4409 files changed, 40334 insertions, 135982 deletions

diff --git a/.github/workflows/duplicates.yml b/.github/workflows/duplicates.yml
new file mode 100644
index 000000000..c6cc040f0
--- /dev/null
+++ b/.github/workflows/duplicates.yml
@@ -0,0 +1,19 @@
+name: duplicates
+
+on:
+  push:
+    branches: [ master ]
+  pull_request:
+    branches: [ master ]
+
+jobs:
+  build:
+    runs-on: ubuntu-latest
+    steps:
+    - uses: actions/checkout@v2
+    - name: Setup master gentoo repository
+      run: |
+        ./scripts/setup-master-gentoo.sh
+    - name: Check for duplicates
+      run: |
+        ./scripts/check-duplicates.sh
diff --git a/.github/workflows/pkgcheck.yml b/.github/workflows/pkgcheck.yml
new file mode 100644
index 000000000..c7440aef2
--- /dev/null
+++ b/.github/workflows/pkgcheck.yml
@@ -0,0 +1,17 @@
+name: pkgcheck
+
+on:
+  push:
+    branches: [ master ]
+  pull_request:
+    branches: [ master ]
+
+jobs:
+  build:
+    runs-on: ubuntu-latest
+    steps:
+    - uses: actions/checkout@v2
+    - name: Run pkgcheck
+      uses: pkgcore/pkgcheck-action@v1
+      with:
+        args: --keywords=-RedundantVersion,-MissingAccountIdentifier,-OldPackageUpdate,-VisibleVcsPkg
diff --git a/.travis.yml b/.travis.yml
deleted file mode 100644
index 241a06e33..000000000
--- a/.travis.yml
+++ /dev/null
@@ -1,39 +0,0 @@
-#
-# Run repoman via travis
-# See https://github.com/mrueg/repoman-travis
-#
-language: python
-cache: pip
-python:
-    - pypy
-env:
-    - PORTAGE_VER="2.3.51"
-before_install:
-    - sudo apt-get -qq update
-install:
-    - pip install lxml PyYAML
-before_script:
-    - sudo chmod a+rwX /etc/passwd /etc/group /etc /usr
-    - mkdir -p travis-overlay /etc/portage /usr/portage/distfiles
-    - mv !(travis-overlay) travis-overlay/
-    - mv .git travis-overlay/
-    - wget "https://raw.githubusercontent.com/mrueg/repoman-travis/master/spinner.sh"
-    - wget -qO - "https://github.com/gentoo/portage/archive/portage-${PORTAGE_VER}.tar.gz" | tar xz
-    - wget -qO - "https://github.com/gentoo-mirror/gentoo/archive/master.tar.gz" | tar xz -C /usr/portage --strip-components=1
-    - chmod a+rwx spinner.sh
-    - echo "portage:x:250:250:portage:/var/tmp/portage:/bin/false" >> /etc/passwd
-    - echo "portage::250:portage,travis" >> /etc/group
-    - wget "https://www.gentoo.org/dtd/metadata.dtd" -O /usr/portage/distfiles/metadata.dtd
-    - ln -s $TRAVIS_BUILD_DIR/portage-portage-${PORTAGE_VER}/cnf/repos.conf /etc/portage/repos.conf
-    - ln -s /usr/portage/profiles/default/linux/amd64/17.1 /etc/portage/make.profile
-    - cd travis-overlay
-script:
-    - ./../spinner.sh "python ../portage-portage-${PORTAGE_VER}/repoman/bin/repoman full -d"
-# You can append own scripts after this line
-
-notifications:
-    irc:
-        channels: "chat.freenode.net#gentoo-science"
-        template:
-            - "%{repository} - %{branch} - %{author}: %{commit_subject} - %{message} - Build details : %{build_url}"
-        use_notice: true
diff --git a/CONTRIBUTING.md b/CONTRIBUTING.md
index 6c4ba5879..f414ef5b5 100644
--- a/CONTRIBUTING.md
+++ b/CONTRIBUTING.md
@@ -36,32 +36,27 @@ Create a [gpg key](http://www.gossamer-threads.com/lists/gentoo/dev/268496?do=po
 
 Now git will sign your commits to the overlay by using the gpg key.
 
-* **Install [hub](http://hub.github.com/)**, the *command-line wrapper for git that makes you better at GitHub*.
+* **Install [pkgdev](https://github.com/pkgcore/pkgdev)**, *A repository commit helper*
 
-*hub* can be used equivalent to to *git* and upstream even recommends *"alias git='hub'*.
+*pkgdev* sanitizes your commit in a convenient way and runs QA checks.
 
-    emerge dev-vcs/hub
-
-* **Install [repo-commit](https://bitbucket.org/gentoo/repo-commit/)**, *A repository commit helper*
-
-*repo-commit* sanitizes your commit in a convenient way.
-
-    emerge app-portage/repo-commit
+    emerge dev-util/pkgdev
 
 ---
 ## Contributing ebuilds
 
+### Fork the overlay
+In order to send pull request and ask for inclusion of your changes you need to have your own fork of the overlay on github. You can do this by clicking the "Fork" button in the top right of our GitHub page.
+
 ### Clone the overlay
 
-Create a local checkout of the overlay
+Create a local checkout of your fork, where `USERNAME` is your GitHub username.
 
-    hub clone gentoo-science/sci
+    git clone git@github.com:USERNAME/sci.git
 
-### Fork the overlay
-In order to send pull request and ask for inclusion of your changes you need to have your own fork of the overlay on github. You can do this by issuing
+To conveniently update your fork later, add the main repository as a second remote
 
-    cd sci
-    hub fork
+    git remote add upstream git@github.com:gentoo/sci.git
 
 ### Branch out for contribution
 It is always convenient for development as well as for the review and merging process, if the development is done in branches. Let's branch the overlay into a local branch named PACKAGE_NAME.
@@ -71,37 +66,38 @@ It is always convenient for development as well as for the review and merging pr
 For the fastest process during merging it is best to have a single branch per package.
 
 ### Work on the package
-Now you are ready to work on your package of interest. Once you are finished you should _always_ use **[repoman](http://dev.gentoo.org/~zmedico/portage/doc/man/repoman.1.html)** to do a static analysis of your work.
+Now you are ready to work on your package of interest. Once you are finished you should _always_ use **[pkgcheck](https://pkgcore.github.io/pkgcheck/man/pkgcheck.html)** to do a static analysis of your work.
 
 This can be done with
 
-    repoman full
+    pkgcheck scan --net
 
 ### Commit your work
 Once *all* reported problems are resolved, you can commit it
 
-    repo-commit "Here we write a comprehensible commit message"
+    pkgdev commit --all
 
-### Push to Github and make a pull request
+### Push to GitHub and make a pull request
 In order to facilitate potential reverts of mistakes, we prefer to keep the git history as linear as possible. For this, always rebase your changes on the latest remote changes.
 
-    hub pull --rebase=preserve github master
+    git pull --rebase=merges upstream master
+
+Next we push back the changes in the PACKAGE_NAME branch to our fork.
 
-Next we push back the changes in the PACKAGE_NAME branch to our fork and send a pull-request to the overlay maintainers.
+    pkgdev push YOUR_GITHUB_USER PACKAGE_NAME
 
-    hub push YOUR_GITHUB_USER PACKAGE_NAME
-    hub pull-request
+Now we are ready to create a Pull Request, go to your GitHub fork and press "Contribute" --> "Open pull request".
 
-Lastly you need to wait for review comments and the merge of your work. If you feel that they are slacking, don't bother to ping them again. In case you need to include some improvements, just commit your work again using *repo-commit* and push it again to your fork. No need to send another pull-request as your new changes will be added to the original one.
+Lastly you need to wait for review comments and the merge of your work. If you feel that they are slacking, don't hesitate to ping them again. In case you need to include some improvements, just commit your work again using `pkgdev commit` and push it again to your fork. No need to send another pull-request as your new changes will be added to the original one.
 
 ### What's next?
-If you would like to get direct access to the overlay, prove some contribution and ping us via sci@gentoo.org or on irc in #gentoo-science @ freenode. If you would like to become a dev yourself, prove some more contributions and again, contact us. We are always looking for new candidates.
+If you would like to get direct access to the overlay, prove some contribution and ping us via sci@gentoo.org or on irc in #gentoo-science @ Libera. If you would like to become a dev yourself, prove some more contributions and again, contact us. We are always looking for new candidates.
 
 ----
 ## Ebuild recommendations
 As the Gentoo Science overlay is a constant work-in-progress, we have some recommendations for prospective contributors:
 
-* **Aim for writing EAPI=6 ebuilds.** For certain eclasses, EAPI=6 is not allowed yet. In such cases you may use EAPI=5. We will not accept EAPI<5 ebuilds.
+* **Aim for writing EAPI=8 ebuilds.** For certain eclasses, `EAPI=8` is not allowed yet. In such cases you may use `EAPI=7`. We will not accept `EAPI<=6` ebuilds.
 * **Version bumps should always follow the latest guidelines.** For instance, a version bump of an ebuild that still employs autotools-utils.eclass should be avoided. Instead, drop 'autotools-utils', move to 'autotools' and call `default` followed by `eautoreconf` in src_prepare().
 
 ----
@@ -109,46 +105,21 @@ As the Gentoo Science overlay is a constant work-in-progress, we have some recom
 
 **It is important, that if you merge a pull request, you should feel as responsible as if you have written the commits yourself!**
 
-
-
 ### Prerequisite
 
-Make sure you have both repos (github & gentoo.org) as remotes defined.
-
-    git remote -v
-
-should give
-
->github	git@github.com:gentoo-science/sci.git (fetch)
->
->github	git@github.com:gentoo-science/sci.git (push)
->
->origin	git+ssh://git@git.overlays.gentoo.org/proj/sci.git (fetch)
->
->origin	git+ssh://git@git.overlays.gentoo.org/proj/sci.git (push)
-
+Install `app-portage/pram`
 
 ### Review process
 
-In the beginning you should review the pull request on github directly and recommend as much improvements as possible. By this you train the new contributor towards becoming a new dev, which should be our final goal.
+In the beginning you should review the pull request on GitHub directly and recommend as much improvements as possible. By this you train the new contributor towards becoming a new dev, which should be our final goal.
 
 #### Checking out the pull-request as local branch
 Once everything is fine or you like to fix the rest yourself, simply use the following command to get the pull-request in a new branch in your repo.
 
-    hub checkout https://github.com/gentoo-science/sci/pull/PULLREQUEST-NUMBER
-
-#### Testing and repoman check
-Now check the package by building and installing it, and run *repoman* in the package dir. Remember, when merging a pull request you take the responsibility for the quality of the commit.
-
-#### Merge the pull-request branch into master
-If this is also fine, merge the branch into the master
-
-    git checkout master
-    git merge USER-BRANCH
-
-#### Merging the two remote HEADs
-Finally use the script **merge-dualHEAD** from the *scripts* directory to merge the github and gentoo.org remote repo.
+    pram -r gentoo/sci PULLREQUEST-NUMBER
 
+#### Testing and pkgcheck check
+Now check the package by building and installing it, and run *pkgcheck* in the package directory. Remember, when merging a pull request you take the responsibility for the quality of the commit.
 
 ---
 #### Contribution to the document
diff --git a/README.md b/README.md
index 6283a58a3..cd47d84a4 100644
--- a/README.md
+++ b/README.md
@@ -1,44 +1,152 @@
-# [Gentoo Science](https://wiki.gentoo.org/wiki/Project:Science/Overlay) Overlay
-[![Build Status](https://travis-ci.org/gentoo/sci.svg?branch=master)](https://travis-ci.org/gentoo/sci)
+# The [Gentoo Science Project](https://wiki.gentoo.org/wiki/Project:Science) Repository    
+[![pkgcheck](https://github.com/gentoo/sci/workflows/pkgcheck/badge.svg)](https://github.com/gentoo/sci/actions?query=workflow%3Apkgcheck)
+[![contributions welcome](https://img.shields.io/badge/contributions-welcome-brightgreen.svg)](https://github.com/gentoo/sci#guide)
+[![chat on libera](https://img.shields.io/badge/chat-on%20libera-brightgreen.svg)](https://web.libera.chat/#gentoo-science)
 
-This is a Gentoo Linux [ebuild repository](https://wiki.gentoo.org/wiki/Ebuild_repository) which provides numerous scientific software packages.
+<table>
+<tr>
+<td width="69%">
 
-## Install
+**This is an official mirror of the Gentoo Science [ebuild repository](https://wiki.gentoo.org/wiki/Ebuild_repository), containing numerous scientific software packages.**
 
-As per the current [Portage specifications](https://dev.gentoo.org/~zmedico/portage/doc/man/portage.5.html), ebuild repositories (a.k.a. overlays) should be managed via file collections under `/etc/portage/repos.conf/`.
-To enable our overlay without the need for additional software, simply run (as root):
+*See [Project:Science](https://wiki.gentoo.org/wiki/Project:Science) for more information on the project.*
 
+</td>
+<td width="27%" style="border-style:solid; border-radius:10px;">
+
+### Contents
+
+1. [Installation](#install)
+  - [Eselect](#install-eselect)
+  - [Manual](#install-manual)
+  - [Layman](#install-layman)
+2. [Usage](#usage)
+3. [Contributing](#contributing)
+
+</td>
+</tr>
+</table>
+
+## Installation <a name="install"></a>
+
+As per the current [Portage specification](https://dev.gentoo.org/~zmedico/portage/doc/man/portage.5.html), ebuild repositories (a.k.a. overlays) can be managed via file collections under `/etc/portage/repos.conf/`, via the new [plug-in sync system](https://wiki.gentoo.org/wiki/Project:Portage/Sync).
+
+### Eselect-repository Install <a name="install-eselect"></a>
+
+The overlay can be enabled via the `repository` extension of the Gentoo `eselect` utility.
+
+```console
+emerge --ask --noreplace --verbose eselect-repository
+eselect repository enable science
 ```
-wget https://gitweb.gentoo.org/proj/sci.git/plain/metadata/science.conf -O /etc/portage/repos.conf/science
+
+### Eselect-repository Uninstall
+
+To disable and remove the overlay, run:
+
+```console
+eselect repository disable science
+eselect repository remove science
 ```
 
-To start using the overlay you now only need to get the ebuilds, via `emerge --sync`.
+### Manual Install <a name="install-manual"></a>
+
+To enable the overlay without the need for dedicated repository software, you need to have `git` installed:
 
-### BLAS and LAPACK Migration
+```console
+emerge --ask --noreplace --verbose dev-vcs/git
+````
 
-There is a long-standing BLAS and LAPACK stack incompatibility between the Science Overlay and the Base Gentoo Overlay.
-A fix [is being considered](https://github.com/gentoo/sci/issues/805), bit is still not scheduled for implementation.
-In the mean time, the most automated and up-to-date solution (building on [the original one](https://wiki.gentoo.org/wiki/User_talk:Houseofsuns)) is to run (as root, and after having installed the overlay):
+Then you can simply download the science repository configuration file, [science.conf](metadata/science.conf):
 
+```console
+wget https://gitweb.gentoo.org/proj/sci.git/plain/metadata/science.conf \
+	-O /etc/portage/repos.conf/science
 ```
-cd ${EPREFIX}/var/lib/overlays/science/scripts
-./lapack-migration.sh
+
+### Manual Uninstall
+
+To disable and remove the overlay, run:
+
+```console
+rm /etc/portage/repos.conf/science
+rm /var/db/repos/science -rf
 ```
 
-### Uninstall
+### Layman Install <a name="install-layman"></a>
 
-To uninstall the overlay run (again, as root):
+You can also install the overlay via the [layman](https://wiki.gentoo.org/wiki/Layman) overlay manager.
 
+```console
+emerge --ask --noreplace --verbose app-portage/layman
+layman --add science
 ```
-rm /etc/portage/repos.conf/science
-rm -rf /var/lib/overlays/science
+
+### Layman Uninstall
+
+To delete the overlay, run:
+
+```console
+layman --delete science
 ```
 
-## Support
+### Using Packages from `::science`
+
+To start using the overlay you now only need to get the newest files, via:
+
+```console
+emerge --sync science
+```
 
-You can ask for help on [Freenode IRC](https://www.gentoo.org/get-involved/irc-channels/) in `#gentoo-science`.
-Alternatively you can report bugs on the [GitHub issues page](https://github.com/gentoo/sci/issues).
+To be able to install `::science` packages you need to make sure that you are accepting the `~${ARCH}` keyword for your respective architecture. This may already be the case globally on your system, and you can check whether this is the case by running:
 
-## Contribute
+```console
+grep "~$(portageq envvar ARCH)" /etc/portage/make.conf
+```
+
+If the above returns empty, you will need to instruct Portage to accept `~${ARCH}` packages.
+
+This can be done for `::science` specifically:
+
+```console
+mkdir -p /etc/portage/package.accept_keywords
+printf '*/*::science ~%s' "$(portageq envvar ARCH)" >> /etc/portage/package.accept_keywords/science
+```
+
+If the above fails with `mkdir: cannot create directory ‘/etc/portage/package.accept_keywords’: File exists` this means you are using a file and not a directory, and you can instead run:
+
+```console
+printf '*/*::science ~%s' "$(portageq envvar ARCH)" >> /etc/portage/package.accept_keywords
+```
+
+Alternatively, and *only if you know what you are doing*, you can accept `~${ARCH}` packages globally:
+
+```console
+printf 'ACCEPT_KEYWORDS="~%s"' "$(portageq envvar ARCH)" >> /etc/portage/make.conf
+```
+
+The downside of this approach is potentially higher instability, the advantage is that often `::science` packages require `~${ARCH}` packages from `::gentoo` as well.
+
+
+## Contributing <a name="contributing"></a>
+
+*If you fork, we will merge!*   
+We welcome new contributors and are happy to include new packages.
+
+### Areas to contribute
+
+- [Current open bugs](https://bugs.gentoo.org/buglist.cgi?no_redirect=1&quicksearch=[science+overlay])
+
+### Resources
+
+For a brief introduction please see our [contributing guide](CONTRIBUTING.md). Further helpful resources are:
+
+- Gentoo Developers Manual - https://devmanual.gentoo.org/ (taking precedence over any other information found here)
+- Contributing to Gentoo - https://wiki.gentoo.org/wiki/Contributing_to_Gentoo
+
+Additionally, please make sure to add the Science Project as an additional maintainer to any new packages you submit. For an example, take a look at the metadata for the [Numba](dev-python/numba) package - [dev-python/numba/metadata.xml](dev-python/numba/metadata.xml)
+
+## Support
 
-Please fork! We will merge! See [our contributing guide](https://github.com/gentoo/sci/blob/master/CONTRIBUTING.md).
+You can ask for help on [Libera IRC](https://www.gentoo.org/get-involved/irc-channels/) in [**#gentoo-science**](https://web.libera.chat/#gentoo-science).
+Alternatively you can report bugs on the [Gentoo Bugzilla](https://bugs.gentoo.org/).
diff --git a/app-admin/eselect/Manifest b/app-admin/eselect/Manifest
deleted file mode 100644
index fc35483d3..000000000
--- a/app-admin/eselect/Manifest
+++ /dev/null
@@ -1 +0,0 @@
-DIST eselect-1.4.13.tar.xz 177848 BLAKE2B 70e5a793759e16119f5233b2c974e0fcc8d213b2033e2b3b76e0a047797b1a0f2feb21ad3beda72f644b498725b4d8ff5c221dcd0870adf5197eaf81c6f3c895 SHA512 5ce10bd288268bc5b52031703f8ac8f3cf07bb22039339bb00c92583ed226162ea8865788f5c1ff4e058d38f0bf25e3557273fb1e839e0391c1fafb9f702bc11
diff --git a/app-admin/eselect/eselect-1.4.13-r101.ebuild b/app-admin/eselect/eselect-1.4.13-r101.ebuild
deleted file mode 100644
index 602a3c8e8..000000000
--- a/app-admin/eselect/eselect-1.4.13-r101.ebuild
+++ /dev/null
@@ -1,73 +0,0 @@
-# Copyright 1999-2018 Gentoo Foundation
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=6
-
-inherit autotools eutils bash-completion-r1
-
-DESCRIPTION="Gentoo's multi-purpose configuration and management tool"
-HOMEPAGE="https://wiki.gentoo.org/wiki/Project:Eselect"
-SRC_URI="https://dev.gentoo.org/~ulm/eselect/${P}.tar.xz"
-
-LICENSE="GPL-2+ || ( GPL-2+ CC-BY-SA-3.0 )"
-SLOT="0"
-KEYWORDS="~amd64 ~x86 ~amd64-linux ~x86-linux"
-IUSE="doc emacs vim-syntax"
-
-RDEPEND="
-	!app-eselect/eselect-blas
-	!app-eselect/eselect-lapack
-	|| (
-		sys-apps/coreutils
-		sys-freebsd/freebsd-bin
-		app-misc/realpath
-	)"
-DEPEND="${RDEPEND}
-	app-arch/xz-utils
-	doc? ( dev-python/docutils )"
-RDEPEND="!app-admin/eselect-news
-	${RDEPEND}
-	sys-apps/file
-	sys-libs/ncurses"
-
-PDEPEND="emacs? ( app-emacs/eselect-mode )
-	vim-syntax? ( app-vim/eselect-syntax )"
-
-PATCHES=( "${FILESDIR}"/${P}-alternatives.patch )
-
-src_prepare() {
-	default
-	AT_M4DIR="." eautoreconf
-}
-
-src_compile() {
-	default
-	use doc && emake html
-}
-
-src_install() {
-	default
-	newbashcomp misc/${PN}.bashcomp ${PN}
-	dodoc AUTHORS ChangeLog NEWS README TODO doc/*.txt
-	use doc && dohtml *.html doc/*
-
-	# needed by news module
-	keepdir /var/lib/gentoo/news
-	if use prefix; then
-		sed -i \
-			"s:ALTERNATIVESDIR_ROOTLESS=\"${EPREFIX}:ALTERNATIVESDIR_ROOTLESS=\":" \
-			"${ED}"/usr/share/eselect/libs/alternatives-common.bash || die
-	else
-		fowners root:portage /var/lib/gentoo/news
-		fperms g+w /var/lib/gentoo/news
-	fi
-}
-
-pkg_postinst() {
-	# fowners in src_install doesn't work for the portage group:
-	# merging changes the group back to root
-	if ! use prefix; then
-		chgrp portage "${EROOT}/var/lib/gentoo/news" \
-			&& chmod g+w "${EROOT}/var/lib/gentoo/news"
-	fi
-}
diff --git a/app-admin/eselect/eselect-9999.ebuild b/app-admin/eselect/eselect-9999.ebuild
deleted file mode 100644
index 8cae96147..000000000
--- a/app-admin/eselect/eselect-9999.ebuild
+++ /dev/null
@@ -1,71 +0,0 @@
-# Copyright 1999-2018 Gentoo Foundation
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=6
-
-inherit autotools git-r3 bash-completion-r1
-
-DESCRIPTION="Gentoo's multi-purpose configuration and management tool"
-HOMEPAGE="https://wiki.gentoo.org/wiki/Project:Eselect"
-EGIT_REPO_URI="git://github.com/gentoo-science/eselect.git"
-EGIT_BRANCH="alternatives"
-
-LICENSE="GPL-2+ || ( GPL-2+ CC-BY-SA-3.0 )"
-SLOT="0"
-IUSE="doc emacs vim-syntax"
-
-RDEPEND="
-	!app-eselect/eselect-blas
-	!app-eselect/eselect-lapack
-	|| (
-		sys-apps/coreutils
-		sys-freebsd/freebsd-bin
-		app-misc/realpath
-	)"
-DEPEND="${RDEPEND}
-	app-arch/xz-utils
-	doc? ( dev-python/docutils )"
-RDEPEND="!app-admin/eselect-news
-	${RDEPEND}
-	sys-apps/file
-	sys-libs/ncurses"
-
-PDEPEND="emacs? ( app-emacs/eselect-mode )
-	vim-syntax? ( app-vim/eselect-syntax )"
-
-src_prepare() {
-	default
-	AT_M4DIR="." eautoreconf
-}
-
-src_compile() {
-	default
-	use doc && emake html
-}
-
-src_install() {
-	default
-	newbashcomp misc/${PN}.bashcomp ${PN}
-	dodoc AUTHORS ChangeLog NEWS README TODO doc/*.txt
-	use doc && dohtml *.html doc/*
-
-	# needed by news module
-	keepdir /var/lib/gentoo/news
-	if use prefix; then
-		sed -i \
-			"s:ALTERNATIVESDIR_ROOTLESS=\"${EPREFIX}:ALTERNATIVESDIR_ROOTLESS=\":" \
-			"${ED}"/usr/share/eselect/libs/alternatives-common.bash || die
-	else
-		fowners root:portage /var/lib/gentoo/news
-		fperms g+w /var/lib/gentoo/news
-	fi
-}
-
-pkg_postinst() {
-	# fowners in src_install doesn't work for the portage group:
-	# merging changes the group back to root
-	if ! use prefix; then
-		chgrp portage "${EROOT}/var/lib/gentoo/news" \
-			&& chmod g+w "${EROOT}/var/lib/gentoo/news"
-	fi
-}
diff --git a/app-admin/eselect/files/eselect-1.4.13-alternatives.patch b/app-admin/eselect/files/eselect-1.4.13-alternatives.patch
deleted file mode 100644
index c47887fe6..000000000
--- a/app-admin/eselect/files/eselect-1.4.13-alternatives.patch
+++ /dev/null
@@ -1,1603 +0,0 @@
- bin/Makefile.am                  |   1 +
- bin/eselect.in                   | 150 +++++++++++-
- libs/Makefile.am                 |   7 +-
- libs/alternatives-common.bash.in | 510 +++++++++++++++++++++++++++++++++++++++
- libs/alternatives.bash.in        | 316 ++++++++++++++++++++++++
- modules/Makefile.am              |   1 +
- modules/alternatives.eselect     | 178 ++++++++++++++
- modules/modules.eselect          | 288 ++++++++++++++--------
- 8 files changed, 1343 insertions(+), 108 deletions(-)
-
-diff --git a/bin/Makefile.am b/bin/Makefile.am
-index 20902c1..ad08867 100644
---- a/bin/Makefile.am
-+++ b/bin/Makefile.am
-@@ -4,6 +4,7 @@ EXTRA_DIST = eselect.in
- dosed = @SED@ -e 's%\@BASH\@%$(BASH)%g' \
- 	      -e 's%\@DATADIR\@%$(datadir)%g' \
- 	      -e 's%\@EPREFIX\@%$(EPREFIX)%g' \
-+	      -e 's%\@LIBEXECDIR\@%$(datadir)%g' \
- 	      -e 's%\@VERSION\@%$(VERSION)$(EXTRAVERSION)%g'
- 
- % : %.in
-diff --git a/bin/eselect.in b/bin/eselect.in
-index 432f4e8..840eb94 100755
---- a/bin/eselect.in
-+++ b/bin/eselect.in
-@@ -22,10 +22,18 @@ ESELECT_DATA_PATH="@DATADIR@/eselect"
- # Where are modules installed by default?
- ESELECT_DEFAULT_MODULES_PATH="${ESELECT_DATA_PATH}/modules"
- 
-+# Where are auto-generated modules placed? (e.g. from alternatives-2.eclass)
-+ESELECT_AUTO_GENERATED_MODULES_PATH="${ESELECT_DEFAULT_MODULES_PATH}/auto"
-+
-+# Where the users store their modules
-+ESELECT_USER_MODULES_PATH="${ROOT}${HOME}/.eselect/modules"
-+
- # Look in these places for modules
--ESELECT_MODULES_PATH=( \
--	"${HOME}/.eselect/modules" \
--	"${ESELECT_DEFAULT_MODULES_PATH}" )
-+ESELECT_MODULES_PATH=(
-+	"${ESELECT_USER_MODULES_PATH}}"
-+	"${ESELECT_DEFAULT_MODULES_PATH}"
-+	"${ESELECT_AUTO_GENERATED_MODULES_PATH}"
-+)
- 
- # Look in this place for libraries
- ESELECT_CORE_PATH="${ESELECT_DATA_PATH}/libs"
-@@ -66,12 +74,27 @@ fi
- # Load core functions
- source "${ESELECT_CORE_PATH}/core.bash" || exit 255
- # Load necessary functions for the main script
--inherit manip output path-manipulation tests
-+inherit manip output path-manipulation tests config
- 
- # Sneaky trick to make die in subshells work. If you don't get
- # it, don't ask...
- trap 'echo "exiting" >&2; exit 250' 15
- 
-+# es_find_module foo
-+# Find and echo the filename of the foo module. If there's no foo module,
-+# die.
-+es_find_module() {
-+    local modname="$1" modpath="" modfile=""
-+	[[ -z ${modname} ]] && die "Usage: ${FUNCNAME} <module>"
-+	for modpath in "${ESELECT_MODULES_PATH[@]}" ; do
-+		[[ -f ${modpath}/${modname}.eselect ]] && break
-+	done
-+
-+	modfile="${modpath}/${modname}.eselect"
-+	[[ -r ${modfile} ]] || die -q "Can't load module ${modname}"
-+	echo ${modfile}
-+}
-+
- # es_do_usage
- # Display eselect usage
- es_do_usage() {
-@@ -83,14 +106,10 @@ es_do_usage() {
- es_do_help() {
- 	es_do_usage
- 	echo
--	# display all recognized global options
--	write_list_start "Global options:"
--	write_kv_list_entry "--brief" "Make output shorter"
--	write_kv_list_entry "--colour=<yes|no|auto>" \
--		"Enable or disable colour output (default 'auto')"
-+	es_do_list-options
- 	echo
- 	# display all available eselect modules
--	do_action modules list
-+	es_do_list-modules
- }
- 
- # es_do_version
-@@ -102,6 +121,114 @@ es_do_version() {
- 	echo "Distributed under the terms of the GNU GPL version 2 or later."
- }
- 
-+# es_do_list-options
-+# Display all recognized global options
-+es_do_list-options() {
-+	write_list_start "Global options:"
-+	write_kv_list_entry "--brief"                   "Make output shorter"
-+	write_kv_list_entry "--colour=<yes|no|auto>"    "Enable or disable colour output (default 'auto')"
-+	write_kv_list_entry "--debug"                   "Debug eselect (enable set -x)"
-+}
-+
-+# es_do_list-modules
-+# Display all available eselect modules DEPRECATED
-+es_do_list-modules() {
-+	do_action modules list $@
-+}
-+
-+### print-* actions, for use with bash_completion and zsh-completion ###
-+
-+# es_do_print-modules
-+#
-+# Display all availble eselect modules in a way that's useful to bash
-+# completion / zsh completion
-+es_do_print-modules() {
-+	local ret=1 path module group groupname want_descriptions
-+
-+	while [[ -n $@ ]]; do
-+		case "${1}" in
-+			--descriptions)
-+				want_descriptions='yes' ;;
-+			--group)
-+				groupname=${2}
-+				[[ -z "$groupname" ]] && die -q "Required option (group name) missing."
-+				shift ;;
-+		esac
-+		shift
-+	done
-+
-+	if [[ ${groupname} == Built-in || -z ${groupname} ]]; then
-+		for module in help usage version print-{modules,actions,options}; do
-+			echo "${module}"
-+		done
-+		[[ ${groupname} == Built-in ]] && return 0
-+	fi
-+
-+	# TODO: factor this out in modules.eselect's do_list()
-+	for path in "${ESELECT_MODULES_PATH[@]}" ; do
-+		[[ -d "${path}" ]] || continue
-+		for file in "${path}"/*.eselect ; do
-+			[[ -f "${file}" ]] || continue
-+			if [[ -n "${groupname}" ]]; then
-+				group=$(load_config "${file}" ESELECT_MODULE_GROUP)
-+				[[ "${groupname}" == "${group}" ||
-+					( "${groupname}" == Extra && -z "${group}" ) ]] || continue
-+			fi
-+			module="${file##*/}"
-+			module="${module%%.eselect}"
-+			echo "${module}${want_descriptions:+:$(load_config "${file}" DESCRIPTION)}"
-+			ret=0
-+		done
-+	done
-+	return $ret
-+}
-+
-+# es_do_print-actions
-+#
-+# Display all available actions for the given module.
-+es_do_print-actions() {
-+	local modfile="$(es_find_module "${1}")" actions action want_descriptions
-+	[[ "${2}" == "--descriptions" ]] && want_descriptions='yes'
-+	(
-+		source "${modfile}" 2>/dev/null \
-+			|| die "Couldn't source ${modfile}"
-+		actions=( $(declare -F \
-+			| sed -n -e 's/^declare\s\+-f\s\+do_//p' \
-+			| egrep -v '^(action|help|usage|version)$' \
-+			| sort ) )
-+		for action in "${actions[@]}" ; do
-+			echo "${action}${want_descriptions:+:$(describe_${action})}"
-+		done
-+	)
-+}
-+
-+# es_do_print-options
-+#
-+# Display all available options for the given module and action
-+es_do_print-options() {
-+	local modfile action want_descriptions
-+
-+	[[ "${1}" == "--descriptions" ]] && want_descriptions='yes' && shift
-+
-+	if [[ -z ${1} ]]; then
-+		echo "--debug${want_descriptions:+:Debug eselect (enable set -x)}"
-+		echo "--no-color${want_descriptions:+:Disable coloured output}"
-+		echo "--no-colour${want_descriptions:+:Disable coloured output}"
-+	elif [[ -n ${2} ]]; then
-+		modfile="$(es_find_module "${1}")"
-+		action=${2}
-+		shift 2
-+		(
-+			source "${modfile}" 2>/dev/null \
-+				|| die "Couldn't source ${modfile}"
-+			is_function options_${action} || return 1
-+			options_${action} ${want_descriptions:+--descriptions} "$@" || return 2
-+		)
-+	else
-+		die "Usage: ${FUNCNAME} [--descriptions] [<module> <action>]"
-+	fi
-+}
-+
- ### main code ###
- 
- # figure out what the action is. we need to know whether we're
-@@ -143,6 +270,9 @@ while [[ ${1##--} != "$1" ]]; do
- 				*) die -q "Invalid argument for ${1%%=*} option" ;;
- 			esac
- 			;;
-+		debug)
-+			set -x
-+			;;
- 		help|version)
- 			[[ -z ${action} ]] || die -q "Too many parameters"
- 			action=${1##--}
-diff --git a/libs/Makefile.am b/libs/Makefile.am
-index 6ebd08e..c19f173 100644
---- a/libs/Makefile.am
-+++ b/libs/Makefile.am
-@@ -1,6 +1,8 @@
- eselectlibsdir = $(datadir)/$(PACKAGE_NAME)/libs/
- 
- eselectlibs_DATA = \
-+	alternatives.bash \
-+	alternatives-common.bash \
- 	config.bash \
- 	core.bash \
- 	default.eselect \
-@@ -14,6 +16,8 @@ eselectlibs_DATA = \
- 	tests.bash
- 
- EXTRA_DIST = \
-+	alternatives.bash.in \
-+	alternatives-common.bash.in \
- 	config.bash.in \
- 	core.bash.in \
- 	default.eselect.in \
-@@ -31,7 +35,8 @@ dosed = @SED@ \
- 	-e 's%\@PORTAGEQ\@%@PORTAGEQ@%g' \
- 	-e 's%\@ENV_UPDATE\@%@ENV_UPDATE@%g' \
- 	-e 's%\@CANONICALISE\@%@CANONICALISE@%g' \
--	-e 's%\@libdir\@%@libdir@%g'
-+	-e 's%\@libdir\@%@libdir@%g' \
-+	-e 's%\@sysconfdir\@%@sysconfdir@%g'
- 
- %.bash : %.bash.in
- 	@$(dosed) $< > $@
-diff --git a/libs/alternatives-common.bash.in b/libs/alternatives-common.bash.in
-new file mode 100644
-index 0000000..8753b89
---- /dev/null
-+++ b/libs/alternatives-common.bash.in
-@@ -0,0 +1,510 @@
-+# Copyright (c) 2005-2015 Gentoo Foundation
-+# Copyright (c) 2008 Mike Kelly
-+# Copyright (c) 2009-2013 David Leverton
-+# Copyright (c) 2009-2014 Bo Ørsted Andresen
-+#
-+# This file is part of the 'eselect' tools framework.
-+#
-+# eselect is free software: you can redistribute it and/or modify it under the
-+# terms of the GNU General Public License as published by the Free Software
-+# Foundation, either version 2 of the License, or (at your option) any later
-+# version.
-+#
-+# eselect is distributed in the hope that it will be useful, but WITHOUT ANY
-+# WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR
-+# A PARTICULAR PURPOSE.  See the GNU General Public License for more details.
-+#
-+# You should have received a copy of the GNU General Public License along with
-+# eselect.  If not, see <http://www.gnu.org/licenses/>.
-+
-+inherit config output path-manipulation tests
-+
-+: "${ALTERNATIVESDIR_ROOTLESS:=@sysconfdir@/env.d/alternatives}"
-+: "${ALTERNATIVESDIR_ROOT:=${ROOT%/}}"
-+ALTERNATIVESDIR="${ALTERNATIVESDIR_ROOT}${ALTERNATIVESDIR_ROOTLESS}"
-+
-+get_current_provider() {
-+	local dieprefix="Could not determine current provider for ${ALTERNATIVE}"
-+	if [[ -L ${ALTERNATIVESDIR}/${ALTERNATIVE}/_current ]]; then
-+		local provider=$(readlink "${ALTERNATIVESDIR}/${ALTERNATIVE}/_current" || die "${dieprefix}: readlink ${symlink} failed")
-+		[[ ${provider} == */* ]] && die "${dieprefix}: malformed target for ${symlink}"
-+
-+		if [[ -L ${ALTERNATIVESDIR}/${ALTERNATIVE}/${provider} ||
-+					( -e ${ALTERNATIVESDIR}/${ALTERNATIVE}/${provider} && ! -d ${ALTERNATIVESDIR}/${ALTERNATIVE}/${provider} ) ]]; then
-+			die "${dieprefix}: ${ALTERNATIVESDIR}/${ALTERNATIVE}/${provider} is not a directory"
-+		fi
-+
-+		echo "${provider}"
-+
-+	elif [[ -e ${ALTERNATIVESDIR}/${ALTERNATIVE}/_current ]]; then
-+		die "${dieprefix}: ${ALTERNATIVESDIR}/${ALTERNATIVE}/_current is not a symlink"
-+	fi
-+}
-+
-+compare_importance() {
-+	local IFS=.
-+	local a=( ${1} ) b=( ${2} )
-+	local -i i=0
-+	while (( i<${#a[@]} && i<${#b[@]} )); do
-+		if (( a[i]<b[i] )); then
-+			return 0
-+		elif (( a[i]>b[i] )); then
-+			return 1
-+		fi
-+		i+=1
-+	done
-+	(( i<${#b[@]} ))
-+}
-+
-+sort_providers() {
-+	local begin=${1:-0}
-+	local count=${2:-${#providers[@]}}
-+	[[ ${count} -le 1 ]] && return 0
-+	sort_providers ${begin} $((count/2))
-+	sort_providers $((begin+count/2)) $((count-count/2))
-+	local left=( "${providers[@]:begin:count/2}" )
-+	local right=( "${providers[@]:begin+count/2:count-count/2}" )
-+	local -i x i=0 j=0
-+	for (( x=begin; x<begin+count; ++x )); do
-+		if (( j>=${#right[@]} )) || { (( i<${#left[@]} )) && compare_importance "${left[i]%%:*}" "${right[j]%%:*}"; }; then
-+			providers[x]=${left[i++]}
-+		else
-+			providers[x]=${right[j++]}
-+		fi
-+	done
-+}
-+
-+get_providers() {
-+	local p= importance providers=()
-+	for p in "${ALTERNATIVESDIR}/${ALTERNATIVE}"/* ; do
-+		[[ -d ${p} && ! -L ${p} ]] || continue
-+		p=${p##*/}
-+
-+		[[ -e "${ALTERNATIVESDIR}/${ALTERNATIVE}/${p}/_importance" ]] && \
-+			importance=$(< "${ALTERNATIVESDIR}/${ALTERNATIVE}/${p}/_importance")
-+		importance=${importance:-0}
-+		[[ "${importance}" =~ ^[0123456789]+(\.[0123456789]+)*$ ]] || die "_importance (${importance}) for ${p} is not a dot-separated list of integers"
-+
-+		providers+=( "${importance}:${p}" )
-+	done
-+
-+	sort_providers
-+	for (( p=${#providers[@]}-1 ; p>=0 ; --p )); do
-+		echo "${providers[p]#*:}"
-+	done
-+}
-+
-+has_provider() {
-+	local provider=${1} item providers=( $(get_providers) )
-+	for item in  ${providers[@]}; do
-+		[[ ${item} == ${provider} ]] && return 0
-+	done
-+	return 1
-+}
-+
-+_options_parameters() {
-+	[[ -n ${2} && ${2} != --descriptions ]] && die -q "Unrecognised option ${2}"
-+	local describe_func=describe_${1#options_}_options descriptions=${2} opt options oldifs=$IFS
-+	if is_function ${describe_func}; then
-+		IFS=$'\n'
-+		options=( $(${describe_func}) )
-+		IFS=$oldifs
-+		for opt in "${options[@]}"; do
-+			[[ ${opt} == --* ]] || continue
-+			if [[ -n ${descriptions} ]]; then
-+				echo "${opt/ : /:}"
-+			else
-+				echo "${opt%% : *}"
-+			fi
-+		done
-+	fi
-+}
-+
-+### set action stub ###
-+
-+# not available in "eselect alternatives", but needed by do_update
-+
-+alternatives_do_set() {
-+	[[ -z "${ALTERNATIVE}" ]] && die "Need to set ALTERNATIVE in the eselect module"
-+
-+	local force provider providers
-+	if [[ ${1} == --force ]]; then
-+		force=yes
-+		shift
-+	fi
-+	local idx=${1}
-+	if [[ ${1} == +(-|+|[[:digit:]]) ]]; then
-+		idx=${1#+(-|+)}
-+		providers=( $(get_providers) )
-+		(( ${idx} <= ${#providers[@]} )) || die -q "The given provider with index (${idx}) does not exist"
-+		provider=${providers[${idx}-1]}
-+	else
-+		provider="${1}"
-+	fi
-+	[[ -z "${provider}" ]] && die -q "Missing required parameter 'provider'"
-+	local dieprefix="Could not set provider ${provider} for alternative ${ALTERNATIVE}"
-+
-+	if [[ ! -d ${ALTERNATIVESDIR}/${ALTERNATIVE}/${provider} ]] ; then
-+		if is_number ${provider} ; then
-+			providers=( $(get_providers) )
-+			[[ -n ${providers[${idx}-1]} ]] && \
-+				die -q "The given provider (${provider}) does not exist"
-+		fi
-+		die -q "The given provider (${provider}) does not exist"
-+	fi
-+
-+	local symlink newsymlinks=() oldsymlinks=()
-+
-+	while read -r -d '' symlink; do
-+		local nicesymlink=${symlink#.}
-+		nicesymlink=${nicesymlink//+(\/)/\/}
-+		[[ ${nicesymlink} == /* ]] || die "${dieprefix}: bad symlink ${symlink}?"
-+		[[ ${nicesymlink} == */ ]] && die "${dieprefix}: bad symlink ${symlink}?"
-+
-+		newsymlinks+=( "${nicesymlink}" )
-+	done < <(
-+		cd "${ALTERNATIVESDIR}/${ALTERNATIVE}/${provider}" || die "${dieprefix}: cd failed"
-+		find . -type l -print0 | LC_ALL=C sort -r -u -z)
-+	[[ ${#newsymlinks[@]} -gt 0 ]] || die "${dieprefix}: does not provide any symlinks?"
-+
-+	if [[ -f ${ALTERNATIVESDIR}/${ALTERNATIVE}/_current_list ]]; then
-+		while read -r -d '' symlink; do
-+			local nicesymlink=${symlink//+(\/)/\/}
-+			[[ ${nicesymlink} == /* ]] || die "${dieprefix}: old provider ${oldcur} provides bad symlink ${symlink}?"
-+			[[ ${nicesymlink} == */ ]] && die "${dieprefix}: old provider ${oldcur} provides bad symlink ${symlink}?"
-+
-+			oldsymlinks+=( "${nicesymlink}" )
-+		done < <(LC_ALL=C sort -r -u -z "${ALTERNATIVESDIR}/${ALTERNATIVE}/_current_list")
-+		[[ ${#oldsymlinks[@]} -gt 0 ]] || die "${dieprefix}: old provider ${oldcur} does not provide any symlinks?"
-+
-+	elif [[ -L ${ALTERNATIVESDIR}/${ALTERNATIVE}/_current_list || -e ${ALTERNATIVESDIR}/${ALTERNATIVE}/_current_list ]]; then
-+		die "${dieprefix}: ${ALTERNATIVESDIR}/${ALTERNATIVE}/_current_list is not a file"
-+	fi
-+
-+	local pass errors=
-+	for pass in check perform; do
-+		local -i new_i=0 old_i=0
-+		while [[ -n ${newsymlinks[new_i]} || -n ${oldsymlinks[old_i]} ]]; do
-+
-+			if ( LC_ALL=C; [[ ${newsymlinks[new_i]} < ${oldsymlinks[old_i]} ]] ); then
-+				if [[ ${pass} == check ]]; then
-+					if [[ -L ${EROOT%/}${oldsymlinks[old_i]} ]]; then
-+						:
-+					elif [[ -d ${EROOT%/}${oldsymlinks[old_i]} ]]; then
-+						write_error_msg "Can't remove ${EROOT%/}${oldsymlinks[old_i]}: is a directory${force:+ which is a fatal error that cannot be ignored by --force}"
-+						errors=yes
-+					elif [[ -e ${EROOT%/}${oldsymlinks[old_i]} ]]; then
-+						if [[ -n ${force} ]]; then
-+							write_warning_msg "Removing ${EROOT%/}${oldsymlinks[old_i]} due to --force: is not a symlink"
-+						else
-+							write_error_msg "Refusing to remove ${EROOT%/}${oldsymlinks[old_i]}: is not a symlink (use --force to override)"
-+							errors=yes
-+						fi
-+					fi
-+
-+				elif [[ ${pass} == perform ]]; then
-+					rm -f "${EROOT%/}${oldsymlinks[old_i]}" || die "${dieprefix}: rm failed"
-+				else
-+					die "${dieprefix}: unknown \${pass} ${pass}???"
-+				fi
-+
-+				old_i+=1
-+
-+			else
-+				local target=${ALTERNATIVESDIR_ROOTLESS#${EPREFIX}/}/${ALTERNATIVE}/_current${newsymlinks[new_i]} dir=${newsymlinks[new_i]%/*}
-+				while [[ -n ${dir} ]]; do
-+					target=../${target}
-+					dir=${dir%/*}
-+				done
-+
-+				if [[ ${pass} == check ]]; then
-+					if [[ -L ${EROOT%/}${newsymlinks[new_i]} ]]; then
-+						:
-+					elif [[ -d ${EROOT%/}${newsymlinks[new_i]} ]]; then
-+						write_error_msg "Can't overwrite ${EROOT%/}${newsymlinks[new_i]}: is a directory${force:+ which is a fatal error that cannot be ignored by --force}"
-+						errors=yes
-+					elif [[ -e ${EROOT%/}${newsymlinks[new_i]} ]]; then
-+						if [[ -n ${force} ]]; then
-+							write_warning_msg "Overwriting ${EROOT%/}${newsymlinks[new_i]} due to --force: is not a symlink"
-+						else
-+							write_error_msg "Refusing to overwrite ${EROOT%/}${newsymlinks[new_i]}: is not a symlink (use --force to override)"
-+							errors=yes
-+						fi
-+					fi
-+
-+				elif [[ ${pass} == perform ]]; then
-+					mkdir -p "${EROOT%/}${newsymlinks[new_i]%/*}" || die "${dieprefix}: mkdir -p failed"
-+					ln -snf "${target#/}" "${EROOT%/}${newsymlinks[new_i]}" || die "${dieprefix}: ln -snf failed"
-+				else
-+					die "${dieprefix}: unknown \${pass} ${pass}???"
-+				fi
-+
-+				[[ ${newsymlinks[new_i]} == ${oldsymlinks[old_i]} ]] && old_i+=1
-+				new_i+=1
-+			fi
-+		done
-+
-+		[[ -n ${errors} ]] && die "${dieprefix}: see previous errors"
-+	done
-+
-+	local oldcur="$(get_current_provider)"
-+	ln -snf "${provider}" "${ALTERNATIVESDIR}/${ALTERNATIVE}/_current" || die "${dieprefix}: ln -snf failed"
-+
-+	: >"${ALTERNATIVESDIR}/${ALTERNATIVE}/_current_list" || die "${dieprefix}: emptying/creating _current_list failed"
-+	for symlink in "${newsymlinks[@]}"; do
-+		echo -n -e "${symlink}\\0" >>"${ALTERNATIVESDIR}/${ALTERNATIVE}/_current_list" || die "${dieprefix}: appending ${symlink} to _current_list failed"
-+	done
-+	return 0
-+}
-+
-+### add action ###
-+alternatives_describe_add() {
-+	echo "Add provider to selected alternative"
-+}
-+
-+alternatives_describe_add_parameters() {
-+	echo "<provider> <importance> <source> <target> [<source> <target> [...]]"
-+}
-+
-+alternatives_describe_add_options() {
-+	echo "<provider> : the name of the alternative provider"
-+	echo "<importance> : interger value, representing the importance of the provider"
-+	echo "<source> : source of the symlink"
-+	echo "<target> : destination for the symlink"
-+}
-+
-+alternatives_do_add() {
-+	[[ -z "${ALTERNATIVE}" ]] && die "Need to set ALTERNATIVE in the eselect module"
-+
-+	(( $# >= 4 )) && (( ($#-2)%2 == 0)) || \
-+		die "exactly 3+N*2 arguments where N>=1 required"
-+	local provider=${1}
-+	local importance=${2}
-+	shift 2
-+	local index src target ret=0
-+	local provider_dir="${ALTERNATIVESDIR}/${ALTERNATIVE}/${provider}"
-+
-+	# Creating base dir
-+	if [[ ! -e "${provider_dir}" ]]; then
-+		mkdir -p "${provider_dir}" || die "Failed to create ${provider_dir}"
-+	elif [[ ! -d "${provider_dir}" ]]; then
-+		die "${provider_dir} exists but is a file"
-+	else
-+		die "${provider_dir} already present. You need to remove it before adding it again"
-+	fi
-+
-+	# Make sure importance is a signed integer
-+	if [[ -n ${importance} ]] && ! [[ ${importance} =~ ^[0-9]+(\.[0-9]+)*$ ]]; then
-+		die "Invalid importance (${importance}) detected"
-+	else
-+		# Setting importance
-+		echo ${importance} > "${provider_dir}/_importance"
-+	fi
-+
-+	# Process source-target pairs
-+	while (( $# >= 2 )); do
-+		src=${1//+(\/)/\/}; target=${2//+(\/)/\/}
-+		if [[ ${src} != /* ]]; then
-+			die "Source path must be absolute, but got ${src}"
-+		else
-+			local reltarget= dir=${provider_dir#${ALTERNATIVESDIR_ROOT}${EPREFIX}}${src%/*}
-+			while [[ -n ${dir} ]]; do
-+				reltarget+=../
-+				dir=${dir%/*}
-+			done
-+
-+			reltarget=${reltarget%/}
-+			[[ ${target} == /* ]] || reltarget+=${src%/*}/
-+			reltarget+=${target}
-+			mkdir -p "${provider_dir}${src%/*}" || die "Failed to create ${provider_dir}${src%/*}"
-+			ln -sf "${reltarget}" "${provider_dir}${src}" || die "Failed to create symlink"
-+			# The -e test will fail if existing symlink points to non-existing target,
-+			# so check for -L also.
-+			# Say ${ED}/sbin/init exists and links to /bin/systemd (which doesn't exist yet).
-+#			if [[ -e ${ED}${src} || -L ${ED}${src} ]]; then
-+#				local fulltarget=${target}
-+#				[[ ${fulltarget} != /* ]] && fulltarget=${src%/*}/${fulltarget}
-+#				if [[ -e ${ED}${fulltarget} || -L ${ED}${fulltarget} ]]; then
-+#					die "${src} defined as provider for ${fulltarget}, but both already exist in \${ED}"
-+#				else
-+#					mv "${ED}${src}" "${ED}${fulltarget}" || die
-+#				fi
-+#			fi
-+		fi
-+		shift 2
-+	done
-+}
-+
-+alternatives_options_add() {
-+	_options_parameters ${FUNCNAME#alternatives_} "$@"
-+}
-+
-+### remove action ###
-+
-+alternatives_describe_remove() {
-+	echo "Remove a provider for selected alternative"
-+}
-+
-+alternatives_describe_remove_parameters() {
-+	echo "<provider>"
-+}
-+
-+alternatives_describe_remove_options() {
-+	echo "<provider> : the name of the alternative provider to be removed"
-+}
-+
-+alternatives_do_remove() {
-+	[[ -z "${ALTERNATIVE}" ]] && die "Need to set ALTERNATIVE in the eselect module"
-+
-+	if [[ -d "${ALTERNATIVESDIR}/${ALTERNATIVE}/${provider}" ]]; then
-+		rm -r "${ALTERNATIVESDIR}/${ALTERNATIVE}/${provider}" || \
-+			die "Failed to remove '${provider}' for '${ALTERNATIVE}'"
-+	else
-+		einfo "'${provider}' is not a provider for '${ALTERNATIVE}'"
-+	fi
-+}
-+
-+alternatives_options_remove() {
-+	_options_parameters ${FUNCNAME#alternatives_} "$@"
-+}
-+
-+### update action ###
-+
-+# available in both "eselect alternatives" and individual modules
-+
-+alternatives_describe_update() {
-+	echo "Set a default provider if no valid one currently exists"
-+}
-+
-+alternatives_describe_update_parameters() {
-+	echo "[--best] [--ignore] <provider>"
-+}
-+
-+alternatives_describe_update_options() {
-+	echo "--best : update to the best provider even if one is already selected"
-+	echo "--ignore : update to any valid provider EXCEPT the specified provider"
-+	echo "<provider> : the name of the provider to use"
-+}
-+
-+alternatives_do_update() {
-+	[[ -z "${ALTERNATIVE}" ]] && die "Need to set ALTERNATIVE in the eselect module"
-+
-+	local p cur=$(get_current_provider) providers=( $(get_providers) ) best ignore
-+	if [[ "--best" == ${1} ]] ; then
-+		shift
-+		best=1
-+	fi
-+	if [[ "--ignore" == ${1} ]] ; then
-+		# Try everything except setting the provider to the given
-+		# one. So, if it isn't the given one, we end up doing
-+		# nothing. Bug #128
-+		shift
-+		ignore=${1}
-+	fi
-+	[[ -n ${best} && -n ${1} && -z ${ignore} ]] && die -q "Cannot specify both --best and a provider"
-+
-+	if [[ -n ${best} ]] ; then
-+		# set best provider
-+		: # fall through to "switch to first available" loop below
-+	elif [[ $# == "0" ]] && [[ -z ${cur} ]]; then
-+		# if nothing is specified
-+		: # fall through to "switch to first available" loop below
-+	elif [[ ${cur} == ${1} && -z ${ignore} ]]; then
-+		# if current provider was just updated, reselect it since it could have changed
-+		alternatives_do_set "${cur}" && return 0
-+	elif [[ -n ${cur} && ${cur} != ${ignore} ]] ; then
-+		# verify existing provider's symlinks
-+		local p= bad=0
-+		while read -r -d '' p ; do
-+			[[ -L "${EROOT%/}${p}" && -e "${EROOT%/}${p}" ]] || (( bad++ ))
-+		done < "${ALTERNATIVESDIR}/${ALTERNATIVE}/_current_list"
-+
-+		[[ "${bad}" -eq 0 ]] && return 0
-+		# fix existing provider if possible
-+		has "${cur}" "${providers[@]}" && alternatives_do_set "${cur}" && return 0
-+	elif has "${1}" "${providers[@]}" && [[ -z ${ignore} ]] ; then
-+		# switch to new provider if none was set before or it can't be fixed
-+		alternatives_do_set "${1}" && return 0
-+	fi
-+
-+	# if no valid provider has been selected switch to first available, valid
-+	# provider, sorted according to importance
-+	for p in "${providers[@]}"; do
-+		[[ ${ignore} != ${p} ]] && alternatives_do_set "${p}" && return 0
-+	done
-+
-+	# if a provider is set but no providers are available anymore cleanup
-+	cur=$(get_current_provider)
-+	if [[ -n ${cur} ]]; then
-+		alternatives_do_unset "${cur}" && return 2
-+	fi
-+	# if no provider is set and none are available that are not ignored, return 2 for cleanup
-+	[[ -z ${providers[@]} || ${providers[@]} == ${ignore} ]] && return 2
-+
-+	# we tried everything to select a valid provider, but failed
-+	return 1
-+}
-+
-+alternatives_options_update() {
-+	_options_parameters ${FUNCNAME#alternatives_} "$@"
-+	if [[ -n ${ALTERNATIVE} ]]; then
-+		get_providers
-+	else
-+		for alt in ${ALTERNATIVESDIR_ROOTLESS}/_*/*/_importance; do
-+			echo ${alt} | cut -d/ -f5
-+		done | sort -u
-+	fi
-+}
-+
-+### unset action stub ###
-+
-+# not available in "eselect alternatives", but needed by do_update
-+
-+alternatives_do_unset() {
-+	[[ -z "${ALTERNATIVE}" ]] && die "Need to set ALTERNATIVE in the eselect module"
-+
-+	local force=
-+	if [[ ${1} == --force ]]; then
-+		force=yes
-+		shift
-+	fi
-+
-+	local cur="$(get_current_provider)" p=
-+	[[ -n "${cur}" ]] || die -q "Nothing to unset"
-+	local dieprefix="Could not unset provider for ${ALTERNATIVE}"
-+
-+	local one=false symlink pass errors=
-+	for pass in check perform; do
-+		while read -r -d '' symlink; do
-+			one=true
-+			if [[ ${pass} == check ]]; then
-+				if [[ -L ${EROOT%/}${symlink} ]]; then
-+					:
-+				elif [[ -d ${EROOT%/}${symlink} ]]; then
-+					write_error_msg "Can't remove ${EROOT%/}${symlink}: is a directory${force:+ which is a fatal error that cannot be ignored by --force}"
-+					errors=yes
-+				elif [[ -e ${EROOT%/}${symlink} ]]; then
-+					if [[ -n ${force} ]]; then
-+						write_warning_msg "Removing ${EROOT%/}${symlink} due to --force: is not a symlink"
-+					else
-+						write_error_msg "Refusing to remove ${EROOT%/}${symlink}: is not a symlink (use --force to override)"
-+						errors=yes
-+					fi
-+				fi
-+
-+			elif [[ ${pass} == perform ]]; then
-+				rm -f "${EROOT%/}${symlink}" || die "${dieprefix}: rm failed"
-+			else
-+				die "${dieprefix}: unknown \${pass} ${pass}???"
-+			fi
-+		done <"${ALTERNATIVESDIR}/${ALTERNATIVE}/_current_list"
-+
-+		[[ -n ${errors} ]] && die "${dieprefix}: see previous errors"
-+	done
-+
-+	${one} || die "${dieprefix}: does not provide any symlinks?"
-+
-+	rm "${ALTERNATIVESDIR}/${ALTERNATIVE}"/{_current,_current_list} || die "${dieprefix}: rm failed"
-+}
-+
-+# vim: set ft=eselect sw=4 sts=4 ts=4 et tw=80 :
-diff --git a/libs/alternatives.bash.in b/libs/alternatives.bash.in
-new file mode 100644
-index 0000000..cf4fa36
---- /dev/null
-+++ b/libs/alternatives.bash.in
-@@ -0,0 +1,316 @@
-+# Copyright (c) 2005-2015 Gentoo Foundation
-+# Copyright (c) 2008 Mike Kelly
-+# Copyright (c) 2009-2013 David Leverton
-+# Copyright (c) 2009-2014 Bo Ørsted Andresen
-+#
-+# This file is part of the 'eselect' tools framework.
-+#
-+# eselect is free software: you can redistribute it and/or modify it under the
-+# terms of the GNU General Public License as published by the Free Software
-+# Foundation, either version 2 of the License, or (at your option) any later
-+# version.
-+#
-+# eselect is distributed in the hope that it will be useful, but WITHOUT ANY
-+# WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR
-+# A PARTICULAR PURPOSE.  See the GNU General Public License for more details.
-+#
-+# You should have received a copy of the GNU General Public License along with
-+# eselect.  If not, see <http://www.gnu.org/licenses/>.
-+
-+inherit alternatives-common
-+
-+### show action ###
-+describe_show() {
-+	echo "Show the current provider in use for ${ALTERNATIVE}"
-+}
-+
-+do_show() {
-+	[[ -z "${ALTERNATIVE}" ]] && die "Need to set ALTERNATIVE in the eselect module"
-+	local current="$(get_current_provider)"
-+	if [[ -z "${current}" ]] ; then
-+		echo "(none)"
-+		return 2
-+	fi
-+	echo "${current}"
-+}
-+
-+options_show() {
-+	:
-+}
-+
-+### list action ###
-+describe_list() {
-+	echo "Lists all available providers for ${ALTERNATIVE}"
-+}
-+
-+do_list() {
-+	[[ -z "${ALTERNATIVE}" ]] && die "Need to set ALTERNATIVE in the eselect module"
-+	local n cur= providers=( $(get_providers) )
-+	write_list_start "Available providers for ${ALTERNATIVE}:"
-+
-+	cur="$(get_current_provider)"
-+
-+	if [[ -n "${providers[@]}" ]] ; then
-+		for (( n = 0 ; n < ${#providers[@]} ; ++n )) ; do
-+			[[ ${cur} ==  "${providers[${n}]}" ]] && \
-+				providers[${n}]="${providers[${n}]} $(highlight '*')"
-+		done
-+		write_numbered_list "${providers[@]}"
-+	else
-+		write_kv_list_entry "(none found)" ""
-+	fi
-+}
-+
-+options_list() {
-+	:
-+}
-+
-+### files action ###
-+describe_files() {
-+	echo "Lists symlinks provided by the currently selected provider"
-+}
-+
-+do_files() {
-+	[[ -z "${ALTERNATIVE}" ]] && die "Need to set ALTERNATIVE in the eselect module"
-+
-+	local cur="$(get_current_provider)" p=
-+	[[ -n "${cur}" ]] || die -q "No selected provider, hence no symlinks provided"
-+	local dieprefix="Could not list symlinks provided for ${ALTERNATIVE}"
-+
-+	local errors symlink rootsymlink
-+	while read -r -d '' symlink; do
-+		rootsymlink="${EROOT%/}${symlink}"
-+		rootsymlink=${rootsymlink//+(\/)/\/}
-+		echo "${rootsymlink}"
-+		if [[ -L ${rootsymlink} ]]; then
-+			if [[ ! -e ${rootsymlink} ]]; then
-+				write_error_msg "${rootsymlink} is dangling symlink"
-+				errors=yes
-+			fi
-+		elif [[ -d ${rootsymlink} ]]; then
-+			write_error_msg "${rootsymlink} is a directory"
-+			errors=yes
-+		elif [[ -e ${rootsymlink} ]]; then
-+			write_error_msg "${rootsymlink} exists but is not a symlink"
-+			errors=yes
-+		else
-+			write_error_msg "${rootsymlink} does not exist"
-+			errors=yes
-+		fi
-+	done <"${ALTERNATIVESDIR}/${ALTERNATIVE}/_current_list"
-+}
-+
-+options_files() {
-+	:
-+}
-+
-+### set action ###
-+
-+describe_set() {
-+	echo "Sets a provider for ${ALTERNATIVE}"
-+}
-+
-+describe_set_parameters() {
-+	echo "[ --force ] <provider>"
-+}
-+
-+describe_set_options() {
-+	echo "--force : overwrite or remove existing non-symlink files (but not directories) if necessary"
-+	echo "<provider> : the name of the provider to use or the index of the provider preceeded by a dash"
-+}
-+
-+do_set() {
-+	# implementation defined in alternatives-common.bash as needed by do_update
-+	alternatives_do_set "$@"
-+}
-+
-+options_set() {
-+	_options_parameters $FUNCNAME "$@"
-+	get_providers
-+}
-+
-+### add action ###
-+
-+describe_add() {
-+	alternatives_describe_add
-+}
-+
-+describe_add_parameters() {
-+	alternatives_describe_add_parameters
-+}
-+
-+describe_add_options() {
-+	alternatives_describe_add_options
-+}
-+
-+do_add() {
-+	alternatives_do_add
-+
-+	# make sure we have something selected
-+	eselect ${provider} show > /dev/null || eselect ${provider} update --best
-+}
-+
-+### remove action ###
-+
-+describe_remove() {
-+	alternatives_describe_remove
-+}
-+
-+describe_remove_parameters() {
-+	alternatives_describe_remove_parameters
-+}
-+
-+describe_remove_options() {
-+	alternatives_describe_remove_options
-+}
-+
-+do_remove() {
-+	local ret
-+	alternatives_do_remove
-+
-+#	if no provider is present, remove whole alternative
-+	eselect ${provider} update --best > /dev/null; ret=$?
-+	case ret in
-+		0)
-+			# All good
-+			:;;
-+		2)
-+			# No provider present anymore
-+			eselect alternatives remove ${ALTERNATIVE};;
-+		*)
-+			write_error_msg "Failed to remove ${ALTERNATIVE}"
-+			errors=yes
-+	esac
-+}
-+
-+### update action ###
-+
-+# all functions implemented in alternatives-common.bash as defined for
-+# both "eselect alternatives" and individual modules
-+
-+describe_update() {
-+	alternatives_describe_update
-+}
-+
-+describe_update_parameters() {
-+	alternatives_describe_update_parameters
-+}
-+
-+describe_update_options() {
-+	alternatives_describe_update_options
-+}
-+
-+do_update() {
-+	alternatives_do_update "$@"
-+}
-+
-+options_update() {
-+	alternatives_options_update
-+}
-+
-+### unset action ###
-+
-+describe_unset() {
-+	echo "Unset any symlinks created for the current provider for ${ALTERNATIVE}."
-+}
-+
-+describe_unset_parameters() {
-+	echo "[ --force ]"
-+}
-+
-+describe_unset_options() {
-+	echo "--force : remove existing non-symlink files (but not directories) if necessary"
-+}
-+
-+do_unset() {
-+	# implementation defined in alternatives-common.bash as needed by do_update
-+	alternatives_do_unset "$@"
-+}
-+
-+options_unset() {
-+	_options_parameters $FUNCNAME "$@"
-+	get_current_provider
-+}
-+
-+### script action ###
-+
-+describe_script() {
-+	echo "Output an evalable script fragment to set PATH, LD_LIBRARY_PATH and MANPATH to use the specified provider"
-+}
-+
-+describe_script_parameters() {
-+	echo "[--sh | --csh] [<provider>]"
-+}
-+
-+describe_script_options() {
-+	echo "--sh : use Bourne shell syntax (default)"
-+	echo "--csh : use C shell syntax"
-+	echo "<provider> : the provider to use or the index of the provider (if not specified, use the system default)"
-+}
-+
-+do_script() {
-+	[[ -z "${ALTERNATIVE}" ]] && die "Need to set ALTERNATIVE in the eselect module"
-+	local syntax=sh provider providers
-+	if [[ ${1} == --sh ]]; then
-+		shift
-+	elif [[ ${1} == --csh ]]; then
-+		syntax=csh
-+		shift
-+	fi
-+
-+	local idx=${!}
-+	if [[ ${idx} == +(-|+|[[:digit:]]) ]]; then
-+		idx=${1#+(-|+)}
-+		providers=( $(get_providers) )
-+		(( ${idx} <= ${#providers[@]} )) || die -q "The given provider with index (${idx}) does not exist"
-+		provider=${providers[${idx}-1]}
-+	else
-+		provider="${idx}"
-+	fi
-+	[[ -z "${provider}" ]] && die -q "Missing required parameter 'provider'"
-+
-+	if [[ ! -d ${ALTERNATIVESDIR}/${ALTERNATIVE}/${provider} ]] ; then
-+		if is_number ${provider} ; then
-+			providers=( $(get_providers) )
-+			[[ -n ${providers[${idx}-1]} ]] && \
-+				die -q "The given provider (${provider}) does not exist"
-+		fi
-+		die -q "The given provider (${provider}) does not exist"
-+	fi
-+
-+	local variables=( PATH LD_LIBRARY_PATH MANPATH )
-+	[[ -n ${!default_*} ]] && local ${!default_*}
-+	local default_LD_LIBRARY_PATH=$(grep '^[^#]' "${EROOT%/}"/etc/ld.so.conf | tr '\n' ':')/lib:/usr/lib
-+	local default_MANPATH=$(MANPATH= man -C"${EROOT%/}"/etc/man.conf -w)
-+
-+	local var IFS=:
-+	for var in "${variables[@]}"; do
-+		local defvar=default_${var} path paths=( )
-+		for path in ${!var}; do
-+			[[ ${path} == ${ALTERNATIVESDIR_ROOTLESS}/${ALTERNATIVE}/* ]] && continue
-+			[[ -n ${provider} && -d ${ALTERNATIVESDIR}/${ALTERNATIVE}/${provider}/${path#/} ]] && paths+=( "${ALTERNATIVESDIR_ROOTLESS}/${ALTERNATIVE}/${provider}/${path#/}" )
-+			paths+=( "${path}" )
-+		done
-+
-+		[[ -n ${provider} ]] && for path in ${!defvar}; do
-+			[[ -d ${ALTERNATIVESDIR}/${ALTERNATIVE}/${provider}/${path#/} ]] && paths+=( "${ALTERNATIVESDIR_ROOTLESS}/${ALTERNATIVE}/${provider}/${path#/}" )
-+		done
-+
-+		local newval=${paths[*]}
-+		if [[ ${newval} != ${!var} ]]; then
-+			newval=${newval//\'/\'\\\'\'}
-+			if [[ ${syntax} == sh ]]; then
-+				echo "${var}='${newval}'; export ${var}"
-+			else
-+				echo "setenv ${var} '${newval}'"
-+			fi
-+		fi
-+	done
-+}
-+
-+options_script() {
-+	_options_parameters $FUNCNAME "$@"
-+	get_providers
-+}
-+
-+# vim: set ft=eselect sw=4 sts=4 ts=4 et tw=80 :
-diff --git a/modules/Makefile.am b/modules/Makefile.am
-index 75ebe02..92127b6 100644
---- a/modules/Makefile.am
-+++ b/modules/Makefile.am
-@@ -1,6 +1,7 @@
- modulesdir=$(datadir)/$(PACKAGE_NAME)/modules/
- 
- modules_DATA = \
-+	alternatives.eselect \
- 	editor.eselect \
- 	env.eselect \
- 	kernel.eselect \
-diff --git a/modules/alternatives.eselect b/modules/alternatives.eselect
-new file mode 100644
-index 0000000..840b9c5
---- /dev/null
-+++ b/modules/alternatives.eselect
-@@ -0,0 +1,178 @@
-+# Copyright (c) 2005-2015 Gentoo Foundation
-+# Copyright (c) 2008 Mike Kelly
-+# Copyright (c) 2009-2013 David Leverton
-+# Copyright (c) 2009-2014 Bo Ørsted Andresen
-+#
-+# This file is part of the 'eselect' tools framework.
-+#
-+# eselect is free software: you can redistribute it and/or modify it under the
-+# terms of the GNU General Public License as published by the Free Software
-+# Foundation, either version 2 of the License, or (at your option) any later
-+# version.
-+#
-+# eselect is distributed in the hope that it will be useful, but WITHOUT ANY
-+# WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR
-+# A PARTICULAR PURPOSE.  See the GNU General Public License for more details.
-+#
-+# You should have received a copy of the GNU General Public License along with
-+# eselect.  If not, see <http://www.gnu.org/licenses/>.
-+
-+inherit alternatives-common
-+
-+DESCRIPTION="Maintain Alternatives symlinks"
-+VERSION="20150521"
-+MAINTAINER="sci@gentoo.org"
-+
-+show_extra_help_text() {
-+	cat <<- ENDOFTEXT
-+	This module is intended for internal use when a package is installed,
-+	updated or removed. For alternatives for which it is likely that
-+	users will need control over which provider is selected, there will be
-+	a separate eselect module installed to do so.
-+	ENDOFTEXT
-+}
-+
-+# all functions implemented in alternatives-common.bash as defined for
-+# both "eselect alternatives" and individual modules
-+
-+### update action ###
-+
-+describe_update() {
-+	alternatives_describe_update
-+}
-+
-+describe_update_parameters() {
-+	echo "<alternative> $(alternatives_describe_update_parameters)"
-+}
-+
-+describe_update_options() {
-+	echo "<alternative> : the name of the alternative to set a provider for"
-+	alternatives_describe_update_options
-+}
-+
-+do_update() {
-+	local ALTERNATIVE=$1
-+	shift
-+	[[ -z "${ALTERNATIVE}" ]] && die -q "Missing required parameter 'alternative'"
-+	alternatives_do_update "$@"
-+}
-+
-+options_update() {
-+	alternatives_options_update
-+}
-+
-+### create action ###
-+
-+describe_create() {
-+	echo "Create a new alternative"
-+}
-+
-+describe_create_parameters() {
-+	echo "<alternative>"
-+}
-+
-+describe_create_options() {
-+	echo "<alternative> : the name of the alternative to create"
-+}
-+
-+do_create() {
-+	[[ $# == 1 ]] || die "Need exactly one alternative name"
-+
-+	local auto_dir="${ESELECT_AUTO_GENERATED_MODULES_PATH}"
-+	local auto_file="${auto_dir}/${1}.eselect"
-+
-+	if [[ ! -e "${auto_file}" ]]; then
-+		if [[ ! -e "${auto_dir}" ]]; then
-+			mkdir -p "${auto_dir}" || die "Failed to create ${auto_dir}"
-+		elif [[ ! -d "${auto_dir}" ]]; then
-+			die "${auto_dir} exists but is a file"
-+		fi
-+		cat >> ${auto_file} <<- ENDOFTEXT
-+			DESCRIPTION="${DESCRIPTION} for ${1}"
-+			VERSION="${VERSION}"
-+			MAINTAINER="${MAINTAINER}"
-+			ESELECT_MODULE_GROUP="Alternatives"
-+
-+			ALTERNATIVE="${1}"
-+
-+			inherit alternatives
-+		ENDOFTEXT
-+	fi
-+}
-+
-+### delete action ###
-+
-+describe_delete() {
-+	echo "Delete an existing alternative"
-+}
-+
-+describe_delete_parameters() {
-+	echo "<alternative>"
-+}
-+
-+describe_delete_options() {
-+	echo "<alternative> : the name of the alternative to delete"
-+}
-+
-+do_delete() {
-+	[[ $# == 1 ]] || die "Need exactly one alternative name"
-+
-+	local auto_dir="${ESELECT_AUTO_GENERATED_MODULES_PATH}"
-+	local auto_file="${auto_dir}/${1}.eselect"
-+
-+	if [[ -e "${auto_file}" ]]; then
-+		rm "${auto_file}" || die "Failed to remove alternative: ${1}"
-+	fi
-+}
-+
-+### add action ###
-+
-+describe_add() {
-+	alternatives_describe_add
-+}
-+
-+describe_add_parameters() {
-+	echo "<alternative> $(alternatives_describe_add_parameters)"
-+}
-+
-+describe_add_options() {
-+	echo "<alternative> : the name of the alternative to add a provider for"
-+	alternatives_describe_add_options
-+}
-+
-+do_add() {
-+	local ALTERNATIVE=$1
-+	shift
-+	[[ -z "${ALTERNATIVE}" ]] && die -q "Missing required parameter 'alternative'"
-+	alternatives_do_add "$@"
-+}
-+
-+options_add() {
-+	alternatives_options_add
-+}
-+
-+### remove action ###
-+
-+describe_remove() {
-+	alternatives_describe_remove
-+}
-+
-+describe_remove_parameters() {
-+	echo "<alternative> $(alternatives_describe_remove_parameters)"
-+}
-+
-+describe_remove_options() {
-+	echo "<alternative> : the name of the alternative to remove a provider from"
-+	alternatives_describe_remove_options
-+}
-+
-+do_remove() {
-+	local ALTERNATIVE=$1
-+	shift
-+	[[ -z "${ALTERNATIVE}" ]] && die -q "Missing required parameter 'alternative'"
-+	alternatives_do_remove "$@"
-+}
-+
-+options_remove() {
-+	alternatives_options_remove
-+}
-diff --git a/modules/modules.eselect b/modules/modules.eselect
-index 5bc78ca..23c1e59 100644
---- a/modules/modules.eselect
-+++ b/modules/modules.eselect
-@@ -2,7 +2,7 @@
- # Copyright 2006-2018 Gentoo Foundation
- # Distributed under the terms of the GNU GPL version 2 or later
- 
--inherit config
-+inherit config output tests
- 
- DESCRIPTION="Query eselect modules"
- MAINTAINER="eselect@gentoo.org"
-@@ -15,57 +15,94 @@ describe_list() {
- 	echo "List all available modules"
- }
- 
--describe_list_options() {
--	echo "--only-names : Output names of modules only"
--}
--
- # List all installed modules
- do_list() {
--	local only_names path file module name desc
--	local -a extra_modules
--
--	if [[ ${1#--} = only-names ]]; then
--		only_names=1
--		shift
--	fi
--	[[ $# -gt 0 ]] && die -q "Too many parameters"
--
--	for path in "${ESELECT_MODULES_PATH[@]}" ; do
--		[[ -d ${path} ]] || continue
--		for file in "${path}"/*.eselect ; do
--			[[ -f ${file} ]] || continue
--			extra_modules=( "${extra_modules[@]}" "${file}" )
--		done
--	done
--
--	if [[ -n ${only_names} ]]; then
--		# This is mainly intended for bash completion
--		echo "help"
--		echo "usage"
--		echo "version"
--		for module in "${extra_modules[@]}" ; do
--			name=${module##*/}
--			echo "${name%%.eselect}"
--		done
--	else
--		write_list_start "Built-in modules:"
--		write_kv_list_entry "help"			"Display a help message"
--		write_kv_list_entry "usage"			"Display a usage message"
--		write_kv_list_entry "version"		"Display version information"
--
--		if [[ ${#extra_modules[@]} -gt 0 ]] ; then
--			echo
--			write_list_start "Extra modules:"
--			for module in "${extra_modules[@]}" ; do
--				name=${module##*/}
--				name=${name%%.eselect}
--				desc=$(ESELECT_MODULE_NAME=${name} \
--					load_config "${module}" DESCRIPTION)
--				desc=${desc:-No description available}
--				write_kv_list_entry "${name}" "${desc}"
--			done
--		fi
--	fi
-+    local path file module name desc group groups Extra_modules
-+
-+    write_list_start "Built-in modules:"
-+    write_kv_list_entry "help"          "Display a help message"
-+    write_kv_list_entry "usage"         "Display a usage message"
-+    write_kv_list_entry "version"       "Display version information"
-+    write_kv_list_entry "print-modules" "Print eselect modules"
-+    write_kv_list_entry "print-actions" "Print actions for a given module"
-+    write_kv_list_entry "print-options" "Print options for a given action"
-+
-+    for path in "${ESELECT_MODULES_PATH[@]}" ; do
-+        [[ -d ${path} ]] || continue
-+        for file in ${path}/*.eselect ; do
-+            [[ -f ${file} ]] || continue
-+            group=$(load_config "${file}" ESELECT_MODULE_GROUP)
-+            if [[ -n ${group} ]]; then
-+                has ${group} ${groups} || groups+=" ${group}"
-+                declare ${group}_modules+=" ${file}"
-+            else
-+                Extra_modules+=" ${file}"
-+            fi
-+        done
-+    done
-+
-+    for group in ${groups} Extra; do
-+        local m
-+        m="${group}_modules"
-+        if [[ -n ${!m} ]] ; then
-+            echo
-+            write_list_start "${group} modules:"
-+            for module in ${!m}; do
-+                name=${module##*/}
-+                name=${name%%.eselect}
-+                desc=$(load_config "${module}" DESCRIPTION)
-+                desc=${desc:-No description available}
-+                write_kv_list_entry "${name}" "${desc}"
-+            done
-+        fi
-+    done
-+}
-+
-+### group action
-+
-+describe_group() {
-+    echo "Lists all available modules belonging to a specified group."
-+}
-+
-+describe_group_parameters() {
-+    echo "<group>"
-+}
-+
-+do_group() {
-+    local path file groupname="$1" group module modules name desc
-+    [[ -z "$groupname" ]] && die -q "Required option (group name) missing."
-+
-+    if [[ ${groupname} == Built-in ]]; then
-+        write_list_start "Built-in modules:"
-+        write_kv_list_entry "help"          "Display a help message"
-+        write_kv_list_entry "usage"         "Display a usage message"
-+        write_kv_list_entry "version"       "Display version information"
-+        return 0
-+    fi
-+
-+    for path in "${ESELECT_MODULES_PATH[@]}" ; do
-+        [[ -d ${path} ]] || continue
-+        for file in ${path}/*.eselect ; do
-+            [[ -f ${file} ]] || continue
-+            group=$(load_config "${file}" ESELECT_MODULE_GROUP)
-+            [[ ${groupname} == ${group} ||
-+                ( ${groupname} == Extra && -z ${group} ) ]] || continue
-+            modules+=" ${file}"
-+        done
-+    done
-+
-+    if [[ -n ${modules} ]] ; then
-+        write_list_start "${groupname} modules:"
-+        for module in ${modules}; do
-+            name=${module##*/}
-+            name=${name%%.eselect}
-+            desc=$(load_config "${module}" DESCRIPTION)
-+            desc=${desc:-No description available}
-+            write_kv_list_entry "${name}" "${desc}"
-+        done
-+    else
-+        die -q "No modules belonging to ${groupname} was found"
-+    fi
- }
- 
- ### has action
-@@ -75,56 +112,113 @@ describe_has() {
- }
- 
- describe_has_parameters() {
--	echo "<module>"
-+    echo "<module>"
- }
- 
- do_has() {
--	[[ -z $1 ]] && die -q "Required option (module name) missing"
--	[[ $# -gt 1 ]] && die -q "Too many parameters"
--
--	local modname=$1 modpath
--	for modpath in "${ESELECT_MODULES_PATH[@]}" ; do
--		[[ -f ${modpath}/${modname}.eselect ]] && return 0
--	done
--	return 1
-+    [[ -z $1 ]] && die -q "Required option (module name) missing"
-+    [[ $# -gt 1 ]] && die -q "Too many parameters"
-+    local modname="$1" modpath
-+    [[ -z "$modname" ]] && die -q "Required option (module name) missing."
-+    for modpath in "${ESELECT_MODULES_PATH[@]}" ; do
-+        [[ -f "${modpath}/${modname}.eselect" ]] && return 0
-+    done
-+    return 1
- }
- 
- ### add action
--# *** Commented out. Do we really want to have an eselect module that is
--# *** installing other modules in a system directory? Also, this should
--# *** go together with a "remove" action.
--
--# describe_add() {
--# 	echo "Install the given module file somewhere that eselect can find it."
--# 	echo "By default, install to \$HOME/.eselect/modules/, unless running as "
--# 	echo "root. Then, install to ${ESELECT_DATA_PATH}/modules/."
--# }
--
--# describe_add_parameters() {
--# 	echo "<module_file>"
--# }
--
--# do_add() {
--# 	local local_path="${ROOT}${HOME}/.eselect/modules/" module_file
--# 	local force_default=0
--#
--# 	if [[ $1 = "--force-default-location" ]] ; then
--# 		force_default=1
--# 		shift
--# 	fi
--# 	module_file=$1
--#
--# 	[[ -z ${module_file} ]] && die -q "Required option (module file) missing"
--#
--# 	# TODO: Don't install the module "somewhere", depending on write access.
--# 	# Add an option to control if it goes to the user's or to the system dir.
--# 	if ! cp "${module_file}" "${ESELECT_DEFAULT_MODULES_PATH}" &> /dev/null ; then
--# 		[[ ${force_default} == 1 ]] \
--# 			&& die -q "Failed to install module file to default modules path"
--#
--# 		mkdir -p "${local_path}" \
--# 			|| die -q "Failed to create module install directory"
--# 		cp "${module_file}" "${local_path}" \
--# 			|| die -q "Failed to install module file"
--# 	fi
--# }
-+
-+describe_add() {
-+    echo "Install a module file"
-+}
-+
-+describe_add_options() {
-+    echo "--default : install as global module (default if root)"
-+    echo "--user : install as user's module"
-+}
-+
-+describe_add_parameters() {
-+    echo "<module_file>"
-+}
-+
-+do_add() {
-+    local module_file module_path
-+    case $1 in
-+	--default)
-+	    module_path="${ESELECT_DEFAULT_MODULES_PATH}"
-+	    shift
-+	    ;;
-+	--user)
-+	    module_path="${ESELECT_USER_MODULES_PATH}"
-+	    mkdir -p "${module_path}" || die -q "Failed to create directory ${module_path}"
-+	    shift
-+	    ;;
-+	*) : ;;
-+    esac
-+    module_file=$1
-+
-+    [[ -z ${module_file} ]] && die -q "Required module file missing"
-+
-+    if [[ -n ${module_path} ]]; then
-+	cp "${module_file}" "${module_path}" &> /dev/null || \
-+	    die -q "Failed to install module file to ${module_path}"
-+    else
-+	if ! cp "${module_file}" "${ESELECT_DEFAULT_MODULES_PATH}" &> /dev/null ; then
-+	    mkdir -p "${ESELECT_USER_MODULES_PATH}" \
-+		|| die -q "Failed to create directory ${ESELECT_USER_MODULES_PATH}"
-+	    cp "${module_file}" "${ESELECT_USER_MODULES_PATH}" \
-+		|| die -q "Failed to install module file ${module_file}"
-+	fi
-+    fi
-+}
-+
-+### remove action
-+
-+describe_remove() {
-+    echo "Remove the given module name"
-+}
-+
-+describe_remove_options() {
-+    echo "--default : remove global module (default if root)"
-+    echo "--alternatives : remove generated alternatives module"
-+    echo "--user : remove user module"
-+}
-+
-+describe_remove_parameters() {
-+    echo "<module>"
-+}
-+
-+do_remove() {
-+    local module_name module_path ret
-+    case $1 in
-+	--alternatives)
-+	    module_path="${ESELECT_GENERATED_MODULES_PATH}"
-+	    shift
-+	    ;;
-+	--default)
-+	    module_path="${ESELECT_DEFAULT_MODULES_PATH}"
-+	    shift
-+	    ;;
-+	--user)
-+	    module_path="${ESELECT_USER_MODULES_PATH}"
-+	    shift
-+			;;
-+	*) : ;;
-+    esac
-+    module_name=$1
-+
-+    [[ -z ${module_name} ]] && die -q "Required module name missing"
-+
-+    if [[ -n ${module_path} ]]; then
-+	rm "${module_path}/${module_name}.eselect" &> /dev/null
-+	ret=$?
-+    else
-+	for module_path in "${ESELECT_MODULES_PATH[@]}" ; do
-+	    rm "${module_path}/${module_name}.eselect" &> /dev/null
-+	    ret=$?
-+	done
-+    fi
-+    [[ ${ret} != 0 ]] && die -q "Failed to remove module ${module_name}"
-+}
-+
-+# vim: set ft=eselect sw=4 sts=4 ts=4 et tw=80 :
diff --git a/app-admin/eselect/metadata.xml b/app-admin/eselect/metadata.xml
deleted file mode 100644
index 8c8d15633..000000000
--- a/app-admin/eselect/metadata.xml
+++ /dev/null
@@ -1,7 +0,0 @@
-<?xml version="1.0" encoding="UTF-8"?>
-<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
-<pkgmetadata>
-	<maintainer type="person">
-		<email>bicatali@gentoo.org</email>
-	</maintainer>
-</pkgmetadata>
diff --git a/app-arch/libdeflate/Manifest b/app-arch/libdeflate/Manifest
deleted file mode 100644
index ae40e25f9..000000000
--- a/app-arch/libdeflate/Manifest
+++ /dev/null
@@ -1 +0,0 @@
-DIST libdeflate-1.2.tar.gz 133494 BLAKE2B cd43b691bda16134ee1d2cdeeea8e5bab7bd8b841dec41fcf93ca0b3383f9c465e095fc7c97b743dc34c2bd6a1d340f8bfda4f4448af832cfec0240965957ffa SHA512 181b53ee9aea96b2520e287824573d111eeacaeae2011e093ca4d4fdd77e4e09bd261d741fac567302cf031058779ccc775dce1f603a05810b0c3b7d96b26fdb
diff --git a/app-arch/libdeflate/files/libdeflate-1.2-respect_EPREFIX.patch b/app-arch/libdeflate/files/libdeflate-1.2-respect_EPREFIX.patch
deleted file mode 100644
index a583d7d2e..000000000
--- a/app-arch/libdeflate/files/libdeflate-1.2-respect_EPREFIX.patch
+++ /dev/null
@@ -1,54 +0,0 @@
---- libdeflate-1.2/Makefile	2019-01-15 06:37:48.000000000 +0100
-+++ libdeflate-1.2/Makefile	2019-01-22 14:06:13.427054892 +0100
-@@ -21,7 +21,7 @@
- 	      1>&2 2>/dev/null; then echo $(1); fi)
- 
- override CFLAGS :=							\
--	$(CFLAGS) -O2 -fomit-frame-pointer -std=c99 -I. -Icommon	\
-+	-O2 $(CFLAGS) -fomit-frame-pointer -std=c99 -I. -Icommon	\
- 	-Wall -Wundef							\
- 	$(call cc-option,-Wpedantic)					\
- 	$(call cc-option,-Wdeclaration-after-statement)			\
-@@ -34,6 +34,9 @@
- ##############################################################################
- 
- PREFIX ?= /usr
-+BINDIR ?= $(PREFIX)/bin
-+INCDIR ?= $(PREFIX)/include
-+LIBDIR ?= $(PREFIX)/lib
- 
- SOVERSION          := 0
- STATIC_LIB_SUFFIX  := .a
-@@ -240,20 +243,20 @@
- all:$(DEFAULT_TARGETS)
- 
- install:all
--	install -Dm644 -t $(DESTDIR)$(PREFIX)/lib $(STATIC_LIB)
--	install -Dm755 -t $(DESTDIR)$(PREFIX)/lib $(SHARED_LIB)
--	ln -sf $(SHARED_LIB) $(DESTDIR)$(PREFIX)/lib/libdeflate.so
--	install -Dm644 -t $(DESTDIR)$(PREFIX)/include libdeflate.h
--	install -Dm755 gzip $(DESTDIR)$(PREFIX)/bin/libdeflate-gzip
--	ln -f $(DESTDIR)$(PREFIX)/bin/libdeflate-gzip $(DESTDIR)$(PREFIX)/bin/libdeflate-gunzip
-+	install -Dm644 -t $(DESTDIR)$(LIBDIR) $(STATIC_LIB)
-+	install -Dm755 -t $(DESTDIR)$(LIBDIR) $(SHARED_LIB)
-+	ln -sf $(SHARED_LIB) $(DESTDIR)$(LIBDIR)/libdeflate.so
-+	install -Dm644 -t $(DESTDIR)$(INCDIR) libdeflate.h
-+	install -Dm755 gzip $(DESTDIR)$(BINDIR)/libdeflate-gzip
-+	ln -f $(DESTDIR)$(BINDIR)/libdeflate-gzip $(DESTDIR)$(BINDIR)/libdeflate-gunzip
- 
- uninstall:
--	rm -f $(DESTDIR)$(PREFIX)/lib/$(STATIC_LIB) \
--		$(DESTDIR)$(PREFIX)/lib/$(SHARED_LIB) \
--		$(DESTDIR)$(PREFIX)/lib/libdeflate.so \
--		$(DESTDIR)$(PREFIX)/include/libdeflate.h \
--		$(DESTDIR)$(PREFIX)/bin/libdeflate-gzip \
--		$(DESTDIR)$(PREFIX)/bin/libdeflate-gunzip
-+	rm -f $(DESTDIR)$(LIBDIR)/$(STATIC_LIB) \
-+		$(DESTDIR)$(LIBDIR)/$(SHARED_LIB) \
-+		$(DESTDIR)$(LIBDIR)/libdeflate.so \
-+		$(DESTDIR)$(INCDIR)/libdeflate.h \
-+		$(DESTDIR)$(BINDIR)/libdeflate-gzip \
-+		$(DESTDIR)$(BINDIR)/libdeflate-gunzip
- 
- test_programs:$(TEST_PROGRAMS)
- 
diff --git a/app-arch/libdeflate/libdeflate-1.2.ebuild b/app-arch/libdeflate/libdeflate-1.2.ebuild
deleted file mode 100644
index 5548ea150..000000000
--- a/app-arch/libdeflate/libdeflate-1.2.ebuild
+++ /dev/null
@@ -1,29 +0,0 @@
-# Copyright 2019 Gentoo Authors
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=7
-
-inherit multilib
-
-DESCRIPTION="Heavily optimized DEFLATE/zlib/gzip (de)compression"
-HOMEPAGE="https://github.com/ebiggers/libdeflate"
-SRC_URI="https://github.com/ebiggers/libdeflate/archive/v1.2.tar.gz -> ${P}.tar.gz"
-
-LICENSE="MIT"
-SLOT="0"
-KEYWORDS="~amd64 ~x86"
-IUSE="static-libs"
-
-DEPEND=""
-RDEPEND="${DEPEND}"
-BDEPEND=""
-
-PATCHES=( "${FILESDIR}"/libdeflate-1.2-respect_EPREFIX.patch )
-
-src_install() {
-	if ! use static-libs; then
-		find "${ED}" -name '*.a' -delete || die
-	fi
-	emake install DESTDIR="${ED}" LIBDIR=/usr/"$(get_libdir)"
-	dodoc NEWS README.md
-}
diff --git a/app-benchmarks/btl/btl-9999.ebuild b/app-benchmarks/btl/btl-9999.ebuild
deleted file mode 100644
index 74bbb1c39..000000000
--- a/app-benchmarks/btl/btl-9999.ebuild
+++ /dev/null
@@ -1,20 +0,0 @@
-# Copyright 1999-2016 Gentoo Foundation
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=6
-
-inherit mercurial
-
-DESCRIPTION="Bench Template Library"
-HOMEPAGE="https://bitbucket.org/spiros/btl"
-EHG_REPO_URI="https://bitbucket.org/spiros/btl"
-
-LICENSE="LGPL-3"
-SLOT="0"
-KEYWORDS=""
-IUSE=""
-
-src_install() {
-	insinto /usr/include/btl
-	doins -r *
-}
diff --git a/app-benchmarks/btl/metadata.xml b/app-benchmarks/btl/metadata.xml
deleted file mode 100644
index 8ebdfe5fd..000000000
--- a/app-benchmarks/btl/metadata.xml
+++ /dev/null
@@ -1,17 +0,0 @@
-<?xml version="1.0" encoding="UTF-8"?>
-<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
-<pkgmetadata>
-	<maintainer type="person">
-		<email>andyspiros@gmail.com</email>
-		<name>Andrea Arteaga</name>
-		<description>Bench Template Library</description>
-	</maintainer>
-	<maintainer type="project">
-		<email>sci@gentoo.org</email>
-		<name>Gentoo Science Project</name>
-	</maintainer>
-	<longdescription>This package contains a modified copy of the BTL.</longdescription>
-	<upstream>
-		<remote-id type="bitbucket">spiros/btl</remote-id>
-	</upstream>
-</pkgmetadata>
diff --git a/app-benchmarks/numbench/Manifest b/app-benchmarks/numbench/Manifest
deleted file mode 100644
index 9ee082cf4..000000000
--- a/app-benchmarks/numbench/Manifest
+++ /dev/null
@@ -1 +0,0 @@
-DIST numbench-0.2.tar.gz 78782 BLAKE2B 762e8139133a2439e23462c55d391733a530b5b5df48bcd9f3717fbeb64726d45950033e0bb9d8f93b5d76a75a78ae1b02d04a1e74a35fb171cc9b6cca5e91ee SHA512 64f177eb63dfcfebb4c20fb821fe8a730443cfbb860494cc432f8ebad717902629236a38002d27e68f6ac6bc0ea8403ac89a6167898b7ec54f23577ec8c37c83
diff --git a/app-benchmarks/numbench/metadata.xml b/app-benchmarks/numbench/metadata.xml
deleted file mode 100644
index 9851d9f74..000000000
--- a/app-benchmarks/numbench/metadata.xml
+++ /dev/null
@@ -1,17 +0,0 @@
-<?xml version="1.0" encoding="UTF-8"?>
-<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
-<pkgmetadata>
-	<maintainer type="person">
-		<email>andyspiros@gmail.com</email>
-		<name>Andrea Arteaga</name>
-		<description>Google Summer of Code 2011 student</description>
-	</maintainer>
-	<maintainer type="project">
-		<email>sci@gentoo.org</email>
-		<name>Gentoo Science Project</name>
-	</maintainer>
-	<longdescription>This package contains a set of scripts developed during the Google Summer of Code 2011 project. It aims to benchmark numerical libraries, and more precisely implementations of the standard BLAS, CBLAS, LAPACK, PBLAS, ScaLAPACK and the library FFTW.</longdescription>
-	<upstream>
-		<remote-id type="github">andyspiros/numbench</remote-id>
-	</upstream>
-</pkgmetadata>
diff --git a/app-benchmarks/numbench/numbench-0.2.ebuild b/app-benchmarks/numbench/numbench-0.2.ebuild
deleted file mode 100644
index f9b79e174..000000000
--- a/app-benchmarks/numbench/numbench-0.2.ebuild
+++ /dev/null
@@ -1,37 +0,0 @@
-# Copyright 1999-2016 Gentoo Foundation
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=6
-
-PYTHON_COMPAT=( python2_7 )
-
-inherit distutils-r1 vcs-snapshot
-
-DESCRIPTION="Automated benchmarks suite"
-HOMEPAGE="http://soc.dev.gentoo.org/~spiros"
-SRC_URI="http://github.com/andyspiros/numbench/tarball/${PV} -> ${P}.tar.gz"
-CID="127a61c"
-
-LICENSE="GPL-2"
-SLOT="0"
-KEYWORDS="~amd64 ~x86"
-
-IUSE=""
-
-RDEPEND="
-	!app-eselect/eselect-blas
-	!app-eselect/eselect-cblas
-	!app-eselect/eselect-lapack
-	>=dev-python/matplotlib-1.0.0
-	>=app-admin/eselect-1.3.2-r100"
-
-python_install_all() {
-	distutils-r1_python_install_all
-
-	python_foreach_impl python_newscript exec.py numbench
-
-	insinto /usr/share/numbench/samples
-	doins samples/*.xml
-
-	doman doc/numbench.1
-}
diff --git a/app-benchmarks/numbench/numbench-9999.ebuild b/app-benchmarks/numbench/numbench-9999.ebuild
deleted file mode 100644
index 831a41d6a..000000000
--- a/app-benchmarks/numbench/numbench-9999.ebuild
+++ /dev/null
@@ -1,37 +0,0 @@
-# Copyright 1999-2016 Gentoo Foundation
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=6
-
-PYTHON_COMPAT=( python2_7 )
-
-inherit distutils-r1 git-r3
-
-DESCRIPTION="Automated benchmarks suite"
-HOMEPAGE="http://soc.dev.gentoo.org/~spiros"
-#EGIT_REPO_URI="git://git.overlays.gentoo.org/proj/auto-numerical-bench.git"
-EGIT_REPO_URI="git://github.com/andyspiros/numbench.git"
-
-LICENSE="GPL-2"
-SLOT="0"
-KEYWORDS=""
-
-IUSE=""
-
-RDEPEND="
-	!app-eselect/eselect-blas
-	!app-eselect/eselect-cblas
-	!app-eselect/eselect-lapack
-	>=dev-python/matplotlib-1.0.0
-	>=app-admin/eselect-1.3.2-r100"
-
-python_install_all() {
-	distutils-r1_python_install_all
-
-	python_foreach_impl python_newscript exec.py numbench
-
-	insinto /usr/share/numbench/samples
-	doins samples/*.xml
-
-	doman doc/numbench.1
-}
diff --git a/app-doc/blacs-docs/Manifest b/app-doc/blacs-docs/Manifest
deleted file mode 100644
index 344d51d14..000000000
--- a/app-doc/blacs-docs/Manifest
+++ /dev/null
@@ -1 +0,0 @@
-DIST blacs-docs-1.1.tar.xz 197992 BLAKE2B b42816b456ad29888bf4149983a4f390cc811b62b31efd74d9c0d765779f9853e469d6c96975cd4e1ff497010964574241cc6bbab94ea281b8c1dbf356a87c90 SHA512 69285f621c77866ea51435b92f8ed9bf9df999d0e2a9bd53a3b80ec61d54793d37156d9ba427382c9c1388f91848f672eb23a68c37cb7962e6695d872f8e3e4f
diff --git a/app-doc/blacs-docs/blacs-docs-1.1.ebuild b/app-doc/blacs-docs/blacs-docs-1.1.ebuild
deleted file mode 100644
index 7bb93e833..000000000
--- a/app-doc/blacs-docs/blacs-docs-1.1.ebuild
+++ /dev/null
@@ -1,19 +0,0 @@
-# Copyright 1999-2016 Gentoo Foundation
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=6
-
-DESCRIPTION="Documentation reference for BLACS implementations"
-HOMEPAGE="http://www.netlib.org/blacs/"
-SRC_URI="https://dev.gentoo.org/~jlec/distfiles/${P}.tar.xz"
-
-LICENSE="BSD"
-SLOT="0"
-KEYWORDS="~amd64 ~x86"
-IUSE=""
-
-S="${WORKDIR}"
-
-src_install() {
-	dodoc *ps
-}
diff --git a/app-doc/blacs-docs/metadata.xml b/app-doc/blacs-docs/metadata.xml
deleted file mode 100644
index 165882922..000000000
--- a/app-doc/blacs-docs/metadata.xml
+++ /dev/null
@@ -1,17 +0,0 @@
-<?xml version="1.0" encoding="UTF-8"?>
-<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
-<pkgmetadata>
-	<maintainer type="project">
-		<email>sci@gentoo.org</email>
-		<name>Gentoo Science Project</name>
-	</maintainer>
-	<longdescription lang="en">
-The BLACS (Basic Linear Algebra Communication Subprograms) project
-is an ongoing investigation whose purpose is to create a linear
-algebra oriented message passing interface that may be implemented
-efficiently and uniformly across a large range of distributed memory
-platforms.
-This package contains manual pages for the routines, and other
-quick reference in postscript format.
-</longdescription>
-</pkgmetadata>
diff --git a/app-doc/blas-docs/Manifest b/app-doc/blas-docs/Manifest
deleted file mode 100644
index 4267db22a..000000000
--- a/app-doc/blas-docs/Manifest
+++ /dev/null
@@ -1,3 +0,0 @@
-DIST blas-report.pdf 2412966 BLAKE2B 3e9f1036e22ea003e8432eae95e8000c7afd850cb0fb2701afbe62e171fa4f32495ce3876c712b606dd8ff0c301697d12dc145e0782143b87c8f74f8d613a31d SHA512 a8a0a8e5eb591461779a7111c130fb7e56dcef0cec3f741c66bd7449b423fced4de61ae7fe9b0f7caa6828119d519198ede72cdeac4c84bf7c698a99e0903e6a
-DIST blasqr.pdf 97443 BLAKE2B 92648b4afbdcce29d3550986db22747bc7f3e592847086c56a1be8ad71547009e677430af2c6db47a96087a8db1ab04a64047c5fa30f48b665cb023855327cdc SHA512 e16f6c4e29df1676b06251c2b71ccfcf83229a73aedbee1a08590a385bffbe3b6668830d213dab6be926c4e6f5adade48c922f96cc0753e9aac19d33abd44168
-DIST lapack-man-3.3.tar.gz 1066170 BLAKE2B 55fbdc7ebd29560db3fd08285e6c5e30e91b423180c4e828a8d2fcf7430a02c64289189b0b8d86358ef7655712eb9c64ed5ff07e9bed25bc80ee9e1999faec72 SHA512 0c437c208bf0509f8183234241bb471cfe5fa7ffe800d52ab3714faa4d6e48ab8be46319555410b0bb2db0db7d289a05110dc8a7c949f40fec13bf1c518c99ee
diff --git a/app-doc/blas-docs/blas-docs-3.3.ebuild b/app-doc/blas-docs/blas-docs-3.3.ebuild
deleted file mode 100644
index 7be6828b3..000000000
--- a/app-doc/blas-docs/blas-docs-3.3.ebuild
+++ /dev/null
@@ -1,30 +0,0 @@
-# Copyright 1999-2016 Gentoo Foundation
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=6
-
-DESCRIPTION="Documentation reference and man pages for blas implementations"
-HOMEPAGE="http://www.netlib.org/blas/"
-SRC_URI="
-	http://dev.gentoo.org/~bicatali/lapack-man-${PV}.tar.gz
-	http://www.netlib.org/blas/blasqr.pdf
-	http://www.netlib.org/blas/blast-forum/blas-report.pdf"
-
-LICENSE="BSD"
-SLOT="0"
-KEYWORDS="~amd64 ~x86 ~amd64-linux ~x86-linux"
-IUSE=""
-
-S="${WORKDIR}/manpages"
-
-src_install() {
-	# rename because doman do not yet understand manl files
-	# Not all systems have the rename command, like say FreeBSD
-	local f t
-	for f in blas/man/manl/*.l; do
-		t="${f%%.l}.n"
-		mv "${f}" "${t}" || die
-	done
-	doman blas/man/manl/*.n
-	dodoc README "${DISTDIR}"/blas{-report,qr}.pdf
-}
diff --git a/app-doc/blas-docs/metadata.xml b/app-doc/blas-docs/metadata.xml
deleted file mode 100644
index dfb4275fa..000000000
--- a/app-doc/blas-docs/metadata.xml
+++ /dev/null
@@ -1,17 +0,0 @@
-<?xml version="1.0" encoding="UTF-8"?>
-<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
-<pkgmetadata>
-	<maintainer type="project">
-		<email>sci@gentoo.org</email>
-		<name>Gentoo Science Project</name>
-	</maintainer>
-	<longdescription lang="en">
-BLAS (Basic Linear Algebra Subroutines) is a set of efficient routines
-for most of the basic vector and matrix operations. They are widely
-used as the basis for other high quality linear algebra software, for
-example lapack and linpack. This implementation is the Fortran 77
-reference implementation found at netlib.
-This package contains manual pages for the routines, and other
-quick reference in postscript format.
-</longdescription>
-</pkgmetadata>
diff --git a/app-doc/lapack-docs/Manifest b/app-doc/lapack-docs/Manifest
deleted file mode 100644
index 91cf6a7f2..000000000
--- a/app-doc/lapack-docs/Manifest
+++ /dev/null
@@ -1,2 +0,0 @@
-DIST lapack-man-3.3.tar.gz 1066170 BLAKE2B 55fbdc7ebd29560db3fd08285e6c5e30e91b423180c4e828a8d2fcf7430a02c64289189b0b8d86358ef7655712eb9c64ed5ff07e9bed25bc80ee9e1999faec72 SHA512 0c437c208bf0509f8183234241bb471cfe5fa7ffe800d52ab3714faa4d6e48ab8be46319555410b0bb2db0db7d289a05110dc8a7c949f40fec13bf1c518c99ee
-DIST lapackqref.ps 72345 BLAKE2B b5c4b7c7d7dae50f622ce06015ca5230a33f880eabba9e8c2b6e27999d51055b6a5b7bae3f7634c1e9313ffb9ffd3cf542b1d68229ae215f51984798cec0b1dc SHA512 b5177910f988002f9b9bc4e735c457b6e65e57e0f4860e237e82e038bd77ef2071d2251b41677374742219dcd0162cd0a92dfba9801279a4b8bb6aa5bdbf0820
diff --git a/app-doc/lapack-docs/lapack-docs-3.3-r1.ebuild b/app-doc/lapack-docs/lapack-docs-3.3-r1.ebuild
deleted file mode 100644
index 314b2fce5..000000000
--- a/app-doc/lapack-docs/lapack-docs-3.3-r1.ebuild
+++ /dev/null
@@ -1,32 +0,0 @@
-# Copyright 1999-2016 Gentoo Foundation
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=6
-
-DESCRIPTION="Documentation reference and man pages for LAPACK implementations"
-HOMEPAGE="http://www.netlib.org/lapack/"
-SRC_URI="
-	http://dev.gentoo.org/~bicatali/lapack-man-${PV}.tar.gz
-	http://www.netlib.org/lapack/lapackqref.ps"
-
-LICENSE="BSD"
-SLOT="0"
-KEYWORDS="~amd64 ~x86 ~amd64-linux ~x86-linux"
-IUSE=""
-
-S="${WORKDIR}/manpages"
-
-src_install() {
-	# These belong to the blas-docs
-	rm -f man/manl/{csrot,lsame,xerbla,xerbla_array,zdrot}.* || die
-
-	# rename because doman do not yet understand manl files
-	# Not all systems have the rename command, like say FreeBSD
-	local f t
-	for f in man/manl/*.l; do
-		t="${f%%.l}.n"
-		mv "${f}" "${t}" || die
-	done
-	doman man/manl/*
-	dodoc README "${DISTDIR}"/lapackqref.ps
-}
diff --git a/app-doc/lapack-docs/metadata.xml b/app-doc/lapack-docs/metadata.xml
deleted file mode 100644
index 19cefda24..000000000
--- a/app-doc/lapack-docs/metadata.xml
+++ /dev/null
@@ -1,16 +0,0 @@
-<?xml version="1.0" encoding="UTF-8"?>
-<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
-<pkgmetadata>
-	<maintainer type="project">
-		<email>sci@gentoo.org</email>
-		<name>Gentoo Science Project</name>
-	</maintainer>
-	<longdescription lang="en">
-LAPACK is a comprehensive FORTRAN library that does linear
-algebra operations including matrix inversions, least squared
-solutions to linear sets of equations, eigenvector analysis, singular
-value decomposition, etc. It is a very comprehensive and reputable
-package that has found extensive use in the scientific community.
-This package contains manual pages for the routines, and a Quick-Reference guide.
-</longdescription>
-</pkgmetadata>
diff --git a/app-doc/scalapack-docs/Manifest b/app-doc/scalapack-docs/Manifest
deleted file mode 100644
index 9078affd2..000000000
--- a/app-doc/scalapack-docs/Manifest
+++ /dev/null
@@ -1 +0,0 @@
-DIST scalapack-docs-2.0.tar.bz2 333002 BLAKE2B 05fd9f07247fa78cdf1d5838daa3e87ae9870dd63d88166b64c9e0ee791e98c64e899b49bbf37f6f2563f513df7d520450dc754f4b995d6a808bae577c3dab8d SHA512 5c9cc1860b12532bb68fc2567aa9decf6e1cf14eb9696fa9f04b79744ef01339796434346136a9ef3cc8aab4195bb7d873b22e8cab1825943f5753aa3115f022
diff --git a/app-doc/scalapack-docs/metadata.xml b/app-doc/scalapack-docs/metadata.xml
deleted file mode 100644
index f404a1788..000000000
--- a/app-doc/scalapack-docs/metadata.xml
+++ /dev/null
@@ -1,18 +0,0 @@
-<?xml version="1.0" encoding="UTF-8"?>
-<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
-<pkgmetadata>
-	<maintainer type="project">
-		<email>sci@gentoo.org</email>
-		<name>Gentoo Science Project</name>
-	</maintainer>
-	<longdescription lang="en">
-The ScaLAPACK (or Scalable LAPACK) library includes a subset of
-LAPACK routines redesigned for distributed memory MIMD parallel
-computers. It is currently written in a Single-Program-Multiple-Data
-style using explicit message passing for interprocessor
-communication. It assumes matrices are laid out in a two-dimensional
-block cyclic decomposition.
-This package contains manual pages for the routines, and quick
-reference guides.
-</longdescription>
-</pkgmetadata>
diff --git a/app-doc/scalapack-docs/scalapack-docs-2.0.ebuild b/app-doc/scalapack-docs/scalapack-docs-2.0.ebuild
deleted file mode 100644
index 6e0caf6a5..000000000
--- a/app-doc/scalapack-docs/scalapack-docs-2.0.ebuild
+++ /dev/null
@@ -1,27 +0,0 @@
-# Copyright 1999-2016 Gentoo Foundation
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=6
-
-DESCRIPTION="Documentation reference and man pages for ScaLAPACK implementations"
-HOMEPAGE="http://www.netlib.org/scalapack/"
-SRC_URI="http://dev.gentoo.org/~bicatali/distfiles/${P}.tar.bz2"
-
-LICENSE="BSD"
-SLOT="0"
-KEYWORDS="~amd64 ~x86 ~amd64-linux ~x86-linux"
-IUSE=""
-
-S="${WORKDIR}"
-
-src_install() {
-	# rename because doman do not yet understand manl files
-	# Not all systems have the rename command, like say FreeBSD
-	local f t
-	for f in MANPAGES/man/manl/*.l; do
-		t="${f%%.l}.n"
-		mv "${f}" "${t}" || die
-	done
-	doman MANPAGES/man/manl/*
-	dodoc *.ps
-}
diff --git a/app-forensics/vine/Manifest b/app-forensics/vine/Manifest
deleted file mode 100644
index 914d14634..000000000
--- a/app-forensics/vine/Manifest
+++ /dev/null
@@ -1 +0,0 @@
-DIST vine-1.0.tar.gz 3401264 BLAKE2B 9afb3e28e95cc76bb273f56dc4937d8babf44ddebf85f2f31b79e2bdfdd01d87c3a180f04ffde1299edfc389f9e65369587c68f9a94671734b0226a812ea72f2 SHA512 9e204fe1954331bc2cfc5f1c648f828e9441adc8ba2e7cdec5f09f805ecc89c97a7995d9bf8a78574b9b37e53cac7b433b3f9b22d7148add2931fbbb8821cf70
diff --git a/app-forensics/vine/files/vine-1.0-binutils.patch b/app-forensics/vine/files/vine-1.0-binutils.patch
deleted file mode 100644
index 737f10ce2..000000000
--- a/app-forensics/vine/files/vine-1.0-binutils.patch
+++ /dev/null
@@ -1,16 +0,0 @@
-https://groups.google.com/d/msg/bitblaze-users/Zpg7Ddzngns/o7LNnR0qqxwJ
-
-Index: libasmir/src/disasm/asm_program.cpp
-===================================================================
---- a/libasmir/src/disasm/asm_program.cpp        (older version)
-+++ b/libasmir/src/disasm/asm_program.cpp        (fixed version)
-@@ -7,6 +7,11 @@
- #include "debug.h"
- #include "asm_program.h"
- #include "objdump.h"
-+/* Some versions of glibc and the binutils libiberty library give 
-+   conflicting prototypes for basename(). We don't use that function
-+   anyway, but to work around the problem, make libliberty.h think
-+   that it has already been declared. */
-+#define HAVE_DECL_BASENAME 1
- #include "libiberty.h"
diff --git a/app-forensics/vine/files/vine-1.0-gcc46.patch b/app-forensics/vine/files/vine-1.0-gcc46.patch
deleted file mode 100644
index 41dc0ae40..000000000
--- a/app-forensics/vine/files/vine-1.0-gcc46.patch
+++ /dev/null
@@ -1,37 +0,0 @@
-https://groups.google.com/d/msg/bitblaze-users/sTTPlFEzWo0/0ZjPL0QYC8IJ
-
-Index: libasmir/src/vex/irtoir-i386.cpp
-===================================================================
---- a/libasmir/src/vex/irtoir-i386.cpp        (old revision)
-+++ b/libasmir/src/vex/irtoir-i386.cpp        (new revision)
-@@ -9,6 +9,13 @@
- web site at: http://bitblaze.cs.berkeley.edu/
- */
- 
-+/* Because we use offsetof() for values that go in switch statement
-+   cases, we need a definition in terms of __builtin_offsetof so that
-+   GCC >= 4.6 can accept the results of offsetof() as a constant
-+   expression. They've stopped supporting the traditional definition
-+   as a macro &((type*)0)->memb, which appears in VEX's headers. */
-+#include <stddef.h>
-+
- #include <string>
- #include <vector>
- #include <iostream>
-Index: libasmir/src/vex/irtoir-arm.cpp
-===================================================================
---- a/libasmir/src/vex/irtoir-arm.cpp        (old revision)
-+++ b/libasmir/src/vex/irtoir-arm.cpp        (new revision)
-@@ -9,6 +9,12 @@
- web site at: http://bitblaze.cs.berkeley.edu/
- */
- 
-+/* Because we use offsetof() for values that go in switch statement
-+   cases, we need a definition in terms of __builtin_offsetof so that
-+   GCC >= 4.6 can accept the results of offsetof() as a constant
-+   expression. They've stopped supporting the traditional definition
-+   as a macro &((type*)0)->memb, which appears in VEX's headers. */
-+#include <stddef.h>
- 
- #include "irtoir-internal.h"
- #include "libvex_guest_arm.h"
diff --git a/app-forensics/vine/files/vine-1.0-install.patch b/app-forensics/vine/files/vine-1.0-install.patch
deleted file mode 100644
index 166bd1c4e..000000000
--- a/app-forensics/vine/files/vine-1.0-install.patch
+++ /dev/null
@@ -1,89 +0,0 @@
---- a/stp/ocaml/Makefile	2009-09-24 15:45:57.000000000 -0600
-+++ b/stp/ocaml/Makefile	2013-03-14 20:22:49.993194747 -0600
-@@ -14,3 +14,6 @@
- 		Makefile
- 
- include $(OCAMLMAKEFILE)
-+
-+install: rawinstall
-+
---- a/stp/ocaml/OCamlMakefile	2009-09-24 15:45:57.000000000 -0600
-+++ b/stp/ocaml/OCamlMakefile	2013-03-14 20:20:23.012069386 -0600
-@@ -1126,10 +1126,10 @@
- .PHONY: rawinstall
- rawinstall:	all
- 	$(QUIET)printf "\nInstalling library to: $(OCAML_LIB_INSTALL)\n"
--	-install -d $(OCAML_LIB_INSTALL)
-+	-install -d $(DESTDIR)$(OCAML_LIB_INSTALL)
- 	for i in $(LIBINSTALL_FILES); do \
- 	  if [ -f $$i ]; then \
--	    install -c -m 0644 $$i $(OCAML_LIB_INSTALL); \
-+	    install -c -m 0644 $$i $(DESTDIR)$(OCAML_LIB_INSTALL); \
- 	  fi; \
- 	done
- 	$(QUIET)printf "\nInstallation successful.\n"
-
---- a/ocaml/Makefile	2009-09-24 15:45:57.000000000 -0600
-+++ b/ocaml/Makefile	2013-03-14 20:22:49.993194747 -0600
-@@ -14,3 +14,6 @@
- 
- 
- include $(OCAMLMAKEFILE)
-+
-+install: rawinstall
-+
---- a/ocaml/OCamlMakefile	2009-09-24 15:45:57.000000000 -0600
-+++ b/ocaml/OCamlMakefile	2013-03-14 20:20:23.012069386 -0600
-@@ -1126,10 +1126,10 @@
- .PHONY: rawinstall
- rawinstall:	all
- 	$(QUIET)printf "\nInstalling library to: $(OCAML_LIB_INSTALL)\n"
--	-install -d $(OCAML_LIB_INSTALL)
-+	-install -d $(DESTDIR)$(OCAML_LIB_INSTALL)
- 	for i in $(LIBINSTALL_FILES); do \
- 	  if [ -f $$i ]; then \
--	    install -c -m 0644 $$i $(OCAML_LIB_INSTALL); \
-+	    install -c -m 0644 $$i $(DESTDIR)$(OCAML_LIB_INSTALL); \
- 	  fi; \
- 	done
- 	$(QUIET)printf "\nInstallation successful.\n"
---- a/trace/Makefile	2009-09-24 15:45:57.000000000 -0600
-+++ b/trace/Makefile	2013-03-14 20:22:49.993194747 -0600
-@@ -14,3 +14,6 @@
- 
- 
- include $(OCAMLMAKEFILE)
-+
-+install: rawinstall
-+
---- a/trace_utils/Makefile	2009-09-24 15:45:57.000000000 -0600
-+++ b/trace_utils/Makefile	2013-03-16 14:31:46.375690732 -0600
-@@ -88,6 +88,8 @@
- #    * subprjs
- 
- 
-+install:
-+	
- 
- %:
- 	make -f $(OCAMLMAKEFILE) subprojs SUBTARGET=$@
---- a/utils/Makefile	2009-09-24 15:45:57.000000000 -0600
-+++ b/utils/Makefile	2013-03-16 14:31:46.375690732 -0600
-@@ -88,6 +88,8 @@
- #    * subprjs
- 
- 
-+install:
-+	
- 
- %:
- 	make -f $(OCAMLMAKEFILE) subprojs SUBTARGET=$@
---- a/doc/Makefile	2009-09-24 15:45:57.000000000 -0600
-+++ b/doc/Makefile	2013-03-16 14:41:59.182926821 -0600
-@@ -17,3 +17,6 @@
- 
- clean:
- 	(cd howto && $(MAKE) clean)
-+
-+install:
-+	
diff --git a/app-forensics/vine/files/vine-1.0-ocamlgraph182.patch b/app-forensics/vine/files/vine-1.0-ocamlgraph182.patch
deleted file mode 100644
index e9a2f5d6a..000000000
--- a/app-forensics/vine/files/vine-1.0-ocamlgraph182.patch
+++ /dev/null
@@ -1,68 +0,0 @@
-Index: ocaml/vine_cfg.mli
-===================================================================
---- a/ocaml/vine_cfg.mli          (old version)
-+++ b/ocaml/vine_cfg.mli          (new version)
-@@ -86,6 +86,11 @@
-     (** [cfg#iter_edges f] calls [f a b] forall [(a,b)] where there is an edge
- vine-1.0-from [a] to [b] in the CFG.  *)
- 
-+  method fold_edges : 'b. ('a bb -> 'a bb -> 'b -> 'b) -> 'b -> 'b
-+    (** [cfg#fold_edges f init] computes [f uN uN (... (f u1 v1
-+init)...)] where [(u1, v1) ... (uN, vN)] is an enumeration of all
-+the edges in the graph, in an unspecified order. *)
-+
-   method get_info : 'a bb -> 'a
-     (** Returns the info associated with the given bb. *)
- 
-@@ -225,6 +230,7 @@
-   val iter_vertex : (bbid -> unit) -> t -> unit
-   val fold_vertex : (vertex -> 'a -> 'a) -> t -> 'a -> 'a
-   val iter_edges_e : (E.t -> unit) -> t -> unit
-+  val fold_edges_e : (E.t -> 'a -> 'a) -> t -> 'a -> 'a
-   val iter_succ : (vertex -> unit) -> t -> vertex -> unit
-   val iter_pred : (vertex -> unit) -> t -> vertex -> unit
-   val in_degree : t -> vertex -> int
-Index: ocaml/vine_cfg.ml
-===================================================================
---- a/ocaml/vine_cfg.ml             (old version)
-+++ b/ocaml/vine_cfg.ml             (new version)
-@@ -115,6 +115,7 @@
-   method iter_bb : ('a bb -> unit) -> unit
-   method fold_bb : 'b. ('a bb -> 'b -> 'b) -> 'b -> 'b
-   method iter_edges : ('a bb -> 'a bb -> unit) -> unit
-+  method fold_edges : 'b. ('a bb -> 'a bb -> 'b -> 'b) -> 'b -> 'b
-   method get_info : 'a bb -> 'a
-   method set_info : 'a bb -> 'a -> unit
-   method get_id : 'a bb -> bbid
-@@ -306,6 +307,14 @@
-     self#iter_bb (fun b -> List.iter (f b) (self#succ b));
-     self#check_graph;
- 
-+  method fold_edges f a =
-+    self#check_graph;
-+    let res = self#fold_bb
-+      (fun b a2 -> List.fold_left (fun a3 b2 -> f b b2 a3) a2 (self#succ b)) a
-+    in
-+      self#check_graph;
-+      res
-+
-   method length = Hashtbl.length blktbl
- 
-   method get_info b =
-@@ -1122,6 +1131,7 @@
-   val iter_vertex : (bbid -> unit) -> t -> unit
-   val fold_vertex : (bbid -> 'a -> 'a) -> t -> 'a -> 'a
-   val iter_edges_e : (E.t -> unit) -> t -> unit
-+  val fold_edges_e : (E.t -> 'a -> 'a) -> t -> 'a -> 'a
-   val iter_succ : (vertex -> unit) -> t -> vertex -> unit
-   val iter_pred : (vertex -> unit) -> t -> vertex -> unit
-   val in_degree : t -> vertex -> int
-@@ -1170,6 +1180,8 @@
-   let fold_vertex f (g:t) a = g#fold_bb (fun b -> f b.id) a 
-   let iter_edges_e f (g:t) =
-     g#iter_edges (fun x y -> f (g#get_id x, g#get_id y))
-+  let fold_edges_e f (g:t) a =
-+    g#fold_edges (fun x y a -> f (g#get_id x, g#get_id y) a) a
-   let iter_succ f g v = List.iter f (bb_succ g v)
-   let iter_pred f g v = List.iter f (bb_pred g v)
-   let in_degree g v = List.length (bb_pred g v)
diff --git a/app-forensics/vine/metadata.xml b/app-forensics/vine/metadata.xml
deleted file mode 100644
index 9dee8db11..000000000
--- a/app-forensics/vine/metadata.xml
+++ /dev/null
@@ -1,8 +0,0 @@
-<?xml version="1.0" encoding="UTF-8"?>
-<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
-<pkgmetadata>
-	<maintainer type="person">
-		<email>ottxor@gentoo.org</email>
-		<name>Christoph Junghans</name>
-	</maintainer>
-</pkgmetadata>
diff --git a/app-forensics/vine/vine-1.0.ebuild b/app-forensics/vine/vine-1.0.ebuild
deleted file mode 100644
index 6ddc2ddbe..000000000
--- a/app-forensics/vine/vine-1.0.ebuild
+++ /dev/null
@@ -1,37 +0,0 @@
-# Copyright 1999-2016 Gentoo Foundation
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=6
-
-inherit eutils toolchain-funcs
-
-DESCRIPTION="The BitBlaze Static Analysis Component"
-HOMEPAGE="http://bitblaze.cs.berkeley.edu/vine.html"
-SRC_URI="http://bitblaze.cs.berkeley.edu/release/${P}/${P}.tar.gz"
-
-LICENSE="GPL-2+"
-SLOT="0"
-KEYWORDS=""
-IUSE=""
-
-DEPEND="
-	dev-lang/ocaml
-	dev-ml/findlib
-	dev-ml/camlidl
-	>=dev-libs/gmetadom-0.2.6-r1[ocaml]
-	dev-ml/extlib
-	dev-ml/ocamlgraph"
-RDEPEND="${DEPEND}"
-
-MAKEOPTS="${MAKEOPTS} -j1"
-
-PATCHES=(
-	"${FILESDIR}"/${P}-binutils.patch
-	"${FILESDIR}"/${P}-gcc46.patch
-	"${FILESDIR}"/${P}-install.patch
-	"${FILESDIR}"/${P}-ocamlgraph182.patch
-)
-
-src_compile() {
-	emake CC=$(tc-getCC) CCFLAGS="${CFLAGS} -fPIC"
-}
diff --git a/app-office/visidata/Manifest b/app-office/visidata/Manifest
new file mode 100644
index 000000000..841bc773a
--- /dev/null
+++ b/app-office/visidata/Manifest
@@ -0,0 +1,4 @@
+DIST visidata-2.11.1.gh.tar.gz 1928973 BLAKE2B bb9c40121175db262d4e0256b4e5b71313228590b9517e42589158d1a6279add0c1eacf1fe0ae5d38bd013b53c3ccad92ba0c4e39d40e27605c1502c84c40a5d SHA512 01905795ae6216e3cf662b43732394c68b43ffc8a4dc40da8552ebefaba4535fa3937aec1825cb108267dd83ab1b6a1072d1e698d416eae883dba915ca40b332
+DIST visidata-2.11.gh.tar.gz 1927455 BLAKE2B 95f868028fabb488f550b2ba15b60104a2d54dff972946ac38996d2906464e306e396adbf8dee32107aaf19a48d0e5d087aeeec82909e1d09b1d84b1e61138b7 SHA512 01512d47da329ba95aa7ceb5678a652fba5e06f6ff7ef0216b6271bf5b63a10712d425a2a1668ef6399b74f9fa9cb8d2d0f7bfa9316488ef5d64285ddcdde31a
+DIST visidata-2.11_p20230217.gh.tar.gz 2062327 BLAKE2B c7cd07ac816a31c2294d431c6426fc44f8a2cf015e7994d8b918c9e60cce2e7700ac77919c5a9e5c3ad5ccf41cb5b04e34fc84016a0c6faa8bd4e8e470275d0a SHA512 eaf2060c6fe6d1fed713cb0318d12233f279151a1a97b11ae3a7ccf07a065d716cf81872b76aa71a15dda3bfd85c09e7e03f9be2fae857f8edbded86e06b597f
+DIST visidata-2.8.gh.tar.gz 1791958 BLAKE2B f7a7dec514bcca37b4ee6ee9c16eb07a625b83e601a5bcf1ca5589a462e50086cbd9997238230ac464b4dc77e9deb421d3ff0bcf0fa39b32f1c1ce0308d2cb7b SHA512 da9bce4e59054ea518024639a1f60d6f19886cd061a52aa49189d7478ea27950e6e97e0d1730456b65815f9298d0225bfcebe4bba5452e1a9a87f5f56aa11dc3
diff --git a/app-office/visidata/metadata.xml b/app-office/visidata/metadata.xml
new file mode 100644
index 000000000..67a30f446
--- /dev/null
+++ b/app-office/visidata/metadata.xml
@@ -0,0 +1,18 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
+<pkgmetadata>
+	<maintainer type="person">
+		<email>chr@chymera.eu</email>
+		<name>Horea Christian</name>
+	</maintainer>
+	<longdescription lang="en">
+		VisiData is an interactive multitool for tabular data. It combines the
+		clarity of a spreadsheet, the efficiency of the terminal, and the power
+		of Python, into a lightweight utility which can handle millions of rows
+		with ease.
+	</longdescription>
+	<upstream>
+		<remote-id type="github">saulpw/visidata</remote-id>
+		<remote-id type="pypi">visidata</remote-id>
+	</upstream>
+</pkgmetadata>
diff --git a/app-office/visidata/visidata-2.11-r1.ebuild b/app-office/visidata/visidata-2.11-r1.ebuild
new file mode 100644
index 000000000..208587336
--- /dev/null
+++ b/app-office/visidata/visidata-2.11-r1.ebuild
@@ -0,0 +1,90 @@
+# Copyright 1999-2023 Gentoo Authors
+# Distributed under the terms of the GNU General Public License v2
+
+EAPI=8
+
+DISTUTILS_USE_PEP517=setuptools
+PYTHON_COMPAT=( python3_{10..11} )
+
+inherit distutils-r1 optfeature
+
+DESCRIPTION="Terminal spreadsheet multitool for discovering and arranging data"
+HOMEPAGE="http://visidata.org"
+SRC_URI="https://github.com/saulpw/${PN}/archive/v${PV}.tar.gz -> ${P}.gh.tar.gz"
+
+LICENSE="GPL-3"
+SLOT="0"
+KEYWORDS="~amd64 ~x86"
+# Tests fail on recent Python:
+# https://github.com/saulpw/visidata/issues/1905
+RESTRICT="test"
+
+RDEPEND="
+	>=dev-python/importlib-metadata-3.6[${PYTHON_USEDEP}]
+	dev-python/python-dateutil[${PYTHON_USEDEP}]
+"
+BDEPEND="
+	test? (
+		dev-python/h5py[${PYTHON_USEDEP}]
+		dev-python/odfpy[${PYTHON_USEDEP}]
+		dev-python/openpyxl[${PYTHON_USEDEP}]
+		dev-python/pandas[${PYTHON_USEDEP}]
+		dev-python/pytest[${PYTHON_USEDEP}]
+		dev-python/requests[${PYTHON_USEDEP}]
+		dev-vcs/git
+		$(python_gen_impl_dep sqlite)
+	)
+"
+
+#distutils_enable_sphinx docs \
+#	dev-python/recommonmark \
+#	dev-python/sphinx-argparse
+# dev-python/sphinx-markdown-tables
+
+distutils_enable_tests pytest
+
+python_prepare_all() {
+	rm tests/load-http.vd || die "Could not remove network-dependent test."
+	rm tests/graph-cursor-nosave.vd || die "Could not remove network-dependent test."
+	rm tests/messenger-nosave.vd || die "Could not remove network-dependent test."
+	rm tests/save-benchmarks.vd || die "Could not benchmarks test"
+	rm tests/graphpr-nosave.vd || die "Could not benchmarks test"
+	rm tests/describe-error.vd || die "Could not remove network-dependent test"
+	rm tests/describe.vd || die "Could not remove network-dependent test"
+	rm tests/edit-type.vd || die "Could not remove network-dependent test"
+
+	distutils-r1_python_prepare_all
+}
+
+python_test() {
+	git init || die "Git init failed."
+	git add tests/golden/ || die "Git add failed."
+	# this test script eventually calls pytest under the hood
+	dev/test.sh || die "Tests failed."
+	rm .git -rf || die "Could not clean up git test directory."
+}
+
+pkg_postinst() {
+	optfeature "integration with yaml" >=dev-python/pyyaml-5.1
+	optfeature "integration with pcap" dev-python/dnslib #dpkt pypcapkit
+	optfeature "integration with png" dev-python/pypng
+	optfeature "integration with http" dev-python/requests
+	optfeature "integration with postgres" dev-python/psycopg-binary
+	optfeature "integration with xlsx" dev-python/openpyxl
+	optfeature "integration with xls" dev-python/xlrd
+	optfeature "integration with hdf5" dev-python/h5py
+	optfeature "integration with ttf/otf" dev-python/fonttools
+	optfeature "integration with xml/htm/html" dev-python/lxml
+	optfeature "integration with dta (Stata)" dev-python/pandas
+	optfeature "integration with shapefiles" sci-libs/pyshp
+	optfeature "integration with namestand" dev-python/graphviz
+	optfeature "integration with pdfminer.six" dev-python/pdfminer-six # in guru
+	optfeature "integration with vobject" dev-python/vobject
+	optfeature "integration with tabulate" dev-python/tabulate
+	optfeature "integration with tabulate (with unicode)" dev-python/wcwidth
+	# optfeature "pdf tables" tabula # no package presently
+	#optfeature "integration with mbtiles" mapbox-vector-tile
+	#optfeature "integration with xpt (SAS)" xport
+	#optfeature "integration with sas7bdat (SAS)" sas7bdat
+	#optfeature "integration with sav (SPSS)" savReaderWriter
+}
diff --git a/app-office/visidata/visidata-2.11.1.ebuild b/app-office/visidata/visidata-2.11.1.ebuild
new file mode 100644
index 000000000..3a5c510b4
--- /dev/null
+++ b/app-office/visidata/visidata-2.11.1.ebuild
@@ -0,0 +1,88 @@
+# Copyright 1999-2023 Gentoo Authors
+# Distributed under the terms of the GNU General Public License v2
+
+EAPI=8
+
+DISTUTILS_USE_PEP517=setuptools
+PYTHON_COMPAT=( python3_11 )
+
+inherit distutils-r1 optfeature
+
+DESCRIPTION="Terminal spreadsheet multitool for discovering and arranging data"
+HOMEPAGE="https://www.visidata.org/"
+SRC_URI="https://github.com/saulpw/visidata/archive/v${PV}.tar.gz -> ${P}.gh.tar.gz"
+
+LICENSE="GPL-3"
+SLOT="0"
+KEYWORDS="~amd64 ~x86"
+
+RDEPEND="
+	>=dev-python/importlib-metadata-3.6[${PYTHON_USEDEP}]
+	dev-python/python-dateutil[${PYTHON_USEDEP}]
+"
+DEPEND="${RDEPEND}"
+BDEPEND="
+	test? (
+		dev-python/h5py[${PYTHON_USEDEP}]
+		dev-python/odfpy[${PYTHON_USEDEP}]
+		dev-python/openpyxl[${PYTHON_USEDEP}]
+		dev-python/pandas[${PYTHON_USEDEP}]
+		dev-python/pytest[${PYTHON_USEDEP}]
+		dev-python/requests[${PYTHON_USEDEP}]
+		dev-vcs/git
+		$(python_gen_impl_dep sqlite)
+	)
+"
+
+#distutils_enable_sphinx docs \
+#	dev-python/recommonmark \
+#	dev-python/sphinx-argparse
+# dev-python/sphinx-markdown-tables
+
+distutils_enable_tests pytest
+
+python_prepare_all() {
+	rm tests/load-http.vd || die "Could not remove network-dependent test."
+	rm tests/graph-cursor-nosave.vd || die "Could not remove network-dependent test."
+	rm tests/messenger-nosave.vd || die "Could not remove network-dependent test."
+	rm tests/save-benchmarks.vd || die "Could not benchmarks test"
+	rm tests/graphpr-nosave.vd || die "Could not benchmarks test"
+	rm tests/describe-error.vd || die "Could not remove network-dependent test"
+	rm tests/describe.vd || die "Could not remove network-dependent test"
+	rm tests/edit-type.vd || die "Could not remove network-dependent test"
+
+	distutils-r1_python_prepare_all
+}
+
+python_test() {
+	git init || die "Git init failed."
+	git add tests/golden/ || die "Git add failed."
+	# this test script eventually calls pytest under the hood
+	dev/test.sh || die "Tests failed."
+	rm .git -rf || die "Could not clean up git test directory."
+}
+
+pkg_postinst() {
+	optfeature "integration with yaml" >=dev-python/pyyaml-5.1
+	optfeature "integration with pcap" dev-python/dnslib #dpkt pypcapkit
+	optfeature "integration with png" dev-python/pypng
+	optfeature "integration with http" dev-python/requests
+	optfeature "integration with postgres" dev-python/psycopg-binary
+	optfeature "integration with xlsx" dev-python/openpyxl
+	optfeature "integration with xls" dev-python/xlrd
+	optfeature "integration with hdf5" dev-python/h5py
+	optfeature "integration with ttf/otf" dev-python/fonttools
+	optfeature "integration with xml/htm/html" dev-python/lxml
+	optfeature "integration with dta (Stata)" dev-python/pandas
+	optfeature "integration with shapefiles" sci-libs/pyshp
+	optfeature "integration with namestand" dev-python/graphviz
+	optfeature "integration with pdfminer.six" dev-python/pdfminer-six # in guru
+	optfeature "integration with vobject" dev-python/vobject
+	optfeature "integration with tabulate" dev-python/tabulate
+	optfeature "integration with tabulate (with unicode)" dev-python/wcwidth
+	# optfeature "pdf tables" tabula # no package presently
+	#optfeature "integration with mbtiles" mapbox-vector-tile
+	#optfeature "integration with xpt (SAS)" xport
+	#optfeature "integration with sas7bdat (SAS)" sas7bdat
+	#optfeature "integration with sav (SPSS)" savReaderWriter
+}
diff --git a/app-office/visidata/visidata-2.11_p20230217-r1.ebuild b/app-office/visidata/visidata-2.11_p20230217-r1.ebuild
new file mode 100644
index 000000000..5edfdcb23
--- /dev/null
+++ b/app-office/visidata/visidata-2.11_p20230217-r1.ebuild
@@ -0,0 +1,90 @@
+# Copyright 1999-2023 Gentoo Authors
+# Distributed under the terms of the GNU General Public License v2
+
+EAPI=8
+
+DISTUTILS_USE_PEP517=setuptools
+PYTHON_COMPAT=( python3_{11..11} )
+
+inherit distutils-r1 optfeature
+
+MY_HASH="5ff7883563eeac32fe192c5b2d4290a4e1e91cc2"
+DESCRIPTION="Terminal spreadsheet multitool for discovering and arranging data"
+HOMEPAGE="http://visidata.org"
+SRC_URI="https://github.com/saulpw/visidata/archive/${MY_HASH}.tar.gz -> ${P}.gh.tar.gz"
+
+LICENSE="GPL-3"
+SLOT="0"
+KEYWORDS="~amd64 ~x86"
+
+RDEPEND="
+	>=dev-python/importlib-metadata-3.6[${PYTHON_USEDEP}]
+	dev-python/python-dateutil[${PYTHON_USEDEP}]
+"
+BDEPEND="
+	test? (
+		dev-python/h5py[${PYTHON_USEDEP}]
+		dev-python/odfpy[${PYTHON_USEDEP}]
+		dev-python/openpyxl[${PYTHON_USEDEP}]
+		dev-python/pandas[${PYTHON_USEDEP}]
+		dev-python/pytest[${PYTHON_USEDEP}]
+		dev-python/requests[${PYTHON_USEDEP}]
+		dev-vcs/git
+		$(python_gen_impl_dep sqlite)
+	)
+"
+
+S="${WORKDIR}/${PN}-${MY_HASH}"
+
+#distutils_enable_sphinx docs \
+#	dev-python/recommonmark \
+#	dev-python/sphinx-argparse
+# dev-python/sphinx-markdown-tables
+
+distutils_enable_tests pytest
+
+python_prepare_all() {
+	rm tests/load-http.vd || die "Could not remove network-dependent test."
+	rm tests/graph-cursor-nosave.vd || die "Could not remove network-dependent test."
+	rm tests/messenger-nosave.vd || die "Could not remove network-dependent test."
+	rm tests/save-benchmarks.vd || die "Could not benchmarks test"
+	rm tests/graphpr-nosave.vd || die "Could not benchmarks test"
+	rm tests/describe-error.vd || die "Could not remove network-dependent test"
+	rm tests/describe.vd || die "Could not remove network-dependent test"
+	rm tests/edit-type.vd || die "Could not remove network-dependent test"
+
+	distutils-r1_python_prepare_all
+}
+
+python_test() {
+	git init || die "Git init failed."
+	git add tests/golden/ || die "Git add failed."
+	# this test script eventually calls pytest under the hood
+	dev/test.sh || die "Tests failed."
+	rm .git -rf || die "Could not clean up git test directory."
+}
+
+pkg_postinst() {
+	optfeature "integration with yaml" >=dev-python/pyyaml-5.1
+	optfeature "integration with pcap" dev-python/dnslib #dpkt pypcapkit
+	optfeature "integration with png" dev-python/pypng
+	optfeature "integration with http" dev-python/requests
+	optfeature "integration with postgres" dev-python/psycopg-binary
+	optfeature "integration with xlsx" dev-python/openpyxl
+	optfeature "integration with xls" dev-python/xlrd
+	optfeature "integration with hdf5" dev-python/h5py
+	optfeature "integration with ttf/otf" dev-python/fonttools
+	optfeature "integration with xml/htm/html" dev-python/lxml
+	optfeature "integration with dta (Stata)" dev-python/pandas
+	optfeature "integration with shapefiles" sci-libs/pyshp
+	optfeature "integration with namestand" dev-python/graphviz
+	optfeature "integration with pdfminer.six" dev-python/pdfminer-six # in guru
+	optfeature "integration with vobject" dev-python/vobject
+	optfeature "integration with tabulate" dev-python/tabulate
+	optfeature "integration with tabulate (with unicode)" dev-python/wcwidth
+	# optfeature "pdf tables" tabula # no package presently
+	#optfeature "integration with mbtiles" mapbox-vector-tile
+	#optfeature "integration with xpt (SAS)" xport
+	#optfeature "integration with sas7bdat (SAS)" sas7bdat
+	#optfeature "integration with sav (SPSS)" savReaderWriter
+}
diff --git a/app-office/visidata/visidata-2.8.ebuild b/app-office/visidata/visidata-2.8.ebuild
new file mode 100644
index 000000000..11c164d7e
--- /dev/null
+++ b/app-office/visidata/visidata-2.8.ebuild
@@ -0,0 +1,88 @@
+# Copyright 1999-2023 Gentoo Authors
+# Distributed under the terms of the GNU General Public License v2
+
+EAPI=8
+
+DISTUTILS_USE_PEP517=setuptools
+PYTHON_COMPAT=( python3_{10..11} )
+
+inherit distutils-r1 optfeature
+
+DESCRIPTION="Terminal spreadsheet multitool for discovering and arranging data"
+HOMEPAGE="http://visidata.org"
+SRC_URI="https://github.com/saulpw/${PN}/archive/v${PV}.tar.gz -> ${P}.gh.tar.gz"
+
+LICENSE="GPL-3"
+SLOT="0"
+KEYWORDS="~amd64 ~x86"
+# Tests fail on recent Python:
+# https://github.com/saulpw/visidata/issues/1905
+RESTRICT="test"
+
+RDEPEND="dev-python/python-dateutil[${PYTHON_USEDEP}]"
+BDEPEND="
+	test? (
+		dev-python/h5py[${PYTHON_USEDEP}]
+		dev-python/odfpy[${PYTHON_USEDEP}]
+		dev-python/openpyxl[${PYTHON_USEDEP}]
+		dev-python/pandas[${PYTHON_USEDEP}]
+		dev-python/pytest[${PYTHON_USEDEP}]
+		dev-python/requests[${PYTHON_USEDEP}]
+		dev-vcs/git
+		$(python_gen_impl_dep sqlite)
+	)
+"
+
+#distutils_enable_sphinx docs \
+#	dev-python/recommonmark \
+#	dev-python/sphinx-argparse
+# dev-python/sphinx-markdown-tables
+
+distutils_enable_tests pytest
+
+python_prepare_all() {
+	rm tests/load-http.vd || die "Could not remove network-dependent test."
+	rm tests/graph-cursor-nosave.vd || die "Could not remove network-dependent test."
+	rm tests/messenger-nosave.vd || die "Could not remove network-dependent test."
+	rm tests/save-benchmarks.vd || die "Could not benchmarks test"
+	rm tests/graph-sincos-nosave.vd || die "Could not benchmarks test"
+	rm tests/graphpr-nosave.vd || die "Could not benchmarks test"
+	rm tests/describe-error.vd || die "Could not remove network-dependent test"
+	rm tests/describe.vd || die "Could not remove network-dependent test"
+	rm tests/edit-type.vd || die "Could not remove network-dependent test"
+
+	distutils-r1_python_prepare_all
+}
+
+python_test() {
+	git init || die "Git init failed."
+	git add tests/golden/ || die "Git add failed."
+	# this test script eventually calls pytest under the hood
+	dev/test.sh || die "Tests failed."
+	rm .git -rf || die "Could not clean up git test directory."
+}
+
+pkg_postinst() {
+	optfeature "integration with yaml" >=dev-python/pyyaml-5.1
+	optfeature "integration with pcap" dev-python/dnslib #dpkt pypcapkit
+	optfeature "integration with png" dev-python/pypng
+	optfeature "integration with http" dev-python/requests
+	optfeature "integration with postgres" dev-python/psycopg-binary
+	optfeature "integration with xlsx" dev-python/openpyxl
+	optfeature "integration with xls" dev-python/xlrd
+	optfeature "integration with hdf5" dev-python/h5py
+	optfeature "integration with ttf/otf" dev-python/fonttools
+	optfeature "integration with xml/htm/html" dev-python/lxml
+	optfeature "integration with dta (Stata)" dev-python/pandas
+	optfeature "integration with shapefiles" sci-libs/pyshp
+	optfeature "integration with namestand" dev-python/graphviz
+	optfeature "integration with pdfminer.six" dev-python/pdfminer-six # in guru
+	optfeature "integration with vobject" dev-python/vobject
+	optfeature "integration with tabulate" dev-python/tabulate
+	optfeature "integration with tabulate (with unicode)" dev-python/wcwidth
+	# optfeature "pdf tables" tabula # no package presently
+	#optfeature "integration with mbtiles" mapbox-vector-tile
+	#optfeature "integration with xpt (SAS)" xport
+	#optfeature "integration with sas7bdat (SAS)" sas7bdat
+	#optfeature "integration with sav (SPSS)" savReaderWriter
+}
diff --git a/app-portage/g-octave/g-octave-9999.ebuild b/app-portage/g-octave/g-octave-9999.ebuild
deleted file mode 100644
index 62316f5cf..000000000
--- a/app-portage/g-octave/g-octave-9999.ebuild
+++ /dev/null
@@ -1,40 +0,0 @@
-# Copyright 1999-2016 Gentoo Foundation
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=6
-
-PYTHON_COMPAT=( python2_7 )
-
-inherit distutils-r1 git-r3
-
-DESCRIPTION="A tool that generates and installs ebuilds for Octave-Forge"
-HOMEPAGE="http://www.g-octave.org/"
-SRC_URI=""
-EGIT_REPO_URI="git://git.overlays.gentoo.org/proj/g-octave.git"
-
-LICENSE="GPL-2"
-SLOT="0"
-KEYWORDS=""
-IUSE="doc test"
-
-DEPEND="
-	dev-python/docutils[${PYTHON_USEDEP}]
-	doc? ( dev-python/sphinx[${PYTHON_USEDEP}] )"
-RDEPEND="sys-apps/portage"
-
-S="${WORKDIR}/${PN}"
-
-python_compile_all() {
-	use doc && emake -C docs html
-}
-
-python_test() {
-	${PYTHON} scripts/run_tests.py || die
-}
-
-python_install_all() {
-	doman ${PN}.1
-	use doc && HTML_DOCS=( docs/_build/html/. )
-	HTML_DOCS+=( ${PN}.html )
-	distutils-r1_python_install_all
-}
diff --git a/app-portage/g-octave/metadata.xml b/app-portage/g-octave/metadata.xml
deleted file mode 100644
index 2388656e8..000000000
--- a/app-portage/g-octave/metadata.xml
+++ /dev/null
@@ -1,16 +0,0 @@
-<?xml version="1.0" encoding="UTF-8"?>
-<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
-<pkgmetadata>
-	<maintainer type="person">
-		<email>rafael@rafaelmartins.eng.br</email>
-		<name>Rafael Goncalves Martins</name>
-	</maintainer>
-	<longdescription lang="en">
-g-octave is a tool that generates and installs ebuilds for Octave-Forge
-packages "on-the-fly" to Gentoo Linux, using Portage. It's capable to
-generate ebuilds and Manifest files for the packages, and to install
-them using an autogenerated overlay (named g-octave). g-octave can also
-handle patches to the packages automatically. The command line interface
-tries to be very similar to the interface of the emerge tool.
-</longdescription>
-</pkgmetadata>
diff --git a/app-text/noweb/Manifest b/app-text/noweb/Manifest
new file mode 100644
index 000000000..2ad9f81df
--- /dev/null
+++ b/app-text/noweb/Manifest
@@ -0,0 +1 @@
+DIST noweb-2.12.tar.gz 579230 BLAKE2B 2b4b252a79df6b030c2e09dff62c2dbb59d4cdfc6dac76eb9d387b355f940a7431bb69f7200bfe0a2269542430cc00720c4391d3dd15978fc39b36e81a9fb5fe SHA512 b4e45f288b6ae99d2457b69628bb5dfca16f7d1ce1bb06722ae598b5ff50a4ed2819313c5f5991cd3d1062c9d306c1308b0336916b6582dba7a405a343958c2a
diff --git a/app-text/noweb/files/50noweb-gentoo.el b/app-text/noweb/files/50noweb-gentoo.el
new file mode 100644
index 000000000..90b971d74
--- /dev/null
+++ b/app-text/noweb/files/50noweb-gentoo.el
@@ -0,0 +1,4 @@
+(add-to-list 'load-path "@SITELISP@")
+(autoload  'noweb-mode "noweb-mode"
+  "Minor meta mode for editing noweb files." t)
+(add-to-list 'auto-mode-alist '("\\.nw\\'" . noweb-mode))
diff --git a/app-text/noweb/files/noweb-2.12-ldflags.patch b/app-text/noweb/files/noweb-2.12-ldflags.patch
new file mode 100644
index 000000000..cc3e0acb8
--- /dev/null
+++ b/app-text/noweb/files/noweb-2.12-ldflags.patch
@@ -0,0 +1,23 @@
+--- a/src/c/Makefile
++++ b/src/c/Makefile
+@@ -41,19 +41,16 @@
+ all:	nt markup mnt finduses nwmktemp
+
+ nt:	$(TANGLEOBJS)
+-	$(CC) $(CFLAGS) -o nt $(TANGLEOBJS)
++	$(CC) $(CFLAGS) $(LDFLAGS) -o nt $(TANGLEOBJS)
+
+ nwmktemp: nwmktemp.o
+ 	$(CC) $(CFLAGS) -o nwmktemp nwmktemp.o
+
+ finduses:	$(FINDUSESOBJS)
+-	$(CC) $(CFLAGS) -o finduses $(FINDUSESOBJS)
+
+ markup:	$(MARKUPOBJS)
+-	$(CC) $(CFLAGS) -o markup $(MARKUPOBJS)
+
+ mnt:	$(MNTOBJS)
+-	$(CC) $(CFLAGS) -o mnt $(MNTOBJS)
+
+ source:	$(SRCS)
+ touch: $(SRCS)
diff --git a/app-text/noweb/files/noweb-2.12-recmake.patch b/app-text/noweb/files/noweb-2.12-recmake.patch
new file mode 100644
index 000000000..b39f9d1c8
--- /dev/null
+++ b/app-text/noweb/files/noweb-2.12-recmake.patch
@@ -0,0 +1,142 @@
+diff -ur a/contrib/norman/Makefile b/contrib/norman/Makefile
+--- a/contrib/norman/Makefile	2018-06-28 23:26:32.000000000 +0200
++++ b/contrib/norman/Makefile	2020-02-25 05:26:26.256610626 +0100
+@@ -1,10 +1,10 @@
+ LIB=/dev/null	# to be overridden
+ DIRS=numarkup
+ 
+-all: ;	for i in $(DIRS); do (cd $$i; make ICONC=$(ICONC) ICONT=$(ICONT) all); done
+-install: ;	for i in $(DIRS); do (cd $$i; make LIB=$(LIB) BIN=$(BIN) install); done
+-source: ;	for i in $(DIRS); do (cd $$i; make source); done
+-clean: ;	for i in $(DIRS); do (cd $$i; make clean); done
++all: ;	for i in $(DIRS); do (cd $$i; $(MAKE) ICONC=$(ICONC) ICONT=$(ICONT) all); done
++install: ;	for i in $(DIRS); do (cd $$i; $(MAKE) LIB=$(LIB) BIN=$(BIN) install); done
++source: ;	for i in $(DIRS); do (cd $$i; $(MAKE) source); done
++clean: ;	for i in $(DIRS); do (cd $$i; $(MAKE) clean); done
+ iconlib:	# cheap hack for slackmake
+ 	true
+ 
+diff -ur a/contrib/norman/numarkup/Makefile b/contrib/norman/numarkup/Makefile
+--- a/contrib/norman/numarkup/Makefile	2018-06-28 23:26:32.000000000 +0200
++++ b/contrib/norman/numarkup/Makefile	2020-02-25 05:32:02.290882144 +0100
+@@ -11,11 +11,11 @@
+ 
+ all: 
+ 	noweb -t numarkup.nw
+-	make $(TARGET)
++	$(MAKE) $(TARGET)
+ 
+ install:
+ 	noweb -t numarkup.nw
+-	make $(TARGET)
++	$(MAKE) $(TARGET)
+ 	strip $(TARGET)
+ 	cp $(TARGET) $(LIB)
+ 
+diff -ur a/Makefile b/Makefile
+--- a/Makefile	2018-06-28 23:26:32.000000000 +0200
++++ b/Makefile	2020-02-25 05:24:54.607975694 +0100
+@@ -12,14 +12,14 @@
+ all:
+ 	@echo "You have no business running 'make' here; please look at the README file"
+ 	@exit 1
+-source: ;	for i in src; do (cd $$i; make source); done
+-www: ;		for i in src/xdoc examples; do (cd $$i; make www); done
++source: ;	for i in src; do (cd $$i; $(MAKE) source); done
++www: ;		for i in src/xdoc examples; do (cd $$i; $(MAKE) www); done
+ 
+ clean:
+-	for i in src examples contrib; do (cd $$i; make clean); done
++	for i in src examples contrib; do (cd $$i; $(MAKE) clean); done
+ 	rm -f nwsrcfilter *~ */*~
+ clobber: clean
+-	for i in src examples contrib; do (cd $$i; make clobber); done
++	for i in src examples contrib; do (cd $$i; $(MAKE) clobber); done
+ 
+ DATE:
+ 	(./echo -n "Version $(VERSION) of "; date) > DATE
+@@ -51,7 +51,7 @@
+ 
+ ctan:	clean source nwsrcfilter DATE emacscheck
+ 	chmod +w src/Makefile
+-	(cd src; make boot)
++	(cd src; $(MAKE) boot)
+ 	rm -f ../noweb-$(VERSION)-ctan.zip
+ 	find ./* ! -type d -not -name FAQ.old -not -name '.git*' -print | ./nwsrcfilter | sed 's@^@noweb/@' | ( ln -s . noweb; zip ../noweb-$(VERSION)-ctan.zip -@; rm -f noweb )
+ 	chmod -w src/Makefile
+@@ -61,6 +61,6 @@
+ 	diff src/elisp/noweb-mode.el $(HOME)/emacs/noweb-mode.el
+ 
+ checkin:
+-	(cd src; make "CINAME=$(CINAME)" "CIMSG=$(CIMSG)" checkin)
++	(cd src; $(MAKE) "CINAME=$(CINAME)" "CIMSG=$(CIMSG)" checkin)
+ 
+ 
+diff -ur a/src/Makefile b/src/Makefile
+--- a/src/Makefile	2020-02-25 05:22:55.103146835 +0100
++++ b/src/Makefile	2020-02-25 05:29:26.557836177 +0100
+@@ -41,9 +41,9 @@
+ TEXNAME=$(TEXINPUTS)
+ 
+ all: 
+-	cd c; make "CC=$(CC)" "$(CFLAGS)" all 
+-	for i in shell lib xdoc tex; do (cd $$i; make all); done
+-	cd $(LIBSRC); make "ICONT=$(ICONT)" "ICONC=$(ICONC)" all
++	cd c; $(MAKE) "CC=$(CC)" "CFLAGS=$(CFLAGS)" all
++	for i in shell lib xdoc tex; do (cd $$i; $(MAKE) all); done
++	cd $(LIBSRC); $(MAKE) "ICONT=$(ICONT)" "ICONC=$(ICONC)" all
+ 
+ FAQ: FAQ.html
+ 	sleep 1; html2ascii FAQ.html > FAQ
+@@ -101,13 +101,13 @@
+ 	mkdir -p $(BIN) $(LIB)
+ 	true c/nt c/markup c/mnt c/finduses c/nwmktemp
+ 	cp c/nt c/markup c/mnt c/finduses c/nwmktemp $(LIB)
+-	cd $(LIBSRC); make ICONT=$(ICONT) ICONC=$(ICONC) LIB=$(LIB) BIN=$(BIN) install
+-	cd lib; make LIB=$(LIB) install
++	cd $(LIBSRC); $(MAKE) ICONT=$(ICONT) ICONC=$(ICONC) LIB=$(LIB) BIN=$(BIN) install
++	cd lib; $(MAKE) LIB=$(LIB) install
+ 
+ uninstall-code: uninstall-shell
+ 	rm -f $(LIB)/nt $(LIB)/markup $(LIB)/mnt $(LIB)/finduses 
+-	cd $(LIBSRC); make ICONT=$(ICONT) ICONC=$(ICONC) LIB=$(LIB) BIN=$(BIN) uninstall
+-	cd lib; make LIB=$(LIB) uninstall
++	cd $(LIBSRC); $(MAKE) ICONT=$(ICONT) ICONC=$(ICONC) LIB=$(LIB) BIN=$(BIN) uninstall
++	cd lib; $(MAKE) LIB=$(LIB) uninstall
+ install-man:
+ 	mkdir -p $(MAN) $(MANDIR) $(MAN7DIR)
+ 	sed -e "s@|LIBDIR|@$(LIBNAME)@" -e "s@|TEXINPUTS|@$(TEXNAME)@" xdoc/cpif.1 > $(MANDIR)/cpif.$(MANEXT)
+@@ -194,26 +194,26 @@
+ uninstall-elisp:
+ 	rm -f $(ELISP)/noweb-mode.el || true
+ checkin:
+-	for i in lib tex xdoc; do (cd $$i; make "CINAME=$(CINAME)" "CIMSG=$(CIMSG)" checkin); done
++	for i in lib tex xdoc; do (cd $$i; $(MAKE) "CINAME=$(CINAME)" "CIMSG=$(CIMSG)" checkin); done
+ 	for i in c icon awk; do (cd $$i; ci -l $(CINAME) $(CIMSG) *.nw Makefile); done
+ 	(cd elisp; ci -l $(CINAME) $(CIMSG) *.el)
+ 	ci -l $(CINAME) $(CIMSG) Makefile.nw INSTALL INSTALL.DOS README FAQ COPYRIGHT nwmake *.nw
+ 
+ source: FAQ
+-	for i in c shell lib xdoc icon awk tex; do (cd $$i; make CPIF=">" source); done
++	for i in c shell lib xdoc icon awk tex; do (cd $$i; $(MAKE) CPIF=">" source); done
+ 	sleep 1
+-	for i in c shell lib xdoc icon awk tex; do (cd $$i; make touch); done
++	for i in c shell lib xdoc icon awk tex; do (cd $$i; $(MAKE) touch); done
+ touch:
+ 	touch FAQ
+-	for i in c shell lib xdoc icon awk tex; do (cd $$i; make touch); done
++	for i in c shell lib xdoc icon awk tex; do (cd $$i; $(MAKE) touch); done
+ boot:
+-	for i in c shell lib xdoc icon awk tex; do (cd $$i; make boot); done
++	for i in c shell lib xdoc icon awk tex; do (cd $$i; $(MAKE) boot); done
+ clean:
+-	for i in c shell lib xdoc icon awk tex; do (cd $$i; make clean); done
++	for i in c shell lib xdoc icon awk tex; do (cd $$i; $(MAKE) clean); done
+ 	rm -f nwsrcfilter *~ */*~
+ 
+ clobber: clean
+-	for i in c shell lib xdoc icon awk tex; do (cd $$i; make clobber); done
++	for i in c shell lib xdoc icon awk tex; do (cd $$i; $(MAKE) clobber); done
+ 
+ Makefile: Makefile.nw
+ 	chmod +w Makefile
diff --git a/app-text/noweb/metadata.xml b/app-text/noweb/metadata.xml
new file mode 100644
index 000000000..6abb9444c
--- /dev/null
+++ b/app-text/noweb/metadata.xml
@@ -0,0 +1,17 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
+<pkgmetadata>
+	<maintainer type="project">
+		<email>sci-mathematics@gentoo.org</email>
+		<name>Gentoo Mathematics Project</name>
+	</maintainer>
+	<upstream>
+		<maintainer>
+			<email>nr@cs.tufts.edu</email>
+			<name>Norman Ramsey</name>
+		</maintainer>
+		<remote-id type="github">nrnrnr/noweb</remote-id>
+	</upstream>
+	<longdescription lang="en">noweb is designed to meet the needs of literate programmers while remaining as simple as possible. Its primary advantages are simplicity, extensibility, and language-independence—especially noticeable when compared with other literate-programming tools. noweb uses 5 control sequences to WEB's 27. The noweb manual is only 4 pages; an additional page explains how to customize its LaTeX output. noweb works ``out of the box'' with any programming language, and supports TeX, latex, HTML, and troff back ends. A back end to support full hypertext or indexing takes about 250 lines; a simpler one can be written in 40 lines of awk. The primary sacrifice relative to WEB is that code is seldom prettyprinted.
+	</longdescription>
+</pkgmetadata>
diff --git a/app-text/noweb/noweb-2.12.ebuild b/app-text/noweb/noweb-2.12.ebuild
new file mode 100644
index 000000000..29fc8cd5a
--- /dev/null
+++ b/app-text/noweb/noweb-2.12.ebuild
@@ -0,0 +1,136 @@
+# Copyright 1999-2021 Gentoo Authors
+# Distributed under the terms of the GNU General Public License v2
+
+EAPI="7"
+
+inherit toolchain-funcs elisp-common
+
+MYPV="$(ver_rs 1 _)"
+
+DESCRIPTION="a literate programming tool, lighter than web"
+HOMEPAGE="https://www.cs.tufts.edu/~nr/noweb/"
+SRC_URI="https://github.com/nrnrnr/${PN}/archive/v${MYPV}.tar.gz -> ${P}.tar.gz"
+
+LICENSE="
+	|| ( BSD-2 noweb )
+	emacs? ( GPL-2 )
+"
+SLOT="0"
+KEYWORDS="~alpha ~amd64 ~hppa ~ia64 ~ppc ~ppc64 ~sparc ~x86 ~ppc-macos ~x64-macos"
+IUSE="emacs examples"
+
+DEPEND="
+	dev-lang/icon
+	sys-apps/debianutils
+	virtual/tex-base
+
+	emacs? ( app-editors/emacs:= )
+"
+RDEPEND="${DEPEND}"
+
+S="${WORKDIR}/${PN}-${MYPV}"
+
+SITEFILE="50${PN}-gentoo.el"
+
+src_prepare() {
+	# glibc2.10 compat (bug 270757)
+#	mkdir d && cp -r c/* d/
+	sed "s/getline (/getline_nonlibc (/" -i src/c/getline.{c,h} || die
+	sed "s/getline(/getline_nonlibc(/" -i src/c/{notangle.c,getline.c,finduses.c} || die
+#	diff -u d/ c/
+
+	# dont run texhash...
+	sed -i -e "s/texhash/true/" src/Makefile || die
+	# dont strip...
+	sed -i -e "s/strip/true/" src/Makefile || die
+
+	sed -i -e "s/CC=gcc -ansi -pedantic -O -Wall -Werror//" src/Makefile || die
+	sed -i -e "s/CFLAGS=//" src/Makefile || die
+	sed -i -e "s/CC=gcc -ansi -pedantic -O -Wall -Werror//" src/c/Makefile || die
+	sed -i -e "s/CFLAGS=//" src/c/Makefile || die
+
+	eapply "${FILESDIR}/${P}-recmake.patch"
+
+	sed -i -e "s/CC = cc//" contrib/norman/numarkup/Makefile || die
+	sed -i -e "s/CFLAGS = -O//" contrib/norman/numarkup/Makefile || die
+
+	eapply "${FILESDIR}/${P}-ldflags.patch"
+	eapply_user
+}
+
+src_compile() {
+	# noweb tries to use notangle and noweb; see bug #50429
+	cd "${S}/src/c"
+
+	emake	ICONC="icont" \
+		CC="$(tc-getCC)" \
+		CFLAGS="${CFLAGS}" \
+		LIBSRC="icon" || die
+
+	export PATH="${PATH}:${T}"
+	cd "${S}/src"
+
+	emake	ICONC="icont" \
+		CC="$(tc-getCC)" \
+		BIN="${T}" \
+		LIB="${T}" \
+		LIBSRC="icon" \
+		install-code || die "make temporal install failed."
+
+	emake	ICONC="icont" \
+		CC="$(tc-getCC)" \
+		CFLAGS="${CFLAGS}" \
+		LIBSRC="icon" || die "make failed"
+
+	# Set awk to awk not nawk
+	./awkname awk
+
+	if use emacs; then
+		elisp-compile elisp/noweb-mode.el || die "elisp-compile failed"
+	fi
+}
+
+src_install () {
+	cd "${S}/src"
+
+	# It needs the directories to exist first...
+	dodir /usr/bin
+	dodir "/usr/libexec/${PN}"
+	dodir /usr/share/man
+	dodir /usr/share/texmf-site/tex/inputs
+
+	emake	ICONC="icont" \
+		BIN="${ED}/usr/bin" \
+		LIBSRC="icon" \
+		LIBNAME="${EPREFIX}/usr/libexec/${PN}" \
+		LIB="${ED}/usr/libexec/${PN}" \
+		MAN="${ED}/usr/share/man" \
+		TEXNAME="${EPREFIX}/usr/share/texmf-site/tex/inputs" \
+		TEXINPUTS="${ED}/usr/share/texmf-site/tex/inputs" \
+		install || die "make install failed"
+
+	cd "${S}"
+
+	if use examples; then
+		insinto "/usr/share/doc/${PF}/examples"
+		doins -r examples/.
+	fi
+
+	if use emacs; then
+		elisp-install "${PN}" "${S}"/src/elisp/noweb-mode.{el,elc} \
+			|| die "elisp-install failed"
+		elisp-site-file-install "${FILESDIR}/${SITEFILE}" \
+			|| die "elisp-site-file-install failed"
+	fi
+	einstalldocs
+}
+
+pkg_postinst() {
+	use emacs && elisp-site-regen
+	einfo "Running texhash to complete installation.."
+	texhash
+}
+
+pkg_postrm() {
+	use emacs && elisp-site-regen
+}
diff --git a/app-vim/vim-gromacs/metadata.xml b/app-vim/vim-gromacs/metadata.xml
index c8a25c291..5b5798e1e 100644
--- a/app-vim/vim-gromacs/metadata.xml
+++ b/app-vim/vim-gromacs/metadata.xml
@@ -5,9 +5,6 @@
 		<email>sci-chemistry@gentoo.org</email>
 		<name>Gentoo Chemistry Project</name>
 	</maintainer>
-	<longdescription lang="en">
-VIM syntax plugin which provides syntax highlighting for the gromacs files.
-</longdescription>
 	<upstream>
 		<remote-id type="github">HubLot/vim-gromacs</remote-id>
 	</upstream>
diff --git a/app-vim/vim-gromacs/vim-gromacs-9999.ebuild b/app-vim/vim-gromacs/vim-gromacs-9999.ebuild
index 2b5661000..1d115fe16 100644
--- a/app-vim/vim-gromacs/vim-gromacs-9999.ebuild
+++ b/app-vim/vim-gromacs/vim-gromacs-9999.ebuild
@@ -1,21 +1,15 @@
-# Copyright 1999-2016 Gentoo Foundation
+# Copyright 1999-2021 Gentoo Authors
 # Distributed under the terms of the GNU General Public License v2
 
-EAPI=6
+EAPI=7
 
 inherit git-r3 vim-plugin
 
 DESCRIPTION="vim plugin: Gromacs file syntax highlighting and some macros"
 HOMEPAGE="https://github.com/HubLot/vim-gromacs"
-SRC_URI=""
-#EGIT_REPO_URI="git://github.com/Reinis/${PN}.git"
-EGIT_REPO_URI="
-	https://github.com/HubLot/${PN}.git
-	git://github.com/HubLot/${PN}.git
-	git://github.com/Reinis/${PN}.git"
+EGIT_REPO_URI="https://github.com/HubLot/${PN}.git"
 
 LICENSE="GPL-3"
 KEYWORDS=""
-IUSE=""
 
 VIM_PLUGIN_MESSAGES="filetype"
diff --git a/dev-cpp/Fastor/Fastor-0.6.3.ebuild b/dev-cpp/Fastor/Fastor-0.6.3.ebuild
new file mode 100644
index 000000000..1dc798191
--- /dev/null
+++ b/dev-cpp/Fastor/Fastor-0.6.3.ebuild
@@ -0,0 +1,22 @@
+# Copyright 1999-2020 Gentoo Authors
+# Distributed under the terms of the GNU General Public License v2
+
+EAPI=7
+
+DESCRIPTION="light-weight high performance tensor algebra framework"
+HOMEPAGE="https://github.com/romeric/Fastor"
+
+if [[ ${PV} == 9999 ]] ; then
+	inherit git-r3
+	EGIT_REPO_URI="https://github.com/romeric/Fastor"
+else
+	SRC_URI="https://github.com/romeric/Fastor/archive/V${PV}.tar.gz -> ${P}.tar.gz"
+	KEYWORDS="~amd64 ~x86"
+fi
+
+LICENSE="MIT"
+SLOT="0"
+
+src_install() {
+	doheader -r Fastor
+}
diff --git a/dev-cpp/Fastor/Fastor-9999.ebuild b/dev-cpp/Fastor/Fastor-9999.ebuild
new file mode 100644
index 000000000..1dc798191
--- /dev/null
+++ b/dev-cpp/Fastor/Fastor-9999.ebuild
@@ -0,0 +1,22 @@
+# Copyright 1999-2020 Gentoo Authors
+# Distributed under the terms of the GNU General Public License v2
+
+EAPI=7
+
+DESCRIPTION="light-weight high performance tensor algebra framework"
+HOMEPAGE="https://github.com/romeric/Fastor"
+
+if [[ ${PV} == 9999 ]] ; then
+	inherit git-r3
+	EGIT_REPO_URI="https://github.com/romeric/Fastor"
+else
+	SRC_URI="https://github.com/romeric/Fastor/archive/V${PV}.tar.gz -> ${P}.tar.gz"
+	KEYWORDS="~amd64 ~x86"
+fi
+
+LICENSE="MIT"
+SLOT="0"
+
+src_install() {
+	doheader -r Fastor
+}
diff --git a/dev-cpp/Fastor/Manifest b/dev-cpp/Fastor/Manifest
new file mode 100644
index 000000000..df2ba44fe
--- /dev/null
+++ b/dev-cpp/Fastor/Manifest
@@ -0,0 +1 @@
+DIST Fastor-0.6.3.tar.gz 910919 BLAKE2B 1d49fea581eb328dfdb3e2ac6ff847bcac1b68b878b1f35fe7578430a62db77c1e69ada66b3b498ea5b265289f7972acf0047e898758fdb1720005aac1f68f4d SHA512 93e3afecf7ef2c1f619b0576c343ddfeeba871d3928eea8e474f6020e1222ef19cf021622981eae5b7d7759647185be2a75371bd28d7280c16444a51b3115af8
diff --git a/dev-cpp/Fastor/metadata.xml b/dev-cpp/Fastor/metadata.xml
new file mode 100644
index 000000000..9937ac435
--- /dev/null
+++ b/dev-cpp/Fastor/metadata.xml
@@ -0,0 +1,15 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
+<pkgmetadata>
+	<maintainer type="person">
+		<email>gentoo@aisha.cc</email>
+		<name>Aisha Tammy</name>
+	</maintainer>
+	<maintainer type="project">
+		<email>sci@gentoo.org</email>
+		<name>Gentoo Science Project</name>
+	</maintainer>
+	<upstream>
+		<remote-id type="github">romeric/Fastor</remote-id>
+	</upstream>
+</pkgmetadata>
diff --git a/dev-cpp/blitz/Manifest b/dev-cpp/blitz/Manifest
new file mode 100644
index 000000000..c490ff809
--- /dev/null
+++ b/dev-cpp/blitz/Manifest
@@ -0,0 +1 @@
+DIST blitz-1.0.3_pre20200524.tar.gz 1297489 BLAKE2B bb2222a63d7763bd9e01b83fd2e895074e2be00bf32617f7ddfbb9e9fc5326daffdb3c5b2a95c257c416238732d53255387df46061a0cca406c33f13747cd060 SHA512 987ee4444b5c2a2d45cb5a66bc7a520e8849461346aab329c14707e53afef7b72325d199b2b619ac7c65c7a1f0995917c6cad2d526166c5ada5e23d0731163aa
diff --git a/dev-cpp/blitz/blitz-1.0.3_pre20200524.ebuild b/dev-cpp/blitz/blitz-1.0.3_pre20200524.ebuild
new file mode 100644
index 000000000..e331bc6c9
--- /dev/null
+++ b/dev-cpp/blitz/blitz-1.0.3_pre20200524.ebuild
@@ -0,0 +1,50 @@
+# Copyright 1999-2022 Gentoo Authors
+# Distributed under the terms of the GNU General Public License v2
+
+EAPI=8
+
+PYTHON_COMPAT=( python3_{10..11} )
+inherit cmake python-any-r1
+
+COMMIT="39f885951a9b8b11f931f917935a16066a945056"
+DESCRIPTION="Multi-dimensional array library for C++"
+HOMEPAGE="https://github.com/blitzpp/blitz"
+SRC_URI="https://github.com/blitzpp/blitz/archive/${COMMIT}.tar.gz -> ${P}.tar.gz"
+S="${WORKDIR}/${PN}-${COMMIT}"
+
+LICENSE="BSD LGPL-3+"
+SLOT="0"
+KEYWORDS="~amd64 ~arm ~arm64 ~ppc64 ~x86"
+IUSE="boost doc test"
+RESTRICT="!test? ( test )"
+
+BDEPEND="
+	${PYTHON_DEPS}
+	doc? ( app-text/doxygen[dot] )
+"
+DEPEND="
+	boost? ( dev-libs/boost:= )
+"
+
+src_configure() {
+	local mycmakeargs=(
+		-DBUILD_DOC=$(usex doc)
+		-DBUILD_TESTING=$(usex test)
+		-DENABLE_SERIALISATION=$(usex boost)
+	)
+	use doc && mycmakeargs+=( -DDISABLE_REFMAN_PDF=ON )
+	cmake_src_configure
+}
+
+src_compile() {
+	cmake_src_compile
+	use doc && cmake_build blitz-doc
+	use test && cmake_build testsuite benchmark examples
+}
+
+src_install() {
+	cmake_src_install
+	if use doc ; then
+		find "${D}" -type f \( -name "*.md5" -o -name "*.map" \) -delete || die
+	fi
+}
diff --git a/dev-cpp/blitz/metadata.xml b/dev-cpp/blitz/metadata.xml
new file mode 100644
index 000000000..c0e5e78aa
--- /dev/null
+++ b/dev-cpp/blitz/metadata.xml
@@ -0,0 +1,22 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
+<pkgmetadata>
+	<maintainer type="person">
+		<email>gentoo@aisha.cc</email>
+		<name>Aisha Tammy</name>
+	</maintainer>
+	<maintainer type="project">
+		<email>sci@gentoo.org</email>
+		<name>Gentoo Science Project</name>
+	</maintainer>
+	<longdescription>
+		Blitz++ is a C++ template class library that provides high-performance
+		multidimensional array containers for scientific compiting.
+	</longdescription>
+	<use>
+		<flag name="boost">Enable serialization support using Boost::Serialization.</flag>
+	</use>
+	<upstream>
+		<remote-id type="github">blitzpp/blitz</remote-id>
+	</upstream>
+</pkgmetadata>
diff --git a/dev-cpp/eigen/Manifest b/dev-cpp/eigen/Manifest
deleted file mode 100644
index fca18c169..000000000
--- a/dev-cpp/eigen/Manifest
+++ /dev/null
@@ -1,4 +0,0 @@
-DIST eigen-3.2.7-cmake.patch 3294 BLAKE2B fcea1faceb2a360ab8ddb56c8bdbcbe061a13115b569e1981c5777973d8317a877372f9f624814badbefeeb3e38e4ff03e5e8fc5a9d5ad72e1b5b4c89c2ab1df SHA512 229c0c1f3d95ae505b5accd1aeba19f59a064218cf9b0d844dbc4c660a4cddb666f818268ba1899370877034a70a87317ca8bf14822e3b85d0bbe7f3bb5c7cf6
-DIST eigen-3.2.7.tar.bz2 1155162 BLAKE2B 2151e5e6bd6d8c6afd595c945f347efab581347992ce29c84aa9d33544ec8149eb34248dd68917760b5d2e2d8cd73bac98e4958417071adb90e20fa58110904f SHA512 6e9beb4fdd69d96a1bb305ea9463547c19cac0072ce908c19bf952d2b7a254c0d674d19a7797a3ba5e8617e1c1bca74dfb7c01971301cb152e467f13eaaed6cc
-DIST eigen-3.2.8-cmake.patch 3294 BLAKE2B fcea1faceb2a360ab8ddb56c8bdbcbe061a13115b569e1981c5777973d8317a877372f9f624814badbefeeb3e38e4ff03e5e8fc5a9d5ad72e1b5b4c89c2ab1df SHA512 229c0c1f3d95ae505b5accd1aeba19f59a064218cf9b0d844dbc4c660a4cddb666f818268ba1899370877034a70a87317ca8bf14822e3b85d0bbe7f3bb5c7cf6
-DIST eigen-3.2.8.tar.bz2 1161201 BLAKE2B 35bace5138f601e73d56412e87bf591ef2f96778050b0a2a4fc8f1e75f02498fb4eb80bf79988dd4bd6b985945a122d44581ccedd925f398f7d282790da06385 SHA512 53c27ba530c985dfef52188e03273eeef33abbc67e3f150cacd3371c8b9ddbd399228730595821c4c56c061d109cf509266c1dab2b8a7c730902cbd6fb18c100
diff --git a/dev-cpp/eigen/eigen-3.2.7-r1.ebuild b/dev-cpp/eigen/eigen-3.2.7-r1.ebuild
deleted file mode 100644
index a00566654..000000000
--- a/dev-cpp/eigen/eigen-3.2.7-r1.ebuild
+++ /dev/null
@@ -1,116 +0,0 @@
-# Copyright 1999-2017 Gentoo Foundation
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=6
-
-FORTRAN_NEEDED=fortran
-
-inherit alternatives-2 cmake-utils fortran-2 multilib numeric vcs-snapshot
-
-DESCRIPTION="C++ template library for linear algebra"
-HOMEPAGE="http://eigen.tuxfamily.org/"
-SRC_URI="
-	https://bitbucket.org/eigen/eigen/get/${PV}.tar.bz2 -> ${P}.tar.bz2
-	https://bitbucket.org/eigen/eigen/commits/1d71b1341c03a7c485289be2c8bd906a259c0487/raw/ -> ${P}-cmake.patch
-"
-
-SLOT="3"
-LICENSE="MPL-2.0"
-KEYWORDS="~amd64 ~x86 ~amd64-linux ~x86-linux"
-IUSE="adolc doc fortran fftw gmp metis mkl pastix sparse static-libs test"
-
-CDEPEND="
-	adolc? ( sci-libs/adolc[sparse?] )
-	fftw? ( sci-libs/fftw:3.0 )
-	gmp? ( dev-libs/gmp:0 dev-libs/mpfr:0 )
-	metis? ( sci-libs/metis )
-	mkl? ( sci-libs/mkl )
-	pastix? ( sci-libs/pastix )
-	sparse? (
-		dev-cpp/sparsehash
-		sci-libs/cholmod[metis?]
-		sci-libs/spqr
-		sci-libs/superlu
-		sci-libs/umfpack
-	)"
-DEPEND="
-	doc? ( app-doc/doxygen[dot,latex] )
-	test? ( ${CDEPEND} )"
-
-RDEPEND="
-	!dev-cpp/eigen:0
-	${CDEPEND}"
-
-PATCHES=( "${DISTDIR}"/${P}-cmake.patch )
-
-src_prepare() {
-	sed -i \
-		-e "s:/usr:${EPREFIX}/usr:g" \
-		-e "s:/bin/bash:${EPREFIX}/bin/bash:g" \
-		cmake/*.cmake || die
-	sed -i \
-		-e "/DESTINATION/s:lib:$(get_libdir):g" \
-		{blas,lapack}/CMakeLists.txt || die
-
-	# TOFIX: static-libs for blas are always built with PIC
-	if ! use static-libs; then
-		sed \
-			-e "/add_dependencies/s/eigen_[a-z]*_static//g" \
-			-e "/TARGETS/s/eigen_[a-z]*_static//g" \
-			-e "/add_library(eigen_[a-z]*_static/d" \
-			-e "/target_link_libraries(eigen_[a-z]*_static/d" \
-			-i {blas,lapack}/CMakeLists.txt || die
-	fi
-
-	sed -i -e "/Unknown build type/d" CMakeLists.txt || die
-
-	sed \
-		-e '/Cflags/s|:.*|: -I${CMAKE_INSTALL_PREFIX}/${INCLUDE_INSTALL_DIR}|g' \
-		-i eigen3.pc.in || die
-
-	cmake-utils_src_prepare
-}
-
-src_configure() {
-	# TOFIX: is it worth fixing all the automagic given no library is built?
-	# cmake has buggy disable_testing feature, so leave it for now
-	local mycmakeargs=(
-		-DDART_TESTING_TIMEOUT=300
-		-DEIGEN_BUILD_BTL=OFF
-	)
-	export VARTEXFONTS="${T}/fonts"
-	export PKG_CONFIG_LIBDIR=/usr/$(get_libdir)/
-
-	cmake-utils_src_configure
-	# use fortran && FORTRAN_LIBS="blas lapack" not ready
-	use fortran && FORTRAN_LIBS="blas"
-}
-
-src_compile() {
-	local targets="${FORTRAN_LIBS}"
-	use doc && targets+=" doc"
-	use test && targets+=" check"
-	cmake-utils_src_compile ${targets}
-}
-
-src_install() {
-	cmake-utils_src_install
-	use doc && dohtml -r "${BUILD_DIR}"/doc/html/*
-	local x
-	for x in ${FORTRAN_LIBS}; do
-		local libname="eigen_${x}"
-		emake DESTDIR="${D}" -C "${BUILD_DIR}/${x}" install ${libname}
-		create_pkgconfig \
-			--description "${DESCRIPTION} ${x^^} implementation" \
-			--libs "-L\${libdir} -l${libname}" \
-			--libs-private "-lm" \
-			$([[ ${x} == lapack ]] && echo "--requires 'blas'") \
-			${libname}
-		alternatives_for ${x} eigen 0 \
-			/usr/$(get_libdir)/pkgconfig/${x}.pc ${libname}.pc
-	done
-
-	# Debian installs it and some projects started using it.
-	insinto /usr/share/cmake/Modules/
-	doins "${S}/cmake/FindEigen3.cmake"
-}
diff --git a/dev-cpp/eigen/eigen-3.2.8-r2.ebuild b/dev-cpp/eigen/eigen-3.2.8-r2.ebuild
deleted file mode 100644
index e93a800aa..000000000
--- a/dev-cpp/eigen/eigen-3.2.8-r2.ebuild
+++ /dev/null
@@ -1,112 +0,0 @@
-# Copyright 1999-2017 Gentoo Foundation
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=6
-
-FORTRAN_NEEDED=fortran
-
-inherit alternatives-2 cmake-utils fortran-2 multilib numeric vcs-snapshot
-
-DESCRIPTION="C++ template library for linear algebra"
-HOMEPAGE="http://eigen.tuxfamily.org/"
-SRC_URI="
-	https://bitbucket.org/eigen/eigen/get/${PV}.tar.bz2 -> ${P}.tar.bz2
-	https://bitbucket.org/eigen/eigen/commits/1d71b1341c03a7c485289be2c8bd906a259c0487/raw/ -> ${P}-cmake.patch
-"
-
-SLOT="3"
-LICENSE="MPL-2.0"
-KEYWORDS="~amd64 ~x86 ~amd64-linux ~x86-linux"
-IUSE="adolc doc fortran fftw gmp metis mkl pastix sparse static-libs test"
-
-CDEPEND="
-	adolc? ( sci-libs/adolc[sparse?] )
-	fftw? ( sci-libs/fftw:3.0 )
-	gmp? ( dev-libs/gmp:0 dev-libs/mpfr:0 )
-	metis? ( sci-libs/metis )
-	mkl? ( sci-libs/mkl )
-	pastix? ( sci-libs/pastix )
-	sparse? (
-		dev-cpp/sparsehash
-		sci-libs/cholmod[metis?]
-		sci-libs/spqr
-		sci-libs/superlu
-		sci-libs/umfpack
-	)"
-DEPEND="
-	doc? ( app-doc/doxygen[dot,latex] )
-	test? ( ${CDEPEND} )"
-
-RDEPEND="
-	!dev-cpp/eigen:0
-	${CDEPEND}"
-
-PATCHES=( "${DISTDIR}"/${P}-cmake.patch )
-
-src_prepare() {
-	sed -i \
-		-e "s:/usr:${EPREFIX}/usr:g" \
-		-e "s:/bin/bash:${EPREFIX}/bin/bash:g" \
-		cmake/*.cmake || die
-	sed -i \
-		-e "/DESTINATION/s:lib:$(get_libdir):g" \
-		{blas,lapack}/CMakeLists.txt || die
-
-	# TOFIX: static-libs for blas are always built with PIC
-	if ! use static-libs; then
-		sed \
-			-e "/add_dependencies/s/eigen_[a-z]*_static//g" \
-			-e "/TARGETS/s/eigen_[a-z]*_static//g" \
-			-e "/add_library(eigen_[a-z]*_static/d" \
-			-e "/target_link_libraries(eigen_[a-z]*_static/d" \
-			-i {blas,lapack}/CMakeLists.txt || die
-	fi
-
-	sed -i -e "/Unknown build type/d" CMakeLists.txt || die
-
-	cmake-utils_src_prepare
-}
-
-src_configure() {
-	# TOFIX: is it worth fixing all the automagic given no library is built?
-	# cmake has buggy disable_testing feature, so leave it for now
-	local mycmakeargs=(
-		-DDART_TESTING_TIMEOUT=300
-		-DEIGEN_BUILD_BTL=OFF
-	)
-	export VARTEXFONTS="${T}/fonts"
-	export PKG_CONFIG_LIBDIR=/usr/$(get_libdir)/
-
-	cmake-utils_src_configure
-	# use fortran && FORTRAN_LIBS="blas lapack" not ready
-	use fortran && FORTRAN_LIBS="blas"
-}
-
-src_compile() {
-	local targets="${FORTRAN_LIBS}"
-	use doc && targets+=" doc"
-	use test && targets+=" check"
-	cmake-utils_src_compile ${targets}
-}
-
-src_install() {
-	cmake-utils_src_install
-	use doc && dohtml -r "${BUILD_DIR}"/doc/html/*
-	local x
-	for x in ${FORTRAN_LIBS}; do
-		local libname="eigen_${x}"
-		emake DESTDIR="${D}" -C "${BUILD_DIR}/${x}" install ${libname}
-		create_pkgconfig \
-			--description "${DESCRIPTION} ${x^^} implementation" \
-			--libs "-L\${libdir} -l${libname}" \
-			--libs-private "-lm" \
-			$([[ ${x} == lapack ]] && echo "--requires 'blas'") \
-			${libname}
-		alternatives_for ${x} eigen 0 \
-			/usr/$(get_libdir)/pkgconfig/${x}.pc ${libname}.pc
-	done
-
-	# Debian installs it and some projects started using it.
-	insinto /usr/share/cmake/Modules/
-	doins "${S}/cmake/FindEigen3.cmake"
-}
diff --git a/dev-cpp/eigen/eigen-9999.ebuild b/dev-cpp/eigen/eigen-9999.ebuild
deleted file mode 100644
index 266a9ed2b..000000000
--- a/dev-cpp/eigen/eigen-9999.ebuild
+++ /dev/null
@@ -1,108 +0,0 @@
-# Copyright 1999-2017 Gentoo Foundation
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=6
-
-FORTRAN_NEEDED=fortran
-
-inherit alternatives-2 cmake-utils fortran-2 mercurial multilib
-
-DESCRIPTION="C++ template library for linear algebra"
-HOMEPAGE="http://eigen.tuxfamily.org/"
-SRC_URI=""
-EHG_REPO_URI="https://bitbucket.org/eigen/eigen"
-
-SLOT="3"
-LICENSE="MPL-2.0"
-KEYWORDS=""
-IUSE="adolc doc fortran fftw gmp metis mkl pastix sparse static-libs test"
-
-CDEPEND="
-	adolc? ( sci-libs/adolc[sparse?] )
-	fftw? ( sci-libs/fftw:3.0 )
-	gmp? ( dev-libs/gmp:0 dev-libs/mpfr:0 )
-	metis? ( sci-libs/metis )
-	mkl? ( sci-libs/mkl )
-	pastix? ( sci-libs/pastix )
-	sparse? (
-		dev-cpp/sparsehash
-		sci-libs/cholmod[metis?]
-		sci-libs/spqr
-		sci-libs/superlu
-		sci-libs/umfpack
-	)"
-DEPEND="
-	doc? ( app-doc/doxygen[dot,latex] )
-	test? ( ${CDEPEND} )"
-
-RDEPEND="
-	!dev-cpp/eigen:0
-	${CDEPEND}"
-
-src_prepare() {
-	sed -i \
-		-e "s:/usr:${EPREFIX}/usr:g" \
-		-e "s:/bin/bash:${EPREFIX}/bin/bash:g" \
-		cmake/*.cmake || die
-	sed -i \
-		-e "/DESTINATION/s:lib:$(get_libdir):g" \
-		{blas,lapack}/CMakeLists.txt || die
-
-	# TOFIX: static-libs for blas are always built with PIC
-	if ! use static-libs; then
-		sed \
-			-e "/add_dependencies/s/eigen_[a-z]*_static//g" \
-			-e "/TARGETS/s/eigen_[a-z]*_static//g" \
-			-e "/add_library(eigen_[a-z]*_static/d" \
-			-e "/target_link_libraries(eigen_[a-z]*_static/d" \
-			-i {blas,lapack}/CMakeLists.txt || die
-	fi
-
-	sed -i -e "/Unknown build type/d" CMakeLists.txt || die
-
-	cmake-utils_src_prepare
-}
-
-src_configure() {
-	# TOFIX: is it worth fixing all the automagic given no library is built?
-	# cmake has buggy disable_testing feature, so leave it for now
-	local mycmakeargs=(
-		-DDART_TESTING_TIMEOUT=300
-		-DEIGEN_BUILD_BTL=OFF
-	)
-	export VARTEXFONTS="${T}/fonts"
-	export PKG_CONFIG_LIBDIR=/usr/$(get_libdir)/
-
-	cmake-utils_src_configure
-	# use fortran && FORTRAN_LIBS="blas lapack" not ready
-	use fortran && FORTRAN_LIBS="blas"
-}
-
-src_compile() {
-	local targets="${FORTRAN_LIBS}"
-	use doc && targets+=" doc"
-	use test && targets+=" check"
-	cmake-utils_src_compile ${targets}
-}
-
-src_install() {
-	cmake-utils_src_install
-	use doc && dohtml -r "${BUILD_DIR}"/doc/html/*
-	local x
-	for x in ${FORTRAN_LIBS}; do
-		local libname="eigen_${x}"
-		emake DESTDIR="${D}" -C "${BUILD_DIR}/${x}" install ${libname}
-		create_pkgconfig \
-			--description "${DESCRIPTION} ${x^^} implementation" \
-			--libs "-L\${libdir} -l${libname}" \
-			--libs-private "-lm" \
-			$([[ ${x} == lapack ]] && echo "--requires 'blas'") \
-			${libname}
-		alternatives_for ${x} eigen 0 \
-			/usr/$(get_libdir)/pkgconfig/${x}.pc ${libname}.pc
-	done
-
-	# Debian installs it and some projects started using it.
-	insinto /usr/share/cmake/Modules/
-	doins "${S}/cmake/FindEigen3.cmake"
-}
diff --git a/dev-cpp/eigen/metadata.xml b/dev-cpp/eigen/metadata.xml
deleted file mode 100644
index ed850b49c..000000000
--- a/dev-cpp/eigen/metadata.xml
+++ /dev/null
@@ -1,34 +0,0 @@
-<?xml version="1.0" encoding="UTF-8"?>
-<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
-<pkgmetadata>
-	<maintainer type="project">
-		<email>sci@gentoo.org</email>
-		<name>Gentoo Science Project</name>
-	</maintainer>
-	<longdescription lang="en">
-Eigen is a lightweight C++ template library for vector and matrix math,
-a.k.a. linear algebra. Unlike most other linear algebra libraries, Eigen
-focuses on the simple mathematical needs of applications: games and other
-OpenGL apps, spreadsheets and other office apps, etc. Eigen is dedicated to
-providing optimal speed with GCC.
-</longdescription>
-	<use>
-		<flag name="adolc">
-Enable automatic differentiation using <pkg>sci-libs/adolc</pkg>
-</flag>
-		<flag name="metis">
-Enable matrix partitioning using <pkg>sci-libs/metis</pkg></flag>
-		<flag name="mkl">
-Use propertary intel blas/lapack implementation through <pkg>sci-libs/mkl</pkg>
-</flag>
-		<flag name="pastix">
-Enable large scale direct solver with using <pkg>sci-libs/pastix</pkg>
-</flag>
-		<flag name="sparse">
-Enable use for extra sparse matrix with <pkg>sci-libs/umfpack</pkg>, <pkg>sci-libs/cholmod</pkg>, <pkg>sci-libs/superlu</pkg> and <pkg>dev-cpp/sparsehash</pkg>
-</flag>
-	</use>
-	<upstream>
-		<remote-id type="bitbucket">eigen/eigen</remote-id>
-	</upstream>
-</pkgmetadata>
diff --git a/dev-cpp/growler-arch/Manifest b/dev-cpp/growler-arch/Manifest
deleted file mode 100644
index ba6b60ea4..000000000
--- a/dev-cpp/growler-arch/Manifest
+++ /dev/null
@@ -1 +0,0 @@
-DIST growler-arch-0.3.7.1.tar.gz 500709 BLAKE2B eec6c82bc03184f06a5fbbc4a66824b9f472c2349560c20ffc5c7e6d583d1353ade24faeeb7c57c8f1421f15df1b2709ceea45547d3ca19c71bc12c4e8e96a27 SHA512 0795aa560c5f9d7b48e1569d666a0ab971f148ddbecfa3a0d4528b758e00be4ec5a2dc26155b9349c60f783960e5a1f8515a23ea76e755fd4a7014b219606790
diff --git a/dev-cpp/growler-arch/growler-arch-0.3.7.1.ebuild b/dev-cpp/growler-arch/growler-arch-0.3.7.1.ebuild
deleted file mode 100644
index 3d75d60c2..000000000
--- a/dev-cpp/growler-arch/growler-arch-0.3.7.1.ebuild
+++ /dev/null
@@ -1,30 +0,0 @@
-# Copyright 1999-2016 Gentoo Foundation
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=6
-
-DESCRIPTION="Growler libraries and utilities"
-HOMEPAGE="http://www.nas.nasa.gov/~bgreen/growler/"
-SRC_URI="${HOMEPAGE}/downloads/growler-arch-${PV}.tar.gz"
-
-SLOT="0"
-LICENSE="NOSA"
-KEYWORDS="~amd64 ~x86"
-IUSE="doc static-libs"
-
-RDEPEND="
-	>=dev-cpp/growler-link-0.3.7
-	>=dev-cpp/growler-thread-0.3.4
-	>=dev-cpp/growler-core-0.3.7"
-
-DEPEND="${RDEPEND}
-	doc? ( app-doc/doxygen dev-libs/libxslt )"
-
-DOCS=( README NEWS AUTHORS NOSA ChangeLog )
-
-src_configure() {
-	econf \
-		$(use_enable doc) \
-		$(use_enable static-libs static) \
-		--enable-fast-install
-}
diff --git a/dev-cpp/growler-arch/metadata.xml b/dev-cpp/growler-arch/metadata.xml
deleted file mode 100644
index 56f547ec6..000000000
--- a/dev-cpp/growler-arch/metadata.xml
+++ /dev/null
@@ -1,9 +0,0 @@
-<?xml version="1.0" encoding="UTF-8"?>
-<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
-<pkgmetadata>
-	<maintainer type="person">
-		<email>bryan.d.green@nasa.gov</email>
-		<name>Bryan Green</name>
-	</maintainer>
-	<longdescription>Growler-Arch is the set growler libraries and utilities that provide a distributed object architecture and environment.</longdescription>
-</pkgmetadata>
diff --git a/dev-cpp/growler-core/Manifest b/dev-cpp/growler-core/Manifest
deleted file mode 100644
index 4a827dbf3..000000000
--- a/dev-cpp/growler-core/Manifest
+++ /dev/null
@@ -1 +0,0 @@
-DIST growler-core-0.3.7.tar.gz 271855 BLAKE2B 4d0b84dc58728ad1e4083e0c6126ed3aa7d22b3f897320ec9bc984e808964a0987a310e18980f2da2452e32d6805b094edc5ad0f5fa7640821e5c1a8de58189a SHA512 18870c6f732967aa720207cc616965336d5123319e1efe2a0a8dcf0b1a19473472f09b1e7b53dac40490dd91fef473be915c90305822d61c4606cd568546b7ab
diff --git a/dev-cpp/growler-core/growler-core-0.3.7.ebuild b/dev-cpp/growler-core/growler-core-0.3.7.ebuild
deleted file mode 100644
index d562bd2e6..000000000
--- a/dev-cpp/growler-core/growler-core-0.3.7.ebuild
+++ /dev/null
@@ -1,29 +0,0 @@
-# Copyright 1999-2016 Gentoo Foundation
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=6
-
-DESCRIPTION="General-purpose classes and functionality"
-HOMEPAGE="http://www.nas.nasa.gov/~bgreen/growler/"
-SRC_URI="${HOMEPAGE}/downloads/growler-core-${PV}.tar.gz"
-
-SLOT="0"
-LICENSE="NOSA"
-KEYWORDS="~amd64 ~x86"
-IUSE="doc static-libs"
-
-RDEPEND="
-	>=dev-cpp/growler-link-0.3.7
-	>=dev-cpp/growler-thread-0.3.4"
-
-DEPEND="${RDEPEND}
-	doc? ( app-doc/doxygen )"
-
-DOCS=( README NEWS AUTHORS NOSA ChangeLog )
-
-src_configure() {
-	econf \
-		$(use_enable doc) \
-		$(use_enable static-libs static) \
-		--enable-fast-install
-}
diff --git a/dev-cpp/growler-core/metadata.xml b/dev-cpp/growler-core/metadata.xml
deleted file mode 100644
index f4b35821b..000000000
--- a/dev-cpp/growler-core/metadata.xml
+++ /dev/null
@@ -1,13 +0,0 @@
-<?xml version="1.0" encoding="UTF-8"?>
-<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
-<pkgmetadata>
-	<maintainer type="person">
-		<email>bryan.d.green@nasa.gov</email>
-		<name>Bryan Green</name>
-	</maintainer>
-	<longdescription>
-Growler-Core provides a large set of mainly general-purpose classes and
-functionality for developing and using the Growler Distributed Component
-Architecture.
-</longdescription>
-</pkgmetadata>
diff --git a/dev-cpp/growler-link/Manifest b/dev-cpp/growler-link/Manifest
deleted file mode 100644
index 27fd5361e..000000000
--- a/dev-cpp/growler-link/Manifest
+++ /dev/null
@@ -1 +0,0 @@
-DIST growler-link-0.3.7.tar.gz 548768 BLAKE2B 80e9502daae403630731595caf6d864a9d70984b0b69a8a0ca22580c92b9a1f80edd4502847fb4c03aaf82cc219445bc51a3bdd301241310b2f2e8386c408902 SHA512 713118a7ba4c0364b3e0bb2f24a551eddfda6998e3b3ea5c5becdb2be49b4deda86eb2961d54e931c9936ef76db64660e3a11a695e3a7287255b22703746117b
diff --git a/dev-cpp/growler-link/files/0.3.7-gcc4.7.patch b/dev-cpp/growler-link/files/0.3.7-gcc4.7.patch
deleted file mode 100644
index f3939be89..000000000
--- a/dev-cpp/growler-link/files/0.3.7-gcc4.7.patch
+++ /dev/null
@@ -1,15 +0,0 @@
- lib/strings.cxx | 1 +
- 1 file changed, 1 insertion(+)
-
-diff --git a/lib/strings.cxx b/lib/strings.cxx
-index 1efa4fd..09488d8 100644
---- a/lib/strings.cxx
-+++ b/lib/strings.cxx
-@@ -26,6 +26,7 @@
- #include <cstdio>
- #include <cerrno>
- #include <stdexcept>
-+#include <unistd.h>
- 
- using namespace std;
- 
diff --git a/dev-cpp/growler-link/files/0.3.7-gcc4.patch b/dev-cpp/growler-link/files/0.3.7-gcc4.patch
deleted file mode 100644
index fcfbf19fb..000000000
--- a/dev-cpp/growler-link/files/0.3.7-gcc4.patch
+++ /dev/null
@@ -1,36 +0,0 @@
-diff --git a/lib/buffer.cxx b/lib/buffer.cxx
-index 7b9eda3..12b87ad 100644
---- a/lib/buffer.cxx
-+++ b/lib/buffer.cxx
-@@ -6,6 +6,7 @@
-  */
- 
- #include <cstdio>
-+#include <cstring>
- #include <memory>
- #include <stdexcept>
- #include <lib/unistd.h>
-diff --git a/lib/daemon.cxx b/lib/daemon.cxx
-index f289783..78d4883 100644
---- a/lib/daemon.cxx
-+++ b/lib/daemon.cxx
-@@ -18,6 +18,7 @@
- #include <sys/stat.h>
- #include <sys/wait.h>
- #include <pwd.h>
-+#include <cstdio>
- 
- #if GR_HAVE_FCNTL_H
- #include <fcntl.h>
-diff --git a/lib/serialize.h b/lib/serialize.h
-index 8fa68f8..0e08c81 100644
---- a/lib/serialize.h
-+++ b/lib/serialize.h
-@@ -23,6 +23,7 @@
- #include <streambuf>
- #include <string>
- #include <cassert>
-+#include <cstdio>
- 
- namespace lib {
- 
diff --git a/dev-cpp/growler-link/growler-link-0.3.7.ebuild b/dev-cpp/growler-link/growler-link-0.3.7.ebuild
deleted file mode 100644
index 2810cf6e9..000000000
--- a/dev-cpp/growler-link/growler-link-0.3.7.ebuild
+++ /dev/null
@@ -1,35 +0,0 @@
-# Copyright 1999-2016 Gentoo Foundation
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=6
-
-inherit fortran-2
-
-DESCRIPTION="The lowest-level Growler library"
-HOMEPAGE="http://www.nas.nasa.gov/~bgreen/growler/"
-SRC_URI="${HOMEPAGE}/downloads/growler-link-${PV}.tar.gz"
-
-SLOT="0"
-LICENSE="NOSA"
-KEYWORDS="~amd64 ~x86"
-IUSE="doc fortran static-libs tcpd"
-
-RDEPEND="
-	dev-libs/boost
-	tcpd? ( sys-apps/tcp-wrappers )"
-DEPEND="${RDEPEND}
-	doc? ( app-doc/doxygen )"
-
-PATCHES=(
-	"${FILESDIR}"/${PV}-gcc4.patch
-	"${FILESDIR}"/${PV}-gcc4.7.patch
-	)
-
-src_configure() {
-	local myeconfargs=(
-		$(use_enable doc)
-		$(use_enable tcpd)
-		$(use_enable static-libs static)
-		)
-	econf ${myeconfargs[@]}
-}
diff --git a/dev-cpp/growler-link/metadata.xml b/dev-cpp/growler-link/metadata.xml
deleted file mode 100644
index 82a8bc1f0..000000000
--- a/dev-cpp/growler-link/metadata.xml
+++ /dev/null
@@ -1,13 +0,0 @@
-<?xml version="1.0" encoding="UTF-8"?>
-<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
-<pkgmetadata>
-	<maintainer type="person">
-		<email>bryan.d.green@nasa.gov</email>
-		<name>Bryan Green</name>
-	</maintainer>
-	<longdescription>
-Growler-Link is the lowest-level Growler package.  It provides basic support for
-dynamic linking, components and modules, as well as several other of Growler's
-commonly used API's, such as Clogger.
-</longdescription>
-</pkgmetadata>
diff --git a/dev-cpp/growler-math/Manifest b/dev-cpp/growler-math/Manifest
deleted file mode 100644
index 0823ee331..000000000
--- a/dev-cpp/growler-math/Manifest
+++ /dev/null
@@ -1 +0,0 @@
-DIST growler-math-0.3.4.1.tar.gz 178883 BLAKE2B aaef7568b350421aa538183f622ed01d9f7df928bc3b7c323c3c4417ba3de39f05a77c7eae6ac705e35b333b86cd3d7f142d3b7f53d1be2670d1cdddf1ab925f SHA512 2894b91b23c2c2c75fedcafe4c2c00e49bb05a7a3de745d764934d33c6b5f656a3c37c6ed7562cd7b70e9fa939c9cb4b686e2cc674a71baad2600413dec7bd69
diff --git a/dev-cpp/growler-math/growler-math-0.3.4.1.ebuild b/dev-cpp/growler-math/growler-math-0.3.4.1.ebuild
deleted file mode 100644
index 0274872c1..000000000
--- a/dev-cpp/growler-math/growler-math-0.3.4.1.ebuild
+++ /dev/null
@@ -1,24 +0,0 @@
-# Copyright 1999-2016 Gentoo Foundation
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=6
-
-DESCRIPTION="Math-related classes and functionality"
-HOMEPAGE="http://www.nas.nasa.gov/~bgreen/growler/"
-SRC_URI="${HOMEPAGE}/downloads/growler-math-${PV}.tar.gz"
-
-SLOT="0"
-LICENSE="NOSA"
-KEYWORDS="~amd64 ~x86"
-IUSE="static-libs"
-
-RDEPEND=">=dev-cpp/growler-core-0.3.7"
-DEPEND="${RDEPEND}"
-
-DOCS=( README NEWS AUTHORS NOSA ChangeLog )
-
-src_configure() {
-	econf \
-		$(use_enable static-libs static) \
-		--enable-fast-install
-}
diff --git a/dev-cpp/growler-math/metadata.xml b/dev-cpp/growler-math/metadata.xml
deleted file mode 100644
index d284223c7..000000000
--- a/dev-cpp/growler-math/metadata.xml
+++ /dev/null
@@ -1,9 +0,0 @@
-<?xml version="1.0" encoding="UTF-8"?>
-<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
-<pkgmetadata>
-	<maintainer type="person">
-		<email>bryan.d.green@nasa.gov</email>
-		<name>Bryan Green</name>
-	</maintainer>
-	<longdescription>Growler-Math provides a set of math-related classes and functionality</longdescription>
-</pkgmetadata>
diff --git a/dev-cpp/growler-thread/Manifest b/dev-cpp/growler-thread/Manifest
deleted file mode 100644
index 863a7095e..000000000
--- a/dev-cpp/growler-thread/Manifest
+++ /dev/null
@@ -1 +0,0 @@
-DIST growler-thread-0.3.4.tar.gz 183150 BLAKE2B 636b443cdcf0e26e8644f167d04e4a820a44c42bb66a2bb16389725131cb6597226b7eebd383cc256d7e8609a0cde8f0ec88dc50b958da85bfbbe3012a9faeaf SHA512 42d44e4c181439c7bf6d2494a5e50da8f52b0858833691e190c2b408b020bdb63655788803fba51b87b40a824260479a08e83f2ec196bacc81fd46aec7784b39
diff --git a/dev-cpp/growler-thread/growler-thread-0.3.4.ebuild b/dev-cpp/growler-thread/growler-thread-0.3.4.ebuild
deleted file mode 100644
index 6a4ec1118..000000000
--- a/dev-cpp/growler-thread/growler-thread-0.3.4.ebuild
+++ /dev/null
@@ -1,26 +0,0 @@
-# Copyright 1999-2016 Gentoo Foundation
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=6
-
-DESCRIPTION="Pthread wrapper library"
-HOMEPAGE="http://www.nas.nasa.gov/~bgreen/growler/"
-SRC_URI="${HOMEPAGE}/downloads/growler-thread-${PV}.tar.gz"
-
-SLOT="0"
-LICENSE="NOSA"
-KEYWORDS="~amd64 ~x86"
-IUSE="doc static-libs"
-
-RDEPEND=">=dev-cpp/growler-link-0.3.7"
-DEPEND="${RDEPEND}
-	doc? ( app-doc/doxygen )"
-
-DOCS=( README NEWS AUTHORS NOSA ChangeLog )
-
-src_configure() {
-	econf \
-		$(use_enable doc) \
-		$(use_enable static-libs static) \
-		--enable-fast-install
-}
diff --git a/dev-cpp/growler-thread/metadata.xml b/dev-cpp/growler-thread/metadata.xml
deleted file mode 100644
index 16f9b1a83..000000000
--- a/dev-cpp/growler-thread/metadata.xml
+++ /dev/null
@@ -1,12 +0,0 @@
-<?xml version="1.0" encoding="UTF-8"?>
-<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
-<pkgmetadata>
-	<maintainer type="person">
-		<email>bryan.d.green@nasa.gov</email>
-		<name>Bryan Green</name>
-	</maintainer>
-	<longdescription>
-Growler-Thread is a pthread wrapper library used by Growler. It provides
-support for creating threads, and for common multithreading tasks
-</longdescription>
-</pkgmetadata>
diff --git a/dev-cpp/growler/growler-0.3.8.2.ebuild b/dev-cpp/growler/growler-0.3.8.2.ebuild
deleted file mode 100644
index c17e38e98..000000000
--- a/dev-cpp/growler/growler-0.3.8.2.ebuild
+++ /dev/null
@@ -1,20 +0,0 @@
-# Copyright 1999-2016 Gentoo Foundation
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=6
-
-DESCRIPTION="Distributed object architecture and environment"
-HOMEPAGE="http://www.nas.nasa.gov/~bgreen/growler/"
-SRC_URI=""
-
-SLOT="0"
-LICENSE="NOSA"
-KEYWORDS="~amd64 ~x86"
-IUSE=""
-
-RDEPEND="
-	>=dev-cpp/growler-link-0.3.7
-	>=dev-cpp/growler-thread-0.3.4
-	>=dev-cpp/growler-core-0.3.7
-	>=dev-cpp/growler-arch-0.3.7.1"
-DEPEND=""
diff --git a/dev-cpp/growler/metadata.xml b/dev-cpp/growler/metadata.xml
deleted file mode 100644
index 7fd7dac50..000000000
--- a/dev-cpp/growler/metadata.xml
+++ /dev/null
@@ -1,9 +0,0 @@
-<?xml version="1.0" encoding="UTF-8"?>
-<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
-<pkgmetadata>
-	<maintainer type="person">
-		<email>bryan.d.green@nasa.gov</email>
-		<name>Bryan Green</name>
-	</maintainer>
-	<longdescription>Growler is a C++-based distributed object and event architecture.</longdescription>
-</pkgmetadata>
diff --git a/dev-cpp/highwayhash/Manifest b/dev-cpp/highwayhash/Manifest
index 40ba9bd4b..a400c0baf 100644
--- a/dev-cpp/highwayhash/Manifest
+++ b/dev-cpp/highwayhash/Manifest
@@ -1 +1 @@
-DIST highwayhash-20180209.tar.gz 152323 BLAKE2B 7151ba6e68ae5c9b32311b962364e77512f609c14bcf43d68f0c938c2ad6ffc5548eb2fb9bfc4b97fe096979a068d3b6342999ca33ea0d51c503a04300845b25 SHA512 00b64db0c27ddc25fe683f4032e21756326ac3fd95e27fa5033cdaf61d89cfec56b990581545e048c596d943ad4fb0efaf4158660ff0ded134e764b1f2db2bc8
+DIST highwayhash-20200922.tar.gz 160264 BLAKE2B f37074a97c8465f0a4720f7f0ebab6eece851da64f872eb8aeb40c6d11ddc073aa6e7e4bfa91908d4ca806b4fd5804a9f40cea729e0fcc6a333f1092ddd33e86 SHA512 4117612b8ea3bc5c10296cefcfda07f6b12f81bac4112a5f5479edee1731c3442fa4d31584f3b0b876c95b02783730ea349ac975ae51d409ff55ace6322bdfe1
diff --git a/dev-cpp/highwayhash/highwayhash-20180209.ebuild b/dev-cpp/highwayhash/highwayhash-20180209.ebuild
deleted file mode 100644
index 2fd3f1349..000000000
--- a/dev-cpp/highwayhash/highwayhash-20180209.ebuild
+++ /dev/null
@@ -1,30 +0,0 @@
-# Copyright 1999-2018 Gentoo Foundation
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=6
-
-DESCRIPTION="Fast strong hash functions: SipHash/HighwayHash"
-HOMEPAGE="https://github.com/google/highwayhash"
-COMMIT="14dedecd1de87cb662f7a882ea1578d2384feb2f"
-SRC_URI="https://github.com/google/highwayhash/archive/${COMMIT}.tar.gz -> ${P}.tar.gz"
-
-LICENSE="Apache-2.0"
-SLOT="0"
-KEYWORDS="~amd64 ~x86"
-IUSE="static-libs"
-
-DEPEND=""
-RDEPEND="${DEPEND}"
-
-S="${WORKDIR}/${PN}-${COMMIT}"
-
-src_prepare() {
-	sed -i "/CXXFLAGS/s/-O3/${CXXFLAGS}/" Makefile || die
-	default
-}
-
-src_install() {
-	emake DESTDIR="${D}" INCDIR="${EPREFIX}/usr/include" LIBDIR="${EPREFIX}/usr/$(get_libdir)" install
-	use static-libs || rm "${D}/${EPREFIX}/usr/$(get_libdir)"/lib*.a || die
-	einstalldocs
-}
diff --git a/dev-cpp/highwayhash/highwayhash-20200922.ebuild b/dev-cpp/highwayhash/highwayhash-20200922.ebuild
new file mode 100644
index 000000000..2eb0ccaa2
--- /dev/null
+++ b/dev-cpp/highwayhash/highwayhash-20200922.ebuild
@@ -0,0 +1,30 @@
+# Copyright 1999-2020 Gentoo Authors
+# Distributed under the terms of the GNU General Public License v2
+
+EAPI=7
+
+DESCRIPTION="Fast strong hash functions: SipHash/HighwayHash"
+HOMEPAGE="https://github.com/google/highwayhash"
+COMMIT="bdd572de8cfa3a1fbef6ba32307c2629db7c4773"
+SRC_URI="https://github.com/google/highwayhash/archive/${COMMIT}.tar.gz -> ${P}.tar.gz"
+S="${WORKDIR}/${PN}-${COMMIT}"
+
+LICENSE="Apache-2.0"
+SLOT="0"
+KEYWORDS="~amd64 ~x86"
+IUSE="static-libs"
+
+src_prepare() {
+	sed -i "/CXXFLAGS/s/-O3/${CXXFLAGS}/" Makefile || die
+	default
+}
+
+src_install() {
+	emake DESTDIR="${ED}"\
+		INCDIR="/usr/include" \
+		LIBDIR="/usr/$(get_libdir)" \
+		install
+	use static-libs || \
+		rm "${ED}/usr/$(get_libdir)"/lib*.a || die
+	einstalldocs
+}
diff --git a/dev-cpp/highwayhash/metadata.xml b/dev-cpp/highwayhash/metadata.xml
index ef6b5dcd5..ce99f4b00 100644
--- a/dev-cpp/highwayhash/metadata.xml
+++ b/dev-cpp/highwayhash/metadata.xml
@@ -5,4 +5,7 @@
 		<email>junghans@gentoo.org</email>
 		<name>Christoph Junghans</name>
 	</maintainer>
+	<upstream>
+		<remote-id type="github">google/highwayhash</remote-id>
+	</upstream>
 </pkgmetadata>
diff --git a/dev-cpp/icnc/icnc-9999.ebuild b/dev-cpp/icnc/icnc-9999.ebuild
deleted file mode 100644
index 180840e95..000000000
--- a/dev-cpp/icnc/icnc-9999.ebuild
+++ /dev/null
@@ -1,50 +0,0 @@
-# Copyright 1999-2017 Gentoo Foundation
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=6
-
-PYTHON_COMPAT=( python2_7 )
-
-inherit cmake-utils git-r3 multilib python-any-r1
-
-DESCRIPTION="Intel Concurrent Collections for C++ - Parallelism without the Pain"
-HOMEPAGE="https://software.intel.com/en-us/articles/intel-concurrent-collections-for-cc"
-EGIT_REPO_URI="https://github.com/icnc/icnc.git"
-
-LICENSE="BSD"
-SLOT="0"
-KEYWORDS=
-IUSE="doc examples mpi test"
-
-RDEPEND="
-	>=dev-cpp/tbb-4.2
-	sys-libs/glibc
-	mpi? ( virtual/mpi )
-	"
-DEPEND="
-	${RDEPEND}
-	doc? ( app-doc/doxygen )
-	test? ( ${PYTHON_DEPS} )
-	"
-
-src_configure() {
-	local mycmakeargs=(
-		$(cmake-utils_use mpi BUILD_LIBS_FOR_MPI)
-		-DLIB=$(get_libdir)
-		$(cmake-utils_use_find_package doc Doxygen)
-		$(cmake-utils_use test ENABLE_TESTING)
-		-DRUN_DIST=OFF
-	)
-	cmake-utils_src_configure
-}
-
-src_install() {
-	cmake-utils_src_install
-	if use doc; then
-		mv "${ED}"/usr/share/{icnc/doc/api,doc/${PF}/html} || die
-		rmdir "${ED}"/usr/share/icnc/doc || die
-	fi
-	if ! use examples; then
-		rm -r "${ED}"/usr/share/icnc/samples || die
-	fi
-}
diff --git a/dev-cpp/icnc/metadata.xml b/dev-cpp/icnc/metadata.xml
deleted file mode 100644
index 9dee8db11..000000000
--- a/dev-cpp/icnc/metadata.xml
+++ /dev/null
@@ -1,8 +0,0 @@
-<?xml version="1.0" encoding="UTF-8"?>
-<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
-<pkgmetadata>
-	<maintainer type="person">
-		<email>ottxor@gentoo.org</email>
-		<name>Christoph Junghans</name>
-	</maintainer>
-</pkgmetadata>
diff --git a/dev-cpp/kokkos/Manifest b/dev-cpp/kokkos/Manifest
deleted file mode 100644
index 7aba01845..000000000
--- a/dev-cpp/kokkos/Manifest
+++ /dev/null
@@ -1 +0,0 @@
-DIST kokkos-2.7.00.tar.gz 2778714 BLAKE2B c90666f61ba693d16456e83bc0d4ed12712439923ff070c2b0d0bc02316359c0f73a35a722f10b41bd6a4420c51fa5a973a2f9cf5298148bedfc7993f2e52db8 SHA512 56c339b6ad168131aaff958213168932d997bc72ed8b58d3082c0d30959261a6f524a79f76ab7963cf91889c7196f058fc6ce5a52bf6983574b083c975d96e03
diff --git a/dev-cpp/kokkos/kokkos-2.7.00.ebuild b/dev-cpp/kokkos/kokkos-2.7.00.ebuild
deleted file mode 100644
index f2adfa3d5..000000000
--- a/dev-cpp/kokkos/kokkos-2.7.00.ebuild
+++ /dev/null
@@ -1,47 +0,0 @@
-# Copyright 1999-2018 Gentoo Foundation
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=6
-
-inherit cmake-utils toolchain-funcs
-
-DESCRIPTION="Kokkos C++ Performance Portability Programming EcoSystem"
-HOMEPAGE="https://github.com/kokkos"
-SRC_URI="https://github.com/${PN}/${PN}/archive/${PV}.tar.gz -> ${P}.tar.gz"
-
-LICENSE="BSD-3"
-SLOT="0"
-KEYWORDS="~amd64 ~x86"
-IUSE="openmp +threads"
-REQUIRED_USE="?? ( openmp threads )"
-
-DEPEND="
-	sys-apps/hwloc
-	"
-RDEPEND="${DEPEND}"
-BDEPEND=""
-
-pkg_setup() {
-	if [[ ${MERGE_TYPE} != binary ]] && \
-		use openmp && ! tc-has-openmp ; then
-			die "Need an OpenMP capable compiler"
-	fi
-}
-
-src_configure() {
-	local mycmakeargs=(
-		-DKOKKOS_ENABLE_HWLOC=ON
-		-DKOKKOS_HWLOC_DIR="${EPREFIX}/usr"
-		-DKOKKOS_ENABLE_OPENMP=$(usex openmp)
-		-DKOKKOS_ENABLE_PTHREAD=$(usex threads)
-		-DKOKKOS_ENABLE_SERIAL=ON
-		-DBUILD_SHARED_LIBS=ON
-	)
-
-	cmake-utils_src_configure
-}
-
-src_install() {
-	cmake-utils_src_install
-	[[ $(get_libdir) = lib ]] || mv "${ED}"/usr/{lib,"$(get_libdir)"} || die
-}
diff --git a/dev-cpp/kokkos/metadata.xml b/dev-cpp/kokkos/metadata.xml
deleted file mode 100644
index ef6b5dcd5..000000000
--- a/dev-cpp/kokkos/metadata.xml
+++ /dev/null
@@ -1,8 +0,0 @@
-<?xml version="1.0" encoding="UTF-8"?>
-<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
-<pkgmetadata>
-	<maintainer type="person">
-		<email>junghans@gentoo.org</email>
-		<name>Christoph Junghans</name>
-	</maintainer>
-</pkgmetadata>
diff --git a/dev-cpp/xor_singleheader/Manifest b/dev-cpp/xor_singleheader/Manifest
new file mode 100644
index 000000000..e0b53a92c
--- /dev/null
+++ b/dev-cpp/xor_singleheader/Manifest
@@ -0,0 +1 @@
+DIST xor_singleheader-0_p20012020.tar.gz 196021 BLAKE2B 1eb25b79f6c28971024374e9c6028965dccc7c18cac1f4f13349d2b392a5c852e81331b0b625194835293d6da672bf35f8720a44c0bbe3c8872b422125aa8017 SHA512 fe0d40c9b1d6dfb6aeeb26439ce06860f8781adbce0fdd7d1aa1037372a9f463690638270365871e0a79a8b3be7e067eb80fca6ee1525b9434afddbe9fdc1f78
diff --git a/dev-cpp/xor_singleheader/metadata.xml b/dev-cpp/xor_singleheader/metadata.xml
new file mode 100644
index 000000000..cebb00f2c
--- /dev/null
+++ b/dev-cpp/xor_singleheader/metadata.xml
@@ -0,0 +1,15 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
+<pkgmetadata>
+	<maintainer type="person">
+		<email>gentoo@aisha.cc</email>
+		<name>Aisha Tammy</name>
+	</maintainer>
+	<maintainer type="project">
+		<email>sci@gentoo.org</email>
+		<name>Gentoo Science Project</name>
+	</maintainer>
+	<upstream>
+		<remote-id type="github">FastFilter/xor_singleheader</remote-id>
+	</upstream>
+</pkgmetadata>
diff --git a/dev-cpp/xor_singleheader/xor_singleheader-0_p20012020.ebuild b/dev-cpp/xor_singleheader/xor_singleheader-0_p20012020.ebuild
new file mode 100644
index 000000000..005e4a582
--- /dev/null
+++ b/dev-cpp/xor_singleheader/xor_singleheader-0_p20012020.ebuild
@@ -0,0 +1,31 @@
+# Copyright 1999-2020 Gentoo Authors
+# Distributed under the terms of the GNU General Public License v2
+
+EAPI=7
+
+DESCRIPTION="single header library for fast XOR filters"
+HOMEPAGE="https://github.com/FastFilter/xor_singleheader"
+
+COMMIT=6cea6a4dcf2f18a0e3b9b9e0b94d6012b804ffa1
+SRC_URI="https://github.com/FastFilter/xor_singleheader/archive/${COMMIT}.tar.gz -> ${P}.tar.gz"
+S="${WORKDIR}"/${PN}-${COMMIT}
+KEYWORDS="~amd64"
+
+LICENSE="Apache-2.0"
+SLOT="0"
+IUSE="test"
+RESTRICT="!test? ( test )"
+
+src_compile() {
+	if use test ; then
+		default
+	fi
+}
+
+src_install() {
+	doheader include/{fusefilter,xorfilter}.h
+}
+
+src_test() {
+	"${S}"/unit || die "failed unittests"
+}
diff --git a/dev-java/fits/Manifest b/dev-java/fits/Manifest
index ecf89b161..dc9abd6bb 100644
--- a/dev-java/fits/Manifest
+++ b/dev-java/fits/Manifest
@@ -1 +1 @@
-DIST fits-1.11.0-src.jar 247303 BLAKE2B 2d836b943229b9d7eda1f144cf3e37a3d94f634a2aff2a177120654aef3fc6cce1bb5ba1c4d45624da5c9f08167d69a67da50cd7a110a5e7d41b47ea5a179ccf SHA512 e4ecebe139dfcd9f475c9e588c4d625472a6b147b67b9ce2eb3f08e5e43b278e9df03d86d597881c9f9a7fffbc3a4dbede75b3a76543742ceb705f136d8a9b27
+DIST fits-1.15.1.jar 531531 BLAKE2B e490d4159ee9ef5bed5359cb3c0972a4a16db9f37c0b52f454c169dfbfd1c51bcf47b941c255b1eb968a22ed3d4bd78c973209a38ab32a621d6eeaf0a7842e30 SHA512 4835bf5ac2766c9c13f3817e2fd48fc8c7304f1cc7c912dc3d5d56dfba9c705d73fcd3093a8b58afb95fb58edd799c7197e7705f189cec7853f2387bafe4fcc5
diff --git a/dev-java/fits/files/01-Use-getResource-to-access-CompressTest-data-for-unit.patch b/dev-java/fits/files/01-Use-getResource-to-access-CompressTest-data-for-unit.patch
deleted file mode 100644
index 389c233d1..000000000
--- a/dev-java/fits/files/01-Use-getResource-to-access-CompressTest-data-for-unit.patch
+++ /dev/null
@@ -1,137 +0,0 @@
-diff --git a/src/nom/tam/fits/test/CompressTest.java b/src/nom/tam/fits/test/CompressTest.java
-index dd3aad0..c6d953e 100644
---- a/src/nom/tam/fits/test/CompressTest.java
-+++ b/src/nom/tam/fits/test/CompressTest.java
-@@ -54,58 +54,57 @@ public class CompressTest {
- 
-     @Test
-     public void testStream() throws Exception {
--        InputStream is;
-+        String is;
- 
--        is = new FileInputStream("test.fits");
-+        is = "test.fits";
-         assertEquals("Stream1", 300, streamRead(is, false, false));
- 
--        is = new FileInputStream("test.fits.Z");
-+        is = "test.fits.Z";
-         assertEquals("Stream2", 300, streamRead(is, false, false));
- 
--        is = new FileInputStream("test.fits.gz");
-+        is = "test.fits.gz";
-         assertEquals("Stream3", 300, streamRead(is, false, false));
- 
--        is = new FileInputStream("test.fits");
-+        is = "test.fits";
-         assertEquals("Stream4", 300, streamRead(is, false, true));
- 
--        is = new FileInputStream("test.fits.Z");
-+        is = "test.fits.Z";
-         assertEquals("Stream5", 300, streamRead(is, false, true));
- 
--        is = new FileInputStream("test.fits.gz");
-+        is = "test.fits.gz";
-         assertEquals("Stream6", 300, streamRead(is, false, true));
- 
--
--        is = new FileInputStream("test.fits.Z");
-+        is = "test.fits.Z";
-         assertEquals("Stream7", 300, streamRead(is, true, true));
- 
--        is = new FileInputStream("test.fits.gz");
-+        is = "test.fits.gz";
-         assertEquals("Stream8", 300, streamRead(is, true, true));
- 
--        is = new FileInputStream("test.fits.bz2");
-+        is = "test.fits.bz2";
-         assertEquals("Stream9", 300, streamRead(is, true, true));
-     }
- 
-     @Test
-     public void testFile() throws Exception {
--        File is = new File("test.fits");
-+        String is = "test.fits";
-         assertEquals("File1", 300, fileRead(is, false, false));
- 
--        is = new File("test.fits.Z");
-+        is = "test.fits.Z";
-         assertEquals("File2", 300, fileRead(is, false, false));
- 
--        is = new File("test.fits.gz");
-+        is = "test.fits.gz";
-         assertEquals("File3", 300, fileRead(is, false, false));
- 
--        is = new File("test.fits");
-+        is = "test.fits";
-         assertEquals("File4", 300, fileRead(is, false, true));
- 
--        is = new File("test.fits.Z");
-+        is = "test.fits.Z";
-         assertEquals("File7", 300, fileRead(is, true, true));
- 
--        is = new File("test.fits.gz");
-+        is = "test.fits.gz";
-         assertEquals("File8", 300, fileRead(is, true, true));
- 
--        is = new File("test.fits.bz2");
-+        is = "test.fits.bz2";
-         assertEquals("File9", 300, fileRead(is, true, true));
-     }
- 
-@@ -131,7 +130,6 @@ public class CompressTest {
- 
-         is = "test.fits.bz2";
-         assertEquals("String8", 300, stringRead(is, true, true));
--
-     }
- 
-     @Test
-@@ -158,13 +156,9 @@ public class CompressTest {
-         assertEquals("String8", 300, urlRead(is, true, true));
-     }
- 
--    int urlRead(String is, boolean comp, boolean useComp)
-+    int urlRead(String filename, boolean comp, boolean useComp)
-             throws Exception {
--        File fil = new File(is);
--
--        String path = fil.getCanonicalPath();
--        URL u = new URL("file://" + path);
--
-+        URL u = CompressTest.class.getResource(filename);
-         Fits f;
-         if (useComp) {
-             f = new Fits(u, comp);
-@@ -176,8 +170,9 @@ public class CompressTest {
-         return total(data);
-     }
- 
--    int streamRead(InputStream is, boolean comp, boolean useComp)
-+    int streamRead(String filename, boolean comp, boolean useComp)
-             throws Exception {
-+        InputStream is = CompressTest.class.getResourceAsStream(filename);
-         Fits f;
-         if (useComp) {
-             f = new Fits(is, comp);
-@@ -190,8 +185,9 @@ public class CompressTest {
-         return total(data);
-     }
- 
--    int fileRead(File is, boolean comp, boolean useComp)
-+    int fileRead(String filename, boolean comp, boolean useComp)
-             throws Exception {
-+        File is = new File(CompressTest.class.getResource(filename).getPath());
-         Fits f;
-         if (useComp) {
-             f = new Fits(is, comp);
-@@ -203,8 +199,9 @@ public class CompressTest {
-         return total(data);
-     }
- 
--    int stringRead(String is, boolean comp, boolean useComp)
-+    int stringRead(String filename, boolean comp, boolean useComp)
-             throws Exception {
-+        String is = CompressTest.class.getResource(filename).getPath();
-         Fits f;
-         if (useComp) {
-             f = new Fits(is, comp);
diff --git a/dev-java/fits/files/02-Update-ArrayFuncsTest.java-to-JUnit-4.patch b/dev-java/fits/files/02-Update-ArrayFuncsTest.java-to-JUnit-4.patch
deleted file mode 100644
index c9cd02d55..000000000
--- a/dev-java/fits/files/02-Update-ArrayFuncsTest.java-to-JUnit-4.patch
+++ /dev/null
@@ -1,223 +0,0 @@
-From b9edd6a86e66d354b0c1d010125246d8359cbb37 Mon Sep 17 00:00:00 2001
-From: W. Trevor King <wking@drexel.edu>
-Date: Fri, 7 Oct 2011 03:44:18 -0400
-Subject: [PATCH 7/8] Update ArrayFuncsTest.java to JUnit-4.
-
----
- src/nom/tam/util/test/ArrayFuncsTest.java |   44 +++++++++++++++++++---------
- 1 files changed, 30 insertions(+), 14 deletions(-)
-
-diff --git a/src/nom/tam/util/test/ArrayFuncsTest.java b/src/nom/tam/util/test/ArrayFuncsTest.java
-index df5efb0..7ad8e51 100644
---- a/src/nom/tam/util/test/ArrayFuncsTest.java
-+++ b/src/nom/tam/util/test/ArrayFuncsTest.java
-@@ -6,6 +6,12 @@
-  */

- package nom.tam.util.test;

- 

-+import org.junit.Test;

-+import static org.junit.Assert.assertEquals;

-+import static org.junit.Assert.assertTrue;

-+import static org.junit.Assert.assertFalse;

-+import static org.junit.Assert.assertSame;

-+import static org.junit.Assert.assertNotSame;

- import junit.framework.*;

- import java.lang.reflect.*;

- import java.util.Arrays;

-@@ -15,21 +21,12 @@ import nom.tam.util.ArrayFuncs;
-  *

-  * @author Thomas McGlynn

-  */

--public class ArrayFuncsTest extends TestCase {

--

--    public ArrayFuncsTest(String testName) {

--        super(testName);

--    }

--

--    protected void setUp() throws Exception {

--    }

--

--    protected void tearDown() throws Exception {

--    }

-+public class ArrayFuncsTest {

- 

-     /**

-      * Test of computeSize method, of class nom.tam.util.ArrayFuncs.

-      */

-+    @Test

-     public void testComputeSize() {

-         System.out.println("computeSize");

- 

-@@ -58,6 +55,7 @@ public class ArrayFuncsTest extends TestCase {
-     /**

-      * Test of nElements method, of class nom.tam.util.ArrayFuncs.

-      */

-+    @Test

-     public void testNElements() {

-         System.out.println("nElements");

- 

-@@ -72,6 +70,7 @@ public class ArrayFuncsTest extends TestCase {
-     /**

-      * Test of deepClone method, of class nom.tam.util.ArrayFuncs.

-      */

-+    @Test

-     public void testDeepClone() {

-         int[][] test = {{0, 1}, {2, 3}, {4, 5}};

-         int[][] result = (int[][]) nom.tam.util.ArrayFuncs.deepClone(test);

-@@ -96,6 +95,7 @@ public class ArrayFuncsTest extends TestCase {
-         }

- 

-         public boolean equals(Object x) {

-+	    System.out.println("checking equality");

-             return (x instanceof CloneTest)

-                     && (((CloneTest) x).value == this.value);

-         }

-@@ -104,6 +104,7 @@ public class ArrayFuncsTest extends TestCase {
-     /**

-      * Test of genericClone method, of class nom.tam.util.ArrayFuncs.

-      */

-+    @Test

-     public void testGenericClone() {

-         System.out.println("genericClone");

- 

-@@ -126,6 +127,7 @@ public class ArrayFuncsTest extends TestCase {
-     /**

-      * Test of copyArray method, of class nom.tam.util.ArrayFuncs.

-      */

-+    @Test

-     public void testCopyArray() {

-         System.out.println("copyArray");

- 

-@@ -138,6 +140,7 @@ public class ArrayFuncsTest extends TestCase {
-     /**

-      * Test of getDimensions method, of class nom.tam.util.ArrayFuncs.

-      */

-+    @Test

-     public void testGetDimensions() {

-         System.out.println("getDimensions");

- 

-@@ -157,6 +160,7 @@ public class ArrayFuncsTest extends TestCase {
-     /**

-      * Test of getBaseArray method, of class nom.tam.util.ArrayFuncs.

-      */

-+    @Test

-     public void testGetBaseArray() {

- 

-         int[][][] test = new int[2][3][4];

-@@ -169,6 +173,7 @@ public class ArrayFuncsTest extends TestCase {
-     /**

-      * Test of getBaseClass method, of class nom.tam.util.ArrayFuncs.

-      */

-+    @Test

-     public void testGetBaseClass() {

-         System.out.println("getBaseClass");

- 

-@@ -179,6 +184,7 @@ public class ArrayFuncsTest extends TestCase {
-     /**

-      * Test of getBaseLength method, of class nom.tam.util.ArrayFuncs.

-      */

-+    @Test

-     public void testGetBaseLength() {

- 

-         assertEquals(ArrayFuncs.getBaseLength(new int[2][3]), 4);

-@@ -195,6 +201,7 @@ public class ArrayFuncsTest extends TestCase {
-     /**

-      * Test of generateArray method, of class nom.tam.util.ArrayFuncs.

-      */

-+    @Test

-     public void testGenerateArray() {

-         System.out.println("generateArray");

- 

-@@ -213,6 +220,7 @@ public class ArrayFuncsTest extends TestCase {
-     /**

-      * Test of testPattern method, of class nom.tam.util.ArrayFuncs.

-      */

-+    @Test

-     public void testTestPattern() {

-         System.out.println("testPattern");

- 

-@@ -229,6 +237,7 @@ public class ArrayFuncsTest extends TestCase {
-     /**

-      * Test of flatten method, of class nom.tam.util.ArrayFuncs.

-      */

-+    @Test

-     public void testFlatten() {

-         System.out.println("flatten");

- 

-@@ -241,6 +250,7 @@ public class ArrayFuncsTest extends TestCase {
-     /**

-      * Test of curl method, of class nom.tam.util.ArrayFuncs.

-      */

-+    @Test

-     public void testCurl() {

-         System.out.println("curl");

- 

-@@ -259,6 +269,7 @@ public class ArrayFuncsTest extends TestCase {
-     /**

-      * Test of mimicArray method, of class nom.tam.util.ArrayFuncs.

-      */

-+    @Test

-     public void testMimicArray() {

-         System.out.println("mimicArray");

- 

-@@ -273,6 +284,7 @@ public class ArrayFuncsTest extends TestCase {
-     /**

-      * Test of convertArray method, of class nom.tam.util.ArrayFuncs.

-      */

-+    @Test

-     public void testConvertArray() {

-         System.out.println("convertArray");

- 

-@@ -286,7 +298,7 @@ public class ArrayFuncsTest extends TestCase {
- 

-         newType = int.class;

-         int[][] ires = (int[][]) ArrayFuncs.convertArray(array, newType, true);

--        assertEquals(array, ires);

-+        assertSame(array, ires);

- 

-         ires = (int[][]) ArrayFuncs.convertArray(array, newType, false);

-         assertNotSame(array, ires);

-@@ -296,6 +308,7 @@ public class ArrayFuncsTest extends TestCase {
-     /**

-      * Test of copyInto method, of class nom.tam.util.ArrayFuncs.

-      */

-+    @Test

-     public void testCopyInto() {

-         System.out.println("copyInto");

- 

-@@ -304,13 +317,14 @@ public class ArrayFuncsTest extends TestCase {
- 

-         ArrayFuncs.copyInto(x, y);

- 

--        assertEquals((double) x[0][0], y[0][0]);

--        assertEquals((double) x[1][2], y[1][2]);

-+        assertEquals((double) x[0][0], y[0][0], 0.01);

-+        assertEquals((double) x[1][2], y[1][2], 0.01);

-     }

- 

-     /**

-      * Test of arrayEquals method, of class nom.tam.util.ArrayFuncs.

-      */

-+    @Test

-     public void testArrayEquals() {

-         System.out.println("arrayEquals");

- 

-@@ -331,6 +345,7 @@ public class ArrayFuncsTest extends TestCase {
-     /**

-      * Test of doubleArrayEquals method, of class nom.tam.util.ArrayFuncs.

-      */

-+    @Test

-     public void testDoubleArrayEquals() {

- 

-         double x[] = {1, 2, 3};

-@@ -349,6 +364,7 @@ public class ArrayFuncsTest extends TestCase {
-     /**

-      * Test of floatArrayEquals method, of class nom.tam.util.ArrayFuncs.

-      */

-+    @Test

-     public void testFloatArrayEquals() {

-         float x[] = {1f, 2f, 3f};

-         float y[] = {1f, 2f, 3f};

--- 
-1.7.3.1.104.gc752e
-
diff --git a/dev-java/fits/files/README.Gentoo b/dev-java/fits/files/README.Gentoo
deleted file mode 100644
index 62c238cdd..000000000
--- a/dev-java/fits/files/README.Gentoo
+++ /dev/null
@@ -1,44 +0,0 @@
-I have been unable to track down a source repository for fits, so this
-ebuild straps a build system onto source unpacked from a source JAR.
-Not the greatest solution, but it's the best I can come up with.  I've
-also had trouble figuring out who holds copyright and what the
-licensing terms are.  If you find more authoritative information, let
-me know!
-
-Authors (listed with the first release note to mention them):
-  Tom McGlynn <thomas.a.mcglynn@nasa.gov> [1,12]
-  Jens Knudstrup [2]
-  Alan Brighton [2]
-  R.J. Mathar [3]
-  Jorgo Bakker [3]
-  Laurent Michel [3]
-  R. Mathar [4]
-  Guillame Belanger [4]
-  A. Kovacs [5]
-  Javier Diaz [6]
-  Juan Carlos Segovia [7]
-  Thomas Granzer [7]
-  L. Michel [8]
-  Mark Taylor [9]
-  Laurent Bourges [10]
-  V. Forchi [11]
-
-From [11]:
-
-> [The] build procedure for FITS library has been changed. The library
-> is now stored as a NetBeans project and the standard NetBeans build
-> script has been modified to generate the fits.jar and fits_src.jar.
-
-
-[1]: http://heasarc.gsfc.nasa.gov/docs/heasarc/fits/java/v0.9/NOTES/NOTE.v091
-[2]: http://heasarc.gsfc.nasa.gov/docs/heasarc/fits/java/v0.9/NOTES/NOTE.v093
-[3]: http://heasarc.gsfc.nasa.gov/docs/heasarc/fits/java/v0.9/NOTES/NOTE.v099
-[4]: http://heasarc.gsfc.nasa.gov/docs/heasarc/fits/java/v0.9/NOTES/NOTE.v099.1
-[5]: http://heasarc.gsfc.nasa.gov/docs/heasarc/fits/java/v0.9/NOTES/NOTE.v099.5
-[6]: http://heasarc.gsfc.nasa.gov/docs/heasarc/fits/java/v1.0/NOTE.v100.1
-[7]: http://heasarc.gsfc.nasa.gov/docs/heasarc/fits/java/v1.0/NOTE.v101.0
-[8]: http://heasarc.gsfc.nasa.gov/docs/heasarc/fits/java/v1.0/NOTE.v102.0
-[9]: http://heasarc.gsfc.nasa.gov/docs/heasarc/fits/java/v1.0/NOTE.v104.0
-[10]: http://heasarc.gsfc.nasa.gov/docs/heasarc/fits/java/v1.0/NOTE.v105.0
-[11]: http://heasarc.gsfc.nasa.gov/docs/heasarc/fits/java/v1.0/NOTE.v105.1
-[12]: http://asd.gsfc.nasa.gov/Thomas.McGlynn/
diff --git a/dev-java/fits/files/build.xml b/dev-java/fits/files/build.xml
deleted file mode 100644
index d8aa41b85..000000000
--- a/dev-java/fits/files/build.xml
+++ /dev/null
@@ -1,84 +0,0 @@
-<?xml version="1.0"?>
-<project name="fits" default="all" basedir=".">
-  <target name="init" description="Sets build properties">
-    <!-- package configuration -->
-    <property name="package.version" value="devel"/>
-    <!-- directory locations -->
-    <property name="src" value="${basedir}/src"/>
-    <property name="build" value="${basedir}/build"/>
-    <property name="doc" value="${basedir}/doc"/>
-    <property name="doc.api" value="${doc}/api"/>
-    <!-- external dependencies -->
-    <property name="junit.jar" value="junit.jar"/>
-    <!-- classpaths -->
-    <path id="project.class.path">
-    </path>
-    <path id="build.class.path">
-      <pathelement location="${junit.jar}"/>
-    </path>
-    <path id="test.class.path">
-      <pathelement location="${build}"/>
-    </path>
-  </target>
-  <target name="all" depends="jar,javadoc"
-          description="Pseudo-target that builds JAR and Javadoc">
-  </target>
-  <target name="build" depends="init"
-          description="Compiles the classes">
-    <mkdir dir="${build}"/>
-    <javac destdir="${build}" srcdir="${src}" debug="true"
-           deprecation="true" includeantruntime="false">
-      <classpath refid="project.class.path"/>
-      <classpath refid="build.class.path"/>
-      <!--compilerarg line="-Xlint:unchecked"/-->
-    </javac>
-    <copy todir="${build}">
-      <mappedresources>
-        <fileset dir="${src}" includes="**/test/test.fits*"/>
-        <globmapper from="*" to="*"/>
-      </mappedresources>
-    </copy>
-  </target>
-  <target name="test" depends="build">
-    <junit>
-      <classpath refid="project.class.path" />
-      <classpath refid="test.class.path"/>
-      <formatter type="brief" usefile="false" />
-      <batchtest>
-        <fileset dir="${build}">
-          <include name="**/test/*.class" />
-          <exclude name="**/*$*.class" />
-        </fileset>
-      </batchtest>
-    </junit>
-  </target>
-  <target name="javadoc" depends="init"
-          description="Generates Javadoc API documentation">
-    <mkdir dir="${doc.api}"/>
-    <javadoc packagenames="*"
-             sourcepath="${src}" destdir="${doc.api}"
-             author="true"       version="true"
-             use="true"          private="true">
-      <classpath refid="project.class.path" />
-      <classpath refid="build.class.path"/>
-    </javadoc>
-  </target>
-  <target name="jar" depends="build"
-          description="Builds a project JAR file">
-    <jar basedir="${build}" jarfile="${build}/fits.jar">
-      <manifest>
-        <attribute name="Version" value="${package.version}"/>
-      </manifest>
-    </jar>
-  </target>
-  <target name="clean" depends="init"
-          description="Erase all generated files and dirs">
-    <delete dir="${build}" verbose="true"/>
-    <delete dir="${doc}/api" verbose="true"/>
-    <delete verbose="true">
-        <fileset dir="${basedir}" includes="*.fits"/>
-        <fileset dir="${basedir}" includes="*.fil"/>
-        <fileset dir="${basedir}" includes="*.hdr"/>
-    </delete>
-  </target>
-</project>
diff --git a/dev-java/fits/fits-1.11.0-r1.ebuild b/dev-java/fits/fits-1.11.0-r1.ebuild
deleted file mode 100644
index 18daa2e84..000000000
--- a/dev-java/fits/fits-1.11.0-r1.ebuild
+++ /dev/null
@@ -1,68 +0,0 @@
-# Copyright 1999-2014 Gentoo Foundation
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=5
-
-JAVA_PKG_IUSE="doc source test"
-
-inherit java-pkg-2 java-ant-2
-
-DESCRIPTION="Java library for FITS input/output"
-HOMEPAGE="http://fits.gsfc.nasa.gov/fits_libraries.html#java_tam"
-SRC_URI="http://heasarc.gsfc.nasa.gov/docs/heasarc/${PN}/java/v1.0/v${PV}/${PN}_src.jar -> ${P}-src.jar"
-
-LICENSE="public-domain"
-SLOT="0"
-KEYWORDS="~amd64 ~x86 ~amd64-linux ~x86-linux"
-IUSE=""
-
-CDEPEND="dev-java/junit:4"
-RDEPEND="${CDEPEND}
-	>=virtual/jre-1.5"
-DEPEND="${CDEPEND}
-	>=virtual/jdk-1.5
-	test? ( dev-java/ant-junit4:0 )"
-
-EANT_EXTRA_ARGS="-Dpackage.version=${PV}"
-JAVA_ANT_REWRITE_CLASSPATH="true"
-EANT_GENTOO_CLASSPATH="junit-4"
-
-src_unpack() {
-	mkdir -p ${P}/src && cd ${P}/src || die
-	unpack ${A}
-}
-
-java_prepare() {
-	cd "${S}" || die
-	cp "${FILESDIR}"/README.Gentoo "${FILESDIR}"/build.xml . || die
-	epatch \
-		"${FILESDIR}"/01-Use-getResource-to-access-CompressTest-data-for-unit.patch \
-		"${FILESDIR}"/02-Update-ArrayFuncsTest.java-to-JUnit-4.patch
-
-	if ! use test; then
-		find "${S}" \( -name "*Test.java" -o -name "*Tester.java" \) -print -delete || die
-	fi
-
-	# from http://heasarc.gsfc.nasa.gov/docs/heasarc/fits/java/v1.0/NOTE.v111.0:
-	# The source code JAR (fits_src.jar) includes a number of new classes for
-	# which the corresponding class files are not included in fits.jar.  These
-	# classes are pre-alpha versions of support for tile compressed data that
-	# is being developed.  Interested Users may take a look at these, but they
-	# definitely are not expected to work today.
-	rm 	src/nom/tam/image/comp/Quantizer.java \
-		src/nom/tam/image/comp/RealStats.java \
-		src/nom/tam/image/comp/TiledImageHDU.java \
-		src/nom/tam/image/QuantizeRandoms.java \
-		src/nom/tam/image/TileDescriptor.java \
-		src/nom/tam/image/TileLooper.java || die
-}
-
-src_test() {
-	ANT_TASKS="ant-junit4" java-pkg-2_src_test
-}
-
-src_install() {
-	java-pkg_dojar build/${PN}.jar
-	use doc && java-pkg_dojavadoc doc/api
-	use source && java-pkg_dosrc src/*
-}
diff --git a/dev-java/fits/fits-1.15.1.ebuild b/dev-java/fits/fits-1.15.1.ebuild
new file mode 100644
index 000000000..59a0801df
--- /dev/null
+++ b/dev-java/fits/fits-1.15.1.ebuild
@@ -0,0 +1,27 @@
+# Copyright 1999-2020 Gentoo Authors
+# Distributed under the terms of the GNU General Public License v2
+
+EAPI=7
+
+inherit java-utils-2
+
+DESCRIPTION="Java library for FITS input/output"
+HOMEPAGE="http://fits.gsfc.nasa.gov/fits_libraries.html#java_tam"
+SRC_URI="http://heasarc.gsfc.nasa.gov/docs/heasarc/${PN}/java/v1.0/v${PV}/${PN}.jar -> ${P}.jar"
+
+LICENSE="public-domain"
+SLOT="0"
+KEYWORDS="~amd64 ~x86"
+
+RDEPEND=">=virtual/jre-1.5"
+
+S="${WORKDIR}"
+
+src_unpack() {
+	# nothing to do here
+	return
+}
+
+src_install() {
+	java-pkg_newjar "${DISTDIR}/${P}.jar" "${PN}.jar"
+}
diff --git a/dev-java/flexdock/Manifest b/dev-java/flexdock/Manifest
deleted file mode 100644
index f5705a1d3..000000000
--- a/dev-java/flexdock/Manifest
+++ /dev/null
@@ -1,2 +0,0 @@
-DIST flexdock-1.1.1-src.zip 6163036 BLAKE2B 3f59d17916913fd0f692a9ef63d9b0154ad338dfee0d112e0f57fec8c32b4ce6cbf98ef1a9be8491b0a5401027c24ef4daa7a84ef3b6656f63c8ee7087fd9fa1 SHA512 104398a573b2aade0ed6b848920f8a3903964feabd755c653d8e62ea986251d9c31a07e88308c9cffe7e696c99109a3dfca249f0ca0357e88a896fc5769170f4
-DIST flexdock-1.2.4.tar.gz 5977054 BLAKE2B f0057d4a09fa994297c437c8ecd3e0f96c922bec5f95b142f19279e154fd352628a342a8dce9dcaab4b5997665b10fc98c8daf59c766a7b83cd7adda50f2b00c SHA512 f20c92d33b0567ed1e779d4c7c843ac9d72e5ae0f0a145d69adf5066bd1dcc426cd8acfe7d0587bd36fc09cab63dd7217f27cd8eee1d5d9b522bec860df9b44f
diff --git a/dev-java/flexdock/files/flexdock-1.1.1-nodemo.patch b/dev-java/flexdock/files/flexdock-1.1.1-nodemo.patch
deleted file mode 100644
index 415301d20..000000000
--- a/dev-java/flexdock/files/flexdock-1.1.1-nodemo.patch
+++ /dev/null
@@ -1,12 +0,0 @@
-diff -urN flexdock-orig/build.xml flexdock/build.xml
---- flexdock-orig/build.xml	2011-12-09 11:11:26.000000000 -0500
-+++ flexdock/build.xml	2011-12-20 18:47:57.277051174 -0500
-@@ -145,8 +145,6 @@
-          <src path="${java.src.drag}"/>
-          <src path="${java.src.perspective}"/>
-       </javac>
--      <javac classpathref="javac.classpath.demo" srcdir="${java.src.demo}" destdir="${bin.dir.demo}" debug="true" source="1.5" target="1.5" includeAntRuntime="no"/>
--      <javac classpathref="javac.classpath.test" srcdir="${java.src.test}" destdir="${bin.dir.test}" debug="true" source="1.5" target="1.5"  includeAntRuntime="no"/>
-    </target>
- 
- 
diff --git a/dev-java/flexdock/files/flexdock-1.2.4-nodemo.patch b/dev-java/flexdock/files/flexdock-1.2.4-nodemo.patch
deleted file mode 100644
index 415301d20..000000000
--- a/dev-java/flexdock/files/flexdock-1.2.4-nodemo.patch
+++ /dev/null
@@ -1,12 +0,0 @@
-diff -urN flexdock-orig/build.xml flexdock/build.xml
---- flexdock-orig/build.xml	2011-12-09 11:11:26.000000000 -0500
-+++ flexdock/build.xml	2011-12-20 18:47:57.277051174 -0500
-@@ -145,8 +145,6 @@
-          <src path="${java.src.drag}"/>
-          <src path="${java.src.perspective}"/>
-       </javac>
--      <javac classpathref="javac.classpath.demo" srcdir="${java.src.demo}" destdir="${bin.dir.demo}" debug="true" source="1.5" target="1.5" includeAntRuntime="no"/>
--      <javac classpathref="javac.classpath.test" srcdir="${java.src.test}" destdir="${bin.dir.test}" debug="true" source="1.5" target="1.5"  includeAntRuntime="no"/>
-    </target>
- 
- 
diff --git a/dev-java/flexdock/flexdock-1.1.1.ebuild b/dev-java/flexdock/flexdock-1.1.1.ebuild
deleted file mode 100644
index 7b1e9f0b0..000000000
--- a/dev-java/flexdock/flexdock-1.1.1.ebuild
+++ /dev/null
@@ -1,48 +0,0 @@
-# Copyright 1999-2014 Gentoo Foundation
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=5
-
-JAVA_PKG_IUSE="doc source"
-
-inherit eutils java-pkg-2 java-ant-2
-
-DESCRIPTION="A Java docking framework for use in cross-platform Swing applications"
-HOMEPAGE="http://flexdock.dev.java.net/"
-SRC_URI="http://forge.scilab.org/index.php/p/flexdock/downloads/get/${P}-src.zip"
-
-LICENSE="MIT"
-SLOT="0"
-KEYWORDS="~amd64 ~x86"
-IUSE=""
-
-RDEPEND=">=virtual/jre-1.4"
-DEPEND="
-	app-arch/unzip
-	dev-java/skinlf
-	dev-java/jgoodies-looks:2.0
-	>=virtual/jdk-1.4"
-
-EANT_DOC_TARGET="doc"
-
-S="${WORKDIR}"
-
-java_prepare() {
-	epatch "${FILESDIR}"/${P}-nodemo.patch
-
-	#some cleanups
-	find . -name '*.so' -exec rm -v {} \;|| die
-	find . -name '*.dll' -exec rm -v {} \;|| die
-
-	#remove built-in jars and use the system ones
-	cd lib || die
-	rm -rvf *.jar jmf|| die
-	java-pkg_jar-from skinlf
-	java-pkg_jar-from jgoodies-looks-2.0 looks.jar
-}
-
-src_install() {
-	java-pkg_newjar "build/${P}.jar" "${PN}.jar"
-	use doc && java-pkg_dojavadoc build/docs/api
-	use source && java-pkg_dosrc src
-}
diff --git a/dev-java/flexdock/flexdock-1.2.4.ebuild b/dev-java/flexdock/flexdock-1.2.4.ebuild
deleted file mode 100644
index 6eae0b579..000000000
--- a/dev-java/flexdock/flexdock-1.2.4.ebuild
+++ /dev/null
@@ -1,44 +0,0 @@
-# Copyright 1999-2014 Gentoo Foundation
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=5
-JAVA_PKG_IUSE="doc source"
-
-inherit java-pkg-2 java-ant-2
-
-DESCRIPTION="A Java docking framework for use in cross-platform Swing applications"
-HOMEPAGE="http://flexdock.dev.java.net/"
-SRC_URI="http://forge.scilab.org/index.php/p/flexdock/downloads/get/${P}.tar.gz"
-
-LICENSE="MIT"
-SLOT="0"
-KEYWORDS="~amd64 ~x86"
-
-IUSE=""
-
-RDEPEND=">=virtual/jre-1.5"
-DEPEND=">=virtual/jdk-1.5
-	app-arch/unzip
-	dev-java/skinlf"
-
-EANT_BUILD_TARGET="jar"
-EANT_DOC_TARGET="doc"
-
-java_prepare() {
-	epatch "${FILESDIR}"/${P}-nodemo.patch
-
-	#some cleanups
-	find . -name '*.so' -exec rm -v {} \;|| die
-	find . -name '*.dll' -exec rm -v {} \;|| die
-
-	#remove built-in jars and use the system ones
-	cd lib || die
-	rm -rvf *.jar jmf|| die
-	java-pkg_jar-from skinlf
-}
-
-src_install() {
-	java-pkg_newjar "build/${P}.jar" "${PN}.jar"
-	use doc && java-pkg_dojavadoc build/docs/api
-	use source && java-pkg_dosrc src
-}
diff --git a/dev-java/flexdock/metadata.xml b/dev-java/flexdock/metadata.xml
deleted file mode 100644
index 11085ca1f..000000000
--- a/dev-java/flexdock/metadata.xml
+++ /dev/null
@@ -1,11 +0,0 @@
-<?xml version="1.0" encoding="UTF-8"?>
-<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
-<pkgmetadata>
-	<maintainer type="project">
-		<email>sci@gentoo.org</email>
-		<name>Gentoo Science Project</name>
-	</maintainer>
-	<longdescription lang="en">
-Java docking framework for use in cross-platform Swing applications.
-</longdescription>
-</pkgmetadata>
diff --git a/dev-java/gluegen/Manifest b/dev-java/gluegen/Manifest
deleted file mode 100644
index c5f36706c..000000000
--- a/dev-java/gluegen/Manifest
+++ /dev/null
@@ -1,4 +0,0 @@
-DIST gluegen-2.1.4.tar.gz 42235490 BLAKE2B 31e5a55c9cc983d0e1c7f53988b7cc0779e01d1c4c0df8a33ca817acd51d0d28e453e6a84e1be65ecfb62883e8900c62a2219f78035dc7a68c26412e7c2b5135 SHA512 196478de92686b168d6f35e2e7141a31f682d22a7f96b5bc84d46905c42eb5bf25bacd74ccc51975fc7894e2e0ba2e236a4a68c101bbabaaa5193e4bdc50f607
-DIST gluegen-2.2.4.tar.gz 43113191 BLAKE2B 8908cff19b4eeaac01eb91ecf51005433c60acbf35a2922e09f7bfe3d11dee46296b466ea22cf570cae5a1013ea6dd9b375fbaa5b0723509d0bad0926014b9fb SHA512 53e973ca8478f4513f9662d1375406af95f2181dae3fb3e3247e4752960e60e741f7eae36981967dba10ac7bc3dc0e85c159c193323c177ce733a9eb0540b98b
-DIST gluegen-20080421.tar.bz2 1044951 SHA256 15ef8f499afc2256615bf453b318fbc22fbe146293ca4c6ca87c98577bf5a026 SHA512 3bffb55ec8723ac452b38d41f1bc596ee3065b1f791b8c7aec06d8acffdfd83d81553d9090fc273b56fa748b501f3a25f8dc4736bad291bc77f15d211957470d WHIRLPOOL 6171345011955517e84c9b82d187e2fe0c96fc1733ee6427248159fd8456472ea15c9cd223bd784a33478a4cfc568ddcfd73ea0addd13daa1b483b7a8cfe66c1
-DIST gluegen-v2.0-rc8.tar.7z 35196696 BLAKE2B 348f331962007d80976287bfa7cfea53c82fc28b2339835aec01045a767bab77886ef36470c6f0870cead7aea6c8b2aceb000541505d4035a002302f1bc9cbb8 SHA512 9845246f9776139cd205f197203349eba28150d5018bd086e6f7484df765b4cd122d78fbf836780a10b0d6395c645eb8ec7a256b8f832453c0b20155a11b3a0f
diff --git a/dev-java/gluegen/files/2.1.4-dont-copy-jars.patch b/dev-java/gluegen/files/2.1.4-dont-copy-jars.patch
deleted file mode 100644
index dca10dce8..000000000
--- a/dev-java/gluegen/files/2.1.4-dont-copy-jars.patch
+++ /dev/null
@@ -1,17 +0,0 @@
-diff --git a/gluegen-2.1.4_rc01/make/build.xml b/gluegen-2.1.4_rc01/make/build.xml
-index 55ef270..bce6d12 100644
---- a/gluegen-2.1.4_rc01/make/build.xml
-+++ b/gluegen-2.1.4_rc01/make/build.xml
-@@ -806,12 +806,6 @@
-       </fileset>
-     </jar>
- 
--    <!-- Copy antlr.jar into build directory for convenience so
--         gluegen.jar can be run via "java -jar". antlr.jar is
--         referenced via a Class-Path entry in the Manifest of
--         gluegen.jar. -->
--    <copy file="${antlr.jar}" todir="${build}" />
--    
-     <!-- copy a jnlp with empty codebase into build folder for local testing 
-          overwrite property in gluegen.proerpties if desired             -->
-     <property name="gluegen.jnlp.codebase" value=""/>
diff --git a/dev-java/gluegen/files/2.1.4-dont-strip.patch b/dev-java/gluegen/files/2.1.4-dont-strip.patch
deleted file mode 100644
index 02020d2ae..000000000
--- a/dev-java/gluegen/files/2.1.4-dont-strip.patch
+++ /dev/null
@@ -1,22 +0,0 @@
-diff --git a/gluegen-2.1.4_rc01/make/gluegen-cpptasks-base.xml b/gluegen-2.1.4_rc01/make/gluegen-cpptasks-base.xml
-index 8b8b82e..ec39aeb 100755
---- a/gluegen-2.1.4_rc01/make/gluegen-cpptasks-base.xml
-+++ b/gluegen-2.1.4_rc01/make/gluegen-cpptasks-base.xml
-@@ -1511,17 +1511,6 @@
-        - Helper strip.libraries for stripping off debug information
-       -->
-     <target name="gluegen.cpptasks.striplibs" depends="gluegen.cpptasks.initialize" if="c.strip.libraries">
--      <echo message="Strip symbols from libs in ${libdir}" />
--      <apply dir="${libdir}" executable="${c.strip.tool}" parallel="false" 
--             failonerror="true">
--        <arg line="${c.strip.args}"/>
--        <fileset dir="${libdir}">
--          <include name="**/*.so"/>     <!-- unix    -->
--          <include name="**/*.dll"/>    <!-- windows -->
--          <include name="**/*.dylib"/>  <!-- macosx  -->
--          <include name="**/*.jnilib"/> <!-- macosx  -->
--        </fileset>
--      </apply>
-     </target>
- 
-     <!-- ================================================================== -->
diff --git a/dev-java/gluegen/files/2.1.4-dont-test-archive.patch b/dev-java/gluegen/files/2.1.4-dont-test-archive.patch
deleted file mode 100644
index 3eb061f27..000000000
--- a/dev-java/gluegen/files/2.1.4-dont-test-archive.patch
+++ /dev/null
@@ -1,16 +0,0 @@
-diff --git a/gluegen-2.1.4_rc01/make/build-test.xml b/gluegen-2.1.4_rc01/make/build-test.xml
-index 31dc773..e872a0a 100644
---- a/gluegen-2.1.4_rc01/make/build-test.xml
-+++ b/gluegen-2.1.4_rc01/make/build-test.xml
-@@ -614,9 +614,11 @@ chmod 644 ${results}/* \${line.separator}
- 
-     <!-- updates / create the test results zip file -->
-     <target name="test-zip-archive" depends="init">
-+    	<!--
-         <archive.7z destfile="${build}/${test.archive.name}.7z"
-                     basedir="${project.root}" 
-                     includes="${rootrel.build}/test/results ${rootrel.build}/test/results-x64 ${rootrel.build}/test/results-x32" />
-+        -->
-     </target>
- 
- 
diff --git a/dev-java/gluegen/files/2.2.4-dont-copy-jars.patch b/dev-java/gluegen/files/2.2.4-dont-copy-jars.patch
deleted file mode 100644
index dca10dce8..000000000
--- a/dev-java/gluegen/files/2.2.4-dont-copy-jars.patch
+++ /dev/null
@@ -1,17 +0,0 @@
-diff --git a/gluegen-2.1.4_rc01/make/build.xml b/gluegen-2.1.4_rc01/make/build.xml
-index 55ef270..bce6d12 100644
---- a/gluegen-2.1.4_rc01/make/build.xml
-+++ b/gluegen-2.1.4_rc01/make/build.xml
-@@ -806,12 +806,6 @@
-       </fileset>
-     </jar>
- 
--    <!-- Copy antlr.jar into build directory for convenience so
--         gluegen.jar can be run via "java -jar". antlr.jar is
--         referenced via a Class-Path entry in the Manifest of
--         gluegen.jar. -->
--    <copy file="${antlr.jar}" todir="${build}" />
--    
-     <!-- copy a jnlp with empty codebase into build folder for local testing 
-          overwrite property in gluegen.proerpties if desired             -->
-     <property name="gluegen.jnlp.codebase" value=""/>
diff --git a/dev-java/gluegen/files/2.2.4-dont-strip.patch b/dev-java/gluegen/files/2.2.4-dont-strip.patch
deleted file mode 100644
index 02020d2ae..000000000
--- a/dev-java/gluegen/files/2.2.4-dont-strip.patch
+++ /dev/null
@@ -1,22 +0,0 @@
-diff --git a/gluegen-2.1.4_rc01/make/gluegen-cpptasks-base.xml b/gluegen-2.1.4_rc01/make/gluegen-cpptasks-base.xml
-index 8b8b82e..ec39aeb 100755
---- a/gluegen-2.1.4_rc01/make/gluegen-cpptasks-base.xml
-+++ b/gluegen-2.1.4_rc01/make/gluegen-cpptasks-base.xml
-@@ -1511,17 +1511,6 @@
-        - Helper strip.libraries for stripping off debug information
-       -->
-     <target name="gluegen.cpptasks.striplibs" depends="gluegen.cpptasks.initialize" if="c.strip.libraries">
--      <echo message="Strip symbols from libs in ${libdir}" />
--      <apply dir="${libdir}" executable="${c.strip.tool}" parallel="false" 
--             failonerror="true">
--        <arg line="${c.strip.args}"/>
--        <fileset dir="${libdir}">
--          <include name="**/*.so"/>     <!-- unix    -->
--          <include name="**/*.dll"/>    <!-- windows -->
--          <include name="**/*.dylib"/>  <!-- macosx  -->
--          <include name="**/*.jnilib"/> <!-- macosx  -->
--        </fileset>
--      </apply>
-     </target>
- 
-     <!-- ================================================================== -->
diff --git a/dev-java/gluegen/files/2.2.4-dont-test-archive.patch b/dev-java/gluegen/files/2.2.4-dont-test-archive.patch
deleted file mode 100644
index 3eb061f27..000000000
--- a/dev-java/gluegen/files/2.2.4-dont-test-archive.patch
+++ /dev/null
@@ -1,16 +0,0 @@
-diff --git a/gluegen-2.1.4_rc01/make/build-test.xml b/gluegen-2.1.4_rc01/make/build-test.xml
-index 31dc773..e872a0a 100644
---- a/gluegen-2.1.4_rc01/make/build-test.xml
-+++ b/gluegen-2.1.4_rc01/make/build-test.xml
-@@ -614,9 +614,11 @@ chmod 644 ${results}/* \${line.separator}
- 
-     <!-- updates / create the test results zip file -->
-     <target name="test-zip-archive" depends="init">
-+    	<!--
-         <archive.7z destfile="${build}/${test.archive.name}.7z"
-                     basedir="${project.root}" 
-                     includes="${rootrel.build}/test/results ${rootrel.build}/test/results-x64 ${rootrel.build}/test/results-x32" />
-+        -->
-     </target>
- 
- 
diff --git a/dev-java/gluegen/gluegen-1_p20080421.ebuild b/dev-java/gluegen/gluegen-1_p20080421.ebuild
deleted file mode 100644
index d3f0aacbc..000000000
--- a/dev-java/gluegen/gluegen-1_p20080421.ebuild
+++ /dev/null
@@ -1,61 +0,0 @@
-# Copyright 1999-2014 Gentoo Foundation
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=5
-
-WANT_ANT_TASKS="ant-antlr"
-JAVA_PKG_IUSE=""
-
-inherit java-pkg-2 java-ant-2
-
-DESCRIPTION="Automatically generate the JNI code necessary to call C libraries"
-HOMEPAGE="http://jogamp.org/gluegen/www/"
-# svn export -r "{2009-05-09}" https://gluegen.dev.java.net/svn/gluegen/trunk
-# gluegen --username xxx --password xxx
-SRC_URI="http://dev.gentoo.org/~ali_bush/distfiles/${PN}-${PV#1_p}.tar.bz2"
-
-LICENSE="BSD"
-SLOT="0"
-KEYWORDS="~amd64 ~x86"
-IUSE=""
-
-RDEPEND="
-	>=virtual/jre-1.4
-	dev-java/antlr:0"
-
-DEPEND="
-	>=virtual/jdk-1.4
-	dev-java/ant-core:0
-	dev-java/antlr:0
-	dev-java/cpptasks:0"
-
-S="${WORKDIR}/${PN}-${PV#1_p}"
-
-java_prepare() {
-	rm make/lib/{cdc_fp,cpptasks}.jar
-	java-pkg_jar-from --build-only --into make/lib cpptasks
-	sed -i -e 's/suncc/sunc89/g' make/${PN}-cpptasks.xml || die
-	java-ant_rewrite-classpath "make/build.xml"
-	sed -i -e 's/\(<target name="generate.c[^"]*" \)/\1 depends="init"/g' \
-		make/build.xml || die
-}
-
-src_compile() {
-	cd make || dir "Unable to enter make directory"
-	local antflags="-Dantlr.jar=$(java-pkg_getjars antlr)"
-	local gcp="$(java-pkg_getjars --build-only ant-core):$(java-config --tools)"
-
-	ANT_TASKS="${WANT_ANT_TASKS}" eant ${antflags} -Dgentoo.classpath="${gcp}" all
-}
-src_install() {
-	cd build || dir "Unable to enter build directory"
-
-	#build copies system antlr.jar here.
-	#So we just need to replace it.
-	rm "${PN}-rt-natives"*.jar || die
-	java-pkg_dojar *.jar
-	java-pkg_doso obj/*.so
-
-	#If we are going to install the source
-	#use source && java-pkg_dosrc src
-}
diff --git a/dev-java/gluegen/gluegen-2.0_rc8.ebuild b/dev-java/gluegen/gluegen-2.0_rc8.ebuild
deleted file mode 100644
index 058e33c83..000000000
--- a/dev-java/gluegen/gluegen-2.0_rc8.ebuild
+++ /dev/null
@@ -1,81 +0,0 @@
-# Copyright 1999-2014 Gentoo Foundation
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=5
-
-JAVA_PKG_IUSE="doc source"
-
-inherit java-pkg-2 java-ant-2
-
-MY_PV=v${PV/_/-}
-MY_P=${PN}-${MY_PV}
-
-DESCRIPTION="Automatically generate the JNI code necessary to call C libraries"
-HOMEPAGE="http://jogamp.org/gluegen/www/"
-SRC_URI="http://jogamp.org/deployment/${MY_PV}/archive/Sources/${MY_P}.tar.7z"
-
-LICENSE="BSD"
-SLOT="2"
-KEYWORDS="~amd64 ~x86"
-IUSE=""
-
-COMMON_DEP="
-	dev-java/ant-core:0
-	dev-java/antlr:0"
-RDEPEND="${COMMON_DEP}
-	>=virtual/jre-1.5"
-DEPEND="${COMMON_DEP}
-	>=virtual/jdk-1.5
-	app-arch/p7zip
-	dev-java/ant-antlr:0
-	dev-java/ant-contrib:0
-	dev-java/ant-nodeps:0
-	dev-java/cpptasks:0
-	dev-java/junit:4"
-
-S=${WORKDIR}/${MY_P}
-
-src_unpack() {
-	default
-	unpack ./${MY_P}.tar
-}
-
-java_prepare() {
-	# preserve android.jar, FIXME can be built form source!
-	mv make/lib/android-sdk "${T}" || die
-	find -name '*.jar' -exec rm -v {} + || die
-	mv "${T}"/android-sdk make/lib/ || die
-}
-
-JAVA_ANT_REWRITE_CLASSPATH="yes"
-
-EANT_BUILD_XML="make/build.xml"
-EANT_BUILD_TARGET="all"
-EANT_DOC_TARGET=""
-EANT_GENTOO_CLASSPATH="antlr,ant-core"
-EANT_NEEDS_TOOLS="yes"
-EANT_ANT_TASKS="ant-antlr ant-contrib ant-nodeps cpptasks"
-src_compile() {
-	# FIXME don't copy around jars
-	EANT_EXTRA_ARGS+=" -Dantlr.jar=\"$(java-pkg_getjar --build-only antlr antlr.jar)\""
-	# FIXME don't build tests just yet
-	EANT_EXTRA_ARGS+=" -Djunit.jar=\"$(java-pkg_getjar --build-only junit-4 junit.jar)\""
-
-	java-pkg-2_src_compile
-}
-
-# FIXME src_test
-
-src_install() {
-	java-pkg_dojar build/${PN}{,-rt}.jar
-	java-pkg_doso build/obj/*.so
-
-	use doc && dohtml -r doc/manual
-	use source && java-pkg_dosrc src/java/*
-
-	# for building jogl
-	insinto /usr/share/${PN}-${SLOT}/make
-	doins -r make/*
-	insinto /usr/share/${PN}-${SLOT}/build
-	doins build/artifact.properties
-}
diff --git a/dev-java/gluegen/gluegen-2.1.4.ebuild b/dev-java/gluegen/gluegen-2.1.4.ebuild
deleted file mode 100644
index ee09ffbdc..000000000
--- a/dev-java/gluegen/gluegen-2.1.4.ebuild
+++ /dev/null
@@ -1,67 +0,0 @@
-# Copyright 1999-2014 Gentoo Foundation
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=5
-
-JAVA_PKG_IUSE="doc source test"
-WANT_ANT_TASKS="ant-antlr ant-contrib dev-java/cpptasks:0"
-
-inherit java-pkg-2 java-ant-2
-
-DESCRIPTION="Automatically generate the JNI code necessary to call C libraries"
-HOMEPAGE="http://jogamp.org/gluegen/www/"
-SRC_URI="https://github.com/sgothel/gluegen/archive/v${PV}.tar.gz -> ${P}.tar.gz"
-
-LICENSE="BSD"
-SLOT="2.1"
-KEYWORDS="~amd64 ~x86"
-IUSE=""
-
-COMMON_DEP="
-	dev-java/ant-core:0
-	dev-java/antlr:0"
-RDEPEND="${COMMON_DEP}
-	>=virtual/jre-1.5"
-
-DEPEND="${COMMON_DEP}
-	>=virtual/jdk-1.5
-	dev-java/cpptasks:0
-	test? (
-		dev-java/junit:4
-		dev-java/ant-junit4
-	)"
-
-JAVA_ANT_REWRITE_CLASSPATH="yes"
-EANT_BUILD_XML="make/build.xml"
-EANT_BUILD_TARGET="all.no_junit"
-EANT_DOC_TARGET=""
-EANT_GENTOO_CLASSPATH="antlr,ant-core"
-EANT_NEEDS_TOOLS="yes"
-EANT_TEST_TARGET="junit.run"
-EANT_TEST_GENTOO_CLASSPATH="${EANT_GENTOO_CLASSPATH},junit-4"
-EANT_GENTOO_CLASSPATH_EXTRA="${S}/build/${PN}{,-rt}.jar"
-EANT_EXTRA_ARGS="-Dc.strip.libraries=false"
-
-java_prepare() {
-	rm -rf make/lib
-	epatch "${FILESDIR}"/${PV}-*.patch
-	java-ant_bsfix_files "${S}/make/build-test.xml"
-}
-
-src_test() {
-	EANT_TASKS="ant-junit4" java-pkg-2_src_test
-}
-
-src_install() {
-	java-pkg_dojar build/${PN}{,-rt}.jar
-	java-pkg_doso build/obj/*.so
-
-	use doc && dohtml -r doc/manual
-	use source && java-pkg_dosrc src/java/*
-
-	# for building jogl
-	insinto /usr/share/${PN}-${SLOT}/make
-	doins -r make/*
-	insinto /usr/share/${PN}-${SLOT}/build
-	doins build/artifact.properties
-}
diff --git a/dev-java/gluegen/gluegen-2.2.4.ebuild b/dev-java/gluegen/gluegen-2.2.4.ebuild
deleted file mode 100644
index 77874b6cc..000000000
--- a/dev-java/gluegen/gluegen-2.2.4.ebuild
+++ /dev/null
@@ -1,67 +0,0 @@
-# Copyright 1999-2015 Gentoo Foundation
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=5
-
-JAVA_PKG_IUSE="doc source test"
-WANT_ANT_TASKS="ant-antlr ant-contrib dev-java/cpptasks:0"
-
-inherit java-pkg-2 java-ant-2
-
-DESCRIPTION="Automatically generate the JNI code necessary to call C libraries"
-HOMEPAGE="http://jogamp.org/gluegen/www/"
-SRC_URI="https://github.com/sgothel/gluegen/archive/v${PV}.tar.gz -> ${P}.tar.gz"
-
-LICENSE="BSD"
-SLOT="2.2"
-KEYWORDS="~amd64 ~x86"
-IUSE=""
-
-COMMON_DEP="
-	dev-java/ant-core:0
-	dev-java/antlr:0"
-RDEPEND="${COMMON_DEP}
-	>=virtual/jre-1.5"
-
-DEPEND="${COMMON_DEP}
-	>=virtual/jdk-1.5
-	dev-java/cpptasks:0
-	test? (
-		dev-java/junit:4
-		dev-java/ant-junit4
-	)"
-
-JAVA_ANT_REWRITE_CLASSPATH="yes"
-EANT_BUILD_XML="make/build.xml"
-EANT_BUILD_TARGET="all.no_junit"
-EANT_DOC_TARGET=""
-EANT_GENTOO_CLASSPATH="antlr,ant-core"
-EANT_NEEDS_TOOLS="yes"
-EANT_TEST_TARGET="junit.run"
-EANT_TEST_GENTOO_CLASSPATH="${EANT_GENTOO_CLASSPATH},junit-4"
-EANT_GENTOO_CLASSPATH_EXTRA="${S}/build/${PN}{,-rt}.jar"
-EANT_EXTRA_ARGS="-Dc.strip.libraries=false"
-
-java_prepare() {
-	rm -rf make/lib
-	epatch "${FILESDIR}"/${PV}-*.patch
-	java-ant_bsfix_files "${S}/make/build-test.xml"
-}
-
-src_test() {
-	EANT_TASKS="ant-junit4" java-pkg-2_src_test
-}
-
-src_install() {
-	java-pkg_dojar build/${PN}{,-rt}.jar
-	java-pkg_doso build/obj/*.so
-
-	use doc && dohtml -r doc/manual
-	use source && java-pkg_dosrc src/java/*
-
-	# for building jogl
-	insinto /usr/share/${PN}-${SLOT}/make
-	doins -r make/*
-	insinto /usr/share/${PN}-${SLOT}/build
-	doins build/artifact.properties
-}
diff --git a/dev-java/gluegen/metadata.xml b/dev-java/gluegen/metadata.xml
deleted file mode 100644
index b81144d5f..000000000
--- a/dev-java/gluegen/metadata.xml
+++ /dev/null
@@ -1,22 +0,0 @@
-<?xml version="1.0" encoding="UTF-8"?>
-<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
-<pkgmetadata>
-	<maintainer type="project">
-		<email>sci@gentoo.org</email>
-		<name>Gentoo Science Project</name>
-	</maintainer>
-	<longdescription lang="en">
-GlueGen is a tool which automatically generates the Java and JNI code necessary
-to call C libraries. It reads as input ANSI C header files and separate
-configuration files which provide control over many aspects of the glue code
-generation. GlueGen uses a complete ANSI C parser and an internal representation
-(IR) capable of representing all C types to represent the APIs for which it
-generates interfaces. It has the ability to perform significant transformations
-on the IR before glue code emission. GlueGen is currently powerful enough to
-bind even low-level APIs such as the Java Native Interface (JNI) and the AWT
-Native Interface (JAWT) back up to the Java programming language.
-</longdescription>
-	<upstream>
-		<remote-id type="github">sgothel/gluegen</remote-id>
-	</upstream>
-</pkgmetadata>
diff --git a/dev-java/hdf-java/Manifest b/dev-java/hdf-java/Manifest
deleted file mode 100644
index ad21ec356..000000000
--- a/dev-java/hdf-java/Manifest
+++ /dev/null
@@ -1 +0,0 @@
-DIST hdf-java-2.9-src.tar 14161920 BLAKE2B 54248013936dcb15c62e37b07060e6e8cd9fa11c4137d23bba211c3f93946f45c844ff4c455a11b656fb48b3514fb7a175c04e5a89283f6c6a87b4a04c178a60 SHA512 6ff9baa2264873411b05f8b6c190d9b72a25deb1e20c4b8633ba192bcf8700e03977e1ef9839e178a3856f3483468bdde432b753e8298e7e09c3a3b669b4c207
diff --git a/dev-java/hdf-java/files/hdf-java-2.9-shared.patch b/dev-java/hdf-java/files/hdf-java-2.9-shared.patch
deleted file mode 100644
index c0894807b..000000000
--- a/dev-java/hdf-java/files/hdf-java-2.9-shared.patch
+++ /dev/null
@@ -1,118 +0,0 @@
---- hdf-java/configure.in.orig	2012-11-13 03:12:03.000000000 +0400
-+++ hdf-java/configure.in	2012-11-25 21:12:40.074363619 +0400
-@@ -177,7 +177,7 @@
-   *)
-     if test -n "$withval" ; then
-         z_lib="`echo $withval |cut -f2 -d, -s`"
--  ZLIB=$z_lib"/libz."$LLEXT
-+  ZLIB="-L$z_lib -lz"
-   HAVE_ZLIB="yes"
-     else
-       ZLIB=""
-@@ -211,7 +211,7 @@
-   *)
-     if test -n "$withval" ; then
-         jpeg_lib="`echo $withval |cut -f2 -d, -s`"
--  JPEGLIB=$jpeg_lib"/libjpeg."$LLEXT
-+  JPEGLIB="-L$jpeg_lib -ljpeg"
-       dnl AC_MSG_RESULT([jpeg found: $JPEGLIB]);
-   HAVE_JPEG="yes"
-     else
-@@ -246,7 +246,7 @@
-   *)
-   if test -n "$withval" ; then
-       sz_lib="`echo $withval |cut -f2 -d, -s`"
--    SZLIB=$sz_lib"/libsz."$LLEXT
-+    SZLIB="-L$sz_lib -lsz"
-     dnl AC_MSG_RESULT([szlib found: $SZLIB]);
-     HAVE_SZIP="yes"
-   else
-@@ -302,7 +302,7 @@
-   ;;
- esac
- if test -n "$HDF4LIB"; then
--  LIBS="$HDF4LIB/libdf.$LLEXT $HDF4LIB/libmfhdf.$LLEXT $LIBS"
-+  LIBS="-L$HDF4LIB -ldf -lmfhdf $LIBS"
-   HAVE_HDF4="yes"
- fi
- AC_MSG_RESULT([$HAVE_HDF4])
-@@ -363,7 +363,7 @@
-   *)
-   if test -n "$withval" ; then
-       hdf5_lib="`echo $withval |cut -f2 -d, -s`"
--    HDF5LIB=$hdf5_lib"/libhdf.$LLEXT"
-+    HDF5LIB="-L$hdf5_lib -lhdf"
-       hdf5_inc="`echo $withval |cut -f1 -d,`"
-       if test -n "$hdf5_inc"; then
-         HDF5INC="$hdf5_inc"
-@@ -380,7 +380,7 @@
-   ;;
- esac
- if test -n "$HDF5LIB"; then
--  LIBS="$HDF5LIB/libhdf5.$LLEXT $LIBS"
-+  LIBS="-L$HDF5LIB -lhdf5 $LIBS"
-   HAVE_HDF5="yes"
- fi
- AC_MSG_RESULT([$HAVE_HDF5])
-@@ -637,10 +637,6 @@
-   if test \( ! -d "$JH45INST" \); then
-     JH45INST_FOUND=0
-   fi
--  if test \( ! -w "$JH45INST" \); then
--    AC_MSG_ERROR( [ $JH45INST : not writable ])
--    JH45INST_FOUND=0
--  fi
- fi
- until test $JH45INST_FOUND -eq 1; do
-   echo "Please type the directory in which to install the JH45"
-@@ -649,10 +645,6 @@
-   if test \( ! -d "$JH45INST" \); then
-     JH45INST_FOUND=0
-   fi
--  if test \( ! -w "$JH45INST" \); then
--    AC_MSG_ERROR( [ $JH45INST : not writable ])
--    JH45INST_FOUND=0
--  fi
- done
- 
- ac_cv_lib_JH45INST=$JH45INST
---- a/native/hdf5lib/Makefile.in
-+++ b/native/hdf5lib/Makefile.in
-@@ -35,7 +35,7 @@
- 
- CFLAGS = -D_FILE_OFFSET_BITS=64 $(DEFS) -I. -I$(HDF5INC) -I$(JAVAINC1) -I$(JAVAINC2)
- 
--LIBS =  $(HDF5LIB)/libhdf5.$(LLEXT) $(ZLIB) $(SZLIB) -lm
-+LIBS =  -L$(HDF5LIB) -lhdf5 $(ZLIB) $(SZLIB) -lm
- 
- # Macro def: object filename used
- OBJECTS =  exceptionImp.o h5Constants.o h5Imp.o h5aImp.o h5dImp.o h5eImp.o h5fImp.o h5gImp.o h5iImp.o h5lImp.o h5oImp.o h5pImp.o h5rImp.o h5sImp.o h5tImp.o nativeData.o h5util.o h5zImp.o
-@@ -47,7 +47,7 @@
- 
- libjhdf5: $(OBJECTS)
- 	-mkdir -p $(LIBDIR);
--	$(LD) $(LDOPT) -o $(LIBDIR)/libjhdf5.$(JSLEXT) $(LDOPT2) $(OBJECTS) $(LIBS)
-+	$(LD) $(LDOPT) $(LDFLAGS) -o $(LIBDIR)/libjhdf5.$(JSLEXT) $(LDOPT2) $(OBJECTS) $(LIBS)
- 
- clean:
- 	$(RM) -f *.o so_locations $(LIBDIR)/libjhdf5.$(JSLEXT)
---- a/native/hdflib/Makefile.in
-+++ b/native/hdflib/Makefile.in
-@@ -41,7 +41,7 @@
- CFLAGS = $(DEFS) -I. -I$(JAVAINC1) -I$(JAVAINC2) -I$(HDFINC)
- 
- # Be sure to add -lbsd if compiling in a SYSV environment
--LIBS =  $(HDFLIB)/libmfhdf.$(LLEXT) $(HDFLIB)/libdf.$(LLEXT) $(SZLIB) $(ZLIB) $(JPEGLIB) -lm
-+LIBS =  -L$(HDFLIB) -lmfhdf -ldf $(SZLIB) $(ZLIB) $(JPEGLIB) -lm
- 
- # Macro def: object filename used
- OBJECTS =  hdfstructsutil.o \
-@@ -60,7 +60,7 @@
- 
- libjhdf: $(OBJECTS) 
- 	-mkdir -p $(LIBDIR);
--	$(LD) $(LDOPT) -o $(LIBDIR)/libjhdf.$(JSLEXT) $(LDOPT2) $(OBJECTS) $(LIBS)
-+	$(LD) $(LDOPT) $(LDFLAGS) -o $(LIBDIR)/libjhdf.$(JSLEXT) $(LDOPT2) $(OBJECTS) $(LIBS)
- 
- clean:
- 	$(RM) -f *.o so_locations $(LIBDIR)/libjhdf.$(JSLEXT)
diff --git a/dev-java/hdf-java/files/hdfview.xml b/dev-java/hdf-java/files/hdfview.xml
deleted file mode 100644
index dd9ab396c..000000000
--- a/dev-java/hdf-java/files/hdfview.xml
+++ /dev/null
@@ -1,13 +0,0 @@
-<mime-info xmlns="http://www.freedesktop.org/standards/shared-mime-info">
-  <mime-type type="application/x-hdf">
-    <comment xml:lang="en">HDF files</comment>
-    <glob pattern="*.hdf"/>
-    <glob pattern="*.h4"/>
-    <glob pattern="*.hdf4"/>
-  </mime-type>
-  <mime-type type="application/x-hdf5">
-    <comment xml:lang="en">HDF5 files</comment>
-    <glob pattern="*.h5"/>
-    <glob pattern="*.hdf5"/>
-  </mime-type>
-</mime-info>
diff --git a/dev-java/hdf-java/hdf-java-2.9.ebuild b/dev-java/hdf-java/hdf-java-2.9.ebuild
deleted file mode 100644
index 248df280d..000000000
--- a/dev-java/hdf-java/hdf-java-2.9.ebuild
+++ /dev/null
@@ -1,130 +0,0 @@
-# Copyright 1999-2015 Gentoo Foundation
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=5
-
-JAVA_PKG_IUSE="doc examples"
-
-inherit autotools eutils fdo-mime java-pkg-2
-
-DESCRIPTION="Java interface to the HDF5 library"
-HOMEPAGE="http://www.hdfgroup.org/hdf-java-html/index.html"
-SRC_URI="https://www.hdfgroup.org/ftp/HDF5/releases/HDF-JAVA/${P}/src/${P}-src.tar"
-
-LICENSE="NCSA-HDF"
-SLOT="0"
-KEYWORDS="~amd64 ~x86"
-IUSE="hdf hdfview szip test zlib"
-
-CDEPEND="
-	>=sci-libs/hdf5-1.8[szip=,zlib=]
-	hdf? ( sci-libs/hdf virtual/jpeg:0 )
-	hdfview? ( dev-java/fits dev-java/netcdf )"
-
-RDEPEND="${CDEPEND}
-	>=virtual/jre-1.5"
-
-DEPEND="${CDEPEND}
-	>=virtual/jdk-1.5
-	test? ( >=dev-java/junit-4 )"
-
-REQUIRED_USE="hdfview? ( hdf )"
-
-# buggy test with incompatible hdf5 library versions
-RESTRICT="test"
-
-S="${WORKDIR}/${PN}"
-
-src_prepare() {
-	epatch "${FILESDIR}"/${P}-shared.patch
-	eautoreconf
-	rm lib/*.jar
-	if use hdfview; then
-		java-pkg_jar-from --into lib fits fits.jar
-		java-pkg_jar-from --into lib netcdf netcdf.jar
-	fi
-	use test && java-pkg_jar-from --into lib junit-4 junit.jar
-}
-
-src_configure() {
-	local stdpath="${EPREFIX}/usr/include,${EPREFIX}/usr/$(get_libdir)"
-	local myconf="--with-hdf4=no --with-libjpeg=no"
-	use hdf && \
-		myconf="--with-libjpeg=${stdpath} --with-hdf4=${stdpath}"
-	use zlib &&	myconf="${myconf} --with-libz=${stdpath}"
-	use szip && myconf="${myconf} --with-libsz=${stdpath}"
-
-	econf \
-		${myconf} \
-		--with-hdf5="${stdpath}" \
-		--with-jdk="$(java-config -o)/include,$(java-config -o)/jre/lib"
-}
-
-src_compile() {
-	# gentoo bug #302621
-	has_version sci-libs/hdf5[mpi] && export CXX=mpicxx CC=mpicc
-
-	# parallel needs work. anyone?
-	emake -j1 ncsa just-hdf5
-
-	if use hdf; then
-		sed -i \
-			-e "s/MAX_VAR_DIMS/H4_MAX_VAR_DIMS/" \
-			native/hdflib/hdfstructsutil.c || die
-		sed -i \
-			-e "s/MAX_NC_NAME/H4_MAX_NC_NAME/" \
-			native/hdflib/hdf{vdata,sds}Imp.c || die
-		emake -j1 just-hdf4
-	fi
-
-	use hdfview && emake -j1 packages
-	use examples && emake -j1 do-examples
-	use doc && emake -j1 javadocs
-}
-
-src_test() {
-	emake -j1 check
-}
-
-src_install() {
-	java-pkg_dojar lib/jhdf5.jar
-	java-pkg_doso lib/linux/libjhdf5.so
-
-	if use hdf; then
-		java-pkg_dojar lib/jhdf.jar
-		java-pkg_doso lib/linux/libjhdf.so
-	fi
-
-	if use hdfview; then
-		java-pkg_dojar lib/jhdf5obj.jar
-		java-pkg_dojar lib/jhdfobj.jar
-		java-pkg_dojar lib/ext/nc2obj.jar
-		java-pkg_dojar lib/ext/fitsobj.jar
-		java-pkg_dojar lib/jhdfview.jar
-		cat <<-EOF > hdfview
-			#!/bin/sh
-			export CLASSPATH=\$(java-config --classpath hdf-java)
-			\$(java-config --java) \
-				-Xmx1000m \
-				-Djava.library.path=\$(java-config --library hdf-java) \
-				ncsa.hdf.view.HDFView \
-				-root "${EROOT}" \$*
-		EOF
-		dobin hdfview
-		insinto /usr/share/mime/packages
-		doins "${FILESDIR}"/hdfview.xml
-		newicon ncsa/hdf/view/icons/hdf_large.gif hdfview.gif
-		make_desktop_entry hdfview "HDF Viewer" hdfview
-	fi
-
-	use doc && java-pkg_dojavadoc docs/javadocs
-	use examples && java-pkg_doexamples examples
-}
-
-pkg_postinst() {
-	use hdfview && fdo-mime_desktop_database_update
-}
-
-pkg_postrm() {
-	use hdfview && fdo-mime_desktop_database_update
-}
diff --git a/dev-java/hdf-java/metadata.xml b/dev-java/hdf-java/metadata.xml
deleted file mode 100644
index 2a2dedfa2..000000000
--- a/dev-java/hdf-java/metadata.xml
+++ /dev/null
@@ -1,20 +0,0 @@
-<?xml version="1.0" encoding="UTF-8"?>
-<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
-<pkgmetadata>
-	<maintainer type="project">
-		<email>sci@gentoo.org</email>
-		<name>Gentoo Science Project</name>
-	</maintainer>
-	<longdescription lang="en">
-HDF is a versatile data model that can represent very complex data
-objects and a wide variety of metadata. It is a completely portable
-file format with no limit on the number or size of data objects in
-the collection. 
-This Java package implements HDF4/HDF5 data objects in an object-oriented
-form. It provides a common Java API for accessing HDF files.
-</longdescription>
-	<use>
-		<flag name="hdf">Add support for the Hierarchical Data Format v.4 (<pkg>sci-libs/hdf</pkg>)</flag>
-		<flag name="hdfview">Build a GUI viewer for all files supported in <pkg>dev-java/hdf-java</pkg></flag>
-	</use>
-</pkgmetadata>
diff --git a/dev-java/htsjdk/Manifest b/dev-java/htsjdk/Manifest
deleted file mode 100644
index c6e15310d..000000000
--- a/dev-java/htsjdk/Manifest
+++ /dev/null
@@ -1,3 +0,0 @@
-DIST htsjdk-2.1.0.tar.gz 11134251 BLAKE2B 3578f1576fd1e52482f8f4068026cd10bfcd870da8cbfbfa5d6162b45ed10371a1162b8b42284c0d11deeca71342c68cd39d4bb33f35f638e22ca8861806bc3d SHA512 a13446fed6e0b8833012e26827d1ecdccbdb1e894f1a6c6b2d41359fb948834ac1cab364a1f5e7e51180b19979a27b34c3f51f326b30fd47c5c4fb71663fa0b9
-DIST htsjdk-2.2.2.tar.gz 11459641 BLAKE2B e7c34e3a9f2747c7668ae28da2f8c598b11dba6ef6b08daf9e43a710403ac578f0437e5f15f7f3e83ec0f13780471a5f3acd6f62a79880a86128b2f40b41bdd3 SHA512 69c4f6be9be16669fbbbcac2e668b564c09793763908b1c4703b760ea46fdbcf747d233f87c48888de3810379b02f2e0d8ebef4d1bf48215128e02cb4053bd10
-DIST htsjdk-2.5.1.tar.gz 9121664 SHA256 78ab25ba4c540805261faf6c7f2ae57755c26f654b93da6d41dc6ff21d59dc00 SHA512 6bc67deb28556664a018dd72a89f7c84f534262dc7f18072d4e1f4bdfc51298d8aeb7086a9d2764d92c44c69844577a9b9a005b00e13fc35f2bd240bde7a347f WHIRLPOOL e5da7f92e4be3271aa1387faaf6966b212a1fbe82d8dc3cea3115f75df9c8188323bb9402b8d34e58191e13b01411d6e529a78687d1f4b963cd239f4512ec88e
diff --git a/dev-java/htsjdk/htsjdk-2.1.0.ebuild b/dev-java/htsjdk/htsjdk-2.1.0.ebuild
deleted file mode 100644
index fc2dd6e8a..000000000
--- a/dev-java/htsjdk/htsjdk-2.1.0.ebuild
+++ /dev/null
@@ -1,47 +0,0 @@
-# Copyright 1999-2016 Gentoo Foundation
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=6
-
-JAVA_PKG_IUSE="doc source"
-
-inherit java-pkg-2 java-ant-2
-
-DESCRIPTION="Java API for high-throughput sequencing data (HTS) formats"
-HOMEPAGE="https://samtools.github.io/htsjdk/"
-SRC_URI="https://github.com/samtools/htsjdk/archive/${PV}.tar.gz -> ${P}.tar.gz"
-
-LICENSE="MIT"
-SLOT="0"
-IUSE=""
-KEYWORDS="~amd64 ~x86"
-
-CDEPEND="dev-java/commons-jexl:2
-	dev-java/commons-compress:0
-	dev-java/commons-logging:0"
-
-DEPEND=">=virtual/jdk-1.8
-	${CDEPEND}"
-RDEPEND=">=virtual/jre-1.8
-	${CDEPEND}"
-
-EANT_BUILD_TARGET="all"
-EANT_NEEDS_TOOLS="true"
-JAVA_ANT_REWRITE_CLASSPATH="true"
-EANT_GENTOO_CLASSPATH="commons-jexl-2,commons-compress,commons-logging"
-
-java_prepare() {
-	default
-	rm -v lib/{commons-compress,commons-jexl,commons-logging}*.jar || die
-}
-
-src_install() {
-	cd dist || die
-
-	for i in *.jar; do
-		java-pkg_newjar $i ${i/-[0-9]*.jar/.jar}
-	done
-
-	use source && java-pkg_dosrc "${S}"/src/java/*
-	use doc && java-pkg_dojavadoc "${S}"/javadoc
-}
diff --git a/dev-java/htsjdk/htsjdk-2.2.2.ebuild b/dev-java/htsjdk/htsjdk-2.2.2.ebuild
deleted file mode 100644
index fc2dd6e8a..000000000
--- a/dev-java/htsjdk/htsjdk-2.2.2.ebuild
+++ /dev/null
@@ -1,47 +0,0 @@
-# Copyright 1999-2016 Gentoo Foundation
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=6
-
-JAVA_PKG_IUSE="doc source"
-
-inherit java-pkg-2 java-ant-2
-
-DESCRIPTION="Java API for high-throughput sequencing data (HTS) formats"
-HOMEPAGE="https://samtools.github.io/htsjdk/"
-SRC_URI="https://github.com/samtools/htsjdk/archive/${PV}.tar.gz -> ${P}.tar.gz"
-
-LICENSE="MIT"
-SLOT="0"
-IUSE=""
-KEYWORDS="~amd64 ~x86"
-
-CDEPEND="dev-java/commons-jexl:2
-	dev-java/commons-compress:0
-	dev-java/commons-logging:0"
-
-DEPEND=">=virtual/jdk-1.8
-	${CDEPEND}"
-RDEPEND=">=virtual/jre-1.8
-	${CDEPEND}"
-
-EANT_BUILD_TARGET="all"
-EANT_NEEDS_TOOLS="true"
-JAVA_ANT_REWRITE_CLASSPATH="true"
-EANT_GENTOO_CLASSPATH="commons-jexl-2,commons-compress,commons-logging"
-
-java_prepare() {
-	default
-	rm -v lib/{commons-compress,commons-jexl,commons-logging}*.jar || die
-}
-
-src_install() {
-	cd dist || die
-
-	for i in *.jar; do
-		java-pkg_newjar $i ${i/-[0-9]*.jar/.jar}
-	done
-
-	use source && java-pkg_dosrc "${S}"/src/java/*
-	use doc && java-pkg_dojavadoc "${S}"/javadoc
-}
diff --git a/dev-java/htsjdk/htsjdk-2.5.1.ebuild b/dev-java/htsjdk/htsjdk-2.5.1.ebuild
deleted file mode 100644
index 755a6fa1f..000000000
--- a/dev-java/htsjdk/htsjdk-2.5.1.ebuild
+++ /dev/null
@@ -1,52 +0,0 @@
-# Copyright 1999-2017 Gentoo Foundation
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=6
-
-JAVA_PKG_IUSE="doc source"
-
-inherit java-pkg-2 java-ant-2
-
-DESCRIPTION="Java API for high-throughput sequencing data (HTS) formats"
-HOMEPAGE="https://samtools.github.io/htsjdk/"
-SRC_URI="https://github.com/samtools/htsjdk/archive/${PV}.tar.gz -> ${P}.tar.gz"
-
-LICENSE="MIT"
-SLOT="0"
-IUSE=""
-KEYWORDS=""
-
-CDEPEND="dev-java/commons-jexl:2
-	dev-java/commons-compress:0
-	dev-java/commons-logging:0"
-
-DEPEND=">=virtual/jdk-1.8
-	${CDEPEND}"
-RDEPEND=">=virtual/jre-1.8
-	${CDEPEND}"
-
-EANT_BUILD_TARGET="all"
-EANT_NEEDS_TOOLS="true"
-JAVA_ANT_REWRITE_CLASSPATH="true"
-EANT_GENTOO_CLASSPATH="commons-jexl-2,commons-compress,commons-logging"
-
-java_prepare(){
-	default
-}
-
-src_compile(){
-	# work around gradle writing $HOME/.gradle and $HOME/.git
-	# https://github.com/samtools/htsjdk/issues/660#issuecomment-232155965
-	GRADLE_USER_HOME="${WORKDIR}" ./gradlew build || die
-}
-
-src_install() {
-	cd dist || die
-
-	for i in *.jar; do
-		java-pkg_newjar $i ${i/-[0-9]*.jar/.jar}
-	done
-
-	use source && java-pkg_dosrc "${S}"/src/java/*
-	use doc && java-pkg_dojavadoc "${S}"/javadoc
-}
diff --git a/dev-java/htsjdk/htsjdk-9999.ebuild b/dev-java/htsjdk/htsjdk-9999.ebuild
deleted file mode 100644
index b4a3c1441..000000000
--- a/dev-java/htsjdk/htsjdk-9999.ebuild
+++ /dev/null
@@ -1,52 +0,0 @@
-# Copyright 1999-2017 Gentoo Foundation
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=6
-
-JAVA_PKG_IUSE="doc source"
-
-inherit git-r3 java-pkg-2 java-ant-2
-
-DESCRIPTION="Java API for high-throughput sequencing data (HTS) formats"
-HOMEPAGE="https://samtools.github.io/htsjdk/"
-EGIT_REPO_URI="https://github.com/samtools/htsjdk.git"
-
-LICENSE="MIT"
-SLOT="0"
-IUSE=""
-KEYWORDS=""
-
-CDEPEND="dev-java/commons-jexl:2
-	dev-java/commons-compress:0
-	dev-java/commons-logging:0"
-
-DEPEND=">=virtual/jdk-1.8
-	${CDEPEND}"
-RDEPEND=">=virtual/jre-1.8
-	${CDEPEND}"
-
-EANT_BUILD_TARGET="all"
-EANT_NEEDS_TOOLS="true"
-JAVA_ANT_REWRITE_CLASSPATH="true"
-EANT_GENTOO_CLASSPATH="commons-jexl-2,commons-compress,commons-logging"
-
-java_prepare(){
-	default
-}
-
-src_compile(){
-	# work around gradle writing $HOME/.gradle and $HOME/.git
-	# https://github.com/samtools/htsjdk/issues/660#issuecomment-232155965
-	GRADLE_USER_HOME="${WORKDIR}" ./gradlew || die
-}
-
-src_install() {
-	cd build/libs || die
-
-	#for i in *-SNAPSHOT.jar; do
-	#	java-pkg_newjar $i ${i/-[0-9]*.jar/.jar}
-	#done
-	java-pkg_newjar "${S}"/build/libs/*-SNAPSHOT.jar htsjdk.jar
-	use source && java-pkg_dosrc "${S}"/build/libs/*-sources.jar
-	use doc && java-pkg_dojavadoc "${S}"/build/libs/*-javadoc.jar
-}
diff --git a/dev-java/htsjdk/metadata.xml b/dev-java/htsjdk/metadata.xml
deleted file mode 100644
index e18a4898a..000000000
--- a/dev-java/htsjdk/metadata.xml
+++ /dev/null
@@ -1,15 +0,0 @@
-<?xml version="1.0" encoding="UTF-8"?>
-<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
-<pkgmetadata>
-	<maintainer type="person">
-		<email>ercpe@gentoo.org</email>
-		<name>Johann Schmitz (ercpe)</name>
-	</maintainer>
-	<maintainer type="project">
-		<email>sci-biology@gentoo.org</email>
-		<name>Gentoo Biology Project</name>
-	</maintainer>
-	<upstream>
-		<remote-id type="github">samtools/htsjdk</remote-id>
-	</upstream>
-</pkgmetadata>
diff --git a/dev-java/jama/Manifest b/dev-java/jama/Manifest
new file mode 100644
index 000000000..47e1c0f12
--- /dev/null
+++ b/dev-java/jama/Manifest
@@ -0,0 +1 @@
+DIST jama-1.0.3-sources.tar.gz 82188 BLAKE2B 35de815f770b192cd1b86a56ddf1919e12675d898ec4473489d3ce2c3899185f9d96eda39b6f7520fc67edfd17fe58b585f788f6a6967220150fc9a334b219ea SHA512 9bedf8f35ea1d400194b5a3b49914ebd04b5a31247959886f1967d062ceffae30993d34cd2f15d3942285a45c6930e2d4518f4ed0cc013ce853cc26aca021b0d
diff --git a/dev-java/jama/jama-1.0.3.ebuild b/dev-java/jama/jama-1.0.3.ebuild
new file mode 100644
index 000000000..9a88f35c4
--- /dev/null
+++ b/dev-java/jama/jama-1.0.3.ebuild
@@ -0,0 +1,32 @@
+# Copyright 1999-2023 Gentoo Authors
+# Distributed under the terms of the GNU General Public License v2
+
+EAPI=8
+
+MY_PN="Jama"
+
+JAVA_PKG_IUSE="doc source test"
+
+inherit java-pkg-2 java-pkg-simple
+
+DESCRIPTION="JAMA is a basic linear algebra package for Java. "
+HOMEPAGE="https://math.nist.gov/javanumerics/jama/"
+
+SRC_URI="https://math.nist.gov/javanumerics/jama/${MY_PN}-${PV}.tar.gz -> ${P}-sources.tar.gz"
+S="${WORKDIR}/${MY_PN}"
+KEYWORDS="~amd64"
+
+LICENSE="public-domain"
+SLOT="0"
+
+BDEPEND=">=virtual/jdk-1.8:*"
+
+RDEPEND=">=virtual/jre-1.8:*"
+
+JAVA_SRC_DIR=(
+	"./"
+	"util"
+)
+JAVA_MAIN_CLASS="gov.math.nist.Main"
+
+JAVA_TEST_SRC_DIR="test"
diff --git a/dev-java/jama/metadata.xml b/dev-java/jama/metadata.xml
new file mode 100644
index 000000000..f3dd4314e
--- /dev/null
+++ b/dev-java/jama/metadata.xml
@@ -0,0 +1,11 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
+<pkgmetadata>
+  <longdescription>
+    JAMA is a basic linear algebra package for Java. It provides user-level classes for constructing and manipulating real, dense matrices. It is meant to provide sufficient functionality for routine problems, packaged in a way that is natural and understandable to non-experts.    
+  </longdescription>
+  <maintainer type="project">
+    <email>sci@gentoo.org</email>
+    <name>Gentoo Science Project</name>
+  </maintainer>
+</pkgmetadata>
diff --git a/dev-java/jeuclid-core/Manifest b/dev-java/jeuclid-core/Manifest
deleted file mode 100644
index 5591eeba1..000000000
--- a/dev-java/jeuclid-core/Manifest
+++ /dev/null
@@ -1 +0,0 @@
-DIST jeuclid-parent-3.1.9-src.zip 8858746 BLAKE2B db3a7b9dc20e7cadd4b8bf6c4820a6e8895c9533bc5e3c55b1a6296c01ec3067d6a7782b0958c475fd0324e8d44587e4016e2af23a54e9a0acf47538a7ebd97c SHA512 ae55ffa469664abbf5545479d7968fd36e003ccc3f21687a43e79d843d6d3855b779ebeca3d38cc0c4a466c2de21bffce8e7d14cb2199f57e125b58ac100f203
diff --git a/dev-java/jeuclid-core/files/jeuclid-core-cast-issue.patch b/dev-java/jeuclid-core/files/jeuclid-core-cast-issue.patch
deleted file mode 100644
index 2ff46700a..000000000
--- a/dev-java/jeuclid-core/files/jeuclid-core-cast-issue.patch
+++ /dev/null
@@ -1,18 +0,0 @@
-Index: jeuclid-parent-3.1.9/jeuclid-core/src/main/java/net/sourceforge/jeuclid/converter/ConverterRegistry.java
-===================================================================
---- jeuclid-parent-3.1.9.orig/jeuclid-core/src/main/java/net/sourceforge/jeuclid/converter/ConverterRegistry.java	2010-02-12 15:10:32.000000000 +0100
-+++ jeuclid-parent-3.1.9/jeuclid-core/src/main/java/net/sourceforge/jeuclid/converter/ConverterRegistry.java	2013-08-20 14:55:16.000000000 +0200
-@@ -52,10 +52,10 @@
-      */
-     @SuppressWarnings("unchecked")
-     protected ConverterRegistry() {
--        final Iterator<ConverterDetector> it = Service
--                .providers(ConverterDetector.class);
-+        final Iterator<Object> it = Service
-+            .providers(ConverterDetector.class);
-         while (it.hasNext()) {
--            final ConverterDetector det = it.next();
-+            final ConverterDetector det = (ConverterDetector) it.next();
-             det.detectConversionPlugins(this);
-         }
-     }
diff --git a/dev-java/jeuclid-core/files/jeuclid-core-no-freehep.patch b/dev-java/jeuclid-core/files/jeuclid-core-no-freehep.patch
deleted file mode 100644
index 798dac293..000000000
--- a/dev-java/jeuclid-core/files/jeuclid-core-no-freehep.patch
+++ /dev/null
@@ -1,10 +0,0 @@
---- build.xml.orig	2010-01-22 17:46:35.000000000 +0000
-+++ build.xml	2010-01-22 17:49:07.000000000 +0000
-@@ -113,6 +113,7 @@
-       <src>
-         <pathelement location="src/main/java"/>
-       </src>
-+      <exclude name="**/FreeHep*" />
-       <classpath refid="libs-build-classpath"/>
-     </javac>
-     <copy todir="${build.output}">
diff --git a/dev-java/jeuclid-core/jeuclid-core-3.1.9-r1.ebuild b/dev-java/jeuclid-core/jeuclid-core-3.1.9-r1.ebuild
deleted file mode 100644
index 73e4e85d6..000000000
--- a/dev-java/jeuclid-core/jeuclid-core-3.1.9-r1.ebuild
+++ /dev/null
@@ -1,49 +0,0 @@
-# Copyright 1999-2015 Gentoo Foundation
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=5
-JAVA_PKG_IUSE="source"
-inherit eutils java-pkg-2 java-ant-2
-
-DESCRIPTION="Core module of MathML rendering solution"
-HOMEPAGE="http://jeuclid.sourceforge.net/"
-SRC_URI="mirror://sourceforge/jeuclid/jeuclid-parent-${PV}-src.zip"
-
-LICENSE="Apache-2.0"
-SLOT="0"
-KEYWORDS=""
-IUSE=""
-
-COMMON_DEPEND="dev-java/ant-core
-	dev-java/batik:1.8=
-	dev-java/commons-logging
-	dev-java/jcip-annotations
-	dev-java/xml-commons-external:1.3
-	dev-java/xmlgraphics-commons:2"
-
-RDEPEND=">=virtual/jre-1.5
-	${COMMON_DEPEND}"
-
-DEPEND=">=virtual/jdk-1.5
-	app-arch/unzip
-	${COMMON_DEPEND}"
-
-S="${WORKDIR}/jeuclid-parent-${PV}/${PN}"
-
-src_prepare() {
-	epatch "${FILESDIR}"/${PN}-no-freehep.patch \
-		"${FILESDIR}"/${PN}-cast-issue.patch
-
-	# create directory for dependencies
-	mkdir lib && cd lib || die
-
-	# add dependencies into the lib dir
-	java-pkg_jar-from ant-core ant.jar
-	java-pkg_jar-from batik-1.8 batik-all.jar
-	java-pkg_jar-from commons-logging,jcip-annotations,xml-commons-external-1.3
-	java-pkg_jar-from xml-commons-external-1.3,xmlgraphics-commons-2
-}
-
-src_install() {
-	java-pkg_dojar target/${PN}.jar
-}
diff --git a/dev-java/jeuclid-core/metadata.xml b/dev-java/jeuclid-core/metadata.xml
deleted file mode 100644
index 8b5c039f5..000000000
--- a/dev-java/jeuclid-core/metadata.xml
+++ /dev/null
@@ -1,21 +0,0 @@
-<?xml version="1.0" encoding="UTF-8"?>
-<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
-<pkgmetadata>
-	<maintainer type="project">
-		<email>sci@gentoo.org</email>
-		<name>Gentoo Science Project</name>
-	</maintainer>
-	<longdescription lang="en">
-JEuclid is a complete MathML rendering solution, consisting of:
-* A MathViewer application
-* Command line converters from MathML to other formats
-* An ant task for automated conversion
-* Display components for AWT and Swing
-* A component for Apache Cocoon
-This package contains the basic JEuclid rendering and document
-handling classes.
-</longdescription>
-	<upstream>
-		<remote-id type="sourceforge">jeuclid</remote-id>
-	</upstream>
-</pkgmetadata>
diff --git a/dev-java/jgraphx/Manifest b/dev-java/jgraphx/Manifest
deleted file mode 100644
index 940eb6906..000000000
--- a/dev-java/jgraphx/Manifest
+++ /dev/null
@@ -1,3 +0,0 @@
-DIST jgraphx-1.4.1.0.zip 4052749 BLAKE2B 12817a161391df4b63f1260af10b76f91cd4f2123f03ebb5e1826f927ced23724ea1210b455320552578a69d6c299fc577f443426a7eecc508ba99d69a9144a7 SHA512 c9d5482abb4876632a794a0c0ea4c7ec1a963ebdc72e7efc9be1ce0ed44edb589879caf3017cc626fbe51e0f8c46ff94c62966c5c242099b1f76c0f63bec58b3
-DIST jgraphx-1.8.0.6.zip 4216848 BLAKE2B beef4e75b001f15de0a77690f7c200f39fc05d1ced11fddf35656372e473d0a69a502bc05a52da62846a2ae2043200d66c15bc019690963191e543be991a735f SHA512 07985168625f094a8de9ab0e5c6050dd1a5d537b21eb6c73e468ad21db2758ac78a272dfedf22b94585eff4f77288ad99f8f1b70b18462754f0f3048ad06e40f
-DIST jgraphx-2.5.0.3.zip 4462094 BLAKE2B 59d0c4461ef836026338a16a07e8b44977b93a6bd67b3664187c7afd681638c63c09673825f5ad6afbd2825632d614d491a4c546fd7c8d9e21683d035c557e66 SHA512 2cdc86c61409f4bba0c25c02dafb26fc6d76a127b584f92d380baa610715ad5e2034c43c1d912f3d7eca4c03464fedcf01573a3dad4fa184c365ff4fc0b2b7ea
diff --git a/dev-java/jgraphx/jgraphx-1.4.1.0.ebuild b/dev-java/jgraphx/jgraphx-1.4.1.0.ebuild
deleted file mode 100644
index 488bafcef..000000000
--- a/dev-java/jgraphx/jgraphx-1.4.1.0.ebuild
+++ /dev/null
@@ -1,45 +0,0 @@
-# Copyright 1999-2014 Gentoo Foundation
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=5
-
-JAVA_PKG_IUSE="doc source"
-
-inherit java-pkg-2 java-ant-2 versionator
-
-MY_PV=$(replace_all_version_separators '_')
-
-DESCRIPTION="Open-source graph component for Java"
-HOMEPAGE="http://www.jgraph.com"
-SRC_URI="http://www.jgraph.com/downloads/jgraphx/archive/${PN}-${MY_PV}.zip -> ${P}.zip"
-
-SLOT="0"
-LICENSE="BSD"
-KEYWORDS="~amd64 ~x86"
-IUSE="doc examples source"
-
-DEPEND="
-	>=virtual/jdk-1.5
-	app-arch/unzip"
-RDEPEND=">=virtual/jre-1.5"
-
-S="${WORKDIR}/${PN}"
-
-src_prepare() {
-	# don't do javadoc always
-	sed -i \
-		-e 's/depends="doc"/depends="compile"/' \
-		build.xml || die "sed failed"
-	rm -rf doc/api lib/jgraphx.jar || die
-}
-
-EANT_BUILD_TARGET="build"
-EANT_DOC_TARGET="doc"
-
-src_install() {
-	java-pkg_dojar lib/${PN}.jar
-
-	use doc && java-pkg_dojavadoc docs/api
-	use source && java-pkg_dosrc src/org
-	use examples && java-pkg_doexamples examples
-}
diff --git a/dev-java/jgraphx/jgraphx-1.8.0.6.ebuild b/dev-java/jgraphx/jgraphx-1.8.0.6.ebuild
deleted file mode 100644
index ae457bf45..000000000
--- a/dev-java/jgraphx/jgraphx-1.8.0.6.ebuild
+++ /dev/null
@@ -1,45 +0,0 @@
-# Copyright 1999-2014 Gentoo Foundation
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=5
-
-JAVA_PKG_IUSE="doc source"
-
-inherit java-pkg-2 java-ant-2 versionator
-
-MY_PV=$(replace_all_version_separators '_')
-
-DESCRIPTION="Open-source graph component for Java"
-HOMEPAGE="http://www.jgraph.com"
-SRC_URI="http://www.jgraph.com/downloads/jgraphx/archive/${PN}-${MY_PV}.zip -> ${P}.zip"
-
-SLOT="1.8"
-LICENSE="BSD"
-KEYWORDS="~amd64 ~x86"
-IUSE="doc examples source"
-
-DEPEND="
-	>=virtual/jdk-1.5
-	app-arch/unzip"
-RDEPEND=">=virtual/jre-1.5"
-
-S="${WORKDIR}/${PN}"
-
-src_prepare() {
-	# don't do javadoc always
-	sed -i \
-		-e 's/depends="doc"/depends="compile"/' \
-		build.xml || die "sed failed"
-	rm -rf doc/api lib/jgraphx.jar || die
-}
-
-EANT_BUILD_TARGET="build"
-EANT_DOC_TARGET="doc"
-
-src_install() {
-	java-pkg_dojar lib/${PN}.jar
-
-	use doc && java-pkg_dojavadoc docs/api
-	use source && java-pkg_dosrc src/org
-	use examples && java-pkg_doexamples examples
-}
diff --git a/dev-java/jgraphx/jgraphx-2.5.0.3.ebuild b/dev-java/jgraphx/jgraphx-2.5.0.3.ebuild
deleted file mode 100644
index 926d260f7..000000000
--- a/dev-java/jgraphx/jgraphx-2.5.0.3.ebuild
+++ /dev/null
@@ -1,41 +0,0 @@
-# Copyright 1999-2014 Gentoo Foundation
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=5
-JAVA_PKG_IUSE="doc source"
-inherit java-pkg-2 java-ant-2 versionator
-
-MY_PV=$(replace_all_version_separators '_')
-
-DESCRIPTION="Open-source graph component for Java"
-SRC_URI="http://www.jgraph.com/downloads/jgraphx/archive/${PN}-${MY_PV}.zip\
-		-> ${P}.zip"
-HOMEPAGE="http://www.jgraph.com"
-IUSE="doc examples source"
-DEPEND=">=virtual/jdk-1.5
-	app-arch/unzip"
-RDEPEND=">=virtual/jre-1.5"
-LICENSE="BSD"
-SLOT="2.5"
-KEYWORDS="~amd64 ~x86"
-
-S="${WORKDIR}/${PN}"
-
-src_prepare() {
-	# don't do javadoc always
-	sed -i \
-		-e 's/depends="doc"/depends="compile"/' \
-		build.xml || die "sed failed"
-	rm -rf doc/api lib/jgraphx.jar || die
-}
-
-EANT_BUILD_TARGET="build"
-EANT_DOC_TARGET="doc"
-
-src_install() {
-	java-pkg_dojar lib/${PN}.jar
-
-	use doc && java-pkg_dojavadoc docs/api
-	use source && java-pkg_dosrc src/org
-	use examples && java-pkg_doexamples examples
-}
diff --git a/dev-java/jgraphx/metadata.xml b/dev-java/jgraphx/metadata.xml
deleted file mode 100644
index 2a4062ae5..000000000
--- a/dev-java/jgraphx/metadata.xml
+++ /dev/null
@@ -1,19 +0,0 @@
-<?xml version="1.0" encoding="UTF-8"?>
-<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
-<pkgmetadata>
-	<maintainer type="project">
-		<email>sci@gentoo.org</email>
-		<name>Gentoo Science Project</name>
-	</maintainer>
-	<longdescription lang="en">
-JGraph X is based on the mxGraph architecture, a re-designed core
-based on JGraph experience.
-Overall, JGraph X provides more features that JGraph, with a far
-smaller code size and complexity. Redesigning the codebase from
-scratch now means implementing common feature extensions are easier
-and require less coding. A number of new loosely coupled
-application-centric features have been added, making prototyping
-even faster, without their usage restricting application
-flexibility.
-</longdescription>
-</pkgmetadata>
diff --git a/dev-java/jlatexmath-fop/Manifest b/dev-java/jlatexmath-fop/Manifest
deleted file mode 100644
index d92e07cb2..000000000
--- a/dev-java/jlatexmath-fop/Manifest
+++ /dev/null
@@ -1 +0,0 @@
-DIST jlatexmath-fop-src-1.0.3.zip 115024 BLAKE2B c45d79c3b57c5439ab0f39fd17926e0cdb8bae4d5ef5bcec476c1daefefecbd197663beded3202dd53f25a3dee71c096f536b0c52b8d366c557c5ed89897abfe SHA512 92e81ab2c2a14cd9ac935028f6cd4370de5925f919e41fb94290a331660e2ea983ab3ca7a5fe7e5fd7c6a2caf34a4bae7ee45c0efc33b4ac0f154f16465c37f8
diff --git a/dev-java/jlatexmath-fop/files/jlatexmath-fop-1.0.3-fixpaths.patch b/dev-java/jlatexmath-fop/files/jlatexmath-fop-1.0.3-fixpaths.patch
deleted file mode 100644
index a03051c36..000000000
--- a/dev-java/jlatexmath-fop/files/jlatexmath-fop-1.0.3-fixpaths.patch
+++ /dev/null
@@ -1,13 +0,0 @@
-diff -urN work-orig/build.xml work/build.xml
---- work-orig/build.xml	2013-04-23 20:42:19.776644942 -0400
-+++ work/build.xml	2013-04-23 20:42:36.821646638 -0400
-@@ -1,7 +1,7 @@
- <?xml version="1.0" encoding="ISO-8859-1"?>
- <project name="jlatexmath-fop" basedir="." default="buildJar">
--  <import file="${basedir}/../../version.xml"/>
--  <property file="../../fop.properties"/>
-+  <import file="${basedir}/version.xml"/>
-+  <property file="fop.properties"/>
- 
-   <path id="libs-build-classpath">
-     <pathelement location="${fop.jar}"/>
diff --git a/dev-java/jlatexmath-fop/files/version.xml b/dev-java/jlatexmath-fop/files/version.xml
deleted file mode 100644
index b538b79a3..000000000
--- a/dev-java/jlatexmath-fop/files/version.xml
+++ /dev/null
@@ -1,5 +0,0 @@
-<?xml version="1.0" encoding="UTF-8"?>
-<project name="version_jlm">
-  <property name="version" value="1.0.3" />
-  <property name="java_version" value="5" />
-</project>
diff --git a/dev-java/jlatexmath-fop/jlatexmath-fop-1.0.3.ebuild b/dev-java/jlatexmath-fop/jlatexmath-fop-1.0.3.ebuild
deleted file mode 100644
index 5cb680271..000000000
--- a/dev-java/jlatexmath-fop/jlatexmath-fop-1.0.3.ebuild
+++ /dev/null
@@ -1,44 +0,0 @@
-# Copyright 1999-2015 Gentoo Foundation
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=5
-
-JAVA_PKG_IUSE="examples source"
-
-inherit java-pkg-2 java-ant-2
-
-DESCRIPTION="jlatexmath plugin for dev-java/fop"
-HOMEPAGE="http://forge.scilab.org/index.php/p/jlatexmath"
-SRC_URI="http://forge.scilab.org/upload/jlatexmath/files/${PN}-src-${PV}.zip"
-
-LICENSE="GPL-2"
-SLOT="1"
-KEYWORDS="~amd64 ~x86"
-IUSE=""
-
-CDEPEND="dev-java/jlatexmath:1
-	dev-java/xmlgraphics-commons:2
-	>=dev-java/fop-2.0-r1:0"
-DEPEND=">=virtual/jdk-1.5
-	${CDEPEND}"
-RDEPEND=">=virtual/jre-1.5
-	${CDEPEND}"
-
-EANT_BUILD_TARGET="buildJar"
-
-S="${WORKDIR}"
-
-src_prepare() {
-	epatch "${FILESDIR}/${P}-fixpaths.patch"
-	cp "${FILESDIR}/version.xml" "${S}" || die
-	echo "fop.jar=$(java-pkg_getjar fop fop.jar)
-xmlgraphics-commons.jar=$(java-pkg_getjar xmlgraphics-commons-2 xmlgraphics-commons.jar)
-jlatexmath.jar=$(java-pkg_getjar jlatexmath-1 jlatexmath.jar)" \
-		 >>fop.properties || die
-}
-
-src_install() {
-	java-pkg_newjar dist/${P}.jar ${PN}.jar
-	use source && java-pkg_dosrc src/org
-	use examples && java-pkg_doexamples examples
-}
diff --git a/dev-java/jlatexmath-fop/metadata.xml b/dev-java/jlatexmath-fop/metadata.xml
deleted file mode 100644
index 9ded36c47..000000000
--- a/dev-java/jlatexmath-fop/metadata.xml
+++ /dev/null
@@ -1,13 +0,0 @@
-<?xml version="1.0" encoding="UTF-8"?>
-<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
-<pkgmetadata>
-	<maintainer type="project">
-		<email>sci@gentoo.org</email>
-		<name>Gentoo Science Project</name>
-	</maintainer>
-	<longdescription lang="en">
-LaTeXmath library provides a set of Java classes for displaying
-(complex) mathematical formulas as part of a Java application with
-LateX style. This package installs the plugin for dev-java/fop.
-</longdescription>
-</pkgmetadata>
diff --git a/dev-java/jlatexmath/Manifest b/dev-java/jlatexmath/Manifest
deleted file mode 100644
index 44a2a7205..000000000
--- a/dev-java/jlatexmath/Manifest
+++ /dev/null
@@ -1 +0,0 @@
-DIST jlatexmath-src-1.0.3.zip 1086238 BLAKE2B 16e420326f5387bb6bae251032d6c3e262334adfa23083e38fc4d5e7552b415c03761172decc0c2a205d9fc3cd63190b949c44a32fa983f964d8a4557be82702 SHA512 85c71568b5bffd897338e7c3fd03be0c0f52fc0543b5d91f54453f20f3f4ec41225cb356667dbaca86df673db1b7ac8afc2b16e57db981ec8037143e26521e82
diff --git a/dev-java/jlatexmath/jlatexmath-1.0.3.ebuild b/dev-java/jlatexmath/jlatexmath-1.0.3.ebuild
deleted file mode 100644
index cda71615d..000000000
--- a/dev-java/jlatexmath/jlatexmath-1.0.3.ebuild
+++ /dev/null
@@ -1,31 +0,0 @@
-# Copyright 1999-2014 Gentoo Foundation
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=5
-
-JAVA_PKG_IUSE="doc examples source"
-
-inherit java-pkg-2 java-ant-2
-
-DESCRIPTION="A Java API to render LaTeX"
-HOMEPAGE="http://forge.scilab.org/index.php/p/jlatexmath"
-SRC_URI="http://forge.scilab.org/upload/jlatexmath/files/${PN}-src-${PV}.zip"
-
-LICENSE="GPL-2"
-SLOT="1"
-KEYWORDS="~amd64 ~x86"
-IUSE=""
-
-DEPEND=">=virtual/jdk-1.5
-		app-arch/unzip"
-RDEPEND=">=virtual/jre-1.5"
-
-EANT_BUILD_TARGET="buildJar"
-EANT_DOC_TARGET="doc"
-
-src_install() {
-	java-pkg_newjar dist/"${P}.jar" "${PN}.jar"
-	use doc && java-pkg_dojavadoc doc
-	use source && java-pkg_dosrc src/org
-	use examples && java-pkg_doexamples examples
-}
diff --git a/dev-java/jlatexmath/metadata.xml b/dev-java/jlatexmath/metadata.xml
deleted file mode 100644
index 7ad985657..000000000
--- a/dev-java/jlatexmath/metadata.xml
+++ /dev/null
@@ -1,13 +0,0 @@
-<?xml version="1.0" encoding="UTF-8"?>
-<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
-<pkgmetadata>
-	<maintainer type="project">
-		<email>sci@gentoo.org</email>
-		<name>Gentoo Science Project</name>
-	</maintainer>
-	<longdescription lang="en">
-LaTeXmath library provides a set of Java classes for displaying
-(complex) mathematical formulas as part of a Java application with
-LateX style.  
-</longdescription>
-</pkgmetadata>
diff --git a/dev-java/jogl/Manifest b/dev-java/jogl/Manifest
deleted file mode 100644
index 385b1874a..000000000
--- a/dev-java/jogl/Manifest
+++ /dev/null
@@ -1,4 +0,0 @@
-DIST jogl-1.1.1a-src.zip 3656870 BLAKE2B 3536ee0ee038278704320e853488537f6ac0758ec75bae317bd415f21afe8706c0c8802ba31c292c4cb3aa15427f392b69802fdfafa009f8e641db5daaac8824 SHA512 6de4273594c3bb4f17a629647a78619ba00d5998fa35cb25ee220e402059647b2c8fd111f1abdada9a78998d1b73052f1b432ed95220d1966e73cb50295b66bf
-DIST jogl-2.1.4.tar.gz 32070918 BLAKE2B 88636fa761addde8d7aba558b6d35382f922dba3ad27f82b7b0c935e5650fa084f9953b62c81495311c57accd6e359dbd4bac06edc7209be52437264d0f0da7c SHA512 9d9f45676f671b1958352fcb7ddb4db539f19fb330db0146df6ce46167bcebf9c4fdc1a09bce72451a4bf2f4632a69cad2b4dd56df61c78f5e26e85a50918a0b
-DIST jogl-2.2.4.tar.gz 50214295 BLAKE2B 984d32e4bd43e33807dca1d0222aae9a9ca453d616002865d4a6b80ec9a8f3e8f833669067daa545103a391af8db6e5c75cfc45501053b3d850c5a28ac311a7e SHA512 79fb054d65e8aa532a75e8c8911f43987d877f7b71584ea24cc0f9152f8aaaddabd4afef7f7504b3df73c4d240bedc123bb8aeb8670d9ae2bd165bd0490e420e
-DIST jogl-v2.0-rc8.tar.7z 18148821 BLAKE2B 88f0d6913741fccfb2dee11b38e2e596ff5f4b767140e1ace1de56d05afe21ad0c467f54ff2b2605f9bef3f00857ebe526a07d0e995a3a84bc538fa995ecc425 SHA512 ce335990dac4c868705f9cd041cab2e97050efcd9b6b0a8fa01e070aa7ee2f27162cb96ebbbd5e9f04a1aa9e7661dde6aa0ba1d02565f38fa76a39deeb48a500
diff --git a/dev-java/jogl/files/1.1.0/fix-solaris-compiler.patch b/dev-java/jogl/files/1.1.0/fix-solaris-compiler.patch
deleted file mode 100644
index 6d77bc3fe..000000000
--- a/dev-java/jogl/files/1.1.0/fix-solaris-compiler.patch
+++ /dev/null
@@ -1,41 +0,0 @@
-diff -Naur gluegen.orig/make/gluegen-cpptasks.xml gluegen/make/gluegen-cpptasks.xml
---- gluegen.orig/make/gluegen-cpptasks.xml	2007-03-14 23:09:20.000000000 +1300
-+++ gluegen/make/gluegen-cpptasks.xml	2007-03-14 23:09:40.000000000 +1300
-@@ -397,16 +397,16 @@
-       <compilerarg value="-fPIC"/>
-     </compiler>
- 
--    <compiler id="compiler.cfg.solaris" name="suncc">
-+    <compiler id="compiler.cfg.solaris" name="gcc">
-     </compiler>
- 
--    <compiler id="compiler.cfg.solaris.sparcv9" name="suncc">
-+    <compiler id="compiler.cfg.solaris.sparcv9" name="gcc">
-       <compilerarg value="-fast" />
-       <compilerarg value="-xchip=ultra" />
-       <compilerarg value="-xarch=v9a" />
-     </compiler>
- 
--    <compiler id="compiler.cfg.solaris.amd64" name="suncc">
-+    <compiler id="compiler.cfg.solaris.amd64" name="gcc">
-       <compilerarg value="-fast" />
-       <compilerarg value="-xchip=opteron" />
-       <compilerarg value="-xarch=amd64" />
-@@ -492,14 +492,14 @@
-     <linker id="linker.cfg.linux.amd64" name="gcc">
-     </linker>
- 
--    <linker id="linker.cfg.solaris" name="suncc">
-+    <linker id="linker.cfg.solaris" name="gcc">
-     </linker>
- 
--    <linker id="linker.cfg.solaris.sparcv9" name="suncc">
-+    <linker id="linker.cfg.solaris.sparcv9" name="gcc">
-       <linkerarg value="-xarch=v9a" />
-     </linker>
- 
--    <linker id="linker.cfg.solaris.amd64" name="suncc">
-+    <linker id="linker.cfg.solaris.amd64" name="gcc">
-       <linkerarg value="-xarch=amd64" />
-     </linker>
- 
diff --git a/dev-java/jogl/files/1.1.0/uncouple-gluegen.patch b/dev-java/jogl/files/1.1.0/uncouple-gluegen.patch
deleted file mode 100644
index a508c610f..000000000
--- a/dev-java/jogl/files/1.1.0/uncouple-gluegen.patch
+++ /dev/null
@@ -1,32 +0,0 @@
-diff -Naur jogl.orig/make/build.xml jogl/make/build.xml
---- jogl.orig/make/build.xml	2007-02-13 17:45:16.000000000 +1300
-+++ jogl/make/build.xml	2007-03-14 22:55:50.000000000 +1300
-@@ -127,7 +127,18 @@
-         <property name="gluegen.build.xml" value="${gluegen.make.dir}/build.xml" />
-         <property name="gluegen.jar" value="../../gluegen/build/gluegen.jar" />
-         <property name="gluegen-rt.jar" value="../../gluegen/build/gluegen-rt.jar" />
--                                                
-+	<!-- This property is used to skip building gluegen if the jar files
-+	   - are already available on the system and have been overridden
-+	   - by the user. The purpose is to allow linux distro's to uncouple
-+	   - gluegen from jogl.
-+	  -->
-+	<condition property="gluegen.prebuilt" >
-+		<and>
-+			<available file="${gluegen.jar}" />
-+			<available file="${gluegen-rt.jar}" />
-+		</and>
-+	</condition>
-+
-         <!-- Names of directories relative to the project root.
-              Some of these are used in FileMappers later for dependence information
-              and need exact string matching, which is why they use file.separator
-@@ -479,7 +490,7 @@
-     <!--
-        - Build GlueGen
-       -->
--    <target name="build.gluegen" depends="init">
-+    <target name="build.gluegen" depends="init" unless="gluegen.prebuilt">
-         <!-- Run the GlueGen build to ensure that the GlueGen ANT task
-            - has been built. -->
-         <!-- FIXME: remove passing down of antlr.jar when gluegen.properties is on all
diff --git a/dev-java/jogl/jogl-1.1.1a.ebuild b/dev-java/jogl/jogl-1.1.1a.ebuild
deleted file mode 100644
index 59e94ddef..000000000
--- a/dev-java/jogl/jogl-1.1.1a.ebuild
+++ /dev/null
@@ -1,79 +0,0 @@
-# Copyright 1999-2014 Gentoo Foundation
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=5
-
-WANT_ANT_TASKS="ant-antlr"
-JAVA_PKG_IUSE="cg source doc"
-
-inherit eutils java-pkg-2 java-ant-2
-
-DESCRIPTION="Java(TM) Binding fot the OpenGL(TM) API"
-HOMEPAGE="https://jogl.dev.java.net/"
-SRC_URI="http://download.java.net/media/${PN}/builds/archive/jsr-231-${PV}/${P}-src.zip"
-
-LICENSE="BSD"
-SLOT="0"
-KEYWORDS="~amd64 ~x86"
-IUSE=""
-
-COMMON_DEPEND="
-	dev-java/ant-core
-	>=dev-java/cpptasks-1.0_beta4-r2
-	dev-java/gluegen:0
-	virtual/opengl
-	x11-libs/libX11
-	x11-libs/libXxf86vm
-	cg? ( media-gfx/nvidia-cg-toolkit )"
-
-DEPEND="
-	app-arch/unzip
-	>=virtual/jdk-1.4
-	${COMMON_DEPEND}"
-
-RDEPEND="
-	>=virtual/jre-1.4
-	${COMMON_DEPEND}"
-
-S="${WORKDIR}/${PN}"
-
-java_prepare() {
-	epatch "${FILESDIR}/1.1.0/uncouple-gluegen.patch"
-	cd "${S}/make" || die
-	mv build.xml build.xml.bak || die
-
-	sed 's_/usr/X11R6_/usr_g' build.xml.bak > build.xml || die
-	sed -i -e 's/suncc/gcc/g' build.xml ../../gluegen/make/gluegen-cpptasks.xml || die
-
-	rm -R "${S}/build/gensrc/classes/javax" || die
-
-	cd "${WORKDIR}/gluegen/make/lib" || die
-	rm -v *.jar || die
-	java-pkg_jar-from cpptasks
-}
-
-src_compile() {
-	cd make/ || die
-	local antflags="-Dgluegen.prebuild=true"
-	antflags="${antflags} -Dantlr.jar=$(java-pkg_getjars --build-only antlr)"
-	local gcp="$(java-pkg_getjars ant-core):$(java-config --tools)"
-
-	local gluegen="-Dgluegen.jar=$(java-pkg_getjar gluegen gluegen.jar)"
-	local gluegenrt="-Dgluegen-rt.jar=$(java-pkg_getjar gluegen gluegen-rt.jar)"
-
-	use cg && antflags="${antflags} -Djogl.cg=1 -Dx11.cg.lib=/usr/lib"
-	# -Dbuild.sysclasspath=ignore fails with missing ant dependencies.
-
-	export ANT_OPTS="-Xmx1g"
-	eant \
-		-Dgentoo.classpath="${gcp}" \
-		${antflags} "${gluegen}" "${gluegenrt}" \
-		all $(use_doc)
-}
-
-src_install() {
-	use source && java-pkg_dosrc src/classes/*
-	java-pkg_doso build/obj/*.so
-	java-pkg_dojar build/*.jar
-	use doc && java-pkg_dojavadoc javadoc_public
-}
diff --git a/dev-java/jogl/jogl-2.0_rc8-r1.ebuild b/dev-java/jogl/jogl-2.0_rc8-r1.ebuild
deleted file mode 100644
index ae3fec701..000000000
--- a/dev-java/jogl/jogl-2.0_rc8-r1.ebuild
+++ /dev/null
@@ -1,95 +0,0 @@
-# Copyright 1999-2014 Gentoo Foundation
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=5
-
-JAVA_PKG_IUSE="doc source"
-
-inherit java-pkg-2 java-ant-2
-
-MY_PV=v${PV/_/-}
-MY_P=${PN}-${MY_PV}
-
-DESCRIPTION="Java(TM) Binding fot the OpenGL(TM) API"
-HOMEPAGE="http://jogamp.org/jogl/www/"
-SRC_URI="http://jogamp.org/deployment/${MY_PV}/archive/Sources/${MY_P}.tar.7z"
-
-LICENSE="BSD"
-SLOT="2"
-KEYWORDS="~amd64 ~x86"
-IUSE="cg"
-
-COMMON_DEP="
-	dev-java/ant-core:0
-	dev-java/ant-junit:0
-	dev-java/antlr:0
-	dev-java/cpptasks:0
-	=dev-java/gluegen-${PV}:${SLOT}
-	dev-java/junit:4
-	dev-java/swt:3.7
-	x11-libs/libX11
-	x11-libs/libXxf86vm
-	virtual/opengl
-	cg? ( media-gfx/nvidia-cg-toolkit )"
-RDEPEND="${COMMON_DEP}
-	>=virtual/jre-1.5"
-DEPEND="${COMMON_DEP}
-	>=virtual/jdk-1.5
-	app-arch/p7zip
-	dev-java/ant-antlr:0
-	dev-java/ant-contrib:0
-	dev-java/ant-nodeps:0
-	dev-java/cpptasks:0"
-
-S=${WORKDIR}/${MY_P}
-
-src_unpack() {
-	default
-	unpack ./${MY_P}.tar
-}
-
-java_prepare() {
-	find -name '*.jar' -exec rm -v {} + || die
-
-	# Empty filesets are never out of date!
-	sed -i -e 's/<outofdate>/<outofdate force="true">/' make/build*xml || die
-}
-
-JAVA_PKG_BSFIX_NAME+=" build-jogl.xml build-nativewindow.xml build-newt.xml build-test.xml"
-JAVA_ANT_REWRITE_CLASSPATH="yes"
-
-EANT_BUILD_XML="make/build.xml"
-EANT_BUILD_TARGET="all"
-EANT_DOC_TARGET="" # FIXME there are a couple javadoc targets, pick one
-EANT_GENTOO_CLASSPATH="ant-core,antlr,swt-3.7,ant-junit"
-EANT_NEEDS_TOOLS="yes"
-EANT_ANT_TASKS="ant-antlr ant-contrib ant-junit ant-nodeps cpptasks"
-
-src_compile() {
-	EANT_EXTRA_ARGS+=" -Dcommon.gluegen.build.done=true"
-	EANT_EXTRA_ARGS+=" -Dgluegen.root=/usr/share/gluegen-${SLOT}/"
-	EANT_EXTRA_ARGS+=" -Dgluegen.jar=$(java-pkg_getjar gluegen-${SLOT} gluegen.jar)"
-	EANT_EXTRA_ARGS+=" -Dgluegen-rt.jar=$(java-pkg_getjar gluegen-${SLOT} gluegen-rt.jar)"
-
-	# FIXME don't build tests just yet
-	EANT_EXTRA_ARGS+=" -Djunit.jar=$(java-pkg_getjar --build-only junit-4 junit.jar)"
-
-	use cg && EANT_EXTRA_ARGS+=" -Djogl.cg=1 -Dx11.cg.lib=/usr/lib"
-
-	java-pkg-2_src_compile
-}
-
-EANT_TEST_TARGET="junit.run"
-# FIXME src_test
-
-src_install() {
-	# There are many more
-	java-pkg_dojar build/jar/*.jar
-	java-pkg_doso build/lib/*.so
-
-	if use doc; then
-		#java-pkg_dojavadoc javadoc_public
-		dodoc -r doc
-	fi
-	use source && java-pkg_dosrc src/jogl/classes/*
-}
diff --git a/dev-java/jogl/jogl-2.1.4.ebuild b/dev-java/jogl/jogl-2.1.4.ebuild
deleted file mode 100644
index fbf84aba8..000000000
--- a/dev-java/jogl/jogl-2.1.4.ebuild
+++ /dev/null
@@ -1,72 +0,0 @@
-# Copyright 1999-2014 Gentoo Foundation
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=5
-
-JAVA_PKG_IUSE="doc source"
-WANT_ANT_TASKS="ant-antlr ant-contrib dev-java/cpptasks:0"
-
-inherit java-pkg-2 java-ant-2
-
-#MY_PV="${PV/_rc/_rc0}"
-#MY_P="${PN}-${MY_PV}"
-
-DESCRIPTION="Java(TM) Binding fot the OpenGL(TM) API"
-HOMEPAGE="http://jogamp.org/jogl/www/"
-SRC_URI="https://github.com/sgothel/jogl/archive/v${PV}.tar.gz -> ${P}.tar.gz"
-
-LICENSE="BSD"
-SLOT="2.1"
-KEYWORDS="~amd64 ~x86"
-IUSE="cg"
-
-CDEPEND="
-	=dev-java/gluegen-${PV}:${SLOT}
-	dev-java/antlr:0
-	dev-java/ant-core:0
-	x11-libs/libX11
-	x11-libs/libXxf86vm
-	dev-java/swt:3.7
-	virtual/opengl
-	cg? ( media-gfx/nvidia-cg-toolkit )"
-
-RDEPEND="${CDEPEND}
-	>=virtual/jre-1.5"
-DEPEND="${CDEPEND}
-	>=virtual/jdk-1.5"
-
-# upstream has a crude way to call the junit tests, which cause a lot of trouble to pass
-# our test classpath...
-RESTRICT="test"
-
-JAVA_PKG_BSFIX_NAME+=" build-jogl.xml build-nativewindow.xml build-newt.xml"
-JAVA_ANT_REWRITE_CLASSPATH="yes"
-EANT_BUILD_XML="make/build.xml"
-EANT_BUILD_TARGET="init build.nativewindow build.jogl build.newt one.dir tag.build"
-EANT_DOC_TARGET=""
-EANT_GENTOO_CLASSPATH="gluegen-${SLOT},antlr,ant-core,swt-3.7"
-EANT_GENTOO_CLASSPATH_EXTRA="${S}/build/${PN}/*.jar:${S}/build/nativewindow/*.jar"
-EANT_NEEDS_TOOLS="yes"
-
-java_prepare() {
-	#we keep make/lib/plugin3/puglin3-public.jar
-	find -name 'make/lib/swt/*.jar' -delete -print || die
-
-	# Empty filesets are never out of date!
-	sed -i -e 's/<outofdate>/<outofdate force="true">/'  make/build*xml || die
-
-	EANT_EXTRA_ARGS+=" -Dcommon.gluegen.build.done=true"
-	EANT_EXTRA_ARGS+=" -Dgluegen.root=/usr/share/gluegen-${SLOT}/"
-	EANT_EXTRA_ARGS+=" -Dgluegen.jar=$(java-pkg_getjar gluegen-${SLOT} gluegen.jar)"
-	EANT_EXTRA_ARGS+=" -Dgluegen-rt.jar=$(java-pkg_getjar gluegen-${SLOT} gluegen-rt.jar)"
-
-	use cg && EANT_EXTRA_ARGS+=" -Djogl.cg=1 -Dx11.cg.lib=/usr/lib"
-}
-
-src_install() {
-	java-pkg_dojar build/jar/*.jar
-	java-pkg_doso build/lib/*.so
-
-	use doc && dodoc -r doc
-	use source && java-pkg_dosrc src/jogl/classes/*
-}
diff --git a/dev-java/jogl/jogl-2.2.4.ebuild b/dev-java/jogl/jogl-2.2.4.ebuild
deleted file mode 100644
index edccee222..000000000
--- a/dev-java/jogl/jogl-2.2.4.ebuild
+++ /dev/null
@@ -1,69 +0,0 @@
-# Copyright 1999-2015 Gentoo Foundation
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=5
-
-JAVA_PKG_IUSE="doc source"
-WANT_ANT_TASKS="ant-antlr ant-contrib dev-java/cpptasks:0"
-
-inherit java-pkg-2 java-ant-2
-
-DESCRIPTION="Java(TM) Binding fot the OpenGL(TM) API"
-HOMEPAGE="http://jogamp.org/jogl/www/"
-SRC_URI="https://github.com/sgothel/jogl/archive/v${PV}.tar.gz -> ${P}.tar.gz"
-
-LICENSE="BSD"
-SLOT="2.2"
-KEYWORDS="~amd64 ~x86"
-IUSE="cg"
-
-CDEPEND="
-	=dev-java/gluegen-${PV}:${SLOT}
-	dev-java/antlr:0
-	dev-java/ant-core:0
-	x11-libs/libX11
-	x11-libs/libXxf86vm
-	dev-java/swt:3.7
-	virtual/opengl
-	cg? ( media-gfx/nvidia-cg-toolkit )"
-
-RDEPEND="${CDEPEND}
-	>=virtual/jre-1.5"
-DEPEND="${CDEPEND}
-	>=virtual/jdk-1.5"
-
-# upstream has a crude way to call the junit tests, which cause a lot of trouble to pass
-# our test classpath...
-RESTRICT="test"
-
-JAVA_PKG_BSFIX_NAME+=" build-jogl.xml build-nativewindow.xml build-newt.xml"
-JAVA_ANT_REWRITE_CLASSPATH="yes"
-EANT_BUILD_XML="make/build.xml"
-EANT_BUILD_TARGET="init build.nativewindow build.jogl build.newt build.oculusvr one.dir tag.build"
-EANT_DOC_TARGET=""
-EANT_GENTOO_CLASSPATH="gluegen-${SLOT},antlr,ant-core,swt-3.7"
-EANT_GENTOO_CLASSPATH_EXTRA="${S}/build/${PN}/*.jar:${S}/build/nativewindow/*.jar"
-EANT_NEEDS_TOOLS="yes"
-
-java_prepare() {
-	#we keep make/lib/plugin3/puglin3-public.jar
-	find -name 'make/lib/swt/*.jar' -delete -print || die
-
-	# Empty filesets are never out of date!
-	sed -i -e 's/<outofdate>/<outofdate force="true">/'  make/build*xml || die
-
-	EANT_EXTRA_ARGS+=" -Dcommon.gluegen.build.done=true"
-	EANT_EXTRA_ARGS+=" -Dgluegen.root=/usr/share/gluegen-${SLOT}/"
-	EANT_EXTRA_ARGS+=" -Dgluegen.jar=$(java-pkg_getjar gluegen-${SLOT} gluegen.jar)"
-	EANT_EXTRA_ARGS+=" -Dgluegen-rt.jar=$(java-pkg_getjar gluegen-${SLOT} gluegen-rt.jar)"
-
-	use cg && EANT_EXTRA_ARGS+=" -Djogl.cg=1 -Dx11.cg.lib=/usr/lib"
-}
-
-src_install() {
-	java-pkg_dojar build/jar/*.jar
-	java-pkg_doso build/lib/*.so
-
-	use doc && dodoc -r doc
-	use source && java-pkg_dosrc src/jogl/classes/*
-}
diff --git a/dev-java/jogl/metadata.xml b/dev-java/jogl/metadata.xml
deleted file mode 100644
index 7751e096e..000000000
--- a/dev-java/jogl/metadata.xml
+++ /dev/null
@@ -1,18 +0,0 @@
-<?xml version="1.0" encoding="UTF-8"?>
-<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
-<pkgmetadata>
-	<maintainer type="project">
-		<email>sci@gentoo.org</email>
-		<name>Gentoo Science Project</name>
-	</maintainer>
-	<longdescription lang="en">
-JOGL provides Java with a Binding for the OpenGL® API (JSR-231), and is designed
-to provide hardware-supported 3D graphics to applications written in Java.
-</longdescription>
-	<use>
-		<flag name="cg">Enable NVidia Cg binding.</flag>
-	</use>
-	<upstream>
-		<remote-id type="github">sgothel/jogl</remote-id>
-	</upstream>
-</pkgmetadata>
diff --git a/dev-java/jrosetta/Manifest b/dev-java/jrosetta/Manifest
deleted file mode 100644
index 3cb51fd1d..000000000
--- a/dev-java/jrosetta/Manifest
+++ /dev/null
@@ -1 +0,0 @@
-DIST jrosetta-1.0.4-sources.jar 94931 BLAKE2B 205a3bf9c9be9f361902f59f7f1756161ba436a29cf5650bf7173f8e431818cab235754cbbc031eb69604bf8857150a17df069bc3f87fff8a1f5f75c2d136f4d SHA512 84b613a0dc6e3ca80414aba8f7c8cf044f013d27ed27c0f18fdbea056a6358c849ee193e3ab7320ffa7368fa17f255d4390fc306e8aa2c0ad70de51f36b6e878
diff --git a/dev-java/jrosetta/files/api-build.xml b/dev-java/jrosetta/files/api-build.xml
deleted file mode 100644
index 6627122ab..000000000
--- a/dev-java/jrosetta/files/api-build.xml
+++ /dev/null
@@ -1,262 +0,0 @@
-<?xml version="1.0" encoding="UTF-8"?>
-
-<!-- ====================================================================== -->
-<!-- Ant build file (http://ant.apache.org/) for Ant 1.6.2 or above.        -->
-<!-- ====================================================================== -->
-
-<!-- ====================================================================== -->
-<!-- ===================== - DO NOT EDIT THIS FILE! - ===================== -->
-<!-- ====================================================================== -->
-<!--                                                                        -->
-<!-- Any modifications will be overwritten.                                 -->
-<!--                                                                        -->
-<!-- Generated by Maven Ant Plugin on 4/12/12 2:43 PM                       -->
-<!-- See: http://maven.apache.org/plugins/maven-ant-plugin/                 -->
-<!--                                                                        -->
-<!-- ====================================================================== -->
-
-<project name="jrosetta-api-from-maven" default="package" basedir=".">
-
-  <!-- ====================================================================== -->
-  <!-- Build environment properties                                           -->
-  <!-- ====================================================================== -->
-
-  <property file="${user.home}/.m2/maven.properties"/>
-  <property file="maven-build.properties"/>
-
-  <property name="maven.build.finalName" value="jrosetta-api-1.0.4"/>
-  <property name="maven.build.dir" value="target"/>
-  <property name="maven.build.outputDir" value="${maven.build.dir}/classes"/>
-  <property name="maven.build.srcDir.0" value="src/main/java"/>
-  <property name="maven.build.resourceDir.0" value="src/main/resources"/>
-  <property name="maven.build.testOutputDir" value="${maven.build.dir}/test-classes"/>
-  <property name="maven.build.testDir.0" value="src/test/java"/>
-  <property name="maven.build.testResourceDir.0" value="src/test/resources"/>
-  <property name="maven.test.reports" value="${maven.build.dir}/test-reports"/>
-  <property name="maven.reporting.outputDirectory" value="${maven.build.dir}/site"/>
-
-  <property name="maven.repo.local" value="${user.home}/.m2/repository"/>
-  <property name="maven.settings.offline" value="true"/>
-  <property name="maven.settings.interactiveMode" value="true"/>
-
-  <!-- ====================================================================== -->
-  <!-- Defining classpaths                                                    -->
-  <!-- ====================================================================== -->
-
-  <path id="build.classpath"/>
-  <path id="build.test.classpath">
-    <pathelement location="${maven.repo.local}/junit/junit/4.10/junit-4.10.jar"/>
-    <pathelement location="${maven.repo.local}/org/hamcrest/hamcrest-core/1.1/hamcrest-core-1.1.jar"/>
-  </path>
-
-  <!-- ====================================================================== -->
-  <!-- Cleaning up target                                                     -->
-  <!-- ====================================================================== -->
-
-  <target name="clean" description="Clean the output directory">
-    <delete dir="${maven.build.dir}"/>
-  </target>
-
-  <!-- ====================================================================== -->
-  <!-- Compilation target                                                     -->
-  <!-- ====================================================================== -->
-
-  <target name="compile" depends="get-deps" description="Compile the code">
-    <mkdir dir="${maven.build.outputDir}"/>
-    <javac destdir="${maven.build.outputDir}" 
-           nowarn="false" 
-           debug="true" 
-           optimize="false" 
-           deprecation="true" 
-           target="1.6" 
-           verbose="false" 
-           fork="false" 
-           source="1.6">
-      <src>
-        <pathelement location="${maven.build.srcDir.0}"/>
-      </src>
-      <classpath refid="build.classpath"/>
-    </javac>
-    <copy todir="${maven.build.outputDir}">
-      <fileset dir="${maven.build.resourceDir.0}"/>
-    </copy>
-  </target>
-
-  <!-- ====================================================================== -->
-  <!-- Test-compilation target                                                -->
-  <!-- ====================================================================== -->
-
-  <target name="compile-tests" 
-          depends="compile" 
-          description="Compile the test code" 
-          unless="maven.test.skip">
-    <mkdir dir="${maven.build.testOutputDir}"/>
-    <javac destdir="${maven.build.testOutputDir}" 
-           nowarn="false" 
-           debug="true" 
-           optimize="false" 
-           deprecation="true" 
-           target="1.6" 
-           verbose="false" 
-           fork="false" 
-           source="1.6">
-      <src>
-        <pathelement location="${maven.build.testDir.0}"/>
-      </src>
-      <classpath>
-        <path refid="build.test.classpath"/>
-        <pathelement location="${maven.build.outputDir}"/>
-      </classpath>
-    </javac>
-    <copy todir="${maven.build.testOutputDir}">
-      <fileset dir="${maven.build.testResourceDir.0}"/>
-    </copy>
-  </target>
-
-  <!-- ====================================================================== -->
-  <!-- Run all tests                                                          -->
-  <!-- ====================================================================== -->
-
-  <target name="test" 
-          depends="compile-tests, junit-missing" 
-          unless="junit.skipped" 
-          description="Run the test cases">
-    <mkdir dir="${maven.test.reports}"/>
-    <junit printSummary="yes" haltonerror="true" haltonfailure="true" fork="true" dir=".">
-      <sysproperty key="basedir" value="."/>
-      <formatter type="xml"/>
-      <formatter type="plain" usefile="false"/>
-      <classpath>
-        <path refid="build.test.classpath"/>
-        <pathelement location="${maven.build.outputDir}"/>
-        <pathelement location="${maven.build.testOutputDir}"/>
-      </classpath>
-      <batchtest todir="${maven.test.reports}" unless="test">
-        <fileset dir="${maven.build.testDir.0}">
-          <include name="**/Test*.java"/>
-          <include name="**/*Test.java"/>
-          <include name="**/*TestCase.java"/>
-          <exclude name="**/*Abstract*Test.java"/>
-        </fileset>
-      </batchtest>
-      <batchtest todir="${maven.test.reports}" if="test">
-        <fileset dir="${maven.build.testDir.0}">
-          <include name="**/${test}.java"/>
-          <exclude name="**/*Abstract*Test.java"/>
-        </fileset>
-      </batchtest>
-    </junit>
-  </target>
-
-  <target name="test-junit-present">
-    <available classname="junit.framework.Test" property="junit.present"/>
-  </target>
-
-  <target name="test-junit-status" 
-          depends="test-junit-present">
-    <condition property="junit.missing">
-      <and>
-        <isfalse value="${junit.present}"/>
-        <isfalse value="${maven.test.skip}"/>
-      </and>
-    </condition>
-    <condition property="junit.skipped">
-      <or>
-        <isfalse value="${junit.present}"/>
-        <istrue value="${maven.test.skip}"/>
-      </or>
-    </condition>
-  </target>
-
-  <target name="junit-missing" 
-          depends="test-junit-status" 
-          if="junit.missing">
-    <echo>=================================== WARNING ===================================</echo>
-    <echo> JUnit is not present in your $ANT_HOME/lib directory. Tests not executed.</echo>
-    <echo>===============================================================================</echo>
-  </target>
-
-  <!-- ====================================================================== -->
-  <!-- Javadoc target                                                         -->
-  <!-- ====================================================================== -->
-
-  <target name="javadoc" description="Generates the Javadoc of the application">
-    <javadoc sourcepath="${maven.build.srcDir.0}" 
-             packagenames="*" 
-             destdir="${maven.reporting.outputDirectory}/apidocs" 
-             access="protected" 
-             old="false" 
-             verbose="false" 
-             version="true" 
-             use="true" 
-             author="true" 
-             splitindex="false" 
-             nodeprecated="false" 
-             nodeprecatedlist="false" 
-             notree="false" 
-             noindex="false" 
-             nohelp="false" 
-             nonavbar="false" 
-             serialwarn="false" 
-             charset="ISO-8859-1" 
-             linksource="false" 
-             breakiterator="false"/>
-  </target>
-
-  <!-- ====================================================================== -->
-  <!-- Package target                                                         -->
-  <!-- ====================================================================== -->
-
-  <target name="package" depends="compile,test" description="Package the application">
-    <jar jarfile="${maven.build.dir}/${maven.build.finalName}.jar" 
-         compress="true" 
-         index="false" 
-         basedir="${maven.build.outputDir}" 
-         excludes="**/package.html">
-      <manifest>
-      </manifest>
-    </jar>
-  </target>
-
-  <!-- ====================================================================== -->
-  <!-- A dummy target for the package named after the type it creates         -->
-  <!-- ====================================================================== -->
-
-  <target name="jar" depends="package" description="Builds the jar for the application"/>
-
-  <!-- ====================================================================== -->
-  <!-- Download dependencies target                                           -->
-  <!-- ====================================================================== -->
-
-  <target name="test-offline">
-    <condition property="maven.mode.offline">
-      <equals arg1="${maven.settings.offline}" arg2="true"/>
-    </condition>
-  </target>
-
-  <target name="get-deps" 
-          depends="test-offline" 
-          description="Download all dependencies" 
-          unless="maven.mode.offline">
-    <mkdir dir="${maven.repo.local}"/>
-    <mkdir dir="${maven.repo.local}/junit/junit/4.10"/>
-    <get src="http://maven.artenum.com/content/groups/public/junit/junit/4.10/junit-4.10.jar" 
-         dest="${maven.repo.local}/junit/junit/4.10/junit-4.10.jar" 
-         usetimestamp="false" 
-         ignoreerrors="true"/>
-    <get src="http://repo.maven.apache.org/maven2/junit/junit/4.10/junit-4.10.jar" 
-         dest="${maven.repo.local}/junit/junit/4.10/junit-4.10.jar" 
-         usetimestamp="false" 
-         ignoreerrors="true"/>
-    <mkdir dir="${maven.repo.local}/org/hamcrest/hamcrest-core/1.1"/>
-    <get src="http://maven.artenum.com/content/groups/public/org/hamcrest/hamcrest-core/1.1/hamcrest-core-1.1.jar" 
-         dest="${maven.repo.local}/org/hamcrest/hamcrest-core/1.1/hamcrest-core-1.1.jar" 
-         usetimestamp="false" 
-         ignoreerrors="true"/>
-    <get src="http://repo.maven.apache.org/maven2/org/hamcrest/hamcrest-core/1.1/hamcrest-core-1.1.jar" 
-         dest="${maven.repo.local}/org/hamcrest/hamcrest-core/1.1/hamcrest-core-1.1.jar" 
-         usetimestamp="false" 
-         ignoreerrors="true"/>
-  </target>
-
-</project>
diff --git a/dev-java/jrosetta/files/build.xml b/dev-java/jrosetta/files/build.xml
deleted file mode 100644
index c6959deb0..000000000
--- a/dev-java/jrosetta/files/build.xml
+++ /dev/null
@@ -1,74 +0,0 @@
-<?xml version="1.0" encoding="UTF-8"?>
-
-<!-- ====================================================================== -->
-<!-- Ant build file (http://ant.apache.org/) for Ant 1.6.2 or above.        -->
-<!-- ====================================================================== -->
-
-<!-- ====================================================================== -->
-<!-- ===================== - DO NOT EDIT THIS FILE! - ===================== -->
-<!-- ====================================================================== -->
-<!--                                                                        -->
-<!-- Any modifications will be overwritten.                                 -->
-<!--                                                                        -->
-<!-- Generated by Maven Ant Plugin on 4/12/12 2:43 PM                       -->
-<!-- See: http://maven.apache.org/plugins/maven-ant-plugin/                 -->
-<!--                                                                        -->
-<!-- ====================================================================== -->
-
-<project name="jrosetta-from-maven" default="package" basedir=".">
-
-  <!-- ====================================================================== -->
-  <!-- Cleaning up target                                                     -->
-  <!-- ====================================================================== -->
-
-  <target name="clean" description="Clean the output directory">
-    <ant antfile="build.xml" dir="modules/jrosetta-api" target="clean"/>
-    <ant antfile="build.xml" dir="modules/jrosetta-engine" target="clean"/>
-  </target>
-
-  <!-- ====================================================================== -->
-  <!-- Compilation target                                                     -->
-  <!-- ====================================================================== -->
-
-  <target name="compile" description="Compile the code">
-    <ant antfile="build.xml" dir="modules/jrosetta-api" target="compile"/>
-    <ant antfile="build.xml" dir="modules/jrosetta-engine" target="compile"/>
-  </target>
-
-  <!-- ====================================================================== -->
-  <!-- Test-compilation target                                                -->
-  <!-- ====================================================================== -->
-
-  <target name="compile-tests" description="Compile the test code">
-    <ant antfile="build.xml" dir="modules/jrosetta-api" target="compile-tests"/>
-    <ant antfile="build.xml" dir="modules/jrosetta-engine" target="compile-tests"/>
-  </target>
-
-  <!-- ====================================================================== -->
-  <!-- Run all tests                                                          -->
-  <!-- ====================================================================== -->
-
-  <target name="test" description="Run the test cases">
-    <ant antfile="build.xml" dir="modules/jrosetta-api" target="test"/>
-    <ant antfile="build.xml" dir="modules/jrosetta-engine" target="test"/>
-  </target>
-
-  <!-- ====================================================================== -->
-  <!-- Javadoc target                                                         -->
-  <!-- ====================================================================== -->
-
-  <target name="javadoc" description="Generates the Javadoc of the application">
-    <ant antfile="build.xml" dir="modules/jrosetta-api" target="javadoc"/>
-    <ant antfile="build.xml" dir="modules/jrosetta-engine" target="javadoc"/>
-  </target>
-
-  <!-- ====================================================================== -->
-  <!-- Package target                                                         -->
-  <!-- ====================================================================== -->
-
-  <target name="package" description="Package the application">
-    <ant antfile="build.xml" dir="modules/jrosetta-api" target="package"/>
-    <ant antfile="build.xml" dir="modules/jrosetta-engine" target="package"/>
-  </target>
-
-</project>
diff --git a/dev-java/jrosetta/files/engine-build.xml b/dev-java/jrosetta/files/engine-build.xml
deleted file mode 100644
index 9ee8429f4..000000000
--- a/dev-java/jrosetta/files/engine-build.xml
+++ /dev/null
@@ -1,274 +0,0 @@
-<?xml version="1.0" encoding="UTF-8"?>
-
-<!-- ====================================================================== -->
-<!-- Ant build file (http://ant.apache.org/) for Ant 1.6.2 or above.        -->
-<!-- ====================================================================== -->
-
-<!-- ====================================================================== -->
-<!-- ===================== - DO NOT EDIT THIS FILE! - ===================== -->
-<!-- ====================================================================== -->
-<!--                                                                        -->
-<!-- Any modifications will be overwritten.                                 -->
-<!--                                                                        -->
-<!-- Generated by Maven Ant Plugin on 4/12/12 2:43 PM                       -->
-<!-- See: http://maven.apache.org/plugins/maven-ant-plugin/                 -->
-<!--                                                                        -->
-<!-- ====================================================================== -->
-
-<project name="jrosetta-engine-from-maven" default="package" basedir=".">
-
-  <!-- ====================================================================== -->
-  <!-- Build environment properties                                           -->
-  <!-- ====================================================================== -->
-
-  <property file="${user.home}/.m2/maven.properties"/>
-  <property file="maven-build.properties"/>
-
-  <property name="maven.build.finalName" value="jrosetta-engine-1.0.4"/>
-  <property name="maven.build.dir" value="target"/>
-  <property name="maven.build.outputDir" value="${maven.build.dir}/classes"/>
-  <property name="maven.build.srcDir.0" value="src/main/java"/>
-  <property name="maven.build.resourceDir.0" value="src/main/resources"/>
-  <property name="maven.build.testOutputDir" value="${maven.build.dir}/test-classes"/>
-  <property name="maven.build.testDir.0" value="src/test/java"/>
-  <property name="maven.build.testResourceDir.0" value="src/test/resources"/>
-  <property name="maven.test.reports" value="${maven.build.dir}/test-reports"/>
-  <property name="maven.reporting.outputDirectory" value="${maven.build.dir}/site"/>
-
-  <property name="maven.repo.local" value="${user.home}/.m2/repository"/>
-  <property name="maven.settings.offline" value="true"/>
-  <property name="maven.settings.interactiveMode" value="true"/>
-
-  <!-- ====================================================================== -->
-  <!-- Defining classpaths                                                    -->
-  <!-- ====================================================================== -->
-
-  <path id="build.classpath">
-    <pathelement location="../jrosetta-api/target/classes"/>
-  </path>
-  <path id="build.test.classpath">
-    <pathelement location="${maven.repo.local}/com/artenum/jrosetta/jrosetta-api/1.0.4/jrosetta-api-1.0.4.jar"/>
-    <pathelement location="${maven.repo.local}/junit/junit/4.10/junit-4.10.jar"/>
-    <pathelement location="${maven.repo.local}/org/hamcrest/hamcrest-core/1.1/hamcrest-core-1.1.jar"/>
-  </path>
-
-  <!-- ====================================================================== -->
-  <!-- Cleaning up target                                                     -->
-  <!-- ====================================================================== -->
-
-  <target name="clean" description="Clean the output directory">
-    <delete dir="${maven.build.dir}"/>
-  </target>
-
-  <!-- ====================================================================== -->
-  <!-- Compilation target                                                     -->
-  <!-- ====================================================================== -->
-
-  <target name="compile" depends="get-deps" description="Compile the code">
-    <mkdir dir="${maven.build.outputDir}"/>
-    <javac destdir="${maven.build.outputDir}" 
-           nowarn="false" 
-           debug="true" 
-           optimize="false" 
-           deprecation="true" 
-           target="1.6" 
-           verbose="false" 
-           fork="false" 
-           source="1.6">
-      <src>
-        <pathelement location="${maven.build.srcDir.0}"/>
-      </src>
-      <classpath refid="build.classpath"/>
-    </javac>
-    <copy todir="${maven.build.outputDir}">
-      <fileset dir="${maven.build.resourceDir.0}"/>
-    </copy>
-  </target>
-
-  <!-- ====================================================================== -->
-  <!-- Test-compilation target                                                -->
-  <!-- ====================================================================== -->
-
-  <target name="compile-tests" 
-          depends="compile" 
-          description="Compile the test code" 
-          unless="maven.test.skip">
-    <mkdir dir="${maven.build.testOutputDir}"/>
-    <javac destdir="${maven.build.testOutputDir}" 
-           nowarn="false" 
-           debug="true" 
-           optimize="false" 
-           deprecation="true" 
-           target="1.6" 
-           verbose="false" 
-           fork="false" 
-           source="1.6">
-      <src>
-        <pathelement location="${maven.build.testDir.0}"/>
-      </src>
-      <classpath>
-        <path refid="build.test.classpath"/>
-        <pathelement location="${maven.build.outputDir}"/>
-      </classpath>
-    </javac>
-    <copy todir="${maven.build.testOutputDir}">
-      <fileset dir="${maven.build.testResourceDir.0}"/>
-    </copy>
-  </target>
-
-  <!-- ====================================================================== -->
-  <!-- Run all tests                                                          -->
-  <!-- ====================================================================== -->
-
-  <target name="test" 
-          depends="compile-tests, junit-missing" 
-          unless="junit.skipped" 
-          description="Run the test cases">
-    <mkdir dir="${maven.test.reports}"/>
-    <junit printSummary="yes" haltonerror="true" haltonfailure="true" fork="true" dir=".">
-      <sysproperty key="basedir" value="."/>
-      <formatter type="xml"/>
-      <formatter type="plain" usefile="false"/>
-      <classpath>
-        <path refid="build.test.classpath"/>
-        <pathelement location="${maven.build.outputDir}"/>
-        <pathelement location="${maven.build.testOutputDir}"/>
-      </classpath>
-      <batchtest todir="${maven.test.reports}" unless="test">
-        <fileset dir="${maven.build.testDir.0}">
-          <include name="**/Test*.java"/>
-          <include name="**/*Test.java"/>
-          <include name="**/*TestCase.java"/>
-          <exclude name="**/*Abstract*Test.java"/>
-        </fileset>
-      </batchtest>
-      <batchtest todir="${maven.test.reports}" if="test">
-        <fileset dir="${maven.build.testDir.0}">
-          <include name="**/${test}.java"/>
-          <exclude name="**/*Abstract*Test.java"/>
-        </fileset>
-      </batchtest>
-    </junit>
-  </target>
-
-  <target name="test-junit-present">
-    <available classname="junit.framework.Test" property="junit.present"/>
-  </target>
-
-  <target name="test-junit-status" 
-          depends="test-junit-present">
-    <condition property="junit.missing">
-      <and>
-        <isfalse value="${junit.present}"/>
-        <isfalse value="${maven.test.skip}"/>
-      </and>
-    </condition>
-    <condition property="junit.skipped">
-      <or>
-        <isfalse value="${junit.present}"/>
-        <istrue value="${maven.test.skip}"/>
-      </or>
-    </condition>
-  </target>
-
-  <target name="junit-missing" 
-          depends="test-junit-status" 
-          if="junit.missing">
-    <echo>=================================== WARNING ===================================</echo>
-    <echo> JUnit is not present in your $ANT_HOME/lib directory. Tests not executed.</echo>
-    <echo>===============================================================================</echo>
-  </target>
-
-  <!-- ====================================================================== -->
-  <!-- Javadoc target                                                         -->
-  <!-- ====================================================================== -->
-
-  <target name="javadoc" description="Generates the Javadoc of the application">
-    <javadoc sourcepath="${maven.build.srcDir.0}" 
-             packagenames="*" 
-             destdir="${maven.reporting.outputDirectory}/apidocs" 
-             access="protected" 
-             old="false" 
-             verbose="false" 
-             version="true" 
-             use="true" 
-             author="true" 
-             splitindex="false" 
-             nodeprecated="false" 
-             nodeprecatedlist="false" 
-             notree="false" 
-             noindex="false" 
-             nohelp="false" 
-             nonavbar="false" 
-             serialwarn="false" 
-             charset="ISO-8859-1" 
-             linksource="false" 
-             breakiterator="false"/>
-  </target>
-
-  <!-- ====================================================================== -->
-  <!-- Package target                                                         -->
-  <!-- ====================================================================== -->
-
-  <target name="package" depends="compile,test" description="Package the application">
-    <jar jarfile="${maven.build.dir}/${maven.build.finalName}.jar" 
-         compress="true" 
-         index="false" 
-         basedir="${maven.build.outputDir}" 
-         excludes="**/package.html">
-      <manifest>
-      </manifest>
-    </jar>
-  </target>
-
-  <!-- ====================================================================== -->
-  <!-- A dummy target for the package named after the type it creates         -->
-  <!-- ====================================================================== -->
-
-  <target name="jar" depends="package" description="Builds the jar for the application"/>
-
-  <!-- ====================================================================== -->
-  <!-- Download dependencies target                                           -->
-  <!-- ====================================================================== -->
-
-  <target name="test-offline">
-    <condition property="maven.mode.offline">
-      <equals arg1="${maven.settings.offline}" arg2="true"/>
-    </condition>
-  </target>
-
-  <target name="get-deps" 
-          depends="test-offline" 
-          description="Download all dependencies" 
-          unless="maven.mode.offline">
-    <mkdir dir="${maven.repo.local}"/>
-    <mkdir dir="${maven.repo.local}/com/artenum/jrosetta/jrosetta-api/1.0.4"/>
-    <get src="http://maven.artenum.com/content/groups/public/com/artenum/jrosetta/jrosetta-api/1.0.4/jrosetta-api-1.0.4.jar" 
-         dest="${maven.repo.local}/com/artenum/jrosetta/jrosetta-api/1.0.4/jrosetta-api-1.0.4.jar" 
-         usetimestamp="false" 
-         ignoreerrors="true"/>
-    <get src="http://repo.maven.apache.org/maven2/com/artenum/jrosetta/jrosetta-api/1.0.4/jrosetta-api-1.0.4.jar" 
-         dest="${maven.repo.local}/com/artenum/jrosetta/jrosetta-api/1.0.4/jrosetta-api-1.0.4.jar" 
-         usetimestamp="false" 
-         ignoreerrors="true"/>
-    <mkdir dir="${maven.repo.local}/junit/junit/4.10"/>
-    <get src="http://maven.artenum.com/content/groups/public/junit/junit/4.10/junit-4.10.jar" 
-         dest="${maven.repo.local}/junit/junit/4.10/junit-4.10.jar" 
-         usetimestamp="false" 
-         ignoreerrors="true"/>
-    <get src="http://repo.maven.apache.org/maven2/junit/junit/4.10/junit-4.10.jar" 
-         dest="${maven.repo.local}/junit/junit/4.10/junit-4.10.jar" 
-         usetimestamp="false" 
-         ignoreerrors="true"/>
-    <mkdir dir="${maven.repo.local}/org/hamcrest/hamcrest-core/1.1"/>
-    <get src="http://maven.artenum.com/content/groups/public/org/hamcrest/hamcrest-core/1.1/hamcrest-core-1.1.jar" 
-         dest="${maven.repo.local}/org/hamcrest/hamcrest-core/1.1/hamcrest-core-1.1.jar" 
-         usetimestamp="false" 
-         ignoreerrors="true"/>
-    <get src="http://repo.maven.apache.org/maven2/org/hamcrest/hamcrest-core/1.1/hamcrest-core-1.1.jar" 
-         dest="${maven.repo.local}/org/hamcrest/hamcrest-core/1.1/hamcrest-core-1.1.jar" 
-         usetimestamp="false" 
-         ignoreerrors="true"/>
-  </target>
-
-</project>
diff --git a/dev-java/jrosetta/jrosetta-1.0.4.ebuild b/dev-java/jrosetta/jrosetta-1.0.4.ebuild
deleted file mode 100644
index dd8a3535e..000000000
--- a/dev-java/jrosetta/jrosetta-1.0.4.ebuild
+++ /dev/null
@@ -1,39 +0,0 @@
-# Copyright 1999-2015 Gentoo Foundation
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=5
-
-inherit java-pkg-2 java-ant-2
-
-DESCRIPTION="Common base for graphical component to build a graphical console"
-HOMEPAGE="http://dev.artenum.com/projects/jrosetta"
-#currently down
-#SRC_URI="http://maven.artenum.com/content/groups/public/com/artenum/${PN}/${PV}/${P}-sources.jar"
-SRC_URI="http://pkgs.fedoraproject.org/repo/pkgs/${PN}/${P}-sources.jar/5c3589d4207f71bad6eeefd4857bce50/${P}-sources.jar"
-
-LICENSE="GPL-2"
-SLOT="0"
-KEYWORDS="~amd64 ~x86"
-IUSE=""
-
-DEPEND="
-	>=virtual/jdk-1.5:*
-	app-arch/unzip"
-RDEPEND=">=virtual/jre-1.5:*"
-
-EANT_BUILD_TARGET="compile package"
-JAVA_ANT_BSFIX_EXTRA_ARGS="--maven-cleaning"
-
-java_prepare () {
-	cp "${FILESDIR}/api-build.xml" modules/jrosetta-api/build.xml || die
-	cp "${FILESDIR}/engine-build.xml" modules/jrosetta-engine/build.xml || die
-	cp "${FILESDIR}/build.xml" . || die
-	echo "${PV}" > modules/jrosetta-engine/src/main/resources/version.txt || die
-}
-
-src_install () {
-	java-pkg_newjar "modules/jrosetta-api/target/jrosetta-api-${PV}.jar" \
-	jrosetta-api.jar
-	java-pkg_newjar "modules/jrosetta-engine/target/jrosetta-engine-${PV}.jar" \
-	jrosetta-engine.jar
-}
diff --git a/dev-java/netcdf/Manifest b/dev-java/netcdf/Manifest
deleted file mode 100644
index e977c681b..000000000
--- a/dev-java/netcdf/Manifest
+++ /dev/null
@@ -1 +0,0 @@
-DIST ncSrc-4.2.zip 59888846 BLAKE2B 08bd2ce623e081dc2c349ba64109abc39feba86c11dc3a536aaf8f18e31e6ce04983411e59807ce4720abe2c310682a82c30c4d2abd21ede7cbc951ceee7edcb SHA512 1cf22c55a43f53bbb573c6bcbc9e40b0020ed9d576c68a0d54639ca9892393735b25bfa0078fcb763c71d5d875fb1f315c6d580d6a859434d362693f6500d652
diff --git a/dev-java/netcdf/metadata.xml b/dev-java/netcdf/metadata.xml
deleted file mode 100644
index 15eb5729e..000000000
--- a/dev-java/netcdf/metadata.xml
+++ /dev/null
@@ -1,12 +0,0 @@
-<?xml version="1.0" encoding="UTF-8"?>
-<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
-<pkgmetadata>
-	<maintainer type="project">
-		<email>sci@gentoo.org</email>
-		<name>Gentoo Science Project</name>
-	</maintainer>
-	<longdescription lang="en">
-The NetCDF-Java Library is a Java interface to NetCDF files,
-as well as to many other types of scientific data formats.
-</longdescription>
-</pkgmetadata>
diff --git a/dev-java/netcdf/netcdf-4.2.ebuild b/dev-java/netcdf/netcdf-4.2.ebuild
deleted file mode 100644
index 1c9c9c42c..000000000
--- a/dev-java/netcdf/netcdf-4.2.ebuild
+++ /dev/null
@@ -1,74 +0,0 @@
-# Copyright 1999-2018 Gentoo Foundation
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=6
-
-JAVA_PKG_IUSE="doc examples source test"
-inherit eutils java-pkg-2 java-ant-2
-
-DESCRIPTION="Java Common Data Model (CDM) interface to to netCDF files"
-HOMEPAGE="http://www.unidata.ucar.edu/software/netcdf-java/"
-SRC_URI="ftp://ftp.unidata.ucar.edu/pub/${PN}-java/v${PV}/ncSrc-${PV}.zip"
-
-LICENSE="netCDF"
-SLOT="0"
-KEYWORDS="~amd64 ~x86"
-IUSE=""
-
-CDEPEND="
-	dev-java/commons-codec
-	dev-java/commons-httpclient
-	dev-java/commons-logging
-	dev-java/ehcache:*
-	dev-java/jcommon
-	dev-java/jdom:*
-	dev-java/jfreechart
-	dev-java/jgoodies-forms:*
-	dev-java/joda-time
-	dev-java/log4j
-	dev-java/slf4j-api
-	dev-java/protobuf-java"
-
-RDEPEND="${CDEPEND}
-	>=virtual/jre-1.5"
-
-DEPEND="${CDEPEND}
-	>=virtual/jdk-1.5
-	test? (
-		dev-java/ant-junit4
-		dev-java/hamcrest-core
-	)"
-
-# There is a from-source maven package in java-overlay, but it hasn't
-# been merged into the Portage trunk yet.
-
-S="${WORKDIR}"
-
-src_prepare() {
-	java-pkg_jar-from --into lib/external commons-codec commons-codec.jar
-	java-pkg_jar-from --into lib/external commons-httpclient-3  commons-httpclient.jar
-	java-pkg_jar-from --into lib/external commons-logging commons-logging.jar
-	java-pkg_jar-from --into lib/external ehcache-1.2 ehcache.jar
-	java-pkg_jar-from --into lib/external jcommon-1.0 jcommon.jar
-	rm -f lib/external/jdom.jar || die
-	java-pkg_jar-from --into lib/external jdom-1.0 jdom.jar
-	java-pkg_jar-from --into lib/external jfreechart-1.0 jfreechart.jar
-	java-pkg_jar-from --into lib/external jgoodies-forms forms.jar jgoodies-forms.jar
-	java-pkg_jar-from --into lib/external joda-time joda-time.jar
-	java-pkg_jar-from --into lib/external junit-4 junit.jar
-	java-pkg_jar-from --into lib/external log4j log4j.jar
-	java-pkg_jar-from --into lib/external protobuf protobuf.jar
-	java-pkg_jar-from --into lib/external slf4j-api slf4j-api.jar
-}
-
-src_compile() {
-	cd "${S}"/cdm && eant
-	use doc && eant javadoc
-}
-
-src_install() {
-	java-pkg_newjar cdm/target/${P}.jar ${PN}.jar
-	use doc && java-pkg_dojavadoc cdm/target/javadoc
-	use source && java-pkg_dosrc cdm/src/main/java/*
-	use examples && java-pkg_doexamples cdm/src/test/java/examples
-}
diff --git a/dev-java/parsington/Manifest b/dev-java/parsington/Manifest
new file mode 100644
index 000000000..970430d78
--- /dev/null
+++ b/dev-java/parsington/Manifest
@@ -0,0 +1 @@
+DIST parsington-3.1.0-sources.tar.gz 45883 BLAKE2B 39d37c772ba12f845fc6a53762e474f534dbb4920bc7178e885d560550a60c4e3949406d94a604b2b8740b9d337a504783111ccf28d480da10454db55abe853c SHA512 d1596e67b691148838116a02a88b2c520f0887952d254939cec0c77f225601be5f7d19f44c6b310126c7d210c726ec3399d77f8d91d590c377a2cd22814a68a7
diff --git a/dev-java/parsington/metadata.xml b/dev-java/parsington/metadata.xml
new file mode 100644
index 000000000..3c4854834
--- /dev/null
+++ b/dev-java/parsington/metadata.xml
@@ -0,0 +1,14 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
+<pkgmetadata>
+  <longdescription>
+    Parsington is an infix-to-postfix and infix-to-syntax-tree expression parser for mathematical expressions written in Java. It is simple yet fancy, handling (customizable) operators, functions, variables and constants in a similar way to what the Java language itself supports.
+  </longdescription>
+  <maintainer type="project">
+    <email>sci@gentoo.org</email>
+    <name>Gentoo Science Project</name>
+  </maintainer>
+  <upstream>
+    <remote-id type="github">scijava/parsington</remote-id>
+  </upstream>
+</pkgmetadata>
diff --git a/dev-java/parsington/parsington-3.1.0.ebuild b/dev-java/parsington/parsington-3.1.0.ebuild
new file mode 100644
index 000000000..c583c89e9
--- /dev/null
+++ b/dev-java/parsington/parsington-3.1.0.ebuild
@@ -0,0 +1,48 @@
+# Copyright 1999-2023 Gentoo Authors
+# Distributed under the terms of the GNU General Public License v2
+
+EAPI=8
+
+JAVA_PKG_IUSE="doc source test"
+JAVA_TESTING_FRAMEWORKS="junit-jupiter"
+
+inherit java-pkg-2 java-pkg-simple
+
+DESCRIPTION="A mathematical expression parser for infix expression strings"
+HOMEPAGE="https://github.com/scijava/parsington"
+
+if [[ ${PV} == 9999 ]]; then
+	inherit git-r3
+	EGIT_REPO_URI="https://github.com/scijava/parsington.git"
+	S="${WORKDIR}/${P}"
+	MAVEN_ID="org.scijava:parsington:9999"
+else
+	SRC_URI="
+		https://github.com/scijava/${PN}/archive/refs/tags/${P}.tar.gz -> ${P}-sources.tar.gz
+	"
+	S="${WORKDIR}/${PN}-${P}"
+	MAVEN_ID="org.scijava:parsington:3.1.0"
+	KEYWORDS="~amd64"
+fi
+
+LICENSE="BSD-2"
+SLOT="0"
+
+CDEPEND=">=dev-java/junit-5.9.1:5"
+
+BDEPEND="
+	>=virtual/jdk-1.8:*
+	test? (
+	      "${CDEPEND}"
+	)
+"
+
+DEPEND="${CDEPEND}"
+
+RDEPEND=">=virtual/jre-1.8:*"
+
+JAVA_SRC_DIR="src/main/java"
+JAVA_MAIN_CLASS="org.scijava.parsington.Main"
+
+JAVA_TEST_GENTOO_CLASSPATH="junit-5"
+JAVA_TEST_SRC_DIR="src/test/java"
diff --git a/dev-java/parsington/parsington-9999.ebuild b/dev-java/parsington/parsington-9999.ebuild
new file mode 100644
index 000000000..c583c89e9
--- /dev/null
+++ b/dev-java/parsington/parsington-9999.ebuild
@@ -0,0 +1,48 @@
+# Copyright 1999-2023 Gentoo Authors
+# Distributed under the terms of the GNU General Public License v2
+
+EAPI=8
+
+JAVA_PKG_IUSE="doc source test"
+JAVA_TESTING_FRAMEWORKS="junit-jupiter"
+
+inherit java-pkg-2 java-pkg-simple
+
+DESCRIPTION="A mathematical expression parser for infix expression strings"
+HOMEPAGE="https://github.com/scijava/parsington"
+
+if [[ ${PV} == 9999 ]]; then
+	inherit git-r3
+	EGIT_REPO_URI="https://github.com/scijava/parsington.git"
+	S="${WORKDIR}/${P}"
+	MAVEN_ID="org.scijava:parsington:9999"
+else
+	SRC_URI="
+		https://github.com/scijava/${PN}/archive/refs/tags/${P}.tar.gz -> ${P}-sources.tar.gz
+	"
+	S="${WORKDIR}/${PN}-${P}"
+	MAVEN_ID="org.scijava:parsington:3.1.0"
+	KEYWORDS="~amd64"
+fi
+
+LICENSE="BSD-2"
+SLOT="0"
+
+CDEPEND=">=dev-java/junit-5.9.1:5"
+
+BDEPEND="
+	>=virtual/jdk-1.8:*
+	test? (
+	      "${CDEPEND}"
+	)
+"
+
+DEPEND="${CDEPEND}"
+
+RDEPEND=">=virtual/jre-1.8:*"
+
+JAVA_SRC_DIR="src/main/java"
+JAVA_MAIN_CLASS="org.scijava.parsington.Main"
+
+JAVA_TEST_GENTOO_CLASSPATH="junit-5"
+JAVA_TEST_SRC_DIR="src/test/java"
diff --git a/dev-java/scijava-common/Manifest b/dev-java/scijava-common/Manifest
new file mode 100644
index 000000000..51c68561b
--- /dev/null
+++ b/dev-java/scijava-common/Manifest
@@ -0,0 +1 @@
+DIST scijava-common-2.97.1-sources.tar.gz 559336 BLAKE2B 4511202aaa7947a57a8fff6420397c05d5768571045519b9d02aa67a5b3ecefd738418d8412f447678d5133e089fa73bd335543979a58ae55b0e31e53eedc8ae SHA512 cf8e47097f608480c59b24d7487dbf1e138c16a63660aa3b5f5de4c600913e509b64e2d9360f7fdb6e5558a1320fb7d6f09bd3184e5e99da2c5265a91050002b
diff --git a/dev-java/scijava-common/metadata.xml b/dev-java/scijava-common/metadata.xml
new file mode 100644
index 000000000..374f9940a
--- /dev/null
+++ b/dev-java/scijava-common/metadata.xml
@@ -0,0 +1,14 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
+<pkgmetadata>
+  <longdescription>
+    SciJava Common is a common library for SciJava software. It provides a plugin framework, with an extensible mechanism for service discovery, backed by its own annotation processor, so that plugins can be loaded dynamically. It is used by both ImageJ2 and SCIFIO.
+  </longdescription>
+  <maintainer type="project">
+    <email>sci@gentoo.org</email>
+    <name>Gentoo Science Project</name>
+  </maintainer>
+  <upstream>
+    <remote-id type="github">scijava/scijava-common</remote-id>
+  </upstream>
+</pkgmetadata>
diff --git a/dev-java/scijava-common/scijava-common-2.97.1.ebuild b/dev-java/scijava-common/scijava-common-2.97.1.ebuild
new file mode 100644
index 000000000..37a9bca8d
--- /dev/null
+++ b/dev-java/scijava-common/scijava-common-2.97.1.ebuild
@@ -0,0 +1,67 @@
+# Copyright 1999-2023 Gentoo Authors
+# Distributed under the terms of the GNU General Public License v2
+
+EAPI=8
+
+JAVA_PKG_IUSE="doc source test"
+
+JAVA_TESTING_FRAMEWORKS="junit-4"
+
+inherit java-pkg-2 java-pkg-simple
+
+DESCRIPTION="SciJava Common is a shared library for SciJava software."
+HOMEPAGE="
+	https://imagej.net/libs/scijava#scijava-common
+	https://github.com/scijava/scijava-common
+	"
+
+if [[ ${PV} == 9999 ]]; then
+	inherit git-r3
+	EGIT_REPO_URI="https://github.com/scijava/scijava-common.git"
+	S="${WORKDIR}/${P}"
+	MAVEN_ID="org.scijava:scijava-common:9999"
+else
+	SRC_URI="
+		https://github.com/scijava/${PN}/archive/refs/tags/${P}.tar.gz -> ${P}-sources.tar.gz
+	"
+	S="${WORKDIR}/${PN}-${P}"
+	MAVEN_ID="org.scijava:scijava-common:2.97.1"
+	KEYWORDS="~amd64"
+fi
+
+LICENSE="BSD-2"
+SLOT="0"
+
+CDEPEND="
+	dev-java/parsington:0
+	dev-java/jaxws-api:0
+	dev-java/jaxb-api:2
+"
+
+BDEPEND="${CDEPEND}
+	>=virtual/jdk-1.8:*
+"
+
+DEPEND="${CDEPEND}
+	test? (
+		>=dev-java/junit-4.13.2
+		>=dev-java/mockito-4.11.0:4
+	)
+"
+
+RDEPEND="${CDEPEND}
+	>=virtual/jre-1.8:*
+"
+
+JAVA_GENTOO_CLASSPATH="parsington,jaxws-api,jaxb-api-2"
+JAVA_SRC_DIR="src/main/java"
+JAVA_MAIN_CLASS=""
+JAVA_RESOURCE_DIRS=(
+	"src/main/resources"
+)
+
+JAVA_TEST_GENTOO_CLASSPATH="junit-4,mockito-4"
+JAVA_TEST_SRC_DIR="src/test/java"
+JAVA_TEST_RESOURCE_DIRS=(
+	"src/test/resources"
+)
diff --git a/dev-java/scijava-common/scijava-common-9999.ebuild b/dev-java/scijava-common/scijava-common-9999.ebuild
new file mode 100644
index 000000000..37a9bca8d
--- /dev/null
+++ b/dev-java/scijava-common/scijava-common-9999.ebuild
@@ -0,0 +1,67 @@
+# Copyright 1999-2023 Gentoo Authors
+# Distributed under the terms of the GNU General Public License v2
+
+EAPI=8
+
+JAVA_PKG_IUSE="doc source test"
+
+JAVA_TESTING_FRAMEWORKS="junit-4"
+
+inherit java-pkg-2 java-pkg-simple
+
+DESCRIPTION="SciJava Common is a shared library for SciJava software."
+HOMEPAGE="
+	https://imagej.net/libs/scijava#scijava-common
+	https://github.com/scijava/scijava-common
+	"
+
+if [[ ${PV} == 9999 ]]; then
+	inherit git-r3
+	EGIT_REPO_URI="https://github.com/scijava/scijava-common.git"
+	S="${WORKDIR}/${P}"
+	MAVEN_ID="org.scijava:scijava-common:9999"
+else
+	SRC_URI="
+		https://github.com/scijava/${PN}/archive/refs/tags/${P}.tar.gz -> ${P}-sources.tar.gz
+	"
+	S="${WORKDIR}/${PN}-${P}"
+	MAVEN_ID="org.scijava:scijava-common:2.97.1"
+	KEYWORDS="~amd64"
+fi
+
+LICENSE="BSD-2"
+SLOT="0"
+
+CDEPEND="
+	dev-java/parsington:0
+	dev-java/jaxws-api:0
+	dev-java/jaxb-api:2
+"
+
+BDEPEND="${CDEPEND}
+	>=virtual/jdk-1.8:*
+"
+
+DEPEND="${CDEPEND}
+	test? (
+		>=dev-java/junit-4.13.2
+		>=dev-java/mockito-4.11.0:4
+	)
+"
+
+RDEPEND="${CDEPEND}
+	>=virtual/jre-1.8:*
+"
+
+JAVA_GENTOO_CLASSPATH="parsington,jaxws-api,jaxb-api-2"
+JAVA_SRC_DIR="src/main/java"
+JAVA_MAIN_CLASS=""
+JAVA_RESOURCE_DIRS=(
+	"src/main/resources"
+)
+
+JAVA_TEST_GENTOO_CLASSPATH="junit-4,mockito-4"
+JAVA_TEST_SRC_DIR="src/test/java"
+JAVA_TEST_RESOURCE_DIRS=(
+	"src/test/resources"
+)
diff --git a/dev-java/scijava-optional/Manifest b/dev-java/scijava-optional/Manifest
new file mode 100644
index 000000000..eb3283b48
--- /dev/null
+++ b/dev-java/scijava-optional/Manifest
@@ -0,0 +1 @@
+DIST scijava-optional-1.0.1-sources.tar.gz 7659 BLAKE2B c5a99b5ffcd5c8a09cc40d360d31796002993352b581509bbb78d4464f0119313b743bdf94b22532bd5bcc3a8baf614273378031154588245805cc6bccf39de5 SHA512 e083586fb6015354bc7520bed04d4c7c745445e01ffb6ba86bb91505f65ba06dfb50cbcecf3971fcb9161c16a2e112af31e247edffae973bf310e13bded99e89
diff --git a/dev-java/scijava-optional/metadata.xml b/dev-java/scijava-optional/metadata.xml
new file mode 100644
index 000000000..e7e56ccca
--- /dev/null
+++ b/dev-java/scijava-optional/metadata.xml
@@ -0,0 +1,11 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
+<pkgmetadata>
+  <maintainer type="project">
+    <email>sci@gentoo.org</email>
+    <name>Gentoo Science Project</name>
+  </maintainer>
+  <upstream>
+    <remote-id type="github">scijava/scijava-optional</remote-id>
+  </upstream>
+</pkgmetadata>
diff --git a/dev-java/scijava-optional/scijava-optional-1.0.1.ebuild b/dev-java/scijava-optional/scijava-optional-1.0.1.ebuild
new file mode 100644
index 000000000..54010f802
--- /dev/null
+++ b/dev-java/scijava-optional/scijava-optional-1.0.1.ebuild
@@ -0,0 +1,44 @@
+# Copyright 1999-2023 Gentoo Authors
+# Distributed under the terms of the GNU General Public License v2
+
+EAPI=8
+
+JAVA_PKG_IUSE="doc source test"
+JAVA_TESTING_FRAMEWORKS="junit-4"
+
+inherit java-pkg-2 java-pkg-simple
+
+DESCRIPTION="Helpers for emulating named and default arguments"
+HOMEPAGE="https://github.com/scijava/scijava-optional"
+
+if [[ ${PV} == 9999 ]]; then
+	inherit git-r3
+	EGIT_REPO_URI="https://github.com/scijava/scijava-optional.git"
+	S="${WORKDIR}/${P}"
+	MAVEN_ID="org.scijava:scijava-optional:9999"
+else
+	SRC_URI="
+		https://github.com/scijava/${PN}/archive/refs/tags/${P}.tar.gz -> ${P}-sources.tar.gz
+	"
+	S="${WORKDIR}/${PN}-${P}"
+	MAVEN_ID="org.scijava:scijava-optional:1.0.2"
+	KEYWORDS="~amd64"
+fi
+
+LICENSE="BSD-2"
+SLOT="0"
+
+BDEPEND="
+	>=virtual/jdk-1.8:*
+	test? (
+		 >=dev-java/junit-4.13.2:4
+	)
+"
+
+RDEPEND=">=virtual/jre-1.8:*"
+
+JAVA_SRC_DIR="src/main/java"
+JAVA_MAIN_CLASS=""
+
+JAVA_TEST_GENTOO_CLASSPATH="junit-4"
+JAVA_TEST_SRC_DIR="src/test/java"
diff --git a/dev-java/scijava-optional/scijava-optional-9999.ebuild b/dev-java/scijava-optional/scijava-optional-9999.ebuild
new file mode 100644
index 000000000..54010f802
--- /dev/null
+++ b/dev-java/scijava-optional/scijava-optional-9999.ebuild
@@ -0,0 +1,44 @@
+# Copyright 1999-2023 Gentoo Authors
+# Distributed under the terms of the GNU General Public License v2
+
+EAPI=8
+
+JAVA_PKG_IUSE="doc source test"
+JAVA_TESTING_FRAMEWORKS="junit-4"
+
+inherit java-pkg-2 java-pkg-simple
+
+DESCRIPTION="Helpers for emulating named and default arguments"
+HOMEPAGE="https://github.com/scijava/scijava-optional"
+
+if [[ ${PV} == 9999 ]]; then
+	inherit git-r3
+	EGIT_REPO_URI="https://github.com/scijava/scijava-optional.git"
+	S="${WORKDIR}/${P}"
+	MAVEN_ID="org.scijava:scijava-optional:9999"
+else
+	SRC_URI="
+		https://github.com/scijava/${PN}/archive/refs/tags/${P}.tar.gz -> ${P}-sources.tar.gz
+	"
+	S="${WORKDIR}/${PN}-${P}"
+	MAVEN_ID="org.scijava:scijava-optional:1.0.2"
+	KEYWORDS="~amd64"
+fi
+
+LICENSE="BSD-2"
+SLOT="0"
+
+BDEPEND="
+	>=virtual/jdk-1.8:*
+	test? (
+		 >=dev-java/junit-4.13.2:4
+	)
+"
+
+RDEPEND=">=virtual/jre-1.8:*"
+
+JAVA_SRC_DIR="src/main/java"
+JAVA_MAIN_CLASS=""
+
+JAVA_TEST_GENTOO_CLASSPATH="junit-4"
+JAVA_TEST_SRC_DIR="src/test/java"
diff --git a/dev-java/scijava-table/Manifest b/dev-java/scijava-table/Manifest
new file mode 100644
index 000000000..ba3cb11b6
--- /dev/null
+++ b/dev-java/scijava-table/Manifest
@@ -0,0 +1 @@
+DIST scijava-table-1.0.2-sources.tar.gz 37037 BLAKE2B 61a6b2da5cb355e00feb49895ae1a9a978ba50ee75e60c4f74d1490d1c167ca3a19452621ba25afccc975f4fbf3636ae09c0d25019e04980c4247fc18d859951 SHA512 17bbb1f798f7ee718fd2fbd9f9c81419cb5054b40d82cac9fa3b9f882e9ba46b410979038d8031d6f6dea53902f0865e68d59e55e1b02ab717da40aed5726b70
diff --git a/dev-java/scijava-table/metadata.xml b/dev-java/scijava-table/metadata.xml
new file mode 100644
index 000000000..d86e34de2
--- /dev/null
+++ b/dev-java/scijava-table/metadata.xml
@@ -0,0 +1,11 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
+<pkgmetadata>
+  <maintainer type="project">
+    <email>sci@gentoo.org</email>
+    <name>Gentoo Science Project</name>
+  </maintainer>
+  <upstream>
+    <remote-id type="github">scijava/scijava-table</remote-id>
+  </upstream>
+</pkgmetadata>
diff --git a/dev-java/scijava-table/scijava-table-1.0.2.ebuild b/dev-java/scijava-table/scijava-table-1.0.2.ebuild
new file mode 100644
index 000000000..c2e06ac37
--- /dev/null
+++ b/dev-java/scijava-table/scijava-table-1.0.2.ebuild
@@ -0,0 +1,54 @@
+# Copyright 1999-2023 Gentoo Authors
+# Distributed under the terms of the GNU General Public License v2
+
+EAPI=8
+
+JAVA_PKG_IUSE="doc source test"
+JAVA_TESTING_FRAMEWORKS="junit-4"
+
+inherit java-pkg-2 java-pkg-simple
+
+DESCRIPTION="Table structures for SciJava."
+HOMEPAGE="https://github.com/scijava/scijava-table"
+
+if [[ ${PV} == 9999 ]]; then
+	inherit git-r3
+	EGIT_REPO_URI="https://github.com/scijava/scijava-table.git"
+	S="${WORKDIR}/${P}"
+	MAVEN_ID="org.scijava:scijava-table:9999"
+else
+	SRC_URI="
+		https://github.com/scijava/${PN}/archive/refs/tags/${P}.tar.gz -> ${P}-sources.tar.gz
+	"
+	S="${WORKDIR}/${PN}-${P}"
+	MAVEN_ID="org.scijava:scijava-table:1.0.3"
+	KEYWORDS="~amd64"
+fi
+
+LICENSE="BSD-2"
+SLOT="0"
+
+CDEPEND="
+	>=dev-java/scijava-common-2.89.0:0
+	>=dev-java/scijava-optional-1.0.1:0
+"
+
+BDEPEND="
+	>=virtual/jdk-1.8:*
+	${CDEPEND}
+	test? ( >=dev-java/junit-4.13.2:4 )
+"
+
+DEPEND="${CDEPEND}"
+
+RDEPEND="
+	>=virtual/jre-1.8:*
+	${CDEPEND}
+"
+
+JAVA_GENTOO_CLASSPATH="scijava-common,scijava-optional"
+JAVA_SRC_DIR="src/main/java"
+JAVA_MAIN_CLASS=""
+
+JAVA_TEST_GENTOO_CLASSPATH="junit-4"
+JAVA_TEST_SRC_DIR="src/test/java"
diff --git a/dev-java/scijava-table/scijava-table-9999.ebuild b/dev-java/scijava-table/scijava-table-9999.ebuild
new file mode 100644
index 000000000..c2e06ac37
--- /dev/null
+++ b/dev-java/scijava-table/scijava-table-9999.ebuild
@@ -0,0 +1,54 @@
+# Copyright 1999-2023 Gentoo Authors
+# Distributed under the terms of the GNU General Public License v2
+
+EAPI=8
+
+JAVA_PKG_IUSE="doc source test"
+JAVA_TESTING_FRAMEWORKS="junit-4"
+
+inherit java-pkg-2 java-pkg-simple
+
+DESCRIPTION="Table structures for SciJava."
+HOMEPAGE="https://github.com/scijava/scijava-table"
+
+if [[ ${PV} == 9999 ]]; then
+	inherit git-r3
+	EGIT_REPO_URI="https://github.com/scijava/scijava-table.git"
+	S="${WORKDIR}/${P}"
+	MAVEN_ID="org.scijava:scijava-table:9999"
+else
+	SRC_URI="
+		https://github.com/scijava/${PN}/archive/refs/tags/${P}.tar.gz -> ${P}-sources.tar.gz
+	"
+	S="${WORKDIR}/${PN}-${P}"
+	MAVEN_ID="org.scijava:scijava-table:1.0.3"
+	KEYWORDS="~amd64"
+fi
+
+LICENSE="BSD-2"
+SLOT="0"
+
+CDEPEND="
+	>=dev-java/scijava-common-2.89.0:0
+	>=dev-java/scijava-optional-1.0.1:0
+"
+
+BDEPEND="
+	>=virtual/jdk-1.8:*
+	${CDEPEND}
+	test? ( >=dev-java/junit-4.13.2:4 )
+"
+
+DEPEND="${CDEPEND}"
+
+RDEPEND="
+	>=virtual/jre-1.8:*
+	${CDEPEND}
+"
+
+JAVA_GENTOO_CLASSPATH="scijava-common,scijava-optional"
+JAVA_SRC_DIR="src/main/java"
+JAVA_MAIN_CLASS=""
+
+JAVA_TEST_GENTOO_CLASSPATH="junit-4"
+JAVA_TEST_SRC_DIR="src/test/java"
diff --git a/dev-java/scirenderer/Manifest b/dev-java/scirenderer/Manifest
deleted file mode 100644
index c6ba9dcf4..000000000
--- a/dev-java/scirenderer/Manifest
+++ /dev/null
@@ -1 +0,0 @@
-DIST scirenderer-1.1.0.tar.gz 113929 BLAKE2B 2008eebfc751597105808e6bb9c19e15de0a1378a05f25aa5e3c1abb2a0fcf41d38d4d88eab3588d65861fd531b87b0fcc3a542522a520cecac4f644e28c9ff7 SHA512 b2f636b65517fd1c472d2eef4bf141f93b7782b1bcf7961f3b18994659ee9e4a4466ca1c63e8c782acdd7250b2f9a20d0140375a4e2e2108a98af1f696894b95
diff --git a/dev-java/scirenderer/metadata.xml b/dev-java/scirenderer/metadata.xml
deleted file mode 100644
index 18259a6ca..000000000
--- a/dev-java/scirenderer/metadata.xml
+++ /dev/null
@@ -1,11 +0,0 @@
-<?xml version="1.0" encoding="UTF-8"?>
-<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
-<pkgmetadata>
-	<maintainer type="project">
-		<email>sci@gentoo.org</email>
-		<name>Gentoo Science Project</name>
-	</maintainer>
-	<longdescription lang="en">
-A rendering library for scilab based on JoGL
-</longdescription>
-</pkgmetadata>
diff --git a/dev-java/scirenderer/scirenderer-1.1.0.ebuild b/dev-java/scirenderer/scirenderer-1.1.0.ebuild
deleted file mode 100644
index 2b74d581b..000000000
--- a/dev-java/scirenderer/scirenderer-1.1.0.ebuild
+++ /dev/null
@@ -1,39 +0,0 @@
-# Copyright 1999-2014 Gentoo Foundation
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=5
-
-JAVA_PKG_IUSE="doc source"
-
-inherit java-pkg-2 java-ant-2
-
-DESCRIPTION="A rendering library based on JoGL"
-SRC_URI="http://forge.scilab.org/index.php/p/${PN}/downloads/get/${P}.tar.gz"
-HOMEPAGE="http://forge.scilab.org/index.php/p/scirenderer/"
-
-IUSE="doc source"
-DEPEND=">=virtual/jdk-1.5
-	=dev-java/jogl-2.0_rc8-r1:2
-	dev-java/jlatexmath:1"
-RDEPEND=">=virtual/jre-1.5"
-
-LICENSE="GPL-2"
-SLOT="1"
-KEYWORDS="~amd64 ~x86"
-
-EANT_DOC_TARGET="doc"
-
-java_prepare() {
-	sed -i \
-	-e "s|jogl2.jar =.*|jogl2.jar =$(java-pkg_getjar jogl-2 jogl.all.jar)|" \
-	-e "s|gluegen2-rt.jar =.*|gluegen2-rt.jar =$(java-pkg_getjar gluegen-2 \
-	gluegen-rt.jar)|" \
-	-e "s|jlatexmath.jar =.*|jlatexmath.jar = $(java-pkg_getjars jlatexmath-1)|" \
-	scirenderer-libs.properties
-}
-
-src_install() {
-	java-pkg_newjar jar/${P}.jar ${PN}.jar
-	use doc && dodoc -r docs/
-	use source && java-pkg_dosrc src/org
-}
diff --git a/dev-lang/berkeley_upc/Manifest b/dev-lang/berkeley_upc/Manifest
index 41c87a169..c4f8eae36 100644
--- a/dev-lang/berkeley_upc/Manifest
+++ b/dev-lang/berkeley_upc/Manifest
@@ -1,4 +1 @@
-DIST berkeley_upc-2.16.2.tar.gz 6544935 BLAKE2B 89fa205b137ac88f716cfb6fa259c2c614767178a89e4a8becb038ccd0376b44214beea0b595a642c6121b6708f2acb98f6744faddf70d7f56e6ad5a1c12060a SHA512 fa7f7f6a36dd2a0c064daf301813f566fbd59a68c9186c81962384a98a2989c0ed26a816dd8196e388a714ca53dcbb34d27fffbdea33f1a29a70217d64cbe8f4
-DIST berkeley_upc-2.18.0.tar.gz 6175945 BLAKE2B 801b68132a41ed6ef2c1facff756d4491d5c3346db29d22161427ee3842a26897a1529e16013d84c8038e241674bfa552238b66a2fd0490d50d899a5dc4c5e1c SHA512 7d213af5f89fd9fda0a08dd8dabfb363227a138d64944dc95245a3f9a9bd0da5d091d1d0456c0a4d2bce16acdae09eaba7ee7c9be856267a135f7c77c98e2536
-DIST berkeley_upc-2.18.2.tar.gz 6888644 BLAKE2B ceff1f7670844d8f2936af56e39168a5cf5a531d7d272a087e739bef0ab2a60f1690919a772a8fd8611557ff378191f8732802db60aeb461d19782196528d756 SHA512 c7c362745003a1001600247654fe694922f397429ecdff7f798d29d4cb268eef709d03783bf082b0aa161586e0c680919631fae09835760b33b88171c717a47a
-DIST berkeley_upc-2.20.0.tar.gz 6914091 BLAKE2B 2a093af3595475b3b7120df160b08297410e9d48d231e75f5730bac3a45fa8f132ac15a52e930bc086379dda65e74e5ad90f2534767643ae0830a4758c5ef033 SHA512 12e3a2b03b840daaaee90fbd03450517abbd61433c53169610719e7febc50353e682bbe85106b542c3405066d6c643d418ed9e35ed46f0162b47402ea5586b94
+DIST berkeley_upc-2020.12.0.tar.gz 5805676 BLAKE2B ec2d5516e9c407e36484a7a39f66edf0a5c464c47580331caa194fb953c711a522b44c962f1d1cd70a8bd05ecbfd07b310b0617908529e1d59c227e8d2607602 SHA512 49e23d46e8234e5e0b9900f074fe5a495ee904fe7da0836fa2a51f68876cb6ba95b2ef76cb2f78aeb404a6e86d32066c907d7d064dd3886978783de2810ca319
diff --git a/dev-lang/berkeley_upc/berkeley_upc-2.16.2.ebuild b/dev-lang/berkeley_upc/berkeley_upc-2.16.2.ebuild
deleted file mode 100644
index 2dd04b9a9..000000000
--- a/dev-lang/berkeley_upc/berkeley_upc-2.16.2.ebuild
+++ /dev/null
@@ -1,57 +0,0 @@
-# Copyright 1999-2014 Gentoo Foundation
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=5
-
-DESCRIPTION="The Berkeley UPC Runtime/driver"
-HOMEPAGE="http://upc.lbl.gov/"
-SRC_URI="http://upc.lbl.gov/download/release/${P}.tar.gz"
-LICENSE="BSD-4"
-
-SLOT="0"
-KEYWORDS="~amd64 ~x86"
-IUSE="mpi mpi-compat pshm +segment-fast segment-large +single +sptr-packed
-	sptr-struct sptr-symmetric threads +udp"
-
-REQUIRED_USE="
-	^^ ( segment-fast segment-large )
-	^^ ( sptr-packed sptr-struct sptr-symmetric )"
-
-DEPEND="mpi? ( virtual/mpi )
-	mpi-compat? ( virtual/mpi )"
-
-pkg_setup() {
-	elog "There is a lot of options for this package,"
-	elog "especially network conduits settings."
-	elog "You can set them using EXTRA_ECONF variable."
-	elog "To see full list of options visit ${HOMEPAGE}download/dist/INSTALL.TXT"
-}
-
-src_configure() {
-	./configure \
-		--prefix="${EPREFIX}"/usr/libexec/${P} \
-		--mandir="${EPREFIX}"/usr/share/man/ \
-		--disable-aligned-segments \
-		--disable-auto-conduit-detect \
-		$(use_enable mpi) \
-		$(use_enable mpi-compat) \
-		$(use_enable pshm) \
-		$(use_enable segment-fast) \
-		$(use_enable segment-large) \
-		$(use_enable single smp) \
-		$(use_enable sptr-packed) \
-		$(use_enable sptr-struct) \
-		$(use_enable sptr-symmetric) \
-		$(use_enable threads par) \
-		$(use_enable udp) \
-		${EXTRA_ECONF} || die
-}
-
-src_install() {
-	default
-	dodir /usr/bin
-	dosym ../libexec/${P}/bin/upc_trace /usr/bin/upc_trace
-	dosym ../libexec/${P}/bin/upcc /usr/bin/upcc
-	dosym ../libexec/${P}/bin/upcdecl /usr/bin/upcdecl
-	dosym ../libexec/${P}/bin/upcrun /usr/bin/upcrun
-}
diff --git a/dev-lang/berkeley_upc/berkeley_upc-2.18.0.ebuild b/dev-lang/berkeley_upc/berkeley_upc-2.18.0.ebuild
deleted file mode 100644
index 2dd04b9a9..000000000
--- a/dev-lang/berkeley_upc/berkeley_upc-2.18.0.ebuild
+++ /dev/null
@@ -1,57 +0,0 @@
-# Copyright 1999-2014 Gentoo Foundation
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=5
-
-DESCRIPTION="The Berkeley UPC Runtime/driver"
-HOMEPAGE="http://upc.lbl.gov/"
-SRC_URI="http://upc.lbl.gov/download/release/${P}.tar.gz"
-LICENSE="BSD-4"
-
-SLOT="0"
-KEYWORDS="~amd64 ~x86"
-IUSE="mpi mpi-compat pshm +segment-fast segment-large +single +sptr-packed
-	sptr-struct sptr-symmetric threads +udp"
-
-REQUIRED_USE="
-	^^ ( segment-fast segment-large )
-	^^ ( sptr-packed sptr-struct sptr-symmetric )"
-
-DEPEND="mpi? ( virtual/mpi )
-	mpi-compat? ( virtual/mpi )"
-
-pkg_setup() {
-	elog "There is a lot of options for this package,"
-	elog "especially network conduits settings."
-	elog "You can set them using EXTRA_ECONF variable."
-	elog "To see full list of options visit ${HOMEPAGE}download/dist/INSTALL.TXT"
-}
-
-src_configure() {
-	./configure \
-		--prefix="${EPREFIX}"/usr/libexec/${P} \
-		--mandir="${EPREFIX}"/usr/share/man/ \
-		--disable-aligned-segments \
-		--disable-auto-conduit-detect \
-		$(use_enable mpi) \
-		$(use_enable mpi-compat) \
-		$(use_enable pshm) \
-		$(use_enable segment-fast) \
-		$(use_enable segment-large) \
-		$(use_enable single smp) \
-		$(use_enable sptr-packed) \
-		$(use_enable sptr-struct) \
-		$(use_enable sptr-symmetric) \
-		$(use_enable threads par) \
-		$(use_enable udp) \
-		${EXTRA_ECONF} || die
-}
-
-src_install() {
-	default
-	dodir /usr/bin
-	dosym ../libexec/${P}/bin/upc_trace /usr/bin/upc_trace
-	dosym ../libexec/${P}/bin/upcc /usr/bin/upcc
-	dosym ../libexec/${P}/bin/upcdecl /usr/bin/upcdecl
-	dosym ../libexec/${P}/bin/upcrun /usr/bin/upcrun
-}
diff --git a/dev-lang/berkeley_upc/berkeley_upc-2.18.2.ebuild b/dev-lang/berkeley_upc/berkeley_upc-2.18.2.ebuild
deleted file mode 100644
index 2dd04b9a9..000000000
--- a/dev-lang/berkeley_upc/berkeley_upc-2.18.2.ebuild
+++ /dev/null
@@ -1,57 +0,0 @@
-# Copyright 1999-2014 Gentoo Foundation
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=5
-
-DESCRIPTION="The Berkeley UPC Runtime/driver"
-HOMEPAGE="http://upc.lbl.gov/"
-SRC_URI="http://upc.lbl.gov/download/release/${P}.tar.gz"
-LICENSE="BSD-4"
-
-SLOT="0"
-KEYWORDS="~amd64 ~x86"
-IUSE="mpi mpi-compat pshm +segment-fast segment-large +single +sptr-packed
-	sptr-struct sptr-symmetric threads +udp"
-
-REQUIRED_USE="
-	^^ ( segment-fast segment-large )
-	^^ ( sptr-packed sptr-struct sptr-symmetric )"
-
-DEPEND="mpi? ( virtual/mpi )
-	mpi-compat? ( virtual/mpi )"
-
-pkg_setup() {
-	elog "There is a lot of options for this package,"
-	elog "especially network conduits settings."
-	elog "You can set them using EXTRA_ECONF variable."
-	elog "To see full list of options visit ${HOMEPAGE}download/dist/INSTALL.TXT"
-}
-
-src_configure() {
-	./configure \
-		--prefix="${EPREFIX}"/usr/libexec/${P} \
-		--mandir="${EPREFIX}"/usr/share/man/ \
-		--disable-aligned-segments \
-		--disable-auto-conduit-detect \
-		$(use_enable mpi) \
-		$(use_enable mpi-compat) \
-		$(use_enable pshm) \
-		$(use_enable segment-fast) \
-		$(use_enable segment-large) \
-		$(use_enable single smp) \
-		$(use_enable sptr-packed) \
-		$(use_enable sptr-struct) \
-		$(use_enable sptr-symmetric) \
-		$(use_enable threads par) \
-		$(use_enable udp) \
-		${EXTRA_ECONF} || die
-}
-
-src_install() {
-	default
-	dodir /usr/bin
-	dosym ../libexec/${P}/bin/upc_trace /usr/bin/upc_trace
-	dosym ../libexec/${P}/bin/upcc /usr/bin/upcc
-	dosym ../libexec/${P}/bin/upcdecl /usr/bin/upcdecl
-	dosym ../libexec/${P}/bin/upcrun /usr/bin/upcrun
-}
diff --git a/dev-lang/berkeley_upc/berkeley_upc-2.20.0.ebuild b/dev-lang/berkeley_upc/berkeley_upc-2.20.0.ebuild
deleted file mode 100644
index 998e9f327..000000000
--- a/dev-lang/berkeley_upc/berkeley_upc-2.20.0.ebuild
+++ /dev/null
@@ -1,57 +0,0 @@
-# Copyright 1999-2015 Gentoo Foundation
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=5
-
-DESCRIPTION="The Berkeley UPC Runtime/driver"
-HOMEPAGE="http://upc.lbl.gov/"
-SRC_URI="http://upc.lbl.gov/download/release/${P}.tar.gz"
-LICENSE="BSD-4"
-
-SLOT="0"
-KEYWORDS="~amd64 ~x86"
-IUSE="mpi mpi-compat pshm +segment-fast segment-large +single +sptr-packed
-	sptr-struct sptr-symmetric threads +udp"
-
-REQUIRED_USE="
-	^^ ( segment-fast segment-large )
-	^^ ( sptr-packed sptr-struct sptr-symmetric )"
-
-DEPEND="mpi? ( virtual/mpi )
-	mpi-compat? ( virtual/mpi )"
-
-pkg_setup() {
-	elog "There is a lot of options for this package,"
-	elog "especially network conduits settings."
-	elog "You can set them using EXTRA_ECONF variable."
-	elog "To see full list of options visit ${HOMEPAGE}download/dist/INSTALL.TXT"
-}
-
-src_configure() {
-	./configure \
-		--prefix="${EPREFIX}"/usr/libexec/${P} \
-		--mandir="${EPREFIX}"/usr/share/man/ \
-		--disable-aligned-segments \
-		--disable-auto-conduit-detect \
-		$(use_enable mpi) \
-		$(use_enable mpi-compat) \
-		$(use_enable pshm) \
-		$(use_enable segment-fast) \
-		$(use_enable segment-large) \
-		$(use_enable single smp) \
-		$(use_enable sptr-packed) \
-		$(use_enable sptr-struct) \
-		$(use_enable sptr-symmetric) \
-		$(use_enable threads par) \
-		$(use_enable udp) \
-		${EXTRA_ECONF} || die
-}
-
-src_install() {
-	default
-	dodir /usr/bin
-	dosym ../libexec/${P}/bin/upc_trace /usr/bin/upc_trace
-	dosym ../libexec/${P}/bin/upcc /usr/bin/upcc
-	dosym ../libexec/${P}/bin/upcdecl /usr/bin/upcdecl
-	dosym ../libexec/${P}/bin/upcrun /usr/bin/upcrun
-}
diff --git a/dev-lang/berkeley_upc/berkeley_upc-2020.12.0.ebuild b/dev-lang/berkeley_upc/berkeley_upc-2020.12.0.ebuild
new file mode 100644
index 000000000..ef148d422
--- /dev/null
+++ b/dev-lang/berkeley_upc/berkeley_upc-2020.12.0.ebuild
@@ -0,0 +1,60 @@
+# Copyright 1999-2021 Gentoo Authors
+# Distributed under the terms of the GNU General Public License v2
+
+EAPI=7
+
+DESCRIPTION="The Berkeley UPC Runtime/driver"
+HOMEPAGE="https://upc.lbl.gov/"
+SRC_URI="https://upc.lbl.gov/download/release/${P}.tar.gz"
+LICENSE="BSD-4"
+
+SLOT="0"
+KEYWORDS="~amd64 ~x86"
+IUSE="mpi mpi-compat pshm +segment-fast segment-large +single +sptr-packed
+	sptr-struct sptr-symmetric threads +udp"
+
+# Requires network access
+RESTRICT="test"
+
+REQUIRED_USE="
+	^^ ( segment-fast segment-large )
+	^^ ( sptr-packed sptr-struct sptr-symmetric )"
+
+DEPEND="mpi? ( virtual/mpi )
+	mpi-compat? ( virtual/mpi )"
+
+pkg_setup() {
+	elog "There is a lot of options for this package,"
+	elog "especially network conduits settings."
+	elog "You can set them using EXTRA_ECONF variable."
+	elog "To see full list of options visit ${HOMEPAGE}download/dist/INSTALL.TXT"
+}
+
+src_configure() {
+	./configure \
+		--prefix="${EPREFIX}"/usr/libexec/${P} \
+		--mandir="${EPREFIX}"/usr/share/man/ \
+		--disable-aligned-segments \
+		--disable-auto-conduit-detect \
+		$(use_enable mpi) \
+		$(use_enable mpi-compat) \
+		$(use_enable pshm) \
+		$(use_enable segment-fast) \
+		$(use_enable segment-large) \
+		$(use_enable single smp) \
+		$(use_enable sptr-packed) \
+		$(use_enable sptr-struct) \
+		$(use_enable sptr-symmetric) \
+		$(use_enable threads par) \
+		$(use_enable udp) \
+		${EXTRA_ECONF} || die
+}
+
+src_install() {
+	default
+	dodir /usr/bin
+	dosym ../libexec/${P}/bin/upc_trace /usr/bin/upc_trace
+	dosym ../libexec/${P}/bin/upcc /usr/bin/upcc
+	dosym ../libexec/${P}/bin/upcdecl /usr/bin/upcdecl
+	dosym ../libexec/${P}/bin/upcrun /usr/bin/upcrun
+}
diff --git a/dev-lang/berkeley_upc_translator/Manifest b/dev-lang/berkeley_upc_translator/Manifest
index f0f254023..0c77a8558 100644
--- a/dev-lang/berkeley_upc_translator/Manifest
+++ b/dev-lang/berkeley_upc_translator/Manifest
@@ -1,3 +1 @@
-DIST berkeley_upc_translator-2.16.2.tar.gz 7257272 BLAKE2B 51fdb47ba3b5d7d203dc1cc0f52df80efff468e04445fe10bb70d7671861f0e3ae3a1ca5e94929ded6b543e59cf0a0cafdbf31913cf3ccf52c6ee159917ef0a5 SHA512 e7bef6697f434d8ed0d7492d1bfc222884ba46aa96f6981949e505e0407feff738bebbbcc00cb74e0690b3b0a91700c6e530aff362d9085023e7cc2e163bb4ba
-DIST berkeley_upc_translator-2.18.0.tar.gz 7257554 BLAKE2B d234361bd5a203d8a42b6d7f8139f43c0463f153a1a619b1f50a47c7b97a37c7dfa2414488cc211c0548e98f1576599d5bb0d724fa567921ca2f40774f18defb SHA512 b9f679a1aae528e22854ddf61b84d76151d25cbafb44ba743cf01e7337f28de1a91010bbd3e3c574cfed9fa5445f2f03b1be8f0b2c59db637190afe1dacc8178
-DIST berkeley_upc_translator-2.18.2.tar.gz 7259552 BLAKE2B 3f20f21eb19be2bc5850c26d146ee3bd34c62d4b598833eeda16d0f4e7ebef17484b56bbbf004e5170afc1e9ef9b4e3bbb929254a90820a646576d95bf00530d SHA512 ec2f306c2690a5e28747b4dfe2f360e89e539e1d7d645a218bff16f6ea5de1965e52891ab5aba4c9da591ea378466c618a2c9917de93a99980285f8bc0df589d
+DIST berkeley_upc_translator-2.28.2.tar.gz 7285825 BLAKE2B 2ec1bdd2dbab604abe52e04dbec9d56a387c3111d0f8d7edd4dd46d651eb8212eeb6fdf671318988f815a1feaeb5e69d03cd5ed07c9c9af12c5622f804ee4ea1 SHA512 b68bdc5185a3559fc27c85cace0c2aa879d9824ec4bbc86509bfa59f12cfc95feb168cdba8bab982819357c1f221e439e0ac909736e87625f2ae1fd57f039692
diff --git a/dev-lang/berkeley_upc_translator/berkeley_upc_translator-2.16.2.ebuild b/dev-lang/berkeley_upc_translator/berkeley_upc_translator-2.16.2.ebuild
deleted file mode 100644
index c625e8a3c..000000000
--- a/dev-lang/berkeley_upc_translator/berkeley_upc_translator-2.16.2.ebuild
+++ /dev/null
@@ -1,30 +0,0 @@
-# Copyright 1999-2014 Gentoo Foundation
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=5
-
-inherit eutils
-
-DESCRIPTION="The Berkeley UPC-to-C translator"
-HOMEPAGE="http://upc.lbl.gov/"
-SRC_URI="http://upc.lbl.gov/download/release/${P}.tar.gz"
-LICENSE="BSD-4"
-
-SLOT="0"
-KEYWORDS="~amd64 ~x86"
-IUSE=""
-
-DEPEND="app-shells/tcsh"
-RDEPEND="dev-lang/berkeley_upc"
-
-src_prepare() {
-	epatch "$FILESDIR/${P}-check-abi.patch"
-}
-
-src_compile() {
-	emake -j1
-}
-
-src_install() {
-	emake install PREFIX="${D}/usr/libexec/${P}"
-}
diff --git a/dev-lang/berkeley_upc_translator/berkeley_upc_translator-2.18.0.ebuild b/dev-lang/berkeley_upc_translator/berkeley_upc_translator-2.18.0.ebuild
deleted file mode 100644
index 35166f22c..000000000
--- a/dev-lang/berkeley_upc_translator/berkeley_upc_translator-2.18.0.ebuild
+++ /dev/null
@@ -1,30 +0,0 @@
-# Copyright 1999-2014 Gentoo Foundation
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=5
-
-inherit eutils
-
-DESCRIPTION="The Berkeley UPC-to-C translator"
-HOMEPAGE="http://upc.lbl.gov/"
-SRC_URI="http://upc.lbl.gov/download/release/${P}.tar.gz"
-LICENSE="BSD-4"
-
-SLOT="0"
-KEYWORDS="~amd64 ~x86"
-IUSE=""
-
-DEPEND="app-shells/tcsh"
-RDEPEND="dev-lang/berkeley_upc"
-
-src_prepare() {
-	epatch "$FILESDIR/${PN}-2.16.2-check-abi.patch"
-}
-
-src_compile() {
-	emake -j1
-}
-
-src_install() {
-	emake install PREFIX="${D}/usr/libexec/${P}"
-}
diff --git a/dev-lang/berkeley_upc_translator/berkeley_upc_translator-2.18.2.ebuild b/dev-lang/berkeley_upc_translator/berkeley_upc_translator-2.18.2.ebuild
deleted file mode 100644
index 35166f22c..000000000
--- a/dev-lang/berkeley_upc_translator/berkeley_upc_translator-2.18.2.ebuild
+++ /dev/null
@@ -1,30 +0,0 @@
-# Copyright 1999-2014 Gentoo Foundation
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=5
-
-inherit eutils
-
-DESCRIPTION="The Berkeley UPC-to-C translator"
-HOMEPAGE="http://upc.lbl.gov/"
-SRC_URI="http://upc.lbl.gov/download/release/${P}.tar.gz"
-LICENSE="BSD-4"
-
-SLOT="0"
-KEYWORDS="~amd64 ~x86"
-IUSE=""
-
-DEPEND="app-shells/tcsh"
-RDEPEND="dev-lang/berkeley_upc"
-
-src_prepare() {
-	epatch "$FILESDIR/${PN}-2.16.2-check-abi.patch"
-}
-
-src_compile() {
-	emake -j1
-}
-
-src_install() {
-	emake install PREFIX="${D}/usr/libexec/${P}"
-}
diff --git a/dev-lang/berkeley_upc_translator/berkeley_upc_translator-2.28.2.ebuild b/dev-lang/berkeley_upc_translator/berkeley_upc_translator-2.28.2.ebuild
new file mode 100644
index 000000000..135ac7393
--- /dev/null
+++ b/dev-lang/berkeley_upc_translator/berkeley_upc_translator-2.28.2.ebuild
@@ -0,0 +1,49 @@
+# Copyright 1999-2021 Gentoo Authors
+# Distributed under the terms of the GNU General Public License v2
+
+EAPI=7
+
+inherit toolchain-funcs
+
+DESCRIPTION="The Berkeley UPC-to-C translator"
+HOMEPAGE="https://upc.lbl.gov/"
+SRC_URI="https://upc.lbl.gov/download/release/${P}.tar.gz"
+
+LICENSE="BSD-4"
+SLOT="0"
+KEYWORDS="~amd64"
+
+BDEPEND="
+	app-shells/tcsh
+	sys-devel/bison
+"
+
+PATCHES=( "${FILESDIR}"/${PN}-2.28.0-makefile.patch )
+
+src_prepare() {
+	default
+
+	# makefiles unset CFLAGS and CXXFLAGS
+	export CXX="$(tc-getCXX) -std=gnu++98 "
+	tc-export CC
+
+	export  BUPC_ABI="${BUPC_ABI:-LP64}" \
+		BUPC_BUILDDIR="${BUPC_BUILDDIR:-build_ia64}"
+}
+
+src_configure() {
+	# their configure is broken
+	# patch should be enough to counter most
+	return
+}
+
+src_compile() {
+	ABI="${BUPC_ABI}" BUILDDIR="${BUPC_BUILDDIR}" \
+	emake -j1 all
+}
+
+src_install() {
+	ABI="${BUPC_ABI}" BUILDDIR="${BUPC_BUILDDIR}" \
+	PREFIX="${ED}/usr/libexec/${P}/" \
+	emake -j1 install
+}
diff --git a/dev-lang/berkeley_upc_translator/files/berkeley_upc_translator-2.16.2-check-abi.patch b/dev-lang/berkeley_upc_translator/files/berkeley_upc_translator-2.16.2-check-abi.patch
deleted file mode 100644
index ba3f8d449..000000000
--- a/dev-lang/berkeley_upc_translator/files/berkeley_upc_translator-2.16.2-check-abi.patch
+++ /dev/null
@@ -1,10 +0,0 @@
---- config-aux/config-builddir
-+++ config-aux/config-builddir
-@@ -1,5 +1,7 @@
- #!/bin/sh
- 
-+unset ABI
-+
- MYDIR=`dirname $0`
- GUESS="$MYDIR/config.guess"
- if test ! -x "$GUESS" ; then
diff --git a/dev-lang/berkeley_upc_translator/files/berkeley_upc_translator-2.28.0-makefile.patch b/dev-lang/berkeley_upc_translator/files/berkeley_upc_translator-2.28.0-makefile.patch
new file mode 100644
index 000000000..19242753f
--- /dev/null
+++ b/dev-lang/berkeley_upc_translator/files/berkeley_upc_translator-2.28.0-makefile.patch
@@ -0,0 +1,70 @@
+diff --git a/Makefile b/Makefile
+index 551228d..b494da7 100644
+--- a/Makefile
++++ b/Makefile
+@@ -1,51 +1,27 @@
+-# C and C++ compilers to use for building the translator
+-CC = gcc
+-CXX = g++
+-
+-# Default location for installation
+-PREFIX = /usr/local/bupc_translator
+-
+-# override default build directory (empty for auto-detect)
+-BUILDDIR=
+-
+ # override if your version of copy doesn't like these flags
+ CPYDIR = cp -R -p
+ 
+ # override if your filesystem has course-grained utimes
+ TOUCHDELAY = 2
+ 
+-# include overrides from configure, if any
+--include Makefile.local
+-
+ #-------------------------------------------------------
+ # You should not need to modify anything below this line
+ 
+ all clean install update-nodist-list:
+-	@echo "------------------------------------------------------------" ; \
+-	if test "$(BUILDDIR)" ; then			\
+-	  echo "WARNING: forcing BUILDDIR=$(BUILDDIR)"; \
+-	  builddir="$(BUILDDIR)" ;			\
+-	else						\
+-	  CC="$(CC)"; export CC;			\
+-	  CXX="$(CXX)"; export CXX;			\
+-	  builddir=`config-aux/config-builddir` ;	\
+-	fi ; 						\
+-	if test "$$builddir" ; then			\
+-	  echo "Making $@ in BUILDDIR=$$builddir" ;	\
+-	  echo " $(CC) is: `$(CC) --version 2>&1 | head -1`" ; \
+-	  echo " $(CXX) is: `$(CXX) --version 2>&1 | head -1`" ; \
+-	  echo " $(MAKE) is: `$(MAKE) --version 2>&1 | head -1`" ; \
+-	  echo "------------------------------------------------------------" ; \
+-	  if test "$$builddir" = "targ_ilp32_osx" -o "$$builddir" = "targ_lp64_osx"; then   \
+-	    strip=NOSTRIP=1 ; export strip ;            \
+-	  fi ;                                          \
+-	  if test -n "$${CFLAGS+set}"; then             \
+-	    echo "WARNING: unsetting CFLAGS" ;          \
+-	    unset CFLAGS ;                              \
+-	  fi ;                                          \
+-	  $(MAKE) BUILDDIR="$$builddir" $$strip $@-internal ;	\
+-	else						\
+-	  exit 1;					\
++	@echo "------------------------------------------------------------" ;	\
++	if test -d "open64/osprey1.0/$(BUILDDIR)" ; then			\
++	  echo "Making $@ in BUILDDIR=$(BUILDDIR)" ;				\
++	  echo " $(CC) is: `$(CC) --version 2>&1 | head -1`" ; 			\
++	  echo " $(CXX) is: `$(CXX) --version 2>&1 | head -1`" ; 		\
++	  echo " $(MAKE) is: `$(MAKE) --version 2>&1 | head -1`" ; 		\
++	  echo "------------------------------------------------------------" ;	\
++	  if test -n "$${CFLAGS+set}"; then					\
++	    echo "WARNING: unsetting CFLAGS" ;					\
++	    unset CFLAGS ;							\
++	  fi ;									\
++	  $(MAKE) BUILDDIR="$(BUILDDIR)" NOSTRIP=1 $@-internal ;		\
++	else									\
++	  exit 1;								\
+ 	fi
+ 
+ all-internal:
diff --git a/dev-lang/berkeley_upc_translator/metadata.xml b/dev-lang/berkeley_upc_translator/metadata.xml
index c8c5e0f03..e97c4322a 100644
--- a/dev-lang/berkeley_upc_translator/metadata.xml
+++ b/dev-lang/berkeley_upc_translator/metadata.xml
@@ -2,7 +2,11 @@
 <!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
 <pkgmetadata>
 	<maintainer type="person">
-		<email>jauhien@gentoo.org</email>
-		<name>Jauhien Piatlicki</name>
+		<email>gentoo@aisha.cc</email>
+		<name>Aisha Tammy</name>
+	</maintainer>
+	<maintainer type="project">
+		<email>sci@gentoo.org</email>
+		<name>Gentoo Science Project</name>
 	</maintainer>
 </pkgmetadata>
diff --git a/dev-lang/conceptual/Manifest b/dev-lang/conceptual/Manifest
deleted file mode 100644
index bb322e2f7..000000000
--- a/dev-lang/conceptual/Manifest
+++ /dev/null
@@ -1 +0,0 @@
-DIST conceptual-1.4.tar.gz 4449879 BLAKE2B 44ab17c66e1d03c842f7526744b8674abad9ba674b2300ee35bf08114307ef12c655d129163a5af66ae6b55bf6dddacccab7d31bc104c2afc8ae12932bb59456 SHA512 a74226ae1d8aaa5ae23585bfa4fa918a5c05bec6bf0fbf388212dd622b0126d9970fe586d79b63820cc3b25e07d5fef7a9d5bd1604e9b3f4eacad45313242931
diff --git a/dev-lang/conceptual/conceptual-1.4.ebuild b/dev-lang/conceptual/conceptual-1.4.ebuild
deleted file mode 100644
index 58da5001f..000000000
--- a/dev-lang/conceptual/conceptual-1.4.ebuild
+++ /dev/null
@@ -1,39 +0,0 @@
-# Copyright 1999-2017 Gentoo Foundation
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=6
-
-PYTHON_COMPAT=( python2_7 )
-JAVA_PKG_OPT_USE="gui"
-
-inherit java-pkg-opt-2 python-single-r1
-
-DESCRIPTION="A Network Correctness and Performance Testing Language"
-HOMEPAGE="http://conceptual.sourceforge.net/"
-SRC_URI="mirror://sourceforge/${PN}/${P}.tar.gz"
-
-SLOT="0"
-LICENSE="BSD-2"
-IUSE="gui test"
-KEYWORDS="~amd64"
-
-REQUIRED_USE="${PYTHON_REQUIRED_USE}"
-
-RDEPEND="
-	virtual/mpi
-	${PYTHON_DEPS}
-	gui? ( virtual/jdk:* )"
-DEPEND="${RDEPEND}"
-
-src_compile() {
-	default
-	use gui && emake gui
-}
-
-src_install () {
-	default
-	if use gui; then
-		java-pkg_newjar gui/ncptlGUI-1.4.jar ${PN}.jar
-		java-pkg_dolauncher
-	fi
-}
diff --git a/dev-lang/conceptual/metadata.xml b/dev-lang/conceptual/metadata.xml
deleted file mode 100644
index c73b3a9fa..000000000
--- a/dev-lang/conceptual/metadata.xml
+++ /dev/null
@@ -1,14 +0,0 @@
-<?xml version="1.0" encoding="UTF-8"?>
-<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
-<pkgmetadata>
-	<maintainer type="person">
-		<email>ottxor@gentoo.org</email>
-		<name>Christoph Junghans</name>
-	</maintainer>
-	<use>
-		<flag name="gui">Build the Java base graphical interface</flag>
-	</use>
-	<upstream>
-		<remote-id type="sourceforge">conceptual</remote-id>
-	</upstream>
-</pkgmetadata>
diff --git a/dev-lang/icc/Manifest b/dev-lang/icc/Manifest
deleted file mode 100644
index ac43ecaf8..000000000
--- a/dev-lang/icc/Manifest
+++ /dev/null
@@ -1 +0,0 @@
-DIST parallel_studio_xe_2018_update2_professional_edition.tgz 3877755304 BLAKE2B c8852df23abf080f482002a37af7781b3fbae3ecec448914ea5a237fa2b925073d1a3dc2dd94ba64002ff0f6c7e9b18b25fa7ada811a83b10344eb9b92cb37ff SHA512 a9b644b0305d83a9d0daa14d146cb3ce79949db55a410afe48d62259414e6256d9ef533a04bb50807103511db2016c4abcbbf769146854a25638f402a6d0f2be
diff --git a/dev-lang/icc/icc-18.0.2.199-r1.ebuild b/dev-lang/icc/icc-18.0.2.199-r1.ebuild
deleted file mode 100644
index 7faa9de54..000000000
--- a/dev-lang/icc/icc-18.0.2.199-r1.ebuild
+++ /dev/null
@@ -1,41 +0,0 @@
-# Copyright 1999-2018 Gentoo Foundation
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=6
-
-INTEL_DIST_SKU=3235
-INTEL_DIST_PV=2018_update2_professional_edition
-
-inherit intel-sdp-r1
-
-DESCRIPTION="Intel C/C++ Compiler"
-HOMEPAGE="http://software.intel.com/en-us/articles/intel-composer-xe/"
-
-IUSE="doc"
-KEYWORDS="-* ~amd64 ~x86 ~amd64-linux ~x86-linux"
-
-# avoid file collision with ifc #476330
-RDEPEND="~dev-libs/intel-common-${PV}[compiler]"
-
-CHECKREQS_DISK_BUILD=500M
-
-INTEL_DIST_DAT_RPMS=(
-	"icc-common-18.0.2-199-18.0.2-199.noarch.rpm"
-	"icc-common-ps-18.0.2-199-18.0.2-199.noarch.rpm"
-	"icc-common-ps-ss-bec-18.0.2-199-18.0.2-199.noarch.rpm")
-INTEL_DIST_AMD64_RPMS=(
-	"icc-18.0.2-199-18.0.2-199.x86_64.rpm"
-	"icc-ps-18.0.2-199-18.0.2-199.x86_64.rpm"
-	"icc-ps-ss-18.0.2-199-18.0.2-199.x86_64.rpm"
-	"icc-ps-ss-bec-18.0.2-199-18.0.2-199.x86_64.rpm")
-INTEL_DIST_X86_RPMS=(
-	"icc-32bit-18.0.2-199-18.0.2-199.x86_64.rpm"
-	"icc-ps-ss-bec-32bit-18.0.2-199-18.0.2-199.x86_64.rpm")
-
-pkg_setup() {
-	if use doc; then
-		INTEL_DIST_DAT_RPMS+=(
-			"icc-doc-18.0-18.0.2-199.noarch.rpm"
-			"icc-doc-ps-18.0-18.0.2-199.noarch.rpm")
-	fi
-}
diff --git a/dev-lang/icc/metadata.xml b/dev-lang/icc/metadata.xml
deleted file mode 100644
index 7c4d1a96d..000000000
--- a/dev-lang/icc/metadata.xml
+++ /dev/null
@@ -1,16 +0,0 @@
-<?xml version="1.0" encoding="UTF-8"?>
-<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
-<pkgmetadata>
-	<maintainer type="project">
-		<email>sci@gentoo.org</email>
-		<name>Gentoo Science Project</name>
-	</maintainer>
-	<longdescription lang="en">
-The Intel® C++ Compiler is a full featured C/C++ compiler for Intel
-based architectures. The compiler supports multi-threading, automatic
-processor dispatch, vectorization, auto-parallelization, OpenMP, data
-prefetching, loop unrolling. The package comes with extensive
-documentation. The product can be installed as a non-commercial as
-well. License, terms of qualifications can be found on the web site.
-</longdescription>
-</pkgmetadata>
diff --git a/dev-lang/ifc/Manifest b/dev-lang/ifc/Manifest
deleted file mode 100644
index ac43ecaf8..000000000
--- a/dev-lang/ifc/Manifest
+++ /dev/null
@@ -1 +0,0 @@
-DIST parallel_studio_xe_2018_update2_professional_edition.tgz 3877755304 BLAKE2B c8852df23abf080f482002a37af7781b3fbae3ecec448914ea5a237fa2b925073d1a3dc2dd94ba64002ff0f6c7e9b18b25fa7ada811a83b10344eb9b92cb37ff SHA512 a9b644b0305d83a9d0daa14d146cb3ce79949db55a410afe48d62259414e6256d9ef533a04bb50807103511db2016c4abcbbf769146854a25638f402a6d0f2be
diff --git a/dev-lang/ifc/ifc-18.0.2.199-r1.ebuild b/dev-lang/ifc/ifc-18.0.2.199-r1.ebuild
deleted file mode 100644
index ce2b3c16d..000000000
--- a/dev-lang/ifc/ifc-18.0.2.199-r1.ebuild
+++ /dev/null
@@ -1,40 +0,0 @@
-# Copyright 1999-2018 Gentoo Foundation
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=6
-
-INTEL_DIST_SKU=3235
-INTEL_DIST_PV=2018_update2_professional_edition
-
-inherit intel-sdp-r1
-
-DESCRIPTION="Intel FORTRAN Compiler"
-HOMEPAGE="http://software.intel.com/en-us/articles/intel-composer-xe/"
-
-IUSE="doc"
-KEYWORDS="-* ~amd64 ~x86 ~amd64-linux ~x86-linux"
-
-RDEPEND="~dev-libs/intel-common-${PV}[compiler]"
-
-CHECKREQS_DISK_BUILD=400M
-
-INTEL_DIST_DAT_RPMS=( "ifort-common-18.0.2-199-18.0.2-199.noarch.rpm" )
-INTEL_DIST_X86_RPMS=( "ifort-32bit-18.0.2-199-18.0.2-199.x86_64.rpm" )
-INTEL_DIST_AMD64_RPMS=( "ifort-18.0.2-199-18.0.2-199.x86_64.rpm" )
-
-pkg_setup() {
-	if use doc; then
-		INTEL_DIST_DAT_RPMS+=( "ifort-doc-18.0-18.0.2-199.noarch.rpm" )
-	fi
-}
-
-src_install() {
-	# already provided in dev-libs/intel-common
-	rm \
-		"${WORKDIR}"/opt/intel/compilers_and_libraries_2018.2.199/linux/compiler/include/omp_lib.f90 \
-		"${WORKDIR}"/opt/intel/compilers_and_libraries_2018.2.199/linux/compiler/include/intel64/omp_lib.mod \
-		"${WORKDIR}"/opt/intel/compilers_and_libraries_2018.2.199/linux/compiler/include/intel64/omp_lib_kinds.mod \
-		|| die "rm failed"
-
-	intel-sdp-r1_src_install
-}
diff --git a/dev-lang/ifc/metadata.xml b/dev-lang/ifc/metadata.xml
deleted file mode 100644
index 0cc12d890..000000000
--- a/dev-lang/ifc/metadata.xml
+++ /dev/null
@@ -1,17 +0,0 @@
-<?xml version="1.0" encoding="UTF-8"?>
-<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
-<pkgmetadata>
-	<maintainer type="project">
-		<email>sci@gentoo.org</email>
-		<name>Gentoo Science Project</name>
-	</maintainer>
-	<longdescription lang="en">
-The Intel® Fortran Compiler is a full featured FORTRAN 77/95 and
-substantial FORTRAN 2003 compiler for Intel based architectures. The
-compiler supports multi-threading with automatic processor dispatch,
-vectorization, auto-parallelization, OpenMP, data prefetching, loop
-unrolling. The package comes with extensive documentation.
-The product can be installed as a non-commercial as well. License,
-terms of qualifications can be found on the web site.
-</longdescription>
-</pkgmetadata>
diff --git a/dev-lang/path64/metadata.xml b/dev-lang/path64/metadata.xml
deleted file mode 100644
index b0cec0934..000000000
--- a/dev-lang/path64/metadata.xml
+++ /dev/null
@@ -1,20 +0,0 @@
-<?xml version="1.0" encoding="UTF-8"?>
-<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
-<pkgmetadata>
-	<maintainer type="person">
-		<email>xarthisius@gentoo.org</email>
-		<name>Kacper Kowalik</name>
-	</maintainer>
-	<longdescription>
-The PathScale EKOPath Compiler Suite offers programmers a rich set of tools and 
-one of the world's most sophisticated optimization infrastructures to maximize 
-program performance on any Intel 64 or AMD64 platform supporting Intel MMX, 
-SSE, SSE2, SSE3, SSSE3, SSE4.1, SSE4.2, AMD SSE4A and AVX.
-</longdescription>
-	<use>
-		<flag name="debugger">Build PathDB debugger</flag>
-		<flag name="assembler">Build PathAS assembler</flag>
-		<flag name="native">Use EKOPath/Path64 for bootstraping</flag>
-		<flag name="valgrind">Support compiler debugging with <pkg>dev-util/valgrind</pkg></flag>
-	</use>
-</pkgmetadata>
diff --git a/dev-lang/path64/path64-9999.ebuild b/dev-lang/path64/path64-9999.ebuild
deleted file mode 100644
index bad943c74..000000000
--- a/dev-lang/path64/path64-9999.ebuild
+++ /dev/null
@@ -1,111 +0,0 @@
-# Copyright 1999-2017 Gentoo Foundation
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=6
-
-inherit cmake-utils git-r3 toolchain-funcs
-
-DESCRIPTION="Path64 Compiler Suite Community Edition"
-HOMEPAGE="http://www.pathscale.com/ekopath-compiler-suite"
-SRC_URI=""
-EGIT_REPO_URI="git://github.com/pathscale/${PN}-suite.git"
-PATH64_URI="compiler assembler"
-PATHSCALE_URI="compiler-rt libcxxrt libdwarf-bsd libunwind stdcxx"
-DBG_URI="git://github.com/path64/debugger.git"
-
-LICENSE="GPL-3"
-SLOT="0"
-KEYWORDS=""
-IUSE="assembler custom-cflags debugger fortran +native +openmp valgrind"
-
-DEPEND="
-	!native? ( sys-devel/gcc:*[vanilla] )
-	native? ( || ( dev-lang/ekopath:* dev-lang/path64 ) )
-	valgrind? ( dev-util/valgrind )"
-RDEPEND="${DEPEND}"
-
-CMAKE_VERBOSE=1
-
-pkg_setup() {
-	if use custom-cflags ; then
-		ewarn "You are trying to build ${PN} with custom-cflags"
-		ewarn "There is a high chance that you will utterly fail!"
-		ewarn "Unless you know what you are doing you'd better stop now"
-		ewarn "Should you decide to proceed, you are on your own..."
-	fi
-}
-
-src_unpack() {
-	git-r3_src_unpack
-	cd "${S}" || die
-	mkdir compiler || die
-	for f in ${PATH64_URI}; do
-		EGIT_REPO_URI="git://github.com/${PN}/${f}.git" \
-		EGIT_DIR="${EGIT_STORE_DIR}/compiler/${f}" \
-		EGIT_SOURCEDIR="${WORKDIR}/${P}/compiler/${f}" git-r3_src_unpack
-	done
-	for f in ${PATHSCALE_URI}; do
-		EGIT_REPO_URI="git://github.com/pathscale/${f}.git" \
-		EGIT_DIR="${EGIT_STORE_DIR}/compiler/${f}" \
-		EGIT_SOURCEDIR="${WORKDIR}/${P}/compiler/${f}" git-r3_src_unpack
-	done
-	EGIT_REPO_URI=${DBG_URI} EGIT_DIR="${EGIT_STORE_DIR}/compiler/pathdb" \
-		EGIT_SOURCEDIR="${WORKDIR}/${P}/compiler/pathdb" git-r3_src_unpack
-}
-
-src_prepare() {
-	local ver=$(grep 'SET(PSC_FULL_VERSION' CMakeLists.txt | cut -d'"' -f2)
-	cat > "98${PN}" <<-EOF
-		PATH=/usr/$(get_libdir)/${PN}/bin
-		ROOTPATH=/usr/$(get_libdir)/${PN}/bin
-		LDPATH=/usr/$(get_libdir)/${PN}/lib:/usr/$(get_libdir)/${PN}/lib/${ver}/x8664/64
-	EOF
-	sed -i -e "s/-Wl,-s //" CMakeLists.txt || die #strip
-}
-
-src_configure() {
-	local linker=$($(tc-getCC) --help -v 2>&1 >/dev/null | \
-		sed -n -e '/dynamic-linker/s:.* -dynamic-linker \([^ ]\+\) .*:\1:p')
-	local libgcc=$($(tc-getCC) -print-libgcc-file-name)
-	use custom-cflags && flags=(
-			-DCMAKE_C_FLAGS="${CFLAGS}"
-			-DCMAKE_CXX_FLAGS="${CXXFLAGS}"
-		)
-
-	# Yup, I know how bad it is, but I'd rather have a working compiler
-	unset FC F90 F77 FCFLAGS F90FLAGS FFLAGS CFLAGS CXXFLAGS
-
-	if use native ; then
-		export CMAKE_BUILD_TYPE=Release
-		export CC=pathcc
-		export CXX=pathCC
-		export MYCMAKEARGS="-UCMAKE_USER_MAKE_RULES_OVERRIDE"
-	else
-		export CMAKE_BUILD_TYPE=Debug
-	fi
-	mycmakeargs=(
-		-DCMAKE_INSTALL_PREFIX=/usr/$(get_libdir)/${PN}
-		-DPATH64_ENABLE_TARGETS="x86_64"
-		-DPATH64_ENABLE_PROFILING=ON
-		-DPATH64_ENABLE_MATHLIBS=ON
-		-DPATH64_ENABLE_PATHOPT2=OFF
-		$(cmake-utils_use assembler PATH64_ENABLE_PATHAS)
-		$(cmake-utils_use assembler PATH64_ENABLE_DEFAULT_PATHAS)
-		$(cmake-utils_use fortran PATH64_ENABLE_FORTRAN)
-		$(cmake-utils_use openmp PATH64_ENABLE_OPENMP)
-		$(cmake-utils_use debugger PATH64_ENABLE_PATHDB)
-		$(cmake-utils_use valgrind PATH64_ENABLE_VALGRIND)
-		-DPSC_CRT_PATH_x86_64=/usr/$(get_libdir)
-		-DPSC_CRTBEGIN_PATH=$(dirname ${libgcc})
-		-DPSC_DYNAMIC_LINKER_x86_64=${linker}
-		-DCMAKE_C_COMPILER="$(tc-getCC)"
-		-DCMAKE_CXX_COMPILER="$(tc-getCXX)"
-		"${flags[@]}"
-	)
-	cmake-utils_src_configure
-}
-
-src_install() {
-	cmake-utils_src_install
-	doenvd "98${PN}"
-}
diff --git a/dev-lang/pgi/Manifest b/dev-lang/pgi/Manifest
deleted file mode 100644
index 27c00897e..000000000
--- a/dev-lang/pgi/Manifest
+++ /dev/null
@@ -1 +0,0 @@
-DIST pgilinux-2013-135.tar.gz 949594228 SHA256 94dc015b5758486905643a729f7ece5c68038667385cbd08406b8799fcf9a22c SHA512 1bbd26f14c6757677c30fc2f4598f2b26072d34f0fe90a8914b55b0e52472adc1d342398372581ee9eef43480b5207d7998322f9621d0993f0a82d9055b7a5c6 WHIRLPOOL ad299eb206748f921ab826093a2a728ea100b0b51f2eca30562a956ed5885791c1b6465d3877586e626bb3ba6d397e6cd0d13e8bc736f2ccbf64e2e5601e7d8f
diff --git a/dev-lang/pgi/files/pgi-13.5-glibc.patch b/dev-lang/pgi/files/pgi-13.5-glibc.patch
deleted file mode 100644
index 434f12cb5..000000000
--- a/dev-lang/pgi/files/pgi-13.5-glibc.patch
+++ /dev/null
@@ -1,31 +0,0 @@
-diff -ru opt/pgi/linux86/13.5/include/bits/types.h opt/pgi-b/linux86/13.5/include/bits/types.h
---- opt/pgi/linux86/13.5/include/bits/types.h	2013-05-07 21:45:39.000000000 +0200
-+++ opt/pgi-b/linux86/13.5/include/bits/types.h	2013-06-02 01:24:19.000000000 +0200
-@@ -136,6 +136,7 @@
- #include <bits/typesizes.h>	/* Defines __*_T_TYPE macros.  */
- 
- 
-+__STD_TYPE __SQUAD_TYPE __syscall_slong_t;
- __STD_TYPE __DEV_T_TYPE __dev_t;	/* Type of device numbers.  */
- __STD_TYPE __UID_T_TYPE __uid_t;	/* Type of user identifications.  */
- __STD_TYPE __GID_T_TYPE __gid_t;	/* Type of group identifications.  */
-diff -ru opt/pgi/linux86-64/13.5/include/bits/types.h opt/pgi-b/linux86-64/13.5/include/bits/types.h
---- opt/pgi/linux86-64/13.5/include/bits/types.h	2013-05-07 21:45:39.000000000 +0200
-+++ opt/pgi-b/linux86-64/13.5/include/bits/types.h	2013-06-02 01:23:51.000000000 +0200
-@@ -135,7 +135,7 @@
- #endif
- #include <bits/typesizes.h>	/* Defines __*_T_TYPE macros.  */
- 
--
-+__STD_TYPE __SQUAD_TYPE __syscall_slong_t;
- __STD_TYPE __DEV_T_TYPE __dev_t;	/* Type of device numbers.  */
- __STD_TYPE __UID_T_TYPE __uid_t;	/* Type of user identifications.  */
- __STD_TYPE __GID_T_TYPE __gid_t;	/* Type of group identifications.  */
-@@ -156,7 +156,6 @@
- __STD_TYPE __SUSECONDS_T_TYPE __suseconds_t; /* Signed count of microseconds.  */
- 
- __STD_TYPE __DADDR_T_TYPE __daddr_t;	/* The type of a disk address.  */
--__STD_TYPE __SWBLK_T_TYPE __swblk_t;	/* Type of a swap block maybe?  */
- __STD_TYPE __KEY_T_TYPE __key_t;	/* Type of an IPC key.  */
- 
- /* Clock ID used in clock and timer functions.  */
diff --git a/dev-lang/pgi/files/pgi-13.5-terminal.patch b/dev-lang/pgi/files/pgi-13.5-terminal.patch
deleted file mode 100644
index 9b5b67474..000000000
--- a/dev-lang/pgi/files/pgi-13.5-terminal.patch
+++ /dev/null
@@ -1,39 +0,0 @@
-diff -ru pgi-a/install pgi/install
---- pgi-a/install	2013-06-01 01:24:11.522714654 +0200
-+++ pgi/install	2013-06-01 01:27:36.372713265 +0200
-@@ -83,7 +83,7 @@
- else 
-   licensefile=$SRC/common/BETA_LICENSE
- fi
--more $licensefile
-+#more $licensefile
- echo
- echo -n 'Do you accept these terms? (accept,decline) '
- read x
-@@ -296,7 +296,7 @@
-   echo
-   echo 'In order to install the ACML software, please read and accept the'
-   echo 'following license.'
--  more $SRC/common/LICENSE_ACML.txt
-+  #more $SRC/common/LICENSE_ACML.txt
-   echo
-   echo -n 'Do you accept these terms? (accept,decline) '
-   read x
-@@ -342,7 +342,7 @@
-   echo
-   echo 'In order to install the CUDA software, please read and accept the'
-   echo 'following license.'
--  more $SRC/common/LICENSE_NVIDIA_CUDA.txt
-+  #more $SRC/common/LICENSE_NVIDIA_CUDA.txt
-   echo
-   echo -n 'Do you accept these terms? (accept,decline) '
-   read x
-@@ -398,7 +398,7 @@
-   echo
-   echo 'In order to install the JAVA software, please read and accept the'
-   echo 'following license.'
--  more $SRC/common/LICENSE_JRE_6U21.txt
-+  #more $SRC/common/LICENSE_JRE_6U21.txt
-   echo
-   echo -n 'Do you accept these terms? (accept,decline) '
-   read x
diff --git a/dev-lang/pgi/metadata.xml b/dev-lang/pgi/metadata.xml
deleted file mode 100644
index c6b14e0fd..000000000
--- a/dev-lang/pgi/metadata.xml
+++ /dev/null
@@ -1,18 +0,0 @@
-<?xml version="1.0" encoding="UTF-8"?>
-<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
-<pkgmetadata>
-	<longdescription>
-PGI is the C/C++/Fortran compiler suite of the Portland Group.
-</longdescription>
-	<maintainer type="person">
-		<email>gentryx@gmx.de</email>
-	</maintainer>
-	<maintainer type="project">
-		<email>cluster@gentoo.org</email>
-		<name>Gentoo Cluster Project</name>
-	</maintainer>
-	<use>
-		<flag name="java">Install a PGI-tuned JRE.</flag>
-		<flag name="cuda">Install PGI's CUDA components (e.g. for OpenACC)</flag>
-	</use>
-</pkgmetadata>
diff --git a/dev-lang/pgi/pgi-13.5.ebuild b/dev-lang/pgi/pgi-13.5.ebuild
deleted file mode 100644
index 19c636132..000000000
--- a/dev-lang/pgi/pgi-13.5.ebuild
+++ /dev/null
@@ -1,105 +0,0 @@
-# Copyright 1999-2017 Gentoo Foundation
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=6
-
-DESCRIPTION="PGI compiler suite"
-HOMEPAGE="http://www.pgroup.com/"
-SRC_URI="pgilinux-2013-135.tar.gz"
-
-LICENSE="PGI"
-SLOT="0"
-KEYWORDS="~amd64 ~x86"
-IUSE="cuda java"
-
-RDEPEND="net-misc/curl"
-
-RESTRICT="mirror strip"
-
-QA_PREBUILT="
-		opt/pgi/linux86/2013/cuda/4.2/lib/lib*.so.*
-		opt/pgi/linux86-64/13.5/bin/*
-		opt/pgi/linux86-64/13.5/lib/lib*
-		opt/pgi/linux86-64/13.5/lib/*.o
-		opt/pgi/linux86-64/13.5/libso/lib*
-		opt/pgi/linux86-64/13.5/libso/*.o
-		opt/pgi/linux86-64/13.5/cray/lib*
-		opt/pgi/linux86-64/13.5/etc/pgi_license_tool/curl
-		opt/pgi/linux86-64/13.5/REDIST/lib*.so
-		opt/pgi/linux86-64/2013/cuda/5.0/nvvm/cicc
-		opt/pgi/linux86-64/2013/cuda/4.2/nvvm/cicc
-		opt/pgi/linux86-64/2013/acml/5.3.0/lib/lib*
-		opt/pgi/linux86-64/2013/acml/5.3.0/libso/lib*.so
-		opt/pgi/linux86/13.5/etc/pgi_license_tool/curl
-		opt/pgi/linux86/13.5/bin/*
-		opt/pgi/linux86/13.5/lib/lib*
-		opt/pgi/linux86/13.5/lib/*.o
-		opt/pgi/linux86/13.5/libso/lib*
-		opt/pgi/linux86/13.5/cray/lib*
-		opt/pgi/linux86/2013/cuda/5.0/nvvm/cicc
-		opt/pgi/linux86/2013/cuda/4.2/nvvm/cicc
-		opt/pgi/linux86/2013/acml/4.4.0/lib/lib*
-		opt/pgi/linux86/2013/acml/4.4.0/libso/lib*.so
-"
-
-S="${WORKDIR}"
-
-PATCHES=( "${FILESDIR}"/${P}-terminal.patch )
-
-pkg_nofetch() {
-	einfo "PGI doesn't provide direct download links. Please download"
-	einfo "${ARCHIVE} from ${HOMEPAGE}"
-}
-
-src_install() {
-	dodir /opt/pgi
-
-	command="accept
-1
-${ED}/opt/pgi"
-
-	command="${command}
-n"
-
-	if use cuda; then
-		command="${command}
-y
-accept"
-	else
-		command="${command}
-n"
-	fi
-
-	if use java; then
-		command="${command}
-
-accept"
-	else
-		command="${command}
-no"
-	fi
-
-	command="${command}
-y
-n
-n
-y
-"
-	./install <<EOF
-${command}
-EOF
-	# fix problems with PGI's C++ compiler and current glibc:
-	cd "${ED}"
-	epatch "${FILESDIR}/${P}-glibc.patch"
-
-	# java symlink might be broken if useflag is disabled:
-	if ! use java; then
-		rm opt/pgi/linux86-64/13.5/jre || die
-	fi
-
-	# replace PGI's curl with the stock version:
-	dodir /opt/pgi/linux86-64/13.5/etc/pgi_license_tool
-	dosym ../../../../../../usr/bin/curl /opt/pgi/linux86-64/13.5/etc/pgi_license_tool/curl
-	dodir /opt/pgi/linux86/13.5/etc/pgi_license_tool
-	dosym ../../../../../../usr/bin/curl /opt/pgi/linux86/13.5/etc/pgi_license_tool/curl
-}
diff --git a/dev-lang/terra/Manifest b/dev-lang/terra/Manifest
deleted file mode 100644
index 9001cea94..000000000
--- a/dev-lang/terra/Manifest
+++ /dev/null
@@ -1,2 +0,0 @@
-DIST LuaJIT-2.0.3.tar.gz 844927 BLAKE2B a6ed54ef562b7af594367cbc0ed6e20295bb64781ceb6b46df81d10d7abd9fdaf902344ab7a6dfdffa6fc38b05e70648ae53c9cffdfb2a866989eba4b02fe9df SHA512 7b3e3de22ac3602299b5918b60801e45a3278e547a15c16fdae7359538d4ada27ba664935d5f97c7409f330c2f8efeaae9ea03415f5e9d5a9d81e022cd5d36e0
-DIST terra-2015.03.12.tar.gz 303867 BLAKE2B e1fea9a2e7842431875b23902787fc0ffb9cebacce2498c7ab44966507b26d208f7d1a4f821ffafe47813e2a12cc7e1e66989b1d3a8651460c254bc49e7a2fac SHA512 abda5cf8126e12ce199c3f8bde8a2fca0e7f7b5bf5f5048a97e3b3b827c83cd8140fb0fba803e116c55cb27a4cda1d13c8695a5cfe95f2383eb2f4515795aa09
diff --git a/dev-lang/terra/metadata.xml b/dev-lang/terra/metadata.xml
deleted file mode 100644
index 684a4dc29..000000000
--- a/dev-lang/terra/metadata.xml
+++ /dev/null
@@ -1,11 +0,0 @@
-<?xml version="1.0" encoding="UTF-8"?>
-<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
-<pkgmetadata>
-	<maintainer type="person">
-		<email>ottxor@gentoo.org</email>
-		<name>Christoph Junghans</name>
-	</maintainer>
-	<upstream>
-		<remote-id type="github">zdevito/terra</remote-id>
-	</upstream>
-</pkgmetadata>
diff --git a/dev-lang/terra/terra-2015.03.12.ebuild b/dev-lang/terra/terra-2015.03.12.ebuild
deleted file mode 100644
index 99421ed5d..000000000
--- a/dev-lang/terra/terra-2015.03.12.ebuild
+++ /dev/null
@@ -1,36 +0,0 @@
-# Copyright 1999-2018 Gentoo Foundation
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=6
-
-DESCRIPTION="A low-level counterpart to Lua"
-HOMEPAGE="http://terralang.org/"
-#cannot be unbundled easily, because needs to compiled with clang
-LUAJIT="LuaJIT-2.0.3.tar.gz"
-SRC_URI="
-	https://github.com/zdevito/terra/archive/release-${PV//./-}.tar.gz -> ${P}.tar.gz
-	http://luajit.org/download/${LUAJIT}"
-
-LICENSE="MIT"
-SLOT="0"
-KEYWORDS="~amd64"
-IUSE="test"
-
-DEPEND="
-	sys-devel/clang:=
-	dev-lang/luajit:2"
-RDEPEND="${DEPEND}"
-
-src_unpack() {
-	unpack "${P}.tar.gz"
-	mv "${PN}"-* "${S}" || die
-	ln -s "${DISTDIR}/${LUAJIT}" "${S}/build" || die
-}
-
-src_install() {
-	cd release || die
-	dobin terra
-	dolib.so libterra.so
-	dodoc README.md
-	doheader include/{terra.h,*.t}
-}
diff --git a/dev-lang/vtune/Manifest b/dev-lang/vtune/Manifest
deleted file mode 100644
index ac43ecaf8..000000000
--- a/dev-lang/vtune/Manifest
+++ /dev/null
@@ -1 +0,0 @@
-DIST parallel_studio_xe_2018_update2_professional_edition.tgz 3877755304 BLAKE2B c8852df23abf080f482002a37af7781b3fbae3ecec448914ea5a237fa2b925073d1a3dc2dd94ba64002ff0f6c7e9b18b25fa7ada811a83b10344eb9b92cb37ff SHA512 a9b644b0305d83a9d0daa14d146cb3ce79949db55a410afe48d62259414e6256d9ef533a04bb50807103511db2016c4abcbbf769146854a25638f402a6d0f2be
diff --git a/dev-lang/vtune/metadata.xml b/dev-lang/vtune/metadata.xml
deleted file mode 100644
index c46d15bb3..000000000
--- a/dev-lang/vtune/metadata.xml
+++ /dev/null
@@ -1,8 +0,0 @@
-<?xml version="1.0" encoding="UTF-8"?>
-<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
-<pkgmetadata>
-	<maintainer type="person">
-		<email>nbigaouette@gmail.com</email>
-		<name>Nicolas Bigaouette</name>
-	</maintainer>
-</pkgmetadata>
diff --git a/dev-lang/vtune/vtune-18.0.2.0.551022.ebuild b/dev-lang/vtune/vtune-18.0.2.0.551022.ebuild
deleted file mode 100644
index 51a0b08c0..000000000
--- a/dev-lang/vtune/vtune-18.0.2.0.551022.ebuild
+++ /dev/null
@@ -1,49 +0,0 @@
-# Copyright 1999-2018 Gentoo Foundation
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=6
-
-INTEL_DIST_SKU=3235
-INTEL_DIST_PV=2018_update2_professional_edition
-INTEL_SUBDIR=vtune_amplifier
-
-inherit intel-sdp-r1
-
-DESCRIPTION="Intel VTune Amplifier XE"
-HOMEPAGE="http://software.intel.com/en-us/articles/intel-vtune-amplifier-xe/"
-
-IUSE="doc"
-KEYWORDS="-* ~amd64 ~x86 ~amd64-linux ~x86-linux"
-
-RDEPEND="~dev-libs/intel-common-18.0.2.199[compiler]"
-
-INTEL_DIST_DAT_RPMS=(
-	"vtune-amplifier-2018-cli-common-2018.2-551022.noarch.rpm"
-	"vtune-amplifier-2018-common-2018.2-551022.noarch.rpm"
-	"vtune-amplifier-2018-common-pset-2018.2-551022.noarch.rpm"
-	"vtune-amplifier-2018-gui-common-2018.2-551022.noarch.rpm"
-	"vtune-amplifier-2018-sep-2018.2-551022.noarch.rpm"
-	"vtune-amplifier-2018-target-2018.2-551022.noarch.rpm")
-INTEL_DIST_AMD64_RPMS=(
-	"vtune-amplifier-2018-cli-2018.2-551022.x86_64.rpm"
-	"vtune-amplifier-2018-collector-64linux-2018.2-551022.x86_64.rpm"
-	"vtune-amplifier-2018-gui-2018.2-551022.x86_64.rpm")
-INTEL_DIST_X86_RPMS=(
-	"vtune-amplifier-2018-cli-32bit-2018.2-551022.i486.rpm"
-	"vtune-amplifier-2018-collector-32linux-2018.2-551022.i486.rpm")
-
-pkg_setup() {
-	if use doc; then
-		INTEL_DIST_DAT_RPMS+=( "vtune-amplifier-2018-doc-2018.2-551022.noarch.rpm" )
-	fi
-}
-
-src_install() {
-	intel-sdp-r1_src_install
-
-	local path="PATH="
-	use abi_x86_64 && path+=":$(isdp_get-sdp-edir)/bin64"
-	use abi_x86_32 && path+=":$(isdp_get-sdp-edir)/bin32"
-	echo "${path}" > "${T}"/35vtune || die
-	doenvd "${T}"/35vtune
-}
diff --git a/dev-lang/yaggo/metadata.xml b/dev-lang/yaggo/metadata.xml
index 138cb7705..61d3a34e2 100644
--- a/dev-lang/yaggo/metadata.xml
+++ b/dev-lang/yaggo/metadata.xml
@@ -9,4 +9,7 @@
 		<email>sci-biology@gentoo.org</email>
 		<name>Gentoo Biology Project</name>
 	</maintainer>
+	<upstream>
+		<remote-id type="github">gmarcais/yaggo</remote-id>
+	</upstream>
 </pkgmetadata>
diff --git a/dev-lang/yaggo/yaggo-1.5.10.ebuild b/dev-lang/yaggo/yaggo-1.5.10.ebuild
index 20f291ce2..3ed91e0ca 100644
--- a/dev-lang/yaggo/yaggo-1.5.10.ebuild
+++ b/dev-lang/yaggo/yaggo-1.5.10.ebuild
@@ -1,7 +1,7 @@
-# Copyright 1999-2017 Gentoo Foundation
+# Copyright 1999-2021 Gentoo Authors
 # Distributed under the terms of the GNU General Public License v2
 
-EAPI=6
+EAPI=7
 
 DESCRIPTION="Tool to generate command line parsers for C++ (aka Gengetopt)"
 HOMEPAGE="https://github.com/gmarcais/yaggo"
@@ -10,10 +10,6 @@ SRC_URI="https://github.com/gmarcais/yaggo/archive/v${PV}.tar.gz -> ${P}.tar.gz"
 LICENSE="GPL-3"
 SLOT="0"
 KEYWORDS="~amd64 ~x86"
-IUSE=""
-
-DEPEND=""
-RDEPEND="${DEPEND}"
 
 src_prepare(){
 	sed -e 's#/usr/local#/usr#g' -i Makefile || die
@@ -22,4 +18,6 @@ src_prepare(){
 
 src_install(){
 	emake install DESTDIR="${ED}"
+	# fix doc path
+	mv "${ED}/usr/share/doc/${PN}" "${ED}/usr/share/doc/${PF}" || die
 }
diff --git a/dev-libs/asmjit/Manifest b/dev-libs/asmjit/Manifest
deleted file mode 100644
index 329d22f72..000000000
--- a/dev-libs/asmjit/Manifest
+++ /dev/null
@@ -1 +0,0 @@
-DIST AsmJit-1.0-beta4.zip 267674 SHA256 f30d76dc01db8d771eda14e7ac194af0a676f905857421e8147ed710e80f5f85 SHA512 dd24f4f9851c546531c0ae9f74c12f8797261e7d064ffa7b0449500ae39b349321e7616356e6e69c1ac89cef73c7862668daf10f357cdcd8afda7fab0bb89ebf WHIRLPOOL c5777d2f76d54a8961b6191a8c1db84bcbb32d97c3d05db1d0a05a82c4d82b6476429df627010ae4bbd2f5728114d6c624ed2f53e9f162948ef0f84f698795b6
diff --git a/dev-libs/asmjit/asmjit-1.0_beta4.ebuild b/dev-libs/asmjit/asmjit-1.0_beta4.ebuild
deleted file mode 100644
index f20a5c087..000000000
--- a/dev-libs/asmjit/asmjit-1.0_beta4.ebuild
+++ /dev/null
@@ -1,42 +0,0 @@
-# Copyright 1999-2014 Gentoo Foundation
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=5
-
-inherit cmake-utils versionator
-
-MY_PN=AsmJit
-MY_PV=$(replace_version_separator _ -)
-MY_PV=${MY_PV/_p/}
-MY_P=${MY_PN}-${MY_PV}
-
-DESCRIPTION="complete x86/x64 JIT-Assembler for C++ language"
-HOMEPAGE="http://code.google.com/p/asmjit/"
-SRC_URI="http://${PN}.googlecode.com/files/${MY_P}.zip"
-
-SLOT="0"
-LICENSE="BSD"
-KEYWORDS="~amd64 ~x86"
-IUSE="test"
-
-DEPEND="app-arch/unzip"
-RDEPEND=""
-
-S=${WORKDIR}/${MY_P}
-
-PATCHES=( "${FILESDIR}"/${PN}-test.patch )
-
-#TODO: Debug is currenlty handled by CMAKE_BUILD_TYPE=debug, fix that
-
-src_prepare() {
-	sed -i -e "s:lib):lib\${LIB_SUFFIX}):" CMakeLists.txt || die
-	cmake-utils_src_prepare
-}
-
-src_configure() {
-	mycmakeargs=(
-	  -DASMJIT_BUILD_LIBRARY=1
-	  $(cmake-utils_use test ASMJIT_BUILD_TEST)
-	)
-	cmake-utils_src_configure
-}
diff --git a/dev-libs/asmjit/files/asmjit-test.patch b/dev-libs/asmjit/files/asmjit-test.patch
deleted file mode 100644
index 3736ee71a..000000000
--- a/dev-libs/asmjit/files/asmjit-test.patch
+++ /dev/null
@@ -1,20 +0,0 @@
-http://code.google.com/p/asmjit/issues/detail?id=22
-
---- CMakeLists.txt
-+++ CMakeLists.txt
-@@ -78,6 +78,7 @@
- 
- # Build AsmJit test executables?
- If(ASMJIT_BUILD_TEST)
-+  Enable_Testing()
-   Set(ASMJIT_TEST_FILES
-     testcorecpu
-     testcoresize
-@@ -105,6 +106,7 @@
-   ForEach(file ${ASMJIT_TEST_FILES})
-     Add_Executable(${file} Test/${file}.cpp)
-     Target_Link_Libraries(${file} AsmJit)
-+    Add_Test(${file} ${EXECUTABLE_OUTPUT_PATH}/${file} ${file})
-   EndForEach(file)
- EndIf(ASMJIT_BUILD_TEST)
- 
diff --git a/dev-libs/asmjit/metadata.xml b/dev-libs/asmjit/metadata.xml
deleted file mode 100644
index a1c96691e..000000000
--- a/dev-libs/asmjit/metadata.xml
+++ /dev/null
@@ -1,24 +0,0 @@
-<?xml version="1.0" encoding="UTF-8"?>
-<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
-<pkgmetadata>
-	<maintainer type="person">
-		<email>xarthisius@gentoo.org</email>
-		<name>Kacper Kowalik</name>
-	</maintainer>
-	<maintainer type="project">
-		<email>sci@gentoo.org</email>
-		<name>Gentoo Science Project</name>
-	</maintainer>
-	<longdescription lang="en">
-AsmJit is complete x86/x64 JIT-Assembler for C++ language. It supports
-32/64-bit x86 processors including all usable extensions (FPU, MMX,
-3dNow, SSE, SSE2, SSE3 and SSE4) through type-safe API that mimics Intel
-assembler syntax and eliminates nearly all common mistakes that can be
-done by developers.
-
-AsmJit contains also high-level code generation classes that can be used
-as a portable way to create JIT code that should run on all supported
-architectures. High-level classes can handle various function
-calling-conventions, register allocation and 32/64-bit mode differences.
-</longdescription>
-</pkgmetadata>
diff --git a/dev-libs/boost-compute/Manifest b/dev-libs/boost-compute/Manifest
index cc8fea806..60b962d99 100644
--- a/dev-libs/boost-compute/Manifest
+++ b/dev-libs/boost-compute/Manifest
@@ -1,2 +1 @@
-DIST boost-compute-0.4.tar.gz 282477 BLAKE2B 0160ae319c54fe93162471b4db5520f08016c1837e9d1140b2362ef403466bb7e486310784a6b29b1aefb38425e575686091f4821b5e33998592ec2ebb401f0f SHA512 7a2b4f227b2f0a46ba44aeddc4b562e125949f262ef057c92b9261c9e0fa7a824323b3dbb0bb5129b76fce4be93bbb1fccf5d681d63663731c83c3ab80e5ceed
-DIST boost-compute-0.5.tar.gz 333192 BLAKE2B 08ef2978db4d3f3dce4c03c00496cb4823cf97947c1bb1780fe9a9e3d0fa8c8233e936a1bedbe16a5ef217ac5abca50bf64d3f11cde5f9d6ac4cb24b8ca9f59a SHA512 1caa067342698ec3a6a8e23aaf194f8ced41ac9d5b5a6d3d195911116af4a8a778667065681a8b0e0004887258d7cae71f3c7187ebc50c390200d66fd8688002
+DIST boost-compute-1.74.0.tar.gz 376653 BLAKE2B 72a1f76ab865e17270561699c02f6fcbfc6efa657fd5b6ce774039590bb8ca2dbd95a22721d669cbaa1764c52b63a360c12112cec19ca830288c6315c23fb888 SHA512 484fa370cc4dc98d40a6d0227d1313ff8097653390fde87928963b32bc30e43b0c81da542cc85bb17cfc6348e801d244fe177e6640f825b7899e5f0a6884ad46
diff --git a/dev-libs/boost-compute/boost-compute-0.4-r1.ebuild b/dev-libs/boost-compute/boost-compute-0.4-r1.ebuild
deleted file mode 100644
index 2c52edf3c..000000000
--- a/dev-libs/boost-compute/boost-compute-0.4-r1.ebuild
+++ /dev/null
@@ -1,25 +0,0 @@
-# Copyright 1999-2015 Gentoo Foundation
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=5
-
-inherit eutils cmake-utils
-
-DESCRIPTION="A header-only C++ Computing Library for OpenCL"
-HOMEPAGE="https://github.com/boostorg/compute"
-SRC_URI="https://github.com/boostorg/compute/archive/v${PV}.tar.gz -> ${P}.tar.gz"
-
-LICENSE="Boost-1.0"
-SLOT="0"
-KEYWORDS="~amd64"
-IUSE=""
-
-RDEPEND="
-	dev-libs/boost
-	virtual/opencl
-"
-DEPEND="${RDEPEND}"
-
-S="${WORKDIR}/compute-${PV}"
-
-PATCHES=( "${FILESDIR}/${P}"-CMakeLists.patch )
diff --git a/dev-libs/boost-compute/boost-compute-0.5.ebuild b/dev-libs/boost-compute/boost-compute-0.5.ebuild
deleted file mode 100644
index 8ae88db9d..000000000
--- a/dev-libs/boost-compute/boost-compute-0.5.ebuild
+++ /dev/null
@@ -1,23 +0,0 @@
-# Copyright 1999-2016 Gentoo Foundation
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=5
-
-inherit eutils cmake-utils
-
-DESCRIPTION="A header-only C++ Computing Library for OpenCL"
-HOMEPAGE="https://github.com/boostorg/compute"
-SRC_URI="https://github.com/boostorg/compute/archive/v${PV}.tar.gz -> ${P}.tar.gz"
-
-LICENSE="Boost-1.0"
-SLOT="0"
-KEYWORDS="~amd64"
-IUSE=""
-
-RDEPEND="
-	dev-libs/boost
-	virtual/opencl
-"
-DEPEND="${RDEPEND}"
-
-S="${WORKDIR}/compute-${PV}"
diff --git a/dev-libs/boost-compute/boost-compute-1.74.0.ebuild b/dev-libs/boost-compute/boost-compute-1.74.0.ebuild
new file mode 100644
index 000000000..3e986bda0
--- /dev/null
+++ b/dev-libs/boost-compute/boost-compute-1.74.0.ebuild
@@ -0,0 +1,50 @@
+# Copyright 1999-2020 Gentoo Authors
+# Distributed under the terms of the GNU General Public License v2
+
+EAPI=7
+
+inherit cmake
+
+DESCRIPTION="A header-only C++ Computing Library for OpenCL"
+HOMEPAGE="https://github.com/boostorg/compute"
+
+if [[ ${PV} == 9999 ]]; then
+	inherit git-r3
+	EGIT_REPO_URI="https://github.com/boostorg/compute"
+else
+	SRC_URI="https://github.com/boostorg/compute/archive/boost-${PV}.tar.gz -> ${P}.tar.gz"
+	S="${WORKDIR}"/compute-boost-${PV}
+	KEYWORDS="~amd64"
+fi
+
+LICENSE="Boost-1.0"
+SLOT="0"
+IUSE="benchmark bolt cache cpp11 cuda eigen examples opencv qt tbb test threads vtk"
+RESTRICT="!test? ( test )"
+
+RDEPEND="
+	dev-libs/boost
+	virtual/opencl
+"
+DEPEND="${RDEPEND}"
+
+PATCHES=( "${FILESDIR}"/${P}-libdir.patch )
+
+src_configure() {
+	local mycmakeargs=(
+		-DBOOST_COMPUTE_USE_OFFLINE_CACHE=$(usex cache)
+		-DBOOST_COMPUTE_USE_CPP11=$(usex cpp11)
+		-DBOOST_COMPUTE_THREAD_SAFE=$(usex threads)
+		-DBOOST_COMPUTE_HAVE_EIGEN=$(usex eigen)
+		-DBOOST_COMPUTE_HAVE_OPENCV=$(usex opencv)
+		-DBOOST_COMPUTE_HAVE_QT=$(usex qt)
+		-DBOOST_COMPUTE_HAVE_VTK=$(usex vtk)
+		-DBOOST_COMPUTE_HAVE_CUDA=$(usex cuda)
+		-DBOOST_COMPUTE_HAVE_TBB=$(usex tbb)
+		-DBOOST_COMPUTE_HAVE_BOLT=$(usex bolt)
+		-DBOOST_COMPUTE_BUILD_TESTS=$(usex test)
+		-DBOOST_COMPUTE_BUILD_BENCHMARKS=$(usex benchmark)
+		-DBOOST_COMPUTE_BUILD_EXAMPLES=$(usex examples)
+	)
+	cmake_src_configure
+}
diff --git a/dev-libs/boost-compute/boost-compute-9999.ebuild b/dev-libs/boost-compute/boost-compute-9999.ebuild
deleted file mode 100644
index fd7276a2d..000000000
--- a/dev-libs/boost-compute/boost-compute-9999.ebuild
+++ /dev/null
@@ -1,23 +0,0 @@
-# Copyright 1999-2015 Gentoo Foundation
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=5
-
-inherit eutils cmake-utils git-r3
-
-DESCRIPTION="A header-only C++ Computing Library for OpenCL"
-HOMEPAGE="https://github.com/boostorg/compute"
-EGIT_REPO_URI="
-	https://github.com/boostorg/compute.git
-	git://github.com/boostorg/compute.git"
-
-LICENSE="Boost-1.0"
-SLOT="0"
-KEYWORDS=""
-IUSE=""
-
-RDEPEND="
-	dev-libs/boost
-	virtual/opencl
-"
-DEPEND="${RDEPEND}"
diff --git a/dev-libs/boost-compute/files/boost-compute-0.4-CMakeLists.patch b/dev-libs/boost-compute/files/boost-compute-0.4-CMakeLists.patch
deleted file mode 100644
index 86d3a9e29..000000000
--- a/dev-libs/boost-compute/files/boost-compute-0.4-CMakeLists.patch
+++ /dev/null
@@ -1,14 +0,0 @@
-Install the BoostComputeConfig to /usr/lib/cmake instead of /usr/share/cmake.
-
-Patch by Marius Brehler.
---- CMakeLists.txt
-+++ CMakeLists.txt
-@@ -81,7 +81,7 @@ configure_file(
- # install cmake config file
- install(
-   FILES ${BoostCompute_BINARY_DIR}/BoostComputeConfig.cmake
--  DESTINATION share/cmake/BoostCompute
-+  DESTINATION lib/cmake/BoostCompute
- )
- 
- # install header files
diff --git a/dev-libs/boost-compute/files/boost-compute-1.74.0-libdir.patch b/dev-libs/boost-compute/files/boost-compute-1.74.0-libdir.patch
new file mode 100644
index 000000000..9b35a5284
--- /dev/null
+++ b/dev-libs/boost-compute/files/boost-compute-1.74.0-libdir.patch
@@ -0,0 +1,13 @@
+diff --git a/CMakeLists.txt b/CMakeLists.txt
+index d0327ca..e52a62a 100644
+--- a/CMakeLists.txt
++++ b/CMakeLists.txt
+@@ -122,7 +122,7 @@ configure_file(
+ # install cmake config file
+ install(
+   FILES ${BoostCompute_BINARY_DIR}/BoostComputeConfig.cmake
+-  DESTINATION lib/cmake/BoostCompute
++  DESTINATION ${CMAKE_INSTALL_LIBDIR}/cmake/BoostCompute
+ )
+ 
+ # install header files
diff --git a/dev-libs/boost-compute/metadata.xml b/dev-libs/boost-compute/metadata.xml
index f41b18fa7..21973c648 100644
--- a/dev-libs/boost-compute/metadata.xml
+++ b/dev-libs/boost-compute/metadata.xml
@@ -2,20 +2,33 @@
 <!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
 <pkgmetadata>
 	<maintainer type="person">
-		<email>marbre@linux.sungazer.de</email>
-		<name>Marius Brehler</name>
+		<email>gentoo@aisha.cc</email>
+		<name>Aisha Tammy</name>
 	</maintainer>
 	<maintainer type="project">
 		<email>sci@gentoo.org</email>
 		<name>Gentoo Science Project</name>
 	</maintainer>
 	<longdescription>
-Boost.Compute is a GPU/parallel-computing library for C++ based on
-OpenCL. The core library is a thin C++ wrapper over the OpenCL API
-and provides access to compute devices, contexts, command queues
-and memory buffers.
-</longdescription>
+		Boost.Compute is a GPU/parallel-computing library for C++ based on
+		OpenCL. The core library is a thin C++ wrapper over the OpenCL API
+		and provides access to compute devices, contexts, command queues
+		and memory buffers.
+	</longdescription>
 	<upstream>
 		<remote-id type="github">boostorg/compute</remote-id>
 	</upstream>
+	<use>
+		<flag name="benchmark">build benchmark examples</flag>
+		<flag name="bolt">build bolt examples and tests</flag>
+		<flag name="cpp11">enable C++11 features in examples and tests</flag>
+		<flag name="cache">use offline cache for opencl binaries in examples and tests</flag>
+		<flag name="cuda">build cuda examples and tests</flag>
+		<flag name="eigen">build eigen examples and tests</flag>
+		<flag name="opencv">build opencv examples and tests</flag>
+		<flag name="qt">build qt examples and tests</flag>
+		<flag name="tbb">build examples and tests using tbb backend</flag>
+		<flag name="threads">build thread safe examples and tests</flag>
+		<flag name="vtk">build vtk examples and tests</flag>
+	</use>
 </pkgmetadata>
diff --git a/dev-libs/fortrancl/Manifest b/dev-libs/fortrancl/Manifest
deleted file mode 100644
index d1b089e47..000000000
--- a/dev-libs/fortrancl/Manifest
+++ /dev/null
@@ -1 +0,0 @@
-DIST fortrancl-0.1alpha3.tar.gz 367740 BLAKE2B 64109abf95434032b75e750fa08a61489791ece3fd0e92044969aa76799a4712b7e0f6f8bc308dbbc6dbabb99f49b387560a6ecedc1b08feafb564d26b0441d3 SHA512 2faeb1d129e7340e2df75a75f004c6d1d1e53f7925bd39abeea49fa7dc794402c64c9e69556046a0dbae2341262040bcd9ad3213045622fc56060e1769167d90
diff --git a/dev-libs/fortrancl/files/fortrancl-0.1_alpha3-gentoo.patch b/dev-libs/fortrancl/files/fortrancl-0.1_alpha3-gentoo.patch
deleted file mode 100644
index 666699b4f..000000000
--- a/dev-libs/fortrancl/files/fortrancl-0.1_alpha3-gentoo.patch
+++ /dev/null
@@ -1,29 +0,0 @@
-Fix pc file
---- a/fortrancl.pc.in
-+++ b/fortrancl.pc.in
-@@ -9,25 +9,3 @@
- URL: @PACKAGE_URL@
- Libs: -L${libdir} -lfortrancl
- Cflags: -I${includedir}/fortrancl
--prefix=@prefix@
--exec_prefix=@exec_prefix@
--libdir=@libdir@
--includedir=@includedir@
--
--Name: @PACKAGE_NAME@
--Description: OpenCL interface for Fortran 90
--Version: @PACKAGE_VERSION@
--URL: @PACKAGE_URL@
--Libs: -L${libdir} -lfortrancl
--Cflags: -I${includedir}/fortrancl
--prefix=@prefix@
--exec_prefix=@exec_prefix@
--libdir=@libdir@
--includedir=@includedir@
--
--Name: @PACKAGE_NAME@
--Description: OpenCL interface for Fortran 90
--Version: @PACKAGE_VERSION@
--URL: @PACKAGE_URL@
--Libs: -L${libdir} -lfortrancl
--Cflags: -I${includedir}/fortrancl
diff --git a/dev-libs/fortrancl/fortrancl-0.1_alpha3.ebuild b/dev-libs/fortrancl/fortrancl-0.1_alpha3.ebuild
deleted file mode 100644
index 1bd3c3938..000000000
--- a/dev-libs/fortrancl/fortrancl-0.1_alpha3.ebuild
+++ /dev/null
@@ -1,36 +0,0 @@
-# Copyright 1999-2015 Gentoo Foundation
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=5
-
-AUTOTOOLS_AUTORECONF=1
-
-inherit autotools-utils fortran-2
-
-MY_PV=${PV/_}
-MY_P=${PN}-${MY_PV}
-
-DESCRIPTION="OpenCL interface for Fortran 90"
-HOMEPAGE="http://code.google.com/p/fortrancl/"
-SRC_URI="http://${PN}.googlecode.com/files/${MY_P}.tar.gz"
-
-LICENSE="LGPL-3"
-SLOT="0"
-KEYWORDS="~amd64"
-IUSE="examples static-libs"
-
-DEPEND="virtual/opencl"
-RDEPEND="${DEPEND}"
-
-S=${WORKDIR}/${MY_P}
-
-DOCS=( AUTHORS ChangeLog README )
-PATCHES=( "${FILESDIR}"/${P}-gentoo.patch )
-
-src_install() {
-	autotools-utils_src_install
-	if use examples ; then
-		insinto /usr/share/doc/${PF}/examples
-		doins examples/*.{f90,cl}
-	fi
-}
diff --git a/dev-libs/fortrancl/metadata.xml b/dev-libs/fortrancl/metadata.xml
deleted file mode 100644
index 3222dfcfc..000000000
--- a/dev-libs/fortrancl/metadata.xml
+++ /dev/null
@@ -1,23 +0,0 @@
-<?xml version="1.0" encoding="UTF-8"?>
-<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
-<pkgmetadata>
-	<maintainer type="person">
-		<email>xarthisius@gentoo.org</email>
-		<name>Kacper Kowalik</name>
-	</maintainer>
-	<maintainer type="project">
-		<email>sci@gentoo.org</email>
-		<name>Gentoo Science Project</name>
-	</maintainer>
-	<longdescription>
-FortranCL is an OpenCL interface for Fortran 90. It allows programmers to call
-the OpenCL parallel programming framework directly from Fortran, so developers
-can accelerate their Fortran code using graphical processing units (GPU) and
-other accelerators.
-The interface is designed to be as close to C OpenCL interface as possible,
-while written in native Fortran 90 with type checking. It was originally
-designed as an OpenCL interface to be used by the Octopus code.
-The interface is not complete but provides all the basic calls required to 
-write a full Fortran 90 OpenCL program. 
-</longdescription>
-</pkgmetadata>
diff --git a/dev-libs/intel-common/Manifest b/dev-libs/intel-common/Manifest
deleted file mode 100644
index ac43ecaf8..000000000
--- a/dev-libs/intel-common/Manifest
+++ /dev/null
@@ -1 +0,0 @@
-DIST parallel_studio_xe_2018_update2_professional_edition.tgz 3877755304 BLAKE2B c8852df23abf080f482002a37af7781b3fbae3ecec448914ea5a237fa2b925073d1a3dc2dd94ba64002ff0f6c7e9b18b25fa7ada811a83b10344eb9b92cb37ff SHA512 a9b644b0305d83a9d0daa14d146cb3ce79949db55a410afe48d62259414e6256d9ef533a04bb50807103511db2016c4abcbbf769146854a25638f402a6d0f2be
diff --git a/dev-libs/intel-common/intel-common-18.0.2.199-r1.ebuild b/dev-libs/intel-common/intel-common-18.0.2.199-r1.ebuild
deleted file mode 100644
index 8f4d6b62f..000000000
--- a/dev-libs/intel-common/intel-common-18.0.2.199-r1.ebuild
+++ /dev/null
@@ -1,95 +0,0 @@
-# Copyright 1999-2018 Gentoo Foundation
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=6
-
-INTEL_DIST_SKU=3235
-INTEL_DIST_PV=2018_update2_professional_edition
-
-inherit intel-sdp-r1
-
-DESCRIPTION="Common libraries and utilities needed for Intel compilers and libraries"
-HOMEPAGE="http://software.intel.com/en-us/articles/intel-compilers/"
-
-IUSE="+compiler doc +mpi +openmp"
-KEYWORDS="-* ~amd64 ~x86 ~amd64-linux ~x86-linux"
-
-CHECKREQS_DISK_BUILD=750M
-
-INTEL_DIST_BIN_RPMS=()
-INTEL_DIST_DAT_RPMS=(
-	"c-comp-common-18.0.2-199-18.0.2-199.noarch.rpm"
-	"comp-l-all-common-18.0.2-199-18.0.2-199.noarch.rpm"
-	"comp-l-all-vars-18.0.2-199-18.0.2-199.noarch.rpm"
-	"comp-nomcu-vars-18.0.2-199-18.0.2-199.noarch.rpm")
-INTEL_DIST_X86_RPMS=(
-	"comp-32bit-18.0.2-199-18.0.2-199.x86_64.rpm"
-	"comp-ps-32bit-18.0.2-199-18.0.2-199.x86_64.rpm"
-	"comp-ps-ss-bec-32bit-18.0.2-199-18.0.2-199.x86_64.rpm")
-INTEL_DIST_AMD64_RPMS=(
-	"comp-18.0.2-199-18.0.2-199.x86_64.rpm"
-	"comp-ps-18.0.2-199-18.0.2-199.x86_64.rpm"
-	"comp-ps-ss-18.0.2-199-18.0.2-199.x86_64.rpm"
-	"comp-ps-ss-bec-18.0.2-199-18.0.2-199.x86_64.rpm")
-
-pkg_setup() {
-	if use doc; then
-		INTEL_DIST_DAT_RPMS+=( "comp-doc-18.0-18.0.2-199.noarch.rpm" )
-	fi
-
-	if use mpi; then
-		INTEL_DIST_AMD64_RPMS+=( "mpi-rt-2018.2-199-2018.2-199.x86_64.rpm" )
-
-		if use doc; then
-			INTEL_DIST_DAT_RPMS+=( "mpi-doc-2018-2018.2-199.x86_64.rpm" )
-		fi
-	fi
-
-	if use openmp; then
-		INTEL_DIST_DAT_RPMS+=( "openmp-common-18.0.2-199-18.0.2-199.noarch.rpm" )
-		INTEL_DIST_AMD64_RPMS+=( "openmp-18.0.2-199-18.0.2-199.x86_64.rpm" )
-		INTEL_DIST_X86_RPMS+=( "openmp-32bit-18.0.2-199-18.0.2-199.x86_64.rpm" )
-
-		if use compiler; then
-			INTEL_DIST_DAT_RPMS+=(
-				"openmp-common-icc-18.0.2-199-18.0.2-199.noarch.rpm"
-				"openmp-common-ifort-18.0.2-199-18.0.2-199.noarch.rpm")
-			INTEL_DIST_AMD64_RPMS+=(
-				"openmp-ifort-18.0.2-199-18.0.2-199.x86_64.rpm")
-			INTEL_DIST_X86_RPMS+=(
-				"openmp-ifort-32bit-18.0.2-199-18.0.2-199.x86_64.rpm")
-		fi
-	fi
-}
-
-src_install() {
-	intel-sdp-r1_src_install
-	local path rootpath ldpath arch fenv=35intelsdp
-	cat > ${fenv} <<-EOF
-		NLSPATH=$(isdp_get-sdp-edir)/linux/compiler/lib/$(isdp_get-native-abi-arch)/locale/en_US/%N
-		INTEL_LICENSE_FILE=${EPREFIX%/}/opt/intel/licenses:$(isdp_get-sdp-edir)/licenses
-	EOF
-	for arch in $(isdp_get-sdp-installed-arches); do
-		path="${path}:$(isdp_get-sdp-edir)/linux/bin/${arch}"
-		rootpath="${rootpath}:$(isdp_get-sdp-edir)/linux/bin/${arch}"
-		ldpath="${ldpath}:$(isdp_get-sdp-edir)/linux/compiler/lib/${arch}"
-	done
-	if use mpi && use amd64; then
-		path="${path}:$(isdp_get-sdp-edir)/linux/mpi/intel64/bin/"
-		rootpath="${rootpath}:$(isdp_get-sdp-edir)/linux/mpi/intel64/bin/"
-		ldpath="${ldpath}:$(isdp_get-sdp-edir)/linux/mpi/intel64/lib/"
-	fi
-	cat >> ${fenv} <<-EOF
-		PATH=${path#:}
-		ROOTPATH=${rootpath#:}
-		LDPATH=${ldpath#:}
-	EOF
-
-	doenvd ${fenv}
-
-	cat >> "${T}"/40-${PN} <<- EOF
-	SEARCH_DIRS_MASK=$(isdp_get-sdp-edir)
-	EOF
-	insinto /etc/revdep-rebuild/
-	doins "${T}"/40-${PN}
-}
diff --git a/dev-libs/intel-common/metadata.xml b/dev-libs/intel-common/metadata.xml
deleted file mode 100644
index 026b5a33d..000000000
--- a/dev-libs/intel-common/metadata.xml
+++ /dev/null
@@ -1,15 +0,0 @@
-<?xml version="1.0" encoding="UTF-8"?>
-<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
-<pkgmetadata>
-	<maintainer type="project">
-		<email>sci@gentoo.org</email>
-		<name>Gentoo Science Project</name>
-	</maintainer>
-	<longdescription lang="en">
-This package contains the core files to be installed for the Intel
-compilers and libraries. Probably useless if installed standalone.
-</longdescription>
-	<use>
-		<flag name="compiler">Install the libraries needed for the icc and ifort compilers</flag>
-	</use>
-</pkgmetadata>
diff --git a/dev-libs/libconfig/libconfig-9999.ebuild b/dev-libs/libconfig/libconfig-9999.ebuild
deleted file mode 100644
index dda594548..000000000
--- a/dev-libs/libconfig/libconfig-9999.ebuild
+++ /dev/null
@@ -1,60 +0,0 @@
-# Copyright 1999-2015 Gentoo Foundation
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=5
-
-AUTOTOOLS_AUTORECONF="1"
-inherit eutils autotools-multilib
-
-DESCRIPTION="Libconfig is a simple library for manipulating structured configuration files"
-HOMEPAGE="http://www.hyperrealm.com/libconfig/libconfig.html"
-
-LICENSE="LGPL-2.1"
-SLOT="0"
-if [[ ${PV} == "9999" ]] ; then
-	EGIT_REPO_URI="https://github.com/hyperrealm/libconfig.git git://github.com/hyperrealm/libconfig.git"
-	inherit git-r3
-	KEYWORDS=""
-else
-	SRC_URI="http://www.hyperrealm.com/${PN}/${P}.tar.gz"
-	KEYWORDS="~amd64 ~arm ~mips ~ppc ~ppc64 ~sparc ~x86 ~x86-linux"
-	PATCHES=( "${FILESDIR}/${P}-out-of-source-build.patch" )
-fi
-
-IUSE="+cxx examples static-libs"
-
-DEPEND="
-	sys-devel/libtool
-	virtual/yacc"
-
-src_prepare() {
-	sed -i configure.ac -e 's|AM_CONFIG_HEADER|AC_CONFIG_HEADERS|g' || die
-	autotools-multilib_src_prepare
-}
-
-multilib_src_configure() {
-	local myeconfargs=(
-		$(use_enable cxx)
-		--disable-examples
-	)
-	autotools-utils_src_configure
-}
-
-multilib_src_test() {
-	# It responds to check but that does not work as intended
-	emake test
-}
-
-multilib_src_install_all() {
-	einstalldocs
-	prune_libtool_files
-
-	if use examples; then
-		find examples/ -name "Makefile.*" -delete || die
-		local dir
-		for dir in examples/c examples/c++; do
-			insinto /usr/share/doc/${PF}/${dir}
-			doins ${dir}/*
-		done
-	fi
-}
diff --git a/dev-libs/libconfig/metadata.xml b/dev-libs/libconfig/metadata.xml
deleted file mode 100644
index 2d70bee59..000000000
--- a/dev-libs/libconfig/metadata.xml
+++ /dev/null
@@ -1,15 +0,0 @@
-<?xml version="1.0" encoding="UTF-8"?>
-<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
-<pkgmetadata>
-	<maintainer type="project">
-		<email>sci@gentoo.org</email>
-		<name>Gentoo Science Project</name>
-	</maintainer>
-	<longdescription lang="en">
-Libconfig is a simple library for processing structured configuration files.
-Libconfig is very compact — a fraction of the size of the expat XML parser library.
-This makes it well-suited for memory-constrained systems like handheld devices.
-The library includes bindings for both the C and C++ languages.
-It works on POSIX-compliant UNIX systems (GNU/Linux, Mac OS X, Solaris, FreeBSD).
-</longdescription>
-</pkgmetadata>
diff --git a/dev-libs/libcuda/files/0001-Fix-detection-of-nouveau-in-case-its-builtin.patch b/dev-libs/libcuda/files/0001-Fix-detection-of-nouveau-in-case-its-builtin.patch
deleted file mode 100644
index aaafd7da7..000000000
--- a/dev-libs/libcuda/files/0001-Fix-detection-of-nouveau-in-case-its-builtin.patch
+++ /dev/null
@@ -1,26 +0,0 @@
-From 605e69e70ce7b4c505be91696612e98649ec383f Mon Sep 17 00:00:00 2001
-From: Alexey Shvetsov <alexxy@gentoo.org>
-Date: Thu, 15 Nov 2012 08:29:04 +0400
-Subject: [PATCH 1/5] Fix detection of nouveau in case its builtin
-
-Signed-off-by: Alexey Shvetsov <alexxy@gentoo.org>
----
- common/autogen.sh | 2 ++
- 1 file changed, 2 insertions(+)
-
-diff --git a/common/autogen.sh b/common/autogen.sh
-index 469d3d8..1dca70f 100644
---- a/common/autogen.sh
-+++ b/common/autogen.sh
-@@ -4,6 +4,8 @@ if [ ! $(lsmod | grep nvidia | wc -l) -eq 0 ] ; then
- 	driver='nvi'
- elif [ ! $(lsmod | grep nouveau | wc -l) -eq 0 ] ; then
- 	driver='nouveau'
-+elif [ ! $(zgrep NOUVEAU /proc/config.gz | grep y | wc -l) -eq 0 ] ; then
-+	driver='nouveau'
- elif [ ! $(lsmod | grep pscnv | wc -l) -eq 0 ] ; then
- 	driver='pscnv'
- else
--- 
-1.7.12.3
-
diff --git a/dev-libs/libcuda/files/0002-Fix-install-target-for-gdev-lib-userspace.patch b/dev-libs/libcuda/files/0002-Fix-install-target-for-gdev-lib-userspace.patch
deleted file mode 100644
index 797136fae..000000000
--- a/dev-libs/libcuda/files/0002-Fix-install-target-for-gdev-lib-userspace.patch
+++ /dev/null
@@ -1,36 +0,0 @@
-From 870f4cddb0233188ec1613a44eb9feb8c94469da Mon Sep 17 00:00:00 2001
-From: Alexey Shvetsov <alexxy@gentoo.org>
-Date: Thu, 15 Nov 2012 08:34:55 +0400
-Subject: [PATCH 2/5] Fix install target for gdev lib userspace
-
-Signed-off-by: Alexey Shvetsov <alexxy@gentoo.org>
----
- lib/user/gdev/Makefile | 12 ++++++------
- 1 file changed, 6 insertions(+), 6 deletions(-)
-
-diff --git a/lib/user/gdev/Makefile b/lib/user/gdev/Makefile
-index d602fa9..5440469 100644
---- a/lib/user/gdev/Makefile
-+++ b/lib/user/gdev/Makefile
-@@ -22,12 +22,12 @@ all: $(OBJS)
- 	$(CC) -fPIC -c $^ -o $@ $(CFLAGS) $(EXTRA_LIBS)
- 
- install:
--	@if test ! -d $(GDEVDIR) ; then mkdir $(GDEVDIR) ; fi ;
--	@if test ! -d $(GDEVDIR)/lib64 ; then mkdir $(GDEVDIR)/lib64 ; fi ;
--	@if test ! -d $(GDEVDIR)/include ; then mkdir $(GDEVDIR)/include ; fi ;
--	cp -f ./$(TARGET).so.1.0.0 $(GDEVDIR)/lib64/
--	ln -sf $(GDEVDIR)/lib64/$(TARGET).so.1.0.0 $(GDEVDIR)/lib64/$(TARGET).so.1
--	ln -sf $(GDEVDIR)/lib64/$(TARGET).so.1 $(GDEVDIR)/lib64/$(TARGET).so
-+	@if test ! -d $(GDEVDIR) ; then mkdir $(DESTDIR)/$(GDEVDIR) ; fi ;
-+	@if test ! -d $(GDEVDIR)/lib64 ; then mkdir $(DESTDIR)/$(GDEVDIR)/lib64 ; fi ;
-+	@if test ! -d $(GDEVDIR)/include ; then mkdir $(DESTDIR)/$(GDEVDIR)/include ; fi ;
-+	cp -f ./$(TARGET).so.1.0.0 $(DESTDIR)/$(GDEVDIR)/lib64/
-+	ln -sf $(GDEVDIR)/lib64/$(TARGET).so.1.0.0 $(DESTDIR)/$(GDEVDIR)/lib64/$(TARGET).so.1
-+	ln -sf $(GDEVDIR)/lib64/$(TARGET).so.1 $(DESTDIR)/$(GDEVDIR)/lib64/$(TARGET).so
- 	cp -f $(HEADERS) $(GDEVDIR)/include
- 
- uninstall:
--- 
-1.7.12.3
-
diff --git a/dev-libs/libcuda/files/0003-Fix-install-target-for-gdev-lib-userspace-part2.patch b/dev-libs/libcuda/files/0003-Fix-install-target-for-gdev-lib-userspace-part2.patch
deleted file mode 100644
index 159ebd737..000000000
--- a/dev-libs/libcuda/files/0003-Fix-install-target-for-gdev-lib-userspace-part2.patch
+++ /dev/null
@@ -1,35 +0,0 @@
-From d99538f4e1f313c385a40ccff6aa3adff62ec55e Mon Sep 17 00:00:00 2001
-From: Alexey Shvetsov <alexxy@gentoo.org>
-Date: Thu, 15 Nov 2012 08:41:13 +0400
-Subject: [PATCH 3/5] Fix install target for gdev lib userspace part2
-
-Signed-off-by: Alexey Shvetsov <alexxy@gentoo.org>
----
- lib/user/gdev/Makefile | 8 ++++----
- 1 file changed, 4 insertions(+), 4 deletions(-)
-
-diff --git a/lib/user/gdev/Makefile b/lib/user/gdev/Makefile
-index 5440469..31bee51 100644
---- a/lib/user/gdev/Makefile
-+++ b/lib/user/gdev/Makefile
-@@ -22,13 +22,13 @@ all: $(OBJS)
- 	$(CC) -fPIC -c $^ -o $@ $(CFLAGS) $(EXTRA_LIBS)
- 
- install:
--	@if test ! -d $(GDEVDIR) ; then mkdir $(DESTDIR)/$(GDEVDIR) ; fi ;
--	@if test ! -d $(GDEVDIR)/lib64 ; then mkdir $(DESTDIR)/$(GDEVDIR)/lib64 ; fi ;
--	@if test ! -d $(GDEVDIR)/include ; then mkdir $(DESTDIR)/$(GDEVDIR)/include ; fi ;
-+	@if test ! -d $(DESTDIR)/$(GDEVDIR) ; then mkdir $(DESTDIR)/$(GDEVDIR) ; fi ;
-+	@if test ! -d $(DESTDIR)/$(GDEVDIR)/lib64 ; then mkdir $(DESTDIR)/$(GDEVDIR)/lib64 ; fi ;
-+	@if test ! -d $(DESTDIR)/$(GDEVDIR)/include ; then mkdir $(DESTDIR)/$(GDEVDIR)/include ; fi ;
- 	cp -f ./$(TARGET).so.1.0.0 $(DESTDIR)/$(GDEVDIR)/lib64/
- 	ln -sf $(GDEVDIR)/lib64/$(TARGET).so.1.0.0 $(DESTDIR)/$(GDEVDIR)/lib64/$(TARGET).so.1
- 	ln -sf $(GDEVDIR)/lib64/$(TARGET).so.1 $(DESTDIR)/$(GDEVDIR)/lib64/$(TARGET).so
--	cp -f $(HEADERS) $(GDEVDIR)/include
-+	cp -f $(HEADERS) $(DESTDIR)/$(GDEVDIR)/include
- 
- uninstall:
- 	rm -f $(GDEVDIR)/lib64/$(TARGET).*
--- 
-1.7.12.3
-
diff --git a/dev-libs/libcuda/files/0004-Respect-extra-CFLAGS-and-LDFLAGS.patch b/dev-libs/libcuda/files/0004-Respect-extra-CFLAGS-and-LDFLAGS.patch
deleted file mode 100644
index 199da0bd2..000000000
--- a/dev-libs/libcuda/files/0004-Respect-extra-CFLAGS-and-LDFLAGS.patch
+++ /dev/null
@@ -1,26 +0,0 @@
-From 4f97a0ec262d190741f16d5d75c9305ee6a4318b Mon Sep 17 00:00:00 2001
-From: Alexey Shvetsov <alexxy@gentoo.org>
-Date: Thu, 15 Nov 2012 08:43:59 +0400
-Subject: [PATCH 4/5] Respect extra CFLAGS and LDFLAGS
-
-Signed-off-by: Alexey Shvetsov <alexxy@gentoo.org>
----
- lib/user/gdev/Makefile | 2 +-
- 1 file changed, 1 insertion(+), 1 deletion(-)
-
-diff --git a/lib/user/gdev/Makefile b/lib/user/gdev/Makefile
-index 31bee51..d9c2200 100644
---- a/lib/user/gdev/Makefile
-+++ b/lib/user/gdev/Makefile
-@@ -16,7 +16,7 @@ OBJS = 	$(DRIVER_NAME)_gdev.o lib$(DRIVER_NAME).o lib$(DRIVER_NAME)_ib.o \
- ZOMBIE  = $(wildcard ./*~)
- 
- all: $(OBJS)
--	$(CC) -shared -Wl,-soname,$(TARGET).so.1 -o ./$(TARGET).so.1.0.0 $(OBJS) $(EXTRA_LIBS)
-+	$(CC) $(LDFLAGS) -shared -Wl,-soname,$(TARGET).so.1 -o ./$(TARGET).so.1.0.0 $(OBJS) $(EXTRA_LIBS)
- 
- %.o:%.c
- 	$(CC) -fPIC -c $^ -o $@ $(CFLAGS) $(EXTRA_LIBS)
--- 
-1.7.12.3
-
diff --git a/dev-libs/libcuda/files/0005-Fix-install-target-for-cuda-lib.patch b/dev-libs/libcuda/files/0005-Fix-install-target-for-cuda-lib.patch
deleted file mode 100644
index 783f3c78b..000000000
--- a/dev-libs/libcuda/files/0005-Fix-install-target-for-cuda-lib.patch
+++ /dev/null
@@ -1,47 +0,0 @@
-From 720760c6a69cd3d8a3d7682327dbb234a5a473f5 Mon Sep 17 00:00:00 2001
-From: Alexey Shvetsov <alexxy@gentoo.org>
-Date: Thu, 15 Nov 2012 09:00:25 +0400
-Subject: [PATCH 5/5] Fix install target for cuda lib
-
-Signed-off-by: Alexey Shvetsov <alexxy@gentoo.org>
----
- cuda/libcuda/Makefile | 18 ++++++++++--------
- 1 file changed, 10 insertions(+), 8 deletions(-)
-
-diff --git a/cuda/libcuda/Makefile b/cuda/libcuda/Makefile
-index 1a296bb..cdfd360 100644
---- a/cuda/libcuda/Makefile
-+++ b/cuda/libcuda/Makefile
-@@ -12,19 +12,21 @@ CUDUMP_OBJS = cudump.o gdev_cuda.o
- ZOMBIE  = $(wildcard ./*~)
- 
- all: $(OBJS)
--	$(CC) -shared -Wl,-soname,$(TARGET).so.1 -o ./$(TARGET).so.1.0.0 $(OBJS) 
--	$(CC) $(CFLAGS) -o ./$(CUDUMP) $(CUDUMP).c gdev_cuda.c
-+	$(CC) $(LDFLAGS)  -shared -Wl,-soname,$(TARGET).so.1 -o ./$(TARGET).so.1.0.0 $(OBJS) 
-+	$(CC) $(LDFLAGS) $(CFLAGS) -o ./$(CUDUMP) $(CUDUMP).c gdev_cuda.c
- 
- %.o:%.c
- 	$(CC) -fPIC -c $^ -o $@ $(CFLAGS)
- 
- install:
--	@if test ! -d $(GDEVDIR)/bin ; then mkdir $(GDEVDIR)/bin ; fi ;
--	cp -f ./$(CUDUMP) $(GDEVDIR)/bin/
--	cp -f ./$(TARGET).so.1.0.0 $(GDEVDIR)/lib64/
--	ln -sf $(GDEVDIR)/lib64/$(TARGET).so.1.0.0 $(GDEVDIR)/lib64/$(TARGET).so.1
--	ln -sf $(GDEVDIR)/lib64/$(TARGET).so.1 $(GDEVDIR)/lib64/$(TARGET).so
--	cp -f ./cuda.h $(GDEVDIR)/include
-+	@if test ! -d $(DESTDIR)/$(GDEVDIR)/bin ; then mkdir -p $(DESTDIR)/$(GDEVDIR)/bin ; fi ;
-+	@if test ! -d $(DESTDIR)/$(GDEVDIR)/lib64 ; then mkdir -p $(DESTDIR)/$(GDEVDIR)/lib64 ; fi ;
-+	@if test ! -d $(DESTDIR)/$(GDEVDIR)/include ; then mkdir -p $(DESTDIR)/$(GDEVDIR)/include ; fi ;
-+	cp -f ./$(CUDUMP) $(DESTDIR)/$(GDEVDIR)/bin/
-+	cp -f ./$(TARGET).so.1.0.0 $(DESTDIR)/$(GDEVDIR)/lib64/
-+	ln -sf $(GDEVDIR)/lib64/$(TARGET).so.1.0.0 $(DESTDIR)/$(GDEVDIR)/lib64/$(TARGET).so.1
-+	ln -sf $(GDEVDIR)/lib64/$(TARGET).so.1 $(DESTDIR)/$(GDEVDIR)/lib64/$(TARGET).so
-+	cp -f ./cuda.h $(DESTDIR)/$(GDEVDIR)/include
- 
- uninstall:
- 	rm -f $(GDEVDIR)/lib64/$(TARGET).*
--- 
-1.7.12.3
-
diff --git a/dev-libs/libcuda/libcuda-9999.ebuild b/dev-libs/libcuda/libcuda-9999.ebuild
deleted file mode 100644
index d42357101..000000000
--- a/dev-libs/libcuda/libcuda-9999.ebuild
+++ /dev/null
@@ -1,43 +0,0 @@
-# Copyright 1999-2014 Gentoo Foundation
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=5
-
-inherit git-r3
-
-DESCRIPTION="Gdev is open-source GPGPU runtime"
-HOMEPAGE="https://github.com/shinpei0208/gdev"
-SRC_URI=""
-EGIT_REPO_URI="
-	git://github.com/shinpei0208/gdev.git
-	https://github.com/shinpei0208/gdev.git"
-
-LICENSE="GPL-2"
-SLOT="0"
-KEYWORDS=""
-IUSE=""
-
-RDEPEND="
-	dev-libs/libgdev
-	x11-libs/libdrm[video_cards_nouveau]
-	x11-misc/envytools"
-DEPEND="
-	virtual/pkgconfig
-	${RDEPEND}"
-
-src_configure() {
-	cd cuda || die
-	mkdir build || die
-	cd build || die
-	../configure || die
-}
-
-src_compile() {
-	cd cuda/build || die
-	emake GDEVDIR="${EPREFIX}/usr"
-}
-
-src_install() {
-	cd cuda/build || die
-	emake GDEVDIR="${EPREFIX}/usr" DESTDIR="${D}" install
-}
diff --git a/dev-libs/libcuda/metadata.xml b/dev-libs/libcuda/metadata.xml
deleted file mode 100644
index 1bee8dd17..000000000
--- a/dev-libs/libcuda/metadata.xml
+++ /dev/null
@@ -1,11 +0,0 @@
-<?xml version="1.0" encoding="UTF-8"?>
-<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
-<pkgmetadata>
-	<maintainer type="person">
-		<email>alexxy@gentoo.org</email>
-		<name>Alexey Shvetsov</name>
-	</maintainer>
-	<upstream>
-		<remote-id type="github">shinpei0208/gdev</remote-id>
-	</upstream>
-</pkgmetadata>
diff --git a/dev-libs/libflatarray/libflatarray-9999.ebuild b/dev-libs/libflatarray/libflatarray-9999.ebuild
deleted file mode 100644
index 12132ab11..000000000
--- a/dev-libs/libflatarray/libflatarray-9999.ebuild
+++ /dev/null
@@ -1,51 +0,0 @@
-# Copyright 1999-2014 Gentoo Foundation
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=5
-
-if [ ${PV} == "9999" ] ; then
-	_SCM=mercurial
-	EHG_REPO_URI="http://bitbucket.org/gentryx/libflatarray"
-	SRC_URI=""
-	KEYWORDS=""
-	CMAKE_USE_DIR="${S}"
-else
-	SRC_URI="http://www.libgeodecomp.org/archive/${P}.tar.bz2"
-	KEYWORDS="~amd64 ~ppc ~x86"
-	S="${WORKDIR}/${P}"
-fi
-
-inherit cmake-utils cuda ${_SCM}
-
-DESCRIPTION="Struct of arrays library with object oriented interface for C++"
-HOMEPAGE="http://www.libgeodecomp.org/libflatarray.html"
-
-SLOT="0"
-LICENSE="Boost-1.0"
-IUSE="cuda doc"
-
-RDEPEND="
-	>=dev-libs/boost-1.48
-	cuda? ( dev-util/nvidia-cuda-toolkit )"
-DEPEND="${RDEPEND}
-	doc? ( app-doc/doxygen )"
-
-src_configure() {
-	local mycmakeargs=(
-		$(cmake-utils_use_with cuda CUDA)
-	)
-	cmake-utils_src_configure
-}
-
-src_compile() {
-	cmake-utils_src_compile
-}
-
-src_install() {
-	DOCS=( README )
-	cmake-utils_src_install
-}
-
-src_test() {
-	cmake-utils_src_make test
-}
diff --git a/dev-libs/libflatarray/metadata.xml b/dev-libs/libflatarray/metadata.xml
deleted file mode 100644
index 124b52db7..000000000
--- a/dev-libs/libflatarray/metadata.xml
+++ /dev/null
@@ -1,22 +0,0 @@
-<?xml version="1.0" encoding="UTF-8"?>
-<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
-<pkgmetadata>
-	<longdescription>
-LibGeoDecomp is a multi-dimensional C++ array class which provides
-an object-oriented view (a.k.a. array of structs, AoS) while
-internally storing data in a struct of arrays (SoA) manner. It
-comes with utilities to move data to CUDA enabled GPUs.
-</longdescription>
-	<maintainer type="person">
-		<email>gentryx@gmx.de</email>
-	</maintainer>
-	<maintainer type="project">
-		<email>cluster@gentoo.org</email>
-		<name>Gentoo Cluster Project</name>
-	</maintainer>
-	<use>
-		<flag name="cuda">
-Enables plugins for NVIDIA GPUs (e.g. CUDAAllocator)
-</flag>
-	</use>
-</pkgmetadata>
diff --git a/dev-libs/libgdev/files/0001-Fix-detection-of-nouveau-in-case-its-builtin.patch b/dev-libs/libgdev/files/0001-Fix-detection-of-nouveau-in-case-its-builtin.patch
deleted file mode 100644
index e8ac9888d..000000000
--- a/dev-libs/libgdev/files/0001-Fix-detection-of-nouveau-in-case-its-builtin.patch
+++ /dev/null
@@ -1,26 +0,0 @@
-From 605e69e70ce7b4c505be91696612e98649ec383f Mon Sep 17 00:00:00 2001
-From: Alexey Shvetsov <alexxy@gentoo.org>
-Date: Thu, 15 Nov 2012 08:29:04 +0400
-Subject: [PATCH 1/4] Fix detection of nouveau in case its builtin
-
-Signed-off-by: Alexey Shvetsov <alexxy@gentoo.org>
----
- common/autogen.sh | 2 ++
- 1 file changed, 2 insertions(+)
-
-diff --git a/common/autogen.sh b/common/autogen.sh
-index 469d3d8..1dca70f 100644
---- a/common/autogen.sh
-+++ b/common/autogen.sh
-@@ -4,6 +4,8 @@ if [ ! $(lsmod | grep nvidia | wc -l) -eq 0 ] ; then
- 	driver='nvi'
- elif [ ! $(lsmod | grep nouveau | wc -l) -eq 0 ] ; then
- 	driver='nouveau'
-+elif [ ! $(zgrep NOUVEAU /proc/config.gz | grep y | wc -l) -eq 0 ] ; then
-+	driver='nouveau'
- elif [ ! $(lsmod | grep pscnv | wc -l) -eq 0 ] ; then
- 	driver='pscnv'
- else
--- 
-1.7.12.3
-
diff --git a/dev-libs/libgdev/files/0002-Fix-install-target-for-gdev-lib-userspace.patch b/dev-libs/libgdev/files/0002-Fix-install-target-for-gdev-lib-userspace.patch
deleted file mode 100644
index 9fe84c100..000000000
--- a/dev-libs/libgdev/files/0002-Fix-install-target-for-gdev-lib-userspace.patch
+++ /dev/null
@@ -1,36 +0,0 @@
-From 870f4cddb0233188ec1613a44eb9feb8c94469da Mon Sep 17 00:00:00 2001
-From: Alexey Shvetsov <alexxy@gentoo.org>
-Date: Thu, 15 Nov 2012 08:34:55 +0400
-Subject: [PATCH 2/4] Fix install target for gdev lib userspace
-
-Signed-off-by: Alexey Shvetsov <alexxy@gentoo.org>
----
- lib/user/gdev/Makefile | 12 ++++++------
- 1 file changed, 6 insertions(+), 6 deletions(-)
-
-diff --git a/lib/user/gdev/Makefile b/lib/user/gdev/Makefile
-index d602fa9..5440469 100644
---- a/lib/user/gdev/Makefile
-+++ b/lib/user/gdev/Makefile
-@@ -22,12 +22,12 @@ all: $(OBJS)
- 	$(CC) -fPIC -c $^ -o $@ $(CFLAGS) $(EXTRA_LIBS)
- 
- install:
--	@if test ! -d $(GDEVDIR) ; then mkdir $(GDEVDIR) ; fi ;
--	@if test ! -d $(GDEVDIR)/lib64 ; then mkdir $(GDEVDIR)/lib64 ; fi ;
--	@if test ! -d $(GDEVDIR)/include ; then mkdir $(GDEVDIR)/include ; fi ;
--	cp -f ./$(TARGET).so.1.0.0 $(GDEVDIR)/lib64/
--	ln -sf $(GDEVDIR)/lib64/$(TARGET).so.1.0.0 $(GDEVDIR)/lib64/$(TARGET).so.1
--	ln -sf $(GDEVDIR)/lib64/$(TARGET).so.1 $(GDEVDIR)/lib64/$(TARGET).so
-+	@if test ! -d $(GDEVDIR) ; then mkdir $(DESTDIR)/$(GDEVDIR) ; fi ;
-+	@if test ! -d $(GDEVDIR)/lib64 ; then mkdir $(DESTDIR)/$(GDEVDIR)/lib64 ; fi ;
-+	@if test ! -d $(GDEVDIR)/include ; then mkdir $(DESTDIR)/$(GDEVDIR)/include ; fi ;
-+	cp -f ./$(TARGET).so.1.0.0 $(DESTDIR)/$(GDEVDIR)/lib64/
-+	ln -sf $(GDEVDIR)/lib64/$(TARGET).so.1.0.0 $(DESTDIR)/$(GDEVDIR)/lib64/$(TARGET).so.1
-+	ln -sf $(GDEVDIR)/lib64/$(TARGET).so.1 $(DESTDIR)/$(GDEVDIR)/lib64/$(TARGET).so
- 	cp -f $(HEADERS) $(GDEVDIR)/include
- 
- uninstall:
--- 
-1.7.12.3
-
diff --git a/dev-libs/libgdev/files/0003-Fix-install-target-for-gdev-lib-userspace-part2.patch b/dev-libs/libgdev/files/0003-Fix-install-target-for-gdev-lib-userspace-part2.patch
deleted file mode 100644
index 39b31be6e..000000000
--- a/dev-libs/libgdev/files/0003-Fix-install-target-for-gdev-lib-userspace-part2.patch
+++ /dev/null
@@ -1,35 +0,0 @@
-From d99538f4e1f313c385a40ccff6aa3adff62ec55e Mon Sep 17 00:00:00 2001
-From: Alexey Shvetsov <alexxy@gentoo.org>
-Date: Thu, 15 Nov 2012 08:41:13 +0400
-Subject: [PATCH 3/4] Fix install target for gdev lib userspace part2
-
-Signed-off-by: Alexey Shvetsov <alexxy@gentoo.org>
----
- lib/user/gdev/Makefile | 8 ++++----
- 1 file changed, 4 insertions(+), 4 deletions(-)
-
-diff --git a/lib/user/gdev/Makefile b/lib/user/gdev/Makefile
-index 5440469..31bee51 100644
---- a/lib/user/gdev/Makefile
-+++ b/lib/user/gdev/Makefile
-@@ -22,13 +22,13 @@ all: $(OBJS)
- 	$(CC) -fPIC -c $^ -o $@ $(CFLAGS) $(EXTRA_LIBS)
- 
- install:
--	@if test ! -d $(GDEVDIR) ; then mkdir $(DESTDIR)/$(GDEVDIR) ; fi ;
--	@if test ! -d $(GDEVDIR)/lib64 ; then mkdir $(DESTDIR)/$(GDEVDIR)/lib64 ; fi ;
--	@if test ! -d $(GDEVDIR)/include ; then mkdir $(DESTDIR)/$(GDEVDIR)/include ; fi ;
-+	@if test ! -d $(DESTDIR)/$(GDEVDIR) ; then mkdir $(DESTDIR)/$(GDEVDIR) ; fi ;
-+	@if test ! -d $(DESTDIR)/$(GDEVDIR)/lib64 ; then mkdir $(DESTDIR)/$(GDEVDIR)/lib64 ; fi ;
-+	@if test ! -d $(DESTDIR)/$(GDEVDIR)/include ; then mkdir $(DESTDIR)/$(GDEVDIR)/include ; fi ;
- 	cp -f ./$(TARGET).so.1.0.0 $(DESTDIR)/$(GDEVDIR)/lib64/
- 	ln -sf $(GDEVDIR)/lib64/$(TARGET).so.1.0.0 $(DESTDIR)/$(GDEVDIR)/lib64/$(TARGET).so.1
- 	ln -sf $(GDEVDIR)/lib64/$(TARGET).so.1 $(DESTDIR)/$(GDEVDIR)/lib64/$(TARGET).so
--	cp -f $(HEADERS) $(GDEVDIR)/include
-+	cp -f $(HEADERS) $(DESTDIR)/$(GDEVDIR)/include
- 
- uninstall:
- 	rm -f $(GDEVDIR)/lib64/$(TARGET).*
--- 
-1.7.12.3
-
diff --git a/dev-libs/libgdev/files/0004-Respect-extra-CFLAGS-and-LDFLAGS.patch b/dev-libs/libgdev/files/0004-Respect-extra-CFLAGS-and-LDFLAGS.patch
deleted file mode 100644
index 44e48daa4..000000000
--- a/dev-libs/libgdev/files/0004-Respect-extra-CFLAGS-and-LDFLAGS.patch
+++ /dev/null
@@ -1,26 +0,0 @@
-From 4f97a0ec262d190741f16d5d75c9305ee6a4318b Mon Sep 17 00:00:00 2001
-From: Alexey Shvetsov <alexxy@gentoo.org>
-Date: Thu, 15 Nov 2012 08:43:59 +0400
-Subject: [PATCH 4/4] Respect extra CFLAGS and LDFLAGS
-
-Signed-off-by: Alexey Shvetsov <alexxy@gentoo.org>
----
- lib/user/gdev/Makefile | 2 +-
- 1 file changed, 1 insertion(+), 1 deletion(-)
-
-diff --git a/lib/user/gdev/Makefile b/lib/user/gdev/Makefile
-index 31bee51..d9c2200 100644
---- a/lib/user/gdev/Makefile
-+++ b/lib/user/gdev/Makefile
-@@ -16,7 +16,7 @@ OBJS = 	$(DRIVER_NAME)_gdev.o lib$(DRIVER_NAME).o lib$(DRIVER_NAME)_ib.o \
- ZOMBIE  = $(wildcard ./*~)
- 
- all: $(OBJS)
--	$(CC) -shared -Wl,-soname,$(TARGET).so.1 -o ./$(TARGET).so.1.0.0 $(OBJS) $(EXTRA_LIBS)
-+	$(CC) $(LDFLAGS) -shared -Wl,-soname,$(TARGET).so.1 -o ./$(TARGET).so.1.0.0 $(OBJS) $(EXTRA_LIBS)
- 
- %.o:%.c
- 	$(CC) -fPIC -c $^ -o $@ $(CFLAGS) $(EXTRA_LIBS)
--- 
-1.7.12.3
-
diff --git a/dev-libs/libgdev/libgdev-9999.ebuild b/dev-libs/libgdev/libgdev-9999.ebuild
deleted file mode 100644
index 39a444fa3..000000000
--- a/dev-libs/libgdev/libgdev-9999.ebuild
+++ /dev/null
@@ -1,44 +0,0 @@
-# Copyright 1999-2014 Gentoo Foundation
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=5
-
-inherit git-r3 toolchain-funcs
-
-DESCRIPTION="Gdev is open-source GPGPU runtime"
-HOMEPAGE="https://github.com/shinpei0208/gdev"
-SRC_URI=""
-EGIT_REPO_URI="
-	git://github.com/shinpei0208/gdev.git
-	https://github.com/shinpei0208/gdev.git"
-
-LICENSE="GPL-2"
-SLOT="0"
-KEYWORDS=""
-IUSE=""
-
-RDEPEND="
-	x11-libs/libdrm[video_cards_nouveau]
-	x11-misc/envytools"
-DEPEND="
-	virtual/pkgconfig
-	${RDEPEND}"
-
-src_configure() {
-	cd lib || die
-	mkdir build || die
-	cd build || die
-	../configure --target=user || die
-}
-
-src_compile() {
-	cd lib/build || die
-	emake \
-		EXTRA_CFLAGS="$($(tc-getPKG_CONFIG) --cflags-only-I libdrm)" \
-		EXTRA_LIBS="$($(tc-getPKG_CONFIG) --libs libdrm_nouveau)"
-}
-
-src_install() {
-	cd lib/build || die
-	emake GDEVDIR="${EPREFIX}/usr" DESTDIR="${D}" install
-}
diff --git a/dev-libs/libgdev/metadata.xml b/dev-libs/libgdev/metadata.xml
deleted file mode 100644
index 1bee8dd17..000000000
--- a/dev-libs/libgdev/metadata.xml
+++ /dev/null
@@ -1,11 +0,0 @@
-<?xml version="1.0" encoding="UTF-8"?>
-<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
-<pkgmetadata>
-	<maintainer type="person">
-		<email>alexxy@gentoo.org</email>
-		<name>Alexey Shvetsov</name>
-	</maintainer>
-	<upstream>
-		<remote-id type="github">shinpei0208/gdev</remote-id>
-	</upstream>
-</pkgmetadata>
diff --git a/dev-libs/libunzip/Manifest b/dev-libs/libunzip/Manifest
deleted file mode 100644
index 596a7c553..000000000
--- a/dev-libs/libunzip/Manifest
+++ /dev/null
@@ -1 +0,0 @@
-DIST unzip552.tar.gz 1140291 BLAKE2B e761d44223fd566c6327a7030f52448217cce7516f61d86696ab0e0f8c9490ec63b9b941607348f7a3ad7819de7804e0a7c1b9106d1c85d93a1c26aa5fa35bba SHA512 9b852687a7cbce3a6696f8da176f97eded1e99b1f10ae5e4b29bf870df374fea3e4266b3a731d7cdfc28ce5c060a01dd8d3f9c3d8250d1d774273de16d70528b
diff --git a/dev-libs/libunzip/files/libunzip-5.52-CVE-2008-0888.patch b/dev-libs/libunzip/files/libunzip-5.52-CVE-2008-0888.patch
deleted file mode 100644
index 368b3eeb1..000000000
--- a/dev-libs/libunzip/files/libunzip-5.52-CVE-2008-0888.patch
+++ /dev/null
@@ -1,35 +0,0 @@
-http://bugs.gentoo.org/213761
-
-fix for CVE-2008-0888
-
---- inflate.c
-+++ inflate.c
-@@ -983,6 +983,7 @@
-   unsigned l;           /* last length */
-   unsigned m;           /* mask for bit lengths table */
-   unsigned n;           /* number of lengths to get */
-+  struct huft *tlp;     
-   struct huft *tl;      /* literal/length code table */
-   struct huft *td;      /* distance code table */
-   unsigned bl;          /* lookup bits for tl */
-@@ -996,6 +997,8 @@
-   int retval = 0;       /* error code returned: initialized to "no error" */
- 
- 
-+  td = tlp = tl = (struct huft *)NULL;
-+
-   /* make local bit buffer */
-   Trace((stderr, "\ndynamic block"));
-   b = G.bb;
-@@ -1047,9 +1050,9 @@
-   while (i < n)
-   {
-     NEEDBITS(bl)
--    j = (td = tl + ((unsigned)b & m))->b;
-+    j = (tlp = tl + ((unsigned)b & m))->b;
-     DUMPBITS(j)
--    j = td->v.n;
-+    j = tlp->v.n;
-     if (j < 16)                 /* length of code in bits (0..15) */
-       ll[i++] = l = j;          /* save last length in l */
-     else if (j == 16)           /* repeat last length 3 to 6 times */
diff --git a/dev-libs/libunzip/files/libunzip-5.52-Makefile.patch b/dev-libs/libunzip/files/libunzip-5.52-Makefile.patch
deleted file mode 100644
index b8787f2f2..000000000
--- a/dev-libs/libunzip/files/libunzip-5.52-Makefile.patch
+++ /dev/null
@@ -1,31 +0,0 @@
---- unix/Makefile	2005-02-26 20:58:34.000000000 +0100
-+++ unix/Makefile.new	2009-04-12 19:49:56.000000000 +0200
-@@ -45,6 +45,7 @@
- CC = cc#	try using "gcc" target rather than changing this (CC and LD
- LD = $(CC)#	must match, else "unresolved symbol:  ___main" is possible)
- AS = as
-+RANLIB =
- LOC = $(LOCAL_UNZIP)
- AF = $(LOC)
- CF = -O -I. -DUNIX $(LOC)
-@@ -810,14 +810,14 @@
- #
- linux_shlib:	unix_make
- #	$(MAKE) objsdll CC=gcc CF="-O3 -Wall -I. -fPIC -DDLL $(LOC)"
--	$(MAKE) objsdll CC=gcc CF="-O3 -Wall -I. -fPIC -DDLL -DASM_CRC $(LOC)"\
--	 AS=gcc AF="-fPIC -Di386 $(AF)" CRC32=crc_gcc
--	ln -sf crc_gcc.pic.o crc32.pic.o
--	gcc -shared -Wl,-soname,libunzip.so.0 -o libunzip.so.0.4 $(OBJSDLL)
-+	$(MAKE) objsdll CC=gcc CF="-O3 -Wall -I. -fPIC -DDLL -DUNIX $(LOC)"
-+	$(LD) $(LDFLAGS) -shared -Wl,-soname,libunzip.so.0 -o libunzip.so.0.4 $(OBJSDLL)
-+	$(AR) $(ARFLAGS) libunzip.a $(OBJSDLL)
-+	$(RANLIB) libunzip.a
- 	ln -sf libunzip.so.0.4 libunzip.so.0
- 	ln -sf libunzip.so.0 libunzip.so
--	gcc -c -O unzipstb.c
--	gcc -o unzip_shlib unzipstb.o -L. -lunzip
-+	$(CC) $(CFLAGS) -c unzipstb.c
-+	$(LD) $(LDFLAGS) -o unzip_shlib unzipstb.o -L. -lunzip
- 
- # Linux ELF shared library, as above, but using inflate() from zlib (libz.so)
- # instead of the original UnZip version.  (libz was libgz prior to 0.94)
diff --git a/dev-libs/libunzip/files/libunzip-5.52-no-exec-stack.patch b/dev-libs/libunzip/files/libunzip-5.52-no-exec-stack.patch
deleted file mode 100644
index e2869bfe8..000000000
--- a/dev-libs/libunzip/files/libunzip-5.52-no-exec-stack.patch
+++ /dev/null
@@ -1,13 +0,0 @@
-Make sure that the asm files don't incorrectly trigger an executable
-stack marking in the final shared library.  That's bad, mmmkay.
-
---- unzip/crc_i386.S
-+++ unzip/crc_i386.S
-@@ -238,3 +238,7 @@
- #endif /* i386 || _i386 || _I386 || __i386 */
- 
- #endif /* !USE_ZLIB */
-+
-+#ifdef __ELF__
-+.section .note.GNU-stack,"",%progbits
-+#endif
diff --git a/dev-libs/libunzip/libunzip-5.52.ebuild b/dev-libs/libunzip/libunzip-5.52.ebuild
deleted file mode 100644
index 15f6ae723..000000000
--- a/dev-libs/libunzip/libunzip-5.52.ebuild
+++ /dev/null
@@ -1,51 +0,0 @@
-# Copyright 1999-2015 Gentoo Foundation
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=5
-
-inherit eutils flag-o-matic toolchain-funcs
-
-MY_PN="${PN#lib}"
-
-DESCRIPTION="libunzip.so"
-HOMEPAGE="http://www.info-zip.org/"
-SRC_URI="mirror://gentoo/${MY_PN}${PV/.}.tar.gz"
-
-LICENSE="Info-ZIP"
-SLOT="0"
-KEYWORDS="~amd64 ~x86"
-IUSE="static-libs"
-
-S="${WORKDIR}/${MY_PN}-${PV}"
-
-src_prepare() {
-	epatch \
-		"${FILESDIR}"/${P}-no-exec-stack.patch \
-		"${FILESDIR}"/${P}-CVE-2008-0888.patch \
-		"${FILESDIR}"/${P}-Makefile.patch
-	sed -i \
-		-e 's:-O3:$(CFLAGS) $(CPPFLAGS):' \
-		-e 's:-O :$(CFLAGS) $(CPPFLAGS) :' \
-		-e "s:CC=gcc :CC=$(tc-getCC) :" \
-		-e "s:CC = cc:CC=$(tc-getCC) :" \
-		-e "s:LD=gcc :LD=$(tc-getCC) :" \
-		-e "s:AS=gcc :AS=$(tc-getCC) :" \
-		-e "s:RANLIB =:RANLIB = $(tc-getRANLIB) :" \
-		-e 's:LF2 = -s:LF2 = :' \
-		-e 's:LF = :LF = $(LDFLAGS) :' \
-		-e 's:SL = :SL = $(LDFLAGS) :' \
-		-e 's:FL = :FL = $(LDFLAGS) :' \
-		unix/Makefile \
-		|| die "sed unix/Makefile failed"
-}
-
-src_compile() {
-	append-lfs-flags #104315
-	emake -f unix/Makefile linux_shlib
-}
-
-src_install() {
-	dolib.so ${PN}.so*
-	use static-libs && dolib.a ${PN}.a
-	doheader unzip.h
-}
diff --git a/dev-libs/libunzip/metadata.xml b/dev-libs/libunzip/metadata.xml
deleted file mode 100644
index 097975e3a..000000000
--- a/dev-libs/libunzip/metadata.xml
+++ /dev/null
@@ -1,4 +0,0 @@
-<?xml version="1.0" encoding="UTF-8"?>
-<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
-<pkgmetadata>
-</pkgmetadata>
diff --git a/dev-libs/lief/Manifest b/dev-libs/lief/Manifest
new file mode 100644
index 000000000..16c730fff
--- /dev/null
+++ b/dev-libs/lief/Manifest
@@ -0,0 +1 @@
+DIST lief-0.11.5.tar.gz 15519537 BLAKE2B 87f16a62df6290652ee1d301b7b067e11882c12066a3abaa4eff750c3a7fd19353001fec6a7d7e70273815064b401707f1afcad9a2006a81c2f1d118fb448d17 SHA512 fa215e6193eadd6be3f8cff92b304ca5a03db24fcb7f48b258318b8f674527fc45f6e3765ca3d6055e7a4e9f2672b2d198df02bbfcc4fa96cb36b9255df7c0c4
diff --git a/dev-libs/lief/lief-0.11.5.ebuild b/dev-libs/lief/lief-0.11.5.ebuild
new file mode 100644
index 000000000..c2c38e5ba
--- /dev/null
+++ b/dev-libs/lief/lief-0.11.5.ebuild
@@ -0,0 +1,128 @@
+# Copyright 1999-2021 Gentoo Authors
+# Distributed under the terms of the GNU General Public License v2
+
+EAPI=7
+
+CMAKE_ECLASS=cmake
+PYTHON_COMPAT=( python3_10 pypy3 )
+
+# Upstream has two alternate approaches to building its Python API:
+# 1. A working "CMakeList.txt" only supporting a single Python target.
+# 2. A non-working "setup.py" supporting multiple Python targets but internally
+#    invoking CMake in mostly non-configurable (and thus broken) ways.
+# We choose working.
+#
+# Note that "cmake-multilib" *MUST* be inherited before "python-single-r1".
+inherit cmake-multilib python-single-r1
+
+DESCRIPTION="Library to instrument executable formats"
+HOMEPAGE="https://lief.quarkslab.com"
+SRC_URI="https://github.com/lief-project/LIEF/archive/${PV}.tar.gz -> ${P}.tar.gz"
+
+LICENSE="Apache-2.0"
+SLOT="0"
+KEYWORDS="~amd64 ~x86"
+
+# Python is not multilib yet
+IUSE="c examples +python static-libs"
+REQUIRED_USE="python? ( ${PYTHON_REQUIRED_USE} !abi_x86_32 !abi_x86_x32 )"
+
+# See "cmake/LIEFDependencies.cmake" for C and C++ dependencies.
+BDEPEND="
+	python? (
+		$(python_gen_cond_dep '
+			>=dev-python/setuptools-31.0.0[${PYTHON_USEDEP}]
+		')
+	)
+"
+#FIXME: Add after bumping to the next stable release:
+#	>=dev-libs/spdlog-1.8.5[${MULTILIB_USEDEP}]
+RDEPEND="python? ( ${PYTHON_DEPS} )"
+DEPEND="${RDEPEND}"
+
+# LIEF tests are non-trivial (if not infeasible) to run in the general case.
+# For example, "tests/CMakeLists.txt" implies all USE flags must be enabled:
+#     if (NOT LIEF_ELF OR NOT LIEF_PE OR NOT LIEF_MACHO)
+#       message(FATAL_ERROR "Tests require all LIEF's modules activated" )
+#     endif()
+RESTRICT="test"
+
+S="${WORKDIR}/LIEF-${PV}"
+
+pkg_setup() {
+	use python && python-single-r1_pkg_setup
+}
+
+#FIXME: Unvender currently vendored dependencies in "third-party/". Ideally,
+#upstream should add one "LIEF_EXTERNAL_${LIBNAME}" CMake option governing each
+#vendored dependency resembling the existing "LIEF_EXTERNAL_SPDLOG" option.
+#Note that LIEF patches the vendored "Boost leaf" and "utfcpp" dependencies.
+src_prepare() {
+	# Respect "multilib"-based lib dirnames.
+	sed -i -e 's~\bDESTINATION lib\(64\)\{0,1\}\b~DESTINATION ${CMAKE_INSTALL_LIBDIR}~' \
+		CMakeLists.txt || die
+
+	# Respect "python"-based installation of Python bindings. Upstream
+	# currently fails to install these bindings, resulting in Gentoo "RUNPATH"
+	# QA notices at installation time. See also:
+	#    https://github.com/lief-project/LIEF/issues/599#issuecomment-889654343
+	cat <<- EOF >> api/python/CMakeLists.txt || die
+		if(LIEF_INSTALL_PYTHON)
+		  install(
+		    TARGETS pyLIEF
+		    DESTINATION "$(python_get_sitedir)"
+		    COMPONENT libraries
+		  )
+		endif()
+	EOF
+
+	cmake_src_prepare
+}
+
+multilib_src_configure() {
+	# See also:
+	# * "cmake/LIEFDependencies.cmake" for a dependency list.
+	# * "cmake/LIEFOptions.cmake" for option descriptions.
+	local mycmakeargs=(
+		-DLIEF_COVERAGE=OFF
+		-DLIEF_DISABLE_FROZEN=OFF
+		-DLIEF_EXTRA_WARNINGS=OFF
+		-DLIEF_FORCE32=OFF  # Defer to "cmake-multilib" for ABI management.
+		-DLIEF_PROFILING=OFF
+		-DLIEF_SUPPORT_CXX14=ON
+		-DLIEF_USE_CCACHE=OFF  # Defer to Portage itself for "ccache" support.
+
+		# Disabling LIEF's format options causes build failures. See also:
+		#    https://github.com/lief-project/LIEF/issues/599
+		-DLIEF_ELF=ON
+		-DLIEF_PE=ON
+		-DLIEF_MACHO=ON
+		-DLIEF_ART=ON
+		-DLIEF_DEX=ON
+		-DLIEF_OAT=ON
+		-DLIEF_VDEX=ON
+
+		-DBUILD_SHARED_LIBS="$(usex static-libs OFF ON)"
+		-DLIEF_C_API="$(usex c ON OFF)"
+		-DLIEF_EXAMPLES="$(usex examples ON OFF)"
+		-DLIEF_FORCE_API_EXPORTS="$(usex python ON OFF)"  # See "setup.py".
+		-DLIEF_PYTHON_API="$(usex python ON OFF)"
+		-DLIEF_INSTALL_PYTHON="$(usex python ON OFF)"
+
+		#FIXME: Add USE flags governing most or all of these options.
+		-DLIEF_ENABLE_JSON=OFF
+		-DLIEF_DOC=OFF
+		-DLIEF_FUZZING=OFF
+		-DLIEF_INSTALL_COMPILED_EXAMPLES=OFF
+		-DLIEF_LOGGING=OFF
+		-DLIEF_LOGGING_DEBUG=OFF
+		-DLIEF_TESTS=OFF
+		-DLIEF_ASAN=OFF
+		-DLIEF_LSAN=OFF
+		-DLIEF_TSAN=OFF
+		-DLIEF_USAN=OFF
+	)
+	use python && mycmakeargs+=( -DPYTHON_EXECUTABLE="${PYTHON}" )
+
+	cmake_src_configure
+}
diff --git a/dev-libs/lief/metadata.xml b/dev-libs/lief/metadata.xml
new file mode 100644
index 000000000..da7baf4c0
--- /dev/null
+++ b/dev-libs/lief/metadata.xml
@@ -0,0 +1,14 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
+<pkgmetadata>
+	<maintainer type="project">
+		<email>sci@gentoo.org</email>
+		<name>Gentoo Science Project</name>
+	</maintainer>
+	<upstream>
+		<remote-id type="github">lief-project/LIEF</remote-id>
+	</upstream>
+	<use>
+		<flag name="c">install C API</flag>
+	</use>
+</pkgmetadata>
diff --git a/dev-libs/memkind/Manifest b/dev-libs/memkind/Manifest
new file mode 100644
index 000000000..b939a9f35
--- /dev/null
+++ b/dev-libs/memkind/Manifest
@@ -0,0 +1,2 @@
+DIST memkind-1.10.1.tar.gz 1031155 BLAKE2B f51f4011cba5a28ad41d54d5c2c64314ff3d190ac537f0dc7fad9f38198c77fb22963df7ddeb2d95ac5810db00b90622c3e975977c9be78e2a708dc7e0142384 SHA512 9fa2eed4e07d0316ee97fcdb594df4fe2e5cf44a509f658a78986aad9b4f56a9c8fbe281073b93ba3c2870734167ad29b8643d69757733fdce25e45e6f0015a0
+DIST memkind-1.11.0.tar.gz 1072455 BLAKE2B 2de2cf053687ba2150f694e8c4143eeca74fc377feee2b6892067b661d8c58d7d5fcacb021fc92a47dad27f52aa4cbc6408cfede3141ab1f8ae81147b49aa6a7 SHA512 0b5bde35b3565c730fa954aebfe2ccbecd1e120c920d05acdbc0a74914731a90aeef8d57101f1f47bd35fd310bc143fa517bc871b32e592b8412384ff652fc05
diff --git a/dev-libs/memkind/memkind-1.10.1.ebuild b/dev-libs/memkind/memkind-1.10.1.ebuild
new file mode 100644
index 000000000..df6efc9e4
--- /dev/null
+++ b/dev-libs/memkind/memkind-1.10.1.ebuild
@@ -0,0 +1,54 @@
+# Copyright 1999-2021 Gentoo Authors
+# Distributed under the terms of the GNU General Public License v2
+
+EAPI=7
+
+inherit autotools linux-info
+
+DESCRIPTION="user extensible heap manager built on top of jemalloc"
+HOMEPAGE="https://memkind.github.io/memkind/"
+
+if [[ ${PV} == 9999 ]]; then
+	inherit git-r3
+	EGIT_REPO_URI="https://github.com/memkind/memkind"
+else
+	SRC_URI="https://github.com/memkind/memkind/archive/v${PV}.tar.gz -> ${P}.tar.gz"
+	KEYWORDS="~amd64 ~x86"
+fi
+
+LICENSE="BSD"
+SLOT="0"
+IUSE="+heap-manager openmp secure +tls"
+RESTRICT="test"
+
+DEPEND="
+	sys-block/ndctl
+	sys-process/numactl
+"
+RDEPEND="${DEPEND}"
+
+src_prepare() {
+	default
+	eautoreconf
+	cd jemalloc && eautoreconf
+}
+
+src_configure() {
+	local myconf=(
+		--disable-silent-rules
+		--enable-shared
+		--enable-static
+		--enable-daxctl
+		$(use_enable heap-manager)
+		$(use_enable openmp)
+		$(use_enable secure)
+		$(use_enable tls)
+	)
+	econf "${myconf[@]}"
+}
+
+src_test() {
+	addwrite /proc/sys/vm/nr_hugepages
+	echo 3000 > /proc/sys/vm/nr_hugepages
+	emake check
+}
diff --git a/dev-libs/memkind/memkind-1.11.0.ebuild b/dev-libs/memkind/memkind-1.11.0.ebuild
new file mode 100644
index 000000000..df6efc9e4
--- /dev/null
+++ b/dev-libs/memkind/memkind-1.11.0.ebuild
@@ -0,0 +1,54 @@
+# Copyright 1999-2021 Gentoo Authors
+# Distributed under the terms of the GNU General Public License v2
+
+EAPI=7
+
+inherit autotools linux-info
+
+DESCRIPTION="user extensible heap manager built on top of jemalloc"
+HOMEPAGE="https://memkind.github.io/memkind/"
+
+if [[ ${PV} == 9999 ]]; then
+	inherit git-r3
+	EGIT_REPO_URI="https://github.com/memkind/memkind"
+else
+	SRC_URI="https://github.com/memkind/memkind/archive/v${PV}.tar.gz -> ${P}.tar.gz"
+	KEYWORDS="~amd64 ~x86"
+fi
+
+LICENSE="BSD"
+SLOT="0"
+IUSE="+heap-manager openmp secure +tls"
+RESTRICT="test"
+
+DEPEND="
+	sys-block/ndctl
+	sys-process/numactl
+"
+RDEPEND="${DEPEND}"
+
+src_prepare() {
+	default
+	eautoreconf
+	cd jemalloc && eautoreconf
+}
+
+src_configure() {
+	local myconf=(
+		--disable-silent-rules
+		--enable-shared
+		--enable-static
+		--enable-daxctl
+		$(use_enable heap-manager)
+		$(use_enable openmp)
+		$(use_enable secure)
+		$(use_enable tls)
+	)
+	econf "${myconf[@]}"
+}
+
+src_test() {
+	addwrite /proc/sys/vm/nr_hugepages
+	echo 3000 > /proc/sys/vm/nr_hugepages
+	emake check
+}
diff --git a/dev-libs/memkind/memkind-9999.ebuild b/dev-libs/memkind/memkind-9999.ebuild
new file mode 100644
index 000000000..df6efc9e4
--- /dev/null
+++ b/dev-libs/memkind/memkind-9999.ebuild
@@ -0,0 +1,54 @@
+# Copyright 1999-2021 Gentoo Authors
+# Distributed under the terms of the GNU General Public License v2
+
+EAPI=7
+
+inherit autotools linux-info
+
+DESCRIPTION="user extensible heap manager built on top of jemalloc"
+HOMEPAGE="https://memkind.github.io/memkind/"
+
+if [[ ${PV} == 9999 ]]; then
+	inherit git-r3
+	EGIT_REPO_URI="https://github.com/memkind/memkind"
+else
+	SRC_URI="https://github.com/memkind/memkind/archive/v${PV}.tar.gz -> ${P}.tar.gz"
+	KEYWORDS="~amd64 ~x86"
+fi
+
+LICENSE="BSD"
+SLOT="0"
+IUSE="+heap-manager openmp secure +tls"
+RESTRICT="test"
+
+DEPEND="
+	sys-block/ndctl
+	sys-process/numactl
+"
+RDEPEND="${DEPEND}"
+
+src_prepare() {
+	default
+	eautoreconf
+	cd jemalloc && eautoreconf
+}
+
+src_configure() {
+	local myconf=(
+		--disable-silent-rules
+		--enable-shared
+		--enable-static
+		--enable-daxctl
+		$(use_enable heap-manager)
+		$(use_enable openmp)
+		$(use_enable secure)
+		$(use_enable tls)
+	)
+	econf "${myconf[@]}"
+}
+
+src_test() {
+	addwrite /proc/sys/vm/nr_hugepages
+	echo 3000 > /proc/sys/vm/nr_hugepages
+	emake check
+}
diff --git a/dev-libs/memkind/metadata.xml b/dev-libs/memkind/metadata.xml
new file mode 100644
index 000000000..c61ea0932
--- /dev/null
+++ b/dev-libs/memkind/metadata.xml
@@ -0,0 +1,20 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
+<pkgmetadata>
+	<maintainer type="person">
+		<email>gentoo@aisha.cc</email>
+		<name>Aisha Tammy</name>
+	</maintainer>
+	<maintainer type="project">
+		<email>sci@gentoo.org</email>
+		<name>Gentoo Science Project</name>
+	</maintainer>
+	<upstream>
+		<remote-id type="github">memkind/memkind</remote-id>
+	</upstream>
+	<use>
+		<flag name="heap-manager">Allow switching allocator at runtime</flag>
+		<flag name="secure">Build libraries with security enhancements</flag>
+		<flag name="tls">Enable thread local storage</flag>
+	</use>
+</pkgmetadata>
diff --git a/dev-libs/mxml/Manifest b/dev-libs/mxml/Manifest
deleted file mode 100644
index 1ee840875..000000000
--- a/dev-libs/mxml/Manifest
+++ /dev/null
@@ -1 +0,0 @@
-DIST mxml-2.9.tar.gz 264379 BLAKE2B d7b77e635466acadc8b876fadc8a3d95f3efd4e692c6e4e7a0a72e2e0ff9adac96a137340340981a212f321ccf94e8ab6c965adfde208dd6960f0dec43e05c8f SHA512 819c506ea43198de07a90d7473f29c9edc7f638638b5a1b215d88ac635b4f4f37441d8a760ce356f7d4bfb14a4f504c304d0e33345f69ecd145db50350e50ad7
diff --git a/dev-libs/mxml/metadata.xml b/dev-libs/mxml/metadata.xml
deleted file mode 100644
index 42a46e0c3..000000000
--- a/dev-libs/mxml/metadata.xml
+++ /dev/null
@@ -1,17 +0,0 @@
-<?xml version="1.0" encoding="UTF-8"?>
-<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
-<pkgmetadata>
-	<maintainer type="person">
-		<email>cjk34@cam.ac.uk</email>
-		<name>Chris Kerr</name>
-		<description>I don't develop this software, I'm just a Gentoo user who
-wanted to install it</description>
-	</maintainer>
-	<maintainer type="project">
-		<email>sci@gentoo.org</email>
-		<name>Gentoo Science Project</name>
-	</maintainer>
-	<longdescription>Mini-XML is a lightweight, ultra-portable XML library
-that requires only an ANSI C compiler and a 'make' program.</longdescription>
-	<use/>
-</pkgmetadata>
diff --git a/dev-libs/mxml/mxml-2.9.ebuild b/dev-libs/mxml/mxml-2.9.ebuild
deleted file mode 100644
index a5b1b8ebc..000000000
--- a/dev-libs/mxml/mxml-2.9.ebuild
+++ /dev/null
@@ -1,18 +0,0 @@
-# Copyright 1999-2015 Gentoo Foundation
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=5
-
-DESCRIPTION="Mini-XML: A lightweight ANSI C XML library"
-HOMEPAGE="http://www.msweet.org/projects.php?Z3"
-SRC_URI="http://www.msweet.org/files/project3/${P}.tar.gz"
-
-LICENSE="LGPL-2-with-linking-exception"
-SLOT="0"
-KEYWORDS="~amd64"
-IUSE=""
-
-src_install() {
-	emake install DSTROOT="${D}"
-	dodoc README ANNOUNCEMENT CHANGES
-}
diff --git a/dev-libs/oneCCL/Manifest b/dev-libs/oneCCL/Manifest
new file mode 100644
index 000000000..2eb21d0f6
--- /dev/null
+++ b/dev-libs/oneCCL/Manifest
@@ -0,0 +1,3 @@
+DIST oneCCL-2021.10.tar.gz 37777252 BLAKE2B fb8d4429cbd7366efdd6e392d8132631c4dbc770962781a49b5b2df6e0c0a9b9b6c97043997066879b22ea85bf76e507bdcc27a78e40beffa7520d2a420b35ef SHA512 3ff845bf28e18c195411f5ed4542f172648feeb385fc456b6222d527018f48625c9be7e96a0f9b973f8af7ad1cc122a83ac8e169eeb59d5a35ed901910fdbace
+DIST oneCCL-2021.7.1.tar.gz 35807233 BLAKE2B 0608b548f42c28983453a1e693c922aff0f6c77ffbf35f92b69113ba9fb02263bf8e1efa94ba47330559bb97b81493923cac10ce2c68c5fb50181677152fcc28 SHA512 e77d836afdcccbc2a1d2f9903916f17698a0d5ad795cd76dbb19a835375e89d0ecfa4695d87758e1ca6078bc23e30416d0a228ad3060816409b91851ad0b0790
+DIST oneCCL-2021.8.tar.gz 36868388 BLAKE2B b27f04efaddf2c31befd70388f0aa84b9cb5266b5d4e4a300064e0dc98e4d7eee3590288dc0b8cc1640fe0a9b928a0dfdf16a2ea45db9bd1517a8ca2dd00bdfe SHA512 879d1b73e594d5ff2c5a5aee08dfb4aded11c4974a9efcc199e7c2ee87b00c2441edb1dcb073bb4ed2587d752efcafe338072959b7b0f89fc1692dc377f748c2
diff --git a/dev-libs/oneCCL/files/oneCCL-2021.7.1-use-system-libs.patch b/dev-libs/oneCCL/files/oneCCL-2021.7.1-use-system-libs.patch
new file mode 100644
index 000000000..e92608f4a
--- /dev/null
+++ b/dev-libs/oneCCL/files/oneCCL-2021.7.1-use-system-libs.patch
@@ -0,0 +1,104 @@
+diff --git a/CMakeLists.txt b/CMakeLists.txt
+index 74c4fc0..92c4d16 100644
+--- a/CMakeLists.txt
++++ b/CMakeLists.txt
+@@ -87,15 +87,13 @@ add_definitions(-DCCL_CXX_COMPILER="${CMAKE_CXX_COMPILER_ID} ${CMAKE_CXX_COMPILE
+ SET(CCL_ENABLE_ZE OFF CACHE BOOL "Enable Level Zero support")
+ 
+ set(CCL_COMMON_INSTALL_PREFIX "intel64")
+-set(CMAKE_INSTALL_LIBDIR "lib")
+ set(CCL_INSTALL_LIB "${CMAKE_INSTALL_PREFIX}/${CMAKE_INSTALL_LIBDIR}")
+ set(CCL_INSTALL_INCLUDE "${CMAKE_INSTALL_PREFIX}/${CMAKE_INSTALL_INCLUDEDIR}")
+ set(CCL_INSTALL_DOC "${CMAKE_INSTALL_PREFIX}/${CMAKE_INSTALL_DOCDIR}")
+ set(CCL_INSTALL_BIN "${CMAKE_INSTALL_PREFIX}/${CMAKE_INSTALL_BINDIR}")
+-set(CCL_INSTALL_ENV "${CMAKE_INSTALL_PREFIX}/env")
+-set(CCL_INSTALL_ETC "${CMAKE_INSTALL_PREFIX}/etc")
+-set(CCL_INSTALL_LICENSE "${CMAKE_INSTALL_PREFIX}/licensing")
+-set(CCL_INSTALL_MODULE "${CMAKE_INSTALL_PREFIX}/modulefiles")
++set(CCL_INSTALL_ENV "${CMAKE_INSTALL_FULL_SYSCONFDIR}/env")
++set(CCL_INSTALL_ETC "${CMAKE_INSTALL_FULL_SYSCONFDIR}")
++set(CCL_INSTALL_MODULE "${CMAKE_INSTALL_FULL_SYSCONFDIR}/modulefiles")
+ set(CCL_INSTALL_EXAMPLES "${CMAKE_INSTALL_PREFIX}/examples")
+ set(CCL_INSTALL_TESTS "${CMAKE_INSTALL_PREFIX}/tests")
+ set(CCL_INSTALL_KERNELS "${CMAKE_INSTALL_PREFIX}/lib/kernels")
+@@ -103,23 +101,23 @@ set(CCL_INSTALL_KERNELS "${CMAKE_INSTALL_PREFIX}/lib/kernels")
+ # setup dependency directories
+ set(DEPS_DIR "${PROJECT_SOURCE_DIR}/deps")
+ 
+-set(MPI_INCLUDE_DIR "${DEPS_DIR}/mpi/include/")
+-set(MPI_LIB_DIR "${DEPS_DIR}/mpi/lib/")
++set(MPI_INCLUDE_DIR "/usr/include/")
++set(MPI_LIB_DIR "/usr/lib64/")
+ message(STATUS "MPI_INCLUDE_DIR: ${MPI_INCLUDE_DIR}")
+ message(STATUS "MPI_LIB_DIR: ${MPI_LIB_DIR}")
+ 
+ if ("${LIBFABRIC_DIR}" STREQUAL "")
+-    set(LIBFABRIC_INCLUDE_DIR "${DEPS_DIR}/ofi/include")
+-    set(LIBFABRIC_LIB_DIR "${DEPS_DIR}/ofi/lib/")
++    set(LIBFABRIC_INCLUDE_DIR "${DEPS_DIR}/ofi/include/")
++    set(LIBFABRIC_LIB_DIR "${DEPS_DIR}/ofi/lib64/")
+ else()
+     set(LIBFABRIC_INCLUDE_DIR "${LIBFABRIC_DIR}/include/")
+-    set(LIBFABRIC_LIB_DIR "${LIBFABRIC_DIR}/lib")
++    set(LIBFABRIC_LIB_DIR "${LIBFABRIC_DIR}/lib64/")
+ endif()
+ message(STATUS "LIBFABRIC_LIB_DIR: ${LIBFABRIC_LIB_DIR}")
+ message(STATUS "LIBFABRIC_INCLUDE_DIR: ${LIBFABRIC_INCLUDE_DIR}")
+ 
+-set(HWLOC_INCLUDE_DIR "${DEPS_DIR}/hwloc/include/")
+-set(HWLOC_LIB_DIR "${DEPS_DIR}/hwloc/lib/")
++set(HWLOC_INCLUDE_DIR "/usr/include/")
++set(HWLOC_LIB_DIR "/usr/lib64/")
+ message(STATUS "HWLOC_INCLUDE_DIR: ${HWLOC_INCLUDE_DIR}")
+ message(STATUS "HWLOC_LIB_DIR: ${HWLOC_LIB_DIR}")
+ 
+@@ -128,7 +126,7 @@ set(ITT_LIB_DIR "${DEPS_DIR}/itt/lib64")
+ message(STATUS "ITT_INCLUDE_DIR: ${ITT_INCLUDE_DIR}")
+ message(STATUS "ITT_LIB_DIR: ${ITT_LIB_DIR}")
+ 
+-set(LEVEL_ZERO_INCLUDE_DIR "${DEPS_DIR}/level_zero/include/")
++set(LEVEL_ZERO_INCLUDE_DIR "/usr/include/level_zero")
+ message(STATUS "LEVEL_ZERO_INCLUDE_DIR: ${LEVEL_ZERO_INCLUDE_DIR}")
+ 
+ set(CMAKE_SKIP_INSTALL_RPATH TRUE)
+@@ -241,8 +239,6 @@ configure_file(third-party-programs.txt ${CMAKE_CURRENT_BINARY_DIR}/third-party-
+ install(PROGRAMS ${CMAKE_CURRENT_BINARY_DIR}/vars.sh DESTINATION ${CCL_INSTALL_ENV})
+ install(PROGRAMS ${CMAKE_CURRENT_BINARY_DIR}/setvars.sh DESTINATION ${CCL_INSTALL_ENV})
+ install(PROGRAMS ${CMAKE_CURRENT_BINARY_DIR}/ccl DESTINATION ${CCL_INSTALL_MODULE})
+-install(PROGRAMS ${CMAKE_CURRENT_BINARY_DIR}/third-party-programs.txt DESTINATION ${CCL_INSTALL_LICENSE})
+-install(PROGRAMS ${PROJECT_SOURCE_DIR}/LICENSE DESTINATION ${CCL_INSTALL_LICENSE})
+ 
+ # copy kernels
+ if (COMPUTE_BACKEND AND EXISTS "${PROJECT_SOURCE_DIR}/src/kernels")
+diff --git a/src/CMakeLists.txt b/src/CMakeLists.txt
+index 7b4cff9..e8296a0 100644
+--- a/src/CMakeLists.txt
++++ b/src/CMakeLists.txt
+@@ -263,8 +263,8 @@ list(APPEND SRC_LINK_LIBS
+      pthread
+      ${EXTERNAL_LIBS}
+      fabric
+-     ${HWLOC_LIB_DIR}/libhwloc.a
+-     ${ITT_LIB_DIR}/libittnotify.a)
++     libhwloc.so
++     libittnotify.so)
+ 
+ if (ENABLE_MPI)
+     set(SRC_C_FLAGS "${SRC_C_FLAGS} -DCCL_ENABLE_MPI")
+@@ -335,16 +335,3 @@ if ("${LIBFABRIC_DIR}" STREQUAL "")
+     install(DIRECTORY ${DEPS_DIR}/ofi/lib/
+             DESTINATION ${CCL_INSTALL_LIB})
+ endif()
+-
+-if (ENABLE_MPI)
+-    file(GLOB mpi_bins "${DEPS_DIR}/mpi/bin/*")
+-    install(PROGRAMS ${mpi_bins} DESTINATION ${CCL_INSTALL_BIN})
+-    install(DIRECTORY ${DEPS_DIR}/mpi/include/
+-            DESTINATION ${CCL_INSTALL_INCLUDE})
+-    install(DIRECTORY ${DEPS_DIR}/mpi/lib/
+-           DESTINATION ${CCL_INSTALL_LIB})
+-    install(DIRECTORY ${DEPS_DIR}/mpi/etc/
+-            DESTINATION ${CCL_INSTALL_ETC})
+-    install(DIRECTORY ${DEPS_DIR}/mpi/licensing/
+-            DESTINATION ${CCL_INSTALL_LICENSE}/mpi/)
+-endif()
diff --git a/dev-libs/oneCCL/files/oneCCL-2021.8-use-system-libs.patch b/dev-libs/oneCCL/files/oneCCL-2021.8-use-system-libs.patch
new file mode 100644
index 000000000..dbb3a9e5f
--- /dev/null
+++ b/dev-libs/oneCCL/files/oneCCL-2021.8-use-system-libs.patch
@@ -0,0 +1,104 @@
+diff --git a/CMakeLists.txt b/CMakeLists.txt
+index 1e65ce9..cabbff9 100644
+--- a/CMakeLists.txt
++++ b/CMakeLists.txt
+@@ -109,15 +109,13 @@ add_definitions(-DCCL_CXX_COMPILER="${CMAKE_CXX_COMPILER_ID} ${CMAKE_CXX_COMPILE
+ SET(CCL_ENABLE_ZE OFF CACHE BOOL "Enable Level Zero support")
+ 
+ set(CCL_COMMON_INSTALL_PREFIX "intel64")
+-set(CMAKE_INSTALL_LIBDIR "lib")
+ set(CCL_INSTALL_LIB "${CMAKE_INSTALL_PREFIX}/${CMAKE_INSTALL_LIBDIR}")
+ set(CCL_INSTALL_INCLUDE "${CMAKE_INSTALL_PREFIX}/${CMAKE_INSTALL_INCLUDEDIR}")
+ set(CCL_INSTALL_DOC "${CMAKE_INSTALL_PREFIX}/${CMAKE_INSTALL_DOCDIR}")
+ set(CCL_INSTALL_BIN "${CMAKE_INSTALL_PREFIX}/${CMAKE_INSTALL_BINDIR}")
+-set(CCL_INSTALL_ENV "${CMAKE_INSTALL_PREFIX}/env")
+-set(CCL_INSTALL_ETC "${CMAKE_INSTALL_PREFIX}/etc")
+-set(CCL_INSTALL_LICENSE "${CMAKE_INSTALL_PREFIX}/licensing")
+-set(CCL_INSTALL_MODULE "${CMAKE_INSTALL_PREFIX}/modulefiles")
++set(CCL_INSTALL_ENV "${CMAKE_INSTALL_FULL_SYSCONFDIR}/env")
++set(CCL_INSTALL_ETC "${CMAKE_INSTALL_FULL_SYSCONFDIR}")
++set(CCL_INSTALL_MODULE "${CMAKE_INSTALL_FULL_SYSCONFDIR}/modulefiles")
+ set(CCL_INSTALL_EXAMPLES "${CMAKE_INSTALL_PREFIX}/examples")
+ set(CCL_INSTALL_TESTS "${CMAKE_INSTALL_PREFIX}/tests")
+ set(CCL_INSTALL_KERNELS "${CMAKE_INSTALL_PREFIX}/lib/kernels")
+@@ -125,23 +123,23 @@ set(CCL_INSTALL_KERNELS "${CMAKE_INSTALL_PREFIX}/lib/kernels")
+ # setup dependency directories
+ set(DEPS_DIR "${PROJECT_SOURCE_DIR}/deps")
+ 
+-set(MPI_INCLUDE_DIR "${DEPS_DIR}/mpi/include/")
+-set(MPI_LIB_DIR "${DEPS_DIR}/mpi/lib/")
++set(MPI_INCLUDE_DIR "/usr/include/")
++set(MPI_LIB_DIR "/usr/lib64/")
+ message(STATUS "MPI_INCLUDE_DIR: ${MPI_INCLUDE_DIR}")
+ message(STATUS "MPI_LIB_DIR: ${MPI_LIB_DIR}")
+ 
+ if ("${LIBFABRIC_DIR}" STREQUAL "")
+-    set(LIBFABRIC_INCLUDE_DIR "${DEPS_DIR}/ofi/include")
+-    set(LIBFABRIC_LIB_DIR "${DEPS_DIR}/ofi/lib/")
++    set(LIBFABRIC_INCLUDE_DIR "${DEPS_DIR}/ofi/include/")
++    set(LIBFABRIC_LIB_DIR "${DEPS_DIR}/ofi/lib64/")
+ else()
+     set(LIBFABRIC_INCLUDE_DIR "${LIBFABRIC_DIR}/include/")
+-    set(LIBFABRIC_LIB_DIR "${LIBFABRIC_DIR}/lib")
++    set(LIBFABRIC_LIB_DIR "${LIBFABRIC_DIR}/lib64/")
+ endif()
+ message(STATUS "LIBFABRIC_LIB_DIR: ${LIBFABRIC_LIB_DIR}")
+ message(STATUS "LIBFABRIC_INCLUDE_DIR: ${LIBFABRIC_INCLUDE_DIR}")
+ 
+-set(HWLOC_INCLUDE_DIR "${DEPS_DIR}/hwloc/include/")
+-set(HWLOC_LIB_DIR "${DEPS_DIR}/hwloc/lib/")
++set(HWLOC_INCLUDE_DIR "/usr/include/")
++set(HWLOC_LIB_DIR "/usr/lib64/")
+ message(STATUS "HWLOC_INCLUDE_DIR: ${HWLOC_INCLUDE_DIR}")
+ message(STATUS "HWLOC_LIB_DIR: ${HWLOC_LIB_DIR}")
+ 
+@@ -150,7 +148,7 @@ set(ITT_LIB_DIR "${DEPS_DIR}/itt/lib64")
+ message(STATUS "ITT_INCLUDE_DIR: ${ITT_INCLUDE_DIR}")
+ message(STATUS "ITT_LIB_DIR: ${ITT_LIB_DIR}")
+ 
+-set(LEVEL_ZERO_INCLUDE_DIR "${DEPS_DIR}/level_zero/include/")
++set(LEVEL_ZERO_INCLUDE_DIR "/usr/include/level_zero")
+ message(STATUS "LEVEL_ZERO_INCLUDE_DIR: ${LEVEL_ZERO_INCLUDE_DIR}")
+ 
+ message(STATUS "DRM_INCLUDE_DIR: ${DRM_INCLUDE_DIR}")
+@@ -290,8 +288,6 @@ configure_file(third-party-programs.txt ${CMAKE_CURRENT_BINARY_DIR}/third-party-
+ install(PROGRAMS ${CMAKE_CURRENT_BINARY_DIR}/vars.sh DESTINATION ${CCL_INSTALL_ENV})
+ install(PROGRAMS ${CMAKE_CURRENT_BINARY_DIR}/setvars.sh DESTINATION ${CCL_INSTALL_ENV})
+ install(PROGRAMS ${CMAKE_CURRENT_BINARY_DIR}/ccl DESTINATION ${CCL_INSTALL_MODULE})
+-install(PROGRAMS ${CMAKE_CURRENT_BINARY_DIR}/third-party-programs.txt DESTINATION ${CCL_INSTALL_LICENSE})
+-install(PROGRAMS ${PROJECT_SOURCE_DIR}/LICENSE DESTINATION ${CCL_INSTALL_LICENSE})
+ 
+ # copy kernels
+ if (COMPUTE_BACKEND AND EXISTS "${PROJECT_SOURCE_DIR}/src/kernels")
+diff --git a/src/CMakeLists.txt b/src/CMakeLists.txt
+index 3948373..168a690 100644
+--- a/src/CMakeLists.txt
++++ b/src/CMakeLists.txt
+@@ -279,8 +279,8 @@ list(APPEND SRC_LINK_LIBS
+      dl
+      pthread
+      ${EXTERNAL_LIBS}
+-     ${HWLOC_LIB_DIR}/libhwloc.a
+-     ${ITT_LIB_DIR}/libittnotify.a)
++     libhwloc.so
++     libittnotify.so)
+ 
+ if (ENABLE_MPI)
+     set(SRC_C_FLAGS "${SRC_C_FLAGS} -DCCL_ENABLE_MPI")
+@@ -350,16 +350,3 @@ if ("${LIBFABRIC_DIR}" STREQUAL "")
+     install(DIRECTORY ${DEPS_DIR}/ofi/lib/
+             DESTINATION ${CCL_INSTALL_LIB})
+ endif()
+-
+-if (ENABLE_MPI)
+-    file(GLOB mpi_bins "${DEPS_DIR}/mpi/bin/*")
+-    install(PROGRAMS ${mpi_bins} DESTINATION ${CCL_INSTALL_BIN})
+-    install(DIRECTORY ${DEPS_DIR}/mpi/include/
+-            DESTINATION ${CCL_INSTALL_INCLUDE})
+-    install(DIRECTORY ${DEPS_DIR}/mpi/lib/
+-           DESTINATION ${CCL_INSTALL_LIB})
+-    install(DIRECTORY ${DEPS_DIR}/mpi/etc/
+-            DESTINATION ${CCL_INSTALL_ETC})
+-    install(DIRECTORY ${DEPS_DIR}/mpi/licensing/
+-            DESTINATION ${CCL_INSTALL_LICENSE}/mpi/)
+-endif()
diff --git a/dev-libs/oneCCL/metadata.xml b/dev-libs/oneCCL/metadata.xml
new file mode 100644
index 000000000..cbb320b12
--- /dev/null
+++ b/dev-libs/oneCCL/metadata.xml
@@ -0,0 +1,11 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
+<pkgmetadata>
+	<maintainer type="project">
+		<email>sci@gentoo.org</email>
+		<name>Gentoo Science Project</name>
+	</maintainer>
+	<upstream>
+		<remote-id type="github">oneapi-src/oneCCL</remote-id>
+	</upstream>
+</pkgmetadata>
diff --git a/dev-libs/oneCCL/oneCCL-2021.10.ebuild b/dev-libs/oneCCL/oneCCL-2021.10.ebuild
new file mode 100644
index 000000000..a67659f4a
--- /dev/null
+++ b/dev-libs/oneCCL/oneCCL-2021.10.ebuild
@@ -0,0 +1,62 @@
+# Copyright 2022 Gentoo Authors
+# Distributed under the terms of the GNU General Public License v2
+
+EAPI=8
+
+inherit cmake
+
+DESCRIPTION="oneAPI Collective Communications Library"
+HOMEPAGE="https://github.com/oneapi-src/oneCCL"
+SRC_URI="https://github.com/oneapi-src/oneCCL/archive/refs/tags/${PV}.tar.gz -> ${P}.tar.gz"
+
+LICENSE="Apache-2.0"
+SLOT="0"
+KEYWORDS="~amd64"
+
+IUSE="mpi"
+
+BDEPEND="sys-devel/DPC++"
+
+DEPEND="
+	dev-libs/level-zero:=
+	sys-apps/hwloc:=
+	sys-block/libfabric:=
+	sys-devel/ittapi
+	sys-cluster/pmix
+	mpi? ( virtual/mpi )
+"
+RDEPEND="${DEPEND}"
+
+PATCHES=(
+	"${FILESDIR}/${PN}-2021.8-use-system-libs.patch"
+)
+
+src_prepare() {
+	# No -Werror
+	find . -name "CMakeLists.txt" -exec sed -i "s/-Werror//g" {} + || die
+
+	# Use system libs instead
+	rm -r deps/* || die
+
+	# DPC++ compiler required for full functionality
+	export CC="${ESYSROOT}/usr/lib/llvm/intel/bin/clang"
+	export CXX="${ESYSROOT}/usr/lib/llvm/intel/bin/clang++"
+
+	cmake_src_prepare
+}
+
+src_configure() {
+	local mycmakeargs=(
+		-DBUILD_EXAMPLES=OFF
+		# BUILD_CONFIG causes sandbox violation
+		-DBUILD_CONFIG=OFF
+		-DCCL_ENABLE_ZE=ON
+		# TODO: Find out how to execute the tests
+		-DBUILD_FT=OFF
+		-DENABLE_MPI_TESTS=OFF
+		-DENABLE_MPI="$(usex mpi)"
+		# Use system fabric
+		-DLIBFABRIC_DIR="${ESYSROOT}/usr"
+	)
+	cmake_src_configure
+}
diff --git a/dev-libs/oneCCL/oneCCL-2021.7.1-r1.ebuild b/dev-libs/oneCCL/oneCCL-2021.7.1-r1.ebuild
new file mode 100644
index 000000000..76ab29af2
--- /dev/null
+++ b/dev-libs/oneCCL/oneCCL-2021.7.1-r1.ebuild
@@ -0,0 +1,61 @@
+# Copyright 2022 Gentoo Authors
+# Distributed under the terms of the GNU General Public License v2
+
+EAPI=8
+
+inherit cmake
+
+DESCRIPTION="oneAPI Collective Communications Library"
+HOMEPAGE="https://github.com/oneapi-src/oneCCL"
+SRC_URI="https://github.com/oneapi-src/oneCCL/archive/refs/tags/${PV}.tar.gz -> ${P}.tar.gz"
+
+LICENSE="Apache-2.0"
+SLOT="0"
+KEYWORDS="~amd64"
+
+IUSE="mpi"
+
+BDEPEND="sys-devel/DPC++"
+
+DEPEND="
+	dev-libs/level-zero:=
+	sys-apps/hwloc:=
+	sys-block/libfabric:=
+	sys-devel/ittapi
+	mpi? ( virtual/mpi )
+"
+RDEPEND="${DEPEND}"
+
+PATCHES=(
+	"${FILESDIR}/${PN}-2021.7.1-use-system-libs.patch"
+)
+
+src_prepare() {
+	# No -Werror
+	find . -name "CMakeLists.txt" -exec sed -i "s/-Werror//g" {} + || die
+
+	# Use system libs instead
+	rm -r deps/* || die
+
+	# DPC++ compiler required for full functionality
+	export CC="${ESYSROOT}/usr/lib/llvm/intel/bin/clang"
+	export CXX="${ESYSROOT}/usr/lib/llvm/intel/bin/clang++"
+
+	cmake_src_prepare
+}
+
+src_configure() {
+	local mycmakeargs=(
+		-DBUILD_EXAMPLES=OFF
+		# BUILD_CONFIG causes sandbox violation
+		-DBUILD_CONFIG=OFF
+		-DCCL_ENABLE_ZE=ON
+		# TODO: Find out how to execute the tests
+		-DBUILD_FT=OFF
+		-DENABLE_MPI_TESTS=OFF
+		-DENABLE_MPI="$(usex mpi)"
+		# Use system fabric
+		-DLIBFABRIC_DIR="${ESYSROOT}/usr"
+	)
+	cmake_src_configure
+}
diff --git a/dev-libs/oneCCL/oneCCL-2021.8.ebuild b/dev-libs/oneCCL/oneCCL-2021.8.ebuild
new file mode 100644
index 000000000..a67659f4a
--- /dev/null
+++ b/dev-libs/oneCCL/oneCCL-2021.8.ebuild
@@ -0,0 +1,62 @@
+# Copyright 2022 Gentoo Authors
+# Distributed under the terms of the GNU General Public License v2
+
+EAPI=8
+
+inherit cmake
+
+DESCRIPTION="oneAPI Collective Communications Library"
+HOMEPAGE="https://github.com/oneapi-src/oneCCL"
+SRC_URI="https://github.com/oneapi-src/oneCCL/archive/refs/tags/${PV}.tar.gz -> ${P}.tar.gz"
+
+LICENSE="Apache-2.0"
+SLOT="0"
+KEYWORDS="~amd64"
+
+IUSE="mpi"
+
+BDEPEND="sys-devel/DPC++"
+
+DEPEND="
+	dev-libs/level-zero:=
+	sys-apps/hwloc:=
+	sys-block/libfabric:=
+	sys-devel/ittapi
+	sys-cluster/pmix
+	mpi? ( virtual/mpi )
+"
+RDEPEND="${DEPEND}"
+
+PATCHES=(
+	"${FILESDIR}/${PN}-2021.8-use-system-libs.patch"
+)
+
+src_prepare() {
+	# No -Werror
+	find . -name "CMakeLists.txt" -exec sed -i "s/-Werror//g" {} + || die
+
+	# Use system libs instead
+	rm -r deps/* || die
+
+	# DPC++ compiler required for full functionality
+	export CC="${ESYSROOT}/usr/lib/llvm/intel/bin/clang"
+	export CXX="${ESYSROOT}/usr/lib/llvm/intel/bin/clang++"
+
+	cmake_src_prepare
+}
+
+src_configure() {
+	local mycmakeargs=(
+		-DBUILD_EXAMPLES=OFF
+		# BUILD_CONFIG causes sandbox violation
+		-DBUILD_CONFIG=OFF
+		-DCCL_ENABLE_ZE=ON
+		# TODO: Find out how to execute the tests
+		-DBUILD_FT=OFF
+		-DENABLE_MPI_TESTS=OFF
+		-DENABLE_MPI="$(usex mpi)"
+		# Use system fabric
+		-DLIBFABRIC_DIR="${ESYSROOT}/usr"
+	)
+	cmake_src_configure
+}
diff --git a/dev-libs/opencl-clhpp/Manifest b/dev-libs/opencl-clhpp/Manifest
deleted file mode 100644
index 4b7bd3ff9..000000000
--- a/dev-libs/opencl-clhpp/Manifest
+++ /dev/null
@@ -1 +0,0 @@
-DIST opencl-clhpp-2.0.10.tar.gz 129954 BLAKE2B 1beb9b41ce1ad8ec88d0ccfa5f1d7a7af931841fa64d79b9eb9db90538f1b43f3cee5c74dc015ba835ee4ded2e926967bc3aa00dcc6ec0f5b65a04f9618ea1a9 SHA512 4a4898540c55422ca0cc6ba7f0c5495b915fc34df50f8add90e7f06dd5ef1d01a767234ecdee3757292980aa2f938e773177bcc73f28ac9c1b42d386863dea58
diff --git a/dev-libs/opencl-clhpp/metadata.xml b/dev-libs/opencl-clhpp/metadata.xml
deleted file mode 100644
index eb09296ba..000000000
--- a/dev-libs/opencl-clhpp/metadata.xml
+++ /dev/null
@@ -1,15 +0,0 @@
-<?xml version="1.0" encoding="UTF-8"?>
-<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
-<pkgmetadata>
-	<maintainer type="person">
-		<email>marbre@linux.sungazer.de</email>
-		<name>Marius Brehler</name>
-	</maintainer>
-	<maintainer type="project">
-		<email>sci@gentoo.org</email>
-		<name>Gentoo Science Project</name>
-	</maintainer>
-	<upstream>
-		<remote-id type="github">KhronosGroup/OpenCL-CLHPP</remote-id>
-	</upstream>
-</pkgmetadata>
diff --git a/dev-libs/opencl-clhpp/opencl-clhpp-2.0.10.ebuild b/dev-libs/opencl-clhpp/opencl-clhpp-2.0.10.ebuild
deleted file mode 100644
index 0ed270d32..000000000
--- a/dev-libs/opencl-clhpp/opencl-clhpp-2.0.10.ebuild
+++ /dev/null
@@ -1,28 +0,0 @@
-# Copyright 1999-2016 Gentoo Foundation
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=6
-
-inherit cmake-utils
-
-MY_PN="OpenCL-CLHPP"
-
-DESCRIPTION="OpenCL Host API C++ bindings (cl.hpp and cl2.hpp)"
-HOMEPAGE="https://github.com/KhronosGroup/OpenCL-CLHPP"
-SRC_URI="https://github.com/KhronosGroup/${MY_PN}/archive/v${PV}.tar.gz -> ${P}.tar.gz"
-KEYWORDS="~amd64"
-
-LICENSE="MIT-KhronosGroup"
-SLOT="0"
-IUSE="examples"
-
-S="${WORKDIR}/${MY_PN}-${PV}"
-
-src_configure() {
-	local mycmakeargs=(
-		-DBUILD_DOCS=OFF
-		-DBUILD_EXAMPLES=OFF
-		-DBUILD_TESTS=OFF
-	)
-	cmake-utils_src_configure
-}
\ No newline at end of file
diff --git a/dev-libs/simclist/Manifest b/dev-libs/simclist/Manifest
index 2ff328fc9..2f6a2d69e 100644
--- a/dev-libs/simclist/Manifest
+++ b/dev-libs/simclist/Manifest
@@ -1 +1 @@
-DIST simclist-1.6.tar.bz2 44280 SHA256 63b47211215466ddfba1643582cb3aaa7b5e9ca1cc5f247290e3199c4e29f147 SHA512 b221b583993470c35d42dbc145af8bce2992c0e717e15f201ed1fe0a1aa3f0d676bb3258930987d85e3080eb27d9c89c4b08f27bd4e56031fd02fbab32e52615 WHIRLPOOL 9b31847ef2cba06f6364dd2ecc486f1dd02727ee7128d88cf3b7a3fe25f10df9a5c31ea2a386e2fa967a2b0c484ea55909c4d73bae390fcc972abce78d46ecdb
+DIST simclist-1.6_p1.tar.gz 47710 BLAKE2B 01153e8de1a2ebe4bc08ba5e995dd8d531151e4125a8f154fc8df1a7f6d64bfa4f0ed2703fbc8f259dbca0a94637dba35006f51f0a7b1bb315b7da88719ef93f SHA512 639ced247de276d95dae6bf2990a0ef8bc4548f45b220593baa2dfcb87e90c14bf4ae16f0898132744fe4ac5377dfa3f97d5ed8e239c6d032f221b3cda17cbb4
diff --git a/dev-libs/simclist/metadata.xml b/dev-libs/simclist/metadata.xml
index 27a2343d7..62c13e1e4 100644
--- a/dev-libs/simclist/metadata.xml
+++ b/dev-libs/simclist/metadata.xml
@@ -6,9 +6,16 @@
 		<name>Gentoo Science Project</name>
 	</maintainer>
 	<longdescription>
-SimCList is a high quality C (C++ embeddable) library for handling
-lists. It exploits several advanced techniques for improving
-performance, including freelists, sentinels, automatic sort algorithm
-selection, sort randomization, mid pointer and optional multithreading.
-</longdescription>
+		SimCList is a high quality C (C++ embeddable) library for handling
+		lists. It exploits several advanced techniques for improving
+		performance, including freelists, sentinels, automatic sort algorithm
+		selection, sort randomization, mid pointer and optional multithreading.
+	</longdescription>
+	<use>
+		<flag name="dump">Disable building of dump and restore functionalities</flag>
+		<flag name="hash">Allow list_hash() to work exclusively on memory locations</flag>
+	</use>
+	<upstream>
+		<remote-id type="github">mij/simclist</remote-id>
+	</upstream>
 </pkgmetadata>
diff --git a/dev-libs/simclist/simclist-1.6.ebuild b/dev-libs/simclist/simclist-1.6.ebuild
deleted file mode 100644
index 179cabbcb..000000000
--- a/dev-libs/simclist/simclist-1.6.ebuild
+++ /dev/null
@@ -1,42 +0,0 @@
-# Copyright 1999-2014 Gentoo Foundation
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=5
-
-inherit cmake-utils
-
-DESCRIPTION="SimCList is a high quality C (C++ embeddable) library for handling lists"
-HOMEPAGE="http://mij.oltrelinux.com/devel/simclist"
-SRC_URI="${HOMEPAGE}/${P/_/}.tar.bz2"
-
-LICENSE="BSD"
-SLOT="0"
-KEYWORDS="~amd64 ~x86"
-IUSE="doc examples"
-
-S="${WORKDIR}/${P/_/}"
-
-DEPEND="doc? ( app-doc/doxygen )"
-RDEPEND=""
-
-src_compile(){
-	cmake-utils_src_compile
-	if use doc; then
-		doxygen || die "doxygen failed"
-	fi
-}
-
-src_install() {
-	mkdir -p "${D}"/usr/include
-	cp simclist.h "${D}"/usr/include/
-	cd "${BUILD_DIR}"
-	dolib libsimclist.so
-	cd "${S}"
-	if use doc; then
-		dohtml -r doc/html/*
-	fi
-	if use examples; then
-		docinto examples
-		dodoc examples/*
-	fi
-}
diff --git a/dev-libs/simclist/simclist-1.6_p1.ebuild b/dev-libs/simclist/simclist-1.6_p1.ebuild
new file mode 100644
index 000000000..41c9151c5
--- /dev/null
+++ b/dev-libs/simclist/simclist-1.6_p1.ebuild
@@ -0,0 +1,52 @@
+# Copyright 1999-2020 Gentoo Authors
+# Distributed under the terms of the GNU General Public License v2
+
+EAPI=7
+
+inherit cmake
+
+DESCRIPTION="SimCList is a high quality C (C++ embeddable) library for handling lists"
+HOMEPAGE="https://mij.oltrelinux.com/devel/simclist"
+COMMIT=6aef848d1743af66045a6f413cd3b8b1f1578c15
+SRC_URI="https://github.com/mij/simclist/archive/${COMMIT}.tar.gz -> ${P}.tar.gz"
+S="${WORKDIR}"/${PN}-${COMMIT}
+
+LICENSE="BSD"
+SLOT="0"
+KEYWORDS="~amd64 ~x86"
+IUSE="debug doc dump hash threads"
+
+BDEPEND="doc? ( app-text/doxygen )"
+
+CMAKE_IN_SOURCE_BUILD=1
+
+src_prepare() {
+	sed -i -e "/-O2/d" CMakeLists.txt || die
+	cmake_src_prepare
+}
+
+src_configure() {
+	local mycmakeargs=(
+		-DSIMCLIST_DEBUG=$(usex debug)
+		-DSIMCLIST_THREADING=$(usex threads)
+		-DSIMCLIST_NO_DUMPRESTORE=$(usex dump)
+		-DSIMCLIST_ALLOW_LOCATIONBASED_HASHES=$(usex hash)
+	)
+	cmake_src_configure
+}
+
+src_compile(){
+	cmake_src_compile
+	if use doc; then
+		doxygen || die "doxygen failed"
+	fi
+}
+
+src_install() {
+	doheader simclist.h
+	dolib.so libsimclist.so
+
+	if use doc ; then
+		dodoc -r doc/html/*
+	fi
+}
diff --git a/dev-libs/utf8proc/Manifest b/dev-libs/utf8proc/Manifest
deleted file mode 100644
index 1163fbcf2..000000000
--- a/dev-libs/utf8proc/Manifest
+++ /dev/null
@@ -1,2 +0,0 @@
-DIST utf8proc-1.2.tar.gz 137294 BLAKE2B 9712699510e05a7abdc51a7d226ae54ee93639f7d7b0684527fd7f5ace5c6b597a354829c5f75b87ed29988b16a19b033c6a6e2d71a892fd9e0a6972feef3bfb SHA512 066b77d599320e0f6d90e52f6ae482c3caf54276920ad4afacaf4d0c4969d94aa33401e63edee14b2887cdf60fdffd07f913d246212aac1a26b480f20cbc24d4
-DIST utf8proc-v1.1.6.tar.gz 105825 BLAKE2B e54975f44517e181b62d1f9631aa1b8d0cb247b948636f262be39477ec1b48bb884e2ed1c4c9f19a758eae9738355815b89bdca90ecbbcd25898ba6f938816a1 SHA512 3bec2388298c201d9d6992cdd36330f1109d26a37b3411ba633f006f40da9e494ba0565051b763a7d3014e6113cd1e7754e6b95d5cbb2d7b50cee55193f0fdc1
diff --git a/dev-libs/utf8proc/files/utf8proc-1.1.6-buildflags.patch b/dev-libs/utf8proc/files/utf8proc-1.1.6-buildflags.patch
deleted file mode 100644
index d9ff3be91..000000000
--- a/dev-libs/utf8proc/files/utf8proc-1.1.6-buildflags.patch
+++ /dev/null
@@ -1,11 +0,0 @@
---- a/Makefile	2014-01-26 18:55:57.400996757 +0000
-+++ b/Makefile	2014-01-26 19:00:10.264164095 +0000
-@@ -3,7 +3,7 @@
- 
- # settings
- 
--cflags = -O2 -std=c99 -pedantic -Wall -fpic $(CFLAGS)
-+cflags = -std=c99 -pedantic -fpic $(CFLAGS)
- cc = $(CC) $(cflags)
- 
- 
diff --git a/dev-libs/utf8proc/files/utf8proc-1.1.6-soname.patch b/dev-libs/utf8proc/files/utf8proc-1.1.6-soname.patch
deleted file mode 100644
index c0463700d..000000000
--- a/dev-libs/utf8proc/files/utf8proc-1.1.6-soname.patch
+++ /dev/null
@@ -1,11 +0,0 @@
---- a/Makefile	2014-01-26 19:01:17.723542649 +0000
-+++ b/Makefile	2014-01-26 19:02:24.532907919 +0000
-@@ -34,7 +34,7 @@
- 	ar rs libutf8proc.a utf8proc.o
- 
- libutf8proc.so: utf8proc.o
--	$(cc) -shared -o libutf8proc.so utf8proc.o
-+	$(cc) -Wl,-soname,libutf8proc.so -shared -o libutf8proc.so utf8proc.o
- 	chmod a-x libutf8proc.so
- 
- libutf8proc.dylib: utf8proc.o
diff --git a/dev-libs/utf8proc/files/utf8proc-1.2-buildflags.patch b/dev-libs/utf8proc/files/utf8proc-1.2-buildflags.patch
deleted file mode 100644
index de8847cdf..000000000
--- a/dev-libs/utf8proc/files/utf8proc-1.2-buildflags.patch
+++ /dev/null
@@ -1,40 +0,0 @@
- Makefile | 9 +++++----
- 1 file changed, 5 insertions(+), 4 deletions(-)
-
-diff --git a/Makefile b/Makefile
-index aba2453..5fab07d 100644
---- a/Makefile
-+++ b/Makefile
-@@ -6,8 +6,8 @@ AR=ar
- INSTALL=install
- 
- # compiler settings
--cflags = -O2 -std=c99 -pedantic -Wall -fpic -DUTF8PROC_EXPORTS $(CFLAGS)
--cc = $(CC) $(cflags)
-+CFLAGS ?= -O2
-+CFLAGS += -std=c99 -pedantic -Wall -fpic -DUTF8PROC_EXPORTS
- 
- # shared-library version MAJOR.MINOR.PATCH ... this may be *different*
- # from the utf8proc version number because it indicates ABI compatibility,
-@@ -54,18 +54,19 @@ data/utf8proc_data.c.new: libutf8proc.$(SHLIB_EXT) data/data_generator.rb data/c
- 	$(MAKE) -C data utf8proc_data.c.new
- 
- utf8proc.o: utf8proc.h utf8proc.c utf8proc_data.c
--	$(cc) -c -o utf8proc.o utf8proc.c
-+	$(CC) $(CFLAGS) -c -o utf8proc.o utf8proc.c
- 
- libutf8proc.a: utf8proc.o
- 	rm -f libutf8proc.a
- 	$(AR) rs libutf8proc.a utf8proc.o
- 
- libutf8proc.so.$(MAJOR).$(MINOR).$(PATCH): utf8proc.o
--	$(cc) -shared -o $@ -Wl,-soname -Wl,libutf8proc.so.$(MAJOR) utf8proc.o
-+	$(CC) $(LDFLAGS) -shared -o $@ -Wl,-soname -Wl,libutf8proc.so.$(MAJOR) utf8proc.o
- 	chmod a-x $@
- 
- libutf8proc.so: libutf8proc.so.$(MAJOR).$(MINOR).$(PATCH)
- 	ln -f -s libutf8proc.so.$(MAJOR).$(MINOR).$(PATCH) $@
-+	ln -f -s libutf8proc.so.$(MAJOR).$(MINOR).$(PATCH) $@.$(MAJOR)
- 
- libutf8proc.$(MAJOR).dylib: utf8proc.o
- 	$(cc) -dynamiclib -o $@ $^ -install_name $(libdir)/$@ -Wl,-compatibility_version -Wl,$(MAJOR) -Wl,-current_version -Wl,$(MAJOR).$(MINOR).$(PATCH)
diff --git a/dev-libs/utf8proc/metadata.xml b/dev-libs/utf8proc/metadata.xml
deleted file mode 100644
index b411feb93..000000000
--- a/dev-libs/utf8proc/metadata.xml
+++ /dev/null
@@ -1,20 +0,0 @@
-<?xml version="1.0" encoding="UTF-8"?>
-<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
-<pkgmetadata>
-	<maintainer type="project">
-		<email>sci@gentoo.org</email>
-		<name>Gentoo Science Project</name>
-	</maintainer>
-	<longdescription>
-utf8proc is a library for processing UTF-8 encoded Unicode
-strings. Some features are Unicode normalization, stripping of
-default ignorable characters, case folding and detection of grapheme
-cluster boundaries. A special character mapping is available, which
-converts for example the characters “Hyphen� (U+2010), “Minus�
-(U+2212) and “Hyphen-Minus� (U+002D, ASCII Minus) all into the ASCII
-minus sign, to make them equal for comparisons.
-</longdescription>
-	<upstream>
-		<remote-id type="github">JuliaLang/utf8proc</remote-id>
-	</upstream>
-</pkgmetadata>
diff --git a/dev-libs/utf8proc/utf8proc-1.1.6.ebuild b/dev-libs/utf8proc/utf8proc-1.1.6.ebuild
deleted file mode 100644
index 0cf65af75..000000000
--- a/dev-libs/utf8proc/utf8proc-1.1.6.ebuild
+++ /dev/null
@@ -1,36 +0,0 @@
-# Copyright 1999-2014 Gentoo Foundation
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=5
-
-inherit eutils
-
-DESCRIPTION="library for processing UTF-8 encoded Unicode strings"
-HOMEPAGE="http://www.public-software-group.org/utf8proc"
-SRC_URI="http://www.public-software-group.org/pub/projects/${PN}/v${PV}/utf8proc-v${PV}.tar.gz"
-S="${WORKDIR}/${PN}-v${PV}"
-
-LICENSE="MIT"
-SLOT="0"
-KEYWORDS="~amd64 ~x86 ~amd64-linux ~x86-linux"
-IUSE="static-libs"
-
-DEPEND=""
-RDEPEND="${DEPEND}"
-
-src_prepare() {
-	epatch \
-		"${FILESDIR}"/${P}-soname.patch \
-		"${FILESDIR}"/${P}-buildflags.patch
-}
-
-src_compile() {
-	emake libutf8proc.so
-	use static-libs & emake libutf8proc.a
-}
-
-src_install() {
-	doheader utf8proc.h
-	dolib.so libutf8proc.so
-	use static-libs && dolib.a libutf8proc.a
-}
diff --git a/dev-libs/utf8proc/utf8proc-1.2-r1.ebuild b/dev-libs/utf8proc/utf8proc-1.2-r1.ebuild
deleted file mode 100644
index d57e4100f..000000000
--- a/dev-libs/utf8proc/utf8proc-1.2-r1.ebuild
+++ /dev/null
@@ -1,35 +0,0 @@
-# Copyright 1999-2015 Gentoo Foundation
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=5
-
-inherit eutils toolchain-funcs
-
-DESCRIPTION="library for processing UTF-8 encoded Unicode strings"
-HOMEPAGE="http://www.public-software-group.org/utf8proc"
-SRC_URI="https://github.com/JuliaLang/${PN}/archive/v1.2.tar.gz -> ${P}.tar.gz"
-
-LICENSE="MIT"
-SLOT="0"
-KEYWORDS="~amd64 ~x86 ~amd64-linux ~x86-linux"
-IUSE="static-libs"
-
-src_prepare() {
-	epatch "${FILESDIR}"/"${P}"-buildflags.patch
-}
-
-src_compile() {
-	emake \
-		libutf8proc.so \
-		$(usex static-libs libutf8proc.a "") \
-		CC=$(tc-getCC) \
-		AR=$(tc-getAR)
-#		CFLAGS="${CFLAGS}"
-#		LDFLAGS="${LDFLAGS} -Wl,--soname,lib${PN}.${PV}"
-}
-
-src_install() {
-	doheader utf8proc.h
-	dolib.so libutf8proc.so*
-	use static-libs && dolib.a libutf8proc.a
-}
diff --git a/dev-lua/lua-md5/Manifest b/dev-lua/lua-md5/Manifest
deleted file mode 100644
index 247b0c1bb..000000000
--- a/dev-lua/lua-md5/Manifest
+++ /dev/null
@@ -1 +0,0 @@
-DIST lua-md5-1.2.tar.gz 29896 BLAKE2B 28188ff00688245df5bed9c06397134b49f2a9f97eea9db979cd1bf1ade20cd54ab592c007d6bef6d6e91415ea6e628e2ec9b101a0f56c0c7bce0415f4a05744 SHA512 1d0925351b4b774581f78147b7dd44df649eec2bc8397db991149feaf1f16c8f26d4b0fce6d8463be656115cebf605339ba8da851bc50d1ae1da8033d4ed564d
diff --git a/dev-lua/lua-md5/files/lua-md5-1.2-respect-DESTDIR.patch b/dev-lua/lua-md5/files/lua-md5-1.2-respect-DESTDIR.patch
deleted file mode 100644
index 9f7e71027..000000000
--- a/dev-lua/lua-md5/files/lua-md5-1.2-respect-DESTDIR.patch
+++ /dev/null
@@ -1,19 +0,0 @@
---- Makefile.ori	2018-09-11 16:35:19.884248326 +0200
-+++ Makefile	2018-09-11 16:35:22.214321658 +0200
-@@ -22,11 +22,11 @@
- 	$(CC) $(CFLAGS) $(LIB_OPTION) -o src/$(DES56_LIBNAME) $(DES56_OBJS) $(COMPAT52_OBJS)
- 
- install: src/$(MD5_LIBNAME) src/$(DES56_LIBNAME)
--	mkdir -p $(LUA_LIBDIR)/md5
--	cp src/$(MD5_LIBNAME) $(LUA_LIBDIR)/md5/core.so
--	mkdir -p $(LUA_DIR)
--	cp $(MD5_LUAS) $(LUA_DIR)
--	cp src/$(DES56_LIBNAME) $(LUA_LIBDIR)
-+	mkdir -p $(DESTDIR)/$(LUA_LIBDIR)/md5
-+	cp src/$(MD5_LIBNAME) $(DESTDIR)/$(LUA_LIBDIR)/md5/core.so
-+	mkdir -p $(DESTDIR)/$(LUA_DIR)
-+	cp $(MD5_LUAS) $(DESTDIR)/$(LUA_DIR)
-+	cp src/$(DES56_LIBNAME) $(DESTDIR)/$(LUA_LIBDIR)
- 
- clean:
- 	rm -f $(MD5_OBJS) src/$(MD5_LIBNAME) $(DES56_OBJS) src/$(DES56_LIBNAME) $(COMPAT52_OBJS)
diff --git a/dev-lua/lua-md5/lua-md5-1.2.ebuild b/dev-lua/lua-md5/lua-md5-1.2.ebuild
deleted file mode 100644
index 14a644702..000000000
--- a/dev-lua/lua-md5/lua-md5-1.2.ebuild
+++ /dev/null
@@ -1,25 +0,0 @@
-# Copyright 1999-2018 Gentoo Foundation
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=6
-
-inherit eutils
-
-DESCRIPTION="Basic cryptographic facilities for Lua 5.0, 5.1 or 5.2"
-HOMEPAGE="http://keplerproject.github.io/md5"
-SRC_URI="https://github.com/keplerproject/md5/archive/v1.2.tar.gz -> ${P}.tar.gz"
-
-LICENSE="MIT"
-SLOT="0"
-KEYWORDS="~amd64 ~x86"
-IUSE=""
-
-DEPEND=""
-RDEPEND="${DEPEND}"
-
-S="${WORKDIR}"/md5-"${PV}"
-
-src_prepare(){
-	epatch "${FILESDIR}"/lua-md5-1.2-respect-DESTDIR.patch
-	default
-}
diff --git a/dev-lua/lua-md5/metadata.xml b/dev-lua/lua-md5/metadata.xml
deleted file mode 100644
index 4163b4b2a..000000000
--- a/dev-lua/lua-md5/metadata.xml
+++ /dev/null
@@ -1,8 +0,0 @@
-<?xml version="1.0" encoding="UTF-8"?>
-<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
-<pkgmetadata>
-	<maintainer type="person">
-		<email>mmokrejs@fold.natur.cuni.cz</email>
-		<name>Martin Mokrejs</name>
-	</maintainer>
-</pkgmetadata>
diff --git a/dev-ml/lacaml/Manifest b/dev-ml/lacaml/Manifest
index 0b14f909a..2dade25f2 100644
--- a/dev-ml/lacaml/Manifest
+++ b/dev-ml/lacaml/Manifest
@@ -1 +1 @@
-DIST lacaml-7.0.3.tar.gz 151742 SHA256 3ebd0b35ae0e4fe5cc5483e61a8bf1fb46ef8fed60f5c89a09e589b91b7ec982 SHA512 5f9267e64e5e2a858ba57b34ea41d64ae8724b5a6a9f9d81b6b2f2d4daeb42eb060f2b18d040d559a1baf356518c93c05db0a00af5bbf34084029e27320ad5b7 WHIRLPOOL 7af11d10e246850e2c1f39f3862b9269d783f2599cd7acd86e75662a5bf43bd2487e3ae3de2374070ea799aaef1377792d9d2d14c268742b8bf1a91975b4a2a9
+DIST lacaml-11.0.8.tar.gz 152679 BLAKE2B fd7884f943c8b7259f9f8e027e17b110c7890b27700b403f40ed129dd9664761e33940895ff692a049c02021f10268b4ec248fe5ddbc9319631a9d8856fa0999 SHA512 5fc3ef09a8acb53b1e3efb128af8a8cd6d78c7c009af423c5a02777de0a4c7d14e817f472a06ab95727745cecb1e0630c9bcf03c56d0cce9ec9355ac82e1df72
diff --git a/dev-ml/lacaml/files/API.odocl b/dev-ml/lacaml/files/API.odocl
deleted file mode 100644
index 4e6cc95b8..000000000
--- a/dev-ml/lacaml/files/API.odocl
+++ /dev/null
@@ -1 +0,0 @@
-lib/Lacaml
diff --git a/dev-ml/lacaml/lacaml-11.0.8.ebuild b/dev-ml/lacaml/lacaml-11.0.8.ebuild
new file mode 100644
index 000000000..7070c04af
--- /dev/null
+++ b/dev-ml/lacaml/lacaml-11.0.8.ebuild
@@ -0,0 +1,28 @@
+# Copyright 1999-2021 Gentoo Authors
+# Distributed under the terms of the GNU General Public License v2
+
+EAPI=7
+
+inherit dune
+
+DESCRIPTION="BLAS/LAPACK interface for OCaml"
+HOMEPAGE="https://mmottl.github.io/lacaml/"
+SRC_URI="https://github.com/mmottl/lacaml/archive/${PV}.tar.gz -> ${P}.tar.gz"
+
+LICENSE="LGPL-2.1-with-linking-exception"
+SLOT="0"
+KEYWORDS="~amd64 ~x86"
+
+IUSE="ocamlopt"
+
+RDEPEND="
+	virtual/blas
+	virtual/lapack
+	dev-ml/dune-configurator
+"
+DEPEND="${RDEPEND}"
+BDEPEND="
+	virtual/pkgconfig
+"
+
+DOCS=( "README.md" "CHANGES.txt" "TODO.md" )
diff --git a/dev-ml/lacaml/lacaml-7.0.3.ebuild b/dev-ml/lacaml/lacaml-7.0.3.ebuild
deleted file mode 100644
index a89c081a6..000000000
--- a/dev-ml/lacaml/lacaml-7.0.3.ebuild
+++ /dev/null
@@ -1,37 +0,0 @@
-# Copyright 1999-2015 Gentoo Foundation
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=5
-
-OASIS_BUILD_DOCS=1
-
-inherit oasis toolchain-funcs
-
-DESCRIPTION="BLAS/LAPACK interface for OCaml"
-HOMEPAGE="http://forge.ocamlcore.org/projects/lacaml"
-SRC_URI="https://bitbucket.org/mmottl/lacaml/downloads/${P}.tar.gz"
-
-LICENSE="LGPL-2.1-with-linking-exception"
-SLOT="0"
-KEYWORDS="~x86"
-IUSE=""
-
-RDEPEND="
-	virtual/blas
-	virtual/lapack"
-DEPEND="${DEPEND}
-	virtual/pkgconfig"
-
-DOCS=( "README.md" "CHANGES.txt" "TODO.md" )
-
-src_prepare() {
-	if use doc; then
-		cp "${FILESDIR}/API.odocl" . || die
-	fi
-	cclib="$($(tc-getPKG_CONFIG) --libs blas lapack)"
-	cclib="[$(echo $cclib|sed -e 's/\(-[a-z0-9]*\) /\"\1\"\;/g' -e \
-	's/\(-[a-z0-9]*\)$/\"\1\"/')]"
-	sed -i "s/cclib = \[\]/cclib = ${cclib}/" setup.conf
-	#would like to do the below, but doesn't work from ebuild
-	#oasis_configure_opts="--override conf_cclib $($(tc-getPKG_CONFIG) --libs blas lapack)"
-}
diff --git a/dev-ml/lacaml/metadata.xml b/dev-ml/lacaml/metadata.xml
index ea2f7445d..24157e1f0 100644
--- a/dev-ml/lacaml/metadata.xml
+++ b/dev-ml/lacaml/metadata.xml
@@ -6,9 +6,15 @@
 		<name>Gentoo Science Project</name>
 	</maintainer>
 	<longdescription lang="en">
-BLAS/LAPACK-interface for OCaml
-</longdescription>
+		This OCaml-library interfaces two widely used mathematical FORTRAN-libraries:
+
+		BLAS - Basic Linear Algebra Subroutines
+		LAPACK - Linear Algebra PACKage
+
+		This allows developers to write high-performance numerical code for applications that require linear algebra.
+	</longdescription>
 	<upstream>
 		<remote-id type="bitbucket">mmottl/lacaml</remote-id>
+		<remote-id type="github">mmottl/lacaml</remote-id>
 	</upstream>
 </pkgmetadata>
diff --git a/dev-ml/mlgmpidl/Manifest b/dev-ml/mlgmpidl/Manifest
deleted file mode 100644
index 79725485c..000000000
--- a/dev-ml/mlgmpidl/Manifest
+++ /dev/null
@@ -1 +0,0 @@
-DIST mlgmpidl-1.1.tgz 194002 BLAKE2B 1fc5b7ef9f6046de7c7357316b37bda5495df22a95b89ba33a7f457e32766218d43d528793b7f2a8fb4dab3cc56354370377670bb21ba496c3b665dd19346e68 SHA512 f7fe74e0e337c2ea33464c49bc1313a3c6a71fee89572d4c23dc26913d8fe1fb41907bfe327d085c39786b63267174be4445b31a5d29acf3e57974ac8b871d2e
diff --git a/dev-ml/mlgmpidl/files/mlgmpidl-1.1-mpfr-3_compat.patch b/dev-ml/mlgmpidl/files/mlgmpidl-1.1-mpfr-3_compat.patch
deleted file mode 100644
index efb07559d..000000000
--- a/dev-ml/mlgmpidl/files/mlgmpidl-1.1-mpfr-3_compat.patch
+++ /dev/null
@@ -1,20 +0,0 @@
-diff -Naurp mlgmpidl/gmp_caml.h mlgmpidl2/gmp_caml.h
---- mlgmpidl/gmp_caml.h	2007-07-11 13:29:31.000000000 +0000
-+++ mlgmpidl2/gmp_caml.h	2010-07-03 16:09:33.000000000 +0000
-@@ -14,6 +14,16 @@
- #if defined(HAS_MPFR)
- #if HAS_MPFR!=0
- #include "mpfr.h"
-+#ifndef GMP_RND_MAX
-+#define GMP_RND_MAX (MPFR_RNDNA - 1)
-+#define mpfr_random(x)	\
-+	{\
-+		gmp_randstate_t s;\
-+		gmp_randinit_default(s);\
-+		mpfr_urandomb(x,s);\
-+		gmp_randclear(s);\
-+	}
-+#endif
- #endif
- #endif
- #include "caml/mlvalues.h"
diff --git a/dev-ml/mlgmpidl/metadata.xml b/dev-ml/mlgmpidl/metadata.xml
deleted file mode 100644
index 8c51f92e4..000000000
--- a/dev-ml/mlgmpidl/metadata.xml
+++ /dev/null
@@ -1,17 +0,0 @@
-<?xml version="1.0" encoding="UTF-8"?>
-<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
-<pkgmetadata>
-	<maintainer type="project">
-		<email>sci-mathematics@gentoo.org</email>
-		<name>Gentoo Mathematics Project</name>
-	</maintainer>
-	<longdescription>
-MLGMPIDL is a package offering an interface to the GMP and MPFR
-libraries for OCaml version 3.07 or higher. The interface offers access
-to almost all the functions of the library, and is decomposed into 7
-submodules.
-</longdescription>
-	<use>
-		<flag name="mpfr">Add support for <pkg>dev-libs/mpfr</pkg></flag>
-	</use>
-</pkgmetadata>
diff --git a/dev-ml/mlgmpidl/mlgmpidl-1.1.ebuild b/dev-ml/mlgmpidl/mlgmpidl-1.1.ebuild
deleted file mode 100644
index 90bc71a8e..000000000
--- a/dev-ml/mlgmpidl/mlgmpidl-1.1.ebuild
+++ /dev/null
@@ -1,55 +0,0 @@
-# Copyright 1999-2015 Gentoo Foundation
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=5
-
-inherit eutils toolchain-funcs
-
-DESCRIPTION="OCaml interface to the GMP and MPFR libraries"
-HOMEPAGE="http://www.inrialpes.fr/pop-art/people/bjeannet/mlxxxidl-forge/mlgmpidl/"
-SRC_URI="https://gforge.inria.fr/frs/download.php/20228/${PN}-${PV}.tgz"
-
-LICENSE="LGPL-2"
-SLOT="0"
-KEYWORDS="~amd64 ~x86"
-IUSE="doc +mpfr"
-
-RDEPEND="
-	>=dev-lang/ocaml-3.09
-	dev-ml/camlidl
-	dev-libs/gmp:0
-	mpfr? ( dev-libs/mpfr:0 )"
-DEPEND="${RDEPEND}
-	doc? (
-		app-text/texlive
-		app-text/ghostscript-gpl
-		)"
-
-S="${WORKDIR}/${PN}"
-
-src_prepare() {
-	rm -R html mlgmpidl.pdf || die
-	mv Makefile.config.model Makefile.config || die
-	sed \
-		-e "s/FLAGS = \\\/FLAGS += \\\/g" \
-		-e "s/-O3 -UNDEBUG/-DUDEBUG/g" \
-		-e "s/MLGMPIDL_PREFIX = /MLGMPIDL_PREFIX = \$(DESTDIR)\/usr/g" \
-		-i Makefile.config || die
-
-	if use !mpfr; then
-		sed -i -e "s/HAS_MPFR=1/#HAS_MPFR=0/g" Makefile.config || die
-	fi
-
-	epatch "${FILESDIR}"/${P}-mpfr-3_compat.patch
-}
-
-src_compile() {
-	emake -j1 all gmprun gmptop
-
-	use doc && emake html mlgmpidl.pdf
-}
-
-src_install(){
-	use doc && DOCS+=( mlgmpidl.pdf )
-	default
-}
diff --git a/dev-perl/Algorithm-Loops/Algorithm-Loops-1.32.ebuild b/dev-perl/Algorithm-Loops/Algorithm-Loops-1.32.ebuild
index 2b7a4126b..f2daf48f5 100644
--- a/dev-perl/Algorithm-Loops/Algorithm-Loops-1.32.ebuild
+++ b/dev-perl/Algorithm-Loops/Algorithm-Loops-1.32.ebuild
@@ -1,7 +1,7 @@
-# Copyright 1999-2016 Gentoo Foundation
+# Copyright 1999-2021 Gentoo Authors
 # Distributed under the terms of the GNU General Public License v2
 
-EAPI=6
+EAPI=7
 
 DIST_AUTHOR="TYEMQ"
 DIST_A_EXT="tar.gz"
@@ -14,7 +14,6 @@ DESCRIPTION="Looping constructs: NestedLoops, MapCar*, Filter, and NextPermute*"
 LICENSE="CC0-1.0"
 SLOT="0"
 KEYWORDS="~amd64 ~x86"
-IUSE=""
 
 DEPEND="dev-lang/perl"
 
diff --git a/dev-perl/BTLib/BTLib-0.19.ebuild b/dev-perl/BTLib/BTLib-0.19.ebuild
index 7aeb5d6f8..6fa1072fb 100644
--- a/dev-perl/BTLib/BTLib-0.19.ebuild
+++ b/dev-perl/BTLib/BTLib-0.19.ebuild
@@ -1,18 +1,19 @@
-# Copyright 1999-2014 Gentoo Foundation
+# Copyright 1999-2021 Gentoo Authors
 # Distributed under the terms of the GNU General Public License v2
 
-EAPI=5
-
-MODULE_AUTHOR=""
+EAPI=7
 
 inherit perl-module
 
 DESCRIPTION="Perl part of the estscan package"
+HOMEPAGE="https://sourceforge.net/projects/estscan/"
 SRC_URI="http://downloads.sourceforge.net/estscan/${P}.tar.gz"
 
-#LICENSE="|| ( Artistic GPL-1 GPL-2 GPL-3 )"
+LICENSE="|| ( Artistic GPL-1 GPL-2 GPL-3 )"
 SLOT="0"
 KEYWORDS="~amd64 ~x86"
-IUSE=""
+
+RDEPEND="
+	!app-misc/sphinx"
 
 SRC_TEST="do"
diff --git a/dev-perl/BTLib/BTLib-0.20.ebuild b/dev-perl/BTLib/BTLib-0.20.ebuild
new file mode 100644
index 000000000..6fa1072fb
--- /dev/null
+++ b/dev-perl/BTLib/BTLib-0.20.ebuild
@@ -0,0 +1,19 @@
+# Copyright 1999-2021 Gentoo Authors
+# Distributed under the terms of the GNU General Public License v2
+
+EAPI=7
+
+inherit perl-module
+
+DESCRIPTION="Perl part of the estscan package"
+HOMEPAGE="https://sourceforge.net/projects/estscan/"
+SRC_URI="http://downloads.sourceforge.net/estscan/${P}.tar.gz"
+
+LICENSE="|| ( Artistic GPL-1 GPL-2 GPL-3 )"
+SLOT="0"
+KEYWORDS="~amd64 ~x86"
+
+RDEPEND="
+	!app-misc/sphinx"
+
+SRC_TEST="do"
diff --git a/dev-perl/BTLib/Manifest b/dev-perl/BTLib/Manifest
index 43486947a..fb421f038 100644
--- a/dev-perl/BTLib/Manifest
+++ b/dev-perl/BTLib/Manifest
@@ -1 +1,2 @@
 DIST BTLib-0.19.tar.gz 36283 BLAKE2B 53d26fdc7fee3325104a7f2041617bbde464421c540b29c7d47381c60d8f837601e7274d9f0ef5694d1b86b3e2cc7e9a0b289090c3c957a343542e3e7305cd50 SHA512 00261daa7fab4d16dec9e9d4f9e382cc804a10c0ed6b813d6223902b53f6b260dc0a242acfab93897afa750e949ab3f21ecae537206d81eb712f06289387f7d2
+DIST BTLib-0.20.tar.gz 35505 BLAKE2B 7cb116601e1641f06e8978a228e562316a0b6b99da99c8acf5d4cd0bc991461235b651e95eecf23e0298f68561743cd1d0b683992bbe056e00e2d02d94af187e SHA512 d130d1d728e57e82d6cd7e990ecf592421bce353e6557a381c4b5b8199db6e82342ccfa15d8527cc2f38272ff5afd303473886345113eedad9a425dff27b4c51
diff --git a/dev-perl/Bio-BigFile/Bio-BigFile-1.07.ebuild b/dev-perl/Bio-BigFile/Bio-BigFile-1.07.ebuild
index 02c7306c5..d695850b9 100644
--- a/dev-perl/Bio-BigFile/Bio-BigFile-1.07.ebuild
+++ b/dev-perl/Bio-BigFile/Bio-BigFile-1.07.ebuild
@@ -1,18 +1,17 @@
-# Copyright 1999-2015 Gentoo Foundation
+# Copyright 1999-2021 Gentoo Authors
 # Distributed under the terms of the GNU General Public License v2
 
-EAPI=5
+EAPI=7
 
-MODULE_AUTHOR="LDS"
+DIST_AUTHOR="LDS"
 
-inherit eutils flag-o-matic perl-module
+inherit flag-o-matic perl-module
 
 DESCRIPTION="BigWig and BigBed file perl-based interface for Gbrowse-2"
 
 LICENSE="|| ( Artistic-2 GPL-1 GPL-2 GPL-3 )"
 SLOT="0"
 KEYWORDS="~amd64 ~x86"
-IUSE=""
 
 RDEPEND="
 	dev-perl/IO-String
@@ -23,8 +22,12 @@ DEPEND="${RDEPEND}
 
 SRC_TEST="do"
 
+PATCHES=(
+	"${FILESDIR}"/Build.PL.patch
+)
+
 src_prepare(){
 	append-cflags -D_REENTRANT -D_GNU_SOURCE -fno-strict-aliasing
 	append-lfs-flags
-	epatch "${FILESDIR}"/Build.PL.patch
+	default
 }
diff --git a/dev-perl/Bio-DB-Das-Chado/Bio-DB-Das-Chado-0.34.ebuild b/dev-perl/Bio-DB-Das-Chado/Bio-DB-Das-Chado-0.34.ebuild
deleted file mode 100644
index e744dec25..000000000
--- a/dev-perl/Bio-DB-Das-Chado/Bio-DB-Das-Chado-0.34.ebuild
+++ /dev/null
@@ -1,22 +0,0 @@
-# Copyright 1999-2015 Gentoo Foundation
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=5
-
-MODULE_AUTHOR="SCAIN"
-
-inherit perl-module
-
-DESCRIPTION="A Chado database interface for Gbrowse-2"
-
-LICENSE="|| ( Artistic-2 GPL-1 GPL-2 GPL-3 )"
-SLOT="0"
-KEYWORDS="~amd64 ~x86"
-IUSE=""
-
-RDEPEND=""
-DEPEND="${RDEPEND}
-	dev-perl/DBD-Pg
-	dev-perl/Module-Build"
-
-SRC_TEST="do"
diff --git a/dev-perl/Bio-DB-Das-Chado/Bio-DB-Das-Chado-0.35.ebuild b/dev-perl/Bio-DB-Das-Chado/Bio-DB-Das-Chado-0.35.ebuild
new file mode 100644
index 000000000..d4a7e1863
--- /dev/null
+++ b/dev-perl/Bio-DB-Das-Chado/Bio-DB-Das-Chado-0.35.ebuild
@@ -0,0 +1,22 @@
+# Copyright 1999-2021 Gentoo Authors
+# Distributed under the terms of the GNU General Public License v2
+
+EAPI=7
+
+DIST_AUTHOR="SCAIN"
+
+inherit perl-module
+
+DESCRIPTION="A Chado database interface for Gbrowse-2"
+
+LICENSE="|| ( Artistic-2 GPL-1 GPL-2 GPL-3 )"
+SLOT="0"
+KEYWORDS="~amd64 ~x86"
+
+RDEPEND=""
+DEPEND="${RDEPEND}
+	dev-perl/DBI
+	dev-perl/DBD-Pg
+	dev-perl/Module-Build"
+
+SRC_TEST="do"
diff --git a/dev-perl/Bio-DB-Das-Chado/Manifest b/dev-perl/Bio-DB-Das-Chado/Manifest
index 13dc8d8ed..1e74a945a 100644
--- a/dev-perl/Bio-DB-Das-Chado/Manifest
+++ b/dev-perl/Bio-DB-Das-Chado/Manifest
@@ -1 +1 @@
-DIST Bio-DB-Das-Chado-0.34.tar.gz 77495 BLAKE2B 66361386760c7fa8f65d2043890a1debf283a9af7540bf88a18244692931df1d7032486ff3e3bfdb2ac8c394ad16b6f2f8c4a43d3b24630acbdf5707b3ae8016 SHA512 e12335304e1cbc81ef261542e8c238aba625bc095e4a2febaf94bdf2eed6226d9daefad78d698341052516be44e670671625c7c903fbe63492c063d0a6843e9a
+DIST Bio-DB-Das-Chado-0.35.tar.gz 78013 BLAKE2B c983cc9a15bbadcb523adcfa52c4e61bde764703d7188503a2e5e84c2be84341b6969a64724ce7663b5050861602709b189b08f9f6d8fbf2996c07efcf0dc9ea SHA512 c31613a92f000c22307763849d389ca02b50fb43d74e4865be5fe88052c49660e70f066e849d54d86c839317f815a98e965a03a687ec40c5e318babb64a742ad
diff --git a/dev-perl/Bio-DB-HTS/Bio-DB-HTS-2.3.ebuild b/dev-perl/Bio-DB-HTS/Bio-DB-HTS-2.3.ebuild
deleted file mode 100644
index 1e7e6ceca..000000000
--- a/dev-perl/Bio-DB-HTS/Bio-DB-HTS-2.3.ebuild
+++ /dev/null
@@ -1,35 +0,0 @@
-# Copyright 1999-2016 Gentoo Foundation
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=5
-
-# this is https://metacpan.org/pod/Bio::DB::HTS and https://github.com/Ensembl/Bio-DB-HTS
-# this is not https://metacpan.org/pod/Bio::HTS
-MODULE_AUTHOR="RISHIDEV"
-inherit perl-module multilib toolchain-funcs
-
-DESCRIPTION="Enable rapid access to bgzipped FASTA files"
-
-#LICENSE="|| ( Artistic GPL-1 GPL-2 GPL-3 )"
-SLOT="0"
-KEYWORDS="~amd64 ~x86"
-IUSE=""
-
-RDEPEND=""
-DEPEND="${RDEPEND}
-	dev-perl/Module-Build
-	sci-libs/htslib[static-libs]"
-
-SRC_TEST="do"
-
-src_prepare(){
-	# https://github.com/Ensembl/Bio-HTS/issues/30
-	export HTSLIB_LIBDIR="${EPREFIX}"/"$(get_libdir)" # currently ignored
-	export HTSLIB_INCDIR="${EPREFIX}"/usr/include/htslib # currently ignored
-	export HTSLIB_DIR="${EPREFIX}"/usr # useless, Build.PL will not invent /usr/lib64/ is the correct answer
-	perl-module_src_prepare
-}
-
-# is the below -rpath acceptable?
-# x86_64-pc-linux-gnu-gcc -shared -O2 -pipe -maes -mpclmul -mpopcnt -mavx -march=native -Wl,-O1 -Wl,--as-needed -o blib/arch/auto/Bio/DB/HTS/HTS.so lib/Bio/DB/HTS.o -L/usr/lib -Wl,-rpath,/usr/lib -lhts -lpthread -lz
-# x86_64-pc-linux-gnu-gcc -shared -O2 -pipe -maes -mpclmul -mpopcnt -mavx -march=native -Wl,-O1 -Wl,--as-needed -o blib/arch/auto/Bio/DB/HTS/Faidx/Faidx.so lib/Bio/DB/HTS/Faidx.o -L/usr/lib -Wl,-rpath,/usr/lib -lhts -lpthread -lz
diff --git a/dev-perl/Bio-DB-HTS/Manifest b/dev-perl/Bio-DB-HTS/Manifest
deleted file mode 100644
index c71a491f1..000000000
--- a/dev-perl/Bio-DB-HTS/Manifest
+++ /dev/null
@@ -1 +0,0 @@
-DIST Bio-DB-HTS-2.3.tar.gz 2187131 BLAKE2B 51b40ad8842faa1891c61cb47daaf2af1df9bff7a831ef7d289908ebfc65a3e3ed46e592c2cb33ae7b895be652749b66217b220846269b7294e0edbc902bd1ae SHA512 837da08534fab6f16f889068cfd67e9bb051b592307c47503c707fb263690e952e4292473bfee54664b109312f8188bd2b6726a7669980f6d129ddd6042be8ed
diff --git a/dev-perl/Bio-EnsEMBL/Bio-EnsEMBL-9999.ebuild b/dev-perl/Bio-EnsEMBL/Bio-EnsEMBL-9999.ebuild
deleted file mode 100644
index d4910ad68..000000000
--- a/dev-perl/Bio-EnsEMBL/Bio-EnsEMBL-9999.ebuild
+++ /dev/null
@@ -1,34 +0,0 @@
-# Copyright 1999-2016 Gentoo Foundation
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=6
-
-MODULE_AUTHOR=""
-inherit perl-module
-
-DESCRIPTION="EnsEMBL Perl API aka ensembl-api exposing Bio::EnsEMBL::Registry"
-SRC_URI="ftp://ftp.ensembl.org/pub/ensembl-api.tar.gz"
-
-#LICENSE="|| ( Artistic GPL-1+ )"
-SLOT="0"
-KEYWORDS=""
-IUSE=""
-
-RDEPEND=""
-DEPEND="${RDEPEND}"
-
-S="${WORKDIR}"
-
-src_install(){
-	perl_set_version
-	insinto "${VENDOR_LIB}" # do not add "${PN}" so the the PERL path starts with Bio/
-	find . -name t | xargs rm -rf || die
-	find . -name test.pl | xargs rm -f || die
-	find . -name \*.example | xargs rm -f || die
-	find . -name \*.json | xargs rm -f || die
-	find . -name README* | xargs rm -rf || die
-	find . -name \*.conf | xargs rm -f || die
-	find . -name travisci | xargs rm -rf || die
-	find . -name sql | xargs rm -rf || die
-	find . -name modules | while read d; do pushd "$d"; doins -r *; popd; done || die
-}
diff --git a/dev-perl/Bio-EnsEMBL/Manifest b/dev-perl/Bio-EnsEMBL/Manifest
deleted file mode 100644
index 0f4a3d2cc..000000000
--- a/dev-perl/Bio-EnsEMBL/Manifest
+++ /dev/null
@@ -1 +0,0 @@
-DIST ensembl-api.tar.gz 59450373 BLAKE2B b775dd932572f7466324af76ea710d8d50bf97d3af967e15ed1c153034a920eef6510f595734ef6a97eb7dac94958e647354252afa141e4a12ffefaa68a4a5a4 SHA512 48cabb86cc687f958f0914f67e33b10ac6dc6605758fe26bdfcd349555fc9dbd4780781f66fb0dbf283296675285a62c472ebcf9ab82a5b274ce1fccb29ce734
diff --git a/dev-perl/Config-Std/Config-Std-0.901.ebuild b/dev-perl/Config-Std/Config-Std-0.901.ebuild
deleted file mode 100644
index 3cc16b153..000000000
--- a/dev-perl/Config-Std/Config-Std-0.901.ebuild
+++ /dev/null
@@ -1,25 +0,0 @@
-# Copyright 1999-2017 Gentoo Foundation
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=5
-
-MODULE_AUTHOR="BRICKER"
-MODULE_A_EXT="tar.gz"
-inherit perl-module
-
-DESCRIPTION="Load and save configuration files in a standard format"
-
-#LICENSE="|| ( Artistic GPL-1+ )"
-SLOT="0"
-KEYWORDS="~amd64 ~x86"
-IUSE="test"
-
-RDEPEND=""
-DEPEND="${RDEPEND}
-	dev-perl/Class-Std
-	dev-perl/Module-Build
-	test? (
-		virtual/perl-Test-Simple
-		dev-perl/Test-Distribution
-		dev-perl/Test-Pod
-	)"
diff --git a/dev-perl/Config-Std/Config-Std-0.903.ebuild b/dev-perl/Config-Std/Config-Std-0.903.ebuild
new file mode 100644
index 000000000..e80b378c4
--- /dev/null
+++ b/dev-perl/Config-Std/Config-Std-0.903.ebuild
@@ -0,0 +1,21 @@
+# Copyright 1999-2020 Gentoo Authors
+# Distributed under the terms of the GNU General Public License v2
+
+EAPI=7
+
+DIST_AUTHOR="BRICKER"
+inherit perl-module
+
+DESCRIPTION="Load and save configuration files in a standard format"
+
+#LICENSE="|| ( Artistic GPL-1+ )"
+SLOT="0"
+KEYWORDS="~amd64 ~x86"
+IUSE="test"
+RESTRICT="!test? ( test )"
+
+RDEPEND="
+	dev-perl/Class-Std
+	dev-perl/Module-Build
+"
+DEPEND="${RDEPEND}"
diff --git a/dev-perl/Config-Std/Manifest b/dev-perl/Config-Std/Manifest
index 3b8346b06..fd26c3dee 100644
--- a/dev-perl/Config-Std/Manifest
+++ b/dev-perl/Config-Std/Manifest
@@ -1 +1 @@
-DIST Config-Std-0.901.tar.gz 21940 BLAKE2B 9a5dd1a4ad8771ad9d44bea3d4ccb6bee3dc814be530146113dc1d6590af05a7945aff474bad466ccc33c3c8f8c27e7d9d0dabf329f075ee7e139eff76ff39c4 SHA512 9ad7622afab9ab960abbf979d297279c8c9ec2ebf8477dfab4db40916cf981ef4b291b272ae1ff78f3a086f97bce8198cebd1888b751dae499026ccc7f28c222
+DIST Config-Std-0.903.tar.gz 21667 BLAKE2B a80e06b7a4be1aed0c788d7ff5881d26b72638e46d1fa344a053cbe16c1fe615bad2c5c1f10fd9d5d04a513380bb439d538ff501d2f099b39b54c4ac24da2b76 SHA512 ad9800fb55631342117600e3fec5be5da7e18cb65e46c7400d0f311de848f013aa69a1b6b659519f6a78338e8b514a4e7e85a939d2c1cc3aa43a98b7d42339ca
diff --git a/dev-perl/DBIx-DBStag/DBIx-DBStag-0.12.ebuild b/dev-perl/DBIx-DBStag/DBIx-DBStag-0.12.ebuild
index d2a550c14..17faeebb7 100644
--- a/dev-perl/DBIx-DBStag/DBIx-DBStag-0.12.ebuild
+++ b/dev-perl/DBIx-DBStag/DBIx-DBStag-0.12.ebuild
@@ -1,9 +1,9 @@
-# Copyright 1999-2014 Gentoo Foundation
+# Copyright 1999-2021 Gentoo Authors
 # Distributed under the terms of the GNU General Public License v2
 
-EAPI=5
+EAPI=7
 
-MODULE_AUTHOR="SCAIN"
+DIST_AUTHOR="SCAIN"
 
 inherit perl-module
 
@@ -12,7 +12,6 @@ DESCRIPTION="Relational Database to Hierarchical (Stag/XML) Mapping"
 LICENSE="|| ( Artistic GPL-1 GPL-2 GPL-3 )"
 SLOT="0"
 KEYWORDS="~amd64 ~x86"
-IUSE=""
 
 DEPEND="
 	>=dev-perl/DBIx-DBSchema-0.39
diff --git a/dev-perl/Data-Types/Data-Types-0.09.ebuild b/dev-perl/Data-Types/Data-Types-0.09.ebuild
deleted file mode 100644
index baccfdb2f..000000000
--- a/dev-perl/Data-Types/Data-Types-0.09.ebuild
+++ /dev/null
@@ -1,23 +0,0 @@
-# Copyright 1999-2017 Gentoo Foundation
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=6
-
-MODULE_AUTHOR="DWHEELER"
-inherit perl-module
-
-DESCRIPTION="Validate and convert data types"
-
-#LICENSE="|| ( Artistic GPL-1+ )"
-SLOT="0"
-KEYWORDS="~amd64 ~x86"
-IUSE="test"
-
-RDEPEND=""
-DEPEND="${RDEPEND}
-	dev-perl/Module-Build
-	test? (
-		virtual/perl-Test-Simple
-		dev-perl/Test-Distribution
-		dev-perl/Test-Pod
-	)"
diff --git a/dev-perl/Lab-VISA/Lab-VISA-2.06.ebuild b/dev-perl/Lab-VISA/Lab-VISA-2.06.ebuild
deleted file mode 100644
index 9d3faf0b8..000000000
--- a/dev-perl/Lab-VISA/Lab-VISA-2.06.ebuild
+++ /dev/null
@@ -1,19 +0,0 @@
-# Copyright 1999-2014 Gentoo Foundation
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=5
-
-inherit perl-module
-
-DESCRIPTION="Perl interface to National Instrument's VISA library"
-HOMEPAGE="http://www.labvisa.de/"
-SRC_URI="mirror://cpan/authors/id/S/SC/SCHROEER/Lab/${P}.tar.gz"
-
-LICENSE="|| ( Artistic GPL-2 )"
-
-SLOT="0"
-KEYWORDS="~amd64 ~x86"
-IUSE=""
-
-DEPEND="dev-lang/perl sci-libs/ni-visa"
-RDEPEND="${DEPEND}"
diff --git a/dev-perl/Lab-VISA/Manifest b/dev-perl/Lab-VISA/Manifest
deleted file mode 100644
index 388f23988..000000000
--- a/dev-perl/Lab-VISA/Manifest
+++ /dev/null
@@ -1 +0,0 @@
-DIST Lab-VISA-2.06.tar.gz 121217 BLAKE2B 5cdb379ad84a01363f4cceaf276c1eaee4f2e4a57f70d00319e1367f6988bde659c3d20570b9def2662a87313f7c728fddc331b48a0fd402741d2094ee5511b3 SHA512 6539d5dbae505a876d5da5c2709b59bca42741a35365830e765185dfd30cfd1524f833762a34778b7cb36cd36f32499d3e07aa7cbe4d9fd1259c4213bc42dea1
diff --git a/dev-perl/Lab-VISA/metadata.xml b/dev-perl/Lab-VISA/metadata.xml
deleted file mode 100644
index 90bb64f30..000000000
--- a/dev-perl/Lab-VISA/metadata.xml
+++ /dev/null
@@ -1,7 +0,0 @@
-<?xml version="1.0" encoding="UTF-8"?>
-<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
-<pkgmetadata>
-	<maintainer type="person">
-		<email>mail@akhuettel.de</email>
-	</maintainer>
-</pkgmetadata>
diff --git a/dev-perl/Log-Cabin/Log-Cabin-0.06.ebuild b/dev-perl/Log-Cabin/Log-Cabin-0.06.ebuild
index b5e385b14..365972f8f 100644
--- a/dev-perl/Log-Cabin/Log-Cabin-0.06.ebuild
+++ b/dev-perl/Log-Cabin/Log-Cabin-0.06.ebuild
@@ -1,11 +1,10 @@
-# Copyright 1999-2014 Gentoo Foundation
+# Copyright 1999-2021 Gentoo Authors
 # Distributed under the terms of the GNU General Public License v2
 
-EAPI=5
+EAPI=7
 
-MODULE_AUTHOR="JORVIS"
-
-MODULE_SECTION="Log-Cabin"
+DIST_AUTHOR="JORVIS"
+DIST_SECTION="Log-Cabin"
 
 inherit perl-module
 
@@ -14,4 +13,3 @@ DESCRIPTION="Partial implementation of Log::Log4perl with reduced disk IO"
 LICENSE="|| ( Artistic GPL-1 GPL-2 GPL-3 )"
 SLOT="0"
 KEYWORDS="~amd64 ~x86"
-IUSE=""
diff --git a/dev-perl/Scalar-Util-Numeric/Scalar-Util-Numeric-0.40.ebuild b/dev-perl/Scalar-Util-Numeric/Scalar-Util-Numeric-0.40.ebuild
index 114425f3d..4833829e7 100644
--- a/dev-perl/Scalar-Util-Numeric/Scalar-Util-Numeric-0.40.ebuild
+++ b/dev-perl/Scalar-Util-Numeric/Scalar-Util-Numeric-0.40.ebuild
@@ -1,10 +1,10 @@
-# Copyright 1999-2016 Gentoo Foundation
+# Copyright 1999-2021 Gentoo Authors
 # Distributed under the terms of the GNU General Public License v2
 
-EAPI=5
+EAPI=7
 
-MODULE_AUTHOR="CHOCOLATE"
-MODULE_A_EXT="tar.gz"
+DIST_AUTHOR="CHOCOLATE"
+DIST_A_EXT="tar.gz"
 
 inherit perl-module
 
@@ -13,8 +13,6 @@ DESCRIPTION="Wrappers around perl's builtin looks_like_number function"
 LICENSE="|| ( Artistic GPL-1 GPL-2 GPL-3 )"
 SLOT="0"
 KEYWORDS="~amd64 ~x86"
-IUSE=""
 
 DEPEND="dev-lang/perl"
-
 RDEPEND="${DEPEND}"
diff --git a/dev-perl/Set-IntSpan-Fast/Set-IntSpan-Fast-1.15.ebuild b/dev-perl/Set-IntSpan-Fast/Set-IntSpan-Fast-1.15.ebuild
index be3fbe77b..c59226cd4 100644
--- a/dev-perl/Set-IntSpan-Fast/Set-IntSpan-Fast-1.15.ebuild
+++ b/dev-perl/Set-IntSpan-Fast/Set-IntSpan-Fast-1.15.ebuild
@@ -1,20 +1,21 @@
-# Copyright 1999-2017 Gentoo Foundation
+# Copyright 1999-2021 Gentoo Authors
 # Distributed under the terms of the GNU General Public License v2
 
-EAPI=5
+EAPI=7
+
+DIST_AUTHOR="ANDYA"
 
-MODULE_AUTHOR="ANDYA"
 inherit perl-module
 
 DESCRIPTION="Fast handling of sets containing integer spans"
 
-#LICENSE="|| ( Artistic GPL-1 GPL-2 GPL-3 )"
+LICENSE="|| ( Artistic GPL-1 GPL-2 GPL-3 )"
 SLOT="0"
-KEYWORDS="~amd64 ~x86"
-IUSE=""
+KEYWORDS="~amd64"
 
 RDEPEND=""
 DEPEND="${RDEPEND}
+	dev-perl/Data-Types
 	dev-perl/Module-Build"
 
 SRC_TEST="do"
diff --git a/dev-perl/Text-Graph/Text-Graph-0.83.ebuild b/dev-perl/Text-Graph/Text-Graph-0.83.ebuild
index 557bcbdbc..1fd5082ea 100644
--- a/dev-perl/Text-Graph/Text-Graph-0.83.ebuild
+++ b/dev-perl/Text-Graph/Text-Graph-0.83.ebuild
@@ -1,10 +1,10 @@
-# Copyright 1999-2016 Gentoo Foundation
+# Copyright 1999-2021 Gentoo Authors
 # Distributed under the terms of the GNU General Public License v2
 
-EAPI=5
+EAPI=7
 
-MODULE_AUTHOR="GWADEJ"
-MODULE_A_EXT="tar.gz"
+DIST_AUTHOR="GWADEJ"
+DIST_A_EXT="tar.gz"
 
 inherit perl-module
 
@@ -13,8 +13,9 @@ DESCRIPTION="Perl module for generating simple text-based graphs"
 LICENSE="|| ( Artistic GPL-1 GPL-2 GPL-3 )"
 SLOT="0"
 KEYWORDS="~amd64 ~x86"
-IUSE=""
-
-DEPEND="dev-lang/perl"
 
+DEPEND="
+	dev-lang/perl
+	dev-perl/Moo
+"
 RDEPEND="${DEPEND}"
diff --git a/dev-perl/Text-ParseWords/Manifest b/dev-perl/Text-ParseWords/Manifest
index 80e2b7737..f7800c632 100644
--- a/dev-perl/Text-ParseWords/Manifest
+++ b/dev-perl/Text-ParseWords/Manifest
@@ -1 +1 @@
-DIST Text-ParseWords-3.27.zip 9740 BLAKE2B 32a8fa88ba1c27116e99d8ceddf67eae7d99e9f3c0f83ea707e1e0c54f32ccb8757802cf7e2a83064f6fbaa1210ab8bfe95bd05c06b3191ec340fb2c07445cdc SHA512 e4a5b53760f8f161eac031589024d6120d5edb3b127db5637eab6732c3f995caee0168778c3cec276335ee6a27082c752624e4e9a2a0e08b155a77cf9d1dcf6e
+DIST Text-ParseWords-3.30.tar.gz 6943 BLAKE2B ed0646c98e44cc0094bdcb10d171d3f00a98cf3307db18eddb7c2b8afbe49f4b67400ede9fe46856f0d153620708a4e1a085a14008f533f36570b81d2d3f5419 SHA512 b148160cd3bd3eeda6f28e16d59a855fc846d314d116ebf88feebb574b452188ddf803b42894c6480324ba69515ef038121def9f6dd6302d31cb37af589344ec
diff --git a/dev-perl/Text-ParseWords/Text-ParseWords-3.27.ebuild b/dev-perl/Text-ParseWords/Text-ParseWords-3.27.ebuild
deleted file mode 100644
index df9259b4c..000000000
--- a/dev-perl/Text-ParseWords/Text-ParseWords-3.27.ebuild
+++ /dev/null
@@ -1,20 +0,0 @@
-# Copyright 1999-2014 Gentoo Foundation
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=5
-
-MODULE_AUTHOR="CHORNY"
-MODULE_A_EXT="zip"
-
-inherit perl-module
-
-DESCRIPTION="Parse strings containing shell-style quoting"
-
-LICENSE="|| ( Artistic GPL-1 GPL-2 GPL-3 )"
-SLOT="0"
-KEYWORDS="~amd64 ~x86"
-IUSE=""
-
-DEPEND="dev-lang/perl"
-
-RDEPEND="${DEPEND}"
diff --git a/dev-perl/Text-ParseWords/Text-ParseWords-3.30.ebuild b/dev-perl/Text-ParseWords/Text-ParseWords-3.30.ebuild
new file mode 100644
index 000000000..d29e96fa0
--- /dev/null
+++ b/dev-perl/Text-ParseWords/Text-ParseWords-3.30.ebuild
@@ -0,0 +1,17 @@
+# Copyright 1999-2020 Gentoo Authors
+# Distributed under the terms of the GNU General Public License v2
+
+EAPI=7
+
+DIST_AUTHOR="CHORNY"
+DIST_A_EXT="tar.gz"
+
+inherit perl-module
+
+DESCRIPTION="Parse strings containing shell-style quoting"
+
+LICENSE="|| ( Artistic GPL-1 GPL-2 GPL-3 )"
+SLOT="0"
+KEYWORDS="~amd64 ~x86"
+IUSE="test"
+RESTRICT="!test? ( test )"
diff --git a/dev-perl/Text-RecordParser/Text-RecordParser-1.6.5.ebuild b/dev-perl/Text-RecordParser/Text-RecordParser-1.6.5.ebuild
index fcb4e8ac7..9392658a2 100644
--- a/dev-perl/Text-RecordParser/Text-RecordParser-1.6.5.ebuild
+++ b/dev-perl/Text-RecordParser/Text-RecordParser-1.6.5.ebuild
@@ -1,9 +1,10 @@
-# Copyright 1999-2017 Gentoo Foundation
+# Copyright 1999-2021 Gentoo Authors
 # Distributed under the terms of the GNU General Public License v2
 
-EAPI=5
+EAPI=7
+
+DIST_AUTHOR="KCLARK"
 
-MODULE_AUTHOR="KCLARK"
 inherit perl-module
 
 DESCRIPTION="Perl module to read record-oriented files"
@@ -11,11 +12,13 @@ DESCRIPTION="Perl module to read record-oriented files"
 LICENSE="|| ( Artistic GPL-1 GPL-2 GPL-3 )"
 SLOT="0"
 KEYWORDS="~amd64 ~x86"
-IUSE=""
 
 RDEPEND="
 	dev-lang/perl
-	dev-perl/Module-Install"
+	dev-perl/Module-Install
+	dev-perl/Readonly
+	dev-perl/Test-Exception
+"
 DEPEND="${RDEPEND}"
 
 SRC_TEST="do"
diff --git a/dev-perl/Time-Progress/Manifest b/dev-perl/Time-Progress/Manifest
index 83b14625a..d17f57c45 100644
--- a/dev-perl/Time-Progress/Manifest
+++ b/dev-perl/Time-Progress/Manifest
@@ -1 +1 @@
-DIST Time-Progress-1.7.tar.gz 4366 BLAKE2B 5aacf0a1f23ef66fa3d97d0f8f08f989a6541ab4b6b312f3aff2b1f25914e8502b37711191cd5ae19058f11506e219b02600a4fd62f62f43dd363514bf224680 SHA512 1cc50a65336e9e60d58ea0ef7532b30a4893fbe133dd6c9aac26d26696b056a98add2feb817f7b129c4f82734d0d1fbfa4c3ab6c6ab98299114422eb8d678769
+DIST Time-Progress-2.12.tar.gz 7455 BLAKE2B 19036b500ead2cfec3a96ac7e20a9c6aa8f41edf7ba400f69a43cc358a1e7133b2f8fd6959adba0b124a3ee9b5ddba5a2cfbd73844ca23945664fb0d9851b2af SHA512 8abe96a51883ed3ff4c9d6cc06b9d5fe985af582b66dbe8792e7eefd351cab3d2e26b577ad7daaf504f6ccfebb05c35c706a98904cd7b6fad8156630606da236
diff --git a/dev-perl/Time-Progress/Time-Progress-1.7.ebuild b/dev-perl/Time-Progress/Time-Progress-1.7.ebuild
deleted file mode 100644
index 4b7091308..000000000
--- a/dev-perl/Time-Progress/Time-Progress-1.7.ebuild
+++ /dev/null
@@ -1,15 +0,0 @@
-# Copyright 1999-2014 Gentoo Foundation
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=5
-
-MODULE_AUTHOR="CADE"
-
-inherit perl-module
-
-DESCRIPTION="Elapsed and estimated finish time reporting"
-
-LICENSE="|| ( Artistic GPL-1 GPL-2 GPL-3 )"
-SLOT="0"
-KEYWORDS="~amd64 ~x86"
-IUSE=""
diff --git a/dev-perl/Time-Progress/Time-Progress-2.12.ebuild b/dev-perl/Time-Progress/Time-Progress-2.12.ebuild
new file mode 100644
index 000000000..7a1985799
--- /dev/null
+++ b/dev-perl/Time-Progress/Time-Progress-2.12.ebuild
@@ -0,0 +1,16 @@
+# Copyright 1999-2020 Gentoo Authors
+# Distributed under the terms of the GNU General Public License v2
+
+EAPI=7
+
+DIST_AUTHOR="CADE"
+DIST_VERSION=2.12
+inherit perl-module
+
+DESCRIPTION="Elapsed and estimated finish time reporting"
+
+LICENSE="|| ( Artistic GPL-1 GPL-2 GPL-3 )"
+SLOT="0"
+KEYWORDS="~amd64 ~x86"
+IUSE="test"
+RESTRICT="!test? ( test )"
diff --git a/dev-perl/go-db-perl/go-db-perl-0.04-r1.ebuild b/dev-perl/go-db-perl/go-db-perl-0.04-r1.ebuild
new file mode 100644
index 000000000..06d4b8c8f
--- /dev/null
+++ b/dev-perl/go-db-perl/go-db-perl-0.04-r1.ebuild
@@ -0,0 +1,23 @@
+# Copyright 1999-2020 Gentoo Authors
+# Distributed under the terms of the GNU General Public License v2
+
+EAPI=7
+
+DIST_VERSION=0.04
+DIST_AUTHOR=SJCARBON
+
+inherit perl-module
+
+DESCRIPTION="Gene Ontology Database perl API"
+
+SLOT="0"
+KEYWORDS="~amd64"
+
+RDEPEND="
+	>=dev-perl/DBIx-DBStag-0.06
+	dev-perl/FreezeThaw
+	dev-perl/go-perl
+	dev-perl/XML-LibXSLT
+"
+
+SRC_TEST=do
diff --git a/dev-perl/go-db-perl/go-db-perl-0.04.ebuild b/dev-perl/go-db-perl/go-db-perl-0.04.ebuild
deleted file mode 100644
index 0b896cc0d..000000000
--- a/dev-perl/go-db-perl/go-db-perl-0.04.ebuild
+++ /dev/null
@@ -1,23 +0,0 @@
-# Copyright 1999-2014 Gentoo Foundation
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=5
-
-MODULE_AUTHOR=SJCARBON
-
-inherit perl-module
-
-DESCRIPTION="Gene Ontology Database perl API"
-
-SLOT="0"
-KEYWORDS="~amd64 ~x86"
-IUSE=""
-
-DEPEND=""
-RDEPEND="${DEPEND}
-	dev-perl/FreezeThaw
-	dev-perl/XML-LibXSLT
-	>=dev-perl/DBIx-DBStag-0.06
-	dev-perl/go-perl"
-
-SRC_TEST=do
diff --git a/dev-perl/go-perl/Manifest b/dev-perl/go-perl/Manifest
deleted file mode 100644
index b8851977c..000000000
--- a/dev-perl/go-perl/Manifest
+++ /dev/null
@@ -1 +0,0 @@
-DIST go-perl-0.13.tar.gz 806739 BLAKE2B 41837c31fa2e1b5c5750c8ddd21038755c1bef942a753ae772d15e51649ce406423baee407c8e77660f60a751648c8a9801e353f72a048adc76527362efa8f2a SHA512 c459748558191975f380bcfce84badbbe93dfc93ab064da764fb5703a76165dcacd00ceb0a55e7a830a055add2e4182554f158b1162736a79e3c7823607c7ac0
diff --git a/dev-perl/go-perl/go-perl-0.13.ebuild b/dev-perl/go-perl/go-perl-0.13.ebuild
deleted file mode 100644
index 480e9563b..000000000
--- a/dev-perl/go-perl/go-perl-0.13.ebuild
+++ /dev/null
@@ -1,20 +0,0 @@
-# Copyright 1999-2014 Gentoo Foundation
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=5
-
-MODULE_AUTHOR="CMUNGALL"
-
-inherit perl-module
-
-DESCRIPTION="GO::Parser parses all GO files formats and types"
-
-LICENSE="|| ( Artistic GPL-1 GPL-2 GPL-3 )"
-SLOT="0"
-KEYWORDS="~amd64 ~x86"
-IUSE=""
-
-DEPEND="
-	>=dev-perl/Data-Stag-0.11
-	dev-lang/perl"
-RDEPEND="${DEPEND}"
diff --git a/dev-perl/go-perl/metadata.xml b/dev-perl/go-perl/metadata.xml
deleted file mode 100644
index 138cb7705..000000000
--- a/dev-perl/go-perl/metadata.xml
+++ /dev/null
@@ -1,12 +0,0 @@
-<?xml version="1.0" encoding="UTF-8"?>
-<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
-<pkgmetadata>
-	<maintainer type="person">
-		<email>mmokrejs@fold.natur.cuni.cz</email>
-		<name>Martin Mokrejs</name>
-	</maintainer>
-	<maintainer type="project">
-		<email>sci-biology@gentoo.org</email>
-		<name>Gentoo Biology Project</name>
-	</maintainer>
-</pkgmetadata>
diff --git a/dev-perl/opal-client/Manifest b/dev-perl/opal-client/Manifest
deleted file mode 100644
index 14d8fa0b5..000000000
--- a/dev-perl/opal-client/Manifest
+++ /dev/null
@@ -1 +0,0 @@
-DIST opal-perl-1.9.2.tar.gz 90429 BLAKE2B b432799fa4ab167f48579b606d16d530f441dfe4e93018af679a5f5130aa07b19dbccc4a9139ad067a491cbc7f78ab69846c8c4878b20502c21c9890ad6ae199 SHA512 e2d9a9638ddf1b86b826c83229246eaca7a96264b66e3b41867cfa83bd7d9dd6ec0441bc7b5390ab96ad8519ffc770a24575f8a8c41b8a15409663e3e66afdc0
diff --git a/dev-perl/opal-client/metadata.xml b/dev-perl/opal-client/metadata.xml
deleted file mode 100644
index f475ca517..000000000
--- a/dev-perl/opal-client/metadata.xml
+++ /dev/null
@@ -1,11 +0,0 @@
-<?xml version="1.0" encoding="UTF-8"?>
-<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
-<pkgmetadata>
-	<maintainer type="project">
-		<email>sci@gentoo.org</email>
-		<name>Gentoo Science Project</name>
-	</maintainer>
-	<upstream>
-		<remote-id type="sourceforge">opaltoolkit</remote-id>
-	</upstream>
-</pkgmetadata>
diff --git a/dev-perl/opal-client/opal-client-1.9.2.ebuild b/dev-perl/opal-client/opal-client-1.9.2.ebuild
deleted file mode 100644
index 3759619ac..000000000
--- a/dev-perl/opal-client/opal-client-1.9.2.ebuild
+++ /dev/null
@@ -1,36 +0,0 @@
-# Copyright 1999-2014 Gentoo Foundation
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=5
-
-PYTHON_COMPAT=( python2_7 )
-
-inherit perl-module python-single-r1
-
-MY_PN="${PN/client/perl}"
-MY_P="${MY_PN}-${PV}"
-
-DESCRIPTION="Perl Opal Web Service Client"
-HOMEPAGE="http://nbcr.net/software/opal/"
-SRC_URI="mirror://sourceforge/opaltoolkit/${MY_P}.tar.gz"
-
-LICENSE="opal"
-SLOT="0"
-KEYWORDS="~amd64 ~x86"
-IUSE=""
-
-RDEPEND="
-	dev-perl/SOAP-Lite
-	dev-lang/perl
-	dev-python/opal-client[${PYTHON_USEDEP}]"
-DEPEND="${RDEPEND}"
-
-S="${WORKDIR}"/${MY_P}
-
-src_install() {
-	insinto ${SITE_LIB}
-	doins *.pm
-	dodoc README etc/* pdb2pqrclient.pl
-	docinto html
-	dodoc docs/*
-}
diff --git a/dev-python/Forthon/Forthon-0.8.13.ebuild b/dev-python/Forthon/Forthon-0.8.13.ebuild
deleted file mode 100644
index cfa00558c..000000000
--- a/dev-python/Forthon/Forthon-0.8.13.ebuild
+++ /dev/null
@@ -1,30 +0,0 @@
-# Copyright 1999-2014 Gentoo Foundation
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=5
-PYTHON_COMPAT=( python{2_7,3_3} )
-
-inherit eutils distutils-r1
-
-DESCRIPTION="Python interface generator for Fortran based codes"
-HOMEPAGE="http://hifweb.lbl.gov/Forthon"
-SRC_URI="http://hifweb.lbl.gov/${PN}/${P}.tgz"
-
-LICENSE="BSD"
-SLOT="0"
-KEYWORDS="~amd64 ~x86 ~amd64-linux ~x86-linux"
-IUSE="examples"
-
-python_prepare_all() {
-	sed -i -e "/data_files/ s/'License.txt',//" setup.py || die
-	distutils-r1_python_prepare_all
-}
-
-python_install_all() {
-	dohtml docs/index.html
-	if use examples ; then
-		docinto /usr/share/doc/${PF}
-		dodoc -r {example,simpleexample}
-	fi
-	distutils-r1_python_install_all
-}
diff --git a/dev-python/Forthon/Manifest b/dev-python/Forthon/Manifest
deleted file mode 100644
index 6821771b9..000000000
--- a/dev-python/Forthon/Manifest
+++ /dev/null
@@ -1 +0,0 @@
-DIST Forthon-0.8.13.tgz 89649 BLAKE2B a1a25eb08609e29a1fdbc8a836129c7a91c567dc05e49100eeb89d84b0427234e2ddd44421146cdc19dba65f2c4ffb2204aede5ef9bd801eade691e22181b8e7 SHA512 06117d0a6743a65d84390f828170c2d681110f6d9912da78402a3b7d611f945f1ece4a475a2cf90aaec605bd604bcf82bf6c1c4635cbea76979c037de206a356
diff --git a/dev-python/Forthon/metadata.xml b/dev-python/Forthon/metadata.xml
deleted file mode 100644
index ac9ace72d..000000000
--- a/dev-python/Forthon/metadata.xml
+++ /dev/null
@@ -1,19 +0,0 @@
-<?xml version="1.0" encoding="UTF-8"?>
-<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
-<pkgmetadata>
-	<maintainer type="person">
-		<email>xarthisius@gentoo.org</email>
-		<name>Kacper Kowalik</name>
-	</maintainer>
-	<longdescription>
-Forthon generates links between Fortran95 and Python. Python is a high
-level, object oriented, interactive and scripting language that allows
-a flexible and versatile interface to computational tools. The Forthon
-package generates the necessary wrapping code which allows access to
-the Fortran database and to the Fortran subroutines and
-functions. This provides a development package where the
-computationally intensive parts of a code can be written in efficient
-Fortran, and the high level controlling code can be written in the
-much more versatile Python language.
-</longdescription>
-</pkgmetadata>
diff --git a/dev-python/GOGrapher/GOGrapher-9999.ebuild b/dev-python/GOGrapher/GOGrapher-9999.ebuild
deleted file mode 100644
index ac8577b5e..000000000
--- a/dev-python/GOGrapher/GOGrapher-9999.ebuild
+++ /dev/null
@@ -1,22 +0,0 @@
-# Copyright 1999-2014 Gentoo Foundation
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=5
-
-PYTHON_COMPAT=( python2_7 )
-
-inherit distutils-r1 subversion
-
-DESCRIPTION="A Gene Ontology Programming Library"
-HOMEPAGE="https://projects.dbbe.musc.edu/trac/GOGrapher"
-ESVN_REPO_URI="https://projects.dbbe.musc.edu/public/GOGrapher/trunk"
-
-LICENSE="GPL-2"
-SLOT="0"
-KEYWORDS=""
-IUSE=""
-
-DEPEND="
-	dev-python/networkx[${PYTHON_USEDEP}]
-	dev-python/pygraphviz[${PYTHON_USEDEP}]"
-RDEPEND="${DEPEND}"
diff --git a/dev-python/GOGrapher/metadata.xml b/dev-python/GOGrapher/metadata.xml
deleted file mode 100644
index 138cb7705..000000000
--- a/dev-python/GOGrapher/metadata.xml
+++ /dev/null
@@ -1,12 +0,0 @@
-<?xml version="1.0" encoding="UTF-8"?>
-<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
-<pkgmetadata>
-	<maintainer type="person">
-		<email>mmokrejs@fold.natur.cuni.cz</email>
-		<name>Martin Mokrejs</name>
-	</maintainer>
-	<maintainer type="project">
-		<email>sci-biology@gentoo.org</email>
-		<name>Gentoo Biology Project</name>
-	</maintainer>
-</pkgmetadata>
diff --git a/dev-python/MagnetoResistance-tool/MagnetoResistance-tool-0.0.2.ebuild b/dev-python/MagnetoResistance-tool/MagnetoResistance-tool-0.0.2.ebuild
new file mode 100644
index 000000000..23e03adcf
--- /dev/null
+++ b/dev-python/MagnetoResistance-tool/MagnetoResistance-tool-0.0.2.ebuild
@@ -0,0 +1,22 @@
+# Copyright 1999-2022 Gentoo Authors
+# Distributed under the terms of the GNU General Public License v2
+
+EAPI=8
+
+PYTHON_COMPAT=( python3_{10..12} )
+DISTUTILS_USE_PEP517=setuptools
+PYPI_NO_NORMALIZE=1
+inherit distutils-r1 pypi
+
+DESCRIPTION="Create calibration matrix to correct for magneto-resistance in resistive sensors"
+HOMEPAGE="https://gitlab.science.ru.nl/hfml/MRcalib"
+
+LICENSE="GPL-3+"
+SLOT="0"
+KEYWORDS="~amd64"
+
+RDEPEND="
+	dev-python/numpy[${PYTHON_USEDEP}]
+	dev-python/pandas[${PYTHON_USEDEP}]
+	dev-python/matplotlib[${PYTHON_USEDEP}]
+"
diff --git a/dev-python/MagnetoResistance-tool/Manifest b/dev-python/MagnetoResistance-tool/Manifest
new file mode 100644
index 000000000..b8d0afd21
--- /dev/null
+++ b/dev-python/MagnetoResistance-tool/Manifest
@@ -0,0 +1 @@
+DIST MagnetoResistance-tool-0.0.2.tar.gz 21657 BLAKE2B 5d1a2f497f742df04aac5db6afe83373e6e3e3cea3891585c22d1585186665f0d597b3dccd5f2adfef4e58bc41f680b974974cb12c56e3ef29f69122407cfff5 SHA512 4866197feb96912edc19691ba7ea54303ed168d8ab72c534ad910a3a77ce6e8ccf0f19744eca5044936c29bde131d4c352abbd57547f1c30b3ae59d4aac36986
diff --git a/dev-python/MagnetoResistance-tool/metadata.xml b/dev-python/MagnetoResistance-tool/metadata.xml
new file mode 100644
index 000000000..aed122741
--- /dev/null
+++ b/dev-python/MagnetoResistance-tool/metadata.xml
@@ -0,0 +1,11 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
+<pkgmetadata>
+	<maintainer type="person">
+		<email>andrewammerlaan@gentoo.org</email>
+		<name>Andrew Ammerlaan</name>
+	</maintainer>
+	<upstream>
+		<remote-id type="pypi">MagnetoResistance-tool</remote-id>
+	</upstream>
+</pkgmetadata>
diff --git a/dev-python/PeakUtils/Manifest b/dev-python/PeakUtils/Manifest
deleted file mode 100644
index c0735ca4e..000000000
--- a/dev-python/PeakUtils/Manifest
+++ /dev/null
@@ -1 +0,0 @@
-DIST PeakUtils-1.0.1.tar.gz 28966 BLAKE2B 85c2a7181a84ed5162f891746a42643edddebe22f41e03aebc3fbc9fb251b8008248030e4615494ec0394285cdfd19503d6cb80bd06649af9061d52394214b33 SHA512 5af07b2fa926f3a083ac9c5f5fc6ecbc7d51c556d51080d020c272c59bbb99fe76ae65839626347785cc9da9fe33101c3e0261b84776d3cca0cf3aa0f784dfaf
diff --git a/dev-python/PeakUtils/PeakUtils-1.0.1.ebuild b/dev-python/PeakUtils/PeakUtils-1.0.1.ebuild
deleted file mode 100644
index d92ad67eb..000000000
--- a/dev-python/PeakUtils/PeakUtils-1.0.1.ebuild
+++ /dev/null
@@ -1,23 +0,0 @@
-# Copyright 1999-2015 Gentoo Foundation
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=5
-PYTHON_COMPAT=( python3_{4,5} )
-
-inherit distutils-r1
-
-MY_PN="pyFFTW"
-
-DESCRIPTION="Peak detection utilities for 1D data"
-HOMEPAGE="https://bitbucket.org/lucashnegri/peakutils"
-SRC_URI="mirror://pypi/${PN:0:1}/${PN}/${P}.tar.gz"
-
-LICENSE="MIT"
-SLOT="0"
-KEYWORDS="~amd64"
-
-RDEPEND="
-	>=dev-python/numpy-1.8.0[${PYTHON_USEDEP}]
-	sci-libs/scipy[${PYTHON_USEDEP}]
-	"
-DEPEND="${RDEPEND}"
diff --git a/dev-python/PeakUtils/metadata.xml b/dev-python/PeakUtils/metadata.xml
deleted file mode 100644
index ba9535089..000000000
--- a/dev-python/PeakUtils/metadata.xml
+++ /dev/null
@@ -1,19 +0,0 @@
-<?xml version="1.0" encoding="UTF-8"?>
-<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
-<pkgmetadata>
-	<maintainer type="project">
-		<email>sci@gentoo.org</email>
-		<name>Gentoo Science Project</name>
-	</maintainer>
-	<longdescription>
-As the name implies, this package provides utilities related to the
-detection of peaks on 1D data. Includes functions to perform
-baseline estimation, to find the indexes of the peaks in the data
-and performing Gaussian fitting or centroid computation to further
-increase the resolution of the peak detection.
-</longdescription>
-	<upstream>
-		<remote-id type="bitbucket">lucashnegri/peakutils</remote-id>
-		<remote-id type="pypi">PeakUtils</remote-id>
-	</upstream>
-</pkgmetadata>
diff --git a/dev-python/PyVISA-py/Manifest b/dev-python/PyVISA-py/Manifest
deleted file mode 100644
index 19c1c9963..000000000
--- a/dev-python/PyVISA-py/Manifest
+++ /dev/null
@@ -1 +0,0 @@
-DIST PyVISA-py-0.2.tar.gz 50244 BLAKE2B ed3c0e249f441c0c44ac07d9b76a5711895cd3bd4fae6b56784d1cc078721004d5e6f47970c99f1c8f8849d60d5d9db123789d93e40660494d5dce01dc61632e SHA512 6ef4d98d37885fb63f2518a0d9a74741fec0c5b833db381cc7d33ce1fbe766d4c65bbc5ba337a2a609c57f8526a80afa15d2e66770a7262336fb0c02f36acb95
diff --git a/dev-python/PyVISA-py/PyVISA-py-0.2.ebuild b/dev-python/PyVISA-py/PyVISA-py-0.2.ebuild
deleted file mode 100644
index b0d4f09dc..000000000
--- a/dev-python/PyVISA-py/PyVISA-py-0.2.ebuild
+++ /dev/null
@@ -1,19 +0,0 @@
-# Copyright 1999-2016 Gentoo Foundation
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=6
-PYTHON_COMPAT=( python2_7 python{3_4,3_5} )
-
-inherit distutils-r1
-
-DESCRIPTION="Python VISA bindings for GPIB, RS232, and USB instruments"
-HOMEPAGE="https://github.com/hgrecco/pyvisa-py"
-SRC_URI="mirror://pypi/${PN:0:1}/${PN}/${P}.tar.gz"
-
-LICENSE="MIT"
-SLOT="0"
-KEYWORDS="~amd64"
-
-RDEPEND="
-	>=dev-python/PyVISA-1.8[${PYTHON_USEDEP}]"
-DEPEND="${RDEPEND}"
diff --git a/dev-python/PyVISA-py/PyVISA-py-9999.ebuild b/dev-python/PyVISA-py/PyVISA-py-9999.ebuild
deleted file mode 100644
index 660858de3..000000000
--- a/dev-python/PyVISA-py/PyVISA-py-9999.ebuild
+++ /dev/null
@@ -1,18 +0,0 @@
-# Copyright 1999-2016 Gentoo Foundation
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=6
-PYTHON_COMPAT=( python2_7 python{3_4,3_5} )
-
-inherit distutils-r1 git-r3
-
-DESCRIPTION="Python VISA bindings for GPIB, RS232, and USB instruments"
-HOMEPAGE="https://github.com/hgrecco/pyvisa-py"
-EGIT_REPO_URI="https://github.com/hgrecco/${PN}.git git://github.com/${hgrecco}/${PN}.git"
-
-LICENSE="MIT"
-SLOT="0"
-
-RDEPEND="
-	>=dev-python/PyVISA-1.8[${PYTHON_USEDEP}]"
-DEPEND="${RDEPEND}"
diff --git a/dev-python/PyVISA-py/metadata.xml b/dev-python/PyVISA-py/metadata.xml
deleted file mode 100644
index b55b92cd3..000000000
--- a/dev-python/PyVISA-py/metadata.xml
+++ /dev/null
@@ -1,20 +0,0 @@
-<?xml version="1.0" encoding="UTF-8"?>
-<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
-<pkgmetadata>
-	<maintainer type="person">
-		<email>marbre@linux.sungazer.de</email>
-		<name>Marius Brehler</name>
-	</maintainer>
-	<maintainer type="project">
-		<email>sci@gentoo.org</email>
-		<name>Gentoo Science Project</name>
-	</maintainer>
-	<longdescription>
-A PyVISA backend that implements a large part of the "Virtual
-Instrument Software Architecture" (VISA) in pure Python.
-</longdescription>
-	<upstream>
-		<remote-id type="github">hgrecco/pyvisa-py</remote-id>
-		<remote-id type="pypi">PyVISA-py</remote-id>
-	</upstream>
-</pkgmetadata>
diff --git a/dev-python/PyVISA/Manifest b/dev-python/PyVISA/Manifest
deleted file mode 100644
index 0325a1839..000000000
--- a/dev-python/PyVISA/Manifest
+++ /dev/null
@@ -1 +0,0 @@
-DIST PyVISA-1.8.tar.gz 429701 BLAKE2B 5e35dba270df0e39fe132cad4adcbaf136146add9c9a06419a724daa5fc7da1e31010aba1d0e1025a4559dff38d33a8d645705051987db3e64b973b8f950c55e SHA512 e3346c0966a97ef09158820df5df74480b0f253c1bde6a3d3621e8011f98f3059d2e9f04c6a361c3332abef433e8e5bb85fc161cbfe737be354d1786336d9254
diff --git a/dev-python/PyVISA/PyVISA-1.8.ebuild b/dev-python/PyVISA/PyVISA-1.8.ebuild
deleted file mode 100644
index e16717b37..000000000
--- a/dev-python/PyVISA/PyVISA-1.8.ebuild
+++ /dev/null
@@ -1,25 +0,0 @@
-# Copyright 1999-2017 Gentoo Foundation
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=6
-PYTHON_COMPAT=( python2_7 python{3_4,3_5} )
-
-inherit distutils-r1
-
-DESCRIPTION="Python VISA bindings for GPIB, RS232, and USB instruments"
-HOMEPAGE="https://github.com/hgrecco/pyvisa"
-SRC_URI="mirror://pypi/${PN:0:1}/${PN}/${P}.tar.gz"
-
-LICENSE="MIT"
-SLOT="0"
-KEYWORDS="~amd64"
-IUSE="test"
-
-RDEPEND="
-	$(python_gen_cond_dep 'dev-python/enum34[${PYTHON_USEDEP}]' python2_7)
-	"
-DEPEND="${RDEPEND}"
-
-python_test() {
-	esetup.py test
-}
diff --git a/dev-python/PyVISA/PyVISA-9999.ebuild b/dev-python/PyVISA/PyVISA-9999.ebuild
deleted file mode 100644
index a51331354..000000000
--- a/dev-python/PyVISA/PyVISA-9999.ebuild
+++ /dev/null
@@ -1,24 +0,0 @@
-# Copyright 1999-2016 Gentoo Foundation
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=6
-PYTHON_COMPAT=( python2_7 python{3_4,3_5} )
-
-inherit distutils-r1 git-r3
-
-DESCRIPTION="Python VISA bindings for GPIB, RS232, and USB instruments"
-HOMEPAGE="https://github.com/hgrecco/pyvisa-py"
-EGIT_REPO_URI="https://github.com/hgrecco/${PN}.git git://github.com/${PN}/${PN}.git"
-
-LICENSE="MIT"
-SLOT="0"
-IUSE="test"
-
-RDEPEND="
-	$(python_gen_cond_dep 'dev-python/enum34[${PYTHON_USEDEP}]' python2_7)
-	"
-DEPEND="${RDEPEND}"
-
-python_test() {
-	esetup.py test
-}
\ No newline at end of file
diff --git a/dev-python/PyVISA/metadata.xml b/dev-python/PyVISA/metadata.xml
deleted file mode 100644
index 1a5f4a861..000000000
--- a/dev-python/PyVISA/metadata.xml
+++ /dev/null
@@ -1,21 +0,0 @@
-<?xml version="1.0" encoding="UTF-8"?>
-<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
-<pkgmetadata>
-	<maintainer type="person">
-		<email>marbre@linux.sungazer.de</email>
-		<name>Marius Brehler</name>
-	</maintainer>
-	<maintainer type="project">
-		<email>sci@gentoo.org</email>
-		<name>Gentoo Science Project</name>
-	</maintainer>
-	<longdescription>
-A Python package for support of the "Virtual Instrument Software
-Architecture" (VISA), in order to control measurement devices and
-test equipment via GPIB, RS232, Ethernet or USB.
-</longdescription>
-	<upstream>
-		<remote-id type="github">hgrecco/pyvisa-py</remote-id>
-		<remote-id type="pypi">PyVISA</remote-id>
-	</upstream>
-</pkgmetadata>
diff --git a/dev-python/RecSQL/RecSQL-9999.ebuild b/dev-python/RecSQL/RecSQL-9999.ebuild
deleted file mode 100644
index a31fdeee1..000000000
--- a/dev-python/RecSQL/RecSQL-9999.ebuild
+++ /dev/null
@@ -1,32 +0,0 @@
-# Copyright 1999-2014 Gentoo Foundation
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=5
-
-PYTHON_COMPAT=( python2_7 )
-PYTHON_REQ_USE="sqlite"
-
-if [[ $PV = *9999* ]]; then
-	scm_eclass=git-r3
-	EGIT_REPO_URI="
-		git://github.com/orbeckst/${PN}.git
-		https://github.com/orbeckst/${PN}.git"
-	SRC_URI=""
-	KEYWORDS=""
-else
-	scm_eclass=vcs-snapshot
-	SRC_URI="https://github.com/orbeckst/${PN}/archive/release-${PV}.tar.gz -> ${P}.tar.gz"
-	KEYWORDS="~amd64 ~x86"
-fi
-
-inherit eutils distutils-r1 ${scm_eclass}
-
-DESCRIPTION="Simple SQL analysis of python records"
-HOMEPAGE="http://orbeckst.github.com/RecSQL/"
-
-LICENSE="GPL-3"
-SLOT="0"
-IUSE=""
-
-DEPEND="dev-python/numpy[${PYTHON_USEDEP}]"
-RDEPEND="${DEPEND}"
diff --git a/dev-python/RecSQL/metadata.xml b/dev-python/RecSQL/metadata.xml
deleted file mode 100644
index a3daeebd2..000000000
--- a/dev-python/RecSQL/metadata.xml
+++ /dev/null
@@ -1,12 +0,0 @@
-<?xml version="1.0" encoding="UTF-8"?>
-<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
-<pkgmetadata>
-	<maintainer type="person">
-		<email>alexxy@gentoo.org</email>
-		<name>Alexey Shvetsov</name>
-	</maintainer>
-	<maintainer type="project">
-		<email>sci@gentoo.org</email>
-		<name>Gentoo Science Project</name>
-	</maintainer>
-</pkgmetadata>
diff --git a/dev-python/absl-py/Manifest b/dev-python/absl-py/Manifest
deleted file mode 100644
index 1cb603ab0..000000000
--- a/dev-python/absl-py/Manifest
+++ /dev/null
@@ -1 +0,0 @@
-DIST absl-py-0.1.13.tar.gz 180047 BLAKE2B d10ff30109cf1a1b21d276b30e1066abc8c002d1c944a13e006a6fa097fc3fc98d4ca4441d194cee61137496aaa9a2314b71408ba507804376fb8750af0130e8 SHA512 ce93346a5f74bd4251789670dffdf983bf557f3e6a90ded9150998c53f8ed3a43fb1aa7b15556695e3d9dfa7a2237bb5462edadc23a8ceeb5f5ce2b87b0623ed
diff --git a/dev-python/absl-py/absl-py-0.1.13.ebuild b/dev-python/absl-py/absl-py-0.1.13.ebuild
deleted file mode 100644
index fd14b09f0..000000000
--- a/dev-python/absl-py/absl-py-0.1.13.ebuild
+++ /dev/null
@@ -1,22 +0,0 @@
-# Copyright 1999-2018 Gentoo Foundation
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=6
-
-PYTHON_COMPAT=( python2_7 python3_{4,5,6} )
-inherit distutils-r1
-
-DESCRIPTION="Abseil Python Common Libraries"
-HOMEPAGE="https://github.com/abseil/abseil-py"
-SRC_URI="https://github.com/abseil/abseil-py/archive/pypi-v${PV}.tar.gz -> ${P}.tar.gz"
-
-LICENSE="Apache-2.0"
-SLOT="0"
-KEYWORDS="~amd64 ~x86"
-IUSE=""
-
-DEPEND="dev-python/six"
-#	test? ( dev-util/bazel )"
-RDEPEND="${DEPEND}"
-
-S="${WORKDIR}/abseil-py-pypi-v${PV}"
diff --git a/dev-python/absl-py/metadata.xml b/dev-python/absl-py/metadata.xml
deleted file mode 100644
index 7f5929aca..000000000
--- a/dev-python/absl-py/metadata.xml
+++ /dev/null
@@ -1,12 +0,0 @@
-<?xml version="1.0" encoding="UTF-8"?>
-<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
-<pkgmetadata>
-	<maintainer type="person">
-		<email>mmokrejs@fold.natur.cuni.cz</email>
-		<name>Martin Mokrejs</name>
-	</maintainer>
-	<maintainer type="project">
-		<email>sci@gentoo.org</email>
-		<name>Gentoo Science Project</name>
-	</maintainer>
-</pkgmetadata>
diff --git a/dev-python/affine/Manifest b/dev-python/affine/Manifest
new file mode 100644
index 000000000..519703c98
--- /dev/null
+++ b/dev-python/affine/Manifest
@@ -0,0 +1 @@
+DIST affine-2.3.0.tar.gz 14860 BLAKE2B 3f1f2bf69e26bc7c73ad7d4fc2fa0a51b3cb5ccea3e88982dd682f377df0c6fde00e037893aa466d89955e7800fa99580b02108ce7acb68fb1b38cb67e4753e6 SHA512 25e3671542a4bcb45c04a3e4a1c312f7e427091470b30b115dd8d0c7a1f3ac008e1b1f9222ca60b08b4717cab90fc224f2e70fc0184ca371ccf918f8c04a23ce
diff --git a/dev-python/affine/affine-2.3.0.ebuild b/dev-python/affine/affine-2.3.0.ebuild
new file mode 100644
index 000000000..7cc363d92
--- /dev/null
+++ b/dev-python/affine/affine-2.3.0.ebuild
@@ -0,0 +1,18 @@
+# Copyright 1999-2022 Gentoo Authors
+# Distributed under the terms of the GNU General Public License v2
+
+EAPI=8
+
+PYTHON_COMPAT=( python3_10 )
+DISTUTILS_USE_PEP517="setuptools"
+inherit distutils-r1
+
+DESCRIPTION="Library for handling affine transformations of the plane"
+HOMEPAGE="https://github.com/rasterio/affine"
+SRC_URI="https://github.com/rasterio/${PN}/archive/refs/tags/${PV}.tar.gz -> ${P}.tar.gz"
+
+LICENSE="BSD"
+SLOT="0"
+KEYWORDS="~amd64 ~x86"
+
+distutils_enable_tests pytest
diff --git a/dev-python/affine/metadata.xml b/dev-python/affine/metadata.xml
new file mode 100644
index 000000000..298f9156d
--- /dev/null
+++ b/dev-python/affine/metadata.xml
@@ -0,0 +1,17 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<!DOCTYPE pkgmetadata SYSTEM "https://www.gentoo.org/dtd/metadata.dtd">
+<pkgmetadata>
+  <maintainer type="project">
+    <email>sci@gentoo.org</email>
+    <name>Gentoo Science Project</name>
+  </maintainer>
+  <longdescription lang="en">
+  Affine is a python library for handling affine transformations of the plane.
+  Georeferenced raster datasets use affine transformations to map from image 
+  coordinates to world coordinates. 
+</longdescription>
+  <upstream>
+    <remote-id type="github">rasterio/affine</remote-id>
+    <remote-id type="pypi">affine</remote-id>
+  </upstream>
+</pkgmetadata>
diff --git a/dev-python/aiohttp-retry/Manifest b/dev-python/aiohttp-retry/Manifest
new file mode 100644
index 000000000..f050b37c0
--- /dev/null
+++ b/dev-python/aiohttp-retry/Manifest
@@ -0,0 +1 @@
+DIST aiohttp-retry-2.8.3.gh.tar.gz 11952 BLAKE2B f2ea6f7b2f13001bd8d49b4529eacb3766cab080ff3a9457e40287bc797afebae10393a628cf78756074ca60a62df78c59c6120f1368316084155f1d7fd7cdfb SHA512 71869c3997e9b5089c298fa6f992b0ed08ca3da0f93c4f37566d8c6b9809bb1873a629cc47f1ffaeccac112d96036851794ee564b11c0f4f1eec00f49413358d
diff --git a/dev-python/aiohttp-retry/aiohttp-retry-2.8.3.ebuild b/dev-python/aiohttp-retry/aiohttp-retry-2.8.3.ebuild
new file mode 100644
index 000000000..25df27ba6
--- /dev/null
+++ b/dev-python/aiohttp-retry/aiohttp-retry-2.8.3.ebuild
@@ -0,0 +1,31 @@
+# Copyright 1999-2023 Gentoo Authors
+# Distributed under the terms of the GNU General Public License v2
+
+EAPI=8
+
+PYTHON_COMPAT=( python3_{10..12} )
+DISTUTILS_USE_PEP517=setuptools
+inherit distutils-r1 pypi
+
+DESCRIPTION="Simple retry client for aiohttp"
+HOMEPAGE="https://github.com/inyutin/aiohttp_retry"
+# Test suite missing from PyPI tarball, reported upstream:
+# https://github.com/inyutin/aiohttp_retry/issues/94
+SRC_URI="https://github.com/inyutin/aiohttp_retry/archive/refs/tags/v${PV}.tar.gz -> ${P}.gh.tar.gz"
+
+LICENSE="MIT"
+SLOT="0"
+KEYWORDS="~amd64 ~arm ~arm64 ~x86"
+IUSE="test"
+RESTRICT="!test? ( test )"
+
+RDEPEND="dev-python/aiohttp[${PYTHON_USEDEP}]"
+
+BDEPEND="
+	test? (
+		dev-python/pytest-aiohttp[${PYTHON_USEDEP}]
+		dev-python/pytest-asyncio[${PYTHON_USEDEP}]
+		dev-python/pytest-tornasync[${PYTHON_USEDEP}]
+	)"
+
+distutils_enable_tests pytest
diff --git a/dev-python/aiohttp-retry/metadata.xml b/dev-python/aiohttp-retry/metadata.xml
new file mode 100644
index 000000000..900a7e9f8
--- /dev/null
+++ b/dev-python/aiohttp-retry/metadata.xml
@@ -0,0 +1,16 @@
+<?xml version='1.0' encoding='UTF-8'?>
+<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
+<pkgmetadata>
+	<maintainer type="person">
+		<email>gentoo@chymera.eu</email>
+		<name>Horea Christian</name>
+	</maintainer>
+	<maintainer type="project">
+		<email>sci@gentoo.org</email>
+		<name>Gentoo Science Project</name>
+	</maintainer>
+	<upstream>
+		<remote-id type="github">inyutin/aiohttp_retry</remote-id>
+		<remote-id type="pypi">aiohttp-retry</remote-id>
+	</upstream>
+</pkgmetadata>
diff --git a/dev-python/annexremote/Manifest b/dev-python/annexremote/Manifest
new file mode 100644
index 000000000..c5eac671a
--- /dev/null
+++ b/dev-python/annexremote/Manifest
@@ -0,0 +1,2 @@
+DIST annexremote-1.5.0.tar.gz 73544 BLAKE2B f5b528faf3d390f9bba6fb97768318ab04224cf05941a2606d49edda7bde30d743bf8e492f277986c0eda62f4000e1446e048d932df436cc2075b1f3e536c7d2 SHA512 7307f5ead82d449eda8b27a83f314b112bfe243a50f556397aed0f563452db6b4ba06b68aacaa27ff722ec9ccd2bdc489a3a8f4f3d849354757bd2fff8ae50d0
+DIST annexremote-1.6.0.tar.gz 74199 BLAKE2B 27956c5ea4789a1bd22bfabe6e0da8a5c8700ba50c3c28610b364d6b358f195124667381094c7786a825fae4464a340b36fd61cd09956477101c7bfd54ba8166 SHA512 1320e06fb3bebe65cce872af6adfb702d9d44cad1671ab8fd432137eb44f22cbd35744b889f11900379da2512fb79da0972c0326fcf3e51c6a404fe497e20ea4
diff --git a/dev-python/annexremote/annexremote-1.5.0.ebuild b/dev-python/annexremote/annexremote-1.5.0.ebuild
new file mode 100644
index 000000000..a6dacd5c9
--- /dev/null
+++ b/dev-python/annexremote/annexremote-1.5.0.ebuild
@@ -0,0 +1,25 @@
+# Copyright 1999-2022 Gentoo Authors
+# Distributed under the terms of the GNU General Public License v2
+
+EAPI=8
+
+DISTUTILS_USE_PEP517=setuptools
+PYTHON_COMPAT=( python3_{10..11} )
+inherit distutils-r1 pypi
+
+DESCRIPTION="Helper module to easily develop git-annex remotes"
+HOMEPAGE="https://github.com/Lykos153/AnnexRemote"
+
+LICENSE="GPL-3"
+SLOT="0"
+KEYWORDS="~amd64 ~x86"
+IUSE="examples"
+# Tests require nose, reported upstream:
+# https://github.com/Lykos153/AnnexRemote/issues/61
+RESTRICT="test"
+
+python_install_all() {
+	distutils-r1_python_install_all
+	dodoc README.md
+	use examples && dodoc -r examples
+}
diff --git a/dev-python/annexremote/annexremote-1.6.0.ebuild b/dev-python/annexremote/annexremote-1.6.0.ebuild
new file mode 100644
index 000000000..a6dacd5c9
--- /dev/null
+++ b/dev-python/annexremote/annexremote-1.6.0.ebuild
@@ -0,0 +1,25 @@
+# Copyright 1999-2022 Gentoo Authors
+# Distributed under the terms of the GNU General Public License v2
+
+EAPI=8
+
+DISTUTILS_USE_PEP517=setuptools
+PYTHON_COMPAT=( python3_{10..11} )
+inherit distutils-r1 pypi
+
+DESCRIPTION="Helper module to easily develop git-annex remotes"
+HOMEPAGE="https://github.com/Lykos153/AnnexRemote"
+
+LICENSE="GPL-3"
+SLOT="0"
+KEYWORDS="~amd64 ~x86"
+IUSE="examples"
+# Tests require nose, reported upstream:
+# https://github.com/Lykos153/AnnexRemote/issues/61
+RESTRICT="test"
+
+python_install_all() {
+	distutils-r1_python_install_all
+	dodoc README.md
+	use examples && dodoc -r examples
+}
diff --git a/dev-python/annexremote/metadata.xml b/dev-python/annexremote/metadata.xml
new file mode 100644
index 000000000..a4bcc5d17
--- /dev/null
+++ b/dev-python/annexremote/metadata.xml
@@ -0,0 +1,22 @@
+<?xml version='1.0' encoding='UTF-8'?>
+<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
+<pkgmetadata>
+	<maintainer type="person">
+		<email>gentoo@chymera.eu</email>
+		<name>Horea Christian</name>
+	</maintainer>
+	<maintainer type="project">
+		<email>sci@gentoo.org</email>
+		<name>Gentoo Science Project</name>
+	</maintainer>
+	<longdescription lang="en">
+		Helper module to easily develop special remotes for git annex. AnnexRemote
+		handles all the protocol stuff for you, so you can focus on the remote
+		itself. It implements the complete external special remote protocol and
+		fulfils all specifications regarding whitespaces etc.
+	</longdescription>
+	<upstream>
+		<remote-id type="github">Lykos153/AnnexRemote</remote-id>
+		<remote-id type="pypi">annexremote</remote-id>
+	</upstream>
+</pkgmetadata>
diff --git a/dev-python/anys/Manifest b/dev-python/anys/Manifest
new file mode 100644
index 000000000..bb3dbee15
--- /dev/null
+++ b/dev-python/anys/Manifest
@@ -0,0 +1 @@
+DIST anys-0.2.1.tar.gz 17850 BLAKE2B c7eda2e245108f9a0a0263af45589d7b0df78767517e9b56768626e43badc5100f01a844d17b10e34a19c0a0fbfa951ba97a374cb8951e7a5560e11867b12d78 SHA512 5a46d9e8aa97401f11dcc7a26a3d8dc759c59b5485222cb6ba1df3d4b2d8d67455102943f044850d289cd3e32bcaf6413ed4a4dfbee26c049a6ef32dfa5cd87e
diff --git a/dev-python/anys/anys-0.2.1.ebuild b/dev-python/anys/anys-0.2.1.ebuild
new file mode 100644
index 000000000..88e61a12e
--- /dev/null
+++ b/dev-python/anys/anys-0.2.1.ebuild
@@ -0,0 +1,29 @@
+# Copyright 1999-2023 Gentoo Authors
+# Distributed under the terms of the GNU General Public License v2
+
+EAPI=8
+
+PYTHON_COMPAT=( python3_{10..11} )
+DISTUTILS_USE_PEP517=setuptools
+inherit distutils-r1
+
+DESCRIPTION="Matchers for pytest"
+HOMEPAGE="https://github.com/jwodder/anys"
+SRC_URI="https://github.com/jwodder/anys/releases/download/v${PV}/${P}.tar.gz"
+
+LICENSE="MIT"
+SLOT="0"
+KEYWORDS="~amd64 ~x86"
+IUSE="test"
+RESTRICT="!test? ( test )"
+
+RDEPEND="
+	dev-python/deprecated[${PYTHON_USEDEP}]
+	dev-python/wheel[${PYTHON_USEDEP}]
+"
+
+PATCHES=(
+	"${FILESDIR}/${PN}-0.2.0-coverage.patch"
+)
+
+distutils_enable_tests pytest
diff --git a/dev-python/anys/files/anys-0.2.0-coverage.patch b/dev-python/anys/files/anys-0.2.0-coverage.patch
new file mode 100644
index 000000000..8091ded2d
--- /dev/null
+++ b/dev-python/anys/files/anys-0.2.0-coverage.patch
@@ -0,0 +1,10 @@
+--- a/tox.ini	2021-09-27 06:43:49.569561395 -0400
++++ b/tox.ini	2021-09-27 06:47:36.549815529 -0400
+@@ -30,7 +30,6 @@
+     mypy src test
+
+ [pytest]
+-addopts = --cov=anys --no-cov-on-fail
+ filterwarnings = error
+ norecursedirs = test/data
+
diff --git a/dev-python/anys/metadata.xml b/dev-python/anys/metadata.xml
new file mode 100644
index 000000000..f0a7bb068
--- /dev/null
+++ b/dev-python/anys/metadata.xml
@@ -0,0 +1,16 @@
+<?xml version='1.0' encoding='UTF-8'?>
+<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
+<pkgmetadata>
+	<maintainer type="person">
+		<email>gentoo@chymera.eu</email>
+		<name>Horea Christian</name>
+	</maintainer>
+	<maintainer type="project">
+		<email>sci@gentoo.org</email>
+		<name>Gentoo Science Project</name>
+	</maintainer>
+	<upstream>
+		<remote-id type="github">jwodder/anys</remote-id>
+		<remote-id type="pypi">anys</remote-id>
+	</upstream>
+</pkgmetadata>
diff --git a/dev-python/archspec/Manifest b/dev-python/archspec/Manifest
new file mode 100644
index 000000000..8ad1830fc
--- /dev/null
+++ b/dev-python/archspec/Manifest
@@ -0,0 +1,2 @@
+DIST archspec-0.1.4.tar.gz 35184 BLAKE2B fe05cab539163d986e639e7e9cf57db208f9cce7ee447d2d3207af0bad68f2d5410e720e5f73376f950b9672602885fe34942fb885d7acbb8ad7e31b7f139ee0 SHA512 28da79ba1469db38ab1424be49feba87378c252ead5ad07fca8ae752dc3503d281f2f3f30391fe6209b118800f357b5219593c2d0d11608d683e56c95ca8f286
+DIST archspec-0.2.2.tar.gz 38306 BLAKE2B c8f8011e122d31a603120231b5f4f034316e06412d64e0bb0fe38886508470d264f7a20da5ef79634fa5ba2f3d3b176b08151f9b5d72d64dbc5c90ce9bd6ff42 SHA512 e2310ca041064109358c918abbdfb581a1494d51d4c0f41e6172fdb9defcefd60f1b80ae2187c8143e37569c815fdc29508d52c048fe88c8c198e85997cef34d
diff --git a/dev-python/archspec/archspec-0.1.4.ebuild b/dev-python/archspec/archspec-0.1.4.ebuild
new file mode 100644
index 000000000..35500e00d
--- /dev/null
+++ b/dev-python/archspec/archspec-0.1.4.ebuild
@@ -0,0 +1,19 @@
+EAPI=8
+
+PYTHON_COMPAT=( python3_{10..11} )
+DISTUTILS_USE_PEP517=poetry
+inherit distutils-r1 pypi
+
+DESCRIPTION="labels for various aspects of a system architecture like CPU, etc."
+HOMEPAGE="https://archspec.readthedocs.io/en/latest/index.html"
+
+LICENSE="MIT"
+SLOT="0"
+KEYWORDS="~amd64"
+
+RDEPEND="
+	>=dev-python/six-1.16.0[${PYTHON_USEDEP}]
+	<=dev-python/six-2.0.0[${PYTHON_USEDEP}]
+	>=dev-python/click-7.1.2[${PYTHON_USEDEP}]
+"
+DEPEND="${RDEPEND}"
diff --git a/dev-python/archspec/archspec-0.2.2.ebuild b/dev-python/archspec/archspec-0.2.2.ebuild
new file mode 100644
index 000000000..a7287fc72
--- /dev/null
+++ b/dev-python/archspec/archspec-0.2.2.ebuild
@@ -0,0 +1,13 @@
+EAPI=8
+
+PYTHON_COMPAT=( python3_{10..12} )
+DISTUTILS_USE_PEP517=poetry
+inherit distutils-r1 pypi
+
+DESCRIPTION="Labels for various aspects of a system architecture like CPU, etc."
+HOMEPAGE="https://archspec.readthedocs.io/en/latest/index.html"
+
+LICENSE="MIT"
+SLOT="0"
+KEYWORDS="~amd64"
+
diff --git a/dev-python/archspec/metadata.xml b/dev-python/archspec/metadata.xml
new file mode 100644
index 000000000..3688592b1
--- /dev/null
+++ b/dev-python/archspec/metadata.xml
@@ -0,0 +1,20 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
+<pkgmetadata>
+	<maintainer type="project">
+		<email>sci@gentoo.org</email>
+		<name>Gentoo Science Project</name>
+	</maintainer>
+	<maintainer type="person">
+		<email>alexander@neuwirth-informatik.de</email>
+		<name>Alexander Puck Neuwirth</name>
+	</maintainer>
+	<longdescription lang="en">
+	Archspec aims at providing a standard set of human-understandable labels for various aspects of a system architecture like CPU, network fabrics, etc. and APIs to detect, query and compare them.
+	</longdescription>
+	<upstream>
+		<remote-id type="pypi">archspec</remote-id>
+		<remote-id type="github">archspec/archspec</remote-id>
+		<bugs-to>https://github.com/archspec/archspec/issues</bugs-to>
+	</upstream>
+</pkgmetadata>
diff --git a/dev-python/arrayfire-python/Manifest b/dev-python/arrayfire-python/Manifest
deleted file mode 100644
index 587a06b33..000000000
--- a/dev-python/arrayfire-python/Manifest
+++ /dev/null
@@ -1,5 +0,0 @@
-DIST arrayfire-3.1.20151111.tar.gz 35015 BLAKE2B 5cfe305aa24e422ebb2cbd662d5a6754fe06047b6d82b62dc50057788244cf525307a486976f19e19196d712ca5fd9c50f3ecc5a2886a162400ede88d733f7a3 SHA512 7a3e359eaf61e7d8234451671941f37f613a77ea4d1d22ac7dc6cd9a0b40a2ca098eb03b8d0778537c5012aca6cb5bc986a056b3cdf15e7d9f23417bf3c6a60d
-DIST arrayfire-3.2.20151224.tar.gz 39158 SHA256 446a8a1e74f2271f0f8cafcc4d144a1cd58d01de50b6f90cc0c2ef48d044434d SHA512 bd3bdab84835c1e112e4d7d159f76d02a0291bc1a82928918202abd524b296b47589dec7d432419006c0348e0741d07e7852d1ad943ae2640b78be3c057f94ed WHIRLPOOL c88e019ed288a05c78de7cd44f590b751c71ebecf957eed7c71d697c3fa026816f4731190de942c73b113c4f98d8f0de8274df619e97ac4c0f8da12b9ad73013
-DIST arrayfire-python-3.3.20160624.tar.gz 104485 BLAKE2B 4294389f7c3f807799df4879e7222a7aca15e2784a5ede141d51443fc5876a88709574dd7557b7f234b2ea3418a4dcac88e931972cd2846fa8d17c08ee7a1623 SHA512 e311470287c099b54961cf7988b57b2c0e3f36b4c77deabcd2ac934f8f3f81d39a97dfe3d10e677a1a58f71d6944010595ac8d30de054b2a7edbe19d599e87d1
-DIST arrayfire-python-3.4.20161126.tar.gz 108299 BLAKE2B 3c92e8849a986f261ce55cee526169be883cb1ac8b46f9c8dfc650b8a48a6dac6899f2d3458bd6c8efb6206d8a5a6835c30b1687fb1a2354ef0440a60cbb47dc SHA512 819d06b3a42922f70352f37a5d1d312c896f8975584cbe8d2bd671e26fc7725247b2826a53ecbcfc00ad4f05c305651a6673fbd89e1d686b514c91d4276820cb
-DIST arrayfire-python-3.4.20170222.tar.gz 111992 BLAKE2B a2540341cd900c7edfe07ae7beea3c61e5b6ee13effd87fb9450ecf338c99146f4077ebf2c8032ee284f7a2b8ba546a055eefbeb670a028081ad87914fb56f3f SHA512 a9c41c7932592df15a023c41d920bd9588da55a58db456d42e2c5b707645564c48aef26ae99345cae8053585a55a4b85b26750e998f2873f81b5d068afe29f71
diff --git a/dev-python/arrayfire-python/arrayfire-python-3.1.20151111.ebuild b/dev-python/arrayfire-python/arrayfire-python-3.1.20151111.ebuild
deleted file mode 100644
index a5518e365..000000000
--- a/dev-python/arrayfire-python/arrayfire-python-3.1.20151111.ebuild
+++ /dev/null
@@ -1,25 +0,0 @@
-# Copyright 1999-2016 Gentoo Foundation
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=6
-PYTHON_COMPAT=( python2_7 python3_{4,5} )
-
-inherit distutils-r1
-
-MY_PN="arrayfire"
-
-DESCRIPTION="Python bindings for ArrayFire"
-HOMEPAGE="http://www.arrayfire.com"
-SRC_URI="mirror://pypi/${MY_PN:0:1}/${MY_PN}/${MY_PN}-${PV}.tar.gz"
-
-LICENSE="BSD"
-SLOT="0"
-KEYWORDS="~amd64"
-
-S="${WORKDIR}/${MY_PN}-${PV}"
-
-RDEPEND="
-	>=sci-libs/arrayfire-3.0.0
-	<sci-libs/arrayfire-3.2
-	"
-DEPEND="${RDEPEND}"
diff --git a/dev-python/arrayfire-python/arrayfire-python-3.2.20151224.ebuild b/dev-python/arrayfire-python/arrayfire-python-3.2.20151224.ebuild
deleted file mode 100644
index 40e30d21e..000000000
--- a/dev-python/arrayfire-python/arrayfire-python-3.2.20151224.ebuild
+++ /dev/null
@@ -1,25 +0,0 @@
-# Copyright 1999-2016 Gentoo Foundation
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=6
-PYTHON_COMPAT=( python2_7 python3_{4,5} )
-
-inherit distutils-r1
-
-MY_PN="arrayfire"
-
-DESCRIPTION="Python bindings for ArrayFire"
-HOMEPAGE="http://www.arrayfire.com"
-SRC_URI="mirror://pypi/${MY_PN:0:1}/${MY_PN}/${MY_PN}-${PV}.tar.gz"
-
-LICENSE="BSD"
-SLOT="0"
-KEYWORDS="~amd64"
-
-S="${WORKDIR}/${MY_PN}-${PV}"
-
-RDEPEND="
-	>=sci-libs/arrayfire-3.2.0
-	<sci-libs/arrayfire-3.3.0
-	"
-DEPEND="${RDEPEND}"
diff --git a/dev-python/arrayfire-python/arrayfire-python-3.3.20160624.ebuild b/dev-python/arrayfire-python/arrayfire-python-3.3.20160624.ebuild
deleted file mode 100644
index 29d275cf3..000000000
--- a/dev-python/arrayfire-python/arrayfire-python-3.3.20160624.ebuild
+++ /dev/null
@@ -1,21 +0,0 @@
-# Copyright 1999-2016 Gentoo Foundation
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=6
-PYTHON_COMPAT=( python2_7 python3_{4,5} )
-
-inherit distutils-r1
-
-DESCRIPTION="Python bindings for ArrayFire"
-HOMEPAGE="http://www.arrayfire.com"
-SRC_URI="https://github.com/arrayfire/arrayfire-python/archive/${PV}.tar.gz -> ${P}.tar.gz"
-
-LICENSE="BSD"
-SLOT="0"
-KEYWORDS="~amd64"
-
-RDEPEND="
-	>=sci-libs/arrayfire-3.3.2
-	<sci-libs/arrayfire-3.4.0
-	"
-DEPEND="${RDEPEND}"
diff --git a/dev-python/arrayfire-python/arrayfire-python-3.4.20161126.ebuild b/dev-python/arrayfire-python/arrayfire-python-3.4.20161126.ebuild
deleted file mode 100644
index cf6980807..000000000
--- a/dev-python/arrayfire-python/arrayfire-python-3.4.20161126.ebuild
+++ /dev/null
@@ -1,26 +0,0 @@
-# Copyright 1999-2016 Gentoo Foundation
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=6
-PYTHON_COMPAT=( python2_7 python3_{4,5} )
-
-inherit distutils-r1
-
-DESCRIPTION="Python bindings for ArrayFire"
-HOMEPAGE="http://www.arrayfire.com"
-SRC_URI="https://github.com/arrayfire/arrayfire-python/archive/${PV}.tar.gz -> ${P}.tar.gz"
-
-LICENSE="BSD"
-SLOT="0"
-IUSE="test"
-KEYWORDS="~amd64"
-
-RDEPEND="
-	>=sci-libs/arrayfire-3.4.0
-	<sci-libs/arrayfire-3.5.0
-	"
-DEPEND="${RDEPEND}"
-
-python_test() {
-	${EPYTHON} -m arrayfire.tests
-}
diff --git a/dev-python/arrayfire-python/arrayfire-python-3.4.20170222.ebuild b/dev-python/arrayfire-python/arrayfire-python-3.4.20170222.ebuild
deleted file mode 100644
index 32818eef8..000000000
--- a/dev-python/arrayfire-python/arrayfire-python-3.4.20170222.ebuild
+++ /dev/null
@@ -1,26 +0,0 @@
-# Copyright 1999-2017 Gentoo Foundation
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=6
-PYTHON_COMPAT=( python2_7 python3_{4,5} )
-
-inherit distutils-r1
-
-DESCRIPTION="Python bindings for ArrayFire"
-HOMEPAGE="http://www.arrayfire.com"
-SRC_URI="https://github.com/arrayfire/arrayfire-python/archive/${PV}.tar.gz -> ${P}.tar.gz"
-
-LICENSE="BSD"
-SLOT="0"
-IUSE="test"
-KEYWORDS="~amd64"
-
-RDEPEND="
-	>=sci-libs/arrayfire-3.4.0
-	<sci-libs/arrayfire-3.5.0
-	"
-DEPEND="${RDEPEND}"
-
-python_test() {
-	${EPYTHON} -m arrayfire.tests
-}
diff --git a/dev-python/arrayfire-python/arrayfire-python-9999.ebuild b/dev-python/arrayfire-python/arrayfire-python-9999.ebuild
deleted file mode 100644
index 5704d5093..000000000
--- a/dev-python/arrayfire-python/arrayfire-python-9999.ebuild
+++ /dev/null
@@ -1,19 +0,0 @@
-# Copyright 1999-2016 Gentoo Foundation
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=6
-PYTHON_COMPAT=( python2_7 python3_{4,5} )
-
-inherit distutils-r1 git-r3
-
-DESCRIPTION="Python bindings for ArrayFire"
-HOMEPAGE="http://www.arrayfire.com"
-EGIT_REPO_URI="https://github.com/arrayfire/${PN}.git git://github.com/arrayfire/${PN}.git"
-
-LICENSE="BSD"
-SLOT="0"
-
-RDEPEND="
-	>=sci-libs/arrayfire-3.0.0
-	"
-DEPEND="${RDEPEND}"
diff --git a/dev-python/arrayfire-python/metadata.xml b/dev-python/arrayfire-python/metadata.xml
deleted file mode 100644
index 8d4d250f0..000000000
--- a/dev-python/arrayfire-python/metadata.xml
+++ /dev/null
@@ -1,21 +0,0 @@
-<?xml version="1.0" encoding="UTF-8"?>
-<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
-<pkgmetadata>
-	<maintainer type="person">
-		<email>marbre@linux.sungazer.de</email>
-		<name>Marius Brehler</name>
-	</maintainer>
-	<maintainer type="project">
-		<email>sci@gentoo.org</email>
-		<name>Gentoo Science Project</name>
-	</maintainer>
-	<longdescription>
-ArrayFire is a high performance library for parallel computing
-wih an easy-to-use API. This package project Python bindings
-for the ArrayFire library.
-</longdescription>
-	<upstream>
-		<remote-id type="github">arrayfire/arrayfire-python</remote-id>
-		<remote-id type="pypi">arrayfire</remote-id>
-	</upstream>
-</pkgmetadata>
diff --git a/dev-python/asciitree/Manifest b/dev-python/asciitree/Manifest
new file mode 100644
index 000000000..5ea004309
--- /dev/null
+++ b/dev-python/asciitree/Manifest
@@ -0,0 +1 @@
+DIST asciitree-0.3.3.tar.gz 8765 BLAKE2B 85b935d9a0df286cd14bb7828335608a2fa2b7acd83707ab61ba29ca58b452a378758ec3553d2845a2536150fd0c9c2bfeb25e95d6bdf02c3d023156e1065e8e SHA512 82ec368db5c3302640860aadeefc89ef2bc74a4336a46729d2688591454b6c1ab1f1fe9fc5305bc956c9998f27bca9e55aeee3bfb82bdf24a67955953e7e37f0
diff --git a/dev-python/asciitree/asciitree-0.3.3.ebuild b/dev-python/asciitree/asciitree-0.3.3.ebuild
new file mode 100644
index 000000000..29d5ecf87
--- /dev/null
+++ b/dev-python/asciitree/asciitree-0.3.3.ebuild
@@ -0,0 +1,19 @@
+# Copyright 1999-2023 Gentoo Authors
+# Distributed under the terms of the GNU General Public License v2
+
+EAPI=8
+
+PYTHON_COMPAT=( python3_{10..11} )
+inherit distutils-r1
+
+DESCRIPTION="ASCII trees in python"
+HOMEPAGE="https://github.com/mbr/asciitree"
+SRC_URI="https://github.com/mbr/asciitree/archive/refs/tags/${PV}.tar.gz -> ${P}.tar.gz"
+
+LICENSE="MIT"
+SLOT="0"
+KEYWORDS="~amd64 ~x86"
+IUSE="test"
+RESTRICT="!test? ( test )"
+
+distutils_enable_tests pytest
diff --git a/dev-python/asciitree/metadata.xml b/dev-python/asciitree/metadata.xml
new file mode 100644
index 000000000..8b000b491
--- /dev/null
+++ b/dev-python/asciitree/metadata.xml
@@ -0,0 +1,15 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
+<pkgmetadata>
+	<maintainer type="person">
+		<email>gentoo@chymera.eu</email>
+		<name>Horea Christian</name>
+	</maintainer>
+	<maintainer type="project">
+		<email>sci@gentoo.org</email>
+		<name>Gentoo Science Project</name>
+	</maintainer>
+	<upstream>
+		<remote-id type="github">mbr/asciitree</remote-id>
+	</upstream>
+</pkgmetadata>
diff --git a/dev-python/asdf/Manifest b/dev-python/asdf/Manifest
new file mode 100644
index 000000000..ac7f18004
--- /dev/null
+++ b/dev-python/asdf/Manifest
@@ -0,0 +1 @@
+DIST asdf-2.14.3.tar.gz 489097 BLAKE2B 26e3da88f4b0ada5a995ff77fdb55a26aa9af1b53c4e90723b36080526ee218581d09295b169bddd998a4055d1b9818e793bfdafdc786a27f5ea87021e9f85e7 SHA512 125015a1d3a26034c8d483bebf609af02489d0710973828e443dea5cfa46cb33826078714b9ccbd385fcc92fd6b2d92253e80c32ca90565a48f45e4ff47b8655
diff --git a/dev-python/asdf/asdf-2.14.3.ebuild b/dev-python/asdf/asdf-2.14.3.ebuild
new file mode 100644
index 000000000..2c935c1fb
--- /dev/null
+++ b/dev-python/asdf/asdf-2.14.3.ebuild
@@ -0,0 +1,46 @@
+# Copyright 1999-2023 Gentoo Authors
+# Distributed under the terms of the GNU General Public License v2
+
+EAPI=8
+
+PYTHON_COMPAT=( python3_{10..11} )
+DISTUTILS_USE_PEP517=setuptools
+
+inherit distutils-r1 pypi
+
+DESCRIPTION="Python library for the Advanced Scientific Data Format"
+HOMEPAGE="https://asdf.readthedocs.io/en/latest/"
+
+LICENSE="BSD"
+SLOT="0"
+KEYWORDS="~amd64 ~x86"
+# Reported upstream:
+# https://github.com/asdf-format/asdf/issues/1319
+RESTRICT="test"
+
+BDEPEND="dev-python/setuptools-scm[${PYTHON_USEDEP}]
+	test? (
+		dev-python/astropy[${PYTHON_USEDEP}]
+		dev-python/pytest-doctestplus[${PYTHON_USEDEP}]
+		dev-python/psutil[${PYTHON_USEDEP}]
+		dev-python/gwcs[${PYTHON_USEDEP}]
+	)
+	doc? ( media-gfx/graphviz )
+"
+
+RDEPEND="
+	>=dev-python/jmespath-0.6.2[${PYTHON_USEDEP}]
+	>=dev-python/jsonschema-3.0.2[${PYTHON_USEDEP}]
+	>=dev-python/numpy-1.10[${PYTHON_USEDEP}]
+	>=dev-python/pyyaml-3.10[${PYTHON_USEDEP}]
+	>=dev-python/semantic-version-2.8[${PYTHON_USEDEP}]
+"
+
+distutils_enable_tests pytest
+distutils_enable_sphinx docs dev-python/astropy dev-python/sphinx-astropy dev-python/matplotlib dev-python/docutils
+
+python_test() {
+	# discovers things in docs dir if we do not
+	# explicitly set it to run on the tests dir
+	epytest asdf/tests
+}
diff --git a/dev-python/asdf/metadata.xml b/dev-python/asdf/metadata.xml
new file mode 100644
index 000000000..332ed9dd0
--- /dev/null
+++ b/dev-python/asdf/metadata.xml
@@ -0,0 +1,11 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
+<pkgmetadata>
+	<maintainer type="project">
+		<email>sci-astronomy@gentoo.org</email>
+		<name>Gentoo Astronomy Project</name>
+	</maintainer>
+	<upstream>
+		<remote-id type="pypi">asdf</remote-id>
+	</upstream>
+</pkgmetadata>
diff --git a/dev-python/astropy-healpix/Manifest b/dev-python/astropy-healpix/Manifest
new file mode 100644
index 000000000..ee0baaaa9
--- /dev/null
+++ b/dev-python/astropy-healpix/Manifest
@@ -0,0 +1 @@
+DIST astropy_healpix-0.7.tar.gz 107330 BLAKE2B c1daed6475b63d59debd19ad97fc3547917df93b9b6998aef51f38a7e4014a543f25f6823dac12e93745fa8cd6c17b418035730b4d37f85b7df250e8d4fd6026 SHA512 33e23a616a0a36880066d96a50b949b1a96b4a1cecc1ebe8584c817a10587d26eb58879fb175c3fd675c3fbc98d4be1cfa9b19aa9ad4ac7a1528a8e6d32f7436
diff --git a/dev-python/astropy-healpix/astropy-healpix-0.7.ebuild b/dev-python/astropy-healpix/astropy-healpix-0.7.ebuild
new file mode 100644
index 000000000..9bf99f7e2
--- /dev/null
+++ b/dev-python/astropy-healpix/astropy-healpix-0.7.ebuild
@@ -0,0 +1,35 @@
+# Copyright 1999-2022 Gentoo Authors
+# Distributed under the terms of the GNU General Public License v2
+
+EAPI=8
+
+PYTHON_COMPAT=( python3_{10..11} )
+DISTUTILS_USE_PEP517=setuptools
+inherit distutils-r1 pypi
+
+DESCRIPTION="HEALPix for Astropy"
+HOMEPAGE="https://github.com/astropy/astropy-healpix"
+S="${WORKDIR}/${P/-/_}"
+
+LICENSE="BSD"
+SLOT="0"
+KEYWORDS="~amd64 ~x86"
+
+#TODO: Package all these pytest deps:
+# 	pytest-doctestplus>=0.2.0
+# 	pytest-remotedata>=0.3.1
+# 	pytest-openfiles>=0.3.1
+# 	pytest-astropy-header>=0.1.2
+# 	pytest-arraydiff>=0.1
+# 	pytest-filter-subpackage>=0.1
+RESTRICT="test"
+
+BDEPEND="dev-python/setuptools-scm[${PYTHON_USEDEP}]"
+
+RDEPEND="
+	>=dev-python/astropy-3.2[${PYTHON_USEDEP}]
+	dev-python/numpy[${PYTHON_USEDEP}]
+"
+
+distutils_enable_sphinx docs dev-python/sphinx-astropy dev-python/matplotlib
+distutils_enable_tests pytest
diff --git a/dev-python/astropy-healpix/metadata.xml b/dev-python/astropy-healpix/metadata.xml
new file mode 100644
index 000000000..2d40d7328
--- /dev/null
+++ b/dev-python/astropy-healpix/metadata.xml
@@ -0,0 +1,12 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
+<pkgmetadata>
+	<maintainer type="project">
+		<email>sci-astronomy@gentoo.org</email>
+		<name>Gentoo Astronomy Project</name>
+	</maintainer>
+	<upstream>
+		<remote-id type="github">astropy/astropy-healpix</remote-id>
+		<remote-id type="pypi">astropy-healpix</remote-id>
+	</upstream>
+</pkgmetadata>
diff --git a/dev-python/astropy-helpers/Manifest b/dev-python/astropy-helpers/Manifest
new file mode 100644
index 000000000..0ada1821b
--- /dev/null
+++ b/dev-python/astropy-helpers/Manifest
@@ -0,0 +1 @@
+DIST astropy-helpers-4.0.1.tar.gz 52904 BLAKE2B c550cbfbf6c64fd354bd212f8954a2c7218f5ec678a5e4ab12ca8af077cb531d7ab8f363a0799f167ee0dd226b920fe4e0077a73f8513f40c987a9763694addf SHA512 11c41f6474b41a8cd89d8cf5b31c5508bba8142e92342761fae602b19694215e0fc97091e83b6a7bc82fbc4b9bc5c4a6cd825f040d63c4629f069ec07119a705
diff --git a/dev-python/astropy-helpers/astropy-helpers-4.0.1-r1.ebuild b/dev-python/astropy-helpers/astropy-helpers-4.0.1-r1.ebuild
new file mode 100644
index 000000000..be72affc7
--- /dev/null
+++ b/dev-python/astropy-helpers/astropy-helpers-4.0.1-r1.ebuild
@@ -0,0 +1,29 @@
+# Copyright 1999-2022 Gentoo Authors
+# Distributed under the terms of the GNU General Public License v2
+
+EAPI=8
+
+PYTHON_COMPAT=( python3_{10..11} )
+DISTUTILS_USE_PEP517=setuptools
+PYPI_NO_NORMALIZE=1
+inherit distutils-r1 pypi xdg-utils
+
+MYPV=${PV/_/}
+S=${WORKDIR}/${PN}-${MYPV}
+
+DESCRIPTION="Helpers for Astropy and Affiliated packages"
+HOMEPAGE="https://github.com/astropy/astropy-helpers"
+
+LICENSE="BSD"
+SLOT="0"
+KEYWORDS="~amd64 ~x86"
+
+python_prepare_all() {
+	sed -e '/import ah_bootstrap/d' \
+		-i setup.py || die "Removing ah_bootstrap failed"
+	xdg_environment_reset
+	distutils-r1_python_prepare_all
+}
+
+# master file /var/tmp/portage/dev-python/astropy-helpers-4.0.1/work/astropy-helpers-4.0.1/astropy_helpers/sphinx/index.rst not found
+#distutils_enable_sphinx astropy_helpers/sphinx dev-python/sphinx-astropy
diff --git a/dev-python/astropy-helpers/astropy-helpers-9999.ebuild b/dev-python/astropy-helpers/astropy-helpers-9999.ebuild
deleted file mode 100644
index fa7d02d33..000000000
--- a/dev-python/astropy-helpers/astropy-helpers-9999.ebuild
+++ /dev/null
@@ -1,27 +0,0 @@
-# Copyright 1999-2014 Gentoo Foundation
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=5
-
-PYTHON_COMPAT=( python{2_7,3_4} )
-inherit distutils-r1
-
-if [ ${PV} == "9999" ] ; then
-	inherit git-r3
-	EGIT_REPO_URI="https://github.com/astropy/${PN}.git"
-else
-	SRC_URI="mirror://pypi/${PN:0:1}/${PN}/${P}.tar.gz"
-	KEYWORDS="~amd64"
-fi
-
-DESCRIPTION="Helpers for Astropy and Affiliated packages"
-HOMEPAGE="https://github.com/astropy/astropy-helpers"
-
-LICENSE="BSD"
-SLOT="0"
-IUSE=""
-
-python_prepare_all() {
-	sed -e '/import ah_bootstrap/d' -i setup.py || die "Removing ah_bootstrap failed"
-	distutils-r1_python_prepare_all
-}
diff --git a/dev-python/astropy-helpers/metadata.xml b/dev-python/astropy-helpers/metadata.xml
index ddf49f5b8..8bd2cb74a 100644
--- a/dev-python/astropy-helpers/metadata.xml
+++ b/dev-python/astropy-helpers/metadata.xml
@@ -1,15 +1,20 @@
 <?xml version="1.0" encoding="UTF-8"?>
 <!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
 <pkgmetadata>
+	<maintainer type="person">
+		<email>davidroman96@gmail.com</email>
+		<name>David Roman</name>
+	</maintainer>
+	<maintainer type="person">
+		<email>gentoo@lotz.li</email>
+		<name>Linus Lotz</name>
+	</maintainer>
 	<maintainer type="project">
 		<email>sci-astronomy@gentoo.org</email>
 		<name>Gentoo Astronomy Project</name>
 	</maintainer>
-	<longdescription lang="en">
-astropy-helpers is a collection of build tools used by astropy
-that may be used by other projects.
-</longdescription>
 	<upstream>
 		<remote-id type="github">astropy/astropy-helpers</remote-id>
+		<remote-id type="pypi">astropy-helpers</remote-id>
 	</upstream>
 </pkgmetadata>
diff --git a/dev-python/astropy-sphinx-theme/Manifest b/dev-python/astropy-sphinx-theme/Manifest
new file mode 100644
index 000000000..af8ce245a
--- /dev/null
+++ b/dev-python/astropy-sphinx-theme/Manifest
@@ -0,0 +1 @@
+DIST astropy-sphinx-theme-1.1.tar.gz 29222 BLAKE2B cc569be457c61e546346ef9d75fd93bcd1ec232dcf36e4837c33b1abe0e53fd5f6e56783ebaceca5630f8fadec9c6eb851e5a992b36a8fa89d295fb7c8074d86 SHA512 534ce3141b0047e5ff86f63ff27416a7b0f081995e72255a6305ff23cb80c40c0c0c736643433c0a3ebdad60e6e6fb655b668d08d556967eb6482e94495c6d01
diff --git a/dev-python/astropy-sphinx-theme/astropy-sphinx-theme-1.1-r1.ebuild b/dev-python/astropy-sphinx-theme/astropy-sphinx-theme-1.1-r1.ebuild
new file mode 100644
index 000000000..5b63931b8
--- /dev/null
+++ b/dev-python/astropy-sphinx-theme/astropy-sphinx-theme-1.1-r1.ebuild
@@ -0,0 +1,19 @@
+# Copyright 1999-2022 Gentoo Authors
+# Distributed under the terms of the GNU General Public License v2
+
+EAPI=8
+
+PYTHON_COMPAT=( python3_{10..11} )
+DISTUTILS_USE_PEP517=setuptools
+PYPI_NO_NORMALIZE=1
+
+inherit distutils-r1 pypi
+
+DESCRIPTION="The sphinx theme for Astropy and affiliated packages"
+HOMEPAGE="https://github.com/astropy/astropy-sphinx-theme"
+
+LICENSE="BSD"
+SLOT="0"
+KEYWORDS="~amd64 ~x86"
+
+distutils_enable_tests pytest
diff --git a/dev-python/astropy-sphinx-theme/metadata.xml b/dev-python/astropy-sphinx-theme/metadata.xml
new file mode 100644
index 000000000..7db317173
--- /dev/null
+++ b/dev-python/astropy-sphinx-theme/metadata.xml
@@ -0,0 +1,12 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
+<pkgmetadata>
+	<maintainer type="project">
+		<email>sci-astronomy@gentoo.org</email>
+		<name>Gentoo Astronomy Project</name>
+	</maintainer>
+	<upstream>
+		<remote-id type="github">astropy/astropy-sphinx-theme</remote-id>
+		<remote-id type="pypi">astropy-sphinx-theme</remote-id>
+	</upstream>
+</pkgmetadata>
diff --git a/dev-python/astropy/Manifest b/dev-python/astropy/Manifest
new file mode 100644
index 000000000..3d86b9bab
--- /dev/null
+++ b/dev-python/astropy/Manifest
@@ -0,0 +1 @@
+DIST astropy-5.2.1.tar.gz 8284422 BLAKE2B ded3556d6b16fe7abbbd019c23c0297f4690b13f054a1b98ab6aaeb20b92debefbc6e7c6c5eff8c65dfaa271826885027d6ba4a92f94218632162501a30b025b SHA512 46da7b065e119fa36233ced928abab31d6022fd116d2ed6825cb88b456ab57130772eea1de8cff7b5b7f30aadf46b933ad56a47cf6d2d68c0fa7593f322a6ea0
diff --git a/dev-python/astropy/astropy-5.2.1.ebuild b/dev-python/astropy/astropy-5.2.1.ebuild
new file mode 100644
index 000000000..b52d1e6f5
--- /dev/null
+++ b/dev-python/astropy/astropy-5.2.1.ebuild
@@ -0,0 +1,60 @@
+# Copyright 1999-2022 Gentoo Authors
+# Distributed under the terms of the GNU General Public License v2
+
+EAPI=8
+
+PYTHON_COMPAT=( python3_{10..11} )
+DISTUTILS_USE_PEP517=setuptools
+
+inherit distutils-r1 pypi
+
+DESCRIPTION="Core functionality for performing astrophysics with Python"
+HOMEPAGE="https://www.astropy.org/"
+
+LICENSE="BSD"
+SLOT="0"
+KEYWORDS="~amd64 ~x86"
+
+#TODO: Package all these pytest deps:
+# 	pytest-remotedata>=0.3.1
+# 	pytest-openfiles>=0.3.1
+# 	pytest-astropy-header>=0.1.2
+# 	pytest-arraydiff>=0.1
+# 	pytest-filter-subpackage>=0.1
+RESTRICT="test"
+
+RDEPEND="
+	dev-libs/expat:0=
+	>=dev-python/numpy-1.18[${PYTHON_USEDEP}]
+	>=dev-python/pyerfa-2.0[${PYTHON_USEDEP}]
+	>=dev-python/pyyaml-3.13[${PYTHON_USEDEP}]
+	>=dev-python/packaging-19.0[${PYTHON_USEDEP}]
+	sci-astronomy/wcslib:0=
+	>=sci-libs/cfitsio-3.350:0=
+	sys-libs/zlib:0=
+"
+DEPEND="${RDEPEND}"
+BDEPEND="
+	dev-python/astropy-helpers[${PYTHON_USEDEP}]
+	dev-python/extension-helpers[${PYTHON_USEDEP}]
+	dev-python/cython[${PYTHON_USEDEP}]
+	dev-python/setuptools-scm[${PYTHON_USEDEP}]
+	test? (
+		dev-libs/libxml2
+		dev-python/h5py[${PYTHON_USEDEP}]
+		dev-python/ipython[${PYTHON_USEDEP}]
+		dev-python/matplotlib[${PYTHON_USEDEP}]
+		dev-python/objgraph[${PYTHON_USEDEP}]
+		dev-python/pytest-xdist[${PYTHON_USEDEP}]
+		dev-python/scipy[${PYTHON_USEDEP}]
+	)"
+
+distutils_enable_tests pytest
+# TODO: Fix this
+# NameError: name 'disabled_intersphinx_mapping' is not defined
+#distutils_enable_sphinx docs \
+# 	dev-python/matplotlib \
+# 	dev-python/graphviz \
+# 	dev-python/sphinx-astropy \
+# 	dev-python/pyyaml \
+# 	dev-python/scipy
diff --git a/dev-python/astropy/astropy-9999.ebuild b/dev-python/astropy/astropy-9999.ebuild
deleted file mode 100644
index 6f031e6f7..000000000
--- a/dev-python/astropy/astropy-9999.ebuild
+++ /dev/null
@@ -1,71 +0,0 @@
-# Copyright 1999-2014 Gentoo Foundation
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=5
-
-PYTHON_COMPAT=( python{2_7,3_4} )
-
-inherit distutils-r1 git-r3
-
-DESCRIPTION="Core functionality for performing astrophysics with Python"
-HOMEPAGE="http://astropy.org/"
-SRC_URI=""
-EGIT_REPO_URI="git://github.com/${PN}/${PN}.git"
-
-LICENSE="BSD"
-SLOT="0"
-KEYWORDS=""
-IUSE="doc test"
-
-RDEPEND="
-	dev-libs/expat:0=
-	dev-python/numpy[${PYTHON_USEDEP}]
-	sci-astronomy/erfa:0=
-	sci-astronomy/wcslib:0=
-	>=sci-libs/cfitsio-3.350:0=
-	sys-libs/zlib:0="
-DEPEND="${RDEPEND}
-	dev-python/astropy-helpers[${PYTHON_USEDEP}]
-	dev-python/cython[${PYTHON_USEDEP}]
-	dev-python/setuptools[${PYTHON_USEDEP}]
-	virtual/pkgconfig
-	doc? (
-		dev-python/matplotlib[${PYTHON_USEDEP}]
-		dev-python/sphinx[${PYTHON_USEDEP}]
-		media-gfx/graphviz
-	)
-	test? (
-		dev-libs/libxml2
-		dev-python/h5py[${PYTHON_USEDEP}]
-		dev-python/matplotlib[${PYTHON_USEDEP}]
-		dev-python/pytest[${PYTHON_USEDEP}]
-		sci-libs/scipy[${PYTHON_USEDEP}]
-	)"
-
-python_prepare_all() {
-	distutils-r1_python_prepare_all
-	sed -e '/import ah_bootstrap/d' -i setup.py || die "Removing ah_bootstrap failed"
-}
-
-python_compile() {
-	distutils-r1_python_compile --use-system-libraries
-}
-
-python_compile_all() {
-	if use doc; then
-		python_export_best
-		VARTEXFONTS="${T}"/fonts \
-			MPLCONFIGDIR="${BUILD_DIR}" \
-			PYTHONPATH="${BUILD_DIR}"/lib \
-			esetup.py build_sphinx
-	fi
-}
-
-python_test() {
-	esetup.py test
-}
-
-python_install_all() {
-	use doc && HTML_DOCS=( docs/_build/html/. )
-	distutils-r1_src_install_all
-}
diff --git a/dev-python/astropy/metadata.xml b/dev-python/astropy/metadata.xml
index 3d1dc456d..3891d8cc8 100644
--- a/dev-python/astropy/metadata.xml
+++ b/dev-python/astropy/metadata.xml
@@ -9,4 +9,7 @@
 		<email>sci-astronomy@gentoo.org</email>
 		<name>Gentoo Astronomy Project</name>
 	</maintainer>
+	<upstream>
+		<remote-id type="pypi">astropy</remote-id>
+	</upstream>
 </pkgmetadata>
diff --git a/dev-python/astropysics/astropysics-9999.ebuild b/dev-python/astropysics/astropysics-9999.ebuild
deleted file mode 100644
index f2368a2c1..000000000
--- a/dev-python/astropysics/astropysics-9999.ebuild
+++ /dev/null
@@ -1,39 +0,0 @@
-# Copyright 1999-2015 Gentoo Foundation
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=5
-
-PYTHON_COMPAT=( python2_7 )
-
-inherit distutils-r1 git-r3
-
-DESCRIPTION="General purpose python library for professional astronomers/astrophysicists"
-HOMEPAGE="http://packages.python.org/Astropysics/"
-SRC_URI=""
-EGIT_REPO_URI="git://github.com/eteq/${PN}.git"
-
-LICENSE="Apache-2.0"
-SLOT="0"
-KEYWORDS=""
-IUSE="doc"
-
-DEPEND="doc? ( dev-python/sphinx[${PYTHON_USEDEP}] )"
-RDEPEND="
-	dev-python/chaco[${PYTHON_USEDEP}]
-	dev-python/ipython[${PYTHON_USEDEP}]
-	dev-python/matplotlib[${PYTHON_USEDEP}]
-	dev-python/networkx[${PYTHON_USEDEP}]
-	dev-python/pygraphviz[${PYTHON_USEDEP}]
-	dev-python/atpy[${PYTHON_USEDEP}]
-	sci-astronomy/sextractor
-	sci-visualization/mayavi[${PYTHON_USEDEP}]
-	sci-libs/scipy[${PYTHON_USEDEP}]"
-
-python_compile_all() {
-	use doc && emake -C docs html
-}
-
-python_install_all() {
-	use doc && HTML_DOCS=( docs/_build/html/. )
-	distutils-r1_python_install_all
-}
diff --git a/dev-python/astropysics/metadata.xml b/dev-python/astropysics/metadata.xml
deleted file mode 100644
index 349a8c1e0..000000000
--- a/dev-python/astropysics/metadata.xml
+++ /dev/null
@@ -1,14 +0,0 @@
-<?xml version="1.0" encoding="UTF-8"?>
-<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
-<pkgmetadata>
-	<maintainer type="project">
-		<email>sci-astronomy@gentoo.org</email>
-		<name>Gentoo Astronomy Project</name>
-	</maintainer>
-	<longdescription lang="en">
-Astropysics leverages a variety of tools already developed for python to simplify 
-quick-and-dirty calculations and streamline really hard ones. When paired with 
-an interactive environment, it aims to be a full-featured replacement for IDL 
-with idlutils/astron or similar.
-</longdescription>
-</pkgmetadata>
diff --git a/dev-python/astroquery/Manifest b/dev-python/astroquery/Manifest
new file mode 100644
index 000000000..2472dec6d
--- /dev/null
+++ b/dev-python/astroquery/Manifest
@@ -0,0 +1 @@
+DIST astroquery-0.4.6.tar.gz 6070636 BLAKE2B 9ea912661e3d0ad59ca42087527eeee5657062c39c389a2635e699a5cb683eb6f4324b9c546e227f26e57b645057ad6bde0b2dad7f71cf5f7b090792ca9f4afc SHA512 4ec5e2fbd9754ae0be614011a0020218fbdd7d7cf4511836b40cefcf99fa0feb88cc247c2c83e556aa11ff10930b9e4d7784d175039f9581a4551bb4667a3529
diff --git a/dev-python/astroquery/astroquery-0.4.6.ebuild b/dev-python/astroquery/astroquery-0.4.6.ebuild
new file mode 100644
index 000000000..3e140280c
--- /dev/null
+++ b/dev-python/astroquery/astroquery-0.4.6.ebuild
@@ -0,0 +1,45 @@
+# Copyright 1999-2021 Gentoo Authors
+# Distributed under the terms of the GNU General Public License v2
+
+EAPI=8
+
+PYTHON_COMPAT=( python3_{10..11} )
+DISTUTILS_USE_PEP517=setuptools
+
+inherit distutils-r1 pypi
+
+DESCRIPTION="A collection of packages to access online astronomical resources"
+HOMEPAGE="https://astroquery.readthedocs.io/"
+
+LICENSE="BSD"
+SLOT="0"
+KEYWORDS="~amd64 ~x86"
+
+#TODO: Package all these pytest deps:
+# 	pytest-doctestplus>=0.2.0
+# 	pytest-remotedata>=0.3.1
+# 	pytest-openfiles>=0.3.1
+# 	pytest-astropy-header>=0.1.2
+# 	pytest-arraydiff>=0.1
+# 	pytest-filter-subpackage>=0.1
+RESTRICT="test"
+
+RDEPEND="
+	>=dev-python/astropy-0.2[${PYTHON_USEDEP}]
+	dev-python/beautifulsoup4[${PYTHON_USEDEP}]
+	dev-python/html5lib[${PYTHON_USEDEP}]
+	dev-python/keyring[${PYTHON_USEDEP}]
+	dev-python/numpy[${PYTHON_USEDEP}]
+	dev-python/requests[${PYTHON_USEDEP}]
+	dev-python/six[${PYTHON_USEDEP}]
+"
+
+BDEPEND="test? (
+	dev-python/photutils[${PYTHON_USEDEP}]
+	dev-python/scipy[${PYTHON_USEDEP}]
+)"
+
+# TODO: Fix this
+# NameError: name 'disabled_intersphinx_mapping' is not defined
+#distutils_enable_sphinx docs dev-python/sphinx-astropy
+distutils_enable_tests pytest
diff --git a/dev-python/astroquery/astroquery-9999.ebuild b/dev-python/astroquery/astroquery-9999.ebuild
deleted file mode 100644
index e4afe9319..000000000
--- a/dev-python/astroquery/astroquery-9999.ebuild
+++ /dev/null
@@ -1,68 +0,0 @@
-# Copyright 1999-2014 Gentoo Foundation
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=5
-
-PYTHON_COMPAT=( python{2_7,3_4} )
-inherit distutils-r1
-
-MY_PV=${PV/_/-}
-
-if [ ${PV} == "9999" ] ; then
-	inherit git-r3
-	EGIT_REPO_URI="https://github.com/astropy/${PN}.git"
-else
-	SRC_URI="mirror://pypi/${PN:0:1}/${PN}/${P}.tar.gz"
-	KEYWORDS="~amd64"
-fi
-
-DESCRIPTION="A collection of packages to access online astronomical resources"
-HOMEPAGE="https://github.com/astropy/astroquery"
-
-LICENSE="MIT"
-SLOT="0"
-IUSE="doc"
-DOCS=( README.rst )
-
-RDEPEND="
-	>=dev-python/astropy-0.2[${PYTHON_USEDEP}]
-	dev-python/astropy-helpers[${PYTHON_USEDEP}]
-	dev-python/requests[${PYTHON_USEDEP}]
-	dev-python/numpy[${PYTHON_USEDEP}]
-	dev-python/beautifulsoup:4[${PYTHON_USEDEP}]
-	dev-python/html5lib[${PYTHON_USEDEP}]"
-DEPEND="${RDEPEND}"
-
-S=${WORKDIR}/${PN}-${MY_PV}
-
-python_prepare_all() {
-	distutils-r1_python_prepare_all
-	sed -e '/import ah_bootstrap/d' -i setup.py || die "Removing ah_bootstrap failed"
-}
-
-python_test() {
-	distutils_install_for_testing
-	cd "${TEST_DIR}" || die
-	"${EPYTHON}" -c "import astroquery, sys;r = astroquery.test();sys.exit(r)" \
-		|| die "tests fail with ${EPYTHON}"
-}
-
-python_compile_all() {
-	if use doc; then
-		python_export_best
-		VARTEXFONTS="${T}"/fonts \
-			MPLCONFIGDIR="${BUILD_DIR}" \
-			PYTHONPATH="${BUILD_DIR}"/lib \
-			esetup.py build_sphinx
-	fi
-}
-
-python_install_all() {
-	use doc && local HTML_DOCS=( docs/_build/html/. )
-	distutils-r1_python_install_all
-}
-
-pkg_postinst() {
-	elog "To use the ESO archive web service, dev-python/keyring"
-	elog "must be installed."
-}
diff --git a/dev-python/astroquery/metadata.xml b/dev-python/astroquery/metadata.xml
index bb6a20b51..b70564de2 100644
--- a/dev-python/astroquery/metadata.xml
+++ b/dev-python/astroquery/metadata.xml
@@ -12,5 +12,6 @@ to support many services with a uniform API.
 </longdescription>
 	<upstream>
 		<remote-id type="github">astropy/astroquery</remote-id>
+		<remote-id type="pypi">astroquery</remote-id>
 	</upstream>
 </pkgmetadata>
diff --git a/dev-python/astroscrappy/Manifest b/dev-python/astroscrappy/Manifest
new file mode 100644
index 000000000..e18b6655d
--- /dev/null
+++ b/dev-python/astroscrappy/Manifest
@@ -0,0 +1 @@
+DIST astroscrappy-1.1.0.tar.gz 368489 BLAKE2B d39caedd8a6b4346959c8af8546fee5fc69d41348f1743911af4c6d5755d5e8b6cdf603907d0962807d65a584422eb8c7355ada1b95c11221c735a1c94a24c5a SHA512 f6e8f7aa2eb930c5def05d33f8eb0788b15f53dda0cd583daae262e02d49b4d57e56b46562583aebf25c5e38295a62caf464b797f78deaf07962ebfca8862f8b
diff --git a/dev-python/astroscrappy/astroscrappy-1.1.0-r1.ebuild b/dev-python/astroscrappy/astroscrappy-1.1.0-r1.ebuild
new file mode 100644
index 000000000..cd34136af
--- /dev/null
+++ b/dev-python/astroscrappy/astroscrappy-1.1.0-r1.ebuild
@@ -0,0 +1,29 @@
+# Copyright 1999-2022 Gentoo Authors
+# Distributed under the terms of the GNU General Public License v2
+
+EAPI=8
+
+PYTHON_COMPAT=( python3_{10..11} )
+DISTUTILS_USE_PEP517=setuptools
+
+inherit distutils-r1 pypi
+
+DESCRIPTION="Speedy Cosmic Ray Annihilation Package in Python"
+HOMEPAGE="https://github.com/astropy/astroscrappy"
+
+LICENSE="BSD"
+SLOT="0"
+KEYWORDS="~amd64 ~x86"
+
+#TODO: Fix this
+RESTRICT="test"
+
+RDEPEND="
+	>=dev-python/astropy-2.0[${PYTHON_USEDEP}]
+	dev-python/numpy[${PYTHON_USEDEP}]
+"
+BDEPEND="dev-python/cython[${PYTHON_USEDEP}]"
+
+# Requires self to already be installed
+#distutils_enable_sphinx docs dev-python/sphinx-astropy
+distutils_enable_tests pytest
diff --git a/dev-python/astroscrappy/metadata.xml b/dev-python/astroscrappy/metadata.xml
new file mode 100644
index 000000000..b308f644b
--- /dev/null
+++ b/dev-python/astroscrappy/metadata.xml
@@ -0,0 +1,12 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
+<pkgmetadata>
+	<maintainer type="project">
+		<email>sci-astronomy@gentoo.org</email>
+		<name>Gentoo Astronomy Project</name>
+	</maintainer>
+	<upstream>
+		<remote-id type="github">astropy/astroscrappy</remote-id>
+		<remote-id type="pypi">astroscrappy</remote-id>
+	</upstream>
+</pkgmetadata>
diff --git a/dev-python/av/Manifest b/dev-python/av/Manifest
new file mode 100644
index 000000000..535dd5295
--- /dev/null
+++ b/dev-python/av/Manifest
@@ -0,0 +1 @@
+DIST av-8.0.3.tar.gz 2321046 BLAKE2B 546c79ab638ad3587d51fd8c598eb72d56455209f93163660e1e1dccbb325c86639d22a413c1b4cc6abce4c4f96e59ae0eb505d6a6604a6444895d594a652f7f SHA512 ba09286f0d786b6e697b91279d0ed8c2c241ef4579c1d74f33dcf4fd35a53e3a819dbbf9901183defd9f40921e94d261a129f1af660666bcd30868c6e4b6ec99
diff --git a/dev-python/av/av-8.0.3.ebuild b/dev-python/av/av-8.0.3.ebuild
new file mode 100644
index 000000000..75236266d
--- /dev/null
+++ b/dev-python/av/av-8.0.3.ebuild
@@ -0,0 +1,22 @@
+# Copyright 2020-2021 Gentoo Authors
+# Distributed under the terms of the GNU General Public License v2
+
+EAPI=8
+
+PYTHON_COMPAT=( python3_10 )
+inherit distutils-r1 pypi
+
+DESCRIPTION="Pythonic bindings for FFmpeg's libraries."
+HOMEPAGE="https://github.com/PyAV-Org/PyAV https://pypi.org/project/av/"
+
+LICENSE="BSD"
+SLOT="0"
+KEYWORDS="~amd64 ~x86"
+
+RESTRICT="test"
+
+DEPEND="media-video/ffmpeg"
+
+distutils_enable_tests setup.py
+# The configuration file (or one of the modules it imports) called sys.exit()
+# distutils_enable_sphinx docs
diff --git a/dev-python/av/metadata.xml b/dev-python/av/metadata.xml
new file mode 100644
index 000000000..2231a73ae
--- /dev/null
+++ b/dev-python/av/metadata.xml
@@ -0,0 +1,12 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
+<pkgmetadata>
+	<maintainer type="person">
+		<email>jpizarrocallejas@gmail.com</email>
+		<name>Jorge Pizarro Callejas</name>
+	</maintainer>
+	<upstream>
+		<remote-id type="github">mikeboers/PyAV</remote-id>
+		<remote-id type="pypi">av</remote-id>
+	</upstream>
+</pkgmetadata>
diff --git a/dev-python/awkward-cpp/Manifest b/dev-python/awkward-cpp/Manifest
new file mode 100644
index 000000000..8d27c5f19
--- /dev/null
+++ b/dev-python/awkward-cpp/Manifest
@@ -0,0 +1 @@
+DIST awkward-cpp-28.tar.gz 1422514 BLAKE2B ec87c37a37e3aceb0a35b580122a8c632070dc9fd284e34de66db2611cf1024dbd7ec8a355f52349783258cdaa91e0f966156689c82427f72574230c8b6ae6e1 SHA512 bbe0df527a7863b192c3c85a90c1295d2eb788eb7670a04a001838294dcdd434b49bdc2b4c3f71e34f5f160b4b9cafdea1cf290206fdcb14c0555005797a666d
diff --git a/dev-python/awkward-cpp/awkward-cpp-28.ebuild b/dev-python/awkward-cpp/awkward-cpp-28.ebuild
new file mode 100644
index 000000000..57634d120
--- /dev/null
+++ b/dev-python/awkward-cpp/awkward-cpp-28.ebuild
@@ -0,0 +1,26 @@
+EAPI=8
+
+PYTHON_COMPAT=( python3_{10..12} )
+
+CMAKE_MAKEFILE_GENERATOR="emake"
+DISTUTILS_USE_PEP517=scikit-build-core
+PYPI_NO_NORMALIZE=1
+
+inherit pypi distutils-r1
+
+DESCRIPTION="awkward-cpp bindings for Python"
+HOMEPAGE="https://github.com/scikit-hep/awkward/"
+
+LICENSE="BSD"
+SLOT="0"
+KEYWORDS="~amd64"
+
+DEPEND="
+	>=dev-python/numpy-1.18.0[${PYTHON_USEDEP}]
+"
+RDEPEND="${DEPEND}"
+BDEPEND="
+	>=dev-python/scikit-build-core-0.2.0[${PYTHON_USEDEP}]
+"
+
+distutils_enable_tests pytest
diff --git a/dev-python/awkward-cpp/metadata.xml b/dev-python/awkward-cpp/metadata.xml
new file mode 100644
index 000000000..a94e99f4b
--- /dev/null
+++ b/dev-python/awkward-cpp/metadata.xml
@@ -0,0 +1,19 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
+<pkgmetadata>
+	<maintainer type="project">
+		<email>sci@gentoo.org</email>
+		<name>Gentoo Science Project</name>
+	</maintainer>
+	<maintainer type="person">
+		<email>alexander@neuwirth-informatik.de</email>
+		<name>Alexander Puck Neuwirth</name>
+	</maintainer>
+	<longdescription lang="en">
+	awkward-cpp provides precompiled routines for the awkward package. It is not useful on its own, only as a dependency for awkward .
+	</longdescription>
+	<upstream>
+		<remote-id type="pypi">awkward</remote-id>
+		<remote-id type="github">scikit-hep/awkward</remote-id>
+	</upstream>
+</pkgmetadata>
diff --git a/dev-python/awkward/Manifest b/dev-python/awkward/Manifest
new file mode 100644
index 000000000..d3422fc99
--- /dev/null
+++ b/dev-python/awkward/Manifest
@@ -0,0 +1 @@
+DIST awkward-2.5.2.tar.gz 5561040 BLAKE2B 4799eeb25fa7433b4889328f9f147b435024c3f507ce66b5cbfcfc5b9c50e63f77131a43b8acd3d9f22d20915eaeb129162e26ffa83fd2071b9a393fbc441e7e SHA512 b6f4f2841e642bfc17aaf40779030d125e9737ef0ded20cc8a898c4b8c15c2932f12c8a0bda3e8c48bb8d13729cf97e181866f15913317bd2dba13b0dad6b929
diff --git a/dev-python/awkward/awkward-2.5.2.ebuild b/dev-python/awkward/awkward-2.5.2.ebuild
new file mode 100644
index 000000000..c11095214
--- /dev/null
+++ b/dev-python/awkward/awkward-2.5.2.ebuild
@@ -0,0 +1,38 @@
+EAPI=8
+
+PYTHON_COMPAT=( python3_{10..12} )
+DISTUTILS_USE_PEP517=hatchling
+export SETUPTOOLS_SCM_PRETEND_VERSION=${PV}
+inherit distutils-r1 pypi
+
+DESCRIPTION="Manipulate JSON-like data with NumPy-like idioms."
+HOMEPAGE="https://github.com/scikit-hep/awkward"
+
+LICENSE="BSD"
+SLOT="0"
+KEYWORDS="~amd64"
+
+RDEPEND="
+	>=dev-python/numpy-1.18.0[${PYTHON_USEDEP}]
+	~dev-python/awkward-cpp-28[${PYTHON_USEDEP}]
+"
+DEPEND="${RDEPEND}"
+BDEPEND="
+	dev-python/packaging[${PYTHON_USEDEP}]
+	dev-python/hatch-vcs[${PYTHON_USEDEP}]
+	dev-python/hatch-fancy-pypi-readme[${PYTHON_USEDEP}]
+	test? (
+		dev-libs/apache-arrow[zstd]
+		dev-python/pyarrow[${PYTHON_USEDEP}]
+		dev-python/fsspec[${PYTHON_USEDEP}]
+		dev-python/numexpr[${PYTHON_USEDEP}]
+		dev-python/pandas[${PYTHON_USEDEP}]
+	)
+"
+
+EPYTEST_IGNORE=(
+	tests-cuda/
+	tests-cuda-kernels/
+)
+
+distutils_enable_tests pytest
diff --git a/dev-python/awkward/metadata.xml b/dev-python/awkward/metadata.xml
new file mode 100644
index 000000000..b3ac679d3
--- /dev/null
+++ b/dev-python/awkward/metadata.xml
@@ -0,0 +1,19 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
+<pkgmetadata>
+	<maintainer type="project">
+		<email>sci@gentoo.org</email>
+		<name>Gentoo Science Project</name>
+	</maintainer>
+	<maintainer type="person">
+		<email>alexander@neuwirth-informatik.de</email>
+		<name>Alexander Puck Neuwirth</name>
+	</maintainer>
+	<longdescription lang="en">
+		Awkward Array is a library for nested, variable-sized data, including arbitrary-length lists, records, mixed types, and missing data, using NumPy-like idioms.
+	</longdescription>
+	<upstream>
+		<remote-id type="pypi">awkward</remote-id>
+		<remote-id type="github">scikit-hep/awkward</remote-id>
+	</upstream>
+</pkgmetadata>
diff --git a/dev-python/bcbio-gff/Manifest b/dev-python/bcbio-gff/Manifest
deleted file mode 100644
index bde632d8d..000000000
--- a/dev-python/bcbio-gff/Manifest
+++ /dev/null
@@ -1 +0,0 @@
-DIST bcbio-gff-0.6.4.tar.gz 18516 BLAKE2B 73b0eda2e5dc33b17fd9af110501300cdf46c330f53c1817b30415ce41c53358d4a480170fd74cb94116e7e06e3caf3ed250cfd3b18819aaedecdabe760f2059 SHA512 8dfe654bf6962ef97f7d7ff5932e50425c3c982df9c86c4c6699a19296a338c90dae7c5ea81323c6bfdc82979fa2cddeb0ec2fb0a6ea23c11c65a79177bb8e38
diff --git a/dev-python/bcbio-gff/bcbio-gff-0.6.4.ebuild b/dev-python/bcbio-gff/bcbio-gff-0.6.4.ebuild
deleted file mode 100644
index 8cebbe010..000000000
--- a/dev-python/bcbio-gff/bcbio-gff-0.6.4.ebuild
+++ /dev/null
@@ -1,19 +0,0 @@
-# Copyright 1999-2017 Gentoo Foundation
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=6
-
-PYTHON_COMPAT=( python2_7 python3_5 )
-inherit distutils-r1
-
-DESCRIPTION="Read and write Generic Feature Format (GFF) with Biopython"
-HOMEPAGE="https://pypi.python.org/pypi/bcbio-gff"
-SRC_URI="https://pypi.python.org/packages/94/df/e2d75cc688ac6eb53f5fb4e2cffd240596bbcd5be28bab8d4f6404a6f86c/bcbio-gff-0.6.4.tar.gz"
-
-LICENSE="HPND" # same as biopython
-SLOT="0"
-KEYWORDS="~amd64 ~x86"
-IUSE=""
-
-DEPEND=""
-RDEPEND="${DEPEND}"
diff --git a/dev-python/bcbio-gff/metadata.xml b/dev-python/bcbio-gff/metadata.xml
deleted file mode 100644
index 138cb7705..000000000
--- a/dev-python/bcbio-gff/metadata.xml
+++ /dev/null
@@ -1,12 +0,0 @@
-<?xml version="1.0" encoding="UTF-8"?>
-<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
-<pkgmetadata>
-	<maintainer type="person">
-		<email>mmokrejs@fold.natur.cuni.cz</email>
-		<name>Martin Mokrejs</name>
-	</maintainer>
-	<maintainer type="project">
-		<email>sci-biology@gentoo.org</email>
-		<name>Gentoo Biology Project</name>
-	</maintainer>
-</pkgmetadata>
diff --git a/dev-python/bokeh/Manifest b/dev-python/bokeh/Manifest
new file mode 100644
index 000000000..54357f721
--- /dev/null
+++ b/dev-python/bokeh/Manifest
@@ -0,0 +1,2 @@
+DIST bokeh-2.4.2.tar.gz 17693785 BLAKE2B 295f79032ded6c63b16a1a95fe81e9850e21a5b1962786b8c99836789d4d267eb9bd51cc3b27b01c03944eb481493f61e6925d4c86a4cef67da7f18afd394de3 SHA512 d1939c095f6109d54060f6963dcbe3ff38c5132ac47d8c468b36a78f894454812838a40ae208af2f9723b02d46ae6eb3d77080ca1b19d8153eb73b89afda6864
+DIST conftest-bokeh-2.4.2.py 1788 BLAKE2B f50dd660a1a55338de345db246d493d4f6d8aad339dbe3dee48921575bfe65c0ecf018e759cca095b28b91423833506137e3d6b16a80a954f09ef953c3db495a SHA512 2b76430f09f39282e2e421c3de7f2a1a9bf2968930b729397374c61c2c6c70aa24e34e5d3a0269e8665bd8909642dc32465579e16802f583b3c17f381a7b8768
diff --git a/dev-python/bokeh/bokeh-2.4.2.ebuild b/dev-python/bokeh/bokeh-2.4.2.ebuild
new file mode 100644
index 000000000..7347e5110
--- /dev/null
+++ b/dev-python/bokeh/bokeh-2.4.2.ebuild
@@ -0,0 +1,78 @@
+# Copyright 1999-2022 Gentoo Authors
+# Distributed under the terms of the GNU General Public License v2
+
+EAPI=8
+
+PYTHON_COMPAT=( python3_{10..12} )
+DISTUTILS_USE_PEP517=setuptools
+inherit distutils-r1 optfeature pypi
+
+DESCRIPTION="Statistical and interactive HTML plots for Python"
+HOMEPAGE="https://bokeh.org/"
+SRC_URI+="
+	https://raw.githubusercontent.com/bokeh/bokeh/${PV}/conftest.py -> conftest-${P}.py
+"
+
+LICENSE="BSD"
+SLOT="0"
+KEYWORDS="~amd64 ~x86"
+
+RDEPEND="
+	>=dev-python/jinja-2.9[${PYTHON_USEDEP}]
+	>=dev-python/numpy-1.11.3[${PYTHON_USEDEP}]
+	>=dev-python/packaging-16.8[${PYTHON_USEDEP}]
+	>=dev-python/pillow-7.1.0[${PYTHON_USEDEP}]
+	>=dev-python/pyyaml-3.10[${PYTHON_USEDEP}]
+	>=dev-python/typing-extensions-3.10.0[${PYTHON_USEDEP}]
+	>=dev-python/tornado-5.1[${PYTHON_USEDEP}]
+"
+BDEPEND="
+	test? (
+		dev-python/beautifulsoup4[${PYTHON_USEDEP}]
+		dev-python/flaky[${PYTHON_USEDEP}]
+		dev-python/ipython_genutils[${PYTHON_USEDEP}]
+		dev-python/mock[${PYTHON_USEDEP}]
+		dev-python/networkx[${PYTHON_USEDEP}]
+		dev-python/nbconvert[${PYTHON_USEDEP}]
+		dev-python/nbformat[${PYTHON_USEDEP}]
+		dev-python/pydot[${PYTHON_USEDEP}]
+		dev-python/pytz[${PYTHON_USEDEP}]
+		dev-python/scipy[${PYTHON_USEDEP}]
+		dev-python/selenium[${PYTHON_USEDEP}]
+	)
+"
+
+distutils_enable_tests pytest
+
+python_prepare_all(){
+	cp "${DISTDIR}"/conftest-${P}.py "${S}"/conftest.py || die
+	distutils-r1_python_prepare_all
+}
+
+python_test() {
+	# disable tests having network calls
+	local SKIP_TESTS=" \
+		not (test___init__ and TestWarnings and test_filters) and \
+		not (test_json__subcommands and test_no_script) and \
+		not (test_standalone and Test_autoload_static) and \
+		not test_nodejs_compile_javascript and \
+		not test_nodejs_compile_less and \
+		not test_inline_extension and \
+		not (test_model and test_select) and \
+		not test_tornado__server and \
+		not test_client_server and \
+		not test_webdriver and \
+		not test_export and \
+		not test_server and \
+		not test_bundle and \
+		not test_ext and \
+		not test_detect_current_filename \
+	"
+	epytest -m "not sampledata" tests/unit -k "${SKIP_TESTS}"
+}
+
+pkg_postinst() {
+	optfeature "integration with amazon S3" dev-python/boto
+	optfeature "pypi integration to publish packages" dev-python/twine
+	optfeature "js library usage" net-libs/nodejs
+}
diff --git a/dev-python/bokeh/metadata.xml b/dev-python/bokeh/metadata.xml
new file mode 100644
index 000000000..001fa0793
--- /dev/null
+++ b/dev-python/bokeh/metadata.xml
@@ -0,0 +1,27 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
+<pkgmetadata>
+  <maintainer type="person">
+    <email>gentoo@aisha.cc</email>
+    <name>Aisha Tammy</name>
+  </maintainer>
+  <maintainer type="project">
+    <email>sci@gentoo.org</email>
+    <name>Gentoo Science Project</name>
+  </maintainer>
+  <longdescription lang="en">
+  Bokeh is a Python interactive visualization library for large
+  datasets that natively uses the latest web technologies. Its goal is
+  to provide elegant, concise construction of novel graphics in the
+  style of Protovis/D3, while delivering high-performance
+  interactivity over large data to thin clients.
+  </longdescription>
+  <upstream>
+    <remote-id type="pypi">bokeh</remote-id>
+    <remote-id type="github">bokeh/bokeh</remote-id>
+    <maintainer status="unknown">
+      <email>info@bokeh.org</email>
+      <name>Bokeh</name>
+    </maintainer>
+  </upstream>
+</pkgmetadata>
diff --git a/dev-python/boost-histogram/Manifest b/dev-python/boost-histogram/Manifest
new file mode 100644
index 000000000..1fb711744
--- /dev/null
+++ b/dev-python/boost-histogram/Manifest
@@ -0,0 +1 @@
+DIST boost_histogram-1.4.0.tar.gz 1329002 BLAKE2B 1636ed04c5df2f6c156468ffc0fed7b82469bb903c316b1b9fd209b7072ebb5b0de9969f4f8b50da69db7ee40009df534959db7734f1161da2c6216bddce858b SHA512 e7f61cc2d013a0664646d9edf1f713eb5f06f000ad2105e90229ef9b01b25a08c8e717a2ac241ed990fa2c082a1bb84af18e17b238640de5679d0ab76ff08af6
diff --git a/dev-python/boost-histogram/boost-histogram-1.4.0.ebuild b/dev-python/boost-histogram/boost-histogram-1.4.0.ebuild
new file mode 100644
index 000000000..96950ebe5
--- /dev/null
+++ b/dev-python/boost-histogram/boost-histogram-1.4.0.ebuild
@@ -0,0 +1,39 @@
+EAPI=8
+
+PYTHON_COMPAT=( python3_{10..12} )
+DISTUTILS_USE_PEP517=setuptools
+inherit distutils-r1 pypi
+
+DESCRIPTION="Python bindings for the C++14 Boost::Histogram library"
+HOMEPAGE="https://github.com/scikit-hep/boost-histogram"
+
+LICENSE="BSD"
+SLOT="0"
+KEYWORDS="~amd64"
+
+RDEPEND="
+	dev-libs/boost:=[python,${PYTHON_USEDEP}]
+	dev-python/numpy[${PYTHON_USEDEP}]
+"
+DEPEND="${RDEPEND}"
+BDEPEND="
+	test? (
+		dev-python/cloudpickle[${PYTHON_USEDEP}]
+		dev-python/hypothesis[${PYTHON_USEDEP}]
+	)
+"
+
+src_prepare() {
+	default
+	sed -i 's/"pytest-benchmark"//g' pyproject.toml || die
+}
+
+distutils_enable_tests pytest
+
+EPYTEST_IGNORE=(
+	tests/test_benchmark_1d.py
+	tests/test_benchmark_2d.py
+	tests/test_benchmark_category_axis.py
+	tests/test_pickle.py
+	tests/test_threaded_fill.py
+)
diff --git a/dev-python/boost-histogram/metadata.xml b/dev-python/boost-histogram/metadata.xml
new file mode 100644
index 000000000..345502cba
--- /dev/null
+++ b/dev-python/boost-histogram/metadata.xml
@@ -0,0 +1,19 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
+<pkgmetadata>
+	<maintainer type="project">
+		<email>sci@gentoo.org</email>
+		<name>Gentoo Science Project</name>
+	</maintainer>
+	<maintainer type="person">
+		<email>alexander@neuwirth-informatik.de</email>
+		<name>Alexander Puck Neuwirth</name>
+	</maintainer>
+	<longdescription lang="en">
+	Python bindings for Boost::Histogram (source), a C++14 library. This is one of the fastest libraries for histogramming, while still providing the power of a full histogram object. See what's new.
+	</longdescription>
+	<upstream>
+		<remote-id type="pypi">boost-histogram</remote-id>
+		<remote-id type="github">scikit-hep/boost-histogram</remote-id>
+	</upstream>
+</pkgmetadata>
diff --git a/dev-python/brewer2mpl/Manifest b/dev-python/brewer2mpl/Manifest
deleted file mode 100644
index a22acfba6..000000000
--- a/dev-python/brewer2mpl/Manifest
+++ /dev/null
@@ -1 +0,0 @@
-DIST brewer2mpl-1.4.1.tar.gz 23593 BLAKE2B cceb880b8f2f7d61e60b29da8fbbf62a10be04a5e005576989be17341a3938ac372405f3a0c6fb7495823584315d812dc194563eb4f6aff8be2dcf31a2c9ab3b SHA512 fe522ca7777117f199c4c82b95d299f91da57d061a8594e6bde59f174b2df243434f4e348f920dc50fb99bd4ebdca93622b1a62b8ec6caff6f790b33871b85dd
diff --git a/dev-python/brewer2mpl/brewer2mpl-1.4.1.ebuild b/dev-python/brewer2mpl/brewer2mpl-1.4.1.ebuild
deleted file mode 100644
index b451e52d7..000000000
--- a/dev-python/brewer2mpl/brewer2mpl-1.4.1.ebuild
+++ /dev/null
@@ -1,24 +0,0 @@
-# Copyright 1999-2015 Gentoo Foundation
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=5
-PYTHON_COMPAT=( python{2_7,3_4} )
-
-inherit distutils-r1
-
-DESCRIPTION="Connect colorbrewer2.org color maps to Python and matplotlib"
-HOMEPAGE="https://github.com/jiffyclub/brewer2mpl"
-
-if [ ${PV} == "9999" ] ; then
-	inherit git-r3
-	EGIT_REPO_URI="https://github.com/jiffyclub/${PN}.git git://github.com/jiffyclub/${PN}.git"
-else
-	SRC_URI="mirror://pypi/${PN:0:1}/${PN}/${P}.tar.gz"
-	KEYWORDS="~amd64"
-fi
-
-LICENSE="MIT"
-SLOT="0"
-
-RDEPEND="dev-python/matplotlib[${PYTHON_USEDEP}]"
-DEPEND="${RDEPEND}"
diff --git a/dev-python/brewer2mpl/brewer2mpl-9999.ebuild b/dev-python/brewer2mpl/brewer2mpl-9999.ebuild
deleted file mode 100644
index b451e52d7..000000000
--- a/dev-python/brewer2mpl/brewer2mpl-9999.ebuild
+++ /dev/null
@@ -1,24 +0,0 @@
-# Copyright 1999-2015 Gentoo Foundation
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=5
-PYTHON_COMPAT=( python{2_7,3_4} )
-
-inherit distutils-r1
-
-DESCRIPTION="Connect colorbrewer2.org color maps to Python and matplotlib"
-HOMEPAGE="https://github.com/jiffyclub/brewer2mpl"
-
-if [ ${PV} == "9999" ] ; then
-	inherit git-r3
-	EGIT_REPO_URI="https://github.com/jiffyclub/${PN}.git git://github.com/jiffyclub/${PN}.git"
-else
-	SRC_URI="mirror://pypi/${PN:0:1}/${PN}/${P}.tar.gz"
-	KEYWORDS="~amd64"
-fi
-
-LICENSE="MIT"
-SLOT="0"
-
-RDEPEND="dev-python/matplotlib[${PYTHON_USEDEP}]"
-DEPEND="${RDEPEND}"
diff --git a/dev-python/brewer2mpl/metadata.xml b/dev-python/brewer2mpl/metadata.xml
deleted file mode 100644
index 7cf56d68d..000000000
--- a/dev-python/brewer2mpl/metadata.xml
+++ /dev/null
@@ -1,22 +0,0 @@
-<?xml version="1.0" encoding="UTF-8"?>
-<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
-<pkgmetadata>
-	<maintainer type="person">
-		<email>marbre@linux.sungazer.de</email>
-		<name>Marius Brehler</name>
-	</maintainer>
-	<maintainer type="project">
-		<email>sci@gentoo.org</email>
-		<name>Gentoo Science Project</name>
-	</maintainer>
-	<longdescription>
-brewer2mpl is a pure Python package for accessing colorbrewer2.org
-color maps from Python. With brewer2mpl you can get the raw RGB
-colors of all 165 colorbrewer2.org color maps. The color map data
-ships with brewer2mpl so no internet connection is required.
-</longdescription>
-	<upstream>
-		<remote-id type="github">jiffyclub/brewer2mpl</remote-id>
-		<remote-id type="pypi">brewer2mpl</remote-id>
-	</upstream>
-</pkgmetadata>
diff --git a/dev-python/ccdproc/Manifest b/dev-python/ccdproc/Manifest
new file mode 100644
index 000000000..e952c66af
--- /dev/null
+++ b/dev-python/ccdproc/Manifest
@@ -0,0 +1 @@
+DIST ccdproc-2.3.0.tar.gz 617350 BLAKE2B 750c9690fecd8f02ce0ca46681ac5959aa6a3810f20204b4698418767df63186a3b47f454fa17357c7fb57f6e6e8e06eab456633c05dcb17502773a023d327cc SHA512 bf68d7c98bb3208f3fab44e85a4dc21e64070b12d1b4e78275e1674e99c99d6a9ae1ff6a1bfeba8fd9cb91ec37ddac8ca8ae8c75e6e8ad15b8ddb713f01e4ff6
diff --git a/dev-python/ccdproc/ccdproc-2.3.0.ebuild b/dev-python/ccdproc/ccdproc-2.3.0.ebuild
new file mode 100644
index 000000000..cdbe1c92c
--- /dev/null
+++ b/dev-python/ccdproc/ccdproc-2.3.0.ebuild
@@ -0,0 +1,36 @@
+# Copyright 1999-2023 Gentoo Authors
+# Distributed under the terms of the GNU General Public License v2
+
+EAPI=8
+
+PYTHON_COMPAT=( python3_10 )
+inherit distutils-r1 pypi
+
+DESCRIPTION="Astropy affiliated package for reducing optical/IR CCD data"
+HOMEPAGE="https://github.com/astropy/ccdproc"
+
+LICENSE="BSD"
+SLOT="0"
+KEYWORDS="~amd64 ~x86"
+
+#TODO: Package all these pytest deps:
+# 	pytest-doctestplus>=0.2.0
+# 	pytest-remotedata>=0.3.1
+# 	pytest-openfiles>=0.3.1
+# 	pytest-astropy-header>=0.1.2
+# 	pytest-arraydiff>=0.1
+# 	pytest-filter-subpackage>=0.1
+RESTRICT="test"
+
+BDEPEND="dev-python/setuptools-scm[${PYTHON_USEDEP}]"
+
+RDEPEND="
+	>=dev-python/astropy-4.0.6[${PYTHON_USEDEP}]
+	>=dev-python/astroscrappy-1.0.8[${PYTHON_USEDEP}]
+	>=dev-python/reproject-0.7[${PYTHON_USEDEP}]
+	dev-python/scikit-image[${PYTHON_USEDEP}]
+	dev-python/scipy[${PYTHON_USEDEP}]
+"
+
+distutils_enable_sphinx docs dev-python/sphinx-astropy dev-python/matplotlib dev-python/pytest-doctestplus
+distutils_enable_tests pytest
diff --git a/dev-python/ccdproc/ccdproc-9999.ebuild b/dev-python/ccdproc/ccdproc-9999.ebuild
deleted file mode 100644
index 9e5439180..000000000
--- a/dev-python/ccdproc/ccdproc-9999.ebuild
+++ /dev/null
@@ -1,58 +0,0 @@
-# Copyright 1999-2014 Gentoo Foundation
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=5
-
-PYTHON_COMPAT=( python{2_7,3_4} )
-inherit distutils-r1
-
-if [ ${PV} == "9999" ] ; then
-	inherit git-r3
-	EGIT_REPO_URI="https://github.com/astropy/${PN}.git"
-else
-	SRC_URI="mirror://pypi/${PN:0:1}/${PN}/${P}.tar.gz"
-	KEYWORDS="~amd64"
-fi
-
-DESCRIPTION="Astropy affiliated package for reducing optical/IR CCD data"
-HOMEPAGE="https://github.com/astropy/ccdproc"
-
-LICENSE="BSD"
-SLOT="0"
-IUSE="doc"
-DOCS=( README.rst )
-
-RDEPEND="
-	>=dev-python/astropy-0.4[${PYTHON_USEDEP}]
-	dev-python/astropy-helpers[${PYTHON_USEDEP}]
-	dev-python/numpy[${PYTHON_USEDEP}]
-	sci-libs/scipy[${PYTHON_USEDEP}]"
-
-DEPEND="${RDEPEND}"
-
-python_prepare_all() {
-	distutils-r1_python_prepare_all
-	sed -e '/import ah_bootstrap/d' -i setup.py || die "Removing ah_bootstrap failed"
-}
-
-python_compile_all() {
-	if use doc; then
-		python_export_best
-		VARTEXFONTS="${T}"/fonts \
-			MPLCONFIGDIR="${BUILD_DIR}" \
-			PYTHONPATH="${BUILD_DIR}"/lib \
-			esetup.py build_sphinx
-	fi
-}
-
-python_test() {
-	distutils_install_for_testing
-	cd "${TEST_DIR}" || die
-	"${EPYTHON}" -c "import ${PN}, sys;r = ${PN}.test(verbose=True);sys.exit(r)" \
-		|| die "tests fail with ${EPYTHON}"
-}
-
-python_install_all() {
-	use doc && local HTML_DOCS=( docs/_build/html/. )
-	distutils-r1_python_install_all
-}
diff --git a/dev-python/ccdproc/metadata.xml b/dev-python/ccdproc/metadata.xml
index 387ed8dcd..72370beb3 100644
--- a/dev-python/ccdproc/metadata.xml
+++ b/dev-python/ccdproc/metadata.xml
@@ -12,5 +12,6 @@ and bad pixel tracking through the reduction steps.
 </longdescription>
 	<upstream>
 		<remote-id type="github">astropy/ccdproc</remote-id>
+		<remote-id type="pypi">ccdproc</remote-id>
 	</upstream>
 </pkgmetadata>
diff --git a/dev-python/cligj/Manifest b/dev-python/cligj/Manifest
new file mode 100644
index 000000000..b3e1ca5dd
--- /dev/null
+++ b/dev-python/cligj/Manifest
@@ -0,0 +1 @@
+DIST cligj-0.7.2.tar.gz 9894 BLAKE2B ebd187a6a7108a8d0a7d348fcb1d617402041d050a89209cb6c242bc47a87be953b679101656af9af31fd40947f1a5b3ded567dce9f3e64f425cce7f0f3036c1 SHA512 292c1a6de4ed5d4926ccd71802d369db383d310a3a8590729233448cebe5e9ad9dd6bff0d0c861890102bc9f23e90fe1b9db62275a9263765e3d77436a0b38b4
diff --git a/dev-python/cligj/cligj-0.7.2.ebuild b/dev-python/cligj/cligj-0.7.2.ebuild
new file mode 100644
index 000000000..28e7f5510
--- /dev/null
+++ b/dev-python/cligj/cligj-0.7.2.ebuild
@@ -0,0 +1,20 @@
+# Copyright 1999-2022 Gentoo Authors
+# Distributed under the terms of the GNU General Public License v2
+
+EAPI=8
+
+PYTHON_COMPAT=( python3_{10..11} )
+DISTUTILS_USE_PEP517="setuptools"
+inherit distutils-r1
+
+DESCRIPTION="Library for processing GeoJSON commands"
+HOMEPAGE="https://github.com/mapbox/cligj"
+SRC_URI="https://github.com/mapbox/${PN}/archive/refs/tags/${PV}.tar.gz -> ${P}.tar.gz"
+
+LICENSE="BSD"
+SLOT="0"
+KEYWORDS="~amd64 ~x86"
+
+RDEPEND="dev-python/click[${PYTHON_USEDEP}]"
+
+distutils_enable_tests pytest
diff --git a/dev-python/cligj/metadata.xml b/dev-python/cligj/metadata.xml
new file mode 100644
index 000000000..9afaefe0d
--- /dev/null
+++ b/dev-python/cligj/metadata.xml
@@ -0,0 +1,17 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<!DOCTYPE pkgmetadata SYSTEM "https://www.gentoo.org/dtd/metadata.dtd">
+<pkgmetadata>
+  <maintainer type="project">
+    <email>sci@gentoo.org</email>
+    <name>Gentoo Science Project</name>
+  </maintainer>
+  <longdescription lang="en">
+  cligj is for Python developers who create command line interfaces for 
+  geospatial data. cligj allows you to quickly build consistent, 
+  well-tested and interoperable CLIs for handling GeoJSON.
+</longdescription>
+  <upstream>
+    <remote-id type="github">mapbox/cligj</remote-id>
+    <remote-id type="pypi">cligj</remote-id>
+  </upstream>
+</pkgmetadata>
diff --git a/dev-python/coards/Manifest b/dev-python/coards/Manifest
deleted file mode 100644
index 41127e449..000000000
--- a/dev-python/coards/Manifest
+++ /dev/null
@@ -1 +0,0 @@
-DIST coards-1.0.5.tar.gz 4658 BLAKE2B 2fa3e3b77baf4fa9f1f616bd5cf55de048e4c1642003c6898a8560438b9e91147e74ebf019608e2bec8aa9de7cfedacde41c83e28516023b171e738e0256dac8 SHA512 2659209d1c67fe30df4ae55867b1f33d57ff9647ea2f115a408e3c1390ecc548021c55032360637503fef6c88f9e3635e33c57009b336b1c8f35f319b113dfd8
diff --git a/dev-python/coards/coards-1.0.5.ebuild b/dev-python/coards/coards-1.0.5.ebuild
deleted file mode 100644
index b0a863f08..000000000
--- a/dev-python/coards/coards-1.0.5.ebuild
+++ /dev/null
@@ -1,22 +0,0 @@
-# Copyright 1999-2014 Gentoo Foundation
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=5
-
-PYTHON_COMPAT=( python2_7 )
-
-inherit distutils-r1
-
-DESCRIPTION="Converts COARDS between time specification and a Python datetime object"
-HOMEPAGE="http://dealmeida.net/"
-SRC_URI="mirror://pypi/${PN:0:1}/${PN}/${P}.tar.gz"
-
-LICENSE="MIT"
-SLOT="0"
-KEYWORDS="~amd64 ~x86"
-IUSE=""
-
-DEPEND="dev-python/setuptools[${PYTHON_USEDEP}]"
-RDEPEND=""
-
-DOCS=( README.rst NEWS.txt )
diff --git a/dev-python/coards/metadata.xml b/dev-python/coards/metadata.xml
deleted file mode 100644
index e36ff5368..000000000
--- a/dev-python/coards/metadata.xml
+++ /dev/null
@@ -1,15 +0,0 @@
-<?xml version="1.0" encoding="UTF-8"?>
-<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
-<pkgmetadata>
-	<maintainer type="person">
-		<email>tim@cerazone.net</email>
-		<name>Tim Cera</name>
-	</maintainer>
-	<longdescription lang="en">
-This module converts between a given COARDS time specification and a Python 
-datetime object, which is much more useful.
-</longdescription>
-	<upstream>
-		<remote-id type="pypi">coards</remote-id>
-	</upstream>
-</pkgmetadata>
diff --git a/dev-python/colorcet/Manifest b/dev-python/colorcet/Manifest
new file mode 100644
index 000000000..a743f1d71
--- /dev/null
+++ b/dev-python/colorcet/Manifest
@@ -0,0 +1 @@
+DIST colorcet-3.0.1.tar.gz 3036207 BLAKE2B fabdd32dafc1828d50236ec93aa78e46aa125fe3564e732c2ece203cb71578d2d23303ccb2d069c938f513bd7df6a35f692b74b0c692546544f9e04fc28e9cae SHA512 92ede4947ef3af8b8cc3a4822c0e738cc8f0730fafb9f58a4a2c9bd3cda9c1e6ed254b9eec92f0306de95643eccd644b8ad955bc079ad20c00ee62e5f611431e
diff --git a/dev-python/colorcet/colorcet-3.0.1.ebuild b/dev-python/colorcet/colorcet-3.0.1.ebuild
new file mode 100644
index 000000000..08ea7d55a
--- /dev/null
+++ b/dev-python/colorcet/colorcet-3.0.1.ebuild
@@ -0,0 +1,27 @@
+# Copyright 1999-2023 Gentoo Authors
+# Distributed under the terms of the GNU General Public License v2
+
+EAPI=8
+
+# Portage incorrectly claims "DISTUTILS_USE_SETUPTOOLS value is probably
+# incorrect" for this package. It isn't. This package imports from neither
+# "distutils", "packaging", "pkg_resources", nor "setuptools" at runtime.
+PYTHON_COMPAT=( python3_{10..11} pypy3 )
+DISTUTILS_USE_PEP517=setuptools
+
+inherit distutils-r1 pypi
+
+DESCRIPTION="Collection of perceptually uniform colormaps"
+HOMEPAGE="https://holoviz.org"
+
+LICENSE="BSD"
+SLOT="0"
+KEYWORDS="~amd64 ~x86"
+
+DEPEND="
+	>=dev-python/param-1.7.0[${PYTHON_USEDEP}]
+	>=dev-python/pyct-0.4.4[${PYTHON_USEDEP}]
+"
+RDEPEND="${DEPEND}"
+
+distutils_enable_tests pytest
diff --git a/dev-python/colorcet/metadata.xml b/dev-python/colorcet/metadata.xml
new file mode 100644
index 000000000..61393b576
--- /dev/null
+++ b/dev-python/colorcet/metadata.xml
@@ -0,0 +1,13 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
+<pkgmetadata>
+	<maintainer type="project">
+		<email>sci@gentoo.org</email>
+		<name>Gentoo Science Project</name>
+	</maintainer>
+	<stabilize-allarches/>
+	<upstream>
+		<remote-id type="pypi">colorcet</remote-id>
+		<remote-id type="github">holoviz/colorcet</remote-id>
+	</upstream>
+</pkgmetadata>
diff --git a/dev-python/colormath/Manifest b/dev-python/colormath/Manifest
new file mode 100644
index 000000000..82abf9e32
--- /dev/null
+++ b/dev-python/colormath/Manifest
@@ -0,0 +1 @@
+DIST colormath-3.0.0.tar.gz 39761 BLAKE2B 3c7cdd08336a3ab35618a79ad31717433c08b23d8ee4fc5484da7305395fce61fa442fc9ff979ff107808c56e809deca9d176677f17106651047be14edc27e9e SHA512 12d1ab931000dadb087fdf7e56280690ff51a299e976347026703eac83373edcacd3310255fd52e05d842aab54d4f7d3ed19deda8db4b78574a7273f1c8cc058
diff --git a/dev-python/colormath/colormath-3.0.0.ebuild b/dev-python/colormath/colormath-3.0.0.ebuild
new file mode 100644
index 000000000..8bd5a2b02
--- /dev/null
+++ b/dev-python/colormath/colormath-3.0.0.ebuild
@@ -0,0 +1,23 @@
+# Copyright 1999-2023 Gentoo Authors
+# Distributed under the terms of the GNU General Public License v2
+
+EAPI=8
+
+DISTUTILS_USE_PEP517=setuptools
+PYTHON_COMPAT=( python3_{10..12} )
+
+inherit pypi distutils-r1
+
+DESCRIPTION="Easy color scales and color conversion for Python"
+HOMEPAGE="https://pypi.org/project/colormath/"
+
+LICENSE="BSD"
+SLOT="0"
+KEYWORDS="~amd64 ~amd64-linux"
+
+RDEPEND="dev-python/networkx[${PYTHON_USEDEP}]
+	dev-python/numpy[${PYTHON_USEDEP}]"
+
+# Nose test no longer supported
+RESTRICT="test"
+#distutils_enable_tests nose
diff --git a/dev-python/colormath/metadata.xml b/dev-python/colormath/metadata.xml
new file mode 100644
index 000000000..a633acfa0
--- /dev/null
+++ b/dev-python/colormath/metadata.xml
@@ -0,0 +1,12 @@
+<?xml version='1.0' encoding='UTF-8'?>
+<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
+<pkgmetadata>
+	<maintainer type="person">
+		<email>mschu.dev@gmail.com</email>
+		<name>Michael Schubert</name>
+	</maintainer>
+	<upstream>
+		<remote-id type="github">gtaylor/python-colormath</remote-id>
+		<remote-id type="pypi">colormath</remote-id>
+	</upstream>
+</pkgmetadata>
diff --git a/dev-python/connection_pool/Manifest b/dev-python/connection_pool/Manifest
new file mode 100644
index 000000000..3e0ede4f4
--- /dev/null
+++ b/dev-python/connection_pool/Manifest
@@ -0,0 +1 @@
+DIST connection_pool-0.0.3.tar.gz 3795 BLAKE2B 6a391b739f2727c69abad3ad95635aef7fa542f86b0f4c8a440ae28dee1af80d3af022733685f8e671ed3be479db291b2f763424b746c0918faf991c4b830981 SHA512 a628608f4b57156b2f3f036ccbc620d9ba457f5958d907fa8749dd8df83a167654efd04f411e20436cf1958d9cf6b3f49bf0a11703bfc8d85332d5fc93b13183
diff --git a/dev-python/connection_pool/connection_pool-0.0.3.ebuild b/dev-python/connection_pool/connection_pool-0.0.3.ebuild
new file mode 100644
index 000000000..96d3c1f62
--- /dev/null
+++ b/dev-python/connection_pool/connection_pool-0.0.3.ebuild
@@ -0,0 +1,16 @@
+# Copyright 1999-2021 Gentoo Authors
+# Distributed under the terms of the GNU General Public License v2
+
+EAPI=8
+
+PYTHON_COMPAT=( python3_{10..11} )
+DISTUTILS_USE_PEP517=setuptools
+
+inherit distutils-r1 pypi
+
+DESCRIPTION="Thread safe connection pool"
+HOMEPAGE="https://github.com/zhouyl/ConnectionPool"
+
+LICENSE="MIT"
+SLOT="0"
+KEYWORDS="~amd64"
diff --git a/dev-python/connection_pool/metadata.xml b/dev-python/connection_pool/metadata.xml
new file mode 100644
index 000000000..efc2a5c9e
--- /dev/null
+++ b/dev-python/connection_pool/metadata.xml
@@ -0,0 +1,12 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
+<pkgmetadata>
+	<maintainer type="project">
+		<email>sci@gentoo.org</email>
+		<name>Gentoo Science Project</name>
+	</maintainer>
+	<upstream>
+		<remote-id type="github">zhouyl/ConnectionPool</remote-id>
+		<remote-id type="pypi">connection_pool</remote-id>
+	</upstream>
+</pkgmetadata>
diff --git a/dev-python/coords/Manifest b/dev-python/coords/Manifest
deleted file mode 100644
index 905d6a94e..000000000
--- a/dev-python/coords/Manifest
+++ /dev/null
@@ -1 +0,0 @@
-DIST coords-0.37.tar.gz 736179 BLAKE2B 70351db789b9abd8637760b9de0f520d395910129433b1e746684fbac786374ce477e3fd50092c650fec856d1a2658a044bc94acb6208b3e01bef5ee7c6b9b8f SHA512 5989a9ec919bf3575dae3cd8a62c58b885ce97eb71ebf13431596f31b9fc7950dccfc6f54a6180c4400cefb2dba7d1f28a64ac80252d4b242092e9c6cb0e7587
diff --git a/dev-python/coords/coords-0.37.ebuild b/dev-python/coords/coords-0.37.ebuild
deleted file mode 100644
index d61e1103d..000000000
--- a/dev-python/coords/coords-0.37.ebuild
+++ /dev/null
@@ -1,24 +0,0 @@
-# Copyright 1999-2014 Gentoo Foundation
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=5
-
-PYTHON_COMPAT=( python2_7 )
-
-inherit distutils-r1
-
-DESCRIPTION="Managing astronomical coordinate systems"
-HOMEPAGE="https://trac6.assembla.com/astrolib/wiki/"
-SRC_URI="http://stsdas.stsci.edu/astrolib/${P}.tar.gz"
-
-LICENSE="AURA"
-SLOT="0"
-KEYWORDS="~amd64 ~x86"
-IUSE=""
-
-DEPEND=""
-RDEPEND="dev-python/numpy[${PYTHON_USEDEP}]"
-
-python_test() {
-	"${PYTHON}" -c "import coords as C; print C._test()" || die
-}
diff --git a/dev-python/coords/metadata.xml b/dev-python/coords/metadata.xml
deleted file mode 100644
index cba3ccd1c..000000000
--- a/dev-python/coords/metadata.xml
+++ /dev/null
@@ -1,12 +0,0 @@
-<?xml version="1.0" encoding="UTF-8"?>
-<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
-<pkgmetadata>
-	<maintainer type="project">
-		<email>sci-astronomy@gentoo.org</email>
-		<name>Gentoo Astronomy Project</name>
-	</maintainer>
-	<longdescription lang="en">
-coords is a part of Astrolib and provide a set of routines for managing 
-astronomical coordinate systems
-</longdescription>
-</pkgmetadata>
diff --git a/dev-python/cosmocalc/Manifest b/dev-python/cosmocalc/Manifest
deleted file mode 100644
index e0f8d4391..000000000
--- a/dev-python/cosmocalc/Manifest
+++ /dev/null
@@ -1 +0,0 @@
-DIST cosmocalc-0.1.2.tar.gz 4830 BLAKE2B da0ecbcde245522f6599afe7d149b291efdd4e8b6b0d69fb07b882f845cf5403a7fb81fac733b7d2fc7ea03586876278ffb9ee77ef835c6f20ab63d2ce2029ab SHA512 64c5b10688c468f88083fb56d5f5a8df310f3a4e3585c7713cb09ec8f8641392a94fd184c224559acc988a99bd98a36f137f0177c96b04cce00cd6ccb42aaf95
diff --git a/dev-python/cosmocalc/cosmocalc-0.1.2-r1.ebuild b/dev-python/cosmocalc/cosmocalc-0.1.2-r1.ebuild
deleted file mode 100644
index c867a6dc2..000000000
--- a/dev-python/cosmocalc/cosmocalc-0.1.2-r1.ebuild
+++ /dev/null
@@ -1,23 +0,0 @@
-# Copyright 1999-2014 Gentoo Foundation
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=5
-
-PYTHON_COMPAT=( python{2_7,3_3} )
-
-inherit distutils-r1
-
-DESCRIPTION="Simple cosmology python module"
-HOMEPAGE="http://cxc.harvard.edu/contrib/cosmocalc/ http://pypi.python.org/pypi/cosmocalc/"
-SRC_URI="http://cxc.harvard.edu/contrib/cosmocalc/downloads/${P}.tar.gz"
-
-LICENSE="GPL-2"
-SLOT="0"
-KEYWORDS="~amd64 ~x86"
-IUSE=""
-
-python_compile() {
-	distutils-r1_python_compile
-	[[ "${PYTHON}" =~ python2 ]] && return
-	2to3 -nw --no-diffs "${BUILD_DIR}" || die
-}
diff --git a/dev-python/cosmocalc/metadata.xml b/dev-python/cosmocalc/metadata.xml
deleted file mode 100644
index 75645dd98..000000000
--- a/dev-python/cosmocalc/metadata.xml
+++ /dev/null
@@ -1,13 +0,0 @@
-<?xml version="1.0" encoding="UTF-8"?>
-<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
-<pkgmetadata>
-	<maintainer type="project">
-		<email>sci-astronomy@gentoo.org</email>
-		<name>Gentoo Astronomy Project</name>
-	</maintainer>
-	<longdescription lang="en">
-Calculate useful values for a given cosmology. This module uses code
-adapted from CC.py (James Schombert) which is a Python version of
-the Cosmology Calculator (Ned Wright).
-</longdescription>
-</pkgmetadata>
diff --git a/dev-python/cymbal/Manifest b/dev-python/cymbal/Manifest
new file mode 100644
index 000000000..600b61b10
--- /dev/null
+++ b/dev-python/cymbal/Manifest
@@ -0,0 +1 @@
+DIST cymbal-1.0.0.tar.gz 4145 BLAKE2B b6da0ce4e32f19f0a91c7e4d917b13c64f1d0d9b37503962b5d73f6b00a37a54637c5d4ebf95d64952e32df2e7652076bde37a51dc316549775c59ea2ab50bb3 SHA512 0bd6bf5996787c5e24d9f9266654b4a501d5479dd1444d064c6a2241ce3e39ddbc12552f4cf22c03e61ba47f0492dc8a6515bb934bcc3523b5a29cb1a4530348
diff --git a/dev-python/cymbal/cymbal-1.0.0.ebuild b/dev-python/cymbal/cymbal-1.0.0.ebuild
new file mode 100644
index 000000000..c5d9eec8e
--- /dev/null
+++ b/dev-python/cymbal/cymbal-1.0.0.ebuild
@@ -0,0 +1,32 @@
+# Copyright 1999-2021 Gentoo Authors
+# Distributed under the terms of the GNU General Public License v2
+
+EAPI=8
+
+PYTHON_COMPAT=( python3_10 )
+inherit distutils-r1 pypi
+
+DESCRIPTION="Add functionality missing from the python libclang bindings"
+HOMEPAGE="https://pypi.org/project/cymbal/"
+
+LICENSE="MIT"
+SLOT="0"
+KEYWORDS="~amd64 ~x86"
+
+DEPEND="dev-python/clang-python[${PYTHON_USEDEP}]"
+RDEPEND="${DEPEND}"
+
+distutils_enable_tests pytest
+
+# Prevent "setup.py" from installing the "tests" package.
+src_prepare() {
+	sed -i -e 's~\(packages     = \)find_packages(),~\1["cymbal"],~' \
+		setup.py || die
+
+	default_src_prepare
+}
+
+# Omit "test_class_template_arg", failing due to outdated clang assumptions.
+python_test() {
+	pytest -k 'not test_class_template_arg' || die
+}
diff --git a/dev-python/cymbal/metadata.xml b/dev-python/cymbal/metadata.xml
new file mode 100644
index 000000000..02975a0d9
--- /dev/null
+++ b/dev-python/cymbal/metadata.xml
@@ -0,0 +1,13 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
+<pkgmetadata>
+	<maintainer type="project">
+		<email>sci@gentoo.org</email>
+		<name>Gentoo Science Project</name>
+	</maintainer>
+	<stabilize-allarches/>
+	<upstream>
+		<remote-id type="pypi">cymbal</remote-id>
+		<remote-id type="github">AndrewWalker/cymbal</remote-id>
+	</upstream>
+</pkgmetadata>
diff --git a/dev-python/dandi-schema/Manifest b/dev-python/dandi-schema/Manifest
new file mode 100644
index 000000000..acdfa9d63
--- /dev/null
+++ b/dev-python/dandi-schema/Manifest
@@ -0,0 +1 @@
+DIST dandi-schema-0.9.1.gh.tar.gz 61794 BLAKE2B f18dda919dad9a685793d075e54c798fd9a0d68926b776f1f5617d414554fed7609684dab3311d35056f385443037f03ab16f7edfb7b57c33f9da1aed9c8016c SHA512 c6ed9763a5a77b8741063ef5f311a889e7e0ba2ef02ab97e2912e1a129da503453d9ccb1b9ed13726f071594af42e564986ef9298b21c07cff6ef48eb3f58fc1
diff --git a/dev-python/dandi-schema/dandi-schema-0.9.1.ebuild b/dev-python/dandi-schema/dandi-schema-0.9.1.ebuild
new file mode 100644
index 000000000..0e7986806
--- /dev/null
+++ b/dev-python/dandi-schema/dandi-schema-0.9.1.ebuild
@@ -0,0 +1,49 @@
+# Copyright 1999-2023 Gentoo Authors
+# Distributed under the terms of the GNU General Public License v2
+
+EAPI=8
+
+DISTUTILS_USE_PEP517=setuptools
+PYTHON_COMPAT=( python3_{10..12} )
+
+inherit distutils-r1
+
+DESCRIPTION="Schemata for DANDI archive project"
+HOMEPAGE="https://github.com/dandi/dandi-schema"
+SRC_URI="https://github.com/dandi/dandi-schema/archive/refs/tags/${PV}.tar.gz -> ${P}.gh.tar.gz"
+
+LICENSE="Apache-2.0"
+SLOT="0"
+KEYWORDS="~amd64 ~x86"
+
+# Package has pydantic version restriction (2.4*), which, however, breaks the test suite:
+# https://github.com/dandi/dandi-schema/issues/228
+# Commented failing tests with upstream version restriction listed below.
+RDEPEND="
+	dev-python/wheel[${PYTHON_USEDEP}]
+	dev-python/jsonschema[${PYTHON_USEDEP}]
+	>=dev-python/pydantic-2.5[${PYTHON_USEDEP}]
+	dev-python/email-validator[${PYTHON_USEDEP}]
+	dev-python/requests[${PYTHON_USEDEP}]
+"
+
+PATCHES=(
+	"${FILESDIR}/${P}-coverage.patch"
+)
+
+src_configure() {
+	echo "__version__ = '${PV}'" >> dandischema/_version.py
+}
+
+#EPYTEST_DESELECT=(
+#	"dandischema/tests/test_metadata.py::test_asset"
+#	"dandischema/tests/test_metadata.py::test_aggregate[files1-summary1]"
+#	"dandischema/tests/test_metadata.py::test_aggregate[files2-summary2]"
+#)
+
+distutils_enable_tests pytest
+
+python_test() {
+	export DANDI_TESTS_NONETWORK=1
+	epytest dandischema
+}
diff --git a/dev-python/dandi-schema/files/dandi-schema-0.3.4-coverage.patch b/dev-python/dandi-schema/files/dandi-schema-0.3.4-coverage.patch
new file mode 100644
index 000000000..a9c7b6c2b
--- /dev/null
+++ b/dev-python/dandi-schema/files/dandi-schema-0.3.4-coverage.patch
@@ -0,0 +1,11 @@
+--- a/tox.ini	2021-09-22 19:31:20.534576095 -0400
++++ b/tox.ini	2021-09-26 16:11:30.080164191 -0400
+@@ -17,7 +17,7 @@
+     flake8 --config=setup.cfg {posargs} dandischema setup.py
+
+ [pytest]
+-addopts = --cov=dandischema --tb=short --durations=10
++addopts = --tb=short --durations=10
+ filterwarnings = error
+
+ [coverage:run]
diff --git a/dev-python/dandi-schema/files/dandi-schema-0.9.1-coverage.patch b/dev-python/dandi-schema/files/dandi-schema-0.9.1-coverage.patch
new file mode 100644
index 000000000..7f9b7dba0
--- /dev/null
+++ b/dev-python/dandi-schema/files/dandi-schema-0.9.1-coverage.patch
@@ -0,0 +1,13 @@
+diff --git a/tox.ini b/tox.ini
+index c32f3b9..d552c6c 100644
+--- a/tox.ini
++++ b/tox.ini
+@@ -30,7 +30,7 @@ commands =
+     mypy dandischema
+ 
+ [pytest]
+-addopts = --cov=dandischema --tb=short --durations=10
++addopts = --tb=short --durations=10
+ filterwarnings =
+     error
+     # <https://github.com/dateutil/dateutil/issues/1284>
diff --git a/dev-python/dandi-schema/metadata.xml b/dev-python/dandi-schema/metadata.xml
new file mode 100644
index 000000000..91cb893fc
--- /dev/null
+++ b/dev-python/dandi-schema/metadata.xml
@@ -0,0 +1,26 @@
+<?xml version='1.0' encoding='UTF-8'?>
+<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
+<pkgmetadata>
+	<maintainer type="person">
+		<email>gentoo@chymera.eu</email>
+		<name>Horea Christian</name>
+	</maintainer>
+	<maintainer type="project">
+		<email>sci@gentoo.org</email>
+		<name>Gentoo Science Project</name>
+	</maintainer>
+	<longdescription lang="en">
+		A Python library for maintaining and managing DANDI metadata schemata.
+		The library helps create and validate DANDI schema-compliant metadata
+		for Dandisets and assets. Every Dandiset and associated asset has a
+		metadata object that can be retrieved using the DANDI API. This
+		library uses Pydantic to implement all the metadata classes. Schemas
+		are generated on schema modifications and placed into this repository.
+		Dandischema generates JSON schema definitions and also an associated
+		context.json file for JSON-LD compliance of the metadata models.
+	</longdescription>
+	<upstream>
+		<remote-id type="github">dandi/dandi-schema</remote-id>
+		<remote-id type="pypi">dandischema</remote-id>
+	</upstream>
+</pkgmetadata>
diff --git a/dev-python/datrie/Manifest b/dev-python/datrie/Manifest
new file mode 100644
index 000000000..2214acc5c
--- /dev/null
+++ b/dev-python/datrie/Manifest
@@ -0,0 +1 @@
+DIST datrie-0.8.2.tar.gz 63278 BLAKE2B 1f58058900c8987ace02d09b893c7df677cdbf7d17d77a2dca8b40f8f6b87d3ddd66b2bda9433afaf092d841e7025d628078976fbd85de469328d013d357db70 SHA512 db1aaa5c50fa4fb6f8abb80200b4b68b05b42e490364b63576492c44ae4208867cbd0ef0dd64ff5a932c6462cd60f41f339d85ac58ade47ef34d34f4f1cf68c6
diff --git a/dev-python/datrie/datrie-0.8.2-r1.ebuild b/dev-python/datrie/datrie-0.8.2-r1.ebuild
new file mode 100644
index 000000000..e8f9f9336
--- /dev/null
+++ b/dev-python/datrie/datrie-0.8.2-r1.ebuild
@@ -0,0 +1,32 @@
+# Copyright 1999-2021 Gentoo Authors
+# Distributed under the terms of the GNU General Public License v2
+
+EAPI=8
+
+PYTHON_COMPAT=( python3_{10..11} )
+# Fails to compile with pep517
+#DISTUTILS_USE_PEP517=setuptools
+
+inherit distutils-r1 pypi
+
+DESCRIPTION="Implements a topological sort algorithm"
+HOMEPAGE="https://github.com/pytries/datrie"
+
+LICENSE="LGPL-2+"
+SLOT="0"
+KEYWORDS="~amd64 ~x86"
+
+BDEPEND="
+	dev-python/cython[${PYTHON_USEDEP}]
+	test? (
+		dev-python/hypothesis[${PYTHON_USEDEP}]
+	)
+"
+
+distutils_enable_tests pytest
+
+python_prepare_all() {
+	# do not depend on pytest-runner
+	sed -i "/pytest-runner/d" setup.py || die
+	distutils-r1_python_prepare_all
+}
diff --git a/dev-python/datrie/metadata.xml b/dev-python/datrie/metadata.xml
new file mode 100644
index 000000000..a399a3d31
--- /dev/null
+++ b/dev-python/datrie/metadata.xml
@@ -0,0 +1,12 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
+<pkgmetadata>
+	<maintainer type="project">
+		<email>sci@gentoo.org</email>
+		<name>Gentoo Science Project</name>
+	</maintainer>
+	<upstream>
+		<remote-id type="github">pytries/datrie</remote-id>
+		<remote-id type="pypi">datrie</remote-id>
+	</upstream>
+</pkgmetadata>
diff --git a/dev-python/delegator/Manifest b/dev-python/delegator/Manifest
new file mode 100644
index 000000000..674027f35
--- /dev/null
+++ b/dev-python/delegator/Manifest
@@ -0,0 +1 @@
+DIST delegator.py-0.1.1.tar.gz 6260 BLAKE2B 2a5c70aa0e07390e801e69ba4ce130ea8da8d98f9dc6bc43e34fdf19386c0402c1d5ba128878c9c7b3bda9f99eeb6aab1b26160e8dab5a4945b411a7dffc9dcb SHA512 7af16f553fafc272056b1bd715ff41c821e0eeccfd6c5e5dcec819333373c9f7daaa95afe9b9aa796244f280869ccb1ddacb075b9fa196ed47a6699096abc143
diff --git a/dev-python/delegator/delegator-0.1.1.ebuild b/dev-python/delegator/delegator-0.1.1.ebuild
new file mode 100644
index 000000000..0a22057ef
--- /dev/null
+++ b/dev-python/delegator/delegator-0.1.1.ebuild
@@ -0,0 +1,20 @@
+# Copyright 1999-2023 Gentoo Authors
+# Distributed under the terms of the GNU General Public License v2
+
+EAPI=8
+
+PYTHON_COMPAT=( python3_{10..11} )
+PYPI_NO_NORMALIZE=1
+PYPI_PN=delegator.py
+inherit distutils-r1 pypi
+
+DESCRIPTION="Subprocesses for Humans 2.0."
+HOMEPAGE="https://github.com/amitt001/delegator.py"
+
+LICENSE="MIT"
+SLOT="0"
+KEYWORDS="~amd64 ~x86"
+
+RDEPEND="dev-python/pexpect[${PYTHON_USEDEP}]"
+
+S="${WORKDIR}/${PN}.py-${PV}"
diff --git a/dev-python/delegator/metadata.xml b/dev-python/delegator/metadata.xml
new file mode 100644
index 000000000..57368da50
--- /dev/null
+++ b/dev-python/delegator/metadata.xml
@@ -0,0 +1,16 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
+<pkgmetadata>
+	<maintainer type="person">
+		<email>gentoo@chymera.eu</email>
+		<name>Horea Christian</name>
+	</maintainer>
+	<maintainer type="project">
+		<email>sci@gentoo.org</email>
+		<name>Gentoo Science Project</name>
+	</maintainer>
+	<upstream>
+		<remote-id type="github">amitt001/delegator.py</remote-id>
+		<remote-id type="pypi">delegator.py</remote-id>
+	</upstream>
+</pkgmetadata>
diff --git a/dev-python/dijitso/Manifest b/dev-python/dijitso/Manifest
deleted file mode 100644
index 51877e8e3..000000000
--- a/dev-python/dijitso/Manifest
+++ /dev/null
@@ -1,2 +0,0 @@
-DIST dijitso-2016.2.0.tar.gz 50947 BLAKE2B 7f7a8feff5f3331601707deca74d313e756b8c8481c64dd41f3f765ed3fc311addb6f1b59eff5cd1eab35b1633604ced321b7defea26101875be6cc34d086c93 SHA512 adae206e2c484db9b373bcf67f974147e3e9196ec4af12cd02cf1698eff3eeb0b1b67ad36383e3588b025844e0437f0f03b701a5c83178f40ee5817f0b47b24a
-DIST dijitso-2017.1.0.tar.gz 51223 BLAKE2B dd36d97ae3051779a4a21f277fddd02460f3572029b70a1fa5a799a54749cbd807bf9e12a41f2138cc917dfa3ea43368a96bb079dc2e99b6be6900f735e425ce SHA512 994c3d88ca207b3d3065f9376546580492a06eda51a340fc16bbd768248dc26a2984af064e9d970657509b003e403db329aea9ca9cca2f428764b7ec0a367040
diff --git a/dev-python/dijitso/dijitso-2016.2.0.ebuild b/dev-python/dijitso/dijitso-2016.2.0.ebuild
deleted file mode 100644
index fb0bc43bd..000000000
--- a/dev-python/dijitso/dijitso-2016.2.0.ebuild
+++ /dev/null
@@ -1,19 +0,0 @@
-# Copyright 1999-2017 Gentoo Foundation
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=6
-
-PYTHON_COMPAT=( python2_7 )
-
-inherit distutils-r1
-
-DESCRIPTION="Python module for distributed just-in-time shared library building"
-HOMEPAGE="https://bitbucket.org/fenics-project/dijitso/"
-SRC_URI="https://bitbucket.org/fenics-project/dijitso/downloads/${P}.tar.gz"
-
-LICENSE="GPL-3"
-SLOT="0"
-KEYWORDS="~amd64 ~x86"
-IUSE=""
-
-RDEPEND="dev-python/mpi4py"
diff --git a/dev-python/dijitso/dijitso-2017.1.0.ebuild b/dev-python/dijitso/dijitso-2017.1.0.ebuild
deleted file mode 100644
index cea6e39ff..000000000
--- a/dev-python/dijitso/dijitso-2017.1.0.ebuild
+++ /dev/null
@@ -1,19 +0,0 @@
-# Copyright 1999-2017 Gentoo Foundation
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=6
-
-PYTHON_COMPAT=( python3_4 python3_5 python3_6 )
-
-inherit distutils-r1
-
-DESCRIPTION="Python module for distributed just-in-time shared library building"
-HOMEPAGE="https://bitbucket.org/fenics-project/dijitso/"
-SRC_URI="https://bitbucket.org/fenics-project/dijitso/downloads/${P}.tar.gz"
-
-LICENSE="GPL-3"
-SLOT="0"
-KEYWORDS="~amd64 ~x86"
-IUSE=""
-
-RDEPEND="dev-python/mpi4py"
diff --git a/dev-python/dijitso/metadata.xml b/dev-python/dijitso/metadata.xml
deleted file mode 100644
index 483c5a2ef..000000000
--- a/dev-python/dijitso/metadata.xml
+++ /dev/null
@@ -1,17 +0,0 @@
-<?xml version="1.0" encoding="UTF-8"?>
-<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
-<pkgmetadata>
-	<maintainer type="project">
-		<email>sci@gentoo.org</email>
-		<name>Gentoo Science Project</name>
-	</maintainer>
-	<longdescription lang="en">
-This module was written to improve a core component of the FEniCS
-framework, namely the just in time compilation of C++ code that is
-generated from Python modules, but is only called from within a C++
-library, and thus do not need wrapping in a nice Python interface.
-</longdescription>
-	<upstream>
-		<remote-id type="bitbucket">fenics-project/dijitso</remote-id>
-	</upstream>
-</pkgmetadata>
diff --git a/dev-python/dimensionful/dimensionful-9999.ebuild b/dev-python/dimensionful/dimensionful-9999.ebuild
deleted file mode 100644
index ec392a1df..000000000
--- a/dev-python/dimensionful/dimensionful-9999.ebuild
+++ /dev/null
@@ -1,28 +0,0 @@
-# Copyright 1999-2014 Gentoo Foundation
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=5
-
-PYTHON_COMPAT=( python2_7 )
-
-inherit distutils-r1 git-r3
-
-DESCRIPTION="A simple library for making your data dimensionful"
-HOMEPAGE="https://github.com/caseywstark/dimensionful"
-SRC_URI=""
-EGIT_REPO_URI="git://github.com/caseywstark/dimensionful.git"
-
-LICENSE="BSD-2"
-SLOT="0"
-KEYWORDS=""
-IUSE=""
-
-DEPEND=""
-RDEPEND="dev-python/sympy[${PYTHON_USEDEP}]"
-
-python_test() {
-	local t
-	for t in test/test_*.py; do
-		${EPYTHON} "${t}" || die
-	done
-}
diff --git a/dev-python/dimensionful/metadata.xml b/dev-python/dimensionful/metadata.xml
deleted file mode 100644
index cd6735682..000000000
--- a/dev-python/dimensionful/metadata.xml
+++ /dev/null
@@ -1,11 +0,0 @@
-<?xml version="1.0" encoding="UTF-8"?>
-<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
-<pkgmetadata>
-	<maintainer type="person">
-		<email>xarthisius@gentoo.org</email>
-		<name>Kacper Kowalik</name>
-	</maintainer>
-	<upstream>
-		<remote-id type="github">caseywstark/dimensionful</remote-id>
-	</upstream>
-</pkgmetadata>
diff --git a/dev-python/distinctipy/.tridesclous-1.6.6.ebuild.swp b/dev-python/distinctipy/.tridesclous-1.6.6.ebuild.swp
new file mode 100644
index 000000000..d281f7480
--- /dev/null
+++ b/dev-python/distinctipy/.tridesclous-1.6.6.ebuild.swp
diff --git a/dev-python/distinctipy/Manifest b/dev-python/distinctipy/Manifest
new file mode 100644
index 000000000..b6e69e178
--- /dev/null
+++ b/dev-python/distinctipy/Manifest
@@ -0,0 +1 @@
+DIST distinctipy-1.2.2.gh.tar.gz 8215214 BLAKE2B c25f34f1b0000751fe22e73845922f31bc3cb1a03a673df608cfb8dda9493765c3694bc151a7318d6702f4ed6d151d9336e75828599ee0cb568d3eaf808786ab SHA512 52ec8189a699fe4dd10e3e3d43f50551ce8825835c4605a7f674db022b766a4a9f1714e6ba312bec8f2f0ce87a4d9d038b784f68c0aae603e2011908529010ec
diff --git a/dev-python/distinctipy/distinctipy-1.2.2.ebuild b/dev-python/distinctipy/distinctipy-1.2.2.ebuild
new file mode 100644
index 000000000..cd4c407d8
--- /dev/null
+++ b/dev-python/distinctipy/distinctipy-1.2.2.ebuild
@@ -0,0 +1,34 @@
+# Copyright 2021-2023 Gentoo Authors
+# Distributed under the terms of the GNU General Public License v2
+
+EAPI=8
+
+PYTHON_COMPAT=( python3_{10..11} )
+DISTUTILS_USE_PEP517=setuptools
+inherit distutils-r1
+
+DESCRIPTION="Lightweight package for generating visually distinct colours"
+HOMEPAGE="
+	https://distinctipy.readthedocs.io/en/latest/
+	https://github.com/alan-turing-institute/distinctipy
+"
+# PyPI archive does not include tests:
+# https://github.com/alan-turing-institute/distinctipy/issues/29
+SRC_URI="https://github.com/alan-turing-institute/distinctipy/archive/refs/tags/v${PV}.tar.gz -> ${P}.gh.tar.gz"
+
+LICENSE="MIT"
+SLOT="0"
+KEYWORDS="~amd64"
+IUSE="test"
+
+RDEPEND="
+	dev-python/numpy[${PYTHON_USEDEP}]
+"
+
+distutils_enable_tests pytest
+
+# Requires networking:
+EPYTEST_DESELECT=(
+	tests/test_examples.py::test_compare_clusters
+	tests/test_examples.py::test_simulate_clusters
+)
diff --git a/dev-python/distinctipy/metadata.xml b/dev-python/distinctipy/metadata.xml
new file mode 100644
index 000000000..eb8a425e8
--- /dev/null
+++ b/dev-python/distinctipy/metadata.xml
@@ -0,0 +1,16 @@
+<?xml version='1.0' encoding='UTF-8'?>
+<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
+<pkgmetadata>
+	<maintainer type="person">
+		<email>gentoo@chymera.eu</email>
+		<name>Horea Christian</name>
+	</maintainer>
+	<maintainer type="project">
+		<email>sci@gentoo.org</email>
+		<name>Gentoo Science Project</name>
+	</maintainer>
+	<upstream>
+		<remote-id type="github">alan-turing-institute/distinctipy</remote-id>
+		<remote-id type="pypi">distinctipy</remote-id>
+	</upstream>
+</pkgmetadata>
diff --git a/dev-python/docstring-parser/Manifest b/dev-python/docstring-parser/Manifest
new file mode 100644
index 000000000..9f508a4f7
--- /dev/null
+++ b/dev-python/docstring-parser/Manifest
@@ -0,0 +1 @@
+DIST docstring_parser-0.16.tar.gz 26565 BLAKE2B 3785bc9176bc06624a43c50a147c3143e344b8093b9c2db90ab49baed807d598a3538344f79a3da7515c16fc2afc90813e26a3a8f3aa5deb6bc2bf1554303d2e SHA512 6bda195f0e60173c9e78f300a05f8ab2d51ec37848c6f3eddccf889f01abc7dd00b1987028bc59058056e2ab4a50e4631d4d0ec10e54180178372001d65c431f
diff --git a/dev-python/docstring-parser/docstring-parser-0.16.ebuild b/dev-python/docstring-parser/docstring-parser-0.16.ebuild
new file mode 100644
index 000000000..1d82de77c
--- /dev/null
+++ b/dev-python/docstring-parser/docstring-parser-0.16.ebuild
@@ -0,0 +1,18 @@
+# Copyright 1999-2023 Gentoo Authors
+# Distributed under the terms of the GNU General Public License v2
+
+EAPI=8
+
+DISTUTILS_USE_PEP517=poetry
+PYTHON_COMPAT=( python3_{10..12} )
+
+inherit distutils-r1 pypi
+
+DESCRIPTION="Parse Python docstrings in various flavors"
+HOMEPAGE="https://github.com/rr-/docstring_parser"
+
+LICENSE="MIT"
+SLOT="0"
+KEYWORDS="~amd64 ~x86"
+
+distutils_enable_tests pytest
diff --git a/dev-python/docstring-parser/metadata.xml b/dev-python/docstring-parser/metadata.xml
new file mode 100644
index 000000000..140ee785a
--- /dev/null
+++ b/dev-python/docstring-parser/metadata.xml
@@ -0,0 +1,16 @@
+<?xml version='1.0' encoding='UTF-8'?>
+<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
+<pkgmetadata>
+	<maintainer type="person">
+		<email>gentoo@chymera.eu</email>
+		<name>Horea Christian</name>
+	</maintainer>
+	<maintainer type="project">
+		<email>sci@gentoo.org</email>
+		<name>Gentoo Science Project</name>
+	</maintainer>
+	<upstream>
+		<remote-id type="pypi">docstring-parser</remote-id>
+		<remote-id type="github">rr-/docstring_parser</remote-id>
+	</upstream>
+</pkgmetadata>
diff --git a/dev-python/dpath/Manifest b/dev-python/dpath/Manifest
new file mode 100644
index 000000000..81aa6ca1c
--- /dev/null
+++ b/dev-python/dpath/Manifest
@@ -0,0 +1 @@
+DIST dpath-2.1.6.tar.gz 28142 BLAKE2B 78cb4a8eb7278cd0c1818ffba9d77a917d89f3454a047a82d9031028b34ea2969fe98ed7086d26f6697a166b81cd50439b7b3bd545ab7e6cadcd0606c24be61e SHA512 2f2dac39b6e1ad2effd8d61ac4acf6619205423389ecebc54061aa10ec11ce3236ea666b632a7dca349e9b7a6579815c97e01c930eaa1a99d965e37b9825b82c
diff --git a/dev-python/dpath/dpath-2.1.6.ebuild b/dev-python/dpath/dpath-2.1.6.ebuild
new file mode 100644
index 000000000..55da56b96
--- /dev/null
+++ b/dev-python/dpath/dpath-2.1.6.ebuild
@@ -0,0 +1,18 @@
+# Copyright 1999-2018 Gentoo Foundation
+# Distributed under the terms of the GNU General Public License v2
+
+EAPI=8
+
+DISTUTILS_USE_PEP517=setuptools
+PYTHON_COMPAT=( python3_{10..12} )
+
+inherit pypi distutils-r1
+
+DESCRIPTION="Accessing and searching dictionaries via /slashed/paths"
+HOMEPAGE="https://pypi.org/project/dpath/"
+
+LICENSE="MIT"
+SLOT="0"
+KEYWORDS="~amd64 ~x86 ~amd64-linux ~x86-linux"
+
+distutils_enable_tests pytest
diff --git a/dev-python/dpath/metadata.xml b/dev-python/dpath/metadata.xml
new file mode 100644
index 000000000..347155fb7
--- /dev/null
+++ b/dev-python/dpath/metadata.xml
@@ -0,0 +1,16 @@
+<?xml version='1.0' encoding='UTF-8'?>
+<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
+<pkgmetadata>
+	<maintainer type="person">
+		<email>mschu.dev@gmail.com</email>
+		<name>Michael Schubert</name>
+	</maintainer>
+	<maintainer type="project">
+		<email>sci@gentoo.org</email>
+		<name>Gentoo Science Project</name>
+	</maintainer>
+	<upstream>
+		<remote-id type="github">dpath-maintainers/dpath-python</remote-id>
+		<remote-id type="pypi">dpath</remote-id>
+	</upstream>
+</pkgmetadata>
diff --git a/dev-python/dpctl/Manifest b/dev-python/dpctl/Manifest
new file mode 100644
index 000000000..d402c3e9e
--- /dev/null
+++ b/dev-python/dpctl/Manifest
@@ -0,0 +1,2 @@
+DIST dpctl-0.14.1_rc2.gh.tar.gz 409028 BLAKE2B 481be08bb6a7b1a439580d600b0e14036f10793e568314f9373ffa46daad7d3e43d33fc66c3c48ec7e3de71e9d0a7256cdfdd984c38fa7f1694dcc0227dae93f SHA512 91ab20a51893e3afc9e140ab9dfd1aa19b24e58227a001faefb9ceba6ffc4aa235214663c7456e977acf556796be097eabacc9b01b94eb42e8c70677a2f2dd9d
+DIST dpctl-0.14.5.gh.tar.gz 552066 BLAKE2B f668ceea99125dad1e0a6989db5bd59df087840d09b1a1538c38cddd0f482f4fc4053ef400e86ddedee4b1906575a441fb97d2caaf3c3718d8aac503d942c0b5 SHA512 6df39eec93da38b86df4cdfdf90350ff11f95d4884bb762289af9b0a6e240d45ed7cc7243677ca7403b042f8938f8acfa42a974d6cff673cd846c0b0f22d0803
diff --git a/dev-python/dpctl/dpctl-0.14.1_rc2.ebuild b/dev-python/dpctl/dpctl-0.14.1_rc2.ebuild
new file mode 100644
index 000000000..4ef429b97
--- /dev/null
+++ b/dev-python/dpctl/dpctl-0.14.1_rc2.ebuild
@@ -0,0 +1,69 @@
+# Copyright 2022 Gentoo Authors
+# Distributed under the terms of the GNU General Public License v2
+
+EAPI=8
+
+PYTHON_COMPAT=( python3_{10..12} )
+DISTUTILS_USE_PEP517=setuptools
+inherit distutils-r1
+
+DESCRIPTION="Data Parallel Control "
+HOMEPAGE="https://github.com/IntelPython/dpctl"
+SRC_URI="https://github.com/IntelPython/dpctl/archive/refs/tags/${PV//_rc/dev}.tar.gz -> ${P}.gh.tar.gz"
+S="${WORKDIR}/${PN}-${PV//_rc/dev}"
+
+LICENSE="Apache-2.0"
+SLOT="0"
+KEYWORDS="~amd64"
+
+BDEPEND="
+	dev-python/cython[${PYTHON_USEDEP}]
+	dev-python/scikit-build[${PYTHON_USEDEP}]
+	dev-python/pybind11[${PYTHON_USEDEP}]
+	dev-python/versioneer[${PYTHON_USEDEP}]
+	dev-build/cmake
+	dev-vcs/git
+	sys-devel/DPC++
+"
+
+DEPEND="
+	dev-libs/level-zero
+	dev-libs/opencl-icd-loader
+	dev-python/numpy[${PYTHON_USEDEP}]
+	dev-python/wheel[${PYTHON_USEDEP}]
+	sci-libs/oneDAL
+	sys-devel/DPC++:0/6
+"
+RDEPEND="${DEPEND}"
+
+PATCHES=(
+	"${FILESDIR}/${PN}-0.14.0-find-opencl.patch"
+	"${FILESDIR}/${PN}-0.14.1_rc2-dont-fetch-level-zero.patch"
+	"${FILESDIR}/${PN}-0.14.1_rc2-dont-fetch-pybind.patch"
+	#"${FILESDIR}/${PN}-0.14.1_rc2-include-tuple.patch"
+)
+
+distutils_enable_tests pytest
+
+python_prepare_all() {
+	# DPC++ compiler required for full functionality
+	export CC="${ESYSROOT}/usr/lib/llvm/intel/bin/clang"
+	export CXX="${ESYSROOT}/usr/lib/llvm/intel/bin/clang++"
+	export DPCPPROOT="${ESYSROOT}/usr/lib/llvm/intel"
+
+	# Build system reads version from git tag
+	git init -q || die
+	git config --global user.email "larry@gentoo.org" || die
+	git config --global user.name "Larry the Cow" || die
+	git add . || die
+	git commit -qm "init" || die
+	git tag -a "${PV}" -m "${PN} version ${PV}" || die
+
+	distutils-r1_python_prepare_all
+}
+
+python_test() {
+	export PYTHONPATH="${BUILD_DIR}/install/usr/lib/${EPYTHON}/site-packages"
+	# We don't use epytest because it overwrites our PYTHONPATH
+	pytest -vv || die
+}
diff --git a/dev-python/dpctl/dpctl-0.14.5.ebuild b/dev-python/dpctl/dpctl-0.14.5.ebuild
new file mode 100644
index 000000000..4ef429b97
--- /dev/null
+++ b/dev-python/dpctl/dpctl-0.14.5.ebuild
@@ -0,0 +1,69 @@
+# Copyright 2022 Gentoo Authors
+# Distributed under the terms of the GNU General Public License v2
+
+EAPI=8
+
+PYTHON_COMPAT=( python3_{10..12} )
+DISTUTILS_USE_PEP517=setuptools
+inherit distutils-r1
+
+DESCRIPTION="Data Parallel Control "
+HOMEPAGE="https://github.com/IntelPython/dpctl"
+SRC_URI="https://github.com/IntelPython/dpctl/archive/refs/tags/${PV//_rc/dev}.tar.gz -> ${P}.gh.tar.gz"
+S="${WORKDIR}/${PN}-${PV//_rc/dev}"
+
+LICENSE="Apache-2.0"
+SLOT="0"
+KEYWORDS="~amd64"
+
+BDEPEND="
+	dev-python/cython[${PYTHON_USEDEP}]
+	dev-python/scikit-build[${PYTHON_USEDEP}]
+	dev-python/pybind11[${PYTHON_USEDEP}]
+	dev-python/versioneer[${PYTHON_USEDEP}]
+	dev-build/cmake
+	dev-vcs/git
+	sys-devel/DPC++
+"
+
+DEPEND="
+	dev-libs/level-zero
+	dev-libs/opencl-icd-loader
+	dev-python/numpy[${PYTHON_USEDEP}]
+	dev-python/wheel[${PYTHON_USEDEP}]
+	sci-libs/oneDAL
+	sys-devel/DPC++:0/6
+"
+RDEPEND="${DEPEND}"
+
+PATCHES=(
+	"${FILESDIR}/${PN}-0.14.0-find-opencl.patch"
+	"${FILESDIR}/${PN}-0.14.1_rc2-dont-fetch-level-zero.patch"
+	"${FILESDIR}/${PN}-0.14.1_rc2-dont-fetch-pybind.patch"
+	#"${FILESDIR}/${PN}-0.14.1_rc2-include-tuple.patch"
+)
+
+distutils_enable_tests pytest
+
+python_prepare_all() {
+	# DPC++ compiler required for full functionality
+	export CC="${ESYSROOT}/usr/lib/llvm/intel/bin/clang"
+	export CXX="${ESYSROOT}/usr/lib/llvm/intel/bin/clang++"
+	export DPCPPROOT="${ESYSROOT}/usr/lib/llvm/intel"
+
+	# Build system reads version from git tag
+	git init -q || die
+	git config --global user.email "larry@gentoo.org" || die
+	git config --global user.name "Larry the Cow" || die
+	git add . || die
+	git commit -qm "init" || die
+	git tag -a "${PV}" -m "${PN} version ${PV}" || die
+
+	distutils-r1_python_prepare_all
+}
+
+python_test() {
+	export PYTHONPATH="${BUILD_DIR}/install/usr/lib/${EPYTHON}/site-packages"
+	# We don't use epytest because it overwrites our PYTHONPATH
+	pytest -vv || die
+}
diff --git a/dev-python/dpctl/files/dpctl-0.14.0-find-opencl.patch b/dev-python/dpctl/files/dpctl-0.14.0-find-opencl.patch
new file mode 100644
index 000000000..3841816ee
--- /dev/null
+++ b/dev-python/dpctl/files/dpctl-0.14.0-find-opencl.patch
@@ -0,0 +1,13 @@
+diff --git a/libsyclinterface/cmake/modules/FindIntelSycl.cmake b/libsyclinterface/cmake/modules/FindIntelSycl.cmake
+index 84e8946..ccc2591 100644
+--- a/libsyclinterface/cmake/modules/FindIntelSycl.cmake
++++ b/libsyclinterface/cmake/modules/FindIntelSycl.cmake
+@@ -134,7 +134,7 @@ if(${clangxx_result} MATCHES "0")
+         find_file(
+             IntelSycl_OPENCL_LIBRARY
+             NAMES "libOpenCL.so"
+-            PATHS ${IntelSycl_LIBRARY_DIR}
++            PATHS /usr/lib64
+         )
+     endif()
+ 
diff --git a/dev-python/dpctl/files/dpctl-0.14.1_rc2-dont-fetch-level-zero.patch b/dev-python/dpctl/files/dpctl-0.14.1_rc2-dont-fetch-level-zero.patch
new file mode 100644
index 000000000..a7a4adf8b
--- /dev/null
+++ b/dev-python/dpctl/files/dpctl-0.14.1_rc2-dont-fetch-level-zero.patch
@@ -0,0 +1,82 @@
+diff --git a/libsyclinterface/cmake/modules/GetLevelZeroHeaders.cmake b/libsyclinterface/cmake/modules/GetLevelZeroHeaders.cmake
+index fe109fc..55595e9 100644
+--- a/libsyclinterface/cmake/modules/GetLevelZeroHeaders.cmake
++++ b/libsyclinterface/cmake/modules/GetLevelZeroHeaders.cmake
+@@ -26,76 +26,10 @@
+ 
+ function(get_level_zero_headers)
+ 
+-    if(EXISTS level-zero)
+-      # Update the checkout
+-        execute_process(
+-            COMMAND ${GIT_EXECUTABLE} fetch
+-            RESULT_VARIABLE result
+-            ERROR_VARIABLE error
+-            WORKING_DIRECTORY ${CMAKE_BINARY_DIR}/level-zero
+-            OUTPUT_STRIP_TRAILING_WHITESPACE
+-            ERROR_STRIP_TRAILING_WHITESPACE
+-        )
+-
+-        if(NOT result EQUAL 0)
+-            message(FATAL_ERROR
+-                "Could not update Level Zero sources. Return code: ${result}"
+-            )
+-        endif()
+-    else()
+-        # Clone the Level Zero git repo
+-        execute_process(
+-            COMMAND ${GIT_EXECUTABLE} clone https://github.com/oneapi-src/level-zero.git
+-            RESULT_VARIABLE result
+-            ERROR_VARIABLE error
+-            OUTPUT_STRIP_TRAILING_WHITESPACE
+-            ERROR_STRIP_TRAILING_WHITESPACE
+-        )
+-
+-        if(NOT result EQUAL 0)
+-            message(FATAL_ERROR
+-                "Could not clone Level Zero sources from github.com/oneapi-src/level-zero. Return code: ${result}"
+-            )
+-        endif()
+-    endif()
+-
+-    # Use git describe to get latest tag name
+-    execute_process(
+-        COMMAND ${GIT_EXECUTABLE} describe --tags --abbrev=0
+-        RESULT_VARIABLE result
+-        OUTPUT_VARIABLE latest_tag
+-        ERROR_VARIABLE error
+-        WORKING_DIRECTORY ${CMAKE_BINARY_DIR}/level-zero
+-        OUTPUT_STRIP_TRAILING_WHITESPACE
+-        ERROR_STRIP_TRAILING_WHITESPACE
+-    )
+-
+-    if(NOT result EQUAL 0)
+-        message(FATAL_ERROR
+-            "Could not get the name for the latest release. Return code: ${result}"
+-        )
+-    endif()
+-
+-    # Use git describe to get latest tag name
+-    execute_process(
+-        COMMAND ${GIT_EXECUTABLE} checkout ${latest_tag}
+-        RESULT_VARIABLE result
+-        ERROR_VARIABLE error
+-        WORKING_DIRECTORY ${CMAKE_BINARY_DIR}/level-zero
+-        OUTPUT_STRIP_TRAILING_WHITESPACE
+-        ERROR_STRIP_TRAILING_WHITESPACE
+-    )
+-
+-    if(NOT result EQUAL 0)
+-        message(FATAL_ERROR
+-            "Could not checkout the latest release. Return code: ${result}"
+-        )
+-    endif()
+-
+     # Populate the path to the headers
+     find_path(LEVEL_ZERO_INCLUDE_DIR
+         NAMES zet_api.h
+-        PATHS ${CMAKE_BINARY_DIR}/level-zero/include
++        PATHS /usr/include/level_zero
+         NO_DEFAULT_PATH
+         NO_CMAKE_ENVIRONMENT_PATH
+         NO_CMAKE_PATH
diff --git a/dev-python/dpctl/files/dpctl-0.14.1_rc2-dont-fetch-pybind.patch b/dev-python/dpctl/files/dpctl-0.14.1_rc2-dont-fetch-pybind.patch
new file mode 100644
index 000000000..d56dc27b3
--- /dev/null
+++ b/dev-python/dpctl/files/dpctl-0.14.1_rc2-dont-fetch-pybind.patch
@@ -0,0 +1,21 @@
+diff --git a/CMakeLists.txt b/CMakeLists.txt
+index d97ca9a..3914bd9 100644
+--- a/CMakeLists.txt
++++ b/CMakeLists.txt
+@@ -32,15 +32,7 @@ install(FILES ${_dpctl_capi_headers}
+ # Define CMAKE_INSTALL_xxx: LIBDIR, INCLUDEDIR
+ include(GNUInstallDirs)
+ 
+-# Fetch pybind11
+-include(FetchContent)
+-
+-FetchContent_Declare(
+-    pybind11
+-    URL https://github.com/pybind/pybind11/archive/refs/tags/v2.10.2.tar.gz
+-    URL_HASH SHA256=93bd1e625e43e03028a3ea7389bba5d3f9f2596abc074b068e70f4ef9b1314ae
+-)
+-FetchContent_MakeAvailable(pybind11)
++include(/usr/share/cmake/pybind11/pybind11Config.cmake)
+ 
+ add_subdirectory(dpctl)
+ 
diff --git a/dev-python/dpctl/metadata.xml b/dev-python/dpctl/metadata.xml
new file mode 100644
index 000000000..06d339ee1
--- /dev/null
+++ b/dev-python/dpctl/metadata.xml
@@ -0,0 +1,12 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
+<pkgmetadata>
+	<maintainer type="project">
+		<email>sci@gentoo.org</email>
+		<name>Gentoo Science Project</name>
+	</maintainer>
+	<upstream>
+		<remote-id type="github">IntelPython/dpctl</remote-id>
+		<remote-id type="pypi">dpctl</remote-id>
+	</upstream>
+</pkgmetadata>
diff --git a/dev-python/dpnp/Manifest b/dev-python/dpnp/Manifest
new file mode 100644
index 000000000..0286f1b8e
--- /dev/null
+++ b/dev-python/dpnp/Manifest
@@ -0,0 +1 @@
+DIST dpnp-0.11.1_rc1.gh.tar.gz 495726 BLAKE2B 13e9696195abd21f41b1a8e6f235f840cd22a4eb1b67f7bbedfdc775f0cb7832157af51309b1d8a5f2d1cde78250c70730a2794f11b01f8bd572e7a1e29f2b47 SHA512 ef58591aaed330123b78268c7b0b04222efc8e688e1bfe2426e13836fe23ae84572f3337d7084525a6dd5e5fcf91dd68c501643b922ebebc7f0fb94115f92749
diff --git a/dev-python/dpnp/dpnp-0.11.1_rc1.ebuild b/dev-python/dpnp/dpnp-0.11.1_rc1.ebuild
new file mode 100644
index 000000000..5d25d62d1
--- /dev/null
+++ b/dev-python/dpnp/dpnp-0.11.1_rc1.ebuild
@@ -0,0 +1,65 @@
+# Copyright 2022 Gentoo Authors
+# Distributed under the terms of the GNU General Public License v2
+
+EAPI=8
+
+PYTHON_COMPAT=( python3_{10..12} )
+# Breaks library installation
+#DISTUTILS_USE_PEP517=setuptools
+inherit distutils-r1
+
+DESCRIPTION="Data Parallel Extension for NumPy"
+HOMEPAGE="https://github.com/IntelPython/dpnp"
+SRC_URI="https://github.com/IntelPython/dpnp/archive/refs/tags/${PV//_rc/dev}.tar.gz -> ${P}.gh.tar.gz"
+S="${WORKDIR}/${PN}-${PV//_rc/dev}"
+
+LICENSE="Apache-2.0"
+SLOT="0"
+KEYWORDS="~amd64"
+
+BDEPEND="
+	dev-python/cython[${PYTHON_USEDEP}]
+	dev-build/cmake
+	sys-devel/DPC++
+"
+
+RDEPEND="
+	dev-cpp/tbb
+	dev-python/dpctl[${PYTHON_USEDEP}]
+	dev-python/numpy[${PYTHON_USEDEP}]
+	sci-libs/mkl
+	sys-devel/DPC++:=
+"
+DEPEND="${RDEPEND}
+	sys-devel/oneDPL
+"
+
+PATCHES=(
+	"${FILESDIR}/${P}-fix-compile.patch"
+)
+
+distutils_enable_tests pytest
+
+python_prepare_all() {
+	# DPC++ compiler required for full functionality
+	export CC="${ESYSROOT}/usr/lib/llvm/intel/bin/clang"
+	export CXX="${ESYSROOT}/usr/lib/llvm/intel/bin/clang++"
+	export DPCPPROOT="${ESYSROOT}/usr/lib/llvm/intel"
+	export DPL_ROOT="${ESYSROOT}/usr/include/include/oneapi/dpl"
+	# Parallel build broken
+	export MAKEOPTS="-j1"
+
+	distutils-r1_python_prepare_all
+}
+
+python_compile() {
+	export BUILD_DIR_LIBS="${BUILD_DIR}/lib/dpnp"
+	distutils-r1_python_compile
+}
+
+python_test() {
+	export PYTHONPATH="${BUILD_DIR}/lib"
+	elog $PYTHONPATH
+	# We don't use epytest because it overwrites our PYTHONPATH
+	pytest -vv || die
+}
diff --git a/dev-python/dpnp/files/dpnp-0.11.1_rc1-fix-compile.patch b/dev-python/dpnp/files/dpnp-0.11.1_rc1-fix-compile.patch
new file mode 100644
index 000000000..25c0d3484
--- /dev/null
+++ b/dev-python/dpnp/files/dpnp-0.11.1_rc1-fix-compile.patch
@@ -0,0 +1,71 @@
+diff --git a/dpnp/backend/CMakeLists.txt b/dpnp/backend/CMakeLists.txt
+index baee709..3202662 100644
+--- a/dpnp/backend/CMakeLists.txt
++++ b/dpnp/backend/CMakeLists.txt
+@@ -99,30 +99,6 @@ string(CONCAT COMMON_LINK_FLAGS
+   "-fsycl "
+   "-fsycl-device-code-split=per_kernel "
+ )
+-if(UNIX)
+-  set(CMAKE_CXX_COMPILER "icpx")
+-  # add_compile_options(-fPIC)
+-elseif(WIN32)
+-  set(CMAKE_CXX_COMPILER "icx")
+-  # set(CMAKE_SHARED_LINKER_FLAGS_INIT "-fuse-ld=lld-link")
+-  # set(CMAKE_LINKER "lld-link")
+-  # include (Platform/Windows-Clang)
+-  # set(CMAKE_LINKER "dpcpp")
+-  # set(CMAKE_AR "llvm-ar")
+-  # set(CMAKE_RANLIB "llvm-ranlib")
+-  # set(CMAKE_CXX_FLAGS "/EHsc")
+-
+-  string(APPEND COMMON_COMPILE_FLAGS
+-    "/EHsc "
+-#    "/Ox "
+-#    "/W3 "
+-#    "/GL "
+-#    "/DNDEBUG "
+-#    "/MD "
+-  )
+-else()
+-  message(FATAL_ERROR "Unsupported system ${CMAKE_SYSTEM} in compiler selection case")
+-endif()
+ 
+ # set language version
+ set(CMAKE_CXX_STANDARD 17)
+@@ -334,6 +310,7 @@ endif()
+ # set_target_properties(dpnp_backend_c PROPERTIES VERSION ${DPNP_VERSION} SOVERSION ${DPNP_API_VERSION})
+ 
+ install(TARGETS dpnp_backend_c
++        DESTINATION ${DPNP_INSTALL_PREFIX}
+         PERMISSIONS OWNER_WRITE OWNER_READ OWNER_EXECUTE GROUP_READ GROUP_EXECUTE WORLD_READ WORLD_EXECUTE
+         )
+ 
+diff --git a/utils/command_build_clib.py b/utils/command_build_clib.py
+index d16bab3..7fd2afa 100644
+--- a/utils/command_build_clib.py
++++ b/utils/command_build_clib.py
+@@ -61,8 +61,8 @@ else:
+ Set compiler for the project
+ """
+ # default variables (for Linux)
+-_project_compiler = "icpx"
+-_project_linker = "icpx"
++_project_compiler = os.environ.get("CXX")
++_project_linker = os.environ.get("CXX")
+ _project_cmplr_flag_sycl_devel = ["-fsycl-device-code-split=per_kernel", "-fno-approx-func", "-fno-finite-math-only"]
+ _project_cmplr_flag_sycl = ["-fsycl"]
+ _project_cmplr_flag_stdcpp_static = []  # This brakes TBB ["-static-libstdc++", "-static-libgcc"]
+diff --git a/utils/command_build_cmake_clib.py b/utils/command_build_cmake_clib.py
+index 0ef0e24..84f2469 100644
+--- a/utils/command_build_cmake_clib.py
++++ b/utils/command_build_cmake_clib.py
+@@ -112,7 +112,7 @@ class custom_build_cmake_clib(build_clib.build_clib):
+             "-S" + backend_directory,
+             "-B" + abs_build_temp_path,
+             "-DCMAKE_BUILD_TYPE=" + config,
+-            "-DDPNP_INSTALL_PREFIX=" + install_directory.replace(os.sep, "/"),  # adjust to cmake requirenments
++            "-DDPNP_INSTALL_PREFIX=" + os.environ.get('BUILD_DIR_LIBS'),  # adjust to cmake requirenments
+             "-DDPNP_INSTALL_STRUCTURED=OFF",
+             # "-DCMAKE_LIBRARY_OUTPUT_DIRECTORY=" + install_directory,
+             "-DDPNP_SYCL_QUEUE_MGR_ENABLE:BOOL=" + _dpctrl_exists,
diff --git a/dev-python/dpnp/metadata.xml b/dev-python/dpnp/metadata.xml
new file mode 100644
index 000000000..868959c89
--- /dev/null
+++ b/dev-python/dpnp/metadata.xml
@@ -0,0 +1,12 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
+<pkgmetadata>
+	<maintainer type="project">
+		<email>sci@gentoo.org</email>
+		<name>Gentoo Science Project</name>
+	</maintainer>
+	<upstream>
+		<remote-id type="github">IntelPython/dpnp</remote-id>
+		<remote-id type="pypi">dpnp</remote-id>
+	</upstream>
+</pkgmetadata>
diff --git a/dev-python/extension-helpers/Manifest b/dev-python/extension-helpers/Manifest
new file mode 100644
index 000000000..33d56a849
--- /dev/null
+++ b/dev-python/extension-helpers/Manifest
@@ -0,0 +1 @@
+DIST extension-helpers-1.0.0.tar.gz 23463 BLAKE2B 0b1edffabc112120ac85c6445255986145143da9552221390a0827516a20e2877cad47e5968f6c7d293550db566574f86c877758d6233e51ca0762c3ff2e9327 SHA512 30234591100e5e8b7bda4392d72421911773a3aabb40c003367e8b335edcea3285f79fd962edd3d09b96ed7b4b936a97086376dfff50b18df85b55c612d61f8d
diff --git a/dev-python/extension-helpers/extension-helpers-1.0.0.ebuild b/dev-python/extension-helpers/extension-helpers-1.0.0.ebuild
new file mode 100644
index 000000000..4532642fa
--- /dev/null
+++ b/dev-python/extension-helpers/extension-helpers-1.0.0.ebuild
@@ -0,0 +1,29 @@
+# Copyright 1999-2022 Gentoo Authors
+# Distributed under the terms of the GNU General Public License v2
+
+EAPI=8
+
+PYTHON_COMPAT=( python3_{10..11} )
+DISTUTILS_USE_PEP517=setuptools
+PYPI_NO_NORMALIZE=1
+
+inherit distutils-r1 pypi
+
+DESCRIPTION="Utilities for building and installing packages in the Astropy ecosystem"
+HOMEPAGE="https://github.com/astropy/astropy-helpers"
+
+LICENSE="BSD"
+SLOT="0"
+KEYWORDS="~amd64 ~x86"
+
+#TODO: Package all these pytest deps:
+# 	pytest-doctestplus>=0.2.0
+# 	pytest-remotedata>=0.3.1
+# 	pytest-openfiles>=0.3.1
+# 	pytest-astropy-header>=0.1.2
+# 	pytest-arraydiff>=0.1
+# 	pytest-filter-subpackage>=0.1
+RESTRICT="test"
+
+distutils_enable_tests pytest
+distutils_enable_sphinx docs dev-python/sphinx-astropy
diff --git a/dev-python/extension-helpers/metadata.xml b/dev-python/extension-helpers/metadata.xml
new file mode 100644
index 000000000..9f1bfe0c4
--- /dev/null
+++ b/dev-python/extension-helpers/metadata.xml
@@ -0,0 +1,12 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
+<pkgmetadata>
+	<maintainer type="project">
+		<email>sci-astronomy@gentoo.org</email>
+		<name>Gentoo Astronomy Project</name>
+	</maintainer>
+	<upstream>
+		<remote-id type="github">astropy/astropy-helpers</remote-id>
+		<remote-id type="pypi">extension-helpers</remote-id>
+	</upstream>
+</pkgmetadata>
diff --git a/dev-python/ezdxf/Manifest b/dev-python/ezdxf/Manifest
new file mode 100644
index 000000000..24626a24c
--- /dev/null
+++ b/dev-python/ezdxf/Manifest
@@ -0,0 +1 @@
+DIST ezdxf-0.16.5.zip 1552408 BLAKE2B d52131c776c5560da659db67b87a5403a0a0f44aa21781d9599555cc71a3a91cd4e92574f985079456bfd6c844fb693cdef5d16277e83dbd6ca378013d5423ca SHA512 1e35aea16bf169bc2fe3bc3accf83f42189371a80cea259f46dcee1e9c75b613f9c09e6e300a2f331510722a1eefa1550052b7d58c08c4e3a0868cebdfe7b330
diff --git a/dev-python/ezdxf/ezdxf-0.16.5.ebuild b/dev-python/ezdxf/ezdxf-0.16.5.ebuild
new file mode 100644
index 000000000..b3a0148f7
--- /dev/null
+++ b/dev-python/ezdxf/ezdxf-0.16.5.ebuild
@@ -0,0 +1,33 @@
+# Copyright 1999-2021 Gentoo Authors
+# Distributed under the terms of the GNU General Public License v2
+
+EAPI=8
+
+#FIXME: Upstream explicitly supports "pypy3", but Gentoo dependencies do not.
+PYTHON_COMPAT=( python3_10 )
+inherit distutils-r1 pypi
+
+DESCRIPTION="Python interface to DXF"
+HOMEPAGE="https://pypi.org/project/ezdxf/"
+SRC_URI="$(pypi_sdist_url ${PN} ${PV} .zip)"
+
+LICENSE="MIT"
+SLOT="0"
+KEYWORDS="~amd64 ~x86"
+IUSE="cython matplotlib qt5"
+
+BDEPEND="
+	cython? ( dev-python/cython[${PYTHON_USEDEP}] )
+	app-arch/unzip
+"
+DEPEND="
+	dev-python/typing-extensions[${PYTHON_USEDEP}]
+	>=dev-python/pyparsing-2.0.1[${PYTHON_USEDEP}]
+"
+RDEPEND="${DEPEND}
+	matplotlib? ( dev-python/matplotlib[${PYTHON_USEDEP}] )
+	qt5? ( dev-python/PyQt5[${PYTHON_USEDEP}] )
+"
+
+#FIXME: Enabling tests requires packaging additional packages (e.g., "geomdl").
+RESTRICT="test"
diff --git a/dev-python/ezdxf/metadata.xml b/dev-python/ezdxf/metadata.xml
new file mode 100644
index 000000000..768dc7877
--- /dev/null
+++ b/dev-python/ezdxf/metadata.xml
@@ -0,0 +1,17 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
+<pkgmetadata>
+	<maintainer type="project">
+		<email>sci@gentoo.org</email>
+		<name>Gentoo Science Project</name>
+	</maintainer>
+	<upstream>
+		<remote-id type="pypi">ezdxf</remote-id>
+		<remote-id type="github">mozman/ezdxf</remote-id>
+	</upstream>
+	<use>
+		<flag name="cython">Build Cython-based C extensions</flag>
+		<flag name="matplotlib">Add support for dev-python/matplotlib</flag>
+		<flag name="qt5">Add support for dev-python/PyQt5</flag>
+	</use>
+</pkgmetadata>
diff --git a/dev-python/ffc/Manifest b/dev-python/ffc/Manifest
deleted file mode 100644
index fb8926bb9..000000000
--- a/dev-python/ffc/Manifest
+++ /dev/null
@@ -1,3 +0,0 @@
-DIST ffc-1.4.0.tar.gz 366090 BLAKE2B 8b47d11c3f19e63119b577822be636bc53e2a508338137913e8dac54fe88a953d055a2ebbdcec9d40f53c8206427f2bc69593baca94d4209455aec1448f6edcd SHA512 94399bb71768b1a1628206f8d4eadcc31e1631682feb68aa42e364c1bb35d2d6d7753bc574b71b3e3ce20b68e13b8c6266dca3e38e48e68ff1c11cf84acdc101
-DIST ffc-2016.2.0.tar.gz 1371814 BLAKE2B 40559fb2a8a064ab936720761f8a506b065ebd8ce26e74290b5cf6d8920583c20c70855078f02151ad33cabd666a288b074f1d62b4a5c60ba8e4008669e56d78 SHA512 173e6e675bcf76efac4655a2ca21798552a193ce4b551f9f2de0a2eff9c059ea9478028b6e069ed8897da9d9c0bc26e14e5b82e7a2be508c33b054bf8f0efd5e
-DIST ffc-2017.1.0.tar.gz 1392845 BLAKE2B 706e75c55446c8670ad613f90ad7a57ff7c7ac0a8391f524566412991c5d06fb2b1e0aeaa32013b68bd5f959efc3727dd38afcf84bad6527d4d9cf1cf6a41b86 SHA512 f0ab58353c68c1db35b41069356b039a89d1ec05f9868cc8010bedc4b598b619bf7d3af92c211894b69c9ce3a9af8a30f6a758bbb5dca8fb2cb6148f0569841c
diff --git a/dev-python/ffc/ffc-1.4.0.ebuild b/dev-python/ffc/ffc-1.4.0.ebuild
deleted file mode 100644
index 55f6e913d..000000000
--- a/dev-python/ffc/ffc-1.4.0.ebuild
+++ /dev/null
@@ -1,25 +0,0 @@
-# Copyright 1999-2016 Gentoo Foundation
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=6
-
-PYTHON_COMPAT=( python2_7 )
-
-inherit distutils-r1
-
-DESCRIPTION="Compiler for multilinear forms by generating C or C++ code"
-HOMEPAGE="https://bitbucket.org/fenics-project/ffc/"
-SRC_URI="https://bitbucket.org/fenics-project/ffc/downloads/${P}.tar.gz"
-
-LICENSE="GPL-3"
-SLOT="0"
-KEYWORDS="~amd64 ~x86"
-IUSE=""
-
-RDEPEND="
-	!sci-mathematics/ufc
-	~dev-python/ufl-${PV}[${PYTHON_USEDEP}]
-	~dev-python/instant-${PV}[${PYTHON_USEDEP}]
-	~dev-python/fiat-${PV}[${PYTHON_USEDEP}]
-	dev-python/numpy[${PYTHON_USEDEP}]
-	"
diff --git a/dev-python/ffc/ffc-2016.2.0.ebuild b/dev-python/ffc/ffc-2016.2.0.ebuild
deleted file mode 100644
index 9dc670306..000000000
--- a/dev-python/ffc/ffc-2016.2.0.ebuild
+++ /dev/null
@@ -1,25 +0,0 @@
-# Copyright 1999-2017 Gentoo Foundation
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=6
-
-PYTHON_COMPAT=( python2_7 )
-
-inherit distutils-r1
-
-DESCRIPTION="Compiler for multilinear forms by generating C or C++ code"
-HOMEPAGE="https://bitbucket.org/fenics-project/ffc/"
-SRC_URI="https://bitbucket.org/fenics-project/ffc/downloads/${P}.tar.gz"
-
-LICENSE="GPL-3"
-SLOT="0"
-KEYWORDS="~amd64 ~x86"
-IUSE=""
-
-RDEPEND="
-	!sci-mathematics/ufc
-	~dev-python/ufl-${PV}[${PYTHON_USEDEP}]
-	~dev-python/instant-${PV}[${PYTHON_USEDEP}]
-	~dev-python/fiat-${PV}[${PYTHON_USEDEP}]
-	dev-python/numpy[${PYTHON_USEDEP}]
-	"
diff --git a/dev-python/ffc/ffc-2017.1.0.ebuild b/dev-python/ffc/ffc-2017.1.0.ebuild
deleted file mode 100644
index 69b633667..000000000
--- a/dev-python/ffc/ffc-2017.1.0.ebuild
+++ /dev/null
@@ -1,25 +0,0 @@
-# Copyright 1999-2017 Gentoo Foundation
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=6
-
-PYTHON_COMPAT=( python3_4 python3_5 python3_6 )
-
-inherit distutils-r1
-
-DESCRIPTION="Compiler for multilinear forms by generating C or C++ code"
-HOMEPAGE="https://bitbucket.org/fenics-project/ffc/"
-SRC_URI="https://bitbucket.org/fenics-project/ffc/downloads/${P}.tar.gz"
-
-LICENSE="GPL-3"
-SLOT="0"
-KEYWORDS="~amd64 ~x86"
-IUSE=""
-
-RDEPEND="
-	!sci-mathematics/ufc
-	~dev-python/ufl-${PV}[${PYTHON_USEDEP}]
-	~dev-python/instant-${PV}[${PYTHON_USEDEP}]
-	~dev-python/fiat-${PV}[${PYTHON_USEDEP}]
-	dev-python/numpy[${PYTHON_USEDEP}]
-	"
diff --git a/dev-python/ffc/metadata.xml b/dev-python/ffc/metadata.xml
deleted file mode 100644
index 744ca900c..000000000
--- a/dev-python/ffc/metadata.xml
+++ /dev/null
@@ -1,19 +0,0 @@
-<?xml version="1.0" encoding="UTF-8"?>
-<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
-<pkgmetadata>
-	<maintainer type="project">
-		<email>sci@gentoo.org</email>
-		<name>Gentoo Science Project</name>
-	</maintainer>
-	<longdescription lang="en">
-FFC works as a compiler for multilinear forms by generating code (C or
-C++) for the evaluation of a multilinear form given in mathematical
-notation. This new approach to form evaluation makes it possible to
-combine generality with efficiency; the form can be given in
-mathematical notation and the generated code is as efficient as
-hand-optimized code.
-</longdescription>
-	<upstream>
-		<remote-id type="bitbucket">fenics-project/ffc</remote-id>
-	</upstream>
-</pkgmetadata>
diff --git a/dev-python/ffnet/Manifest b/dev-python/ffnet/Manifest
deleted file mode 100644
index b7f7bb4cd..000000000
--- a/dev-python/ffnet/Manifest
+++ /dev/null
@@ -1,2 +0,0 @@
-DIST ffnet-0.7.1.tar.gz 58608 BLAKE2B bddf4f20529c49e2ca9774b0446990f8160aeffba23e4424845024d9c9ecc422341d5299b52bc1537018c04e1b8a6f3521e8b7b4d0b64809dc30c4645c0bf565 SHA512 eafb961716020f473b0cad6c37bdef42e9eb487076fd2b4b263ca045ad4db83441bb85acffa0068f3a1149c9f99a8d6919d27e0e33d40d9db9627448aac02ae3
-DIST ffnet-0.8.3.tar.gz 69148 BLAKE2B 8f1af3d5ea491e2e2b31dfc1f35fd3a572d1d0bffb4d5e4374567bc2c36a1840d0d5d4fa21a0ece9353e8a1b4c0bbbc6fcb833adbbf4d81dfc3f7ce3f53d74ab SHA512 acd5b3a4c094e803f12247cf9ddf8268fb7d3a22e68f89e2cca1bf0f9f9bd95d2806861c5a6183f1e62f484fb1423d2163ac19095fc9d48a7e924386f8ea24ea
diff --git a/dev-python/ffnet/ffnet-0.7.1.ebuild b/dev-python/ffnet/ffnet-0.7.1.ebuild
deleted file mode 100644
index 0cc21ebb0..000000000
--- a/dev-python/ffnet/ffnet-0.7.1.ebuild
+++ /dev/null
@@ -1,41 +0,0 @@
-# Copyright 1999-2016 Gentoo Foundation
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=6
-
-PYTHON_COMPAT=( python2_7 )
-
-inherit distutils-r1 fortran-2 flag-o-matic
-
-DESCRIPTION="Feed-forward neural network for python"
-HOMEPAGE="http://ffnet.sourceforge.net/"
-SRC_URI="mirror://sourceforge/${PN}/${P}.tar.gz"
-
-SLOT="0"
-LICENSE="GPL-2"
-KEYWORDS="~amd64 ~x86"
-IUSE="examples graphviz matplotlib"
-
-DEPEND="${PYTHON_DEPS}
-	dev-python/networkx[${PYTHON_USEDEP}]
-	dev-python/numpy[${PYTHON_USEDEP}]
-	sci-libs/scipy[${PYTHON_USEDEP}]
-	matplotlib? ( dev-python/matplotlib[${PYTHON_USEDEP}] )
-	graphviz? ( dev-python/pygraphviz[${PYTHON_USEDEP}] )"
-RDEPEND="${DEPEND}"
-
-python_prepare_all() {
-	export FCONFIG="config_fc --noopt --noarch"
-	append-ldflags -shared
-	append-fflags -fPIC
-	distutils-r1_python_prepare_all
-}
-
-src_compile() {
-	distutils-r1_src_compile ${FCONFIG}
-}
-
-python_install_all() {
-	distutils-r1_python_install_all
-	use examples && dodoc -r examples
-}
diff --git a/dev-python/ffnet/ffnet-0.8.3.ebuild b/dev-python/ffnet/ffnet-0.8.3.ebuild
deleted file mode 100644
index 5684807e4..000000000
--- a/dev-python/ffnet/ffnet-0.8.3.ebuild
+++ /dev/null
@@ -1,40 +0,0 @@
-# Copyright 1999-2016 Gentoo Foundation
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=6
-
-PYTHON_COMPAT=( python2_7 python3_{3,4} )
-
-inherit distutils-r1 fortran-2 flag-o-matic
-
-DESCRIPTION="Feed-forward neural network for python"
-HOMEPAGE="http://ffnet.sourceforge.net/"
-SRC_URI="mirror://pypi/${PN:0:1}/${PN}/${P}.tar.gz"
-
-SLOT="0"
-LICENSE="LGPL-3"
-KEYWORDS="~amd64 ~x86"
-IUSE="examples matplotlib"
-
-DEPEND="${PYTHON_DEPS}
-	dev-python/networkx[${PYTHON_USEDEP}]
-	dev-python/numpy[${PYTHON_USEDEP}]
-	sci-libs/scipy[${PYTHON_USEDEP}]
-	matplotlib? ( dev-python/matplotlib[${PYTHON_USEDEP}] )"
-RDEPEND="${DEPEND}"
-
-python_prepare_all() {
-	export FCONFIG="config_fc --noopt --noarch"
-	append-ldflags -shared
-	append-fflags -fPIC
-	distutils-r1_python_prepare_all
-}
-
-src_compile() {
-	distutils-r1_src_compile ${FCONFIG}
-}
-
-python_install_all() {
-	distutils-r1_python_install_all
-	use examples && dodoc -r examples
-}
diff --git a/dev-python/ffnet/metadata.xml b/dev-python/ffnet/metadata.xml
deleted file mode 100644
index 7dfe9ca51..000000000
--- a/dev-python/ffnet/metadata.xml
+++ /dev/null
@@ -1,19 +0,0 @@
-<?xml version="1.0" encoding="UTF-8"?>
-<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
-<pkgmetadata>
-	<maintainer type="project">
-		<email>sci@gentoo.org</email>
-		<name>Gentoo Science Project</name>
-	</maintainer>
-	<longdescription lang="en">
-ffnet is a fast and easy-to-use feed-forward neural
-network training library for python.
-</longdescription>
-	<use>
-		<flag name="matplotlib">Use matplotlib for drawing</flag>
-	</use>
-	<upstream>
-		<remote-id type="pypi">ffnet</remote-id>
-		<remote-id type="sourceforge">ffnet</remote-id>
-	</upstream>
-</pkgmetadata>
diff --git a/dev-python/ffnetui/Manifest b/dev-python/ffnetui/Manifest
deleted file mode 100644
index 1d8e5da2c..000000000
--- a/dev-python/ffnetui/Manifest
+++ /dev/null
@@ -1 +0,0 @@
-DIST ffnetui-0.8.3.2.tar.gz 286481 BLAKE2B f2397ca567900096353634884de52e62fce59f3be71a0dfba23690a11faed8883c9deb7501a9b9c37caf949d2f5ca917922a5a2eff820183577f42ba33bf62fb SHA512 3749fdb817644502f4ef46515f9c9ad4bbd94e14b9a1e6340cdc3875dc2a4580b963b70a65dedc313948c90a19e4356fd46a8c14f163798cfa8e155f0f147192
diff --git a/dev-python/ffnetui/ffnetui-0.8.3.2.ebuild b/dev-python/ffnetui/ffnetui-0.8.3.2.ebuild
deleted file mode 100644
index 605cafd71..000000000
--- a/dev-python/ffnetui/ffnetui-0.8.3.2.ebuild
+++ /dev/null
@@ -1,23 +0,0 @@
-# Copyright 1999-2016 Gentoo Foundation
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=6
-
-PYTHON_COMPAT=( python2_7 )
-
-inherit distutils-r1
-
-DESCRIPTION="GUI for ffnet - feed forward neural network for python"
-HOMEPAGE="http://ffnet.sourceforge.net"
-SRC_URI="mirror://pypi/${PN:0:1}/${PN}/${P}.tar.gz"
-
-SLOT="0"
-LICENSE="GPL-3"
-KEYWORDS="~amd64 ~x86"
-IUSE=""
-
-DEPEND="${PYTHON_DEPS}
-	>=dev-python/ffnet-0.8.3[${PYTHON_USEDEP}]
-	>=dev-python/matplotlib-1.4[${PYTHON_USEDEP}]
-	dev-python/traitsui[${PYTHON_USEDEP}]"
-RDEPEND="${DEPEND}"
diff --git a/dev-python/ffnetui/metadata.xml b/dev-python/ffnetui/metadata.xml
deleted file mode 100644
index 1b18e7538..000000000
--- a/dev-python/ffnetui/metadata.xml
+++ /dev/null
@@ -1,15 +0,0 @@
-<?xml version="1.0" encoding="UTF-8"?>
-<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
-<pkgmetadata>
-	<maintainer type="project">
-		<email>sci@gentoo.org</email>
-		<name>Gentoo Science Project</name>
-	</maintainer>
-	<longdescription lang="en">
-GUI for ffnet - feed forward neural network for python
-</longdescription>
-	<upstream>
-		<remote-id type="pypi">ffnetui</remote-id>
-		<remote-id type="sourceforge">ffnet</remote-id>
-	</upstream>
-</pkgmetadata>
diff --git a/dev-python/fiat/Manifest b/dev-python/fiat/Manifest
deleted file mode 100644
index ad573d4d1..000000000
--- a/dev-python/fiat/Manifest
+++ /dev/null
@@ -1,3 +0,0 @@
-DIST fiat-1.4.0.tar.gz 57087 BLAKE2B ae774cfbf50471858f6d6ccdb3c1b54df4f9ad23ac144867ebc228d5ab177a5224e6e3d995a1589dd2fdacfd96b6c64684bffb8f6594cc0bb27f4c6da3c1e894 SHA512 4566d2b5b74fbf6fb5ea640a0c86b33009f29e818cbf6d6f19e96b413220bb3ad29ade1ed3739cf2eb4d97caa603ceaafcc77fccff06c5cef7070e87eac37467
-DIST fiat-2016.2.0.tar.gz 97293 BLAKE2B f4ea65a59a012cd423a465808175d134026e81f3d6dccd6a5dbbf816c6d05953e5b80c290c5a62a3d02b312f1677cbeae7b2310052565100903277c094144503 SHA512 a058da6ed913eb7e6962f469c75959dfac8756268006a5224a5b6b7f3c56df8a796cee5b20f0c5dcc76f61dea50b7beca2e2f4dcaa90a8e78887cedf4743490a
-DIST fiat-2017.1.0.tar.gz 99849 BLAKE2B bac0bbb23312bbbda6564b4f78e32d174b1c21160f6aa6ca6151a180883a2c302f390eb5c9ad1a7aff4a5b1b33badf4d265f805aa805be3f22c6963e04c22a79 SHA512 86219bddd21349c90e187963b61d67982af4a11e31f0cf69107b54a5031ed26c5d636bba6358df9d5fdd6304d3be668390e53c7dc70fe8f8d33ecc77aeb7a690
diff --git a/dev-python/fiat/fiat-1.4.0.ebuild b/dev-python/fiat/fiat-1.4.0.ebuild
deleted file mode 100644
index c01e789b0..000000000
--- a/dev-python/fiat/fiat-1.4.0.ebuild
+++ /dev/null
@@ -1,23 +0,0 @@
-# Copyright 1999-2016 Gentoo Foundation
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=6
-
-PYTHON_COMPAT=( python2_7 )
-
-inherit distutils-r1
-
-DESCRIPTION="FInite element Automatic Tabulator"
-HOMEPAGE="https://bitbucket.org/fenics-project/fiat"
-SRC_URI="https://bitbucket.org/fenics-project/fiat/downloads/${P}.tar.gz"
-
-LICENSE="LGPL-3"
-SLOT="0"
-KEYWORDS="~amd64 ~x86"
-IUSE=""
-
-DEPEND=""
-RDEPEND="
-	dev-python/scientificpython[${PYTHON_USEDEP}]
-	dev-python/numpy[${PYTHON_USEDEP}]
-	"
diff --git a/dev-python/fiat/fiat-2016.2.0.ebuild b/dev-python/fiat/fiat-2016.2.0.ebuild
deleted file mode 100644
index 33ab972fe..000000000
--- a/dev-python/fiat/fiat-2016.2.0.ebuild
+++ /dev/null
@@ -1,22 +0,0 @@
-# Copyright 1999-2017 Gentoo Foundation
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=6
-
-PYTHON_COMPAT=( python2_7 )
-
-inherit distutils-r1
-
-DESCRIPTION="FInite element Automatic Tabulator"
-HOMEPAGE="https://bitbucket.org/fenics-project/fiat"
-SRC_URI="https://bitbucket.org/fenics-project/fiat/downloads/${P}.tar.gz"
-
-LICENSE="LGPL-3"
-SLOT="0"
-KEYWORDS="~amd64 ~x86"
-IUSE=""
-
-DEPEND=""
-RDEPEND="
-	dev-python/numpy[${PYTHON_USEDEP}]
-	"
diff --git a/dev-python/fiat/fiat-2017.1.0.ebuild b/dev-python/fiat/fiat-2017.1.0.ebuild
deleted file mode 100644
index 21d3b22e3..000000000
--- a/dev-python/fiat/fiat-2017.1.0.ebuild
+++ /dev/null
@@ -1,22 +0,0 @@
-# Copyright 1999-2017 Gentoo Foundation
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=6
-
-PYTHON_COMPAT=( python3_4 python3_5 python3_6 )
-
-inherit distutils-r1
-
-DESCRIPTION="FInite element Automatic Tabulator"
-HOMEPAGE="https://bitbucket.org/fenics-project/fiat"
-SRC_URI="https://bitbucket.org/fenics-project/fiat/downloads/${P}.tar.gz"
-
-LICENSE="LGPL-3"
-SLOT="0"
-KEYWORDS="~amd64 ~x86"
-IUSE=""
-
-DEPEND=""
-RDEPEND="
-	dev-python/numpy[${PYTHON_USEDEP}]
-	"
diff --git a/dev-python/fiat/metadata.xml b/dev-python/fiat/metadata.xml
deleted file mode 100644
index d08e0d509..000000000
--- a/dev-python/fiat/metadata.xml
+++ /dev/null
@@ -1,21 +0,0 @@
-<?xml version="1.0" encoding="UTF-8"?>
-<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
-<pkgmetadata>
-	<maintainer type="project">
-		<email>sci@gentoo.org</email>
-		<name>Gentoo Science Project</name>
-	</maintainer>
-	<longdescription lang="en">
-The FInite element Automatic Tabulator FIAT supports generation of
-arbitrary order instances of the Lagrange elements on lines, triangles,
-and tetrahedra. It is also capable of generating arbitrary order
-instances of Jacobi-type quadrature rules on the same element shapes.
-Further, H(div) and H(curl) conforming finite element spaces such as the
-families of Raviart-Thomas, Brezzi-Douglas-Marini and Nedelec are
-supported on triangles and tetrahedra. Upcoming versions will also
-support Hermite and nonconforming elements.
-</longdescription>
-	<upstream>
-		<remote-id type="bitbucket">fenics-project/fiat</remote-id>
-	</upstream>
-</pkgmetadata>
diff --git a/dev-python/fiona/Manifest b/dev-python/fiona/Manifest
new file mode 100644
index 000000000..bed2fa4ce
--- /dev/null
+++ b/dev-python/fiona/Manifest
@@ -0,0 +1 @@
+DIST fiona-1.9.0.gh.tar.gz 290797 BLAKE2B 1cd2a4a26d23d057433889937b4fecefb1e1585dc6b507e297ef3bab8cf72f734bc080bab8487d58c636312bca1330960f78fc2916d27c9a7247df087818c9b3 SHA512 f59d148cfc4f1cab6d89660146522920fab8b6fb1120ad8f3d3e8349d5fa823860984f8fd331e2fc3183a4a186a165508db8dcbcbdf4b943a7dad82d8d51d866
diff --git a/dev-python/fiona/fiona-1.9.0.ebuild b/dev-python/fiona/fiona-1.9.0.ebuild
new file mode 100644
index 000000000..7bc415b14
--- /dev/null
+++ b/dev-python/fiona/fiona-1.9.0.ebuild
@@ -0,0 +1,76 @@
+# Copyright 1999-2023 Gentoo Authors
+# Distributed under the terms of the GNU General Public License v2
+
+EAPI=8
+
+PYTHON_COMPAT=( python3_{10..11} )
+DISTUTILS_USE_PEP517="setuptools"
+inherit distutils-r1
+
+DESCRIPTION="API for reading/writing vector geospatial data"
+HOMEPAGE="https://github.com/Toblerity/fiona"
+SRC_URI="https://github.com/Toblerity/${PN}/archive/refs/tags/${PV}.tar.gz -> ${P}.gh.tar.gz"
+S="${WORKDIR}/Fiona-${PV}"
+
+LICENSE="BSD"
+SLOT="0"
+KEYWORDS="~amd64 ~x86"
+
+RDEPEND="
+	sci-libs/gdal[geos,sqlite]
+	dev-python/attrs[${PYTHON_USEDEP}]
+	dev-python/click-plugins[${PYTHON_USEDEP}]
+	dev-python/cligj[${PYTHON_USEDEP}]
+	dev-python/munch[${PYTHON_USEDEP}]
+	dev-python/certifi[${PYTHON_USEDEP}]
+"
+
+BDEPEND="
+	dev-python/cython[${PYTHON_USEDEP}]
+	test? (
+		dev-python/boto3[${PYTHON_USEDEP}]
+		sci-libs/gdal[geos,sqlite]
+	)
+"
+
+distutils_enable_tests pytest
+
+python_test() {
+	local deselect=(
+		# disable tests due to networking blocked
+		tests/test_vfs.py::test_open_http
+		tests/test_vfs.py::test_open_zip_https
+		tests/test_collection.py::test_collection_http
+		tests/test_collection.py::test_collection_zip_http
+
+		# disable tests failing due to deprecated GDAL features
+		tests/test_data_paths.py::test_gdal_data_wheel
+		tests/test_data_paths.py::test_proj_data_wheel
+		tests/test_data_paths.py::test_env_gdal_data_wheel
+		tests/test_data_paths.py::test_env_proj_data_wheel
+		tests/test_datetime.py::test_datefield[GPSTrackMaker-datetime]
+		tests/test_datetime.py::test_datefield_null[GPSTrackMaker-datetime]
+		tests/test_drvsupport.py::test_write_or_driver_error[GPSTrackMaker]
+		tests/test_drvsupport.py::test_no_append_driver_cannot_append[GPSTrackMaker]
+		tests/test_drvsupport.py::test_no_append_driver_cannot_append[PCIDSK]
+		tests/test_drvsupport.py::test_write_or_driver_error[DGN]
+
+		# failure in flatgeobuf impl
+		tests/test_drvsupport.py::test_no_append_driver_cannot_append[FlatGeobuf]
+
+		# geos
+		#tests/test_collection.py::test_mask_polygon_triangle
+		#tests/test_collection.py::test_mask_polygon_triangle
+		#tests/test_collection.py::test_mask_polygon_triangle
+
+		# sqlite
+		#tests/test_schema.py::test_geometry_only_schema_write[GPKG]
+		#tests/test_schema.py::test_geometry_only_schema_update[GPKG]
+		#tests/test_schema.py::test_property_only_schema_write[GPKG]
+		#tests/test_schema.py::test_property_only_schema_update[GPKG]
+	)
+
+	mv fiona{,.bak} || die # Avoid non-working local import
+	epytest ${deselect[@]/#/--deselect }
+	mv fiona{.bak,} || die
+}
diff --git a/dev-python/fiona/metadata.xml b/dev-python/fiona/metadata.xml
new file mode 100644
index 000000000..e1e191ee0
--- /dev/null
+++ b/dev-python/fiona/metadata.xml
@@ -0,0 +1,18 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<!DOCTYPE pkgmetadata SYSTEM "https://www.gentoo.org/dtd/metadata.dtd">
+<pkgmetadata>
+  <maintainer type="project">
+    <email>sci@gentoo.org</email>
+    <name>Gentoo Science Project</name>
+  </maintainer>
+  <longdescription lang="en">
+  Fiona reads and writes geographic data files and thereby helps Python 
+  programmers integrate geographic information systems with other 
+  computer systems. Fiona contains extension modules that link the 
+  Geospatial Data Abstraction Library (GDAL).
+</longdescription>
+  <upstream>
+    <remote-id type="github">Toblerity/fiona</remote-id>
+    <remote-id type="pypi">Fiona</remote-id>
+  </upstream>
+</pkgmetadata>
diff --git a/dev-python/fscacher/Manifest b/dev-python/fscacher/Manifest
new file mode 100644
index 000000000..779c470e4
--- /dev/null
+++ b/dev-python/fscacher/Manifest
@@ -0,0 +1,2 @@
+DIST fscacher-0.1.4.gh.tar.gz 35097 BLAKE2B 32cd904d9d3bd36b4b14a55a4d618a99f73afda2807a1f655931b8b26e8ce0b1126773c5b242af824e2014cf634200a17f95d547c75ec4f6a3dd959ee5c37e23 SHA512 e3e85cee4c446552215b6d7092bdc72c31709e05dee7efb52fc6fc985992a3ece338c5a0dee54ed7e6aec797d4b7e2bd77b00f634112134c61f402b604103b5c
+DIST fscacher-0.2.0.gh.tar.gz 37693 BLAKE2B 4e6493d5ec1bb56b53ab72842b6861fbfb916698b80021bbb5c8a8c89be9d90661c78bef9f5b09d3f681b40e45fa52b06dc93231df2228e3a00ee13f913544d8 SHA512 eca32e84f2b317b57aca749644fb76e6c7a0e65384903def29ff70d23740cf2cac8c29e78985dc516f2e01544a0173846fe700e3abb1543fd47c17e9a44ceb9e
diff --git a/dev-python/fscacher/files/fscacher-0.1.4-coverage.patch b/dev-python/fscacher/files/fscacher-0.1.4-coverage.patch
new file mode 100644
index 000000000..ce87d33b3
--- /dev/null
+++ b/dev-python/fscacher/files/fscacher-0.1.4-coverage.patch
@@ -0,0 +1,9 @@
+--- a/tox.ini	2021-09-27 01:00:33.935464308 -0400
++++ b/tox.ini	2021-09-27 02:48:34.349729243 -0400
+@@ -27,7 +27,6 @@
+     asv run {posargs}
+
+ [pytest]
+-addopts = --cov=fscacher --no-cov-on-fail
+ filterwarnings = error
+ norecursedirs = test/data
diff --git a/dev-python/fscacher/files/fscacher-0.2.0-coverage.patch b/dev-python/fscacher/files/fscacher-0.2.0-coverage.patch
new file mode 100644
index 000000000..c5c7f85e2
--- /dev/null
+++ b/dev-python/fscacher/files/fscacher-0.2.0-coverage.patch
@@ -0,0 +1,10 @@
+--- a/tox.ini	2021-09-27 01:00:33.935464308 -0400
++++ b/tox.ini	2021-09-27 02:48:34.349729243 -0400
+@@ -31,7 +31,6 @@
+     asv run --strict {posargs} HEAD^1..HEAD
+
+ [pytest]
+-addopts = --cov=fscacher --no-cov-on-fail
+ filterwarnings =
+     error
+     ignore:The distutils package is deprecated:DeprecationWarning:joblib
diff --git a/dev-python/fscacher/fscacher-0.1.4.ebuild b/dev-python/fscacher/fscacher-0.1.4.ebuild
new file mode 100644
index 000000000..50dcd6914
--- /dev/null
+++ b/dev-python/fscacher/fscacher-0.1.4.ebuild
@@ -0,0 +1,32 @@
+# Copyright 1999-2023 Gentoo Authors
+# Distributed under the terms of the GNU General Public License v2
+
+EAPI=8
+
+PYTHON_COMPAT=( python3_{10..11} )
+inherit distutils-r1
+
+DESCRIPTION="Cache results of operations on heavy file trees"
+HOMEPAGE="https://github.com/con/fscacher"
+SRC_URI="https://github.com/con/fscacher/archive/refs/tags/${PV}.tar.gz -> ${P}.gh.tar.gz"
+
+SLOT="0"
+LICENSE="MIT"
+KEYWORDS="~amd64 ~x86"
+RESTRICT="test"
+
+RDEPEND="
+	dev-python/appdirs[${PYTHON_USEDEP}]
+	dev-python/joblib[${PYTHON_USEDEP}]
+"
+DEPEND="
+	test? (
+		dev-python/pytest-mock[${PYTHON_USEDEP}]
+	)
+"
+
+PATCHES=(
+	"${FILESDIR}/${PN}-0.1.4-coverage.patch"
+)
+
+distutils_enable_tests pytest
diff --git a/dev-python/fscacher/fscacher-0.2.0.ebuild b/dev-python/fscacher/fscacher-0.2.0.ebuild
new file mode 100644
index 000000000..f466d0675
--- /dev/null
+++ b/dev-python/fscacher/fscacher-0.2.0.ebuild
@@ -0,0 +1,31 @@
+# Copyright 1999-2023 Gentoo Authors
+# Distributed under the terms of the GNU General Public License v2
+
+EAPI=8
+
+PYTHON_COMPAT=( python3_{10..11} )
+inherit distutils-r1
+
+DESCRIPTION="Cache results of operations on heavy file trees"
+HOMEPAGE="https://github.com/con/fscacher"
+SRC_URI="https://github.com/con/fscacher/archive/refs/tags/${PV}.tar.gz -> ${P}.gh.tar.gz"
+
+SLOT="0"
+LICENSE="MIT"
+KEYWORDS="~amd64 ~x86"
+
+RDEPEND="
+	dev-python/appdirs[${PYTHON_USEDEP}]
+	dev-python/joblib[${PYTHON_USEDEP}]
+"
+DEPEND="
+	test? (
+		dev-python/pytest-mock[${PYTHON_USEDEP}]
+	)
+"
+
+PATCHES=(
+	"${FILESDIR}/${PN}-0.2.0-coverage.patch"
+)
+
+distutils_enable_tests pytest
diff --git a/dev-python/fscacher/metadata.xml b/dev-python/fscacher/metadata.xml
new file mode 100644
index 000000000..460ce9d09
--- /dev/null
+++ b/dev-python/fscacher/metadata.xml
@@ -0,0 +1,23 @@
+<?xml version='1.0' encoding='UTF-8'?>
+<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
+<pkgmetadata>
+	<maintainer type="person">
+		<email>gentoo@chymera.eu</email>
+		<name>Horea Christian</name>
+	</maintainer>
+	<maintainer type="project">
+		<email>sci@gentoo.org</email>
+		<name>Gentoo Science Project</name>
+	</maintainer>
+	<longdescription lang="en">
+		fscacher provides a cache and decorator for memoizing functions whose
+		outputs depend upon the contents of a file argument. If you have a
+		function `foo()` that takes a file path as its first argument, and if
+		the behavior of `foo()` is pure in the contents of the path and the
+		values of its other arguments, fscacher can help cache that function,
+	</longdescription>
+	<upstream>
+		<remote-id type="github">con/fscacher</remote-id>
+		<remote-id type="pypi">fscacher</remote-id>
+	</upstream>
+</pkgmetadata>
diff --git a/dev-python/fslpy/Manifest b/dev-python/fslpy/Manifest
new file mode 100644
index 000000000..f2c52a88e
--- /dev/null
+++ b/dev-python/fslpy/Manifest
@@ -0,0 +1 @@
+DIST fslpy-3.10.0.tar.gz 4695461 BLAKE2B 9ce74ed6175fb84fe0f123375273a9450c03b659c977b48e3fb874509d5b3f728c75aff850931e1af4fd398fb5eda80a6eef90b2a582e8db3f2135704b4124ed SHA512 b9b12350308d2aee5d10c16582abd96f17b56893287fc32ab3942e8edce8add1f96e1f5c83cca761707be9b2442262e28d961879d5d02e1001006805a74e1cda
diff --git a/dev-python/fslpy/fslpy-3.10.0.ebuild b/dev-python/fslpy/fslpy-3.10.0.ebuild
new file mode 100644
index 000000000..3f6262707
--- /dev/null
+++ b/dev-python/fslpy/fslpy-3.10.0.ebuild
@@ -0,0 +1,47 @@
+# Copyright 1999-2023 Gentoo Authors
+# Distributed under the terms of the GNU General Public License v2
+
+EAPI=8
+
+PYTHON_COMPAT=( python3_{10..11} )
+DISTUTILS_USE_PEP517=setuptools
+inherit distutils-r1 virtualx
+
+DESCRIPTION="The FSL Python Library"
+HOMEPAGE="https://git.fmrib.ox.ac.uk/fsl/fslpy"
+SRC_URI="https://git.fmrib.ox.ac.uk/fsl/${PN}/-/archive/${PV}/${P}.tar.gz"
+
+LICENSE="BSD"
+SLOT="0"
+KEYWORDS="~amd64 ~x86"
+
+RDEPEND="
+	dev-python/dill[${PYTHON_USEDEP}]
+	>=dev-python/h5py-2.9[${PYTHON_USEDEP}]
+	>=dev-python/indexed-gzip-0.7.0[${PYTHON_USEDEP}]
+	>=dev-python/numpy-1[${PYTHON_USEDEP}]
+	>=dev-python/pillow-3.2.0[${PYTHON_USEDEP}]
+	>=dev-python/trimesh-2.37.29[${PYTHON_USEDEP}]
+	=dev-python/wxpython-4*[${PYTHON_USEDEP}]
+	>=sci-libs/rtree-0.8.3[${PYTHON_USEDEP}]
+	>=sci-libs/nibabel-2.4[${PYTHON_USEDEP}]
+	>=dev-python/scipy-0.18[${PYTHON_USEDEP}]
+"
+
+distutils_enable_tests pytest
+distutils_enable_sphinx doc dev-python/sphinx-rtd-theme
+
+python_prepare_all() {
+	# Do not depend on coverage
+	sed -i -e 's/--cov=fsl//g' setup.cfg || die
+
+	distutils-r1_python_prepare_all
+}
+
+src_test() {
+	virtx distutils-r1_src_test
+}
+
+python_test() {
+	epytest -m "not (dicomtest or longtest or fsltest)" || die "Tests failed with ${EPYTHON}"
+}
diff --git a/dev-python/fslpy/metadata.xml b/dev-python/fslpy/metadata.xml
new file mode 100644
index 000000000..d8a7dd52f
--- /dev/null
+++ b/dev-python/fslpy/metadata.xml
@@ -0,0 +1,18 @@
+<?xml version='1.0' encoding='UTF-8'?>
+<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
+<pkgmetadata>
+	<maintainer type="person">
+		<email>gentoo@chymera.eu</email>
+		<name>Horea Christian</name>
+	</maintainer>
+	<maintainer type="project">
+		<email>sci@gentoo.org</email>
+		<name>Gentoo Science Project</name>
+	</maintainer>
+	<longdescription lang="en">
+		The fslpy project is an FSL programming library written (for the processing
+		of neuroimaging data) in Python. It is used by the FSLeyes visualization
+		packag visualization
+		package.
+	</longdescription>
+</pkgmetadata>
diff --git a/dev-python/gammapy/Manifest b/dev-python/gammapy/Manifest
new file mode 100644
index 000000000..6cd1ed25d
--- /dev/null
+++ b/dev-python/gammapy/Manifest
@@ -0,0 +1 @@
+DIST gammapy-1.0.tar.gz 3548471 BLAKE2B c6f66a5fe3158d42fefbae3e14a659d2d637b935cede97e0dfefad32d0aa39a3d5ece23b19e95436deb1299e60b472c7ed01bd5c9c4c1e009618d8dead8b1951 SHA512 acf8f7940b910cdd1277a876e14fde9e962c40d7742610dd8c37b7769b132485bb0aa6fadbd0f68af37858c110985d34679e6f3f4fe52c28a11bd4d56dcf3699
diff --git a/dev-python/gammapy/gammapy-1.0.ebuild b/dev-python/gammapy/gammapy-1.0.ebuild
new file mode 100644
index 000000000..6357014ed
--- /dev/null
+++ b/dev-python/gammapy/gammapy-1.0.ebuild
@@ -0,0 +1,58 @@
+# Copyright 1999-2021 Gentoo Authors
+# Distributed under the terms of the GNU General Public License v2
+
+EAPI=8
+
+PYTHON_COMPAT=( python3_{10..11} )
+DISTUTILS_USE_PEP517=setuptools
+
+inherit distutils-r1 pypi optfeature
+
+DESCRIPTION="A Python package for gamma-ray astronomy"
+HOMEPAGE="https://github.com/gammapy/gammapy"
+
+LICENSE="BSD"
+SLOT="0"
+KEYWORDS="~amd64 ~x86"
+
+#TODO: Package all these pytest deps:
+# 	pytest-doctestplus>=0.2.0
+# 	pytest-remotedata>=0.3.1
+# 	pytest-openfiles>=0.3.1
+# 	pytest-astropy-header>=0.1.2
+# 	pytest-arraydiff>=0.1
+# 	pytest-filter-subpackage>=0.1
+RESTRICT="test"
+
+RDEPEND="
+	dev-python/click[${PYTHON_USEDEP}]
+	>=dev-python/astropy-0.4[${PYTHON_USEDEP}]
+	dev-python/numpy[${PYTHON_USEDEP}]
+	dev-python/pydantic[${PYTHON_USEDEP}]
+	dev-python/pyyaml[${PYTHON_USEDEP}]
+	dev-python/regions[${PYTHON_USEDEP}]
+	dev-python/scipy[${PYTHON_USEDEP}]
+"
+
+# TODO: fix this
+# There is a programmable error in your configuration file:
+# KeyError: 'build_docs'
+#distutils_enable_sphinx docs dev-python/sphinx-astropy
+distutils_enable_tests pytest
+
+pkg_postinst() {
+	elog "To get additional features, a number of optional runtime"
+	elog "dependencies may be installed:"
+	elog ""
+	optfeature "Plotting" dev-python/matplotlib
+	optfeature "Plotting Astronomical Images" dev-python/aplpy
+	optfeature "Read/write CVS files" dev-python/pandas
+	optfeature "Image Processing" dev-python/scikit-image
+	optfeature "Conversion helper functions" dev-python/rootpy
+
+	# In science overlay:
+	optfeature "Image photometry" dev-python/photutils
+	optfeature "Image Utility Functions" dev-python/imageutils
+
+	# Not packaged: Gammalib, ctools, sherpa, imfun, uncertainties, reproject
+}
diff --git a/dev-python/gammapy/gammapy-9999.ebuild b/dev-python/gammapy/gammapy-9999.ebuild
deleted file mode 100644
index 5d608a6fc..000000000
--- a/dev-python/gammapy/gammapy-9999.ebuild
+++ /dev/null
@@ -1,75 +0,0 @@
-# Copyright 1999-2014 Gentoo Foundation
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=5
-
-PYTHON_COMPAT=( python{2_7,3_4} )
-inherit distutils-r1 eutils
-
-if [ ${PV} == "9999" ] ; then
-	inherit git-r3
-	EGIT_REPO_URI="https://github.com/gammapy/${PN}.git"
-else
-	SRC_URI="mirror://pypi/${PN:0:1}/${PN}/${P}.tar.gz"
-	KEYWORDS="~amd64"
-fi
-
-DESCRIPTION="A Python package for gamma-ray astronomy"
-HOMEPAGE="https://github.com/gammapy/gammapy"
-
-LICENSE="BSD"
-SLOT="0"
-IUSE="doc"
-DOCS=( README.rst )
-
-RDEPEND="
-	>=dev-python/astropy-0.4[${PYTHON_USEDEP}]
-	dev-python/astropy-helpers[${PYTHON_USEDEP}]
-	dev-python/numpy[${PYTHON_USEDEP}]"
-
-DEPEND="${RDEPEND}"
-
-python_prepare_all() {
-	distutils-r1_python_prepare_all
-	sed -e '/import ah_bootstrap/d' -i setup.py || die "Removing ah_bootstrap failed"
-}
-
-python_compile_all() {
-	if use doc; then
-		python_export_best
-		VARTEXFONTS="${T}"/fonts \
-			MPLCONFIGDIR="${BUILD_DIR}" \
-			PYTHONPATH="${BUILD_DIR}"/lib \
-			esetup.py build_sphinx
-	fi
-}
-
-python_test() {
-	distutils_install_for_testing
-	cd "${TEST_DIR}" || die
-	"${EPYTHON}" -c "import ${PN}, sys;r = ${PN}.test(verbose=True);sys.exit(r)" \
-		|| die "tests fail with ${EPYTHON}"
-}
-
-python_install_all() {
-	use doc && local HTML_DOCS=( docs/_build/html/. )
-	distutils-r1_python_install_all
-}
-
-pkg_postinst() {
-	elog "To get additional features, a number of optional runtime"
-	elog "dependencies may be installed:"
-	elog ""
-	optfeature "Numerical Methods" sci-libs/scipy
-	optfeature "Plotting" dev-python/matplotlib
-	optfeature "Plotting Astronomical Images" dev-python/aplpy
-	optfeature "Read/write CVS files" dev-python/pandas
-	optfeature "Image Processing" sci-libs/scikits_image
-	optfeature "Conversion helper functions" dev-python/rootpy
-
-	# In science overlay:
-	optfeature "Image photometry" dev-python/photutils
-	optfeature "Image Utility Functions" dev-python/imageutils
-
-	# Not packaged: Gammalib, ctools, sherpa, imfun, uncertainties, reproject
-}
diff --git a/dev-python/gammapy/metadata.xml b/dev-python/gammapy/metadata.xml
index a9f88e7d8..f4a01e639 100644
--- a/dev-python/gammapy/metadata.xml
+++ b/dev-python/gammapy/metadata.xml
@@ -12,5 +12,6 @@ H.E.S.S, and CTA in primarily Galactic plane survey studies.
 </longdescription>
 	<upstream>
 		<remote-id type="github">gammapy/gammapy</remote-id>
+		<remote-id type="pypi">gammapy</remote-id>
 	</upstream>
 </pkgmetadata>
diff --git a/dev-python/geopandas/Manifest b/dev-python/geopandas/Manifest
new file mode 100644
index 000000000..037a125d3
--- /dev/null
+++ b/dev-python/geopandas/Manifest
@@ -0,0 +1 @@
+DIST geopandas-0.13.2.gh.tar.gz 6388249 BLAKE2B 910f32ea7d798bbdeee77be190c57daf7bdc719901a2183b5328ec13619ff9b4145d1717afed8fc71da154d84f388ce2bc30c541478f95ed121c7d8681c691ae SHA512 4dff4bfeca2490081c02c41edf92037fa8a8f4b030b6f6a0cdc231b3119f829604af39277125db9535c66aac0698d2d4dcfac2bb58b92d31bea83f0ee296e21a
diff --git a/dev-python/geopandas/geopandas-0.13.2.ebuild b/dev-python/geopandas/geopandas-0.13.2.ebuild
new file mode 100644
index 000000000..921c13417
--- /dev/null
+++ b/dev-python/geopandas/geopandas-0.13.2.ebuild
@@ -0,0 +1,42 @@
+# Copyright 1999-2023 Gentoo Authors
+# Distributed under the terms of the GNU General Public License v2
+
+EAPI=8
+
+PYTHON_COMPAT=( python3_{10..11} )
+DISTUTILS_USE_PEP517=setuptools
+inherit distutils-r1 optfeature
+
+DESCRIPTION="Python tools for geographic data"
+HOMEPAGE="https://github.com/geopandas/geopandas https://pypi.org/project/geopandas/"
+SRC_URI="https://github.com/geopandas/${PN}/archive/refs/tags/v${PV}.tar.gz -> ${P}.gh.tar.gz"
+
+LICENSE="BSD"
+SLOT="0"
+KEYWORDS="~amd64 ~x86"
+
+RDEPEND="
+	dev-python/pandas[${PYTHON_USEDEP}]
+	dev-python/shapely[${PYTHON_USEDEP}]
+	dev-python/fiona[${PYTHON_USEDEP}]
+	dev-python/pyproj[${PYTHON_USEDEP}]"
+
+distutils_enable_tests pytest
+
+python_test() {
+	local deselect=(
+		# needs network access
+		geopandas/io/tests/test_file.py::test_read_file_url
+		# fails with RuntimeError thrown by matplotlib
+		geopandas/tests/test_plotting.py::TestGeoplotAccessor::test_pandas_kind
+	)
+
+	epytest ${deselect[@]/#/--deselect }
+}
+
+pkg_postinst() {
+	optfeature "plotting" dev-python/matplotlib
+	optfeature "spatial indexes and spatial joins" sci-libs/rtree
+	optfeature "geocoding" sci-geosciences/geopy
+	optfeature "geodatabase access" dev-python/psycopg dev-python/sqlalchemy
+}
diff --git a/dev-python/geopandas/metadata.xml b/dev-python/geopandas/metadata.xml
new file mode 100644
index 000000000..a102c7148
--- /dev/null
+++ b/dev-python/geopandas/metadata.xml
@@ -0,0 +1,19 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<!DOCTYPE pkgmetadata SYSTEM "https://www.gentoo.org/dtd/metadata.dtd">
+<pkgmetadata>
+	<maintainer type="project">
+		<email>sci@gentoo.org</email>
+		<name>Gentoo Science Project</name>
+	</maintainer>
+	<longdescription lang="en">
+		GeoPandas is a project to add support for geographic data to pandas 
+		objects. It currently implements GeoSeries and GeoDataFrame types 
+		which are subclasses of pandas.Series and pandas.DataFrame 
+		respectively. GeoPandas objects can act on shapely geometry objects 
+		and perform geometric operations.
+	</longdescription>
+	<upstream>
+		<remote-id type="github">geopandas/geopandas</remote-id>
+		<remote-id type="pypi">geopandas</remote-id>
+	</upstream>
+</pkgmetadata>
diff --git a/dev-python/gffpandas/Manifest b/dev-python/gffpandas/Manifest
new file mode 100644
index 000000000..1a3ae3b5f
--- /dev/null
+++ b/dev-python/gffpandas/Manifest
@@ -0,0 +1 @@
+DIST gffpandas-1.2.0.gh.tar.gz 32040 BLAKE2B 66f53357876d417997366cdcbacd778f2b17e7df113d21f2a836b082719f549ede5e06a9a6c46e9c5bee2d86946871e68ab1f9b7af0defcaa8a55ae8ef93b274 SHA512 feb67ea93a078547103c1c6b8f32bd6bbd69ab669b93b90aa5f48bc0ebc25ea23e35130976bf1a89ff5e92fdbd054c4df98cc961278c7caaf28b48c202a662d7
diff --git a/dev-python/gffpandas/gffpandas-1.2.0.ebuild b/dev-python/gffpandas/gffpandas-1.2.0.ebuild
new file mode 100644
index 000000000..e0fe2f621
--- /dev/null
+++ b/dev-python/gffpandas/gffpandas-1.2.0.ebuild
@@ -0,0 +1,29 @@
+# Copyright 2021-2023 Gentoo Authors
+# Distributed under the terms of the GNU General Public License v2
+
+EAPI=8
+
+PYTHON_COMPAT=( python3_10 )
+
+inherit distutils-r1
+
+DESCRIPTION="Python library to Filter and sort GFF3 annotations"
+HOMEPAGE="https://github.com/foerstner-lab/gffpandas
+	https://gffpandas.readthedocs.io/en/latest/"
+SRC_URI="https://github.com/foerstner-lab/${PN}/archive/v${PV}.tar.gz -> ${P}.gh.tar.gz"
+
+LICENSE="ISC"
+SLOT="0"
+KEYWORDS="~amd64 ~x86"
+
+RDEPEND="dev-python/pandas[${PYTHON_USEDEP}]"
+
+distutils_enable_tests pytest
+distutils_enable_sphinx docs/source dev-python/sphinx-rtd-theme
+
+python_prepare_all() {
+	# Do not depend on pytest-runner
+	sed -i -e '/pytest-runner/d' setup.py || die
+
+	distutils-r1_python_prepare_all
+}
diff --git a/dev-python/gffpandas/metadata.xml b/dev-python/gffpandas/metadata.xml
new file mode 100644
index 000000000..c3d31ba1d
--- /dev/null
+++ b/dev-python/gffpandas/metadata.xml
@@ -0,0 +1,16 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
+<pkgmetadata>
+	<maintainer type="person">
+		<email>mmokrejs@fold.natur.cuni.cz</email>
+		<name>Martin Mokrejs</name>
+	</maintainer>
+	<maintainer type="project">
+		<email>sci-biology@gentoo.org</email>
+		<name>Gentoo Biology Project</name>
+	</maintainer>
+	<upstream>
+		<remote-id type="github">foerstner-lab/gffpandas</remote-id>
+		<remote-id type="pypi">gffpandas</remote-id>
+	</upstream>
+</pkgmetadata>
diff --git a/dev-python/gmsh_interop/Manifest b/dev-python/gmsh_interop/Manifest
new file mode 100644
index 000000000..2780b9e2e
--- /dev/null
+++ b/dev-python/gmsh_interop/Manifest
@@ -0,0 +1 @@
+DIST gmsh_interop-2021.1.1.tar.gz 24654 BLAKE2B c2959a6b2b7950d4f1bbc4961e3c77c5f28b7ccc53d74410fe851782b471feea14235828f5882bdc57ad8f93719e6e9591cbe0d336670d0f79c77ddfb6486a28 SHA512 b60694dad4bd6e79bc8417812f1df9568599b9f0adfab5f5d2e56b9d1667ff3fd9893b6dc0d1a22ba1aefc7fa214c45aa97464f78af1713dd85eab0a6102ea5c
diff --git a/dev-python/gmsh_interop/gmsh_interop-2021.1.1.ebuild b/dev-python/gmsh_interop/gmsh_interop-2021.1.1.ebuild
new file mode 100644
index 000000000..3185102ba
--- /dev/null
+++ b/dev-python/gmsh_interop/gmsh_interop-2021.1.1.ebuild
@@ -0,0 +1,26 @@
+# Copyright 1999-2022 Gentoo Authors
+# Distributed under the terms of the GNU General Public License v2
+
+EAPI=8
+
+PYTHON_COMPAT=( python3_10 )
+inherit distutils-r1 pypi
+
+DESCRIPTION="Interoperability with Gmsh for Python"
+HOMEPAGE="https://github.com/inducer/gmsh_interop/"
+
+LICENSE="MIT"
+SLOT="0"
+KEYWORDS="~amd64"
+
+RDEPEND="${PYTHON_DEPS}
+	>=dev-python/numpy-1.6.0[${PYTHON_USEDEP}]
+	dev-python/pytools[${PYTHON_USEDEP}]
+	sci-libs/gmsh[blas]
+"
+BDEPEND="
+	test? (
+		dev-python/joblib[${PYTHON_USEDEP}]
+	)
+"
+distutils_enable_tests pytest
diff --git a/dev-python/gmsh_interop/metadata.xml b/dev-python/gmsh_interop/metadata.xml
new file mode 100644
index 000000000..ed015f298
--- /dev/null
+++ b/dev-python/gmsh_interop/metadata.xml
@@ -0,0 +1,16 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
+<pkgmetadata>
+    <maintainer type="person">
+        <email>gentoo@aisha.cc</email>
+        <name>Aisha Tammy</name>
+    </maintainer>
+    <maintainer type="project">
+        <email>sci@gentoo.org</email>
+        <name>Gentoo Science Project</name>
+    </maintainer>
+    <upstream>
+        <remote-id type="pypi">gmsh_interop</remote-id>
+        <remote-id type="github">inducer/gmsh_interop</remote-id>
+    </upstream>
+</pkgmetadata>
diff --git a/dev-python/google-cloud-storage/Manifest b/dev-python/google-cloud-storage/Manifest
new file mode 100644
index 000000000..6bd5af5b0
--- /dev/null
+++ b/dev-python/google-cloud-storage/Manifest
@@ -0,0 +1 @@
+DIST google-cloud-storage-2.7.0.tar.gz 5490914 BLAKE2B 582fcf9a84bedcff41de2b26558ccae96474cbbe91c86bbe6bf53ff6a2fe38d7eb8dbe396fccd36ad252f171ed7eda45974ca9e7867e3ee9542c85570a951aef SHA512 89c4208781735bb0e8b0978202877af324154d5233d7abafd1b2b14b4bb381c18572cfdc791e42577ad929f3c4ded0857d9bd9f4eb52a93ed74e8884d797b365
diff --git a/dev-python/google-cloud-storage/google-cloud-storage-2.7.0.ebuild b/dev-python/google-cloud-storage/google-cloud-storage-2.7.0.ebuild
new file mode 100644
index 000000000..403f75dee
--- /dev/null
+++ b/dev-python/google-cloud-storage/google-cloud-storage-2.7.0.ebuild
@@ -0,0 +1,25 @@
+# Copyright 2021 Gentoo Authors
+# Distributed under the terms of the GNU General Public License v2
+
+EAPI=8
+
+PYTHON_COMPAT=( python3_{10..11} )
+DISTUTILS_USE_PEP517=setuptools
+PYPI_NO_NORMALIZE=1
+
+inherit distutils-r1 pypi
+
+DESCRIPTION="Google Cloud Storage API client library"
+HOMEPAGE="https://github.com/googleapis/python-storage"
+
+LICENSE="Apache-2.0"
+SLOT="0"
+KEYWORDS="~amd64"
+
+RDEPEND="
+	dev-python/google-auth[${PYTHON_USEDEP}]
+	dev-python/google-api-core[${PYTHON_USEDEP}]
+	dev-python/requests[${PYTHON_USEDEP}]
+"
+
+distutils_enable_tests pytest
diff --git a/dev-python/google-cloud-storage/metadata.xml b/dev-python/google-cloud-storage/metadata.xml
new file mode 100644
index 000000000..d67c6b09f
--- /dev/null
+++ b/dev-python/google-cloud-storage/metadata.xml
@@ -0,0 +1,12 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<!DOCTYPE pkgmetadata SYSTEM "https://www.gentoo.org/dtd/metadata.dtd">
+<pkgmetadata>
+    <maintainer type="project">
+        <email>sci@gentoo.org</email>
+        <name>Gentoo Science Project</name>
+    </maintainer>
+    <upstream>
+        <remote-id type="github">googleapis/python-storage</remote-id>
+        <remote-id type="pypi">google-cloud-storage</remote-id>
+    </upstream>
+</pkgmetadata>
diff --git a/dev-python/grabbit/Manifest b/dev-python/grabbit/Manifest
index 77c260c37..eb58b981b 100644
--- a/dev-python/grabbit/Manifest
+++ b/dev-python/grabbit/Manifest
@@ -1,2 +1 @@
-DIST grabbit-0.1.1.tar.gz 70145 BLAKE2B dffde22513697f28f89dfe76f0f8ae827a9a25046090a7abc1759cbc38a3cb1b77a01b8ddca86b347610345560fa93260a72573457496dde924b2dd0acb4776b SHA512 ae816a7c1a3a2ed1e521ba3e87473c447411d9b6efead824ee78707ca34bea24798609bbdec889a97948413021f2720be143bf3d8c4b081dccd243960a543232
 DIST grabbit-0.2.6.tar.gz 94284 BLAKE2B f5ec8da12ac5e6b2060ba9f6f07ea74c17ac143e8b392f4aac48d0fc7d3368995df239a8ed414c19ef109d2f51ace3d34b5be35fe5f55ec05d2812bfefd13115 SHA512 d9a46c06f8bee00a42b2dbb8daa5b440a2f7da35adc4833f001d632ac9ef6ba114aa0e7221eee10149bbb1a0212e983ffb054195de6beba754cad50e6440d549
diff --git a/dev-python/grabbit/grabbit-0.1.1.ebuild b/dev-python/grabbit/grabbit-0.1.1.ebuild
deleted file mode 100644
index dd6a7e6a9..000000000
--- a/dev-python/grabbit/grabbit-0.1.1.ebuild
+++ /dev/null
@@ -1,27 +0,0 @@
-# Copyright 1999-2018 Gentoo Foundation
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=7
-
-PYTHON_COMPAT=( python{2_7,3_4,3_5,3_6} )
-
-inherit distutils-r1
-
-DESCRIPTION="Get grabby with file trees"
-HOMEPAGE="https://github.com/grabbles/grabbit"
-SRC_URI="https://github.com/grabbles/grabbit/archive/${PV}.tar.gz -> ${P}.tar.gz"
-
-LICENSE="MIT"
-SLOT="0"
-KEYWORDS="~amd64"
-IUSE="test"
-
-DEPEND="
-	dev-python/setuptools[${PYTHON_USEDEP}]
-	test? ( >=dev-python/pytest-3.4.1[${PYTHON_USEDEP}] )
-	"
-RDEPEND=""
-
-python_test() {
-	py.test -v || die
-}
diff --git a/dev-python/grabbit/grabbit-0.2.6.ebuild b/dev-python/grabbit/grabbit-0.2.6.ebuild
index 009db3338..722048089 100644
--- a/dev-python/grabbit/grabbit-0.2.6.ebuild
+++ b/dev-python/grabbit/grabbit-0.2.6.ebuild
@@ -1,9 +1,9 @@
-# Copyright 1999-2019 Gentoo Authors
+# Copyright 1999-2023 Gentoo Authors
 # Distributed under the terms of the GNU General Public License v2
 
-EAPI=7
+EAPI=8
 
-PYTHON_COMPAT=( python{2_7,3_4,3_5,3_6} )
+PYTHON_COMPAT=( python3_{10..11} )
 
 inherit distutils-r1
 
@@ -17,11 +17,8 @@ KEYWORDS="~amd64"
 IUSE="test"
 
 DEPEND="
-	dev-python/setuptools[${PYTHON_USEDEP}]
-	test? ( >=dev-python/pytest-3.4.1[${PYTHON_USEDEP}] )
+	test? ( dev-python/pytest[${PYTHON_USEDEP}] )
 	"
 RDEPEND=""
 
-python_test() {
-	py.test -v || die
-}
+distutils_enable_tests pytest
diff --git a/dev-python/grabbit/metadata.xml b/dev-python/grabbit/metadata.xml
index f297bae41..777d8901a 100644
--- a/dev-python/grabbit/metadata.xml
+++ b/dev-python/grabbit/metadata.xml
@@ -2,7 +2,7 @@
 <!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
 <pkgmetadata>
 	<maintainer type="person">
-		<email>horea.christ@gmail.com</email>
+		<email>gentoo@chymera.eu</email>
 		<name>Horea Christian</name>
 	</maintainer>
 	<maintainer type="project">
diff --git a/dev-python/gwcs/Manifest b/dev-python/gwcs/Manifest
new file mode 100644
index 000000000..4e040149b
--- /dev/null
+++ b/dev-python/gwcs/Manifest
@@ -0,0 +1 @@
+DIST gwcs-0.18.3.tar.gz 184361 BLAKE2B a4afcf3d6281f65f1ff6733bb83f82ba089fc56d2a21c2d6f5fd8370ef518b97376ebe718a9e4f9fa34ae80fc66baecf9e32835bb18f1737bf3f47e972e31118 SHA512 51aac4dd1f3b835b274f265cf26d4f9cf757435bb8355d43a31b7eba665991c233b46f9e0a87d22985c04fdabc0455958b99f37aeb55a04a9c0b4901d5069891
diff --git a/dev-python/gwcs/gwcs-0.18.3-r1.ebuild b/dev-python/gwcs/gwcs-0.18.3-r1.ebuild
new file mode 100644
index 000000000..eef5aeb36
--- /dev/null
+++ b/dev-python/gwcs/gwcs-0.18.3-r1.ebuild
@@ -0,0 +1,42 @@
+# Copyright 1999-2023 Gentoo Authors
+# Distributed under the terms of the GNU General Public License v2
+
+EAPI=8
+
+PYTHON_COMPAT=( python3_{10..11} )
+DISTUTILS_USE_PEP517=setuptools
+
+inherit distutils-r1 pypi
+
+DESCRIPTION="Generalized World Coordinate System"
+HOMEPAGE="https://gwcs.readthedocs.io/en/latest/"
+
+LICENSE="BSD"
+SLOT="0"
+KEYWORDS="~amd64 ~x86"
+# Tests do not pass, reported upstream:
+# https://github.com/spacetelescope/gwcs/issues/437
+RESTRICT=test
+
+BDEPEND="dev-python/setuptools-scm[${PYTHON_USEDEP}]
+	test? (
+		dev-python/pytest-doctestplus[${PYTHON_USEDEP}]
+	)
+"
+
+RDEPEND="
+	dev-python/asdf[${PYTHON_USEDEP}]
+	>=dev-python/astropy-4.1[${PYTHON_USEDEP}]
+	dev-python/numpy[${PYTHON_USEDEP}]
+	dev-python/scipy[${PYTHON_USEDEP}]
+"
+
+# TODO: package stsci-rtd-theme
+#distutils_enable_sphinx docs dev-python/sphinx-astropy dev-python/sphinx-automodapi dev-python/sphinx_rtd_theme
+distutils_enable_tests pytest
+
+python_test() {
+	# discovers things in docs dir if we do not
+	# explicitly set it to run on the tests dir
+	epytest gwcs/tests
+}
diff --git a/dev-python/gwcs/metadata.xml b/dev-python/gwcs/metadata.xml
new file mode 100644
index 000000000..d7b713ef5
--- /dev/null
+++ b/dev-python/gwcs/metadata.xml
@@ -0,0 +1,11 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
+<pkgmetadata>
+	<maintainer type="project">
+		<email>sci-astronomy@gentoo.org</email>
+		<name>Gentoo Astronomy Project</name>
+	</maintainer>
+	<upstream>
+		<remote-id type="pypi">gwcs</remote-id>
+	</upstream>
+</pkgmetadata>
diff --git a/dev-python/hdbscan/Manifest b/dev-python/hdbscan/Manifest
new file mode 100644
index 000000000..7ffc42c8b
--- /dev/null
+++ b/dev-python/hdbscan/Manifest
@@ -0,0 +1 @@
+DIST hdbscan-0.8.29.tar.gz 11666106 BLAKE2B de324386d7d2178f74ea958fa75e5eccb9dcdeba3d85cecce1150930e2d687caecbc79469de6ad62806c5bd860962bba57f27323c69f3abc6b0d4694a553656d SHA512 fd349c1c6c09f0288a9a2501eb7794fb03139c11261a835d90f1c9cd80955a4d8d075ff3864ddb9cfcbc204a3d0662011074bdb29b66b72d5469f76bc4f7ecca
diff --git a/dev-python/hdbscan/hdbscan-0.8.29.ebuild b/dev-python/hdbscan/hdbscan-0.8.29.ebuild
new file mode 100644
index 000000000..33947fd22
--- /dev/null
+++ b/dev-python/hdbscan/hdbscan-0.8.29.ebuild
@@ -0,0 +1,32 @@
+# Copyright 2021-2023 Gentoo Authors
+# Distributed under the terms of the GNU General Public License v2
+
+EAPI=8
+
+PYTHON_COMPAT=( python3_{10..11} )
+DISTUTILS_USE_PEP517=setuptools
+inherit distutils-r1 pypi
+
+DESCRIPTION="A high performance implementation of HDBSCAN clustering."
+HOMEPAGE="https://github.com/scikit-learn-contrib/hdbscan"
+
+LICENSE="BSD"
+SLOT="0"
+KEYWORDS="~amd64 ~x86"
+IUSE="test"
+# Reported upstream:
+# https://github.com/scikit-learn-contrib/hdbscan/issues/501
+RESTRICT="test"
+
+DEPEND=""
+RDEPEND="
+	dev-python/cython[${PYTHON_USEDEP}]
+	dev-python/joblib[${PYTHON_USEDEP}]
+	dev-python/numpy[${PYTHON_USEDEP}]
+	dev-python/scipy[${PYTHON_USEDEP}]
+	dev-python/six[${PYTHON_USEDEP}]
+	sci-libs/scikit-learn[${PYTHON_USEDEP}]
+"
+BDEPEND=""
+
+distutils_enable_tests pytest
diff --git a/dev-python/hdbscan/metadata.xml b/dev-python/hdbscan/metadata.xml
new file mode 100644
index 000000000..3e9aab1c5
--- /dev/null
+++ b/dev-python/hdbscan/metadata.xml
@@ -0,0 +1,29 @@
+<?xml version='1.0' encoding='UTF-8'?>
+<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
+<pkgmetadata>
+	<maintainer type="person">
+		<email>gentoo@chymera.eu</email>
+		<name>Horea Christian</name>
+	</maintainer>
+	<maintainer type="project">
+		<email>sci@gentoo.org</email>
+		<name>Gentoo Science Project</name>
+	</maintainer>
+	<longdescription lang="en">
+		HDBSCAN - Hierarchical Density-Based Spatial Clustering of Applications with
+		Noise. Performs DBSCAN over varying epsilon values and integrates the result
+		to find a clustering that gives the best stability over epsilon. This allows
+		HDBSCAN to find clusters of varying densities (unlike DBSCAN), and be more
+		robust to parameter selection.
+
+		In practice this means that HDBSCAN returns a good clustering straight away
+		with little or no parameter tuning -- and the primary parameter, minimum
+		cluster size, is intuitive and easy to select. HDBSCAN is ideal for
+		exploratory data analysis; it's a fast and robust algorithm that you can
+		trust to return meaningful clusters (if there are any).
+	</longdescription>
+	<upstream>
+		<remote-id type="github">scikit-learn-contrib/hdbscan</remote-id>
+		<remote-id type="pypi">hdbscan</remote-id>
+	</upstream>
+</pkgmetadata>
diff --git a/dev-python/hdf5storage/Manifest b/dev-python/hdf5storage/Manifest
index 0679b631e..caea5df39 100644
--- a/dev-python/hdf5storage/Manifest
+++ b/dev-python/hdf5storage/Manifest
@@ -1,2 +1 @@
-DIST hdf5storage-0.1.13.zip 115134 BLAKE2B 9f0de9351063c901a8d2487f892d4721c849ed9dfef06448a34cf916462c2e6003ec5a3d75d6da7c4d4d0e336aa5cb5f5709a5af3b4915a774940fa85d3cbc6b SHA512 d6c4259e3f387bf58fbd1d4db739a3172b5c3c716b6930e4b65d431d852a93299c4e2e3075c1714ec184106d559f8e4e560b36338eb5ced1adb454e377a079df
-DIST hdf5storage-0.1.14.zip 118087 BLAKE2B 6c247a72399196da8be5b897b149d4e1ae783afcae1f419fbd1c2ae9b8517f8bbfbbc5818ff1d2789eb77a8eab58e79a5e822a1ecebd0f0771d094171ba9c073 SHA512 15029b7eef4afeb52c189e42b0a22ee75f50c7f09617712d5322c81ac11674afc014b8d8aa5882f3350702871849aa8fcbc31ee4a8bb1cccac42a6fbba6867ec
+DIST hdf5storage-0.1.19.tar.gz 92294 BLAKE2B b4379e9c6b69af1c205072d0d8b29f6322c3271cc1f5e56ab81a4ec3c09db9f9ac107b912e4d74772253ade269db589ed4ac140cde6cfd95346de7fcdc6dc752 SHA512 0ea4068be1af2521bba3fba3b0b020c0faff64be487644c46350ef19f4f3997593af90438db5b0d9b80ac303ff99755a0f59504ad34cfa27f1bc8c7881f024ce
diff --git a/dev-python/hdf5storage/hdf5storage-0.1.13.ebuild b/dev-python/hdf5storage/hdf5storage-0.1.13.ebuild
deleted file mode 100644
index ed7954124..000000000
--- a/dev-python/hdf5storage/hdf5storage-0.1.13.ebuild
+++ /dev/null
@@ -1,21 +0,0 @@
-# Copyright 1999-2017 Gentoo Foundation
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=6
-PYTHON_COMPAT=( python2_7 python3_{4,5} )
-
-inherit distutils-r1
-
-DESCRIPTION="Read/write Python types to/from HDF5 files, including MATLAB v7.3 MAT files"
-HOMEPAGE="https://github.com/frejanordsiek/hdf5storage"
-SRC_URI="mirror://pypi/${PN:0:1}/${PN}/${P}.zip"
-
-LICENSE="BSD-2"
-SLOT="0"
-KEYWORDS="~amd64"
-
-RDEPEND="
-	dev-python/numpy[${PYTHON_USEDEP}]
-	dev-python/h5py[${PYTHON_USEDEP}]
-	"
-DEPEND="${RDEPEND}"
\ No newline at end of file
diff --git a/dev-python/hdf5storage/hdf5storage-0.1.14.ebuild b/dev-python/hdf5storage/hdf5storage-0.1.14.ebuild
deleted file mode 100644
index ed7954124..000000000
--- a/dev-python/hdf5storage/hdf5storage-0.1.14.ebuild
+++ /dev/null
@@ -1,21 +0,0 @@
-# Copyright 1999-2017 Gentoo Foundation
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=6
-PYTHON_COMPAT=( python2_7 python3_{4,5} )
-
-inherit distutils-r1
-
-DESCRIPTION="Read/write Python types to/from HDF5 files, including MATLAB v7.3 MAT files"
-HOMEPAGE="https://github.com/frejanordsiek/hdf5storage"
-SRC_URI="mirror://pypi/${PN:0:1}/${PN}/${P}.zip"
-
-LICENSE="BSD-2"
-SLOT="0"
-KEYWORDS="~amd64"
-
-RDEPEND="
-	dev-python/numpy[${PYTHON_USEDEP}]
-	dev-python/h5py[${PYTHON_USEDEP}]
-	"
-DEPEND="${RDEPEND}"
\ No newline at end of file
diff --git a/dev-python/hdf5storage/hdf5storage-0.1.19.ebuild b/dev-python/hdf5storage/hdf5storage-0.1.19.ebuild
new file mode 100644
index 000000000..ab64fefbc
--- /dev/null
+++ b/dev-python/hdf5storage/hdf5storage-0.1.19.ebuild
@@ -0,0 +1,25 @@
+# Copyright 1999-2022 Gentoo Authors
+# Distributed under the terms of the GNU General Public License v2
+
+EAPI=8
+PYTHON_COMPAT=( python3_{10..11} )
+DISTUTILS_USE_PEP517=setuptools
+
+inherit distutils-r1
+
+DESCRIPTION="Read/write Python types to/from HDF5 files, including MATLAB v7.3 MAT files"
+HOMEPAGE="https://github.com/frejanordsiek/hdf5storage"
+
+SRC_URI="https://github.com/frejanordsiek/hdf5storage/archive/refs/tags/v${PV}.tar.gz -> ${P}.tar.gz"
+KEYWORDS="~amd64 ~x86"
+
+LICENSE="BSD"
+SLOT="0"
+
+RDEPEND="
+	dev-python/numpy[${PYTHON_USEDEP}]
+	dev-python/h5py[${PYTHON_USEDEP}]
+"
+DEPEND="${RDEPEND}"
+
+distutils_enable_tests pytest
diff --git a/dev-python/hdf5storage/hdf5storage-9999.ebuild b/dev-python/hdf5storage/hdf5storage-9999.ebuild
index 194a845ce..1bcf35a57 100644
--- a/dev-python/hdf5storage/hdf5storage-9999.ebuild
+++ b/dev-python/hdf5storage/hdf5storage-9999.ebuild
@@ -1,14 +1,24 @@
-# Copyright 1999-2017 Gentoo Foundation
+# Copyright 1999-2022 Gentoo Authors
 # Distributed under the terms of the GNU General Public License v2
 
-EAPI=6
-PYTHON_COMPAT=( python2_7 python3_{4,5} )
+EAPI=8
+PYTHON_COMPAT=( python3_{10..11} )
+DISTUTILS_USE_PEP517=setuptools
 
-inherit distutils-r1 git-r3
+inherit distutils-r1
 
 DESCRIPTION="Read/write Python types to/from HDF5 files, including MATLAB v7.3 MAT files"
 HOMEPAGE="https://github.com/frejanordsiek/hdf5storage"
-EGIT_REPO_URI="https://github.com/frejanordsiek/${PN}.git git://github.com/frejanordsiek/${PN}.git"
+
+if [[ ${PV} == 9999 ]]; then
+	inherit git-r3
+	EGIT_REPO_URI="https://github.com/frejanordsiek/hdf5storage"
+else
+	COMMIT=09dfc5fb3a6a3f9c32c2479a896c7f14d3c8d830
+	SRC_URI="https://github.com/frejanordsiek/hdf5storage/archive/${COMMIT}.tar.gz -> ${P}.tar.gz"
+	S="${WORKDIR}"/${PN}-${COMMIT}
+	KEYWORDS="~amd64"
+fi
 
 LICENSE="BSD"
 SLOT="0"
@@ -16,5 +26,7 @@ SLOT="0"
 RDEPEND="
 	dev-python/numpy[${PYTHON_USEDEP}]
 	dev-python/h5py[${PYTHON_USEDEP}]
-	"
-DEPEND="${RDEPEND}"
\ No newline at end of file
+"
+DEPEND="${RDEPEND}"
+
+distutils_enable_tests pytest
diff --git a/dev-python/hdmf-zarr/Manifest b/dev-python/hdmf-zarr/Manifest
new file mode 100644
index 000000000..6b7d2418b
--- /dev/null
+++ b/dev-python/hdmf-zarr/Manifest
@@ -0,0 +1 @@
+DIST hdmf_zarr-0.5.0.tar.gz 3095566 BLAKE2B f824b480bb99ffbf495b18505d561a3511af60f654df66f89c2c5c081ba49889512e29cb31b6eb617ef7abac58472fa4b6d9f23cd9c33be436a77ceb2d54130a SHA512 205dd5b2de1a403fc7098e7ba26e4bbba1949b8f50641173ea614011e821a77a461ab255f19afefddcd5fa019ed0e7c047fd7c940a2d09a1f63c5de5f1ac50cb
diff --git a/dev-python/hdmf-zarr/files/hdmf-zarr-0.5.0-coverage.patch b/dev-python/hdmf-zarr/files/hdmf-zarr-0.5.0-coverage.patch
new file mode 100644
index 000000000..d82c30960
--- /dev/null
+++ b/dev-python/hdmf-zarr/files/hdmf-zarr-0.5.0-coverage.patch
@@ -0,0 +1,28 @@
+diff --git a/pyproject.toml b/pyproject.toml
+index 4008b3b..40e281a 100644
+--- a/pyproject.toml
++++ b/pyproject.toml
+@@ -62,9 +62,6 @@ exclude = [".git_archival.txt"]
+ [tool.hatch.build.targets.wheel]
+ packages = ["src/hdmf_zarr"]
+
+-[tool.pytest.ini_options]
+-addopts = "--cov --cov-report html"
+-
+ [tool.codespell]
+ skip = "htmlcov,.git,.mypy_cache,.pytest_cache,.coverage,*.pdf,*.svg,venvs,.tox,./docs/_build/*,*.ipynb"
+ ignore-words-list = "datas"
+diff --git a/tox.ini b/tox.ini
+index 720a97f..66d0df3 100644
+--- a/tox.ini
++++ b/tox.ini
+@@ -28,8 +28,7 @@ commands =
+ [testenv:localcoverage]
+ basepython = python3.11
+ commands =
+-    pytest --cov=hdmf_zarr
+-    coverage html -d tests/coverage/htmlcov
++    pytest
+
+ # Test with python 3.11; pinned dev and optional reqs
+ [testenv:py311-optional]
diff --git a/dev-python/hdmf-zarr/hdmf-zarr-0.5.0.ebuild b/dev-python/hdmf-zarr/hdmf-zarr-0.5.0.ebuild
new file mode 100644
index 000000000..692197867
--- /dev/null
+++ b/dev-python/hdmf-zarr/hdmf-zarr-0.5.0.ebuild
@@ -0,0 +1,32 @@
+# Copyright 1999-2022 Gentoo Authors
+# Distributed under the terms of the GNU General Public License v2
+
+EAPI=8
+PYTHON_COMPAT=( python3_{10..11} )
+DISTUTILS_USE_PEP517=hatchling
+
+inherit distutils-r1 pypi
+
+DESCRIPTION="Zarr I/O backend for HDMF"
+HOMEPAGE="https://github.com/hdmf-dev/hdmf-zarr"
+#SRC_URI="https://github.com/hdmf-dev/hdmf-zarr/archive/refs/tags/${PV}.tar.gz -> ${P}.tar.gz"
+KEYWORDS="~amd64 ~x86"
+
+LICENSE="BSD"
+SLOT="0"
+
+RDEPEND="
+	dev-python/hdmf[${PYTHON_USEDEP}]
+	dev-python/numcodecs[${PYTHON_USEDEP}]
+	dev-python/numpy[${PYTHON_USEDEP}]
+	dev-python/pynwb[${PYTHON_USEDEP}]
+	dev-python/threadpoolctl[${PYTHON_USEDEP}]
+	dev-python/zarr[${PYTHON_USEDEP}]
+"
+DEPEND="${RDEPEND}"
+
+PATCHES=(
+	"${FILESDIR}/${P}-coverage.patch"
+)
+
+distutils_enable_tests pytest
diff --git a/dev-python/hdmf-zarr/metadata.xml b/dev-python/hdmf-zarr/metadata.xml
new file mode 100644
index 000000000..1ced471a1
--- /dev/null
+++ b/dev-python/hdmf-zarr/metadata.xml
@@ -0,0 +1,16 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
+<pkgmetadata>
+	<maintainer type="person">
+		<email>gentoo@chymera.eu</email>
+		<name>Horea Christian</name>
+	</maintainer>
+	<maintainer type="project">
+		<email>sci@gentoo.org</email>
+		<name>Gentoo Science Project</name>
+	</maintainer>
+	<upstream>
+		<remote-id type="github">hdmf-dev/hdmf-zarr</remote-id>
+		<remote-id type="pypi">hdmf-zarr</remote-id>
+	</upstream>
+</pkgmetadata>
diff --git a/dev-python/hdmf/Manifest b/dev-python/hdmf/Manifest
new file mode 100644
index 000000000..204753b4e
--- /dev/null
+++ b/dev-python/hdmf/Manifest
@@ -0,0 +1 @@
+DIST hdmf-3.13.0.tar.gz 15855926 BLAKE2B 8eb386540768a83954745c02f7142d2a0b466ef670baaf13a1dfee0ce02261f0f89a9b173dfb8d2673d1f538c35e800117f6f0fe2ca77e5ca6a94b01e9908917 SHA512 5d6f97abb28b46136b3a62f915f8c14cc48e49c1ec3d44e3d863b1c3e7aebb1cfea428b77311ca51dbf5ef9a1e529e73cdb477d863e3d0cd6641fbf79a043f20
diff --git a/dev-python/hdmf/files/hdmf-3.11.0-no_test_coverage.patch b/dev-python/hdmf/files/hdmf-3.11.0-no_test_coverage.patch
new file mode 100644
index 000000000..e44a68902
--- /dev/null
+++ b/dev-python/hdmf/files/hdmf-3.11.0-no_test_coverage.patch
@@ -0,0 +1,10 @@
+--- a/pyproject.toml	2020-02-01 19:00:00.000000000 -0500
++++ b/pyproject.toml	2023-12-11 12:00:19.368474488 -0500
+@@ -76,7 +76,6 @@
+ # verbose = 1
+
+ [tool.pytest.ini_options]
+-addopts = "--cov --cov-report html"
+ norecursedirs = "tests/unit/helpers"
+
+ [tool.codespell]
diff --git a/dev-python/hdmf/hdmf-3.13.0.ebuild b/dev-python/hdmf/hdmf-3.13.0.ebuild
new file mode 100644
index 000000000..7068afb01
--- /dev/null
+++ b/dev-python/hdmf/hdmf-3.13.0.ebuild
@@ -0,0 +1,31 @@
+# Copyright 1999-2023 Gentoo Authors
+# Distributed under the terms of the GNU General Public License v2
+
+EAPI=8
+
+DISTUTILS_USE_PEP517=hatchling
+PYTHON_COMPAT=( python3_{10..12} )
+inherit distutils-r1 pypi
+
+DESCRIPTION="The Hierarchical Data Modeling Framework"
+HOMEPAGE="https://github.com/hdmf-dev/hdmf"
+SRC_URI="$(pypi_sdist_url hdmf)"
+
+SLOT="0"
+LICENSE="BSD"
+KEYWORDS="~amd64 ~x86"
+
+RDEPEND="
+	dev-python/h5py[${PYTHON_USEDEP}]
+	dev-python/jsonschema[${PYTHON_USEDEP}]
+	dev-python/numpy[${PYTHON_USEDEP}]
+	dev-python/pandas[${PYTHON_USEDEP}]
+	dev-python/ruamel-yaml[${PYTHON_USEDEP}]
+	dev-python/scipy[${PYTHON_USEDEP}]
+	"
+
+PATCHES=(
+	"${FILESDIR}/${PN}-3.11.0-no_test_coverage.patch"
+	)
+
+distutils_enable_tests pytest
diff --git a/dev-python/hdmf/metadata.xml b/dev-python/hdmf/metadata.xml
new file mode 100644
index 000000000..ac3f7a6cb
--- /dev/null
+++ b/dev-python/hdmf/metadata.xml
@@ -0,0 +1,22 @@
+<?xml version='1.0' encoding='UTF-8'?>
+<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
+<pkgmetadata>
+	<maintainer type="person">
+		<email>gentoo@chymera.eu</email>
+		<name>Horea Christian</name>
+	</maintainer>
+	<maintainer type="project">
+		<email>sci@gentoo.org</email>
+		<name>Gentoo Science Project</name>
+	</maintainer>
+	<longdescription lang="en">
+		The Hierarchical Data Modeling Framework, or HDMF, is a Python package
+		for working with hierarchical data. It provides APIs for specifying
+		data models, reading and writing data to different storage backends,
+		and representing data with Python object.
+	</longdescription>
+	<upstream>
+		<remote-id type="github">hdmf-dev/hdmf</remote-id>
+		<remote-id type="pypi">hdmf</remote-id>
+	</upstream>
+</pkgmetadata>
diff --git a/dev-python/heudiconv/Manifest b/dev-python/heudiconv/Manifest
new file mode 100644
index 000000000..fe38a3307
--- /dev/null
+++ b/dev-python/heudiconv/Manifest
@@ -0,0 +1,2 @@
+DIST heudiconv-0.13.0.tar.gz 9158053 BLAKE2B 9f87fbcd5ea8ccca39cc029f1bdd84906412a22e5d18e2afe280d19737f0dda4c03248ba93f58c06aae4b15366477e8a5d1c41d09d1b1d3a10ff673aaa050e26 SHA512 b867ee0a60ad98099a3802e290ebb24b858befbd45e93772fafe437a87ea867c5076680ea3ed7856272397267c740ef2eade9f64ffc0d4216d4a37be39add158
+DIST heudiconv-1.0.0.tar.gz 9158631 BLAKE2B af5b3dee2448a025a231fad0ac9692b13d431288ea0ca19b4919d9ae83c86a7c72cf11f9bd3a0ec6b18259d2f8e8cecf9372a0fae605ecb5e9cac0bd4975693a SHA512 165bd814e3c7f25b51ed8884bddde45b82dc226ee93af5984b822aa53ad5e7504aae57088cd1f777c62835669e8816d95dbf84de7fb379038308dca7871d8739
diff --git a/dev-python/heudiconv/heudiconv-0.13.0.ebuild b/dev-python/heudiconv/heudiconv-0.13.0.ebuild
new file mode 100644
index 000000000..7f7db0b0e
--- /dev/null
+++ b/dev-python/heudiconv/heudiconv-0.13.0.ebuild
@@ -0,0 +1,42 @@
+# Copyright 1999-2023 Gentoo Authors
+# Distributed under the terms of the GNU General Public License v2
+
+EAPI=8
+
+DISTUTILS_USE_PEP517=setuptools
+PYTHON_COMPAT=( python3_{10..11} )
+inherit distutils-r1 pypi
+
+DESCRIPTION="Flexible DICOM conversion to structured directory layouts"
+HOMEPAGE="
+	https://github.com/nipy/heudiconv
+	https://heudiconv.readthedocs.io/en/latest/
+"
+
+SLOT="0"
+LICENSE="Apache-2.0"
+KEYWORDS="~amd64 ~x86"
+
+RDEPEND="
+	dev-python/filelock[${PYTHON_USEDEP}]
+	dev-python/versioningit[${PYTHON_USEDEP}]
+	sci-biology/dcm2niix
+	sci-biology/dcmstack[${PYTHON_USEDEP}]
+	sci-libs/nibabel[${PYTHON_USEDEP}]
+	sci-libs/nipype[${PYTHON_USEDEP}]
+	sci-libs/pydicom[${PYTHON_USEDEP}]
+	"
+BDEPEND="
+	test? (
+		dev-python/mock[${PYTHON_USEDEP}]
+		dev-python/six[${PYTHON_USEDEP}]
+	)
+"
+
+# Reported upstream:
+# https://github.com/nipy/heudiconv/issues/679
+EPYTEST_DESELECT=(
+	heudiconv/tests/test_main.py::test_prepare_for_datalad
+)
+
+distutils_enable_tests pytest
diff --git a/dev-python/heudiconv/heudiconv-1.0.0.ebuild b/dev-python/heudiconv/heudiconv-1.0.0.ebuild
new file mode 100644
index 000000000..7f7db0b0e
--- /dev/null
+++ b/dev-python/heudiconv/heudiconv-1.0.0.ebuild
@@ -0,0 +1,42 @@
+# Copyright 1999-2023 Gentoo Authors
+# Distributed under the terms of the GNU General Public License v2
+
+EAPI=8
+
+DISTUTILS_USE_PEP517=setuptools
+PYTHON_COMPAT=( python3_{10..11} )
+inherit distutils-r1 pypi
+
+DESCRIPTION="Flexible DICOM conversion to structured directory layouts"
+HOMEPAGE="
+	https://github.com/nipy/heudiconv
+	https://heudiconv.readthedocs.io/en/latest/
+"
+
+SLOT="0"
+LICENSE="Apache-2.0"
+KEYWORDS="~amd64 ~x86"
+
+RDEPEND="
+	dev-python/filelock[${PYTHON_USEDEP}]
+	dev-python/versioningit[${PYTHON_USEDEP}]
+	sci-biology/dcm2niix
+	sci-biology/dcmstack[${PYTHON_USEDEP}]
+	sci-libs/nibabel[${PYTHON_USEDEP}]
+	sci-libs/nipype[${PYTHON_USEDEP}]
+	sci-libs/pydicom[${PYTHON_USEDEP}]
+	"
+BDEPEND="
+	test? (
+		dev-python/mock[${PYTHON_USEDEP}]
+		dev-python/six[${PYTHON_USEDEP}]
+	)
+"
+
+# Reported upstream:
+# https://github.com/nipy/heudiconv/issues/679
+EPYTEST_DESELECT=(
+	heudiconv/tests/test_main.py::test_prepare_for_datalad
+)
+
+distutils_enable_tests pytest
diff --git a/dev-python/heudiconv/metadata.xml b/dev-python/heudiconv/metadata.xml
new file mode 100644
index 000000000..a98cbf459
--- /dev/null
+++ b/dev-python/heudiconv/metadata.xml
@@ -0,0 +1,16 @@
+<?xml version='1.0' encoding='UTF-8'?>
+<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
+<pkgmetadata>
+	<maintainer type="person">
+		<email>gentoo@chymera.eu</email>
+		<name>Horea Christian</name>
+	</maintainer>
+	<maintainer type="project">
+		<email>sci@gentoo.org</email>
+		<name>Gentoo Science Project</name>
+	</maintainer>
+	<upstream>
+		<remote-id type="pypi">heudiconv</remote-id>
+		<remote-id type="github">nipy/heudiconv</remote-id>
+	</upstream>
+</pkgmetadata>
diff --git a/dev-python/hist/Manifest b/dev-python/hist/Manifest
new file mode 100644
index 000000000..722ab9aa8
--- /dev/null
+++ b/dev-python/hist/Manifest
@@ -0,0 +1 @@
+DIST hist-2.7.2.tar.gz 991866 BLAKE2B 6785114e1a5b3e38b9917c5d8b660e6d03dbe56d7a3238c971686ffc03ec1e9c6361ea6ed73ed61b10a4074b13d4ad785b676a61a856069ba23789985949787e SHA512 92a320a80509eaeaa496c2713b349e3b1442c46a7aeda04e362fdd692aea3f43f06e5bdb35293ca70f9b24536c24494fa1c806e9f9e8573559c13abeee22c4ce
diff --git a/dev-python/hist/hist-2.7.2.ebuild b/dev-python/hist/hist-2.7.2.ebuild
new file mode 100644
index 000000000..082844a5f
--- /dev/null
+++ b/dev-python/hist/hist-2.7.2.ebuild
@@ -0,0 +1,26 @@
+EAPI=8
+
+PYTHON_COMPAT=( python3_{10..12} )
+DISTUTILS_USE_PEP517=hatchling
+SETUPTOOLS_SCM_PRETEND_VERSION=${PV}
+inherit distutils-r1 pypi
+
+DESCRIPTION="Histogramming for analysis powered by boost-histogram "
+HOMEPAGE="https://github.com/scikit-hep/hist"
+
+LICENSE="BSD"
+SLOT="0"
+KEYWORDS="~amd64"
+
+RDEPEND="
+	>=dev-python/boost-histogram-1.3.1[${PYTHON_USEDEP}]
+	>=dev-python/histoprint-2.2.0[${PYTHON_USEDEP}]
+	>=dev-python/numpy-1.14.5[${PYTHON_USEDEP}]
+"
+BDEPEND="
+	dev-python/hatch-vcs[${PYTHON_USEDEP}]
+"
+
+RESTRICT="test"
+# needs mplhep and dask_histogram ...
+#distutils_enable_tests pytest
diff --git a/dev-python/hist/metadata.xml b/dev-python/hist/metadata.xml
new file mode 100644
index 000000000..566083fe3
--- /dev/null
+++ b/dev-python/hist/metadata.xml
@@ -0,0 +1,19 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
+<pkgmetadata>
+	<maintainer type="project">
+		<email>sci@gentoo.org</email>
+		<name>Gentoo Science Project</name>
+	</maintainer>
+	<maintainer type="person">
+		<email>alexander@neuwirth-informatik.de</email>
+		<name>Alexander Puck Neuwirth</name>
+	</maintainer>
+	<longdescription lang="en">
+	Hist is an analyst-friendly front-end for boost-histogram, designed for Python 3.7+ (3.6 users get version 2.4)
+	</longdescription>
+	<upstream>
+		<remote-id type="pypi">hist</remote-id>
+		<remote-id type="github">scikit-hep/hist</remote-id>
+	</upstream>
+</pkgmetadata>
diff --git a/dev-python/histoprint/Manifest b/dev-python/histoprint/Manifest
new file mode 100644
index 000000000..2914a2419
--- /dev/null
+++ b/dev-python/histoprint/Manifest
@@ -0,0 +1 @@
+DIST histoprint-2.4.0.tar.gz 359154 BLAKE2B f10abcff02875f1a27b31256c5daf00500e0177986052f3fc9b013a0be0f63daf58f9d9b7bf2b6b5510758e080a118c6ad07801b055019e7e226ee631da57154 SHA512 bbf7c90acb66c298588304a15c7ae3ec0536fb01a468b4aa7b944115e242a0ef3e2ef21c181e8476845f5d7611a944f43de0c9cf80faeab2ddbb8422432e2fa6
diff --git a/dev-python/histoprint/histoprint-2.4.0.ebuild b/dev-python/histoprint/histoprint-2.4.0.ebuild
new file mode 100644
index 000000000..b6395b898
--- /dev/null
+++ b/dev-python/histoprint/histoprint-2.4.0.ebuild
@@ -0,0 +1,20 @@
+EAPI=8
+
+PYTHON_COMPAT=( python3_{10..12} )
+DISTUTILS_USE_PEP517=setuptools
+inherit distutils-r1 pypi
+
+DESCRIPTION="Pretty print histograms to the console"
+HOMEPAGE="https://github.com/scikit-hep/histoprint"
+
+LICENSE="MIT"
+SLOT="0"
+KEYWORDS="~amd64"
+
+RDEPEND="
+	dev-python/numpy[${PYTHON_USEDEP}]
+	>=dev-python/click-7.0.0[${PYTHON_USEDEP}]
+	>=dev-python/uhi-0.2.1[${PYTHON_USEDEP}]
+"
+
+distutils_enable_tests pytest
diff --git a/dev-python/histoprint/metadata.xml b/dev-python/histoprint/metadata.xml
new file mode 100644
index 000000000..78373f05f
--- /dev/null
+++ b/dev-python/histoprint/metadata.xml
@@ -0,0 +1,19 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
+<pkgmetadata>
+	<maintainer type="project">
+		<email>sci@gentoo.org</email>
+		<name>Gentoo Science Project</name>
+	</maintainer>
+	<maintainer type="person">
+		<email>alexander@neuwirth-informatik.de</email>
+		<name>Alexander Puck Neuwirth</name>
+	</maintainer>
+	<longdescription lang="en">
+	Histoprint uses a mix of terminal color codes and Unicode trickery (i.e. combining characters) to plot overlaying histograms. Some terminals are not able to display Unicode combining characters correctly. Histoprint can still be used in those terminals, but the character set needs to be constrained to the non-combining ones (see below).
+	</longdescription>
+	<upstream>
+		<remote-id type="pypi">histoprint</remote-id>
+		<remote-id type="github">scikit-hep/histoprint</remote-id>
+	</upstream>
+</pkgmetadata>
diff --git a/dev-python/holoviews/Manifest b/dev-python/holoviews/Manifest
new file mode 100644
index 000000000..ec3bb1815
--- /dev/null
+++ b/dev-python/holoviews/Manifest
@@ -0,0 +1 @@
+DIST holoviews-1.15.3.tar.gz 6905214 BLAKE2B 60bb7008dd5af474295245eb0dbce240cfb4dcaf4122bc6073561e829c506b670201ac7d2b7ae1eea640929eb0993148c22c1a3e8d8ccb8e00582a2fbd3e696b SHA512 b1d4b64503511c61ede67d6d45472acde1afb854e19f7a30acb35d7fab2400ffe1e43db7b6e85eefe542b8353982af9cb41d505412bb0674cb20926c24f76494
diff --git a/dev-python/holoviews/holoviews-1.15.3.ebuild b/dev-python/holoviews/holoviews-1.15.3.ebuild
new file mode 100644
index 000000000..154b7195d
--- /dev/null
+++ b/dev-python/holoviews/holoviews-1.15.3.ebuild
@@ -0,0 +1,45 @@
+# Copyright 1999-2023 Gentoo Authors
+# Distributed under the terms of the GNU General Public License v2
+
+EAPI=8
+
+PYTHON_COMPAT=( python3_{10..11} )
+
+# HoloViews imports from "distutils" at runtime.
+DISTUTILS_USE_SETUPTOOLS=rdepend
+
+inherit distutils-r1 pypi
+
+DESCRIPTION="Make data analysis and visualization seamless and simple"
+HOMEPAGE="https://holoviews.org"
+
+LICENSE="BSD"
+SLOT="0"
+KEYWORDS="~amd64"
+# Reported upstream:
+# https://github.com/holoviz/holoviews/issues/5592
+RESTRICT="test"
+
+DEPEND="
+	>=dev-python/param-1.9.3[${PYTHON_USEDEP}]
+	>=dev-python/pyct-0.4.4[${PYTHON_USEDEP}]
+"
+BDEPEND="
+	test? (
+		dev-python/bokeh[${PYTHON_USEDEP}]
+		dev-python/matplotlib[${PYTHON_USEDEP}]
+		dev-python/nbconvert[${PYTHON_USEDEP}]
+		dev-python/pillow[${PYTHON_USEDEP}]
+		dev-python/plotly[${PYTHON_USEDEP}]
+		sci-visualization/dash[${PYTHON_USEDEP}]
+	)
+"
+RDEPEND="${DEPEND}
+	dev-python/colorcet[${PYTHON_USEDEP}]
+	dev-python/pandas[${PYTHON_USEDEP}]
+	>=dev-python/numpy-1.0.0[${PYTHON_USEDEP}]
+	>=dev-python/panel-0.8.0[${PYTHON_USEDEP}]
+	>=dev-python/pyviz_comms-0.7.4[${PYTHON_USEDEP}]
+"
+
+distutils_enable_tests pytest
diff --git a/dev-python/holoviews/metadata.xml b/dev-python/holoviews/metadata.xml
new file mode 100644
index 000000000..e2afe391a
--- /dev/null
+++ b/dev-python/holoviews/metadata.xml
@@ -0,0 +1,13 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
+<pkgmetadata>
+	<maintainer type="project">
+		<email>sci@gentoo.org</email>
+		<name>Gentoo Science Project</name>
+	</maintainer>
+	<stabilize-allarches/>
+	<upstream>
+		<remote-id type="pypi">holoviews</remote-id>
+		<remote-id type="github">holoviz/holoviews</remote-id>
+	</upstream>
+</pkgmetadata>
diff --git a/dev-python/hopcroftkarp/Manifest b/dev-python/hopcroftkarp/Manifest
new file mode 100644
index 000000000..dbe9fb11b
--- /dev/null
+++ b/dev-python/hopcroftkarp/Manifest
@@ -0,0 +1 @@
+DIST hopcroftkarp-1.2.5_p1.tar.gz 25754 BLAKE2B 78401cb878d84abaaaef3f06e4764bf34b1711f332957493c4bf8b2c46082f293a48a70d06d9600f36fe949298860e10dce27cbe09b518e5d1b1f4225be1733f SHA512 f6b265273ed72f3927dd604c1279d8ce225ba88600faf83f052b875b1dc62ea733faac82d4665ba43d296bad089a122600b7dee968f3b4e001ed18803a22cabf
diff --git a/dev-python/hopcroftkarp/files/hopcroftkarp-1.2.5_p1-setup_py.patch b/dev-python/hopcroftkarp/files/hopcroftkarp-1.2.5_p1-setup_py.patch
new file mode 100644
index 000000000..b76b882e9
--- /dev/null
+++ b/dev-python/hopcroftkarp/files/hopcroftkarp-1.2.5_p1-setup_py.patch
@@ -0,0 +1,13 @@
+diff --git a/setup.py b/setup.py
+index 552ab4e..022b5d3 100644
+--- a/setup.py
++++ b/setup.py
+@@ -10,7 +10,7 @@ setup(
+ 	url='https://github.com/sofiat-olaosebikan/hopcroftkarp',
+ 	license = 'GPL',
+ 	keywords = 'hopcroftkarp algorithm, maximum cardinality matching, bipartite graphs',
+-	packages=find_packages(),
++	packages=[ 'hopcroftkarp' ],
+ 	zip_safe=True,
+ 	package_dir={'hopcroftkarp': 'hopcroftkarp'},
+ 	test_suite='test',
diff --git a/dev-python/hopcroftkarp/hopcroftkarp-1.2.5_p1-r1.ebuild b/dev-python/hopcroftkarp/hopcroftkarp-1.2.5_p1-r1.ebuild
new file mode 100644
index 000000000..29c57f90a
--- /dev/null
+++ b/dev-python/hopcroftkarp/hopcroftkarp-1.2.5_p1-r1.ebuild
@@ -0,0 +1,23 @@
+# Copyright 1999-2023 Gentoo Authors
+# Distributed under the terms of the GNU General Public License v2
+
+EAPI=8
+
+PYTHON_COMPAT=( python3_{10..11} )
+DISTUTILS_USE_PEP517=setuptools
+
+inherit distutils-r1
+
+DESCRIPTION="python frontend for the fast ripser tda tool"
+HOMEPAGE="https://ripser.scikit-tda.org/ https://github.com/sofiatolaosebikan/hopcroftkarp"
+COMMIT="2846e1dd3265d95d2bddb0cf4190b830cbb4efe6"
+SRC_URI="https://github.com/sofiatolaosebikan/hopcroftkarp/archive/${COMMIT}.tar.gz -> ${P}.tar.gz"
+S="${WORKDIR}"/${PN}-${COMMIT}
+
+LICENSE="MIT"
+SLOT="0"
+KEYWORDS="~amd64 ~x86"
+
+PATCHES=( "${FILESDIR}"/${P}-setup_py.patch )
+
+distutils_enable_tests pytest
diff --git a/dev-python/hopcroftkarp/metadata.xml b/dev-python/hopcroftkarp/metadata.xml
new file mode 100644
index 000000000..6959005e7
--- /dev/null
+++ b/dev-python/hopcroftkarp/metadata.xml
@@ -0,0 +1,15 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
+<pkgmetadata>
+	<maintainer type="person">
+		<email>gentoo@aisha.cc</email>
+		<name>Aisha Tammy</name>
+	</maintainer>
+	<maintainer type="project">
+		<email>sci@gentoo.org</email>
+		<name>Gentoo Science Project</name>
+	</maintainer>
+	<upstream>
+		<remote-id type="github">sofiatolaosebikan/hopcroftkarp</remote-id>
+	</upstream>
+</pkgmetadata>
diff --git a/dev-python/imageutils/imageutils-9999.ebuild b/dev-python/imageutils/imageutils-9999.ebuild
deleted file mode 100644
index 1e04e3394..000000000
--- a/dev-python/imageutils/imageutils-9999.ebuild
+++ /dev/null
@@ -1,57 +0,0 @@
-# Copyright 1999-2014 Gentoo Foundation
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=5
-
-PYTHON_COMPAT=( python{2_7,3_4} )
-inherit distutils-r1
-
-if [ ${PV} == "9999" ] ; then
-	inherit git-r3
-	EGIT_REPO_URI="https://github.com/astropy/${PN}.git"
-else
-	SRC_URI="mirror://pypi/${PN:0:1}/${PN}/${P}.tar.gz"
-	KEYWORDS="~amd64"
-fi
-
-DESCRIPTION="Image processing utilities for Astropy"
-HOMEPAGE="https://github.com/astropy/imageutils"
-
-LICENSE="BSD"
-SLOT="0"
-IUSE="doc"
-
-DOCS=( README.rst )
-
-RDEPEND="
-	>=dev-python/astropy-0.4[${PYTHON_USEDEP}]
-	dev-python/astropy-helpers[${PYTHON_USEDEP}]
-	dev-python/numpy[${PYTHON_USEDEP}]"
-DEPEND="${RDEPEND}"
-
-python_prepare_all() {
-	distutils-r1_python_prepare_all
-	sed -e '/import ah_bootstrap/d' -i setup.py || die "Removing ah_bootstrap failed"
-}
-
-python_test() {
-	distutils_install_for_testing
-	cd "${TEST_DIR}" || die
-	"${EPYTHON}" -c "import ${PN}, sys;r = ${PN}.test(verbose=True);sys.exit(r)" \
-		|| die "tests fail with ${EPYTHON}"
-}
-
-python_compile_all() {
-	if use doc; then
-		python_export_best
-		VARTEXFONTS="${T}"/fonts \
-			MPLCONFIGDIR="${BUILD_DIR}" \
-			PYTHONPATH="${BUILD_DIR}"/lib \
-			esetup.py build_sphinx
-	fi
-}
-
-python_install_all() {
-	use doc && local HTML_DOCS=( docs/_build/html/. )
-	distutils-r1_python_install_all
-}
diff --git a/dev-python/imageutils/metadata.xml b/dev-python/imageutils/metadata.xml
deleted file mode 100644
index b75b1ab3a..000000000
--- a/dev-python/imageutils/metadata.xml
+++ /dev/null
@@ -1,16 +0,0 @@
-<?xml version="1.0" encoding="UTF-8"?>
-<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
-<pkgmetadata>
-	<maintainer type="project">
-		<email>sci-astronomy@gentoo.org</email>
-		<name>Gentoo Astronomy Project</name>
-	</maintainer>
-	<longdescription lang="en">
-imageutils is a collection of image processing utilities that are generally
-useful to astronomers. These will likely become part of the core AstroPy
-package before the 1.0 release.
-</longdescription>
-	<upstream>
-		<remote-id type="github">astropy/imageutils</remote-id>
-	</upstream>
-</pkgmetadata>
diff --git a/dev-python/inference/Manifest b/dev-python/inference/Manifest
deleted file mode 100644
index da7b1529b..000000000
--- a/dev-python/inference/Manifest
+++ /dev/null
@@ -1 +0,0 @@
-DIST inference-0.4.tar.xz 811572 BLAKE2B 93ba8499fe14bb24793b10cf689aa9c84b746e733257152ab8633b6e52d89c35fa8eef07baded5b361e23d8d46a7eac0876eb8ea5d472d5054fc332b5989c6da SHA512 49af21fd9874ec845435515220a5dd0cf8a5012fbae866c477304eb1f6958fdd2b372bd71010bfa80137afe2580df06c099c153c6ea6588839f27ab1f3729e75
diff --git a/dev-python/inference/inference-0.4.ebuild b/dev-python/inference/inference-0.4.ebuild
deleted file mode 100644
index faf123a18..000000000
--- a/dev-python/inference/inference-0.4.ebuild
+++ /dev/null
@@ -1,50 +0,0 @@
-# Copyright 1999-2015 Gentoo Foundation
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=5
-
-PYTHON_COMPAT=( python2_7 )
-
-inherit distutils-r1 flag-o-matic fortran-2
-
-DESCRIPTION="Collection of Python modules for statistical inference"
-HOMEPAGE="http://inference.astro.cornell.edu/"
-SRC_URI="http://dev.gentoo.org/~jlec/distfiles/${P}.tar.xz"
-
-SLOT="0"
-LICENSE="all-rights-reserved"
-KEYWORDS="~amd64 ~x86"
-IUSE=""
-
-DEPEND="sci-libs/scipy[${PYTHON_USEDEP}]"
-RDEPEND="${DEPEND}
-	dev-python/matplotlib[${PYTHON_USEDEP}]"
-
-# buggy tests
-RESTRICT="test"
-
-S="${WORKDIR}"/${P}/package
-
-pkg_setup() {
-	fortran-2_pkg_setup
-}
-
-python_prepare_all() {
-	# The usual numpy.distutils hacks when fortran is used
-	append-ldflags -shared
-	append-fflags -fPIC
-	export NUMPY_FCONFIG="config_fc --noopt --noarch"
-	distutils-r1_python_prepare_all
-}
-
-python_compile() {
-	distutils-r1_python_compile ${NUMPY_CONFIG}
-}
-
-python_test() {
-	nosetests --verbose --verbosity=3 || die
-}
-
-python_install() {
-	distutils-r1_python_install ${NUMPY_FCONFIG}
-}
diff --git a/dev-python/inference/metadata.xml b/dev-python/inference/metadata.xml
deleted file mode 100644
index 9e0d8673e..000000000
--- a/dev-python/inference/metadata.xml
+++ /dev/null
@@ -1,16 +0,0 @@
-<?xml version="1.0" encoding="UTF-8"?>
-<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
-<pkgmetadata>
-	<maintainer type="project">
-		<email>sci@gentoo.org</email>
-		<name>Gentoo Science Project</name>
-	</maintainer>
-	<longdescription lang="en">
-The inference package is a collection of Python modules implementing
-a variety of methods targeting the statistical inference
-problems—and the statistical modeling style—of the physical
-sciences. The target discipline is astronomy, and the choice of
-problems and methods most directly targets the needs of astronomers,
-but many tools here may be of use to other physical scientists. 
-</longdescription>
-</pkgmetadata>
diff --git a/dev-python/instant/Manifest b/dev-python/instant/Manifest
deleted file mode 100644
index 7c546bbfc..000000000
--- a/dev-python/instant/Manifest
+++ /dev/null
@@ -1,3 +0,0 @@
-DIST instant-1.4.0.tar.gz 147300 BLAKE2B dfbbf001fe01186e2c4224f455b3d40a8b9d84c1b71ae47fec1711ea820088c08496bf64d86243eb010dcf1f20987dd98ade12f1edee2c15f5dcced8358d8d80 SHA512 80144935f6810d1b20b0b2539f2931ff0e5f6fbdd38b2356eb2d1012bcf28291616564766e9066b748de132e2c100db0788c6f1866a59964d6380fa8380595b8
-DIST instant-2016.2.0.tar.gz 74052 BLAKE2B 0e0e2047859370147d7debca5ab159939b50ad2846863beb8d3b5cd60576658f738cffb99d9a92dd6c0d436029df4061c05f4dbd0beadf648999026d0b0a31a1 SHA512 b9752a98d9ae7b08c7113eeae45f3c3c028dd25d538d26c59cb84e90f8cdbac58126dff55b336d56ea2ba1a5fe3ae08b614046738d76978ec91b28e53c491ae2
-DIST instant-2017.1.0.tar.gz 74482 BLAKE2B cd53bb1ba6af26e6be12b9ee54dfbc6954c7af59b1988c6e664a54f7f460466cd111f44802b7056534175a906caa182d83e7056cc5f6f3e1368f572e786a86e1 SHA512 e0623d4718b08481061de4beec10d05b8ac05128a0396caffe705cb0e75dc79b58e900a4a71bba2d1960d3e1eb9bcccb6abf5798ed8f99825e4710df9dc07aef
diff --git a/dev-python/instant/instant-1.4.0.ebuild b/dev-python/instant/instant-1.4.0.ebuild
deleted file mode 100644
index d72f562a0..000000000
--- a/dev-python/instant/instant-1.4.0.ebuild
+++ /dev/null
@@ -1,20 +0,0 @@
-# Copyright 1999-2014 Gentoo Foundation
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=5
-
-PYTHON_COMPAT=( python2_7 )
-
-inherit distutils-r1
-
-DESCRIPTION="Instant inlining of C and C++ code in Python"
-HOMEPAGE="https://bitbucket.org/fenics-project/instant/"
-SRC_URI="https://bitbucket.org/fenics-project/instant/downloads/${P}.tar.gz"
-
-LICENSE="GPL-2"
-SLOT="0"
-KEYWORDS="~amd64 ~x86"
-IUSE=""
-
-DEPEND="dev-lang/swig"
-RDEPEND="dev-python/numpy[${PYTHON_USEDEP}]"
diff --git a/dev-python/instant/instant-2016.2.0.ebuild b/dev-python/instant/instant-2016.2.0.ebuild
deleted file mode 100644
index d9ee9318b..000000000
--- a/dev-python/instant/instant-2016.2.0.ebuild
+++ /dev/null
@@ -1,20 +0,0 @@
-# Copyright 1999-2017 Gentoo Foundation
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=6
-
-PYTHON_COMPAT=( python2_7 )
-
-inherit distutils-r1
-
-DESCRIPTION="Instant inlining of C and C++ code in Python"
-HOMEPAGE="https://bitbucket.org/fenics-project/instant/"
-SRC_URI="https://bitbucket.org/fenics-project/instant/downloads/${P}.tar.gz"
-
-LICENSE="GPL-2"
-SLOT="0"
-KEYWORDS="~amd64 ~x86"
-IUSE=""
-
-DEPEND="dev-lang/swig"
-RDEPEND="dev-python/numpy[${PYTHON_USEDEP}]"
diff --git a/dev-python/instant/instant-2017.1.0.ebuild b/dev-python/instant/instant-2017.1.0.ebuild
deleted file mode 100644
index 5e6cf2907..000000000
--- a/dev-python/instant/instant-2017.1.0.ebuild
+++ /dev/null
@@ -1,20 +0,0 @@
-# Copyright 1999-2017 Gentoo Foundation
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=6
-
-PYTHON_COMPAT=( python3_4 python3_5 python3_6 )
-
-inherit distutils-r1
-
-DESCRIPTION="Instant inlining of C and C++ code in Python"
-HOMEPAGE="https://bitbucket.org/fenics-project/instant/"
-SRC_URI="https://bitbucket.org/fenics-project/instant/downloads/${P}.tar.gz"
-
-LICENSE="GPL-2"
-SLOT="0"
-KEYWORDS="~amd64 ~x86"
-IUSE=""
-
-DEPEND="dev-lang/swig"
-RDEPEND="dev-python/numpy[${PYTHON_USEDEP}]"
diff --git a/dev-python/instant/metadata.xml b/dev-python/instant/metadata.xml
deleted file mode 100644
index bd49e87a7..000000000
--- a/dev-python/instant/metadata.xml
+++ /dev/null
@@ -1,16 +0,0 @@
-<?xml version="1.0" encoding="UTF-8"?>
-<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
-<pkgmetadata>
-	<maintainer type="project">
-		<email>sci@gentoo.org</email>
-		<name>Gentoo Science Project</name>
-	</maintainer>
-	<longdescription lang="en">
-Instant is a Python module that allows for instant inlining of C and C++
-code in Python. It is a small Python module built on top of SWIG and
-Distutils. It is part of the FEniCS Project (http://www.fenics.org)
-</longdescription>
-	<upstream>
-		<remote-id type="bitbucket">fenics-project/instant</remote-id>
-	</upstream>
-</pkgmetadata>
diff --git a/dev-python/interleave/Manifest b/dev-python/interleave/Manifest
new file mode 100644
index 000000000..6040d8f7d
--- /dev/null
+++ b/dev-python/interleave/Manifest
@@ -0,0 +1 @@
+DIST interleave-0.2.0.tar.gz 15879 BLAKE2B 72056882821415b68f404e757098b8cb89968feef717fec61bae7a92d97d90a68a2e2aff490c5acc07d55410c28c6310b6882d122f0be64eaada4348ddf6c588 SHA512 ed47603fb0b917e7355c9e461584b5c92ba4beef2416e602da0c8b70f36d9d5d5bc57fa3a71bb00e96e35bd580873dca10cdd19280ace7b717765a8386576a0f
diff --git a/dev-python/interleave/files/interleave-0.2.0-drop-coverage.patch b/dev-python/interleave/files/interleave-0.2.0-drop-coverage.patch
new file mode 100644
index 000000000..5f358f6aa
--- /dev/null
+++ b/dev-python/interleave/files/interleave-0.2.0-drop-coverage.patch
@@ -0,0 +1,18 @@
+--- a/tox.ini
++++ b/tox.ini
+@@ -8,8 +8,6 @@
+ passenv = CI
+ deps =
+     pytest~=7.0
+-    pytest-cov~=3.0
+-    pytest-rerunfailures~=10.0
+ commands =
+     pytest {posargs} test
+
+@@ -31,7 +29,6 @@
+     mypy src test
+
+ [pytest]
+-addopts = --cov=interleave --no-cov-on-fail
+ filterwarnings = error
+ norecursedirs = test/data
diff --git a/dev-python/interleave/interleave-0.2.0.ebuild b/dev-python/interleave/interleave-0.2.0.ebuild
new file mode 100644
index 000000000..4434b8fdd
--- /dev/null
+++ b/dev-python/interleave/interleave-0.2.0.ebuild
@@ -0,0 +1,24 @@
+# Copyright 1999-2023 Gentoo Authors
+# Distributed under the terms of the GNU General Public License v2
+
+EAPI=8
+
+DISTUTILS_USE_PEP517=setuptools
+PYTHON_COMPAT=( python3_{10..11} )
+
+inherit distutils-r1 pypi
+
+DESCRIPTION="Yield from multiple iterators as values become available"
+HOMEPAGE="https://github.com/jwodder/interleave"
+
+LICENSE="MIT"
+SLOT="0"
+KEYWORDS="~amd64 ~arm ~arm64 ~x86 ~amd64-linux ~x86-linux"
+
+RDEPEND="
+	dev-python/wheel[${PYTHON_USEDEP}]
+"
+
+PATCHES=( "${FILESDIR}/${PN}-0.2.0-drop-coverage.patch" )
+
+distutils_enable_tests pytest
diff --git a/dev-python/interleave/metadata.xml b/dev-python/interleave/metadata.xml
new file mode 100644
index 000000000..66b4383b6
--- /dev/null
+++ b/dev-python/interleave/metadata.xml
@@ -0,0 +1,21 @@
+<?xml version='1.0' encoding='UTF-8'?>
+<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
+<pkgmetadata>
+	<maintainer type="person">
+		<email>gentoo@chymera.eu</email>
+		<name>Horea Christian</name>
+	</maintainer>
+	<maintainer type="project">
+		<email>sci@gentoo.org</email>
+		<name>Gentoo Science Project</name>
+	</maintainer>
+	<longdescription lang="en">
+		The interleave package provides a function of the same name that
+		takes a number of iterators, runs them in separate threads, and
+		yields the values produced as soon as each one is available.
+	</longdescription>
+	<upstream>
+		<remote-id type="github">jwodder/interleave</remote-id>
+		<remote-id type="pypi">interleave</remote-id>
+	</upstream>
+</pkgmetadata>
diff --git a/dev-python/ipykernel/ipykernel-9999.ebuild b/dev-python/ipykernel/ipykernel-9999.ebuild
deleted file mode 100644
index 3f00e4588..000000000
--- a/dev-python/ipykernel/ipykernel-9999.ebuild
+++ /dev/null
@@ -1,34 +0,0 @@
-# Copyright 1999-2017 Gentoo Foundation
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=6
-
-PYTHON_COMPAT=( python2_7 python3_{4,5} )
-PYTHON_REQ_USE="threads(+)"
-
-inherit distutils-r1 git-r3
-
-DESCRIPTION="IPython Kernel for Jupyter"
-HOMEPAGE="https://github.com/ipython/ipykernel"
-EGIT_REPO_URI="https://github.com/ipython/${PN}.git git://github.com/ipython/${PN}.git"
-
-LICENSE="BSD"
-SLOT="0"
-KEYWORDS=""
-IUSE="test"
-
-RDEPEND="
-	>=dev-python/ipython-4.0.0[${PYTHON_USEDEP}]
-	dev-python/jupyter_client[${PYTHON_USEDEP}]
-	>=www-servers/tornado-4.0[${PYTHON_USEDEP}]
-	dev-python/traitlets[${PYTHON_USEDEP}]
-	"
-DEPEND="${RDEPEND}
-	test? (
-		dev-python/nose[${PYTHON_USEDEP}]
-	)
-	"
-
-python_test() {
-	nosetests --verbose ipykernel || die
-}
diff --git a/dev-python/ipykernel/metadata.xml b/dev-python/ipykernel/metadata.xml
deleted file mode 100644
index d1399a897..000000000
--- a/dev-python/ipykernel/metadata.xml
+++ /dev/null
@@ -1,14 +0,0 @@
-<?xml version="1.0" encoding="UTF-8"?>
-<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
-<pkgmetadata>
-	<maintainer type="project">
-		<email>sci@gentoo.org</email>
-		<name>Gentoo Science Project</name>
-	</maintainer>
-	<longdescription>
-This package provides the IPython kernel for Jupyter.
-</longdescription>
-	<upstream>
-		<remote-id type="github">ipython/ipykernel</remote-id>
-	</upstream>
-</pkgmetadata>
diff --git a/dev-python/ipyparallel/ipyparallel-9999.ebuild b/dev-python/ipyparallel/ipyparallel-9999.ebuild
deleted file mode 100644
index 90da1d810..000000000
--- a/dev-python/ipyparallel/ipyparallel-9999.ebuild
+++ /dev/null
@@ -1,60 +0,0 @@
-# Copyright 1999-2017 Gentoo Foundation
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=6
-
-PYTHON_COMPAT=( python2_7 python3_{4,5} )
-PYTHON_REQ_USE="threads(+)"
-
-inherit distutils-r1 git-r3
-
-DESCRIPTION="Interactive Parallel Computing with IPython"
-HOMEPAGE="http://ipython.org/"
-EGIT_REPO_URI="https://github.com/ipython/${PN}.git git://github.com/ipython/${PN}.git"
-
-LICENSE="BSD"
-SLOT="0"
-KEYWORDS=""
-IUSE="doc test"
-
-RDEPEND="
-	dev-python/ipython_genutils[${PYTHON_USEDEP}]
-	dev-python/decorator[${PYTHON_USEDEP}]
-	>=dev-python/pyzmq-14.4.0[${PYTHON_USEDEP}]
-	dev-python/ipykernel[${PYTHON_USEDEP}]
-	!<dev-python/ipython-4.0.0[smp]
-	>=dev-python/ipython-4.0.0[${PYTHON_USEDEP}]
-	dev-python/notebook[${PYTHON_USEDEP}]
-	dev-python/jupyter_client[${PYTHON_USEDEP}]
-	www-servers/tornado[${PYTHON_USEDEP}]
-	"
-DEPEND="${RDEPEND}
-	doc? ( dev-python/sphinx[${PYTHON_USEDEP}] )
-	test? (
-		dev-python/mock[${PYTHON_USEDEP}]
-		dev-python/nose[${PYTHON_USEDEP}]
-		dev-python/requests[${PYTHON_USEDEP}]
-	)
-	"
-
-python_prepare_all() {
-	# Prevent un-needed download during build
-	if use doc; then
-		sed -e "/^    'sphinx.ext.intersphinx',/d" -i docs/source/conf.py || die
-	fi
-
-	distutils-r1_python_prepare_all
-}
-
-python_compile_all() {
-	use doc && emake -C docs html
-}
-
-python_test() {
-	iptest ipyparallel.tests -- -vsx || die
-}
-
-python_install_all() {
-	use doc && HTML_DOCS=( docs/build/html/. )
-	distutils-r1_python_install_all
-}
diff --git a/dev-python/ipyparallel/metadata.xml b/dev-python/ipyparallel/metadata.xml
deleted file mode 100644
index 1d9e7c2d3..000000000
--- a/dev-python/ipyparallel/metadata.xml
+++ /dev/null
@@ -1,12 +0,0 @@
-<?xml version="1.0" encoding="UTF-8"?>
-<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
-<pkgmetadata>
-	<maintainer type="project">
-		<email>sci@gentoo.org</email>
-		<name>Gentoo Science Project</name>
-	</maintainer>
-	<longdescription>
-Interactive Parallel Computing with IPython.
-ipyparallel is the new home of IPython.parallel.
-</longdescription>
-</pkgmetadata>
diff --git a/dev-python/ipython_genutils/ipython_genutils-9999.ebuild b/dev-python/ipython_genutils/ipython_genutils-9999.ebuild
deleted file mode 100644
index 807e4588a..000000000
--- a/dev-python/ipython_genutils/ipython_genutils-9999.ebuild
+++ /dev/null
@@ -1,28 +0,0 @@
-# Copyright 1999-2017 Gentoo Foundation
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=6
-
-PYTHON_COMPAT=( python2_7 python3_{4,5} )
-
-inherit distutils-r1 git-r3
-
-DESCRIPTION="Vestigial utilities from IPython"
-HOMEPAGE="https://github.com/ipython/ipython_genutils"
-EGIT_REPO_URI="https://github.com/ipython/${PN}.git git://github.com/ipython/${PN}.git"
-
-LICENSE="BSD"
-SLOT="0"
-KEYWORDS=""
-IUSE="test"
-
-DEPEND="
-	test? (
-		dev-python/nose[${PYTHON_USEDEP}]
-		dev-python/coverage[${PYTHON_USEDEP}]
-	)
-	"
-
-python_test() {
-	nosetests --with-coverage --cover-package=ipython_genutils ipython_genutils || die
-}
diff --git a/dev-python/ipython_genutils/metadata.xml b/dev-python/ipython_genutils/metadata.xml
deleted file mode 100644
index 05e43b726..000000000
--- a/dev-python/ipython_genutils/metadata.xml
+++ /dev/null
@@ -1,17 +0,0 @@
-<?xml version="1.0" encoding="UTF-8"?>
-<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
-<pkgmetadata>
-	<maintainer type="project">
-		<email>sci@gentoo.org</email>
-		<name>Gentoo Science Project</name>
-	</maintainer>
-	<longdescription>
-This package contains some common utilities shared by Jupyter and
-IPython projects during The Big Split. As soon as possible, those
-packages will remove their dependency on this, and this repo will
-go away. No packages outside IPython/Jupyter should depend on it.
-</longdescription>
-	<upstream>
-		<remote-id type="github">ipython/ipython_genutils</remote-id>
-	</upstream>
-</pkgmetadata>
diff --git a/dev-python/ipywidgets/Manifest b/dev-python/ipywidgets/Manifest
deleted file mode 100644
index c60d344cd..000000000
--- a/dev-python/ipywidgets/Manifest
+++ /dev/null
@@ -1 +0,0 @@
-DIST ipywidgets-4.1.1.tar.gz 321646 BLAKE2B bb2a82d979d195bee420c4b9e780391e9b8764f49932115fe916f766b7311624b67228d6812a0be0e8cff4c6b85e192319b4f72962befc86d8031334ddc00fa4 SHA512 53b18ae432f72d3305333e92f488f62bb36f83d37fab59e4d103fb77a7ee266d03b96e6de4ffcc2a0f67d6fd892ed1d984c0b188d6cbd527ff3e950e885a5fe4
diff --git a/dev-python/ipywidgets/ipywidgets-4.1.1.ebuild b/dev-python/ipywidgets/ipywidgets-4.1.1.ebuild
deleted file mode 100644
index 5497fcc79..000000000
--- a/dev-python/ipywidgets/ipywidgets-4.1.1.ebuild
+++ /dev/null
@@ -1,36 +0,0 @@
-# Copyright 1999-2017 Gentoo Foundation
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=6
-
-PYTHON_COMPAT=( python2_7 python3_{4,5} )
-PYTHON_REQ_USE="threads(+)"
-
-inherit distutils-r1
-
-DESCRIPTION="IPython HTML widgets for Jupyter"
-HOMEPAGE="http://ipython.org/"
-SRC_URI="mirror://pypi/${PN:0:1}/${PN}/${P}.tar.gz"
-
-LICENSE="BSD"
-SLOT="0"
-KEYWORDS="~amd64 ~x86"
-IUSE="test"
-
-RDEPEND="
-	dev-python/traitlets[${PYTHON_USEDEP}]
-	dev-python/ipykernel[${PYTHON_USEDEP}]
-	"
-DEPEND="${RDEPEND}
-	test? (
-		$(python_gen_cond_dep 'dev-python/mock[${PYTHON_USEDEP}]' python2_7)
-		dev-python/nose[${PYTHON_USEDEP}]
-		dev-python/coverage[${PYTHON_USEDEP}]
-	)
-	"
-
-python_test() {
-	nosetests --with-coverage --cover-package=ipywidgets ipywidgets || die
-
-	"${PYTHON}" -m ipywidgets.jstest || die
-}
diff --git a/dev-python/ipywidgets/ipywidgets-9999.ebuild b/dev-python/ipywidgets/ipywidgets-9999.ebuild
deleted file mode 100644
index c32dbb3e1..000000000
--- a/dev-python/ipywidgets/ipywidgets-9999.ebuild
+++ /dev/null
@@ -1,37 +0,0 @@
-# Copyright 1999-2016 Gentoo Foundation
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=6
-
-PYTHON_COMPAT=( python2_7 python3_{4,5} )
-PYTHON_REQ_USE="threads(+)"
-
-inherit distutils-r1 git-r3
-
-DESCRIPTION="IPython HTML widgets for Jupyter"
-HOMEPAGE="http://ipython.org/"
-EGIT_REPO_URI="https://github.com/ipython/${PN}.git git://github.com/ipython/${PN}.git"
-
-LICENSE="BSD"
-SLOT="0"
-KEYWORDS=""
-IUSE="test"
-
-RDEPEND="
-	>=dev-python/traitlets-4.2.0[${PYTHON_USEDEP}]
-	>=dev-python/ipykernel-4.2.2[${PYTHON_USEDEP}]
-	>=dev-python/widgetsnbextension-1.2.3[${PYTHON_USEDEP}]
-	"
-DEPEND="${RDEPEND}
-	test? (
-		$(python_gen_cond_dep 'dev-python/mock[${PYTHON_USEDEP}]' python2_7)
-		dev-python/nose[${PYTHON_USEDEP}]
-		dev-python/coverage[${PYTHON_USEDEP}]
-	)
-	"
-
-python_test() {
-	nosetests --with-coverage --cover-package=ipywidgets ipywidgets || die
-
-	"${PYTHON}" -m ipywidgets.jstest || die
-}
diff --git a/dev-python/ipywidgets/metadata.xml b/dev-python/ipywidgets/metadata.xml
deleted file mode 100644
index 0349df8c5..000000000
--- a/dev-python/ipywidgets/metadata.xml
+++ /dev/null
@@ -1,15 +0,0 @@
-<?xml version="1.0" encoding="UTF-8"?>
-<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
-<pkgmetadata>
-	<maintainer type="project">
-		<email>sci@gentoo.org</email>
-		<name>Gentoo Science Project</name>
-	</maintainer>
-	<longdescription>
-Interactive HTML widgets for Jupyter notebooks and the IPython
-kernel.
-</longdescription>
-	<upstream>
-		<remote-id type="pypi">ipywidgets</remote-id>
-	</upstream>
-</pkgmetadata>
diff --git a/dev-python/jacobi/Manifest b/dev-python/jacobi/Manifest
new file mode 100644
index 000000000..be04d75f2
--- /dev/null
+++ b/dev-python/jacobi/Manifest
@@ -0,0 +1,2 @@
+DIST jacobi-0.8.1.tar.gz 997020 BLAKE2B ba54654e8a202976242674afa79de06d486d03c6d78b5566711df7df4ddcf5bbaa0e536eb9feeb0b0d6aaa9a444f677dfbbfa9928e38431aa9377c97132d4a26 SHA512 4a9a280cfae81926563c9736bf1805a3fe379809fe51421bdd0659651008d07d9f772df5006a1b796959311956822839791289eacb03af39823dd5a671b3845a
+DIST jacobi-0.9.2.tar.gz 998268 BLAKE2B 93ed0a03e8984143229929d04dd7b166c71bf10e98b98d396c58a5cea556b2b8da7977538a419cfbff26a5f681885df2f952a7aef98822dea885b408e12033a7 SHA512 ef91d8aceab8823913820c46e33db43a3daba90bfacf640167987cd92006c4b253ec17166fc1750902afec69385d35559fede17a8ed227dab582f1490711bff1
diff --git a/dev-python/jacobi/jacobi-0.8.1.ebuild b/dev-python/jacobi/jacobi-0.8.1.ebuild
new file mode 100644
index 000000000..93afcbf16
--- /dev/null
+++ b/dev-python/jacobi/jacobi-0.8.1.ebuild
@@ -0,0 +1,24 @@
+EAPI=8
+
+PYTHON_COMPAT=( python3_{10..12} )
+DISTUTILS_USE_PEP517=setuptools
+inherit distutils-r1 pypi
+
+DESCRIPTION="Numerical derivatives for analytic functions with arbitrary precision."
+HOMEPAGE="https://github.com/HDembinski/jacobi"
+
+LICENSE="MIT"
+SLOT="0"
+KEYWORDS="~amd64"
+
+RDEPEND="
+	>=dev-python/numpy-1.10[${PYTHON_USEDEP}]
+"
+DEPEND="${RDEPEND}"
+
+distutils_enable_tests pytest
+
+EPYTEST_IGNORE=(
+	tests/bench.py
+)
+
diff --git a/dev-python/jacobi/jacobi-0.9.2.ebuild b/dev-python/jacobi/jacobi-0.9.2.ebuild
new file mode 100644
index 000000000..806967a38
--- /dev/null
+++ b/dev-python/jacobi/jacobi-0.9.2.ebuild
@@ -0,0 +1,26 @@
+EAPI=8
+
+PYTHON_COMPAT=( python3_{11..12} )
+DISTUTILS_USE_PEP517=setuptools
+inherit distutils-r1 pypi
+
+DESCRIPTION="Numerical derivatives for analytic functions with arbitrary precision."
+HOMEPAGE="https://github.com/HDembinski/jacobi"
+
+LICENSE="MIT"
+SLOT="0"
+KEYWORDS="~amd64"
+
+RDEPEND="
+	>=dev-python/numpy-1.10[${PYTHON_USEDEP}]
+"
+DEPEND="${RDEPEND}"
+
+distutils_enable_tests pytest
+
+python_test() {
+	local EPYTEST_IGNORE=(
+		tests/bench.py
+	)
+	epytest
+}
diff --git a/dev-python/jacobi/metadata.xml b/dev-python/jacobi/metadata.xml
new file mode 100644
index 000000000..ebbabb06c
--- /dev/null
+++ b/dev-python/jacobi/metadata.xml
@@ -0,0 +1,21 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
+<pkgmetadata>
+	<maintainer type="project">
+		<email>sci@gentoo.org</email>
+		<name>Gentoo Science Project</name>
+	</maintainer>
+	<maintainer type="person">
+		<email>alexander@neuwirth-informatik.de</email>
+		<name>Alexander Puck Neuwirth</name>
+	</maintainer>
+	<longdescription lang="en">
+	Robustly compute the generalised Jacobi matrix for an arbitrary real analytic mapping �� → ��¹ × ... × ���
+	Returns error estimates for derivatives
+	Perform statistical error propagation based on numerically computed jacobian
+	</longdescription>
+	<upstream>
+		<remote-id type="pypi">jacobi</remote-id>
+		<remote-id type="github">HDembinski/jacobi</remote-id>
+	</upstream>
+</pkgmetadata>
diff --git a/dev-python/jupyter_client/jupyter_client-9999.ebuild b/dev-python/jupyter_client/jupyter_client-9999.ebuild
deleted file mode 100644
index 272acefb7..000000000
--- a/dev-python/jupyter_client/jupyter_client-9999.ebuild
+++ /dev/null
@@ -1,35 +0,0 @@
-# Copyright 1999-2017 Gentoo Foundation
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=6
-
-PYTHON_COMPAT=( python2_7 python3_{4,5} )
-PYTHON_REQ_USE="threads(+)"
-
-inherit distutils-r1 git-r3
-
-DESCRIPTION="Jupyter protocol implementation and client libraries"
-HOMEPAGE="http://jupyter.org"
-EGIT_REPO_URI="https://github.com/jupyter/${PN}.git git://github.com/jupyter/${PN}.git"
-
-LICENSE="BSD"
-SLOT="0"
-IUSE="test"
-
-RDEPEND="
-	dev-python/traitlets[${PYTHON_USEDEP}]
-	dev-python/jupyter_core[${PYTHON_USEDEP}]
-	>=dev-python/pyzmq-14.4.0[${PYTHON_USEDEP}]
-	"
-DEPEND="${RDEPEND}
-	test? (
-		dev-python/nose[${PYTHON_USEDEP}]
-		dev-python/coverage[${PYTHON_USEDEP}]
-		$(python_gen_cond_dep 'dev-python/mock[${PYTHON_USEDEP}]' python2_7)
-		dev-python/ipykernel[${PYTHON_USEDEP}]
-	)
-	"
-
-python_test() {
-	nosetests --with-coverage --cover-package jupyter_client jupyter_client || die
-}
diff --git a/dev-python/jupyter_client/metadata.xml b/dev-python/jupyter_client/metadata.xml
deleted file mode 100644
index c8a2d03e4..000000000
--- a/dev-python/jupyter_client/metadata.xml
+++ /dev/null
@@ -1,14 +0,0 @@
-<?xml version="1.0" encoding="UTF-8"?>
-<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
-<pkgmetadata>
-	<maintainer type="project">
-		<email>sci@gentoo.org</email>
-		<name>Gentoo Science Project</name>
-	</maintainer>
-	<longdescription>
-Contains the reference implementation of the Jupyter protocol. It
-also provides client and kernel management APIs for working with
-kernels. It also provides the jupyter kernelspec entrypoint for
-installing kernelspecs for use with Jupyter frontends.
-</longdescription>
-</pkgmetadata>
diff --git a/dev-python/jupyter_console/jupyter_console-9999.ebuild b/dev-python/jupyter_console/jupyter_console-9999.ebuild
deleted file mode 100644
index fc4eb50d0..000000000
--- a/dev-python/jupyter_console/jupyter_console-9999.ebuild
+++ /dev/null
@@ -1,54 +0,0 @@
-# Copyright 1999-2017 Gentoo Foundation
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=6
-
-PYTHON_COMPAT=( python2_7 python3_{4,5} )
-
-inherit distutils-r1 git-r3
-
-DESCRIPTION="A terminal-based console frontend for Jupyter kernels"
-HOMEPAGE="http://jupyter.org"
-EGIT_REPO_URI="https://github.com/jupyter/${PN}.git git://github.com/jupyter/${PN}.git"
-
-LICENSE="BSD"
-SLOT="0"
-IUSE="doc test"
-
-RDEPEND="
-	dev-python/ipython[${PYTHON_USEDEP}]
-	dev-python/ipykernel[${PYTHON_USEDEP}]
-	dev-python/jupyter_client[${PYTHON_USEDEP}]
-	>=dev-python/prompt_toolkit-1.0.0[${PYTHON_USEDEP}]
-	dev-python/pygments[${PYTHON_USEDEP}]
-	"
-DEPEND="${RDEPEND}
-	doc? ( dev-python/sphinx[${PYTHON_USEDEP}] )
-	test? (
-		$(python_gen_cond_dep 'dev-python/mock[${PYTHON_USEDEP}]' python2_7)
-		dev-python/pexpect[${PYTHON_USEDEP}]
-		>=dev-python/nose-0.10.1[${PYTHON_USEDEP}]
-	)
-	"
-
-python_prepare_all() {
-	# Prevent un-needed download during build
-	if use doc; then
-		sed -e "/^    'sphinx.ext.intersphinx',/d" -i docs/conf.py || die
-	fi
-
-	distutils-r1_python_prepare_all
-}
-
-python_compile_all() {
-	use doc && emake -C docs html
-}
-
-python_test() {
-	nosetests --with-coverage --cover-package=jupyter_console jupyter_console || die
-}
-
-python_install_all() {
-	use doc && HTML_DOCS=( docs/_build/html/. )
-	distutils-r1_python_install_all
-}
diff --git a/dev-python/jupyter_console/metadata.xml b/dev-python/jupyter_console/metadata.xml
deleted file mode 100644
index d7078d3ee..000000000
--- a/dev-python/jupyter_console/metadata.xml
+++ /dev/null
@@ -1,12 +0,0 @@
-<?xml version="1.0" encoding="UTF-8"?>
-<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
-<pkgmetadata>
-	<maintainer type="project">
-		<email>sci@gentoo.org</email>
-		<name>Gentoo Science Project</name>
-	</maintainer>
-	<longdescription>
-A terminal-based console frontend for Jupyter kernels.
-This code is based on the single-process IPython terminal.
-</longdescription>
-</pkgmetadata>
diff --git a/dev-python/jupyter_core/jupyter_core-9999.ebuild b/dev-python/jupyter_core/jupyter_core-9999.ebuild
deleted file mode 100644
index f75ca798b..000000000
--- a/dev-python/jupyter_core/jupyter_core-9999.ebuild
+++ /dev/null
@@ -1,52 +0,0 @@
-# Copyright 1999-2017 Gentoo Foundation
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=6
-
-PYTHON_COMPAT=( python2_7 python3_{4,5} )
-
-inherit distutils-r1 git-r3
-
-DESCRIPTION="Core common functionality of Jupyter projects"
-HOMEPAGE="http://jupyter.org"
-EGIT_REPO_URI="https://github.com/jupyter/${PN}.git git://github.com/jupyter/${PN}.git"
-
-LICENSE="BSD"
-SLOT="0"
-IUSE="doc test"
-
-RDEPEND="
-	dev-python/traitlets[${PYTHON_USEDEP}]
-	"
-DEPEND="${RDEPEND}
-	doc? ( dev-python/sphinx[${PYTHON_USEDEP}] )
-	test? (
-		dev-python/pytest[${PYTHON_USEDEP}]
-		$(python_gen_cond_dep 'dev-python/mock[${PYTHON_USEDEP}]' python2_7)
-		>=dev-python/ipython-4.0.1[${PYTHON_USEDEP}]
-	)
-	"
-
-python_prepare_all() {
-	# Prevent un-needed download during build
-	if use doc; then
-		sed -e "/^    'sphinx.ext.intersphinx',/d" -i docs/conf.py || die
-	fi
-
-	distutils-r1_python_prepare_all
-}
-
-python_compile_all() {
-	use doc && emake -C docs html
-}
-
-python_test() {
-	distutils_install_for_testing
-	cd "${TEST_DIR}"/lib || die
-	py.test jupyter_core || die
-}
-
-python_install_all() {
-	use doc && HTML_DOCS=( docs/_build/html/. )
-	distutils-r1_python_install_all
-}
diff --git a/dev-python/jupyter_core/metadata.xml b/dev-python/jupyter_core/metadata.xml
deleted file mode 100644
index 73840fc5c..000000000
--- a/dev-python/jupyter_core/metadata.xml
+++ /dev/null
@@ -1,13 +0,0 @@
-<?xml version="1.0" encoding="UTF-8"?>
-<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
-<pkgmetadata>
-	<maintainer type="project">
-		<email>sci@gentoo.org</email>
-		<name>Gentoo Science Project</name>
-	</maintainer>
-	<longdescription>
-Core common functionality of Jupyter projects.
-This package contains base application classes and configuration
-inhertited by other projects. It doesn't do much on its own.
-</longdescription>
-</pkgmetadata>
diff --git a/dev-python/kmapper/Manifest b/dev-python/kmapper/Manifest
new file mode 100644
index 000000000..0eeec60f6
--- /dev/null
+++ b/dev-python/kmapper/Manifest
@@ -0,0 +1 @@
+DIST kmapper-2.0.1.gh.tar.gz 6686101 BLAKE2B 8afa79a2479370c335debb4cee7375b0d47b0e79d02649ff53681d006e2a80cd6175f8aeb3c3a6fa0ac32d0cf30ba8217d348f6158b9ee1bc7c683d0a5b4290e SHA512 751f02ee3f5a55eb74b55b0a9204e54d05c9af2a816f8070082a73d4213c1fb7842e41e3e27316d69efaa2cf3e2f9b2d967870905ace8d9e9a3e67f9ea181ed2
diff --git a/dev-python/kmapper/kmapper-2.0.1-r1.ebuild b/dev-python/kmapper/kmapper-2.0.1-r1.ebuild
new file mode 100644
index 000000000..22f35fbda
--- /dev/null
+++ b/dev-python/kmapper/kmapper-2.0.1-r1.ebuild
@@ -0,0 +1,43 @@
+# Copyright 1999-2021 Gentoo Authors
+# Distributed under the terms of the GNU General Public License v2
+
+EAPI=8
+
+PYTHON_COMPAT=( python3_{10..11} )
+DISTUTILS_USE_PEP517=setuptools
+
+inherit distutils-r1
+
+DESCRIPTION="Python implementation of Mapper algorithm for Topological Data Analysis"
+HOMEPAGE="https://kepler-mapper.scikit-tda.org"
+SRC_URI="https://github.com/scikit-tda/kepler-mapper/archive/refs/tags/v${PV}.tar.gz -> ${P}.gh.tar.gz"
+S="${WORKDIR}"/kepler-mapper-${PV}
+
+LICENSE="MIT"
+SLOT="0"
+KEYWORDS="~amd64"
+
+RDEPEND="${PYTHON_DEPS}
+	dev-python/jinja[${PYTHON_USEDEP}]
+	dev-python/joblib[${PYTHON_USEDEP}]
+	dev-python/markupsafe[${PYTHON_USEDEP}]
+	dev-python/numpy[${PYTHON_USEDEP}]
+	dev-python/plotly[${PYTHON_USEDEP}]
+	dev-python/python-igraph[${PYTHON_USEDEP}]
+	sci-libs/scikit-learn[${PYTHON_USEDEP}]
+"
+DEPEND="${RDEPEND}"
+BDEPEND="
+	test? (
+		dev-python/networkx[${PYTHON_USEDEP}]
+		dev-python/matplotlib[${PYTHON_USEDEP}]
+		dev-python/ipywidgets[${PYTHON_USEDEP}]
+	)
+"
+
+distutils_enable_tests pytest
+
+python_prepare_all() {
+	rm "${S}"/test/test_plotly.py || die
+	distutils-r1_python_prepare_all
+}
diff --git a/dev-python/kmapper/metadata.xml b/dev-python/kmapper/metadata.xml
new file mode 100644
index 000000000..4dee7702f
--- /dev/null
+++ b/dev-python/kmapper/metadata.xml
@@ -0,0 +1,16 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
+<pkgmetadata>
+	<maintainer type="person">
+		<email>gentoo@aisha.cc</email>
+		<name>Aisha Tammy</name>
+	</maintainer>
+	<maintainer type="project">
+		<email>sci@gentoo.org</email>
+		<name>Gentoo Science Project</name>
+	</maintainer>
+	<upstream>
+		<remote-id type="github">scikit-tda/kepler-mapper</remote-id>
+		<remote-id type="pypi">kmapper</remote-id>
+	</upstream>
+</pkgmetadata>
diff --git a/dev-python/lasagne/lasagne-0.1_p20180608.ebuild b/dev-python/lasagne/lasagne-0.1_p20180608.ebuild
deleted file mode 100644
index 1dee8a0f4..000000000
--- a/dev-python/lasagne/lasagne-0.1_p20180608.ebuild
+++ /dev/null
@@ -1,34 +0,0 @@
-# Copyright 1999-2018 Gentoo Foundation
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=7
-
-PYTHON_COMPAT=( python{2_7,3_4,3_5,3_6} )
-
-inherit distutils-r1 git-r3
-
-DESCRIPTION="Lightweight library to build and train neural networks in Theano"
-HOMEPAGE="https://github.com/Lasagne/Lasagne"
-SRC_URI=""
-EGIT_REPO_URI="https://github.com/Lasagne/Lasagne"
-EGIT_COMMIT="18f7ee0e500a023a50904f62d34d90a73624d021"
-
-LICENSE="MIT"
-SLOT="0"
-KEYWORDS="~amd64"
-IUSE="test"
-
-DEPEND="
-	test? (
-		dev-python/pytest[${PYTHON_USEDEP}]
-		dev-python/pytest-cov[${PYTHON_USEDEP}]
-		dev-python/pytest-pep8[${PYTHON_USEDEP}]
-		)
-	"
-RDEPEND="
-	>=dev-python/theano-0.8.2
-	"
-
-python_test() {
-	py.test --runslow --cov-config=.coveragerc-nogpu || die
-}
diff --git a/dev-python/lasagne/lasagne-9999.ebuild b/dev-python/lasagne/lasagne-9999.ebuild
deleted file mode 100644
index 9d05a3380..000000000
--- a/dev-python/lasagne/lasagne-9999.ebuild
+++ /dev/null
@@ -1,33 +0,0 @@
-# Copyright 1999-2018 Gentoo Foundation
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=7
-
-PYTHON_COMPAT=( python{2_7,3_4,3_5,3_6} )
-
-inherit distutils-r1 git-r3
-
-DESCRIPTION="Lightweight library to build and train neural networks in Theano"
-HOMEPAGE="https://github.com/Lasagne/Lasagne"
-SRC_URI=""
-EGIT_REPO_URI="https://github.com/Lasagne/Lasagne"
-
-LICENSE="MIT"
-SLOT="0"
-KEYWORDS=""
-IUSE="test"
-
-DEPEND="
-	test? (
-		dev-python/pytest[${PYTHON_USEDEP}]
-		dev-python/pytest-cov[${PYTHON_USEDEP}]
-		dev-python/pytest-pep8[${PYTHON_USEDEP}]
-		)
-	"
-RDEPEND="
-	>=dev-python/theano-0.8.2
-	"
-
-python_test() {
-	py.test --runslow --cov-config=.coveragerc-nogpu || die
-}
diff --git a/dev-python/lasagne/metadata.xml b/dev-python/lasagne/metadata.xml
deleted file mode 100644
index 6d2de971f..000000000
--- a/dev-python/lasagne/metadata.xml
+++ /dev/null
@@ -1,21 +0,0 @@
-<?xml version="1.0" encoding="UTF-8"?>
-<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
-<pkgmetadata>
-	<maintainer type="person">
-		<email>horea.christ@gmail.com</email>
-		<name>Horea Christian</name>
-	</maintainer>
-	<maintainer type="project">
-		<email>sci@gentoo.org</email>
-		<name>Gentoo Science Project</name>
-	</maintainer>
-	<longdescription lang="en">
-		Lasagne is a lightweight library to build and train neural networks in Theano.
-		It supports feed-forward networks such as Convolutional Neural Networks
-		(CNNs), recurrent networks including Long Short-Term Memory (LSTM), and any
-		combination thereof.
-	</longdescription>
-	<upstream>
-		<remote-id type="github">Lasagne/Lasagne</remote-id>
-	</upstream>
-</pkgmetadata>
diff --git a/dev-python/latexify_py/Manifest b/dev-python/latexify_py/Manifest
new file mode 100644
index 000000000..7a500fe7d
--- /dev/null
+++ b/dev-python/latexify_py/Manifest
@@ -0,0 +1 @@
+DIST latexify_py-0.2.0.tar.gz 30995 BLAKE2B 2b55c83ea073b221096b4e44fad362d421f5d526bdff79a825b67a5fb419ff6185cd9f18a49727b988409f257318845a90f78223cf6eb9dd264ce6d1c0b71b82 SHA512 17250784d7a009705854d3f6118b3c854c4e86e007a45740c2b6d314ff25503b3561327b610b17e49652fa59ff6612bae8e74ea4caedeaa4f6a0b1e446fe086c
diff --git a/dev-python/latexify_py/latexify_py-0.2.0.ebuild b/dev-python/latexify_py/latexify_py-0.2.0.ebuild
new file mode 100644
index 000000000..bd42c3cf3
--- /dev/null
+++ b/dev-python/latexify_py/latexify_py-0.2.0.ebuild
@@ -0,0 +1,34 @@
+# Copyright 1999-2022 Gentoo Authors
+# Distributed under the terms of the GNU General Public License v2
+
+EAPI=8
+
+PYTHON_COMPAT=( python3_{10..11} )
+DISTUTILS_USE_PEP517=hatchling
+
+inherit distutils-r1
+
+DESCRIPTION="Generate LaTeX expression from Python code"
+HOMEPAGE="https://github.com/google/latexify_py"
+SRC_URI="https://github.com/google/${PN}/archive/refs/tags/v${PV}.tar.gz -> ${P}.tar.gz"
+
+LICENSE="Apache-2.0"
+SLOT="0"
+KEYWORDS="~amd64"
+
+RDEPEND="
+	dev-python/dill[${PYTHON_USEDEP}]
+"
+
+BDEPEND="test? (
+	dev-python/notebook[${PYTHON_USEDEP}]
+	dev-python/twine[${PYTHON_USEDEP}]
+)"
+
+distutils_enable_tests pytest
+
+DOCS=( README.md docs )
+
+python_test() {
+	PYTHONPATH="${S}/src" epytest
+}
diff --git a/dev-java/jrosetta/metadata.xml b/dev-python/latexify_py/metadata.xml
index ae9640ffb..ae9640ffb 100644
--- a/dev-java/jrosetta/metadata.xml
+++ b/dev-python/latexify_py/metadata.xml
diff --git a/dev-python/lazy_ops/Manifest b/dev-python/lazy_ops/Manifest
new file mode 100644
index 000000000..b5b4cce5e
--- /dev/null
+++ b/dev-python/lazy_ops/Manifest
@@ -0,0 +1 @@
+DIST lazy_ops-0.2.0.tar.gz 5284 BLAKE2B ba8747ba9028103fad7e0cab5eb53ebfefca5e886dcd39a499c8c8c6c8c466dcdb85438fc012f32cff7b98e486fe8154ef4e3c08241c3c9c738f0a399a6f91af SHA512 b0c7e49d37553f56f491d7e7aaeee8e6e18d44f6f34f7148ed98a596573dc26523e9cbc7bb6dce04bae99dbe59cecd35759173985fc203d7e59dfa61592e6955
diff --git a/dev-python/lazy_ops/lazy_ops-0.2.0.ebuild b/dev-python/lazy_ops/lazy_ops-0.2.0.ebuild
new file mode 100644
index 000000000..d624fb2aa
--- /dev/null
+++ b/dev-python/lazy_ops/lazy_ops-0.2.0.ebuild
@@ -0,0 +1,26 @@
+# Copyright 1999-2023 Gentoo Authors
+# Distributed under the terms of the GNU General Public License v2
+
+EAPI=8
+
+PYTHON_COMPAT=( python3_{10..11} )
+DISTUTILS_USE_PEP517=setuptools
+inherit distutils-r1 pypi
+
+DESCRIPTION="Lazy transposing and slicing of h5py and Zarr data"
+HOMEPAGE="https://github.com/catalystneuro/lazy_ops"
+
+LICENSE="BSD"
+SLOT="0"
+KEYWORDS="~amd64 ~x86"
+IUSE="test"
+# There are no source archive with tests available:
+# https://github.com/catalystneuro/lazy_ops/issues/29
+RESTRICT="test"
+
+RDEPEND="
+	dev-python/h5py[${PYTHON_USEDEP}]
+	dev-python/zarr[${PYTHON_USEDEP}]
+"
+
+distutils_enable_tests pytest
diff --git a/dev-python/lazy_ops/metadata.xml b/dev-python/lazy_ops/metadata.xml
new file mode 100644
index 000000000..d5101128a
--- /dev/null
+++ b/dev-python/lazy_ops/metadata.xml
@@ -0,0 +1,16 @@
+<?xml version='1.0' encoding='UTF-8'?>
+<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
+<pkgmetadata>
+	<maintainer type="person">
+		<email>gentoo@chymera.eu</email>
+		<name>Horea Christian</name>
+	</maintainer>
+	<maintainer type="project">
+		<email>sci@gentoo.org</email>
+		<name>Gentoo Science Project</name>
+	</maintainer>
+	<upstream>
+		<remote-id type="github">catalystneuro/lazy_ops</remote-id>
+		<remote-id type="pypi">lazy_ops</remote-id>
+	</upstream>
+</pkgmetadata>
diff --git a/dev-python/linesep/Manifest b/dev-python/linesep/Manifest
new file mode 100644
index 000000000..99369e648
--- /dev/null
+++ b/dev-python/linesep/Manifest
@@ -0,0 +1 @@
+DIST linesep-0.5.0.tar.gz 23979 BLAKE2B 78413c41b5002c8d4edf28c97eb8867416710ed5164d872bce845debfd4d17ac6aa03d7f4a36ef3e22160f517913e1f57c2d99a1ef4963941001892211f0386f SHA512 fe91aea8f4f36e722edc025fbfc452488bcef9a8dfef85b36a446f33a5a0c079102538a0f141ec7474325d5948214082790c53a928d1b7453d7d1e56622714fb
diff --git a/dev-python/linesep/files/linesep-0.5.0-nocov.patch b/dev-python/linesep/files/linesep-0.5.0-nocov.patch
new file mode 100644
index 000000000..a27bbd4b8
--- /dev/null
+++ b/dev-python/linesep/files/linesep-0.5.0-nocov.patch
@@ -0,0 +1,12 @@
+diff --git a/tox.ini b/tox.ini
+index 4d45597..cdd9e18 100644
+--- a/tox.ini
++++ b/tox.ini
+@@ -31,7 +31,6 @@ commands =
+     mypy src test
+ 
+ [pytest]
+-addopts = --cov=linesep --no-cov-on-fail
+ asyncio_mode = strict
+ doctest_optionflags = IGNORE_EXCEPTION_DETAIL
+ filterwarnings = error
diff --git a/dev-python/linesep/linesep-0.5.0.ebuild b/dev-python/linesep/linesep-0.5.0.ebuild
new file mode 100644
index 000000000..148ff0883
--- /dev/null
+++ b/dev-python/linesep/linesep-0.5.0.ebuild
@@ -0,0 +1,25 @@
+# Copyright 1999-2022 Gentoo Authors
+# Distributed under the terms of the GNU General Public License v2
+
+EAPI=8
+
+DISTUTILS_USE_PEP517=setuptools
+PYTHON_COMPAT=( python3_{10..12} )
+inherit distutils-r1 pypi
+
+DESCRIPTION="Handling lines with arbitrary separators"
+HOMEPAGE="https://github.com/jwodder/linesep"
+
+LICENSE="MIT"
+SLOT="0"
+KEYWORDS="~amd64 ~x86"
+
+BDEPEND="
+	test? (
+		dev-python/pytest-subtests[${PYTHON_USEDEP}]
+	)
+"
+
+PATCHES=( "${FILESDIR}/${P}-nocov.patch" )
+
+distutils_enable_tests pytest
diff --git a/dev-python/linesep/metadata.xml b/dev-python/linesep/metadata.xml
new file mode 100644
index 000000000..017856905
--- /dev/null
+++ b/dev-python/linesep/metadata.xml
@@ -0,0 +1,16 @@
+<?xml version='1.0' encoding='UTF-8'?>
+<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
+<pkgmetadata>
+	<maintainer type="person">
+		<email>gentoo@chymera.eu</email>
+		<name>Horea Christian</name>
+	</maintainer>
+	<maintainer type="project">
+		<email>sci@gentoo.org</email>
+		<name>Gentoo Science Project</name>
+	</maintainer>
+	<upstream>
+		<remote-id type="github">jwodder/linesep</remote-id>
+		<remote-id type="pypi">linesep</remote-id>
+	</upstream>
+</pkgmetadata>
diff --git a/dev-python/logzero/Manifest b/dev-python/logzero/Manifest
new file mode 100644
index 000000000..73c1e0244
--- /dev/null
+++ b/dev-python/logzero/Manifest
@@ -0,0 +1 @@
+DIST logzero-1.7.0.tar.gz 577803 BLAKE2B d54c16ee55e105bf026695dcac21065f58f04bc1d6a66d0d80f4a8f2a0dddabbca8c901dd596643977010ca1aae29fddaf194ef8f2882fd6660b764ce9070d98 SHA512 6c9647e81f16479a09b11383a9b6e7fb1068e61007cf9884d59469535706850a4ef2893d7393feb68dcdeb0793dcb8c41f8f3865289792de97dd20a5d32224bb
diff --git a/dev-python/logzero/logzero-1.7.0.ebuild b/dev-python/logzero/logzero-1.7.0.ebuild
new file mode 100644
index 000000000..2c3f44eb1
--- /dev/null
+++ b/dev-python/logzero/logzero-1.7.0.ebuild
@@ -0,0 +1,16 @@
+# Copyright 1999-2021 Gentoo Authors
+# Distributed under the terms of the GNU General Public License v2
+
+EAPI=8
+
+PYTHON_COMPAT=( python3_10 pypy3 )
+inherit distutils-r1 pypi
+
+DESCRIPTION="Robust and effective logging for Python 2 and 3"
+HOMEPAGE="https://pypi.org/project/logzero"
+
+LICENSE="MIT"
+SLOT="0"
+KEYWORDS="~amd64 ~x86"
+
+distutils_enable_tests pytest
diff --git a/dev-python/logzero/metadata.xml b/dev-python/logzero/metadata.xml
new file mode 100644
index 000000000..3bdc37964
--- /dev/null
+++ b/dev-python/logzero/metadata.xml
@@ -0,0 +1,13 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
+<pkgmetadata>
+	<maintainer type="project">
+		<email>sci@gentoo.org</email>
+		<name>Gentoo Science Project</name>
+	</maintainer>
+	<stabilize-allarches/>
+	<upstream>
+		<remote-id type="pypi">logzero</remote-id>
+		<remote-id type="github">metachris/logzero</remote-id>
+	</upstream>
+</pkgmetadata>
diff --git a/dev-python/lzstring/Manifest b/dev-python/lzstring/Manifest
new file mode 100644
index 000000000..f44e5e773
--- /dev/null
+++ b/dev-python/lzstring/Manifest
@@ -0,0 +1 @@
+DIST lzstring-1.0.4.tar.gz 4256 BLAKE2B e1a205f980de050635114e26a86d7251e0822a4459c44042291e80d55129d815f0753ff2b45a179fb468e9020a0a6255748566bc4e62fc98e7e041b07ae073f3 SHA512 0d61fe04402aaa5325d3ab555b9b83132048124a2ff11ae3a947a188d5507f1043b0522fcb7024009d75cf3efd3afbb64d24c238c4c2181346a823c77cb4ea02
diff --git a/dev-python/lzstring/lzstring-1.0.4.ebuild b/dev-python/lzstring/lzstring-1.0.4.ebuild
new file mode 100644
index 000000000..bfdb76a67
--- /dev/null
+++ b/dev-python/lzstring/lzstring-1.0.4.ebuild
@@ -0,0 +1,16 @@
+# Copyright 1999-2023 Gentoo Authors
+# Distributed under the terms of the GNU General Public License v2
+
+EAPI=8
+
+DISTUTILS_USE_PEP517=setuptools
+PYTHON_COMPAT=( python3_{10..11} )
+
+inherit pypi distutils-r1
+
+DESCRIPTION="String encoding/decoding of binary data"
+HOMEPAGE="https://pypi.org/project/lzstring/"
+
+LICENSE="BSD"
+SLOT="0"
+KEYWORDS="~amd64 ~amd64-linux"
diff --git a/dev-python/lzstring/metadata.xml b/dev-python/lzstring/metadata.xml
new file mode 100644
index 000000000..4dde9fdd9
--- /dev/null
+++ b/dev-python/lzstring/metadata.xml
@@ -0,0 +1,12 @@
+<?xml version='1.0' encoding='UTF-8'?>
+<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
+<pkgmetadata>
+	<maintainer type="person">
+		<email>mschu.dev@gmail.com</email>
+		<name>Michael Schubert</name>
+	</maintainer>
+	<upstream>
+		<remote-id type="github">gkovacs/lz-string-python</remote-id>
+		<remote-id type="pypi">lzstring</remote-id>
+	</upstream>
+</pkgmetadata>
diff --git a/dev-python/matlab_wrapper/Manifest b/dev-python/matlab_wrapper/Manifest
deleted file mode 100644
index 1e1c05f4f..000000000
--- a/dev-python/matlab_wrapper/Manifest
+++ /dev/null
@@ -1 +0,0 @@
-DIST matlab_wrapper-0.9.6.tar.gz 22673 BLAKE2B a6630dd5dd18a4611088facb91d4f6b717f05ca8cf9081827f4922774a90f5a1f1cd7411f0a874d417ecbf47e25a6b87ccc613d67735d6d2321a06754b8b64cb SHA512 b0de8b96b996fd6e02ac50e8b2c82b3d5859400ac16ce8bcc54c1d83cda921f1bb65a9c752c5c4b55d80903573aefeff6d0d046e8ee6780d0820c5e0d3d2ebef
diff --git a/dev-python/matlab_wrapper/matlab_wrapper-0.9.6.ebuild b/dev-python/matlab_wrapper/matlab_wrapper-0.9.6.ebuild
deleted file mode 100644
index 948dc7c5d..000000000
--- a/dev-python/matlab_wrapper/matlab_wrapper-0.9.6.ebuild
+++ /dev/null
@@ -1,24 +0,0 @@
-# Copyright 1999-2015 Gentoo Foundation
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=5
-PYTHON_COMPAT=( python2_7 )
-
-inherit distutils-r1
-
-DESCRIPTION="MATLAB wrapper for Python"
-HOMEPAGE="https://github.com/mrkrd/matlab_wrapper"
-
-if [ ${PV} == "9999" ] ; then
-	inherit git-r3
-	EGIT_REPO_URI="https://github.com/mrkrd/${PN}.git git://github.com/mrkrd/${PN}.git"
-else
-	SRC_URI="mirror://pypi/${PN:0:1}/${PN}/${P}.tar.gz"
-	KEYWORDS="~amd64"
-fi
-
-LICENSE="GPL-3+"
-SLOT="0"
-
-RDEPEND="dev-python/numpy[${PYTHON_USEDEP}]"
-DEPEND="${RDEPEND}"
diff --git a/dev-python/matlab_wrapper/matlab_wrapper-9999.ebuild b/dev-python/matlab_wrapper/matlab_wrapper-9999.ebuild
deleted file mode 100644
index 948dc7c5d..000000000
--- a/dev-python/matlab_wrapper/matlab_wrapper-9999.ebuild
+++ /dev/null
@@ -1,24 +0,0 @@
-# Copyright 1999-2015 Gentoo Foundation
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=5
-PYTHON_COMPAT=( python2_7 )
-
-inherit distutils-r1
-
-DESCRIPTION="MATLAB wrapper for Python"
-HOMEPAGE="https://github.com/mrkrd/matlab_wrapper"
-
-if [ ${PV} == "9999" ] ; then
-	inherit git-r3
-	EGIT_REPO_URI="https://github.com/mrkrd/${PN}.git git://github.com/mrkrd/${PN}.git"
-else
-	SRC_URI="mirror://pypi/${PN:0:1}/${PN}/${P}.tar.gz"
-	KEYWORDS="~amd64"
-fi
-
-LICENSE="GPL-3+"
-SLOT="0"
-
-RDEPEND="dev-python/numpy[${PYTHON_USEDEP}]"
-DEPEND="${RDEPEND}"
diff --git a/dev-python/matlab_wrapper/metadata.xml b/dev-python/matlab_wrapper/metadata.xml
deleted file mode 100644
index 4981c3b8a..000000000
--- a/dev-python/matlab_wrapper/metadata.xml
+++ /dev/null
@@ -1,23 +0,0 @@
-<?xml version="1.0" encoding="UTF-8"?>
-<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
-<pkgmetadata>
-	<maintainer type="person">
-		<email>marbre@linux.sungazer.de</email>
-		<name>Marius Brehler</name>
-	</maintainer>
-	<maintainer type="project">
-		<email>sci@gentoo.org</email>
-		<name>Gentoo Science Project</name>
-	</maintainer>
-	<longdescription>
-matlab_wrapper allows you to use MATLAB in a convenient way in
-Python. You can call MATLAB functions and access workspace
-variables directly from your Python scripts and interactive
-shell. MATLAB session is started in the background and appears
-as a regular Python module.
-</longdescription>
-	<upstream>
-		<remote-id type="github">mrkrd/matlab_wrapper</remote-id>
-		<remote-id type="pypi">matlab_wrapper</remote-id>
-	</upstream>
-</pkgmetadata>
diff --git a/dev-python/matlabengine/Manifest b/dev-python/matlabengine/Manifest
new file mode 100644
index 000000000..8704c974e
--- /dev/null
+++ b/dev-python/matlabengine/Manifest
@@ -0,0 +1 @@
+DIST matlabengine-9.13.7.tar.gz 18796 BLAKE2B ccc5dae8fb9bc7a7cf240021f6066d4779d86d266b76cad3a610ed1fb455e1eefbef00cc5b1fe425f1f4f033dcb7721c2d1d3856c026fba13d2155604bfbf81f SHA512 b8d5d4d99f657fd24226f2accab676340a34739464fd289f1ca1c2db28a22f4b1288dfe160e8e193926e5db3e4fda0fcbbbf67b67f9a509910429e023b9cc3fb
diff --git a/dev-python/matlabengine/matlabengine-9.13.7.ebuild b/dev-python/matlabengine/matlabengine-9.13.7.ebuild
new file mode 100644
index 000000000..d65b1c0e5
--- /dev/null
+++ b/dev-python/matlabengine/matlabengine-9.13.7.ebuild
@@ -0,0 +1,17 @@
+# Copyright 1999-2022 Gentoo Authors
+# Distributed under the terms of the GNU General Public License v2
+
+EAPI=8
+
+PYTHON_COMPAT=( python3_10 ) # No 3.11 according to setup.py
+DISTUTILS_USE_PEP517=setuptools
+inherit distutils-r1 pypi
+
+DESCRIPTION="A module to call MATLAB from Python"
+HOMEPAGE="https://github.com/mathworks/matlab-engine-for-python"
+
+LICENSE="MathWorks"
+SLOT="0"
+KEYWORDS="-* ~amd64"
+
+RESTRICT="bindist mirror"
diff --git a/dev-python/matlabengine/metadata.xml b/dev-python/matlabengine/metadata.xml
new file mode 100644
index 000000000..83a61da06
--- /dev/null
+++ b/dev-python/matlabengine/metadata.xml
@@ -0,0 +1,12 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
+<pkgmetadata>
+	<maintainer type="person">
+		<email>sci@gentoo.org</email>
+		<name>Gentoo Science Project</name>
+	</maintainer>
+	<upstream>
+		<remote-id type="pypi">matlabengine</remote-id>
+		<remote-id type="github">mathworks/matlab-engine-for-python</remote-id>
+	</upstream>
+</pkgmetadata>
diff --git a/dev-python/matplotlib-venn/Manifest b/dev-python/matplotlib-venn/Manifest
deleted file mode 100644
index 396987c6c..000000000
--- a/dev-python/matplotlib-venn/Manifest
+++ /dev/null
@@ -1 +0,0 @@
-DIST matplotlib-venn-0.11.zip 38853 BLAKE2B d9215fdf87965ba8a5cf33eb8d654b3ed5e1e8344741e30227e0eb16b387fefa088ea15f450f2c4858230c7c0f5b0b1f6110a9db63533b97f13fef7b62e1ed37 SHA512 e45c96933471166233c7b3231c17fd5a6f8cc67c934f377d56bd1fe161b05e8aca8d39fee5b9d83d184359996fa983a473c20c3c15d0d04349596e4fe1073287
diff --git a/dev-python/matplotlib-venn/matplotlib-venn-0.11.ebuild b/dev-python/matplotlib-venn/matplotlib-venn-0.11.ebuild
deleted file mode 100644
index fd1949a32..000000000
--- a/dev-python/matplotlib-venn/matplotlib-venn-0.11.ebuild
+++ /dev/null
@@ -1,30 +0,0 @@
-# Copyright 1999-2016 Gentoo Foundation
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=6
-
-PYTHON_COMPAT=( python2_7 python3_4 python3_5)
-
-inherit distutils-r1
-
-DESCRIPTION="Routines for plotting area-weighted two- and three-circle venn diagrams"
-HOMEPAGE="http://pysurfer.github.com"
-SRC_URI="mirror://pypi/m/${PN}/${P}.zip"
-
-LICENSE="MIT"
-SLOT="0"
-KEYWORDS="~amd64"
-IUSE="test"
-
-RDEPEND="
-	dev-python/matplotlib[${PYTHON_USEDEP}]
-	dev-python/numpy[${PYTHON_USEDEP}]
-	sci-libs/scipy[${PYTHON_USEDEP}]
-	"
-DEPEND="
-	dev-python/setuptools[${PYTHON_USEDEP}]
-	test? ( dev-python/pytest[${PYTHON_USEDEP}] )"
-
-python_test() {
-	py.test --verbose || die
-}
diff --git a/dev-python/matplotlib-venn/matplotlib-venn-9999.ebuild b/dev-python/matplotlib-venn/matplotlib-venn-9999.ebuild
deleted file mode 100644
index 8a8aab123..000000000
--- a/dev-python/matplotlib-venn/matplotlib-venn-9999.ebuild
+++ /dev/null
@@ -1,32 +0,0 @@
-# Copyright 1999-2015 Gentoo Foundation
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=5
-
-PYTHON_COMPAT=( python2_7 )
-
-inherit distutils-r1 git-r3
-
-DESCRIPTION="Routines for plotting area-weighted two- and three-circle venn diagrams"
-HOMEPAGE="http://pysurfer.github.com"
-SRC_URI=""
-EGIT_REPO_URI="https://github.com/konstantint/matplotlib-venn"
-
-LICENSE="MIT"
-SLOT="0"
-KEYWORDS=""
-IUSE="test"
-
-RDEPEND="
-	dev-python/matplotlib[${PYTHON_USEDEP}]
-	dev-python/numpy[${PYTHON_USEDEP}]
-	sci-libs/scipy[${PYTHON_USEDEP}]"
-DEPEND="test? (
-		${RDEPEND}
-		dev-python/pytest[${PYTHON_USEDEP}]
-	)
-	dev-python/setuptools[${PYTHON_USEDEP}]"
-
-python_test() {
-	py.test || die "Tests fail with ${EPYTHON}"
-}
diff --git a/dev-python/matplotlib-venn/metadata.xml b/dev-python/matplotlib-venn/metadata.xml
deleted file mode 100644
index 6c79256de..000000000
--- a/dev-python/matplotlib-venn/metadata.xml
+++ /dev/null
@@ -1,11 +0,0 @@
-<?xml version="1.0" encoding="UTF-8"?>
-<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
-<pkgmetadata>
-	<maintainer type="project">
-		<email>sci@gentoo.org</email>
-		<name>Gentoo Science Project</name>
-	</maintainer>
-	<upstream>
-		<remote-id type="pypi">matplotlib-venn</remote-id>
-	</upstream>
-</pkgmetadata>
diff --git a/dev-python/matplotlib2tikz/files/matplotlib2tikz-0.6-init_pipdated.patch b/dev-python/matplotlib2tikz/files/matplotlib2tikz-0.6-init_pipdated.patch
deleted file mode 100644
index 2acf79738..000000000
--- a/dev-python/matplotlib2tikz/files/matplotlib2tikz-0.6-init_pipdated.patch
+++ /dev/null
@@ -1,15 +0,0 @@
-Remove version checks using pipdated.
-
-Patch by Marius Brehler <marbre@linux.sungazer.de>
---- a/matplotlib2tikz/__init__.py
-+++ b/matplotlib2tikz/__init__.py
-@@ -15,9 +15,3 @@ from matplotlib2tikz.__about__ import (
-         )
- 
- from matplotlib2tikz.save import save
--
--import pipdated
--if pipdated.needs_checking('matplotlib2tikz'):
--    msg = pipdated.check('matplotlib2tikz', __version__)
--    if msg:
--        print(msg)
diff --git a/dev-python/matplotlib2tikz/matplotlib2tikz-9999.ebuild b/dev-python/matplotlib2tikz/matplotlib2tikz-9999.ebuild
deleted file mode 100644
index 47853ce1e..000000000
--- a/dev-python/matplotlib2tikz/matplotlib2tikz-9999.ebuild
+++ /dev/null
@@ -1,26 +0,0 @@
-# Copyright 1999-2017 Gentoo Foundation
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=6
-
-PYTHON_COMPAT=( python2_7 python3_{4,5} )
-
-inherit distutils-r1 git-r3
-
-DESCRIPTION="Convert matplotlib figures into TikZ/PGFPlots"
-HOMEPAGE="https://github.com/nschloe/matplotlib2tikz"
-EGIT_REPO_URI="https://github.com/nschloe/${PN}.git git://github.com/nschloe/${PN}.git"
-KEYWORDS=""
-
-LICENSE="MIT"
-SLOT="0"
-IUSE=""
-
-PATCHES=( "${FILESDIR}/${PN}-0.6-init_pipdated.patch" )
-
-RDEPEND="
-	dev-python/matplotlib[${PYTHON_USEDEP}]
-	dev-python/numpy[${PYTHON_USEDEP}]
-	dev-python/pillow[${PYTHON_USEDEP}]"
-DEPEND="${RDEPEND}"
-	#test? ( dev-python/pytest[${PYTHON_USEDEP}] )"
diff --git a/dev-python/matplotlib2tikz/metadata.xml b/dev-python/matplotlib2tikz/metadata.xml
deleted file mode 100644
index 7e9013abe..000000000
--- a/dev-python/matplotlib2tikz/metadata.xml
+++ /dev/null
@@ -1,16 +0,0 @@
-<?xml version="1.0" encoding="UTF-8"?>
-<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
-<pkgmetadata>
-	<maintainer type="person">
-		<email>marbre@linux.sungazer.de</email>
-		<name>Marius Brehler</name>
-	</maintainer>
-	<maintainer type="project">
-		<email>sci@gentoo.org</email>
-		<name>Gentoo Science Project</name>
-	</maintainer>
-	<longdescription>matplotlib2tikz is a Python tool for converting matplotlib figures into PGFPlots (TikZ) figures like for native inclusion into LaTeX documents. The output of matplotlib2tikz is in PGFPlots, a LaTeX library that sits on top of TikZ and describes graphs in terms of axes, data etc. Consequently, the output of matplotlib2tikz retains more information, can be more easily understood, and is more easily editable than raw TikZ output.</longdescription>
-	<upstream>
-		<remote-id type="github">nschloe/matplotlib2tikz</remote-id>
-	</upstream>
-</pkgmetadata>
diff --git a/dev-python/matrix2latex/Manifest b/dev-python/matrix2latex/Manifest
deleted file mode 100644
index a59826c27..000000000
--- a/dev-python/matrix2latex/Manifest
+++ /dev/null
@@ -1 +0,0 @@
-DIST matrix2latex-1.0.0.tar.gz 183350 BLAKE2B daae91c8b91e9b21fdf62a1c6936a20390988ea1b6f2d4b6a2c34c14441b25274b1b3f4cd907311d52340dde7deb962bacded06b2a459f98e21a8e07777f3730 SHA512 fd116bba7a40303851ceb7d63b55545b9345cc5721e2d33350ca167f0752bc47f802ebfa5d3794fe45148f08a6005e64fb569f0d60072a4ac3edaf9a42bb1ce0
diff --git a/dev-python/matrix2latex/matrix2latex-1.0.0.ebuild b/dev-python/matrix2latex/matrix2latex-1.0.0.ebuild
deleted file mode 100644
index 1577e94db..000000000
--- a/dev-python/matrix2latex/matrix2latex-1.0.0.ebuild
+++ /dev/null
@@ -1,19 +0,0 @@
-# Copyright 1999-2015 Gentoo Foundation
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=5
-
-PYTHON_COMPAT=( python{2_7,3_4} )
-
-inherit distutils-r1 multilib
-
-DESCRIPTION="A tool to create LaTeX tables from python lists and arrays"
-HOMEPAGE="https://github.com/TheChymera/matrix2latex"
-SRC_URI="https://github.com/TheChymera/${PN}/blob/master/archive/${PN}Python-${PV}.tar.gz?raw=true -> ${P}.tar.gz"
-
-LICENSE="GPL-3"
-SLOT="0"
-KEYWORDS="~amd64"
-IUSE=""
-
-S="${WORKDIR}/${PN}Python${PV}"
diff --git a/dev-python/matrix2latex/matrix2latex-9999.ebuild b/dev-python/matrix2latex/matrix2latex-9999.ebuild
deleted file mode 100644
index e206c1d0f..000000000
--- a/dev-python/matrix2latex/matrix2latex-9999.ebuild
+++ /dev/null
@@ -1,17 +0,0 @@
-# Copyright 1999-2015 Gentoo Foundation
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=5
-
-PYTHON_COMPAT=( python{2_7,3_4} )
-
-inherit distutils-r1 git-r3 multilib
-
-DESCRIPTION="A tool to create LaTeX tables from python lists and arrays"
-HOMEPAGE="https://github.com/TheChymera/matrix2latex"
-EGIT_REPO_URI="https://github.com/TheChymera/matrix2latex"
-
-LICENSE="GPL-3"
-SLOT="0"
-KEYWORDS=""
-IUSE=""
diff --git a/dev-python/matrix2latex/metadata.xml b/dev-python/matrix2latex/metadata.xml
deleted file mode 100644
index 62facfd12..000000000
--- a/dev-python/matrix2latex/metadata.xml
+++ /dev/null
@@ -1,16 +0,0 @@
-<?xml version="1.0" encoding="UTF-8"?>
-<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
-<pkgmetadata>
-	<maintainer type="project">
-		<email>sci@gentoo.org</email>
-		<name>Gentoo Science Project</name>
-	</maintainer>
-	<longdescription lang="en">
-A tool for converting Python or MATLAB matrices to
-LaTeX tables, that can optionally create self-sustained
-LATeX documents and compile them.
-</longdescription>
-	<upstream>
-		<remote-id type="github">TheChymera/matrix2latex</remote-id>
-	</upstream>
-</pkgmetadata>
diff --git a/dev-python/meshpy/Manifest b/dev-python/meshpy/Manifest
index d00662118..b39e4ba75 100644
--- a/dev-python/meshpy/Manifest
+++ b/dev-python/meshpy/Manifest
@@ -1,2 +1 @@
-DIST MeshPy-2013.1.2.tar.gz 1885753 BLAKE2B beb95592cc3013e4bb5dab23a02015eac2a6b679464e721e7a9b2b8f78f74421f113f7aea3de63d55ad50715807fcb919c83c0909442e537bd2c665f3d2f4505 SHA512 6004a609fc62ff44e5770a0d041da42eea1e185def5b1efca357d4cac3dcd34a7ccb5b0ca2d2f7fb4ba81bbc0251b8c998eb64bcff828f05cfc1a0a49385b9ae
-DIST MeshPy-2014.1.tar.gz 1851120 BLAKE2B 1daac481c25b2605e485037842b89881d552e51e333a9cc2a52c02f0182167adda93e873eae5df4393cbeaaa3ba3ff7358267b95aa824c58bc2e800b71a4070e SHA512 d8d7823df60250382577f67bb5ffd3b6523c84729c013220eaddccfa4b227839c2e0ffb285f87e752cf0dc5292eb1e5c693d04139d2fb33a05877e0b2b1bcecc
+DIST meshpy-2020.1.tar.gz 482475 BLAKE2B fe59de6fae837db584c38ee0f8ad7d9e242624df360fa0c0eb2778f1d2ea6233e6f92f113014dfc73f570dbb47c65582775ec3c615cd887b5aefdb7030794b90 SHA512 d328a546f14db44a40e885554cf3bfff1e522a1ce38b312acaf6ac7ddc6fd909299fb78793229482ec51ccb2484baee13c2c09406be937a073555cc120f6f2df
diff --git a/dev-python/meshpy/meshpy-2013.1.2.ebuild b/dev-python/meshpy/meshpy-2013.1.2.ebuild
deleted file mode 100644
index c5e501f4b..000000000
--- a/dev-python/meshpy/meshpy-2013.1.2.ebuild
+++ /dev/null
@@ -1,38 +0,0 @@
-# Copyright 1999-2014 Gentoo Foundation
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=5
-
-PYTHON_COMPAT=( python2_7 )
-
-inherit distutils-r1
-
-MY_PN="MeshPy"
-
-DESCRIPTION="Quality triangular and tetrahedral mesh generation for Python"
-HOMEPAGE="http://mathema.tician.de/software/meshpy http://pypi.python.org/pypi/MeshPy"
-SRC_URI="mirror://pypi/M/${MY_PN}/${MY_PN}-${PV}.tar.gz"
-
-LICENSE="MIT"
-SLOT="0"
-KEYWORDS="~amd64 ~x86"
-IUSE=""
-
-RDEPEND="
-	dev-libs/boost[python,${PYTHON_USEDEP}]
-	dev-python/pyvtk[${PYTHON_USEDEP}]"
-DEPEND="${RDEPEND}
-	dev-python/setuptools[${PYTHON_USEDEP}]"
-
-S="${WORKDIR}/${MY_PN}-${PV}"
-
-python_prepare_all() {
-	sed 's: delay = 10: delay = 1:g' -i aksetup_helper.py || die
-	distutils-r1_python_prepare_all
-}
-
-python_compile() {
-	mkdir "${BUILD_DIR}" || die
-	echo "BOOST_PYTHON_LIBNAME = [\'boost_${EPYTHON}-mt\']">> "${BUILD_DIR}"/siteconf.py
-	distutils-r1_python_compile
-}
diff --git a/dev-python/meshpy/meshpy-2014.1.ebuild b/dev-python/meshpy/meshpy-2014.1.ebuild
deleted file mode 100644
index 790c10023..000000000
--- a/dev-python/meshpy/meshpy-2014.1.ebuild
+++ /dev/null
@@ -1,45 +0,0 @@
-# Copyright 1999-2015 Gentoo Foundation
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=6
-
-PYTHON_COMPAT=( python2_7 python3_{4,5} )
-
-inherit distutils-r1
-
-MY_PN="MeshPy"
-
-DESCRIPTION="Quality triangular and tetrahedral mesh generation for Python"
-HOMEPAGE="http://mathema.tician.de/software/meshpy http://pypi.python.org/pypi/MeshPy"
-SRC_URI="mirror://pypi/M/${MY_PN}/${MY_PN}-${PV}.tar.gz"
-
-LICENSE="MIT"
-SLOT="0"
-KEYWORDS="~amd64 ~x86"
-IUSE="test"
-
-RDEPEND="
-	dev-libs/boost[python,${PYTHON_USEDEP}]
-	dev-python/numpy[${PYTHON_USEDEP}]
-	dev-python/pytools[${PYTHON_USEDEP}]
-	dev-python/six[${PYTHON_USEDEP}]"
-DEPEND="${RDEPEND}
-	dev-python/setuptools[${PYTHON_USEDEP}]
-	test? ( dev-python/pytest[${PYTHON_USEDEP}] )"
-
-S="${WORKDIR}/${MY_PN}-${PV}"
-
-python_prepare_all() {
-	sed 's: delay = 10: delay = 1:g' -i aksetup_helper.py || die
-	distutils-r1_python_prepare_all
-}
-
-python_compile() {
-	mkdir "${BUILD_DIR}" || die
-	echo "BOOST_PYTHON_LIBNAME = [\'boost_${EPYTHON}-mt\']">> "${BUILD_DIR}"/siteconf.py
-	distutils-r1_python_compile
-}
-
-python_test() {
-	py.test || die
-}
diff --git a/dev-python/meshpy/meshpy-2020.1.ebuild b/dev-python/meshpy/meshpy-2020.1.ebuild
new file mode 100644
index 000000000..78ee45fbc
--- /dev/null
+++ b/dev-python/meshpy/meshpy-2020.1.ebuild
@@ -0,0 +1,41 @@
+# Copyright 1999-2022 Gentoo Authors
+# Distributed under the terms of the GNU General Public License v2
+
+EAPI=8
+
+DISTUTILS_IN_SOURCE_BUILD=1
+PYTHON_COMPAT=( python3_10 )
+
+inherit distutils-r1
+
+MY_PN="MeshPy"
+
+DESCRIPTION="Quality triangular and tetrahedral mesh generation for Python"
+HOMEPAGE="https://mathema.tician.de/software/meshpy
+	https://pypi.python.org/pypi/MeshPy
+"
+SRC_URI="https://github.com/inducer/meshpy/archive/v${PV}.tar.gz -> ${P}.tar.gz"
+
+LICENSE="MIT"
+SLOT="0"
+KEYWORDS="~amd64"
+
+# ModuleNotFoundError: No module named 'meshpy._internals'
+RESTRICT="test"
+
+RDEPEND="
+	dev-libs/boost[python,${PYTHON_USEDEP}]
+	dev-python/gmsh_interop[${PYTHON_USEDEP}]
+	dev-python/numpy[${PYTHON_USEDEP}]
+	dev-python/pybind11[${PYTHON_USEDEP}]
+	dev-python/pytools[${PYTHON_USEDEP}]
+	sci-libs/gmsh
+"
+DEPEND="${RDEPEND}"
+
+distutils_enable_tests --install pytest
+
+python_prepare_all() {
+	sed 's:delay=10:delay=1:g' -i aksetup_helper.py || die
+	distutils-r1_python_prepare_all
+}
diff --git a/dev-python/meshpy/metadata.xml b/dev-python/meshpy/metadata.xml
index fff86775c..77991f7a8 100644
--- a/dev-python/meshpy/metadata.xml
+++ b/dev-python/meshpy/metadata.xml
@@ -15,5 +15,6 @@ Hang Si. Both are included in the package in slightly modified versions.
 </longdescription>
 	<upstream>
 		<remote-id type="pypi">MeshPy</remote-id>
+		<remote-id type="github">inducer/meshpy</remote-id>
 	</upstream>
 </pkgmetadata>
diff --git a/dev-python/metakernel/Manifest b/dev-python/metakernel/Manifest
deleted file mode 100644
index 57eabeb65..000000000
--- a/dev-python/metakernel/Manifest
+++ /dev/null
@@ -1,3 +0,0 @@
-DIST metakernel-0.12.2.tar.gz 90147 BLAKE2B 920efab7dc60494a56588edcc77b256448e08aa4576988878f12d944c9fa7eb6996afe7561abe070f95d52ff4b13abc817f2fe5ce5d50ab00fce09b0b01f0bd7 SHA512 fafbe0638cf21f4d0532f014b4a3602c095b1928597de89fd418d2a5c33fe4496998da39bf288a861464894e35b964fa93fc83cdc6c71b993eca52cbc57d0c47
-DIST metakernel-0.12.6.tar.gz 90203 BLAKE2B 1165a3d4f915aadb69016a95be864933d71d38d5429c3d8d9aac4a2dd85a851c79d2d5f7dfc62dc422731a3a02a894ffe1980125f779c96982354fd26887170f SHA512 1d1f2ad59879b2f7c78696b26a68cbdbc2612c5052138b72e26b8ec14f58a1455d9d1614dbe6957d9d7ecd965f91f6e20ecc939b2293cd682f87f6d5d2e21373
-DIST metakernel-0.18.4.tar.gz 67008 BLAKE2B 3eea325e1d6e9df19e9fa7479292fcef82d7a4e9147f73053b38201eb9c2247c936803d41999ce88070739620fcb5ede58d2395e3cb3062212f51c96f7f40340 SHA512 74c8321069ee7bfc338fc24d4c74dcafba3aee262324c5167e8568ed09afa03ba74f9eb565488b697dca20d5414e017538697156407a14fe774381930093a282
diff --git a/dev-python/metakernel/metadata.xml b/dev-python/metakernel/metadata.xml
deleted file mode 100644
index 1a16e93ec..000000000
--- a/dev-python/metakernel/metadata.xml
+++ /dev/null
@@ -1,17 +0,0 @@
-<?xml version="1.0" encoding="UTF-8"?>
-<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
-<pkgmetadata>
-	<maintainer type="project">
-		<email>sci@gentoo.org</email>
-		<name>Gentoo Science Project</name>
-	</maintainer>
-	<longdescription>
-A Jupyter/IPython kernel template which includes core magic
-functions (including help, command and file path completion,
-parallel and distributed processing, downloads, and much more).
-</longdescription>
-	<upstream>
-		<remote-id type="github">Calysto/metakernel</remote-id>
-		<remote-id type="pypi">metakernel</remote-id>
-	</upstream>
-</pkgmetadata>
diff --git a/dev-python/metakernel/metakernel-0.12.2.ebuild b/dev-python/metakernel/metakernel-0.12.2.ebuild
deleted file mode 100644
index c89a49abb..000000000
--- a/dev-python/metakernel/metakernel-0.12.2.ebuild
+++ /dev/null
@@ -1,37 +0,0 @@
-# Copyright 1999-2017 Gentoo Foundation
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=6
-
-PYTHON_COMPAT=( python{2_7,3_{4,5}} )
-
-inherit distutils-r1
-
-DESCRIPTION="Metakernel for Jupyter"
-HOMEPAGE="https://github.com/Calysto/metakernel"
-SRC_URI="mirror://pypi/${PN:0:1}/${PN}/${P}.tar.gz"
-
-LICENSE="BSD"
-SLOT="0"
-IUSE="test"
-KEYWORDS="~amd64"
-
-RDEPEND="
-	>=dev-python/ipython-3.0[${PYTHON_USEDEP}]
-	"
-DEPEND="${RDEPEND}
-	test? (
-		dev-python/nose[${PYTHON_USEDEP}]
-		dev-python/coverage[${PYTHON_USEDEP}]
-		>=dev-python/metakernel_python-0.11.3[${PYTHON_USEDEP}]
-	)
-"
-
-# tests currently fail and the dying/stopping of ipcluster needs to be fixed
-RESTRICT="test"
-
-python_test() {
-	ipcluster start -n=3 &
-	nosetests --with-doctest --with-coverage --cover-package metakernel || die
-	ipcluster stop
-}
diff --git a/dev-python/metakernel/metakernel-0.12.6.ebuild b/dev-python/metakernel/metakernel-0.12.6.ebuild
deleted file mode 100644
index c89a49abb..000000000
--- a/dev-python/metakernel/metakernel-0.12.6.ebuild
+++ /dev/null
@@ -1,37 +0,0 @@
-# Copyright 1999-2017 Gentoo Foundation
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=6
-
-PYTHON_COMPAT=( python{2_7,3_{4,5}} )
-
-inherit distutils-r1
-
-DESCRIPTION="Metakernel for Jupyter"
-HOMEPAGE="https://github.com/Calysto/metakernel"
-SRC_URI="mirror://pypi/${PN:0:1}/${PN}/${P}.tar.gz"
-
-LICENSE="BSD"
-SLOT="0"
-IUSE="test"
-KEYWORDS="~amd64"
-
-RDEPEND="
-	>=dev-python/ipython-3.0[${PYTHON_USEDEP}]
-	"
-DEPEND="${RDEPEND}
-	test? (
-		dev-python/nose[${PYTHON_USEDEP}]
-		dev-python/coverage[${PYTHON_USEDEP}]
-		>=dev-python/metakernel_python-0.11.3[${PYTHON_USEDEP}]
-	)
-"
-
-# tests currently fail and the dying/stopping of ipcluster needs to be fixed
-RESTRICT="test"
-
-python_test() {
-	ipcluster start -n=3 &
-	nosetests --with-doctest --with-coverage --cover-package metakernel || die
-	ipcluster stop
-}
diff --git a/dev-python/metakernel/metakernel-0.18.4.ebuild b/dev-python/metakernel/metakernel-0.18.4.ebuild
deleted file mode 100644
index c89a49abb..000000000
--- a/dev-python/metakernel/metakernel-0.18.4.ebuild
+++ /dev/null
@@ -1,37 +0,0 @@
-# Copyright 1999-2017 Gentoo Foundation
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=6
-
-PYTHON_COMPAT=( python{2_7,3_{4,5}} )
-
-inherit distutils-r1
-
-DESCRIPTION="Metakernel for Jupyter"
-HOMEPAGE="https://github.com/Calysto/metakernel"
-SRC_URI="mirror://pypi/${PN:0:1}/${PN}/${P}.tar.gz"
-
-LICENSE="BSD"
-SLOT="0"
-IUSE="test"
-KEYWORDS="~amd64"
-
-RDEPEND="
-	>=dev-python/ipython-3.0[${PYTHON_USEDEP}]
-	"
-DEPEND="${RDEPEND}
-	test? (
-		dev-python/nose[${PYTHON_USEDEP}]
-		dev-python/coverage[${PYTHON_USEDEP}]
-		>=dev-python/metakernel_python-0.11.3[${PYTHON_USEDEP}]
-	)
-"
-
-# tests currently fail and the dying/stopping of ipcluster needs to be fixed
-RESTRICT="test"
-
-python_test() {
-	ipcluster start -n=3 &
-	nosetests --with-doctest --with-coverage --cover-package metakernel || die
-	ipcluster stop
-}
diff --git a/dev-python/metakernel_bash/Manifest b/dev-python/metakernel_bash/Manifest
deleted file mode 100644
index f10b54516..000000000
--- a/dev-python/metakernel_bash/Manifest
+++ /dev/null
@@ -1 +0,0 @@
-DIST metakernel_bash-0.11.3.tar.gz 1801 BLAKE2B b85b8d13298dfe915ad5053b82211ae7d2e1aaba785074ad8ae176daef9259c5f4c6d50eb697f33d805fec10d2186fbd0cffa45cd7b3561455405d327b7ce822 SHA512 8a96580d7bbb409c461c227d5255d9075968c4c423a4e7fc329713dcf097c0194031a8a9c747146e18ccdcf58958478e99233f586b715601514741ceb1b67c75
diff --git a/dev-python/metakernel_bash/files/kernel.json b/dev-python/metakernel_bash/files/kernel.json
deleted file mode 100644
index a8e06d478..000000000
--- a/dev-python/metakernel_bash/files/kernel.json
+++ /dev/null
@@ -1 +0,0 @@
-{"argv": ["/usr/bin/python", "-m", "metakernel_bash", "-f", "{connection_file}"], "display_name": "MetaKernel Bash", "language": "bash", "name": "metakernel_bash"}
diff --git a/dev-python/metakernel_bash/metadata.xml b/dev-python/metakernel_bash/metadata.xml
deleted file mode 100644
index e63da5337..000000000
--- a/dev-python/metakernel_bash/metadata.xml
+++ /dev/null
@@ -1,15 +0,0 @@
-<?xml version="1.0" encoding="UTF-8"?>
-<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
-<pkgmetadata>
-	<maintainer type="project">
-		<email>sci@gentoo.org</email>
-		<name>Gentoo Science Project</name>
-	</maintainer>
-	<longdescription>
-A Bash kernel for Jupyter/IPython, based on MetaKernel.
-</longdescription>
-	<upstream>
-		<remote-id type="github">Calysto/metakernel</remote-id>
-		<remote-id type="pypi">metakernel_bash</remote-id>
-	</upstream>
-</pkgmetadata>
diff --git a/dev-python/metakernel_bash/metakernel_bash-0.11.3-r1.ebuild b/dev-python/metakernel_bash/metakernel_bash-0.11.3-r1.ebuild
deleted file mode 100644
index b31e6754e..000000000
--- a/dev-python/metakernel_bash/metakernel_bash-0.11.3-r1.ebuild
+++ /dev/null
@@ -1,27 +0,0 @@
-# Copyright 1999-2016 Gentoo Foundation
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=6
-PYTHON_COMPAT=( python2_7 python{3_4,3_5} )
-
-inherit distutils-r1
-
-DESCRIPTION="A Bash kernel for Jupyter/IPython"
-HOMEPAGE="https://github.com/Calysto/metakernel"
-SRC_URI="mirror://pypi/${PN:0:1}/${PN}/${P}.tar.gz"
-KEYWORDS="~amd64"
-
-LICENSE="BSD"
-SLOT="0"
-
-RDEPEND="
-	>=dev-python/metakernel-0.11.0[${PYTHON_USEDEP}]
-	"
-DEPEND="${RDEPEND}"
-
-python_install_all() {
-	insinto /usr/share/jupyter/kernels/${PN}
-	doins "${FILESDIR}"/kernel.json
-
-	distutils-r1_python_install_all
-}
\ No newline at end of file
diff --git a/dev-python/metakernel_python/Manifest b/dev-python/metakernel_python/Manifest
deleted file mode 100644
index e886b758a..000000000
--- a/dev-python/metakernel_python/Manifest
+++ /dev/null
@@ -1 +0,0 @@
-DIST metakernel_python-0.11.3.tar.gz 1856 BLAKE2B 018acc77077da997f166cb167e5f03ef58c4cf6e03db32eafb961ad6b37640214d04c2758a70984f6d537701777ee8ba4fd6068efbfd36c307674bac138d23b2 SHA512 13cc9ee62047a6048b1ea469a3850c34e369a426a16b6c43e002427601f07a585f109c4162bfd30e6607186233affbff7333ae84b12ca6749ecbbc2cea2a1915
diff --git a/dev-python/metakernel_python/files/kernel.json b/dev-python/metakernel_python/files/kernel.json
deleted file mode 100644
index 0a561584a..000000000
--- a/dev-python/metakernel_python/files/kernel.json
+++ /dev/null
@@ -1 +0,0 @@
-{"argv": ["/usr/bin/python", "-m", "metakernel_python", "-f", "{connection_file}"], "display_name": "MetaKernel Python", "language": "python", "name": "metakernel_python"}
diff --git a/dev-python/metakernel_python/metadata.xml b/dev-python/metakernel_python/metadata.xml
deleted file mode 100644
index 0abf27730..000000000
--- a/dev-python/metakernel_python/metadata.xml
+++ /dev/null
@@ -1,15 +0,0 @@
-<?xml version="1.0" encoding="UTF-8"?>
-<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
-<pkgmetadata>
-	<maintainer type="project">
-		<email>sci@gentoo.org</email>
-		<name>Gentoo Science Project</name>
-	</maintainer>
-	<longdescription>
-A Python kernel for Jupyter/IPython, based on MetaKernel.
-</longdescription>
-	<upstream>
-		<remote-id type="github">Calysto/metakernel</remote-id>
-		<remote-id type="pypi">metakernel_python</remote-id>
-	</upstream>
-</pkgmetadata>
diff --git a/dev-python/metakernel_python/metakernel_python-0.11.3-r1.ebuild b/dev-python/metakernel_python/metakernel_python-0.11.3-r1.ebuild
deleted file mode 100644
index bac43de96..000000000
--- a/dev-python/metakernel_python/metakernel_python-0.11.3-r1.ebuild
+++ /dev/null
@@ -1,28 +0,0 @@
-# Copyright 1999-2016 Gentoo Foundation
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=6
-PYTHON_COMPAT=( python2_7 python{3_4,3_5} )
-
-inherit distutils-r1
-
-DESCRIPTION="A Python kernel for Jupyter/IPython"
-HOMEPAGE="https://github.com/Calysto/metakernel"
-SRC_URI="mirror://pypi/${PN:0:1}/${PN}/${P}.tar.gz"
-KEYWORDS="~amd64"
-
-LICENSE="BSD"
-SLOT="0"
-
-RDEPEND="
-	>=dev-python/metakernel-0.11.0[${PYTHON_USEDEP}]
-	dev-python/jedi[${PYTHON_USEDEP}]
-	"
-DEPEND="${RDEPEND}"
-
-python_install_all() {
-	insinto /usr/share/jupyter/kernels/${PN}
-	doins "${FILESDIR}"/kernel.json
-
-	distutils-r1_python_install_all
-}
\ No newline at end of file
diff --git a/dev-python/methodtools/Manifest b/dev-python/methodtools/Manifest
new file mode 100644
index 000000000..f11018f95
--- /dev/null
+++ b/dev-python/methodtools/Manifest
@@ -0,0 +1 @@
+DIST methodtools-0.4.7.gh.tar.gz 6789 BLAKE2B 83da6aae76dc8fe7035e21a03396398c3c72ab7e94bf5850da233dbc95da0c549f2f64a24e3ace4cc093243e846f418e97a6427f66a8ad9ba910bafd11217d61 SHA512 78fbdd3232673159bbef0ea53d8bc1502d70335751e6e91106a02ff9ddea99d44a69037506516492b3e864137b80819b1679809b287049270e623b4ebe667554
diff --git a/dev-python/methodtools/files/methodtools-0.4.7-nocov.patch b/dev-python/methodtools/files/methodtools-0.4.7-nocov.patch
new file mode 100644
index 000000000..e2ff8a4c1
--- /dev/null
+++ b/dev-python/methodtools/files/methodtools-0.4.7-nocov.patch
@@ -0,0 +1,9 @@
+--- a/setup.cfg	2023-02-05 08:15:17.000000000 -0500
++++ b/setup.cfg	2024-05-06 11:19:57.822360100 -0400
+@@ -35,6 +35,5 @@
+ [aliases]
+ test=pytest
+ [tool:pytest]
+-addopts=--verbose --cov-config .coveragerc --cov methodtools
+ python_files = tests/test*.py
+ norecursedirs=.git py ci
diff --git a/dev-python/methodtools/metadata.xml b/dev-python/methodtools/metadata.xml
new file mode 100644
index 000000000..e85efd512
--- /dev/null
+++ b/dev-python/methodtools/metadata.xml
@@ -0,0 +1,16 @@
+<?xml version='1.0' encoding='UTF-8'?>
+<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
+<pkgmetadata>
+	<maintainer type="person">
+		<email>gentoo@chymera.eu</email>
+		<name>Horea Christian</name>
+	</maintainer>
+	<maintainer type="project">
+		<email>sci@gentoo.org</email>
+		<name>Gentoo Science Project</name>
+	</maintainer>
+	<upstream>
+		<remote-id type="github">youknowone/methodtools</remote-id>
+		<remote-id type="pypi">methodtools</remote-id>
+	</upstream>
+</pkgmetadata>
diff --git a/dev-python/methodtools/methodtools-0.4.7.ebuild b/dev-python/methodtools/methodtools-0.4.7.ebuild
new file mode 100644
index 000000000..79e7739c5
--- /dev/null
+++ b/dev-python/methodtools/methodtools-0.4.7.ebuild
@@ -0,0 +1,24 @@
+# Copyright 1999-2022 Gentoo Authors
+# Distributed under the terms of the GNU General Public License v2
+
+EAPI=8
+
+DISTUTILS_USE_PEP517=setuptools
+PYTHON_COMPAT=( python3_{10..12} )
+inherit distutils-r1
+
+DESCRIPTION="Expand functools features to methods, classmethods, staticmethods"
+HOMEPAGE="https://github.com/youknowone/methodtools"
+# Not using PyPI archive because it misses test files:
+# https://github.com/youknowone/methodtools/issues/24
+SRC_URI="https://github.com/youknowone/methodtools/archive/refs/tags/${PV}.tar.gz -> ${P}.gh.tar.gz"
+
+LICENSE="MIT"
+SLOT="0"
+KEYWORDS="~amd64 ~x86"
+
+RDEPEND="dev-python/wirerope[${PYTHON_USEDEP}]"
+
+PATCHES=( "${FILESDIR}/${P}-nocov.patch" )
+
+distutils_enable_tests pytest
diff --git a/dev-python/mkl-service/Manifest b/dev-python/mkl-service/Manifest
new file mode 100644
index 000000000..f0b775c11
--- /dev/null
+++ b/dev-python/mkl-service/Manifest
@@ -0,0 +1 @@
+DIST mkl-service-2.4.0.gh.tar.gz 18705 BLAKE2B 12896adba1c001a581ff10a18cf11b3b87344687807307ae7ee002583281ac8072730b9496ce94c48d8d9ded5ae815c432e1944715091043c222bd93e2728ed8 SHA512 fc33b0a3670fcac5564c020ee870a800b113b93f344eddf63874303347c7151b7f00052adf5a9544ff7557892aefb6088ee9c53cce043536f4456bd9903dc232
diff --git a/dev-python/mkl-service/metadata.xml b/dev-python/mkl-service/metadata.xml
new file mode 100644
index 000000000..813808eb0
--- /dev/null
+++ b/dev-python/mkl-service/metadata.xml
@@ -0,0 +1,12 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
+<pkgmetadata>
+	<maintainer type="project">
+		<email>sci@gentoo.org</email>
+		<name>Gentoo Science Project</name>
+	</maintainer>
+	<upstream>
+		<remote-id type="github">IntelPython/mkl-service</remote-id>
+		<remote-id type="pypi">mkl-service</remote-id>
+	</upstream>
+</pkgmetadata>
diff --git a/dev-python/mkl-service/mkl-service-2.4.0.ebuild b/dev-python/mkl-service/mkl-service-2.4.0.ebuild
new file mode 100644
index 000000000..decfc57bb
--- /dev/null
+++ b/dev-python/mkl-service/mkl-service-2.4.0.ebuild
@@ -0,0 +1,38 @@
+# Copyright 2022 Gentoo Authors
+# Distributed under the terms of the GNU General Public License v2
+
+EAPI=8
+
+PYTHON_COMPAT=( python3_{10..11} )
+DISTUTILS_USE_PEP517=setuptools
+inherit distutils-r1
+
+DESCRIPTION="Python hooks for Intel Math Kernel Library runtime control settings"
+HOMEPAGE="https://github.com/IntelPython/mkl-service"
+SRC_URI="https://github.com/IntelPython/mkl-service/archive/refs/tags/v${PV}.tar.gz -> ${P}.gh.tar.gz"
+
+LICENSE="BSD"
+SLOT="0"
+KEYWORDS="~amd64"
+
+BDEPEND="
+	dev-python/cython[${PYTHON_USEDEP}]
+	sys-devel/DPC++
+"
+
+RDEPEND="
+	sci-libs/mkl
+"
+DEPEND="${RDEPEND}"
+
+distutils_enable_tests pytest
+
+python_prepare_all() {
+	# DPC++ compiler required for full functionality
+	export CC="${ESYSROOT}/usr/lib/llvm/intel/bin/clang"
+	export CXX="${ESYSROOT}/usr/lib/llvm/intel/bin/clang++"
+	export DPCPPROOT="${ESYSROOT}/usr/lib/llvm/intel"
+	export MKLROOT="${ESYSROOT}/opt/intel/oneapi/mkl/latest"
+
+	distutils-r1_python_prepare_all
+}
diff --git a/dev-python/mkl_fft/Manifest b/dev-python/mkl_fft/Manifest
new file mode 100644
index 000000000..24960cd58
--- /dev/null
+++ b/dev-python/mkl_fft/Manifest
@@ -0,0 +1 @@
+DIST mkl_fft-1.3.1.gh.tar.gz 41796 BLAKE2B 880c5fef47e8f489c51c7ae69516ca073fe49583a1a11c16289d5313161190d0f4fe2be43defe51b26c6d1f5a4df8c40da8fe65c10911f40483e0400d177f859 SHA512 5d9bb76a5d5dfcf93a05fe6e1ebc267ba7011370ef40e84d6e017e90db301cedb1fb202b1f0851133537fa8bf09260bc9b3f5eb497efc049d6153a4de088854f
diff --git a/dev-python/mkl_fft/metadata.xml b/dev-python/mkl_fft/metadata.xml
new file mode 100644
index 000000000..95348817f
--- /dev/null
+++ b/dev-python/mkl_fft/metadata.xml
@@ -0,0 +1,12 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
+<pkgmetadata>
+	<maintainer type="project">
+		<email>sci@gentoo.org</email>
+		<name>Gentoo Science Project</name>
+	</maintainer>
+	<upstream>
+		<remote-id type="github">IntelPython/mkl_fft</remote-id>
+		<remote-id type="pypi">mkl-fft</remote-id>
+	</upstream>
+</pkgmetadata>
diff --git a/dev-python/mkl_fft/mkl_fft-1.3.1.ebuild b/dev-python/mkl_fft/mkl_fft-1.3.1.ebuild
new file mode 100644
index 000000000..9b9c72d41
--- /dev/null
+++ b/dev-python/mkl_fft/mkl_fft-1.3.1.ebuild
@@ -0,0 +1,39 @@
+# Copyright 2022 Gentoo Authors
+# Distributed under the terms of the GNU General Public License v2
+
+EAPI=8
+
+PYTHON_COMPAT=( python3_{10..11} )
+DISTUTILS_USE_PEP517=setuptools
+inherit distutils-r1
+
+DESCRIPTION="NumPy-based Python interface to Intel MKL FFT functionality"
+HOMEPAGE="https://github.com/IntelPython/mkl_fft"
+SRC_URI="https://github.com/IntelPython/mkl_fft/archive/refs/tags/v${PV}.tar.gz -> ${P}.gh.tar.gz"
+
+LICENSE="BSD"
+SLOT="0"
+KEYWORDS="~amd64"
+
+BDEPEND="
+	dev-python/cython[${PYTHON_USEDEP}]
+	sys-devel/DPC++
+"
+
+RDEPEND="
+	dev-python/numpy[${PYTHON_USEDEP}]
+	sci-libs/mkl
+"
+DEPEND="${RDEPEND}"
+
+distutils_enable_tests pytest
+
+python_prepare_all() {
+	# DPC++ compiler required for full functionality
+	export CC="${ESYSROOT}/usr/lib/llvm/intel/bin/clang"
+	export CXX="${ESYSROOT}/usr/lib/llvm/intel/bin/clang++"
+	export DPCPPROOT="${ESYSROOT}/usr/lib/llvm/intel"
+	export MKLROOT="${ESYSROOT}/opt/intel/oneapi/mkl/latest"
+
+	distutils-r1_python_prepare_all
+}
diff --git a/dev-python/mkl_random/Manifest b/dev-python/mkl_random/Manifest
new file mode 100644
index 000000000..a826880d4
--- /dev/null
+++ b/dev-python/mkl_random/Manifest
@@ -0,0 +1 @@
+DIST mkl_random-1.2.2.gh.tar.gz 80274 BLAKE2B f59091c2bdb4b0136e218e3a1341d1852aa9fcec097dc435330f9b175a71aefc1d7fe7fb56411f562f4f56bbff52fa46dec3506a36f73fecd91646b7b1ac56d4 SHA512 dd691fb9873cf54e4f488a20de9c85993536bbeaedb7fbd731e9c021e3b40992f45a01268f3166ce08e766b9374745ac2ee81e99eb013c7406d40d365241cb31
diff --git a/dev-python/mkl_random/metadata.xml b/dev-python/mkl_random/metadata.xml
new file mode 100644
index 000000000..394347ca5
--- /dev/null
+++ b/dev-python/mkl_random/metadata.xml
@@ -0,0 +1,12 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
+<pkgmetadata>
+	<maintainer type="project">
+		<email>sci@gentoo.org</email>
+		<name>Gentoo Science Project</name>
+	</maintainer>
+	<upstream>
+		<remote-id type="github">IntelPython/mkl_random</remote-id>
+		<remote-id type="pypi">mkl-random</remote-id>
+	</upstream>
+</pkgmetadata>
diff --git a/dev-python/mkl_random/mkl_random-1.2.2.ebuild b/dev-python/mkl_random/mkl_random-1.2.2.ebuild
new file mode 100644
index 000000000..7bd845de9
--- /dev/null
+++ b/dev-python/mkl_random/mkl_random-1.2.2.ebuild
@@ -0,0 +1,41 @@
+# Copyright 2022 Gentoo Authors
+# Distributed under the terms of the GNU General Public License v2
+
+EAPI=8
+
+PYTHON_COMPAT=( python3_{10..11} )
+DISTUTILS_USE_PEP517=setuptools
+inherit distutils-r1
+
+DESCRIPTION="Python interface to Intel Math Kernel Library's random number generation"
+HOMEPAGE="https://github.com/IntelPython/mkl_random"
+SRC_URI="https://github.com/IntelPython/mkl_random/archive/refs/tags/v${PV}.tar.gz -> ${P}.gh.tar.gz"
+
+LICENSE="BSD"
+SLOT="0"
+KEYWORDS="~amd64"
+
+BDEPEND="
+	dev-python/cython[${PYTHON_USEDEP}]
+	sys-devel/DPC++
+"
+
+RDEPEND="
+	dev-python/numpy[${PYTHON_USEDEP}]
+	sci-libs/mkl
+"
+DEPEND="${RDEPEND}"
+
+distutils_enable_tests pytest
+
+python_prepare_all() {
+	# DPC++ compiler required for full functionality
+	export CC="${ESYSROOT}/usr/lib/llvm/intel/bin/clang"
+	export CXX="${ESYSROOT}/usr/lib/llvm/intel/bin/clang++"
+	export DPCPPROOT="${ESYSROOT}/usr/lib/llvm/intel"
+	export MKLROOT="${ESYSROOT}/opt/intel/oneapi/mkl/latest"
+	export C_INCLUDE_PATH="${ESYSROOT}/opt/intel/oneapi/mkl/latest/include/"
+	export CPLUS_INCLUDE_PATH="${ESYSROOT}/opt/intel/oneapi/mkl/latest/include/"
+
+	distutils-r1_python_prepare_all
+}
diff --git a/dev-python/mkl_umath/Manifest b/dev-python/mkl_umath/Manifest
new file mode 100644
index 000000000..6e1df7796
--- /dev/null
+++ b/dev-python/mkl_umath/Manifest
@@ -0,0 +1 @@
+DIST mkl_umath-0.1.1.gh.tar.gz 47263 BLAKE2B cb336ad38853298152ebef56e20dac5c6154352a1e443097db27c21ef3099b1ce93ba14a8a9d93ec163aecd0bef2ad8bbff436ae3f4f35ff1029ac6c34a808f5 SHA512 7e545c294d879ca602d2527945b9bb6782cf4e01c44cbde617c3ffcf8d639e428fecc3c9427b4089d70dbc8ae723630a8148917df18109b9c1727a25ad651775
diff --git a/dev-python/mkl_umath/metadata.xml b/dev-python/mkl_umath/metadata.xml
new file mode 100644
index 000000000..f23ce9644
--- /dev/null
+++ b/dev-python/mkl_umath/metadata.xml
@@ -0,0 +1,12 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
+<pkgmetadata>
+	<maintainer type="project">
+		<email>sci@gentoo.org</email>
+		<name>Gentoo Science Project</name>
+	</maintainer>
+	<upstream>
+		<remote-id type="github">IntelPython/mkl_umath</remote-id>
+		<remote-id type="pypi">mkl-umath</remote-id>
+	</upstream>
+</pkgmetadata>
diff --git a/dev-python/mkl_umath/mkl_umath-0.1.1.ebuild b/dev-python/mkl_umath/mkl_umath-0.1.1.ebuild
new file mode 100644
index 000000000..1210fdfd8
--- /dev/null
+++ b/dev-python/mkl_umath/mkl_umath-0.1.1.ebuild
@@ -0,0 +1,37 @@
+# Copyright 2022 Gentoo Authors
+# Distributed under the terms of the GNU General Public License v2
+
+EAPI=8
+
+PYTHON_COMPAT=( python3_{10..11} )
+DISTUTILS_USE_PEP517=setuptools
+inherit distutils-r1
+
+DESCRIPTION="Package implementing NumPy's UFuncs based on SVML and MKL VML"
+HOMEPAGE="https://github.com/IntelPython/mkl_umath"
+SRC_URI="https://github.com/IntelPython/mkl_umath/archive/refs/tags/v${PV}.tar.gz -> ${P}.gh.tar.gz"
+
+LICENSE="BSD"
+SLOT="0"
+KEYWORDS="~amd64"
+
+BDEPEND="
+	dev-python/cython[${PYTHON_USEDEP}]
+	sys-devel/DPC++
+"
+
+RDEPEND="
+	dev-python/numpy[${PYTHON_USEDEP}]
+	sci-libs/mkl
+"
+DEPEND="${RDEPEND}"
+
+python_prepare_all() {
+	# DPC++ compiler required for full functionality
+	export CC="${ESYSROOT}/usr/lib/llvm/intel/bin/clang"
+	export CXX="${ESYSROOT}/usr/lib/llvm/intel/bin/clang++"
+	export DPCPPROOT="${ESYSROOT}/usr/lib/llvm/intel"
+	export MKLROOT="${ESYSROOT}/opt/intel/oneapi/mkl/latest"
+
+	distutils-r1_python_prepare_all
+}
diff --git a/dev-python/multimethod/Manifest b/dev-python/multimethod/Manifest
new file mode 100644
index 000000000..2b7c7d4a6
--- /dev/null
+++ b/dev-python/multimethod/Manifest
@@ -0,0 +1 @@
+DIST multimethod-1.8.gh.tar.gz 15364 BLAKE2B e16a42a9d35387b4a972e0b88299af215df20dd5025ad5a2fa4314410f667ba4cea401c0d050dfa3e45612117774c4a6627f6b84c33bc55ed0e4c4ec42f5fec3 SHA512 433a2c72a6c98129df70aa09d1e640f2f23be6c42236cb88ad4ef9dee89406a9b6a2c01771b2b7e69ffa8d6b6cae05a8e0cd273d77c2eed86c5b8ee0c6887c8c
diff --git a/dev-python/multimethod/metadata.xml b/dev-python/multimethod/metadata.xml
new file mode 100644
index 000000000..cd5b00a2b
--- /dev/null
+++ b/dev-python/multimethod/metadata.xml
@@ -0,0 +1,12 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
+<pkgmetadata>
+	<maintainer type="project">
+		<email>sci@gentoo.org</email>
+		<name>Gentoo Science Project</name>
+	</maintainer>
+	<stabilize-allarches/>
+	<upstream>
+		<remote-id type="github">coady/multimethod</remote-id>
+	</upstream>
+</pkgmetadata>
diff --git a/dev-python/multimethod/multimethod-1.8.ebuild b/dev-python/multimethod/multimethod-1.8.ebuild
new file mode 100644
index 000000000..595a728a4
--- /dev/null
+++ b/dev-python/multimethod/multimethod-1.8.ebuild
@@ -0,0 +1,20 @@
+# Copyright 1999-2022 Gentoo Authors
+# Distributed under the terms of the GNU General Public License v2
+
+EAPI=8
+
+DISTUTILS_USE_PEP517=setuptools
+PYTHON_COMPAT=( python3_10 )
+
+inherit distutils-r1
+
+DESCRIPTION="Library allowing Python function overloads based on argument types"
+HOMEPAGE="https://github.com/coady/multimethod"
+
+SRC_URI="https://github.com/coady/multimethod/archive/refs/tags/v${PV}.tar.gz -> ${P}.gh.tar.gz"
+
+LICENSE="Apache-2.0"
+KEYWORDS="~amd64 ~x86"
+SLOT="0"
+
+distutils_enable_tests pytest
diff --git a/dev-python/nbconvert/metadata.xml b/dev-python/nbconvert/metadata.xml
deleted file mode 100644
index 5e646a7e0..000000000
--- a/dev-python/nbconvert/metadata.xml
+++ /dev/null
@@ -1,12 +0,0 @@
-<?xml version="1.0" encoding="UTF-8"?>
-<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
-<pkgmetadata>
-	<maintainer type="project">
-		<email>sci@gentoo.org</email>
-		<name>Gentoo Science Project</name>
-	</maintainer>
-	<longdescription>
-Jupyter NBConvert converts Jupyter notebooks to various other
-formats via Jinja templates.
-</longdescription>
-</pkgmetadata>
diff --git a/dev-python/nbconvert/nbconvert-9999.ebuild b/dev-python/nbconvert/nbconvert-9999.ebuild
deleted file mode 100644
index f2c7c93bd..000000000
--- a/dev-python/nbconvert/nbconvert-9999.ebuild
+++ /dev/null
@@ -1,71 +0,0 @@
-# Copyright 1999-2017 Gentoo Foundation
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=6
-
-PYTHON_COMPAT=( python2_7 python3_{4,5} )
-
-inherit distutils-r1 git-r3
-
-DESCRIPTION="Converting Jupyter Notebooks"
-HOMEPAGE="http://jupyter.org"
-EGIT_REPO_URI="https://github.com/jupyter/${PN}.git git://github.com/jupyter/${PN}.git"
-
-LICENSE="BSD"
-SLOT="0"
-IUSE="doc test"
-
-RDEPEND="
-	dev-python/jupyter_core[${PYTHON_USEDEP}]
-	dev-python/nbformat[${PYTHON_USEDEP}]
-	dev-python/mistune[${PYTHON_USEDEP}]
-	dev-python/jinja[${PYTHON_USEDEP}]
-	dev-python/pygments[${PYTHON_USEDEP}]
-	dev-python/traitlets[${PYTHON_USEDEP}]
-	dev-python/entrypoints[${PYTHON_USEDEP}]
-	"
-DEPEND="${RDEPEND}
-	doc? (
-		dev-python/ipython[${PYTHON_USEDEP}]
-		dev-python/jupyter_client[${PYTHON_USEDEP}]
-		dev-python/sphinx[${PYTHON_USEDEP}]
-		app-text/pandoc
-	)
-	test? (
-		dev-python/nose[${PYTHON_USEDEP}]
-		dev-python/coverage[${PYTHON_USEDEP}]
-		dev-python/ipykernel[${PYTHON_USEDEP}]
-	)
-	"
-
-python_prepare_all() {
-	# Prevent un-needed download during build
-	if use doc; then
-		sed -e "/^    'sphinx.ext.intersphinx',/d" -i docs/source/conf.py || die
-	fi
-
-	distutils-r1_python_prepare_all
-}
-
-python_compile_all() {
-	use doc && emake -C docs html
-}
-
-python_test() {
-	distutils_install_for_testing
-	cd "${TEST_DIR}"/lib || die
-	nosetests --with-coverage --cover-package=nbconvert nbconvert || die
-}
-
-python_install_all() {
-	use doc && HTML_DOCS=( docs/build/html/. )
-	distutils-r1_python_install_all
-}
-
-pkg_postinst() {
-	if ! has_version app-text/pandoc ; then
-		einfo "Pandoc is required for converting to formats other than Python,"
-		einfo "HTML, and Markdown. If you need this functionality, install"
-		einfo "app-text/pandoc."
-	fi
-}
diff --git a/dev-python/nbdime/metadata.xml b/dev-python/nbdime/metadata.xml
deleted file mode 100644
index b3a30b1ae..000000000
--- a/dev-python/nbdime/metadata.xml
+++ /dev/null
@@ -1,20 +0,0 @@
-<?xml version="1.0" encoding="UTF-8"?>
-<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
-<pkgmetadata>
-	<maintainer type="person">
-		<email>marbre@linux.sungazer.de</email>
-		<name>Marius Brehler</name>
-	</maintainer>
-	<maintainer type="project">
-		<email>sci@gentoo.org</email>
-		<name>Gentoo Science Project</name>
-	</maintainer>
-	<longdescription>
-nbdime provides tools for diffing and merging of Jupyter Notebooks.
-</longdescription>
-	<use>
-		<flag name="webtools">
-Install web-based diff and merge tools.
-</flag>
-	</use>
-</pkgmetadata>
diff --git a/dev-python/nbdime/nbdime-9999.ebuild b/dev-python/nbdime/nbdime-9999.ebuild
deleted file mode 100644
index 29ba0908f..000000000
--- a/dev-python/nbdime/nbdime-9999.ebuild
+++ /dev/null
@@ -1,53 +0,0 @@
-# Copyright 1999-2017 Gentoo Foundation
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=6
-
-PYTHON_COMPAT=( python3_{4,5} )
-
-inherit distutils-r1 git-r3
-
-DESCRIPTION="Diff and merge of Jupyter Notebooks"
-HOMEPAGE="http://jupyter.org"
-EGIT_REPO_URI="https://github.com/jupyter/${PN}.git"
-
-LICENSE="BSD"
-SLOT="0"
-IUSE="test webtools"
-
-RDEPEND="
-	dev-python/nbformat[${PYTHON_USEDEP}]
-	dev-python/six[${PYTHON_USEDEP}]
-	dev-python/colorama[${PYTHON_USEDEP}]
-	dev-python/requests[${PYTHON_USEDEP}]
-	www-servers/tornado[${PYTHON_USEDEP}]
-	webtools? ( net-libs/nodejs[npm] )
-	"
-DEPEND="${RDEPEND}
-	test? (
-		dev-python/pytest[${PYTHON_USEDEP}]
-		dev-python/pytest-cov[${PYTHON_USEDEP}]
-		dev-python/pytest-timeout[${PYTHON_USEDEP}]
-		dev-python/jsonschema[${PYTHON_USEDEP}]
-		dev-python/mock[${PYTHON_USEDEP}]
-		dev-python/requests[${PYTHON_USEDEP}]
-	)
-	"
-# The package recommonmark is required to build the docs, not in portage yet.
-# Furthermore, backports.shutil_which is required for python2_7.
-
-python_configure_all() {
-	if ! use webtools; then
-		mydistutilsargs=( --skip-npm )
-	fi
-}
-
-python_test() {
-	# user.email and user.name are not configured in the sandbox.
-	git config --global user.email "you@example.com" || die
-	git config --global user.name "Your Name" || die
-
-	distutils_install_for_testing
-
-	py.test -l || die
-}
diff --git a/dev-python/nbformat/metadata.xml b/dev-python/nbformat/metadata.xml
deleted file mode 100644
index 0bd1894f0..000000000
--- a/dev-python/nbformat/metadata.xml
+++ /dev/null
@@ -1,14 +0,0 @@
-<?xml version="1.0" encoding="UTF-8"?>
-<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
-<pkgmetadata>
-	<maintainer type="project">
-		<email>sci@gentoo.org</email>
-		<name>Gentoo Science Project</name>
-	</maintainer>
-	<longdescription>
-Jupyther nbformat contains the reference implementation of the
-Jupyter Notebook format, and Python APIs for working with
-notebooks. There is also a JSON schema for notebook format
-versions &gt;= 3.
-</longdescription>
-</pkgmetadata>
diff --git a/dev-python/nbformat/nbformat-9999.ebuild b/dev-python/nbformat/nbformat-9999.ebuild
deleted file mode 100644
index 9549f6909..000000000
--- a/dev-python/nbformat/nbformat-9999.ebuild
+++ /dev/null
@@ -1,59 +0,0 @@
-# Copyright 1999-2017 Gentoo Foundation
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=6
-
-PYTHON_COMPAT=( python2_7 python3_{4,5} )
-PYTHON_REQ_USE='sqlite'
-
-inherit distutils-r1 git-r3
-
-DESCRIPTION="Reference implementation of the Jupyter Notebook format"
-HOMEPAGE="http://jupyter.org"
-EGIT_REPO_URI="https://github.com/jupyter/${PN}.git git://github.com/jupyter/${PN}.git"
-
-LICENSE="BSD"
-SLOT="0"
-IUSE="doc test"
-
-RDEPEND="
-	>=dev-python/jsonschema-2.4.0[${PYTHON_USEDEP}]
-	dev-python/ipython_genutils[${PYTHON_USEDEP}]
-	>=dev-python/traitlets-4.1[${PYTHON_USEDEP}]
-	dev-python/jupyter_core[${PYTHON_USEDEP}]
-	"
-DEPEND="${RDEPEND}
-	doc? (
-		dev-python/sphinx[${PYTHON_USEDEP}]
-		dev-python/numpydoc[${PYTHON_USEDEP}]
-	)
-	test? (
-		dev-python/testpath[${PYTHON_USEDEP}]
-		dev-python/pytest[${PYTHON_USEDEP}]
-		dev-python/pytest-cov[${PYTHON_USEDEP}]
-	)
-	"
-
-python_prepare_all() {
-	# Prevent un-needed download during build
-	if use doc; then
-		sed -e "/^    'sphinx.ext.intersphinx',/d" -i docs/conf.py || die
-	fi
-
-	distutils-r1_python_prepare_all
-}
-
-python_compile_all() {
-	use doc && emake -C docs html
-}
-
-python_test() {
-	distutils_install_for_testing
-	cd "${TEST_DIR}"/lib || die
-	py.test -v --cov nbformat nbformat || die
-}
-
-python_install_all() {
-	use doc && HTML_DOCS=( docs/_build/html/. )
-	distutils-r1_python_install_all
-}
diff --git a/dev-python/nbviewer/metadata.xml b/dev-python/nbviewer/metadata.xml
deleted file mode 100644
index b7acb9324..000000000
--- a/dev-python/nbviewer/metadata.xml
+++ /dev/null
@@ -1,13 +0,0 @@
-<?xml version="1.0" encoding="UTF-8"?>
-<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
-<pkgmetadata>
-	<maintainer type="project">
-		<email>sci@gentoo.org</email>
-		<name>Gentoo Science Project</name>
-	</maintainer>
-	<longdescription>
-Jupyter nbviewer is the web application behind The Jupyter Notebook
-Viewer, which is graciously hosted by Rackspace. Run this locally
-to get most of the features of nbviewer on your own network.
-</longdescription>
-</pkgmetadata>
diff --git a/dev-python/nbviewer/nbviewer-9999.ebuild b/dev-python/nbviewer/nbviewer-9999.ebuild
deleted file mode 100644
index 219ae21be..000000000
--- a/dev-python/nbviewer/nbviewer-9999.ebuild
+++ /dev/null
@@ -1,32 +0,0 @@
-# Copyright 1999-2015 Gentoo Foundation
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=5
-PYTHON_COMPAT=( python3_{4,5} )
-
-inherit distutils-r1
-
-DESCRIPTION="Nbconvert as a webservice (rendering ipynb to static HTML)"
-HOMEPAGE="http://jupyter.org"
-
-if [ ${PV} == "9999" ] ; then
-	inherit git-r3
-	EGIT_REPO_URI="https://github.com/jupyter/${PN}.git git://github.com/jupyter/${PN}.git"
-else
-	SRC_URI=""
-	KEYWORDS="~amd64"
-fi
-
-LICENSE="BSD-4"
-SLOT="0"
-
-RDEPEND="
-	>=dev-python/ipython-4.0.0[notebook,${PYTHON_USEDEP}]
-	>=www-servers/tornado-3.1.1[${PYTHON_USEDEP}]
-	dev-python/pycurl[${PYTHON_USEDEP}]
-	dev-python/pylibmc[${PYTHON_USEDEP}]
-	dev-python/newrelic[${PYTHON_USEDEP}]
-	dev-python/markdown[${PYTHON_USEDEP}]
-	dev-python/elasticsearch-py[${PYTHON_USEDEP}]
-	"
-DEPEND="${RDEPEND}"
diff --git a/dev-python/neo/Manifest b/dev-python/neo/Manifest
new file mode 100644
index 000000000..346e022b8
--- /dev/null
+++ b/dev-python/neo/Manifest
@@ -0,0 +1,3 @@
+DIST neo-0.11.0.tar.gz 9411608 BLAKE2B 9257fd8ff9eea8ec80b0a4eb701b63a9db10d51e6f145b704eb5e9a394dd13a5c6e567cb3469fa4d86f538637f80e9c660823d358bb7ddfd651291dc5df73450 SHA512 dab4832317c8dc6a794ffc9fb118124734fa2428c0527eb9c86bc3d35195a34bdb162bc0a44a3604cb8067fff7263ab5b106c0f9871007a093e7185df5ba9993
+DIST neo-0.11.1.tar.gz 3906151 BLAKE2B 26b60c715d6f3ec017cdb909c1f54b1509db4862f0630ab6d60b4b07153d5cb8512fbf16dd9039d1998b08e0f9e828bb271d4f482cc2d34a5d17a010ef4d203b SHA512 1f93a9eea020ee40f792f038bef76e053ff4f6e05951f78afa70bf4009bac3da8222be57c2cee88ae5e7539c5c8978cf50bf52cce787dbacafe6d5450d5e1aa7
+DIST neo-0.12.0.tar.gz 28377158 BLAKE2B efc6ae96d8cf8325355367af482d4e6dcc0dc3e3c5f3d449076a1c3ef32f530f777a2b125c946360b05a070cd75ae3f04b31a9e63d9bee7fecf437c3a19fc284 SHA512 1849c5074afb71cba7e90a78fa51b9967b27cb3f0b6242cfbadc3c29faf7a4a13da0a15a1c43cf43df810a5c0ed0b45cf60b42f3ed83520689acc27d3bde07b9
diff --git a/dev-python/neo/metadata.xml b/dev-python/neo/metadata.xml
new file mode 100644
index 000000000..5a50da2a7
--- /dev/null
+++ b/dev-python/neo/metadata.xml
@@ -0,0 +1,23 @@
+<?xml version='1.0' encoding='UTF-8'?>
+<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
+<pkgmetadata>
+	<maintainer type="person">
+		<email>gentoo@chymera.eu</email>
+		<name>Horea Christian</name>
+	</maintainer>
+	<maintainer type="project">
+		<email>sci@gentoo.org</email>
+		<name>Gentoo Science Project</name>
+	</maintainer>
+	<longdescription lang="en">
+		Neo is a Python package for working with electrophysiology data in Python,
+		together with support for reading a wide range of neurophysiology file
+		formats, including Spike2, NeuroExplorer, AlphaOmega, Axon, Blackrock,
+		Plexon, Tdt, and support for writing to a subset of these formats plus
+		non-proprietary formats including HDF5.
+	</longdescription>
+	<upstream>
+		<remote-id type="github">NeuralEnsemble/python-neo</remote-id>
+		<remote-id type="pypi">neo</remote-id>
+	</upstream>
+</pkgmetadata>
diff --git a/dev-python/neo/neo-0.11.0.ebuild b/dev-python/neo/neo-0.11.0.ebuild
new file mode 100644
index 000000000..dedbcea6e
--- /dev/null
+++ b/dev-python/neo/neo-0.11.0.ebuild
@@ -0,0 +1,61 @@
+# Copyright 2021-2023 Gentoo Authors
+# Distributed under the terms of the GNU General Public License v2
+
+EAPI=8
+
+PYTHON_COMPAT=( python3_{10..11} )
+DISTUTILS_USE_PEP517=setuptools
+inherit distutils-r1 pypi
+
+MY_PN="python-neo"
+
+DESCRIPTION="Read and represent a wide range of neurophysiology file formats in Python"
+HOMEPAGE="https://github.com/NeuralEnsemble/python-neo"
+
+LICENSE="MIT"
+SLOT="0"
+KEYWORDS="~amd64"
+IUSE="test"
+
+RDEPEND="
+	dev-python/numpy[${PYTHON_USEDEP}]
+	dev-python/quantities[${PYTHON_USEDEP}]
+"
+BDEPEND="
+	test? (
+		${RDEPEND}
+		dev-python/scipy[${PYTHON_USEDEP}]
+		dev-python/h5py[${PYTHON_USEDEP}]
+		dev-python/matplotlib[${PYTHON_USEDEP}]
+		dev-python/pillow[${PYTHON_USEDEP}]
+		dev-python/probeinterface[${PYTHON_USEDEP}]
+		dev-python/pynwb[${PYTHON_USEDEP}]
+		dev-python/tqdm[${PYTHON_USEDEP}]
+		dev-vcs/datalad[${PYTHON_USEDEP}]
+	)
+"
+# Testing deps also need:
+# igor
+# pyedflib https://github.com/holgern/pyedflib
+# klusta
+# nixio
+# sonpy
+# ipython
+
+S="${WORKDIR}/${MY_PN}-${PV}"
+
+distutils_enable_tests pytest
+
+EPYTEST_DESELECT=(
+	neo/test/utils/test_datasets.py::TestDownloadDataset::test_download_dataset
+)
+
+# Reported upstream
+# https://github.com/NeuralEnsemble/python-neo/issues/1037
+python_test() {
+	local EPYTEST_IGNORE=(
+		neo/test/iotest/*
+		neo/test/rawiotest/*
+	)
+	epytest
+}
diff --git a/dev-python/neo/neo-0.11.1.ebuild b/dev-python/neo/neo-0.11.1.ebuild
new file mode 100644
index 000000000..6f43494f8
--- /dev/null
+++ b/dev-python/neo/neo-0.11.1.ebuild
@@ -0,0 +1,53 @@
+# Copyright 2021-2023 Gentoo Authors
+# Distributed under the terms of the GNU General Public License v2
+
+EAPI=8
+
+PYTHON_COMPAT=( python3_{10..11} )
+DISTUTILS_USE_PEP517=setuptools
+inherit distutils-r1 pypi
+
+DESCRIPTION="Read and represent a wide range of neurophysiology file formats in Python"
+HOMEPAGE="https://github.com/NeuralEnsemble/python-neo"
+
+LICENSE="MIT"
+SLOT="0"
+KEYWORDS="~amd64"
+IUSE="test"
+
+RDEPEND="
+	dev-python/numpy[${PYTHON_USEDEP}]
+	dev-python/quantities[${PYTHON_USEDEP}]
+"
+BDEPEND="
+	test? (
+		${RDEPEND}
+		dev-python/scipy[${PYTHON_USEDEP}]
+		dev-python/h5py[${PYTHON_USEDEP}]
+		dev-python/matplotlib[${PYTHON_USEDEP}]
+		dev-python/pillow[${PYTHON_USEDEP}]
+		dev-python/probeinterface[${PYTHON_USEDEP}]
+		dev-python/pynwb[${PYTHON_USEDEP}]
+		dev-python/tqdm[${PYTHON_USEDEP}]
+		dev-vcs/datalad[${PYTHON_USEDEP}]
+	)
+"
+# Testing deps also need:
+# igor
+# pyedflib https://github.com/holgern/pyedflib
+# klusta
+# nixio
+# sonpy
+# ipython
+
+distutils_enable_tests pytest
+
+# Reported upstream
+# https://github.com/NeuralEnsemble/python-neo/issues/1037
+python_test() {
+	local EPYTEST_IGNORE=(
+		neo/test/iotest/*
+		neo/test/rawiotest/*
+	)
+	epytest
+}
diff --git a/dev-python/neo/neo-0.12.0.ebuild b/dev-python/neo/neo-0.12.0.ebuild
new file mode 100644
index 000000000..6e058728e
--- /dev/null
+++ b/dev-python/neo/neo-0.12.0.ebuild
@@ -0,0 +1,57 @@
+# Copyright 2021-2023 Gentoo Authors
+# Distributed under the terms of the GNU General Public License v2
+
+EAPI=8
+
+PYTHON_COMPAT=( python3_{10..11} )
+DISTUTILS_USE_PEP517=setuptools
+inherit distutils-r1 pypi
+
+DESCRIPTION="Read and represent a wide range of neurophysiology file formats in Python"
+HOMEPAGE="https://github.com/NeuralEnsemble/python-neo"
+
+LICENSE="MIT"
+SLOT="0"
+KEYWORDS="~amd64"
+IUSE="test"
+
+RDEPEND="
+	dev-python/numpy[${PYTHON_USEDEP}]
+	dev-python/quantities[${PYTHON_USEDEP}]
+"
+BDEPEND="
+	test? (
+		${RDEPEND}
+		dev-python/scipy[${PYTHON_USEDEP}]
+		dev-python/h5py[${PYTHON_USEDEP}]
+		dev-python/matplotlib[${PYTHON_USEDEP}]
+		dev-python/pillow[${PYTHON_USEDEP}]
+		dev-python/probeinterface[${PYTHON_USEDEP}]
+		dev-python/pynwb[${PYTHON_USEDEP}]
+		dev-python/tqdm[${PYTHON_USEDEP}]
+		dev-vcs/datalad[${PYTHON_USEDEP}]
+	)
+"
+# Testing deps also need:
+# igor
+# pyedflib https://github.com/holgern/pyedflib
+# klusta
+# nixio
+# sonpy
+# ipython
+
+distutils_enable_tests pytest
+
+python_test() {
+	# Reported upstream
+	# https://github.com/NeuralEnsemble/python-neo/issues/1037
+	local EPYTEST_IGNORE=(
+		neo/test/iotest/*
+		neo/test/rawiotest/*
+	)
+	# Requires dynamic data download
+	local EPYTEST_DESELECT=(
+		neo/test/utils/test_datasets.py::TestDownloadDataset::test_download_dataset
+	)
+	epytest
+}
diff --git a/dev-python/newrelic/Manifest b/dev-python/newrelic/Manifest
deleted file mode 100644
index 31a6c137a..000000000
--- a/dev-python/newrelic/Manifest
+++ /dev/null
@@ -1,2 +0,0 @@
-DIST newrelic-2.44.0.36.tar.gz 656605 BLAKE2B 7cc423ee88a2f678a0b10aa2be16e105267348d66f2acf07c1e6d19083b667294fe0b7b6a647d79994c37cb4ca87bb9de1818cacae0709c49deace3123317bed SHA512 2e9b7b6afd74c562c82813d0245822a194e151abf1e32827915b83677db811032711418ae2bd0c26b3ea4727323ca53d538862957d8cd07f7f6a2ce26630a682
-DIST newrelic-2.50.0.39.tar.gz 662564 BLAKE2B 17eb9f914e558bd063553460b3ada06316f7e5300ee8c136820c5c2095dfc27987e7b515eb86ed7303968eb587575fa7c2ced456e2fad681faaed4735a7e3e38 SHA512 935973b7897348113ab40ac4f1ea173cf31886057569a0384e4a26d96463220a43768a4dd88ac4e4a8a7db01ab4fe6fde7825860a7fbd62911ead5fc2e3f0774
diff --git a/dev-python/newrelic/metadata.xml b/dev-python/newrelic/metadata.xml
deleted file mode 100644
index 7f0f33d60..000000000
--- a/dev-python/newrelic/metadata.xml
+++ /dev/null
@@ -1,15 +0,0 @@
-<?xml version="1.0" encoding="UTF-8"?>
-<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
-<pkgmetadata>
-	<maintainer type="project">
-		<email>sci@gentoo.org</email>
-		<name>Gentoo Science Project</name>
-	</maintainer>
-	<longdescription>
-Python agent for the New Relic web application performance
-monitoring service.
-</longdescription>
-	<upstream>
-		<remote-id type="pypi">newrelic</remote-id>
-	</upstream>
-</pkgmetadata>
diff --git a/dev-python/newrelic/newrelic-2.44.0.36.ebuild b/dev-python/newrelic/newrelic-2.44.0.36.ebuild
deleted file mode 100644
index d954b20de..000000000
--- a/dev-python/newrelic/newrelic-2.44.0.36.ebuild
+++ /dev/null
@@ -1,34 +0,0 @@
-# Copyright 1999-2017 Gentoo Foundation
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=6
-
-PYTHON_COMPAT=( python{2_7,3_{4,5}} )
-
-inherit distutils-r1
-
-MY_PN="newrelic"
-
-DESCRIPTION="New Relic Python Agent"
-HOMEPAGE="http://newrelic.com/docs/python/new-relic-for-python"
-SRC_URI="mirror://pypi/${PN:0:1}/${PN}/${P}.tar.gz"
-
-LICENSE="newrelic"
-SLOT="0"
-KEYWORDS="~amd64"
-IUSE=""
-
-RDEPEND="
-	|| (
-		dev-python/bottle[${PYTHON_USEDEP}]
-		dev-python/cherrypy[${PYTHON_USEDEP}]
-		dev-python/django[${PYTHON_USEDEP}]
-		dev-python/flask[${PYTHON_USEDEP}]
-		dev-python/pyramid[${PYTHON_USEDEP}]
-	)"
-	#|| (
-	#	dev-python/cython[${PYTHON_USEDEP}]
-	#	virtual/pypy
-	#	virtual/pypy3
-	#)"
-DEPEND="${RDEPEND}"
diff --git a/dev-python/newrelic/newrelic-2.50.0.39.ebuild b/dev-python/newrelic/newrelic-2.50.0.39.ebuild
deleted file mode 100644
index 3812ed990..000000000
--- a/dev-python/newrelic/newrelic-2.50.0.39.ebuild
+++ /dev/null
@@ -1,39 +0,0 @@
-# Copyright 1999-2017 Gentoo Foundation
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=6
-
-PYTHON_COMPAT=( python{2_7,3_{4,5}} )
-
-inherit distutils-r1
-
-MY_PN="newrelic"
-
-DESCRIPTION="New Relic Python Agent"
-HOMEPAGE="http://newrelic.com/docs/python/new-relic-for-python"
-SRC_URI="mirror://pypi/${PN:0:1}/${PN}/${P}.tar.gz"
-
-LICENSE="newrelic"
-SLOT="0"
-KEYWORDS="~amd64"
-IUSE=""
-
-RDEPEND="
-	|| (
-		dev-python/bottle[${PYTHON_USEDEP}]
-		dev-python/cherrypy[${PYTHON_USEDEP}]
-		dev-python/django[${PYTHON_USEDEP}]
-		dev-python/flask[${PYTHON_USEDEP}]
-		dev-python/pyramid[${PYTHON_USEDEP}]
-	)"
-	#|| (
-	#	dev-python/cython[${PYTHON_USEDEP}]
-	#	virtual/pypy
-	#	virtual/pypy3
-	#)"
-DEPEND="${RDEPEND}"
-
-src_install() {
-	default
-	dobin scripts/newrelic-admin
-}
diff --git a/dev-python/ngslib/Manifest b/dev-python/ngslib/Manifest
deleted file mode 100644
index 38135f6df..000000000
--- a/dev-python/ngslib/Manifest
+++ /dev/null
@@ -1 +0,0 @@
-DIST ngslib-1.1.19.tar.gz 1064346 BLAKE2B ee6782c1b1ffb1ebec0ae04d3763c653bbe8a36d2e801b58c6ce6000fd3aa42c8f724251ff62a7e58067c59a8f8357301eefe4a4218bc66c24aed62a01609446 SHA512 c92b577145d94ad5f34996e38cbc5cf146465d1faedd342a053357eeb7a59c29880e8e1541104c6b6205129751a93f39e3a3f8186ab911e9ccdd800779cc62d9
diff --git a/dev-python/ngslib/metadata.xml b/dev-python/ngslib/metadata.xml
deleted file mode 100644
index 138cb7705..000000000
--- a/dev-python/ngslib/metadata.xml
+++ /dev/null
@@ -1,12 +0,0 @@
-<?xml version="1.0" encoding="UTF-8"?>
-<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
-<pkgmetadata>
-	<maintainer type="person">
-		<email>mmokrejs@fold.natur.cuni.cz</email>
-		<name>Martin Mokrejs</name>
-	</maintainer>
-	<maintainer type="project">
-		<email>sci-biology@gentoo.org</email>
-		<name>Gentoo Biology Project</name>
-	</maintainer>
-</pkgmetadata>
diff --git a/dev-python/ngslib/ngslib-1.1.19.ebuild b/dev-python/ngslib/ngslib-1.1.19.ebuild
deleted file mode 100644
index 5885bce3c..000000000
--- a/dev-python/ngslib/ngslib-1.1.19.ebuild
+++ /dev/null
@@ -1,23 +0,0 @@
-# Copyright 1999-2017 Gentoo Foundation
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=6
-
-PYTHON_COMPAT=( python2_7 )
-inherit distutils-r1
-
-DESCRIPTION="Work with BED, WIG, BigWIG, 2bit files in python"
-HOMEPAGE="https://pypi.python.org/pypi/ngslib"
-SRC_URI="https://pypi.python.org/packages/da/90/862bde7ea3e7a1f064872f51200b1558efa7c58df8131c39352f1c35fbdd/${P}.tar.gz"
-
-LICENSE="GPL-3" # but Jim Kent's lib is 'for personal, academic and non-profit use only'
-SLOT="0"
-KEYWORDS="~amd64 ~x86"
-IUSE=""
-
-DEPEND="
-	>=sci-biology/pysam-0.8.2
-	>=dev-python/numpy-1.4.1"
-RDEPEND="${DEPEND}"
-
-# contains bundled Jim Kent's library jkweb.a, probab;y do 'rm -rf ./external'
diff --git a/dev-python/notebook/Manifest b/dev-python/notebook/Manifest
deleted file mode 100644
index d402bf197..000000000
--- a/dev-python/notebook/Manifest
+++ /dev/null
@@ -1 +0,0 @@
-DIST notebook-4.0.6.tar.gz 6705277 BLAKE2B a2ea87ca39951bab1bfa5c6ca5952653dda5ce7a12abeaa0a80c4a334a649618f5832d950d8ceffedeaff260035b247e44fd1d10572140875131e7e55ffc39fd SHA512 9ce9ca21adcb967725aeb7a18543ace8aca4e88497d3d2fd708a603511e8ef4a932b39337d134d684df03b273bbc442958a37ced8cd499cb7b97a1c29758eeb0
diff --git a/dev-python/notebook/metadata.xml b/dev-python/notebook/metadata.xml
deleted file mode 100644
index 9b08c7c0f..000000000
--- a/dev-python/notebook/metadata.xml
+++ /dev/null
@@ -1,15 +0,0 @@
-<?xml version="1.0" encoding="UTF-8"?>
-<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
-<pkgmetadata>
-	<maintainer type="project">
-		<email>sci@gentoo.org</email>
-		<name>Gentoo Science Project</name>
-	</maintainer>
-	<longdescription>
-The Jupyter HTML notebook is a web-based notebook environment
-for interactive computing.
-</longdescription>
-	<upstream>
-		<remote-id type="pypi">notebook</remote-id>
-	</upstream>
-</pkgmetadata>
diff --git a/dev-python/notebook/notebook-4.0.6.ebuild b/dev-python/notebook/notebook-4.0.6.ebuild
deleted file mode 100644
index c704eaf44..000000000
--- a/dev-python/notebook/notebook-4.0.6.ebuild
+++ /dev/null
@@ -1,91 +0,0 @@
-# Copyright 1999-2017 Gentoo Foundation
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=5
-
-PYTHON_COMPAT=( python2_7 python3_{4,5} )
-PYTHON_REQ_USE="threads(+)"
-
-inherit distutils-r1
-
-DESCRIPTION="Jupyter Interactive Notebook"
-HOMEPAGE="http://jupyter.org"
-SRC_URI="mirror://pypi/${PN:0:1}/${PN}/${P}.tar.gz"
-KEYWORDS="~amd64 ~x86"
-
-LICENSE="BSD"
-SLOT="0"
-IUSE="doc test"
-RDEPEND="
-	>=dev-libs/mathjax-2.4
-	dev-python/jinja[${PYTHON_USEDEP}]
-	>=dev-python/terminado-0.3.3[${PYTHON_USEDEP}]
-	>=www-servers/tornado-4.0[${PYTHON_USEDEP}]
-	dev-python/ipython_genutils[${PYTHON_USEDEP}]
-	dev-python/traitlets[${PYTHON_USEDEP}]
-	dev-python/jupyter_core[${PYTHON_USEDEP}]
-	dev-python/jupyter_client[${PYTHON_USEDEP}]
-	dev-python/nbformat[${PYTHON_USEDEP}]
-	dev-python/nbconvert[${PYTHON_USEDEP}]
-	dev-python/ipykernel[${PYTHON_USEDEP}]
-	"
-DEPEND="${RDEPEND}
-	dev-python/setuptools[${PYTHON_USEDEP}]
-	test? (
-		$(python_gen_cond_dep 'dev-python/mock[${PYTHON_USEDEP}]' python2_7)
-		>=dev-python/nose-0.10.1[${PYTHON_USEDEP}]
-		dev-python/requests[${PYTHON_USEDEP}]
-		dev-python/coverage[${PYTHON_USEDEP}]
-	)
-	doc? (
-		app-text/pandoc
-		>=dev-python/ipython-4.0.0[${PYTHON_USEDEP}]
-		>=dev-python/sphinx-1.1[${PYTHON_USEDEP}]
-	)
-	"
-
-python_prepare_all() {
-	sed \
-		-e "/import setup/s:$:\nimport setuptools:g" \
-		-i setup.py || die
-
-	# disable bundled mathjax
-	sed -i 's/^.*MathJax.*$//' bower.json || die
-	sed -i 's/mj(/#mj(/' setupbase.py || die
-
-	# Prevent un-needed download during build
-	if use doc; then
-		sed -e "/^    'sphinx.ext.intersphinx',/d" -i docs/source/conf.py || die
-	fi
-
-	distutils-r1_python_prepare_all
-}
-
-python_compile_all() {
-	use doc && emake -C docs html
-}
-
-python_test() {
-	nosetests --with-coverage --cover-package=notebook notebook || die
-
-	"${PYTHON}" -m notebook.jstest base || die
-	"${PYTHON}" -m notebook.jstest notebook || die
-	"${PYTHON}" -m notebook.jstest services || die
-	"${PYTHON}" -m notebook.jstest tree || die
-}
-
-python_install() {
-	distutils-r1_python_install
-
-	ln -sf "${EPREFIX}/usr/share/mathjax" "${D}$(python_get_sitedir)/notebook/static/components/MathJax" || die
-}
-
-python_install_all() {
-	use doc && HTML_DOCS=( docs/build/html/. )
-	distutils-r1_python_install_all
-}
-
-pkg_preinst() {
-	# remove old mathjax folder if present
-	rm -rf "${EROOT}"/usr/lib*/python*/site-packages/notebook/static/components/MathJax
-}
diff --git a/dev-python/notebook/notebook-9999.ebuild b/dev-python/notebook/notebook-9999.ebuild
deleted file mode 100644
index e54ee851c..000000000
--- a/dev-python/notebook/notebook-9999.ebuild
+++ /dev/null
@@ -1,90 +0,0 @@
-# Copyright 1999-2016 Gentoo Foundation
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=6
-
-PYTHON_COMPAT=( python2_7 python3_{4,5} )
-PYTHON_REQ_USE="threads(+)"
-
-inherit distutils-r1 git-r3
-
-DESCRIPTION="Jupyter Interactive Notebook"
-HOMEPAGE="http://jupyter.org"
-EGIT_REPO_URI="https://github.com/jupyter/${PN}.git git://github.com/jupyter/${PN}.git"
-
-LICENSE="BSD"
-SLOT="0"
-IUSE="doc test"
-RDEPEND="
-	>=dev-libs/mathjax-2.4
-	dev-python/jinja[${PYTHON_USEDEP}]
-	>=dev-python/terminado-0.3.3[${PYTHON_USEDEP}]
-	>=www-servers/tornado-4.0[${PYTHON_USEDEP}]
-	dev-python/ipython_genutils[${PYTHON_USEDEP}]
-	dev-python/traitlets[${PYTHON_USEDEP}]
-	dev-python/jupyter_core[${PYTHON_USEDEP}]
-	dev-python/jupyter_client[${PYTHON_USEDEP}]
-	dev-python/nbformat[${PYTHON_USEDEP}]
-	>=dev-python/nbconvert-4.2.0[${PYTHON_USEDEP}]
-	dev-python/ipykernel[${PYTHON_USEDEP}]
-	"
-DEPEND="${RDEPEND}
-	dev-python/setuptools[${PYTHON_USEDEP}]
-	test? (
-		$(python_gen_cond_dep 'dev-python/mock[${PYTHON_USEDEP}]' python2_7)
-		>=dev-python/nose-0.10.1[${PYTHON_USEDEP}]
-		dev-python/requests[${PYTHON_USEDEP}]
-		dev-python/coverage[${PYTHON_USEDEP}]
-	)
-	doc? (
-		app-text/pandoc
-		>=dev-python/ipython-4.0.0[${PYTHON_USEDEP}]
-		>=dev-python/sphinx-1.1[${PYTHON_USEDEP}]
-	)
-	"
-
-python_prepare_all() {
-	sed \
-		-e "/import setup/s:$:\nimport setuptools:g" \
-		-i setup.py || die
-
-	# disable bundled mathjax
-	sed -i 's/^.*MathJax.*$//' bower.json || die
-	sed -i 's/mj(/#mj(/' setupbase.py || die
-
-	# Prevent un-needed download during build
-	if use doc; then
-		sed -e "/^    'sphinx.ext.intersphinx',/d" -i docs/source/conf.py || die
-	fi
-
-	distutils-r1_python_prepare_all
-}
-
-python_compile_all() {
-	use doc && emake -C docs html
-}
-
-python_test() {
-	nosetests --with-coverage --cover-package=notebook notebook || die
-
-	"${PYTHON}" -m notebook.jstest base || die
-	"${PYTHON}" -m notebook.jstest notebook || die
-	"${PYTHON}" -m notebook.jstest services || die
-	"${PYTHON}" -m notebook.jstest tree || die
-}
-
-python_install() {
-	distutils-r1_python_install
-
-	ln -sf "${EPREFIX}/usr/share/mathjax" "${D}$(python_get_sitedir)/notebook/static/components/MathJax" || die
-}
-
-python_install_all() {
-	use doc && HTML_DOCS=( docs/build/html/. )
-	distutils-r1_python_install_all
-}
-
-pkg_preinst() {
-	# remove old mathjax folder if present
-	rm -rf "${EROOT}"/usr/lib*/python*/site-packages/notebook/static/components/MathJax
-}
diff --git a/dev-python/nptyping/Manifest b/dev-python/nptyping/Manifest
new file mode 100644
index 000000000..8a541f60d
--- /dev/null
+++ b/dev-python/nptyping/Manifest
@@ -0,0 +1 @@
+DIST nptyping-2.5.0.gh.tar.gz 72870 BLAKE2B 16c6cb90c36bbf0b97da5ff74cee7030c641ef76d055cc5691b9d83adab2714d6e3515fd4e8616fece74606e109e6b115348964614b408df06b4f5c3cbccce37 SHA512 2cde9c5f7694d4f916b85c93b86df7f72709a70b2ffa91b7bbc98c5884236f5b36bb545a89c37e8c02a9b460065c97151d77c64f8d93b92fd93bcff406f039d9
diff --git a/dev-python/nptyping/metadata.xml b/dev-python/nptyping/metadata.xml
new file mode 100644
index 000000000..45345f0dc
--- /dev/null
+++ b/dev-python/nptyping/metadata.xml
@@ -0,0 +1,16 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<!DOCTYPE pkgmetadata SYSTEM "https://www.gentoo.org/dtd/metadata.dtd">
+<pkgmetadata>
+	<maintainer type="project">
+		<email>sci@gentoo.org</email>
+		<name>Gentoo Science Project</name>
+	</maintainer>
+	<maintainer type="person">
+		<email>gentoo@chymera.eu</email>
+		<name>Horea Christian</name>
+	</maintainer>
+	<upstream>
+		<remote-id type="pypi">nptyping</remote-id>
+		<remote-id type="github">ramonhagenaars/nptyping</remote-id>
+	</upstream>
+</pkgmetadata>
diff --git a/dev-python/nptyping/nptyping-2.5.0.ebuild b/dev-python/nptyping/nptyping-2.5.0.ebuild
new file mode 100644
index 000000000..f6e8864df
--- /dev/null
+++ b/dev-python/nptyping/nptyping-2.5.0.ebuild
@@ -0,0 +1,66 @@
+# Copyright 2022-2023 Gentoo Authors
+# Distributed under the terms of the GNU General Public License v2
+
+EAPI=8
+
+DISTUTILS_USE_PEP517=setuptools
+PYTHON_COMPAT=( python3_{9..11} )
+
+inherit distutils-r1
+
+DESCRIPTION="Type hints for Numpy"
+HOMEPAGE="
+	https://pypi.org/project/nptyping/
+	https://github.com/ramonhagenaars/nptyping/
+"
+SRC_URI="
+	https://github.com/ramonhagenaars/nptyping/archive/v${PV}.tar.gz
+		-> ${P}.gh.tar.gz
+"
+
+LICENSE="MIT"
+SLOT="0"
+KEYWORDS="~amd64"
+
+RDEPEND="
+	dev-python/numpy[${PYTHON_USEDEP}]
+"
+BDEPEND="
+	test? (
+		dev-python/mypy[${PYTHON_USEDEP}]
+		dev-python/pandas-stubs[${PYTHON_USEDEP}]
+		dev-python/typeguard[${PYTHON_USEDEP}]
+		dev-python/beartype[${PYTHON_USEDEP}]
+	)
+"
+
+EPYTEST_IGNORE=(
+	# requires pyright, which is not yet packaged
+	tests/test_pyright.py
+	# requires Internet + feedparser, meaningless for users
+	tests/test_package_info.py
+	# relying on Internet access to fetch packages for pip
+	tests/test_wheel.py
+	tests/pandas_/test_fork_sync.py
+)
+
+EPYTEST_DESELECT=(
+	# Reported upstream:
+	# https://github.com/ramonhagenaars/nptyping/issues/113
+	tests/test_mypy.py::MyPyTest::test_mypy_accepts_ndarray_with_any
+	tests/test_mypy.py::MyPyTest::test_mypy_accepts_ndarray_with_shape
+	tests/test_mypy.py::MyPyTest::test_mypy_accepts_ndarray_with_structure
+	tests/test_mypy.py::MyPyTest::test_mypy_accepts_ndarrays_as_function_arguments
+	tests/test_mypy.py::MyPyTest::test_mypy_accepts_ndarrays_as_variable_hints
+	tests/test_mypy.py::MyPyTest::test_mypy_accepts_nptyping_types
+	tests/test_mypy.py::MyPyTest::test_mypy_accepts_numpy_types
+	tests/test_mypy.py::MyPyTest::test_mypy_accepts_recarray_with_structure
+	tests/test_mypy.py::MyPyTest::test_mypy_disapproves_ndarray_with_wrong_function_arguments
+	tests/test_mypy.py::MyPyTest::test_mypy_knows_of_ndarray_methods
+	tests/test_typeguard.py::TypeguardTest::test_success
+	tests/pandas_/test_mypy_dataframe.py::MyPyDataFrameTest::test_mypy_accepts_dataframe
+	tests/pandas_/test_mypy_dataframe.py::MyPyDataFrameTest::test_mypy_disapproves_dataframe_with_wrong_function_arguments
+	tests/pandas_/test_mypy_dataframe.py::MyPyDataFrameTest::test_mypy_knows_of_dataframe_methods
+)
+
+distutils_enable_tests pytest
diff --git a/dev-python/num2words/Manifest b/dev-python/num2words/Manifest
index 669f70f9c..5a0bcf9bb 100644
--- a/dev-python/num2words/Manifest
+++ b/dev-python/num2words/Manifest
@@ -1 +1 @@
-DIST num2words-0.5.6.tar.gz 55475 BLAKE2B 954c314762cb63ecf229eee465a7a88688eec00b940a73f6a2fe843a55bee65ce4590a865e607ae665d2248158cb69f196e5e5d9e6d91867305496fe6192de33 SHA512 6f6d979f8352268ee139681b3fecb659e67ba885806801e2424700b6a002883f6326b85497438e721a476b92a145e6f61a61929ec6bd885309f555f86959b66e
+DIST num2words-0.5.10.tar.gz 114781 BLAKE2B 799df95e048ebc4a1868b1cbc7498301724d4e10c950e2202f04211653dbcca85cce30709434b28e9fef1a5c01ac0259d1046bcbecf84d24cef5528fdacae88b SHA512 16938cc3af36719975986b2d9caeb3853ca5a11fa7d982531420296f4c3730b096efb16d24d84a5260a2510914ab86436083dc9c63a372728cf745f3a1a5ba77
diff --git a/dev-python/num2words/metadata.xml b/dev-python/num2words/metadata.xml
index c98623ef2..f3e4e8fcd 100644
--- a/dev-python/num2words/metadata.xml
+++ b/dev-python/num2words/metadata.xml
@@ -2,7 +2,7 @@
 <!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
 <pkgmetadata>
 	<maintainer type="person">
-		<email>horea.christ@gmail.com</email>
+		<email>gentoo@chymera.eu</email>
 		<name>Horea Christian</name>
 	</maintainer>
 	<maintainer type="project">
@@ -16,6 +16,7 @@
 		(although this last feature is a bit buggy for some languages at the moment).
 	</longdescription>
 	<upstream>
-		<remote-id type="github">savoirefairelinux/num2words</remote-id>
+		<remote-id type="github">savoirfairelinux/num2words</remote-id>
+		<remote-id type="pypi">num2words</remote-id>
 	</upstream>
 </pkgmetadata>
diff --git a/dev-python/num2words/num2words-0.5.10.ebuild b/dev-python/num2words/num2words-0.5.10.ebuild
new file mode 100644
index 000000000..f57281b6e
--- /dev/null
+++ b/dev-python/num2words/num2words-0.5.10.ebuild
@@ -0,0 +1,22 @@
+# Copyright 1999-2023 Gentoo Authors
+# Distributed under the terms of the GNU General Public License v2
+
+EAPI=8
+
+PYTHON_COMPAT=( python3_{10..11} )
+inherit distutils-r1 pypi
+
+DESCRIPTION="Modules to convert numbers to words."
+HOMEPAGE="https://github.com/savoirfairelinux/num2words"
+
+LICENSE="MIT"
+SLOT="0"
+KEYWORDS="~amd64 ~x86"
+
+RDEPEND="dev-python/docopt[${PYTHON_USEDEP}]"
+
+BDEPEND="
+	test? ( dev-python/delegator[${PYTHON_USEDEP}] )
+"
+
+distutils_enable_tests pytest
diff --git a/dev-python/num2words/num2words-0.5.6.ebuild b/dev-python/num2words/num2words-0.5.6.ebuild
deleted file mode 100644
index 214bd8907..000000000
--- a/dev-python/num2words/num2words-0.5.6.ebuild
+++ /dev/null
@@ -1,26 +0,0 @@
-# Copyright 1999-2018 Gentoo Foundation
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=7
-
-PYTHON_COMPAT=( python{2_7,3_4,3_5,3_6} )
-
-inherit distutils-r1
-
-DESCRIPTION="Modules to convert numbers to words."
-HOMEPAGE="https://github.com/savoirfairelinux/num2words"
-SRC_URI="https://github.com/savoirfairelinux/num2words/archive/${PV}.tar.gz -> ${P}.tar.gz"
-
-LICENSE="MIT"
-SLOT="0"
-KEYWORDS="~amd64"
-IUSE=""
-
-DEPEND="
-	dev-python/setuptools[${PYTHON_USEDEP}]
-	"
-RDEPEND=""
-
-python_test() {
-	${EPYTHON} setup.py test || die
-}
diff --git a/dev-python/numcodecs/Manifest b/dev-python/numcodecs/Manifest
new file mode 100644
index 000000000..b14e3311b
--- /dev/null
+++ b/dev-python/numcodecs/Manifest
@@ -0,0 +1,2 @@
+DIST numcodecs-0.11.0.tar.gz 4512454 BLAKE2B 8144120856437ca272e275430c6e169d3e2a88c12c54f71518a7f262a77f13161f61e36b8da75abc0ab4efc02cf0807e86272c1bcf5e21bfb76fba7c4cbc8863 SHA512 cd0bcd87320e3c5a4cc97f8b6b11062361ce007c55bf23d07afab7a85df256bf7bc3f16d49958e9238901e70b26deb90faaa7a006207b6325fdbe225b99139d2
+DIST numcodecs-0.12.1.tar.gz 4091415 BLAKE2B d7fa8cc549495c7c54130898f2047eb409559541b299640fb34a2332d874049afa64d5c14151426b24a1ab04c0e0444245477aa26f9336ce3ba7aefc8043abcf SHA512 716a1144c17b08cc1737bd429517b5434a7e5dbc9626ed613ca9ab4f9cda356ed97cb4ef0e2bba747a7681dc5b43818cb07c6db7f5537b4910790f6ea23c696c
diff --git a/dev-python/numcodecs/files/numcodecs-0.11.0-nocov.patch b/dev-python/numcodecs/files/numcodecs-0.11.0-nocov.patch
new file mode 100644
index 000000000..2d5e7f86e
--- /dev/null
+++ b/dev-python/numcodecs/files/numcodecs-0.11.0-nocov.patch
@@ -0,0 +1,11 @@
+--- a/pyproject.toml
++++ b/pyproject.toml
+@@ -87,7 +87,7 @@ exclude_lines = [
+ ]
+ 
+ [tool.pytest.ini_options]
+-addopts = "--cov=numcodecs --cov-report xml --doctest-modules --doctest-glob=*.pyx"
++addopts = "--pyargs numcodecs --doctest-modules --doctest-glob=*.pyx"
+ doctest_optionflags = [
+     "NORMALIZE_WHITESPACE",
+     "ELLIPSIS",
diff --git a/dev-python/numcodecs/metadata.xml b/dev-python/numcodecs/metadata.xml
new file mode 100644
index 000000000..ab018028a
--- /dev/null
+++ b/dev-python/numcodecs/metadata.xml
@@ -0,0 +1,16 @@
+<?xml version='1.0' encoding='UTF-8'?>
+<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
+<pkgmetadata>
+	<maintainer type="person">
+		<email>gentoo@chymera.eu</email>
+		<name>Horea Christian</name>
+	</maintainer>
+	<maintainer type="project">
+		<email>sci@gentoo.org</email>
+		<name>Gentoo Science Project</name>
+	</maintainer>
+	<upstream>
+		<remote-id type="github">zarr-developers/numcodecs</remote-id>
+		<remote-id type="pypi">numcodecs</remote-id>
+	</upstream>
+</pkgmetadata>
diff --git a/dev-python/numcodecs/numcodecs-0.11.0.ebuild b/dev-python/numcodecs/numcodecs-0.11.0.ebuild
new file mode 100644
index 000000000..500a52b89
--- /dev/null
+++ b/dev-python/numcodecs/numcodecs-0.11.0.ebuild
@@ -0,0 +1,49 @@
+# Copyright 1999-2023 Gentoo Authors
+# Distributed under the terms of the GNU General Public License v2
+
+EAPI=8
+
+PYTHON_COMPAT=( python3_{10..11} )
+DISTUTILS_USE_PEP517=setuptools
+inherit distutils-r1 pypi
+
+DESCRIPTION="Data storage buffer compression and transformation codecs"
+HOMEPAGE="https://github.com/zarr-developers/numcodecs"
+
+LICENSE="MIT"
+SLOT="0"
+KEYWORDS="~amd64 ~x86"
+IUSE="test"
+
+RDEPEND="
+	dev-python/cython[${PYTHON_USEDEP}]
+	dev-python/entrypoints[${PYTHON_USEDEP}]
+	dev-python/msgpack[${PYTHON_USEDEP}]
+	dev-python/numpy[${PYTHON_USEDEP}]
+	dev-python/py-cpuinfo[${PYTHON_USEDEP}]
+"
+
+DEPEND="
+	test? (
+		${RDEPEND}
+		dev-python/entrypoints[${PYTHON_USEDEP}]
+	)
+"
+
+PATCHES=(
+	"${FILESDIR}/${P}-nocov.patch"
+)
+
+# Reported upstream:
+# https://github.com/zarr-developers/numcodecs/issues/436
+EPYTEST_DESELECT=(
+	tests/test_json.py::test_non_numpy_inputs
+	tests/test_msgpacks.py::test_non_numpy_inputs
+)
+
+distutils_enable_tests pytest
+
+python_test() {
+	cd "${T}" || die
+	epytest --pyargs numcodecs
+}
diff --git a/dev-python/numcodecs/numcodecs-0.12.1-r2.ebuild b/dev-python/numcodecs/numcodecs-0.12.1-r2.ebuild
new file mode 100644
index 000000000..3d20684ba
--- /dev/null
+++ b/dev-python/numcodecs/numcodecs-0.12.1-r2.ebuild
@@ -0,0 +1,43 @@
+# Copyright 1999-2023 Gentoo Authors
+# Distributed under the terms of the GNU General Public License v2
+
+EAPI=8
+
+PYTHON_COMPAT=( python3_{10..11} )
+DISTUTILS_USE_PEP517=setuptools
+inherit distutils-r1 pypi
+
+DESCRIPTION="Data storage buffer compression and transformation codecs"
+HOMEPAGE="https://github.com/zarr-developers/numcodecs"
+
+LICENSE="MIT"
+SLOT="0"
+KEYWORDS="~amd64 ~x86"
+IUSE="test"
+
+RDEPEND="
+	dev-python/cython[${PYTHON_USEDEP}]
+	dev-python/entrypoints[${PYTHON_USEDEP}]
+	dev-python/msgpack[${PYTHON_USEDEP}]
+	dev-python/numpy[${PYTHON_USEDEP}]
+	dev-python/py-cpuinfo[${PYTHON_USEDEP}]
+"
+DEPEND="
+	test? (
+		${RDEPEND}
+		dev-python/entrypoints[${PYTHON_USEDEP}]
+	)
+"
+
+distutils_enable_tests pytest
+
+python_compile() {
+	local -x DISABLE_NUMCODECS_AVX2=1
+	local -x DISABLE_NUMCODECS_SSE2=1
+	distutils-r1_python_compile
+}
+
+python_test() {
+	cd "${T}" || die
+	epytest --pyargs numcodecs
+}
diff --git a/dev-python/nwbinspector/Manifest b/dev-python/nwbinspector/Manifest
new file mode 100644
index 000000000..d4db5e2f3
--- /dev/null
+++ b/dev-python/nwbinspector/Manifest
@@ -0,0 +1,2 @@
+DIST nwbinspector-0.4.19.gh.tar.gz 570101 BLAKE2B f3950a8e24225fe490a6454ab5cd429bcb741eeee9cf12591089508600d283b4242ef70427e116960d16367e16c6d5a5869cfcedd829500ce920387d8ebca916 SHA512 3ecd7d1db1d53c0ec5db986a211e56b4818c165a376d15e7a79ede9c8ca45560b6f302e3c9b1e960153d632bfa759660be4e44540399e272be3728d76fd52a7c
+DIST nwbinspector-0.4.26.gh.tar.gz 575576 BLAKE2B 5ec888fc578dd0225b346426b93193f1a08cf92fa9c11e7653773c6bd74603c9e3456514209b3e2a12cf9d868f6004b64700c98212f3837b4b77096dff23ea72 SHA512 901df8422aa3b8666f01e9a6389c22f7caca30007494cb8680ee228bb58a9192f4f35a2426f38f068df5e938fe192db6db4d5626d00ca96e766114dd301efce3
diff --git a/dev-python/nwbinspector/metadata.xml b/dev-python/nwbinspector/metadata.xml
new file mode 100644
index 000000000..ccdbc7f6d
--- /dev/null
+++ b/dev-python/nwbinspector/metadata.xml
@@ -0,0 +1,16 @@
+<?xml version='1.0' encoding='UTF-8'?>
+<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
+<pkgmetadata>
+	<maintainer type="person">
+		<email>gentoo@chymera.eu</email>
+		<name>Horea Christian</name>
+	</maintainer>
+	<maintainer type="project">
+		<email>sci@gentoo.org</email>
+		<name>Gentoo Science Project</name>
+	</maintainer>
+	<upstream>
+		<remote-id type="github">NeurodataWithoutBorders/nwbinspector</remote-id>
+		<remote-id type="pypi">nwbinspector</remote-id>
+	</upstream>
+</pkgmetadata>
diff --git a/dev-python/nwbinspector/nwbinspector-0.4.19.ebuild b/dev-python/nwbinspector/nwbinspector-0.4.19.ebuild
new file mode 100644
index 000000000..b4b5f7448
--- /dev/null
+++ b/dev-python/nwbinspector/nwbinspector-0.4.19.ebuild
@@ -0,0 +1,31 @@
+# Copyright 2022-2023 Gentoo Authors
+# Distributed under the terms of the GNU General Public License v2
+
+EAPI=8
+
+DISTUTILS_USE_PEP517=setuptools
+PYTHON_COMPAT=( python3_{10..11} )
+inherit distutils-r1
+
+DESCRIPTION="Inspect NWB files for compliance with NWB Best Practices"
+HOMEPAGE="https://github.com/NeurodataWithoutBorders/nwbinspector"
+SRC_URI="https://github.com/NeurodataWithoutBorders/nwbinspector/archive/refs/tags/v${PV}.tar.gz -> ${P}.gh.tar.gz"
+
+LICENSE="BSD"
+SLOT="0"
+KEYWORDS="~amd64 ~x86"
+IUSE="test"
+RESTRICT="!test? ( test )"
+
+DEPEND=""
+RDEPEND="
+	dev-python/click[${PYTHON_USEDEP}]
+	dev-python/jsonschema[${PYTHON_USEDEP}]
+	dev-python/natsort[${PYTHON_USEDEP}]
+	dev-python/pynwb[${PYTHON_USEDEP}]
+	dev-python/pyyaml[${PYTHON_USEDEP}]
+	dev-python/tqdm[${PYTHON_USEDEP}]
+"
+BDEPEND=""
+
+distutils_enable_tests pytest
diff --git a/dev-python/nwbinspector/nwbinspector-0.4.26-r1.ebuild b/dev-python/nwbinspector/nwbinspector-0.4.26-r1.ebuild
new file mode 100644
index 000000000..271dbfb1d
--- /dev/null
+++ b/dev-python/nwbinspector/nwbinspector-0.4.26-r1.ebuild
@@ -0,0 +1,32 @@
+# Copyright 2022-2023 Gentoo Authors
+# Distributed under the terms of the GNU General Public License v2
+
+EAPI=8
+
+DISTUTILS_USE_PEP517=setuptools
+PYTHON_COMPAT=( python3_{10..11} )
+inherit distutils-r1
+
+DESCRIPTION="Inspect NWB files for compliance with NWB Best Practices"
+HOMEPAGE="https://github.com/NeurodataWithoutBorders/nwbinspector"
+SRC_URI="https://github.com/NeurodataWithoutBorders/nwbinspector/archive/refs/tags/v${PV}.tar.gz -> ${P}.gh.tar.gz"
+
+LICENSE="BSD"
+SLOT="0"
+KEYWORDS="~amd64 ~x86"
+IUSE="test"
+RESTRICT="!test? ( test )"
+
+DEPEND=""
+RDEPEND="
+	dev-python/click[${PYTHON_USEDEP}]
+	dev-python/isodate[${PYTHON_USEDEP}]
+	dev-python/jsonschema[${PYTHON_USEDEP}]
+	dev-python/natsort[${PYTHON_USEDEP}]
+	dev-python/pynwb[${PYTHON_USEDEP}]
+	dev-python/pyyaml[${PYTHON_USEDEP}]
+	dev-python/tqdm[${PYTHON_USEDEP}]
+"
+BDEPEND=""
+
+distutils_enable_tests pytest
diff --git a/dev-python/omniorbpy/Manifest b/dev-python/omniorbpy/Manifest
deleted file mode 100644
index 45baa94eb..000000000
--- a/dev-python/omniorbpy/Manifest
+++ /dev/null
@@ -1 +0,0 @@
-DIST omniORBpy-3.4.tar.gz 721891 BLAKE2B 16a57423c8fa9a5238a6804caa64b059d052fff404c7aa00c6ed70fd2b74a8fb346f67e6adab4a9fe05ac4dbae5e59ab9da263e6721521c5657346f89707d15d SHA512 a9f13e78a8aa216aa1357589c7a9d363b3ef4d1d79e6fe763dab78fe0df3ad0b1d7b19d4efb9a09f25fc507d657164e390e897c8e85c3f50c8882c2522043780
diff --git a/dev-python/omniorbpy/metadata.xml b/dev-python/omniorbpy/metadata.xml
deleted file mode 100644
index 39a7f8b65..000000000
--- a/dev-python/omniorbpy/metadata.xml
+++ /dev/null
@@ -1,11 +0,0 @@
-<?xml version="1.0" encoding="UTF-8"?>
-<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
-<pkgmetadata>
-	<maintainer type="project">
-		<email>sci@gentoo.org</email>
-		<name>Gentoo Science Project</name>
-	</maintainer>
-	<upstream>
-		<remote-id type="sourceforge">omniorb</remote-id>
-	</upstream>
-</pkgmetadata>
diff --git a/dev-python/omniorbpy/omniorbpy-3.4.ebuild b/dev-python/omniorbpy/omniorbpy-3.4.ebuild
deleted file mode 100644
index 4f67c53da..000000000
--- a/dev-python/omniorbpy/omniorbpy-3.4.ebuild
+++ /dev/null
@@ -1,66 +0,0 @@
-# Copyright 1999-2015 Gentoo Foundation
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=5
-
-PYTHON_COMPAT=( python2_7 )
-
-inherit autotools-utils eutils multilib python-r1
-
-MY_P=${P/omniorb/omniORB}
-
-DESCRIPTION="A robust high-performance CORBA ORB for Python"
-HOMEPAGE="http://omniorb.sourceforge.net/"
-SRC_URI="mirror://sourceforge/omniorb/${MY_P}.tar.gz"
-
-LICENSE="LGPL-2.1"
-SLOT="0"
-KEYWORDS="~amd64 ~x86"
-IUSE="ssl"
-
-REQUIRED_USE="${PYTHON_REQUIRED_USE}"
-
-DEPEND="${PYTHON_DEPS}
-	>=net-misc/omniORB-4.1.3[${PYTHON_USEDEP}]
-	ssl? ( dev-libs/openssl:0= )"
-RDEPEND=${DEPEND}
-
-S=${WORKDIR}/${MY_P}
-
-src_prepare() {
-	sed \
-		-e "s/^CXXDEBUGFLAGS.*/CXXDEBUGFLAGS = ${CXXFLAGS}/" \
-		-e "s/^CDEBUGFLAGS.*/CDEBUGFLAGS = ${CFLAGS}/" \
-		-e "s/'prefix[\t ]*:= \/usr'/'prefix := \${DESTDIR}\/usr'/" \
-		-i "${S}"/mk/beforeauto.mk.in || die
-	sed \
-		-e 's#^.*compileall[^\\]*#${EPREFIX}/bin/true;#' \
-		-i "${S}"/python/dir.mk \
-		"${S}"/python/omniORB/dir.mk \
-		"${S}"/python/COS/dir.mk \
-		"${S}"/python/CosNaming/dir.mk || die
-	autotools-utils_src_prepare
-}
-
-src_configure() {
-	local myeconfargs=( --with-omniorb="${EPREFIX}/usr" )
-
-	use ssl && myconf+=( --with-openssl="${EPREFIX}/usr" )
-
-	python_foreach_impl autotools-utils_src_configure
-}
-
-src_compile() {
-	python_foreach_impl autotools-utils_src_compile
-}
-
-src_install() {
-	python_foreach_impl autotools-utils_src_install
-
-	HTML_DOCS=( doc/omniORBpy )
-	DOCS=( doc/omniORBpy.p* doc/tex/* )
-	einstalldocs
-
-	insinto /usr/share/doc/${PF}/
-	doins -r examples
-}
diff --git a/dev-python/opal-client/Manifest b/dev-python/opal-client/Manifest
deleted file mode 100644
index 8e353ba9b..000000000
--- a/dev-python/opal-client/Manifest
+++ /dev/null
@@ -1 +0,0 @@
-DIST opal-py-2.4.1.tar.gz 1089581 BLAKE2B b084b1a2c0380649e38ce907912fb389a6bd5fe2eb9c99cbd6fcfa3dbb62f296853bfff6ed23bc8a8e8d88638c95e2d088ef428345f7a61f0b5706f535f1dacf SHA512 8b8563507d5905a2bc2d36552b52a9ce4da555910496242cfed207ea573da973ac78678fff158066db91154a6f38b5dc8701b8484781143ebd4134b440d01292
diff --git a/dev-python/opal-client/metadata.xml b/dev-python/opal-client/metadata.xml
deleted file mode 100644
index bd5beea0b..000000000
--- a/dev-python/opal-client/metadata.xml
+++ /dev/null
@@ -1,11 +0,0 @@
-<?xml version="1.0" encoding="UTF-8"?>
-<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
-<pkgmetadata>
-	<maintainer type="project">
-		<email>sci-biology@gentoo.org</email>
-		<name>Gentoo Biology Project</name>
-	</maintainer>
-	<upstream>
-		<remote-id type="sourceforge">opaltoolkit</remote-id>
-	</upstream>
-</pkgmetadata>
diff --git a/dev-python/opal-client/opal-client-2.4.1.ebuild b/dev-python/opal-client/opal-client-2.4.1.ebuild
deleted file mode 100644
index 6b0b7df47..000000000
--- a/dev-python/opal-client/opal-client-2.4.1.ebuild
+++ /dev/null
@@ -1,40 +0,0 @@
-# Copyright 1999-2014 Gentoo Foundation
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=5
-
-PYTHON_COMPAT=( python2_7 )
-
-inherit python-r1 versionator
-
-MY_PN="${PN/client/py}"
-MY_P="${MY_PN}-${PV}"
-
-DESCRIPTION="Python Opal Web Service Client"
-HOMEPAGE="http://www.nbcr.net/data/docs/opal/documentation.html"
-SRC_URI="mirror://sourceforge/opaltoolkit/opal-python/$(get_version_component_range 1-2)/${MY_P}.tar.gz"
-
-LICENSE="opal"
-SLOT="0"
-KEYWORDS="~amd64 ~x86"
-IUSE=""
-
-REQUIRED_USE="${PYTHON_REQUIRED_USE}"
-
-RDEPEND="${PYTHON_DEPS}
-	>=dev-python/zsi-2.1_alpha1[${PYTHON_USEDEP}]
-	!=sci-chemistry/apbs-1.1.0"
-DEPEND="${RDEPEND}"
-
-S="${WORKDIR}"/${MY_P}
-
-src_install() {
-	"${EPREFIX}"/usr/bin/wsdl2py  wsdl/opal.wsdl || die
-
-	python_moduleinto AppService
-	python_foreach_impl python_domodule AppService_*.py
-	python_foreach_impl python_optimize
-
-	dodoc README CHANGELOG etc/* *Client.py
-	dohtml docs/*
-}
diff --git a/dev-python/pamela/Manifest b/dev-python/pamela/Manifest
deleted file mode 100644
index 09a551427..000000000
--- a/dev-python/pamela/Manifest
+++ /dev/null
@@ -1 +0,0 @@
-DIST pamela-0.2.1.tar.gz 5314 BLAKE2B acfcd678a6fd5e6ae8e9a1cce4a3dfdf1dc0d923704e550f09cbac40e37ef7afd10250eebaf50010acc13dcdc87c4500b73188666a30a7b9f03c3c49b6617474 SHA512 c0393c7f6d1d8cb257d025577fda3ae0c5839a32cd0748210d298df1745466afebb0e917498440c7550d0a0f0437b908ef712080fb02aa0a1b4c9d3d29cbdf07
diff --git a/dev-python/pamela/metadata.xml b/dev-python/pamela/metadata.xml
deleted file mode 100644
index e458bccf6..000000000
--- a/dev-python/pamela/metadata.xml
+++ /dev/null
@@ -1,16 +0,0 @@
-<?xml version="1.0" encoding="UTF-8"?>
-<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
-<pkgmetadata>
-	<maintainer type="project">
-		<email>sci@gentoo.org</email>
-		<name>Gentoo Science Project</name>
-	</maintainer>
-	<longdescription>
-An interface to the Pluggable Authentication Modules (PAM) library,
-written in pure Python (using ctypes).
-</longdescription>
-	<upstream>
-		<remote-id type="github">minrk/pamela</remote-id>
-		<remote-id type="pypi">pamela</remote-id>
-	</upstream>
-</pkgmetadata>
diff --git a/dev-python/pamela/pamela-0.2.1.ebuild b/dev-python/pamela/pamela-0.2.1.ebuild
deleted file mode 100644
index 307894d13..000000000
--- a/dev-python/pamela/pamela-0.2.1.ebuild
+++ /dev/null
@@ -1,15 +0,0 @@
-# Copyright 1999-2015 Gentoo Foundation
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=5
-PYTHON_COMPAT=( python2_7 python3_{3,4,5} )
-
-inherit distutils-r1
-
-DESCRIPTION="PAM interface using ctypes"
-HOMEPAGE="https://github.com/minrk/pamela"
-SRC_URI="mirror://pypi/${PN:0:1}/${PN}/${P}.tar.gz"
-KEYWORDS="~amd64"
-
-LICENSE="MIT"
-SLOT="0"
diff --git a/dev-python/pamela/pamela-9999.ebuild b/dev-python/pamela/pamela-9999.ebuild
deleted file mode 100644
index 6450b7e24..000000000
--- a/dev-python/pamela/pamela-9999.ebuild
+++ /dev/null
@@ -1,22 +0,0 @@
-# Copyright 1999-2015 Gentoo Foundation
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=5
-PYTHON_COMPAT=( python2_7 python3_{3,4,5} )
-
-inherit distutils-r1 git-r3
-
-DESCRIPTION="PAM interface using ctypes"
-HOMEPAGE="https://github.com/minrk/pamela"
-EGIT_REPO_URI="https://github.com/minrk/${PN}.git git://github.com/minrk/${PN}.git"
-KEYWORDS=""
-
-LICENSE="MIT"
-SLOT="0"
-IUSE="test"
-
-DEPEND="test? ( dev-python/pytest[${PYTHON_USEDEP}] )"
-
-python_test() {
-	py.test --assert=plain test_pamela.py
-}
diff --git a/dev-python/pandas-stubs/Manifest b/dev-python/pandas-stubs/Manifest
new file mode 100644
index 000000000..856ff2fe2
--- /dev/null
+++ b/dev-python/pandas-stubs/Manifest
@@ -0,0 +1 @@
+DIST pandas-stubs-2.1.1.230928.gh.tar.gz 192865 BLAKE2B f3604def27a3ba7444969473c5800f7cc72fd4487f2363f326de6d637f1b6b60d2a8707f6cbb2647389691fbd856a2e7e5cf3710c0ad014ae106472c76dfb1c8 SHA512 5f9e71f187d1532388a98e0139852098c00d44d3ddf32fc3bad1c5199291c7dd4af82b2d73605b1e16b09a79f3b9df02752b37cf87fcb222faee9e704f52dd47
diff --git a/dev-python/pandas-stubs/metadata.xml b/dev-python/pandas-stubs/metadata.xml
new file mode 100644
index 000000000..8cbc804ad
--- /dev/null
+++ b/dev-python/pandas-stubs/metadata.xml
@@ -0,0 +1,16 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<!DOCTYPE pkgmetadata SYSTEM "https://www.gentoo.org/dtd/metadata.dtd">
+<pkgmetadata>
+	<maintainer type="project">
+		<email>python@gentoo.org</email>
+		<name>Gentoo Python Project</name>
+	</maintainer>
+	<maintainer type="person">
+		<email>gentoo@chymera.eu</email>
+		<name>Horea Christian</name>
+	</maintainer>
+	<upstream>
+		<remote-id type="github">pandas-dev/pandas-stubs</remote-id>
+		<remote-id type="pypi">pandas-stubs</remote-id>
+	</upstream>
+</pkgmetadata>
diff --git a/dev-python/pandas-stubs/pandas-stubs-2.1.1.230928.ebuild b/dev-python/pandas-stubs/pandas-stubs-2.1.1.230928.ebuild
new file mode 100644
index 000000000..e10fd1aca
--- /dev/null
+++ b/dev-python/pandas-stubs/pandas-stubs-2.1.1.230928.ebuild
@@ -0,0 +1,52 @@
+# Copyright 2023 Gentoo Authors
+# Distributed under the terms of the GNU General Public License v2
+
+EAPI=8
+
+DISTUTILS_USE_PEP517=poetry
+PYTHON_COMPAT=( python3_{10..11} )
+inherit distutils-r1
+
+DESCRIPTION="Public type stubs for pandas"
+HOMEPAGE="https://github.com/pandas-dev/pandas-stubs"
+SRC_URI="https://github.com/pandas-dev/pandas-stubs/archive/refs/tags/v${PV}.tar.gz -> ${P}.gh.tar.gz"
+
+LICENSE="BSD"
+SLOT="0"
+KEYWORDS="~amd64"
+# Allegedly also needs dev-python/types-pytz (available in ::guru), but somehow works without it...
+# https://github.com/pandas-dev/pandas-stubs/blob/3c2affdaeb1cb03777cc59832dcdd4b030add27d/pyproject.toml#L34
+RDEPEND="
+	dev-python/numpy[${PYTHON_USEDEP}]
+"
+BDEPEND="
+	test? (
+		dev-python/xarray[${PYTHON_USEDEP}]
+		dev-python/pyarrow[${PYTHON_USEDEP}]
+	)
+"
+
+EPYTEST_DESELECT=(
+	# Package has a bunch of test deps missing from ::gentoo and ::science
+	tests/test_frame.py::test_to_markdown
+	tests/test_frame.py::test_types_to_feather
+	tests/test_io.py::test_orc
+	tests/test_io.py::test_orc_path
+	tests/test_io.py::test_orc_buffer
+	tests/test_io.py::test_orc_columns
+	tests/test_io.py::test_orc_bytes
+	tests/test_io.py::test_hdf
+	tests/test_io.py::test_hdfstore
+	tests/test_io.py::test_read_hdf_iterator
+	tests/test_io.py::test_hdf_context_manager
+	tests/test_io.py::test_hdf_series
+	tests/test_io.py::test_spss
+	tests/test_io.py::test_parquet
+	tests/test_io.py::test_parquet_options
+	tests/test_io.py::test_excel_writer_engine
+	tests/test_io.py::test_all_read_without_lxml_dtype_backend
+	tests/test_series.py::test_types_agg
+	tests/test_series.py::test_types_aggregate
+)
+
+distutils_enable_tests pytest
diff --git a/dev-python/panel/Manifest b/dev-python/panel/Manifest
new file mode 100644
index 000000000..459ed3f61
--- /dev/null
+++ b/dev-python/panel/Manifest
@@ -0,0 +1 @@
+DIST panel-0.14.2.tar.gz 20352366 BLAKE2B 429a2da7e92cc1b0f3a42fc120eddc4a8a54e3805c1ca249aad7c243cef0092959e62a13b0f9c64c4765a6d2533b6519a90640e85d4d512a257df40fff1a4522 SHA512 c611e4bc592edeca5920441102cf7baea336016b9f90778c05fc61c57a4b8b48c80e16c182daa1763440be10c6a0ffabb80699bf6aaa96e03566b4ac55b56f4b
diff --git a/dev-python/panel/files/panel-0.14.1-disable_lite_build.patch b/dev-python/panel/files/panel-0.14.1-disable_lite_build.patch
new file mode 100644
index 000000000..387cfb61b
--- /dev/null
+++ b/dev-python/panel/files/panel-0.14.1-disable_lite_build.patch
@@ -0,0 +1,47 @@
+Subject: Prevent Panel from violating network sandboxing.
+
+     * By default, "setup.py" invokes "npm" to rebuild Node.js packages bundled with Panel.
+     * Without this patch we get `error: HTTPSConnectionPool`
+     * A `sed` fix of the `_build_paneljs()` line will break the syntax.
+     * Using the `PANEL_LITE_BUILD` variable might do the trick instead of a patch, but thus far it didn't 
+Author: Horea Christian <gentoo@chymera.eu>
+diff --git a/setup.py b/setup.py
+index d2541dfb..8cfbf933 100644
+--- a/setup.py
++++ b/setup.py
+@@ -54,8 +54,6 @@ class CustomDevelopCommand(develop):
+     """Custom installation for development mode."""
+
+     def run(self):
+-        if not PANEL_LITE_BUILD:
+-            _build_paneljs()
+         develop.run(self)
+
+
+@@ -63,8 +61,6 @@ class CustomInstallCommand(install):
+     """Custom installation for install mode."""
+
+     def run(self):
+-        if not PANEL_LITE_BUILD:
+-            _build_paneljs()
+         install.run(self)
+
+
+@@ -72,8 +68,6 @@ class CustomSdistCommand(sdist):
+     """Custom installation for sdist mode."""
+
+     def run(self):
+-        if not PANEL_LITE_BUILD:
+-            _build_paneljs()
+         sdist.run(self)
+
+
+@@ -92,8 +86,6 @@ try:
+
+         def run(self):
+             """Do nothing so the command intentionally fails."""
+-            if not PANEL_LITE_BUILD:
+-                _build_paneljs()
+             bdist_wheel.run(self)
+
+     _COMMANDS['bdist_wheel'] = CustomBdistWheelCommand
diff --git a/dev-python/panel/metadata.xml b/dev-python/panel/metadata.xml
new file mode 100644
index 000000000..892a7d01f
--- /dev/null
+++ b/dev-python/panel/metadata.xml
@@ -0,0 +1,13 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
+<pkgmetadata>
+	<maintainer type="project">
+		<email>sci@gentoo.org</email>
+		<name>Gentoo Science Project</name>
+	</maintainer>
+	<stabilize-allarches/>
+	<upstream>
+		<remote-id type="pypi">panel</remote-id>
+		<remote-id type="github">holoviz/panel</remote-id>
+	</upstream>
+</pkgmetadata>
diff --git a/dev-python/panel/panel-0.14.2-r1.ebuild b/dev-python/panel/panel-0.14.2-r1.ebuild
new file mode 100644
index 000000000..4674f8161
--- /dev/null
+++ b/dev-python/panel/panel-0.14.2-r1.ebuild
@@ -0,0 +1,63 @@
+# Copyright 1999-2023 Gentoo Authors
+# Distributed under the terms of the GNU General Public License v2
+
+EAPI=8
+
+PYTHON_COMPAT=( python3_{10..11} )
+DISTUTILS_USE_PEP517=setuptools
+# Panel imports from "distutils" at runtime.
+#DISTUTILS_USE_SETUPTOOLS=rdepend
+inherit distutils-r1 pypi
+
+DESCRIPTION="High-level app and dashboarding solution for Python"
+HOMEPAGE="https://panel.holoviz.org"
+
+LICENSE="BSD"
+SLOT="0"
+KEYWORDS="~amd64 ~x86"
+
+# "setup.py" imports from Bokeh to rebuild Node.js packages, but we patch that
+# away below. Our patched Panel thus requires Bokeh only at runtime.
+DEPEND="
+	>=dev-python/param-1.10.0[${PYTHON_USEDEP}]
+	>=dev-python/pyct-0.4.4[${PYTHON_USEDEP}]
+	dev-python/bleach[${PYTHON_USEDEP}]
+"
+RDEPEND="${DEPEND}
+	dev-python/markdown[${PYTHON_USEDEP}]
+	dev-python/requests[${PYTHON_USEDEP}]
+	dev-python/tqdm[${PYTHON_USEDEP}]
+	>=dev-python/bokeh-2.3.0[${PYTHON_USEDEP}]
+	>=dev-python/pyviz_comms-0.7.4[${PYTHON_USEDEP}]
+	>=net-libs/nodejs-15.11.0
+"
+
+PATCHES=( "${FILESDIR}/${PN}-0.14.1-disable_lite_build.patch" )
+
+# This does not work, need to patch..
+#export PANEL_LITE_BUILD=1
+
+src_prepare() {
+	# Install Jupyter configuration files to "/etc" rather than "/usr/etc".
+	sed -i -e 's~"etc/jupyter~"/etc/jupyter~' setup.py || die
+
+	default_src_prepare
+}
+
+# This also does not work, still need patch :(
+#src_compile() {
+#	export PANEL_LITE_BUILD=1
+#	distutils-r1_src_compile
+#}
+
+pkg_postinst() {
+	panel_pkg_postinst() {
+		PANEL_DIR="$(${EPYTHON} -c 'import os, panel; print(os.path.dirname(panel.__file__))')"
+		elog "Node.js packages bundled with Panel under ${EPYTHON} may be"
+		elog "desynchronized from Bokeh and require manual rebuilding with:"
+		elog "    sudo ${EPYTHON} -m panel build \"${PANEL_DIR}\""
+		elog
+	}
+
+	python_foreach_impl panel_pkg_postinst
+}
diff --git a/dev-python/param/Manifest b/dev-python/param/Manifest
new file mode 100644
index 000000000..d26e110b2
--- /dev/null
+++ b/dev-python/param/Manifest
@@ -0,0 +1,2 @@
+DIST param-1.10.1.gh.tar.gz 132562 BLAKE2B ec4f8f6fada02aa91049cc665efddc75ab289a4f86cbd8951d9720c8174b5236415df884e630ede57b76d01da62b477a5db50b97cb46d04d46e37503ec0410a0 SHA512 ca035325829bbb9fdcfadc8fabac8d5a690e38b0942d30d8963f14259f0dc8ebeeba84723904aae8804898f6ea6d5cfa97d2a1103db29f0d6d3355577abe8d14
+DIST param-1.12.3.gh.tar.gz 460593 BLAKE2B 45e004f4df4d70ceb3d5ff654e260d2fdb28cd47c904408ccda86233502464907bc2e709840b060189a81242f348d3cd6e3f021a157be67962365f93a0b08327 SHA512 c7181dfb7ccffaab7521744566d601470678dc35a2ecd9b55fc5adda73a7cd4998f583f4a7b5930a5c811913cd5a9f2152fbc270a541b749c32b0901985cead2
diff --git a/dev-python/param/metadata.xml b/dev-python/param/metadata.xml
new file mode 100644
index 000000000..a853e1f59
--- /dev/null
+++ b/dev-python/param/metadata.xml
@@ -0,0 +1,13 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
+<pkgmetadata>
+	<maintainer type="project">
+		<email>sci@gentoo.org</email>
+		<name>Gentoo Science Project</name>
+	</maintainer>
+	<stabilize-allarches/>
+	<upstream>
+		<remote-id type="pypi">param</remote-id>
+		<remote-id type="github">holoviz/param</remote-id>
+	</upstream>
+</pkgmetadata>
diff --git a/dev-python/param/param-1.10.1.ebuild b/dev-python/param/param-1.10.1.ebuild
new file mode 100644
index 000000000..8e8ec8053
--- /dev/null
+++ b/dev-python/param/param-1.10.1.ebuild
@@ -0,0 +1,22 @@
+# Copyright 1999-2023 Gentoo Authors
+# Distributed under the terms of the GNU General Public License v2
+
+EAPI=8
+
+PYTHON_COMPAT=( python3_{10..11} pypy3 )
+DISTUTILS_USE_PEP517=setuptools
+
+inherit distutils-r1
+
+DESCRIPTION="Make Python code clearer and more reliable by declaring Parameters"
+HOMEPAGE="https://param.holoviz.org"
+# Pypi sources do not include tests
+#SRC_URI="mirror://pypi/${PN:0:1}/${PN}/${P}.tar.gz"
+SRC_URI="https://github.com/holoviz/param/archive/refs/tags/v${PV}.tar.gz -> ${P}.gh.tar.gz"
+
+LICENSE="BSD"
+KEYWORDS="~amd64 ~x86"
+SLOT="0"
+
+# Some tests require nose:
+#distutils_enable_tests unittest
diff --git a/dev-python/param/param-1.12.3.ebuild b/dev-python/param/param-1.12.3.ebuild
new file mode 100644
index 000000000..9ce9e3762
--- /dev/null
+++ b/dev-python/param/param-1.12.3.ebuild
@@ -0,0 +1,22 @@
+# Copyright 1999-2023 Gentoo Authors
+# Distributed under the terms of the GNU General Public License v2
+
+EAPI=8
+
+PYTHON_COMPAT=( python3_{10..11} pypy3 )
+DISTUTILS_USE_PEP517=setuptools
+
+inherit distutils-r1
+
+DESCRIPTION="Make Python code clearer and more reliable by declaring Parameters"
+HOMEPAGE="https://param.holoviz.org"
+# Pypi sources do not include tests, reported upstream:
+# https://github.com/holoviz/param/issues/678
+#SRC_URI="mirror://pypi/${PN:0:1}/${PN}/${P}.tar.gz"
+SRC_URI="https://github.com/holoviz/param/archive/refs/tags/v${PV}.tar.gz -> ${P}.gh.tar.gz"
+
+LICENSE="BSD"
+KEYWORDS="~amd64 ~x86"
+SLOT="0"
+
+distutils_enable_tests pytest
diff --git a/dev-python/persim/Manifest b/dev-python/persim/Manifest
new file mode 100644
index 000000000..b45fc4da3
--- /dev/null
+++ b/dev-python/persim/Manifest
@@ -0,0 +1 @@
+DIST persim-0.3.1.tar.gz 50438 BLAKE2B 774f0adc67ec6af7e297e73a75a3c4eb6004b0ec43d685eca29e20b0b6ef214fafed638e4c1c6eb10b5dad0b836883f3396c6ed323d4530d832c2e655f5353c2 SHA512 b35884d202a98449b719527987fdf07b88b42252d403f7f0b18a2507f63db496d49e389eca5019c540ebcdc99b63b07df73f43bc7780488a6e7e6958e0017b70
diff --git a/dev-python/persim/metadata.xml b/dev-python/persim/metadata.xml
new file mode 100644
index 000000000..ea34f9f89
--- /dev/null
+++ b/dev-python/persim/metadata.xml
@@ -0,0 +1,15 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
+<pkgmetadata>
+    <maintainer type="person">
+        <email>gentoo@aisha.cc</email>
+        <name>Aisha Tammy</name>
+    </maintainer>
+    <maintainer type="project">
+        <email>sci@gentoo.org</email>
+        <name>Gentoo Science Project</name>
+    </maintainer>
+    <upstream>
+        <remote-id type="pypi">persim</remote-id>
+    </upstream>
+</pkgmetadata>
diff --git a/dev-python/persim/persim-0.3.1.ebuild b/dev-python/persim/persim-0.3.1.ebuild
new file mode 100644
index 000000000..994dca206
--- /dev/null
+++ b/dev-python/persim/persim-0.3.1.ebuild
@@ -0,0 +1,46 @@
+# Copyright 1999-2023 Gentoo Authors
+# Distributed under the terms of the GNU General Public License v2
+
+EAPI=8
+
+PYTHON_COMPAT=( python3_{10..11} )
+DISTUTILS_USE_PEP517=setuptools
+
+inherit distutils-r1 pypi
+
+DESCRIPTION="Distances and representations of persistence diagrams"
+HOMEPAGE="https://persim.scikit-tda.org/"
+
+LICENSE="MIT"
+SLOT="0"
+KEYWORDS="~amd64"
+
+RDEPEND="
+	dev-python/hopcroftkarp[${PYTHON_USEDEP}]
+	dev-python/matplotlib[${PYTHON_USEDEP}]
+	dev-python/numpy[${PYTHON_USEDEP}]
+	dev-python/plotly[${PYTHON_USEDEP}]
+	dev-python/scipy[${PYTHON_USEDEP}]
+	sci-libs/scikit-learn[${PYTHON_USEDEP}]
+"
+BDEPEND="test? ( dev-python/deprecated[${PYTHON_USEDEP}] )"
+
+distutils_enable_tests pytest
+
+EPYTEST_DESELECT=(
+	# Reported upsream:
+	# https://github.com/scikit-tda/persim/issues/66
+	test/test_landscapes.py::TestPersLandscapeExact::test_exact_critical_pairs
+	test/test_persim.py::test_integer_diagrams
+	test/test_persim.py::TestEmpty::test_empyt_diagram_list
+	test/test_persim.py::TestTransforms::test_lists_of_lists
+	test/test_persim.py::TestTransforms::test_n_pixels
+	test/test_persim.py::TestTransforms::test_multiple_diagrams
+	test/test_persistence_imager.py::test_empty_diagram_list
+	test/test_persistence_imager.py::test_fit_diagram
+	test/test_persistence_imager.py::test_fit_diagram_list
+	test/test_persistence_imager.py::test_mixed_pairs
+	test/test_persistence_imager.py::TestTransformOutput::test_lists_of_lists
+	test/test_persistence_imager.py::TestTransformOutput::test_n_pixels
+	test/test_persistence_imager.py::TestTransformOutput::test_multiple_diagrams
+)
diff --git a/dev-python/photutils/Manifest b/dev-python/photutils/Manifest
new file mode 100644
index 000000000..00cdad6e8
--- /dev/null
+++ b/dev-python/photutils/Manifest
@@ -0,0 +1 @@
+DIST photutils-1.6.0.tar.gz 1062334 BLAKE2B dd694299ab52e561f3ba419bd3f2329d73017cefd2ab84dcd278dd93b290fb45457ccc6b9bd0cac769f0bce9a4e3ddd15c097a8345fc5a63af52b5c9aa577f4c SHA512 6d7e20f032f7417cedaaf29692b790a597b1a0e8a2d4e25605c2e598e6908de7e1a76e075f02cb1f281df586d9e6d45d0d61bc16eb3996c41568c9d1478725ed
diff --git a/dev-python/photutils/metadata.xml b/dev-python/photutils/metadata.xml
index 5c3d380b2..8069e65c7 100644
--- a/dev-python/photutils/metadata.xml
+++ b/dev-python/photutils/metadata.xml
@@ -12,5 +12,6 @@ centroid and shape parameters, and performing photometry.
 </longdescription>
 	<upstream>
 		<remote-id type="github">astropy/photutils</remote-id>
+		<remote-id type="pypi">photutils</remote-id>
 	</upstream>
 </pkgmetadata>
diff --git a/dev-python/photutils/photutils-1.6.0.ebuild b/dev-python/photutils/photutils-1.6.0.ebuild
new file mode 100644
index 000000000..a1fa5f2d2
--- /dev/null
+++ b/dev-python/photutils/photutils-1.6.0.ebuild
@@ -0,0 +1,40 @@
+# Copyright 1999-2021 Gentoo Authors
+# Distributed under the terms of the GNU General Public License v2
+
+EAPI=8
+
+PYTHON_COMPAT=( python3_{10..11} )
+DISTUTILS_USE_PEP517=setuptools
+
+inherit distutils-r1 pypi
+
+DESCRIPTION="Affiliated package for image photometry utilities"
+HOMEPAGE="https://github.com/astropy/photutils"
+
+LICENSE="BSD"
+SLOT="0"
+KEYWORDS="~amd64 ~x86"
+
+#TODO: Package all these pytest deps:
+# 	pytest-doctestplus>=0.2.0
+# 	pytest-remotedata>=0.3.1
+# 	pytest-openfiles>=0.3.1
+# 	pytest-astropy-header>=0.1.2
+# 	pytest-arraydiff>=0.1
+# 	pytest-filter-subpackage>=0.1
+RESTRICT="test"
+
+RDEPEND="
+	>=dev-python/astropy-0.4[${PYTHON_USEDEP}]
+	dev-python/numpy[${PYTHON_USEDEP}]
+"
+
+distutils_enable_tests pytest
+# TODO: Fix this
+# NameError: name 'disabled_intersphinx_mapping' is not defined
+#distutils_enable_sphinx docs \
+# 	dev-python/sphinx-astropy \
+# 	dev-python/scipy \
+# 	dev-python/matplotlib \
+# 	sci-libs/scikit-learn \
+# 	dev-python/scikit-image \
diff --git a/dev-python/photutils/photutils-9999.ebuild b/dev-python/photutils/photutils-9999.ebuild
deleted file mode 100644
index 0a4b3a0d7..000000000
--- a/dev-python/photutils/photutils-9999.ebuild
+++ /dev/null
@@ -1,60 +0,0 @@
-# Copyright 1999-2014 Gentoo Foundation
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=5
-
-PYTHON_COMPAT=( python{2_7,3_4} )
-inherit distutils-r1
-
-if [ ${PV} == "9999" ] ; then
-	inherit git-r3
-	EGIT_REPO_URI="https://github.com/astropy/${PN}.git"
-else
-	SRC_URI="mirror://pypi/${PN:0:1}/${PN}/${P}.tar.gz"
-	KEYWORDS="~amd64"
-fi
-
-DESCRIPTION="Affiliated package for image photometry utilities"
-HOMEPAGE="https://github.com/astropy/photutils"
-
-LICENSE="BSD"
-SLOT="0"
-IUSE="doc"
-DOCS=( README.rst )
-
-RDEPEND="
-	>=dev-python/astropy-0.4[${PYTHON_USEDEP}]
-	dev-python/astropy-helpers[${PYTHON_USEDEP}]
-	dev-python/imageutils[${PYTHON_USEDEP}]
-	dev-python/matplotlib[${PYTHON_USEDEP}]
-	dev-python/numpy[${PYTHON_USEDEP}]
-	sci-libs/scipy[${PYTHON_USEDEP}]"
-
-DEPEND="${RDEPEND}"
-
-python_prepare_all() {
-	distutils-r1_python_prepare_all
-	sed -e '/import ah_bootstrap/d' -i setup.py || die "Removing ah_bootstrap failed"
-}
-
-python_compile_all() {
-	if use doc; then
-		python_export_best
-		VARTEXFONTS="${T}"/fonts \
-			MPLCONFIGDIR="${BUILD_DIR}" \
-			PYTHONPATH="${BUILD_DIR}"/lib \
-			esetup.py build_sphinx
-	fi
-}
-
-python_test() {
-	distutils_install_for_testing
-	cd "${TEST_DIR}" || die
-	"${EPYTHON}" -c "import ${PN}, sys;r = ${PN}.test(verbose=True);sys.exit(r)" \
-		|| die "tests fail with ${EPYTHON}"
-}
-
-python_install_all() {
-	use doc && local HTML_DOCS=( docs/_build/html/. )
-	distutils-r1_python_install_all
-}
diff --git a/dev-python/pickleshare/metadata.xml b/dev-python/pickleshare/metadata.xml
deleted file mode 100644
index 4898921bd..000000000
--- a/dev-python/pickleshare/metadata.xml
+++ /dev/null
@@ -1,20 +0,0 @@
-<?xml version="1.0" encoding="UTF-8"?>
-<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
-<pkgmetadata>
-	<maintainer type="project">
-		<email>sci@gentoo.org</email>
-		<name>Gentoo Science Project</name>
-	</maintainer>
-	<longdescription>
-Like shelve, a PickleShareDB object acts like a normal dictionary.
-Unlike shelve, many processes can access the database
-simultaneously. Changing a value in database is immediately visible
-to other processes accessing the same database.
-Concurrency is possible because the values are stored in separate
-files. Hence the "database" is a directory where all files are
-governed by PickleShare.
-</longdescription>
-	<upstream>
-		<remote-id type="github">pickleshare/pickleshare</remote-id>
-	</upstream>
-</pkgmetadata>
diff --git a/dev-python/pickleshare/pickleshare-9999.ebuild b/dev-python/pickleshare/pickleshare-9999.ebuild
deleted file mode 100644
index 95306c174..000000000
--- a/dev-python/pickleshare/pickleshare-9999.ebuild
+++ /dev/null
@@ -1,29 +0,0 @@
-# Copyright 1999-2017 Gentoo Foundation
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=6
-
-PYTHON_COMPAT=( python2_7 python3_{4,5} )
-
-inherit distutils-r1 git-r3
-
-DESCRIPTION="A small 'shelve' like datastore with concurrency support"
-HOMEPAGE="https://github.com/pickleshare/pickleshare"
-EGIT_REPO_URI="https://github.com/${PN}/${PN}.git git://github.com/${PN}/${PN}.git"
-
-LICENSE="MIT"
-SLOT="0"
-KEYWORDS=""
-IUSE="test"
-
-RDEPEND="
-	dev-python/path-py[${PYTHON_USEDEP}]"
-DEPEND="${RDEPEND}
-	test? ( dev-python/pytest[${PYTHON_USEDEP}] )"
-
-python_test() {
-	distutils_install_for_testing
-	cd "${TEST_DIR}"/lib || die
-	cp "${S}"/test_pickleshare.py "${TEST_DIR}"/lib/ || die
-	py.test || die
-}
diff --git a/dev-python/plac/Manifest b/dev-python/plac/Manifest
new file mode 100644
index 000000000..f50e462dc
--- /dev/null
+++ b/dev-python/plac/Manifest
@@ -0,0 +1 @@
+DIST plac-1.4.2.tar.gz 37595 BLAKE2B 5205e9d8a5a775eb2e23ea7ad30e576417a8ba944cb196ccb7a16b514b6c4902856a7191b1bbf71ab0176910b5d8dc163ab36fe3fb0c5bb5765c02d16ae347b1 SHA512 c8c320cabda42f33071d7675b64befab8344bde746d0befe661a9bb26f658559435d2895dad0a27dc1d7c2dc59f07a359b529880e115d900b4fca8f245186742
diff --git a/dev-python/plac/metadata.xml b/dev-python/plac/metadata.xml
new file mode 100644
index 000000000..98f0f918b
--- /dev/null
+++ b/dev-python/plac/metadata.xml
@@ -0,0 +1,16 @@
+<?xml version='1.0' encoding='UTF-8'?>
+<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
+<pkgmetadata>
+	<maintainer type="person">
+		<email>mschu.dev@gmail.com</email>
+		<name>Michael Schubert</name>
+	</maintainer>
+	<maintainer type="project">
+		<email>sci@gentoo.org</email>
+		<name>Gentoo Science Project</name>
+	</maintainer>
+	<upstream>
+		<remote-id type="github">ialbert/plac</remote-id>
+		<remote-id type="pypi">plac</remote-id>
+	</upstream>
+</pkgmetadata>
diff --git a/dev-python/plac/plac-1.4.2.ebuild b/dev-python/plac/plac-1.4.2.ebuild
new file mode 100644
index 000000000..50b269f42
--- /dev/null
+++ b/dev-python/plac/plac-1.4.2.ebuild
@@ -0,0 +1,23 @@
+# Copyright 1999-2018 Gentoo Foundation
+# Distributed under the terms of the GNU General Public License v2
+
+EAPI=8
+
+DISTUTILS_USE_PEP517=setuptools
+PYTHON_COMPAT=( pypy3 python3_{10..12} )
+
+inherit pypi distutils-r1
+
+DESCRIPTION="Parsing the Command Line the Easy Way"
+HOMEPAGE="https://pypi.org/project/plac/"
+
+LICENSE="BSD"
+SLOT="0"
+KEYWORDS="~amd64 ~x86 ~amd64-linux ~x86-linux"
+
+EPYTEST_DESELECT=(
+	# Missing index.rst
+	doc/test_plac.py::test_doctest
+)
+
+distutils_enable_tests pytest
diff --git a/dev-python/prettyplotlib/Manifest b/dev-python/prettyplotlib/Manifest
deleted file mode 100644
index 02f17d730..000000000
--- a/dev-python/prettyplotlib/Manifest
+++ /dev/null
@@ -1 +0,0 @@
-DIST prettyplotlib-0.1.7.tar.gz 697060 BLAKE2B 3d4b8bf61d872ffb70f629019606133ac43f513ffcfc9a78ac4e1cff9853d5da11e977ebd0e95633f9d74d7b06168f4d654cdedd179765bb81f5f69342ef754e SHA512 f1bd2018a7498dd27d8decf12c25ecaae238379a99b27b4c4a87629286ea5e6548a918832ebadab7eb8d46d53a52c75dd96596bfd1af6b47a9adc85be2988a5e
diff --git a/dev-python/prettyplotlib/metadata.xml b/dev-python/prettyplotlib/metadata.xml
deleted file mode 100644
index 6f1686f39..000000000
--- a/dev-python/prettyplotlib/metadata.xml
+++ /dev/null
@@ -1,15 +0,0 @@
-<?xml version="1.0" encoding="UTF-8"?>
-<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
-<pkgmetadata>
-	<maintainer type="person">
-		<email>marbre@linux.sungazer.de</email>
-		<name>Marius Brehler</name>
-	</maintainer>
-	<longdescription>
-Python matplotlib-enhancer library which painlessly creates
-beautiful default matplotlib plots.
-</longdescription>
-	<upstream>
-		<remote-id type="pypi">prettyplotlib</remote-id>
-	</upstream>
-</pkgmetadata>
diff --git a/dev-python/prettyplotlib/prettyplotlib-0.1.7.ebuild b/dev-python/prettyplotlib/prettyplotlib-0.1.7.ebuild
deleted file mode 100644
index dad43b864..000000000
--- a/dev-python/prettyplotlib/prettyplotlib-0.1.7.ebuild
+++ /dev/null
@@ -1,29 +0,0 @@
-# Copyright 1999-2015 Gentoo Foundation
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=5
-PYTHON_COMPAT=( python{2_7,3_4} )
-
-inherit distutils-r1
-
-DESCRIPTION="Painlessly create beautiful matplotlib plots"
-HOMEPAGE="http://blog.olgabotvinnik.com/prettyplotlib/"
-
-if [ ${PV} == "9999" ] ; then
-	inherit git-r3
-	EGIT_REPO_URI="https://github.com/olgabot/${PN}.git git://github.com/olgabot/${PN}.git"
-else
-	SRC_URI="mirror://pypi/${PN:0:1}/${PN}/${P}.tar.gz"
-	KEYWORDS="~amd64"
-fi
-
-LICENSE="MIT"
-SLOT="0"
-
-RDEPEND="
-	sci-libs/scipy[${PYTHON_USEDEP}]
-	>=dev-python/matplotlib-1.4.0[${PYTHON_USEDEP}]
-	dev-python/brewer2mpl[${PYTHON_USEDEP}]
-	dev-python/six[${PYTHON_USEDEP}]
-	dev-python/numpy[${PYTHON_USEDEP}]"
-DEPEND="${RDEPEND}"
diff --git a/dev-python/prettyplotlib/prettyplotlib-9999.ebuild b/dev-python/prettyplotlib/prettyplotlib-9999.ebuild
deleted file mode 100644
index dad43b864..000000000
--- a/dev-python/prettyplotlib/prettyplotlib-9999.ebuild
+++ /dev/null
@@ -1,29 +0,0 @@
-# Copyright 1999-2015 Gentoo Foundation
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=5
-PYTHON_COMPAT=( python{2_7,3_4} )
-
-inherit distutils-r1
-
-DESCRIPTION="Painlessly create beautiful matplotlib plots"
-HOMEPAGE="http://blog.olgabotvinnik.com/prettyplotlib/"
-
-if [ ${PV} == "9999" ] ; then
-	inherit git-r3
-	EGIT_REPO_URI="https://github.com/olgabot/${PN}.git git://github.com/olgabot/${PN}.git"
-else
-	SRC_URI="mirror://pypi/${PN:0:1}/${PN}/${P}.tar.gz"
-	KEYWORDS="~amd64"
-fi
-
-LICENSE="MIT"
-SLOT="0"
-
-RDEPEND="
-	sci-libs/scipy[${PYTHON_USEDEP}]
-	>=dev-python/matplotlib-1.4.0[${PYTHON_USEDEP}]
-	dev-python/brewer2mpl[${PYTHON_USEDEP}]
-	dev-python/six[${PYTHON_USEDEP}]
-	dev-python/numpy[${PYTHON_USEDEP}]"
-DEPEND="${RDEPEND}"
diff --git a/dev-python/probeinterface/Manifest b/dev-python/probeinterface/Manifest
new file mode 100644
index 000000000..189bbfcaf
--- /dev/null
+++ b/dev-python/probeinterface/Manifest
@@ -0,0 +1,3 @@
+DIST probeinterface-0.2.14.gh.tar.gz 210232 BLAKE2B 5a2c4fb5bc0f1315777a70b4292a30b135022e3a70608584070088c5ff42b0e1474714472a306196b390e103b45eea70cb89e01cc5dca90b0c31ac4f44810c24 SHA512 e0f5cf5b6560f8c4e578cab708308c36ecf81446c0db684b520e1436e864f2f4e0dce0015461c7cfcba19a0c1c54345b2d55b972de5f4338b02b90731cff52c2
+DIST probeinterface-0.2.16.gh.tar.gz 302386 BLAKE2B e2124774f2f50779f1dc67b682085d87691c935909ab81591f005abd756c0925837b97e97bf651e2a84e2276f57bf6fd1df6de6289431b16227dc9caa6cea51c SHA512 7c38534dbcab837df1289074db054e31c0768bceefafeb6d70051f88a6ac289d664d77cd6c456f40e7c52a7b60a09e80a4a4fe5e8f491121157b0bbb4d5c1f84
+DIST probeinterface-0.2.20.gh.tar.gz 1930434 BLAKE2B 0087f82f8cea3e1eb225ba188487eb3862de8444cadb0cf76ebba1046f194eb1f369bab7b3ff35eb6b99c054409b902c1907037d42aa84d0d4253a47fa6009ce SHA512 16cee1845d4cd40f1bfdea654fff99ea5949fbd8606ffc038ea0ca27d6a4f3faa65e2dd448bcda1066c0d2984ce7e3995a0ead028ef57ae59743c34c6c5a4c39
diff --git a/dev-python/probeinterface/metadata.xml b/dev-python/probeinterface/metadata.xml
new file mode 100644
index 000000000..58f800ce0
--- /dev/null
+++ b/dev-python/probeinterface/metadata.xml
@@ -0,0 +1,15 @@
+<?xml version='1.0' encoding='UTF-8'?>
+<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
+<pkgmetadata>
+	<maintainer type="person">
+		<email>gentoo@chymera.eu</email>
+		<name>Horea Christian</name>
+	</maintainer>
+	<maintainer type="project">
+		<email>sci@gentoo.org</email>
+		<name>Gentoo Science Project</name>
+	</maintainer>
+	<upstream>
+		<remote-id type="github">SpikeInterface/probeinterface</remote-id>
+	</upstream>
+</pkgmetadata>
diff --git a/dev-python/probeinterface/probeinterface-0.2.14.ebuild b/dev-python/probeinterface/probeinterface-0.2.14.ebuild
new file mode 100644
index 000000000..75dd43bd4
--- /dev/null
+++ b/dev-python/probeinterface/probeinterface-0.2.14.ebuild
@@ -0,0 +1,37 @@
+# Copyright 2021-2023 Gentoo Authors
+# Distributed under the terms of the GNU General Public License v2
+
+EAPI=8
+
+DISTUTILS_USE_PEP517=setuptools
+PYTHON_COMPAT=( python3_{10..11} )
+inherit distutils-r1
+
+DESCRIPTION="Python package to handle probe layout, geometry and wiring to device"
+HOMEPAGE="https://github.com/SpikeInterface/probeinterface"
+SRC_URI="https://github.com/SpikeInterface/probeinterface/archive/refs/tags/${PV}.tar.gz -> ${P}.gh.tar.gz"
+# upstream doesn't pus test dir to pypi, https://github.com/SpikeInterface/probeinterface/issues/145
+#SRC_URI="mirror://pypi/${PN:0:1}/${PN}/${P}.tar.gz"
+
+LICENSE="MIT"
+SLOT="0"
+KEYWORDS="~amd64 ~x86"
+
+RDEPEND="dev-python/numpy[${PYTHON_USEDEP}]"
+BDEPEND="
+	test? (
+		dev-python/matplotlib[${PYTHON_USEDEP}]
+		dev-python/pandas[${PYTHON_USEDEP}]
+		dev-python/scipy[${PYTHON_USEDEP}]
+	)
+"
+
+EPYTEST_DESELECT=(
+	# Requires network access:
+	# https://github.com/SpikeInterface/probeinterface/issues/70
+	tests/test_library.py::test_download_probeinterface_file
+	tests/test_library.py::test_get_from_cache
+	tests/test_library.py::test_get_probe
+	tests/test_wiring.py::test_wire_probe
+)
+distutils_enable_tests pytest
diff --git a/dev-python/probeinterface/probeinterface-0.2.16.ebuild b/dev-python/probeinterface/probeinterface-0.2.16.ebuild
new file mode 100644
index 000000000..75dd43bd4
--- /dev/null
+++ b/dev-python/probeinterface/probeinterface-0.2.16.ebuild
@@ -0,0 +1,37 @@
+# Copyright 2021-2023 Gentoo Authors
+# Distributed under the terms of the GNU General Public License v2
+
+EAPI=8
+
+DISTUTILS_USE_PEP517=setuptools
+PYTHON_COMPAT=( python3_{10..11} )
+inherit distutils-r1
+
+DESCRIPTION="Python package to handle probe layout, geometry and wiring to device"
+HOMEPAGE="https://github.com/SpikeInterface/probeinterface"
+SRC_URI="https://github.com/SpikeInterface/probeinterface/archive/refs/tags/${PV}.tar.gz -> ${P}.gh.tar.gz"
+# upstream doesn't pus test dir to pypi, https://github.com/SpikeInterface/probeinterface/issues/145
+#SRC_URI="mirror://pypi/${PN:0:1}/${PN}/${P}.tar.gz"
+
+LICENSE="MIT"
+SLOT="0"
+KEYWORDS="~amd64 ~x86"
+
+RDEPEND="dev-python/numpy[${PYTHON_USEDEP}]"
+BDEPEND="
+	test? (
+		dev-python/matplotlib[${PYTHON_USEDEP}]
+		dev-python/pandas[${PYTHON_USEDEP}]
+		dev-python/scipy[${PYTHON_USEDEP}]
+	)
+"
+
+EPYTEST_DESELECT=(
+	# Requires network access:
+	# https://github.com/SpikeInterface/probeinterface/issues/70
+	tests/test_library.py::test_download_probeinterface_file
+	tests/test_library.py::test_get_from_cache
+	tests/test_library.py::test_get_probe
+	tests/test_wiring.py::test_wire_probe
+)
+distutils_enable_tests pytest
diff --git a/dev-python/probeinterface/probeinterface-0.2.20.ebuild b/dev-python/probeinterface/probeinterface-0.2.20.ebuild
new file mode 100644
index 000000000..75dd43bd4
--- /dev/null
+++ b/dev-python/probeinterface/probeinterface-0.2.20.ebuild
@@ -0,0 +1,37 @@
+# Copyright 2021-2023 Gentoo Authors
+# Distributed under the terms of the GNU General Public License v2
+
+EAPI=8
+
+DISTUTILS_USE_PEP517=setuptools
+PYTHON_COMPAT=( python3_{10..11} )
+inherit distutils-r1
+
+DESCRIPTION="Python package to handle probe layout, geometry and wiring to device"
+HOMEPAGE="https://github.com/SpikeInterface/probeinterface"
+SRC_URI="https://github.com/SpikeInterface/probeinterface/archive/refs/tags/${PV}.tar.gz -> ${P}.gh.tar.gz"
+# upstream doesn't pus test dir to pypi, https://github.com/SpikeInterface/probeinterface/issues/145
+#SRC_URI="mirror://pypi/${PN:0:1}/${PN}/${P}.tar.gz"
+
+LICENSE="MIT"
+SLOT="0"
+KEYWORDS="~amd64 ~x86"
+
+RDEPEND="dev-python/numpy[${PYTHON_USEDEP}]"
+BDEPEND="
+	test? (
+		dev-python/matplotlib[${PYTHON_USEDEP}]
+		dev-python/pandas[${PYTHON_USEDEP}]
+		dev-python/scipy[${PYTHON_USEDEP}]
+	)
+"
+
+EPYTEST_DESELECT=(
+	# Requires network access:
+	# https://github.com/SpikeInterface/probeinterface/issues/70
+	tests/test_library.py::test_download_probeinterface_file
+	tests/test_library.py::test_get_from_cache
+	tests/test_library.py::test_get_probe
+	tests/test_wiring.py::test_wire_probe
+)
+distutils_enable_tests pytest
diff --git a/dev-python/prov/Manifest b/dev-python/prov/Manifest
index 48e1571ca..afbcb1608 100644
--- a/dev-python/prov/Manifest
+++ b/dev-python/prov/Manifest
@@ -1 +1 @@
-DIST prov-1.4.0.tar.gz 92617 BLAKE2B 7fd28b3e726e083f878f7d32d62e14a40d2b3ebdafc7eaad5aad91d14136622054a433dda4af1ea3bdd6c56811e1862897bee14adf5b95be7d15088b4c25d39c SHA512 fa253668ae63f1178d3f766cebc5273d06d11c3020a8a30d0c7e03d06a24260f9146f396cad267db01998ab921230a52356cff85a40b7aacdf4742ff5515e1bd
+DIST prov-2.0.0.tar.gz 131878 BLAKE2B 65f14ad3a7dc6e10d03b0d778be02d3a3a7e4cae7b8aedf54117446eefe51546fb30e9ca602b2d5780fab8abde4ed1d56ed7385815db64a7879623a481b050be SHA512 6d05c88855f23d5dc22b0eccce0af935c0ad3d227b7a257ff205ad8566ed9607f614c13427ac8dd922e79bd477ca125b9d3f9492f5f65ae55ab8e8f3b9b97307
diff --git a/dev-python/prov/metadata.xml b/dev-python/prov/metadata.xml
index d73a01129..d1559163d 100644
--- a/dev-python/prov/metadata.xml
+++ b/dev-python/prov/metadata.xml
@@ -1,18 +1,14 @@
 <?xml version="1.0" encoding="UTF-8"?>
-<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
+<!DOCTYPE pkgmetadata SYSTEM "https://www.gentoo.org/dtd/metadata.dtd">
 <pkgmetadata>
-	<maintainer type="person">
-		<email>horea.christ@gmail.com</email>
-		<name>Horea Christian</name>
-	</maintainer>
-	<maintainer type="project">
-		<email>sci@gentoo.org</email>
-		<name>Gentoo Science Project</name>
-	</maintainer>
+	<!-- maintainer-needed -->
 	<longdescription lang="en">
-A library for W3C Provenance Data Model supporting PROV-JSON and PROV-XML import/export
-</longdescription>
+		A library for W3C Provenance Data Model supporting PROV-O
+		(RDF), PROV-XML, PROV-JSON import/export Interface to
+		Graphviz’s Dot language.
+	</longdescription>
 	<upstream>
 		<remote-id type="pypi">prov</remote-id>
+		<remote-id type="github">trungdong/prov</remote-id>
 	</upstream>
 </pkgmetadata>
diff --git a/dev-python/prov/prov-1.4.0.ebuild b/dev-python/prov/prov-1.4.0.ebuild
deleted file mode 100644
index 2fff38574..000000000
--- a/dev-python/prov/prov-1.4.0.ebuild
+++ /dev/null
@@ -1,31 +0,0 @@
-# Copyright 1999-2016 Gentoo Foundation
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=6
-
-PYTHON_COMPAT=( python{2_7,3_4,3_5} )
-
-inherit distutils-r1
-
-DESCRIPTION="W3C provenance data dodel library"
-HOMEPAGE="https://pypi.python.org/pypi/prov"
-SRC_URI="mirror://pypi/p/${PN}/${P}.tar.gz"
-
-LICENSE="MIT"
-SLOT="0"
-KEYWORDS="~amd64 ~x86"
-IUSE="test"
-
-DEPEND="
-	test? ( dev-python/pydotplus[${PYTHON_USEDEP}] )
-	dev-python/setuptools[${PYTHON_USEDEP}]
-	"
-RDEPEND="dev-python/python-dateutil[${PYTHON_USEDEP}]
-	dev-python/lxml[${PYTHON_USEDEP}]
-	>=dev-python/networkx-1.10[${PYTHON_USEDEP}]
-	>=dev-python/six-1.10[${PYTHON_USEDEP}]
-	"
-
-python_test() {
-	${EPYTHON} -m unittest discover || die
-}
diff --git a/dev-python/prov/prov-2.0.0.ebuild b/dev-python/prov/prov-2.0.0.ebuild
new file mode 100644
index 000000000..a87b15c6f
--- /dev/null
+++ b/dev-python/prov/prov-2.0.0.ebuild
@@ -0,0 +1,43 @@
+# Copyright 1999-2023 Gentoo Authors
+# Distributed under the terms of the GNU General Public License v2
+
+EAPI=8
+
+DISTUTILS_USE_PEP517=setuptools
+PYTHON_COMPAT=( python3_{9..12} )
+inherit distutils-r1 pypi
+
+DESCRIPTION="W3C provenance data dodel library"
+HOMEPAGE="https://pypi.org/project/prov/"
+
+LICENSE="MIT"
+SLOT="0"
+KEYWORDS="~amd64 ~x86"
+
+RDEPEND="
+	dev-python/pydot[${PYTHON_USEDEP}]
+	dev-python/python-dateutil[${PYTHON_USEDEP}]
+	dev-python/lxml[${PYTHON_USEDEP}]
+	>=dev-python/networkx-1.10[${PYTHON_USEDEP}]
+	dev-python/rdflib[${PYTHON_USEDEP}]
+"
+
+distutils_enable_tests pytest
+
+# Reported upstream:
+# https://github.com/trungdong/prov/issues/156
+EPYTEST_DESELECT=(
+	src/prov/tests/test_model.py::TestAttributesBase
+	src/prov/tests/test_rdf.py::TestStatementsBase
+	src/prov/tests/test_rdf.py::TestAttributesBase2
+	src/prov/tests/test_rdf.py::TestQualifiedNamesBase
+	src/prov/tests/test_rdf.py::TestAttributesBase
+	src/prov/tests/test_model.py::TestStatementsBase
+	src/prov/tests/test_model.py::TestExamplesBase::test_all_examples
+	src/prov/tests/test_model.py::TestQualifiedNamesBase
+	src/prov/tests/test_rdf.py::RoundTripRDFTests::test_namespace_inheritance
+	src/prov/tests/test_rdf.py::RoundTripRDFTests::test_default_namespace_inheritance
+	src/prov/tests/test_rdf.py::TestRDFSerializer::test_json_to_ttl_match
+	src/prov/tests/test_rdf.py::TestJSONExamplesBase::test_all_examples
+	src/prov/tests/test_rdf.py::TestExamplesBase::test_all_examples
+)
diff --git a/dev-python/psubprocess/Manifest b/dev-python/psubprocess/Manifest
deleted file mode 100644
index 8defb267a..000000000
--- a/dev-python/psubprocess/Manifest
+++ /dev/null
@@ -1 +0,0 @@
-DIST psubprocess-0.1.2.tar.gz 178830 SHA256 271bc35c98a3a2c8181e8415f87648f0a1d95113fba010f4f19c8efbf6e2c767 SHA512 01ccf58ed8130124a192155775fdfa8cfe0896f364c1325f78a15e7bce0f309a183ef2577c45e295d797e56cde76fdec926ebe69100183198d0769de78eb09a2 WHIRLPOOL e9d9f9afb7154123c76916bfb55d861f2b0aeb5fc98da5e4210d2f7f3a475aa553c86b8ddd3dacf5b6cd88594b65b1c05ce4854f5778fe88d22d981ab75b7b62
diff --git a/dev-python/psubprocess/metadata.xml b/dev-python/psubprocess/metadata.xml
deleted file mode 100644
index 138cb7705..000000000
--- a/dev-python/psubprocess/metadata.xml
+++ /dev/null
@@ -1,12 +0,0 @@
-<?xml version="1.0" encoding="UTF-8"?>
-<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
-<pkgmetadata>
-	<maintainer type="person">
-		<email>mmokrejs@fold.natur.cuni.cz</email>
-		<name>Martin Mokrejs</name>
-	</maintainer>
-	<maintainer type="project">
-		<email>sci-biology@gentoo.org</email>
-		<name>Gentoo Biology Project</name>
-	</maintainer>
-</pkgmetadata>
diff --git a/dev-python/psubprocess/psubprocess-0.1.2.ebuild b/dev-python/psubprocess/psubprocess-0.1.2.ebuild
deleted file mode 100644
index f95a93f0b..000000000
--- a/dev-python/psubprocess/psubprocess-0.1.2.ebuild
+++ /dev/null
@@ -1,20 +0,0 @@
-# Copyright 1999-2014 Gentoo Foundation
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=5
-
-PYTHON_COMPAT=( python2_7 )
-
-inherit distutils-r1
-
-DESCRIPTION="Execute tasks in parallel"
-HOMEPAGE="http://bioinf.comav.upv.es/psubprocess"
-SRC_URI="http://bioinf.comav.upv.es/_downloads/"${P}".tar.gz"
-
-LICENSE="GPL-3"
-SLOT="0"
-KEYWORDS="~amd64"
-IUSE=""
-
-DEPEND=""
-RDEPEND="${DEPEND}"
diff --git a/dev-python/ptyprocess/metadata.xml b/dev-python/ptyprocess/metadata.xml
deleted file mode 100644
index 33094cdb7..000000000
--- a/dev-python/ptyprocess/metadata.xml
+++ /dev/null
@@ -1,11 +0,0 @@
-<?xml version="1.0" encoding="UTF-8"?>
-<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
-<pkgmetadata>
-	<maintainer type="project">
-		<email>sci@gentoo.org</email>
-		<name>Gentoo Science Project</name>
-	</maintainer>
-	<upstream>
-		<remote-id type="github">pexpect/ptyprocess</remote-id>
-	</upstream>
-</pkgmetadata>
diff --git a/dev-python/ptyprocess/ptyprocess-9999.ebuild b/dev-python/ptyprocess/ptyprocess-9999.ebuild
deleted file mode 100644
index 73da68ab7..000000000
--- a/dev-python/ptyprocess/ptyprocess-9999.ebuild
+++ /dev/null
@@ -1,24 +0,0 @@
-# Copyright 1999-2017 Gentoo Foundation
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=5
-
-PYTHON_COMPAT=( python2_7 python3_{4,5} )
-
-inherit distutils-r1 git-r3
-
-DESCRIPTION="Run a subprocess in a pseudo terminal"
-HOMEPAGE="https://github.com/pexpect/ptyprocess"
-SRC_URI=""
-EGIT_REPO_URI="https://github.com/pexpect/${PN}.git git://github.com/pexpect/${PN}.git"
-
-LICENSE="ISC"
-SLOT="0"
-KEYWORDS=""
-IUSE="test"
-
-DEPEND="test? ( dev-python/pytest[${PYTHON_USEDEP}] )"
-
-python_test() {
-	py.test --verbose --verbose || die
-}
diff --git a/dev-python/py2bit/Manifest b/dev-python/py2bit/Manifest
index d2694e454..afd79913c 100644
--- a/dev-python/py2bit/Manifest
+++ b/dev-python/py2bit/Manifest
@@ -1 +1,2 @@
-DIST py2bit-0.2.1.tar.gz 15206 BLAKE2B 75d8c7bd1bfb7224679538196d678a48f610c4de062df6caf78eb9100d8f6c5e68d7d233e3fd801d7128b52a06b36c18a573a6fcd2676a882cef11fe9035203e SHA512 b6a6a52488c432622df757e794b15ff8348e019b1547f750c9f66217fbe07758b6577261a28d8d75f81f63b2edf6b6b5d93b92ece60a64e0b5985407ea42e2fc
+DIST py2bit-0.3.0.tar.gz 16059 BLAKE2B b66621b91db8c0370933d1531c25e3e9d2cf34cc453e085f5acf92175f16bc4a87368d5b97f4ad1f6b0aeb715ac91e02f752f27d660e733cbcf9788f7fb9ff0b SHA512 914ee4490605a005c5c83e914e5d469dcb860a76cf52dd2337086954d9a37f21addca7a581eb8ff612b77f7969334057de4ab5d5ce2c6e15fb88e56abd36e193
+DIST py2bit-0.3.1.tar.gz 16771 BLAKE2B 044f6c638bc001694a5ee1c0924bebfeccd26616dbeb7f7a692df71dde6937851227d8a4263c9f0c4e44a34d53900340bdf95818aa2c9c699d26b36a75e64158 SHA512 e9cb16e6f617f5f9c4a324abc949562da8aa0b4792e7011148103462ec49f3f38ab29a2c1821a374ec99726c292de2888de506966510a10211ee24295e9f775c
diff --git a/dev-python/py2bit/py2bit-0.2.1.ebuild b/dev-python/py2bit/py2bit-0.2.1.ebuild
deleted file mode 100644
index d33e9798f..000000000
--- a/dev-python/py2bit/py2bit-0.2.1.ebuild
+++ /dev/null
@@ -1,20 +0,0 @@
-# Copyright 1999-2017 Gentoo Foundation
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=6
-
-PYTHON_COMPAT=( python2_7 python3_5 )
-
-inherit distutils-r1
-
-DESCRIPTION="Python library for accessing 2bit files"
-HOMEPAGE="https://github.com/dpryan79/py2bit"
-SRC_URI="https://github.com/dpryan79/py2bit/archive/0.2.1.tar.gz -> ${P}.tar.gz"
-
-LICENSE="MIT"
-SLOT="0"
-KEYWORDS="~amd64 ~x86"
-IUSE=""
-
-DEPEND="sci-libs/lib2bit"
-RDEPEND="${DEPEND}"
diff --git a/dev-python/py2bit/py2bit-0.3.0.ebuild b/dev-python/py2bit/py2bit-0.3.0.ebuild
new file mode 100644
index 000000000..4b1c29658
--- /dev/null
+++ b/dev-python/py2bit/py2bit-0.3.0.ebuild
@@ -0,0 +1,32 @@
+# Copyright 1999-2023 Gentoo Authors
+# Distributed under the terms of the GNU General Public License v2
+
+EAPI=8
+
+PYTHON_COMPAT=( python3_{10..11} )
+DISTUTILS_USE_PEP517=setuptools
+
+inherit distutils-r1
+
+DESCRIPTION="Python library for accessing 2bit files"
+HOMEPAGE="https://github.com/dpryan79/py2bit"
+
+if [[ ${PV} == 9999 ]] ; then
+	inherit git-r3
+	EGIT_REPO_URI="https://github.com/dpryan79/py2bit"
+else
+	SRC_URI="https://github.com/dpryan79/py2bit/archive/${PV}.tar.gz -> ${P}.tar.gz"
+	KEYWORDS="~amd64 ~x86"
+fi
+
+LICENSE="MIT"
+SLOT="0"
+
+DEPEND="sci-libs/lib2bit"
+RDEPEND="${DEPEND}"
+
+distutils_enable_tests pytest
+
+python_test() {
+	epytest "py2bitTest/test.py"
+}
diff --git a/dev-python/py2bit/py2bit-0.3.1.ebuild b/dev-python/py2bit/py2bit-0.3.1.ebuild
new file mode 100644
index 000000000..4b1c29658
--- /dev/null
+++ b/dev-python/py2bit/py2bit-0.3.1.ebuild
@@ -0,0 +1,32 @@
+# Copyright 1999-2023 Gentoo Authors
+# Distributed under the terms of the GNU General Public License v2
+
+EAPI=8
+
+PYTHON_COMPAT=( python3_{10..11} )
+DISTUTILS_USE_PEP517=setuptools
+
+inherit distutils-r1
+
+DESCRIPTION="Python library for accessing 2bit files"
+HOMEPAGE="https://github.com/dpryan79/py2bit"
+
+if [[ ${PV} == 9999 ]] ; then
+	inherit git-r3
+	EGIT_REPO_URI="https://github.com/dpryan79/py2bit"
+else
+	SRC_URI="https://github.com/dpryan79/py2bit/archive/${PV}.tar.gz -> ${P}.tar.gz"
+	KEYWORDS="~amd64 ~x86"
+fi
+
+LICENSE="MIT"
+SLOT="0"
+
+DEPEND="sci-libs/lib2bit"
+RDEPEND="${DEPEND}"
+
+distutils_enable_tests pytest
+
+python_test() {
+	epytest "py2bitTest/test.py"
+}
diff --git a/dev-python/py2bit/py2bit-9999.ebuild b/dev-python/py2bit/py2bit-9999.ebuild
new file mode 100644
index 000000000..4b1c29658
--- /dev/null
+++ b/dev-python/py2bit/py2bit-9999.ebuild
@@ -0,0 +1,32 @@
+# Copyright 1999-2023 Gentoo Authors
+# Distributed under the terms of the GNU General Public License v2
+
+EAPI=8
+
+PYTHON_COMPAT=( python3_{10..11} )
+DISTUTILS_USE_PEP517=setuptools
+
+inherit distutils-r1
+
+DESCRIPTION="Python library for accessing 2bit files"
+HOMEPAGE="https://github.com/dpryan79/py2bit"
+
+if [[ ${PV} == 9999 ]] ; then
+	inherit git-r3
+	EGIT_REPO_URI="https://github.com/dpryan79/py2bit"
+else
+	SRC_URI="https://github.com/dpryan79/py2bit/archive/${PV}.tar.gz -> ${P}.tar.gz"
+	KEYWORDS="~amd64 ~x86"
+fi
+
+LICENSE="MIT"
+SLOT="0"
+
+DEPEND="sci-libs/lib2bit"
+RDEPEND="${DEPEND}"
+
+distutils_enable_tests pytest
+
+python_test() {
+	epytest "py2bitTest/test.py"
+}
diff --git a/dev-python/pyBigWig/Manifest b/dev-python/pyBigWig/Manifest
index 88325560d..b27a43a9b 100644
--- a/dev-python/pyBigWig/Manifest
+++ b/dev-python/pyBigWig/Manifest
@@ -1 +1,2 @@
-DIST pyBigWig-0.3.4.tar.gz 59804 BLAKE2B 305f63925428332095341d69ed77c50b337bab9dcbc7c15ee68112b0d1ecba6d1b051a08fee7af16fe470dc8bdf1417fac2213ad50f1a6c0ab843dcc4c5f8e42 SHA512 9d7c174aa9d8242a5fb88a9a696201c7b5637ac66ae1aef730a5c4cc695f150094d830e0d575614f3f4a5cdf177bbc37a9fe06ced7ccc866906420288e24f319
+DIST pyBigWig-0.3.17.tar.gz 65490 BLAKE2B 5ae3ad5792357ae36082022aa34548fb7ad105909eccc27305064f8f948714f462e1d239c3af7f9b75b84f5658bcb03231d7d1d3b0ebc8025c96d2e7835f1bfb SHA512 b52fec3a85984708660dd454f5569900a5cce7804d02e719bddbdc7ed2f9f4ab1131e55b0a01ae977b18bb0bbd079e13ec887d5df108d8abfebdd04ad56e503f
+DIST pyBigWig-0.3.18.tar.gz 66478 BLAKE2B 0d2e20bed5f59fb8c79026f453c4d5c3e4f9b663e96614b3ef8cbb939357c8895edfa92184da018efdd40e14bbf357f13cc32f898d9cf89419382e7be89b01c8 SHA512 e782f059a8c47043498b2c4b1c0b63f3a1863d03f641c469995536bded220714c61fe0a2f1dbe5841152fe54d0d43b544e14ec4999447d4d808e01b452fa5e88
diff --git a/dev-python/pyBigWig/pyBigWig-0.3.17.ebuild b/dev-python/pyBigWig/pyBigWig-0.3.17.ebuild
new file mode 100644
index 000000000..acaca2306
--- /dev/null
+++ b/dev-python/pyBigWig/pyBigWig-0.3.17.ebuild
@@ -0,0 +1,25 @@
+# Copyright 1999-2023 Gentoo Authors
+# Distributed under the terms of the GNU General Public License v2
+
+EAPI=8
+
+PYTHON_COMPAT=( python3_{10..11} )
+DISTUTILS_USE_PEP517=setuptools
+inherit distutils-r1
+
+DESCRIPTION="quick access to and creation of bigWig files"
+HOMEPAGE="https://github.com/dpryan79/pyBigWig"
+
+if [[ ${PV} == 9999 ]] ; then
+	inherit git-r3
+	EGIT_REPO_URI="https://github.com/dpryan79/pyBigWig"
+else
+	SRC_URI="https://github.com/dpryan79/pyBigWig/archive/${PV}.tar.gz -> ${P}.tar.gz"
+	KEYWORDS="~amd64 ~x86"
+fi
+
+LICENSE="MIT"
+SLOT="0"
+
+DEPEND="sci-biology/libBigWig"
+RDEPEND="${DEPEND}"
diff --git a/dev-python/pyBigWig/pyBigWig-0.3.18.ebuild b/dev-python/pyBigWig/pyBigWig-0.3.18.ebuild
new file mode 100644
index 000000000..acaca2306
--- /dev/null
+++ b/dev-python/pyBigWig/pyBigWig-0.3.18.ebuild
@@ -0,0 +1,25 @@
+# Copyright 1999-2023 Gentoo Authors
+# Distributed under the terms of the GNU General Public License v2
+
+EAPI=8
+
+PYTHON_COMPAT=( python3_{10..11} )
+DISTUTILS_USE_PEP517=setuptools
+inherit distutils-r1
+
+DESCRIPTION="quick access to and creation of bigWig files"
+HOMEPAGE="https://github.com/dpryan79/pyBigWig"
+
+if [[ ${PV} == 9999 ]] ; then
+	inherit git-r3
+	EGIT_REPO_URI="https://github.com/dpryan79/pyBigWig"
+else
+	SRC_URI="https://github.com/dpryan79/pyBigWig/archive/${PV}.tar.gz -> ${P}.tar.gz"
+	KEYWORDS="~amd64 ~x86"
+fi
+
+LICENSE="MIT"
+SLOT="0"
+
+DEPEND="sci-biology/libBigWig"
+RDEPEND="${DEPEND}"
diff --git a/dev-python/pyBigWig/pyBigWig-0.3.4.ebuild b/dev-python/pyBigWig/pyBigWig-0.3.4.ebuild
deleted file mode 100644
index ba8e24b6a..000000000
--- a/dev-python/pyBigWig/pyBigWig-0.3.4.ebuild
+++ /dev/null
@@ -1,22 +0,0 @@
-# Copyright 1999-2017 Gentoo Foundation
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=6
-
-PYTHON_COMPAT=( python2_7 python 3_5 )
-
-PYTHON_COMPAT=( python2_7 python3_5 )
-
-inherit distutils-r1
-
-DESCRIPTION="Python extension written in C for quick access to and creation of bigWig files"
-HOMEPAGE="https://github.com/dpryan79/pyBigWig"
-SRC_URI="https://github.com/dpryan79/pyBigWig/archive/0.3.4.tar.gz -> ${P}.tar.gz"
-
-LICENSE="MIT"
-SLOT="0"
-KEYWORDS="~amd64 ~x86"
-IUSE=""
-
-DEPEND="sci-biology/libBigWig"
-RDEPEND="${DEPEND}"
diff --git a/dev-python/pyBigWig/pyBigWig-9999.ebuild b/dev-python/pyBigWig/pyBigWig-9999.ebuild
index 169e6198f..acaca2306 100644
--- a/dev-python/pyBigWig/pyBigWig-9999.ebuild
+++ b/dev-python/pyBigWig/pyBigWig-9999.ebuild
@@ -1,20 +1,25 @@
-# Copyright 1999-2017 Gentoo Foundation
+# Copyright 1999-2023 Gentoo Authors
 # Distributed under the terms of the GNU General Public License v2
 
-EAPI=5
+EAPI=8
 
-PYTHON_COMPAT=( python2_7 python3_5 )
+PYTHON_COMPAT=( python3_{10..11} )
+DISTUTILS_USE_PEP517=setuptools
+inherit distutils-r1
 
-inherit git-r3 distutils-r1
-
-DESCRIPTION="Python extension written in C for quick access to and creation of bigWig files"
+DESCRIPTION="quick access to and creation of bigWig files"
 HOMEPAGE="https://github.com/dpryan79/pyBigWig"
-EGIT_REPO_URI="https://github.com/dpryan79/pyBigWig.git"
+
+if [[ ${PV} == 9999 ]] ; then
+	inherit git-r3
+	EGIT_REPO_URI="https://github.com/dpryan79/pyBigWig"
+else
+	SRC_URI="https://github.com/dpryan79/pyBigWig/archive/${PV}.tar.gz -> ${P}.tar.gz"
+	KEYWORDS="~amd64 ~x86"
+fi
 
 LICENSE="MIT"
 SLOT="0"
-KEYWORDS=""
-IUSE=""
 
 DEPEND="sci-biology/libBigWig"
 RDEPEND="${DEPEND}"
diff --git a/dev-python/pyaml-env/Manifest b/dev-python/pyaml-env/Manifest
new file mode 100644
index 000000000..06b54d70e
--- /dev/null
+++ b/dev-python/pyaml-env/Manifest
@@ -0,0 +1 @@
+DIST pyaml_env-1.2.1.tar.gz 12759 BLAKE2B 5a037ccefaaa3c60ce393dae5847777eb43745549a31b763ef2f50feb3a6e216ef793f9501df9e80cb381f78782e54b888ee4b043736dc05bcd01619d839ff86 SHA512 1ef873fa66660e4949dc1064260405244c8b3a2ee4391831a0a52be30e503e99d0b80b087c78db78683e9fe2fc1fd73f2e30c1eacc4c94a1394000d8526c9d68
diff --git a/dev-python/pyaml-env/metadata.xml b/dev-python/pyaml-env/metadata.xml
new file mode 100644
index 000000000..44769bf23
--- /dev/null
+++ b/dev-python/pyaml-env/metadata.xml
@@ -0,0 +1,12 @@
+<?xml version='1.0' encoding='UTF-8'?>
+<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
+<pkgmetadata>
+	<maintainer type="person">
+		<email>mschu.dev@gmail.com</email>
+		<name>Michael Schubert</name>
+	</maintainer>
+	<upstream>
+		<remote-id type="github">mkaranasou/pyaml_env</remote-id>
+		<remote-id type="pypi">pyaml-env</remote-id>
+	</upstream>
+</pkgmetadata>
diff --git a/dev-python/pyaml-env/pyaml-env-1.2.1.ebuild b/dev-python/pyaml-env/pyaml-env-1.2.1.ebuild
new file mode 100644
index 000000000..a5169040a
--- /dev/null
+++ b/dev-python/pyaml-env/pyaml-env-1.2.1.ebuild
@@ -0,0 +1,22 @@
+# Copyright 1999-2023 Gentoo Authors
+# Distributed under the terms of the GNU General Public License v2
+
+EAPI=8
+
+DISTUTILS_USE_PEP517=setuptools
+PYTHON_COMPAT=( python3_{10..12} )
+
+inherit pypi distutils-r1
+
+DESCRIPTION="Parse YAML configuration with environment variables in Python"
+HOMEPAGE="https://pypi.org/project/pyaml-env/"
+
+LICENSE="MIT"
+SLOT="0"
+KEYWORDS="~amd64 ~amd64-linux"
+
+RDEPEND="dev-python/pyyaml[${PYTHON_USEDEP}]"
+
+# tests not included in pypi tarball
+RESTRICT="test"
+#distutils_enable_tests pytest
diff --git a/dev-python/pybind11-stubgen/Manifest b/dev-python/pybind11-stubgen/Manifest
new file mode 100644
index 000000000..7b5f755b5
--- /dev/null
+++ b/dev-python/pybind11-stubgen/Manifest
@@ -0,0 +1 @@
+DIST pybind11-stubgen-0.10.4.tar.gz 12605 BLAKE2B 5cb3e4301a896066ac26a7e6b9af83c77fb16fd5a3e48713a597e981a68e41cd90ddf0e351c177b7385966e8720100ef03b0524dfd381f17c87a2016a6eba808 SHA512 b43795c5fef6eee5198ec7590338f8a2dabbc4a2530de49f50a3b1a410da60188da86f7148a74ff014068c8d9ce5b058695902e236407ab221d640ac9b15903d
diff --git a/dev-python/pybind11-stubgen/metadata.xml b/dev-python/pybind11-stubgen/metadata.xml
new file mode 100644
index 000000000..ad7b36abc
--- /dev/null
+++ b/dev-python/pybind11-stubgen/metadata.xml
@@ -0,0 +1,16 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
+<pkgmetadata>
+    <maintainer type="person">
+        <email>gentoo@aisha.cc</email>
+        <name>Aisha Tammy</name>
+    </maintainer>
+    <maintainer type="project">
+        <email>sci@gentoo.org</email>
+        <name>Gentoo Science Project</name>
+    </maintainer>
+    <upstream>
+        <remote-id type="github">sizmailov/pybind11-stubgen</remote-id>
+        <remote-id type="pypi">pybind11-stubgen</remote-id>
+    </upstream>
+</pkgmetadata>
diff --git a/dev-python/pybind11-stubgen/pybind11-stubgen-0.10.4.ebuild b/dev-python/pybind11-stubgen/pybind11-stubgen-0.10.4.ebuild
new file mode 100644
index 000000000..e1aaab3b6
--- /dev/null
+++ b/dev-python/pybind11-stubgen/pybind11-stubgen-0.10.4.ebuild
@@ -0,0 +1,19 @@
+# Copyright 1999-2022 Gentoo Authors
+# Distributed under the terms of the GNU General Public License v2
+
+EAPI=8
+
+PYTHON_COMPAT=( python3_{10..11} )
+PYPI_NO_NORMALIZE=1
+inherit distutils-r1 pypi
+
+DESCRIPTION="PEP 561 type stubs generator for pybind11 modules"
+HOMEPAGE="https://github.com/sizmailov/pybind11-stubgen"
+
+LICENSE="BSD"
+SLOT="0"
+KEYWORDS="~amd64 ~x86"
+
+DEPEND="
+	dev-python/pybind11[${PYTHON_USEDEP}]
+"
diff --git a/dev-python/pyct/Manifest b/dev-python/pyct/Manifest
new file mode 100644
index 000000000..f46ddb65e
--- /dev/null
+++ b/dev-python/pyct/Manifest
@@ -0,0 +1 @@
+DIST pyct-0.4.8.tar.gz 16265 BLAKE2B 13bd6e3405ef0b2b69bc27135b2758668f636fbe2cfec7e7cea8d8d24ec5ed855bd7225caa599622e7df80b08ef46da981098fd58508c7aee0471ed7f0354e51 SHA512 8570b06d9e7c6d19c7a3c6a0c7977fdd1810b4c3dea89423a06459b98cc941164d70f021157be32fa4405699e7ee1ef66a5bb522d752aed153d93ece23fdf1a0
diff --git a/dev-python/pyct/metadata.xml b/dev-python/pyct/metadata.xml
new file mode 100644
index 000000000..23a8fe7c2
--- /dev/null
+++ b/dev-python/pyct/metadata.xml
@@ -0,0 +1,13 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
+<pkgmetadata>
+	<maintainer type="project">
+		<email>sci@gentoo.org</email>
+		<name>Gentoo Science Project</name>
+	</maintainer>
+	<stabilize-allarches/>
+	<upstream>
+		<remote-id type="pypi">pyct</remote-id>
+		<remote-id type="github">pyviz-dev/pyct</remote-id>
+	</upstream>
+</pkgmetadata>
diff --git a/dev-python/pyct/pyct-0.4.8.ebuild b/dev-python/pyct/pyct-0.4.8.ebuild
new file mode 100644
index 000000000..d8ef9bfa2
--- /dev/null
+++ b/dev-python/pyct/pyct-0.4.8.ebuild
@@ -0,0 +1,21 @@
+# Copyright 1999-2023 Gentoo Authors
+# Distributed under the terms of the GNU General Public License v2
+
+EAPI=8
+
+PYTHON_COMPAT=( python3_{10..11} pypy3 )
+# HoloViews imports from "distutils" at runtime.
+DISTUTILS_USE_SETUPTOOLS=rdepend
+inherit distutils-r1 pypi
+
+DESCRIPTION="Python packaging Common Tasks"
+HOMEPAGE="https://holoviz.org"
+
+LICENSE="BSD"
+SLOT="0"
+KEYWORDS="~amd64 ~x86"
+
+DEPEND=">=dev-python/param-1.7.0[${PYTHON_USEDEP}]"
+RDEPEND="${DEPEND}"
+
+distutils_enable_tests pytest
diff --git a/dev-python/pydotplus/Manifest b/dev-python/pydotplus/Manifest
deleted file mode 100644
index 397f4ef92..000000000
--- a/dev-python/pydotplus/Manifest
+++ /dev/null
@@ -1 +0,0 @@
-DIST pydotplus-2.0.2.tar.gz 278677 BLAKE2B 879271ba7e2104134a71caef7676082420770dcdb34aeabfe76232ad8f9774d3e90a9f7ca5fb407a7a4e8e0c4e5e01824bd0d5936fe77554cc661839fcc0dc7b SHA512 6f06a1f284401123a4514f9e9a4974dee8dc8d01e6b7c40a797fb70eed22b99fe774272f8b106b5632a33f524b356349fe1ff9633101ff61ef2fc3fe69d641ac
diff --git a/dev-python/pydotplus/metadata.xml b/dev-python/pydotplus/metadata.xml
deleted file mode 100644
index aa8f9c150..000000000
--- a/dev-python/pydotplus/metadata.xml
+++ /dev/null
@@ -1,19 +0,0 @@
-<?xml version="1.0" encoding="UTF-8"?>
-<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
-<pkgmetadata>
-	<maintainer type="person">
-		<email>horea.christ@gmail.com</email>
-		<name>Horea Christian</name>
-	</maintainer>
-	<maintainer type="project">
-		<email>sci@gentoo.org</email>
-		<name>Gentoo Science Project</name>
-	</maintainer>
-	<longdescription lang="en">
-PyDotPlus is an improved version of the old pydot project that provides a Python Interface to
-Graphviz’s Dot language.
-</longdescription>
-	<upstream>
-		<remote-id type="pypi">pydotplus</remote-id>
-	</upstream>
-</pkgmetadata>
diff --git a/dev-python/pydotplus/pydotplus-2.0.2.ebuild b/dev-python/pydotplus/pydotplus-2.0.2.ebuild
deleted file mode 100644
index 50f99069f..000000000
--- a/dev-python/pydotplus/pydotplus-2.0.2.ebuild
+++ /dev/null
@@ -1,28 +0,0 @@
-# Copyright 1999-2016 Gentoo Foundation
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=6
-
-PYTHON_COMPAT=( python{2_7,3_4,3_5} )
-
-inherit distutils-r1
-
-DESCRIPTION="Improved version of the old pydot project"
-HOMEPAGE="http://pydotplus.readthedocs.org/"
-SRC_URI="mirror://pypi/p/${PN}/${P}.tar.gz"
-
-LICENSE="MIT"
-SLOT="0"
-KEYWORDS="~amd64 ~x86"
-IUSE="test"
-
-DEPEND="
-	dev-python/setuptools[${PYTHON_USEDEP}]
-	"
-RDEPEND="
-	dev-python/pyparsing[${PYTHON_USEDEP}]
-	"
-
-python_test() {
-	${EPYTHON} -m unittest discover || die
-}
diff --git a/dev-python/pyerfa/Manifest b/dev-python/pyerfa/Manifest
new file mode 100644
index 000000000..29344f9fb
--- /dev/null
+++ b/dev-python/pyerfa/Manifest
@@ -0,0 +1 @@
+DIST pyerfa-2.0.0.1.tar.gz 808497 BLAKE2B b9c6973330236f4a983fdbb6b0f3faefc3fd8ec8a2187b5cd37d3d4a97ab9aa7da4008c1d77f9b2465282b164cdf338f41e816344f5ba15af3fda48ccb71d3b8 SHA512 420e7bb2d00a9bd7d2290b6b0598b5963404ac021f713ae7bbf607135b9db6605f63dd89694d2cf406eb230b58b1028f2458f96ed834127ce9a398810cfea589
diff --git a/dev-python/pyerfa/metadata.xml b/dev-python/pyerfa/metadata.xml
new file mode 100644
index 000000000..5615e25d7
--- /dev/null
+++ b/dev-python/pyerfa/metadata.xml
@@ -0,0 +1,12 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
+<pkgmetadata>
+	<maintainer type="project">
+		<email>sci-astronomy@gentoo.org</email>
+		<name>Gentoo Astronomy Project</name>
+	</maintainer>
+	<upstream>
+		<remote-id type="github">liberfa/pyerfa</remote-id>
+		<remote-id type="pypi">pyerfa</remote-id>
+	</upstream>
+</pkgmetadata>
diff --git a/dev-python/pyerfa/pyerfa-2.0.0.1-r2.ebuild b/dev-python/pyerfa/pyerfa-2.0.0.1-r2.ebuild
new file mode 100644
index 000000000..11a68c169
--- /dev/null
+++ b/dev-python/pyerfa/pyerfa-2.0.0.1-r2.ebuild
@@ -0,0 +1,33 @@
+# Copyright 1999-2022 Gentoo Authors
+# Distributed under the terms of the GNU General Public License v2
+
+EAPI=8
+
+PYTHON_COMPAT=( python3_{10..11} )
+DISTUTILS_USE_PEP517=setuptools
+
+inherit distutils-r1 pypi
+
+DESCRIPTION="Python bindings for ERFA"
+HOMEPAGE="https://github.com/liberfa/pyerfa/"
+
+LICENSE="BSD"
+SLOT="0"
+KEYWORDS="~amd64 ~x86"
+
+# ImportError: cannot import name 'ufunc' from 'erfa'
+RESTRICT="test"
+
+RDEPEND="
+	sci-astronomy/erfa:0=
+	>=dev-python/numpy-1.17[${PYTHON_USEDEP}]
+"
+DEPEND="${RDEPEND}"
+BDEPEND="
+	dev-python/setuptools-scm[${PYTHON_USEDEP}]
+	test? (
+		dev-python/pytest-doctestplus[${PYTHON_USEDEP}]
+	)"
+
+distutils_enable_tests pytest
+#distutils_enable_sphinx docs dev-python/sphinx-astropy
diff --git a/dev-python/pyfftw/Manifest b/dev-python/pyfftw/Manifest
deleted file mode 100644
index 9fae200c5..000000000
--- a/dev-python/pyfftw/Manifest
+++ /dev/null
@@ -1,2 +0,0 @@
-DIST pyFFTW-0.10.4.tar.gz 365496 BLAKE2B 5b16fc01f64cf5726292ba386da9682b018f1709c7d6f510614ae35ed50bcaa7fd9ceaa84fb76adddd132eb57e62509dde73d7ba4e3bf6861b07f5810b1a801f SHA512 6848133e30a02ee51bb86613f53a5fdbf9b5a0fea3cab01b8ca7d365f924a966ac9b94f4ed62979d418f9f847369f8c50568ca855e472035fa37e86e630fb9fd
-DIST pyFFTW-0.9.2.tar.gz 336928 BLAKE2B 089f354b5d2d7621dbf7a2171505b60727c77220c310dbe3cdef9b2f087aac72b943b822add12d4057911f292872bd4429bb961754da4915634cc43aa451a6b4 SHA512 f77e52ce36c9375dbd48ebfd848884c9d9a1e080df920f28f10db5350549011de62fa1cb3ec96d1b1450d8a45209e97a0b20ece43eea16d7e543581c8444d194
diff --git a/dev-python/pyfftw/metadata.xml b/dev-python/pyfftw/metadata.xml
deleted file mode 100644
index c93b316f7..000000000
--- a/dev-python/pyfftw/metadata.xml
+++ /dev/null
@@ -1,19 +0,0 @@
-<?xml version="1.0" encoding="UTF-8"?>
-<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
-<pkgmetadata>
-	<maintainer type="person">
-		<email>marbre@linux.sungazer.de</email>
-		<name>Marius Brehler</name>
-	</maintainer>
-	<maintainer type="project">
-		<email>sci@gentoo.org</email>
-		<name>Gentoo Science Project</name>
-	</maintainer>
-	<longdescription>
-A pythonic wrapper around FFTW, the FFT library, presenting a
-unified interface for all the supported transforms.
-</longdescription>
-	<upstream>
-		<remote-id type="pypi">pyFFTW</remote-id>
-	</upstream>
-</pkgmetadata>
diff --git a/dev-python/pyfftw/pyfftw-0.10.4.ebuild b/dev-python/pyfftw/pyfftw-0.10.4.ebuild
deleted file mode 100644
index d6d6e7bbc..000000000
--- a/dev-python/pyfftw/pyfftw-0.10.4.ebuild
+++ /dev/null
@@ -1,40 +0,0 @@
-# Copyright 1999-2017 Gentoo Foundation
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=6
-PYTHON_COMPAT=( python2_7 python3_{4,5} )
-
-inherit distutils-r1
-
-MY_PN="pyFFTW"
-
-DESCRIPTION="FFTW wrapper for python"
-HOMEPAGE="http://hgomersall.github.io/pyFFTW/"
-SRC_URI="mirror://pypi/${MY_PN:0:1}/${MY_PN}/${MY_PN}-${PV}.tar.gz"
-
-LICENSE="BSD"
-SLOT="0"
-IUSE="test"
-KEYWORDS="~amd64"
-
-S="${WORKDIR}/${MY_PN}-${PV}"
-
-RDEPEND="
-	>=dev-python/numpy-1.8.0[${PYTHON_USEDEP}]
-	sci-libs/scipy[${PYTHON_USEDEP}]
-	>=sci-libs/fftw-3.3.3
-	>=dev-python/cython-0.19.1[${PYTHON_USEDEP}]
-	"
-DEPEND="${RDEPEND}"
-
-#current python_test() broken
-RESTRICT="test"
-
-python_test() {
-	distutils_install_for_testing
-	cd "${TEST_DIR}"/lib || die
-
-	cp "${S}"/setup.py "${TEST_DIR}"/lib/ || die
-	cp -r "${S}"/test "${TEST_DIR}"/lib/ || die
-	esetup.py test || die
-}
diff --git a/dev-python/pyfftw/pyfftw-0.9.2.ebuild b/dev-python/pyfftw/pyfftw-0.9.2.ebuild
deleted file mode 100644
index 7a5b2d505..000000000
--- a/dev-python/pyfftw/pyfftw-0.9.2.ebuild
+++ /dev/null
@@ -1,35 +0,0 @@
-# Copyright 1999-2017 Gentoo Foundation
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=6
-PYTHON_COMPAT=( python2_7 python3_{4,5} )
-
-inherit distutils-r1
-
-MY_PN="pyFFTW"
-
-DESCRIPTION="FFTW wrapper for python"
-HOMEPAGE="http://hgomersall.github.io/pyFFTW/"
-SRC_URI="mirror://pypi/${MY_PN:0:1}/${MY_PN}/${MY_PN}-${PV}.tar.gz"
-
-LICENSE="BSD"
-SLOT="0"
-IUSE="test"
-KEYWORDS="~amd64"
-
-S="${WORKDIR}/${MY_PN}-${PV}"
-
-RDEPEND="
-	>=dev-python/numpy-1.8.0[${PYTHON_USEDEP}]
-	>=sci-libs/fftw-3.3.3
-	>=dev-python/cython-0.19.1[${PYTHON_USEDEP}]
-	"
-DEPEND="${RDEPEND}"
-
-python_test() {
-	distutils_install_for_testing
-	cd "${TEST_DIR}"/lib || die
-	cp "${S}"/setup.py "${TEST_DIR}"/lib/ || die
-	cp -r "${S}"/test "${TEST_DIR}"/lib/ || die
-	esetup.py test || die
-}
diff --git a/dev-python/pyfftw/pyfftw-9999.ebuild b/dev-python/pyfftw/pyfftw-9999.ebuild
deleted file mode 100644
index 7a7f4257d..000000000
--- a/dev-python/pyfftw/pyfftw-9999.ebuild
+++ /dev/null
@@ -1,33 +0,0 @@
-# Copyright 1999-2017 Gentoo Foundation
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=6
-PYTHON_COMPAT=( python2_7 python3_{4,5} )
-
-inherit distutils-r1 git-r3
-
-MY_PN="pyFFTW"
-
-DESCRIPTION="FFTW wrapper for python"
-HOMEPAGE="http://hgomersall.github.io/pyFFTW/"
-EGIT_REPO_URI="https://github.com/${MY_PN}/${MY_PN}.git git://github.com/${MY_PN}/${MY_PN}.git"
-
-LICENSE="BSD"
-SLOT="0"
-IUSE="test"
-
-RDEPEND="
-	>=dev-python/numpy-1.8.0[${PYTHON_USEDEP}]
-	sci-libs/scipy[${PYTHON_USEDEP}]
-	>=sci-libs/fftw-3.3.3
-	>=dev-python/cython-0.19.1[${PYTHON_USEDEP}]
-	"
-DEPEND="${RDEPEND}"
-
-python_test() {
-	distutils_install_for_testing
-	cd "${TEST_DIR}"/lib || die
-	cp "${S}"/setup.py "${TEST_DIR}"/lib/ || die
-	cp -r "${S}"/test "${TEST_DIR}"/lib/ || die
-	esetup.py test || die
-}
diff --git a/dev-python/pyhdf/Manifest b/dev-python/pyhdf/Manifest
deleted file mode 100644
index 8993244ca..000000000
--- a/dev-python/pyhdf/Manifest
+++ /dev/null
@@ -1 +0,0 @@
-DIST pyhdf-0.8.3.tar.gz 346412 BLAKE2B d6336d1c8f1a7af8483be5ced528c50a8aa4d71a7d3d916c1b5a69a84fb6ab53015f3c6d68cc4b975855cc2f070cf4af7889ae917842a68c87a4b2ec5d5da50a SHA512 d6a23930210dd25380454af96cb0caa15473a13979824276de4c7a477d6f9aaae78af5d566d72cb359a50ac98b306fa8dffe38db0063e43a8384593d10c264d3
diff --git a/dev-python/pyhdf/metadata.xml b/dev-python/pyhdf/metadata.xml
deleted file mode 100644
index 6a3e3ff5d..000000000
--- a/dev-python/pyhdf/metadata.xml
+++ /dev/null
@@ -1,18 +0,0 @@
-<?xml version="1.0" encoding="UTF-8"?>
-<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
-<pkgmetadata>
-	<maintainer type="person">
-		<email>gorkypl@gmail.com</email>
-		<name>Paweł Rumian</name>
-	</maintainer>
-	<maintainer type="project">
-		<email>sci@gentoo.org</email>
-		<name>Gentoo Science Project</name>
-	</maintainer>
-	<use>
-		<flag name="szip">Allow to use <pkg>sci-libs/szip</pkg> for SZIP compression method in SDsetcompress()</flag>
-	</use>
-	<upstream>
-		<remote-id type="sourceforge">pysclint</remote-id>
-	</upstream>
-</pkgmetadata>
diff --git a/dev-python/pyhdf/pyhdf-0.8.3.ebuild b/dev-python/pyhdf/pyhdf-0.8.3.ebuild
deleted file mode 100644
index 3f1ceb391..000000000
--- a/dev-python/pyhdf/pyhdf-0.8.3.ebuild
+++ /dev/null
@@ -1,40 +0,0 @@
-# Copyright 1999-2014 Gentoo Foundation
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=5
-
-PYTHON_COMPAT=( python2_7 )
-
-inherit distutils-r1
-
-DESCRIPTION="Python interface to NCSA HDF4 library"
-HOMEPAGE="http://pysclint.sourceforge.net/pycdf/ http://pypi.python.org/pypi/pyhdf"
-SRC_URI="mirror://sourceforge/pysclint/${PN}/${PV}/${P}.tar.gz"
-
-LICENSE="PSF-2"
-SLOT="0"
-KEYWORDS="~amd64 ~x86"
-IUSE="examples szip"
-
-RDEPEND="
-	dev-python/numpy[${PYTHON_USEDEP}]
-	sci-libs/hdf[szip=]"
-DEPEND="${RDEPEND}
-	dev-python/setuptools[${PYTHON_USEDEP}]"
-
-python_compile() {
-	use szip || export NOSZIP=1
-	distutils-r1_python_compile
-}
-
-python_install_all() {
-	distutils-r1_python_install_all
-
-	dohtml doc/*.html
-	dodoc CHANGES doc/*.txt
-
-	if use examples; then
-		insinto /usr/share/doc/${PF}
-		doins -r examples
-	fi
-}
diff --git a/dev-python/pylibconfig2/Manifest b/dev-python/pylibconfig2/Manifest
deleted file mode 100644
index e22de5a93..000000000
--- a/dev-python/pylibconfig2/Manifest
+++ /dev/null
@@ -1 +0,0 @@
-DIST pylibconfig2-0.2.5.tar.gz 5293 BLAKE2B c5c678cf10b8dc41309d520e52a326dd7fd368c1cda665eea68bdacc21119081f6902a5e94e65514ba99cf064bf0f372f697fafd1c5ae72d79e208837e4aec25 SHA512 e9b7b969ce895b1ca8b1d88bf59b3b56f179e8c669ccb472e7d71e51d8461db353dce343c19b97f82fc10d5b88be5e6d549329f2d4d352b23336ce38dbe725cc
diff --git a/dev-python/pylibconfig2/metadata.xml b/dev-python/pylibconfig2/metadata.xml
deleted file mode 100644
index cbff41127..000000000
--- a/dev-python/pylibconfig2/metadata.xml
+++ /dev/null
@@ -1,25 +0,0 @@
-<?xml version="1.0" encoding="UTF-8"?>
-<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
-<pkgmetadata>
-	<maintainer type="person">
-		<email>marbre@linux.sungazer.de</email>
-		<name>Marius Brehler</name>
-	</maintainer>
-	<maintainer type="project">
-		<email>sci@gentoo.org</email>
-		<name>Gentoo Science Project</name>
-	</maintainer>
-	<longdescription>
-Pure python library for libconfig syntax.
-IO works via strings, and include directives.
-
-Scalar types are pythons basic types str, int, long, float, bool.
-The libconfig types Array, List, Group are implemented as ConfArray,
-ConfList, ConfGroup, respectively. A config is setup from a string
-only, and represented as a string automatically.
-</longdescription>
-	<upstream>
-		<remote-id type="github">heinzK1X/pylibconfig2</remote-id>
-		<remote-id type="pypi">pylibconfig2</remote-id>
-	</upstream>
-</pkgmetadata>
diff --git a/dev-python/pylibconfig2/pylibconfig2-0.2.5.ebuild b/dev-python/pylibconfig2/pylibconfig2-0.2.5.ebuild
deleted file mode 100644
index 5d35c0e7f..000000000
--- a/dev-python/pylibconfig2/pylibconfig2-0.2.5.ebuild
+++ /dev/null
@@ -1,20 +0,0 @@
-# Copyright 1999-2016 Gentoo Foundation
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=6
-PYTHON_COMPAT=( python2_7 python{3_4,3_5} )
-
-inherit distutils-r1
-
-DESCRIPTION="Pure python library for libconfig syntax"
-HOMEPAGE="https://github.com/heinzK1X/pylibconfig2"
-SRC_URI="mirror://pypi/${PN:0:1}/${PN}/${P}.tar.gz"
-
-LICENSE="BSD"
-SLOT="0"
-KEYWORDS="~amd64 ~x86"
-
-RDEPEND="
-	dev-python/pyparsing[${PYTHON_USEDEP}]
-	"
-DEPEND="${RDEPEND}"
diff --git a/dev-python/pylibconfig2/pylibconfig2-9999.ebuild b/dev-python/pylibconfig2/pylibconfig2-9999.ebuild
deleted file mode 100644
index 197e6ce54..000000000
--- a/dev-python/pylibconfig2/pylibconfig2-9999.ebuild
+++ /dev/null
@@ -1,26 +0,0 @@
-# Copyright 1999-2016 Gentoo Foundation
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=6
-PYTHON_COMPAT=( python2_7 python{3_4,3_5} )
-
-inherit distutils-r1 git-r3
-
-DESCRIPTION="Pure python library for libconfig syntax"
-HOMEPAGE="https://github.com/heinzK1X/pylibconfig2"
-EGIT_REPO_URI="https://github.com/heinzK1X/${PN}.git git://github.com/heinzK1X/${PN}.git"
-
-LICENSE="BSD"
-SLOT="0"
-KEYWORDS=""
-IUSE="test"
-
-RDEPEND="
-	dev-python/pyparsing[${PYTHON_USEDEP}]
-	"
-DEPEND="${RDEPEND}"
-
-python_test() {
-	distutils_install_for_testing
-	esetup.py test || die
-}
diff --git a/dev-python/pynomo/Manifest b/dev-python/pynomo/Manifest
deleted file mode 100644
index df46a96bd..000000000
--- a/dev-python/pynomo/Manifest
+++ /dev/null
@@ -1 +0,0 @@
-DIST PyNomo-0.2.2.tar.gz 101609 BLAKE2B f9199c639be959d146c9513bdc1a4ad0cd9de3705cd6d772924432840d7ab27c27e57528e5743b723ec4d44d41a1ab2c26ab8089e547689f651574ea373445cd SHA512 089456926e2e7a55d88b965ba6a879648aac489ff12847c492ddbfb0320278475e8b41955ed211760b2d758ff52b31f34f57e2263d3ad0f43d5a61e84f1aea0c
diff --git a/dev-python/pynomo/metadata.xml b/dev-python/pynomo/metadata.xml
deleted file mode 100644
index 9e69d00fa..000000000
--- a/dev-python/pynomo/metadata.xml
+++ /dev/null
@@ -1,15 +0,0 @@
-<?xml version="1.0" encoding="UTF-8"?>
-<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
-<pkgmetadata>
-	<maintainer type="person">
-		<email>witold.pilat@gmail.com</email>
-	</maintainer>
-	<longdescription>
-Pynomo is a program to create (pdf) nomographs
-(nomograms) using Python interpreter. A nomograph (nomogram) is a
-graphical solution to an equation.
-</longdescription>
-	<upstream>
-		<remote-id type="sourceforge">pynomo</remote-id>
-	</upstream>
-</pkgmetadata>
diff --git a/dev-python/pynomo/pynomo-0.2.2.ebuild b/dev-python/pynomo/pynomo-0.2.2.ebuild
deleted file mode 100644
index fe1d91481..000000000
--- a/dev-python/pynomo/pynomo-0.2.2.ebuild
+++ /dev/null
@@ -1,34 +0,0 @@
-# Copyright 1999-2014 Gentoo Foundation
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=5
-
-PYTHON_COMPAT=( python2_7 )
-
-inherit distutils-r1
-
-MY_PN="PyNomo"
-MY_P="${MY_PN}-${PV}"
-
-DESCRIPTION="PyNomo is a program to create nomographs (nomograms) using Python interpreter"
-HOMEPAGE="http://pynomo.org/
-	http://sourceforge.net/projects/pynomo/"
-SRC_URI="mirror://sourceforge/${PN}/${MY_P}.tar.gz"
-
-LICENSE="GPL-3+"
-KEYWORDS="~amd64 ~x86"
-SLOT="0"
-IUSE="examples"
-
-RDEPEND="dev-python/numpy[${PYTHON_USEDEP}]
-	dev-python/pyx[${PYTHON_USEDEP}]
-	sci-libs/scipy[${PYTHON_USEDEP}]"
-DEPEND="dev-python/setuptools[${PYTHON_USEDEP}]"
-
-S="${WORKDIR}/${MY_P}"
-DOCS=( AUTHORS.txt CHANGES.txt README.txt )
-
-python_install_all() {
-	use examples && local EXAMPLES=( examples/. )
-	distutils-r1_python_install_all
-}
diff --git a/dev-python/pynrrd/Manifest b/dev-python/pynrrd/Manifest
index da7214fcf..e174359e3 100644
--- a/dev-python/pynrrd/Manifest
+++ b/dev-python/pynrrd/Manifest
@@ -1 +1,3 @@
-DIST pynrrd-0.2.2.tar.gz 14444 BLAKE2B 4db61bb02a0ff88f1961ee041dcbab2ad4d19b6858d2ec762d47e05e0cb188e59699bd0ba54783047f6c8f499f81eb04acd644df03103f74bd3cb00112608d90 SHA512 50f659c97342a0b87d9836817b171dc5ebdd501d21c7cd128edcc91064d157f69d48e94ea69a03cbd23c37a9eba0b9fefdb10b093b92f8b62b41df9270782434
+DIST pynrrd-0.4.2.tar.gz 43129 BLAKE2B 2001d151e38bbd02a648759475af13dd1be4bb7c12b7f8a3c7294e7fe1c281aeb9b35e39cce8254088b1c2f766aabe7343be0da4d48208375bb21be6dce9ba61 SHA512 8c5e4c1cb89dc84be3cf06e40d3f5bd45ea355c4e103027a62b088c4a73b03d1032cea1de0b153ef13fefd9b06d5a9b1954456a4542ae27cb74a278835b759ca
+DIST pynrrd-0.4.3.tar.gz 43162 BLAKE2B 266c57029e48e923dd5371184f59471e069890668ac15a75cfafc178cfe1a718f33bc6bcc704172e0fca0bdc9c52091da79e404b6bfb85838eef0c3e0807409c SHA512 d6264fce3b270e5ae9d889e7d58a18ae7bf3fecf5a1fe168dc584dece2052efd32170b21a02fa630c35e0e45e7109c745069710169ec38819639a4585344e0f6
+DIST pynrrd-1.0.0.tar.gz 45061 BLAKE2B c08bcd70c3565cd690b228793651e57e08d2095a72b7f7102e6274f1518873acb1ee5645302fbb68b7cf1afafe3c5c734a33e561eea1caaacb5434c049dcc325 SHA512 c622812a4e000e6a4b5d82db2eac02822968c38bb9b8ab5d35cfa498a636bf221078d8722f8ac2cdd91b0430f0b5b6768fb33a63112c3045038f6d44d121e7b5
diff --git a/dev-python/pynrrd/metadata.xml b/dev-python/pynrrd/metadata.xml
index 5375bfa89..93fdc88d6 100644
--- a/dev-python/pynrrd/metadata.xml
+++ b/dev-python/pynrrd/metadata.xml
@@ -2,7 +2,7 @@
 <!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
 <pkgmetadata>
 	<maintainer type="person">
-		<email>horea.christ@gmail.com</email>
+		<email>gentoo@chymera.eu</email>
 		<name>Horea Christian</name>
 	</maintainer>
 	<maintainer type="project">
diff --git a/dev-python/pynrrd/pynrrd-0.2.2.ebuild b/dev-python/pynrrd/pynrrd-0.2.2.ebuild
deleted file mode 100644
index 1933dd639..000000000
--- a/dev-python/pynrrd/pynrrd-0.2.2.ebuild
+++ /dev/null
@@ -1,24 +0,0 @@
-# Copyright 1999-2018 Gentoo Foundation
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=7
-
-PYTHON_COMPAT=( python{2_7,3_4,3_5,3_6} )
-
-inherit distutils-r1
-
-DESCRIPTION="Simple pure-python module for reading and writing nrrd files"
-HOMEPAGE="https://github.com/mhe/pynrrd"
-SRC_URI="https://github.com/mhe/pynrrd/archive/v${PV}.tar.gz -> ${P}.tar.gz"
-
-LICENSE="BSD"
-SLOT="0"
-KEYWORDS="~amd64"
-IUSE="test"
-
-RDEPEND="dev-python/numpy[${PYTHON_USEDEP}]"
-DEPEND="test? ( ${RDEPEND} )"
-
-python_test() {
-	${EPYTHON} tests/test_nrrd.py || die
-}
diff --git a/dev-python/pynrrd/pynrrd-0.4.2.ebuild b/dev-python/pynrrd/pynrrd-0.4.2.ebuild
new file mode 100644
index 000000000..2993f8f3a
--- /dev/null
+++ b/dev-python/pynrrd/pynrrd-0.4.2.ebuild
@@ -0,0 +1,27 @@
+# Copyright 1999-2023 Gentoo Authors
+# Distributed under the terms of the GNU General Public License v2
+
+EAPI=8
+
+DISTUTILS_USE_PEP517=setuptools
+PYTHON_COMPAT=( python3_{10..11} )
+
+inherit distutils-r1
+
+DESCRIPTION="Simple pure-python module for reading and writing nrrd files"
+HOMEPAGE="https://github.com/mhe/pynrrd"
+SRC_URI="https://github.com/mhe/pynrrd/archive/v${PV}.tar.gz -> ${P}.tar.gz"
+
+LICENSE="BSD"
+SLOT="0"
+KEYWORDS="~amd64"
+
+RDEPEND="dev-python/numpy[${PYTHON_USEDEP}]"
+DEPEND="test? ( ${RDEPEND} )"
+
+distutils_enable_tests unittest
+
+python_test() {
+	${EPYTHON} -m unittest discover -v nrrd/tests || \
+		die "unittests failed for ${EPYTHON}"
+}
diff --git a/dev-python/pynrrd/pynrrd-0.4.3.ebuild b/dev-python/pynrrd/pynrrd-0.4.3.ebuild
new file mode 100644
index 000000000..2993f8f3a
--- /dev/null
+++ b/dev-python/pynrrd/pynrrd-0.4.3.ebuild
@@ -0,0 +1,27 @@
+# Copyright 1999-2023 Gentoo Authors
+# Distributed under the terms of the GNU General Public License v2
+
+EAPI=8
+
+DISTUTILS_USE_PEP517=setuptools
+PYTHON_COMPAT=( python3_{10..11} )
+
+inherit distutils-r1
+
+DESCRIPTION="Simple pure-python module for reading and writing nrrd files"
+HOMEPAGE="https://github.com/mhe/pynrrd"
+SRC_URI="https://github.com/mhe/pynrrd/archive/v${PV}.tar.gz -> ${P}.tar.gz"
+
+LICENSE="BSD"
+SLOT="0"
+KEYWORDS="~amd64"
+
+RDEPEND="dev-python/numpy[${PYTHON_USEDEP}]"
+DEPEND="test? ( ${RDEPEND} )"
+
+distutils_enable_tests unittest
+
+python_test() {
+	${EPYTHON} -m unittest discover -v nrrd/tests || \
+		die "unittests failed for ${EPYTHON}"
+}
diff --git a/dev-python/pynrrd/pynrrd-1.0.0.ebuild b/dev-python/pynrrd/pynrrd-1.0.0.ebuild
new file mode 100644
index 000000000..d46aba486
--- /dev/null
+++ b/dev-python/pynrrd/pynrrd-1.0.0.ebuild
@@ -0,0 +1,30 @@
+# Copyright 1999-2023 Gentoo Authors
+# Distributed under the terms of the GNU General Public License v2
+
+EAPI=8
+
+DISTUTILS_USE_PEP517=setuptools
+PYTHON_COMPAT=( python3_{10..11} )
+
+inherit distutils-r1
+
+DESCRIPTION="Simple pure-python module for reading and writing nrrd files"
+HOMEPAGE="https://github.com/mhe/pynrrd"
+SRC_URI="https://github.com/mhe/pynrrd/archive/v${PV}.tar.gz -> ${P}.tar.gz"
+
+LICENSE="BSD"
+SLOT="0"
+KEYWORDS="~amd64"
+
+RDEPEND="
+	dev-python/nptyping[${PYTHON_USEDEP}]
+	dev-python/numpy[${PYTHON_USEDEP}]
+"
+DEPEND="test? ( ${RDEPEND} )"
+
+distutils_enable_tests unittest
+
+python_test() {
+	${EPYTHON} -m unittest discover -v nrrd/tests || \
+		die "unittests failed for ${EPYTHON}"
+}
diff --git a/dev-python/pynwb/Manifest b/dev-python/pynwb/Manifest
new file mode 100644
index 000000000..0dffbb9ab
--- /dev/null
+++ b/dev-python/pynwb/Manifest
@@ -0,0 +1,2 @@
+DIST pynwb-2.5.0.tar.gz 620770 BLAKE2B 470f5127560bf79f112061e9e8af208051d76833e449a66b03e31bb0828ffbfd6aa0b9efc136ecc0b7efba758334c3f15525a41ec4540c6f55d02f8afbd55ab2 SHA512 cad84e3ac6c3c67c3c28e3c3ec44402bfc94c4cf988fbe64ddfa461a67115398b24bb9bcac1bd00933e1b63d73048d9b20ec6cd736a51d9f2c7bf4d294edb261
+DIST pynwb-2.6.0.tar.gz 625188 BLAKE2B ac179af7e3c9de6ec4fb841dfd6279a1c3ba191b9d786553af02397a49c511f4a257a0e62f3b57a217ebb08588ad8ca64219fd435b3ec25776775d05e6a9ab9b SHA512 5c830cb37e8c6fe0643bd5bfee947565ddb1d0eff16dadadd3ebec7ec14a6e1ebcf34c3909ad05c3eedd8dd5f9e3669348216d695123f2013de0e969a403ec1c
diff --git a/dev-python/pynwb/metadata.xml b/dev-python/pynwb/metadata.xml
new file mode 100644
index 000000000..1e30097b2
--- /dev/null
+++ b/dev-python/pynwb/metadata.xml
@@ -0,0 +1,24 @@
+<?xml version='1.0' encoding='UTF-8'?>
+<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
+<pkgmetadata>
+	<maintainer type="person">
+		<email>gentoo@chymera.eu</email>
+		<name>Horea Christian</name>
+	</maintainer>
+	<maintainer type="project">
+		<email>sci@gentoo.org</email>
+		<name>Gentoo Science Project</name>
+	</maintainer>
+	<longdescription lang="en">
+		PyNWB is a Python package for working with NWB files. It provides a
+		high-level API for efficiently working with Neurodata stored in the NWB
+		format. Neurodata Without Borders: Neurophysiology (NWB:N) is a project
+		to develop a unified data format for cellular-based neurophysiology
+		data, focused on the dynamics of groups of neurons measured under a
+		large range of experimental conditions.
+	</longdescription>
+	<upstream>
+		<remote-id type="pypi">pynwb</remote-id>
+		<remote-id type="github">NeurodataWithoutBorders/pynwb</remote-id>
+	</upstream>
+</pkgmetadata>
diff --git a/dev-python/pynwb/pynwb-2.5.0.ebuild b/dev-python/pynwb/pynwb-2.5.0.ebuild
new file mode 100644
index 000000000..ca11c3dbe
--- /dev/null
+++ b/dev-python/pynwb/pynwb-2.5.0.ebuild
@@ -0,0 +1,50 @@
+# Copyright 1999-2023 Gentoo Authors
+# Distributed under the terms of the GNU General Public License v2
+
+EAPI=8
+
+DISTUTILS_USE_PEP517=setuptools
+PYTHON_COMPAT=( python3_{10..11} )
+inherit distutils-r1 pypi
+
+DESCRIPTION="A Python API for working with Neurodata stored in the NWB Format "
+HOMEPAGE="https://github.com/NeurodataWithoutBorders/pynwb"
+
+SLOT="0"
+LICENSE="BSD"
+KEYWORDS="~amd64 ~x86"
+
+RDEPEND="
+	>=dev-python/hdmf-3.3.2[${PYTHON_USEDEP}]
+	>=sci-libs/hdf5-1.12.2
+	dev-python/h5py[${PYTHON_USEDEP}]
+	dev-python/numpy[${PYTHON_USEDEP}]
+	dev-python/pandas[${PYTHON_USEDEP}]
+	dev-python/python-dateutil[${PYTHON_USEDEP}]
+	dev-python/requests[${PYTHON_USEDEP}]
+	"
+
+EPYTEST_DESELECT=(
+	# Reported upsream:
+	# https://github.com/NeurodataWithoutBorders/pynwb/issues/1580
+	tests/validation/test_validate.py::TestValidateCLI::test_validate_file_cached
+	tests/validation/test_validate.py::TestValidateCLI::test_validate_file_cached_bad_ns
+	tests/validation/test_validate.py::TestValidateCLI::test_validate_file_cached_core
+	tests/validation/test_validate.py::TestValidateCLI::test_validate_file_cached_extension
+	tests/validation/test_validate.py::TestValidateCLI::test_validate_file_cached_extension_pass_ns
+	tests/validation/test_validate.py::TestValidateCLI::test_validate_file_cached_hdmf_common
+	tests/validation/test_validate.py::TestValidateCLI::test_validate_file_cached_ignore
+	tests/validation/test_validate.py::TestValidateCLI::test_validate_file_invalid
+	tests/validation/test_validate.py::TestValidateCLI::test_validate_file_list_namespaces_core
+	tests/validation/test_validate.py::TestValidateCLI::test_validate_file_list_namespaces_extension
+	tests/validation/test_validate.py::TestValidateCLI::test_validate_file_no_cache
+	tests/validation/test_validate.py::TestValidateCLI::test_validate_file_no_cache_bad_ns
+	# Reported upstream:
+	# https://github.com/NeurodataWithoutBorders/pynwb/issues/1800
+	tests/unit/test_file.py::TestNoCacheSpec::test_simple
+	# Not sandboxed, reported upstream:
+	# https://github.com/NeurodataWithoutBorders/pynwb/issues/1800
+	tests/read_dandi/test_read_dandi.py::TestReadNWBDandisets::test_read_first_nwb_asset
+)
+
+distutils_enable_tests pytest
diff --git a/dev-python/pynwb/pynwb-2.6.0.ebuild b/dev-python/pynwb/pynwb-2.6.0.ebuild
new file mode 100644
index 000000000..2f403981c
--- /dev/null
+++ b/dev-python/pynwb/pynwb-2.6.0.ebuild
@@ -0,0 +1,51 @@
+# Copyright 1999-2023 Gentoo Authors
+# Distributed under the terms of the GNU General Public License v2
+
+EAPI=8
+
+DISTUTILS_USE_PEP517=setuptools
+PYTHON_COMPAT=( python3_{10..11} )
+inherit distutils-r1 pypi
+
+DESCRIPTION="A Python API for working with Neurodata stored in the NWB Format "
+HOMEPAGE="https://github.com/NeurodataWithoutBorders/pynwb"
+
+SLOT="0"
+LICENSE="BSD"
+KEYWORDS="~amd64 ~x86"
+
+RDEPEND="
+	>=dev-python/hdmf-3.3.2[${PYTHON_USEDEP}]
+	>=sci-libs/hdf5-1.12.2
+	dev-python/h5py[${PYTHON_USEDEP}]
+	dev-python/numpy[${PYTHON_USEDEP}]
+	dev-python/pandas[${PYTHON_USEDEP}]
+	dev-python/python-dateutil[${PYTHON_USEDEP}]
+	dev-python/requests[${PYTHON_USEDEP}]
+	"
+
+EPYTEST_DESELECT=(
+	# Reported upsream:
+	# https://github.com/NeurodataWithoutBorders/pynwb/issues/1580
+	tests/validation/test_validate.py::TestValidateCLI::test_validate_file_cached
+	tests/validation/test_validate.py::TestValidateCLI::test_validate_file_cached_bad_ns
+	tests/validation/test_validate.py::TestValidateCLI::test_validate_file_cached_core
+	tests/validation/test_validate.py::TestValidateCLI::test_validate_file_cached_extension
+	tests/validation/test_validate.py::TestValidateCLI::test_validate_file_cached_extension_pass_ns
+	tests/validation/test_validate.py::TestValidateCLI::test_validate_file_cached_hdmf_common
+	tests/validation/test_validate.py::TestValidateCLI::test_validate_file_cached_ignore
+	tests/validation/test_validate.py::TestValidateCLI::test_validate_file_invalid
+	tests/validation/test_validate.py::TestValidateCLI::test_validate_file_list_namespaces_core
+	tests/validation/test_validate.py::TestValidateCLI::test_validate_file_list_namespaces_extension
+	tests/validation/test_validate.py::TestValidateCLI::test_validate_file_no_cache
+	tests/validation/test_validate.py::TestValidateCLI::test_validate_file_no_cache_bad_ns
+	# Reported upstream:
+	# https://github.com/NeurodataWithoutBorders/pynwb/issues/1800
+	tests/unit/test_file.py::TestNoCacheSpec::test_simple
+	# Not sandboxed, reported upstream:
+	# https://github.com/NeurodataWithoutBorders/pynwb/issues/1800
+	tests/read_dandi/test_read_dandi.py::TestReadNWBDandisets::test_read_first_nwb_asset
+	tests/unit/test_base.py::TestTimeSeries::test_repr_html
+)
+
+distutils_enable_tests pytest
diff --git a/dev-python/pyout/Manifest b/dev-python/pyout/Manifest
new file mode 100644
index 000000000..5878b2e20
--- /dev/null
+++ b/dev-python/pyout/Manifest
@@ -0,0 +1,2 @@
+DIST pyout-0.7.2.tar.gz 181753 BLAKE2B 780e536921151f81097e5dee7c74cfa086153f916fc9b9fd684f01008ada34102ba33ee7bdd3dd8cc4ccf89a8d9821ec0aecdbd87bc356abf25c6e4fe32d4c5a SHA512 e7be6f7829f6b09ead64c596cfdecfa45073af0a1da15401702327e141bbfae10e7968ee5e332358aa04bfc7ddf71b7b6caf2d5877aca8514e4ba544d3b1670a
+DIST pyout-0.7.3.tar.gz 45726 BLAKE2B 4c5bc42b835fefd3db5d97db46c086ec2a7ca488a339813937f6e795a5fef699451dd67cd5078737f4f2bc47a36c96e2cb9f0010645fa45ebd288d24b5e0c3ba SHA512 784a7dd5b1eb811073466828f81783f89e3a251e05bc49edf124cdfc916c2447982299c83b087942845b61791481850f8c89379eea920e91d35c8abc2cbeb8ef
diff --git a/dev-python/pyout/files/pyout-0.7.2-blessed.patch b/dev-python/pyout/files/pyout-0.7.2-blessed.patch
new file mode 100644
index 000000000..89e189916
--- /dev/null
+++ b/dev-python/pyout/files/pyout-0.7.2-blessed.patch
@@ -0,0 +1,140 @@
+From 0f7c6d6f2abb304c9c473afb504cb03d17fef036 Mon Sep 17 00:00:00 2001
+From: Horea Christian <chr@chymera.eu>
+Date: Sat, 7 Jan 2023 21:49:32 -0500
+Subject: [PATCH 1/2] Accepting either bless* library
+
+---
+ pyout/field.py                | 7 ++++++-
+ pyout/tabular.py              | 9 +++++++--
+ pyout/tests/terminal.py       | 9 +++++++--
+ pyout/tests/test_interface.py | 7 ++++++-
+ pyout/tests/test_tabular.py   | 7 ++++++-
+ 5 files changed, 32 insertions(+), 7 deletions(-)
+
+diff --git a/pyout/field.py b/pyout/field.py
+index 5105081..99c310f 100644
+--- a/pyout/field.py
++++ b/pyout/field.py
+@@ -495,7 +495,12 @@ class TermProcessors(StyleProcessors):
+ 
+     Parameters
+     ----------
+-    term : blessings.Terminal
++    term : blessed.Terminal or blessings.Terminal
++
++    Notes
++    -----
++    * Eventually we may want to retire blessings:
++        https://github.com/pyout/pyout/issues/136
+     """
+ 
+     def __init__(self, term):
+diff --git a/pyout/tabular.py b/pyout/tabular.py
+index 2a776a1..0d4797a 100644
+--- a/pyout/tabular.py
++++ b/pyout/tabular.py
+@@ -7,7 +7,12 @@
+ from logging import getLogger
+ import os
+ 
+-from blessings import Terminal
++# Eventually we may want to retire blessings:
++# https://github.com/pyout/pyout/issues/136
++try:
++    from blessed import Terminal
++except ImportError:
++    from blessings import Terminal
+ 
+ from pyout import interface
+ from pyout.field import TermProcessors
+@@ -16,7 +21,7 @@
+ 
+ 
+ class TerminalStream(interface.Stream):
+-    """Stream interface implementation using blessings.Terminal.
++    """Stream interface implementation using blessed/blessings.Terminal.
+     """
+ 
+     def __init__(self, stream=None, interactive=None):
+diff --git a/pyout/tests/terminal.py b/pyout/tests/terminal.py
+index 53aabd7..2d8857c 100644
+--- a/pyout/tests/terminal.py
++++ b/pyout/tests/terminal.py
+@@ -6,12 +6,17 @@
+ from functools import partial
+ import re
+ 
+-import blessings
++# Eventually we may want to retire blessings:
++# https://github.com/pyout/pyout/issues/136
++try:
++    import blessed as bls
++except ImportError:
++    import blessings as bls
+ 
+ from pyout.tests.utils import assert_contains
+ 
+ 
+-class Terminal(blessings.Terminal):
++class Terminal(bls.Terminal):
+ 
+     def __init__(self, *args, **kwargs):
+         super(Terminal, self).__init__(
+diff --git a/pyout/tests/test_interface.py b/pyout/tests/test_interface.py
+index 5205ef3..8348323 100644
+--- a/pyout/tests/test_interface.py
++++ b/pyout/tests/test_interface.py
+@@ -1,6 +1,11 @@
+ import pytest
+ 
+-pytest.importorskip("blessings")
++# Eventually we may want to retire blessings:
++# https://github.com/pyout/pyout/issues/136
++try:
++    pytest.importorskip("blessed")
++except pytest.skip.Exception:
++    pytest.importorskip("blessings")
+ 
+ import inspect
+ 
+diff --git a/pyout/tests/test_tabular.py b/pyout/tests/test_tabular.py
+index 2044e92..a1d35e5 100644
+--- a/pyout/tests/test_tabular.py
++++ b/pyout/tests/test_tabular.py
+@@ -1,7 +1,12 @@
+ # -*- coding: utf-8 -*-
+ import pytest
+ 
+-pytest.importorskip("blessings")
++# Eventually we may want to retire blessings:
++# https://github.com/pyout/pyout/issues/136
++try:
++    pytest.importorskip("blessed")
++except pytest.skip.Exception:
++    pytest.importorskip("blessings")
+ 
+ from collections import Counter
+ from collections import OrderedDict
+
+From 5f6691c114578217a124d2ac1b24468993178e27 Mon Sep 17 00:00:00 2001
+From: Horea Christian <chr@chymera.eu>
+Date: Sat, 7 Jan 2023 23:48:37 -0500
+Subject: [PATCH 2/2] Preferring blessings
+
+---
+ setup.py | 2 +-
+ 1 file changed, 1 insertion(+), 1 deletion(-)
+
+diff --git a/setup.py b/setup.py
+index b376c2e..43005e7 100644
+--- a/setup.py
++++ b/setup.py
+@@ -2,7 +2,7 @@
+ 
+ requires = {
+     "core": [
+-        "blessings; sys_platform != 'win32'",
++        "blessed; sys_platform != 'win32'",
+         "jsonschema>=3.0.0",
+     ],
+     "tests": ["pytest", "pytest-timeout"],
diff --git a/dev-python/pyout/metadata.xml b/dev-python/pyout/metadata.xml
new file mode 100644
index 000000000..712a48169
--- /dev/null
+++ b/dev-python/pyout/metadata.xml
@@ -0,0 +1,24 @@
+<?xml version='1.0' encoding='UTF-8'?>
+<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
+<pkgmetadata>
+	<maintainer type="person">
+		<email>gentoo@chymera.eu</email>
+		<name>Horea Christian</name>
+	</maintainer>
+	<maintainer type="project">
+		<email>sci@gentoo.org</email>
+		<name>Gentoo Science Project</name>
+	</maintainer>
+	<longdescription lang="en">
+		pyout is a Python package that defines an interface for writing
+		structured records as a table in a terminal. It is being developed to
+		replace custom code for displaying tabular data in in ReproMan and
+		DataLad. See the Examples folder for how to get started. A primary
+		goal of the interface is the separation of content from style and
+		presentation.
+	</longdescription>
+	<upstream>
+		<remote-id type="github">pyout/pyout</remote-id>
+		<remote-id type="pypi">pyout</remote-id>
+	</upstream>
+</pkgmetadata>
diff --git a/dev-python/pyout/pyout-0.7.2-r1.ebuild b/dev-python/pyout/pyout-0.7.2-r1.ebuild
new file mode 100644
index 000000000..7e262b158
--- /dev/null
+++ b/dev-python/pyout/pyout-0.7.2-r1.ebuild
@@ -0,0 +1,34 @@
+# Copyright 1999-2022 Gentoo Authors
+# Distributed under the terms of the GNU General Public License v2
+
+EAPI=8
+
+PYTHON_COMPAT=( python3_{10..11} )
+inherit distutils-r1
+
+DESCRIPTION="Terminal styling for structured data"
+HOMEPAGE="https://github.com/pyout/pyout"
+SRC_URI="https://github.com/pyout/pyout/archive/refs/tags/v${PV}.tar.gz -> ${P}.tar.gz"
+
+SLOT="0"
+LICENSE="MIT"
+KEYWORDS="~amd64 ~x86"
+
+RDEPEND="
+	dev-python/jsonschema[${PYTHON_USEDEP}]
+	dev-python/blessed[${PYTHON_USEDEP}]
+"
+DEPEND="
+	test? (
+		dev-python/pytest-timeout[${PYTHON_USEDEP}]
+	)
+"
+
+distutils_enable_tests pytest
+
+PATCHES=( "${FILESDIR}/${P}-blessed.patch"  )
+
+python_prepare_all() {
+	sed -i -e '/pytest-runner/d' setup.py || die
+	distutils-r1_python_prepare_all
+}
diff --git a/dev-python/pyout/pyout-0.7.3.ebuild b/dev-python/pyout/pyout-0.7.3.ebuild
new file mode 100644
index 000000000..7246139ee
--- /dev/null
+++ b/dev-python/pyout/pyout-0.7.3.ebuild
@@ -0,0 +1,35 @@
+# Copyright 1999-2022 Gentoo Authors
+# Distributed under the terms of the GNU General Public License v2
+
+EAPI=8
+
+DISTUTILS_USE_PEP517=setuptools
+PYTHON_COMPAT=( python3_{10..12} )
+inherit distutils-r1 pypi
+
+DESCRIPTION="Terminal styling for structured data"
+HOMEPAGE="https://github.com/pyout/pyout"
+#SRC_URI="https://github.com/pyout/pyout/archive/refs/tags/v${PV}.tar.gz -> ${P}.tar.gz"
+
+SLOT="0"
+LICENSE="MIT"
+KEYWORDS="~amd64 ~x86"
+
+RDEPEND="
+	dev-python/jsonschema[${PYTHON_USEDEP}]
+	dev-python/blessed[${PYTHON_USEDEP}]
+"
+DEPEND="
+	test? (
+		dev-python/pytest-timeout[${PYTHON_USEDEP}]
+	)
+"
+
+distutils_enable_tests pytest
+
+#PATCHES=( "${FILESDIR}/${PN}-0.7.2-blessed.patch"  )
+
+python_prepare_all() {
+	sed -i -e '/pytest-runner/d' setup.py || die
+	distutils-r1_python_prepare_all
+}
diff --git a/dev-python/pysolar/Manifest b/dev-python/pysolar/Manifest
index 0b453c83d..d353c6cbd 100644
--- a/dev-python/pysolar/Manifest
+++ b/dev-python/pysolar/Manifest
@@ -1 +1 @@
-DIST pysolar-0.5.tar.gz 1858367 BLAKE2B 034ddf4be458cfbb4cc43fd9b4ab3c265f0ae47d02a8d9b4956eaadf400a1c0e63a4f1e81aa27f6e195b8c81bb8c46fe8da0be12fb9c42506a5047b7e2eaf566 SHA512 0fc34de7ccf2afd02a05042e4d8dd2ecd165a0b968a2bb1f854e187e6bd00991256c4671a12db76249dfd579e4f9dae7e2ac9a11ccb7fc912a73b8305158ff71
+DIST pysolar-0.10.tar.gz 1569021 BLAKE2B f1f30b32030e6dda00635257b6d2cbc5d75bf8122f27db2db6c0471339b73f4123627b116008c262a7547b5ca7a0664318ad90a92d6d4fc0b53d65de708cde29 SHA512 bccb41874bb6f344a64db694b8ed81137ddaa7c0df9b6011192c3ce3acb4b8f4d934e70000d91ced005936c5e1751043a80ad96b5d262ebf1d96ee061326e114
diff --git a/dev-python/pysolar/metadata.xml b/dev-python/pysolar/metadata.xml
index 6776625c7..6b8874754 100644
--- a/dev-python/pysolar/metadata.xml
+++ b/dev-python/pysolar/metadata.xml
@@ -6,12 +6,12 @@
 		<name>Gentoo Astronomy Project</name>
 	</maintainer>
 	<longdescription lang="en">
-Pysolar is a collection of Python libraries for simulating the
-irradiation of any point on earth by the sun. It includes code for
-extremely precise ephemeris calculations, and more. Pysolar can
-calculate the location of the sun or the shading percentage as a
-function of time for a row of 2-axis tracked panels.
-</longdescription>
+		Pysolar is a collection of Python libraries for simulating the
+		irradiation of any point on earth by the sun. It includes code for
+		extremely precise ephemeris calculations, and more. Pysolar can
+		calculate the location of the sun or the shading percentage as a
+		function of time for a row of 2-axis tracked panels.
+	</longdescription>
 	<upstream>
 		<remote-id type="github">pingswept/pysolar</remote-id>
 	</upstream>
diff --git a/dev-python/pysolar/pysolar-0.10.ebuild b/dev-python/pysolar/pysolar-0.10.ebuild
new file mode 100644
index 000000000..0e11e7967
--- /dev/null
+++ b/dev-python/pysolar/pysolar-0.10.ebuild
@@ -0,0 +1,38 @@
+# Copyright 1999-2021 Gentoo Authors
+# Distributed under the terms of the GNU General Public License v2
+
+EAPI=8
+
+PYTHON_COMPAT=( python3_{10..11} )
+DISTUTILS_USE_PEP517=setuptools
+
+AUTHOR=pingswept
+
+inherit distutils-r1
+
+DESCRIPTION="Collection of Python libraries for simulating the irradiation by the sun"
+HOMEPAGE="https://pysolar.org/"
+SRC_URI="https://github.com/${AUTHOR}/${PN}/archive/${PV}.tar.gz -> ${P}.tar.gz"
+
+LICENSE="GPL-3"
+SLOT="0"
+KEYWORDS="~amd64 ~x86"
+
+# Still depends on nose
+RESTRICT="test"
+
+RDEPEND="
+	dev-python/numpy[${PYTHON_USEDEP}]
+	dev-python/pytz[${PYTHON_USEDEP}]
+	dev-python/scipy[${PYTHON_USEDEP}]
+"
+
+distutils_enable_tests pytest
+
+python_prepare_all() {
+	sed \
+		-e "s:'testsolar', ::" \
+		-e "s:'shade_test', ::" \
+		-i setup.py || die # don't install tests
+	distutils-r1_python_prepare_all
+}
diff --git a/dev-python/pysolar/pysolar-0.5.ebuild b/dev-python/pysolar/pysolar-0.5.ebuild
deleted file mode 100644
index ee3339a1f..000000000
--- a/dev-python/pysolar/pysolar-0.5.ebuild
+++ /dev/null
@@ -1,49 +0,0 @@
-# Copyright 1999-2014 Gentoo Foundation
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=5
-
-PYTHON_COMPAT=( python2_7 )
-
-AUTHOR=pingswept
-
-inherit distutils-r1 vcs-snapshot
-
-DESCRIPTION="Collection of Python libraries for simulating the irradiation by the sun"
-HOMEPAGE="http://pysolar.org/"
-SRC_URI="https://github.com/${AUTHOR}/${PN}/tarball/${PV} -> ${P}.tar.gz"
-
-LICENSE="GPL-3"
-SLOT="0"
-KEYWORDS="~amd64 ~x86 ~amd64-linux ~x86-linux"
-IUSE="doc"
-
-DEPEND="doc? ( dev-python/numpydoc )"
-RDEPEND="
-	dev-python/pillow[${PYTHON_USEDEP}]
-	dev-python/matplotlib[${PYTHON_USEDEP}]
-	dev-python/numpy[${PYTHON_USEDEP}]
-	dev-python/pygtk:2[${PYTHON_USEDEP}]
-	dev-python/pytz[${PYTHON_USEDEP}]
-	sci-libs/scipy[${PYTHON_USEDEP}]"
-
-python_prepare_all() {
-	sed \
-		-e "s:'testsolar', ::" \
-		-e "s:'shade_test', ::" \
-		-i setup.py || die # don't install tests
-	distutils-r1_python_prepare_all
-}
-
-python_compile_all() {
-	use doc && PYTHONPATH=".." emake -C doc html
-}
-
-python_test() {
-	${EPYTHON} Pysolar/testsolar.py || die
-}
-
-python_install_all() {
-	use doc && HTML_DOCS=( doc/.build/html/. )
-	distutils-r1_python_install_all
-}
diff --git a/dev-python/pytest-doctestplus/Manifest b/dev-python/pytest-doctestplus/Manifest
new file mode 100644
index 000000000..fa08cd21b
--- /dev/null
+++ b/dev-python/pytest-doctestplus/Manifest
@@ -0,0 +1 @@
+DIST pytest-doctestplus-0.12.1.tar.gz 36434 BLAKE2B 95baa9f6185423fdd3e61ec0c269de54a4cf3298f2db90087b1413608663e4200e48158240cf565c8cc267244fbf8d60a0a5241b3b8f1fa8c1187e34824b17ae SHA512 46b999abd5632fa5c5743900b8b78ee7b6be742959daeb85296ebdf820d7533cff0a78d1c8aed7f5d5a15436998b2f7fe3e571133be14fce056276900493fef9
diff --git a/dev-python/pytest-doctestplus/metadata.xml b/dev-python/pytest-doctestplus/metadata.xml
new file mode 100644
index 000000000..33e3f0e33
--- /dev/null
+++ b/dev-python/pytest-doctestplus/metadata.xml
@@ -0,0 +1,11 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
+<pkgmetadata>
+	<maintainer type="project">
+		<email>sci-astronomy@gentoo.org</email>
+		<name>Gentoo Astronomy Project</name>
+	</maintainer>
+	<upstream>
+		<remote-id type="pypi">pytest-doctestplus</remote-id>
+	</upstream>
+</pkgmetadata>
diff --git a/dev-python/pytest-doctestplus/pytest-doctestplus-0.12.1.ebuild b/dev-python/pytest-doctestplus/pytest-doctestplus-0.12.1.ebuild
new file mode 100644
index 000000000..89f6c46eb
--- /dev/null
+++ b/dev-python/pytest-doctestplus/pytest-doctestplus-0.12.1.ebuild
@@ -0,0 +1,41 @@
+# Copyright 1999-2022 Gentoo Authors
+# Distributed under the terms of the GNU General Public License v2
+
+EAPI=8
+
+PYTHON_COMPAT=( python3_{10..11} )
+DISTUTILS_USE_PEP517=setuptools
+PYPI_NO_NORMALIZE=1
+
+inherit distutils-r1 pypi
+
+DESCRIPTION="Pytest plugin with advanced doctest features"
+HOMEPAGE="https://astropy.org/"
+
+LICENSE="BSD"
+SLOT="0"
+KEYWORDS="~amd64 ~x86"
+
+RDEPEND="
+	dev-python/pytest[${PYTHON_USEDEP}]
+	dev-python/packaging[${PYTHON_USEDEP}]
+"
+
+BDEPEND="
+	dev-python/setuptools-scm[${PYTHON_USEDEP}]
+	test? (
+		dev-python/numpy[${PYTHON_USEDEP}]
+	)
+"
+
+# Skip the remote tests
+EPYTEST_DESELECT=(
+	tests/test_doctestplus.py::test_remote_data_url
+	tests/test_doctestplus.py::test_remote_data_float_cmp
+	tests/test_doctestplus.py::test_remote_data_ignore_whitespace
+	tests/test_doctestplus.py::test_remote_data_ellipsis
+	tests/test_doctestplus.py::test_remote_data_requires
+	tests/test_doctestplus.py::test_remote_data_ignore_warnings
+)
+
+distutils_enable_tests pytest
diff --git a/dev-python/python-gantt/Manifest b/dev-python/python-gantt/Manifest
new file mode 100644
index 000000000..607c0bbc8
--- /dev/null
+++ b/dev-python/python-gantt/Manifest
@@ -0,0 +1 @@
+DIST python-gantt-0.6.0_p20200809.tar.gz 32423 BLAKE2B e1e34276707d757e5c8386a75318863550dc7cabc1fa9cee161043ec757633819ac2efbd237b20d8497ce2b037aa72f44396dbcbd4c206f264eef4601985323a SHA512 62811ab5ac8aa26bdfa2ec10b621e1aeae84612e628be6555eb71548694dce4d474cc8d0bd56d5db8a40ffee4ac161c8aa11b7a250f8260df6a8175b3672e50b
diff --git a/dev-python/python-gantt/metadata.xml b/dev-python/python-gantt/metadata.xml
new file mode 100644
index 000000000..18071f943
--- /dev/null
+++ b/dev-python/python-gantt/metadata.xml
@@ -0,0 +1,19 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
+<pkgmetadata>
+	<maintainer type="person">
+		<email>gentoo@chymera.eu</email>
+		<name>Horea Christian</name>
+	</maintainer>
+	<maintainer type="project">
+		<email>sci@gentoo.org</email>
+		<name>Gentoo Science Project</name>
+	</maintainer>
+	<longdescription lang="en">
+		Python-Gantt makes it possible to easily draw gantt charts from Python
+		and export outputs as scalable vector graphics (SVG).
+	</longdescription>
+	<upstream>
+		<remote-id type="github">stefanSchinkel/gantt</remote-id>
+	</upstream>
+</pkgmetadata>
diff --git a/dev-python/python-gantt/python-gantt-0.6.0_p20200809.ebuild b/dev-python/python-gantt/python-gantt-0.6.0_p20200809.ebuild
new file mode 100644
index 000000000..b5fdf845b
--- /dev/null
+++ b/dev-python/python-gantt/python-gantt-0.6.0_p20200809.ebuild
@@ -0,0 +1,36 @@
+# Copyright 1999-2022 Gentoo Authors
+# Distributed under the terms of the GNU General Public License v2
+
+EAPI=8
+PYTHON_COMPAT=( python3_10 )
+
+inherit distutils-r1
+
+MY_HASH="2bdacef4d1f4d760f6c8b5397db56928ea223563"
+
+DESCRIPTION="Draw Gantt charts from Python"
+HOMEPAGE="https://pypi.org/project/python-gantt/"
+SRC_URI="https://github.com/stefanSchinkel/gantt/archive/${MY_HASH}.tar.gz -> ${P}.tar.gz"
+#SRC_URI="mirror://pypi/${PN:0:1}/${PN}/${P}.tar.gz"
+
+LICENSE="GPL-3"
+SLOT="0"
+KEYWORDS="~amd64 ~x86"
+
+DEPEND="test? ( >=dev-python/pytest-5.1.2[${PYTHON_USEDEP}] )"
+RDEPEND="
+	>=dev-python/matplotlib-3.0.3[${PYTHON_USEDEP}]
+	>=dev-python/numpy-1.16.3[${PYTHON_USEDEP}]
+	"
+
+S="${WORKDIR}/gantt-${MY_HASH}"
+
+python_prepare() {
+	sed -i\
+		-e "s/matplotlib==3.0.3/matplotlib/g"\
+		-e "s/numpy==1.16.3/numpy/g"\
+		setup.py || die
+	python_prepare_all
+}
+
+distutils_enable_tests pytest
diff --git a/dev-python/python-igraph/Manifest b/dev-python/python-igraph/Manifest
new file mode 100644
index 000000000..335664088
--- /dev/null
+++ b/dev-python/python-igraph/Manifest
@@ -0,0 +1 @@
+DIST igraph-0.10.4.tar.gz 4209850 BLAKE2B 2f3b75569ea93d08b50c4af7331a1e072d1ded66a6437d52ca054ee2603f60cbbec9371107d8c6eeda5a8215b0fa5ee6eac420dbda9247ab2246d70b01d25aa5 SHA512 675388c3a9a346534c66ec96f4a427b34e88e15a1d401af4f283ee7f1f17fad85bd1636a85af58b6d1969238b40e0314d7b6db4b84723e0eb1f3afbc660f0300
diff --git a/dev-python/python-igraph/metadata.xml b/dev-python/python-igraph/metadata.xml
new file mode 100644
index 000000000..4a86617fb
--- /dev/null
+++ b/dev-python/python-igraph/metadata.xml
@@ -0,0 +1,15 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
+<pkgmetadata>
+	<maintainer type="person">
+		<email>gentoo@aisha.cc</email>
+		<name>Aisha Tammy</name>
+	</maintainer>
+	<maintainer type="project">
+		<email>sci@gentoo.org</email>
+		<name>Gentoo Science Project</name>
+	</maintainer>
+	<upstream>
+		<remote-id type="pypi">python-igraph</remote-id>
+	</upstream>
+</pkgmetadata>
diff --git a/dev-python/python-igraph/python-igraph-0.10.4.ebuild b/dev-python/python-igraph/python-igraph-0.10.4.ebuild
new file mode 100644
index 000000000..3ee6e1eb4
--- /dev/null
+++ b/dev-python/python-igraph/python-igraph-0.10.4.ebuild
@@ -0,0 +1,50 @@
+# Copyright 1999-2021 Gentoo Authors
+# Distributed under the terms of the GNU General Public License v2
+
+EAPI=8
+
+PYTHON_COMPAT=( python3_{10..11} )
+DISTUTILS_USE_PEP517=setuptools
+inherit distutils-r1 pypi
+
+DESCRIPTION="Python interface for igraph"
+HOMEPAGE="https://igraph.org"
+SRC_URI="$(pypi_sdist_url igraph)"
+S="${WORKDIR}/igraph-${PV}"
+
+LICENSE="MIT"
+SLOT="0"
+KEYWORDS="~amd64"
+
+RDEPEND="
+	>=dev-libs/igraph-$(ver_cut 1-2)
+	>=dev-python/texttable-1.6.2[${PYTHON_USEDEP}]
+"
+DEPEND="${RDEPEND}"
+BDEPEND="
+	test? (
+		dev-python/cairocffi[${PYTHON_USEDEP}]
+		dev-python/matplotlib[${PYTHON_USEDEP}]
+		dev-python/networkx[${PYTHON_USEDEP}]
+		dev-python/numpy[${PYTHON_USEDEP}]
+		dev-python/pandas[${PYTHON_USEDEP}]
+		dev-python/plotly[${PYTHON_USEDEP}]
+		dev-python/scipy[${PYTHON_USEDEP}]
+	)
+"
+
+distutils_enable_tests pytest
+
+python_prepare_all() {
+	# fix the igraph include path
+	cd src || die
+	find -type f -name "*.h" -exec sed -i -e 's@#include <igraph@#include <igraph/igraph@g' {} + || die
+	find -type f -name "*.c" -exec sed -i -e 's@#include <igraph@#include <igraph/igraph@g' {} + || die
+	cd .. || die
+
+	distutils-r1_python_prepare_all
+}
+
+python_compile() {
+	distutils-r1_python_compile --use-pkg-config
+}
diff --git a/dev-python/python-ivi/Manifest b/dev-python/python-ivi/Manifest
deleted file mode 100644
index 64deacd7f..000000000
--- a/dev-python/python-ivi/Manifest
+++ /dev/null
@@ -1 +0,0 @@
-DIST python-ivi-0.14.9.tar.gz 209201 BLAKE2B 002c2282f84fe86e1dbe256fff4c78e8f801c864ec66214f5f16d493376b2569251d13cc30050a4f163143e019a31e833d141fb06dd1eca70a8693c992cbacea SHA512 60ddaaa66163374221530b6fb1ff19e1f5c0e9ac9051db6c95c34cdd6dc1b96279dd42c7f022ef1025852c9cd0277f94fa3a2f2bc73c621842cc1a4dba555e4d
diff --git a/dev-python/python-ivi/metadata.xml b/dev-python/python-ivi/metadata.xml
deleted file mode 100644
index 0b9069525..000000000
--- a/dev-python/python-ivi/metadata.xml
+++ /dev/null
@@ -1,21 +0,0 @@
-<?xml version="1.0" encoding="UTF-8"?>
-<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
-<pkgmetadata>
-	<maintainer type="person">
-		<email>marbre@linux.sungazer.de</email>
-		<name>Marius Brehler</name>
-	</maintainer>
-	<maintainer type="project">
-		<email>sci@gentoo.org</email>
-		<name>Gentoo Science Project</name>
-	</maintainer>
-	<longdescription>
-Python IVI is a Python-based interpretation of the Interchangeable
-Virtual Instrument standard from the IVI foundation. Python IVI can
-use Python VXI-11, Python USBTMC, PyVISA, pySerial and linux-gpib to
-connect to instruments.
-</longdescription>
-	<upstream>
-		<remote-id type="github">python-ivi/python-ivi</remote-id>
-	</upstream>
-</pkgmetadata>
diff --git a/dev-python/python-ivi/python-ivi-0.14.9.ebuild b/dev-python/python-ivi/python-ivi-0.14.9.ebuild
deleted file mode 100644
index 842bef44e..000000000
--- a/dev-python/python-ivi/python-ivi-0.14.9.ebuild
+++ /dev/null
@@ -1,23 +0,0 @@
-# Copyright 1999-2016 Gentoo Foundation
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=6
-PYTHON_COMPAT=( python2_7 python{3_4,3_5} )
-
-inherit distutils-r1
-
-DESCRIPTION="Python-based interpretation of the Interchangeable Virtual Instrument standard"
-HOMEPAGE="https://github.com/python-ivi/python-ivi"
-SRC_URI="https://github.com/${PN}/${PN}/archive/v${PV}.tar.gz -> ${P}.tar.gz"
-
-LICENSE="MIT"
-SLOT="0"
-KEYWORDS="~amd64"
-
-RDEPEND="
-	|| (
-		dev-python/python-vxi11[${PYTHON_USEDEP}]
-		sci-libs/linux-gpib
-	)
-	dev-python/numpy[${PYTHON_USEDEP}]"
-DEPEND="${RDEPEND}"
diff --git a/dev-python/python-ivi/python-ivi-9999.ebuild b/dev-python/python-ivi/python-ivi-9999.ebuild
deleted file mode 100644
index 1820ab353..000000000
--- a/dev-python/python-ivi/python-ivi-9999.ebuild
+++ /dev/null
@@ -1,22 +0,0 @@
-# Copyright 1999-2016 Gentoo Foundation
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=6
-PYTHON_COMPAT=( python2_7 python{3_4,3_5} )
-
-inherit distutils-r1 git-r3
-
-DESCRIPTION="Python-based interpretation of the Interchangeable Virtual Instrument standard"
-HOMEPAGE="https://github.com/python-ivi/python-ivi"
-EGIT_REPO_URI="https://github.com/${PN}/${PN}.git git://github.com/${PN}/${PN}.git"
-
-LICENSE="MIT"
-SLOT="0"
-
-RDEPEND="
-	|| (
-		dev-python/python-vxi11[${PYTHON_USEDEP}]
-		sci-libs/linux-gpib
-	)
-	dev-python/numpy[${PYTHON_USEDEP}]"
-DEPEND="${RDEPEND}"
diff --git a/dev-python/python-vxi11/Manifest b/dev-python/python-vxi11/Manifest
deleted file mode 100644
index d2928e820..000000000
--- a/dev-python/python-vxi11/Manifest
+++ /dev/null
@@ -1 +0,0 @@
-DIST python-vxi11-0.8.tar.gz 19664 BLAKE2B 0bcdce1d1384ea1e40b71265a46fcf6f1c5e8cfbb947695c82a133edddf3b1b19d5c80b80b9a336c6ea16801949220a856f251f350346efaa71cee24ec8e4860 SHA512 fbd2bf54d161527135d7f7739cf3921f31173511da30078042c02dabc28ef61fafa296eb65d4908e0f6559fd08604c690c91e27564041186a4d7892940658f3f
diff --git a/dev-python/python-vxi11/metadata.xml b/dev-python/python-vxi11/metadata.xml
deleted file mode 100644
index 80031f312..000000000
--- a/dev-python/python-vxi11/metadata.xml
+++ /dev/null
@@ -1,20 +0,0 @@
-<?xml version="1.0" encoding="UTF-8"?>
-<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
-<pkgmetadata>
-	<maintainer type="person">
-		<email>marbre@linux.sungazer.de</email>
-		<name>Marius Brehler</name>
-	</maintainer>
-	<maintainer type="project">
-		<email>sci@gentoo.org</email>
-		<name>Gentoo Science Project</name>
-	</maintainer>
-	<longdescription>
-Python VXI-11 is a Python implementation of the VXI-11 Ethernet
-instrument control protocol. It is compatible with VXI-11,
-LXI instruments and VXI-11 to GPIB bridges (HP E2050A, etc.).
-</longdescription>
-	<upstream>
-		<remote-id type="github">python-ivi/python-vxi11</remote-id>
-	</upstream>
-</pkgmetadata>
diff --git a/dev-python/python-vxi11/python-vxi11-0.8.ebuild b/dev-python/python-vxi11/python-vxi11-0.8.ebuild
deleted file mode 100644
index 0c4b25d06..000000000
--- a/dev-python/python-vxi11/python-vxi11-0.8.ebuild
+++ /dev/null
@@ -1,15 +0,0 @@
-# Copyright 1999-2016 Gentoo Foundation
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=6
-PYTHON_COMPAT=( python2_7 python{3_4,3_5} )
-
-inherit distutils-r1
-
-DESCRIPTION="Provides a pure Python VXI-11 driver for controlling instruments over Ethernet"
-HOMEPAGE="https://github.com/python-ivi/python-vxi11"
-SRC_URI="https://github.com/python-ivi/${PN}/archive/v${PV}.tar.gz -> ${P}.tar.gz"
-
-LICENSE="MIT"
-SLOT="0"
-KEYWORDS="~amd64"
diff --git a/dev-python/python-vxi11/python-vxi11-9999.ebuild b/dev-python/python-vxi11/python-vxi11-9999.ebuild
deleted file mode 100644
index f0da2f343..000000000
--- a/dev-python/python-vxi11/python-vxi11-9999.ebuild
+++ /dev/null
@@ -1,14 +0,0 @@
-# Copyright 1999-2016 Gentoo Foundation
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=6
-PYTHON_COMPAT=( python2_7 python{3_4,3_5} )
-
-inherit distutils-r1 git-r3
-
-DESCRIPTION="Provides a pure Python VXI-11 driver for controlling instruments over Ethernet"
-HOMEPAGE="https://github.com/python-ivi/python-vxi11"
-EGIT_REPO_URI="https://github.com/python-ivi/${PN}.git git://github.com/python-ivi/${PN}.git"
-
-LICENSE="MIT"
-SLOT="0"
\ No newline at end of file
diff --git a/dev-python/pythoncgns/Manifest b/dev-python/pythoncgns/Manifest
deleted file mode 100644
index 7381ba937..000000000
--- a/dev-python/pythoncgns/Manifest
+++ /dev/null
@@ -1 +0,0 @@
-DIST CGNS-2009.10.30.tar.gz 24185 BLAKE2B 042c8d1e12065ac316eec46e60bf1a32061ba977526c8777c775366cbdc9fe473c6e5f2d51bd73eef29840833e383f16c99f05f0effe7ba5ead51e6c5a9b87d3 SHA512 01aa7980ed95c39f9f925cd3a6acff1a28419fbf07e5c4163dd5c35263aa0a6b08eec985ab081bddc9d45ef4c799aed997d613229a9f2c926df141aef7c7e082
diff --git a/dev-python/pythoncgns/metadata.xml b/dev-python/pythoncgns/metadata.xml
deleted file mode 100644
index ba0b86026..000000000
--- a/dev-python/pythoncgns/metadata.xml
+++ /dev/null
@@ -1,11 +0,0 @@
-<?xml version="1.0" encoding="UTF-8"?>
-<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
-<pkgmetadata>
-	<maintainer type="project">
-		<email>sci@gentoo.org</email>
-		<name>Gentoo Science Project</name>
-	</maintainer>
-	<upstream>
-		<remote-id type="pypi">CGNS</remote-id>
-	</upstream>
-</pkgmetadata>
diff --git a/dev-python/pythoncgns/pythoncgns-2009.10.30.ebuild b/dev-python/pythoncgns/pythoncgns-2009.10.30.ebuild
deleted file mode 100644
index 2365f31e6..000000000
--- a/dev-python/pythoncgns/pythoncgns-2009.10.30.ebuild
+++ /dev/null
@@ -1,26 +0,0 @@
-# Copyright 1999-2014 Gentoo Foundation
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=5
-
-PYTHON_COMPAT=( python2_7 )
-
-inherit distutils-r1
-
-MY_PN="CGNS"
-MY_P="${MY_PN}-${PV}"
-
-DESCRIPTION="Python language bindings for the CGNS library"
-HOMEPAGE="http://pypi.python.org/pypi/CGNS/"
-SRC_URI="mirror://pypi/C/${MY_PN}/${MY_P}.tar.gz"
-
-LICENSE="GPL-3"
-KEYWORDS="~amd64 ~x86"
-SLOT="0"
-IUSE=""
-
-RDEPEND="sci-libs/cgnslib"
-DEPEND="${RDEPEND}
-	dev-lang/swig"
-
-S="${WORKDIR}/${MY_P}"
diff --git a/dev-python/pyvcf/Manifest b/dev-python/pyvcf/Manifest
deleted file mode 100644
index 8ab357349..000000000
--- a/dev-python/pyvcf/Manifest
+++ /dev/null
@@ -1 +0,0 @@
-DIST pyvcf-0.6.8.tar.gz 34961 BLAKE2B 4176ae6c48ce057d84f980c6257ecf82d652f9ee36e4855cd87227c687d20ba2f474a561871de1b114f676973ef8dc8ba758fabc60d7721e0cf11616066401ff SHA512 adf08769422bf198bb017be43082d0bf3e08c5c4ba06380ed9b08e60dd9a3289ca966b9cd4a534168dfcd668d25284029920af84cc09bed9d764b87ce9b2b548
diff --git a/dev-python/pyvcf/metadata.xml b/dev-python/pyvcf/metadata.xml
deleted file mode 100644
index 138cb7705..000000000
--- a/dev-python/pyvcf/metadata.xml
+++ /dev/null
@@ -1,12 +0,0 @@
-<?xml version="1.0" encoding="UTF-8"?>
-<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
-<pkgmetadata>
-	<maintainer type="person">
-		<email>mmokrejs@fold.natur.cuni.cz</email>
-		<name>Martin Mokrejs</name>
-	</maintainer>
-	<maintainer type="project">
-		<email>sci-biology@gentoo.org</email>
-		<name>Gentoo Biology Project</name>
-	</maintainer>
-</pkgmetadata>
diff --git a/dev-python/pyvcf/pyvcf-0.6.8.ebuild b/dev-python/pyvcf/pyvcf-0.6.8.ebuild
deleted file mode 100644
index 5f2fde4a9..000000000
--- a/dev-python/pyvcf/pyvcf-0.6.8.ebuild
+++ /dev/null
@@ -1,22 +0,0 @@
-# Copyright 1999-2017 Gentoo Foundation
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=6
-
-PYTHON_COMPAT=( python2_7 python3_5 )
-inherit distutils-r1
-
-DESCRIPTION="Work with VCF files in python"
-HOMEPAGE="https://pypi.python.org/pypi/PyVCF"
-SRC_URI="https://pypi.python.org/packages/20/b6/36bfb1760f6983788d916096193fc14c83cce512c7787c93380e09458c09/PyVCF-${PV}.tar.gz -> ${P}.tar.gz"
-
-LICENSE="pyvcf"
-SLOT="0"
-KEYWORDS="~amd64 ~x86"
-IUSE=""
-
-DEPEND=">=sci-biology/pysam-0.8.0
-	dev-python/cython"
-RDEPEND="${DEPEND}"
-
-S="${WORKDIR}"/PyVCF-"${PV}"
diff --git a/dev-python/pyvista/Manifest b/dev-python/pyvista/Manifest
new file mode 100644
index 000000000..0fa9b89d4
--- /dev/null
+++ b/dev-python/pyvista/Manifest
@@ -0,0 +1 @@
+DIST pyvista-0.33.2.tar.gz 1383071 BLAKE2B bebd90489ac37566dc9f9161ce9348d48bc758c8dfe6ffa4f7d3085061f49db30dcc515d4a2c6f470150667f23e498a165f8492391b42115556b17868d684865 SHA512 bf6a6d921bcb5f86e4fb05c42ff50d90cb24800d930bd41d7d13b112b476dcaf6888d598354ca50e58313e05682a92160dbdfe633955f48f8895d464669aeb59
diff --git a/dev-python/pyvista/metadata.xml b/dev-python/pyvista/metadata.xml
new file mode 100644
index 000000000..0137fea97
--- /dev/null
+++ b/dev-python/pyvista/metadata.xml
@@ -0,0 +1,13 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
+<pkgmetadata>
+	<maintainer type="project">
+		<email>sci@gentoo.org</email>
+		<name>Gentoo Science Project</name>
+	</maintainer>
+	<stabilize-allarches/>
+	<upstream>
+		<remote-id type="pypi">pyvista</remote-id>
+		<remote-id type="github">pyvista/pyvista</remote-id>
+	</upstream>
+</pkgmetadata>
diff --git a/dev-python/pyvista/pyvista-0.33.2.ebuild b/dev-python/pyvista/pyvista-0.33.2.ebuild
new file mode 100644
index 000000000..d59653fae
--- /dev/null
+++ b/dev-python/pyvista/pyvista-0.33.2.ebuild
@@ -0,0 +1,27 @@
+# Copyright 1999-2023 Gentoo Authors
+# Distributed under the terms of the GNU General Public License v2
+
+EAPI=8
+
+PYTHON_COMPAT=( python3_{10..10} )
+DISTUTILS_SINGLE_IMPL=1  # because "sci-libs/vtk" inherits "python-single-r1"
+inherit distutils-r1 pypi
+
+DESCRIPTION="Easier Pythonic interface to VTK"
+HOMEPAGE="https://docs.pyvista.org"
+
+LICENSE="MIT"
+KEYWORDS="~amd64 ~x86"
+SLOT="0"
+
+RDEPEND="
+	sci-libs/vtk[python,imaging,rendering,views,${PYTHON_SINGLE_USEDEP}]
+	$(python_gen_cond_dep '
+		dev-python/appdirs[${PYTHON_USEDEP}]
+		dev-python/imageio[${PYTHON_USEDEP}]
+		dev-python/numpy[${PYTHON_USEDEP}]
+		dev-python/pillow[${PYTHON_USEDEP}]
+		>=dev-python/scooby-0.5.1[${PYTHON_USEDEP}]
+	')
+"
+DEPEND="${RDEPEND}"
diff --git a/dev-python/pyviz_comms/Manifest b/dev-python/pyviz_comms/Manifest
new file mode 100644
index 000000000..0d6a5ac51
--- /dev/null
+++ b/dev-python/pyviz_comms/Manifest
@@ -0,0 +1 @@
+DIST pyviz_comms-2.2.0.tar.gz 31910 BLAKE2B 42175d8750e9cb8dea4888970028898a9ee1e34b2ca5c895d2a1db40d9eec2f7eb86aec41090431b723ffcfdd0411016c04015e286d467a4c9d89eb710e7e08c SHA512 de6dba5b5d93a9a496b6895f4bf884dd80afd4124e1519bbd243b7672827f04f51d353f3941678be3780a250640e03b0c4ea0a3f87b8b9892980845bdca07439
diff --git a/dev-python/pyviz_comms/metadata.xml b/dev-python/pyviz_comms/metadata.xml
new file mode 100644
index 000000000..3a0ec5dc8
--- /dev/null
+++ b/dev-python/pyviz_comms/metadata.xml
@@ -0,0 +1,13 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
+<pkgmetadata>
+	<maintainer type="project">
+		<email>sci@gentoo.org</email>
+		<name>Gentoo Science Project</name>
+	</maintainer>
+	<stabilize-allarches/>
+	<upstream>
+		<remote-id type="pypi">pyviz-comms</remote-id>
+		<remote-id type="github">holoviz/pyviz_comms</remote-id>
+	</upstream>
+</pkgmetadata>
diff --git a/dev-python/pyviz_comms/pyviz_comms-2.2.0.ebuild b/dev-python/pyviz_comms/pyviz_comms-2.2.0.ebuild
new file mode 100644
index 000000000..7f50fc279
--- /dev/null
+++ b/dev-python/pyviz_comms/pyviz_comms-2.2.0.ebuild
@@ -0,0 +1,20 @@
+# Copyright 1999-2023 Gentoo Authors
+# Distributed under the terms of the GNU General Public License v2
+
+EAPI=8
+
+PYTHON_COMPAT=( python3_{10..11} )
+inherit distutils-r1 pypi
+
+DESCRIPTION="Bidirectional communication for the HoloViz ecosystem"
+HOMEPAGE="https://holoviz.org"
+
+LICENSE="BSD"
+SLOT="0"
+KEYWORDS="~amd64 ~x86"
+
+RDEPEND="dev-python/param[${PYTHON_USEDEP}]"
+
+# Tarballs do not include tests, reported upstream:
+# https://github.com/holoviz/pyviz_comms/issues/104
+#distutils_enable_tests pytest
diff --git a/dev-python/pyvote/Manifest b/dev-python/pyvote/Manifest
new file mode 100644
index 000000000..1dbafe013
--- /dev/null
+++ b/dev-python/pyvote/Manifest
@@ -0,0 +1 @@
+DIST pyvote-0.1.tar.gz 17689 BLAKE2B 67f97f265995203fb1cdc69947b73c664c96668a1e11b573efe87874023d4f77554abb93310477fe22155cc759248c55a1d2204cad2a85e52a297d25bc93fcbe SHA512 be6a0b5aa71ef4e151a5d95411c8614d956217d71ab53d3b0ff3f1a209c7980efa87545ab234465b6411daa1d9b63722670500323aff55e27240cc1d5ce8aa88
diff --git a/dev-python/pyvote/metadata.xml b/dev-python/pyvote/metadata.xml
new file mode 100644
index 000000000..5fbf687f3
--- /dev/null
+++ b/dev-python/pyvote/metadata.xml
@@ -0,0 +1,22 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
+<pkgmetadata>
+	<maintainer type="person">
+		<email>gentoo@chymera.eu</email>
+		<name>Horea Christian</name>
+	</maintainer>
+	<maintainer type="project">
+		<email>sci@gentoo.org</email>
+		<name>Gentoo Science Project</name>
+	</maintainer>
+	<longdescription lang="en">
+		This package provides a Python module and a Bash interface which can
+		compute the probability of a 2-choice popular election being decided by
+		one vote. Predictions are based on either a series of forecasts, a beta
+		(or normal) probability density function for outcomes, or a fixed
+		outcome probability.
+	</longdescription>
+	<upstream>
+		<remote-id type="github">TheChymera/pyvote</remote-id>
+	</upstream>
+</pkgmetadata>
diff --git a/dev-python/pyvote/pyvote-0.1.ebuild b/dev-python/pyvote/pyvote-0.1.ebuild
new file mode 100644
index 000000000..95d95cb1b
--- /dev/null
+++ b/dev-python/pyvote/pyvote-0.1.ebuild
@@ -0,0 +1,22 @@
+# Copyright 1999-2022 Gentoo Authors
+# Distributed under the terms of the GNU General Public License v2
+
+EAPI=8
+
+PYTHON_COMPAT=( python3_10 )
+
+inherit distutils-r1
+
+DESCRIPTION="Estimate the probability of votes changing election outcomes"
+HOMEPAGE="https://github.com/TheChymera/pyvote.git"
+SRC_URI="https://github.com/TheChymera/pyvote/archive/${PV}.tar.gz -> ${P}.tar.gz"
+
+LICENSE="GPL-3"
+SLOT="0"
+KEYWORDS="~amd64 ~x86"
+
+RDEPEND="
+	dev-python/argh[${PYTHON_USEDEP}]
+	dev-python/mpmath[${PYTHON_USEDEP}]
+	dev-python/numpy[${PYTHON_USEDEP}]
+"
diff --git a/dev-python/pywcsgrid2/metadata.xml b/dev-python/pywcsgrid2/metadata.xml
deleted file mode 100644
index c240a7553..000000000
--- a/dev-python/pywcsgrid2/metadata.xml
+++ /dev/null
@@ -1,14 +0,0 @@
-<?xml version="1.0" encoding="UTF-8"?>
-<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
-<pkgmetadata>
-	<maintainer type="project">
-		<email>sci-astronomy@gentoo.org</email>
-		<name>Gentoo Astronomy Project</name>
-	</maintainer>
-	<longdescription lang="en">
-pywcsgrid2 provides a custom Axes class (derived from matplotlib's
-original Axes class) suitable for displaying fits images. Its main
-functionality is to draw ticks, ticklabels, and grids in an
-appropriate sky coordinates.
-</longdescription>
-</pkgmetadata>
diff --git a/dev-python/pywcsgrid2/pywcsgrid2-9999.ebuild b/dev-python/pywcsgrid2/pywcsgrid2-9999.ebuild
deleted file mode 100644
index d544c5cfa..000000000
--- a/dev-python/pywcsgrid2/pywcsgrid2-9999.ebuild
+++ /dev/null
@@ -1,23 +0,0 @@
-# Copyright 1999-2015 Gentoo Foundation
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=5
-
-PYTHON_COMPAT=( python2_7 python3_{3,4} )
-
-inherit distutils-r1 git-r3
-
-DESCRIPTION="Custom Matplotlib Axes class for displaying astronomical fits images"
-HOMEPAGE="http://leejjoon.github.io/pywcsgrid2/"
-EGIT_REPO_URI="https://github.com/leejjoon/pywcsgrid2.git"
-
-LICENSE="MIT"
-SLOT="0"
-KEYWORDS=""
-IUSE=""
-
-RDEPEND="
-	dev-python/astropy[${PYTHON_USEDEP}]
-	dev-python/numpy[${PYTHON_USEDEP}]
-	dev-python/matplotlib[${PYTHON_USEDEP}]"
-DEPEND="${RDEPEND}"
diff --git a/dev-python/pyzo/Manifest b/dev-python/pyzo/Manifest
new file mode 100644
index 000000000..781107b6f
--- /dev/null
+++ b/dev-python/pyzo/Manifest
@@ -0,0 +1 @@
+DIST pyzo-4.12.7.gh.tar.gz 2280468 BLAKE2B c71e29730c677cc0e75a16a10f752b26dd5675ab978493e98049a3cb6ff51449e554c22d9b171ade7e96d8908fcf4b09842c9107d09cbfee2b4e488a3ef3ed28 SHA512 974e4166227afb42ffb950f0abd8733264e57fbf5cb1c23fc72f76a41940be5cf7cc9bc39bc93353ce392aaf204a420853e62313c139814771fff92729dbe032
diff --git a/dev-python/pyzo/metadata.xml b/dev-python/pyzo/metadata.xml
new file mode 100644
index 000000000..8019eb9d1
--- /dev/null
+++ b/dev-python/pyzo/metadata.xml
@@ -0,0 +1,11 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
+<pkgmetadata>
+	<maintainer type="project">
+		<email>sci@gentoo.org</email>
+		<name>Gentoo Science Project</name>
+	</maintainer>
+	<upstream>
+		<remote-id type="github">pyzo/pyzo</remote-id>
+	</upstream>
+</pkgmetadata>
diff --git a/dev-python/pyzo/pyzo-4.12.7.ebuild b/dev-python/pyzo/pyzo-4.12.7.ebuild
new file mode 100644
index 000000000..f65ebcc7d
--- /dev/null
+++ b/dev-python/pyzo/pyzo-4.12.7.ebuild
@@ -0,0 +1,67 @@
+# Copyright 1999-2021 Gentoo Authors
+# Distributed under the terms of the GNU General Public License v2
+
+EAPI=8
+
+PYTHON_COMPAT=( python3_{10..11} )
+DISTUTILS_USE_PEP517=setuptools
+
+inherit distutils-r1 virtualx desktop xdg
+
+DESCRIPTION="The Python IDE for scientific computing"
+HOMEPAGE="https://pyzo.org/"
+SRC_URI="https://github.com/${PN}/${PN}/archive/refs/tags/v${PV}.tar.gz -> ${P}.gh.tar.gz"
+
+LICENSE="BSD-2"
+SLOT="0"
+KEYWORDS="~amd64"
+
+# For some reason this requires network access
+# Qt: Session management error: Could not open network socket
+PROPERTIES="test_network"
+RESTRICT="test"
+
+RDEPEND="
+	dev-python/QtPy[${PYTHON_USEDEP}]
+"
+BDEPEND="
+	dev-python/packaging[${PYTHON_USEDEP}]
+	test? (
+		dev-python/visvis[${PYTHON_USEDEP}]
+	)
+"
+
+distutils_enable_tests pytest
+distutils_enable_sphinx doc
+
+python_prepare_all() {
+	# Use relative path to avoid access violation
+	# Do not install the license file, install other data_files manually
+	sed -i \
+		-e 's:/usr/share/metainfo:share/metainfo:g' \
+		-e '/LICENSE.md/d' \
+		setup.py || die
+
+	distutils-r1_python_prepare_all
+}
+
+python_test() {
+	virtx epytest
+}
+
+python_install() {
+	 distutils-r1_python_install
+	 python_doscript pyzolauncher.py
+}
+
+python_install_all() {
+	insinto /usr/share/metainfo/
+	doins pyzo.appdata.xml
+
+	for size in 16 32 48 64 128; do
+		newicon -s ${size} "${PN}/resources/appicons/pyzologo${size}.png" pyzologo.png
+	done
+	domenu "${PN}/resources/${PN}.desktop"
+
+	distutils-r1_python_install_all
+}
diff --git a/dev-python/qtconsole/metadata.xml b/dev-python/qtconsole/metadata.xml
deleted file mode 100644
index d90e4df14..000000000
--- a/dev-python/qtconsole/metadata.xml
+++ /dev/null
@@ -1,12 +0,0 @@
-<?xml version="1.0" encoding="UTF-8"?>
-<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
-<pkgmetadata>
-	<maintainer type="project">
-		<email>sci@gentoo.org</email>
-		<name>Gentoo Science Project</name>
-	</maintainer>
-	<longdescription>
-A rich Qt-based console for working with Jupyter kernels,
-supporting rich media output, session export, and more.
-</longdescription>
-</pkgmetadata>
diff --git a/dev-python/qtconsole/qtconsole-9999.ebuild b/dev-python/qtconsole/qtconsole-9999.ebuild
deleted file mode 100644
index 6d023675b..000000000
--- a/dev-python/qtconsole/qtconsole-9999.ebuild
+++ /dev/null
@@ -1,67 +0,0 @@
-# Copyright 1999-2017 Gentoo Foundation
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=6
-
-PYTHON_COMPAT=( python2_7 python3_{4,5} )
-PYTHON_REQ_USE="threads(+)"
-
-inherit distutils-r1 git-r3
-
-DESCRIPTION="Qt-based console for Jupyter with support for rich media output"
-HOMEPAGE="http://jupyter.org"
-EGIT_REPO_URI="https://github.com/jupyter/${PN}.git git://github.com/jupyter/${PN}.git"
-
-LICENSE="BSD"
-SLOT="0"
-KEYWORDS=""
-IUSE="doc test"
-
-RDEPEND="
-	dev-python/ipykernel[${PYTHON_USEDEP}]
-	>=dev-python/jupyter_client-4.1.1[${PYTHON_USEDEP}]
-	"
-DEPEND="${RDEPEND}
-	doc? (
-		>=dev-python/ipython-4.0.0-r2[${PYTHON_USEDEP}]
-		>=dev-python/sphinx-1.3.1-r1[${PYTHON_USEDEP}]
-	)
-	test? (
-		>=dev-python/nose-0.10.1[${PYTHON_USEDEP}]
-	)
-	|| (
-		dev-python/pyside[${PYTHON_USEDEP},svg]
-		dev-python/PyQt4[${PYTHON_USEDEP},svg]
-		dev-python/PyQt5[${PYTHON_USEDEP},svg]
-	)
-	dev-python/pygments[${PYTHON_USEDEP}]
-	>=dev-python/pyzmq-13[${PYTHON_USEDEP}]
-	"
-PDEPEND="dev-python/ipython[${PYTHON_USEDEP}]"
-
-python_prepare_all() {
-	# Prevent un-needed download during build
-	if use doc; then
-		sed -e "/^    'sphinx.ext.intersphinx',/d" -i docs/source/conf.py || die
-	fi
-
-	distutils-r1_python_prepare_all
-}
-
-python_compile_all() {
-	use doc && emake -C docs html
-}
-
-python_test() {
-	# jupyter qtconsole --generate-config ... jupyter-qtconsole: cannot connect to X server
-	# ERROR
-	sed \
-		-e 's:test_generate_config:_&:g' \
-		-i qtconsole/tests/test_app.py || die
-	virtx nosetests --verbosity=2 qtconsole
-}
-
-python_install_all() {
-	use doc && HTML_DOCS=( docs/build/html/. )
-	distutils-r1_python_install_all
-}
diff --git a/dev-python/rasterio/Manifest b/dev-python/rasterio/Manifest
new file mode 100644
index 000000000..a87aed058
--- /dev/null
+++ b/dev-python/rasterio/Manifest
@@ -0,0 +1 @@
+DIST rasterio-1.2.10.tar.gz 12888995 BLAKE2B e6e4e55ae2fc7c10839625331f52a3366815672412dee7ee2332d32ce842c35ebbbb81e446d03a92a1cb6f877ecc377de1509d2d8c857ab7034dd246996b0318 SHA512 97559778163a36982b733137f6b5a879649c9591583cf80ccb38739f6565bf65c6b198d499242811ebb7342a3a4ef3756451bc3c7d1b431f8d1e568c6bae41d5
diff --git a/dev-python/rasterio/metadata.xml b/dev-python/rasterio/metadata.xml
new file mode 100644
index 000000000..88f92bb1c
--- /dev/null
+++ b/dev-python/rasterio/metadata.xml
@@ -0,0 +1,18 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<!DOCTYPE pkgmetadata SYSTEM "https://www.gentoo.org/dtd/metadata.dtd">
+<pkgmetadata>
+  <maintainer type="project">
+    <email>sci@gentoo.org</email>
+    <name>Gentoo Science Project</name>
+  </maintainer>
+  <longdescription lang="en">
+  Rasterio reads and writes geospatial raster data. Geographic information 
+  systems use GeoTIFF and other formats to organize and store gridded, 
+  or raster, datasets. Rasterio reads and writes these formats and 
+  provides a Python API based on N-D arrays.
+</longdescription>
+  <upstream>
+    <remote-id type="github">rasterio/rasterio</remote-id>
+    <remote-id type="pypi">rasterio</remote-id>
+  </upstream>
+</pkgmetadata>
diff --git a/dev-python/rasterio/rasterio-1.2.10-r1.ebuild b/dev-python/rasterio/rasterio-1.2.10-r1.ebuild
new file mode 100644
index 000000000..c2aa347f1
--- /dev/null
+++ b/dev-python/rasterio/rasterio-1.2.10-r1.ebuild
@@ -0,0 +1,109 @@
+# Copyright 1999-2022 Gentoo Authors
+# Distributed under the terms of the GNU General Public License v2
+
+EAPI=8
+
+PYTHON_COMPAT=( python3_10 )
+DISTUTILS_USE_PEP517="setuptools"
+inherit distutils-r1
+
+DESCRIPTION="Command line tool and API for geospatial raster data"
+HOMEPAGE="https://github.com/rasterio/rasterio"
+SRC_URI="https://github.com/rasterio/${PN}/archive/refs/tags/${PV}.tar.gz -> ${P}.tar.gz"
+
+LICENSE="BSD"
+SLOT="0"
+KEYWORDS="~amd64 ~x86"
+
+RDEPEND="
+	sci-libs/gdal:=[aux-xml(+),jpeg,png,threads(+)]
+	dev-python/affine[${PYTHON_USEDEP}]
+	dev-python/attrs[${PYTHON_USEDEP}]
+	dev-python/certifi[${PYTHON_USEDEP}]
+	dev-python/click[${PYTHON_USEDEP}]
+	dev-python/cligj[${PYTHON_USEDEP}]
+	dev-python/numpy[${PYTHON_USEDEP}]
+	dev-python/click-plugins[${PYTHON_USEDEP}]
+	dev-python/snuggs[${PYTHON_USEDEP}]
+"
+
+#DEPEND="${RDEPEND}"
+BDEPEND="
+	dev-python/cython[${PYTHON_USEDEP}]
+	test? (
+		dev-python/boto3[${PYTHON_USEDEP}]
+		dev-python/hypothesis[${PYTHON_USEDEP}]
+		dev-python/shapely[${PYTHON_USEDEP}]
+		sci-libs/gdal:=[aux-xml(+),jpeg,png,threads(+)]
+	)
+"
+
+distutils_enable_tests pytest
+
+python_test() {
+	local deselect=(
+		# disable tests failing for unknown reason
+		tests/test_env.py::test_rio_env_no_credentials
+		tests/test_rio_info.py::test_info_azure_unsigned
+
+		tests/test__env.py::test_search_debian_gdal_data
+		tests/test__env.py::test_search_gdal_data_debian
+		tests/test_warp.py::test_reproject_resampling[Resampling.cubic]
+		tests/test_warp.py::test_reproject_resampling[Resampling.lanczos]
+		tests/test_warp.py::test_reproject_resampling_alpha[Resampling.cubic]
+		tests/test_warp.py::test_reproject_resampling_alpha[Resampling.lanczos]
+
+		#tests/test_warp.py::test_warp_from_to_file_multi
+
+		# aux-xml
+		#tests/test_dataset.py::test_files
+		#tests/test_gcps.py::test_write_read_gcps_buffereddatasetwriter
+		#tests/test_rio_edit_info.py::test_delete_nodata
+		#tests/test_update.py::test_update_nodatavals_none
+
+		# curl
+		#tests/test_warp.py::test_reproject_error_propagation
+
+		# geos
+		#tests/test_warp.py::test_transform_geom_polygon_offset
+		#tests/test_warp.py::test_transform_geom_polygon_cutting
+
+		# png
+		#tests/test_colormap.py::test_write_colormap
+		#tests/test_no_georef.py::test_write
+		#tests/test_png.py::test_write_ubyte
+		#tests/test_rio_convert.py::test_autodetect_format
+		#tests/test_rio_merge.py::test_merge_output_dataset
+		#tests/test_shutil.py::test_delete[None-png]
+		#tests/test_shutil.py::test_delete[PNG-png]
+		#tests/test_write.py::test_write__autodetect_driver[png-PNG]
+		#tests/test_write.py::test_issue2088[PNG]
+
+		# jpeg
+		#tests/test_blocks.py::test_block_size_exception
+		#tests/test_crs.py::test_read_no_crs
+		#tests/test_memoryfile.py::test_zip_file_object_read
+		#tests/test_memoryfile.py::test_vrt_memfile
+		#tests/test_memoryfile.py::test_write_plus_model_jpeg
+		#tests/test_rio_convert.py::test_format
+		#tests/test_rio_convert.py::test_format_short
+		#tests/test_rio_convert.py::test_output_opt
+		#tests/test_rio_convert.py::test_convert_overwrite_without_option
+		#tests/test_rio_convert.py::test_convert_overwrite_with_option
+		#tests/test_rio_stack.py::test_format_jpeg
+		#tests/test_rio_warp.py::test_warp_vrt_gcps
+		#tests/test_shutil.py::test_copy_strict_failure
+		#tests/test_shutil.py::test_copy_strict_silent_failure
+		#tests/test_write.py::test_write__autodetect_driver[jpg-JPEG]
+		#tests/test_write.py::test_write__autodetect_driver[jpeg-JPEG]
+		#tests/test_write.py::test_issue2088[JPEG]
+
+		# threads
+		#tests/test_thread_pool_executor.py::test_threads_main_env
+		#tests/test_threading.py::test_child_thread_inherits_env
+	)
+
+	mv rasterio{,.bak} || die # Avoid non-working local import
+	epytest ${deselect[@]/#/--deselect }
+	mv rasterio{.bak,} || die
+}
diff --git a/dev-python/rasterstats/Manifest b/dev-python/rasterstats/Manifest
new file mode 100644
index 000000000..261dbac3d
--- /dev/null
+++ b/dev-python/rasterstats/Manifest
@@ -0,0 +1 @@
+DIST rasterstats-0.16.0.tar.gz 610224 BLAKE2B bc84e93e7aa9d4ca32516d85b6f01d3c1badd42af2a211d6116a78614252b9bd5488a21b3a3a1000f1fd0bd205e2009e598df8953add000f4eee2d572a4d6c61 SHA512 c3174d1a8aa18f663d5bf05beb4f56aeaf768939220b29d26d5b892936309a48b8777ee16a88b009011f718fbd7432056deaffaac917161631532b0670c0263e
diff --git a/dev-python/rasterstats/metadata.xml b/dev-python/rasterstats/metadata.xml
new file mode 100644
index 000000000..ab1322912
--- /dev/null
+++ b/dev-python/rasterstats/metadata.xml
@@ -0,0 +1,18 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<!DOCTYPE pkgmetadata SYSTEM "https://www.gentoo.org/dtd/metadata.dtd">
+<pkgmetadata>
+  <maintainer type="project">
+    <email>sci@gentoo.org</email>
+    <name>Gentoo Science Project</name>
+  </maintainer>
+  <longdescription lang="en">
+  rasterstats is a Python module for summarizing geospatial raster datasets 
+  based on vector geometries. It includes functions for zonal statistics 
+  and interpolated point queries. The command-line interface allows for 
+  easy interoperability with other GeoJSON tools.
+</longdescription>
+  <upstream>
+    <remote-id type="github">perrygeo/python-rasterstats</remote-id>
+    <remote-id type="pypi">rasterstats</remote-id>
+  </upstream>
+</pkgmetadata>
diff --git a/dev-python/rasterstats/rasterstats-0.16.0.ebuild b/dev-python/rasterstats/rasterstats-0.16.0.ebuild
new file mode 100644
index 000000000..5074a1566
--- /dev/null
+++ b/dev-python/rasterstats/rasterstats-0.16.0.ebuild
@@ -0,0 +1,30 @@
+# Copyright 1999-2022 Gentoo Authors
+# Distributed under the terms of the GNU General Public License v2
+
+EAPI=8
+
+PYTHON_COMPAT=( python3_10 )
+DISTUTILS_USE_PEP517="setuptools"
+inherit distutils-r1
+
+DESCRIPTION="Python module for summarizing geospatial raster datasets based on vectors"
+HOMEPAGE="https://github.com/perrygeo/python-rasterstats"
+SRC_URI="https://github.com/perrygeo/python-${PN}/archive/refs/tags/${PV}.tar.gz -> ${P}.tar.gz"
+
+LICENSE="BSD"
+SLOT="0"
+KEYWORDS="~amd64 ~x86"
+
+RDEPEND="
+	dev-python/affine[${PYTHON_USEDEP}]
+	dev-python/shapely[${PYTHON_USEDEP}]
+	dev-python/numpy[${PYTHON_USEDEP}]
+	dev-python/rasterio[${PYTHON_USEDEP}]
+	dev-python/cligj[${PYTHON_USEDEP}]
+	dev-python/fiona[${PYTHON_USEDEP}]
+	dev-python/simplejson[${PYTHON_USEDEP}]
+"
+
+S="${WORKDIR}/python-${P}"
+
+distutils_enable_tests pytest
diff --git a/dev-python/regions/Manifest b/dev-python/regions/Manifest
new file mode 100644
index 000000000..7e2e2f89a
--- /dev/null
+++ b/dev-python/regions/Manifest
@@ -0,0 +1 @@
+DIST regions-0.7.tar.gz 666091 BLAKE2B 7fd8cc1c9c34b236301c0493e11b99a3d2177e31c15c3ef43f38053eec653f8a68b84c4e0568395e38c940e987fcdf3a52a06e012a387a741de0cb46ec1995e8 SHA512 0e86b1cda4e479e29c00d151079788630a5b434f3d721d21ee81b4abcb03ea959e04351d61f48bfc19713dc938396fc9383c00998ba947f50fbbf9477db7d760
diff --git a/dev-python/regions/metadata.xml b/dev-python/regions/metadata.xml
new file mode 100644
index 000000000..b0d9fd489
--- /dev/null
+++ b/dev-python/regions/metadata.xml
@@ -0,0 +1,17 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
+<pkgmetadata>
+	<maintainer type="project">
+		<email>sci-astronomy@gentoo.org</email>
+		<name>Gentoo Astronomy Project</name>
+	</maintainer>
+	<longdescription lang="en">
+Gammapy is a package for simulating and analysing gamma-ray sky data.
+It is currently designed to support users of telescopes such as Fermi,
+H.E.S.S, and CTA in primarily Galactic plane survey studies.
+</longdescription>
+	<upstream>
+		<remote-id type="github">gammapy/gammapy</remote-id>
+		<remote-id type="pypi">regions</remote-id>
+	</upstream>
+</pkgmetadata>
diff --git a/dev-python/regions/regions-0.7.ebuild b/dev-python/regions/regions-0.7.ebuild
new file mode 100644
index 000000000..ef412a153
--- /dev/null
+++ b/dev-python/regions/regions-0.7.ebuild
@@ -0,0 +1,31 @@
+# Copyright 1999-2021 Gentoo Authors
+# Distributed under the terms of the GNU General Public License v2
+
+EAPI=8
+
+PYTHON_COMPAT=( python3_{10..11} )
+DISTUTILS_USE_PEP517=setuptools
+
+inherit distutils-r1 pypi
+
+DESCRIPTION="Astropy affilated package for region handling"
+HOMEPAGE="https://github.com/astropy/regions"
+
+LICENSE="BSD"
+SLOT="0"
+KEYWORDS="~amd64 ~x86"
+
+# TODO: fix this
+# E   ModuleNotFoundError: No module named 'regions._geometry.circular_overlap'
+RESTRICT="test"
+
+RDEPEND="
+	>=dev-python/astropy-0.4[${PYTHON_USEDEP}]
+	dev-python/numpy[${PYTHON_USEDEP}]
+	dev-python/six[${PYTHON_USEDEP}]
+"
+
+# TODO: fix this
+# NameError: name 'disabled_intersphinx_mapping' is not defined
+#distutils_enable_sphinx docs dev-python/sphinx-astropy
+distutils_enable_tests pytest
diff --git a/dev-python/reproject/Manifest b/dev-python/reproject/Manifest
new file mode 100644
index 000000000..76c6dd3c9
--- /dev/null
+++ b/dev-python/reproject/Manifest
@@ -0,0 +1 @@
+DIST reproject-0.8.tar.gz 774255 BLAKE2B bf66cf2038f436567b6b0a66cc19608c96f98d2bf1624aa33c7b07e1e42c8bfdecc46072d410699f2a0c2f3db52a0ee04d0ce64f58464fd1abd28e33d704933d SHA512 48fba585de3fc67fdb39390390021e6e8295297e31d2c3fccbead53a592f512232ef182e8914906f21190108f87266faf5ad57d5982a76a50c30eeca630fd6ed
diff --git a/dev-python/reproject/metadata.xml b/dev-python/reproject/metadata.xml
new file mode 100644
index 000000000..56a54a20b
--- /dev/null
+++ b/dev-python/reproject/metadata.xml
@@ -0,0 +1,11 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
+<pkgmetadata>
+	<maintainer type="project">
+		<email>sci-astronomy@gentoo.org</email>
+		<name>Gentoo Astronomy Project</name>
+	</maintainer>
+	<upstream>
+		<remote-id type="pypi">reproject</remote-id>
+	</upstream>
+</pkgmetadata>
diff --git a/dev-python/reproject/reproject-0.8.ebuild b/dev-python/reproject/reproject-0.8.ebuild
new file mode 100644
index 000000000..cf57e7d73
--- /dev/null
+++ b/dev-python/reproject/reproject-0.8.ebuild
@@ -0,0 +1,36 @@
+# Copyright 1999-2022 Gentoo Authors
+# Distributed under the terms of the GNU General Public License v2
+
+EAPI=8
+
+PYTHON_COMPAT=( python3_10 )
+inherit distutils-r1 pypi
+
+DESCRIPTION="Reproject astronomical images"
+HOMEPAGE="https://reproject.readthedocs.io/"
+
+LICENSE="BSD"
+SLOT="0"
+KEYWORDS="~amd64 ~x86"
+
+#TODO: Package all these pytest deps:
+# 	pytest-doctestplus>=0.2.0
+# 	pytest-remotedata>=0.3.1
+# 	pytest-openfiles>=0.3.1
+# 	pytest-astropy-header>=0.1.2
+# 	pytest-arraydiff>=0.1
+# 	pytest-filter-subpackage>=0.1
+RESTRICT="test"
+
+BDEPEND="dev-python/setuptools-scm[${PYTHON_USEDEP}]"
+
+RDEPEND="
+	>=dev-python/astropy-3.2[${PYTHON_USEDEP}]
+	>=dev-python/astropy-healpix-0.6[${PYTHON_USEDEP}]
+	>=dev-python/numpy-1.14[${PYTHON_USEDEP}]
+	>=dev-python/scipy-1.1[${PYTHON_USEDEP}]
+"
+
+# requires self to be installed
+# distutils_enable_sphinx docs dev-python/sphinx-astropy dev-python/matplotlib
+distutils_enable_tests --install pytest
diff --git a/dev-python/repsep_utils/Manifest b/dev-python/repsep_utils/Manifest
new file mode 100644
index 000000000..1c65b16d9
--- /dev/null
+++ b/dev-python/repsep_utils/Manifest
@@ -0,0 +1,3 @@
+DIST repsep_utils-0.2.tar.gz 11147 BLAKE2B 89726b7e163c954ae9826a32c6997f4c678e6586240db52b37355ca59c16743b8c19e89d12d175cb55435aced5498a22e9e825d0c2d95f9046a52ac6daadefb3 SHA512 ba499cecb3dac38c1ca8e91eee3e1f9edafbc906e8acc046cd1eaead8253a9ac61f489ffca23cdb4ac6a595ecef40cc6a3374b3618c8162a4f38f499c1a4cc4e
+DIST repsep_utils-0.3.1.tar.gz 12021 BLAKE2B cfe6e0dbeaddf751a1f222a19e7c430b4c3acd4ea28061164ecc213cadccb7bcb42e9b1fe16bf73f93d735edba3887553ac49b04f763ec888177ab653d05b07b SHA512 a5897a6b2a778d8079f9d5947b22def7c42922d0c607e711f2c2957b569991098f1ed3ce53ff2f74183cb4466b87f87596aafec9f2e4c1efb38c317ef29df8da
+DIST repsep_utils-0.3.tar.gz 11893 BLAKE2B b02ec74d55bbfbe15052573049660a39c87681862ff3d38a7560666191b9b2cec6ea230898349c8feef4d5654e1524b16fa90c13b1238ea1d5d51ae6eaffa283 SHA512 9df1fb77d09d18387625e7cceed9aa31faf35fd72d076425cbabc30c7020e6f8257161628940f131f6209ac2aab6336c07ffb3aa333c2ec48e2a3c47708cc2b4
diff --git a/dev-python/repsep_utils/metadata.xml b/dev-python/repsep_utils/metadata.xml
new file mode 100644
index 000000000..228d0e4bf
--- /dev/null
+++ b/dev-python/repsep_utils/metadata.xml
@@ -0,0 +1,18 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
+<pkgmetadata>
+	<maintainer type="person">
+		<email>chr@chymera.eu</email>
+		<name>Horea Christian</name>
+	</maintainer>
+	<longdescription lang="en">
+		Utilities for compiling and developing RepSeP-style articles, such as the
+		reference implementation. The package contains generic boilerplate code for
+		PythonTeX-interaction, as used by all RepSeP-style articles, as well as an
+		executable file allowing single-script execution for development and
+		debugging purposes.
+	</longdescription>
+	<upstream>
+		<remote-id type="github">TheChymera/repsep_utils</remote-id>
+	</upstream>
+</pkgmetadata>
diff --git a/dev-python/repsep_utils/repsep_utils-0.2.ebuild b/dev-python/repsep_utils/repsep_utils-0.2.ebuild
new file mode 100644
index 000000000..670b44a0f
--- /dev/null
+++ b/dev-python/repsep_utils/repsep_utils-0.2.ebuild
@@ -0,0 +1,22 @@
+# Copyright 2019-2021 Gentoo Authors
+# Distributed under the terms of the GNU General Public License v2
+
+EAPI=7
+
+DESCRIPTION="Utilities Supporting RepSeP-style documents"
+HOMEPAGE="https://github.com/TheChymera/repsep_utils"
+SRC_URI="https://github.com/TheChymera/repsep_utils/archive/${PV}.tar.gz -> ${P}.tar.gz"
+
+LICENSE="GPL-2"
+SLOT="0"
+KEYWORDS="~amd64 ~x86"
+
+DEPEND=""
+RDEPEND="dev-tex/pythontex"
+
+src_install() {
+	dobin "bin/repsep"
+
+	insinto "/usr/share/repsep"
+	doins repsep/*
+}
diff --git a/dev-python/repsep_utils/repsep_utils-0.3.1.ebuild b/dev-python/repsep_utils/repsep_utils-0.3.1.ebuild
new file mode 100644
index 000000000..975d97f9d
--- /dev/null
+++ b/dev-python/repsep_utils/repsep_utils-0.3.1.ebuild
@@ -0,0 +1,22 @@
+# Copyright 2019-2023 Gentoo Authors
+# Distributed under the terms of the GNU General Public License v2
+
+EAPI=8
+
+DESCRIPTION="Utilities Supporting RepSeP-style documents"
+HOMEPAGE="https://github.com/TheChymera/repsep_utils"
+SRC_URI="https://github.com/TheChymera/repsep_utils/archive/${PV}.tar.gz -> ${P}.tar.gz"
+
+LICENSE="GPL-2"
+SLOT="0"
+KEYWORDS="~amd64 ~x86"
+
+DEPEND=""
+RDEPEND="dev-tex/pythontex"
+
+src_install() {
+	dobin "bin/repsep"
+
+	insinto "/usr/share/repsep"
+	doins repsep/*
+}
diff --git a/dev-python/repsep_utils/repsep_utils-0.3.ebuild b/dev-python/repsep_utils/repsep_utils-0.3.ebuild
new file mode 100644
index 000000000..975d97f9d
--- /dev/null
+++ b/dev-python/repsep_utils/repsep_utils-0.3.ebuild
@@ -0,0 +1,22 @@
+# Copyright 2019-2023 Gentoo Authors
+# Distributed under the terms of the GNU General Public License v2
+
+EAPI=8
+
+DESCRIPTION="Utilities Supporting RepSeP-style documents"
+HOMEPAGE="https://github.com/TheChymera/repsep_utils"
+SRC_URI="https://github.com/TheChymera/repsep_utils/archive/${PV}.tar.gz -> ${P}.tar.gz"
+
+LICENSE="GPL-2"
+SLOT="0"
+KEYWORDS="~amd64 ~x86"
+
+DEPEND=""
+RDEPEND="dev-tex/pythontex"
+
+src_install() {
+	dobin "bin/repsep"
+
+	insinto "/usr/share/repsep"
+	doins repsep/*
+}
diff --git a/dev-python/reretry/Manifest b/dev-python/reretry/Manifest
new file mode 100644
index 000000000..af408dac3
--- /dev/null
+++ b/dev-python/reretry/Manifest
@@ -0,0 +1 @@
+DIST reretry-0.11.8.gh.tar.gz 6629 BLAKE2B eb13ecce1ca29ce29932566e08b57a05d3f2426f41633b33b1c51eed1c4d880c5520adda4e5386ac13d064f7ff6bdc3831ce612c64c8dd24e63164a55907ae3b SHA512 e499e64cc06af8e1bb7e9fdd857c02305dcb76fd3205de128d389332a94493696c85a705efaf1e9ac0110b94a1cd443a44d49856f26b31a7eba8ad317f7deba4
diff --git a/dev-python/reretry/metadata.xml b/dev-python/reretry/metadata.xml
new file mode 100644
index 000000000..64af0841d
--- /dev/null
+++ b/dev-python/reretry/metadata.xml
@@ -0,0 +1,12 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
+<pkgmetadata>
+	<maintainer type="project">
+		<email>sci@gentoo.org</email>
+		<name>Gentoo Science Project</name>
+	</maintainer>
+	<upstream>
+		<remote-id type="github">leshchenko1979/reretry</remote-id>
+		<remote-id type="pypi">reretry</remote-id>
+	</upstream>
+</pkgmetadata>
diff --git a/dev-python/reretry/reretry-0.11.8.ebuild b/dev-python/reretry/reretry-0.11.8.ebuild
new file mode 100644
index 000000000..64da7215b
--- /dev/null
+++ b/dev-python/reretry/reretry-0.11.8.ebuild
@@ -0,0 +1,25 @@
+# Copyright 1999-2021 Gentoo Authors
+# Distributed under the terms of the GNU General Public License v2
+
+EAPI=8
+
+PYTHON_COMPAT=( python3_{10..11} )
+DISTUTILS_USE_PEP517=setuptools
+
+inherit distutils-r1
+
+DESCRIPTION="An easy-to-use but functional retry decorator in python"
+HOMEPAGE="https://github.com/leshchenko1979/reretry"
+SRC_URI="https://github.com/leshchenko1979/reretry/archive/refs/tags/${PV}.tar.gz -> ${P}.gh.tar.gz"
+
+LICENSE="Apache-2.0"
+SLOT="0"
+KEYWORDS="~amd64"
+
+BDEPEND="
+	test? (
+		dev-python/pytest-asyncio[${PYTHON_USEDEP}]
+	)
+"
+
+distutils_enable_tests pytest
diff --git a/dev-python/rich-click/Manifest b/dev-python/rich-click/Manifest
new file mode 100644
index 000000000..ae8d92c2f
--- /dev/null
+++ b/dev-python/rich-click/Manifest
@@ -0,0 +1 @@
+DIST rich-click-1.7.2.tar.gz 39362 BLAKE2B c4ad70d449ce9ceb3d9bbbccf7c7d3cd43386c35061d60c6395ff7845f606558af36a7c465a3393484008ece244f8e684ca9d71cea14463f04cac21803108543 SHA512 f4046e54874c4f3cc4f77651fdeb1f888d9435ff282f54d320c16c7c42f57c48018c0159230e780684336d29edff6e654454b8940b5b8df5a19139d2219c671b
diff --git a/dev-python/rich-click/metadata.xml b/dev-python/rich-click/metadata.xml
new file mode 100644
index 000000000..79a5238bd
--- /dev/null
+++ b/dev-python/rich-click/metadata.xml
@@ -0,0 +1,12 @@
+<?xml version='1.0' encoding='UTF-8'?>
+<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
+<pkgmetadata>
+	<maintainer type="person">
+		<email>mschu.dev@gmail.com</email>
+		<name>Michael Schubert</name>
+	</maintainer>
+	<upstream>
+		<remote-id type="github">ewels/rich-click</remote-id>
+		<remote-id type="pypi">rich-click</remote-id>
+	</upstream>
+</pkgmetadata>
diff --git a/dev-python/rich-click/rich-click-1.7.2.ebuild b/dev-python/rich-click/rich-click-1.7.2.ebuild
new file mode 100644
index 000000000..e642303e2
--- /dev/null
+++ b/dev-python/rich-click/rich-click-1.7.2.ebuild
@@ -0,0 +1,25 @@
+# Copyright 1999-2023 Gentoo Authors
+# Distributed under the terms of the GNU General Public License v2
+
+EAPI=8
+
+DISTUTILS_USE_PEP517=setuptools
+PYTHON_COMPAT=( python3_{10..12} )
+
+PYPI_NO_NORMALIZE=1
+inherit pypi distutils-r1
+
+DESCRIPTION="Format click help output nicely with rich"
+HOMEPAGE="https://pypi.org/project/rich-click/"
+
+LICENSE="MIT"
+SLOT="0"
+KEYWORDS="~amd64 ~amd64-linux"
+
+RDEPEND="dev-python/click[${PYTHON_USEDEP}]
+	dev-python/rich[${PYTHON_USEDEP}]
+	dev-python/typing-extensions[${PYTHON_USEDEP}]"
+
+RESTRICT="test"
+# ModuleNotFoundError: No module named 'tests.conftest'
+#distutils_enable_tests pytest
diff --git a/dev-python/ripser/Manifest b/dev-python/ripser/Manifest
new file mode 100644
index 000000000..4f2515c0a
--- /dev/null
+++ b/dev-python/ripser/Manifest
@@ -0,0 +1 @@
+DIST ripser-0.6.4.tar.gz 74642 BLAKE2B a6d7a39671415a86978ae4514f1f915f13ec791f246e632d3974553b53c398b971989e25b3cca2027a910831404c478994e646ed6e03010350b1e95438d7fc10 SHA512 b3fc216e75c807666e24d9f797a96296f2e1ffbddf3bba499220dab385690cdb6f47138cb55977eb68678dfbff9d750d7f1c4bcd8ea9267a940c9949a8dae360
diff --git a/dev-python/ripser/metadata.xml b/dev-python/ripser/metadata.xml
new file mode 100644
index 000000000..f983c3d4c
--- /dev/null
+++ b/dev-python/ripser/metadata.xml
@@ -0,0 +1,15 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
+<pkgmetadata>
+    <maintainer type="person">
+        <email>gentoo@aisha.cc</email>
+        <name>Aisha Tammy</name>
+    </maintainer>
+    <maintainer type="project">
+        <email>sci@gentoo.org</email>
+        <name>Gentoo Science Project</name>
+    </maintainer>
+    <upstream>
+        <remote-id type="pypi">ripser</remote-id>
+    </upstream>
+</pkgmetadata>
diff --git a/dev-python/ripser/ripser-0.6.4.ebuild b/dev-python/ripser/ripser-0.6.4.ebuild
new file mode 100644
index 000000000..21d6b6ccd
--- /dev/null
+++ b/dev-python/ripser/ripser-0.6.4.ebuild
@@ -0,0 +1,31 @@
+# Copyright 1999-2020 Gentoo Authors
+# Distributed under the terms of the GNU General Public License v2
+
+EAPI=8
+
+PYTHON_COMPAT=( python3_{10..11} )
+DISTUTILS_USE_PEP517=setuptools
+
+inherit distutils-r1 pypi
+
+DESCRIPTION="python frontend for the fast ripser tda tool"
+HOMEPAGE="https://ripser.scikit-tda.org/"
+
+LICENSE="MIT"
+SLOT="0"
+KEYWORDS="~amd64"
+
+RDEPEND="
+	dev-python/cython[${PYTHON_USEDEP}]
+	dev-python/numpy[${PYTHON_USEDEP}]
+	dev-python/persim[${PYTHON_USEDEP}]
+	dev-python/scipy[${PYTHON_USEDEP}]
+	sci-libs/scikit-learn[${PYTHON_USEDEP}]
+"
+BDEPEND="
+	test? (
+		dev-python/hopcroftkarp[${PYTHON_USEDEP}]
+		dev-python/joblib[${PYTHON_USEDEP}]
+	)
+"
+distutils_enable_tests pytest
diff --git a/dev-python/scooby/Manifest b/dev-python/scooby/Manifest
new file mode 100644
index 000000000..0a16de485
--- /dev/null
+++ b/dev-python/scooby/Manifest
@@ -0,0 +1 @@
+DIST scooby-0.5.7.tar.gz 15770 BLAKE2B 08f9cf7c7e35c6c87cb80314b5287d2cbebaf46471e58e574d8f6725eb18fe95488c1043412a0abcd88040cb157713cb2076f425318c28ac02d3ad193df64b54 SHA512 4f8cc4c03c0af707115e11c11d6bbb5fb730d6221ff32598ad56e9592e1bcb2e22f56af189d05ca50fefcefd5262233594dd9b1d0dfd374d66f42700c7553d48
diff --git a/dev-python/scooby/metadata.xml b/dev-python/scooby/metadata.xml
new file mode 100644
index 000000000..c48aae2cf
--- /dev/null
+++ b/dev-python/scooby/metadata.xml
@@ -0,0 +1,13 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
+<pkgmetadata>
+	<maintainer type="project">
+		<email>sci@gentoo.org</email>
+		<name>Gentoo Science Project</name>
+	</maintainer>
+	<stabilize-allarches/>
+	<upstream>
+		<remote-id type="pypi">scooby</remote-id>
+		<remote-id type="github">banesullivan/scooby</remote-id>
+	</upstream>
+</pkgmetadata>
diff --git a/dev-python/scooby/scooby-0.5.7.ebuild b/dev-python/scooby/scooby-0.5.7.ebuild
new file mode 100644
index 000000000..4cd053b50
--- /dev/null
+++ b/dev-python/scooby/scooby-0.5.7.ebuild
@@ -0,0 +1,14 @@
+# Copyright 1999-2021 Gentoo Authors
+# Distributed under the terms of the GNU General Public License v2
+
+EAPI=7
+
+PYTHON_COMPAT=( python3_10 )
+inherit distutils-r1 pypi
+
+DESCRIPTION="Easily report Python package versions and hardware resources"
+HOMEPAGE="https://pypi.org/project/scooby/"
+
+LICENSE="MIT"
+KEYWORDS="~amd64 ~x86"
+SLOT="0"
diff --git a/dev-python/shove/Manifest b/dev-python/shove/Manifest
deleted file mode 100644
index fbd71bc63..000000000
--- a/dev-python/shove/Manifest
+++ /dev/null
@@ -1 +0,0 @@
-DIST shove-0.6.6.tar.gz 19442 BLAKE2B 924f54f6d1f4d9d06c368d963a892a733f6e04c33e473d6a4eae7b5afa88fc9a89aad9625d8cdcd6abe14fbd89989d5837064f6127e34459737fc72f973e7c34 SHA512 aa3386eea6ac3806fe6f475c411fb2a80124029d6c6a26f42a2197db904065d467431b75ae47baf85cdfe1762708eb53096575c8d72188633499cdb3b02a456d
diff --git a/dev-python/shove/metadata.xml b/dev-python/shove/metadata.xml
deleted file mode 100644
index 597a68368..000000000
--- a/dev-python/shove/metadata.xml
+++ /dev/null
@@ -1,15 +0,0 @@
-<?xml version="1.0" encoding="UTF-8"?>
-<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
-<pkgmetadata>
-	<maintainer type="person">
-		<email>mmokrejs@fold.natur.cuni.cz</email>
-		<name>Martin Mokrejs</name>
-	</maintainer>
-	<maintainer type="project">
-		<email>sci-biology@gentoo.org</email>
-		<name>Gentoo Biology Project</name>
-	</maintainer>
-	<upstream>
-		<remote-id type="github">lcrees/shove</remote-id>
-	</upstream>
-</pkgmetadata>
diff --git a/dev-python/shove/shove-0.6.6.ebuild b/dev-python/shove/shove-0.6.6.ebuild
deleted file mode 100644
index dd5a25e73..000000000
--- a/dev-python/shove/shove-0.6.6.ebuild
+++ /dev/null
@@ -1,20 +0,0 @@
-# Copyright 1999-2017 Gentoo Foundation
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=6
-
-PYTHON_COMPAT=( python2_7 python3_5 )
-inherit distutils-r1
-
-DESCRIPTION="Object storage frontend to DBM/fs/mem/sqlite backends"
-HOMEPAGE="https://github.com/lcrees/shove
-	https://pypi.python.org/pypi/shove"
-SRC_URI="https://github.com/lcrees/shove/archive/0.6.6.tar.gz -> ${P}.tar.gz"
-
-LICENSE="BSD"
-SLOT="0"
-KEYWORDS="~amd64 ~x86"
-IUSE=""
-
-DEPEND=""
-RDEPEND="${DEPEND}"
diff --git a/dev-python/smart-open/Manifest b/dev-python/smart-open/Manifest
new file mode 100644
index 000000000..37703129f
--- /dev/null
+++ b/dev-python/smart-open/Manifest
@@ -0,0 +1 @@
+DIST smart-open-6.3.0.gh.tar.gz 131300 BLAKE2B 816b2e42fca7783891eefbe767ac28423c533fe726707bf40be2b53107d7c928e74dec904db79542f7b0d41100f5aada78598478c9bc6ca23d3dbe2341575ad4 SHA512 78a63b22fc00b1ab9b60161ab0ea79d7c760539f1c69386cba1c9844099b597dc8a8a77940e019f126cb989ae63c3f2418493f4e8e86f6605662d7f2904108e4
diff --git a/dev-python/smart-open/metadata.xml b/dev-python/smart-open/metadata.xml
new file mode 100644
index 000000000..6c86761f0
--- /dev/null
+++ b/dev-python/smart-open/metadata.xml
@@ -0,0 +1,12 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
+<pkgmetadata>
+	<maintainer type="project">
+		<email>sci@gentoo.org</email>
+		<name>Gentoo Science Project</name>
+	</maintainer>
+	<upstream>
+		<remote-id type="github">RaRe-Technologies/smart_open</remote-id>
+		<remote-id type="pypi">smart-open</remote-id>
+	</upstream>
+</pkgmetadata>
diff --git a/dev-python/smart-open/smart-open-6.3.0.ebuild b/dev-python/smart-open/smart-open-6.3.0.ebuild
new file mode 100644
index 000000000..b585f1d4b
--- /dev/null
+++ b/dev-python/smart-open/smart-open-6.3.0.ebuild
@@ -0,0 +1,35 @@
+# Copyright 1999-2021 Gentoo Authors
+# Distributed under the terms of the GNU General Public License v2
+
+EAPI=8
+
+PYTHON_COMPAT=( python3_{10..11} )
+DISTUTILS_USE_PEP517=setuptools
+
+inherit distutils-r1
+
+DESCRIPTION="Utils for streaming large files (S3, HDFS, gzip, bz2...) "
+HOMEPAGE="https://github.com/RaRe-Technologies/smart_open"
+SRC_URI="https://github.com/RaRe-Technologies/smart_open/archive/refs/tags/v${PV}.tar.gz -> ${P}.gh.tar.gz"
+S="${WORKDIR}/${PN//-/_}-${PV}"
+
+LICENSE="MIT"
+SLOT="0"
+KEYWORDS="~amd64"
+
+RDEPEND="
+	dev-python/boto3[${PYTHON_USEDEP}]
+	dev-python/google-cloud-storage[${PYTHON_USEDEP}]
+	dev-python/requests[${PYTHON_USEDEP}]
+	dev-python/paramiko[${PYTHON_USEDEP}]
+"
+
+BDEPEND="
+	test? (
+		dev-python/moto[${PYTHON_USEDEP}]
+		dev-python/responses[${PYTHON_USEDEP}]
+		dev-python/pytest-rerunfailures[${PYTHON_USEDEP}]
+	)
+"
+
+distutils_enable_tests pytest
diff --git a/dev-python/snakemake/Manifest b/dev-python/snakemake/Manifest
index 3242ed813..eca03bc0e 100644
--- a/dev-python/snakemake/Manifest
+++ b/dev-python/snakemake/Manifest
@@ -1 +1 @@
-DIST snakemake-3.4.2.tar.gz 64681 BLAKE2B 3025dc9ce351069c3bb42ddeac64640d2e09e0de329c8aa4149b6a1c704c361eb9501d1a9229508213c6524d24385ccbc2406362328fbd7f7f52957b3b4d6ae4 SHA512 0c1422b5cfa38a1abcb4fd936eff5e9a9f0712e352a5414b21e255edc97c117adff57754a8c5c9d2ba298e9a3e00f0158805ba0aac693bdfd808fd9f82677214
+DIST snakemake-7.32.4.gh.tar.gz 8885863 BLAKE2B 6bb7ff4722dd06f0edf5e8079b42f5e54d6f55f41e2987b7dae7f9b75df0d4d836138e28340e5977107a5cc0b5afe793b0d7897c501246cc1b4340eb4eca2f17 SHA512 34fef61528b18facab798652c88ed5c698ef02161e023255fdd024b7c7781c4e582cdb04b2740fdff9b6f3600acaec719742984acee57920bb48ef3b5af99d9a
diff --git a/dev-python/snakemake/metadata.xml b/dev-python/snakemake/metadata.xml
index cff648bf6..74c76cce1 100644
--- a/dev-python/snakemake/metadata.xml
+++ b/dev-python/snakemake/metadata.xml
@@ -6,11 +6,11 @@
 		<name>Michael Schubert</name>
 	</maintainer>
 	<maintainer type="project">
-		<email>python@gentoo.org</email>
-		<name>Python</name>
+		<email>sci@gentoo.org</email>
+		<name>Gentoo Science Project</name>
 	</maintainer>
 	<upstream>
-		<remote-id type="bitbucket">johanneskoester/snakemake</remote-id>
 		<remote-id type="pypi">snakemake</remote-id>
+		<remote-id type="github">snakemake/snakemake</remote-id>
 	</upstream>
 </pkgmetadata>
diff --git a/dev-python/snakemake/snakemake-3.4.2.ebuild b/dev-python/snakemake/snakemake-3.4.2.ebuild
deleted file mode 100644
index db58e6fed..000000000
--- a/dev-python/snakemake/snakemake-3.4.2.ebuild
+++ /dev/null
@@ -1,16 +0,0 @@
-# Copyright 1999-2014 Gentoo Foundation
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=5
-
-PYTHON_COMPAT=( python{3_4,3_5} )
-
-inherit distutils-r1
-
-DESCRIPTION="Make-like task language"
-HOMEPAGE="https://bitbucket.org/johanneskoester/snakemake/wiki/Home"
-SRC_URI="mirror://pypi/${PN:0:1}/${PN}/${P}.tar.gz"
-
-LICENSE="MIT"
-SLOT="0"
-KEYWORDS="~amd64 ~x86 ~amd64-linux ~x86-linux"
diff --git a/dev-python/snakemake/snakemake-7.32.4.ebuild b/dev-python/snakemake/snakemake-7.32.4.ebuild
new file mode 100644
index 000000000..711aac286
--- /dev/null
+++ b/dev-python/snakemake/snakemake-7.32.4.ebuild
@@ -0,0 +1,67 @@
+# Copyright 1999-2022 Gentoo Authors
+# Distributed under the terms of the GNU General Public License v2
+
+EAPI=8
+
+PYTHON_COMPAT=( python3_{10..11} )
+DISTUTILS_USE_PEP517=setuptools
+
+inherit distutils-r1
+
+DESCRIPTION="Make-like task language"
+HOMEPAGE="https://snakemake.readthedocs.io"
+SRC_URI="https://github.com/${PN}/${PN}/archive/v${PV}.tar.gz -> ${P}.gh.tar.gz"
+
+LICENSE="MIT"
+SLOT="0"
+KEYWORDS="~amd64"
+
+# cannot import name '_helpers' from 'google.cloud'
+RESTRICT="test"
+
+BDEPEND="
+	dev-python/tomli[${PYTHON_USEDEP}]
+	test? (
+		dev-python/requests-mock[${PYTHON_USEDEP}]
+		dev-python/google-api-python-client[${PYTHON_USEDEP}]
+		dev-python/networkx[${PYTHON_USEDEP}]
+		dev-python/pygments[${PYTHON_USEDEP}]
+		dev-python/pygraphviz[${PYTHON_USEDEP}]
+		net-libs/google-cloud-cpp
+	)
+"
+
+RDEPEND="
+	dev-python/appdirs[${PYTHON_USEDEP}]
+	dev-python/ConfigArgParse[${PYTHON_USEDEP}]
+	dev-python/connection_pool[${PYTHON_USEDEP}]
+	dev-python/datrie[${PYTHON_USEDEP}]
+	dev-python/docutils[${PYTHON_USEDEP}]
+	dev-python/GitPython[${PYTHON_USEDEP}]
+	dev-python/humanfriendly[${PYTHON_USEDEP}]
+	dev-python/jinja[${PYTHON_USEDEP}]
+	dev-python/jsonschema[${PYTHON_USEDEP}]
+	dev-python/nbformat[${PYTHON_USEDEP}]
+	dev-python/packaging[${PYTHON_USEDEP}]
+	dev-python/psutil[${PYTHON_USEDEP}]
+	dev-python/pyyaml[${PYTHON_USEDEP}]
+	dev-python/requests[${PYTHON_USEDEP}]
+	dev-python/reretry[${PYTHON_USEDEP}]
+	dev-python/smart-open[${PYTHON_USEDEP}]
+	dev-python/stopit[${PYTHON_USEDEP}]
+	dev-python/tabulate[${PYTHON_USEDEP}]
+	dev-python/throttler[${PYTHON_USEDEP}]
+	dev-python/toposort[${PYTHON_USEDEP}]
+	dev-python/wrapt[${PYTHON_USEDEP}]
+	dev-python/yte[${PYTHON_USEDEP}]
+	sci-mathematics/pulp[${PYTHON_USEDEP}]
+"
+
+distutils_enable_sphinx docs \
+	dev-python/sphinxcontrib-napoleon \
+	dev-python/sphinx-argparse \
+	dev-python/sphinx-rtd-theme \
+	dev-python/docutils \
+	dev-python/recommonmark \
+	dev-python/myst-parser
+distutils_enable_tests pytest
diff --git a/dev-python/snuggs/Manifest b/dev-python/snuggs/Manifest
new file mode 100644
index 000000000..d9ccc74fd
--- /dev/null
+++ b/dev-python/snuggs/Manifest
@@ -0,0 +1 @@
+DIST snuggs-1.4.7.tar.gz 7762 BLAKE2B fae10c4e6f759219cbecdbea4b8f49001980824fe1d43fba9d5b62837a88183d1ecb6f55e191b637048e03856b1c6466cb17a9c38dfa332537d8968c8510fc25 SHA512 c1f40e521d1b0cf15075b22b04000c74ecbd0522cdd820b8c159aac812924d877349b3f3bca93b09eed5b025a34c26665a41c7a52a8145419558b115cf8ef361
diff --git a/dev-python/snuggs/metadata.xml b/dev-python/snuggs/metadata.xml
new file mode 100644
index 000000000..19390156e
--- /dev/null
+++ b/dev-python/snuggs/metadata.xml
@@ -0,0 +1,17 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<!DOCTYPE pkgmetadata SYSTEM "https://www.gentoo.org/dtd/metadata.dtd">
+<pkgmetadata>
+  <maintainer type="project">
+    <email>sci@gentoo.org</email>
+    <name>Gentoo Science Project</name>
+  </maintainer>
+  <longdescription lang="en">
+  Snuggs library parses S-expressions using numpy. Available function 
+  include arithmetic and logical operators.  Also members of the numpy 
+  module such as "asarray()", "mean()" and "where" are available.
+</longdescription>
+  <upstream>
+    <remote-id type="github">mapbox/snuggs</remote-id>
+    <remote-id type="pypi">snuggs</remote-id>
+  </upstream>
+</pkgmetadata>
diff --git a/dev-python/snuggs/snuggs-1.4.7.ebuild b/dev-python/snuggs/snuggs-1.4.7.ebuild
new file mode 100644
index 000000000..be3395de7
--- /dev/null
+++ b/dev-python/snuggs/snuggs-1.4.7.ebuild
@@ -0,0 +1,26 @@
+# Copyright 1999-2022 Gentoo Authors
+# Distributed under the terms of the GNU General Public License v2
+
+EAPI=8
+
+PYTHON_COMPAT=( python3_10 )
+DISTUTILS_USE_PEP517="setuptools"
+inherit distutils-r1
+
+DESCRIPTION="S-expressions for numpy"
+HOMEPAGE="https://github.com/mapbox/snuggs"
+SRC_URI="https://github.com/mapbox/${PN}/archive/refs/tags/${PV}.tar.gz -> ${P}.tar.gz"
+
+LICENSE="MIT"
+SLOT="0"
+KEYWORDS="~amd64 ~x86"
+
+RDEPEND="
+	dev-python/numpy[${PYTHON_USEDEP}]
+	dev-python/pyparsing[${PYTHON_USEDEP}]
+"
+BDEPEND="
+	test? ( dev-python/hypothesis[${PYTHON_USEDEP}] )
+"
+
+distutils_enable_tests pytest
diff --git a/dev-python/spectra/Manifest b/dev-python/spectra/Manifest
new file mode 100644
index 000000000..97bcfc93a
--- /dev/null
+++ b/dev-python/spectra/Manifest
@@ -0,0 +1 @@
+DIST spectra-0.0.11.tar.gz 18819 BLAKE2B 45ceefa8d2bab051a8fa8ee687f9fa25f6436e66987bb84c6982f64a522fb0b04120e068ef890f4b04f6626a130c5df1e81090913c143df1e82bda5ca3a01d4d SHA512 7b4e244ba200df8c6d7cff19ddf36a5af6cfe8cf6f89283f8dbb64345a3eb85b4f62456e3c75b7c8ce2d24e01c8a123a5763605b1e702903fe16839966e47b32
diff --git a/dev-python/spectra/metadata.xml b/dev-python/spectra/metadata.xml
new file mode 100644
index 000000000..9332eceee
--- /dev/null
+++ b/dev-python/spectra/metadata.xml
@@ -0,0 +1,12 @@
+<?xml version='1.0' encoding='UTF-8'?>
+<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
+<pkgmetadata>
+	<maintainer type="person">
+		<email>mschu.dev@gmail.com</email>
+		<name>Michael Schubert</name>
+	</maintainer>
+	<upstream>
+		<remote-id type="github">jsvine/spectra</remote-id>
+		<remote-id type="pypi">spectra</remote-id>
+	</upstream>
+</pkgmetadata>
diff --git a/dev-python/spectra/spectra-0.0.11.ebuild b/dev-python/spectra/spectra-0.0.11.ebuild
new file mode 100644
index 000000000..d0df23724
--- /dev/null
+++ b/dev-python/spectra/spectra-0.0.11.ebuild
@@ -0,0 +1,22 @@
+# Copyright 1999-2023 Gentoo Authors
+# Distributed under the terms of the GNU General Public License v2
+
+EAPI=8
+
+DISTUTILS_USE_PEP517=setuptools
+PYTHON_COMPAT=( python3_{10..12} )
+
+inherit pypi distutils-r1
+
+DESCRIPTION="Easy color scales and color conversion for Python"
+HOMEPAGE="https://pypi.org/project/spectra/"
+
+LICENSE="MIT"
+SLOT="0"
+KEYWORDS="~amd64 ~amd64-linux"
+
+RDEPEND="dev-python/colormath[${PYTHON_USEDEP}]"
+
+# requires nose
+RESTRICT="test"
+#distutils_enable_tests pytest
diff --git a/dev-python/specutils/Manifest b/dev-python/specutils/Manifest
new file mode 100644
index 000000000..9ee9c42c5
--- /dev/null
+++ b/dev-python/specutils/Manifest
@@ -0,0 +1 @@
+DIST specutils-1.9.1.tar.gz 665564 BLAKE2B 733bfecfdc61a03f85bc7f7588724eac869db66e135c4ef22993c3b1d537b67ef6ca784d03a0182741684282c4a7385642352f20d3fce948f0b26a4e950ba82f SHA512 f06e878539173b3c8a9220fd87f8deff15db744c3d267405afb1a43f98c181440c160c5396c636d2f6e2ed4373055537e6274e4a65e5f4e82f9163a446a6d450
diff --git a/dev-python/specutils/metadata.xml b/dev-python/specutils/metadata.xml
index d8e354751..1055c50cb 100644
--- a/dev-python/specutils/metadata.xml
+++ b/dev-python/specutils/metadata.xml
@@ -12,5 +12,6 @@ into a class with special handling of 1D spectra.
 </longdescription>
 	<upstream>
 		<remote-id type="github">astropy/specutils</remote-id>
+		<remote-id type="pypi">specutils</remote-id>
 	</upstream>
 </pkgmetadata>
diff --git a/dev-python/specutils/specutils-1.9.1.ebuild b/dev-python/specutils/specutils-1.9.1.ebuild
new file mode 100644
index 000000000..c77a1078d
--- /dev/null
+++ b/dev-python/specutils/specutils-1.9.1.ebuild
@@ -0,0 +1,38 @@
+# Copyright 1999-2021 Gentoo Authors
+# Distributed under the terms of the GNU General Public License v2
+
+EAPI=8
+
+PYTHON_COMPAT=( python3_{10..11} )
+DISTUTILS_USE_PEP517=setuptools
+
+inherit distutils-r1 pypi
+
+DESCRIPTION="Package for spectroscopic astronomical data"
+HOMEPAGE="https://github.com/astropy/specutils"
+
+LICENSE="BSD"
+SLOT="0"
+KEYWORDS="~amd64 ~x86"
+
+# Requires access to the internet
+RESTRICT="test"
+
+RDEPEND="
+	dev-python/asdf[${PYTHON_USEDEP}]
+	>=dev-python/astropy-4.0[${PYTHON_USEDEP}]
+	dev-python/astropy-helpers[${PYTHON_USEDEP}]
+	dev-python/gwcs[${PYTHON_USEDEP}]
+	dev-python/scipy[${PYTHON_USEDEP}]
+"
+
+# Bug: https://bugs.gentoo.org/703778
+#distutils_enable_sphinx docs dev-python/sphinx-astropy
+distutils_enable_tests pytest
+
+python_prepare_all() {
+	# do not depend on pytest-datafiles
+	sed -i -e '/addopts =/d' setup.cfg || die
+
+	distutils-r1_python_prepare_all
+}
diff --git a/dev-python/specutils/specutils-9999.ebuild b/dev-python/specutils/specutils-9999.ebuild
deleted file mode 100644
index e91b20477..000000000
--- a/dev-python/specutils/specutils-9999.ebuild
+++ /dev/null
@@ -1,58 +0,0 @@
-# Copyright 1999-2014 Gentoo Foundation
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=5
-
-PYTHON_COMPAT=( python{2_7,3_4} )
-inherit distutils-r1
-
-if [ ${PV} == "9999" ] ; then
-	inherit git-r3
-	EGIT_REPO_URI="https://github.com/astropy/${PN}.git"
-else
-	SRC_URI="mirror://pypi/${PN:0:1}/${PN}/${P}.tar.gz"
-	KEYWORDS="~amd64"
-fi
-
-DESCRIPTION="Affiliated package for 1D spectral operations"
-HOMEPAGE="https://github.com/astropy/specutils"
-
-LICENSE="BSD"
-SLOT="0"
-IUSE="doc"
-DOCS=( README.rst )
-
-RDEPEND="
-	>=dev-python/astropy-0.4[${PYTHON_USEDEP}]
-	dev-python/astropy-helpers[${PYTHON_USEDEP}]
-	dev-python/matplotlib[${PYTHON_USEDEP}]
-	dev-python/numpy[${PYTHON_USEDEP}]"
-
-DEPEND="${RDEPEND}"
-
-python_prepare_all() {
-	distutils-r1_python_prepare_all
-	sed -e '/import ah_bootstrap/d' -i setup.py || die "Removing ah_bootstrap failed"
-}
-
-python_compile_all() {
-	if use doc; then
-		python_export_best
-		VARTEXFONTS="${T}"/fonts \
-			MPLCONFIGDIR="${BUILD_DIR}" \
-			PYTHONPATH="${BUILD_DIR}"/lib \
-			esetup.py build_sphinx
-	fi
-}
-
-python_test() {
-	distutils_install_for_testing
-	cd "${TEST_DIR}" || die
-	"${EPYTHON}" -c "import ${PN}, sys;r = ${PN}.test(verbose=True);sys.exit(r)" \
-		|| die "tests fail with ${EPYTHON}"
-}
-
-python_install_all() {
-	use doc && local HTML_DOCS=( docs/_build/html/. )
-	distutils-r1_python_install_all
-}
diff --git a/dev-python/sphinx-astropy/Manifest b/dev-python/sphinx-astropy/Manifest
new file mode 100644
index 000000000..7cbf6d7c8
--- /dev/null
+++ b/dev-python/sphinx-astropy/Manifest
@@ -0,0 +1 @@
+DIST sphinx-astropy-1.8.0.tar.gz 18310 BLAKE2B 0d13ba59b2ffcb792e66e58d2a87057b79da811d38e6fd101b074b0edbf5ad6d76e79300f5863521b0bbb1b40921ba6773f8d37c32d68dd36078cb2d0497e2ff SHA512 f02fe8d3ed58ffeff190492c07e2df91a2bd5bcc8e82c6685002e543585a5fc1294ebd46821b7dc0a364540f3a45adacf1b90261b7da95657bc99dcd6130f4d5
diff --git a/dev-python/sphinx-astropy/metadata.xml b/dev-python/sphinx-astropy/metadata.xml
new file mode 100644
index 000000000..8d01c3b18
--- /dev/null
+++ b/dev-python/sphinx-astropy/metadata.xml
@@ -0,0 +1,11 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
+<pkgmetadata>
+	<maintainer type="project">
+		<email>sci-astronomy@gentoo.org</email>
+		<name>Gentoo Astronomy Project</name>
+	</maintainer>
+	<upstream>
+		<remote-id type="pypi">sphinx-astropy</remote-id>
+	</upstream>
+</pkgmetadata>
diff --git a/dev-python/sphinx-astropy/sphinx-astropy-1.8.0.ebuild b/dev-python/sphinx-astropy/sphinx-astropy-1.8.0.ebuild
new file mode 100644
index 000000000..89d58fc6b
--- /dev/null
+++ b/dev-python/sphinx-astropy/sphinx-astropy-1.8.0.ebuild
@@ -0,0 +1,32 @@
+# Copyright 1999-2022 Gentoo Authors
+# Distributed under the terms of the GNU General Public License v2
+
+EAPI=8
+
+PYTHON_COMPAT=( python3_{10..11} )
+DISTUTILS_USE_PEP517=setuptools
+PYPI_NO_NORMALIZE=1
+
+inherit distutils-r1 pypi
+
+DESCRIPTION="Sphinx extensions and configuration specific to the Astropy project"
+HOMEPAGE="https://www.astropy.org/"
+
+LICENSE="BSD"
+SLOT="0"
+KEYWORDS="~amd64 ~x86"
+
+# Requires access to the internet
+RESTRICT="test"
+
+RDEPEND="
+	dev-python/packaging[${PYTHON_USEDEP}]
+	dev-python/astropy-sphinx-theme[${PYTHON_USEDEP}]
+	dev-python/numpydoc[${PYTHON_USEDEP}]
+	>=dev-python/sphinx-1.7[${PYTHON_USEDEP}]
+	dev-python/sphinx-automodapi[${PYTHON_USEDEP}]
+	dev-python/sphinx-gallery[${PYTHON_USEDEP}]
+	dev-python/pillow[${PYTHON_USEDEP}]
+"
+
+distutils_enable_tests pytest
diff --git a/dev-python/sphinx-automodapi/Manifest b/dev-python/sphinx-automodapi/Manifest
new file mode 100644
index 000000000..31e6f3c8b
--- /dev/null
+++ b/dev-python/sphinx-automodapi/Manifest
@@ -0,0 +1 @@
+DIST sphinx-automodapi-0.14.1.tar.gz 45504 BLAKE2B 1d6aa247c9991260c0d6421dbeb80adccec72f60e6e0035ef892d6582e62608dd526a77da6c4b5066c9c100228fd6aceb77a9965eab76c0b9117a96d76ee221a SHA512 fae2927f8f9ec29f5e8e945b2902a0fa94231446b514be884ddab1a8644b4e305408e986b74a4506447baf00c4941cf9e7585f0c8e82820935a3d831bcfa6374
diff --git a/dev-python/sphinx-automodapi/metadata.xml b/dev-python/sphinx-automodapi/metadata.xml
new file mode 100644
index 000000000..092a8c5e9
--- /dev/null
+++ b/dev-python/sphinx-automodapi/metadata.xml
@@ -0,0 +1,11 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
+<pkgmetadata>
+	<maintainer type="project">
+		<email>sci-astronomy@gentoo.org</email>
+		<name>Gentoo Astronomy Project</name>
+	</maintainer>
+	<upstream>
+		<remote-id type="pypi">sphinx-automodapi</remote-id>
+	</upstream>
+</pkgmetadata>
diff --git a/dev-python/sphinx-automodapi/sphinx-automodapi-0.14.1-r1.ebuild b/dev-python/sphinx-automodapi/sphinx-automodapi-0.14.1-r1.ebuild
new file mode 100644
index 000000000..e64b9a0e0
--- /dev/null
+++ b/dev-python/sphinx-automodapi/sphinx-automodapi-0.14.1-r1.ebuild
@@ -0,0 +1,24 @@
+# Copyright 1999-2022 Gentoo Authors
+# Distributed under the terms of the GNU General Public License v2
+
+EAPI=8
+
+PYTHON_COMPAT=( python3_{10..11} )
+DISTUTILS_USE_PEP517=setuptools
+PYPI_NO_NORMALIZE=1
+
+inherit distutils-r1 pypi
+
+DESCRIPTION="Sphinx extension for auto-generating API documentation for entire modules"
+HOMEPAGE="https://www.astropy.org/"
+
+LICENSE="BSD"
+SLOT="0"
+KEYWORDS="~amd64 ~x86"
+
+# Requires network for some reason
+RESTRICT="test"
+
+RDEPEND="dev-python/sphinx[${PYTHON_USEDEP}]"
+
+distutils_enable_tests pytest
diff --git a/dev-python/sphinxcontrib-napoleon/Manifest b/dev-python/sphinxcontrib-napoleon/Manifest
new file mode 100644
index 000000000..fdfb3f5ec
--- /dev/null
+++ b/dev-python/sphinxcontrib-napoleon/Manifest
@@ -0,0 +1 @@
+DIST sphinxcontrib-napoleon-0.7.tar.gz 21232 BLAKE2B c64433a9e42d7f68ffca0f3d45e927a10ff8a67e47d0d05f19614c1625db29633774155a9ddb48fb1a32fe04710ecb597fc13b393738afb7266afc6e62526346 SHA512 000fc00b21148ed38b3f0beed5163e232f50642369641a940fd77b30c3c426d799144b3e1c7fbc4dd86b5b1f526656b56be7d77239d4cd3a14dd93178c0e13f8
diff --git a/dev-python/sphinxcontrib-napoleon/metadata.xml b/dev-python/sphinxcontrib-napoleon/metadata.xml
new file mode 100644
index 000000000..ca93985fb
--- /dev/null
+++ b/dev-python/sphinxcontrib-napoleon/metadata.xml
@@ -0,0 +1,9 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
+
+<pkgmetadata>
+	<maintainer type="project">
+		<email>sci@gentoo.org</email>
+		<name>Gentoo Science Project</name>
+	</maintainer>
+</pkgmetadata>
diff --git a/dev-python/sphinxcontrib-napoleon/sphinxcontrib-napoleon-0.7-r1.ebuild b/dev-python/sphinxcontrib-napoleon/sphinxcontrib-napoleon-0.7-r1.ebuild
new file mode 100644
index 000000000..0a962fd5e
--- /dev/null
+++ b/dev-python/sphinxcontrib-napoleon/sphinxcontrib-napoleon-0.7-r1.ebuild
@@ -0,0 +1,30 @@
+# Copyright 1999-2022 Gentoo Authors
+# Distributed under the terms of the GNU General Public License v2
+
+EAPI=8
+
+PYTHON_COMPAT=( python3_{10..11} )
+DISTUTILS_USE_PEP517=setuptools
+PYPI_NO_NORMALIZE=1
+
+inherit distutils-r1 pypi
+
+DESCRIPTION="Allow a different format in dosctrings for better clarity"
+HOMEPAGE="https://sphinxcontrib-napoleon.readthedocs.io/"
+
+LICENSE="BSD"
+SLOT="0"
+KEYWORDS="~amd64 ~x86"
+
+RDEPEND="
+	dev-python/sphinx[${PYTHON_USEDEP}]
+"
+DEPEND="
+	dev-python/pockets[${PYTHON_USEDEP}]
+	dev-python/six[${PYTHON_USEDEP}]
+"
+
+python_install_all() {
+	distutils-r1_python_install_all
+	find "${ED}" -name '*.pth' -delete || die
+}
diff --git a/dev-python/spikeinterface/Manifest b/dev-python/spikeinterface/Manifest
new file mode 100644
index 000000000..bdf3e4b60
--- /dev/null
+++ b/dev-python/spikeinterface/Manifest
@@ -0,0 +1,3 @@
+DIST spikeinterface-0.96.1.tar.gz 1596455 BLAKE2B 52b5d4f0b435433396e7d06b9a2ed83646280ebefb1f62f179f068a060f43898a822e41bf1500ec53087ad5410ee060806f415988606b0197d13d7a671a5603a SHA512 12de90a8d27e900489d36d0ca14edaac3d1abab1a29f0c41ff1d1648fbf11be09c6c01cb0bd1cc4e1d00a81303fab5ffcb4de596ae69be9508e0503edab768ef
+DIST spikeinterface-0.97.0.tar.gz 6735715 BLAKE2B c11bee4306f8d96ae5cd09cf1b852e267c1db6caa13565f6364cd65ee36fe62c04589e8e0657517003ed1dd6d76d25f60bef226820403111db4ed7717e8a20cd SHA512 befdf3382de6aad2ef2c72e3bbdf64fbee1c1f72f83610ca8bba2f8693992c84b515f8c000dc6b3609825347b0bcd85b026747633e90777d7fdd30dc0ae0ef13
+DIST spikeinterface-0.99.1.tar.gz 11475537 BLAKE2B 9427079f70020b882c7bdbaadb9b60508827f1131f3aeb4fa8fdaaada73f2aa2cb3ec018f87467cd2a7505bea435d6bcf04d9784d921829533ebf41d686d72bb SHA512 4dd513aa6eb8af58fa9d1a80671973b01cb81643588c4522f3f87cfd0ccebcfb7a1f2926e554bc7dadbb2201fc0b2f2873b0003483dd5ca578b5a76d4cce05a2
diff --git a/dev-python/spikeinterface/metadata.xml b/dev-python/spikeinterface/metadata.xml
new file mode 100644
index 000000000..f91c7a26c
--- /dev/null
+++ b/dev-python/spikeinterface/metadata.xml
@@ -0,0 +1,19 @@
+<?xml version='1.0' encoding='UTF-8'?>
+<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
+<pkgmetadata>
+	<maintainer type="person">
+		<email>gentoo@chymera.eu</email>
+		<name>Horea Christian</name>
+	</maintainer>
+	<maintainer type="project">
+		<email>sci@gentoo.org</email>
+		<name>Gentoo Science Project</name>
+	</maintainer>
+	<use>
+		<flag name="extractors">support for all extractors</flag>
+		<flag name="full">support for all optional processing features</flag>
+	</use>
+	<upstream>
+		<remote-id type="github">SpikeInterface/spikeinterface</remote-id>
+	</upstream>
+</pkgmetadata>
diff --git a/dev-python/spikeinterface/spikeinterface-0.96.1.ebuild b/dev-python/spikeinterface/spikeinterface-0.96.1.ebuild
new file mode 100644
index 000000000..ef6a472f4
--- /dev/null
+++ b/dev-python/spikeinterface/spikeinterface-0.96.1.ebuild
@@ -0,0 +1,93 @@
+# Copyright 2021-2023 Gentoo Authors
+# Distributed under the terms of the GNU General Public License v2
+
+EAPI=8
+
+PYTHON_COMPAT=( python3_{10..11} )
+DISTUTILS_USE_PEP517=setuptools
+inherit distutils-r1
+
+DESCRIPTION="A Python-based module for creating flexible and robust spike sorting pipelines."
+HOMEPAGE="https://github.com/SpikeInterface/spikeinterface"
+SRC_URI="https://github.com/SpikeInterface/spikeinterface/archive/refs/tags/${PV}.tar.gz -> ${P}.tar.gz"
+
+LICENSE="MIT"
+SLOT="0"
+KEYWORDS="~amd64"
+IUSE="extractors full test"
+
+RDEPEND="
+	dev-python/joblib[${PYTHON_USEDEP}]
+	dev-python/neo[${PYTHON_USEDEP}]
+	dev-python/numpy[${PYTHON_USEDEP}]
+	dev-python/probeinterface[${PYTHON_USEDEP}]
+	dev-python/threadpoolctl[${PYTHON_USEDEP}]
+	dev-python/tqdm[${PYTHON_USEDEP}]
+	extractors? (
+		dev-python/pynwb[${PYTHON_USEDEP}]
+		dev-python/lxml[${PYTHON_USEDEP}]
+		dev-python/scipy[${PYTHON_USEDEP}]
+	)
+	full? (
+		dev-python/distinctipy[${PYTHON_USEDEP}]
+		dev-python/h5py[${PYTHON_USEDEP}]
+		dev-python/matplotlib[${PYTHON_USEDEP}]
+		dev-python/networkx[${PYTHON_USEDEP}]
+		dev-python/pandas[${PYTHON_USEDEP}]
+		dev-python/scipy[${PYTHON_USEDEP}]
+		dev-python/xarray[${PYTHON_USEDEP}]
+		dev-python/zarr[${PYTHON_USEDEP}]
+		sci-libs/scikit-learn[${PYTHON_USEDEP}]
+	)
+"
+# Also wants:
+# # Extractors:
+# 	MEArec
+# 	pyedflib
+# 	sonpy
+# 	dev-python/hdf5storage (in ::science, masked)
+
+distutils_enable_tests pytest
+
+# Test failures reported upstream:
+# https://github.com/SpikeInterface/spikeinterface/issues/307
+python_test() {
+	# Network sandboxing, mostly (?)
+	local EPYTEST_DESELECT=(
+		spikeinterface/core/tests/test_datasets.py::test_download_dataset
+		spikeinterface/sortingcomponents/tests/test_motion_estimation.py::test_motion_functions
+		spikeinterface/sortingcomponents/tests/test_motion_estimation.py::test_estimate_motion_rigid
+		spikeinterface/sortingcomponents/tests/test_motion_estimation.py::test_estimate_motion_non_rigid
+		spikeinterface/comparison/tests/test_multisortingcomparison.py::test_compare_multiple_sorters
+		spikeinterface/curation/tests/test_sortingview_curation.py::test_sortingview_curation
+		spikeinterface/exporters/tests/test_export_to_phy.py::test_export_to_phy
+		spikeinterface/exporters/tests/test_export_to_phy.py::test_export_to_phy_by_sparsity
+		spikeinterface/exporters/tests/test_report.py::test_export_report
+		spikeinterface/extractors/tests/test_neoextractors.py
+		spikeinterface/sorters/tests/test_launcher.py::test_run_sorters_with_dict
+		spikeinterface/sorters/tests/test_launcher.py::test_sorter_installation
+		spikeinterface/sorters/tests/test_runsorter.py::test_run_sorter_local
+		spikeinterface/sorters/tests/test_runsorter.py::test_run_sorter_docker
+		spikeinterface/sorters/tests/test_runsorter.py::test_run_sorter_singularity
+		spikeinterface/sorters/tests/test_si_based_sorters.py::SpykingCircus2SorterCommonTestSuite
+		spikeinterface/sorters/tests/test_si_based_sorters.py::Tridesclous2SorterCommonTestSuite::test_with_class
+		spikeinterface/sorters/tests/test_si_based_sorters.py::Tridesclous2SorterCommonTestSuite::test_with_run
+		spikeinterface/sortingcomponents/tests/test_clustering.py::test_find_cluster_from_peaks
+		spikeinterface/sortingcomponents/tests/test_features_from_peaks.py::test_features_from_peaks
+		spikeinterface/sortingcomponents/tests/test_peak_detection.py::test_detect_peaks
+		spikeinterface/sortingcomponents/tests/test_peak_localization.py::test_localize_peaks
+		spikeinterface/sortingcomponents/tests/test_peak_pipeline.py::test_run_peak_pipeline
+		spikeinterface/sortingcomponents/tests/test_peak_selection.py::test_detect_peaks
+		spikeinterface/sortingcomponents/tests/test_template_matching.py::test_find_spikes_from_templates
+		spikeinterface/widgets/tests/test_widgets.py::TestWidgets
+	)
+	# Reported upstream:
+	# https://github.com/SpikeInterface/spikeinterface/issues/307#issuecomment-1410840998
+	EPYTEST_DESELECT+=(
+		spikeinterface/sorters/tests/test_launcher.py::test_collect_sorting_outputs
+	)
+	local EPYTEST_IGNORE=(
+		spikeinterface/widgets/_legacy_mpl_widgets/tests/*
+	)
+	epytest
+}
diff --git a/dev-python/spikeinterface/spikeinterface-0.97.0.ebuild b/dev-python/spikeinterface/spikeinterface-0.97.0.ebuild
new file mode 100644
index 000000000..2a25d4eee
--- /dev/null
+++ b/dev-python/spikeinterface/spikeinterface-0.97.0.ebuild
@@ -0,0 +1,93 @@
+# Copyright 2021-2023 Gentoo Authors
+# Distributed under the terms of the GNU General Public License v2
+
+EAPI=8
+
+PYTHON_COMPAT=( python3_{10..11} )
+DISTUTILS_USE_PEP517=setuptools
+inherit distutils-r1
+
+DESCRIPTION="A Python-based module for creating flexible and robust spike sorting pipelines."
+HOMEPAGE="https://github.com/SpikeInterface/spikeinterface"
+SRC_URI="https://github.com/SpikeInterface/spikeinterface/archive/refs/tags/${PV}.tar.gz -> ${P}.tar.gz"
+
+LICENSE="MIT"
+SLOT="0"
+KEYWORDS="~amd64"
+IUSE="extractors full test"
+
+RDEPEND="
+	dev-python/joblib[${PYTHON_USEDEP}]
+	dev-python/neo[${PYTHON_USEDEP}]
+	dev-python/numpy[${PYTHON_USEDEP}]
+	>=dev-python/probeinterface-0.2.16[${PYTHON_USEDEP}]
+	dev-python/threadpoolctl[${PYTHON_USEDEP}]
+	dev-python/tqdm[${PYTHON_USEDEP}]
+	extractors? (
+		dev-python/pynwb[${PYTHON_USEDEP}]
+		dev-python/lxml[${PYTHON_USEDEP}]
+		dev-python/scipy[${PYTHON_USEDEP}]
+	)
+	full? (
+		dev-python/distinctipy[${PYTHON_USEDEP}]
+		dev-python/h5py[${PYTHON_USEDEP}]
+		dev-python/matplotlib[${PYTHON_USEDEP}]
+		dev-python/networkx[${PYTHON_USEDEP}]
+		dev-python/pandas[${PYTHON_USEDEP}]
+		dev-python/scipy[${PYTHON_USEDEP}]
+		dev-python/xarray[${PYTHON_USEDEP}]
+		dev-python/zarr[${PYTHON_USEDEP}]
+		sci-libs/scikit-learn[${PYTHON_USEDEP}]
+	)
+"
+# Also wants:
+# # Extractors:
+# 	MEArec
+# 	pyedflib
+# 	sonpy
+# 	dev-python/hdf5storage (in ::science, masked)
+
+distutils_enable_tests pytest
+
+# Test failures reported upstream:
+# https://github.com/SpikeInterface/spikeinterface/issues/307
+python_test() {
+	# Network sandboxing, mostly (?)
+	local EPYTEST_DESELECT=(
+		spikeinterface/core/tests/test_datasets.py::test_download_dataset
+		spikeinterface/sortingcomponents/tests/test_motion_estimation.py::test_motion_functions
+		spikeinterface/sortingcomponents/tests/test_motion_estimation.py::test_estimate_motion_rigid
+		spikeinterface/sortingcomponents/tests/test_motion_estimation.py::test_estimate_motion_non_rigid
+		spikeinterface/comparison/tests/test_multisortingcomparison.py::test_compare_multiple_sorters
+		spikeinterface/curation/tests/test_sortingview_curation.py::test_sortingview_curation
+		spikeinterface/exporters/tests/test_export_to_phy.py::test_export_to_phy
+		spikeinterface/exporters/tests/test_export_to_phy.py::test_export_to_phy_by_sparsity
+		spikeinterface/exporters/tests/test_report.py::test_export_report
+		spikeinterface/extractors/tests/test_neoextractors.py
+		spikeinterface/sorters/tests/test_launcher.py::test_run_sorters_with_dict
+		spikeinterface/sorters/tests/test_launcher.py::test_sorter_installation
+		spikeinterface/sorters/tests/test_runsorter.py::test_run_sorter_local
+		spikeinterface/sorters/tests/test_runsorter.py::test_run_sorter_docker
+		spikeinterface/sorters/tests/test_runsorter.py::test_run_sorter_singularity
+		spikeinterface/sorters/tests/test_si_based_sorters.py::SpykingCircus2SorterCommonTestSuite
+		spikeinterface/sorters/tests/test_si_based_sorters.py::Tridesclous2SorterCommonTestSuite::test_with_class
+		spikeinterface/sorters/tests/test_si_based_sorters.py::Tridesclous2SorterCommonTestSuite::test_with_run
+		spikeinterface/sortingcomponents/tests/test_clustering.py::test_find_cluster_from_peaks
+		spikeinterface/sortingcomponents/tests/test_features_from_peaks.py::test_features_from_peaks
+		spikeinterface/sortingcomponents/tests/test_peak_detection.py::test_detect_peaks
+		spikeinterface/sortingcomponents/tests/test_peak_localization.py::test_localize_peaks
+		spikeinterface/sortingcomponents/tests/test_peak_pipeline.py::test_run_peak_pipeline
+		spikeinterface/sortingcomponents/tests/test_peak_selection.py::test_detect_peaks
+		spikeinterface/sortingcomponents/tests/test_template_matching.py::test_find_spikes_from_templates
+		spikeinterface/widgets/tests/test_widgets.py::TestWidgets
+	)
+	# Reported upstream:
+	# https://github.com/SpikeInterface/spikeinterface/issues/307#issuecomment-1410840998
+	EPYTEST_DESELECT+=(
+		spikeinterface/sorters/tests/test_launcher.py::test_collect_sorting_outputs
+	)
+	local EPYTEST_IGNORE=(
+		spikeinterface/widgets/_legacy_mpl_widgets/tests/*
+	)
+	epytest
+}
diff --git a/dev-python/spikeinterface/spikeinterface-0.99.1.ebuild b/dev-python/spikeinterface/spikeinterface-0.99.1.ebuild
new file mode 100644
index 000000000..a428775eb
--- /dev/null
+++ b/dev-python/spikeinterface/spikeinterface-0.99.1.ebuild
@@ -0,0 +1,53 @@
+# Copyright 2021-2023 Gentoo Authors
+# Distributed under the terms of the GNU General Public License v2
+
+EAPI=8
+
+PYTHON_COMPAT=( python3_{10..11} )
+DISTUTILS_USE_PEP517=setuptools
+inherit distutils-r1
+
+DESCRIPTION="A Python-based module for creating flexible and robust spike sorting pipelines."
+HOMEPAGE="https://github.com/SpikeInterface/spikeinterface"
+SRC_URI="https://github.com/SpikeInterface/spikeinterface/archive/refs/tags/${PV}.tar.gz -> ${P}.tar.gz"
+
+LICENSE="MIT"
+SLOT="0"
+KEYWORDS="~amd64"
+IUSE="extractors full test"
+# Reported upstream:
+# https://github.com/SpikeInterface/spikeinterface/issues/2339
+RESTRICT="test"
+
+RDEPEND="
+	dev-python/joblib[${PYTHON_USEDEP}]
+	dev-python/neo[${PYTHON_USEDEP}]
+	dev-python/numpy[${PYTHON_USEDEP}]
+	>=dev-python/probeinterface-0.2.16[${PYTHON_USEDEP}]
+	dev-python/threadpoolctl[${PYTHON_USEDEP}]
+	dev-python/tqdm[${PYTHON_USEDEP}]
+	extractors? (
+		dev-python/pynwb[${PYTHON_USEDEP}]
+		dev-python/lxml[${PYTHON_USEDEP}]
+		dev-python/scipy[${PYTHON_USEDEP}]
+	)
+	full? (
+		dev-python/distinctipy[${PYTHON_USEDEP}]
+		dev-python/h5py[${PYTHON_USEDEP}]
+		dev-python/matplotlib[${PYTHON_USEDEP}]
+		dev-python/networkx[${PYTHON_USEDEP}]
+		dev-python/pandas[${PYTHON_USEDEP}]
+		dev-python/scipy[${PYTHON_USEDEP}]
+		dev-python/xarray[${PYTHON_USEDEP}]
+		dev-python/zarr[${PYTHON_USEDEP}]
+		sci-libs/scikit-learn[${PYTHON_USEDEP}]
+	)
+"
+# Also wants:
+# # Extractors:
+# 	MEArec
+# 	pyedflib
+# 	sonpy
+# 	dev-python/hdf5storage (in ::science, masked)
+
+distutils_enable_tests pytest
diff --git a/dev-python/stopit/Manifest b/dev-python/stopit/Manifest
new file mode 100644
index 000000000..8509ce69f
--- /dev/null
+++ b/dev-python/stopit/Manifest
@@ -0,0 +1 @@
+DIST stopit-1.1.2.tar.gz 18281 BLAKE2B 500c4c60f7a1ae65231f546c28c6406bb1b01c48b43ac97757b87db1c6cfe460b9fb96543a46ec4ff36640e6aa758dbea543f75628bf7bf237e1f76acd54e62e SHA512 5ddf93c12ac19e2a2bf52a22838de13da1cf50f1a4d2ef8958dc3ddccd1884b7edaa629edc29121071ba231bfc1e3188bfa089da6e8fc994364c134f0c7aa0c8
diff --git a/dev-python/stopit/metadata.xml b/dev-python/stopit/metadata.xml
new file mode 100644
index 000000000..21d0546f4
--- /dev/null
+++ b/dev-python/stopit/metadata.xml
@@ -0,0 +1,11 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
+<pkgmetadata>
+	<maintainer type="project">
+		<email>sci@gentoo.org</email>
+		<name>Gentoo Science Project</name>
+	</maintainer>
+	<upstream>
+		<remote-id type="pypi">stopit</remote-id>
+	</upstream>
+</pkgmetadata>
diff --git a/dev-python/stopit/stopit-1.1.2.ebuild b/dev-python/stopit/stopit-1.1.2.ebuild
new file mode 100644
index 000000000..64d63502a
--- /dev/null
+++ b/dev-python/stopit/stopit-1.1.2.ebuild
@@ -0,0 +1,16 @@
+# Copyright 1999-2021 Gentoo Authors
+# Distributed under the terms of the GNU General Public License v2
+
+EAPI=8
+
+PYTHON_COMPAT=( python3_{10..11} )
+DISTUTILS_USE_PEP517=setuptools
+
+inherit distutils-r1 pypi
+
+DESCRIPTION="Timeout control decorator and context managers"
+HOMEPAGE="https://pypi.org/project/stopit"
+
+LICENSE="MIT"
+SLOT="0"
+KEYWORDS="~amd64"
diff --git a/dev-python/symengine/metadata.xml b/dev-python/symengine/metadata.xml
deleted file mode 100644
index e8f764b63..000000000
--- a/dev-python/symengine/metadata.xml
+++ /dev/null
@@ -1,15 +0,0 @@
-<?xml version="1.0" encoding="UTF-8"?>
-<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
-<pkgmetadata>
-	<maintainer type="person">
-		<email>mschu.dev@gmail.com</email>
-		<name>Michael Schubert</name>
-	</maintainer>
-	<maintainer type="project">
-		<email>sci-mathematics@gentoo.org</email>
-		<name>Gentoo Mathematics Project</name>
-	</maintainer>
-	<upstream>
-		<remote-id type="github">sympy/symengine.py</remote-id>
-	</upstream>
-</pkgmetadata>
diff --git a/dev-python/symengine/symengine-9999.ebuild b/dev-python/symengine/symengine-9999.ebuild
deleted file mode 100644
index 3d2a11f2c..000000000
--- a/dev-python/symengine/symengine-9999.ebuild
+++ /dev/null
@@ -1,31 +0,0 @@
-# Copyright 1999-2015 Gentoo Foundation
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=5
-
-PYTHON_COMPAT=( python{2_7,3_4,3_5} )
-
-inherit distutils-r1 git-r3
-
-DESCRIPTION="Python wrappers to the symengine C++ library"
-HOMEPAGE="https://github.com/sympy/symengine.py"
-SRC_URI=""
-EGIT_REPO_URI="https://github.com/symengine/symengine.py.git"
-
-LICENSE="MIT"
-SLOT="0"
-KEYWORDS="~amd64 ~x86 ~amd64-linux ~x86-linux"
-
-RDEPEND="
-	dev-python/numpy[${PYTHON_USEDEP}]
-	=sci-libs/symengine-9999"
-DEPEND="${RDEPEND}
-	dev-python/cython[${PYTHON_USEDEP}]
-	dev-python/setuptools[${PYTHON_USEDEP}]"
-
-# if this is not set python2 .so is linked to python3
-DISTUTILS_IN_SOURCE_BUILD=1
-
-python_install_all() {
-	newdoc README.md ${PN}_py.md
-}
diff --git a/dev-python/testpath/files/testpath-0.2-setup.py.patch b/dev-python/testpath/files/testpath-0.2-setup.py.patch
deleted file mode 100644
index 1dc73e77a..000000000
--- a/dev-python/testpath/files/testpath-0.2-setup.py.patch
+++ /dev/null
@@ -1,28 +0,0 @@
-Patch to bring back setup.py from
-https://github.com/jupyter/testpath/blob/086bd1bd1ec7da1b3dacfed1705c0c99fae231b3/setup.py
---- /dev/null
-+++ b/setup.py
-@@ -0,0 +1,22 @@
-+from distutils.core import setup
-+
-+with open("README.rst", "r") as f:
-+    readme = f.read()
-+
-+setup(name='testpath',
-+      version='0.3',
-+      description='Test utilities for code working with files and commands',
-+      long_description = readme,
-+      author='Thomas Kluyver',
-+      author_email='thomas@kluyver.me.uk',
-+      url='https://github.com/takluyver/testpath',
-+      packages=['testpath'],
-+      classifiers=[
-+          'Intended Audience :: Developers',
-+          'License :: OSI Approved :: MIT License',
-+          'Programming Language :: Python',
-+          'Programming Language :: Python :: 2',
-+          'Programming Language :: Python :: 3',
-+          'Topic :: Software Development :: Testing',
-+      ]
-+)
-\ No newline at end of file
diff --git a/dev-python/testpath/metadata.xml b/dev-python/testpath/metadata.xml
deleted file mode 100644
index 8129b08bc..000000000
--- a/dev-python/testpath/metadata.xml
+++ /dev/null
@@ -1,14 +0,0 @@
-<?xml version="1.0" encoding="UTF-8"?>
-<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
-<pkgmetadata>
-	<maintainer type="project">
-		<email>sci@gentoo.org</email>
-		<name>Gentoo Science Project</name>
-	</maintainer>
-	<longdescription>
-Testpath is a collection of utilities for Python code working with
-files and commands. It contains functions to check things on the
-filesystem, and tools for mocking system commands and recording
-calls to those.
-</longdescription>
-</pkgmetadata>
diff --git a/dev-python/testpath/testpath-9999.ebuild b/dev-python/testpath/testpath-9999.ebuild
deleted file mode 100644
index 70fcabfd1..000000000
--- a/dev-python/testpath/testpath-9999.ebuild
+++ /dev/null
@@ -1,53 +0,0 @@
-# Copyright 1999-2017 Gentoo Foundation
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=6
-
-PYTHON_COMPAT=( python2_7 python3_{4,5} )
-
-inherit distutils-r1 git-r3
-
-DESCRIPTION="Test utilities for code working with files and commands"
-HOMEPAGE="http://jupyter.org"
-EGIT_REPO_URI="https://github.com/jupyter/${PN}.git git://github.com/jupyter/${PN}.git"
-
-LICENSE="BSD"
-SLOT="0"
-IUSE="doc test"
-
-DEPEND="
-	test? (
-		dev-python/pytest[${PYTHON_USEDEP}]
-		virtual/python-pathlib[${PYTHON_USEDEP}]
-	)
-	doc? ( dev-python/sphinx[${PYTHON_USEDEP}] )
-	"
-
-PATCHES=(
-	"${FILESDIR}/${PN}"-0.2-setup.py.patch
-	)
-
-python_prepare_all() {
-	# Prevent un-needed download during build
-	if use doc; then
-		sed -e "/^    'sphinx.ext.intersphinx',/d" -i doc/conf.py || die
-	fi
-
-distutils-r1_python_prepare_all
-}
-
-python_compile_all() {
-	use doc && emake -C doc html
-}
-
-python_install_all() {
-	use doc && HTML_DOCS=( doc/_build/html/. )
-	distutils-r1_python_install_all
-	}
-
-python_test() {
-	distutils_install_for_testing
-	cd "${TEST_DIR}"/lib || die
-	cp -r "${S}"/tests "${TEST_DIR}"/lib/ || die
-	py.test || die
-}
diff --git a/dev-python/texext/Manifest b/dev-python/texext/Manifest
new file mode 100644
index 000000000..3300b31c6
--- /dev/null
+++ b/dev-python/texext/Manifest
@@ -0,0 +1 @@
+DIST texext-0.6.7.gh.tar.gz 42823 BLAKE2B 224cb700f5ee74de75c41d8248a1cbb494f773f8124638974fbabdbffcd2bf72237c55b15e12ea8e5a5086dab02fde798efe5f3519befddb1a4535ed233414a3 SHA512 abdc57f9fd38b3d6e261347a3ba2d7d7400d8b7bd79c2763a40cc34aa72a079fe55dae1fc0117f2da604331a449b2d9168f320a6ecc2f13c62a6615c000523f8
diff --git a/dev-python/texext/metadata.xml b/dev-python/texext/metadata.xml
new file mode 100644
index 000000000..026cdb22b
--- /dev/null
+++ b/dev-python/texext/metadata.xml
@@ -0,0 +1,8 @@
+<?xml version='1.0' encoding='UTF-8'?>
+<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
+<pkgmetadata>
+	<maintainer type="project">
+		<email>sci@gentoo.org</email>
+		<name>Gentoo Science Project</name>
+	</maintainer>
+</pkgmetadata>
diff --git a/dev-python/texext/texext-0.6.7.ebuild b/dev-python/texext/texext-0.6.7.ebuild
new file mode 100644
index 000000000..fdeb2350a
--- /dev/null
+++ b/dev-python/texext/texext-0.6.7.ebuild
@@ -0,0 +1,33 @@
+# Copyright 1999-2021 Gentoo Authors
+# Distributed under the terms of the GNU General Public License v2
+
+EAPI=8
+
+PYTHON_COMPAT=( python3_10 )
+DISTUTILS_USE_PEP517=setuptools
+inherit distutils-r1
+
+DESCRIPTION="Sphinx extensions for working with LaTeX math"
+HOMEPAGE="https://github.com/matthew-brett/texext"
+SRC_URI="https://github.com/matthew-brett/texext/archive/refs/tags/${PV}.tar.gz -> ${P}.gh.tar.gz"
+
+LICENSE="BSD"
+SLOT="0"
+KEYWORDS="~amd64 ~x86"
+
+# TODO: package sphinxtesters
+# E   ModuleNotFoundError: No module named 'sphinxtesters'
+RESTRICT="test"
+
+RDEPEND="
+	dev-python/sphinx[${PYTHON_USEDEP}]
+	dev-python/six[${PYTHON_USEDEP}]
+	dev-python/docutils[${PYTHON_USEDEP}]
+"
+
+BDEPEND="test? (
+	dev-python/matplotlib[${PYTHON_USEDEP}]
+	dev-python/sympy[${PYTHON_USEDEP}]
+)"
+
+distutils_enable_tests pytest
diff --git a/dev-python/throttler/Manifest b/dev-python/throttler/Manifest
new file mode 100644
index 000000000..fcd07b799
--- /dev/null
+++ b/dev-python/throttler/Manifest
@@ -0,0 +1 @@
+DIST throttler-1.2.2.gh.tar.gz 8874 BLAKE2B f4f62059483551d2516e0d744ce4de4de1d83c5d169583944f2fba390acc2f6aadd5f212158de2c59b85356d71396a02404051e9206dfffec25be95ae983686a SHA512 a45cba0400e2e6225bcc396d1a216e781be9264345c215aa0c9e009d463bb80fca449ef0cc6a67657c443f9624e0864644cd5187351e815292894176dd6f13bb
diff --git a/dev-python/throttler/metadata.xml b/dev-python/throttler/metadata.xml
new file mode 100644
index 000000000..dff8139fd
--- /dev/null
+++ b/dev-python/throttler/metadata.xml
@@ -0,0 +1,12 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
+<pkgmetadata>
+	<maintainer type="project">
+		<email>sci@gentoo.org</email>
+		<name>Gentoo Science Project</name>
+	</maintainer>
+	<upstream>
+		<remote-id type="github">uburuntu/throttler</remote-id>
+		<remote-id type="pypi">throttler</remote-id>
+	</upstream>
+</pkgmetadata>
diff --git a/dev-python/throttler/throttler-1.2.2.ebuild b/dev-python/throttler/throttler-1.2.2.ebuild
new file mode 100644
index 000000000..0d0d62a16
--- /dev/null
+++ b/dev-python/throttler/throttler-1.2.2.ebuild
@@ -0,0 +1,25 @@
+# Copyright 1999-2021 Gentoo Authors
+# Distributed under the terms of the GNU General Public License v2
+
+EAPI=8
+
+PYTHON_COMPAT=( python3_{10..11} )
+DISTUTILS_USE_PEP517=setuptools
+
+inherit distutils-r1
+
+DESCRIPTION="Easy throttling with asyncio support"
+HOMEPAGE="https://github.com/uburuntu/throttler"
+SRC_URI="https://github.com/uburuntu/throttler/archive/refs/tags/v${PV}.tar.gz -> ${P}.gh.tar.gz"
+
+LICENSE="MIT"
+SLOT="0"
+KEYWORDS="~amd64"
+
+BDEPEND="
+	test? (
+		dev-python/pytest-asyncio[${PYTHON_USEDEP}]
+	)
+"
+
+distutils_enable_tests pytest
diff --git a/dev-python/traitlets/metadata.xml b/dev-python/traitlets/metadata.xml
deleted file mode 100644
index 3f68d9cc7..000000000
--- a/dev-python/traitlets/metadata.xml
+++ /dev/null
@@ -1,16 +0,0 @@
-<?xml version="1.0" encoding="UTF-8"?>
-<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
-<pkgmetadata>
-	<maintainer type="project">
-		<email>sci@gentoo.org</email>
-		<name>Gentoo Science Project</name>
-	</maintainer>
-	<longdescription>
-A lightweight pure-Python derivative of Enthought Traits,
-used for configuring Python objects. This package powers
-the config system of IPython and Jupyter.
-</longdescription>
-	<upstream>
-		<remote-id type="github">ipython/traitlets</remote-id>
-	</upstream>
-</pkgmetadata>
diff --git a/dev-python/traitlets/traitlets-9999.ebuild b/dev-python/traitlets/traitlets-9999.ebuild
deleted file mode 100644
index 889a831f4..000000000
--- a/dev-python/traitlets/traitlets-9999.ebuild
+++ /dev/null
@@ -1,53 +0,0 @@
-# Copyright 1999-2017 Gentoo Foundation
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=6
-
-PYTHON_COMPAT=( python2_7 python3_{4,5} )
-
-inherit distutils-r1 git-r3
-
-DESCRIPTION="A configuration system for Python applications"
-HOMEPAGE="https://github.com/ipython/traitlets"
-EGIT_REPO_URI="https://github.com/ipython/${PN}.git git://github.com/ipython/${PN}.git"
-
-LICENSE="BSD"
-SLOT="0"
-KEYWORDS=""
-IUSE="doc test"
-
-RDEPEND="
-	dev-python/decorator[${PYTHON_USEDEP}]
-	dev-python/ipython_genutils[${PYTHON_USEDEP}]
-	"
-DEPEND="
-	doc? (
-		dev-python/ipython_genutils[${PYTHON_USEDEP}]
-		dev-python/sphinx[${PYTHON_USEDEP}]
-	)
-	test? (
-		dev-python/nose[${PYTHON_USEDEP}]
-		dev-python/coverage[${PYTHON_USEDEP}]
-	)"
-
-python_prepare_all() {
-	# Prevent un-needed download during build
-	if use doc; then
-		sed -e "/^    'sphinx.ext.intersphinx',/d" -i docs/source/conf.py || die
-	fi
-
-	distutils-r1_python_prepare_all
-}
-
-python_compile_all() {
-	use doc && emake -C docs html
-}
-
-python_test() {
-	nosetests --with-coverage --cover-package traitlets traitlets || die
-}
-
-python_install_all() {
-	use doc && HTML_DOCS=( docs/build/html/. )
-	distutils-r1_python_install_all
-}
diff --git a/dev-python/traits/Manifest b/dev-python/traits/Manifest
index 961583d00..c33b93d1f 100644
--- a/dev-python/traits/Manifest
+++ b/dev-python/traits/Manifest
@@ -1,3 +1,2 @@
-DIST traits-4.5.0.tar.gz 4853612 BLAKE2B 6c3d83718751de1e0553487a45d073c285ada96686558133fe61472c29c3d4661e1c0bce68340bada9667f3f9e0c8ed11050a714bc0c55424dbd4ebd17e3ad8e SHA512 d506b4395395898eb824896d299bfcde609e100025cf9a55cd7d7c47615545efd3b007e46549e564fbfb2d5882b36ae676843f211f168b2557c504849c5ef582
-DIST traits-4.6.0.tar.gz 434937 BLAKE2B 91d457b411f78b74a077f3bfaa8e3f627d0ddb959784ba0ce9e07e3fc8b76cddcaee1fd7293d8336c4fc0630d49527fd29e1a9ccba6b724846069f6282c643e8 SHA512 0fce336696e4cbb1d4ba63a07ad42867cb179a9efa6c348623036bd6d2eb791302539ae89994b11acd5a9f1be42a0febeb517db1716342b78aa71ca1277fde99
-DIST traits-5.0.0.tar.gz 437001 BLAKE2B bfc9c69e4abbc341aaf8a62efcd443933097ce0612a5c6f98c2d16c7e21825f94d8fee0ec9cfbd7b30d406e68d4e006a3a12f629d507856c93093851334929cd SHA512 11e3b9b1f12d73df037fa95e4a5e48de7b7968a9598225a6c8de33e6250ff51c6b5ed056c0b55d90132139cb83b2b19121254152023408cb036c93971d3fa0e6
+DIST traits-6.3.2.tar.gz 9517139 BLAKE2B 9c6209a24fd07def86699174a66e2e0b3332670d974a75ead9486187c37e1c2c25b2a0c47e5444a03577931411ce6938b3b9ba195261a46c86d660c5abe9b502 SHA512 792004d88d2a00a1e9ba03974d58ec692b620f3c45aaf3bd82f93396818df8663a86903d43806c877230a66c5c8fee4d68268ed9355c166af00b5d060ba14c7d
+DIST traits-6.4.1.tar.gz 9527016 BLAKE2B 12036eeb845cc3014b0cba9984e1c1686a6720630678d440a2059c47916c08284b1f823ca566dcb6c1c86594ebec5400bb2a8c44d43d765a25d00e157fbbda74 SHA512 04b936195d57320c02fee9f0d5e7dbcfee28add422c151bd4aaa6d1c58c59f8de7fe54b4df039bb2023ffc9dae9570bba52210cd015ce462e0f736e9439327e5
diff --git a/dev-python/traits/metadata.xml b/dev-python/traits/metadata.xml
index 0e2713e31..2e84467ab 100644
--- a/dev-python/traits/metadata.xml
+++ b/dev-python/traits/metadata.xml
@@ -2,12 +2,12 @@
 <!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
 <pkgmetadata>
 	<maintainer type="person">
-		<email>horea.christ@gmail.com</email>
+		<email>gentoo@chymera.eu</email>
 		<name>Horea Christian</name>
 	</maintainer>
 	<maintainer type="project">
-		<email>proxy-maint@gentoo.org</email>
-		<name>Proxy Maintainers</name>
+		<email>sci@gentoo.org</email>
+		<name>Gentoo Science Project</name>
 	</maintainer>
 	<longdescription lang="en">
 		The traits package from the Enthought Tool Suite provides a
@@ -21,6 +21,7 @@
 		* Visualization: With the TraitsUI package, GUIs can be generated automatically from traited objects.
 	</longdescription>
 	<upstream>
+		<remote-id type="github">enthought/traits</remote-id>
 		<remote-id type="pypi">traits</remote-id>
 	</upstream>
 </pkgmetadata>
diff --git a/dev-python/traits/traits-4.5.0.ebuild b/dev-python/traits/traits-4.5.0.ebuild
deleted file mode 100644
index 528d28b25..000000000
--- a/dev-python/traits/traits-4.5.0.ebuild
+++ /dev/null
@@ -1,38 +0,0 @@
-# Copyright 1999-2019 Gentoo Authors
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=7
-
-PYTHON_COMPAT=( python2_7 )
-
-inherit distutils-r1 virtualx
-
-DESCRIPTION="Enthought Tool Suite: Explicitly typed attributes for Python"
-HOMEPAGE="http://docs.enthought.com/traits/
-	https://github.com/enthought/traits
-	https://pypi.org/project/traits/"
-SRC_URI="mirror://pypi/${PN:0:1}/${PN}/${P}.tar.gz"
-
-LICENSE="BSD"
-SLOT="0"
-KEYWORDS="~amd64 ~ppc ~ppc64 ~x86 ~amd64-linux ~x86-linux"
-IUSE="test"
-
-RDEPEND="dev-python/numpy[${PYTHON_USEDEP}]"
-DEPEND="dev-python/setuptools[${PYTHON_USEDEP}]
-	test? ( ${RDEPEND} )"
-
-python_prepare_all() {
-	sed -i -e "s/'-O3'//g" setup.py || die
-	distutils-r1_python_prepare_all
-}
-
-python_compile() {
-	local -x CFLAGS="${CFLAGS} -fno-strict-aliasing"
-	distutils-r1_python_compile
-}
-
-python_test() {
-	cd "${BUILD_DIR}"/lib || die
-	nosetests || die
-}
diff --git a/dev-python/traits/traits-4.6.0.ebuild b/dev-python/traits/traits-4.6.0.ebuild
deleted file mode 100644
index 5685ceeb5..000000000
--- a/dev-python/traits/traits-4.6.0.ebuild
+++ /dev/null
@@ -1,43 +0,0 @@
-# Copyright 1999-2019 Gentoo Authors
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=7
-
-PYTHON_COMPAT=( python{2_7,3_4,3_5,3_6} )
-
-inherit distutils-r1 virtualx
-
-DESCRIPTION="Enthought Tool Suite: Explicitly typed attributes for Python"
-HOMEPAGE="http://docs.enthought.com/traits/
-	https://github.com/enthought/traits
-	https://pypi.org/project/traits/"
-SRC_URI="mirror://pypi/${PN:0:1}/${PN}/${P}.tar.gz"
-
-LICENSE="BSD"
-SLOT="0"
-KEYWORDS="~amd64 ~ppc ~ppc64 ~x86 ~amd64-linux ~x86-linux"
-IUSE="test"
-
-RDEPEND="dev-python/numpy[${PYTHON_USEDEP}]"
-
-DEPEND="
-	dev-python/setuptools[${PYTHON_USEDEP}]
-	test? (
-		dev-python/nose[${PYTHON_USEDEP}]
-		${RDEPEND}
-		)"
-
-python_prepare_all() {
-	sed -i -e "s/'-O3'//g" setup.py || die
-	distutils-r1_python_prepare_all
-}
-
-python_compile() {
-	python_is_python3 || local -x CFLAGS="${CFLAGS} -fno-strict-aliasing"
-	distutils-r1_python_compile
-}
-
-python_test() {
-	cd "${BUILD_DIR}"/lib || die
-	nosetests || die
-}
diff --git a/dev-python/traits/traits-5.0.0.ebuild b/dev-python/traits/traits-5.0.0.ebuild
deleted file mode 100644
index f0b7d6dd0..000000000
--- a/dev-python/traits/traits-5.0.0.ebuild
+++ /dev/null
@@ -1,50 +0,0 @@
-# Copyright 1999-2019 Gentoo Authors
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=7
-
-PYTHON_COMPAT=( python{2_7,3_4,3_5,3_6} )
-
-inherit distutils-r1 virtualx
-
-DESCRIPTION="Enthought Tool Suite: Explicitly typed attributes for Python"
-HOMEPAGE="http://docs.enthought.com/traits/
-	https://github.com/enthought/traits
-	https://pypi.org/project/traits/"
-SRC_URI="mirror://pypi/${PN:0:1}/${PN}/${P}.tar.gz"
-
-LICENSE="BSD"
-SLOT="0"
-KEYWORDS="~amd64 ~ppc ~ppc64 ~x86 ~amd64-linux ~x86-linux"
-IUSE="test"
-
-RDEPEND="dev-python/numpy[${PYTHON_USEDEP}]"
-
-DEPEND="
-	dev-python/setuptools[${PYTHON_USEDEP}]
-	test? (
-		dev-python/nose[${PYTHON_USEDEP}]
-		${RDEPEND}
-		)"
-
-python_prepare_all() {
-	sed -i -e "s/'-O3'//g" setup.py || die
-	if use test; then
-		# Errors reported upstream: https://github.com/enthought/traits/issues/458
-		sed -i \
-			-e '1s/^/from nose.plugins.skip import SkipTest \n/' \
-			-e "/class TraitTypesTest(unittest.TestCase):/i@SkipTest" \
-            traits/tests/test_trait_types.py || die
-	fi
-	distutils-r1_python_prepare_all
-}
-
-python_compile() {
-	python_is_python3 || local -x CFLAGS="${CFLAGS} -fno-strict-aliasing"
-	distutils-r1_python_compile
-}
-
-python_test() {
-	cd "${BUILD_DIR}"/lib || die
-	nosetests || die
-}
diff --git a/dev-python/traits/traits-6.3.2.ebuild b/dev-python/traits/traits-6.3.2.ebuild
new file mode 100644
index 000000000..4d3c699a5
--- /dev/null
+++ b/dev-python/traits/traits-6.3.2.ebuild
@@ -0,0 +1,35 @@
+# Copyright 1999-2023 Gentoo Authors
+# Distributed under the terms of the GNU General Public License v2
+
+EAPI=8
+
+PYTHON_COMPAT=( python3_{10..11} )
+
+inherit distutils-r1 pypi
+
+DESCRIPTION="Enthought Tool Suite: Explicitly typed attributes for Python"
+HOMEPAGE="
+	https://docs.enthought.com/traits/
+	https://github.com/enthought/traits
+"
+
+LICENSE="BSD"
+SLOT="0"
+KEYWORDS="~amd64 ~ppc ~ppc64 ~x86"
+
+RDEPEND="dev-python/numpy[${PYTHON_USEDEP}]"
+
+distutils_enable_tests unittest
+# ToDo: Fix doc building:
+# AttributeError: 'NoDefaultSpecified' object has no attribute '__name__'
+#distutils_enable_sphinx docs/source --no-autodoc
+
+python_prepare_all() {
+	sed -i -e "s/'-O3'//g" setup.py || die
+	distutils-r1_python_prepare_all
+}
+
+python_test() {
+	cd "${BUILD_DIR}"/lib || die
+	${EPYTHON} -m unittest discover || die
+}
diff --git a/dev-python/traits/traits-6.4.1.ebuild b/dev-python/traits/traits-6.4.1.ebuild
new file mode 100644
index 000000000..ebd3fb97a
--- /dev/null
+++ b/dev-python/traits/traits-6.4.1.ebuild
@@ -0,0 +1,36 @@
+# Copyright 1999-2023 Gentoo Authors
+# Distributed under the terms of the GNU General Public License v2
+
+EAPI=8
+
+DISTUTILS_USE_PEP517=setuptools
+PYTHON_COMPAT=( python3_{10..11} )
+
+inherit distutils-r1 pypi
+
+DESCRIPTION="Enthought Tool Suite: Explicitly typed attributes for Python"
+HOMEPAGE="
+	https://docs.enthought.com/traits/
+	https://github.com/enthought/traits
+"
+
+LICENSE="BSD"
+SLOT="0"
+KEYWORDS="~amd64 ~ppc ~ppc64 ~x86"
+
+RDEPEND="dev-python/numpy[${PYTHON_USEDEP}]"
+
+distutils_enable_tests pytest
+# ToDo: Fix doc building:
+# AttributeError: 'NoDefaultSpecified' object has no attribute '__name__'
+#distutils_enable_sphinx docs/source --no-autodoc
+
+python_prepare_all() {
+	sed -i -e "s/'-O3'//g" setup.py || die
+	distutils-r1_python_prepare_all
+}
+
+python_test() {
+	cd "${T}" || die
+	epytest --pyargs traits
+}
diff --git a/dev-python/transforms3d/Manifest b/dev-python/transforms3d/Manifest
new file mode 100644
index 000000000..00bbff4f5
--- /dev/null
+++ b/dev-python/transforms3d/Manifest
@@ -0,0 +1 @@
+DIST transforms3d-0.3.1.tar.gz 62812 BLAKE2B 0f279bfd9cc6bac451ea311d4dc8eb779b391cbbb8a00169271838bbdbe2400a64d8d8f1a7bae91d48de36c2d49ab985f1cc87ea27d0a86b5a5760947e1b6d6d SHA512 bee42558d600f62a01b2ec08049a4680e278cff3b2c47bf9f12bc9f7d67d0b220895187d050678f347443ed02f41be0902ed1b14d976f4034bde7b849ffbc6dd
diff --git a/dev-python/transforms3d/metadata.xml b/dev-python/transforms3d/metadata.xml
new file mode 100644
index 000000000..594eae127
--- /dev/null
+++ b/dev-python/transforms3d/metadata.xml
@@ -0,0 +1,13 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
+<pkgmetadata>
+	<maintainer type="project">
+		<email>sci@gentoo.org</email>
+		<name>Gentoo Science Project</name>
+	</maintainer>
+	<stabilize-allarches/>
+	<upstream>
+		<remote-id type="pypi">transforms3d</remote-id>
+		<remote-id type="github">matthew-brett/transforms3d</remote-id>
+	</upstream>
+</pkgmetadata>
diff --git a/dev-python/transforms3d/transforms3d-0.3.1.ebuild b/dev-python/transforms3d/transforms3d-0.3.1.ebuild
new file mode 100644
index 000000000..661d78acb
--- /dev/null
+++ b/dev-python/transforms3d/transforms3d-0.3.1.ebuild
@@ -0,0 +1,22 @@
+# Copyright 1999-2021 Gentoo Authors
+# Distributed under the terms of the GNU General Public License v2
+
+EAPI=8
+
+PYTHON_COMPAT=( python3_{10..11} )
+DISTUTILS_USE_PEP517=setuptools
+
+inherit distutils-r1 pypi
+
+DESCRIPTION="Functions for 3D coordinate transformations"
+HOMEPAGE="https://matthew-brett.github.io/transforms3d/"
+
+LICENSE="BSD-2"
+KEYWORDS="~amd64 ~x86"
+SLOT="0"
+
+RDEPEND="
+	>=dev-python/numpy-1.5.1[${PYTHON_USEDEP}]
+"
+
+distutils_enable_tests pytest
diff --git a/dev-python/trimesh/Manifest b/dev-python/trimesh/Manifest
deleted file mode 100644
index bfba01e62..000000000
--- a/dev-python/trimesh/Manifest
+++ /dev/null
@@ -1 +0,0 @@
-DIST trimesh-2.34.3.tar.gz 8390792 BLAKE2B c15fd2e7fe407b6c459995d8cfac3c4fdd369cd842cb4e2025ecfd66f6fafc4c324d16d21060b57e4b4a6eb743003288085a20ea31bdab3830b69de8c388a7e0 SHA512 2f3eb685a8ba35ff3e16bb81502f14c5fcbf82394466484c27a61b8b2c87c3287ebf2725270abd91ad01ed8a2068e559a2eaf1fc72f5e1814b26810ab984f3fc
diff --git a/dev-python/trimesh/files/trimesh-2.34.3-suppress-xvfb-test.patch b/dev-python/trimesh/files/trimesh-2.34.3-suppress-xvfb-test.patch
deleted file mode 100644
index 948c57281..000000000
--- a/dev-python/trimesh/files/trimesh-2.34.3-suppress-xvfb-test.patch
+++ /dev/null
@@ -1,11 +0,0 @@
---- a/tests/test_export.py	2018-10-02 22:46:48.992653740 +0200
-+++ b/tests/test_export.py	2018-10-07 01:52:37.793858817 +0200
-@@ -139,7 +139,7 @@
-                         g.log.error('failed to export {}'.format(
-                             option))
-                         # raise the error again
-+                        return
--                        raise E
- 
-                     # load meshlabs export back into trimesh
-                     r = g.trimesh.load(temp_off.name)
diff --git a/dev-python/trimesh/metadata.xml b/dev-python/trimesh/metadata.xml
deleted file mode 100644
index 7e0eebddb..000000000
--- a/dev-python/trimesh/metadata.xml
+++ /dev/null
@@ -1,19 +0,0 @@
-<?xml version='1.0' encoding='UTF-8'?>
-<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
-<pkgmetadata>
-	<maintainer type="person">
-		<email>horea.christ@gmail.com</email>
-		<name>Horea Christian</name>
-	</maintainer>
-	<maintainer type="project">
-		<email>sci@gentoo.org</email>
-		<name>Gentoo Science Project</name>
-	</maintainer>
-	<longdescription lang="en">
-		Trimesh is a pure Python library for loading and using triangular meshes
-		with an emphasis on single- body watertight surfaces. The goal of the
-		library is to provide a full featured and well tested Trimesh object which
-		allows for easy manipulation and analysis, in the style of the Polygon
-		object in the Shapely library.
-	</longdescription>
-</pkgmetadata>
diff --git a/dev-python/trimesh/trimesh-2.34.3.ebuild b/dev-python/trimesh/trimesh-2.34.3.ebuild
deleted file mode 100644
index 5b7e69232..000000000
--- a/dev-python/trimesh/trimesh-2.34.3.ebuild
+++ /dev/null
@@ -1,49 +0,0 @@
-# Copyright 1999-2018 Gentoo Authors
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=7
-
-PYTHON_COMPAT=( python2_7 python3_{5,6} )
-
-inherit distutils-r1
-
-DESCRIPTION="Python library for loading and using triangular meshes."
-HOMEPAGE="https://trimsh.org/"
-SRC_URI="https://github.com/mikedh/trimesh/archive/${PV}.tar.gz -> ${P}.tar.gz"
-
-LICENSE="MIT"
-SLOT="0"
-KEYWORDS="~amd64 ~x86"
-IUSE="test"
-
-DEPEND="
-	test? (
-		${RDEPEND}
-		dev-python/pytest[${PYTHON_USEDEP}]
-		)
-	dev-python/setuptools[${PYTHON_USEDEP}]
-	dev-python/numpy[${PYTHON_USEDEP}]
-	sci-libs/scipy[${PYTHON_USEDEP}]
-	dev-python/networkx[${PYTHON_USEDEP}]
-"
-RDEPEND="
-	dev-libs/xxhash
-	dev-python/colorlog[${PYTHON_USEDEP}]
-	dev-python/deprecation[${PYTHON_USEDEP}]
-	dev-python/lxml[${PYTHON_USEDEP}]
-	dev-python/msgpack[${PYTHON_USEDEP}]
-	dev-python/pillow[${PYTHON_USEDEP}]
-	dev-python/pyglet[${PYTHON_USEDEP}]
-	dev-python/requests[${PYTHON_USEDEP}]
-	dev-python/svg-path[${PYTHON_USEDEP}]
-	dev-python/sympy[${PYTHON_USEDEP}]
-	=dev-python/six-1*[${PYTHON_USEDEP}]
-	sci-libs/Shapely[${PYTHON_USEDEP}]
-	sci-libs/Rtree[${PYTHON_USEDEP}]
-"
-
-PATCHES=( "${FILESDIR}/${P}-suppress-xvfb-test.patch" )
-
-python_test() {
-	pytest -vv || die
-}
diff --git a/dev-python/typish/Manifest b/dev-python/typish/Manifest
new file mode 100644
index 000000000..809dd7e09
--- /dev/null
+++ b/dev-python/typish/Manifest
@@ -0,0 +1 @@
+DIST typish-1.9.3.gh.tar.gz 22997 BLAKE2B f399f5d9b3ae8f85f3b719de77d675b142ac45b6535f66d9d0d999411bc5bfc9100523667ea4c1d2be60c15a4bf35ec931ded9e1181a4545bbaa9b96fb27d0dd SHA512 baad9d2229ac289c4eb1d6e64bac0313efd4680f42a95270e0c1141d511392e6a95a5fea767943ddf432f5f0d48d95a05bbf26e06df188079ac177d321e4fa5c
diff --git a/dev-python/typish/metadata.xml b/dev-python/typish/metadata.xml
new file mode 100644
index 000000000..603d0691e
--- /dev/null
+++ b/dev-python/typish/metadata.xml
@@ -0,0 +1,13 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<!DOCTYPE pkgmetadata SYSTEM "https://www.gentoo.org/dtd/metadata.dtd">
+<pkgmetadata>
+  <maintainer type="project">
+      <email>sci@gentoo.org</email>
+      <name>Gentoo Science Project</name>
+  </maintainer>
+  <stabilize-allarches/>
+  <upstream>
+    <remote-id type="pypi">typish</remote-id>
+    <remote-id type="github">ramonhagenaars/typish</remote-id>
+  </upstream>
+</pkgmetadata>
diff --git a/dev-python/typish/typish-1.9.3.ebuild b/dev-python/typish/typish-1.9.3.ebuild
new file mode 100644
index 000000000..a4ecbb65f
--- /dev/null
+++ b/dev-python/typish/typish-1.9.3.ebuild
@@ -0,0 +1,29 @@
+# Copyright 2022 Gentoo Authors
+# Distributed under the terms of the GNU General Public License v2
+
+EAPI=8
+
+DISTUTILS_USE_PEP517=setuptools
+PYTHON_COMPAT=( python3_10 )
+inherit distutils-r1
+
+DESCRIPTION="Functionality for types"
+HOMEPAGE="https://pypi.org/project/typish/
+	https://github.com/ramonhagenaars/typish"
+SRC_URI="
+	https://github.com/ramonhagenaars/typish/archive/v${PV}.tar.gz
+		-> ${P}.gh.tar.gz
+"
+
+LICENSE="MIT"
+SLOT="0"
+KEYWORDS="~amd64"
+
+BDEPEND="
+	test? (
+		dev-python/numpy[${PYTHON_USEDEP}]
+		dev-python/nptyping[${PYTHON_USEDEP}]
+	)
+"
+
+distutils_enable_tests pytest
diff --git a/dev-python/ufl/Manifest b/dev-python/ufl/Manifest
deleted file mode 100644
index 071ee42c2..000000000
--- a/dev-python/ufl/Manifest
+++ /dev/null
@@ -1,3 +0,0 @@
-DIST ufl-1.4.0.tar.gz 294109 BLAKE2B f04b1f1df6c0b1c302175eeeb53e2b644ca80ec7af1f0d2f6221b20123f822e0f09bfabdc1b26c43baa9dd9dc2a86f7efa528c5fa9941feb2b78aa5854a831f7 SHA512 b2d41f58d3ad3493f7714a9944a3a9bdee7f6530e20cdde2d3f4610e81667f4181da172c01afcd46eca8afbc43c84fc214b76e4895253cd2572594a6e7398d2b
-DIST ufl-2016.2.0.tar.gz 302202 BLAKE2B 836acad8c77bdfac742c9c43306ab3289beed233109fb16f65d23716284bf2a8112519b46b43062a6527f6f707fbcb9ae46c80d3bbd9bf05b9876c5f6c5dc189 SHA512 af95bc663a323e7c4efbb84d61bd0a8c8ca7aa85c9313aecff1c7f161703657165ca83ff4a21c59c7fbc396a0f47ee639c09c3113f4c7a4a2bfe2792b0e7de43
-DIST ufl-2017.1.0.tar.gz 306145 BLAKE2B 84a0602072cb82d96a26999ffe81bb9788c6e0d5a601b432c52e1d32ed8062e95c4320aab5d760615e7065822ddb2118aeab2e378251d708a2cd6282d2ad8f78 SHA512 3f2912c9cb5411095c7ff9fd05574c99cc0bd214b789c9196216098f9c833eda4940d90dd65eeecd05cd2d2c152f7954fad2d899f97bc142acd8eaa9a766f2a3
diff --git a/dev-python/ufl/metadata.xml b/dev-python/ufl/metadata.xml
deleted file mode 100644
index 142da2a70..000000000
--- a/dev-python/ufl/metadata.xml
+++ /dev/null
@@ -1,18 +0,0 @@
-<?xml version="1.0" encoding="UTF-8"?>
-<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
-<pkgmetadata>
-	<maintainer type="project">
-		<email>sci@gentoo.org</email>
-		<name>Gentoo Science Project</name>
-	</maintainer>
-	<longdescription lang="en">
-The Unified Form Language (UFL) is a domain specific language for
-declaration of finite element discretizations of variational forms. More
-precisely, it defines a flexible interface for choosing finite element
-spaces and defining expressions for weak forms in a notation close to
-mathematical notation.
-</longdescription>
-	<upstream>
-		<remote-id type="bitbucket">fenics-project/ufl</remote-id>
-	</upstream>
-</pkgmetadata>
diff --git a/dev-python/ufl/ufl-1.4.0.ebuild b/dev-python/ufl/ufl-1.4.0.ebuild
deleted file mode 100644
index 0922a2b4a..000000000
--- a/dev-python/ufl/ufl-1.4.0.ebuild
+++ /dev/null
@@ -1,23 +0,0 @@
-# Copyright 1999-2016 Gentoo Foundation
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=6
-
-PYTHON_COMPAT=( python2_7 )
-
-inherit distutils-r1 eutils
-
-DESCRIPTION="Unified Form Language for declaration of for FE discretizations"
-HOMEPAGE="https://bitbucket.org/fenics-project/ufl/"
-SRC_URI="https://bitbucket.org/fenics-project/ufl/downloads/${P}.tar.gz"
-
-LICENSE="GPL-3"
-SLOT="0"
-KEYWORDS="~amd64 ~x86"
-IUSE=""
-
-RDEPEND="dev-python/numpy[${PYTHON_USEDEP}]"
-
-pkg_postinst() {
-	optfeature "Support for evaluating Bessel functions" sci-libs/scipy
-}
diff --git a/dev-python/ufl/ufl-2016.2.0.ebuild b/dev-python/ufl/ufl-2016.2.0.ebuild
deleted file mode 100644
index 78ce49375..000000000
--- a/dev-python/ufl/ufl-2016.2.0.ebuild
+++ /dev/null
@@ -1,23 +0,0 @@
-# Copyright 1999-2017 Gentoo Foundation
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=6
-
-PYTHON_COMPAT=( python2_7 )
-
-inherit distutils-r1 eutils
-
-DESCRIPTION="Unified Form Language for declaration of for FE discretizations"
-HOMEPAGE="https://bitbucket.org/fenics-project/ufl/"
-SRC_URI="https://bitbucket.org/fenics-project/ufl/downloads/${P}.tar.gz"
-
-LICENSE="GPL-3"
-SLOT="0"
-KEYWORDS="~amd64 ~x86"
-IUSE=""
-
-RDEPEND="dev-python/numpy[${PYTHON_USEDEP}]"
-
-pkg_postinst() {
-	optfeature "Support for evaluating Bessel functions" sci-libs/scipy
-}
diff --git a/dev-python/ufl/ufl-2017.1.0.ebuild b/dev-python/ufl/ufl-2017.1.0.ebuild
deleted file mode 100644
index a7c1e2d9a..000000000
--- a/dev-python/ufl/ufl-2017.1.0.ebuild
+++ /dev/null
@@ -1,23 +0,0 @@
-# Copyright 1999-2017 Gentoo Foundation
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=6
-
-PYTHON_COMPAT=( python3_4 python3_5 python3_6 )
-
-inherit distutils-r1 eutils
-
-DESCRIPTION="Unified Form Language for declaration of for FE discretizations"
-HOMEPAGE="https://bitbucket.org/fenics-project/ufl/"
-SRC_URI="https://bitbucket.org/fenics-project/ufl/downloads/${P}.tar.gz"
-
-LICENSE="GPL-3"
-SLOT="0"
-KEYWORDS="~amd64 ~x86"
-IUSE=""
-
-RDEPEND="dev-python/numpy[${PYTHON_USEDEP}]"
-
-pkg_postinst() {
-	optfeature "Support for evaluating Bessel functions" sci-libs/scipy
-}
diff --git a/dev-python/uhi/Manifest b/dev-python/uhi/Manifest
new file mode 100644
index 000000000..199ee2a62
--- /dev/null
+++ b/dev-python/uhi/Manifest
@@ -0,0 +1 @@
+DIST uhi-0.4.0.tar.gz 52953 BLAKE2B b0c16c58c676f405d7b46398507968e92e4c3939a53224b49cbd935c3473800341903a9e9c5e3c598d68f171a9ec098feedaa774b2bbfe780581a663e99b2592 SHA512 4f7f0bdce3fef14c8789e0860956d6d4d2ab91e48eb95b6bceb67aef47b23a260f0f33a565c052fe48933f108adfe32f4c28c8cf874cc908929d407687bbc385
diff --git a/dev-python/uhi/metadata.xml b/dev-python/uhi/metadata.xml
new file mode 100644
index 000000000..c1ee047a1
--- /dev/null
+++ b/dev-python/uhi/metadata.xml
@@ -0,0 +1,19 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
+<pkgmetadata>
+	<maintainer type="project">
+		<email>sci@gentoo.org</email>
+		<name>Gentoo Science Project</name>
+	</maintainer>
+	<maintainer type="person">
+		<email>alexander@neuwirth-informatik.de</email>
+		<name>Alexander Puck Neuwirth</name>
+	</maintainer>
+	<longdescription lang="en">
+	This is a package meant primarily for documenting histogram indexing and the PlottableHistogram Protocol and any future cross-library standards. It also contains the code for the PlottableHistogram Protocol, to be used in type checking libraries wanting to conform to the protocol. Eventually, it might gain a set of tools for testing conformance to UHI indexing, as well. It is not usually a runtime dependency, but only a type checking, testing, and/or docs dependency in support of other libraries (such as boost-histogram 0.13+, hist 2.1+, mplhep 0.2.15+, uproot 4+, and histoprint 2+). There are a few useful runtime usable components (listed below). It requires Python 3.6+. See what's new.
+	</longdescription>
+	<upstream>
+		<remote-id type="pypi">uhi</remote-id>
+		<remote-id type="github">scikit-hep/uhi</remote-id>
+	</upstream>
+</pkgmetadata>
diff --git a/dev-python/uhi/uhi-0.4.0.ebuild b/dev-python/uhi/uhi-0.4.0.ebuild
new file mode 100644
index 000000000..380e3bdbd
--- /dev/null
+++ b/dev-python/uhi/uhi-0.4.0.ebuild
@@ -0,0 +1,27 @@
+EAPI=8
+
+PYTHON_COMPAT=( python3_{10..12} )
+DISTUTILS_USE_PEP517=hatchling
+SETUPTOOLS_SCM_PRETEND_VERSION=${PV}
+inherit distutils-r1 pypi
+
+DESCRIPTION="Universal Histogram Interface"
+HOMEPAGE="https://github.com/scikit-hep/uhi"
+
+LICENSE="BSD"
+SLOT="0"
+KEYWORDS="~amd64"
+
+RDEPEND="
+	>=dev-python/numpy-1.13.3[${PYTHON_USEDEP}]
+	test? (
+		dev-python/pytest[${PYTHON_USEDEP}]
+		dev-python/boost-histogram[${PYTHON_USEDEP}]
+	)
+"
+BDEPEND="
+	${RDEPEND}
+	dev-python/hatch-vcs[${PYTHON_USEDEP}]
+"
+
+distutils_enable_tests pytest
diff --git a/dev-python/vector/Manifest b/dev-python/vector/Manifest
new file mode 100644
index 000000000..df652f966
--- /dev/null
+++ b/dev-python/vector/Manifest
@@ -0,0 +1,3 @@
+DIST vector-1.1.1.tar.gz 289916 BLAKE2B 35281c498f244b0307d744a20d0364c4cf664d0bd08a4f17d8d3110aa4eae6d7f66e3b51b4e9847f31d3a6ab943248115221dee4dcd3c3f2f8c47842001b553a SHA512 b1e195751de35ca2c67749b6b2b330db8a29e023f42e9b454adc8fc2408c29b5926b39e9ed6dc6a93f97006fbfb286a2217be8b14cb0eb2b96c9538f6c3943e6
+DIST vector-1.3.1.tar.gz 299581 BLAKE2B 36e99e814b5e8afc7a0179acce74f399db8f76e3c3c59ebbb5a2616bfa8f34ca2cfabe9e42752226dbabbdcd77fc15a4725c4e296f5329533a85cade8fcfae0c SHA512 524752789f6ea0201e1bb3dc09e7396a8bc64a1ee78ccab383bbe968134783bbf7499948784b141353612649f8188d0cb93147b53afdf37ba26f812d8ebd84b0
+DIST vector-1.4.0.tar.gz 368490 BLAKE2B 443922bc00bfddd3601a414af1a2ba70bed0caff0dd5516573a557d736b65ebf42f191c6de776a3a28b2399d4cbe3db56f69864051758839a00e2703e6b3b53c SHA512 f8caba973fe7739537c41b5a86b435134bfa1f59b355a2246ae0cff76b6be5ea8ddae90c11326d439e4c31aacbbf21061479fa0d1d9e644292307bf2a77c416e
diff --git a/dev-python/vector/metadata.xml b/dev-python/vector/metadata.xml
new file mode 100644
index 000000000..b6aaa9af7
--- /dev/null
+++ b/dev-python/vector/metadata.xml
@@ -0,0 +1,19 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
+<pkgmetadata>
+	<maintainer type="project">
+		<email>sci@gentoo.org</email>
+		<name>Gentoo Science Project</name>
+	</maintainer>
+	<maintainer type="person">
+		<email>alexander@neuwirth-informatik.de</email>
+		<name>Alexander Puck Neuwirth</name>
+	</maintainer>
+	<longdescription lang="en">
+	Vector is a Python 3.8+ library (Python 3.6 and 3.7 supported till v0.9.0 and v1.0.0, respectively) for 2D, 3D, and Lorentz vectors, especially arrays of vectors, to solve common physics problems in a NumPy-like way.
+	</longdescription>
+	<upstream>
+		<remote-id type="pypi">vector</remote-id>
+		<remote-id type="github">scikit-hep/vector</remote-id>
+	</upstream>
+</pkgmetadata>
diff --git a/dev-python/vector/vector-1.1.1.ebuild b/dev-python/vector/vector-1.1.1.ebuild
new file mode 100644
index 000000000..8b5a45c3d
--- /dev/null
+++ b/dev-python/vector/vector-1.1.1.ebuild
@@ -0,0 +1,22 @@
+EAPI=8
+
+PYTHON_COMPAT=( python3_{10..12} )
+DISTUTILS_USE_PEP517=hatchling
+inherit distutils-r1 pypi
+
+DESCRIPTION="Vector classes and utilities"
+HOMEPAGE="https://github.com/scikit-hep/vector"
+
+LICENSE="BSD"
+SLOT="0"
+KEYWORDS="~amd64"
+
+RDEPEND="
+	>=dev-python/numpy-1.13.3[${PYTHON_USEDEP}]
+"
+DEPEND="${RDEPEND}"
+BDEPEND="
+	dev-python/hatch-vcs[${PYTHON_USEDEP}]
+"
+
+export SETUPTOOLS_SCM_PRETEND_VERSION=${PV}
diff --git a/dev-python/vector/vector-1.3.1.ebuild b/dev-python/vector/vector-1.3.1.ebuild
new file mode 100644
index 000000000..8b5a45c3d
--- /dev/null
+++ b/dev-python/vector/vector-1.3.1.ebuild
@@ -0,0 +1,22 @@
+EAPI=8
+
+PYTHON_COMPAT=( python3_{10..12} )
+DISTUTILS_USE_PEP517=hatchling
+inherit distutils-r1 pypi
+
+DESCRIPTION="Vector classes and utilities"
+HOMEPAGE="https://github.com/scikit-hep/vector"
+
+LICENSE="BSD"
+SLOT="0"
+KEYWORDS="~amd64"
+
+RDEPEND="
+	>=dev-python/numpy-1.13.3[${PYTHON_USEDEP}]
+"
+DEPEND="${RDEPEND}"
+BDEPEND="
+	dev-python/hatch-vcs[${PYTHON_USEDEP}]
+"
+
+export SETUPTOOLS_SCM_PRETEND_VERSION=${PV}
diff --git a/dev-python/vector/vector-1.4.0.ebuild b/dev-python/vector/vector-1.4.0.ebuild
new file mode 100644
index 000000000..a57240b49
--- /dev/null
+++ b/dev-python/vector/vector-1.4.0.ebuild
@@ -0,0 +1,34 @@
+EAPI=8
+
+PYTHON_COMPAT=( python3_{10..12} )
+DISTUTILS_USE_PEP517=hatchling
+inherit distutils-r1 pypi optfeature
+
+DESCRIPTION="Vector classes and utilities"
+HOMEPAGE="
+	https://github.com/scikit-hep/vector
+	https://vector.readthedocs.io/
+	https://doi.org/10.5281/zenodo.7054478
+"
+
+LICENSE="BSD"
+SLOT="0"
+KEYWORDS="~amd64"
+# tests need numba
+RESTRICT="test"
+
+RDEPEND="
+	>=dev-python/numpy-1.13.3[${PYTHON_USEDEP}]
+	>=dev-python/packaging-19[${PYTHON_USEDEP}]
+"
+DEPEND="${RDEPEND}"
+BDEPEND="
+	dev-python/hatch-vcs[${PYTHON_USEDEP}]
+"
+
+export SETUPTOOLS_SCM_PRETEND_VERSION=${PV}
+
+pkg_postinst() {
+	optfeature "awkward array support" dev-python/awkward
+	optfeature "sympy support" dev-python/sympy
+}
diff --git a/dev-python/viper/Manifest b/dev-python/viper/Manifest
deleted file mode 100644
index c4ce40e5e..000000000
--- a/dev-python/viper/Manifest
+++ /dev/null
@@ -1 +0,0 @@
-DIST viper-1.0.1.tar.gz 192880 BLAKE2B 6997ce51328f7a94134c8d58261e2746c8ef03779fc0a202eb7661df63c6a1344a742987201aa38eba5db3ccc8dd9fdaf1551fbefcd839a988bfb7dac8f9ed69 SHA512 f56c93058a3fcc904a2e2f4f5780e8b027d97a10d09867c0f66048475e07282760798f2ff446915704d49e5d1e31bb55367d3902edbce331be4936a71ca85caf
diff --git a/dev-python/viper/metadata.xml b/dev-python/viper/metadata.xml
deleted file mode 100644
index 6c82f77b4..000000000
--- a/dev-python/viper/metadata.xml
+++ /dev/null
@@ -1,16 +0,0 @@
-<?xml version="1.0" encoding="UTF-8"?>
-<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
-<pkgmetadata>
-	<maintainer type="project">
-		<email>sci@gentoo.org</email>
-		<name>Gentoo Science Project</name>
-	</maintainer>
-	<longdescription lang="en">
-Viper is a minimalistic scientific plotter and run-time visualization
-module. Viper has support for visualizing meshes and solutions in
-DOLFIN.
-</longdescription>
-	<upstream>
-		<remote-id type="launchpad">fenics-viper</remote-id>
-	</upstream>
-</pkgmetadata>
diff --git a/dev-python/viper/viper-1.0.1.ebuild b/dev-python/viper/viper-1.0.1.ebuild
deleted file mode 100644
index 0ba65e117..000000000
--- a/dev-python/viper/viper-1.0.1.ebuild
+++ /dev/null
@@ -1,17 +0,0 @@
-# Copyright 1999-2014 Gentoo Foundation
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=5
-
-PYTHON_COMPAT=( python2_7 )
-
-inherit distutils-r1
-
-DESCRIPTION="Minimalistic scientific plotter and run-time visualization module"
-HOMEPAGE="https://launchpad.net/fenics-viper"
-SRC_URI="https://launchpad.net/fenics-viper/1.0.x/${PV}/+download/${P}.tar.gz"
-
-LICENSE="LGPL-3"
-SLOT="0"
-KEYWORDS="~amd64 ~x86"
-IUSE=""
diff --git a/dev-python/visvis/Manifest b/dev-python/visvis/Manifest
new file mode 100644
index 000000000..2caf8e4e4
--- /dev/null
+++ b/dev-python/visvis/Manifest
@@ -0,0 +1 @@
+DIST visvis-1.14.0.tar.gz 4892032 BLAKE2B 564e328d4265676bec35798149ff1283b7289fe04e946ca78b6068ae6f70d1dff809a4ec19b94b1d49a9c3ac7f0b186996070736d3eb4ba4897feac7d03edb6a SHA512 d056ec8a83ac9cee4cbb05806145287fa9dab8064fbc910463255d4510f082ca29f393c309c7b649c6d625f1c368bf5ef28f44de1ebb30ccd1d5650fadb76a81
diff --git a/dev-python/visvis/metadata.xml b/dev-python/visvis/metadata.xml
new file mode 100644
index 000000000..7eac38327
--- /dev/null
+++ b/dev-python/visvis/metadata.xml
@@ -0,0 +1,12 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
+<pkgmetadata>
+	<maintainer type="project">
+		<email>sci@gentoo.org</email>
+		<name>Gentoo Science Project</name>
+	</maintainer>
+	<upstream>
+		<remote-id type="pypi">visvis</remote-id>
+		<remote-id type="github">almarklein/visvis</remote-id>
+	</upstream>
+</pkgmetadata>
diff --git a/dev-python/visvis/visvis-1.14.0.ebuild b/dev-python/visvis/visvis-1.14.0.ebuild
new file mode 100644
index 000000000..1f210c0b4
--- /dev/null
+++ b/dev-python/visvis/visvis-1.14.0.ebuild
@@ -0,0 +1,24 @@
+# Copyright 1999-2021 Gentoo Authors
+# Distributed under the terms of the GNU General Public License v2
+
+EAPI=8
+
+PYTHON_COMPAT=( python3_{10..11} )
+DISTUTILS_USE_PEP517=setuptools
+
+inherit distutils-r1 pypi
+
+DESCRIPTION="An object oriented approach to visualization of 1D to 4D data"
+HOMEPAGE="https://github.com/almarklein/visvis"
+
+LICENSE="BSD"
+SLOT="0"
+KEYWORDS="~amd64"
+
+RDEPEND="
+	dev-python/numpy[${PYTHON_USEDEP}]
+	dev-python/pyopengl[${PYTHON_USEDEP}]
+	dev-python/imageio[${PYTHON_USEDEP}]
+"
+
+distutils_enable_tests pytest
diff --git a/dev-python/widgetsnbextension/Manifest b/dev-python/widgetsnbextension/Manifest
deleted file mode 100644
index d8a798627..000000000
--- a/dev-python/widgetsnbextension/Manifest
+++ /dev/null
@@ -1 +0,0 @@
-DIST widgetsnbextension-1.2.2.tar.gz 721558 BLAKE2B 94b9b88602097818dcd9fc3688fdb826b08b55b005eaeb540aa3bbd4959d396eac6cd36f0763fc76b5b911b66cb90d060aea021de1cb384b28c09d4ebfae9313 SHA512 40f0939bb61ca39360873ec7f85ef035b7f033be65ca7d2d0b4219efd343d886c24f53b0e30d00e1b82da55e47c552ec7a7e23a62511c993f679e080e9b18ddf
diff --git a/dev-python/widgetsnbextension/metadata.xml b/dev-python/widgetsnbextension/metadata.xml
deleted file mode 100644
index 3df0fc455..000000000
--- a/dev-python/widgetsnbextension/metadata.xml
+++ /dev/null
@@ -1,14 +0,0 @@
-<?xml version="1.0" encoding="UTF-8"?>
-<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
-<pkgmetadata>
-	<maintainer type="project">
-		<email>sci@gentoo.org</email>
-		<name>Gentoo Science Project</name>
-	</maintainer>
-	<longdescription>
-Interactive HTML widgets for Jupyter notebooks.
-</longdescription>
-	<upstream>
-		<remote-id type="pypi">widgetsnbextension</remote-id>
-	</upstream>
-</pkgmetadata>
diff --git a/dev-python/widgetsnbextension/widgetsnbextension-1.2.2.ebuild b/dev-python/widgetsnbextension/widgetsnbextension-1.2.2.ebuild
deleted file mode 100644
index 637a642a4..000000000
--- a/dev-python/widgetsnbextension/widgetsnbextension-1.2.2.ebuild
+++ /dev/null
@@ -1,23 +0,0 @@
-# Copyright 1999-2016 Gentoo Foundation
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=6
-
-PYTHON_COMPAT=( python2_7 python3_{4,5} )
-PYTHON_REQ_USE="threads(+)"
-
-inherit distutils-r1
-
-DESCRIPTION="IPython HTML widgets for Jupyter"
-HOMEPAGE="http://ipython.org/"
-SRC_URI="mirror://pypi/${PN:0:1}/${PN}/${P}.tar.gz"
-
-LICENSE="BSD"
-SLOT="0"
-KEYWORDS="~amd64 ~x86"
-IUSE=""
-
-RDEPEND="
-	>=dev-python/notebook-4.2.0[${PYTHON_USEDEP}]
-	"
-DEPEND="${RDEPEND}"
diff --git a/dev-python/wirerope/Manifest b/dev-python/wirerope/Manifest
new file mode 100644
index 000000000..ae2ee16cb
--- /dev/null
+++ b/dev-python/wirerope/Manifest
@@ -0,0 +1 @@
+DIST wirerope-0.4.7.gh.tar.gz 12220 BLAKE2B 1ed861b71cfbfb4c0d18a2c09f6cf96f545d9a88617e7618053c4e5459317532e12195a02e3f3d99a0cc91bf0601c39404b80e4e631a86b24a5926718b4cb287 SHA512 cfa7222503a9c03f9afe6cab9acc45d7115795169325692c5c519913406f8abc4d78d84769d24ff123ca47333f7ea8dde3a8a7961d34d0e20aebc02e0a420aaf
diff --git a/dev-python/wirerope/files/wirerope-0.4.7-nocov.patch b/dev-python/wirerope/files/wirerope-0.4.7-nocov.patch
new file mode 100644
index 000000000..64d47d0b7
--- /dev/null
+++ b/dev-python/wirerope/files/wirerope-0.4.7-nocov.patch
@@ -0,0 +1,10 @@
+--- a/setup.cfg	2023-02-05 08:00:42.000000000 -0500
++++ b/setup.cfg	2024-05-06 11:01:02.896234948 -0400
+@@ -33,7 +33,6 @@
+     sphinx
+ 
+ [tool:pytest]
+-addopts=--verbose --cov-config .coveragerc --cov wirerope
+ python_files = tests/test_*.py
+ norecursedirs=.git py ci
+ [flake8]
diff --git a/dev-python/wirerope/metadata.xml b/dev-python/wirerope/metadata.xml
new file mode 100644
index 000000000..6e39bae5d
--- /dev/null
+++ b/dev-python/wirerope/metadata.xml
@@ -0,0 +1,16 @@
+<?xml version='1.0' encoding='UTF-8'?>
+<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
+<pkgmetadata>
+	<maintainer type="person">
+		<email>gentoo@chymera.eu</email>
+		<name>Horea Christian</name>
+	</maintainer>
+	<maintainer type="project">
+		<email>sci@gentoo.org</email>
+		<name>Gentoo Science Project</name>
+	</maintainer>
+	<upstream>
+		<remote-id type="github">youknowone/wirerope</remote-id>
+		<remote-id type="pypi">wirerope</remote-id>
+	</upstream>
+</pkgmetadata>
diff --git a/dev-python/wirerope/wirerope-0.4.7.ebuild b/dev-python/wirerope/wirerope-0.4.7.ebuild
new file mode 100644
index 000000000..74e7f40bd
--- /dev/null
+++ b/dev-python/wirerope/wirerope-0.4.7.ebuild
@@ -0,0 +1,26 @@
+# Copyright 1999-2022 Gentoo Authors
+# Distributed under the terms of the GNU General Public License v2
+
+EAPI=8
+
+DISTUTILS_USE_PEP517=setuptools
+PYTHON_COMPAT=( python3_{10..12} )
+inherit distutils-r1
+
+DESCRIPTION="A wrapper interface for python callables"
+HOMEPAGE="https://github.com/youknowone/wirerope"
+# Not using PyPI archive because it misses test files:
+# https://github.com/youknowone/wirerope/issues/20
+SRC_URI="https://github.com/youknowone/wirerope/archive/refs/tags/${PV}.tar.gz -> ${P}.gh.tar.gz"
+
+LICENSE="MIT"
+SLOT="0"
+KEYWORDS="~amd64 ~x86"
+
+RDEPEND="
+	dev-python/six[${PYTHON_USEDEP}]
+"
+
+PATCHES=( "${FILESDIR}/${P}-nocov.patch" )
+
+distutils_enable_tests pytest
diff --git a/dev-python/wraps/Manifest b/dev-python/wraps/Manifest
new file mode 100644
index 000000000..44510a1dd
--- /dev/null
+++ b/dev-python/wraps/Manifest
@@ -0,0 +1 @@
+DIST wraps-0.2.0.tar.gz 25308 BLAKE2B b68359d34995f7bc39535e97458807a5d55e3547124ccb8b34f9cd34fe1d3b38921a3a0c16df031410022f74d414aba97af9e9f60a20fb635428030bc400b130 SHA512 daf72785c3215db06f4bf06704f02c7ecfd1ef5c58dbf5c50b2dee14755d73b519f8a13be9658bf825c296689d9b3effd08aec4254779812583c1024522751f0
diff --git a/dev-python/wraps/files/wraps-0.1.0-poetry_groups.patch b/dev-python/wraps/files/wraps-0.1.0-poetry_groups.patch
new file mode 100644
index 000000000..c1b2ccd3e
--- /dev/null
+++ b/dev-python/wraps/files/wraps-0.1.0-poetry_groups.patch
@@ -0,0 +1,63 @@
+--- a/pyproject.toml	2022-06-28 11:08:09.624127900 -0400
++++ b/pyproject.toml	2022-07-11 16:33:14.810411482 -0400
+@@ -36,31 +36,6 @@
+
+ typing-extensions = ">= 4.3.0"
+
+-[tool.poetry.group.format]
+-optional = true
+-
+-[tool.poetry.group.format.dependencies]
+-black = "22.8.0"
+-
+-[tool.poetry.group.format.dependencies.isort]
+-version = "5.10.1"
+-python = "^3.7"
+-
+-[tool.poetry.group.check]
+-optional = true
+-
+-[tool.poetry.group.check.dependencies]
+-mypy = "0.971"
+-
+-[tool.poetry.group.test]
+-optional = true
+-
+-[tool.poetry.group.test.dependencies]
+-pytest = "7.1.3"
+-pytest-cov = "3.0.0"
+-anyio = "3.6.1"
+-trio = "0.21.0"
+-
+ [tool.poetry.group.docs]
+ optional = true
+
+@@ -67,29 +44,6 @@
+ line_length = 100
+ profile = "black"
+
+-[tool.pytest.ini_options]
+-addopts = "--cov wraps"
+-testpaths = ["tests"]
+-
+-[tool.coverage.run]
+-source = ["wraps"]
+-
+-[tool.coverage.report]
+-ignore_errors = true
+-exclude_lines = [
+-    "pragma: never",
+-    "pragma: no cover",
+-    "if TYPE_CHECKING",
+-    "@overload",
+-    "@abstractmethod",
+-    "raise NotImplementedError",
+-    "raise AssertionError",
+-    "def __repr__",
+-]
+-
+-[tool.coverage.html]
+-directory = "coverage"
+-
+ [tool.mypy]
+ show_column_numbers = true
diff --git a/dev-python/wraps/metadata.xml b/dev-python/wraps/metadata.xml
new file mode 100644
index 000000000..d94ee3bee
--- /dev/null
+++ b/dev-python/wraps/metadata.xml
@@ -0,0 +1,16 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
+<pkgmetadata>
+	<maintainer type="person">
+		<email>gentoo@chymera.eu</email>
+		<name>Horea Christian</name>
+	</maintainer>
+	<maintainer type="project">
+		<email>sci@gentoo.org</email>
+		<name>Gentoo Science Project</name>
+	</maintainer>
+	<upstream>
+		<remote-id type="github">nekitdev/wraps</remote-id>
+		<remote-id type="pypi">wraps</remote-id>
+	</upstream>
+</pkgmetadata>
diff --git a/dev-python/wraps/wraps-0.2.0.ebuild b/dev-python/wraps/wraps-0.2.0.ebuild
new file mode 100644
index 000000000..b06b511cd
--- /dev/null
+++ b/dev-python/wraps/wraps-0.2.0.ebuild
@@ -0,0 +1,28 @@
+# Copyright 1999-2022 Gentoo Authors
+# Distributed under the terms of the GNU General Public License v2
+
+EAPI=8
+
+DISTUTILS_USE_PEP517=poetry
+PYTHON_COMPAT=( python3_{10..11} )
+inherit distutils-r1 pypi
+
+DESCRIPTION=" Meaningful and safe wrapping types. "
+HOMEPAGE="https://github.com/nekitdev/wraps"
+
+LICENSE="MIT"
+SLOT="0"
+KEYWORDS="~amd64 ~x86"
+RESTRICT="test"
+# package does not have test suite (yet)
+
+RDEPEND="
+	>=dev-python/attrs-21.4.0[${PYTHON_USEDEP}]
+	>=dev-python/typing-extensions-4.2.0[${PYTHON_USEDEP}]
+	"
+
+PATCHES=(
+	"${FILESDIR}/${PN}-0.1.0-poetry_groups.patch"
+)
+
+distutils_enable_tests pytest
diff --git a/dev-python/xgboost/Manifest b/dev-python/xgboost/Manifest
new file mode 100644
index 000000000..b76de8dcc
--- /dev/null
+++ b/dev-python/xgboost/Manifest
@@ -0,0 +1,2 @@
+DIST xgboost-1.6.2.tar.gz 790950 BLAKE2B 07c7e65f6969d75b5741e7fb0d113dd98007d7fe296eb2f62cd02d88b39ec4d87c2e51e8f866ee9fb76d9cf73fbb2e0defea3a9d4d78373d170f9298a991ca22 SHA512 6e5221cf569765848484a7476acc1d8ccc7260807c70695047d0dac839404bd191e0f521a91d9e088af2c125770aec7c6a651c4bb830059c04482c4c799bb62b
+DIST xgboost-2.0.3.tar.gz 1048322 BLAKE2B 2140b805aaed441da956e47cbfe08d84db1b0af96844771f4912480b05346b18632051886b237bef3e2b55a80f09c1db996be4dfeff48c942220079c4a4a149c SHA512 93614a9ad9d0a256cc31586b701c46eef4353df76c3eac26f39df23c8c02fa9ec95e72a0cea0b51bc3e416b81b3ac557ed361afeda246376a7b561bb6f7da579
diff --git a/dev-python/xgboost/metadata.xml b/dev-python/xgboost/metadata.xml
new file mode 100644
index 000000000..f862a0379
--- /dev/null
+++ b/dev-python/xgboost/metadata.xml
@@ -0,0 +1,11 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<!DOCTYPE pkgmetadata
+SYSTEM 'http://www.gentoo.org/dtd/metadata.dtd'>
+<pkgmetadata>
+	<maintainer type="person">
+		<email>heroxbd@gentoo.org</email>
+	</maintainer>
+	<upstream>
+		<remote-id type="pypi">xgboost</remote-id>
+	</upstream>
+</pkgmetadata>
diff --git a/dev-python/xgboost/xgboost-1.6.2.ebuild b/dev-python/xgboost/xgboost-1.6.2.ebuild
new file mode 100644
index 000000000..780adec11
--- /dev/null
+++ b/dev-python/xgboost/xgboost-1.6.2.ebuild
@@ -0,0 +1,20 @@
+# Copyright 1999-2021 Gentoo Authors
+# Distributed under the terms of the GNU General Public License v2
+
+EAPI=8
+
+PYTHON_COMPAT=( python3_{10..11} )
+DISTUTILS_USE_PEP517=setuptools
+inherit distutils-r1 pypi
+
+DESCRIPTION="XGBoost Python Package"
+HOMEPAGE="https://xgboost.readthedocs.io"
+
+LICENSE="Apache-2.0"
+SLOT="0"
+KEYWORDS="~amd64 ~x86"
+
+RDEPEND="
+	dev-python/numpy[${PYTHON_USEDEP}]
+	dev-python/scipy[${PYTHON_USEDEP}]
+"
diff --git a/dev-python/xgboost/xgboost-2.0.3.ebuild b/dev-python/xgboost/xgboost-2.0.3.ebuild
new file mode 100644
index 000000000..60302a1cb
--- /dev/null
+++ b/dev-python/xgboost/xgboost-2.0.3.ebuild
@@ -0,0 +1,27 @@
+# Copyright 1999-2021 Gentoo Authors
+# Distributed under the terms of the GNU General Public License v2
+
+EAPI=8
+
+PYTHON_COMPAT=( python3_{10..12} )
+DISTUTILS_USE_PEP517="standalone"
+inherit distutils-r1 pypi
+
+DESCRIPTION="XGBoost Python Package"
+HOMEPAGE="
+	https://xgboost.readthedocs.io
+	https://github.com/dmlc/xgboost/
+"
+
+REQUIRED_USE="
+	${PYTHON_REQUIRED_USE}
+"
+
+LICENSE="Apache-2.0"
+SLOT="0"
+KEYWORDS="~amd64 ~x86"
+
+RDEPEND="
+	dev-python/numpy[${PYTHON_USEDEP}]
+	dev-python/scipy[${PYTHON_USEDEP}]
+"
diff --git a/dev-python/xopen/Manifest b/dev-python/xopen/Manifest
deleted file mode 100644
index a4b7d016b..000000000
--- a/dev-python/xopen/Manifest
+++ /dev/null
@@ -1 +0,0 @@
-DIST xopen-0.1.1.tar.gz 4217 BLAKE2B 8ca7084a6cec3d9bc764b60568cd4694a5e4b69ff5923f74d2184e09af4264ec404bd8c344c7c1d74bbb37e191c8a98d2c42e1026757b51b441aaae869fbb39f SHA512 9fa710bce16da4e95e7d2aa1444c6fed1c942e977c7fe1e7e2a7f44ec792a459a8cf384b44b5345b6e5420af3d671e6a53bbfd79f6edd5ecb538d5441a48e6a6
diff --git a/dev-python/xopen/metadata.xml b/dev-python/xopen/metadata.xml
deleted file mode 100644
index 138cb7705..000000000
--- a/dev-python/xopen/metadata.xml
+++ /dev/null
@@ -1,12 +0,0 @@
-<?xml version="1.0" encoding="UTF-8"?>
-<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
-<pkgmetadata>
-	<maintainer type="person">
-		<email>mmokrejs@fold.natur.cuni.cz</email>
-		<name>Martin Mokrejs</name>
-	</maintainer>
-	<maintainer type="project">
-		<email>sci-biology@gentoo.org</email>
-		<name>Gentoo Biology Project</name>
-	</maintainer>
-</pkgmetadata>
diff --git a/dev-python/xopen/xopen-0.1.1.ebuild b/dev-python/xopen/xopen-0.1.1.ebuild
deleted file mode 100644
index 18d1911b5..000000000
--- a/dev-python/xopen/xopen-0.1.1.ebuild
+++ /dev/null
@@ -1,19 +0,0 @@
-# Copyright 1999-2017 Gentoo Foundation
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=6
-
-PYTHON_COMPAT=( python2_7 python3_5 )
-inherit distutils-r1
-
-DESCRIPTION="Open compressed files transparently"
-HOMEPAGE="https://pypi.python.org/pypi/xopen"
-SRC_URI="mirror://pypi/${PN:0:1}/${PN}/${P}.tar.gz"
-
-LICENSE="MIT"
-SLOT="0"
-KEYWORDS="~amd64 ~x86"
-IUSE=""
-
-DEPEND=""
-RDEPEND="${DEPEND}"
diff --git a/dev-python/yte/Manifest b/dev-python/yte/Manifest
new file mode 100644
index 000000000..2ad6d3366
--- /dev/null
+++ b/dev-python/yte/Manifest
@@ -0,0 +1 @@
+DIST yte-1.5.4.tar.gz 6352 BLAKE2B f304d1846c0f54949397570564f6bf9d048cd26a99a87feb62f8944403fd0f619546ed0989a2f9fda381c0f39adaa4d987ff66eb4e3bcbce107a460091c1b775 SHA512 eb61553d4c17f6d39f954ea5ab1a09a83009ab8f6f653afbf780b7a30f355e149b4508f8e3755a804f245246e0a1184c74be995f1477e1d2d27bc536bc1ff1f7
diff --git a/dev-python/yte/metadata.xml b/dev-python/yte/metadata.xml
new file mode 100644
index 000000000..ea4e4616a
--- /dev/null
+++ b/dev-python/yte/metadata.xml
@@ -0,0 +1,16 @@
+<?xml version='1.0' encoding='UTF-8'?>
+<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
+<pkgmetadata>
+	<maintainer type="person">
+		<email>mschu.dev@gmail.com</email>
+		<name>Michael Schubert</name>
+	</maintainer>
+	<maintainer type="project">
+		<email>sci@gentoo.org</email>
+		<name>Gentoo Science Project</name>
+	</maintainer>
+	<upstream>
+		<remote-id type="github">yte-template-engine/yte</remote-id>
+		<remote-id type="pypi">yte</remote-id>
+	</upstream>
+</pkgmetadata>
diff --git a/dev-python/yte/yte-1.5.4.ebuild b/dev-python/yte/yte-1.5.4.ebuild
new file mode 100644
index 000000000..ad7b669b1
--- /dev/null
+++ b/dev-python/yte/yte-1.5.4.ebuild
@@ -0,0 +1,22 @@
+# Copyright 1999-2018 Gentoo Foundation
+# Distributed under the terms of the GNU General Public License v2
+
+EAPI=8
+
+DISTUTILS_USE_PEP517=poetry
+PYTHON_COMPAT=( python3_{10..12} )
+
+inherit pypi distutils-r1
+
+DESCRIPTION="A YAML template engine with Python expressions"
+HOMEPAGE="https://pypi.org/project/yte/"
+
+LICENSE="MIT"
+SLOT="0"
+KEYWORDS="~amd64 ~x86 ~amd64-linux ~x86-linux"
+
+RDEPEND="
+	dev-python/dpath[${PYTHON_USEDEP}]
+	dev-python/plac[${PYTHON_USEDEP}]
+	dev-python/pyyaml[${PYTHON_USEDEP}]
+"
diff --git a/dev-python/zarr/Manifest b/dev-python/zarr/Manifest
new file mode 100644
index 000000000..bb2213da1
--- /dev/null
+++ b/dev-python/zarr/Manifest
@@ -0,0 +1,3 @@
+DIST zarr-2.12.0.tar.gz 3571172 BLAKE2B f8c628d0ff1fdb75fa46dc923de413f4de5f7aeed822a14523c3c2277b2692852f4896c80d160c503c787d510270c25fc813a9556f1a1f54ed2ffa0147f41763 SHA512 300fc20e22def9b444629c5bb7d5ae9d8178100b88f02b5dc4ddeabc2007cc9d19e7fe9b1710f3b69ebf1aa2154f7e03b11b1a78809be9285caf294d4d49c4ee
+DIST zarr-2.14.2.tar.gz 3589944 BLAKE2B 5e7de6c3a2bd9bd970b07bdfe1d51f14ad0e50bac37f2fbad91d98066d5239d237fa5af8cfef2f0a1ab4461dba4eeaed1db9fa0a4a1bfcd1757d54da4bbb15f7 SHA512 cc1eb40cd3723e87916e84f958d26df6353fc1e767e33a986068e182ad2a83c2dd7eb4939bf12ff45d4de49d822a0e6cb0afb5a5f1292d4c196f812d48939191
+DIST zarr-2.16.1.tar.gz 3597771 BLAKE2B 459f8022b3a4e3298b0f9650738713f6c13bb474ae50005b9387fefc87360f6358e4899037b26b9893d87298b14606d7b29bc1539fc8fa1479a08b30f2c8323b SHA512 e3b7c234c6376bea535d47304d83ee5b4d8b4bfc6952dde5e0bf1276833c1f427c98a7af0867f351e0139404d3729024b591a1f9b2242e219846a994e0762ee5
diff --git a/dev-python/zarr/metadata.xml b/dev-python/zarr/metadata.xml
new file mode 100644
index 000000000..036ff8b45
--- /dev/null
+++ b/dev-python/zarr/metadata.xml
@@ -0,0 +1,16 @@
+<?xml version='1.0' encoding='UTF-8'?>
+<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
+<pkgmetadata>
+	<maintainer type="person">
+		<email>gentoo@chymera.eu</email>
+		<name>Horea Christian</name>
+	</maintainer>
+	<maintainer type="project">
+		<email>sci@gentoo.org</email>
+		<name>Gentoo Science Project</name>
+	</maintainer>
+	<upstream>
+		<remote-id type="github">zarr-developers/zarr-python</remote-id>
+		<remote-id type="pypi">zarr</remote-id>
+	</upstream>
+</pkgmetadata>
diff --git a/dev-python/zarr/zarr-2.12.0.ebuild b/dev-python/zarr/zarr-2.12.0.ebuild
new file mode 100644
index 000000000..f18e92d44
--- /dev/null
+++ b/dev-python/zarr/zarr-2.12.0.ebuild
@@ -0,0 +1,61 @@
+# Copyright 1999-2023 Gentoo Authors
+# Distributed under the terms of the GNU General Public License v2
+
+EAPI=8
+
+DISTUTILS_USE_PEP517=setuptools
+PYTHON_COMPAT=( python3_{10..11} )
+
+inherit distutils-r1 pypi
+
+DESCRIPTION="Chunked, compressed, N-dimensional arrays for Python"
+HOMEPAGE="https://github.com/zarr-developers/zarr-python"
+
+LICENSE="MIT"
+SLOT="0"
+KEYWORDS="~amd64 ~x86"
+IUSE="test"
+RESTRICT="!test? ( test )"
+
+RDEPEND="
+	dev-python/asciitree[${PYTHON_USEDEP}]
+	dev-python/fasteners[${PYTHON_USEDEP}]
+	>=dev-python/numcodecs-0.6.4[${PYTHON_USEDEP}]
+	>=dev-python/numpy-1.7[${PYTHON_USEDEP}]
+"
+
+DEPEND="
+	test? (
+		dev-python/msgpack[${PYTHON_USEDEP}]
+	)
+"
+
+# Reported upsream
+# https://github.com/zarr-developers/zarr-python/issues/961
+EPYTEST_DESELECT=(
+	zarr/tests/test_core.py::TestArray::test_object_arrays_vlen_bytes
+	zarr/tests/test_core.py::TestArrayWithPath::test_object_arrays_vlen_bytes
+	zarr/tests/test_core.py::TestArrayWithChunkStore::test_object_arrays_vlen_bytes
+	zarr/tests/test_core.py::TestArrayWithDirectoryStore::test_object_arrays_vlen_bytes
+	zarr/tests/test_core.py::TestArrayWithNestedDirectoryStore::test_object_arrays_vlen_bytes
+	zarr/tests/test_core.py::TestArrayWithDBMStore::test_object_arrays_vlen_bytes
+	zarr/tests/test_core.py::TestArrayWithSQLiteStore::test_object_arrays_vlen_bytes
+	zarr/tests/test_core.py::TestArrayWithNoCompressor::test_object_arrays_vlen_bytes
+	zarr/tests/test_core.py::TestArrayWithBZ2Compressor::test_object_arrays_vlen_bytes
+	zarr/tests/test_core.py::TestArrayWithBloscCompressor::test_object_arrays_vlen_bytes
+	zarr/tests/test_core.py::TestArrayWithLZMACompressor::test_object_arrays_vlen_bytes
+	zarr/tests/test_core.py::TestArrayWithCustomMapping::test_object_arrays_vlen_bytes
+	zarr/tests/test_core.py::TestArrayNoCache::test_object_arrays_vlen_bytes
+	zarr/tests/test_core.py::TestArrayWithStoreCache::test_object_arrays_vlen_bytes
+	zarr/tests/test_sync.py::TestArray::test_object_arrays_vlen_bytes
+	zarr/tests/test_sync.py::TestArrayWithThreadSynchronizer::test_object_arrays_vlen_bytes
+	zarr/tests/test_sync.py::TestArrayWithProcessSynchronizer::test_object_arrays_vlen_bytes
+	zarr/tests/test_core.py::TestArrayWithFSStore::test_object_arrays_vlen_bytes
+	zarr/tests/test_core.py::TestArrayWithFSStoreFromFilesystem::test_object_arrays_vlen_bytes
+	zarr/tests/test_core.py::TestArrayWithFSStorePartialRead::test_object_arrays_vlen_bytes
+	zarr/tests/test_core.py::TestArrayWithFSStoreNested::test_object_arrays_vlen_bytes
+	zarr/tests/test_core.py::TestArrayWithFSStoreNestedPartialRead::test_object_arrays_vlen_bytes
+)
+
+distutils_enable_tests pytest
+distutils_enable_sphinx docs dev-python/numpydoc dev-python/sphinx-issues dev-python/sphinx-rtd-theme
diff --git a/dev-python/zarr/zarr-2.14.2.ebuild b/dev-python/zarr/zarr-2.14.2.ebuild
new file mode 100644
index 000000000..f18e92d44
--- /dev/null
+++ b/dev-python/zarr/zarr-2.14.2.ebuild
@@ -0,0 +1,61 @@
+# Copyright 1999-2023 Gentoo Authors
+# Distributed under the terms of the GNU General Public License v2
+
+EAPI=8
+
+DISTUTILS_USE_PEP517=setuptools
+PYTHON_COMPAT=( python3_{10..11} )
+
+inherit distutils-r1 pypi
+
+DESCRIPTION="Chunked, compressed, N-dimensional arrays for Python"
+HOMEPAGE="https://github.com/zarr-developers/zarr-python"
+
+LICENSE="MIT"
+SLOT="0"
+KEYWORDS="~amd64 ~x86"
+IUSE="test"
+RESTRICT="!test? ( test )"
+
+RDEPEND="
+	dev-python/asciitree[${PYTHON_USEDEP}]
+	dev-python/fasteners[${PYTHON_USEDEP}]
+	>=dev-python/numcodecs-0.6.4[${PYTHON_USEDEP}]
+	>=dev-python/numpy-1.7[${PYTHON_USEDEP}]
+"
+
+DEPEND="
+	test? (
+		dev-python/msgpack[${PYTHON_USEDEP}]
+	)
+"
+
+# Reported upsream
+# https://github.com/zarr-developers/zarr-python/issues/961
+EPYTEST_DESELECT=(
+	zarr/tests/test_core.py::TestArray::test_object_arrays_vlen_bytes
+	zarr/tests/test_core.py::TestArrayWithPath::test_object_arrays_vlen_bytes
+	zarr/tests/test_core.py::TestArrayWithChunkStore::test_object_arrays_vlen_bytes
+	zarr/tests/test_core.py::TestArrayWithDirectoryStore::test_object_arrays_vlen_bytes
+	zarr/tests/test_core.py::TestArrayWithNestedDirectoryStore::test_object_arrays_vlen_bytes
+	zarr/tests/test_core.py::TestArrayWithDBMStore::test_object_arrays_vlen_bytes
+	zarr/tests/test_core.py::TestArrayWithSQLiteStore::test_object_arrays_vlen_bytes
+	zarr/tests/test_core.py::TestArrayWithNoCompressor::test_object_arrays_vlen_bytes
+	zarr/tests/test_core.py::TestArrayWithBZ2Compressor::test_object_arrays_vlen_bytes
+	zarr/tests/test_core.py::TestArrayWithBloscCompressor::test_object_arrays_vlen_bytes
+	zarr/tests/test_core.py::TestArrayWithLZMACompressor::test_object_arrays_vlen_bytes
+	zarr/tests/test_core.py::TestArrayWithCustomMapping::test_object_arrays_vlen_bytes
+	zarr/tests/test_core.py::TestArrayNoCache::test_object_arrays_vlen_bytes
+	zarr/tests/test_core.py::TestArrayWithStoreCache::test_object_arrays_vlen_bytes
+	zarr/tests/test_sync.py::TestArray::test_object_arrays_vlen_bytes
+	zarr/tests/test_sync.py::TestArrayWithThreadSynchronizer::test_object_arrays_vlen_bytes
+	zarr/tests/test_sync.py::TestArrayWithProcessSynchronizer::test_object_arrays_vlen_bytes
+	zarr/tests/test_core.py::TestArrayWithFSStore::test_object_arrays_vlen_bytes
+	zarr/tests/test_core.py::TestArrayWithFSStoreFromFilesystem::test_object_arrays_vlen_bytes
+	zarr/tests/test_core.py::TestArrayWithFSStorePartialRead::test_object_arrays_vlen_bytes
+	zarr/tests/test_core.py::TestArrayWithFSStoreNested::test_object_arrays_vlen_bytes
+	zarr/tests/test_core.py::TestArrayWithFSStoreNestedPartialRead::test_object_arrays_vlen_bytes
+)
+
+distutils_enable_tests pytest
+distutils_enable_sphinx docs dev-python/numpydoc dev-python/sphinx-issues dev-python/sphinx-rtd-theme
diff --git a/dev-python/zarr/zarr-2.16.1.ebuild b/dev-python/zarr/zarr-2.16.1.ebuild
new file mode 100644
index 000000000..f18e92d44
--- /dev/null
+++ b/dev-python/zarr/zarr-2.16.1.ebuild
@@ -0,0 +1,61 @@
+# Copyright 1999-2023 Gentoo Authors
+# Distributed under the terms of the GNU General Public License v2
+
+EAPI=8
+
+DISTUTILS_USE_PEP517=setuptools
+PYTHON_COMPAT=( python3_{10..11} )
+
+inherit distutils-r1 pypi
+
+DESCRIPTION="Chunked, compressed, N-dimensional arrays for Python"
+HOMEPAGE="https://github.com/zarr-developers/zarr-python"
+
+LICENSE="MIT"
+SLOT="0"
+KEYWORDS="~amd64 ~x86"
+IUSE="test"
+RESTRICT="!test? ( test )"
+
+RDEPEND="
+	dev-python/asciitree[${PYTHON_USEDEP}]
+	dev-python/fasteners[${PYTHON_USEDEP}]
+	>=dev-python/numcodecs-0.6.4[${PYTHON_USEDEP}]
+	>=dev-python/numpy-1.7[${PYTHON_USEDEP}]
+"
+
+DEPEND="
+	test? (
+		dev-python/msgpack[${PYTHON_USEDEP}]
+	)
+"
+
+# Reported upsream
+# https://github.com/zarr-developers/zarr-python/issues/961
+EPYTEST_DESELECT=(
+	zarr/tests/test_core.py::TestArray::test_object_arrays_vlen_bytes
+	zarr/tests/test_core.py::TestArrayWithPath::test_object_arrays_vlen_bytes
+	zarr/tests/test_core.py::TestArrayWithChunkStore::test_object_arrays_vlen_bytes
+	zarr/tests/test_core.py::TestArrayWithDirectoryStore::test_object_arrays_vlen_bytes
+	zarr/tests/test_core.py::TestArrayWithNestedDirectoryStore::test_object_arrays_vlen_bytes
+	zarr/tests/test_core.py::TestArrayWithDBMStore::test_object_arrays_vlen_bytes
+	zarr/tests/test_core.py::TestArrayWithSQLiteStore::test_object_arrays_vlen_bytes
+	zarr/tests/test_core.py::TestArrayWithNoCompressor::test_object_arrays_vlen_bytes
+	zarr/tests/test_core.py::TestArrayWithBZ2Compressor::test_object_arrays_vlen_bytes
+	zarr/tests/test_core.py::TestArrayWithBloscCompressor::test_object_arrays_vlen_bytes
+	zarr/tests/test_core.py::TestArrayWithLZMACompressor::test_object_arrays_vlen_bytes
+	zarr/tests/test_core.py::TestArrayWithCustomMapping::test_object_arrays_vlen_bytes
+	zarr/tests/test_core.py::TestArrayNoCache::test_object_arrays_vlen_bytes
+	zarr/tests/test_core.py::TestArrayWithStoreCache::test_object_arrays_vlen_bytes
+	zarr/tests/test_sync.py::TestArray::test_object_arrays_vlen_bytes
+	zarr/tests/test_sync.py::TestArrayWithThreadSynchronizer::test_object_arrays_vlen_bytes
+	zarr/tests/test_sync.py::TestArrayWithProcessSynchronizer::test_object_arrays_vlen_bytes
+	zarr/tests/test_core.py::TestArrayWithFSStore::test_object_arrays_vlen_bytes
+	zarr/tests/test_core.py::TestArrayWithFSStoreFromFilesystem::test_object_arrays_vlen_bytes
+	zarr/tests/test_core.py::TestArrayWithFSStorePartialRead::test_object_arrays_vlen_bytes
+	zarr/tests/test_core.py::TestArrayWithFSStoreNested::test_object_arrays_vlen_bytes
+	zarr/tests/test_core.py::TestArrayWithFSStoreNestedPartialRead::test_object_arrays_vlen_bytes
+)
+
+distutils_enable_tests pytest
+distutils_enable_sphinx docs dev-python/numpydoc dev-python/sphinx-issues dev-python/sphinx-rtd-theme
diff --git a/dev-python/zarr_checksum/Manifest b/dev-python/zarr_checksum/Manifest
new file mode 100644
index 000000000..5ca7cc376
--- /dev/null
+++ b/dev-python/zarr_checksum/Manifest
@@ -0,0 +1,2 @@
+DIST zarr_checksum-0.2.8.tar.gz 11824 BLAKE2B b26b6e1b9559e6572c95fb3700afada3c9040dfa1d26f736dcf6edfe4272c2e513f209286e24d7690de9fa2789297075469258f65edc8a2999fa2c4eee58f3ee SHA512 5c79611568decc8b9a353002e96c6ca73ec2c378debcba11f89feecb62089a78a4c3a8f4948971dd1a120a476dba7f357b23ba0b6edcf93d3f44dbb7c531feb5
+DIST zarr_checksum-0.4.0.tar.gz 11618 BLAKE2B 90c963f6540fd9a7a667f0a683b6c3d4a70230b4d71eb08f62a1cfecb20b7eb46b515b4cafc12b90fbc6c80fb83d5c5779682c6313bc56a819a4a8a5ff1843dc SHA512 e903bbc04847767dd14a0e0ad7e2fae47e97b18b813911b3bdb835e75454f573e8e1021c68f79cbf44fa21af64a4833f41ecb754a5b263e5d46dc0c7dc83447f
diff --git a/dev-python/zarr_checksum/metadata.xml b/dev-python/zarr_checksum/metadata.xml
new file mode 100644
index 000000000..57bdec31a
--- /dev/null
+++ b/dev-python/zarr_checksum/metadata.xml
@@ -0,0 +1,16 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
+<pkgmetadata>
+	<maintainer type="person">
+		<email>gentoo@chymera.eu</email>
+		<name>Horea Christian</name>
+	</maintainer>
+	<maintainer type="project">
+		<email>sci@gentoo.org</email>
+		<name>Gentoo Science Project</name>
+	</maintainer>
+	<upstream>
+		<remote-id type="github">dandi/zarr_checksum</remote-id>
+		<remote-id type="pypi">zarr_checksum</remote-id>
+	</upstream>
+</pkgmetadata>
diff --git a/dev-python/zarr_checksum/zarr_checksum-0.2.8.ebuild b/dev-python/zarr_checksum/zarr_checksum-0.2.8.ebuild
new file mode 100644
index 000000000..58cb87329
--- /dev/null
+++ b/dev-python/zarr_checksum/zarr_checksum-0.2.8.ebuild
@@ -0,0 +1,26 @@
+# Copyright 1999-2023 Gentoo Authors
+# Distributed under the terms of the GNU General Public License v2
+
+EAPI=8
+
+PYTHON_COMPAT=( python3_{10..11} )
+DISTUTILS_USE_PEP517=poetry
+
+inherit distutils-r1 pypi
+
+DESCRIPTION="Calculatine zarr checksums from local or cloud storage"
+HOMEPAGE="https://github.com/dandi/zarr_checksum"
+
+LICENSE="Apache-2.0"
+SLOT="0"
+KEYWORDS="~amd64 ~x86"
+
+RDEPEND="
+	dev-python/boto3[${PYTHON_USEDEP}]
+	dev-python/click[${PYTHON_USEDEP}]
+	dev-python/pydantic[${PYTHON_USEDEP}]
+	dev-python/tqdm[${PYTHON_USEDEP}]
+	dev-python/zarr[${PYTHON_USEDEP}]
+"
+
+distutils_enable_tests pytest
diff --git a/dev-python/zarr_checksum/zarr_checksum-0.4.0.ebuild b/dev-python/zarr_checksum/zarr_checksum-0.4.0.ebuild
new file mode 100644
index 000000000..58cb87329
--- /dev/null
+++ b/dev-python/zarr_checksum/zarr_checksum-0.4.0.ebuild
@@ -0,0 +1,26 @@
+# Copyright 1999-2023 Gentoo Authors
+# Distributed under the terms of the GNU General Public License v2
+
+EAPI=8
+
+PYTHON_COMPAT=( python3_{10..11} )
+DISTUTILS_USE_PEP517=poetry
+
+inherit distutils-r1 pypi
+
+DESCRIPTION="Calculatine zarr checksums from local or cloud storage"
+HOMEPAGE="https://github.com/dandi/zarr_checksum"
+
+LICENSE="Apache-2.0"
+SLOT="0"
+KEYWORDS="~amd64 ~x86"
+
+RDEPEND="
+	dev-python/boto3[${PYTHON_USEDEP}]
+	dev-python/click[${PYTHON_USEDEP}]
+	dev-python/pydantic[${PYTHON_USEDEP}]
+	dev-python/tqdm[${PYTHON_USEDEP}]
+	dev-python/zarr[${PYTHON_USEDEP}]
+"
+
+distutils_enable_tests pytest
diff --git a/dev-tcltk/img_rotate/Manifest b/dev-tcltk/img_rotate/Manifest
deleted file mode 100644
index 072ab7548..000000000
--- a/dev-tcltk/img_rotate/Manifest
+++ /dev/null
@@ -1 +0,0 @@
-DIST img_rotate-1.1.zip 11368 BLAKE2B 25f37276857deeccb26d35b6190cc30706d63fdc483c202e55631ef71e7321240d503cd72b3c6a7ebe1665b7840dd8d1fd357e5d6f1725d67c29ea31580fe2a8 SHA512 4b6ba324a2e54432e2bbd2c2c1ebd378cb16de916a08758c442d40cd8382d92895a05b1ea84469d02076b273961a23a898a34d9b6c95b695df5ceb5203caef89
diff --git a/dev-tcltk/img_rotate/img_rotate-1.1.ebuild b/dev-tcltk/img_rotate/img_rotate-1.1.ebuild
deleted file mode 100644
index 8e17bd218..000000000
--- a/dev-tcltk/img_rotate/img_rotate-1.1.ebuild
+++ /dev/null
@@ -1,26 +0,0 @@
-# Copyright 1999-2015 Gentoo Foundation
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=5
-
-inherit multilib
-
-DESCRIPTION="Image rotation package"
-HOMEPAGE="http://cardtable.sourceforge.net/tcltk/"
-SRC_URI="http://cardtable.sourceforge.net/tcltk/img_rotate.zip -> ${P}.zip"
-
-LICENSE="tcltk"
-SLOT="0"
-KEYWORDS="~amd64 ~x86"
-IUSE=""
-
-RDEPEND="dev-lang/tcl:0="
-DEPEND="${RDEPEND}
-	app-arch/unzip"
-
-S="${WORKDIR}"
-
-src_install() {
-	insinto /usr/$(get_libdir)/${P}
-	doins *
-}
diff --git a/dev-tcltk/img_rotate/metadata.xml b/dev-tcltk/img_rotate/metadata.xml
deleted file mode 100644
index f1310b451..000000000
--- a/dev-tcltk/img_rotate/metadata.xml
+++ /dev/null
@@ -1,11 +0,0 @@
-<?xml version="1.0" encoding="UTF-8"?>
-<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
-<pkgmetadata>
-	<maintainer type="project">
-		<email>sci@gentoo.org</email>
-		<name>Gentoo Science Project</name>
-	</maintainer>
-	<upstream>
-		<remote-id type="sourceforge">cardtable</remote-id>
-	</upstream>
-</pkgmetadata>
diff --git a/dev-tcltk/togl/Manifest b/dev-tcltk/togl/Manifest
deleted file mode 100644
index 382534c12..000000000
--- a/dev-tcltk/togl/Manifest
+++ /dev/null
@@ -1 +0,0 @@
-DIST Togl-1.7.tar.gz 205532 BLAKE2B 5a05356d0e3c7655135f0c6ccaa77f61cb38cc1209d9b9d3122591649358c6739b5bef7a9aebd3ffe26c1d450c1eb28470a34ec0b17bfef2b3f5885a6a35112c SHA512 86dccaf1585767fc2e217cee3172619fe08b1d054beb679bd1db140195a100ec90daef02ac9b85d3e6c2b805d0a7668a540b80754023aee85138cefa7275e84a
diff --git a/dev-tcltk/togl/metadata.xml b/dev-tcltk/togl/metadata.xml
deleted file mode 100644
index c191e6dbe..000000000
--- a/dev-tcltk/togl/metadata.xml
+++ /dev/null
@@ -1,11 +0,0 @@
-<?xml version="1.0" encoding="UTF-8"?>
-<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
-<pkgmetadata>
-	<maintainer type="project">
-		<email>sci@gentoo.org</email>
-		<name>Gentoo Science Project</name>
-	</maintainer>
-	<upstream>
-		<remote-id type="sourceforge">togl</remote-id>
-	</upstream>
-</pkgmetadata>
diff --git a/dev-tcltk/togl/togl-1.7-r1.ebuild b/dev-tcltk/togl/togl-1.7-r1.ebuild
deleted file mode 100644
index 714cae183..000000000
--- a/dev-tcltk/togl/togl-1.7-r1.ebuild
+++ /dev/null
@@ -1,39 +0,0 @@
-# Copyright 1999-2015 Gentoo Foundation
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=5
-
-MY_P="Togl-${PV}"
-
-DESCRIPTION="A Tk widget for OpenGL rendering"
-HOMEPAGE="http://togl.sourceforge.net/"
-SRC_URI="mirror://sourceforge/${PN}/${MY_P}.tar.gz"
-
-LICENSE="BSD"
-SLOT="1.7"
-KEYWORDS="~amd64 ~x86"
-IUSE="debug +threads"
-
-RDEPEND="
-	dev-lang/tk:0
-	virtual/opengl"
-DEPEND="${RDEPEND}"
-
-# tests directory is missing
-RESTRICT="test"
-
-S=${WORKDIR}/${MY_P}
-
-src_configure() {
-	econf \
-		$(use_enable debug symbols) \
-		$(use_enable amd64 64bit) \
-		$(use_enable threads)
-}
-
-src_install() {
-	default
-	rm "${D}"/usr/include/* || die
-	insinto /usr/include/${PN}-${SLOT}
-	doins togl*.h
-}
diff --git a/dev-tex/pythontex/Manifest b/dev-tex/pythontex/Manifest
deleted file mode 100644
index ecf789f79..000000000
--- a/dev-tex/pythontex/Manifest
+++ /dev/null
@@ -1,2 +0,0 @@
-DIST pythontex-0.14.tar.gz 9704671 BLAKE2B 5d4644acfb53f08cae5b45f068c363236406f42438539c52d1c2ced30b613ec71d35383e8b1233e85c6dd46acb26ce7e494990fc7c2ca2c55abd7c1a5b1bba0a SHA512 dc37e3ac112ace95d4ac253f51fe08074cf465537fa8e686637dd2342edb397e89a1e9ee1111fd6b93bcf4194b8bbbcb5cbcc5256d4c451809bf96bb28ae3db6
-DIST pythontex-0.15.tar.gz 1765050 BLAKE2B b70415e453310d97a8c50781ea2a65656cdae7a78060a8f789af36368e024ca9dd75fdb4bec55216eec982be9c31ccb0894cd258924aa5649dc46a53cb34bccb SHA512 cbca1dc9208028bfe1a8ab47f6c145ec2bd0af0ad2c733ef80e1f9ee77199670c8701d30e7634207064dd073e5456bb1d1853ce4e1729f64c44967a52111b0d8
diff --git a/dev-tex/pythontex/metadata.xml b/dev-tex/pythontex/metadata.xml
deleted file mode 100644
index 02c7c504c..000000000
--- a/dev-tex/pythontex/metadata.xml
+++ /dev/null
@@ -1,14 +0,0 @@
-<?xml version="1.0" encoding="UTF-8"?>
-<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
-<pkgmetadata>
-	<maintainer type="project">
-		<email>sci@gentoo.org</email>
-		<name>Gentoo Science Project</name>
-	</maintainer>
-	<use>
-		<flag name="highlighting">PLEASE FIX MY DESCRIPTION</flag>
-	</use>
-	<upstream>
-		<remote-id type="github">gpoore/pythontex</remote-id>
-	</upstream>
-</pkgmetadata>
diff --git a/dev-tex/pythontex/pythontex-0.14-r1.ebuild b/dev-tex/pythontex/pythontex-0.14-r1.ebuild
deleted file mode 100644
index 63645e881..000000000
--- a/dev-tex/pythontex/pythontex-0.14-r1.ebuild
+++ /dev/null
@@ -1,55 +0,0 @@
-# Copyright 1999-2015 Gentoo Foundation
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=5
-
-PYTHON_COMPAT=( python2_7 python3_{3,4} )
-
-inherit latex-package python-r1
-
-DESCRIPTION="Fast Access to Python from within LaTeX"
-HOMEPAGE="https://github.com/gpoore/pythontex"
-SRC_URI="https://github.com/gpoore/pythontex/archive/v${PV}.tar.gz -> ${P}.tar.gz"
-
-SLOT="0"
-LICENSE="LPPL-1.3 BSD"
-KEYWORDS="~amd64"
-IUSE="highlighting"
-
-REQUIRED_USE="${PYTHON_REQUIRED_USE}"
-
-DEPEND="${PYTHON_DEPS}
-	dev-texlive/texlive-latex"
-RDEPEND="${DEPEND}
-	dev-texlive/texlive-latex
-	highlighting? ( dev-python/pygments[${PYTHON_USEDEP}] )"
-
-TEXMF=/usr/share/texmf-site
-
-src_compile() {
-	cd ${PN} || die
-	ebegin "Compiling ${PN}"
-	rm ${PN}.sty || die
-	VARTEXFONTS="${T}/fonts" latex ${PN}.ins extra || die
-	eend
-}
-
-src_install() {
-	dodoc ${PN}/README "${S}"/*rst ${PN}_quickstart/*
-
-	cd ${PN} || die
-
-	installation() {
-		if python_is_python3; then
-			python_domodule {de,}${PN}3.py
-		else
-			python_domodule {de,}${PN}2.py
-		fi
-		python_domodule ${PN}_{engines,utils}.py
-		python_doscript {de,}${PN}.py syncpdb.py
-		python_optimize
-	}
-	python_foreach_impl installation
-
-	latex-package_src_doinstall dtx ins sty
-}
diff --git a/dev-tex/pythontex/pythontex-0.15.ebuild b/dev-tex/pythontex/pythontex-0.15.ebuild
deleted file mode 100644
index 6526b9fc6..000000000
--- a/dev-tex/pythontex/pythontex-0.15.ebuild
+++ /dev/null
@@ -1,55 +0,0 @@
-# Copyright 1999-2017 Gentoo Foundation
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=6
-
-PYTHON_COMPAT=( python2_7 python3_{4,5} )
-
-inherit latex-package python-r1
-
-DESCRIPTION="Fast Access to Python from within LaTeX"
-HOMEPAGE="https://github.com/gpoore/pythontex"
-SRC_URI="https://github.com/gpoore/pythontex/archive/v${PV}.tar.gz -> ${P}.tar.gz"
-
-SLOT="0"
-LICENSE="LPPL-1.3 BSD"
-KEYWORDS="~amd64"
-IUSE="highlighting"
-
-REQUIRED_USE="${PYTHON_REQUIRED_USE}"
-
-DEPEND="${PYTHON_DEPS}
-	>=dev-texlive/texlive-latex-2016"
-RDEPEND="${DEPEND}
-	>=dev-texlive/texlive-latex-2016
-	highlighting? ( dev-python/pygments[${PYTHON_USEDEP}] )"
-
-TEXMF=/usr/share/texmf-site
-
-src_compile() {
-	cd ${PN} || die
-	ebegin "Compiling ${PN}"
-	rm ${PN}.sty || die
-	VARTEXFONTS="${T}/fonts" latex ${PN}.ins extra || die
-	eend
-}
-
-src_install() {
-	dodoc ${PN}/README "${S}"/*rst ${PN}_quickstart/*
-
-	cd ${PN} || die
-
-	installation() {
-		if python_is_python3; then
-			python_domodule {de,}${PN}3.py
-		else
-			python_domodule {de,}${PN}2.py
-		fi
-		python_domodule ${PN}_{engines,utils}.py
-		python_doscript {de,}${PN}.py syncpdb.py
-		python_optimize
-	}
-	python_foreach_impl installation
-
-	latex-package_src_doinstall dtx ins sty
-}
diff --git a/dev-tex/pythontex/pythontex-9999.ebuild b/dev-tex/pythontex/pythontex-9999.ebuild
deleted file mode 100644
index b5bc2fd02..000000000
--- a/dev-tex/pythontex/pythontex-9999.ebuild
+++ /dev/null
@@ -1,56 +0,0 @@
-# Copyright 1999-2015 Gentoo Foundation
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=5
-
-PYTHON_COMPAT=( python2_7 python3_{3,4} )
-
-inherit latex-package python-r1 git-r3
-
-DESCRIPTION="Fast Access to Python from within LaTeX"
-HOMEPAGE="https://github.com/gpoore/pythontex"
-SRC_URI=""
-EGIT_REPO_URI="https://github.com/gpoore/pythontex.git"
-
-SLOT="0"
-LICENSE="LPPL-1.3 BSD"
-KEYWORDS=""
-IUSE="highlighting"
-
-REQUIRED_USE="${PYTHON_REQUIRED_USE}"
-
-DEPEND="${PYTHON_DEPS}
-	dev-texlive/texlive-latex"
-RDEPEND="${DEPEND}
-	dev-texlive/texlive-latex
-	highlighting? ( dev-python/pygments[${PYTHON_USEDEP}] )"
-
-TEXMF=/usr/share/texmf-site
-
-src_compile() {
-	cd ${PN} || die
-	ebegin "Compiling ${PN}"
-	rm ${PN}.sty || die
-	VARTEXFONTS="${T}/fonts" latex ${PN}.ins extra || die
-	eend
-}
-
-src_install() {
-	dodoc ${PN}/README "${S}"/*rst ${PN}_quickstart/*
-
-	cd ${PN} || die
-
-	installation() {
-		if python_is_python3; then
-			python_domodule {de,}${PN}3.py
-		else
-			python_domodule {de,}${PN}2.py
-		fi
-		python_domodule ${PN}_{engines,utils}.py
-		python_doscript {de,}${PN}.py syncpdb.py
-		python_optimize
-	}
-	python_foreach_impl installation
-
-	latex-package_src_doinstall dtx ins sty
-}
diff --git a/dev-util/VampirTrace/Manifest b/dev-util/VampirTrace/Manifest
deleted file mode 100644
index 541640406..000000000
--- a/dev-util/VampirTrace/Manifest
+++ /dev/null
@@ -1,2 +0,0 @@
-DIST dcount.php?package=gputrace&get=VampirTrace-5.14.4-gpu2.tar.gz 5930789 BLAKE2B 4c3500c11c815c2ff7971081e8583c85a01f659a9d94b30ba2397905894d1060e51886b0f2f79a6c9148f8beff2581de7a240781a7488a21c9d36d288ed54b27 SHA512 ea76ccf3bcd21a395a3fa233d16804f1e287449b3fef2a71c0e16d8df45dab9b62434dae3fa644479ac58784e5b198cd89ab2975dc9813163a4849f332aeb47d
-DIST dcount.php?package=vampirtrace&get=VampirTrace-5.14.3.tar.gz 5956627 SHA256 d3bc18662ee48c9c02de0b5933c52213849cbb79b21a3b4ec786bc21e3126209 SHA512 2b1faa707d12b672ba12b399f6b1c14c8d3cff0b3f961f70b81adb1e5ba69960a217ae228cbacd1ffd3f54aab1b30697ef66748a4fd604e8684910d98041d458 WHIRLPOOL 2bcf401f25f4ed500e92739e36265979cab1c5c0caebb53555caf6f293411b4ac8c542254bc95cad5a81f3458ccb74126580450873ff53a9df3e944f67cb9d48
diff --git a/dev-util/VampirTrace/VampirTrace-5.14.3.ebuild b/dev-util/VampirTrace/VampirTrace-5.14.3.ebuild
deleted file mode 100644
index f31fb00d3..000000000
--- a/dev-util/VampirTrace/VampirTrace-5.14.3.ebuild
+++ /dev/null
@@ -1,35 +0,0 @@
-# Copyright 1999-2016 Gentoo Foundation
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=6
-
-inherit eutils cuda
-
-DESCRIPTION="Library for detailed logging of program execution for parallel applications"
-HOMEPAGE="http://www.tu-dresden.de/die_tu_dresden/zentrale_einrichtungen/zih/forschung/software_werkzeuge_zur_unterstuetzung_von_programmierung_und_optimierung/vampirtrace"
-SRC_URI="http://wwwpub.zih.tu-dresden.de/%7Emlieber/dcount/dcount.php?package=vampirtrace&get=${P}.tar.gz"
-
-SLOT="0"
-LICENSE="vampir"
-KEYWORDS="~amd64"
-IUSE="cuda"
-
-DEPEND="
-	virtual/mpi
-	cuda? ( >=dev-util/nvidia-cuda-toolkit-4.0.0 )"
-
-src_prepare() {
-	use cuda && cuda_src_prepare
-}
-
-src_configure() {
-	econf $(use_with cuda cuda-dir "${EPREFIX}"/opt/cuda)
-}
-
-src_install() {
-	default
-	# avoid collisions with app-text/lcdf-typetools:
-	mv "${ED}"/usr/bin/otfinfo{,.vampir} || die
-	# libtool is already installed:
-	rm "${ED}"/usr/share/libtool || die
-}
diff --git a/dev-util/VampirTrace/VampirTrace-5.14.4.ebuild b/dev-util/VampirTrace/VampirTrace-5.14.4.ebuild
deleted file mode 100644
index ace9370fe..000000000
--- a/dev-util/VampirTrace/VampirTrace-5.14.4.ebuild
+++ /dev/null
@@ -1,40 +0,0 @@
-# Copyright 1999-2016 Gentoo Foundation
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=6
-
-inherit eutils cuda
-
-MY_PV="${PV}-gpu2"
-MY_P="${PN}-${MY_PV}"
-
-DESCRIPTION="Library for detailed logging of program execution for parallel applications"
-HOMEPAGE="http://tu-dresden.de/die_tu_dresden/zentrale_einrichtungen/zih/forschung/projekte/vampirtrace/accelerator"
-SRC_URI="http://wwwpub.zih.tu-dresden.de/~mlieber/dcount/dcount.php?package=gputrace&get=${MY_P}.tar.gz"
-
-SLOT="0"
-LICENSE="vampir"
-KEYWORDS="~amd64"
-IUSE="cuda"
-
-S="${WORKDIR}/${MY_P}"
-
-DEPEND="
-	virtual/mpi
-	cuda? ( >=dev-util/nvidia-cuda-toolkit-4.0.0 )"
-
-src_prepare() {
-	use cuda && cuda_src_prepare
-}
-
-src_configure() {
-	econf $(use_with cuda cuda-dir "${EPREFIX}"/opt/cuda)
-}
-
-src_install() {
-	default
-	# avoid collisions with app-text/lcdf-typetools:
-	mv "${ED}"/usr/bin/otfinfo{,.vampir} || die
-	# libtool is already installed:
-	rm "${ED}"/usr/share/libtool || die
-}
diff --git a/dev-util/VampirTrace/metadata.xml b/dev-util/VampirTrace/metadata.xml
deleted file mode 100644
index 08eda31af..000000000
--- a/dev-util/VampirTrace/metadata.xml
+++ /dev/null
@@ -1,19 +0,0 @@
-<?xml version="1.0" encoding="UTF-8"?>
-<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
-<pkgmetadata>
-	<longdescription>
-VampirTrace is an open source library that allows detailed logging of program execution for parallel applications using message passing (MPI) and threads (OpenMP), Pthreads). Besides these typical parallelization paradigms, VampirTrace is capable of tracing GPU accelerated applications and generates exact time stamps for all GPU related events.
-</longdescription>
-	<maintainer type="person">
-		<email>gentryx@gmx.de</email>
-	</maintainer>
-	<maintainer type="project">
-		<email>cluster@gentoo.org</email>
-		<name>Gentoo Cluster Project</name>
-	</maintainer>
-	<use>
-		<flag name="cuda">
-Enable tracing of CUDA calls and GPU kernels.
-</flag>
-	</use>
-</pkgmetadata>
diff --git a/dev-util/amdapp/Manifest b/dev-util/amdapp/Manifest
deleted file mode 100644
index 60a7fd05f..000000000
--- a/dev-util/amdapp/Manifest
+++ /dev/null
@@ -1,4 +0,0 @@
-DIST AMD-APP-SDKInstaller-v3.0.130.135-GA-linux32.tar.bz2 175232929 SHA256 8e1ad82b4cd2fcf58649daf4e43574d9d5c654cd2e07fcbb4bae7cc6d2f3daf6 SHA512 8f62ec26bf6655e71948418113553f39bfcff8588a857cb8706c2538c4742ab0e95d3843e1084acd7a8d0e8b26593a140677316b8aa285aca454828e545402a6 WHIRLPOOL 54001052fa9e8903a21916ec6265c5882d7e0d69180d2041ddde6d9ce9412a4188f7bf39d67f51792505b9a4e75b9dada2c78fcdc5e3ecadf522a8b5bda68091
-DIST AMD-APP-SDKInstaller-v3.0.130.135-GA-linux64.tar.bz2 175434609 SHA256 27a6145a73910d2320fd017159cf72f16601c375c2b304644c31566f45cc26a6 SHA512 c73ea4b4fa3f383e63755233d78203f1f5d387de1202875b40ed8e9a8b1e5a3bd6e9731244aac1086cdc1a764974ff95daca34261295a2746ddd478d0774460b WHIRLPOOL a11c878347e713b57343a7734acac505055154678cfb453cd1da84279f3e4100685d89151fb3be8ff16155f6459fa05fa9b12b5a634e28b86945023505fac810
-DIST AMD-APP-SDKInstaller-v3.0.130.136-GA-linux32.tar.bz2 195906870 SHA256 181fb9815e735c90ca5713acc27a6f9ed7f85135d2f2a085bed7b4c7ed157b94 SHA512 f3483a0db9afbf99b4ee07f26deaab589eb6ba20f9831564959121969c78690634929031dc2ba49147d2968ca084cd10848723d2b061ba80e5ec634a4adf1a68 WHIRLPOOL 09a3f4676829e5757647b58f7524b172abf35a3009b0b2a2fcff36397f5c68a7d9a9829b4fdfff9cc2176944239a262f07333f8408e49ff96a648d2fb22fb942
-DIST AMD-APP-SDKInstaller-v3.0.130.136-GA-linux64.tar.bz2 195996744 SHA256 0aa436acd334b686820bd3caab9f09014608741b92e3996d3642d0b148ede0f7 SHA512 573b60c7d2d2a46318e4490b9d14a991f317b3cc19be1b785f4f06e59925e801069329f5383b2249c227f64f0484194f44483edcc51443ed5870bc34134d2417 WHIRLPOOL ce649d422dc0f4fb283e12abd126262d726abde04c7fb1f99b639ddfe7dd8afcb88180858c0c4cbc97ce4e9d6f30401215a8356481e140b34aaebfc8834ff612
diff --git a/dev-util/amdapp/amdapp-3.0-r1.ebuild b/dev-util/amdapp/amdapp-3.0-r1.ebuild
deleted file mode 100644
index 359aa2f57..000000000
--- a/dev-util/amdapp/amdapp-3.0-r1.ebuild
+++ /dev/null
@@ -1,73 +0,0 @@
-# Copyright 1999-2017 Gentoo Foundation
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=6
-
-inherit unpacker versionator
-
-MY_V="$(get_version_component_range 1).$(get_version_component_range 2).130.135-GA"
-
-X86_AT="AMD-APP-SDKInstaller-v${MY_V}-linux32.tar.bz2"
-AMD64_AT="AMD-APP-SDKInstaller-v${MY_V}-linux64.tar.bz2"
-
-MY_P_AMD64="AMD-APP-SDK-v${MY_V}-linux64.sh"
-MY_P_AMD32="AMD-APP-SDK-v${MY_V}-linux32.sh"
-
-DESCRIPTION="AMD Accelerated Parallel Processing (APP) SDK"
-HOMEPAGE="http://developer.amd.com/tools-and-sdks/opencl-zone/amd-accelerated-parallel-processing-app-sdk"
-SRC_URI="
-	amd64? ( ${AMD64_AT} )
-	x86? ( ${X86_AT} )"
-
-LICENSE="AMD-APPSDK"
-SLOT="0"
-KEYWORDS="~amd64 ~x86"
-IUSE="examples"
-
-RDEPEND="
-	!<dev-util/amdstream-2.6
-	app-eselect/eselect-opencl
-	app-eselect/eselect-opengl
-	media-libs/freeglut
-	media-libs/mesa[video_cards_radeonsi]
-	sys-devel/gcc:*
-	sys-devel/llvm:*
-	virtual/opencl
-	examples? ( media-libs/glew:0= )"
-DEPEND="
-	${RDEPEND}
-	dev-util/patchelf
-	dev-lang/perl
-	sys-apps/fakeroot
-"
-
-RESTRICT="mirror strip"
-
-S="${WORKDIR}"
-
-pkg_nofetch() {
-	einfo "AMD doesn't provide direct download links. Please download"
-	einfo "${ARCHIVE} from ${HOMEPAGE}"
-}
-
-src_unpack() {
-	default
-
-	cd "${WORKDIR}" || die
-
-	if use amd64 || use amd64-linux ; then
-		unpacker ./${MY_P_AMD64}
-	else
-		unpacker ./${MY_P_X86}
-	fi
-}
-
-src_compile() {
-	MAKEOPTS+=" -j1"
-	use examples && cd samples/opencl && default
-}
-
-src_install() {
-	dodir /opt/AMDAPP
-	cp -R "${S}/"* "${ED}/opt/AMDAPP" || die "Install failed!"
-}
diff --git a/dev-util/amdapp/amdapp-3.0-r2.ebuild b/dev-util/amdapp/amdapp-3.0-r2.ebuild
deleted file mode 100644
index bfa63a332..000000000
--- a/dev-util/amdapp/amdapp-3.0-r2.ebuild
+++ /dev/null
@@ -1,89 +0,0 @@
-# Copyright 1999-2017 Gentoo Foundation
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=6
-
-inherit multilib unpacker versionator
-
-MY_V="$(get_version_component_range 1).$(get_version_component_range 2).130.136-GA"
-
-X86_AT="AMD-APP-SDKInstaller-v${MY_V}-linux32.tar.bz2"
-AMD64_AT="AMD-APP-SDKInstaller-v${MY_V}-linux64.tar.bz2"
-
-MY_P_AMD64="AMD-APP-SDK-v${MY_V}-linux64.sh"
-MY_P_AMD32="AMD-APP-SDK-v${MY_V}-linux32.sh"
-
-DESCRIPTION="AMD Accelerated Parallel Processing (APP) SDK"
-HOMEPAGE="http://developer.amd.com/tools-and-sdks/opencl-zone/amd-accelerated-parallel-processing-app-sdk"
-SRC_URI="
-	amd64? ( ${AMD64_AT} )
-	x86? ( ${X86_AT} )"
-LICENSE="AMD-APPSDK"
-SLOT="0"
-KEYWORDS="~amd64 ~x86"
-IUSE="examples"
-
-RDEPEND="
-	!<dev-util/amdstream-2.6
-	app-eselect/eselect-opencl
-	app-eselect/eselect-opengl
-	media-libs/freeglut
-	media-libs/mesa[video_cards_radeonsi]
-	sys-devel/gcc:*
-	sys-devel/llvm:*
-	virtual/opencl
-	examples? ( media-libs/glew:0= )"
-DEPEND="
-	${RDEPEND}
-	dev-util/patchelf
-	dev-lang/perl
-	sys-apps/fakeroot
-"
-
-RESTRICT="mirror strip"
-
-S="${WORKDIR}"
-
-OPT_DIR="/opt/AMDAPP"
-
-pkg_nofetch() {
-	einfo "AMD doesn't provide direct download links. Please download"
-	einfo "${ARCHIVE} from ${HOMEPAGE}"
-}
-
-src_unpack() {
-	default
-
-	cd "${WORKDIR}" || die
-
-	if use amd64 || use amd64-linux ; then
-		unpacker ./${MY_P_AMD64}
-	else
-		unpacker ./${MY_P_X86}
-	fi
-}
-
-src_compile() {
-	MAKEOPTS+=" -j1"
-	use examples && cd samples/opencl && default
-}
-
-src_install() {
-	# Copy everything
-	insinto $OPT_DIR
-	doins -r *
-
-	# Set executable bits
-	exeinto $OPT_DIR/bin/x86_64/
-	doexe bin/x86_64/clinfo
-
-	exeinto $OPT_DIR/bin/x86/
-	doexe bin/x86/clinfo
-
-	# Delete archive - already unpacked
-	if use amd64 || use amd64-linux ; then
-		rm "${D}/${OPT_DIR}/${MY_P_AMD64}" || die
-	else
-		rm "${D}/${OPT_DIR}/${MY_P_X86}" || die
-	fi
-}
diff --git a/dev-util/amdapp/metadata.xml b/dev-util/amdapp/metadata.xml
deleted file mode 100644
index c5c89b820..000000000
--- a/dev-util/amdapp/metadata.xml
+++ /dev/null
@@ -1,18 +0,0 @@
-<?xml version="1.0" encoding="UTF-8"?>
-<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
-<pkgmetadata>
-	<longdescription>
-AMD Accelerated Parallel Processing (APP) is an SDK which includes
-the Bolt libraries and an OpenCL implementation for AMD's CPUs and GPUs.
-</longdescription>
-	<maintainer type="person">
-		<email>gentryx@gmx.de</email>
-	</maintainer>
-	<maintainer type="project">
-		<email>cluster@gentoo.org</email>
-		<name>Gentoo Cluster Project</name>
-	</maintainer>
-	<use>
-		<flag name="examples">Build the OpenCL example programs</flag>
-	</use>
-</pkgmetadata>
diff --git a/dev-util/bazel/Manifest b/dev-util/bazel/Manifest
deleted file mode 100644
index 686aebe99..000000000
--- a/dev-util/bazel/Manifest
+++ /dev/null
@@ -1 +0,0 @@
-DIST bazel-0.13.0-dist.zip 90105262 BLAKE2B cb065025524123babef187bac2e1f54f43645d08cb1282a5fe8f8c8b090e595570646072e2380836e2c43403f7953f97321becc24b743d7b9ab43ad208cf2c2d SHA512 3c128e551cff1b685250a68892ca3e1ad6be8b152ee2b8eb527c94adbb8fd50c70e703a363bb938916275030ddb14d756c14e4dc238e7a7b40289c700c5d53c7
diff --git a/dev-util/bazel/bazel-0.13.0.ebuild b/dev-util/bazel/bazel-0.13.0.ebuild
deleted file mode 100644
index 797c062b0..000000000
--- a/dev-util/bazel/bazel-0.13.0.ebuild
+++ /dev/null
@@ -1,104 +0,0 @@
-# Copyright 1999-2018 Gentoo Foundation
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=6
-
-inherit bash-completion-r1 java-pkg-2
-
-DESCRIPTION="Fast and correct automated build system"
-HOMEPAGE="http://bazel.io/"
-SRC_URI="https://github.com/bazelbuild/bazel/releases/download/${PV}/${P}-dist.zip"
-
-LICENSE="Apache-2.0"
-SLOT="0"
-KEYWORDS="~amd64"
-IUSE="examples tools zsh-completion"
-# strip corrupts the bazel binary
-RESTRICT="strip"
-RDEPEND="virtual/jdk:1.8"
-DEPEND="${RDEPEND}
-	app-arch/unzip
-	app-arch/zip"
-
-S="${WORKDIR}"
-
-pkg_setup() {
-	echo ${PATH} | grep -q ccache && \
-		ewarn "${PN} usually fails to compile with ccache, you have been warned"
-	java-pkg-2_pkg_setup
-}
-
-bazel-get-flags() {
-	local fs=""
-	for i in ${CFLAGS}; do
-		[[ -n "${fs}" ]] && fs+=" "
-		fs+="--copt=${i}"
-	done
-	for i in ${CXXFLAGS}; do
-		[[ -n "${fs}" ]] && fs+=" "
-		fs+="--cxxopt=${i}"
-	done
-	for i in ${CPPFLAGS}; do
-		[[ -n "${fs}" ]] && fs+=" "
-		fs+="--copt=${i}"
-		fs+="--cxxopt=${i}"
-	done
-	for i in ${LDFLAGS}; do
-		[[ -n "${fs}" ]] && fs+=" "
-		fs+="--linkopt=${i}"
-	done
-	echo "${fs}"
-}
-
-src_compile() {
-	# F: fopen_wr
-	# S: deny
-	# P: /proc/self/setgroups
-	# A: /proc/self/setgroups
-	# R: /proc/24939/setgroups
-	# C: /usr/lib/systemd/systemd
-	addpredict /proc
-	VERBOSE=yes ./compile.sh || die
-	# Use standalone strategy to deactivate the bazel sandbox, since it
-	# conflicts with FEATURES=sandbox.
-	echo "build --verbose_failures --spawn_strategy=standalone --genrule_strategy=standalone" \
-		 > "${T}/bazelrc" || die
-	einfo "output/bazel --bazelrc=\"${T}/bazelrc\" build \\"
-	einfo "    $(bazel-get-flags) \\"
-	einfo "    scripts:bazel-complete.bash"
-	output/bazel --bazelrc="${T}/bazelrc" build $(bazel-get-flags) \
-		scripts:bazel-complete.bash || die
-	mv bazel-bin/scripts/bazel-complete.bash output/ || die
-}
-
-src_test() {
-	output/bazel test \
-		--verbose_failures \
-		--spawn_strategy=standalone \
-		--genrule_strategy=standalone \
-		--verbose_test_summary \
-		examples/cpp:hello-success_test || die
-}
-
-src_install() {
-	output/bazel shutdown
-	dobin output/bazel
-	newbashcomp output/bazel-complete.bash ${PN}
-	bashcomp_alias ${PN} ibazel
-	if use zsh-completion ; then
-		insinto /usr/share/zsh/site-functions
-		doins scripts/zsh_completion/_bazel
-	fi
-	if use examples; then
-		docinto examples
-		dodoc -r examples/*
-		docompress -x /usr/share/doc/${PF}/examples
-	fi
-	# could really build tools but I don't know which ones
-	# are actually used
-	if use tools; then
-		docinto tools
-		dodoc -r tools/*
-		docompress -x /usr/share/doc/${PF}/tools
-	fi
-}
diff --git a/dev-util/bazel/metadata.xml b/dev-util/bazel/metadata.xml
deleted file mode 100644
index e7d5f3b34..000000000
--- a/dev-util/bazel/metadata.xml
+++ /dev/null
@@ -1,20 +0,0 @@
-<?xml version="1.0" encoding="UTF-8"?>
-<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
-<pkgmetadata>
-	<maintainer type="person">
-		<email>zmedico@gentoo.org</email>
-	</maintainer>
-	<upstream>
-		<remote-id type="github">bazelbuild/bazel</remote-id>
-	</upstream>
-	<longdescription>
-		Bazel is Google's own build tool. Bazel has built-in support for
-		building both client and server software, including client
-		applications for both Android and iOS platforms. It also provides
-		an extensible framework that you can use to develop your own build
-		rules.
-	</longdescription>
-	<use>
-		<flag name="tools">Install extra bazel tools to build from sources</flag>
-	</use>
-</pkgmetadata>
diff --git a/dev-util/f90cache/Manifest b/dev-util/f90cache/Manifest
index 7e4a6cb88..e3e4d6b65 100644
--- a/dev-util/f90cache/Manifest
+++ b/dev-util/f90cache/Manifest
@@ -1 +1 @@
-DIST f90cache-0.99.tar.bz2 64842 BLAKE2B b7f84bc424fbda4bce5c0d89ddd9b76cc71e9f1604a134fd1f9235e2f0fc1f210658eba4120a4a609fddc7671dec4333ab0f04490efde5780a5f25355166fa45 SHA512 f188d774faa364fd8379d5c42fe36c301e59f9fc2bf49cd273ba1da6e8219cb544ce9a22ccba4b3a645dedfa695abab5b1e2e5975a00ce4ae25b393c2b51b6f7
+DIST f90cache-0.99c.tar.gz 78078 BLAKE2B d808210cffff070702aa0228e3275e3e42a3591a7b9c911b7b03d2a0f9e04ab8c1f613e59d2bc8e82129c4098738acbfb43028c6688241ae8d9bf278b4198894 SHA512 6c3aea0a333e4ece7abc56d70a939064ca5d1a5f905bca007d608325e5275db3dbecc9b0a8d4362f0b82d9f79e859332251b1ba6efea8eee1b558e507323a7ca
diff --git a/dev-util/f90cache/f90cache-0.99.ebuild b/dev-util/f90cache/f90cache-0.99.ebuild
deleted file mode 100644
index 1bc36389a..000000000
--- a/dev-util/f90cache/f90cache-0.99.ebuild
+++ /dev/null
@@ -1,37 +0,0 @@
-# Copyright 1999-2017 Gentoo Foundation
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=6
-
-inherit fortran-2 multilib toolchain-funcs
-
-DESCRIPTION="Compiler cache for fortran"
-HOMEPAGE="http://people.irisa.fr/Edouard.Canot/f90cache/"
-SRC_URI="http://people.irisa.fr/Edouard.Canot/${PN}/${P}.tar.bz2"
-
-LICENSE="GPL-3"
-SLOT="0"
-KEYWORDS="~amd64 ~x86"
-IUSE=""
-
-DEPEND=""
-RDEPEND="dev-util/ccache"
-
-src_prepare() {
-	default
-	sed -i -e '/OBJS/s/CFLAGS/LDFLAGS/' -e '/strip/d' Makefile.in || die
-}
-
-src_install() {
-	default
-
-	#we depend on ccache, put links in there so that portage find it
-	#TODO improve this
-	dosym ../../../bin/f90cache "${ROOT}/usr/$(get_libdir)/ccache/bin/gfortran"
-}
-
-pkg_postinst() {
-	elog "Please add F90CACHE_DIR=\"${ROOT%/}/var/tmp/f90cache\""
-	elog "to your make.conf otherwise f90cache files end up in"
-	elog "home of the user executing portage"
-}
diff --git a/dev-util/f90cache/f90cache-0.99c.ebuild b/dev-util/f90cache/f90cache-0.99c.ebuild
new file mode 100644
index 000000000..cc5024c91
--- /dev/null
+++ b/dev-util/f90cache/f90cache-0.99c.ebuild
@@ -0,0 +1,35 @@
+# Copyright 1999-2021 Gentoo Authors
+# Distributed under the terms of the GNU General Public License v2
+
+EAPI=7
+
+inherit fortran-2
+
+DESCRIPTION="Compiler cache for fortran"
+HOMEPAGE="https://perso.univ-rennes1.fr/edouard.canot//f90cache/"
+SRC_URI="https://perso.univ-rennes1.fr/edouard.canot//f90cache/${P}.tar.gz"
+
+LICENSE="GPL-3"
+SLOT="0"
+KEYWORDS="~amd64 ~x86"
+
+RDEPEND="dev-util/ccache"
+
+src_prepare() {
+	default
+	sed -i -e '/OBJS/s/CFLAGS/LDFLAGS/' -e '/strip/d' Makefile.in || die
+}
+
+src_install() {
+	default
+
+	#we depend on ccache, put links in there so that portage find it
+	#TODO improve this
+	dosym ../../../bin/f90cache "/usr/$(get_libdir)/ccache/bin/gfortran"
+}
+
+pkg_postinst() {
+	elog "Please add F90CACHE_DIR=\"${ROOT}/var/tmp/f90cache\""
+	elog "to your make.conf otherwise f90cache files end up in"
+	elog "home of the user executing portage"
+}
diff --git a/dev-util/mad-numdiff/Manifest b/dev-util/mad-numdiff/Manifest
index e62ff8fb5..2c7d9f66e 100644
--- a/dev-util/mad-numdiff/Manifest
+++ b/dev-util/mad-numdiff/Manifest
@@ -1 +1 @@
-DIST mad-numdiff-20150724.tar.gz 1212994 BLAKE2B c5ccc00e5fb95ca00c66a2502ab8fdd56bc17c787edb6fff064fe0828ef06d8b13dc1d58d01e25de089080954670ebb42dca29ade369a6681b7d5e70dbb266fb SHA512 2c01c37e1e34045c38386111d39225850053bde4efbfaccd8f684e900b9f155c6629e25a8b7935d45e5d02ab0f7b7a973064b5407a842970c52299b2fe965ff3
+DIST mad-numdiff-20180125.tar.gz 1213204 BLAKE2B 4ee36965f292230d0d7ef721d468a5c7c93839bd026bd4ba63ea82f13048c64909544aac54ccffc0c73a24ed4fe340a7d6dc3d2da15d9bb17e992baf4fbed1e1 SHA512 a4c3c75e8c22c8c6df7d000f9d1ca95f4c85008fb9e575fe907ee5c6cd29158aa893ec35eec5e8d5713e86e2483dd4e786967285b80486c831af47a9c8ed5948
diff --git a/dev-util/mad-numdiff/mad-numdiff-20150724.ebuild b/dev-util/mad-numdiff/mad-numdiff-20150724.ebuild
deleted file mode 100644
index 141df3952..000000000
--- a/dev-util/mad-numdiff/mad-numdiff-20150724.ebuild
+++ /dev/null
@@ -1,19 +0,0 @@
-# Copyright 1999-2017 Gentoo Foundation
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=6
-
-inherit cmake-utils vcs-snapshot
-
-DESCRIPTION="compare unformatted text files with numerical content"
-HOMEPAGE="https://github.com/quinoacomputing/ndiff"
-COMMIT="3154ade48853851bd82251f3e98dded92c9998f0"
-SRC_URI="${HOMEPAGE}/archive/${COMMIT}.tar.gz -> ${P}.tar.gz"
-
-LICENSE="GPL-3"
-SLOT="0"
-KEYWORDS="~amd64 ~x86"
-IUSE=""
-
-DEPEND=""
-RDEPEND="${DEPEND}"
diff --git a/dev-util/mad-numdiff/mad-numdiff-20180125.ebuild b/dev-util/mad-numdiff/mad-numdiff-20180125.ebuild
new file mode 100644
index 000000000..720edea32
--- /dev/null
+++ b/dev-util/mad-numdiff/mad-numdiff-20180125.ebuild
@@ -0,0 +1,21 @@
+# Copyright 1999-2021 Gentoo Authors
+# Distributed under the terms of the GNU General Public License v2
+
+EAPI=7
+
+inherit cmake vcs-snapshot
+
+DESCRIPTION="compare unformatted text files with numerical content"
+HOMEPAGE="https://github.com/quinoacomputing/ndiff"
+
+if [[ ${PV} == 9999 ]]; then
+	inherit git-r3
+	EGIT_REPO_URI="${HOMEPAGE}"
+else
+	COMMIT="a2be3a91e9f541a7b357f672c21b2e6fa491d794"
+	SRC_URI="https://github.com/quinoacomputing/ndiff/archive/${COMMIT}.tar.gz -> ${P}.tar.gz"
+	KEYWORDS="~amd64 ~x86"
+fi
+
+LICENSE="GPL-3"
+SLOT="0"
diff --git a/dev-util/mad-numdiff/mad-numdiff-9999.ebuild b/dev-util/mad-numdiff/mad-numdiff-9999.ebuild
index 3eac8de10..f74cbab89 100644
--- a/dev-util/mad-numdiff/mad-numdiff-9999.ebuild
+++ b/dev-util/mad-numdiff/mad-numdiff-9999.ebuild
@@ -1,9 +1,9 @@
-# Copyright 1999-2017 Gentoo Foundation
+# Copyright 1999-2021 Gentoo Authors
 # Distributed under the terms of the GNU General Public License v2
 
-EAPI=6
+EAPI=7
 
-inherit cmake-utils vcs-snapshot
+inherit cmake vcs-snapshot
 
 DESCRIPTION="compare unformatted text files with numerical content"
 HOMEPAGE="https://github.com/quinoacomputing/ndiff"
@@ -13,13 +13,9 @@ if [[ ${PV} == 9999 ]]; then
 	EGIT_REPO_URI="${HOMEPAGE}"
 else
 	COMMIT="3154ade48853851bd82251f3e98dded92c9998f0"
-	SRC_URI="${HOMEPAGE}/archive/${COMMIT}.tar.gz -> ${P}.tar.gz"
+	SRC_URI="https://github.com/quinoacomputing/ndiff/archive/${COMMIT}.tar.gz -> ${P}.tar.gz"
 	KEYWORDS="~amd64 ~x86"
 fi
 
 LICENSE="GPL-3"
 SLOT="0"
-IUSE=""
-
-DEPEND=""
-RDEPEND="${DEPEND}"
diff --git a/dev-util/makefile2graph/makefile2graph-1.5.0.ebuild b/dev-util/makefile2graph/makefile2graph-1.5.0.ebuild
index a934ce2cb..3d5943c64 100644
--- a/dev-util/makefile2graph/makefile2graph-1.5.0.ebuild
+++ b/dev-util/makefile2graph/makefile2graph-1.5.0.ebuild
@@ -1,21 +1,36 @@
-# Copyright 1999-2018 Gentoo Foundation
+# Copyright 1999-2021 Gentoo Authors
 # Distributed under the terms of the GNU General Public License v2
 
-EAPI=6
+EAPI=7
+
+inherit toolchain-funcs
 
 DESCRIPTION="Create a graph of dependencies from GNU Make"
 HOMEPAGE="https://github.com/lindenb/makefile2graph"
-SRC_URI="https://github.com/lindenb/makefile2graph/archive/v1.5.0.tar.gz -> ${P}.tar.gz"
+if [[ "${PV}" = 9999 ]]; then
+	inherit git-r3
+	EGIT_REPO_URI="https://github.com/lindenb/makefile2graph"
+else
+	SRC_URI="https://github.com/lindenb/makefile2graph/archive/v${PV}.tar.gz -> ${P}.tar.gz"
+	KEYWORDS="~amd64 ~x86"
+fi
 
 LICENSE="MIT"
 SLOT="0"
-KEYWORDS="~amd64 ~x86"
-IUSE=""
+IUSE="test"
+RESTRICT="!test? ( test )"
 
-DEPEND=""
-RDEPEND="${DEPEND}"
+BDEPEND="test? ( media-gfx/graphviz )"
 
 src_prepare(){
-	sed -e 's#/usr/local#/usr#' -i Makefile || die
+	sed -e "s|/usr/local|${EPREFIX}/usr|" -i Makefile || die
 	default
 }
+
+src_compile() {
+	CC="$(tc-getCC)" default
+}
+
+src_test() {
+	CC="$(tc-getCC)" emake test
+}
diff --git a/dev-util/makefile2graph/makefile2graph-9999.ebuild b/dev-util/makefile2graph/makefile2graph-9999.ebuild
new file mode 100644
index 000000000..3d5943c64
--- /dev/null
+++ b/dev-util/makefile2graph/makefile2graph-9999.ebuild
@@ -0,0 +1,36 @@
+# Copyright 1999-2021 Gentoo Authors
+# Distributed under the terms of the GNU General Public License v2
+
+EAPI=7
+
+inherit toolchain-funcs
+
+DESCRIPTION="Create a graph of dependencies from GNU Make"
+HOMEPAGE="https://github.com/lindenb/makefile2graph"
+if [[ "${PV}" = 9999 ]]; then
+	inherit git-r3
+	EGIT_REPO_URI="https://github.com/lindenb/makefile2graph"
+else
+	SRC_URI="https://github.com/lindenb/makefile2graph/archive/v${PV}.tar.gz -> ${P}.tar.gz"
+	KEYWORDS="~amd64 ~x86"
+fi
+
+LICENSE="MIT"
+SLOT="0"
+IUSE="test"
+RESTRICT="!test? ( test )"
+
+BDEPEND="test? ( media-gfx/graphviz )"
+
+src_prepare(){
+	sed -e "s|/usr/local|${EPREFIX}/usr|" -i Makefile || die
+	default
+}
+
+src_compile() {
+	CC="$(tc-getCC)" default
+}
+
+src_test() {
+	CC="$(tc-getCC)" emake test
+}
diff --git a/dev-util/makefile2graph/metadata.xml b/dev-util/makefile2graph/metadata.xml
index 138cb7705..41bb35aa0 100644
--- a/dev-util/makefile2graph/metadata.xml
+++ b/dev-util/makefile2graph/metadata.xml
@@ -9,4 +9,7 @@
 		<email>sci-biology@gentoo.org</email>
 		<name>Gentoo Biology Project</name>
 	</maintainer>
+	<upstream>
+		<remote-id type="github">lindenb/makefile2graph</remote-id>
+	</upstream>
 </pkgmetadata>
diff --git a/dev-util/ndiff/ndiff-2.00.ebuild b/dev-util/ndiff/ndiff-2.00.ebuild
index 4353d65cd..1b3e06b9c 100644
--- a/dev-util/ndiff/ndiff-2.00.ebuild
+++ b/dev-util/ndiff/ndiff-2.00.ebuild
@@ -1,7 +1,7 @@
-# Copyright 1999-2015 Gentoo Foundation
+# Copyright 1999-2021 Gentoo Authors
 # Distributed under the terms of the GNU General Public License v2
 
-EAPI=5
+EAPI=7
 
 DESCRIPTION="A diff program that ignores small numeric differences"
 HOMEPAGE="http://www.math.utah.edu/~beebe/software/ndiff/"
@@ -12,6 +12,9 @@ SLOT="0"
 KEYWORDS="~amd64 ~x86"
 IUSE="doc"
 
+# Sandbox violation to /tmp/
+RESTRICT="test"
+
 DEPEND="dev-libs/gmp:0="
 RDEPEND="${DEPEND}"
 
diff --git a/dev-util/nvidia-cuda-gdk/Manifest b/dev-util/nvidia-cuda-gdk/Manifest
deleted file mode 100644
index 9183dec8d..000000000
--- a/dev-util/nvidia-cuda-gdk/Manifest
+++ /dev/null
@@ -1 +0,0 @@
-DIST cuda_352_79_gdk_linux.run 3947168 BLAKE2B 0a1e765488e9e85220605d1961d81b5b7284c59da7e82f871c871b183d7ed4ba65c2d1a6013144fcb17f8b19c617eacde98364abda3a84042b46f243034f6ff9 SHA512 1f1d41c5b7bbc5ebc85a05e595d7fcd9e04fdcecece620c2e571eb83a38b5741965e2d5a0abe4fdd28c5e63fc6a4a3b82fe2f459fd2f33e38ad7b2025728a5c9
diff --git a/dev-util/nvidia-cuda-gdk/files/nvidia-healthmon b/dev-util/nvidia-cuda-gdk/files/nvidia-healthmon
deleted file mode 100644
index caf1b004e..000000000
--- a/dev-util/nvidia-cuda-gdk/files/nvidia-healthmon
+++ /dev/null
@@ -1,9 +0,0 @@
-#!/bin/bash
-
-while getopts ":c" opt
-do
-	case $opt in
-		c) exec /opt/cuda/gdk/nvidia-healthmon/nvidia-healthmon "$@";;
-		*) exec /opt/cuda/gdk/nvidia-healthmon/nvidia-healthmon -c /etc/nvidia-healthmon/nvidia-healthmon.conf "$@";;
-	esac
-done
\ No newline at end of file
diff --git a/dev-util/nvidia-cuda-gdk/metadata.xml b/dev-util/nvidia-cuda-gdk/metadata.xml
deleted file mode 100644
index d335675d1..000000000
--- a/dev-util/nvidia-cuda-gdk/metadata.xml
+++ /dev/null
@@ -1,24 +0,0 @@
-<?xml version="1.0" encoding="UTF-8"?>
-<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
-<pkgmetadata>
-	<maintainer type="person">
-		<email>marbre@linux.sungazer.de</email>
-		<name>Marius Brehler</name>
-	</maintainer>
-	<maintainer type="project">
-		<email>sci@gentoo.org</email>
-		<name>Gentoo Science Project</name>
-	</maintainer>
-	<longdescription>
-The GPU Deployment Kit (previously known as the Tesla Deployment
-Kit) is a set of tools provided for the NVIDIA Teslaâ„¢, GRIDâ„¢ and
-Quadroâ„¢ GPUs.
-</longdescription>
-	<use>
-		<flag name="healthmon">Install nvidia-healthmon.</flag>
-		<flag name="nvml">Install the NVIDIA Managment Library.</flag>
-		<flag name="nvvs">
-Install the NVIDIA Validation Suite.
-</flag>
-	</use>
-</pkgmetadata>
diff --git a/dev-util/nvidia-cuda-gdk/nvidia-cuda-gdk-352.79.ebuild b/dev-util/nvidia-cuda-gdk/nvidia-cuda-gdk-352.79.ebuild
deleted file mode 100644
index 6a815da47..000000000
--- a/dev-util/nvidia-cuda-gdk/nvidia-cuda-gdk-352.79.ebuild
+++ /dev/null
@@ -1,187 +0,0 @@
-# Copyright 1999-2018 Gentoo Foundation
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=6
-
-inherit eutils portability toolchain-funcs unpacker versionator
-
-MYD=$(get_version_component_range 1)_$(get_version_component_range 2)
-
-HEALTMON_PV="${PV}"
-NVVS_PV="${PV}"
-
-DESCRIPTION="NVIDIA GPU Deployment Kit"
-HOMEPAGE="http://developer.nvidia.com/cuda"
-SRC_URI="http://developer.download.nvidia.com/compute/cuda/7.5/Prod/local_installers/cuda_${MYD}_gdk_linux.run"
-
-LICENSE="NVIDIA-gdk"
-SLOT="0"
-KEYWORDS="-* ~amd64"
-IUSE="+healthmon +nvml +doc examples +nvvs"
-
-RDEPEND="
-	>=dev-util/nvidia-cuda-toolkit-7.5
-	media-libs/freeglut
-	examples? ( >=x11-drivers/nvidia-drivers-352.79[uvm] )
-	nvvs? (	>=x11-drivers/nvidia-drivers-352.79[uvm] )
-	"
-DEPEND="${RDEPEND}"
-
-S="${WORKDIR}/payload"
-
-QA_PREBUILT=(
-	/opt/cuda/gdk/nvidia-healthmon/nvidia-healthmon
-	/opt/cuda/gdk/nvidia-healthmon/nvidia-healthmon-tests/gpu_rdma_bw
-	/opt/cuda/gdk/nvidia-healthmon/nvidia-healthmon-tests/ibv_rdma_bw
-	/opt/cuda/gdk/nvml/lib/libnvidia-ml.so.1
-	/opt/cuda/gdk/nvvs/plugins/libPcie.so.1
-	/opt/cuda/gdk/nvvs/plugins/libSmPerformance.so.1
-	/opt/cuda/gdk/nvvs/plugins/libPerformance.so
-	/opt/cuda/gdk/nvvs/plugins/libPower.so.1
-	/opt/cuda/gdk/nvvs/plugins/libMemory.so.1
-	/opt/cuda/gdk/nvvs/plugins/libPerformance.so.1
-	/opt/cuda/gdk/nvvs/plugins/libDeployment.so.1
-	/opt/cuda/gdk/nvvs/plugins/libSmPerformance.so
-	/opt/cuda/gdk/nvvs/plugins/libPower.so
-	/opt/cuda/gdk/nvvs/nvvs
-)
-
-src_unpack() {
-	unpacker
-}
-
-src_compile() {
-	use examples || return
-	cd "${S}"/nvml/example || die
-	default
-}
-
-src_install() {
-	local i j f t
-
-	if use doc; then
-		if use healthmon ; then
-			ebegin "Installing healthmon docs..."
-				doman nvidia-healthmon/docs/man/man8/nvidia-healthmon.8
-				cd "${S}/nvidia-healthmon/nvidia-healthmon-amd64-${HEALTMON_PV}" || die
-				treecopy \
-					$(find -type f \( -name README.txt -name COPYING.txt -o -name "*.pdf" \)) \
-					"${ED}"/usr/share/doc/${PF}/nvidia-healthmon/
-				docompress -x \
-					$(find "${ED}"/usr/share/doc/${PF}/nvidia-healthmon/ -type f -name readme.txt | sed -e "s:${ED}::")
-				cd "${S}/" || die
-			eend
-		fi
-
-		if use nvml ; then
-			ebegin "Installing nvml docs..."
-				doman nvml/doc/man/man3/*.3
-				cd "${S}/nvml/" || die
-				treecopy \
-					$(find -type f \( -name README.txt -name COPYRIGHT.txt -o -name "*.pdf" \)) \
-					"${ED}"/usr/share/doc/${PF}/nvml/
-				docompress -x \
-					$(find "${ED}"/usr/share/doc/${PF}/nvml/ -type f -name readme.txt | sed -e "s:${ED}::")
-				cd "${S}/" || die
-			eend
-		fi
-
-		if use nvvs ; then
-			ebegin "Installing validation suite docs..."
-				dodoc "nvidia-validation-suite/nvidia-validation-suite-amd64-${NVVS_PV}/docs/NVIDIA_Validation_Suite_User_Guide.pdf"
-				doman "nvidia-validation-suite/nvidia-validation-suite-amd64-${NVVS_PV}/docs/man/man8/nvvs.8"
-			eend
-		fi
-
-	fi
-
-	ebegin "Cleaning before installation..."
-		find -type f \
-			\( -name "*.o" -o -name "*.pdf" -o -name "*.txt" -o -name "*.3" -o -name "*.8" \) -delete \
-			|| die
-		rm -f "${S}"/nvml/lib/libnvidia-ml.so
-		rm -f "${S}/nvidia-validation-suite/nvidia-validation-suite-amd64-${NVVS_PV}/plugins"/libDeployment.so
-		rm -f "${S}/nvidia-validation-suite/nvidia-validation-suite-amd64-${NVVS_PV}/plugins"/libMemory.so
-		rm -f "${S}/nvidia-validation-suite/nvidia-validation-suite-amd64-${NVVS_PV}/plugins"/libPcie.so
-		rm -f "${S}/nvidia-validation-suite/nvidia-validation-suite-amd64-${NVVS_PV}/plugins"/libPerformance.so
-		rm -f "${S}/nvidia-validation-suite/nvidia-validation-suite-amd64-${NVVS_PV}/plugins"/libPower.so
-		rm -f "${S}/nvidia-validation-suite/nvidia-validation-suite-amd64-${NVVS_PV}/plugins"/libSmPerformance.so
-		rm -f "${S}/nvidia-validation-suite/nvidia-validation-suite-amd64-${NVVS_PV}"/nvidia-vs
-	eend
-
-	if use healthmon; then
-		ebegin "Installing nvidia-healthmon"
-			exeinto /opt/cuda/gdk/nvidia-healthmon/nvidia-healthmon-tests/
-			doexe "nvidia-healthmon/nvidia-healthmon-amd64-${HEALTMON_PV}/bin"/{*,*.*}
-			exeinto /opt/cuda/gdk/nvidia-healthmon/
-			doexe "nvidia-healthmon/nvidia-healthmon-amd64-${HEALTMON_PV}"/nvidia-healthmon
-			insinto /etc/nvidia-healthmon/
-			doins "nvidia-healthmon/nvidia-healthmon-amd64-${HEALTMON_PV}"/nvidia-healthmon.conf
-
-			# install launch script
-			exeinto /opt/bin
-			doexe "${FILESDIR}"/nvidia-healthmon
-		eend
-	fi
-
-	if use nvml; then
-		ebegin "Installing nvml"
-			cd "${S}/nvml" || die
-			for f in $(find .); do
-				local t="$(dirname ${f})"
-				if [[ "${t/obj\/}" != "${t}" || "${t##*.}" == "a" ]]; then
-					continue
-				fi
-
-				if [[ ! -d "${f}" ]]; then
-					if [[ -x "${f}" ]]; then
-						exeinto "/opt/cuda/gdk/nvml/${t}"
-						doexe "${f}"
-					else
-						insinto "/opt/cuda/gdk/nvml/${t}"
-						doins "${f}"
-					fi
-				fi
-			done
-
-			dosym libnvidia-ml.so.1 /opt/cuda/gdk/nvml/lib/libnvidia-ml.so
-			cd "${S}/" || die
-		eend
-	fi
-
-	if use nvvs; then
-		ebegin "Installing validation suite"
-			cd "${S}/nvidia-validation-suite/nvidia-validation-suite-amd64-${NVVS_PV}/" || die
-
-			insinto /etc/nvidia-validation-suite/
-			doins nvvs.conf
-			rm nvvs.conf || die
-
-			for f in $(find .); do
-				local t="$(dirname ${f})"
-				if [[ "${t/obj\/}" != "${t}" || "${t##*.}" == "a" ]]; then
-					continue
-				fi
-
-				if [[ ! -d "${f}" ]]; then
-					if [[ -x "${f}" ]]; then
-						exeinto "/opt/cuda/gdk/nvvs/${t}"
-						doexe "${f}"
-					else
-						insinto "/opt/cuda/gdk/nvvs/${t}"
-						doins "${f}"
-					fi
-				fi
-			done
-
-			dosym libDeployment.so.1 /opt/cuda/gdk/nvvs/plugins/libDeployment.so
-			dosym libMemory.so.1 /opt/cuda/gdk/nvvs/plugins/libMemory.so
-			dosym libPcie.so.1 /opt/cuda/gdk/nvvs/plugins/libPcie.so
-			dosym libPerformance.so.1 /opt/cuda/gdk/nvvs/plugins/libPerformance.so
-			dosym libPower.so.1 /opt/cuda/gdk/nvvs/plugins/libPower.so
-			dosym libSmPerformance.so.1 /opt/cuda/gdk/nvvs/plugins/libSmPerformance.so
-
-			dosym ../cuda/gdk/nvvs/nvvs /opt/bin/nvidia-vs
-		eend
-	fi
-}
diff --git a/dev-util/plog/Manifest b/dev-util/plog/Manifest
new file mode 100644
index 000000000..c5b00b7ca
--- /dev/null
+++ b/dev-util/plog/Manifest
@@ -0,0 +1 @@
+DIST plog-1.1.5.tar.gz 40453 BLAKE2B 41176a9cb70c796f337ebaa451f511c8d8d70fe95abfb8affa5b67f9f5d7b12355cb8458fc0c441eddcee9eeeeaa47484774140e26efd53408d6b0baaf892f5d SHA512 c16b428e1855c905c486130c8610d043962bedc2b40d1d986c250c8f7fd7139540164a3cbb408ed08298370aa150d5937f358c13ccae2728ce8ea47fa897fd0b
diff --git a/dev-util/plog/metadata.xml b/dev-util/plog/metadata.xml
new file mode 100644
index 000000000..40a8e36c6
--- /dev/null
+++ b/dev-util/plog/metadata.xml
@@ -0,0 +1,10 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
+<pkgmetadata>
+	<maintainer type="person">
+		<email>heroxbd@gentoo.org</email>
+	</maintainer>
+	<upstream>
+		<remote-id type="github">SergiusTheBest/plog</remote-id>
+	</upstream>
+</pkgmetadata>
diff --git a/dev-util/plog/plog-1.1.5.ebuild b/dev-util/plog/plog-1.1.5.ebuild
new file mode 100644
index 000000000..9bfddba07
--- /dev/null
+++ b/dev-util/plog/plog-1.1.5.ebuild
@@ -0,0 +1,23 @@
+# Copyright 1999-2020 Gentoo Authors
+# Distributed under the terms of the GNU General Public License v2
+
+EAPI=7
+
+DESCRIPTION="Portable, simple and extensible C++ logging library"
+HOMEPAGE="https://github.com/SergiusTheBest/plog"
+
+if [[ ${PV} == 9999 ]]; then
+	inherit git-r3
+	EGIT_REPO_URI="https://github.com/SergiusTheBest/plog"
+else
+	SRC_URI="https://github.com/SergiusTheBest/plog/archive/${PV}.tar.gz -> ${P}.tar.gz"
+	KEYWORDS="~amd64 ~arm64 ~x86"
+fi
+
+LICENSE="MPL-2.0"
+SLOT="0"
+
+src_install() {
+	doheader -r include/plog
+	dodoc README.md
+}
diff --git a/dev-util/plog/plog-9999.ebuild b/dev-util/plog/plog-9999.ebuild
new file mode 100644
index 000000000..9bfddba07
--- /dev/null
+++ b/dev-util/plog/plog-9999.ebuild
@@ -0,0 +1,23 @@
+# Copyright 1999-2020 Gentoo Authors
+# Distributed under the terms of the GNU General Public License v2
+
+EAPI=7
+
+DESCRIPTION="Portable, simple and extensible C++ logging library"
+HOMEPAGE="https://github.com/SergiusTheBest/plog"
+
+if [[ ${PV} == 9999 ]]; then
+	inherit git-r3
+	EGIT_REPO_URI="https://github.com/SergiusTheBest/plog"
+else
+	SRC_URI="https://github.com/SergiusTheBest/plog/archive/${PV}.tar.gz -> ${P}.tar.gz"
+	KEYWORDS="~amd64 ~arm64 ~x86"
+fi
+
+LICENSE="MPL-2.0"
+SLOT="0"
+
+src_install() {
+	doheader -r include/plog
+	dodoc README.md
+}
diff --git a/dev-vcs/dandi-cli/Manifest b/dev-vcs/dandi-cli/Manifest
new file mode 100644
index 000000000..f84e21730
--- /dev/null
+++ b/dev-vcs/dandi-cli/Manifest
@@ -0,0 +1,2 @@
+DIST dandi-0.61.0.tar.gz 306755 BLAKE2B 8d279fddf4a9c390c91d09915d978f5709c297bb4284e8c8f3026ef9c94a9b2bab4b24409ff1d915550ab2564f8398a1afb236b226a41303264898de51deed42 SHA512 3cbd5c81c024cfca01c94fd2f9c794b22170f830a39c283f5cde1dfd998447287559457e324f81f46154fa38bf065720736da3be13a5668bc7453d091dd51869
+DIST dandi-0.61.2.tar.gz 306867 BLAKE2B 9a51c26f36d462e518241d40604726973727f17c70855136b6ea8e8402fb2c30ecc3adbbf7db6ed967bdb8c63a11da0809c09ae61f3a4996784b0b2083c1ec3a SHA512 9f4f3a02e62a3c4af3496a29faa18c696263e71dd2baf56c2925696c09e4c633a3a28a1fe30329764b98cba3006e4ccfe0884f5bae3d580f643f4cf946b2d291
diff --git a/dev-vcs/dandi-cli/dandi-cli-0.61.0.ebuild b/dev-vcs/dandi-cli/dandi-cli-0.61.0.ebuild
new file mode 100644
index 000000000..35ac320f5
--- /dev/null
+++ b/dev-vcs/dandi-cli/dandi-cli-0.61.0.ebuild
@@ -0,0 +1,80 @@
+# Copyright 1999-2024 Gentoo Authors
+# Distributed under the terms of the GNU General Public License v2
+
+EAPI=8
+
+DISTUTILS_USE_PEP517=setuptools
+PYTHON_COMPAT=( python3_{10..11} )
+
+inherit distutils-r1 pypi
+
+MY_PN="dandi"
+MY_P="${MY_PN}-${PV}"
+
+DESCRIPTION="DANDI command line client to facilitate common operations"
+HOMEPAGE="https://github.com/dandi/dandi-cli"
+SRC_URI="$(pypi_sdist_url dandi)"
+
+LICENSE="Apache-2.0"
+SLOT="0"
+KEYWORDS="~amd64"
+IUSE="test etelemetry"
+
+RDEPEND="
+	>=dev-python/dandi-schema-0.9.0[${PYTHON_USEDEP}]
+	>=dev-python/pydantic-2.0.0[${PYTHON_USEDEP}]
+	>=sci-biology/bidsschematools-0.7.0[${PYTHON_USEDEP}]
+	dev-python/click-didyoumean[${PYTHON_USEDEP}]
+	dev-python/click[${PYTHON_USEDEP}]
+	dev-python/fasteners[${PYTHON_USEDEP}]
+	dev-python/fscacher[${PYTHON_USEDEP}]
+	dev-python/humanize[${PYTHON_USEDEP}]
+	dev-python/interleave[${PYTHON_USEDEP}]
+	dev-python/joblib[${PYTHON_USEDEP}]
+	dev-python/keyring[${PYTHON_USEDEP}]
+	dev-python/keyrings-alt[${PYTHON_USEDEP}]
+	dev-python/nwbinspector[${PYTHON_USEDEP}]
+	dev-python/packaging[${PYTHON_USEDEP}]
+	dev-python/platformdirs[${PYTHON_USEDEP}]
+	dev-python/pycryptodome[${PYTHON_USEDEP}]
+	dev-python/pynwb[${PYTHON_USEDEP}]
+	dev-python/pyout[${PYTHON_USEDEP}]
+	dev-python/python-dateutil[${PYTHON_USEDEP}]
+	dev-python/requests[${PYTHON_USEDEP}]
+	dev-python/ruamel-yaml[${PYTHON_USEDEP}]
+	dev-python/semantic-version[${PYTHON_USEDEP}]
+	dev-python/tenacity[${PYTHON_USEDEP}]
+	dev-python/versioneer[${PYTHON_USEDEP}]
+	dev-python/wheel[${PYTHON_USEDEP}]
+	dev-python/zarr[${PYTHON_USEDEP}]
+	>=dev-python/zarr_checksum-0.4.0[${PYTHON_USEDEP}]
+"
+
+BDEPEND="
+	test? (
+		dev-python/anys[${PYTHON_USEDEP}]
+		dev-python/pyfakefs[${PYTHON_USEDEP}]
+		dev-python/pytest-mock[${PYTHON_USEDEP}]
+		dev-python/pytest-rerunfailures[${PYTHON_USEDEP}]
+		dev-python/responses[${PYTHON_USEDEP}]
+		dev-python/vcrpy[${PYTHON_USEDEP}]
+		media-libs/opencv[ffmpeg,${PYTHON_USEDEP}]
+	)
+"
+# Upstream might be amenable to dropping opencv:
+# https://github.com/dandi/dandi-cli/issues/944
+
+S="${WORKDIR}/${MY_P}"
+
+EPYTEST_DESELECT=(
+	# Reported upstream:
+	# https://github.com/dandi/dandi-cli/issues/1394
+	dandi/cli/tests/test_command.py::test_no_heavy_imports
+)
+
+distutils_enable_tests pytest
+
+python_test() {
+	export DANDI_TESTS_NONETWORK=1
+	epytest
+}
diff --git a/dev-vcs/dandi-cli/dandi-cli-0.61.2.ebuild b/dev-vcs/dandi-cli/dandi-cli-0.61.2.ebuild
new file mode 100644
index 000000000..760fb32b4
--- /dev/null
+++ b/dev-vcs/dandi-cli/dandi-cli-0.61.2.ebuild
@@ -0,0 +1,81 @@
+# Copyright 1999-2024 Gentoo Authors
+# Distributed under the terms of the GNU General Public License v2
+
+EAPI=8
+
+DISTUTILS_USE_PEP517=setuptools
+PYTHON_COMPAT=( python3_{10..11} )
+
+inherit distutils-r1 pypi
+
+MY_PN="dandi"
+MY_P="${MY_PN}-${PV}"
+
+DESCRIPTION="DANDI command line client to facilitate common operations"
+HOMEPAGE="https://github.com/dandi/dandi-cli"
+SRC_URI="$(pypi_sdist_url dandi)"
+
+S="${WORKDIR}/${MY_P}"
+
+LICENSE="Apache-2.0"
+SLOT="0"
+KEYWORDS="~amd64"
+IUSE="test etelemetry"
+
+RDEPEND="
+	>=dev-python/dandi-schema-0.9.0[${PYTHON_USEDEP}]
+	>=dev-python/pydantic-2.0.0[${PYTHON_USEDEP}]
+	>=sci-biology/bidsschematools-0.7.0[${PYTHON_USEDEP}]
+	>=dev-python/zarr_checksum-0.4.0[${PYTHON_USEDEP}]
+	dev-python/click-didyoumean[${PYTHON_USEDEP}]
+	dev-python/click[${PYTHON_USEDEP}]
+	dev-python/fasteners[${PYTHON_USEDEP}]
+	dev-python/fscacher[${PYTHON_USEDEP}]
+	dev-python/humanize[${PYTHON_USEDEP}]
+	dev-python/interleave[${PYTHON_USEDEP}]
+	dev-python/joblib[${PYTHON_USEDEP}]
+	dev-python/keyring[${PYTHON_USEDEP}]
+	dev-python/keyrings-alt[${PYTHON_USEDEP}]
+	dev-python/nwbinspector[${PYTHON_USEDEP}]
+	dev-python/packaging[${PYTHON_USEDEP}]
+	dev-python/platformdirs[${PYTHON_USEDEP}]
+	dev-python/pycryptodome[${PYTHON_USEDEP}]
+	dev-python/pynwb[${PYTHON_USEDEP}]
+	dev-python/pyout[${PYTHON_USEDEP}]
+	dev-python/python-dateutil[${PYTHON_USEDEP}]
+	dev-python/requests[${PYTHON_USEDEP}]
+	dev-python/ruamel-yaml[${PYTHON_USEDEP}]
+	dev-python/semantic-version[${PYTHON_USEDEP}]
+	dev-python/tenacity[${PYTHON_USEDEP}]
+	dev-python/versioneer[${PYTHON_USEDEP}]
+	dev-python/wheel[${PYTHON_USEDEP}]
+	dev-python/yarl[${PYTHON_USEDEP}]
+	dev-python/zarr[${PYTHON_USEDEP}]
+"
+
+BDEPEND="
+	test? (
+		dev-python/anys[${PYTHON_USEDEP}]
+		dev-python/pyfakefs[${PYTHON_USEDEP}]
+		dev-python/pytest-mock[${PYTHON_USEDEP}]
+		dev-python/pytest-rerunfailures[${PYTHON_USEDEP}]
+		dev-python/responses[${PYTHON_USEDEP}]
+		dev-python/vcrpy[${PYTHON_USEDEP}]
+		media-libs/opencv[ffmpeg,${PYTHON_USEDEP}]
+	)
+"
+# Upstream might be amenable to dropping opencv:
+# https://github.com/dandi/dandi-cli/issues/944
+
+EPYTEST_DESELECT=(
+	# Reported upstream:
+	# https://github.com/dandi/dandi-cli/issues/1394
+	dandi/cli/tests/test_command.py::test_no_heavy_imports
+)
+
+distutils_enable_tests pytest
+
+python_test() {
+	export DANDI_TESTS_NONETWORK=1
+	epytest
+}
diff --git a/dev-vcs/dandi-cli/files/dandi-cli-0.28.0-no-etelemetry.patch b/dev-vcs/dandi-cli/files/dandi-cli-0.28.0-no-etelemetry.patch
new file mode 100644
index 000000000..6822e1abf
--- /dev/null
+++ b/dev-vcs/dandi-cli/files/dandi-cli-0.28.0-no-etelemetry.patch
@@ -0,0 +1,30 @@
+--- a/dandi/utils.py	2021-09-21 11:51:39.799524534 -0400
++++ b/dandi/utils.py	2021-10-06 04:58:00.506440719 -0400
+@@ -734,27 +734,4 @@
+ def check_dandi_version():
+     if os.environ.get("DANDI_NO_ET"):
+         return
+-    try:
+-        import etelemetry
+-
+-        try:
+-            etelemetry.check_available_version(
+-                "dandi/dandi-cli", __version__, lgr=lgr, raise_exception=True
+-            )
+-        except etelemetry.client.BadVersionError:
+-            # note: SystemExit is based of BaseException, so is not Exception
+-            raise SystemExit(
+-                "DANDI CLI has detected that you are using a version that is known to "
+-                "contain bugs, is incompatible with our current data archive, or has "
+-                "other significant performance limitations. "
+-                "To continue using DANDI CLI, please upgrade your dandi client to a newer "
+-                "version (e.g., using pip install --upgrade dandi if you installed using pip). "
+-                "If you have any issues, please contact the DANDI "
+-                "helpdesk at https://github.com/dandi/helpdesk/issues/new/choose ."
+-            )
+-    except Exception as exc:
+-        lgr.warning(
+-            "Failed to check for a more recent version available with etelemetry: %s",
+-            exc,
+-        )
+     os.environ["DANDI_NO_ET"] = "1"
diff --git a/dev-vcs/dandi-cli/files/dandi-cli-0.55.0-hdf5.patch b/dev-vcs/dandi-cli/files/dandi-cli-0.55.0-hdf5.patch
new file mode 100644
index 000000000..4cd55ca7e
--- /dev/null
+++ b/dev-vcs/dandi-cli/files/dandi-cli-0.55.0-hdf5.patch
@@ -0,0 +1,29 @@
+From d16bf0855e9ef7c029e8aca969ddfa04c1d7fdfd Mon Sep 17 00:00:00 2001
+From: "John T. Wodder II" <git@varonathe.org>
+Date: Thu, 25 May 2023 14:17:36 -0400
+Subject: [PATCH] Fix test for newer hdf5
+
+---
+ dandi/tests/test_files.py | 9 ++++++++-
+ 1 file changed, 8 insertions(+), 1 deletion(-)
+
+diff --git a/dandi/tests/test_files.py b/dandi/tests/test_files.py
+index 4dbf0f223..3e44cf6b1 100644
+--- a/dandi/tests/test_files.py
++++ b/dandi/tests/test_files.py
+@@ -374,7 +374,14 @@ def test_validate_bogus(tmp_path):
+     errors = dandi_file(path).get_validation_errors()
+     # ATM we would get 2 errors -- since could not be open in two places,
+     # but that would be too rigid to test. Let's just see that we have expected errors
+-    assert any(e.message.startswith("Unable to open file") for e in errors)
++    assert any(
++        e.message.startswith(
++            ("Unable to open file", "Unable to synchronously open file")
++        )
++        for e in errors
++    )
++    # Recent versions of hdf5 changed the error message, hence the need to
++    # check for two different patterns.
+ 
+ 
+ def test_upload_zarr(new_dandiset, tmp_path):
diff --git a/dev-vcs/dandi-cli/files/dandi-cli-0.59.0-no-etelemetry.patch b/dev-vcs/dandi-cli/files/dandi-cli-0.59.0-no-etelemetry.patch
new file mode 100644
index 000000000..4d4f42a03
--- /dev/null
+++ b/dev-vcs/dandi-cli/files/dandi-cli-0.59.0-no-etelemetry.patch
@@ -0,0 +1,40 @@
+diff --git a/dandi/files/bases.py b/dandi/files/bases.py
+index 45f5929f..38bde34f 100644
+--- a/dandi/files/bases.py
++++ b/dandi/files/bases.py
+@@ -18,7 +18,6 @@ from dandischema.digests.dandietag import DandiETag
+ from dandischema.models import BareAsset, CommonModel
+ from dandischema.models import Dandiset as DandisetMeta
+ from dandischema.models import get_schema_version
+-from etelemetry import get_project
+ from packaging.version import Version
+ from pydantic import ValidationError
+ import requests
+@@ -737,6 +736,7 @@ def _get_nwb_inspector_version():
+     _current_nwbinspector_version = get_package_version(name="nwbinspector")
+     # Ensure latest version of NWB Inspector is installed and used client-side
+     try:
++        from etelemetry import get_project
+         max_version = Version(
+             get_project(repo="NeurodataWithoutBorders/nwbinspector")["version"]
+         )
+diff --git a/setup.cfg b/setup.cfg
+--- a/setup.cfg	2024-01-09 14:08:33.952653200 -0500
++++ b/setup.cfg	2024-01-25 01:45:34.594335960 -0500
+@@ -34,7 +34,6 @@
+ 	click >= 7.1
+ 	click-didyoumean
+ 	dandischema ~= 0.8.0
+-	etelemetry >= 0.2.2
+ 	fasteners
+ 	fscacher >= 0.3.0
+ 	hdmf != 3.5.0
+@@ -147,9 +146,6 @@
+ [mypy-click_didyoumean.*]
+ ignore_missing_imports = True
+
+-[mypy-etelemetry.*]
+-ignore_missing_imports = True
+-
+ [mypy-fasteners.*]
+ ignore_missing_imports = True
diff --git a/dev-vcs/dandi-cli/metadata.xml b/dev-vcs/dandi-cli/metadata.xml
new file mode 100644
index 000000000..9565a2184
--- /dev/null
+++ b/dev-vcs/dandi-cli/metadata.xml
@@ -0,0 +1,26 @@
+<?xml version='1.0' encoding='UTF-8'?>
+<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
+<pkgmetadata>
+	<maintainer type="person">
+		<email>gentoo@chymera.eu</email>
+		<name>Horea Christian</name>
+	</maintainer>
+	<maintainer type="project">
+		<email>sci@gentoo.org</email>
+		<name>Gentoo Science Project</name>
+	</maintainer>
+	<longdescription lang="en">
+		This package provides a dandi command line utility with a basic interface
+		which should assist you in preparing and uploading your data to and/or
+		obtaining data from the http://dandiarchive.org . Each of the commands
+		has a set of options to alter their behavior. Please run
+		`dandi COMMAND --help` to get more information
+	</longdescription>
+	<use>
+		<flag name="etelemetry">version checking to respect server schema version</flag>
+	</use>
+	<upstream>
+		<remote-id type="github">dandi/dandi-cli</remote-id>
+		<remote-id type="pypi">dandi</remote-id>
+	</upstream>
+</pkgmetadata>
diff --git a/dev-vcs/datalad-fuse/Manifest b/dev-vcs/datalad-fuse/Manifest
new file mode 100644
index 000000000..cebf299ec
--- /dev/null
+++ b/dev-vcs/datalad-fuse/Manifest
@@ -0,0 +1 @@
+DIST datalad-fuse-0.5.1.gh.tar.gz 66846 BLAKE2B 7b6311060bc8434ff48006775199c8bcac30a37feb55a516dd5df754a2c81f062bcd6717f977365d4db08f97e587fc105e7721ff54e08ae90db159b2fb1c81c3 SHA512 9e479008325b6673bb0714dcfc86776361a6764f2218ed70ca229a76ac04e352c76b7c41e1aba13939ccfec186f2ad00b0c1a15eefc42f9b81af4041fcb4fe32
diff --git a/dev-vcs/datalad-fuse/datalad-fuse-0.5.1.ebuild b/dev-vcs/datalad-fuse/datalad-fuse-0.5.1.ebuild
new file mode 100644
index 000000000..1359f4e0d
--- /dev/null
+++ b/dev-vcs/datalad-fuse/datalad-fuse-0.5.1.ebuild
@@ -0,0 +1,43 @@
+# Copyright 1999-2023 Gentoo Authors
+# Distributed under the terms of the GNU General Public License v2
+
+EAPI=8
+
+DISTUTILS_USE_PEP517=setuptools
+PYTHON_COMPAT=( python3_{10..11} )
+inherit distutils-r1
+
+DESCRIPTION="Keep code, data, containers under control with git and git-annex"
+HOMEPAGE="https://github.com/datalad/datalad"
+SRC_URI="https://github.com/datalad/datalad-fuse/archive/refs/tags/${PV}.tar.gz -> ${P}.gh.tar.gz"
+
+LICENSE="MIT"
+SLOT="0"
+KEYWORDS="~amd64"
+
+RDEPEND="
+	dev-python/aiohttp-retry[${PYTHON_USEDEP}]
+	dev-python/fsspec[${PYTHON_USEDEP}]
+	dev-python/methodtools[${PYTHON_USEDEP}]
+	dev-python/linesep[${PYTHON_USEDEP}]
+	dev-vcs/datalad[${PYTHON_USEDEP}]
+	sys-fs/fuse
+"
+
+distutils_enable_tests pytest
+
+PATCHES=(
+	"${FILESDIR}/${P}-git_config.patch"
+)
+
+python_test() {
+	#git init -q || die
+	#git config --global user.email "placeholder@gentoo.org" || die
+	#git config --global user.name "Place Holder" || die
+	#git add . || die
+	#git commit -m "init" || die
+	##GIT_AUTHOR_NAME="Place Holder" GIT_AUTHOR_EMAIL="placeholder@gentoo.org" epytest
+	##export GIT_AUTHOR_NAME="Place Holder"
+	##export GIT_AUTHOR_EMAIL="placeholder@gentoo.org"
+	epytest
+}
diff --git a/dev-vcs/datalad-fuse/files/datalad-fuse-0.5.1-git_config.patch b/dev-vcs/datalad-fuse/files/datalad-fuse-0.5.1-git_config.patch
new file mode 100644
index 000000000..f62fc412e
--- /dev/null
+++ b/dev-vcs/datalad-fuse/files/datalad-fuse-0.5.1-git_config.patch
@@ -0,0 +1,15 @@
+Upstreamed and perhaps removable for future releases:
+https://github.com/datalad/datalad-fuse/pull/113
+diff --git a/datalad_fuse/tests/test_fsspec_head.py b/datalad_fuse/tests/test_fsspec_head.py
+index 75a6efc..1ffc60f 100644
+--- a/datalad_fuse/tests/test_fsspec_head.py
++++ b/datalad_fuse/tests/test_fsspec_head.py
+@@ -131,6 +131,8 @@ def test_git_repo(tmp_path):
+     TEXT = (Path(__file__).with_name("data") / "text.txt").read_bytes()
+     (tmp_path / "text.txt").write_bytes(TEXT)
+     subprocess.run(["git", "add", "text.txt"], cwd=tmp_path, check=True)
++    subprocess.run(["git", "config", "user.email", "place@holder.org"], cwd=tmp_path, check=True)
++    subprocess.run(["git", "config", "user.name", "Place Holder"], cwd=tmp_path, check=True)
+     subprocess.run(["git", "commit", "-m", "Add a file"], cwd=tmp_path, check=True)
+     ds = Dataset(tmp_path)
+     assert_in_results(
diff --git a/dev-vcs/datalad-fuse/metadata.xml b/dev-vcs/datalad-fuse/metadata.xml
new file mode 100644
index 000000000..97f1a33f3
--- /dev/null
+++ b/dev-vcs/datalad-fuse/metadata.xml
@@ -0,0 +1,16 @@
+<?xml version='1.0' encoding='UTF-8'?>
+<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
+<pkgmetadata>
+	<maintainer type="person">
+		<email>gentoo@chymera.eu</email>
+		<name>Horea Christian</name>
+	</maintainer>
+	<maintainer type="project">
+		<email>sci@gentoo.org</email>
+		<name>Gentoo Science Project</name>
+	</maintainer>
+	<upstream>
+		<remote-id type="github">datalad/datalad-fuse</remote-id>
+		<remote-id type="pypi">datalad-fuse</remote-id>
+	</upstream>
+</pkgmetadata>
diff --git a/dev-vcs/datalad/Manifest b/dev-vcs/datalad/Manifest
new file mode 100644
index 000000000..7875ed2b6
--- /dev/null
+++ b/dev-vcs/datalad/Manifest
@@ -0,0 +1 @@
+DIST datalad-0.19.6.tar.gz 1420979 BLAKE2B 49d8e19449652f284f89f99e6696c6d1abf7ddcc58a8eb00004c657be38ce2532ed9c11855dca4a0a8f82c55fbf1633f53ff2bdea063fd18ad946145d27a3404 SHA512 db7cd807a8106727f0b6f587be8c0ce3abcf0dc7cf72b4757e6b44650adca05482e6b0a6c1719050fba37660dcd5de2a6f27df044a8db180ac6855ee7ff8cbda
diff --git a/dev-vcs/datalad/datalad-0.19.6-r1.ebuild b/dev-vcs/datalad/datalad-0.19.6-r1.ebuild
new file mode 100644
index 000000000..c95bc935f
--- /dev/null
+++ b/dev-vcs/datalad/datalad-0.19.6-r1.ebuild
@@ -0,0 +1,73 @@
+# Copyright 1999-2023 Gentoo Authors
+# Distributed under the terms of the GNU General Public License v2
+
+EAPI=8
+
+DISTUTILS_USE_PEP517=setuptools
+PYTHON_COMPAT=( python3_{10..11} )
+inherit distutils-r1 pypi
+
+DESCRIPTION="Keep code, data, containers under control with git and git-annex"
+HOMEPAGE="https://github.com/datalad/datalad"
+#SRC_URI="https://github.com/datalad/datalad/archive/refs/tags/${PV}.tar.gz -> ${P}.tar.gz"
+
+LICENSE="MIT"
+SLOT="0"
+KEYWORDS="~amd64"
+IUSE="test +downloaders +metadata +publish misc"
+RESTRICT="!test? ( test )"
+
+RDEPEND="
+	>=dev-python/chardet-3.0.4[${PYTHON_USEDEP}]
+	app-arch/p7zip
+	app-arch/patool[${PYTHON_USEDEP}]
+	dev-python/annexremote[${PYTHON_USEDEP}]
+	dev-python/distro[${PYTHON_USEDEP}]
+	dev-python/fasteners[${PYTHON_USEDEP}]
+	dev-python/humanize[${PYTHON_USEDEP}]
+	dev-python/iso8601[${PYTHON_USEDEP}]
+	dev-python/looseversion[${PYTHON_USEDEP}]
+	dev-python/platformdirs[${PYTHON_USEDEP}]
+	dev-python/tqdm[${PYTHON_USEDEP}]
+	dev-python/wraps[${PYTHON_USEDEP}]
+	dev-vcs/git-annex
+	downloaders? (
+		dev-python/keyring[${PYTHON_USEDEP}]
+		dev-python/keyrings-alt[${PYTHON_USEDEP}]
+		dev-python/msgpack[${PYTHON_USEDEP}]
+		dev-python/requests[${PYTHON_USEDEP}]
+	)
+	metadata? (
+		dev-python/simplejson[${PYTHON_USEDEP}]
+		dev-python/whoosh[${PYTHON_USEDEP}]
+	)
+	misc? (
+		dev-python/argcomplete[${PYTHON_USEDEP}]
+		dev-python/pyperclip[${PYTHON_USEDEP}]
+		dev-python/python-dateutil[${PYTHON_USEDEP}]
+	)
+	publish? (
+		dev-vcs/python-gitlab[${PYTHON_USEDEP}]
+	)
+"
+BDEPEND="
+	dev-python/packaging[${PYTHON_USEDEP}]
+	test? (
+		${RDEPEND}
+		dev-python/beautifulsoup4[${PYTHON_USEDEP}]
+		dev-python/httpretty[${PYTHON_USEDEP}]
+		dev-python/mypy[${PYTHON_USEDEP}]
+		dev-python/vcrpy[${PYTHON_USEDEP}]
+	)
+"
+# Also wants test dep:
+# dev-python/types-requests
+# dev-python/types-python-dateutil
+
+distutils_enable_tests pytest
+
+python_test() {
+	local -x DATALAD_TESTS_NONETWORK=1
+	# see test groups in "tox.ini"
+	epytest -k "not turtle and not slow and not usecase"
+}
diff --git a/dev-vcs/datalad/metadata.xml b/dev-vcs/datalad/metadata.xml
new file mode 100644
index 000000000..9c40d4f36
--- /dev/null
+++ b/dev-vcs/datalad/metadata.xml
@@ -0,0 +1,31 @@
+<?xml version='1.0' encoding='UTF-8'?>
+<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
+<pkgmetadata>
+	<maintainer type="person">
+		<email>gentoo@chymera.eu</email>
+		<name>Horea Christian</name>
+	</maintainer>
+	<maintainer type="project">
+		<email>sci@gentoo.org</email>
+		<name>Gentoo Science Project</name>
+	</maintainer>
+	<longdescription lang="en">
+		DataLad makes data management and data distribution more accessible. To
+		do that, it stands on the shoulders of Git and Git-annex to deliver a
+		decentralized system for data exchange. This includes automated
+		ingestion of data from online portals and exposing it in readily usable
+		form as Git(-annex) repositories, so-called datasets. The actual data
+		storage and permission management, however, remains with the original
+		data providers.
+	</longdescription>
+	<use>
+		<flag name="downloaders">Extended support for download resources</flag>
+		<flag name="metadata">Annotated metadata support for datasets</flag>
+		<flag name="misc">Dataset publishing support</flag>
+		<flag name="publish">Dataset publishing support</flag>
+	</use>
+	<upstream>
+		<remote-id type="github">datalad/datalad</remote-id>
+		<remote-id type="pypi">datalad</remote-id>
+	</upstream>
+</pkgmetadata>
diff --git a/docs/meetings/logs/20130130.log b/docs/meetings/logs/20130130.log
deleted file mode 100644
index cde74b5cc..000000000
--- a/docs/meetings/logs/20130130.log
+++ /dev/null
@@ -1,262 +0,0 @@
-[22:01:44] *** Joins: jlec (~jlec@gentoo/developer/jlec)
-[22:01:53] <tomka> here
-[22:01:53] <willikins> tomka, you have notes! [17:16] <darkside_> thats a fun OSX error o_0 [18:46] <hwoarang> how about moving the tatt source code to the arch-tools repository please?!
-[22:02:13] <jlec> hi
-[22:02:59] <bicatali> let's wait another minute or so, although not sure we'll be so many of us
-[22:03:53] <jlec> Actually the science channel looks quite full
-[22:04:32] <bicatali> may be we should switch the meeting there then
-[22:04:53] <bicatali> ok, let's start
-[22:05:06] <jlec> I am supressing the join/part messages so I don't know when they all joined
-[22:05:06] <bicatali> 1. alternatives
-[22:05:26] <jlec> Who is willing to work on that?
-[22:06:03] <bicatali> i'm working on an eselect fork, some fixes are already on github.com/gentoo-science/eselect.git
-[22:06:31] <tomka> I'm mostly in maintenance mode, not going to take over new projects, sorry.
-[22:06:33] <jlec> How much work do you think needs to be done until we can start merging it into the main eselect?
-[22:06:45] <bicatali> more fixes will follow this week end to do the alternatives_for into the eselect
-[22:07:04] <jlec> is ulm following the changes?
-[22:07:15] <bicatali> these last fixes should be enough for ulm to review and pull
-[22:07:24] <jlec> perfect.
-[22:07:41] <jlec> That you are taking care of eselect.
-[22:07:45] <bicatali> then there is the ldscript issue, which i have not started
-[22:07:46] <bicatali> yep
-[22:08:12] <jlec> yeah about the ldscript thing.
-[22:08:12] *** Joins: heroxbd (~user@gentoo/developer/heroxbd)
-[22:08:17] <bicatali> after those fixes the eclass will need to be rewritten, but it should be much more simple
-[22:08:31] <heroxbd> sorry I'm late, it's 5am here.
-[22:08:44] <jlec> no problem
-[22:08:48] <jlec> we just started
-[22:08:55] <heroxbd> ;)
-[22:09:07] <jlec> bicatali:	so we are waiting for you to fix eselect
-[22:09:21] <bicatali> so has anyone tried the eselect-9999 from the science overlay?
-[22:09:39] <jlec> not yet, but I will switch to tomorrow
-[22:10:11] * heroxbd is wondering if it is about blas/atlas/gotoblas selection
-[22:10:19] <bicatali> i would like a tester for the current eclass/eselect with multiple blas
-[22:10:25] <jlec> heroxbd: alternatives framework
-[22:10:32] <heroxbd> I see
-[22:10:53] <bicatali> heroxbd: you need to unmask eselect-9999::science
-[22:11:13] <heroxbd> bicatali: I'd like to be a tester, too.
-[22:11:19] <bicatali> the other issue is what we do with library sonames
-[22:11:31] <jlec> right
-[22:11:43] <jlec> But I still disagree with equalizing them
-[22:12:02] <jlec> You are right we reduce the rebuilding when one implementation is drop
-[22:12:04] <jlec> ped
-[22:12:07] <bicatali> so debian changes soname for atlas and openblas to blas
-[22:12:28] <jlec> But we loose the ability to use different blas implementations for different programms
-[22:13:31] <jlec> What do we gain in addition to the rebuilds to set all sonames to blas?
-[22:13:33] <bicatali> i don't think we want users to compile R against openblas-threaded and octave against atlas
-[22:13:49] <jlec> Why not?
-[22:14:37] <bicatali> it's calling for bugs while rebuilding, and what do we do if the user removes one provider?
-[22:15:00] <jlec> portage should catch that and preserve libs.
-[22:15:03] <bicatali> and truely, once you choose one, you don't move
-[22:15:25] <jlec> Not that I would recommend using different blas for different apps
-[22:15:31] <jlec> But it's about choice
-[22:15:35] <bicatali> we could do more eselect modules: blas-threads, blas-serial, blas-int64
-[22:16:21] <heroxbd> just to confirm, they cannot be made ABI at all. So we are exclued with this probability, is that true?
-[22:16:27] <jlec> so instead of splitting into different providers, splitting into different types of implementation.
-[22:16:30] <heroxbd> ABI-compatible I mean
-[22:16:59] <jlec> bicatali: that sounds like a good idea
-[22:17:29] <bicatali> yes, so we would use the mutlibuild eclass for each, then add some use flags threads, int64, etc... for the dependent packages
-[22:18:02] <jlec> bicatali: but what about the libs which are splitted in to different so files? How do you handle sonames there?
-[22:18:15] <bicatali> this makes sense: sometimes a threaded program does want a serial blas to avoid oversuscribing
-[22:18:38] <bicatali> same soname for a given eselect module?
-[22:19:20] <bicatali> right now i would suggest lets split, then later on let's worry about soname/ldscript
-[22:19:49] <jlec> split what?
-[22:20:22] <bicatali> let's make several blas eselect modules: blas-serial, blas-threads, ...
-[22:20:59] <bicatali> and add use flags to virtual/blas
-[22:22:15] <jlec> And would that look for different providers for e.g. blas-serial?
-[22:22:30] <jlec> so atlas and reference are installed and provide serial
-[22:22:40] <jlec> How can the user choose?
-[22:22:51] <bicatali> use flag?
-[22:23:19] <bicatali> threads? ( virtual/blas[threads] )
-[22:23:56] <jlec> so we have can do eselect blas-thread set atlas ?
-[22:23:59] <bicatali> the worry about this is: much work to change ebuilds
-[22:24:34] <bicatali> eselect blas-threads to select atlas-threads
-[22:24:47] <bicatali> eselect blas-serial to select atlas...
-[22:25:14] <jlec> and what if want now reference ?
-[22:25:44] <bicatali> only on eselect blas-serial and virtual/blas with -threads
-[22:26:25] <jlec> So you want to control everything over virtual/blas?
-[22:26:57] <bicatali> on the package level yes, or do several virtual/blas-*
-[22:27:30] <bicatali> it seems it needs more thinking, so let's set this for another time
-[22:27:56] <jlec> yes fine. Perhaps you could write up a draft of your ideas
-[22:28:34] * heroxbd considers a written guideline for us and the users necessary
-[22:28:41] <bicatali> so actions: i'll finish the eselect, heroxbd will test the current builds with it
-[22:28:55] <jlec> I will also test
-[22:29:13] <jlec> sounds good
-[22:29:14] <bicatali> anyone wants to investigate multibuilds?
-[22:29:16] <heroxbd> no problem
-[22:29:29] <heroxbd> I've been googling for it
-[22:29:34] <jlec> bicatali: I can take a look
-[22:29:49] <jlec> but we need to have a chat about your exact ideas
-[22:30:08] <bicatali> yes. and let's start an alternatives wiki page
-[22:30:37] <bicatali> btw anyone with another word than 'alternatives' is welcome
-[22:31:05] * jlec slowly gets bicatali plan
-[22:31:39] <bicatali> time to switch to the 2. documentation
-[22:31:52] <jlec> WE need more.
-[22:32:04] <heroxbd> exactly
-[22:32:23] <jlec> I am trying to work on the whole contribution/community part
-[22:32:43] <jlec> And I am currently in progress to move the mpi.eclass/empi thing to the tree.
-[22:33:08] <jlec> This also need more documentation, which is probably more a business of the clusterteam
-[22:33:31] <jlec> Which other documentations are top priority?
-[22:33:33] <bicatali> regarding https://wiki.gentoo.org/wiki/Project:Science: it would be nice if everyone reads all the pages/subpages and resources 
-[22:34:36] <bicatali> like the Gentoo Electronics project and herd are empty
-[22:34:49] <bicatali> but is it?
-[22:34:56] <bicatali> the mail alias is not
-[22:35:26] <jlec> bicatali: I will go through it and send mails to the aliases.
-[22:35:57] <jlec> !herd sci-electronics
-[22:36:00] <willikins> jlec: (sci-electronics) calchan, rafaelmartins, tomjbe, xmw
-[22:37:38] <jlec> And wee need to increase the staffing needs
-[22:37:45] <jlec> As we really need staff
-[22:37:58] <jlec> BTW please try to recruit
-[22:38:19] <bicatali> so let's push some jobs in the next gmn
-[22:38:19] <jlec> we are super fast in recruiting currently so the process is really fast
-[22:38:28] <jlec> good idea
-[22:39:10] <bicatali> who would like to review all the wiki pages to make them consistent?
-[22:39:30] <heroxbd> I can, haven't read it carefully yet
-[22:39:32] <bicatali> i've tried quite a bit already, but it needs more reviewing
-[22:39:46] <tomka> What's inconsistent?
-[22:39:57] <bicatali> jlec: want to ping the herds to include themselves in the wiki?
-[22:40:06] <jlec> It seems to be quite consistent
-[22:40:12] <bicatali> herds, members and mail aliases
-[22:40:18] <jlec> bicatali: ask for input on their pages
-[22:40:29] <jlec> I will also go through it
-[22:41:04] <tomka> Recruitment looks pretty much boilerplate.
-[22:41:09] <tomka> It's the same on every sub-page.
-[22:41:23] <tomka> But missing on sci-biology
-[22:41:27] <bicatali> just want to make sure we can get rid of http://www.gentoo.org/proj/en/science/index.xml
-[22:41:28] <tomka> are they fully staffed?
-[22:41:42] <bicatali> which is still the first google result for gentoo science
-[22:43:08] <jlec> I will first take a look that everything from the old xml site is covered by the wiki and then clean/improve the wiki pages.
-[22:43:12] <heroxbd> so the task is to review the wiki to make sure it has the full coverage of proj/science/xml and then redirect it.
-[22:43:48] <bicatali> yes, the blas-lapack page i will start the rewrite with the alternatives
-[22:43:48] <heroxbd> !herd sci-biology
-[22:43:49] <willikins> heroxbd: (sci-biology) je_fro, jlec, weaver
-[22:44:05] <bicatali> !herd sci-geosciences
-[22:44:06] <willikins> bicatali: (sci-geosciences) fordfrog
-[22:44:06] <jlec> heroxbd: it's just me
-[22:44:20] <heroxbd> ;)
-[22:44:32] <bicatali> so these sub-projects make sense?
-[22:44:59] <jlec> you mean the packages in the wiki or the herd subdivision?
-[22:45:05] <heroxbd> I think so, there would be more stuff.
-[22:45:36] <bicatali> we have both sub-herds and sub-projects
-[22:46:00] <bicatali> ok, let's keep it that way and get more people i guess
-[22:46:28] <jlec> sub-projects don't make really sense. 
-[22:46:33] <jlec> sub-herds do
-[22:47:17] <jlec> I think the sub-projects should be things like the alternative framework rather then different science fields
-[22:47:29] <bicatali> well we had this: http://www.gentoo.org/proj/en/science/electronics/
-[22:48:09] <jlec> so we can add the electronics test bench sub project
-[22:48:36] <bicatali> first make sure that electronics is active...
-[22:49:02] <jlec> So I will ask the current sub-projects if they are willing to merge into the parent
-[22:49:14] <jlec> or otherwise maintain their subpage
-[22:49:24] <bicatali> yes, and then re-organize the wiki
-[22:49:26] <jlec> rafaelmartins: what about sci-electronics?
-[22:49:34] <jlec> !seen rafaelmartins
-[22:49:37] <willikins> jlec: rafaelmartins was last seen 4 hours, 44 minutes and 31 seconds ago, joining #gentoo-prefix
-[22:50:35] <heroxbd> we can make alternative framework itself a subproject in parallel to the fields.
-[22:51:22] <bicatali> i'd rather see the alternatives part of the eselect, i'll talk to ulm
-[22:51:32] <jlec> kk
-[22:52:00] <rafaelmartins> jlec: hello
-[22:52:05] <jlec> hi
-[22:52:08] * rafaelmartins jumps in the meeting
-[22:52:18] <heroxbd> hi
-[22:52:21] <jlec> I will send around mails
-[22:52:26] <jlec> that's better
-[22:52:30] <rafaelmartins> so, we are having low activity lately
-[22:52:31] <bicatali> actions: wiki review herobxd, jlec. wiki reorg: jlec?. alternatives write-up start: bicatali
-[22:52:37] <bicatali> rafaelmartins: oi
-[22:52:45] <rafaelmartins> bicatali: oi :)
-[22:53:01] <jlec> bicatali: I will take care of the wiki
-[22:54:14] <bicatali> finally: 3. new leader
-[22:54:21] <bicatali> i nominate jlec 
-[22:54:46] * heroxbd nods
-[22:54:46] <jlec> Thanks. I accept the nomination.
-[22:54:53] <tomka> I second that.
-[22:54:59] <rafaelmartins> about electronics, quickly:
-[22:55:33] <rafaelmartins> I'am not doing a lot of work on this. mainly maintaining just the stuff I use to play for fun, not working with any eng-related stuff at this point
-[22:56:12] <rafaelmartins> I assumed as lead mainly because calchan wasn't able to do it at that time, my plan is to schedule a subproject lead election soon
-[22:56:37] <bicatali> rafaelmartins: pushing for new recruits and updating the wiki should be enough for electronics to survive
-[22:56:42] <jlec> rafaelmartins: I will take care of the wiki and do the rest by mail to the alias
-[22:56:50] <rafaelmartins> so, the subproject still exists, but with quite low activity at this point
-[22:56:59] <heroxbd> rafaelmartins: or would like to merge the sub project into science?
-[22:57:10] <rafaelmartins> bicatali: yeah, we got some people interested, but they disappear :(
-[22:57:34] <rafaelmartins> heroxbd: I'd like to hear calchan's opinion on this
-[22:57:52] <heroxbd> rafaelmartins: ok
-[22:57:59] <rafaelmartins> we can keep everything as is now, just migrating the project page to the wiki and decide on it later
-[22:58:05] <bicatali> rafaelmartins: could you help jlec merging the old page into https://wiki.gentoo.org/wiki/Project:Electronics
-[22:58:16] <rafaelmartins> bicatali: of course
-[22:58:49] *** Joins: fbissey (~fbissey@132.181.64.206)
-[22:58:53] <bicatali> ok voting: i vote for jlec as new leader
-[22:59:08] <rafaelmartins> +1 for jlec
-[22:59:10] <fbissey> Just in time for the vote
-[22:59:17] <bicatali> hey fbissey 
-[22:59:23] <heroxbd> I vote for jlec, too
-[22:59:27] <heroxbd> fbissey: hi
-[22:59:39] <fbissey> no surprise that jlec is put in the driving seat
-[22:59:52] <tomka> +1 for jlec
-[23:00:49] <bicatali> jlec: clearly you are our new leader, please someone kicks me out from this channel!
-[23:01:08] <jlec> THank you everbody
-[23:01:12] <heroxbd> bicatali: ;)
-[23:01:15] <fbissey> congrats!
-[23:01:50] <jlec> ANd thank you bicatali doing the work the last years
-[23:01:55] <heroxbd> jlec: hey you haven't voted yet
-[23:01:59] <tomka> yeah thanks bicatali 
-[23:02:24] <fbissey> thanks for putting up with us bicatali
-[23:02:50] <heroxbd> bicatali: yeah, thanks. And may I ask why you stepped down and what's your plan with science herd next?
-[23:03:02] <bicatali> i'll try to clean up my leadership with a bug free alternatives
-[23:03:36] <fbissey> I remember jlec and I came to gentoo at the same time and he is lead and I haven't made it to developer yet
-[23:03:52] <bicatali> heroxbd: jlec is more involved than me. i'm going to work on an automated gentoo
-[23:04:07] <heroxbd> fbissey: wow
-[23:04:38] <jlec> I think we set some nice clean up for the next months.
-[23:04:39] <heroxbd> bicatali: that's cluster deployment?
-[23:04:58] <jlec> Getting the alternatives into the tree should be top priority.
-[23:05:11] <heroxbd> jlec: agreed.
-[23:05:43] <heroxbd> jlec: and as the wiki reorg/review overlaps, you can assign me some jobs in detail.
-[23:05:59] <bicatali> heroxbd: no, some minimal gentoo core + cvmfs ala coreos to automate stabilizing 
-[23:06:20] <bicatali> anyone keeping logs?
-[23:06:31] <jlec> I am logging
-[23:06:54] <heroxbd> ain't there a 4. open floor?
-[23:07:15] <heroxbd> just some FYI: first some news from roverlay.
-[23:07:18] <bicatali> heroxbd: yes you are right
-[23:08:27] <heroxbd> I started co-maintaining the roverlay with calchan, it is automated generatedfrom cran. once it's mature, I'll write up some doc
-[23:08:49] <bicatali> that is good news
-[23:09:13] <heroxbd> sorry, creepy internet connection
-[23:09:32] <bicatali> jlec: want to post meeting log on the wiki then?
-[23:09:48] <jlec> bicatali: I will
-[23:09:56] <fbissey> heroxbd: can it take other R repo like bioconductor?
-[23:11:04] <heroxbd> fbissey, I think it high possible, as the overlay generation tools are actively developed by another student.
-[23:11:13] <heroxbd> *highly
-[23:11:32] <heroxbd> it has been a google summer of code project
-[23:12:57] <heroxbd> FYI2, among the Prefix users, many are from academic field. They submit bugs, and are good candidatesfor recruitment.
-[23:14:38] <jlec> heroxbd: sounds great.
-[23:14:45] <bicatali> ok folks, thanks, i'm off the meeting
-[23:14:53] <jlec> make them fix the quizzes and get them a bug
-[23:14:57] <fbissey> bye bicatali
-[23:15:05] <jlec> bicatali thanks for all
-[23:15:07] <jlec> bye
-[23:15:28] <heroxbd> bicatali: see you
-[23:17:30] <jlec> Okay guys, anymore more openfloor topics?
-[23:17:34] <heroxbd> are we waiting for closing the meeting?
-[23:18:08] <fbissey> I have some stuff but I will probably post on list for discusion
-[23:18:19] <jlec> If there is nothing else, I would close it
-[23:18:47] <jlec> We can schedule the next meeting sooner, in 1-2 months or so
-[23:19:12] <jlec> fbissey: Or do you want to discuss now. It is up to you.
-[23:19:31] <fbissey> I can introduce it.
-[23:19:58] <fbissey> blas/lapack setup in python package is horrible
-[23:20:26] <fbissey> motivated by work I am doing with people in sage I trying to get stuff to simplify that
-[23:20:27] <jlec> We should wait for this a little
-[23:20:39] <heroxbd> fbissey: python build system tries to do all the smart but wrong guessing 
-[23:21:00] <jlec> After bicatali fixed eselect and we decided about the soname thing, we shoudl have an ldscript
-[23:21:10] <jlec> then it will become easier
-[23:21:13] <fbissey> there is a python module to interface with pkg-config that makes some things easier
-[23:21:22] <heroxbd> good idea
-[23:21:42] <jlec> fbissey: best would be to simply have libblas.so as ldscript
-[23:21:57] <jlec> but that should be implemented after we fixed the rest
-[23:21:59] <fbissey> that make things easy agreed.
-[23:23:57] <fbissey> nothing more from me
-[23:24:05] <jlec> fine
-[23:24:18] <jlec> So I will close the meeting here. Thanks for attending.
-[23:24:29] <jlec> I will post the meeting log on the wiki
-[23:24:36] <heroxbd> Thanks all
-[23:24:47] <tomka> thanks
-[23:25:30] *** Parts: fbissey (~fbissey@132.181.64.206) ("Konversation terminated!")
-[23:33:09] *** Quits: tomka (~tomka@gentoo/developer/tomka) (Quit: tomka)
-[23:44:50] *** Joins: Calchan (~calchan@gentoo/developer/calchan)
diff --git a/docs/meetings/sci-electronics-201010-agenda b/docs/meetings/sci-electronics-201010-agenda
deleted file mode 100644
index 2e3c18a3c..000000000
--- a/docs/meetings/sci-electronics-201010-agenda
+++ /dev/null
@@ -1,14 +0,0 @@
-Topics
-------
-
-- Open bugs (http://xrl.us/bh4cdg).
-- Packages lacking in the main tree:
-  - Add your package here...
-- Creation of the sci-electronics subproject.
-
-
-Schedule
---------
-
-- When: 2010-10-17 2000 UTC (rafaelmartins, dilfridge)
-- Where: #gentoo-meetings @ Freenode
diff --git a/docs/proj/blas-lapack.xml b/docs/proj/blas-lapack.xml
deleted file mode 100644
index f4ef31cee..000000000
--- a/docs/proj/blas-lapack.xml
+++ /dev/null
@@ -1,492 +0,0 @@
-<?xml version="1.0" encoding="UTF-8"?>
-<!DOCTYPE guide SYSTEM "/dtd/guide.dtd">
-
-<guide link="/proj/en/science/blas-lapack.xml">
-<title>Using multiple versions of BLAS and LAPACK with Gentoo/Linux</title>
-
-<author title="Author">
-  <mail link="bicatali@gentoo.org">Sébastien Fabbro</mail>
-</author>
-<author title="Author">
-  <mail link="markusle@gentoo.org">Markus Dittrich</mail>
-</author>
-<author title="Editor">
-  <mail link="nightmorph@gentoo.org">Joshua Saddler</mail>
-</author>
-
-<abstract>
-This guide explains the use of the different implementations of the BLAS
-and LAPACK libraries that are available via Portage.
-</abstract>
-
-<!-- The content of this document is licensed under the CC-BY-SA license -->
-<!-- See http://creativecommons.org/licenses/by-sa/2.5 -->
-<license/>
-
-<version>1.0</version>
-<date>2007-10-22</date>
-
-<chapter>
-<title>Introduction</title>
-<section>
-<body>
-
-<p>
-The Basic Linear Algebra Subroutines (BLAS) and Linear Algebra PACKage (LAPACK)
-are well designed linear algebra software libraries developed by the
-High Performance Computing (HPC) community. BLAS
-implements dense matrix and vectors products, while LAPACK provides routines for 
-solving systems of linear equations. Both are widely used in
-many scientific applications and it is, therefore, important to 
-have efficient implementations available.
-</p>
-
-<p>
-Originally written in FORTRAN 77, a number of additional language
-wrappers have been developed for languages like C, C++, FORTRAN 95, and others.
-The following legacy libraries are available via the reference ebuilds:
-</p>
-
-<ul>
-  <li>
-    <uri link="http://netlib.org/blas">BLAS</uri>: FORTRAN 77 implementation of
-    BLAS
-  </li>
-  <li>
-    <uri link="http://netlib.org/blas">CBLAS</uri>: C implementation of BLAS
-  </li>
-  <li>
-    <uri link="http://netlib.org/lapack">LAPACK</uri>: FORTRAN 77 implementation
-    of LAPACK
-  </li>
-</ul>
-
-<p>
-In addition, Gentoo provides a number of optimized BLAS and LAPACK implementations
-that will be described below. Different implementations are bundled together with
-Gentoo's <c>eselect</c> system and the widely used <c>pkg-config</c> tool.
-</p>
-
-<p> It is important to note that if you require, e.g., a well performing 
-BLAS implementation, simply emerging X over Y often is not enough. Rather, you will have
-to carefully benchmark your applications since performance may depend 
-on many factors,
-such as hardware or network.
-If you are simply looking for a well performing and well tested
-implementation, the reference ebuilds will likely be your best choice.
-</p>
-
-
-</body>
-</section>
-</chapter>
-
-<chapter>
-<title>For Users</title>
-<section>
-<title>Installing</title>
-<body>
-
-<p>
-If best possible performance is not of paramount importance for you 
-and you simply
-need BLAS and/or LAPACK, just emerge the virtual packages:
-</p>
-
-<pre caption="Installing">
-# <i>emerge blas cblas lapack</i>
-</pre>
-
-<p>
-These will install the reference legacy	packages from
-<uri>http://netlib.org</uri>. They are well tested, easy to debug
-implementations. They should satisfy most users; if they're all you need, you're
-done reading.
-</p>
-
-<p>
-However, if:
-</p>
-
-<ul>
-  <li>BLAS/LAPACK are critical for the speed of your applications</li>
-  <li>you absolutely need to build the fastest computer</li>
-  <li>you want to help Gentoo sci project to improve their packages</li>
-</ul>
-
-<p>
-... then read on, and be sure to file bugs both to Gentoo and upstream.
-</p>
-
-<p>
-There is a number of optimized implementations of these libraries in the Portage
-tree:
-</p>
-
-<ul>
-  <li>
-   <uri link="http://math-atlas.sourceforge.net">ATLAS</uri>: Automatically
-   Tuned Linear Algebra Software is an open-source package that empirically
-   tunes the library to the machine it is being compiled on. It provides BLAS
-   (FORTRAN 77 and C), and LAPACK implementations on various architectures.
-  </li>
-  <li>
-   <uri
-   link="http://www.tacc.utexas.edu/resources/software/software.php">GotoBLAS</uri>:
-   Goto BLAS provide open-source, free for academic use, hand-coded
-   machine language, processor optimized versions of the FORTRAN 77 BLAS
-   routines. Claims to be the fastest BLAS.
-  </li>
-  <li>
-    <uri link="http://developer.intel.com/software/products/mkl/">MKL</uri>:
-    Intel® Math Kernel Library is a closed-source but free package for
-    non-commercial use containing BLAS (FORTRAN 77 and C), LAPACK optimized for
-    Intel® based architectures: x86, amd64 and ia64.
-  </li>
-</ul>
-
-<p>
-Usually performance gain is noticeable mainly with BLAS, since LAPACK routines
-depend on BLAS kernels.
-</p>
-
-</body>
-</section>
-<section>
-<title>Compiling and linking with installed libraries</title>
-<body>
-
-<p>
-We took great care to make sure that each package provides consistent pkg-config files.
-Hence, compiling and linking with BLAS/LAPACK should be simple and straightforward:
-</p>
-
-<pre caption="Compiling and linking BLAS/LAPACK">
-# <i>pkg-config --libs blas</i>    <comment>(To link with FORTRAN 77 BLAS library)</comment>
-# <i>pkg-config --cflags cblas</i> <comment>(To compile against C BLAS library)</comment>
-# <i>pkg-config --libs cblas</i>   <comment>(To link with C BLAS library)</comment>
-# <i>pkg-config --libs lapack</i>  <comment>(To link with FORTRAN 77 LAPACK library)</comment>
-</pre>
-
-<p>
-<c>pkg-config</c> files are available for whichever implementation you select with <c>eselect</c>.
-More information on using <c>pkg-config</c> can be obtained with <c>man pkg-config</c>. 
-</p>
-
-</body>
-</section>
-<section>
-<title>Choosing libraries</title>
-<body>
-
-<p>
-You can easily switch BLAS, CBLAS and LAPACK implementations with
-<c>eselect</c>. At this point, you probably have <c>eselect-blas</c>,
-<c>eselect-cblas</c> and <c>eselect-lapack</c> installed. If you do not,
-install them now! Using eselect, you can view which implementations of CBLAS
-are available.
-</p>
-
-<pre caption="Viewing available implementations">
-# <i>eselect cblas list</i>
-Installed CBLAS for library directory lib64
-[1]   atlas
-[2]   atlas-threads
-[3]   gsl
-[4]   mkl-threads *
-[5]   reference
-</pre>
-
-<p>
-The implementation marked with an asterisk (*) is the currently
-selected implementation. To switch implementations, run:
-</p>
-
-<pre caption="Switching to the ATLAS implementation of LAPACK">
-# <i>eselect lapack set atlas</i>
-</pre>
-
-<p>
-To learn more about the <c>eselect</c> tool, visit the 
-<uri link="http://www.gentoo.org/proj/en/eselect/user-guide.xml">eselect guide</uri>
-</p>
-
-<p>
-When selecting blas, cblas or lapack profiles try to avoid mixing
-different implementations since we don't have any mechanism to enforce
-reasonable profiles. However, here is a list of well performing
-profile combinations that have been used successfully in the past:
-</p>
-<ul>
-  <li> Most CPUs:
-    <ul>
-      <li>blas,cblas: atlas (or atlas-threads with multi-processor)</li>
-      <li>lapack:atlas</li>
-    </ul>
-  </li>
-  <li> Most CPUs:
-    <ul>
-      <li>blas: goto </li>
-      <li>cblas,lapack: reference</li>
-    </ul>
-  </li>
-  <li> AMD based CPUs:
-    <ul>
-      <li>cblas: reference</li>
-    </ul>
-  </li>
-  <li> Intel based CPUs:
-    <ul>
-      <li>blas,cblas,lapack: mkl-threads</li>
-    </ul>
-  </li>
-</ul>
-
-</body>
-</section>
-
-<section>
-<title>Choosing a compiler</title>
-<body>
-
-<p>
-Most of the libraries can compile with both the GNU compiler collection and the
-Intel® compilers on the x86, amd64 and ia64 architectures. By default, you are
-probably using <c>gcc</c>. You can also compile the <c>*-reference</c> packages
-with <c>ifort</c> and <c>icc</c>. To do this, you need to define the F77
-environment variable and don't forget the FFLAGS.
-</p>
-
-<pre caption="Using non-GCC compilers">
-# <i>F77=ifort FFLAGS="-O2 -mp" emerge blas-reference</i>
-</pre>
-
-<p>
-Depending on your hardware, a small performance gain can be noticed thanks to
-vectorization. The <c>-mp</c> flag maintains floating-point precision, since by
-default ifort is pretty aggressive on floating point arithmetic, and we are
-actually compiling a math package. Try <c>man ifort</c> to see additional flags
-to fit your hardware.
-</p>
-
-<p>
-Some of the implementations let you specify the Intel® C compiler as
-well. Please beware that not all libraries compile with all
-combinations.  You should receive an error during the emerge in case you have
-chosen an incompatible combination.
-</p>
-
-<p>
-As usual for Gentoo, there are many combinations of USE flags and
-compilers with which you could compile a package. Unfortunately
-switching compilers between BLAS and LAPACK might not be always
-compatible. For example: 
-</p>
-
-<pre caption="Incompatible combinations">
-# <i>F77=gfortran FFLAGS="-O2" emerge lapack-reference</i>
-</pre>
-
-<p>
-This will most likely break things or not even compile.
-</p>
-
-<p>
-Try to be consistent in your choice. Stay with the GCC most of the time will
-avoid you some trouble, unless you want to use the MKL, in which case the Intel®
-C and FORTRAN compilers make a good combination.
-</p>
-
-</body>
-</section>
-<section>
-<title>Documentation</title>
-<body>
-
-<p>
-If you need BLAS or LAPACK to develop your own programs, the documentation
-becomes pretty handy. Setting the USE="doc" flag for the corresponding BLAS or
-LAPACK package will install man pages and quick reference sheets from the
-<c>app-doc/blas-docs</c> and <c>app-doc/lapack-docs</c> packages. They are
-standard and valid for all implementations. For optimized packages, the
-USE="doc" flags will usually install extra doc in PDF or HTML format.
-</p>
-
-</body>
-</section>
-</chapter>
-
-<chapter>
-<title>For Developers</title>
-<section>
-<title>Providing new implementations</title>
-<body>
-
-<p>
-The Portage tree contains many ebuilds that depend on the BLAS/CBLAS/LAPACK
-libraries. As there is more than one possible implementation, the Gentoo
-Scientific Project reorganized all the packages to provide <c>virtual/blas</c>,
-<c>virtual/cblas</c>, and <c>virtual/lapack</c>. All ebuilds using BLAS should
-depend on this virtual package, unless it is explicitly known to break with
-different BLAS implementations.
-</p>
-
-<p>
-To work with Gentoo's configuration tools
-<c>app-admin/eselect-{blas,cblas,lapack}</c>, and the virtual, every ebuild that
-installs a BLAS implementation must fulfill following requirements:
-</p>
-
-<ol>
-  <li>
-    The ebuild must install an eselect file for each profile it provides. The
-    libraries should link to the ones in <path>/usr/$(get_libdir)</path>
-    directories and the include files in <path>/usr/include</path>:
-    <ul>
-      <li>
-	<path>libblas.so[.0]</path> - Shared object for FORTRAN BLAS
-	applications
-      </li>
-      <li>
-        <path>libblas.a</path> - Static library for FORTRAN BLAS applications
-      </li>
-      <li>
-        <path>libcblas.so[.0]</path> - Shared object for C/C++ CBLAS applications
-      </li>
-      <li>
-        <path>libcblas.a</path> - Static library for C/C++ CBLAS applications
-      </li>
-      <li><path>cblas.h</path> - Include header for C/C++ applications</li>
-      <li>
-        <path>liblapack.so[.0]</path> - Shared object for FORTRAN LAPACK
-	applications
-      </li>
-      <li>
-        <path>liblapack.a</path> - Static library for FORTRAN LAPACK applications
-      </li>
-    </ul>
-  </li>
-  <li>
-    The ebuild must install a <path>blas.pc</path>, <path>cblas.pc</path> and/or
-    <path>lapack.pc</path> pkg-config file and therefore RDEPEND on
-    <c>dev-util/pkgconfig</c>.  They should also be included in the eselect
-    files, and link to the <path>/usr/$(get_libdir)/pkgconfig</path> directory:
-    <ul>
-      <li><path>blas.pc</path> - BLAS pkg-config file</li>
-      <li><path>cblas.pc</path> - CBLAS pkg-config file</li>
-      <li><path>lapack.pc</path> - LAPACK pkg-config file</li>
-    </ul>
-  </li>
-  <li>Be included in the virtual package as a possible provider:
-    <ul>
-      <li><c>virtual/blas</c> - BLAS virtual package</li>
-      <li><c>virtual/cblas</c> - CBLAS virtual package</li>
-      <li><c>virtual/lapack</c> - LAPACK virtual package</li>
-    </ul>
-  </li>
-</ol>
- 
-<p>
-The easiest way of understanding all this is probably getting inspiration from
-one of the available packages.  Currently the Portage tree provide the following
-virtuals:
-</p>
-
-<table>
-<tr>
-  <th>Package name</th>
-  <th>virtual/blas</th>
-  <th>virtual/cblas</th>
-  <th>virtual/lapack</th>
-</tr>
-<tr>
-  <ti><c>sci-libs/blas-atlas</c></ti>
-  <ti>*</ti>
-  <ti>*</ti>
-  <ti></ti>
-</tr>
-<tr>
-  <ti><c>sci-libs/blas-goto</c></ti>
-  <ti>*</ti>
-  <ti></ti>
-  <ti></ti>
-</tr>
-<tr>
-  <ti><c>sci-libs/blas-reference</c></ti>
-  <ti>*</ti>
-  <ti></ti>
-  <ti></ti>
-</tr>
-<tr>
-  <ti><c>sci-libs/cblas-reference</c></ti>
-  <ti></ti>
-  <ti>*</ti>
-  <ti></ti>
-</tr>
-<tr>
-  <ti><c>sci-libs/gsl</c></ti>
-  <ti></ti>
-  <ti>*</ti>
-  <ti></ti>
-</tr>
-<tr>
-  <ti><c>sci-libs/lapack-atlas</c></ti>
-  <ti></ti>
-  <ti></ti>
-  <ti>*</ti>
-</tr>
-<tr>
-  <ti><c>sci-libs/lapack-reference</c></ti>
-  <ti></ti>
-  <ti></ti>
-  <ti>*</ti>
-</tr>
-<tr>
-  <ti><c>sci-libs/mkl</c></ti>
-  <ti>*</ti>
-  <ti>*</ti>
-  <ti>*</ti>
-</tr>
-</table>
-
-</body>
-</section>
-<section>
-<title>Packages with BLAS/LAPACK dependencies</title>
-<body>
-
-<p>
-Simply use <c>virtual/{blas,cblas,lapack}</c> as a [R]DEPEND. To build some
-packages, you might need to use the pkg-config tool. If you are lucky, the
-package uses autotools together with common BLAS and LAPACK M4 macros.In this
-case, the configuration step becomes simple. For example:
-</p>
-
-<pre caption="Sample package configuration">
-<keyword>econf</keyword> --with-blas="<var>$(pkg-config --libs blas)</var>"
-</pre>
-
-<impo>
-Don't forget to add <c>dev-util/pkgconfig</c> in DEPEND.
-</impo>
-
-</body>
-</section>
-</chapter>
-
-<chapter>
-<title>In the near future</title>
-<section>
-<body>
-
-<p>
-We plan to include more standard BLAS, LAPACK libraries: BLAS 95, LAPACK 95,
-Sparse BLAS, ScaLAPACK. If you feel inclined to write an ebuild for these, you
-are more than welcomed to file it on our <uri
-link="http://bugs.gentoo.org">Bugzilla</uri>.
-</p>
-
-</body>
-</section>
-</chapter>
-</guide>
diff --git a/docs/proj/contrib.xml b/docs/proj/contrib.xml
deleted file mode 100644
index fd474808b..000000000
--- a/docs/proj/contrib.xml
+++ /dev/null
@@ -1,182 +0,0 @@
-<?xml version="1.0" encoding="UTF-8"?>
-<!DOCTYPE guide SYSTEM "/dtd/guide.dtd">
-<guide link="/doc/en/" lang="en">
-
-  <title>Contributing to the Scientific Project</title>
-
-  <author title="Author">
-    <mail link="bicatali@gentoo.org">Sébastien Fabbro</mail>
-    <!-- others add your name here -->
-  </author>
-
-  <abstract>
-    This document provides information on how one can get involved and 
-    help out with the Gentoo Scientific Project
-  </abstract>
-
-  <!-- The content of this document is licensed under the CC-BY-SA license -->
-  <!-- See http://creativecommons.org/licenses/by-sa/2.5 -->
-  <license/>
-
-  <version>0.1</version>
-  <date>2009-01-21</date>
-
-  <chapter>
-    <title>Overview</title>
-    <section>
-      <body>
-        <p>
-          This document aims to provide information on how one can get
-          involved and help out with the Gentoo Scientific Project.
-	  Scientific packages are very diverse and many of us want our
-          pet application in the main tree for easy installation. Due to
-          the small size of our team, we can not implement all of
-          them, so we really appreciate any contribution.
-        </p>
-	<p>
-	  There are few obvious areas where one can help as we
-	  describe below. The Scientific Project tends to set strong
-	  requirements on testing, especially on core packages.
-	  Comments, thoughts, and feedback is greatly welcomed!
-	</p>
-      </body>
-    </section>
-  </chapter>
-
-  <chapter>
-    <title>Bugs</title>
-    <section>
-      <title>Reporting</title>
-      <body>
-        <p>
-          All good software has bugs. They are too many combinations of
-          compilers, USE flags and versions to test them all. So if
-          you find the time to report them, we would love to hear
-          about it. We have the standard bugzilla system for
-          this. Don't be afraid of all these fields to fill in, it's
-          not that bad!
-        </p>
-      </body>
-    </section>
-    <section>
-      <title>Resolving</title>
-      <body>
-        <p>
-	  The Scientific Team in Gentoo has always had a high number of
-	  bugs. Fortunately, many of them are new packages. Any help in resolving
-	  issues, improving submitted ebuilds is greatly appreciated.
-        </p>
-        <p>
-	  <uri link="http://tinyurl.com/2qxmvu">Bugs for the Scientific Team.</uri>
-	  <uri link="http://tinyurl.com/2nm6ag">Bugs for the Biology Team.</uri>
-	  <uri link="http://tinyurl.com/368f2d">Bugs for the Chemistry Team.</uri>
-	  <uri link="http://tinyurl.com/2lknlo">Bugs for the Electronics Team.</uri>
-	  <uri link="http://tinyurl.com/2pcntk">Bugs for the Mathematics Team.</uri>
-	  <uri link="http://tinyurl.com/3789aa">Bugs for the Physics Team.</uri>
-        </p>
-      </body>
-    </section>
-  </chapter>
-
-  <chapter>
-    <title>Writing ebuilds</title>
-    <section>
-      <body>
-        <p>
-	  You don't see your application in the main tree or in the
-	  overlays and you don't want to wait for someone else to
-	  create the ebuilds? The most obvious solution is to develop
-	  your own ebuilds. If you do so, it's always nice to share
-	  them. You can post them to our bugzilla system and then one
-	  of our devs will comment out. The <uri link="http://overlays.gentoo.org/proj/sunrise">sunrise
-	  overlay</uri> allows you more directly to commit your
-	  ebuilds if you don't want to wait for science access.
-	</p>
-      </body>
-    </section>
-  </chapter>
-
-  <chapter>
-    <title>Communication</title>
-    <section>
-      <title>Mailing List</title>
-      <body>
-        <p>
-          Join our
-          <uri link="http://www.gentoo.org/main/en/lists.xml"> gentoo-science mailing list
-          </uri> and asking/answering questions. 
-        </p>
-      </body>
-    </section>
-    <section>
-      <title>IRC</title>
-      <body>
-        <p>
-          Meet some of us in #gentoo-science. It is a fairly quiet
-          channel, but slowly growing and we are responsive. We can
-          answer your questions, help you developing your ebuilds,
-          share ideas, etc...
-        </p>
-      </body>
-    </section>
-      <title>Direct emails</title>
-      <body>
-        <p>
-	  If you feel your questions are more private and don't need
-	  to be known from the rest of the world, you can always
-	  directly send an email to our developers
-	  listed <uri link="http://www.gentoo.org/main/en/proj/science/index.xml">here</uri>
-	  and the listed sub-projects. If you want to mail all of us, send a mail to the herd.
-        </p>
-      </body>
-  </chapter>
-
-  <chapter>
-    <title>Writing Documentation</title>
-      <body>
-	<section>
-          <p>
-	    You may not be interested in fixing ebuilds and testing
-	    packages, but want to share your knowledge about some
-	    software, configuration or tips and tricks. The best way to
-	    do this is to write some documentation. You can even write
-	    official Gentoo documentation such as our
-	    <uri link="http://www.gentoo.org/main/en/proj/science/blas-lapack.xml">blas/lapack
-	      guide</uri>.
-	  </p>
-	</section>
-      </body>
-  </chapter>
-
-  <chapter>
-    <title>Seriously getting involved</title>
-    <section>
-      <body>
-        <p>
-          If you would like to join our team of volunteers and become
-          an official Gentoo Developer, show activity in anywhere you
-          can: bugzilla, overlays, mailing lists, irc, forums,...
-	  Please refer to
-	  <uri link="http://www.gentoo.org/proj/en/devrel/handbook/handbook.xml?part=1&amp;chap=2">
-	  Becoming a Developer</uri> in the
-	  <uri link="http://www.gentoo.org/proj/en/devrel/handbook/handbook.xml">
-	  Gentoo Developer Handbook</uri>.
-        </p>
-	<p> 
-	  Benefits are huge :-) :
-          <dl>
-            <dd>
-              <ul>
-		<li>Receive a warm welcome from us</li>
-		<li>Impress your geek friends</li>
-		<!--<li>Loose your social life, but</li>-->
-		<li>Get a free beer first time we meet in person!</li>
-              </ul>
-            </dd>
-          </dl>	  
-	</p>
-
-      </body>
-    </section>
-  </chapter>
-</guide>
diff --git a/docs/proj/index.xml b/docs/proj/index.xml
deleted file mode 100644
index 98656304d..000000000
--- a/docs/proj/index.xml
+++ /dev/null
@@ -1,107 +0,0 @@
-<?xml version="1.0" encoding="UTF-8"?>
-<?xml-stylesheet href="/xsl/project.xsl" type="text/xsl"?>
-<?xml-stylesheet href="/xsl/guide.xsl" type="text/xsl"?>
-<!DOCTYPE project SYSTEM "/dtd/project.dtd"> 
-
-<project>
-  <name>Science</name>
-  <longname>The Gentoo Scientific Project</longname>
-  <date>2009-01-21</date>
-  <author title="author">
-    <mail link="sci@gentoo.org">Science Team</mail>
-  </author>
-    
-  <description>
-    The Gentoo Scientific Project handles all Gentoo related Math and Science items.
-  </description>
-
-  <longdescription>
-    <p>
-      The Gentoo Scientific Project handles math and science related activities in Gentoo.
-      This includes maintaining packages that belong to various math
-      and science related herds, fortran compilers, documentations and communications.
-    </p>
-  </longdescription>
-
-  <goals>
-    <p>
-      The goals of Scientific Gentoo are to provide a simple but optimal
-      installation and configuration of a wide variety of math and
-      science applications. Scientific computing is an area where custom optimization
-      provides great benefit. We also provide tools to easily switch configurations, and relevant
-      documentations. We give special attention to ways to test the
-      packages, through regression suites, and benchmarks.
-    </p>
-  </goals>
-
-
-  <!-- Staff -->	
-  <dev role="member" description="General package maintainer">bicatali</dev>
-  <dev role="contributor" description="Ebuild development, general bug fixing, electronics and physics">dilfridge</dev>
-  <dev role="member" description="General package maintainer">je_fro</dev>
-  <dev role="contributor" description="Ebuild development (sage), general bug fixing and keep opendx running">kiwifb</dev>
-  <dev role="member" description="General package maintainer, g-octave developer">rafaelmartins</dev>
-  <dev role="member" description="General package maintainer">xarthisius</dev>
-  <dev role="member" description="g-cran developer">tulcod</dev>
-  <dev role="member" description="General package maintainer, sci-electronics">tomjbe</dev>
-  <dev role="my role in the science project" description="what i do mainly">dev-username</dev>
-
-  <!-- Subprojects 
-  <subproject ref="/proj/en/science/astronomy/index.xml" />
-  <subproject ref="/proj/en/science/biology/index.xml" />
-  <subproject ref="/proj/en/science/chemistry/index.xml" />
-  <subproject ref="/proj/en/science/electronics/index.xml" />
-  <subproject ref="/proj/en/science/math/index.xml" />
-  <subproject ref="/proj/en/science/physics/index.xml" />
-  -->
-
-  <resource link="blas-lapack.xml">Guide on using BLAS/LAPACK</resource>
-  <resource link="contrib.xml">Guide on contributing to the science project</resource>
-  <resource link="http://overlays.gentoo.org/proj/science">Official overlay</resource>
-  <resource link="http://news.gmane.org/gmane.linux.gentoo.science/">Mailing list archives</resource>
-  <resource link="irc://irc.freenode.net/gentoo-science">#gentoo-science IRC Channel</resource>
-
-<extrachapter position="bottom">
-<title>The Science Overlay</title>
-<section>
-<body>
-<p>
-  New packages and more complex version bumps are held in
-  an <uri link="http://overlays.gentoo.org/proj/science/">Overlay</uri>. They
-  help both the science and hp-cluster team and the wiki contains some
-  temporary information.
-</p>
-</body>
-</section>
-</extrachapter>
-
-<recruitment>
-  <job>
-    <summary>Scientific package maintainer</summary>
-    <details>
-      The sci team and its various subprojects are always looking for a
-      general package maintainer to help our understaffed
-      team. Tasks are troubleshooting, version bumping and
-      stabilizing, new ebuilds and eclassed introduction.
-    </details>
-    <requirements>
-      Experience with Linux, various package build systems (autotools, cmake)
-      and makefiles, and bash.
-    </requirements>
-    <contact>sci</contact>
-  </job>
-  <job>
-    <summary>CAD Programs</summary>
-    <details>
-      Computer Aided Design open source programs are getting more popular
-      and yet to have decent support in Gentoo. We need to put an end
-      on this.
-    </details>
-    <requirements>
-      Knowledge of a few CAD programs and good ebuild skills.
-    </requirements>
-    <contact>sci</contact>
-  </job>
-</recruitment>
-
-</project>
diff --git a/docs/proj/linalg.xml b/docs/proj/linalg.xml
deleted file mode 100644
index 02ce98bf4..000000000
--- a/docs/proj/linalg.xml
+++ /dev/null
@@ -1,530 +0,0 @@
-<?xml version="1.0" encoding="UTF-8"?>
-<!DOCTYPE guide SYSTEM "/dtd/guide.dtd">
-
-<guide link="/proj/en/science/linalg.xml">
-<title>Linear Algebra on Gentoo</title>
-
-<author title="Author">
-  <mail link="bicatali@gentoo.org">Sébastien Fabbro</mail>
-</author>
-
-<abstract>
-  This guide explains the use of linear algebra libraries and focus on
-  how to use the different implementations of BLAS and LAPACK available on Gentoo.
-</abstract>
-
-<!-- The content of this document is licensed under the CC-BY-SA license -->
-<!-- See http://creativecommons.org/licenses/by-sa/2.5 -->
-<license/>
-
-<version>1.0</version>
-<date>2010-12-22</date>
-
-<chapter>
-<title>Introduction</title>
-<section>
-<body>
-
-<p>
-  There are <uri link="http://en.wikipedia.org/wiki/List_of_numerical_libraries">many</uri>
-  performant numerical libraries available. 
-  The Basic Linear Algebra Subprograms (BLAS) and the Linear Algebra PACKage (LAPACK)
-  are well designed linear algebra libraries developed by the
-  High Performance Computing (HPC) community. BLAS is an API of dense
-  matrix and vectors products, while LAPACK provides routines for
-  solving systems of linear equations. Both are widely used in
-  many scientific applications and it is, therefore, important to 
-  have efficient implementations available.
-</p>
-
-<p>
-  BLAS and LAPACK were originally written in FORTRAN 77. Since then, a
-  number of additional language wrappers have been developed for
-  languages like C, C++, FORTRAN 95, Java, Python, etc...
-  Netlib offers exact implementations of the APIs and they are called
-  "reference" libraries.
-</p>
-
-<ul>
-<li>
-  <uri link="http://www.netlib.org/blas/">BLAS</uri>: FORTRAN 77 and C
-  (CBLAS) implementations of BLAS
-</li>
-<li>
-  <uri link="http://www.netlib.org/lapack/">LAPACK</uri>: FORTRAN 77 and
-  C (LAPACKE) implementations of LAPACK
-</li>
-</ul>
-
-<p>
-  
-</p>
-
-<ul>
-<li>
-  <uri link="http://www.netlib.org/blacs/">BLACS</uri>: FORTRAN 77 and C
-  implementations of BLACS
-</li>
-<li>
-  <uri link="http://www.netlib.org/scalapack/">ScaLAPACK</uri>: FORTRAN 77 and
-  C implementations of PBLAS and ScaLAPACK
-</li>
-</ul>
-
-<p>
-  In addition, Gentoo provides a number of optimized implementations
-  of the above linear algebra libraries that will be described
-  below. You can switch between implementations with the
-  Gentoo's <c>eselect</c> system and the widely used <c>pkg-config</c>
-  tool.
-</p>
-
-<p>
-  It is important to note that if you require, e.g., a well performing 
-  BLAS implementation, simply emerging X over Y often is not enough. Rather, you will have
-  to carefully benchmark your applications since performance may depend 
-  on many factors,
-  such as hardware or network.
-  If you are simply looking for a well performing and well tested
-  implementation, the reference ebuilds will likely be your best choice.
-</p>
-
-
-</body>
-</section>
-</chapter>
-
-<chapter>
-<title>For Users</title>
-<section>
-<title>Installing</title>
-<body>
-
-<p>
-  If best possible performance is not of paramount importance for you 
-  and you simply need BLAS and/or LAPACK, just emerge the virtual
-  package:
-</p>
-
-<pre caption="Installing">
-# <i>emerge lapack</i>
-</pre>
-
-<p>
-  This will install both <><> and <><> the reference packages from
-  <uri>http://www.netlib.org/</uri> . They are well tested, easy to debug
-  implementations. They should satisfy most users; if they're all you need, you're
-  done reading.
-</p>
-
-<p>
-However, if:
-</p>
-
-<ul>
-  <li>linear algebra libraries are critical for the speed of your applications</li>
-  <li>you absolutely need to build the fastest computer</li>
-  <li>you want to help Gentoo sci project to improve their packages</li>
-</ul>
-
-<p>
-... then read on, and be sure to file bugs both to Gentoo and upstream.
-</p>
-
-<p>
-  There is a number of optimized implementations of these libraries in the Portage
-  tree:
-</p>
-
-<ul>
-  <li>
-   <uri link="http://math-atlas.sourceforge.net">ATLAS</uri>: Automatically
-   Tuned Linear Algebra Software is an open-source package that empirically
-   tunes the library to the machine it is being compiled on. It provides BLAS
-   (FORTRAN 77 and C), and LAPACK implementations on various architectures.
-  </li>
-  <li>
-   <uri
-   link="http://www.tacc.utexas.edu/tacc-projects/gotoblas2/">GotoBLAS</uri>:
-   Goto BLAS provides open-source, free for academic use, hand-coded
-   machine language, processor optimized versions of the FORTRAN 77
-   and C BLAS routines. Still claims to be the fastest BLAS.
-  </li>
-  <li>
-    <uri link="http://software.intel.com/en-us/articles/intel-mkl/">MKL</uri>:
-    Intel® Math Kernel Library is a closed-source but free package for
-    non-commercial use on Linux systems containing implementations of all the linear
-    algebra libraries mentioned here.
-  </li>
-</ul>
-
-<p>
-  Usually performance gain is noticeable mainly with BLAS, since LAPACK routines
-  depend on BLAS kernels.
-</p>
-
-</body>
-</section>
-
-
-<section>
-<title>Developping with the installed linear algebra libraries</title>
-<body>
-
-<p>
-  We took great care to make sure that each package provides
-  consistent pkg-config files generated by us.
-  Compiling and linking becomes straightforward:
-</p>
-
-<pre caption="Compiling and linking linear algebra libraries">
-# <i>pkg-config --libs blas</i>    <comment>(To link with FORTRAN 77 BLAS library)</comment>
-# <i>pkg-config --cflags cblas</i> <comment>(To compile against C BLAS library)</comment>
-# <i>pkg-config --libs cblas</i>   <comment>(To link with C BLAS library)</comment>
-# <i>pkg-config --libs scalapack</i>  <comment>(To link with the ScaLAPACK library)</comment>
-</pre>
-
-<p>
-  <c>pkg-config</c> files are available for all implementations and
-  various alternatives within implementations. The default names of
-  the implementations are: blas, cblas, lapack, lapacke, blacs and
-  scalapack, and they can be chosen with <c>eselect</c>. You can also always compile or link
-  with an library not selected for the 
-  More information on using <c>pkg-config</c> can be obtained with <c>man pkg-config</c>. 
-</p>
-
-</body>
-</section>
-<section>
-<title>Selecting libraries</title>
-<body>
-
-<p>
-  You can switch BLAS, CBLAS and LAPACK implementations with
-  <c>eselect</c>. you can view which implementations of CBLAS
-  are available.
-</p>
-
-<pre caption="Viewing available implementations of CBLAS">
-# <i>eselect cblas list</i>
-Installed CBLAS for library directory lib64
-[1]   atlas
-[2]   atlas-threads
-[3]   gsl
-[4]   mkl-threads *
-[5]   reference
-</pre>
-
-<p>
-  The implementation marked with an asterisk (*) is the currently
-  selected implementation. To switch implementations, run:
-</p>
-
-<pre caption="Switching to the threaded ATLAS implementation of BLAS">
-# <i>eselect blas set atlas-threads</i>
-</pre>
-
-<p>
-  To learn more about the <c>eselect</c> tool, visit the 
-  <uri link="http://www.gentoo.org/proj/en/eselect/user-guide.xml">eselect guide</uri>
-</p>
-
-<p>
-  When selecting your linear algebra profiles try to avoid mixing
-  different implementations since we don't have any mechanism to enforce
-  reasonable profiles. However, here is a list of well performing
-  profile combinations that have been used successfully in the past:
-</p>
-<ul>
-  <li> performant on most CPUs:
-    <ul>
-      <li>blas, cblas: atlas (or atlas-threads with multi-processor)</li>
-      <li>lapack, lapacke: atlas</li>
-    </ul>
-  </li>
-  <li> performant on most CPUs:
-    <ul>
-      <li>blas, cblas: goto2 </li>
-      <li>lapack, lapacke: reference</li>
-    </ul>
-  </li>
-  <li> performant on AMD based CPUs:
-    <ul>
-      <li>cblas: reference</li>
-    </ul>
-  </li>
-  <li> performant on Intel based CPUs:
-    <ul>
-      <li>blas,cblas,lapack: mkl-threads</li>
-    </ul>
-  </li>
-</ul>
-
-</body>
-</section>
-
-<section>
-<title>Choosing a compiler</title>
-<body>
-
-<p>
-  All the above libraries have been tested with the GNU compiler
-  collections (gcc, gfortran).
-  There are many available C compilers and a few FORTRAN (ifort,
-  Open64) compilers on Gentoo and many other FORTRAN compilers outside
-  of Gentoo ().
-</p>
-
-<pre caption="Installing BLAS with the Intel FORTRAN compiler">
-# <i>F77=ifort FFLAGS="-O2 -mp1" emerge blas-reference</i>
-</pre>
-
-<p>
-  Depending on your hardware, a small performance gain can be noticed thanks to
-  vectorization. The <c>-mp</c> flag maintains floating-point precision, since by
-  default ifort is pretty aggressive on floating point arithmetic, and we are
-  actually compiling a math package. Try <c>man ifort</c> to see additional flags
-  to fit your hardware.
-</p>
-
-<p>
-  Some of the implementations let you specify the Intel® C compiler as
-  well. Please beware that not all libraries compile with all
-  combinations.  You should receive an error during the emerge in case you have
-  chosen an incompatible combination.
-</p>
-
-<p>
-  As usual for Gentoo, there are many combinations of USE flags and
-  compilers with which you could compile a package. Unfortunately
-  switching compilers between BLAS and LAPACK might not be always
-  compatible. For example: 
-</p>
-
-<pre caption="Looking for trouble combinations">
-# <i>FC=gfortran FFLAGS="-O2" emerge lapack-reference</i>
-</pre>
-
-<p>
-  This will most likely break things or not even compile.
-</p>
-
-<p>
-  Try to be consistent in your choice. Stay with the GCC most of the time will
-  avoid you some trouble, unless you want to use the MKL, in which case the Intel
-  compilers make a good combination.
-</p>
-
-</body>
-</section>
-<section>
-<title>Documentation</title>
-<body>
-
-<p>
-  If you need BLAS or LAPACK to develop your own programs, the documentation
-  becomes pretty handy. Setting the USE="doc" flag for the corresponding BLAS or
-  LAPACK package will install man pages and quick reference sheets from the
-  <c>app-doc/blas-docs</c> and <c>app-doc/lapack-docs</c> packages. They are
-  standard and valid for all implementations. For optimized packages, the
-  USE="doc" flags will usually install extra doc in PDF or HTML format.
-</p>
-
-</body>
-</section>
-</chapter>
-
-<chapter>
-<title>For ebuild developers</title>
-<section>
-
-<section>
-<title>Packages with BLAS/LAPACK dependencies</title>
-<body>
-
-<p>
-  You need two things:
-  set [R]DEPEND to <c>virtual/<imp></c>. To build some
-  packages, you m need to use the pkg-config tool. If you are lucky, the
-  package uses autotools together with the autoconf <>AX_BLAS and <>AX_LAPACK M4
-  macros. In this case, the configuration step becomes simple. For example:
-</p>
-
-<pre caption="Sample package configuration with autotools">
-<keyword>econf</keyword> --with-blas="<var>$(pkg-config --libs blas)</var>"
-</pre>
-
-</body>
-</section>
-
-
-
-<title>Providing new implementations</title>
-<body>
-
-<p>
-  The Portage tree contains many ebuilds that depend on the
-  BLAS/CBLAS/LAPACK/BLACS/ScaLAPACK libraries. As there is more than
-  one possible implementation, the Gentoo Science Project
-  reorganized all the packages to provide <c>virtual</c>. All ebuilds using
-  should depend on this virtual package, unless it is explicitly
-  known to break with a specific implementation.
-</p>
-
-<p>
-  To work with Gentoo's configuration tools
-  <c>app-admin/eselect-{blas,cblas,lapack}</c>, and the virtual, every ebuild that
-  installs a BLAS implementation must fulfill following requirements:
-</p>
-
-<ol>
-<li>
-  The ebuild must install an eselect file for each profile it provides. The
-  libraries should link to the ones in <path>/usr/$(get_libdir)</path>
-  directories and the include files in <path>/usr/include</path>:
- <ul>
-      <li>
-	<path>libblas.so[.0]</path> - Shared object for FORTRAN BLAS
-	applications
-      </li>
-      <li>
-        <path>libblas.a</path> - Static library for FORTRAN BLAS applications
-      </li>
-      <li>
-        <path>libcblas.so[.0]</path> - Shared object for C/C++ CBLAS applications
-      </li>
-      <li>
-        <path>libcblas.a</path> - Static library for C/C++ CBLAS applications
-      </li>
-      <li><path>cblas.h</path> - Include header for C/C++ applications</li>
-      <li>
-        <path>liblapack.so[.0]</path> - Shared object for FORTRAN LAPACK
-	applications
-      </li>
-      <li>
-        <path>liblapack.a</path> - Static library for FORTRAN LAPACK applications
-      </li>
-    </ul>
-  </li>
-  <li>
-    The ebuild must install a <path>blas.pc</path>, <path>cblas.pc</path> and/or
-    <path>lapack.pc</path> pkg-config file and therefore RDEPEND on
-    <c>dev-util/pkgconfig</c>.  They should also be included in the eselect
-    files, and link to the <path>/usr/$(get_libdir)/pkgconfig</path> directory:
-    <ul>
-      <li><path>blas.pc</path> - BLAS pkg-config file</li>
-      <li><path>cblas.pc</path> - CBLAS pkg-config file</li>
-      <li><path>lapack.pc</path> - LAPACK pkg-config file</li>
-    </ul>
-  </li>
-  <li>Be included in the virtual package as a possible provider:
-    <ul>
-      <li><c>virtual/blas</c> - BLAS virtual package</li>
-      <li><c>virtual/cblas</c> - CBLAS virtual package</li>
-      <li><c>virtual/lapack</c> - LAPACK virtual package</li>
-    </ul>
-  </li>
-</ol>
- 
-<p>
-  The easiest way of understanding all this is probably getting inspiration from
-  one of the available packages. Currently the Portage tree provide the following
-  virtual packages:
-</p>
-
-<table>
-<tr>
-  <th>Package name</th>
-  <th>virtual/blas</th>
-  <th>virtual/cblas</th>
-  <th>virtual/lapack</th>
-  <th>virtual/lapacke</th>
-  <th>virtual/blacs</th>
-  <th>virtual/scalapack</th>
-</tr>
-<tr>
-  <ti><c>sci-libs/atlas</c></ti>
-  <ti>*</ti>
-  <ti>*</ti>
-  <ti>*</ti>
-  <ti>*</ti>
-  <ti></ti>
-  <ti></ti>
-</tr>
-<tr>
-  <ti><c>sci-libs/gotoblas2</c></ti>
-  <ti>*</ti>
-  <ti>*</ti>
-  <ti></ti>
-  <ti></ti>
-  <ti></ti>
-  <ti></ti>
-</tr>
-<tr>
-  <ti><c>sci-libs/blas-reference</c></ti>
-  <ti>*</ti>
-  <ti></ti>
-  <ti></ti>
-  <ti></ti>
-  <ti></ti>
-  <ti></ti>
-</tr>
-<tr>
-  <ti><c>sci-libs/cblas-reference</c></ti>
-  <ti></ti>
-  <ti>*</ti>
-  <ti></ti>
-  <ti></ti>
-  <ti></ti>
-  <ti></ti>
-</tr>
-<tr>
-  <ti><c>sci-libs/gsl</c></ti>
-  <ti></ti>
-  <ti>*</ti>
-  <ti></ti>
-  <ti></ti>
-  <ti></ti>
-  <ti></ti>
-</tr>
-<tr>
-  <ti><c>sci-libs/lapack-reference</c></ti>
-  <ti></ti>
-  <ti></ti>
-  <ti>*</ti>
-  <ti></ti>
-  <ti></ti>
-  <ti></ti>
-</tr>
-<tr>
-  <ti><c>sci-libs/mkl</c></ti>
-  <ti>*</ti>
-  <ti>*</ti>
-  <ti>*</ti>
-  <ti>*</ti>
-  <ti>*</ti>
-  <ti>*</ti>
-</tr>
-</table>
-
-</body>
-</section>
-
-</chapter>
-
-<chapter>
-<title>Benchmarks</title>
-<section>
-<body>
-
-<p>
-  If you feel inclined to write an ebuild for these, you
-  are more than welcomed to file it on our <uri
-  link="http://bugs.gentoo.org">Bugzilla</uri>.
-</p>
-
-</body>
-</section>
-</chapter>
-
-</guide>
diff --git a/eclass/alternatives-2.eclass b/eclass/alternatives-2.eclass
deleted file mode 100644
index 7237f0db3..000000000
--- a/eclass/alternatives-2.eclass
+++ /dev/null
@@ -1,142 +0,0 @@
-# Copyright 2010-2017 Gentoo Foundation
-# Distributed under the terms of the GNU General Public License v2
-
-# Based in part upon 'alternatives.exlib' from Exherbo, which is:
-# Copyright 2008, 2009 Bo Ørsted Andresen
-# Copyright 2008, 2009 Mike Kelly
-# Copyright 2009 David Leverton
-
-# @ECLASS: alternatives-2.eclass
-# @MAINTAINER:
-# Gentoo Science Project <sci@gentoo.org>
-# @BLURB: Manage alternative implementations.
-# @DESCRIPTION:
-# Autogenerate eselect modules for alternatives and ensure that valid provider
-# is set.
-#
-# Remove eselect modules when last provider is unmerged.
-#
-# If your package provides pkg_postinst or pkg_prerm phases, you need to be
-# sure you explicitly run alternatives-2_pkg_{postinst,prerm} where appropriate.
-
-case "${EAPI:-0}" in
-	0|1|2|3|4)
-		die "Unsupported EAPI=${EAPI:-0} (too old) for ${ECLASS}"
-		;;
-	5|6|7)
-		;;
-	*)
-		die "Unsupported EAPI=${EAPI} (unknown) for ${ECLASS}"
-		;;
-esac
-
-DEPEND=">=app-admin/eselect-1.4.13-r101"
-RDEPEND="${DEPEND}
-	!app-eselect/eselect-blas
-	!app-eselect/eselect-cblas
-	!app-eselect/eselect-lapack"
-
-# @ECLASS-VARIABLE: ALTERNATIVES_DIR
-# @INTERNAL
-# @DESCRIPTION:
-# Alternatives directory with symlinks managed by eselect.
-ALTERNATIVES_DIR="/etc/env.d/alternatives"
-
-# @FUNCTION: alternatives_for
-# @USAGE: <alternative> <provider> <importance> <source> <target> [<source> <target> [...]]
-# @DESCRIPTION:
-# Set up alternative provider.
-#
-# EXAMPLE:
-# @CODE
-# alternatives_for sh bash 0 \
-#     /usr/bin/sh bash
-# @CODE
-alternatives_for() {
-	debug-print-function ${FUNCNAME} "${@}"
-
-	dodir /etc/env.d/alternatives
-
-	ALTERNATIVESDIR_ROOT="${D%/}" \
-		eselect alternatives add ${@} || die
-
-	ALTERNATIVES_CREATED+=( ${1} )
-}
-
-# @FUNCTION: cleanup_old_alternatives_module
-# @USAGE: <alternative>
-# @DESCRIPTION:
-# Remove old alternatives module.
-cleanup_old_alternatives_module() {
-	debug-print-function ${FUNCNAME} "${@}"
-
-	local alt=${1} old_module="${EROOT%/}/usr/share/eselect/modules/${alt}.eselect"
-
-	if [[ -f "${old_module}" && $(grep 'ALTERNATIVE=' "${old_module}" | cut -d '=' -f 2) == "${alt}" ]]; then
-		local version="$(grep 'VERSION=' "${old_module}" | grep -o '[0-9.]\+')"
-		if [[ "${version}" == "0.1" || "${version}" == "20080924" ]]; then
-			einfo "rm ${old_module}"
-			rm "${old_module}" || eerror "rm ${old_module} failed"
-		fi
-	fi
-}
-
-# @FUNCTION: alternatives-2_pkg_postinst
-# @DESCRIPTION:
-# Create eselect modules for all provided alternatives if necessary and ensure
-# that valid provider is set.
-#
-# Also remove old eselect modules for provided alternatives.
-#
-# Provided alternatives are set up using alternatives_for().
-alternatives-2_pkg_postinst() {
-	debug-print-function ${FUNCNAME} "${@}"
-
-	local alt
-
-	for alt in ${ALTERNATIVES_CREATED[@]}; do
-		if ! eselect ${alt} show > /dev/null; then
-			einfo "Creating Alternative for ${alt}"
-			eselect alternatives create ${alt}
-		fi
-
-		# Set alternative provider if there is no valid provider selected
-		eselect alternatives update "${alt}"
-
-		cleanup_old_alternatives_module ${alt}
-	done
-}
-
-# @FUNCTION: alternatives-2_pkg_prerm
-# @DESCRIPTION:
-# Ensure a valid provider is set in case the package is unmerged and
-# remove autogenerated eselect modules for alternative when last
-# provider is unmerged.
-#
-# Provided alternatives are set up using alternatives_for().
-alternatives-2_pkg_prerm() {
-	debug-print-function ${FUNCNAME} "${@}"
-
-	local alt ret
-
-	# If we are uninstalling, update alternatives to valid provider
-	[[ -n ${REPLACED_BY_VERSION} ]] || ignore="--ignore"
-	for alt in ${ALTERNATIVES_CREATED[@]}; do
-		eselect alternatives update "${alt}"
-		ret=$?
-
-		case ${ret} in
-			0) : ;;
-			2)
-				# This was last provider for the alternative, remove eselect module
-				einfo "Cleaning up unused alternatives module for ${alt}"
-				eselect alternatives delete "${alt}" || eerror "Failed to remove ${alt}"
-				;;
-			*)
-				eerror "eselect alternatives update returned \"${ret}\""
-				;;
-		esac
-	done
-}
-
-EXPORT_FUNCTIONS pkg_postinst pkg_prerm
diff --git a/eclass/intel-sdp-r1.eclass b/eclass/intel-sdp-r1.eclass
deleted file mode 100644
index 12d1f868d..000000000
--- a/eclass/intel-sdp-r1.eclass
+++ /dev/null
@@ -1,571 +0,0 @@
-# Copyright 1999-2017 Gentoo Foundation
-# Distributed under the terms of the GNU General Public License v2
-
-# @ECLASS: intel-sdp-r1.eclass
-# @MAINTAINER:
-# Justin Lecher <jlec@gentoo.org>
-# David Seifert <soap@gentoo.org>
-# Sci Team <sci@gentoo.org>
-# @BLURB: Handling of Intel's Software Development Products package management
-
-MULTILIB_COMPAT=( abi_x86_{32,64} )
-
-inherit check-reqs eutils multilib-build versionator
-
-EXPORT_FUNCTIONS src_unpack src_install pkg_postinst pkg_postrm pkg_pretend
-
-if [[ ! ${_INTEL_SDP_R1_ECLASS_} ]]; then
-
-case "${EAPI}" in
-	6) ;;
-	*) die "EAPI=${EAPI} is not supported" ;;
-esac
-
-# @ECLASS-VARIABLE: INTEL_DIST_NAME
-# @DESCRIPTION:
-# The package name to download from Intel.
-# To determine its value, see the links to download in
-# https://registrationcenter.intel.com/RegCenter/MyProducts.aspx
-#
-# e.g. parallel_studio_xe
-#
-# Must be defined before inheriting the eclass.
-: ${INTEL_DIST_NAME:=parallel_studio_xe}
-
-# @ECLASS-VARIABLE: INTEL_DIST_PV
-# @DEFAULT_UNSET
-# @DESCRIPTION:
-# The package download version from Intel.
-# To determine its value, see the links to download in
-# https://registrationcenter.intel.com/RegCenter/MyProducts.aspx
-#
-# e.g. 2016_update1
-#
-# Must be defined before inheriting the eclass.
-
-# @ECLASS-VARIABLE: INTEL_DIST_TARX
-# @DESCRIPTION:
-# The package distfile suffix.
-# To determine its value, see the links to download in
-# https://registrationcenter.intel.com/RegCenter/MyProducts.aspx
-#
-# e.g. tgz
-#
-# Must be defined before inheriting the eclass.
-: ${INTEL_DIST_TARX:=tgz}
-
-# @ECLASS-VARIABLE: INTEL_SUBDIR
-# @DESCRIPTION:
-# The package sub-directory (without version numbers) where it will end-up in /opt/intel
-#
-# e.g. compilers_and_libraries
-#
-# To determine its value, you have to do a raw install from the Intel tarball.
-: ${INTEL_SUBDIR:=compilers_and_libraries}
-
-# @ECLASS-VARIABLE: INTEL_SKIP_LICENSE
-# @DEFAULT_UNSET
-# @DESCRIPTION:
-# Possibility to skip the mandatory check for licenses. Only set this if there
-# is really no fix.
-
-# @ECLASS-VARIABLE: INTEL_RPMS_DIR
-# @DESCRIPTION:
-# Main subdirectory which contains the rpms to extract.
-: ${INTEL_RPMS_DIR:=rpm}
-
-# @ECLASS-VARIABLE: INTEL_DIST_BIN_RPMS
-# @DESCRIPTION:
-# Functional name of rpm without any version/arch tag.
-# Has to be a bash array
-#
-# e.g. ("icc-l-all-devel")
-#
-# if the rpm is located in a directory other than INTEL_RPMS_DIR you can
-# specify the full path
-#
-# e.g. ("CLI_install/rpm/intel-vtune-amplifier-xe-cli")
-[[ ${INTEL_DIST_BIN_RPMS[@]} ]] || INTEL_DIST_BIN_RPMS=()
-
-# @ECLASS-VARIABLE: INTEL_DIST_AMD64_RPMS
-# @DESCRIPTION:
-# AMD64 single arch rpms. Same syntax as INTEL_DIST_BIN_RPMS.
-# Has to be a bash array.
-[[ ${INTEL_DIST_AMD64_RPMS[@]} ]] || INTEL_DIST_AMD64_RPMS=()
-
-# @ECLASS-VARIABLE: INTEL_DIST_X86_RPMS
-# @DESCRIPTION:
-# X86 single arch rpms. Same syntax as INTEL_DIST_BIN_RPMS.
-# Has to be a bash array.
-[[ ${INTEL_DIST_X86_RPMS[@]} ]] || INTEL_DIST_X86_RPMS=()
-
-# @ECLASS-VARIABLE: INTEL_DIST_DAT_RPMS
-# @DESCRIPTION:
-# Functional name of rpm of common data which are arch free
-# without any version tag. Has to be a bash array.
-#
-# e.g. ("openmp-l-all-devel")
-#
-# if the rpm is located in a directory different to INTEL_RPMS_DIR you can
-# specify the full path
-#
-# e.g. ("CLI_install/rpm/intel-vtune-amplifier-xe-cli-common")
-[[ ${INTEL_DIST_DAT_RPMS[@]} ]] || INTEL_DIST_DAT_RPMS=()
-
-# @ECLASS-VARIABLE: INTEL_DIST_SPLIT_ARCH
-# @DESCRIPTION:
-# Set to "true" if arches are to be fetched separately, instead of using
-# the combined tarball.
-: ${INTEL_DIST_SPLIT_ARCH:=false}
-
-# @FUNCTION: _isdp_path_exists
-# @INTERNAL
-# @USAGE: [-a|-o] <paths>
-# @DESCRIPTION:
-# Check if the specified paths exist.  Works for all types of paths
-# (files/dirs/etc...).  The -a and -o flags control the requirements
-# of the paths.  They correspond to "and" and "or" logic.  So the -a
-# flag means all the paths must exist while the -o flag means at least
-# one of the paths must exist.  The default behavior is "and".  If no
-# paths are specified, then the return value is "false".
-_isdp_path_exists() {
-       local opt=$1
-       [[ ${opt} == -[ao] ]] && shift || opt="-a"
-
-       # no paths -> return false
-       # same behavior as: [[ -e "" ]]
-       [[ $# -eq 0 ]] && return 1
-
-       local p r=0
-       for p in "$@" ; do
-               [[ -e ${p} ]]
-               : $(( r += $? ))
-       done
-
-       case ${opt} in
-               -a) return $(( r != 0 )) ;;
-               -o) return $(( r == $# )) ;;
-       esac
-       eerror "path_exists has been removed.  Please see the following post"
-       eerror "for a replacement snippet:"
-       eerror "https://blogs.gentoo.org/mgorny/2018/08/09/inlining-path_exists/"
-       die "path_exists is banned"
-}
-
-# @FUNCTION: _isdp_get-sdp-year
-# @INTERNAL
-# @DESCRIPTION:
-# Gets the year component from INTEL_DIST_PV
-_isdp_get-sdp-year() {
-	local _intel_sdp_year
-	_intel_sdp_year=${INTEL_DIST_PV}
-	_intel_sdp_year=${_intel_sdp_year%_sp*}
-	_intel_sdp_year=${_intel_sdp_year%_update*}
-	echo "${_intel_sdp_year}"
-}
-
-# @FUNCTION: isdp_get-sdp-dir
-# @DESCRIPTION:
-# Gets the full rootless path to the installation directory
-#
-#     e.g. opt/intel/compilers_and_libraries_2016.1.150
-#          opt/intel/vtune_amplifier_2018.2.0.551022
-isdp_get-sdp-dir() {
-	local _intel_sdp_dir="opt/intel/${INTEL_SUBDIR}_$(_isdp_get-sdp-year).$(get_version_component_range 3-)"
-	echo "${_intel_sdp_dir}"
-}
-
-# @FUNCTION: isdp_get-sdp-edir
-# @DESCRIPTION:
-# Gets the full rooted/prefixed path to the installation directory
-#
-#     e.g. /opt/intel/compilers_and_libraries_2016.1.150
-isdp_get-sdp-edir() {
-	local _intel_sdp_edir="${EPREFIX%/}/$(isdp_get-sdp-dir)"
-	echo "${_intel_sdp_edir}"
-}
-
-SRC_URI="${INTEL_DIST_NAME}_${INTEL_DIST_PV}.${INTEL_DIST_TARX}"
-LICENSE="Intel-SDP"
-# TODO: Proper slotting
-# Future work, #394411
-SLOT="0"
-
-RESTRICT="mirror fetch"
-
-RDEPEND=""
-DEPEND="app-arch/rpm2targz"
-
-S="${WORKDIR}"
-
-QA_PREBUILT="$(isdp_get-sdp-dir)/*"
-
-# @FUNCTION: isdp_convert2intel-arch
-# @USAGE: <arch>
-# @DESCRIPTION:
-# Convert between portage arch (e.g. amd64, x86) and intel installed arch
-# nomenclature (e.g. intel64, ia32)
-isdp_convert2intel-arch() {
-	debug-print-function ${FUNCNAME} "${@}"
-
-	case $1 in
-		*amd64*|abi_x86_64)
-			echo "intel64"
-			;;
-		*x86*)
-			echo "ia32"
-			;;
-		*)
-			die "Abi \'$1\' is unsupported"
-			;;
-	esac
-}
-
-# @FUNCTION: isdp_get-native-abi-arch
-# @DESCRIPTION:
-# Determine the the intel arch string of the native ABI
-isdp_get-native-abi-arch() {
-	debug-print-function ${FUNCNAME} "${@}"
-
-	use amd64 && echo "$(isdp_convert2intel-arch abi_x86_64)"
-	use x86 && echo "$(isdp_convert2intel-arch abi_x86_32)"
-}
-
-# @FUNCTION: isdp_get-sdp-installed-arches
-# @DESCRIPTION:
-# Returns a space separated list of the arch suffixes used in directory
-# names for enabled ABIs. Intel uses "ia32" for x86 and "intel64" for
-# amd64. The result would be "ia32 intel64" if both ABIs were enabled.
-isdp_get-sdp-installed-arches() {
-	local arch=()
-	use abi_x86_64 && arch+=($(isdp_convert2intel-arch abi_x86_64))
-	use abi_x86_32 && arch+=($(isdp_convert2intel-arch abi_x86_32))
-	echo "${arch[*]}"
-}
-
-# @FUNCTION: _isdp_generate-list-install-rpms
-# @INTERNAL
-# @DESCRIPTION:
-# Generates the list of fully expanded RPMs to be extracted.
-_isdp_generate-list-install-rpms() {
-	debug-print-function ${FUNCNAME} "${@}"
-
-	# Expand components into full RPM filenames
-	expand_component_into_full_rpm() {
-		local deref_var="${1}[@]"
-		local p rpm_prefix expanded_full_rpms=()
-
-		for p in "${!deref_var}"; do
-			# check if a directory is prefixed
-			if [[ "${p}" == "${p##*/}" ]]; then
-				rpm_prefix="${INTEL_RPMS_DIR}/intel-"
-			else
-				rpm_prefix=""
-			fi
-			expanded_full_rpms+=( "${rpm_prefix}${p}" )
-		done
-		echo ${expanded_full_rpms[*]}
-	}
-
-	local vars_to_expand=("INTEL_DIST_BIN_RPMS" "INTEL_DIST_DAT_RPMS")
-	if use abi_x86_32; then
-		vars_to_expand+=("INTEL_DIST_X86_RPMS")
-	fi
-	if use abi_x86_64; then
-		vars_to_expand+=("INTEL_DIST_AMD64_RPMS")
-	fi
-
-	local i fully_expanded_intel_rpms=()
-	for ((i=0; i<${#vars_to_expand[@]}; i++)); do
-		fully_expanded_intel_rpms+=($(expand_component_into_full_rpm "${vars_to_expand[i]}"))
-	done
-	echo ${fully_expanded_intel_rpms[*]}
-}
-
-# @FUNCTION: _isdp_big-warning
-# @USAGE: [pre-check | test-failed]
-# @INTERNAL
-# @DESCRIPTION:
-# warn user that we really require a license
-_isdp_big-warning() {
-	debug-print-function ${FUNCNAME} "${@}"
-
-	case ${1} in
-		pre-check )
-			ewarn "License file not found!"
-			;;
-
-		test-failed )
-			ewarn "Function test failed. Most probably due to an invalid license."
-			ewarn "This means you already tried to bypass the license check once."
-			;;
-	esac
-
-	ewarn
-	ewarn "Make sure you have received an Intel license."
-	ewarn "To receive a non-commercial license, you need to register at:"
-	ewarn "https://software.intel.com/en-us/qualify-for-free-software"
-	ewarn "Install the license file into ${EPREFIX}/opt/intel/licenses"
-
-	case ${1} in
-		pre-check )
-			ewarn "before proceeding with installation of ${P}"
-			;;
-		* )
-			;;
-	esac
-}
-
-# @FUNCTION: _isdp_version_test
-# @INTERNAL
-# @DESCRIPTION:
-# Testing for valid license by asking for version information of the compiler.
-_isdp_version_test() {
-	debug-print-function ${FUNCNAME} "${@}"
-
-	local comp
-	case ${PN} in
-		ifc )
-			debug-print "Testing ifort"
-			comp=ifort
-			;;
-		icc )
-			debug-print "Testing icc"
-			comp=icc
-			;;
-		*)
-			die "${PN} is not supported for testing"
-			;;
-	esac
-
-	local comp_full arch warn
-	for arch in $(isdp_get-sdp-installed-arches); do
-		case ${EBUILD_PHASE} in
-			install )
-				comp_full="${ED%/}/$(isdp_get-sdp-dir)/linux/bin/${arch}/${comp}"
-				;;
-			postinst )
-				comp_full="$(isdp_get-sdp-edir)/linux/bin/${arch}/${comp}"
-				;;
-			* )
-				die "Compile test not supported in ${EBUILD_PHASE}"
-				;;
-		esac
-
-		debug-print "LD_LIBRARY_PATH=\"$(isdp_get-sdp-edir)/linux/bin/${arch}/\" \"${comp_full}\" -V"
-
-		LD_LIBRARY_PATH="$(isdp_get-sdp-edir)/linux/bin/${arch}/" "${comp_full}" -V &>/dev/null || warn=yes
-	done
-	[[ ${warn} == yes ]] && _isdp_big-warning test-failed
-}
-
-# @FUNCTION: _isdp_run-test
-# @INTERNAL
-# @DESCRIPTION:
-# Test if installed compiler is working.
-_isdp_run-test() {
-	debug-print-function ${FUNCNAME} "${@}"
-
-	if [[ -z ${INTEL_SKIP_LICENSE} ]]; then
-		case ${PN} in
-			ifc | icc )
-				_isdp_version_test
-				;;
-			* )
-				debug-print "No test available for ${PN}"
-				;;
-		esac
-	fi
-}
-
-# @FUNCTION: intel-sdp-r1_pkg_pretend
-# @DESCRIPTION:
-#
-# * Check for a (valid) license before proceeding.
-#
-# * Check for space requirements being fulfilled.
-#
-intel-sdp-r1_pkg_pretend() {
-	debug-print-function ${FUNCNAME} "${@}"
-
-	local warn=1 dir dirs ret arch a p
-
-	: ${CHECKREQS_DISK_BUILD:=256M}
-	check-reqs_pkg_pretend
-
-	if [[ -z ${INTEL_SKIP_LICENSE} ]]; then
-		if [[ ${INTEL_LICENSE_FILE} == *@* ]]; then
-			einfo "Looks like you are using following license server:"
-			einfo "   ${INTEL_LICENSE_FILE}"
-			return 0
-		fi
-
-		dirs=(
-			"${EPREFIX}/opt/intel/licenses"
-			"$(isdp_get-sdp-edir)/licenses"
-			"$(isdp_get-sdp-edir)/Licenses"
-			)
-		for dir in "${dirs[@]}" ; do
-			ebegin "Checking for a license in: ${dir}"
-			_isdp_path_exists "${dir}"/*lic && warn=0
-			eend ${warn} && break
-		done
-		if [[ ${warn} == 1 ]]; then
-			_isdp_big-warning pre-check
-			die "Could not find license file"
-		fi
-	else
-		eqawarn "The ebuild doesn't check for presence of a proper intel license!"
-		eqawarn "This shouldn't be done unless there is a very good reason."
-	fi
-}
-
-# @FUNCTION: intel-sdp-r1_pkg_nofetch
-# @DESCRIPTION:
-# Advice user to download the parallel studio tarball
-pkg_nofetch() {
-	einfo "Please download"
-	einfo "    ${SRC_URI}"
-	einfo "from"
-	einfo "    https://registrationcenter.intel.com/RegCenter/MyProducts.aspx"
-	einfo "and place the tarball in your DISTDIR directory."
-}
-
-# @FUNCTION: intel-sdp-r1_src_unpack
-# @DESCRIPTION:
-# Unpacking necessary rpms from tarball, extract them and rearrange the output.
-intel-sdp-r1_src_unpack() {
-	local t
-	for t in ${A}; do
-		local r list=() source_rpms=($(_isdp_generate-list-install-rpms))
-		for r in "${source_rpms[@]}"; do
-			list+=( ${t%%.*}/${r} )
-		done
-
-		local debug_list
-		debug_list="$(IFS=$'\n'; echo ${list[@]} )"
-
-		debug-print "Adding to decompression list:"
-		debug-print ${debug_list}
-
-		tar -xvf "${DISTDIR}"/${t} ${list[@]} &> "${T}"/rpm-extraction.log
-
-		for r in ${list[@]}; do
-			einfo "Unpacking ${r}"
-			printf "\nUnpacking %s\n" "${r}" >> "${T}"/rpm-extraction.log
-			rpm2tar -O ${r} | tar -xvf - &>> "${T}"/rpm-extraction.log; assert "Unpacking ${r} failed"
-		done
-	done
-}
-
-# @FUNCTION: intel-sdp-r1_src_install
-# @DESCRIPTION:
-# Install everything
-intel-sdp-r1_src_install() {
-	debug-print-function ${FUNCNAME} "${@}"
-
-	local i
-	# remove uninstall information
-	ebegin "Cleaning out uninstall"
-	while IFS='\n' read -r -d '' i; do
-		rm -r "${i}" || die
-	done < <(find opt -regextype posix-extended -regex '.*(uninstall|uninstall.sh)$' -print0)
-	eend
-
-	# handle documentation
-	if _isdp_path_exists "opt/intel/documentation_$(_isdp_get-sdp-year)"; then
-		# normal man pages
-		if _isdp_path_exists "opt/intel/documentation_$(_isdp_get-sdp-year)/en/man/common/man1"; then
-			doman opt/intel/documentation_"$(_isdp_get-sdp-year)"/en/man/common/man1/*
-			rm -r opt/intel/documentation_"$(_isdp_get-sdp-year)"/en/man || die
-		fi
-
-		use doc && dodoc -r opt/intel/documentation_"$(_isdp_get-sdp-year)"/*
-
-		ebegin "Cleaning out documentation"
-		rm -r "opt/intel/documentation_$(_isdp_get-sdp-year)" || die
-		rm -rf "$(isdp_get-sdp-dir)"/linux/{documentation,man} || die
-		eend
-	fi
-
-	# MPI man pages
-	if _isdp_path_exists "$(isdp_get-sdp-dir)/linux/mpi/man/man3"; then
-		doman "$(isdp_get-sdp-dir)"/linux/mpi/man/man3/*
-		rm -r "$(isdp_get-sdp-dir)"/linux/mpi/man || die
-	fi
-
-	# licensing docs
-	if _isdp_path_exists "$(isdp_get-sdp-dir)/licensing/documentation"; then
-		dodoc -r "$(isdp_get-sdp-dir)/licensing/documentation"/*
-		rm -rf "$(isdp_get-sdp-dir)/licensing/documentation" || die
-	fi
-
-	if _isdp_path_exists opt/intel/"${INTEL_DIST_NAME}"*/licensing; then
-		dodoc -r opt/intel/"${INTEL_DIST_NAME}"*/licensing
-		rm -rf opt/intel/"${INTEL_DIST_NAME}"* || die
-	fi
-
-	# handle examples
-	if _isdp_path_exists "opt/intel/samples_$(_isdp_get-sdp-year)"; then
-		use examples && dodoc -r opt/intel/samples_"$(_isdp_get-sdp-year)"/*
-
-		ebegin "Cleaning out examples"
-		rm -r "opt/intel/samples_$(_isdp_get-sdp-year)" || die
-		eend
-	fi
-
-	# remove eclipse unconditionally
-	ebegin "Cleaning out eclipse files"
-	rm -rf opt/intel/ide_support_* || die
-	eend
-
-	# repair shell scripts used for sourcing PATH (iccvars.sh and such)
-	ebegin "Tagging ${PN}"
-	find opt -name \*sh -type f -exec sed -i \
-		-e "s:<.*DIR>:$(isdp_get-sdp-edir)/linux:g" \
-		'{}' + || die
-	eend
-
-	ebegin "Removing broken symlinks"
-	while IFS='\n' read -r -d '' i; do
-		rm "${i}" || die
-	done < <(find opt -xtype l -print0)
-	eend
-
-	mv opt "${ED%/}"/ || die "moving files failed"
-
-	keepdir "$(isdp_get-sdp-dir)"/licenses /opt/intel/ism/rm
-}
-
-# @FUNCTION: intel-sdp-r1_pkg_postinst
-# @DESCRIPTION:
-# Test for all things working
-intel-sdp-r1_pkg_postinst() {
-	debug-print-function ${FUNCNAME} "${@}"
-
-	_isdp_run-test
-
-	if [[ ${PN} = icc ]] && has_version ">=dev-util/ccache-3.1.9-r2" ; then
-		#add ccache links as icc might get installed after ccache
-		"${EROOT}"/usr/bin/ccache-config --install-links
-	fi
-
-	elog "Beginning with the 2016 suite of Intel tools, Gentoo has removed"
-	elog "support for the eclipse plugin. If you require the IDE support,"
-	elog "you will have to install the suite on your own, outside portage."
-}
-
-# @FUNCTION: intel-sdp-r1_pkg_postrm
-# @DESCRIPTION:
-# Sanitize cache links
-intel-sdp-r1_pkg_postrm() {
-	debug-print-function ${FUNCNAME} "${@}"
-
-	if [[ ${PN} = icc ]] && has_version ">=dev-util/ccache-3.1.9-r2" && [[ -z ${REPLACED_BY_VERSION} ]]; then
-		# --remove-links would remove all links, --install-links updates them
-		"${EROOT}"/usr/bin/ccache-config --install-links
-	fi
-}
-
-_INTEL_SDP_R1_ECLASS_=1
-fi
diff --git a/eclass/mpi.eclass b/eclass/mpi.eclass
deleted file mode 100644
index 3c6537196..000000000
--- a/eclass/mpi.eclass
+++ /dev/null
@@ -1,478 +0,0 @@
-# Copyright 1999-2017 Gentoo Foundation
-# Distributed under the terms of the GNU General Public License v2
-
-# @ECLASS: mpi.eclass
-# @MAINTAINER:
-#	Justin Bronder <jsbronder@gentoo.org>
-# @BLURB: Common functions for mpi-pkg.eclass and mpi-imp.eclass
-
-# History:
-#	2009-06-26 (jsbronder):  Add ability to require common use flags.
-#		Remove dep on eselect-mpi (it's in sys-cluster/empi)
-#		Use virtual/$class to get imp dep in mpi_pkg_deplist.
-#	2008-11-20 (jsbronder):  Initial rewrite from old mpi.eclass
-
-if [[ ! ${_MPI_ECLASS} ]]; then
-
-case ${EAPI:-0} in
-	2|3|4|5)
-		inherit multilib ;;
-	6) ;;
-	*) die "EAPI=${EAPI} is not supported" ;;
-esac
-
-#####################
-# Private Variables #
-#####################
-
-# @ECLASS-VARIABLE: __MPI_ALL_IMPLEMENTATION_PNS
-# @INTERNAL
-# @DESCRIPTION:
-# All known mpi implementations
-__MPI_ALL_IMPLEMENTATION_PNS="mpich mpich2 openmpi lam-mpi openib-mvapich2"
-
-# @ECLASS-VARIABLE: __MPI_ALL_CLASSABLE_PNS
-# @INTERNAL
-# @DESCRIPTION:
-# All mpi implentations that can be classed.
-__MPI_ALL_CLASSABLE_PNS="mpich openmpi mpich2 lam-mpi"
-
-
-
-###################################################################
-# Generic Functions that are used by Implementations and Packages #
-###################################################################
-
-# @ECLASS-VARIABLE: MPI_UNCLASSED_DEP_STR
-# @DEFAULT_UNSET
-# @DESCRIPTION:
-# String inserted into the deplist when not using a classed
-# install.
-
-# @FUNCTION: mpi_classed
-# @RETURN: True if this build is classed.
-mpi_classed() {
-	[[ ${CATEGORY} == mpi-* ]]
-}
-
-#empi has no support for multilib yet
-mpi_classed && [[ ${_MULTILIB_BUILD} ]] && REQUIRED_USE="abi_x86_64? ( !abi_x86_32 )"
-
-# @FUNCTION: mpi_class
-# @RETURN: The name of the current class, or nothing if unclassed.
-mpi_class() {
-	mpi_classed && echo "${CATEGORY}"
-}
-
-# @FUNCTION: mpi_root
-# @RETURN: The root path that packages should start installing to.  In the end,
-# the majority of a package will will install to ${ROOT}$(mpi_root).
-mpi_root() {
-	if mpi_classed; then
-		echo "/usr/$(get_libdir)/mpi/$(mpi_class)/"
-	else
-		echo "/"
-	fi
-}
-
-# @FUNCTION: mpi_econf_args
-# @DESCRIPTION:
-# If classed, returns a list of arguments for econf that sets the
-# default install locations correctly.  Should be first in the list of arguments
-# to econf so that any unsuitable options can be overwritten.
-mpi_econf_args() {
-	if mpi_classed; then
-		local d=$(mpi_root)
-		local c=$(mpi_class)
-		local a="
-			--prefix=${d}usr
-			--mandir=${d}usr/share/man
-			--infodir=${d}usr/share/info
-			--datadir=${d}usr/share
-			--sysconfdir=/etc/${c}
-			--localstatedir=/var/lib/${c}"
-		echo "${a}"
-	fi
-}
-
-# @FUNCTION: _mpi_do
-# @USAGE: <Standard ebuild command to replicate>
-# @DESCRIPTION:
-# Large wrapping class for all of the {do,new}* commands that need
-# to respect the new root to install to.  Works with unclassed builds as well.
-# Currently supports:
-#
-# @CODE
-# dobin    newbin    dodoc     newdoc
-# doexe    newexe    dohtml    dolib
-# dolib.a  newlib.a  dolib.so  newlib.so
-# dosbin   newsbin   doman     newman
-# doinfo   dodir     dohard    doins
-# dosym
-# @CODE
-_mpi_do() {
-	local rc prefix d
-	local cmd=${1}
-	local ran=1
-	local slash=/
-	local mdir="$(mpi_root)"
-
-	if ! mpi_classed; then
-		$*
-		return ${?}
-	fi
-
-	shift
-	if [ "${cmd#do}" != "${cmd}" ]; then
-		prefix="do"; cmd=${cmd#do}
-	elif [ "${cmd#new}" != "${cmd}" ]; then
-		prefix="new"; cmd=${cmd#new}
-	else
-		die "Unknown command passed to _mpi_do: ${cmd}"
-	fi
-	case ${cmd} in
-		bin|lib|lib.a|lib.so|sbin)
-			DESTTREE="${mdir}usr" ${prefix}${cmd} $*
-			rc=$?;;
-		doc)
-			_E_DOCDESTTREE_="../../../../${mdir}usr/share/doc/${PF}/${_E_DOCDESTTREE_}" \
-				${prefix}${cmd} $*
-			rc=$?
-			for d in "/share/doc/${P}" "/share/doc" "/share"; do
-				rmdir ${D}/usr${d} &>/dev/null
-			done
-			;;
-		html)
-			_E_DOCDESTTREE_="../../../../${mdir}usr/share/doc/${PF}/www/${_E_DOCDESTTREE_}" \
-				${prefix}${cmd} $*
-			rc=$?
-			for d in "/share/doc/${P}/html" "/share/doc/${P}" "/share/doc" "/share"; do
-				rmdir ${D}/usr${d} &>/dev/null
-			done
-			;;
-		exe)
-			_E_EXEDESTTREE_="${mdir}${_E_EXEDESTTREE_}" ${prefix}${cmd} $*
-			rc=$?;;
-		man|info)
-			[ -d "${D}"usr/share/${cmd} ] && mv "${D}"usr/share/${cmd}{,-orig}
-			[ ! -d "${D}"${mdir}usr/share/${cmd} ] \
-				&& install -d "${D}"${mdir}usr/share/${cmd}
-			[ ! -d "${D}"usr/share ] \
-				&& install -d "${D}"usr/share
-
-			ln -snf ../../${mdir}usr/share/${cmd} ${D}usr/share/${cmd}
-			${prefix}${cmd} $*
-			rc=$?
-			rm "${D}"usr/share/${cmd}
-			[ -d "${D}"usr/share/${cmd}-orig ] \
-				&& mv "${D}"usr/share/${cmd}{-orig,}
-			[ "$(find "${D}"usr/share/)" == "${D}usr/share/" ] \
-				&& rmdir "${D}usr/share"
-			;;
-		dir)
-			dodir "${@/#${slash}/${mdir}${slash}}"; rc=$?;;
-		hard|sym)
-			${prefix}${cmd} "${mdir}$1" "${mdir}/$2"; rc=$?;;
-		ins)
-			INSDESTTREE="${mdir}${INSTREE}" ${prefix}${cmd} $*; rc=$?;;
-		*)
-			rc=0;;
-	esac
-
-	[[ ${ran} -eq 0 ]] && die "mpi_do passed unknown command: ${cmd}"
-	return ${rc}
-}
-mpi_dobin()     { _mpi_do "dobin"        $*; }
-mpi_newbin()    { _mpi_do "newbin"       $*; }
-mpi_dodoc()     { _mpi_do "dodoc"        $*; }
-mpi_newdoc()    { _mpi_do "newdoc"       $*; }
-mpi_doexe()     { _mpi_do "doexe"        $*; }
-mpi_newexe()    { _mpi_do "newexe"       $*; }
-mpi_dohtml()    { _mpi_do "dohtml"       $*; }
-mpi_dolib()     { _mpi_do "dolib"        $*; }
-mpi_dolib.a()   { _mpi_do "dolib.a"      $*; }
-mpi_newlib.a()  { _mpi_do "newlib.a"     $*; }
-mpi_dolib.so()  { _mpi_do "dolib.so"     $*; }
-mpi_newlib.so() { _mpi_do "newlib.so"    $*; }
-mpi_dosbin()    { _mpi_do "dosbin"       $*; }
-mpi_newsbin()   { _mpi_do "newsbin"      $*; }
-mpi_doman()     { _mpi_do "doman"        $*; }
-mpi_newman()    { _mpi_do "newman"       $*; }
-mpi_doinfo()    { _mpi_do "doinfo"       $*; }
-mpi_dodir()     { _mpi_do "dodir"        $*; }
-mpi_dohard()    { _mpi_do "dohard"       $*; }
-mpi_doins()     { _mpi_do "doins"        $*; }
-mpi_dosym()     { _mpi_do "dosym"        $*; }
-
-
-###########################################
-# Functions for MPI Implementation Builds #
-###########################################
-
-# @FUNCTION: mpi_imp_deplist
-# @DESCRIPTION:
-# To be written
-# @RETURNS: Returns a deplist that handles the blocking between mpi
-# implementations, and any blockers as specified in MPI_UNCLASSED_DEP_STR
-mpi_imp_deplist() {
-	local c="sys-cluster"
-	local pn ver
-
-	mpi_classed && c="${CATEGORY}"
-	ver=""
-	for pn in ${__MPI_ALL_IMPLEMENTATION_PNS}; do
-		ver="${ver} !${c}/${pn}"
-	done
-	if ! mpi_classed && [ -n "${MPI_UNCLASSED_DEP_STR}" ]; then
-		ver="${ver} ${MPI_UNCLASSED_DEP_STR}"
-	else
-		ver="${ver} sys-cluster/empi"
-	fi
-	echo "${ver}"
-}
-
-# @FUNCTION: mpi_imp_add_eselect
-# @DESCRIPTION:
-# To be written
-mpi_imp_add_eselect() {
-	mpi_classed || return 0
-	local c=$(mpi_class)
-	cp "${FILESDIR}"/${MPI_ESELECT_FILE} ${T}/${c}.eselect || die
-	sed -i \
-		-e "s|@ROOT@|$(mpi_root)|g" \
-		-e "s|@LIBDIR@|$(get_libdir)|g" \
-		-e "s|@BASE_IMP@|${PN}|g" \
-		${T}/${c}.eselect || die
-
-	eselect mpi add "${T}"/${c}.eselect || die
-}
-
-
-
-########################################
-# Functions for packages requiring MPI #
-########################################
-
-# @ECLASS-VARIABLE: MPI_PKG_NEED_IMPS
-# @DESCRIPTION:
-# List of package names (${PN}) that this package is compatible
-# with.  Default is the list of all mpi implementations
-MPI_PKG_NEED_IMPS="${MPI_PKG_NEED_IMPS:-${__MPI_ALL_CLASSABLE_PNS}}"
-
-
-# @ECLASS-VARIABLE: MPI_PKG_USE_CXX
-# @DESCRIPTION:
-# Require a mpi implementation with c++ enabled.
-# This feature requires EAPI 2 style use dependencies
-MPI_PKG_USE_CXX="${MPI_PKG_USE_CXX:-0}"
-
-# @ECLASS-VARIABLE: MPI_PKG_USE_FC
-# @DESCRIPTION:
-# Require a mpi implementation with fortran enabled.
-# This feature requires EAPI 2 style use dependencies
-MPI_PKG_USE_FC="${MPI_PKG_USE_FC:-0}"
-
-# @ECLASS-VARIABLE: MPI_PKG_USE_ROMIO
-# @DESCRIPTION:
-# Require a mpi implementation with romio enabled.
-# This feature requires EAPI 2 style use dependencies
-MPI_PKG_USE_ROMIO="${MPI_PKG_USE_ROMIO:-0}"
-
-# @ECLASS-VARIABLE: MPI_PKG_USE_THREADS
-# @DESCRIPTION:
-# Require a mpi implementation with threads enabled.
-# This feature requires EAPI 2 style use dependencies
-MPI_PKG_USE_THREADS="${MPI_PKG_USE_THREADS:-0}"
-
-# @ECLASS-VARIABLE: MPI_PKG_USE_DEPS
-# @DESCRIPTION:
-# Set the use deps for the virtual mpi package
-# directly.  For instance, if set to 'fortran=,threads?' then a dep on
-# virtual/mpi[fortran=,threads?] will be added.
-# This feature requires EAPI 2 style use dependencies
-MPI_PKG_USE_DEPS="${MPI_PKG_USE_DEPS}"
-
-
-# @FUNCTION: mpi_pkg_deplist
-# @DESCRIPTION:
-# To be written
-# @RETURN: Returns a deplist comprised of valid implementations and any blockers
-# depending on if this package is building with mpi class support.
-mpi_pkg_deplist() {
-	local pn pn2 ver usedeps invalid_imps inval
-
-	case "${EAPI}" in
-		2|3|4|5)
-			[[ ${MPI_PKG_USE_CXX} -ne 0 ]] \
-				&& usedeps=",cxx"
-			[[ ${MPI_PKG_USE_FC} -ne 0 ]] \
-				&& usedeps="${usedeps},fortran"
-			[[ ${MPI_PKG_USE_ROMIO} -ne 0 ]] \
-				&& usedeps="${usedeps},romio"
-			[[ "${MPI_PKG_USE_THREADS}" -ne 0 ]] \
-				&& usedeps="${usedeps},threads"
-			[ -n "${MPI_PKG_USE_DEPS}" ] \
-				&& usedeps="${usedeps},${MPI_PKG_USE_DEPS}"
-			;;
-		*)
-			;;
-	esac
-
-	if mpi_classed; then
-		ver="sys-cluster/empi virtual/$(mpi_class)"
-	else
-		ver="virtual/mpi"
-	fi
-
-	if [ -n "${usedeps}" ]; then
-		ver="${ver}[${usedeps:1}]"
-	fi
-
-	if ! mpi_classed && [ -n "${MPI_UNCLASSED_DEP_STR}" ]; then
-		ver="${ver} ${MPI_UNCLASSED_DEP_STR}"
-	fi
-
-	for pn in ${__MPI_ALL_IMPLEMENTATION_PNS}; do
-		inval=1
-		for pn2 in ${MPI_PKG_NEED_IMPS}; do
-			if [ "${pn}" == "${pn2}" ]; then
-				inval=0
-				break;
-			fi
-		done
-		[[ ${inval} -eq 1 ]] \
-			&& invalid_imps="${invalid_imps} ${pn}"
-	done
-
-	for pn in ${inval_imps}; do
-		ver="${ver} !${c}/${pn}"
-	done
-	echo "${ver}"
-}
-
-# @FUNCTION: mpi_pkg_base_imp
-# @DESCRIPTION:
-# To be written
-# @RETURNS:
-# Returns the ${PN} of the package providing mpi support.   Works
-# even when using an unclassed mpi build.
-mpi_pkg_base_imp() {
-	if mpi_classed; then
-		echo "$(_get_eselect_var CLASS_BASE_MPI_IMP)"
-	else
-		local pn
-		for pn in ${MPI_PKG_NEED_IMPS}; do
-			if has_version "sys-cluster/${pn}"; then
-				echo "${PN}"
-			fi
-		done
-	fi
-}
-
-# @FUNCTION: mpi_pkg_cc
-# @DESCRIPTION:
-#  Returns the full path to the mpi C compiler.  Trys to find one
-# even if this build is unclassed.  If return is empty, user should assume the
-# implementation does not support this compiler
-mpi_pkg_cc()  { _mpi_pkg_compiler "MPI_CC"  "cc";      }
-
-# @FUNCTION: mpi_pkg_cxx
-# @DESCRIPTION:
-# Returns the full path to the mpi C++ compiler.  Trys to find one
-# even if this build is unclassed.  If return is empty, user should assume the
-# implementation does not support this compiler
-mpi_pkg_cxx() { _mpi_pkg_compiler "MPI_CXX" "cxx c++"; }
-
-# @FUNCTION: mpi_pkg_fc
-# @DESCRIPTION:
-# Returns the full path to the mpi f90 compiler.  Trys to find one
-# even if this build is unclassed.  If return is empty, user should assume the
-# implementation does not support this compiler
-mpi_pkg_fc()  { _mpi_pkg_compiler "MPI_FC"  "f90 fc";  }
-
-# @FUNCTION: mpi_pkg_f77
-# @DESCRIPTION:
-# Returns the full path to the mpi f77 compiler.  Trys to find one
-# even if this build is unclassed.  If return is empty, user should assume the
-# implementation does not support this compiler
-mpi_pkg_f77() { _mpi_pkg_compiler "MPI_F77" "f77";     }
-
-
-# @FUNCTION:  mpi_pkg_set_ld_library_path
-# @DESCRIPTION:
-# Adds the correct path(s) to the end of LD_LIBRARY_PATH.  Does
-# nothing if the build is unclassed.
-mpi_pkg_set_ld_library_path() {
-	if mpi_classed; then
-		export LD_LIBRARY_PATH="${LD_LIBRARY_PATH}:$(_get_eselect_var LD_LIBRARY_PATH)"
-	fi
-}
-
-# @FUNCTION: _mpi_pkg_compiler
-# @DESCRIPTION:
-# If classed, we can ask eselect-mpi.  Otherwise we'll look for some common
-# executable names in ${ROOT}usr/bin.
-_mpi_pkg_compiler() {
-	if mpi_classed; then
-		echo "$(eselect mpi printvar $(mpi_class) ${1})"
-	else
-		local suffixes=${2}
-		local p
-
-		for p in ${suffixes}; do
-			if [ -x ${ROOT}usr/bin/mpi${p} ]; then
-				echo "${ROOT}usr/bin/mpi${p}"
-				break
-			fi
-		done
-	fi
-}
-
-# @FUNCTION: mpi_pkg_set_env
-# @DESCRIPTION:
-# Exports 'some influential environment variables'.  CC, CXX, F77, FC
-mpi_pkg_set_env() {
-	if mpi_classed; then
-		_mpi_oCC=$CC
-		_mpi_oCXX=$CXX
-		_mpi_oF77=$F77
-		_mpi_oFC=$FC
-		_mpi_oPCP=${PKG_CONFIG_PATH}
-		_mpi_oLLP=${LD_LIBRARY_PATH}
-		export CC=$(mpi_pkg_cc)
-		export CXX=$(mpi_pkg_cxx)
-		export F77=$(mpi_pkg_f77)
-		export FC=$(mpi_pkg_fc)
-		export PKG_CONFIG_PATH="$(mpi_root)$(get_libdir)/pkgconfig:${PKG_CONFIG_PATH}"
-		mpi_pkg_set_ld_library_path
-	fi
-}
-
-# @FUNCTION: mpi_pkg_restore_env
-# @DESCRIPTION:
-# Attempts to undo the damage done by mpi_pkg_set_env
-mpi_pkg_restore_env() {
-	if mpi_classed; then
-		export CC=$_mpi_oCC
-		export CXX=$_mpi_oCXX
-		export F77=$_mpi_oF77
-		export FC=$_mpi_oFC
-		export PKG_CONFIG_PATH=$_mpi_oPCP
-		export LD_LIBRARY_PATH=$_mpi_oLLP
-	fi
-}
-
-
-
-# @FUNCTION: _get_eselect_var
-# @USAGE: <Variable to get from the class definition>
-# @RETURN: If classed, and given a valid variable, the contents; empty
-# otherwise.
-_get_eselect_var() {
-	if mpi_classed && [ -n "${1}" ]; then
-		echo "$(eselect mpi printvar $(mpi_class) ${1} 2>/dev/null)"
-	fi
-}
-
-_MPI_ECLASS=1
-fi
diff --git a/eclass/numeric-int64-multibuild.eclass b/eclass/numeric-int64-multibuild.eclass
deleted file mode 100644
index f720356a3..000000000
--- a/eclass/numeric-int64-multibuild.eclass
+++ /dev/null
@@ -1,414 +0,0 @@
-# Copyright 1999-2017 Gentoo Foundation
-# Distributed under the terms of the GNU General Public License v2
-
-# @ECLASS: numeric-int64-multilib.eclass
-# @MAINTAINER:
-# sci team <sci@gentoo.org>
-# @AUTHOR:
-# Author: Mark Wright <gienah@gentoo.org>
-# Author: Justin Lecher <jlec@gentoo.org>
-# @BLURB: Build functions for Fortran multilib int64 multibuild packages
-# @DESCRIPTION:
-# The numeric-int64-multilib.eclass exports USE flags and utility functions
-# necessary to build packages for multilib int64 multibuild in a clean
-# and uniform manner.
-
-if [[ ! ${_NUMERIC_INT64_MULTILIB_ECLASS} ]]; then
-
-# EAPI=5 is required for meaningful MULTILIB_USEDEP.
-case ${EAPI:-0} in
-	5)
-		inherit multilib ;;
-	6|7) ;;
-	*) die "EAPI=${EAPI} is not supported" ;;
-esac
-
-inherit alternatives-2 eutils fortran-2 multilib-build numeric toolchain-funcs
-
-IUSE="int64"
-
-# @ECLASS-VARIABLE: NUMERIC_INT32_SUFFIX
-# @INTERNAL
-# @DESCRIPTION:
-# MULTIBUILD_ID suffix for int32 build
-NUMERIC_INT32_SUFFIX="int32"
-
-# @ECLASS-VARIABLE: NUMERIC_INT64_SUFFIX
-# @INTERNAL
-# @DESCRIPTION:
-# MULTIBUILD_ID suffix for int64 build
-NUMERIC_INT64_SUFFIX="int64"
-
-# @ECLASS-VARIABLE: NUMERIC_STATIC_SUFFIX
-# @INTERNAL
-# @DESCRIPTION:
-# MULTIBUILD_ID suffix for static build
-NUMERIC_STATIC_SUFFIX="static"
-
-# @FUNCTION: numeric-int64_is_int64_build
-# @DESCRIPTION:
-# Returns shell true if the current multibuild is a int64 build,
-# else returns shell false.
-#
-# Example:
-#
-# @CODE
-#	$(numeric-int64_is_int64_build) && \
-#		openblas_abi_cflags+=" -DOPENBLAS_USE64BITINT"
-# @CODE
-numeric-int64_is_int64_build() {
-	debug-print-function ${FUNCNAME} "${@}"
-	if [[ "${MULTIBUILD_ID}" =~ "${NUMERIC_INT64_SUFFIX}" ]]; then
-		return 0
-	else
-		return 1
-	fi
-}
-
-# @FUNCTION: numeric-int64_is_static_build
-# @DESCRIPTION:
-# Returns shell true if current multibuild is a static build,
-# else returns shell false.
-#
-# Example:
-#
-# @CODE
-#	if $(numeric-int64_is_static_build); then
-#		dolib.a lib*a
-#	fi
-# @CODE
-numeric-int64_is_static_build() {
-	debug-print-function ${FUNCNAME} "${@}"
-	if [[ "${MULTIBUILD_ID}" =~ "${NUMERIC_STATIC_SUFFIX}" ]]; then
-		return 0
-	else
-		return 1
-	fi
-}
-
-# @FUNCTION: numeric-int64_get_module_name
-# @USAGE: [<module_name>]
-# @DESCRIPTION:
-# Return the numeric module name, without the .pc extension,
-# for the current fortran int64 build.  If the current build is not an int64
-# build, and the ebuild does not have dynamic, threads or openmp USE flags or
-# they are disabled, then the module_name is ${NUMERIC_MODULE_NAME} or
-# <module_name> if <module_name> is specified.
-#
-# Takes an optional <module_name> parameter.  If no <module_name> is specified,
-# uses ${NUMERIC_MODULE_NAME} as the base to calculate the module_name for the
-# current build.
-#
-# Example:
-#
-# @CODE
-#	NUMERIC_MODULE_NAME=blas
-#	profname=$(numeric-int64_get_module_name)
-#
-#	int32 build:
-#	-> profname == blas
-#
-#	int64 build:
-#	-> profname == blas-int64
-# @CODE
-numeric-int64_get_module_name() {
-	debug-print-function ${FUNCNAME} "${@}"
-	local module_name="${1:-${NUMERIC_MODULE_NAME}}"
-	if has dynamic ${IUSE} && use dynamic; then
-		module_name+="-dynamic"
-	fi
-	if $(numeric-int64_is_int64_build); then
-		module_name+="-${NUMERIC_INT64_SUFFIX}"
-	fi
-	# choose posix threads over openmp when the two are set
-	# yet to see the need of having the two profiles simultaneously
-	if use_if_iuse threads; then
-		module_name+="-threads"
-	elif use_if_iuse openmp; then
-		module_name+="-openmp"
-	fi
-	echo "${module_name}"
-}
-
-# @FUNCTION: _numeric-int64_get_numeric_alternative
-# @INTERNAL
-_numeric-int64_get_numeric_alternative() {
-	debug-print-function ${FUNCNAME} "${@}"
-	local alternative_name="${1}"
-	if $(numeric-int64_is_int64_build); then
-		alternative_name+="-${NUMERIC_INT64_SUFFIX}"
-	fi
-	echo "${alternative_name}"
-}
-
-# @FUNCTION: numeric-int64_get_blas_alternative
-# @DESCRIPTION:
-# Returns the eselect blas alternative for the current
-# int build type. Which is blas-int64 if called from an int64 build,
-# or blas otherwise.
-numeric-int64_get_blas_alternative() {
-	debug-print-function ${FUNCNAME} "${@}"
-	_numeric-int64_get_numeric_alternative blas
-}
-
-# @FUNCTION: numeric-int64_get_cblas_alternative
-# @DESCRIPTION:
-# Returns the eselect cblas alternative for the current
-# int build type. Which is cblas-int64 if called from an int64 build,
-# or cblas otherwise.
-numeric-int64_get_cblas_alternative() {
-	debug-print-function ${FUNCNAME} "${@}"
-	_numeric-int64_get_numeric_alternative cblas
-}
-
-# @FUNCTION: numeric-int64_get_xblas_alternative
-# @DESCRIPTION:
-# Returns the eselect xblas alternative for the current
-# int build type. Which is xblas-int64 if called from an int64 build,
-# or xblas otherwise.
-numeric-int64_get_xblas_alternative() {
-	debug-print-function ${FUNCNAME} "${@}"
-	_numeric-int64_get_numeric_alternative xblas
-}
-
-# @FUNCTION: numeric-int64_get_lapack_alternative
-# @DESCRIPTION:
-# Returns the eselect lapack alternative for the current
-# int build type. Which is lapack-int64 if called from an int64 build,
-# or lapack otherwise.
-numeric-int64_get_lapack_alternative() {
-	debug-print-function ${FUNCNAME} "${@}"
-	_numeric-int64_get_numeric_alternative lapack
-}
-
-# @FUNCTION: numeric-int64_get_blas_module_name
-# @DESCRIPTION:
-# Returns the pkg-config file name, without the .pc extension,
-# for the currently selected blas-int64 module if we are performing an int64
-# build, or the currently selected blas module otherwise.
-numeric-int64_get_blas_module_name() {
-	debug-print-function ${FUNCNAME} "${@}"
-	local blas_alternative=$(numeric-int64_get_blas_alternative)
-	local blas_symlinks=( $(eselect "${blas_alternative}" files) )
-	local blas_prof_symlink="$(readlink -f ${blas_symlinks[0]})"
-	local blas_prof_file="${blas_prof_symlink##*/}"
-	echo "${blas_prof_file%.pc}"
-}
-
-# @FUNCTION: numeric-int64_get_xblas_module_name
-# @DESCRIPTION:
-# Returns the xblas pkg-config file name,
-# without the .pc extension, for the current build. Which is xblas-int64 if
-# we are performing an int64 build, or xblas otherwise.
-numeric-int64_get_xblas_module_name() {
-	debug-print-function ${FUNCNAME} "${@}"
-	local xblas_provider="xblas"
-	if $(numeric-int64_is_int64_build); then
-		xblas_provider+="-${INT64_SUFFIX}"
-	fi
-	echo "${xblas_provider}"
-}
-
-# @FUNCTION: numeric-int64_get_fortran_int64_abi_fflags
-# @DESCRIPTION:
-# Return the Fortran compiler flag to enable 64 bit integers for
-# array indices if we are performing an int64 build, or the empty string
-# otherwise.
-#
-# Example:
-#
-# @CODE
-# src_configure() {
-#	my_configure() {
-#		export FCFLAGS="${FCFLAGS} $(get_abi_CFLAGS) $(numeric-int64_get_fortran_int64_abi_fflags)"
-#		econf $(use_enable fortran)
-#	}
-#	numeric-int64-multibuild_foreach_all_abi_variants run_in_build_dir my_configure
-# }
-# @CODE
-numeric-int64_get_fortran_int64_abi_fflags() {
-	debug-print-function ${FUNCNAME} "${@}"
-	$(numeric-int64_is_int64_build) && echo "$(fortran_int64_abi_fflags)"
-}
-
-# @FUNCTION: numeric-int64_get_multibuild_int_variants
-# @DESCRIPTION:
-# Returns the array of int64 and int32
-# multibuild combinations.
-numeric-int64_get_multibuild_int_variants() {
-	debug-print-function ${FUNCNAME} "${@}"
-	local MULTIBUILD_VARIANTS=( int32 ) variant
-
-	use_if_iuse int64 && MULTIBUILD_VARIANTS+=( int64 )
-
-	echo "${MULTIBUILD_VARIANTS[@]}"
-}
-
-# @FUNCTION: numeric-int64_get_multibuild_variants
-# @DESCRIPTION:
-# Returns the array of int64, int32 and static
-# multibuild combinations.
-numeric-int64_get_multibuild_variants() {
-	debug-print-function ${FUNCNAME} "${@}"
-	local MULTIBUILD_VARIANTS=$(numeric-int64_get_multibuild_int_variants)
-	if use_if_iuse static-libs; then
-		for variant in ${MULTIBUILD_VARIANTS[@]}; do
-			MULTIBUILD_VARIANTS+=( static_${variant} )
-		done
-	fi
-	echo "${MULTIBUILD_VARIANTS[@]}"
-}
-
-# @FUNCTION: numeric-int64_get_all_abi_variants
-# @DESCRIPTION:
-# Returns the array of int64, int32 and static build combinations
-# combined with all multilib ABI variants.
-numeric-int64_get_all_abi_variants() {
-	debug-print-function ${FUNCNAME} "${@}"
-	local abi ret=() variant
-
-	for abi in $(multilib_get_enabled_abi_pairs); do
-		for variant in $(numeric-int64_get_multibuild_variants); do
-			if [[ ${variant} =~ int64 ]]; then
-				[[ ${abi} =~ amd64 ]] && ret+=( ${abi}_${variant} )
-			else
-				ret+=( ${abi}_${variant} )
-			fi
-		done
-	done
-	echo "${ret[@]}"
-}
-
-# @FUNCTION: numeric-int64_ensure_blas_int_support
-# @DESCRIPTION:
-# Check the blas supports the necessary int types in the currently
-# selected blas module.
-#
-# Example:
-#
-# @CODE
-# src_prepare() {
-#	numeric-int64_ensure_blas_int_support
-#	...
-# @CODE
-numeric-int64_ensure_blas_int_support() {
-	local MULTILIB_INT64_VARIANTS=( $(numeric-int64_get_multibuild_variants) )
-	local MULTIBUILD_ID
-	for MULTIBUILD_ID in "${MULTILIB_INT64_VARIANTS[@]}"; do
-		local blas_module_name=$(numeric-int64_get_blas_module_name)
-		$(tc-getPKG_CONFIG) --exists "${blas_module_name}" \
-			|| die "${PN} requires the pkgbuild module ${blas_module_name}"
-	done
-}
-
-# @FUNCTION: numeric-int64-multibuild_install_alternative
-# @USAGE: <alternative name> <provider name> [extra files sources] [extra files dest]
-# @DESCRIPTION:
-# Install alternatives pc file and extra files for all providers for all multilib ABIs.
-numeric-int64-multibuild_install_alternative() {
-	debug-print-function ${FUNCNAME} "${@}"
-	[[ $# -lt 2 ]] && die "${FUNCNAME} needs at least two arguments"
-	pc_file()  {
-		debug-print-function ${FUNCNAME} "${@}"
-		numeric-int64_is_static_build && return
-		local alternative=$(_numeric-int64_get_numeric_alternative "$1")
-		local module_name=$(numeric-int64_get_module_name)
-		printf \
-			"/usr/$(get_libdir)/pkgconfig/${alternative}.pc ${module_name}.pc " \
-			>> "${T}"/alternative-${alternative}.sh || die
-	}
-	pc_install() {
-		debug-print-function ${FUNCNAME} "${@}"
-		numeric-int64_is_static_build && return
-		local alternative=$(_numeric-int64_get_numeric_alternative "$1")
-		local module_name=$(numeric-int64_get_module_name $2)
-		shift 2
-		alternatives_for \
-			${alternative} ${module_name} 0 \
-			$(cat "${T}"/alternative-${alternative}.sh) ${@}
-		rm "${T}"/alternative-${alternative}.sh || die
-	}
-	numeric-int64-multibuild_foreach_all_abi_variants pc_file ${@}
-	numeric-int64-multibuild_foreach_int_abi pc_install ${@}
-}
-
-# @FUNCTION: numeric-int64-multibuild_multilib_wrapper
-# @USAGE: <argv>...
-# @DESCRIPTION:
-# Initialize the environment for ABI selected for multibuild.
-#
-# Example:
-#
-# @CODE
-# 	multibuild_foreach_variant run_in_build_dir \
-# 		numeric-int64-multibuild_multilib_wrapper my_src_install
-# @CODE
-numeric-int64-multibuild_multilib_wrapper() {
-	debug-print-function ${FUNCNAME} "${@}"
-
-	local v="${MULTIBUILD_VARIANT%_*}"
-	# MULTIBUILD_VARIANT could be abi_x86_64.amd64_static_int32
-	v=${v%_${NUMERIC_STATIC_SUFFIX}}
-	local ABI="${v#*.}"
-	# hack: our int64 and int32 ABIs can correspond to the same ABI
-	# in multilib, resulting in multiple sed replacements of headers
-	# and thus error like "Flag not listed in wrapper template."
-	# Using MULTILIB_ABI_FLAG="${ABI}", the corresponding header
-	# is ignored.
-	local MULTILIB_ABI_FLAG
-	case ${MULTIBUILD_VARIANT} in
-	*_${NUMERIC_STATIC_SUFFIX}*|*_${NUMERIC_INT64_SUFFIX})
-		MULTILIB_ABI_FLAG="${ABI}"
-		;;
-	*_${NUMERIC_INT32_SUFFIX})
-		MULTILIB_ABI_FLAG="${v%.*}"
-		;;
-	esac
-
-	multilib_toolchain_setup "${ABI}"
-	readonly ABI
-	"${@}" || die
-}
-
-# @FUNCTION: numeric-int64-multibuild_foreach_int_abi
-# @USAGE: <argv> ...
-# @DESCRIPTION:
-# Run command for each enabled numeric variant (e.g. int32, int64)
-numeric-int64-multibuild_foreach_int_abi() {
-	debug-print-function ${FUNCNAME} "${@}"
-	local MULTIBUILD_VARIANTS=( $(numeric-int64_get_multibuild_int_variants) )
-	multibuild_foreach_variant numeric-int64-multibuild_multilib_wrapper "${@}"
-}
-
-# @FUNCTION: numeric-int64-multibuild_foreach_variant
-# @USAGE: <argv> ...
-# @DESCRIPTION:
-# Run command for each enabled numeric abi and static-libs (e.g. int32, int64, static)
-numeric-int64-multibuild_foreach_variant() {
-	debug-print-function ${FUNCNAME} "${@}"
-	local MULTIBUILD_VARIANTS=( $(numeric-int64_get_multibuild_variants) )
-	multibuild_foreach_variant numeric-int64-multibuild_multilib_wrapper "${@}"
-}
-
-# @FUNCTION: numeric-int64-multibuild_foreach_all_abi_variants
-# @USAGE: <argv> ...
-# @DESCRIPTION:
-# Run command for each enabled numeric variant (e.g. int32, int64, static) _AND_
-# enabled multilib ABI
-numeric-int64-multibuild_foreach_all_abi_variants() {
-	debug-print-function ${FUNCNAME} "${@}"
-	local MULTIBUILD_VARIANTS=( $(numeric-int64_get_all_abi_variants) )
-	multibuild_foreach_variant numeric-int64-multibuild_multilib_wrapper "${@}"
-}
-
-# @FUNCTION: numeric-int64-multibuild_copy_sources
-# @DESCRIPTION:
-# Thin wrapper around multibuild_copy_sources()
-numeric-int64-multibuild_copy_sources() {
-	debug-print-function ${FUNCNAME} "${@}"
-	local MULTIBUILD_VARIANTS=( $(numeric-int64_get_all_abi_variants) )
-	multibuild_copy_sources
-}
-
-_NUMERIC_INT64_MULTILIB_ECLASS=1
-fi
diff --git a/eclass/numeric.eclass b/eclass/numeric.eclass
deleted file mode 100644
index 431b7afec..000000000
--- a/eclass/numeric.eclass
+++ /dev/null
@@ -1,138 +0,0 @@
-# Copyright 1999-2017 Gentoo Foundation
-# Distributed under the terms of the GNU General Public License v2
-
-# @ECLASS: numeric.eclass
-# @MAINTAINER:
-# jlec@gentoo.org
-# @BLURB: Maintance bits needed for *lapack* and *blas* packages
-# @DESCRIPTION:
-# Various functions which make the maintenance  numerical algebra packages
-# easier.
-
-if [[ ! ${_NUMERIC_ECLASS} ]]; then
-
-case ${EAPI:-0} in
-	0|1|2|3|4|5)
-		inherit multilib ;;
-	6|7) ;;
-	*) die "EAPI=${EAPI} is not supported" ;;
-esac
-
-# @VARIABLE: NUMERIC_MODULE_NAME
-# @DESCRIPTION:
-# The base pkg-config module name of the package being built.
-# NUMERIC_MODULE_NAME is used by the numeric-int64_get_module_name to
-# determine the pkg-config module name based on whether the package
-# has dynamic, threads or openmp USE flags and if so, if the user has
-# turned them or, and if the current multibuild is a int64 build or not.
-#
-# @CODE
-# NUMERIC_MODULE_NAME="openblas"
-# inherit ... numeric-int64-multibuild
-# @CODE
-: ${NUMERIC_MODULE_NAME:=blas}
-
-# @FUNCTION: create_pkgconfig
-# @USAGE: [ additional arguments ]
-# @DESCRIPTION:
-# Creates and installs pkg-config file. The function should only be executed in
-# src_install(). For further information about optional arguments please consult
-# http://people.freedesktop.org/~dbn/pkg-config-guide.html
-#
-# @CODE
-# Optional arguments are:
-#
-#   -p | --prefix       Offset for current package               (${EPREFIX}/usr)
-#   -e | --exec-prefix  Offset for current package               (${prefix})
-#   -L | --libdir       Libdir to use                            (${prefix}/$(get_libdir))
-#   -I | --includedir   Includedir to use                        (${prefix}/include)
-#   -n | --name         A human-readable name                    (PN}
-#   -d | --description  A brief description                      (DESCRIPTION)
-#   -V | --version      Version of the package                   (PV)
-#   -u | --url          Web presents                             (HOMEPAGE)
-#   -r | --requires     Packages required by this package        (unset)
-#   -l | --libs         Link flags specific to this package      (unset)
-#   -c | --cflags       Compiler flags specific to this package  (unset)
-#   --requires-private  Like --requires, but not exposed         (unset)
-#   --conflicts         Packages that this one conflicts with    (unset)
-#   --libs-private      Like --libs, but not exposed             (unset)
-# @CODE
-create_pkgconfig() {
-	debug-print-function ${FUNCNAME} "${@}"
-	local pcfilename pcrequires pcrequirespriv pcconflicts pclibs pclibspriv pccflags
-	local pcprefix="${EPREFIX}/usr"
-	local pcexecprefix="${pcprefix}"
-	local pclibdir="${EPREFIX}/usr/$(get_libdir)"
-	local pcincldir="${pcprefix}/include"
-	local pcname=${PN}
-	local pcdescription="${DESCRIPTION}"
-	local pcurl=${HOMEPAGE}
-	local pcversion=${PV}
-
-	[[ "${EBUILD_PHASE}" != "install" ]] && \
-		die "create_pkgconfig should only be used in src_install()"
-
-	while (($#)); do
-		case ${1} in
-			-p | --prefix )
-				shift; pcprefix=${1} ;;
-			-e | --exec-prefix )
-				shift; pcexecprefix=${1} ;;
-			-L | --libdir )
-				shift; pclibdir=${1} ;;
-			-I | --includedir )
-				shift; pcincldir=${1} ;;
-			-n | --name )
-				shift; pcname=${1} ;;
-			-d | --description )
-				shift; pcdescription=${1} ;;
-			-V | --version )
-				shift; pcversion=${1} ;;
-			-u | --url )
-				shift; pcurl=${1} ;;
-			-r | --requires )
-				shift; pcrequires=${1} ;;
-			--requires-private )
-				shift; pcrequirespriv=${1} ;;
-			--conflicts )
-				shift; pcconflicts=${1};;
-			-l | --libs )
-				shift; pclibs=${1} ;;
-			--libs-private )
-				shift; pclibspriv=${1} ;;
-			-c | --cflags )
-				shift; pccflags=${1} ;;
-			-* )
-				ewarn "Unknown option ${1}" ;;
-			* )
-				pcfilename=${1} ;;
-		esac
-		shift
-	done
-
-	[[ -z ${pcfilename} ]] && die "Missing name for pkg-config file"
-
-	cat > "${T}"/${pcfilename}.pc <<- EOF
-	prefix="${pcprefix}"
-	exec_prefix="${pcexecprefix}"
-	libdir="${pclibdir}"
-	includedir="${pcincldir}"
-
-	Name: ${pcname}
-	Description: ${pcdescription}
-	Version: ${pcversion}
-	URL: ${pcurl}
-	Requires: ${pcrequires}
-	Requires.private: ${pcrequirespriv}
-	Conflicts: ${pcconflicts}
-	Libs: -L\${libdir} ${pclibs}
-	Libs.private: ${pclibspriv}
-	Cflags: -I\${includedir} ${pccflags}
-	EOF
-
-	insinto /usr/$(get_libdir)/pkgconfig
-	doins "${T}"/${pcfilename}.pc
-}
-
-_NUMERIC_ECLASS=1
-fi
diff --git a/licenses/AMD-APPSDK b/licenses/AMD-APPSDK
deleted file mode 100644
index fece351dd..000000000
--- a/licenses/AMD-APPSDK
+++ /dev/null
@@ -1,267 +0,0 @@
-
-		SOFTWARE DEVELOPMENT KIT LICENSE AGREEMENT
-			(Linux APP SDK Installer)
-
-IMPORTANT-READ CAREFULLY:  This is a legal agreement 
-("Agreement") between you and Advanced Micro Devices, Inc. 
-("AMD"). Your use of this AMD Software Development Kit, (the 
-"SDK") including software, tools, utilities,
-Documentation, and to the extent provided hereunder, Libraries, 
-Sample Code, header files, any related AMD materials, and 
-updates thereto (collectively, "Licensed Materials"), are 
-subject to the following terms and conditions.
-Do not use these Licensed Materials until you have carefully 
-read the following terms and conditions. By downloading or 
-using the Licensed Materials obtained herewith, you are 
-expressly agreeing to all of the following
-terms:
-WARRANTIES, SUPPORT, RIGHTS, AND DAMAGES ARE DISCLAIMED AND/OR 
-LIMITED BELOW, PLEASE READ ENTIRELY AND CAREFULLY.  IF YOU DO 
-NOT AGREE TO THE TERMS OF THIS AGREEMENT, DO NOT DOWNLOAD OR 
-USE THE LICENSED MATERIALS OR ANY PORTION THEREOF.  DOWNLOADING 
-OR USING THE LICENSED MATERIALS OR ANY PORTION THEREOF 
-CONSTITUTES YOUR ACCEPTANCE OF THIS AGREEMENT.
-
-1. Definitions.
-
-   1.1. "Documentation" means install scripts and online or 
-electronic 		documentation included with the Licensed 
-Materials, or portions thereof.
-
-   1.2. "Free Software License" means an open source or other 
-license that requires, as a condition of use, modification or 
-distribution, that any resulting software must be (a) disclosed 
-or distributed in source code form; (b) licensed for the 
-purpose of making derivative works; or (c) re-distributable at 
-no charge.
-
-   1.3. "Licensee Software" means any software developed or 
-modified by you using the Licensed Materials, and which may 
-include any Libraries, Sample Code and/or derivative works of 
-Sample Code.
-
-   1.4. "Intellectual Property Rights" means all copyrights, 
-trademarks, trade secrets, patents, mask works, and all 
-related, similar, or other intellectual property rights 
-recognized in any jurisdiction worldwide, including all 
-applications and registrations with respect thereto.
-
-   1.5. "Libraries" means any run-times or other functionality 
-provided in Object Code including but not limited to codecs and 
-video processing libraries.
-
-   1.6. "Object Code" means machine readable computer 
-programming code files, which is not in a human readable form.
-
-   1.7. "Sample Code" means the Source Code identified within 
-the SDK as sample code.
-
-   1.8. "Source Code" means computer programming code in human 
-readable form and related system level documentation, including 
-all comments, symbols and any procedural code such as job 
-control language.
-
-2 License Grants.
-
-   2.1 Internal Use.  Subject to the terms and conditions of 
-this Agreement, AMD hereby grants to you a non-exclusive, non-
-transferable, royalty-free copyright license solely for your 
-internal use in developing Licensee Software for use with 
-products based on or incorporating AMD products (a) to use the 
-Licensed Materials, (b) to download, use, copy, and create 
-derivative works of Sample Code in Source Code and to create 
-compilations of same in Object Code form, and (c) to download, 
-use and copy the Libraries.
-
-	2.2 Restrictions.  This Agreement does not grant you any 
-rights, by license, implication or otherwise, in or to any 
-associated materials or technology, except as is expressly 
-provided herein.  Furthermore, you acknowledge that except as 
-expressly provided herein, the Licensed Materials provided by 
-AMD hereunder are for your internal use only and you may not 
-sell, transfer, assign, sublicense or distribute the Licensed 
-Materials, in whole or in part, in any manner.  Except as 
-expressly specified in Section 2.1, you will have no right to 
-make or have made derivatives of the Licensed Materials, to 
-reverse engineer, modify, disassemble or to decompile the 
-Licensed Materials, or otherwise reduce any part of the 
-Licensed Materials to any human readable form.  You will not 
-use the Licensed Materials in applications intended to support 
-or sustain life, or in which the failure of your product could 
-create a situation where personal injury, death, or severe 
-property or environmental damage may occur. You will not use or 
-distribute with any Licensee Software any code that is licensed 
-under a Free Software License.  No portion of the Licensed 
-Materials may in any event be distributed on a stand-alone 
-basis or other than in the form of Licensee Software.  You must 
-not alter or remove any copyright, trademark or patent notice 
-in the Licensed Materials.  You must reproduce all AMD 
-trademark and/or copyright notices on any derivative work that 
-incorporates Sample Code or Libraries.  You may not use AMD's 
-trademarks in the Licensee Software name or advertising in a 
-way that suggests the Licensee Software comes from or is 
-endorsed by AMD.
-
-	2.3 Third Party Materials.  Together with the Licensed 
-Materials, AMD may include third party technologies (e.g. third 
-party libraries) for which you must obtain licenses from 
-parties other than AMD.  You agree that AMD has not obtained or 
-conveyed to you, and that you shall be responsible for 
-obtaining, Intellectual Property Rights to use and/or 
-distribute the applicable, underlying Intellectual Property 
-Rights related to the third party technologies.  These third 
-party technologies are not licensed as part of the Licensed 
-Materials and are not licensed under this Agreement.
-
-	2.4 Other AMD Software Components.  The Licensed 
-Materials may be accompanied by AMD software components (e.g. 
-libraries, sample code) which are licensed to you under the 
-terms and conditions of their respective licenses located in 
-the directory with the software component.
-
-	2.5 Feedback.  You have no obligation to give AMD any 
-suggestions, comments or other feedback ("Feedback") relating 
-to the Licensed Materials.  However, AMD may use and include 
-any Feedback that you voluntarily provide to improve the 
-Licensed Materials or other AMD products and technologies.  
-Accordingly, if you provide Feedback, you grant AMD and its 
-affiliates and subsidiaries a worldwide, non-exclusive, 
-irrevocable, royalty-free, perpetual license to use, reproduce, 
-license, sublicense, distribute, make, have made, sell and 
-otherwise commercialize the Feedback in the Licensed Materials 
-or other AMD technologies.  You further agree not to provide 
-any Feedback that (a) you know is subject to any patent, 
-copyright or other intellectual property claim or right of any 
-third party; or (b) is subject to a Free Software License.
-
-3 Ownership and Copyright Notices.  The Licensed Materials are 
-owned or licensed by AMD and are protected by United States and 
-foreign intellectual property laws and international treaty 
-provisions.  All title and copyrights in and to the Licensed 
-Materials, all copies thereof (in whole or in part, and in any 
-form), and all rights therein will remain vested in AMD.  
-Except as expressly provided herein, AMD does not grant any 
-express or implied right to you under AMD patents, copyrights, 
-trademarks, or trade secrets. You agree the Licensed Materials 
-are licensed, not sold by AMD.
-
-4 Support.  You will not be entitled to any support of any kind 
-from AMD or AMD's licensors.  Furthermore, you will be solely 
-responsible for providing support to your end users for the 
-Licensee Software distributed by you or your
-products.  AMD may, in its sole discretion, provide to you 
-updates to the Licensed Materials. 
-
-5 Warranty, Limitations of Liability and Indemnification.
-
-	5.1 THE LICENSED MATERIALS ARE PROVIDED "AS IS," WITH ALL 
-FAULTS, AND WITHOUT WARRANTY OF ANY KIND.  AMD DISCLAIMS ALL 
-WARRANTIES, EXPRESS, IMPLIED, OR STATUTORY, INCLUDING BUT NOT 
-LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY, FITNESS 
-FOR A PARTICULAR PURPOSE, TITLE, AND NON-INFRINGEMENT.  AMD 
-DOES NOT WARRANT THAT THE LICENSED MATERIALS ARE ERROR FREE OR 
-THAT THE LICENSED MATERIALS WILL RUN CONTINUOUSLY.
-
-	5.2 AMD WILL NOT, UNDER ANY CIRCUMSTANCES, BE LIABLE TO 
-YOU FOR CONSEQUENTIAL, INCIDENTAL, PUNITIVE OR SPECIAL DAMAGES, 
-INCLUDING BUT NOT LIMITED TO, LOSS OF USE, DATA OR PROFITS, 
-ARISING FROM THIS AGREEMENT, EVEN IF AMD HAS BEEN APPRISED OF 
-THE LIKELIHOOD OF SUCH DAMAGES.  In no event will AMD's total 
-liability to you for all damages, losses, and causes of action 
-(whether in contract, tort (including negligence) or otherwise) 
-exceed the amount of $100 USD.
-
-	5.3 You agree to defend, indemnify and hold harmless AMD 
-and its licensors, and any of their directors, officers, 
-employees, affiliates or agents, from and against any and all 
-loss, damage, liability and other expenses (including 
-reasonable attorneys' fees), resulting from (a) your improper 
-use of the Licensed Materials or (b) use of Licensee Software.
-
-6 Termination.  Either party may terminate this Agreement upon 
-thirty (30) days prior written notice to the other party.  This 
-Agreement will terminate immediately without notice from AMD or 
-judicial resolution if you fail to comply
-with any provisions of this Agreement or upon AMD's written 
-request for return of the Licensed Materials.  Upon termination 
-of this Agreement, you will cease using the Licensed Materials. 
-Termination of this Agreement will have no effect on any sub-
-licenses properly granted by you to end users under Section 2, 
-which sub-licenses will survive in accordance with their terms.
-
-7 Survival.  Notwithstanding the foregoing, Sections 2.2, 2.3, 
-2.4, 2.5, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12 and 13 will survive 
-any expiration or termination of this Agreement, until by their 
-own terms they are fulfilled.
-
-8 Export Restrictions.  You shall adhere to all applicable 
-U.S., European, and other export laws, including but not 
-limited to the U.S. Export Administration Regulations ("EAR"), 
-(15 C.F.R. Sections 730 through 774), and E.U. Council 
-Regulation (EC) No 428/2009 of 5 May 2009.  Further, pursuant 
-to Section 740.6 of the EAR, you hereby certify that, except 
-pursuant to a license granted by the United States Department 
-of Commerce Bureau of Industry and Security or as otherwise 
-permitted pursuant to a License Exception under the EAR, you 
-will not (1) export, re-export or release to a national of a 
-country in Country Groups D:1, E:1 or E:2 any restricted 
-technology, software, or source code you receive from AMD, or 
-(2) export to Country Groups D:1, E:1 or E:2 the direct product 
-of such technology or software, if such foreign produced direct 
-product is subject to national security controls as identified 
-on the Commerce Control List (currently found in Supplement 1 
-to Part 774 of EAR).  For the most current Country Group 
-listings, or for additional information about the EAR or your 
-obligations under those regulations, please refer to the U.S. 
-Bureau of Industry and Security's website at 
-http://www.bis.doc.gov/.
-
-9. U.S. Government Restricted Rights.  The Licensed Materials 
-are provided with "RESTRICTED RIGHTS."  Use, duplication or 
-disclosure by the Government is subject to restrictions as set 
-forth in FAR 52.227-14 and DFAR 252.227-7013, et seq., or its 
-successor.  Use of the Licensed Materials by the Government 
-constitutes acknowledgement of AMD's proprietary rights in 
-them.
-
-10. Governing Law.  This Agreement will be governed under the 
-laws of Texas, excluding the conflicts of law rules, and is 
-deemed to have been executed and performed in Austin, Texas.
-
-11.	Equitable Remedies.  You acknowledge that your breach of 
-this Agreement may cause irreparable damage to AMD and agree 
-that AMD shall be entitled to seek injunctive relief under this 
-Agreement, as well as such further relief as may be granted by 
-a court of competent jurisdiction.
-
-12. General.  You may not assign this Agreement.  Any attempted 
-assignment by you will be null and void. The parties do not 
-intend that any agency or partnership relationship be created 
-between them by this Agreement.  Each
-provision of this Agreement shall be interpreted in such a 
-manner as to be effective and valid under applicable law. 
-However, in the event that any provision of this Agreement 
-becomes or is declared unenforceable by any court of
-competent jurisdiction, such provision shall be deemed deleted 
-and the remainder of this Agreement shall remain in full force 
-and effect
-
-13. Entire Agreement.  This Agreement sets forth the entire 
-agreement and understanding between the parties and supersedes 
-and merges all prior and contemporaneous oral and/or written 
-agreements, discussions and
-understandings concerning the subject matter hereof.  This 
-Agreement may not be modified except by a written instrument 
-executed by the parties.  No waiver or modification of any 
-provision of this Agreement shall be binding unless made in 
-writing and signed by an authorized representative of each 
-party.
-
-If you agree to abide by the terms and conditions of this 
-Agreement, please press "Accept."  If you do not agree to abide 
-by the terms and conditions of this Agreement, press "Decline" 
-and you may not use or access the Licensed
-Materials.
-
-By clicking accept, you confirm that you are neither a resident 
-nor a national of Cuba, Iran, North Korea, the Sudan or Syria.
diff --git a/licenses/ATLAS b/licenses/ATLAS
deleted file mode 100644
index e6f11a8c9..000000000
--- a/licenses/ATLAS
+++ /dev/null
@@ -1,48 +0,0 @@
-NON-COMMERCIAL LICENSE AGREEMENT
-
-This Non-commercial License Agreement (Agreement) has been adopted for use by Baylor College of Medicine (BCM), a Texas non-profit corporation, for the licensing of software programs for use for internal research purposes only by individuals or employees of an academic institution or private company. 
-
- 1.DEFINITIONS
-
- 1.1 The term Licensed Code shall mean the software entitled Atlas Whole Genome Assembly Suite, developed
-by (in alphabetical order): Rui Chen, James Durbin, Amy Egan, Paul Havlak, and Yanru Ren (collectively the Authors), employees of BCM.  
-
- 2.GRANT OF LICENSE
-
- 2.1 BCM hereby grants to you, or the corporation or institution you represent, identified in the above form (LICENSEE), a non-exclusive and non-transferable, right and license to use, modify, prepare derivative works of and execute solely for internal, research (non-commercial) purposes, the Licensed Code. This license shall be for use only by the LICENSEE only at the site (physical address) where the code is downloaded.  The foregoing license does not include the right to copy the Licensed Code, or portions thereof, to another site for any reason.
-
- 2.2 LICENSEE acknowledges that the Licensed Code, including, but not limited to, all rights under federal copyright laws, are and shall remain at all times the exclusive property of BCM. Any modifications or derivative works based on the Licensed Code are and shall be considered part of the Licensed Code and ownership thereof is retained by or vested in BCM.  LICENSEE shall provide to BCM reports of such modifications or derivative works and such modifications or derivative works shall be made available to BCM upon receipt of a written request for such from BCM.
-
- 2.3 LICENSEE shall not distribute or transfer the Licensed Code, or any portion thereof, to any other company, 
-institution or individual without the prior written permission of BCM.
-
- 3.NO UPGRADES/NO SERVICE/DELIVERED AS IS
-
- 3.1 It is expressly understood and agreed that the Licensed Code and Manuals will be delivered to LICENSEE on as "AS IS" basis as of the Agreement Date and that neither BCM nor the Authors will be responsible for future support of the Licensed Code.
-
- 3.2 LICENSEE acknowledges that LICENSEE will not be entitled to any Licensed Code upgrades and that BCM will not provide maintenance for the Licensed Code.  If LICENSEE finds defects, bugs, in the Licensed Code, LICENSEE shall notify BCM of the existence of the bugs. Neither BCM nor the Authors shall, however, have any obligation to fix any bugs in the Licensed Code.
-
- 4.DISCLAIMER OF WARRANTY
-
- BCM MAKES NO WARRANTIES OR REPRESENTATIONS, EXPRESS OR IMPLIED, INCLUDING, BUT NOT LIMITED TO, WARRANTIES OF FITNESS OR MERCHANTABILITY, REGARDING OR WITH RESPECT TO THE LICENSED CODE. BCM MAKES NO WARRANTIES OR REPRESENTATIONS, EXPRESS OR IMPLIED, OF THE PATENTABILITY OR COPYRIGHTABILITY OF ANY OF THE LICENSED CODE OR OF THE ENFORCEABILITY OF ANY PATENTS OR COPYRIGHTS ISSUING THEREUPON, IF ANY, OR THAT THE LICENSED CODE, IS OR SHALL BE FREE FROM INFRINGEMENT OF ANY PATENT, COPYRIGHT OR OTHER RIGHTS OF THIRD PARTIES. BCM MAKES NO WARRANTIES OR REPRESENTATIONS, EXPRESS OR IMPLIED, THAT THE LICENSED CODE SATISFIES REGULATORY REQUIREMENTS. LICENSEE ACKNOWLEDGE THAT THE LICENSED CODE IS BEING LICENSED AS IS. BCM HAS NOT TESTED THE LICENSED CODE FOR VIRUSES OR OTHER DEFECTS NOR HAS BCM COMPLETED TESTING THE LICENSED CODE.
-
- 5.LIMITATION OF DAMAGES
-
- BCM shall not be liable for any monetary damages whatsoever with respect to LICENSEE's use of the Licensed Code nor shall BCM be liable for any special, indirect, incidental or consequential damages arising out of or related to this Agreement, even if BCM is advised of such damages.
-
- 6.INDEMNIFICATION
-
- LICENSEE will indemnify and hold BCM, BCM's trustees, officers, agents, employees, students, persons holding academic appointments within BCM, and affiliated hospitals (the Indemnified parties) harmless from and against any and all claims, causes of action or lawsuits for personal injury (including death), property damage, and any other losses of any nature together with related expenses (including attorney's fees) made against the Indemnified parties resulting directly or indirectly from the use or possession of the Licensed Code by LICENSEE, regardless of whether such claim, causes of action, lawsuits, other proceedings and the costs (including attorney's fees) related thereto result in whole or in part from the negligence of any of the Indemnified parties.
-
-7.   BCM shall have the right to terminate this Agreement for any reason by giving ninety (90) days written 
-notice to LICENSEE.  Upon termination for any reason, LICENSEE agrees to destroy the original and all copies, 
-including partial copies of the Program.
-
-8.  The parties agree that this Agreement is the entire Agreement, and shall not be subject to any change or modification except in writing by both parties.
-
-9. The provisions of this Agreement are severable, and if any provisions of this Agreement are determined to 
-be invalid or unenforceable, such determination shall not in any way affect the validity or enforceability of the remaining provisions.
-
-----------------------------------------------------------------
-
-
diff --git a/licenses/AURA b/licenses/AURA
deleted file mode 100644
index 8ffca19cd..000000000
--- a/licenses/AURA
+++ /dev/null
@@ -1,29 +0,0 @@
-Copyright (C) 2008 Association of Universities for Research in Astronomy (AURA)
-
-Redistribution and use in source and binary forms, with or without
-modification, are permitted provided that the following conditions are met:
-
-    1. Redistributions of source code must retain the above copyright
-      notice, this list of conditions and the following disclaimer.
-
-    2. Redistributions in binary form must reproduce the above
-      copyright notice, this list of conditions and the following
-      disclaimer in the documentation and/or other materials provided
-      with the distribution.
-
-    3. The name of AURA and its representatives may not be used to
-      endorse or promote products derived from this software without
-      specific prior written permission.
-
-THIS SOFTWARE IS PROVIDED BY AURA ``AS IS'' AND ANY EXPRESS OR IMPLIED
-WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES OF
-MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE
-DISCLAIMED. IN NO EVENT SHALL AURA BE LIABLE FOR ANY DIRECT, INDIRECT,
-INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING,
-BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS
-OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND
-ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR
-TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE
-USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH
-DAMAGE.
-
diff --git a/licenses/Artistic-Manatee b/licenses/Artistic-Manatee
deleted file mode 100644
index 266b5db33..000000000
--- a/licenses/Artistic-Manatee
+++ /dev/null
@@ -1,50 +0,0 @@
-The Artistic License
-
-Preamble
-
-The intent of this document is to state the conditions under which a Package may be copied, such that the Copyright Holder maintains some semblance of artistic control over the development of the package, while giving the users of the package the right to use and distribute the Package in a more-or-less customary fashion, plus the right to make reasonable modifications.
-
-Definitions:
-
-    * "Package" refers to the collection of files distributed by the Copyright Holder, and derivatives of that collection of files created through textual modification.
-    * "Standard Version" refers to such a Package if it has not been modified, or has been modified in accordance with the wishes of the Copyright Holder.
-    * "Copyright Holder" is whoever is named in the copyright or copyrights for the package.
-    * "You" is you, if you're thinking about copying or distributing this Package.
-    * "Reasonable copying fee" is whatever you can justify on the basis of media cost, duplication charges, time of people involved, and so on. (You will not be required to justify it to the Copyright Holder, but only to the computing community at large as a market that must bear the fee.)
-    * "Freely Available" means that no fee is charged for the item itself, though there may be fees involved in handling the item. It also means that recipients of the item may redistribute it under the same conditions they received it.
-
-1. You may make and give away verbatim copies of the source form of the Standard Version of this Package without restriction, provided that you duplicate all of the original copyright notices and associated disclaimers.
-
-2. You may apply bug fixes, portability fixes and other modifications derived from the Public Domain or from the Copyright Holder. A Package modified in such a way shall still be considered the Standard Version.
-
-3. You may otherwise modify your copy of this Package in any way, provided that you insert a prominent notice in each changed file stating how and when you changed that file, and provided that you do at least ONE of the following:
-
-    a) place your modifications in the Public Domain or otherwise make them Freely Available, such as by posting said modifications to Usenet or an equivalent medium, or placing the modifications on a major archive site such as ftp.uu.net, or by allowing the Copyright Holder to include your modifications in the Standard Version of the Package.
-
-    b) use the modified Package only within your corporation or organization.
-
-    c) rename any non-standard executables so the names do not conflict with standard executables, which must also be provided, and provide a separate manual page for each non-standard executable that clearly documents how it differs from the Standard Version.
-
-    d) make other distribution arrangements with the Copyright Holder.
-
-4. You may distribute the programs of this Package in object code or executable form, provided that you do at least ONE of the following:
-
-    a) distribute a Standard Version of the executables and library files, together with instructions (in the manual page or equivalent) on where to get the Standard Version.
-
-    b) accompany the distribution with the machine-readable source of the Package with your modifications.
-
-    c) accompany any non-standard executables with their corresponding Standard Version executables, giving the non-standard executables non-standard names, and clearly documenting the differences in manual pages (or equivalent), together with instructions on where to get the Standard Version.
-
-    d) make other distribution arrangements with the Copyright Holder.
-
-5. You may charge a reasonable copying fee for any distribution of this Package. You may charge any fee you choose for support of this Package. You may not charge a fee for this Package itself. However, you may distribute this Package in aggregate with other (possibly commercial) programs as part of a larger (possibly commercial) software distribution provided that you do not advertise this Package as a product of your own.
-
-6. The scripts and library files supplied as input to or produced as output from the programs of this Package do not automatically fall under the copyright of this Package, but belong to whomever generated them, and may be sold commercially, and may be aggregated with this Package.
-
-7. C or perl subroutines supplied by you and linked into this Package shall not be considered part of this Package.
-
-8. The name of the Copyright Holder may not be used to endorse or promote products derived from this software without specific prior written permission.
-
-9. THIS PACKAGE IS PROVIDED "AS IS" AND WITHOUT ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, WITHOUT LIMITATION, THE IMPLIED WARRANTIES OF MERCHANTIBILITY AND FITNESS FOR A PARTICULAR PURPOSE.
-
-The End
diff --git a/licenses/BSD-3 b/licenses/BSD-3
deleted file mode 100644
index 3e6ae8250..000000000
--- a/licenses/BSD-3
+++ /dev/null
@@ -1,26 +0,0 @@
-Copyright (c) 2009-2018, Broad Institute, Inc. All rights reserved.
-
-Redistribution and use in source and binary forms, with or without
-modification, are permitted provided that the following conditions are met:
-
-* Redistributions of source code must retain the above copyright notice, this
-  list of conditions and the following disclaimer.
-
-* Redistributions in binary form must reproduce the above copyright notice,
-  this list of conditions and the following disclaimer in the documentation
-  and/or other materials provided with the distribution.
-
-* Neither the name Broad Institute, Inc. nor the names of its
-  contributors may be used to endorse or promote products derived from
-  this software without specific prior written permission.
-
-THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
-AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE
-IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE
-DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR CONTRIBUTORS BE LIABLE
-FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL
-DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR
-SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER
-CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY,
-OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE
-OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
diff --git a/licenses/CeCILL-1.1 b/licenses/CeCILL-1.1
deleted file mode 100644
index b4efe1181..000000000
--- a/licenses/CeCILL-1.1
+++ /dev/null
@@ -1,513 +0,0 @@
-                FREE SOFTWARE LICENSING AGREEMENT CeCILL
-                ========================================
-
-
-Notice
-------
-
-
-This Agreement is a free software license that is the result of  discussions
-between its authors  in  order  to  ensure  compliance  with  the  two  main
-principles guiding its drafting:
-   - firstly, its conformity with French law, both as  regards  the  law  of
-     torts and intellectual property law, and the protection that it offers
-     to authors and the holders of economic rights over software.
-   - secondly, compliance with the principles for the distribution  of  free
-     software: access to source codes, extended user-rights.
-
-The following bodies are the authors of this license CeCILL (Ce : CEA, C :
-CNRS, I : INRIA, LL : Logiciel Libre):
-
-Commissariat à l'Energie Atomique - CEA, a public scientific, technical  and
-industrial establishment, having its principal place of  business  at  31-33
-rue de la Fédération, 75752 PARIS cedex 15, France.
-
-Centre National de la Recherche Scientifique -  CNRS,  a  public  scientific
-and technological establishment, having its principal place of  business  at
-3 rue Michel-Ange 75794 Paris cedex 16, France.
-
-Institut National de Recherche en Informatique et en Automatique - INRIA,  a
-public scientific and  technological  establishment,  having  its  principal
-place of business at Domaine de Voluceau, Rocquencourt,  BP  105,  78153  Le
-Chesnay cedex.
-
-
-PREAMBLE
---------
-
-
-The purpose of this Free Software Licensing Agreement is to grant users  the
-right to modify and redistribute  the  software  governed  by  this  license
-within the framework of an "open source" distribution model.
-
-The exercising of these rights is conditional upon certain  obligations  for
-users  so  as  to  ensure  that  this  status  is  retained  for  subsequent
-redistribution operations.
-
-As a counterpart to the access to the source code and rights to copy, modify
-and redistribute granted by the license,  users are provided only with  a
-limited warranty and  the software's author, the holder of the economic
-rights,  and  the  successive licensors only have limited liability.
-
-In this respect, it is brought to the user's attention that the risks
-associated  with loading, using, modifying and/or developing or reproducing
-the  software  by the user given its nature of Free Software,  that  may  
-mean that it is complicated to manipulate, and that also therefore means 
-that it is reserved for developers and experienced professionals having
-in-depth computer knowledge. Users are therefore encouraged to load and test
-the Software's suitability  as  regards  their  requirements  in  conditions
-enabling  the security of their systems and/or data to be ensured and, more
-generally,  to use and operate  it  in  the  same  conditions  of security.
-This Agreement may be  freely  reproduced  and  published, provided  it  is
-not altered, and that no Articles are either added or removed herefrom. 
-
-This Agreement may apply to any or all software for which the holder of  the
-economic rights decides to submit the operation thereof to its provisions.
-
-
-Article 1  - DEFINITIONS
-------------------------
-
-
-For the purposes of this Agreement, when the following expressions  commence
-with a capital letter, they shall have the following meaning:
-
-Agreement: means this Licensing Agreement, and any or all of its  subsequent
-versions.
-
-Software: means the software in its Object  Code  and/or  Source  Code  form
-and, where applicable, its documentation, "as  is"  at  the  time  when  the
-Licensee accepts the Agreement.
-
-Initial Software: means the Software in its Source Code and/or  Object  Code
-form and, where applicable, its documentation, "as is" at the time  when  it
-is distributed for the first time under the  terms  and  conditions  of  the
-Agreement.
-
-Modified  Software:  means  the  Software   modified   by   at   least   one
-Contribution.
-
-Source Code: means all the Software's  instructions  and  program  lines  to
-which access is required so as to modify the Software.
-
-Object Code: means the binary files originating from the compilation of  the
-Source Code.
-
-Holder: means  the  holder  of  the  economic  rights  over  the  Initial
-Software.
-
-Licensee(s): mean(s) the Software user(s) having accepted the Agreement.
-
-Contributor: means a Licensee having made at least one Contribution.
-
-Licensor: means the Holder, or any or all other individual or legal  entity,
-that distributes the Software under the Agreement.
-
-Contributions: mean any or  all  modifications,  corrections,  translations,
-adaptations and/or new functionalities integrated into the Software  by  any
-or all Contributor, and the Static Modules.
-
-Module: means a set of sources files  including  their  documentation  that,
-once compiled in executable form, enables supplementary  functionalities  or
-services to be developed in addition to those offered by the Software.
-
-Dynamic Module: means any or all module, created by  the  Contributor,  that
-is independent of the Software, so that this module and the Software are  in
-two different executable forms that are  run  in  separate  address  spaces,
-with one calling the other when they are run.
-
-Static Module: means any or all  module,  created  by  the  Contributor  and
-connected to the Software by a static link that  makes  their  object  codes
-interdependent. This module and the Software to which it is  connected,  are
-combined in a single executable.
-
-Parties: mean both the Licensee and the Licensor.
-
-These expressions may be used both in singular and plural form.
-
-
-Article 2 - PURPOSE
--------------------
-
-
-The purpose of the  Agreement  is  to  enable  the  Licensor  to  grant  the
-Licensee a free, non-exclusive, transferable and worldwide License  for  the
-Software as set forth in  Article  5  hereinafter  for  the  whole  term  of
-protection of the rights over said Software.
-
-
-Article 3 - ACCEPTANCE
-----------------------
-
-
-3.1. The  Licensee  shall  be  deemed  as  having  accepted  the  terms  and
-conditions of  this  Agreement  by  the  occurrence  of  the  first  of  the
-following events:
-- (i) loading the Software by any or all means, notably,  by  downloading
-  from a remote server, or by loading from a physical medium;
-- (ii) the first time the Licensee exercises any of  the  rights  granted
-  hereunder.
-
-3.2. One copy  of  the  Agreement,  containing  a  notice  relating  to  the
-specific nature of the  Software,  to  the  limited  warranty,  and  to  the
-limitation to use by experienced users has been  provided  to  the  Licensee
-prior to its acceptance as set forth in Article  3.1  hereinabove,  and  the
-Licensee hereby acknowledges that it is aware thereof.
-
-
-Article 4 - EFFECTIVE DATE AND TERM
------------------------------------
-
-
-4.1. EFFECTIVE DATE
-
-The Agreement shall become effective on the date when it is accepted by  the
-Licensee as set forth in Article 3.1.
-
-4.2. TERM
-
-The Agreement  shall  remain  in  force  during  the  whole  legal  term  of
-protection of the economic rights over the Software.
-
-
-Article 5 - SCOPE OF THE RIGHTS GRANTED
----------------------------------------
-
-
-The  Licensor  hereby  grants  to  the  Licensee,  that  accepts  such,  the
-following rights as regards the Software for any or all  use,  and  for  the
-term of the Agreement, on the basis of the terms and  conditions  set  forth
-hereinafter.
-
-Otherwise, the Licensor grants to the Licensee free of  charge  exploitation
-rights on  the  patents  he  holds  on  whole  or  part  of  the  inventions
-implemented in the Software.
-
-5.1. RIGHTS OF USE
-
-The Licensee is authorized to use the Software, unrestrictedly,  as  regards
-the fields of application, with it being  hereinafter  specified  that  this
-relates to:
-- permanent or temporary reproduction of all or part of the Software  by
-  any or all means and in any or all form.
-- loading, displaying, running, or storing the Software on any or all
-  medium.
-- entitlement to observe, study or test the operation thereof so  as  to
-  establish the ideas and principles that form the basis for any or  all
-  constituent elements of said  Software.  This  shall  apply  when  the
-  Licensee  carries  out  any  or  all  loading,  displaying,   running,
-  transmission or storage operation as regards the Software, that it  is
-  entitled to carry out hereunder.
-
-5.2. entitlement to make CONTRIBUTIONS
-
-The right to make Contributions includes  the  right  to  translate,  adapt,
-arrange, or make any or all modification to the Software, and the  right  to
-reproduce the resulting Software.
-
-The Licensee is authorized to make any or all Contribution to  the  Software
-provided that it  explicitly  mentions  its  name  as  the  author  of  said
-Contribution and the date of the development thereof.
-
-5.3. DISTRIBUTION AND PUBLICATION RIGHTS
-
-In particular, the right of distribution and publication includes the  right
-to transmit and communicate the Software to the general  public  on  any  or
-all medium, and by any or all means, and the  right  to  market,  either  in
-consideration of a fee, or free of charge, a  copy or copies of the Software 
-by means of any or all process.
-The Licensee is further authorized to redistribute copies  of  the  modified
-or  unmodified  Software  to  third  parties  according  to  the  terms  and
-conditions set forth hereinafter.
-
-5.3.1. REDISTRIBUTION OF SOFTWARE WITHOUT MODIFICATION
-
-The Licensee is authorized to redistribute true copies of  the  Software  in
-Source Code or Object Code form, provided that said redistribution  complies
-with all the provisions of the Agreement and is accompanied by:
-- a copy of the Agreement,
-- a notice relating to the limitation of both  the  Licensor's  warranty
-  and liability as set forth in Articles 8 and 9,
-and  that,  in  the  event  that  only  the  Software's   Object   Code   is
-redistributed, the Licensee allows future  Licensees  unhindered  access  to
-the Software's full Source  Code  by  providing  them  with  the  terms  and
-conditions for access thereto, it being understood that the additional  cost
-of acquiring the Source Code shall not exceed the cost of  transferring  the
-data.
-
-5.3.2. REDISTRIBUTION OF MODIFIED  SOFTWARE
-
-When the Licensee makes a  Contribution  to  the  Software,  the  terms  and
-conditions for the redistribution of the Modified  Software  shall  then  be
-subject to all the provisions hereof.
-
-The Licensee is authorized to redistribute the Modified Software, in  Source
-Code or Object Code form, provided that said  redistribution  complies  with
-all the provisions of the Agreement and is accompanied by:
-- a copy of the Agreement,
-- a notice relating to the limitation of both  the  Licensor's  warranty
-  and liability as set forth in Articles 8 and 9,
-and that, in the event that only the  Modified  Software's  Object  Code  is
-redistributed, the Licensee allows future  Licensees  unhindered  access  to
-the Modified Software's full Source Code by providing them  with  the  terms
-and conditions for access thereto, it being understood that  the  additional
-cost of acquiring the Source Code shall not exceed the cost of  transferring
-the data.
-
-
-5.3.3. redistribution OF DYNAMIC MODULES
-
-When the Licensee has developed a Dynamic Module, the terms  and  conditions
-hereof do not apply to said Dynamic Module, that  may  be  distributed under 
-a separate Licensing Agreement.
-
-5.3.4. COMPATIBILITY WITH THE GPL LICENSE
-
-In the event that the Modified or unmodified Software is included in a code
-that is subject to the provisions of the GPL License, the Licensee is
-authorized to redistribute the whole under the GPL License.
-
-In the event that the Modified Software includes a code that is  subject  to
-the  provisions  of  the  GPL  License,  the  Licensee  is   authorized   to
-redistribute the Modified Software under the GPL License.
-
-
-Article 6  - INTELLECTUAL PROPERTY
-----------------------------------
-
-
-6.1. OVER THE INITIAL SOFTWARE
-
-The Holder owns the economic rights over the Initial Software.  Any  or  all
-use of the Initial Software is subject to  compliance  with  the  terms  and
-conditions under which the Holder has elected to distribute its work and  no
-one shall be entitled to  and it shall have sole entitlement to  modify  the
-terms and conditions for the distribution of said Initial Software.
-
-The Holder undertakes to maintain the distribution of the  Initial  Software
-under the conditions of  the  Agreement,  for  the  duration  set  forth  in
-article 4.2..
-
-6.2. OVER THE CONTRIBUTIONS
-
-The intellectual property rights over the Contributions belong to  the
-holder of the economic rights as designated by effective legislation.
-
-6.3. OVER THE DYNAMIC MODULES
-
-The Licensee having  developed  a  Dynamic  Module  is  the  holder  of  the
-intellectual property rights over said Dynamic Module and is free to  choose
-the agreement that shall govern its distribution.
-
-6.4. JOINT PROVISIONS
-
-6.4.1. The Licensee expressly undertakes:
-- not to remove, or modify, in  any  or  all  manner,  the  intellectual
-  property notices affixed to the Software;
-- to reproduce said notices, in an identical manner, in  the  copies  of
-  the Software.
-
-6.4.2. The Licensee undertakes not to directly or  indirectly  infringe  the
-intellectual property rights of the Holder and/or Contributors and to  take,
-where applicable, vis-à-vis its staff,  any  or  all  measures  required  to
-ensure respect for said intellectual property rights of  the  Holder  and/or
-Contributors.
-
-
-Article 7  - RELATED SERVICES
------------------------------
-
-
-7.1. Under no circumstances shall  the  Agreement  oblige  the  Licensor  to
-provide technical assistance or maintenance services for the Software.
-
-However, the Licensor is entitled to offer  this  type  of  service. The
-terms  and  conditions  of  such  technical  assistance,  and/or   such 
-maintenance, shall then be set forth in  a  separate  instrument.  Only  the
-Licensor offering said  maintenance  and/or  technical  assistance  services
-shall incur liability therefor.
-
-7.2. Similarly, any or all Licensor  shall  be  entitled  to  offer  to  its
-Licensees, under its own responsibility, a  warranty,  that  shall  only  be
-binding upon itself, for the  redistribution  of  the  Software  and/or  the
-Modified Software, under terms and conditions  that  it  shall  decide  upon
-itself. Said warranty,  and  the  financial  terms  and  conditions  of  its
-application, shall be subject to a separate instrument executed between  the
-Licensor and the Licensee.
-
-
-Article 8  - LIABILITY
-----------------------
-
-
-8.1. Subject to the provisions of Article 8.2, should the Licensor  fail  to
-fulfill all or part of its obligations  hereunder,  the  Licensee  shall  be
-entitled to claim compensation for the direct loss suffered  as a result of
-a fault on the part of the Licensor, subject to providing evidence of it. 
-
-8.2. The Licensor's liability is limited to the commitments made under  this
-Licensing Agreement and shall not be incurred as a result ,  in  particular:
-(i) of loss due the Licensee's total  or  partial  failure  to  fulfill  its
-obligations, (ii) direct or consequential loss due to the Software's use  or
-performance that  is  suffered  by  the  Licensee,  when  the  latter  is  a
-professional  using  said  Software  for  professional  purposes  and  (iii)
-consequential loss due to the Software's use  or  performance.  The  Parties
-expressly agree that any or all pecuniary or business  loss  (i.e.  loss  of
-data, loss  of  profits,  operating  loss,  loss  of  customers  or  orders,
-opportunity cost, any disturbance to business  activities)  or  any  or  all
-legal proceedings instituted against the Licensee by a  third  party,  shall
-constitute consequential loss and shall not provide entitlement  to  any  or
-all compensation from the Licensor.
-
-
-Article 9  - WARRANTY
----------------------
-
-
-9.1. The  Licensee  acknowledges  that  the  current  situation  as  regards
-scientific and  technical  know-how  at  the  time  when  the  Software  was
-distributed did not enable all possible uses to be tested and verified,  nor
-for the presence of any or all faults to be detected. In this  respect,  the
-Licensee's attention has been drawn to the risks  associated  with  loading,
-using, modifying and/or developing and reproducing  the  Software  that  are
-reserved for experienced users.
-
-The Licensee shall be responsible for verifying, by any or  all  means,  the
-product's suitability for its requirements, its due and proper  functioning,
-and for ensuring that it  shall  not  cause  damage  to  either  persons  or
-property.
-
-9.2. The Licensor hereby represents, in good faith, that it is  entitled  to
-grant all the rights on the  Software (including in  particular  the  rights
-set forth in Article 5 hereof over the Software).
-
-9.3. The Licensee acknowledges that the Software is supplied "as is" by  the
-Licensor without any or all other express  or  tacit  warranty,  other  than
-that provided for in Article 9.2 and, in  particular,  without  any  or  all
-warranty as to its market  value,  its  secured,  innovative  or  relevant
-nature.
-
-Specifically, the Licensor does not warrant that the Software is  free  from
-any or all error, that it shall  operate  continuously,  that  it  shall  be
-compatible  with   the   Licensee's   own   equipment   and   its   software
-configuration, nor that it shall meet the Licensee's requirements.
-
-9.4. The Licensor does not either expressly  or  tacitly  warrant  that  the
-Software does not  infringe  any  or  all  third  party  intellectual  right
-relating to a patent, software or  to  any  or  all  other  property  right.
-Moreover, the Licensor shall not hold the Licensee harmless against  any  or
-all proceedings for infringement that may be instituted in  respect  of  the
-use, modification and redistribution of the Software.  Nevertheless,  should
-such proceedings be instituted against  the  Licensee,  the  Licensor  shall
-provide it with  technical  and  legal  assistance  for  its  defense.  Such
-technical and legal assistance shall  be  decided  upon  on  a  case-by-case
-basis  between  the  relevant  Licensor  and  the  Licensee  pursuant  to  a
-memorandum of understanding. The Licensor disclaims any or all liability  as
-regards the Licensee's use of the Software's  name.  No  warranty  shall  be
-provided as regards the existence of prior  rights  over  the  name  of  the
-Software and as regards the existence of a trademark.
-
-
-Article 10  - TERMINATION
--------------------------
-
-
-10.1. In  the  event  of  a  breach  by  the  Licensee  of  its  obligations
-hereunder, the Licensor may automatically terminate  this  Agreement  thirty
-(30) days after notice has been  sent  to  the  Licensee  and  has  remained
-ineffective.
-
-10.2. The  Licensee  whose  Agreement  is  terminated  shall  no  longer  be
-authorized to use, modify or distribute the Software. However,  any  or  all
-licenses that it may have granted prior to  termination  of  the  Agreement
-shall remain valid subject to their having been granted in  compliance  with
-the terms and conditions hereof.
-
-
-Article 11  - MISCELLANEOUS PROVISIONS
---------------------------------------
-
-
-11.1. EXCUSABLE EVENTS
-
-Neither Party shall be liable for any or all delay, or  failure  to  perform
-the Agreement, that may be attributable to an event  of  force  majeure,  an
-act of God or an outside cause, such as, notably, defective functioning,  or
-interruptions affecting  the  electricity  or  telecommunications  networks,
-blocking of the network following a virus attack, the  intervention  of  the
-government authorities, natural disasters, water damage, earthquakes,  fire,
-explosions, strikes and labor unrest, war, etc.
-
-11.2. The fact that either Party may fail, on one or several  occasions,  to
-invoke  one  or  several  of  the  provisions   hereof,   shall   under   no
-circumstances be interpreted as being a waiver by the  interested  Party  of
-its entitlement to invoke said provision(s) subsequently.
-
-11.3. The Agreement cancels and replaces  any  or  all  previous  agreement,
-whether written or oral, between the Parties and having  the  same  purpose,
-and  constitutes  the  entirety  of  the  agreement  between  said   Parties
-concerning said purpose. No supplement or  modification  to  the  terms  and
-conditions hereof shall be effective as regards the  Parties  unless  it  is
-made in writing and signed by their duly authorized representatives.
-
-11.4. In the event that one or several of  the  provisions  hereof  were  to
-conflict with a current or future applicable act or legislative  text,  said
-act or legislative text shall take precedence, and the  Parties  shall  make
-the necessary amendments so  as  to  be  in  compliance  with  said  act  or
-legislative  text.  All  the  other  provisions  shall   remain   effective.
-Similarly, the fact that a provision of  the  Agreement  may   be  null  and
-void, for any reason whatsoever, shall not cause the Agreement  as  a  whole
-to be null and void.
-
-11.5. LANGUAGE
-
-The Agreement is drafted in both French and  English.  In  the  event  of  a
-conflict as  regards  construction,  the  French  version  shall  be  deemed
-authentic.
-
-
-Article 12  - NEW VERSIONS OF THE AGREEMENT
--------------------------------------------
-
-
-12.1. Any or all person is authorized to duplicate and distribute copies  of
-this Agreement.
-
-12.2. So as to ensure coherence, the wording of this Agreement is  protected
-and may only be modified by the authors of the  License,  that  reserve  the
-right to periodically publish updates or  new  versions  of  the  Agreement,
-each with a separate number. These subsequent versions may address new issues
-encountered by Free Software.
-
-12.3. Any  or  all  Software  distributed  under  a  given  version  of  the
-Agreement may only be subsequently distributed under  the  same  version  of
-the Agreement, or  a  subsequent  version,  subject  to  the  provisions  of
-article 5.3.4.
-
-
-Article 13 - GOVERNING LAW AND JURISDICTION
--------------------------------------------
-
-
-13.1. The Agreement is  governed  by  French  law.   The  Parties  agree  to
-endeavor to settle the disagreements or disputes that may arise  during  the
-performance of the Agreement out-of-court.
-
-13.2. In the absence of an out-of-court settlement within two (2) months  as
-from their occurrence, and unless emergency proceedings are  necessary,  the
-disagreements or disputes shall be  referred  to  the  Paris  Courts  having
-jurisdiction, by the first Party to take action.
-
-
-                                                   Version 1.1 of 10/26/2004
-
-
-
-
-
-
-
-
-
-
-
diff --git a/licenses/CeCILL-2.0 b/licenses/CeCILL-2.0
deleted file mode 100644
index 9061494b8..000000000
--- a/licenses/CeCILL-2.0
+++ /dev/null
@@ -1,505 +0,0 @@
-CeCILL FREE SOFTWARE LICENSE AGREEMENT
-
-
-    Notice
-
-This Agreement is a Free Software license agreement that is the result
-of discussions between its authors in order to ensure compliance with
-the two main principles guiding its drafting:
-
-    * firstly, compliance with the principles governing the distribution
-      of Free Software: access to source code, broad rights granted to
-      users,
-    * secondly, the election of a governing law, French law, with which
-      it is conformant, both as regards the law of torts and
-      intellectual property law, and the protection that it offers to
-      both authors and holders of the economic rights over software.
-
-The authors of the CeCILL (for Ce[a] C[nrs] I[nria] L[ogiciel] L[ibre])
-license are:
-
-Commissariat  l'Energie Atomique - CEA, a public scientific, technical
-and industrial research establishment, having its principal place of
-business at 25 rue Leblanc, immeuble Le Ponant D, 75015 Paris, France.
-
-Centre National de la Recherche Scientifique - CNRS, a public scientific
-and technological establishment, having its principal place of business
-at 3 rue Michel-Ange, 75794 Paris cedex 16, France.
-
-Institut National de Recherche en Informatique et en Automatique -
-INRIA, a public scientific and technological establishment, having its
-principal place of business at Domaine de Voluceau, Rocquencourt, BP
-105, 78153 Le Chesnay cedex, France.
-
-
-    Preamble
-
-The purpose of this Free Software license agreement is to grant users
-the right to modify and redistribute the software governed by this
-license within the framework of an open source distribution model.
-
-The exercising of these rights is conditional upon certain obligations
-for users so as to preserve this status for all subsequent redistributions.
-
-In consideration of access to the source code and the rights to copy,
-modify and redistribute granted by the license, users are provided only
-with a limited warranty and the software's author, the holder of the
-economic rights, and the successive licensors only have limited liability.
-
-In this respect, the risks associated with loading, using, modifying
-and/or developing or reproducing the software by the user are brought to
-the user's attention, given its Free Software status, which may make it
-complicated to use, with the result that its use is reserved for
-developers and experienced professionals having in-depth computer
-knowledge. Users are therefore encouraged to load and test the
-suitability of the software as regards their requirements in conditions
-enabling the security of their systems and/or data to be ensured and,
-more generally, to use and operate it in the same conditions of
-security. This Agreement may be freely reproduced and published,
-provided it is not altered, and that no provisions are either added or
-removed herefrom.
-
-This Agreement may apply to any or all software for which the holder of
-the economic rights decides to submit the use thereof to its provisions.
-
-
-    Article 1 - DEFINITIONS
-
-For the purpose of this Agreement, when the following expressions
-commence with a capital letter, they shall have the following meaning:
-
-Agreement: means this license agreement, and its possible subsequent
-versions and annexes.
-
-Software: means the software in its Object Code and/or Source Code form
-and, where applicable, its documentation, "as is" when the Licensee
-accepts the Agreement.
-
-Initial Software: means the Software in its Source Code and possibly its
-Object Code form and, where applicable, its documentation, "as is" when
-it is first distributed under the terms and conditions of the Agreement.
-
-Modified Software: means the Software modified by at least one
-Contribution.
-
-Source Code: means all the Software's instructions and program lines to
-which access is required so as to modify the Software.
-
-Object Code: means the binary files originating from the compilation of
-the Source Code.
-
-Holder: means the holder(s) of the economic rights over the Initial
-Software.
-
-Licensee: means the Software user(s) having accepted the Agreement.
-
-Contributor: means a Licensee having made at least one Contribution.
-
-Licensor: means the Holder, or any other individual or legal entity, who
-distributes the Software under the Agreement.
-
-Contribution: means any or all modifications, corrections, translations,
-adaptations and/or new functions integrated into the Software by any or
-all Contributors, as well as any or all Internal Modules.
-
-Module: means a set of sources files including their documentation that
-enables supplementary functions or services in addition to those offered
-by the Software.
-
-External Module: means any or all Modules, not derived from the
-Software, so that this Module and the Software run in separate address
-spaces, with one calling the other when they are run.
-
-Internal Module: means any or all Module, connected to the Software so
-that they both execute in the same address space.
-
-GNU GPL: means the GNU General Public License version 2 or any
-subsequent version, as published by the Free Software Foundation Inc.
-
-Parties: mean both the Licensee and the Licensor.
-
-These expressions may be used both in singular and plural form.
-
-
-    Article 2 - PURPOSE
-
-The purpose of the Agreement is the grant by the Licensor to the
-Licensee of a non-exclusive, transferable and worldwide license for the
-Software as set forth in Article 5 hereinafter for the whole term of the
-protection granted by the rights over said Software. 
-
-
-    Article 3 - ACCEPTANCE
-
-3.1 The Licensee shall be deemed as having accepted the terms and
-conditions of this Agreement upon the occurrence of the first of the
-following events:
-
-    * (i) loading the Software by any or all means, notably, by
-      downloading from a remote server, or by loading from a physical
-      medium;
-    * (ii) the first time the Licensee exercises any of the rights
-      granted hereunder.
-
-3.2 One copy of the Agreement, containing a notice relating to the
-characteristics of the Software, to the limited warranty, and to the
-fact that its use is restricted to experienced users has been provided
-to the Licensee prior to its acceptance as set forth in Article 3.1
-hereinabove, and the Licensee hereby acknowledges that it has read and
-understood it.
-
-
-    Article 4 - EFFECTIVE DATE AND TERM
-
-
-      4.1 EFFECTIVE DATE
-
-The Agreement shall become effective on the date when it is accepted by
-the Licensee as set forth in Article 3.1.
-
-
-      4.2 TERM
-
-The Agreement shall remain in force for the entire legal term of
-protection of the economic rights over the Software.
-
-
-    Article 5 - SCOPE OF RIGHTS GRANTED
-
-The Licensor hereby grants to the Licensee, who accepts, the following
-rights over the Software for any or all use, and for the term of the
-Agreement, on the basis of the terms and conditions set forth hereinafter.
-
-Besides, if the Licensor owns or comes to own one or more patents
-protecting all or part of the functions of the Software or of its
-components, the Licensor undertakes not to enforce the rights granted by
-these patents against successive Licensees using, exploiting or
-modifying the Software. If these patents are transferred, the Licensor
-undertakes to have the transferees subscribe to the obligations set
-forth in this paragraph.
-
-
-      5.1 RIGHT OF USE
-
-The Licensee is authorized to use the Software, without any limitation
-as to its fields of application, with it being hereinafter specified
-that this comprises:
-
-   1. permanent or temporary reproduction of all or part of the Software
-      by any or all means and in any or all form.
-
-   2. loading, displaying, running, or storing the Software on any or
-      all medium.
-
-   3. entitlement to observe, study or test its operation so as to
-      determine the ideas and principles behind any or all constituent
-      elements of said Software. This shall apply when the Licensee
-      carries out any or all loading, displaying, running, transmission
-      or storage operation as regards the Software, that it is entitled
-      to carry out hereunder.
-
-
-      5.2 ENTITLEMENT TO MAKE CONTRIBUTIONS
-
-The right to make Contributions includes the right to translate, adapt,
-arrange, or make any or all modifications to the Software, and the right
-to reproduce the resulting software.
-
-The Licensee is authorized to make any or all Contributions to the
-Software provided that it includes an explicit notice that it is the
-author of said Contribution and indicates the date of the creation thereof.
-
-
-      5.3 RIGHT OF DISTRIBUTION
-
-In particular, the right of distribution includes the right to publish,
-transmit and communicate the Software to the general public on any or
-all medium, and by any or all means, and the right to market, either in
-consideration of a fee, or free of charge, one or more copies of the
-Software by any means.
-
-The Licensee is further authorized to distribute copies of the modified
-or unmodified Software to third parties according to the terms and
-conditions set forth hereinafter.
-
-
-        5.3.1 DISTRIBUTION OF SOFTWARE WITHOUT MODIFICATION
-
-The Licensee is authorized to distribute true copies of the Software in
-Source Code or Object Code form, provided that said distribution
-complies with all the provisions of the Agreement and is accompanied by:
-
-   1. a copy of the Agreement,
-
-   2. a notice relating to the limitation of both the Licensor's
-      warranty and liability as set forth in Articles 8 and 9,
-
-and that, in the event that only the Object Code of the Software is
-redistributed, the Licensee allows future Licensees unhindered access to
-the full Source Code of the Software by indicating how to access it, it
-being understood that the additional cost of acquiring the Source Code
-shall not exceed the cost of transferring the data.
-
-
-        5.3.2 DISTRIBUTION OF MODIFIED SOFTWARE
-
-When the Licensee makes a Contribution to the Software, the terms and
-conditions for the distribution of the resulting Modified Software
-become subject to all the provisions of this Agreement.
-
-The Licensee is authorized to distribute the Modified Software, in
-source code or object code form, provided that said distribution
-complies with all the provisions of the Agreement and is accompanied by:
-
-   1. a copy of the Agreement,
-
-   2. a notice relating to the limitation of both the Licensor's
-      warranty and liability as set forth in Articles 8 and 9,
-
-and that, in the event that only the object code of the Modified
-Software is redistributed, the Licensee allows future Licensees
-unhindered access to the full source code of the Modified Software by
-indicating how to access it, it being understood that the additional
-cost of acquiring the source code shall not exceed the cost of
-transferring the data.
-
-
-        5.3.3 DISTRIBUTION OF EXTERNAL MODULES
-
-When the Licensee has developed an External Module, the terms and
-conditions of this Agreement do not apply to said External Module, that
-may be distributed under a separate license agreement.
-
-
-        5.3.4 COMPATIBILITY WITH THE GNU GPL
-
-The Licensee can include a code that is subject to the provisions of one
-of the versions of the GNU GPL in the Modified or unmodified Software,
-and distribute that entire code under the terms of the same version of
-the GNU GPL.
-
-The Licensee can include the Modified or unmodified Software in a code
-that is subject to the provisions of one of the versions of the GNU GPL,
-and distribute that entire code under the terms of the same version of
-the GNU GPL.
-
-
-    Article 6 - INTELLECTUAL PROPERTY
-
-
-      6.1 OVER THE INITIAL SOFTWARE
-
-The Holder owns the economic rights over the Initial Software. Any or
-all use of the Initial Software is subject to compliance with the terms
-and conditions under which the Holder has elected to distribute its work
-and no one shall be entitled to modify the terms and conditions for the
-distribution of said Initial Software.
-
-The Holder undertakes that the Initial Software will remain ruled at
-least by this Agreement, for the duration set forth in Article 4.2.
-
-
-      6.2 OVER THE CONTRIBUTIONS
-
-The Licensee who develops a Contribution is the owner of the
-intellectual property rights over this Contribution as defined by
-applicable law.
-
-
-      6.3 OVER THE EXTERNAL MODULES
-
-The Licensee who develops an External Module is the owner of the
-intellectual property rights over this External Module as defined by
-applicable law and is free to choose the type of agreement that shall
-govern its distribution.
-
-
-      6.4 JOINT PROVISIONS
-
-The Licensee expressly undertakes:
-
-   1. not to remove, or modify, in any manner, the intellectual property
-      notices attached to the Software;
-
-   2. to reproduce said notices, in an identical manner, in the copies
-      of the Software modified or not.
-
-The Licensee undertakes not to directly or indirectly infringe the
-intellectual property rights of the Holder and/or Contributors on the
-Software and to take, where applicable, vis--vis its staff, any and all
-measures required to ensure respect of said intellectual property rights
-of the Holder and/or Contributors.
-
-
-    Article 7 - RELATED SERVICES
-
-7.1 Under no circumstances shall the Agreement oblige the Licensor to
-provide technical assistance or maintenance services for the Software.
-
-However, the Licensor is entitled to offer this type of services. The
-terms and conditions of such technical assistance, and/or such
-maintenance, shall be set forth in a separate instrument. Only the
-Licensor offering said maintenance and/or technical assistance services
-shall incur liability therefor.
-
-7.2 Similarly, any Licensor is entitled to offer to its licensees, under
-its sole responsibility, a warranty, that shall only be binding upon
-itself, for the redistribution of the Software and/or the Modified
-Software, under terms and conditions that it is free to decide. Said
-warranty, and the financial terms and conditions of its application,
-shall be subject of a separate instrument executed between the Licensor
-and the Licensee.
-
-
-    Article 8 - LIABILITY
-
-8.1 Subject to the provisions of Article 8.2, the Licensee shall be
-entitled to claim compensation for any direct loss it may have suffered
-from the Software as a result of a fault on the part of the relevant
-Licensor, subject to providing evidence thereof.
-
-8.2 The Licensor's liability is limited to the commitments made under
-this Agreement and shall not be incurred as a result of in particular:
-(i) loss due the Licensee's total or partial failure to fulfill its
-obligations, (ii) direct or consequential loss that is suffered by the
-Licensee due to the use or performance of the Software, and (iii) more
-generally, any consequential loss. In particular the Parties expressly
-agree that any or all pecuniary or business loss (i.e. loss of data,
-loss of profits, operating loss, loss of customers or orders,
-opportunity cost, any disturbance to business activities) or any or all
-legal proceedings instituted against the Licensee by a third party,
-shall constitute consequential loss and shall not provide entitlement to
-any or all compensation from the Licensor.
-
-
-    Article 9 - WARRANTY
-
-9.1 The Licensee acknowledges that the scientific and technical
-state-of-the-art when the Software was distributed did not enable all
-possible uses to be tested and verified, nor for the presence of
-possible defects to be detected. In this respect, the Licensee's
-attention has been drawn to the risks associated with loading, using,
-modifying and/or developing and reproducing the Software which are
-reserved for experienced users.
-
-The Licensee shall be responsible for verifying, by any or all means,
-the suitability of the product for its requirements, its good working
-order, and for ensuring that it shall not cause damage to either persons
-or properties.
-
-9.2 The Licensor hereby represents, in good faith, that it is entitled
-to grant all the rights over the Software (including in particular the
-rights set forth in Article 5).
-
-9.3 The Licensee acknowledges that the Software is supplied "as is" by
-the Licensor without any other express or tacit warranty, other than
-that provided for in Article 9.2 and, in particular, without any warranty 
-as to its commercial value, its secured, safe, innovative or relevant
-nature.
-
-Specifically, the Licensor does not warrant that the Software is free
-from any error, that it will operate without interruption, that it will
-be compatible with the Licensee's own equipment and software
-configuration, nor that it will meet the Licensee's requirements.
-
-9.4 The Licensor does not either expressly or tacitly warrant that the
-Software does not infringe any third party intellectual property right
-relating to a patent, software or any other property right. Therefore,
-the Licensor disclaims any and all liability towards the Licensee
-arising out of any or all proceedings for infringement that may be
-instituted in respect of the use, modification and redistribution of the
-Software. Nevertheless, should such proceedings be instituted against
-the Licensee, the Licensor shall provide it with technical and legal
-assistance for its defense. Such technical and legal assistance shall be
-decided on a case-by-case basis between the relevant Licensor and the
-Licensee pursuant to a memorandum of understanding. The Licensor
-disclaims any and all liability as regards the Licensee's use of the
-name of the Software. No warranty is given as regards the existence of
-prior rights over the name of the Software or as regards the existence
-of a trademark.
-
-
-    Article 10 - TERMINATION
-
-10.1 In the event of a breach by the Licensee of its obligations
-hereunder, the Licensor may automatically terminate this Agreement
-thirty (30) days after notice has been sent to the Licensee and has
-remained ineffective.
-
-10.2 A Licensee whose Agreement is terminated shall no longer be
-authorized to use, modify or distribute the Software. However, any
-licenses that it may have granted prior to termination of the Agreement
-shall remain valid subject to their having been granted in compliance
-with the terms and conditions hereof.
-
-
-    Article 11 - MISCELLANEOUS
-
-
-      11.1 EXCUSABLE EVENTS
-
-Neither Party shall be liable for any or all delay, or failure to
-perform the Agreement, that may be attributable to an event of force
-majeure, an act of God or an outside cause, such as defective
-functioning or interruptions of the electricity or telecommunications
-networks, network paralysis following a virus attack, intervention by
-government authorities, natural disasters, water damage, earthquakes,
-fire, explosions, strikes and labor unrest, war, etc.
-
-11.2 Any failure by either Party, on one or more occasions, to invoke
-one or more of the provisions hereof, shall under no circumstances be
-interpreted as being a waiver by the interested Party of its right to
-invoke said provision(s) subsequently.
-
-11.3 The Agreement cancels and replaces any or all previous agreements,
-whether written or oral, between the Parties and having the same
-purpose, and constitutes the entirety of the agreement between said
-Parties concerning said purpose. No supplement or modification to the
-terms and conditions hereof shall be effective as between the Parties
-unless it is made in writing and signed by their duly authorized
-representatives.
-
-11.4 In the event that one or more of the provisions hereof were to
-conflict with a current or future applicable act or legislative text,
-said act or legislative text shall prevail, and the Parties shall make
-the necessary amendments so as to comply with said act or legislative
-text. All other provisions shall remain effective. Similarly, invalidity
-of a provision of the Agreement, for any reason whatsoever, shall not
-cause the Agreement as a whole to be invalid.
-
-
-      11.5 LANGUAGE
-
-The Agreement is drafted in both French and English and both versions
-are deemed authentic.
-
-
-    Article 12 - NEW VERSIONS OF THE AGREEMENT
-
-12.1 Any person is authorized to duplicate and distribute copies of this
-Agreement.
-
-12.2 So as to ensure coherence, the wording of this Agreement is
-protected and may only be modified by the authors of the License, who
-reserve the right to periodically publish updates or new versions of the
-Agreement, each with a separate number. These subsequent versions may
-address new issues encountered by Free Software.
-
-12.3 Any Software distributed under a given version of the Agreement may
-only be subsequently distributed under the same version of the Agreement
-or a subsequent version, subject to the provisions of Article 5.3.4.
-
-
-    Article 13 - GOVERNING LAW AND JURISDICTION
-
-13.1 The Agreement is governed by French law. The Parties agree to
-endeavor to seek an amicable solution to any disagreements or disputes
-that may arise during the performance of the Agreement.
-
-13.2 Failing an amicable solution within two (2) months as from their
-occurrence, and unless emergency proceedings are necessary, the
-disagreements or disputes shall be referred to the Paris Courts having
-jurisdiction, by the more diligent Party.
-
-
-Version 2.0 dated 2006-09-05.
diff --git a/licenses/CeCILL-2.1 b/licenses/CeCILL-2.1
deleted file mode 100644
index b705f37a2..000000000
--- a/licenses/CeCILL-2.1
+++ /dev/null
@@ -1,519 +0,0 @@
-
-  CeCILL FREE SOFTWARE LICENSE AGREEMENT
-
-Version 2.1 dated 2013-06-21
-
-
-    Notice
-
-This Agreement is a Free Software license agreement that is the result
-of discussions between its authors in order to ensure compliance with
-the two main principles guiding its drafting:
-
-  * firstly, compliance with the principles governing the distribution
-    of Free Software: access to source code, broad rights granted to users,
-  * secondly, the election of a governing law, French law, with which it
-    is conformant, both as regards the law of torts and intellectual
-    property law, and the protection that it offers to both authors and
-    holders of the economic rights over software.
-
-The authors of the CeCILL (for Ce[a] C[nrs] I[nria] L[ogiciel] L[ibre]) 
-license are: 
-
-Commissariat à l'énergie atomique et aux énergies alternatives - CEA, a
-public scientific, technical and industrial research establishment,
-having its principal place of business at 25 rue Leblanc, immeuble Le
-Ponant D, 75015 Paris, France.
-
-Centre National de la Recherche Scientifique - CNRS, a public scientific
-and technological establishment, having its principal place of business
-at 3 rue Michel-Ange, 75794 Paris cedex 16, France.
-
-Institut National de Recherche en Informatique et en Automatique -
-Inria, a public scientific and technological establishment, having its
-principal place of business at Domaine de Voluceau, Rocquencourt, BP
-105, 78153 Le Chesnay cedex, France.
-
-
-    Preamble
-
-The purpose of this Free Software license agreement is to grant users
-the right to modify and redistribute the software governed by this
-license within the framework of an open source distribution model.
-
-The exercising of this right is conditional upon certain obligations for
-users so as to preserve this status for all subsequent redistributions.
-
-In consideration of access to the source code and the rights to copy,
-modify and redistribute granted by the license, users are provided only
-with a limited warranty and the software's author, the holder of the
-economic rights, and the successive licensors only have limited liability.
-
-In this respect, the risks associated with loading, using, modifying
-and/or developing or reproducing the software by the user are brought to
-the user's attention, given its Free Software status, which may make it
-complicated to use, with the result that its use is reserved for
-developers and experienced professionals having in-depth computer
-knowledge. Users are therefore encouraged to load and test the
-suitability of the software as regards their requirements in conditions
-enabling the security of their systems and/or data to be ensured and,
-more generally, to use and operate it in the same conditions of
-security. This Agreement may be freely reproduced and published,
-provided it is not altered, and that no provisions are either added or
-removed herefrom.
-
-This Agreement may apply to any or all software for which the holder of
-the economic rights decides to submit the use thereof to its provisions.
-
-Frequently asked questions can be found on the official website of the
-CeCILL licenses family (http://www.cecill.info/index.en.html) for any 
-necessary clarification.
-
-
-    Article 1 - DEFINITIONS
-
-For the purpose of this Agreement, when the following expressions
-commence with a capital letter, they shall have the following meaning:
-
-Agreement: means this license agreement, and its possible subsequent
-versions and annexes.
-
-Software: means the software in its Object Code and/or Source Code form
-and, where applicable, its documentation, "as is" when the Licensee
-accepts the Agreement.
-
-Initial Software: means the Software in its Source Code and possibly its
-Object Code form and, where applicable, its documentation, "as is" when
-it is first distributed under the terms and conditions of the Agreement.
-
-Modified Software: means the Software modified by at least one
-Contribution.
-
-Source Code: means all the Software's instructions and program lines to
-which access is required so as to modify the Software.
-
-Object Code: means the binary files originating from the compilation of
-the Source Code.
-
-Holder: means the holder(s) of the economic rights over the Initial
-Software.
-
-Licensee: means the Software user(s) having accepted the Agreement.
-
-Contributor: means a Licensee having made at least one Contribution.
-
-Licensor: means the Holder, or any other individual or legal entity, who
-distributes the Software under the Agreement.
-
-Contribution: means any or all modifications, corrections, translations,
-adaptations and/or new functions integrated into the Software by any or
-all Contributors, as well as any or all Internal Modules.
-
-Module: means a set of sources files including their documentation that
-enables supplementary functions or services in addition to those offered
-by the Software.
-
-External Module: means any or all Modules, not derived from the
-Software, so that this Module and the Software run in separate address
-spaces, with one calling the other when they are run.
-
-Internal Module: means any or all Module, connected to the Software so
-that they both execute in the same address space.
-
-GNU GPL: means the GNU General Public License version 2 or any
-subsequent version, as published by the Free Software Foundation Inc.
-
-GNU Affero GPL: means the GNU Affero General Public License version 3 or
-any subsequent version, as published by the Free Software Foundation Inc.
-
-EUPL: means the European Union Public License version 1.1 or any
-subsequent version, as published by the European Commission.
-
-Parties: mean both the Licensee and the Licensor.
-
-These expressions may be used both in singular and plural form.
-
-
-    Article 2 - PURPOSE
-
-The purpose of the Agreement is the grant by the Licensor to the
-Licensee of a non-exclusive, transferable and worldwide license for the
-Software as set forth in Article 5 <#scope> hereinafter for the whole
-term of the protection granted by the rights over said Software.
-
-
-    Article 3 - ACCEPTANCE
-
-3.1 The Licensee shall be deemed as having accepted the terms and
-conditions of this Agreement upon the occurrence of the first of the
-following events:
-
-  * (i) loading the Software by any or all means, notably, by
-    downloading from a remote server, or by loading from a physical medium;
-  * (ii) the first time the Licensee exercises any of the rights granted
-    hereunder.
-
-3.2 One copy of the Agreement, containing a notice relating to the
-characteristics of the Software, to the limited warranty, and to the
-fact that its use is restricted to experienced users has been provided
-to the Licensee prior to its acceptance as set forth in Article 3.1
-<#accepting> hereinabove, and the Licensee hereby acknowledges that it
-has read and understood it.
-
-
-    Article 4 - EFFECTIVE DATE AND TERM
-
-
-      4.1 EFFECTIVE DATE
-
-The Agreement shall become effective on the date when it is accepted by
-the Licensee as set forth in Article 3.1 <#accepting>.
-
-
-      4.2 TERM
-
-The Agreement shall remain in force for the entire legal term of
-protection of the economic rights over the Software.
-
-
-    Article 5 - SCOPE OF RIGHTS GRANTED
-
-The Licensor hereby grants to the Licensee, who accepts, the following
-rights over the Software for any or all use, and for the term of the
-Agreement, on the basis of the terms and conditions set forth hereinafter.
-
-Besides, if the Licensor owns or comes to own one or more patents
-protecting all or part of the functions of the Software or of its
-components, the Licensor undertakes not to enforce the rights granted by
-these patents against successive Licensees using, exploiting or
-modifying the Software. If these patents are transferred, the Licensor
-undertakes to have the transferees subscribe to the obligations set
-forth in this paragraph.
-
-
-      5.1 RIGHT OF USE
-
-The Licensee is authorized to use the Software, without any limitation
-as to its fields of application, with it being hereinafter specified
-that this comprises:
-
- 1. permanent or temporary reproduction of all or part of the Software
-    by any or all means and in any or all form.
-
- 2. loading, displaying, running, or storing the Software on any or all
-    medium.
-
- 3. entitlement to observe, study or test its operation so as to
-    determine the ideas and principles behind any or all constituent
-    elements of said Software. This shall apply when the Licensee
-    carries out any or all loading, displaying, running, transmission or
-    storage operation as regards the Software, that it is entitled to
-    carry out hereunder.
-
-
-      5.2 ENTITLEMENT TO MAKE CONTRIBUTIONS
-
-The right to make Contributions includes the right to translate, adapt,
-arrange, or make any or all modifications to the Software, and the right
-to reproduce the resulting software.
-
-The Licensee is authorized to make any or all Contributions to the
-Software provided that it includes an explicit notice that it is the
-author of said Contribution and indicates the date of the creation thereof.
-
-
-      5.3 RIGHT OF DISTRIBUTION
-
-In particular, the right of distribution includes the right to publish,
-transmit and communicate the Software to the general public on any or
-all medium, and by any or all means, and the right to market, either in
-consideration of a fee, or free of charge, one or more copies of the
-Software by any means.
-
-The Licensee is further authorized to distribute copies of the modified
-or unmodified Software to third parties according to the terms and
-conditions set forth hereinafter.
-
-
-        5.3.1 DISTRIBUTION OF SOFTWARE WITHOUT MODIFICATION
-
-The Licensee is authorized to distribute true copies of the Software in
-Source Code or Object Code form, provided that said distribution
-complies with all the provisions of the Agreement and is accompanied by:
-
- 1. a copy of the Agreement,
-
- 2. a notice relating to the limitation of both the Licensor's warranty
-    and liability as set forth in Articles 8 and 9,
-
-and that, in the event that only the Object Code of the Software is
-redistributed, the Licensee allows effective access to the full Source
-Code of the Software for a period of at least three years from the
-distribution of the Software, it being understood that the additional
-acquisition cost of the Source Code shall not exceed the cost of the
-data transfer.
-
-
-        5.3.2 DISTRIBUTION OF MODIFIED SOFTWARE
-
-When the Licensee makes a Contribution to the Software, the terms and
-conditions for the distribution of the resulting Modified Software
-become subject to all the provisions of this Agreement.
-
-The Licensee is authorized to distribute the Modified Software, in
-source code or object code form, provided that said distribution
-complies with all the provisions of the Agreement and is accompanied by:
-
- 1. a copy of the Agreement,
-
- 2. a notice relating to the limitation of both the Licensor's warranty
-    and liability as set forth in Articles 8 and 9,
-
-and, in the event that only the object code of the Modified Software is
-redistributed,
-
- 3. a note stating the conditions of effective access to the full source
-    code of the Modified Software for a period of at least three years
-    from the distribution of the Modified Software, it being understood
-    that the additional acquisition cost of the source code shall not
-    exceed the cost of the data transfer.
-
-
-        5.3.3 DISTRIBUTION OF EXTERNAL MODULES
-
-When the Licensee has developed an External Module, the terms and
-conditions of this Agreement do not apply to said External Module, that
-may be distributed under a separate license agreement.
-
-
-        5.3.4 COMPATIBILITY WITH OTHER LICENSES
-
-The Licensee can include a code that is subject to the provisions of one
-of the versions of the GNU GPL, GNU Affero GPL and/or EUPL in the
-Modified or unmodified Software, and distribute that entire code under
-the terms of the same version of the GNU GPL, GNU Affero GPL and/or EUPL.
-
-The Licensee can include the Modified or unmodified Software in a code
-that is subject to the provisions of one of the versions of the GNU GPL,
-GNU Affero GPL and/or EUPL and distribute that entire code under the
-terms of the same version of the GNU GPL, GNU Affero GPL and/or EUPL.
-
-
-    Article 6 - INTELLECTUAL PROPERTY
-
-
-      6.1 OVER THE INITIAL SOFTWARE
-
-The Holder owns the economic rights over the Initial Software. Any or
-all use of the Initial Software is subject to compliance with the terms
-and conditions under which the Holder has elected to distribute its work
-and no one shall be entitled to modify the terms and conditions for the
-distribution of said Initial Software.
-
-The Holder undertakes that the Initial Software will remain ruled at
-least by this Agreement, for the duration set forth in Article 4.2 <#term>.
-
-
-      6.2 OVER THE CONTRIBUTIONS
-
-The Licensee who develops a Contribution is the owner of the
-intellectual property rights over this Contribution as defined by
-applicable law.
-
-
-      6.3 OVER THE EXTERNAL MODULES
-
-The Licensee who develops an External Module is the owner of the
-intellectual property rights over this External Module as defined by
-applicable law and is free to choose the type of agreement that shall
-govern its distribution.
-
-
-      6.4 JOINT PROVISIONS
-
-The Licensee expressly undertakes:
-
- 1. not to remove, or modify, in any manner, the intellectual property
-    notices attached to the Software;
-
- 2. to reproduce said notices, in an identical manner, in the copies of
-    the Software modified or not.
-
-The Licensee undertakes not to directly or indirectly infringe the
-intellectual property rights on the Software of the Holder and/or
-Contributors, and to take, where applicable, vis-à-vis its staff, any
-and all measures required to ensure respect of said intellectual
-property rights of the Holder and/or Contributors.
-
-
-    Article 7 - RELATED SERVICES
-
-7.1 Under no circumstances shall the Agreement oblige the Licensor to
-provide technical assistance or maintenance services for the Software.
-
-However, the Licensor is entitled to offer this type of services. The
-terms and conditions of such technical assistance, and/or such
-maintenance, shall be set forth in a separate instrument. Only the
-Licensor offering said maintenance and/or technical assistance services
-shall incur liability therefor.
-
-7.2 Similarly, any Licensor is entitled to offer to its licensees, under
-its sole responsibility, a warranty, that shall only be binding upon
-itself, for the redistribution of the Software and/or the Modified
-Software, under terms and conditions that it is free to decide. Said
-warranty, and the financial terms and conditions of its application,
-shall be subject of a separate instrument executed between the Licensor
-and the Licensee.
-
-
-    Article 8 - LIABILITY
-
-8.1 Subject to the provisions of Article 8.2, the Licensee shall be
-entitled to claim compensation for any direct loss it may have suffered
-from the Software as a result of a fault on the part of the relevant
-Licensor, subject to providing evidence thereof.
-
-8.2 The Licensor's liability is limited to the commitments made under
-this Agreement and shall not be incurred as a result of in particular:
-(i) loss due the Licensee's total or partial failure to fulfill its
-obligations, (ii) direct or consequential loss that is suffered by the
-Licensee due to the use or performance of the Software, and (iii) more
-generally, any consequential loss. In particular the Parties expressly
-agree that any or all pecuniary or business loss (i.e. loss of data,
-loss of profits, operating loss, loss of customers or orders,
-opportunity cost, any disturbance to business activities) or any or all
-legal proceedings instituted against the Licensee by a third party,
-shall constitute consequential loss and shall not provide entitlement to
-any or all compensation from the Licensor.
-
-
-    Article 9 - WARRANTY
-
-9.1 The Licensee acknowledges that the scientific and technical
-state-of-the-art when the Software was distributed did not enable all
-possible uses to be tested and verified, nor for the presence of
-possible defects to be detected. In this respect, the Licensee's
-attention has been drawn to the risks associated with loading, using,
-modifying and/or developing and reproducing the Software which are
-reserved for experienced users.
-
-The Licensee shall be responsible for verifying, by any or all means,
-the suitability of the product for its requirements, its good working
-order, and for ensuring that it shall not cause damage to either persons
-or properties.
-
-9.2 The Licensor hereby represents, in good faith, that it is entitled
-to grant all the rights over the Software (including in particular the
-rights set forth in Article 5 <#scope>).
-
-9.3 The Licensee acknowledges that the Software is supplied "as is" by
-the Licensor without any other express or tacit warranty, other than
-that provided for in Article 9.2 <#good-faith> and, in particular,
-without any warranty as to its commercial value, its secured, safe,
-innovative or relevant nature.
-
-Specifically, the Licensor does not warrant that the Software is free
-from any error, that it will operate without interruption, that it will
-be compatible with the Licensee's own equipment and software
-configuration, nor that it will meet the Licensee's requirements.
-
-9.4 The Licensor does not either expressly or tacitly warrant that the
-Software does not infringe any third party intellectual property right
-relating to a patent, software or any other property right. Therefore,
-the Licensor disclaims any and all liability towards the Licensee
-arising out of any or all proceedings for infringement that may be
-instituted in respect of the use, modification and redistribution of the
-Software. Nevertheless, should such proceedings be instituted against
-the Licensee, the Licensor shall provide it with technical and legal
-expertise for its defense. Such technical and legal expertise shall be
-decided on a case-by-case basis between the relevant Licensor and the
-Licensee pursuant to a memorandum of understanding. The Licensor
-disclaims any and all liability as regards the Licensee's use of the
-name of the Software. No warranty is given as regards the existence of
-prior rights over the name of the Software or as regards the existence
-of a trademark.
-
-
-    Article 10 - TERMINATION
-
-10.1 In the event of a breach by the Licensee of its obligations
-hereunder, the Licensor may automatically terminate this Agreement
-thirty (30) days after notice has been sent to the Licensee and has
-remained ineffective.
-
-10.2 A Licensee whose Agreement is terminated shall no longer be
-authorized to use, modify or distribute the Software. However, any
-licenses that it may have granted prior to termination of the Agreement
-shall remain valid subject to their having been granted in compliance
-with the terms and conditions hereof.
-
-
-    Article 11 - MISCELLANEOUS
-
-
-      11.1 EXCUSABLE EVENTS
-
-Neither Party shall be liable for any or all delay, or failure to
-perform the Agreement, that may be attributable to an event of force
-majeure, an act of God or an outside cause, such as defective
-functioning or interruptions of the electricity or telecommunications
-networks, network paralysis following a virus attack, intervention by
-government authorities, natural disasters, water damage, earthquakes,
-fire, explosions, strikes and labor unrest, war, etc.
-
-11.2 Any failure by either Party, on one or more occasions, to invoke
-one or more of the provisions hereof, shall under no circumstances be
-interpreted as being a waiver by the interested Party of its right to
-invoke said provision(s) subsequently.
-
-11.3 The Agreement cancels and replaces any or all previous agreements,
-whether written or oral, between the Parties and having the same
-purpose, and constitutes the entirety of the agreement between said
-Parties concerning said purpose. No supplement or modification to the
-terms and conditions hereof shall be effective as between the Parties
-unless it is made in writing and signed by their duly authorized
-representatives.
-
-11.4 In the event that one or more of the provisions hereof were to
-conflict with a current or future applicable act or legislative text,
-said act or legislative text shall prevail, and the Parties shall make
-the necessary amendments so as to comply with said act or legislative
-text. All other provisions shall remain effective. Similarly, invalidity
-of a provision of the Agreement, for any reason whatsoever, shall not
-cause the Agreement as a whole to be invalid.
-
-
-      11.5 LANGUAGE
-
-The Agreement is drafted in both French and English and both versions
-are deemed authentic.
-
-
-    Article 12 - NEW VERSIONS OF THE AGREEMENT
-
-12.1 Any person is authorized to duplicate and distribute copies of this
-Agreement.
-
-12.2 So as to ensure coherence, the wording of this Agreement is
-protected and may only be modified by the authors of the License, who
-reserve the right to periodically publish updates or new versions of the
-Agreement, each with a separate number. These subsequent versions may
-address new issues encountered by Free Software.
-
-12.3 Any Software distributed under a given version of the Agreement may
-only be subsequently distributed under the same version of the Agreement
-or a subsequent version, subject to the provisions of Article 5.3.4
-<#compatibility>.
-
-
-    Article 13 - GOVERNING LAW AND JURISDICTION
-
-13.1 The Agreement is governed by French law. The Parties agree to
-endeavor to seek an amicable solution to any disagreements or disputes
-that may arise during the performance of the Agreement.
-
-13.2 Failing an amicable solution within two (2) months as from their
-occurrence, and unless emergency proceedings are necessary, the
-disagreements or disputes shall be referred to the Paris Courts having
-jurisdiction, by the more diligent Party.
-
diff --git a/licenses/CeCILL-B b/licenses/CeCILL-B
deleted file mode 100644
index 3ad4deaa3..000000000
--- a/licenses/CeCILL-B
+++ /dev/null
@@ -1,515 +0,0 @@
-
-CeCILL-B FREE SOFTWARE LICENSE AGREEMENT
-
-
-    Notice
-
-This Agreement is a Free Software license agreement that is the result
-of discussions between its authors in order to ensure compliance with
-the two main principles guiding its drafting:
-
-    * firstly, compliance with the principles governing the distribution
-      of Free Software: access to source code, broad rights granted to
-      users,
-    * secondly, the election of a governing law, French law, with which
-      it is conformant, both as regards the law of torts and
-      intellectual property law, and the protection that it offers to
-      both authors and holders of the economic rights over software.
-
-The authors of the CeCILL-B (for Ce[a] C[nrs] I[nria] L[ogiciel] L[ibre])
-license are: 
-
-Commissariat à l'Energie Atomique - CEA, a public scientific, technical
-and industrial research establishment, having its principal place of
-business at 25 rue Leblanc, immeuble Le Ponant D, 75015 Paris, France.
-
-Centre National de la Recherche Scientifique - CNRS, a public scientific
-and technological establishment, having its principal place of business
-at 3 rue Michel-Ange, 75794 Paris cedex 16, France.
-
-Institut National de Recherche en Informatique et en Automatique -
-INRIA, a public scientific and technological establishment, having its
-principal place of business at Domaine de Voluceau, Rocquencourt, BP
-105, 78153 Le Chesnay cedex, France.
-
-
-    Preamble
-
-This Agreement is an open source software license intended to give users
-significant freedom to modify and redistribute the software licensed
-hereunder.
-
-The exercising of this freedom is conditional upon a strong obligation
-of giving credits for everybody that distributes a software
-incorporating a software ruled by the current license so as all
-contributions to be properly identified and acknowledged.
-
-In consideration of access to the source code and the rights to copy,
-modify and redistribute granted by the license, users are provided only
-with a limited warranty and the software's author, the holder of the
-economic rights, and the successive licensors only have limited liability.
-
-In this respect, the risks associated with loading, using, modifying
-and/or developing or reproducing the software by the user are brought to
-the user's attention, given its Free Software status, which may make it
-complicated to use, with the result that its use is reserved for
-developers and experienced professionals having in-depth computer
-knowledge. Users are therefore encouraged to load and test the
-suitability of the software as regards their requirements in conditions
-enabling the security of their systems and/or data to be ensured and,
-more generally, to use and operate it in the same conditions of
-security. This Agreement may be freely reproduced and published,
-provided it is not altered, and that no provisions are either added or
-removed herefrom.
-
-This Agreement may apply to any or all software for which the holder of
-the economic rights decides to submit the use thereof to its provisions.
-
-
-    Article 1 - DEFINITIONS
-
-For the purpose of this Agreement, when the following expressions
-commence with a capital letter, they shall have the following meaning:
-
-Agreement: means this license agreement, and its possible subsequent
-versions and annexes.
-
-Software: means the software in its Object Code and/or Source Code form
-and, where applicable, its documentation, "as is" when the Licensee
-accepts the Agreement.
-
-Initial Software: means the Software in its Source Code and possibly its
-Object Code form and, where applicable, its documentation, "as is" when
-it is first distributed under the terms and conditions of the Agreement.
-
-Modified Software: means the Software modified by at least one
-Contribution.
-
-Source Code: means all the Software's instructions and program lines to
-which access is required so as to modify the Software.
-
-Object Code: means the binary files originating from the compilation of
-the Source Code.
-
-Holder: means the holder(s) of the economic rights over the Initial
-Software.
-
-Licensee: means the Software user(s) having accepted the Agreement.
-
-Contributor: means a Licensee having made at least one Contribution.
-
-Licensor: means the Holder, or any other individual or legal entity, who
-distributes the Software under the Agreement.
-
-Contribution: means any or all modifications, corrections, translations,
-adaptations and/or new functions integrated into the Software by any or
-all Contributors, as well as any or all Internal Modules.
-
-Module: means a set of sources files including their documentation that
-enables supplementary functions or services in addition to those offered
-by the Software.
-
-External Module: means any or all Modules, not derived from the
-Software, so that this Module and the Software run in separate address
-spaces, with one calling the other when they are run.
-
-Internal Module: means any or all Module, connected to the Software so
-that they both execute in the same address space.
-
-Parties: mean both the Licensee and the Licensor.
-
-These expressions may be used both in singular and plural form.
-
-
-    Article 2 - PURPOSE
-
-The purpose of the Agreement is the grant by the Licensor to the
-Licensee of a non-exclusive, transferable and worldwide license for the
-Software as set forth in Article 5 hereinafter for the whole term of the
-protection granted by the rights over said Software.
-
-
-    Article 3 - ACCEPTANCE
-
-3.1 The Licensee shall be deemed as having accepted the terms and
-conditions of this Agreement upon the occurrence of the first of the
-following events:
-
-    * (i) loading the Software by any or all means, notably, by
-      downloading from a remote server, or by loading from a physical
-      medium;
-    * (ii) the first time the Licensee exercises any of the rights
-      granted hereunder.
-
-3.2 One copy of the Agreement, containing a notice relating to the
-characteristics of the Software, to the limited warranty, and to the
-fact that its use is restricted to experienced users has been provided
-to the Licensee prior to its acceptance as set forth in Article 3.1
-hereinabove, and the Licensee hereby acknowledges that it has read and
-understood it.
-
-
-    Article 4 - EFFECTIVE DATE AND TERM
-
-
-      4.1 EFFECTIVE DATE
-
-The Agreement shall become effective on the date when it is accepted by
-the Licensee as set forth in Article 3.1.
-
-
-      4.2 TERM
-
-The Agreement shall remain in force for the entire legal term of
-protection of the economic rights over the Software.
-
-
-    Article 5 - SCOPE OF RIGHTS GRANTED
-
-The Licensor hereby grants to the Licensee, who accepts, the following
-rights over the Software for any or all use, and for the term of the
-Agreement, on the basis of the terms and conditions set forth hereinafter.
-
-Besides, if the Licensor owns or comes to own one or more patents
-protecting all or part of the functions of the Software or of its
-components, the Licensor undertakes not to enforce the rights granted by
-these patents against successive Licensees using, exploiting or
-modifying the Software. If these patents are transferred, the Licensor
-undertakes to have the transferees subscribe to the obligations set
-forth in this paragraph.
-
-
-      5.1 RIGHT OF USE
-
-The Licensee is authorized to use the Software, without any limitation
-as to its fields of application, with it being hereinafter specified
-that this comprises:
-
-   1. permanent or temporary reproduction of all or part of the Software
-      by any or all means and in any or all form.
-
-   2. loading, displaying, running, or storing the Software on any or
-      all medium.
-
-   3. entitlement to observe, study or test its operation so as to
-      determine the ideas and principles behind any or all constituent
-      elements of said Software. This shall apply when the Licensee
-      carries out any or all loading, displaying, running, transmission
-      or storage operation as regards the Software, that it is entitled
-      to carry out hereunder.
-
-
-      5.2 ENTITLEMENT TO MAKE CONTRIBUTIONS
-
-The right to make Contributions includes the right to translate, adapt,
-arrange, or make any or all modifications to the Software, and the right
-to reproduce the resulting software.
-
-The Licensee is authorized to make any or all Contributions to the
-Software provided that it includes an explicit notice that it is the
-author of said Contribution and indicates the date of the creation thereof.
-
-
-      5.3 RIGHT OF DISTRIBUTION
-
-In particular, the right of distribution includes the right to publish,
-transmit and communicate the Software to the general public on any or
-all medium, and by any or all means, and the right to market, either in
-consideration of a fee, or free of charge, one or more copies of the
-Software by any means.
-
-The Licensee is further authorized to distribute copies of the modified
-or unmodified Software to third parties according to the terms and
-conditions set forth hereinafter.
-
-
-        5.3.1 DISTRIBUTION OF SOFTWARE WITHOUT MODIFICATION
-
-The Licensee is authorized to distribute true copies of the Software in
-Source Code or Object Code form, provided that said distribution
-complies with all the provisions of the Agreement and is accompanied by:
-
-   1. a copy of the Agreement,
-
-   2. a notice relating to the limitation of both the Licensor's
-      warranty and liability as set forth in Articles 8 and 9,
-
-and that, in the event that only the Object Code of the Software is
-redistributed, the Licensee allows effective access to the full Source
-Code of the Software at a minimum during the entire period of its
-distribution of the Software, it being understood that the additional
-cost of acquiring the Source Code shall not exceed the cost of
-transferring the data.
-
-
-        5.3.2 DISTRIBUTION OF MODIFIED SOFTWARE
-
-If the Licensee makes any Contribution to the Software, the resulting
-Modified Software may be distributed under a license agreement other
-than this Agreement subject to compliance with the provisions of Article
-5.3.4.
-
-
-        5.3.3 DISTRIBUTION OF EXTERNAL MODULES
-
-When the Licensee has developed an External Module, the terms and
-conditions of this Agreement do not apply to said External Module, that
-may be distributed under a separate license agreement.
-
-
-        5.3.4 CREDITS
-
-Any Licensee who may distribute a Modified Software hereby expressly
-agrees to:
-
-   1. indicate in the related documentation that it is based on the
-      Software licensed hereunder, and reproduce the intellectual
-      property notice for the Software,
-
-   2. ensure that written indications of the Software intended use,
-      intellectual property notice and license hereunder are included in
-      easily accessible format from the Modified Software interface,
-
-   3. mention, on a freely accessible website describing the Modified
-      Software, at least throughout the distribution term thereof, that
-      it is based on the Software licensed hereunder, and reproduce the
-      Software intellectual property notice,
-
-   4. where it is distributed to a third party that may distribute a
-      Modified Software without having to make its source code
-      available, make its best efforts to ensure that said third party
-      agrees to comply with the obligations set forth in this Article .
-
-If the Software, whether or not modified, is distributed with an
-External Module designed for use in connection with the Software, the
-Licensee shall submit said External Module to the foregoing obligations.
-
-
-        5.3.5 COMPATIBILITY WITH THE CeCILL AND CeCILL-C LICENSES
-
-Where a Modified Software contains a Contribution subject to the CeCILL
-license, the provisions set forth in Article 5.3.4 shall be optional.
-
-A Modified Software may be distributed under the CeCILL-C license. In
-such a case the provisions set forth in Article 5.3.4 shall be optional.
-
-
-    Article 6 - INTELLECTUAL PROPERTY
-
-
-      6.1 OVER THE INITIAL SOFTWARE
-
-The Holder owns the economic rights over the Initial Software. Any or
-all use of the Initial Software is subject to compliance with the terms
-and conditions under which the Holder has elected to distribute its work
-and no one shall be entitled to modify the terms and conditions for the
-distribution of said Initial Software.
-
-The Holder undertakes that the Initial Software will remain ruled at
-least by this Agreement, for the duration set forth in Article 4.2.
-
-
-      6.2 OVER THE CONTRIBUTIONS
-
-The Licensee who develops a Contribution is the owner of the
-intellectual property rights over this Contribution as defined by
-applicable law.
-
-
-      6.3 OVER THE EXTERNAL MODULES
-
-The Licensee who develops an External Module is the owner of the
-intellectual property rights over this External Module as defined by
-applicable law and is free to choose the type of agreement that shall
-govern its distribution.
-
-
-      6.4 JOINT PROVISIONS
-
-The Licensee expressly undertakes:
-
-   1. not to remove, or modify, in any manner, the intellectual property
-      notices attached to the Software;
-
-   2. to reproduce said notices, in an identical manner, in the copies
-      of the Software modified or not.
-
-The Licensee undertakes not to directly or indirectly infringe the
-intellectual property rights of the Holder and/or Contributors on the
-Software and to take, where applicable, vis-à-vis its staff, any and all
-measures required to ensure respect of said intellectual property rights
-of the Holder and/or Contributors.
-
-
-    Article 7 - RELATED SERVICES
-
-7.1 Under no circumstances shall the Agreement oblige the Licensor to
-provide technical assistance or maintenance services for the Software.
-
-However, the Licensor is entitled to offer this type of services. The
-terms and conditions of such technical assistance, and/or such
-maintenance, shall be set forth in a separate instrument. Only the
-Licensor offering said maintenance and/or technical assistance services
-shall incur liability therefor.
-
-7.2 Similarly, any Licensor is entitled to offer to its licensees, under
-its sole responsibility, a warranty, that shall only be binding upon
-itself, for the redistribution of the Software and/or the Modified
-Software, under terms and conditions that it is free to decide. Said
-warranty, and the financial terms and conditions of its application,
-shall be subject of a separate instrument executed between the Licensor
-and the Licensee.
-
-
-    Article 8 - LIABILITY
-
-8.1 Subject to the provisions of Article 8.2, the Licensee shall be
-entitled to claim compensation for any direct loss it may have suffered
-from the Software as a result of a fault on the part of the relevant
-Licensor, subject to providing evidence thereof.
-
-8.2 The Licensor's liability is limited to the commitments made under
-this Agreement and shall not be incurred as a result of in particular:
-(i) loss due the Licensee's total or partial failure to fulfill its
-obligations, (ii) direct or consequential loss that is suffered by the
-Licensee due to the use or performance of the Software, and (iii) more
-generally, any consequential loss. In particular the Parties expressly
-agree that any or all pecuniary or business loss (i.e. loss of data,
-loss of profits, operating loss, loss of customers or orders,
-opportunity cost, any disturbance to business activities) or any or all
-legal proceedings instituted against the Licensee by a third party,
-shall constitute consequential loss and shall not provide entitlement to
-any or all compensation from the Licensor.
-
-
-    Article 9 - WARRANTY
-
-9.1 The Licensee acknowledges that the scientific and technical
-state-of-the-art when the Software was distributed did not enable all
-possible uses to be tested and verified, nor for the presence of
-possible defects to be detected. In this respect, the Licensee's
-attention has been drawn to the risks associated with loading, using,
-modifying and/or developing and reproducing the Software which are
-reserved for experienced users.
-
-The Licensee shall be responsible for verifying, by any or all means,
-the suitability of the product for its requirements, its good working
-order, and for ensuring that it shall not cause damage to either persons
-or properties.
-
-9.2 The Licensor hereby represents, in good faith, that it is entitled
-to grant all the rights over the Software (including in particular the
-rights set forth in Article 5).
-
-9.3 The Licensee acknowledges that the Software is supplied "as is" by
-the Licensor without any other express or tacit warranty, other than
-that provided for in Article 9.2 and, in particular, without any warranty 
-as to its commercial value, its secured, safe, innovative or relevant 
-nature.
-
-Specifically, the Licensor does not warrant that the Software is free
-from any error, that it will operate without interruption, that it will
-be compatible with the Licensee's own equipment and software
-configuration, nor that it will meet the Licensee's requirements.
-
-9.4 The Licensor does not either expressly or tacitly warrant that the
-Software does not infringe any third party intellectual property right
-relating to a patent, software or any other property right. Therefore,
-the Licensor disclaims any and all liability towards the Licensee
-arising out of any or all proceedings for infringement that may be
-instituted in respect of the use, modification and redistribution of the
-Software. Nevertheless, should such proceedings be instituted against
-the Licensee, the Licensor shall provide it with technical and legal
-assistance for its defense. Such technical and legal assistance shall be
-decided on a case-by-case basis between the relevant Licensor and the
-Licensee pursuant to a memorandum of understanding. The Licensor
-disclaims any and all liability as regards the Licensee's use of the
-name of the Software. No warranty is given as regards the existence of
-prior rights over the name of the Software or as regards the existence
-of a trademark.
-
-
-    Article 10 - TERMINATION
-
-10.1 In the event of a breach by the Licensee of its obligations
-hereunder, the Licensor may automatically terminate this Agreement
-thirty (30) days after notice has been sent to the Licensee and has
-remained ineffective.
-
-10.2 A Licensee whose Agreement is terminated shall no longer be
-authorized to use, modify or distribute the Software. However, any
-licenses that it may have granted prior to termination of the Agreement
-shall remain valid subject to their having been granted in compliance
-with the terms and conditions hereof.
-
-
-    Article 11 - MISCELLANEOUS
-
-
-      11.1 EXCUSABLE EVENTS
-
-Neither Party shall be liable for any or all delay, or failure to
-perform the Agreement, that may be attributable to an event of force
-majeure, an act of God or an outside cause, such as defective
-functioning or interruptions of the electricity or telecommunications
-networks, network paralysis following a virus attack, intervention by
-government authorities, natural disasters, water damage, earthquakes,
-fire, explosions, strikes and labor unrest, war, etc.
-
-11.2 Any failure by either Party, on one or more occasions, to invoke
-one or more of the provisions hereof, shall under no circumstances be
-interpreted as being a waiver by the interested Party of its right to
-invoke said provision(s) subsequently.
-
-11.3 The Agreement cancels and replaces any or all previous agreements,
-whether written or oral, between the Parties and having the same
-purpose, and constitutes the entirety of the agreement between said
-Parties concerning said purpose. No supplement or modification to the
-terms and conditions hereof shall be effective as between the Parties
-unless it is made in writing and signed by their duly authorized
-representatives.
-
-11.4 In the event that one or more of the provisions hereof were to
-conflict with a current or future applicable act or legislative text,
-said act or legislative text shall prevail, and the Parties shall make
-the necessary amendments so as to comply with said act or legislative
-text. All other provisions shall remain effective. Similarly, invalidity
-of a provision of the Agreement, for any reason whatsoever, shall not
-cause the Agreement as a whole to be invalid.
-
-
-      11.5 LANGUAGE
-
-The Agreement is drafted in both French and English and both versions
-are deemed authentic.
-
-
-    Article 12 - NEW VERSIONS OF THE AGREEMENT
-
-12.1 Any person is authorized to duplicate and distribute copies of this
-Agreement.
-
-12.2 So as to ensure coherence, the wording of this Agreement is
-protected and may only be modified by the authors of the License, who
-reserve the right to periodically publish updates or new versions of the
-Agreement, each with a separate number. These subsequent versions may
-address new issues encountered by Free Software.
-
-12.3 Any Software distributed under a given version of the Agreement may
-only be subsequently distributed under the same version of the Agreement
-or a subsequent version.
-
-
-    Article 13 - GOVERNING LAW AND JURISDICTION
-
-13.1 The Agreement is governed by French law. The Parties agree to
-endeavor to seek an amicable solution to any disagreements or disputes
-that may arise during the performance of the Agreement.
-
-13.2 Failing an amicable solution within two (2) months as from their
-occurrence, and unless emergency proceedings are necessary, the
-disagreements or disputes shall be referred to the Paris Courts having
-jurisdiction, by the more diligent Party.
-
-
-Version 1.0 dated 2006-09-05.
diff --git a/licenses/ECL-2.0 b/licenses/ECL-2.0
deleted file mode 100644
index 012da6c80..000000000
--- a/licenses/ECL-2.0
+++ /dev/null
@@ -1,97 +0,0 @@
-Educational Community License, Version 2.0 (ECL-2.0)
-(plain text)
-Educational Community License
-
-Version 2.0, April 2007
-
-http://www.osedu.org/licenses/
-
-The Educational Community License version 2.0 ("ECL") consists of the Apache 2.0 license, modified to change the scope of the patent grant in section 3 to be specific to the needs of the education communities using this license. The original Apache 2.0 license can be found at: http://www.apache.org/licenses/LICENSE-2.0
-
-TERMS AND CONDITIONS FOR USE, REPRODUCTION, AND DISTRIBUTION
-
-1. Definitions.
-
-"License" shall mean the terms and conditions for use, reproduction, and distribution as defined by Sections 1 through 9 of this document.
-
-"Licensor" shall mean the copyright owner or entity authorized by the copyright owner that is granting the License.
-
-"Legal Entity" shall mean the union of the acting entity and all other entities that control, are controlled by, or are under common control with that entity. For the purposes of this definition, "control" means (i) the power, direct or indirect, to cause the direction or management of such entity, whether by contract or otherwise, or (ii) ownership of fifty percent (50%) or more of the outstanding shares, or (iii) beneficial ownership of such entity.
-
-"You" (or "Your") shall mean an individual or Legal Entity exercising permissions granted by this License.
-
-"Source" form shall mean the preferred form for making modifications, including but not limited to software source code, documentation source, and configuration files.
-
-"Object" form shall mean any form resulting from mechanical transformation or translation of a Source form, including but not limited to compiled object code, generated documentation, and conversions to other media types.
-
-"Work" shall mean the work of authorship, whether in Source or Object form, made available under the License, as indicated by a copyright notice that is included in or attached to the work (an example is provided in the Appendix below).
-
-"Derivative Works" shall mean any work, whether in Source or Object form, that is based on (or derived from) the Work and for which the editorial revisions, annotations, elaborations, or other modifications represent, as a whole, an original work of authorship. For the purposes of this License, Derivative Works shall not include works that remain separable from, or merely link (or bind by name) to the interfaces of, the Work and Derivative Works thereof.
-
-"Contribution" shall mean any work of authorship, including the original version of the Work and any modifications or additions to that Work or Derivative Works thereof, that is intentionally submitted to Licensor for inclusion in the Work by the copyright owner or by an individual or Legal Entity authorized to submit on behalf of the copyright owner. For the purposes of this definition, "submitted" means any form of electronic, verbal, or written communication sent to the Licensor or its representatives, including but not limited to communication on electronic mailing lists, source code control systems, and issue tracking systems that are managed by, or on behalf of, the Licensor for the purpose of discussing and improving the Work, but excluding communication that is conspicuously marked or otherwise designated in writing by the copyright owner as "Not a Contribution."
-
-"Contributor" shall mean Licensor and any individual or Legal Entity on behalf of whom a Contribution has been received by Licensor and subsequently incorporated within the Work.
-
-2. Grant of Copyright License.
-
-Subject to the terms and conditions of this License, each Contributor hereby grants to You a perpetual, worldwide, non-exclusive, no-charge, royalty-free, irrevocable copyright license to reproduce, prepare Derivative Works of, publicly display, publicly perform, sublicense, and distribute the Work and such Derivative Works in Source or Object form.
-
-3. Grant of Patent License.
-
-Subject to the terms and conditions of this License, each Contributor hereby grants to You a perpetual, worldwide, non-exclusive, no-charge, royalty-free, irrevocable (except as stated in this section) patent license to make, have made, use, offer to sell, sell, import, and otherwise transfer the Work, where such license applies only to those patent claims licensable by such Contributor that are necessarily infringed by their Contribution(s) alone or by combination of their Contribution(s) with the Work to which such Contribution(s) was submitted. If You institute patent litigation against any entity (including a cross-claim or counterclaim in a lawsuit) alleging that the Work or a Contribution incorporated within the Work constitutes direct or contributory patent infringement, then any patent licenses granted to You under this License for that Work shall terminate as of the date such litigation is filed. Any patent license granted hereby with respect to contributions by an individual employed by an institution or organization is limited to patent claims where the individual that is the author of the Work is also the inventor of the patent claims licensed, and where the organization or institution has the right to grant such license under applicable grant and research funding agreements. No other express or implied licenses are granted.
-
-4. Redistribution.
-
-You may reproduce and distribute copies of the Work or Derivative Works thereof in any medium, with or without modifications, and in Source or Object form, provided that You meet the following conditions:
-
-You must give any other recipients of the Work or Derivative Works a copy of this License; and
-You must cause any modified files to carry prominent notices stating that You changed the files; and
-You must retain, in the Source form of any Derivative Works that You distribute, all copyright, patent, trademark, and attribution notices from the Source form of the Work, excluding those notices that do not pertain to any part of the Derivative Works; and
-If the Work includes a "NOTICE" text file as part of its distribution, then any Derivative Works that You distribute must include a readable copy of the attribution notices contained within such NOTICE file, excluding those notices that do not pertain to any part of the Derivative Works, in at least one of the following places: within a NOTICE text file distributed as part of the Derivative Works; within the Source form or documentation, if provided along with the Derivative Works; or, within a display generated by the Derivative Works, if and wherever such third-party notices normally appear. The contents of the NOTICE file are for informational purposes only and do not modify the License. You may add Your own attribution notices within Derivative Works that You distribute, alongside or as an addendum to the NOTICE text from the Work, provided that such additional attribution notices cannot be construed as modifying the License.
-You may add Your own copyright statement to Your modifications and may provide additional or different license terms and conditions for use, reproduction, or distribution of Your modifications, or for any such Derivative Works as a whole, provided Your use, reproduction, and distribution of the Work otherwise complies with the conditions stated in this License.
-
-5. Submission of Contributions.
-
-Unless You explicitly state otherwise, any Contribution intentionally submitted for inclusion in the Work by You to the Licensor shall be under the terms and conditions of this License, without any additional terms or conditions. Notwithstanding the above, nothing herein shall supersede or modify the terms of any separate license agreement you may have executed with Licensor regarding such Contributions.
-
-6. Trademarks.
-
-This License does not grant permission to use the trade names, trademarks, service marks, or product names of the Licensor, except as required for reasonable and customary use in describing the origin of the Work and reproducing the content of the NOTICE file.
-
-7. Disclaimer of Warranty.
-
-Unless required by applicable law or agreed to in writing, Licensor provides the Work (and each Contributor provides its Contributions) on an "AS IS" BASIS, WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied, including, without limitation, any warranties or conditions of TITLE, NON-INFRINGEMENT, MERCHANTABILITY, or FITNESS FOR A PARTICULAR PURPOSE. You are solely responsible for determining the appropriateness of using or redistributing the Work and assume any risks associated with Your exercise of permissions under this License.
-
-8. Limitation of Liability.
-
-In no event and under no legal theory, whether in tort (including negligence), contract, or otherwise, unless required by applicable law (such as deliberate and grossly negligent acts) or agreed to in writing, shall any Contributor be liable to You for damages, including any direct, indirect, special, incidental, or consequential damages of any character arising as a result of this License or out of the use or inability to use the Work (including but not limited to damages for loss of goodwill, work stoppage, computer failure or malfunction, or any and all other commercial damages or losses), even if such Contributor has been advised of the possibility of such damages.
-
-9. Accepting Warranty or Additional Liability.
-
-While redistributing the Work or Derivative Works thereof, You may choose to offer, and charge a fee for, acceptance of support, warranty, indemnity, or other liability obligations and/or rights consistent with this License. However, in accepting such obligations, You may act only on Your own behalf and on Your sole responsibility, not on behalf of any other Contributor, and only if You agree to indemnify, defend, and hold each Contributor harmless for any liability incurred by, or claims asserted against, such Contributor by reason of your accepting any such warranty or additional liability.
-
-END OF TERMS AND CONDITIONS
-
-APPENDIX: How to apply the Educational Community License to your work
-
-To apply the Educational Community License to your work, attach
-the following boilerplate notice, with the fields enclosed by
-brackets "[]" replaced with your own identifying information.
-(Don't include the brackets!) The text should be enclosed in the
-appropriate comment syntax for the file format. We also recommend
-that a file or class name and description of purpose be included on
-the same "printed page" as the copyright notice for easier
-identification within third-party archives.
-
-	Copyright [yyyy] [name of copyright owner] Licensed under the
-	Educational Community License, Version 2.0 (the "License"); you may
-	not use this file except in compliance with the License. You may
-	obtain a copy of the License at
-
-http://www.osedu.org/licenses/ECL-2.0
-
-	Unless required by applicable law or agreed to in writing,
-	software distributed under the License is distributed on an "AS IS"
-	BASIS, WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express
-	or implied. See the License for the specific language governing
-	permissions and limitations under the License.
\ No newline at end of file
diff --git a/licenses/GSL b/licenses/GSL
new file mode 100644
index 000000000..38014b153
--- /dev/null
+++ b/licenses/GSL
@@ -0,0 +1,221 @@
+   END USER LICENSE AGREEMENT
+
+   NOTICE: THIS SOFTWARE END USER LICENSE AGREEMENT ("EULA") IS A LEGAL
+   AGREEMENT BETWEEN YOU (EITHER AS AN INDIVIDUAL OR AN ENTITY) AND GSL
+   BIOTECH LLC ("GSL"). PLEASE READ IT CAREFULLY BEFORE COMPLETING THE
+   INSTALLATION PROCESS AND USING THE SOFTWARE. THIS AGREEMENT PROVIDES A
+   LICENSE TO USE THE SOFTWARE AND CONTAINS WARRANTY INFORMATION AND
+   LIABILITY DISCLAIMERS. BY INSTALLING AND USING THE SOFTWARE, YOU ARE
+   CONFIRMING YOUR ACCEPTANCE OF THE SOFTWARE AND AGREEING TO BECOME BOUND BY
+   THE TERMS OF THIS AGREEMENT. IF YOU DO NOT AGREE TO BE BOUND BY THESE
+   TERMS, THEN DO NOT INSTALL THE SOFTWARE, AND RETURN THE SOFTWARE TO GSL.
+
+    1. Recitals
+
+         1. This End User License Agreement ("EULA") is a legal agreement
+            between you (either an individual person or a single legal
+            entity, who will be referred to in this EULA as "End User", and
+            GSL Biotech LLC ("GSL") for the SnapGene software product
+            ("Software") or SnapGene Viewer software product ("Freeware")
+            that accompanies this EULA, including any associated media,
+            printed materials and electronic documentation.
+         2. The Software or Freeware also includes any software updates,
+            add-on components, web services and/or supplements that GSL may
+            provide to End User or make available to End User after the date
+            End User obtains the initial copy of the Software or Freeware, to
+            the extent that such items are not accompanied by a separate
+            license agreement or terms of use. By installing, copying,
+            downloading, accessing or otherwise using the Software or
+            Freeware, End User agrees to be bound by the terms of this EULA.
+            If End User does not agree to the terms of this EULA, End User
+            should not install, access or use the Software or Freeware.
+
+    2. License Grants
+
+         1. Freeware License. GSL grants End User an unlimited license to use
+            the Freeware. The install packages for the Freeware can be
+            redistributed without restriction, and can be used for both
+            commercial and non-commercial purposes.
+         2. Trial Period License. End User may download and use the Software
+            for free for thirty (30) days after installation ("Trial
+            Period"). During the Trial Period, GSL grants End User a limited,
+            non-exclusive, non-transferable, non-renewable license to copy
+            and use the Software for evaluation purposes only. At GSL's
+            discretion, GSL may provide limited support through email or
+            discussion forums at GSL's website. The evaluation copy of the
+            Software contains a feature that will automatically disable
+            certain features of the Software at the end of Trial Period. GSL
+            will have no liability to End User if this feature disables the
+            Software.
+         3. License After Trial Period. This Software is licensed, not sold.
+            End User has the option of paying a license fee in order to use
+            the Software after the expiration of the Trial Period. Upon
+            payment of the license fee, GSL provides End User with a
+            registration number, and grants End User a limited,
+            non-exclusive, non-transferable license as outlined in Sections
+            2.d through Section 2.g and in Section 3.
+         4. Computer-Specific License. Under the terms of a Computer-Specific
+            License for the Software, End User may activate each license only
+            on a single computer, and may use the Software only on that
+            computer. The Software may not be accessed remotely.
+         5. Floating License. Under the terms of a Floating License for the
+            Software, End User may install the Software on an unlimited
+            number of computers. All computers using the Software must have
+            the ability to communicate with a license server. The number of
+            users who may run the Software concurrently must not at any time
+            exceed the number of Floating Licenses purchased.
+         6. Unlimited License. Under the terms of an Unlimited License for
+            the Software, End User may install and use the Software on an
+            unlimited number of computers with IP addresses in a specified IP
+            range as agreed to by GSL and End User.
+         7. The Software or Freeware is for educational and non-commercial or
+            commercial research purposes only. GSL makes no representation
+            that the Software or Freeware is a clinically approved medical
+            device, and End User understands and accepts that any result or
+            its display presented in whatever form obtained using the
+            Software or Freeware must not be used for any purpose other than
+            education or research.
+
+    3. License Restrictions
+
+         1. End User may use the Software only on the permitted number of
+            computers.
+         2. End User may make one copy of the Software solely for backup
+            purposes. Any backup copy must contain all copyright notices and
+            any other proprietary legends on the original copy of the
+            Software. End User may not sell or transfer any copy of the
+            Software made for backup purposes.
+         3. End User's license rights under this EULA are non-exclusive and
+            non-assignable.
+         4. Other than as set forth in Section 3.b, End User may not make
+            copies of the Software or electronically transfer the Software
+            from one computer to another.
+         5. End User may not alter, merge, modify, adapt, translate,
+            decompile, reverse engineer, disassemble, or otherwise reduce the
+            Software to a human-perceivable form.
+         6. End User may not rent, lease, or sublicense the Software.
+         7. End User may not create derivative works based upon the Software.
+         8. End User may not export the Software into any country to which
+            such export is prohibited by the United States Export
+            Administration Act.
+         9. In the event that End User fails to comply with this EULA, GSL
+            and its distributors may, in addition to seeking any damages,
+            terminate the license. Upon termination, End User must destroy
+            all copies of the Software (with all other rights of both parties
+            and all other provisions of this EULA surviving any such
+            termination).
+
+    4. Ownership
+
+       The foregoing license gives End User a limited license to use the
+       Software. GSL retains all rights, title and interest, including all
+       copyright and intellectual property rights, in and to the Software and
+       all copies thereof. The Software is protected by the copyright laws of
+       the United States and other countries. All rights not expressly
+       granted in this EULA are reserved by GSL.
+
+    5. LIMITED WARRANTY AND DISCLAIMER
+
+         1. GSL warrants that, for a period of ninety (90) days, the Software
+            will perform in substantial conformance with published
+            specifications for the Software.
+         2. EXCEPT AS SET FORTH IN THE FOREGOING LIMITED WARRANTY WITH
+            RESPECT TO THE SOFTWARE, GSL DISCLAIMS ALL OTHER WARRANTIES AND
+            REPRESENTATIONS, WHETHER EXPRESS, IMPLIED, OR OTHERWISE,
+            INCLUDING THE WARRANTIES OF MERCHANTABILITY OR FITNESS FOR A
+            PARTICULAR PURPOSE. ALSO, THERE IS NO WARRANTY OF
+            NON-INFRINGEMENT AND TITLE OR QUIET ENJOYMENT. GSL DOES NOT
+            WARRANT THAT THE SOFTWARE IS ERROR-FREE OR WILL OPERATE WITHOUT
+            INTERRUPTION. THE SOFTWARE IS NOT DESIGNED, INTENDED OR LICENSED
+            FOR USE IN HAZARDOUS ENVIRONMENTS REQUIRING FAIL-SAFE CONTROLS.
+         3. IF APPLICABLE LAW REQUIRES ANY WARRANTIES WITH RESPECT TO THE
+            SOFTWARE, ALL SUCH WARRANTIES ARE LIMITED IN DURATION TO NINETY
+            (90) DAYS FROM THE DATE OF DELIVERY.
+         4. NO ORAL OR WRITTEN INFORMATION OR ADVICE GIVEN BY GSL SHALL
+            CREATE A WARRANTY OR IN ANY WAY INCREASE THE SCOPE OF ANY
+            WARRANTY PROVIDED HEREIN.
+         5. (USA only) SOME STATES DO NOT ALLOW THE EXCLUSION OF IMPLIED
+            WARRANTIES, SO THE ABOVE EXCLUSION MAY NOT APPLY TO END USER.
+            THIS WARRANTY GIVES END USER SPECIFIC LEGAL RIGHTS AND END USER
+            MAY ALSO HAVE OTHER LEGAL RIGHTS THAT VARY FROM STATE TO STATE.
+
+    6. Exclusive Remedy
+
+       End User's exclusive remedy is to return the Software to GSL. Provided
+       that any non-compliance with the above warranty is reported in writing
+       to GSL no more than ninety (90) days following delivery to End User,
+       GSL will use reasonable commercial efforts to supply End User with a
+       replacement copy of the Software that substantially conforms to
+       published specifications, provide a replacement for defective media,
+       or refund to End User the purchase price for the Software, at its
+       option. GSL shall have no responsibility if the Software has been
+       altered in any way, or if the media has been damaged by misuse,
+       accident, abuse, modification or misapplication. Any such misuse,
+       accident, abuse, modification or misapplication of the Software will
+       void the warranty above. THIS REMEDY IS THE SOLE AND EXCLUSIVE REMEDY
+       AVAILABLE TO END USER FOR BREACH OF EXPRESS OR IMPLIED WARRANTIES WITH
+       RESPECT TO THE SOFTWARE.
+
+    7. LIMITATION OF LIABILITY
+
+         1. GSL SHALL NOT BE LIABLE TO END USER OR ANY THIRD PARTY FOR ANY
+            INDIRECT, SPECIAL, INCIDENTAL, PUNITIVE, COVER OR CONSEQUENTIAL
+            DAMAGES (INCLUDING, BUT NOT LIMITED TO, DAMAGES FOR THE INABILITY
+            TO USE EQUIPMENT OR ACCESS DATA, LOSS OF BUSINESS, LOSS OF
+            PROFITS, BUSINESS INTERRUPTION OR THE LIKE), ARISING OUT OF THE
+            USE OF, OR INABILITY TO USE, THE SOFTWARE AND BASED ON ANY THEORY
+            OF LIABILITY INCLUDING BREACH OF CONTRACT, BREACH OF WARRANTY,
+            TORT (INCLUDING NEGLIGENCE), PRODUCT LIABILITY OR OTHERWISE, EVEN
+            IF GSL OR ITS REPRESENTATIVES HAVE BEEN ADVISED OF THE
+            POSSIBILITY OF SUCH DAMAGES AND EVEN IF A REMEDY SET FORTH HEREIN
+            IS FOUND TO HAVE FAILED IN ITS ESSENTIAL PURPOSE.
+         2. GSL'S TOTAL LIABILITY TO END USER FOR ACTUAL DAMAGES FOR ANY
+            CAUSE WHATSOEVER WILL BE LIMITED TO THE AMOUNT END USER PAID FOR
+            THE SOFTWARE.
+         3. (USA only) SOME STATES DO NOT ALLOW THE LIMITATION OR EXCLUSION
+            OF LIABILITY FOR INCIDENTAL OR CONSEQUENTIAL DAMAGES, SO THE
+            ABOVE LIMITATION OR EXCLUSION MAY NOT APPLY TO END USER AND END
+            USER MAY ALSO HAVE OTHER LEGAL RIGHTS THAT VARY FROM STATE TO
+            STATE.
+         4. THE FOREGOING LIMITATIONS ON LIABILITY ARE INTENDED TO APPLY TO
+            THE WARRANTIES AND DISCLAIMERS ABOVE AND ALL OTHER ASPECTS OF
+            THIS EULA.
+
+    8. U.S. GOVERNMENT RESTRICTED RIGHTS LEGEND
+
+       This Software and the documentation are provided with "RESTRICTED
+       RIGHTS" applicable to private and public licenses alike. Without
+       limiting the foregoing, use, duplication, or disclosure by the U.S.
+       Government is subject to restrictions as set forth in this EULA and as
+       provided in DFARS 227.7202-1(a) and 227.7202-3(a) (1995), DFARS
+       252.227-7013 (c)(1)(ii)(OCT 1988), FAR 12.212(a)(1995), FAR 52.227-19,
+       or FAR 52.227-14, as applicable. Manufacturer: GSL Biotech LLC
+
+    9. General
+
+       This EULA shall be governed by the internal laws of the State of
+       Illinois, USA. In each case this EULA shall be construed and enforced
+       without regard to the United Nations Convention on the International
+       Sale of Goods.
+
+       This EULA contains the complete agreement between the parties with
+       respect to the subject matter hereof, and supersedes all prior or
+       contemporaneous agreements or understandings, whether oral or written.
+       End User agrees that any varying or additional terms contained in any
+       purchase order or other written notification or document issued by End
+       User in relation to the Software licensed hereunder shall be of no
+       effect. The failure or delay of GSL to exercise any of its rights
+       under this EULA or upon any breach of this EULA shall not be deemed a
+       waiver of those rights or of the breach.
+
+       If any provision of this EULA shall be held by a court of competent
+       jurisdiction to be contrary to law, then that provision will be
+       enforced to the maximum extent permissible and the remaining
+       provisions of this EULA will remain in full force and effect.
+
+       All questions concerning this EULA shall be directed to GSL. This EULA
+       does not authorize End User to use the trademarks of GSL or its
+       suppliers.
+
+   GSL Biotech LLC
+   July 18th, 2017
diff --git a/licenses/HDecodeCambridge b/licenses/HDecodeCambridge
deleted file mode 100644
index fda09a633..000000000
--- a/licenses/HDecodeCambridge
+++ /dev/null
@@ -1,68 +0,0 @@
-                        HDecode END USER LICENSE AGREEMENT
-
-1. Definitions
-
-   Licensed Software:  All source code, object or executable code,
-                       associated technical documentation and any 
-                       data files in this HDecode extension to HTK.
-
-   Licensor         :  University of Cambridge
-
-   Licensee         :  The person/organisation who downloads the HDecode
-                       extension to HTK or any part of it.
-                 
-
-2. License Rights and Obligations
-
-   2.1 The Licensor hereby grants the Licensee a non-exclusive license to a) make 
-   copies of the Licensed Software in source and object code form for use 
-   within the Licensee's organisation for research purposes only; b) modify 
-   copies of the Licensed Software to create derivative works thereof for use within 
-   the Licensee's organisation for research purposes only; c) make use of models 
-   derived using the licensed Software for research and non-research purposes. 
-
-   2.2 The Licensed Software either in whole or in part can not be distributed
-   or sub-licensed to any third party in any form.
-
-   2.3 The Licensee agrees not to remove any copyright, trademark or patent notices 
-   that appear in the Licensed Software.
-
-   2.4 THE LICENSED SOFTWARE IS PROVIDED "AS IS" WITHOUT ANY WARRANTY OF ANY KIND.
-   TO THE MAXIMUM EXTENT PERMITTED BY LAW, ANY AND ALL EXPRESS AND IMPLIED 
-   WARRANTIES OF ANY KIND WHATSOEVER, INCLUDING BUT NOT LIMITED TO THOSE OF 
-   MERCHANTABILITY, OF FITNESS FOR A PARTICULAR PURPOSE, OF ACCURACY OR COMPLETENESS 
-   OF RESPONSES, OF RESULTS, OF REASONABLE CARE OR WORKMANLIKE EFFORT, OF LACK OF 
-   NEGLIGENCE, AND/OR OF A LACK OF VIRUSES, ALL WITH REGARD TO THE LICENSED SOFTWARE, 
-   ARE EXPRESSLY EXCLUDED.  
-
-   2.5 THE LICENSEE AGREES THAT LICENSOR SHALL NOT BE 
-   LIABLE FOR ANY CONSEQUENTIAL, INCIDENTAL, INDIRECT, ECONOMIC OR PUNITIVE DAMAGES 
-   WHATSOEVER (INCLUDING BUT NOT LIMITED TO DAMAGES FOR LOSS OF BUSINESS OR PERSONAL 
-   PROFITS, BUSINESS INTERRUPTION, LOSS OF BUSINESS OR PERSONAL OR CONFIDENTIAL 
-   INFORMATION, OR ANY OTHER PECUNIARY LOSS, DAMAGES FOR LOSS OF PRIVACY, OR FOR FAILURE 
-   TO MEET ANY DUTY, INCLUDING ANY DUTY OF GOOD FAITH, OR TO EXERCISE COMMERCIALLY 
-   REASONABLE CARE OR FOR NEGLIGENCE) ARISING OUT OF OR IN ANY WAY RELATED TO THE 
-   USE OF OR INABILITY TO USE THE LICENSED SOFTWARE. 
-
-
-3. Term of Agreement
-
-   This agreement is effective upon the download of the Licensed Software and 
-   shall remain in effect until terminated. Termination by the Licensee should be 
-   accompanied by the complete destruction of the Licensed Software and any complete 
-   or partial copies thereof. The Licensor may only terminate this  agreement if 
-   the Licensee has failed to abide by the terms of this agreement in which case 
-   termination may be without notice. All provisions of this agreement relating 
-   to disclaimers of warranties, limitation of liability, remedies or damage 
-   and the Licensor's proprietary rights shall survive termination.
-
-
-4. Governing Law
-
-   This agreement shall be construed and interpreted in accordance with the laws 
-   of England.
-
-
-5. Though not a license condition, Licensees are strongly encouraged to
-   a) report all bugs, where possible with bug fixes, that are found.
-   b) reference the use of HDecode and HTK in any publications that use the Licensed Software.
diff --git a/licenses/HGSC-BCM b/licenses/HGSC-BCM
deleted file mode 100644
index 2f7b5bec0..000000000
--- a/licenses/HGSC-BCM
+++ /dev/null
@@ -1,8 +0,0 @@
-© 2011 Human Genome Sequencing Center, Baylor College of Medicine. All rights reserved.
-
-Redistribution and use in source and binary forms, with or without modification, are permitted provided that the following conditions are met:
-
-    Redistributions of source code must retain the above copyright notice, this list of conditions and the following disclaimer.
-
-    Redistributions in binary form must reproduce the above copyright notice, this list of conditions and the following disclaimer in the documentation and/or other materials provided with the distribution.
-
diff --git a/licenses/HTKCambridge b/licenses/HTKCambridge
deleted file mode 100644
index b57936427..000000000
--- a/licenses/HTKCambridge
+++ /dev/null
@@ -1,76 +0,0 @@
-                        HTK END USER LICENSE AGREEMENT
-
-1. Definitions
-
-   Licensed Software:  All source code, object or executable code,
-                       associated technical documentation and any 
-                       data files in this HTK distribution.
-
-   Licensor         :  University of Cambridge
-
-   Licensee         :  The person/organisation who downloads the HTK
-                       distribution or any part of it.
-                 
-
-2. License Rights and Obligations
-
-   2.1 The Licensor hereby grants the Licensee a non-exclusive license to a) make 
-   copies of the Licensed Software in source and object code form for use 
-   within the Licensee's organisation; b) modify copies of the Licensed Software 
-   to create derivative works thereof for use within the Licensee's organisation.
-
-   2.2 The Licensed Software either in whole or in part can not be distributed
-   or sub-licensed to any third party in any form.
-
-   2.3 The Licensee agrees not to remove any copyright, trademark or patent notices 
-   that appear in the Licensed Software.
-
-   2.4 THE LICENSED SOFTWARE IS PROVIDED "AS IS" WITHOUT ANY WARRANTY OF ANY KIND.
-   TO THE MAXIMUM EXTENT PERMITTED BY LAW, ANY AND ALL EXPRESS AND IMPLIED 
-   WARRANTIES OF ANY KIND WHATSOEVER, INCLUDING BUT NOT LIMITED TO THOSE OF 
-   MERCHANTABILITY, OF FITNESS FOR A PARTICULAR PURPOSE, OF ACCURACY OR COMPLETENESS 
-   OF RESPONSES, OF RESULTS, OF REASONABLE CARE OR WORKMANLIKE EFFORT, OF LACK OF 
-   NEGLIGENCE, AND/OR OF A LACK OF VIRUSES, ALL WITH REGARD TO THE LICENSED SOFTWARE, 
-   ARE EXPRESSLY EXCLUDED.  NEITHER LICENSOR, ENTROPIC OR MICROSOFT MAKE ANY WARRANTY 
-   THAT THE LICENSED SOFTWARE WILL OPERATE PROPERLY AS INTEGRATED IN YOUR PRODUCT(S) 
-   OR ON ANY CUSTOMER SYSTEM(S). 
-
-   2.5 THE LICENSEE AGREES THAT NEITHER LICENSOR, ENTROPIC OR MICROSOFT SHALL BE 
-   LIABLE FOR ANY CONSEQUENTIAL, INCIDENTAL, INDIRECT, ECONOMIC OR PUNITIVE DAMAGES 
-   WHATSOEVER (INCLUDING BUT NOT LIMITED TO DAMAGES FOR LOSS OF BUSINESS OR PERSONAL 
-   PROFITS, BUSINESS INTERRUPTION, LOSS OF BUSINESS OR PERSONAL OR CONFIDENTIAL 
-   INFORMATION, OR ANY OTHER PECUNIARY LOSS, DAMAGES FOR LOSS OF PRIVACY, OR FOR FAILURE 
-   TO MEET ANY DUTY, INCLUDING ANY DUTY OF GOOD FAITH, OR TO EXERCISE COMMERCIALLY 
-   REASONABLE CARE OR FOR NEGLIGENCE) ARISING OUT OF OR IN ANY WAY RELATED TO THE 
-   USE OF OR INABILITY TO USE THE LICENSED SOFTWARE, EVEN IF ENTROPIC HAS BEEN 
-   ADVISED OF THE POSSIBILITY OF SUCH DAMAGES. 
-
-
-3. Term of Agreement
-
-   This agreement is effective upon the download of the Licensed Software and 
-   shall remain in effect until terminated. Termination by the Licensee should be 
-   accompanied by the complete destruction of the Licensed Software and any complete 
-   or partial copies thereof. The Licensor may only terminate this  agreement if 
-   the Licensee has failed to abide by the terms of this agreement in which case 
-   termination may be without notice. All provisions of this agreement relating 
-   to disclaimers of warranties, limitation of liability, remedies or damage 
-   and the Licensor's proprietary rights shall survive termination.
-
-
-4. Governing Law
-
-   This agreement shall be construed and interpreted in accordance with the laws 
-   of England.
-
-
-5. Though not a license condition, Licensees are strongly encouraged to
-   a) report all bugs, where possible with bug fixes, that are found.
-   b) reference the use of HTK in any publications that use the Licensed Software.
-
-
-6. Contributions to HTK 
-
-   We strongly encourage contributions to the HTK source code base. These will 
-   in general be additional tools or library modules which will not fall under this 
-   HTK License Agreement.
diff --git a/licenses/ICS b/licenses/ICS
deleted file mode 100644
index 042cd9e47..000000000
--- a/licenses/ICS
+++ /dev/null
@@ -1,14 +0,0 @@
-Copyright (c) <YOUR NAME>, and CONTRIBUTORS
-Copyright (c) <YEAR> <YOUR INSTITUTION>
-
-Permission to use, copy, modify, and distribute this software for any
-purpose with or without fee is hereby granted, provided that the above
-copyright notice and this permission notice appear in all copies.
-
-THE SOFTWARE IS PROVIDED "AS IS" AND THE AUTHOR DISCLAIMS ALL WARRANTIES
-WITH REGARD TO THIS SOFTWARE INCLUDING ALL IMPLIED WARRANTIES OF
-MERCHANTABILITY AND FITNESS. IN NO EVENT SHALL THE AUTHOR BE LIABLE FOR
-ANY SPECIAL, DIRECT, INDIRECT, OR CONSEQUENTIAL DAMAGES OR ANY DAMAGES
-WHATSOEVER RESULTING FROM LOSS OF USE, DATA OR PROFITS, WHETHER IN AN
-ACTION OF CONTRACT, NEGLIGENCE OR OTHER TORTIOUS ACTION, ARISING OUT OF
-OR IN CONNECTION WITH THE USE OR PERFORMANCE OF THIS SOFTWARE.
diff --git a/licenses/Intel-SDP b/licenses/Intel-SDP
deleted file mode 100644
index be409eb57..000000000
--- a/licenses/Intel-SDP
+++ /dev/null
@@ -1,369 +0,0 @@
-IMPORTANT - READ BEFORE COPYING, INSTALLING OR USING.

-Do not copy, install, or use the Materials provided under this license agreement

-("Agreement"), until you have carefully read the following terms and conditions.

-

-By copying, installing, or otherwise using the Materials, you agree to be bound 

-by the terms of this Agreement. If you do not agree to the terms of this 

-Agreement, do not copy, install, or use the Materials.

-

-End User License Agreement for the Intel(R) Software Development Products

-

-1.	LICENSE DEFINITIONS: 

-

-A.	"Materials" are defined as the software, documentation, license key codes 

-and other materials, including any updates and upgrade thereto, that are 

-provided to you under this Agreement. Materials also include the 

-Redistributables, Cluster OpenMP Library, and Sample Source as defined below.

-

-B.	"Redistributables" are the files listed in the following text files that 

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-time. A separate license is required for each additional use and/or individual

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-v.	NODE-LOCKED LICENSE: If you are using the Materials under the control of 

-a Node-Locked license, you may use the Materials only on a single designated 

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-vi.	FLOATING LICENSE: If you are using the Materials under the control of a 

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-computers that are connected to the designated network and (b) use the Material

-by no more than the authorized number of concurrent users. A separate license 

-is required for each additional concurrent user and/or network on which the 

-Materials are used. Intel will provide you with a license code key that 

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-concurrent users. If you obtained a time-limited Floating license, the duration

-(time period) of your license and your ability to use the Materials is limited 

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-key code for the Materials. Intel Library Floating License: If the Materials 

-are the Intel(R) Math Kernel Library or the Intel(R) Integrated Performance 

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-such, in addition to the terms and conditions above, the Intel Library may only

-be used by the authorized concurrent users of that Intel Compiler Floating 

-license.

-

-D.	DISTRIBUTION: Distribution of the Redistributables is also subject to the

-following limitations: You (i) shall be solely responsible to your customers 

-for any update or support obligation or other liability which may arise from the

-distribution, (ii) shall not make any statement that your product is 

-"certified", or that its performance is guaranteed, by Intel, (iii) shall not 

-use Intel's name or trademarks to market your product without written 

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-reverse engineering of the Redistributables, (v) shall indemnify, hold harmless,

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-including attorney's fees, that arise or result from your distribution of any 

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-E.	Intel(R) Integrated Performance Primitives (Intel IPP). The following 

-terms and conditions apply only to the Intel IPP.

-

-i.	 Notwithstanding anything in this Agreement to the contrary, if you 

-implement the Sample Sources in your application or if you use Intel IPP to 

-implement algorithms that are protected by others' licenses then you may need 

-additional licenses from various entities. Should any such additional licenses

-be required, you are solely responsible for obtaining any such licenses and 

-agree to obtain any such licenses at your own expense.

-

-ii.	Notwithstanding anything herein to the contrary, a valid license to Intel

-IPP is a prerequisite to any license for Sample Source, and possession of Sample

-Source does not grant any license to Intel IPP (or any portion thereof). To 

-access Sample Source, you must first register your licensed copy of the Intel 

-IPP with Intel. By downloading, installing or copying any Sample Source file, 

-you agree to be bound by terms of this Agreement.

-

-F.	SOFTWARE TRANSFER: You may permanently transfer the Materials and all of

-your rights under this Agreement to another party ("Recipient") only if you 

-notify Intel of the transfer by sending a letter to Intel certifying that you 

-retain no copies of the Materials and that the Recipient has agreed in writing

-to be bound by all of the terms and conditions of this Agreement. Please send

-such letter to:

-

-Intel Corporation

-2111 NE 25th Avenue

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-Attn: DPD Contracts Management, JF1-15

-

-4.	COPYRIGHT: Title to the Materials and all copies thereof remain with Intel

-or its suppliers. The Materials are copyrighted and are protected by United 

-States copyright laws and international treaty provisions. You will not remove

-any copyright notice from the Materials. You agree to prevent any unauthorized

-copying of the Materials. Except as expressly provided herein, no license or 

-right is granted to you directly or by implication, inducement, estoppel or 

-otherwise, specifically Intel does not grant any express or implied right to you

-under Intel patents, copyrights, trademarks, or trade secret information.

-

-5.	NO WARRANTY AND LIMITED REPLACEMENT: THE MATERIALS AND INFORMATION ARE 

-PROVIDED "AS IS" WITH NO WARRANTIES, EXPRESS OR IMPLIED, INCLUDING BUT NOT 

-LIMITED TO ANY IMPLIED WARRANTY OF MERCHANTABILITY, FITNESS FOR A PARTICULAR 

-PURPOSE, NON-INFRINGEMENT OF INTELLECTUAL PROPERTY RIGHTS, OR ANY WARRANTY 

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-receipt, Intel's entire liability and your exclusive remedy shall be the 

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-

-6.	LIMITATION OF LIABILITY: THE ABOVE REPLACEMENT PROVISION IS THE ONLY 

-WARRANTY OF ANY KIND. INTEL OFFERS NO OTHER WARRANTY EITHER EXPRESS OR IMPLIED 

-INCLUDING THOSE OF MERCHANTABILITY, NONINFRINGEMENT OF THIRD- PARTY 

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-OF BUSINESS INFORMATION, OR OTHER LOSS) ARISING OUT OF THE USE OF OR INABILITY 

-TO USE THE SOFTWARE, EVEN IF INTEL HAS BEEN ADVISED OF THE POSSIBILITY OF SUCH 

-DAMAGES. BECAUSE SOME JURISDICTIONS PROHIBIT THE EXCLUSION OR LIMITATION OF 

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-APPLY TO YOU.

-

-7.	UNAUTHORIZED USE: THE MATERIALS ARE NOT DESIGNED, INTENDED, OR AUTHORIZED 

-FOR USE IN ANY TYPE OF SYSTEM OR APPLICATION IN WHICH THE FAILURE OF THE 

-MATERIALS COULD CREATE A SITUATION WHERE PERSONAL INJURY OR DEATH MAY OCCUR 

-(E.G MEDICAL SYSTEMS, LIFE SUSTAINING OR LIFE SAVING SYSTEMS). Should the buyer 

-purchase or use the Materials for any such unintended or unauthorized use, the 

-buyer shall indemnify and hold Intel and its officers, subsidiaries and 

-affiliates harmless against all claims, costs, damages, and expenses, and 

-reasonable attorney fees arising out of, directly or indirectly, any claim of 

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-unauthorized use, even if such claim alleges that Intel was negligent regarding

-the design or manufacture of the part.

-

-8.	USER SUBMISSIONS: You agree that any material, information or other 

-communication you transmit or post to an Intel website or provide to Intel under

-this Agreement related to the features, functions, performance or use of the 

-Materials will be considered non-confidential and non-proprietary 

-("Communications"). Intel will have no obligations with respect to the 

-Communications. You hereby grant to Intel a non-exclusive, perpetual, 

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-multiple tiers of distribution and licensees, incorporate and otherwise use the

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-If you wish to provide Intel with your confidential information, Intel requires

-a non-disclosure agreement ("NDA") to receive such confidential information, so

-please contact your Intel representative to ensure the proper NDA is in place.

-

-9.	CONSENT. You agree that Intel, its subsidiaries or suppliers may collect

-and use technical and related information, including but not limited to 

-technical information about your computer, system and application software, and

-peripherals, that is gathered periodically to facilitate the provision of 

-software updates, product support and other services to you (if any) related to

-the Materials, and to verify compliance with the terms of this Agreement.

-Intel may use this information, as long as it is in a form that does not 

-personally identify you, to improve our products or to provide services or 

-technologies to you.

-

-10.	TERMINATION OF THIS LICENSE: This Agreement becomes effective on the date

-you accept this Agreement and will continue until terminated as provided for in

-this Agreement. If you are using the Materials under the control of a 

-time-limited license, for example an Evaluation License, this Agreement 

-terminates without notice on the last day of the time period, which is specified

-elsewhere in the Materials, and/or controlled by the license key code for the 

-Materials. Intel may terminate this license immediately if you are in breach of

-any of its terms and conditions and such breach is not cured within thirty (30)

-days of written notice from Intel. Upon termination, you will immediately 

-return to Intel or destroy the Materials and all copies thereof. Any 

-distribution of the Redistributables conducted in accordance with the terms and

-conditions of this Agreement shall survive termination of this Agreement.

-

-11.	U.S. GOVERNMENT RESTRICTED RIGHTS: The technical data and computer 

-software covered by this license is a "Commercial Item," as such term is defined

-by the FAR 2.101 (48 C.F.R. 2.101) and is "commercial computer software" and 

-"commercial computer software documentation" as specified under FAR 12.212 

-(48 C.F.R. 12.212) or DFARS 227.7202 (48 C.F.R. 227.7202), as applicable. This

-commercial computer software and related documentation is provided to end users

-for use by and on behalf of the U.S. Government, with only those rights as are

-granted to all other end users pursuant to the terms and conditions herein. Use

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-official. This use by or for the U.S. Government clause is in lieu of, and 

-supersedes, any other FAR, DFARS, or other provision that addresses Government

-rights in the computer software or documentation covered by this license. All 

-copyright licenses granted to the U.S. Government are coextensive with the 

-technical data and computer software licenses granted herein. The U.S. 

-Government shall only have the right to reproduce, distribute, perform, display,

-and prepare derivative works as needed to implement those rights.

-

-12.	GENERAL PROVISIONS

-

-A.	ENTIRE AGREEMENT: This Agreement is intended to be the entire agreement

-between you and Intel with respect to matters contained herein, and supersedes

-all prior or contemporaneous agreements and negotiations with respect to those

-matters. No waiver of any breach or default shall constitute a waiver of any

-subsequent breach or default. If any provision of this Agreement is determined

-by a court to be unenforceable, you and Intel will deem the provision to be 

-modified to the extent necessary to allow it to be enforced to the extent

-permitted by law, or if it cannot be modified, the provision will be severed and

-deleted from this Agreement, and the remainder of the Agreement will continue in

-effect. Any change, modification or waiver to this Agreement must be in writing

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-

-B.	APPLICABLE LAWS: Any claim arising under or relating to this Agreement 

-shall be governed by the internal substantive laws of the State of Delaware,

-without regard to principles of conflict of laws. You agree that the terms of

-the United Nations Convention on Contracts for the Sale of Goods do not apply

-to this Agreement. You agree that your distribution and export/re-export of the

-Software and permitted modifications shall be in compliance with the laws,

-regulations, orders or other restrictions of applicable export laws.

-

-13.	THIRD PARTY PROGRAMS. The Materials may include third party programs or

-materials. The license terms with those programs or materials apply to your use

-of them, and Intel is not liable for them.

-

-* Other names and brands may be claimed as the property of others

-	November 2010

-

diff --git a/licenses/Janelia-1.2 b/licenses/Janelia-1.2
new file mode 100644
index 000000000..76ce9337b
--- /dev/null
+++ b/licenses/Janelia-1.2
@@ -0,0 +1,9 @@
+The Janelia Research Campus Software License 1.2
+Copyright (c) 2019, Howard Hughes Medical Institute, All rights reserved.
+
+Redistribution and use in source and binary forms, with or without modification, are permitted provided that the following conditions are met:
+
+Redistributions of source code must retain the above copyright notice, this list of conditions and the following disclaimer.
+Redistributions in binary form must reproduce the above copyright notice, this list of conditions and the following disclaimer in the documentation and/or other materials provided with the distribution.
+Neither the name of the Howard Hughes Medical Institute nor the names of its contributors may be used to endorse or promote products derived from this software without specific prior written permission.
+THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, ANY IMPLIED WARRANTIES OF MERCHANTABILITY, NON-INFRINGEMENT, OR FITNESS FOR A PARTICULAR PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT OWNER OR CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; REASONABLE ROYALTIES; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
diff --git a/licenses/LNLL-BSD b/licenses/LNLL-BSD
deleted file mode 100644
index 5d9e89279..000000000
--- a/licenses/LNLL-BSD
+++ /dev/null
@@ -1,57 +0,0 @@
-Copyright (c) 2012, Lawrence Livermore National Security, LLC.
-Produced at the Lawrence Livermore National Laboratory
-Written by David Grote, grote1@llnl.gov.
-LLNL-CODE-544231
-All rights reserved.
-
-This file is part of Forthon. For details, see http://hifweb.lbl.gov/Forthon.
-Please also read below, an Additional BSD Notice.
-
-Redistribution and use in source and binary forms, with or without
-modification, are permitted provided that the following conditions are met:
-
-   * Redistributions of source code must retain the above copyright notice,
-     this list of conditions and the disclaimer below.
-
-   * Redistributions in binary form must reproduce the above copyright
-     notice, this list of conditions and the disclaimer (as noted below) in
-     the documentation and/or other materials provided with the distribution.
-
-   * Neither the name of the LLNS/LLNL nor the names of its contributors may
-     be used to endorse or promote products derived from this software
-     without specific prior written permission.
-
-THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
-AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE
-IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE
-ARE DISCLAIMED. IN NO EVENT SHALL LAWRENCE LIVERMORE NATIONAL SECURITY, LLC,
-THE U.S. DEPARTMENT OF ENERGY OR CONTRIBUTORS BE LIABLE FOR ANY DIRECT,
-INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES
-(INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES;
-LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND
-ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT
-(INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS
-SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
-
-Additional BSD Notice
-
-1. This notice is required to be provided under our contract with the U.S.
-Department of Energy (DOE). This work was produced at Lawrence Livermore
-National Laboratory under Contract No. DE-AC52-07NA27344 with the DOE.
-
-2. Neither the United States Government nor Lawrence Livermore National
-Security, LLC nor any of their employees, makes any warranty, express or
-implied, or assumes any liability or responsibility for the accuracy,
-completeness, or usefulness of any information, apparatus, product, or
-process disclosed, or represents that its use would not infringe
-privately-owned rights.
-
-3. Also, reference herein to any specific commercial products, process, or
-services by trade name, trademark, manufacturer or otherwise does not
-necessarily constitute or imply its endorsement, recommendation, or favoring
-by the United States Government or Lawrence Livermore National Security, LLC.
-The views and opinions of authors expressed herein do not necessarily state
-or reflect those of the United States Government or Lawrence Livermore
-National Security, LLC, and shall not be used for advertising or product
-endorsement purposes.
-
diff --git a/licenses/MGLTOOLS b/licenses/MGLTOOLS
deleted file mode 100644
index 3e5895974..000000000
--- a/licenses/MGLTOOLS
+++ /dev/null
@@ -1,41 +0,0 @@
-1. Grant Of Limited License; Software Use Restrictions. The programs
-     received by you will be used only for NON COMMERCIAL purposes.
-     This license is issued to you as an individual.
-
-     For COMMERCIAL use done with the software please contact Michel F. 
-     Sanner for details about commercial usage license agreements.
-     
-     For any question regarding license agreements, please contact
-             Michel Sanner:
-	     TSRI, Molecular Biology Department, TCP 26,
-	     10550 North Torrey Pines Road, La Jolla, CA 92037
-	     sanner@scripps.edu
-	     tel (858) 784-7742
-	     fax (858) 784-2341
-
-  2. COMMERCIAL USAGE is defined as revenues generating activities. These
-     include using this software for consulting activities and selling
-     applications built on top of, or using this software. Scientific 
-     research in an academic environment and teaching are considered 
-     NON COMMERCIAL.
-
-  3.  Copying Restrictions. You will not sell or otherwise distribute commercially 
-     these programs or derivatives to any other party, whether with or without 
-     consideration.
-
-  4. Ownership of Software. You will not obtain, and will not attempt to 
-     obtain copyright coverage thereon without the express purpose written 
-     consent of The Scripps Research Institute and Dr. Sanner.
-
-  5. IN NO EVENT SHALL THE AUTHORS OR DISTRIBUTORS BE LIABLE TO ANY PARTY
-     FOR DIRECT, INDIRECT, SPECIAL, INCIDENTAL, OR CONSEQUENTIAL DAMAGES
-     ARISING OUT OF THE USE OF THIS SOFTWARE, ITS DOCUMENTATION, OR ANY
-     DERIVATIVES THEREOF, EVEN IF THE AUTHORS HAVE BEEN ADVISED OF THE
-     POSSIBILITY OF SUCH DAMAGE.
-
-  6. THE AUTHORS AND DISTRIBUTORS SPECIFICALLY DISCLAIM ANY WARRANTIES,
-     INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY,
-     FITNESS FOR A PARTICULAR PURPOSE, AND NON-INFRINGEMENT.  THIS SOFTWARE
-     IS PROVIDED ON AN "AS IS" BASIS, AND THE AUTHORS AND DISTRIBUTORS HAVE
-     NO OBLIGATION TO PROVIDE MAINTENANCE, SUPPORT, UPDATES, ENHANCEMENTS, OR
-     MODIFICATIONS.
\ No newline at end of file
diff --git a/licenses/MIT-KhronosGroup b/licenses/MIT-KhronosGroup
deleted file mode 100644
index e022241b4..000000000
--- a/licenses/MIT-KhronosGroup
+++ /dev/null
@@ -1,25 +0,0 @@
-Copyright (c) 2008-2015 The Khronos Group Inc.
- 
-Permission is hereby granted, free of charge, to any person obtaining a
-copy of this software and/or associated documentation files (the
-"Materials"), to deal in the Materials without restriction, including
-without limitation the rights to use, copy, modify, merge, publish,
-distribute, sublicense, and/or sell copies of the Materials, and to
-permit persons to whom the Materials are furnished to do so, subject to
-the following conditions:
-
-The above copyright notice and this permission notice shall be included
-in all copies or substantial portions of the Materials.
-
-MODIFICATIONS TO THIS FILE MAY MEAN IT NO LONGER ACCURATELY REFLECTS
-KHRONOS STANDARDS. THE UNMODIFIED, NORMATIVE VERSIONS OF KHRONOS
-SPECIFICATIONS AND HEADER INFORMATION ARE LOCATED AT
-    https://www.khronos.org/registry/
-
-THE MATERIALS ARE PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND,
-EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF
-MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT.
-IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY
-CLAIM, DAMAGES OR OTHER LIABILITY, WHETHER IN AN ACTION OF CONTRACT,
-TORT OR OTHERWISE, ARISING FROM, OUT OF OR IN CONNECTION WITH THE
-MATERIALS OR THE USE OR OTHER DEALINGS IN THE MATERIALS.
diff --git a/licenses/MSR-LA b/licenses/MSR-LA
deleted file mode 100644
index 2b25654cf..000000000
--- a/licenses/MSR-LA
+++ /dev/null
@@ -1,104 +0,0 @@
-Microsoft Research License Agreement
-Non-Commercial Use Only 
-Z3
-_____________________________________________________________________
-This Microsoft Research License Agreement, including all exhibits ("MSR-LA") is 
-a legal agreement between you and Microsoft Corporation ("Microsoft" or "we") 
-for the data identified above, which may include associated materials, text or 
-speech files, associated media and "online" or electronic documentation and any 
-updates we provide in our discretion (together, the "Software"). 
-
-By installing, copying, or otherwise using this Software, you agree to be bound 
-by the terms of this MSR-LA. If you do not agree, do not install copy or use the 
-Software. The Software is protected by copyright and other intellectual property 
-laws and is licensed, not sold. 
-
-SCOPE OF RIGHTS:
-You may use, copy, reproduce, and distribute this Software for any 
-non-commercial purpose, subject to the restrictions in this MSR-LA. Some 
-purposes which can be non-commercial are teaching, academic research, public 
-demonstrations and personal experimentation. You may also distribute this 
-Software with books or other teaching materials, or publish the Software on 
-Websites, that are intended to teach the use of the Software for academic or 
-other non-commercial purposes.
-
-You may not use or distribute this Software or any derivative works in any form 
-for commercial purposes. Examples of commercial purposes would be running 
-business operations, licensing, leasing, or selling the Software, distributing 
-the Software for use with commercial products, using the Software in the 
-creation or use of commercial products or any other activity which purpose is 
-to procure a commercial gain to you or others.
-
-You may create derivative works of the Software source code and distribute the 
-modified Software solely for non-commercial academic purposes, as provided  
-herein. If you distribute the Software or any derivative works of the Software, 
-you will distribute them under the same terms and conditions as in this 
-license, and you will not grant other rights to the Software or derivative 
-works that are different from those provided by this MSR-LA. 
-
-If you have created derivative works of the Software, and distribute such 
-derivative works, you will cause the modified files to carry prominent notices 
-so that recipients know that they are not receiving the original Software. Such 
-notices must state: (i) that you have changed the Software; and (ii) the date 
-of any changes.
-In return, we simply require that you agree: 
-
-1. That you will not remove any copyright or other notices from the Software.
-
-2. That if any of the Software is in binary format, you will not attempt to 
-modify such portions of the Software, or to reverse engineer or decompile them, 
-except and only to the extent authorized by applicable law. 
-
-3. That Microsoft is granted back, without any restrictions or limitations, a 
-non-exclusive, perpetual, irrevocable, royalty-free, assignable and 
-sub-licensable license, to reproduce, publicly perform or display, install, 
-use, modify, post, distribute, make and have made, sell and transfer your 
-modifications to and/or derivative works of the Software source code or data, 
-for any purpose. 
-
-4. That any feedback about the Software provided by you to us is voluntarily 
-given, and Microsoft shall be free to use the feedback as it sees fit without 
-obligation or restriction of any kind, even if the feedback is designated by 
-you as confidential. 
-
-5. THAT THE SOFTWARE COMES "AS IS", WITH NO WARRANTIES. THIS MEANS NO EXPRESS, 
-IMPLIED OR STATUTORY WARRANTY, INCLUDING WITHOUT LIMITATION, WARRANTIES OF 
-MERCHANTABILITY OR FITNESS FOR A PARTICULAR PURPOSE, ANY WARRANTY AGAINST 
-INTERFERENCE WITH YOUR ENJOYMENT OF THE SOFTWARE OR ANY WARRANTY OF TITLE OR 
-NON-INFRINGEMENT. THERE IS NO WARRANTY THAT THIS SOFTWARE WILL FULFILL ANY OF 
-YOUR PARTICULAR PURPOSES OR NEEDS. ALSO, YOU MUST PASS THIS DISCLAIMER ON 
-WHENEVER YOU DISTRIBUTE THE SOFTWARE OR DERIVATIVE WORKS.
-
-6. THAT NEITHER MICROSOFT NOR ANY CONTRIBUTOR TO THE SOFTWARE WILL BE LIABLE 
-FOR ANY DAMAGES RELATED TO THE SOFTWARE OR THIS MSR-LA, INCLUDING DIRECT, 
-INDIRECT, SPECIAL, CONSEQUENTIAL OR INCIDENTAL DAMAGES, TO THE MAXIMUM EXTENT 
-THE LAW PERMITS, NO MATTER WHAT LEGAL THEORY IT IS BASED ON. ALSO, YOU MUST 
-PASS THIS LIMITATION OF LIABILITY ON WHENEVER YOU DISTRIBUTE THE SOFTWARE OR 
-DERIVATIVE WORKS.
-
-7. That we have no duty of reasonable care or lack of negligence, and we are 
-not obligated to (and will not) provide technical support for the Software.
-
-8. That if you breach this MSR-LA or if you sue anyone over patents that you 
-think may apply to or read on the Software or anyone's use of the Software, 
-this MSR-LA (and your license and rights obtained herein) terminate 
-automatically. Upon any such termination, you shall destroy all of your copies 
-of the Software immediately. Sections 3, 4, 5, 6, 7, 8, 11 and 12 of this 
-MSR-LA shall survive any termination of this MSR-LA.
-
-9. That the patent rights, if any, granted to you in this MSR-LA only apply to 
-the Software, not to any derivative works you make.
-
-10. That the Software may be subject to U.S. export jurisdiction at the time it 
-is licensed to you, and it may be subject to additional export or import laws 
-in other places. You agree to comply with all such laws and regulations that 
-may apply to the Software after delivery of the Software to you.
-
-11. That all rights not expressly granted to you in this MSR-LA are reserved.
-
-12. That this MSR-LA shall be construed and controlled by the laws of the State 
-of Washington, USA, without regard to conflicts of law. If any provision of 
-this MSR-LA shall be deemed unenforceable or contrary to law, the rest of this 
-MSR-LA shall remain in full effect and interpreted in an enforceable manner 
-that most nearly captures the intent of the original language. 
-
diff --git a/licenses/MathWorks b/licenses/MathWorks
new file mode 100644
index 000000000..d42c4d7a3
--- /dev/null
+++ b/licenses/MathWorks
@@ -0,0 +1,7 @@
+Copyright (c) 2022, The MathWorks, Inc.
+All rights reserved.
+Redistribution and use in source and binary forms, with or without modification, are permitted provided that the following conditions are met:
+1. Redistributions of source code must retain the above copyright notice, this list of conditions and the following disclaimer.
+2. Redistributions in binary form must reproduce the above copyright notice, this list of conditions and the following disclaimer in the documentation and/or other materials provided with the distribution.
+3. In all cases, the software is, and all modifications and derivatives of the software shall be, licensed to you solely for use in conjunction with MathWorks products and service offerings. 
+THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
\ No newline at end of file
diff --git a/licenses/Montage b/licenses/Montage
deleted file mode 100644
index f33d7c8c3..000000000
--- a/licenses/Montage
+++ /dev/null
@@ -1,90 +0,0 @@
-CALTECH/JPL
-NON-EXCLUSIVE, NON-COMMERCIAL
-SOFTWARE LICENSE AGREEMENT
-
---MONTAGE(TM)
-SOURCE CODE ALLOCATION
---CLICKWRAP LICENSE AGREEMENT--
-
-BY CLICKING THE "I AGREE" BUTTON OR BY USING THE SOFTWARE AFTER VIEWING THIS LICENSE, YOU ARE AGREEING TO THE TERMS OF THIS LICENSE AGREEMENT.
-
-This is a license agreement and not an agreement for sale.  This license agreement (Agreement) is between your Company or self for your personal use, and the California Institute of Technology (hereinafter called "LICENSOR" or alternatively CALTECH, through the operating division, Jet Propulsion Laboratory (JPL) of LICENSOR" and gives Licensee certain limited rights to use the proprietary "Montage" Software and Related Material.   All rights not specifically granted in this Agreement are reserved to Caltech/JPL.   Licensor warrants that it has the right to grant this license of the Software and Related Materials.
-
-RESERVATION OF OWNERSHIP AND GRANT OF LICENSE:  Caltech/JPL retains exclusive ownership of any copy of the Software (as defined below) licensed under this Agreement and hereby grants to Licensee a personal, non-exclusive, non-transferable license to use the Software and Related Materials, without the right to sublicense, for research purposes, and pursuant to the terms and conditions of this Agreement.  From the date of receipt, Licensee agrees to use reasonable effort to protect the Software from unauthorized use, reproduction, distribution, or publication. 
-
-CONFIDENTIALITY:  Licensee acknowledges that the Software provided under this Agreement is proprietary to Caltech/JPL, and as such, Licensee agrees to receive all such materials in confidence and use the Software only in accordance with the terms of this Agreement.  
-
-COPYRIGHT:   The Software is owned by Caltech/JPL and is protected by United States copyright laws and applicable international treaties and/or conventions. The United States Government may have prior rights to use some or all of the Software as determined under applicable contracts and license agreements with Caltech/JPL.
-
-DEFINITIONS:  As used herein, the following words, phrases, or terms in this Agreement shall have the following meanings:
-
-"Montage(TM)" means the suite of programs, scripts, manuals and procedures received from Caltech/JPL for the purpose of providing a portable, compute-intensive service that will deliver science-grade custom astronomical image mosaics on demand, with requests made through existing portals.
-
-"Internal" means within the Licensee’s own organization which has been granted this license.
-
-"Executable Code" means machine-readable code compiled by a high-level compiler.
-
-"Noncommercial" means for research purposes only, wherein LICENSEE shall earn no fees or costs whatsoever for use of Software and/or Related Materials, and shall not develop or manufacture a Product either directly or indirectly from the Software.
-
-"Source Code" means code written in human-readable format or in a high-level program language.
-
-"Software" means the actual copy of all or any portion of the allocated source or executable code for program routines delivered on the media, inclusive of backups, updates, or merged copies permitted hereunder or subsequently supplied by Caltech/JPL. It includes file structures, programming instructions, user interfaces and screen formats and sequences.
-
-"Related Materials" means all of the printed materials, user documentation, training documentation and confidential software activation code supplied by Caltech/JPL under this Agreement.
-
-
-PERMITTED USES: 
-
-Noncommercial Research:
-
-The Software may be used for Licensee's own internal research and development or experimental use.  Licensee shall report any performance problems to Caltech/JPL for improvement of the software. 
-
-Backups:  Licensee may make and maintain backup copies provided Licensee or its archive service delegatee keeps possession of each backup.  In addition, Licensee may make that number of copies of the Software necessary for its licensed site provided that all information appearing in or on the original labels, including the copyright and trademark notices are copied onto the labels of the copies.
-
-USES NOT PERMITTED:
-
-Licensee has not been granted any trademark license as part of this agreement and may not use the name or mark "Montage" or any rendition thereof for any purpose outside of the purpose stated herein.
-
-THIRD PARTIES:  LICENSEE MAY NOT SELL, RENT, LEASE, SUBLICENSE, LEND, TIME-SHARE OR TRANSFER, IN WHOLE OR IN PART, OR PROVIDE UNLICENSED THIRD PARTIES ACCESS, TO PRIOR OR PRESENT VERSIONS (OR ANY PARTS THEREOF) OF THE SOFTWARE AND RELATED MATERIALS, ANY UPDATES, OR LICENSEE'S RIGHTS UNDER THIS AGREEMENT.  THE CODE MAY BE ACCESSED INDEPENDENTLY, AFTER CLICKING THE "I AGREE" BUTTON AND FILLING OUT AN INFORMATION FORM, THROUGH THE WWW SITE: HTTP://MONTAGE.IPAC.CALTECH.EDU.
-
-Licensee may not remove or obscure any copyright or trademark notices.
-
-The Software and Related Materials shall not become subject to application for patent or copyright by Licensee.
-
-Assignment: Licensee shall not assign this Agreement or Licensee's rights hereunder without the prior written consent of Caltech/JPL.  Any purported assignment without such consent shall be null and void.
-
-Term:   The term of the license granted by this Agreement is from the effective date of this agreement until terminated. 
-
-You may terminate this license at any time by destroying the program and documentation and the permitted backup copy. Upon termination, you will destroy all copies of the Software.
-
-This license automatically terminates if you fail to comply with any provision of this Agreement.  Licensee will then return to Caltech/JPL the Software, Related Materials and any whole or partial copies, codes, modifications, and merged portions in any form.  The parties hereby agree that all provisions, which operate to protect the proprietary rights of Caltech/JPL shall remain in force should breach occur and that the obligation of confidentiality described survives the term of the Agreement.
-
-Fee:   Whereas Licensee will use said Software solely for the uses stated above, and agrees not to permit or sublicense third-party use of this Software, and to comply with any applicable "Restricted Rights" requirements, there is no fee for this license.  
-
-NO WARRANTY:
-
-DISCLAIMER
-
-THE SOFTWARE AND/OR RELATED MATERIALS ARE PROVIDED "AS-IS" WITHOUT WARRANTY OF ANY KIND INCLUDING ANY WARRANTIES OF PERFORMANCE OR MERCHANTABILITY OR FITNESS FOR A PARTICULAR PURPOSE (AS SET FORTH IN UCC §2312 2313) OR FOR ANY PURPOSE WHATSOEVER, FOR THE LICENSED PRODUCT, HOWEVER USED.  
-
-IN NO EVENT SHALL CALTECH/JPL BE LIABLE FOR INCIDENTAL OR CONSEQUENTIAL DAMAGES OF ANY KIND, INCLUDING ECONOMIC DAMAGE OR INJURY TO PROPERTY AND LOST PROFITS, REGARDLESS OF WHETHER CALTECH/JPL SHALL BE ADVISED, HAVE REASON TO KNOW, OR IN FACT SHALL KNOW OF THE POSSIBILITY.
-
-USER BEARS ALL RISK RELATING TO QUALITY AND PERFORMANCE OF THE SOFTWARE AND/OR RELATED MATERIALS. 
-
-Exclusive Remedy and Limitation of Liability:  Caltech/JPL shall not be liable for indirect, special, incidental, or consequential damages or lost profits related to Licensee's use of the Software and Related Materials, even if Caltech/JPL is advised of the possibility of such damage.
-
-Restricted Rights Legend
-
-Use, duplication, or disclosure by the Government is subject to the restrictions as set forth in FAR s52.227-14 (JUN 1987) Alternate III (g)(3), FAR s52.227-19 (JUN 1987), DFARS  s252.211-7015 (MAY 1991) or DFARS s252.227-7013 (c)(1)(ii) (OCT 1988), as applicable.
-
-Support and Maintenance:  No software support or training by the Licensor is provided as part of this agreement. 
-
-Export Regulation:  When exporting Caltech/JPL software or product incorporating such software to a foreign entity, licensee shall comply with all federal export laws and statutes.  In the event an export license is required to execute the transfer, licensee shall apply and obtain approval for such license through the appropriate U.S. government agency.  
-
-Severability: If any provision(s) of this Agreement shall be held to be invalid, illegal, or unenforceable by a court or other tribunal of competent jurisdiction, the validity, legality and enforceability of the remaining provisions shall not in any way be affected or impaired thereby.
-
-No Implied Waivers: No failure or delay by Caltech/JPL in enforcing any right or remedy under this Agreement shall be construed as a waiver of any future or other exercise of such right or remedy by Caltech/JPL.
-
-Governing Law: Except with respect to Copyright or Patent rights, which shall be governed by federal laws, this Agreement shall be construed and enforced in accordance with the laws of the State of California. 
-
-BY CLICKING THE "I AGREE" BUTTON OR BY USING THE SOFTWARE AFTER VIEWING THIS LICENSE, YOU ARE AGREEING TO THE TERMS OF THIS LICENSE AGREEMENT.
diff --git a/licenses/NOSA b/licenses/NOSA
deleted file mode 100644
index 298f1e588..000000000
--- a/licenses/NOSA
+++ /dev/null
@@ -1,258 +0,0 @@
-NASA OPEN SOURCE AGREEMENT VERSION 1.3
-
-THIS OPEN SOURCE AGREEMENT ("AGREEMENT") DEFINES THE RIGHTS OF USE,
-REPRODUCTION, DISTRIBUTION, MODIFICATION AND REDISTRIBUTION OF CERTAIN
-COMPUTER SOFTWARE ORIGINALLY RELEASED BY THE UNITED STATES GOVERNMENT
-AS REPRESENTED BY THE GOVERNMENT AGENCY LISTED BELOW ("GOVERNMENT
-AGENCY").  THE UNITED STATES GOVERNMENT, AS REPRESENTED BY GOVERNMENT
-AGENCY, IS AN INTENDED THIRD-PARTY BENEFICIARY OF ALL SUBSEQUENT
-DISTRIBUTIONS OR REDISTRIBUTIONS OF THE SUBJECT SOFTWARE.  ANYONE WHO
-USES, REPRODUCES, DISTRIBUTES, MODIFIES OR REDISTRIBUTES THE SUBJECT
-SOFTWARE, AS DEFINED HEREIN, OR ANY PART THEREOF, IS, BY THAT ACTION,
-ACCEPTING IN FULL THE RESPONSIBILITIES AND OBLIGATIONS CONTAINED IN
-THIS AGREEMENT.
-
-Government Agency: National Aeronautics and Space Administration (NASA) 
-Government Agency Original Software Designation: ARC-15277
-Government Agency Original Software Title: growler 0.1
-User Registration Requested.  Please Visit http://opensource.arc.nasa.gov/
-Government Agency Point of Contact for Original Software: bgreen@nas.nasa.gov
-
-1. DEFINITIONS
-
-A. "Contributor" means Government Agency, as the developer of the
-Original Software, and any entity that makes a Modification.
-
-B. "Covered Patents" mean patent claims licensable by a Contributor
-that are necessarily infringed by the use or sale of its Modification
-alone or when combined with the Subject Software.
-
-C. "Display" means the showing of a copy of the Subject Software,
-either directly or by means of an image, or any other device.
-
-D. "Distribution" means conveyance or transfer of the Subject
-Software, regardless of means, to another.
-
-E. "Larger Work" means computer software that combines Subject
-Software, or portions thereof, with software separate from the Subject
-Software that is not governed by the terms of this Agreement.
-
-F.  "Modification" means any alteration of, including addition to or
-deletion from, the substance or structure of either the Original
-Software or Subject Software, and includes derivative works, as that
-term is defined in the Copyright Statute, 17 USC 101.  However, the
-act of including Subject Software as part of a Larger Work does not in
-and of itself constitute a Modification.
-
-G. "Original Software" means the computer software first released
-under this Agreement by Government Agency with Government Agency
-designation ARC-15277 and entitled growler, including source code,
-object code and accompanying documentation, if any.
-
-H. "Recipient" means anyone who acquires the Subject Software under
-this Agreement, including all Contributors.
-
-I. "Redistribution" means Distribution of the Subject Software after a
-Modification has been made.
-
-J. "Reproduction" means the making of a counterpart, image or copy of
-the Subject Software.
-
-K. "Sale" means the exchange of the Subject Software for money or
-equivalent value.
-
-L. "Subject Software" means the Original Software, Modifications, or
-any respective parts thereof.
-
-M. "Use" means the application or employment of the Subject Software
-for any purpose.
-
-2. GRANT OF RIGHTS
-
-A. Under Non-Patent Rights: Subject to the terms and conditions of
-this Agreement, each Contributor, with respect to its own contribution
-to the Subject Software, hereby grants to each Recipient a
-non-exclusive, world-wide, royalty-free license to engage in the
-following activities pertaining to the Subject Software:
-
-1. Use
-2. Distribution
-3. Reproduction
-4. Modification
-5. Redistribution
-6. Display
-
-B. Under Patent Rights: Subject to the terms and conditions of this
-Agreement, each Contributor, with respect to its own contribution to
-the Subject Software, hereby grants to each Recipient under Covered
-Patents a non-exclusive, world-wide, royalty-free license to engage in
-the following activities pertaining to the Subject Software:
-
-1. Use
-2. Distribution
-3. Reproduction
-4. Sale
-5. Offer for Sale
-
-C. The rights granted under Paragraph B. also apply to the combination
-of a Contributor's Modification and the Subject Software if, at the
-time the Modification is added by the Contributor, the addition of
-such Modification causes the combination to be covered by the Covered
-Patents.  It does not apply to any other combinations that include a
-Modification.
-
-D. The rights granted in Paragraphs A. and B. allow the Recipient to
-sublicense those same rights.  Such sublicense must be under the same
-terms and conditions of this Agreement.
-
-3. OBLIGATIONS OF RECIPIENT
-
-A. Distribution or Redistribution of the Subject Software must be made
-under this Agreement except for additions covered under paragraph 3H.
-
-1. Whenever a Recipient distributes or redistributes the Subject
-   Software, a copy of this Agreement must be included with each copy
-   of the Subject Software; and
-2. If Recipient distributes or redistributes the Subject Software in
-   any form other than source code, Recipient must also make the
-   source code freely available, and must provide with each copy of
-   the Subject Software information on how to obtain the source code
-   in a reasonable manner on or through a medium customarily used for
-   software exchange.
-
-B. Each Recipient must ensure that the following copyright notice
-appears prominently in the Subject Software:
-
-Copyright ã 2004 United States Government as represented by the
-Administrator of the National Aeronautics and Space Administration.
-All Rights Reserved.
-
-C. Each Contributor must characterize its alteration of the Subject
-Software as a Modification and must identify itself as the originator
-of its Modification in a manner that reasonably allows subsequent
-Recipients to identify the originator of the Modification.  In
-fulfillment of these requirements, Contributor must include a file
-(e.g., a change log file) that describes the alterations made and the
-date of the alterations, identifies Contributor as originator of the
-alterations, and consents to characterization of the alterations as a
-Modification, for example, by including a statement that the
-Modification is derived, directly or indirectly, from Original
-Software provided by Government Agency. Once consent is granted, it
-may not thereafter be revoked.
-
-D. A Contributor may add its own copyright notice to the Subject
-Software.  Once a copyright notice has been added to the Subject
-Software, a Recipient may not remove it without the express permission
-of the Contributor who added the notice.
-
-E. A Recipient may not make any representation in the Subject Software
-or in any promotional, advertising or other material that may be
-construed as an endorsement by Government Agency or by any prior
-Recipient of any product or service provided by Recipient, or that may
-seek to obtain commercial advantage by the fact of Government Agency's
-or a prior Recipient's participation in this Agreement.
-
-F. In an effort to track usage and maintain accurate records of the
-Subject Software, each Recipient, upon receipt of the Subject
-Software, is requested to register with Government Agency by visiting
-the following website: http://opensource.arc.nasa.gov.  Recipient's
-name and personal information shall be used for statistical purposes
-only. Once a Recipient makes a Modification available, it is requested
-that the Recipient inform Government Agency at the web site provided
-above how to access the Modification.
-
-G. Each Contributor represents that that its Modification is believed
-to be Contributor's original creation and does not violate any
-existing agreements, regulations, statutes or rules, and further that
-Contributor has sufficient rights to grant the rights conveyed by this
-Agreement.
-
-H. A Recipient may choose to offer, and to charge a fee for, warranty,
-support, indemnity and/or liability obligations to one or more other
-Recipients of the Subject Software.  A Recipient may do so, however,
-only on its own behalf and not on behalf of Government Agency or any
-other Recipient.  Such a Recipient must make it absolutely clear that
-any such warranty, support, indemnity and/or liability obligation is
-offered by that Recipient alone.  Further, such Recipient agrees to
-indemnify Government Agency and every other Recipient for any
-liability incurred by them as a result of warranty, support, indemnity
-and/or liability offered by such Recipient.
-
-I. A Recipient may create a Larger Work by combining Subject Software
-with separate software not governed by the terms of this agreement and
-distribute the Larger Work as a single product. In such case, the
-Recipient must make sure Subject Software, or portions thereof,
-included in the Larger Work is subject to this Agreement.
-
-J. Notwithstanding any provisions contained herein, Recipient is
-hereby put on notice that export of any goods or technical data from
-the United States may require some form of export license from the
-U.S. Government.  Failure to obtain necessary export licenses may
-result in criminal liability under U.S. laws.  Government Agency
-neither represents that a license shall not be required nor that, if
-required, it shall be issued.  Nothing granted herein provides any
-such export license.
-
-4. DISCLAIMER OF WARRANTIES AND LIABILITIES; WAIVER AND INDEMNIFICATION
-
-A. No Warranty: THE SUBJECT SOFTWARE IS PROVIDED "AS IS" WITHOUT ANY
-WARRANTY OF ANY KIND, EITHER EXPRESSED, IMPLIED, OR STATUTORY,
-INCLUDING, BUT NOT LIMITED TO, ANY WARRANTY THAT THE SUBJECT SOFTWARE
-WILL CONFORM TO SPECIFICATIONS, ANY IMPLIED WARRANTIES OF
-MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE, OR FREEDOM FROM
-INFRINGEMENT, ANY WARRANTY THAT THE SUBJECT SOFTWARE WILL BE ERROR
-FREE, OR ANY WARRANTY THAT DOCUMENTATION, IF PROVIDED, WILL CONFORM TO
-THE SUBJECT SOFTWARE. THIS AGREEMENT DOES NOT, IN ANY MANNER,
-CONSTITUTE AN ENDORSEMENT BY GOVERNMENT AGENCY OR ANY PRIOR RECIPIENT
-OF ANY RESULTS, RESULTING DESIGNS, HARDWARE, SOFTWARE PRODUCTS OR ANY
-OTHER APPLICATIONS RESULTING FROM USE OF THE SUBJECT SOFTWARE.
-FURTHER, GOVERNMENT AGENCY DISCLAIMS ALL WARRANTIES AND LIABILITIES
-REGARDING THIRD-PARTY SOFTWARE, IF PRESENT IN THE ORIGINAL SOFTWARE,
-AND DISTRIBUTES IT "AS IS."
-
-B. Waiver and Indemnity: RECIPIENT AGREES TO WAIVE ANY AND ALL CLAIMS
-AGAINST THE UNITED STATES GOVERNMENT, ITS CONTRACTORS AND
-SUBCONTRACTORS, AS WELL AS ANY PRIOR RECIPIENT.  IF RECIPIENT'S USE OF
-THE SUBJECT SOFTWARE RESULTS IN ANY LIABILITIES, DEMANDS, DAMAGES,
-EXPENSES OR LOSSES ARISING FROM SUCH USE, INCLUDING ANY DAMAGES FROM
-PRODUCTS BASED ON, OR RESULTING FROM, RECIPIENT'S USE OF THE SUBJECT
-SOFTWARE, RECIPIENT SHALL INDEMNIFY AND HOLD HARMLESS THE UNITED
-STATES GOVERNMENT, ITS CONTRACTORS AND SUBCONTRACTORS, AS WELL AS ANY
-PRIOR RECIPIENT, TO THE EXTENT PERMITTED BY LAW.  RECIPIENT'S SOLE
-REMEDY FOR ANY SUCH MATTER SHALL BE THE IMMEDIATE, UNILATERAL
-TERMINATION OF THIS AGREEMENT.
-
-
-5. GENERAL TERMS
-
-A. Termination: This Agreement and the rights granted hereunder will
-terminate automatically if a Recipient fails to comply with these
-terms and conditions, and fails to cure such noncompliance within
-thirty (30) days of becoming aware of such noncompliance.  Upon
-termination, a Recipient agrees to immediately cease use and
-distribution of the Subject Software.  All sublicenses to the Subject
-Software properly granted by the breaching Recipient shall survive any
-such termination of this Agreement.
-
-B. Severability: If any provision of this Agreement is invalid or
-unenforceable under applicable law, it shall not affect the validity
-or enforceability of the remainder of the terms of this Agreement.
-
-C. Applicable Law: This Agreement shall be subject to United States
-federal law only for all purposes, including, but not limited to,
-determining the validity of this Agreement, the meaning of its
-provisions and the rights, obligations and remedies of the parties.
-
-D. Entire Understanding: This Agreement constitutes the entire
-understanding and agreement of the parties relating to release of the
-Subject Software and may not be superseded, modified or amended except
-by further written agreement duly executed by the parties.
-
-E. Binding Authority: By accepting and using the Subject Software
-under this Agreement, a Recipient affirms its authority to bind the
-Recipient to all terms and conditions of this Agreement and that that
-Recipient hereby agrees to all terms and conditions herein.
-
-F. Point of Contact: Any Recipient contact with Government Agency is
-to be directed to the designated representative as follows:
-bgreen@nas.nasa.gov.
diff --git a/licenses/NVIDIA-CUDA b/licenses/NVIDIA-CUDA
deleted file mode 100644
index e101b27e5..000000000
--- a/licenses/NVIDIA-CUDA
+++ /dev/null
@@ -1,2297 +0,0 @@
-End User License Agreement
---------------------------
-
-
-Preface
--------
-
-The following contains specific license terms and conditions
-for four separate NVIDIA products. By accepting this
-agreement, you agree to comply with all the terms and
-conditions applicable to the specific product(s) included
-herein.
-
-
-NVIDIA CUDA Toolkit
-
-
-Description
-
-The NVIDIA CUDA Toolkit provides command-line and graphical
-tools for building, debugging and optimizing the performance
-of applications accelerated by NVIDIA GPUs, runtime and math
-libraries, and documentation including programming guides,
-user manuals, and API references. The NVIDIA CUDA Toolkit
-License Agreement is available in Chapter 1.
-
-
-Default Install Location of CUDA Toolkit
-
-Windows platform:
-
-%ProgramFiles%\NVIDIA GPU Computing Toolkit\CUDA\v#.#
-
-Linux platform:
-
-/usr/local/cuda-#.#
-
-Mac platform:
-
-/Developer/NVIDIA/CUDA-#.#
-
-
-NVIDIA CUDA Samples
-
-
-Description
-
-This package includes over 100+ CUDA examples that demonstrate
-various CUDA programming principles, and efficient CUDA
-implementation of algorithms in specific application domains.
-The NVIDIA CUDA Samples License Agreement is available in
-Chapter 2.
-
-
-Default Install Location of CUDA Samples
-
-Windows platform:
-
-%ProgramData%\NVIDIA Corporation\CUDA Samples\v#.#
-
-Linux platform:
-
-/usr/local/cuda-#.#/samples
-
-and
-
-$HOME/NVIDIA_CUDA-#.#_Samples
-
-Mac platform:
-
-/Developer/NVIDIA/CUDA-#.#/samples
-
-
-NVIDIA Driver
-
-
-Description
-
-This package contains the operating system driver and
-fundamental system software components for NVIDIA GPUs. The
-NVIDIA Driver License for the Windows platform is available in
-Chapter 3, and the NVIDIA Driver License for the Linux and Mac
-OSX platforms is available in Chapter 4.
-
-
-NVIDIA Nsight Visual Studio Edition (Windows only)
-
-
-Description
-
-NVIDIA Nsight Development Platform, Visual Studio Edition is a
-development environment integrated into Microsoft Visual
-Studio that provides tools for debugging, profiling, analyzing
-and optimizing your GPU computing and graphics applications.
-The NVIDIA Nsight Visual Studio Edition License Agreement is
-available in Chapter 5.
-
-
-Default Install Location of Nsight Visual Studio Edition
-
-Windows platform:
-
-%ProgramFiles(x86)%\NVIDIA Corporation\Nsight Visual Studio Edition #.#
-
-
-NVIDIA CUDA General Terms
-
-
-Description
-
-General terms that apply to all of the software components are
-available in Chapter 6.
-
-
-1. NVIDIA CUDA Toolkit License Agreement
-----------------------------------------
-
-
-Important Notice
-----------------
-
-READ CAREFULLY: This Software License Agreement ("Agreement")
-for NVIDIA CUDA Toolkit, including computer software and
-associated documentation ("Software"), is the Agreement which
-governs use of the SOFTWARE of NVIDIA Corporation and its
-subsidiaries ("NVIDIA") downloadable herefrom. By downloading,
-installing, copying, or otherwise using the SOFTWARE, You (as
-defined below) agree to be bound by the terms of this
-Agreement. If You do not agree to the terms of this Agreement,
-do not download the SOFTWARE.
-
-
-Recitals
---------
-
-Use of NVIDIA's SOFTWARE requires three elements: the
-SOFTWARE, an NVIDIA GPU or application processor ("NVIDIA
-Hardware"), and a computer system. The SOFTWARE is protected
-by copyright laws and international copyright treaties, as
-well as other intellectual property laws and treaties. The
-SOFTWARE is not sold, and instead is only licensed for Your
-use, strictly in accordance with this Agreement. The NVIDIA
-Hardware is protected by various patents, and is sold, but
-this Agreement does not cover the sale or use of such
-hardware, since it may not necessarily be sold as a package
-with the SOFTWARE. This Agreement sets forth the terms and
-conditions of the SOFTWARE only.
-
-
-1.1. Definitions
-
-
-1.1.1. Licensee
-
-"You", or "Your" shall mean the entity or individual that
-downloads and uses the SOFTWARE.
-
-
-1.1.2. Redistributable Software
-
-"Redistributable Software" shall mean the redistributable
-libraries referenced in Attachment A of this Agreement.
-
-
-1.1.3. Software
-
-"SOFTWARE" shall mean the deliverables provided pursuant to
-this Agreement. SOFTWARE may be provided in either source or
-binary form, at NVIDIA's discretion.
-
-
-1.2. Grant of License
-
-
-1.2.1. Rights and Limitations of Grant
-
-Provided that Licensee complies with the terms of this
-Agreement, NVIDIA hereby grants Licensee the following
-limited, non-exclusive, non-transferable, non-sublicensable
-(except as expressly permitted otherwise for Redistributable
-Software in Section 1.2.1.1 and Section 1.2.1.3 of this
-Agreement) right to use the SOFTWARE -- and, if the SOFTWARE
-is provided in source form, to compile the SOFTWARE -- with
-the following limitations:
-
-
-1.2.1.1. Redistribution Rights
-
-Licensee may transfer, redistribute, and sublicense certain
-files of the Redistributable SOFTWARE, as defined in
-Attachment A of this Agreement, provided, however, that (a)
-the Redistributable SOFTWARE shall be distributed solely in
-binary form to Licensee's licensees ("Customers") only as a
-component of Licensee's own software products (each, a
-"Licensee Application"); (b) Licensee shall design the
-Licensee Application such that the Redistributable SOFTWARE
-files are installed only in a private (non-shared) directory
-location that is used only by the Licensee Application; (c)
-Licensee shall obtain each Customer's written or clickwrap
-agreement to the license terms under a written, legally
-enforceable agreement that has the effect of protecting the
-SOFTWARE and the rights of NVIDIA under terms no less
-restrictive than this Agreement.
-
-
-1.2.1.2. Usage Rights
-
-Licensee may install and use multiple copies of the SOFTWARE
-on a shared computer or concurrently on different computers,
-and make multiple back-up copies of the SOFTWARE, solely for
-Licensee's use within Licensee's Enterprise. "Enterprise"
-shall mean individual use by Licensee or any legal entity
-(such as a corporation or university) and the subsidiaries it
-owns by more than 50 percent.
-
-
-1.2.1.3. Further Redistribution Rights
-
-Subject to the terms and conditions of the Agreement, Licensee
-may authorize Customers to further redistribute the
-Redistributable SOFTWARE that such Customers receive as part
-of the Licensee Application, solely in binary form, provided,
-however, that Licensee shall require in their standard
-software license agreements with Customers that all such
-redistributions must be made pursuant to a license agreement
-that has the effect of protecting the SOFTWARE and the rights
-of NVIDIA whose terms and conditions are at least as
-restrictive as those in the applicable Licensee software
-license agreement covering the Licensee Application. For
-avoidance of doubt, termination of this Agreement shall not
-affect rights previously granted by Licensee to its Customers
-under this Agreement to the extent validly granted to
-Customers under Section 1.2.1.1.
-
-
-1.2.1.4. Linux/FreeBSD Exception
-
-Notwithstanding the foregoing terms of Section 1.2.1.2,
-Section 1.2.1.1 and Section 1.2.1.3, SOFTWARE designed
-exclusively for use on the Linux or FreeBSD operating systems,
-or other operating systems derived from the source code to
-these operating systems, may be copied and redistributed,
-provided that the binary files thereof are not modified in any
-way (except for unzipping of compressed files).
-
-
-1.2.1.5. Additional Licensing Obligations
-
-Licensee acknowledges and agrees that its use of certain third
-party components included with the SOFTWARE may be subject to
-additional licensing terms and conditions as set forth or
-referenced in Attachment B of this Agreement.
-
-
-1.2.1.6. Limitations
-
-No Reverse Engineering
-
-If the SOFTWARE is provided in binary form, Licensee may not
-reverse engineer, decompile, or disassemble the SOFTWARE, nor
-attempt in any other manner to obtain the source code.
-
-No Separation of Components
-
-The SOFTWARE is licensed as a single product. Except as
-authorized in this Agreement, Software component parts of the
-Software may not be separated for use on more than one
-computer, nor otherwise used separately from the other parts.
-
-No Rental
-
-Licensee may not rent or lease the SOFTWARE to someone else.
-
-No Modifications
-
-If the SOFTWARE is provided in source form, Licensee may not
-modify or create derivative works of the SOFTWARE.
-
-
-1.3. Term and Termination
-
-This Agreement will continue in effect for two (2) years
-("Initial Term") after Your initial download and use of the
-SOFTWARE, subject to the exclusive right of NVIDIA to
-terminate as provided herein. The term of this Agreement will
-automatically renew for successive one (1) year renewal terms
-after the Initial Term, unless either party provides to the
-other party at least three (3) months prior written notice of
-termination before the end of the applicable renewal term.
-
-This Agreement will automatically terminate if Licensee fails
-to comply with any of the terms and conditions hereof. In such
-event, Licensee must destroy all copies of the SOFTWARE and
-all of its component parts.
-
-
-Defensive Suspension
-
-If Licensee commences or participates in any legal proceeding
-against NVIDIA, then NVIDIA may, in its sole discretion,
-suspend or terminate all license grants and any other rights
-provided under this Agreement during the pendency of such
-legal proceedings.
-
-
-1.4. Copyright
-
-All rights, title, interest and copyrights in and to the
-SOFTWARE (including but not limited to all images,
-photographs, animations, video, audio, music, text, and other
-information incorporated into the SOFTWARE), the accompanying
-printed materials, and any copies of the SOFTWARE, are owned
-by NVIDIA, or its suppliers. The SOFTWARE is protected by
-copyright laws and international treaty provisions.
-Accordingly, Licensee is required to treat the SOFTWARE like
-any other copyrighted material, except as otherwise allowed
-pursuant to this Agreement and that it may make one copy of
-the SOFTWARE solely for backup or archive purposes.
-
-RESTRICTED RIGHTS NOTICE. Software has been developed entirely
-at private expense and is commercial computer software
-provided with RESTRICTED RIGHTS. Use, duplication or
-disclosure by the U.S. Government or a U.S. Government
-subcontractor is subject to the restrictions set forth in the
-Agreement under which Software was obtained pursuant to DFARS
-227.7202-3(a) or as set forth in subparagraphs (c)(1) and (2)
-of the Commercial Computer Software - Restricted Rights clause
-at FAR 52.227-19, as applicable. Contractor/manufacturer is
-NVIDIA, 2701 San Tomas Expressway, Santa Clara, CA 95050.
-
-
-1.5. Applicable Law
-
-This Agreement shall be deemed to have been made in, and shall
-be construed pursuant to, the laws of the State of Delaware.
-The United Nations Convention on Contracts for the
-International Sale of Goods is specifically disclaimed. The
-courts of Santa Clara County, California shall have exclusive
-jurisdiction and venue over any dispute arising out of or
-relating to this Agreement.
-
-
-1.6. Disclaimer of Warranties and Limitations on Liability
-
-
-1.6.1. No Warranties
-
-TO THE MAXIMUM EXTENT PERMITTED BY APPLICABLE LAW, THE
-SOFTWARE IS PROVIDED "AS IS" AND NVIDIA AND ITS SUPPLIERS
-DISCLAIM ALL WARRANTIES, EITHER EXPRESS OR IMPLIED, INCLUDING,
-BUT NOT LIMITED TO, IMPLIED WARRANTIES OF MERCHANTABILITY,
-FITNESS FOR A PARTICULAR PURPOSE, OR NONINFRINGEMENT.
-
-
-1.6.2. No Liability for Consequential Damages
-
-TO THE MAXIMUM EXTENT PERMITTED BY APPLICABLE LAW, IN NO EVENT
-SHALL NVIDIA OR ITS SUPPLIERS BE LIABLE FOR ANY SPECIAL,
-INCIDENTAL, INDIRECT, OR CONSEQUENTIAL DAMAGES WHATSOEVER
-(INCLUDING, WITHOUT LIMITATION, DAMAGES FOR LOSS OF BUSINESS
-PROFITS, BUSINESS INTERRUPTION, LOSS OF BUSINESS INFORMATION,
-OR ANY OTHER PECUNIARY LOSS) ARISING OUT OF THE USE OF OR
-INABILITY TO USE THE SOFTWARE, EVEN IF NVIDIA HAS BEEN ADVISED
-OF THE POSSIBILITY OF SUCH DAMAGES.
-
-
-1.6.3. No Support
-
-NVIDIA has no obligation to support or to provide any updates
-of the Software.
-
-
-1.7. Miscellaneous
-
-
-1.7.1. Feedback
-
-Notwithstanding any Non-Disclosure Agreement executed by and
-between the parties, the parties agree that in the event
-Licensee or NVIDIA provides Feedback (as defined below) to the
-other party on how to design, implement, or improve the
-SOFTWARE or Licensee's product(s) for use with the SOFTWARE,
-the following terms and conditions apply the Feedback:
-
-
-1.7.1.1. Exchange of Feedback
-
-Both parties agree that neither party has an obligation to
-give the other party any suggestions, comments or other
-feedback, whether verbally or in written or source code form,
-relating to (i) the SOFTWARE; (ii) Licensee's products; (iii)
-Licensee's use of the SOFTWARE; or (iv)
-optimization/interoperability of Licensee's product with the
-SOFTWARE (collectively defined as "Feedback"). In the event
-either party provides Feedback to the other party, the party
-receiving the Feedback may use any Feedback that the other
-party voluntarily provides to improve the (i) SOFTWARE or
-other related NVIDIA technologies, respectively for the
-benefit of NVIDIA; or (ii) Licensee's product or other related
-Licensee technologies, respectively for the benefit of
-Licensee. Accordingly, if either party provides Feedback to
-the other party, both parties agree that the other party and
-its respective licensees may freely use, reproduce, license,
-distribute, and otherwise commercialize the Feedback in the
-(i) SOFTWARE or other related technologies; or (ii) Licensee's
-products or other related technologies, respectively, without
-the payment of any royalties or fees.
-
-
-1.7.1.2. Residual Rights
-
-Licensee agrees that NVIDIA shall be free to use any general
-knowledge, skills and experience, (including, but not limited
-to, ideas, concepts, know-how, or techniques) ("Residuals"),
-contained in the (i) Feedback provided by Licensee to NVIDIA;
-(ii) Licensee's products shared or disclosed to NVIDIA in
-connection with the Feedback; or (c) Licensee's confidential
-information voluntarily provided to NVIDIA in connection with
-the Feedback, which are retained in the memories of NVIDIA's
-employees, agents, or contractors who have had access to such
-Residuals. Subject to the terms and conditions of this
-Agreement, NVIDIA's employees, agents, or contractors shall
-not be prevented from using Residuals as part of such
-employee's, agent's or contractor's general knowledge, skills,
-experience, talent, and/or expertise. NVIDIA shall not have
-any obligation to limit or restrict the assignment of such
-employees, agents or contractors or to pay royalties for any
-work resulting from the use of Residuals.
-
-
-1.7.1.3. Disclaimer of Warranty
-
-FEEDBACK FROM EITHER PARTY IS PROVIDED FOR THE OTHER PARTY'S
-USE "AS IS" AND BOTH PARTIES DISCLAIM ALL WARRANTIES, EXPRESS,
-IMPLIED AND STATUTORY INCLUDING, WITHOUT LIMITATION, THE
-IMPLIED WARRANTIES OF MERCHANTABILITY, FITNESS FOR A
-PARTICULAR PURPOSE, OR NONINFRINGEMENT. BOTH PARTIES DO NOT
-REPRESENT OR WARRANT THAT THE FEEDBACK WILL MEET THE OTHER
-PARTY'S REQUIREMENTS OR THAT THE OPERATION OR IMPLEMENTATION
-OF THE FEEDBACK WILL BE UNINTERRUPTED OR ERROR-FREE.
-
-
-1.7.1.4. No Liability for Consequential Damages
-
-TO THE MAXIMUM EXTENT PERMITTED BY APPLICABLE LAW, IN NO EVENT
-SHALL EITHER PARTY OR ITS SUPPLIERS BE LIABLE FOR ANY SPECIAL,
-INCIDENTAL, INDIRECT, OR CONSEQUENTIAL DAMAGES WHATSOEVER
-(INCLUDING, WITHOUT LIMITATION, DAMAGES FOR LOSS OF BUSINESS
-PROFITS, BUSINESS INTERRUPTION, LOSS OF BUSINESS INFORMATION,
-OR ANY OTHER PECUNIARY LOSS) ARISING OUT OF THE USE OF OR
-INABILITY TO USE THE FEEDBACK, EVEN IF THE OTHER PARTY HAS
-BEEN ADVISED OF THE POSSIBILITY OF SUCH DAMAGES.
-
-
-1.7.2. Freedom of Action
-
-Licensee agrees that this Agreement is nonexclusive and NVIDIA
-may currently or in the future be developing software, other
-technology or confidential information internally, or
-receiving confidential information from other parties that
-maybe similar to the Feedback and Licensee's confidential
-information (as provided in Section 1.7.1.2 above), which may
-be provided to NVIDIA in connection with Feedback by Licensee.
-Accordingly, Licensee agrees that nothing in this Agreement
-will be construed as a representation or inference that NVIDIA
-will not develop, design, manufacture, acquire, market
-products, or have products developed, designed, manufactured,
-acquired, or marketed for NVIDIA, that compete with the
-Licensee's products or confidential information.
-
-
-1.7.3. No Implied Licenses
-
-Under no circumstances should anything in this Agreement be
-construed as NVIDIA granting by implication, estoppel or
-otherwise, (i) a license to any NVIDIA product or technology
-other than the SOFTWARE; or (ii) any additional license rights
-for the SOFTWARE other than the licenses expressly granted in
-this Agreement.
-
-
-1.7.4. 
-
-If any provision of this Agreement is inconsistent with, or
-cannot be fully enforced under, the law, such provision will
-be construed as limited to the extent necessary to be
-consistent with and fully enforceable under the law. This
-Agreement is the final, complete and exclusive agreement
-between the parties relating to the subject matter hereof, and
-supersedes all prior or contemporaneous understandings and
-agreements relating to such subject matter, whether oral or
-written. This Agreement may only be modified in writing signed
-by an authorized officer of NVIDIA. Licensee agrees that it
-will not ship, transfer or export the SOFTWARE into any
-country, or use the SOFTWARE in any manner, prohibited by the
-United States Bureau of Industry and Security or any export
-laws, restrictions or regulations.
-
-
-1.7.5. 
-
-The parties agree that the following sections of the Agreement
-will survive the termination of the License: Section 1.2.1.4,
-Section 1.4, Section 1.5, Section 1.6, and Section 1.7.
-
-
-1.8. Attachment A
-
-
-Redistributable Software
-
-In connection with Section 1.2.1.1 of this Agreement, the
-following files may be redistributed with software
-applications developed by Licensee, including certain
-variations of these files that have version number or
-architecture specific information embedded in the file name -
-as an example only, for release version 6.0 of the 64-bit
-Windows software, the file cudart64_60.dll is redistributable.
-
-Component : CUDA Runtime
-  Windows : cudart.dll, cudart_static.lib, cudadevrt.lib
-  Mac OSX : libcudart.dylib, libcudart_static.a, libcudadevrt.a
-  Linux   : libcudart.so, libcudart_static.a, libcudadevrt.a
-  Android : libcudart.so, libcudart_static.a, libcudadevrt.a
-
-Component : CUDA FFT Library
-  Windows : cufft.dll, cufftw.dll
-  Mac OSX : libcufft.dylib, libcufft_static.a, libcufftw.dylib, libcufftw_static.a
-  Linux   : libcufft.so, libcufft_static.a, libcufftw.so, libcufftw_static.a
-  Android : libcufft.so, libcufft_static.a, libcufftw.so, libcufftw_static.a
-
-Component : CUDA BLAS Library
-  Windows : cublas.dll, cublas_device.lib
-  Mac OSX : libcublas.dylib, libcublas_static.a, libcublas_device.a
-  Linux   : libcublas.so, libcublas_static.a, libcublas_device.a
-  Android : libcublas.so, libcublas_static.a, libcublas_device.a
-
-Component : NVIDIA "Drop-in" BLAS Library
-  Windows : nvblas.dll
-  Mac OSX : libnvblas.dylib
-  Linux   : libnvblas.so
-
-Component : CUDA Sparse Matrix Library
-  Windows : cusparse.dll
-  Mac OSX : libcusparse.dylib, libcusparse_static.a
-  Linux   : libcusparse.so, libcusparse_static.a
-  Android : libcusparse.so, libcusparse_static.a
-
-Component : CUDA Linear Solver Library
-  Windows : cusolver.dll
-  Mac OSX : libcusolver.dylib, libcusolver_static.a
-  Linux   : libcusolver.so, libcusolver_static.a
-  Android : libcusolver.so, libcusolver_static.a
-
-Component : CUDA Random Number Generation Library
-  Windows : curand.dll
-  Mac OSX : libcurand.dylib, libcurand_static.a
-  Linux   : libcurand.so, libcurand_static.a
-  Android : libcurand.so, libcurand_static.a
-
-Component : NVIDIA Performance Primitives Library
-  Windows : nppc.dll, nppi.dll, npps.dll
-  Mac OSX : libnppc.dylib, libnppi.dylib, libnpps.dylib, libnppc_static.a, libnpps_static.a, libnppi_static.a
-  Linux   : libnppc.so, libnppi.so, libnpps.so, libnppc_static.a, libnpps_static.a, libnppi_static.a
-  Android : libnppc.so, libnppi.so, libnpps.so, libnppc_static.a, libnpps_static.a, libnppi_static.a
-
-Component : Internal common library required for statically linking to cuBLAS, cuSPARSE, cuFFT, cuRAND and NPP
-  Mac OSX : libculibos.a
-  Linux   : libculibos.a
-
-Component : NVIDIA Runtime Compilation Library
-  Windows : nvrtc.dll, nvrtc-builtins.dll
-  Mac OSX : libnvrtc.dylib, libnvrtc-builtins.dylib
-  Linux   : libnvrtc.so, libnvrtc-builtins.so
-
-Component : NVIDIA Optimizing Compiler Library
-  Windows : nvvm.dll
-  Mac OSX : libnvvm.dylib
-  Linux   : libnvvm.so
-
-Component : NVIDIA Common Device Math Functions Library
-  Windows : libdevice.compute_20.bc, libdevice.compute_30.bc, libdevice.compute_35.bc
-  Mac OSX : libdevice.compute_20.bc, libdevice.compute_30.bc, libdevice.compute_35.bc
-  Linux   : libdevice.compute_20.bc, libdevice.compute_30.bc, libdevice.compute_35.bc
-
-Component : CUDA Occupancy Calculation Header Library
-  All     : cuda_occupancy.h
-
-Component : Profiling Tools Interface Library
-  Windows : cupti.dll
-  Mac OSX : libcupti.dylib
-  Linux   : libcupti.so
-      
-
-
-1.9. Attachment B
-
-
-Additional Licensing Obligations
-
-The following third party components included in the SOFTWARE
-are licensed to Licensee pursuant to the following terms and
-conditions:
-
-  1. Licensee's use of the GDB third party component is
-    subject to the terms and conditions of GNU GPL v3:
-
-    This product includes copyrighted third-party software licensed
-    under the terms of the GNU General Public License v3 ("GPL v3").
-    All third-party software packages are copyright by their respective
-    authors. GPL v3 terms and conditions are hereby incorporated into
-    the Agreement by this reference:     http://www.gnu.org/licenses/gpl.txt
-
-    Consistent with these licensing requirements, the software
-    listed below is provided under the terms of the specified
-    open source software licenses. To obtain source code for
-    software provided under licenses that require
-    redistribution of source code, including the GNU General
-    Public License (GPL) and GNU Lesser General Public License
-    (LGPL), contact oss-requests@nvidia.com. This offer is
-    valid for a period of three (3) years from the date of the
-    distribution of this product by NVIDIA CORPORATION.
-
-    Component          License
-    CUDA-GDB           GPL v3  
-
-  2. Licensee represents and warrants that any and all third
-    party licensing and/or royalty payment obligations in
-    connection with Licensee's use of the H.264 video codecs
-    are solely the responsibility of Licensee.
-
-  3. Licensee's use of the Thrust library is subject to the
-    terms and conditions of the Apache License Version 2.0.
-    All third-party software packages are copyright by their
-    respective authors. Apache License Version 2.0 terms and
-    conditions are hereby incorporated into the Agreement by
-    this reference.
-    http://www.apache.org/licenses/LICENSE-2.0.html
-
-    In addition, Licensee acknowledges the following notice:
-    Thrust includes source code from the Boost Iterator,
-    Tuple, System, and Random Number libraries.
-
-    Boost Software License - Version 1.0 - August 17th, 2003
-    . . . .
-    
-    Permission is hereby granted, free of charge, to any person or 
-    organization obtaining a copy of the software and accompanying 
-    documentation covered by this license (the "Software") to use, 
-    reproduce, display, distribute, execute, and transmit the Software, 
-    and to prepare derivative works of the Software, and to permit 
-    third-parties to whom the Software is furnished to do so, all 
-    subject to the following:
-    
-    The copyright notices in the Software and this entire statement, 
-    including the above license grant, this restriction and the following 
-    disclaimer, must be included in all copies of the Software, in whole 
-    or in part, and all derivative works of the Software, unless such 
-    copies or derivative works are solely in the form of machine-executable 
-    object code generated by a source language processor.
-    
-    THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, 
-    EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF 
-    MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE, TITLE AND 
-    NON-INFRINGEMENT. IN NO EVENT SHALL THE COPYRIGHT HOLDERS OR 
-    ANYONE DISTRIBUTING THE SOFTWARE BE LIABLE FOR ANY DAMAGES OR 
-    OTHER LIABILITY, WHETHER IN CONTRACT, TORT OR OTHERWISE, ARISING 
-    FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR 
-    OTHER DEALINGS IN THE SOFTWARE.  
-
-  4. Licensee's use of the LLVM third party component is
-    subject to the following terms and conditions:
-
-    ======================================================
-    LLVM Release License
-    ======================================================
-    University of Illinois/NCSA
-    Open Source License
-    
-    Copyright (c) 2003-2010 University of Illinois at Urbana-Champaign.
-    All rights reserved.
-    
-    Developed by:
-    
-        LLVM Team
-    
-        University of Illinois at Urbana-Champaign
-    
-        http://llvm.org
-    
-    Permission is hereby granted, free of charge, to any person obtaining a copy
-    of this software and associated documentation files (the "Software"), to 
-    deal with the Software without restriction, including without limitation the
-    rights to use, copy, modify, merge, publish, distribute, sublicense, and/or 
-    sell copies of the Software, and to permit persons to whom the Software is 
-    furnished to do so, subject to the following conditions:
-    
-    *  Redistributions of source code must retain the above copyright notice, 
-       this list of conditions and the following disclaimers.
-    
-    *  Redistributions in binary form must reproduce the above copyright 
-       notice, this list of conditions and the following disclaimers in the 
-       documentation and/or other materials provided with the distribution.
-    
-    *  Neither the names of the LLVM Team, University of Illinois at Urbana-
-       Champaign, nor the names of its contributors may be used to endorse or
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-  5. Licensee's use of the PCRE third party component is
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-
-    ------------
-    PCRE LICENCE
-    ------------
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-    
-    THE BASIC LIBRARY FUNCTIONS
-    ---------------------------
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-    Copyright (c) 1997-2012 University of Cambridge
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-    PCRE JUST-IN-TIME COMPILATION SUPPORT
-    -------------------------------------
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-    Emain domain:     freemail.hu
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-    
-    THE C++ WRAPPER FUNCTIONS
-    -------------------------
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-    THE "BSD" LICENCE
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-    Copyright (c) 2008-2009 Davide Barbieri @ University of Rome Tor Vergata.
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-  9. Some of the cuBLAS library routines were written by or
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-    derived from code written by Ahmad M. Abdelfattah, David
-    Keyes, and Hatem Ltaief, and are subject to the Apache
-    License, Version 2.0, as follows:
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-     -- (C) Copyright 2013 King Abdullah University of Science and Technology
-      Authors:
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-      David Keyes (david.keyes@kaust.edu.sa)
-      Hatem Ltaief (hatem.ltaief@kaust.edu.sa)
-    
-      Redistribution  and  use  in  source and binary forms, with or without
-      modification,  are  permitted  provided  that the following conditions
-      are met:
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-      * Redistributions  of  source  code  must  retain  the above copyright
-        notice,  this  list  of  conditions  and  the  following  disclaimer.
-      * Redistributions  in  binary  form must reproduce the above copyright
-        notice,  this list of conditions and the following disclaimer in the
-        documentation  and/or other materials provided with the distribution.
-      * Neither  the  name of the King Abdullah University of Science and
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-        or promote products derived from this software without specific prior 
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-    Developed by: IMPACT Group, University of Illinois, http://impact.crhc.illinois.edu
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-    SOFTWARE.  
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-  12. Some of the cuRAND library routines were written by or
-    derived from code written by Mutsuo Saito and Makoto
-    Matsumoto and are subject to the following license:
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-    Copyright (c) 2009, 2010 Mutsuo Saito, Makoto Matsumoto and Hiroshima
-    University. All rights reserved.
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-  13. Some of the cuRAND library routines were derived from
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-between the parties, the parties agree that in the event
-Licensee or NVIDIA provides Feedback (as defined below) to the
-other party on how to design, implement, or improve the
-SOFTWARE or Licensee's product(s) for use with the SOFTWARE,
-the following terms and conditions apply the Feedback:
-
-
-2.8.1. Exchange of Feedback
-
-Both parties agree that neither party has an obligation to
-give the other party any suggestions, comments or other
-feedback, whether verbally or in written or source code form,
-relating to (i) the SOFTWARE; (ii) Licensee's products; (iii)
-Licensee's use of the SOFTWARE; or (iv)
-optimization/interoperability of Licensee's product with the
-SOFTWARE (collectively defined as "Feedback"). In the event
-either party provides Feedback to the other party, the party
-receiving the Feedback may use any Feedback that the other
-party voluntarily provides to improve the (i) SOFTWARE or
-other related NVIDIA technologies, respectively for the
-benefit of NVIDIA; or (ii) Licensee's product or other related
-Licensee technologies, respectively for the benefit of
-Licensee. Accordingly, if either party provides Feedback to
-the other party, both parties agree that the other party and
-its respective licensees may freely use, reproduce, license,
-distribute, and otherwise commercialize the Feedback in the
-(i) SOFTWARE or other related technologies; or (ii) Licensee's
-products or other related technologies, respectively, without
-the payment of any royalties or fees.
-
-
-2.8.2. Residual Rights
-
-Licensee agrees that NVIDIA shall be free to use any general
-knowledge, skills and experience, (including, but not limited
-to, ideas, concepts, know-how, or techniques) ("Residuals"),
-contained in the (i) Feedback provided by Licensee to NVIDIA;
-(ii) Licensee's products shared or disclosed to NVIDIA in
-connection with the Feedback; or (c) Licensee's confidential
-information voluntarily provided to NVIDIA in connection with
-the Feedback, which are retained in the memories of NVIDIA's
-employees, agents, or contractors who have had access to such
-Residuals. Subject to the terms and conditions of this
-Agreement, NVIDIA's employees, agents, or contractors shall
-not be prevented from using Residuals as part of such
-employee's, agent's or contractor's general knowledge, skills,
-experience, talent, and/or expertise. NVIDIA shall not have
-any obligation to limit or restrict the assignment of such
-employees, agents or contractors or to pay royalties for any
-work resulting from the use of Residuals.
-
-
-2.8.3. Disclaimer of Warranty
-
-FEEDBACK FROM EITHER PARTY IS PROVIDED FOR THE OTHER PARTY'S
-USE "AS IS" AND BOTH PARTIES DISCLAIM ALL WARRANTIES, EXPRESS,
-IMPLIED AND STATUTORY INCLUDING, WITHOUT LIMITATION, THE
-IMPLIED WARRANTIES OF MERCHANTABILITY, FITNESS FOR A
-PARTICULAR PURPOSE, OR NONINFRINGEMENT. BOTH PARTIES DO NOT
-REPRESENT OR WARRANT THAT THE FEEDBACK WILL MEET THE OTHER
-PARTY'S REQUIREMENTS OR THAT THE OPERATION OR IMPLEMENTATION
-OF THE FEEDBACK WILL BE UNINTERRUPTED OR ERROR-FREE.
-
-
-2.8.4. No Liability for Consequential Damages
-
-TO THE MAXIMUM EXTENT PERMITTED BY APPLICABLE LAW, IN NO EVENT
-SHALL EITHER PARTY OR ITS SUPPLIERS BE LIABLE FOR ANY SPECIAL,
-INCIDENTAL, INDIRECT, OR CONSEQUENTIAL DAMAGES WHATSOEVER
-(INCLUDING, WITHOUT LIMITATION, DAMAGES FOR LOSS OF BUSINESS
-PROFITS, BUSINESS INTERRUPTION, LOSS OF BUSINESS INFORMATION,
-OR ANY OTHER PECUNIARY LOSS) ARISING OUT OF THE USE OF OR
-INABILITY TO USE THE FEEDBACK, EVEN IF THE OTHER PARTY HAS
-BEEN ADVISED OF THE POSSIBILITY OF SUCH DAMAGES.
-
-
-2.9. Freedom of Action
-
-Developer agrees that this Agreement is nonexclusive and
-NVIDIA may currently or in the future be developing software,
-other technology or confidential information internally, or
-receiving confidential information from other parties that
-maybe similar to the Feedback and Developer's confidential
-information (as provided in subsection 2 above), which may be
-provided to NVIDIA in connection with Feedback by Developer.
-Accordingly, Developer agrees that nothing in this Agreement
-will be construed as a representation or inference that NVIDIA
-will not develop, design, manufacture, acquire, market
-products, or have products developed, designed, manufactured,
-acquired, or marketed for NVIDIA, that compete with the
-Developer's products or confidential information.
-
-
-2.10. Restricted Rights Notice
-
-Materials have been developed entirely at private expense and
-is commercial computer software provided with RESTRICTED
-RIGHTS. Use, duplication or disclosure by the U.S. Government
-or a U.S. Government subcontractor is subject to the
-restrictions set forth in the license agreement under which
-Materials was obtained pursuant to DFARS 227.7202-3(a) or as
-set forth in subparagraphs (c)(1) and (2) of the Commercial
-Computer Software - Restricted Rights clause at FAR 52.227-19,
-as applicable. Contractor/manufacturer is NVIDIA, 2701 San
-Tomas Expressway, Santa Clara, CA 95050.
-
-
-2.11. Miscellaneous
-
-If any provision of this Agreement is inconsistent with, or
-cannot be fully enforced under, the law, such provision will
-be construed as limited to the extent necessary to be
-consistent with and fully enforceable under the law. This
-Agreement is the final, complete and exclusive agreement
-between the parties relating to the subject matter hereof, and
-supersedes all prior or contemporaneous understandings and
-agreements relating to such subject matter, whether oral or
-written. This Agreement may only be modified in writing signed
-by an authorized officer of NVIDIA. Developer agrees that it
-will not ship, transfer or export the Materials into any
-country, or use the Materials in any manner, prohibited by the
-United States Bureau of Industry and Security or any export
-laws, restrictions or regulations.
-
-
-2.12. Attachment C
-
-
-Additional Licensing Obligations
-
-Licensee's use of the "libfreeimage" third party component is
-subject to the following terms and conditions:
-
-The contents of this file are subject to the FreeImage Public
-License Version 1.0 (the "License"); you may not use this file
-except in compliance with the License. You may obtain a copy
-of the License at
-http://freeimage.sourceforge.net/freeimage-license.txt.
-
-Software distributed under the License is distributed on an
-"AS IS" basis, WITHOUT WARRANTY OF ANY KIND, either express or
-implied. See the License for the specific language governing
-rights and limitations under the License.
-
-
-3. NVIDIA Driver License for Customer Use of NVIDIA Software
-on Windows
-------------------------------------------------------------
-
-
-IMPORTANT NOTICE -- READ CAREFULLY:
------------------------------------
-
-This License For Customer Use of NVIDIA Software ("LICENSE")
-is the agreement which governs use of the software of NVIDIA
-Corporation and its subsidiaries ("NVIDIA") downloadable
-herefrom, including GeForce Experience, computer software
-(including drivers downloaded in connection with GeForce
-Experience) and associated printed materials ("SOFTWARE"). By
-downloading, installing, copying, or otherwise using the
-SOFTWARE, you agree to be bound by the terms of this LICENSE.
-If you do not agree to the terms of this LICENSE, do not
-download the SOFTWARE.
-
-
-RECITALS:
----------
-
-Use of NVIDIA's products requires three elements: the
-SOFTWARE, the hardware on a graphics controller board, and a
-personal computer (collectively, such hardware and personal
-computer is defined herein as "CUSTOMER SYSTEM"). The SOFTWARE
-is protected by copyright laws and international copyright
-treaties, as well as other intellectual property laws and
-treaties. The SOFTWARE is not sold, and instead is only
-licensed for use, strictly in accordance with this document.
-The hardware is protected by various patents, and is sold, but
-this LICENSE does not cover that sale, since it may not
-necessarily be sold as a package with the SOFTWARE. This
-LICENSE sets forth the terms and conditions of the SOFTWARE
-LICENSE only.
-
-
-3.1. Definitions
-
-
-3.1.1. Customer
-
-Customer means the entity or individual that downloads and/or
-installs the SOFTWARE.
-
-
-3.2. Grant of License
-
-
-3.2.1. Rights and Limitations of Grant
-
-Provided Customer complies with the terms in this LICENSE,
-NVIDIA hereby grants Customer the following non-exclusive,
-non-transferable right to use the SOFTWARE in the manner and
-for the purposes described in the associated printed
-materials, with the following limitations:
-
-
-3.2.1.1. Rights
-
-Customer may install and use multiple copies of the SOFTWARE
-on a shared computer or concurrently on different computers,
-and make multiple back-up copies of the SOFTWARE, solely for
-Customer's use within Customer's Enterprise. "Enterprise"
-shall mean individual use by Customer or any legal entity
-(such as a corporation or university) and the subsidiaries it
-owns by more than fifty percent (50%).
-
-
-3.2.1.2. Limitations
-
-No Reverse Engineering
-
-Customer may not reverse engineer, decompile, or disassemble
-the SOFTWARE, nor attempt in any other manner to obtain the
-source code. You may not remove any copyright notices from the
-SOFTWARE. The SOFTWARE is licensed as a single product. Its
-component parts may not be separated for use on more than one
-computer, nor otherwise used separately from the other parts.
-
-No Rental
-
-Customer may not rent or lease the SOFTWARE to someone else.
-
-
-3.2.2. Additional Information
-
-7-Zip. The SOFTWARE includes the 7-Zip software program
-("7-Zip"). Use of the source code for 7-Zip is subject to the
-terms and conditions at www.7-zip.org.
-
-
-3.3. Consent to Collection and Use of Information
-
-Customer hereby acknowledges that the SOFTWARE accesses and
-collects non-personally identifiable information about
-Customer and CUSTOMER SYSTEM as well as configures CUSTOMER
-SYSTEM in order to (a) properly optimize such system for use
-with the SOFTWARE, (b) deliver content through the SOFTWARE,
-and (c) improve NVIDIA products and services. Information
-collected by the SOFTWARE includes, but is not limited to,
-CUSTOMER SYSTEM'S (a) hardware configuration and ID, (b)
-operating system and driver configuration, (c) installed games
-and applications, (d) games and applications settings,
-performance, and usage data, and (e) usage metrics of the
-SOFTWARE. To the extent that Customer uses the SOFTWARE,
-Customer hereby consents to all of the foregoing, and
-represents and warrants that Customer has the right to grant
-such consent. In addition, Customer agrees that Customer is
-solely responsible for maintaining appropriate data backups
-and system restore points for CUSTOMER SYSTEM, and that NVIDIA
-will have no responsibility for any damage or loss to CUSTOMER
-SYSTEM (including loss of data or access) arising from or
-relating to (a) any changes to the configuration, application
-settings, environment variables, registry, drivers, BIOS, or
-other attributes of CUSTOMER SYSTEM (or any part of CUSTOMER
-SYSTEM) initiated through the SOFTWARE; or (b) installation of
-any SOFTWARE or third party software patches initiated through
-the SOFTWARE. The SOFTWARE may contain links to websites and
-services. We encourage you to review the privacy statements on
-those sites and services that you choose to visit so that you
-can understand how they may collect, use and share your
-personal information. NVIDIA is not responsible for the
-privacy statements or practices of sites and services
-controlled by other companies or organizations.
-
-Customer and CUSTOMER SYSTEM information collection rules can
-be configured on the "Preferences" tab of GeForce Experience.
-For more information on NVIDIA's collection and use of
-information policies for this SOFTWARE, visit
-http://www.geforce.com/drivers/geforce-experience/faq.
-
-Customer represents and warrants that the non-personally
-identifiable information that Customer has furnished in
-connection with its registration for the SOFTWARE is complete
-and accurate. Customer also acknowledges that from time to
-time, NVIDIA may collect, use, and disclose such information
-about Customer and/or Customer's system in connection with the
-SOFTWARE in accordance with NVIDIA's privacy policy, available
-at URL http://www.nvidia.com/object/privacy_policy.html.
-
-
-3.4. Termination
-
-This LICENSE will automatically terminate if Customer fails to
-comply with any of the terms and conditions hereof. In such
-event, Customer must destroy all copies of the SOFTWARE and
-all of its component parts.
-
-Defensive Suspension. If Customer commences or participates in
-any legal proceeding against NVIDIA, then NVIDIA may, in its
-sole discretion, suspend or terminate all license grants and
-any other rights provided under this LICENSE during the
-pendency of such legal proceedings.
-
-
-3.5. Copyright
-
-All title and copyrights in and to the SOFTWARE (including but
-not limited to all images, photographs, animations, video,
-audio, music, text, and other information incorporated into
-the SOFTWARE), the accompanying printed materials, and any
-copies of the SOFTWARE, are owned by NVIDIA, or its licensors
-or suppliers. The SOFTWARE is protected by copyright laws and
-international treaty provisions. Accordingly, Customer is
-required to treat the SOFTWARE like any other copyrighted
-material, except as otherwise allowed pursuant to this LICENSE
-and that it may make one copy of the SOFTWARE solely for
-backup or archive purposes. The algorithms, structure,
-organization and source code of the Software are the valuable
-trade secrets and confidential information of NVIDIA. Except
-as otherwise expressly provided herein, neither this LICENSE
-nor NVIDIA grants Customer any express or implied right under
-any NVIDIA patents, copyrights, trademarks, or other
-intellectual property rights in the SOFTWARE, and all rights,
-title and interest in and to the SOFTWARE not expressly
-granted are reserved by NVIDIA or its licensors or suppliers.
-
-
-3.6. Applicable Law
-
-This LICENSE shall be deemed to have been made in, and shall
-be construed pursuant to, the laws of the State of Delaware.
-The United Nations Convention on Contracts for the
-International Sale of Goods is specifically disclaimed. The
-state and/or federal courts residing in Santa Clara County,
-California shall have exclusive jurisdiction over any dispute
-or claim arising out of this Agreement. Customer may not
-export the SOFTWARE in violation of applicable export laws and
-regulations.
-
-
-3.7. Disclaimer of Warranties and Limitations on Liability
-
-
-3.7.1. No Warranties
-
-THE SOFTWARE IS PROVIDED "AS IS" AND TO THE MAXIMUM EXTENT
-PERMITTED BY APPLICABLE LAW, NVIDIA AND ITS SUPPLIERS DISCLAIM
-ALL WARRANTIES, EITHER EXPRESS OR IMPLIED, INCLUDING, BUT NOT
-LIMITED TO, IMPLIED WARRANTIES OF MERCHANTABILITY,
-NONINFRINGEMENT, TITLE AND FITNESS FOR A PARTICULAR PURPOSE.
-Without limiting the foregoing, you are solely responsible for
-determining and verifying that the SOFTWARE that you obtain
-and install is the appropriate version for your model of
-graphics controller board, operating system, and computer
-hardware.
-
-
-3.7.2. No Liability for Consequential Damages
-
-TO THE MAXIMUM EXTENT PERMITTED BY APPLICABLE LAW, IN NO EVENT
-SHALL NVIDIA OR ITS SUPPLIERS BE LIABLE FOR ANY DIRECT,
-SPECIAL, INCIDENTAL, INDIRECT, OR CONSEQUENTIAL DAMAGES
-WHATSOEVER (INCLUDING, WITHOUT LIMITATION, DAMAGES FOR LOSS OF
-BUSINESS PROFITS, LOSS OF DATA, BUSINESS INTERRUPTION, LOSS OF
-BUSINESS INFORMATION, OR ANY OTHER PECUNIARY LOSS) ARISING OUT
-OF THE USE OF OR INABILITY TO USE THE SOFTWARE, EVEN IF NVIDIA
-HAS BEEN ADVISED OF THE POSSIBILITY OF SUCH DAMAGES. SOME
-JURISDICTIONS PROHIBIT EXCLUSION OR LIMITATION OF LIABILITY
-FOR IMPLIED WARRANTIES OR CONSEQUENTIAL OR INCIDENTAL DAMAGES,
-SO THE ABOVE LIMITATION MAY NOT APPLY TO YOU. YOU MAY ALSO
-HAVE OTHER LEGAL RIGHTS THAT VARY FROM JURISDICTION TO
-JURISDICTION. NOTWITHSTANDING THE FOREGOING, NVIDIA'S
-AGGREGATE LIABILITY ARISING OUT OF THIS LICENSE AGREEMENT
-SHALL NOT EXCEED ONE THOUSAND UNITED STATES DOLLARS
-(USD$1000).
-
-
-3.8. Miscellaneous
-
-If any provision of this LICENSE is inconsistent with, or
-cannot be fully enforced under, the law, such provision will
-be construed as limited to the extent necessary to be
-consistent with and fully enforceable under the law. This
-LICENSE is the final, complete and exclusive agreement between
-the parties relating to the subject matter hereof, and
-supersedes all prior or contemporaneous understandings and
-agreements relating to such subject matter, whether oral or
-written. This LICENSE may only be modified in writing signed
-by an authorized officer of NVIDIA. Customer agrees that it
-will not ship, transfer or export the SOFTWARE into any
-country, or use the SOFTWARE in any manner, prohibited by the
-United States Bureau of Industry and Security or any export
-laws, restrictions or regulations.
-
-
-4. NVIDIA Driver License for Customer Use of NVIDIA Software
-on Linux and Mac OSX
-------------------------------------------------------------
-
-
-IMPORTANT NOTICE -- READ CAREFULLY:
------------------------------------
-
-This License For Customer Use of NVIDIA Software ("LICENSE")
-is the agreement which governs use of the software of NVIDIA
-Corporation and its subsidiaries ("NVIDIA") downloadable
-herefrom, including computer software and associated printed
-materials ("SOFTWARE"). By downloading, installing, copying,
-or otherwise using the SOFTWARE, you agree to be bound by the
-terms of this LICENSE. If you do not agree to the terms of
-this LICENSE, do not download the SOFTWARE.
-
-
-RECITALS:
----------
-
-Use of NVIDIA's products requires three elements: the
-SOFTWARE, the hardware on a graphics controller board, and a
-personal computer. The SOFTWARE is protected by copyright laws
-and international copyright treaties, as well as other
-intellectual property laws and treaties. The SOFTWARE is not
-sold, and instead is only licensed for use, strictly in
-accordance with this document. The hardware is protected by
-various patents, and is sold, but this agreement does not
-cover that sale, since it may not necessarily be sold as a
-package with the SOFTWARE. This agreement sets forth the terms
-and conditions of the SOFTWARE LICENSE only.
-
-
-4.1. DEFINITIONS
-
-
-4.1.1. Customer
-
-Customer means the entity or individual that downloads the
-SOFTWARE.
-
-
-4.2. GRANT OF LICENSE
-
-
-4.2.1. Rights and Limitations of Grant
-
-NVIDIA hereby grants Customer the following non-exclusive,
-non-transferable right to use the SOFTWARE, with the following
-limitations:
-
-
-4.2.1.1. Rights
-
-Customer may install and use multiple copies of the SOFTWARE
-on a shared computer or concurrently on different computers,
-and make multiple back-up copies of the SOFTWARE, solely for
-Customer's use within Customer's Enterprise. "Enterprise"
-shall mean individual use by Customer or any legal entity
-(such as a corporation or university) and the subsidiaries it
-owns by more than fifty percent (50%).
-
-
-4.2.1.2. Linux/FreeBSD Exception
-
-Notwithstanding the foregoing terms of Section 4.2.1.1,
-SOFTWARE designed exclusively for use on the Linux or FreeBSD
-operating systems, or other operating systems derived from the
-source code to these operating systems, may be copied and
-redistributed, provided that the binary files thereof are not
-modified in any way (except for unzipping of compressed
-files).
-
-
-4.2.1.3. Limitations
-
-No Reverse Engineering
-
-Customer may not reverse engineer, decompile, or disassemble
-the SOFTWARE, nor attempt in any other manner to obtain the
-source code.
-
-No Separation of Components
-
-The SOFTWARE is licensed as a single product. Its component
-parts may not be separated for use on more than one computer,
-nor otherwise used separately from the other parts.
-
-No Rental
-
-Customer may not rent or lease the SOFTWARE to someone else.
-
-
-4.3. TERMINATION
-
-This LICENSE will automatically terminate if Customer fails to
-comply with any of the terms and conditions hereof. In such
-event, Customer must destroy all copies of the SOFTWARE and
-all of its component parts.
-
-Defensive Suspension. If Customer commences or participates in
-any legal proceeding against NVIDIA, then NVIDIA may, in its
-sole discretion, suspend or terminate all license grants and
-any other rights provided under this LICENSE during the
-pendency of such legal proceedings.
-
-
-4.4. COPYRIGHT
-
-All title and copyrights in and to the SOFTWARE (including but
-not limited to all images, photographs, animations, video,
-audio, music, text, and other information incorporated into
-the SOFTWARE), the accompanying printed materials, and any
-copies of the SOFTWARE, are owned by NVIDIA, or its suppliers.
-The SOFTWARE is protected by copyright laws and international
-treaty provisions. Accordingly, Customer is required to treat
-the SOFTWARE like any other copyrighted material, except as
-otherwise allowed pursuant to this LICENSE and that it may
-make one copy of the SOFTWARE solely for backup or archive
-purposes.
-
-
-4.5. APPLICABLE LAW
-
-This agreement shall be deemed to have been made in, and shall
-be construed pursuant to, the laws of the State of California.
-
-
-4.6. DISCLAIMER OF WARRANTIES AND LIMITATION ON LIABILITY
-
-
-4.6.1. No Warranties
-
-TO THE MAXIMUM EXTENT PERMITTED BY APPLICABLE LAW, THE
-SOFTWARE IS PROVIDED "AS IS" AND NVIDIA AND ITS SUPPLIERS
-DISCLAIM ALL WARRANTIES, EITHER EXPRESS OR IMPLIED, INCLUDING,
-BUT NOT LIMITED TO, IMPLIED WARRANTIES OF MERCHANTABILITY AND
-FITNESS FOR A PARTICULAR PURPOSE.
-
-
-4.6.2. No Liability for Consequential Damages
-
-TO THE MAXIMUM EXTENT PERMITTED BY APPLICABLE LAW, IN NO EVENT
-SHALL NVIDIA OR ITS SUPPLIERS BE LIABLE FOR ANY SPECIAL,
-INCIDENTAL, INDIRECT, OR CONSEQUENTIAL DAMAGES WHATSOEVER
-(INCLUDING, WITHOUT LIMITATION, DAMAGES FOR LOSS OF BUSINESS
-PROFITS, BUSINESS INTERRUPTION, LOSS OF BUSINESS INFORMATION,
-OR ANY OTHER PECUNIARY LOSS) ARISING OUT OF THE USE OF OR
-INABILITY TO USE THE SOFTWARE, EVEN IF NVIDIA HAS BEEN ADVISED
-OF THE POSSIBILITY OF SUCH DAMAGES.
-
-
-4.7. MISCELLANEOUS
-
-The United Nations Convention on Contracts for the
-International Sale of Goods is specifically disclaimed. If any
-provision of this LICENSE is inconsistent with, or cannot be
-fully enforced under, the law, such provision will be
-construed as limited to the extent necessary to be consistent
-with and fully enforceable under the law. This agreement is
-the final, complete and exclusive agreement between the
-parties relating to the subject matter hereof, and supersedes
-all prior or contemporaneous understandings and agreements
-relating to such subject matter, whether oral or written.
-Customer agrees that it will not ship, transfer or export the
-SOFTWARE into any country, or use the SOFTWARE in any manner,
-prohibited by the United States Bureau of Export
-Administration or any export laws, restrictions or
-regulations. This LICENSE may only be modified in writing
-signed by an authorized officer of NVIDIA.
-
-
-5. NVIDIA Nsight Development Platform, Visual Studio Edition
-Software License Agreement (Windows only)
-------------------------------------------------------------
-
-
-IMPORTANT - READ BEFORE COPYING, INSTALLING OR USING
-----------------------------------------------------
-
-Do not use or load this software and any associated materials
-provided by NVIDIA on its extranet (collectively the
-"Software") until You have carefully read the following terms
-and conditions. By loading or using the Software, You agree to
-fully comply with the terms and conditions of this Software
-License Agreement ("Agreement") by and between NVIDIA
-Corporation, a Delaware corporation with its principal place
-of business at 2701 San Tomas Expressway, Santa Clara,
-California 95050 U.S.A. ("NVIDIA"), and You. If You do not
-wish to so agree, do not install or use the Software.
-
-For the purposes of this Agreement:
-
-"Licensee," "You" and/or "Your" shall mean, collectively and
-individually, Original Equipment Manufacturers, Independent
-Hardware Vendors, Independent Software Vendors, and End-Users
-of the Software pursuant to the terms and conditions of this
-Agreement.
-
-"Intellectual Property Rights" shall mean all proprietary
-rights, including all patents, trademarks, copyrights,
-know-how, trade secrets, mask works, including all
-applications and registrations thereto, and any other similar
-protected rights in any country.
-
-
-5.1. Grant of License
-
-NVIDIA agrees to provide the Software and any associated
-materials pursuant to this Agreement. Subject to the terms of
-this Agreement, NVIDIA grants to You a nonexclusive,
-transferable, worldwide, revocable, limited, royalty-free,
-fully paid-up license under NVIDIA's copyrights to install,
-deploy, use, have used execute, reproduce, display, perform,
-run, the object code of the Software, to create Your products
-to interoperate with NVIDIA hardware and software.
-
-Unless otherwise authorized in the Agreement, You shall not
-otherwise assign, sublicense, lease, or in any other way
-transfer or disclose Software to any third party. Unless
-otherwise authorized in the Agreement, You shall not reverse-
-compile, disassemble, reverse-engineer, or in any manner
-attempt to derive the source code of the Software from the
-object code portions of the Software.
-
-Except as expressly stated in this Agreement, no license or
-right is granted to You directly or by implication,
-inducement, estoppels or otherwise. NVIDIA shall have the
-right to inspect or have an independent auditor inspect Your
-relevant records to verify Your compliance with the terms and
-conditions of this Agreement.
-
-
-5.2. Confidentiality
-
-If applicable, any exchange of Confidential Information (as
-defined in the NDA) shall be made pursuant to the terms and
-conditions of a separately signed Non-Disclosure Agreement
-("NDA") by and between NVIDIA and You. For the sake of
-clarity, You agree that (a) the Software; and (b) Your use of
-the Software/participation in the Software's pre-production
-release is considered Confidential Information of NVIDIA.
-
-If You wish to have a third party consultant or subcontractor
-("Contractor") perform work on Your behalf which involves
-access to or use of Software, You shall obtain a written
-confidentiality agreement from the Contractor which contains
-terms and obligations with respect to access to or use of
-Software no less restrictive than those set forth in this
-Agreement and excluding any distribution or sublicense rights,
-and use for any other purpose than permitted in this
-Agreement. Otherwise, You shall not disclose the terms or
-existence of this Agreement or use NVIDIA's name in any
-publications, advertisements, or other announcements without
-NVIDIA's prior written consent. Unless otherwise provided in
-this Agreement, You do not have any rights to use any NVIDIA
-trademarks or logos.
-
-
-5.3. Ownership of Software and Intellectual Property Rights
-
-All rights, title and interest to all copies of the Software
-remain with NVIDIA, subsidiaries, licensors, or its suppliers.
-The Software is copyrighted and protected by the laws of the
-United States and other countries, and international treaty
-provisions. You may not remove any copyright notices from the
-Software. NVIDIA may make changes to the Software, or to items
-referenced therein, at any time and without notice, but is not
-obligated to support or update the Software. Except as
-otherwise expressly provided, NVIDIA grants no express or
-implied right under any NVIDIA patents, copyrights,
-trademarks, or other intellectual property rights.
-
-You have no obligation to give NVIDIA any suggestions,
-comments or other feedback ("Feedback") relating to the
-Software. However, NVIDIA may use and include any Feedback
-that You voluntarily provide to improve the Software or other
-related NVIDIA technologies. Accordingly, if You provide
-Feedback, You agree NVIDIA and its licensees may freely use,
-reproduce, license, distribute, and otherwise commercialize
-the Feedback in the Software or other related technologies
-without the payment of any royalties or fees. You also agree
-that the Software may collect application specific session
-data and target device information that shall be sent to
-NVIDIA, solely for use by NVIDIA in improving the Software.
-
-
-5.4. No Warranties
-
-THE SOFTWARE IS PROVIDED "AS IS" WITHOUT ANY EXPRESS OR
-IMPLIED WARRANTY OF ANY KIND, INCLUDING WARRANTIES OF
-MERCHANTABILITY, NONINFRINGEMENT, OR FITNESS FOR A PARTICULAR
-PURPOSE. NVIDIA does not warrant or assume responsibility for
-the accuracy or completeness of any information, text,
-graphics, links or other items contained within the Software.
-NVIDIA does not represent that errors or other defects will be
-identified or corrected.
-
-
-5.5. Limitation of Liability
-
-EXCEPT WITH RESPECT TO THE MISUSE OF THE OTHER PARTY'S
-INTELLECTUAL PROPERTY OR DISCLOSURE OF THE OTHER PARTY'S
-CONFIDENTIAL INFORMATION IN BREACH OF THIS AGREEMENT, IN NO
-EVENT SHALL NVIDIA, SUBSIDIARIES, LICENSORS, OR ITS SUPPLIERS
-BE LIABLE FOR ANY DAMAGES WHATSOEVER (INCLUDING, WITHOUT
-LIMITATION, INDIRECT, LOST PROFITS, CONSEQUENTIAL, BUSINESS
-INTERRUPTION OR LOST INFORMATION) ARISING OUT OF THE USE OF OR
-INABILITY TO USE THE SOFTWARE, EVEN IF NVIDIA HAS BEEN ADVISED
-OF THE POSSIBILITY OF SUCH DAMAGES. SOME JURISDICTIONS
-PROHIBIT EXCLUSION OR LIMITATION OF LIABILITY FOR IMPLIED
-WARRANTIES OR CONSEQUENTIAL OR INCIDENTAL DAMAGES, SO THE
-ABOVE LIMITATION MAY NOT APPLY TO YOU. YOU MAY ALSO HAVE OTHER
-LEGAL RIGHTS THAT VARY FROM JURISDICTION TO JURISDICTION.
-NOTWITHSTANDING THE FOREGOING, NVIDIA'S AGGREGATE LIABILITY
-ARISING OUT OF THIS AGREEMENT SHALL NOT EXCEED ONE HUNDRED
-UNITED STATES DOLLARS (USD$100).
-
-
-5.6. Term
-
-This Agreement and the licenses granted hereunder shall be
-effective as of the date You install/download the Software
-("Effective Date") and continue perpetually, unless terminated
-earlier in accordance with the "Termination" provision of this
-Agreement.
-
-
-5.7. Termination
-
-NVIDIA may terminate this Agreement at any time if You violate
-its terms. Upon termination, You will immediately destroy the
-Software or return all copies of the Software to NVIDIA, and
-certify to NVIDIA in writing that such actions have been
-completed.
-
-
-5.8. Miscellaneous
-
-
-5.8.1. Survival
-
-Those provisions in this Agreement, which by their nature need
-to survive the termination or expiration of this Agreement,
-shall survive termination or expiration of the Agreement,
-including but not limited to Section  5.2, Section 5.3,
-Section 5.4, Section 5.5, Section 5.7, and Section 5.8.
-
-
-5.8.2. Applicable Laws
-
-Claims arising under this Agreement shall be governed by the
-laws of Delaware, excluding its principles of conflict of laws
-and the United Nations Convention on Contracts for the Sale of
-Goods. The state and/or federal courts residing in Santa Clara
-County, California shall have exclusive jurisdiction over any
-dispute or claim arising out of this Agreement. You may not
-export the Software in violation of applicable export laws and
-regulations.
-
-
-5.8.3. Amendment
-
-The Agreement shall not be modified except by a written
-agreement that names this Agreement and any provision to be
-modified, is dated subsequent to the Effective Date, and is
-signed by duly authorized representatives of both parties.
-
-
-5.8.4. No Waiver
-
-No failure or delay on the part of either party in the
-exercise of any right, power or remedy under this Agreement or
-under law, or to insist upon or enforce performance by the
-other party of any of the provisions of this Agreement or
-under law, shall operate as a waiver thereof, nor shall any
-single or partial exercise of any right, power or remedy
-preclude other or further exercise thereof, or the exercise of
-any other right, power or remedy; rather the provision, right,
-or remedy shall be and remain in full force and effect.
-
-
-5.8.5. No Assignment
-
-This Agreement and Licensee's rights and obligations herein,
-may not be assigned, subcontracted, delegated, or otherwise
-transferred by Licensee without NVIDIA's prior written
-consent, and any attempted assignment, subcontract,
-delegation, or transfer in violation of the foregoing will be
-null and void. The terms of this Agreement shall be binding
-upon Licensee's assignees.
-
-
-5.8.6. Government Restricted Rights
-
-The parties acknowledge that the Software is subject to U.S.
-export control laws and regulations. The parties agree to
-comply with all applicable international and national laws
-that apply to the Software, including the U.S. Export
-Administration Regulations, as well as end-user, end-use and
-destination restrictions issued by U.S. and other governments.
-
-The Software has been developed entirely at private expense
-and is commercial computer software provided with RESTRICTED
-RIGHTS. Use, duplication or disclosure of the Software by the
-U.S. Government or a U.S. Government subcontractor is subject
-to the restrictions set forth in the Agreement under which the
-Software was obtained pursuant to DFARS 227.7202-3(a) or as
-set forth in subparagraphs (c)(1) and (2) of the Commercial
-Computer Software - Restricted Rights clause at FAR 52.227-19,
-as applicable. Contractor/manufacturer is NVIDIA, 2701 San
-Tomas Expressway, Santa Clara, CA 95050. Use of the Software
-by the Government constitutes acknowledgment of NVIDIA's
-proprietary rights therein.
-
-
-5.8.7. Independent Contractors
-
-Licensee's relationship to NVIDIA is that of an independent
-contractor, and neither party is an agent or partner of the
-other. Licensee will not have, and will not represent to any
-third party that it has, any authority to act on behalf of
-NVIDIA.
-
-
-5.8.8. Severability
-
-If for any reason a court of competent jurisdiction finds any
-provision of this Agreement, or portion thereof, to be
-unenforceable, that provision of the Agreement will be
-enforced to the maximum extent permissible so as to affect the
-intent of the parties, and the remainder of this Agreement
-will continue in full force and effect. This Agreement has
-been negotiated by the parties and their respective counsel
-and will be interpreted fairly in accordance with its terms
-and without any strict construction in favor of or against
-either party.
-
-
-5.8.9. Entire Agreement
-
-This Agreement and NDA constitute the entire agreement between
-the parties with respect to the subject matter contemplated
-herein, and merges all prior and contemporaneous
-communications.
-
-MICROSOFT SOFTWARE LICENSE TERMS
-MICROSOFT DIRECTX END USER RUNTIME
-
-These license terms are an agreement between Microsoft Corporation (or based on
-where you live, one of its affiliates) and you.  Please read them.  They apply
-to the software named above, which includes the media on which you received it,
-if any.  The terms also apply to any Microsoft
-
-* updates,
-* supplements,
-* Internet-based services, and 
-* support services
-
-for this software, unless other terms accompany those items.  If so, those
-terms apply.
-
-BY USING THE SOFTWARE, YOU ACCEPT THESE TERMS.  IF YOU DO NOT ACCEPT THEM, DO
-NOT USE THE SOFTWARE.
-
-If you comply with these license terms, you have the rights below.
-
-1. INSTALLATION AND USE RIGHTS.  You may install and use any number of copies
-of the software on your devices.
-
-2. SCOPE OF LICENSE.  The software is licensed, not sold. This agreement only
-gives you some rights to use the software.  Microsoft reserves all other
-rights.  Unless applicable law gives you more rights despite this limitation,
-you may use the software only as expressly permitted in this agreement.  In
-doing so, you must comply with any technical limitations in the software that
-only allow you to use it in certain ways.  You may not
-
-* work around any technical limitations in the software;
-* reverse engineer, decompile or disassemble the software, except and only to
-  the extent that applicable law expressly permits, despite this limitation;
-* make more copies of the software than specified in this agreement or allowed
-  by applicable law, despite this limitation;
-* publish the software for others to copy;
-* rent, lease or lend the software;
-* transfer the software or this agreement to any third party; or
-* use the software for commercial software hosting services.
-
-3. BACKUP COPY.  You may make one backup copy of the software.  You may use it
-only to reinstall the software.
-
-4. DOCUMENTATION.  Any person that has valid access to your computer or
-internal network may copy and use the documentation for your internal,
-reference purposes.
-
-5. EXPORT RESTRICTIONS.  The software is subject to United States export laws
-and regulations.  You must comply with all domestic and international export
-laws and regulations that apply to the software.  These laws include
-restrictions on destinations, end users and end use.  For additional
-information, see www.microsoft.com/exporting.
-
-6. SUPPORT SERVICES. Because this software is "as is," we may not provide
-support services for it.
-
-7. ENTIRE AGREEMENT.  This agreement, and the terms for supplements, updates,
-Internet-based services and support services that you use, are the entire
-agreement for the software and support services.
-
-8. APPLICABLE LAW.
-
-a. United States.  If you acquired the software in the United States,
-Washington state law governs the interpretation of this agreement and applies
-to claims for breach of it, regardless of conflict of laws principles.  The
-laws of the state where you live govern all other claims, including claims
-under state consumer protection laws, unfair competition laws, and in tort.
-
-b. Outside the United States.  If you acquired the software in any other
-country, the laws of that country apply.
-
-9. LEGAL EFFECT.  This agreement describes certain legal rights.  You may have
-other rights under the laws of your country.  You may also have rights with
-respect to the party from whom you acquired the software.  This agreement does
-not change your rights under the laws of your country if the laws of your
-country do not permit it to do so.
-
-10. DISCLAIMER OF WARRANTY.   THE SOFTWARE IS LICENSED "AS-IS."  YOU BEAR THE
-RISK OF USING IT.  MICROSOFT GIVES NO EXPRESS WARRANTIES, GUARANTEES OR
-CONDITIONS.  YOU MAY HAVE ADDITIONAL CONSUMER RIGHTS UNDER YOUR LOCAL LAWS
-WHICH THIS AGREEMENT CANNOT CHANGE.  TO THE EXTENT PERMITTED UNDER YOUR LOCAL
-LAWS, MICROSOFT EXCLUDES THE IMPLIED WARRANTIES OF MERCHANTABILITY, FITNESS FOR
-A PARTICULAR PURPOSE AND NON-INFRINGEMENT.
-
-11. LIMITATION ON AND EXCLUSION OF REMEDIES AND DAMAGES.  YOU CAN RECOVER FROM
-MICROSOFT AND ITS SUPPLIERS ONLY DIRECT DAMAGES UP TO U.S. $5.00.  YOU CANNOT
-RECOVER ANY OTHER DAMAGES, INCLUDING CONSEQUENTIAL, LOST PROFITS, SPECIAL,
-INDIRECT OR INCIDENTAL DAMAGES.
-
-This limitation applies to
-
-* anything related to the software, services, content (including code) on third
-  party Internet sites, or third party programs; and
-* claims for breach of contract, breach of warranty, guarantee or condition,
-  strict liability, negligence, or other tort to the extent permitted by
-  applicable law.
-
-It also applies even if Microsoft knew or should have known about the
-possibility of the damages.  The above limitation or exclusion may not apply to
-you because your country may not allow the exclusion or limitation of
-incidental, consequential or other damages.
-
-The Software contains components, as listed below that are
-licensed to Licensee pursuant to the terms and conditions of
-their respective End User License Agreements:
-
-  * NVIDIA CUDA Samples
-
-  * NVIDIA CUDA Toolkit
-
-  * NVIDIA DirectX SDK
-
-More information, including licensing information, about the
-NVIDIA CUDA Toolkit and the NVIDIA CUDA Samples can be found
-at: http://www.nvidia.com/getcuda
-
-More information, including licensing information, about the
-NVIDIA DirectX SDK can be found at:
-http://developer.nvidia.com/object/sdk_home.html
-
-
-6. NVIDIA CUDA General Terms
-----------------------------
-
-The Software, on the Windows platform, may collect
-non-personally identifiable information for the purposes of
-customizing information delivered to you and improving future
-versions of the Software. Such information, including IP
-address and system configuration, will only be collected on an
-anonymous basis and cannot be linked to any personally
-identifiable information. Personally identifiable information
-such as your username or hostname is not collected.
-
--------------------------------------------------------------
diff --git a/licenses/NVIDIA-gdk b/licenses/NVIDIA-gdk
deleted file mode 100644
index 769c505a7..000000000
--- a/licenses/NVIDIA-gdk
+++ /dev/null
@@ -1,32 +0,0 @@
-Copyright 1993-2014 NVIDIA Corporation.  All rights reserved.
-
-NOTICE TO USER:   
-
-This source code is subject to NVIDIA ownership rights under U.S. and 
-international Copyright laws.  Users and possessors of this source code 
-are hereby granted a nonexclusive, royalty-free license to use this code 
-in individual and commercial software.
-
-NVIDIA MAKES NO REPRESENTATION ABOUT THE SUITABILITY OF THIS SOURCE 
-CODE FOR ANY PURPOSE.  IT IS PROVIDED "AS IS" WITHOUT EXPRESS OR 
-IMPLIED WARRANTY OF ANY KIND.  NVIDIA DISCLAIMS ALL WARRANTIES WITH 
-REGARD TO THIS SOURCE CODE, INCLUDING ALL IMPLIED WARRANTIES OF 
-MERCHANTABILITY, NONINFRINGEMENT, AND FITNESS FOR A PARTICULAR PURPOSE.
-IN NO EVENT SHALL NVIDIA BE LIABLE FOR ANY SPECIAL, INDIRECT, INCIDENTAL, 
-OR CONSEQUENTIAL DAMAGES, OR ANY DAMAGES WHATSOEVER RESULTING FROM LOSS 
-OF USE, DATA OR PROFITS,  WHETHER IN AN ACTION OF CONTRACT, NEGLIGENCE 
-OR OTHER TORTIOUS ACTION,  ARISING OUT OF OR IN CONNECTION WITH THE USE 
-OR PERFORMANCE OF THIS SOURCE CODE.  
-
-U.S. Government End Users.   This source code is a "commercial item" as 
-that term is defined at  48 C.F.R. 2.101 (OCT 1995), consisting  of 
-"commercial computer  software"  and "commercial computer software 
-documentation" as such terms are  used in 48 C.F.R. 12.212 (SEPT 1995) 
-and is provided to the U.S. Government only as a commercial end item.  
-Consistent with 48 C.F.R.12.212 and 48 C.F.R. 227.7202-1 through 
-227.7202-4 (JUNE 1995), all U.S. Government End Users acquire the 
-source code with only those rights set forth herein. 
-
-Any use of this source code in individual and commercial software must 
-include, in the user documentation and internal comments to the code,
-the above Disclaimer and U.S. Government End Users Notice.
diff --git a/licenses/OBO-Edit b/licenses/OBO-Edit
deleted file mode 100644
index 4c2b496ae..000000000
--- a/licenses/OBO-Edit
+++ /dev/null
@@ -1,9 +0,0 @@
-OBO-Edit License Agreement
-Copyright (C) 2000-2007, Berkeley Bioinformatics and Ontologies Project
-Author: John Richter (jrichter@berkeleybop.org)
-
-OBO-Edit is hearby released to the public under the terms of the Artistic License
-contained in this archive in the file ARTISTIC_LICENSE. 
-
-OBO-Edit makes use of the org.bbop toolkit, which is free to distribute and
-modify.
\ No newline at end of file
diff --git a/licenses/PGI b/licenses/PGI
deleted file mode 100644
index a54f86c9b..000000000
--- a/licenses/PGI
+++ /dev/null
@@ -1,262 +0,0 @@
-PGI End-User License Agreement

-

-NOTICE: PLEASE READ THIS DOCUMENT CAREFULLY BEFORE DOWNLOADING, COPYING OR

-USING THE LICENSED SOFTWARE.  THIS END-USER LICENSE AGREEMENT ("ELA") IS A

-LEGAL AGREEMENT BETWEEN YOU, THE LICENSEE (A SINGLE PERSON, INSTITUTION, OR

-LEGAL ENTITY) ("YOU"), AND STMICROELECTRONICS, N.V., A DUTCH CORPORATION,

-HAVING ITS PRINCIPAL PLACE OF BUSINESS AT STRAWINSKYLAAN 1725, TOWER B 17TH

-FLOOR, 1077 XX AMSTERDAM, THE NETHERLANDS, ACTING FOR THE PURPOSE OF THIS

-ELA THROUGH ITS SWISS BRANCH, 39, CHEMIN DU CHAMP DES FILLES, C. P. 21, CH

-1228 PLAN-LES-OUATES, GENEVA, SWITZERLAND ("ST") FOR THE LICENSED SOFTWARE,

-ASSOCIATED MEDIA, PRINTED MATERIAL, ELECTRONIC DOCUMENTATION OR ANY PORTION

-THEREOF ("SOFTWARE").  ST IS WILLING TO LICENSE THE SOFTWARE TO YOU ONLY

-UPON THE CONDITION THAT YOU ACCEPT ALL OF THE TERMS CONTAINED IN THIS ELA.

-PLEASE READ THE ELA CAREFULLY.  BY DOWNLOADING OR INSTALLING THIS SOFTWARE,

-YOU ACCEPT ALL OF THE TERMS OF THE ELA. PLEASE INDICATE YOUR ACCEPTANCE OF

-ALL OF THE THESE TERMS BY SELECTING THE "ACCEPT" BUTTON AT THE BOTTOM OF

-THE ELA. IF YOU ARE UNWILLING TO BE BOUND BY ALL OF THE TERMS, PLEASE

-SELECT THE "DECLINE" BUTTON AT THE BOTTOM OF THE ELA AND THE DOWNLOAD OR

-INSTALL PROCESS WILL STOP.

-

-

-1)	Ownership

-

-	The Software distributed and licensed to You hereunder, including, if

-	and when provided, any updates furnished to You for free or for

-	additional fees, is proprietary to ST or its licensors (ST and

-	licensors hereafter referred to as "Licensor").  The Licensors retain

-	title to and ownership of the Software, including the copy provided

-	herein, and reserve all rights not expressly granted in this ELA.

-

-2)	Granting of License

-

-2A)	Except as set forth in Sections 3 and 4 below, under the terms and

-	conditions of this ELA, You are hereby granted a limited, revocable,

-	nontransferable, and nonexclusive license to use the Software subject

-	to the restrictions and other terms within.  That use must be

-	(i)	only by You,

-	(ii)	only on a computer system running a specific operating system

-		on which the Software is designed to run and for which portions

-		of the Software and subsequent components in the compilation

-		process are intended to produce an executable image ("Target

-		Systems") for which the corresponding fee has been paid,

-	(iii)	only on the network(s) and only by the number of users for

-		which the corresponding fee has been paid, and

-	(iv)	only to target no more than the maximum number of CPUs, or

-		the maximum number of processes, for which the corresponding

-		fee has been paid.

-	Except as set forth in Section 2B below, any other use of the

-	Software is strictly prohibited.

-

-2B)	You may distribute an end-user application that You build with the

-	Software that provides significant functionality distinct from that

-	included with the Software ("End-User Application") to users within

-	Your organization as well as third party users outside Your

-	organization ("Sublicensees") for only such uses and/or Target

-	Systems for which the Software was designed and	intended.  You agree

-	that any sublicense shall not relieve You from Your obligations under

-	this ELA.  The Software includes the run-time files, libraries and

-	executables ("Run-Time Files") that are bound into Your application

-	by the linker or otherwise required by Your application.  You may

-	also distribute separate dynamically-linked or executable Run-Time

-	Files required during the execution of Your End-User Application.

-	Whenever an End-User Application is used internally within Your

-	organization or by outside third parties, You shall contractually

-	require that all Sublicensees abide by the following restrictions:

-	(i)	they shall not use the "PGI", "The Portland Group", "ST", or

-		"STMicroelectronics" name, logo, or trademarks in marketing the

-		End-User Application without prior written permission from ST,

-	(ii)	they will maintain a valid copyright on the End-User

-		Application,

-	(iii)	they will, without limitation, indemnify, hold harmless, and

-		defend ST and other applicable Licensors and their respective

-		affiliates and suppliers from and against any and all claims,

-		lawsuits, costs, and expenses, including attorney's fees, that

-		arise or result from their use or distribution of the End-User

-		Application, and

-	(iv)	they shall strictly prohibit the further distribution of the

-		Run-Time Files by the user of the End-User Application.

-	Notwithstanding the above, the only Run-Time Files that may be

-	distributed as noted in this Section 2B are in the folders or

-	directories whose names begin with "REDIST".

-

-3)	Software from Microsoft

-	

-	You acknowledge that as part of the Software You may receive Run-Time

-	Files in the form of Microsoft Foundation Classes ("MFCs"), Active

-	Template Libraries ("ATLs"), and/or "C" Runtime files ("CRTs") in

-	binary form only ("Microsoft Distributable Code").  Notwithstanding

-	any other provision of this ELA, You acknowledge and agree

-	(A)	that You have a limited right to use the Microsoft

-		Distributable Code to design,	develop, or test for use with the

-		Software only,

-	(B)	that You or Your end-users of the Microsoft Distributable Code

-		may only use it to create programs that run natively on

-		Microsoft platforms, and

-	(C)	to the following restrictions: You and Your end-users:

-		(i)   will not alter any copyright, trademark, patent, or other

-		      legal notice or disclaimer in the Microsoft Distributable

-		      Code,

-		(ii)  will not run the Microsoft Distributable Code on a

-		      platform other than a Microsoft platform, and

-		(iii) will not include Microsoft Distributable Code in

-		      malicious, deceptive, or unlawful programs.

-	Further, You will require end	users of the Microsoft Distributable

-	Code to agree to terms at least as protective as this ELA.

-

-4)	Software from Sun Microsystems and/or Oracle America, Inc.

-

-	You acknowledge that as part of the Software you are receiving access

-	to Java(tm) 2 Runtime Environment (J2RE), version 1.4.2 or subsequent

-	versions ("Java Code").  Notwithstanding any other provision of this

-	ELA, You are hereby granted a limited, revocable, nontransferable,

-	and nonexclusive license, without the right to sublicense, to use the

-	Java Code complete and unmodified for the sole purpose of running

-	Java applets and applications intended to run on the JavaTM 2

-	Platform Standard Edition 5.0 (J2SE 5.0) or subsequent versions on

-	Java-enabled general purpose desktop computers and servers.

-

-5)	Restrictions

-      

-5A)	You may make one (1) copy of the Software in machine-readable form,

-	solely for archival or backup purposes, provided the copyright notice

-	and other proprietary legends on the Software are included on any

-	archival/backup copies.  You may not modify, adapt, translate,

-	reverse engineer, de-compile, disassemble, or create derivative

-	works, in whole or in part, based on the Software.  You may not rent,

-	lease, loan, share, or electronically transfer the Software to

-	others.

-

-5B)	The term "proprietary" as used in this ELA or in the Software does

-	not establish a confidential relationship between the Licensor and

-	You and does not in itself provide You any rights to the Software.

-	You acknowledge that the  Licensors have valuable intellectual

-	property rights in the Software and agree to respect and protect such

-	intellectual property rights.  No right, title, or interest in or to

-	any trademark, service mark, logo or trade name of the Licensors is

-	granted under this ELA.

-

-5C)	You acknowledge and agree that the Software is not designed or

-	intended for use in nuclear activities or life support systems.  The

-	Licensors disclaim any express or implied warranty of fitness for

-	such uses.

-      

-5D)	You will not modify or distribute any of the Software so that any

-	part of it becomes subject to an Excluded License.  As used in this

-	ELA, an "Excluded License" is one that requires, as a condition of

-	use, modification, or distribution, that

-	(i)	the Software be disclosed or distributed in source code form; or

-	(ii)	others have a right to modify it, or

-	(iii)	the Software loses its proprietary nature.

-	Therefore, without the prior written permission of the applicable

-	Licensors, You may not modify the Software directly in any way.  In

-	particular, You may not introduce or commingle with the Software any

-	source or object code that is governed by an open source or public

-	license of any kind.

-

-6)	Limited Warranty  

-

-	THE SOFTWARE IS PROVIDED "AS IS" WITHOUT WARRANTY OF ANY KIND.  TO

-	THE MAXIMUM EXTENT PERMITTED BY APPLICABLE LAW, THE LICENSORS FURTHER

-	DISCLAIM ALL WARRANTIES, INCLUDING WITHOUT LIMITATION ANY IMPLIED

-	WARRANTIES OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE, AND

-	NONINFRINGEMENT.  THE ENTIRE RISK ARISING OUT OF THE USE OR

-	PERFORMANCE OF THE SOFTWARE AND DOCUMENTATION REMAINS WITH YOU. TO

-	THE MAXIMUM EXTENT PERMITTED BY APPLICABLE LAW,  IN NO EVENT SHALL

-	THE LICENSORS BE LIABLE FOR ANY CONSEQUENTIAL, INCIDENTAL, INDIRECT,

-	SPECIAL, PUNITIVE, OR OTHER DAMAGES WHATSOEVER (INCLUDING, WITHOUT

-	LIMITATION, DAMAGES FOR	LOSS OF BUSINESS PROFITS, BUSINESS

-	INTERRUPTION, LOSS OF BUSINESS INFORMATION, LOSS OF DATA OR OTHER

-	PECUNIARY LOSS) ARISING OUT OF THIS ELA OR THE USE OF OR INABILITY TO

-	USE THE SOFTWARE, EVEN IF THE LICENSORS HAVE BEEN ADVISED OF THE

-	POSSIBILITY OF SUCH DAMAGES. NOTWITHSTANDING THE FOREGOING, TO THE

-	EXTENT THAT ST MAY BE HELD LEGALLY LIABLE TO YOU BY A COURT OF

-	COMPETENT JURISDICTION UNDER CONTRACT, TORT, OR ANY OTHER LEGAL

-	THEORY, THE MAXIMUM LIABILITY OF THE LICENSORS SHALL NOT EXCEED THE

-	APPLICABLE PURCHASE PRICE OF THE SOFTWARE OR ONE THOUSAND DOLLARS

-	($1,000), WHICHEVER IS GREATER.

-

-7)	Indemnity and Audit

-

-7A)	You agree to indemnify, defend, and hold the Licensors harmless from

-	and against any and all claims, liabilities, damages, penalties,

-	settlements, and costs and expenses (including, without limitation,

-	reasonable attorneys' fees and court or arbitration costs), asserted

-	by any and all third parties (collectively "Claims") against the

-	Licensors, and their respective employees, directors, officers, and

-	agents alleging or resulting from:

-	(i)	Your breach of any term or condition of this ELA;

-	(ii)	alleged or actual infringement of the intellectual property or

-		other proprietary rights of a third party by You or Your

-		sublicensees; unauthorized alteration of the Software or

-		derivative products by You or Your sublicensees;

-	(iii)	combination of the Software or derivative products with other

-		software, products or materials not in accordance with the

-		terms	of this ELA; or

-	(iv)	any acts or omissions by You, Your employees, directors,

-		officers, and agents or sublicensees either under this ELA or

-		outside its scope, including personal injury, death, or

-		property damage to anyone or anything.

-

-7B)	ST reserves the right, upon reasonable prior written notice to You

-	and during Your normal business hours, to audit Your use of the

-	Software and any derivative products made therefrom to confirm Your

-	compliance with the terms of this ELA.

-

-8)	Software Export

-

-	All Software and technical data delivered under this ELA are subject

-	to US export control laws and may be subject to export or import

-	regulations in other countries.  You agree to comply strictly with

-	all such laws and regulations and acknowledge that You have the

-	responsibility to obtain such licenses to export, re-export, or

-	import as may be required after delivery to You.

-

-9)	Software Manuals

-

-	All proprietary documentation provided with the Software is copyrighted

-	and may not be copied, photographed, reproduced, translated or reduced

-	to any electronic medium or machine-readable form in whole or in part

-	without the express, written, prior approval of ST.

-

-10)	Government Use 

-

-	The Software is a "commercial item," as that term is defined at 48

-	C.F.R. 2.101 (OCT 1995), consisting of "commercial computer software"

-	and "commercial computer software documentation," as such terms are

-	used in 48 C.F.R. 12.212 (SEPT 1995) and is provided to the U.S.

-	Government only as a commercial end item.  Consistent with 48 C.F.R.

-	12.212 and 48 C.F.R. 227.7202-1 through 227.7202-4 (JUNE 1995), all

-	U.S. Government licensees and end users acquire the Software with

-	only those rights set forth herein. 

-

-11)	Termination  

-

-	The license granted to You in this ELA is effective until terminated.

-	The license may be terminated by ST at any time without prior notice.

-	You may terminate the license at any time by returning and/or

-	destroying the Software together with all copies.  Upon termination

-	of the license for any reason, you agree to destroy all copies of the

-	Software.

-      

-12)	Surviving Terms

-

-	In the event this ELA is terminated for any reason, the following

-	provisions shall survive termination and shall remain in full force

-	and effect: 1, 5, 6, 7, 8, 9, 10, 12, and 13.

-

-13)	Controlling Law and Complete Agreement  

-

-	This Agreement shall be construed and interpreted under the laws of

-	the state of New York, not including its conflict of laws principles.

-	If any provision of this ELA, or portion thereof, is found to be

-	unenforceable, that provision shall be enforced to the maximum extent

-	possible and the remainder of this ELA shall continue in full force

-	and effect.

-

-YOU ACKNOWLEDGE THAT YOU HAVE READ THIS ELA AND AGREE TO BE BOUND BY ITS

-TERMS.  YOU FURTHER AGREE THAT IT IS THE COMPLETE AND EXCLUSIVE STATEMENT

-OF AGREEMENT BETWEEN YOU AND ST AND THAT IT SUPERSEDES ANY PRIOR AGREEMENT,

-ORAL OR WRITTEN, ANY PROPOSAL, AND ANY OTHER COMMUNICATIONS BETWEEN YOU AND

-ST RELATING TO THE SUBJECT MATTER OF THIS ELA.

-

diff --git a/licenses/PMEL-FERRET b/licenses/PMEL-FERRET
deleted file mode 100644
index 6c2d24b79..000000000
--- a/licenses/PMEL-FERRET
+++ /dev/null
@@ -1,33 +0,0 @@
-US Department of Commerce (DOC)
-Software License for PMEL Ferret
-
-Scope of License. Subject to all the terms and conditions of this license, DOC
-grants USER the royalty-free, nonexclusive, nontransferable, and worldwide
-rights to reproduce, modify, and distribute PMEL Ferret, herein referred to as
-the Product.
-
-Conditions and Limitations of Use Warranties. Neither the U.S. Government, nor
-any agency or employee thereof, makes any warranties, expressed or implied,
-with respect to the Product provided under this License, including but not
-limited to the implied warranties or merchantability and fitness for any
-particular purpose.
-
-Liability. In no event shall the U.S. Government, nor any agency or employee
-thereof, be liable for any direct, indirect, or consequential damages flowing
-from the use of the Product provided under this License.
-
-Non-Assignment. Neither this License nor any rights granted hereunder are
-transferable or assignable without the explicit prior written consent of DOC.
-
-Names and Logos. USER shall not substitute its name or logo for the name or
-logo of DOC, or any of its agencies, in identification of the Product.
-
-Export of technology. USER shall comply with all U.S. laws and regulations
-restricting the export of the Product to other countries.
-
-Governing Law. This License shall be governed by the laws of United States as
-interpreted and applied by the Federal courts in the District of Columbia.
-
-Term of License. This License shall remain in effect as long as USER uses the
-Product in accordance with Paragraphs 1 and 2.
-
diff --git a/licenses/Tablet b/licenses/Tablet
deleted file mode 100644
index 296b09c7f..000000000
--- a/licenses/Tablet
+++ /dev/null
@@ -1,10 +0,0 @@
-Copyright (c) 2009-2014, Information & Computational Sciences, The James Hutton Institute.
-All rights reserved.
-
-Redistribution and use in source and binary forms, with or without modification, are permitted provided that the following conditions are met:
-
-1. Redistributions of source code must retain the above copyright notice, this list of conditions and the following disclaimer.
-
-2. Redistributions in binary form must reproduce the above copyright notice, this list of conditions and the following disclaimer in the documentation and/or other materials provided with the distribution.
-
-THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS “AS IS� AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
diff --git a/licenses/UCSF-Motioncor2 b/licenses/UCSF-Motioncor2
new file mode 100644
index 000000000..8a63c50d8
--- /dev/null
+++ b/licenses/UCSF-Motioncor2
@@ -0,0 +1,19 @@
+UCSF MotionCor2 Non-Commercial Software License Agreement
+
+This license agreement ("License"), effective today, is made by and between you ("Licensee") and The Regents of the University of California, a California corporation having its statewide administrative offices at 1111 Franklin Street, Oakland, California 94607-5200 ("The Regents"), acting through its Office of Technology Management, University of California San Francisco ("UCSF"), 3333 California Street, Suite S-11, San Francisco, California 94143, and concerns certain software known as "MotionCor2," a software for correction of electron beam-induced sample motion in cryo-electron microscopy, for research purposes and includes executable code, source code, and documentation ("Software"). The Software was developed by the Keck Advanced Microscopy Laboratory and by Dr. David Agard at UCSF while Dr. Agard was an employee of Howard Hughes Medical Institute (“HHMI�). 
+
+1.	General. A non-exclusive, nontransferable, perpetual license is granted to the Licensee to install and use the Software for academic, non-profit, or government-sponsored research purposes. Use of the Software under this License is restricted to non-commercial purposes. Commercial use of the Software requires a separately executed written license agreement.
+
+2.	Permitted Use and Restrictions. Licensee agrees that it will use the Software, and any modifications, improvements, or derivatives to the Software that the Licensee may create (collectively, "Improvements") solely for internal, non-commercial purposes and shall not distribute or transfer the Software or Improvements to any person or third parties without prior written permission from The Regents. The term "non-commercial," as used in this License, means academic or other scholarly research which (a) is not undertaken for profit, or (b) is not intended to produce works, services, or data for commercial use, or (c) is neither conducted, nor funded, by a person or an entity engaged in the commercial use, application or exploitation of works similar to the Software.
+
+3.	Ownership and Assignment of Copyright. The Licensee acknowledges that The Regents hold copyright in the Software and associated documentation, and the Software and associated documentation are the property of The Regents. The Licensee agrees that any Improvements made by Licensee shall be subject to the same terms and conditions as the Software. Licensee agrees not to assert a claim of infringement in Licensee copyrights in Improvements in the event The Regents prepares substantially similar modifications or derivative works. The Licensee agrees to use his/her reasonable best efforts to protect the contents of the Software and to prevent unauthorized disclosure by its agents, officers, employees, and consultants. If the Licensee receives a request to furnish all or any portion of the Software to a third party, Licensee will not fulfill such a request but will refer the third party to the UCSF CryoEM Software web page so that the third party's use of this Software will be subject to the terms and conditions of this License. Notwithstanding the above, Licensee may disclose any Improvements that do not involve disclosure of the Software.
+
+4.	Copies. The Licensee may make a reasonable number of copies of the Software for the purposes of backup, maintenance of the Software or the development of derivative works based on the Software. These additional copies shall carry the copyright notice and shall be controlled by this License, and will be destroyed along with the original by the Licensee upon termination of the License.
+
+5.	Acknowledgement. Licensee agrees that any publication of results obtained with the Software will acknowledge its use by an appropriate citation as specified in the documentation.
+
+6.	Disclaimer of Warranties and Limitation of Liability. THE LICENSEE AGREES THAT ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE DISCLAIMED. THE REGENTS MAKES NO REPRESENTATION OR WARRANTY THAT THE SOFTWARE WILL NOT INFRINGE ANY PATENT OR OTHER PROPRIETARY RIGHT. IN NO EVENT SHALL THE REGENTS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
+
+7.	Termination. This License is effective until terminated by either party. Licensee's rights under this License will terminate automatically without notice from The Regents if Licensee fails to comply with any term(s) of this License. Licensee may terminate the License by giving written notice of termination to The Regents. Upon termination of this License, Licensee shall immediately discontinue all use of the Software and destroy the original and all copies, full or partial, of the Software, including any modifications or derivative works, and associated documentation.
+
+8.	Governing Law and General Provisions. This License shall be governed by the laws of the State of California, excluding the application of its conflicts of law rules. This License shall not be governed by the United Nations Convention on Contracts for the International Sale of Goods, the application of which is expressly excluded. If any provisions of this License are held invalid or unenforceable for any reason, the remaining provisions shall remain in full force and effect. This License is binding upon any heirs and assigns of the Licensee. The License granted to Licensee hereunder may not be assigned or transferred to any other person or entity without the express consent of The Regents. This License constitutes the entire agreement between the parties with respect to the use of the Software licensed hereunder and supersedes all other previous or contemporaneous agreements or understandings between the parties, whether verbal or written, concerning the subject matter. Any translation of this License is done for local requirements and in the event of a dispute between the English and any non-English versions, the English version of this License shall govern.
diff --git a/licenses/UPennState b/licenses/UPennState
deleted file mode 100644
index 8d2c6b44f..000000000
--- a/licenses/UPennState
+++ /dev/null
@@ -1,7 +0,0 @@
-Copyright (c) 2012 University of Pennsylvania
-
-Permission is hereby granted, free of charge, to any person obtaining a copy of this software and associated documentation files (the "Software"), to deal in the Software without restriction, including without limitation the rights to use, copy, modify, merge, publish, distribute, sublicense, and/or sell copies of the Software, and to permit persons to whom the Software is furnished to do so, subject to the following conditions:
-
-The above copyright notice and this permission notice shall be included in all copies or substantial portions of the Software.
-
-THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE SOFTWARE.
diff --git a/licenses/UTPackages b/licenses/UTPackages
deleted file mode 100644
index 61f1975be..000000000
--- a/licenses/UTPackages
+++ /dev/null
@@ -1,115 +0,0 @@
-TERMS AND CONDITIONS FOR COPYING,
-DISTRIBUTION AND MODIFICATION
-1. This software is the copyright of
-THE UNIVERSITY OF TEXAS AT AUSTIN, 2005.
-
-2. The software is available under multiple licenses.
-
-3. For non commercial educational and non commercial academic use,
-the software including source code, interface definitions and compile
-scripts are freely available. Any distribution of code, library
-or executables which contains any modules from this software should
-contain, conspicously and appropriately, on each copy, this copyright
-and license notice and should be freely distributed.
-
-4. If you wish to incorporate parts of the Library into other free programs
-whose distribution conditions are incompatible with these, write to the
-author to ask for permission. For software which is copyrighted by the
-Free Software Foundation, write to the Free Software Foundation.
-
-5. For any other purpose, including commercial purposes,
-please contact The University of  Texas at Austin for a different license.
-
-6. Credits:
-
-This software has been developed at the Computational and
-Visualization center under
-
-    Dr Chandrajit Bajaj,
-    Computational Applied Mathematics Chair in Visualization,
-    Professor of Computer Sciences,
-    Director of Center for Computational Visualization,
-    Department of Computer Sciences &
-    The Institute of Computational Engineering and Sciences,
-     Center for Computational Visualization,
-    201 East 24th Street, ACES 2.324A,
-    1 University Station, C0200,
-    Austin, TX 78712-0027.
-
-We request that you agree to acknowledge the use of the software that
-results in any published work, including scientific papers, films and
-videotapes by citing the references listed below
-
-For UTblur:
-
-C. Bajaj, V. Siddavanahalli
-Fast Feature Adaptive Surfaces and Derivatives Computation for
-Volumetric Particle Data
-ICES and CS technical reports, The University of Texas at Austin, 2005.
-
-For UTisocontour:
-
-C. Bajaj, V. Pascucci, D. Schikore
-Accelerated IsoContouring of Scalar Fields
-Data Visualization Techniques, edited by C. Bajaj, John Wiley and Sons (1998).
-
-C. Bajaj, V. Pascucci, D. Schikore
-Fast Isocontouring for Improved Interactivity
-Proceedings: ACM Siggraph/IEEE Symposium on Volume Visualization,
-ACM Press, (1996), San Francisco, CA. Pages: 39-46 99
-
-For UTmesh:
-
-Y. Zhang, C. Bajaj
-Adaptive and Quality Quadrilateral/Hexahedral Meshing from
-Volumetric Data Computer Methods in Applied Mechanics
-and Engineering (CMAME), in press, 2005.
-
-Y. Zhang, C. Bajaj, B-S. Sohn
-3D Finite Element Meshing from Imaging Data
-The special issue of Computer Methods in Applied Mechanics and
-Engineering (CMAME) on Unstructured
-Mesh Generation, 194(48-49):5083-5106, 2005.
-
-For UTsdf:
-
-C. Bajaj, V. Siddavanahalli
-An Adaptive Grid Based Method for Computing Molecular Surfaces
-and Properties ICES and CS Technical Reports,
-The University of Texas at Austin, 2005.
-
-For UTvolrend:
-
-C. Bajaj, Z. Yu, M. Auer
-Volumetric Feature Extraction and Visualization of Tomographic
-Molecular Imaging. Journal of Structural Biology,
-Volume 144, Issues 1-2, October 2003, Pages 132-143
-
-For UTmolderivatives:
-
-C. Bajaj, V. Siddavanahalli
-Fast Feature Adaptive Surfaces and Derivatives Computation for Volumetric
-Particle Data ICES and CS Technical Reports,
-The University of Texas at Austin, 2005.
-
-7. No warranty
-
-7a. Because the library is licensed free of charge, there is no warranty
-for the library, to the extent permitted by applicable law. except when
-otherwise stated in writing the copyright holders and/or other parties
-provide the library "as is" without warranty of any kind, either
-expressed or implied, including, but not limited to, the implied warranties
-of merchantability and fitness for a particular purpose. the entire risk as
-to the quality and performance of the library is with you. should the library
-prove defective, you assume the cost of all necessary servicing,
-repair or correction.
-
-7b. In no event unless required by applicable law or agreed to in writing
-will any copyright holder, or any other party who may modify and/or
-redistribute the library as permitted above, be liable to you for damages,
-including any general, special, incidental or consequential damages
-arising out of the use or inability to use the library (including but
-not limited to loss of data or data being rendered inaccurate or
-losses sustained by you or third parties or a failure of the
-library to operate with any other software), even if such holder
-or other party has been advised of the possibility of such damages.
\ No newline at end of file
diff --git a/licenses/XPLOR-NIH b/licenses/XPLOR-NIH
deleted file mode 100644
index 5465e23ea..000000000
--- a/licenses/XPLOR-NIH
+++ /dev/null
@@ -1,37 +0,0 @@
-	 LICENSE FOR NON-PROFIT INSTITUTIONS TO USE XPLOR-NIH
-
-                         Terms of Agreement
-
-By downloading or using the Xplor-NIH software you agree to the
-following terms:  
-
-- You shall not use the software for any purpose (research or
-  otherwise) that is supported by a "for profit" organization without
-  prior written authorization.
-
-- You agree that the software is furnished on an "as is" basis and
-  that the authors in no way warrant the software or any of its
-  results and is in no way liable for any use you make of the software.
-
-- Ownership of software and documentation is retained by the
-  appropriate, respective organizations.
-
-- You shall not disclose in any form either the delivered software or
-  documentation to third parties without prior written authorization. 
-
-
-In addition, we request that you adhere to the following practices:
-
-- Please report modifications and additions to the software back to
-  the Xplor-NIH authors. We would like the modified source code and a
-  test script, such that we can include the modifications in future
-  versions of the software.
-
-- In reports or publication of results obtained using Xplor-NIH,
-  please acknowledge use of the software by citing the article:
-
-
-    C.D. Schwieters, J.J. Kuszewski, N. Tjandra, G.M. Clore, ``The
-    Xplor-NIH NMR Molecular Structure Determination Package,'' 
-    J. Magn. Res., 160, 66-74 (2003).
-
diff --git a/licenses/XVIEW b/licenses/XVIEW
index 114a7416a..02e2fb693 100644
--- a/licenses/XVIEW
+++ b/licenses/XVIEW
@@ -1,3 +1,28 @@
+This is Debian GNU/Linux's prepackaged version of Sun's xview/olwm/olvwm.
+Miscellaneous patches were contributed by:
+Kenneth Osterberg <lmfken@lmf.ericsson.se>
+Joern Lubkoll <lumpi@dobag.in-berlin.de>
+Oleg Kibirev <oleg@gd.cs.CSUFresno.EDU>
+Wolfram Gloger <Gloger@lrz.uni-muenchen.de>
+E. Zimmermann <edz@bsn.com>
+Rainer Wiesner <RainerRW@aol.com>
+Sven Rudolph <sr1@os.inf.tu-dresden.de>
+Sebastiano Suraci <suraci@uniud.it>
+Frodo Looijaard <frodol@dds.nl>
+Roman Hodek <Roman.Hodek@informatik.uni-erlangen.de>
+Martin Buck <mbuck@debian.org>
+
+This package was put together by Sven Rudolph <sr1@inf.tu-dresden.de>,
+from sources obtained from:
+sunsite.unc.edu:/pub/Linux/libs/X/xview/xview3.2p1-X11R6-LinuxELF.2.src.tar.gz
+
+Starting with xview-3.2p1.4-1, the XView packages are maintained by Martin
+Buck <mbuck@debian.org>, who also maintains the upstream version
+ftp://sunsite.unc.edu/pub/Linux/libs/X/xview/xview3.2p1.4.src.tar.gz at the
+moment.
+
+Copyright:
+
 	NOTICE TO USER: The source code, including the glyphs or icons 
 	forming a par of the OPEN LOOK TM Graphic User Interface, on this 
 	tape and in these files is copyrighted under U.S. and international
diff --git a/licenses/atsas b/licenses/atsas
deleted file mode 100644
index 16d0e700f..000000000
--- a/licenses/atsas
+++ /dev/null
@@ -1,211 +0,0 @@
-ACADEMIC SOFTWARE LICENSE AGREEMENT FOR END-USERS AT PUBLIC FUNDED ACADEMIC,
-EDUCATION OR RESEARCH INSTITUTIONS FOR THE USE OF ATSAS 2.6
-
-By clicking the Acceptance button for the ATSAS 2.6 Software ("Licensed
-Software"), you are consenting to be bound by and become a party to this
-agreement as the "Licensee". If you do not agree to all of the terms of
-this agreement, you must not click the Acceptance button, not install
-the product nor use the product, and you do not become a LICENSEE under
-this agreement.
-
-If you are not a member of a public funded Academic and/or Education and/
-or Research Institution you must obtain a commercial license from EMBLEM
-(Info@embl-em.de).
-
-This software license agreement is entered into by and between EMBL Enter-
-prise Management GmbH (hereinafter "EMBLEM") located at Boxberg Ring 107,
-D-69126 Heidelberg, Germany and the "LICENSEE".
-
-WHEREAS EMBLEM has the right to license all copyrights and other property
-rights in the Licensed Software identified as ATSAS 2.6 and developed by
-EMBL (European Molecular Biology Laboratory, Meyerhofstrasse 1, 69117
-Heidelberg, Germany), and EMBLEM desires to license the Software so that
-it becomes available for public use and benefit.
-
-WHEREAS LICENSEE is a public funded Academic and/or Education and/or
-Research Institution.
-
-WHEREAS LICENSEE desires to acquire a free non-exclusive license to use
-the Software for internal research purposes only.
-
-NOW, THEREFORE, in consideration of the mutual promises and covenants
-contained herein, the parties agree as follows:
-
-1. Definitions
-"Licensed Software" means the current version 2.6 of the ATSAS computer
-package developed by ATSAS team at EMBL-Hamburg, collectively the "Authors",
-pursuant to this Agreement.
-
-Any opinion, findings, conclusions or recommendations expressed in the
-ATSAS 2.6 suite are those of the authors and do not necessarily reflect
-the views of EMBL and EMBLEM.
-
-2. License
-Subject to the terms and conditions of this Agreement a non-exclusive,
-non-transferable License to use and copy the Licensed Software is made
-available free of charge for the LICENSEE which is a non-profit educational,
-academic and/or research institution. The License is only granted for
-personal and internal use in research only at one Site, where a Site
-is defined as a set of contiguous buildings in one location. The software
-will be used at only one location of LICENSEE.
-
-This license does not entitle Licensee to receive from EMBLEM copies of
-the Licensed software on disks, tapes or CD's, hard-copy documentation,
-technical support, telephone assistance, or enhancements or updates to
-the Licensed Software.
-
-The user and any research assistants, co-workers or other workers who may
-use the Software agree to not give the source code to third parties or
-grant licenses on software, which include the Software, alone or integrated
-into other software, to third parties. Modification of the source code
-is prohibited without the prior written consent of EMBLEM.
-
-3. Ownership
-Except as expressly licensed in this Agreement, EMBL shall retain title to 
-the Licensed Software, and any upgrades and modifications created by EMBL.
-
-4. Consideration
-In consideration for the license rights granted by EMBLEM, LICENSEE will
-obtain this academic license free of charge.
-
-5. Copies
-LICENSEE shall have the right to make copies of the Licensed Software for
-internal use at the Site and for back-up purposes under this Agreement,
-but agrees that all such copies shall contain the copyright notices and
-all other reasonable and appropriate proprietary markings or confidential
-legends that appear on the Licensed Software provided hereunder.
-
-6. Support
-EMBLEM shall have no obligation to offer support services to LICENSEE, and
-nothing contained herein shall be interpreted as to require EMBLEM to provide
-maintenance, installation services, debugging, consultation or end-user
-support of any kind. EMBLEM will provide any available updates for a period
-of one year, without additional cost.
-
-7. Software Protection
-LICENSEE acknowledges that the ATSAS Software is proprietary to EMBLEM.
-The software code shall be treated as trade secrets and confidential
-information of EMBLEM, and LICENSEE agrees to use best efforts to hold
-the same in confidence. LICENSEE's obligation for confidentiality shall
-not extend to any information which is or becomes generally available
-to the public, is already known to or subsequently disclosed by third
-parties to LICENSEE and at its free disposal, or is independently
-developed by LICENSEE or its affiliates without the use of the confidential
-information disclosed by EMBLEM, or is required by law or legal process.
-
-Except as other wise expressly permitted in this Agreement, LICENSEE may
-not (i) modify or create any derivative works of the Licensed Software or
-documentation, including customisation, translation or localization; (ii)
-decompile, disassemble, reverse engineer, or otherwise attempt to derive
-the source code for the Product; (iii) redistribute, encumber, sell, rent,
-lease, sublicense, or otherwise transfer rights to the Licensed Software;
-(iv) remove or alter any trademark, logo, copyright or other proprietary
-notices, legends, symbols or labels in the Product; or (v) publish any
-results of benchmark tests run on the Product to a third party without
-EMBLEM's prior written consent.
-
-8. Representations of EMBLEM to LICENSEE 
-EMBLEM represents to LICENSEE that (i) EMBLEM has the right to grant the
-License and to enter into this agreement, (ii) that, to the best of
-EMBLEM's knowledge, the Licensed software does not infringe any patent,
-copyright or trade secrets of any third party, provided however that such
-representation and warranty shall not apply to any addition to, or
-modifications or adaptation of, the Licensed Software made by LICENSEE and
-(iii) EMBLEM undertakes to use best efforts to cooperate with and assist
-LICENSEE, at LICENSEE's expense, in defending itself against any action
-based on the alleged infringement of any third party patent, copyright or
-trade secret rights resulting from or relating to the use or licensing of
-the Licensed Software by LICENSEE.
-
-9. Indemnity and Disclaimer of Warranties
-Except as expressly set forth in this agreement, EMBLEM makes no
-representations or warranties, express or implied.
-
-The product is provided free of charge, and, therefore, on an "as is" basis,
-without warranty of any kind, express or implied, including without limitation
-the warranties that it is free of defects, virus free, able to operate on an
-uninterrupted basis, merchantable, fit for a particular purpose or non-inter-
-fering. The entire risk as to the quality and performance of the Licensed
-Software is borne by LICENSEE.
-
-By way of example, but not limitation, EMBLEM makes no representations or
-warranties of merchantability or fitness for any particular application or,
-except as set forth in paragraph 8, that the use of the Software will not
-infringe any patents, copyrights or trademarks or other rights of third
-parties. The entire risk as to the quality and performance of the product
-is borne by LICENSEE. EMBLEM shall not be liable for any liability or
-damages with respect to any claim by LICENSEE or any third party on account
-of, or arising from the license or use of the Software.
-
-Should the Licensed Software prove defective in any respect, LICENSEE and
-not LICENSOR or it's affiliates should assume the entire cost of any service
-and repair. This disclaimer of warranty constitutes an essential part of
-this agreement. No use of the licensed product is authorized hereunder except
-under this disclaimer.
-
-In no event will LICENSOR or its affiliates be liable for any indirect,
-special, incidental or consequential damages arising out of the use of
-or inability to use the product, including, without limitation, damages
-for lost profits, loss of goodwill, work stoppage, computer failure or
-malfunction, or any and all other commercial damages or losses, even if
-advised of the possibility thereof, and regardless of the legal or
-equitable theory (contract, tort or otherwise) upon which the claim
-is based.
-
-10. Promotional Advertising & References
-LICENSEE may not use the name "ATSAS" in its promotional advertising, product
-literature, and other similar promotional materials to be disseminated to the
-public or any portion thereof. LICENSEE agrees not to identify EMBL in any
-promotional advertising or other promotional materials to be disseminated to
-the public, or any portion thereof without EMBLEM's prior written consent.
-LICENSEE agrees that any reference to the software for crystallographic
-computations will cite one or more publications as set forth in the manual
-and in agreement with common scientific practice. EMBLEM or EMBL shall not
-use LICENSEE's name in publicity or advertising involving this Agreement or
-otherwise without LICENSEE's prior written consent which may be withheld at
-LICENSEE's sole discretion.
-
-
-11. Term
-This Agreement and the license rights granted herein shall become effective
-as of the date this Agreement is executed by both parties and shall be
-perpetual unless terminated in accordance with this Section.
-
-EMBLEM may terminate this Agreement at any time.
-
-Either party may terminate this Agreement at any time effective upon the
-other party's breach of any agreement, covenant, or representation made
-in this Agreement, such breach remaining uncorrected sixty (60) days after
-written notice thereof.
-
-LICENSEE shall have the right, at any time, to terminate this Agreement
-without cause by written notice to EMBLEM specifying the date of termination.
-
-Upon termination, LICENSEE shall destroy all full and partial copies of the
-Licensed Software
-
-12. Governing Law
-This Agreement shall be construed in accordance with the laws of Germany.
-
-13. General
-The parties agree that this Agreement is the complete and exclusive agreement
-among the parties and supersedes all proposals and prior agreements whether
-written or oral, and all other communications among the parties relating to
-the subject matter of this Agreement. This Agreement cannot be modified except
-in writing and signed by both parties. Failure by either party at any time to
-enforce any of the provisions of this Agreement shall not constitute a waiver
-by such party of such provision nor in any way affect the validity of this
-Agreement.
-
-The invalidity of singular provisions does not affect the validity of the
-entire understanding. The parties are obligated, however, to replace the
-invalidprovisions by a regulation which comes closest to the economic
-intent of the invalid provision. The same shall apply mutatis mutandis in
-case of a gap.
-
-IN WITNESS WHEREOF, the LICENSEE hereto have caused this Agreement to be
-duly executed on the date of the download of the software and by accepting
-the license conditions by pressing the Acceptance button.
-
-I have read this License Agreement and I agree to uphold the terms and
-conditions of this license.
diff --git a/licenses/bambino b/licenses/bambino
deleted file mode 100644
index 0931f923c..000000000
--- a/licenses/bambino
+++ /dev/null
@@ -1,32 +0,0 @@
-PROVIDER: The National Cancer Institute at the National Institutes of Health, an Agency of the Federal Government 

-

-Definitions: 

-The term "SOFTWARE" throughout this agreement means the machine readable, binary, object code form and related documentation for the modules of the Bambino software package, which is a graphical viewer and variant detector for next-generation sequencing files in SAM/BAM format. 

-

-The term "RECIPIENT" means the party that downloads the software.

-

-By downloading or otherwise receiving the SOFTWARE, RECIPIENT may use the SOFTWARE subject to RECIPIENT's agreement to the following terms:

-

-1. THE SOFTWARE SHALL NOT BE USED IN THE TREATMENT OR DIAGNOSIS OF HUMAN SUBJECTS.

-

-2. RECIPIENT shall not distribute the SOFTWARE, in whole or in part without express advance written approval of PROVIDER.

-

-3. The SOFTWARE may be used for research and academic purposes only. The SOFTWARE may not be used for commercial purposes. RECIPIENT will not license or sell or use the SOFTWARE for commercial purposes or applications.

-

-4. RECIPIENT shall not modify, extend, decompile, make derivatives of, merge, publish, reverse engineer or distribute the SOFTWARE without written permission from PROVIDER.

-

-5. RECIPIENT agrees to comply with all regulations applicable to the use of the SOFTWARE. 

- 

-6. RECIPIENT may publish or otherwise publicly disclose the results of using the SOFTWARE. RECIPIENT agrees to acknowledge PROVIDER's contribution of the SOFTWARE in all written publications containing any data or information regarding or resulting from use of the SOFTWARE.

-

-7. THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE PROVIDER OR THE INDIVIDUAL DEVELOPERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY OF ANY KIND.  USE OF THE SOFTWARE BY RECIPIENT IS AT RECIPIENT'S OWN RISK. PROVIDER makes no representations that the use of SOFTWARE will not infringe any patent or proprietary rights of third parties.

-

-8. No indemnification for any loss, claim, damage, or liability is intended or provided by either Party under this Agreement.  Each Party shall be liable for any loss, claim, damage, or liability that said Party incurs as a result of said Party's activities under this Agreement, except that Provider, as an agency of the United States, assumes liability only to the extent as provided under the Federal Tort Claims Act (28 U.S.C. Chapter 171 Sections 2671-2680).

-

-9. RECIPIENT agrees not to claim, infer, or imply endorsement by the United States Government, or any of its organizational units, contractors or employees.  RECIPIENT agrees that it will not use any trademarks, service marks, trade names, logos or product names of NCI except as required to comply with the terms of this agreement.

-

-10. By conveying the SOFTWARE herein, the PROVIDER and the individual developers will not be obligated to provide to the RECIPIENT, or any other party, support in any form nor will Provider be obligated to replace the SOFTWARE should it become erased or otherwise destroyed.  Accordingly, the PROVIDER and the individual developers shall be under no obligation to provide RECIPIENT any service, guidance, updates or assistance.

-

-11. Title in the SOFTWARE shall remain with the PROVIDER.  It is understood that nothing herein will be deemed to constitute, by implication or otherwise, the grant to either Party by the other of any license or other rights under any patent, patent application or other intellectual property right or interest.  PROVIDER reserves the right to distribute the SOFTWARE to others and to use it for PROVIDER's own purposes.   The United States Government explicitly retains all rights to use the SOFTWARE for any purpose, to have it used on the Government's behalf or to allow others to use it.

-

-

diff --git a/licenses/bcca_2010 b/licenses/bcca_2010
deleted file mode 100644
index c8874f8c5..000000000
--- a/licenses/bcca_2010
+++ /dev/null
@@ -1,453 +0,0 @@
-BC CANCER AGENCY SOFTWARE LICENSE AGREEMENT (ACADEMIC USE)
-
-CAREFULLY READ THE FOLLOWING TERMS AND CONDITIONS. This License
-
-Agreement (the "Agreement") is a legal contract between you, your
-
-employer, educational institution or organization (collectively, "You")
-
-and the British Columbia Cancer Agency ("BCCA") with respect to the
-
-license of the software, including all associated documentation
-
-(collectively, the "Product").
-
- 
-
-BCCA is willing to license the Product to You only if You accept the
-
-terms and conditions of this Agreement. By clicking on the "I ACCEPT"
-
-button, or by copying, downloading, accessing or otherwise using the
-
-Product, You automatically agree to be bound by the terms of this
-
-Agreement. IF YOU DO NOT WISH TO BE BOUND BY THE TERMS OF THIS
-
-AGREEMENT, DO NOT COPY, DOWNLOAD, ACCESS OR OTHERWISE USE THE
-
-PRODUCT.
-
- 
-
-1. AUTHORITY: In the event that You are an educational institution or
-
-organization, Your representative who is clicking the "I ACCEPT"
-
-button, or otherwise copying, downloading, accessing or using the
-
-Product hereby, in their personal capacity, represents and warrants
-
-that they possess the legal authority to enter into this Agreement
-
-on Your behalf and to bind You to the terms of this Agreement.
-
- 
-
-2. LICENSE TO USE: BCCA hereby grants to You a personal, non-exclusive,
-
-non-transferable, limited license to use the Product solely for
-
-internal, non-commercial use for non-profit research or educational
-
-purposes only on the terms and conditions contained in this Agreement.
-
-The Product may be installed at a single site at Your premises only. A
-
-copy of the Product installed on a single common machine or cluster of
-
-machines may be shared for internal use by Qualified Users only. In
-
-order to be a "Qualified User", an individual must be a student,
-
-researcher, professor, instructor or staff member of a non-profit
-
-educational institution or organization who uses the Product solely for
-
-non-profit research or educational purposes.
-
- 
-
-3. RESTRICTIONS: You acknowledge and agree that You shall not, and
-
-shall not authorize any third party to:
-
-(a) make copies of the Product, except as provided in Section 2 and
-
-except for a single backup copy, and any such copy together with the
-
-original must be kept in Your possession or control;
-
-(b) modify, adapt, decompile, disassemble, translate into another
-
-computer language, create derivative works of, or otherwise reverse
-
-engineer the Product, or disclose any trade secrets relating to the
-
-Product, except as permitted in Section 5;
-
-(c) license, sublicense, distribute, sell, lease, transfer, assign,
-
-trade, rent or publish the Product or any part thereof and/or copies
-
-thereof, to any third party;
-
-(d) use the Product to process any data other than Your own;
-
-(e) use the Product or any part thereof for any commercial or
-
-for-profit purpose or any other purpose other than as permitted in
-
-Section 2; or
-
-(f) use, without its express permission, the name of BCCA.
-
- 
-
-4. INTELLECTUAL PROPERTY RIGHTS: Subject to Section 5 below, all
-
-patents, copyrights, trade secrets, service marks, trademarks and
-
-other proprietary rights in or related to the Product and any
-
-improvements, modifications and enhancements thereof are and will
-
-remain the exclusive property of BCCA or its licensors. You agree
-
-that You will not, either during or after the termination of this
-
-Agreement, contest or challenge the title to or the intellectual
-
-property rights of BCCA or its licensors in the Product or any
-
-portion thereof.
-
- 
-
-5. OWNERSHIP OF IMPROVEMENTS: In the event that the Product, in the
-
-form provided to You, includes source code (the "Source Code"),
-
-You are entitled to make improvements, modifications and
-
-enhancements to the Source Code (collectively, "Improvements")
-
-which Improvements are to be used by You for non-profit research
-
-and educational purposes only and You shall be the owner of those
-
-Improvements that You directly make and of all intellectual
-
-property rights to such Improvements, subject to the foregoing
-
-limits on Your use and distribution of such Improvements. You
-
-hereby grant to BCCA a perpetual, non-exclusive, worldwide,
-
-fully-paid, irrevocable license to use such Improvements for any
-
-purposes whatsoever, and to sublicense such Improvements including
-
-the right for third parties to sublicense the same, in perpetuity
-
-to the extent such rights are not limited in duration under
-
-applicable law, without identifying or seeking Your
-
-consent. Notwithstanding the foregoing, You acknowledge that BCCA
-
-and its licensors will retain or own all rights in and to any
-
-pre-existing code or other technology, content and data that may be
-
-incorporated in the Improvements. For greater certainty, this
-
-Section applies solely to the Source Code and shall not give You
-
-any rights with respect to the object code or any other portion or
-
-format of the Product which use, for greater certainty, is limited
-
-as set forth in this Agreement including as set out in Section 3(b)
-
-above. You acknowledge and agree that you will provide copies of
-
-Improvements to BCCA in such format as reasonably requested by BCCA
-
-at any time upon the request of BCCA.
-
- 
-
-6. CONFIDENTIALITY: You acknowledge that the Product is and
-
-incorporates confidential and proprietary information developed,
-
-acquired by or licensed to BCCA. You will take all reasonable
-
-precautions necessary to safeguard the confidentiality of the
-
-Product, and will not disclose any information about the Product to
-
-any other person without BCCA's prior written consent. You will
-
-not allow the removal or defacement of any confidential or
-
-proprietary notice placed on the Product. You acknowledge that any
-
-breach of this Section 6 will cause irreparable harm to BCCA and
-
-its licensors.
-
- 
-
-7. NO WARRANTIES: THIS PRODUCT IS PROVIDED TO YOU BY BCCA IN ORDER TO
-
-ALLOW YOU TO OBTAIN ACCESS TO LEADING ACADEMIC RESEARCH. THE PRODUCT
-
-IS PROVIDED TO YOU ON AN "AS IS" BASIS WITHOUT WARRANTY OF ANY
-
-KIND. NO WARRANTY, REPRESENTATION OR CONDITION EITHER EXPRESS OR
-
-IMPLIED, INCLUDING WITHOUT LIMITATION, ANY IMPLIED WARRANTY OR
-
-CONDITION OF MERCHANTABILITY, NON-INFRINGEMENT, PERFORMANCE,
-
-DURABILITY OR FITNESS FOR A PARTICULAR PURPOSE OR USE SHALL
-
-APPLY. BCCA DOES NOT WARRANT THAT THE PRODUCT WILL OPERATE ON A
-
-CONTINUOUS OR TROUBLE FREE BASIS.
-
- 
-
-8. LIMITATION OF LIABILITY: TO THE MAXIMUM EXTENT PERMITTED BY
-
-APPLICABLE LAW, IN NO EVENT SHALL THE AGGREGATE LIABILITY OF BCCA TO
-
-YOU EXCEED THE AMOUNT YOU HAVE PAID TO ACQUIRE THE PRODUCT ("MAXIMUM
-
-AMOUNT") AND WHERE YOU HAVE NOT PAID ANY AMOUNT FOR THE PRODUCT THEN
-
-THE MAXIMUM AMOUNT SHALL BE DEEMED TO BE CDN$100.00. IN NO EVENT SHALL
-
-BCCA BE LIABLE FOR ANY INDIRECT, INCIDENTAL, CONSEQUENTIAL, OR SPECIAL
-
-DAMAGES, INCLUDING WITHOUT LIMITATION ANY DAMAGES FOR LOST PROFITS OR
-
-SAVINGS, REGARDLESS OF WHETHER THEY HAVE BEEN ADVISED OF THE
-
-POSSIBILITY OF SUCH DAMAGE. EXCEPT TO THE EXTENT THAT THE LAWS OF A
-
-COMPETENT JURISDICTION REQUIRE LIABILITIES BEYOND AND DESPITE THESE
-
-LIMITATIONS, EXCLUSIONS AND DISCLAIMERS, THESE LIMITATIONS, EXCLUSIONS
-
-AND DISCLAIMERS SHALL APPLY WHETHER AN ACTION, CLAIM OR DEMAND ARISES
-
-FROM A BREACH OF WARRANTY OR CONDITION, BREACH OF CONTRACT,
-
-NEGLIGENCE, STRICT LIABILITY OR ANY OTHER KIND OF CIVIL OR STATUTORY
-
-LIABILITY CONNECTED WITH OR ARISING FROM THIS AGREEMENT. YOU AGREE
-
-THAT THE FOREGOING DISCLAIMER OF WARRANTIES AND LIMITATION OF
-
-LIABILITY ARE FAIR IN LIGHT OF THE NATURE OF THE RIGHTS GRANTED HEREIN
-
-AND THE AMOUNT OF FEES PAID BY YOU IN RESPECT OF THE PRODUCT.
-
- 
-
-9. INDEMNITY: You will indemnify, defend and hold harmless BCCA, its
-
-board of directors, staff and agents from and against any and all
-
-liability, loss, damage, action, claim or expense (including
-
-attorney's fees and costs at trial and appellate levels) in
-
-connection with any claim, suit, action, demand or judgement
-
-(collectively, "Claim") arising out of, connected with, resulting
-
-from, or sustained as a result of Your use of the Product or the
-
-downloading of the Product, including without limitation, any Claim
-
-relating to infringement of BCCA's intellectual property rights or
-
-the intellectual property rights of any third party.
-
- 
-
-10. SUPPORT AND MAINTENANCE: You acknowledge and agree that, unless
-
-and to the extent expressly agreed by BCCA in a separate written
-
-document, the Product is provided to You without any support or
-
-maintenance from BCCA and, for greater certainty, BCCA shall have
-
-no obligation to issue any update or upgrade to any Product.
-
- 
-
-11. TERM: This Agreement is effective until terminated. You may
-
-terminate this Agreement at any time by ceasing use of the Product
-
-and destroying or deleting any copies of the Product. This
-
-Agreement will terminate immediately without notice from BCCA if
-
-You fail to comply with any provision of this Agreement. BCCA may
-
-terminate this Agreement at any time upon notice to you where BCCA
-
-determines, in its sole discretion, that any continued use of the
-
-Product could infringe the rights of any third parties. Upon
-
-termination of this Agreement, and in any event upon BCCA
-
-delivering You notice of termination, You shall immediately purge
-
-all Products from Your computer system(s), return to BCCA all
-
-copies of the Product that are in Your possession or control, and
-
-cease any further development of any Improvements. On any
-
-termination of this Agreement Sections 1, 4, 6, 7, 8, 9, 13 and 14
-
-shall survive such termination.
-
- 
-
-12. GOVERNMENT END USERS: Where any of the Product is used, duplicated
-
-or disclosed by or to the United States government or a government
-
-contractor or sub contractor, it is provided with RESTRICTED
-
-RIGHTS as defined in Title 48 CFR 52.227-19 and is subject to the
-
-following: Title 48 CFR 2.101, 52.227-19, 227.7201 through
-
-227.7202-4, FAR 52.227-14, and FAR 52.227-19(c)(1-2) and (6/87),
-
-and where applicable, the customary software license, as described
-
-in Title 48 CFR 227-7202 with respect to commercial software and
-
-commercial software documentation including DFAR 252.227-7013,
-
-DFAR 252,227-7014, DFAR 252.227-7015 and DFAR 252.7018, all as
-
-applicable.
-
- 
-
-13. USE OF THE DOWNLOAD SERVICE: You acknowledge and agree that you
-
-will be responsible for all costs, charges and taxes (where
-
-applicable) arising out of Your use of the Product and the
-
-downloading of the Product. You acknowledge that You are
-
-responsible for supplying any hardware or software necessary to
-
-use the Product pursuant to this Agreement.
-
- 
-
-14. GENERAL PROVISIONS:
-
-(a) This Agreement will be governed by the laws of the Province of
-
-British Columbia, and the laws of Canada applicable therein, excluding
-
-any rules of private international law that lead to the application of
-
-the laws of any other jurisdiction. The United Nations Convention on
-
-Contracts for the International Sale of Goods (1980) does not apply to
-
-this Agreement. The courts of the Province of British Columbia shall
-
-have non-exclusive jurisdiction to hear any matter arising in
-
-connection with this Agreement.
-
-(b) USE OF THE PRODUCT IS PROHIBITED IN ANY JURISDICTION WHICH DOES
-
-NOT GIVE EFFECT TO THE TERMS OF THIS AGREEMENT.
-
-(c) You agree that no joint venture, partnership, employment,
-
-consulting or agency relationship exists between You and BCCA as a
-
-result of this Agreement or Your use of the Product.
-
-(d) You hereby consent to Your contact information and any other
-
-personally identifiable information that You provide to us being
-
-disclosed to and maintained and used by us and our business partners
-
-for the purposes of (i) managing and developing our respective
-
-businesses and operations; (ii) marketing products and services to You
-
-and your staff; and (iii) developing new and enhancing existing
-
-products. You further agree that we may provide this information to
-
-other persons as required to satisfy any legal requirements and to any
-
-person that acquires some or all of the assets of BCCA. Where any of
-
-the personally identifiable information that You provide to us is in
-
-respect of individuals other than Yourself (such as Your staff) then
-
-You represent and warrant to use that You have obtained all necessary
-
-consents and authorizations from such individuals in order to comply
-
-with this provision. Please see the BCCA website for further
-
-information regarding personally identifiable information.
-
-(e) This Agreement is the entire Agreement between You and BCCA
-
-relating to this subject matter. You will not contest the validity of
-
-this Agreement merely because it is in electronic form. No
-
-modification of this Agreement will be binding, unless in writing and
-
-accepted by an authorized representative of each party.
-
-(f) The provisions of this Agreement are severable in that if any
-
-provision in the Agreement is determined to be invalid or
-
-unenforceable under any controlling body of law, that will not affect
-
-the validity or enforceability of the remaining provisions of the
-
-Agreement.
-
-(g) You agree to print out or download a copy of this Agreement and
-
-retain it for Your records.
-
-(h) You consent to the use of the English language in this Agreement.
-
-(i) You may not assign this Agreement or any of Your rights or
-
-obligations hereunder without BCCA's prior written consent. BCCA, at
-
-its sole discretion may assign this Agreement without notice to You.
\ No newline at end of file
diff --git a/licenses/direx b/licenses/direx
deleted file mode 100644
index cdda29cdc..000000000
--- a/licenses/direx
+++ /dev/null
@@ -1,53 +0,0 @@
-
-
-LICENSE FOR ACADEMIC (NON-PROFIT) INSTITUTIONS
-                    TO USE DIREX V0.2
-
-AUTHOR: GUNNAR SCHROEDER
-
-                         TERMS OF AGREEMENT
-
-BY DOWNLOADING OR USING DIREX V0.2 YOU AGREE TO THE FOLLOWING TERMS:
-
-- THE AUTHOR RETAINS OWNERSHIP OF ALL MATERIALS (INCLUDING
-  SOFTWARE AND DOCUMENTATION). REPORTS OF MODIFICATIONS OR DERIVATIVE
-  WORKS ARE TO BE MADE TO THE AUTHOR, AND ARE TO BE MADE AVAILABLE
-  ON REQUEST.
-
-- YOU SHALL NOT USE THE SOFTWARE FOR ANY PURPOSE (RESEARCH OR
-  OTHERWISE) THAT IS SUPPORTED BY A "FOR PROFIT" ORGANIZATION WITHOUT
-  PRIOR WRITTEN AUTHORIZATION.
-
-- YOU SHALL NOT DISCLOSE IN ANY FORM EITHER THE DELIVERED SOFTWARE OR
-  DOCUMENTATION OR ANY MODIFICATIONS OR DERIVATIVE WORKS BASED ON THE
-  SOFTWARE OR DOCUMENTATION TO THIRD PARTIES WITHOUT PRIOR WRITTEN
-  AUTHORIZATION.
-
-- IF YOU RECEIVE A REQUEST TO FURNISH ALL OR ANY PORTION OF THE
-  SOFTWARE TO ANY THIRD PARTY, YOU WILL NOT FULFILL SUCH A REQUEST AND
-  WILL REFER IT IN WRITING TO THE AUTHOR.
-
-- YOU AGREE THAT THE SOFTWARE IS FURNISHED ON AN "AS IS" BASIS AND
-  THAT THE AUTHOR IN NO WAY WARRANTS THE SOFTWARE OR ANY OF ITS
-  RESULTS AND IS IN NO WAY LIABLE FOR ANY USE YOU MAKE OF THE SOFTWARE.
-  EXCEPT AS OTHERWISE PROVIDED IN THIS SECTION, THE AUTHOR
-  DISCLAIMS ALL WARRANTIES, REPRESENTATIONS, AND STATEMENTS, EXPRESS
-  OR IMPLIED, STATUTORY OR OTHERWISE, INCLUDING, WITHOUT LIMITATION, ANY
-  IMPLIED WARRANTIES OF MERCHANTABILITY OR FITNESS FOR A PARTICULAR
-  PURPOSE. IN NO EVENT SHALL THE AUTHOR BE LIABLE FOR ANY ACTUAL,
-  DIRECT, INDIRECT, SPECIAL, CONSEQUENTIAL, OR INCIDENTAL DAMAGES,
-  HOWEVER CAUSED, INCLUDING, WITHOUT LIMITATION, ANY DAMAGES ARISING OUT
-  OF THE USE OR OPERATION OF THE SOFTWARE, LOSS OF USE OF THE SOFTWARE,
-  OR DAMAGE OF ANY SORT TO THE USER.
-
-- YOU AGREE THAT ANY REPORTS OR PUBLICATION OF RESULTS OBTAINED WITH
-  THE SOFTWARE WILL ACKNOWLEDGE ITS USE BY CITATION OF THE FOLLOWING
-  ARTICLE:
-
-    'COMBINING EFFICIENT CONFORMATIONAL SAMPLING WITH A
-     DEFORMABLE ELASTIC NETWORK MODEL FACILITATES STRUCTURE
-     REFINEMENT AT LOW RESOLUTION'.
-     G.F.SCHRODER, A.T.BRUNGER, AND M.LEVITT
-     STRUCTURE, VOL 15, 1630-1641, (2007)
-
-
diff --git a/licenses/estscan b/licenses/estscan
deleted file mode 100644
index 46089aab6..000000000
--- a/licenses/estscan
+++ /dev/null
@@ -1,88 +0,0 @@
-                       ESTScan license
-                       ---------------
-
-Copyright (c) Swiss Institute of Bioinformatics, Ludwig Institute for
-Cancer Research (LICR), and Swiss Institute for Experimental Cancer
-Research (ISREC), 1999, 2004. For the purposes of this copyright, the
-Swiss Institute of Bioinformatics acts on behalf of its partners, LICR
-and ISREC.
-
-The ESTScan software is the exclusive property of the copyright
-owners, at UNIL - BEP, CH-1015 LAUSANNE, Switzerland.  The Swiss
-Institute of Bioinformatics provides the ESTScan program WITHOUT ANY
-WARRANTY OF MERCHANTABILITY OR FITNESS FOR ANY PARTICULAR PURPOSE, OR
-ANY OTHER WARRANTY, EXPRESS OR IMPLIED.
-
-
-License Terms:
-
-Use, Modification and Redistribution (including distribution of any
-modified or derived work) in source and binary forms is permitted only
-if each of the following conditions is met:
-
-1. Redistributions qualify as "freeware" or "Open Source Software" under
-   one of the following terms:
-
-   (a) Redistributions are made at no charge beyond the reasonable cost of
-       materials and delivery.
-
-   (b) Redistributions are accompanied by a copy of the Source Code or by an
-       irrevocable offer to provide a copy of the Source Code for up to three
-       years at the cost of materials and delivery.  Such redistributions
-       must allow further use, modification, and redistribution of the Source
-       Code under substantially the same terms as this license.  For the
-       purposes of redistribution "Source Code" means the complete source
-       code of ESTScan including all modifications.
-
-   Other forms of redistribution are allowed only under a separate royalty-
-   free agreement permitting such redistribution subject to standard
-   commercial terms and conditions.  A copy of such agreement may be
-   obtained from the Swiss Institute of Bioinformatics at the above address.
-
-2. Redistributions of source code must retain the copyright notices as they
-   appear in each source code file, these license terms, and the
-   disclaimer/limitation of liability set forth in the introductory paragraph.
-
-3. Redistributions in binary form must reproduce the Copyright Notice,
-   these license terms, and the disclaimer/limitation of liability set
-   forth as above, in the documentation and/or other materials
-   provided with the distribution.  For the purposes of binary distribution
-   the "Copyright Notice" refers to the following language:
-   "Copyright (c) 1999, 2004 Swiss Institute of Bioinformatics.
-    All rights reserved."
-
-4. Neither the name of the Swiss Institute of Bioinformatics nor
-   the names of its contributors may be used to endorse or promote
-   products derived from this software without specific prior written
-   permission.
-
-5. All redistributions must comply with the conditions imposed by the
-   Swiss Institute of Bioinformatics on certain embedded code, whose copyright
-   notice and conditions for redistribution are as follows:
-
-   (a) Copyright (c) 1999, 2004 Swiss Institute of Bioinformatics.
-       All rights reserved.
-
-   (b) Redistribution and use in source and binary forms, with or without
-       modification, are permitted provided that the following conditions
-       are met:
-
-      (i)   Redistributions of source code must retain the above copyright
-            notice, this list of conditions and the above disclaimer.
-
-      (ii)  Redistributions in binary form must reproduce the above
-            copyright notice, this list of conditions and the following
-            disclaimer in the documentation and/or other materials provided
-            with the distribution.
-
-      (iii) All advertising materials mentioning features or use of this
-            software must display the following acknowledgement:  "This
-            product includes software developed by the Swiss Institute of
-            Bioinformatics and its contributors."
-
-      (iv)  Neither the name of the Institute nor the names of its
-            contributors may be used to endorse or promote products derived
-            from this software without specific prior written permission.
-
-($Id: COPYRIGHT,v 1.1.1.1 2004/12/16 12:44:29 c4chris Exp $
-Version 1.1, last updated 9 December 2004)
diff --git a/licenses/gDEBugger b/licenses/gDEBugger
deleted file mode 100644
index 0a1588503..000000000
--- a/licenses/gDEBugger
+++ /dev/null
@@ -1,232 +0,0 @@
-END USER LICENSE AGREEMENT
-AMD gDEBugger SOFTWARE
-(No Redistribution)
-IMPORTANT-READ CAREFULLY:  This is a legal agreement ("Agreement") between you
-(either an individual or an entity on whose behalf you sign this Agreement)
-("You") and Advanced Micro Devices, Inc., related companies and affiliates
-("AMD").  Do not install, copy or use the enclosed Materials (defined below),
-until You have carefully read and agreed to the following terms and conditions.
- If You do not agree to the terms of this Agreement including the collection,
-transmission and storage of Your personal information, do not install, copy or
-use the Materials or any portion thereof.  By loading or using the Materials
-provided herewith You agree to all of the terms of this Agreement.  
-
-1.      USE:  
-        a.      Subject to the terms and conditions of this Agreement, AMD
-grants You the following non-exclusive, non-transferable, royalty-free,
-limited, copyright license to (1) install, copy and use the object code version
-of the gDEBugger software and materials associated with this Agreement,
-including without limitation, the user guide and other documentation,
-(collectively, "Materials") for internal testing, debugging and application
-profiling, and (2) modify the gDEBugger software for Your internal use and
-reverse engineer only for debugging such modifications.  
-        b.      You may make a limited number of copies of the object code
-version of the Materials only as required for back-up purposes. In making
-copies of the Materials for back-up purposes, You agree to include all
-copyright legends and other legal notices that may appear in the Materials, as
-well as this Agreement in its entirety.  Except for the limited license granted
-herein, You shall have no other rights in the Materials, whether express,
-implied, arising by estoppel or otherwise.
-        c.      AMD reserves the right to replace, modify or upgrade the
-Materials at any time.  AMD may also offer You a replacement or modified
-version of the Materials.  AMD reserves the right to charge for such
-replacement, modification or upgrade.  Any such replacement or modified
-Materials code or upgrade to the Materials offered to You by AMD shall be
-considered part of the Materials and subject to the terms of this Agreement
-(unless this Agreement is superseded by a further Agreement accompanying such
-replacement or modified version of or upgrade to the Materials).  In the event
-that AMD offers a replacement or modified version of or any upgrade to the
-Materials, (i) Your continued use of the Materials is conditioned on Your
-acceptance of such replacement or modified version of or upgrade to the
-Materials and any accompanying superseding Agreement; and (ii) in the case of
-the replacement or modified Materials, Your use of all prior versions of the
-Materials is terminated.
-        d.      You do not have the right to (i) distribute, rent, lease, sell,
-sublicense, assign, or otherwise transfer the Materials, in whole or in part,
-to third parties for commercial or for non-commercial use; (ii) modify,
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-the Materials to any third party for outsourcing or any other purpose without
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-        e.      AMD is under no obligation to support or provide maintenance
-for the Materials or to provide any updates, modifications, enhancements or
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-2.      FEEDBACK:  You may provide AMD feedback, suggestions or opinions as to
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-3.      OWNERSHIP AND COPYRIGHT OF MATERIALS: You agree that the Materials are
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-AMD does not grant any express or implied right to You under AMD and/or its
-licensor(s) patents, copyrights, trademarks, know how or trade secret
-information.
-
-4.      CONFIDENTIAL INFORMATION:  You shall refrain from disclosing any
-Confidential Information to third parties and will take reasonable security
-precautions, at least as great as the precautions it takes to protect Your own
-confidential information, but no less than reasonable care, to keep
-confidential the Confidential Information.  For the purposes hereof,
-"Confidential Information" means all information disclosed between the parties
-in connection with this Agreement, including the Materials and any other
-business or technical information provided to You by AMD.  You will only
-disclose the Confidential Information to Your employees or on-site
-subcontractors (i) who have a need to know in furtherance of this Agreement;
-and (ii) who have signed a confidentiality agreement with You at least as
-restrictive as this Agreement.  If at any future time AMD, directly or
-indirectly, discloses any other related technology or information to You,
-including without limitation any updates, modifications, enhancements or
-        upgrades of the Materials, such disclosure will also be deemed to be
-confidential, part of the Materials and will be subject to the provisions of
-this Agreement. You may disclose Confidential Information in accordance with a
-judicial or other governmental order, provided that You give AMD reasonable
-notice prior to such disclosure to allow AMD a reasonable opportunity to seek a
-protective order or equivalent.  
-
-5.      NOTICES: To the extent that the Materials include any software licensed
-under the FreeImage License, notice is hereby given that any terms that differ
-in this Agreement from the terms in FreeImage license are offered by AMD alone
-and not any developer or contributor to the FreeImage code or project. The
-gDEBugger software uses the Qt library. Use of the Qt library is governed by
-the GNU Lesser General Public License version 2.1 (LGPL v 2.1).
-
-6.      LINKS:  AMD may create links to other web sites within the Materials.
- AMD will make a reasonable effort to link only to sites that have practices to
-maintain individual's right to privacy.  AMD cannot control these links and is
-not responsible for any content appearing on these sites.
-
-7.      COMMUNICATIONS AND YOUR PERSONAL INFORMATION: During use, the Materials
-may send information about You, the Materials and the system to AMD.  This
-information may include the version and other support metadata about the
-Materials, computer hardware, software, the Internet protocol address of the
-computer and your name, company name (if applicable), e-mail, phone number and
-other personal information submitted by You.  AMD may use this information to
-identify or contact You.  By using the Materials, You consent to the
-collection, transmission and storage of Your information and AMD's use of Your
-information.  If You do not consent to the transmission of this information do
-not install or use the Materials.  You can view AMD's privacy statement at:
-http://www.amd.com/us/aboutamd/Pages/privacy.aspx
-
-8.      WARRANTY DISCLAIMER:  You expressly acknowledge and agree that use of
-the Materials are at Your sole risk.  The Materials are provided "AS IS" and
-without warranty of any kind and AMD EXPRESSLY DISCLAIMS ALL WARRANTIES,
-EXPRESS AND IMPLIED, INCLUDING, BUT NOT LIMITED TO, ANY IMPLIED WARRANTIES OF
-MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE OR NON-INFRINGEMENT.  AMD
-DOES NOT WARRANT THAT THE FUNCTIONS CONTAINED IN THE MATERIALS WILL MEET YOUR
-REQUIREMENTS, OR THAT THE OPERATION OF THE MATERIALS WILL BE UNINTERRUPTED OR
-ERROR-FREE, OR THAT DEFECTS IN THE MATERIALS WILL BE CORRECTED.  THE ENTIRE
-RISK AS TO THE RESULTS AND PERFORMANCE OF THE MATERIALS IS ASSUMED BY YOU.
- FURTHERMORE, AMD DOES NOT WARRANT OR MAKE ANY REPRESENTATIONS REGARDING THE
-USE OR THE RESULTS OF THE USE OF THE MATERIALS IN TERMS OF THEIR CORRECTNESS,
-ACCURACY, RELIABILITY, CURRENT-NESS, OR OTHERWISE. NO ORAL OR WRITTEN
-INFORMATION OR ADVICE GIVEN BY AMD OR AMD PARTIES (DEFINED BELOW) SHALL CREATE
-A WARRANTY OR IN ANY WAY INCREASE
-        THE SCOPE OF THIS WARRANTY.  SHOULD THE MATERIALS PROVE DEFECTIVE, YOU
-(AND NOT AMD OR AMD PARTIES) ASSUME THE ENTIRE COST OF ALL NECESSARY SERVICING,
-REPAIR OR CORRECTION.  THE MATERIALS ARE NOT INTENDED FOR USE IN MEDICAL, LIFE
-SAVING OR LIFE SUSTAINING, NUCLEAR OR WEAPONS RELATED APPLICATIONS.  SOME
-JURISDICTIONS DO NOT ALLOW THE EXCLUSION OF IMPLIED WARRANTIES, SO THE ABOVE
-EXCLUSION MAY NOT APPLY TO YOU.  
-
-9.      INDEMNIFICATION: You will indemnify, defend, and hold AMD Parties
-(defined below) harmless from any and all actions, causes of action, claims,
-demands, costs, liabilities, expenses and damages, including reasonable
-attorneys' fees, arising out of or in connection with any breach of Your
-obligations under this Agreement.
-
-10.     LIMITATION OF LIABILITY:  IN NO EVENT SHALL AMD OR ANY OF THEIR
-DIRECTORS, OFFICERS, EMPLOYEES AND AGENTS, OR ANY OF THEIR SUPPLIERS OR
-LICENSORS ("AMD PARTIES") BE LIABLE TO YOU OR ANY THIRD PARTIES IN RECEIPT OF
-THE MATERIALS UNDER ANY THEORY OF LIABILITY, WHETHER EQUITABLE, LEGAL OR COMMON
-LAW ACTION ARISING HEREUNDER FOR CONTRACT, STRICT LIABILITY, INDEMNITY, TORT
-(INCLUDING NEGLIGENCE), OR OTHERWISE FOR DAMAGES WHICH, IN THE AGGREGATE EXCEED
-ONE HUNDRED DOLLARS ($100.00).  IN NO EVENT SHALL AMD PARTIES BE LIABLE FOR ANY
-CONSEQUENTIAL, INCIDENTAL, PUNITIVE OR SPECIAL DAMAGES, INCLUDING, BUT NOT
-LIMITED TO, LOSS OF PROFITS, BUSINESS INTERRUPTION, OR LOSS OF INFORMATION
-ARISING OUT OF THE USE OF OR INABILITY TO USE THE MATERIALS, EVEN IF AMD
-PARTIES HAVE BEEN ADVISED OF THE POSSIBILITY OF SUCH DAMAGES.  BY USING THE
-MATERIALS WITHOUT CHARGE, YOU ACCEPT THIS ALLOCATION OF RISK.  Because some
-jurisdictions prohibit the exclusion or limitation of liability for
-consequential or incidental damages, the above    limitation may not apply to
-You.
-
-11.     EXPORT RESTRICTIONS: You shall adhere to all applicable U.S., European,
-and other export laws, including but not limited to the U.S. Export
-Administration Regulations ("EAR"), (15 C.F.R. Sections 730 through 774), and
-E.U. Council Regulation (EC) No 1334/2000 of 22 June 2000.  Further, pursuant
-to Section 740.6 of the EAR, You hereby certify that, except pursuant to a
-license granted by the United States Department of Commerce Bureau of Industry
-and Security or as otherwise permitted pursuant to a License Exception under
-the EAR, You will not (1) export, re-export or release to a national of a
-country in Country Groups D:1, E:1 or E:2 any restricted technology, Materials,
-or source code it receives from AMD, or (2) export to Country Groups D:1, E:
-1 or E:2 the direct product of such technology or Materials, if such foreign
-produced direct product is subject to national security controls as identified
-on the Commerce Control List (currently found in Supplement 1 to Part 774 of
-EAR).  For the most current
-        Country Group listings, or for additional information about the EAR or
-Your obligations under those regulations, please refer to the U.S. Bureau of
-Industry and Security's website at http://www.bis.doc.gov/.
-
-12.     U.S. GOVERNMENT RESTRICTED RIGHTS: The Materials are provided with
-"RESTRICTED RIGHTS." Use, duplication, or disclosure by the Government is
-subject to the restrictions as set forth in FAR 52.227-14 and DFAR252.227-7013,
-et seq., or its successor.  Use of the Materials by the Government constitutes
-acknowledgement of AMD's proprietary rights in them.
-
-13.     TERMINATION OF LICENSE: This Agreement is effective until terminated.
- You can terminate this Agreement at any time by destroying the Materials, and
-all copies You have made.  AMD may terminate this Agreement upon thirty (30)
-days' prior notice with or without cause.  This Agreement will terminate
-immediately without notice from AMD if You fail to comply with any provision of
-this Agreement.  Upon termination You must destroy the Materials and all copies
-You have made.  
-
-14.     SURVIVAL:  Sections 1(c)-(e) (and Section 1(a)(2) only as it applies to
-section 1(d(ii)), 2-18, inclusive, shall survive any expiration or termination
-of this Agreement.
-
-15.     APPLICABLE LAWS:  Any claim arising under or relating to this Agreement
-shall be governed by and construed in accordance with the substantive laws of
-the State of California, without regard to principles of conflict of laws.
-   Each party hereto submits to the jurisdiction of the state and federal
-courts of Santa Clara County and the Northern District of California for the
-purposes of all legal proceedings arising out of or relating to this Agreement
-or the subject matter hereof.  Each party waives any objection which it may
-have to contest such forum.
-
-16.     SEVERABILITY:  Should any term of this Agreement be declared void or
-unenforceable by any court of competent jurisdiction, such declaration shall
-have no effect on the remaining terms hereof.
-
-17.     NO WAIVER:  The failure of either party to enforce any rights granted
-hereunder or to take action against the other party in the event of any breach
-hereunder shall not be deemed a waiver by that party as to subsequent
-enforcement of rights or subsequent actions in the event of future breaches.
-
-18.     ENTIRE AGREEMENT:  This Agreement constitutes the entire agreement
-between the parties and supersedes any prior or contemporaneous oral or written
-agreements with respect to the subject matter of this Agreement.
-
-Rev. June 2011  - 2 -   END USER LICENSE AGREEMENT
diff --git a/licenses/hoomd-blue b/licenses/hoomd-blue
deleted file mode 100644
index 4e38f05d2..000000000
--- a/licenses/hoomd-blue
+++ /dev/null
@@ -1,46 +0,0 @@
-Highly Optimized Object-oriented Many-particle Dynamics -- Blue Edition
-(HOOMD-blue) Open Source Software License Copyright 2009-2014 The Regents of
-the University of Michigan All rights reserved.
-
-HOOMD-blue may contain modifications ("Contributions") provided, and to which
-copyright is held, by various Contributors who have granted The Regents of the
-University of Michigan the right to modify and/or distribute such Contributions.
-
-You may redistribute, use, and create derivate works of HOOMD-blue, in source
-and binary forms, provided you abide by the following conditions:
-
-* Redistributions of source code must retain the above copyright notice, this
-list of conditions, and the following disclaimer both in the code and
-prominently in any materials provided with the distribution.
-
-* Redistributions in binary form must reproduce the above copyright notice, this
-list of conditions, and the following disclaimer in the documentation and/or
-other materials provided with the distribution.
-
-* All publications and presentations based on HOOMD-blue, including any reports
-or published results obtained, in whole or in part, with HOOMD-blue, will
-acknowledge its use according to the terms posted at the time of submission on:
-http://codeblue.umich.edu/hoomd-blue/citations.html
-
-* Any electronic documents citing HOOMD-Blue will link to the HOOMD-Blue website:
-http://codeblue.umich.edu/hoomd-blue/
-
-* Apart from the above required attributions, neither the name of the copyright
-holder nor the names of HOOMD-blue's contributors may be used to endorse or
-promote products derived from this software without specific prior written
-permission.
-
-Disclaimer
-
-THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDER AND CONTRIBUTORS ``AS IS'' AND
-ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED
-WARRANTIES OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE, AND/OR ANY
-WARRANTIES THAT THIS SOFTWARE IS FREE OF INFRINGEMENT ARE DISCLAIMED.
-
-IN NO EVENT SHALL THE COPYRIGHT HOLDER OR CONTRIBUTORS BE LIABLE FOR ANY DIRECT,
-INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING,
-BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE,
-DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF
-LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE
-OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF
-ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
diff --git a/licenses/jing b/licenses/jing
new file mode 100644
index 000000000..0833c55c8
--- /dev/null
+++ b/licenses/jing
@@ -0,0 +1,85 @@
+<html xmlns="http://www.w3.org/1999/xhtml">
+<head>
+<title>Jing Copying Conditions</title>
+</head>
+
+<body>
+<h1>Jing Copying Conditions</h1>
+
+<p>Copyright (c) 2001-2003 Thai Open Source Software Center Ltd<br />
+All rights reserved.</p>
+
+<p>Redistribution and use in source and binary forms, with or without
+modification, are permitted provided that the following conditions are
+met:</p>
+
+<ul>
+    <li>Redistributions of source code must retain the above copyright
+    notice, this list of conditions and the following disclaimer.</li>
+
+    <li>Redistributions in binary form must reproduce the above copyright
+    notice, this list of conditions and the following disclaimer in
+    the documentation and/or other materials provided with the
+    distribution.</li>
+
+    <li>Neither the name of the Thai Open Source Software Center Ltd nor
+    the names of its contributors may be used to endorse or promote
+    products derived from this software without specific prior written
+    permission.</li>
+</ul>
+
+<p>THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS
+"AS IS" AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT
+LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR
+A PARTICULAR PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE REGENTS OR
+CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL,
+EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO,
+PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR
+PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF
+LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING
+NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS
+SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.</p>
+
+<h2>Third-party JARs</h2>
+
+<p>This distribution includes some additional JAR files, which have
+their own copying conditions:</p>
+
+<dl>
+
+<dt><code>saxon.jar</code></dt>
+
+<dd>Comes from the <a href="http://saxon.sourceforge.net/">Saxon</a>
+6.5.2 distribution and is covered by these <a
+href="http://saxon.sourceforge.net/saxon6.5.2/conditions.html">conditions</a></dd>
+
+<dt><code>xercesImpl.jar</code></dt>
+<dt><code>xml-apis.jar</code></dt>
+<dd>Come from the <a href="http://xml.apache.org/xerces2-j/">Xerces-J</a> 2.4.0
+distribution and are covered by the <a href="xerces.copying.txt">Apache
+Software License</a></dd>
+
+<dt><code>isorelax.jar</code></dt>
+<dd>Comes from <a href="http://sourceforge.net/projects/iso-relax/">ISO RELAX</a>
+2003/01/08 distribution and is covered by the following license:
+
+<p>Copyright (c) 2001-2002, SourceForge ISO-RELAX Project (ASAMI Tomoharu, Daisuke
+Okajima, Kohsuke Kawaguchi, and MURATA Makoto)</p>
+ 
+<p>Permission is hereby granted, free of charge, to any person obtaining a copy of
+this software and associated documentation files (the "Software"), to deal in the Software without restriction, including without limitation the rights to use,
+copy, modify, merge, publish, distribute, sublicense, and/or sell copies of the
+Software, and to permit persons to whom the Software is furnished to do so, subject to the following conditions:</p>
+ 
+<p>The above copyright notice and this permission notice shall be included in all copies or substantial portions of the Software.</p>
+ 
+<p>THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, FITNESS FOR
+A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY, WHETHER IN AN
+ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE SOFTWARE.</p>
+</dd>
+
+</dl>
+
+</body>
+
+</html>
diff --git a/licenses/kash b/licenses/kash
deleted file mode 100644
index 8e4985af8..000000000
--- a/licenses/kash
+++ /dev/null
@@ -1,19 +0,0 @@
-KASH can be copied and distributed freely for any non-commercial purpose.
-
-If you copy KASH for somebody else, you may ask this person to refund your expenses. This should cover cost of media, copying and shipping. You are not allowed to ask for more than this. In any case you must give a copy of this copyright notice along with the program.
-
-If you obtain KASH please send us a short notice to that effect, e.g., an e-mail message to the address kant@math.tu-berlin.de containing your full name and address. This allows us to keep track of the number of KASH users.
-
-If you publish a mathematical result that was partly obtained using KASH, please cite
-
-    M. Daberkow, C. Fieker, J. Klüners, M. Pohst, K. Roegner and K. Wildanger: KANT V4, in J. Symbolic Comp. 24 (1997), 267-283. 
-
-Also we would appreciate it if you could inform us about such a paper.
-
-You are permitted to modify and redistribute KASH, but you are not allowed to restrict further redistribution. That is to say proprietary modifications will not be allowed. We want all versions of KASH to remain free. If you modify any part of KASH and redistribute it, you must supply a `README' document. This should specify what modifications you made in which files. We do not want to take credit or be blamed for your modifications.
-
-Of course we are interested in all of your modifications. In particular we would like to see bug-fixes, improvements and new functions. So again we would appreciate it if you would inform us about all modifications you make.
-
-KASH is distributed by us without any warranty, to the extent permitted by applicable state law. We distribute KASH *as is* without warranty of any kind, either expressed or implied, including, but not limited to, the implied warranties of merchantability and fitness for a particular purpose.
-
-The entire risk as to the quality and performance of the program is with you. Should KASH prove defective, you assume the cost of all necessary servicing, repair or correction. In no case unless required by applicable law will we, and/or any other party who may modify and redistribute KASH as permitted above, be liable to you for damages, including lost profits, lost monies or other special, incidental or consequential damages arising out of the use or inability to use KASH.
diff --git a/licenses/ligplot+ b/licenses/ligplot+
deleted file mode 100644
index 7457f6622..000000000
--- a/licenses/ligplot+
+++ /dev/null
@@ -1,138 +0,0 @@
-LIGPLOT - Automated representation of protein-ligand interactions
-  ----------------------------------------------------------------
-
-			CONFIDENTIALITY AGREEMENT
-			-------------------------
-
-
-
-In regard to the LIGPLOT , specified in the Appendix herewith 
-(the Software) supplied to us, the copyright and other
-intellectual property rights to which belong to the authors, we
-
-
-    __________________________________________________________________
-
-undertake to the authors that we shall be bound by the following terms 
-and conditions:-
-
-1. We will receive the Software and any related documentation in 
-confidence and will not use the same except for the purpose of the
-department's own research. The Software will be used only by such of 
-our officers or employees to whom it must reasonably be communicated 
-to enable us to undertake our research and who agree to be bound by 
-the same confidence.  The department shall procure and enforce such
-agreement from its staff for the benefit of the authors.
-
-2. The publication of research using the Software must reference
-"Wallace A C, Laskowski R A, Thornton J M (1995). LIGPLOT: A program
-to generate schematic diagrams of protein-ligand interactions. Protein 
-Engineering, 8, 127-134."
-
-3. Research shall take place solely at the department's premises at
-
-
-    __________________________________________________________________
-
-4. All forms of the Software will be kept in a reasonably secure place
- to prevent unauthorised access.
-
-5. Each copy of the Software or, if not practicable then, any package
-associated therewith shall be suitably marked (and such marking 
-maintained) with the following copyright notice: " Copyright 1994
-A C Wallace, R A Laskowski, & J M Thornton All Rights Reserved".
-
-6. The Software may be modified but any changes made shall be made
-available to the authors.
-
-7. The Software shall be used exclusively for academic teaching and
-research. The Software will not be used for any commercial research or
-research associated with an industrial company.
-
-8. The confidentiality obligation in paragraph one shall not apply:
-
-   (i)  to information and data known to the department at the time of
-	receipt hereunder (as evidenced by its written records);
-
-  (ii)	to information and data which was at the time of receipt in the 
-	public domain or thereafter becomes so through no wrongful act of
-	the department;
-
- (iii)	to information and data which the department receives from a third
-	party not in breach of any obligation of confidentiality owed to
-	the authors.
-
-Please sign this Undertaking and return a copy of it to indicate that you 
-have read, understood and accepted the above terms.
-
-
-
-		      For and on behalf of _____________________________
-
-		      _________________________________________________
-		     
-		      ..................................................
-
-		      Dated ............................................
-
-
-
-e-mail address ___________________________
-
-
-
-Please complete the above form, sign it, and then send it, or fax it, to:-
-
-
-Roman Laskowski
-European Bioinformatics Institute,
-Wellcome Trust Genome Campus,
-Hinxton,
-Cambridge, CB10 1SD,
-United Kingdom
- 
-Fax:- +44 (0)1223 494 468
- 
-roman@ebi.ac.uk
-
-
-If you have any problems either installing the software or running it,
-please e-mail your problems to:-
-
-     roman@ebi.ac.uk
-
-
-APPENDIX - Files supplied as part of the LIGPLOT program
---------------------------------------------------------
-
-Source program files:-
-1. ligplot.c
-2. ligplot.h
-3. hbadd.c
-4. hbadd.h
-5. dimer.c
-6. dimer.h
-
-Script files:-
-1. ligplot.scr
-2. ligonly.scr
-3. dimplot.scr
-4. dimonly.scr
-
-Parameter file:-
-1. ligplot.prm
-
-Installation instructions:-
-1. install.doc
-
-Documentation:-
-1. manual.tar.Z
-2. README
-
-Confidentiality Agreement:-
-1. confid.txt
-
-
-
-                                                   v.4.4.2 - 7 Mar 2003
-
diff --git a/licenses/mRNAmarkup b/licenses/mRNAmarkup
deleted file mode 100644
index 884ed1bd3..000000000
--- a/licenses/mRNAmarkup
+++ /dev/null
@@ -1,25 +0,0 @@
-Copyright (c) 2000 Volker Brendel
-All Rights Reserved. E-mail: vbrendel@iastate.edu
-
-Permission to use, copy, modify, and distribute this software and its
-documentation for educational, research and non-profit purposes, without fee,
-and without a written agreement is hereby granted, provided that the above
-copyright notice, this paragraph and the following three paragraphs appear in
-all copies. If you modify this file or included files you must cause the
-modified files to carry prominent notices stating that you changed the files.
-
-Inqueries for permission to incorporate this software into commercial products
-should be directed to the Office of Intellectual Property and Technology
-Transfer, 310 Lab of Mechanics, Iowa State University, Ames, IA 50011, phone:
-(515) 294-4740, E-mail: Licensing@iastate.edu.
-
-IN NO EVENT SHALL THE AUTHOR OR IOWA STATE UNIVERSITY BE LIABLE TO ANY PARTY FOR
-DIRECT, INDIRECT, SPECIAL, INCIDENTAL, OR CONSEQUENTIAL DAMAGES, INCLUDING LOST
-PROFITS, ARISING OUT OF THE USE OF THIS SOFTWARE AND ITS DOCUMENTATION, EVEN IF
-IOWA STATE UNIVERSITY HAS BEEN ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
-
-IOWA STATE UNIVERSITY SPECIFICALLY DISCLAIMS ANY WARRANTIES, INCLUDING, BUT NOT
-LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A
-PARTICULAR PURPOSE.  THE SOFTWARE PROVIDED HEREUNDER IS ON AN "AS IS" BASIS,
-AND IOWA STATE UNIVERSITY HAS NO OBLIGATIONS TO PROVIDE MAINTENANCE, SUPPORT,
-UPDATES, ENHANCEMENTS, OR MODIFICATIONS.
diff --git a/licenses/mavid b/licenses/mavid
deleted file mode 100644
index ea7b1490d..000000000
--- a/licenses/mavid
+++ /dev/null
@@ -1,29 +0,0 @@
-Copyright B)2003.  The Regents of the University of California (Regents). All
-Rights Reserved. Created by Nicolas Bray and Lior Pachter, Department of
-Mathematics, University of California, Berkeley.
-
-
-
-Permission is hereby granted to use, copy, modify, display and distribute
-this software and documentation for educational, academic and nonprofit
-purposes only, provided that the above copyright notice, this paragraph, and
-the following two paragraphs appear in all copies, modifications, displays
-and distributions.  For use of this software and documentation for purposes
-other than educational purposes, contact the Office of Technology Licensing,
-UC Berkeley, 2150 Shattuck Avenue, Suite 510, Berkeley, CA  94720-1620;
-(510) 643-7201.
-
-
-
-IN NO EVENT SHALL REGENTS BE LIABLE TO ANY PARTY FOR DIRECT, INDIRECT,
-SPECIAL, INCIDENTAL, OR CONSEQUENTIAL DAMAGES, INCLUDING LOST PROFITS,
-ARISING OUT OF THE USE OF THIS SOFTWARE AND ITS DOCUMENTATION, EVEN IF
-REGENTS HAS BEEN ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
-
-
-
-REGENTS SPECIFICALLY DISCLAIMS ANY WARRANTIES, INCLUDING, BUT NOT LIMITED
-TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR
-PURPOSE. THE SOFTWARE AND ACCOMPANYING DOCUMENTATION, IF ANY, PROVIDED
-HEREUNDER IS PROVIDED "AS IS". REGENTS HAS NO OBLIGATION TO PROVIDE
-MAINTENANCE, SUPPORT, UPDATES, ENHANCEMENTS, OR MODIFICATIONS.
diff --git a/licenses/mddnmr b/licenses/mddnmr
deleted file mode 100644
index dd5c9e910..000000000
--- a/licenses/mddnmr
+++ /dev/null
@@ -1,39 +0,0 @@
-Copyright and Legal Information 
-
-Copyright (C) V. Orekhov, V. Jaravine, M. Mayzel, K. Kazimierczuk, Swedish NMR Center, University of Gothenburg, 2004-2011.
-
-Date: Jul 3, 2011 
-
-DESCRIPTION 
-MddNMR is a program for processing uniformly and non-uniformly sampled (sparse) NMR spectra. 
-The following is legal information pertaining to the use of the MddNMR program. It applies to all MddNMR source files, executable (binary) files, configuration and documentation files contained in the official MddNMR archives. (Certain portions refer to custom versions of the software, there are specific rules listed below for these versions also.) All of these are referred to here as "the software".  
-
-THIS NOTICE MUST ACCOMPANY ALL OFFICIAL OR CUSTOM MddNMR FILES. IT MAY NOT BE REMOVED OR MODIFIED. THIS INFORMATION PERTAINS TO ALL USE OF THE PACKAGE WORLDWIDE. THIS DOCUMENT SUPERSEDES ALL PREVIOUS LICENSES OR DISTRIBUTION POLICIES.  
-
-IMPORTANT LEGAL INFORMATION 
-While the use MddNMR is essentially free of any costs for noncommercial purposes, commercial users and software developers, who wish to bundle MddNMR with other software, will be asked for support of the research and development of MddNMR. For commercial purposes of MddNMR please contact the copyright holders. Permission is granted to use the MddNMR program and all associated files in this package for making calculations. Use of the software for academic and educational purposes is free. The user retains all rights to the results and may use them for any noncommercial purpose. The following legal information exclusively concerns distribution and use of the software for noncommercial purposes.
-
-When results obtained by MddNMR are used in lectures, publications or other similar occasions, then a reference to the authors and at least one of the following papers is to be made: 
-(1) Orekhov, V.Y. and V.A. Jaravine, Analysis of non-?uniformly sampled spectra with Multi-?Dimensional Decomposition. Prog. Nucl. Magn. Reson. Spectrosc., 2011, in press, doi:10.1016/j.pnmrs.2011.02.002 	
-	
-(2) Kazimierczuk, K. and V.Y. Orekhov, Accelerated NMR Spectroscopy by Using Compressed Sensing. Angew. Chem.-Int. Edit., 2011, 123, 5670-3 
-
-
-This software package and all of the files in this archive are copyrighted by the authors, which are represented by Prof. Vladislav Orekhov for distribution, copyright and other legal issues (VO). The software may only be distributed and/or modified according to the guidelines listed below. The spirit of the guidelines below is to provide the MddNMR package freely to as many users as possible, prevent MddNMR users and developers from being taken advantage of, enhance the life quality of those who come in contact with MddNMR. This legal document was created so these goals could be realized. You are legally bound to follow these rules, but we hope you will follow them as a matter of ethics, rather than fear of litigation. 
-
-No portion of this package may be separated from the package and distributed separately other than under the conditions specified in the guidelines below. This package may only be bundled in other software packages with the explicit permission of the copyright holders. This package may only be posted in the Internet and/or included in software compilations using media such as, but not limited to, floppy disk, CD-ROM, tape backup, optical disks, hard disks, or memory cards with the explicit permission of the copyright holders. 
-
-CUSTOM VERSIONS
-With a separate agreement a user may be granted the privilege to modify and compile the source for their own use in any fashion they see fit. What you do with the software in your home or lab is your business, however, in such cases the activity is usually limited by the agreement or defined by the collaborative project. If the user wishes to distribute a modified version of the software, documentation or other parts of the package (here after referred to as a "custom version") they must follow the guidelines listed below. These guidelines have been established to promote the growth of MddNMR and prevent difficulties for users and developers alike. Please follow them carefully for the benefit of all concerned when creating a custom version. You may not incorporate any portion of the MddNMR source code in any software other than a custom version of MddNMR without the explicit permission of the copyright holders. However authors who contribute source to MddNMR may still retain all rights to use their contributed code for any purpose as described below. The user is encouraged to send enhancements and bug fixes to the MddNMR authors, but the authors are in no way required to utilize these enhancements or fixes. By sending material to the authors, the contributor asserts that he owns the materials or has the right to distribute these materials. He authorizes the MddNMR authors to use the materials any way they like. The contributor still retains rights to the donated material, but by donating you grant equal rights to the MddNMR authors. The MddNMR authors don't have to use the material, but if we do, you do not acquire any rights related to MddNMR. We will give you credit if applicable. 
-
-CONDITIONS FOR DISTRIBUTION OF CUSTOM VERSIONS 
-The permission to distribute compiled custom version of the software may be granted in advance with specific permission from VO. Typical conditions include but not limited to following conditions are met. These conditions also apply to custom documentation based on our files. - Mark your version clearly on all modified files stating this to be a modified and unofficial version. - Make all of your modifications to MddNMR freely and publicly   available. - Include clear and obvious information on how to obtain the   official MddNMR. - Include contact and support information for your version. - Include all credits and credit screens for the official   version. - Include a copy of this document. The MddNMR authors are not obligated to provide you or your users any technical support. 
-
-GENERAL RULES FOR ALL DISTRIBUTION
-All requests to acquire the software should be sent to VO, who normally distributes the software on behalf of all co-authors. The permission to distribute this package under certain very specific conditions is granted in advance to other persons or organizations, provided that the above and following conditions are met. The software archives must not be renamed or re-archived using a different method without the explicit permission of the authors. The full software package, as described in the next section, must always be distributed. All forms of commercial and non-profit distribution are only allowed with explicit permission of the copyright holders represented by VO. Clear reference to the copyright holders (at least to VO) must be present in any description/synopsis of software. The copyright holders reserve the right to withdraw distribution privileges from any group, individual, or organization for any reason. 
-
-DEFINITION OF "MddNMR PACKAGE" MddNMR is distributed as a number of  archive containing executables, installation scripts, examples, and documentation. MddNMR is officially distributed for PC (LINUX) and Intel MAC (OS X 10.6 and later). Other systems may be added in the future. Distributors may support different platforms but for each platform they support the full package must be distributed. 
-
-DISCLAIMER 
-This software is provided as is without any guarantees or warranty. Although the authors have attempted to find and correct any bugs in the package, they are not responsible for any damage or losses of any kind caused by the use or misuse of the package. The authors are under no obligation to provide service, corrections, or upgrades to this package. 
-[End of Legal Information] 
diff --git a/licenses/modeller b/licenses/modeller
deleted file mode 100644
index 4921a6462..000000000
--- a/licenses/modeller
+++ /dev/null
@@ -1,19 +0,0 @@
-End-User Software License Agreement for MODELLER
-
-   1. Andrej Sali (``LICENSOR'') grants to (``LICENSEE'') a fully-paid, non-exclusive, and non-transferable license to use the ``MODELLER'' computer software program and associated documentation furnished hereunder (hereinafter called the ``PROGRAM''), upon the terms and conditions hereinafter set out and until termination of this license as set forth below.
-
-   2. LICENSEE understands that this Agreement is license for use of, not sale of, the PROGRAM. Consequently, no Purchase Orders can be accepted by LICENSOR.
-
-   3. LICENSEE acknowledges that the PROGRAM is a research tool still in the development stage, that is being supplied ``as is'', without any accompanying services or improvements from LICENSOR and that this license is entered into in order to enable others to utilize the PROGRAM in their scholarly activities.
-
-   4. LICENSOR MAKES NO REPRESENTATIONS OR WARRANTIES, EXPRESS OR IMPLIED. By way of example, but not limitation, LICENSOR MAKES NO REPRESENTATIONS OR WARRANTIES OF MERCHANTABILITY OR FITNESS FOR ANY PARTICULAR PURPOSE OR THAT THE USE OF THE PROGRAM WILL NOT INFRINGE ANY PATENTS, COPYRIGHTS, TRADEMARKS OR OTHER RIGHTS. LICENSOR shall have no liability nor be liable for an direct, indirect or consequential damages with respect to any claim by LICENSEE or any third party on account of or arising from this Agreement or use of the PROGRAM.
-
-   5. LICENSEE agrees that it will use the PROGRAM, and any modifications, improvements, or derivatives to PROGRAM that LICENSEE may create (collectively, ``IMPROVEMENTS'') solely for internal, non-commercial purposes and shall not distribute or transfer the PROGRAM OR IMPROVEMENTS to any person without prior written permission from LICENSOR. The term ``non-commercial'', as used in this Agreement, means academic or other scholarly research which (a) is not undertaken for profit, or (b) is not intended to produce works, services, or data for commercial use, or (c) is neither conducted, nor funded, by a person or an entity engaged in the commercial use, application or exploitation of works similar to the PROGRAM.
-
-   6. LICENSEE agrees to notify LICENSOR of any IMPROVEMENTS made to the PROGRAM, as described in Section 5, above, and hereby (a) agrees to supply LICENSOR with a copy of same, and (b) grants LICENSOR a worldwide, perpetual license, with the right to sublicense (at any tier), such IMPROVEMENTS without any royalty or other obligation to LICENSEE.
-
-   7. Ownership of all rights, including copyright in the PROGRAM and in any material associated therewith, shall at all times remain with LICENSOR and LICENSEE agrees to preserve same. LICENSEE agrees not to use any portion of the PROGRAM in any machine-readable form outside the PROGRAM, nor to make any copies except for its internal use, without prior written consent of LICENSOR. LICENSEE agrees to place the appropriate copyright notice on any such copies.
-
-   8. This Agreement shall be construed, interpreted and applied in accordance with the Commonwealth of Massachusetts and any legal action arising out of this Agreement or use of the PROGRAM shall be filed in a court in the Commonwealth of Massachusetts.
-
-   9. This license shall be for a term of 5 years except that upon any breach of this Agreement by LICENSEE, LICENSOR shall have the right to terminate this license immediately upon notice to LICENSEE.
diff --git a/licenses/mpich b/licenses/mpich
deleted file mode 100644
index a9216d495..000000000
--- a/licenses/mpich
+++ /dev/null
@@ -1,39 +0,0 @@
-
-				  COPYRIGHT
-
-The following is a notice of limited availability of the code, and disclaimer
-which must be included in the prologue of the code and in all source listings
-of the code.
-
-Copyright Notice
- + 2002 University of Chicago
-
-Permission is hereby granted to use, reproduce, prepare derivative works, and
-to redistribute to others.  This software was authored by:
-
-Mathematics and Computer Science Division
-Argonne National Laboratory, Argonne IL 60439
-
-(and)
-
-Department of Computer Science
-University of Illinois at Urbana-Champaign
-
-
-			      GOVERNMENT LICENSE
-
-Portions of this material resulted from work developed under a U.S.
-Government Contract and are subject to the following license: the Government
-is granted for itself and others acting on its behalf a paid-up, nonexclusive,
-irrevocable worldwide license in this computer software to reproduce, prepare
-derivative works, and perform publicly and display publicly.
-
-				  DISCLAIMER
-
-This computer code material was prepared, in part, as an account of work
-sponsored by an agency of the United States Government.  Neither the United
-States, nor the University of Chicago, nor any of their employees, makes any
-warranty express or implied, or assumes any legal liability or responsibility
-for the accuracy, completeness, or usefulness of any information, apparatus,
-product, or process disclosed, or represents that its use would not infringe
-privately owned rights.
diff --git a/licenses/mpich2 b/licenses/mpich2
deleted file mode 100644
index a9216d495..000000000
--- a/licenses/mpich2
+++ /dev/null
@@ -1,39 +0,0 @@
-
-				  COPYRIGHT
-
-The following is a notice of limited availability of the code, and disclaimer
-which must be included in the prologue of the code and in all source listings
-of the code.
-
-Copyright Notice
- + 2002 University of Chicago
-
-Permission is hereby granted to use, reproduce, prepare derivative works, and
-to redistribute to others.  This software was authored by:
-
-Mathematics and Computer Science Division
-Argonne National Laboratory, Argonne IL 60439
-
-(and)
-
-Department of Computer Science
-University of Illinois at Urbana-Champaign
-
-
-			      GOVERNMENT LICENSE
-
-Portions of this material resulted from work developed under a U.S.
-Government Contract and are subject to the following license: the Government
-is granted for itself and others acting on its behalf a paid-up, nonexclusive,
-irrevocable worldwide license in this computer software to reproduce, prepare
-derivative works, and perform publicly and display publicly.
-
-				  DISCLAIMER
-
-This computer code material was prepared, in part, as an account of work
-sponsored by an agency of the United States Government.  Neither the United
-States, nor the University of Chicago, nor any of their employees, makes any
-warranty express or implied, or assumes any legal liability or responsibility
-for the accuracy, completeness, or usefulness of any information, apparatus,
-product, or process disclosed, or represents that its use would not infringe
-privately owned rights.
diff --git a/licenses/netCDF b/licenses/netCDF
deleted file mode 100644
index 780ba9ee5..000000000
--- a/licenses/netCDF
+++ /dev/null
@@ -1,31 +0,0 @@
-Copyright 1993-2012 University Corporation for Atmospheric Research/Unidata
-
-Portions of this software were developed by the Unidata Program at the
-University Corporation for Atmospheric Research.
-
-Access and use of this software shall impose the following obligations
-and understandings on the user. The user is granted the right, without
-any fee or cost, to use, copy, modify, alter, enhance and distribute
-this software, and any derivative works thereof, and its supporting
-documentation for any purpose whatsoever, provided that this entire
-notice appears in all copies of the software, derivative works and
-supporting documentation. Further, UCAR requests that the user credit
-UCAR/Unidata in any publications that result from the use of this
-software or in any product that includes this software, although this
-is not an obligation. The names UCAR and/or Unidata, however, may not
-be used in any advertising or publicity to endorse or promote any
-products or commercial entity unless specific written permission is
-obtained from UCAR/Unidata. The user also understands that
-UCAR/Unidata is not obligated to provide the user with any support,
-consulting, training or assistance of any kind with regard to the use,
-operation and performance of this software nor to provide the user
-with any updates, revisions, new versions or "bug fixes."
-
-THIS SOFTWARE IS PROVIDED BY UCAR/UNIDATA "AS IS" AND ANY EXPRESS OR
-IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED
-WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE
-DISCLAIMED. IN NO EVENT SHALL UCAR/UNIDATA BE LIABLE FOR ANY SPECIAL,
-INDIRECT OR CONSEQUENTIAL DAMAGES OR ANY DAMAGES WHATSOEVER RESULTING
-FROM LOSS OF USE, DATA OR PROFITS, WHETHER IN AN ACTION OF CONTRACT,
-NEGLIGENCE OR OTHER TORTIOUS ACTION, ARISING OUT OF OR IN CONNECTION
-WITH THE ACCESS, USE OR PERFORMANCE OF THIS SOFTWARE.
diff --git a/licenses/ni-visa b/licenses/ni-visa
deleted file mode 100644
index e295937eb..000000000
--- a/licenses/ni-visa
+++ /dev/null
@@ -1,318 +0,0 @@
-NATIONAL INSTRUMENTS SOFTWARE LICENSE AGREEMENT (LINUX DRIVER SOFTWARE)
-
-
-INSTALLATION NOTICE: THIS IS A CONTRACT. BEFORE YOU DOWNLOAD THE SOFTWARE AND/OR
-COMPLETE THE INSTALLATION PROCESS, CAREFULLY READ THIS AGREEMENT. BY DOWNLOADING
-THE SOFTWARE AND/OR ENTERING 'y' TO COMPLETE THE INSTALLATION PROCESS, YOU
-CONSENT TO THE TERMS OF THIS AGREEMENT AND YOU AGREE TO BE BOUND BY THIS
-AGREEMENT. IF YOU DO NOT WISH TO BECOME A PARTY TO THIS AGREEMENT AND BE BOUND
-BY ALL OF ITS TERMS AND CONDITIONS, ENTER 'n' OR 'q' TO CANCEL THE INSTALLATION
-PROCESS, DO NOT INSTALL OR USE THE SOFTWARE, AND RETURN THE SOFTWARE (INCLUDING,
-IF APPLICABLE, ALL ACCOMPANYING WRITTEN MATERIALS, ALONG WITH THEIR CONTAINERS)
-WITHIN THIRTY (30) DAYS OF RECEIPT OF THE SOFTWARE TO THE PLACE YOU OBTAINED
-THEM. ALL RETURNS SHALL BE SUBJECT TO NI'S THEN CURRENT RETURN POLICY.
-
-
-1. Definitions. As used in this Agreement, the following terms have the
-following meanings:
-
-A. "You." Means you the individual using the SOFTWARE as well as your employer
-if you are using the SOFTWARE within the scope of your employment.
-
-B. "NI." Means (i) National Instruments Corporation, a company organized under
-the laws of the State of Delaware, U.S.A., if the SOFTWARE is manufactured in
-the U.S.A.; (ii) National Instruments Ireland Resources Ltd., a company
-organized under the laws of the Republic of Ireland, if the SOFTWARE is
-manufactured in the Republic of Ireland; and (iii) National Instruments Europe
-Kft, a limited liability company organized under the laws of Hungary, if the
-SOFTWARE is manufactured in Hungary. If you are not sure where the SOFTWARE is
-manufactured, please contact National Instruments Corporation, 11500 N. Mopac
-Expressway, Austin, Texas, U.S.A. 78759-3504 (Attention: Legal Department).
-
-C. "Software." Means all files (including, but not limited to, libraries,
-modules, and programs) provided with this Agreement and which are being
-installed or otherwise used. SOFTWARE includes all Upgrades that may be provided
-by NI in its discretion.
-
-D. "Upgrade." Means any supplemental or replacement code for computer software
-you have previously licensed from NI.
-
-
-2. Grant of License. In consideration of payment of the applicable fees to NI,
-NI is willing to provide you with a limited, non-exclusive right to use the
-SOFTWARE, but only pursuant to the terms and conditions of this Agreement. The
-SOFTWARE is in "use" when loaded into temporary memory (i.e., RAM) or installed
-into permanent memory (e.g., hard disk, CD-ROM, network storage device, or other
-storage device). Floating, concurrent, or shared use is not permitted under this
-Agreement (i.e., allocating an individual license or one seat of a volume
-license to non-simultaneous use of the SOFTWARE (in whole or part) on multiple
-machines). The specific use rights granted you are as follows:
-
-You may install and use the SOFTWARE on as many computers in your workplace as
-you desire; provided, however, that you separately install the SOFTWARE (using
-the accompanying installer) on each such machine.
-
-Notes. The following applies:
-
-Source Code Component. One component of the SOFTWARE, the Kernel Abstraction
-Layer ("KAL"), is provided to you in source code form. All other components of
-the SOFTWARE are provided to you in object code form. You understand that you
-must configure and compile the KAL for use under this Agreement. This
-configuration and compilation process, however, will be completed on your behalf
-by the installer.
-
-
-3. Restrictions. You may not: (i) for those components of the SOFTWARE
-provided in object code form, reverse engineer, decompile, or disassemble the
-SOFTWARE (except to the extent such foregoing restriction is expressly
-prohibited by applicable law); (ii) sub-license, lease, or rent the SOFTWARE (in
-whole or part); (iii) (other than as expressly permitted under this Agreement)
-distribute in whole or part, modify, or create derivatives of the SOFTWARE; and
-(iv) directly or indirectly, export, re-export, download, or ship the SOFTWARE
-(in whole or part) in violation of the laws and regulations of the U.S.A. and
-the laws and regulations of the applicable jurisdiction in which you use or are
-downloading the SOFTWARE. Under no circumstance is "floating" or shared use
-permitted under this Agreement. Nothing in this Agreement, however, is intended
-to prevent you from creating your own driver interface software for use with
-other NI software and third party hardware; provided, however, that in doing so
-you do not modify or use (in whole or part) any of the SOFTWARE.
-
-
-4. Transfer. The license rights granted hereunder are non-transferable. Except
-for the installation rights granted above, you may not distribute or otherwise
-provide the SOFTWARE to any third party.
-
-
-5. Upgrades. If the SOFTWARE is an Upgrade, you may only use the SOFTWARE if
-you have (at the time you receive the Upgrade) a valid license to use the
-pre-existing SOFTWARE. Further, the license agreement accompanying the Upgrade
-applies to your use of the Upgrade. While you may continue to use the
-pre-existing SOFTWARE, you may only use it on the same machine upon which the
-Upgrade is used and the license that accompanied the pre-existing SOFTWARE will
-continue to apply to your use of the pre-existing SOFTWARE.
-
-
-6. Copyright; No Other Licenses. The SOFTWARE is owned by NI or its suppliers
-and is protected by applicable copyright laws and international treaty
-provisions. Therefore, you must treat the SOFTWARE like any other copyrighted
-material. You may, however, copy the SOFTWARE solely for backup or archival
-purposes. All rights not expressly granted to you in this Agreement are reserved
-to NI. Further, and without limiting the foregoing, no license or any right of
-any kind (whether by express license, implied license, the doctrine of
-exhaustion, or otherwise) is granted under any NI patents (whether identified
-herein or not) or other intellectual property right of NI with respect to any
-other product(s) of NI or of any third party, including without limitation, the
-right to use any of these other products.
-
-
-7. Patent and Trademark Notice. For patents covering National Instruments
-products, refer to the appropriate location: Help>>Patents in your software, the
-patents.txt file on your CD, or ni.com/patents. ComponentWorks, CVI, FieldPoint,
-IMAQ, Lookout, LabVIEW, LabWindows/CVI, Measurement Studio, NI-488.2, NI-CAN,
-NI-DAQ, NI-FBUS, NI-VISA, NI-VXI and TestStand are the trademarks of National
-Instruments Corporation. DIAdem and DASYLab are the trademarks of National
-Instruments Ireland Resources Ltd. Further, all other product and company names
-used herein are (or may be) trademarks or trade names of their respective
-companies.
-
-
-8. Limited Warranty. NI warrants, for your benefit alone, that for a period of
-ninety (90) days from the date the SOFTWARE is shipped to you (i) the SOFTWARE
-will (when used with the applicable NI hardware) perform substantially in
-accordance with the accompanying written materials, and (ii) the medium on which
-the SOFTWARE is recorded will be free from defects in materials and workmanship
-under normal use and service. Any replacement SOFTWARE will be warranted for the
-remainder of the original warranty period or thirty (30) days, whichever is
-longer. Some states/jurisdictions do not allow limitations on duration of an
-express or implied warranty, so the above or any other limitation provided
-herein may not apply to you. In such event, such warranties are limited to the
-minimum warranty period allowed by applicable law. You must obtain a Return
-Material Authorization number from NI before returning the SOFTWARE under
-warranty to NI and you agree to pay expenses for shipment to and from NI. The
-Limited Warranty is void if failure of the SOFTWARE has resulted from accident,
-abuse, misapplication, improper calibration by you, third party products (i.e.,
-hardware or software) used by you which are not intended by National Instruments
-for use with the SOFTWARE, utilization of an improper hardware or software key
-(if applicable), or unauthorized maintenance of the SOFTWARE.
-
-
-9. Customer Remedies. NI's sole obligation (and your sole remedy) with respect
-to the foregoing Limited Warranty shall be to, at NI's option, return the fees
-paid or repair/replace the SOFTWARE, provided that NI receives written notice of
-applicable defects during the warranty period. You may not bring an action to
-enforce your remedies under the foregoing Limited Warranty more than one (1)
-year after the accrual of such cause of action.
-
-
-10. No Other Warranties. EXCEPT AS EXPRESSLY SET FORTH ABOVE, THE SOFTWARE IS
-PROVIDED "AS IS" WITHOUT WARRANTY OF ANY KIND, AND NO OTHER WARRANTIES, EITHER
-EXPRESSED OR IMPLIED ARE MADE WITH RESPECT TO THE SOFTWARE, INCLUDING BUT NOT
-LIMITED TO ANY IMPLIED WARRANTIES OF MERCHANTABILITY, FITNESS FOR A PARTICULAR
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-NI EXPRESSLY DISCLAIMS ANY WARRANTIES NOT STATED HEREIN.
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-
-11. Intellectual Property Liability. NI shall, at its own expense, defend any
-claim resulting from your use of the SOFTWARE as authorized by your license to
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-copyright, or trademark protected by the laws of the U.S.A., Canada, Mexico,
-Japan, Australia, Switzerland, Norway, or the European Union, provided that such
-claim does not arise from your use of the SOFTWARE in combination with equipment
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-NI, and further provided that you notify NI in writing immediately upon your
-obtaining notice of such impending claim and your full cooperation with NI in
-preparing a defense. If you provide to NI the authority, assistance, and
-information NI needs to defend or settle such claim, NI shall pay any final
-award of damages or settlement with respect to such claim and any expense you
-incur at NI's written request, but NI shall not be liable for a settlement made
-without its prior written consent. If the SOFTWARE is held to be infringing of
-the rights stated above and the use thereof is enjoined or if NI believes the
-SOFTWARE may be held to infringe a third party's intellectual property rights,
-NI shall, at its option, either (i) procure for you the right to use the
-SOFTWARE, (ii) replace or modify the SOFTWARE with other software which does not
-infringe, or (iii) receive your return of the SOFTWARE and refund to you the
-license fee payment(s) made by you to NI. The foregoing states your sole remedy
-for, and NI's entire liability and responsibility for, infringement of any
-patent, trademark, copyright, or other intellectual property right relating to
-the SOFTWARE. THIS LIMITED INDEMNITY IS IN LIEU OF ANY OTHER STATUTORY OR
-IMPLIED WARRANTY AGAINST INFRINGEMENT. THE FOREGOING INDEMNIFICATION OBLIGATIONS
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-PARTY MANUFACTURER WITH RESPECT TO ANY CLAIMS FOR INFRINGEMENT INVOLVING THIRD
-PARTY PRODUCTS.
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-
-12. Limitation On Liability. The entire liability of NI and its licensors,
-distributors, and suppliers (including its and their directors, officers,
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-be liable for any damages, including, but not limited to, any special, direct,
-indirect, incidental, exemplary, or consequential damages, expenses, lost
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-possibility of such damages. You acknowledge that the applicable fees and prices
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-is determined by a court of competent jurisdiction in a final, non-appealable
-judgment to be defective and to have directly caused bodily injury, death, or
-property damage, in no event shall NI's liability for property damage exceed
-$500 (U.S.).
-
-
-13. Warning. (1) NI PRODUCTS ARE NOT DESIGNED WITH COMPONENTS AND TESTING FOR
-A LEVEL OF RELIABILITY SUITABLE FOR USE IN OR IN CONNECTION WITH SURGICAL
-IMPLANTS OR AS CRITICAL COMPONENTS IN ANY LIFE SUPPORT SYSTEMS WHOSE FAILURE TO
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-IN ANY APPLICATION, INCLUDING THE ABOVE, RELIABILITY OF OPERATION OF THE
-SOFTWARE PRODUCTS CAN BE IMPAIRED BY ADVERSE FACTORS, INCLUDING BUT NOT LIMITED
-TO FLUCTUATIONS IN ELECTRICAL POWER SUPPLY, COMPUTER HARDWARE MALFUNCTIONS,
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-HARDWARE COMPATIBILITY PROBLEMS, MALFUNCTIONS OR FAILURES OF ELECTRONIC
-MONITORING OR CONTROL DEVICES, TRANSIENT FAILURES OF ELECTRONIC SYSTEMS
-(HARDWARE AND/OR SOFTWARE), UNANTICIPATED USES OR MISUSES, OR ERRORS ON THE PART
-OF THE USER OR APPLICATIONS DESIGNER (ADVERSE FACTORS SUCH AS THESE ARE
-HEREAFTER COLLECTIVELY TERMED "SYSTEM FAILURES"). ANY APPLICATION WHERE A SYSTEM
-FAILURE WOULD CREATE A RISK OF HARM TO PROPERTY OR PERSONS (INCLUDING THE RISK
-OF BODILY INJURY AND DEATH) SHOULD NOT BE RELIANT SOLELY UPON ONE FORM OF
-ELECTRONIC SYSTEM DUE TO THE RISK OF SYSTEM FAILURE. TO AVOID DAMAGE, INJURY, OR
-DEATH, THE USER OR APPLICATION DESIGNER MUST TAKE REASONABLY PRUDENT STEPS TO
-PROTECT AGAINST SYSTEM FAILURES, INCLUDING BUT NOT LIMITED TO BACK-UP OR SHUT
-DOWN MECHANISMS. BECAUSE EACH END-USER SYSTEM IS CUSTOMIZED AND DIFFERS FROM
-NI'S TESTING PLATFORMS AND BECAUSE A USER OR APPLICATION DESIGNER MAY USE NI
-PRODUCTS IN COMBINATION WITH OTHER PRODUCTS IN A MANNER NOT EVALUATED OR
-CONTEMPLATED BY NI, THE USER OR APPLICATION DESIGNER IS ULTIMATELY RESPONSIBLE
-FOR VERIFYING AND VALIDATING THE SUITABILITY OF NI PRODUCTS WHENEVER NI PRODUCTS
-ARE INCORPORATED IN A SYSTEM OR APPLICATION, INCLUDING, WITHOUT LIMITATION, THE
-APPROPRIATE DESIGN, PROCESS, AND SAFETY LEVEL OF SUCH SYSTEM OR APPLICATION.
-
-
-14. U.S. Government Restricted Rights. If you are an agency, department, or
-other entity of the United States Government ("Government"), the use,
-duplication, reproduction, release, modification, disclosure, or transfer of the
-SOFTWARE, or any related documentation of any kind, including technical data or
-manuals, is restricted in accordance with Federal Acquisition Regulation 12.212
-(as amended or supplanted) for civilian agencies and Defense Federal Acquisition
-Regulation Supplement 227.7202 (as amended or supplanted) for military agencies.
-The SOFTWARE is commercial computer software and the related documentation is
-commercial computer software documentation. The use of the SOFTWARE and related
-documentation is further restricted in accordance with the terms of this
-Agreement, or any modification hereto. The Contractor/Manufacturer is National
-Instruments Corporation, 11500 North Mopac Expressway, Austin, Texas, U.S.A.,
-78759-3504.
-
-
-15. Compliance. You agree to make all applicable records available for review
-by NI during your normal business hours so as to permit NI (upon reasonable
-notice to you) to verify your compliance with the terms and conditions of this
-Agreement. Further, if you are a business or other entity, you agree that upon
-the request of NI or NI's authorized representative, you will promptly document
-and certify in writing to NI that your and your employees' use of the SOFTWARE
-complies with the terms and conditions of this Agreement. NI may (upon written
-notice) inspect your use of the SOFTWARE during your normal business hours to
-ensure your compliance with this Agreement. If the results of any such
-inspection indicate the underpayment by you of applicable fees due and payable
-to NI, you shall: (i) immediately pay such amounts to NI and (ii) reimburse NI
-for the cost of such inspection.
-
-
-16. Termination. This Agreement shall automatically terminate upon failure by
-you to comply with its terms. Upon termination of this Agreement, regardless of
-the reason, you must destroy all copies of the SOFTWARE.
-
-
-17. General.
-
-A. If the SOFTWARE is manufactured in the U.S.A., (i) this Agreement is
-governed by the laws of the State of Texas, U.S.A., exclusive of any provisions
-of the United Nations Convention on the International Sale of Goods, and without
-regard to principles of conflicts of law and (ii) the non-exclusive venue for
-all actions under this Agreement shall be in the courts located in Travis
-County, Texas, U.S.A. and the parties agree to submit to the jurisdiction of
-such courts.
-
-B. If the SOFTWARE is manufactured in the Republic of Ireland or the SOFTWARE
-is DIAdem, DIAdem Clip, DIAdem Insight, or DASYLab, (i) this Agreement is
-governed by the laws of the Republic of Ireland, exclusive of any provisions of
-the United Nations Convention on the International Sale of Goods, and without
-regard to principles of conflicts of law and (ii) the non-exclusive venue for
-all actions under this Agreement shall be in the courts located in Dublin, the
-Republic of Ireland and the parties agree to submit to the jurisdiction of such
-courts.
-
-C. If the SOFTWARE is manufactured in Hungary, (i) this Agreement is governed
-by the laws of Hungary, exclusive of any provisions of the United Nations
-Convention on the International Sale of Goods, and without regard to principles
-of conflicts of law and (ii) the non-exclusive venue for all actions under this
-Agreement shall be in the courts located in Hungary and the parties agree to
-submit to the jurisdiction of such courts.
-
-D. This Agreement constitutes the complete agreement between you and NI
-regarding the SOFTWARE and it supersedes any oral or written proposals, prior
-agreements, purchase orders, or any other communication between you and NI
-relating to the subject matter of this Agreement.
-
-E. If any action is brought by either party to this Agreement against the
-other regarding the subject matter hereof, the prevailing party shall be
-entitled to recover, in addition to any relief granted, reasonable attorney fees
-and court costs. If any provision of this Agreement is held invalid, the
-offending clause will be modified so as to be enforceable and, as modified,
-shall be fully enforced, and the remainder of this Agreement will continue in
-full force and effect. If you are downloading the SOFTWARE, you represent and
-warrant that you are not located in or under the control of any country which
-the export laws and regulations of such country or of the United States prohibit
-the exportation of the SOFTWARE to.
-
-
-(c) 2004-2005 National Instruments Corporation. All Rights Reserved.
-371460B-01
-March 2005
diff --git a/licenses/noweb b/licenses/noweb
new file mode 100644
index 000000000..e1f338458
--- /dev/null
+++ b/licenses/noweb
@@ -0,0 +1,22 @@
+Noweb is copyright 1989-2000 by Norman Ramsey.  All rights reserved.
+
+Noweb is protected by copyright.  It is not public-domain
+software or shareware, and it is not protected by a ``copyleft''
+agreement like the one used by the Free Software Foundation.
+
+Noweb is available free for any use in any field of endeavor.  You may
+redistribute noweb in whole or in part provided you acknowledge its
+source and include this COPYRIGHT file.  You may modify noweb and
+create derived works, provided you retain this copyright notice, but
+the result may not be called noweb without my written consent.
+
+You may sell noweb if you wish.  For example, you may sell a CD-ROM
+including noweb.
+
+You may sell a derived work, provided that all source code for your
+derived work is available, at no additional charge, to anyone who buys
+your derived work in any form.  You must give permisson for said
+source code to be used and modified under the terms of this license.
+You must state clearly that your work uses or is based on noweb and
+that noweb is available free of change.  You must also request that
+bug reports on your work be reported to you.
diff --git a/licenses/oncotator b/licenses/oncotator
deleted file mode 100644
index 0528987f4..000000000
--- a/licenses/oncotator
+++ /dev/null
@@ -1,46 +0,0 @@
-By downloading the PROGRAM you agree to the following terms of use:
-
-BROAD INSTITUTE SOFTWARE LICENSE AGREEMENT
-FOR ACADEMIC NON-COMMERCIAL RESEARCH PURPOSES ONLY
-
-This Agreement is made between the Broad Institute, Inc. with a principal address at 7 Cambridge Center, Cambridge, MA 02142 ("BROAD") and the LICENSEE and is effective at the date the downloading is completed ("EFFECTIVE DATE").
-
-WHEREAS, LICENSEE desires to license the PROGRAM, as defined hereinafter, and BROAD wishes to have this PROGRAM utilized in the public interest, subject only to the royalty-free, nonexclusive, nontransferable license rights of the United States Government pursuant to 48 CFR 52.227-14; and 
-
-WHEREAS, LICENSEE desires to license the PROGRAM and BROAD desires to grant a license on the following terms and conditions.
-
-NOW, THEREFORE, in consideration of the promises and covenants made herein, the parties hereto agree as follows:
-
-1. DEFINITIONS
-1.1 "PROGRAM" shall mean the object code and source code known as Oncotator 1.0 and related documentation, if any, as they exist on the EFFECTIVE DATE and can be downloaded from http://www.broadinstitute.org/cancer/cga/oncotator on the EFFECTIVE DATE.  BROAD acknowledges that the PROGRAM employs one or more public domain code(s) that are freely available for public use.
-
-2. LICENSE
-2.1   Grant. Subject to the terms of this Agreement, BROAD hereby grants to LICENSEE, solely for academic non-commercial research purposes, a non-exclusive, non-transferable license to: (a) download, execute and display the PROGRAM and (b) create bug fixes and modify the PROGRAM.  LICENSEE hereby automatically grants to BROAD a non-exclusive, royalty-free, irrevocable license to any LICENSEE bug fixes or modifications to the PROGRAM with unlimited rights to sublicense and/or distribute.  LICENSEE agrees to provide any such modifications and bug fixes to BROAD promptly upon their creation.  The LICENSEE may apply the PROGRAM in a pipeline to data owned by users other than the LICENSEE and provide these users the results of the PROGRAM provided LICENSEE does so for academic non-commercial purposes only.  For clarification purposes, academic sponsored research is not a commercial use under the terms of this Agreement.
-2.2  No Sublicensing or Additional Rights. LICENSEE shall not sublicense or distribute the PROGRAM, in whole or in part, without prior written permission from BROAD.  LICENSEE shall ensure that all of its users agree to the terms of this Agreement.  LICENSEE further agrees that it shall not put the PROGRAM on a network, server, or other similar technology that may be accessed by anyone other than the LICENSEE and its employees and users who have agreed to the terms of this agreement.
-2.3  License Limitations. Nothing in this Agreement shall be construed to confer any rights upon LICENSEE by implication, estoppel, or otherwise to any computer software, trademark, intellectual property, or patent rights of BROAD, or of any other entity, except as expressly granted herein. LICENSEE agrees that the PROGRAM, in whole or part, shall not be used for any commercial purpose, including without limitation, as the basis of a commercial software or hardware product or to provide services. LICENSEE further agrees that the PROGRAM shall not be copied or otherwise adapted in order to circumvent the need for obtaining a license for use of the PROGRAM.
-
-3. OWNERSHIP OF INTELLECTUAL PROPERTY
-LICENSEE acknowledges that title to the PROGRAM shall remain with BROAD. The PROGRAM is marked with the following BROAD copyright notice and notice of attribution to contributors. LICENSEE shall retain such notice on all copies.  LICENSEE agrees to include appropriate attribution if any results obtained from use of the PROGRAM are included in any publication.
-
-Copyright 2014 Broad Institute, Inc.
-Notice of attribution:  The Oncotator 1.0 program was made available through the generosity of the Broad Institute, Inc.
-
-LICENSEE shall not use any trademark or trade name of BROAD, or any variation, adaptation, or abbreviation, of such marks or trade names, or any names of officers, faculty, students, employees, or agents of BROAD except as states above for attribution purposes.
-
-4. INDEMNIFICATION
-LICENSEE shall indemnify, defend, and hold harmless BROAD, and their respective officers, faculty, students, employees, associated investigators and agents, and their respective successors, heirs and assigns, ("Indemnitees"), against any liability, damage, loss, or expense (including reasonable attorney fees and expenses) incurred by or imposed upon any of the Indemnitees in connection with any claims, suits, actions, demands or judgments arising out of any theory of liability (including, without limitation, actions in the form of tort, warranty, or strict liability and regardless of whether such action has any factual basis) pursuant to any right or license granted under this Agreement.
-
-5. NO REPRESENTATIONS OR WARRANTIES
-THE PROGRAM IS DELIVERED "AS IS."  BROAD MAKES NO REPRESENTATIONS OR WARRANTIES OF ANY KIND CONCERNING THE PROGRAM OR THE COPYRIGHT, EXPRESS OR IMPLIED, INCLUDING, WITHOUT LIMITATION, WARRANTIES OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE, NONINFRINGEMENT, OR THE ABSENCE OF LATENT OR OTHER DEFECTS, WHETHER OR NOT DISCOVERABLE. BROAD EXTENDS NO WARRANTIES OF ANY KIND AS TO PROGRAM CONFORMITY WITH WHATEVER USER MANUALS OR OTHER LITERATURE MAY BE ISSUED FROM TIME TO TIME.  IN NO EVENT SHALL BROAD OR ITS RESPECTIVE DIRECTORS, OFFICERS, EMPLOYEES, AFFILIATED INVESTIGATORS AND AFFILIATES BE LIABLE FOR INCIDENTAL OR CONSEQUENTIAL DAMAGES OF ANY KIND, INCLUDING, WITHOUT LIMITATION, ECONOMIC DAMAGES OR INJURY TO PROPERTY AND LOST PROFITS, REGARDLESS OF WHETHER BROAD SHALL BE ADVISED, SHALL HAVE OTHER REASON TO KNOW, OR IN FACT SHALL KNOW OF THE POSSIBILITY OF THE FOREGOING.
-
-6. ASSIGNMENT
-This Agreement is personal to LICENSEE and any rights or obligations assigned by LICENSEE without the prior written consent of BROAD shall be null and void.
-
-7. MISCELLANEOUS
-7.1 Export Control. LICENSEE gives assurance that it will comply with all United States export control laws and regulations controlling the export of the PROGRAM, including, without limitation, all Export Administration Regulations of the United States Department of Commerce. Among other things, these laws and regulations prohibit, or require a license for, the export of certain types of software to specified countries.
-7.2 Termination. LICENSEE shall have the right to terminate this Agreement for any reason upon prior written notice to BROAD. If LICENSEE breaches any provision hereunder, and fails to cure such breach within thirty (30) days, BROAD may terminate this Agreement immediately. Upon termination, LICENSEE shall provide BROAD with written assurance that the original and all copies of the PROGRAM have been destroyed, except that, upon prior written authorization from BROAD, LICENSEE may retain a copy for archive purposes.
-7.3 Survival. The following provisions shall survive the expiration or termination of this Agreement: Articles 1, 3, 4, 5 and Sections 2.2, 2.3, 7.3, and 7.4.
-7.4 Notice. Any notices under this Agreement shall be in writing, shall specifically refer to this Agreement, and shall be sent by hand, recognized national overnight courier, confirmed facsimile transmission, confirmed electronic mail, or registered or certified mail, postage prepaid, return receipt requested.  All notices under this Agreement shall be deemed effective upon receipt.
-7.5 Amendment and Waiver; Entire Agreement. This Agreement may be amended, supplemented, or otherwise modified only by means of a written instrument signed by all parties. Any waiver of any rights or failure to act in a specific instance shall relate only to such instance and shall not be construed as an agreement to waive any rights or fail to act in any other instance, whether or not similar. This Agreement constitutes the entire agreement among the parties with respect to its subject matter and supersedes prior agreements or understandings between the parties relating to its subject matter.
-7.6 Binding Effect; Headings. This Agreement shall be binding upon and inure to the benefit of the parties and their respective permitted successors and assigns. All headings are for convenience only and shall not affect the meaning of any provision of this Agreement.
-7.7 Governing Law. This Agreement shall be construed, governed, interpreted and applied in accordance with the internal laws of the Commonwealth of Massachusetts, U.S.A., without regard to conflict of laws principles.
diff --git a/licenses/opal b/licenses/opal
deleted file mode 100644
index 182ba127f..000000000
--- a/licenses/opal
+++ /dev/null
@@ -1,38 +0,0 @@
-COPYRIGHT AND LICENCE
-
-Copyright (c) 2005-2008 The Regents of the University of California.
-All rights reserved.
-
-Redistribution and use in source and binary forms, with or
-without modification, are permitted provided that the following
-conditions are met:
-
-1. Redistributions of source code must retain the above copyright
-notice, this list of conditions and the following disclaimer.
-
-2. Redistributions in binary form must reproduce the above
-copyright notice, this list of conditions and the following
-disclaimer in the documentation and/or other materials provided
-with the distribution.
-
-3. All advertising materials mentioning features or use of this
-software must display the following acknowledgement: This product
-includes software developed by the San Diego Supercomputer Center
-, the National Biomedical Computation Resource, and their contributors.
-
-4. Neither the names of the Centers nor the names of the contributors
-may be used to endorse or promote products derived from this
-software without specific prior written permission.
-
-THIS SOFTWARE IS PROVIDED BY THE REGENTS AND CONTRIBUTORS ``AS IS''
-AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED
-TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A
-PARTICULAR PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE REGENTS
-OR CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL,
-SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT
-LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF
-USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED
-AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT
-LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN
-ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE
-POSSIBILITY OF SUCH DAMAGE.
diff --git a/licenses/phaser b/licenses/phaser
deleted file mode 100644
index e03a57a14..000000000
--- a/licenses/phaser
+++ /dev/null
@@ -1,280 +0,0 @@
-Software: PHASER
-Version: 1.3
-
-This End User Licence Agreement is a legal agreement between you the
-"Licensee" (in your capacity as an individual and as an agent for your
-institution or other entity) 
-and
-Cambridge University Technical Services Limited ("CUTS") whose registered
-office is at 16 Mill Lane, Cambridge, CB2 1SB UK.
-
-CUTS is a company wholly owned by the Chancellor, Masters and Scholars of the
-University of Cambridge which holds title in intellectual property rights
-including in the Software and carries on trading, business and technology
-transfer transactions on behalf of the University of Cambridge.
-
-CUTS is the entire legal and beneficial owner and licensor of the Software and
-desires to grant on the Software non-exclusive, restricted-use licences for
-in-house use to appropriate academic and non-commercial third parties.  
-
-Downloading the Software from its internet publication site (restricted access
-via user ID and password) at
-http://www-structmed.cimr.cam.ac.uk/phaser/download.html, installing, or
-using of the Software by you indicates your agreement to be bound by the terms
-and conditions of this Agreement.  If you do not agree to these terms and
-conditions, do not download, install or use the Software.
-
-AGREED TERMS
-
-1. DEFINITIONS
-
-1.1 In this Agreement the following words and phrases shall, unless the
-context otherwise requires, have the following meanings:
-
-Commencement Date means the initial date of download of the Software from its
-internet publication site by the Licensee; 
-
-Derivatives means computer programs in machine readable object code or source
-code form developed or otherwise acquired by the Licensee which are a
-modification of, enhancement to, derived from or based upon the Software;
-
-Intellectual Property Rights means all patents, copyrights, design rights,
-trade marks, service marks, trade secrets, know-how, database rights and other
-rights in the nature of intellectual property rights (whether registered or
-unregistered) and all applications for the same, anywhere in the world;
-
-Parties means CUTS and the Licensee and "Party" shall mean either of them;
-
-Software means the computer program and version listed at the head of this
-Agreement.
-
-2. GRANT OF LICENCE
-
-2.1 CUTS hereby grants to the Licensee and the Licensee hereby accepts a
-non-exclusive, non-transferable, royalty-free licence, commencing on the
-Commencement Date and for a term of five years therefrom, to download, install
-and use the Software subject to the following terms and conditions:
-
-(a) the Licensee may use the Software solely for its internal use and the
-Licensee shall not sell, give, disclose, lend, transfer, sublicense or
-otherwise distribute the Software to any third party, or allow the Software to
-be accessed over the internet or in any other manner that would allow access
-to the Software by anyone other than the Licensee's employees (and consultants
-and contractors provided such use is solely for the Licensee's internal use
-and subject to the provisions of this Agreement); 
-
-(b) the Licensee may create Derivatives solely for its own internal use but
-shall not distribute the Software or any Derivatives in whole or in part to
-any third party; 
-
-(c) the Software may be installed and used only on computers owned or leased
-by the Licensee;
-
-(d) the Licensee may copy the Software solely to the extent necessary to
-exercise this Licence, and for backup, disaster recovery and archival
-purposes, provided that the Licensee shall retain on all copies of the
-Software the following copyright notice: © 2000-2005. Cambridge University
-Technical Services Limited.  All rights reserved.
-
-3. INTELLECTUAL PROPERTY RIGHTS
-
-3.1 The Licensee acknowledges that all Intellectual Property Rights in the
-Software and any copies thereof belong and shall belong to CUTS and the
-Licensee shall have no rights in or to the Software other than the right to
-use it in accordance with the terms of the Licence in this Agreement.
-
-3.2 Title to and ownership of any portion of the Software incorporated into
-Derivatives shall at all times remain with CUTS and the Licensee shall not
-have any title or ownership interest therein.
-
-3.3 Title to and ownership of any portion of Derivatives created by the
-Licensee and not owned by CUTS pursuant to Clauses 3.1 and 3.2 above shall be
-held by the Licensee.  Nothing contained in this Licence shall be construed to
-limit CUTS rights to modify or to develop other derivatives of the Software
-which are similar to or offer the same or similar improvements as any
-Derivatives developed by the Licensee.
-
-3.4 Error fixes, bug fixes, technical suggestions, comments and suggested
-improvements to the Software and its code are welcome by the authors of the
-Software and CUTS, and in agreeing to provide these to the authors or to CUTS
-the Licensee hereby assigns the Intellectual Property Rights in error fixes,
-bug fixes, or technical improvements to CUTS which are communicated in any
-manner or medium to the authors of the Software or CUTS with a reservation of
-use of those improvements and suggestions by the Licensee subject to the terms
-and conditions of the Licence in this Agreement.
-
-4. NO MAINTENANCE OR SUPPORT
-
-4.1 CUTS is under no obligation whatsoever to:
-
-(a) provide maintenance or support for the Software; or
-
-(b) notify the Licensee of error fixes, bug fixes, patches, or upgrades to
-the features, functionality or performance of the Software ("Enhancements")
-(if any), whether developed by CUTS or third parties.  If, in its sole
-discretion, CUTS makes an Enhancement available to the Licensee and CUTS does
-not separately enter into a written licence agreement with the Licensee
-relating to such bug fix, patch or upgrade, then it shall be deemed
-incorporated into the Software and subject to this Agreement.
-
-5. DISCLAIMER OF WARRANTIES
-
-5.1 CUTS warrants that the Software will conform substantially with its
-functional specifications.  Otherwise the Software is supplied "as is" without
-warranty of any kind.  CUTS, its licensors and its employees:
-
-(a) disclaim any warranties, express or implied, including but not limited to
-any implied warranties of merchantability, fitness for a particular purpose,
-title or non-infringement of third party rights;
-
-(b) do not assume any legal liability or responsibility for the accuracy,
-completeness, or usefulness of the Software;
-
-(c) do not represent that use of the Software will not infringe privately
-owned rights;
-
-(d) do not warrant that the Software will function uninterrupted, that it is
-error-free or that any errors will be corrected.
-
-6. LIMITATION OF LIABILITY
-
-6.1 The Software is provided for academic non-commercial purposes only.
-Therefore, in no event will CUTS or its licensors or its employees be liable
-to the Licensee for any indirect, incidental, consequential, special or
-punitive damages of any kind or nature, including but not limited to loss of
-profits or loss of data, for any reason whatsoever, whether such liability is
-asserted on the basis of contract, tort (including negligence or strict
-liability), or otherwise, even if CUTS has been warned of the possibility of
-such loss or damages.
-
-6.2 The limitations and exclusions in this Agreement shall not apply in
-respect of claims for personal injury or death caused by the negligence of
-CUTS, its licensors or its employees or in respect of fraud or fraudulent
-misrepresentation.  
-
-7. INDEMNITY
-
-7.1 The Licensee shall indemnify CUTS, the Software authors, the Software
-sponsors, and their agents, officers, and employees, against any and all
-claims, suits, losses, damages, costs, fees, and expenses arising out of or in
-connection with any claim or threatened claim by any third party relating to
-or arising from the use of the Software by the Licensee.  The Licensee shall
-pay all costs incurred by CUTS in enforcing this provision.
-
-8. TERM AND TERMINATION
-
-8.1 This Agreement and the Licence granted herein shall come into effect
-on the Commencement Date and will continue for the duration of five years
-therefrom unless terminated by CUTS in accordance with this Agreement.  If the
-Licensee breaches any term of this Agreement, and fails to cure such breach
-within thirty (30) days of the date of written notice, this Agreement shall
-immediately terminate.  Upon such termination the Licensee shall immediately
-cease using the Software, return to CUTS or destroy all copies of the
-Software, and provide CUTS with written certification of the Licensee's
-compliance with the foregoing.  Termination shall not relieve the Licensee
-from its obligations arising prior to such termination.  Notwithstanding any
-provision of this Agreement to the contrary, Sections 3, 5, 6, 7, 8, 9, 10,
-13, 14 and 18 shall survive termination of this Agreement.  
-
-9. CONFIDENTIALITY
-
-9.1 The Licensee agrees and undertakes that during the term of the Licence in
-this Agreement and thereafter it will keep confidential all, and will not use
-for its own purposes nor without the prior written consent of CUTS disclose to
-any third party any information of a confidential nature (including trade
-secrets and information of commercial value) which may become known to the
-Licensee and which relates to CUTS unless such information is public knowledge
-or already known to the Licensee at the time of disclosure or subsequently
-becomes public knowledge other by breach of the Licence in this Agreement or
-subsequently comes lawfully into the possession of the Licensee from a third
-party.
-
-10. NO SUBLICENSING AND NO ASSIGNMENT 
-
-10.1 The Licensee shall have no right to sub-license or to assign,
-transfer, charge or deal in any other manner the benefit or burden of the
-Licence in this Agreement in whole or in part or to allow the Software to
-become the subject of any charge, lien or encumbrance without the prior
-written consent of CUTS such consent may be withheld without giving any
-reasons.
-
-11. WAIVER
-
-11.1 No forbearance or delay by either party in enforcing its rights will
-prejudice or restrict the rights of that party, and no waiver of any such
-rights or of any breach of any contractual terms will be deemed to be a waiver
-of any other right or of any later breach.
-
-12. SEVERABILITY
-
-12.1 If any provision of the Licence in this Agreement is judged to be
-illegal or unenforceable, the continuation in full force and effect of the
-remainder of the provisions will not be prejudiced.
-
-13. NO AGENCY OR PARTNERSHIP
-
-13.1 Nothing contained or implied in this Agreement constitutes a Party the
-partner, agent, or legal representative of another party or of the other Party
-for any purpose or creates any partnership, agency or trust, and no Party has
-any authority to bind the other Party in any way.
-
-14. THE CONTRACTS (RIGHTS OF THIRD PARTIES) ACT 1999
-
-14.1 The Contracts (Rights of Third Parties) Act 1999 shall not apply to
-this Agreement and nothing in this Agreement shall confer or purport to confer
-on or operate to give any third Party any benefit or any right to enforce any
-term of this Agreement.
-
-15. NOTICES
-
-15.1 Any notice to be given under this Agreement shall be in writing and
-delivered by hand, prepaid registered post or facsimile to a Party at the
-address set out at the head of this Agreement or to such other address or fax
-number as any Party may specify in writing to another.  Notices are deemed to
-have been given:
-
-(a) if delivered by hand, at the time of delivery unless delivered after 5pm
-in the place of receipt or on a non-business day, in which case the notice is
-deemed to have been given at 9am the next business day;
-
-(b) if sent by registered post from within the United Kingdom, three
-business days after posting (or seven business days if posted from outside the
-United Kingdom); and
-
-(c) if sent by facsimile, at the time the facsimile is received shown in
-the transmission report as the time that the whole facsimile was sent unless
-received after 5pm in the place of receipt or on a non-business day, in which
-case the notice is deemed to have been given at 9am the next business day.
-Any notice served by facsimile transmission shall be confirmed by post.
-
-16. ENTIRE AGREEMENT
-
-16.1 This Agreement constitutes the entire agreement and understanding of the
-Parties and supersedes all negotiations, understandings or previous agreement
-between the Parties relating to the subject matter of this Agreement.
-
-17. GOVERNING LAW
-
-17.1 This Agreement and any documents to be entered into pursuant to it
-shall be governed by and construed in accordance with English law and each
-Party irrevocably submits to the exclusive jurisdiction of the courts of
-England over any claim or matter arising under or in connection with this
-Agreement and the documents entered into pursuant to it.
-
-18. EXPORT CONTROL REGULATIONS
-
-18.1 'Export Control Regulations' means any United Nations trade sanctions
-or EU or UK legislation or regulation, from time to time in force, which
-impose arms embargoes or control of export of goods, technology or software.
-
-18.2 The Licensee shall ensure that, in using the Software it shall not and
-nor shall its employees breach or compromise directly of indirectly compliance
-with any Export Control Regulations.
-
-
-
-If you have any questions or feedback concerning the Software, contact
-University of Cambridge, Department of Haematology, Cambridge Institute for
-Medical Research, Wellcome Trust/MRC Building, Cambridge CB2 0XY UK.  
-Attn: Professor Randy Read, or via email at cimr-phaser@lists.cam.ac.uk
-
diff --git a/licenses/phaser-com b/licenses/phaser-com
deleted file mode 100644
index 3c1b3a03c..000000000
--- a/licenses/phaser-com
+++ /dev/null
@@ -1,290 +0,0 @@
-Software: PHASER
-Version: 1.3
-
-This End User Licence Agreement ("Agreement") is a legal agreement between
-your company the "Licensee" 
-and
-CAMBRIDGE UNIVERSITY TECHNICAL SERVICES LIMITED ("CUTS") whose registered
-office is at 16 Mill Lane, Cambridge, CB2 1SB UK.
-
-CUTS is a company wholly owned by the Chancellor, Masters and Scholars of the
-University of Cambridge which holds title in intellectual property rights
-including in the Software and carries on trading, business and technology
-transfer transactions on behalf of the University of Cambridge.
-
-CUTS is the entire legal and beneficial owner and licensor of the Software and
-is willing to license use of the Software by the Licensee.  As a condition
-precedent to the execution and performance of this Licence, the Licensee
-(and/or any of its Affiliates, if applicable, the Licensee and its Affiliates
-collectively referred to as the "Licensee" for the purposes of this Agreement)
-will have paid up annual fees to the PHENIX Industry Consortium for use of
-software, including the Software which is the subject of the Licence in this
-Agreement, which has been assembled for the PHENIX Industry Consortium.
-
-Downloading the Software from its internet publication site (restricted access
-via user ID and password) at
-http://www-structmed.cimr.cam.ac.uk/phaser/download.html, installing, or use
-of the Software by the Licensee indicates the Licensee's agreement to be bound
-by the terms and conditions of this Agreement.  If the Licensee does not agree
-to these terms and conditions, the Licensee may not download, install or use
-the Software.
-
-AGREED TERMS
-
-1. DEFINITIONS
-
-1.1 In this Agreement the following words and phrases shall, unless the
-context otherwise requires, have the following meanings:
-
-Commencement Date means the initial date of download of the Software from its
-internet publication site by the Licensee; 
-
-Derivatives means computer programs in machine readable object code or source
-code form developed or otherwise acquired by the Licensee which are a
-modification of, enhancement to, derived from or based upon the Software;
-
-Fee means the annual licence fee payable by the Licensee to the PHENIX
-Industry Consortium;
-
-Intellectual Property Rights means all patents, copyrights, design rights,
-trade marks, service marks, trade secrets, know-how, database rights and other
-rights in the nature of intellectual property rights (whether registered or
-unregistered) and all applications for the same, anywhere in the world;
-
-Parties means CUTS and the Licensee and "Party" shall mean either of them;
-
-Software means the computer program and version listed at the head of this
-Agreement.
-
-2. GRANT OF LICENCE
-
-2.1 In consideration of the Fee, CUTS hereby grants to the Licensee a
-non-exclusive, non-transferable, royalty-free licence, commencing on the
-Commencement Date and for the duration of payment of the Fee, to download,
-install and use the Software subject to the following terms and conditions:
-
-(a) the Licensee may use the Software solely for its internal use and the
-Licensee shall not sell, give, disclose, lend, transfer, sublicense or
-otherwise distribute the Software to any third party, or allow the Software to
-be accessed over the internet or in any other manner that would allow access
-to the Software by anyone other than the Licensee's employees (and consultants
-and contractors provided such use is solely for the Licensee's internal use
-and subject to the provisions of this Agreement); 
-
-(b) the Licensee may create Derivatives solely for its own internal use but
-shall not distribute the Software or any Derivatives in whole or in part to
-any third party; 
-
-(c) the Software may be installed and used only on computers owned or leased
-by the Licensee;
-
-(d) the Licensee may copy the Software solely to the extent necessary to
-exercise this Licence, and for backup, disaster recovery and archival
-purposes, provided that the Licensee shall retain on all copies of the
-Software the following copyright notice: © 2000-2005. Cambridge University
-Technical Services Limited.  All rights reserved.
-
-3. INTELLECTUAL PROPERTY RIGHTS
-
-3.1 The Licensee acknowledges that all Intellectual Property Rights in the
-Software belong and shall belong to CUTS and the Licensee shall have no rights
-in or to the Software other than the right to use it in accordance with the
-terms of the Licence in this Agreement.
-
-3.2 Title to and ownership of any portion of the Software incorporated into
-Derivatives shall at all times remain with CUTS and the Licensee shall not
-have any title or ownership interest therein.
-
-3.3 Title to and ownership of any portion of Derivatives created by the
-Licensee and not owned by CUTS pursuant to Clauses 3.1 and 3.2 above shall be
-held by the Licensee.  Nothing contained in this Licence shall be construed to
-limit CUTS rights to modify or to develop other derivatives of the Software
-which are similar to or offer the same or similar improvements as any
-Derivatives developed by the Licensee.
-
-3.4 Error fixes, bug fixes, technical suggestions, comments and suggested
-improvements to the Software and its code are welcome by the authors of the
-Software and CUTS, and in agreeing to provide these to the authors or to CUTS
-the Licensee hereby assigns the Intellectual Property Rights in error fixes,
-bug fixes, or technical improvements to CUTS which are communicated in any
-manner or medium to the authors of the Software or CUTS with a reservation of
-use of those improvements and suggestions by the Licensee subject to the terms
-and conditions of the Licence in this Agreement.
-
-4. NO MAINTENANCE OR SUPPORT
-
-4.1 CUTS is under no obligation whatsoever to:
-
-(a) provide maintenance or support for the Software; or
-
-(b) notify the Licensee of error fixes, bug fixes, patches, or upgrades to
-the features, functionality or performance of the Software ("Enhancements")
-(if any), whether developed by CUTS or third parties.  If, in its sole
-discretion, CUTS makes an Enhancement available to the Licensee and CUTS does
-not separately enter into a written licence agreement with the Licensee
-relating to such bug fix, patch or upgrade, then it shall be deemed
-incorporated into the Software and subject to this Agreement.
-
-5. DISCLAIMER OF WARRANTIES
-
-5.1 CUTS warrants that the Software will conform substantially with its
-functional specifications.  Otherwise the Software is supplied "as is" without
-warranty of any kind.  CUTS, its licensors and its employees:
-
-(a) disclaim any warranties, express or implied, including but not limited to
-any implied warranties of merchantability, fitness for a particular purpose,
-title or non-infringement of third party rights;
-
-(b) do not assume any legal liability or responsibility for the accuracy,
-completeness, or usefulness of the Software;
-
-(c) do not represent that use of the Software will not infringe privately
-owned rights;
-
-(d) do not warrant that the Software will function uninterrupted, that it is
-error-free or that any errors will be corrected.
-
-6. LIMITATION OF LIABILITY
-
-6.1 In no event will CUTS or its licensors or its employees be liable to
-the Licensee for any indirect, incidental, consequential, special or punitive
-damages of any kind or nature, including but not limited to loss of profits or
-loss of data, for any reason whatsoever, whether such liability is asserted on
-the basis of contract, tort (including negligence or strict liability), or
-otherwise, even if CUTS has been warned of the possibility of such loss or
-damages.  In no event shall CUTS' liability arising from or in connection with
-this Agreement exceed a sum equivalent to the annual Fee paid by the Licensee
-to the PHENIX Industry Consortium for use of the Software.
-
-6.2 The limitations and exclusions in this Agreement shall not apply in
-respect of claims for personal injury or death caused by the negligence of
-CUTS, its licensors or its employees or in respect of fraud or fraudulent
-misrepresentation.
-
-7. INDEMNITY
-
-7.1 The Licensee shall indemnify CUTS, the Software authors, the Software
-sponsors, and their agents, officers, and employees, against any and all
-claims, suits, losses, damages, costs, fees, and expenses arising out of or in
-connection with any claim or threatened claim by any third party relating to
-or arising from the use of the Software by the Licensee.  The Licensee shall
-pay all costs incurred by CUTS in enforcing this provision.
-
-8. TERM AND TERMINATION
-
-8.1 This Agreement and the Licence granted herein shall come into effect
-on the Commencement Date and will continue for the duration of payment of the
-Fee unless terminated by CUTS in accordance with this Agreement.  If the
-Licensee breaches any term of this Agreement, and fails to cure such breach
-within thirty (30) days of the date of written notice, this Agreement shall
-immediately terminate.  Upon such termination the Licensee shall immediately
-cease using the Software, return to CUTS or destroy all copies of the
-Software, and provide CUTS with written certification of the Licensee's
-compliance with the foregoing.  Termination shall not relieve the Licensee
-from its obligations arising prior to such termination.  Notwithstanding any
-provision of this Agreement to the contrary, Sections 3, 5, 6, 7, 8, 9, 10,
-13, 14 and 18 shall survive termination of this Agreement.  
-
-9. CONFIDENTIALITY
-
-9.1 The Licensee agrees and undertakes that during the term of the Licence in
-this Agreement and thereafter it will keep confidential all, and will not use
-for its own purposes nor without the prior written consent of CUTS disclose to
-any third party any information of a confidential nature (including trade
-secrets and information of commercial value) which may become known to the
-Licensee and which relates to CUTS unless such information is public knowledge
-or already known to the Licensee at the time of disclosure or subsequently
-becomes public knowledge other by breach of the Licence in this Agreement or
-subsequently comes lawfully into the possession of the Licensee from a third
-party.
-
-10. NO SUBLICENSING AND NO ASSIGNMENT 
-
-10.1 The Licensee shall have no right to sub-license or to assign,
-transfer, charge or deal in any other manner the benefit or burden of the
-Licence in this Agreement in whole or in part or to allow the Software to
-become the subject of any charge, lien or encumbrance without the prior
-written consent of CUTS such consent may be withheld without giving any
-reasons.
-
-11. WAIVER
-
-11.1 No forbearance or delay by either party in enforcing its rights will
-prejudice or restrict the rights of that party, and no waiver of any such
-rights or of any breach of any contractual terms will be deemed to be a waiver
-of any other right or of any later breach.
-
-12. SEVERABILITY
-
-12.1 If any provision of the Licence in this Agreement is judged to be
-illegal or unenforceable, the continuation in full force and effect of the
-remainder of the provisions will not be prejudiced.
-
-13. NO AGENCY OR PARTNERSHIP
-
-13.1 Nothing contained or implied in this Agreement constitutes a Party the
-partner, agent, or legal representative of another party or of the other Party
-for any purpose or creates any partnership, agency or trust, and no Party has
-any authority to bind the other Party in any way.
-
-14. THE CONTRACTS (RIGHTS OF THIRD PARTIES) ACT 1999
-
-14.1 The Contracts (Rights of Third Parties) Act 1999 shall not apply to
-this Agreement and nothing in this Agreement shall confer or purport to confer
-on or operate to give any third Party any benefit or any right to enforce any
-term of this Agreement except as expressly provided in this Agreement.
-
-15. NOTICES
-
-15.1 Any notice to be given under this Agreement shall be in writing and
-delivered by hand, prepaid registered post or facsimile to a Party at the
-address set out at the head of this Agreement or to such other address or fax
-number as any Party may specify in writing to another.  Notices are deemed to
-have been given:
-
-(a) if delivered by hand, at the time of delivery unless delivered after 5pm
-in the place of receipt or on a non-business day, in which case the notice is
-deemed to have been given at 9am the next business day;
-
-(b) if sent by registered post from within the United Kingdom, three
-business days after posting (or seven business days if posted from outside the
-United Kingdom); and
-
-(c) if sent by facsimile, at the time the facsimile is received shown in
-the transmission report as the time that the whole facsimile was sent unless
-received after 5pm in the place of receipt or on a non-business day, in which
-case the notice is deemed to have been given at 9am the next business day.
-Any notice served by facsimile transmission shall be confirmed by post.
-
-16. ENTIRE AGREEMENT
-
-16.1 This Agreement constitutes the entire agreement and understanding of
-the Parties and supersedes all negotiations, understandings or previous
-agreement between the Parties relating to the subject matter of this
-Agreement.
-
-17. GOVERNING LAW
-
-17.1 This Agreement and any documents to be entered into pursuant to it
-shall be governed by and construed in accordance with English law and each
-Party irrevocably submits to the exclusive jurisdiction of the courts of
-England over any claim or matter arising under or in connection with this
-Agreement and the documents entered into pursuant to it.
-
-18. EXPORT CONTROL REGULATIONS
-
-18.1 'Export Control Regulations' means any United Nations trade sanctions
-or EU or UK legislation or regulation, from time to time in force, which
-impose arms embargoes or control of export of goods, technology or software.
-
-18.2 The Licensee shall ensure that, in using the Software it shall not and
-nor shall its employees or consultants or contractors breach or compromise
-directly of indirectly compliance with any Export Control Regulations.
-
-
-
-If you have any questions or feedback concerning the Software, contact
-University of Cambridge, Department of Haematology, Cambridge Institute for
-Medical Research, Wellcome Trust/MRC Building, Cambridge CB2 0XY UK.  
-Attn: Professor Randy Read, or via email at cimr-phaser@lists.cam.ac.uk
-
diff --git a/licenses/phenix b/licenses/phenix
deleted file mode 100644
index 0b6c5c08c..000000000
--- a/licenses/phenix
+++ /dev/null
@@ -1,174 +0,0 @@
-NON-COMMERCIAL END USER 
-SOURCE  CODE  &  BINARY  LICENSE  AGREEMENT
-
-Software: PHENIX (LBNL Ref. CR-1770)
-Version:  1 Alpha, Beta and General 
-
-Software: LABELIT (LBNL Ref. CR-1960)
-Version:  1.1.4
-
-IMPORTANT - READ CAREFULLY: This License Agreement ("Agreement") is a
-legal agreement between you (in your capacity as an individual and as
-an agent for your company, institution or other entity) and The
-Regents of the University of California, Department of Energy
-contract-operators of the Ernest Orlando Lawrence Berkeley National
-Laboratory ("Berkeley Lab").  Downloading, installing, using, or
-copying of the Software (as defined below) by you or by a third party
-on your behalf indicates your agreement to be bound by the terms and
-conditions of this Agreement.  If you do not agree to these terms and
-conditions, do not download, install or use the Software.
-
-1.  LICENSE GRANT. Berkeley Lab grants you, and you hereby accept, a
-non-exclusive, royalty-free perpetual license to install, use, modify,
-and prepare derivative works the version noted above of the computer
-software program noted above, in binary and source code format, or any
-derivative work thereof, together with any associated media, printed
-materials, and on-line or electronic documentation (if any) provided
-by Berkeley Lab (collectively, the "Software") FOR INTERNAL,
-NON-COMMERCIAL, RESEARCH AND DEVELOPMENT PURPOSES ONLY, subject to the
-following terms and conditions: (i) you may not distribute, rent,
-lease, loan, or sublicense the Software to any third party, nor may
-you distribute the Software as incorporated into any derivative work
-you may create.  This version of the Software constitutes a research
-prototype and may be changed substantially.  The license grant set
-forth above is subject to receipt by Berkeley Lab of any required
-U.S. Department of Energy approvals.
-
-2.  COPYRIGHT; RETENTION OF RIGHTS.  The above license grant is
-conditioned on the following: (i) you must reproduce all copyright
-notices and other proprietary notices on any copies of the Software
-and you must not remove such notices; and (ii) in the event you
-compile the Software, you will include the copyright notice with the
-binary in such a manner as to allow it to be easily viewable.  All
-copies of the Software shall be subject to the terms of this
-Agreement.  Subject to approval by the U.S. Department of Energy: (a)
-you hereby acknowledge that the Software is protected by United States
-copyright law and international treaty provisions; (b) Berkeley Lab,
-and its licensors (if any), hereby reserve all rights in the Software
-which are not explicitly granted to you herein; (c) without limiting
-the generality of the foregoing, Berkeley Lab and its licensors retain
-all title, copyright, and other proprietary interests in the Software
-and any copies thereof, and you do not acquire any rights, express or
-implied, in the Software, other than those specifically set forth in
-this Agreement.  Subject to Berkeley Lab's underlying copyright in the
-Software pursuant to the above, you retain all title, copyright, and
-other proprietary interests in any derivative works of the Software
-that you create and any copies thereof, and Berkeley Lab does not
-acquire any rights, express or implied, in such derivative works.
-
-3.  NO MAINTENANCE OR SUPPORT; TREATMENT OF ENHANCEMENTS YOU CHOOSE TO
-PROVIDE TO BERKELEY LAB.  Berkeley Lab is under no obligation
-whatsoever to: (i) provide maintenance or support for the Software; or
-(ii) notify you of bug fixes, patches, or upgrades to the features,
-functionality or performance of the Software ("Enhancements") (if
-any), whether developed by Berkeley Lab or third parties.  If, in its
-sole discretion, Berkeley Lab makes an Enhancement available to you
-and Berkeley Lab does not separately enter into a written license
-agreement with you relating to such bug fix, patch or upgrade, then it
-shall be deemed incorporated into the Software and subject to this
-Agreement.  You are under no obligation whatsoever to provide any
-Enhancements to Berkeley Lab that you may develop over time; however,
-if you choose to provide your Enhancements to Berkeley Lab in source
-code form without contemporaneously requiring Berkeley Lab to enter
-into a separate written license agreement for such Enhancements, then
-you hereby grant Berkeley Lab a non-exclusive, royalty-free perpetual
-license to install, use, modify, prepare derivative works, incorporate
-into the Software or other computer software, distribute, and
-sublicense your Enhancements or derivative works thereof, in binary
-and source code form.
-
-4.  U.S. GOVERNMENT RIGHTS.  The Software was developed under funding
-from the U.S. Department of Energy and the U.S. Government
-consequently retains certain rights as follows: the U.S. Government
-has been granted for itself and others acting on its behalf a paid-up,
-nonexclusive, irrevocable, worldwide license in the Software to
-reproduce, prepare derivative works, and perform publicly and display
-publicly.  Beginning five (5) years after the date permission to
-assert copyright was granted by the U.S. Dept. of Energy, and subject
-to any subsequent five (5) year renewals, the U.S. Government is
-granted for itself and others acting on its behalf a paid-up,
-nonexclusive, irrevocable, worldwide license in the Software to
-reproduce, prepare derivative works, distribute copies to the public,
-perform publicly and display publicly, and to permit others to do so.
-
-5.  CONFIDENTIALITY.  You agree to take appropriate steps to ensure
-that the source code form of the Software remains confidential and is
-protected against unauthorized disclosure, use, or release, and will
-treat it with at least the same level of care as you would use to
-protect and secure your own confidential information, but in any event
-using no less than a reasonable standard of care.
-
-6.  WARRANTY DISCLAIMER.  THE SOFTWARE IS SUPPLIED "AS IS" WITHOUT
-WARRANTY OF ANY KIND.  BERKELEY LAB, ITS LICENSORS, THE UNITED STATES,
-THE UNITED STATES DEPARTMENT OF ENERGY, AND THEIR EMPLOYEES: (1)
-DISCLAIM ANY WARRANTIES, EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED
-TO ANY IMPLIED WARRANTIES OF MERCHANTABILITY, FITNESS FOR A PARTICULAR
-PURPOSE, TITLE OR NON-INFRINGEMENT, (2) DO NOT ASSUME ANY LEGAL
-LIABILITY OR RESPONSIBILITY FOR THE ACCURACY, COMPLETENESS, OR
-USEFULNESS OF THE SOFTWARE, (3) DO NOT REPRESENT THAT USE OF THE
-SOFTWARE WOULD NOT INFRINGE PRIVATELY OWNED RIGHTS, (4) DO NOT WARRANT
-THAT THE SOFTWARE WILL FUNCTION UNINTERRUPTED, THAT IT IS ERROR-FREE
-OR THAT ANY ERRORS WILL BE CORRECTED.
-
-7.  LIMITATION OF LIABILITY. IN NO EVENT WILL BERKELEY LAB OR ITS
-LICENSORS BE LIABLE FOR ANY INDIRECT, INCIDENTAL, CONSEQUENTIAL,
-SPECIAL OR PUNITIVE DAMAGES OF ANY KIND OR NATURE, INCLUDING BUT NOT
-LIMITED TO LOSS OF PROFITS OR LOSS OF DATA, FOR ANY REASON WHATSOEVER,
-WHETHER SUCH LIABILITY IS ASSERTED ON THE BASIS OF CONTRACT, TORT
-(INCLUDING NEGLIGENCE OR STRICT LIABILITY), OR OTHERWISE, EVEN IF
-BERKELEY LAB HAS BEEN WARNED OF THE POSSIBILITY OF SUCH LOSS OR
-DAMAGES.  IN NO EVENT SHALL BERKELEY LAB'S LIABILITY FOR DAMAGES
-ARISING FROM OR IN CONNECTION WITH THIS AGREEMENT EXCEED THE AMOUNT
-PAID BY YOU FOR THE SOFTWARE.
-
-8.  INDEMNITY.  You shall indemnify, defend, and hold harmless
-Berkeley Lab, the U.S. Government, the Software developers, the
-Software sponsors, and their agents, officers, and employees, against
-any and all claims, suits, losses, damage, costs, fees, and expenses
-arising out of or in connection with this Agreement.  You shall pay
-all costs incurred by Berkeley Lab in enforcing this provision,
-including reasonable attorney fees.
-
-9.  TERM AND TERMINATION.  The license granted to you under this
-Agreement will continue perpetually unless terminated by Berkeley Lab
-in accordance with this Agreement.  If you breach any term of this
-Agreement, and fail to cure such breach within thirty (30) days of the
-date of written notice, this Agreement shall immediately
-terminate. Upon such termination, you shall immediately cease using
-the Software, return to Berkeley Lab, or destroy, all copies of the
-Software, and provide Berkeley Lab with written certification of your
-compliance with the foregoing.  Termination shall not relieve you from
-your obligations arising prior to such termination.  Notwithstanding
-any provision of this Agreement to the contrary, Sections 5 through 12
-shall survive termination of this Agreement.
-
-10.  EXPORT CONTROLS. You shall observe all applicable United States
-and foreign laws and regulations (if any) with respect to the export,
-re-export, diversion or transfer of the Software, related technical
-data and direct products thereof, including, without limitation, the
-International Traffic in Arms Regulations (ITAR) and the Export
-Administration Regulations.
-
-11.  NO ENDORSEMENT.  In accordance with California Education Code
-Section 92000, you shall not use in advertising, publicity or other
-promotional activities any name, trade name, trademark, or other
-designation of the University of California, nor shall you so use
-"Ernest Orlando Lawrence Berkeley National Laboratory" or "United
-States Department of Energy" (including any contraction, abbreviation,
-or simulation of any of the foregoing) without Berkeley Lab's prior
-written consent.
-
-12.  GENERAL.  This Agreement shall be governed by the laws of the
-State of California, excluding its rules governing conflicts of laws.
-No provision in either party's purchase orders, or in any other
-business forms employed by either party will supersede the terms of
-this Agreement, and no modification or amendment of this Agreement is
-binding, unless in writing signed by a duly authorized representative
-of each party.  This Agreement is binding upon and shall inure to the
-benefit of Berkeley Lab, its successors and assigns.  This Agreement
-represents the entire understanding of the parties, and supersedes all
-previous communications, written or oral, relating to the subject of
-this Agreement. If you have any questions concerning this license,
-contact Lawrence Berkeley National Laboratory, Technology Transfer
-Department, One Cyclotron Road, MS 90R1070, Berkeley, CA 94720, Attn:
-Software Licensing or via e-mail at TTD@lbl.gov. (rev 010903)
diff --git a/licenses/phrap b/licenses/phrap
deleted file mode 100644
index 0e1df110a..000000000
--- a/licenses/phrap
+++ /dev/null
@@ -1,210 +0,0 @@
-ACADEMIC USER AGREEMENT
-
-Please read the entire agreement, fill in the information in the
-indicated positions (such as "NAME:"), and return the entire document
-to the indicated people.  Please send the document as the message--not
-as an attachment.
-
-Phrap:  A program for assembling DNA sequence data.
-
-Swat:  A program for searching one or more DNA or protein query sequences
-against a sequence database, using (an efficient implementation of) the
-Smith-Waterman-Gotoh algorithm.
-
-Cross_Match:  A general-purpose utility based on Swat for comparing any
-two sets of (long or short) DNA sequences.
-
-Phred:  A program that reads DNA sequencer trace data, calls bases,
-assigns quality values to the bases, and writes the base calls and quality
-values to output files.
-
-Consed:  A program for viewing and editing Phrap assemblies.
-
-To receive any of these programs you will need to agree to the following
-conditions. They should be taken seriously!
-
-1) You agree to read the documentation.  We welcome feedback on any
-inaccuracies.
-
-2) You agree to report any bugs to us.  (To fix bugs, we will need
-from you a dataset and a procedure that reproduces the problem; but do
-not send datasets without first emailing us to describe the nature of
-the bug.)
-
-3) You agree not to make the programs (including source code,
-executables, or any part thereof, in modified or unmodified form)
-available to anyone outside your group, and not to put them where they
-may be accessible to outside individuals without your direct knowledge
-(e.g. on a computer to which people outside your group have login
-privileges).  The documentation however may be freely distributed.
-Refer any requests for the programs to the authors.  If you are
-operating a computer facility which provides access to several
-independent investigators, you agree to set the permissions on the
-executables and source code to allow execute but not read access, so
-that the programs may not be copied. Investigators who want copies of
-the software for their own use must return a separate copy of this
-agreement.
-
-4) You agree not to use the programs for any commercial purpose,
-including but not limited to commercially restricted sequencing
-(defined as sequencing for which a company retains patenting or
-licensing rights regarding the sequence, or the right to restrict or
-delay dissemination of the sequence; with the sole exception that
-sequencing is not considered to be commercially restricted if it is
-federally funded and the investigators adopt the data release policies
-endorsed at the Wellcome Trust-sponsored Bermuda meeting,
-i.e. immediate release of data as it is generated).
- [If you wish to obtain the software for commercially restricted
-sequencing or any other commercial purposes, you will need to execute
-a separate licensing agreement with the University of Washington and
-pay a fee. In that case please contact:
-
-Lisa Heinz
-University of Washington TechTransfer, Digital Ventures
-Box 354990
-4311-11th Avenue NE, Suite 500
-Seattle, WA  98105-4608
-
-http://depts.washington.edu/techtran
-
-206-616-3451  FAX: 206-616-3322
-swxfr@u.washington.edu
-
-Do not contact her if the academic license applies.]
-
-5) You acknowledge that the software is experimental in nature and is
-supplied "AS IS", without obligation by the authors or the University
-of Washington to provide accompanying services or support.  The entire
-risk as to the quality and performance of the Software is with you.
-UW AND THE AUTHORS EXPRESSLY DISCLAIM ANY AND ALL WARRANTIES
-REGARDING THE SOFTWARE, WHETHER EXPRESS OR IMPLIED, INCLUDING BUT NOT
-LIMITED TO WARRANTIES PERTAINING TO MERCHANTABILITY OR FITNESS FOR A
-PARTICULAR PURPOSE.
-
-6) All members of your group with access to the software agree to the
-same conditions.
-
-
-
-Having read the above, if you are still interested in obtaining the
-programs, please return a copy of this entire message (which MUST be
-included so that it is clear what you are agreeing to) by email
-together with the following information:
-
-NAME: Your name in first name/last name order.
-
-NAME:  
-
-
-Example:
-NAME: John Dracula
-(Please do not use all capitals such as John DRACULA)
-
-ACKNOWLEDGEMENT: An acknowledgement that you and the members of your
-group agree to these conditions.
-
-ACKNOWLEDGEMENT:
-
-Example:
-ACKNOWLEDGEMENT: I agree to the license.
-
-PROGRAMS: Which programs you want (phrap,cross_match, and swat are
-distributed together). You must cc the message to each appropriate
-individual (Brent Ewing, David Gordon, and/or Phil Green) at the email
-addresses below so that they will know to send you the appropriate
-program.
-
-PROGRAMS:
-
-Example:
-PROGRAMS: phred, phrap, consed
-
-INSTITUTION: Your academic or government institution (give full name,
-not abbreviation)
-
-INSTITUTION: 
-
-Example:
-INSTITUTION:  University of Lower Transylvania
-
-DEPARTMENT: Your department
-
-DEPARTMENT:
-
-Example:
-DEPARTMENT:  Department of Hematology
-
-EMAIL: Your email address for all future correspondence. Ideally this
-should be a Unix computer running a generic mail program, since
-several of the programs are sent as uuencoded files which may be
-corrupted by some mail programs.
-  If this address is not at the institution & department listed above,
-please explain the discrepancy.
-
-EMAIL: 
-
-Example:
-EMAIL: john.dracula@utrans.edu
-
-OS: (Consed requestors only) Which platform(s) you want Consed for:
-solaris 2.5.1, solaris 2.6, solaris 2.7 (solaris 7), solaris 8,
-solaris 9, digital unix 4.0 (or better), hp-ux 11.x, sgi irix 6.2,
-6.3, 6.4, or 6.5, linux (normal 32 bit) (Redhat 7.1-1 or better),
-linux (Itanium), linux (AMD64), ibm aix 5.2 (or better), macosx 10.2
-(Darwin kernel 6.0) (or better), or solaris-intel (2.8 or better).
-
-OS:
-
-Example:
-OS: hpux
-
-Note: Consed is not available for PC's running Windows, XP, NT, or
-2000.
-
-IP: (Consed requestors only) The ip address of the computer on which
-you will be running a web browser to download consed.  This does not
-have to be the same computer as the one on which you will run consed.
-Please view page
-http://bozeman.mbt.washington.edu/consed/find_ip_address.html
-which will tell you what my computer thinks is your ip address.
-
-(Even if you think you know your ip address, firewalls and proxies can
-cause your browser to transmit a different ip address, and thus my
-webserver would deny you access to consed.  So it would be a good idea
-to view the page above and send me the ip address it shows, even if
-this isn't your real ip address.)
-
-IP:
-
-Example:
-IP: 123.49.74.80
-
-
-If you want Consed/Autofinish, you must include OS and IP (above).
-Consed cannot be obtained without them.
-
-Please return this entire agreement so it is clear what you are
-agreeing to.
-
-Please send all of this, including the agreement, as part of the
-email message--not as an attachment.  
-
-Send it to each of the relevant individuals below:
-
-Contacts for obtaining the programs and for questions, bug reports,
-suggestions:
-
-      Phrap/cross_match/swat:  Phil Green, phg (at) u.washington.edu
-      Phred: Brent Ewing, bge (at) u.washington.edu
-      Consed: David Gordon, gordon (at) genome.washington.edu
-
-where the " (at) " is replaced by "@".
-
-It can take up to 2 weeks for a license application to be processed,
-so please be patient.
-
-
-
-
-
-
diff --git a/licenses/polyphen b/licenses/polyphen
deleted file mode 100644
index 250b86ed7..000000000
--- a/licenses/polyphen
+++ /dev/null
@@ -1,7 +0,0 @@
-The software provided herein is free for academic instruction and research
-use only. Commercial licenses are available to legal entities, including
-companies and organizations (both for-profit and non-profit), requiring the
-software for general commercial use. To obtain a commercial license please,
-contact us via e-mail.
-
-e-mail: iadzhubey@rics.bwh.harvard.edu
\ No newline at end of file
diff --git a/licenses/pydap b/licenses/pydap
deleted file mode 100644
index cdf41977a..000000000
--- a/licenses/pydap
+++ /dev/null
@@ -1,20 +0,0 @@
-Copyright (c) 2003?2009 Roberto De Almeida
-
-Permission is hereby granted, free of charge, to any person obtaining a copy of
-this software and associated documentation files (the ?Software?), to deal in
-the Software without restriction, including without limitation the rights to
-use, copy, modify, merge, publish, distribute, sublicense, and/or sell copies
-of the Software, and to permit persons to whom the Software is furnished to do
-so, subject to the following conditions:
-
-The above copyright notice and this permission notice shall be included in all
-copies or substantial portions of the Software.
-
-THE SOFTWARE IS PROVIDED ?AS IS?, WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
-IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
-FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
-AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
-LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
-OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
-SOFTWARE.
-
diff --git a/licenses/pyvcf b/licenses/pyvcf
deleted file mode 100644
index f37927b3a..000000000
--- a/licenses/pyvcf
+++ /dev/null
@@ -1,46 +0,0 @@
-Copyright (c) 2011-2012, Population Genetics Technologies Ltd, All rights reserved.
-
-Redistribution and use in source and binary forms, with or without
-modification, are permitted provided that the following conditions are met:
-
-1. Redistributions of source code must retain the above copyright notice, this
-list of conditions and the following disclaimer.  
-
-2. Redistributions in binary form must reproduce the above copyright notice, this
-list of conditions and the following disclaimer in the documentation and/or
-other materials provided with the distribution.  
-
-3. Neither the name of the Population Genetics Technologies Ltd nor the names of
-its contributors may be used to endorse or promote products derived from this
-software without specific prior written permission.  
-
-THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" AND
-ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED
-WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE
-DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR CONTRIBUTORS BE LIABLE
-FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL
-DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR
-SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER
-CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY,
-OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE
-OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
-
-
-Copyright (c) 2011 John Dougherty
-
-Permission is hereby granted, free of charge, to any person obtaining a copy of
-this software and associated documentation files (the "Software"), to deal in
-the Software without restriction, including without limitation the rights to
-use, copy, modify, merge, publish, distribute, sublicense, and/or sell copies of
-the Software, and to permit persons to whom the Software is furnished to do so,
-subject to the following conditions:
-
-The above copyright notice and this permission notice shall be included in all
-copies or substantial portions of the Software.
-
-THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
-IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, FITNESS
-FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR
-COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY, WHETHER
-IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, OUT OF OR IN
-CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE SOFTWARE.
diff --git a/licenses/rosetta-academic b/licenses/rosetta-academic
deleted file mode 100644
index 48e58aa27..000000000
--- a/licenses/rosetta-academic
+++ /dev/null
@@ -1,52 +0,0 @@
-Rosetta++
-License:
-Rosetta++ Software
-Academic License Agreement
-
-The University of Washington (“UW�) and the developers of the Rosetta software (Developers) give permission for you (“You�) and your Institution (“Institution�) to use the Rosetta++ protein prediction software (“Software�). Software was developed through support from the National Institutes of Health, Human Frontier Science Program Grant, National Science Foundation, Office of Naval Research, Packard Foundation, the Damon Runyon Cancer Research Foundation, Jane Coffin Childs Foundation, Los Alamos National Lab, and in part by researchers of the Howard Hughes Medical Institute (HHMI) at UW. UW and the Developers allow researchers at your Institution to copy and modify Software, for internal, non-profit research purposes, on the following conditions:
-
-1.       The Software remains at your Institution and is not published, distributed, or otherwise transferred or made available to other than Institution employees and students involved in research under your supervision.
-
-2.       You agree to make protein sequences, models and structures generated by using Software available to other academic researchers for non-profit research purposes. If You wish to obtain Software for any commercial purposes, including fee-based service projects, You will need to execute a separate licensing agreement with the University of Washington and pay a fee. In that case please contact: license@u.washington.edu
-
-3.       You retain in Software and any modifications to Software, the copyright, trademark, or other notices pertaining to Software as provided by UW.
-
-4.       You provide the Developers with feedback on the use of the Software in your research, and that the Developers and UW are permitted to use any information You provide in making changes to the Software. All bug reports and technical questions shall be sent to the email address: general-support@rosettacommons.org
-
-5.       You acknowledge that the Developers, HHMI, UW and its licensees may develop modifications to Software that may be substantially similar to your modifications of Software, and that the Developers, HHMI, UW and its licensees shall not be constrained in any way by You in HHMI’s, UW’s or its licensees’ use or management of such modifications. You acknowledge the right of the Developers, HHMI, and UW to prepare and publish modifications to Software that may be substantially similar or functionally equivalent to your modifications and improvements, and if You obtain patent protection for any modification or improvement to Software You agree not to allege or enjoin infringement of your patent by the Developers, HHMI, the UW or by any of UW’s licensees obtaining modifications or improvements to Software from the University of Washington or the Developers.
-
-6.       We will acknowledge in our publications contributions we make to each other’s research involving or based on the Software. The current citations for Software are:
-
-Rosetta ab initio structure prediction
-Bonneau R, Strauss CE, Rohl CA, Chivian D, Bradley P, Malmstrom L, Robertson T, Baker D. (2002) De novo prediction of three-dimensional structures for major protein families. J Mol Biol 322(1):65-78.
-
-Bonneau R, Tsai J, Ruczinski I, Chivian D, Rohl C, Strauss CE, Baker D. (2001) Rosetta in CASP4: progress in ab initio protein structure prediction. Proteins Suppl 5:119-26.
-
-Simons KT, Ruczinski I, Kooperberg C, Fox B, Bystroff C, Baker D. (1999) Improved recognition of native-like protein structures using a combination of sequence-dependent and sequence-independent features of proteins. Proteins 34(1) 82-95.
-
-Simons KT, Kooperberg C, Huang E, Baker, D. (1997) Assembly of protein tertiary structures from fragments with similar local sequences using simulate anealing and Bayesian scoring functions. J Mol Biol 268:209-25.
-
-RosettaDock
-Protein-Protein Docking with Simultaneous Optimization of Rigid Body Displacement and Side Chain Conformations, J.J. Gray, S.E. Moughan, C. Wang, O. Schueler-Furman, B. Kuhlman, C.A. Rohl and D. Baker, J. Mol. Biol., 331(1), 281-299, 2003.
-
-Protein-Protein Docking Predictions for the CAPRI Experiment, J.J. Gray, S.E. Moughan, T. Kortemme, O. Schueler-Furman, K.M.S. Misura, A.V. Morozov, and D. Baker, Proteins, 52(1), 118-122, 2003.
-
-RosettaDesign
-Dantas, G., Kuhlman, B., Callender, D., Wong, M., D. Baker: A large scale test of computational protein design: folding and stability of nine completely redesigned globular proteins. J Mol Biol 332: (2) 449-60 Sep 12 2003.
-
-Kuhlman B, Dantas G, Ireton G, Varani G, Stoddard B, Baker D: Design of a novel globular protein fold with atomic level accuracy. Science, 302, 1364-1368, Nov 21 2003.
-
-RosettaNMR
-Rohl CA and Baker D. (2002) De novo determination of protein backbone structure from residual dipolar couplings using Rosetta. J Am Chem Soc 124:2723-9.
-
-Bowers PM, Strauss CE, Baker D. (2000) De novo protein structure determination using sparse NMR data. J Biomol NMR 18(4):311-8.
-
-RosettaNucleicAcids
-Havranek, J. J., Duarte, C. M., Baker, D. (2004). A simple physical model for the prediction and design of protein-DNA interactions J Mol Biol 344, 59-70.
-
-RosettaLigand
-Meiler J, Baker D. (2006). ROSETTALIGAND: protein-small molecule docking with full side-chain flexibility. Proteins 65(3):538-48.
-
-7.       Any risk associated with using the Software at your institution is with You and your Institution. Software is experimental in nature and is made available as a research courtesy "AS IS," without obligation by UW to provide accompanying services or support.
-
-8.       UW AND THE AUTHORS EXPRESSLY DISCLAIM ANY AND ALL WARRANTIES REGARDING THE SOFTWARE, WHETHER EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO WARRANTIES PERTAINING TO NON-INFRINGEMENT, MERCHANTABILITY OR FITNESS FOR A PARTICULAR PURPOSE.
diff --git a/licenses/rosetta-commercial b/licenses/rosetta-commercial
deleted file mode 100644
index 0f22be5f6..000000000
--- a/licenses/rosetta-commercial
+++ /dev/null
@@ -1,26 +0,0 @@
-ROSETTA++ EXPRESS LICENSE
-Instructions for Licensing of ROSETTA++ for Commercial Use
-Non-Exclusive Software Site License Agreement
-Commercial users are required to obtain this license in order to use Rosetta++. Please fill out the
-license agreement and return it to UW TechTransfer.
-Procedure for filling out the license:
-    1.   Print out the attached license agreement form and Attachments A & B.
-    2.   Complete the license fee and contact information on Attachment B.
-    3.   Have the license agreement signed by an authorized representative of your institution.
-    4.   Fax the completed agreement to (206) 616-3322. You may also send a Purchase Order.
-    5.   UW TechTransfer will review the agreement, countersign it or contact you. When the
-         license is complete, you will receive a copy of the executed agreement with an invoice.
-    6.   Your invoice will include a license agreement number.
-    7.   Include the license and invoice numbers on your check. A confirmation by facsimile of
-         the wire transfer amount and date by the issuing bank will substitute for confirmation by
-         UW. You can mail your fee to: Contracts Manager, UW TechTransfer Digital Ventures.
-         University of Washington. 4311 11th Ave NE Suite 500, Seattle, WA 98105-4608.
-    8.   Software access information will be sent to the Technical Contact via email upon receipt
-         of payment.
-    9.   Please contact our office if you have any questions about this process
-         UW Tech Transfer Digital Ventures
-         University of Washington
-         Phone: (206) 616-3451
-         Fax: (206) 616-3322
-         Email: license@u.washington.edu
-
diff --git a/licenses/signalp b/licenses/signalp
deleted file mode 100644
index 7e5b15f19..000000000
--- a/licenses/signalp
+++ /dev/null
@@ -1,218 +0,0 @@
-  ACADEMIC SOFTWARE LICENSE AGREEMENT FOR END-USERS AT PUBLICLY FUNDED
-  ACADEMIC, EDUCATION OR RESEARCH INSTITUTIONS FOR THE USE OF SignalP 3.0
-  
-  By downloading the Software you are consenting to be bound by and become
-  a party to this agreement as the "Licensee". If you do not agree to all
-  of the terms of this agreement, you must not click the Acceptance
-  button, not install the product nor use the product, and you do not
-  become a LICENSEE under this agreement. 
-  
-  If you are not a member of a publicly funded Academic and/or Education
-  and/or Research Institution you must obtain a commercial license, please
-  send mail to (software@cbs.dtu.dk). This software license agreement is
-  entered into by and between Center for Biological Sequence Analysis,
-  Technical University of Denmark (hereinafter "CBS") and the "LICENSEE". 
-  
-  WHEREAS CBS has the right to license all copyrights and other property
-  rights in the Licensed Software identified as SignalP 3.0 and developed
-  by CBS and CBS desires to license the Software so that it becomes
-  available for public use and benefit. 
-  
-  WHEREAS LICENSEE is a public funded Academic and/or Education and/or
-  Research Institution. 
-  
-  WHEREAS LICENSEE desires to acquire a free non-exclusive license to use
-  the Software for internal research purposes only. 
-  
-  NOW, THEREFORE, in consideration of the mutual promises and covenants
-  contained herein, the parties agree as follows: 
-  
-  1. Definitions 
-  
-  "Licensed Software" means the specific version SignalP 3.0 pursuant
-  to this Agreement. Any opinion, findings, conclusions or recommendations
-  expressed in the Licensed Software are those of the authors and do not
-  necessarily reflect the views of CBS. 
-  
-  2. License 
-  
-  Subject to the terms and conditions of this Agreement a non-exclusive,
-  non-transferable License to use and copy the Licensed Software is made
-  available free of charge for the LICENSEE which is a non-profit
-  educational, academic and/or research institution. The License is only
-  granted for personal and internal use in research only at one Site,
-  where a Site is defined as a set of contiguous buildings in one
-  location. The software will be used at only one location of LICENSEE. 
-  
-  This license does not entitle Licensee to receive from CBS copies of the
-  Licensed software on disks, tapes or CD's, hard-copy documentation,
-  technical support, telephone assistance, or enhancements or updates to
-  the Licensed Software. 
-  
-  The user and any research assistants, co-workers or other workers who
-  may use the Software agree to not give the program to third parties or
-  grant licenses on software, which include the Software, alone or
-  integrated into other software, to third parties. Modification of the
-  source code is prohibited without the prior written consent of CBS. 
-  
-  3. Ownership 
-  
-  Except as expressly licensed in this Agreement, CBS shall retain title
-  to the Licensed Software, and any upgrades and modifications created by
-  CBS. 
-  
-  4. Consideration 
-  
-  In consideration for the license rights granted by CBS, LICENSEE will
-  obtain this academic license free of charge. 
-  
-  5. Copies 
-  
-  LICENSEE shall have the right to make copies of the Licensed Software
-  for internal use at the Site and for back-up purposes under this
-  Agreement, but agrees that all such copies shall contain the copyright
-  notices and all other reasonable and appropriate proprietary markings or
-  confidential legends that appear on the Licensed Software provided
-  hereunder. 
-  
-  6. Support 
-  
-  CBS shall have no obligation to offer support services to LICENSEE, and
-  nothing contained herein shall be interpreted as to require CBS to
-  provide maintenance, installation services, version updates, debugging,
-  consultation or end-user support of any kind. 
-  
-  7. Software Protection 
-  
-  LICENSEE acknowledges that the Licensed Software is proprietary to CBS.
-  The software code shall be treated as trade secrets and confidential
-  information of CBS, and LICENSEE agrees to use best efforts to hold the
-  same in confidence. LICENSEE's obligation for confidentiality shall not
-  extend to any information which is or becomes generally available to the
-  public, is already known to or subsequently disclosed by third parties
-  to LICENSEE and at its free disposal, or is independently developed by
-  LICENSEE or its affiliates without the use of the confidential
-  information disclosed by CBS, or is required by law or legal process. 
-  
-  Except as other wise expressly permitted in this Agreement, Licensee my
-  not (i) modify or create any derivative works of the Licensed Software
-  or documentation, including customization, translation or localization;
-  (ii) decompile, disassemble, reverse engineer, or otherwise attempt to
-  derive the source code for the Product; (iii) redistribute, encumber,
-  sell, rent, lease, sublicense, or otherwise transfer rights to the
-  Licensed Software; (iv) remove or alter any trademark, logo, copyright
-  or other proprietary notices, legends, symbols or labels in the Product;
-  or (v) publish any results of benchmark tests run on the Product to a
-  third party without CBS's prior written consent. 
-  
-  8. Representations of CBS to LICENSEE 
-  
-  CBS represents to LICENSEE that (i) CBS has the right to grant the
-  License and to enter into this agreement, (ii) that, to the best of
-  CBS's knowledge, the Licensed software does not infringe any patent,
-  copyright or trade secrets of any third party, provided however that
-  such representation and warranty shall not apply to any addition to, or
-  modifications or adaptation of, the Licensed Software made by LICENSEE
-  and (iii) CBS undertakes to use best efforts to cooperate with and
-  assist LICENSEE, at LICENSEE's expense, in defending itself against any
-  action based on the alleged infringement of any third party patent,
-  copyright or trade secret rights resulting from or relating to the use
-  or licensing of the Licensed Software by LICENSEE. 
-  
-  9. Indemnity and Disclaimer of Warranties 
-  
-  Except as expressly set forth in this agreement, CBS makes no
-  representations or warranties, express or implied. 
-  
-  The product is provided free of charge, and, therefore, on an "as is"
-  basis, without warranty of any kind, express or implied, including
-  without limitation the warranties that it is free of defects, virus
-  free, able to operate on an uninterrupted basis, merchantable, fit for a
-  particular purpose or non-interfering. The entire risk as to the quality
-  and performance of the Licensed Software is borne by LICENSEE. 
-  
-  By way of example, but not limitation, CBS makes no representations or
-  warranties of merchantability or fitness for any particular application
-  or, except as set forth in paragraph 8, that the use of the Software
-  will not infringe any patents, copyrights or trademarks or other rights
-  of third parties. The entire risk as to the quality and performance of
-  the product is borne by LICENSEE. CBS shall not be liable for any
-  liability or damages with respect to any claim by LICENSEE or any third
-  party on account of, or arising from the license or use of the Software.
-  
-  Should the Licensed Software prove defective in any respect, LICENSEE
-  and not LICENSOR or it's affiliates should assume the entire cost of any
-  service and repair. This disclaimer of warranty constitutes an essential
-  part of this agreement. No use of the licensed product is authorized
-  hereunder except under this disclaimer. 
-  
-  In no event will LICENSOR or its affiliates be liable for any indirect,
-  special, incidental or consequential damages arising out of the use of
-  or inability to use the product, including, without limitation, damages
-  for lost profits, loss of goodwill, work stoppage, computer failure or
-  malfunction, or any and all other commercial damages or losses, even if
-  advised of the possibility thereof, and regardless of the legal or
-  equitable theory (contract, tort or otherwise) upon which the claim is
-  based. 
-  
-  10. Promotional Advertising & References 
-  
-  LICENSEE may not use the name of the Licensed Software in its
-  promotional advertising, product literature, and other similar
-  promotional materials to be disseminated to the public or any portion
-  thereof. LICENSEE agrees not to identify CBS in any promotional
-  advertising or other promotional materials to be disseminated to the
-  public, or any portion thereof without CBS's prior written consent.
-  LICENSEE agrees that any reference to the software for crystallographic
-  computations will cite one or more publications as set forth in the
-  manual and in agreement with common scientific practice. CBS shall not
-  use LICENSEE's name in publicity or advertising involving this Agreement
-  or otherwise without LICENSEE's prior written consent which may be
-  withheld at LICENSEE's sole discretion. 
-  
-  11. Term 
-  
-  This Agreement and the license rights granted herein shall become
-  effective as of the date this Agreement is executed by both parties and
-  shall be perpetual unless terminated in accordance with this Section. 
-  
-  CBS may terminate this Agreement at any time. 
-  
-  Either party may terminate this Agreement at any time effective upon the
-  other party's breach of any agreement, covenant, or representation made
-  in this Agreement, such breach remaining uncorrected sixty (60) days
-  after written notice thereof. 
-  
-  LICENSEE shall have the right, at any time, to terminate this Agreement
-  without cause by written notice to CBS specifying the date of
-  termination. 
-  
-  Upon termination, LICENSEE shall destroy all full and partial copies of
-  the Licensed Software. 
-  
-  12. Governing Law 
-  
-  This Agreement shall be construed in accordance with the laws of
-  Denmark. 
-  
-  13. General 
-  
-  The parties agree that this Agreement is the complete and exclusive
-  agreement among the parties and supersedes all proposals and prior
-  agreements whether written or oral, and all other communications among
-  the parties relating to the subject matter of this Agreement. This
-  Agreement cannot be modified except in writing and signed by both
-  parties. Failure by either party at any time to enforce any of the
-  provisions of this Agreement shall not constitute a waiver by such party
-  of such provision nor in any way affect the validity of this Agreement. 
-  
-  The invalidity of singular provisions does not affect the validity of
-  the entire understanding. The parties are obligated, however, to replace
-  the invalid provisions by a regulation which comes closest to the
-  economic intent of the invalid provision. The same shall apply mutatis
-  mutandis in case of a gap. 
-  
-  IN WITNESS WHEREOF, the LICENSEE hereto have caused this Agreement to be
-  duly executed on the date of the download of the software and by
-  accepting the license conditions by pressing the Acceptance button. 
-  
diff --git a/licenses/smartgit b/licenses/smartgit
deleted file mode 100644
index c1ff2a6f1..000000000
--- a/licenses/smartgit
+++ /dev/null
@@ -1,120 +0,0 @@
-License Agreement for SmartGit
-
-Last date of change: 2014-08-15
-
-1 Subject of the Contract: The license terms of syntevo GmbH (hereinafter called "licensor") are applied for the concession of the rights of use for the entire or partly use of the object code of the software SmartGit (hereinafter called "SOFTWARE") to contractors, juristic persons under public law or official fund assets in terms of §310 in conjunction with §14 BGB [Civil Code] (hereinafter called "licensee"). Herewith the inclusion of the licensee's own terms and conditions is contradicted, unless their validity has explicitly been agreed to.
-
-2 Scope of the Rights of Use
-
-2.1 The following terms are valid for the assignment and use of the SOFTWARE for an unlimited period of time including any documentation and the license file (a file that is custom-made for each individual granting of a license, the file being necessary for the operation of the SOFTWARE).
-
-2.2 They are not valid for additional services such as installation, integration, parameterization and customization of the SOFTWARE to the licensee's requirements.
-
-3 Rights of Use
-
-3.1 The SOFTWARE is partly copyrighted in favour of the licensor and partly in favour of other holders of rights.
-
-3.2 The SOFTWARE is handed over to the licensee for its intended use. The scope of the intended use as well as the kind and scope of the rights of use result from the assignment contract and said license terms. They especially depend on whether the licensee gets a
-
-SOFTWARE Non-Commercial License,
-SOFTWARE Commercial License,
-SOFTWARE Enterprise License.
-3.2.1 If a SOFTWARE Non-Commercial License is agreed upon with the licensee, the licensor grants to licensee the non-exclusive, non-transferable right, which is terminable according to the terms of clause 5 and terminated according to the terms of clause 3.2.1.1, to have the SOFTWARE used
-
-on a arbitrary number of single-user computers or on a central server or via terminal server clients,
-simultaneously by a arbitrary number of users,
-solely for non-commercial purposes. A purpose is non-commercial only if it is in no manner primarily intended for or directed toward commercial advantage or private monetary compensation.
-Examples of non-commercial purposes:
-you are using the SOFTWARE to work on open-source projects,
-you are a student and you are using the SOFTWARE for your academic projects,
-you are using the SOFTWARE in your spare time to manage the website source of your local football club for free.
-Examples of commercial purposes, i.e. when you will need a Commercial License:
-you are using the SOFTWARE to work on open-source as well as on your company's projects,
-you are a student and you are using the SOFTWARE for your work as a freelancer,
-you are using the SOFTWARE in your spare time to manage the website source code of your local football club and you are getting paid for that.
-3.2.1.1 The Non-Commercial License is only valid for the latest version of the SOFTWARE as it is published on licensor's website and for all versions which have been first published not earlier than 3 months prior to the latest published version ('License Transition Period'). The SOFTWARE may contain a feature which enforces the termination of the Non-Commercial License for older versions by making them stop working after the License Transition Period.
-
-3.2.2 If a SOFTWARE Commercial License or a SOFTWARE Enterprise License is agreed upon with the licensee, the licensor grants to licensee the non-exclusive, non-transferable right, which is terminable according to the terms of clause 5 or permanent, to have the SOFTWARE used
-
-on a central server or via terminal server clients or as an in situ installation on single-user computers
-by the agreed-upon number of all users nameable on demand, that means to have the SOFTWARE saved, loaded, displayed and run permanently or temporarily. Every user known by name can be replaced by another user known by name only once in a month. From that time on, said first user must not use the SOFTWARE anymore and said second user may start to use the SOFTWARE. At no time must the number of the users known by name exceed the number of the acquired licenses (example: If the licensee has bought the SOFTWARE for five users whose names he can indicate on demand, only these five users may use the SOFTWARE. This is true independently of the number of the respective installations and of the fact if they are done on a central server or via terminal server clients or as a local installation on single-user computers).
-3.3 The licensee undertakes to take care that the intended use of the SOFTWARE is assured by appropriate technical and organizational measures.
-
-3.4 The licensee is obliged to back up the data orderly and regularly (especially with respect to working copies and repositories).
-
-3.5 The licensee is entitled to produce one backup from the SOFTWARE.
-
-3.6 The licensee is not entitled to translate, process, arrange the SOFTWARE differently or adapt or alter it and to copy the achieved results.
-
-3.7 The licensee is not entitled to distribute the SOFTWARE. This comprises any form of sublicensing, especially selling, letting, leasing or lending. Passing on the license file, a text file showing name and address of the licensee as well as an electronic signature which allows the technical exploitation of the SOFTWARE is also considered to be a form of distribution.
-
-3.8 The licensee is not entitled to make the SOFTWARE publicly accessible in such a way that it is accessible to the public at any place and at any time.
-
-3.9 The licensee undertakes not to decompile the SOFTWARE.
-
-4 Demo
-
-4.1 If the SOFTWARE is handed over only for test purposes, the licensor grants the licensee the non-exclusive, non-transferable right, limited to the test period of thirty-one (31) days, to have a non-registered copy of the SOFTWARE (demo) used on a arbitrary number of single-user computers or on a central server or via terminal server clients by a arbitrary number of users simultaneously for test purposes only, that means not productively, which again means to have the SOFTWARE saved, loaded, displayed and run permanently or temporarily.
-
-4.2 The demo of the SOFTWARE includes a function that terminates the use of the SOFTWARE after the expiration of the test period. After the payment of the agreed-upon license fee and the agreement to said license terms within the agreed-upon scope, this function is deactivated and the licensee gets the agreed-upon rights of use according to these license terms. Bypassing this technical protective function results in an immediate loss of all conceded rights of use. In this case a termination according to clause 5 is no longer applicable.
-
-5 Check for Updates/Internal Error reporting
-
-5.1 The SOFTWARE contains features which will automatically connect to licensor's servers to
-
-check for a new program version
-in case of an internal error, report a "crash footprint"
-The sent data contains NO POTENTIALLY SENSITIVE INFORMATION. The user can opt-out from both SOFTWARE features.
-
-5.2 Only upon user confirmation the SOFTWARE will send a full "bug report" to licensor for investigation. The contents of a full "bug report" may contain POTENTIALLY SENSITIVE INFORMATION and should be reviewed before sending.
-
-6 Liability
-
-6.1 When the SOFTWARE is handed over cost-free or for test purposes, the licensor is only liable in case that malice or gross negligence are blamed on him.
-
-6.2 The licensee's rights on indemnification due to a certain lack are excluded, if, for example, he has known the lack at the conclusion of the contract, especially when there had been a test phase before that date. If the licensee has not known of a lack due to gross negligence, he can only claim rights with respect to that lack if the licensor had fraudulently concealed the lack or had taken over a guarantee for the quality of that object.
-
-6.3 In case of data loss the licensor is only liable for the effort that would have been necessary for the recovery of the data, provided that the data backup was properly executed by the licensee.
-
-6.4 For the rest, kind and scope of liability are fixed in the respective sales contracts.
-
-6.5 If a third party asserts rights against the licensee because of claimed infringement of the SOFTWARE, the licensee is entitled to the rights defined in the corresponding sales contract. However this only applies, if the licensee immediately notifies the licensor about the claims of the third party, does not accept any claimed infringement and either leaves any legal actions, including possible out-of-court arrangements, to the licensee or only consummates them in agreement with the licensee.
-
-7 Cancellation of the Rights of Use
-
-7.1 If the licensee culpably and seriously violates the agreed-upon rights of use or intellectual property rights of the entitled person, the licensor can cancel the rights to use the respective SOFTWARE. In this case the fee will not be refunded.
-
-7.2 In case of cancellation the licensee is obliged to destroy the original of the SOFTWARE affected by the cancellation including any documentation and all copies or to return them to the licensor. If demanded by the licensor, the licensee will deliver a statement certifying the destruction.
-
-7.3 The other legal provisions remain untouched.
-
-8 Applicable Law and Place of Jurisdiction
-
-8.1 The law of the Federal Republic of Germany is applicable for all legal relationships of the parties excluding the laws on the international sale of goods.
-
-8.2 If the licensee is a merchant, a juristic person under public law or a person having special property under public law, the exclusive place of jurisdiction for all disputes from this contract will be the licensor's place of business. The same is applicable for the case when the licensee does not have a domestic place of general jurisdiction in Germany or the licensor's residence or habitual abode are not known at the time of filing an action. The licensor's capacity to apply to the court of a different place of jurisdiction remains untouched.
-
-9 The following third parties have rights on parts of the SOFTWARE:
-
-Hg4J, copyright by TMate Software s.r.o. (http://hg4j.com/). The corresponding license agreement can be found in the file licenses/HG4J-LICENSE.
-Java-Prettify, copyright by Chan Wai Shing (https://code.google.com/p/java-prettify/).
-The corresponding license agreement (Apache License 2.0) can be found at https://code.google.com/p/java-prettify/.
-JGit, copyright by various authors (http://repo.or.cz/w/jgit.git and http://jgit.org).
-The corresponding license agreement can be found at http://repo.or.cz/w/jgit.git/blob/HEAD:/LICENSE or in the file licenses/JGIT-LICENSE within the installation directory of SmartGit.
-JNA, copyright 2008 by Timothy Wall and Wayne Meissner (https://jna.dev.java.net)
-The corresponding license agreement can be found at http://www.gnu.org/licenses/old-licenses/lgpl-2.1.html or in the file licenses/JNA-LICENSE within the installation directory of SmartGit.
-JOpt-Simple, copyright by various authors (http://sourceforge.net/projects/jopt-simple/). The corresponding license agreement can be found in the file licenses/JOPT-SIMPLE-LICENSE (MIT license) within the installation directory of SmartGit.
-JSon-Simple, copyright by various authors (https://code.google.com/p/json-simple/). The corresponding license agreement (Apache License 2.0) can be found at https://code.google.com/p/json-simple/.
-JMySpell, copyright 2007 by DreamTangerine (dreamtangerine@hotmail.com)
-The corresponding license agreement can be found at http://javahispano.net/projects/jmyspell/ or in the file licenses/JMYSPELL-LICENSE within the installation directory of SmartGit.
-Log4j, copyright by Apache Software Foundation
-The corresponding license agreement can be found at http://www.apache.org/licenses/LICENSE-2.0 or in the file licenses/LOG4J-LICENSE within the installation directory of SmartGit.
-Parboiled, copyright by Mathias Doenitz
-The corresponding license agreement can be found at https://github.com/sirthias/parboiled/blob/master/LICENSE or in the file licenses/PARBOILED-LICENSE within the installation directory of SmartGit.
-Pegdown, copyright by Mathias Doenitz
-The corresponding license agreement can be found at https://github.com/sirthias/pegdown/blob/master/LICENSE or in the file licenses/PEGDOWN-LICENSE within the installation directory of SmartGit.
-SWT, copyright by Eclipse (http://eclipse.org). The corresponding license agreement can be found at http://www.eclipse.org/legal/epl-v10.html.
-SVNKit, copyright by TMate Software s.r.o. (http://svnkit.com/) The corresponding license agreement can be found in the file licenses/SVNKIT-LICENSE within the installation directory of SmartGit.
-Trilead SSH API, Copyright (c) 2007 Trilead AG (http://www.trilead.com). All rights reserved.
-The corresponding license agreement can be found at http://www.trilead.com/Products/Trilead_SSH_for_Java/license/ or in the file licenses/TRILEAD-LICENSE within the installation directory of SmartGit.
-The licensee is obliged to abide by these third parties license terms. Consequently they are part of this license agreement.
\ No newline at end of file
diff --git a/licenses/staden b/licenses/staden
deleted file mode 100644
index f2e77291a..000000000
--- a/licenses/staden
+++ /dev/null
@@ -1,76 +0,0 @@
-=============================================================================
-
-The Staden Package
-
-Copyright (c) 2003 MEDICAL RESEARCH COUNCIL
-All rights reserved
-
-Redistribution and use in source and binary forms, with or without 
-modification, are permitted provided that the following conditions are met:
-
-   . Redistributions of source code must retain the above copyright notice, 
-this list of conditions and the following disclaimer.
-
-   . Redistributions in binary form must reproduce the above copyright notice, 
-this list of conditions and the following disclaimer in the documentation 
-and/or other materials provided with the distribution.
-
-   . Neither the name of the MEDICAL RESEARCH COUNCIL, THE LABORATORY OF 
-MOLECULAR BIOLOGY nor the names of its contributors may be used to endorse or 
-promote products derived from this software without specific prior written 
-permission.
-
-THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" AND 
-ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED 
-WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE 
-DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT OWNER OR CONTRIBUTORS BE LIABLE FOR 
-ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES 
-(INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; 
-LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON 
-ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT 
-(INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS 
-SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
-
-=============================================================================
-
-Portions of this code have been modified by the Wellcome Trust Sanger
-Institute (Genome Research Limited). In some cases entirely new
-programs and/or source files have been created. These are licenced
-under essentially the same conditions as the MRC code (with just name
-changes).
-
-The following licence only applies to files bearing the Genome
-Research Limited copyright notice:
-
-
-
-Copyright (c) 2004 GENOME RESEARCH LIMITED
-All rights reserved
-
-Redistribution and use in source and binary forms, with or without 
-modification, are permitted provided that the following conditions are met:
-
-   . Redistributions of source code must retain the above copyright notice, 
-this list of conditions and the following disclaimer.
-
-   . Redistributions in binary form must reproduce the above copyright notice, 
-this list of conditions and the following disclaimer in the documentation 
-and/or other materials provided with the distribution.
-
-   . Neither the name of the GENOME RESEARCH LIMITED, the WELLCOME TRUST
-SANGER INSTITUTE nor the names of its contributors may be used to endorse or 
-promote products derived from this software without specific prior written 
-permission.
-
-THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" AND 
-ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED 
-WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE 
-DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT OWNER OR CONTRIBUTORS BE LIABLE FOR 
-ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES 
-(INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; 
-LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON 
-ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT 
-(INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS 
-SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
-
-=============================================================================
diff --git a/licenses/stampy-academic b/licenses/stampy-academic
deleted file mode 100644
index 31eaa61b6..000000000
--- a/licenses/stampy-academic
+++ /dev/null
@@ -1,22 +0,0 @@
-This is a release version.  Permission is granted for the normal 
-use of the program and its output in an academic setting, including
-in publications.  If the program is used to generate data for a 
-publication, please cite this paper:
-
-  G. Lunter and M. Goodson.  Stampy: A statistical algorithm for 
-  sensitive and fast mapping of Illumina sequence reads.  Genome
-  Res. 2011 21:936-939.
-
-The program itself may not be modified in any way, and may not be
-reverse-engineered.
-
-This license does not allow the use of this program for any 
-commercial purpose.  If you wish to use this program for commercial 
-purposes, please contact the author.
-
-No guarantees are given as to the program's correctness, or the 
-accuracy or completeness of its output.  The author accepts no 
-liability for damage or otherwise following from using and 
-interpreting the output of this program.  The software is supplied 
-"as is", without obligation by the author to provide any services 
-or support.
diff --git a/licenses/sun-bcla-jhall b/licenses/sun-bcla-jhall
new file mode 100644
index 000000000..5dfad9d6e
--- /dev/null
+++ b/licenses/sun-bcla-jhall
@@ -0,0 +1,234 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 3.2//EN"><html><head>
+	<meta http-equiv="CONTENT-TYPE" content="text/html; charset=iso-8859-1"><title></title>
+	
+	<meta name="GENERATOR" content="StarOffice 6.0  (Solaris Sparc)">
+	<meta name="AUTHOR" content="douglass hall">
+	<meta name="CREATED" content="20010118;13284400">
+	<meta name="CHANGED" content="20030905;13512000"></head>
+
+<body lang="en-US">
+<p align="center"><font size="4">Sun Microsystems, Inc.</font> <br><font size="4">Binary
+Code License Agreement</font></p>
+<p>READ THE TERMS OF THIS AGREEMENT AND ANY PROVIDED SUPPLEMENTAL
+LICENSE TERMS (COLLECTIVELY "AGREEMENT") CAREFULLY BEFORE
+OPENING THE SOFTWARE MEDIA PACKAGE.á BY OPENING THE SOFTWARE
+MEDIA PACKAGE, YOU AGREE TO THE TERMS OF THIS AGREEMENT.á IF YOU
+ARE ACCESSING THE SOFTWARE ELECTRONICALLY, INDICATE YOUR ACCEPTANCE
+OF THESE TERMS BY SELECTING THE "ACCEPT" BUTTON AT THE END
+OF THIS AGREEMENT.á IF YOU DO NOT AGREE TO ALL THESE TERMS,
+PROMPTLY RETURN THE UNUSED SOFTWARE TO YOUR PLACE OF PURCHASE FOR A
+REFUND OR, IF THE SOFTWARE IS ACCESSED ELECTRONICALLY, SELECT THE
+"DECLINE" BUTTON AT THE END OF THIS AGREEMENT. 
+</p>
+<p><b>1.á LICENSE TO USE.</b>á Sun grants you a
+non-exclusive and non-transferable license for the internal use only
+of the accompanying software and documentation and any error
+corrections provided by Sun (collectively "Software"), by
+the number of users and the class of computer hardware for which the
+corresponding fee has been paid. 
+</p>
+<p><b>2.á RESTRICTIONS.á</b> Software is confidential and
+copyrighted. Title to Software and all associated intellectual
+property rights is retained by Sun and/or its licensors.á Except
+as specifically authorized in any Supplemental License Terms, you may
+not make copies of Software, other than a single copy of Software for
+archival purposes.á Unless enforcement is prohibited by
+applicable law, you may not modify, decompile, or reverse engineer
+Software.á You acknowledge that Software is not designed,
+licensed or intended for use in the design, construction, operation
+or maintenance of any nuclear facility.á Sun disclaims any
+express or implied warranty of fitness for such uses.á No right,
+title or interest in or to any trademark, service mark, logo or trade
+name of Sun or its licensors is granted under this Agreement. 
+</p>
+<p><b>3. LIMITED WARRANTY.</b>á Sun warrants to you that for a
+period of ninety (90) days from the date of purchase, as evidenced by
+a copy of the receipt, the media on which Software is furnished (if
+any) will be free of defects in materials and workmanship under
+normal use.á Except for the foregoing, Software is provided "AS
+IS".á Your exclusive remedy and Sun's entire liability
+under this limited warranty will be at Sun's option to replace
+Software media or refund the fee paid for Software. 
+</p>
+<p><b>4.á DISCLAIMER OF WARRANTY.á</b> UNLESS SPECIFIED IN
+THIS AGREEMENT, ALL EXPRESS OR IMPLIED CONDITIONS, REPRESENTATIONS
+AND WARRANTIES, INCLUDING ANY IMPLIED WARRANTY OF MERCHANTABILITY,
+FITNESS FOR A PARTICULAR PURPOSE OR NON-INFRINGEMENT ARE DISCLAIMED,
+EXCEPT TO THE EXTENT THAT THESE DISCLAIMERS ARE HELD TO BE LEGALLY
+INVALID. 
+</p>
+<p><b>5.á LIMITATION OF LIABILITY.</b>á TO THE EXTENT NOT
+PROHIBITED BY LAW, IN NO EVENT WILL SUN OR ITS LICENSORS BE LIABLE
+FOR ANY LOST REVENUE, PROFIT OR DATA, OR FOR SPECIAL, INDIRECT,
+CONSEQUENTIAL, INCIDENTAL OR PUNITIVE DAMAGES, HOWEVER CAUSED
+REGARDLESS OF THE THEORY OF LIABILITY, ARISING OUT OF OR RELATED TO
+THE USE OF OR INABILITY TO USE SOFTWARE, EVEN IF SUN HAS BEEN ADVISED
+OF THE POSSIBILITY OF SUCH DAMAGES.á In no event will Sun's
+liability to you, whether in contract, tort (including negligence),
+or otherwise, exceed the amount paid by you for Software under this
+Agreement.á The foregoing limitations will apply even if the
+above stated warranty fails of its essential purpose. 
+</p>
+<p><b>6.á Termination.</b>á This Agreement is effective
+until terminated.á You may terminate this Agreement at any time
+by destroying all copies of Software.á This Agreement will
+terminate immediately without notice from Sun if you fail to comply
+with any provision of this Agreement.á Upon Termination, you
+must destroy all copies of Software. 
+</p>
+<p><b>7. Export Regulations.</b> All Software and technical data
+delivered under this Agreement are subject to US export control laws
+and may be subject to export or import regulations in other
+countries.á You agree to comply strictly with all such laws and
+regulations and acknowledge that you have the responsibility to
+obtain such licenses to export, re-export, or import as may be
+required after delivery to you. 
+</p>
+<p><b>8.áá U.S. Government Restricted Rights.á</b> If
+Software is being acquired by or on behalf of the U.S. Government or
+by a U.S. Government prime contractor or subcontractor (at any tier),
+then the Government's rights in Software and accompanying
+documentation will be only as set forth in this Agreement; this is in
+accordance with 48 CFR 227.7201 through 227.7202-4 (for Department of
+Defense (DOD) acquisitions) and with 48 CFR 2.101 and 12.212 (for
+non-DOD acquisitions). 
+</p>
+<p><b>9.á Governing Law.</b>á Any action related to this
+Agreement will be governed by California law and controlling U.S.
+federal law.á No choice of law rules of any jurisdiction will
+apply. 
+</p>
+<p><b>10.á Severability.</b> If any provision of this Agreement
+is held to be unenforceable, this Agreement will remain in effect
+with the provision omitted, unless omission would frustrate the
+intent of the parties, in which case this Agreement will immediately
+terminate. 
+</p>
+<p><b>11.á Integration.</b>á This Agreement is the entire
+agreement between you and Sun relating to its subject matter.á
+It supersedes all prior or contemporaneous oral or written
+communications, proposals, representations and warranties and
+prevails over any conflicting or additional terms of any quote,
+order, acknowledgment, or other communication between the parties
+relating to its subject matter during the term of this Agreement.á
+No modification of this Agreement will be binding, unless in writing
+and signed by an authorized representative of each party. 
+</p>
+<p align="center" style="margin-bottom: 0cm;"><font size="4"><font color="#000000">JAVAHELP</font>(TM)<font color="#000000"><font size="2" style="font-size: 9pt;">
+</font>VERSION 2.0</font></font><br><font size="4">SUPPLEMENTAL LICENSE
+TERMS</font></p>
+<p align="center" style="margin-bottom: 0cm;"><br>
+</p>
+<p>These supplemental license terms ("Supplemental Terms")
+add to or modify the terms of the Binary Code License Agreement
+(collectively, the "Agreement"). Capitalized terms not
+defined in these Supplemental Terms shall have the same meanings
+ascribed to them in the Agreement. These Supplemental Terms shall
+supersede any inconsistent or conflicting terms in the Agreement, or
+in any license contained within the Software. 
+</p>
+<p style="margin-bottom: 0.51cm;"><font color="#000000"><b>1. Software
+Internal Use and Development License Grant.</b> Subject to the terms
+and conditions of this Agreement, including, but not limited to
+Section 4 (Java(TM) Technology Restrictions) of these Supplemental
+Terms, Sun grants you a non-exclusive, non-transferable, limited
+license to reproduce internally and use internally the binary form of
+the Software complete and unmodified for the sole purpose of
+designing, developing and testing your Java applets and applications
+intended to run on the Java platform ("Programs"). </font>
+</p>
+<p style="margin-bottom: 0.51cm;"><font color="#000000"><b>2. License
+to Distribute Software.</b>á In addition to the license granted
+in Section 1 (Software Internal Use and Development License Grant) of
+these Supplemental Terms, subject to the terms and conditions of this
+Agreement, including but not limited to Section 4 (Java Technology
+Restrictions), Sun grants you a non-exclusive, non-transferable,
+limited license to reproduce and distribute the Software in binary
+form only, provided that you (i) distribute the Software complete and
+unmodified and only bundled as part of your Programs, (ii) do not
+distribute additional software intended to replace any component(s)
+of the Software, (iii) do not remove or alter any proprietary legends
+or notices contained in the Software, (iv) only distribute the
+Software subject to a license agreement that protects Sun's interests
+consistent with the terms contained in this Agreement, and (v) agree
+to defend and indemnify Sun and its licensors from and against any
+damages, costs, liabilities, settlement amounts and/or expenses
+(including attorneys' fees) incurred in connection with any claim,
+lawsuit or action by any third party that arises or results from the
+use or distribution of any and all Programs and/or Software. </font>
+</p>
+<p style="margin-bottom: 0.51cm;"><font color="#000000"><b>3. License
+to Distribute Redistributables.</b>á In addition to the license
+granted in Section 1 (Software Internal Use and Development License
+Grant) of these Supplemental Terms, subject to the terms and
+conditions of this Agreement, including but not limited to Section 3
+(Java Technology Restrictions) of these Supplemental Terms, Sun
+grants you a non-exclusive, non-transferable, limited license to
+reproduce and distribute those files specifically identified as
+redistributable in the Software "README" file
+("Redistributables") provided that: (i) you distribute the
+Redistributables complete and unmodified (unless otherwise specified
+in the applicable README file), and only bundled as part of your
+Programs, (ii) you do not distribute additional software intended to
+supersede any component(s) of the Redistributables, (iii) you do not
+remove or alter any proprietary legends or notices contained in or on
+the Redistributables, (iv) you only distribute the Redistributables
+pursuant to a license agreement that protects Sun's interests
+consistent with the terms contained in the Agreement, and (v) you
+agree to defend and indemnify Sun and its licensors from and against
+any damages, costs, liabilities, settlement amounts and/or expenses
+(including attorneys' fees) incurred in connection with any claim,
+lawsuit or action by any third party that arises or results from the
+use or distribution of any and all Programs and/or Software. </font>
+</p>
+<p style="margin-bottom: 0.51cm;"><b><font color="#000000">4. Java
+Techn</font>ology Restrictions.</b> You may not modify the Java
+Platform Interface ("JPI", identified as classes contained
+within the "java" package or any subpackages of the "java"
+package), by creating additional classes within the JPI or otherwise
+causing the addition to or modification of the classes in the JPI.á
+In the event that you create an additional class and associated
+API(s) which (i) extends the functionality of the Java platform, and
+(ii) is exposed to third party software developers for the purpose of
+developing additional software which invokes such additional API, you
+must promptly publish broadly an accurate specification for such API
+for free use by all developers. You may not create, or authorize your
+licensees to create, additional classes, interfaces, or subpackages
+that are in any way identified as "java", "javax",
+"sun" or similar convention as specified by Sun in any
+naming convention designation. 
+</p>
+<p style="margin-bottom: 0.51cm;"><b>5. Java Runtime Availability.</b>á
+Refer to the appropriate version of the Java Runtime Environment
+binary code license (currently located at
+http://www.java.sun.com/jdk/index.html) for the availability of
+runtime code which may be distributed with Java applets and
+applications. 
+</p>
+<p style="margin-bottom: 0.51cm;"><b>6. Trademarks and Logos.</b> You
+acknowledge and agree as between you and Sun that Sun owns the SUN,
+SOLARIS, JAVA, JINI, FORTE, and iPLANET trademarks and all SUN,
+SOLARIS, JAVA, JINI, FORTE, and iPLANET-related trademarks, service
+marks, logos and other brand designations ("Sun Marks"),
+and you agree to comply with the Sun Trademark and Logo Usage
+Requirements currently located at
+http://www.sun.com/policies/trademarks. Any use you make of the Sun
+Marks inures to Sun's benefit. 
+</p>
+<p style="margin-bottom: 0.51cm;"><b>7. Source Code.</b> Software may
+contain source code that is provided solely for reference purposes
+pursuant to the terms of this Agreement.  Source code may not be
+redistributed unless expressly provided for in this Agreement. Some
+source code may contain alternative license terms that apply only to
+that source code file.</p>
+<p style="margin-bottom: 0.51cm;"><b>8. Termination for Infringement.</b>á
+Either party may terminate this Agreement immediately should any
+Software become, or in either party's opinion be likely to become,
+the subject of a claim of infringement of any intellectual property
+right. 
+</p>
+<p style="margin-bottom: 0.51cm;"><font face="Thorndale"><font color="#000000">For
+inquiries please contact: Sun Microsystems, Inc. 4150 Network Circle,
+Santa Clara, California 95054.</font></font> <br><i>(LFI#135834/Form
+ID#011801)</i></p>
+</body></html>
\ No newline at end of file
diff --git a/licenses/tmhmm b/licenses/tmhmm
deleted file mode 100644
index 529d135d5..000000000
--- a/licenses/tmhmm
+++ /dev/null
@@ -1,217 +0,0 @@
-  ACADEMIC SOFTWARE LICENSE AGREEMENT FOR END-USERS AT PUBLICLY FUNDED
-  ACADEMIC, EDUCATION OR RESEARCH INSTITUTIONS FOR THE USE OF TMHMM 2.0c
-  
-  By downloading the Software you are consenting to be bound by and become
-  a party to this agreement as the "Licensee". If you do not agree to all
-  of the terms of this agreement, you must not click the Acceptance
-  button, not install the product nor use the product, and you do not
-  become a LICENSEE under this agreement. 
-  
-  If you are not a member of a publicly funded Academic and/or Education
-  and/or Research Institution you must obtain a commercial license, please
-  send mail to (software@cbs.dtu.dk). This software license agreement is
-  entered into by and between Center for Biological Sequence Analysis,
-  Technical University of Denmark (hereinafter "CBS") and the "LICENSEE". 
-  
-  WHEREAS CBS has the right to license all copyrights and other property
-  rights in the Licensed Software identified as TMHMM 2.0c and developed
-  by CBS and CBS desires to license the Software so that it becomes
-  available for public use and benefit. 
-  
-  WHEREAS LICENSEE is a public funded Academic and/or Education and/or
-  Research Institution. 
-  
-  WHEREAS LICENSEE desires to acquire a free non-exclusive license to use
-  the Software for internal research purposes only. 
-  
-  NOW, THEREFORE, in consideration of the mutual promises and covenants
-  contained herein, the parties agree as follows: 
-  
-  1. Definitions 
-  
-  "Licensed Software" means the specific version TMHMM 2.0c pursuant
-  to this Agreement. Any opinion, findings, conclusions or recommendations
-  expressed in the Licensed Software are those of the authors and do not
-  necessarily reflect the views of CBS. 
-  
-  2. License 
-  
-  Subject to the terms and conditions of this Agreement a non-exclusive,
-  non-transferable License to use and copy the Licensed Software is made
-  available free of charge for the LICENSEE which is a non-profit
-  educational, academic and/or research institution. The License is only
-  granted for personal and internal use in research only at one Site,
-  where a Site is defined as a set of contiguous buildings in one
-  location. The software will be used at only one location of LICENSEE. 
-  
-  This license does not entitle Licensee to receive from CBS copies of the
-  Licensed software on disks, tapes or CD's, hard-copy documentation,
-  technical support, telephone assistance, or enhancements or updates to
-  the Licensed Software. 
-  
-  The user and any research assistants, co-workers or other workers who
-  may use the Software agree to not give the program to third parties or
-  grant licenses on software, which include the Software, alone or
-  integrated into other software, to third parties. Modification of the
-  source code is prohibited without the prior written consent of CBS. 
-  
-  3. Ownership 
-  
-  Except as expressly licensed in this Agreement, CBS shall retain title
-  to the Licensed Software, and any upgrades and modifications created by
-  CBS. 
-  
-  4. Consideration 
-  
-  In consideration for the license rights granted by CBS, LICENSEE will
-  obtain this academic license free of charge. 
-  
-  5. Copies 
-  
-  LICENSEE shall have the right to make copies of the Licensed Software
-  for internal use at the Site and for back-up purposes under this
-  Agreement, but agrees that all such copies shall contain the copyright
-  notices and all other reasonable and appropriate proprietary markings or
-  confidential legends that appear on the Licensed Software provided
-  hereunder. 
-  
-  6. Support 
-  
-  CBS shall have no obligation to offer support services to LICENSEE, and
-  nothing contained herein shall be interpreted as to require CBS to
-  provide maintenance, installation services, version updates, debugging,
-  consultation or end-user support of any kind. 
-  
-  7. Software Protection 
-  
-  LICENSEE acknowledges that the Licensed Software is proprietary to CBS.
-  The software code shall be treated as trade secrets and confidential
-  information of CBS, and LICENSEE agrees to use best efforts to hold the
-  same in confidence. LICENSEE's obligation for confidentiality shall not
-  extend to any information which is or becomes generally available to the
-  public, is already known to or subsequently disclosed by third parties
-  to LICENSEE and at its free disposal, or is independently developed by
-  LICENSEE or its affiliates without the use of the confidential
-  information disclosed by CBS, or is required by law or legal process. 
-  
-  Except as other wise expressly permitted in this Agreement, Licensee my
-  not (i) modify or create any derivative works of the Licensed Software
-  or documentation, including customization, translation or localization;
-  (ii) decompile, disassemble, reverse engineer, or otherwise attempt to
-  derive the source code for the Product; (iii) redistribute, encumber,
-  sell, rent, lease, sublicense, or otherwise transfer rights to the
-  Licensed Software; (iv) remove or alter any trademark, logo, copyright
-  or other proprietary notices, legends, symbols or labels in the Product;
-  or (v) publish any results of benchmark tests run on the Product to a
-  third party without CBS's prior written consent. 
-  
-  8. Representations of CBS to LICENSEE 
-  
-  CBS represents to LICENSEE that (i) CBS has the right to grant the
-  License and to enter into this agreement, (ii) that, to the best of
-  CBS's knowledge, the Licensed software does not infringe any patent,
-  copyright or trade secrets of any third party, provided however that
-  such representation and warranty shall not apply to any addition to, or
-  modifications or adaptation of, the Licensed Software made by LICENSEE
-  and (iii) CBS undertakes to use best efforts to cooperate with and
-  assist LICENSEE, at LICENSEE's expense, in defending itself against any
-  action based on the alleged infringement of any third party patent,
-  copyright or trade secret rights resulting from or relating to the use
-  or licensing of the Licensed Software by LICENSEE. 
-  
-  9. Indemnity and Disclaimer of Warranties 
-  
-  Except as expressly set forth in this agreement, CBS makes no
-  representations or warranties, express or implied. 
-  
-  The product is provided free of charge, and, therefore, on an "as is"
-  basis, without warranty of any kind, express or implied, including
-  without limitation the warranties that it is free of defects, virus
-  free, able to operate on an uninterrupted basis, merchantable, fit for a
-  particular purpose or non-interfering. The entire risk as to the quality
-  and performance of the Licensed Software is borne by LICENSEE. 
-  
-  By way of example, but not limitation, CBS makes no representations or
-  warranties of merchantability or fitness for any particular application
-  or, except as set forth in paragraph 8, that the use of the Software
-  will not infringe any patents, copyrights or trademarks or other rights
-  of third parties. The entire risk as to the quality and performance of
-  the product is borne by LICENSEE. CBS shall not be liable for any
-  liability or damages with respect to any claim by LICENSEE or any third
-  party on account of, or arising from the license or use of the Software.
-  
-  Should the Licensed Software prove defective in any respect, LICENSEE
-  and not LICENSOR or it's affiliates should assume the entire cost of any
-  service and repair. This disclaimer of warranty constitutes an essential
-  part of this agreement. No use of the licensed product is authorized
-  hereunder except under this disclaimer. 
-  
-  In no event will LICENSOR or its affiliates be liable for any indirect,
-  special, incidental or consequential damages arising out of the use of
-  or inability to use the product, including, without limitation, damages
-  for lost profits, loss of goodwill, work stoppage, computer failure or
-  malfunction, or any and all other commercial damages or losses, even if
-  advised of the possibility thereof, and regardless of the legal or
-  equitable theory (contract, tort or otherwise) upon which the claim is
-  based. 
-  
-  10. Promotional Advertising & References 
-  
-  LICENSEE may not use the name of the Licensed Software in its
-  promotional advertising, product literature, and other similar
-  promotional materials to be disseminated to the public or any portion
-  thereof. LICENSEE agrees not to identify CBS in any promotional
-  advertising or other promotional materials to be disseminated to the
-  public, or any portion thereof without CBS's prior written consent.
-  LICENSEE agrees that any reference to the software for crystallographic
-  computations will cite one or more publications as set forth in the
-  manual and in agreement with common scientific practice. CBS shall not
-  use LICENSEE's name in publicity or advertising involving this Agreement
-  or otherwise without LICENSEE's prior written consent which may be
-  withheld at LICENSEE's sole discretion. 
-  
-  11. Term 
-  
-  This Agreement and the license rights granted herein shall become
-  effective as of the date this Agreement is executed by both parties and
-  shall be perpetual unless terminated in accordance with this Section. 
-  
-  CBS may terminate this Agreement at any time. 
-  
-  Either party may terminate this Agreement at any time effective upon the
-  other party's breach of any agreement, covenant, or representation made
-  in this Agreement, such breach remaining uncorrected sixty (60) days
-  after written notice thereof. 
-  
-  LICENSEE shall have the right, at any time, to terminate this Agreement
-  without cause by written notice to CBS specifying the date of
-  termination. 
-  
-  Upon termination, LICENSEE shall destroy all full and partial copies of
-  the Licensed Software. 
-  
-  12. Governing Law 
-  
-  This Agreement shall be construed in accordance with the laws of
-  Denmark. 
-  
-  13. General 
-  
-  The parties agree that this Agreement is the complete and exclusive
-  agreement among the parties and supersedes all proposals and prior
-  agreements whether written or oral, and all other communications among
-  the parties relating to the subject matter of this Agreement. This
-  Agreement cannot be modified except in writing and signed by both
-  parties. Failure by either party at any time to enforce any of the
-  provisions of this Agreement shall not constitute a waiver by such party
-  of such provision nor in any way affect the validity of this Agreement. 
-  
-  The invalidity of singular provisions does not affect the validity of
-  the entire understanding. The parties are obligated, however, to replace
-  the invalid provisions by a regulation which comes closest to the
-  economic intent of the invalid provision. The same shall apply mutatis
-  mutandis in case of a gap. 
-  
-  IN WITNESS WHEREOF, the LICENSEE hereto have caused this Agreement to be
-  duly executed on the date of the download of the software and by
-  accepting the license conditions by pressing the Acceptance button. 
diff --git a/licenses/unio b/licenses/unio
deleted file mode 100644
index 55b34fa4a..000000000
--- a/licenses/unio
+++ /dev/null
@@ -1,133 +0,0 @@
-This legal document has to accompany all official or custom UNIO files. It may not be
-removed or modified. This document pertains to all use of the software package
-worldwide. This document supersedes all previous licenses or distribution policies.
-Contract for license of software
-between
-
-ETH Zurich
-Represented by Kurt Wüthrich
-(licensor)
-
-and
-
-the licensee
-
-1. Definition of the Software
-UNIO is a software package for automated NMR data analysis. It provides the
-functionalities of the four existing algorithms: MATCH, for automated backbone
-assignment, ASCAN, for automated side-chain assignment, ATNOS, for automated
-peak picking and NOE identification in 2D homonuclear and 3D heteronuclear-
-resolved NOESY spectra, and CANDID, for automated NOE assignment of NOESY
-cross peaks in conjunction with protein three-dimensional structure calculation.
-Details are to learn from the following publications:
-Herrmann, T., Güntert, P. & Wüthrich, K.
-"Protein NMR structure determination with automated NOE-identification in the NOESY spectra using the new
-software ATNOS."
-J. Biomol. NMR 2002 Nov; 24(3): 171-189.
-Herrmann, T., Güntert, P. & Wüthrich, K.
-"Protein NMR structure determination with automated NOE assignment using the new software CANDID and the
-torsion angle dynamics algorithm DYANA."
-J. Mol. Biol. 2002 May; 319(1): 209-227.
-Volk, J.; Herrmann, T.; Wüthrich, K.
-“Automated sequence-specific protein NMR assignment using the memetic algorithm MATCH.�
-J. Biomol.NMR. 2008, 41, 127-138.
-Fiorito, F.; Damberger, F.F.; Herrmann, T.; Wüthrich, K.
-“Automated amino acid side-chain assignment of proteins using 13C- and 15N resolved 3D [1H, 1H]-NOESY.�
-J. Biomol. NMR 2008, 42, 23-33.
-This Software is composed of 3 types of files: executable (binary) files, configuration
-files and documentation files. Not included is the source code.
-(together “Software�)
-2. License of ETH Zurich
-ETH Zurich hereby grants a single, non-exclusive, world-wide, royalty-free license to
-use Software subject to all the terms and conditions of this Contract to the licensee.
-3. The scope of the license
-a. Use
-The Software may be used exclusively for research purposes in academic
-institutions. The licensee retains all rights to results from such use.
-Only the use for non-commercial purposes is allowed. Prohibited is for example:
-i. selling, licensing or renting the Software to third parties for a fee, payment of
-money or other compensation
-ii.
-using the Software to provide services or products to others for which the
-licensee is compensated in any manner (by payment of money or otherwise),
-including providing support or maintenance for the Software
-iii.
-using the Software to develop a similar application on any platform for
-commercial distribution.
-b. Reproduction
-Reproduction is prohibited except for the provisions of the applicable law (article 21
-URG [Bundesgesetz über das Urheberrecht, SR 231.1]).
-c. Modification
-Neither modification, combination with other commercial applications or other
-preparation of derivative works of the Software, nor reverse engeneering,
-decompilation, disassembly or other reduction of any portion of the Software is
-permitted except for the provisions of the applicable law (article 21 URG
-[Bundesgesetz über das Urheberrecht, SR 231.1]).
-d. Distribution
-Assignment to a third party is prohibited.
-4. Obligations of licensee
-a. Use
-Any report or publication of results obtained by the Software has to be acknowledged
-by citing the following four publications:
-Herrmann, T., Güntert, P. & Wüthrich, K.
-"Protein NMR structure determination with automated NOE-identification in the NOESY spectra using the new
-software ATNOS."
-J. Biomol. NMR 2002 Nov; 24(3): 171-189.
-Herrmann, T., Güntert, P. & Wüthrich, K.
-"Protein NMR structure determination with automated NOE assignment using the new software CANDID and the
-torsion angle dynamics algorithm DYANA."
-J. Mol. Biol. 2002 May; 319(1): 209-227.
-Volk, J.; Herrmann, T.; Wüthrich, K.
-“Automated sequence-specific protein NMR assignment using the memetic algorithm MATCH.�
-J. Biomol.NMR. 2008, 41, 127-138.
-Fiorito, F.; Damberger, F.F.; Herrmann, T.; Wüthrich, K.
-“Automated amino acid side-chain assignment of proteins using 13C- and 15N resolved 3D [1H, 1H]-NOESY.�
-J. Biomol. NMR 2008, 42, 23-33.
-b. Modification
-Reports of modifications or derivative works are to be made to ETH Zurich, and are
-to be made available on request.
-5. Intellectual property and other rights
-Ownership and intellectual property rights in and to the Software shall remain in ETH
-Zurich. ETH Zurich reserves the right to withdraw distribution privileges from any group,
-individual, or organization for any reason.
-6. Maintenance, support, upgrades or new releases
-ETH Zurich doesn’t have any obligation of maintenance, support, upgrades or new
-releases and disclaims all costs associated with serving, repair or correction.
-7. Warranty
-The Software is provided “as is�. ETH Zurich does not make any warranty of any
-kind. Disclaimed warranties include for example:
-i. warranty of merchantability, satisfactory quality and fitness for a particular
-purpose
-ii.
-warranty of accuracy of results, of the quality and performance of the Software
-iii.
-warranty of noninfringement of the intellectual property rights of third parties.
-8. Liability
-ETH Zurich disclaims all liabilities. ETH Zurich shall not have any liability for any
-direct or indirect damage except for the provisions of the applicable law (article 100
-OR [Schweizerisches Obligationenrecht]).
-9. Termination
-This Contract may be terminated by ETH Zurich at any time. On termination all
-copies of the Software has to be destroyed.
-10. Severability
-If any provisions of this Contract will become invalid or unenforceable, such invalidity
-or enforceability shall not affect the other provisions of Contract which shall remain in
-full force and effect provided that the basic intent of the parties is preserved. The
-parties will in good faith negotiate substitute provisions to replace invalid or
-unenforceable provisions which reflect the orginal intentions of the parties as closely
-as possible and maintain the economic balance between the parties.
-11. Applicable law
-This Contract as well as any and all matters arising out of it shall exclusively be
-governed by and interpreted in accordance with the laws of Switzerland, excluding its
-principles of conflict of laws.
-12. Jurisdiction
-If any dispute, controversy or difference arises between the Parties hereto in
-connection with or out of this Contract, the parties hereto shall first attempt to settle it
-amicably.
-Should settlement not be achieved, the Courts of Zurich-City shall have exclusive
-jurisdiction.
-By using this software you indicate your acceptance.
-For commercial use of the Software please contact torsten.herrmann@ens-lyon.fr.
-In case of any problems, comments, questions, please contact the UNIO authors
-using the E-mail address torsten.herrmann@ens-lyon.fr
-
diff --git a/licenses/vampir b/licenses/vampir
deleted file mode 100644
index 70f15aa22..000000000
--- a/licenses/vampir
+++ /dev/null
@@ -1,36 +0,0 @@
-Copyright (c) 2005-2013, ZIH, TU Dresden, Federal Republic of Germany
-
-Copyright (c) 1998-2005, Forschungszentrum Juelich, Juelich Supercomputing
-                         Centre, Federal Republic of Germany
-
-Copyright (c) 2007-2008, High Performance Computing Center Stuttgart,
-                         Federal Republic of Germany
-
-All rights reserved.
-
-Redistribution and use in source and binary forms, with or without modification,
-are permitted provided that the following conditions are met:
-
-- Redistributions of source code must retain the above copyright notice,
-this list of conditions and the following disclaimer.
-
-- Redistributions in binary form must reproduce the above copyright notice,
-this list of conditions and the following disclaimer in the documentation and/or
-other materials provided with the distribution.
-
-- Neither the name of ZIH, TU Dresden, Forschungszentrum Juelich, Juelich
-Supercomputing Centre, or High Performance Computing Center Stuttgart, nor the
-names of its contributors may be used to endorse or promote products derived
-from this software without pecific prior written permission.
-
-THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" AND
-ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED
-WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE
-DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT OWNER OR CONTRIBUTORS BE LIABLE FOR
-ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES
-(INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES;
-LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON
-ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT
-(INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS
-SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
-
diff --git a/media-gfx/PhiloGL/Manifest b/media-gfx/PhiloGL/Manifest
deleted file mode 100644
index f045b5183..000000000
--- a/media-gfx/PhiloGL/Manifest
+++ /dev/null
@@ -1 +0,0 @@
-DIST PhiloGL-1.4.3.zip 2484628 BLAKE2B 43adf2b1fea3c98a4970fbca8ce5b3f5feef8b61b085043c897f36d7e18e0abb5c0ec44ce24723d6a99e7cfb4d5ab285cc11982630e239827d624dbcfab1e49d SHA512 5483b92e0ed282734f08a42f231f8b871a821c977d0ba8fd59169bf557d41761a7d03252f1f8bc4807d912edb96bedf0fa21f0b330a521079708580d002ddc4b
diff --git a/media-gfx/PhiloGL/PhiloGL-1.4.3.ebuild b/media-gfx/PhiloGL/PhiloGL-1.4.3.ebuild
deleted file mode 100644
index 2b9792e69..000000000
--- a/media-gfx/PhiloGL/PhiloGL-1.4.3.ebuild
+++ /dev/null
@@ -1,37 +0,0 @@
-# Copyright 1999-2014 Gentoo Foundation
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=5
-
-DESCRIPTION="WebGL Framework for Data Vis, Creative Coding and Game Development"
-HOMEPAGE="http://www.senchalabs.org/philogl/"
-SRC_URI="http://www.senchalabs.org/philogl/downloads/${P}.zip"
-
-LICENSE="MIT"
-SLOT="0"
-KEYWORDS="~amd64 ~x86"
-IUSE="examples"
-
-S=${WORKDIR}
-
-src_prepare() {
-	if use examples ; then
-		for f in $(find "${S}"/examples -name index.html); do
-	   		sed -e "s:../../../build:/usr/share/${PN}/build:g" \
-				-e "s:../../build:/usr/share/${PN}/build:g" \
-				-i ${f} || die
-		done
-		sed -e "s:../../../shaders/:/usr/share/${PN}/shaders/:" \
-			-i examples/lessons/{14,15,16}/index.js || die
-	fi
-}
-
-src_install() {
-	insinto /usr/share/${PN}
-	doins -r build shaders
-
-	if use examples ; then
-		insinto /usr/share/doc/${PF}
-		doins -r examples
-	fi
-}
diff --git a/media-gfx/PhiloGL/metadata.xml b/media-gfx/PhiloGL/metadata.xml
deleted file mode 100644
index c62a87f48..000000000
--- a/media-gfx/PhiloGL/metadata.xml
+++ /dev/null
@@ -1,8 +0,0 @@
-<?xml version="1.0" encoding="UTF-8"?>
-<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
-<pkgmetadata>
-	<maintainer type="person">
-		<email>xarthisius@gentoo.org</email>
-		<name>Kacper Kowalik</name>
-	</maintainer>
-</pkgmetadata>
diff --git a/media-gfx/brlcad/Manifest b/media-gfx/brlcad/Manifest
index 76543bcb6..0ead205b0 100644
--- a/media-gfx/brlcad/Manifest
+++ b/media-gfx/brlcad/Manifest
@@ -1,3 +1 @@
-DIST brlcad-7.22.0.tar.gz 80633583 BLAKE2B 4641f4d3003d160decc96f04dfeeefcc21f8db0d85a81afca30a847a2bf6c1cc0dda9d3c924869e7f92c2cdc2a68815a3b8fb4f590718ba9fceb60c14186af09 SHA512 515df65cf0e6a7a2109309c05a31abfad80889a40236f79bf09fe92528cd35742be76a3074d3aa12320c8e85a32d35661af8c7e2acef0b2a2a588de885a0e30d
-DIST brlcad-7.24.0.tar.gz 80060095 BLAKE2B 7d0235459b319515e14c81703892e247db1eef61a1909b0e9c228e532aa5dad123ffe38b2b6983331818f918194ae7fa52c60e638a872a752565563a91b031d6 SHA512 53c549173b95640125fa22ee7eec8a891c327bb1a8d3d046cc23a53a8e34d4a1b03c1729be30ad69aa9e28f05ec2880786d0a972707fa974e50ff227677b3b51
-DIST brlcad-7.24.2.tar.gz 81355643 BLAKE2B f66599f1d7dfedbcb1eea0aa405e340e05bf26590e1d1da5643e944498d8a18377df95e84b6fc9ae7cd45a4176c2040f66528de93e1114fd8e0ed502ecb198c1 SHA512 c0280bd55ad07c267fc77c643f8d687f91c7b193dc40d23fb6757d43378891121be762e07fdefeb621d72bcde0be42fb6a7ad67088446cf97df3ec299c86db88
+DIST brlcad-7.32.4.tar.gz 124190135 BLAKE2B 44366199aa5274853d3c8482d6a741e6774a9dc3c8dd8f14ac7c0379c0a776d640d1a48870fdd2c916c6edb2d871f3aacf9402fe73dc64682607b9d998caa02e SHA512 14388ec1a63e70bd5418372711f9231a371de0468bc3d535b772149f910a1825f457810547fdc2cf0efae2236f87edaf49439e209bff2c62f26f3f0cfc097e1a
diff --git a/media-gfx/brlcad/brlcad-7.22.0.ebuild b/media-gfx/brlcad/brlcad-7.22.0.ebuild
deleted file mode 100644
index 2d611e73b..000000000
--- a/media-gfx/brlcad/brlcad-7.22.0.ebuild
+++ /dev/null
@@ -1,110 +0,0 @@
-# Copyright 1999-2015 Gentoo Foundation
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=5
-inherit cmake-utils eutils java-pkg-2 flag-o-matic
-
-DESCRIPTION="Constructive solid geometry modeling system"
-HOMEPAGE="http://brlcad.org/"
-SRC_URI="mirror://sourceforge/${PN}/${P}.tar.gz"
-
-LICENSE="LGPL-2 BSD"
-SLOT="0"
-KEYWORDS="~amd64 ~x86"
-IUSE="benchmarks debug doc examples java opengl smp"
-
-RDEPEND="media-libs/libpng:0
-	sys-libs/zlib
-	>=sci-libs/tnt-3
-	sci-libs/jama
-	<dev-lang/tcl-8.6:0
-	<dev-lang/tk-8.6:0
-	<dev-tcltk/itcl-4.0
-	<dev-tcltk/itk-4.0
-	dev-tcltk/iwidgets
-	dev-tcltk/tkimg
-	dev-tcltk/tkpng
-	sys-libs/libtermcap-compat
-	media-libs/urt
-	x11-libs/libXt
-	x11-libs/libXi
-	java? ( >=virtual/jre-1.5:* )
-	"
-
-DEPEND="${RDEPEND}
-	sys-devel/bison
-	sys-devel/flex
-	dev-tcltk/tktable
-	>=virtual/jre-1.5:*
-	doc? (
-		dev-libs/libxslt
-		app-doc/doxygen
-	)"
-
-BRLCAD_DIR="${EPREFIX}/usr/${PN}"
-
-#src_prepare() {
-#	epatch "${FILESDIR}/${P}-cmake.patch"
-#}
-
-src_configure() {
-filter-flags -std=c++0x
-	if use Debug; then
-		CMAKE_BUILD_TYPE=Debug
-		else
-		CMAKE_BUILD_TYPE=Release
-		fi
-	local mycmakeargs=(
-		-DCMAKE_INSTALL_PREFIX="${BRLCAD_DIR}"
-		-DBRLCAD_ENABLE_STRICT=OFF
-		-DBRLCAD-ENABLE_STRICT=OFF
-		-DBRLCAD-ENABLE_COMPILER_WARNINGS=OFF
-		-DBRLCAD_FLAGS_OPTIMIZATION=ON
-		-DBRLCAD_ENABLE_X11=ON
-		-DBRLCAD_BUNDLED_LIBS=AUTO
-		)
-
-			# use flag triggered options
-	if use debug; then
-		mycmakeargs += "-DCMAKE_BUILD_TYPE=Debug"
-	else
-		mycmakeargs += "-DCMAKE_BUILD_TYPE=Release"
-	fi
-	mycmakeargs+=(
-		$(cmake-utils_use opengl BRLCAD_ENABLE_OPENGL)
-#experimental RTGL support
-	#	$(cmake-utils_use opengl BRLCAD_ENABLE_RTGL)
-		$(cmake-utils_use amd64 BRLCAD_ENABLE_64BIT)
-		$(cmake-utils_use smp BRLCAD_ENABLE_SMP)
-	#	$(cmake-utils_use java BRLCAD_ENABLE_RTSERVER)
-		$(cmake-utils_use examples BRLCAD_INSTALL_EXAMPLE_GEOMETRY)
-		$(cmake-utils_use doc BRLCAD_EXTRADOCS)
-		$(cmake-utils_use doc BRLCAD_EXTRADOCS_PDF)
-		$(cmake-utils_use doc BRLCAD_EXTRADOCS_MAN)
-		$(cmake-utils_use debug BRLCAD_ENABLE_VERBOSE_PROGRESS)
-			)
-	cmake-utils_src_configure
-}
-
-src_compile() {
-	cmake-utils_src_compile
-}
-
-src_test() {
-	cmake-utils_src_test
-	#emake check || die "emake check failed"
-	if use benchmarks; then
-		emake benchmark
-	fi
-}
-
-src_install() {
-	cmake-utils_src_install
-	rm -f "${D}"usr/share/brlcad/{README,NEWS,AUTHORS,HACKING,INSTALL,COPYING}
-	dodoc AUTHORS NEWS README HACKING TODO BUGS ChangeLog
-	echo "PATH=\"${BRLCAD_DIR}/bin\"" >  99brlcad
-	echo "MANPATH=\"${BRLCAD_DIR}/man\"" >> 99brlcad
-	doenvd 99brlcad
-	newicon misc/macosx/Resources/ReadMe.rtfd/brlcad_logo_tiny.png brlcad.png
-	make_desktop_entry mged "BRL-CAD" brlcad "Graphics;Engineering"
-}
diff --git a/media-gfx/brlcad/brlcad-7.24.0.ebuild b/media-gfx/brlcad/brlcad-7.24.0.ebuild
deleted file mode 100644
index 417f0bfdf..000000000
--- a/media-gfx/brlcad/brlcad-7.24.0.ebuild
+++ /dev/null
@@ -1,110 +0,0 @@
-# Copyright 1999-2015 Gentoo Foundation
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=5
-inherit cmake-utils eutils java-pkg-2 flag-o-matic
-
-DESCRIPTION="Constructive solid geometry modeling system"
-HOMEPAGE="http://brlcad.org/"
-SRC_URI="mirror://sourceforge/${PN}/${P}.tar.gz"
-
-LICENSE="LGPL-2 BSD"
-SLOT="0"
-KEYWORDS="~amd64 ~x86"
-IUSE="benchmarks debug doc examples java opengl smp"
-
-RDEPEND="media-libs/libpng:0
-	sys-libs/zlib
-	>=sci-libs/tnt-3
-	sci-libs/jama
-	<dev-lang/tcl-8.6:0
-	<dev-lang/tk-8.6:0
-	<dev-tcltk/itcl-4.0
-	<dev-tcltk/itk-4.0
-	dev-tcltk/iwidgets
-	dev-tcltk/tkimg
-	dev-tcltk/tkpng
-	sys-libs/libtermcap-compat
-	media-libs/urt
-	x11-libs/libXt
-	x11-libs/libXi
-	java? ( >=virtual/jre-1.5:* )
-	"
-
-DEPEND="${RDEPEND}
-	sys-devel/bison
-	sys-devel/flex
-	dev-tcltk/tktable
-	>=virtual/jre-1.5:*
-	doc? (
-		dev-libs/libxslt
-		app-doc/doxygen
-	)"
-
-BRLCAD_DIR="${EPREFIX}/usr/${PN}"
-
-#src_prepare() {
-#	epatch "${FILESDIR}/${P}-cmake.patch"
-#}
-
-src_configure() {
-filter-flags -std=c++0x
-	if use Debug; then
-		CMAKE_BUILD_TYPE=Debug
-		else
-		CMAKE_BUILD_TYPE=Release
-		fi
-	local mycmakeargs=(
-		-DCMAKE_INSTALL_PREFIX="${BRLCAD_DIR}"
-		-DBRLCAD_ENABLE_STRICT=NO
-		-DBRLCAD-ENABLE_COMPILER_WARNINGS=NO
-		-DBRLCAD_BUNDLED_LIBS=ON
-		-DBRLCAD_FLAGS_OPTIMIZATION=ON
-		-DBRLCAD_ENABLE_X11=ON
-		-DCMAKE_BUILD_TYPE=Release
-		)
-
-			# use flag triggered options
-	if use debug; then
-		mycmakeargs += "-DCMAKE_BUILD_TYPE=Debug"
-	else
-		mycmakeargs += "-DCMAKE_BUILD_TYPE=Release"
-	fi
-	mycmakeargs+=(
-		$(cmake-utils_use opengl BRLCAD_ENABLE_OPENGL)
-#experimental RTGL support
-	#	$(cmake-utils_use opengl BRLCAD_ENABLE_RTGL)
-		$(cmake-utils_use amd64 BRLCAD_ENABLE_64BIT)
-		$(cmake-utils_use smp BRLCAD_ENABLE_SMP)
-	#	$(cmake-utils_use java BRLCAD_ENABLE_RTSERVER)
-		$(cmake-utils_use examples BRLCAD_INSTALL_EXAMPLE_GEOMETRY)
-		$(cmake-utils_use doc BRLCAD_EXTRADOCS)
-		$(cmake-utils_use doc BRLCAD_EXTRADOCS_PDF)
-		$(cmake-utils_use doc BRLCAD_EXTRADOCS_MAN)
-		$(cmake-utils_use debug BRLCAD_ENABLE_VERBOSE_PROGRESS)
-			)
-	cmake-utils_src_configure
-}
-
-src_compile() {
-	cmake-utils_src_compile
-}
-
-src_test() {
-	cmake-utils_src_test
-	#emake check || die "emake check failed"
-	if use benchmarks; then
-		emake benchmark
-	fi
-}
-
-src_install() {
-	cmake-utils_src_install
-	rm -f "${D}"usr/share/brlcad/{README,NEWS,AUTHORS,HACKING,INSTALL,COPYING}
-	dodoc AUTHORS NEWS README HACKING TODO BUGS ChangeLog
-	echo "PATH=\"${BRLCAD_DIR}/bin\"" >  99brlcad
-	echo "MANPATH=\"${BRLCAD_DIR}/man\"" >> 99brlcad
-	doenvd 99brlcad
-	newicon misc/macosx/Resources/ReadMe.rtfd/brlcad_logo_tiny.png brlcad.png
-	make_desktop_entry mged "BRL-CAD" brlcad "Graphics;Engineering"
-}
diff --git a/media-gfx/brlcad/brlcad-7.24.2.ebuild b/media-gfx/brlcad/brlcad-7.24.2.ebuild
deleted file mode 100644
index 1bca8bb59..000000000
--- a/media-gfx/brlcad/brlcad-7.24.2.ebuild
+++ /dev/null
@@ -1,109 +0,0 @@
-# Copyright 1999-2015 Gentoo Foundation
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=5
-inherit cmake-utils eutils java-pkg-2 flag-o-matic
-
-DESCRIPTION="Constructive solid geometry modeling system"
-HOMEPAGE="http://brlcad.org/"
-SRC_URI="mirror://sourceforge/${PN}/${P}.tar.gz"
-
-LICENSE="LGPL-2 BSD"
-SLOT="0"
-KEYWORDS="~amd64 ~x86"
-IUSE="benchmarks debug doc examples java opengl smp"
-
-RDEPEND="
-	java? (
-		>=virtual/jre-1.5:*
-	)
-	"
-
-DEPEND="${RDEPEND}
-	>=sci-libs/tnt-3
-	sys-devel/bison
-	sys-devel/flex
-	media-libs/libpng:0
-	<dev-lang/tcl-8.6:0/8.5
-	<dev-lang/tk-8.6:0/8.5
-	dev-tcltk/tktable
-	sys-libs/zlib
-	sys-libs/libtermcap-compat
-	media-libs/urt
-	x11-libs/libXt
-	x11-libs/libXi
-	java? (
-		sci-libs/jama
-		>=virtual/jre-1.5:*
-	)
-	doc? (
-		dev-libs/libxslt
-		app-doc/doxygen
-	)"
-
-BRLCAD_DIR="${EPREFIX}/usr/${PN}"
-
-src_prepare() {
-	epatch "${FILESDIR}/${P}-cmake.patch"
-}
-
-src_configure() {
-	append-cflags "-w"
-	if use debug; then
-		CMAKE_BUILD_TYPE=Debug
-		else
-		CMAKE_BUILD_TYPE=Release
-		fi
-	local mycmakeargs=(
-		-DCMAKE_INSTALL_PREFIX="${BRLCAD_DIR}"
-		-DBRLCAD_ENABLE_STRICT=NO
-		-DBRLCAD-ENABLE_COMPILER_WARNINGS=NO
-		-DBRLCAD_BUNDLED_LIBS=AUTO
-		-DBRLCAD_FLAGS_OPTIMIZATION=ON
-		-DBRLCAD_ENABLE_X11=ON
-		-DBRLCAD_ENABLE_VERBOSE_PROGRESS=ON
-		)
-
-			# use flag triggered options
-	if use debug; then
-		mycmakeargs += "-DCMAKE_BUILD_TYPE=Debug"
-	else
-		mycmakeargs += "-DCMAKE_BUILD_TYPE=Release"
-	fi
-	mycmakeargs+=(
-		$(cmake-utils_use opengl BRLCAD_ENABLE_OPENGL)
-#experimental RTGL support
-#		$(cmake-utils_use opengl BRLCAD_ENABLE_RTGL)
-		$(cmake-utils_use amd64 BRLCAD_ENABLE_64BIT)
-		$(cmake-utils_use smp BRLCAD_ENABLE_SMP)
-		$(cmake-utils_use java BRLCAD_ENABLE_RTSERVER)
-		$(cmake-utils_use examples BRLCAD_INSTALL_EXAMPLE_GEOMETRY)
-		$(cmake-utils_use doc BRLCAD_EXTRADOCS)
-		$(cmake-utils_use doc BRLCAD_EXTRADOCS_PDF)
-		$(cmake-utils_use doc BRLCAD_EXTRADOCS_MAN)
-		)
-	cmake-utils_src_configure
-}
-
-src_compile() {
-	cmake-utils_src_compile
-}
-
-src_test() {
-	cmake-utils_src_test
-	emake check
-	if use benchmarks; then
-		emake benchmark
-	fi
-}
-
-src_install() {
-	cmake-utils_src_install
-	rm -f "${D}"usr/share/brlcad/{README,NEWS,AUTHORS,HACKING,INSTALL,COPYING}
-	dodoc AUTHORS NEWS README HACKING TODO BUGS ChangeLog
-	echo "PATH=\"${BRLCAD_DIR}/bin\"" >  99brlcad
-	echo "MANPATH=\"${BRLCAD_DIR}/man\"" >> 99brlcad
-	doenvd 99brlcad
-	newicon misc/macosx/Resources/ReadMe.rtfd/brlcad_logo_tiny.png brlcad.png
-	make_desktop_entry mged "BRL-CAD" brlcad "Graphics;Engineering"
-}
diff --git a/media-gfx/brlcad/brlcad-7.32.4.ebuild b/media-gfx/brlcad/brlcad-7.32.4.ebuild
new file mode 100644
index 000000000..180542cac
--- /dev/null
+++ b/media-gfx/brlcad/brlcad-7.32.4.ebuild
@@ -0,0 +1,137 @@
+# Copyright 1999-2022 Gentoo Authors
+# Distributed under the terms of the GNU General Public License v2
+
+EAPI=8
+
+inherit cmake desktop java-pkg-2 flag-o-matic
+
+DESCRIPTION="Constructive solid geometry modeling system"
+HOMEPAGE="https://brlcad.org/ https://github.com/BRL-CAD/brlcad"
+SRC_URI="https://github.com/BRL-CAD/${PN}/archive/refs/tags/rel-${PV//./-}.tar.gz -> ${P}.tar.gz"
+S="${WORKDIR}/${PN}-rel-${PV//./-}"
+
+LICENSE="LGPL-2 BSD"
+SLOT="0"
+KEYWORDS="~amd64 ~x86"
+IUSE="benchmarks debug doc examples java opengl smp"
+
+RDEPEND="
+	java? (
+		>=virtual/jre-1.8:*
+	)
+	"
+
+DEPEND="${RDEPEND}
+	dev-util/astyle
+	dev-util/re2c
+	>=sci-libs/tnt-3
+	sci-libs/proj
+	sci-libs/lemon
+	sys-devel/bison
+	sys-devel/flex
+	media-libs/libpng:0
+	>=dev-lang/tcl-8.6:0/8.6
+	>=dev-lang/tk-8.6:0/8.6
+	sys-libs/zlib
+	sys-libs/libtermcap-compat
+	media-libs/urt
+	x11-libs/libXt
+	x11-libs/libXi
+	java? (
+		sci-libs/jama
+		>=virtual/jre-1.8:*
+	)
+	doc? (
+		dev-libs/libxslt
+		app-text/doxygen
+	)"
+
+# Install into /usr/ not recommended by upstream due to possible file conflicts
+# with bundled libraries!
+BRLCAD_DIR="${EPREFIX}/usr/${PN}"
+
+PATCHES=( "${FILESDIR}/${P}-skip-gstep.patch" )
+
+src_prepare() {
+	cmake_src_prepare
+}
+
+src_configure() {
+	append-cflags "-w"
+	if use debug; then
+		CMAKE_BUILD_TYPE=Debug
+	else
+		CMAKE_BUILD_TYPE=Release
+	fi
+	local mycmakeargs=(
+		-DCMAKE_INSTALL_PREFIX="${BRLCAD_DIR}"
+		-DBRLCAD_ENABLE_STRICT=NO
+		-DBRLCAD-ENABLE_COMPILER_WARNINGS=NO
+		-DBRLCAD_BUNDLED_LIBS=AUTO
+		-DBRLCAD_FLAGS_OPTIMIZATION=ON
+		-DBRLCAD_ENABLE_X11=ON
+		-DBRLCAD_ENABLE_VERBOSE_PROGRESS=ON
+		-DACCEPT_USE_OF_DEPRECATED_PROJ_API_H=ON
+# requires itk/itcl version 3, not packaged, use bundled instead
+# 		-DBRLCAD_TKTABLE=OFF
+# 		-DBRLCAD_IWIDGETS=OFF
+# 		-DBRLCAD_ITCL=OFF
+# 		-DBRLCAD_ITK=OFF
+#		-DBRLCAD_TKPNG=OFF
+# Not packaged, use bundled
+# 		-DBRLCAD_GDIAM
+# 		-DBRLCAD_VDS
+# 		-DBRLCAD_SC
+# 		-DBRLCAD_OPENNURBS
+# 		-DBRLCAD_TKHTML
+# 		-DBRLCAD_UTAHRLE
+# 		-DBRLCAD_TERMLIB
+# 		-DBRLCAD_XMLLINT
+# 		-DBRLCAD_XSLTPROC
+# 		-DBRLCAD_PERPLEX
+	)
+
+	# use flag triggered options
+	if use debug; then
+		mycmakeargs+=( -DCMAKE_BUILD_TYPE="Debug" )
+	else
+		mycmakeargs+=( -DCMAKE_BUILD_TYPE="Release" )
+	fi
+	mycmakeargs+=(
+		$(usex opengl BRLCAD_ENABLE_OPENGL)
+		$(usex opengl BRLCAD_ENABLE_RTGL)
+		$(usex amd64 BRLCAD_ENABLE_64BIT)
+		$(usex smp BRLCAD_ENABLE_SMP)
+		$(usex java BRLCAD_ENABLE_RTSERVER)
+		$(usex examples BRLCAD_INSTALL_EXAMPLE_GEOMETRY)
+		$(usex doc BRLCAD_EXTRADOCS)
+		$(usex doc BRLCAD_EXTRADOCS_PDF)
+		$(usex doc BRLCAD_EXTRADOCS_MAN)
+	)
+	cmake_src_configure
+}
+
+src_compile() {
+	cmake_src_compile
+}
+
+src_test() {
+	cmake_src_test
+	emake check
+	if use benchmarks; then
+		emake benchmark
+	fi
+}
+
+src_install() {
+	cmake_src_install
+	rm -f "${D}"/usr/share/brlcad/{README,NEWS,AUTHORS,HACKING,INSTALL,COPYING}
+	dodoc AUTHORS NEWS README HACKING TODO BUGS ChangeLog
+	echo "PATH=\"${BRLCAD_DIR}/bin\"" >  99brlcad
+	echo "MANPATH=\"${BRLCAD_DIR}/man\"" >> 99brlcad
+	doenvd 99brlcad
+	for size in {16,24,36,48,64,96,128,256}; do
+		doicon misc/debian/icons/${size}x${size}/*
+	done
+	domenu misc/debian/*.desktop
+}
diff --git a/media-gfx/brlcad/brlcad-9999.ebuild b/media-gfx/brlcad/brlcad-9999.ebuild
index eefc481a3..5f7c0ad4c 100644
--- a/media-gfx/brlcad/brlcad-9999.ebuild
+++ b/media-gfx/brlcad/brlcad-9999.ebuild
@@ -1,32 +1,35 @@
-# Copyright 1999-2015 Gentoo Foundation
+# Copyright 1999-2022 Gentoo Authors
 # Distributed under the terms of the GNU General Public License v2
 
-EAPI=5
-inherit cmake-utils eutils subversion java-pkg-2 flag-o-matic
+EAPI=8
+
+inherit cmake desktop git-r3 java-pkg-2 flag-o-matic
 
 DESCRIPTION="Constructive solid geometry modeling system"
-HOMEPAGE="http://brlcad.org/"
-ESVN_REPO_URI="https://brlcad.svn.sourceforge.net/svnroot/${PN}/${PN}/trunk"
+HOMEPAGE="https://brlcad.org/ https://github.com/BRL-CAD/brlcad"
+EGIT_REPO_URI="https://github.com/BRL-CAD/brlcad"
 
 LICENSE="LGPL-2 BSD"
 SLOT="0"
-KEYWORDS=""
 IUSE="benchmarks debug doc examples java opengl smp"
 
 RDEPEND="
 	java? (
-		>=virtual/jre-1.5:*
+		>=virtual/jre-1.8:*
 	)
 	"
 
 DEPEND="${RDEPEND}
+	dev-util/astyle
+	dev-util/re2c
 	>=sci-libs/tnt-3
+	sci-libs/proj
+	sci-libs/lemon
 	sys-devel/bison
 	sys-devel/flex
 	media-libs/libpng:0
-	<dev-lang/tcl-8.6:0/8.5
-	<dev-lang/tk-8.6:0/8.5
-	dev-tcltk/tktable
+	>=dev-lang/tcl-8.6:0/8.6
+	>=dev-lang/tk-8.6:0/8.6
 	sys-libs/zlib
 	sys-libs/libtermcap-compat
 	media-libs/urt
@@ -34,22 +37,28 @@ DEPEND="${RDEPEND}
 	x11-libs/libXi
 	java? (
 		sci-libs/jama
-		>=virtual/jre-1.5:*
+		>=virtual/jre-1.8:*
 	)
 	doc? (
 		dev-libs/libxslt
-		app-doc/doxygen
+		app-text/doxygen
 	)"
 
+# Install into /usr/ not recommended by upstream due to possible file conflicts
+# with bundled libraries!
 BRLCAD_DIR="${EPREFIX}/usr/${PN}"
 
+src_prepare() {
+	cmake_src_prepare
+}
+
 src_configure() {
 	append-cflags "-w"
 	if use debug; then
 		CMAKE_BUILD_TYPE=Debug
-		else
+	else
 		CMAKE_BUILD_TYPE=Release
-		fi
+	fi
 	local mycmakeargs=(
 		-DCMAKE_INSTALL_PREFIX="${BRLCAD_DIR}"
 		-DBRLCAD_ENABLE_STRICT=NO
@@ -58,48 +67,67 @@ src_configure() {
 		-DBRLCAD_FLAGS_OPTIMIZATION=ON
 		-DBRLCAD_ENABLE_X11=ON
 		-DBRLCAD_ENABLE_VERBOSE_PROGRESS=ON
-		)
+		-DACCEPT_USE_OF_DEPRECATED_PROJ_API_H=ON
+# requires itk/itcl version 3, not packaged, use bundled instead
+# 		-DBRLCAD_TKTABLE=OFF
+# 		-DBRLCAD_IWIDGETS=OFF
+# 		-DBRLCAD_ITCL=OFF
+# 		-DBRLCAD_ITK=OFF
+#		-DBRLCAD_TKPNG=OFF
+# Not packaged, use bundled
+# 		-DBRLCAD_GDIAM
+# 		-DBRLCAD_VDS
+# 		-DBRLCAD_SC
+# 		-DBRLCAD_OPENNURBS
+# 		-DBRLCAD_TKHTML
+# 		-DBRLCAD_UTAHRLE
+# 		-DBRLCAD_TERMLIB
+# 		-DBRLCAD_XMLLINT
+# 		-DBRLCAD_XSLTPROC
+# 		-DBRLCAD_PERPLEX
+	)
 
-			# use flag triggered options
+	# use flag triggered options
 	if use debug; then
-		mycmakeargs += "-DCMAKE_BUILD_TYPE=Debug"
+		mycmakeargs+=( -DCMAKE_BUILD_TYPE="Debug" )
 	else
-		mycmakeargs += "-DCMAKE_BUILD_TYPE=Release"
+		mycmakeargs+=( -DCMAKE_BUILD_TYPE="Release" )
 	fi
 	mycmakeargs+=(
-		$(cmake-utils_use opengl BRLCAD_ENABLE_OPENGL)
-#experimental RTGL support
-#		$(cmake-utils_use opengl BRLCAD_ENABLE_RTGL)
-		$(cmake-utils_use amd64 BRLCAD_ENABLE_64BIT)
-		$(cmake-utils_use smp BRLCAD_ENABLE_SMP)
-		$(cmake-utils_use java BRLCAD_ENABLE_RTSERVER)
-		$(cmake-utils_use examples BRLCAD_INSTALL_EXAMPLE_GEOMETRY)
-		$(cmake-utils_use doc BRLCAD_EXTRADOCS)
-		$(cmake-utils_use doc BRLCAD_EXTRADOCS_PDF)
-		$(cmake-utils_use doc BRLCAD_EXTRADOCS_MAN)
-		)
-	cmake-utils_src_configure
+		$(usex opengl BRLCAD_ENABLE_OPENGL)
+		$(usex opengl BRLCAD_ENABLE_RTGL)
+		$(usex amd64 BRLCAD_ENABLE_64BIT)
+		$(usex smp BRLCAD_ENABLE_SMP)
+		$(usex java BRLCAD_ENABLE_RTSERVER)
+		$(usex examples BRLCAD_INSTALL_EXAMPLE_GEOMETRY)
+		$(usex doc BRLCAD_EXTRADOCS)
+		$(usex doc BRLCAD_EXTRADOCS_PDF)
+		$(usex doc BRLCAD_EXTRADOCS_MAN)
+	)
+	cmake_src_configure
 }
 
 src_compile() {
-	cmake-utils_src_compile
+	cmake_src_compile
 }
 
 src_test() {
-	cmake-utils_src_test
-	#emake check || die "emake check failed"
+	cmake_src_test
+	emake check
 	if use benchmarks; then
 		emake benchmark
 	fi
 }
 
 src_install() {
-	cmake-utils_src_install
-	rm -f "${D}"usr/share/brlcad/{README,NEWS,AUTHORS,HACKING,INSTALL,COPYING}
+	cmake_src_install
+	rm -f "${D}"/usr/share/brlcad/{README,NEWS,AUTHORS,HACKING,INSTALL,COPYING}
 	dodoc AUTHORS NEWS README HACKING TODO BUGS ChangeLog
 	echo "PATH=\"${BRLCAD_DIR}/bin\"" >  99brlcad
 	echo "MANPATH=\"${BRLCAD_DIR}/man\"" >> 99brlcad
 	doenvd 99brlcad
-	newicon misc/macosx/Resources/ReadMe.rtfd/brlcad_logo_tiny.png brlcad.png
-	make_desktop_entry mged "BRL-CAD" brlcad "Graphics;Engineering"
+	for size in {16,24,36,48,64,96,128,256}; do
+		doicon misc/debian/icons/${size}x${size}/*
+	done
+	domenu misc/debian/*.desktop
 }
diff --git a/media-gfx/brlcad/files/brlcad-7.18.4-libpng15.patch b/media-gfx/brlcad/files/brlcad-7.18.4-libpng15.patch
deleted file mode 100644
index e0d42d1e2..000000000
--- a/media-gfx/brlcad/files/brlcad-7.18.4-libpng15.patch
+++ /dev/null
@@ -1,42 +0,0 @@
-http://bugs.gentoo.org/378273
-
---- src/libged/png.c
-+++ src/libged/png.c
-@@ -30,6 +30,8 @@
- #include <string.h>
- #include "bio.h"
- 
-+#include <zlib.h> /* Z_BEST_COMPRESSION */
-+
- #include "png.h"
- #include "bu.h"
- #include "vmath.h"
---- src/fb/fb-png.c	2011-04-12 14:31:56.000000000 -0400
-+++ src/fb/fb-png.c.new	2011-09-19 13:18:08.000000000 -0400
-@@ -38,13 +38,13 @@
- #  include <unistd.h>
- #endif
- 
-+#include "zlib.h"
- #include "png.h"
- #include "bu.h"
- #include "fb.h"
- 
- #include "pkg.h"
- 
--
- /* in cmap-crunch.c */
- extern void cmap_crunch(RGBpixel (*scan_buf), int pixel_ct, ColorMap *colormap);
- 
---- src/util/pix-png.c	2011-04-12 14:34:24.000000000 -0400
-+++ src/util/pix-png.c.new	2011-09-19 13:18:59.000000000 -0400
-@@ -36,7 +36,8 @@
- #include "bio.h"
- 
- #include "zlib.h"
--#include "pngconf.h"
-+/* removed as png.h includes this and including it in the wrong order seems to cause bugs
-+#include "pngconf.h" */
- #include "png.h"
- 
- #include "bu.h"
diff --git a/media-gfx/brlcad/files/brlcad-7.20.4-cmake.patch b/media-gfx/brlcad/files/brlcad-7.20.4-cmake.patch
deleted file mode 100644
index 1dd79c2da..000000000
--- a/media-gfx/brlcad/files/brlcad-7.20.4-cmake.patch
+++ /dev/null
@@ -1,20 +0,0 @@
---- brlcad-7.20.4/CMakeLists.txt	2012-02-11 22:21:21.407311510 -0500
-+++ brlcad-7.20.4/CMakeLists.txt	2012-02-11 22:21:33.220804265 -0500
-@@ -1394,7 +1394,7 @@
- 	ENDFOREACH()
- 	FOREACH(path_label ${PATH_LABELS})
- 		SET(CURRENT_LABEL ${${path_label}_LABEL})
--		STRING(LENGTH ${CURRENT_LABEL} CURRENT_LENGTH)
-+		STRING(LENGTH "${CURRENT_LABEL}" CURRENT_LENGTH)
- 		WHILE(${PATH_LABEL_LENGTH} GREATER ${CURRENT_LENGTH})
- 			SET(CURRENT_LABEL " ${CURRENT_LABEL}")
- 			STRING(LENGTH "${CURRENT_LABEL}" CURRENT_LENGTH)
-@@ -1436,7 +1436,7 @@
- 	ENDFOREACH()
- 	FOREACH(setting_label ${SETTINGLABELS})
- 		SET(CURRENT_LABEL ${${setting_label}_LABEL})
--		STRING(LENGTH ${CURRENT_LABEL} CURRENT_LENGTH)
-+		STRING(LENGTH "${CURRENT_LABEL}" CURRENT_LENGTH)
- 		WHILE(${SETTING_LABEL_LENGTH} GREATER ${CURRENT_LENGTH})
- 			SET(CURRENT_LABEL "${CURRENT_LABEL} ")
- 			STRING(LENGTH ${CURRENT_LABEL} CURRENT_LENGTH)
diff --git a/media-gfx/brlcad/files/brlcad-7.24.2-cmake.patch b/media-gfx/brlcad/files/brlcad-7.24.2-cmake.patch
deleted file mode 100644
index 52d423d75..000000000
--- a/media-gfx/brlcad/files/brlcad-7.24.2-cmake.patch
+++ /dev/null
@@ -1,13 +0,0 @@
---- a/misc/CMake/BRLCAD_CMakeFiles.cmake	2015-04-27 12:18:13.159285916 -0400
-+++ b/misc/CMake/BRLCAD_CMakeFiles.cmake	2015-04-27 12:19:40.722856052 -0400
-@@ -82,6 +82,10 @@
- 	endif("${ITEM}" MATCHES "${TARGET_FLAG}")
-       endforeach(TARGET_FLAG ${FUZZY_TARGET_FLAGS})
- 
-+      if("${ITEM}" MATCHES "MODULE")
-+            set(CMAKEFILES_DO_TEST 0)
-+      endif("")
-+
-       # Handled target flags, proceeding with tests.
-       if(CMAKEFILES_DO_TEST)
- 	get_filename_component(ITEM_PATH "${ITEM}" PATH)
diff --git a/media-gfx/brlcad/files/brlcad-7.32.4-skip-gstep.patch b/media-gfx/brlcad/files/brlcad-7.32.4-skip-gstep.patch
new file mode 100644
index 000000000..5768ad63a
--- /dev/null
+++ b/media-gfx/brlcad/files/brlcad-7.32.4-skip-gstep.patch
@@ -0,0 +1,12 @@
+--- a/db/nist/CMakeLists.txt
++++ b/db/nist/CMakeLists.txt
+@@ -10,7 +10,8 @@ set(NIST_SAMPLE_MODELS
+ )
+ 
+ foreach(im ${NIST_SAMPLE_MODELS})
+-  ADD_G_TARGET(${im} "BRL-CAD Geometry Models/Sample")
++#  disabled because this often segfaults
++#  ADD_G_TARGET(${im} "BRL-CAD Geometry Models/Sample")
+ endforeach(im ${NIST_SAMPLE_MODELS})
+ 
+ CMAKEFILES(
diff --git a/media-gfx/brlcad/metadata.xml b/media-gfx/brlcad/metadata.xml
index 5a5505b09..51a1c2468 100644
--- a/media-gfx/brlcad/metadata.xml
+++ b/media-gfx/brlcad/metadata.xml
@@ -32,9 +32,9 @@ photon mapping.
 	<use>
 		<flag name="benchmarks">
 Run benchmarks during test phase (need test option enabled)
-</flag>
+		</flag>
 	</use>
 	<upstream>
-		<remote-id type="sourceforge">brlcad</remote-id>
+		<remote-id type="github">BRL-CAD/brlcad</remote-id>
 	</upstream>
 </pkgmetadata>
diff --git a/media-libs/avbin-bin/Manifest b/media-libs/avbin-bin/Manifest
deleted file mode 100644
index 9ee5e3fb3..000000000
--- a/media-libs/avbin-bin/Manifest
+++ /dev/null
@@ -1,2 +0,0 @@
-DIST avbin-linux-x86-32-v8.1.tar.bz2 2361130 SHA256 9c4a44296abbb3d17f7d5f1257cb21e2965d35f50b6336262d18335ee1870732 SHA512 419c9d8238792121c010454760938899d6f6a31d51f11bf0d5fdbc81d0f7e573ab4d3173e4655a7f3e56baf4d372301fec56bf6092f308843c8aeb1893ed2e17 WHIRLPOOL 6c6b46f38ac8d2916daf4de5f581bd096c5f0e08128fc6d00f279ee95be64b9e77e78586f7357a910df29c26cb240a06946366f97ef9f215321ce99e234603aa
-DIST avbin-linux-x86-64-v8.1.tar.bz2 2330125 BLAKE2B dd17a2890c1e2bfe39dd755d4cd698149f0082666a14f2bbefbbe24b3054b9e24189c6d8a3f10e69f0bd4323708b00508c382be4bed1a8e7075457a626159301 SHA512 a04a8ef901fb0996197905b52d55a18e88689e4d6845222adcc24afba20613d5ba7b35646af4124e4df92ae41b7c04fd4c6726a38e3076312cd98dceaf421dbb
diff --git a/media-libs/avbin-bin/avbin-bin-8.1.ebuild b/media-libs/avbin-bin/avbin-bin-8.1.ebuild
deleted file mode 100644
index 13eb02661..000000000
--- a/media-libs/avbin-bin/avbin-bin-8.1.ebuild
+++ /dev/null
@@ -1,27 +0,0 @@
-# Copyright 1999-2016 Gentoo Foundation
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=6
-
-DESCRIPTION="A thin wrapper around FFmpeg"
-HOMEPAGE="http://avbin.github.io/"
-SRC_URI="
-	amd64? ( mirror://github/AVbin/AVbin/avbin-linux-x86-64-v${PV}.tar.bz2 )
-	x86? ( mirror://github/AVbin/AVbin/avbin-linux-x86-32-v${PV}.tar.bz2 )"
-
-LICENSE="GPL-3 LGPL-3"
-SLOT="0"
-KEYWORDS="-* ~amd64 ~x86"
-IUSE=""
-
-pkg_setup(){
-	if use amd64; then
-		S="${WORKDIR}"/avbin-linux-x86-64-v${PV}
-	elif use x86; then
-		S="${WORKDIR}"/avbin-linux-x86-32-v${PV}
-	fi
-}
-src_install() {
-	ln -s libavbin.so.${PV} libavbin.so || die
-	dolib libavbin.so*
-}
diff --git a/media-libs/avbin-bin/metadata.xml b/media-libs/avbin-bin/metadata.xml
deleted file mode 100644
index 633797339..000000000
--- a/media-libs/avbin-bin/metadata.xml
+++ /dev/null
@@ -1,13 +0,0 @@
-<?xml version="1.0" encoding="UTF-8"?>
-<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
-<pkgmetadata>
-	<maintainer type="person">
-		<email>grozin@gentoo.org</email>
-		<name>Andrey Grozin</name>
-	</maintainer>
-	<maintainer type="project">
-		<email>sci@gentoo.org</email>
-		<name>Gentoo Science Project</name>
-	</maintainer>
-	<longdescription>AVbin is a thin wrapper around FFmpeg</longdescription>
-</pkgmetadata>
diff --git a/media-libs/charls/Manifest b/media-libs/charls/Manifest
new file mode 100644
index 000000000..5275ba74f
--- /dev/null
+++ b/media-libs/charls/Manifest
@@ -0,0 +1 @@
+DIST charls-2.3.4.tar.gz 9483782 BLAKE2B 655bbe2f143df1c3b86f2bbb033217c9fa30f39cf9b449cb84ffd56ef2e3eb0ceb7088c8757cc1a59d6d9462363e59e62acee7dabcbe5a16fb68be0d5036b3eb SHA512 3f6e1a054d5f7cfa5309e3d1b280d0dbaaeac7f06b08619cefe15677367631d9f6eb96e54b3e5ec921ac50793a570c39178c3e4b52ce9837b731bbccd6a3d0ad
diff --git a/media-libs/charls/charls-2.3.4.ebuild b/media-libs/charls/charls-2.3.4.ebuild
new file mode 100644
index 000000000..155e910a8
--- /dev/null
+++ b/media-libs/charls/charls-2.3.4.ebuild
@@ -0,0 +1,30 @@
+# Copyright 2022 Gentoo Authors
+# Distributed under the terms of the GNU General Public License v2
+
+EAPI=8
+
+inherit cmake
+
+DESCRIPTION="C++ JPEG-LS library implementation"
+HOMEPAGE="https://github.com/team-charls/charls"
+SRC_URI="https://github.com/team-charls/charls/archive/refs/tags/${PV}.tar.gz -> ${P}.tar.gz"
+
+LICENSE="BSD"
+SLOT="0"
+KEYWORDS="~amd64 ~x86"
+
+DEPEND=""
+RDEPEND="${DEPEND}"
+BDEPEND=""
+
+src_configure() {
+	# It doesn't seem like there is an automated way to run the test programs
+	# The samples option builds them, but do not install the resulting binaries
+	local mycmakeargs=(
+		-DCHARLS_BUILD_TESTS=OFF
+		-DCHARLS_BUILD_FUZZ_TEST=OFF
+		-DCHARLS_BUILD_SAMPLES=OFF
+		-DBUILD_SHARED_LIBS=ON
+	)
+	cmake_src_configure
+}
diff --git a/media-libs/charls/metadata.xml b/media-libs/charls/metadata.xml
new file mode 100644
index 000000000..3eef65eb8
--- /dev/null
+++ b/media-libs/charls/metadata.xml
@@ -0,0 +1,11 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<!DOCTYPE pkgmetadata SYSTEM "https://www.gentoo.org/dtd/metadata.dtd">
+<pkgmetadata>
+	<maintainer type="person">
+		<email>fx.carton91@gmail.com</email>
+		<name>François-Xavier Carton</name>
+	</maintainer>
+	<upstream>
+		<remote-id type="github">team-charls/charls</remote-id>
+	</upstream>
+</pkgmetadata>
diff --git a/media-libs/embree-bin/Manifest b/media-libs/embree-bin/Manifest
new file mode 100644
index 000000000..b884b5159
--- /dev/null
+++ b/media-libs/embree-bin/Manifest
@@ -0,0 +1,4 @@
+DIST embree-bin-3.12.0.tar.gz 95209715 BLAKE2B 74b6a9c94ff596ebab64b7f3a1e506a4b08afabf2c86823520004bb46d67d27d136e54e20e5ae238a261a9e14372139da8d5f22a8a5db3597c43a6dc78ba5140 SHA512 5cc69d9c9dacc15433a9b9a6d50893e6f4fd4146f0a0c805802504aa7c079c8960d8cacb6bbe61195d5ee61b6b688cc9b358e5c79951a7d8371ac39d5ded02c5
+DIST embree-bin-3.12.1.tar.gz 95241868 BLAKE2B 6d65916a7bf95209269ee948d4dd1c2ee2218bd186f074501abd8086bdcaa5a270fa1cd8c3029763d1da746e375a29890b7c02577992edeaa8829d0b31ed0e0f SHA512 e8c8bc63e0c56360ef02c3794c18237151554d1ebcc761a50cc887bfbc4df528e56b27c4c83f7ca0fdf952b269e207b966ecc4ffbc159b75a2172541f8b5e3fe
+DIST embree-bin-3.12.2.tar.gz 95365459 BLAKE2B 234aa46a6e6936591c8ad10a5bdb9f29107e1bb9a82b0f256ea23629344884fbee588dc7cf03c5bde8a8b479548cd350a645702a245452d40749b3a315357f27 SHA512 dc01aee95bef18561ec01cbc53f44c3765ffa7d25ff9289a647f86be81ab44916a6d8ba61e377de85026cac0f37eee7ccfc6c5e371cccc6d40289a8d44e4b70d
+DIST embree-bin-3.13.0.tar.gz 96162228 BLAKE2B 4cb0430beca487dba34b946e0d8f05c0f8d4cc19c373e68390b26efe5c8767282367fe13a662334da04cbb80588b36787344946954fbe4ccdf52d562c468cfc8 SHA512 f7bf28d6a50fcb5bb8ac3b87841fc8f23e78865b4be8217fc12268f2e831cdc088a97bd80f1721171ac7c7d772175a4b2bf22a48af5ad18b3835c02340435272
diff --git a/media-libs/embree-bin/embree-bin-3.12.0.ebuild b/media-libs/embree-bin/embree-bin-3.12.0.ebuild
new file mode 100644
index 000000000..479c2eb90
--- /dev/null
+++ b/media-libs/embree-bin/embree-bin-3.12.0.ebuild
@@ -0,0 +1,54 @@
+# Copyright 1999-2020 Gentoo Authors
+# Distributed under the terms of the GNU General Public License v2
+
+EAPI=7
+
+DESCRIPTION="high-performance ray tracing kernels from intel"
+HOMEPAGE="https://github.com/embree/embree"
+SRC_URI="https://github.com/embree/embree/releases/download/v${PV}/embree-${PV}.x86_64.linux.tar.gz -> ${P}.tar.gz"
+S="${WORKDIR}"/embree-${PV}.x86_64.linux
+RESTRICT="mirror"
+
+LICENSE="Apache-2.0"
+KEYWORDS="~amd64"
+SLOT="0"
+
+QA_PREBUILT="opt/embree/bin/.*"
+QA_PRESTRIPPED="opt/embree/lib/libembree3.so.3"
+
+RDEPEND="
+	dev-cpp/tbb
+	dev-lang/ispc
+	media-libs/glfw
+	media-libs/glu
+	media-libs/libjpeg-turbo:0
+	virtual/opengl
+	x11-libs/libxcb
+	x11-libs/libX11
+	x11-libs/libXau
+	x11-libs/libXdmcp
+"
+
+src_compile() {
+	true
+}
+
+src_install() {
+	dodir /opt/embree
+	cp -r "${S}"/* "${ED}"/opt/embree/ || die
+
+	doenvd "${FILESDIR}"/00embree_bin
+}
+
+pkg_postinst() {
+	elog "Embree has been installed to /opt/embree"
+	elog "you are all set to start using it as binary package"
+	elog "after you refresh your environment with"
+	elog "  env-update && . /etc/profile"
+	elog "If you want to use embree as a library and wist to"
+	elog "do development using embree, you need to source"
+	elog "the appropriate shell script from either"
+	elog "  . /opt/embree/embree-vars.sh"
+	elog "or if you are using csh"
+	elog "  . /opt/embree/embree-vars.csh"
+}
diff --git a/media-libs/embree-bin/embree-bin-3.12.1.ebuild b/media-libs/embree-bin/embree-bin-3.12.1.ebuild
new file mode 100644
index 000000000..479c2eb90
--- /dev/null
+++ b/media-libs/embree-bin/embree-bin-3.12.1.ebuild
@@ -0,0 +1,54 @@
+# Copyright 1999-2020 Gentoo Authors
+# Distributed under the terms of the GNU General Public License v2
+
+EAPI=7
+
+DESCRIPTION="high-performance ray tracing kernels from intel"
+HOMEPAGE="https://github.com/embree/embree"
+SRC_URI="https://github.com/embree/embree/releases/download/v${PV}/embree-${PV}.x86_64.linux.tar.gz -> ${P}.tar.gz"
+S="${WORKDIR}"/embree-${PV}.x86_64.linux
+RESTRICT="mirror"
+
+LICENSE="Apache-2.0"
+KEYWORDS="~amd64"
+SLOT="0"
+
+QA_PREBUILT="opt/embree/bin/.*"
+QA_PRESTRIPPED="opt/embree/lib/libembree3.so.3"
+
+RDEPEND="
+	dev-cpp/tbb
+	dev-lang/ispc
+	media-libs/glfw
+	media-libs/glu
+	media-libs/libjpeg-turbo:0
+	virtual/opengl
+	x11-libs/libxcb
+	x11-libs/libX11
+	x11-libs/libXau
+	x11-libs/libXdmcp
+"
+
+src_compile() {
+	true
+}
+
+src_install() {
+	dodir /opt/embree
+	cp -r "${S}"/* "${ED}"/opt/embree/ || die
+
+	doenvd "${FILESDIR}"/00embree_bin
+}
+
+pkg_postinst() {
+	elog "Embree has been installed to /opt/embree"
+	elog "you are all set to start using it as binary package"
+	elog "after you refresh your environment with"
+	elog "  env-update && . /etc/profile"
+	elog "If you want to use embree as a library and wist to"
+	elog "do development using embree, you need to source"
+	elog "the appropriate shell script from either"
+	elog "  . /opt/embree/embree-vars.sh"
+	elog "or if you are using csh"
+	elog "  . /opt/embree/embree-vars.csh"
+}
diff --git a/media-libs/embree-bin/embree-bin-3.12.2.ebuild b/media-libs/embree-bin/embree-bin-3.12.2.ebuild
new file mode 100644
index 000000000..10bd17f02
--- /dev/null
+++ b/media-libs/embree-bin/embree-bin-3.12.2.ebuild
@@ -0,0 +1,55 @@
+# Copyright 1999-2021 Gentoo Authors
+# Distributed under the terms of the GNU General Public License v2
+
+EAPI=7
+
+DESCRIPTION="high-performance ray tracing kernels from intel"
+HOMEPAGE="https://github.com/embree/embree"
+SRC_URI="https://github.com/embree/embree/releases/download/v${PV}/embree-${PV}.x86_64.linux.tar.gz -> ${P}.tar.gz"
+S="${WORKDIR}"/embree-${PV}.x86_64.linux
+RESTRICT="mirror"
+
+LICENSE="Apache-2.0"
+KEYWORDS="~amd64"
+SLOT="0"
+RESTRICT="strip"
+
+QA_PREBUILT="opt/embree/bin/.*"
+QA_PRESTRIPPED="opt/embree/lib/libembree3.so.3"
+
+RDEPEND="
+	dev-cpp/tbb
+	dev-lang/ispc
+	media-libs/glfw
+	media-libs/glu
+	media-libs/libjpeg-turbo:0
+	virtual/opengl
+	x11-libs/libxcb
+	x11-libs/libX11
+	x11-libs/libXau
+	x11-libs/libXdmcp
+"
+
+src_compile() {
+	true
+}
+
+src_install() {
+	dodir /opt/embree
+	cp -r "${S}"/* "${ED}"/opt/embree/ || die
+
+	doenvd "${FILESDIR}"/00embree_bin
+}
+
+pkg_postinst() {
+	elog "Embree has been installed to /opt/embree"
+	elog "you are all set to start using it as binary package"
+	elog "after you refresh your environment with"
+	elog "  env-update && . /etc/profile"
+	elog "If you want to use embree as a library and wist to"
+	elog "do development using embree, you need to source"
+	elog "the appropriate shell script from either"
+	elog "  . /opt/embree/embree-vars.sh"
+	elog "or if you are using csh"
+	elog "  . /opt/embree/embree-vars.csh"
+}
diff --git a/media-libs/embree-bin/embree-bin-3.13.0.ebuild b/media-libs/embree-bin/embree-bin-3.13.0.ebuild
new file mode 100644
index 000000000..ac7de32f4
--- /dev/null
+++ b/media-libs/embree-bin/embree-bin-3.13.0.ebuild
@@ -0,0 +1,58 @@
+# Copyright 1999-2021 Gentoo Authors
+# Distributed under the terms of the GNU General Public License v2
+
+EAPI=7
+
+DESCRIPTION="high-performance ray tracing kernels from intel"
+HOMEPAGE="https://github.com/embree/embree"
+SRC_URI="https://github.com/embree/embree/releases/download/v${PV}/embree-${PV}.x86_64.linux.tar.gz -> ${P}.tar.gz"
+S="${WORKDIR}"/embree-${PV}.x86_64.linux
+RESTRICT="mirror"
+
+LICENSE="Apache-2.0"
+KEYWORDS="~amd64"
+SLOT="0"
+RESTRICT="strip"
+
+QA_PREBUILT="
+	/opt/embree/bin/.*
+	/opt/embree/lib/.*
+"
+QA_PRESTRIPPED="${QA_PREBUILT}"
+
+RDEPEND="
+	dev-cpp/tbb
+	dev-lang/ispc
+	media-libs/glfw
+	media-libs/glu
+	media-libs/libjpeg-turbo:0
+	virtual/opengl
+	x11-libs/libxcb
+	x11-libs/libX11
+	x11-libs/libXau
+	x11-libs/libXdmcp
+"
+
+src_compile() {
+	true
+}
+
+src_install() {
+	dodir /opt/embree
+	cp -r "${S}"/* "${ED}"/opt/embree/ || die
+
+	doenvd "${FILESDIR}"/00embree_bin
+}
+
+pkg_postinst() {
+	elog "Embree has been installed to /opt/embree"
+	elog "you are all set to start using it as binary package"
+	elog "after you refresh your environment with"
+	elog "  env-update && . /etc/profile"
+	elog "If you want to use embree as a library and wist to"
+	elog "do development using embree, you need to source"
+	elog "the appropriate shell script from either"
+	elog "  . /opt/embree/embree-vars.sh"
+	elog "or if you are using csh"
+	elog "  . /opt/embree/embree-vars.csh"
+}
diff --git a/media-libs/embree-bin/files/00embree_bin b/media-libs/embree-bin/files/00embree_bin
new file mode 100644
index 000000000..9588b61e8
--- /dev/null
+++ b/media-libs/embree-bin/files/00embree_bin
@@ -0,0 +1 @@
+PATH="/opt/embree/bin"
diff --git a/media-libs/embree-bin/metadata.xml b/media-libs/embree-bin/metadata.xml
new file mode 100644
index 000000000..e97c4322a
--- /dev/null
+++ b/media-libs/embree-bin/metadata.xml
@@ -0,0 +1,12 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
+<pkgmetadata>
+	<maintainer type="person">
+		<email>gentoo@aisha.cc</email>
+		<name>Aisha Tammy</name>
+	</maintainer>
+	<maintainer type="project">
+		<email>sci@gentoo.org</email>
+		<name>Gentoo Science Project</name>
+	</maintainer>
+</pkgmetadata>
diff --git a/media-libs/glbinding/Manifest b/media-libs/glbinding/Manifest
index 03c0fb0c8..122510b11 100644
--- a/media-libs/glbinding/Manifest
+++ b/media-libs/glbinding/Manifest
@@ -1 +1 @@
-DIST glbinding-2.1.1.tar.gz 3147406 SHA256 253671f2b730a6efa55de92a704938bb0f1761d151f3f8e87c043c51d46ea1e4 SHA512 3d4035294b1383aa71d693f34691bc5e865267e73aa21010f418126b28e4b7850a28a03d8bf3af23bb566f2ca1b53d74ce4a4ee0be962c7df6a3256eb54bb60e WHIRLPOOL 7a5f6bd10611a7c0e7a768a53a0876a3445cd0c14d833824b7b91bb9a1900ef56f5311cc009ba0821fdda5ed0166b6a7fd47bfeba0a40206ad6eaea02af92878
+DIST glbinding-3.1.0_p1.tar.gz 2803219 BLAKE2B 5886fcde037ae5aede3d3a1661321c175b3b54fc2ba0cd4062f04f83c45f8a74a8fae051d2fab5a099b006270ef888907df85b8a455f538c8390803891f92dc7 SHA512 d062412e3455c03ecf7f927f6425786bc04add3ab934b0fdab7d9603ec61d4b5021c68418849885cd11f64f6567a29f933ece5f80efa6790f660a4e58d0d33a1
diff --git a/media-libs/glbinding/files/glbinding-2.1.1-CMakeLists.patch b/media-libs/glbinding/files/glbinding-2.1.1-CMakeLists.patch
deleted file mode 100644
index 8c4b50577..000000000
--- a/media-libs/glbinding/files/glbinding-2.1.1-CMakeLists.patch
+++ /dev/null
@@ -1,19 +0,0 @@
---- a/CMakeLists.txt
-+++ b/CMakeLists.txt
-@@ -159,16 +159,8 @@ add_subdirectory(deploy)
- # Deployment (global project files)

- # 

- 

--# Install version file

--install(FILES "${PROJECT_BINARY_DIR}/VERSION" DESTINATION ${INSTALL_ROOT} COMPONENT runtime)

--

- # Install cmake find script for the project

- install(FILES ${META_PROJECT_NAME}-config.cmake DESTINATION ${INSTALL_ROOT} COMPONENT dev)

- 

--# Install the project meta files

--install(FILES AUTHORS   DESTINATION ${INSTALL_ROOT} COMPONENT runtime)

--install(FILES LICENSE   DESTINATION ${INSTALL_ROOT} COMPONENT runtime)

--install(FILES README.md DESTINATION ${INSTALL_ROOT} COMPONENT runtime)

--

- # Install runtime data

- install(DIRECTORY ${PROJECT_SOURCE_DIR}/data DESTINATION ${INSTALL_DATA} COMPONENT examples_data)

diff --git a/media-libs/glbinding/files/glbinding-3.1.0_p1-CMakeLists.patch b/media-libs/glbinding/files/glbinding-3.1.0_p1-CMakeLists.patch
new file mode 100644
index 000000000..7486939e7
--- /dev/null
+++ b/media-libs/glbinding/files/glbinding-3.1.0_p1-CMakeLists.patch
@@ -0,0 +1,41 @@
+diff --git a/CMakeLists.txt b/CMakeLists.txt
+index 45f9981..2c71349 100644
+--- a/CMakeLists.txt
++++ b/CMakeLists.txt
+@@ -143,8 +143,8 @@ if(UNIX AND SYSTEM_DIR_INSTALL)
+     set(INSTALL_EXAMPLES  "share/${project}")       # /usr/[local]/share/<project>

+     set(INSTALL_DATA      "share/${project}")       # /usr/[local]/share/<project>

+     set(INSTALL_BIN       "bin")                    # /usr/[local]/bin

+-    set(INSTALL_SHARED    "lib")                    # /usr/[local]/lib

+-    set(INSTALL_LIB       "lib")                    # /usr/[local]/lib

++    set(INSTALL_SHARED    "${CMAKE_INSTALL_LIBDIR}")                    # /usr/[local]/lib

++    set(INSTALL_LIB       "${CMAKE_INSTALL_LIBDIR}")                    # /usr/[local]/lib

+     set(INSTALL_INCLUDE   "include")                # /usr/[local]/include

+     set(INSTALL_DOC       "share/doc/${project}")   # /usr/[local]/share/doc/<project>

+     set(INSTALL_SHORTCUTS "share/applications")     # /usr/[local]/share/applications

+@@ -157,8 +157,8 @@ else()
+     set(INSTALL_EXAMPLES  ".")                      # ./

+     set(INSTALL_DATA      ".")                      # ./

+     set(INSTALL_BIN       ".")                      # ./

+-    set(INSTALL_SHARED    "lib")                    # ./lib

+-    set(INSTALL_LIB       "lib")                    # ./lib

++    set(INSTALL_SHARED    "${CMAKE_INSTALL_LIBDIR}")                    # ./lib

++    set(INSTALL_LIB       "${CMAKE_INSTALL_LIBDIR}")                    # ./lib

+     set(INSTALL_INCLUDE   "include")                # ./include

+     set(INSTALL_DOC       "doc")                    # ./doc

+     set(INSTALL_SHORTCUTS "misc")                   # ./misc

+@@ -210,3 +210,14 @@ install(FILES README.md DESTINATION ${INSTALL_ROOT} COMPONENT runtime)
+ if (TARGET cubescape OR TARGET cubescape-log OR TARGET cubescape-qt)

+     install(DIRECTORY ${PROJECT_SOURCE_DIR}/data DESTINATION ${INSTALL_DATA} COMPONENT examples_data)

+ endif()

++
++MESSAGE(STATUS "<<< Gentoo configuration >>>
++Build type      ${CMAKE_BUILD_TYPE}
++Install path    ${CMAKE_INSTALL_PREFIX}
++Compiler flags:
++C               ${CMAKE_C_FLAGS}
++C++             ${CMAKE_CXX_FLAGS}
++Linker flags:
++Executable      ${CMAKE_EXE_LINKER_FLAGS}
++Module          ${CMAKE_MODULE_LINKER_FLAGS}
++Shared          ${CMAKE_SHARED_LINKER_FLAGS}\n")
diff --git a/media-libs/glbinding/files/glbinding-3.1.0_p1-source_CMakeLists.patch b/media-libs/glbinding/files/glbinding-3.1.0_p1-source_CMakeLists.patch
new file mode 100644
index 000000000..88d11dc3a
--- /dev/null
+++ b/media-libs/glbinding/files/glbinding-3.1.0_p1-source_CMakeLists.patch
@@ -0,0 +1,12 @@
+diff --git a/source/CMakeLists.txt b/source/CMakeLists.txt
+index 757217b..19da804 100644
+--- a/source/CMakeLists.txt
++++ b/source/CMakeLists.txt
+@@ -13,7 +13,6 @@ configure_file(version.h.in ${CMAKE_CURRENT_BINARY_DIR}/include/${META_PROJECT_N
+ 
+ # 3rdParties
+ set(IDE_FOLDER "3rdparty")
+-add_subdirectory("3rdparty/KHR")
+ 
+ # Libraries
+ set(IDE_FOLDER "")
diff --git a/media-libs/glbinding/glbinding-2.1.1.ebuild b/media-libs/glbinding/glbinding-2.1.1.ebuild
deleted file mode 100644
index 408093fb5..000000000
--- a/media-libs/glbinding/glbinding-2.1.1.ebuild
+++ /dev/null
@@ -1,36 +0,0 @@
-# Copyright 1999-2016 Gentoo Foundation
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=6
-
-inherit cmake-utils
-
-DESCRIPTION="Cross-platform C++ binding for the OpenGL API"
-HOMEPAGE="https://github.com/cginternals/glbinding"
-SRC_URI="https://github.com/cginternals/${PN}/archive/v${PV}.tar.gz -> ${P}.tar.gz"
-
-LICENSE="MIT"
-SLOT="0"
-KEYWORDS="~amd64"
-IUSE=""
-
-RDEPEND="
-	>=media-libs/glfw-3.1.1
-	"
-DEPEND="${RDEPEND}
-	>=dev-util/cmake-3.2.2
-	"
-
-PATCHES=(
-	"${FILESDIR}/${P}"-CMakeLists.patch
-)
-
-src_configure() {
-	local mycmakeargs=(
-	   -DOPTION_BUILD_TESTS=OFF
-	   -DOPTION_BUILD_GPU_TESTS=OFF
-	   -DOPTION_BUILD_DOCS=OFF
-	   -DOPTION_BUILD_EXAMPLES=OFF
-	)
-	cmake-utils_src_configure
-}
diff --git a/media-libs/glbinding/glbinding-3.1.0_p1.ebuild b/media-libs/glbinding/glbinding-3.1.0_p1.ebuild
new file mode 100644
index 000000000..9999b537f
--- /dev/null
+++ b/media-libs/glbinding/glbinding-3.1.0_p1.ebuild
@@ -0,0 +1,45 @@
+# Copyright 2020 Gentoo Authors
+# Distributed under the terms of the GNU General Public License v2
+
+EAPI=7
+
+inherit cmake
+
+DESCRIPTION="Cross-platform C++ binding for the OpenGL API"
+HOMEPAGE="https://github.com/cginternals/glbinding"
+COMMIT="55634e35bd8d8bf58cb36f6ed81af0a0f0939973"
+SRC_URI="https://github.com/cginternals/glbinding/archive/${COMMIT}.tar.gz -> ${P}.tar.gz"
+S="${WORKDIR}/${PN}-${COMMIT}"
+
+LICENSE="MIT"
+SLOT="0"
+KEYWORDS="~amd64"
+
+RDEPEND="
+	media-libs/glfw
+	media-libs/libglvnd
+"
+DEPEND="${RDEPEND}"
+BDEPEND="
+	dev-vcs/git
+"
+
+PATCHES=(
+	"${FILESDIR}/${P}"-CMakeLists.patch
+	"${FILESDIR}/${P}"-source_CMakeLists.patch
+)
+
+src_configure() {
+	local mycmakeargs=(
+		-DBUILD_SHARED_LIBS=ON
+		-DOPTION_SELF_CONTAINED=OFF
+		-DOPTION_BUILD_TESTS=OFF
+		-DOPTION_BUILD_DOCS=OFF
+		-DOPTION_BUILD_EXAMPLES=OFF
+		-DOPTION_BUILD_WITH_BOOST_THREAD=OFF
+		-DOPTION_BUILD_CHECK=OFF
+		-DOPTION_BUILD_OWN_KHR_HEADERS=OFF
+		-DOPTION_BUILD_WITH_LTO=OFF
+	)
+	cmake_src_configure
+}
diff --git a/media-libs/glbinding/metadata.xml b/media-libs/glbinding/metadata.xml
index 7e15e92be..706402ab4 100644
--- a/media-libs/glbinding/metadata.xml
+++ b/media-libs/glbinding/metadata.xml
@@ -5,22 +5,26 @@
 		<email>marbre@linux.sungazer.de</email>
 		<name>Marius Brehler</name>
 	</maintainer>
+	<maintainer type="person">
+		<email>gentoo@aisha.cc</email>
+		<name>Aisha Tammy</name>
+	</maintainer>
 	<maintainer type="project">
 		<email>sci@gentoo.org</email>
 		<name>Gentoo Science Project</name>
 	</maintainer>
 	<longdescription>
-glbinding leverages modern C++11 features like enum classes,
-lambdas, and variadic templates, instead of relying on macros; all
-OpenGL symbols are real functions and variables. It provides
-type-safe parameters, per feature API header, lazy function
-resolution, multi-context and multi-thread support, global and local
-function callbacks, meta information about the generated OpenGL
-binding and the OpenGL runtime, as well as tools and examples for
-quick-starting your projects. Based on the OpenGL API specification
-(gl.xml) glbinding is generated using python scripts and templates
-that can be easily adapted to fit custom needs.
-</longdescription>
+		glbinding leverages modern C++11 features like enum classes,
+		lambdas, and variadic templates, instead of relying on macros; all
+		OpenGL symbols are real functions and variables. It provides
+		type-safe parameters, per feature API header, lazy function
+		resolution, multi-context and multi-thread support, global and local
+		function callbacks, meta information about the generated OpenGL
+		binding and the OpenGL runtime, as well as tools and examples for
+		quick-starting your projects. Based on the OpenGL API specification
+		(gl.xml) glbinding is generated using python scripts and templates
+		that can be easily adapted to fit custom needs.
+	</longdescription>
 	<upstream>
 		<remote-id type="github">cginternals/glbinding</remote-id>
 	</upstream>
diff --git a/media-libs/imglib2/Manifest b/media-libs/imglib2/Manifest
new file mode 100644
index 000000000..eaae671d4
--- /dev/null
+++ b/media-libs/imglib2/Manifest
@@ -0,0 +1 @@
+DIST imglib2-6.3.0-sources.tar.gz 1100228 BLAKE2B 65aba1c43980e98018154972bc143093d25e000148805d8ee75459f43dbe301cb0ae10463585fccc51dab28c926900e7c43df13696d408e79d2b4cb55ffadfc6 SHA512 9f6159379d1be6478a9cd53ee88241277761a5e569cd2042e26363f43394abc85d3ea2f72e592a57cff6f8b5f8f4cd46821a4168bf76939f7f77680844231748
diff --git a/media-libs/imglib2/imglib2-6.3.0.ebuild b/media-libs/imglib2/imglib2-6.3.0.ebuild
new file mode 100644
index 000000000..4233e6795
--- /dev/null
+++ b/media-libs/imglib2/imglib2-6.3.0.ebuild
@@ -0,0 +1,53 @@
+# Copyright 1999-2023 Gentoo Authors
+# Distributed under the terms of the GNU General Public License v2
+
+EAPI=8
+
+JAVA_PKG_IUSE="doc source test"
+JAVA_TESTING_FRAMEWORKS="junit-4"
+
+inherit java-pkg-2 java-pkg-simple
+
+DESCRIPTION="A multidimensional, type-agnostic image processing library."
+HOMEPAGE="
+	http://imglib2.net/
+	https://github.com/imglib/imglib2
+"
+
+if [[ ${PV} == 9999 ]]; then
+	inherit git-r3
+	EGIT_REPO_URI="https://github.com/imglib/imglib2.git"
+	S="${WORKDIR}/${P}"
+	MAVEN_ID="net.imglib2:imglib2:9999"
+else
+	SRC_URI="
+		https://github.com/imglib/${PN}/archive/refs/tags/${P}.tar.gz -> ${P}-sources.tar.gz
+	"
+	S="${WORKDIR}/${PN}-${P}"
+	MAVEN_ID="net.imglib2:imglib2:6.3.0"
+	KEYWORDS="~amd64"
+fi
+
+LICENSE="BSD-2"
+SLOT="0"
+
+# jmh-core: According to the pom version 1.36 is required,
+# however, jmh-core-1.35 is latest available in Gentoo
+BDEPEND="
+	>=virtual/jdk-1.8:*
+	test? (
+		>=dev-java/jama-1.0.3
+		>=dev-java/junit-4.13.2
+		>=dev-java/jmh-core-1.35
+	)
+"
+
+RDEPEND="
+	>=virtual/jre-1.8:*
+"
+
+JAVA_SRC_DIR="src/main/java"
+JAVA_MAIN_CLASS=""
+
+JAVA_TEST_GENTOO_CLASSPATH="jama,junit-4,jmh-core"
+JAVA_TEST_SRC_DIR="src/test/java"
diff --git a/media-libs/imglib2/imglib2-9999.ebuild b/media-libs/imglib2/imglib2-9999.ebuild
new file mode 100644
index 000000000..4233e6795
--- /dev/null
+++ b/media-libs/imglib2/imglib2-9999.ebuild
@@ -0,0 +1,53 @@
+# Copyright 1999-2023 Gentoo Authors
+# Distributed under the terms of the GNU General Public License v2
+
+EAPI=8
+
+JAVA_PKG_IUSE="doc source test"
+JAVA_TESTING_FRAMEWORKS="junit-4"
+
+inherit java-pkg-2 java-pkg-simple
+
+DESCRIPTION="A multidimensional, type-agnostic image processing library."
+HOMEPAGE="
+	http://imglib2.net/
+	https://github.com/imglib/imglib2
+"
+
+if [[ ${PV} == 9999 ]]; then
+	inherit git-r3
+	EGIT_REPO_URI="https://github.com/imglib/imglib2.git"
+	S="${WORKDIR}/${P}"
+	MAVEN_ID="net.imglib2:imglib2:9999"
+else
+	SRC_URI="
+		https://github.com/imglib/${PN}/archive/refs/tags/${P}.tar.gz -> ${P}-sources.tar.gz
+	"
+	S="${WORKDIR}/${PN}-${P}"
+	MAVEN_ID="net.imglib2:imglib2:6.3.0"
+	KEYWORDS="~amd64"
+fi
+
+LICENSE="BSD-2"
+SLOT="0"
+
+# jmh-core: According to the pom version 1.36 is required,
+# however, jmh-core-1.35 is latest available in Gentoo
+BDEPEND="
+	>=virtual/jdk-1.8:*
+	test? (
+		>=dev-java/jama-1.0.3
+		>=dev-java/junit-4.13.2
+		>=dev-java/jmh-core-1.35
+	)
+"
+
+RDEPEND="
+	>=virtual/jre-1.8:*
+"
+
+JAVA_SRC_DIR="src/main/java"
+JAVA_MAIN_CLASS=""
+
+JAVA_TEST_GENTOO_CLASSPATH="jama,junit-4,jmh-core"
+JAVA_TEST_SRC_DIR="src/test/java"
diff --git a/media-libs/imglib2/metadata.xml b/media-libs/imglib2/metadata.xml
new file mode 100644
index 000000000..b5cf3918a
--- /dev/null
+++ b/media-libs/imglib2/metadata.xml
@@ -0,0 +1,16 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
+<pkgmetadata>
+  <longdescription>
+    ImgLib2 is a general-purpose, multidimensional image processing library.
+
+    It provides an interface-driven design that supports numeric and non-numeric data types (8-bit unsigned integer, 32-bit floating point, etc.) in an extensible way. It implements several data sources and sample organizations, including one single primitive array, one array per plane, N-dimensional array “cells� cached to and from disk on demand, and planes read on demand from disk.
+  </longdescription>
+  <maintainer type="project">
+    <email>sci@gentoo.org</email>
+    <name>Gentoo Science Project</name>
+  </maintainer>
+  <upstream>
+    <remote-id type="github">imglib/imglib2</remote-id>
+  </upstream>
+</pkgmetadata>
diff --git a/media-libs/libgfx/Manifest b/media-libs/libgfx/Manifest
index c18a5b7eb..68c9b5f8d 100644
--- a/media-libs/libgfx/Manifest
+++ b/media-libs/libgfx/Manifest
@@ -1 +1,2 @@
 DIST libgfx-1.1.0.tar.gz 145470 BLAKE2B bbf80adc726f9b4030c22365526af284a3843cf487fb5f606318d651af39d3866cb02d846969735e65aba0c857b715d4c10fcf443f22bb2cb3f65ac642999e29 SHA512 b23744225a63a77f17a78eb49b39e89a5d8c695cac62e1a399516c0e1728074ca80275fccb91cb3a128f20c2a8c66a6756005ba2d2ef9c251be36e3b3ba95d9b
+DIST libgfx-1.1.1.tar.gz 145075 BLAKE2B dab3bf0c4ddde672a3588fa88dc931db5deeef2e5e51ee6adb80ab500796677d200d4cec157828011cde5146c883cad80aae2cd69603e8f68dc67996ef84fc95 SHA512 264288a91ee9a1062bd36fa6ef381f27813e7c87949e8a1e7723f936fc1827d0a63252f2897b393f90ad0c6d47d0d413b5779194b05141efd618fc841b6bb6ff
diff --git a/media-libs/libgfx/files/1.1.0-gcc-4.3.patch b/media-libs/libgfx/files/1.1.0-gcc-4.3.patch
new file mode 100644
index 000000000..ba5eba38a
--- /dev/null
+++ b/media-libs/libgfx/files/1.1.0-gcc-4.3.patch
@@ -0,0 +1,24 @@
+cstring now contains memcpy.
+Written and tested by Lucas Mitrak.
+
+--- a/src/raster-png.cxx
++++ b/src/raster-png.cxx
+@@ -12,6 +12,7 @@
+ #include <vector>
+ #include <gfx/gfx.h>
+ #include <gfx/raster.h>
++#include <cstring>
+ 
+ #ifdef HAVE_LIBPNG
+ 
+--- a/src/raster.cxx
++++ b/src/raster.cxx
+@@ -9,7 +9,7 @@
+ #include <gfx/gfx.h>
+ #include <gfx/raster.h>
+ 
+-#include <string>
++#include <cstring>
+ #include <cctype>
+ 
+ namespace gfx
diff --git a/media-libs/libgfx/files/1.1.0-gcc4.3.patch b/media-libs/libgfx/files/1.1.0-gcc4.3.patch
deleted file mode 100644
index 811d5dbcc..000000000
--- a/media-libs/libgfx/files/1.1.0-gcc4.3.patch
+++ /dev/null
@@ -1,11 +0,0 @@
---- a/src/raster.cxx	2004-09-27 06:45:31.000000000 +0200
-+++ b/src/raster.cxx.new	2009-05-17 23:48:58.417607175 +0200
-@@ -9,7 +9,7 @@
- #include <gfx/gfx.h>
- #include <gfx/raster.h>
- 
--#include <string>
-+#include <cstring>
- #include <cctype>
- 
- namespace gfx
diff --git a/media-libs/libgfx/files/1.1.0-libPNG-1.2.5.patch b/media-libs/libgfx/files/1.1.0-libPNG-1.2.5.patch
new file mode 100644
index 000000000..0d648d06e
--- /dev/null
+++ b/media-libs/libgfx/files/1.1.0-libPNG-1.2.5.patch
@@ -0,0 +1,24 @@
+Changes the png buffer pointer to the new function call.
+Written and tested by Lucas Mitrak.
+https://bugs.gentoo.org/756061
+
+--- a/src/raster-png.cxx
++++ b/src/raster-png.cxx
+@@ -43,7 +43,7 @@ ByteRaster *read_png_image(const char *file_name)
+    // Because we didn't set up any error handlers, we need to be
+    // prepared to handle longjmps out of the library on error
+    // conditions.
+-   if( setjmp(png_ptr->jmpbuf) )
++   if( setjmp(png_jmpbuf(png_ptr)) )
+    {
+       png_destroy_read_struct(&png_ptr, &info_ptr, NULL);
+       fclose(fp);
+@@ -133,7 +133,7 @@ bool write_png_image(const char *file_name, const ByteRaster& img)
+       return false;
+    }
+ 
+-   if( setjmp(png_ptr->jmpbuf) )
++   if( setjmp(png_jmpbuf(png_ptr)) )
+    {
+       fclose(fp);
+       png_destroy_write_struct(&png_ptr,  (png_infopp)NULL);
diff --git a/media-libs/libgfx/libgfx-1.1.0.ebuild b/media-libs/libgfx/libgfx-1.1.0.ebuild
index c3671ce07..01f5c7f71 100644
--- a/media-libs/libgfx/libgfx-1.1.0.ebuild
+++ b/media-libs/libgfx/libgfx-1.1.0.ebuild
@@ -1,7 +1,7 @@
-# Copyright 1999-2017 Gentoo Foundation
+# Copyright 1999-2021 Gentoo Authors
 # Distributed under the terms of the GNU General Public License v2
 
-EAPI=6
+EAPI=7
 
 DESCRIPTION="Simplify the creation of computer graphics software"
 HOMEPAGE="http://mgarland.org/software/libgfx.html"
@@ -12,7 +12,17 @@ SLOT="0"
 KEYWORDS="~amd64 ~x86"
 IUSE="static-libs"
 
-PATCHES=( "${FILESDIR}"/${PV}-gcc4.3.patch )
+DEPEND="
+	virtual/opengl
+	x11-libs/fltk
+"
+
+RDEPEND="${DEPEND}"
+
+PATCHES=(
+	"${FILESDIR}"/${PV}-gcc-4.3.patch
+	"${FILESDIR}"/${PV}-libPNG-1.2.5.patch
+)
 
 src_compile() {
 	cd src || die
@@ -23,5 +33,11 @@ src_install() {
 	use static-libs && dolib.a src/*.a
 	doheader include/gfx/gfx.h
 
-	dohtml doc/*
+	dodoc doc/*
+}
+
+src_test() {
+	cd tests || die
+	sed -i -e 's/t-vec.cxx t-img.cxx t-gui.cxx t-glimg.cxx t-script.cxx t-glext.cxx/t-vec.cxx t-img.cxx t-script.cxx/' Makefile
+	emake
 }
diff --git a/media-libs/libgfx/libgfx-1.1.1.ebuild b/media-libs/libgfx/libgfx-1.1.1.ebuild
new file mode 100644
index 000000000..6cbedc968
--- /dev/null
+++ b/media-libs/libgfx/libgfx-1.1.1.ebuild
@@ -0,0 +1,41 @@
+# Copyright 1999-2021 Gentoo Authors
+# Distributed under the terms of the GNU General Public License v2
+
+EAPI=8
+
+DESCRIPTION="Simplify the creation of computer graphics software"
+HOMEPAGE="http://mgarland.org/software/libgfx.html"
+
+COMMIT="f28ca5f0df3044f6399d6214faf66daa36712b91"
+SRC_URI="https://github.com/mjgarland/libgfx/archive/${COMMIT}.tar.gz -> ${P}.tar.gz"
+S="${WORKDIR}/${PN}-${COMMIT}"
+
+LICENSE="LGPL-2.1"
+SLOT="0"
+KEYWORDS="~amd64 ~x86"
+IUSE="static-libs"
+
+DEPEND="
+	virtual/opengl
+	x11-libs/fltk
+"
+
+RDEPEND="${DEPEND}"
+
+src_compile() {
+	cd src || die
+	default
+}
+
+src_install() {
+	use static-libs && dolib.a src/*.a
+	doheader include/gfx/gfx.h
+
+	dodoc doc/*
+}
+
+src_test() {
+	cd tests || die
+	sed -i -e 's/t-vec.cxx t-img.cxx t-gui.cxx t-glimg.cxx t-script.cxx t-glext.cxx/t-vec.cxx t-img.cxx t-script.cxx/' Makefile
+	emake
+}
diff --git a/media-libs/libgfx/metadata.xml b/media-libs/libgfx/metadata.xml
index ae9640ffb..2103548da 100644
--- a/media-libs/libgfx/metadata.xml
+++ b/media-libs/libgfx/metadata.xml
@@ -5,4 +5,7 @@
 		<email>sci@gentoo.org</email>
 		<name>Gentoo Science Project</name>
 	</maintainer>
+	<upstream>
+		<remote-id type="github">mjgarland/libgfx</remote-id>
+	</upstream>
 </pkgmetadata>
diff --git a/media-libs/mmg/Manifest b/media-libs/mmg/Manifest
new file mode 100644
index 000000000..4f3ca75ef
--- /dev/null
+++ b/media-libs/mmg/Manifest
@@ -0,0 +1,3 @@
+DIST mmg-5.5.0.tar.gz 9569999 BLAKE2B a544b2c06d6ea8653bc7ba1f0ba7276addd9a4eb4aeac6e520de5987925d5e6279f99c3e5625db2df87b41fe338a6e012a9738979b718ae6cf3dc0710921ea7e SHA512 15c493c3e66e84b4d2b73044b0575473aee17190c44e096fa77be1a8f8eab94e5e11f1750f0d86e7be085bdc3bce72d01af928ed321a6134f6e9cbc4457f2de8
+DIST mmg-5.5.1.tar.gz 9569862 BLAKE2B a51fc5d8f416a2bec3629756a3f1c2a4e54b37884e2d14d85735bdfa45ac7ff4094627cc4f17dfb0262123c73bb91f68a566971beee467907d2b3c4fb9b7aab9 SHA512 75c86e9d3cc5b630032421e53d540a00da0d1595524a8041a2fca2e81d4c9dd1936e1dc2593e2dbb906f76fcb75cef22c0f6c745d5530fa5efc20fb255373d05
+DIST mmg-5.5.2.tar.gz 9570653 BLAKE2B 741c751b9abab109f500d11c9b421aab59e22e7b8c0ce83168e186017e3dd8dd135e86b68e83e43c52729277aee7adfe8646483867869ccf896e688010b9dbd1 SHA512 8cc6b69d9a339d1ca710b7a60858ff290137c444d20062f27d9434f238bb7cc982787efa4957b59e2e182cb36f76bf24f66098909fb1e40a107496dc51384750
diff --git a/media-libs/mmg/metadata.xml b/media-libs/mmg/metadata.xml
new file mode 100644
index 000000000..bd7221f19
--- /dev/null
+++ b/media-libs/mmg/metadata.xml
@@ -0,0 +1,19 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
+<pkgmetadata>
+	<maintainer type="person">
+		<email>gentoo@aisha.cc</email>
+		<name>Aisha Tammy</name>
+	</maintainer>
+	<maintainer type="project">
+		<email>sci@gentoo.org</email>
+		<name>Gentoo Science Project</name>
+	</maintainer>
+	<use>
+		<flag name="scotch">Use SCOTCH TOOL for renumbering</flag>
+		<flag name="vtk">Use VTK I/O</flag>
+	</use>
+	<upstream>
+		<remote-id type="github">MmgTools/mmg</remote-id>
+	</upstream>
+</pkgmetadata>
diff --git a/media-libs/mmg/mmg-5.5.0.ebuild b/media-libs/mmg/mmg-5.5.0.ebuild
new file mode 100644
index 000000000..1e8e4d8cb
--- /dev/null
+++ b/media-libs/mmg/mmg-5.5.0.ebuild
@@ -0,0 +1,40 @@
+# Copyright 1999-2020 Gentoo Authors
+# Distributed under the terms of the GNU General Public License v2
+
+EAPI=7
+
+inherit cmake fortran-2
+CMAKE_BUILD_TYPE=MMG
+FORTRAN_NEED_OPENMP=1
+
+DESCRIPTION="bidimensional and tridimensional remesher"
+HOMEPAGE="https://www.mmgtools.org/"
+SRC_URI="https://github.com/MmgTools/mmg/archive/v${PV}.tar.gz -> ${P}.tar.gz"
+
+LICENSE="GPL-3 LGPL-3"
+KEYWORDS="~amd64"
+SLOT="0"
+IUSE="scotch vtk"
+
+DEPEND="
+	scotch? ( sci-libs/scotch )
+	vtk? ( sci-libs/vtk )
+"
+RDEPEND="${DEPEND}"
+BDEPEND="
+	app-text/doxygen
+"
+
+src_configure() {
+	local mycmakeargs=(
+		-DUSE_VTK=$(usex vtk)
+		-DUSE_SCOTCH=$(usex scotch)
+		-DBUILD_SHARED_LIBS=ON
+		-DLIBMMG2D_SHARED=ON
+		-DLIBMMGS_SHARED=ON
+		-DLIBMMG3D_SHARED=ON
+	)
+	cmake_src_configure
+}
+
+# no tests present
diff --git a/media-libs/mmg/mmg-5.5.1.ebuild b/media-libs/mmg/mmg-5.5.1.ebuild
new file mode 100644
index 000000000..1e8e4d8cb
--- /dev/null
+++ b/media-libs/mmg/mmg-5.5.1.ebuild
@@ -0,0 +1,40 @@
+# Copyright 1999-2020 Gentoo Authors
+# Distributed under the terms of the GNU General Public License v2
+
+EAPI=7
+
+inherit cmake fortran-2
+CMAKE_BUILD_TYPE=MMG
+FORTRAN_NEED_OPENMP=1
+
+DESCRIPTION="bidimensional and tridimensional remesher"
+HOMEPAGE="https://www.mmgtools.org/"
+SRC_URI="https://github.com/MmgTools/mmg/archive/v${PV}.tar.gz -> ${P}.tar.gz"
+
+LICENSE="GPL-3 LGPL-3"
+KEYWORDS="~amd64"
+SLOT="0"
+IUSE="scotch vtk"
+
+DEPEND="
+	scotch? ( sci-libs/scotch )
+	vtk? ( sci-libs/vtk )
+"
+RDEPEND="${DEPEND}"
+BDEPEND="
+	app-text/doxygen
+"
+
+src_configure() {
+	local mycmakeargs=(
+		-DUSE_VTK=$(usex vtk)
+		-DUSE_SCOTCH=$(usex scotch)
+		-DBUILD_SHARED_LIBS=ON
+		-DLIBMMG2D_SHARED=ON
+		-DLIBMMGS_SHARED=ON
+		-DLIBMMG3D_SHARED=ON
+	)
+	cmake_src_configure
+}
+
+# no tests present
diff --git a/media-libs/mmg/mmg-5.5.2.ebuild b/media-libs/mmg/mmg-5.5.2.ebuild
new file mode 100644
index 000000000..1e8e4d8cb
--- /dev/null
+++ b/media-libs/mmg/mmg-5.5.2.ebuild
@@ -0,0 +1,40 @@
+# Copyright 1999-2020 Gentoo Authors
+# Distributed under the terms of the GNU General Public License v2
+
+EAPI=7
+
+inherit cmake fortran-2
+CMAKE_BUILD_TYPE=MMG
+FORTRAN_NEED_OPENMP=1
+
+DESCRIPTION="bidimensional and tridimensional remesher"
+HOMEPAGE="https://www.mmgtools.org/"
+SRC_URI="https://github.com/MmgTools/mmg/archive/v${PV}.tar.gz -> ${P}.tar.gz"
+
+LICENSE="GPL-3 LGPL-3"
+KEYWORDS="~amd64"
+SLOT="0"
+IUSE="scotch vtk"
+
+DEPEND="
+	scotch? ( sci-libs/scotch )
+	vtk? ( sci-libs/vtk )
+"
+RDEPEND="${DEPEND}"
+BDEPEND="
+	app-text/doxygen
+"
+
+src_configure() {
+	local mycmakeargs=(
+		-DUSE_VTK=$(usex vtk)
+		-DUSE_SCOTCH=$(usex scotch)
+		-DBUILD_SHARED_LIBS=ON
+		-DLIBMMG2D_SHARED=ON
+		-DLIBMMGS_SHARED=ON
+		-DLIBMMG3D_SHARED=ON
+	)
+	cmake_src_configure
+}
+
+# no tests present
diff --git a/media-libs/scifio-jai-imageio/Manifest b/media-libs/scifio-jai-imageio/Manifest
new file mode 100644
index 000000000..3d8ce4b51
--- /dev/null
+++ b/media-libs/scifio-jai-imageio/Manifest
@@ -0,0 +1 @@
+DIST scifio-jai-imageio-1.1.1-sources.tar.gz 826853 BLAKE2B 5bd31431f2b3b1286005ac740d0847281d46f2a4784d823f2a668544a0a69fd006b8b449919008bb51a15a07031a2c8f8c41046ed2f240632c4e7a47616b66da SHA512 041c743c3d5d64110d0f20396bf8d40e06b7806addc40165d6cde1e00edd37ffa22fc1b9887a00c14c701f59c549b3aebf9a7238a71efdac91d018627764e73a
diff --git a/media-libs/scifio-jai-imageio/metadata.xml b/media-libs/scifio-jai-imageio/metadata.xml
new file mode 100644
index 000000000..ff4226a63
--- /dev/null
+++ b/media-libs/scifio-jai-imageio/metadata.xml
@@ -0,0 +1,14 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
+<pkgmetadata>
+  <longdescription>
+    SCIFIO version of the Java Advanced Imaging Image I/O Tools API Core. Java API to handle JPEG and JPEG2000 files. Used by Bio-Formats to read images compressed with JPEG2000 and lossless JPEG.
+  </longdescription>
+  <maintainer type="project">
+    <email>sci@gentoo.org</email>
+    <name>Gentoo Science Project</name>
+  </maintainer>
+  <upstream>
+    <remote-id type="github">scifio/scifio-jai-imageio</remote-id>
+  </upstream>
+</pkgmetadata>
diff --git a/media-libs/scifio-jai-imageio/scifio-jai-imageio-1.1.1.ebuild b/media-libs/scifio-jai-imageio/scifio-jai-imageio-1.1.1.ebuild
new file mode 100644
index 000000000..bdc989735
--- /dev/null
+++ b/media-libs/scifio-jai-imageio/scifio-jai-imageio-1.1.1.ebuild
@@ -0,0 +1,37 @@
+# Copyright 1999-2023 Gentoo Authors
+# Distributed under the terms of the GNU General Public License v2
+
+EAPI=8
+
+JAVA_PKG_IUSE="doc source"
+
+inherit java-pkg-2 java-pkg-simple
+
+DESCRIPTION="SCIFIO version of the Java Advanced Imaging Image I/O Tools API Core."
+HOMEPAGE="http://jai-imageio.dev.java.net/"
+
+if [[ ${PV} == 9999 ]]; then
+	inherit git-r3
+	EGIT_REPO_URI="https://github.com/scifio/scifio-jai-imageio.git"
+	S="${WORKDIR}/${P}"
+	MAVEN_ID="io.scif:scifio-jai-imageio:9999"
+else
+	SRC_URI="
+		https://github.com/scifio/${PN}/archive/refs/tags/${P}.tar.gz -> ${P}-sources.tar.gz
+	"
+	S="${WORKDIR}/${PN}-${P}"
+	MAVEN_ID="io.scif:scifio-jai-imageio:1.1.2"
+	KEYWORDS="~amd64"
+fi
+
+LICENSE="BSD-2"
+SLOT="0"
+
+DEPEND=">=virtual/jdk-1.8:*"
+RDEPEND=">=virtual/jre-1.8:*"
+
+JAVA_SRC_DIR="src/main/java"
+JAVA_MAIN_CLASS=""
+JAVA_RESOURCE_DIRS=(
+	"src/main/resources"
+)
diff --git a/media-libs/scifio-jai-imageio/scifio-jai-imageio-9999.ebuild b/media-libs/scifio-jai-imageio/scifio-jai-imageio-9999.ebuild
new file mode 100644
index 000000000..bdc989735
--- /dev/null
+++ b/media-libs/scifio-jai-imageio/scifio-jai-imageio-9999.ebuild
@@ -0,0 +1,37 @@
+# Copyright 1999-2023 Gentoo Authors
+# Distributed under the terms of the GNU General Public License v2
+
+EAPI=8
+
+JAVA_PKG_IUSE="doc source"
+
+inherit java-pkg-2 java-pkg-simple
+
+DESCRIPTION="SCIFIO version of the Java Advanced Imaging Image I/O Tools API Core."
+HOMEPAGE="http://jai-imageio.dev.java.net/"
+
+if [[ ${PV} == 9999 ]]; then
+	inherit git-r3
+	EGIT_REPO_URI="https://github.com/scifio/scifio-jai-imageio.git"
+	S="${WORKDIR}/${P}"
+	MAVEN_ID="io.scif:scifio-jai-imageio:9999"
+else
+	SRC_URI="
+		https://github.com/scifio/${PN}/archive/refs/tags/${P}.tar.gz -> ${P}-sources.tar.gz
+	"
+	S="${WORKDIR}/${PN}-${P}"
+	MAVEN_ID="io.scif:scifio-jai-imageio:1.1.2"
+	KEYWORDS="~amd64"
+fi
+
+LICENSE="BSD-2"
+SLOT="0"
+
+DEPEND=">=virtual/jdk-1.8:*"
+RDEPEND=">=virtual/jre-1.8:*"
+
+JAVA_SRC_DIR="src/main/java"
+JAVA_MAIN_CLASS=""
+JAVA_RESOURCE_DIRS=(
+	"src/main/resources"
+)
diff --git a/metadata/layout.conf b/metadata/layout.conf
index 91f5b7f8c..0719596ad 100644
--- a/metadata/layout.conf
+++ b/metadata/layout.conf
@@ -22,8 +22,7 @@ manifest-required-hashes = BLAKE2B
 # 2015-10-11 council meeting deprecated EAPI 4.
 # 2016-01-10 council meeting banned EAPI 3.
 # 2018-05-13 council meeting deprecated EAPI 5 for ebuilds.
-eapis-banned = 0 1 2 3 4
-eapis-deprecated = 5 6
+eapis-banned = 0 1 2 3 4 5 6
 
 # Bug #337853 - gentoo's council says to enable
 # --echangelog by default for the "gentoo" repo
diff --git a/metadata/news/2020-12-20-visa-packages-removed/2020-12-20-visa-packages-removed.en.txt b/metadata/news/2020-12-20-visa-packages-removed/2020-12-20-visa-packages-removed.en.txt
new file mode 100644
index 000000000..0468a5aef
--- /dev/null
+++ b/metadata/news/2020-12-20-visa-packages-removed/2020-12-20-visa-packages-removed.en.txt
@@ -0,0 +1,17 @@
+Title: national instrument packages moved to natinst overlay
+Author: Aisha Tammy <gentoo@aisha.cc>
+Posted: 2020-12-20
+Revision: 1
+News-Item-Format: 2.0
+
+The VISA packages have been removed from the science overlay
+and are now available in the natinst overlay which also
+maintains the packages from National Instruments:
+   https://github.com/AndrewAmmerlaan/natinst
+
+The following packages have been moved
+
+  dev-perl/Lab-VISA
+  dev-python/PyVISA
+  dev-python/PyVISA-py
+  sci-libs/ni-visa
diff --git a/metadata/pkgcheck.conf b/metadata/pkgcheck.conf
new file mode 100644
index 000000000..b39b6e490
--- /dev/null
+++ b/metadata/pkgcheck.conf
@@ -0,0 +1,2 @@
+[DEFAULT]
+profiles = stable,dev,-default/linux/amd64/17.0/musl,-default/linux/amd64/17.0/x32
diff --git a/metadata/science.conf b/metadata/science.conf
index 2a1e51cca..fdcdb2ede 100644
--- a/metadata/science.conf
+++ b/metadata/science.conf
@@ -1,5 +1,5 @@
 #put this in /etc/portage/repos.conf/
 [science]
-location = /var/lib/overlays/science
+location = /var/db/repos/science
 sync-type = git
 sync-uri = git://git.gentoo.org/proj/sci.git
diff --git a/net-ftp/bbftp-client/Manifest b/net-ftp/bbftp-client/Manifest
deleted file mode 100644
index 73900ed62..000000000
--- a/net-ftp/bbftp-client/Manifest
+++ /dev/null
@@ -1 +0,0 @@
-DIST bbftp-client-3.2.1.tar.gz 245320 BLAKE2B 92d369d19893d9e9e87ef630d08f288aff9429c8ec3c42ef5f4181c1fd4dbc8226523fc4ccb4e4f50badde08bcf9ab8e09d9b9916122eabcc41960f2a1015f59 SHA512 18447b70fbb7eb9db50500f197d43e9e0d78649e26c4471c9c6f96e8b4a357c88192a8e5097d53fd092d5a7aaf7c65a7d503c6ff7e327bfa8004a64677114a2f
diff --git a/net-ftp/bbftp-client/bbftp-client-3.2.1.ebuild b/net-ftp/bbftp-client/bbftp-client-3.2.1.ebuild
deleted file mode 100644
index da3141fec..000000000
--- a/net-ftp/bbftp-client/bbftp-client-3.2.1.ebuild
+++ /dev/null
@@ -1,43 +0,0 @@
-# Copyright 1999-2017 Gentoo Foundation
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=6
-
-inherit toolchain-funcs
-
-DESCRIPTION="Secure file transfer optimized for files larger than 2GB"
-HOMEPAGE="http://doc.in2p3.fr/bbftp/"
-SRC_URI="http://doc.in2p3.fr/bbftp/dist/${P}.tar.gz"
-
-LICENSE="GPL-2"
-SLOT="0"
-KEYWORDS="~amd64 ~x86"
-IUSE="ssl"
-
-DEPEND="ssl? ( dev-libs/openssl:0 )"
-RDEPEND="${DEPEND}"
-
-S="${WORKDIR}/${P}/bbftpc"
-
-src_prepare() {
-	sed \
-		-e '/@INSTALL@\|mkdir/s:${\(prefix\|mandir\|bindir\)}:${DESTDIR}${\1}:' \
-		-e '/\/etc/d' \
-		-i Makefile.in || die
-	tc-export CC
-	default
-}
-
-src_configure() {
-	econf \
-		$(use_with ssl) \
-		--with-gzip \
-		--without-rfio \
-		--without-afs
-}
-
-src_install() {
-	DOCS=( ../README ../ChangeLog ../TODO ../doc/. )
-	default
-	doman ../doc/bbftp.1
-}
diff --git a/net-ftp/bbftp-client/metadata.xml b/net-ftp/bbftp-client/metadata.xml
deleted file mode 100644
index a5b1bdacc..000000000
--- a/net-ftp/bbftp-client/metadata.xml
+++ /dev/null
@@ -1,13 +0,0 @@
-<?xml version="1.0" encoding="UTF-8"?>
-<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
-<pkgmetadata>
-	<maintainer type="project">
-		<email>sci@gentoo.org</email>
-		<name>Gentoo Science Project</name>
-	</maintainer>
-	<longdescription>
-bbFTP is a file transfer software. It implements its own transfer protocol,
-which is optimized for large files (larger than 2GB) and secure as it does not
-read the password in a file and encrypts the connection information.
-</longdescription>
-</pkgmetadata>
diff --git a/net-ftp/bbftp-server/Manifest b/net-ftp/bbftp-server/Manifest
deleted file mode 100644
index 74bafa390..000000000
--- a/net-ftp/bbftp-server/Manifest
+++ /dev/null
@@ -1 +0,0 @@
-DIST bbftp-server-3.2.1.tar.gz 234731 BLAKE2B 43e0419b44aa7f19ef442cbf25ce8a43e739b668d97940be758dcc51dd531ca9f14eb84502578fe916f7c508c3d42b6ef41169a3af5614a0dde91d12d6fa7101 SHA512 7a11af95cd6724fbe70077e3ee2406cdd4c0ca66d7f74b568dfeedf34637838142cbeca646ab32827fc934634269fe7472cfaa2b0622983807b46ed1803aefec
diff --git a/net-ftp/bbftp-server/bbftp-server-3.2.1.ebuild b/net-ftp/bbftp-server/bbftp-server-3.2.1.ebuild
deleted file mode 100644
index 6c1c61c30..000000000
--- a/net-ftp/bbftp-server/bbftp-server-3.2.1.ebuild
+++ /dev/null
@@ -1,54 +0,0 @@
-# Copyright 1999-2017 Gentoo Foundation
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=6
-
-inherit eutils toolchain-funcs
-
-DESCRIPTION="Secure file transfer optimized for files larger than 2GB"
-HOMEPAGE="http://doc.in2p3.fr/bbftp/"
-SRC_URI="http://doc.in2p3.fr/bbftp/dist/${P}.tar.gz"
-
-LICENSE="GPL-2"
-SLOT="0"
-KEYWORDS="~amd64"
-IUSE="pam ssl"
-
-DEPEND="ssl? ( dev-libs/openssl:0 )"
-RDEPEND="${DEPEND}"
-
-S="${WORKDIR}/${P}/bbftpd"
-
-PATCHES=( "${FILESDIR}"/${PV}-deffixes.patch )
-
-src_prepare() {
-	default
-	sed \
-		-e '/@INSTALL@\|mkdir/s:${\(prefix\|mandir\|bindir\)}:${DESTDIR}${\1}:' \
-		-e '/\/etc/d' \
-		-i Makefile.in
-
-	tc-export CC
-}
-
-src_configure() {
-	econf \
-		$(use_with ssl) \
-		$(use_with pam) \
-		--with-gzip \
-		--without-rfio \
-		--without-afs
-}
-
-src_install() {
-	DOCS=( ../README ../ChangeLog ../TODO ../doc/. )
-	default
-
-	newinitd "${FILESDIR}"/bbftpd.init.d bbftpd
-	doman ../doc/bbftpd.1
-	if use pam; then
-		echo -e "#%PAM-1.0\nauth include system-auth\naccount include system-auth" >> "${T}"/bbftp.pam
-		insinto /etc/pam.d
-		newins "${T}"/bbftp.pam bbftp
-	fi
-}
diff --git a/net-ftp/bbftp-server/files/3.2.0-deffixes.patch b/net-ftp/bbftp-server/files/3.2.0-deffixes.patch
deleted file mode 100644
index ad9d35c84..000000000
--- a/net-ftp/bbftp-server/files/3.2.0-deffixes.patch
+++ /dev/null
@@ -1,77 +0,0 @@
---- includes/common.h	2010-01-07 12:07:45.623549385 -0800
-+++ includes/common.h.new	2010-01-07 12:10:54.585550305 -0800
-@@ -31,6 +31,18 @@
- 
- *****************************************************************************/
- 
-+/* add includes for missing definitions - bgreen 01/07/2010 */
-+#include <stddef.h>  /* for definition of NULL */
-+#ifdef HAVE_STDLIB_H
-+#include <stdlib.h>  /* for free(), exit(), etc. */
-+#endif
-+#ifdef HAVE_STRING_H
-+#include <string.h>
-+#endif
-+#ifdef HAVE_STDIO_H
-+#include <stdio.h>
-+#endif
-+
- /* COMPRESSION and NOCOMPRESSION :
- **		Often used in routine call (more readable than 0 or 1)
- */
---- bbftpd/signals_routines.c	2004-06-30 10:38:52.000000000 -0700
-+++ bbftpd/signals_routines.c.new	2010-01-07 12:15:34.049612507 -0800
-@@ -41,6 +41,12 @@
- #if HAVE_STRING_H
- # include <string.h>
- #endif
-+#if HAVE_STDIO_H
-+# include <stdio.h>
-+#endif
-+#if HAVE_STDLIB_H
-+#include <stdlib.h>
-+#endif
- 
- #include <daemon.h>
- #include <daemon_proto.h>
---- bbftpd/bbftpd_signals.c	2005-03-29 04:55:55.000000000 -0800
-+++ bbftpd/bbftpd_signals.c.new	2010-01-07 12:18:41.923611939 -0800
-@@ -54,6 +54,12 @@
- #if HAVE_STRING_H
- # include <string.h>
- #endif
-+#if HAVE_STDIO_H
-+# include <stdio.h>
-+#endif
-+#if HAVE_STDLIB_H
-+#include <stdlib.h>
-+#endif
- 
- #include <daemon.h>
- #include <daemon_proto.h>
---- bbftpd/bbftpd_utils.c	2003-03-11 04:34:36.000000000 -0800
-+++ bbftpd/bbftpd_utils.c.new	2010-01-07 12:22:38.237550132 -0800
-@@ -31,6 +31,8 @@
-             
- *****************************************************************************/
- #include <stdio.h>
-+#include <string.h>
-+#include <stdlib.h>
- 
- extern char *curfilename ;
- extern char *realfilename ;
---- bbftpd/signals_routines.c	2004-06-30 10:38:52.000000000 -0700
-+++ bbftpd/signals_routines.c.new	2010-01-07 12:24:12.840550139 -0800
-@@ -41,6 +41,12 @@
- #if HAVE_STRING_H
- # include <string.h>
- #endif
-+#if HAVE_STDIO_H
-+# include <stdio.h>
-+#endif
-+#if HAVE_STDLIB_H
-+# include <stdlib.h>
-+#endif
- 
- #include <daemon.h>
- #include <daemon_proto.h>
diff --git a/net-ftp/bbftp-server/files/bbftpd.init.d b/net-ftp/bbftp-server/files/bbftpd.init.d
deleted file mode 100644
index c78ed6642..000000000
--- a/net-ftp/bbftp-server/files/bbftpd.init.d
+++ /dev/null
@@ -1,27 +0,0 @@
-#!/sbin/openrc-run
-# Copyright 1999-2017 Gentoo Foundation
-# Distributed under the terms of the GNU General Public License v2
-
-# Based on opensm script from openfabrics.org,
-#  Copyright (c) 2006 Mellanox Technologies. All rights reserved.
-#  Distributed under the terms of the GNU General Public License v2
-
-depend() {
-    after net    # ip net seems to be needed to perform management.
-}
-
-prog=/usr/bin/bbftpd
-pidfile=/var/run/bbftpd.pid
-
-start() {
-    ebegin "Starting bbftpd"
-    start-stop-daemon --start --pidfile $pidfile --exec $prog -- -b $OPTIONS
-    eend $?
-}
-
-stop() {
-    ebegin "Stopping bbftpd"
-    start-stop-daemon --stop --pidfile $pidfile --exec $prog
-    eend $?
-}
-
diff --git a/net-ftp/bbftp-server/metadata.xml b/net-ftp/bbftp-server/metadata.xml
deleted file mode 100644
index a5b1bdacc..000000000
--- a/net-ftp/bbftp-server/metadata.xml
+++ /dev/null
@@ -1,13 +0,0 @@
-<?xml version="1.0" encoding="UTF-8"?>
-<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
-<pkgmetadata>
-	<maintainer type="project">
-		<email>sci@gentoo.org</email>
-		<name>Gentoo Science Project</name>
-	</maintainer>
-	<longdescription>
-bbFTP is a file transfer software. It implements its own transfer protocol,
-which is optimized for large files (larger than 2GB) and secure as it does not
-read the password in a file and encrypts the connection information.
-</longdescription>
-</pkgmetadata>
diff --git a/net-misc/bbscp/Manifest b/net-misc/bbscp/Manifest
deleted file mode 100644
index 959010183..000000000
--- a/net-misc/bbscp/Manifest
+++ /dev/null
@@ -1 +0,0 @@
-DIST bbscp-1.0.6.tar.gz 17798 BLAKE2B a95c0dbc89b75106a7deab15f0554a32dafcb5ddefb00d783b32befeff854198272cd93f3f9434b725b1690281428e2fe1b35958da6c53297f27f8ea80f9c4b1 SHA512 8b16d60d23be75dae87607674f97bffee92f90bf83af1d135d62d69c1ae5b7e8b4367d047db882257ebfed23d92c81d69359e5101f42cb153e05a0a9608e6f08
diff --git a/net-misc/bbscp/bbscp-1.0.6.ebuild b/net-misc/bbscp/bbscp-1.0.6.ebuild
deleted file mode 100644
index 14dfbdb63..000000000
--- a/net-misc/bbscp/bbscp-1.0.6.ebuild
+++ /dev/null
@@ -1,23 +0,0 @@
-# Copyright 1999-2014 Gentoo Foundation
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=5
-
-DESCRIPTION="SCP-like interface to bbFTP"
-HOMEPAGE="http://www.nas.nasa.gov/Users/Documentation/Networks/BBSCP/bbscp.html"
-SRC_URI="http://www.nas.nasa.gov/hecc/support/kb/file/4/ -> ${P}.tar.gz"
-
-LICENSE="NOSA"
-SLOT="0"
-KEYWORDS="~amd64 ~x86 ~amd64-linux ~x86-linux"
-IUSE=""
-
-DEPEND=""
-RDEPEND="${DEPEND}
-	net-ftp/bbftp-client"
-
-src_install() {
-	dobin ${PN}
-	dodoc NOSA.txt
-	doman man/bbscp.1
-}
diff --git a/net-misc/bbscp/metadata.xml b/net-misc/bbscp/metadata.xml
deleted file mode 100644
index b398694d2..000000000
--- a/net-misc/bbscp/metadata.xml
+++ /dev/null
@@ -1,11 +0,0 @@
-<?xml version="1.0" encoding="UTF-8"?>
-<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
-<pkgmetadata>
-	<maintainer type="project">
-		<email>sci@gentoo.org</email>
-		<name>Gentoo Science Project</name>
-	</maintainer>
-	<longdescription>
-bbSCP is a wrapper that provides an SCP-like interface to bbFTP.
-</longdescription>
-</pkgmetadata>
diff --git a/net-misc/cernbox-client/Manifest b/net-misc/cernbox-client/Manifest
index 9cc363d55..5916259b7 100644
--- a/net-misc/cernbox-client/Manifest
+++ b/net-misc/cernbox-client/Manifest
@@ -1,2 +1,4 @@
-DIST cernbox-client-2.2.4-1.1.src.rpm 14208412 SHA256 1835b660026026a1fd30ef45c2f0d76fbf8efb2970399c24467c9e1611745838 SHA512 24b2a56eb7cc520271ea5f4900f86852cf34ff500b5339b63984b74a40288e30fe785fc9815937637211e7c3d8d7fde7f509f0319d676522641e04ef8192db1e WHIRLPOOL af3c11d30b77d6722c67bb561d1d6e3ab125824d3a25265d25227dfc0ef4f2198d0dfe733b0ca5a3098f59b6da08fbcdb2fac81d02b025ca3215196bf2a4e337
-DIST owncloudclient-2.3.2.tar.xz 12266008 BLAKE2B 53d08aec4971ae309b4fd07cea4e6ed9643411d4f6921c82213d55ec757abcd61ee64abc81e359ea0808b54d8447e3742fdec5394ed55b2e09805616f5430a75 SHA512 8abe071c28b365c100eb30ed91610640a25a7385f4347f5527289f4664788bda375e9618396ffa3e441c7e473da55bdaf7a5cdd99c8fd5801de78cb945fabb9c
+DIST cernbox-client-4.1.0-11373.src.rpm 4621882 BLAKE2B db5106e4e214cee38f729543017adc45a7f4a00e95e57953c6d18b5272e6db88a7d5d820e68272e17d80c3ce962ad3ce689f053a2cff5fe0b7ec2788885cc0d8 SHA512 2deb9c19cbfffd7c37ac06c244c94e996a369ac511d4d71634b7f86f16093cfe7e6d44a97446bcf919924ded392669903344ea38da8bb70cc47317729d355cee
+DIST libregraphapi-1.0.1.tar.gz 105266 BLAKE2B b5122ca5bb757c58bba0f29eaf119685c0ed119a9a72951f4098d8180e5bf05332b36fa6c884ca29b0414051c9c6d6ca081e3c7eeb7b9810202f11c1a70c5190 SHA512 aaa710642c36b4038dc61e7df4fc904a82a2ab6c34da03c3f5328075e41ab319f6616866b7f9ae472ff256b421751f8f5ce7ce0a6d3451bda75cfa3b307df082
+DIST ownCloud-4.1.0.11250.tar.xz 4122856 BLAKE2B 63bdd6047a75e07f6097fec37fb8092675ede50aada272bb8817e0d6ac1aa690cb7257a3d984bac58ed6320543f038cd2c89c49d9161d70ec8a3268997c42af3 SHA512 5f8f43cc8e3ceb2beeebe11fd93937df54e66ce9020a628da232523176815968364667a093cdea6bdf44dca9e1b67878ef76f38c48287327efc0fc3f85f22fb5
+DIST ownCloud-4.2.0.11670.tar.xz 4126004 BLAKE2B 60a5855239b32bfb6769d38de3eced3dcb6c642d702fa33439dfebdc97947dfaed1f0081d2ec8913edc7ab8688872115abd739e21eae7d06e96cbcd92abb5565 SHA512 277d18581155f663c0c18b44a6c0fb9b31c84695e0980da486028b91c1d1c9f5a7ba956afbc11fb2e7fc4679e46a30c2d737667208f5c0599a39bf91a109ce99
diff --git a/net-misc/cernbox-client/cernbox-client-2.3.2.ebuild b/net-misc/cernbox-client/cernbox-client-2.3.2.ebuild
deleted file mode 100644
index 9513b064b..000000000
--- a/net-misc/cernbox-client/cernbox-client-2.3.2.ebuild
+++ /dev/null
@@ -1,104 +0,0 @@
-# Copyright 1999-2018 Gentoo Foundation
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=6
-
-inherit cmake-utils rpm
-
-# Origin is classic owncloud-client, branded for CERN during compilation.
-ORIGIN_P="owncloudclient"
-BRANDED_P="cernbox"
-BRANDED_PV="2.2.4"
-BRANDED_REL="1.1"
-
-DESCRIPTION="Synchronize files from CERNbox EOS with your computer"
-HOMEPAGE="https://cernbox.cern.ch/"
-SRC_URI="
-	http://download.owncloud.com/desktop/stable/${ORIGIN_P}-${PV}.tar.xz
-	https://cernbox.cern.ch/cernbox/doc/Linux/repo/CentOS_7/src/${PN}-${BRANDED_PV}-${BRANDED_REL}.src.rpm"
-
-LICENSE="CC-BY-3.0 GPL-2"
-SLOT="0"
-KEYWORDS="~amd64 ~x86"
-IUSE="doc dolphin nautilus samba +sftp test"
-
-COMMON_DEPEND="
-	>=dev-db/sqlite-3.4:3
-	dev-libs/qtkeychain
-	dev-qt/qtconcurrent:5
-	dev-qt/qtcore:5
-	dev-qt/qtdbus:5
-	dev-qt/qtgui:5
-	dev-qt/qtnetwork:5
-	dev-qt/qtsql:5
-	dev-qt/qtwebkit:5
-	sys-fs/inotify-tools
-	virtual/libiconv
-	dolphin? (
-		kde-frameworks/kcoreaddons:5
-		kde-frameworks/kio:5
-	)
-	nautilus? ( dev-python/nautilus-python )
-	samba? ( >=net-fs/samba-3.5 )
-	sftp? ( >=net-libs/libssh-0.5 )
-"
-RDEPEND="${COMMON_DEPEND}
-	!net-misc/ocsync
-	!net-misc/nextcloud-client
-"
-DEPEND="${COMMON_DEPEND}
-	dev-qt/linguist-tools:5
-	doc? (
-		dev-python/sphinx
-		dev-texlive/texlive-latexextra
-		virtual/latex-base
-	)
-	dolphin? ( kde-frameworks/extra-cmake-modules )
-	test? (
-		dev-util/cmocka
-		dev-qt/qttest:5
-	)
-"
-
-S=${WORKDIR}/owncloudclient-${PV}
-
-src_unpack() {
-	rpm_src_unpack ${PN}-${BRANDED_PV}-${BRANDED_REL}.src.rpm
-	mv ${PN/-}-${BRANDED_PV}/cernbox "${S}" || die "failed to extract branding"
-}
-
-src_prepare() {
-	# Keep tests in ${T}
-	sed -i -e "s#\"/tmp#\"${T}#g" test/test*.cpp || die "sed failed"
-
-	if ! use nautilus; then
-		pushd shell_integration > /dev/null || die
-		cmake_comment_add_subdirectory nautilus
-		popd > /dev/null || die
-	fi
-	default
-}
-
-src_configure() {
-	local mycmakeargs=(
-		-DSYSCONF_INSTALL_DIR="${EPREFIX}"/etc
-		-DCMAKE_INSTALL_DOCDIR=/usr/share/doc/${PF}
-		-DWITH_ICONV=ON
-		-DWITH_DOC=$(usex doc)
-		-DCMAKE_DISABLE_FIND_PACKAGE_KF5=$(usex !dolphin)
-		-DBUILD_WITH_QT4=OFF
-		-DCMAKE_DISABLE_FIND_PACKAGE_Libsmbclient=$(usex !samba)
-		-DCMAKE_DISABLE_FIND_PACKAGE_LibSSH=$(usex !sftp)
-		-DUNIT_TESTING=$(usex test)
-		-DOEM_THEME_DIR=${PWD}/${BRANDED_P}/mirall
-	)
-
-	cmake-utils_src_configure
-}
-
-pkg_postinst() {
-	if ! use doc ; then
-		elog "Documentation and man pages not installed"
-		elog "Enable doc USE-flag to generate them"
-	fi
-}
diff --git a/net-misc/cernbox-client/cernbox-client-4.1.0.11250.ebuild b/net-misc/cernbox-client/cernbox-client-4.1.0.11250.ebuild
new file mode 100644
index 000000000..741aa66f1
--- /dev/null
+++ b/net-misc/cernbox-client/cernbox-client-4.1.0.11250.ebuild
@@ -0,0 +1,92 @@
+# Copyright 1999-2023 Gentoo Authors
+# Distributed under the terms of the GNU General Public License v2
+
+EAPI=8
+
+inherit cmake rpm xdg
+
+DESCRIPTION="Synchronize files from CERNBox EOS with your computer"
+
+# Origin is classic owncloud-client, branded for CERN during compilation.
+ORIGIN_PN="ownCloud"
+BRANDED_P="cernbox"
+BRANDED_PV="4.1.0"
+BRANDED_REL="11373"
+REGRAPHAPI_PV="1.0.1"
+HOMEPAGE="https://cernbox.cern.ch/"
+SRC_URI="https://download.owncloud.com/desktop/${ORIGIN_PN}/stable/${PV}/source/${ORIGIN_PN}-${PV}.tar.xz
+	https://cernboxdistr.web.cern.ch/cernboxdistr/Linux/repo.future/Fedora_38/src/${PN}-${BRANDED_PV}-${BRANDED_REL}.src.rpm
+	https://cern.ch/ofreyerm/gentoo/cernbox/${PN}-${BRANDED_PV}-${BRANDED_REL}.src.rpm
+	https://github.com/owncloud/libre-graph-api-cpp-qt-client/archive/refs/tags/v${REGRAPHAPI_PV}.tar.gz
+		-> libregraphapi-${REGRAPHAPI_PV}.tar.gz"
+
+LICENSE="CC-BY-3.0 GPL-2"
+SLOT="0"
+KEYWORDS="~amd64 ~x86"
+IUSE="dolphin keyring nautilus test"
+RESTRICT="!test? ( test )"
+
+RDEPEND=">=dev-db/sqlite-3.4:3
+	dev-libs/qtkeychain[keyring?,qt5(+)]
+	dev-qt/qtconcurrent:5
+	dev-qt/qtcore:5
+	dev-qt/qtdbus:5
+	dev-qt/qtgui:5
+	dev-qt/qtnetwork:5[ssl]
+	dev-qt/qtsql:5
+	dev-qt/qtwidgets:5
+	dev-qt/qtxml:5
+	sys-fs/inotify-tools
+	dolphin? (
+		kde-frameworks/kcoreaddons:5
+		kde-frameworks/kio:5
+	)
+	nautilus? ( dev-python/nautilus-python )"
+
+DEPEND="${RDEPEND}
+	test? (
+		dev-util/cmocka
+		dev-qt/qttest:5
+	)"
+
+BDEPEND="
+	dev-qt/linguist-tools:5
+	kde-frameworks/extra-cmake-modules"
+
+S=${WORKDIR}/${ORIGIN_PN}-${PV}
+
+src_unpack() {
+	rpm_src_unpack ${PN}-${BRANDED_PV}-${BRANDED_REL}.src.rpm || die "failed to extract branding RPM"
+	mv ${PN%-*}-${BRANDED_PV}.${BRANDED_REL}/branding "${S}" || die "failed to extract branding"
+}
+
+PATCHES=(
+	"${FILESDIR}"/owncloud-client-3.1.0.9872-no_cmake_fetch.patch
+	"${FILESDIR}"/owncloud-client-3.2.0.10193-no_fortify_override.patch
+	"${FILESDIR}"/owncloud-client-4.1.0.11250-fix-mirall.patch
+)
+
+src_prepare() {
+	mv ../libre-graph-api-cpp-qt-client-${REGRAPHAPI_PV} \
+		src/libsync/libregraphapisrc-src || die
+
+	# Keep tests in ${T}
+	sed -i -e "s#\"/tmp#\"${T}#g" test/test*.cpp || die
+
+	if ! use nautilus; then
+		pushd shell_integration > /dev/null || die
+		cmake_comment_add_subdirectory nautilus
+		popd > /dev/null || die
+	fi
+	cmake_src_prepare
+}
+
+src_configure() {
+	local mycmakeargs=(
+		-DCMAKE_INSTALL_DOCDIR=/usr/share/doc/${PF}
+		-DBUILD_SHELL_INTEGRATION_DOLPHIN=$(usex dolphin)
+		-DBUILD_TESTING=$(usex test)
+	)
+
+	cmake_src_configure
+}
diff --git a/net-misc/cernbox-client/cernbox-client-4.2.0.11670.ebuild b/net-misc/cernbox-client/cernbox-client-4.2.0.11670.ebuild
new file mode 100644
index 000000000..741aa66f1
--- /dev/null
+++ b/net-misc/cernbox-client/cernbox-client-4.2.0.11670.ebuild
@@ -0,0 +1,92 @@
+# Copyright 1999-2023 Gentoo Authors
+# Distributed under the terms of the GNU General Public License v2
+
+EAPI=8
+
+inherit cmake rpm xdg
+
+DESCRIPTION="Synchronize files from CERNBox EOS with your computer"
+
+# Origin is classic owncloud-client, branded for CERN during compilation.
+ORIGIN_PN="ownCloud"
+BRANDED_P="cernbox"
+BRANDED_PV="4.1.0"
+BRANDED_REL="11373"
+REGRAPHAPI_PV="1.0.1"
+HOMEPAGE="https://cernbox.cern.ch/"
+SRC_URI="https://download.owncloud.com/desktop/${ORIGIN_PN}/stable/${PV}/source/${ORIGIN_PN}-${PV}.tar.xz
+	https://cernboxdistr.web.cern.ch/cernboxdistr/Linux/repo.future/Fedora_38/src/${PN}-${BRANDED_PV}-${BRANDED_REL}.src.rpm
+	https://cern.ch/ofreyerm/gentoo/cernbox/${PN}-${BRANDED_PV}-${BRANDED_REL}.src.rpm
+	https://github.com/owncloud/libre-graph-api-cpp-qt-client/archive/refs/tags/v${REGRAPHAPI_PV}.tar.gz
+		-> libregraphapi-${REGRAPHAPI_PV}.tar.gz"
+
+LICENSE="CC-BY-3.0 GPL-2"
+SLOT="0"
+KEYWORDS="~amd64 ~x86"
+IUSE="dolphin keyring nautilus test"
+RESTRICT="!test? ( test )"
+
+RDEPEND=">=dev-db/sqlite-3.4:3
+	dev-libs/qtkeychain[keyring?,qt5(+)]
+	dev-qt/qtconcurrent:5
+	dev-qt/qtcore:5
+	dev-qt/qtdbus:5
+	dev-qt/qtgui:5
+	dev-qt/qtnetwork:5[ssl]
+	dev-qt/qtsql:5
+	dev-qt/qtwidgets:5
+	dev-qt/qtxml:5
+	sys-fs/inotify-tools
+	dolphin? (
+		kde-frameworks/kcoreaddons:5
+		kde-frameworks/kio:5
+	)
+	nautilus? ( dev-python/nautilus-python )"
+
+DEPEND="${RDEPEND}
+	test? (
+		dev-util/cmocka
+		dev-qt/qttest:5
+	)"
+
+BDEPEND="
+	dev-qt/linguist-tools:5
+	kde-frameworks/extra-cmake-modules"
+
+S=${WORKDIR}/${ORIGIN_PN}-${PV}
+
+src_unpack() {
+	rpm_src_unpack ${PN}-${BRANDED_PV}-${BRANDED_REL}.src.rpm || die "failed to extract branding RPM"
+	mv ${PN%-*}-${BRANDED_PV}.${BRANDED_REL}/branding "${S}" || die "failed to extract branding"
+}
+
+PATCHES=(
+	"${FILESDIR}"/owncloud-client-3.1.0.9872-no_cmake_fetch.patch
+	"${FILESDIR}"/owncloud-client-3.2.0.10193-no_fortify_override.patch
+	"${FILESDIR}"/owncloud-client-4.1.0.11250-fix-mirall.patch
+)
+
+src_prepare() {
+	mv ../libre-graph-api-cpp-qt-client-${REGRAPHAPI_PV} \
+		src/libsync/libregraphapisrc-src || die
+
+	# Keep tests in ${T}
+	sed -i -e "s#\"/tmp#\"${T}#g" test/test*.cpp || die
+
+	if ! use nautilus; then
+		pushd shell_integration > /dev/null || die
+		cmake_comment_add_subdirectory nautilus
+		popd > /dev/null || die
+	fi
+	cmake_src_prepare
+}
+
+src_configure() {
+	local mycmakeargs=(
+		-DCMAKE_INSTALL_DOCDIR=/usr/share/doc/${PF}
+		-DBUILD_SHELL_INTEGRATION_DOLPHIN=$(usex dolphin)
+		-DBUILD_TESTING=$(usex test)
+	)
+
+	cmake_src_configure
+}
diff --git a/net-misc/cernbox-client/files/owncloud-client-3.1.0.9872-no_cmake_fetch.patch b/net-misc/cernbox-client/files/owncloud-client-3.1.0.9872-no_cmake_fetch.patch
new file mode 100644
index 000000000..d9762292e
--- /dev/null
+++ b/net-misc/cernbox-client/files/owncloud-client-3.1.0.9872-no_cmake_fetch.patch
@@ -0,0 +1,17 @@
+Index: ownCloud-3.1.0.9872/src/libsync/CMakeLists.txt
+--- ownCloud-3.1.0.9872/src/libsync/CMakeLists.txt.orig
++++ ownCloud-3.1.0.9872/src/libsync/CMakeLists.txt
+@@ -3,12 +3,7 @@ set(LibreGraphAPIVersion v0.13.2)
+ find_package(LibreGraphAPI QUIET)
+ if (NOT TARGET OpenAPI::LibreGraphAPI)
+     message(WARNING "Failed to find system OpenAPI::LibreGraphAPI: fetching ${LibreGraphAPIVersion}")
+-    include(FetchContent)
+-    FetchContent_Populate(LibreGraphAPISrc
+-                        QUIET
+-                        GIT_REPOSITORY https://github.com/owncloud/libre-graph-api-cpp-qt-client.git
+-                        GIT_TAG ${LibreGraphAPIVersion})
+-    add_subdirectory(${libregraphapisrc_SOURCE_DIR}/client ${libregraphapisrc_BINARY_DIR}/client EXCLUDE_FROM_ALL)
++    add_subdirectory(libregraphapisrc-src/client libregraphapisrc-src/client EXCLUDE_FROM_ALL)
+ endif()
+ 
+ set(libsync_SRCS
diff --git a/net-misc/cernbox-client/files/owncloud-client-3.2.0.10193-no_fortify_override.patch b/net-misc/cernbox-client/files/owncloud-client-3.2.0.10193-no_fortify_override.patch
new file mode 100644
index 000000000..266596b7b
--- /dev/null
+++ b/net-misc/cernbox-client/files/owncloud-client-3.2.0.10193-no_fortify_override.patch
@@ -0,0 +1,16 @@
+diff -Naur ownCloud-3.2.0.10193.orig/src/CMakeLists.txt ownCloud-3.2.0.10193/src/CMakeLists.txt
+--- ownCloud-3.2.0.10193.orig/src/CMakeLists.txt	2023-02-15 18:27:55.000000000 +0100
++++ ownCloud-3.2.0.10193/src/CMakeLists.txt	2023-02-22 22:55:29.352847663 +0100
+@@ -16,12 +16,6 @@
+       set(CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} -fstack-protector-strong")
+     endif()
+   endif()
+-
+-  string(TOLOWER "${CMAKE_BUILD_TYPE}" CMAKE_BUILD_TYPE_LOWER)
+-  if(CMAKE_BUILD_TYPE_LOWER MATCHES "(release|relwithdebinfo|minsizerel)")
+-    set(CMAKE_C_FLAGS "${CMAKE_C_FLAGS} -D_FORTIFY_SOURCE=2")
+-    set(CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} -D_FORTIFY_SOURCE=2")
+-  endif()
+ endif()
+ 
+ if(WIN32)
diff --git a/net-misc/cernbox-client/files/owncloud-client-4.1.0.11250-fix-mirall.patch b/net-misc/cernbox-client/files/owncloud-client-4.1.0.11250-fix-mirall.patch
new file mode 100644
index 000000000..5e00e23aa
--- /dev/null
+++ b/net-misc/cernbox-client/files/owncloud-client-4.1.0.11250-fix-mirall.patch
@@ -0,0 +1,73 @@
+From: Fabian Müller <fmueller@owncloud.com>
+Bug: https://github.com/owncloud/client/pull/10969
+
+Fix installation of branded client in parallel to unbranded client.
+
+diff --git a/src/CMakeLists.txt b/src/CMakeLists.txt
+index 4d73f2cc3..49228dbb6 100644
+--- a/src/CMakeLists.txt
++++ b/src/CMakeLists.txt
+@@ -54,10 +54,12 @@ endif(NOT BUILD_LIBRARIES_ONLY)
+ 
+ add_subdirectory(plugins)
+ 
+-install(EXPORT ownCloudConfig DESTINATION "${KDE_INSTALL_CMAKEPACKAGEDIR}/ownCloud"  NAMESPACE ownCloud::)
++install(EXPORT ${APPLICATION_SHORTNAME}Config DESTINATION "${KDE_INSTALL_CMAKEPACKAGEDIR}/${APPLICATION_SHORTNAME}" NAMESPACE ownCloud::)
+ 
+-ecm_setup_version(PROJECT VARIABLE_PREFIX ownCloud
+-                        PACKAGE_VERSION_FILE "${CMAKE_CURRENT_BINARY_DIR}/ownCloudConfigVersion.cmake"
+-                        SOVERSION ${MIRALL_SOVERSION})
++ecm_setup_version(PROJECT
++    VARIABLE_PREFIX ${APPLICATION_SHORTNAME}
++    PACKAGE_VERSION_FILE "${CMAKE_CURRENT_BINARY_DIR}/${APPLICATION_SHORTNAME}ConfigVersion.cmake"
++    SOVERSION ${MIRALL_SOVERSION}
++)
+ 
+-install(FILES "${CMAKE_CURRENT_BINARY_DIR}/ownCloudConfigVersion.cmake" DESTINATION "${KDE_INSTALL_CMAKEPACKAGEDIR}/ownCloud")
++install(FILES "${CMAKE_CURRENT_BINARY_DIR}/${APPLICATION_SHORTNAME}ConfigVersion.cmake" DESTINATION "${KDE_INSTALL_CMAKEPACKAGEDIR}/${APPLICATION_SHORTNAME}")
+diff --git a/src/csync/CMakeLists.txt b/src/csync/CMakeLists.txt
+index fcf665e44..15c0a8130 100644
+--- a/src/csync/CMakeLists.txt
++++ b/src/csync/CMakeLists.txt
+@@ -98,10 +98,10 @@ INSTALL(
+         ../common/filesystembase.h
+         ../common/utility.h
+     DESTINATION
+-        ${INCLUDE_INSTALL_DIR}/ownCloud/common
++        ${INCLUDE_INSTALL_DIR}/${APPLICATION_SHORTNAME}/common
+ )
+ 
+-INSTALL(TARGETS csync EXPORT ownCloudConfig ${KDE_INSTALL_TARGETS_DEFAULT_ARGS})
++INSTALL(TARGETS csync EXPORT ${APPLICATION_SHORTNAME}Config ${KDE_INSTALL_TARGETS_DEFAULT_ARGS})
+ 
+ configure_file(config_csync.h.cmake ${CMAKE_CURRENT_BINARY_DIR}/config_csync.h)
+ 
+diff --git a/src/libsync/CMakeLists.txt b/src/libsync/CMakeLists.txt
+index 3995bcfe9..eeaef8450 100644
+--- a/src/libsync/CMakeLists.txt
++++ b/src/libsync/CMakeLists.txt
+@@ -85,7 +85,7 @@ INSTALL(
+         ${CMAKE_CURRENT_BINARY_DIR}/owncloudlib.h
+         logger.h
+         accessmanager.h
+-    DESTINATION ${INCLUDE_INSTALL_DIR}/ownCloud/libsync
++    DESTINATION ${INCLUDE_INSTALL_DIR}/${APPLICATION_SHORTNAME}/libsync
+ )
+ 
+ add_library(libsync SHARED ${libsync_SRCS})
+@@ -138,4 +138,4 @@ set_target_properties(libsync PROPERTIES
+         VERSION ${MIRALL_VERSION}
+         SOVERSION ${MIRALL_SOVERSION}
+ )
+-install(TARGETS libsync EXPORT ownCloudConfig ${KDE_INSTALL_TARGETS_DEFAULT_ARGS})
++install(TARGETS libsync EXPORT ${APPLICATION_SHORTNAME}Config ${KDE_INSTALL_TARGETS_DEFAULT_ARGS})
+diff --git a/src/resources/CMakeLists.txt b/src/resources/CMakeLists.txt
+index 6f50bf3be..7e0ff05b7 100644
+--- a/src/resources/CMakeLists.txt
++++ b/src/resources/CMakeLists.txt
+@@ -42,4 +42,4 @@ if(Qt5LinguistTools_FOUND)
+     )
+ endif()
+ 
+-install(TARGETS owncloudResources EXPORT ownCloudConfig ${KDE_INSTALL_TARGETS_DEFAULT_ARGS})
++install(TARGETS owncloudResources EXPORT ${APPLICATION_SHORTNAME}Config ${KDE_INSTALL_TARGETS_DEFAULT_ARGS})
diff --git a/net-misc/cernbox-client/metadata.xml b/net-misc/cernbox-client/metadata.xml
index ac0a4fc58..e8384eb02 100644
--- a/net-misc/cernbox-client/metadata.xml
+++ b/net-misc/cernbox-client/metadata.xml
@@ -1,27 +1,32 @@
 <?xml version="1.0" encoding="UTF-8"?>
-<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
+<!DOCTYPE pkgmetadata SYSTEM "https://www.gentoo.org/dtd/metadata.dtd">
 <pkgmetadata>
+	<maintainer type="person">
+		<email>o.freyermuth@googlemail.com</email>
+		<name>Oliver Freyermuth</name>
+	</maintainer>
 	<maintainer type="project">
 		<email>sci-physics@gentoo.org</email>
 		<name>Gentoo Physics Project</name>
 	</maintainer>
 	<longdescription lang="en">
-This service provides a cloud synchronisation service for all CERN users between personal devices (like a laptop) and a centrally-managed data storage.
+		This service provides a cloud synchronisation service for all CERN users between personal devices (like a laptop) and a centrally-managed data storage.
 
-Available to all CERN users. This service provides synchronisation capabilities:
-everyone having a CERN computing account can use box to synchronise data (files and directories) across a series of (mobile) devices (smartphones, tablet, laptop, desktop).
-Major software distributions are supported (notably recent Mac, Linux and Windows).
+		Available to all CERN users. This service provides synchronisation capabilities:
+		everyone having a CERN computing account can use box to synchronise data (files and directories) across a series of (mobile) devices (smartphones, tablet, laptop, desktop).
+		Major software distributions are supported (notably recent Mac, Linux and Windows).
 
-The service provides off-line eventually synchronised access to data and it is also meant for data sharing across collaborators (for example to share presentations or text documents).
+		The service provides off-line eventually synchronised access to data and it is also meant for data sharing across collaborators (for example to share presentations or text documents).
 
-The service is not suitable for critical-path activities like data acquisition, world-wide data distribution and massive batch processing.
-</longdescription>
+		The service is not suitable for critical-path activities like data acquisition, world-wide data distribution and massive batch processing.
+	</longdescription>
 	<use>
 		<flag name="dolphin">Install the <pkg>kde-apps/dolphin</pkg> extension</flag>
 		<flag name="nautilus">Install the <pkg>gnome-base/nautilus</pkg> extension</flag>
-		<flag name="sftp">Enable sftp transfer support via <pkg>net-libs/libssh</pkg></flag>
 	</use>
 	<upstream>
-		<doc>http://cernbox.web.cern.ch/cernbox/00_getting_started/index.html</doc>
+		<doc>https://cernbox.web.cern.ch/cernbox/</doc>
+		<remote-id type="github">owncloud/client</remote-id>
+		<remote-id type="github">owncloud/libre-graph-api-cpp-qt-client</remote-id>
 	</upstream>
 </pkgmetadata>
diff --git a/patches/0002-LU-3319-procfs-move-mdd-ofd-proc-handling-to-seq_fil.patch b/patches/0002-LU-3319-procfs-move-mdd-ofd-proc-handling-to-seq_fil.patch
deleted file mode 100644
index 813446c38..000000000
--- a/patches/0002-LU-3319-procfs-move-mdd-ofd-proc-handling-to-seq_fil.patch
+++ /dev/null
@@ -1,2082 +0,0 @@
-From 9071634fd9db37a6121fdfbd817162f782661202 Mon Sep 17 00:00:00 2001
-From: James Simmons <uja.ornl@gmail.com>
-Date: Mon, 5 May 2014 10:02:21 -0400
-Subject: [PATCH 2/3] LU-3319 procfs: move mdd/ofd proc handling to seq_files
-
-With 3.10 linux kernel and above proc handling now only
-uses struct seq_files. This patch migrates the mdd/ofd
-layer proc entries over to using seq_files.
-
-Signed-off-by: James Simmons <uja.ornl@gmail.com>
-Change-Id: I61b7df6bfd5efd0f12e3ca1a1813b7b62d493168
----
- lustre/include/lustre_lfsck.h  |   6 +-
- lustre/lfsck/lfsck_internal.h  |   9 +-
- lustre/lfsck/lfsck_layout.c    | 132 ++++-------
- lustre/lfsck/lfsck_lib.c       |  88 +++-----
- lustre/lfsck/lfsck_namespace.c |  75 ++-----
- lustre/mdd/mdd_device.c        |  25 +--
- lustre/mdd/mdd_internal.h      |   1 -
- lustre/mdd/mdd_lproc.c         | 302 ++++++++++++-------------
- lustre/ofd/lproc_ofd.c         | 490 +++++++++++++++++++++--------------------
- lustre/ofd/ofd_dev.c           |  90 ++++----
- lustre/ofd/ofd_internal.h      |   6 +-
- 11 files changed, 543 insertions(+), 681 deletions(-)
-
-diff --git a/lustre/include/lustre_lfsck.h b/lustre/include/lustre_lfsck.h
-index 0d6f666..5adbffe 100644
---- a/lustre/include/lustre_lfsck.h
-+++ b/lustre/include/lustre_lfsck.h
-@@ -148,12 +148,12 @@ int lfsck_in_notify(const struct lu_env *env, struct dt_device *key,
- int lfsck_query(const struct lu_env *env, struct dt_device *key,
- 		struct lfsck_request *lr);
- 
--int lfsck_get_speed(struct dt_device *key, void *buf, int len);
-+int lfsck_get_speed(struct seq_file *m, struct dt_device *key);
- int lfsck_set_speed(struct dt_device *key, int val);
--int lfsck_get_windows(struct dt_device *key, void *buf, int len);
-+int lfsck_get_windows(struct seq_file *m, struct dt_device *key);
- int lfsck_set_windows(struct dt_device *key, int val);
- 
--int lfsck_dump(struct dt_device *key, void *buf, int len, enum lfsck_type type);
-+int lfsck_dump(struct seq_file *m, struct dt_device *key, enum lfsck_type type);
- 
- static inline void lfsck_pack_rfa(struct lfsck_request *lr,
- 				  const struct lu_fid *fid)
-diff --git a/lustre/lfsck/lfsck_internal.h b/lustre/lfsck/lfsck_internal.h
-index 24b84ae..203ad74 100644
---- a/lustre/lfsck/lfsck_internal.h
-+++ b/lustre/lfsck/lfsck_internal.h
-@@ -303,8 +303,7 @@ struct lfsck_operations {
- 
- 	int (*lfsck_dump)(const struct lu_env *env,
- 			  struct lfsck_component *com,
--			  char *buf,
--			  int len);
-+			  struct seq_file *m);
- 
- 	int (*lfsck_double_scan)(const struct lu_env *env,
- 				 struct lfsck_component *com);
-@@ -590,10 +589,10 @@ void lfsck_component_cleanup(const struct lu_env *env,
- 			     struct lfsck_component *com);
- void lfsck_instance_cleanup(const struct lu_env *env,
- 			    struct lfsck_instance *lfsck);
--int lfsck_bits_dump(char **buf, int *len, int bits, const char *names[],
-+int lfsck_bits_dump(struct seq_file *m, int bits, const char *names[],
- 		    const char *prefix);
--int lfsck_time_dump(char **buf, int *len, __u64 time, const char *prefix);
--int lfsck_pos_dump(char **buf, int *len, struct lfsck_position *pos,
-+int lfsck_time_dump(struct seq_file *m, __u64 time, const char *prefix);
-+int lfsck_pos_dump(struct seq_file *m, struct lfsck_position *pos,
- 		   const char *prefix);
- void lfsck_pos_fill(const struct lu_env *env, struct lfsck_instance *lfsck,
- 		    struct lfsck_position *pos, bool init);
-diff --git a/lustre/lfsck/lfsck_layout.c b/lustre/lfsck/lfsck_layout.c
-index ced2e4d..e2df62d 100644
---- a/lustre/lfsck/lfsck_layout.c
-+++ b/lustre/lfsck/lfsck_layout.c
-@@ -492,7 +492,7 @@ static struct lfsck_rbtree_node *lfsck_rbtree_new(const struct lu_env *env,
- 		return ERR_PTR(-ENOMEM);
- 	}
- 
--	rb_init_node(&lrn->lrn_node);
-+	RB_CLEAR_NODE(&lrn->lrn_node);
- 	lrn->lrn_seq = fid_seq(fid);
- 	lrn->lrn_first_oid = fid_oid(fid) & ~LFSCK_RBTREE_BITMAP_MASK;
- 	atomic_set(&lrn->lrn_known_count, 0);
-@@ -4873,69 +4873,53 @@ static int lfsck_layout_slave_post(const struct lu_env *env,
- }
- 
- static int lfsck_layout_dump(const struct lu_env *env,
--			     struct lfsck_component *com, char *buf, int len)
-+			     struct lfsck_component *com, struct seq_file *m)
- {
- 	struct lfsck_instance	*lfsck = com->lc_lfsck;
- 	struct lfsck_bookmark	*bk    = &lfsck->li_bookmark_ram;
- 	struct lfsck_layout	*lo    = com->lc_file_ram;
--	int			 save  = len;
--	int			 ret   = -ENOSPC;
- 	int			 rc;
- 
- 	down_read(&com->lc_sem);
--	rc = snprintf(buf, len,
--		      "name: lfsck_layout\n"
-+	seq_printf(m, "name: lfsck_layout\n"
- 		      "magic: %#x\n"
- 		      "version: %d\n"
- 		      "status: %s\n",
- 		      lo->ll_magic,
- 		      bk->lb_version,
- 		      lfsck_status2names(lo->ll_status));
--	if (rc <= 0)
--		goto out;
- 
--	buf += rc;
--	len -= rc;
--	rc = lfsck_bits_dump(&buf, &len, lo->ll_flags, lfsck_flags_names,
--			     "flags");
-+	rc = lfsck_bits_dump(m, lo->ll_flags, lfsck_flags_names, "flags");
- 	if (rc < 0)
- 		goto out;
- 
--	rc = lfsck_bits_dump(&buf, &len, bk->lb_param, lfsck_param_names,
--			     "param");
-+	rc = lfsck_bits_dump(m, bk->lb_param, lfsck_param_names, "param");
- 	if (rc < 0)
- 		goto out;
- 
--	rc = lfsck_time_dump(&buf, &len, lo->ll_time_last_complete,
-+	rc = lfsck_time_dump(m, lo->ll_time_last_complete,
- 			     "time_since_last_completed");
- 	if (rc < 0)
- 		goto out;
- 
--	rc = lfsck_time_dump(&buf, &len, lo->ll_time_latest_start,
-+	rc = lfsck_time_dump(m, lo->ll_time_latest_start,
- 			     "time_since_latest_start");
- 	if (rc < 0)
- 		goto out;
- 
--	rc = lfsck_time_dump(&buf, &len, lo->ll_time_last_checkpoint,
-+	rc = lfsck_time_dump(m, lo->ll_time_last_checkpoint,
- 			     "time_since_last_checkpoint");
- 	if (rc < 0)
- 		goto out;
- 
--	rc = snprintf(buf, len,
--		      "latest_start_position: "LPU64"\n"
-+	seq_printf(m, "latest_start_position: "LPU64"\n"
- 		      "last_checkpoint_position: "LPU64"\n"
- 		      "first_failure_position: "LPU64"\n",
- 		      lo->ll_pos_latest_start,
- 		      lo->ll_pos_last_checkpoint,
- 		      lo->ll_pos_first_inconsistent);
--	if (rc <= 0)
--		goto out;
- 
--	buf += rc;
--	len -= rc;
--
--	rc = snprintf(buf, len,
--		      "success_count: %u\n"
-+	seq_printf(m, "success_count: %u\n"
- 		      "repaired_dangling: "LPU64"\n"
- 		      "repaired_unmatched_pair: "LPU64"\n"
- 		      "repaired_multiple_referenced: "LPU64"\n"
-@@ -4955,11 +4939,6 @@ static int lfsck_layout_dump(const struct lu_env *env,
- 		      lo->ll_objs_skipped,
- 		      lo->ll_objs_failed_phase1,
- 		      lo->ll_objs_failed_phase2);
--	if (rc <= 0)
--		goto out;
--
--	buf += rc;
--	len -= rc;
- 
- 	if (lo->ll_status == LS_SCANNING_PHASE1) {
- 		__u64 pos;
-@@ -4977,8 +4956,7 @@ static int lfsck_layout_dump(const struct lu_env *env,
- 			do_div(new_checked, duration);
- 		if (rtime != 0)
- 			do_div(speed, rtime);
--		rc = snprintf(buf, len,
--			      "checked_phase1: "LPU64"\n"
-+		seq_printf(m, "checked_phase1: "LPU64"\n"
- 			      "checked_phase2: "LPU64"\n"
- 			      "run_time_phase1: %u seconds\n"
- 			      "run_time_phase2: %u seconds\n"
-@@ -4992,11 +4970,6 @@ static int lfsck_layout_dump(const struct lu_env *env,
- 			      lo->ll_run_time_phase2,
- 			      speed,
- 			      new_checked);
--		if (rc <= 0)
--			goto out;
--
--		buf += rc;
--		len -= rc;
- 
- 		LASSERT(lfsck->li_di_oit != NULL);
- 
-@@ -5009,12 +4982,8 @@ static int lfsck_layout_dump(const struct lu_env *env,
- 		pos = iops->store(env, lfsck->li_di_oit);
- 		if (!lfsck->li_current_oit_processed)
- 			pos--;
--		rc = snprintf(buf, len, "current_position: "LPU64"\n", pos);
--		if (rc <= 0)
--			goto out;
-+		seq_printf(m, "current_position: "LPU64"\n", pos);
- 
--		buf += rc;
--		len -= rc;
- 	} else if (lo->ll_status == LS_SCANNING_PHASE2) {
- 		cfs_duration_t duration = cfs_time_current() -
- 					  lfsck->li_time_last_checkpoint;
-@@ -5032,29 +5001,26 @@ static int lfsck_layout_dump(const struct lu_env *env,
- 			do_div(speed1, lo->ll_run_time_phase1);
- 		if (rtime != 0)
- 			do_div(speed2, rtime);
--		rc = snprintf(buf, len,
--			      "checked_phase1: "LPU64"\n"
--			      "checked_phase2: "LPU64"\n"
--			      "run_time_phase1: %u seconds\n"
--			      "run_time_phase2: %u seconds\n"
--			      "average_speed_phase1: "LPU64" items/sec\n"
--			      "average_speed_phase2: "LPU64" items/sec\n"
--			      "real-time_speed_phase1: N/A\n"
--			      "real-time_speed_phase2: "LPU64" items/sec\n"
--			      "current_position: "DFID"\n",
--			      lo->ll_objs_checked_phase1,
--			      checked,
--			      lo->ll_run_time_phase1,
--			      rtime,
--			      speed1,
--			      speed2,
--			      new_checked,
--			      PFID(&com->lc_fid_latest_scanned_phase2));
-+		rc = seq_printf(m, "checked_phase1: "LPU64"\n"
-+				"checked_phase2: "LPU64"\n"
-+				"run_time_phase1: %u seconds\n"
-+				"run_time_phase2: %u seconds\n"
-+				"average_speed_phase1: "LPU64" items/sec\n"
-+				"average_speed_phase2: "LPU64" items/sec\n"
-+				"real-time_speed_phase1: N/A\n"
-+				"real-time_speed_phase2: "LPU64" items/sec\n"
-+				"current_position: "DFID"\n",
-+				lo->ll_objs_checked_phase1,
-+				checked,
-+				lo->ll_run_time_phase1,
-+				rtime,
-+				speed1,
-+				speed2,
-+				new_checked,
-+				PFID(&com->lc_fid_latest_scanned_phase2));
- 		if (rc <= 0)
- 			goto out;
- 
--		buf += rc;
--		len -= rc;
- 	} else {
- 		__u64 speed1 = lo->ll_objs_checked_phase1;
- 		__u64 speed2 = lo->ll_objs_checked_phase2;
-@@ -5063,34 +5029,26 @@ static int lfsck_layout_dump(const struct lu_env *env,
- 			do_div(speed1, lo->ll_run_time_phase1);
- 		if (lo->ll_run_time_phase2 != 0)
- 			do_div(speed2, lo->ll_run_time_phase2);
--		rc = snprintf(buf, len,
--			      "checked_phase1: "LPU64"\n"
--			      "checked_phase2: "LPU64"\n"
--			      "run_time_phase1: %u seconds\n"
--			      "run_time_phase2: %u seconds\n"
--			      "average_speed_phase1: "LPU64" items/sec\n"
--			      "average_speed_phase2: "LPU64" objs/sec\n"
--			      "real-time_speed_phase1: N/A\n"
--			      "real-time_speed_phase2: N/A\n"
--			      "current_position: N/A\n",
--			      lo->ll_objs_checked_phase1,
--			      lo->ll_objs_checked_phase2,
--			      lo->ll_run_time_phase1,
--			      lo->ll_run_time_phase2,
--			      speed1,
--			      speed2);
--		if (rc <= 0)
--			goto out;
--
--		buf += rc;
--		len -= rc;
-+		seq_printf(m, "checked_phase1: "LPU64"\n"
-+			   "checked_phase2: "LPU64"\n"
-+			   "run_time_phase1: %u seconds\n"
-+			   "run_time_phase2: %u seconds\n"
-+			   "average_speed_phase1: "LPU64" items/sec\n"
-+			   "average_speed_phase2: "LPU64" objs/sec\n"
-+			   "real-time_speed_phase1: N/A\n"
-+			   "real-time_speed_phase2: N/A\n"
-+			   "current_position: N/A\n",
-+			   lo->ll_objs_checked_phase1,
-+			   lo->ll_objs_checked_phase2,
-+			   lo->ll_run_time_phase1,
-+			   lo->ll_run_time_phase2,
-+			   speed1,
-+			   speed2);
- 	}
--	ret = save - len;
--
- out:
- 	up_read(&com->lc_sem);
- 
--	return ret;
-+	return rc;
- }
- 
- static int lfsck_layout_master_double_scan(const struct lu_env *env,
-diff --git a/lustre/lfsck/lfsck_lib.c b/lustre/lfsck/lfsck_lib.c
-index db73616..f6f1cce 100644
---- a/lustre/lfsck/lfsck_lib.c
-+++ b/lustre/lfsck/lfsck_lib.c
-@@ -900,21 +900,15 @@ static inline int lfsck_instance_add(struct lfsck_instance *lfsck)
- 	return 0;
- }
- 
--int lfsck_bits_dump(char **buf, int *len, int bits, const char *names[],
-+int lfsck_bits_dump(struct seq_file *m, int bits, const char *names[],
- 		    const char *prefix)
- {
--	int save = *len;
- 	int flag;
--	int rc;
- 	int i;
- 	bool newline = (bits != 0 ? false : true);
- 
--	rc = snprintf(*buf, *len, "%s:%c", prefix, newline ? '\n' : ' ');
--	if (rc <= 0)
--		return -ENOSPC;
-+	seq_printf(m, "%s:%c", prefix, bits != 0 ? ' ' : '\n');
- 
--	*buf += rc;
--	*len -= rc;
- 	for (i = 0, flag = 1; bits != 0; i++, flag = 1 << i) {
- 		if (flag & bits) {
- 			bits &= ~flag;
-@@ -922,69 +916,43 @@ int lfsck_bits_dump(char **buf, int *len, int bits, const char *names[],
- 				if (bits == 0)
- 					newline = true;
- 
--				rc = snprintf(*buf, *len, "%s%c", names[i],
--					      newline ? '\n' : ',');
--				if (rc <= 0)
--					return -ENOSPC;
--
--				*buf += rc;
--				*len -= rc;
-+				seq_printf(m, "%s%c", names[i],
-+					   newline ? '\n' : ',');
- 			}
- 		}
- 	}
- 
--	if (!newline) {
--		rc = snprintf(*buf, *len, "\n");
--		if (rc <= 0)
--			return -ENOSPC;
--
--		*buf += rc;
--		*len -= rc;
--	}
--
--	return save - *len;
-+	if (!newline)
-+		seq_printf(m, "\n");
-+	return 0;
- }
- 
--int lfsck_time_dump(char **buf, int *len, __u64 time, const char *prefix)
-+int lfsck_time_dump(struct seq_file *m, __u64 time, const char *prefix)
- {
--	int rc;
--
- 	if (time != 0)
--		rc = snprintf(*buf, *len, "%s: "LPU64" seconds\n", prefix,
--			      cfs_time_current_sec() - time);
-+		seq_printf(m, "%s: "LPU64" seconds\n", prefix,
-+			  cfs_time_current_sec() - time);
- 	else
--		rc = snprintf(*buf, *len, "%s: N/A\n", prefix);
--	if (rc <= 0)
--		return -ENOSPC;
--
--	*buf += rc;
--	*len -= rc;
--	return rc;
-+		seq_printf(m, "%s: N/A\n", prefix);
-+	return 0;
- }
- 
--int lfsck_pos_dump(char **buf, int *len, struct lfsck_position *pos,
-+int lfsck_pos_dump(struct seq_file *m, struct lfsck_position *pos,
- 		   const char *prefix)
- {
--	int rc;
--
- 	if (fid_is_zero(&pos->lp_dir_parent)) {
- 		if (pos->lp_oit_cookie == 0)
--			rc = snprintf(*buf, *len, "%s: N/A, N/A, N/A\n",
--				      prefix);
-+			seq_printf(m, "%s: N/A, N/A, N/A\n",
-+				   prefix);
- 		else
--			rc = snprintf(*buf, *len, "%s: "LPU64", N/A, N/A\n",
--				      prefix, pos->lp_oit_cookie);
-+			seq_printf(m, "%s: "LPU64", N/A, N/A\n",
-+				   prefix, pos->lp_oit_cookie);
- 	} else {
--		rc = snprintf(*buf, *len, "%s: "LPU64", "DFID", "LPU64"\n",
--			      prefix, pos->lp_oit_cookie,
--			      PFID(&pos->lp_dir_parent), pos->lp_dir_cookie);
-+		seq_printf(m, "%s: "LPU64", "DFID", "LPU64"\n",
-+			   prefix, pos->lp_oit_cookie,
-+			   PFID(&pos->lp_dir_parent), pos->lp_dir_cookie);
- 	}
--	if (rc <= 0)
--		return -ENOSPC;
--
--	*buf += rc;
--	*len -= rc;
--	return rc;
-+	return 0;
- }
- 
- void lfsck_pos_fill(const struct lu_env *env, struct lfsck_instance *lfsck,
-@@ -1670,7 +1638,7 @@ int lfsck_async_request(const struct lu_env *env, struct obd_export *exp,
- 
- /* external interfaces */
- 
--int lfsck_get_speed(struct dt_device *key, void *buf, int len)
-+int lfsck_get_speed(struct seq_file *m, struct dt_device *key)
- {
- 	struct lu_env		env;
- 	struct lfsck_instance  *lfsck;
-@@ -1683,8 +1651,7 @@ int lfsck_get_speed(struct dt_device *key, void *buf, int len)
- 
- 	lfsck = lfsck_instance_find(key, true, false);
- 	if (likely(lfsck != NULL)) {
--		rc = snprintf(buf, len, "%u\n",
--			      lfsck->li_bookmark_ram.lb_speed_limit);
-+		seq_printf(m, "%u\n", lfsck->li_bookmark_ram.lb_speed_limit);
- 		lfsck_instance_put(&env, lfsck);
- 	} else {
- 		rc = -ENXIO;
-@@ -1724,7 +1691,7 @@ int lfsck_set_speed(struct dt_device *key, int val)
- }
- EXPORT_SYMBOL(lfsck_set_speed);
- 
--int lfsck_get_windows(struct dt_device *key, void *buf, int len)
-+int lfsck_get_windows(struct seq_file *m, struct dt_device *key)
- {
- 	struct lu_env		env;
- 	struct lfsck_instance  *lfsck;
-@@ -1737,8 +1704,7 @@ int lfsck_get_windows(struct dt_device *key, void *buf, int len)
- 
- 	lfsck = lfsck_instance_find(key, true, false);
- 	if (likely(lfsck != NULL)) {
--		rc = snprintf(buf, len, "%u\n",
--			      lfsck->li_bookmark_ram.lb_async_windows);
-+		seq_printf(m, "%u\n", lfsck->li_bookmark_ram.lb_async_windows);
- 		lfsck_instance_put(&env, lfsck);
- 	} else {
- 		rc = -ENXIO;
-@@ -1788,7 +1754,7 @@ int lfsck_set_windows(struct dt_device *key, int val)
- }
- EXPORT_SYMBOL(lfsck_set_windows);
- 
--int lfsck_dump(struct dt_device *key, void *buf, int len, enum lfsck_type type)
-+int lfsck_dump(struct seq_file *m, struct dt_device *key, enum lfsck_type type)
- {
- 	struct lu_env		env;
- 	struct lfsck_instance  *lfsck;
-@@ -1804,7 +1770,7 @@ int lfsck_dump(struct dt_device *key, void *buf, int len, enum lfsck_type type)
- 	if (likely(lfsck != NULL)) {
- 		com = lfsck_component_find(lfsck, type);
- 		if (likely(com != NULL)) {
--			rc = com->lc_ops->lfsck_dump(&env, com, buf, len);
-+			rc = com->lc_ops->lfsck_dump(&env, com, m);
- 			lfsck_component_put(&env, com);
- 		} else {
- 			rc = -ENOTSUPP;
-diff --git a/lustre/lfsck/lfsck_namespace.c b/lustre/lfsck/lfsck_namespace.c
-index 4dccb70..fc9a0dc 100644
---- a/lustre/lfsck/lfsck_namespace.c
-+++ b/lustre/lfsck/lfsck_namespace.c
-@@ -1099,65 +1099,56 @@ static int lfsck_namespace_post(const struct lu_env *env,
- 
- static int
- lfsck_namespace_dump(const struct lu_env *env, struct lfsck_component *com,
--		     char *buf, int len)
-+		     struct seq_file *m)
- {
- 	struct lfsck_instance	*lfsck = com->lc_lfsck;
- 	struct lfsck_bookmark	*bk    = &lfsck->li_bookmark_ram;
- 	struct lfsck_namespace	*ns    = com->lc_file_ram;
--	int			 save  = len;
--	int			 ret   = -ENOSPC;
- 	int			 rc;
- 
- 	down_read(&com->lc_sem);
--	rc = snprintf(buf, len,
--		      "name: lfsck_namespace\n"
--		      "magic: %#x\n"
--		      "version: %d\n"
--		      "status: %s\n",
--		      ns->ln_magic,
--		      bk->lb_version,
--		      lfsck_status2names(ns->ln_status));
--	if (rc <= 0)
--		goto out;
--
--	buf += rc;
--	len -= rc;
--	rc = lfsck_bits_dump(&buf, &len, ns->ln_flags, lfsck_flags_names,
--			     "flags");
-+	seq_printf(m, "name: lfsck_namespace\n"
-+		   "magic: %#x\n"
-+		   "version: %d\n"
-+		   "status: %s\n",
-+		   ns->ln_magic,
-+		   bk->lb_version,
-+		   lfsck_status2names(ns->ln_status));
-+
-+	rc = lfsck_bits_dump(m, ns->ln_flags, lfsck_flags_names, "flags");
- 	if (rc < 0)
- 		goto out;
- 
--	rc = lfsck_bits_dump(&buf, &len, bk->lb_param, lfsck_param_names,
--			     "param");
-+	rc = lfsck_bits_dump(m, bk->lb_param, lfsck_param_names, "param");
- 	if (rc < 0)
- 		goto out;
- 
--	rc = lfsck_time_dump(&buf, &len, ns->ln_time_last_complete,
-+	rc = lfsck_time_dump(m, ns->ln_time_last_complete,
- 			     "time_since_last_completed");
- 	if (rc < 0)
- 		goto out;
- 
--	rc = lfsck_time_dump(&buf, &len, ns->ln_time_latest_start,
-+	rc = lfsck_time_dump(m, ns->ln_time_latest_start,
- 			     "time_since_latest_start");
- 	if (rc < 0)
- 		goto out;
- 
--	rc = lfsck_time_dump(&buf, &len, ns->ln_time_last_checkpoint,
-+	rc = lfsck_time_dump(m, ns->ln_time_last_checkpoint,
- 			     "time_since_last_checkpoint");
- 	if (rc < 0)
- 		goto out;
- 
--	rc = lfsck_pos_dump(&buf, &len, &ns->ln_pos_latest_start,
-+	rc = lfsck_pos_dump(m, &ns->ln_pos_latest_start,
- 			    "latest_start_position");
- 	if (rc < 0)
- 		goto out;
- 
--	rc = lfsck_pos_dump(&buf, &len, &ns->ln_pos_last_checkpoint,
-+	rc = lfsck_pos_dump(m, &ns->ln_pos_last_checkpoint,
- 			    "last_checkpoint_position");
- 	if (rc < 0)
- 		goto out;
- 
--	rc = lfsck_pos_dump(&buf, &len, &ns->ln_pos_first_inconsistent,
-+	rc = lfsck_pos_dump(m, &ns->ln_pos_first_inconsistent,
- 			    "first_failure_position");
- 	if (rc < 0)
- 		goto out;
-@@ -1177,8 +1168,7 @@ lfsck_namespace_dump(const struct lu_env *env, struct lfsck_component *com,
- 			do_div(new_checked, duration);
- 		if (rtime != 0)
- 			do_div(speed, rtime);
--		rc = snprintf(buf, len,
--			      "checked_phase1: "LPU64"\n"
-+		seq_printf(m, "checked_phase1: "LPU64"\n"
- 			      "checked_phase2: "LPU64"\n"
- 			      "updated_phase1: "LPU64"\n"
- 			      "updated_phase2: "LPU64"\n"
-@@ -1214,11 +1204,6 @@ lfsck_namespace_dump(const struct lu_env *env, struct lfsck_component *com,
- 			      ns->ln_run_time_phase2,
- 			      speed,
- 			      new_checked);
--		if (rc <= 0)
--			goto out;
--
--		buf += rc;
--		len -= rc;
- 
- 		LASSERT(lfsck->li_di_oit != NULL);
- 
-@@ -1247,9 +1232,7 @@ lfsck_namespace_dump(const struct lu_env *env, struct lfsck_component *com,
- 			pos.lp_dir_cookie = 0;
- 		}
- 		spin_unlock(&lfsck->li_lock);
--		rc = lfsck_pos_dump(&buf, &len, &pos, "current_position");
--		if (rc <= 0)
--			goto out;
-+		lfsck_pos_dump(m, &pos, "current_position");
- 	} else if (ns->ln_status == LS_SCANNING_PHASE2) {
- 		cfs_duration_t duration = cfs_time_current() -
- 					  lfsck->li_time_last_checkpoint;
-@@ -1267,8 +1250,7 @@ lfsck_namespace_dump(const struct lu_env *env, struct lfsck_component *com,
- 			do_div(speed1, ns->ln_run_time_phase1);
- 		if (rtime != 0)
- 			do_div(speed2, rtime);
--		rc = snprintf(buf, len,
--			      "checked_phase1: "LPU64"\n"
-+		seq_printf(m, "checked_phase1: "LPU64"\n"
- 			      "checked_phase2: "LPU64"\n"
- 			      "updated_phase1: "LPU64"\n"
- 			      "updated_phase2: "LPU64"\n"
-@@ -1307,11 +1289,6 @@ lfsck_namespace_dump(const struct lu_env *env, struct lfsck_component *com,
- 			      speed2,
- 			      new_checked,
- 			      PFID(&ns->ln_fid_latest_scanned_phase2));
--		if (rc <= 0)
--			goto out;
--
--		buf += rc;
--		len -= rc;
- 	} else {
- 		__u64 speed1 = ns->ln_items_checked;
- 		__u64 speed2 = ns->ln_objs_checked_phase2;
-@@ -1320,8 +1297,7 @@ lfsck_namespace_dump(const struct lu_env *env, struct lfsck_component *com,
- 			do_div(speed1, ns->ln_run_time_phase1);
- 		if (ns->ln_run_time_phase2 != 0)
- 			do_div(speed2, ns->ln_run_time_phase2);
--		rc = snprintf(buf, len,
--			      "checked_phase1: "LPU64"\n"
-+		seq_printf(m, "checked_phase1: "LPU64"\n"
- 			      "checked_phase2: "LPU64"\n"
- 			      "updated_phase1: "LPU64"\n"
- 			      "updated_phase2: "LPU64"\n"
-@@ -1358,17 +1334,10 @@ lfsck_namespace_dump(const struct lu_env *env, struct lfsck_component *com,
- 			      ns->ln_run_time_phase2,
- 			      speed1,
- 			      speed2);
--		if (rc <= 0)
--			goto out;
--
--		buf += rc;
--		len -= rc;
- 	}
--	ret = save - len;
--
- out:
- 	up_read(&com->lc_sem);
--	return ret;
-+	return 0;
- }
- 
- static int lfsck_namespace_double_scan_main(void *args)
-diff --git a/lustre/mdd/mdd_device.c b/lustre/mdd/mdd_device.c
-index 4f0baa4..f6deaca 100644
---- a/lustre/mdd/mdd_device.c
-+++ b/lustre/mdd/mdd_device.c
-@@ -889,16 +889,16 @@ static int mdd_process_config(const struct lu_env *env,
-         ENTRY;
- 
-         switch (cfg->lcfg_command) {
--        case LCFG_PARAM: {
--                struct lprocfs_static_vars lvars;
--
--                lprocfs_mdd_init_vars(&lvars);
--                rc = class_process_proc_param(PARAM_MDD, lvars.obd_vars, cfg,m);
--                if (rc > 0 || rc == -ENOSYS)
--                        /* we don't understand; pass it on */
--                        rc = next->ld_ops->ldo_process_config(env, next, cfg);
--                break;
--        }
-+	case LCFG_PARAM: {
-+		struct obd_device *obd = mdd2obd_dev(m);
-+
-+		rc = class_process_proc_seq_param(PARAM_MDD, obd->obd_vars,
-+						  cfg, m);
-+		if (rc > 0 || rc == -ENOSYS)
-+			/* we don't understand; pass it on */
-+			rc = next->ld_ops->ldo_process_config(env, next, cfg);
-+		break;
-+	}
-         case LCFG_SETUP:
-                 rc = next->ld_ops->ldo_process_config(env, next, cfg);
-                 if (rc)
-@@ -1566,11 +1566,8 @@ LU_CONTEXT_KEY_DEFINE(mdd, LCT_MD_THREAD);
- 
- static int __init mdd_mod_init(void)
- {
--	struct lprocfs_static_vars lvars;
- 	int rc;
- 
--	lprocfs_mdd_init_vars(&lvars);
--
- 	rc = lu_kmem_init(mdd_caches);
- 	if (rc)
- 		return rc;
-@@ -1586,7 +1583,7 @@ static int __init mdd_mod_init(void)
- 
- 	rc = class_register_type(&mdd_obd_device_ops, NULL, true, NULL,
- #ifndef HAVE_ONLY_PROCFS_SEQ
--				 lvars.module_vars,
-+				 NULL,
- #endif
- 				 LUSTRE_MDD_NAME, &mdd_device_type);
- 	if (rc)
-diff --git a/lustre/mdd/mdd_internal.h b/lustre/mdd/mdd_internal.h
-index 4411892..37698f8 100644
---- a/lustre/mdd/mdd_internal.h
-+++ b/lustre/mdd/mdd_internal.h
-@@ -248,7 +248,6 @@ int orph_declare_index_delete(const struct lu_env *, struct mdd_object *,
-                               struct thandle *);
- 
- /* mdd_lproc.c */
--void lprocfs_mdd_init_vars(struct lprocfs_static_vars *lvars);
- int mdd_procfs_init(struct mdd_device *mdd, const char *name);
- int mdd_procfs_fini(struct mdd_device *mdd);
- 
-diff --git a/lustre/mdd/mdd_lproc.c b/lustre/mdd/mdd_lproc.c
-index de379b3..7ac4afa 100644
---- a/lustre/mdd/mdd_lproc.c
-+++ b/lustre/mdd/mdd_lproc.c
-@@ -49,56 +49,14 @@
- #include <libcfs/libcfs_string.h>
- #include "mdd_internal.h"
- 
--int mdd_procfs_init(struct mdd_device *mdd, const char *name)
--{
--        struct lprocfs_static_vars lvars;
--        struct obd_type     *type;
--        int                  rc;
--        ENTRY;
--
--	/* at the moment there is no linkage between lu_type
--	 * and obd_type, so we lookup obd_type this way */
--	type = class_search_type(LUSTRE_MDD_NAME);
--
--        LASSERT(name != NULL);
--        LASSERT(type != NULL);
--
--        /* Find the type procroot and add the proc entry for this device */
--        lprocfs_mdd_init_vars(&lvars);
--        mdd->mdd_proc_entry = lprocfs_register(name, type->typ_procroot,
--                                               lvars.obd_vars, mdd);
--        if (IS_ERR(mdd->mdd_proc_entry)) {
--                rc = PTR_ERR(mdd->mdd_proc_entry);
--                CERROR("Error %d setting up lprocfs for %s\n",
--                       rc, name);
--                mdd->mdd_proc_entry = NULL;
--                GOTO(out, rc);
--        }
--
--	rc = 0;
--
--        EXIT;
--out:
--        if (rc)
--               mdd_procfs_fini(mdd);
--        return rc;
--}
--
--int mdd_procfs_fini(struct mdd_device *mdd)
--{
--        if (mdd->mdd_proc_entry) {
--                 lprocfs_remove(&mdd->mdd_proc_entry);
--                 mdd->mdd_proc_entry = NULL;
--        }
--        RETURN(0);
--}
--
--static int lprocfs_wr_atime_diff(struct file *file, const char *buffer,
--                                 unsigned long count, void *data)
-+static ssize_t
-+mdd_atime_diff_seq_write(struct file *file, const char *buffer,
-+			 size_t count, loff_t *off)
- {
--        struct mdd_device *mdd = data;
--        char kernbuf[20], *end;
--        unsigned long diff = 0;
-+	struct seq_file *m = file->private_data;
-+	struct mdd_device *mdd = m->private;
-+	char kernbuf[20], *end;
-+	unsigned long diff = 0;
- 
-         if (count > (sizeof(kernbuf) - 1))
-                 return -EINVAL;
-@@ -116,37 +74,35 @@ static int lprocfs_wr_atime_diff(struct file *file, const char *buffer,
-         return count;
- }
- 
--static int lprocfs_rd_atime_diff(char *page, char **start, off_t off,
--                                 int count, int *eof, void *data)
-+static int mdd_atime_diff_seq_show(struct seq_file *m, void *data)
- {
--        struct mdd_device *mdd = data;
-+	struct mdd_device *mdd = m->private;
- 
--        *eof = 1;
--        return snprintf(page, count, "%lu\n", mdd->mdd_atime_diff);
-+	return seq_printf(m, "%lu\n", mdd->mdd_atime_diff);
- }
--
-+LPROC_SEQ_FOPS(mdd_atime_diff);
- 
- /**** changelogs ****/
--static int lprocfs_rd_changelog_mask(char *page, char **start, off_t off,
--                                     int count, int *eof, void *data)
-+static int mdd_changelog_mask_seq_show(struct seq_file *m, void *data)
- {
--        struct mdd_device *mdd = data;
--        int i = 0, rc = 0;
--
--        *eof = 1;
--        while (i < CL_LAST) {
--                if (mdd->mdd_cl.mc_mask & (1 << i))
--                        rc += snprintf(page + rc, count - rc, "%s ",
--                                       changelog_type2str(i));
--                i++;
--        }
--        return rc;
-+	struct mdd_device *mdd = m->private;
-+	int i = 0;
-+
-+	while (i < CL_LAST) {
-+		if (mdd->mdd_cl.mc_mask & (1 << i))
-+			seq_printf(m, "%s ", changelog_type2str(i));
-+		i++;
-+	}
-+	seq_printf(m, "\n");
-+	return 0;
- }
- 
--static int lprocfs_wr_changelog_mask(struct file *file, const char *buffer,
--				     unsigned long count, void *data)
-+static ssize_t
-+mdd_changelog_mask_seq_write(struct file *file, const char *buffer,
-+			     size_t count, loff_t *off)
- {
--	struct mdd_device *mdd = data;
-+	struct seq_file *m = file->private_data;
-+	struct mdd_device *mdd = m->private;
- 	char *kernbuf;
- 	int rc;
- 	ENTRY;
-@@ -168,45 +124,32 @@ out:
- 	OBD_FREE(kernbuf, PAGE_CACHE_SIZE);
- 	return rc;
- }
--
--struct cucb_data {
--        char *page;
--        int count;
--        int idx;
--};
-+LPROC_SEQ_FOPS(mdd_changelog_mask);
- 
- static int lprocfs_changelog_users_cb(const struct lu_env *env,
- 				      struct llog_handle *llh,
- 				      struct llog_rec_hdr *hdr, void *data)
- {
--        struct llog_changelog_user_rec *rec;
--        struct cucb_data *cucb = (struct cucb_data *)data;
-+	struct llog_changelog_user_rec *rec;
-+	struct seq_file *m = data;
- 
--        LASSERT(llh->lgh_hdr->llh_flags & LLOG_F_IS_PLAIN);
-+	LASSERT(llh->lgh_hdr->llh_flags & LLOG_F_IS_PLAIN);
- 
--        rec = (struct llog_changelog_user_rec *)hdr;
-+	rec = (struct llog_changelog_user_rec *)hdr;
- 
--        cucb->idx += snprintf(cucb->page + cucb->idx, cucb->count - cucb->idx,
--                              CHANGELOG_USER_PREFIX"%-3d "LPU64"\n",
--                              rec->cur_id, rec->cur_endrec);
--        if (cucb->idx >= cucb->count)
--                return -ENOSPC;
--
--        return 0;
-+	seq_printf(m, CHANGELOG_USER_PREFIX"%-3d "LPU64"\n",
-+		   rec->cur_id, rec->cur_endrec);
-+	return 0;
- }
- 
--static int lprocfs_rd_changelog_users(char *page, char **start, off_t off,
--                                      int count, int *eof, void *data)
-+static int mdd_changelog_users_seq_show(struct seq_file *m, void *data)
- {
- 	struct lu_env		 env;
--	struct mdd_device	*mdd = data;
-+	struct mdd_device	*mdd = m->private;
- 	struct llog_ctxt	*ctxt;
--	struct cucb_data	 cucb;
- 	__u64			 cur;
- 	int			 rc;
- 
--        *eof = 1;
--
-         ctxt = llog_get_context(mdd2obd_dev(mdd),
- 				LLOG_CHANGELOG_USER_ORIG_CTXT);
-         if (ctxt == NULL)
-@@ -223,37 +166,32 @@ static int lprocfs_rd_changelog_users(char *page, char **start, off_t off,
- 	cur = mdd->mdd_cl.mc_index;
- 	spin_unlock(&mdd->mdd_cl.mc_lock);
- 
--        cucb.count = count;
--        cucb.page = page;
--        cucb.idx = 0;
--
--        cucb.idx += snprintf(cucb.page + cucb.idx, cucb.count - cucb.idx,
--                              "current index: "LPU64"\n", cur);
--
--        cucb.idx += snprintf(cucb.page + cucb.idx, cucb.count - cucb.idx,
--                              "%-5s %s\n", "ID", "index");
-+	seq_printf(m, "current index: "LPU64"\n", cur);
-+	seq_printf(m, "%-5s %s\n", "ID", "index");
- 
- 	llog_cat_process(&env, ctxt->loc_handle, lprocfs_changelog_users_cb,
--			 &cucb, 0, 0);
-+			 m, 0, 0);
- 
- 	lu_env_fini(&env);
- 	llog_ctxt_put(ctxt);
--	return cucb.idx;
-+	return 0;
- }
-+LPROC_SEQ_FOPS_RO(mdd_changelog_users);
- 
--static int lprocfs_rd_sync_perm(char *page, char **start, off_t off,
--                                int count, int *eof, void *data)
-+static int mdd_sync_perm_seq_show(struct seq_file *m, void *data)
- {
--        struct mdd_device *mdd = data;
-+	struct mdd_device *mdd = m->private;
- 
--        LASSERT(mdd != NULL);
--        return snprintf(page, count, "%d\n", mdd->mdd_sync_permission);
-+	LASSERT(mdd != NULL);
-+	return seq_printf(m, "%d\n", mdd->mdd_sync_permission);
- }
- 
--static int lprocfs_wr_sync_perm(struct file *file, const char *buffer,
--                                unsigned long count, void *data)
-+static ssize_t
-+mdd_sync_perm_seq_write(struct file *file, const char *buffer,
-+			size_t count, loff_t *off)
- {
--        struct mdd_device *mdd = data;
-+	struct seq_file *m = file->private_data;
-+	struct mdd_device *mdd = m->private;
-         int val, rc;
- 
-         LASSERT(mdd != NULL);
-@@ -264,22 +202,22 @@ static int lprocfs_wr_sync_perm(struct file *file, const char *buffer,
-         mdd->mdd_sync_permission = !!val;
-         return count;
- }
-+LPROC_SEQ_FOPS(mdd_sync_perm);
- 
--static int lprocfs_rd_lfsck_speed_limit(char *page, char **start, off_t off,
--					int count, int *eof, void *data)
-+static int mdd_lfsck_speed_limit_seq_show(struct seq_file *m, void *data)
- {
--	struct mdd_device *mdd = data;
-+	struct mdd_device *mdd = m->private;
- 
- 	LASSERT(mdd != NULL);
--	*eof = 1;
--
--	return lfsck_get_speed(mdd->mdd_bottom, page, count);
-+	return lfsck_get_speed(m, mdd->mdd_bottom);
- }
- 
--static int lprocfs_wr_lfsck_speed_limit(struct file *file, const char *buffer,
--					unsigned long count, void *data)
-+static ssize_t
-+mdd_lfsck_speed_limit_seq_write(struct file *file, const char *buffer,
-+				size_t count, loff_t *off)
- {
--	struct mdd_device *mdd = data;
-+	struct seq_file *m = file->private_data;
-+	struct mdd_device *mdd = m->private;
- 	__u32 val;
- 	int rc;
- 
-@@ -291,25 +229,22 @@ static int lprocfs_wr_lfsck_speed_limit(struct file *file, const char *buffer,
- 	rc = lfsck_set_speed(mdd->mdd_bottom, val);
- 	return rc != 0 ? rc : count;
- }
-+LPROC_SEQ_FOPS(mdd_lfsck_speed_limit);
- 
--static int lprocfs_rd_lfsck_async_windows(char *page, char **start, off_t off,
--					  int count, int *eof, void *data)
-+static int mdd_lfsck_async_windows_seq_show(struct seq_file *m, void *data)
- {
--	struct mdd_device *mdd = data;
--	int		   rc;
-+	struct mdd_device *mdd = m->private;
- 
- 	LASSERT(mdd != NULL);
--	*eof = 1;
--
--	rc = lfsck_get_windows(mdd->mdd_bottom, page, count);
--
--	return rc != 0 ? rc : count;
-+	return lfsck_get_windows(m, mdd->mdd_bottom);
- }
- 
--static int lprocfs_wr_lfsck_async_windows(struct file *file, const char *buffer,
--					  unsigned long count, void *data)
-+static ssize_t
-+mdd_lfsck_async_windows_seq_write(struct file *file, const char *buffer,
-+				  size_t count, loff_t *off)
- {
--	struct mdd_device *mdd = data;
-+	struct seq_file   *m = file->private_data;
-+	struct mdd_device *mdd = m->private;
- 	__u32		   val;
- 	int		   rc;
- 
-@@ -320,54 +255,87 @@ static int lprocfs_wr_lfsck_async_windows(struct file *file, const char *buffer,
- 
- 	return rc != 0 ? rc : count;
- }
-+LPROC_SEQ_FOPS(mdd_lfsck_async_windows);
- 
--static int lprocfs_rd_lfsck_namespace(char *page, char **start, off_t off,
--				      int count, int *eof, void *data)
-+static int mdd_lfsck_namespace_seq_show(struct seq_file *m, void *data)
- {
--	struct mdd_device *mdd = data;
--	int rc;
-+	struct mdd_device *mdd = m->private;
- 
- 	LASSERT(mdd != NULL);
--	*eof = 1;
- 
--	rc = lfsck_dump(mdd->mdd_bottom, page, count, LT_NAMESPACE);
--	return rc;
-+	return lfsck_dump(m, mdd->mdd_bottom, LT_NAMESPACE);
- }
-+LPROC_SEQ_FOPS_RO(mdd_lfsck_namespace);
- 
--static int lprocfs_rd_lfsck_layout(char *page, char **start, off_t off,
--				   int count, int *eof, void *data)
-+static int mdd_lfsck_layout_seq_show(struct seq_file *m, void *data)
- {
--	struct mdd_device *mdd = data;
-+	struct mdd_device *mdd = m->private;
- 
- 	LASSERT(mdd != NULL);
--	*eof = 1;
- 
--	return lfsck_dump(mdd->mdd_bottom, page, count, LT_LAYOUT);
-+	return lfsck_dump(m, mdd->mdd_bottom, LT_LAYOUT);
- }
--
--static struct lprocfs_vars lprocfs_mdd_obd_vars[] = {
--        { "atime_diff",      lprocfs_rd_atime_diff, lprocfs_wr_atime_diff, 0 },
--        { "changelog_mask",  lprocfs_rd_changelog_mask,
--                             lprocfs_wr_changelog_mask, 0 },
--        { "changelog_users", lprocfs_rd_changelog_users, 0, 0},
--        { "sync_permission", lprocfs_rd_sync_perm, lprocfs_wr_sync_perm, 0 },
--	{ "lfsck_speed_limit", lprocfs_rd_lfsck_speed_limit,
--			       lprocfs_wr_lfsck_speed_limit, 0 },
--	{ "lfsck_async_windows", lprocfs_rd_lfsck_async_windows,
--				 lprocfs_wr_lfsck_async_windows, 0 },
--	{ "lfsck_namespace", lprocfs_rd_lfsck_namespace, 0, 0 },
--	{ "lfsck_layout", lprocfs_rd_lfsck_layout, 0, 0 },
-+LPROC_SEQ_FOPS_RO(mdd_lfsck_layout);
-+
-+static struct lprocfs_seq_vars lprocfs_mdd_obd_vars[] = {
-+	{ .name =	"atime_diff",
-+	  .fops =	&mdd_atime_diff_fops		},
-+	{ .name =	"changelog_mask",
-+	  .fops =	&mdd_changelog_mask_fops	},
-+	{ .name =	"changelog_users",
-+	  .fops =	&mdd_changelog_users_fops	},
-+	{ .name =	"sync_permission",
-+	  .fops =	&mdd_sync_perm_fops		},
-+	{ .name =	"lfsck_speed_limit",
-+	  .fops =	&mdd_lfsck_speed_limit_fops	},
-+	{ .name =	"lfsck_async_windows",
-+	  .fops =	&mdd_lfsck_async_windows_fops	},
-+	{ .name =	"lfsck_namespace",
-+	  .fops =	&mdd_lfsck_namespace_fops	},
-+	{ .name	=	"lfsck_layout",
-+	  .fops	=	&mdd_lfsck_layout_fops		},
- 	{ 0 }
- };
- 
--static struct lprocfs_vars lprocfs_mdd_module_vars[] = {
--        { "num_refs",   lprocfs_rd_numrefs, 0, 0 },
--        { 0 }
--};
--
--void lprocfs_mdd_init_vars(struct lprocfs_static_vars *lvars)
-+int mdd_procfs_init(struct mdd_device *mdd, const char *name)
- {
--        lvars->module_vars  = lprocfs_mdd_module_vars;
--        lvars->obd_vars     = lprocfs_mdd_obd_vars;
-+	struct obd_device *obd = class_name2obd(name);
-+	struct obd_type   *type;
-+	int		   rc;
-+	ENTRY;
-+
-+	/* at the moment there is no linkage between lu_type
-+	 * and obd_type, so we lookup obd_type this way */
-+	type = class_search_type(LUSTRE_MDD_NAME);
-+
-+	LASSERT(name != NULL);
-+	LASSERT(type != NULL);
-+	LASSERT(obd  != NULL);
-+
-+	/* Find the type procroot and add the proc entry for this device */
-+	obd->obd_vars = lprocfs_mdd_obd_vars;
-+	mdd->mdd_proc_entry = lprocfs_seq_register(name, type->typ_procroot,
-+						   obd->obd_vars, mdd);
-+	if (IS_ERR(mdd->mdd_proc_entry)) {
-+		rc = PTR_ERR(mdd->mdd_proc_entry);
-+		CERROR("Error %d setting up lprocfs for %s\n",
-+		       rc, name);
-+		mdd->mdd_proc_entry = NULL;
-+		GOTO(out, rc);
-+	}
-+	rc = 0;
-+	EXIT;
-+out:
-+	if (rc)
-+		mdd_procfs_fini(mdd);
-+	return rc;
- }
- 
-+int mdd_procfs_fini(struct mdd_device *mdd)
-+{
-+	if (mdd->mdd_proc_entry) {
-+		lprocfs_remove(&mdd->mdd_proc_entry);
-+		mdd->mdd_proc_entry = NULL;
-+	}
-+	RETURN(0);
-+}
-diff --git a/lustre/ofd/lproc_ofd.c b/lustre/ofd/lproc_ofd.c
-index 359b373..fcde82a 100644
---- a/lustre/ofd/lproc_ofd.c
-+++ b/lustre/ofd/lproc_ofd.c
-@@ -47,81 +47,75 @@
- 
- #ifdef LPROCFS
- 
--static int lprocfs_ofd_rd_seqs(char *page, char **start, off_t off,
--				int count, int *eof, void *data)
-+static int ofd_seqs_seq_show(struct seq_file *m, void *data)
- {
--	struct obd_device *obd = (struct obd_device *)data;
-+	struct obd_device *obd = m->private;
- 	struct ofd_device *ofd = ofd_dev(obd->obd_lu_dev);
- 
--	*eof = 1;
--	return snprintf(page, count, "%u\n", ofd->ofd_seq_count);
-+	return seq_printf(m, "%u\n", ofd->ofd_seq_count);
- }
-+LPROC_SEQ_FOPS_RO(ofd_seqs);
- 
--static int lprocfs_ofd_rd_tot_dirty(char *page, char **start, off_t off,
--				    int count, int *eof, void *data)
-+static int ofd_tot_dirty_seq_show(struct seq_file *m, void *data)
- {
--	struct obd_device *obd = (struct obd_device *)data;
-+	struct obd_device *obd = m->private;
- 	struct ofd_device *ofd;
- 
- 	LASSERT(obd != NULL);
- 	ofd = ofd_dev(obd->obd_lu_dev);
--	*eof = 1;
--	return snprintf(page, count, LPU64"\n", ofd->ofd_tot_dirty);
-+	return seq_printf(m, LPU64"\n", ofd->ofd_tot_dirty);
- }
-+LPROC_SEQ_FOPS_RO(ofd_tot_dirty);
- 
--static int lprocfs_ofd_rd_tot_granted(char *page, char **start, off_t off,
--				      int count, int *eof, void *data)
-+static int ofd_tot_granted_seq_show(struct seq_file *m, void *data)
- {
--	struct obd_device *obd = (struct obd_device *)data;
-+	struct obd_device *obd = m->private;
- 	struct ofd_device *ofd;
- 
- 	LASSERT(obd != NULL);
- 	ofd = ofd_dev(obd->obd_lu_dev);
--	*eof = 1;
--	return snprintf(page, count, LPU64"\n", ofd->ofd_tot_granted);
-+	return seq_printf(m, LPU64"\n", ofd->ofd_tot_granted);
- }
-+LPROC_SEQ_FOPS_RO(ofd_tot_granted);
- 
--static int lprocfs_ofd_rd_tot_pending(char *page, char **start, off_t off,
--				      int count, int *eof, void *data)
-+static int ofd_tot_pending_seq_show(struct seq_file *m, void *data)
- {
--	struct obd_device *obd = (struct obd_device *)data;
-+	struct obd_device *obd = m->private;
- 	struct ofd_device *ofd;
- 
- 	LASSERT(obd != NULL);
- 	ofd = ofd_dev(obd->obd_lu_dev);
--	*eof = 1;
--	return snprintf(page, count, LPU64"\n", ofd->ofd_tot_pending);
-+	return seq_printf(m, LPU64"\n", ofd->ofd_tot_pending);
- }
-+LPROC_SEQ_FOPS_RO(ofd_tot_pending);
- 
--static int lprocfs_ofd_rd_grant_precreate(char *page, char **start, off_t off,
--					  int count, int *eof, void *data)
-+static int ofd_grant_precreate_seq_show(struct seq_file *m, void *data)
- {
--	struct obd_device *obd = (struct obd_device *)data;
-+	struct obd_device *obd = m->private;
- 
- 	LASSERT(obd != NULL);
--	*eof = 1;
--	return snprintf(page, count, "%ld\n",
--			obd->obd_self_export->exp_filter_data.fed_grant);
-+	return seq_printf(m, "%ld\n",
-+			  obd->obd_self_export->exp_filter_data.fed_grant);
- }
-+LPROC_SEQ_FOPS_RO(ofd_grant_precreate);
- 
--static int lprocfs_ofd_rd_grant_ratio(char *page, char **start, off_t off,
--				      int count, int *eof, void *data)
-+static int ofd_grant_ratio_seq_show(struct seq_file *m, void *data)
- {
--	struct obd_device *obd = (struct obd_device *)data;
-+	struct obd_device *obd = m->private;
- 	struct ofd_device *ofd;
- 
- 	LASSERT(obd != NULL);
- 	ofd = ofd_dev(obd->obd_lu_dev);
--	*eof = 1;
--	return snprintf(page, count, "%d%%\n",
--			(int) ofd_grant_reserved(ofd, 100));
-+	return seq_printf(m, "%d%%\n",
-+			  (int) ofd_grant_reserved(ofd, 100));
- }
- 
--static int lprocfs_ofd_wr_grant_ratio(struct file *file,
--				      const char __user *buffer,
--				      unsigned long count, void *data)
-+static ssize_t
-+ofd_grant_ratio_seq_write(struct file *file, const char __user *buffer,
-+			  size_t count, loff_t *off)
- {
--	struct obd_device	*obd = (struct obd_device *)data;
-+	struct seq_file         *m = file->private_data;
-+	struct obd_device       *obd = m->private;
- 	struct ofd_device	*ofd = ofd_dev(obd->obd_lu_dev);
- 	int			 val;
- 	int			 rc;
-@@ -145,24 +139,24 @@ static int lprocfs_ofd_wr_grant_ratio(struct file *file,
- 	spin_unlock(&ofd->ofd_grant_lock);
- 	return count;
- }
-+LPROC_SEQ_FOPS(ofd_grant_ratio);
- 
--static int lprocfs_ofd_rd_precreate_batch(char *page, char **start, off_t off,
--					  int count, int *eof, void *data)
-+static int ofd_precreate_batch_seq_show(struct seq_file *m, void *data)
- {
--	struct obd_device *obd = (struct obd_device *)data;
-+	struct obd_device *obd = m->private;
- 	struct ofd_device *ofd;
- 
- 	LASSERT(obd != NULL);
- 	ofd = ofd_dev(obd->obd_lu_dev);
--	*eof = 1;
--	return snprintf(page, count, "%d\n", ofd->ofd_precreate_batch);
-+	return seq_printf(m, "%d\n", ofd->ofd_precreate_batch);
- }
- 
--static int lprocfs_ofd_wr_precreate_batch(struct file *file,
--					  const char __user *buffer,
--					  unsigned long count, void *data)
-+static ssize_t
-+ofd_precreate_batch_seq_write(struct file *file, const char __user *buffer,
-+			      size_t count, loff_t *off)
- {
--	struct obd_device *obd = (struct obd_device *)data;
-+	struct seq_file	  *m = file->private_data;
-+	struct obd_device *obd = m->private;
- 	struct ofd_device *ofd = ofd_dev(obd->obd_lu_dev);
- 	int val;
- 	int rc;
-@@ -179,11 +173,11 @@ static int lprocfs_ofd_wr_precreate_batch(struct file *file,
- 	spin_unlock(&ofd->ofd_batch_lock);
- 	return count;
- }
-+LPROC_SEQ_FOPS(ofd_precreate_batch);
- 
--static int lprocfs_ofd_rd_last_id(char *page, char **start, off_t off,
--				  int count, int *eof, void *data)
-+static int ofd_last_id_seq_show(struct seq_file *m, void *data)
- {
--	struct obd_device	*obd = data;
-+	struct obd_device	*obd = m->private;
- 	struct ofd_device	*ofd;
- 	struct ofd_seq		*oseq = NULL;
- 	int			retval = 0, rc;
-@@ -201,35 +195,32 @@ static int lprocfs_ofd_rd_last_id(char *page, char **start, off_t off,
- 		      fid_idif_seq(ostid_id(&oseq->os_oi),
- 				   ofd->ofd_lut.lut_lsd.lsd_osd_index) :
- 		      ostid_seq(&oseq->os_oi);
--		rc = snprintf(page, count, DOSTID"\n", seq,
--			      ostid_id(&oseq->os_oi));
-+		rc = seq_printf(m, DOSTID"\n", seq, ostid_id(&oseq->os_oi));
- 		if (rc < 0) {
- 			retval = rc;
- 			break;
- 		}
--		page += rc;
--		count -= rc;
- 		retval += rc;
- 	}
- 	read_unlock(&ofd->ofd_seq_list_lock);
- 	return retval;
- }
-+LPROC_SEQ_FOPS_RO(ofd_last_id);
- 
--int lprocfs_ofd_rd_fmd_max_num(char *page, char **start, off_t off,
--			       int count, int *eof, void *data)
-+static int ofd_fmd_max_num_seq_show(struct seq_file *m, void *data)
- {
--	struct obd_device	*obd = data;
--	struct ofd_device	*ofd = ofd_dev(obd->obd_lu_dev);
--	int			 rc;
-+	struct obd_device *obd = m->private;
-+	struct ofd_device *ofd = ofd_dev(obd->obd_lu_dev);
- 
--	rc = snprintf(page, count, "%u\n", ofd->ofd_fmd_max_num);
--	return rc;
-+	return seq_printf(m, "%u\n", ofd->ofd_fmd_max_num);
- }
- 
--int lprocfs_ofd_wr_fmd_max_num(struct file *file, const char __user *buffer,
--			       unsigned long count, void *data)
-+static ssize_t
-+ofd_fmd_max_num_seq_write(struct file *file, const char __user *buffer,
-+			  size_t count, loff_t *off)
- {
--	struct obd_device	*obd = data;
-+	struct seq_file		*m = file->private_data;
-+	struct obd_device	*obd = m->private;
- 	struct ofd_device	*ofd = ofd_dev(obd->obd_lu_dev);
- 	int			 val;
- 	int			 rc;
-@@ -244,22 +235,22 @@ int lprocfs_ofd_wr_fmd_max_num(struct file *file, const char __user *buffer,
- 	ofd->ofd_fmd_max_num = val;
- 	return count;
- }
-+LPROC_SEQ_FOPS(ofd_fmd_max_num);
- 
--int lprocfs_ofd_rd_fmd_max_age(char *page, char **start, off_t off,
--			       int count, int *eof, void *data)
-+static int ofd_fmd_max_age_seq_show(struct seq_file *m, void *data)
- {
--	struct obd_device	*obd = data;
--	struct ofd_device	*ofd = ofd_dev(obd->obd_lu_dev);
--	int			 rc;
-+	struct obd_device *obd = m->private;
-+	struct ofd_device *ofd = ofd_dev(obd->obd_lu_dev);
- 
--	rc = snprintf(page, count, "%ld\n", ofd->ofd_fmd_max_age / HZ);
--	return rc;
-+	return seq_printf(m, "%ld\n", ofd->ofd_fmd_max_age / HZ);
- }
- 
--int lprocfs_ofd_wr_fmd_max_age(struct file *file, const char __user *buffer,
--			       unsigned long count, void *data)
-+static ssize_t
-+ofd_fmd_max_age_seq_write(struct file *file, const char __user *buffer,
-+			  size_t count, loff_t *off)
- {
--	struct obd_device	*obd = data;
-+	struct seq_file		*m = file->private_data;
-+	struct obd_device	*obd = m->private;
- 	struct ofd_device	*ofd = ofd_dev(obd->obd_lu_dev);
- 	int			 val;
- 	int			 rc;
-@@ -274,22 +265,22 @@ int lprocfs_ofd_wr_fmd_max_age(struct file *file, const char __user *buffer,
- 	ofd->ofd_fmd_max_age = val * HZ;
- 	return count;
- }
-+LPROC_SEQ_FOPS(ofd_fmd_max_age);
- 
--static int lprocfs_ofd_rd_capa(char *page, char **start, off_t off,
--			       int count, int *eof, void *data)
-+static int ofd_capa_seq_show(struct seq_file *m, void *data)
- {
--	struct obd_device	*obd = data;
--	int			 rc;
-+	struct obd_device	*obd = m->private;
- 
--	rc = snprintf(page, count, "capability on: %s\n",
--		      obd->u.filter.fo_fl_oss_capa ? "oss" : "");
--	return rc;
-+	return seq_printf(m, "capability on: %s\n",
-+			  obd->u.filter.fo_fl_oss_capa ? "oss" : "");
- }
- 
--static int lprocfs_ofd_wr_capa(struct file *file, const char __user *buffer,
--			       unsigned long count, void *data)
-+static ssize_t
-+ofd_capa_seq_write(struct file *file, const char *__user buffer, size_t count,
-+		   loff_t *off)
- {
--	struct obd_device	*obd = data;
-+	struct seq_file		*m = file->private_data;
-+	struct obd_device	*obd = m->private;
- 	int			 val, rc;
- 
- 	rc = lprocfs_write_helper(buffer, count, &val);
-@@ -308,28 +299,29 @@ static int lprocfs_ofd_wr_capa(struct file *file, const char __user *buffer,
- 		      val ? "enabled" : "disabled");
- 	return count;
- }
-+LPROC_SEQ_FOPS(ofd_capa);
- 
--static int lprocfs_ofd_rd_capa_count(char *page, char **start, off_t off,
--				     int count, int *eof, void *data)
-+static int ofd_capa_count_seq_show(struct seq_file *m, void *data)
- {
--	return snprintf(page, count, "%d %d\n",
--			capa_count[CAPA_SITE_CLIENT],
--			capa_count[CAPA_SITE_SERVER]);
-+	return seq_printf(m, "%d %d\n", capa_count[CAPA_SITE_CLIENT],
-+			  capa_count[CAPA_SITE_SERVER]);
- }
-+LPROC_SEQ_FOPS_RO(ofd_capa_count);
- 
--int lprocfs_ofd_rd_degraded(char *page, char **start, off_t off,
--			    int count, int *eof, void *data)
-+static int ofd_degraded_seq_show(struct seq_file *m, void *data)
- {
--	struct obd_device *obd = data;
-+	struct obd_device *obd = m->private;
- 	struct ofd_device *ofd = ofd_dev(obd->obd_lu_dev);
- 
--	return snprintf(page, count, "%u\n", ofd->ofd_raid_degraded);
-+	return seq_printf(m, "%u\n", ofd->ofd_raid_degraded);
- }
- 
--int lprocfs_ofd_wr_degraded(struct file *file, const char __user *buffer,
--			    unsigned long count, void *data)
-+static ssize_t
-+ofd_degraded_seq_write(struct file *file, const char __user *buffer,
-+		       size_t count, loff_t *off)
- {
--	struct obd_device	*obd = data;
-+	struct seq_file		*m = file->private_data;
-+	struct obd_device	*obd = m->private;
- 	struct ofd_device	*ofd = ofd_dev(obd->obd_lu_dev);
- 	int			 val, rc;
- 
-@@ -340,38 +332,37 @@ int lprocfs_ofd_wr_degraded(struct file *file, const char __user *buffer,
- 	spin_lock(&ofd->ofd_flags_lock);
- 	ofd->ofd_raid_degraded = !!val;
- 	spin_unlock(&ofd->ofd_flags_lock);
--
- 	return count;
- }
-+LPROC_SEQ_FOPS(ofd_degraded);
- 
--int lprocfs_ofd_rd_fstype(char *page, char **start, off_t off, int count,
--			  int *eof, void *data)
-+static int ofd_fstype_seq_show(struct seq_file *m, void *data)
- {
--	struct obd_device *obd = data;
-+	struct obd_device *obd = m->private;
- 	struct ofd_device *ofd = ofd_dev(obd->obd_lu_dev);
- 	struct lu_device  *d;
- 
- 	LASSERT(ofd->ofd_osd);
- 	d = &ofd->ofd_osd->dd_lu_dev;
- 	LASSERT(d->ld_type);
--	return snprintf(page, count, "%s\n", d->ld_type->ldt_name);
-+	return seq_printf(m, "%s\n", d->ld_type->ldt_name);
- }
-+LPROC_SEQ_FOPS_RO(ofd_fstype);
- 
--int lprocfs_ofd_rd_syncjournal(char *page, char **start, off_t off,
--			       int count, int *eof, void *data)
-+static int ofd_syncjournal_seq_show(struct seq_file *m, void *data)
- {
--	struct obd_device	*obd = data;
-+	struct obd_device	*obd = m->private;
- 	struct ofd_device	*ofd = ofd_dev(obd->obd_lu_dev);
--	int			 rc;
- 
--	rc = snprintf(page, count, "%u\n", ofd->ofd_syncjournal);
--	return rc;
-+	return seq_printf(m, "%u\n", ofd->ofd_syncjournal);
- }
- 
--int lprocfs_ofd_wr_syncjournal(struct file *file, const char __user *buffer,
--			       unsigned long count, void *data)
-+static ssize_t
-+ofd_syncjournal_seq_write(struct file *file, const char __user *buffer,
-+			  size_t count, loff_t *off)
- {
--	struct obd_device	*obd = data;
-+	struct seq_file		*m = file->private_data;
-+	struct obd_device	*obd = m->private;
- 	struct ofd_device	*ofd = ofd_dev(obd->obd_lu_dev);
- 	int			 val;
- 	int			 rc;
-@@ -390,6 +381,7 @@ int lprocfs_ofd_wr_syncjournal(struct file *file, const char __user *buffer,
- 
- 	return count;
- }
-+LPROC_SEQ_FOPS(ofd_syncjournal);
- 
- /* This must be longer than the longest string below */
- #define SYNC_STATES_MAXLEN 16
-@@ -397,23 +389,21 @@ static char *sync_on_cancel_states[] = {"never",
- 					"blocking",
- 					"always" };
- 
--int lprocfs_ofd_rd_sync_lock_cancel(char *page, char **start, off_t off,
--				    int count, int *eof, void *data)
-+static int ofd_sync_lock_cancel_seq_show(struct seq_file *m, void *data)
- {
--	struct obd_device	*obd = data;
-+	struct obd_device	*obd = m->private;
- 	struct lu_target	*tgt = obd->u.obt.obt_lut;
--	int			 rc;
- 
--	rc = snprintf(page, count, "%s\n",
--		      sync_on_cancel_states[tgt->lut_sync_lock_cancel]);
--	return rc;
-+	return seq_printf(m, "%s\n",
-+			  sync_on_cancel_states[tgt->lut_sync_lock_cancel]);
- }
- 
--int lprocfs_ofd_wr_sync_lock_cancel(struct file *file,
--				    const char __user *buffer,
--				    unsigned long count, void *data)
-+static ssize_t
-+ofd_sync_lock_cancel_seq_write(struct file *file, const char __user *buffer,
-+			       size_t count, loff_t *off)
- {
--	struct obd_device	*obd = data;
-+	struct seq_file		*m = file->private_data;
-+	struct obd_device	*obd = m->private;
- 	struct lu_target	*tgt = obd->u.obt.obt_lut;
- 	char			 kernbuf[SYNC_STATES_MAXLEN];
- 	int			 val = -1;
-@@ -455,23 +445,23 @@ int lprocfs_ofd_wr_sync_lock_cancel(struct file *file,
- 	spin_unlock(&tgt->lut_flags_lock);
- 	return count;
- }
-+LPROC_SEQ_FOPS(ofd_sync_lock_cancel);
- 
--int lprocfs_ofd_rd_grant_compat_disable(char *page, char **start, off_t off,
--					int count, int *eof, void *data)
-+static int ofd_grant_compat_disable_seq_show(struct seq_file *m, void *data)
- {
--	struct obd_device	*obd = data;
--	struct ofd_device	*ofd = ofd_dev(obd->obd_lu_dev);
--	int			 rc;
-+	struct obd_device *obd = m->private;
-+	struct ofd_device *ofd = ofd_dev(obd->obd_lu_dev);
- 
--	rc = snprintf(page, count, "%u\n", ofd->ofd_grant_compat_disable);
--	return rc;
-+	return seq_printf(m, "%u\n", ofd->ofd_grant_compat_disable);
- }
- 
--int lprocfs_ofd_wr_grant_compat_disable(struct file *file,
--					const char __user *buffer,
--					unsigned long count, void *data)
-+static ssize_t
-+ofd_grant_compat_disable_seq_write(struct file *file,
-+				   const char __user *buffer,
-+				   size_t count, loff_t *off)
- {
--	struct obd_device	*obd = data;
-+	struct seq_file		*m = file->private_data;
-+	struct obd_device	*obd = m->private;
- 	struct ofd_device	*ofd = ofd_dev(obd->obd_lu_dev);
- 	int			 val;
- 	int			 rc;
-@@ -489,42 +479,43 @@ int lprocfs_ofd_wr_grant_compat_disable(struct file *file,
- 
- 	return count;
- }
-+LPROC_SEQ_FOPS(ofd_grant_compat_disable);
- 
--int lprocfs_ofd_rd_soft_sync_limit(char *page, char **start, off_t off,
--				   int count, int *eof, void *data)
-+static int ofd_soft_sync_limit_seq_show(struct seq_file *m, void *data)
- {
--	struct obd_device	*obd = data;
-+	struct obd_device	*obd = m->private;
- 	struct ofd_device	*ofd = ofd_dev(obd->obd_lu_dev);
- 
--	return lprocfs_rd_uint(page, start, off, count, eof,
--			       &ofd->ofd_soft_sync_limit);
-+	return lprocfs_uint_seq_show(m, &ofd->ofd_soft_sync_limit);
- }
- 
--int lprocfs_ofd_wr_soft_sync_limit(struct file *file, const char __user *buffer,
--				   unsigned long count, void *data)
-+static ssize_t
-+ofd_soft_sync_limit_seq_write(struct file *file, const char __user *buffer,
-+			      size_t count, loff_t *off)
- {
--	struct obd_device	*obd = data;
--	struct ofd_device	*ofd = ofd_dev(obd->obd_lu_dev);
-+	struct seq_file	  *m = file->private_data;
-+	struct obd_device *obd = m->private;
-+	struct ofd_device *ofd = ofd_dev(obd->obd_lu_dev);
- 
--	return lprocfs_wr_uint(file, buffer, count, &ofd->ofd_soft_sync_limit);
-+	return lprocfs_uint_seq_write(file, buffer, count,
-+				      (loff_t *) &ofd->ofd_soft_sync_limit);
- }
-+LPROC_SEQ_FOPS(ofd_soft_sync_limit);
- 
--static int lprocfs_rd_lfsck_speed_limit(char *page, char **start, off_t off,
--					int count, int *eof, void *data)
-+static int ofd_lfsck_speed_limit_seq_show(struct seq_file *m, void *data)
- {
--	struct obd_device	*obd = data;
-+	struct obd_device       *obd = m->private;
- 	struct ofd_device	*ofd = ofd_dev(obd->obd_lu_dev);
- 
--	*eof = 1;
--
--	return lfsck_get_speed(ofd->ofd_osd, page, count);
-+	return lfsck_get_speed(m, ofd->ofd_osd);
- }
- 
--static int lprocfs_wr_lfsck_speed_limit(struct file *file,
--					const char __user *buffer,
--					unsigned long count, void *data)
-+static ssize_t
-+ofd_lfsck_speed_limit_seq_write(struct file *file, const char __user *buffer,
-+				size_t count, loff_t *off)
- {
--	struct obd_device	*obd = data;
-+	struct seq_file		*m = file->private_data;
-+	struct obd_device	*obd = m->private;
- 	struct ofd_device	*ofd = ofd_dev(obd->obd_lu_dev);
- 	__u32			 val;
- 	int			 rc;
-@@ -537,38 +528,35 @@ static int lprocfs_wr_lfsck_speed_limit(struct file *file,
- 
- 	return rc != 0 ? rc : count;
- }
-+LPROC_SEQ_FOPS(ofd_lfsck_speed_limit);
- 
--static int lprocfs_rd_lfsck_layout(char *page, char **start, off_t off,
--				   int count, int *eof, void *data)
-+static int ofd_lfsck_layout_seq_show(struct seq_file *m, void *data)
- {
--	struct obd_device	*obd = data;
--	struct ofd_device	*ofd = ofd_dev(obd->obd_lu_dev);
--
--	*eof = 1;
-+	struct obd_device *obd = m->private;
-+	struct ofd_device *ofd = ofd_dev(obd->obd_lu_dev);
- 
--	return lfsck_dump(ofd->ofd_osd, page, count, LT_LAYOUT);
-+	return lfsck_dump(m, ofd->ofd_osd, LT_LAYOUT);
- }
-+LPROC_SEQ_FOPS_RO(ofd_lfsck_layout);
- 
--static int lprocfs_rd_lfsck_verify_pfid(char *page, char **start, off_t off,
--					int count, int *eof, void *data)
-+static int ofd_lfsck_verify_pfid_seq_show(struct seq_file *m, void *data)
- {
--	struct obd_device	*obd = data;
--	struct ofd_device	*ofd = ofd_dev(obd->obd_lu_dev);
--
--	*eof = 1;
-+	struct obd_device *obd = m->private;
-+	struct ofd_device *ofd = ofd_dev(obd->obd_lu_dev);
- 
--	return snprintf(page, count,
--			"switch: %s\ndetected: "LPU64"\nrepaired: "LPU64"\n",
--			ofd->ofd_lfsck_verify_pfid ? "on" : "off",
--			ofd->ofd_inconsistency_self_detected,
--			ofd->ofd_inconsistency_self_repaired);
-+	return seq_printf(m,
-+			  "switch: %s\ndetected: "LPU64"\nrepaired: "LPU64"\n",
-+			  ofd->ofd_lfsck_verify_pfid ? "on" : "off",
-+			  ofd->ofd_inconsistency_self_detected,
-+			  ofd->ofd_inconsistency_self_repaired);
- }
- 
--static int lprocfs_wr_lfsck_verify_pfid(struct file *file,
--					const char __user *buffer,
--					unsigned long count, void *data)
-+static ssize_t
-+ofd_lfsck_verify_pfid_seq_write(struct file *file, const char __user *buffer,
-+				size_t count, loff_t *off)
- {
--	struct obd_device	*obd = data;
-+	struct seq_file		*m = file->private_data;
-+	struct obd_device	*obd = m->private;
- 	struct ofd_device	*ofd = ofd_dev(obd->obd_lu_dev);
- 	__u32			 val;
- 	int			 rc;
-@@ -581,75 +569,101 @@ static int lprocfs_wr_lfsck_verify_pfid(struct file *file,
- 
- 	return count;
- }
--
--static struct lprocfs_vars lprocfs_ofd_obd_vars[] = {
--	{ "uuid",		 lprocfs_rd_uuid, 0, 0 },
--	{ "blocksize",		 lprocfs_rd_blksize, 0, 0 },
--	{ "kbytestotal",	 lprocfs_rd_kbytestotal, 0, 0 },
--	{ "kbytesfree",		 lprocfs_rd_kbytesfree, 0, 0 },
--	{ "kbytesavail",	 lprocfs_rd_kbytesavail, 0, 0 },
--	{ "filestotal",		 lprocfs_rd_filestotal, 0, 0 },
--	{ "filesfree",		 lprocfs_rd_filesfree, 0, 0 },
--	{ "seqs_allocated",	 lprocfs_ofd_rd_seqs, 0, 0 },
--	{ "fstype",		 lprocfs_ofd_rd_fstype, 0, 0 },
--	{ "last_id",		 lprocfs_ofd_rd_last_id, 0, 0 },
--	{ "tot_dirty",		 lprocfs_ofd_rd_tot_dirty,   0, 0 },
--	{ "tot_pending",	 lprocfs_ofd_rd_tot_pending, 0, 0 },
--	{ "tot_granted",	 lprocfs_ofd_rd_tot_granted, 0, 0 },
--	{ "grant_precreate",	 lprocfs_ofd_rd_grant_precreate, 0, 0 },
--	{ "grant_ratio",	 lprocfs_ofd_rd_grant_ratio,
--				 lprocfs_ofd_wr_grant_ratio, 0, 0 },
--	{ "precreate_batch",	 lprocfs_ofd_rd_precreate_batch,
--				 lprocfs_ofd_wr_precreate_batch, 0 },
--	{ "recovery_status",	 lprocfs_obd_rd_recovery_status, 0, 0 },
--	{ "recovery_time_soft",	 lprocfs_obd_rd_recovery_time_soft,
--				 lprocfs_obd_wr_recovery_time_soft, 0},
--	{ "recovery_time_hard",  lprocfs_obd_rd_recovery_time_hard,
--				 lprocfs_obd_wr_recovery_time_hard, 0},
--	{ "evict_client",	 0, lprocfs_wr_evict_client, 0,
--				 &lprocfs_evict_client_fops},
--	{ "num_exports",	 lprocfs_rd_num_exports,   0, 0 },
--	{ "degraded",		 lprocfs_ofd_rd_degraded,
--				 lprocfs_ofd_wr_degraded, 0},
--	{ "sync_journal",	 lprocfs_ofd_rd_syncjournal,
--				 lprocfs_ofd_wr_syncjournal, 0 },
--	{ "sync_on_lock_cancel", lprocfs_ofd_rd_sync_lock_cancel,
--				 lprocfs_ofd_wr_sync_lock_cancel, 0 },
--	{ "instance",		 lprocfs_target_rd_instance, 0 },
--	{ "ir_factor",		 lprocfs_obd_rd_ir_factor,
--				 lprocfs_obd_wr_ir_factor, 0},
--	{ "grant_compat_disable", lprocfs_ofd_rd_grant_compat_disable,
--				  lprocfs_ofd_wr_grant_compat_disable, 0 },
--	{ "client_cache_count",	 lprocfs_ofd_rd_fmd_max_num,
--				 lprocfs_ofd_wr_fmd_max_num, 0 },
--	{ "client_cache_seconds", lprocfs_ofd_rd_fmd_max_age,
--				  lprocfs_ofd_wr_fmd_max_age, 0 },
--	{ "capa",		 lprocfs_ofd_rd_capa,
--				 lprocfs_ofd_wr_capa, 0 },
--	{ "capa_count",		 lprocfs_ofd_rd_capa_count, 0, 0 },
--	{ "job_cleanup_interval", lprocfs_rd_job_interval,
--				  lprocfs_wr_job_interval, 0},
--	{ "soft_sync_limit",	 lprocfs_ofd_rd_soft_sync_limit,
--				 lprocfs_ofd_wr_soft_sync_limit, 0},
--	{ "lfsck_speed_limit",	lprocfs_rd_lfsck_speed_limit,
--				lprocfs_wr_lfsck_speed_limit, 0 },
--	{ "lfsck_layout",	lprocfs_rd_lfsck_layout, 0, 0 },
--	{ "lfsck_verify_pfid",	lprocfs_rd_lfsck_verify_pfid,
--				lprocfs_wr_lfsck_verify_pfid, 0 },
--	{ 0 }
--};
--
--static struct lprocfs_vars lprocfs_ofd_module_vars[] = {
--	{ "num_refs",	  lprocfs_rd_numrefs,	0, 0 },
-+LPROC_SEQ_FOPS(ofd_lfsck_verify_pfid);
-+
-+LPROC_SEQ_FOPS_RO_TYPE(ofd, uuid);
-+LPROC_SEQ_FOPS_RO_TYPE(ofd, blksize);
-+LPROC_SEQ_FOPS_RO_TYPE(ofd, kbytestotal);
-+LPROC_SEQ_FOPS_RO_TYPE(ofd, kbytesfree);
-+LPROC_SEQ_FOPS_RO_TYPE(ofd, kbytesavail);
-+LPROC_SEQ_FOPS_RO_TYPE(ofd, filestotal);
-+LPROC_SEQ_FOPS_RO_TYPE(ofd, filesfree);
-+
-+LPROC_SEQ_FOPS_RO_TYPE(ofd, recovery_status);
-+LPROC_SEQ_FOPS_RW_TYPE(ofd, recovery_time_soft);
-+LPROC_SEQ_FOPS_RW_TYPE(ofd, recovery_time_hard);
-+LPROC_SEQ_FOPS_WO_TYPE(ofd, evict_client);
-+LPROC_SEQ_FOPS_RO_TYPE(ofd, num_exports);
-+LPROC_SEQ_FOPS_RO_TYPE(ofd, target_instance);
-+LPROC_SEQ_FOPS_RW_TYPE(ofd, ir_factor);
-+LPROC_SEQ_FOPS_RW_TYPE(ofd, job_interval);
-+
-+struct lprocfs_seq_vars lprocfs_ofd_obd_vars[] = {
-+	{ .name =	"uuid",
-+	  .fops =	&ofd_uuid_fops			},
-+	{ .name =	"blocksize",
-+	  .fops =	&ofd_blksize_fops		},
-+	{ .name =	"kbytestotal",
-+	  .fops =	&ofd_kbytestotal_fops		},
-+	{ .name =	"kbytesfree",
-+	  .fops =	&ofd_kbytesfree_fops		},
-+	{ .name =	"kbytesavail",
-+	  .fops =	&ofd_kbytesavail_fops		},
-+	{ .name =	"filestotal",
-+	  .fops =	&ofd_filestotal_fops		},
-+	{ .name =	"filesfree",
-+	  .fops =	&ofd_filesfree_fops		},
-+	{ .name =	"seqs_allocated",
-+	  .fops =	&ofd_seqs_fops			},
-+	{ .name =	"fstype",
-+	  .fops =	&ofd_fstype_fops		},
-+	{ .name =	"last_id",
-+	  .fops =	&ofd_last_id_fops		},
-+	{ .name =	"tot_dirty",
-+	  .fops =	&ofd_tot_dirty_fops		},
-+	{ .name =	"tot_pending",
-+	  .fops =	&ofd_tot_pending_fops		},
-+	{ .name =	"tot_granted",
-+	  .fops =	&ofd_tot_granted_fops		},
-+	{ .name =	"grant_precreate",
-+	  .fops =	&ofd_grant_precreate_fops	},
-+	{ .name =	"grant_ratio",
-+	  .fops =	&ofd_grant_ratio_fops		},
-+	{ .name =	"precreate_batch",
-+	  .fops =	&ofd_precreate_batch_fops	},
-+	{ .name =	"recovery_status",
-+	  .fops =	&ofd_recovery_status_fops	},
-+	{ .name =	"recovery_time_soft",
-+	  .fops =	&ofd_recovery_time_soft_fops	},
-+	{ .name =	"recovery_time_hard",
-+	  .fops =	&ofd_recovery_time_hard_fops	},
-+	{ .name =	"evict_client",
-+	  .fops =	&ofd_evict_client_fops		},
-+	{ .name =	"num_exports",
-+	  .fops =	&ofd_num_exports_fops		},
-+	{ .name =	"degraded",
-+	  .fops =	&ofd_degraded_fops		},
-+	{ .name =	"sync_journal",
-+	  .fops =	&ofd_syncjournal_fops		},
-+	{ .name =	"sync_on_lock_cancel",
-+	  .fops =	&ofd_sync_lock_cancel_fops	},
-+	{ .name =	"instance",
-+	  .fops =	&ofd_target_instance_fops	},
-+	{ .name =	"ir_factor",
-+	  .fops =	&ofd_ir_factor_fops		},
-+	{ .name =	"grant_compat_disable",
-+	  .fops =	&ofd_grant_compat_disable_fops	},
-+	{ .name =	"client_cache_count",
-+	  .fops =	&ofd_fmd_max_num_fops		},
-+	{ .name =	"client_cache_seconds",
-+	  .fops =	&ofd_fmd_max_age_fops		},
-+	{ .name =	"capa",
-+	  .fops =	&ofd_capa_fops			},
-+	{ .name =	"capa_count",
-+	  .fops =	&ofd_capa_count_fops		},
-+	{ .name =	"job_cleanup_interval",
-+	  .fops =	&ofd_job_interval_fops		},
-+	{ .name =	"soft_sync_limit",
-+	  .fops =	&ofd_soft_sync_limit_fops	},
-+	{ .name =	"lfsck_speed_limit",
-+	  .fops =	&ofd_lfsck_speed_limit_fops	},
-+	{ .name =	"lfsck_layout",
-+	  .fops =	&ofd_lfsck_layout_fops		},
-+	{ .name	=	"lfsck_verify_pfid",
-+	  .fops	=	&ofd_lfsck_verify_pfid_fops	},
- 	{ 0 }
- };
- 
--void lprocfs_ofd_init_vars(struct lprocfs_static_vars *lvars)
--{
--	lvars->module_vars  = lprocfs_ofd_module_vars;
--	lvars->obd_vars     = lprocfs_ofd_obd_vars;
--}
--
- void ofd_stats_counter_init(struct lprocfs_stats *stats)
- {
- 	LASSERT(stats && stats->ls_num >= LPROC_OFD_STATS_LAST);
-diff --git a/lustre/ofd/ofd_dev.c b/lustre/ofd/ofd_dev.c
-index 0f0d51a..6172913 100644
---- a/lustre/ofd/ofd_dev.c
-+++ b/lustre/ofd/ofd_dev.c
-@@ -239,8 +239,7 @@ static int ofd_process_config(const struct lu_env *env, struct lu_device *d,
- 
- 	switch (cfg->lcfg_command) {
- 	case LCFG_PARAM: {
--		struct lprocfs_static_vars lvars;
--
-+		struct obd_device	*obd = ofd_obd(m);
- 		/* For interoperability */
- 		struct cfg_interop_param   *ptr = NULL;
- 		struct lustre_cfg	   *old_cfg = NULL;
-@@ -278,8 +277,7 @@ static int ofd_process_config(const struct lu_env *env, struct lu_device *d,
- 			break;
- 		}
- 
--		lprocfs_ofd_init_vars(&lvars);
--		rc = class_process_proc_param(PARAM_OST, lvars.obd_vars, cfg,
-+		rc = class_process_proc_seq_param(PARAM_OST, obd->obd_vars, cfg,
- 					      d->ld_obd);
- 		if (rc > 0 || rc == -ENOSYS) {
- 			CDEBUG(D_CONFIG, "pass param %s down the stack.\n",
-@@ -485,9 +483,10 @@ static struct lu_device_operations ofd_lu_ops = {
- 	.ldo_prepare		= ofd_prepare,
- };
- 
-+LPROC_SEQ_FOPS(lprocfs_nid_stats_clear);
-+
- static int ofd_procfs_init(struct ofd_device *ofd)
- {
--	struct lprocfs_static_vars	 lvars;
- 	struct obd_device		*obd = ofd_obd(ofd);
- 	cfs_proc_dir_entry_t		*entry;
- 	int				 rc = 0;
-@@ -496,8 +495,8 @@ static int ofd_procfs_init(struct ofd_device *ofd)
- 
- 	/* lprocfs must be setup before the ofd so state can be safely added
- 	 * to /proc incrementally as the ofd is setup */
--	lprocfs_ofd_init_vars(&lvars);
--	rc = lprocfs_obd_setup(obd, lvars.obd_vars);
-+	obd->obd_vars = lprocfs_ofd_obd_vars;
-+	rc = lprocfs_seq_obd_setup(obd);
- 	if (rc) {
- 		CERROR("%s: lprocfs_obd_setup failed: %d.\n",
- 		       obd->obd_name, rc);
-@@ -513,7 +512,8 @@ static int ofd_procfs_init(struct ofd_device *ofd)
- 
- 	obd->obd_uses_nid_stats = 1;
- 
--	entry = lprocfs_register("exports", obd->obd_proc_entry, NULL, NULL);
-+	entry = lprocfs_seq_register("exports", obd->obd_proc_entry, NULL,
-+				     NULL);
- 	if (IS_ERR(entry)) {
- 		rc = PTR_ERR(entry);
- 		CERROR("%s: error %d setting up lprocfs for %s\n",
-@@ -523,8 +523,10 @@ static int ofd_procfs_init(struct ofd_device *ofd)
- 	obd->obd_proc_exports_entry = entry;
- 
- 	entry = lprocfs_add_simple(obd->obd_proc_exports_entry, "clear",
--				   lprocfs_nid_stats_clear_read,
--				   lprocfs_nid_stats_clear_write, obd, NULL);
-+#ifndef HAVE_ONLY_PROCFS_SEQ
-+				   NULL, NULL,
-+#endif
-+				   obd, &lprocfs_nid_stats_clear_fops);
- 	if (IS_ERR(entry)) {
- 		rc = PTR_ERR(entry);
- 		CERROR("%s: add proc entry 'clear' failed: %d.\n",
-@@ -540,7 +542,7 @@ static int ofd_procfs_init(struct ofd_device *ofd)
- 		GOTO(remove_entry_clear, rc);
- 	RETURN(0);
- remove_entry_clear:
--	lprocfs_remove_proc_entry("clear", obd->obd_proc_exports_entry);
-+	lprocfs_remove(&obd->obd_proc_exports_entry);
- obd_cleanup:
- 	lprocfs_obd_cleanup(obd);
- 	lprocfs_free_obd_stats(obd);
-@@ -548,51 +550,48 @@ obd_cleanup:
- 	return rc;
- }
- 
-+/**
-+ * ofd_procfs_add_brw_stats_symlink - expose osd stats to ofd layer
-+ *
-+ * The osd interfaces to the backend file system exposes useful data
-+ * such as brw_stats and read or write cache states. This same data
-+ * needs to be exposed into the obdfilter (ofd) layer to maintain
-+ * backwards compatibility. This function creates the symlinks in the
-+ * proc layer to enable this.
-+ */
- static void ofd_procfs_add_brw_stats_symlink(struct ofd_device *ofd)
- {
- 	struct obd_device	*obd = ofd_obd(ofd);
- 	struct obd_device	*osd_obd = ofd->ofd_osd_exp->exp_obd;
--	cfs_proc_dir_entry_t	*osd_root = osd_obd->obd_type->typ_procroot;
--	cfs_proc_dir_entry_t	*osd_dir;
- 
--	osd_dir = lprocfs_srch(osd_root, obd->obd_name);
--	if (osd_dir == NULL)
-+	if (obd->obd_proc_entry == NULL)
- 		return;
- 
--	if (lprocfs_srch(osd_dir, "brw_stats") != NULL)
--		lprocfs_add_symlink("brw_stats", obd->obd_proc_entry,
--				    "../../%s/%s/brw_stats",
--				    osd_root->name, osd_dir->name);
--
--	if (lprocfs_srch(osd_dir, "read_cache_enable") != NULL)
--		lprocfs_add_symlink("read_cache_enable", obd->obd_proc_entry,
--				    "../../%s/%s/read_cache_enable",
--				    osd_root->name, osd_dir->name);
--
--	if (lprocfs_srch(osd_dir, "readcache_max_filesize") != NULL)
--		lprocfs_add_symlink("readcache_max_filesize",
--				    obd->obd_proc_entry,
--				    "../../%s/%s/readcache_max_filesize",
--				    osd_root->name, osd_dir->name);
--
--	if (lprocfs_srch(osd_dir, "writethrough_cache_enable") != NULL)
--		lprocfs_add_symlink("writethrough_cache_enable",
--				    obd->obd_proc_entry,
--				    "../../%s/%s/writethrough_cache_enable",
--				    osd_root->name, osd_dir->name);
-+	lprocfs_add_symlink("brw_stats", obd->obd_proc_entry,
-+			    "../../%s/%s/brw_stats",
-+			    osd_obd->obd_type->typ_name, obd->obd_name);
-+
-+	lprocfs_add_symlink("read_cache_enable", obd->obd_proc_entry,
-+			    "../../%s/%s/read_cache_enable",
-+			    osd_obd->obd_type->typ_name, obd->obd_name);
-+
-+	lprocfs_add_symlink("readcache_max_filesize",
-+			    obd->obd_proc_entry,
-+			    "../../%s/%s/readcache_max_filesize",
-+			    osd_obd->obd_type->typ_name, obd->obd_name);
-+
-+	lprocfs_add_symlink("writethrough_cache_enable",
-+			    obd->obd_proc_entry,
-+			    "../../%s/%s/writethrough_cache_enable",
-+			    osd_obd->obd_type->typ_name, obd->obd_name);
- }
- 
- static void ofd_procfs_fini(struct ofd_device *ofd)
- {
- 	struct obd_device *obd = ofd_obd(ofd);
- 
--	lprocfs_remove_proc_entry("writethrough_cache_enable",
--				  obd->obd_proc_entry);
--	lprocfs_remove_proc_entry("readcache_max_filesize",
--				  obd->obd_proc_entry);
--	lprocfs_remove_proc_entry("read_cache_enable", obd->obd_proc_entry);
--	lprocfs_remove_proc_entry("brw_stats", obd->obd_proc_entry);
--	lprocfs_remove_proc_entry("clear", obd->obd_proc_exports_entry);
-+	lprocfs_remove(&obd->obd_proc_exports_entry);
-+	lprocfs_remove(&obd->obd_proc_entry);
- 	lprocfs_free_per_client_stats(obd);
- 	lprocfs_obd_cleanup(obd);
- 	lprocfs_free_obd_stats(obd);
-@@ -2377,7 +2376,6 @@ static struct lu_device_type ofd_device_type = {
- 
- int __init ofd_init(void)
- {
--	struct lprocfs_static_vars	lvars;
- 	int				rc;
- 
- 	rc = lu_kmem_init(ofd_caches);
-@@ -2390,11 +2388,9 @@ int __init ofd_init(void)
- 		return(rc);
- 	}
- 
--	lprocfs_ofd_init_vars(&lvars);
--
- 	rc = class_register_type(&ofd_obd_ops, NULL, true, NULL,
- #ifndef HAVE_ONLY_PROCFS_SEQ
--				 lvars.module_vars,
-+				 NULL,
- #endif
- 				 LUSTRE_OST_NAME, &ofd_device_type);
- 	return rc;
-diff --git a/lustre/ofd/ofd_internal.h b/lustre/ofd/ofd_internal.h
-index 4f12506..2e75de5 100644
---- a/lustre/ofd/ofd_internal.h
-+++ b/lustre/ofd/ofd_internal.h
-@@ -403,13 +403,9 @@ int ofd_txn_stop_cb(const struct lu_env *env, struct thandle *txn,
- 
- /* lproc_ofd.c */
- #ifdef LPROCFS
--void lprocfs_ofd_init_vars(struct lprocfs_static_vars *lvars);
-+extern struct lprocfs_seq_vars lprocfs_ofd_obd_vars[];
- void ofd_stats_counter_init(struct lprocfs_stats *stats);
- #else
--static void lprocfs_ofd_init_vars(struct lprocfs_static_vars *lvars)
--{
--	memset(lvars, 0, sizeof(*lvars));
--}
- static inline void ofd_stats_counter_init(struct lprocfs_stats *stats) {}
- #endif
- 
--- 
-1.9.3
-
diff --git a/patches/07_doxygen.patch b/patches/07_doxygen.patch
deleted file mode 100644
index 6df24ea2e..000000000
--- a/patches/07_doxygen.patch
+++ /dev/null
@@ -1,1804 +0,0 @@
-Index: dcmtk-3.6.0/doxygen/htmldocs.cfg
-===================================================================
---- dcmtk-3.6.0.orig/doxygen/htmldocs.cfg	2011-11-23 15:49:41.000000000 +0100
-+++ dcmtk-3.6.0/doxygen/htmldocs.cfg	2011-11-23 15:50:00.000000000 +0100
-@@ -1,4 +1,4 @@
--# Doxyfile 1.5.1
-+# Doxyfile 1.7.1
- 
- # This file describes the settings to be used by the documentation system
- # doxygen (www.doxygen.org) for a project
-@@ -14,438 +14,560 @@
- # Project related configuration options
- #---------------------------------------------------------------------------
- 
--# The PROJECT_NAME tag is a single word (or a sequence of words surrounded 
-+# This tag specifies the encoding used for all characters in the config file
-+# that follow. The default is UTF-8 which is also the encoding used for all
-+# text before the first occurrence of this tag. Doxygen uses libiconv (or the
-+# iconv built into libc) for the transcoding. See
-+# http://www.gnu.org/software/libiconv for the list of possible encodings.
-+
-+DOXYFILE_ENCODING      = UTF-8
-+
-+# The PROJECT_NAME tag is a single word (or a sequence of words surrounded
- # by quotes) that should identify the project.
- 
- PROJECT_NAME           = "OFFIS DCMTK"
- 
--# The PROJECT_NUMBER tag can be used to enter a project or revision number. 
--# This could be handy for archiving the generated documentation or 
-+# The PROJECT_NUMBER tag can be used to enter a project or revision number.
-+# This could be handy for archiving the generated documentation or
- # if some version control system is used.
- 
- PROJECT_NUMBER         = "Version @DCMTK_VERSION@"
- 
--# The OUTPUT_DIRECTORY tag is used to specify the (relative or absolute) 
--# base path where the generated documentation will be put. 
--# If a relative path is entered, it will be relative to the location 
-+# The OUTPUT_DIRECTORY tag is used to specify the (relative or absolute)
-+# base path where the generated documentation will be put.
-+# If a relative path is entered, it will be relative to the location
- # where doxygen was started. If left blank the current directory will be used.
- 
--OUTPUT_DIRECTORY       = 
-+OUTPUT_DIRECTORY       =
- 
--# If the CREATE_SUBDIRS tag is set to YES, then doxygen will create 
--# 4096 sub-directories (in 2 levels) under the output directory of each output 
--# format and will distribute the generated files over these directories. 
--# Enabling this option can be useful when feeding doxygen a huge amount of 
--# source files, where putting all generated files in the same directory would 
-+# If the CREATE_SUBDIRS tag is set to YES, then doxygen will create
-+# 4096 sub-directories (in 2 levels) under the output directory of each output
-+# format and will distribute the generated files over these directories.
-+# Enabling this option can be useful when feeding doxygen a huge amount of
-+# source files, where putting all generated files in the same directory would
- # otherwise cause performance problems for the file system.
- 
- CREATE_SUBDIRS         = NO
- 
--# The OUTPUT_LANGUAGE tag is used to specify the language in which all 
--# documentation generated by doxygen is written. Doxygen will use this 
--# information to generate all constant output in the proper language. 
--# The default language is English, other supported languages are: 
--# Afrikaans, Arabic, Brazilian, Catalan, Chinese, Chinese-Traditional, 
--# Croatian, Czech, Danish, Dutch, Finnish, French, German, Greek, Hungarian, 
--# Italian, Japanese, Japanese-en (Japanese with English messages), Korean, 
--# Korean-en, Lithuanian, Norwegian, Polish, Portuguese, Romanian, Russian, 
--# Serbian, Slovak, Slovene, Spanish, Swedish, and Ukrainian.
-+# The OUTPUT_LANGUAGE tag is used to specify the language in which all
-+# documentation generated by doxygen is written. Doxygen will use this
-+# information to generate all constant output in the proper language.
-+# The default language is English, other supported languages are:
-+# Afrikaans, Arabic, Brazilian, Catalan, Chinese, Chinese-Traditional,
-+# Croatian, Czech, Danish, Dutch, Esperanto, Farsi, Finnish, French, German,
-+# Greek, Hungarian, Italian, Japanese, Japanese-en (Japanese with English
-+# messages), Korean, Korean-en, Lithuanian, Norwegian, Macedonian, Persian,
-+# Polish, Portuguese, Romanian, Russian, Serbian, Serbian-Cyrilic, Slovak,
-+# Slovene, Spanish, Swedish, Ukrainian, and Vietnamese.
- 
- OUTPUT_LANGUAGE        = English
- 
--# This tag can be used to specify the encoding used in the generated output. 
--# The encoding is not always determined by the language that is chosen, 
--# but also whether or not the output is meant for Windows or non-Windows users. 
--# In case there is a difference, setting the USE_WINDOWS_ENCODING tag to YES 
--# forces the Windows encoding (this is the default for the Windows binary), 
--# whereas setting the tag to NO uses a Unix-style encoding (the default for 
--# all platforms other than Windows).
--
--USE_WINDOWS_ENCODING   = NO
--
--# If the BRIEF_MEMBER_DESC tag is set to YES (the default) Doxygen will 
--# include brief member descriptions after the members that are listed in 
--# the file and class documentation (similar to JavaDoc). 
-+# If the BRIEF_MEMBER_DESC tag is set to YES (the default) Doxygen will
-+# include brief member descriptions after the members that are listed in
-+# the file and class documentation (similar to JavaDoc).
- # Set to NO to disable this.
- 
- BRIEF_MEMBER_DESC      = YES
- 
--# If the REPEAT_BRIEF tag is set to YES (the default) Doxygen will prepend 
--# the brief description of a member or function before the detailed description. 
--# Note: if both HIDE_UNDOC_MEMBERS and BRIEF_MEMBER_DESC are set to NO, the 
-+# If the REPEAT_BRIEF tag is set to YES (the default) Doxygen will prepend
-+# the brief description of a member or function before the detailed description.
-+# Note: if both HIDE_UNDOC_MEMBERS and BRIEF_MEMBER_DESC are set to NO, the
- # brief descriptions will be completely suppressed.
- 
- REPEAT_BRIEF           = YES
- 
--# This tag implements a quasi-intelligent brief description abbreviator 
--# that is used to form the text in various listings. Each string 
--# in this list, if found as the leading text of the brief description, will be 
--# stripped from the text and the result after processing the whole list, is 
--# used as the annotated text. Otherwise, the brief description is used as-is. 
--# If left blank, the following values are used ("$name" is automatically 
--# replaced with the name of the entity): "The $name class" "The $name widget" 
--# "The $name file" "is" "provides" "specifies" "contains" 
-+# This tag implements a quasi-intelligent brief description abbreviator
-+# that is used to form the text in various listings. Each string
-+# in this list, if found as the leading text of the brief description, will be
-+# stripped from the text and the result after processing the whole list, is
-+# used as the annotated text. Otherwise, the brief description is used as-is.
-+# If left blank, the following values are used ("$name" is automatically
-+# replaced with the name of the entity): "The $name class" "The $name widget"
-+# "The $name file" "is" "provides" "specifies" "contains"
- # "represents" "a" "an" "the"
- 
--ABBREVIATE_BRIEF       = 
-+ABBREVIATE_BRIEF       =
- 
--# If the ALWAYS_DETAILED_SEC and REPEAT_BRIEF tags are both set to YES then 
--# Doxygen will generate a detailed section even if there is only a brief 
-+# If the ALWAYS_DETAILED_SEC and REPEAT_BRIEF tags are both set to YES then
-+# Doxygen will generate a detailed section even if there is only a brief
- # description.
- 
- ALWAYS_DETAILED_SEC    = NO
- 
--# If the INLINE_INHERITED_MEMB tag is set to YES, doxygen will show all 
--# inherited members of a class in the documentation of that class as if those 
--# members were ordinary class members. Constructors, destructors and assignment 
-+# If the INLINE_INHERITED_MEMB tag is set to YES, doxygen will show all
-+# inherited members of a class in the documentation of that class as if those
-+# members were ordinary class members. Constructors, destructors and assignment
- # operators of the base classes will not be shown.
- 
- INLINE_INHERITED_MEMB  = NO
- 
--# If the FULL_PATH_NAMES tag is set to YES then Doxygen will prepend the full 
--# path before files name in the file list and in the header files. If set 
-+# If the FULL_PATH_NAMES tag is set to YES then Doxygen will prepend the full
-+# path before files name in the file list and in the header files. If set
- # to NO the shortest path that makes the file name unique will be used.
- 
- FULL_PATH_NAMES        = YES
- 
--# If the FULL_PATH_NAMES tag is set to YES then the STRIP_FROM_PATH tag 
--# can be used to strip a user-defined part of the path. Stripping is 
--# only done if one of the specified strings matches the left-hand part of 
--# the path. The tag can be used to show relative paths in the file list. 
--# If left blank the directory from which doxygen is run is used as the 
-+# If the FULL_PATH_NAMES tag is set to YES then the STRIP_FROM_PATH tag
-+# can be used to strip a user-defined part of the path. Stripping is
-+# only done if one of the specified strings matches the left-hand part of
-+# the path. The tag can be used to show relative paths in the file list.
-+# If left blank the directory from which doxygen is run is used as the
- # path to strip.
- 
- STRIP_FROM_PATH        = ..
- 
--# The STRIP_FROM_INC_PATH tag can be used to strip a user-defined part of 
--# the path mentioned in the documentation of a class, which tells 
--# the reader which header file to include in order to use a class. 
--# If left blank only the name of the header file containing the class 
--# definition is used. Otherwise one should specify the include paths that 
-+# The STRIP_FROM_INC_PATH tag can be used to strip a user-defined part of
-+# the path mentioned in the documentation of a class, which tells
-+# the reader which header file to include in order to use a class.
-+# If left blank only the name of the header file containing the class
-+# definition is used. Otherwise one should specify the include paths that
- # are normally passed to the compiler using the -I flag.
- 
--STRIP_FROM_INC_PATH    = 
-+STRIP_FROM_INC_PATH    =
- 
--# If the SHORT_NAMES tag is set to YES, doxygen will generate much shorter 
--# (but less readable) file names. This can be useful is your file systems 
-+# If the SHORT_NAMES tag is set to YES, doxygen will generate much shorter
-+# (but less readable) file names. This can be useful is your file systems
- # doesn't support long names like on DOS, Mac, or CD-ROM.
- 
- SHORT_NAMES            = NO
- 
--# If the JAVADOC_AUTOBRIEF tag is set to YES then Doxygen 
--# will interpret the first line (until the first dot) of a JavaDoc-style 
--# comment as the brief description. If set to NO, the JavaDoc 
--# comments will behave just like the Qt-style comments (thus requiring an 
--# explicit @brief command for a brief description.
-+# If the JAVADOC_AUTOBRIEF tag is set to YES then Doxygen
-+# will interpret the first line (until the first dot) of a JavaDoc-style
-+# comment as the brief description. If set to NO, the JavaDoc
-+# comments will behave just like regular Qt-style comments
-+# (thus requiring an explicit @brief command for a brief description.)
- 
- JAVADOC_AUTOBRIEF      = YES
- 
--# The MULTILINE_CPP_IS_BRIEF tag can be set to YES to make Doxygen 
--# treat a multi-line C++ special comment block (i.e. a block of //! or /// 
--# comments) as a brief description. This used to be the default behaviour. 
--# The new default is to treat a multi-line C++ comment block as a detailed 
-+# If the QT_AUTOBRIEF tag is set to YES then Doxygen will
-+# interpret the first line (until the first dot) of a Qt-style
-+# comment as the brief description. If set to NO, the comments
-+# will behave just like regular Qt-style comments (thus requiring
-+# an explicit \brief command for a brief description.)
-+
-+QT_AUTOBRIEF           = NO
-+
-+# The MULTILINE_CPP_IS_BRIEF tag can be set to YES to make Doxygen
-+# treat a multi-line C++ special comment block (i.e. a block of //! or ///
-+# comments) as a brief description. This used to be the default behaviour.
-+# The new default is to treat a multi-line C++ comment block as a detailed
- # description. Set this tag to YES if you prefer the old behaviour instead.
- 
- MULTILINE_CPP_IS_BRIEF = NO
- 
--# If the DETAILS_AT_TOP tag is set to YES then Doxygen 
--# will output the detailed description near the top, like JavaDoc.
--# If set to NO, the detailed description appears after the member 
--# documentation.
--
--DETAILS_AT_TOP         = NO
--
--# If the INHERIT_DOCS tag is set to YES (the default) then an undocumented 
--# member inherits the documentation from any documented member that it 
-+# If the INHERIT_DOCS tag is set to YES (the default) then an undocumented
-+# member inherits the documentation from any documented member that it
- # re-implements.
- 
- INHERIT_DOCS           = NO
- 
--# If the SEPARATE_MEMBER_PAGES tag is set to YES, then doxygen will produce 
--# a new page for each member. If set to NO, the documentation of a member will 
-+# If the SEPARATE_MEMBER_PAGES tag is set to YES, then doxygen will produce
-+# a new page for each member. If set to NO, the documentation of a member will
- # be part of the file/class/namespace that contains it.
- 
- SEPARATE_MEMBER_PAGES  = NO
- 
--# The TAB_SIZE tag can be used to set the number of spaces in a tab. 
-+# The TAB_SIZE tag can be used to set the number of spaces in a tab.
- # Doxygen uses this value to replace tabs by spaces in code fragments.
- 
- TAB_SIZE               = 4
- 
--# This tag can be used to specify a number of aliases that acts 
--# as commands in the documentation. An alias has the form "name=value". 
--# For example adding "sideeffect=\par Side Effects:\n" will allow you to 
--# put the command \sideeffect (or @sideeffect) in the documentation, which 
--# will result in a user-defined paragraph with heading "Side Effects:". 
-+# This tag can be used to specify a number of aliases that acts
-+# as commands in the documentation. An alias has the form "name=value".
-+# For example adding "sideeffect=\par Side Effects:\n" will allow you to
-+# put the command \sideeffect (or @sideeffect) in the documentation, which
-+# will result in a user-defined paragraph with heading "Side Effects:".
- # You can put \n's in the value part of an alias to insert newlines.
- 
--ALIASES                = 
-+ALIASES                =
- 
--# Set the OPTIMIZE_OUTPUT_FOR_C tag to YES if your project consists of C 
--# sources only. Doxygen will then generate output that is more tailored for C. 
--# For instance, some of the names that are used will be different. The list 
-+# Set the OPTIMIZE_OUTPUT_FOR_C tag to YES if your project consists of C
-+# sources only. Doxygen will then generate output that is more tailored for C.
-+# For instance, some of the names that are used will be different. The list
- # of all members will be omitted, etc.
- 
- OPTIMIZE_OUTPUT_FOR_C  = NO
- 
--# Set the OPTIMIZE_OUTPUT_JAVA tag to YES if your project consists of Java 
--# sources only. Doxygen will then generate output that is more tailored for Java. 
--# For instance, namespaces will be presented as packages, qualified scopes 
--# will look different, etc.
-+# Set the OPTIMIZE_OUTPUT_JAVA tag to YES if your project consists of Java
-+# sources only. Doxygen will then generate output that is more tailored for
-+# Java. For instance, namespaces will be presented as packages, qualified
-+# scopes will look different, etc.
- 
- OPTIMIZE_OUTPUT_JAVA   = NO
- 
--# If you use STL classes (i.e. std::string, std::vector, etc.) but do not want to 
--# include (a tag file for) the STL sources as input, then you should 
--# set this tag to YES in order to let doxygen match functions declarations and 
--# definitions whose arguments contain STL classes (e.g. func(std::string); v.s. 
--# func(std::string) {}). This also make the inheritance and collaboration 
-+# Set the OPTIMIZE_FOR_FORTRAN tag to YES if your project consists of Fortran
-+# sources only. Doxygen will then generate output that is more tailored for
-+# Fortran.
-+
-+OPTIMIZE_FOR_FORTRAN   = NO
-+
-+# Set the OPTIMIZE_OUTPUT_VHDL tag to YES if your project consists of VHDL
-+# sources. Doxygen will then generate output that is tailored for
-+# VHDL.
-+
-+OPTIMIZE_OUTPUT_VHDL   = NO
-+
-+# Doxygen selects the parser to use depending on the extension of the files it
-+# parses. With this tag you can assign which parser to use for a given extension.
-+# Doxygen has a built-in mapping, but you can override or extend it using this
-+# tag. The format is ext=language, where ext is a file extension, and language
-+# is one of the parsers supported by doxygen: IDL, Java, Javascript, CSharp, C,
-+# C++, D, PHP, Objective-C, Python, Fortran, VHDL, C, C++. For instance to make
-+# doxygen treat .inc files as Fortran files (default is PHP), and .f files as C
-+# (default is Fortran), use: inc=Fortran f=C. Note that for custom extensions
-+# you also need to set FILE_PATTERNS otherwise the files are not read by doxygen.
-+
-+EXTENSION_MAPPING      =
-+
-+# If you use STL classes (i.e. std::string, std::vector, etc.) but do not want
-+# to include (a tag file for) the STL sources as input, then you should
-+# set this tag to YES in order to let doxygen match functions declarations and
-+# definitions whose arguments contain STL classes (e.g. func(std::string); v.s.
-+# func(std::string) {}). This also make the inheritance and collaboration
- # diagrams that involve STL classes more complete and accurate.
- 
- BUILTIN_STL_SUPPORT    = NO
- 
--# If member grouping is used in the documentation and the DISTRIBUTE_GROUP_DOC 
--# tag is set to YES, then doxygen will reuse the documentation of the first 
--# member in the group (if any) for the other members of the group. By default 
-+# If you use Microsoft's C++/CLI language, you should set this option to YES to
-+# enable parsing support.
-+
-+CPP_CLI_SUPPORT        = NO
-+
-+# Set the SIP_SUPPORT tag to YES if your project consists of sip sources only.
-+# Doxygen will parse them like normal C++ but will assume all classes use public
-+# instead of private inheritance when no explicit protection keyword is present.
-+
-+SIP_SUPPORT            = NO
-+
-+# For Microsoft's IDL there are propget and propput attributes to indicate getter
-+# and setter methods for a property. Setting this option to YES (the default)
-+# will make doxygen to replace the get and set methods by a property in the
-+# documentation. This will only work if the methods are indeed getting or
-+# setting a simple type. If this is not the case, or you want to show the
-+# methods anyway, you should set this option to NO.
-+
-+IDL_PROPERTY_SUPPORT   = YES
-+
-+# If member grouping is used in the documentation and the DISTRIBUTE_GROUP_DOC
-+# tag is set to YES, then doxygen will reuse the documentation of the first
-+# member in the group (if any) for the other members of the group. By default
- # all members of a group must be documented explicitly.
- 
- DISTRIBUTE_GROUP_DOC   = NO
- 
--# Set the SUBGROUPING tag to YES (the default) to allow class member groups of 
--# the same type (for instance a group of public functions) to be put as a 
--# subgroup of that type (e.g. under the Public Functions section). Set it to 
--# NO to prevent subgrouping. Alternatively, this can be done per class using 
-+# Set the SUBGROUPING tag to YES (the default) to allow class member groups of
-+# the same type (for instance a group of public functions) to be put as a
-+# subgroup of that type (e.g. under the Public Functions section). Set it to
-+# NO to prevent subgrouping. Alternatively, this can be done per class using
- # the \nosubgrouping command.
- 
- SUBGROUPING            = YES
- 
-+# When TYPEDEF_HIDES_STRUCT is enabled, a typedef of a struct, union, or enum
-+# is documented as struct, union, or enum with the name of the typedef. So
-+# typedef struct TypeS {} TypeT, will appear in the documentation as a struct
-+# with name TypeT. When disabled the typedef will appear as a member of a file,
-+# namespace, or class. And the struct will be named TypeS. This can typically
-+# be useful for C code in case the coding convention dictates that all compound
-+# types are typedef'ed and only the typedef is referenced, never the tag name.
-+
-+TYPEDEF_HIDES_STRUCT   = NO
-+
-+# The SYMBOL_CACHE_SIZE determines the size of the internal cache use to
-+# determine which symbols to keep in memory and which to flush to disk.
-+# When the cache is full, less often used symbols will be written to disk.
-+# For small to medium size projects (<1000 input files) the default value is
-+# probably good enough. For larger projects a too small cache size can cause
-+# doxygen to be busy swapping symbols to and from disk most of the time
-+# causing a significant performance penality.
-+# If the system has enough physical memory increasing the cache will improve the
-+# performance by keeping more symbols in memory. Note that the value works on
-+# a logarithmic scale so increasing the size by one will rougly double the
-+# memory usage. The cache size is given by this formula:
-+# 2^(16+SYMBOL_CACHE_SIZE). The valid range is 0..9, the default is 0,
-+# corresponding to a cache size of 2^16 = 65536 symbols
-+
-+SYMBOL_CACHE_SIZE      = 0
-+
- #---------------------------------------------------------------------------
- # Build related configuration options
- #---------------------------------------------------------------------------
- 
--# If the EXTRACT_ALL tag is set to YES doxygen will assume all entities in 
--# documentation are documented, even if no documentation was available. 
--# Private class members and static file members will be hidden unless 
-+# If the EXTRACT_ALL tag is set to YES doxygen will assume all entities in
-+# documentation are documented, even if no documentation was available.
-+# Private class members and static file members will be hidden unless
- # the EXTRACT_PRIVATE and EXTRACT_STATIC tags are set to YES
- 
- EXTRACT_ALL            = NO
- 
--# If the EXTRACT_PRIVATE tag is set to YES all private members of a class 
-+# If the EXTRACT_PRIVATE tag is set to YES all private members of a class
- # will be included in the documentation.
- 
- EXTRACT_PRIVATE        = YES
- 
--# If the EXTRACT_STATIC tag is set to YES all static members of a file 
-+# If the EXTRACT_STATIC tag is set to YES all static members of a file
- # will be included in the documentation.
- 
- EXTRACT_STATIC         = YES
- 
--# If the EXTRACT_LOCAL_CLASSES tag is set to YES classes (and structs) 
--# defined locally in source files will be included in the documentation. 
-+# If the EXTRACT_LOCAL_CLASSES tag is set to YES classes (and structs)
-+# defined locally in source files will be included in the documentation.
- # If set to NO only classes defined in header files are included.
- 
- EXTRACT_LOCAL_CLASSES  = YES
- 
--# This flag is only useful for Objective-C code. When set to YES local 
--# methods, which are defined in the implementation section but not in 
--# the interface are included in the documentation. 
-+# This flag is only useful for Objective-C code. When set to YES local
-+# methods, which are defined in the implementation section but not in
-+# the interface are included in the documentation.
- # If set to NO (the default) only methods in the interface are included.
- 
- EXTRACT_LOCAL_METHODS  = NO
- 
--# If the HIDE_UNDOC_MEMBERS tag is set to YES, Doxygen will hide all 
--# undocumented members of documented classes, files or namespaces. 
--# If set to NO (the default) these members will be included in the 
--# various overviews, but no documentation section is generated. 
-+# If this flag is set to YES, the members of anonymous namespaces will be
-+# extracted and appear in the documentation as a namespace called
-+# 'anonymous_namespace{file}', where file will be replaced with the base
-+# name of the file that contains the anonymous namespace. By default
-+# anonymous namespace are hidden.
-+
-+EXTRACT_ANON_NSPACES   = NO
-+
-+# If the HIDE_UNDOC_MEMBERS tag is set to YES, Doxygen will hide all
-+# undocumented members of documented classes, files or namespaces.
-+# If set to NO (the default) these members will be included in the
-+# various overviews, but no documentation section is generated.
- # This option has no effect if EXTRACT_ALL is enabled.
- 
- HIDE_UNDOC_MEMBERS     = NO
- 
--# If the HIDE_UNDOC_CLASSES tag is set to YES, Doxygen will hide all 
--# undocumented classes that are normally visible in the class hierarchy. 
--# If set to NO (the default) these classes will be included in the various 
-+# If the HIDE_UNDOC_CLASSES tag is set to YES, Doxygen will hide all
-+# undocumented classes that are normally visible in the class hierarchy.
-+# If set to NO (the default) these classes will be included in the various
- # overviews. This option has no effect if EXTRACT_ALL is enabled.
- 
- HIDE_UNDOC_CLASSES     = NO
- 
--# If the HIDE_FRIEND_COMPOUNDS tag is set to YES, Doxygen will hide all 
--# friend (class|struct|union) declarations. 
--# If set to NO (the default) these declarations will be included in the 
-+# If the HIDE_FRIEND_COMPOUNDS tag is set to YES, Doxygen will hide all
-+# friend (class|struct|union) declarations.
-+# If set to NO (the default) these declarations will be included in the
- # documentation.
- 
- HIDE_FRIEND_COMPOUNDS  = NO
- 
--# If the HIDE_IN_BODY_DOCS tag is set to YES, Doxygen will hide any 
--# documentation blocks found inside the body of a function. 
--# If set to NO (the default) these blocks will be appended to the 
-+# If the HIDE_IN_BODY_DOCS tag is set to YES, Doxygen will hide any
-+# documentation blocks found inside the body of a function.
-+# If set to NO (the default) these blocks will be appended to the
- # function's detailed documentation block.
- 
- HIDE_IN_BODY_DOCS      = NO
- 
--# The INTERNAL_DOCS tag determines if documentation 
--# that is typed after a \internal command is included. If the tag is set 
--# to NO (the default) then the documentation will be excluded. 
-+# The INTERNAL_DOCS tag determines if documentation
-+# that is typed after a \internal command is included. If the tag is set
-+# to NO (the default) then the documentation will be excluded.
- # Set it to YES to include the internal documentation.
- 
- INTERNAL_DOCS          = NO
- 
--# If the CASE_SENSE_NAMES tag is set to NO then Doxygen will only generate 
--# file names in lower-case letters. If set to YES upper-case letters are also 
--# allowed. This is useful if you have classes or files whose names only differ 
--# in case and if your file system supports case sensitive file names. Windows 
-+# If the CASE_SENSE_NAMES tag is set to NO then Doxygen will only generate
-+# file names in lower-case letters. If set to YES upper-case letters are also
-+# allowed. This is useful if you have classes or files whose names only differ
-+# in case and if your file system supports case sensitive file names. Windows
- # and Mac users are advised to set this option to NO.
- 
- CASE_SENSE_NAMES       = YES
- 
--# If the HIDE_SCOPE_NAMES tag is set to NO (the default) then Doxygen 
--# will show members with their full class and namespace scopes in the 
-+# If the HIDE_SCOPE_NAMES tag is set to NO (the default) then Doxygen
-+# will show members with their full class and namespace scopes in the
- # documentation. If set to YES the scope will be hidden.
- 
- HIDE_SCOPE_NAMES       = NO
- 
--# If the SHOW_INCLUDE_FILES tag is set to YES (the default) then Doxygen 
--# will put a list of the files that are included by a file in the documentation 
-+# If the SHOW_INCLUDE_FILES tag is set to YES (the default) then Doxygen
-+# will put a list of the files that are included by a file in the documentation
- # of that file.
- 
- SHOW_INCLUDE_FILES     = NO
- 
--# If the INLINE_INFO tag is set to YES (the default) then a tag [inline] 
-+# If the FORCE_LOCAL_INCLUDES tag is set to YES then Doxygen
-+# will list include files with double quotes in the documentation
-+# rather than with sharp brackets.
-+
-+FORCE_LOCAL_INCLUDES   = NO
-+
-+# If the INLINE_INFO tag is set to YES (the default) then a tag [inline]
- # is inserted in the documentation for inline members.
- 
- INLINE_INFO            = YES
- 
--# If the SORT_MEMBER_DOCS tag is set to YES (the default) then doxygen 
--# will sort the (detailed) documentation of file and class members 
--# alphabetically by member name. If set to NO the members will appear in 
-+# If the SORT_MEMBER_DOCS tag is set to YES (the default) then doxygen
-+# will sort the (detailed) documentation of file and class members
-+# alphabetically by member name. If set to NO the members will appear in
- # declaration order.
- 
- SORT_MEMBER_DOCS       = YES
- 
--# If the SORT_BRIEF_DOCS tag is set to YES then doxygen will sort the 
--# brief documentation of file, namespace and class members alphabetically 
--# by member name. If set to NO (the default) the members will appear in 
-+# If the SORT_BRIEF_DOCS tag is set to YES then doxygen will sort the
-+# brief documentation of file, namespace and class members alphabetically
-+# by member name. If set to NO (the default) the members will appear in
- # declaration order.
- 
- SORT_BRIEF_DOCS        = NO
- 
--# If the SORT_BY_SCOPE_NAME tag is set to YES, the class list will be 
--# sorted by fully-qualified names, including namespaces. If set to 
--# NO (the default), the class list will be sorted only by class name, 
--# not including the namespace part. 
-+# If the SORT_MEMBERS_CTORS_1ST tag is set to YES then doxygen
-+# will sort the (brief and detailed) documentation of class members so that
-+# constructors and destructors are listed first. If set to NO (the default)
-+# the constructors will appear in the respective orders defined by
-+# SORT_MEMBER_DOCS and SORT_BRIEF_DOCS.
-+# This tag will be ignored for brief docs if SORT_BRIEF_DOCS is set to NO
-+# and ignored for detailed docs if SORT_MEMBER_DOCS is set to NO.
-+
-+SORT_MEMBERS_CTORS_1ST = NO
-+
-+# If the SORT_GROUP_NAMES tag is set to YES then doxygen will sort the
-+# hierarchy of group names into alphabetical order. If set to NO (the default)
-+# the group names will appear in their defined order.
-+
-+SORT_GROUP_NAMES       = NO
-+
-+# If the SORT_BY_SCOPE_NAME tag is set to YES, the class list will be
-+# sorted by fully-qualified names, including namespaces. If set to
-+# NO (the default), the class list will be sorted only by class name,
-+# not including the namespace part.
- # Note: This option is not very useful if HIDE_SCOPE_NAMES is set to YES.
--# Note: This option applies only to the class list, not to the 
-+# Note: This option applies only to the class list, not to the
- # alphabetical list.
- 
- SORT_BY_SCOPE_NAME     = NO
- 
--# The GENERATE_TODOLIST tag can be used to enable (YES) or 
--# disable (NO) the todo list. This list is created by putting \todo 
-+# The GENERATE_TODOLIST tag can be used to enable (YES) or
-+# disable (NO) the todo list. This list is created by putting \todo
- # commands in the documentation.
- 
- GENERATE_TODOLIST      = NO
- 
--# The GENERATE_TESTLIST tag can be used to enable (YES) or 
--# disable (NO) the test list. This list is created by putting \test 
-+# The GENERATE_TESTLIST tag can be used to enable (YES) or
-+# disable (NO) the test list. This list is created by putting \test
- # commands in the documentation.
- 
- GENERATE_TESTLIST      = NO
- 
--# The GENERATE_BUGLIST tag can be used to enable (YES) or 
--# disable (NO) the bug list. This list is created by putting \bug 
-+# The GENERATE_BUGLIST tag can be used to enable (YES) or
-+# disable (NO) the bug list. This list is created by putting \bug
- # commands in the documentation.
- 
- GENERATE_BUGLIST       = NO
- 
--# The GENERATE_DEPRECATEDLIST tag can be used to enable (YES) or 
--# disable (NO) the deprecated list. This list is created by putting 
-+# The GENERATE_DEPRECATEDLIST tag can be used to enable (YES) or
-+# disable (NO) the deprecated list. This list is created by putting
- # \deprecated commands in the documentation.
- 
- GENERATE_DEPRECATEDLIST= YES
- 
--# The ENABLED_SECTIONS tag can be used to enable conditional 
-+# The ENABLED_SECTIONS tag can be used to enable conditional
- # documentation sections, marked by \if sectionname ... \endif.
- 
--ENABLED_SECTIONS       = # MODULE_DCMJP2K MODULE_DCMPPS MODULE_DCMSTCOM MODULE_DCMRT
-+ENABLED_SECTIONS       =
- 
--# The MAX_INITIALIZER_LINES tag determines the maximum number of lines 
--# the initial value of a variable or define consists of for it to appear in 
--# the documentation. If the initializer consists of more lines than specified 
--# here it will be hidden. Use a value of 0 to hide initializers completely. 
--# The appearance of the initializer of individual variables and defines in the 
--# documentation can be controlled using \showinitializer or \hideinitializer 
-+# The MAX_INITIALIZER_LINES tag determines the maximum number of lines
-+# the initial value of a variable or define consists of for it to appear in
-+# the documentation. If the initializer consists of more lines than specified
-+# here it will be hidden. Use a value of 0 to hide initializers completely.
-+# The appearance of the initializer of individual variables and defines in the
-+# documentation can be controlled using \showinitializer or \hideinitializer
- # command in the documentation regardless of this setting.
- 
- MAX_INITIALIZER_LINES  = 30
- 
--# Set the SHOW_USED_FILES tag to NO to disable the list of files generated 
--# at the bottom of the documentation of classes and structs. If set to YES the 
-+# Set the SHOW_USED_FILES tag to NO to disable the list of files generated
-+# at the bottom of the documentation of classes and structs. If set to YES the
- # list will mention the files that were used to generate the documentation.
- 
- SHOW_USED_FILES        = YES
- 
--# If the sources in your project are distributed over multiple directories 
--# then setting the SHOW_DIRECTORIES tag to YES will show the directory hierarchy 
-+# If the sources in your project are distributed over multiple directories
-+# then setting the SHOW_DIRECTORIES tag to YES will show the directory hierarchy
- # in the documentation. The default is NO.
- 
- SHOW_DIRECTORIES       = NO
- 
--# The FILE_VERSION_FILTER tag can be used to specify a program or script that 
--# doxygen should invoke to get the current version for each file (typically from the 
--# version control system). Doxygen will invoke the program by executing (via 
--# popen()) the command <command> <input-file>, where <command> is the value of 
--# the FILE_VERSION_FILTER tag, and <input-file> is the name of an input file 
--# provided by doxygen. Whatever the program writes to standard output 
-+# Set the SHOW_FILES tag to NO to disable the generation of the Files page.
-+# This will remove the Files entry from the Quick Index and from the
-+# Folder Tree View (if specified). The default is YES.
-+
-+SHOW_FILES             = YES
-+
-+# Set the SHOW_NAMESPACES tag to NO to disable the generation of the
-+# Namespaces page.
-+# This will remove the Namespaces entry from the Quick Index
-+# and from the Folder Tree View (if specified). The default is YES.
-+
-+SHOW_NAMESPACES        = YES
-+
-+# The FILE_VERSION_FILTER tag can be used to specify a program or script that
-+# doxygen should invoke to get the current version for each file (typically from
-+# the version control system). Doxygen will invoke the program by executing (via
-+# popen()) the command <command> <input-file>, where <command> is the value of
-+# the FILE_VERSION_FILTER tag, and <input-file> is the name of an input file
-+# provided by doxygen. Whatever the program writes to standard output
- # is used as the file version. See the manual for examples.
- 
--FILE_VERSION_FILTER    = 
-+FILE_VERSION_FILTER    =
-+
-+# The LAYOUT_FILE tag can be used to specify a layout file which will be parsed
-+# by doxygen. The layout file controls the global structure of the generated
-+# output files in an output format independent way. The create the layout file
-+# that represents doxygen's defaults, run doxygen with the -l option.
-+# You can optionally specify a file name after the option, if omitted
-+# DoxygenLayout.xml will be used as the name of the layout file.
-+
-+LAYOUT_FILE            =
- 
- #---------------------------------------------------------------------------
- # configuration options related to warning and progress messages
- #---------------------------------------------------------------------------
- 
--# The QUIET tag can be used to turn on/off the messages that are generated 
-+# The QUIET tag can be used to turn on/off the messages that are generated
- # by doxygen. Possible values are YES and NO. If left blank NO is used.
- 
- QUIET                  = NO
- 
--# The WARNINGS tag can be used to turn on/off the warning messages that are 
--# generated by doxygen. Possible values are YES and NO. If left blank 
-+# The WARNINGS tag can be used to turn on/off the warning messages that are
-+# generated by doxygen. Possible values are YES and NO. If left blank
- # NO is used.
- 
- WARNINGS               = YES
- 
--# If WARN_IF_UNDOCUMENTED is set to YES, then doxygen will generate warnings 
--# for undocumented members. If EXTRACT_ALL is set to YES then this flag will 
-+# If WARN_IF_UNDOCUMENTED is set to YES, then doxygen will generate warnings
-+# for undocumented members. If EXTRACT_ALL is set to YES then this flag will
- # automatically be disabled.
- 
- WARN_IF_UNDOCUMENTED   = YES
- 
--# If WARN_IF_DOC_ERROR is set to YES, doxygen will generate warnings for 
--# potential errors in the documentation, such as not documenting some 
--# parameters in a documented function, or documenting parameters that 
-+# If WARN_IF_DOC_ERROR is set to YES, doxygen will generate warnings for
-+# potential errors in the documentation, such as not documenting some
-+# parameters in a documented function, or documenting parameters that
- # don't exist or using markup commands wrongly.
- 
- WARN_IF_DOC_ERROR      = YES
- 
--# This WARN_NO_PARAMDOC option can be abled to get warnings for 
--# functions that are documented, but have no documentation for their parameters 
--# or return value. If set to NO (the default) doxygen will only warn about 
--# wrong or incomplete parameter documentation, but not about the absence of 
-+# This WARN_NO_PARAMDOC option can be abled to get warnings for
-+# functions that are documented, but have no documentation for their parameters
-+# or return value. If set to NO (the default) doxygen will only warn about
-+# wrong or incomplete parameter documentation, but not about the absence of
- # documentation.
- 
- WARN_NO_PARAMDOC       = NO
- 
--# The WARN_FORMAT tag determines the format of the warning messages that 
--# doxygen can produce. The string should contain the $file, $line, and $text 
--# tags, which will be replaced by the file and line number from which the 
--# warning originated and the warning text. Optionally the format may contain 
--# $version, which will be replaced by the version of the file (if it could 
-+# The WARN_FORMAT tag determines the format of the warning messages that
-+# doxygen can produce. The string should contain the $file, $line, and $text
-+# tags, which will be replaced by the file and line number from which the
-+# warning originated and the warning text. Optionally the format may contain
-+# $version, which will be replaced by the version of the file (if it could
- # be obtained via FILE_VERSION_FILTER)
- 
- WARN_FORMAT            = "$file:$line: $text"
- 
--# The WARN_LOGFILE tag can be used to specify a file to which warning 
--# and error messages should be written. If left blank the output is written 
-+# The WARN_LOGFILE tag can be used to specify a file to which warning
-+# and error messages should be written. If left blank the output is written
- # to stderr.
- 
- WARN_LOGFILE           = htmldocs.log
-@@ -454,98 +576,117 @@
- # configuration options related to the input files
- #---------------------------------------------------------------------------
- 
--# The INPUT tag can be used to specify the files and/or directories that contain 
--# documented source files. You may enter file names like "myfile.cpp" or 
--# directories like "/usr/src/myproject". Separate the files or directories 
-+# The INPUT tag can be used to specify the files and/or directories that contain
-+# documented source files. You may enter file names like "myfile.cpp" or
-+# directories like "/usr/src/myproject". Separate the files or directories
- # with spaces.
- 
- INPUT                  = @DOXYGEN_INPUT_DIR@
- 
--# If the value of the INPUT tag contains directories, you can use the 
--# FILE_PATTERNS tag to specify one or more wildcard pattern (like *.cpp 
--# and *.h) to filter out the source-files in the directories. If left 
--# blank the following patterns are tested: 
--# *.c *.cc *.cxx *.cpp *.c++ *.java *.ii *.ixx *.ipp *.i++ *.inl *.h *.hh *.hxx 
--# *.hpp *.h++ *.idl *.odl *.cs *.php *.php3 *.inc *.m *.mm *.py
-+# This tag can be used to specify the character encoding of the source files
-+# that doxygen parses. Internally doxygen uses the UTF-8 encoding, which is
-+# also the default input encoding. Doxygen uses libiconv (or the iconv built
-+# into libc) for the transcoding. See http://www.gnu.org/software/libiconv for
-+# the list of possible encodings.
-+
-+INPUT_ENCODING         = UTF-8
-+
-+# If the value of the INPUT tag contains directories, you can use the
-+# FILE_PATTERNS tag to specify one or more wildcard pattern (like *.cpp
-+# and *.h) to filter out the source-files in the directories. If left
-+# blank the following patterns are tested:
-+# *.c *.cc *.cxx *.cpp *.c++ *.java *.ii *.ixx *.ipp *.i++ *.inl *.h *.hh *.hxx
-+# *.hpp *.h++ *.idl *.odl *.cs *.php *.php3 *.inc *.m *.mm *.py *.f90
- 
- FILE_PATTERNS          = *.h \
-                          *.man \
-                          *.dox
- 
--# The RECURSIVE tag can be used to turn specify whether or not subdirectories 
--# should be searched for input files as well. Possible values are YES and NO. 
-+# The RECURSIVE tag can be used to turn specify whether or not subdirectories
-+# should be searched for input files as well. Possible values are YES and NO.
- # If left blank NO is used.
- 
- RECURSIVE              = YES
- 
--# The EXCLUDE tag can be used to specify files and/or directories that should 
--# excluded from the INPUT source files. This way you can easily exclude a 
-+# The EXCLUDE tag can be used to specify files and/or directories that should
-+# excluded from the INPUT source files. This way you can easily exclude a
- # subdirectory from a directory tree whose root is specified with the INPUT tag.
- 
- EXCLUDE                = @DOXYGEN_INPUT_DIR@/config/include \
-                          @DOXYGEN_INPUT_DIR@/docs
- 
--# The EXCLUDE_SYMLINKS tag can be used select whether or not files or 
--# directories that are symbolic links (a Unix filesystem feature) are excluded 
-+# The EXCLUDE_SYMLINKS tag can be used select whether or not files or
-+# directories that are symbolic links (a Unix filesystem feature) are excluded
- # from the input.
- 
- EXCLUDE_SYMLINKS       = NO
- 
--# If the value of the INPUT tag contains directories, you can use the 
--# EXCLUDE_PATTERNS tag to specify one or more wildcard patterns to exclude 
--# certain files from those directories. Note that the wildcards are matched 
--# against the file with absolute path, so to exclude all test directories 
-+# If the value of the INPUT tag contains directories, you can use the
-+# EXCLUDE_PATTERNS tag to specify one or more wildcard patterns to exclude
-+# certain files from those directories. Note that the wildcards are matched
-+# against the file with absolute path, so to exclude all test directories
- # for example use the pattern */test/*
- 
--EXCLUDE_PATTERNS       = 
-+EXCLUDE_PATTERNS       =
-+
-+# The EXCLUDE_SYMBOLS tag can be used to specify one or more symbol names
-+# (namespaces, classes, functions, etc.) that should be excluded from the
-+# output. The symbol name can be a fully qualified name, a word, or if the
-+# wildcard * is used, a substring. Examples: ANamespace, AClass,
-+# AClass::ANamespace, ANamespace::*Test
-+
-+EXCLUDE_SYMBOLS        =
- 
--# The EXAMPLE_PATH tag can be used to specify one or more files or 
--# directories that contain example code fragments that are included (see 
-+# The EXAMPLE_PATH tag can be used to specify one or more files or
-+# directories that contain example code fragments that are included (see
- # the \include command).
- 
- EXAMPLE_PATH           = @DOXYGEN_INPUT_DIR@
- 
--# If the value of the EXAMPLE_PATH tag contains directories, you can use the 
--# EXAMPLE_PATTERNS tag to specify one or more wildcard pattern (like *.cpp 
--# and *.h) to filter out the source-files in the directories. If left 
-+# If the value of the EXAMPLE_PATH tag contains directories, you can use the
-+# EXAMPLE_PATTERNS tag to specify one or more wildcard pattern (like *.cpp
-+# and *.h) to filter out the source-files in the directories. If left
- # blank all files are included.
- 
--EXAMPLE_PATTERNS       = 
-+EXAMPLE_PATTERNS       =
- 
--# If the EXAMPLE_RECURSIVE tag is set to YES then subdirectories will be 
--# searched for input files to be used with the \include or \dontinclude 
--# commands irrespective of the value of the RECURSIVE tag. 
-+# If the EXAMPLE_RECURSIVE tag is set to YES then subdirectories will be
-+# searched for input files to be used with the \include or \dontinclude
-+# commands irrespective of the value of the RECURSIVE tag.
- # Possible values are YES and NO. If left blank NO is used.
- 
- EXAMPLE_RECURSIVE      = YES
- 
--# The IMAGE_PATH tag can be used to specify one or more files or 
--# directories that contain image that are included in the documentation (see 
-+# The IMAGE_PATH tag can be used to specify one or more files or
-+# directories that contain image that are included in the documentation (see
- # the \image command).
- 
--IMAGE_PATH             = 
-+IMAGE_PATH             =
- 
--# The INPUT_FILTER tag can be used to specify a program that doxygen should 
--# invoke to filter for each input file. Doxygen will invoke the filter program 
--# by executing (via popen()) the command <filter> <input-file>, where <filter> 
--# is the value of the INPUT_FILTER tag, and <input-file> is the name of an 
--# input file. Doxygen will then use the output that the filter program writes 
--# to standard output.  If FILTER_PATTERNS is specified, this tag will be 
-+# The INPUT_FILTER tag can be used to specify a program that doxygen should
-+# invoke to filter for each input file. Doxygen will invoke the filter program
-+# by executing (via popen()) the command <filter> <input-file>, where <filter>
-+# is the value of the INPUT_FILTER tag, and <input-file> is the name of an
-+# input file. Doxygen will then use the output that the filter program writes
-+# to standard output.
-+# If FILTER_PATTERNS is specified, this tag will be
- # ignored.
- 
--INPUT_FILTER           = 
-+INPUT_FILTER           =
- 
--# The FILTER_PATTERNS tag can be used to specify filters on a per file pattern 
--# basis.  Doxygen will compare the file name with each pattern and apply the 
--# filter if there is a match.  The filters are a list of the form: 
--# pattern=filter (like *.cpp=my_cpp_filter). See INPUT_FILTER for further 
--# info on how filters are used. If FILTER_PATTERNS is empty, INPUT_FILTER 
-+# The FILTER_PATTERNS tag can be used to specify filters on a per file pattern
-+# basis.
-+# Doxygen will compare the file name with each pattern and apply the
-+# filter if there is a match.
-+# The filters are a list of the form:
-+# pattern=filter (like *.cpp=my_cpp_filter). See INPUT_FILTER for further
-+# info on how filters are used. If FILTER_PATTERNS is empty, INPUT_FILTER
- # is applied to all files.
- 
--FILTER_PATTERNS        = 
-+FILTER_PATTERNS        =
- 
--# If the FILTER_SOURCE_FILES tag is set to YES, the input filter (if set using 
--# INPUT_FILTER) will be used to filter the input files when producing source 
-+# If the FILTER_SOURCE_FILES tag is set to YES, the input filter (if set using
-+# INPUT_FILTER) will be used to filter the input files when producing source
- # files to browse (i.e. when SOURCE_BROWSER is set to YES).
- 
- FILTER_SOURCE_FILES    = NO
-@@ -554,32 +695,32 @@
- # configuration options related to source browsing
- #---------------------------------------------------------------------------
- 
--# If the SOURCE_BROWSER tag is set to YES then a list of source files will 
--# be generated. Documented entities will be cross-referenced with these sources. 
--# Note: To get rid of all source code in the generated output, make sure also 
-+# If the SOURCE_BROWSER tag is set to YES then a list of source files will
-+# be generated. Documented entities will be cross-referenced with these sources.
-+# Note: To get rid of all source code in the generated output, make sure also
- # VERBATIM_HEADERS is set to NO.
- 
- SOURCE_BROWSER         = YES
- 
--# Setting the INLINE_SOURCES tag to YES will include the body 
-+# Setting the INLINE_SOURCES tag to YES will include the body
- # of functions and classes directly in the documentation.
- 
- INLINE_SOURCES         = NO
- 
--# Setting the STRIP_CODE_COMMENTS tag to YES (the default) will instruct 
--# doxygen to hide any special comment blocks from generated source code 
-+# Setting the STRIP_CODE_COMMENTS tag to YES (the default) will instruct
-+# doxygen to hide any special comment blocks from generated source code
- # fragments. Normal C and C++ comments will always remain visible.
- 
- STRIP_CODE_COMMENTS    = YES
- 
--# If the REFERENCED_BY_RELATION tag is set to YES (the default) 
--# then for each documented function all documented 
-+# If the REFERENCED_BY_RELATION tag is set to YES
-+# then for each documented function all documented
- # functions referencing it will be listed.
- 
- REFERENCED_BY_RELATION = YES
- 
--# If the REFERENCES_RELATION tag is set to YES (the default) 
--# then for each documented function all documented entities 
-+# If the REFERENCES_RELATION tag is set to YES
-+# then for each documented function all documented entities
- # called/used by that function will be listed.
- 
- REFERENCES_RELATION    = YES
-@@ -587,20 +728,21 @@
- # If the REFERENCES_LINK_SOURCE tag is set to YES (the default)
- # and SOURCE_BROWSER tag is set to YES, then the hyperlinks from
- # functions in REFERENCES_RELATION and REFERENCED_BY_RELATION lists will
--# link to the source code.  Otherwise they will link to the documentation.
-+# link to the source code.
-+# Otherwise they will link to the documentation.
- 
- REFERENCES_LINK_SOURCE = YES
- 
--# If the USE_HTAGS tag is set to YES then the references to source code 
--# will point to the HTML generated by the htags(1) tool instead of doxygen 
--# built-in source browser. The htags tool is part of GNU's global source 
--# tagging system (see http://www.gnu.org/software/global/global.html). You 
-+# If the USE_HTAGS tag is set to YES then the references to source code
-+# will point to the HTML generated by the htags(1) tool instead of doxygen
-+# built-in source browser. The htags tool is part of GNU's global source
-+# tagging system (see http://www.gnu.org/software/global/global.html). You
- # will need version 4.8.6 or higher.
- 
- USE_HTAGS              = NO
- 
--# If the VERBATIM_HEADERS tag is set to YES (the default) then Doxygen 
--# will generate a verbatim copy of the header file for each class for 
-+# If the VERBATIM_HEADERS tag is set to YES (the default) then Doxygen
-+# will generate a verbatim copy of the header file for each class for
- # which an include is specified. Set to NO to disable this.
- 
- VERBATIM_HEADERS       = YES
-@@ -609,279 +751,488 @@
- # configuration options related to the alphabetical class index
- #---------------------------------------------------------------------------
- 
--# If the ALPHABETICAL_INDEX tag is set to YES, an alphabetical index 
--# of all compounds will be generated. Enable this if the project 
-+# If the ALPHABETICAL_INDEX tag is set to YES, an alphabetical index
-+# of all compounds will be generated. Enable this if the project
- # contains a lot of classes, structs, unions or interfaces.
- 
- ALPHABETICAL_INDEX     = YES
- 
--# If the alphabetical index is enabled (see ALPHABETICAL_INDEX) then 
--# the COLS_IN_ALPHA_INDEX tag can be used to specify the number of columns 
-+# If the alphabetical index is enabled (see ALPHABETICAL_INDEX) then
-+# the COLS_IN_ALPHA_INDEX tag can be used to specify the number of columns
- # in which this list will be split (can be a number in the range [1..20])
- 
- COLS_IN_ALPHA_INDEX    = 3
- 
--# In case all classes in a project start with a common prefix, all 
--# classes will be put under the same header in the alphabetical index. 
--# The IGNORE_PREFIX tag can be used to specify one or more prefixes that 
-+# In case all classes in a project start with a common prefix, all
-+# classes will be put under the same header in the alphabetical index.
-+# The IGNORE_PREFIX tag can be used to specify one or more prefixes that
- # should be ignored while generating the index headers.
- 
--IGNORE_PREFIX          = 
-+IGNORE_PREFIX          =
- 
- #---------------------------------------------------------------------------
- # configuration options related to the HTML output
- #---------------------------------------------------------------------------
- 
--# If the GENERATE_HTML tag is set to YES (the default) Doxygen will 
-+# If the GENERATE_HTML tag is set to YES (the default) Doxygen will
- # generate HTML output.
- 
- GENERATE_HTML          = YES
- 
--# The HTML_OUTPUT tag is used to specify where the HTML docs will be put. 
--# If a relative path is entered the value of OUTPUT_DIRECTORY will be 
-+# The HTML_OUTPUT tag is used to specify where the HTML docs will be put.
-+# If a relative path is entered the value of OUTPUT_DIRECTORY will be
- # put in front of it. If left blank `html' will be used as the default path.
- 
- HTML_OUTPUT            = htmldocs
- 
--# The HTML_FILE_EXTENSION tag can be used to specify the file extension for 
--# each generated HTML page (for example: .htm,.php,.asp). If it is left blank 
-+# The HTML_FILE_EXTENSION tag can be used to specify the file extension for
-+# each generated HTML page (for example: .htm,.php,.asp). If it is left blank
- # doxygen will generate files with .html extension.
- 
- HTML_FILE_EXTENSION    = .html
- 
--# The HTML_HEADER tag can be used to specify a personal HTML header for 
--# each generated HTML page. If it is left blank doxygen will generate a 
-+# The HTML_HEADER tag can be used to specify a personal HTML header for
-+# each generated HTML page. If it is left blank doxygen will generate a
- # standard header.
- 
--HTML_HEADER            = 
-+HTML_HEADER            =
- 
--# The HTML_FOOTER tag can be used to specify a personal HTML footer for 
--# each generated HTML page. If it is left blank doxygen will generate a 
-+# The HTML_FOOTER tag can be used to specify a personal HTML footer for
-+# each generated HTML page. If it is left blank doxygen will generate a
- # standard footer.
- 
- HTML_FOOTER            = @DOXYGEN_DATA_DIR@/footer.html
- 
--# The HTML_STYLESHEET tag can be used to specify a user-defined cascading 
--# style sheet that is used by each HTML page. It can be used to 
--# fine-tune the look of the HTML output. If the tag is left blank doxygen 
--# will generate a default style sheet. Note that doxygen will try to copy 
--# the style sheet file to the HTML output directory, so don't put your own 
-+# The HTML_STYLESHEET tag can be used to specify a user-defined cascading
-+# style sheet that is used by each HTML page. It can be used to
-+# fine-tune the look of the HTML output. If the tag is left blank doxygen
-+# will generate a default style sheet. Note that doxygen will try to copy
-+# the style sheet file to the HTML output directory, so don't put your own
- # stylesheet in the HTML output directory as well, or it will be erased!
- 
--HTML_STYLESHEET        = 
-+HTML_STYLESHEET        =
-+
-+# The HTML_COLORSTYLE_HUE tag controls the color of the HTML output.
-+# Doxygen will adjust the colors in the stylesheet and background images
-+# according to this color. Hue is specified as an angle on a colorwheel,
-+# see http://en.wikipedia.org/wiki/Hue for more information.
-+# For instance the value 0 represents red, 60 is yellow, 120 is green,
-+# 180 is cyan, 240 is blue, 300 purple, and 360 is red again.
-+# The allowed range is 0 to 359.
-+
-+HTML_COLORSTYLE_HUE    = 220
-+
-+# The HTML_COLORSTYLE_SAT tag controls the purity (or saturation) of
-+# the colors in the HTML output. For a value of 0 the output will use
-+# grayscales only. A value of 255 will produce the most vivid colors.
- 
--# If the HTML_ALIGN_MEMBERS tag is set to YES, the members of classes, 
--# files or namespaces will be aligned in HTML using tables. If set to 
-+HTML_COLORSTYLE_SAT    = 100
-+
-+# The HTML_COLORSTYLE_GAMMA tag controls the gamma correction applied to
-+# the luminance component of the colors in the HTML output. Values below
-+# 100 gradually make the output lighter, whereas values above 100 make
-+# the output darker. The value divided by 100 is the actual gamma applied,
-+# so 80 represents a gamma of 0.8, The value 220 represents a gamma of 2.2,
-+# and 100 does not change the gamma.
-+
-+HTML_COLORSTYLE_GAMMA  = 80
-+
-+# If the HTML_TIMESTAMP tag is set to YES then the footer of each generated HTML
-+# page will contain the date and time when the page was generated. Setting
-+# this to NO can help when comparing the output of multiple runs.
-+
-+HTML_TIMESTAMP         = YES
-+
-+# If the HTML_ALIGN_MEMBERS tag is set to YES, the members of classes,
-+# files or namespaces will be aligned in HTML using tables. If set to
- # NO a bullet list will be used.
- 
- HTML_ALIGN_MEMBERS     = YES
- 
--# If the GENERATE_HTMLHELP tag is set to YES, additional index files 
--# will be generated that can be used as input for tools like the 
--# Microsoft HTML help workshop to generate a compressed HTML help file (.chm) 
-+# If the HTML_DYNAMIC_SECTIONS tag is set to YES then the generated HTML
-+# documentation will contain sections that can be hidden and shown after the
-+# page has loaded. For this to work a browser that supports
-+# JavaScript and DHTML is required (for instance Mozilla 1.0+, Firefox
-+# Netscape 6.0+, Internet explorer 5.0+, Konqueror, or Safari).
-+
-+HTML_DYNAMIC_SECTIONS  = NO
-+
-+# If the GENERATE_DOCSET tag is set to YES, additional index files
-+# will be generated that can be used as input for Apple's Xcode 3
-+# integrated development environment, introduced with OSX 10.5 (Leopard).
-+# To create a documentation set, doxygen will generate a Makefile in the
-+# HTML output directory. Running make will produce the docset in that
-+# directory and running "make install" will install the docset in
-+# ~/Library/Developer/Shared/Documentation/DocSets so that Xcode will find
-+# it at startup.
-+# See http://developer.apple.com/tools/creatingdocsetswithdoxygen.html
-+# for more information.
-+
-+GENERATE_DOCSET        = NO
-+
-+# When GENERATE_DOCSET tag is set to YES, this tag determines the name of the
-+# feed. A documentation feed provides an umbrella under which multiple
-+# documentation sets from a single provider (such as a company or product suite)
-+# can be grouped.
-+
-+DOCSET_FEEDNAME        = "Doxygen generated docs"
-+
-+# When GENERATE_DOCSET tag is set to YES, this tag specifies a string that
-+# should uniquely identify the documentation set bundle. This should be a
-+# reverse domain-name style string, e.g. com.mycompany.MyDocSet. Doxygen
-+# will append .docset to the name.
-+
-+DOCSET_BUNDLE_ID       = org.doxygen.Project
-+
-+# When GENERATE_PUBLISHER_ID tag specifies a string that should uniquely identify
-+# the documentation publisher. This should be a reverse domain-name style
-+# string, e.g. com.mycompany.MyDocSet.documentation.
-+
-+DOCSET_PUBLISHER_ID    = org.doxygen.Publisher
-+
-+# The GENERATE_PUBLISHER_NAME tag identifies the documentation publisher.
-+
-+DOCSET_PUBLISHER_NAME  = Publisher
-+
-+# If the GENERATE_HTMLHELP tag is set to YES, additional index files
-+# will be generated that can be used as input for tools like the
-+# Microsoft HTML help workshop to generate a compiled HTML help file (.chm)
- # of the generated HTML documentation.
- 
- GENERATE_HTMLHELP      = NO
- 
--# If the GENERATE_HTMLHELP tag is set to YES, the CHM_FILE tag can 
--# be used to specify the file name of the resulting .chm file. You 
--# can add a path in front of the file if the result should not be 
-+# If the GENERATE_HTMLHELP tag is set to YES, the CHM_FILE tag can
-+# be used to specify the file name of the resulting .chm file. You
-+# can add a path in front of the file if the result should not be
- # written to the html output directory.
- 
- CHM_FILE               = dcmtk354.chm
- 
--# If the GENERATE_HTMLHELP tag is set to YES, the HHC_LOCATION tag can 
--# be used to specify the location (absolute path including file name) of 
--# the HTML help compiler (hhc.exe). If non-empty doxygen will try to run 
-+# If the GENERATE_HTMLHELP tag is set to YES, the HHC_LOCATION tag can
-+# be used to specify the location (absolute path including file name) of
-+# the HTML help compiler (hhc.exe). If non-empty doxygen will try to run
- # the HTML help compiler on the generated index.hhp.
- 
--HHC_LOCATION           = 
-+HHC_LOCATION           =
- 
--# If the GENERATE_HTMLHELP tag is set to YES, the GENERATE_CHI flag 
--# controls if a separate .chi index file is generated (YES) or that 
-+# If the GENERATE_HTMLHELP tag is set to YES, the GENERATE_CHI flag
-+# controls if a separate .chi index file is generated (YES) or that
- # it should be included in the master .chm file (NO).
- 
- GENERATE_CHI           = NO
- 
--# If the GENERATE_HTMLHELP tag is set to YES, the BINARY_TOC flag 
--# controls whether a binary table of contents is generated (YES) or a 
-+# If the GENERATE_HTMLHELP tag is set to YES, the CHM_INDEX_ENCODING
-+# is used to encode HtmlHelp index (hhk), content (hhc) and project file
-+# content.
-+
-+CHM_INDEX_ENCODING     =
-+
-+# If the GENERATE_HTMLHELP tag is set to YES, the BINARY_TOC flag
-+# controls whether a binary table of contents is generated (YES) or a
- # normal table of contents (NO) in the .chm file.
- 
- BINARY_TOC             = NO
- 
--# The TOC_EXPAND flag can be set to YES to add extra items for group members 
-+# The TOC_EXPAND flag can be set to YES to add extra items for group members
- # to the contents of the HTML help documentation and to the tree view.
- 
- TOC_EXPAND             = YES
- 
--# The DISABLE_INDEX tag can be used to turn on/off the condensed index at 
--# top of each HTML page. The value NO (the default) enables the index and 
-+# If the GENERATE_QHP tag is set to YES and both QHP_NAMESPACE and
-+# QHP_VIRTUAL_FOLDER are set, an additional index file will be generated
-+# that can be used as input for Qt's qhelpgenerator to generate a
-+# Qt Compressed Help (.qch) of the generated HTML documentation.
-+
-+GENERATE_QHP           = NO
-+
-+# If the QHG_LOCATION tag is specified, the QCH_FILE tag can
-+# be used to specify the file name of the resulting .qch file.
-+# The path specified is relative to the HTML output folder.
-+
-+QCH_FILE               =
-+
-+# The QHP_NAMESPACE tag specifies the namespace to use when generating
-+# Qt Help Project output. For more information please see
-+# http://doc.trolltech.com/qthelpproject.html#namespace
-+
-+QHP_NAMESPACE          = org.doxygen.Project
-+
-+# The QHP_VIRTUAL_FOLDER tag specifies the namespace to use when generating
-+# Qt Help Project output. For more information please see
-+# http://doc.trolltech.com/qthelpproject.html#virtual-folders
-+
-+QHP_VIRTUAL_FOLDER     = doc
-+
-+# If QHP_CUST_FILTER_NAME is set, it specifies the name of a custom filter to
-+# add. For more information please see
-+# http://doc.trolltech.com/qthelpproject.html#custom-filters
-+
-+QHP_CUST_FILTER_NAME   =
-+
-+# The QHP_CUST_FILT_ATTRS tag specifies the list of the attributes of the
-+# custom filter to add. For more information please see
-+# <a href="http://doc.trolltech.com/qthelpproject.html#custom-filters">
-+# Qt Help Project / Custom Filters</a>.
-+
-+QHP_CUST_FILTER_ATTRS  =
-+
-+# The QHP_SECT_FILTER_ATTRS tag specifies the list of the attributes this
-+# project's
-+# filter section matches.
-+# <a href="http://doc.trolltech.com/qthelpproject.html#filter-attributes">
-+# Qt Help Project / Filter Attributes</a>.
-+
-+QHP_SECT_FILTER_ATTRS  =
-+
-+# If the GENERATE_QHP tag is set to YES, the QHG_LOCATION tag can
-+# be used to specify the location of Qt's qhelpgenerator.
-+# If non-empty doxygen will try to run qhelpgenerator on the generated
-+# .qhp file.
-+
-+QHG_LOCATION           =
-+
-+# If the GENERATE_ECLIPSEHELP tag is set to YES, additional index files
-+#  will be generated, which together with the HTML files, form an Eclipse help
-+# plugin. To install this plugin and make it available under the help contents
-+# menu in Eclipse, the contents of the directory containing the HTML and XML
-+# files needs to be copied into the plugins directory of eclipse. The name of
-+# the directory within the plugins directory should be the same as
-+# the ECLIPSE_DOC_ID value. After copying Eclipse needs to be restarted before
-+# the help appears.
-+
-+GENERATE_ECLIPSEHELP   = NO
-+
-+# A unique identifier for the eclipse help plugin. When installing the plugin
-+# the directory name containing the HTML and XML files should also have
-+# this name.
-+
-+ECLIPSE_DOC_ID         = org.doxygen.Project
-+
-+# The DISABLE_INDEX tag can be used to turn on/off the condensed index at
-+# top of each HTML page. The value NO (the default) enables the index and
- # the value YES disables it.
- 
- DISABLE_INDEX          = NO
- 
--# This tag can be used to set the number of enum values (range [1..20]) 
-+# This tag can be used to set the number of enum values (range [1..20])
- # that doxygen will group on one line in the generated HTML documentation.
- 
- ENUM_VALUES_PER_LINE   = 4
- 
--# If the GENERATE_TREEVIEW tag is set to YES, a side panel will be
--# generated containing a tree-like index structure (just like the one that 
--# is generated for HTML Help). For this to work a browser that supports 
--# JavaScript, DHTML, CSS and frames is required (for instance Mozilla 1.0+, 
--# Netscape 6.0+, Internet explorer 5.0+, or Konqueror). Windows users are 
--# probably better off using the HTML help feature.
-+# The GENERATE_TREEVIEW tag is used to specify whether a tree-like index
-+# structure should be generated to display hierarchical information.
-+# If the tag value is set to YES, a side panel will be generated
-+# containing a tree-like index structure (just like the one that
-+# is generated for HTML Help). For this to work a browser that supports
-+# JavaScript, DHTML, CSS and frames is required (i.e. any modern browser).
-+# Windows users are probably better off using the HTML help feature.
- 
- GENERATE_TREEVIEW      = NO
- 
--# If the treeview is enabled (see GENERATE_TREEVIEW) then this tag can be 
--# used to set the initial width (in pixels) of the frame in which the tree 
-+# By enabling USE_INLINE_TREES, doxygen will generate the Groups, Directories,
-+# and Class Hierarchy pages using a tree view instead of an ordered list.
-+
-+USE_INLINE_TREES       = NO
-+
-+# If the treeview is enabled (see GENERATE_TREEVIEW) then this tag can be
-+# used to set the initial width (in pixels) of the frame in which the tree
- # is shown.
- 
- TREEVIEW_WIDTH         = 250
- 
-+# When the EXT_LINKS_IN_WINDOW option is set to YES doxygen will open
-+# links to external symbols imported via tag files in a separate window.
-+
-+EXT_LINKS_IN_WINDOW    = NO
-+
-+# Use this tag to change the font size of Latex formulas included
-+# as images in the HTML documentation. The default is 10. Note that
-+# when you change the font size after a successful doxygen run you need
-+# to manually remove any form_*.png images from the HTML output directory
-+# to force them to be regenerated.
-+
-+FORMULA_FONTSIZE       = 10
-+
-+# Use the FORMULA_TRANPARENT tag to determine whether or not the images
-+# generated for formulas are transparent PNGs. Transparent PNGs are
-+# not supported properly for IE 6.0, but are supported on all modern browsers.
-+# Note that when changing this option you need to delete any form_*.png files
-+# in the HTML output before the changes have effect.
-+
-+FORMULA_TRANSPARENT    = YES
-+
-+# When the SEARCHENGINE tag is enabled doxygen will generate a search box
-+# for the HTML output. The underlying search engine uses javascript
-+# and DHTML and should work on any modern browser. Note that when using
-+# HTML help (GENERATE_HTMLHELP), Qt help (GENERATE_QHP), or docsets
-+# (GENERATE_DOCSET) there is already a search function so this one should
-+# typically be disabled. For large projects the javascript based search engine
-+# can be slow, then enabling SERVER_BASED_SEARCH may provide a better solution.
-+
-+SEARCHENGINE           = NO
-+
-+# When the SERVER_BASED_SEARCH tag is enabled the search engine will be
-+# implemented using a PHP enabled web server instead of at the web client
-+# using Javascript. Doxygen will generate the search PHP script and index
-+# file to put on the web server. The advantage of the server
-+# based approach is that it scales better to large projects and allows
-+# full text search. The disadvances is that it is more difficult to setup
-+# and does not have live searching capabilities.
-+
-+SERVER_BASED_SEARCH    = NO
-+
- #---------------------------------------------------------------------------
- # configuration options related to the LaTeX output
- #---------------------------------------------------------------------------
- 
--# If the GENERATE_LATEX tag is set to YES (the default) Doxygen will 
-+# If the GENERATE_LATEX tag is set to YES (the default) Doxygen will
- # generate Latex output.
- 
- GENERATE_LATEX         = NO
- 
--# The LATEX_OUTPUT tag is used to specify where the LaTeX docs will be put. 
--# If a relative path is entered the value of OUTPUT_DIRECTORY will be 
-+# The LATEX_OUTPUT tag is used to specify where the LaTeX docs will be put.
-+# If a relative path is entered the value of OUTPUT_DIRECTORY will be
- # put in front of it. If left blank `latex' will be used as the default path.
- 
- LATEX_OUTPUT           = latex
- 
--# The LATEX_CMD_NAME tag can be used to specify the LaTeX command name to be 
-+# The LATEX_CMD_NAME tag can be used to specify the LaTeX command name to be
- # invoked. If left blank `latex' will be used as the default command name.
-+# Note that when enabling USE_PDFLATEX this option is only used for
-+# generating bitmaps for formulas in the HTML output, but not in the
-+# Makefile that is written to the output directory.
- 
- LATEX_CMD_NAME         = latex
- 
--# The MAKEINDEX_CMD_NAME tag can be used to specify the command name to 
--# generate index for LaTeX. If left blank `makeindex' will be used as the 
-+# The MAKEINDEX_CMD_NAME tag can be used to specify the command name to
-+# generate index for LaTeX. If left blank `makeindex' will be used as the
- # default command name.
- 
- MAKEINDEX_CMD_NAME     = makeindex
- 
--# If the COMPACT_LATEX tag is set to YES Doxygen generates more compact 
--# LaTeX documents. This may be useful for small projects and may help to 
-+# If the COMPACT_LATEX tag is set to YES Doxygen generates more compact
-+# LaTeX documents. This may be useful for small projects and may help to
- # save some trees in general.
- 
- COMPACT_LATEX          = NO
- 
--# The PAPER_TYPE tag can be used to set the paper type that is used 
--# by the printer. Possible values are: a4, a4wide, letter, legal and 
-+# The PAPER_TYPE tag can be used to set the paper type that is used
-+# by the printer. Possible values are: a4, a4wide, letter, legal and
- # executive. If left blank a4wide will be used.
- 
- PAPER_TYPE             = a4wide
- 
--# The EXTRA_PACKAGES tag can be to specify one or more names of LaTeX 
-+# The EXTRA_PACKAGES tag can be to specify one or more names of LaTeX
- # packages that should be included in the LaTeX output.
- 
--EXTRA_PACKAGES         = 
-+EXTRA_PACKAGES         =
- 
--# The LATEX_HEADER tag can be used to specify a personal LaTeX header for 
--# the generated latex document. The header should contain everything until 
--# the first chapter. If it is left blank doxygen will generate a 
-+# The LATEX_HEADER tag can be used to specify a personal LaTeX header for
-+# the generated latex document. The header should contain everything until
-+# the first chapter. If it is left blank doxygen will generate a
- # standard header. Notice: only use this tag if you know what you are doing!
- 
--LATEX_HEADER           = 
-+LATEX_HEADER           =
- 
--# If the PDF_HYPERLINKS tag is set to YES, the LaTeX that is generated 
--# is prepared for conversion to pdf (using ps2pdf). The pdf file will 
--# contain links (just like the HTML output) instead of page references 
-+# If the PDF_HYPERLINKS tag is set to YES, the LaTeX that is generated
-+# is prepared for conversion to pdf (using ps2pdf). The pdf file will
-+# contain links (just like the HTML output) instead of page references
- # This makes the output suitable for online browsing using a pdf viewer.
- 
- PDF_HYPERLINKS         = YES
- 
--# If the USE_PDFLATEX tag is set to YES, pdflatex will be used instead of 
--# plain latex in the generated Makefile. Set this option to YES to get a 
-+# If the USE_PDFLATEX tag is set to YES, pdflatex will be used instead of
-+# plain latex in the generated Makefile. Set this option to YES to get a
- # higher quality PDF documentation.
- 
- USE_PDFLATEX           = NO
- 
--# If the LATEX_BATCHMODE tag is set to YES, doxygen will add the \\batchmode. 
--# command to the generated LaTeX files. This will instruct LaTeX to keep 
--# running if errors occur, instead of asking the user for help. 
-+# If the LATEX_BATCHMODE tag is set to YES, doxygen will add the \\batchmode.
-+# command to the generated LaTeX files. This will instruct LaTeX to keep
-+# running if errors occur, instead of asking the user for help.
- # This option is also used when generating formulas in HTML.
- 
- LATEX_BATCHMODE        = YES
- 
--# If LATEX_HIDE_INDICES is set to YES then doxygen will not 
--# include the index chapters (such as File Index, Compound Index, etc.) 
-+# If LATEX_HIDE_INDICES is set to YES then doxygen will not
-+# include the index chapters (such as File Index, Compound Index, etc.)
- # in the output.
- 
- LATEX_HIDE_INDICES     = NO
- 
-+# If LATEX_SOURCE_CODE is set to YES then doxygen will include
-+# source code with syntax highlighting in the LaTeX output.
-+# Note that which sources are shown also depends on other settings
-+# such as SOURCE_BROWSER.
-+
-+LATEX_SOURCE_CODE      = NO
-+
- #---------------------------------------------------------------------------
- # configuration options related to the RTF output
- #---------------------------------------------------------------------------
- 
--# If the GENERATE_RTF tag is set to YES Doxygen will generate RTF output 
--# The RTF output is optimized for Word 97 and may not look very pretty with 
-+# If the GENERATE_RTF tag is set to YES Doxygen will generate RTF output
-+# The RTF output is optimized for Word 97 and may not look very pretty with
- # other RTF readers or editors.
- 
- GENERATE_RTF           = NO
- 
--# The RTF_OUTPUT tag is used to specify where the RTF docs will be put. 
--# If a relative path is entered the value of OUTPUT_DIRECTORY will be 
-+# The RTF_OUTPUT tag is used to specify where the RTF docs will be put.
-+# If a relative path is entered the value of OUTPUT_DIRECTORY will be
- # put in front of it. If left blank `rtf' will be used as the default path.
- 
- RTF_OUTPUT             = rtf
- 
--# If the COMPACT_RTF tag is set to YES Doxygen generates more compact 
--# RTF documents. This may be useful for small projects and may help to 
-+# If the COMPACT_RTF tag is set to YES Doxygen generates more compact
-+# RTF documents. This may be useful for small projects and may help to
- # save some trees in general.
- 
- COMPACT_RTF            = NO
- 
--# If the RTF_HYPERLINKS tag is set to YES, the RTF that is generated 
--# will contain hyperlink fields. The RTF file will 
--# contain links (just like the HTML output) instead of page references. 
--# This makes the output suitable for online browsing using WORD or other 
--# programs which support those fields. 
-+# If the RTF_HYPERLINKS tag is set to YES, the RTF that is generated
-+# will contain hyperlink fields. The RTF file will
-+# contain links (just like the HTML output) instead of page references.
-+# This makes the output suitable for online browsing using WORD or other
-+# programs which support those fields.
- # Note: wordpad (write) and others do not support links.
- 
- RTF_HYPERLINKS         = NO
- 
--# Load stylesheet definitions from file. Syntax is similar to doxygen's 
--# config file, i.e. a series of assignments. You only have to provide 
-+# Load stylesheet definitions from file. Syntax is similar to doxygen's
-+# config file, i.e. a series of assignments. You only have to provide
- # replacements, missing definitions are set to their default value.
- 
--RTF_STYLESHEET_FILE    = 
-+RTF_STYLESHEET_FILE    =
- 
--# Set optional variables used in the generation of an rtf document. 
-+# Set optional variables used in the generation of an rtf document.
- # Syntax is similar to doxygen's config file.
- 
--RTF_EXTENSIONS_FILE    = 
-+RTF_EXTENSIONS_FILE    =
- 
- #---------------------------------------------------------------------------
- # configuration options related to the man page output
- #---------------------------------------------------------------------------
- 
--# If the GENERATE_MAN tag is set to YES (the default) Doxygen will 
-+# If the GENERATE_MAN tag is set to YES (the default) Doxygen will
- # generate man pages
- 
- GENERATE_MAN           = NO
- 
--# The MAN_OUTPUT tag is used to specify where the man pages will be put. 
--# If a relative path is entered the value of OUTPUT_DIRECTORY will be 
-+# The MAN_OUTPUT tag is used to specify where the man pages will be put.
-+# If a relative path is entered the value of OUTPUT_DIRECTORY will be
- # put in front of it. If left blank `man' will be used as the default path.
- 
- MAN_OUTPUT             = man
- 
--# The MAN_EXTENSION tag determines the extension that is added to 
-+# The MAN_EXTENSION tag determines the extension that is added to
- # the generated man pages (default is the subroutine's section .3)
- 
- MAN_EXTENSION          = .3
- 
--# If the MAN_LINKS tag is set to YES and Doxygen generates man output, 
--# then it will generate one additional man file for each entity 
--# documented in the real man page(s). These additional files 
--# only source the real man page, but without them the man command 
-+# If the MAN_LINKS tag is set to YES and Doxygen generates man output,
-+# then it will generate one additional man file for each entity
-+# documented in the real man page(s). These additional files
-+# only source the real man page, but without them the man command
- # would be unable to find the correct page. The default is NO.
- 
- MAN_LINKS              = NO
-@@ -890,33 +1241,33 @@
- # configuration options related to the XML output
- #---------------------------------------------------------------------------
- 
--# If the GENERATE_XML tag is set to YES Doxygen will 
--# generate an XML file that captures the structure of 
-+# If the GENERATE_XML tag is set to YES Doxygen will
-+# generate an XML file that captures the structure of
- # the code including all documentation.
- 
- GENERATE_XML           = NO
- 
--# The XML_OUTPUT tag is used to specify where the XML pages will be put. 
--# If a relative path is entered the value of OUTPUT_DIRECTORY will be 
-+# The XML_OUTPUT tag is used to specify where the XML pages will be put.
-+# If a relative path is entered the value of OUTPUT_DIRECTORY will be
- # put in front of it. If left blank `xml' will be used as the default path.
- 
- XML_OUTPUT             = xml
- 
--# The XML_SCHEMA tag can be used to specify an XML schema, 
--# which can be used by a validating XML parser to check the 
-+# The XML_SCHEMA tag can be used to specify an XML schema,
-+# which can be used by a validating XML parser to check the
- # syntax of the XML files.
- 
--XML_SCHEMA             = 
-+XML_SCHEMA             =
- 
--# The XML_DTD tag can be used to specify an XML DTD, 
--# which can be used by a validating XML parser to check the 
-+# The XML_DTD tag can be used to specify an XML DTD,
-+# which can be used by a validating XML parser to check the
- # syntax of the XML files.
- 
--XML_DTD                = 
-+XML_DTD                =
- 
--# If the XML_PROGRAMLISTING tag is set to YES Doxygen will 
--# dump the program listings (including syntax highlighting 
--# and cross-referencing information) to the XML output. Note that 
-+# If the XML_PROGRAMLISTING tag is set to YES Doxygen will
-+# dump the program listings (including syntax highlighting
-+# and cross-referencing information) to the XML output. Note that
- # enabling this will significantly increase the size of the XML output.
- 
- XML_PROGRAMLISTING     = YES
-@@ -925,10 +1276,10 @@
- # configuration options for the AutoGen Definitions output
- #---------------------------------------------------------------------------
- 
--# If the GENERATE_AUTOGEN_DEF tag is set to YES Doxygen will 
--# generate an AutoGen Definitions (see autogen.sf.net) file 
--# that captures the structure of the code including all 
--# documentation. Note that this feature is still experimental 
-+# If the GENERATE_AUTOGEN_DEF tag is set to YES Doxygen will
-+# generate an AutoGen Definitions (see autogen.sf.net) file
-+# that captures the structure of the code including all
-+# documentation. Note that this feature is still experimental
- # and incomplete at the moment.
- 
- GENERATE_AUTOGEN_DEF   = NO
-@@ -937,82 +1288,84 @@
- # configuration options related to the Perl module output
- #---------------------------------------------------------------------------
- 
--# If the GENERATE_PERLMOD tag is set to YES Doxygen will 
--# generate a Perl module file that captures the structure of 
--# the code including all documentation. Note that this 
--# feature is still experimental and incomplete at the 
-+# If the GENERATE_PERLMOD tag is set to YES Doxygen will
-+# generate a Perl module file that captures the structure of
-+# the code including all documentation. Note that this
-+# feature is still experimental and incomplete at the
- # moment.
- 
- GENERATE_PERLMOD       = NO
- 
--# If the PERLMOD_LATEX tag is set to YES Doxygen will generate 
--# the necessary Makefile rules, Perl scripts and LaTeX code to be able 
-+# If the PERLMOD_LATEX tag is set to YES Doxygen will generate
-+# the necessary Makefile rules, Perl scripts and LaTeX code to be able
- # to generate PDF and DVI output from the Perl module output.
- 
- PERLMOD_LATEX          = NO
- 
--# If the PERLMOD_PRETTY tag is set to YES the Perl module output will be 
--# nicely formatted so it can be parsed by a human reader.  This is useful 
--# if you want to understand what is going on.  On the other hand, if this 
--# tag is set to NO the size of the Perl module output will be much smaller 
-+# If the PERLMOD_PRETTY tag is set to YES the Perl module output will be
-+# nicely formatted so it can be parsed by a human reader.
-+# This is useful
-+# if you want to understand what is going on.
-+# On the other hand, if this
-+# tag is set to NO the size of the Perl module output will be much smaller
- # and Perl will parse it just the same.
- 
- PERLMOD_PRETTY         = YES
- 
--# The names of the make variables in the generated doxyrules.make file 
--# are prefixed with the string contained in PERLMOD_MAKEVAR_PREFIX. 
--# This is useful so different doxyrules.make files included by the same 
-+# The names of the make variables in the generated doxyrules.make file
-+# are prefixed with the string contained in PERLMOD_MAKEVAR_PREFIX.
-+# This is useful so different doxyrules.make files included by the same
- # Makefile don't overwrite each other's variables.
- 
--PERLMOD_MAKEVAR_PREFIX = 
-+PERLMOD_MAKEVAR_PREFIX =
- 
- #---------------------------------------------------------------------------
--# Configuration options related to the preprocessor   
-+# Configuration options related to the preprocessor
- #---------------------------------------------------------------------------
- 
--# If the ENABLE_PREPROCESSING tag is set to YES (the default) Doxygen will 
--# evaluate all C-preprocessor directives found in the sources and include 
-+# If the ENABLE_PREPROCESSING tag is set to YES (the default) Doxygen will
-+# evaluate all C-preprocessor directives found in the sources and include
- # files.
- 
- ENABLE_PREPROCESSING   = YES
- 
--# If the MACRO_EXPANSION tag is set to YES Doxygen will expand all macro 
--# names in the source code. If set to NO (the default) only conditional 
--# compilation will be performed. Macro expansion can be done in a controlled 
-+# If the MACRO_EXPANSION tag is set to YES Doxygen will expand all macro
-+# names in the source code. If set to NO (the default) only conditional
-+# compilation will be performed. Macro expansion can be done in a controlled
- # way by setting EXPAND_ONLY_PREDEF to YES.
- 
- MACRO_EXPANSION        = NO
- 
--# If the EXPAND_ONLY_PREDEF and MACRO_EXPANSION tags are both set to YES 
--# then the macro expansion is limited to the macros specified with the 
-+# If the EXPAND_ONLY_PREDEF and MACRO_EXPANSION tags are both set to YES
-+# then the macro expansion is limited to the macros specified with the
- # PREDEFINED and EXPAND_AS_DEFINED tags.
- 
- EXPAND_ONLY_PREDEF     = NO
- 
--# If the SEARCH_INCLUDES tag is set to YES (the default) the includes files 
-+# If the SEARCH_INCLUDES tag is set to YES (the default) the includes files
- # in the INCLUDE_PATH (see below) will be search if a #include is found.
- 
- SEARCH_INCLUDES        = YES
- 
--# The INCLUDE_PATH tag can be used to specify one or more directories that 
--# contain include files that are not input files but should be processed by 
-+# The INCLUDE_PATH tag can be used to specify one or more directories that
-+# contain include files that are not input files but should be processed by
- # the preprocessor.
- 
--INCLUDE_PATH           = 
-+INCLUDE_PATH           =
- 
--# You can use the INCLUDE_FILE_PATTERNS tag to specify one or more wildcard 
--# patterns (like *.h and *.hpp) to filter out the header-files in the 
--# directories. If left blank, the patterns specified with FILE_PATTERNS will 
-+# You can use the INCLUDE_FILE_PATTERNS tag to specify one or more wildcard
-+# patterns (like *.h and *.hpp) to filter out the header-files in the
-+# directories. If left blank, the patterns specified with FILE_PATTERNS will
- # be used.
- 
--INCLUDE_FILE_PATTERNS  = 
-+INCLUDE_FILE_PATTERNS  =
- 
--# The PREDEFINED tag can be used to specify one or more macro names that 
--# are defined before the preprocessor is started (similar to the -D option of 
--# gcc). The argument of the tag is a list of macros of the form: name 
--# or name=definition (no spaces). If the definition and the = are 
--# omitted =1 is assumed. To prevent a macro definition from being 
--# undefined via #undef or recursively expanded use the := operator 
-+# The PREDEFINED tag can be used to specify one or more macro names that
-+# are defined before the preprocessor is started (similar to the -D option of
-+# gcc). The argument of the tag is a list of macros of the form: name
-+# or name=definition (no spaces). If the definition and the = are
-+# omitted =1 is assumed. To prevent a macro definition from being
-+# undefined via #undef or recursively expanded use the := operator
- # instead of the = operator.
- 
- PREDEFINED             = WITH_OPENSSL \
-@@ -1104,7 +1457,7 @@
- # toolkit from AT&T and Lucent Bell Labs. The other options in this section 
- # have no effect if this option is set to NO (the default)
- 
--HAVE_DOT               = NO
-+HAVE_DOT               = YES
- 
- # If the CLASS_GRAPH and HAVE_DOT tags are set to YES then doxygen 
- # will generate a graph for each documented class showing the direct and 
-@@ -1182,7 +1535,7 @@
- # generated by dot. Possible values are png, jpg, or gif
- # If left blank png will be used.
- 
--DOT_IMAGE_FORMAT       = png
-+DOT_IMAGE_FORMAT       = svg
- 
- # The tag DOT_PATH can be used to specify the path where the dot tool can be 
- # found. If left blank, it is assumed the dot tool can be found in the path.
diff --git a/patches/bigdft-abi-1.0.4-0005.patch b/patches/bigdft-abi-1.0.4-0005.patch
deleted file mode 100644
index ae59b7ba1..000000000
--- a/patches/bigdft-abi-1.0.4-0005.patch
+++ /dev/null
@@ -1,5317 +0,0 @@
-diff -urN bigdft-abi-1.0.4.old/configure.ac bigdft-abi-1.0.4.new/configure.ac
---- bigdft-abi-1.0.4.old/configure.ac	2012-07-09 16:43:33.000000000 +0200
-+++ bigdft-abi-1.0.4.new/configure.ac	2013-06-11 16:51:00.000000000 +0200
-@@ -806,8 +806,8 @@
-     
-     dnl Test the given implementation of libabinit.
-     AC_CHECK_LIB(abinit, symbrav, withlibabinit=yes, withlibabinit=no)
--    AC_CHECK_FILE($ac_libabinit_dir/include/ab6_moldyn.$ax_fc_mod_ext, moldyn="yes", moldyn="no")
--    AC_CHECK_FILE($ac_libabinit_dir/include/ab6_symmetry.$ax_fc_mod_ext, sym="yes", sym="no")
-+    AC_CHECK_FILE($ac_libabinit_dir/include/ab7_moldyn.$ax_fc_mod_ext, moldyn="yes", moldyn="no")
-+    AC_CHECK_FILE($ac_libabinit_dir/include/ab7_symmetry.$ax_fc_mod_ext, sym="yes", sym="no")
-     AC_CHECK_FILE($ac_libabinit_dir/include/libxc_functionals.$ax_fc_mod_ext, libxc="yes", libxc="no")
-     if test "$withlibabinit" = "yes" -a "$moldyn" = "yes" -a "$sym" = "yes" -a "$libxc" = "yes"; then
-       ac_use_libabinit="yes"
-diff -urN bigdft-abi-1.0.4.old/libABINIT/src/10_defs/defs_basis.F90 bigdft-abi-1.0.4.new/libABINIT/src/10_defs/defs_basis.F90
---- bigdft-abi-1.0.4.old/libABINIT/src/10_defs/defs_basis.F90	2012-07-09 16:43:33.000000000 +0200
-+++ bigdft-abi-1.0.4.new/libABINIT/src/10_defs/defs_basis.F90	2013-06-11 16:51:00.000000000 +0200
-@@ -211,18 +211,18 @@
-  integer, parameter :: abinit_comm_serial = -12345
- 
-  ! Error codes used by the bindings.
-- integer, parameter, public :: AB6_NO_ERROR                 =  0
-- integer, parameter, public :: AB6_ERROR_OBJ                =  1
-- integer, parameter, public :: AB6_ERROR_ARG                =  2
-- integer, parameter, public :: AB6_ERROR_INVARS_ATT         =  3
-- integer, parameter, public :: AB6_ERROR_INVARS_ID          =  4
-- integer, parameter, public :: AB6_ERROR_INVARS_SIZE        =  5
-- integer, parameter, public :: AB6_ERROR_SYM_NOT_PRIMITIVE  =  6
-- integer, parameter, public :: AB6_ERROR_SYM_BRAVAIS_XRED   =  7
-- integer, parameter, public :: AB6_ERROR_MIXING_ARG         =  8
-- integer, parameter, public :: AB6_ERROR_MIXING_CONVERGENCE =  9
-- integer, parameter, public :: AB6_ERROR_MIXING_INTERNAL    = 10
-- integer, parameter, public :: AB6_ERROR_MIXING_INC_NNSLOOP = 11
-+ integer, parameter, public :: AB7_NO_ERROR                 =  0
-+ integer, parameter, public :: AB7_ERROR_OBJ                =  1
-+ integer, parameter, public :: AB7_ERROR_ARG                =  2
-+ integer, parameter, public :: AB7_ERROR_INVARS_ATT         =  3
-+ integer, parameter, public :: AB7_ERROR_INVARS_ID          =  4
-+ integer, parameter, public :: AB7_ERROR_INVARS_SIZE        =  5
-+ integer, parameter, public :: AB7_ERROR_SYM_NOT_PRIMITIVE  =  6
-+ integer, parameter, public :: AB7_ERROR_SYM_BRAVAIS_XRED   =  7
-+ integer, parameter, public :: AB7_ERROR_MIXING_ARG         =  8
-+ integer, parameter, public :: AB7_ERROR_MIXING_CONVERGENCE =  9
-+ integer, parameter, public :: AB7_ERROR_MIXING_INTERNAL    = 10
-+ integer, parameter, public :: AB7_ERROR_MIXING_INC_NNSLOOP = 11
- 
- ! Values of optdriver corresponding to the different run-levels. 
-  integer, parameter, public :: RUNL_GSTATE     = 0
-diff -urN bigdft-abi-1.0.4.old/libABINIT/src/14_hidewrite/wrtout.F90 bigdft-abi-1.0.4.new/libABINIT/src/14_hidewrite/wrtout.F90
---- bigdft-abi-1.0.4.old/libABINIT/src/14_hidewrite/wrtout.F90	2012-07-09 16:43:33.000000000 +0200
-+++ bigdft-abi-1.0.4.new/libABINIT/src/14_hidewrite/wrtout.F90	2013-06-11 16:51:00.000000000 +0200
-@@ -62,7 +62,7 @@
- !!      ioniondist,irrzg,isfile,jellium,klocal,kpgio,kpgsph,kpgstr
- !!      kramerskronig,ks_ddiago,kxc_alda,kxc_eok,ladielmt,lattice,lavnl
- !!      leave_new,leave_test,linemin,listkk,lobpcgIIwf,lobpcgccIIwf,lobpcgccwf
--!!      lobpcgwf,loop3dte,loper3,lwf,m_ab6_invars_f90,m_abilasi,m_atom
-+!!      lobpcgwf,loop3dte,loper3,lwf,m_ab7_invars_f90,m_abilasi,m_atom
- !!      m_bands_sym,m_bs_defs,m_bz_mesh,m_coulombian,m_crystal,m_dyson_solver
- !!      m_ebands,m_errors,m_fft_mesh,m_fftw3,m_geometry,m_green,m_gsphere
- !!      m_gwdefs,m_hamiltonian,m_hidecudarec,m_initcuda,m_io_kss,m_io_screening
-diff -urN bigdft-abi-1.0.4.old/libABINIT/src/16_hideleave/leave_new.F90 bigdft-abi-1.0.4.new/libABINIT/src/16_hideleave/leave_new.F90
---- bigdft-abi-1.0.4.old/libABINIT/src/16_hideleave/leave_new.F90	2012-07-09 16:43:33.000000000 +0200
-+++ bigdft-abi-1.0.4.new/libABINIT/src/16_hideleave/leave_new.F90	2013-06-11 16:51:00.000000000 +0200
-@@ -54,7 +54,7 @@
- !!      inupper,invars0,invars1,invars1m,invars2,invars9,invcb,inwffil,inwffil3
- !!      ioarr,ioddb8_in,iofn1,iofn2,irrzg,isfile,jellium,klocal,kpgsph,kpgstr
- !!      kxc_alda,kxc_eok,ladielmt,lavnl,linemin,listkk,lobpcgIIwf,lobpcgccIIwf
--!!      loper3,lwf,m_ab6_invars_f90,m_errors,m_green,m_libxc_functionals
-+!!      loper3,lwf,m_ab7_invars_f90,m_errors,m_green,m_libxc_functionals
- !!      m_matlu,m_matrix,m_oper,m_paw_dmft,m_special_funcs,m_wffile
- !!      mat_mlms2jmj,mat_slm2ylm,matcginv,matcginv_dpc,mati3inv,matrginv
- !!      matrixelmt_g,mean_fftr,meanvalue_g,memana,metcon,metric,metstr,mka2f
-diff -urN bigdft-abi-1.0.4.old/libABINIT/src/18_timing/timab.F90 bigdft-abi-1.0.4.new/libABINIT/src/18_timing/timab.F90
---- bigdft-abi-1.0.4.old/libABINIT/src/18_timing/timab.F90	2012-07-09 16:43:33.000000000 +0200
-+++ bigdft-abi-1.0.4.new/libABINIT/src/18_timing/timab.F90	2013-06-11 16:51:00.000000000 +0200
-@@ -50,7 +50,7 @@
- !!      getgsc,getngrec,gran_potrec,green_kernel,gstate,gstateimg,hartre
- !!      hartre1,initylmg,inkpts,invars2,inwffil,inwffil3,kpgio,kpgsph,ladielmt
- !!      lavnl,leave_test,lobpcgIIwf,lobpcgccIIwf,lobpcgccwf,lobpcgwf,loop3dte
--!!      loper3,m_ab6_invars_f90,m_hidecudarec,m_screening,matrixelmt_g
-+!!      loper3,m_ab7_invars_f90,m_hidecudarec,m_screening,matrixelmt_g
- !!      mean_fftr,meanvalue_g,mkcore,mkffnl,mklocl_realspace,mklocl_recipspace
- !!      mkresi,mkrho,mkrho3,mkvxc3,mkvxcstr3,newkpt,newocc,newrho,newvtr
- !!      newvtr3,nhatgrid,nlenergyrec,nonlinear,nonlop,nstdy3,nstwf3,odamix
-diff -urN bigdft-abi-1.0.4.old/libABINIT/src/32_util/mati3inv.F90 bigdft-abi-1.0.4.new/libABINIT/src/32_util/mati3inv.F90
---- bigdft-abi-1.0.4.old/libABINIT/src/32_util/mati3inv.F90	2012-07-09 16:43:33.000000000 +0200
-+++ bigdft-abi-1.0.4.new/libABINIT/src/32_util/mati3inv.F90	2013-06-11 16:51:00.000000000 +0200
-@@ -32,7 +32,7 @@
- !! TODO
- !!
- !! PARENTS
--!!      ab6_symmetry_f90,debug_tools,get_full_kgrid,getkgrid,ingeo,invars2m
-+!!      ab7_symmetry_f90,debug_tools,get_full_kgrid,getkgrid,ingeo,invars2m
- !!      m_bands_sym,m_crystal,m_fft_mesh,m_io_kss,nstdy3,optic,outscfcv,rdddb9
- !!      read_gkk,setsym,strainsym,symdij,symdyma,wfconv
- !!
-diff -urN bigdft-abi-1.0.4.old/libABINIT/src/42_geometry/chkprimit.F90 bigdft-abi-1.0.4.new/libABINIT/src/42_geometry/chkprimit.F90
---- bigdft-abi-1.0.4.old/libABINIT/src/42_geometry/chkprimit.F90	2012-07-09 16:43:33.000000000 +0200
-+++ bigdft-abi-1.0.4.new/libABINIT/src/42_geometry/chkprimit.F90	2013-06-11 16:51:00.000000000 +0200
-@@ -32,7 +32,7 @@
- !
- !!
- !! PARENTS
--!!      ingeo,ab6_symmetry_f90
-+!!      ingeo,ab7_symmetry_f90
- !!
- !! CHILDREN
- !!      leave_new,wrtout
-diff -urN bigdft-abi-1.0.4.old/libABINIT/src/42_geometry/m_ab6_symmetry.F90 bigdft-abi-1.0.4.new/libABINIT/src/42_geometry/m_ab6_symmetry.F90
---- bigdft-abi-1.0.4.old/libABINIT/src/42_geometry/m_ab6_symmetry.F90	2012-07-09 16:43:33.000000000 +0200
-+++ bigdft-abi-1.0.4.new/libABINIT/src/42_geometry/m_ab6_symmetry.F90	1970-01-01 01:00:00.000000000 +0100
-@@ -1,1088 +0,0 @@
--!* * Fortran90 source file *
--!*
--!* Copyright (c) 2008-2010 ABINIT Group (Damien Caliste)
--!* All rights reserved.
--!*
--!* This file is part of the ABINIT software package. For license information,
--!* please see the COPYING file in the top-level directory of the ABINIT source
--!* distribution.
--!*
--!*
--
--module m_ab6_symmetry
--
--  use defs_basis
--
--  implicit none
--
--  private
--
--  integer, parameter, public :: AB6_MAX_SYMMETRIES = 384
--
--  type, public :: symmetry_type
--     ! The input characteristics
--     real(dp) :: tolsym
--     real(dp) :: rprimd(3,3), gprimd(3,3), rmet(3,3)
--     integer :: nAtoms
--     integer, pointer :: typeAt(:)
--     real(dp), pointer :: xRed(:,:)
--
--     logical :: withField
--     real(dp) :: field(3)
--
--     logical :: withJellium
--
--     integer :: withSpin
--     real(dp), pointer :: spinAt(:,:)
--
--     logical :: withSpinOrbit
--
--     integer :: vacuum(3)
--
--     ! The output characteristics
--     ! The bravais parameters
--     integer :: nBravSym
--     integer :: bravais(11), bravSym(3, 3, AB6_MAX_SYMMETRIES)
--     ! The symmetry matrices
--     logical  :: auto
--     integer  :: nSym
--     integer, pointer  :: sym(:,:,:)
--     real(dp), pointer :: transNon(:,:)
--     integer, pointer  :: symAfm(:)
--     ! Some additional information
--     integer          :: multiplicity
--     real(dp)         :: genAfm(3)
--     integer          :: spaceGroup, pointGroupMagn
--     integer, pointer :: indexingAtoms(:,:,:)
--  end type symmetry_type
--
--  ! We store here a list of symmetry objects to be able to
--  ! call several symmetry operations on different objects.
--  ! The simplest portable way to do it, is to create
--  ! a list of Fortran structure and to use the list index
--  ! as an identifier that can be given to the other languages.
--  type, private :: symmetry_list
--     integer                       :: id
--     type(symmetry_list),  pointer :: next
--     type(symmetry_type)           :: data
--  end type symmetry_list
--  type(symmetry_list), pointer :: my_symmetries
--  integer :: n_symmetries = 0
--
--  logical, private, parameter :: AB_DBG = .false.
--
--  public :: symmetry_new
--  public :: symmetry_free
--  public :: symmetry_set_tolerance
--  public :: symmetry_set_lattice
--  public :: symmetry_set_structure
--  public :: symmetry_set_collinear_spin
--  public :: symmetry_set_spin
--  public :: symmetry_set_spin_orbit
--  public :: symmetry_set_field
--  public :: symmetry_set_jellium
--  public :: symmetry_set_periodicity
--  public :: symmetry_set_n_sym
--
--  public :: symmetry_get_from_id
--  public :: symmetry_get_n_atoms
--  public :: symmetry_get_n_sym
--  public :: symmetry_get_multiplicity
--  public :: symmetry_get_bravais
--  public :: symmetry_get_matrices
--  public :: symmetry_get_matrices_p
--  public :: symmetry_get_group
--  public :: symmetry_get_equivalent_atom
--
--contains
--
--  subroutine new_item(token)
--
--
--!This section has been created automatically by the script Abilint (TD).
--!Do not modify the following lines by hand.
--!End of the abilint section
--
--    type(symmetry_list), pointer :: token
--
--    ! We allocate a new list token and prepend it.
--    if (AB_DBG) write(0,*) "AB symmetry: create a new token."
--
--    ! Init case, very first call.
--    if (n_symmetries == 0) then
--       nullify(my_symmetries)
--    end if
--
--    ! Normal treatment.
--    n_symmetries = n_symmetries + 1
--
--    allocate(token)
--    token%id = n_symmetries
--    call new_symmetry(token%data)
--    token%next => my_symmetries
--
--    my_symmetries => token
--    if (AB_DBG) write(0,*) "AB symmetry: creation OK with id ", token%id
--  end subroutine new_item
--
--  subroutine free_item(token)
--
--
--!This section has been created automatically by the script Abilint (TD).
--!Do not modify the following lines by hand.
--!End of the abilint section
--
--    type(symmetry_list), pointer :: token
--
--    type(symmetry_list), pointer :: tmp
--
--    if (.not. associated(token)) then
--       return
--    end if
--
--    call free_symmetry(token%data)
--
--    if (AB_DBG) write(0,*) "AB symmetry: free request on token ", token%id
--    ! We remove token from the list.
--    if (my_symmetries%id == token%id) then
--       my_symmetries => token%next
--    else
--       tmp => my_symmetries
--       do
--          if (.not.associated(tmp)) then
--             return
--          end if
--          if (associated(tmp%next) .and. tmp%next%id == token%id) then
--             exit
--          end if
--          tmp => tmp%next
--       end do
--       tmp%next => token%next
--    end if
--    deallocate(token)
--    if (AB_DBG) write(0,*) "AB symmetry: free done"
--  end subroutine free_item
--
--  subroutine get_item(token, id)
--
--
--    type(symmetry_list), pointer :: token
--    integer, intent(in) :: id
--
--    type(symmetry_list), pointer :: tmp
--
--    if (AB_DBG) write(0,*) "AB symmetry: request list element ", id
--    nullify(token)
--
--    tmp => my_symmetries
--    do
--       if (.not. associated(tmp)) then
--          exit
--       end if
--       if (tmp%id == id) then
--          token => tmp
--          return
--       end if
--       tmp => tmp%next
--    end do
--  end subroutine get_item
--
--  subroutine symmetry_get_from_id(sym, id, errno)
--
--    type(symmetry_type), pointer :: sym
--    integer, intent(in) :: id
--    integer, intent(out) :: errno
--
--    type(symmetry_list), pointer :: token
--
--    errno = AB6_NO_ERROR
--    call get_item(token, id)
--    if (associated(token)) then
--       sym => token%data
--       if (sym%nSym <= 0) then
--          ! We do the computation of the matrix part.
--          call compute_matrices(sym, errno)
--       end if
--    else
--       errno = AB6_ERROR_OBJ
--       nullify(sym)
--    end if
--  end subroutine symmetry_get_from_id
--
--  subroutine new_symmetry(sym)
--
--
--    type(symmetry_type), intent(out) :: sym
--
--    if (AB_DBG) write(0,*) "AB symmetry: create a new symmetry object."
--    nullify(sym%xRed)
--    nullify(sym%spinAt)
--    nullify(sym%typeAt)
--    sym%tolsym   = tol8
--    sym%auto     = .true.
--    sym%nSym     = 0
--    nullify(sym%sym)
--    nullify(sym%symAfm)
--    nullify(sym%transNon)
--    sym%nBravSym = -1
--    sym%withField   = .false.
--    sym%withJellium = .false.
--    sym%withSpin = 1
--    sym%withSpinOrbit = .false.
--    sym%multiplicity = -1
--    nullify(sym%indexingAtoms)
--    sym%vacuum = 0
--  end subroutine new_symmetry
--
--  subroutine free_symmetry(sym)
--
--
--    type(symmetry_type), intent(inout) :: sym
--
--    if (AB_DBG) write(0,*) "AB symmetry: free a symmetry."
--
--    if (associated(sym%xRed)) deallocate(sym%xRed)
--    if (associated(sym%spinAt)) deallocate(sym%spinAt)
--    if (associated(sym%typeAt)) deallocate(sym%typeAt)
--    if (associated(sym%indexingAtoms)) deallocate(sym%indexingAtoms)
--    if (associated(sym%sym)) deallocate(sym%sym)
--    if (associated(sym%symAfm)) deallocate(sym%symAfm)
--    if (associated(sym%transNon)) deallocate(sym%transNon)
--  end subroutine free_symmetry
--
--
--
--
--
--  subroutine symmetry_new(id)
--
--
--!This section has been created automatically by the script Abilint (TD).
--!Do not modify the following lines by hand.
--!End of the abilint section
--
--    integer, intent(out) :: id
--
--    type(symmetry_list), pointer :: token
--
--    if (AB_DBG) write(0,*) "AB symmetry: call new symmetry."
--    call new_item(token)
--    id = token%id
--  end subroutine symmetry_new
--
--  subroutine symmetry_free(id)
--
--
--!This section has been created automatically by the script Abilint (TD).
--!Do not modify the following lines by hand.
--!End of the abilint section
--
--    integer, intent(in) :: id
--
--    type(symmetry_list), pointer :: token
--
--    if (AB_DBG) write(0,*) "AB symmetry: call free symmetry."
--
--    call get_item(token, id)
--    if (associated(token)) call free_item(token)
--  end subroutine symmetry_free
--
--  subroutine symmetry_set_tolerance(id, tolsym, errno)
--
--
--!This section has been created automatically by the script Abilint (TD).
--!Do not modify the following lines by hand.
--!End of the abilint section
--
--    integer, intent(in) :: id
--    real(dp), intent(in) :: tolsym
--    integer, intent(out) :: errno
--
--    type(symmetry_list), pointer :: token
--
--    if (AB_DBG) write(0,*) "AB symmetry: call set tolerance."
--
--    errno = AB6_NO_ERROR
--    call get_item(token, id)
--    if (.not. associated(token)) then
--       errno = AB6_ERROR_OBJ
--       return
--    end if
--
--    token%data%tolsym = tolsym
--
--    ! We unset all the computed symmetries
--    token%data%nBravSym = -1
--    if (token%data%auto) then
--       token%data%nSym  = 0
--    end if
--  end subroutine symmetry_set_tolerance
--
--  subroutine symmetry_set_lattice(id, rprimd, errno)
--
--
--!This section has been created automatically by the script Abilint (TD).
--!Do not modify the following lines by hand.
--  use interfaces_42_geometry
--!End of the abilint section
--
--    integer, intent(in) :: id
--    real(dp), intent(in) :: rprimd(3,3)
--    integer, intent(out) :: errno
--
--    type(symmetry_list), pointer :: token
--    real(dp) :: ucvol
--    real(dp) :: gmet(3,3)
--
--    if (AB_DBG) write(0,*) "AB symmetry: call set lattice."
--    if (AB_DBG) write(0, "(A,3F12.6,A)") "  (", rprimd(:,1), ")"
--    if (AB_DBG) write(0, "(A,3F12.6,A)") "  (", rprimd(:,2), ")"
--    if (AB_DBG) write(0, "(A,3F12.6,A)") "  (", rprimd(:,3), ")"
--
--    errno = AB6_NO_ERROR
--    call get_item(token, id)
--    if (.not. associated(token)) then
--       errno = AB6_ERROR_OBJ
--       return
--    end if
--
--    token%data%rprimd = rprimd
--    call metric(gmet, token%data%gprimd, -1, token%data%rmet, rprimd, ucvol)
--
--    ! We unset all the computed symmetries
--    token%data%nBravSym = -1
--    if (token%data%auto) then
--       token%data%nSym  = 0
--    end if
--  end subroutine symmetry_set_lattice
--
--  subroutine symmetry_set_structure(id, nAtoms, typeAt, xRed, errno)
--
--
--!This section has been created automatically by the script Abilint (TD).
--!Do not modify the following lines by hand.
--!End of the abilint section
--
--    integer, intent(in) :: id
--    integer, intent(in) :: nAtoms
--    integer, intent(in) :: typeAt(nAtoms)
--    real(dp), intent(in) :: xRed(3,nAtoms)
--    integer, intent(out) :: errno
--
--    type(symmetry_list), pointer :: token
--    integer :: i
--
--    if (AB_DBG) write(0,*) "AB symmetry: call set structure."
--    if (AB_DBG) write(0, "(A,I3,A)") "  ", nAtoms, " atoms"
--    if (AB_DBG) then
--       do i = 1, nAtoms, 1
--          write(0, "(A,3F12.6,I3)") "  ", xRed(:, i), typeAt(i)
--       end do
--    end if
--
--    errno = AB6_NO_ERROR
--    call get_item(token, id)
--    if (.not. associated(token)) then
--       errno = AB6_ERROR_OBJ
--       return
--    end if
--
--    token%data%nAtoms =  nAtoms
--    allocate(token%data%typeAt(nAtoms))
--    token%data%typeAt = typeAt
--    allocate(token%data%xRed(3, nAtoms))
--    token%data%xRed   = xRed
--
--    ! We unset only the symmetries
--    if (token%data%auto) then
--       token%data%nSym = 0
--    end if
--    if (associated(token%data%indexingAtoms)) deallocate(token%data%indexingAtoms)
--  end subroutine symmetry_set_structure
--
--  subroutine symmetry_set_spin(id, nAtoms, spinAt, errno)
--
--
--!This section has been created automatically by the script Abilint (TD).
--!Do not modify the following lines by hand.
--!End of the abilint section
--
--    integer, intent(in) :: id
--    integer, intent(in) :: nAtoms
--    real(dp), intent(in) :: spinAt(3,nAtoms)
--    integer, intent(out) :: errno
--
--    type(symmetry_list), pointer :: token
--    integer :: i
--
--    if (AB_DBG) write(0,*) "AB symmetry: call set spin."
--    if (AB_DBG) then
--       do i = 1, nAtoms, 1
--          write(0, "(A,3F12.6)") "  ", spinAt(:, i)
--       end do
--    end if
--
--    errno = AB6_NO_ERROR
--    call get_item(token, id)
--    if (.not. associated(token)) then
--       errno = AB6_ERROR_OBJ
--       return
--    end if
--    if (token%data%nAtoms /= nAtoms) then
--       errno = AB6_ERROR_ARG
--       return
--    end if
--
--    token%data%withSpin = 4
--    allocate(token%data%spinAt(3, nAtoms))
--    token%data%spinAt = spinAt
--
--    ! We unset only the symmetries
--    if (token%data%auto) then
--       token%data%nSym  = 0
--    end if
--  end subroutine symmetry_set_spin
--
--  subroutine symmetry_set_collinear_spin(id, nAtoms, spinAt, errno)
--
--
--!This section has been created automatically by the script Abilint (TD).
--!Do not modify the following lines by hand.
--!End of the abilint section
--
--    integer, intent(in) :: id
--    integer, intent(in) :: nAtoms
--    integer, intent(in) :: spinAt(nAtoms)
--    integer, intent(out) :: errno
--
--    type(symmetry_list), pointer :: token
--    integer :: i
--
--    if (AB_DBG) write(0,*) "AB symmetry: call set collinear spin."
--    if (AB_DBG) then
--       do i = 1, nAtoms, 1
--          write(0, "(A,I3)") "  ", spinAt(i)
--       end do
--    end if
--
--    errno = AB6_NO_ERROR
--    call get_item(token, id)
--    if (.not. associated(token)) then
--       errno = AB6_ERROR_OBJ
--       return
--    end if
--    if (token%data%nAtoms /= nAtoms) then
--       errno = AB6_ERROR_ARG
--       return
--    end if
--
--    token%data%withSpin = 2
--    allocate(token%data%spinAt(1, nAtoms))
--    token%data%spinAt = real(reshape(spinAt, (/ 1, nAtoms /)), dp)
--
--    ! We unset only the symmetries
--    if (token%data%auto) then
--       token%data%nSym  = 0
--    end if
--  end subroutine symmetry_set_collinear_spin
--
--  subroutine symmetry_set_spin_orbit(id, withSpinOrbit, errno)
--
--
--!This section has been created automatically by the script Abilint (TD).
--!Do not modify the following lines by hand.
--!End of the abilint section
--
--    integer, intent(in) :: id
--    logical, intent(in) :: withSpinOrbit
--    integer, intent(out) :: errno
--
--    type(symmetry_list), pointer :: token
--
--    if (AB_DBG) write(0,*) "AB symmetry: call set spin orbit."
--
--    errno = AB6_NO_ERROR
--    call get_item(token, id)
--    if (.not. associated(token)) then
--       errno = AB6_ERROR_OBJ
--       return
--    end if
--
--    token%data%withSpinOrbit = withSpinOrbit
--
--    ! We unset only the symmetries
--    if (token%data%auto) then
--       token%data%nSym  = 0
--    end if
--  end subroutine symmetry_set_spin_orbit
--
--  subroutine symmetry_set_field(id, field, errno)
--
--
--!This section has been created automatically by the script Abilint (TD).
--!Do not modify the following lines by hand.
--!End of the abilint section
--
--    integer, intent(in) :: id
--    real(dp), intent(in) :: field(3)
--    integer, intent(out) :: errno
--
--    type(symmetry_list), pointer :: token
--
--    if (AB_DBG) write(0,*) "AB symmetry: call set field."
--
--    errno = AB6_NO_ERROR
--    call get_item(token, id)
--    if (.not. associated(token)) then
--       errno = AB6_ERROR_OBJ
--       return
--    end if
--
--    token%data%withField = .true.
--    token%data%field = field
--
--    ! We unset all the computed symmetries
--    token%data%nBravSym = -1
--    if (token%data%auto) then
--       token%data%nSym  = 0
--    end if
--  end subroutine symmetry_set_field
--
--  subroutine symmetry_set_jellium(id, jellium, errno)
--
--
--!This section has been created automatically by the script Abilint (TD).
--!Do not modify the following lines by hand.
--!End of the abilint section
--
--    integer, intent(in) :: id
--    logical, intent(in) :: jellium
--    integer, intent(out) :: errno
--
--    type(symmetry_list), pointer :: token
--
--    if (AB_DBG) write(0,*) "AB symmetry: call set jellium."
--
--    errno = AB6_NO_ERROR
--    call get_item(token, id)
--    if (.not. associated(token)) then
--       errno = AB6_ERROR_OBJ
--       return
--    end if
--
--    token%data%withJellium = jellium
--
--    ! We unset only the symmetries
--    if (token%data%auto) then
--       token%data%nSym  = 0
--    end if
--  end subroutine symmetry_set_jellium
--
--  subroutine symmetry_set_periodicity(id, periodic, errno)
--
--
--!This section has been created automatically by the script Abilint (TD).
--!Do not modify the following lines by hand.
--!End of the abilint section
--
--    integer, intent(in) :: id
--    logical, intent(in) :: periodic(3)
--    integer, intent(out) :: errno
--
--    type(symmetry_list), pointer :: token
--
--    if (AB_DBG) write(0,*) "AB symmetry: call set periodicity."
--    if (AB_DBG) write(0, "(A,3L1,A)") "  (", periodic, ")"
--
--    errno = AB6_NO_ERROR
--    call get_item(token, id)
--    if (.not. associated(token)) then
--       errno = AB6_ERROR_OBJ
--       return
--    end if
--
--    token%data%vacuum = 0
--    if (.not. periodic(1)) token%data%vacuum(1) = 1
--    if (.not. periodic(2)) token%data%vacuum(2) = 1
--    if (.not. periodic(3)) token%data%vacuum(3) = 1
--  end subroutine symmetry_set_periodicity
--
--
--
--
--
--  subroutine symmetry_get_n_atoms(id, nAtoms, errno)
--    !scalars
--
--!This section has been created automatically by the script Abilint (TD).
--!Do not modify the following lines by hand.
--!End of the abilint section
--
--    integer, intent(in) :: id
--    integer, intent(out) :: errno
--    integer, intent(out) :: nAtoms
--
--    type(symmetry_list), pointer :: token
--
--    if (AB_DBG) write(0,*) "AB symmetry: call get nAtoms."
--
--    errno = AB6_NO_ERROR
--    call get_item(token, id)
--    if (.not. associated(token)) then
--       errno = AB6_ERROR_OBJ
--       return
--    end if
--
--    nAtoms = token%data%nAtoms
--  end subroutine symmetry_get_n_atoms
--
--  subroutine compute_bravais(sym)
--
--
--!This section has been created automatically by the script Abilint (TD).
--!Do not modify the following lines by hand.
--  use interfaces_42_geometry
--!End of the abilint section
--
--    type(symmetry_type), intent(inout) :: sym
--
--    integer :: berryopt
--
--    ! We do the computation
--    if (sym%withField) then
--       berryopt = 4
--    else
--       berryopt = 0
--    end if
--    if (AB_DBG) write(0,*) "AB symmetry: call ABINIT symlatt."
--    call symlatt(sym%bravais, AB6_MAX_SYMMETRIES, &
--         & sym%nBravSym, sym%bravSym, sym%rprimd, sym%tolsym)
--    if (AB_DBG) write(0,*) "AB symmetry: call ABINIT OK."
--    if (AB_DBG) write(0, "(A,I3)") "  nSymBrav :", sym%nBravSym
--    if (AB_DBG) write(0, "(A,I3)") "  holohedry:", sym%bravais(1)
--    if (AB_DBG) write(0, "(A,I3)") "  center   :", sym%bravais(2)
--  end subroutine compute_bravais
--
--  subroutine symmetry_get_bravais(id, bravais, holohedry, center, &
--       & nBravSym, bravSym, errno)
--    !scalars
--
--!This section has been created automatically by the script Abilint (TD).
--!Do not modify the following lines by hand.
--!End of the abilint section
--
--    integer, intent(in) :: id
--    integer, intent(out) :: errno
--    integer, intent(out) :: nBravSym, holohedry, center
--    !arrays
--    integer, intent(out) :: bravais(3,3), bravSym(3, 3, AB6_MAX_SYMMETRIES)
--
--    type(symmetry_list), pointer :: token
--
--    if (AB_DBG) write(0,*) "AB symmetry: call get bravais."
--
--    errno = AB6_NO_ERROR
--    call get_item(token, id)
--    if (.not. associated(token)) then
--       errno = AB6_ERROR_OBJ
--       return
--    end if
--
--    if (token%data%nBravSym < 0) then
--       ! We do the computation
--       call compute_bravais(token%data)
--    end if
--    
--    holohedry = token%data%bravais(1)
--    center    = token%data%bravais(2)
--    bravais   = reshape(token%data%bravais(3:11), (/ 3,3 /))
--    nBravSym  = token%data%nBravSym
--    bravSym(:, :, 1:nBravSym) = token%data%bravSym(:, :, 1:nBravSym)
--  end subroutine symmetry_get_bravais
--
--  subroutine compute_matrices(sym, errno)
--
--
--!This section has been created automatically by the script Abilint (TD).
--!Do not modify the following lines by hand.
--  use interfaces_42_geometry
--!End of the abilint section
--
--    type(symmetry_type), intent(inout) :: sym
--    integer, intent(out) :: errno
--
--    integer :: berryopt, jellslab, noncol
--    integer :: use_inversion
--    real(dp), pointer :: spinAt_(:,:)
--    integer  :: sym_(3, 3, AB6_MAX_SYMMETRIES)
--    real(dp) :: transNon_(3, AB6_MAX_SYMMETRIES)
--    integer  :: symAfm_(AB6_MAX_SYMMETRIES)
--
--    errno = AB6_NO_ERROR
--
--    if (sym%nBravSym < 0) then
--       ! We do the computation of the Bravais part.
--       call compute_bravais(sym)
--    end if
--
--    if (sym%withField) then
--       berryopt = 4
--    else
--       berryopt = 0
--    end if
--    if (sym%withJellium) then
--       jellslab = 1
--    else
--       jellslab = 0
--    end if
--    if (sym%withSpin == 4) then
--       noncol = 1
--       spinAt_ => sym%spinAt
--    else if (sym%withSpin == 2) then
--       noncol = 0
--       spinAt_ => sym%spinAt
--    else
--       noncol = 0
--       allocate(spinAt_(3, sym%nAtoms))
--       spinAt_ = 0
--    end if
--    if (sym%withSpinOrbit) then
--       use_inversion = 0
--    else
--       use_inversion = 1
--    end if
--
--    if (sym%nsym == 0) then
--       if (AB_DBG) write(0,*) "AB symmetry: call ABINIT symfind."
--       call symfind(berryopt, sym%field, sym%gprimd, jellslab, AB6_MAX_SYMMETRIES, &
--            & sym%nAtoms, noncol, sym%nBravSym, sym%nSym, sym%bravSym, spinAt_, &
--            & symAfm_, sym_, transNon_, sym%tolsym, sym%typeAt, &
--            & use_inversion, sym%xRed)
--       if (AB_DBG) write(0,*) "AB symmetry: call ABINIT OK."
--       if (AB_DBG) write(0, "(A,I3)") "  nSym:", sym%nSym
--       if (associated(sym%sym)) deallocate(sym%sym)
--       if (associated(sym%symAfm)) deallocate(sym%symAfm)
--       if (associated(sym%transNon)) deallocate(sym%transNon)
--       allocate(sym%sym(3, 3, sym%nSym))
--       sym%sym(:,:,:) = sym_(:,:, 1:sym%nSym)
--       allocate(sym%symAfm(sym%nSym))
--       sym%symAfm(:) = symAfm_(1:sym%nSym)
--       allocate(sym%transNon(3, sym%nSym))
--       sym%transNon(:,:) = transNon_(:, 1:sym%nSym)
--    else if (sym%nsym < 0) then
--       sym%nsym = -sym%nsym
--       sym_(:,:, 1:sym%nSym) = sym%sym(:,:,:)
--       transNon_(:, 1:sym%nSym) = sym%transNon(:,:)
--       symAfm_(1:sym%nSym) = sym%symAfm(:)
--    end if
--
--    if (sym%withSpin == 1) then
--       deallocate(spinAt_)
--    end if
--    
--    if (AB_DBG) write(0,*) "AB symmetry: call ABINIT symanal."
--    call symanal(sym%bravais, 0, sym%genAfm, AB6_MAX_SYMMETRIES, sym%nSym, &
--         & sym%pointGroupMagn, sym%rprimd, sym%spaceGroup, symAfm_, &
--         & sym_, transNon_, sym%tolsym)
--    if (AB_DBG) write(0,*) "AB symmetry: call ABINIT OK."
--    sym%transNon(:,:) = transNon_(:, 1:sym%nSym)
--
--    if (sym%bravais(1) < 0) then
--       sym%multiplicity = 2
--    else
--       sym%multiplicity = 1
--    end if
--    if (AB_DBG) write(0, "(A,I3)") "  multi:", sym%multiplicity
--    if (AB_DBG) write(0, "(A,I3)") "  space:", sym%spaceGroup
--  end subroutine compute_matrices
--
--  subroutine symmetry_get_n_sym(id, nSym, errno)
--    !scalars
--
--!This section has been created automatically by the script Abilint (TD).
--!Do not modify the following lines by hand.
--!End of the abilint section
--
--    integer, intent(in) :: id
--    integer, intent(out) :: errno
--    integer, intent(out) :: nSym
--
--    type(symmetry_list), pointer :: token
--
--    if (AB_DBG) write(0,*) "AB symmetry: call get nSym."
--
--    errno = AB6_NO_ERROR
--    call get_item(token, id)
--    if (.not. associated(token)) then
--       errno = AB6_ERROR_OBJ
--       return
--    end if
--
--    if (token%data%nSym <= 0) then
--       ! We do the computation of the matrix part.
--       call compute_matrices(token%data, errno)
--    end if
--
--    nSym = token%data%nSym
--  end subroutine symmetry_get_n_sym
--
--  subroutine symmetry_set_n_sym(id, nSym, sym, transNon, symAfm, errno)
--    !scalars
--
--!This section has been created automatically by the script Abilint (TD).
--!Do not modify the following lines by hand.
--!End of the abilint section
--
--    integer, intent(in)  :: id
--    integer, intent(in)  :: nSym
--    integer, intent(in)  :: sym(3, 3, nSym)
--    real(dp), intent(in) :: transNon(3, nSym)
--    integer, intent(in)  :: symAfm(nSym)
--    integer, intent(out) :: errno
--
--    type(symmetry_list), pointer :: token
--
--    if (AB_DBG) write(0,*) "AB symmetry: call get nSym."
--
--    errno = AB6_NO_ERROR
--    call get_item(token, id)
--    if (.not. associated(token)) then
--       errno = AB6_ERROR_OBJ
--       return
--    end if
--
--    if (nSym <= 0) then
--       errno = AB6_ERROR_ARG
--       return
--    else
--       allocate(token%data%sym(3, 3, nSym))
--       token%data%sym(:,:,:) = sym(:,:,:)
--       allocate(token%data%symAfm(nSym))
--       token%data%symAfm(:) = symAfm(:)
--       allocate(token%data%transNon(3, nSym))
--       token%data%transNon(:,:) = transNon(:,:)
--
--       token%data%auto = .false.
--       token%data%nsym = -nSym
--    end if
--
--    ! We do the computation of the matrix part.
--    call compute_matrices(token%data, errno)
--  end subroutine symmetry_set_n_sym
--
--  subroutine symmetry_get_matrices(id, nSym, sym, transNon, symAfm, errno)
--
--
--!This section has been created automatically by the script Abilint (TD).
--!Do not modify the following lines by hand.
--!End of the abilint section
--
--    integer, intent(in) :: id
--    integer, intent(out) :: errno
--    integer, intent(out) :: nSym
--    integer, intent(out)  :: sym(3, 3, AB6_MAX_SYMMETRIES)
--    integer, intent(out)  :: symAfm(AB6_MAX_SYMMETRIES)
--    real(dp), intent(out) :: transNon(3, AB6_MAX_SYMMETRIES)
--
--    type(symmetry_list), pointer :: token
--
--    if (AB_DBG) write(0,*) "AB symmetry: call get matrices."
--
--    errno = AB6_NO_ERROR
--    call get_item(token, id)
--    if (.not. associated(token)) then
--       errno = AB6_ERROR_OBJ
--       return
--    end if
--
--    if (token%data%nSym <= 0) then
--       ! We do the computation of the matrix part.
--       call compute_matrices(token%data, errno)
--    end if
--
--    nSym                = token%data%nSym
--    sym(:, :, 1:nSym)   = token%data%sym(:, :,:)
--    symAfm(1:nSym)      = token%data%symAfm(:)
--    transNon(:, 1:nSym) = token%data%transNon(:,:)
--  end subroutine symmetry_get_matrices
--
--  subroutine symmetry_get_matrices_p(id, nSym, sym, transNon, symAfm, errno)
--
--
--!This section has been created automatically by the script Abilint (TD).
--!Do not modify the following lines by hand.
--!End of the abilint section
--
--    integer, intent(in) :: id
--    integer, intent(out) :: errno
--    integer, intent(out) :: nSym
--    integer, pointer  :: sym(:,:,:)
--    integer, pointer  :: symAfm(:)
--    real(dp), pointer :: transNon(:,:)
--
--    type(symmetry_list), pointer :: token
--
--    if (AB_DBG) write(0,*) "AB symmetry: call get matrices as pointers."
--
--    errno = AB6_NO_ERROR
--    call get_item(token, id)
--    if (.not. associated(token)) then
--       errno = AB6_ERROR_OBJ
--       return
--    end if
--
--    if (token%data%nSym <= 0) then
--       ! We do the computation of the matrix part.
--       call compute_matrices(token%data, errno)
--    end if
--
--    nSym     =  token%data%nSym
--    sym      => token%data%sym
--    symAfm   => token%data%symAfm
--    transNon => token%data%transNon
--  end subroutine symmetry_get_matrices_p
--
--  subroutine symmetry_get_multiplicity(id, multiplicity, errno)
--
--
--!This section has been created automatically by the script Abilint (TD).
--!Do not modify the following lines by hand.
--!End of the abilint section
--
--    integer, intent(in) :: id
--    integer, intent(out) :: multiplicity, errno
--
--    type(symmetry_list), pointer :: token
--
--    if (AB_DBG) write(0,*) "AB symmetry: call get multiplicity."
--
--    errno = AB6_NO_ERROR
--    call get_item(token, id)
--    if (.not. associated(token)) then
--       errno = AB6_ERROR_OBJ
--       return
--    end if
--
--    if (token%data%multiplicity < 0) then
--       ! We do the computation of the matrix part.
--       call compute_matrices(token%data, errno)
--    end if
--    multiplicity = token%data%multiplicity
--  end subroutine symmetry_get_multiplicity
--
--  subroutine symmetry_get_group(id, spaceGroup, spaceGroupId, &
--       & pointGroupMagn, genAfm, errno)
--
--
--!This section has been created automatically by the script Abilint (TD).
--!Do not modify the following lines by hand.
--  use interfaces_42_geometry
--!End of the abilint section
--
--    integer, intent(in)            :: id
--    integer, intent(out)           :: errno
--    real(dp), intent(out)          :: genAfm(3)
--    character(len=15), intent(out) :: spaceGroup
--    integer, intent(out)           :: spaceGroupId, pointGroupMagn
--
--    type(symmetry_list), pointer  :: token
--    integer :: sporder
--    character(len=1)  :: brvLattice
--    character(len=15) :: ptintsb,ptschsb,schsb,spgrp
--    character(len=35) :: intsbl
--
--    if (AB_DBG) write(0,*) "AB symmetry: call get group."
--
--    errno = AB6_NO_ERROR
--    call get_item(token, id)
--    if (.not. associated(token)) then
--       errno = AB6_ERROR_OBJ
--       return
--    end if
--
--    if (token%data%multiplicity < 0) then
--       ! We do the computation of the matrix part.
--       call compute_matrices(token%data, errno)
--    end if
--
--    if (token%data%multiplicity /= 1) then
--       errno = AB6_ERROR_SYM_NOT_PRIMITIVE
--       return
--    end if
--
--    call spgdata(brvLattice,spgrp,intsbl,ptintsb,ptschsb,&
--         &  schsb,1,token%data%spaceGroup,sporder,1)
--
--    write(spaceGroup, "(3A)") brvLattice, " ", trim(spgrp(1:13))
--    pointGroupMagn = token%data%pointGroupMagn
--    spaceGroupId   = token%data%spaceGroup
--    genAfm         = token%data%genAfm
--  end subroutine symmetry_get_group
--
--  subroutine compute_equivalent_atoms(sym)
--
--
--!This section has been created automatically by the script Abilint (TD).
--!Do not modify the following lines by hand.
--  use interfaces_32_util
--  use interfaces_42_geometry
--!End of the abilint section
--
--    type(symmetry_type), intent(inout) :: sym
--
--    integer, allocatable :: symrec(:,:,:)
--    integer :: isym
--
--    if (.not. associated(sym%indexingAtoms)) &
--         & allocate(sym%indexingAtoms(4, sym%nSym, sym%nAtoms))
--
--    !Get the symmetry matrices in terms of reciprocal basis
--    allocate(symrec(3, 3, sym%nSym))
--    do isym = 1, sym%nSym, 1
--       call mati3inv(sym%sym(:,:,isym), symrec(:,:,isym))
--    end do
--    
--    !Obtain a list of rotated atom labels:
--    call symatm(sym%indexingAtoms, sym%nAtoms, sym%nSym, symrec, &
--         & sym%transNon, sym%tolsym, sym%typeAt, sym%xRed)
--
--    deallocate(symrec)
--  end subroutine compute_equivalent_atoms
--
--  subroutine symmetry_get_equivalent_atom(id, equiv, iAtom, errno)
--
--
--!This section has been created automatically by the script Abilint (TD).
--!Do not modify the following lines by hand.
--!End of the abilint section
--
--    integer, intent(in)  :: id
--    integer, intent(in)  :: iAtom
--    integer, intent(out) :: equiv(4, AB6_MAX_SYMMETRIES)
--    integer, intent(out) :: errno
--
--    type(symmetry_list), pointer  :: token
--
--    if (AB_DBG) write(0,*) "AB symmetry: call get equivalent."
--
--    errno = AB6_NO_ERROR
--    call get_item(token, id)
--    if (.not. associated(token)) then
--       errno = AB6_ERROR_OBJ
--       return
--    end if
--
--    if (iAtom < 1 .or. iAtom > token%data%nAtoms) then
--       errno = AB6_ERROR_ARG
--       return
--    end if
--
--    if (.not. associated(token%data%indexingAtoms)) then
--       ! We do the computation of the matrix part.
--       call compute_equivalent_atoms(token%data)
--    end if
--
--    equiv(:, 1:token%data%nSym) = token%data%indexingAtoms(:,:,iAtom)
--  end subroutine symmetry_get_equivalent_atom
--
--end module m_ab6_symmetry
-diff -urN bigdft-abi-1.0.4.old/libABINIT/src/42_geometry/m_ab7_symmetry.F90 bigdft-abi-1.0.4.new/libABINIT/src/42_geometry/m_ab7_symmetry.F90
---- bigdft-abi-1.0.4.old/libABINIT/src/42_geometry/m_ab7_symmetry.F90	1970-01-01 01:00:00.000000000 +0100
-+++ bigdft-abi-1.0.4.new/libABINIT/src/42_geometry/m_ab7_symmetry.F90	2013-06-11 16:51:00.000000000 +0200
-@@ -0,0 +1,1088 @@
-+!* * Fortran90 source file *
-+!*
-+!* Copyright (c) 2008-2010 ABINIT Group (Damien Caliste)
-+!* All rights reserved.
-+!*
-+!* This file is part of the ABINIT software package. For license information,
-+!* please see the COPYING file in the top-level directory of the ABINIT source
-+!* distribution.
-+!*
-+!*
-+
-+module m_ab7_symmetry
-+
-+  use defs_basis
-+
-+  implicit none
-+
-+  private
-+
-+  integer, parameter, public :: AB7_MAX_SYMMETRIES = 384
-+
-+  type, public :: symmetry_type
-+     ! The input characteristics
-+     real(dp) :: tolsym
-+     real(dp) :: rprimd(3,3), gprimd(3,3), rmet(3,3)
-+     integer :: nAtoms
-+     integer, pointer :: typeAt(:)
-+     real(dp), pointer :: xRed(:,:)
-+
-+     logical :: withField
-+     real(dp) :: field(3)
-+
-+     logical :: withJellium
-+
-+     integer :: withSpin
-+     real(dp), pointer :: spinAt(:,:)
-+
-+     logical :: withSpinOrbit
-+
-+     integer :: vacuum(3)
-+
-+     ! The output characteristics
-+     ! The bravais parameters
-+     integer :: nBravSym
-+     integer :: bravais(11), bravSym(3, 3, AB7_MAX_SYMMETRIES)
-+     ! The symmetry matrices
-+     logical  :: auto
-+     integer  :: nSym
-+     integer, pointer  :: sym(:,:,:)
-+     real(dp), pointer :: transNon(:,:)
-+     integer, pointer  :: symAfm(:)
-+     ! Some additional information
-+     integer          :: multiplicity
-+     real(dp)         :: genAfm(3)
-+     integer          :: spaceGroup, pointGroupMagn
-+     integer, pointer :: indexingAtoms(:,:,:)
-+  end type symmetry_type
-+
-+  ! We store here a list of symmetry objects to be able to
-+  ! call several symmetry operations on different objects.
-+  ! The simplest portable way to do it, is to create
-+  ! a list of Fortran structure and to use the list index
-+  ! as an identifier that can be given to the other languages.
-+  type, private :: symmetry_list
-+     integer                       :: id
-+     type(symmetry_list),  pointer :: next
-+     type(symmetry_type)           :: data
-+  end type symmetry_list
-+  type(symmetry_list), pointer :: my_symmetries
-+  integer :: n_symmetries = 0
-+
-+  logical, private, parameter :: AB_DBG = .false.
-+
-+  public :: symmetry_new
-+  public :: symmetry_free
-+  public :: symmetry_set_tolerance
-+  public :: symmetry_set_lattice
-+  public :: symmetry_set_structure
-+  public :: symmetry_set_collinear_spin
-+  public :: symmetry_set_spin
-+  public :: symmetry_set_spin_orbit
-+  public :: symmetry_set_field
-+  public :: symmetry_set_jellium
-+  public :: symmetry_set_periodicity
-+  public :: symmetry_set_n_sym
-+
-+  public :: symmetry_get_from_id
-+  public :: symmetry_get_n_atoms
-+  public :: symmetry_get_n_sym
-+  public :: symmetry_get_multiplicity
-+  public :: symmetry_get_bravais
-+  public :: symmetry_get_matrices
-+  public :: symmetry_get_matrices_p
-+  public :: symmetry_get_group
-+  public :: symmetry_get_equivalent_atom
-+
-+contains
-+
-+  subroutine new_item(token)
-+
-+
-+!This section has been created automatically by the script Abilint (TD).
-+!Do not modify the following lines by hand.
-+!End of the abilint section
-+
-+    type(symmetry_list), pointer :: token
-+
-+    ! We allocate a new list token and prepend it.
-+    if (AB_DBG) write(0,*) "AB symmetry: create a new token."
-+
-+    ! Init case, very first call.
-+    if (n_symmetries == 0) then
-+       nullify(my_symmetries)
-+    end if
-+
-+    ! Normal treatment.
-+    n_symmetries = n_symmetries + 1
-+
-+    allocate(token)
-+    token%id = n_symmetries
-+    call new_symmetry(token%data)
-+    token%next => my_symmetries
-+
-+    my_symmetries => token
-+    if (AB_DBG) write(0,*) "AB symmetry: creation OK with id ", token%id
-+  end subroutine new_item
-+
-+  subroutine free_item(token)
-+
-+
-+!This section has been created automatically by the script Abilint (TD).
-+!Do not modify the following lines by hand.
-+!End of the abilint section
-+
-+    type(symmetry_list), pointer :: token
-+
-+    type(symmetry_list), pointer :: tmp
-+
-+    if (.not. associated(token)) then
-+       return
-+    end if
-+
-+    call free_symmetry(token%data)
-+
-+    if (AB_DBG) write(0,*) "AB symmetry: free request on token ", token%id
-+    ! We remove token from the list.
-+    if (my_symmetries%id == token%id) then
-+       my_symmetries => token%next
-+    else
-+       tmp => my_symmetries
-+       do
-+          if (.not.associated(tmp)) then
-+             return
-+          end if
-+          if (associated(tmp%next) .and. tmp%next%id == token%id) then
-+             exit
-+          end if
-+          tmp => tmp%next
-+       end do
-+       tmp%next => token%next
-+    end if
-+    deallocate(token)
-+    if (AB_DBG) write(0,*) "AB symmetry: free done"
-+  end subroutine free_item
-+
-+  subroutine get_item(token, id)
-+
-+
-+    type(symmetry_list), pointer :: token
-+    integer, intent(in) :: id
-+
-+    type(symmetry_list), pointer :: tmp
-+
-+    if (AB_DBG) write(0,*) "AB symmetry: request list element ", id
-+    nullify(token)
-+
-+    tmp => my_symmetries
-+    do
-+       if (.not. associated(tmp)) then
-+          exit
-+       end if
-+       if (tmp%id == id) then
-+          token => tmp
-+          return
-+       end if
-+       tmp => tmp%next
-+    end do
-+  end subroutine get_item
-+
-+  subroutine symmetry_get_from_id(sym, id, errno)
-+
-+    type(symmetry_type), pointer :: sym
-+    integer, intent(in) :: id
-+    integer, intent(out) :: errno
-+
-+    type(symmetry_list), pointer :: token
-+
-+    errno = AB7_NO_ERROR
-+    call get_item(token, id)
-+    if (associated(token)) then
-+       sym => token%data
-+       if (sym%nSym <= 0) then
-+          ! We do the computation of the matrix part.
-+          call compute_matrices(sym, errno)
-+       end if
-+    else
-+       errno = AB7_ERROR_OBJ
-+       nullify(sym)
-+    end if
-+  end subroutine symmetry_get_from_id
-+
-+  subroutine new_symmetry(sym)
-+
-+
-+    type(symmetry_type), intent(out) :: sym
-+
-+    if (AB_DBG) write(0,*) "AB symmetry: create a new symmetry object."
-+    nullify(sym%xRed)
-+    nullify(sym%spinAt)
-+    nullify(sym%typeAt)
-+    sym%tolsym   = tol8
-+    sym%auto     = .true.
-+    sym%nSym     = 0
-+    nullify(sym%sym)
-+    nullify(sym%symAfm)
-+    nullify(sym%transNon)
-+    sym%nBravSym = -1
-+    sym%withField   = .false.
-+    sym%withJellium = .false.
-+    sym%withSpin = 1
-+    sym%withSpinOrbit = .false.
-+    sym%multiplicity = -1
-+    nullify(sym%indexingAtoms)
-+    sym%vacuum = 0
-+  end subroutine new_symmetry
-+
-+  subroutine free_symmetry(sym)
-+
-+
-+    type(symmetry_type), intent(inout) :: sym
-+
-+    if (AB_DBG) write(0,*) "AB symmetry: free a symmetry."
-+
-+    if (associated(sym%xRed)) deallocate(sym%xRed)
-+    if (associated(sym%spinAt)) deallocate(sym%spinAt)
-+    if (associated(sym%typeAt)) deallocate(sym%typeAt)
-+    if (associated(sym%indexingAtoms)) deallocate(sym%indexingAtoms)
-+    if (associated(sym%sym)) deallocate(sym%sym)
-+    if (associated(sym%symAfm)) deallocate(sym%symAfm)
-+    if (associated(sym%transNon)) deallocate(sym%transNon)
-+  end subroutine free_symmetry
-+
-+
-+
-+
-+
-+  subroutine symmetry_new(id)
-+
-+
-+!This section has been created automatically by the script Abilint (TD).
-+!Do not modify the following lines by hand.
-+!End of the abilint section
-+
-+    integer, intent(out) :: id
-+
-+    type(symmetry_list), pointer :: token
-+
-+    if (AB_DBG) write(0,*) "AB symmetry: call new symmetry."
-+    call new_item(token)
-+    id = token%id
-+  end subroutine symmetry_new
-+
-+  subroutine symmetry_free(id)
-+
-+
-+!This section has been created automatically by the script Abilint (TD).
-+!Do not modify the following lines by hand.
-+!End of the abilint section
-+
-+    integer, intent(in) :: id
-+
-+    type(symmetry_list), pointer :: token
-+
-+    if (AB_DBG) write(0,*) "AB symmetry: call free symmetry."
-+
-+    call get_item(token, id)
-+    if (associated(token)) call free_item(token)
-+  end subroutine symmetry_free
-+
-+  subroutine symmetry_set_tolerance(id, tolsym, errno)
-+
-+
-+!This section has been created automatically by the script Abilint (TD).
-+!Do not modify the following lines by hand.
-+!End of the abilint section
-+
-+    integer, intent(in) :: id
-+    real(dp), intent(in) :: tolsym
-+    integer, intent(out) :: errno
-+
-+    type(symmetry_list), pointer :: token
-+
-+    if (AB_DBG) write(0,*) "AB symmetry: call set tolerance."
-+
-+    errno = AB7_NO_ERROR
-+    call get_item(token, id)
-+    if (.not. associated(token)) then
-+       errno = AB7_ERROR_OBJ
-+       return
-+    end if
-+
-+    token%data%tolsym = tolsym
-+
-+    ! We unset all the computed symmetries
-+    token%data%nBravSym = -1
-+    if (token%data%auto) then
-+       token%data%nSym  = 0
-+    end if
-+  end subroutine symmetry_set_tolerance
-+
-+  subroutine symmetry_set_lattice(id, rprimd, errno)
-+
-+
-+!This section has been created automatically by the script Abilint (TD).
-+!Do not modify the following lines by hand.
-+  use interfaces_42_geometry
-+!End of the abilint section
-+
-+    integer, intent(in) :: id
-+    real(dp), intent(in) :: rprimd(3,3)
-+    integer, intent(out) :: errno
-+
-+    type(symmetry_list), pointer :: token
-+    real(dp) :: ucvol
-+    real(dp) :: gmet(3,3)
-+
-+    if (AB_DBG) write(0,*) "AB symmetry: call set lattice."
-+    if (AB_DBG) write(0, "(A,3F12.6,A)") "  (", rprimd(:,1), ")"
-+    if (AB_DBG) write(0, "(A,3F12.6,A)") "  (", rprimd(:,2), ")"
-+    if (AB_DBG) write(0, "(A,3F12.6,A)") "  (", rprimd(:,3), ")"
-+
-+    errno = AB7_NO_ERROR
-+    call get_item(token, id)
-+    if (.not. associated(token)) then
-+       errno = AB7_ERROR_OBJ
-+       return
-+    end if
-+
-+    token%data%rprimd = rprimd
-+    call metric(gmet, token%data%gprimd, -1, token%data%rmet, rprimd, ucvol)
-+
-+    ! We unset all the computed symmetries
-+    token%data%nBravSym = -1
-+    if (token%data%auto) then
-+       token%data%nSym  = 0
-+    end if
-+  end subroutine symmetry_set_lattice
-+
-+  subroutine symmetry_set_structure(id, nAtoms, typeAt, xRed, errno)
-+
-+
-+!This section has been created automatically by the script Abilint (TD).
-+!Do not modify the following lines by hand.
-+!End of the abilint section
-+
-+    integer, intent(in) :: id
-+    integer, intent(in) :: nAtoms
-+    integer, intent(in) :: typeAt(nAtoms)
-+    real(dp), intent(in) :: xRed(3,nAtoms)
-+    integer, intent(out) :: errno
-+
-+    type(symmetry_list), pointer :: token
-+    integer :: i
-+
-+    if (AB_DBG) write(0,*) "AB symmetry: call set structure."
-+    if (AB_DBG) write(0, "(A,I3,A)") "  ", nAtoms, " atoms"
-+    if (AB_DBG) then
-+       do i = 1, nAtoms, 1
-+          write(0, "(A,3F12.6,I3)") "  ", xRed(:, i), typeAt(i)
-+       end do
-+    end if
-+
-+    errno = AB7_NO_ERROR
-+    call get_item(token, id)
-+    if (.not. associated(token)) then
-+       errno = AB7_ERROR_OBJ
-+       return
-+    end if
-+
-+    token%data%nAtoms =  nAtoms
-+    allocate(token%data%typeAt(nAtoms))
-+    token%data%typeAt = typeAt
-+    allocate(token%data%xRed(3, nAtoms))
-+    token%data%xRed   = xRed
-+
-+    ! We unset only the symmetries
-+    if (token%data%auto) then
-+       token%data%nSym = 0
-+    end if
-+    if (associated(token%data%indexingAtoms)) deallocate(token%data%indexingAtoms)
-+  end subroutine symmetry_set_structure
-+
-+  subroutine symmetry_set_spin(id, nAtoms, spinAt, errno)
-+
-+
-+!This section has been created automatically by the script Abilint (TD).
-+!Do not modify the following lines by hand.
-+!End of the abilint section
-+
-+    integer, intent(in) :: id
-+    integer, intent(in) :: nAtoms
-+    real(dp), intent(in) :: spinAt(3,nAtoms)
-+    integer, intent(out) :: errno
-+
-+    type(symmetry_list), pointer :: token
-+    integer :: i
-+
-+    if (AB_DBG) write(0,*) "AB symmetry: call set spin."
-+    if (AB_DBG) then
-+       do i = 1, nAtoms, 1
-+          write(0, "(A,3F12.6)") "  ", spinAt(:, i)
-+       end do
-+    end if
-+
-+    errno = AB7_NO_ERROR
-+    call get_item(token, id)
-+    if (.not. associated(token)) then
-+       errno = AB7_ERROR_OBJ
-+       return
-+    end if
-+    if (token%data%nAtoms /= nAtoms) then
-+       errno = AB7_ERROR_ARG
-+       return
-+    end if
-+
-+    token%data%withSpin = 4
-+    allocate(token%data%spinAt(3, nAtoms))
-+    token%data%spinAt = spinAt
-+
-+    ! We unset only the symmetries
-+    if (token%data%auto) then
-+       token%data%nSym  = 0
-+    end if
-+  end subroutine symmetry_set_spin
-+
-+  subroutine symmetry_set_collinear_spin(id, nAtoms, spinAt, errno)
-+
-+
-+!This section has been created automatically by the script Abilint (TD).
-+!Do not modify the following lines by hand.
-+!End of the abilint section
-+
-+    integer, intent(in) :: id
-+    integer, intent(in) :: nAtoms
-+    integer, intent(in) :: spinAt(nAtoms)
-+    integer, intent(out) :: errno
-+
-+    type(symmetry_list), pointer :: token
-+    integer :: i
-+
-+    if (AB_DBG) write(0,*) "AB symmetry: call set collinear spin."
-+    if (AB_DBG) then
-+       do i = 1, nAtoms, 1
-+          write(0, "(A,I3)") "  ", spinAt(i)
-+       end do
-+    end if
-+
-+    errno = AB7_NO_ERROR
-+    call get_item(token, id)
-+    if (.not. associated(token)) then
-+       errno = AB7_ERROR_OBJ
-+       return
-+    end if
-+    if (token%data%nAtoms /= nAtoms) then
-+       errno = AB7_ERROR_ARG
-+       return
-+    end if
-+
-+    token%data%withSpin = 2
-+    allocate(token%data%spinAt(1, nAtoms))
-+    token%data%spinAt = real(reshape(spinAt, (/ 1, nAtoms /)), dp)
-+
-+    ! We unset only the symmetries
-+    if (token%data%auto) then
-+       token%data%nSym  = 0
-+    end if
-+  end subroutine symmetry_set_collinear_spin
-+
-+  subroutine symmetry_set_spin_orbit(id, withSpinOrbit, errno)
-+
-+
-+!This section has been created automatically by the script Abilint (TD).
-+!Do not modify the following lines by hand.
-+!End of the abilint section
-+
-+    integer, intent(in) :: id
-+    logical, intent(in) :: withSpinOrbit
-+    integer, intent(out) :: errno
-+
-+    type(symmetry_list), pointer :: token
-+
-+    if (AB_DBG) write(0,*) "AB symmetry: call set spin orbit."
-+
-+    errno = AB7_NO_ERROR
-+    call get_item(token, id)
-+    if (.not. associated(token)) then
-+       errno = AB7_ERROR_OBJ
-+       return
-+    end if
-+
-+    token%data%withSpinOrbit = withSpinOrbit
-+
-+    ! We unset only the symmetries
-+    if (token%data%auto) then
-+       token%data%nSym  = 0
-+    end if
-+  end subroutine symmetry_set_spin_orbit
-+
-+  subroutine symmetry_set_field(id, field, errno)
-+
-+
-+!This section has been created automatically by the script Abilint (TD).
-+!Do not modify the following lines by hand.
-+!End of the abilint section
-+
-+    integer, intent(in) :: id
-+    real(dp), intent(in) :: field(3)
-+    integer, intent(out) :: errno
-+
-+    type(symmetry_list), pointer :: token
-+
-+    if (AB_DBG) write(0,*) "AB symmetry: call set field."
-+
-+    errno = AB7_NO_ERROR
-+    call get_item(token, id)
-+    if (.not. associated(token)) then
-+       errno = AB7_ERROR_OBJ
-+       return
-+    end if
-+
-+    token%data%withField = .true.
-+    token%data%field = field
-+
-+    ! We unset all the computed symmetries
-+    token%data%nBravSym = -1
-+    if (token%data%auto) then
-+       token%data%nSym  = 0
-+    end if
-+  end subroutine symmetry_set_field
-+
-+  subroutine symmetry_set_jellium(id, jellium, errno)
-+
-+
-+!This section has been created automatically by the script Abilint (TD).
-+!Do not modify the following lines by hand.
-+!End of the abilint section
-+
-+    integer, intent(in) :: id
-+    logical, intent(in) :: jellium
-+    integer, intent(out) :: errno
-+
-+    type(symmetry_list), pointer :: token
-+
-+    if (AB_DBG) write(0,*) "AB symmetry: call set jellium."
-+
-+    errno = AB7_NO_ERROR
-+    call get_item(token, id)
-+    if (.not. associated(token)) then
-+       errno = AB7_ERROR_OBJ
-+       return
-+    end if
-+
-+    token%data%withJellium = jellium
-+
-+    ! We unset only the symmetries
-+    if (token%data%auto) then
-+       token%data%nSym  = 0
-+    end if
-+  end subroutine symmetry_set_jellium
-+
-+  subroutine symmetry_set_periodicity(id, periodic, errno)
-+
-+
-+!This section has been created automatically by the script Abilint (TD).
-+!Do not modify the following lines by hand.
-+!End of the abilint section
-+
-+    integer, intent(in) :: id
-+    logical, intent(in) :: periodic(3)
-+    integer, intent(out) :: errno
-+
-+    type(symmetry_list), pointer :: token
-+
-+    if (AB_DBG) write(0,*) "AB symmetry: call set periodicity."
-+    if (AB_DBG) write(0, "(A,3L1,A)") "  (", periodic, ")"
-+
-+    errno = AB7_NO_ERROR
-+    call get_item(token, id)
-+    if (.not. associated(token)) then
-+       errno = AB7_ERROR_OBJ
-+       return
-+    end if
-+
-+    token%data%vacuum = 0
-+    if (.not. periodic(1)) token%data%vacuum(1) = 1
-+    if (.not. periodic(2)) token%data%vacuum(2) = 1
-+    if (.not. periodic(3)) token%data%vacuum(3) = 1
-+  end subroutine symmetry_set_periodicity
-+
-+
-+
-+
-+
-+  subroutine symmetry_get_n_atoms(id, nAtoms, errno)
-+    !scalars
-+
-+!This section has been created automatically by the script Abilint (TD).
-+!Do not modify the following lines by hand.
-+!End of the abilint section
-+
-+    integer, intent(in) :: id
-+    integer, intent(out) :: errno
-+    integer, intent(out) :: nAtoms
-+
-+    type(symmetry_list), pointer :: token
-+
-+    if (AB_DBG) write(0,*) "AB symmetry: call get nAtoms."
-+
-+    errno = AB7_NO_ERROR
-+    call get_item(token, id)
-+    if (.not. associated(token)) then
-+       errno = AB7_ERROR_OBJ
-+       return
-+    end if
-+
-+    nAtoms = token%data%nAtoms
-+  end subroutine symmetry_get_n_atoms
-+
-+  subroutine compute_bravais(sym)
-+
-+
-+!This section has been created automatically by the script Abilint (TD).
-+!Do not modify the following lines by hand.
-+  use interfaces_42_geometry
-+!End of the abilint section
-+
-+    type(symmetry_type), intent(inout) :: sym
-+
-+    integer :: berryopt
-+
-+    ! We do the computation
-+    if (sym%withField) then
-+       berryopt = 4
-+    else
-+       berryopt = 0
-+    end if
-+    if (AB_DBG) write(0,*) "AB symmetry: call ABINIT symlatt."
-+    call symlatt(sym%bravais, AB7_MAX_SYMMETRIES, &
-+         & sym%nBravSym, sym%bravSym, sym%rprimd, sym%tolsym)
-+    if (AB_DBG) write(0,*) "AB symmetry: call ABINIT OK."
-+    if (AB_DBG) write(0, "(A,I3)") "  nSymBrav :", sym%nBravSym
-+    if (AB_DBG) write(0, "(A,I3)") "  holohedry:", sym%bravais(1)
-+    if (AB_DBG) write(0, "(A,I3)") "  center   :", sym%bravais(2)
-+  end subroutine compute_bravais
-+
-+  subroutine symmetry_get_bravais(id, bravais, holohedry, center, &
-+       & nBravSym, bravSym, errno)
-+    !scalars
-+
-+!This section has been created automatically by the script Abilint (TD).
-+!Do not modify the following lines by hand.
-+!End of the abilint section
-+
-+    integer, intent(in) :: id
-+    integer, intent(out) :: errno
-+    integer, intent(out) :: nBravSym, holohedry, center
-+    !arrays
-+    integer, intent(out) :: bravais(3,3), bravSym(3, 3, AB7_MAX_SYMMETRIES)
-+
-+    type(symmetry_list), pointer :: token
-+
-+    if (AB_DBG) write(0,*) "AB symmetry: call get bravais."
-+
-+    errno = AB7_NO_ERROR
-+    call get_item(token, id)
-+    if (.not. associated(token)) then
-+       errno = AB7_ERROR_OBJ
-+       return
-+    end if
-+
-+    if (token%data%nBravSym < 0) then
-+       ! We do the computation
-+       call compute_bravais(token%data)
-+    end if
-+    
-+    holohedry = token%data%bravais(1)
-+    center    = token%data%bravais(2)
-+    bravais   = reshape(token%data%bravais(3:11), (/ 3,3 /))
-+    nBravSym  = token%data%nBravSym
-+    bravSym(:, :, 1:nBravSym) = token%data%bravSym(:, :, 1:nBravSym)
-+  end subroutine symmetry_get_bravais
-+
-+  subroutine compute_matrices(sym, errno)
-+
-+
-+!This section has been created automatically by the script Abilint (TD).
-+!Do not modify the following lines by hand.
-+  use interfaces_42_geometry
-+!End of the abilint section
-+
-+    type(symmetry_type), intent(inout) :: sym
-+    integer, intent(out) :: errno
-+
-+    integer :: berryopt, jellslab, noncol
-+    integer :: use_inversion
-+    real(dp), pointer :: spinAt_(:,:)
-+    integer  :: sym_(3, 3, AB7_MAX_SYMMETRIES)
-+    real(dp) :: transNon_(3, AB7_MAX_SYMMETRIES)
-+    integer  :: symAfm_(AB7_MAX_SYMMETRIES)
-+
-+    errno = AB7_NO_ERROR
-+
-+    if (sym%nBravSym < 0) then
-+       ! We do the computation of the Bravais part.
-+       call compute_bravais(sym)
-+    end if
-+
-+    if (sym%withField) then
-+       berryopt = 4
-+    else
-+       berryopt = 0
-+    end if
-+    if (sym%withJellium) then
-+       jellslab = 1
-+    else
-+       jellslab = 0
-+    end if
-+    if (sym%withSpin == 4) then
-+       noncol = 1
-+       spinAt_ => sym%spinAt
-+    else if (sym%withSpin == 2) then
-+       noncol = 0
-+       spinAt_ => sym%spinAt
-+    else
-+       noncol = 0
-+       allocate(spinAt_(3, sym%nAtoms))
-+       spinAt_ = 0
-+    end if
-+    if (sym%withSpinOrbit) then
-+       use_inversion = 0
-+    else
-+       use_inversion = 1
-+    end if
-+
-+    if (sym%nsym == 0) then
-+       if (AB_DBG) write(0,*) "AB symmetry: call ABINIT symfind."
-+       call symfind(berryopt, sym%field, sym%gprimd, jellslab, AB7_MAX_SYMMETRIES, &
-+            & sym%nAtoms, noncol, sym%nBravSym, sym%nSym, sym%bravSym, spinAt_, &
-+            & symAfm_, sym_, transNon_, sym%tolsym, sym%typeAt, &
-+            & use_inversion, sym%xRed)
-+       if (AB_DBG) write(0,*) "AB symmetry: call ABINIT OK."
-+       if (AB_DBG) write(0, "(A,I3)") "  nSym:", sym%nSym
-+       if (associated(sym%sym)) deallocate(sym%sym)
-+       if (associated(sym%symAfm)) deallocate(sym%symAfm)
-+       if (associated(sym%transNon)) deallocate(sym%transNon)
-+       allocate(sym%sym(3, 3, sym%nSym))
-+       sym%sym(:,:,:) = sym_(:,:, 1:sym%nSym)
-+       allocate(sym%symAfm(sym%nSym))
-+       sym%symAfm(:) = symAfm_(1:sym%nSym)
-+       allocate(sym%transNon(3, sym%nSym))
-+       sym%transNon(:,:) = transNon_(:, 1:sym%nSym)
-+    else if (sym%nsym < 0) then
-+       sym%nsym = -sym%nsym
-+       sym_(:,:, 1:sym%nSym) = sym%sym(:,:,:)
-+       transNon_(:, 1:sym%nSym) = sym%transNon(:,:)
-+       symAfm_(1:sym%nSym) = sym%symAfm(:)
-+    end if
-+
-+    if (sym%withSpin == 1) then
-+       deallocate(spinAt_)
-+    end if
-+    
-+    if (AB_DBG) write(0,*) "AB symmetry: call ABINIT symanal."
-+    call symanal(sym%bravais, 0, sym%genAfm, AB7_MAX_SYMMETRIES, sym%nSym, &
-+         & sym%pointGroupMagn, sym%rprimd, sym%spaceGroup, symAfm_, &
-+         & sym_, transNon_, sym%tolsym)
-+    if (AB_DBG) write(0,*) "AB symmetry: call ABINIT OK."
-+    sym%transNon(:,:) = transNon_(:, 1:sym%nSym)
-+
-+    if (sym%bravais(1) < 0) then
-+       sym%multiplicity = 2
-+    else
-+       sym%multiplicity = 1
-+    end if
-+    if (AB_DBG) write(0, "(A,I3)") "  multi:", sym%multiplicity
-+    if (AB_DBG) write(0, "(A,I3)") "  space:", sym%spaceGroup
-+  end subroutine compute_matrices
-+
-+  subroutine symmetry_get_n_sym(id, nSym, errno)
-+    !scalars
-+
-+!This section has been created automatically by the script Abilint (TD).
-+!Do not modify the following lines by hand.
-+!End of the abilint section
-+
-+    integer, intent(in) :: id
-+    integer, intent(out) :: errno
-+    integer, intent(out) :: nSym
-+
-+    type(symmetry_list), pointer :: token
-+
-+    if (AB_DBG) write(0,*) "AB symmetry: call get nSym."
-+
-+    errno = AB7_NO_ERROR
-+    call get_item(token, id)
-+    if (.not. associated(token)) then
-+       errno = AB7_ERROR_OBJ
-+       return
-+    end if
-+
-+    if (token%data%nSym <= 0) then
-+       ! We do the computation of the matrix part.
-+       call compute_matrices(token%data, errno)
-+    end if
-+
-+    nSym = token%data%nSym
-+  end subroutine symmetry_get_n_sym
-+
-+  subroutine symmetry_set_n_sym(id, nSym, sym, transNon, symAfm, errno)
-+    !scalars
-+
-+!This section has been created automatically by the script Abilint (TD).
-+!Do not modify the following lines by hand.
-+!End of the abilint section
-+
-+    integer, intent(in)  :: id
-+    integer, intent(in)  :: nSym
-+    integer, intent(in)  :: sym(3, 3, nSym)
-+    real(dp), intent(in) :: transNon(3, nSym)
-+    integer, intent(in)  :: symAfm(nSym)
-+    integer, intent(out) :: errno
-+
-+    type(symmetry_list), pointer :: token
-+
-+    if (AB_DBG) write(0,*) "AB symmetry: call get nSym."
-+
-+    errno = AB7_NO_ERROR
-+    call get_item(token, id)
-+    if (.not. associated(token)) then
-+       errno = AB7_ERROR_OBJ
-+       return
-+    end if
-+
-+    if (nSym <= 0) then
-+       errno = AB7_ERROR_ARG
-+       return
-+    else
-+       allocate(token%data%sym(3, 3, nSym))
-+       token%data%sym(:,:,:) = sym(:,:,:)
-+       allocate(token%data%symAfm(nSym))
-+       token%data%symAfm(:) = symAfm(:)
-+       allocate(token%data%transNon(3, nSym))
-+       token%data%transNon(:,:) = transNon(:,:)
-+
-+       token%data%auto = .false.
-+       token%data%nsym = -nSym
-+    end if
-+
-+    ! We do the computation of the matrix part.
-+    call compute_matrices(token%data, errno)
-+  end subroutine symmetry_set_n_sym
-+
-+  subroutine symmetry_get_matrices(id, nSym, sym, transNon, symAfm, errno)
-+
-+
-+!This section has been created automatically by the script Abilint (TD).
-+!Do not modify the following lines by hand.
-+!End of the abilint section
-+
-+    integer, intent(in) :: id
-+    integer, intent(out) :: errno
-+    integer, intent(out) :: nSym
-+    integer, intent(out)  :: sym(3, 3, AB7_MAX_SYMMETRIES)
-+    integer, intent(out)  :: symAfm(AB7_MAX_SYMMETRIES)
-+    real(dp), intent(out) :: transNon(3, AB7_MAX_SYMMETRIES)
-+
-+    type(symmetry_list), pointer :: token
-+
-+    if (AB_DBG) write(0,*) "AB symmetry: call get matrices."
-+
-+    errno = AB7_NO_ERROR
-+    call get_item(token, id)
-+    if (.not. associated(token)) then
-+       errno = AB7_ERROR_OBJ
-+       return
-+    end if
-+
-+    if (token%data%nSym <= 0) then
-+       ! We do the computation of the matrix part.
-+       call compute_matrices(token%data, errno)
-+    end if
-+
-+    nSym                = token%data%nSym
-+    sym(:, :, 1:nSym)   = token%data%sym(:, :,:)
-+    symAfm(1:nSym)      = token%data%symAfm(:)
-+    transNon(:, 1:nSym) = token%data%transNon(:,:)
-+  end subroutine symmetry_get_matrices
-+
-+  subroutine symmetry_get_matrices_p(id, nSym, sym, transNon, symAfm, errno)
-+
-+
-+!This section has been created automatically by the script Abilint (TD).
-+!Do not modify the following lines by hand.
-+!End of the abilint section
-+
-+    integer, intent(in) :: id
-+    integer, intent(out) :: errno
-+    integer, intent(out) :: nSym
-+    integer, pointer  :: sym(:,:,:)
-+    integer, pointer  :: symAfm(:)
-+    real(dp), pointer :: transNon(:,:)
-+
-+    type(symmetry_list), pointer :: token
-+
-+    if (AB_DBG) write(0,*) "AB symmetry: call get matrices as pointers."
-+
-+    errno = AB7_NO_ERROR
-+    call get_item(token, id)
-+    if (.not. associated(token)) then
-+       errno = AB7_ERROR_OBJ
-+       return
-+    end if
-+
-+    if (token%data%nSym <= 0) then
-+       ! We do the computation of the matrix part.
-+       call compute_matrices(token%data, errno)
-+    end if
-+
-+    nSym     =  token%data%nSym
-+    sym      => token%data%sym
-+    symAfm   => token%data%symAfm
-+    transNon => token%data%transNon
-+  end subroutine symmetry_get_matrices_p
-+
-+  subroutine symmetry_get_multiplicity(id, multiplicity, errno)
-+
-+
-+!This section has been created automatically by the script Abilint (TD).
-+!Do not modify the following lines by hand.
-+!End of the abilint section
-+
-+    integer, intent(in) :: id
-+    integer, intent(out) :: multiplicity, errno
-+
-+    type(symmetry_list), pointer :: token
-+
-+    if (AB_DBG) write(0,*) "AB symmetry: call get multiplicity."
-+
-+    errno = AB7_NO_ERROR
-+    call get_item(token, id)
-+    if (.not. associated(token)) then
-+       errno = AB7_ERROR_OBJ
-+       return
-+    end if
-+
-+    if (token%data%multiplicity < 0) then
-+       ! We do the computation of the matrix part.
-+       call compute_matrices(token%data, errno)
-+    end if
-+    multiplicity = token%data%multiplicity
-+  end subroutine symmetry_get_multiplicity
-+
-+  subroutine symmetry_get_group(id, spaceGroup, spaceGroupId, &
-+       & pointGroupMagn, genAfm, errno)
-+
-+
-+!This section has been created automatically by the script Abilint (TD).
-+!Do not modify the following lines by hand.
-+  use interfaces_42_geometry
-+!End of the abilint section
-+
-+    integer, intent(in)            :: id
-+    integer, intent(out)           :: errno
-+    real(dp), intent(out)          :: genAfm(3)
-+    character(len=15), intent(out) :: spaceGroup
-+    integer, intent(out)           :: spaceGroupId, pointGroupMagn
-+
-+    type(symmetry_list), pointer  :: token
-+    integer :: sporder
-+    character(len=1)  :: brvLattice
-+    character(len=15) :: ptintsb,ptschsb,schsb,spgrp
-+    character(len=35) :: intsbl
-+
-+    if (AB_DBG) write(0,*) "AB symmetry: call get group."
-+
-+    errno = AB7_NO_ERROR
-+    call get_item(token, id)
-+    if (.not. associated(token)) then
-+       errno = AB7_ERROR_OBJ
-+       return
-+    end if
-+
-+    if (token%data%multiplicity < 0) then
-+       ! We do the computation of the matrix part.
-+       call compute_matrices(token%data, errno)
-+    end if
-+
-+    if (token%data%multiplicity /= 1) then
-+       errno = AB7_ERROR_SYM_NOT_PRIMITIVE
-+       return
-+    end if
-+
-+    call spgdata(brvLattice,spgrp,intsbl,ptintsb,ptschsb,&
-+         &  schsb,1,token%data%spaceGroup,sporder,1)
-+
-+    write(spaceGroup, "(3A)") brvLattice, " ", trim(spgrp(1:13))
-+    pointGroupMagn = token%data%pointGroupMagn
-+    spaceGroupId   = token%data%spaceGroup
-+    genAfm         = token%data%genAfm
-+  end subroutine symmetry_get_group
-+
-+  subroutine compute_equivalent_atoms(sym)
-+
-+
-+!This section has been created automatically by the script Abilint (TD).
-+!Do not modify the following lines by hand.
-+  use interfaces_32_util
-+  use interfaces_42_geometry
-+!End of the abilint section
-+
-+    type(symmetry_type), intent(inout) :: sym
-+
-+    integer, allocatable :: symrec(:,:,:)
-+    integer :: isym
-+
-+    if (.not. associated(sym%indexingAtoms)) &
-+         & allocate(sym%indexingAtoms(4, sym%nSym, sym%nAtoms))
-+
-+    !Get the symmetry matrices in terms of reciprocal basis
-+    allocate(symrec(3, 3, sym%nSym))
-+    do isym = 1, sym%nSym, 1
-+       call mati3inv(sym%sym(:,:,isym), symrec(:,:,isym))
-+    end do
-+    
-+    !Obtain a list of rotated atom labels:
-+    call symatm(sym%indexingAtoms, sym%nAtoms, sym%nSym, symrec, &
-+         & sym%transNon, sym%tolsym, sym%typeAt, sym%xRed)
-+
-+    deallocate(symrec)
-+  end subroutine compute_equivalent_atoms
-+
-+  subroutine symmetry_get_equivalent_atom(id, equiv, iAtom, errno)
-+
-+
-+!This section has been created automatically by the script Abilint (TD).
-+!Do not modify the following lines by hand.
-+!End of the abilint section
-+
-+    integer, intent(in)  :: id
-+    integer, intent(in)  :: iAtom
-+    integer, intent(out) :: equiv(4, AB7_MAX_SYMMETRIES)
-+    integer, intent(out) :: errno
-+
-+    type(symmetry_list), pointer  :: token
-+
-+    if (AB_DBG) write(0,*) "AB symmetry: call get equivalent."
-+
-+    errno = AB7_NO_ERROR
-+    call get_item(token, id)
-+    if (.not. associated(token)) then
-+       errno = AB7_ERROR_OBJ
-+       return
-+    end if
-+
-+    if (iAtom < 1 .or. iAtom > token%data%nAtoms) then
-+       errno = AB7_ERROR_ARG
-+       return
-+    end if
-+
-+    if (.not. associated(token%data%indexingAtoms)) then
-+       ! We do the computation of the matrix part.
-+       call compute_equivalent_atoms(token%data)
-+    end if
-+
-+    equiv(:, 1:token%data%nSym) = token%data%indexingAtoms(:,:,iAtom)
-+  end subroutine symmetry_get_equivalent_atom
-+
-+end module m_ab7_symmetry
-diff -urN bigdft-abi-1.0.4.old/libABINIT/src/42_geometry/symfind.F90 bigdft-abi-1.0.4.new/libABINIT/src/42_geometry/symfind.F90
---- bigdft-abi-1.0.4.old/libABINIT/src/42_geometry/symfind.F90	2012-07-09 16:43:33.000000000 +0200
-+++ bigdft-abi-1.0.4.new/libABINIT/src/42_geometry/symfind.F90	2013-06-11 16:51:00.000000000 +0200
-@@ -49,7 +49,7 @@
- !!  be 0 0 0 each for a symmorphic space group)
- !!
- !! PARENTS
--!!      ingeo,ab6_symmetry_f90
-+!!      ingeo,ab7_symmetry_f90
- !!
- !! CHILDREN
- !!      leave_new,wrtout
-diff -urN bigdft-abi-1.0.4.old/libABINIT/src/56_mixing/findminscf.F90 bigdft-abi-1.0.4.new/libABINIT/src/56_mixing/findminscf.F90
---- bigdft-abi-1.0.4.old/libABINIT/src/56_mixing/findminscf.F90	2012-07-09 16:43:33.000000000 +0200
-+++ bigdft-abi-1.0.4.new/libABINIT/src/56_mixing/findminscf.F90	2013-06-11 16:51:00.000000000 +0200
-@@ -92,7 +92,7 @@
- !write(6,*)' choice,lambda_1,lambda_2=',choice,lambda_1,lambda_2
- !ENDDEBUG
- 
-- errid = AB6_NO_ERROR
-+ errid = AB7_NO_ERROR
-  d_lambda=lambda_1-lambda_2
- 
-  if(choice==1) then
-@@ -111,7 +111,7 @@
- &   +0.5_dp*d2edv2_1*(lambda_2-lambda_1)**2
- 
-    if(d2edv2_mid<0.0_dp)then
--      errid = AB6_ERROR_MIXING_INTERNAL
-+      errid = AB7_ERROR_MIXING_INTERNAL
-      write(errmess, '(a,a,a,a,es18.10,a)' ) ch10,&
- &     ' findminscf : WARNING -',ch10,&
- &     '  (scfcge) The second derivative is negative, equal to',d2edv2_mid        ,'.'
-@@ -128,7 +128,7 @@
-    d2edv2_2=d2edv2_1
-    d2edv2_predict=d2edv2_1
-    if(d2edv2_predict<0.0_dp)then
--      errid = AB6_ERROR_MIXING_INTERNAL
-+      errid = AB7_ERROR_MIXING_INTERNAL
-      write(errmess, '(a,a,a,a,es18.10,a,a,a)' ) ch10,&
- &     ' findmin : WARNING -',ch10,&
- &     '  (scfcge) The second derivative is negative, equal to',d2edv2_predict,'.',&
-diff -urN bigdft-abi-1.0.4.old/libABINIT/src/56_mixing/m_ab6_mixing.F90 bigdft-abi-1.0.4.new/libABINIT/src/56_mixing/m_ab6_mixing.F90
---- bigdft-abi-1.0.4.old/libABINIT/src/56_mixing/m_ab6_mixing.F90	2012-07-09 16:43:33.000000000 +0200
-+++ bigdft-abi-1.0.4.new/libABINIT/src/56_mixing/m_ab6_mixing.F90	1970-01-01 01:00:00.000000000 +0100
-@@ -1,688 +0,0 @@
--#if defined HAVE_CONFIG_H
--#include "config.h"
--#endif
--  
--  module m_ab6_mixing
--
--    use m_profiling
--    use defs_basis
--
--    implicit none
--
--    private
--
--    integer, parameter, public :: AB6_MIXING_NONE        = 0
--    integer, parameter, public :: AB6_MIXING_EIG         = 1
--    integer, parameter, public :: AB6_MIXING_SIMPLE      = 2
--    integer, parameter, public :: AB6_MIXING_ANDERSON    = 3
--    integer, parameter, public :: AB6_MIXING_ANDERSON_2  = 4
--    integer, parameter, public :: AB6_MIXING_CG_ENERGY   = 5
--    integer, parameter, public :: AB6_MIXING_CG_ENERGY_2 = 6
--    integer, parameter, public :: AB6_MIXING_PULAY       = 7
--
--    integer, parameter, public :: AB6_MIXING_POTENTIAL  = 0
--    integer, parameter, public :: AB6_MIXING_DENSITY    = 1
--
--    integer, parameter, public :: AB6_MIXING_REAL_SPACE     = 1
--    integer, parameter, public :: AB6_MIXING_FOURRIER_SPACE = 2
--
--    type, public :: ab6_mixing_object
--       integer :: iscf
--       integer :: nfft, nspden, kind, space
--
--       logical :: useprec
--       integer :: mffmem
--       character(len = fnlen) :: diskCache
--       integer :: n_index, n_fftgr, n_pulayit, n_pawmix
--       integer, dimension(:), pointer :: i_rhor, i_vtrial, i_vresid, i_vrespc
--       real(dp), dimension(:,:,:), pointer :: f_fftgr, f_atm
--       real(dp), dimension(:,:), pointer :: f_paw
--
--       ! Private
--       integer :: n_atom
--       real(dp), pointer :: xred(:,:), dtn_pc(:,:)
--    end type ab6_mixing_object
--
--    public :: ab6_mixing_new
--    public :: ab6_mixing_deallocate
--
--    public :: ab6_mixing_use_disk_cache
--    public :: ab6_mixing_use_moving_atoms
--    public :: ab6_mixing_copy_current_step
--
--    public :: ab6_mixing_eval_allocate
--    public :: ab6_mixing_eval
--    public :: ab6_mixing_eval_deallocate
--
--  contains
--
--    subroutine init_(mix)
--      implicit none
--
--      type(ab6_mixing_object), intent(out) :: mix
--
--      ! Default values.
--      mix%iscf      = AB6_MIXING_NONE
--      mix%mffmem    = 1
--      mix%n_index   = 0
--      mix%n_fftgr   = 0
--      mix%n_pulayit = 7
--      mix%n_pawmix  = 0
--      mix%n_atom    = 0
--      mix%useprec   = .true.
--
--      call nullify_(mix)
--    end subroutine init_
--
--    subroutine nullify_(mix)
--
--
--      implicit none
--
--      type(ab6_mixing_object), intent(inout) :: mix
--
--      ! Nullify internal pointers.
--      nullify(mix%i_rhor)
--      nullify(mix%i_vtrial)
--      nullify(mix%i_vresid)
--      nullify(mix%i_vrespc)
--      nullify(mix%f_fftgr)
--      nullify(mix%f_atm)
--      nullify(mix%f_paw)
--      nullify(mix%dtn_pc)
--      nullify(mix%xred)
--    end subroutine nullify_
--
--    subroutine ab6_mixing_new(mix, iscf, kind, space, nfft, nspden, &
--         & npawmix, errid, errmess, npulayit, useprec)
--      implicit none
--
--      type(ab6_mixing_object), intent(out) :: mix
--      integer, intent(in) :: iscf, kind, space, nfft, nspden, npawmix
--      integer, intent(out) :: errid
--      character(len = 500), intent(out) :: errmess
--      integer, intent(in), optional :: npulayit
--      logical, intent(in), optional :: useprec
--      
--      integer :: ii, i_stat
--      character(len = *), parameter :: subname = "ab6_mixing_new"
--
--      ! Set default values.
--      call init_(mix)
--
--      ! Argument checkings.
--      if (kind /= AB6_MIXING_POTENTIAL .and. kind /= AB6_MIXING_DENSITY) then
--         errid = AB6_ERROR_MIXING_ARG
--         write(errmess, '(a,a,a,a)' )ch10,&
--              & ' ab6_mixing_set_arrays: ERROR -',ch10,&
--              & '  Mixing must be done on density or potential only.'
--         return
--      end if
--      if (space /= AB6_MIXING_REAL_SPACE .and. &
--           & space /= AB6_MIXING_FOURRIER_SPACE) then
--         errid = AB6_ERROR_MIXING_ARG
--         write(errmess, '(a,a,a,a)' )ch10,&
--              & ' ab6_mixing_set_arrays: ERROR -',ch10,&
--              & '  Mixing must be done in real or Fourrier space only.'
--         return
--      end if
--      if (iscf /= AB6_MIXING_EIG .and. iscf /= AB6_MIXING_SIMPLE .and. &
--           & iscf /= AB6_MIXING_ANDERSON .and. &
--           & iscf /= AB6_MIXING_ANDERSON_2 .and. &
--           & iscf /= AB6_MIXING_CG_ENERGY .and. &
--           & iscf /= AB6_MIXING_PULAY .and. &
--           & iscf /= AB6_MIXING_CG_ENERGY_2) then
--         errid = AB6_ERROR_MIXING_ARG
--         write(errmess, "(A,I0,A)") "Unknown mixing scheme (", iscf, ")."
--         return
--      end if
--      errid = AB6_NO_ERROR
--
--      ! Mandatory arguments.
--      mix%iscf     = iscf
--      mix%kind     = kind
--      mix%space    = space
--      mix%nfft     = nfft
--      mix%nspden   = nspden
--      mix%n_pawmix = npawmix
--
--      ! Optional arguments.
--      if (present(useprec)) mix%useprec = useprec
--
--      ! Set-up internal dimensions.
--      !These arrays are needed only in the self-consistent case
--      if (iscf == AB6_MIXING_EIG) then
--         !    For iscf==1, five additional vectors are needed
--         !    The index 1 is attributed to the old trial potential,
--         !    The new residual potential, and the new
--         !    preconditioned residual potential receive now a temporary index
--         !    The indices number 4 and 5 are attributed to work vectors.
--         mix%n_fftgr=5 ; mix%n_index=1
--      else if(iscf == AB6_MIXING_SIMPLE) then
--         !    For iscf==2, three additional vectors are needed.
--         !    The index number 1 is attributed to the old trial vector
--         !    The new residual potential, and the new preconditioned
--         !    residual potential, receive now a temporary index.
--         mix%n_fftgr=3 ; mix%n_index=1
--         if (.not. mix%useprec) mix%n_fftgr = 2
--      else if(iscf == AB6_MIXING_ANDERSON) then
--         !    For iscf==3 , four additional vectors are needed.
--         !    The index number 1 is attributed to the old trial vector
--         !    The new residual potential, and the new and old preconditioned
--         !    residual potential, receive now a temporary index.
--         mix%n_fftgr=4 ; mix%n_index=2
--         if (.not. mix%useprec) mix%n_fftgr = 3
--      else if (iscf == AB6_MIXING_ANDERSON_2) then
--         !    For iscf==4 , six additional vectors are needed.
--         !    The indices number 1 and 2 are attributed to two old trial vectors
--         !    The new residual potential, and the new and two old preconditioned
--         !    residual potentials, receive now a temporary index.
--         mix%n_fftgr=6 ; mix%n_index=3
--         if (.not. mix%useprec) mix%n_fftgr = 5
--      else if(iscf == AB6_MIXING_CG_ENERGY .or. iscf == AB6_MIXING_CG_ENERGY_2) then
--         !    For iscf==5 or 6, ten additional vectors are needed
--         !    The index number 1 is attributed to the old trial vector
--         !    The index number 6 is attributed to the search vector
--         !    Other indices are attributed now. Altogether ten vectors
--         mix%n_fftgr=10 ; mix%n_index=3
--      else if(iscf == AB6_MIXING_PULAY) then
--         !    For iscf==7, lot of additional vectors are needed
--         !    The index number 1 is attributed to the old trial vector
--         !    The index number 2 is attributed to the old residual
--         !    The indices number 2 and 3 are attributed to two old precond. residuals
--         !    Other indices are attributed now.
--         if (present(npulayit)) mix%n_pulayit = npulayit
--         mix%n_fftgr=2+2*mix%n_pulayit ; mix%n_index=1+mix%n_pulayit
--         if (.not. mix%useprec) mix%n_fftgr = 1+2*mix%n_pulayit
--      end if ! iscf cases
--
--      ! Allocate new arrays.
--      allocate(mix%i_rhor(mix%n_index), stat = i_stat)
--      call memocc(i_stat, mix%i_rhor, 'mix%i_rhor', subname)
--      allocate(mix%i_vtrial(mix%n_index), stat = i_stat)
--      call memocc(i_stat, mix%i_vtrial, 'mix%i_vtrial', subname)
--      allocate(mix%i_vresid(mix%n_index), stat = i_stat)
--      call memocc(i_stat, mix%i_vresid, 'mix%i_vresid', subname)
--      allocate(mix%i_vrespc(mix%n_index), stat = i_stat)
--      call memocc(i_stat, mix%i_vrespc, 'mix%i_vrespc', subname)
--
--      ! Setup initial values.
--      if (iscf == AB6_MIXING_EIG) then
--         mix%i_vtrial(1)=1 ; mix%i_vresid(1)=2 ; mix%i_vrespc(1)=3
--      else if(iscf == AB6_MIXING_SIMPLE) then
--         mix%i_vtrial(1)=1 ; mix%i_vresid(1)=2 ; mix%i_vrespc(1)=3
--         if (.not. mix%useprec) mix%i_vrespc(1)=2
--      else if(iscf == AB6_MIXING_ANDERSON) then
--         mix%i_vtrial(1)=1 ; mix%i_vresid(1)=2
--         if (mix%useprec) then
--            mix%i_vrespc(1)=3 ; mix%i_vrespc(2)=4
--         else
--            mix%i_vrespc(1)=2 ; mix%i_vrespc(2)=3
--         end if
--      else if (iscf == AB6_MIXING_ANDERSON_2) then
--         mix%i_vtrial(1)=1 ; mix%i_vtrial(2)=2
--         mix%i_vresid(1)=3
--         if (mix%useprec) then
--            mix%i_vrespc(1)=4 ; mix%i_vrespc(2)=5 ; mix%i_vrespc(3)=6
--         else
--            mix%i_vrespc(1)=3 ; mix%i_vrespc(2)=4 ; mix%i_vrespc(3)=5
--         end if
--      else if(iscf == AB6_MIXING_CG_ENERGY .or. &
--           & iscf == AB6_MIXING_CG_ENERGY_2) then
--         mix%n_fftgr=10 ; mix%n_index=3
--         mix%i_vtrial(1)=1
--         mix%i_vresid(1)=2 ; mix%i_vresid(2)=4 ; mix%i_vresid(3)=7
--         mix%i_vrespc(1)=3 ; mix%i_vrespc(2)=5 ; mix%i_vrespc(3)=8
--         mix%i_rhor(2)=9 ; mix%i_rhor(3)=10
--      else if(iscf == AB6_MIXING_PULAY) then
--         do ii=1,mix%n_pulayit
--            mix%i_vtrial(ii)=2*ii-1 ; mix%i_vrespc(ii)=2*ii
--         end do
--         mix%i_vrespc(mix%n_pulayit+1)=2*mix%n_pulayit+1
--         mix%i_vresid(1)=2*mix%n_pulayit+2
--         if (.not. mix%useprec) mix%i_vresid(1)=2
--      end if ! iscf cases
--    end subroutine ab6_mixing_new
--
--    subroutine ab6_mixing_use_disk_cache(mix, fnametmp_fft)
--
--
--      implicit none
--
--
--      type(ab6_mixing_object), intent(inout) :: mix
--      character(len = *), intent(in) :: fnametmp_fft
--      
--      if (len(trim(fnametmp_fft)) > 0) then
--         mix%mffmem = 0
--         write(mix%diskCache, "(A)") fnametmp_fft
--      else
--         mix%mffmem = 1
--      end if
--    end subroutine ab6_mixing_use_disk_cache
--
--    subroutine ab6_mixing_use_moving_atoms(mix, natom, xred, dtn_pc)
--
--
--      type(ab6_mixing_object), intent(inout) :: mix
--      integer, intent(in) :: natom
--      real(dp), intent(in), target :: dtn_pc(3, natom)
--      real(dp), intent(in), target :: xred(3, natom)
--
--      mix%n_atom = natom
--      mix%dtn_pc => dtn_pc
--      mix%xred => xred
--    end subroutine ab6_mixing_use_moving_atoms
--
--    subroutine ab6_mixing_copy_current_step(mix, arr_resid, errid, errmess, &
--         & arr_respc, arr_paw_resid, arr_paw_respc, arr_atm)
--
--
--      type(ab6_mixing_object), intent(inout) :: mix
--      real(dp), intent(in) :: arr_resid(mix%space * mix%nfft, mix%nspden)
--      integer, intent(out) :: errid
--      character(len = 500), intent(out) :: errmess
--      real(dp), intent(in), optional :: arr_respc(mix%space * mix%nfft, mix%nspden)
--      real(dp), intent(in), optional :: arr_paw_resid(mix%n_pawmix), &
--           & arr_paw_respc(mix%n_pawmix)
--      real(dp), intent(in), optional :: arr_atm(3, mix%n_atom)
--
--      if (.not. associated(mix%f_fftgr)) then
--         errid = AB6_ERROR_MIXING_ARG
--         write(errmess, '(a,a,a,a)' )ch10,&
--              & ' ab6_mixing_set_arr_current_step: ERROR -',ch10,&
--              & '  Working arrays not yet allocated.'
--         return
--      end if
--      errid = AB6_NO_ERROR
--
--      mix%f_fftgr(:,:,mix%i_vresid(1)) = arr_resid(:,:)
--      if (present(arr_respc)) mix%f_fftgr(:,:,mix%i_vrespc(1)) = arr_respc(:,:)
--      if (present(arr_paw_resid)) mix%f_paw(:, mix%i_vresid(1)) = arr_paw_resid(:)
--      if (present(arr_paw_respc)) mix%f_paw(:, mix%i_vrespc(1)) = arr_paw_respc(:)
--      if (present(arr_atm)) mix%f_atm(:,:, mix%i_vresid(1)) = arr_atm(:,:)
--    end subroutine ab6_mixing_copy_current_step
--
--    subroutine ab6_mixing_eval_allocate(mix, istep)
--
--
--!This section has been created automatically by the script Abilint (TD).
--!Do not modify the following lines by hand.
-- use interfaces_18_timing
--!End of the abilint section
--
--      implicit none
--
--      type(ab6_mixing_object), intent(inout) :: mix
--      integer, intent(in), optional :: istep
--
--      integer :: istep_, i_stat, usepaw
--      real(dp) :: tsec(2)
--      character(len = *), parameter :: subname = "ab6_mixing_eval_allocate"
--
--      istep_ = 1
--      if (present(istep)) istep_ = istep
--
--      ! Allocate work array.
--      if (.not. associated(mix%f_fftgr)) then
--         allocate(mix%f_fftgr(mix%space * mix%nfft,mix%nspden,mix%n_fftgr), stat = i_stat)
--         call memocc(i_stat, mix%f_fftgr, 'mix%f_fftgr', subname)
--         mix%f_fftgr(:,:,:)=zero
--         if (mix%mffmem == 0 .and. istep_ > 1) then
--            call timab(83,1,tsec)
--            open(unit=tmp_unit,file=mix%diskCache,form='unformatted',status='old')
--            rewind(tmp_unit)
--            read(tmp_unit) mix%f_fftgr
--            if (mix%n_pawmix == 0) close(unit=tmp_unit)
--            call timab(83,2,tsec)
--         end if
--      end if
--      ! Allocate PAW work array.
--      if (.not. associated(mix%f_paw)) then
--         usepaw = 0
--         if (mix%n_pawmix > 0) usepaw = 1
--         allocate(mix%f_paw(max(1,mix%n_pawmix),max(1,mix%n_fftgr * usepaw)), &
--              & stat = i_stat)
--         call memocc(i_stat, mix%f_paw, 'mix%f_paw', subname)
--         if (mix%n_pawmix > 0) then
--            mix%f_paw(:,:)=zero
--            if (mix%mffmem == 0 .and. istep_ > 1) then
--               read(tmp_unit) mix%f_paw
--               close(unit=tmp_unit)
--               call timab(83,2,tsec)
--            end if
--         end if
--      end if
--      ! Allocate atom work array.
--      if (.not. associated(mix%f_atm)) then
--         allocate(mix%f_atm(3,mix%n_atom,mix%n_fftgr), stat = i_stat)
--         call memocc(i_stat, mix%f_atm, 'mix%f_atm', subname)
--      end if
--    end subroutine ab6_mixing_eval_allocate
--
--    subroutine ab6_mixing_eval_deallocate(mix)
--
--
--!This section has been created automatically by the script Abilint (TD).
--!Do not modify the following lines by hand.
-- use interfaces_18_timing
--!End of the abilint section
--
--      implicit none
--
--      type(ab6_mixing_object), intent(inout) :: mix
--
--      integer :: i_all, i_stat
--      real(dp) :: tsec(2)
--      character(len = *), parameter :: subname = "ab6_mixing_eval_deallocate"
--
--      ! Save on disk and deallocate work array in case on disk cache only.
--      if (mix%mffmem == 0) then
--         call timab(83,1,tsec)
--         open(unit=tmp_unit,file=mix%diskCache,form='unformatted',status='unknown')
--         rewind(tmp_unit)
--         ! VALGRIND complains not all of f_fftgr_disk is initialized
--         write(tmp_unit) mix%f_fftgr
--         if (mix%n_pawmix > 0) then
--            write(tmp_unit) mix%f_paw
--         end if
--         close(unit=tmp_unit)
--         call timab(83,2,tsec)
--         i_all = -product(shape(mix%f_fftgr))*kind(mix%f_fftgr)
--         deallocate(mix%f_fftgr, stat = i_stat)
--         call memocc(i_stat, i_all, 'mix%f_atm', subname)
--         nullify(mix%f_fftgr)
--         if (associated(mix%f_paw)) then
--            i_all = -product(shape(mix%f_paw))*kind(mix%f_paw)
--            deallocate(mix%f_paw, stat = i_stat)
--            call memocc(i_stat, i_all, 'mix%f_paw', subname)
--            nullify(mix%f_paw)
--         end if
--      end if
--    end subroutine ab6_mixing_eval_deallocate
--
--    subroutine ab6_mixing_eval(mix, arr, istep, nfftot, ucvol, &
--         & mpi_comm, mpi_summarize, errid, errmess, &
--         & reset, isecur, pawarr, pawopt, response, etotal, potden, &
--         & resnrm, fnrm, fdot, user_data)
--
--
--!This section has been created automatically by the script Abilint (TD).
--!Do not modify the following lines by hand.
-- use interfaces_56_mixing
--!End of the abilint section
--
--      implicit none
--
--      type(ab6_mixing_object), intent(inout) :: mix
--      integer, intent(in) :: istep, nfftot, mpi_comm
--      logical, intent(in) :: mpi_summarize
--      real(dp), intent(in) :: ucvol
--      real(dp), intent(inout) :: arr(mix%space * mix%nfft,mix%nspden)
--      integer, intent(out) :: errid
--      character(len = 500), intent(out) :: errmess
--
--      logical, intent(in), optional :: reset
--      integer, intent(in), optional :: isecur, pawopt, response
--      real(dp), intent(inout), optional, target :: pawarr(mix%n_pawmix)
--      real(dp), intent(in), optional :: etotal
--      real(dp), intent(in), optional :: potden(mix%space * mix%nfft,mix%nspden)
--      real(dp), intent(out), optional :: resnrm
--      optional :: fnrm, fdot
--      integer, intent(in), optional :: user_data(:)
--
--      interface
--         function fdot(x,y,cplex,nfft,nspden,opt_denpot,user_data)
--           integer, intent(in) :: cplex,nfft,nspden,opt_denpot
--           double precision, intent(in) :: x(*), y(*)
--           integer, intent(in) :: user_data(:)
--
--           double precision :: fdot
--         end function fdot
--
--         function fnrm(x,cplex,nfft,nspden,opt_denpot,user_data)
--           integer, intent(in) :: cplex,nfft,nspden,opt_denpot
--           double precision, intent(in) :: x(*)
--           integer, intent(in) :: user_data(:)
--
--           double precision :: fnrm
--         end function fnrm
--      end interface
--
--      character(len = *), parameter :: subname = "ab6_mixing_eval"
--      integer :: moveAtm, dbl_nnsclo, initialized, isecur_
--      integer :: usepaw, pawoptmix_, response_, i_stat, i_all
--      integer :: user_data_(2)
--      real(dp) :: resnrm_
--      real(dp), pointer :: pawarr_(:)
--
--      ! Argument checkings.
--      if (mix%iscf == AB6_MIXING_NONE) then
--         errid = AB6_ERROR_MIXING_ARG
--         write(errmess, '(a,a,a,a)' )ch10,&
--              & ' ab6_mixing_eval: ERROR -',ch10,&
--              & '  No method has been chosen.'
--         return
--      end if
--      if (mix%n_pawmix > 0 .and. .not. present(pawarr)) then
--         errid = AB6_ERROR_MIXING_ARG
--         write(errmess, '(a,a,a,a)' )ch10,&
--              & ' ab6_mixing_eval: ERROR -',ch10,&
--              & '  PAW is used, but no pawarr argument provided.'
--         return
--      end if
--      if (mix%n_atom > 0 .and. (.not. associated(mix%dtn_pc) .or. &
--           & .not. associated(mix%xred))) then
--         errid = AB6_ERROR_MIXING_ARG
--         write(errmess, '(a,a,a,a)' )ch10,&
--              & ' ab6_mixing_eval: ERROR -',ch10,&
--              & '  Moving atoms is used, but no xred or dtn_pc attributes provided.'
--         return
--      end if
--      if ((present(fnrm) .or. present(fdot) .or. present(user_data)) .and. &
--           & .not. (present(fnrm) .and. present(fdot) .and. present(user_data))) then
--         errid = AB6_ERROR_MIXING_ARG
--         write(errmess, '(a,a,a,a)' )ch10,&
--              & ' ab6_mixing_eval: ERROR -',ch10,&
--              & '  Passing optional norm and dot product routines without user_data argument.'
--         return
--      end if
--      errid = AB6_NO_ERROR
--
--      ! Miscellaneous
--      moveAtm = 0
--      if (mix%n_atom > 0) moveAtm = 1
--      initialized = 1
--      if (present(reset)) then
--         if (reset) initialized = 0
--      end if
--      isecur_ = 0
--      if (present(isecur)) isecur_ = isecur
--      usepaw = 0
--      if (mix%n_pawmix > 0) usepaw = 1
--      pawoptmix_ = 0
--      if (present(pawopt)) pawoptmix_ = pawopt
--      response_ = 0
--      if (present(response)) response_ = response
--      if (present(pawarr)) then
--         pawarr_ => pawarr
--      else
--         allocate(pawarr_(1), stat = i_stat)
--         call memocc(i_stat, pawarr_, 'pawarr_', subname)
--      end if
--
--      ! Norm and dot products.
--      if (.not. present(user_data)) then
--         user_data_(1) = 0
--         if (mpi_summarize) user_data_(1) = 1
--         user_data_(2) = mpi_comm
--      end if
--
--      ! Do the mixing.
--      resnrm_ = 0.d0
--      if (mix%iscf == AB6_MIXING_EIG) then
--         !  This routine compute the eigenvalues of the SCF operator
--         call scfeig(istep, mix%space * mix%nfft, mix%nspden, &
--              & mix%f_fftgr(:,:,mix%i_vrespc(1)), arr, &
--              & mix%f_fftgr(:,:,1), mix%f_fftgr(:,:,4:5), errid, errmess)
--      else if (mix%iscf == AB6_MIXING_SIMPLE .or. &
--           & mix%iscf == AB6_MIXING_ANDERSON .or. &
--           & mix%iscf == AB6_MIXING_ANDERSON_2 .or. &
--           & mix%iscf == AB6_MIXING_PULAY) then
--         if (present(user_data)) then
--            call scfopt(mix%space, mix%f_fftgr,mix%f_paw,mix%iscf,istep,&
--                 & mix%i_vrespc,mix%i_vtrial, mix%nfft,mix%n_pawmix,mix%nspden, &
--                 & mix%n_fftgr,mix%n_index,mix%kind,pawoptmix_,usepaw,pawarr_, &
--                 & resnrm_, arr, fnrm, fdot, user_data, errid, errmess)
--         else
--            call scfopt(mix%space, mix%f_fftgr,mix%f_paw,mix%iscf,istep,&
--                 & mix%i_vrespc,mix%i_vtrial, mix%nfft,mix%n_pawmix,mix%nspden, &
--                 & mix%n_fftgr,mix%n_index,mix%kind,pawoptmix_,usepaw,pawarr_, &
--                 & resnrm_, arr, fnrm_default, fdot_default, user_data_, errid, errmess)
--         end if
--         !  Change atomic positions
--         if((istep==1 .or. mix%iscf==AB6_MIXING_SIMPLE) .and. mix%n_atom > 0)then
--            !    GAF: 2009-06-03
--            !    Apparently there are not reason
--            !    to restrict iscf=2 for ionmov=5
--            mix%xred(:,:) = mix%xred(:,:) + mix%dtn_pc(:,:)
--         end if
--      else if (mix%iscf == AB6_MIXING_CG_ENERGY .or. &
--           & mix%iscf == AB6_MIXING_CG_ENERGY_2) then
--         !  Optimize next vtrial using an algorithm based
--         !  on the conjugate gradient minimization of etotal
--         if (.not. present(etotal) .or. .not. present(potden)) then
--            errid = AB6_ERROR_MIXING_ARG
--            write(errmess, '(a,a,a,a)' )ch10,&
--                 & ' ab6_mixing_eval: ERROR -',ch10,&
--                 & '  Arguments etotal or potden are missing for CG on energy methods.'
--            return
--         end if
--         if (mix%n_atom == 0) then
--            allocate(mix%xred(3,0), stat = i_stat)
--            call memocc(i_stat, mix%xred, 'mix%xred', subname)
--            allocate(mix%dtn_pc(3,0), stat = i_stat)
--            call memocc(i_stat, mix%dtn_pc, 'mix%dtn_pc', subname)
--         end if
--         if (present(user_data)) then
--            call scfcge(mix%space,dbl_nnsclo,mix%dtn_pc,etotal,mix%f_atm,&
--                 & mix%f_fftgr,initialized,mix%iscf,isecur_,istep,&
--                 & mix%i_rhor,mix%i_vresid,mix%i_vrespc,moveAtm,&
--                 & mix%n_atom,mix%nfft,nfftot,&
--                 & mix%nspden,mix%n_fftgr,mix%n_index,mix%kind,&
--                 & response_,potden,ucvol,arr,mix%xred, &
--                 & fnrm, fdot, user_data, errid, errmess)
--         else
--            call scfcge(mix%space,dbl_nnsclo,mix%dtn_pc,etotal,mix%f_atm,&
--                 & mix%f_fftgr,initialized,mix%iscf,isecur_,istep,&
--                 & mix%i_rhor,mix%i_vresid,mix%i_vrespc,moveAtm,&
--                 & mix%n_atom,mix%nfft,nfftot,&
--                 & mix%nspden,mix%n_fftgr,mix%n_index,mix%kind,&
--                 & response_,potden,ucvol,arr,mix%xred, fnrm_default, &
--                 & fdotn_default, user_data_, errid, errmess)
--         end if
--         if (mix%n_atom == 0) then
--            i_all = -product(shape(mix%xred))*kind(mix%xred)
--            deallocate(mix%xred, stat = i_stat)
--            call memocc(i_stat, i_all, 'mix%xred', subname)
--            i_all = -product(shape(mix%dtn_pc))*kind(mix%dtn_pc)
--            deallocate(mix%dtn_pc, stat = i_stat)
--            call memocc(i_stat, i_all, 'mix%dtn_pc', subname)
--         end if
--         if (dbl_nnsclo == 1) errid = AB6_ERROR_MIXING_INC_NNSLOOP
--      end if
--      
--      if (present(resnrm)) resnrm = resnrm_
--      if (.not. present(pawarr)) then
--         i_all = -product(shape(pawarr_))*kind(pawarr_)
--         deallocate(pawarr_, stat = i_stat)
--         call memocc(i_stat, i_all, 'pawarr_', subname)
--      end if
--    end subroutine ab6_mixing_eval
--
--    subroutine ab6_mixing_deallocate(mix)
--      implicit none
--
--      type(ab6_mixing_object), intent(inout) :: mix
--
--      integer :: i_all, i_stat
--      character(len = *), parameter :: subname = "ab6_mixing_deallocate"
--
--      if (associated(mix%i_rhor)) then
--         i_all = -product(shape(mix%i_rhor))*kind(mix%i_rhor)
--         deallocate(mix%i_rhor, stat = i_stat)
--         call memocc(i_stat, i_all, 'mix%i_rhor', subname)
--      end if
--      if (associated(mix%i_vtrial)) then
--         i_all = -product(shape(mix%i_vtrial))*kind(mix%i_vtrial)
--         deallocate(mix%i_vtrial, stat = i_stat)
--         call memocc(i_stat, i_all, 'mix%i_vtrial', subname)
--      end if
--      if (associated(mix%i_vresid)) then
--         i_all = -product(shape(mix%i_vresid))*kind(mix%i_vresid)
--         deallocate(mix%i_vresid, stat = i_stat)
--         call memocc(i_stat, i_all, 'mix%i_vresid', subname)
--      end if
--      if (associated(mix%i_vrespc)) then
--         i_all = -product(shape(mix%i_vrespc))*kind(mix%i_vrespc)
--         deallocate(mix%i_vrespc, stat = i_stat)
--         call memocc(i_stat, i_all, 'mix%i_vrespc', subname)
--      end if
--      if (associated(mix%f_fftgr)) then
--         i_all = -product(shape(mix%f_fftgr))*kind(mix%f_fftgr)
--         deallocate(mix%f_fftgr, stat = i_stat)
--         call memocc(i_stat, i_all, 'mix%f_fftgr', subname)
--      end if
--      if (associated(mix%f_paw)) then
--         i_all = -product(shape(mix%f_paw))*kind(mix%f_paw)
--         deallocate(mix%f_paw, stat = i_stat)
--         call memocc(i_stat, i_all, 'mix%f_paw', subname)
--      end if
--      if (associated(mix%f_atm)) then
--         i_all = -product(shape(mix%f_atm))*kind(mix%f_atm)
--         deallocate(mix%f_atm, stat = i_stat)
--         call memocc(i_stat, i_all, 'mix%f_atm', subname)
--      end if
--
--      call nullify_(mix)
--    end subroutine ab6_mixing_deallocate
--
--    function fnrm_default(x,cplex,nfft,nspden,opt_denpot,user_data)
--      integer, intent(in) :: cplex,nfft,nspden,opt_denpot
--      double precision, intent(in) :: x(*)
--      integer, intent(in) :: user_data(:)
--
--      double precision :: fnrm_default
--      real(dp) :: resid_new(1)
--
--      call sqnormm_v(cplex,1,user_data(2),(user_data(1) /= 0),1,&
--           & nfft,resid_new,1,nspden,opt_denpot,x)
--      fnrm_default = resid_new(1)
--    end function fnrm_default
--
--    function fdot_default(x,y,cplex,nfft,nspden,opt_denpot,user_data)
--      integer, intent(in) :: cplex,nfft,nspden,opt_denpot
--      double precision, intent(in) :: x(*), y(*)
--      integer, intent(in) :: user_data(:)
--
--      double precision :: fdot_default
--      real(dp) :: prod_resid(1)
--
--      call dotprodm_v(cplex,1,prod_resid,1,1,user_data(2),(user_data(1) /= 0),1,1,&
--           & nfft,1,1,nspden,opt_denpot,x,y)
--      fdot_default = prod_resid(1)
--    end function fdot_default
--
--    function fdotn_default(x,y,cplex,nfft,nspden,opt_denpot,user_data)
--      integer, intent(in) :: cplex,nfft,nspden,opt_denpot
--      double precision, intent(in) :: x(*), y(*)
--      integer, intent(in) :: user_data(:)
--
--      double precision :: fdotn_default
--      real(dp) :: prod_resid(1,1,1)
--
--      call dotprodm_vn(cplex,1,x,prod_resid,1,1,user_data(2),(user_data(1) /= 0),1,1,&
--           & 1,nfft,1,nspden,y)
--      fdotn_default = prod_resid(1,1,1)
--    end function fdotn_default
--  end module m_ab6_mixing
-diff -urN bigdft-abi-1.0.4.old/libABINIT/src/56_mixing/m_ab7_mixing.F90 bigdft-abi-1.0.4.new/libABINIT/src/56_mixing/m_ab7_mixing.F90
---- bigdft-abi-1.0.4.old/libABINIT/src/56_mixing/m_ab7_mixing.F90	1970-01-01 01:00:00.000000000 +0100
-+++ bigdft-abi-1.0.4.new/libABINIT/src/56_mixing/m_ab7_mixing.F90	2013-06-11 16:51:00.000000000 +0200
-@@ -0,0 +1,688 @@
-+#if defined HAVE_CONFIG_H
-+#include "config.h"
-+#endif
-+  
-+  module m_ab7_mixing
-+
-+    use m_profiling
-+    use defs_basis
-+
-+    implicit none
-+
-+    private
-+
-+    integer, parameter, public :: AB7_MIXING_NONE        = 0
-+    integer, parameter, public :: AB7_MIXING_EIG         = 1
-+    integer, parameter, public :: AB7_MIXING_SIMPLE      = 2
-+    integer, parameter, public :: AB7_MIXING_ANDERSON    = 3
-+    integer, parameter, public :: AB7_MIXING_ANDERSON_2  = 4
-+    integer, parameter, public :: AB7_MIXING_CG_ENERGY   = 5
-+    integer, parameter, public :: AB7_MIXING_CG_ENERGY_2 = 6
-+    integer, parameter, public :: AB7_MIXING_PULAY       = 7
-+
-+    integer, parameter, public :: AB7_MIXING_POTENTIAL  = 0
-+    integer, parameter, public :: AB7_MIXING_DENSITY    = 1
-+
-+    integer, parameter, public :: AB7_MIXING_REAL_SPACE     = 1
-+    integer, parameter, public :: AB7_MIXING_FOURRIER_SPACE = 2
-+
-+    type, public :: ab7_mixing_object
-+       integer :: iscf
-+       integer :: nfft, nspden, kind, space
-+
-+       logical :: useprec
-+       integer :: mffmem
-+       character(len = fnlen) :: diskCache
-+       integer :: n_index, n_fftgr, n_pulayit, n_pawmix
-+       integer, dimension(:), pointer :: i_rhor, i_vtrial, i_vresid, i_vrespc
-+       real(dp), dimension(:,:,:), pointer :: f_fftgr, f_atm
-+       real(dp), dimension(:,:), pointer :: f_paw
-+
-+       ! Private
-+       integer :: n_atom
-+       real(dp), pointer :: xred(:,:), dtn_pc(:,:)
-+    end type ab7_mixing_object
-+
-+    public :: ab7_mixing_new
-+    public :: ab7_mixing_deallocate
-+
-+    public :: ab7_mixing_use_disk_cache
-+    public :: ab7_mixing_use_moving_atoms
-+    public :: ab7_mixing_copy_current_step
-+
-+    public :: ab7_mixing_eval_allocate
-+    public :: ab7_mixing_eval
-+    public :: ab7_mixing_eval_deallocate
-+
-+  contains
-+
-+    subroutine init_(mix)
-+      implicit none
-+
-+      type(ab7_mixing_object), intent(out) :: mix
-+
-+      ! Default values.
-+      mix%iscf      = AB7_MIXING_NONE
-+      mix%mffmem    = 1
-+      mix%n_index   = 0
-+      mix%n_fftgr   = 0
-+      mix%n_pulayit = 7
-+      mix%n_pawmix  = 0
-+      mix%n_atom    = 0
-+      mix%useprec   = .true.
-+
-+      call nullify_(mix)
-+    end subroutine init_
-+
-+    subroutine nullify_(mix)
-+
-+
-+      implicit none
-+
-+      type(ab7_mixing_object), intent(inout) :: mix
-+
-+      ! Nullify internal pointers.
-+      nullify(mix%i_rhor)
-+      nullify(mix%i_vtrial)
-+      nullify(mix%i_vresid)
-+      nullify(mix%i_vrespc)
-+      nullify(mix%f_fftgr)
-+      nullify(mix%f_atm)
-+      nullify(mix%f_paw)
-+      nullify(mix%dtn_pc)
-+      nullify(mix%xred)
-+    end subroutine nullify_
-+
-+    subroutine ab7_mixing_new(mix, iscf, kind, space, nfft, nspden, &
-+         & npawmix, errid, errmess, npulayit, useprec)
-+      implicit none
-+
-+      type(ab7_mixing_object), intent(out) :: mix
-+      integer, intent(in) :: iscf, kind, space, nfft, nspden, npawmix
-+      integer, intent(out) :: errid
-+      character(len = 500), intent(out) :: errmess
-+      integer, intent(in), optional :: npulayit
-+      logical, intent(in), optional :: useprec
-+      
-+      integer :: ii, i_stat
-+      character(len = *), parameter :: subname = "ab7_mixing_new"
-+
-+      ! Set default values.
-+      call init_(mix)
-+
-+      ! Argument checkings.
-+      if (kind /= AB7_MIXING_POTENTIAL .and. kind /= AB7_MIXING_DENSITY) then
-+         errid = AB7_ERROR_MIXING_ARG
-+         write(errmess, '(a,a,a,a)' )ch10,&
-+              & ' ab7_mixing_set_arrays: ERROR -',ch10,&
-+              & '  Mixing must be done on density or potential only.'
-+         return
-+      end if
-+      if (space /= AB7_MIXING_REAL_SPACE .and. &
-+           & space /= AB7_MIXING_FOURRIER_SPACE) then
-+         errid = AB7_ERROR_MIXING_ARG
-+         write(errmess, '(a,a,a,a)' )ch10,&
-+              & ' ab7_mixing_set_arrays: ERROR -',ch10,&
-+              & '  Mixing must be done in real or Fourrier space only.'
-+         return
-+      end if
-+      if (iscf /= AB7_MIXING_EIG .and. iscf /= AB7_MIXING_SIMPLE .and. &
-+           & iscf /= AB7_MIXING_ANDERSON .and. &
-+           & iscf /= AB7_MIXING_ANDERSON_2 .and. &
-+           & iscf /= AB7_MIXING_CG_ENERGY .and. &
-+           & iscf /= AB7_MIXING_PULAY .and. &
-+           & iscf /= AB7_MIXING_CG_ENERGY_2) then
-+         errid = AB7_ERROR_MIXING_ARG
-+         write(errmess, "(A,I0,A)") "Unknown mixing scheme (", iscf, ")."
-+         return
-+      end if
-+      errid = AB7_NO_ERROR
-+
-+      ! Mandatory arguments.
-+      mix%iscf     = iscf
-+      mix%kind     = kind
-+      mix%space    = space
-+      mix%nfft     = nfft
-+      mix%nspden   = nspden
-+      mix%n_pawmix = npawmix
-+
-+      ! Optional arguments.
-+      if (present(useprec)) mix%useprec = useprec
-+
-+      ! Set-up internal dimensions.
-+      !These arrays are needed only in the self-consistent case
-+      if (iscf == AB7_MIXING_EIG) then
-+         !    For iscf==1, five additional vectors are needed
-+         !    The index 1 is attributed to the old trial potential,
-+         !    The new residual potential, and the new
-+         !    preconditioned residual potential receive now a temporary index
-+         !    The indices number 4 and 5 are attributed to work vectors.
-+         mix%n_fftgr=5 ; mix%n_index=1
-+      else if(iscf == AB7_MIXING_SIMPLE) then
-+         !    For iscf==2, three additional vectors are needed.
-+         !    The index number 1 is attributed to the old trial vector
-+         !    The new residual potential, and the new preconditioned
-+         !    residual potential, receive now a temporary index.
-+         mix%n_fftgr=3 ; mix%n_index=1
-+         if (.not. mix%useprec) mix%n_fftgr = 2
-+      else if(iscf == AB7_MIXING_ANDERSON) then
-+         !    For iscf==3 , four additional vectors are needed.
-+         !    The index number 1 is attributed to the old trial vector
-+         !    The new residual potential, and the new and old preconditioned
-+         !    residual potential, receive now a temporary index.
-+         mix%n_fftgr=4 ; mix%n_index=2
-+         if (.not. mix%useprec) mix%n_fftgr = 3
-+      else if (iscf == AB7_MIXING_ANDERSON_2) then
-+         !    For iscf==4 , six additional vectors are needed.
-+         !    The indices number 1 and 2 are attributed to two old trial vectors
-+         !    The new residual potential, and the new and two old preconditioned
-+         !    residual potentials, receive now a temporary index.
-+         mix%n_fftgr=6 ; mix%n_index=3
-+         if (.not. mix%useprec) mix%n_fftgr = 5
-+      else if(iscf == AB7_MIXING_CG_ENERGY .or. iscf == AB7_MIXING_CG_ENERGY_2) then
-+         !    For iscf==5 or 6, ten additional vectors are needed
-+         !    The index number 1 is attributed to the old trial vector
-+         !    The index number 6 is attributed to the search vector
-+         !    Other indices are attributed now. Altogether ten vectors
-+         mix%n_fftgr=10 ; mix%n_index=3
-+      else if(iscf == AB7_MIXING_PULAY) then
-+         !    For iscf==7, lot of additional vectors are needed
-+         !    The index number 1 is attributed to the old trial vector
-+         !    The index number 2 is attributed to the old residual
-+         !    The indices number 2 and 3 are attributed to two old precond. residuals
-+         !    Other indices are attributed now.
-+         if (present(npulayit)) mix%n_pulayit = npulayit
-+         mix%n_fftgr=2+2*mix%n_pulayit ; mix%n_index=1+mix%n_pulayit
-+         if (.not. mix%useprec) mix%n_fftgr = 1+2*mix%n_pulayit
-+      end if ! iscf cases
-+
-+      ! Allocate new arrays.
-+      allocate(mix%i_rhor(mix%n_index), stat = i_stat)
-+      call memocc(i_stat, mix%i_rhor, 'mix%i_rhor', subname)
-+      allocate(mix%i_vtrial(mix%n_index), stat = i_stat)
-+      call memocc(i_stat, mix%i_vtrial, 'mix%i_vtrial', subname)
-+      allocate(mix%i_vresid(mix%n_index), stat = i_stat)
-+      call memocc(i_stat, mix%i_vresid, 'mix%i_vresid', subname)
-+      allocate(mix%i_vrespc(mix%n_index), stat = i_stat)
-+      call memocc(i_stat, mix%i_vrespc, 'mix%i_vrespc', subname)
-+
-+      ! Setup initial values.
-+      if (iscf == AB7_MIXING_EIG) then
-+         mix%i_vtrial(1)=1 ; mix%i_vresid(1)=2 ; mix%i_vrespc(1)=3
-+      else if(iscf == AB7_MIXING_SIMPLE) then
-+         mix%i_vtrial(1)=1 ; mix%i_vresid(1)=2 ; mix%i_vrespc(1)=3
-+         if (.not. mix%useprec) mix%i_vrespc(1)=2
-+      else if(iscf == AB7_MIXING_ANDERSON) then
-+         mix%i_vtrial(1)=1 ; mix%i_vresid(1)=2
-+         if (mix%useprec) then
-+            mix%i_vrespc(1)=3 ; mix%i_vrespc(2)=4
-+         else
-+            mix%i_vrespc(1)=2 ; mix%i_vrespc(2)=3
-+         end if
-+      else if (iscf == AB7_MIXING_ANDERSON_2) then
-+         mix%i_vtrial(1)=1 ; mix%i_vtrial(2)=2
-+         mix%i_vresid(1)=3
-+         if (mix%useprec) then
-+            mix%i_vrespc(1)=4 ; mix%i_vrespc(2)=5 ; mix%i_vrespc(3)=6
-+         else
-+            mix%i_vrespc(1)=3 ; mix%i_vrespc(2)=4 ; mix%i_vrespc(3)=5
-+         end if
-+      else if(iscf == AB7_MIXING_CG_ENERGY .or. &
-+           & iscf == AB7_MIXING_CG_ENERGY_2) then
-+         mix%n_fftgr=10 ; mix%n_index=3
-+         mix%i_vtrial(1)=1
-+         mix%i_vresid(1)=2 ; mix%i_vresid(2)=4 ; mix%i_vresid(3)=7
-+         mix%i_vrespc(1)=3 ; mix%i_vrespc(2)=5 ; mix%i_vrespc(3)=8
-+         mix%i_rhor(2)=9 ; mix%i_rhor(3)=10
-+      else if(iscf == AB7_MIXING_PULAY) then
-+         do ii=1,mix%n_pulayit
-+            mix%i_vtrial(ii)=2*ii-1 ; mix%i_vrespc(ii)=2*ii
-+         end do
-+         mix%i_vrespc(mix%n_pulayit+1)=2*mix%n_pulayit+1
-+         mix%i_vresid(1)=2*mix%n_pulayit+2
-+         if (.not. mix%useprec) mix%i_vresid(1)=2
-+      end if ! iscf cases
-+    end subroutine ab7_mixing_new
-+
-+    subroutine ab7_mixing_use_disk_cache(mix, fnametmp_fft)
-+
-+
-+      implicit none
-+
-+
-+      type(ab7_mixing_object), intent(inout) :: mix
-+      character(len = *), intent(in) :: fnametmp_fft
-+      
-+      if (len(trim(fnametmp_fft)) > 0) then
-+         mix%mffmem = 0
-+         write(mix%diskCache, "(A)") fnametmp_fft
-+      else
-+         mix%mffmem = 1
-+      end if
-+    end subroutine ab7_mixing_use_disk_cache
-+
-+    subroutine ab7_mixing_use_moving_atoms(mix, natom, xred, dtn_pc)
-+
-+
-+      type(ab7_mixing_object), intent(inout) :: mix
-+      integer, intent(in) :: natom
-+      real(dp), intent(in), target :: dtn_pc(3, natom)
-+      real(dp), intent(in), target :: xred(3, natom)
-+
-+      mix%n_atom = natom
-+      mix%dtn_pc => dtn_pc
-+      mix%xred => xred
-+    end subroutine ab7_mixing_use_moving_atoms
-+
-+    subroutine ab7_mixing_copy_current_step(mix, arr_resid, errid, errmess, &
-+         & arr_respc, arr_paw_resid, arr_paw_respc, arr_atm)
-+
-+
-+      type(ab7_mixing_object), intent(inout) :: mix
-+      real(dp), intent(in) :: arr_resid(mix%space * mix%nfft, mix%nspden)
-+      integer, intent(out) :: errid
-+      character(len = 500), intent(out) :: errmess
-+      real(dp), intent(in), optional :: arr_respc(mix%space * mix%nfft, mix%nspden)
-+      real(dp), intent(in), optional :: arr_paw_resid(mix%n_pawmix), &
-+           & arr_paw_respc(mix%n_pawmix)
-+      real(dp), intent(in), optional :: arr_atm(3, mix%n_atom)
-+
-+      if (.not. associated(mix%f_fftgr)) then
-+         errid = AB7_ERROR_MIXING_ARG
-+         write(errmess, '(a,a,a,a)' )ch10,&
-+              & ' ab7_mixing_set_arr_current_step: ERROR -',ch10,&
-+              & '  Working arrays not yet allocated.'
-+         return
-+      end if
-+      errid = AB7_NO_ERROR
-+
-+      mix%f_fftgr(:,:,mix%i_vresid(1)) = arr_resid(:,:)
-+      if (present(arr_respc)) mix%f_fftgr(:,:,mix%i_vrespc(1)) = arr_respc(:,:)
-+      if (present(arr_paw_resid)) mix%f_paw(:, mix%i_vresid(1)) = arr_paw_resid(:)
-+      if (present(arr_paw_respc)) mix%f_paw(:, mix%i_vrespc(1)) = arr_paw_respc(:)
-+      if (present(arr_atm)) mix%f_atm(:,:, mix%i_vresid(1)) = arr_atm(:,:)
-+    end subroutine ab7_mixing_copy_current_step
-+
-+    subroutine ab7_mixing_eval_allocate(mix, istep)
-+
-+
-+!This section has been created automatically by the script Abilint (TD).
-+!Do not modify the following lines by hand.
-+ use interfaces_18_timing
-+!End of the abilint section
-+
-+      implicit none
-+
-+      type(ab7_mixing_object), intent(inout) :: mix
-+      integer, intent(in), optional :: istep
-+
-+      integer :: istep_, i_stat, usepaw
-+      real(dp) :: tsec(2)
-+      character(len = *), parameter :: subname = "ab7_mixing_eval_allocate"
-+
-+      istep_ = 1
-+      if (present(istep)) istep_ = istep
-+
-+      ! Allocate work array.
-+      if (.not. associated(mix%f_fftgr)) then
-+         allocate(mix%f_fftgr(mix%space * mix%nfft,mix%nspden,mix%n_fftgr), stat = i_stat)
-+         call memocc(i_stat, mix%f_fftgr, 'mix%f_fftgr', subname)
-+         mix%f_fftgr(:,:,:)=zero
-+         if (mix%mffmem == 0 .and. istep_ > 1) then
-+            call timab(83,1,tsec)
-+            open(unit=tmp_unit,file=mix%diskCache,form='unformatted',status='old')
-+            rewind(tmp_unit)
-+            read(tmp_unit) mix%f_fftgr
-+            if (mix%n_pawmix == 0) close(unit=tmp_unit)
-+            call timab(83,2,tsec)
-+         end if
-+      end if
-+      ! Allocate PAW work array.
-+      if (.not. associated(mix%f_paw)) then
-+         usepaw = 0
-+         if (mix%n_pawmix > 0) usepaw = 1
-+         allocate(mix%f_paw(max(1,mix%n_pawmix),max(1,mix%n_fftgr * usepaw)), &
-+              & stat = i_stat)
-+         call memocc(i_stat, mix%f_paw, 'mix%f_paw', subname)
-+         if (mix%n_pawmix > 0) then
-+            mix%f_paw(:,:)=zero
-+            if (mix%mffmem == 0 .and. istep_ > 1) then
-+               read(tmp_unit) mix%f_paw
-+               close(unit=tmp_unit)
-+               call timab(83,2,tsec)
-+            end if
-+         end if
-+      end if
-+      ! Allocate atom work array.
-+      if (.not. associated(mix%f_atm)) then
-+         allocate(mix%f_atm(3,mix%n_atom,mix%n_fftgr), stat = i_stat)
-+         call memocc(i_stat, mix%f_atm, 'mix%f_atm', subname)
-+      end if
-+    end subroutine ab7_mixing_eval_allocate
-+
-+    subroutine ab7_mixing_eval_deallocate(mix)
-+
-+
-+!This section has been created automatically by the script Abilint (TD).
-+!Do not modify the following lines by hand.
-+ use interfaces_18_timing
-+!End of the abilint section
-+
-+      implicit none
-+
-+      type(ab7_mixing_object), intent(inout) :: mix
-+
-+      integer :: i_all, i_stat
-+      real(dp) :: tsec(2)
-+      character(len = *), parameter :: subname = "ab7_mixing_eval_deallocate"
-+
-+      ! Save on disk and deallocate work array in case on disk cache only.
-+      if (mix%mffmem == 0) then
-+         call timab(83,1,tsec)
-+         open(unit=tmp_unit,file=mix%diskCache,form='unformatted',status='unknown')
-+         rewind(tmp_unit)
-+         ! VALGRIND complains not all of f_fftgr_disk is initialized
-+         write(tmp_unit) mix%f_fftgr
-+         if (mix%n_pawmix > 0) then
-+            write(tmp_unit) mix%f_paw
-+         end if
-+         close(unit=tmp_unit)
-+         call timab(83,2,tsec)
-+         i_all = -product(shape(mix%f_fftgr))*kind(mix%f_fftgr)
-+         deallocate(mix%f_fftgr, stat = i_stat)
-+         call memocc(i_stat, i_all, 'mix%f_atm', subname)
-+         nullify(mix%f_fftgr)
-+         if (associated(mix%f_paw)) then
-+            i_all = -product(shape(mix%f_paw))*kind(mix%f_paw)
-+            deallocate(mix%f_paw, stat = i_stat)
-+            call memocc(i_stat, i_all, 'mix%f_paw', subname)
-+            nullify(mix%f_paw)
-+         end if
-+      end if
-+    end subroutine ab7_mixing_eval_deallocate
-+
-+    subroutine ab7_mixing_eval(mix, arr, istep, nfftot, ucvol, &
-+         & mpi_comm, mpi_summarize, errid, errmess, &
-+         & reset, isecur, pawarr, pawopt, response, etotal, potden, &
-+         & resnrm, fnrm, fdot, user_data)
-+
-+
-+!This section has been created automatically by the script Abilint (TD).
-+!Do not modify the following lines by hand.
-+ use interfaces_56_mixing
-+!End of the abilint section
-+
-+      implicit none
-+
-+      type(ab7_mixing_object), intent(inout) :: mix
-+      integer, intent(in) :: istep, nfftot, mpi_comm
-+      logical, intent(in) :: mpi_summarize
-+      real(dp), intent(in) :: ucvol
-+      real(dp), intent(inout) :: arr(mix%space * mix%nfft,mix%nspden)
-+      integer, intent(out) :: errid
-+      character(len = 500), intent(out) :: errmess
-+
-+      logical, intent(in), optional :: reset
-+      integer, intent(in), optional :: isecur, pawopt, response
-+      real(dp), intent(inout), optional, target :: pawarr(mix%n_pawmix)
-+      real(dp), intent(in), optional :: etotal
-+      real(dp), intent(in), optional :: potden(mix%space * mix%nfft,mix%nspden)
-+      real(dp), intent(out), optional :: resnrm
-+      optional :: fnrm, fdot
-+      integer, intent(in), optional :: user_data(:)
-+
-+      interface
-+         function fdot(x,y,cplex,nfft,nspden,opt_denpot,user_data)
-+           integer, intent(in) :: cplex,nfft,nspden,opt_denpot
-+           double precision, intent(in) :: x(*), y(*)
-+           integer, intent(in) :: user_data(:)
-+
-+           double precision :: fdot
-+         end function fdot
-+
-+         function fnrm(x,cplex,nfft,nspden,opt_denpot,user_data)
-+           integer, intent(in) :: cplex,nfft,nspden,opt_denpot
-+           double precision, intent(in) :: x(*)
-+           integer, intent(in) :: user_data(:)
-+
-+           double precision :: fnrm
-+         end function fnrm
-+      end interface
-+
-+      character(len = *), parameter :: subname = "ab7_mixing_eval"
-+      integer :: moveAtm, dbl_nnsclo, initialized, isecur_
-+      integer :: usepaw, pawoptmix_, response_, i_stat, i_all
-+      integer :: user_data_(2)
-+      real(dp) :: resnrm_
-+      real(dp), pointer :: pawarr_(:)
-+
-+      ! Argument checkings.
-+      if (mix%iscf == AB7_MIXING_NONE) then
-+         errid = AB7_ERROR_MIXING_ARG
-+         write(errmess, '(a,a,a,a)' )ch10,&
-+              & ' ab7_mixing_eval: ERROR -',ch10,&
-+              & '  No method has been chosen.'
-+         return
-+      end if
-+      if (mix%n_pawmix > 0 .and. .not. present(pawarr)) then
-+         errid = AB7_ERROR_MIXING_ARG
-+         write(errmess, '(a,a,a,a)' )ch10,&
-+              & ' ab7_mixing_eval: ERROR -',ch10,&
-+              & '  PAW is used, but no pawarr argument provided.'
-+         return
-+      end if
-+      if (mix%n_atom > 0 .and. (.not. associated(mix%dtn_pc) .or. &
-+           & .not. associated(mix%xred))) then
-+         errid = AB7_ERROR_MIXING_ARG
-+         write(errmess, '(a,a,a,a)' )ch10,&
-+              & ' ab7_mixing_eval: ERROR -',ch10,&
-+              & '  Moving atoms is used, but no xred or dtn_pc attributes provided.'
-+         return
-+      end if
-+      if ((present(fnrm) .or. present(fdot) .or. present(user_data)) .and. &
-+           & .not. (present(fnrm) .and. present(fdot) .and. present(user_data))) then
-+         errid = AB7_ERROR_MIXING_ARG
-+         write(errmess, '(a,a,a,a)' )ch10,&
-+              & ' ab7_mixing_eval: ERROR -',ch10,&
-+              & '  Passing optional norm and dot product routines without user_data argument.'
-+         return
-+      end if
-+      errid = AB7_NO_ERROR
-+
-+      ! Miscellaneous
-+      moveAtm = 0
-+      if (mix%n_atom > 0) moveAtm = 1
-+      initialized = 1
-+      if (present(reset)) then
-+         if (reset) initialized = 0
-+      end if
-+      isecur_ = 0
-+      if (present(isecur)) isecur_ = isecur
-+      usepaw = 0
-+      if (mix%n_pawmix > 0) usepaw = 1
-+      pawoptmix_ = 0
-+      if (present(pawopt)) pawoptmix_ = pawopt
-+      response_ = 0
-+      if (present(response)) response_ = response
-+      if (present(pawarr)) then
-+         pawarr_ => pawarr
-+      else
-+         allocate(pawarr_(1), stat = i_stat)
-+         call memocc(i_stat, pawarr_, 'pawarr_', subname)
-+      end if
-+
-+      ! Norm and dot products.
-+      if (.not. present(user_data)) then
-+         user_data_(1) = 0
-+         if (mpi_summarize) user_data_(1) = 1
-+         user_data_(2) = mpi_comm
-+      end if
-+
-+      ! Do the mixing.
-+      resnrm_ = 0.d0
-+      if (mix%iscf == AB7_MIXING_EIG) then
-+         !  This routine compute the eigenvalues of the SCF operator
-+         call scfeig(istep, mix%space * mix%nfft, mix%nspden, &
-+              & mix%f_fftgr(:,:,mix%i_vrespc(1)), arr, &
-+              & mix%f_fftgr(:,:,1), mix%f_fftgr(:,:,4:5), errid, errmess)
-+      else if (mix%iscf == AB7_MIXING_SIMPLE .or. &
-+           & mix%iscf == AB7_MIXING_ANDERSON .or. &
-+           & mix%iscf == AB7_MIXING_ANDERSON_2 .or. &
-+           & mix%iscf == AB7_MIXING_PULAY) then
-+         if (present(user_data)) then
-+            call scfopt(mix%space, mix%f_fftgr,mix%f_paw,mix%iscf,istep,&
-+                 & mix%i_vrespc,mix%i_vtrial, mix%nfft,mix%n_pawmix,mix%nspden, &
-+                 & mix%n_fftgr,mix%n_index,mix%kind,pawoptmix_,usepaw,pawarr_, &
-+                 & resnrm_, arr, fnrm, fdot, user_data, errid, errmess)
-+         else
-+            call scfopt(mix%space, mix%f_fftgr,mix%f_paw,mix%iscf,istep,&
-+                 & mix%i_vrespc,mix%i_vtrial, mix%nfft,mix%n_pawmix,mix%nspden, &
-+                 & mix%n_fftgr,mix%n_index,mix%kind,pawoptmix_,usepaw,pawarr_, &
-+                 & resnrm_, arr, fnrm_default, fdot_default, user_data_, errid, errmess)
-+         end if
-+         !  Change atomic positions
-+         if((istep==1 .or. mix%iscf==AB7_MIXING_SIMPLE) .and. mix%n_atom > 0)then
-+            !    GAF: 2009-06-03
-+            !    Apparently there are not reason
-+            !    to restrict iscf=2 for ionmov=5
-+            mix%xred(:,:) = mix%xred(:,:) + mix%dtn_pc(:,:)
-+         end if
-+      else if (mix%iscf == AB7_MIXING_CG_ENERGY .or. &
-+           & mix%iscf == AB7_MIXING_CG_ENERGY_2) then
-+         !  Optimize next vtrial using an algorithm based
-+         !  on the conjugate gradient minimization of etotal
-+         if (.not. present(etotal) .or. .not. present(potden)) then
-+            errid = AB7_ERROR_MIXING_ARG
-+            write(errmess, '(a,a,a,a)' )ch10,&
-+                 & ' ab7_mixing_eval: ERROR -',ch10,&
-+                 & '  Arguments etotal or potden are missing for CG on energy methods.'
-+            return
-+         end if
-+         if (mix%n_atom == 0) then
-+            allocate(mix%xred(3,0), stat = i_stat)
-+            call memocc(i_stat, mix%xred, 'mix%xred', subname)
-+            allocate(mix%dtn_pc(3,0), stat = i_stat)
-+            call memocc(i_stat, mix%dtn_pc, 'mix%dtn_pc', subname)
-+         end if
-+         if (present(user_data)) then
-+            call scfcge(mix%space,dbl_nnsclo,mix%dtn_pc,etotal,mix%f_atm,&
-+                 & mix%f_fftgr,initialized,mix%iscf,isecur_,istep,&
-+                 & mix%i_rhor,mix%i_vresid,mix%i_vrespc,moveAtm,&
-+                 & mix%n_atom,mix%nfft,nfftot,&
-+                 & mix%nspden,mix%n_fftgr,mix%n_index,mix%kind,&
-+                 & response_,potden,ucvol,arr,mix%xred, &
-+                 & fnrm, fdot, user_data, errid, errmess)
-+         else
-+            call scfcge(mix%space,dbl_nnsclo,mix%dtn_pc,etotal,mix%f_atm,&
-+                 & mix%f_fftgr,initialized,mix%iscf,isecur_,istep,&
-+                 & mix%i_rhor,mix%i_vresid,mix%i_vrespc,moveAtm,&
-+                 & mix%n_atom,mix%nfft,nfftot,&
-+                 & mix%nspden,mix%n_fftgr,mix%n_index,mix%kind,&
-+                 & response_,potden,ucvol,arr,mix%xred, fnrm_default, &
-+                 & fdotn_default, user_data_, errid, errmess)
-+         end if
-+         if (mix%n_atom == 0) then
-+            i_all = -product(shape(mix%xred))*kind(mix%xred)
-+            deallocate(mix%xred, stat = i_stat)
-+            call memocc(i_stat, i_all, 'mix%xred', subname)
-+            i_all = -product(shape(mix%dtn_pc))*kind(mix%dtn_pc)
-+            deallocate(mix%dtn_pc, stat = i_stat)
-+            call memocc(i_stat, i_all, 'mix%dtn_pc', subname)
-+         end if
-+         if (dbl_nnsclo == 1) errid = AB7_ERROR_MIXING_INC_NNSLOOP
-+      end if
-+      
-+      if (present(resnrm)) resnrm = resnrm_
-+      if (.not. present(pawarr)) then
-+         i_all = -product(shape(pawarr_))*kind(pawarr_)
-+         deallocate(pawarr_, stat = i_stat)
-+         call memocc(i_stat, i_all, 'pawarr_', subname)
-+      end if
-+    end subroutine ab7_mixing_eval
-+
-+    subroutine ab7_mixing_deallocate(mix)
-+      implicit none
-+
-+      type(ab7_mixing_object), intent(inout) :: mix
-+
-+      integer :: i_all, i_stat
-+      character(len = *), parameter :: subname = "ab7_mixing_deallocate"
-+
-+      if (associated(mix%i_rhor)) then
-+         i_all = -product(shape(mix%i_rhor))*kind(mix%i_rhor)
-+         deallocate(mix%i_rhor, stat = i_stat)
-+         call memocc(i_stat, i_all, 'mix%i_rhor', subname)
-+      end if
-+      if (associated(mix%i_vtrial)) then
-+         i_all = -product(shape(mix%i_vtrial))*kind(mix%i_vtrial)
-+         deallocate(mix%i_vtrial, stat = i_stat)
-+         call memocc(i_stat, i_all, 'mix%i_vtrial', subname)
-+      end if
-+      if (associated(mix%i_vresid)) then
-+         i_all = -product(shape(mix%i_vresid))*kind(mix%i_vresid)
-+         deallocate(mix%i_vresid, stat = i_stat)
-+         call memocc(i_stat, i_all, 'mix%i_vresid', subname)
-+      end if
-+      if (associated(mix%i_vrespc)) then
-+         i_all = -product(shape(mix%i_vrespc))*kind(mix%i_vrespc)
-+         deallocate(mix%i_vrespc, stat = i_stat)
-+         call memocc(i_stat, i_all, 'mix%i_vrespc', subname)
-+      end if
-+      if (associated(mix%f_fftgr)) then
-+         i_all = -product(shape(mix%f_fftgr))*kind(mix%f_fftgr)
-+         deallocate(mix%f_fftgr, stat = i_stat)
-+         call memocc(i_stat, i_all, 'mix%f_fftgr', subname)
-+      end if
-+      if (associated(mix%f_paw)) then
-+         i_all = -product(shape(mix%f_paw))*kind(mix%f_paw)
-+         deallocate(mix%f_paw, stat = i_stat)
-+         call memocc(i_stat, i_all, 'mix%f_paw', subname)
-+      end if
-+      if (associated(mix%f_atm)) then
-+         i_all = -product(shape(mix%f_atm))*kind(mix%f_atm)
-+         deallocate(mix%f_atm, stat = i_stat)
-+         call memocc(i_stat, i_all, 'mix%f_atm', subname)
-+      end if
-+
-+      call nullify_(mix)
-+    end subroutine ab7_mixing_deallocate
-+
-+    function fnrm_default(x,cplex,nfft,nspden,opt_denpot,user_data)
-+      integer, intent(in) :: cplex,nfft,nspden,opt_denpot
-+      double precision, intent(in) :: x(*)
-+      integer, intent(in) :: user_data(:)
-+
-+      double precision :: fnrm_default
-+      real(dp) :: resid_new(1)
-+
-+      call sqnormm_v(cplex,1,user_data(2),(user_data(1) /= 0),1,&
-+           & nfft,resid_new,1,nspden,opt_denpot,x)
-+      fnrm_default = resid_new(1)
-+    end function fnrm_default
-+
-+    function fdot_default(x,y,cplex,nfft,nspden,opt_denpot,user_data)
-+      integer, intent(in) :: cplex,nfft,nspden,opt_denpot
-+      double precision, intent(in) :: x(*), y(*)
-+      integer, intent(in) :: user_data(:)
-+
-+      double precision :: fdot_default
-+      real(dp) :: prod_resid(1)
-+
-+      call dotprodm_v(cplex,1,prod_resid,1,1,user_data(2),(user_data(1) /= 0),1,1,&
-+           & nfft,1,1,nspden,opt_denpot,x,y)
-+      fdot_default = prod_resid(1)
-+    end function fdot_default
-+
-+    function fdotn_default(x,y,cplex,nfft,nspden,opt_denpot,user_data)
-+      integer, intent(in) :: cplex,nfft,nspden,opt_denpot
-+      double precision, intent(in) :: x(*), y(*)
-+      integer, intent(in) :: user_data(:)
-+
-+      double precision :: fdotn_default
-+      real(dp) :: prod_resid(1,1,1)
-+
-+      call dotprodm_vn(cplex,1,x,prod_resid,1,1,user_data(2),(user_data(1) /= 0),1,1,&
-+           & 1,nfft,1,nspden,y)
-+      fdotn_default = prod_resid(1,1,1)
-+    end function fdotn_default
-+  end module m_ab7_mixing
-diff -urN bigdft-abi-1.0.4.old/libABINIT/src/56_mixing/scfcge.F90 bigdft-abi-1.0.4.new/libABINIT/src/56_mixing/scfcge.F90
---- bigdft-abi-1.0.4.old/libABINIT/src/56_mixing/scfcge.F90	2012-07-09 16:43:33.000000000 +0200
-+++ bigdft-abi-1.0.4.new/libABINIT/src/56_mixing/scfcge.F90	2013-06-11 16:51:00.000000000 +0200
-@@ -182,7 +182,7 @@
- !DEBUG
- !write(6,*)' scfcge : enter '
- !ENDDEBUG
-- errid = AB6_NO_ERROR
-+ errid = AB7_NO_ERROR
-  dbl_nnsclo = 0
- 
- !reduction gives the level of reduction of the error in
-@@ -318,7 +318,7 @@
- &     d2edv2_new,d2edv2_old,d2edv2_predict,&
- &     etotal,etotal_old,etotal_predict,&
- &     lambda_new,lambda_old,lambda_predict,errid_,message)
--     if (errid_ /= AB6_NO_ERROR) then
-+     if (errid_ /= AB7_NO_ERROR) then
-         call wrtout(std_out,message,'COLL')
-      end if
- 
-@@ -388,7 +388,7 @@
- &   (abs(lambda_predict)<0.005_dp*lambda_adapt .and. iscf==6).or.  &
- &   ilinmin==mlinmin                                      )     )then
-      if(number_of_restart>12)then
--        errid = AB6_ERROR_MIXING_CONVERGENCE
-+        errid = AB7_ERROR_MIXING_CONVERGENCE
-         write(errmess, '(a,a,a,a,a,i3,a,a,a,a,a)' ) ch10,&
- &       ' scfcge : ERROR -',ch10,&
- &       '  Potential-based CG line minimization not',&
-@@ -572,7 +572,7 @@
- &     d2edv2_new,d2edv2_old,d2edv2_predict,&
- &     etotal,etotal_old,etotal_predict,&
- &     lambda_new,lambda_old,lambda_predict,errid_,message)
--     if (errid_ /= AB6_NO_ERROR) then
-+     if (errid_ /= AB7_NO_ERROR) then
-         call wrtout(std_out,message,'COLL')
-      end if
-      lambda_predict2=0.0_dp
-@@ -836,7 +836,7 @@
- !  End of choice between initialisation or more developed
- !  parts of the CG algorithm
-  else
--    errid = AB6_ERROR_MIXING_ARG
-+    errid = AB7_ERROR_MIXING_ARG
-    write(errmess, '(a,a,a,a)' ) ch10,&
- &   ' scfcge : BUG ',ch10,&
- &   '  You should not be here ! '
-diff -urN bigdft-abi-1.0.4.old/libABINIT/src/56_mixing/scfeig.F90 bigdft-abi-1.0.4.new/libABINIT/src/56_mixing/scfeig.F90
---- bigdft-abi-1.0.4.old/libABINIT/src/56_mixing/scfeig.F90	2012-07-09 16:43:33.000000000 +0200
-+++ bigdft-abi-1.0.4.new/libABINIT/src/56_mixing/scfeig.F90	2013-06-11 16:51:00.000000000 +0200
-@@ -71,10 +71,10 @@
- 
- ! *************************************************************************
-  
-- errid = AB6_NO_ERROR
-+ errid = AB7_NO_ERROR
- 
-  if(nspden==4)then
--    errid = AB6_ERROR_MIXING_ARG
-+    errid = AB7_ERROR_MIXING_ARG
-     write(errmess, *) ' scfeig : does not work yet for nspden=4'
-     return
-  end if
-@@ -103,7 +103,7 @@
- &   ' scfeig : initial PC_residual square =',resid_old
-    call wrtout(std_out,message,'COLL')
-    if(resid_old>1.0d-8)then
--      errid = AB6_ERROR_MIXING_ARG
-+      errid = AB7_ERROR_MIXING_ARG
-       write(errmess,'(a,a,a,a,a,a,a,a,a,a)') ch10,&
- &     ' scfeig : ERROR -',ch10,&
- &     '  This value is not good enough to allow',ch10,&
-diff -urN bigdft-abi-1.0.4.old/libABINIT/src/56_mixing/scfopt.F90 bigdft-abi-1.0.4.new/libABINIT/src/56_mixing/scfopt.F90
---- bigdft-abi-1.0.4.old/libABINIT/src/56_mixing/scfopt.F90	2012-07-09 16:43:33.000000000 +0200
-+++ bigdft-abi-1.0.4.new/libABINIT/src/56_mixing/scfopt.F90	2013-06-11 16:51:00.000000000 +0200
-@@ -136,7 +136,7 @@
- !DEBUG
- !write(6,*)' scfopt : enter ; istep,iscf ',istep,iscf
- !ENDDEBUG
-- errid = AB6_NO_ERROR
-+ errid = AB7_NO_ERROR
- 
-  i_vstore=i_vtrial(1)
-  if (iscf==4) i_vstore=i_vtrial(2)
-@@ -322,7 +322,7 @@
-    call wrtout(std_out,message,'COLL')
- 
-    if (npulay>npulaymax) then
--      errid = AB6_ERROR_MIXING_CONVERGENCE
-+      errid = AB7_ERROR_MIXING_CONVERGENCE
-       write(errmess, '(4a)' ) ch10,&
- &     ' scfopt : ERROR - ',ch10,&
- &     '  Too much iterations required for Pulay algorithm (<50) !'
-diff -urN bigdft-abi-1.0.4.old/libABINIT/src/56_recipspace/m_ab6_kpoints.F90 bigdft-abi-1.0.4.new/libABINIT/src/56_recipspace/m_ab6_kpoints.F90
---- bigdft-abi-1.0.4.old/libABINIT/src/56_recipspace/m_ab6_kpoints.F90	2012-07-09 16:43:33.000000000 +0200
-+++ bigdft-abi-1.0.4.new/libABINIT/src/56_recipspace/m_ab6_kpoints.F90	1970-01-01 01:00:00.000000000 +0100
-@@ -1,281 +0,0 @@
--!* * Fortran90 source file *
--!*
--!* Copyright (C) 2008-2011 ABINIT Group (Damien Caliste)
--!* All rights reserved.
--!*
--!* This file is part of the ABINIT software package. For license information,
--!* please see the COPYING file in the top-level directory of the ABINIT source
--!* distribution.
--!*
--!*
--
--#if defined HAVE_CONFIG_H
--#include "config.inc"
--#endif
--
--module m_ab6_kpoints
--
--  use defs_basis
--  use m_ab6_symmetry
--
--  implicit none
--
--  private
--
--  logical, private, parameter :: AB_DBG = .false.
--
--  public :: kpoints_get_irreductible_zone
--
--  public :: kpoints_get_mp_k_grid
--  public :: kpoints_get_auto_k_grid
--
--  public :: kpoints_binding_mp_k_1
--  public :: kpoints_binding_mp_k_2
--  public :: kpoints_binding_auto_k_1
--  public :: kpoints_binding_auto_k_2
--
--contains
--
--  subroutine kpoints_get_irreductible_zone(irrzon, phnons, &
--       & n1, n2, n3, nsppol, nspden, symid, errno)
--
--
--!This section has been created automatically by the script Abilint (TD).
--!Do not modify the following lines by hand.
-- use interfaces_56_recipspace
--!End of the abilint section
--
--    integer, intent(in)   :: symid
--    integer, intent(in)   :: n1, n2, n3, nsppol, nspden
--    integer, intent(out)  :: irrzon(n1*n2*n3,2,(nspden/nsppol)-3*(nspden/4))
--    real(dp), intent(out) :: phnons(2,n1*n2*n3,(nspden/nsppol)-3*(nspden/4))
--    integer, intent(out)  :: errno
--
--    type(symmetry_type), pointer  :: sym
--
--    if (AB_DBG) write(std_err,*) "AB kpoints: call get irreductible zone."
--
--    errno = AB6_NO_ERROR
--    call symmetry_get_from_id(sym, symid, errno)
--    if (errno /= AB6_NO_ERROR) return
--
--    if (sym%withSpin /= nspden) then
--       errno = AB6_ERROR_ARG
--       return
--    end if
--
--    call irrzg(irrzon, nspden, nsppol, sym%nSym, n1, n2, n3, phnons, &
--         & sym%symAfm, sym%sym, sym%transNon)
--  end subroutine kpoints_get_irreductible_zone
--
--
--
--  subroutine kpoints_binding_mp_k_1(symid, nkpt, ngkpt, &
--       & kptrlatt, kptrlen, nshiftk, shiftk, errno)
--
--
--!This section has been created automatically by the script Abilint (TD).
--!Do not modify the following lines by hand.
-- use interfaces_56_recipspace
--!End of the abilint section
--
--    integer, intent(in)  :: symid
--    integer, intent(out) :: errno
--    integer, intent(in) :: ngkpt(3)
--    integer, intent(inout) :: nshiftk
--    real(dp), intent(inout) :: shiftk(3, 8)
--    real(dp), intent(out) :: kptrlen
--    integer, intent(out) :: kptrlatt(3,3)
--    integer, intent(out) :: nkpt
--
--    type(symmetry_type), pointer  :: sym
--    real(dp) :: kpt(3,1), wkpt(1)
--
--    if (AB_DBG) write(std_err,*) "AB symmetry: call get k grid1."
--
--    errno = AB6_NO_ERROR
--    call symmetry_get_from_id(sym, symid, errno)
--    if (errno /= AB6_NO_ERROR) return
--
--    ! First, compute the number of kpoints
--    kptrlatt(:,:) = 0
--    kptrlatt(1,1) = ngkpt(1)
--    kptrlatt(2,2) = ngkpt(2)
--    kptrlatt(3,3) = ngkpt(3)
--    kptrlen = 20.
--
--    call getkgrid(6, 1, kpt, 1, kptrlatt, kptrlen, &
--         & AB6_MAX_SYMMETRIES, 0, nkpt, nshiftk, sym%nSym, &
--         & sym%rprimd, shiftk, sym%symAfm, sym%sym, &
--         & sym%vacuum, wkpt)
--  end subroutine kpoints_binding_mp_k_1
--
--  subroutine kpoints_binding_mp_k_2(symid, nkpt, kpt, wkpt, &
--       & kptrlatt, kptrlen, nshiftk, shiftk, errno)
--
--
--!This section has been created automatically by the script Abilint (TD).
--!Do not modify the following lines by hand.
-- use interfaces_56_recipspace
--!End of the abilint section
--
--    integer, intent(in)  :: symid
--    integer, intent(out) :: errno
--    integer, intent(inout) :: nshiftk
--    real(dp), intent(inout) :: shiftk(3, 8)
--    integer, intent(in) :: nkpt
--    real(dp), intent(out) :: kpt(3,nkpt), wkpt(nkpt)
--    real(dp), intent(inout) :: kptrlen
--    integer, intent(inout) :: kptrlatt(3,3)
--
--    type(symmetry_type), pointer  :: sym
--    integer :: nkpt_
--
--    if (AB_DBG) write(std_err,*) "AB symmetry: call get k grid2."
--
--    errno = AB6_NO_ERROR
--    call symmetry_get_from_id(sym, symid, errno)
--    if (errno /= AB6_NO_ERROR) return
--
--    ! Then, we call it again to get the actual values for the k points.
--    call getkgrid(6, 1, kpt, 1, kptrlatt, kptrlen, &
--         & AB6_MAX_SYMMETRIES, nkpt, nkpt_, nshiftk, sym%nSym, &
--         & sym%rprimd, shiftk, sym%symAfm, sym%sym, &
--         & sym%vacuum, wkpt)
--  end subroutine kpoints_binding_mp_k_2
--
--
--  subroutine kpoints_get_mp_k_grid(symid, nkpt, kpt, wkpt, &
--       & ngkpt, nshiftk, shiftk, errno)
--
--    integer, intent(in)  :: symid
--    integer, intent(out) :: errno
--    integer, intent(in) :: ngkpt(3)
--    integer, intent(in) :: nshiftk
--    real(dp), intent(in) :: shiftk(3, nshiftk)
--    integer, intent(out) :: nkpt
--    real(dp), pointer :: kpt(:,:), wkpt(:)
--
--    real(dp) :: kptrlen
--    integer :: kptrlatt(3,3)
--    integer :: nshiftk_
--    real(dp) :: shiftk_(3, 8)
--
--    if (AB_DBG) write(std_err,*) "AB symmetry: call get k grid."
--
--    nshiftk_ = nshiftk
--    shiftk_(:,1:nshiftk_) = shiftk(:,:)
--
--    call kpoints_binding_mp_k_1(symid, nkpt, ngkpt, kptrlatt, kptrlen, &
--         & nshiftk_, shiftk_, errno)
--    if (errno /= AB6_NO_ERROR) return
--    allocate(kpt(3, nkpt))
--    allocate(wkpt(nkpt))
--    call kpoints_binding_mp_k_2(symid, nkpt, kpt, wkpt, &
--       & kptrlatt, kptrlen, nshiftk_, shiftk_, errno)
--  end subroutine kpoints_get_mp_k_grid
--
--
--
--  subroutine kpoints_binding_auto_k_1(symid, nkpt, kptrlatt, kptrlen, &
--       & nshiftk, shiftk, errno)
--
--
--!This section has been created automatically by the script Abilint (TD).
--!Do not modify the following lines by hand.
-- use interfaces_56_recipspace
--!End of the abilint section
--
--    integer, intent(in)  :: symid
--    integer, intent(out) :: errno
--    integer, intent(out) :: nkpt
--    real(dp), intent(inout) :: kptrlen
--    integer, intent(out) :: nshiftk
--    real(dp), intent(out) :: shiftk(3, 8)
--    integer, intent(out) :: kptrlatt(3,3)
--
--    type(symmetry_type), pointer  :: sym
--    real(dp), allocatable :: kpt(:,:), wkpt(:)
--
--    if (AB_DBG) write(std_err,*) "AB symmetry: call get auto k grid1."
--
--    errno = AB6_NO_ERROR
--    call symmetry_get_from_id(sym, symid, errno)
--    if (errno /= AB6_NO_ERROR) return
--
--    !  The parameters of the k lattice are not known, compute
--    !  kptrlatt, nshiftk, shiftk.
--    call testkgrid(sym%bravais,6,kptrlatt,kptrlen,&
--         & AB6_MAX_SYMMETRIES,nshiftk,sym%nSym,0,sym%rprimd,&
--         & shiftk,sym%symAfm,sym%sym,sym%vacuum)
--    if (AB_DBG) write(std_err,*) "AB symmetry: testkgrid -> kptrlatt=", kptrlatt
--
--    call getkgrid(6, 1, kpt, 1, kptrlatt, kptrlen, &
--         & AB6_MAX_SYMMETRIES, 0, nkpt, nshiftk, sym%nSym, &
--         & sym%rprimd, shiftk, sym%symAfm, sym%sym, &
--         & sym%vacuum, wkpt)
--    if (AB_DBG) write(std_err,*) "AB symmetry: getkgrid -> nkpt=", nkpt
--  end subroutine kpoints_binding_auto_k_1
--
--
--  subroutine kpoints_binding_auto_k_2(symid, nkpt, kpt, wkpt, kptrlatt, kptrlen, &
--       & nshiftk, shiftk, errno)
--
--
--!This section has been created automatically by the script Abilint (TD).
--!Do not modify the following lines by hand.
-- use interfaces_56_recipspace
--!End of the abilint section
--
--    integer, intent(in)  :: symid
--    integer, intent(out) :: errno
--    integer, intent(in) :: nkpt
--    real(dp), intent(out) :: kpt(3,nkpt), wkpt(nkpt)
--    real(dp), intent(inout) :: kptrlen
--    integer, intent(inout) :: nshiftk
--    real(dp), intent(inout) :: shiftk(3, 8)
--    integer, intent(inout) :: kptrlatt(3,3)
--
--    type(symmetry_type), pointer  :: sym
--    integer :: nkpt_
--
--    if (AB_DBG) write(std_err,*) "AB symmetry: call get auto k grid2."
--
--    errno = AB6_NO_ERROR
--    call symmetry_get_from_id(sym, symid, errno)
--    if (errno /= AB6_NO_ERROR) return
--
--    ! Then, we call it again to get the actual values for the k points.
--    call getkgrid(6, 1, kpt, 1, kptrlatt, kptrlen, &
--         & AB6_MAX_SYMMETRIES, nkpt, nkpt_, nshiftk, sym%nSym, &
--         & sym%rprimd, shiftk, sym%symAfm, sym%sym, &
--         & sym%vacuum, wkpt)
--  end subroutine kpoints_binding_auto_k_2
--
--  subroutine kpoints_get_auto_k_grid(symid, nkpt, kpt, wkpt, &
--       & kptrlen, errno)
--
--    integer, intent(in)  :: symid
--    integer, intent(out) :: errno
--    integer, intent(out) :: nkpt
--    real(dp), intent(in) :: kptrlen
--    real(dp), pointer :: kpt(:,:), wkpt(:)
--
--    real(dp) :: kptrlen_
--    integer :: kptrlatt(3,3)
--    integer :: nshiftk
--    real(dp) :: shiftk(3, 8)
--
--    if (AB_DBG) write(std_err,*) "AB symmetry: call get auto k grid."
--
--    kptrlen_ = kptrlen
--    call kpoints_binding_auto_k_1(symid, nkpt, kptrlatt, kptrlen_, &
--       & nshiftk, shiftk, errno)
--    if (errno /= AB6_NO_ERROR) return
--    allocate(kpt(3, nkpt))
--    allocate(wkpt(nkpt))
--    call kpoints_binding_auto_k_2(symid, nkpt, kpt, wkpt, kptrlatt, kptrlen_, &
--       & nshiftk, shiftk, errno)
--  end subroutine kpoints_get_auto_k_grid
--
--end module m_ab6_kpoints
-diff -urN bigdft-abi-1.0.4.old/libABINIT/src/56_recipspace/m_ab7_kpoints.F90 bigdft-abi-1.0.4.new/libABINIT/src/56_recipspace/m_ab7_kpoints.F90
---- bigdft-abi-1.0.4.old/libABINIT/src/56_recipspace/m_ab7_kpoints.F90	1970-01-01 01:00:00.000000000 +0100
-+++ bigdft-abi-1.0.4.new/libABINIT/src/56_recipspace/m_ab7_kpoints.F90	2013-06-11 16:51:00.000000000 +0200
-@@ -0,0 +1,281 @@
-+!* * Fortran90 source file *
-+!*
-+!* Copyright (C) 2008-2011 ABINIT Group (Damien Caliste)
-+!* All rights reserved.
-+!*
-+!* This file is part of the ABINIT software package. For license information,
-+!* please see the COPYING file in the top-level directory of the ABINIT source
-+!* distribution.
-+!*
-+!*
-+
-+#if defined HAVE_CONFIG_H
-+#include "config.inc"
-+#endif
-+
-+module m_ab7_kpoints
-+
-+  use defs_basis
-+  use m_ab7_symmetry
-+
-+  implicit none
-+
-+  private
-+
-+  logical, private, parameter :: AB_DBG = .false.
-+
-+  public :: kpoints_get_irreductible_zone
-+
-+  public :: kpoints_get_mp_k_grid
-+  public :: kpoints_get_auto_k_grid
-+
-+  public :: kpoints_binding_mp_k_1
-+  public :: kpoints_binding_mp_k_2
-+  public :: kpoints_binding_auto_k_1
-+  public :: kpoints_binding_auto_k_2
-+
-+contains
-+
-+  subroutine kpoints_get_irreductible_zone(irrzon, phnons, &
-+       & n1, n2, n3, nsppol, nspden, symid, errno)
-+
-+
-+!This section has been created automatically by the script Abilint (TD).
-+!Do not modify the following lines by hand.
-+ use interfaces_56_recipspace
-+!End of the abilint section
-+
-+    integer, intent(in)   :: symid
-+    integer, intent(in)   :: n1, n2, n3, nsppol, nspden
-+    integer, intent(out)  :: irrzon(n1*n2*n3,2,(nspden/nsppol)-3*(nspden/4))
-+    real(dp), intent(out) :: phnons(2,n1*n2*n3,(nspden/nsppol)-3*(nspden/4))
-+    integer, intent(out)  :: errno
-+
-+    type(symmetry_type), pointer  :: sym
-+
-+    if (AB_DBG) write(std_err,*) "AB kpoints: call get irreductible zone."
-+
-+    errno = AB7_NO_ERROR
-+    call symmetry_get_from_id(sym, symid, errno)
-+    if (errno /= AB7_NO_ERROR) return
-+
-+    if (sym%withSpin /= nspden) then
-+       errno = AB7_ERROR_ARG
-+       return
-+    end if
-+
-+    call irrzg(irrzon, nspden, nsppol, sym%nSym, n1, n2, n3, phnons, &
-+         & sym%symAfm, sym%sym, sym%transNon)
-+  end subroutine kpoints_get_irreductible_zone
-+
-+
-+
-+  subroutine kpoints_binding_mp_k_1(symid, nkpt, ngkpt, &
-+       & kptrlatt, kptrlen, nshiftk, shiftk, errno)
-+
-+
-+!This section has been created automatically by the script Abilint (TD).
-+!Do not modify the following lines by hand.
-+ use interfaces_56_recipspace
-+!End of the abilint section
-+
-+    integer, intent(in)  :: symid
-+    integer, intent(out) :: errno
-+    integer, intent(in) :: ngkpt(3)
-+    integer, intent(inout) :: nshiftk
-+    real(dp), intent(inout) :: shiftk(3, 8)
-+    real(dp), intent(out) :: kptrlen
-+    integer, intent(out) :: kptrlatt(3,3)
-+    integer, intent(out) :: nkpt
-+
-+    type(symmetry_type), pointer  :: sym
-+    real(dp) :: kpt(3,1), wkpt(1)
-+
-+    if (AB_DBG) write(std_err,*) "AB symmetry: call get k grid1."
-+
-+    errno = AB7_NO_ERROR
-+    call symmetry_get_from_id(sym, symid, errno)
-+    if (errno /= AB7_NO_ERROR) return
-+
-+    ! First, compute the number of kpoints
-+    kptrlatt(:,:) = 0
-+    kptrlatt(1,1) = ngkpt(1)
-+    kptrlatt(2,2) = ngkpt(2)
-+    kptrlatt(3,3) = ngkpt(3)
-+    kptrlen = 20.
-+
-+    call getkgrid(6, 1, kpt, 1, kptrlatt, kptrlen, &
-+         & AB7_MAX_SYMMETRIES, 0, nkpt, nshiftk, sym%nSym, &
-+         & sym%rprimd, shiftk, sym%symAfm, sym%sym, &
-+         & sym%vacuum, wkpt)
-+  end subroutine kpoints_binding_mp_k_1
-+
-+  subroutine kpoints_binding_mp_k_2(symid, nkpt, kpt, wkpt, &
-+       & kptrlatt, kptrlen, nshiftk, shiftk, errno)
-+
-+
-+!This section has been created automatically by the script Abilint (TD).
-+!Do not modify the following lines by hand.
-+ use interfaces_56_recipspace
-+!End of the abilint section
-+
-+    integer, intent(in)  :: symid
-+    integer, intent(out) :: errno
-+    integer, intent(inout) :: nshiftk
-+    real(dp), intent(inout) :: shiftk(3, 8)
-+    integer, intent(in) :: nkpt
-+    real(dp), intent(out) :: kpt(3,nkpt), wkpt(nkpt)
-+    real(dp), intent(inout) :: kptrlen
-+    integer, intent(inout) :: kptrlatt(3,3)
-+
-+    type(symmetry_type), pointer  :: sym
-+    integer :: nkpt_
-+
-+    if (AB_DBG) write(std_err,*) "AB symmetry: call get k grid2."
-+
-+    errno = AB7_NO_ERROR
-+    call symmetry_get_from_id(sym, symid, errno)
-+    if (errno /= AB7_NO_ERROR) return
-+
-+    ! Then, we call it again to get the actual values for the k points.
-+    call getkgrid(6, 1, kpt, 1, kptrlatt, kptrlen, &
-+         & AB7_MAX_SYMMETRIES, nkpt, nkpt_, nshiftk, sym%nSym, &
-+         & sym%rprimd, shiftk, sym%symAfm, sym%sym, &
-+         & sym%vacuum, wkpt)
-+  end subroutine kpoints_binding_mp_k_2
-+
-+
-+  subroutine kpoints_get_mp_k_grid(symid, nkpt, kpt, wkpt, &
-+       & ngkpt, nshiftk, shiftk, errno)
-+
-+    integer, intent(in)  :: symid
-+    integer, intent(out) :: errno
-+    integer, intent(in) :: ngkpt(3)
-+    integer, intent(in) :: nshiftk
-+    real(dp), intent(in) :: shiftk(3, nshiftk)
-+    integer, intent(out) :: nkpt
-+    real(dp), pointer :: kpt(:,:), wkpt(:)
-+
-+    real(dp) :: kptrlen
-+    integer :: kptrlatt(3,3)
-+    integer :: nshiftk_
-+    real(dp) :: shiftk_(3, 8)
-+
-+    if (AB_DBG) write(std_err,*) "AB symmetry: call get k grid."
-+
-+    nshiftk_ = nshiftk
-+    shiftk_(:,1:nshiftk_) = shiftk(:,:)
-+
-+    call kpoints_binding_mp_k_1(symid, nkpt, ngkpt, kptrlatt, kptrlen, &
-+         & nshiftk_, shiftk_, errno)
-+    if (errno /= AB7_NO_ERROR) return
-+    allocate(kpt(3, nkpt))
-+    allocate(wkpt(nkpt))
-+    call kpoints_binding_mp_k_2(symid, nkpt, kpt, wkpt, &
-+       & kptrlatt, kptrlen, nshiftk_, shiftk_, errno)
-+  end subroutine kpoints_get_mp_k_grid
-+
-+
-+
-+  subroutine kpoints_binding_auto_k_1(symid, nkpt, kptrlatt, kptrlen, &
-+       & nshiftk, shiftk, errno)
-+
-+
-+!This section has been created automatically by the script Abilint (TD).
-+!Do not modify the following lines by hand.
-+ use interfaces_56_recipspace
-+!End of the abilint section
-+
-+    integer, intent(in)  :: symid
-+    integer, intent(out) :: errno
-+    integer, intent(out) :: nkpt
-+    real(dp), intent(inout) :: kptrlen
-+    integer, intent(out) :: nshiftk
-+    real(dp), intent(out) :: shiftk(3, 8)
-+    integer, intent(out) :: kptrlatt(3,3)
-+
-+    type(symmetry_type), pointer  :: sym
-+    real(dp), allocatable :: kpt(:,:), wkpt(:)
-+
-+    if (AB_DBG) write(std_err,*) "AB symmetry: call get auto k grid1."
-+
-+    errno = AB7_NO_ERROR
-+    call symmetry_get_from_id(sym, symid, errno)
-+    if (errno /= AB7_NO_ERROR) return
-+
-+    !  The parameters of the k lattice are not known, compute
-+    !  kptrlatt, nshiftk, shiftk.
-+    call testkgrid(sym%bravais,6,kptrlatt,kptrlen,&
-+         & AB7_MAX_SYMMETRIES,nshiftk,sym%nSym,0,sym%rprimd,&
-+         & shiftk,sym%symAfm,sym%sym,sym%vacuum)
-+    if (AB_DBG) write(std_err,*) "AB symmetry: testkgrid -> kptrlatt=", kptrlatt
-+
-+    call getkgrid(6, 1, kpt, 1, kptrlatt, kptrlen, &
-+         & AB7_MAX_SYMMETRIES, 0, nkpt, nshiftk, sym%nSym, &
-+         & sym%rprimd, shiftk, sym%symAfm, sym%sym, &
-+         & sym%vacuum, wkpt)
-+    if (AB_DBG) write(std_err,*) "AB symmetry: getkgrid -> nkpt=", nkpt
-+  end subroutine kpoints_binding_auto_k_1
-+
-+
-+  subroutine kpoints_binding_auto_k_2(symid, nkpt, kpt, wkpt, kptrlatt, kptrlen, &
-+       & nshiftk, shiftk, errno)
-+
-+
-+!This section has been created automatically by the script Abilint (TD).
-+!Do not modify the following lines by hand.
-+ use interfaces_56_recipspace
-+!End of the abilint section
-+
-+    integer, intent(in)  :: symid
-+    integer, intent(out) :: errno
-+    integer, intent(in) :: nkpt
-+    real(dp), intent(out) :: kpt(3,nkpt), wkpt(nkpt)
-+    real(dp), intent(inout) :: kptrlen
-+    integer, intent(inout) :: nshiftk
-+    real(dp), intent(inout) :: shiftk(3, 8)
-+    integer, intent(inout) :: kptrlatt(3,3)
-+
-+    type(symmetry_type), pointer  :: sym
-+    integer :: nkpt_
-+
-+    if (AB_DBG) write(std_err,*) "AB symmetry: call get auto k grid2."
-+
-+    errno = AB7_NO_ERROR
-+    call symmetry_get_from_id(sym, symid, errno)
-+    if (errno /= AB7_NO_ERROR) return
-+
-+    ! Then, we call it again to get the actual values for the k points.
-+    call getkgrid(6, 1, kpt, 1, kptrlatt, kptrlen, &
-+         & AB7_MAX_SYMMETRIES, nkpt, nkpt_, nshiftk, sym%nSym, &
-+         & sym%rprimd, shiftk, sym%symAfm, sym%sym, &
-+         & sym%vacuum, wkpt)
-+  end subroutine kpoints_binding_auto_k_2
-+
-+  subroutine kpoints_get_auto_k_grid(symid, nkpt, kpt, wkpt, &
-+       & kptrlen, errno)
-+
-+    integer, intent(in)  :: symid
-+    integer, intent(out) :: errno
-+    integer, intent(out) :: nkpt
-+    real(dp), intent(in) :: kptrlen
-+    real(dp), pointer :: kpt(:,:), wkpt(:)
-+
-+    real(dp) :: kptrlen_
-+    integer :: kptrlatt(3,3)
-+    integer :: nshiftk
-+    real(dp) :: shiftk(3, 8)
-+
-+    if (AB_DBG) write(std_err,*) "AB symmetry: call get auto k grid."
-+
-+    kptrlen_ = kptrlen
-+    call kpoints_binding_auto_k_1(symid, nkpt, kptrlatt, kptrlen_, &
-+       & nshiftk, shiftk, errno)
-+    if (errno /= AB7_NO_ERROR) return
-+    allocate(kpt(3, nkpt))
-+    allocate(wkpt(nkpt))
-+    call kpoints_binding_auto_k_2(symid, nkpt, kpt, wkpt, kptrlatt, kptrlen_, &
-+       & nshiftk, shiftk, errno)
-+  end subroutine kpoints_get_auto_k_grid
-+
-+end module m_ab7_kpoints
-diff -urN bigdft-abi-1.0.4.old/libABINIT/src/72_geomoptim/ab6_moldyn.F90 bigdft-abi-1.0.4.new/libABINIT/src/72_geomoptim/ab6_moldyn.F90
---- bigdft-abi-1.0.4.old/libABINIT/src/72_geomoptim/ab6_moldyn.F90	2012-07-09 16:43:33.000000000 +0200
-+++ bigdft-abi-1.0.4.new/libABINIT/src/72_geomoptim/ab6_moldyn.F90	1970-01-01 01:00:00.000000000 +0100
-@@ -1,42 +0,0 @@
--module ab6_moldyn
--
--  use defs_basis
--
--  implicit none
--
--  interface
--     subroutine scfloop_main(acell, epot, fcart, grad, itime, me, natom, rprimd, xred)
--       use defs_basis
--
--       integer, intent(in) :: natom, itime, me
--       real(dp), intent(out) :: epot
--       real(dp), intent(in) :: acell(3)
--       real(dp), intent(in) :: rprimd(3,3), xred(3,natom)
--       real(dp), intent(out) :: fcart(3, natom), grad(3, natom)
--     end subroutine scfloop_main
--  end interface
--
--  interface
--     subroutine scfloop_output(acell, epot, ekin, fred, itime, me, natom, rprimd, vel, xred)
--       use defs_basis
--
--       integer, intent(in) :: natom, itime, me
--       real(dp), intent(in) :: epot, ekin
--       real(dp), intent(in) :: acell(3)
--       real(dp), intent(in) :: rprimd(3,3), xred(3,natom)
--       real(dp), intent(in) :: fred(3, natom), vel(3, natom)
--     end subroutine scfloop_output
--  end interface
--
--contains
--
--  include "velocity_verlet.F90"
--  include "quenched.F90"
--  include "langevin.F90"
--  include "nose.F90"
--  include "isokinetic.F90"
--  include "isotemp.F90"
--  include "isothermal.F90"
--  include "moldyn.F90"
--
--end module ab6_moldyn
-diff -urN bigdft-abi-1.0.4.old/libABINIT/src/72_geomoptim/ab7_moldyn.F90 bigdft-abi-1.0.4.new/libABINIT/src/72_geomoptim/ab7_moldyn.F90
---- bigdft-abi-1.0.4.old/libABINIT/src/72_geomoptim/ab7_moldyn.F90	1970-01-01 01:00:00.000000000 +0100
-+++ bigdft-abi-1.0.4.new/libABINIT/src/72_geomoptim/ab7_moldyn.F90	2013-06-11 16:51:00.000000000 +0200
-@@ -0,0 +1,42 @@
-+module ab7_moldyn
-+
-+  use defs_basis
-+
-+  implicit none
-+
-+  interface
-+     subroutine scfloop_main(acell, epot, fcart, grad, itime, me, natom, rprimd, xred)
-+       use defs_basis
-+
-+       integer, intent(in) :: natom, itime, me
-+       real(dp), intent(out) :: epot
-+       real(dp), intent(in) :: acell(3)
-+       real(dp), intent(in) :: rprimd(3,3), xred(3,natom)
-+       real(dp), intent(out) :: fcart(3, natom), grad(3, natom)
-+     end subroutine scfloop_main
-+  end interface
-+
-+  interface
-+     subroutine scfloop_output(acell, epot, ekin, fred, itime, me, natom, rprimd, vel, xred)
-+       use defs_basis
-+
-+       integer, intent(in) :: natom, itime, me
-+       real(dp), intent(in) :: epot, ekin
-+       real(dp), intent(in) :: acell(3)
-+       real(dp), intent(in) :: rprimd(3,3), xred(3,natom)
-+       real(dp), intent(in) :: fred(3, natom), vel(3, natom)
-+     end subroutine scfloop_output
-+  end interface
-+
-+contains
-+
-+  include "velocity_verlet.F90"
-+  include "quenched.F90"
-+  include "langevin.F90"
-+  include "nose.F90"
-+  include "isokinetic.F90"
-+  include "isotemp.F90"
-+  include "isothermal.F90"
-+  include "moldyn.F90"
-+
-+end module ab7_moldyn
-diff -urN bigdft-abi-1.0.4.old/libABINIT/src/Makefile.am bigdft-abi-1.0.4.new/libABINIT/src/Makefile.am
---- bigdft-abi-1.0.4.old/libABINIT/src/Makefile.am	2012-11-08 11:12:57.000000000 +0100
-+++ bigdft-abi-1.0.4.new/libABINIT/src/Makefile.am	2013-06-11 16:51:00.000000000 +0200
-@@ -85,7 +85,7 @@
- 	42_geometry/getspinrot.F90 \
- 	42_geometry/gridgcart.F90 \
- 	42_geometry/holocell.F90 \
--	42_geometry/m_ab6_symmetry.F90 \
-+	42_geometry/m_ab7_symmetry.F90 \
- 	42_geometry/metric.F90 \
- 	42_geometry/mkrdim.F90 \
- 	42_geometry/operat.F90 \
-@@ -128,14 +128,14 @@
- 	56_mixing/dotprodm_vn.F90 \
- 	56_mixing/findminscf.F90 \
- 	56_mixing/interfaces_56_mixing.F90 \
--	56_mixing/m_ab6_mixing.F90 \
-+	56_mixing/m_ab7_mixing.F90 \
- 	56_mixing/scfcge.F90 \
- 	56_mixing/scfeig.F90 \
- 	56_mixing/scfopt.F90 \
- 	56_mixing/sqnormm_v.F90 \
- 	56_recipspace/interfaces_56_recipspace.F90 \
- 	56_recipspace/irrzg.F90 \
--	56_recipspace/m_ab6_kpoints.F90 \
-+	56_recipspace/m_ab7_kpoints.F90 \
- 	56_recipspace/getkgrid.F90 \
- 	56_recipspace/smpbz.F90 \
- 	56_recipspace/symkpt.F90 \
-@@ -159,7 +159,7 @@
-         67_common/ewald2.F90 \
- 	67_common/fconv.F90 \
- 	67_common/prtxvf.F90 \
--	72_geomoptim/ab6_moldyn.F90 \
-+	72_geomoptim/ab7_moldyn.F90 \
- 	72_geomoptim/xfpack.F90
- 
- CLEANFILES = mpif.h *.@MODULE_EXT@
-diff -urN bigdft-abi-1.0.4.old/libABINIT/src/Makefile.in bigdft-abi-1.0.4.new/libABINIT/src/Makefile.in
---- bigdft-abi-1.0.4.old/libABINIT/src/Makefile.in	2013-01-28 14:39:34.000000000 +0100
-+++ bigdft-abi-1.0.4.new/libABINIT/src/Makefile.in	2013-06-11 16:51:00.000000000 +0200
-@@ -91,7 +91,7 @@
- 	gensymshub4.$(OBJEXT) gensymshub.$(OBJEXT) \
- 	gensymspgr.$(OBJEXT) getptgroupma.$(OBJEXT) \
- 	getspinrot.$(OBJEXT) gridgcart.$(OBJEXT) holocell.$(OBJEXT) \
--	m_ab6_symmetry.$(OBJEXT) metric.$(OBJEXT) mkrdim.$(OBJEXT) \
-+	m_ab7_symmetry.$(OBJEXT) metric.$(OBJEXT) mkrdim.$(OBJEXT) \
- 	operat.$(OBJEXT) prtspgroup.$(OBJEXT) ptgmadata.$(OBJEXT) \
- 	smallprim.$(OBJEXT) spgdata.$(OBJEXT) strainsym.$(OBJEXT) \
- 	strconv.$(OBJEXT) stresssym.$(OBJEXT) sym2cart.$(OBJEXT) \
-@@ -106,10 +106,10 @@
- 	symzat.$(OBJEXT) xredxcart.$(OBJEXT) defs_abitypes.$(OBJEXT) \
- 	aprxdr.$(OBJEXT) dotprodm_v.$(OBJEXT) dotprodm_vn.$(OBJEXT) \
- 	findminscf.$(OBJEXT) interfaces_56_mixing.$(OBJEXT) \
--	m_ab6_mixing.$(OBJEXT) scfcge.$(OBJEXT) scfeig.$(OBJEXT) \
-+	m_ab7_mixing.$(OBJEXT) scfcge.$(OBJEXT) scfeig.$(OBJEXT) \
- 	scfopt.$(OBJEXT) sqnormm_v.$(OBJEXT) \
- 	interfaces_56_recipspace.$(OBJEXT) irrzg.$(OBJEXT) \
--	m_ab6_kpoints.$(OBJEXT) getkgrid.$(OBJEXT) smpbz.$(OBJEXT) \
-+	m_ab7_kpoints.$(OBJEXT) getkgrid.$(OBJEXT) smpbz.$(OBJEXT) \
- 	symkpt.$(OBJEXT) testkgrid.$(OBJEXT) \
- 	interfaces_56_xc.$(OBJEXT) drivexc.$(OBJEXT) invcb.$(OBJEXT) \
- 	mkdenpos.$(OBJEXT) m_libxc_functionals.$(OBJEXT) \
-@@ -117,7 +117,7 @@
- 	xclb.$(OBJEXT) xcpbe.$(OBJEXT) xcpzca.$(OBJEXT) \
- 	xcspol.$(OBJEXT) xctetr.$(OBJEXT) xcwign.$(OBJEXT) \
- 	xcxalp.$(OBJEXT) ewald.$(OBJEXT) ewald2.$(OBJEXT) \
--	fconv.$(OBJEXT) prtxvf.$(OBJEXT) ab6_moldyn.$(OBJEXT) \
-+	fconv.$(OBJEXT) prtxvf.$(OBJEXT) ab7_moldyn.$(OBJEXT) \
- 	xfpack.$(OBJEXT)
- libabinit_a_OBJECTS = $(am_libabinit_a_OBJECTS)
- DEFAULT_INCLUDES = -I.@am__isrc@ -I$(top_builddir)
-@@ -352,7 +352,7 @@
- 	42_geometry/getspinrot.F90 \
- 	42_geometry/gridgcart.F90 \
- 	42_geometry/holocell.F90 \
--	42_geometry/m_ab6_symmetry.F90 \
-+	42_geometry/m_ab7_symmetry.F90 \
- 	42_geometry/metric.F90 \
- 	42_geometry/mkrdim.F90 \
- 	42_geometry/operat.F90 \
-@@ -395,14 +395,14 @@
- 	56_mixing/dotprodm_vn.F90 \
- 	56_mixing/findminscf.F90 \
- 	56_mixing/interfaces_56_mixing.F90 \
--	56_mixing/m_ab6_mixing.F90 \
-+	56_mixing/m_ab7_mixing.F90 \
- 	56_mixing/scfcge.F90 \
- 	56_mixing/scfeig.F90 \
- 	56_mixing/scfopt.F90 \
- 	56_mixing/sqnormm_v.F90 \
- 	56_recipspace/interfaces_56_recipspace.F90 \
- 	56_recipspace/irrzg.F90 \
--	56_recipspace/m_ab6_kpoints.F90 \
-+	56_recipspace/m_ab7_kpoints.F90 \
- 	56_recipspace/getkgrid.F90 \
- 	56_recipspace/smpbz.F90 \
- 	56_recipspace/symkpt.F90 \
-@@ -426,7 +426,7 @@
-         67_common/ewald2.F90 \
- 	67_common/fconv.F90 \
- 	67_common/prtxvf.F90 \
--	72_geomoptim/ab6_moldyn.F90 \
-+	72_geomoptim/ab7_moldyn.F90 \
- 	72_geomoptim/xfpack.F90
- 
- CLEANFILES = mpif.h *.@MODULE_EXT@
-@@ -633,8 +633,8 @@
- holocell.obj: 42_geometry/holocell.F90
- 	$(FC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(AM_FCFLAGS) $(FCFLAGS) -c -o holocell.obj `if test -f '42_geometry/holocell.F90'; then $(CYGPATH_W) '42_geometry/holocell.F90'; else $(CYGPATH_W) '$(srcdir)/42_geometry/holocell.F90'; fi`
- 
--m_ab6_symmetry.obj: 42_geometry/m_ab6_symmetry.F90
--	$(FC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(AM_FCFLAGS) $(FCFLAGS) -c -o m_ab6_symmetry.obj `if test -f '42_geometry/m_ab6_symmetry.F90'; then $(CYGPATH_W) '42_geometry/m_ab6_symmetry.F90'; else $(CYGPATH_W) '$(srcdir)/42_geometry/m_ab6_symmetry.F90'; fi`
-+m_ab7_symmetry.obj: 42_geometry/m_ab7_symmetry.F90
-+	$(FC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(AM_FCFLAGS) $(FCFLAGS) -c -o m_ab7_symmetry.obj `if test -f '42_geometry/m_ab7_symmetry.F90'; then $(CYGPATH_W) '42_geometry/m_ab7_symmetry.F90'; else $(CYGPATH_W) '$(srcdir)/42_geometry/m_ab7_symmetry.F90'; fi`
- 
- metric.obj: 42_geometry/metric.F90
- 	$(FC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(AM_FCFLAGS) $(FCFLAGS) -c -o metric.obj `if test -f '42_geometry/metric.F90'; then $(CYGPATH_W) '42_geometry/metric.F90'; else $(CYGPATH_W) '$(srcdir)/42_geometry/metric.F90'; fi`
-@@ -762,8 +762,8 @@
- interfaces_56_mixing.obj: 56_mixing/interfaces_56_mixing.F90
- 	$(FC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(AM_FCFLAGS) $(FCFLAGS) -c -o interfaces_56_mixing.obj `if test -f '56_mixing/interfaces_56_mixing.F90'; then $(CYGPATH_W) '56_mixing/interfaces_56_mixing.F90'; else $(CYGPATH_W) '$(srcdir)/56_mixing/interfaces_56_mixing.F90'; fi`
- 
--m_ab6_mixing.obj: 56_mixing/m_ab6_mixing.F90
--	$(FC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(AM_FCFLAGS) $(FCFLAGS) -c -o m_ab6_mixing.obj `if test -f '56_mixing/m_ab6_mixing.F90'; then $(CYGPATH_W) '56_mixing/m_ab6_mixing.F90'; else $(CYGPATH_W) '$(srcdir)/56_mixing/m_ab6_mixing.F90'; fi`
-+m_ab7_mixing.obj: 56_mixing/m_ab7_mixing.F90
-+	$(FC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(AM_FCFLAGS) $(FCFLAGS) -c -o m_ab7_mixing.obj `if test -f '56_mixing/m_ab7_mixing.F90'; then $(CYGPATH_W) '56_mixing/m_ab7_mixing.F90'; else $(CYGPATH_W) '$(srcdir)/56_mixing/m_ab7_mixing.F90'; fi`
- 
- scfcge.obj: 56_mixing/scfcge.F90
- 	$(FC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(AM_FCFLAGS) $(FCFLAGS) -c -o scfcge.obj `if test -f '56_mixing/scfcge.F90'; then $(CYGPATH_W) '56_mixing/scfcge.F90'; else $(CYGPATH_W) '$(srcdir)/56_mixing/scfcge.F90'; fi`
-@@ -783,8 +783,8 @@
- irrzg.obj: 56_recipspace/irrzg.F90
- 	$(FC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(AM_FCFLAGS) $(FCFLAGS) -c -o irrzg.obj `if test -f '56_recipspace/irrzg.F90'; then $(CYGPATH_W) '56_recipspace/irrzg.F90'; else $(CYGPATH_W) '$(srcdir)/56_recipspace/irrzg.F90'; fi`
- 
--m_ab6_kpoints.obj: 56_recipspace/m_ab6_kpoints.F90
--	$(FC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(AM_FCFLAGS) $(FCFLAGS) -c -o m_ab6_kpoints.obj `if test -f '56_recipspace/m_ab6_kpoints.F90'; then $(CYGPATH_W) '56_recipspace/m_ab6_kpoints.F90'; else $(CYGPATH_W) '$(srcdir)/56_recipspace/m_ab6_kpoints.F90'; fi`
-+m_ab7_kpoints.obj: 56_recipspace/m_ab7_kpoints.F90
-+	$(FC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(AM_FCFLAGS) $(FCFLAGS) -c -o m_ab7_kpoints.obj `if test -f '56_recipspace/m_ab7_kpoints.F90'; then $(CYGPATH_W) '56_recipspace/m_ab7_kpoints.F90'; else $(CYGPATH_W) '$(srcdir)/56_recipspace/m_ab7_kpoints.F90'; fi`
- 
- getkgrid.obj: 56_recipspace/getkgrid.F90
- 	$(FC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(AM_FCFLAGS) $(FCFLAGS) -c -o getkgrid.obj `if test -f '56_recipspace/getkgrid.F90'; then $(CYGPATH_W) '56_recipspace/getkgrid.F90'; else $(CYGPATH_W) '$(srcdir)/56_recipspace/getkgrid.F90'; fi`
-@@ -855,8 +855,8 @@
- prtxvf.obj: 67_common/prtxvf.F90
- 	$(FC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(AM_FCFLAGS) $(FCFLAGS) -c -o prtxvf.obj `if test -f '67_common/prtxvf.F90'; then $(CYGPATH_W) '67_common/prtxvf.F90'; else $(CYGPATH_W) '$(srcdir)/67_common/prtxvf.F90'; fi`
- 
--ab6_moldyn.obj: 72_geomoptim/ab6_moldyn.F90
--	$(FC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(AM_FCFLAGS) $(FCFLAGS) -c -o ab6_moldyn.obj `if test -f '72_geomoptim/ab6_moldyn.F90'; then $(CYGPATH_W) '72_geomoptim/ab6_moldyn.F90'; else $(CYGPATH_W) '$(srcdir)/72_geomoptim/ab6_moldyn.F90'; fi`
-+ab7_moldyn.obj: 72_geomoptim/ab7_moldyn.F90
-+	$(FC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(AM_FCFLAGS) $(FCFLAGS) -c -o ab7_moldyn.obj `if test -f '72_geomoptim/ab7_moldyn.F90'; then $(CYGPATH_W) '72_geomoptim/ab7_moldyn.F90'; else $(CYGPATH_W) '$(srcdir)/72_geomoptim/ab7_moldyn.F90'; fi`
- 
- xfpack.obj: 72_geomoptim/xfpack.F90
- 	$(FC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(AM_FCFLAGS) $(FCFLAGS) -c -o xfpack.obj `if test -f '72_geomoptim/xfpack.F90'; then $(CYGPATH_W) '72_geomoptim/xfpack.F90'; else $(CYGPATH_W) '$(srcdir)/72_geomoptim/xfpack.F90'; fi`
-@@ -1268,11 +1268,11 @@
- 	interfaces_42_geometry.o
- 	$(PPFCCOMPILE) -c -o symptgroup.o `test -f '42_geometry/symptgroup.F90' || echo '$(srcdir)/'`42_geometry/symptgroup.F90
- 
--m_ab6_symmetry.o: 42_geometry/m_ab6_symmetry.F90 \
-+m_ab7_symmetry.o: 42_geometry/m_ab7_symmetry.F90 \
- 	defs_basis.o \
- 	interfaces_32_util.o \
- 	interfaces_42_geometry.o
--	$(PPFCCOMPILE) -c -o m_ab6_symmetry.o `test -f '42_geometry/m_ab6_symmetry.F90' || echo '$(srcdir)/'`42_geometry/m_ab6_symmetry.F90
-+	$(PPFCCOMPILE) -c -o m_ab7_symmetry.o `test -f '42_geometry/m_ab7_symmetry.F90' || echo '$(srcdir)/'`42_geometry/m_ab7_symmetry.F90
- 
- symchk.o: 42_geometry/symchk.F90 \
- 	defs_basis.o
-@@ -1498,11 +1498,11 @@
- 	interfaces_56_recipspace.o
- 	$(PPFCCOMPILE) -c -o getkgrid.o `test -f '56_recipspace/getkgrid.F90' || echo '$(srcdir)/'`56_recipspace/getkgrid.F90
- 
--m_ab6_kpoints.o: 56_recipspace/m_ab6_kpoints.F90 \
-+m_ab7_kpoints.o: 56_recipspace/m_ab7_kpoints.F90 \
- 	defs_basis.o \
- 	interfaces_56_recipspace.o \
--	m_ab6_symmetry.o
--	$(PPFCCOMPILE) -c -o m_ab6_kpoints.o `test -f '56_recipspace/m_ab6_kpoints.F90' || echo '$(srcdir)/'`56_recipspace/m_ab6_kpoints.F90
-+	m_ab7_symmetry.o
-+	$(PPFCCOMPILE) -c -o m_ab7_kpoints.o `test -f '56_recipspace/m_ab7_kpoints.F90' || echo '$(srcdir)/'`56_recipspace/m_ab7_kpoints.F90
- 
- interfaces_56_recipspace.o: 56_recipspace/interfaces_56_recipspace.F90 \
- 	defs_abitypes.o \
-@@ -1647,7 +1647,7 @@
- 	defs_datatypes.o
- 	$(PPFCCOMPILE) -c -o moldyn.o `test -f '72_geomoptim/moldyn.F90' || echo '$(srcdir)/'`72_geomoptim/moldyn.F90
- 
--ab6_moldyn.o: 72_geomoptim/ab6_moldyn.F90 \
-+ab7_moldyn.o: 72_geomoptim/ab7_moldyn.F90 \
- 	defs_basis.o \
- 	defs_basis.o \
- 	72_geomoptim/isokinetic.F90 \
-@@ -1669,7 +1669,7 @@
- 	72_geomoptim/quenched.F90 \
- 	defs_basis.o \
- 	72_geomoptim/velocity_verlet.F90
--	$(PPFCCOMPILE) -c -o ab6_moldyn.o `test -f '72_geomoptim/ab6_moldyn.F90' || echo '$(srcdir)/'`72_geomoptim/ab6_moldyn.F90
-+	$(PPFCCOMPILE) -c -o ab7_moldyn.o `test -f '72_geomoptim/ab7_moldyn.F90' || echo '$(srcdir)/'`72_geomoptim/ab7_moldyn.F90
- 
- velocity_verlet.o: 72_geomoptim/velocity_verlet.F90 \
- 	defs_basis.o
-@@ -1768,12 +1768,12 @@
- 	interfaces_14_hidewrite.o
- 	$(PPFCCOMPILE) -c -o scfeig.o `test -f '56_mixing/scfeig.F90' || echo '$(srcdir)/'`56_mixing/scfeig.F90
- 
--m_ab6_mixing.o: 56_mixing/m_ab6_mixing.F90 \
-+m_ab7_mixing.o: 56_mixing/m_ab7_mixing.F90 \
- 	defs_basis.o \
- 	interfaces_18_timing.o \
- 	interfaces_56_mixing.o \
- 	m_profiling.o
--	$(PPFCCOMPILE) -c -o m_ab6_mixing.o `test -f '56_mixing/m_ab6_mixing.F90' || echo '$(srcdir)/'`56_mixing/m_ab6_mixing.F90
-+	$(PPFCCOMPILE) -c -o m_ab7_mixing.o `test -f '56_mixing/m_ab7_mixing.F90' || echo '$(srcdir)/'`56_mixing/m_ab7_mixing.F90
- 
- dotprodm_vn.o: 56_mixing/dotprodm_vn.F90 \
- 	defs_abitypes.o \
-diff -urN bigdft-abi-1.0.4.old/libABINIT/src/deps bigdft-abi-1.0.4.new/libABINIT/src/deps
---- bigdft-abi-1.0.4.old/libABINIT/src/deps	2012-11-08 11:13:29.000000000 +0100
-+++ bigdft-abi-1.0.4.new/libABINIT/src/deps	2013-06-11 16:51:00.000000000 +0200
-@@ -194,11 +194,11 @@
- 	interfaces_42_geometry.o
- 	$(PPFCCOMPILE) -c -o symptgroup.o `test -f '42_geometry/symptgroup.F90' || echo '$(srcdir)/'`42_geometry/symptgroup.F90
- 
--m_ab6_symmetry.o: 42_geometry/m_ab6_symmetry.F90 \
-+m_ab7_symmetry.o: 42_geometry/m_ab7_symmetry.F90 \
- 	defs_basis.o \
- 	interfaces_32_util.o \
- 	interfaces_42_geometry.o
--	$(PPFCCOMPILE) -c -o m_ab6_symmetry.o `test -f '42_geometry/m_ab6_symmetry.F90' || echo '$(srcdir)/'`42_geometry/m_ab6_symmetry.F90
-+	$(PPFCCOMPILE) -c -o m_ab7_symmetry.o `test -f '42_geometry/m_ab7_symmetry.F90' || echo '$(srcdir)/'`42_geometry/m_ab7_symmetry.F90
- 
- symchk.o: 42_geometry/symchk.F90 \
- 	defs_basis.o
-@@ -424,11 +424,11 @@
- 	interfaces_56_recipspace.o
- 	$(PPFCCOMPILE) -c -o getkgrid.o `test -f '56_recipspace/getkgrid.F90' || echo '$(srcdir)/'`56_recipspace/getkgrid.F90
- 
--m_ab6_kpoints.o: 56_recipspace/m_ab6_kpoints.F90 \
-+m_ab7_kpoints.o: 56_recipspace/m_ab7_kpoints.F90 \
- 	defs_basis.o \
- 	interfaces_56_recipspace.o \
--	m_ab6_symmetry.o
--	$(PPFCCOMPILE) -c -o m_ab6_kpoints.o `test -f '56_recipspace/m_ab6_kpoints.F90' || echo '$(srcdir)/'`56_recipspace/m_ab6_kpoints.F90
-+	m_ab7_symmetry.o
-+	$(PPFCCOMPILE) -c -o m_ab7_kpoints.o `test -f '56_recipspace/m_ab7_kpoints.F90' || echo '$(srcdir)/'`56_recipspace/m_ab7_kpoints.F90
- 
- interfaces_56_recipspace.o: 56_recipspace/interfaces_56_recipspace.F90 \
- 	defs_abitypes.o \
-@@ -573,7 +573,7 @@
- 	defs_datatypes.o
- 	$(PPFCCOMPILE) -c -o moldyn.o `test -f '72_geomoptim/moldyn.F90' || echo '$(srcdir)/'`72_geomoptim/moldyn.F90
- 
--ab6_moldyn.o: 72_geomoptim/ab6_moldyn.F90 \
-+ab7_moldyn.o: 72_geomoptim/ab7_moldyn.F90 \
- 	defs_basis.o \
- 	defs_basis.o \
- 	72_geomoptim/isokinetic.F90 \
-@@ -595,7 +595,7 @@
- 	72_geomoptim/quenched.F90 \
- 	defs_basis.o \
- 	72_geomoptim/velocity_verlet.F90
--	$(PPFCCOMPILE) -c -o ab6_moldyn.o `test -f '72_geomoptim/ab6_moldyn.F90' || echo '$(srcdir)/'`72_geomoptim/ab6_moldyn.F90
-+	$(PPFCCOMPILE) -c -o ab7_moldyn.o `test -f '72_geomoptim/ab7_moldyn.F90' || echo '$(srcdir)/'`72_geomoptim/ab7_moldyn.F90
- 
- velocity_verlet.o: 72_geomoptim/velocity_verlet.F90 \
- 	defs_basis.o
-@@ -694,12 +694,12 @@
- 	interfaces_14_hidewrite.o
- 	$(PPFCCOMPILE) -c -o scfeig.o `test -f '56_mixing/scfeig.F90' || echo '$(srcdir)/'`56_mixing/scfeig.F90
- 
--m_ab6_mixing.o: 56_mixing/m_ab6_mixing.F90 \
-+m_ab7_mixing.o: 56_mixing/m_ab7_mixing.F90 \
- 	defs_basis.o \
- 	interfaces_18_timing.o \
- 	interfaces_56_mixing.o \
- 	m_profiling.o
--	$(PPFCCOMPILE) -c -o m_ab6_mixing.o `test -f '56_mixing/m_ab6_mixing.F90' || echo '$(srcdir)/'`56_mixing/m_ab6_mixing.F90
-+	$(PPFCCOMPILE) -c -o m_ab7_mixing.o `test -f '56_mixing/m_ab7_mixing.F90' || echo '$(srcdir)/'`56_mixing/m_ab7_mixing.F90
- 
- dotprodm_vn.o: 56_mixing/dotprodm_vn.F90 \
- 	defs_abitypes.o \
-diff -urN bigdft-abi-1.0.4.old/src/abscalc.f90 bigdft-abi-1.0.4.new/src/abscalc.f90
---- bigdft-abi-1.0.4.old/src/abscalc.f90	2012-07-09 16:43:33.000000000 +0200
-+++ bigdft-abi-1.0.4.new/src/abscalc.f90	2013-06-11 16:51:00.000000000 +0200
-@@ -13,7 +13,7 @@
-    use module_base
-    use module_types
-    use module_interfaces
--   use m_ab6_symmetry
-+   use m_ab7_symmetry
-    !  use minimization, only: parameterminimization 
- 
-    implicit none
-@@ -323,9 +323,9 @@
-    use module_xc
-    use vdwcorrection
-    use esatto
--   use m_ab6_symmetry
--   use m_ab6_mixing
--   use m_ab6_kpoints
-+   use m_ab7_symmetry
-+   use m_ab7_mixing
-+   use m_ab7_kpoints
-    implicit none
-    integer, intent(in) :: nproc,iproc
-    real(gp), intent(inout) :: hx_old,hy_old,hz_old
-diff -urN bigdft-abi-1.0.4.old/src/cluster.f90 bigdft-abi-1.0.4.new/src/cluster.f90
---- bigdft-abi-1.0.4.old/src/cluster.f90	2012-11-29 11:18:04.000000000 +0100
-+++ bigdft-abi-1.0.4.new/src/cluster.f90	2013-06-11 16:51:00.000000000 +0200
-@@ -192,7 +192,7 @@
- !  use Poisson_Solver
-   use module_xc
- !  use vdwcorrection
--  use m_ab6_mixing
-+  use m_ab7_mixing
-   use yaml_output
-   implicit none
-   integer, intent(in) :: nproc,iproc
-@@ -1140,7 +1140,7 @@
-   use module_types
-   use module_interfaces, except_this_one => kswfn_optimization_loop
-   use yaml_output
--  use m_ab6_mixing
-+  use m_ab7_mixing
-   implicit none
-   real(dp), dimension(6), intent(out) :: xcstr
-   integer, intent(in) :: iproc, nproc, idsx, inputpsi
-@@ -1306,7 +1306,7 @@
-               if (nproc > 1) call MPI_BARRIER(MPI_COMM_WORLD,ierr)
-               !call kswfn_free_scf_data(KSwfn, (nproc > 1))
-               !if (opt%iscf /= SCF_KIND_DIRECT_MINIMIZATION) then
--              !   call ab6_mixing_deallocate(denspot%mix)
-+              !   call ab7_mixing_deallocate(denspot%mix)
-               !   deallocate(denspot%mix)
-               !end if
-               !>todo: change this return into a clean out of the routine, so the YAML is clean.
-diff -urN bigdft-abi-1.0.4.old/src/distances.f90 bigdft-abi-1.0.4.new/src/distances.f90
---- bigdft-abi-1.0.4.old/src/distances.f90	2012-07-09 16:43:33.000000000 +0200
-+++ bigdft-abi-1.0.4.new/src/distances.f90	2013-06-11 16:51:00.000000000 +0200
-@@ -275,7 +275,7 @@
-   subroutine box_features(whichone,contcar,nrep,nat,ntypes,iatype,pos,factor)
-     use BigDFT_API
-     use module_interfaces
--    use m_ab6_symmetry
-+    use m_ab7_symmetry
-     implicit none
-     character(len=1), intent(in) :: whichone
-     character(len=40), intent(in) :: contcar
-@@ -375,7 +375,7 @@
- subroutine read_pos(iunit,whichone,nat,pos,nrep)
-   use BigDFT_API
-   use module_interfaces
--  use m_ab6_symmetry
-+  use m_ab7_symmetry
-   implicit none
-   character(len=1), intent(in) :: whichone
-   integer, intent(in) :: iunit,nat,nrep
-diff -urN bigdft-abi-1.0.4.old/src/forces.f90 bigdft-abi-1.0.4.new/src/forces.f90
---- bigdft-abi-1.0.4.old/src/forces.f90	2012-07-09 16:43:33.000000000 +0200
-+++ bigdft-abi-1.0.4.new/src/forces.f90	2013-06-11 16:51:00.000000000 +0200
-@@ -3757,7 +3757,7 @@
- subroutine symm_stress(dump,tens,symobj)
-   use defs_basis
-   use module_base, only: verbose,gp
--  use m_ab6_symmetry
-+  use m_ab7_symmetry
-   use module_types
-   implicit none
-   !Arguments
-@@ -3773,7 +3773,7 @@
-   real(gp),dimension(3,3) :: symtens
- 
-   call symmetry_get_matrices_p(symObj, nsym, sym, transNon, symAfm, errno)
--  if (errno /= AB6_NO_ERROR) stop
-+  if (errno /= AB7_NO_ERROR) stop
-   if (nsym < 2) return
- 
-   if (dump)&
-@@ -3824,7 +3824,7 @@
- !> Symmetrize the atomic forces (needed with special k points)
- subroutine symmetrise_forces(iproc, fxyz, at)
-   use defs_basis
--  use m_ab6_symmetry
-+  use m_ab7_symmetry
-   use module_types
- 
-   implicit none
-@@ -3833,7 +3833,7 @@
-   type(atoms_data), intent(in) :: at
-   real(gp), intent(inout) :: fxyz(3, at%nat)
-   integer :: ia, mu, isym, errno, ind, nsym
--  integer :: indsym(4, AB6_MAX_SYMMETRIES)
-+  integer :: indsym(4, AB7_MAX_SYMMETRIES)
-   real(gp) :: summ
-   real(gp) :: alat(3)
-   real(gp), allocatable :: dedt(:,:)
-@@ -3843,7 +3843,7 @@
-   real(gp), pointer :: transNon(:,:)
- 
-   call symmetry_get_matrices_p(at%sym%symObj, nsym, sym, transNon, symAfm, errno)
--  if (errno /= AB6_NO_ERROR) stop
-+  if (errno /= AB7_NO_ERROR) stop
-   if (nsym < 2) return
- 
-   if (iproc == 0) write(*,"(1x,A,I0,A)") "Symmetrise forces with ", nsym, " symmetries."
-@@ -3866,7 +3866,7 @@
-   ! actually conduct symmetrization
-   do ia = 1, at%nat
-      call symmetry_get_equivalent_atom(at%sym%symObj, indsym, ia, errno)
--     if (errno /= AB6_NO_ERROR) stop
-+     if (errno /= AB7_NO_ERROR) stop
-      do mu = 1, 3
-         summ = real(0, gp)
-         do isym = 1, nsym
-diff -urN bigdft-abi-1.0.4.old/src/frequencies.f90 bigdft-abi-1.0.4.new/src/frequencies.f90
---- bigdft-abi-1.0.4.old/src/frequencies.f90	2012-07-09 16:43:33.000000000 +0200
-+++ bigdft-abi-1.0.4.new/src/frequencies.f90	2013-06-11 16:51:00.000000000 +0200
-@@ -20,7 +20,7 @@
-    use module_base
-    use module_types
-    use module_interfaces
--   use m_ab6_symmetry
-+   use m_ab7_symmetry
-    use yaml_output
-    implicit none
- 
-diff -urN bigdft-abi-1.0.4.old/src/geometry.f90 bigdft-abi-1.0.4.new/src/geometry.f90
---- bigdft-abi-1.0.4.old/src/geometry.f90	2012-07-09 16:43:33.000000000 +0200
-+++ bigdft-abi-1.0.4.new/src/geometry.f90	2013-06-11 16:51:00.000000000 +0200
-@@ -159,7 +159,7 @@
-   use module_base
-   use module_types
-   use scfloop_API
--  use ab6_moldyn
-+  use ab7_moldyn
-   implicit none
-   integer, intent(in) :: nproc,iproc
-   integer, intent(inout) :: ncount_bigdft
-diff -urN bigdft-abi-1.0.4.old/src/hpsiortho.f90 bigdft-abi-1.0.4.new/src/hpsiortho.f90
---- bigdft-abi-1.0.4.old/src/hpsiortho.f90	2013-01-30 10:10:56.000000000 +0100
-+++ bigdft-abi-1.0.4.new/src/hpsiortho.f90	2013-06-11 16:51:00.000000000 +0200
-@@ -17,7 +17,7 @@
-   use module_types
-   use module_interfaces, fake_name => psitohpsi
-   use Poisson_Solver
--  use m_ab6_mixing
-+  use m_ab7_mixing
-   use yaml_output
-   implicit none
-   logical, intent(in) :: scf
-@@ -144,7 +144,7 @@
- 
-      !here the density can be mixed
-      if (iscf > SCF_KIND_DIRECT_MINIMIZATION ) then
--        if (denspot%mix%kind == AB6_MIXING_DENSITY) then
-+        if (denspot%mix%kind == AB7_MIXING_DENSITY) then
-            call mix_rhopot(iproc,nproc,denspot%mix%nfft*denspot%mix%nspden,alphamix,denspot%mix,&
-                 denspot%rhov,itrp,wfn%Lzd%Glr%d%n1i,wfn%Lzd%Glr%d%n2i,wfn%Lzd%Glr%d%n3i,&
-                 atoms%alat1*atoms%alat2*atoms%alat3,&!hx*hy*hz,& !volume should be used
-@@ -215,7 +215,7 @@
- 
-      !here the potential can be mixed
-      if (iscf > SCF_KIND_DIRECT_MINIMIZATION ) then
--        if (denspot%mix%kind == AB6_MIXING_POTENTIAL) then
-+        if (denspot%mix%kind == AB7_MIXING_POTENTIAL) then
-            call mix_rhopot(iproc,nproc,denspot%mix%nfft*denspot%mix%nspden,alphamix,denspot%mix,&
-                 denspot%rhov,itrp,wfn%Lzd%Glr%d%n1i,wfn%Lzd%Glr%d%n2i,wfn%Lzd%Glr%d%n3i,&
-                 atoms%alat1*atoms%alat2*atoms%alat3,&!volume should be used 
-diff -urN bigdft-abi-1.0.4.old/src/init/atoms.f90 bigdft-abi-1.0.4.new/src/init/atoms.f90
---- bigdft-abi-1.0.4.old/src/init/atoms.f90	2012-07-09 16:43:33.000000000 +0200
-+++ bigdft-abi-1.0.4.new/src/init/atoms.f90	2013-06-11 16:51:00.000000000 +0200
-@@ -210,7 +210,7 @@
-   use module_base
-   use module_types
-   use defs_basis
--  use m_ab6_symmetry
-+  use m_ab7_symmetry
-   implicit none
-   type(atoms_data), intent(inout) :: atoms
-   real(gp), dimension(3,atoms%nat), intent(in) :: rxyz
-@@ -1901,8 +1901,8 @@
- subroutine symmetry_set_irreductible_zone(sym, geocode, n1i, n2i, n3i, nspin)
-   use module_base
-   use module_types
--  use m_ab6_kpoints
--  use m_ab6_symmetry
-+  use m_ab7_kpoints
-+  use m_ab7_symmetry
-   implicit none
-   type(symmetry_data), intent(inout) :: sym
-   integer, intent(in) :: n1i, n2i, n3i, nspin
-diff -urN bigdft-abi-1.0.4.old/src/init/denspotd.f90 bigdft-abi-1.0.4.new/src/init/denspotd.f90
---- bigdft-abi-1.0.4.old/src/init/denspotd.f90	2012-07-09 16:43:33.000000000 +0200
-+++ bigdft-abi-1.0.4.new/src/init/denspotd.f90	2013-06-11 16:51:00.000000000 +0200
-@@ -95,7 +95,7 @@
-      & n1i, n2i) !to be removed arguments when denspot has dimensions
-   use module_base
-   use module_types
--  use m_ab6_mixing
-+  use m_ab7_mixing
-   implicit none
-   type(DFT_local_fields), intent(inout) :: denspot
-   integer, intent(in) :: iscf, n1i, n2i, nspin
-@@ -104,20 +104,20 @@
-   character(len=500) :: errmess
- 
-   if (iscf < 10) then
--     potden = AB6_MIXING_POTENTIAL
-+     potden = AB7_MIXING_POTENTIAL
-      npoints = n1i*n2i*denspot%dpbox%n3p
-      if (denspot%dpbox%n3p==0) npoints=1
-   else
--     potden = AB6_MIXING_DENSITY
-+     potden = AB7_MIXING_DENSITY
-      npoints = n1i*n2i*denspot%dpbox%n3d
-      if (denspot%dpbox%n3d==0) npoints=1
-   end if
-   if (iscf > SCF_KIND_DIRECT_MINIMIZATION) then
-      allocate(denspot%mix)
--     call ab6_mixing_new(denspot%mix, modulo(iscf, 10), potden, &
--          AB6_MIXING_REAL_SPACE, npoints, nspin, 0, &
-+     call ab7_mixing_new(denspot%mix, modulo(iscf, 10), potden, &
-+          AB7_MIXING_REAL_SPACE, npoints, nspin, 0, &
-           ierr, errmess, useprec = .false.)
--     call ab6_mixing_eval_allocate(denspot%mix)
-+     call ab7_mixing_eval_allocate(denspot%mix)
-   else
-      nullify(denspot%mix)
-   end if
-@@ -125,12 +125,12 @@
- 
- subroutine denspot_free_history(denspot)
-   use module_types
--  use m_ab6_mixing
-+  use m_ab7_mixing
-   implicit none
-   type(DFT_local_fields), intent(inout) :: denspot
-   
-   if (associated(denspot%mix)) then
--     call ab6_mixing_deallocate(denspot%mix)
-+     call ab7_mixing_deallocate(denspot%mix)
-      deallocate(denspot%mix)
-   end if
- end subroutine denspot_free_history
-@@ -396,7 +396,7 @@
-   use module_base
-   use module_types
-   use module_interfaces, except_this_one => allocateRhoPot
--  use m_ab6_mixing
-+  use m_ab7_mixing
-   implicit none
-   integer, intent(in) :: iproc,nspin
-   type(locreg_descriptors), intent(in) :: Glr
-diff -urN bigdft-abi-1.0.4.old/src/init/sysprop.f90 bigdft-abi-1.0.4.new/src/init/sysprop.f90
---- bigdft-abi-1.0.4.old/src/init/sysprop.f90	2012-07-09 16:43:33.000000000 +0200
-+++ bigdft-abi-1.0.4.new/src/init/sysprop.f90	2013-06-11 16:51:00.000000000 +0200
-@@ -879,7 +879,7 @@
-   use module_base
-   use module_types
-   use module_xc
--  use m_ab6_symmetry
-+  use m_ab7_symmetry
-   implicit none
-   character (len=*), intent(in) :: fileocc
-   type(atoms_data), intent(inout) :: atoms
-diff -urN bigdft-abi-1.0.4.old/src/input_variables.f90 bigdft-abi-1.0.4.new/src/input_variables.f90
---- bigdft-abi-1.0.4.old/src/input_variables.f90	2012-07-09 16:43:33.000000000 +0200
-+++ bigdft-abi-1.0.4.new/src/input_variables.f90	2013-06-11 16:51:00.000000000 +0200
-@@ -908,7 +908,7 @@
-   use module_base
-   use module_types
-   use defs_basis
--  use m_ab6_kpoints
-+  use m_ab7_kpoints
-   use module_input
-   implicit none
-   character(len=*), intent(in) :: filename
-@@ -958,7 +958,7 @@
-           comment='Equivalent length of K-space resolution (Bohr)')
-      call kpoints_get_auto_k_grid(sym%symObj, in%nkpt, in%kpt, in%wkpt, &
-           & kptrlen, ierror)
--     if (ierror /= AB6_NO_ERROR) then
-+     if (ierror /= AB7_NO_ERROR) then
-         if (iproc==0) write(*,*) " ERROR in symmetry library. Error code is ", ierror
-         stop
-      end if
-@@ -984,7 +984,7 @@
-      end do
-      call kpoints_get_mp_k_grid(sym%symObj, in%nkpt, in%kpt, in%wkpt, &
-           & ngkpt, nshiftk, shiftk, ierror)
--     if (ierror /= AB6_NO_ERROR) then
-+     if (ierror /= AB7_NO_ERROR) then
-         if (iproc==0) write(*,*) " ERROR in symmetry library. Error code is ", ierror
-         stop
-      end if
-@@ -1126,7 +1126,7 @@
-   use module_base
-   use module_types
-   use defs_basis
--  use m_ab6_kpoints
-+  use m_ab7_kpoints
-   implicit none
-   character(len=*), intent(in) :: filename
-   integer, intent(in) :: iproc
-@@ -1178,11 +1178,11 @@
-      call check()
-      call kpoints_get_auto_k_grid(atoms%sym%symObj, in%nkpt, in%kpt, in%wkpt, &
-           & kptrlen, ierror)
--     if (ierror /= AB6_NO_ERROR) then
-+     if (ierror /= AB7_NO_ERROR) then
-         if (iproc==0) write(*,*) " ERROR in symmetry library. Error code is ", ierror
-         stop
-      end if
--     ! in%kpt and in%wkpt will be allocated by ab6_symmetry routine.
-+     ! in%kpt and in%wkpt will be allocated by ab7_symmetry routine.
-      call memocc(0,in%kpt,'in%kpt',subname)
-      call memocc(0,in%wkpt,'in%wkpt',subname)
-   else if (trim(type) == "MPgrid" .or. trim(type) == "mpgrid") then
-@@ -1198,11 +1198,11 @@
-      if (atoms%geocode == 'F') ngkpt = 1
-      call kpoints_get_mp_k_grid(atoms%sym%symObj, in%nkpt, in%kpt, in%wkpt, &
-           & ngkpt, nshiftk, shiftk, ierror)
--     if (ierror /= AB6_NO_ERROR) then
-+     if (ierror /= AB7_NO_ERROR) then
-         if (iproc==0) write(*,*) " ERROR in symmetry library. Error code is ", ierror
-         stop
-      end if
--     ! in%kpt and in%wkpt will be allocated by ab6_symmetry routine.
-+     ! in%kpt and in%wkpt will be allocated by ab7_symmetry routine.
-      call memocc(0,in%kpt,'in%kpt',subname)
-      call memocc(0,in%wkpt,'in%wkpt',subname)
-   else if (trim(type) == "manual" .or. trim(type) == "Manual") then
-@@ -1858,7 +1858,7 @@
-    use module_base
-    use module_types
-    use module_interfaces, except_this_one => read_atomic_file
--   use m_ab6_symmetry
-+   use m_ab7_symmetry
-    use position_files
-    implicit none
-    character(len=*), intent(in) :: file
-@@ -2430,7 +2430,7 @@
-   use module_base
-   use module_types
-   use module_interfaces, except_this_one => initialize_atomic_file
--  use m_ab6_symmetry
-+  use m_ab7_symmetry
-   implicit none
-   integer, intent(in) :: iproc
-   type(atoms_data), intent(inout) :: atoms
-diff -urN bigdft-abi-1.0.4.old/src/memguess.f90 bigdft-abi-1.0.4.new/src/memguess.f90
---- bigdft-abi-1.0.4.old/src/memguess.f90	2012-07-09 16:43:33.000000000 +0200
-+++ bigdft-abi-1.0.4.new/src/memguess.f90	2013-06-11 16:51:00.000000000 +0200
-@@ -16,7 +16,7 @@
-    use module_types
-    use module_interfaces
-    use module_xc
--   use m_ab6_symmetry
-+   use m_ab7_symmetry
- 
-    implicit none
-    character(len=*), parameter :: subname='memguess'
-diff -urN bigdft-abi-1.0.4.old/src/modules/defs.F90 bigdft-abi-1.0.4.new/src/modules/defs.F90
---- bigdft-abi-1.0.4.old/src/modules/defs.F90	2012-07-09 16:43:33.000000000 +0200
-+++ bigdft-abi-1.0.4.new/src/modules/defs.F90	2013-06-11 16:51:00.000000000 +0200
-@@ -1074,7 +1074,7 @@
-     end subroutine herk_double
- 
-     function fnrm_denpot(x,cplex,nfft,nspden,opt_denpot,user_data)
--      use m_ab6_mixing
-+      use m_ab7_mixing
-       implicit none
-       integer, intent(in) :: cplex,nfft,nspden,opt_denpot
-       double precision, intent(in) :: x(*)
-@@ -1084,7 +1084,7 @@
-       double precision :: fnrm_denpot, ar, nrm_local, dnrm2
- 
-       ! In case of density, we use nscatterarr.
--      if (opt_denpot == AB6_MIXING_DENSITY) then
-+      if (opt_denpot == AB7_MIXING_DENSITY) then
-          call MPI_COMM_RANK(MPI_COMM_WORLD,iproc,ierr)
-          if (ierr /= 0) then
-             call MPI_ABORT(MPI_COMM_WORLD, ierr, ie)
-@@ -1125,7 +1125,7 @@
-     end function fnrm_denpot
- 
-     function fdot_denpot(x,y,cplex,nfft,nspden,opt_denpot,user_data)
--      use m_ab6_mixing
-+      use m_ab7_mixing
-       implicit none
-       integer, intent(in) :: cplex,nfft,nspden,opt_denpot
-       double precision, intent(in) :: x(*), y(*)
-@@ -1135,7 +1135,7 @@
-       double precision :: fdot_denpot, ar, dot_local, ddot
- 
-       ! In case of density, we use nscatterarr.
--      if (opt_denpot == AB6_MIXING_DENSITY) then
-+      if (opt_denpot == AB7_MIXING_DENSITY) then
-          call MPI_COMM_RANK(MPI_COMM_WORLD,iproc,ierr)
-          if (ierr /= 0) then
-             call MPI_ABORT(MPI_COMM_WORLD, ierr, ie)
-diff -urN bigdft-abi-1.0.4.old/src/modules/interfaces.f90 bigdft-abi-1.0.4.new/src/modules/interfaces.f90
---- bigdft-abi-1.0.4.old/src/modules/interfaces.f90	2013-01-03 10:10:13.000000000 +0100
-+++ bigdft-abi-1.0.4.new/src/modules/interfaces.f90	2013-06-11 16:51:00.000000000 +0200
-@@ -5857,7 +5857,7 @@
-             energs,rpnrm,xcstr,proj_G,paw)
-          use module_base
-          use module_types
--         use m_ab6_mixing
-+         use m_ab7_mixing
-          implicit none
-          logical, intent(in) :: scf
-          integer, intent(in) :: iproc,nproc,itrp,iscf,ixc,linflag,itwfn
-diff -urN bigdft-abi-1.0.4.old/src/modules/types.f90 bigdft-abi-1.0.4.new/src/modules/types.f90
---- bigdft-abi-1.0.4.old/src/modules/types.f90	2013-01-03 10:18:08.000000000 +0100
-+++ bigdft-abi-1.0.4.new/src/modules/types.f90	2013-06-11 16:51:00.000000000 +0200
-@@ -12,7 +12,7 @@
- !!  and the routines of allocations and de-allocations
- module module_types
- 
--  use m_ab6_mixing, only : ab6_mixing_object
-+  use m_ab7_mixing, only : ab7_mixing_object
-   use module_base, only : gp,wp,dp,tp,uninitialized
-   implicit none
- 
-@@ -828,7 +828,7 @@
-   type, public :: DFT_local_fields
-      real(dp), dimension(:), pointer :: rhov !< generic workspace. What is there is indicated by rhov_is
-      
--     type(ab6_mixing_object), pointer :: mix          !< History of rhov, allocated only when using diagonalisation
-+     type(ab7_mixing_object), pointer :: mix          !< History of rhov, allocated only when using diagonalisation
-      !local fields which are associated to their name
-      !normally given in parallel distribution
-      real(dp), dimension(:,:), pointer :: rho_psi !< density as given by square of el. WFN
-@@ -1658,7 +1658,7 @@
- 
-   subroutine deallocate_symmetry(sym, subname)
-     use module_base
--    use m_ab6_symmetry
-+    use m_ab7_symmetry
-     implicit none
-     type(symmetry_data), intent(inout) :: sym
-     character(len = *), intent(in) :: subname
-diff -urN bigdft-abi-1.0.4.old/src/output.f90 bigdft-abi-1.0.4.new/src/output.f90
---- bigdft-abi-1.0.4.old/src/output.f90	2012-07-09 16:43:33.000000000 +0200
-+++ bigdft-abi-1.0.4.new/src/output.f90	2013-06-11 16:51:00.000000000 +0200
-@@ -63,7 +63,7 @@
-   use module_base
-   use module_types
-   use defs_basis
--  use m_ab6_symmetry
-+  use m_ab7_symmetry
-   implicit none
-   !Arguments
-   integer, intent(in) :: nproc
-@@ -71,9 +71,9 @@
-   type(atoms_data), intent(in) :: atoms
- 
-   integer :: nSym, ierr, ityp, iat, i, lg
--  integer :: sym(3, 3, AB6_MAX_SYMMETRIES)
--  integer :: symAfm(AB6_MAX_SYMMETRIES)
--  real(gp) :: transNon(3, AB6_MAX_SYMMETRIES)
-+  integer :: sym(3, 3, AB7_MAX_SYMMETRIES)
-+  integer :: symAfm(AB7_MAX_SYMMETRIES)
-+  real(gp) :: transNon(3, AB7_MAX_SYMMETRIES)
-   real(gp) :: genAfm(3)
-   character(len=15) :: spaceGroup
-   integer :: spaceGroupId, pointGroupMagn
-@@ -138,7 +138,7 @@
-      call symmetry_get_matrices(atoms%sym%symObj, nSym, sym, transNon, symAfm, ierr)
-      call symmetry_get_group(atoms%sym%symObj, spaceGroup, &
-           & spaceGroupId, pointGroupMagn, genAfm, ierr)
--     if (ierr == AB6_ERROR_SYM_NOT_PRIMITIVE) write(spaceGroup, "(A)") "not prim."
-+     if (ierr == AB7_ERROR_SYM_NOT_PRIMITIVE) write(spaceGroup, "(A)") "not prim."
-      write(add(1), '(a,i0)')       "N. sym.   = ", nSym
-      write(add(2), '(a,a,a)')      "Sp. group = ", trim(spaceGroup)
-   else if (atoms%geocode /= 'F' .and. input%disableSym) then
-diff -urN bigdft-abi-1.0.4.old/src/splinedsaddle.f90 bigdft-abi-1.0.4.new/src/splinedsaddle.f90
---- bigdft-abi-1.0.4.old/src/splinedsaddle.f90	2012-07-09 16:43:33.000000000 +0200
-+++ bigdft-abi-1.0.4.new/src/splinedsaddle.f90	2013-06-11 16:51:00.000000000 +0200
-@@ -14,7 +14,7 @@
-   use module_base
-   use module_types
-   use module_interfaces
--  use m_ab6_symmetry
-+  use m_ab7_symmetry
-   use yaml_output
-   implicit none
-   character(len=*), parameter :: subname='BigDFT'
-diff -urN bigdft-abi-1.0.4.old/src/sumrho.f90 bigdft-abi-1.0.4.new/src/sumrho.f90
---- bigdft-abi-1.0.4.old/src/sumrho.f90	2012-07-09 16:43:33.000000000 +0200
-+++ bigdft-abi-1.0.4.new/src/sumrho.f90	2013-06-11 16:51:00.000000000 +0200
-@@ -719,7 +719,7 @@
-      sym)
-   use module_base!, only: gp,dp,wp,ndebug,memocc
-   use module_types
--  use m_ab6_symmetry
-+  use m_ab7_symmetry
- 
-   implicit none
-   integer, intent(in) :: iproc,nproc,nspin, n1i, n2i, n3i
-diff -urN bigdft-abi-1.0.4.old/src/test_forces.f90 bigdft-abi-1.0.4.new/src/test_forces.f90
---- bigdft-abi-1.0.4.old/src/test_forces.f90	2012-07-09 16:43:33.000000000 +0200
-+++ bigdft-abi-1.0.4.new/src/test_forces.f90	2013-06-11 16:51:00.000000000 +0200
-@@ -22,7 +22,7 @@
-    use module_base
-    use module_types
-    use module_interfaces
--   use m_ab6_symmetry
-+   use m_ab7_symmetry
- 
-    implicit none
-    character(len=*), parameter :: subname='test_forces'
-diff -urN bigdft-abi-1.0.4.old/src/wfn_opt/diis.f90 bigdft-abi-1.0.4.new/src/wfn_opt/diis.f90
---- bigdft-abi-1.0.4.old/src/wfn_opt/diis.f90	2012-08-22 09:55:24.000000000 +0200
-+++ bigdft-abi-1.0.4.new/src/wfn_opt/diis.f90	2013-06-11 16:51:00.000000000 +0200
-@@ -459,13 +459,13 @@
- subroutine mix_rhopot(iproc,nproc,npoints,alphamix,mix,rhopot,istep,&
-      & n1,n2,n3,ucvol,rpnrm,nscatterarr)
-   use module_base
--  use defs_basis, only: AB6_NO_ERROR
--  use m_ab6_mixing
-+  use defs_basis, only: AB7_NO_ERROR
-+  use m_ab7_mixing
-   implicit none
-   integer, intent(in) :: npoints, istep, n1, n2, n3, nproc, iproc
-   real(gp), intent(in) :: alphamix, ucvol
-   integer, dimension(0:nproc-1,4), intent(in) :: nscatterarr
--  type(ab6_mixing_object), intent(inout) :: mix
-+  type(ab7_mixing_object), intent(inout) :: mix
-   real(dp), dimension(npoints), intent(inout) :: rhopot
-   real(gp), intent(out) :: rpnrm
-   !local variables
-@@ -497,10 +497,10 @@
-   end do
- 
-   ! Do the mixing 
--  call ab6_mixing_eval(mix, rhopot, istep, n1 * n2 * n3, ucvol, &
-+  call ab7_mixing_eval(mix, rhopot, istep, n1 * n2 * n3, ucvol, &
-        & MPI_COMM_WORLD, (nproc > 1), ierr, errmess, resnrm = rpnrm, &
-        & fnrm = fnrm_denpot, fdot = fdot_denpot, user_data = user_data)
--  if (ierr /= AB6_NO_ERROR) then
-+  if (ierr /= AB7_NO_ERROR) then
-      if (iproc == 0) write(0,*) errmess
-      call MPI_ABORT(MPI_COMM_WORLD, ierr, ie)
-   end if
diff --git a/perl-core/encoding-warnings/Manifest b/perl-core/encoding-warnings/Manifest
deleted file mode 100644
index dbd39aa0e..000000000
--- a/perl-core/encoding-warnings/Manifest
+++ /dev/null
@@ -1 +0,0 @@
-DIST encoding-warnings-0.11.tar.gz 16110 BLAKE2B 2868398b6d477c1708238e77fd2c42c47090d550cdbe8878e6e81eb0c6464bf2467a9c4bb770d8a5ad5643ef09f7677a5f51ebf18a3b18596c25c5bfc0397f81 SHA512 9c8ff27f500cc343c4c2de3c4faafcf4553e3a951143443746394cd8916ffb1c01272c2e7adce14ba2308b2a8f542c31acd3f2dda32e633989885db9fe1ecd3d
diff --git a/perl-core/encoding-warnings/encoding-warnings-0.11.ebuild b/perl-core/encoding-warnings/encoding-warnings-0.11.ebuild
deleted file mode 100644
index bf8ca2a8c..000000000
--- a/perl-core/encoding-warnings/encoding-warnings-0.11.ebuild
+++ /dev/null
@@ -1,19 +0,0 @@
-# Copyright 1999-2014 Gentoo Foundation
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=5
-
-inherit perl-module
-
-DESCRIPTION="Warn on implicit encoding conversions"
-HOMEPAGE="http://search.cpan.org/~audreyt/encoding-warnings-0.11/lib/encoding/warnings.pm"
-SRC_URI="mirror://cpan/authors/id/A/AU/AUDREYT/encoding-warnings-0.11.tar.gz"
-
-LICENSE="|| ( Artistic GPL-2 )"
-
-SLOT="0"
-KEYWORDS="~amd64 ~x86"
-IUSE=""
-
-DEPEND="dev-lang/perl"
-RDEPEND="${DEPEND}"
diff --git a/perl-core/encoding-warnings/metadata.xml b/perl-core/encoding-warnings/metadata.xml
deleted file mode 100644
index 90bb64f30..000000000
--- a/perl-core/encoding-warnings/metadata.xml
+++ /dev/null
@@ -1,7 +0,0 @@
-<?xml version="1.0" encoding="UTF-8"?>
-<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
-<pkgmetadata>
-	<maintainer type="person">
-		<email>mail@akhuettel.de</email>
-	</maintainer>
-</pkgmetadata>
diff --git a/profiles/arch.list b/profiles/arch.list
deleted file mode 100644
index a917db833..000000000
--- a/profiles/arch.list
+++ /dev/null
@@ -1,35 +0,0 @@
-alpha
-amd64
-amd64-fbsd
-arm
-arm64
-hppa
-ia64
-m68k
-mips
-ppc
-ppc64
-s390
-sh
-sparc
-x86
-x86-fbsd
-
-# Prefix keywords
-ppc-aix
-amd64-linux
-arm-linux
-arm64-linux
-ppc64-linux
-x86-linux
-ppc-macos
-x86-macos
-x64-macos
-m68k-mint
-sparc-solaris
-sparc64-solaris
-x64-solaris
-x86-solaris
-x86-winnt
-x64-cygwin
-x86-cygwin
diff --git a/profiles/arch/arm/use.mask b/profiles/arch/arm/use.mask
deleted file mode 100644
index f7203065e..000000000
--- a/profiles/arch/arm/use.mask
+++ /dev/null
@@ -1,9 +0,0 @@
-# Copyright 1999-2017 Gentoo Foundation
-# Distributed under the terms of the GNU General Public License v2
-
-# Unmask the flag which corresponds to ARCH.
--arm
-
-# Mark Wright <gienah@gentoo.org> (26 Apr 2014)
-# mask int64 flag for 32 bits arches
-int64
diff --git a/profiles/arch/m68k/use.mask b/profiles/arch/m68k/use.mask
deleted file mode 100644
index 7a8f25dbd..000000000
--- a/profiles/arch/m68k/use.mask
+++ /dev/null
@@ -1,9 +0,0 @@
-# Copyright 1999-2017 Gentoo Foundation
-# Distributed under the terms of the GNU General Public License v2
-
-# Unmask the flag which corresponds to ARCH.
--m68k
-
-# Mark Wright <gienah@gentoo.org> (26 Apr 2014)
-# mask int64 flag for 32 bits arches
-int64
diff --git a/profiles/arch/sparc/use.mask b/profiles/arch/sparc/use.mask
deleted file mode 100644
index 5f4ec9f0c..000000000
--- a/profiles/arch/sparc/use.mask
+++ /dev/null
@@ -1,9 +0,0 @@
-# Copyright 1999-2017 Gentoo Foundation
-# Distributed under the terms of the GNU General Public License v2
-
-# Unmask the flag which corresponds to ARCH.
--sparc
-
-# Mark Wright <gienah@gentoo.org> (26 Apr 2014)
-# mask int64 flag for 32 bits arches
-int64
diff --git a/profiles/arch/x86-fbsd/use.mask b/profiles/arch/x86-fbsd/use.mask
deleted file mode 100644
index 4233375d6..000000000
--- a/profiles/arch/x86-fbsd/use.mask
+++ /dev/null
@@ -1,9 +0,0 @@
-# Copyright 1999-2017 Gentoo Foundation
-# Distributed under the terms of the GNU General Public License v2
-
-# Unmask the flag which corresponds to ARCH.
--x86-fbsd
-
-# Mark Wright <gienah@gentoo.org> (26 Apr 2014)
-# mask int64 flag for 32 bits arches
-int64
diff --git a/profiles/arch/x86/use.mask b/profiles/arch/x86/use.mask
deleted file mode 100644
index cc38655e2..000000000
--- a/profiles/arch/x86/use.mask
+++ /dev/null
@@ -1,9 +0,0 @@
-# Copyright 1999-2017 Gentoo Foundation
-# Distributed under the terms of the GNU General Public License v2
-
-# Unmask the flag which corresponds to ARCH.
--x86
-
-# Mark Wright <gienah@gentoo.org> (26 Apr 2014)
-# mask int64 flag for 32 bits arches
-int64
diff --git a/profiles/categories b/profiles/categories
deleted file mode 100644
index 3d47d6ca4..000000000
--- a/profiles/categories
+++ /dev/null
@@ -1,163 +0,0 @@
-app-accessibility
-app-admin
-app-antivirus
-app-arch
-app-backup
-app-benchmarks
-app-cdr
-app-crypt
-app-dicts
-app-doc
-app-editors
-app-emacs
-app-emulation
-app-eselect
-app-forensics
-app-i18n
-app-laptop
-app-leechcraft
-app-misc
-app-mobilephone
-app-office
-app-officeext
-app-pda
-app-portage
-app-shells
-app-text
-app-vim
-app-xemacs
-dev-ada
-dev-cpp
-dev-db
-dev-dotnet
-dev-embedded
-dev-erlang
-dev-games
-dev-go
-dev-haskell
-dev-java
-dev-lang
-dev-libs
-dev-lisp
-dev-lua
-dev-ml
-dev-perl
-dev-php
-dev-python
-dev-qt
-dev-ros
-dev-ruby
-dev-scheme
-dev-tcltk
-dev-tex
-dev-texlive
-dev-util
-dev-vcs
-games-action
-games-arcade
-games-board
-games-emulation
-games-engines
-games-fps
-games-kids
-games-misc
-games-mud
-games-puzzle
-games-roguelike
-games-rpg
-games-server
-games-simulation
-games-sports
-games-strategy
-games-util
-gnome-base
-gnome-extra
-gnustep-apps
-gnustep-base
-gnustep-libs
-java-virtuals
-kde-apps
-kde-frameworks
-kde-misc
-kde-plasma
-lxde-base
-lxqt-base
-mail-client
-mail-filter
-mail-mta
-mate-base
-mate-extra
-media-fonts
-media-gfx
-media-libs
-media-plugins
-media-radio
-media-sound
-media-tv
-media-video
-net-analyzer
-net-dialup
-net-dns
-net-firewall
-net-fs
-net-ftp
-net-im
-net-irc
-net-libs
-net-mail
-net-misc
-net-nds
-net-news
-net-nntp
-net-p2p
-net-print
-net-proxy
-net-voip
-net-wireless
-perl-core
-ros-meta
-sci-astronomy
-sci-biology
-sci-calculators
-sci-chemistry
-sci-electronics
-sci-geosciences
-sci-libs
-sci-mathematics
-sci-misc
-sci-physics
-sci-visualization
-sec-policy
-sys-apps
-sys-auth
-sys-block
-sys-boot
-sys-cluster
-sys-devel
-sys-fabric
-sys-firmware
-sys-freebsd
-sys-fs
-sys-kernel
-sys-libs
-sys-power
-sys-process
-virtual
-www-apache
-www-apps
-www-client
-www-misc
-www-plugins
-www-servers
-x11-apps
-x11-base
-x11-drivers
-x11-libs
-x11-misc
-x11-plugins
-x11-proto
-x11-terms
-x11-themes
-x11-wm
-xfce-base
-xfce-extra
diff --git a/profiles/desc/lhapdf_sets.desc b/profiles/desc/lhapdf_sets.desc
new file mode 100644
index 000000000..66da0763c
--- /dev/null
+++ b/profiles/desc/lhapdf_sets.desc
@@ -0,0 +1,19 @@
+# Copyright 2022 Gentoo Authors
+# Distributed under the terms of the GNU General Public License v2
+
+# This file contains descriptions of LHAPDF_SETS USE_EXPAND flags.
+
+nnpdf31_nnlo_as_0118_luxqed - NNPDF31_nnlo_as_0118_luxqed LHAPDF grid
+pdf4lhc15_nlo_asvar - PDF4LHC15_nlo_asvar LHAPDF grid
+ct14qed_proton - CT14qed_proton LHAPDF grid
+ct14lo - CT14lo LHAPDF grid
+ct14nlo - CT14nlo LHAPDF grid
+ct10 - CT10 LHAPDF grid
+mrst2007lomod - MRST2007lomod LHAPDF grid
+nnpdf23_nlo_as_0119_qed_mc - NNPDF23_nlo_as_0119_qed_mc LHAPDF grid
+nnpdf23_nnlo_as_0119_qed_mc - NNPDF23_nnlo_as_0119_qed_mc LHAPDF grid
+cteq66 - CTEQ66 LHAPDF grid
+cteq6l1 - CTEQ6L1 LHAPDF grid
+mrst2004qed - MRST2004qed LHAPDF grid
+nnpdf23_nlo_as_0118 - nnpdf23_nlo_as_0118 grid
+nnpdf31_nnlo_as_0118 - nnpdf31_nnlo_as_0118 grid
\ No newline at end of file
diff --git a/profiles/license_groups b/profiles/license_groups
index c23a2a105..5221d37f1 100644
--- a/profiles/license_groups
+++ b/profiles/license_groups
@@ -1,2 +1 @@
-EULA AMD-APPSDK NVIDIA-gdk NVIDIA-CUDA OpenSIFT
-MISC-FREE CeCILL-B
+EULA OpenSIFT MathWorks
diff --git a/profiles/make.defaults b/profiles/make.defaults
new file mode 100644
index 000000000..88d3fe603
--- /dev/null
+++ b/profiles/make.defaults
@@ -0,0 +1 @@
+USE_EXPAND="LHAPDF_SETS"
\ No newline at end of file
diff --git a/profiles/package.mask b/profiles/package.mask
index 9f3e2465b..48068ccf9 100644
--- a/profiles/package.mask
+++ b/profiles/package.mask
@@ -30,19 +30,9 @@
 
 #--- END OF EXAMPLES ---
 
-# Horea Christian <horea.christ@gmail.com> (26 Jun 2018)
-# All versions depend on hard-masked sci-biology/afni.
-sci-biology/samri
+# Andrew Ammerlaan <andrewammerlaan@gentoo.org> (2024-04-24)
+# Dependencies dev-python/future removed
+sci-biology/multiqc
 
-# Horea Christian <horea.christ@gmail.com> (26 Jun 2018)
-# Serious bundling issues, upstream does not support Gentoo
-# or more generally unbundling. Masked until unbundling
-# efforts ( https://github.com/afni/afni/pull/60 ) come to
-# fruition.
-=sci-biology/afni-19.0.21
-=sci-biology/afni-18.1.04
-
-# Sebastien Fabbro <bicatali@gentoo.org> (23 Aug 2011)
-# mask old blas from main tree to allow smoother transition to
-# new blas/lapack framework
-=sci-libs/blas-reference-20070226*
+# Andrew Ammerlaan <andrewammerlaan@gentoo.org> (2024-04-24)
+# reverse deps
diff --git a/profiles/package.use.mask b/profiles/package.use.mask
index 4814b71b9..39a6df0b7 100644
--- a/profiles/package.use.mask
+++ b/profiles/package.use.mask
@@ -1,4 +1,4 @@
-# Copyright 1999-2017 Gentoo Foundation
+# Copyright 1999-2020 Gentoo Foundation
 # Distributed under the terms of the GNU General Public License v2
 
 # When you add an entry to the top of this file, add your name, the date, and
@@ -15,34 +15,6 @@
 ## =media-video/mplayer-0.90_pre5-r1 foo
 #
 
-# Matthias Maier <tamiko@gentoo.org) (25 May 2017)
-# sci-libs/parmetis-4* is masked
-sci-mathematics/petsc metis
-sci-libs/dealii metis
-
-# Andrew Savchenko <bircoph@gentoo.org> (02 Jun 2016)
-# doesn't link with plotutils-2.6
-sci-physics/qcl plotutils
-
-# Christoph Junghans <ottxor@gentoo.org> (12 Sep 2014)
-# icc and ifc don't work on no-multilib
-sci-biology/estscan icc ifc
-
-# Justin Lecher <jlec@gntoo.org> (06 Jan 2014)
-# Missing dep dev-python/scikits-cuda
-sci-biology/mne-python cuda
-
-# Andreas Schäfer <gentryx@gmx.de> (21 Nov 2013)
-# cuda only works on x86 and amd64
-sys-cluster/openmpi -cuda
-
-# Andreas Schäfer <gentryx@gmx.de> (21 Nov 2013)
-# cuda only works on x86 and amd64
-sys-cluster/openmpi -cuda
-# Christoph Junghans <ottxor@gentoo.org> (05 Nov 2013)
-# gui sandbox error
-dev-lang/conceptual gui
-
-# Kacper Kowalik <xarthisius@gentoo.org> (23 Jul 2011)
-# mask assembler as it currently doesn't work
-dev-lang/path64 assembler
+# Andrew Ammerlaan <andrewammerlaan@gentoo.org> (23 Aug 2022)
+# vtk<9 no longer available in ::gentoo
+sci-libs/gdcm python
diff --git a/profiles/profiles.desc b/profiles/profiles.desc
deleted file mode 100644
index 8b1378917..000000000
--- a/profiles/profiles.desc
+++ /dev/null
@@ -1 +0,0 @@
-
diff --git a/profiles/updates/1Q-2011 b/profiles/updates/1Q-2011
index 85c91332b..fc246d419 100644
--- a/profiles/updates/1Q-2011
+++ b/profiles/updates/1Q-2011
@@ -1,6 +1,6 @@
 move www-apps/SwishE www-apps/py-swish-e
 move sys-cluster/os-mpi sys-cluster/native-mpi
 move sci-misc/freecad media-gfx/freecad
-move app-doc/votca-manual app-doc/votca-csg-manual 
+move app-doc/votca-manual app-doc/votca-csg-manual
 move sci-chemistry/inchi sci-libs/inchi
 move sci-chemistry/stdinchi sci-libs/inchi
diff --git a/profiles/updates/1Q-2021 b/profiles/updates/1Q-2021
new file mode 100644
index 000000000..4e6e845aa
--- /dev/null
+++ b/profiles/updates/1Q-2021
@@ -0,0 +1,9 @@
+move virtual/blacs sci-libs/mkl
+move sci-libs/elmer-eio sci-misc/elmer-fem
+move sci-libs/elmer-hutiter sci-misc/elmer-fem
+move sci-misc/elmer-elmergrid sci-misc/elmer-fem
+move sci-misc/elmer-front sci-misc/elmer-fem
+move sci-misc/elmer-meshgend2d sci-misc/elmer-fem
+move sci-misc/elmer-post sci-misc/elmer-fem
+move sci-misc/elmer-meta sci-misc/elmer-fem
+move sci-biology/phusion  sci-biology/phusion2
diff --git a/profiles/updates/1Q-2022 b/profiles/updates/1Q-2022
new file mode 100644
index 000000000..8b44d82fa
--- /dev/null
+++ b/profiles/updates/1Q-2022
@@ -0,0 +1 @@
+move sci-biology/sra_sdk sci-biology/sra-tools
diff --git a/profiles/updates/2Q-2021 b/profiles/updates/2Q-2021
new file mode 100644
index 000000000..6b04562b8
--- /dev/null
+++ b/profiles/updates/2Q-2021
@@ -0,0 +1 @@
+move media-libs/libredwg media-gfx/libredwg
diff --git a/profiles/updates/4Q-2020 b/profiles/updates/4Q-2020
new file mode 100644
index 000000000..533fbbee0
--- /dev/null
+++ b/profiles/updates/4Q-2020
@@ -0,0 +1,2 @@
+move sci-libs/amdlibm sci-libs/aocl-libm
+move sys-cluster/Lmod sys-cluster/lmod
diff --git a/profiles/updates/4Q-2021 b/profiles/updates/4Q-2021
new file mode 100644
index 000000000..63c17f4be
--- /dev/null
+++ b/profiles/updates/4Q-2021
@@ -0,0 +1 @@
+move sys-apps/ndctl sys-block/ndctl
diff --git a/profiles/updates/4Q-2022 b/profiles/updates/4Q-2022
new file mode 100644
index 000000000..b80d5a910
--- /dev/null
+++ b/profiles/updates/4Q-2022
@@ -0,0 +1 @@
+move sci-mathematics/netgen media-gfx/netgen
diff --git a/sci-astronomy/bpz/Manifest b/sci-astronomy/bpz/Manifest
deleted file mode 100644
index 2e8d7e16b..000000000
--- a/sci-astronomy/bpz/Manifest
+++ /dev/null
@@ -1 +0,0 @@
-DIST bpz-1.99.3.tar.gz 1353654 SHA256 f0c40e837aa90123cd087ee792169da6e478cc54912ce0767eafdb2fe1f7e584 SHA512 d00a2da6852a0314088e3cf76d89c4ea2317c620a4a6d94fe8da5b4a3d147957af249efc41de79c21b0a01882b6063f1061a7c2f8820fe7737ce1eae22ca9cf0 WHIRLPOOL 1738c44a1dd9af7ded03af42a3983c5f0ab5394bb665f7965d098b1aff3c3328b85e1d263e73c8d5b2eee2ed851f7d28ec09d9217ab7c9920456d32f4f80a3c5
diff --git a/sci-astronomy/bpz/bpz-1.99.3.ebuild b/sci-astronomy/bpz/bpz-1.99.3.ebuild
deleted file mode 100644
index c651aa3d8..000000000
--- a/sci-astronomy/bpz/bpz-1.99.3.ebuild
+++ /dev/null
@@ -1,57 +0,0 @@
-# Copyright 1999-2014 Gentoo Foundation
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=5
-
-PYTHON_COMPAT=( python2_7 )
-
-inherit python-single-r1
-
-DESCRIPTION="Bayesian Photometric Redshifts"
-HOMEPAGE="http://www.its.caltech.edu/~coe/BPZ/"
-SRC_URI="${HOMEPAGE}/${P}.tar.gz"
-
-LICENSE="all-rights-reserved"
-SLOT="0"
-KEYWORDS="~amd64 ~x86"
-IUSE="test"
-
-REQUIRED_USE="${PYTHON_REQUIRED_USE}"
-
-RDEPEND="${PYTHON_DEPS}
-	dev-python/numpy[${PYTHON_USEDEP}]
-	|| (
-		dev-python/matplotlib[${PYTHON_USEDEP}]
-		dev-python/python-biggles[${PYTHON_USEDEP}]
-		)"
-DEPEND="${PYTHON_DEPS}
-	test? ( ${RDEPEND} )"
-
-src_prepare() {
-	sed \
-		-e 's/TkAgg/Agg/g' \
-		-i bpz.py plots/probplot.py plots/coeplot.py || die
-}
-
-src_test() {
-	cd test
-	export BPZPATH="${S}" PYTHONPATH="${S}"
-	${EPYTHON} ../bpz.py UDFtest.cat -INTERP 2 || die
-	${EPYTHON} ../bpzfinalize.py UDFtest || die
-	${EPYTHON} ../plots/webpage.py UDFtest || die
-}
-
-src_install() {
-	insinto /usr/share/bpz
-	doins -r FILTER SED AB
-	python_moduleinto ${PN}
-	python_domodule *.py plots
-
-	cat <<-EOF > bpz
-		#!$(type -P sh)
-		sitedir=$(python_get_sitedir)
-		BPZPATH="${EPREFIX}"/usr/share/bpz ${EPYTHON} \${sitedir}/bpz/bpz.py \$@
-	EOF
-
-	dobin bpz
-}
diff --git a/sci-astronomy/bpz/metadata.xml b/sci-astronomy/bpz/metadata.xml
deleted file mode 100644
index 008ef62b2..000000000
--- a/sci-astronomy/bpz/metadata.xml
+++ /dev/null
@@ -1,12 +0,0 @@
-<?xml version="1.0" encoding="UTF-8"?>
-<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
-<pkgmetadata>
-	<maintainer type="project">
-		<email>sci-astronomy@gentoo.org</email>
-		<name>Gentoo Astronomy Project</name>
-	</maintainer>
-	<longdescription lang="en">
-Bayesian Photometric Redshifts is a method to infere photometric
-redshifts of galaxies.
-</longdescription>
-</pkgmetadata>
diff --git a/sci-astronomy/casapy-bin/Manifest b/sci-astronomy/casapy-bin/Manifest
deleted file mode 100644
index b31ef5857..000000000
--- a/sci-astronomy/casapy-bin/Manifest
+++ /dev/null
@@ -1,3 +0,0 @@
-DIST casa-release-4.4.0-el6.tar.gz 1028567130 BLAKE2B e44260cf0ce14329781299ff131697c2348c5cf28340154db2b7de2156d3e8bb8790695203e840c8d1a733ad8ff15b9e0cddda7e53fb9951d4e68b97504bb1ef SHA512 ee71bd6d80c18db570f42e54d8d0d2d8cc512497ee885e316a81cc1f71480abb21681a8ef39991fe3673a70d036e1418a7f7d77909b3bc7ff2b32c8be004409f
-DIST casapy-42.1.29047-001-1-64b.tar.gz 985311640 BLAKE2B 7752c2c69b5ac8c2bcde43a9da8198488890196d7303199942b5d7c7d4facf016cd2014dcae478ab84eb85908a5cdeb671602dfd4b16a4d758a7a865ee4de46f SHA512 506a7d173a4196106d437ba234a48b186d036b82d524d89fbe476045de979992c438db12bcaa4eb42b551f1f9c65fd83fce3c7469a8c8ef60a4692d71bab40dc
-DIST casapy-42.2.30986-1-64b.tar.gz 1000907646 SHA256 e178b8005efeb9eee60f809f1eef6d55a5cd29b9b62b1a5a3103277635188f0c SHA512 2410b0e802752a1992a0add4cd23bd0f0dc9a0ca21895f1cd88ffb81ab5566b8bd1ff2c6c64759760105e65d0f844efa453b6ab52b2f86bc4017f5337fa66f5e WHIRLPOOL 340e99f95892a49b40ca1fb3da11110a99fda36f882b01de2cb9fee4c4f0b8609c07c46271d299146bbaeb1661aad18e409f2143f21be90f605e9e7a82e3d2cb
diff --git a/sci-astronomy/casapy-bin/casapy-bin-4.2.1.29047.001_p1.ebuild b/sci-astronomy/casapy-bin/casapy-bin-4.2.1.29047.001_p1.ebuild
deleted file mode 100644
index 386a3b0ba..000000000
--- a/sci-astronomy/casapy-bin/casapy-bin-4.2.1.29047.001_p1.ebuild
+++ /dev/null
@@ -1,68 +0,0 @@
-# Copyright 1999-2014 Gentoo Foundation
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=5
-inherit versionator
-
-DESCRIPTION="Software package to calibrate, image, and analyze radioastronomical data"
-HOMEPAGE="http://casa.nrao.edu/"
-
-MY_P=$(version_format_string '${PN%-bin}-$1$2.$3.$4-$5-${6#p}-64b')
-SRC_URI="https://svn.cv.nrao.edu/casa/linux_distro/old/${MY_P}.tar.gz"
-
-LICENSE="LGPL-2.1+"
-SLOT="0"
-KEYWORDS="~amd64"
-IUSE=""
-
-DEPEND=""
-RDEPEND="
-	app-crypt/mit-krb5
-	dev-db/sqlite
-	dev-libs/glib
-	dev-libs/icu
-	dev-libs/libxslt
-	media-libs/alsa-lib
-	media-libs/fontconfig
-	media-libs/freetype
-	media-libs/gst-plugins-base
-	media-libs/libjpeg-turbo
-	media-libs/mesa
-	media-libs/tiff
-	sci-libs/gsl
-	sci-libs/pgplot
-	sys-apps/keyutils
-	sys-apps/util-linux
-	sys-devel/gcc[fortran]
-	virtual/libffi
-	x11-libs/libdrm
-	x11-libs/libSM
-	x11-libs/libXau
-	x11-libs/libXcursor
-	x11-libs/libXdmcp
-	x11-libs/libXi
-	x11-libs/libXinerama
-	x11-libs/libXrandr
-"
-
-S="${WORKDIR}/${MY_P}"
-QA_PREBUILT="/opt/casapy/* /opt/casapy/sbin/* /opt/casapy/lib64/*"
-
-src_compile() { :; }
-
-src_install() {
-	dodir /opt/
-	cp -R "${S}" "${D}/opt/casapy" || die "Could not copy casapy into ${D}/opt"
-
-	dodir /opt/bin
-	cd "${D}/opt/casapy/bin"
-	for binary in `ls`
-	do
-		dosym ../casapy/$binary /opt/bin/$binary
-	done
-}
-
-pkg_postinst() {
-	einfo "CASA will use media-gfx/graphviz if this package is installed."
-	ewarn "Upstream warns that SElinux must be disabled, set to permissive, or configured to allow execheap."
-}
diff --git a/sci-astronomy/casapy-bin/casapy-bin-4.2.2.30986_p1.ebuild b/sci-astronomy/casapy-bin/casapy-bin-4.2.2.30986_p1.ebuild
deleted file mode 100644
index 993c588e8..000000000
--- a/sci-astronomy/casapy-bin/casapy-bin-4.2.2.30986_p1.ebuild
+++ /dev/null
@@ -1,68 +0,0 @@
-# Copyright 1999-2014 Gentoo Foundation
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=5
-inherit versionator
-
-DESCRIPTION="Software package to calibrate, image, and analyze radioastronomical data"
-HOMEPAGE="http://casa.nrao.edu/"
-
-MY_P=$(version_format_string '${PN%-bin}-$1$2.$3.$4-${5#p}-64b')
-SRC_URI="https://svn.cv.nrao.edu/casa/linux_distro/${MY_P}.tar.gz"
-
-LICENSE="LGPL-2.1+"
-SLOT="0"
-KEYWORDS="~amd64"
-IUSE=""
-
-DEPEND=""
-RDEPEND="
-	app-crypt/mit-krb5
-	dev-db/sqlite
-	dev-libs/glib
-	dev-libs/icu
-	dev-libs/libxslt
-	media-libs/alsa-lib
-	media-libs/fontconfig
-	media-libs/freetype
-	media-libs/gst-plugins-base
-	media-libs/libjpeg-turbo
-	media-libs/mesa
-	media-libs/tiff
-	sci-libs/gsl
-	sci-libs/pgplot
-	sys-apps/keyutils
-	sys-apps/util-linux
-	sys-devel/gcc[fortran]
-	virtual/libffi
-	x11-libs/libdrm
-	x11-libs/libSM
-	x11-libs/libXau
-	x11-libs/libXcursor
-	x11-libs/libXdmcp
-	x11-libs/libXi
-	x11-libs/libXinerama
-	x11-libs/libXrandr
-"
-
-S="${WORKDIR}/${MY_P}"
-QA_PREBUILT="/opt/casapy/* /opt/casapy/sbin/* /opt/casapy/lib64/*"
-
-src_compile() { :; }
-
-src_install() {
-	dodir /opt/
-	cp -R "${S}" "${D}/opt/casapy" || die "Could not copy casapy into ${D}/opt"
-
-	dodir /opt/bin
-	cd "${D}/opt/casapy/bin"
-	for binary in `ls`
-	do
-		dosym ../casapy/$binary /opt/bin/$binary
-	done
-}
-
-pkg_postinst() {
-	einfo "CASA will use media-gfx/graphviz if this package is installed."
-	ewarn "Upstream warns that SElinux must be disabled, set to permissive, or configured to allow execheap."
-}
diff --git a/sci-astronomy/casapy-bin/casapy-bin-4.4.0.ebuild b/sci-astronomy/casapy-bin/casapy-bin-4.4.0.ebuild
deleted file mode 100644
index 8c45d6097..000000000
--- a/sci-astronomy/casapy-bin/casapy-bin-4.4.0.ebuild
+++ /dev/null
@@ -1,68 +0,0 @@
-# Copyright 1999-2015 Gentoo Foundation
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=5
-inherit versionator
-
-DESCRIPTION="Software package to calibrate, image, and analyze radioastronomical data"
-HOMEPAGE="http://casa.nrao.edu/"
-
-MY_P=${P/py-bin/-release}-el6
-SRC_URI="https://svn.cv.nrao.edu/casa/linux_distro/release/el6/${MY_P}.tar.gz"
-
-LICENSE="LGPL-2.1+"
-SLOT="0"
-KEYWORDS="~amd64"
-IUSE=""
-
-DEPEND=""
-RDEPEND="
-	app-crypt/mit-krb5
-	dev-db/sqlite
-	dev-libs/glib
-	dev-libs/icu
-	dev-libs/libxslt
-	media-libs/alsa-lib
-	media-libs/fontconfig
-	media-libs/freetype
-	media-libs/gst-plugins-base
-	media-libs/libjpeg-turbo
-	media-libs/mesa
-	media-libs/tiff
-	sci-libs/gsl
-	sci-libs/pgplot
-	sys-apps/keyutils
-	sys-apps/util-linux
-	sys-devel/gcc[fortran]
-	virtual/libffi
-	x11-libs/libdrm
-	x11-libs/libSM
-	x11-libs/libXau
-	x11-libs/libXcursor
-	x11-libs/libXdmcp
-	x11-libs/libXi
-	x11-libs/libXinerama
-	x11-libs/libXrandr
-"
-
-S="${WORKDIR}/${MY_P}"
-QA_PREBUILT="/opt/casapy/* /opt/casapy/sbin/* /opt/casapy/lib64/*"
-
-src_compile() { :; }
-
-src_install() {
-	dodir /opt/
-	cp -R "${S}" "${D}/opt/casapy" || die "Could not copy casapy into ${D}/opt"
-
-	dodir /opt/bin
-	cd "${D}/opt/casapy/bin"
-	for binary in `ls`
-	do
-		dosym ../casapy/$binary /opt/bin/$binary
-	done
-}
-
-pkg_postinst() {
-	einfo "CASA will use media-gfx/graphviz if this package is installed."
-	ewarn "Upstream warns that SElinux must be disabled, set to permissive, or configured to allow execheap."
-}
diff --git a/sci-astronomy/casapy-bin/metadata.xml b/sci-astronomy/casapy-bin/metadata.xml
deleted file mode 100644
index ef1c2d6cc..000000000
--- a/sci-astronomy/casapy-bin/metadata.xml
+++ /dev/null
@@ -1,13 +0,0 @@
-<?xml version="1.0" encoding="UTF-8"?>
-<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
-<pkgmetadata>
-	<maintainer type="project">
-		<email>sci-astronomy@gentoo.org</email>
-		<name>Gentoo Astronomy Project</name>
-	</maintainer>
-	<longdescription>
-CASA, the Common Astronomy Software Applications package, is being developed
-with the primary goal of supporting the data post-processing needs of the
-next generation of radio astronomical telescopes such as ALMA and VLA.
-</longdescription>
-</pkgmetadata>
diff --git a/sci-astronomy/eazy/Manifest b/sci-astronomy/eazy/Manifest
deleted file mode 100644
index 72e4134e8..000000000
--- a/sci-astronomy/eazy/Manifest
+++ /dev/null
@@ -1 +0,0 @@
-DIST eazy-1.00.tar.gz 4111352 BLAKE2B 1e90abcc6da80c3abad3a4f2530f70384dce68b97cb9832f31fdda16749e0f2816afe5d679c0d2fa8b008f79e3a1c598e0d92c77abc6f555e77e716f9a62604f SHA512 b841b4d5c3bd853cd1bcb575bc6be6cde4437521399fe978c92a448d037ace9edcdf88e8a9eef3157a722a524b8d0bb5f656559d865c6c66e52d2f07b300f78a
diff --git a/sci-astronomy/eazy/eazy-1.00.ebuild b/sci-astronomy/eazy/eazy-1.00.ebuild
deleted file mode 100644
index 971409000..000000000
--- a/sci-astronomy/eazy/eazy-1.00.ebuild
+++ /dev/null
@@ -1,48 +0,0 @@
-# Copyright 1999-2014 Gentoo Foundation
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=5
-
-inherit eutils
-
-DESCRIPTION="Photometric redshift estimator for galaxies"
-HOMEPAGE="http://www.astro.yale.edu/eazy/?home"
-SRC_URI="http://www.astro.yale.edu/eazy/download/${P}.tar.gz"
-
-LICENSE="all-rights-reserved"
-SLOT="0"
-KEYWORDS="~amd64 ~x86"
-IUSE="doc examples"
-
-RDEPEND=""
-DEPEND="${RDEPEND}
-	doc? ( virtual/latex-base )"
-
-src_prepare() {
-	epatch "${FILESDIR}"/${P}-makefile.patch
-}
-
-src_compile() {
-	emake -C src
-	use doc && emake -C doc
-}
-
-src_test() {
-	cd inputs
-	../src/eazy
-	mv zphot.param.default zphot.param
-	../src/eazy || die
-}
-
-src_install() {
-	dobin src/eazy
-	insinto /usr/share/eazy
-	doins -r templates
-	use doc && dodoc doc/eazy_manual.pdf
-	if use examples; then
-		cd inputs
-		rm templates
-		insinto /usr/share/doc/${PF}
-		doins -r *
-	fi
-}
diff --git a/sci-astronomy/eazy/files/eazy-1.00-makefile.patch b/sci-astronomy/eazy/files/eazy-1.00-makefile.patch
deleted file mode 100644
index 40ce53894..000000000
--- a/sci-astronomy/eazy/files/eazy-1.00-makefile.patch
+++ /dev/null
@@ -1,21 +0,0 @@
---- src/makefile.orig	2012-05-11 04:15:35.000000000 +0100
-+++ src/makefile	2012-05-11 04:15:53.000000000 +0100
-@@ -1,16 +1,14 @@
- # -pg -lc_p for profiling
--.c.o:
--	gcc -msse2 -c -O3 -Wall $<
- 
- all: eazy 
- 
- eazy: main.o output_files.o zeropoints.o getpar.o makegrid.o interpol.o getphotz.o  kmag_prior.o 
--	gcc -o eazy main.o output_files.o zeropoints.o getpar.o makegrid.o interpol.o getphotz.o kmag_prior.o  -lm 
-+	$(CC) $(LDFLAGS) main.o output_files.o zeropoints.o getpar.o makegrid.o interpol.o getphotz.o kmag_prior.o  -lm -o eazy
- 
- main.o output_files.o zeropoints.o getpar.o makegrid.o interpol.o getphotz.o temperr.o kmag_prior.o : defs.h
- 
- temperr: temperr.o  getpar.o
--	gcc -o temperr temperr.o getpar.o -lm
-+	$(CC) $(LDFLAGS) temperr.o getpar.o -lm -o temperr
- 
- clean:
- 	rm *.o eazy 
diff --git a/sci-astronomy/eazy/metadata.xml b/sci-astronomy/eazy/metadata.xml
deleted file mode 100644
index 66032a84a..000000000
--- a/sci-astronomy/eazy/metadata.xml
+++ /dev/null
@@ -1,13 +0,0 @@
-<?xml version="1.0" encoding="UTF-8"?>
-<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
-<pkgmetadata>
-	<maintainer type="project">
-		<email>sci-astronomy@gentoo.org</email>
-		<name>Gentoo Astronomy Project</name>
-	</maintainer>
-	<longdescription lang="en">
-Easy and Accurate Zphot from Yale is a photometric redshift code
-designed to produce high-quality redshifts from 0 to 4 for situations
-where complete spectroscopic calibration samples are not available.
-</longdescription>
-</pkgmetadata>
diff --git a/sci-astronomy/eye/eye-9999.ebuild b/sci-astronomy/eye/eye-9999.ebuild
deleted file mode 100644
index 2ec0f52ff..000000000
--- a/sci-astronomy/eye/eye-9999.ebuild
+++ /dev/null
@@ -1,36 +0,0 @@
-# Copyright 1999-2016 Gentoo Foundation
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=6
-
-inherit subversion
-
-ESVN_REPO_URI="https://astromatic.net/pubsvn/software/${PN}/trunk"
-ESVN_OPTIONS="--trust-server-cert-failures=unknown-ca"
-
-SRC_URI=""
-KEYWORDS=""
-
-DESCRIPTION="Enhance astronomical object extraction with neural network filters"
-HOMEPAGE="http://www.astromatic.net/software/eye"
-
-LICENSE="GPL-3"
-SLOT="0"
-IUSE="doc threads"
-
-RDEPEND=""
-DEPEND="${RDEPEND}"
-
-src_prepare() {
-	default
-	subversion_src_prepare
-}
-
-src_configure() {
-	econf $(use_enable threads)
-}
-
-src_install () {
-	default
-	use doc && dodoc doc/*
-}
diff --git a/sci-astronomy/eye/metadata.xml b/sci-astronomy/eye/metadata.xml
deleted file mode 100644
index 0bbded1cf..000000000
--- a/sci-astronomy/eye/metadata.xml
+++ /dev/null
@@ -1,17 +0,0 @@
-<?xml version="1.0" encoding="UTF-8"?>
-<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
-<pkgmetadata>
-	<maintainer type="project">
-		<email>sci-astronomy@gentoo.org</email>
-		<name>Gentoo Astronomy Project</name>
-	</maintainer>
-	<longdescription lang="en">
-In EyE (Enhance Your Extraction) an artificial neural network
-connected to pixels of a moving window (retina) is trained to
-associate these input stimuli to the corresponding response in one
-or several output image(s). The resulting filter can be loaded in
-SExtractor to operate complex, wildly non-linear filters on
-astronomical images. Typical applications of EyE include adaptive
-filtering, feature detection and cosmetic corrections.
-</longdescription>
-</pkgmetadata>
diff --git a/sci-astronomy/galfit-bin/Manifest b/sci-astronomy/galfit-bin/Manifest
deleted file mode 100644
index fa02e4bac..000000000
--- a/sci-astronomy/galfit-bin/Manifest
+++ /dev/null
@@ -1,4 +0,0 @@
-DIST galfit-bin-3.0.5-amd64.tar.gz 1487754 BLAKE2B 1f997504695c55a728b1cb29c3ab5d84f63a44b27306c7cb85640d5cc5c84086b658949aefcdc915efd32102ab1b111218c4fa699a5c91429c96e086082e7299 SHA512 016481bb27e63ee02756da9b13d08ebd726f8f0c947a5c31b2e2837bcf4f3778e07018aeaaf69d6d047e499649788b7d3dae029848be6c355404727781273c33
-DIST galfit-bin-3.0.5-x86.tar.gz 1043378 BLAKE2B 99ea5c273a4669cb3accbfe3c8f390c1480f9df505d1120a9e042fbca4a07619b84fdb259c559362585b63a88770afe31f2aacb3af5fcb8bdabf7de91c8c339e SHA512 4a222dda8f9b9b06cc4c7d1b67de2a18986222418000093e73a535e80af2638deb0fde5d6b5f6a6f142807143260549180627e528744f91e4c3fd7a68fa42452
-DIST galfit-ex.tar.gz 1918422 BLAKE2B dbae80db44e19167acc5f1af99236d96442836cb3172aa7641179b8d1c291345605eda9ce2499482765f46af7e44192864d5f1c7efe77e12dc98d27d2a0db627 SHA512 cea08755bbae9e074c30bcd8c35da9358d29cdff0450af578d9363f5c9a813696d3506ad9cfb2d4e10dfe1f7469ab397c075427473e1f250b5397e5aa82d981a
-DIST galfit.pdf 2039018 BLAKE2B d10c919e7176c586aa845b1d729568a713bc1e7da82d42e1ee21083c58df8aa53d68b4b20691fb9836d9a7a5cfdddc96b160c299c01b09658eb372cb3c689758 SHA512 e28491d61276911995142726a742bdea86069c216d41103c494b821943ee3d48a96cc5e5c1dc73fc65cb682922828e366b29405c62eeb2614c314c4bab8c1824
diff --git a/sci-astronomy/galfit-bin/galfit-bin-3.0.5.ebuild b/sci-astronomy/galfit-bin/galfit-bin-3.0.5.ebuild
deleted file mode 100644
index 438d104d2..000000000
--- a/sci-astronomy/galfit-bin/galfit-bin-3.0.5.ebuild
+++ /dev/null
@@ -1,45 +0,0 @@
-# Copyright 1999-2014 Gentoo Foundation
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=5
-
-MYPN=galfit
-
-inherit multilib
-
-DESCRIPTION="Galaxy morphology fitting program"
-HOMEPAGE="http://users.obs.carnegiescience.edu/peng/work/galfit/galfit.html"
-CURI="http://users.obs.carnegiescience.edu/peng/work/${MYPN}"
-SRC_URI="
-	amd64? ( ${CURI}/${MYPN}3-debian64.tar.gz -> ${P}-amd64.tar.gz )
-	x86? ( ${CURI}/${MYPN}3-debian32.tar.gz -> ${P}-x86.tar.gz )
-	doc? ( ${CURI}/README.pdf -> ${MYPN}.pdf )
-	examples? ( ${CURI}/${MYPN}-ex.tar.gz )
-	test? ( ${CURI}/${MYPN}-ex.tar.gz )"
-
-LICENSE="all-rights-reserved"
-SLOT="0"
-KEYWORDS="-* ~amd64 ~x86 ~amd64-linux ~x86-linux"
-IUSE="doc examples test"
-
-RDEPEND="sys-libs/ncurses[tinfo]"
-DEPEND=""
-
-RESTRICT="mirror"
-
-S="${WORKDIR}"
-
-src_test() {
-	chmod +x ${MYPN}
-	cd ${MYPN}-example/EXAMPLE
-	LD_LIBRARY_PATH=../.. ../../${MYPN} ${MYPN}.feedme
-}
-
-src_install () {
-	dobin ${MYPN}
-	use doc && newdoc "${DISTDIR}"/${MYPN}.pdf README.pdf
-	if use examples; then
-		insinto /usr/share/doc/${PF}/examples
-		doins ${MYPN}-example/*
-	fi
-}
diff --git a/sci-astronomy/galfit-bin/metadata.xml b/sci-astronomy/galfit-bin/metadata.xml
deleted file mode 100644
index 90190836d..000000000
--- a/sci-astronomy/galfit-bin/metadata.xml
+++ /dev/null
@@ -1,12 +0,0 @@
-<?xml version="1.0" encoding="UTF-8"?>
-<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
-<pkgmetadata>
-	<maintainer type="project">
-		<email>sci-astronomy@gentoo.org</email>
-		<name>Gentoo Astronomy Project</name>
-	</maintainer>
-	<longdescription lang="en">
-GALFIT is a data analysis algorithm that fits 2-D analytic functions
-to galaxies and point sources directly to digital images.
-</longdescription>
-</pkgmetadata>
diff --git a/sci-astronomy/lephare/Manifest b/sci-astronomy/lephare/Manifest
deleted file mode 100644
index c01ed47de..000000000
--- a/sci-astronomy/lephare/Manifest
+++ /dev/null
@@ -1 +0,0 @@
-DIST lephare_dev_v2.2.tar.gz 44360090 SHA256 11bafb4e7fde8ca25eca4633a8c10a7a5d9a17361c5ee5824d81a1aa8f4a4aba SHA512 a4f46b1539df9b4fb03dbbbb0429f19dc1070c40d0e2ab4c2c63cc114c212d162555a462f8197aa35f72ff543f6d3461fc5a4db6566b571863913a06df7665d0 WHIRLPOOL 8af505c08418917db16b46e4d12778b503e752a82109b0b30b05cb3bf5e46bc68764abb03714c596524786fd9003903022dfe2fbb0595409358ed1c114e96f07
diff --git a/sci-astronomy/lephare/lephare-2.2.ebuild b/sci-astronomy/lephare/lephare-2.2.ebuild
deleted file mode 100644
index 7d7828146..000000000
--- a/sci-astronomy/lephare/lephare-2.2.ebuild
+++ /dev/null
@@ -1,63 +0,0 @@
-# Copyright 1999-2015 Gentoo Foundation
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=5
-
-inherit eutils check-reqs fortran-2 versionator
-
-MYP=${PN}_dev_v$(replace_version_separator 2 '')
-
-DESCRIPTION="Photometric Analysis for Redshift Estimate for galaxies"
-HOMEPAGE="http://www.cfht.hawaii.edu/~arnouts/LEPHARE/lephare.html"
-SRC_URI="http://www.cfht.hawaii.edu/~arnouts/LEPHARE/DOWNLOAD/${MYP}.tar.gz"
-
-LICENSE="GPL-3"
-SLOT="0"
-KEYWORDS="~amd64 ~x86 ~amd64-linux ~x86-linux"
-IUSE="doc"
-
-S="${WORKDIR}/${PN}_dev/source"
-
-CHECKREQS_DISK_BUILD="400M"
-
-src_prepare() {
-	export LEPHAREDIR="${WORKDIR}/${PN}_dev" LEPHAREWORK="${WORKDIR}"
-	# clean up mac left over crap
-	find . -name ._\* -delete || die
-	# respect user flags and compiler
-	sed -i -e '/^FC/d' -e '/^FFLAGS/d' Makefile || die
-}
-
-src_test() {
-	# from pdf manual
-	cd ${LEPHAREDIR}/test || die
-	${LEPHAREDIR}/source/sedtolib -t S -c ../config/zphot.para || die
-	${LEPHAREDIR}/source/sedtolib -t Q -c ../config/zphot.para || die
-	${LEPHAREDIR}/source/sedtolib -t G -c ../config/zphot.para || die
-	${LEPHAREDIR}/source/filter -c ../config/zphot.para || die
-	${LEPHAREDIR}/source/mag_star -c ../config/zphot.para || die
-	${LEPHAREDIR}/source/mag_gal -t Q -c ../config/zphot.para -EB_V 0. || die
-	${LEPHAREDIR}/source/mag_gal -t G -c ../config/zphot.para -MOD_EXTINC 4,8 -LIB_ASCII YES || die
-	${LEPHAREDIR}/source/zphota -c ../config/zphot.para || die
-}
-
-src_install() {
-	# FILES target in Makefile
-	dobin \
-		sedtolib \
-		filter \
-		filter_info \
-		filter_extinc \
-		mag_star \
-		mag_gal \
-		zphota \
-		mag_zform
-	dodoc README_TECH
-	insinto /usr/share/${PN}
-	cd .. || die
-	doins -r {ext,filt,config,opa,sed,simul,test,tools,vega}
-	echo "LEPHAREDIR=${EPREFIX}/usr/share/${PN}" > 99lephare
-	doenvd 99lephare
-	newdoc INSTALL README
-	use doc && dodoc doc/*.pdf
-}
diff --git a/sci-astronomy/lephare/metadata.xml b/sci-astronomy/lephare/metadata.xml
deleted file mode 100644
index 0c2cbc460..000000000
--- a/sci-astronomy/lephare/metadata.xml
+++ /dev/null
@@ -1,12 +0,0 @@
-<?xml version="1.0" encoding="UTF-8"?>
-<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
-<pkgmetadata>
-	<maintainer type="project">
-		<email>sci-astronomy@gentoo.org</email>
-		<name>Gentoo Astronomy Project</name>
-	</maintainer>
-	<longdescription lang="en">
-Le Photometric Analysis for Redshift Estimate is a set of commands
-to compute photometric redshifts and to perform SED fitting.
-</longdescription>
-</pkgmetadata>
diff --git a/sci-astronomy/libthesky/Manifest b/sci-astronomy/libthesky/Manifest
index 240414b04..aed369dea 100644
--- a/sci-astronomy/libthesky/Manifest
+++ b/sci-astronomy/libthesky/Manifest
@@ -1,2 +1,2 @@
-DIST libthesky-0.3.2.tar.gz 124598 BLAKE2B a70db5dea8aa7ce478a5eb5ac3a837e2580b90c4ede2539059c57033e90eee56f453ea4efc811795bbbad5896190d8455315b41e3b5e147650f0f3c8e2263b1a SHA512 64fae18cf410c37d6bda5d65f8890a045734fa3bbaa23c76a8080ef06e15443af5159baf779b69594e24bb1fc8b0719ba03174764d46abed66f61750e8e9e68e
-DIST libthesky-data-20131020.tar.bz2 3945800 BLAKE2B 317556d3f045fb154f692caa37d40001713ae382810edec9843685868facc89e90d74a01c4169232ffe765536e2c4a0504dd94be4ff01699d76069bb43f7f18e SHA512 2bbc2eaeb37a52f383625ecbb0c8d455741631b8cf212e5b8839a9d4276ca8bfc638087aca6d94a458e2889e8e0b9a37cd0392828fe24fb1f653d5956c27b27d
+DIST libthesky-0.4.2.tar.gz 217861 BLAKE2B 8197878a299b93e6c6f98aef5555bbbb4304ade0fff10714a4fb33cf6eac89ccd4ae24400f5ee0262dca877cf770e85525787ceca2b95700407ddd3f5fa5e133 SHA512 70bcc525d54f1645cff65fc0ac702fb0a19445d74fa3c567aa07fed027b966c4753146becb9efc46e81521d1788846c460c47ec88d6611cec0524c2dad7cb646
+DIST libthesky-data-20160409.tar.bz2 3780265 BLAKE2B 9331156f7536d634f8523e776209190d73c10158800ff73694ac499292b2be80948810e6aaa531b51d878b5018f7304188b855fcbc976a1b1c285829555d2f4e SHA512 b790aa70b60c6c35db85a54de3487aa5ef47710121cb6c6c13069d4d8adba822b61449eb59ce7ec9203fb4d9cf33570222ec9a65b36ac21f5d4506cddd0b35a3
diff --git a/sci-astronomy/libthesky/libthesky-0.3.2.ebuild b/sci-astronomy/libthesky/libthesky-0.3.2.ebuild
deleted file mode 100644
index 5a12fc708..000000000
--- a/sci-astronomy/libthesky/libthesky-0.3.2.ebuild
+++ /dev/null
@@ -1,35 +0,0 @@
-# Copyright 1999-2015 Gentoo Foundation
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=5
-
-inherit cmake-utils fortran-2
-
-DESCRIPTION="Fortran library to compute positions of celestial bodies"
-HOMEPAGE="http://libthesky.sourceforge.net/"
-SRC_URI="mirror://sourceforge/${PN}/${P}.tar.gz
-mirror://sourceforge/${PN}/libthesky-data-20131020.tar.bz2"
-
-LICENSE="GPL-3"
-SLOT="0"
-KEYWORDS="~amd64 ~x86"
-IUSE="static-libs"
-
-DEPEND=">=sci-libs/libsufr-0.5.4"
-RDEPEND="${DEPEND}"
-
-src_configure() {
-	mycmakeargs=(
-		$(cmake-utils_use static-libs CREATE_STATICLIB)
-	)
-	cmake-utils_src_configure
-}
-
-# Install the data files as well as the libraries:
-src_install() {
-	insinto /usr/share/libTheSky
-	doins "${WORKDIR}"/data/*
-	cmake-utils_src_install
-}
-
-DOCS="CHANGELOG README VERSION"
diff --git a/sci-astronomy/libthesky/libthesky-0.4.2.ebuild b/sci-astronomy/libthesky/libthesky-0.4.2.ebuild
new file mode 100644
index 000000000..c7d2bd0c3
--- /dev/null
+++ b/sci-astronomy/libthesky/libthesky-0.4.2.ebuild
@@ -0,0 +1,37 @@
+# Copyright 1999-2022 Gentoo Authors
+# Distributed under the terms of the GNU General Public License v2
+
+EAPI=8
+
+CMAKE_BUILD_TYPE=Release
+CMAKE_MAKEFILE_GENERATOR="emake"
+inherit cmake fortran-2
+
+DESCRIPTION="Fortran library to compute positions of celestial bodies"
+HOMEPAGE="http://libthesky.sourceforge.net/"
+SRC_URI="https://downloads.sourceforge.net/${PN}/${P}.tar.gz
+	https://downloads.sourceforge.net/${PN}/libthesky-data-20160409.tar.bz2
+"
+
+LICENSE="GPL-3"
+SLOT="0"
+KEYWORDS="~amd64 ~x86"
+IUSE="static-libs"
+
+DEPEND="sci-libs/libsufr[static-libs?]"
+RDEPEND="${DEPEND}"
+
+src_unpack() {
+	default
+	gunzip -r "${S}"/man || die
+	mv "${WORKDIR}"/data "${S}" || die
+}
+
+src_configure() {
+	local mycmakeargs=(
+		-DCMAKE_VERBOSE_MAKEFILE=ON
+		-DCREATE_SHAREDLIB=ON
+		-DCREATE_STATICLIB=$(usex static-libs)
+	)
+	cmake_src_configure
+}
diff --git a/sci-astronomy/libthesky/metadata.xml b/sci-astronomy/libthesky/metadata.xml
index 1ce9631c7..08c750857 100644
--- a/sci-astronomy/libthesky/metadata.xml
+++ b/sci-astronomy/libthesky/metadata.xml
@@ -2,8 +2,8 @@
 <!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
 <pkgmetadata>
 	<maintainer type="person">
-		<email>AstroFloyd@gmail.com</email>
-		<name>AstroFloyd</name>
+		<email>git@vandersluys.nl</email>
+		<name>MarcvdSluys</name>
 	</maintainer>
 	<maintainer type="project">
 		<email>sci-astronomy@gentoo.org</email>
diff --git a/sci-astronomy/missfits/metadata.xml b/sci-astronomy/missfits/metadata.xml
deleted file mode 100644
index 136e880c2..000000000
--- a/sci-astronomy/missfits/metadata.xml
+++ /dev/null
@@ -1,16 +0,0 @@
-<?xml version="1.0" encoding="UTF-8"?>
-<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
-<pkgmetadata>
-	<maintainer type="project">
-		<email>sci-astronomy@gentoo.org</email>
-		<name>Gentoo Astronomy Project</name>
-	</maintainer>
-	<longdescription lang="en">
-MissFITS is a program that performs basic maintenance and packaging
-tasks on FITS files using an optimised FITS library. MissFITS can:
-* add/edit/remove FITS header keywords
-* split/join Multi-Extension-FITS (MEF) files
-* unpile/pile FITS data-cubes
-* create/check/update FITS checksums, using R. Seaman’s protocol.
-</longdescription>
-</pkgmetadata>
diff --git a/sci-astronomy/missfits/missfits-9999.ebuild b/sci-astronomy/missfits/missfits-9999.ebuild
deleted file mode 100644
index dbea211b2..000000000
--- a/sci-astronomy/missfits/missfits-9999.ebuild
+++ /dev/null
@@ -1,32 +0,0 @@
-# Copyright 1999-2016 Gentoo Foundation
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=6
-
-inherit subversion
-
-ESVN_REPO_URI="https://astromatic.net/pubsvn/software/${PN}/trunk"
-ESVN_OPTIONS="--trust-server-cert-failures=unknown-ca"
-
-SRC_URI=""
-KEYWORDS=""
-
-DESCRIPTION="Performs basic maintenance and packaging tasks on FITS files"
-HOMEPAGE="http://www.astromatic.net/software/missfits/"
-
-LICENSE="GPL-3"
-SLOT="0"
-IUSE="doc"
-
-RDEPEND=""
-DEPEND="${RDEPEND}"
-
-src_prepare() {
-	default
-	subversion_src_prepare
-}
-
-src_install () {
-	default
-	use doc && dodoc doc/*
-}
diff --git a/sci-astronomy/psfex/metadata.xml b/sci-astronomy/psfex/metadata.xml
deleted file mode 100644
index e1b68e8d9..000000000
--- a/sci-astronomy/psfex/metadata.xml
+++ /dev/null
@@ -1,17 +0,0 @@
-<?xml version="1.0" encoding="UTF-8"?>
-<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
-<pkgmetadata>
-	<maintainer type="project">
-		<email>sci-astronomy@gentoo.org</email>
-		<name>Gentoo Astronomy Project</name>
-	</maintainer>
-	<longdescription lang="en">
-PSFEx  (“PSF Extractor�) extracts models of the Point Spread
-Function (PSF) from FITS images processed with <pkg>sci-libs/sextractor</pkg>, and
-measures the quality of images. The generated PSF models can be used
-for model-fitting photometry or morphological analyses.
-</longdescription>
-	<use>
-		<flag name="plplot">Build with <pkg>sci-libs/plplot</pkg> to allow diagnostic plots during processing</flag>
-	</use>
-</pkgmetadata>
diff --git a/sci-astronomy/psfex/psfex-9999.ebuild b/sci-astronomy/psfex/psfex-9999.ebuild
deleted file mode 100644
index 84c1b4262..000000000
--- a/sci-astronomy/psfex/psfex-9999.ebuild
+++ /dev/null
@@ -1,58 +0,0 @@
-# Copyright 1999-2016 Gentoo Foundation
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=6
-
-inherit subversion autotools
-
-ESVN_REPO_URI="https://astromatic.net/pubsvn/software/${PN}/trunk"
-ESVN_OPTIONS="--trust-server-cert-failures=unknown-ca"
-SRC_URI=""
-KEYWORDS=""
-
-DESCRIPTION="Extracts models of the Point Spread Function from FITS images"
-HOMEPAGE="http://www.astromatic.net/software/psfex"
-
-LICENSE="GPL-3"
-SLOT="0"
-IUSE="doc threads plplot"
-
-RDEPEND="
-	sci-libs/atlas[lapack,threads=]
-	sci-libs/fftw:3.0
-	plplot? ( sci-libs/plplot:= )"
-DEPEND="${RDEPEND}"
-
-src_prepare() {
-	default
-	local mycblas=atlcblas  myclapack=atlclapack
-	if use threads; then
-		[[ -e ${EPREFIX}/usr/$(get_libdir)/libptcblas.so ]] && \
-			mycblas=ptcblas
-		[[ -e ${EPREFIX}/usr/$(get_libdir)/libptclapack.so ]] &&
-		myclapack=ptclapack
-	fi
-	# fix the configure and not the acx_atlas.m4. the eautoreconf will
-	# produce a configure giving  a wrong install Makefile target (to fix)
-	sed -e "s/-lcblas/-l${mycblas}/g" \
-		-e "s/AC_CHECK_LIB(cblas/AC_CHECK_LIB(${mycblas}/g" \
-		-e "s/-llapack/-l${myclapack}/g" \
-		-e "s/\(lapack_lib=\).*/\1${myclapack}/g" \
-		-e "s/AC_CHECK_LIB(lapack/AC_CHECK_LIB(${myclapack}/g" \
-		-i acx_atlas.m4 || die
-
-	eautoreconf
-	subversion_src_prepare
-}
-
-src_configure() {
-	econf \
-		--with-atlas-incdir="${EPREFIX}/usr/include/atlas" \
-		$(use_enable plplot) \
-		$(use_enable threads)
-}
-
-src_install () {
-	default
-	use doc && dodoc doc/*
-}
diff --git a/sci-astronomy/scamp/metadata.xml b/sci-astronomy/scamp/metadata.xml
deleted file mode 100644
index d4357bf76..000000000
--- a/sci-astronomy/scamp/metadata.xml
+++ /dev/null
@@ -1,16 +0,0 @@
-<?xml version="1.0" encoding="UTF-8"?>
-<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
-<pkgmetadata>
-	<maintainer type="project">
-		<email>sci-astronomy@gentoo.org</email>
-		<name>Gentoo Astronomy Project</name>
-	</maintainer>
-	<longdescription lang="en">
-SCAMP computes astrometric and photometric solutions from SExtractor catalogs
-and stores them in header files. These headers files can be read by SWarp to
-coadd images.
-</longdescription>
-	<use>
-		<flag name="plplot">Build with <pkg>sci-libs/plplot</pkg> to allow diagnostic plots during processing</flag>
-	</use>
-</pkgmetadata>
diff --git a/sci-astronomy/scamp/scamp-9999.ebuild b/sci-astronomy/scamp/scamp-9999.ebuild
deleted file mode 100644
index b5fa5eff4..000000000
--- a/sci-astronomy/scamp/scamp-9999.ebuild
+++ /dev/null
@@ -1,54 +0,0 @@
-# Copyright 1999-2016 Gentoo Foundation
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=6
-
-inherit subversion autotools
-
-ESVN_REPO_URI="https://astromatic.net/pubsvn/software/${PN}/trunk"
-ESVN_OPTIONS="--trust-server-cert-failures=unknown-ca"
-SRC_URI=""
-KEYWORDS=""
-
-DESCRIPTION="Astrometric and photometric solutions for astronomical images"
-HOMEPAGE="http://www.astromatic.net/software/scamp"
-
-LICENSE="GPL-3"
-SLOT="0"
-IUSE="doc plplot threads"
-
-RDEPEND="
-	net-misc/curl:=
-	sci-libs/atlas[lapack,threads=]
-	sci-libs/fftw:3.0
-	plplot? ( sci-libs/plplot:= )"
-DEPEND="${RDEPEND}"
-
-src_prepare() {
-	default
-	local mycblas=atlcblas myclapack=atlclapack
-	if use threads; then
-		[[ -e "${EPREFIX}"/usr/$(get_libdir)/libptcblas.so ]] && \
-			mycblas=ptcblas
-		[[ -e "${EPREFIX}"/usr/$(get_libdir)/libptclapack.so ]] && \
-			myclapack=ptclapack
-	fi
-	sed -e "s/-lcblas/-l${mycblas}/g"\
-		-e "/SEARCH_LIBS/s/ cblas,/${mycblas},/g" \
-		-e "/SEARCH_LIBS/s/lapack_atlas/${myclapack}/g" \
-		-i acx_atlas.m4 || die
-	eautoreconf
-	subversion_src_prepare
-}
-
-src_configure() {
-	econf \
-		--with-atlas-incdir="${EPREFIX}/usr/include/atlas" \
-		$(use_enable plplot) \
-		$(use_enable threads)
-}
-
-src_install () {
-	default
-	use doc && dodoc doc/*
-}
diff --git a/sci-astronomy/sextractor/metadata.xml b/sci-astronomy/sextractor/metadata.xml
deleted file mode 100644
index 9564e71e6..000000000
--- a/sci-astronomy/sextractor/metadata.xml
+++ /dev/null
@@ -1,22 +0,0 @@
-<?xml version="1.0" encoding="UTF-8"?>
-<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
-<pkgmetadata>
-	<maintainer type="project">
-		<email>sci-astronomy@gentoo.org</email>
-		<name>Gentoo Astronomy Project</name>
-	</maintainer>
-	<longdescription lang="en">
-SExtractor (Source Extractor) is a program that builds a catalogue of
-objects from an astronomical image. Although it is particularly
-oriented towards reduction of large scale galaxy-survey data, it
-performs rather well on moderately crowded star fields. It has the
-ability to automatically separate stars and galaxy using neural
-networks.
-</longdescription>
-	<use>
-		<flag name="modelfit">
-Enable profile model fitting, needs <pkg>sci-libs/atlas</pkg>
-and <pkg>sci-libs/fftw</pkg>
-</flag>
-	</use>
-</pkgmetadata>
diff --git a/sci-astronomy/sextractor/sextractor-9999.ebuild b/sci-astronomy/sextractor/sextractor-9999.ebuild
deleted file mode 100644
index 2837c4ab3..000000000
--- a/sci-astronomy/sextractor/sextractor-9999.ebuild
+++ /dev/null
@@ -1,66 +0,0 @@
-# Copyright 1999-2016 Gentoo Foundation
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=6
-
-inherit subversion autotools
-
-ESVN_REPO_URI="https://astromatic.net/pubsvn/software/${PN}/trunk"
-ESVN_OPTIONS="--trust-server-cert-failures=unknown-ca"
-SRC_URI=""
-KEYWORDS=""
-
-DESCRIPTION="Extract catalogs of sources from astronomical FITS images"
-HOMEPAGE="http://www.astromatic.net/software/sextractor"
-
-LICENSE="GPL-3"
-SLOT="0"
-
-IUSE="doc modelfit test threads"
-
-RDEPEND="
-	modelfit? ( sci-libs/atlas[lapack,threads=] sci-libs/fftw:3.0 )"
-DEPEND="${RDEPEND}"
-
-REQUIRED_USE="test? ( modelfit )"
-
-src_prepare() {
-	default
-	if use modelfit; then
-		local mycblas=atlcblas myclapack=atlclapack
-		if use threads; then
-			[[ -e "${EPREFIX}"/usr/$(get_libdir)/libptcblas.so ]] && \
-				mycblas=ptcblas
-			[[ -e "${EPREFIX}"/usr/$(get_libdir)/libptclapack.so ]] && \
-			myclapack=ptclapack
-		fi
-		sed -i \
-			-e "s/-lcblas/-l${mycblas}/g" \
-			-e "s/AC_CHECK_LIB(cblas/AC_CHECK_LIB(${mycblas}/g" \
-			-e "s/-llapack/-l${myclapack}/g" \
-			-e "s/AC_CHECK_LIB(lapack/AC_CHECK_LIB(${myclapack}/g" \
-			acx_atlas.m4 || die
-		eautoreconf
-	fi
-	subversion_src_prepare
-}
-
-src_configure() {
-	econf \
-		--with-atlas-incdir="${EPREFIX}/usr/include/atlas" \
-		$(use_enable modelfit model-fitting) \
-		$(use_enable threads)
-}
-
-src_install () {
-	default
-	CONFDIR=/usr/share/sextractor
-	insinto ${CONFDIR}
-	doins config/*
-	use doc && dodoc doc/*
-}
-
-pkg_postinst() {
-	elog "SExtractor examples configuration files are located in"
-	elog "${EROOT%/}/${CONFDIR} and are not loaded anymore by default."
-}
diff --git a/sci-astronomy/skymaker/metadata.xml b/sci-astronomy/skymaker/metadata.xml
deleted file mode 100644
index 268814ffc..000000000
--- a/sci-astronomy/skymaker/metadata.xml
+++ /dev/null
@@ -1,15 +0,0 @@
-<?xml version="1.0" encoding="UTF-8"?>
-<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
-<pkgmetadata>
-	<maintainer type="project">
-		<email>sci-astronomy@gentoo.org</email>
-		<name>Gentoo Astronomy Project</name>
-	</maintainer>
-	<longdescription lang="en">
-SkyMaker is a program that simulates astronomical images. It accepts
-object lists in ASCII generated by the Stuff program to produce
-realistic astronomical fields. There are various options for the user:
-build a realistic Point Spread Function, generate a list of stars and
-galaxies. Galaxies are modeled analytically.
-</longdescription>
-</pkgmetadata>
diff --git a/sci-astronomy/skymaker/skymaker-9999.ebuild b/sci-astronomy/skymaker/skymaker-9999.ebuild
deleted file mode 100644
index ef8ece542..000000000
--- a/sci-astronomy/skymaker/skymaker-9999.ebuild
+++ /dev/null
@@ -1,30 +0,0 @@
-# Copyright 1999-2016 Gentoo Foundation
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=6
-
-inherit subversion
-
-ESVN_REPO_URI="https://astromatic.net/pubsvn/software/${PN}/trunk"
-ESVN_OPTIONS="--trust-server-cert-failures=unknown-ca"
-SRC_URI=""
-KEYWORDS=""
-
-DESCRIPTION="Program that simulates astronomical images"
-HOMEPAGE="http://www.astromatic.net/software/skymaker"
-
-LICENSE="GPL-3"
-SLOT="0"
-IUSE="threads"
-
-RDEPEND="sci-libs/fftw:3.0"
-DEPEND="${RDEPEND}"
-
-src_prepare() {
-	default
-	subversion_src_prepare
-}
-
-src_configure() {
-	econf $(use_enable threads)
-}
diff --git a/sci-astronomy/starlink-bin/Manifest b/sci-astronomy/starlink-bin/Manifest
deleted file mode 100644
index e307212b5..000000000
--- a/sci-astronomy/starlink-bin/Manifest
+++ /dev/null
@@ -1,2 +0,0 @@
-DIST starlink-hikianalia-Linux-32bit.tar.gz 805812419 SHA256 166e8a6e8cf29cf7d0d6ed0d25c65372c2658b4028f8fe106f2bfd026789418a SHA512 776e72770986eeda6e539f56c7e4a35495dd856d5687bc399ed5a66f121259ae3f8c8f6191103e29ae2bd85147b27d568c8699f4d3073e8bacecdfaf8c1f764f WHIRLPOOL 441f2b1801a6b5306fdeef49635cf8af6fcb1d3afbb4aff5930957dc7d380efd36d774e2d015f3a9f52dd18bc9b9e5c2763e2c6ac98086209e7c866cce1f16c7
-DIST starlink-hikianalia-Linux-64bit.tar.gz 814753889 SHA256 ab7b06304dc5bcc19b60263f7d75515449959f96c3cec556555556d8654b3f06 SHA512 b0f085eda46c352a17984f2e7fd3f54dbd2c0bd0aeccbce46eaf3e24384538fc70ad5c3b7c616de2c82290922415f3fd76ed36a234b3d96624c7709b1579906a WHIRLPOOL 1a4363328fcc157ace804b613be7256cf5761e54b1f13b19e6ffb58d8aa3099511ce6a3132310d75ee396d720865f6f3d57d682c1d7920400eabcdf288a2d144
diff --git a/sci-astronomy/starlink-bin/metadata.xml b/sci-astronomy/starlink-bin/metadata.xml
deleted file mode 100644
index ef0e61480..000000000
--- a/sci-astronomy/starlink-bin/metadata.xml
+++ /dev/null
@@ -1,14 +0,0 @@
-<?xml version="1.0" encoding="UTF-8"?>
-<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
-<pkgmetadata>
-	<maintainer type="project">
-		<email>sci-astronomy@gentoo.org</email>
-		<name>Gentoo Astronomy Project</name>
-	</maintainer>
-	<longdescription lang="en">
-The Starlink Project, referred to by users as Starlink and by
-developers as simply The Project, was a UK astronomical computing
-project which supplied general-purpose data reduction
-software.
-</longdescription>
-</pkgmetadata>
diff --git a/sci-astronomy/starlink-bin/starlink-bin-20130413.ebuild b/sci-astronomy/starlink-bin/starlink-bin-20130413.ebuild
deleted file mode 100644
index 0632636b7..000000000
--- a/sci-astronomy/starlink-bin/starlink-bin-20130413.ebuild
+++ /dev/null
@@ -1,29 +0,0 @@
-# Copyright 1999-2014 Gentoo Foundation
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=5
-
-SP=starlink
-SR=hikianalia
-SRC_COM="http://ftp.jach.hawaii.edu/${SP}/${SR}/${SP}-${SR}"
-
-DESCRIPTION="Astronomical data processing software suite"
-HOMEPAGE="http://starlink.jach.hawaii.edu/starlink"
-SRC_URI="amd64? ( ${SRC_COM}-Linux-64bit.tar.gz )
-	x86? ( ${SRC_COM}-Linux-32bit.tar.gz )"
-
-LICENSE="GPL-2"
-SLOT="0"
-KEYWORDS="-* ~amd64 ~x86 ~amd64-linux ~x86-linux"
-IUSE=""
-
-RDEPEND=""
-DEPEND=""
-S="${WORKDIR}"
-
-src_install () {
-	dodir /usr
-	mv star-${SR} "${ED}"/usr || die
-	echo >> 99starlink "STARLINK_DIR=${EROOT%/}/usr/star-${SR}"
-	doenvd 99starlink
-}
diff --git a/sci-astronomy/stiff/metadata.xml b/sci-astronomy/stiff/metadata.xml
deleted file mode 100644
index c100b1037..000000000
--- a/sci-astronomy/stiff/metadata.xml
+++ /dev/null
@@ -1,13 +0,0 @@
-<?xml version="1.0" encoding="UTF-8"?>
-<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
-<pkgmetadata>
-	<maintainer type="project">
-		<email>sci-astronomy@gentoo.org</email>
-		<name>Gentoo Astronomy Project</name>
-	</maintainer>
-	<longdescription lang="en">
-STIFF is a program that convert scientific FITS images to the
-more popular TIFF, in 8 (grayscale) or 24 (true colour: 3 times 8) bits per
-pixel.
-</longdescription>
-</pkgmetadata>
diff --git a/sci-astronomy/stiff/stiff-9999.ebuild b/sci-astronomy/stiff/stiff-9999.ebuild
deleted file mode 100644
index debf04b3c..000000000
--- a/sci-astronomy/stiff/stiff-9999.ebuild
+++ /dev/null
@@ -1,39 +0,0 @@
-# Copyright 1999-2016 Gentoo Foundation
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=6
-
-inherit subversion
-
-ESVN_REPO_URI="https://astromatic.net/pubsvn/software/${PN}/trunk"
-ESVN_OPTIONS="--trust-server-cert-failures=unknown-ca"
-
-SRC_URI=""
-KEYWORDS=""
-
-DESCRIPTION="Converts astronomical FITS images to the TIFF format"
-HOMEPAGE="http://www.astromatic.net/software/stiff"
-
-LICENSE="GPL-3"
-SLOT="0"
-IUSE="doc threads"
-
-RDEPEND="
-	media-libs/tiff:0=
-	virtual/jpeg:0
-	sys-libs/zlib:0="
-DEPEND="${RDEPEND}"
-
-src_prepare() {
-	default
-	subversion_src_prepare
-}
-
-src_configure() {
-	econf $(use_enable threads)
-}
-
-src_install () {
-	default
-	use doc && dodoc doc/*
-}
diff --git a/sci-astronomy/stilts/Manifest b/sci-astronomy/stilts/Manifest
deleted file mode 100644
index 48b0fc9af..000000000
--- a/sci-astronomy/stilts/Manifest
+++ /dev/null
@@ -1 +0,0 @@
-DIST stilts-2.5.1.jar 10785962 BLAKE2B 151b7951b80daba76ef8dafd360e023e2f7f6ee75ffca73ef09c9f1edde67b2da2112f40946f701a5294b7b83f7b757650014ef696f1dd52dfeda090eeba1146 SHA512 bf67205fb8dcc6d38c812d842ff2e3b4f5a365f74341c109275499da2b8aa3437d74f3fa2aa0759c9eb921f389ccdc05067bb1145c150e5df01c447b7957518e
diff --git a/sci-astronomy/stilts/metadata.xml b/sci-astronomy/stilts/metadata.xml
deleted file mode 100644
index f2c84722f..000000000
--- a/sci-astronomy/stilts/metadata.xml
+++ /dev/null
@@ -1,17 +0,0 @@
-<?xml version="1.0" encoding="UTF-8"?>
-<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
-<pkgmetadata>
-	<maintainer type="project">
-		<email>sci-astronomy@gentoo.org</email>
-		<name>Gentoo Astronomy Project</name>
-	</maintainer>
-	<longdescription lang="en">
-The Starlink Tables Infrastructure Library Tool Set is a set of
-command-line tools based on STIL, the Starlink Tables Infrastructure
-Library. It deals with the processing of tabular data; the package
-has been designed for, but is not restricted to, astronomical tables
-such as object catalogues. Some of the tools are generic and can
-work with multiple formats (including FITS, VOTable, CSV, SQL and
-ASCII), and others are specific to the VOTable format.
-</longdescription>
-</pkgmetadata>
diff --git a/sci-astronomy/stilts/stilts-2.5.1.ebuild b/sci-astronomy/stilts/stilts-2.5.1.ebuild
deleted file mode 100644
index 5387c41d6..000000000
--- a/sci-astronomy/stilts/stilts-2.5.1.ebuild
+++ /dev/null
@@ -1,27 +0,0 @@
-# Copyright 1999-2014 Gentoo Foundation
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=5
-
-inherit java-pkg-2 versionator
-
-MYPV=$(replace_version_separator 2 '-')
-
-DESCRIPTION="Command line tools to process astronomical tables"
-HOMEPAGE="http://www.star.bris.ac.uk/~mbt/stilts/"
-SRC_URI="ftp://andromeda.star.bris.ac.uk/pub/star/${PN}/v${MYPV}/${PN}.jar -> ${P}.jar"
-
-LICENSE="GPL-2"
-SLOT="0"
-KEYWORDS="~amd64 ~x86 ~amd64-linux ~x86-linux"
-IUSE=""
-
-RDEPEND=">=virtual/jre-1.5"
-DEPEND=""
-
-S="${WORKDIR}"
-
-src_install() {
-	java-pkg_newjar "${DISTDIR}"/${P}.jar
-	java-pkg_dolauncher ${PN}
-}
diff --git a/sci-astronomy/stuff/metadata.xml b/sci-astronomy/stuff/metadata.xml
deleted file mode 100644
index ade4c41c5..000000000
--- a/sci-astronomy/stuff/metadata.xml
+++ /dev/null
@@ -1,13 +0,0 @@
-<?xml version="1.0" encoding="UTF-8"?>
-<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
-<pkgmetadata>
-	<maintainer type="project">
-		<email>sci-astronomy@gentoo.org</email>
-		<name>Gentoo Astronomy Project</name>
-	</maintainer>
-	<longdescription lang="en">
-Stuff is a program that simulates “perfect� astronomical
-catalogues. It generate object lists in ASCII which can read by the
-SkyMaker program to produce realistic astronomical fields.
-</longdescription>
-</pkgmetadata>
diff --git a/sci-astronomy/stuff/stuff-9999.ebuild b/sci-astronomy/stuff/stuff-9999.ebuild
deleted file mode 100644
index 03b5a2b8f..000000000
--- a/sci-astronomy/stuff/stuff-9999.ebuild
+++ /dev/null
@@ -1,31 +0,0 @@
-# Copyright 1999-2016 Gentoo Foundation
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=6
-
-inherit subversion
-
-ESVN_REPO_URI="https://astromatic.net/pubsvn/software/${PN}/trunk"
-ESVN_OPTIONS="--trust-server-cert-failures=unknown-ca"
-
-SRC_URI=""
-KEYWORDS=""
-
-DESCRIPTION="Tool for automatic generation of astronomical catalogs"
-HOMEPAGE="http://www.astromatic.net/software/stuff/"
-
-LICENSE="GPL-3"
-SLOT="0"
-IUSE="threads"
-
-RDEPEND=""
-DEPEND="${RDEPEND}"
-
-src_prepare() {
-	default
-	subversion_src_prepare
-}
-
-src_configure() {
-	econf $(use_enable threads)
-}
diff --git a/sci-astronomy/swarp/metadata.xml b/sci-astronomy/swarp/metadata.xml
deleted file mode 100644
index 209ee5d8f..000000000
--- a/sci-astronomy/swarp/metadata.xml
+++ /dev/null
@@ -1,12 +0,0 @@
-<?xml version="1.0" encoding="UTF-8"?>
-<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
-<pkgmetadata>
-	<maintainer type="project">
-		<email>sci-astronomy@gentoo.org</email>
-		<name>Gentoo Astronomy Project</name>
-	</maintainer>
-	<longdescription lang="en">
-SWarp takes astronomical FITS images with a WCS-like projection,
-resample and stack them all.
-</longdescription>
-</pkgmetadata>
diff --git a/sci-astronomy/swarp/swarp-9999.ebuild b/sci-astronomy/swarp/swarp-9999.ebuild
deleted file mode 100644
index 1b51d9193..000000000
--- a/sci-astronomy/swarp/swarp-9999.ebuild
+++ /dev/null
@@ -1,36 +0,0 @@
-# Copyright 1999-2016 Gentoo Foundation
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=6
-
-inherit subversion
-
-ESVN_REPO_URI="https://astromatic.net/pubsvn/software/${PN}/trunk"
-ESVN_OPTIONS="--trust-server-cert-failures=unknown-ca"
-SRC_URI=""
-KEYWORDS=""
-
-DESCRIPTION="Resample and coadd astronomical FITS images"
-HOMEPAGE="http://www.astromatic.net/software/swarp"
-
-LICENSE="GPL-3"
-SLOT="0"
-
-IUSE="doc threads"
-
-RDEPEND=""
-DEPEND="${RDEPEND}"
-
-src_prepare() {
-	default
-	subversion_src_prepare
-}
-
-src_configure() {
-	econf $(use_enable threads)
-}
-
-src_install () {
-	default
-	use doc && dodoc doc/*
-}
diff --git a/sci-astronomy/topcat/Manifest b/sci-astronomy/topcat/Manifest
deleted file mode 100644
index 62ab2d457..000000000
--- a/sci-astronomy/topcat/Manifest
+++ /dev/null
@@ -1,2 +0,0 @@
-DIST topcat-4.0.1-full.jar 26377995 BLAKE2B a56af802e17f0377a33e57272e7b84f592b51489f6fc35ae05a6a97965527c849d28d79cc732608db65ba65424f622b17345f30ffe9fa70d96f076a63f9143e6 SHA512 112876a177a2a2de3a086a8b72f4100472608733f9701360e4f25376907b6803550fc79e0567405165daafb739bd7bb077f3e0928a36637ab5443f9dfaa15e55
-DIST topcat-4.0.1-lite.jar 19636175 BLAKE2B ea9fd114457d87060a20cb487d7bd1b051fad8e58d2e7e8daf16f790beb2c25f5c2522395c43ae09423807048437b598624d7243ad2902e394cfbedfd2ce304a SHA512 9e88a859fec50dcd97b546acc5d24179f0652e3f6335403357bb832ce29c51aa23143da086a60bb5fae35884870ce161e22ecca02aaaff23dd58f60f0b3fa2e4
diff --git a/sci-astronomy/topcat/metadata.xml b/sci-astronomy/topcat/metadata.xml
deleted file mode 100644
index 65b998b7d..000000000
--- a/sci-astronomy/topcat/metadata.xml
+++ /dev/null
@@ -1,17 +0,0 @@
-<?xml version="1.0" encoding="UTF-8"?>
-<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
-<pkgmetadata>
-	<maintainer type="project">
-		<email>sci-astronomy@gentoo.org</email>
-		<name>Gentoo Astronomy Project</name>
-	</maintainer>
-	<longdescription lang="en">
-Tool for OPerations on Catalogues And Tables is an interactive
-graphical viewer and editor for tabular data. Its aim is to provide
-most of the facilities that astronomers need for analysis and
-manipulation of source catalogues and other tables, though it can be
-used for non-astronomical data as well. It understands a number of
-different astronomically important formats (including FITS and
-VOTable) and more formats can be added. 
-</longdescription>
-</pkgmetadata>
diff --git a/sci-astronomy/topcat/topcat-4.0.1.ebuild b/sci-astronomy/topcat/topcat-4.0.1.ebuild
deleted file mode 100644
index 9695a4f2d..000000000
--- a/sci-astronomy/topcat/topcat-4.0.1.ebuild
+++ /dev/null
@@ -1,35 +0,0 @@
-# Copyright 1999-2014 Gentoo Foundation
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=5
-
-inherit java-pkg-2 versionator
-MYPV=$(replace_version_separator 2 '-')
-
-DESCRIPTION="Interactive graphical viewer and editor for astronomical tables"
-HOMEPAGE="http://www.star.bris.ac.uk/~mbt/topcat/"
-SRC_COM="ftp://andromeda.star.bris.ac.uk/pub/star/${PN}/v${MYPV}"
-SRC_URI="${SRC_COM}/${PN}-lite.jar -> ${P}-lite.jar
-	!minimal? ( ${SRC_COM}/${PN}-full.jar -> ${P}-full.jar )"
-
-LICENSE="GPL-2"
-SLOT="0"
-KEYWORDS="~amd64 ~x86 ~amd64-linux ~x86-linux"
-IUSE="+minimal"
-
-RDEPEND=">=virtual/jre-1.5"
-DEPEND=""
-
-S="${WORKDIR}"
-
-src_install() {
-	java-pkg_newjar "${DISTDIR}"/${P}-lite.jar ${PN}-lite.jar
-	java-pkg_dolauncher ${PN}-lite
-	if use minimal; then
-		dosym ${PN}-lite /usr/bin/${PN}
-	else
-		java-pkg_newjar "${DISTDIR}"/${P}-full.jar
-		java-pkg_dolauncher ${PN}-full
-		dosym ${PN}-full /usr/bin/${PN}
-	fi
-}
diff --git a/sci-astronomy/weightwatcher/metadata.xml b/sci-astronomy/weightwatcher/metadata.xml
deleted file mode 100644
index 8af502859..000000000
--- a/sci-astronomy/weightwatcher/metadata.xml
+++ /dev/null
@@ -1,14 +0,0 @@
-<?xml version="1.0" encoding="UTF-8"?>
-<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
-<pkgmetadata>
-	<maintainer type="project">
-		<email>sci-astronomy@gentoo.org</email>
-		<name>Gentoo Astronomy Project</name>
-	</maintainer>
-	<longdescription lang="en">
-WeightWatcher is a program that combines weight-maps, flag-maps and
-polygon data in order to produce control maps which can directly be
-used in astronomical image-processing packages like Drizzle,
-<pkg>sci-astronomy/sextractor</pkg> or <pkg>sci-astronomy/swarp</pkg>.
-</longdescription>
-</pkgmetadata>
diff --git a/sci-astronomy/weightwatcher/weightwatcher-9999.ebuild b/sci-astronomy/weightwatcher/weightwatcher-9999.ebuild
deleted file mode 100644
index 35633e2d4..000000000
--- a/sci-astronomy/weightwatcher/weightwatcher-9999.ebuild
+++ /dev/null
@@ -1,32 +0,0 @@
-# Copyright 1999-2016 Gentoo Foundation
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=6
-
-inherit subversion
-
-ESVN_REPO_URI="https://astromatic.net/pubsvn/software/${PN}/trunk"
-ESVN_OPTIONS="--trust-server-cert-failures=unknown-ca"
-
-SRC_URI=""
-KEYWORDS=""
-
-DESCRIPTION="Combine weight maps and polygon for astronomical images weighting"
-HOMEPAGE="http://www.astromatic.net/software/weightwatcher/"
-
-LICENSE="GPL-3"
-SLOT="0"
-IUSE="doc"
-
-RDEPEND=""
-DEPEND="${RDEPEND}"
-
-src_prepare() {
-	default
-	subversion_src_prepare
-}
-
-src_install () {
-	default
-	use doc && dodoc doc/*
-}
diff --git a/sci-astronomy/zebra/Manifest b/sci-astronomy/zebra/Manifest
deleted file mode 100644
index 50c07d577..000000000
--- a/sci-astronomy/zebra/Manifest
+++ /dev/null
@@ -1 +0,0 @@
-DIST zebra-1.01.tar.gz 1574479 BLAKE2B 54b52f25312a9bf5c24cc7ba9dacb66a1fb0e7d931e4926788c80757cf7e4e114fc4b7c47498906e6ba32838be3236d894ffeddddf885c3d9d53f0c6eb258cec SHA512 68372227d095b84301099f5fbc541778642de6dcbdb2d76f33215263752ef452145fb061132a940c14fb488617f7b95ddc6aea298063cba44e0c17bd4d626f80
diff --git a/sci-astronomy/zebra/metadata.xml b/sci-astronomy/zebra/metadata.xml
deleted file mode 100644
index b9760ac17..000000000
--- a/sci-astronomy/zebra/metadata.xml
+++ /dev/null
@@ -1,25 +0,0 @@
-<?xml version="1.0" encoding="UTF-8"?>
-<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
-<pkgmetadata>
-	<maintainer type="project">
-		<email>sci-astronomy@gentoo.org</email>
-		<name>Gentoo Astronomy Project</name>
-	</maintainer>
-	<longdescription lang="en">
-The Zurich Extragalactic Bayesian Redshift Analyzer is a software to
-compute and analyze photometric redshifts of galaxies.
-ZEBRA combines and extends several of the classical approaches to
-produce accurate photometric redshifts down to faint magnitudes. In
-particular, ZEBRA uses the template-fitting approach to produce
-Maximum Likelihood and Bayesian redshift estimates based on:
-* An automatic iterative technique to correct the original set of
-galaxy templates to best represent the SEDs of real galaxies at
-different redshifts;
-* A training set of spectroscopic redshifts for a small fraction of
-the photometric sample, to improve the robustness of the
-photometric redshift estimates; and
-* An iterative technique for Bayesian redshift estimates, which
-extracts the full two-dimensional redshift and template likelihood
-function for each galaxy.
-</longdescription>
-</pkgmetadata>
diff --git a/sci-astronomy/zebra/zebra-1.01.ebuild b/sci-astronomy/zebra/zebra-1.01.ebuild
deleted file mode 100644
index b8949e212..000000000
--- a/sci-astronomy/zebra/zebra-1.01.ebuild
+++ /dev/null
@@ -1,42 +0,0 @@
-# Copyright 1999-2014 Gentoo Foundation
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=5
-
-inherit autotools-utils toolchain-funcs
-
-DESCRIPTION="Galaxy redhift Bayesian analyzer"
-HOMEPAGE="http://www.astro.phys.ethz.ch/exgal_ocosm/zebra/index.html"
-SRC_URI="http://www.astro.phys.ethz.ch/exgal_ocosm/zebra/tar/${P}.tar.gz"
-
-LICENSE="GPL-3"
-SLOT="0"
-KEYWORDS="~amd64 ~x86"
-IUSE="doc examples"
-
-RDEPEND="
-	sci-libs/gsl
-	sci-libs/lapackpp
-	virtual/blas
-	virtual/cblas
-	virtual/lapack"
-DEPEND="${RDEPEND}
-	virtual/pkgconfig"
-
-src_configure() {
-	myeconfargs+=(
-		--with-blas="$($(tc-getPKG_CONFIG) --libs blas)"
-		--with-cblas="$($(tc-getPKG_CONFIG) --libs cblas)"
-		--with-lapack="$($(tc-getPKG_CONFIG) --libs lapack)"
-	)
-	autotools-utils_src_configure
-}
-
-src_install() {
-	autotools-utils_src_install
-	use doc && dodoc doc/*.pdf
-	if use examples; then
-		insinto /usr/share/doc/${PF}
-		doins -r scripts examples
-	fi
-}
diff --git a/sci-astronomy/zpeg/Manifest b/sci-astronomy/zpeg/Manifest
deleted file mode 100644
index ce1489fe2..000000000
--- a/sci-astronomy/zpeg/Manifest
+++ /dev/null
@@ -1 +0,0 @@
-DIST zpeg_5.23.tar.gz 37541120 BLAKE2B 9d43befef6d25a47c4f4c0ddc1376879e6e8f89938fa9ce7419668c47dabfe4ed78ba30fa6a52511e99c1409e7dfa8fcd37501a398b19c189011a75e67bb8939 SHA512 4bc05bb504531317de7dbb76b9f949ee346b401d3ab90e5a4a08d1b268f98aa1f2ca2895003a48a136e0f9316e976daa5ee2198e31353eaf7462ad40a302cadc
diff --git a/sci-astronomy/zpeg/metadata.xml b/sci-astronomy/zpeg/metadata.xml
deleted file mode 100644
index fbf281467..000000000
--- a/sci-astronomy/zpeg/metadata.xml
+++ /dev/null
@@ -1,17 +0,0 @@
-<?xml version="1.0" encoding="UTF-8"?>
-<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
-<pkgmetadata>
-	<maintainer type="project">
-		<email>sci-astronomy@gentoo.org</email>
-		<name>Gentoo Astronomy Project</name>
-	</maintainer>
-	<longdescription lang="en">
-Z-PEG is a software anybody can use to compute photometric
-redshifts. In short, Z-PEG performs a chi square minimization of the
-distance between observed photometric bands and synthetic photometry
-from galaxies simulated by the evolutionary code PEGASE.
-</longdescription>
-	<use>
-		<flag name="gdl">Install GDL/IDL plotting routines</flag>
-	</use>
-</pkgmetadata>
diff --git a/sci-astronomy/zpeg/zpeg-5.23.ebuild b/sci-astronomy/zpeg/zpeg-5.23.ebuild
deleted file mode 100644
index b1c9e406d..000000000
--- a/sci-astronomy/zpeg/zpeg-5.23.ebuild
+++ /dev/null
@@ -1,62 +0,0 @@
-# Copyright 1999-2014 Gentoo Foundation
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=5
-
-inherit fortran-2
-
-MYP=${PN}_${PV}
-
-DESCRIPTION="Galaxy photometric redshifts from evolutionary synthesis"
-HOMEPAGE="http://imacdlb.iap.fr:8080/cgi-bin/zpeg/zpeg.pl"
-SRC_URI="ftp://ftp.iap.fr/pub/from_users/leborgne/${PN}/${MYP}.tar.gz"
-
-SLOT="0"
-LICENSE="GPL-2"
-KEYWORDS="~amd64 ~x86 ~amd64-linux ~x86-linux"
-IUSE="gdl"
-
-RDEPEND="gdl? ( dev-lang/gdl )"
-DEPEND=""
-
-S="${WORKDIR}/${MYP}"
-
-FORTRAN_STANDARD="90"
-
-src_prepare() {
-	# save configure for tests
-	cp configure{,.orig} || die
-	# install data in FHS
-	sed -i \
-		-e "s:ZPEG_ROOT=.*:ZPEG_ROOT=${EPREFIX}/usr/share/${PN}:" \
-		configure || die
-}
-
-src_compile() {
-	# not worth debugging parallel build failures which is due to
-	# fortran modules missing dependencies)
-	emake -j1 -C src
-}
-
-src_test() {
-	# test only works with hardcoded path, so reconfigure and recompile
-	mv bin/zpeg{,.orig} || die
-	mv configure{.orig,} || die
-	emake -C src clean && econf && emake -j1 -C src
-	cd test
-	../bin/zpeg -V ZPEG1_cata.cat -o hdf.zpeg -p hdf.par -t hdf.par.tmp || die
-	mv bin/zpeg{.orig,} || die
-}
-
-src_install() {
-	dobin bin/zpeg
-	insinto /usr/share/${PN}
-	doins -r data VERSION
-	dodoc HISTORY
-	echo > 99zpeg "ZPEG_ROOT=${EROOT}/usr/share/${PN}"
-	doenvd 99zpeg
-	if use gdl; then
-		insinto /usr/share/gnudatalanguage/${PN}
-		doins idl/*.pro
-	fi
-}
diff --git a/sci-biology/ABI-connectivity-data/ABI-connectivity-data-0.1-r1.ebuild b/sci-biology/ABI-connectivity-data/ABI-connectivity-data-0.1-r1.ebuild
new file mode 100644
index 000000000..fe4926644
--- /dev/null
+++ b/sci-biology/ABI-connectivity-data/ABI-connectivity-data-0.1-r1.ebuild
@@ -0,0 +1,32 @@
+# Copyright 1999-2023 Gentoo Authors
+# Distributed under the terms of the GNU General Public License v2
+
+EAPI=8
+
+inherit check-reqs
+
+DESCRIPTION="Connectivity data from the Allen Mouse Brain data portal"
+HOMEPAGE="https://github.com/IBT-FMI/ABI-connectivity-data_generator"
+SRC_URI="https://resources.chymera.eu/distfiles/${P}.tar.xz"
+
+LICENSE="fairuse"
+SLOT="0"
+KEYWORDS="~amd64 ~x86 ~amd64-linux ~x86-linux"
+
+RDEPEND=""
+DEPEND=""
+
+pkg_pretend() {
+	CHECKREQS_DISK_BUILD="3G"
+	CHECKREQS_DISK_USR="3G"
+	CHECKREQS_DISK_VAR="3G"
+	check-reqs_pkg_pretend
+}
+
+# We disable this phase to not check requirements twice.
+pkg_setup() { :; }
+
+src_install() {
+	insinto "/usr/share/${PN}"
+	doins -r *
+}
diff --git a/sci-biology/ABI-connectivity-data/ABI-connectivity-data-0.1.ebuild b/sci-biology/ABI-connectivity-data/ABI-connectivity-data-0.1.ebuild
deleted file mode 100644
index cc3bb4bad..000000000
--- a/sci-biology/ABI-connectivity-data/ABI-connectivity-data-0.1.ebuild
+++ /dev/null
@@ -1,32 +0,0 @@
-# Copyright 1999-2019 Gentoo Authors
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=7
-
-inherit check-reqs
-
-DESCRIPTION="Connectivity data from the Allen Mouse Brain data portal"
-HOMEPAGE="https://github.com/IBT-FMI/ABI-connectivity-data"
-SRC_URI="http://chymera.eu/distfiles/${P}.tar.xz"
-
-LICENSE="fairuse"
-SLOT="0"
-KEYWORDS="~amd64 ~x86 ~amd64-linux ~x86-linux"
-
-RDEPEND=""
-DEPEND=""
-
-pkg_pretend() {
-	CHECKREQS_DISK_BUILD="3G"
-	CHECKREQS_DISK_USR="3G"
-	CHECKREQS_DISK_VAR="3G"
-	check-reqs_pkg_pretend
-}
-
-# We disable this phase to not check requirements twice.
-pkg_setup() { :; }
-
-src_install() {
-	insinto "/usr/share/${PN}"
-	doins -r *
-}
diff --git a/sci-biology/ABI-connectivity-data/ABI-connectivity-data-0.2.ebuild b/sci-biology/ABI-connectivity-data/ABI-connectivity-data-0.2.ebuild
new file mode 100644
index 000000000..fe4926644
--- /dev/null
+++ b/sci-biology/ABI-connectivity-data/ABI-connectivity-data-0.2.ebuild
@@ -0,0 +1,32 @@
+# Copyright 1999-2023 Gentoo Authors
+# Distributed under the terms of the GNU General Public License v2
+
+EAPI=8
+
+inherit check-reqs
+
+DESCRIPTION="Connectivity data from the Allen Mouse Brain data portal"
+HOMEPAGE="https://github.com/IBT-FMI/ABI-connectivity-data_generator"
+SRC_URI="https://resources.chymera.eu/distfiles/${P}.tar.xz"
+
+LICENSE="fairuse"
+SLOT="0"
+KEYWORDS="~amd64 ~x86 ~amd64-linux ~x86-linux"
+
+RDEPEND=""
+DEPEND=""
+
+pkg_pretend() {
+	CHECKREQS_DISK_BUILD="3G"
+	CHECKREQS_DISK_USR="3G"
+	CHECKREQS_DISK_VAR="3G"
+	check-reqs_pkg_pretend
+}
+
+# We disable this phase to not check requirements twice.
+pkg_setup() { :; }
+
+src_install() {
+	insinto "/usr/share/${PN}"
+	doins -r *
+}
diff --git a/sci-biology/ABI-connectivity-data/Manifest b/sci-biology/ABI-connectivity-data/Manifest
index 7eba5b6fb..59b871e12 100644
--- a/sci-biology/ABI-connectivity-data/Manifest
+++ b/sci-biology/ABI-connectivity-data/Manifest
@@ -1 +1,2 @@
-DIST ABI-connectivity-data-0.1.tar.xz 2748929360 BLAKE2B 1380c6a8442136ab8a4f4d8ad7ff0cec844836243deb877f771582f93375ecdf8437b9095919a4eb291bca91775114d0d695eb1fe70c2992a6837371fcf6b78b SHA512 eec1fb1f7a96c8442a134172f476e5b00522f78dda2bc72564daef838e8604a92fdacd2b7de3288b3fb529891af1b68e7f76bca3184fa63796804b2ffeee9cb9
+DIST ABI-connectivity-data-0.1.tar.xz 2748905328 BLAKE2B c404798d2ecbe740d7cfae295aeab52d99086e3effa6dc23eca42409990a7ed2cdf7d448010fc0f08178a7dfd638a083fb87afcc66797dc4bf7b5095cec02253 SHA512 91643114456362327e617db682636bc564c131ebd797dc4edda493c2d96c2beb9567ef87b3baf8bce77815a755de8ea010fa6399460a839070f1a179d07b755d
+DIST ABI-connectivity-data-0.2.tar.xz 2746778304 BLAKE2B 70ca32dd0a40fe6d6f3c402af9e4c8e1884d9ef8ecf98fd9751f0cd0c4f10b1923e6be4f0137e4d424705009bbbe1ca3c74ef5145189fa18c9970c40fc8f9fa5 SHA512 60538a45defaec32b126f7dd639f61fb030d9ef4830ff9ebb63736087493935312209dbd6591eb245a72be1217c35a3f877a7549918cc1bc39dfd34b2c23d478
diff --git a/sci-biology/ABI-connectivity-data/metadata.xml b/sci-biology/ABI-connectivity-data/metadata.xml
index 15c6fa66f..4f11f95ba 100644
--- a/sci-biology/ABI-connectivity-data/metadata.xml
+++ b/sci-biology/ABI-connectivity-data/metadata.xml
@@ -9,8 +9,7 @@
 		<email>sci@gentoo.org</email>
 		<name>Gentoo Science Project</name>
 	</maintainer>
-	<longdescription lang="en">
-		A data library of neural projections collected 
-		from the Allen Mouse Brain Connectivity data portal.
-	</longdescription>
+	<upstream>
+		<remote-id type="github">IBT-FMI/ABI-connectivity-data_generator</remote-id>
+	</upstream>
 </pkgmetadata>
diff --git a/sci-biology/ABI-expression-data/ABI-expression-data-0.1.ebuild b/sci-biology/ABI-expression-data/ABI-expression-data-0.1.ebuild
deleted file mode 100644
index 8fc372e55..000000000
--- a/sci-biology/ABI-expression-data/ABI-expression-data-0.1.ebuild
+++ /dev/null
@@ -1,34 +0,0 @@
-# Copyright 1999-2019 Gentoo Authors
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=7
-
-inherit check-reqs
-
-DESCRIPTION="Gene expression data form the Allen Mouse Brain data portal"
-HOMEPAGE="https://github.com/IBT-FMI/ABI-geneexpression-data"
-SRC_URI="
-	http://chymera.eu/distfiles/${P}.tar.xz
-	"
-
-LICENSE="fairuse"
-SLOT="0"
-KEYWORDS="~amd64 ~x86 ~amd64-linux ~x86-linux"
-
-RDEPEND=""
-DEPEND=""
-
-pkg_pretend() {
-	CHECKREQS_DISK_BUILD="7G"
-	CHECKREQS_DISK_USR="7G"
-	CHECKREQS_DISK_VAR="7G"
-	check-reqs_pkg_pretend
-}
-
-# We disable this phase to not check requirements twice.
-pkg_setup() { :; }
-
-src_install() {
-	insinto "/usr/share/${PN}"
-	doins -r *
-}
diff --git a/sci-biology/ABI-expression-data/ABI-expression-data-0.2.ebuild b/sci-biology/ABI-expression-data/ABI-expression-data-0.2.ebuild
new file mode 100644
index 000000000..2016de083
--- /dev/null
+++ b/sci-biology/ABI-expression-data/ABI-expression-data-0.2.ebuild
@@ -0,0 +1,34 @@
+# Copyright 1999-2021 Gentoo Authors
+# Distributed under the terms of the GNU General Public License v2
+
+EAPI=7
+
+inherit check-reqs
+
+DESCRIPTION="Gene expression data form the Allen Mouse Brain data portal"
+HOMEPAGE="https://github.com/IBT-FMI/ABI-expression-data_generator"
+SRC_URI="
+	https://resources.chymera.eu/distfiles/${P}.tar.xz
+	"
+
+LICENSE="fairuse"
+SLOT="0"
+KEYWORDS="~amd64 ~x86 ~amd64-linux ~x86-linux"
+
+RDEPEND=""
+DEPEND=""
+
+pkg_pretend() {
+	CHECKREQS_DISK_BUILD="7G"
+	CHECKREQS_DISK_USR="7G"
+	CHECKREQS_DISK_VAR="7G"
+	check-reqs_pkg_pretend
+}
+
+# We disable this phase to not check requirements twice.
+pkg_setup() { :; }
+
+src_install() {
+	insinto "/usr/share/${PN}"
+	doins -r *
+}
diff --git a/sci-biology/ABI-expression-data/Manifest b/sci-biology/ABI-expression-data/Manifest
index 78ec76e0c..dc4f3d13a 100644
--- a/sci-biology/ABI-expression-data/Manifest
+++ b/sci-biology/ABI-expression-data/Manifest
@@ -1 +1 @@
-DIST ABI-expression-data-0.1.tar.xz 4059922432 BLAKE2B 367db2c707c83423c4b0d0755abdb823acc376f75e56be3dd1ff27b7fbed216dd0497874bbd4889c2621b6391e3891bd4c3ce20aaade9f0455bddf462a4f449b SHA512 6d152a5c17389135b6e6f8bce6af59a3adf244c166d87e8ea9bb29300f28e298c95016123dedeb59c262b2edd4fa51041b1d6adedd84c474d770d19f90f6f111
+DIST ABI-expression-data-0.2.tar.xz 5945203160 BLAKE2B e34891b51360c79818e696fd3ace5565151ff9acd8c62c72c59bd09d8ad433e53db0ae6b78b291bdef2955afa4b23b2ce13e9cef90a2bd0585121458fad8f3ed SHA512 ba2346b9904782f32216b24bb969928ef5eddb7d9d5d5aef0ccd5a60fe9e441d017a9f43f4df2fb258af51e27aed39f9b8a44d192894eb9fcc742d6655599c62
diff --git a/sci-biology/ABI-expression-data/metadata.xml b/sci-biology/ABI-expression-data/metadata.xml
index 3c5138f6b..6de417d21 100644
--- a/sci-biology/ABI-expression-data/metadata.xml
+++ b/sci-biology/ABI-expression-data/metadata.xml
@@ -9,8 +9,4 @@
 		<email>sci@gentoo.org</email>
 		<name>Gentoo Science Project</name>
 	</maintainer>
-	<longdescription lang="en">
-		A data library of gene expression maps collected
-		from the Allen Mouse Brain data portal.
-	</longdescription>
 </pkgmetadata>
diff --git a/sci-biology/ANGLE-bin/ANGLE-bin-20080813-r1.ebuild b/sci-biology/ANGLE-bin/ANGLE-bin-20080813-r1.ebuild
index 5716596e3..f6453cd6a 100644
--- a/sci-biology/ANGLE-bin/ANGLE-bin-20080813-r1.ebuild
+++ b/sci-biology/ANGLE-bin/ANGLE-bin-20080813-r1.ebuild
@@ -1,7 +1,9 @@
-# Copyright 1999-2016 Gentoo Foundation
+# Copyright 1999-2021 Gentoo Authors
 # Distributed under the terms of the GNU General Public License v2
 
-EAPI=6
+EAPI=7
+
+inherit perl-functions
 
 DESCRIPTION="CDS prediction overcoming sequencing errors in unfinished cDNA"
 HOMEPAGE="http://bioinformatics.cenargen.embrapa.br/portrait/download"
@@ -14,15 +16,18 @@ SRC_URI="http://bioinformatics.cenargen.embrapa.br/portrait/download/angle.tar.g
 LICENSE="BSD"
 SLOT="0"
 KEYWORDS="~amd64 ~x86"
-IUSE=""
 
-S="${WORKDIR}"/angle
+S="${WORKDIR}/angle"
+
+RDEPEND="
+	sys-libs/libstdc++-v3
+	dev-lang/perl
+"
 
 QA_PREBUILT="opt/*"
 
 src_install(){
-	into /opt
-	dobin *.pl
+	perl_domodule *.pl
 	use amd64 && dobin ANGLE-linux64 ANGLE-linux64DP
 	use x86 && dobin ANGLE-linux32 ANGLE-linux32DP
 	dodoc README.txt
diff --git a/sci-biology/AlignGraph/AlignGraph-9999.ebuild b/sci-biology/AlignGraph/AlignGraph-9999.ebuild
index 46d1029fd..f48b436ee 100644
--- a/sci-biology/AlignGraph/AlignGraph-9999.ebuild
+++ b/sci-biology/AlignGraph/AlignGraph-9999.ebuild
@@ -1,20 +1,16 @@
-# Copyright 1999-2015 Gentoo Foundation
+# Copyright 1999-2021 Gentoo Authors
 # Distributed under the terms of the GNU General Public License v2
 
-EAPI=5
+EAPI=7
 
 inherit toolchain-funcs
 
-if [ "$PV" == "9999" ]; then
-	inherit git-r3
-fi
-
 DESCRIPTION="Reference-genome-assisted asssembly of contigs/scaffolds using PE reads"
 HOMEPAGE="https://github.com/baoe/AlignGraph
 	http://bioinformatics.oxfordjournals.org/content/30/12/i319.long"
 if [ "$PV" == "9999" ]; then
+	inherit git-r3
 	EGIT_REPO_URI="https://github.com/baoe/AlignGraph.git"
-	KEYWORDS=""
 else
 	SRC_URI=""
 	KEYWORDS=""
@@ -22,13 +18,13 @@ fi
 
 LICENSE="Artistic-2"
 SLOT="0"
-IUSE=""
 
 DEPEND=""
 RDEPEND="${DEPEND}
 	sci-biology/mummer
 	sci-biology/blat
-	sci-biology/bowtie"
+	sci-biology/bowtie
+"
 
 # AlignGraph runs the alignment steps with BLAT and Bowtie2 automatically, but both
 # need to be installed on the system. AlignGraph’s run time is currently 23–57 min
diff --git a/sci-biology/Atlas-Link/Atlas-Link-0.01-r1.ebuild b/sci-biology/Atlas-Link/Atlas-Link-0.01-r1.ebuild
deleted file mode 100644
index 9324bc4f8..000000000
--- a/sci-biology/Atlas-Link/Atlas-Link-0.01-r1.ebuild
+++ /dev/null
@@ -1,26 +0,0 @@
-# Copyright 1999-2016 Gentoo Foundation
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=6
-
-inherit perl-module
-
-DESCRIPTION="Link and orient genome sequence contigs using mate-pair information"
-HOMEPAGE="https://www.hgsc.bcm.edu/software/atlas-link"
-SRC_URI="https://www.hgsc.bcm.edu/sites/default/files/software/Atlas_Link/Atlas-link.tar.gz -> ${P}.tar.gz"
-
-LICENSE="HGSC-BCM"
-SLOT="0"
-KEYWORDS=""
-IUSE=""
-
-# https://github.com/gitpan/Algorithm-ClusterPoints
-DEPEND="
-	dev-lang/perl
-	dev-perl/Graph
-	dev-perl/Algorithm-ClusterPoints
-	dev-perl/XML-DOM
-	dev-perl/Statistics-Descriptive"
-RDEPEND="${DEPEND}"
-
-S="${WORKDIR}"/Atlas-link
diff --git a/sci-biology/Atlas-Link/Manifest b/sci-biology/Atlas-Link/Manifest
deleted file mode 100644
index 3adee8c10..000000000
--- a/sci-biology/Atlas-Link/Manifest
+++ /dev/null
@@ -1 +0,0 @@
-DIST Atlas-Link-0.01.tar.gz 4212464 BLAKE2B ab82fc21560ca1f04490df8e0c67df74f4c662965d6788f85c6306990f407cfb6bf48b74b1607c484445ea375ff397a9d11d2e5973376ee151c2948c7c52b5d0 SHA512 ac3595ca81034de2eb2b4dc206e6e29c59fbb4fededfd2dee3b597ce47bc436907587fc59ac753d81c4ca0fc627e0a9961ebebd7bfcc002df634466c17fd2bce
diff --git a/sci-biology/Atlas-Link/metadata.xml b/sci-biology/Atlas-Link/metadata.xml
deleted file mode 100644
index 138cb7705..000000000
--- a/sci-biology/Atlas-Link/metadata.xml
+++ /dev/null
@@ -1,12 +0,0 @@
-<?xml version="1.0" encoding="UTF-8"?>
-<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
-<pkgmetadata>
-	<maintainer type="person">
-		<email>mmokrejs@fold.natur.cuni.cz</email>
-		<name>Martin Mokrejs</name>
-	</maintainer>
-	<maintainer type="project">
-		<email>sci-biology@gentoo.org</email>
-		<name>Gentoo Biology Project</name>
-	</maintainer>
-</pkgmetadata>
diff --git a/sci-biology/Atlas/Atlas-2005.ebuild b/sci-biology/Atlas/Atlas-2005.ebuild
deleted file mode 100644
index cfe09e0f7..000000000
--- a/sci-biology/Atlas/Atlas-2005.ebuild
+++ /dev/null
@@ -1,40 +0,0 @@
-# Copyright 1999-2016 Gentoo Foundation
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=5
-
-inherit toolchain-funcs
-
-DESCRIPTION="Atlas Whole Genome Assembly Suite"
-HOMEPAGE="https://www.hgsc.bcm.edu/software/atlas-whole-genome-assembly-suite"
-SRC_URI="https://www.hgsc.bcm.edu/sites/default/files/software/Atlas/atlas-src.tgz"
-# https://www.hgsc.bcm.edu/sites/default/files/software/Atlas/atlas2005-linux.tgz
-
-LICENSE="ATLAS"
-SLOT="0"
-KEYWORDS=""
-IUSE=""
-
-DEPEND="dev-libs/boost"
-RDEPEND="${DEPEND}"
-
-S="${WORKDIR}"/atlas-src/CBT
-
-src_prepare(){
-	sed -e "s/^CC = .*/CC = $(tc-getCC)/" -e "s/^GCC = .*/GCC = $(tc-getCXX)/" -i Makefile || die
-	sed -e "s/^CC = .*/CC = $(tc-getCC)/" -e "s/^GCC = .*/GCC = $(tc-getCXX)/" -i ../CBTApps/Makefile.in || die
-	sed -e "s@^# CBT_DEVEL_USER = .*@CBT_DEVEL_USER = ${EPREFIX}/@" -i Makefile || die
-	sed -e "s@^# CBT_DEVEL_USER = .*@CBT_DEVEL_USER = ${EPREFIX}/@" -i Makefile.in || die
-	sed -e "s#^CBT_INSTALL_LIB = /home/hgsc/lib/#CBT_INSTALL_LIB = ${EPREFIX}/usr/lib/#" -i Makefile || die
-	sed -e "s#^CBT_INSTALL_LIB = /home/hgsc/lib/#CBT_INSTALL_LIB = ${EPREFIX}/usr/lib/#" -i Makefile.in || die
-	sed -e "s#^BOOST_DIR = .*#BOOST_DIR = ${EPREFIX}/usr/lib/#" -i Makefile || die
-	sed -e "s#^BOOST_DIR = .*#BOOST_DIR = ${EPREFIX}/usr/lib/#" -i Makefile.in || die
-	sed -e "s#^CXX = .*#CXX = $(tc-getCXX)#" -i gzstream/Makefile || die
-}
-
-src_compile(){
-	# install headers, bins and libs into CBT_DEVEL_USER, then compile apps
-	emake CBT_DEVEL_DIR="${WORKDIR}/atlas-src/CBT" CBT_INSTALL_DIR="${D}"/"${EPREFIX}"
-	cd ../CBTApps || die
-	emake CBT_DEVEL_DIR="${WORKDIR}/atlas-src/CBTApps" CBT_INSTALL_DIR="${D}"/"${EPREFIX}"
-}
diff --git a/sci-biology/Atlas/Manifest b/sci-biology/Atlas/Manifest
deleted file mode 100644
index 4001534d5..000000000
--- a/sci-biology/Atlas/Manifest
+++ /dev/null
@@ -1 +0,0 @@
-DIST atlas-src.tgz 645758 BLAKE2B 2f0afa31dba2f10aaa6dd8e98248adb6eb1bad4c00a06553c27db9d8312b47266e34b1f38186f4e8d2da207220c633b2ec2a801fef4541c6f35d5d03bed86b9b SHA512 12d31642fbab52ae06a681dda8a3aae675f8898f357e2ffa9a5d37933ad327bef157784fbe936076cba17d774187296b0b8b516eced48a45914bba879165b8d9
diff --git a/sci-biology/Atlas/metadata.xml b/sci-biology/Atlas/metadata.xml
deleted file mode 100644
index 138cb7705..000000000
--- a/sci-biology/Atlas/metadata.xml
+++ /dev/null
@@ -1,12 +0,0 @@
-<?xml version="1.0" encoding="UTF-8"?>
-<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
-<pkgmetadata>
-	<maintainer type="person">
-		<email>mmokrejs@fold.natur.cuni.cz</email>
-		<name>Martin Mokrejs</name>
-	</maintainer>
-	<maintainer type="project">
-		<email>sci-biology@gentoo.org</email>
-		<name>Gentoo Biology Project</name>
-	</maintainer>
-</pkgmetadata>
diff --git a/sci-biology/Atlas2/Atlas2-1.4.3.ebuild b/sci-biology/Atlas2/Atlas2-1.4.3.ebuild
deleted file mode 100644
index 2305fb15d..000000000
--- a/sci-biology/Atlas2/Atlas2-1.4.3.ebuild
+++ /dev/null
@@ -1,40 +0,0 @@
-# Copyright 1999-2017 Gentoo Foundation
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=6
-
-USE_RUBY="ruby22 ruby23 ruby24"
-
-inherit ruby-fakegem
-
-DESCRIPTION="Variant analysis tools from whole exome capture sequencing (WECS)"
-HOMEPAGE="https://www.hgsc.bcm.edu/software/atlas2"
-SRC_URI="http://downloads.sourceforge.net/project/atlas2/Atlas2_v1.4.3.zip"
-
-LICENSE="BSD"
-SLOT="0"
-KEYWORDS=""
-IUSE=""
-
-DEPEND="
-	sci-biology/samtools:0
-	sci-biology/blat
-	sci-biology/phrap
-	sci-biology/ucsc-genome-browser" # that provides bigWig.h and jkweb.a, aka Jim Kent's src
-RDEPEND="${DEPEND}"
-
-S="${WORKDIR}"/all/"${PN}"_v"${PV}"
-
-src_compile(){
-	cd SOLiD-SNP-caller || die
-	default
-
-	cd ../vcfPrinter || die
-	# TODO: install the *.rb files
-
-	cd ../Atlas-Indel2 || die
-	# TODO: install the *.rb and files in lib/
-
-	cd ../Atlas-SNP2 || die
-	# TODO: install
-}
diff --git a/sci-biology/Atlas2/Manifest b/sci-biology/Atlas2/Manifest
deleted file mode 100644
index ad6a78081..000000000
--- a/sci-biology/Atlas2/Manifest
+++ /dev/null
@@ -1 +0,0 @@
-DIST Atlas2_v1.4.3.zip 979109 BLAKE2B 5807adfbdac63520f750a0eeedca5d296391813e5eb6b5181bc2875982d6b5b85566ad3e7153f42737084053e3e07fd89a5c944723bc7f33e1d8b7f05164dda8 SHA512 bad8f4b4bb3b5e26e2d01e21a1bc1b3cd9b6ab77acf943892052f4f1632d13789919d857c211b1c657069a0672807bf5daa70fc78e0afce460013ad33fe0ddb5
diff --git a/sci-biology/Atlas2/metadata.xml b/sci-biology/Atlas2/metadata.xml
deleted file mode 100644
index 7ce5225f5..000000000
--- a/sci-biology/Atlas2/metadata.xml
+++ /dev/null
@@ -1,21 +0,0 @@
-<?xml version="1.0" encoding="UTF-8"?>
-<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
-<pkgmetadata>
-	<maintainer type="person">
-		<email>mmokrejs@fold.natur.cuni.cz</email>
-		<name>Martin Mokrejs</name>
-	</maintainer>
-	<maintainer type="project">
-		<email>sci-biology@gentoo.org</email>
-		<name>Gentoo Biology Project</name>
-	</maintainer>
-	<longdescription>
-Atlas2 is a next-generation sequencing suite of variant analysis
-tools specializing in the separation of true SNPs and insertions
-and deletions (indels) from sequencing and mapping errors in Whole
-Exome Capture Sequencing (WECS) data.
-</longdescription>
-	<upstream>
-		<remote-id type="sourceforge">downloads</remote-id>
-	</upstream>
-</pkgmetadata>
diff --git a/sci-biology/Atlas_GapFill/Atlas_GapFill-2.2.ebuild b/sci-biology/Atlas_GapFill/Atlas_GapFill-2.2.ebuild
deleted file mode 100644
index 935134f09..000000000
--- a/sci-biology/Atlas_GapFill/Atlas_GapFill-2.2.ebuild
+++ /dev/null
@@ -1,23 +0,0 @@
-# Copyright 1999-2017 Gentoo Foundation
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=5
-
-DESCRIPTION="Close gaps using BWA-identified reads and reassemble"
-HOMEPAGE="https://www.hgsc.bcm.edu/software/atlas-gapfill"
-SRC_URI="
-	https://www.hgsc.bcm.edu/sites/default/files/software/ATLAS_GapFill_V2_2/ATLAS_GapFill_V2.2_release.tar.bz2
-	https://www.hgsc.bcm.edu/sites/default/files/software/ATLAS_GapFill_V2_2/README -> ATLAS_GapFill_V2_2.README"
-
-LICENSE="ATLAS"
-SLOT="0"
-KEYWORDS=""
-IUSE=""
-
-# is there an ebuild for newbler so we could add it to DEPEND?
-RDEPEND="
-	dev-lang/perl
-	sci-biology/phrap
-	sci-biology/bwa
-	sci-biology/velvet"
-DEPEND=""
diff --git a/sci-biology/Atlas_GapFill/Manifest b/sci-biology/Atlas_GapFill/Manifest
deleted file mode 100644
index 479998ee1..000000000
--- a/sci-biology/Atlas_GapFill/Manifest
+++ /dev/null
@@ -1,2 +0,0 @@
-DIST ATLAS_GapFill_V2.2_release.tar.bz2 467649030 BLAKE2B 5d6f5942aeb031c4b546a84be8e60bd4e73cf01e5d4f9725ac4d63e31dca9e8cf4778dfcb06c5290c662e6656634c1dbe8a6c727091fcdb26eb0886e80b6faa8 SHA512 7194cdc085d7a6157de91c3e7ea8968132c107917ae5a46abc05f53d6a8351ef310713108710cba1dc242646117b90a2bde18a99bc9cd08b6d265c8b8892dafd
-DIST ATLAS_GapFill_V2_2.README 19029 BLAKE2B 38aa8b2fc3a9d01afe4a05a4dee2537d4554b13e7d7dd8d5468a58c5e64620d3d13afc22c8205d01737cd74d67f9e44e3eb1deb4fc4e8822e3a82598763a53d6 SHA512 fa3408884da4218890074c446317f6e163d657a450c941cb34c59f41f746586a20b11c4142a79fd963986d3e984f7e751d52bb285fa3a520fbe4c28ee84e8404
diff --git a/sci-biology/Atlas_GapFill/metadata.xml b/sci-biology/Atlas_GapFill/metadata.xml
deleted file mode 100644
index 138cb7705..000000000
--- a/sci-biology/Atlas_GapFill/metadata.xml
+++ /dev/null
@@ -1,12 +0,0 @@
-<?xml version="1.0" encoding="UTF-8"?>
-<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
-<pkgmetadata>
-	<maintainer type="person">
-		<email>mmokrejs@fold.natur.cuni.cz</email>
-		<name>Martin Mokrejs</name>
-	</maintainer>
-	<maintainer type="project">
-		<email>sci-biology@gentoo.org</email>
-		<name>Gentoo Biology Project</name>
-	</maintainer>
-</pkgmetadata>
diff --git a/sci-biology/BBmap/BBmap-34.97.ebuild b/sci-biology/BBmap/BBmap-34.97.ebuild
deleted file mode 100644
index cf80ed6c8..000000000
--- a/sci-biology/BBmap/BBmap-34.97.ebuild
+++ /dev/null
@@ -1,43 +0,0 @@
-# Copyright 1999-2017 Gentoo Foundation
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=5
-
-inherit java-pkg-2 java-ant-2
-
-DESCRIPTION="Short read aligner, K-mer-based error-correct and normalize, FASTA/Q tool"
-HOMEPAGE="http://sourceforge.net/projects/bbmap/"
-SRC_URI="http://sourceforge.net/projects/bbmap/files/BBMap_"${PV}".tar.gz"
-
-LICENSE="BSD"
-SLOT="0"
-KEYWORDS="~amd64 ~x86"
-IUSE=""
-
-DEPEND="
-	sys-cluster/openmpi[java]
-	>=virtual/jdk-1.7:*
-	dev-java/ant-core"
-RDEPEND="${DEPEND}
-	>=virtual/jre-1.7:*"
-
-S="${WORKDIR}"/bbmap
-
-src_prepare(){
-	# fix the line in build.xml to point to mpi.jar location
-	# <property name="mpijar" location="/tmp/mpi.jar" ></property>
-	# see bug #542700
-	sed -e 's#/usr/common/usg/hpc/openmpi/gnu4.6/sge/1.8.1/ib_2.1-1.0.0/lib/mpi.jar#/usr/share/openmpi/lib/mpi.jar#' -i build.xml
-	sed -e 's#compiler="${jcompiler}" ##' -i build.xml
-	epatch "${FILESDIR}"/UnicodeToAscii.patch
-}
-
-src_compile(){
-	ant dist || die
-}
-
-src_install(){
-	dobin *.sh
-	dodoc docs/readme.txt
-	java-pkg_dojar dist/lib/BBTools.jar
-}
diff --git a/sci-biology/BBmap/BBmap-35.92.ebuild b/sci-biology/BBmap/BBmap-35.92.ebuild
deleted file mode 100644
index d8d2042ce..000000000
--- a/sci-biology/BBmap/BBmap-35.92.ebuild
+++ /dev/null
@@ -1,42 +0,0 @@
-# Copyright 1999-2017 Gentoo Foundation
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=5
-
-inherit java-pkg-2 java-ant-2
-
-DESCRIPTION="Short read aligner, K-mer-based error-correct and normalize, FASTA/Q tool"
-HOMEPAGE="http://sourceforge.net/projects/bbmap/"
-SRC_URI="http://sourceforge.net/projects/bbmap/files/BBMap_"${PV}".tar.gz"
-
-LICENSE="BSD"
-SLOT="0"
-KEYWORDS="~amd64 ~x86"
-IUSE=""
-
-DEPEND="
-	sys-cluster/openmpi[java]
-	>=virtual/jdk-1.7:*
-	dev-java/ant-core"
-RDEPEND="${DEPEND}
-	>=virtual/jre-1.7:*"
-
-S="${WORKDIR}"/bbmap
-
-src_prepare(){
-	# fix the line in build.xml to point to mpi.jar location
-	# <property name="mpijar" location="/tmp/mpi.jar" ></property>
-	# see bug #542700
-	sed -e 's#/usr/common/usg/hpc/openmpi/gnu4.6/sge/1.8.1/ib_2.1-1.0.0/lib/mpi.jar#/usr/share/openmpi/lib/mpi.jar#' -i build.xml
-	sed -e 's#compiler="${jcompiler}" ##' -i build.xml
-}
-
-src_compile(){
-	ant dist || die
-}
-
-src_install(){
-	dobin *.sh
-	dodoc docs/readme.txt
-	java-pkg_dojar dist/lib/BBTools.jar
-}
diff --git a/sci-biology/BBmap/BBmap-36.02.ebuild b/sci-biology/BBmap/BBmap-36.02.ebuild
deleted file mode 100644
index d8d2042ce..000000000
--- a/sci-biology/BBmap/BBmap-36.02.ebuild
+++ /dev/null
@@ -1,42 +0,0 @@
-# Copyright 1999-2017 Gentoo Foundation
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=5
-
-inherit java-pkg-2 java-ant-2
-
-DESCRIPTION="Short read aligner, K-mer-based error-correct and normalize, FASTA/Q tool"
-HOMEPAGE="http://sourceforge.net/projects/bbmap/"
-SRC_URI="http://sourceforge.net/projects/bbmap/files/BBMap_"${PV}".tar.gz"
-
-LICENSE="BSD"
-SLOT="0"
-KEYWORDS="~amd64 ~x86"
-IUSE=""
-
-DEPEND="
-	sys-cluster/openmpi[java]
-	>=virtual/jdk-1.7:*
-	dev-java/ant-core"
-RDEPEND="${DEPEND}
-	>=virtual/jre-1.7:*"
-
-S="${WORKDIR}"/bbmap
-
-src_prepare(){
-	# fix the line in build.xml to point to mpi.jar location
-	# <property name="mpijar" location="/tmp/mpi.jar" ></property>
-	# see bug #542700
-	sed -e 's#/usr/common/usg/hpc/openmpi/gnu4.6/sge/1.8.1/ib_2.1-1.0.0/lib/mpi.jar#/usr/share/openmpi/lib/mpi.jar#' -i build.xml
-	sed -e 's#compiler="${jcompiler}" ##' -i build.xml
-}
-
-src_compile(){
-	ant dist || die
-}
-
-src_install(){
-	dobin *.sh
-	dodoc docs/readme.txt
-	java-pkg_dojar dist/lib/BBTools.jar
-}
diff --git a/sci-biology/BBmap/BBmap-36.86.ebuild b/sci-biology/BBmap/BBmap-36.86.ebuild
deleted file mode 100644
index d8d2042ce..000000000
--- a/sci-biology/BBmap/BBmap-36.86.ebuild
+++ /dev/null
@@ -1,42 +0,0 @@
-# Copyright 1999-2017 Gentoo Foundation
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=5
-
-inherit java-pkg-2 java-ant-2
-
-DESCRIPTION="Short read aligner, K-mer-based error-correct and normalize, FASTA/Q tool"
-HOMEPAGE="http://sourceforge.net/projects/bbmap/"
-SRC_URI="http://sourceforge.net/projects/bbmap/files/BBMap_"${PV}".tar.gz"
-
-LICENSE="BSD"
-SLOT="0"
-KEYWORDS="~amd64 ~x86"
-IUSE=""
-
-DEPEND="
-	sys-cluster/openmpi[java]
-	>=virtual/jdk-1.7:*
-	dev-java/ant-core"
-RDEPEND="${DEPEND}
-	>=virtual/jre-1.7:*"
-
-S="${WORKDIR}"/bbmap
-
-src_prepare(){
-	# fix the line in build.xml to point to mpi.jar location
-	# <property name="mpijar" location="/tmp/mpi.jar" ></property>
-	# see bug #542700
-	sed -e 's#/usr/common/usg/hpc/openmpi/gnu4.6/sge/1.8.1/ib_2.1-1.0.0/lib/mpi.jar#/usr/share/openmpi/lib/mpi.jar#' -i build.xml
-	sed -e 's#compiler="${jcompiler}" ##' -i build.xml
-}
-
-src_compile(){
-	ant dist || die
-}
-
-src_install(){
-	dobin *.sh
-	dodoc docs/readme.txt
-	java-pkg_dojar dist/lib/BBTools.jar
-}
diff --git a/sci-biology/BBmap/BBmap-37.67.ebuild b/sci-biology/BBmap/BBmap-37.67.ebuild
deleted file mode 100644
index d8d2042ce..000000000
--- a/sci-biology/BBmap/BBmap-37.67.ebuild
+++ /dev/null
@@ -1,42 +0,0 @@
-# Copyright 1999-2017 Gentoo Foundation
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=5
-
-inherit java-pkg-2 java-ant-2
-
-DESCRIPTION="Short read aligner, K-mer-based error-correct and normalize, FASTA/Q tool"
-HOMEPAGE="http://sourceforge.net/projects/bbmap/"
-SRC_URI="http://sourceforge.net/projects/bbmap/files/BBMap_"${PV}".tar.gz"
-
-LICENSE="BSD"
-SLOT="0"
-KEYWORDS="~amd64 ~x86"
-IUSE=""
-
-DEPEND="
-	sys-cluster/openmpi[java]
-	>=virtual/jdk-1.7:*
-	dev-java/ant-core"
-RDEPEND="${DEPEND}
-	>=virtual/jre-1.7:*"
-
-S="${WORKDIR}"/bbmap
-
-src_prepare(){
-	# fix the line in build.xml to point to mpi.jar location
-	# <property name="mpijar" location="/tmp/mpi.jar" ></property>
-	# see bug #542700
-	sed -e 's#/usr/common/usg/hpc/openmpi/gnu4.6/sge/1.8.1/ib_2.1-1.0.0/lib/mpi.jar#/usr/share/openmpi/lib/mpi.jar#' -i build.xml
-	sed -e 's#compiler="${jcompiler}" ##' -i build.xml
-}
-
-src_compile(){
-	ant dist || die
-}
-
-src_install(){
-	dobin *.sh
-	dodoc docs/readme.txt
-	java-pkg_dojar dist/lib/BBTools.jar
-}
diff --git a/sci-biology/BBmap/BBmap-38.87.ebuild b/sci-biology/BBmap/BBmap-38.87.ebuild
new file mode 100644
index 000000000..7e196a47d
--- /dev/null
+++ b/sci-biology/BBmap/BBmap-38.87.ebuild
@@ -0,0 +1,42 @@
+# Copyright 1999-2021 Gentoo Authors
+# Distributed under the terms of the GNU General Public License v2
+
+EAPI=7
+
+inherit java-pkg-2 java-ant-2
+
+DESCRIPTION="Short read aligner, K-mer-based error-correct and normalize, FASTA/Q tool"
+HOMEPAGE="https://sourceforge.net/projects/bbmap/"
+SRC_URI="https://sourceforge.net/projects/bbmap/files/BBMap_${PV}.tar.gz"
+
+LICENSE="BSD"
+SLOT="0"
+KEYWORDS="~amd64 ~x86"
+
+DEPEND="
+	sys-cluster/openmpi[java(-)]
+	>=virtual/jdk-1.7:*
+	dev-java/ant-core"
+RDEPEND="${DEPEND}
+	>=virtual/jre-1.7:*"
+
+S="${WORKDIR}/bbmap"
+
+src_prepare(){
+	default
+	# fix the line in build.xml to point to mpi.jar location
+	# <property name="mpijar" location="/tmp/mpi.jar" ></property>
+	# see bug #542700
+	sed -e 's#/usr/common/usg/hpc/openmpi/gnu4.6/sge/1.8.1/ib_2.1-1.0.0/lib/mpi.jar#/usr/share/openmpi/lib/mpi.jar#' -i build.xml
+	sed -e 's#compiler="${jcompiler}" ##' -i build.xml
+}
+
+src_compile(){
+	ant dist || die
+}
+
+src_install(){
+	dobin *.sh
+	dodoc docs/readme.txt
+	java-pkg_dojar dist/lib/BBTools.jar
+}
diff --git a/sci-biology/BBmap/Manifest b/sci-biology/BBmap/Manifest
index 7752e7d6b..b6276cf14 100644
--- a/sci-biology/BBmap/Manifest
+++ b/sci-biology/BBmap/Manifest
@@ -1,5 +1 @@
-DIST BBMap_34.97.tar.gz 3986036 BLAKE2B 79989c6c9444ed0e11dd460b06a9ed8f419f815d3b0ebf9face00bf0310c8e9fa8763bc652ac5393f25518144d220dd5a1d2e591df7300ecddcc9d039987c1b9 SHA512 ddc43fe281af775946a8688805ec352431340a1e28ae0e8bd90dc8f2ef51435d03af73d3d90f2c0d04cf932d744acb43576bf89cd392e79f02393f9a6188598a
-DIST BBMap_35.92.tar.gz 4481029 BLAKE2B 0d5dc2378a8d00ea4bf863e4dbc368d3edfc614b71d657ea1253f35b161b74617a1d39ae3615195bec4ceae9751786a85e4f6250cc5f75cfbceceea4068af48d SHA512 d9d43d40d8791826ad9d9a639a2cf9f08fd92460d37a19564ca460b9c5ace988c91052bb4e7c7ca49eb807efa2d3869153bdd5615df0f5900d623a3aae930dc5
-DIST BBMap_36.02.tar.gz 4545396 BLAKE2B 92fbea1acd387ab251f541e27113cffe0c703d0fef4c1ef81c8c0bef0e251a62bb9b67823a76957b835ee5af6860b9917821484004db64f37023d27bc139bf31 SHA512 4e960bd8d3b665333bbcd2c8f1b74e5b40a8172ef3b92f0512f1f9ea26cd83116f1284147e3f2e4f7340f7fb472159b47442c082336d3c45bf42ecb99f911fad
-DIST BBMap_36.86.tar.gz 5290221 BLAKE2B 6350f455f7af73f8f656ae9f1528b78131d9a602447011c1e9b73985ba1fc3796ca19f75b37d6bb5ba415c81a4460b96e26f2f8a995845caedccdb66a6afbc1a SHA512 fc263572d8d3ecd8096594643cb4b955d48daf3c44538393c9f2f212838503ad00b5dfab969121e80091b1079752dd3e35428ca658959dd8549bda667396e8b0
-DIST BBMap_37.67.tar.gz 6697061 BLAKE2B 9dc9dec257aab50867c4e5e20ddcfb0971f77ea643d087cc885e5677e413dceaac32a323944d95d4e08a0a9a9f9a625f76bbe6c7eed06bedc62cfdfad4d431c6 SHA512 d2a945a9ada73d268ef3cb9bce26837e193b90701ce0c69b3214fa35b31f215d57db9c52fb654b0f75b233fdbfe86e3b3cf50b2035bf5c2c31afe7ea5ba975dd
+DIST BBMap_38.87.tar.gz 10476117 BLAKE2B 9fa4b5b0127766f58d48b094a376fb5299fec2066b308804fe7576ef605eaf103ad957e5dddda9c7412993ea6a272afde07ea37171e49c760ba8afc591a1201d SHA512 54069131e87953888a0aa0d67f3f3770a88d3fc5bbc116b6a034e4ba359ac54d9aa4a75b66b007fa11d396294eb440b99b9af0df6e0899a6269c518ad83baf9a
diff --git a/sci-biology/BBmap/files/UnicodeToAscii.patch b/sci-biology/BBmap/files/UnicodeToAscii.patch
deleted file mode 100644
index 36e5a36e5..000000000
--- a/sci-biology/BBmap/files/UnicodeToAscii.patch
+++ /dev/null
@@ -1,17 +0,0 @@
---- bbmap/current/jgi/UnicodeToAscii.java.ori	2015-11-12 20:24:13.704471341 +0100
-+++ bbmap/current/jgi/UnicodeToAscii.java	2015-11-12 20:27:12.564474322 +0100
-@@ -20,14 +20,6 @@
- public class UnicodeToAscii {

- 	

- 	public static void main(String[] args){

--//		try {

--//			System.err.println("AêñüC");

--//			System.err.println(new String("AêñüC".getBytes("UTF8"), "UTF8"));

--//		} catch (Exception e) {

--//			// TODO Auto-generated catch block

--//			e.printStackTrace();

--//		}

--//		assert(false);

- 		

- 		Timer t=new Timer();

- 		t.start();

diff --git a/sci-biology/BEP032tools/BEP032tools-0.0.1_alpha.ebuild b/sci-biology/BEP032tools/BEP032tools-0.0.1_alpha.ebuild
new file mode 100644
index 000000000..ec394603d
--- /dev/null
+++ b/sci-biology/BEP032tools/BEP032tools-0.0.1_alpha.ebuild
@@ -0,0 +1,44 @@
+# Copyright 1999-2023 Gentoo Authors
+# Distributed under the terms of the GNU General Public License v2
+
+EAPI=8
+
+DISTUTILS_USE_PEP517=setuptools
+PYTHON_COMPAT=( python3_{10..11} )
+
+inherit distutils-r1
+
+MY_HASH="a7059ef691e74aeb018edaf37df49c99f6efed60"
+
+DESCRIPTION="Conversion and validation tools for BEP 032"
+HOMEPAGE="https://github.com/INT-NIT/BEP032tools"
+SRC_URI="https://github.com/INT-NIT/BEP032tools/archive/${MY_HASH}.tar.gz -> ${P}.gh.tar.gz"
+
+LICENSE="MIT"
+SLOT="0"
+KEYWORDS="~amd64"
+
+RDEPEND="
+	dev-python/pandas[${PYTHON_USEDEP}]
+	dev-python/pynwb[${PYTHON_USEDEP}]
+	dev-python/neo[${PYTHON_USEDEP}]
+"
+BDEPEND="
+	dev-python/parameterized[${PYTHON_USEDEP}]
+"
+
+S="${WORKDIR}/${PN}-${MY_HASH}"
+
+# Require nixio
+EPYTEST_DESELECT=(
+	"bep032tools/generator/tests/test_BEP032Generator.py::Test_BEP032Data_ece::test_data_file_conversion_0_nix"
+	"bep032tools/generator/tests/test_BEP032Generator.py::Test_BEP032Data_ece::test_data_file_conversion_multi_split"
+	"bep032tools/generator/tests/test_BEP032Generator.py::Test_BEP032Data_ice::test_data_file_conversion_0_nix"
+)
+# Require dynamically fetched data
+EPYTEST_DESELECT+=(
+	"bep032tools/generator/tests/test_nwb2bidsgenerator.py::TestNwbBIDSGenerator::test_nwb_to_bids"
+	"bep032tools/generator/tests/test_nwb2bidsgenerator.py::TestNwbBIDSGenerator::test_validation"
+)
+
+distutils_enable_tests pytest
diff --git a/sci-biology/BEP032tools/Manifest b/sci-biology/BEP032tools/Manifest
new file mode 100644
index 000000000..1e97ed9b1
--- /dev/null
+++ b/sci-biology/BEP032tools/Manifest
@@ -0,0 +1 @@
+DIST BEP032tools-0.0.1_alpha.gh.tar.gz 79175 BLAKE2B dc3d999401d2d4361bfc66b72a39fa02bd6148a377bf63b5bdcc788f4018e486e89743b35ad8f61e232b22f79fed6199dad462aaab60e3bbd1425de117b9c576 SHA512 bf929e5f00cfdd47bbdb9f2240bab97468da5bcb72857e8272eb25857ce7d525b6a97cbc459ace8629d67eb9238b8ddd537e2b6269b73d0173a945b39d5eb59e
diff --git a/sci-biology/BEP032tools/metadata.xml b/sci-biology/BEP032tools/metadata.xml
new file mode 100644
index 000000000..8d24d17e7
--- /dev/null
+++ b/sci-biology/BEP032tools/metadata.xml
@@ -0,0 +1,16 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
+<pkgmetadata>
+	<maintainer type="person">
+		<email>gentoo@chymera.eu</email>
+		<name>Horea Christian</name>
+	</maintainer>
+	<maintainer type="project">
+		<email>sci@gentoo.org</email>
+		<name>Gentoo Science Project</name>
+	</maintainer>
+	<upstream>
+		<remote-id type="github">INT-NIT/BEP032tools</remote-id>
+		<remote-id type="pypi">BEP032tools</remote-id>
+	</upstream>
+</pkgmetadata>
diff --git a/sci-biology/BG7/BG7-9999.ebuild b/sci-biology/BG7/BG7-9999.ebuild
deleted file mode 100644
index 35ae6ea50..000000000
--- a/sci-biology/BG7/BG7-9999.ebuild
+++ /dev/null
@@ -1,23 +0,0 @@
-# Copyright 1999-2017 Gentoo Foundation
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=6
-
-inherit java-pkg-2 java-ant-2 git-r3
-
-DESCRIPTION="Bacterial genome annotation system"
-HOMEPAGE="http://bg7.ohnosequences.com"
-#SRC_URI=""
-EGIT_REPO_URI="https://github.com/bg7/BG7"
-
-LICENSE="AGPL-3"
-SLOT="0"
-KEYWORDS=""
-IUSE=""
-
-DEPEND="
-	>=virtual/jre-1.5:*
-	dev-java/ant-core"
-RDEPEND="${DEPEND}
-	>=virtual/jre-1.5:*
-	sci-biology/ncbi-tools++"
diff --git a/sci-biology/BG7/metadata.xml b/sci-biology/BG7/metadata.xml
deleted file mode 100644
index ae9640ffb..000000000
--- a/sci-biology/BG7/metadata.xml
+++ /dev/null
@@ -1,8 +0,0 @@
-<?xml version="1.0" encoding="UTF-8"?>
-<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
-<pkgmetadata>
-	<maintainer type="project">
-		<email>sci@gentoo.org</email>
-		<name>Gentoo Science Project</name>
-	</maintainer>
-</pkgmetadata>
diff --git a/sci-biology/BRAKER/BRAKER-2.1.0.ebuild b/sci-biology/BRAKER/BRAKER-2.1.0.ebuild
deleted file mode 100644
index 13d63d4b8..000000000
--- a/sci-biology/BRAKER/BRAKER-2.1.0.ebuild
+++ /dev/null
@@ -1,45 +0,0 @@
-# Copyright 1999-2018 Gentoo Foundation
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=5
-
-PERL_EXPORT_PHASE_FUNCTIONS=no
-inherit perl-module
-
-DESCRIPTION="Gene prediction based on RNA-Seq using GeneMark-ET and AUGUSTUS"
-# http://bioinf.uni-greifswald.de/bioinf/publications/pag2015.pdf
-HOMEPAGE="http://bioinf.uni-greifswald.de/bioinf/braker
-	http://bioinf.uni-greifswald.de/augustus/downloads"
-SRC_URI="http://bioinf.uni-greifswald.de/augustus/binaries/BRAKER_v"${PV}".tar.gz -> ${P}.tar.gz"
-# Example data for testing the BRAKER2 pipeline is available at
-# http://bioinf.uni-greifswald.de/augustus/binaries/BRAKER2examples.tar.gz (1.1 GB).
-
-# BRAKER2 is using the Artistic-1.0 version without clause 8 about
-# commercial distribution
-# See discussion at https://opensource.org/licenses/artistic-license-1.0
-# Practically the license is same as http://dev.perl.org/licenses/artistic.html
-LICENSE="Artistic"
-SLOT="0"
-KEYWORDS="~amd64 ~x86"
-IUSE=""
-
-DEPEND=""
-RDEPEND="${DEPEND}
-	dev-perl/Scalar-Util-Numeric
-	sci-biology/augustus"
-	#>=sci-biology/GeneMark_ET-bin-4.29"
-
-S="${WORKDIR}"/BRAKER_v"${PV}"
-
-src_install(){
-	perl_set_version
-	dobin *.pl
-	insinto ${VENDOR_LIB}/${PN}
-	doins *.pm
-	dodoc userguide.pdf
-}
-
-pkg_postinst(){
-	einfo "Please install sci-biology/GeneMark_ET after obtaininig a license and binaries from"
-	einfo "http://exon.gatech.edu/GeneMark/gmes_instructions.html"
-}
diff --git a/sci-biology/BRAKER/BRAKER-2.1.2.ebuild b/sci-biology/BRAKER/BRAKER-2.1.2.ebuild
new file mode 100644
index 000000000..150bf55a1
--- /dev/null
+++ b/sci-biology/BRAKER/BRAKER-2.1.2.ebuild
@@ -0,0 +1,41 @@
+# Copyright 1999-2021 Gentoo Authors
+# Distributed under the terms of the GNU General Public License v2
+
+EAPI=7
+
+inherit perl-module
+
+DESCRIPTION="Gene prediction based on RNA-Seq using GeneMark-ET and AUGUSTUS"
+# http://bioinf.uni-greifswald.de/bioinf/publications/pag2015.pdf
+HOMEPAGE="https://github.com/Gaius-Augustus/BRAKER
+	http://bioinf.uni-greifswald.de/bioinf/braker
+	http://bioinf.uni-greifswald.de/augustus/downloads"
+SRC_URI="https://github.com/Gaius-Augustus/BRAKER/archive/v${PV}.tar.gz -> ${P}.tar.gz"
+# Example data for testing the BRAKER2 pipeline is available at
+# http://bioinf.uni-greifswald.de/augustus/binaries/BRAKER2examples.tar.gz (1.1 GB).
+
+# BRAKER2 is using the Artistic-1.0 version without clause 8 about
+# commercial distribution
+# See discussion at https://opensource.org/licenses/artistic-license-1.0
+# Practically the license is same as http://dev.perl.org/licenses/artistic.html
+LICENSE="Artistic"
+SLOT="0"
+KEYWORDS="~amd64 ~x86"
+
+DEPEND=""
+RDEPEND="${DEPEND}
+	dev-perl/Scalar-Util-Numeric
+	sci-biology/augustus"
+	#>=sci-biology/GeneMark_ET-bin-4.29"
+
+src_install(){
+	perl_set_version
+	dobin scripts/*.pl
+	perl_domodule scripts/*.pm
+	dodoc docs/userguide.pdf
+}
+
+pkg_postinst(){
+	einfo "Please install sci-biology/GeneMark_ET after obtaininig a license and binaries from"
+	einfo "http://exon.gatech.edu/GeneMark/gmes_instructions.html"
+}
diff --git a/sci-biology/BRAKER/Manifest b/sci-biology/BRAKER/Manifest
index 0f3e0caf5..f7daf9f3f 100644
--- a/sci-biology/BRAKER/Manifest
+++ b/sci-biology/BRAKER/Manifest
@@ -1 +1 @@
-DIST BRAKER-2.1.0.tar.gz 444207 BLAKE2B a764303ba7b6d95cd4205f90e723f383afbe339a84f2d55e5b098cec5ef80b288caf82517af64ed761032bcfca24393bd112c50826fb0efe90d63eeeb5214a3b SHA512 0f2c9df14a2ce7bf655c14cbdaa943c01adc0aea15cd7c4bd538710f7809f22dabbf34dbddfb028352b13a7fc1cd5237882fb240c2b544aa4584461067ea54d8
+DIST BRAKER-2.1.2.tar.gz 10492582 BLAKE2B 5b18fb1bff68b27217cfed1d33691d5689cafd0560964252eb5a66f6b21dbf2296bf39fe823187ffee120f95be87efe735b38ae3ea1344a8500b0e113caf393e SHA512 1189bf67e9881d6580af11b3926d6d6a067f479bf5f21592068b2e5e48b2a5fd5f687bd2a3e02cdd876f678ad62ac02c87db232d921402a66011a50598687c6e
diff --git a/sci-biology/BRAKER/metadata.xml b/sci-biology/BRAKER/metadata.xml
index 138cb7705..aa4766e73 100644
--- a/sci-biology/BRAKER/metadata.xml
+++ b/sci-biology/BRAKER/metadata.xml
@@ -9,4 +9,7 @@
 		<email>sci-biology@gentoo.org</email>
 		<name>Gentoo Biology Project</name>
 	</maintainer>
+	<upstream>
+		<remote-id type="github">Gaius-Augustus/BRAKER</remote-id>
+	</upstream>
 </pkgmetadata>
diff --git a/sci-biology/BRANCH/BRANCH-9999.ebuild b/sci-biology/BRANCH/BRANCH-9999.ebuild
index 1700c4a09..409cc3b12 100644
--- a/sci-biology/BRANCH/BRANCH-9999.ebuild
+++ b/sci-biology/BRANCH/BRANCH-9999.ebuild
@@ -1,17 +1,15 @@
-# Copyright 1999-2015 Gentoo Foundation
+# Copyright 1999-2021 Gentoo Authors
 # Distributed under the terms of the GNU General Public License v2
 
-EAPI=5
+EAPI=7
 
-[ "$PV" == "9999" ] && inherit git-r3
-
-inherit eutils toolchain-funcs
+inherit toolchain-funcs
 
 DESCRIPTION="Extend partial transcripts with sequence from other reads or genomic contigs"
 HOMEPAGE="https://github.com/baoe/BRANCH"
 if [ "$PV" == "9999" ]; then
+	inherit git-r3
 	EGIT_REPO_URI="https://github.com/baoe/BRANCH"
-	KEYWORDS=""
 else
 	SRC_URI=""
 	KEYWORDS=""
@@ -19,11 +17,11 @@ fi
 
 LICENSE="Artistic-2"
 SLOT="0"
-IUSE=""
 
 DEPEND="
 	sci-biology/blat
-	sci-libs/lemon"
+	sci-libs/lemon
+"
 RDEPEND="${DEPEND}"
 
 src_compile(){
diff --git a/sci-biology/BamView/BamView-1.2.11.ebuild b/sci-biology/BamView/BamView-1.2.11.ebuild
deleted file mode 100644
index afc6ecb38..000000000
--- a/sci-biology/BamView/BamView-1.2.11.ebuild
+++ /dev/null
@@ -1,22 +0,0 @@
-# Copyright 1999-2015 Gentoo Foundation
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=5
-
-inherit java-pkg-2 java-ant-2 eutils
-
-DESCRIPTION="Display read alignments in BAM files, is a part of Artemis"
-HOMEPAGE="http://bamview.sourceforge.net/"
-SRC_URI="http://bamview.sourceforge.net/v"${PV}"/BamView_v"${PV}".jar"
-
-#http://www.ncbi.nlm.nih.gov/pubmed/20071372
-LICENSE="GPL-2"
-SLOT="0"
-KEYWORDS=""
-IUSE=""
-
-DEPEND="
-	>=virtual/jdk-1.6:*
-	dev-java/ant-core"
-RDEPEND="${DEPEND}
-	>=virtual/jre-1.6:*"
diff --git a/sci-biology/BamView/Manifest b/sci-biology/BamView/Manifest
deleted file mode 100644
index 57de2aae8..000000000
--- a/sci-biology/BamView/Manifest
+++ /dev/null
@@ -1 +0,0 @@
-DIST BamView_v1.2.11.jar 9844743 BLAKE2B 38981e8c03e74db01071e1b544c5f3b1865bbbb573250681dda162a1fd50092dc007e18558aa40753c98d01793109852c6ac720075423533d0ff1f6780a47df4 SHA512 81f5eb4aea181a4e0c8262c63873d7d898484e3ba675af633b25d6363786d2b6b926e3f6ba5b7001ce22581167e1d6b7f8b058ee7c304f3ce1ac07bae5b5f78a
diff --git a/sci-biology/BamView/metadata.xml b/sci-biology/BamView/metadata.xml
deleted file mode 100644
index 93e06748e..000000000
--- a/sci-biology/BamView/metadata.xml
+++ /dev/null
@@ -1,14 +0,0 @@
-<?xml version="1.0" encoding="UTF-8"?>
-<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
-<pkgmetadata>
-	<maintainer type="person">
-		<email>mmokrejs@fold.natur.cuni.cz</email>
-	</maintainer>
-	<maintainer type="project">
-		<email>sci-biology@gentoo.org</email>
-		<name>Gentoo Biology Project</name>
-	</maintainer>
-	<upstream>
-		<remote-id type="sourceforge">bamview</remote-id>
-	</upstream>
-</pkgmetadata>
diff --git a/sci-biology/BlastToSam/BlastToSam-1.1.ebuild b/sci-biology/BlastToSam/BlastToSam-1.1.ebuild
deleted file mode 100644
index 6053606ad..000000000
--- a/sci-biology/BlastToSam/BlastToSam-1.1.ebuild
+++ /dev/null
@@ -1,32 +0,0 @@
-# Copyright 1999-2018 Gentoo Foundation
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=6
-
-inherit git-r3 java-pkg-2 java-ant-2
-
-DESCRIPTION="Convert NCBI BLAST+ Pairwise/XML (-outfmt 0 or 5) output to SAM v1.4"
-HOMEPAGE="https://github.com/AstrorEnales/BlastToSam"
-EGIT_REPO_URI="https://github.com/AstrorEnales/BlastToSam.git"
-EGIT_COMMIT="8f543ff1640b64e44701cb534e2959ff46469b2e"
-
-LICENSE="MIT"
-SLOT="0"
-KEYWORDS="~amd64 ~x86"
-IUSE=""
-
-RDEPEND=">=virtual/jre-1.5:*"
-DEPEND="${RDEPEND}
-	>=virtual/jdk-1.5:*
-	dev-java/ant-core
-	dev-java/jython"
-
-src_compile() {
-	ant compile || die
-}
-
-src_install() {
-	java-pkg_dojar build/jar/BlastToSam.jar
-	java-pkg_dolauncher
-	dodoc README.md
-}
diff --git a/sci-biology/BlastToSam/metadata.xml b/sci-biology/BlastToSam/metadata.xml
deleted file mode 100644
index 5a3c7d51d..000000000
--- a/sci-biology/BlastToSam/metadata.xml
+++ /dev/null
@@ -1,15 +0,0 @@
-<?xml version="1.0" encoding="UTF-8"?>
-<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
-<pkgmetadata>
-	<maintainer type="person">
-		<email>mmokrejs@fold.natur.cuni.cz</email>
-		<name>Martin Mokrejs</name>
-	</maintainer>
-	<maintainer type="project">
-		<email>sci-biology@gentoo.org</email>
-		<name>Gentoo Biology Project</name>
-	</maintainer>
-	<upstream>
-		<remote-id type="github">AstrorEnales/BlastToSam</remote-id>
-	</upstream>
-</pkgmetadata>
diff --git a/sci-biology/CAT/CAT-1.3.ebuild b/sci-biology/CAT/CAT-1.3.ebuild
index 44d099524..508ca4c36 100644
--- a/sci-biology/CAT/CAT-1.3.ebuild
+++ b/sci-biology/CAT/CAT-1.3.ebuild
@@ -1,14 +1,10 @@
-# Copyright 2019 Gentoo Authors
+# Copyright 2019-2021 Gentoo Authors
 # Distributed under the terms of the GNU General Public License v2
 
 EAPI=7
 
 DESCRIPTION="Codon usage bias (composition) and its statistical significance"
-HOMEPAGE="
-	http://bigd.big.ac.cn/tools/cat
-	http://cbb.big.ac.cn/Software
-	http://code.google.com/p/composition-analysis-toolkit
-	http://www.cbrc.kaust.edu.sa/CAT"
+HOMEPAGE="https://bigd.big.ac.cn/tools/cat"
 SRC_URI="ftp://download.big.ac.cn/bigd/tools/${PN}${PV}.tar.gz -> ${P}.tar.gz"
 
 LICENSE="GPL-3+"
diff --git a/sci-biology/DisEMBL/DisEMBL-1.4.ebuild b/sci-biology/DisEMBL/DisEMBL-1.4.ebuild
deleted file mode 100644
index 712766d33..000000000
--- a/sci-biology/DisEMBL/DisEMBL-1.4.ebuild
+++ /dev/null
@@ -1,35 +0,0 @@
-# Copyright 1999-2016 Gentoo Foundation
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=5
-
-inherit toolchain-funcs
-
-DESCRIPTION="Intrinsic Protein Disorder Prediction"
-HOMEPAGE="http://dis.embl.de"
-SRC_URI="http://dis.embl.de/${P}.tgz"
-
-LICENSE="GPL-2"
-SLOT="0"
-KEYWORDS="~amd64"
-IUSE=""
-
-# The smoothing function sav_gol.c cannot be re-distributed but can be downloaded from TISEAN.
-# http://www.mpipks-dresden.mpg.de/~tisean/
-
-DEPEND="sci-mathematics/tisean"
-RDEPEND="${DEPEND}
-	sci-biology/biopython"
-
-src_prepare(){
-	sed -e 's@/usr/local/bin/@ /usr/bin/env @' -i DisEMBL.py || die
-}
-
-src_compile(){
-	$(tc-getCC) ${CFLAGS} ${LDFLAGS} disembl.c -o disembl
-}
-
-src_install(){
-	dobin DisEMBL.py disembl
-	dodoc INSTALL CHANGELOG
-}
diff --git a/sci-biology/DisEMBL/Manifest b/sci-biology/DisEMBL/Manifest
deleted file mode 100644
index 26eb31cda..000000000
--- a/sci-biology/DisEMBL/Manifest
+++ /dev/null
@@ -1 +0,0 @@
-DIST DisEMBL-1.4.tgz 626226 BLAKE2B 80cb7ead8239fae6bc46e2e422f953e34e7a017e5c1bc0d4994d142788fee8f882841e19c53c4805fb4def3529b71261b44194c17e8aec690682b778d616b3e6 SHA512 3544324b9456f03f021b5cfeaaf8c168aa9ddb1862383b746fb52e44579c9774f0e8cc8552fe50f8662ad7fee8d37c731244cde44c3ee09ce574aab1401cca2f
diff --git a/sci-biology/DisEMBL/metadata.xml b/sci-biology/DisEMBL/metadata.xml
deleted file mode 100644
index 138cb7705..000000000
--- a/sci-biology/DisEMBL/metadata.xml
+++ /dev/null
@@ -1,12 +0,0 @@
-<?xml version="1.0" encoding="UTF-8"?>
-<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
-<pkgmetadata>
-	<maintainer type="person">
-		<email>mmokrejs@fold.natur.cuni.cz</email>
-		<name>Martin Mokrejs</name>
-	</maintainer>
-	<maintainer type="project">
-		<email>sci-biology@gentoo.org</email>
-		<name>Gentoo Biology Project</name>
-	</maintainer>
-</pkgmetadata>
diff --git a/sci-biology/EBARDenovo/EBARDenovo-1.2.2.ebuild b/sci-biology/EBARDenovo/EBARDenovo-1.2.2.ebuild
deleted file mode 100644
index 3ac057f6d..000000000
--- a/sci-biology/EBARDenovo/EBARDenovo-1.2.2.ebuild
+++ /dev/null
@@ -1,24 +0,0 @@
-# Copyright 1999-2015 Gentoo Foundation
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=5
-
-DESCRIPTION="Transcriptome de novo assembler with chimera detection"
-HOMEPAGE="http://ebardenovo.sourceforge.net"
-SRC_URI="http://downloads.sourceforge.net/project/ebardenovo/EBARDenovo-1.2.2-20130404.zip"
-
-# This software package (with patent pending) is free of charge for academic use only
-LICENSE="CPL-1.0"
-SLOT="0"
-KEYWORDS="~amd64"
-IUSE=""
-
-DEPEND="dev-lang/mono"
-RDEPEND="${DEPEND}"
-
-S="${WORKDIR}"/EBARDenovo-1.2.2-20130404
-
-src_install(){
-	dobin EBARDenovo.exe
-	dodoc EBARDenovoManual.pdf ReleaseNote.txt README.txt
-}
diff --git a/sci-biology/EBARDenovo/Manifest b/sci-biology/EBARDenovo/Manifest
deleted file mode 100644
index b1b00b49a..000000000
--- a/sci-biology/EBARDenovo/Manifest
+++ /dev/null
@@ -1 +0,0 @@
-DIST EBARDenovo-1.2.2-20130404.zip 8319322 BLAKE2B d11c8f22a5b766d34eb2f7fdde19781d5f478f14b43069c7ee18706a825c9e09ed6c8e864fa56bd1e3c03dba65beec0f42704b0442a542081c9d3863f66b1daf SHA512 34b5b3942686da14f0dc55855ff2f2e8e321c3147adb3cb854e4abe13f3c3162e859af769ebf447917609a54bff816f1fb0a0fa61abbee7b4d7a61bee4e4b4f3
diff --git a/sci-biology/EBARDenovo/metadata.xml b/sci-biology/EBARDenovo/metadata.xml
deleted file mode 100644
index 0f267b755..000000000
--- a/sci-biology/EBARDenovo/metadata.xml
+++ /dev/null
@@ -1,15 +0,0 @@
-<?xml version="1.0" encoding="UTF-8"?>
-<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
-<pkgmetadata>
-	<maintainer type="person">
-		<email>mmokrejs@fold.natur.cuni.cz</email>
-		<name>Martin Mokrejs</name>
-	</maintainer>
-	<maintainer type="project">
-		<email>sci-biology@gentoo.org</email>
-		<name>Gentoo Biology Project</name>
-	</maintainer>
-	<upstream>
-		<remote-id type="sourceforge">downloads</remote-id>
-	</upstream>
-</pkgmetadata>
diff --git a/sci-biology/ESTate/ESTate-0.5.ebuild b/sci-biology/ESTate/ESTate-0.5.ebuild
deleted file mode 100644
index f24e85106..000000000
--- a/sci-biology/ESTate/ESTate-0.5.ebuild
+++ /dev/null
@@ -1,50 +0,0 @@
-# Copyright 1999-2017 Gentoo Foundation
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=5
-
-inherit eutils
-
-DESCRIPTION="ORF finding despite frameshifts, EST clustering"
-HOMEPAGE="http://www.ebi.ac.uk/~guy/estate"
-SRC_URI="
-	http://www.ebi.ac.uk/~guy/estate/estate.tar.gz
-	http://www.ebi.ac.uk/~guy/estate/thesis.ps.gz"
-
-LICENSE="GPL-2"
-SLOT="0"
-KEYWORDS="~amd64"
-IUSE=""
-
-S="${WORKDIR}"/estate
-
-src_prepare(){
-	sed \
-		-e "s/^CC/#CC/" \
-		-e "s/^LDFLAGS/#LDFLAGS/" \
-		-e "s/^CFLAGS/#CFLAGS/" \
-		-e "s/LDFLAGS/CFLAGS/" \
-		-i src/Makefile || die
-}
-
-src_install(){
-	# prevent file collision with sci-biology/hmmer-2.3.2
-	newbin bin/{revcomp,revcomp_ESTate}
-	rm bin/revcomp || die
-	newbin bin/{translate,translate_ESTate}
-	rm bin/translate || die
-	dobin bin/*
-	doman doc/man/man1/*.1 doc/man/man7/*.7
-
-	insinto /usr/share/ESTate/etc
-	doins etc/ESTaterc
-
-	insinto /usr/share/ESTate/example
-	doins example/embl59* example/drosophila*
-
-	dodoc ANNOUNCE.txt README.txt "${DISTDIR}"/thesis.ps.gz
-}
-
-pkg_postinst() {
-	optfeature "additional features" sci-biology/wcd
-}
diff --git a/sci-biology/ESTate/Manifest b/sci-biology/ESTate/Manifest
deleted file mode 100644
index 1d8f539be..000000000
--- a/sci-biology/ESTate/Manifest
+++ /dev/null
@@ -1,2 +0,0 @@
-DIST estate.tar.gz 465176 BLAKE2B 2690e84d658a85d916d9fec123f94749d46cef496a33955bcb151144cbd2342f7e797517373b9e91debf3a1906c22ee0267358a0010358cf78567ce4e25c251b SHA512 a33d9718fb55d421d9ed02e32bfb3d92150a72ee44fbf259886747c3c5ffe0e40fbe55675e9e36775af350f79310e2f994ff2e68266a1d44d1b9e34da20d7812
-DIST thesis.ps.gz 613820 SHA256 ffacc8aef617ee924461c2c4cd74820fde8056667c98c8148f65ff234b568b1b SHA512 d8a289e059b775751b1d0f3089ac8cf15936e7134bf33e5128b6c344d26d2e93c4387688b3261dabeebdcdca05c0a1decfde4ac7f4177a3c6f33a01d4c66d17e WHIRLPOOL 47e86754d9d7b906d1b889490000556c3b5edb4678125923839d6c3114a461e063fe05a765db6a494ff2a664883493a2774b22a0233f5845e5a06c2d9e96c9ad
diff --git a/sci-biology/ESTate/metadata.xml b/sci-biology/ESTate/metadata.xml
deleted file mode 100644
index 138cb7705..000000000
--- a/sci-biology/ESTate/metadata.xml
+++ /dev/null
@@ -1,12 +0,0 @@
-<?xml version="1.0" encoding="UTF-8"?>
-<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
-<pkgmetadata>
-	<maintainer type="person">
-		<email>mmokrejs@fold.natur.cuni.cz</email>
-		<name>Martin Mokrejs</name>
-	</maintainer>
-	<maintainer type="project">
-		<email>sci-biology@gentoo.org</email>
-		<name>Gentoo Biology Project</name>
-	</maintainer>
-</pkgmetadata>
diff --git a/sci-biology/FLASH/FLASH-1.2.11.ebuild b/sci-biology/FLASH/FLASH-1.2.11.ebuild
new file mode 100644
index 000000000..89d401a8e
--- /dev/null
+++ b/sci-biology/FLASH/FLASH-1.2.11.ebuild
@@ -0,0 +1,17 @@
+# Copyright 1999-2021 Gentoo Authors
+# Distributed under the terms of the GNU General Public License v2
+
+EAPI=7
+
+DESCRIPTION="Paired-end mates merge from fragments"
+HOMEPAGE="https://sourceforge.net/projects/flashpage/"
+SRC_URI="https://downloads.sourceforge.net/project/flashpage/${P}.tar.gz"
+
+LICENSE="GPL-3"
+SLOT="0"
+KEYWORDS="~amd64"
+
+src_install(){
+	dobin flash
+	dodoc NEWS README
+}
diff --git a/sci-biology/FLASH/FLASH-1.2.9.ebuild b/sci-biology/FLASH/FLASH-1.2.9.ebuild
deleted file mode 100644
index 823f2eba7..000000000
--- a/sci-biology/FLASH/FLASH-1.2.9.ebuild
+++ /dev/null
@@ -1,18 +0,0 @@
-# Copyright 1999-2017 Gentoo Foundation
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=6
-
-DESCRIPTION="Paired-end mates merge from fragments"
-HOMEPAGE="http://sourceforge.net/projects/flashpage"
-SRC_URI="http://downloads.sourceforge.net/project/flashpage/FLASH-1.2.9.tar.gz"
-
-LICENSE="GPL-3"
-SLOT="0"
-KEYWORDS="~amd64"
-IUSE=""
-
-src_install(){
-	dobin flash
-	dodoc NEWS README
-}
diff --git a/sci-biology/FLASH/Manifest b/sci-biology/FLASH/Manifest
index 7e3eca53f..d20beabb2 100644
--- a/sci-biology/FLASH/Manifest
+++ b/sci-biology/FLASH/Manifest
@@ -1 +1 @@
-DIST FLASH-1.2.9.tar.gz 46870 BLAKE2B c3b0b2fd1b012f7f49651dac1c67c8e4d6f21dfb6faecb9c1be09b84e48b1cd91901926211db8f98359951c02387ad34bf0366d88b66d38483e093b2dbe2dc1f SHA512 2113c717d3e7043d98f6058eabc510f1df713c580b4e8374560e9d30bebe33b58dd0e0ab5c594cc10b70622721073ba370b80b9fef8f7db9d505d3a3d3a32ff5
+DIST FLASH-1.2.11.tar.gz 48889 BLAKE2B 7e1beb9a4975352ff803ff5a94fe5a7c9b823d35465619a1d7ad8fbf61e40bda98c85b36655dfe9658c53459a7cc41775ed3b2052f34f626893bbeadae7add99 SHA512 d0357b925db8ab58054e893912381d9c2cd78ef8f3a7cc0182dd924f6959daafd595ca2b1a1e395b65af61558791a51abbfdaad3f9aaf8b462bb1fcda3e90268
diff --git a/sci-biology/FLASH/metadata.xml b/sci-biology/FLASH/metadata.xml
index 0f267b755..7dc91092f 100644
--- a/sci-biology/FLASH/metadata.xml
+++ b/sci-biology/FLASH/metadata.xml
@@ -10,6 +10,6 @@
 		<name>Gentoo Biology Project</name>
 	</maintainer>
 	<upstream>
-		<remote-id type="sourceforge">downloads</remote-id>
+		<remote-id type="sourceforge">flashpage</remote-id>
 	</upstream>
 </pkgmetadata>
diff --git a/sci-biology/Fastaq/Fastaq-3.17.0.ebuild b/sci-biology/Fastaq/Fastaq-3.17.0.ebuild
new file mode 100644
index 000000000..443fb3342
--- /dev/null
+++ b/sci-biology/Fastaq/Fastaq-3.17.0.ebuild
@@ -0,0 +1,21 @@
+# Copyright 1999-2023 Gentoo Authors
+# Distributed under the terms of the GNU General Public License v2
+
+EAPI=8
+
+PYTHON_COMPAT=( python3_{10..11} )
+DISTUTILS_USE_PEP517=setuptools
+
+inherit distutils-r1
+
+DESCRIPTION="Manipulate FASTA/Q, GFF3, EMBL, GBK files with API for developers"
+HOMEPAGE="https://github.com/sanger-pathogens/Fastaq"
+SRC_URI="https://github.com/sanger-pathogens/Fastaq/archive/v${PV}.tar.gz -> ${P}.tar.gz"
+
+LICENSE="GPL-3"
+SLOT="0"
+KEYWORDS="~amd64"
+
+distutils_enable_tests pytest
+# Nominally upstream still uses nose, though it does not encumber us, and tests pass:
+# https://github.com/sanger-pathogens/Fastaq/issues/84
diff --git a/sci-biology/Fastaq/Fastaq-9999.ebuild b/sci-biology/Fastaq/Fastaq-9999.ebuild
deleted file mode 100644
index 3a99df177..000000000
--- a/sci-biology/Fastaq/Fastaq-9999.ebuild
+++ /dev/null
@@ -1,20 +0,0 @@
-# Copyright 1999-2018 Gentoo Foundation
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=6
-
-PYTHON_COMPAT=( python3_3 python3_4 python3_5 python3_6 python3_7 )
-
-inherit distutils-r1 git-r3
-
-DESCRIPTION="Manipulate FASTA/Q, GFF3, EMBL, GBK files with API for developers"
-HOMEPAGE="https://github.com/sanger-pathogens/Fastaq"
-EGIT_REPO_URI="https://github.com/sanger-pathogens/Fastaq.git"
-
-LICENSE="GPL-3"
-SLOT="0"
-KEYWORDS=""
-IUSE=""
-
-DEPEND=""
-RDEPEND="${DEPEND}"
diff --git a/sci-biology/Fastaq/Manifest b/sci-biology/Fastaq/Manifest
new file mode 100644
index 000000000..1c9e549fd
--- /dev/null
+++ b/sci-biology/Fastaq/Manifest
@@ -0,0 +1 @@
+DIST Fastaq-3.17.0.tar.gz 71324 BLAKE2B 317ddcd0ce823f655d60e372f2c02afdaba4a1f9c13b6213f72337ad018c1a11f7ca52657f8615712631b2332682fdaf7eb735cd92e9d05a8bf12a6ed4b0cf14 SHA512 e32470384324be365476d27334e223ecb428f58398f5c02b1365713f8ef51362d9b2b9bc5d3244fff064fb8086cbb81be0f20c6c12ccbe870dbd11f47fa20464
diff --git a/sci-biology/GAL/GAL-0.2.2.ebuild b/sci-biology/GAL/GAL-0.2.2.ebuild
deleted file mode 100644
index ac019eded..000000000
--- a/sci-biology/GAL/GAL-0.2.2.ebuild
+++ /dev/null
@@ -1,43 +0,0 @@
-# Copyright 1999-2017 Gentoo Foundation
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=5
-
-inherit eutils perl-module
-
-DESCRIPTION="Genome Annotation Library (incl. fasta_tool)"
-HOMEPAGE="http://www.sequenceontology.org/software/GAL.html"
-SRC_URI="http://www.sequenceontology.org/software/GAL_Code/${PN}_${PV}.tar.gz"
-
-LICENSE="( GPL-1+ Artistic )"
-SLOT="0"
-KEYWORDS=""
-IUSE=""
-
-DEPEND="
-	>=dev-lang/perl-5.6.1
-	dev-perl/Module-Build
-	dev-perl/Config-Std
-	virtual/perl-Data-Dumper
-	dev-perl/Data-Types
-	dev-perl/DBD-SQLite
-	dev-perl/DBIx-Class
-	dev-perl/IO-All
-	dev-perl/Number-Format
-	virtual/perl-Scalar-List-Utils
-	dev-perl/Set-IntSpan-Fast
-	dev-perl/Statistics-Descriptive-Discrete
-	dev-perl/Template-Toolkit
-	dev-perl/Text-Graph
-	dev-perl/Text-RecordParser
-	dev-perl/Text-Table
-	dev-perl/Exception-Class
-	dev-perl/Test-Warn
-	dev-perl/URI"
-RDEPEND="${DEPEND}"
-
-S="${WORKDIR}/${PN}_${PV}"
-
-src_prepare(){
-	epatch "${FILESDIR}"/Build.PL.patch
-}
diff --git a/sci-biology/GAL/GAL-0.2.2_p20200508.ebuild b/sci-biology/GAL/GAL-0.2.2_p20200508.ebuild
new file mode 100644
index 000000000..f02907368
--- /dev/null
+++ b/sci-biology/GAL/GAL-0.2.2_p20200508.ebuild
@@ -0,0 +1,47 @@
+# Copyright 1999-2022 Gentoo Authors
+# Distributed under the terms of the GNU General Public License v2
+
+EAPI=8
+
+inherit perl-module
+
+COMMIT="94af39622aab5ba48eb693f2327f6e90f1d202ed"
+
+DESCRIPTION="Genome Annotation Library (incl. fasta_tool)"
+HOMEPAGE="https://github.com/The-Sequence-Ontology/GAL"
+SRC_URI="https://github.com/The-Sequence-Ontology/GAL/archive/${COMMIT}.tar.gz -> ${P}.tar.gz"
+S="${WORKDIR}/${PN}-${COMMIT}"
+
+LICENSE="( GPL-1+ Artistic )"
+SLOT="0"
+KEYWORDS="~amd64"
+
+RESTRICT="test"
+
+DEPEND="
+	dev-perl/Config-Std
+	virtual/perl-Data-Dumper
+	dev-perl/Data-Types
+	dev-perl/DBD-SQLite
+	dev-perl/DBIx-Class
+	dev-perl/IO-All
+	dev-perl/Number-Format
+	virtual/perl-Scalar-List-Utils
+	dev-perl/Set-IntSpan-Fast
+	dev-perl/Statistics-Descriptive
+	dev-perl/Statistics-Descriptive-Discrete
+	dev-perl/Template-Toolkit
+	dev-perl/Text-Graph
+	dev-perl/Text-RecordParser
+	dev-perl/Text-Table
+	dev-perl/Exception-Class
+	dev-perl/Test-Warn
+	dev-perl/URI
+	sci-biology/fasta
+"
+RDEPEND="${DEPEND}"
+BDEPEND="dev-perl/Module-Build"
+
+PATCHES=(
+	"${FILESDIR}/Build.PL.patch"
+)
diff --git a/sci-biology/GAL/Manifest b/sci-biology/GAL/Manifest
index 35e71f97e..4ade9c0d1 100644
--- a/sci-biology/GAL/Manifest
+++ b/sci-biology/GAL/Manifest
@@ -1 +1 @@
-DIST GAL_0.2.2.tar.gz 108786594 BLAKE2B c66a22d3623278317e9feb18938faea33bbb114df153e684bb2c6b1bf6c1c2a13c6bd3306497d80ff066fa65301fdde74e70dc33f73757e9f4bf34074e145780 SHA512 a90b396b7a703da875c2b7ad67a86f477f5b98e68353c94ab7d5876e613bfe386ba8f59d130c4f8fc62e2137742256e95ba9686c14f21b85b21d64fdc4c1be1b
+DIST GAL-0.2.2_p20200508.tar.gz 49788822 BLAKE2B 694030ad1d2963884bfdd7c25cb0df77be5ed12472c708d40a3bd1d5d837a99bf61a5cc1a2ba55a517cc90b53a896256cc4e2e875f89451af6232f3df3a90469 SHA512 cd06af20a895db2874d0f1b18e698706352968c5f60a610f73a3237ffabbd965e07d0cad4e1f6c542f4434a331a93178e49ee677393b7ca18c65e20466651058
diff --git a/sci-biology/GAL/files/Build.PL.patch b/sci-biology/GAL/files/Build.PL.patch
index 6d881f249..eee4fb60d 100644
--- a/sci-biology/GAL/files/Build.PL.patch
+++ b/sci-biology/GAL/files/Build.PL.patch
@@ -1,16 +1,11 @@
-diff -ruN GAL_0.2.2.orig/Build.PL GAL_0.2.2/Build.PL
---- GAL_0.2.2.orig/Build.PL	2014-01-30 01:35:11.000000000 +0100
-+++ GAL_0.2.2/Build.PL	2016-01-02 12:09:16.212623256 +0100
-@@ -6,26 +6,6 @@
- my $class = Module::Build->subclass
-   (
-    class => 'Module::Build::Custom',
--   code => q{
--       sub ACTION_build {
--	 my $self = shift;
--	 $self->SUPER::ACTION_build;
--	 $self->dispatch('installdeps');
--       }
+diff --git a/Build.PL b/Build.PL
+index 5915ca8..61eceb3 100644
+--- a/Build.PL
++++ b/Build.PL
+@@ -12,19 +12,6 @@ my $class = Module::Build->subclass
+ 	 $self->SUPER::ACTION_build;
+ 	 $self->dispatch('installdeps');
+        }
 -       sub ACTION_install {
 -	   my $self = shift;
 -	   print "\n\nGAL does not do a system wide install\n\n";
@@ -24,7 +19,6 @@ diff -ruN GAL_0.2.2.orig/Build.PL GAL_0.2.2/Build.PL
 -	   print "remove the entire subroutine (ACTION_install) where this message\n";
 -	   print "is printed run Build realclean and re-install.\n\n";
 -       }
--     },
+      },
    );
  
- my $builder = $class->new(
diff --git a/sci-biology/GAL/metadata.xml b/sci-biology/GAL/metadata.xml
index 138cb7705..480ba370b 100644
--- a/sci-biology/GAL/metadata.xml
+++ b/sci-biology/GAL/metadata.xml
@@ -9,4 +9,7 @@
 		<email>sci-biology@gentoo.org</email>
 		<name>Gentoo Biology Project</name>
 	</maintainer>
+	<upstream>
+		<remote-id type="github">The-Sequence-Ontology/GAL</remote-id>
+	</upstream>
 </pkgmetadata>
diff --git a/sci-biology/ICC/ICC-2.0.1.ebuild b/sci-biology/ICC/ICC-2.0.1.ebuild
deleted file mode 100644
index b6e13294a..000000000
--- a/sci-biology/ICC/ICC-2.0.1.ebuild
+++ /dev/null
@@ -1,54 +0,0 @@
-# Copyright 1999-2015 Gentoo Foundation
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=5
-
-DESCRIPTION="Error corrector for Roche/454 and IonTorrent data"
-HOMEPAGE="http://indra.mullins.microbiol.washington.edu/ICC"
-SRC_URI="http://indra.mullins.microbiol.washington.edu/cgi-bin/ICC/info.cgi?ID=ICC_v2.0.1.zip -> ICC_v2.0.1.zip"
-
-LICENSE="all-rights-reserved"
-SLOT="0"
-KEYWORDS=""
-IUSE=""
-
-DEPEND="
-	dev-lang/perl
-	dev-perl/Parallel-ForkManager
-	sci-biology/ncbi-tools++"
-RDEPEND="${DEPEND}"
-
-S="${WORKDIR}"
-
-src_install(){
-	dobin Scripts/*.pl
-	dodoc README.txt
-}
-
-#    testing: Blast/Linux/LICENSE      OK
-#    testing: Example/exampleReads.fas   OK
-#    testing: Example/exampleReads.qual   OK
-#    testing: Example/exampleReference.fas   OK
-#    testing: README.md                OK
-#    testing: README.txt               OK
-#    testing: Scripts/                 OK
-#    testing: Scripts/CC.pl            OK
-#    testing: Scripts/HIC.pl           OK
-#    testing: Scripts/IC.pl            OK
-#    testing: Scripts/alignRegion.pl   OK
-#    testing: Scripts/config.pl        OK
-#    testing: Scripts/lib/             OK
-#    testing: Scripts/lib/.DS_Store    OK
-#    testing: Scripts/lib/Parallel/    OK
-#    testing: Scripts/lib/Parallel/ForkManager.pm   OK
-#    testing: Scripts/lib/paths.pm     OK
-#    testing: Scripts/lib/seqAlign.pm   OK
-#    testing: Scripts/lib/utils.pm     OK
-#    testing: Scripts/ntFreq.pl        OK
-#    testing: Scripts/readQualFilter.pl   OK
-#    testing: Scripts/retrieveRegion.pl   OK
-#    testing: Scripts/retrieveWindows.pl   OK
-#    testing: Scripts/runBLAST.pl      OK
-#    testing: Scripts/runICC.pl        OK
-#    testing: Scripts/uniqueReads.pl   OK
-#    testing: VersionHistory.txt       OK
diff --git a/sci-biology/ICC/Manifest b/sci-biology/ICC/Manifest
deleted file mode 100644
index 375391637..000000000
--- a/sci-biology/ICC/Manifest
+++ /dev/null
@@ -1 +0,0 @@
-DIST ICC_v2.0.1.zip 63756669 SHA256 475eb33c8a9c49babc746823a988494f645f2d437ddb46c6988fbd14df39b833 SHA512 2952c5489e81f0702d3854a5a6f9591c4674b559a58be647bcd24c9837e8208ed1187721063a95abc120dffd860e13bd996a4f89f5e90de2d56ccd3750cce42e WHIRLPOOL 23bad2bf3daef731a5ffe967fe99e2dac698131f6b5e7becc2e9f4eaf3e9aa791f34b346382c84247f08e6717c07977c2e0104b1adb6877db6f29129ea4b4b43
diff --git a/sci-biology/ICC/metadata.xml b/sci-biology/ICC/metadata.xml
deleted file mode 100644
index 138cb7705..000000000
--- a/sci-biology/ICC/metadata.xml
+++ /dev/null
@@ -1,12 +0,0 @@
-<?xml version="1.0" encoding="UTF-8"?>
-<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
-<pkgmetadata>
-	<maintainer type="person">
-		<email>mmokrejs@fold.natur.cuni.cz</email>
-		<name>Martin Mokrejs</name>
-	</maintainer>
-	<maintainer type="project">
-		<email>sci-biology@gentoo.org</email>
-		<name>Gentoo Biology Project</name>
-	</maintainer>
-</pkgmetadata>
diff --git a/sci-biology/IMAGE/IMAGE-2.4.1.ebuild b/sci-biology/IMAGE/IMAGE-2.4.1.ebuild
index 82447fb2b..df06eb8eb 100644
--- a/sci-biology/IMAGE/IMAGE-2.4.1.ebuild
+++ b/sci-biology/IMAGE/IMAGE-2.4.1.ebuild
@@ -1,19 +1,28 @@
-# Copyright 1999-2015 Gentoo Foundation
+# Copyright 1999-2021 Gentoo Authors
 # Distributed under the terms of the GNU General Public License v2
 
-EAPI=5
+EAPI=7
+
+inherit perl-functions
 
 DESCRIPTION="Iterative Mapping and Assembly for Gap Elimination using paired-end Illumina"
 HOMEPAGE="https://sourceforge.net/apps/mediawiki/image2"
-SRC_URI="http://sourceforge.net/projects/image2/files/IMAGE_version2.4.1_64bit.zip"
+SRC_URI="https://sourceforge.net/projects/image2/files/IMAGE_version${PV}_64bit.zip"
 
 #http://genomebiology.com/2010/11/4/R41
 LICENSE="CC-BY-2.0"
 SLOT="0"
-KEYWORDS=""
-IUSE=""
+KEYWORDS="~amd64"
 
 # contains bundled binaries:
 # nucmer smalt_x86_64 ssaha2 ssaha2Build velvetg velveth
 DEPEND=""
 RDEPEND="${DEPEND}"
+BDEPEND="app-arch/unzip"
+
+S="${WORKDIR}/${PN}_version2.4"
+
+src_install() {
+	perl_doexamples example/
+	perl_domodule *.pl
+}
diff --git a/sci-biology/InterMine/InterMine-0.98.ebuild b/sci-biology/InterMine/InterMine-0.98.ebuild
deleted file mode 100644
index 2159f4dba..000000000
--- a/sci-biology/InterMine/InterMine-0.98.ebuild
+++ /dev/null
@@ -1,23 +0,0 @@
-# Copyright 1999-2015 Gentoo Foundation
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=5
-
-[ "$PV" == "9999" ] && inherit git-r3
-
-DESCRIPTION="Biological data warehouse integrating complex data"
-HOMEPAGE="http://github.com/intermine/intermine"
-if [ "$PV" == "9999" ]; then
-	EGIT_REPO_URI="https://github.com/intermine/intermine"
-	KEYWORDS=""
-else
-	SRC_URI=""
-	KEYWORDS="~amd64"
-fi
-
-LICENSE="LGPL-2.1+"
-SLOT="0"
-IUSE=""
-
-DEPEND=""
-RDEPEND="${DEPEND}"
diff --git a/sci-biology/InterMine/metadata.xml b/sci-biology/InterMine/metadata.xml
deleted file mode 100644
index 0114515a6..000000000
--- a/sci-biology/InterMine/metadata.xml
+++ /dev/null
@@ -1,15 +0,0 @@
-<?xml version="1.0" encoding="UTF-8"?>
-<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
-<pkgmetadata>
-	<maintainer type="person">
-		<email>mmokrejs@fold.natur.cuni.cz</email>
-		<name>Martin Mokrejs</name>
-	</maintainer>
-	<maintainer type="project">
-		<email>sci-biology@gentoo.org</email>
-		<name>Gentoo Biology Project</name>
-	</maintainer>
-	<upstream>
-		<remote-id type="github">intermine/intermine</remote-id>
-	</upstream>
-</pkgmetadata>
diff --git a/sci-biology/KING/KING-2.2.7.ebuild b/sci-biology/KING/KING-2.2.7.ebuild
new file mode 100644
index 000000000..6d01ca794
--- /dev/null
+++ b/sci-biology/KING/KING-2.2.7.ebuild
@@ -0,0 +1,24 @@
+# Copyright 1999-2021 Gentoo Authors
+# Distributed under the terms of the GNU General Public License v2
+
+EAPI=7
+
+inherit toolchain-funcs
+
+MY_P="KING${PV}"
+DESCRIPTION="Check family relationship and infer population structure"
+HOMEPAGE="https://kingrelatedness.com"
+SRC_URI="https://www.kingrelatedness.com/executables/${MY_P}code.tar.gz -> ${P}.tar.gz"
+S="${WORKDIR}"
+
+LICENSE="all-rights-reserved" # Our robust relationship inference algorithm is implemented in a freely available software package
+SLOT="0"
+KEYWORDS="~amd64 ~x86"
+
+src_compile(){
+	$(tc-getCXX) ${CXXFLAGS} -lm -lz -fopenmp -o king *.cpp
+}
+
+src_install(){
+	newbin {king,KING}
+}
diff --git a/sci-biology/KING/KING-20161017.ebuild b/sci-biology/KING/KING-20161017.ebuild
deleted file mode 100644
index 95ba91702..000000000
--- a/sci-biology/KING/KING-20161017.ebuild
+++ /dev/null
@@ -1,33 +0,0 @@
-# Copyright 1999-2017 Gentoo Foundation
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=6
-
-inherit eutils toolchain-funcs
-
-DESCRIPTION="Check family relationship and infer population structure"
-HOMEPAGE="http://people.virginia.edu/~wc9c/KING
-	http://people.virginia.edu/~wc9c/publications/pdf/BI26_2867.pdf"
-SRC_URI="http://people.virginia.edu/~wc9c/KING/KINGcode.tar.gz -> ${P}.tar.gz
-	http://people.virginia.edu/~wc9c/KING/manual.html -> ${PN}_relationship_inference.html
-	http://people.virginia.edu/~wc9c/KING/kingpopulation.html -> ${PN}.kingpopulation.html"
-
-LICENSE="all-rights-reserved" # Our robust relationship inference algorithm is implemented in a freely available software package
-SLOT="0"
-KEYWORDS="~amd64 ~x86"
-IUSE=""
-
-DEPEND=""
-RDEPEND="${DEPEND}"
-
-S="${WORKDIR}"
-
-src_compile(){
-	$(tc-getCXX) ${CXXFLAGS} -lm -lz -fopenmp -o king *.cpp
-}
-
-src_install(){
-	newbin {king,KING}
-	insinto /usr/share/doc/"${PN}"
-	dodoc "${DISTDIR}"/"${PN}"_relationship_inference.html "${DISTDIR}"/"${PN}".kingpopulation.html
-}
diff --git a/sci-biology/KING/Manifest b/sci-biology/KING/Manifest
index 5901c92b2..5c06973e1 100644
--- a/sci-biology/KING/Manifest
+++ b/sci-biology/KING/Manifest
@@ -1,3 +1 @@
-DIST KING-20161017.tar.gz 367891 SHA256 94b8cbca543c02ecff4bdd81c95957cde7e935eaeb4708db423fd79358a38e28 SHA512 27602b1be3ce241ba9edf5806f308940387af309232cd6d3e8058d28034481e32ad11ab99f496dc6abd86d22e7c27d64922971bb0902e9e91fd3ec64c3ad1dea WHIRLPOOL 3b7cbe762b1d0d51fe3e8d088e707198e5610be02c564bd68ff943a501c12d641f61cd41d627d05eee6db455c71117e43ff1d41051f56347a0994d9b060341cc
-DIST KING.kingpopulation.html 8679 SHA256 3dab294ecd03aafff647d972bcdbad2c25271f3a80877a6eac1078b27e392e55 SHA512 799752b9d23652c56ef2a7341840811439e7760f181f9804b9b14a41ba06bd3873b1611cbf0ceafd32177e511937aaed37eb84a82d29bc1b5d207529577ecb24 WHIRLPOOL ff044f1c67f72d3228baf226ccbe21c14b4971928a609b57fa044ebe1b733d2f8d1e90bb72ed1770ec6c7803925fe6820243b027722cb0bd0bd8554fcee69ff3
-DIST KING_relationship_inference.html 13084 SHA256 24ad49ed36f589c3a07ebfe6c655c7b49fafe432782a4374f14175cfcdde5223 SHA512 e3e516e642cc7696e189871fc3a1a16629c92cdcdc651cff5a8488dd8dc8e9dc44eb065746a2a51a2e269f4c70c7c2840a5fc5f494d6ee35e0003a3eb3df3381 WHIRLPOOL f9860f5baf88f6d4a6e6bdb2281c6f5988ce88927008899b007bdc53165deda35a6f01fcf683e7044bfdb5d03450870bda4bf3cff94876520a8c84e6ff6b58c5
+DIST KING-2.2.7.tar.gz 527147 BLAKE2B cdc294de47895088ce7917e9aae8aafce0dc293e542636c02d6356c5f42cfbb2f17986d1bf1f05b450528f27b9e9596483440134fc4cb576206742c9a8253160 SHA512 0953d4c5396395518599cc9abd31f645a804d096d19e9f33ae75362c9cf9649fbdfd3acf2d3969cc0dd17c98e7b18f1db7af4500621c55aba411b045f7b8d5de
diff --git a/sci-biology/KaKs_Calculator/KaKs_Calculator-1.2.ebuild b/sci-biology/KaKs_Calculator/KaKs_Calculator-1.2.ebuild
index 929117604..38383a14d 100644
--- a/sci-biology/KaKs_Calculator/KaKs_Calculator-1.2.ebuild
+++ b/sci-biology/KaKs_Calculator/KaKs_Calculator-1.2.ebuild
@@ -1,13 +1,12 @@
-# Copyright 1999-2019 Gentoo Authors
+# Copyright 1999-2021 Gentoo Authors
 # Distributed under the terms of the GNU General Public License v2
 
 EAPI=7
 
-inherit eutils toolchain-funcs
+inherit toolchain-funcs
 
 DESCRIPTION="Calculate nonsynonymous (Ka) and synonymous (Ks) substitution rates"
-HOMEPAGE="https://code.google.com/p/kaks-calculator
-	http://bigd.big.ac.cn/tools/kaks"
+HOMEPAGE="https://bigd.big.ac.cn/tools/kaks"
 SRC_URI="
 	https://storage.googleapis.com/google-code-archive-downloads/v2/code.google.com/kaks-calculator/KaKs_Calculator"${PV}".tar.gz -> ${P}.tar.gz
 	https://storage.googleapis.com/google-code-archive-downloads/v2/code.google.com/kaks-calculator/parseFastaIntoAXT.pl
diff --git a/sci-biology/KaKs_Calculator/KaKs_Calculator-2.0.ebuild b/sci-biology/KaKs_Calculator/KaKs_Calculator-2.0.ebuild
index 5edd1323a..c01f01587 100644
--- a/sci-biology/KaKs_Calculator/KaKs_Calculator-2.0.ebuild
+++ b/sci-biology/KaKs_Calculator/KaKs_Calculator-2.0.ebuild
@@ -1,17 +1,17 @@
-# Copyright 1999-2019 Gentoo Authors
+# Copyright 1999-2021 Gentoo Authors
 # Distributed under the terms of the GNU General Public License v2
 
 EAPI=7
 
-inherit eutils toolchain-funcs
+inherit toolchain-funcs
 
 DESCRIPTION="Calculate nonsynonymous (Ka) and synonymous (Ks) substitution rates"
-HOMEPAGE="https://code.google.com/p/kaks-calculator
+HOMEPAGE="
 	https://sourceforge.net/projects/kakscalculator2/
 	https://www.sciencedirect.com/science/article/pii/S1672022910600083"
 SRC_URI="
 	https://netcologne.dl.sourceforge.net/project/kakscalculator2/${PN}${PV}.tar.gz -> ${P}.tar.gz
-	https://github.com/WilsonSayresLab/AlignmentProcessor/blob/master/KaKs_Calculator/${PN}${PV}/${PN}${PV}_manual.pdf -> ${P}_manual.pdf
+	https://raw.githubusercontent.com/WilsonSayresLab/AlignmentProcessor/master/${PN}/${PN}${PV}/${PN}${PV}_manual.pdf -> ${P}_manual.pdf
 	https://s3.amazonaws.com/fumba.me/share+files/1-s2.0-S1672022907600072-main.pdf -> ${PN}-Zhang_et_al_2006.pdf"
 
 LICENSE="GPL-3"
diff --git a/sci-biology/KaKs_Calculator/Manifest b/sci-biology/KaKs_Calculator/Manifest
index 9e3f8a37d..4db8e2068 100644
--- a/sci-biology/KaKs_Calculator/Manifest
+++ b/sci-biology/KaKs_Calculator/Manifest
@@ -1,6 +1,6 @@
 DIST KaKs_Calculator-1.2.tar.gz 2301729 BLAKE2B d8d7812d61b26bce8868e9de59511c0d119c43f725d1f5b4bfbf2b7cddd3c3844e348c9003126ddaff4b0d3d0a0ada2ce1733cda0b1129b7b801114eaaf74f86 SHA512 a1a18229d89262425f879695a1f44ebecbe473c32bcf7ee0d2a2d5d36d34a45b88f5fdcedbacdf0070eb5f0feedff9d74616849aff3cf44f210fdbc65ed56e2c
 DIST KaKs_Calculator-1.2_manual.pdf 72922 BLAKE2B 7c0db9bbca331ecec0e088938217c33c9a70b61732355568a99426663328b2071501c0abf9268d36661ad04af6ea1bf10cb35f72fba03956dc455ff36217e942 SHA512 11c99c4421449ae22d80bf35b063214e3b39d2fa1bd7e7de7a2cfa89aeb0f309f5d1e1cb2fe7cb646c0277d36a951dce04fca00fb957bb713e072d82c9c67566
 DIST KaKs_Calculator-2.0.tar.gz 2104721 BLAKE2B 1782f7ae96695b4a1c01a9f317412bf5e1b910bafbd6f911f97a40eaf459eb2b3b1b65728a7478dff30c00db337f1f4dbae741de569019d2d063688b4f7438d9 SHA512 db8edbd22624a2adb17b3adebc392b1ac327ce0404d6fb184dc9dd8fa3d3b670408b8dc993a29625121610db07ad92bba7613e80abe372ad14bd63248aeda587
-DIST KaKs_Calculator-2.0_manual.pdf 55736 BLAKE2B b8f5103cf7032106e9783fbbddd6417ab1989c090ec770fc474432853d9ca62881c71752a94ea9a0bbbb4442a191ff30b0980d08f78e139f25f99fa471537263 SHA512 ac66a5ec665081778162fc557c609765ae13f30513b3d7cc80d3d400d2f44fbbb54329e2460f7da0c6d8e3fdd26b77c0e86737a0fe721636c34f3ab433dee401
+DIST KaKs_Calculator-2.0_manual.pdf 370524 BLAKE2B 049a4bf338300a323b748b29ca610ff987da8cdba97a6590c38259cac7b4fbd19aa83b7f8654990373436ad935041caf19faa735c8b310bc6bd16d9ba6d5ef57 SHA512 44434b7756995a161c35d3e89c1d8fd0f9139cd74c11db9b7b1fae0335c057a514689a054c949e2cd1d6d694e8a14f542bbb12254e9548f7ed32a459b30482f6
 DIST KaKs_Calculator-Zhang_et_al_2006.pdf 160940 BLAKE2B 2f7e74f44be783f7d7c9973f5d481e54f989733392dee9143a3dc439817d359c3da369d91865c48b4d82ef04d2001cb0ea6d0cea14e1a3a36043ee53b6ac3df1 SHA512 e9a15a41ec4919d302c38f65654beed9cb5a71d9a25f49458dca8a7431a015fa4b955855b97185c2a1d1d19a8fc1f2b0af78f5ab38db3dffec9f14adaa47697a
 DIST parseFastaIntoAXT.pl 1483 BLAKE2B 5fb82e508bd277cdf1df1b3df63e3449c9569d3334db8f1a259ef69fe45981b40265290c92ba6120b2463809830641878e2cb207118b7dbfc163fad9869e62d9 SHA512 38d39d0fe1f788cf45d742e9fd6b0918a78973faecdb10d98d39384670abdef7212dbd2cdea777f0d5fcbbf202f5331f9fe178ef0f48fafe9e0a31625ab532a1
diff --git a/sci-biology/LINKS/LINKS-2.0.1.ebuild b/sci-biology/LINKS/LINKS-2.0.1.ebuild
new file mode 100644
index 000000000..c1c9cc5d8
--- /dev/null
+++ b/sci-biology/LINKS/LINKS-2.0.1.ebuild
@@ -0,0 +1,21 @@
+# Copyright 1999-2022 Gentoo Authors
+# Distributed under the terms of the GNU General Public License v2
+
+EAPI=8
+
+DESCRIPTION="Scaffold genome assemblies by Chromium/PacBio/Nanopore reads"
+HOMEPAGE="https://github.com/bcgsc/LINKS"
+SRC_URI="https://github.com/bcgsc/LINKS/releases/download/v${PV}/links-v${PV}.tar.gz -> ${P}.tar.gz"
+S="${WORKDIR}/links-${PV}"
+
+LICENSE="GPL-3"
+SLOT="0"
+KEYWORDS="~amd64"
+
+RDEPEND="
+	>=dev-lang/perl-1.6
+	dev-util/cppcheck
+"
+DEPEND="${RDEPEND}
+	dev-lang/swig
+"
diff --git a/sci-biology/LINKS/Manifest b/sci-biology/LINKS/Manifest
new file mode 100644
index 000000000..e57aae29d
--- /dev/null
+++ b/sci-biology/LINKS/Manifest
@@ -0,0 +1 @@
+DIST LINKS-2.0.1.tar.gz 4566466 BLAKE2B 0713278c17b5d6fce3d6c0bbfffd2decd71599464b9d4c7da5b82997dfc6f2e1be7435dc26bc96eb6ce23ba0bd8136f8ca714e327de465137e0435ebdaa19d9c SHA512 2bbcc264da6dbe361d8224e2a123983c4f09a4b051490d599f193e3f02463e4e8ff2fadf72b8be2df6adee6db886b76d59eee179648cfed6a025c31d7fe2c696
diff --git a/app-arch/libdeflate/metadata.xml b/sci-biology/LINKS/metadata.xml
index 138cb7705..138cb7705 100644
--- a/app-arch/libdeflate/metadata.xml
+++ b/sci-biology/LINKS/metadata.xml
diff --git a/sci-biology/MaSuRCA/MaSuRCA-3.2.2.ebuild b/sci-biology/MaSuRCA/MaSuRCA-3.2.2.ebuild
deleted file mode 100644
index 2f2f9ddbd..000000000
--- a/sci-biology/MaSuRCA/MaSuRCA-3.2.2.ebuild
+++ /dev/null
@@ -1,35 +0,0 @@
-# Copyright 1999-2017 Gentoo Foundation
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=6
-
-DESCRIPTION="de Bruijn and OLC assembler for Sanger, Roche 454, Illumina, Pacbio, Nanopore"
-HOMEPAGE="http://www.genome.umd.edu/masurca.html
-	http://bioinformatics.oxfordjournals.org/content/29/21/2669
-	http://biorxiv.org/content/biorxiv/early/2016/07/26/066100.full.pdf"
-SRC_URI="${P}.tar.gz
-	ftp://ftp.genome.umd.edu/pub/MaSuRCA/MaSuRCA_QuickStartGuide.pdf"
-
-LICENSE="BSD GPL-2 GPL-3"
-SLOT="0"
-KEYWORDS=""
-IUSE=""
-
-DEPEND=">=dev-lang/perl-5.8
-		app-arch/bzip2"
-RDEPEND="${DEPEND}"
-
-RESTRICT="fetch"
-
-src_configure(){
-	./install.sh || die
-}
-
-src_compile(){
-	./install.sh || die
-}
-
-src_install(){
-	dobin masurca
-	dodoc sr_config_example.txt
-}
diff --git a/sci-biology/MaSuRCA/MaSuRCA-4.0.1.ebuild b/sci-biology/MaSuRCA/MaSuRCA-4.0.1.ebuild
new file mode 100644
index 000000000..7b070e595
--- /dev/null
+++ b/sci-biology/MaSuRCA/MaSuRCA-4.0.1.ebuild
@@ -0,0 +1,29 @@
+# Copyright 1999-2023 Gentoo Authors
+# Distributed under the terms of the GNU General Public License v2
+
+EAPI=8
+
+DESCRIPTION="de Bruijn and OLC assembler for Sanger, Roche 454, Illumina, Pacbio, Nanopore"
+HOMEPAGE="http://www.genome.umd.edu/masurca.html
+	http://bioinformatics.oxfordjournals.org/content/29/21/2669
+	https://github.com/alekseyzimin/masurca"
+SRC_URI="https://github.com/alekseyzimin/masurca/releases/download/v${PV}/${P}.tar.gz"
+
+LICENSE="BSD GPL-2 GPL-3"
+SLOT="0"
+# Known to produce build failure:
+# https://github.com/alekseyzimin/masurca/issues/323
+KEYWORDS=""
+
+DEPEND="
+	>=dev-lang/perl-5.8
+	app-arch/bzip2
+"
+RDEPEND="${DEPEND}"
+
+src_compile(){
+	./install.sh || die
+}
+src_install(){
+	dobin masurca
+}
diff --git a/sci-biology/MaSuRCA/MaSuRCA-4.1.0.ebuild b/sci-biology/MaSuRCA/MaSuRCA-4.1.0.ebuild
new file mode 100644
index 000000000..7b070e595
--- /dev/null
+++ b/sci-biology/MaSuRCA/MaSuRCA-4.1.0.ebuild
@@ -0,0 +1,29 @@
+# Copyright 1999-2023 Gentoo Authors
+# Distributed under the terms of the GNU General Public License v2
+
+EAPI=8
+
+DESCRIPTION="de Bruijn and OLC assembler for Sanger, Roche 454, Illumina, Pacbio, Nanopore"
+HOMEPAGE="http://www.genome.umd.edu/masurca.html
+	http://bioinformatics.oxfordjournals.org/content/29/21/2669
+	https://github.com/alekseyzimin/masurca"
+SRC_URI="https://github.com/alekseyzimin/masurca/releases/download/v${PV}/${P}.tar.gz"
+
+LICENSE="BSD GPL-2 GPL-3"
+SLOT="0"
+# Known to produce build failure:
+# https://github.com/alekseyzimin/masurca/issues/323
+KEYWORDS=""
+
+DEPEND="
+	>=dev-lang/perl-5.8
+	app-arch/bzip2
+"
+RDEPEND="${DEPEND}"
+
+src_compile(){
+	./install.sh || die
+}
+src_install(){
+	dobin masurca
+}
diff --git a/sci-biology/MaSuRCA/Manifest b/sci-biology/MaSuRCA/Manifest
index f15817f90..fd6029f04 100644
--- a/sci-biology/MaSuRCA/Manifest
+++ b/sci-biology/MaSuRCA/Manifest
@@ -1,2 +1,2 @@
-DIST MaSuRCA-3.2.2.tar.gz 23269939 SHA256 b0535e9cca6fa3699290d5a31f3d30b6270ba3c75f8197d8bd142ba81eed5202 SHA512 274184de19e20e7e6eb31bdd62f69e02ea77657da1821207edb5c0f3a9c0d829426d14e4551d594411a17ca2ae8fdc81c3b2b19ae6c3978b641e60b8a80a2032 WHIRLPOOL 7e24c3150771083ed5cf9792c98db9db79d3b25178e693c5de93899f6bf028cc90b15027b6e68bbf36e4fff60010351db2cee6f60d5e5248b66eb308298021f8
-DIST MaSuRCA_QuickStartGuide.pdf 153680 BLAKE2B 608a7f962fbec2982626f14a0fe3d7c7aa8e57582b9366c48e8981706edadce44f304f3addecb1f4f556de9fdd57500760a82bd9e00a85d34e7f35a3d003a8d4 SHA512 d887c36ec30cb89ecbde73517055592fd370721bb8945f293c508d0ca6851160326bf2d2b3ade89324611ea5d4bc238068f422df4c5693672623961383635f24
+DIST MaSuRCA-4.0.1.tar.gz 26502309 BLAKE2B 658c3a85d3d16bc966f50def9b0f98503f25f89893a18f6b7c361592dc2b20875f4c2b78e55e7279e47d0d381e9f973185da7cf7a1529c617c82b0789dea4183 SHA512 5a52dc6667b501ef5ee33f8c30a516a466b39b061ae3bee93f3e6a9cc9dd21503365671d93858165290b3200c859772324fdb12f8bdab235b3ff08c158c4dd66
+DIST MaSuRCA-4.1.0.tar.gz 26532049 BLAKE2B 93cf8cc2bcb4d2c56961f66c0e045ad7776011b4a5f78e5944c5e9b74004c553fc38e542a163aa2efca0aff0e2726fc38eea1aba8f2da287c5154c9eae4e9bcf SHA512 6de57abff87de2fd8c30bcc7efbd6c37358d37eab518d36ccbe48f036af6e1bc22a655abb59f32df613d99c84a5deca272c8c894395f255bcbceb4da5368e64a
diff --git a/sci-biology/MaSuRCA/metadata.xml b/sci-biology/MaSuRCA/metadata.xml
index 138cb7705..8a631d677 100644
--- a/sci-biology/MaSuRCA/metadata.xml
+++ b/sci-biology/MaSuRCA/metadata.xml
@@ -9,4 +9,7 @@
 		<email>sci-biology@gentoo.org</email>
 		<name>Gentoo Biology Project</name>
 	</maintainer>
+	<upstream>
+		<remote-id type="github">alekseyzimin/masurca</remote-id>
+	</upstream>
 </pkgmetadata>
diff --git a/sci-biology/MagicViewer/MagicViewer-1.2.1.ebuild b/sci-biology/MagicViewer/MagicViewer-1.2.1.ebuild
deleted file mode 100644
index 403b99d9b..000000000
--- a/sci-biology/MagicViewer/MagicViewer-1.2.1.ebuild
+++ /dev/null
@@ -1,23 +0,0 @@
-# Copyright 1999-2017 Gentoo Foundation
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=6
-
-inherit java-pkg-2 java-ant-2
-
-DESCRIPTION="Display short reads alignment"
-HOMEPAGE="http://bioinformatics.zj.cn/magicviewer"
-SRC_URI="
-	http://59.79.168.90/soft/${PN}_${PV}_x86_64_linux.tar.gz
-	http://59.79.168.90/soft/${PN}_${PV}_x86_32_linux.tar.gz"
-
-LICENSE="GRL"
-SLOT="0"
-KEYWORDS=""
-IUSE=""
-
-DEPEND=">=virtual/jdk-1.6:*"
-RDEPEND=">=virtual/jre-1.6:*"
-
-# TODO: install either contents from
-#          MagicViewer_1.2.1_x86_32_linux/ subdir or MagicViewer_1.2.1_x86_64_linux/
diff --git a/sci-biology/MagicViewer/Manifest b/sci-biology/MagicViewer/Manifest
deleted file mode 100644
index 88cdf0a48..000000000
--- a/sci-biology/MagicViewer/Manifest
+++ /dev/null
@@ -1,2 +0,0 @@
-DIST MagicViewer_1.2.1_x86_32_linux.tar.gz 27177280 SHA256 0e61e53a2765abcdaa2eba782e4ad834062e274da38bbcef6abb74a161840118 SHA512 5435fd4b859c8db3d90aab345788ae569647826cae025edec3a2b5f38fa5d7238d7cccb8f742e611551ee64720d37e0bd1b9bab5bb1820bb47be9d16048e136c WHIRLPOOL f467d62ca555ffab2ee2c74843e063496f9c35f8966d5a1030d3e19032ee58508520790a36c43ea8aa2a4629a3baf9a76e477e57a27d86ef3b63564c9497e9c2
-DIST MagicViewer_1.2.1_x86_64_linux.tar.gz 26976321 SHA256 daa1b624ff04952faf232a449ce3e01e990168357f8bc5d22c7c01042b963fa0 SHA512 aa37746c287bcae81d3a3df97e6042ee611aad5f7ef42f4b1355425011ccd0fb305d6852bcf4c82eb9c43346cb9a4ba0c894d925a5c6ec5a8c007501cd820302 WHIRLPOOL ae8a96fd00bb44188c474e75eae3c03f0a518428fa6108bd3b77245eba5227759e4015364e58b5e0b8f986775faa99952d5ede2a489ac3080de0632a74d9d44b
diff --git a/sci-biology/MagicViewer/metadata.xml b/sci-biology/MagicViewer/metadata.xml
deleted file mode 100644
index 138cb7705..000000000
--- a/sci-biology/MagicViewer/metadata.xml
+++ /dev/null
@@ -1,12 +0,0 @@
-<?xml version="1.0" encoding="UTF-8"?>
-<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
-<pkgmetadata>
-	<maintainer type="person">
-		<email>mmokrejs@fold.natur.cuni.cz</email>
-		<name>Martin Mokrejs</name>
-	</maintainer>
-	<maintainer type="project">
-		<email>sci-biology@gentoo.org</email>
-		<name>Gentoo Biology Project</name>
-	</maintainer>
-</pkgmetadata>
diff --git a/sci-biology/MeV/Manifest b/sci-biology/MeV/Manifest
index 0a8f99e09..a3c7b3e5c 100644
--- a/sci-biology/MeV/Manifest
+++ b/sci-biology/MeV/Manifest
@@ -1 +1 @@
-DIST MeV_4_8_1_r2727_linux.tar.gz 81391795 BLAKE2B ef3010a8116ce9b23f7dc2a84de26aa08f26a541b2e07f45d57ffd6b489172eaa51e273b43b964e4ddc64b62f6594ef15030818862be2b67d948d6fae812b5a0 SHA512 60a6a17fefbbb57f50d97edf23f2c69aae5c9423400aecf9d1f4d19374356637d52aee53e63e87d65a02ef19d8bd3ca08b63c783ec483ab0214e01a5ea71c7ce
+DIST MeV-4.8.1.tar.gz 81391795 BLAKE2B ef3010a8116ce9b23f7dc2a84de26aa08f26a541b2e07f45d57ffd6b489172eaa51e273b43b964e4ddc64b62f6594ef15030818862be2b67d948d6fae812b5a0 SHA512 60a6a17fefbbb57f50d97edf23f2c69aae5c9423400aecf9d1f4d19374356637d52aee53e63e87d65a02ef19d8bd3ca08b63c783ec483ab0214e01a5ea71c7ce
diff --git a/sci-biology/MeV/MeV-4.8.1.ebuild b/sci-biology/MeV/MeV-4.8.1.ebuild
index 50ec72254..eb605976e 100644
--- a/sci-biology/MeV/MeV-4.8.1.ebuild
+++ b/sci-biology/MeV/MeV-4.8.1.ebuild
@@ -1,23 +1,20 @@
-# Copyright 1999-2016 Gentoo Foundation
+# Copyright 1999-2021 Gentoo Authors
 # Distributed under the terms of the GNU General Public License v2
 
-EAPI=5
+EAPI=7
 
-#MY_PV="${PV/./_/}"
-MY_PV="4_8_1"
+MY_PV="${PV//./_}"
 
-inherit java-pkg-2 java-ant-2 eutils
+inherit java-pkg-2 java-ant-2
 
 DESCRIPTION="Multiple experiment Viewer for genomic data analysis"
-HOMEPAGE="http://mev-tm4.sourceforge.net"
-SRC_URI="http://downloads.sourceforge.net/project/mev-tm4/mev-tm4/MeV%20${PV}/MeV_${MY_PV}_r2727_linux.tar.gz"
+HOMEPAGE="https://sourceforge.net/projects/mev-tm4/"
+SRC_URI="https://downloads.sourceforge.net/project/mev-tm4/mev-tm4/MeV%20${PV}/MeV_${MY_PV}_r2727_linux.tar.gz -> ${P}.tar.gz"
 
 LICENSE="Artistic-2"
 SLOT="0"
-KEYWORDS=""
-IUSE=""
+KEYWORDS="~amd64"
 
-DEPEND=""
 RDEPEND=">=virtual/jre-1.5:*
 	${DEPEND}"
 DEPEND="${RDEPEND}
@@ -25,4 +22,12 @@ DEPEND="${RDEPEND}
 		dev-java/ant-core
 		"
 
-S="${WORKDIR}"/"${PN}"_"${MY_PV}"
+S="${WORKDIR}/${PN}_${MY_PV}"
+
+src_install() {
+	dodoc -r documentation/*
+	rm -r documentation
+	insinto "/opt/${PN}"
+	doins -r *
+	dosym ../${PN}/tmev.sh /opt/bin/tmev
+}
diff --git a/sci-biology/MeV/metadata.xml b/sci-biology/MeV/metadata.xml
index bd7adb92f..334d55097 100644
--- a/sci-biology/MeV/metadata.xml
+++ b/sci-biology/MeV/metadata.xml
@@ -9,6 +9,6 @@
 		<name>Gentoo Biology Project</name>
 	</maintainer>
 	<upstream>
-		<remote-id type="sourceforge">downloads</remote-id>
+		<remote-id type="sourceforge">mev-tm4</remote-id>
 	</upstream>
 </pkgmetadata>
diff --git a/sci-biology/MochiView/Manifest b/sci-biology/MochiView/Manifest
new file mode 100644
index 000000000..86278527b
--- /dev/null
+++ b/sci-biology/MochiView/Manifest
@@ -0,0 +1 @@
+DIST MochiView_v146.zip 12300500 BLAKE2B a85169437bc04e420e4e483f4eb98401e3e72dab1a096a5063e51c7d6d1917b3d455a91c4deb2b51c1c4be9fea18c36b97399331737ab7f217c124493dec3fb7 SHA512 c0fb8e101b1193c973d532191521b57b20ccf4843769691850d825eb750cfd76fb7f225b6becb65839a8b57fd162143787158329a5f6b8201e03b17ffcd4fd10
diff --git a/sci-biology/MochiView/MochiView-1.45.ebuild b/sci-biology/MochiView/MochiView-1.45.ebuild
deleted file mode 100644
index 61e0be859..000000000
--- a/sci-biology/MochiView/MochiView-1.45.ebuild
+++ /dev/null
@@ -1,16 +0,0 @@
-# Copyright 1999-2015 Gentoo Foundation
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=5
-
-DESCRIPTION="Genome browser and analysis"
-HOMEPAGE="http://johnsonlab.ucsf.edu/mochi.html"
-SRC_URI=""
-
-LICENSE="MIT"
-SLOT="0"
-KEYWORDS=""
-IUSE=""
-
-DEPEND=""
-RDEPEND="${DEPEND}"
diff --git a/sci-biology/MochiView/MochiView-1.46.ebuild b/sci-biology/MochiView/MochiView-1.46.ebuild
new file mode 100644
index 000000000..c3e69194b
--- /dev/null
+++ b/sci-biology/MochiView/MochiView-1.46.ebuild
@@ -0,0 +1,23 @@
+# Copyright 1999-2021 Gentoo Authors
+# Distributed under the terms of the GNU General Public License v2
+
+EAPI=7
+
+inherit java-utils-2
+
+DESCRIPTION="Genome browser and analysis"
+HOMEPAGE="https://www.johnsonlab.ucsf.edu/mochi.html"
+SRC_URI="https://www.johnsonlab.ucsf.edu/s/MochiView_v${PV//.}.zip"
+
+LICENSE="MIT LGPL-3 MPL-1.1 Apache-2.0"
+SLOT="0"
+KEYWORDS="~amd64"
+
+RDEPEND=">=virtual/jre-1.7:*"
+BDEPEND="app-arch/unzip"
+
+S="${WORKDIR}/${PN}_v${PV}"
+
+src_install() {
+	java-pkg_dojar INTERNAL_USE/*.jar
+}
diff --git a/sci-biology/MolBioLib/Manifest b/sci-biology/MolBioLib/Manifest
deleted file mode 100644
index fcfe68414..000000000
--- a/sci-biology/MolBioLib/Manifest
+++ /dev/null
@@ -1 +0,0 @@
-DIST MolBioLib_public.version5.tar.gz 2414384 BLAKE2B 845ac366ed41886cc0d3d96376dc9a97bae3d84bfc41d5f9e5be4fa274a6d64a981fcbcc12de28e1518212313af12330b08cac5488e7db9a2738c7846b981cb7 SHA512 056c38bcb65b845b32678fb8c5d758023154c07085414194e98e58281e61e475dca7321c8d684955c88bf459bc92c9d39f8b6091d0b804581e6f6e6ecabe3832
diff --git a/sci-biology/MolBioLib/MolBioLib-5.ebuild b/sci-biology/MolBioLib/MolBioLib-5.ebuild
deleted file mode 100644
index 681758724..000000000
--- a/sci-biology/MolBioLib/MolBioLib-5.ebuild
+++ /dev/null
@@ -1,39 +0,0 @@
-# Copyright 1999-2017 Gentoo Foundation
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=6
-
-DESCRIPTION="C++11 framework for rapid develop and deploy of bioinformatic tasks"
-HOMEPAGE="https://sourceforge.net/projects/molbiolib"
-SRC_URI="https://sourceforge.net/projects/molbiolib/files/MolBioLib_public.version${PV}.tar.gz"
-
-LICENSE="GPL-3"
-SLOT="0"
-KEYWORDS="" # does not build
-IUSE="doc"
-
-# contains bundled samtools-0.1.18 and bamtools (pezmaster31-bamtools-d553a62) which contains jsoncpp
-# also needs app-doc/doxygen
-DEPEND="
-	dev-lang/perl
-	sys-devel/gcc:*
-	sys-devel/clang:*
-	>=sci-biology/samtools-0.1.18:0
-	<sci-biology/samtools-1:0
-	doc? ( app-doc/doxygen )"
-RDEPEND="${DEPEND}"
-
-S="${WORKDIR}"/MolBioLib
-
-src_prepare(){
-	# edit MakeAllApps.pl
-	default
-}
-
-src_compile(){
-	perl MakeAllApps.pl || die
-}
-
-src_install(){
-	dodoc -r docs/doxygen/*
-}
diff --git a/sci-biology/MolBioLib/metadata.xml b/sci-biology/MolBioLib/metadata.xml
deleted file mode 100644
index 3b9e38617..000000000
--- a/sci-biology/MolBioLib/metadata.xml
+++ /dev/null
@@ -1,15 +0,0 @@
-<?xml version="1.0" encoding="UTF-8"?>
-<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
-<pkgmetadata>
-	<maintainer type="person">
-		<email>mmokrejs@fold.natur.cuni.cz</email>
-		<name>Martin Mokrejs</name>
-	</maintainer>
-	<maintainer type="project">
-		<email>sci-biology@gentoo.org</email>
-		<name>Gentoo Biology Project</name>
-	</maintainer>
-	<upstream>
-		<remote-id type="sourceforge">molbiolib</remote-id>
-	</upstream>
-</pkgmetadata>
diff --git a/sci-biology/MuSeqBox/Manifest b/sci-biology/MuSeqBox/Manifest
index 4b2bfab1f..e9472a450 100644
--- a/sci-biology/MuSeqBox/Manifest
+++ b/sci-biology/MuSeqBox/Manifest
@@ -1 +1 @@
-DIST MuSeqBox-4-8-2015.tar.gz 86427 BLAKE2B 5152da22a0fdf4694e9a3bea51d95e819d06bf9d27863d9af04bdc1159eec42f90f7eaab426c8e9b3db3988e6da34bfaff4ea9d6d5feb9b07ccc39e0d27af99a SHA512 09644994e682ed6e7307f950ec61e78e8dff7cdba5d70324b8529f33ed9339481f647fd3f45eb272ffa941afa6138a23a26769651dd4c22e3a1a16d2275d14b8
+DIST MuSeqBox-5-7-2021.tar.gz 105192 BLAKE2B f9cd38ab403a1b6ff4ae46f4bc07739e38b84f30e48eebeadb7519b9c8954ae83c8ecd4034acd8b80c74327a55b746093aa9652ad0f4ccad83b06f232d1145a5 SHA512 81aaf6c8a9065a944821fb974031c939b8fdf90efddf08303d3c095aebe7a82dc4655b3cd2c682fa67a45a3bd732f44dc2c583c8ad06f1bf403bf56e30c97d6c
diff --git a/sci-biology/MuSeqBox/MuSeqBox-5.4.ebuild b/sci-biology/MuSeqBox/MuSeqBox-5.4.ebuild
deleted file mode 100644
index 326e0d7c0..000000000
--- a/sci-biology/MuSeqBox/MuSeqBox-5.4.ebuild
+++ /dev/null
@@ -1,36 +0,0 @@
-# Copyright 1999-2016 Gentoo Foundation
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=5
-
-inherit toolchain-funcs
-
-DESCRIPTION="Parse and filter BLAST output into tab-delimited file"
-HOMEPAGE="http://brendelgroup.org/bioinformatics2go/MuSeqBox.php"
-SRC_URI="http://www.brendelgroup.org/bioinformatics2go/Download/MuSeqBox-4-8-2015.tar.gz"
-# code will move to https://github.com/BrendelGroup
-
-LICENSE="GPL-3"
-SLOT="0"
-KEYWORDS="~amd64"
-IUSE=""
-
-DEPEND=""
-RDEPEND="${DEPEND}"
-
-S="${WORKDIR}/MUSEQBOX5.4"
-
-src_compile(){
-	cd src || die
-	$(tc-getCXX) ${CFLAGS} -DLINUX -c MuSeqBox.C || die
-	$(tc-getCXX) ${CFLAGS} ${LDFLAGS} -DLINUX MuSeqBox.o -o ../bin/MuSeqBox || die
-}
-
-src_install(){
-	dobin bin/*
-	dodoc 0README
-	insinto /usr/share/"${PN}"
-	doins doc/*.ps doc/*.pdf
-	doins -r data
-	doman doc/MuSeqBox.1
-}
diff --git a/sci-biology/MuSeqBox/MuSeqBox-5.7.2021.ebuild b/sci-biology/MuSeqBox/MuSeqBox-5.7.2021.ebuild
new file mode 100644
index 000000000..49bd7da9c
--- /dev/null
+++ b/sci-biology/MuSeqBox/MuSeqBox-5.7.2021.ebuild
@@ -0,0 +1,31 @@
+# Copyright 1999-2021 Gentoo Authors
+# Distributed under the terms of the GNU General Public License v2
+
+EAPI=8
+
+inherit toolchain-funcs
+
+DESCRIPTION="Parse and filter BLAST output into tab-delimited file"
+HOMEPAGE="http://brendelgroup.org/bioinformatics2go/MuSeqBox.php"
+SRC_URI="http://www.brendelgroup.org/bioinformatics2go/Download/MuSeqBox-${PV//./-}.tar.gz"
+
+LICENSE="GPL-3"
+SLOT="0"
+KEYWORDS="~amd64"
+
+S="${WORKDIR}/MUSEQBOX$(ver_cut 1-2)"
+
+src_compile(){
+	cd src || die
+	$(tc-getCXX) ${CFLAGS} -DLINUX -c MuSeqBox.C || die
+	$(tc-getCXX) ${CFLAGS} ${LDFLAGS} -DLINUX MuSeqBox.o -o ../bin/MuSeqBox || die
+}
+
+src_install(){
+	dobin bin/*
+	dodoc 0README
+	insinto /usr/share/"${PN}"
+	doins doc/*.ps doc/*.pdf
+	doins -r data
+	doman doc/MuSeqBox.1
+}
diff --git a/sci-biology/NGSEPcore-bin/Manifest b/sci-biology/NGSEPcore-bin/Manifest
new file mode 100644
index 000000000..282ee5abc
--- /dev/null
+++ b/sci-biology/NGSEPcore-bin/Manifest
@@ -0,0 +1,4 @@
+DIST NGSEPcore-bin-4.0.3_QuickStart.txt 21313 BLAKE2B b897e25945d337f85f0c525ce93221440f6f1577ad1bde6fa3884a74e4366c2e17d7ef1d8603acba02ab21bdaa63fdfcc4d4251273f5e77b938e2318b13bdc19 SHA512 f5d528555c6115cdbddddbfc1c24939d1ca4776b16a5b848b4b9321cb882903d70eeef00c08e032dce4b6fe5551cea881570fc6f5975837e4f9eaf646de0c363
+DIST NGSEPcore-bin-4.0.3_Tutorial.txt 16946 BLAKE2B 0f397c6cd6d0f57f219d3f7963df32263347345a2e6231c7ccbc1a433d8de6350c6653e1a260182aa3ea5fa6a0bf88f47b659df236c78c8289914823b92f5778 SHA512 b110a0058962e1dc899183d3ca73cdfdd5f9b729561d35fe8d25e2fbeaa9b4647cbb768b047fa6df80b7926b1a34e4dc87c13979b66e6e6fe83f6f0c991fe6a8
+DIST NGSEPcore-bin-4.0.3_UserManual.pdf 10516580 BLAKE2B abe69a790413851181cbd210c8389fd302d917a1f6b4d425fbda2389808234290d38f31532933c0fc8505ca8b530f1b778bb58ce041783d184a85c2d5a716cd9 SHA512 cff9176f0a791b5b3e24fdba681bd71a3c39cb4593c01631e722e60e238140c80f292286454b7337a741a2f54fa6d5db30146c5bfdb02d5d5dd8d65322e3dc6e
+DIST NGSEPcore_4.0.3.jar 3122004 BLAKE2B 363ecc94cb8b3afb55c360b1479705a048de062d0200db183b25ed36c675e95cc9d4337826e207ff5513be07f4e61e919e2bd1edb579332e38673f363e833dde SHA512 856db7958f1bed5c41f29dd5ee4bc275032edabc1b7d75f61063236d77713716f7f946b6d93eeef8322f12e64ea808e509fac5517eb5d964a330e93df253bca5
diff --git a/sci-biology/NGSEPcore-bin/NGSEPcore-bin-4.0.3.ebuild b/sci-biology/NGSEPcore-bin/NGSEPcore-bin-4.0.3.ebuild
new file mode 100644
index 000000000..a47524cf8
--- /dev/null
+++ b/sci-biology/NGSEPcore-bin/NGSEPcore-bin-4.0.3.ebuild
@@ -0,0 +1,36 @@
+# Copyright 1999-2021 Gentoo Authors
+# Distributed under the terms of the GNU General Public License v2
+
+EAPI=7
+
+inherit java-pkg-2
+
+DESCRIPTION="NGSEP (CNV and indel discovery)"
+HOMEPAGE="https://sourceforge.net/p/ngsep/wiki/Home
+	https://github.com/NGSEP/NGSEPcore"
+SRC_URI="https://sourceforge.net/projects/ngsep/files/Library/NGSEPcore_${PV}.jar
+	https://sourceforge.net/projects/ngsep/files/training/ManualNGSEP_v${PV}.pdf -> ${P}_UserManual.pdf
+	https://sourceforge.net/projects/ngsep/files/training/Tutorial.txt -> ${P}_Tutorial.txt
+	https://sourceforge.net/projects/ngsep/files/training/QuickStart.txt -> ${P}_QuickStart.txt"
+
+LICENSE="GPL-3"
+SLOT="0"
+KEYWORDS="~amd64 ~x86"
+
+RDEPEND="
+	!sci-biology/NGSEPcore
+	>=virtual/jdk-1.8:*"
+DEPEND="${RDEPEND}"
+
+S="${WORKDIR}"
+
+src_unpack(){
+	return
+}
+
+src_install(){
+	java-pkg_dojar "${DISTDIR}"/*.jar
+	dodoc "${DISTDIR}"/${P}_UserManual.pdf \
+		"${DISTDIR}"/${P}_Tutorial.txt \
+		"${DISTDIR}"/${P}_QuickStart.txt
+}
diff --git a/sci-biology/NGSTools/metadata.xml b/sci-biology/NGSEPcore-bin/metadata.xml
index 642261079..642261079 100644
--- a/sci-biology/NGSTools/metadata.xml
+++ b/sci-biology/NGSEPcore-bin/metadata.xml
diff --git a/sci-biology/NGSEPcore/Manifest b/sci-biology/NGSEPcore/Manifest
new file mode 100644
index 000000000..ef9c10376
--- /dev/null
+++ b/sci-biology/NGSEPcore/Manifest
@@ -0,0 +1,4 @@
+DIST NGSEPcore-4.0.3_QuickStart.txt 21313 BLAKE2B b897e25945d337f85f0c525ce93221440f6f1577ad1bde6fa3884a74e4366c2e17d7ef1d8603acba02ab21bdaa63fdfcc4d4251273f5e77b938e2318b13bdc19 SHA512 f5d528555c6115cdbddddbfc1c24939d1ca4776b16a5b848b4b9321cb882903d70eeef00c08e032dce4b6fe5551cea881570fc6f5975837e4f9eaf646de0c363
+DIST NGSEPcore-4.0.3_Tutorial.txt 16946 BLAKE2B 0f397c6cd6d0f57f219d3f7963df32263347345a2e6231c7ccbc1a433d8de6350c6653e1a260182aa3ea5fa6a0bf88f47b659df236c78c8289914823b92f5778 SHA512 b110a0058962e1dc899183d3ca73cdfdd5f9b729561d35fe8d25e2fbeaa9b4647cbb768b047fa6df80b7926b1a34e4dc87c13979b66e6e6fe83f6f0c991fe6a8
+DIST NGSEPcore-4.0.3_UserManual.pdf 10516580 BLAKE2B abe69a790413851181cbd210c8389fd302d917a1f6b4d425fbda2389808234290d38f31532933c0fc8505ca8b530f1b778bb58ce041783d184a85c2d5a716cd9 SHA512 cff9176f0a791b5b3e24fdba681bd71a3c39cb4593c01631e722e60e238140c80f292286454b7337a741a2f54fa6d5db30146c5bfdb02d5d5dd8d65322e3dc6e
+DIST NGSEPcore_4.0.3.tar.gz 11668258 BLAKE2B de8bdeee18c8647e93dcf8adf0751660618bb54208160a15de184680459122ef6fb62ea6c1ae8d3e81b6ada11ab4a1b2f18ee575b4fdc4543f3c30b9077ffc1d SHA512 12c73243cc026fc37424fc8b5112179288bf569c3e06208bfc768420874dc676a23f10a8fd067eb0120fa8f188556e2a91e22fc4e54a8cd3e7851a0b2e32e036
diff --git a/sci-biology/NGSEPcore/NGSEPcore-4.0.3.ebuild b/sci-biology/NGSEPcore/NGSEPcore-4.0.3.ebuild
new file mode 100644
index 000000000..49b13a169
--- /dev/null
+++ b/sci-biology/NGSEPcore/NGSEPcore-4.0.3.ebuild
@@ -0,0 +1,44 @@
+# Copyright 1999-2021 Gentoo Authors
+# Distributed under the terms of the GNU General Public License v2
+
+EAPI=7
+
+inherit java-pkg-2
+
+DESCRIPTION="NGSEP (CNV and indel discovery)"
+HOMEPAGE="https://sourceforge.net/p/ngsep/wiki/Home
+	https://github.com/NGSEP/NGSEPcore"
+SRC_URI="https://sourceforge.net/projects/ngsep/files/SourceCode/NGSEPcore_${PV}.tar.gz
+	https://sourceforge.net/projects/ngsep/files/training/ManualNGSEP_v${PV}.pdf -> ${P}_UserManual.pdf
+	https://sourceforge.net/projects/ngsep/files/training/Tutorial.txt -> ${P}_Tutorial.txt
+	https://sourceforge.net/projects/ngsep/files/training/QuickStart.txt -> ${P}_QuickStart.txt"
+
+LICENSE="GPL-3"
+SLOT="0"
+KEYWORDS="~amd64 ~x86"
+
+RDEPEND=">=virtual/jdk-1.8:="
+DEPEND="${RDEPEND}"
+
+S="${WORKDIR}/${PN}_${PV}"
+
+src_prepare(){
+	# recent versions of htsjdk now use gradle,
+	# which is not supported by portage
+	#rm lib/htsjdk-2.22.jar || die
+	# TODO: package dev-java/jsci
+	#rm lib/jsci-core.jar || die
+	default
+}
+
+src_compile(){
+	emake -j1
+}
+
+src_install(){
+	java-pkg_dojar *.jar lib/*.jar
+	dodoc "${DISTDIR}"/${P}_UserManual.pdf \
+	"${DISTDIR}"/${P}_Tutorial.txt \
+	"${DISTDIR}"/${P}_QuickStart.txt \
+	README.txt
+}
diff --git a/sci-biology/NGSEPcore/metadata.xml b/sci-biology/NGSEPcore/metadata.xml
new file mode 100644
index 000000000..642261079
--- /dev/null
+++ b/sci-biology/NGSEPcore/metadata.xml
@@ -0,0 +1,15 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
+<pkgmetadata>
+	<maintainer type="person">
+		<email>mmokrejs@fold.natur.cuni.cz</email>
+		<name>Martin Mokrejs</name>
+	</maintainer>
+	<maintainer type="project">
+		<email>sci-biology@gentoo.org</email>
+		<name>Gentoo Biology Project</name>
+	</maintainer>
+	<upstream>
+		<remote-id type="sourceforge">ngsep</remote-id>
+	</upstream>
+</pkgmetadata>
diff --git a/sci-biology/NGSTools/Manifest b/sci-biology/NGSTools/Manifest
deleted file mode 100644
index 09d9be941..000000000
--- a/sci-biology/NGSTools/Manifest
+++ /dev/null
@@ -1 +0,0 @@
-DIST NGSTools_2.0.5.tar.gz 1366288 BLAKE2B 8cf11e3824a37634072c42d031d1753b55a2ac56e771f8f962b22ed9d20904f8c07856009e6bbb8c1677d0bb91a37c1dca30d0aa77c0ff63b392dfdd02b4823a SHA512 05ef3bf3aac397aa4a471ed86a35f279cb97f8af9f827881751a0f3b11612d683724ece5d24a9848978a1a88f75aa102ee2765d5204f65b7a94da3149412bfa4
diff --git a/sci-biology/NGSTools/NGSTools-2.0.5.ebuild b/sci-biology/NGSTools/NGSTools-2.0.5.ebuild
deleted file mode 100644
index 862983fec..000000000
--- a/sci-biology/NGSTools/NGSTools-2.0.5.ebuild
+++ /dev/null
@@ -1,20 +0,0 @@
-# Copyright 1999-2014 Gentoo Foundation
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=5
-
-inherit java-pkg-2 java-ant-2 eutils
-
-S="${PV/-/_}"
-
-DESCRIPTION="Next Generation Sequencing Eclipse Plugin (CNV and indel discovery), aka NGSEP"
-HOMEPAGE="https://sourceforge.net/p/ngsep/wiki/Home"
-SRC_URI="http://sourceforge.net/projects/ngsep/files/SourceCode/NGSTools_2.0.5.tar.gz"
-
-LICENSE="GPL-3"
-SLOT="0"
-KEYWORDS=""
-IUSE=""
-
-DEPEND="dev-util/eclipse-sdk"
-RDEPEND="${DEPEND}"
diff --git a/sci-biology/OBO-Edit/Manifest b/sci-biology/OBO-Edit/Manifest
deleted file mode 100644
index 7b4f34232..000000000
--- a/sci-biology/OBO-Edit/Manifest
+++ /dev/null
@@ -1,4 +0,0 @@
-DIST OBO-Edit_ReleaseNotes-2.1.1.6.txt 38066 SHA256 7b7c44c39897469dc1f535866292050d7fd45639d31fbc9c64589fa717146839 SHA512 abb46c2671edf5227d0e083104af4202974adafedb879900685c4681f3a0de09037907edfb1e3e14144b3aea27c04a17822250f778b3b6ef0371e81f7e3cdb49 WHIRLPOOL 3b8b361b04ab31d003a416de15676ada324b9c33a36690416d135fa96bfe56d70c992b089cb5496ab24c2eb31dd8648e4e1b66be6544c532976f27ea6c5f982e
-DIST OBO-Edit_unix_install4j-2.1.0.sh 44395414 SHA256 22fa3801c5ddbb7d1f5a8445574850263a3d2ddf676311f6f21bfebffd6d894f SHA512 f63fd9af367ae67ad1eab7e0a93921efabcef7da3ff155cc74ac38ba4e53dccb6cf5dc944718f938681b52c22bbb2eef4e7a29e4c8c663c3c694bad1a87771e1 WHIRLPOOL 8f87631fcae9e4c589ab7635ff488ea81d099b3fc9db28835f27e01d61097c01b267097f4d577a4f900c09b1b62723117000af66911613e7e59493cb9111f197
-DIST OBO-Edit_unix_install4j-2.1.1.6.sh 46660658 SHA256 9779f89d54dc3d72e3acb4f76d16f04fb0f2d1715c5dd2ea74d7e3da01c78cb3 SHA512 0bacd2fc4a5684ccedeadc5e5304ea917c53e68a57089bd5450cff083f4591ddb6875a54b2198446ef6910e44b73a339a5350146b86dde4e9e95b8aacdb4e8b0 WHIRLPOOL 769947720eb99dc6406692908e8f95e02088a409de4d2e39530d9f7f071b13ce0b9843f36434ce910c6ffaaad3fb4a985ecc0687082f5d023878473dbd6e58fb
-DIST ReleaseNotes-2.1.0.txt 33593 SHA256 e906e9a53148f7d21d0f820d878342a989773f4549303b2dc49007d9c23fe564 SHA512 9d93967eedd21a9f823c361f451533acdbccd860a6bffdfffa57095a7d783e9942a8849c6fff16b89c30e805f9def6bf5d250377f8808b0c335bf4ed9b03f344 WHIRLPOOL 736ef94b100e404b8c6bfc0450c286d34d86fb9194a82e354134311f637d8466ec70673e7f34890bf18ccbd525beb48c8c763aa8e8920fe898b35b546db33989
diff --git a/sci-biology/OBO-Edit/OBO-Edit-2.1.0.ebuild b/sci-biology/OBO-Edit/OBO-Edit-2.1.0.ebuild
deleted file mode 100644
index 4b948623a..000000000
--- a/sci-biology/OBO-Edit/OBO-Edit-2.1.0.ebuild
+++ /dev/null
@@ -1,53 +0,0 @@
-# Copyright 1999-2016 Gentoo Foundation
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=5
-
-inherit eutils toolchain-funcs versionator java-pkg-2
-
-MY_PV=$(replace_all_version_separators '-')
-
-DESCRIPTION="Java-based editor optimized for the OBO biological ontology file format"
-HOMEPAGE="http://www.oboedit.org/"
-SRC_URI="
-	http://sourceforge.net/projects/geneontology/files/OBO-Edit%202%20%5BLatest%20versions%5D/OBO-Edit%20${PV}/${MY_PV}_unix_install4j.sh/download -> OBO-Edit_unix_install4j-${PV}.sh
-	http://sourceforge.net/projects/geneontology/files/OBO-Edit%202%20%5BLatest%20versions%5D/OBO-Edit%20${PV}/ReleaseNotes-${PV}.txt"
-
-LICENSE="OBO-Edit" # Artistic-like
-SLOT="0"
-KEYWORDS="~amd64 ~x86"
-IUSE=""
-
-DEPEND="app-arch/rpm2targz"
-RDEPEND="virtual/jre"
-
-S="${WORKDIR}"
-
-src_install(){
-	dodir /opt/OBO-Edit2/.install4j
-
-	sed \
-		-e "s#\"\${D}\"#"${D}"#g" \
-		"${FILESDIR}"/response.varfile \
-		> "${D}"/opt/OBO-Edit2/.install4j/response.varfile || die "sed failed"
-
-	sed \
-		-e "s#/bin/java\" -Dinstall4j.jvmDir#/bin/java\" -Duser.home="${D}"/../temp -Dinstall4j.jvmDir#" \
-		-i "${DISTDIR}"/OBO-Edit_unix_install4j-"${PV}".sh || die "failed to set userHome value"
-
-	sh "${DISTDIR}"/OBO-Edit_unix_install4j-"${PV}".sh \
-		-q -overwrite \
-		--varfile="${D}"/opt/OBO-Edit2/.install4j/response.varfile \
-		--destination="${D}"/opt/OBO-Edit2 \
-		-dir "${D}"/opt/OBO-Edit2 \
-		|| die "Failed to run the self-extracting ${DISTDIR}/OBO-Edit_unix_install4j-"${PV}".sh file"
-	find . -name firstrun -delete || die
-
-	esvn_clean
-
-	insinto /opt/
-	doins -r OBO-Edit2
-	chmod 755 "${ED}"/opt/OBO-Edit2/* || die
-
-	dodoc "${DISTDIR}"/ReleaseNotes-2.1.0.txt
-}
diff --git a/sci-biology/OBO-Edit/OBO-Edit-2.1.1.6.ebuild b/sci-biology/OBO-Edit/OBO-Edit-2.1.1.6.ebuild
deleted file mode 100644
index 6163c6728..000000000
--- a/sci-biology/OBO-Edit/OBO-Edit-2.1.1.6.ebuild
+++ /dev/null
@@ -1,82 +0,0 @@
-# Copyright 1999-2016 Gentoo Foundation
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=5
-
-inherit eutils toolchain-funcs versionator java-pkg-2
-
-# MY_PV=$(replace_all_version_separators '-')
-MY_PV="oboedit_2_1_1-b6"
-MY_VER="2.1.1-b6"
-MY_PV=$(replace_all_version_separators '-')
-
-DESCRIPTION="Java-based editor optimized for the OBO biological ontology file format"
-HOMEPAGE="http://www.oboedit.org/"
-SRC_URI="
-	http://downloads.sourceforge.net/project/geneontology/OBO-Edit%202%20%5BLatest%20versions%5D/${MY_VER}/${MY_PV}_unix_install4j.sh -> ${PN}_unix_install4j-${PV}.sh
-	http://sourceforge.net/projects/geneontology/files/OBO-Edit%202%20%5BLatest%20versions%5D/${MY_PV}/ReleaseNotes-${MY_VER}.txt -> ${PN}_ReleaseNotes-${PV}.txt"
-
-LICENSE="OBO-Edit" # Artistic-like
-SLOT="0"
-KEYWORDS="~amd64 ~x86"
-IUSE=""
-
-DEPEND="app-arch/rpm2targz"
-RDEPEND="virtual/jre"
-
-S="${WORKDIR}"
-
-pkg_setup() {
-	einfo "Fixing java access violations ..."
-	# learned from bug #387227
-	# opened a bug #402507 to get this .systemPrefs directory pre-created for everybody
-	addpredict /opt/icedtea-bin-7.2.0/jre/.systemPrefs
-	addpredict /usr/local/bin/OBO-Edit
-}
-
-src_prepare(){
-	dodir /opt/OBO-Edit2/.install4j /usr/bin
-
-	# /var/tmp/portage/sci-biology/OBO-Edit-2.1.1.6/image//opt/OBO-Edit2/.install4j/response.varfile
-	sed -e "s#\"\${D}\"#"${D}"#g" "${FILESDIR}"/response.varfile | \
-	sed -e "s#\"\${TMPDIR}\"#"${TMPDIR}"#g" | \
-	sed -e "s@sys.symlinkDir=/usr/local/bin@#sys.symlinkDir=/usr/local/bin@" \
-	> "${D}"/opt/OBO-Edit2/.install4j/response.varfile || die "sed failed"
-	cp -r "${D}"/opt/OBO-Edit2/.install4j "${TMPDIR}" || die
-
-	# for user root install4j writes into /opt/icedtea-bin-7.2.0/jre/.systemPrefs or whatever it
-	# found via JAVA_HOME or similar variables
-	# for other users it writes into $HOME/.java/.userPrefs/
-
-	# trick setting -Djava.util.prefs.systemRoot="${TMPDIR}" does not work
-	sed \
-		-e "s@/bin/java\" -Dinstall4j.jvmDir=\"\$app_java_home\"@/bin/java\" -Duser.home="${TMPDIR}" -Dinstall4j.jvmDir="${TMPDIR}" -Dsys.symlinkDir="${D}"usr/bin -Djava.util.prefs.systemRoot="${TMPDIR}"@" \
-		-i "${DISTDIR}"/"${PN}"_unix_install4j-"${PV}".sh \
-		|| die "failed to set userHome and jvmDir where JAVA .systemPrefs can be found"
-
-	chmod u+rx "${DISTDIR}"/"${PN}"_unix_install4j-"${PV}".sh || die
-}
-
-src_install(){
-	# it looks install4j removes the target installation direcotry before writing into it :((
-	#
-	# cat "${TMPDIR}"/.install4j/response.varfile
-	# chmod a-w "${TMPDIR}"/.install4j/response.varfile
-
-	INSTALL4J_KEEP_TEMP="yes" \
-		HOME="${TMPDIR}" \
-		sh "${DISTDIR}"/"${PN}"_unix_install4j-"${PV}".sh -q \
-		--varfile="${TMPDIR}"/.install4j/response.varfile \
-		--destination="${D}"/opt/OBO-Edit2 \
-		-dir "${D}"/opt/OBO-Edit2 \
-		|| die "Failed to run the self-extracting ${DISTDIR}/${PN}_unix_install4j-${PV}.sh file"
-
-	find . -name firstrun -delete || die
-
-	esvn_clean
-
-	dodoc "${DISTDIR}"/"${PN}"_ReleaseNotes-"${PV}".txt
-
-	echo "PATH=/opt/OBO-Edit2" > 99OBO-Edit || die
-	doenvd 99OBO-Edit
-}
diff --git a/sci-biology/OBO-Edit/files/response.varfile b/sci-biology/OBO-Edit/files/response.varfile
deleted file mode 100644
index 8c4361d01..000000000
--- a/sci-biology/OBO-Edit/files/response.varfile
+++ /dev/null
@@ -1,10 +0,0 @@
-#install4j response file for OBO-Edit2 2.1.1-b6
-#Tue Feb 07 03:08:04 MET 2012
-sys.component.89$Boolean=false
-createDesktopLinkAction$Boolean=false
-oboedit.memoryAlloc$Integer=3456
-sys.programGroupDisabled$Boolean=true
-sys.component.61$Boolean=true
-sys.symlinkDir="${D}"usr/bin
-sys.languageId=en
-sys.installationDir="${D}"opt/OBO-Edit2
diff --git a/sci-biology/OBO-Edit/metadata.xml b/sci-biology/OBO-Edit/metadata.xml
deleted file mode 100644
index acbbc35a4..000000000
--- a/sci-biology/OBO-Edit/metadata.xml
+++ /dev/null
@@ -1,15 +0,0 @@
-<?xml version="1.0" encoding="UTF-8"?>
-<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
-<pkgmetadata>
-	<maintainer type="person">
-		<email>mmokrejs@fold.natur.cuni.cz</email>
-		<name>Martin Mokrejs</name>
-	</maintainer>
-	<maintainer type="project">
-		<email>sci-biology@gentoo.org</email>
-		<name>Gentoo Biology Project</name>
-	</maintainer>
-	<upstream>
-		<remote-id type="sourceforge">geneontology</remote-id>
-	</upstream>
-</pkgmetadata>
diff --git a/sci-biology/ONTO-PERL/Manifest b/sci-biology/ONTO-PERL/Manifest
index b3a2be6db..d346d127d 100644
--- a/sci-biology/ONTO-PERL/Manifest
+++ b/sci-biology/ONTO-PERL/Manifest
@@ -1 +1 @@
-DIST ONTO-PERL-1.41.tar.gz 724171 BLAKE2B 71f3f966ee62bf97412790981de7fe9dc726468cd0eb9a9f92cb33d015a82b611c1bf5ff8ee47f8070783183c4945a18d11e5d243c6cacef1496d414915ada23 SHA512 cff9601ac55cf0c46b1a820c9b93d82d48683081491667d132b4806597c46280fd977e565cb9ca43ec230e3ac9371987a90d167ac2f1fa297ab34f5fa080395e
+DIST ONTO-PERL-1.45.tar.gz 731993 BLAKE2B eec1d9bde08768c5c8531fb6d32f60e488301e31de0d8b64283adc3716d0f42147464df40127d31c35a66f548ea4ad59120c4b3deae05aa9a7ff99206578e7e5 SHA512 d563afba6faf333f0bba21c2dcb08a46e9081e3c71fa54af6e9323e776027274fa415baa4e8f12d05305f189dbff955c04a5559e06a37725faf880b22db3ffa9
diff --git a/sci-biology/ONTO-PERL/ONTO-PERL-1.41.ebuild b/sci-biology/ONTO-PERL/ONTO-PERL-1.41.ebuild
deleted file mode 100644
index 39d35e1e3..000000000
--- a/sci-biology/ONTO-PERL/ONTO-PERL-1.41.ebuild
+++ /dev/null
@@ -1,26 +0,0 @@
-# Copyright 1999-2016 Gentoo Foundation
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=6
-
-MODULE_AUTHOR=EASR
-
-inherit multilib perl-module
-
-DESCRIPTION="Manipulates OBO- and OWL-formatted ontologies (like the Gene Ontology)"
-SRC_URI="mirror://cpan/authors/id/E/EA/${MODULE_AUTHOR}/${PN}/${P}.tar.gz"
-
-SLOT="0"
-KEYWORDS="~amd64 ~x86"
-IUSE=""
-
-RDEPEND="
-	>=sci-biology/swissknife-1.65
-	dev-perl/Date-Manip
-	>=dev-perl/XML-Simple-2.16
-	>=dev-perl/XML-Parser-2.34
-	virtual/perl-File-Path"
-DEPEND="${RDEPEND}"
-
-SRC_TEST=do
-#myconf="LIBS=-L/usr/$(get_libdir)"
diff --git a/sci-biology/ONTO-PERL/ONTO-PERL-1.45.ebuild b/sci-biology/ONTO-PERL/ONTO-PERL-1.45.ebuild
new file mode 100644
index 000000000..67423c48c
--- /dev/null
+++ b/sci-biology/ONTO-PERL/ONTO-PERL-1.45.ebuild
@@ -0,0 +1,26 @@
+# Copyright 1999-2021 Gentoo Authors
+# Distributed under the terms of the GNU General Public License v2
+
+EAPI=7
+
+MODULE_AUTHOR=EASR
+
+inherit perl-module
+
+DESCRIPTION="Manipulates OBO- and OWL-formatted ontologies (like the Gene Ontology)"
+HOMEPAGE="https://metacpan.org/release/ONTO-PERL"
+SRC_URI="mirror://cpan/authors/id/E/EA/${MODULE_AUTHOR}/${PN}/${P}.tar.gz"
+
+SLOT="0"
+KEYWORDS="~amd64 ~x86"
+
+RDEPEND="
+	>=sci-biology/swissknife-1.65
+	dev-perl/Date-Manip
+	>=dev-perl/XML-Simple-2.16
+	>=dev-perl/XML-Parser-2.34
+	virtual/perl-File-Path"
+DEPEND="${RDEPEND}"
+
+SRC_TEST=do
+#myconf="LIBS=-L/usr/$(get_libdir)"
diff --git a/sci-biology/ORFcor/Manifest b/sci-biology/ORFcor/Manifest
deleted file mode 100644
index 43ecf7822..000000000
--- a/sci-biology/ORFcor/Manifest
+++ /dev/null
@@ -1 +0,0 @@
-DIST ORFcor.tar.gz 3499343 BLAKE2B 5ebeb3614496d37f22d79c3d8d1f0bbabec7c16d834dbc60994f35fa9849050409a42e48955d695de2518c1ab33f071c03eb4d060efff21160040e807ceb1801 SHA512 2a0c57e94a71294f115c769aced754e8e3f6d0f8ad2b577add8f65f9f45fed2486946244ea99109dbac7dfcaf3bae1a14ebe4d6ffb194c285675e361ddd12141
diff --git a/sci-biology/ORFcor/ORFcor-20130507.ebuild b/sci-biology/ORFcor/ORFcor-20130507.ebuild
deleted file mode 100644
index 31c863dda..000000000
--- a/sci-biology/ORFcor/ORFcor-20130507.ebuild
+++ /dev/null
@@ -1,30 +0,0 @@
-# Copyright 1999-2015 Gentoo Foundation
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=5
-
-DESCRIPTION="Automated editor of protein-coding sequences"
-HOMEPAGE="http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0058387"
-SRC_URI="http://www.currielab.wisc.edu/files/ORFcor.tar.gz"
-
-LICENSE="BSD"
-SLOT="0"
-KEYWORDS="~amd64"
-IUSE=""
-
-DEPEND="dev-lang/perl
-	sci-biology/muscle
-	dev-perl/Parallel-ForkManager"
-	# >=sci-biology/hmmer-3.0
-RDEPEND="${DEPEND}"
-
-S="${WORKDIR}"/ORFcor
-
-src_install(){
-	dobin *.pl
-	dodoc README
-	insinto /usr/share/${PN}
-	doins 31_HMM*
-	insinto /usr/share/${PN}/test_data
-	doins test_data/*
-}
diff --git a/sci-biology/ORFcor/metadata.xml b/sci-biology/ORFcor/metadata.xml
deleted file mode 100644
index 138cb7705..000000000
--- a/sci-biology/ORFcor/metadata.xml
+++ /dev/null
@@ -1,12 +0,0 @@
-<?xml version="1.0" encoding="UTF-8"?>
-<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
-<pkgmetadata>
-	<maintainer type="person">
-		<email>mmokrejs@fold.natur.cuni.cz</email>
-		<name>Martin Mokrejs</name>
-	</maintainer>
-	<maintainer type="project">
-		<email>sci-biology@gentoo.org</email>
-		<name>Gentoo Biology Project</name>
-	</maintainer>
-</pkgmetadata>
diff --git a/sci-biology/ParaAT/ParaAT-1.0.ebuild b/sci-biology/ParaAT/ParaAT-1.0.ebuild
index d806d90eb..fd2007274 100644
--- a/sci-biology/ParaAT/ParaAT-1.0.ebuild
+++ b/sci-biology/ParaAT/ParaAT-1.0.ebuild
@@ -1,18 +1,16 @@
-# Copyright 1999-2019 Gentoo Authors
+# Copyright 1999-2021 Gentoo Authors
 # Distributed under the terms of the GNU General Public License v2
 
-EAPI=6
+EAPI=7
 
 DESCRIPTION="Create multiple protein-coding DNA alignments and back-Translation"
-HOMEPAGE="https://code.google.com/p/paraat
-	http://cbb.big.ac.cn/software
+HOMEPAGE="http://cbb.big.ac.cn/software
 	https://www.sciencedirect.com/science/article/pii/S0006291X12003518"
 SRC_URI="https://storage.googleapis.com/google-code-archive-downloads/v2/code.google.com/paraat/${PN}${PV}.tar.gz -> ${P}.tar.gz"
 
 LICENSE="GPL-3"
 SLOT="0"
 KEYWORDS="~amd64 ~x86"
-IUSE=""
 
 DEPEND="dev-lang/perl"
 RDEPEND="${DEPEND}"
diff --git a/sci-biology/RADtools/Manifest b/sci-biology/RADtools/Manifest
deleted file mode 100644
index b6ae8f0c8..000000000
--- a/sci-biology/RADtools/Manifest
+++ /dev/null
@@ -1,2 +0,0 @@
-DIST RADmanual.pdf 90937 BLAKE2B f757c3d9d1a2d34f09fb394ebbfbdca06d59dbb2fd2c8110299cb43f1edb50b41f9be582124c7b74544e53bdb683ca5f95855540ceb281d4a843638158ae3825 SHA512 4647edd9f14c59484ed04cbcdff3c99b841f169ea41a3ed678c28b6dd5f228cbc88d94f3f75bb5abbba2604cae7aefc2b77960178b4d7868e48c6717f90d08e1
-DIST RADtools_1.2.4.tar.gz 125243 BLAKE2B 0159e63e3db583b97504b94bec965a0807283e81c5502b2cbc03cdd09c9d277900f03951d173d73ddfc05139e2716c9ea20712d86e3996d01805182485a3212d SHA512 556323e8debadac6f5607ff639bbd5c73dc0a070a88c1d257fae06215a40cb4b615455a118cb7f5dab7a1a4a9a09d0c0138c02290f3c1e5eba41be11e47b5bbf
diff --git a/sci-biology/RADtools/RADtools-1.2.4.ebuild b/sci-biology/RADtools/RADtools-1.2.4.ebuild
deleted file mode 100644
index dc608b93b..000000000
--- a/sci-biology/RADtools/RADtools-1.2.4.ebuild
+++ /dev/null
@@ -1,32 +0,0 @@
-# Copyright 1999-2017 Gentoo Foundation
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=5
-
-PERL_EXPORT_PHASE_FUNCTIONS=no
-inherit eutils perl-module
-
-DESCRIPTION="Tools for processing RAD Sequencing Illumina reads"
-HOMEPAGE="https://www.wiki.ed.ac.uk/display/RADSequencing/Home"
-SRC_URI="
-	https://www.wiki.ed.ac.uk/download/attachments/68630442/RADtools_${PV}.tar.gz
-	https://www.wiki.ed.ac.uk/download/attachments/68630442/RADmanual.pdf"
-
-LICENSE="GPL-3"
-SLOT="0"
-KEYWORDS="~amd64"
-IUSE=""
-
-DEPEND=">=dev-lang/perl-5.10
-	dev-perl/Parallel-ForkManager"
-RDEPEND="${DEPEND}"
-
-S="${WORKDIR}"
-
-src_install() {
-	dobin RADMIDs RADmarkers RADpools RADtags
-	dodoc CHANGELOG RADmanual.pdf RADmanual.tex README
-	perl_set_version
-	insinto "${VENDOR_LIB}"
-	doins *.pm
-}
diff --git a/sci-biology/RADtools/RADtools-9999.ebuild b/sci-biology/RADtools/RADtools-9999.ebuild
deleted file mode 100644
index bdee24f78..000000000
--- a/sci-biology/RADtools/RADtools-9999.ebuild
+++ /dev/null
@@ -1,29 +0,0 @@
-# Copyright 1999-2018 Gentoo Foundation
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=5
-
-PERL_EXPORT_PHASE_FUNCTIONS=no
-inherit eutils perl-module git-r3
-
-DESCRIPTION="Tools for processing RAD Sequencing Illumina reads"
-HOMEPAGE="https://www.wiki.ed.ac.uk/display/RADSequencing/Home"
-EGIT_REPO_URI="https://github.com/johnomics/RADtools.git"
-
-LICENSE="GPL-3"
-SLOT="0"
-KEYWORDS=""
-IUSE=""
-
-DEPEND="
-	>=dev-lang/perl-5.10
-	dev-perl/Parallel-ForkManager"
-RDEPEND="${DEPEND}"
-
-src_install() {
-	dobin RADMIDs RADmarkers RADpools RADtags
-	dodoc CHANGELOG RADmanual.pdf RADmanual.tex README
-	perl_set_version
-	insinto "${VENDOR_LIB}"
-	doins *.pm
-}
diff --git a/sci-biology/RADtools/metadata.xml b/sci-biology/RADtools/metadata.xml
deleted file mode 100644
index 138cb7705..000000000
--- a/sci-biology/RADtools/metadata.xml
+++ /dev/null
@@ -1,12 +0,0 @@
-<?xml version="1.0" encoding="UTF-8"?>
-<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
-<pkgmetadata>
-	<maintainer type="person">
-		<email>mmokrejs@fold.natur.cuni.cz</email>
-		<name>Martin Mokrejs</name>
-	</maintainer>
-	<maintainer type="project">
-		<email>sci-biology@gentoo.org</email>
-		<name>Gentoo Biology Project</name>
-	</maintainer>
-</pkgmetadata>
diff --git a/sci-biology/RAILS/Manifest b/sci-biology/RAILS/Manifest
index f31fe08bc..d9f432dff 100644
--- a/sci-biology/RAILS/Manifest
+++ b/sci-biology/RAILS/Manifest
@@ -1 +1 @@
-DIST RAILS-1.4.1.tar.gz 758732 BLAKE2B e2ec3b06a00dddf87220f3f492a274e7a9dd80a35c93d5326c5baf8f8281729d36444f4af0ae246429b4ac4182ceed8cd16ff877d9b07970b733e1cea17e1a6d SHA512 eb44b25ed7237fc38cba3d435c76ac813385fe2e6906144103279888107102fb30d280a4ff2256ae744291d769aba5d87125c77c348fb7300dcbd319520450fd
+DIST RAILS-1.5.1.tar.gz 1100024 BLAKE2B 64938481a333a1e9cb54798540327413f5dc95be38f4b5a88fc4bc38f31ab889da19804f9470bc90f63c690342acecb9907c12cb68e7f359d7cd8885fb6248e6 SHA512 37b6c4d35858c0b41a9ca04076a360aa732a12ab0f9bfa170aa307b2c7bbe28b6ba7b2f5b9f3ba949036fb274c96c934ad34e675b468608a8580cf3fdb7dba32
diff --git a/sci-biology/RAILS/RAILS-1.4.1.ebuild b/sci-biology/RAILS/RAILS-1.4.1.ebuild
deleted file mode 100644
index 9360c6040..000000000
--- a/sci-biology/RAILS/RAILS-1.4.1.ebuild
+++ /dev/null
@@ -1,30 +0,0 @@
-# Copyright 2018 Gentoo Authors
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=7
-
-DESCRIPTION="Cobbler and RAILS scaffolding tools"
-HOMEPAGE="https://github.com/bcgsc/RAILS"
-SRC_URI="https://github.com/bcgsc/RAILS/archive/v1.4.1.tar.gz -> ${P}.tar.gz"
-
-LICENSE="GPL-3+"
-SLOT="0"
-KEYWORDS="~amd64 ~x86"
-IUSE=""
-
-DEPEND=""
-RDEPEND="${DEPEND}
-	dev-lang/perl
-	sci-biology/samtools"
-BDEPEND=""
-
-src_prepare(){
-	# remove hardcoded PATHs
-	sed -e 's@^\.\./@@g' -e 's@^export PATH=/gsc/btl/linuxbrew@#&1@' -i bin/runRAILS.sh || die
-	default
-}
-
-src_install(){
-	dobin bin/*
-	dodoc readme.md paper/paper.pdf
-}
diff --git a/sci-biology/RAILS/RAILS-1.5.1.ebuild b/sci-biology/RAILS/RAILS-1.5.1.ebuild
new file mode 100644
index 000000000..df5f0ea4a
--- /dev/null
+++ b/sci-biology/RAILS/RAILS-1.5.1.ebuild
@@ -0,0 +1,34 @@
+# Copyright 2018-2020 Gentoo Authors
+# Distributed under the terms of the GNU General Public License v2
+
+EAPI=7
+
+DESCRIPTION="Cobbler and RAILS scaffolding tools acting on SAM streams"
+HOMEPAGE="https://github.com/bcgsc/RAILS"
+SRC_URI="https://github.com/bcgsc/RAILS/archive/v${PV}.tar.gz -> ${P}.tar.gz"
+
+LICENSE="GPL-3+"
+SLOT="0"
+KEYWORDS="~amd64 ~x86"
+IUSE=""
+
+DEPEND=""
+RDEPEND="${DEPEND}
+	dev-lang/perl
+	sci-biology/samtools
+	sci-biology/bwa
+"
+# bin/runRAILSminimap.sh calls minimap2 but one can stream the SAM data directly
+BDEPEND=""
+
+src_prepare(){
+	# remove hardcoded PATHs
+	# https://github.com/bcgsc/RAILS/issues/8
+	sed -e 's@^\.\./@@g' -e 's@^export PATH=/gsc/btl/linuxbrew@#&1@' -i bin/*.sh || die
+	default
+}
+
+src_install(){
+	dobin bin/*
+	dodoc readme.md paper/paper.pdf
+}
diff --git a/sci-biology/RAILS/metadata.xml b/sci-biology/RAILS/metadata.xml
index 138cb7705..a3f152e56 100644
--- a/sci-biology/RAILS/metadata.xml
+++ b/sci-biology/RAILS/metadata.xml
@@ -9,4 +9,7 @@
 		<email>sci-biology@gentoo.org</email>
 		<name>Gentoo Biology Project</name>
 	</maintainer>
+	<upstream>
+		<remote-id type="github">bcgsc/RAILS</remote-id>
+	</upstream>
 </pkgmetadata>
diff --git a/sci-biology/RSeQC/Manifest b/sci-biology/RSeQC/Manifest
deleted file mode 100644
index 4fac5c0d9..000000000
--- a/sci-biology/RSeQC/Manifest
+++ /dev/null
@@ -1,2 +0,0 @@
-DIST RSeQC-2.6.1.tar.gz 1654756 BLAKE2B 401ffe1f45c685339bb39378d9b318e366eac1598eccec1eb5249ecf17f7da522f939569fe6ea211a12bdbbf75b550944c347a8fc530f6dbc2f95f6f5cbe86f9 SHA512 9adf44be989764c4095e91a4de76d5d96842956ff855392c11d644f99010c2e06ded80ab2373e636e59f544fb508839ea6d4ed6e202695ff31c42a68c1ceb86b
-DIST fetchChromSizes 2695 BLAKE2B a41f8e0085121f097c0fe93922b221b276f00a5d6af1da76f347ca121882e5d899d482900f51a0da4bff22b0b3158f0e274a67c60d7b7499c1bc3ead96beccd6 SHA512 23405beabb4f42b5cc5b569d9948d070e354ef2be10030b51ba3510865ab4e25bee8aab7283d9b6cbd7df454159a6f89e58ad8f5ee6a541046ad5a72f65019e8
diff --git a/sci-biology/RSeQC/RSeQC-2.6.1.ebuild b/sci-biology/RSeQC/RSeQC-2.6.1.ebuild
deleted file mode 100644
index ad9e1ce54..000000000
--- a/sci-biology/RSeQC/RSeQC-2.6.1.ebuild
+++ /dev/null
@@ -1,28 +0,0 @@
-# Copyright 1999-2016 Gentoo Foundation
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=6
-
-PYTHON_COMPAT=( python2_7 )
-
-inherit distutils-r1
-
-DESCRIPTION="Utilities for RNA-seq data quality control"
-HOMEPAGE="http://rseqc.sourceforge.net"
-SRC_URI="http://sourceforge.net/projects/rseqc/files/RSeQC-2.6.1.tar.gz
-	http://sourceforge.net/projects/rseqc/files/other/fetchChromSizes"
-
-LICENSE="GPL-3"
-SLOT="0"
-KEYWORDS="~amd64"
-IUSE=""
-
-DEPEND=">=sci-biology/pysam-0.7.5[${PYTHON_USEDEP}]"
-RDEPEND="${DEPEND}"
-
-# pysam (v0.7.5) was built in RSeQC. The latest version of pysam may not be compatible with RSeQC.
-python_install(){
-	distutils-r1_python_install
-	rm -r "${D}$(python_get_sitedir)"/pysam
-	dobin "${DISTDIR}"/fetchChromSizes
-}
diff --git a/sci-biology/RSeQC/metadata.xml b/sci-biology/RSeQC/metadata.xml
deleted file mode 100644
index 5c8442330..000000000
--- a/sci-biology/RSeQC/metadata.xml
+++ /dev/null
@@ -1,15 +0,0 @@
-<?xml version="1.0" encoding="UTF-8"?>
-<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
-<pkgmetadata>
-	<maintainer type="person">
-		<email>mmokrejs@fold.natur.cuni.cz</email>
-		<name>Martin Mokrejs</name>
-	</maintainer>
-	<maintainer type="project">
-		<email>sci-biology@gentoo.org</email>
-		<name>Gentoo Biology Project</name>
-	</maintainer>
-	<upstream>
-		<remote-id type="sourceforge">rseqc</remote-id>
-	</upstream>
-</pkgmetadata>
diff --git a/sci-biology/Ray/Manifest b/sci-biology/Ray/Manifest
deleted file mode 100644
index 756a824dd..000000000
--- a/sci-biology/Ray/Manifest
+++ /dev/null
@@ -1 +0,0 @@
-DIST Ray-2.3.0.tar.bz2 444056 BLAKE2B 438e6b602cc8fd81e08ca8d443037064e9befc2ef171ad4fb16363378341b0228528562664626c58417364a5e7c6efd57aad32d95758056c5d37c9334eae03c7 SHA512 91305e6ab0c6de668ba878965dcef14b02010873bcc494d20200850357bf74f07f60c1d7a15f4e5f53a266b0b2528566bd429335eaba85445b50ab396595eb87
diff --git a/sci-biology/Ray/Ray-2.3.0.ebuild b/sci-biology/Ray/Ray-2.3.0.ebuild
deleted file mode 100644
index aa21e2a25..000000000
--- a/sci-biology/Ray/Ray-2.3.0.ebuild
+++ /dev/null
@@ -1,22 +0,0 @@
-# Copyright 1999-2017 Gentoo Foundation
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=6
-
-DESCRIPTION="Assembler for metagenomes, genomes and transcriptomes using MPI"
-HOMEPAGE="http://denovoassembler.sourceforge.net/"
-SRC_URI="http://sourceforge.net/projects/denovoassembler/files/Ray-"${PV}".tar.bz2"
-
-LICENSE="LGPL-3 GPL-3"
-SLOT="0"
-KEYWORDS="~amd64"
-IUSE="static-libs"
-
-DEPEND="virtual/mpi"
-RDEPEND="${DEPEND}
-	sys-cluster/osc-mpiexec"
-
-src_install(){
-	dobin Ray
-	use static-libs && dolib.a libRayPlatform.a libRay.a
-}
diff --git a/sci-biology/Ray/metadata.xml b/sci-biology/Ray/metadata.xml
deleted file mode 100644
index 982286fb0..000000000
--- a/sci-biology/Ray/metadata.xml
+++ /dev/null
@@ -1,15 +0,0 @@
-<?xml version="1.0" encoding="UTF-8"?>
-<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
-<pkgmetadata>
-	<maintainer type="person">
-		<email>mmokrejs@fold.natur.cuni.cz</email>
-		<name>Martin Mokrejs</name>
-	</maintainer>
-	<maintainer type="project">
-		<email>sci-biology@gentoo.org</email>
-		<name>Gentoo Biology Project</name>
-	</maintainer>
-	<upstream>
-		<remote-id type="sourceforge">denovoassembler</remote-id>
-	</upstream>
-</pkgmetadata>
diff --git a/sci-biology/Rcorrector/Manifest b/sci-biology/Rcorrector/Manifest
new file mode 100644
index 000000000..b6eaa3f0e
--- /dev/null
+++ b/sci-biology/Rcorrector/Manifest
@@ -0,0 +1 @@
+DIST Rcorrector-1.0.4.tar.gz 44316 BLAKE2B 07130d782ee7742fe552ae4209b69036db654461b7a0009dd83c6b727c17b63b78b106ac78eed7e8225996096ed76fea0fad091e38901bb3c7e1be5cf7e4f234 SHA512 9ef80d408675a88b4c96aa846f5c445b8ee281f5af5c9c383f7246e65f4e40cd6d691921f1c9fad21a6d82a4356d48879d89f833620c41c898cd15983c03ab59
diff --git a/sci-biology/Rcorrector/Rcorrector-1.0.4.ebuild b/sci-biology/Rcorrector/Rcorrector-1.0.4.ebuild
new file mode 100644
index 000000000..7522e86d3
--- /dev/null
+++ b/sci-biology/Rcorrector/Rcorrector-1.0.4.ebuild
@@ -0,0 +1,36 @@
+# Copyright 1999-2021 Gentoo Authors
+# Distributed under the terms of the GNU General Public License v2
+
+EAPI=7
+
+DESCRIPTION="Error correction for Illumina RNA-seq reads"
+HOMEPAGE="https://github.com/mourisl/Rcorrector"
+SRC_URI="https://github.com/mourisl/Rcorrector/archive/v${PV}.tar.gz -> ${P}.tar.gz"
+
+LICENSE="GPL-2+"
+SLOT="0"
+KEYWORDS="~amd64"
+
+DEPEND=">=sci-biology/jellyfish-2.1.3:2"
+RDEPEND="${DEPEND}
+	dev-lang/perl"
+
+PATCHES=(
+	"${FILESDIR}"/Rcorrector-rename-jellyfish.patch
+)
+
+src_prepare(){
+	default
+	# prevent building of jellyfish from bundled sources
+	mkdir -p ./jellyfish/bin/ || die
+	touch ./jellyfish/bin/jellyfish2 || die
+	sed -e "s#-Wall -O3#${CXXFLAGS}#" -i Makefile || die
+}
+
+src_install(){
+	dobin rcorrector run_rcorrector.pl
+}
+
+pkg_postinst(){
+	einfo "Note that the default kmer size 23 is suboptimal, use k=31 instead"
+}
diff --git a/sci-biology/Rcorrector/Rcorrector-9999.ebuild b/sci-biology/Rcorrector/Rcorrector-9999.ebuild
deleted file mode 100644
index 58007a73b..000000000
--- a/sci-biology/Rcorrector/Rcorrector-9999.ebuild
+++ /dev/null
@@ -1,37 +0,0 @@
-# Copyright 1999-2018 Gentoo Foundation
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=6
-
-inherit git-r3 eutils
-
-DESCRIPTION="Error correction for Illumina RNA-seq reads"
-HOMEPAGE="https://github.com/mourisl/Rcorrector"
-SRC_URI=""
-EGIT_REPO_URI="https://github.com/mourisl/Rcorrector.git"
-
-LICENSE="GPL-2+"
-SLOT="0"
-KEYWORDS=""
-IUSE=""
-
-DEPEND=">=sci-biology/jellyfish-2.1.3:2"
-RDEPEND="${DEPEND}
-	dev-lang/perl"
-
-src_prepare(){
-	default
-	epatch "${FILESDIR}"/Rcorrector-rename-jellyfish.patch
-	# prevent building of jellyfish from bundled sources
-	mkdir -p ./jellyfish/bin/ || die
-	touch ./jellyfish/bin/jellyfish2 || die
-	sed -e "s#-Wall -O3#${CXXFLAGS}#" -i Makefile || die
-}
-
-src_install(){
-	dobin rcorrector run_rcorrector.pl
-}
-
-pkg_postinst(){
-	einfo "Note that the default kmer size 23 is suboptimal, use k=31 instead"
-}
diff --git a/sci-biology/Rcorrector/files/Rcorrector-rename-jellyfish.patch b/sci-biology/Rcorrector/files/Rcorrector-rename-jellyfish.patch
index 08b9918d4..12962e124 100644
--- a/sci-biology/Rcorrector/files/Rcorrector-rename-jellyfish.patch
+++ b/sci-biology/Rcorrector/files/Rcorrector-rename-jellyfish.patch
@@ -1,5 +1,5 @@
---- Makefile.ori	2018-04-21 17:47:38.017147315 +0200
-+++ Makefile	2018-04-21 17:48:29.038679685 +0200
+--- a/Makefile	2018-04-21 17:47:38.017147315 +0200
++++ b/Makefile	2018-04-21 17:48:29.038679685 +0200
 @@ -2,14 +2,14 @@
  CXXFLAGS= -O2 -pipe -mpclmul -mpopcnt -march=native -ftree-vectorize -std=c++0x
  LINKFLAGS = -I . -lpthread -lz 
@@ -18,8 +18,8 @@
  		then \
  			wget -O jellyfish.tar.gz https://github.com/gmarcais/Jellyfish/releases/download/v2.2.4/jellyfish-2.2.4.tar.gz ;\
  			tar -xzf jellyfish.tar.gz ; mv jellyfish-2.2.4 jellyfish ; rm jellyfish.tar.gz ; cd jellyfish && ./configure && make ;\
---- run_rcorrector.pl.ori	2018-04-21 17:48:43.459112787 +0200
-+++ run_rcorrector.pl	2018-04-21 17:49:18.070152287 +0200
+--- a/run_rcorrector.pl	2018-04-21 17:48:43.459112787 +0200
++++ b/run_rcorrector.pl	2018-04-21 17:49:18.070152287 +0200
 @@ -42,10 +42,10 @@
  	die "$usage\n" ;
  }
diff --git a/sci-biology/SEECER/SEECER-0.1.3-r2.ebuild b/sci-biology/SEECER/SEECER-0.1.3-r2.ebuild
index 49ebd3879..c30b872a7 100644
--- a/sci-biology/SEECER/SEECER-0.1.3-r2.ebuild
+++ b/sci-biology/SEECER/SEECER-0.1.3-r2.ebuild
@@ -1,9 +1,7 @@
-# Copyright 1999-2018 Gentoo Foundation
+# Copyright 1999-2021 Gentoo Authors
 # Distributed under the terms of the GNU General Public License v2
 
-EAPI=6
-
-inherit eutils
+EAPI=7
 
 DESCRIPTION="SEquence Error Corrector for RNA-Seq reads"
 HOMEPAGE="http://sb.cs.cmu.edu/seecer/"
@@ -13,7 +11,6 @@ SRC_URI="
 
 LICENSE="GPL-3"
 SLOT="0"
-IUSE=""
 KEYWORDS="~amd64"
 
 # although has bundled jellyfish-1.1.11 copy it just calls the executable during runtime
@@ -24,7 +21,7 @@ DEPEND="
 RDEPEND="${DEPEND}
 	sci-biology/jellyfish:1"
 
-S="${S}"/SEECER
+S="${WORKDIR}/${P}/SEECER"
 
 PATCHES=(
 	"${FILESDIR}"/remove-hardcoded-paths.patch
diff --git a/sci-biology/SEECER/SEECER-0.1.3-r3.ebuild b/sci-biology/SEECER/SEECER-0.1.3-r3.ebuild
new file mode 100644
index 000000000..e41bbb19d
--- /dev/null
+++ b/sci-biology/SEECER/SEECER-0.1.3-r3.ebuild
@@ -0,0 +1,66 @@
+# Copyright 1999-2021 Gentoo Authors
+# Distributed under the terms of the GNU General Public License v2
+
+EAPI=8
+
+inherit autotools toolchain-funcs
+
+DESCRIPTION="SEquence Error Corrector for RNA-Seq reads"
+HOMEPAGE="http://sb.cs.cmu.edu/seecer/"
+SRC_URI="
+	http://sb.cs.cmu.edu/seecer/downloads/"${P}".tar.gz
+	http://sb.cs.cmu.edu/seecer/downloads/manual.pdf -> "${PN}"-manual.pdf"
+
+LICENSE="GPL-3"
+SLOT="0"
+KEYWORDS="~amd64"
+
+# although has bundled jellyfish-1.1.11 copy it just calls the executable during runtime
+# seems jellyfish-2 does not accept same commandline arguments
+DEPEND="
+	sci-libs/gsl:0=
+	sci-biology/seqan:0="
+RDEPEND="${DEPEND}
+	sci-biology/jellyfish:1"
+
+S="${WORKDIR}/${P}/SEECER"
+
+PATCHES=(
+	"${FILESDIR}"/remove-hardcoded-paths.patch
+	"${FILESDIR}"/run_seecer.sh.patch
+	"${FILESDIR}"/run_jellyfish.sh.patch
+	"${FILESDIR}"/${PN}-increase-max-sequence-length.patch
+	"${FILESDIR}"/${PN}-remove-flags.patch
+)
+
+pkg_pretend(){
+	# openmp is a hard requirement due to no gomp switch and source code assuming it is available
+	[[ ${MERGE_TYPE} != "binary" ]] && tc-check-openmp
+}
+
+pkg_setup(){
+	[[ ${MERGE_TYPE} != "binary" ]] && tc-check-openmp
+}
+
+src_prepare(){
+	rm bin/.run*.swp || die
+	rm src/*.o pipeline/*.o || die
+	rm -r seqan-cxx || die
+	default
+	eautoreconf -i
+}
+
+src_configure(){
+	econf \
+		--with-seqan-include-path=/usr/include/seqan \
+		CXXFLAGS="${CXXFLAGS}"
+}
+
+src_install(){
+	dobin bin/seecer bin/random_sub_N bin/replace_ids bin/run_jellyfish.sh bin/run_seecer.sh
+	dodoc README "${DISTDIR}"/"${PN}"-manual.pdf
+}
+
+pkg_postinst(){
+	einfo "Note that the default kmer size 17 is terribly suboptimal, use k=31 instead"
+}
diff --git a/sci-biology/SEECER/files/SEECER-increase-max-sequence-length.patch b/sci-biology/SEECER/files/SEECER-increase-max-sequence-length.patch
new file mode 100644
index 000000000..be6b320a9
--- /dev/null
+++ b/sci-biology/SEECER/files/SEECER-increase-max-sequence-length.patch
@@ -0,0 +1,44 @@
+Increase the max sequence length from 256 to 10000
+Patch created from an updated replace_ids.cc downloaded from an archived upstream email list that is no longer online
+https://web.archive.org/web/20150911132231/http://seecer-rna-read-error-correction-mailing-list.21961.x6.nabble.com/Segmentation-fault-in-step-4-td41.html
+
+--- SEECER-0.1.3/pipeline/replace_ids.cc
++++ SEECER-0.1.3/pipeline/replace_ids.cc
+@@ -5,6 +5,7 @@
+ 
+ #include <vector>
+ using namespace std;
++#define MAXSEQLENGTH 10000  
+ 
+ char* getread(int& rid, char* annot, char* seq, FILE* f2, FILE* f3) {
+   char a;
+@@ -47,10 +48,10 @@ void closeFiles(vector<FILE*>& files) {
+ 
+ bool ReadNextLines(FILE* f, char* id, char* seq) {
+     assert(!feof(f));
+-    fgets(id, 256, f);
++    fgets(id, MAXSEQLENGTH, f);
+     if (id[0] == '+') {
+-	if (!fgets(id, 256, f)) return false;
+-	if (!fgets(id, 256, f)) return false;
++	if (!fgets(id, MAXSEQLENGTH, f)) return false;
++	if (!fgets(id, MAXSEQLENGTH, f)) return false;
+     }
+     int i = 0;
+     while (id[i+1] != '\0' && id[i+1] != '\n') {
+@@ -78,11 +79,10 @@ int main(int argc, char* argv[]) {
+       && origs.size() == output.size()) {
+ 
+     int n = origs.size();
+-  
+-    char id[256];
+-    char seq[256];
+-    char seqc[256];
+-    char annot[256];
++    char id[MAXSEQLENGTH];
++    char seq[MAXSEQLENGTH];
++    char seqc[MAXSEQLENGTH];
++    char annot[MAXSEQLENGTH];
+     int rid;
+     char a;
+ 
diff --git a/sci-biology/SEECER/files/SEECER-remove-flags.patch b/sci-biology/SEECER/files/SEECER-remove-flags.patch
new file mode 100644
index 000000000..455ab4a7a
--- /dev/null
+++ b/sci-biology/SEECER/files/SEECER-remove-flags.patch
@@ -0,0 +1,30 @@
+Remove CXXFLAGS, CFLAGS, LDCLAGS set in configure.ac and Makefile.am
+Written and tested by Lucas Mitrak
+
+--- SEECER-0.1.3/Makefile.am
++++ SEECER-0.1.3/Makefile.am
+@@ -1,6 +1,6 @@
+ AM_LDFLAGS = -lgomp
+ AM_CPPFLAGS = -Wno-deprecated -Wall $(SEQAN_CFLAGS) -fopenmp
+-AM_CXXFLAGS = -O3 -g
++AM_CXXFLAGS =
+ 
+ bin_PROGRAMS = bin/seecer \
+ 	bin/random_sub_N \
+--- SEECER-0.1.3/configure.ac
++++ SEECER-0.1.3/configure.ac
+@@ -2,10 +2,10 @@ AC_INIT([seecer], [1.0], [hple@cs.cmu.edu,maschulz@cs.cmu.edu])
+ AM_INIT_AUTOMAKE([-Wall subdir-objects  foreign])
+ AC_PREREQ(2.62)
+ 
+-: ${CXXFLAGS=""}
+-CFLAGS="$CFLAGS -I/opt/local/include"
+-CXXFLAGS="$CXXFLAGS -I/opt/local/include"
+-LDFLAGS="$LDFLAGS -L/opt/local/lib"
++#: ${CXXFLAGS=""}
++#CFLAGS="$CFLAGS -I/opt/local/include"
++#CXXFLAGS="$CXXFLAGS -I/opt/local/include"
++#LDFLAGS="$LDFLAGS -L/opt/local/lib"
+ AC_PROG_CXX
+ 
+ AC_CONFIG_HEADERS([config.h])
diff --git a/sci-biology/SOAPdenovo2/Manifest b/sci-biology/SOAPdenovo2/Manifest
deleted file mode 100644
index 047465b7e..000000000
--- a/sci-biology/SOAPdenovo2/Manifest
+++ /dev/null
@@ -1 +0,0 @@
-DIST SOAPdenovo2-241.tar.gz 1532760 BLAKE2B 3229ca63b8ecb5012cc8eaa16991ea1385c63da1d7b78c8a3ade6b5fe0b90be08c08d18d3f5e5d708e3af50d5a06e9413807b00e6512965fbc2b8b07ec2dcc6b SHA512 7b0cd992e437f9e5c6f4878c3d3b1fa93f3f8aa3d40895f88cc7a99f7cd69003c4db4d27d7aaa1c2f9f43741f048a74c2479aced44ce4b9432405195749af2e2
diff --git a/sci-biology/SOAPdenovo2/SOAPdenovo2-241.ebuild b/sci-biology/SOAPdenovo2/SOAPdenovo2-241.ebuild
deleted file mode 100644
index e3679664d..000000000
--- a/sci-biology/SOAPdenovo2/SOAPdenovo2-241.ebuild
+++ /dev/null
@@ -1,47 +0,0 @@
-# Copyright 1999-2018 Gentoo Foundation
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=6
-
-inherit toolchain-funcs eutils
-
-DESCRIPTION="Whole genome shotgun assembler (sparse de Bruijn graph) (now MEGAHIT)"
-HOMEPAGE="https://github.com/aquaskyline/SOAPdenovo2
-	http://gigascience.biomedcentral.com/articles/10.1186/2047-217X-1-18"
-SRC_URI="https://github.com/aquaskyline/SOAPdenovo2/archive/r241.tar.gz -> ${P}.tar.gz"
-
-LICENSE="GPL-3"
-SLOT="0"
-KEYWORDS=""
-IUSE=""
-
-DEPEND="dev-libs/libaio
-	sci-biology/samtools:0.1-legacy"
-RDEPEND="${DEPEND}"
-
-S="${WORKDIR}"/"${PN}"-r"${PV}" # version is 2.04-r241
-
-src_prepare(){
-	epatch "${FILESDIR}"/SOAPdenovo2-r241-Makefile.patch
-	# this will be partly covered by
-	# https://github.com/aquaskyline/SOAPdenovo2/pull/44
-	#
-	for f in Makefile standardPregraph/Makefile sparsePregraph/Makefile; do
-		sed -e 's#^INCLUDES =#INCLUDES = -I/usr/include/bam-0.1-legacy -I./inc#;s#-lbam#-lbam-0.1-legacy#' -i $f || die
-	done
-	rm -f standardPregraph/*.a standardPregraph/inc/sam.h standardPregraph/inc/bam.h standardPregraph/inc/bgzf.h \
-		sparsePregraph/inc/sam.h sparsePregraph/inc/bam.h sparsePregraph/inc/bgzf.h standardPregraph/inc/zlib.h \
-		standardPregraph/inc/zconf.h sparsePregraph/inc/zlib.h sparsePregraph/inc/zconf.h standardPregraph/inc/*.so \
-		sparsePregraph/*.a || die
-	default
-}
-
-src_compile(){
-	cd standardPregraph && emake -j1 63mer=1
-	cd ../standardPregraph && emake -j1 127mer=1
-	cd ../sparsePregraph && emake -j1
-}
-
-src_install(){
-	doman "${FILESDIR}"/SOAPdenovo2.1
-}
diff --git a/sci-biology/SOAPdenovo2/files/SOAPdenovo2-r241-Makefile.patch b/sci-biology/SOAPdenovo2/files/SOAPdenovo2-r241-Makefile.patch
deleted file mode 100644
index a710c2d86..000000000
--- a/sci-biology/SOAPdenovo2/files/SOAPdenovo2-r241-Makefile.patch
+++ /dev/null
@@ -1,204 +0,0 @@
---- sparsePregraph/Makefile.ori	2017-01-03 21:34:59.000000000 +0100
-+++ sparsePregraph/Makefile	2018-04-22 22:07:47.303546845 +0200
-@@ -1,28 +1,28 @@
--CC=            g++
-+CXX ?= g++
- ifdef debug
--CFLAGS=         -O0 -g -fomit-frame-pointer
-+CXXFLAGS ?= -O0 -g -fomit-frame-pointer
- else
--CFLAGS=         -O3 -fomit-frame-pointer -w
-+CXXFLAGS ?= -O3 -fomit-frame-pointer -w
- endif
- 
--DFLAGS=         
--OBJS=		build_graph.o build_edge.o multi_threads.o \
--			build_preArc.o pregraph_sparse.o io_func.o\
--			global.o convert_soapdenovo.o
--PROG=           
--INCLUDES=	-I./inc
--SUBDIRS=    . 
--LIBPATH=	-L/usr/lib64
--LIBS=       -pthread -lz -L./inc
-+DFLAGS =         
-+OBJS = build_graph.o build_edge.o multi_threads.o \
-+	build_preArc.o pregraph_sparse.o io_func.o\
-+	global.o convert_soapdenovo.o
-+PROG =           
-+INCLUDES = -I./inc
-+SUBDIRS = . 
-+LIBPATH = -L/usr/lib64
-+LIBS = -pthread -lz -L./inc
- EXTRA_FLAGS=
--VERSION =    1.0.3
-+VERSION = 1.0.3
- 
- ifdef 127mer
--CFLAGS += -D_127MER_
-+CXXFLAGS += -D_127MER_
- PROG = pregraph_sparse_127mer.v$(VERSION)
- 
- else
--CFLAGS += -D_63MER_
-+CXXFLAGS += -D_63MER_
- PROG = pregraph_sparse_63mer.v$(VERSION)
- endif
- 
-@@ -38,22 +38,22 @@
- endif
- 
- ifneq (,$(findstring $(shell uname -m), x86_64))
--CFLAGS += -m64
-+CXXFLAGS += -m64
- endif
- 
- ifneq (,$(findstring $(shell uname -m), ia64))
--CFLAGS += 
-+CXXFLAGS += 
- endif
- 
- ifneq (,$(findstring $(shell uname -m), ppc64))
--CFLAGS += -mpowerpc64
-+CXXFLAGS += -mpowerpc64
- endif
- 
- .SUFFIXES:.cpp .o
- 
- .cpp.o:
- 		@printf "Compiling $<...                               \r"
--		@$(CC) -c $(CFLAGS) $(DFLAGS) $(INCLUDES) $< || echo "Error in command: $(CC) -c $(CFLAGS) $(DFLAGS) $(INCLUDES) $<"
-+		@$(CXX) -c $(CXXFLAGS) $(DFLAGS) $(INCLUDES) $< || echo "Error in command: $(CXX) -c $(CXXFLAGS) $(DFLAGS) $(INCLUDES) $<"
- 
- all:		$(OBJS) 
- 		@printf "$(PROG) objects generated.                    \n"
-@@ -66,7 +66,7 @@
- 
- pregraph_sparse: clean envTest $(OBJS)
- 		@printf "Linking...                                     \r"
--		@$(CC) $(CFLAGS)$(INCLUDES) -o $(PROG)  $(OBJS) $(LIBPATH) $(LIBS) $(ENTRAFLAGS)
-+		@$(CXX) $(CXXFLAGS)$(INCLUDES) -o $(PROG)  $(OBJS) $(LIBPATH) $(LIBS) $(ENTRAFLAGS)
- 		@printf "$(PROG) compilation done.                      \n"
- 
- clean:
---- Makefile.ori	2017-01-03 21:34:59.000000000 +0100
-+++ Makefile	2018-04-22 22:09:16.526124921 +0200
-@@ -1,17 +1,17 @@
- MAKEFLAGS += --no-print-directory
--CC = g++
-+CXX ?= g++
- ifdef debug
--CFLAGS=         -O0 -g -fomit-frame-pointer
-+CXXFLAGS ?= -O0 -g -fomit-frame-pointer
- else
--CFLAGS=         -O3 -fomit-frame-pointer
-+CXXFLAGS ?= -O3 -fomit-frame-pointer
- endif
- 
- SUBDIRS = sparsePregraph standardPregraph fusion
--PROG=       SOAPdenovo-63mer SOAPdenovo-127mer SOAPdenovo-fusion
--INCLUDES=   -I./sparsePregraph/inc -I./standardPregraph/inc
-+PROG = SOAPdenovo-63mer SOAPdenovo-127mer SOAPdenovo-fusion
-+INCLUDES = -I./sparsePregraph/inc -I./standardPregraph/inc
- 
--LIBPATH=    -L/lib64 -L/usr/lib64 -L./sparsePregraph/inc -L./standardPregraph/inc
--LIBS=       -pthread -lz -lm
-+LIBPATH = -L./sparsePregraph/inc -L./standardPregraph/inc
-+LIBS = -pthread -lz -lm
- EXTRA_FLAGS= 
- 
- BIT_ERR = 0
-@@ -25,15 +25,15 @@
- endif
- 
- ifneq (,$(findstring $(shell uname -m), x86_64))
--CFLAGS += -m64
-+CXXFLAGS += -m64
- endif
- 
- ifneq (,$(findstring $(shell uname -m), ia64))
--CFLAGS +=
-+CXXFLAGS +=
- endif
- 
- ifneq (,$(findstring $(shell uname -m), ppc64))
--CFLAGS += -mpowerpc64
-+CXXFLAGS += -mpowerpc64
- endif
- 
- 
-@@ -46,20 +46,20 @@
- SOAPdenovo-63mer:
- 	@cd sparsePregraph;make 63mer=1 debug=1;cd ..;
- 	@cd standardPregraph;make 63mer=1 debug=1;cd ..;
--	@$(CC) sparsePregraph/*.o standardPregraph/*.o $(LIBPATH) $(LIBS) $(EXTRA_FLAGS) -o SOAPdenovo-63mer
-+	@$(CXX) sparsePregraph/*.o standardPregraph/*.o $(LIBPATH) $(LIBS) $(EXTRA_FLAGS) -o SOAPdenovo-63mer
- SOAPdenovo-127mer:
- 	@cd sparsePregraph;make 127mer=1 debug=1;cd ..;
- 	@cd standardPregraph;make 127mer=1 debug=1;cd ..;
--	@$(CC) sparsePregraph/*.o standardPregraph/*.o $(LIBPATH) $(LIBS) $(EXTRA_FLAGS) -o SOAPdenovo-127mer
-+	@$(CXX) sparsePregraph/*.o standardPregraph/*.o $(LIBPATH) $(LIBS) $(EXTRA_FLAGS) -o SOAPdenovo-127mer
- else
- SOAPdenovo-63mer:
- 	@cd sparsePregraph;make 63mer=1;cd ..;
- 	@cd standardPregraph;make 63mer=1;cd ..;
--	@$(CC) sparsePregraph/*.o standardPregraph/*.o $(LIBPATH) $(LIBS) $(EXTRA_FLAGS) -o SOAPdenovo-63mer
-+	@$(CXX) sparsePregraph/*.o standardPregraph/*.o $(LIBPATH) $(LIBS) $(EXTRA_FLAGS) -o SOAPdenovo-63mer
- SOAPdenovo-127mer:
- 	@cd sparsePregraph;make 127mer=1;cd ..;
- 	@cd standardPregraph;make 127mer=1;cd ..;
--	@$(CC) sparsePregraph/*.o standardPregraph/*.o $(LIBPATH) $(LIBS) $(EXTRA_FLAGS) -o SOAPdenovo-127mer
-+	@$(CXX) sparsePregraph/*.o standardPregraph/*.o $(LIBPATH) $(LIBS) $(EXTRA_FLAGS) -o SOAPdenovo-127mer
- endif
- 
- clean:
---- standardPregraph/Makefile.ori	2017-01-03 21:34:59.000000000 +0100
-+++ standardPregraph/Makefile	2018-04-22 22:10:33.108337752 +0200
-@@ -5,13 +5,13 @@
- #
- ###################################
- 
--CC=             gcc
-+CC ?= gcc
- GCCVERSIONMAJOR := $(shell expr `$(CC) -dumpversion | cut -f1 -d.` \>= 4)
- GCCVERSIONMINOR := $(shell expr `$(CC) -dumpversion | cut -f2 -d.` \>= 4)
- ifdef debug
--CFLAGS=         -O0 -g -fomit-frame-pointer #-msse4.2
-+CFLAGS ?= -O0 -g -fomit-frame-pointer #-msse4.2
- else
--CFLAGS=         -O3 -fomit-frame-pointer -w #-msse4.2
-+CFLAGS ?= -O3 -fomit-frame-pointer -w #-msse4.2
- endif
- DFLAGS=         
- OBJS=		arc.o attachPEinfo.o bubble.o check.o compactEdge.o \
-@@ -24,12 +24,12 @@
- 		prlRead2path.o prlReadFillGap.o read2scaf.o readInterval.o stack.o\
- 		readseq1by1.o scaffold.o searchPath.o seq.o splitReps.o \
- 		cutTip_graph2.o linearEdge.o kmerhash.o read2edge.o iterate.o
--PROG=       SOAPdenovo-63mer
--INCLUDES=   -Iinc
--SUBDIRS=    .
--LIBPATH=    -L/lib64 -L/usr/lib64 -L./inc
--LIBS=       -pthread -lz -lm 
--EXTRA_FLAGS=
-+PROG = SOAPdenovo-63mer
-+INCLUDES = -Iinc
-+SUBDIRS = .
-+LIBPATH = -L./inc
-+LIBS = -pthread -lz -lm 
-+EXTRA_FLAGS =
- 
- BIT_ERR = 0
- ifeq (,$(findstring $(shell uname -m), x86_64 ppc64 ia64))
---- fusion/Makefile.ori	2017-01-03 21:34:59.000000000 +0100
-+++ fusion/Makefile	2018-04-22 22:11:21.209727636 +0200
-@@ -6,8 +6,8 @@
- libdir = 
- mandir = 
- 
--CC = gcc
--CCOPT = -O3 -fprefetch-loop-arrays -funroll-loops -fomit-frame-pointer -w 
-+CC ?= gcc
-+CCOPT ?= -O3 -fprefetch-loop-arrays -funroll-loops -fomit-frame-pointer -w 
- LIBS = -lm -lpthread
- INCDIRS = -Iinc/
- CFLAGS = ${CCOPT} ${INCDIRS}
diff --git a/sci-biology/SOAPdenovo2/files/soapdenovo2.1 b/sci-biology/SOAPdenovo2/files/soapdenovo2.1
deleted file mode 100644
index 337618ace..000000000
--- a/sci-biology/SOAPdenovo2/files/soapdenovo2.1
+++ /dev/null
@@ -1,22 +0,0 @@
-.TH soapdenovo2 1  "February 09, 2013" "version 2.2.3" "USER COMMANDS"
-.SH NAME
-soapdenovo2 \-  Short-read assembly method that can build a de novo draft assembly
-.SH SYNOPSIS
-.B soapdenovo_63mer soapdenovo_127mer
-
-.SH Introduction
-
-SOAPdenovo is a novel short-read assembly method that can build a de novo draft assembly for the human-sized genomes. The program is specially designed to assemble Illumina GA short reads. It creates new opportunities for building reference sequences and carrying out accurate analyses of unexplored genomes in a cost effective way.
-
-1) Support large kmer up to 127 to utilize long reads. Three version are provided.
-    I. The 31mer version support kmer only <=31.
-    II. The 63mer version support kmer only <=63 and doubles the memory consumption than 31mer version, even being used with kmer <=31.
-    III. The 127mer version support kmer only <=127 and double the memory consumption than 63mer version, even being used with kmer <=63.
-
-Please notice that, with longer kmer, the quantity of nodes would decrease significantly, thus the memory consumption is usually smaller than double with shifted version.
-
-For more information, look at the MANUAL in /usr/share/doc/soapdenovo2 or on soapdenovo web site.
-
-.SH AUTHOR
-Olivier Sallou (olivier.sallou (at) irisa.fr) - Man page and packaging
-
diff --git a/sci-biology/SOAPdenovo2/metadata.xml b/sci-biology/SOAPdenovo2/metadata.xml
deleted file mode 100644
index 138cb7705..000000000
--- a/sci-biology/SOAPdenovo2/metadata.xml
+++ /dev/null
@@ -1,12 +0,0 @@
-<?xml version="1.0" encoding="UTF-8"?>
-<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
-<pkgmetadata>
-	<maintainer type="person">
-		<email>mmokrejs@fold.natur.cuni.cz</email>
-		<name>Martin Mokrejs</name>
-	</maintainer>
-	<maintainer type="project">
-		<email>sci-biology@gentoo.org</email>
-		<name>Gentoo Biology Project</name>
-	</maintainer>
-</pkgmetadata>
diff --git a/sci-biology/SPAdes/Manifest b/sci-biology/SPAdes/Manifest
index fba8980d4..cf724a82a 100644
--- a/sci-biology/SPAdes/Manifest
+++ b/sci-biology/SPAdes/Manifest
@@ -1,5 +1,4 @@
-DIST SPAdes-3.13.0.tar.gz 8634070 BLAKE2B 8876c1ebfb7dd6485f5511a6b8b171b05eeb086ac610371833d4f9d24a175d44b7b96fdac010f5ef5ccb63bd9a839c4f83c7c2e1699b5f9239cff5dff28572b2 SHA512 2df8173debad0edb845302dc8e1fed0b459d247c4cb2d92d711ed05e5a1a2bfbb19f97aeec3aab4e991593bc90ba445347cf7e7d528147f76044a5e7f564af10
-DIST SPAdes-3.13.0_dipspades_manual.html 12561 BLAKE2B adacd4a195a1ae4ce400907d728aa9df9398ffd8545777dc2d5a69cab4396e73825e4e8f42d3d590cf82ec4f6cbb0e4783d3d731b6637b0ce8cf8afe2ebe689b SHA512 618284c899b5c0f167b91638ac3ca4d7ee2c932f5acbfa6225f43276b073259000022f12afa3d8df26dfd967085b3d2d11ca006766169199afc02de111a78db4
-DIST SPAdes-3.13.0_manual.html 64051 BLAKE2B 6217855724637fd7615d194747fcec6a94f259e3534c52574183d8bcb9cc2bf75435989f75e77774b19d6268aa6eeeb525db8ee305d02419480e285637db971a SHA512 4c80ec091ca3478e26c911313465a886c7768f87574b69a651e7e1519eef73e2bdf147e2d4136993fd309802c0fc9380ffff9a05f2da3aec5db69bbf7cd3af75
-DIST SPAdes-3.13.0_rnaspades_manual.html 7109 BLAKE2B c560e781b97899b02abf1324506a505fafa8819dd2dcf33a60886b19ddb4af515901d3ee4ac98a0d9aa21939e1afa040b0063b287f46b9b02202d5a562ba28b4 SHA512 26761374a6baa706139c108e2695ec56aef8aa1433c72e20b8b73a5e8204a225a9b1e79fddb4f627196005c7e843be8df4a7cd02a653cc47f3a9f8934d96160f
-DIST SPAdes-3.13.0_truspades_manual.html 10769 BLAKE2B ec2788a9dfdb783b8e922517263d54177595c4c6b6feee7d4c6122c3c7db561a8e2f31d210af1d6384aeb9554fb551a3ddb9937bcaf185ad6707d8c3f049f48a SHA512 e19a9385ae63f32cb232c90abd16eb8563b6b8f0abcdb2aadcfdf35cfe4aee8cf329fc97e5a2a7149ac9c6fce40791b5a89c9431de90d6e1d3651b6f0a5e221b
+DIST SPAdes-3.15.5.tar.gz 13692466 BLAKE2B c4fe59e6b253c91a6e409cf3c2e5a8181f3c0e93892e3b87f603aa75a6d025d5f1466a87ada5c86d6602f74de9048639e9b057d2abfbe449265f9c1796c608d1 SHA512 98b17f1ab0019a45e6abaf1bc7128a5edb5102120d50a47ddfbd5e30fc7130c7895a096cef16ba8e40be71c8a1f0feff38da54f02f9d2e62bd39d2d91a54f9bd
+DIST SPAdes-3.15.5_manual.html 91156 BLAKE2B e5776ec98e972f52eb630cb2048f8cd12318f0cfc020ce464bbe72e14f3716b72199d5ea34f219351d79b3fd0f4201c99f68ca487edde0d258d8794aea1f4675 SHA512 b21cc705a1f3a224dad882fce26e15dfd6d249c46627172189b285584a11d2846d0fa3c4b5aa01ca6436a494cec552122cffd4b79f6cc31446a03d610486dfaa
+DIST SPAdes-3.15.5_rnaspades_manual.html 8624 BLAKE2B b549a6cae6b02c98cae08fd5d8975210f3593c47f2b4757f19a9445a759e332229620885a6fa2f1dc0662096974548e3d0362079d12c47e6738c0261d755a2af SHA512 2d0b169efd8aa7064d59bed8ad406477c72150f23ae0438227903645071c8f66f26fe062f7dd44b584edf8ef7c709ad6c220237e68917ec23c63cfb3139666b8
+DIST SPAdes-3.15.5_truspades_manual.html 10821 BLAKE2B eb466697f774d3421053cf0fd290c82d9b2059cafd787f10c616c1363537c59960cb8ca41a8a02983ec199e0e1a27567c5850009ad6d2173df45e38f7d3120f7 SHA512 1f3bcdbe5397a23ee94820f6aaf3b85c48aca357276f58f66607140d25529c28b31298c5c8e681df3c61dabed478ac67abeb0975885aa9b7e365e14d6aac06fd
diff --git a/sci-biology/SPAdes/SPAdes-3.13.0.ebuild b/sci-biology/SPAdes/SPAdes-3.13.0.ebuild
deleted file mode 100644
index 00ccc4f27..000000000
--- a/sci-biology/SPAdes/SPAdes-3.13.0.ebuild
+++ /dev/null
@@ -1,74 +0,0 @@
-# Copyright 1999-2018 Gentoo Foundation
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=6
-
-PYTHON_COMPAT=( python{2_7,3_{4,5}} )
-
-inherit eutils toolchain-funcs
-
-DESCRIPTION="De novo de Bruijn genome assembler overcoming uneven coverage"
-HOMEPAGE="http://cab.spbu.ru/software/spades"
-SRC_URI="
-	https://github.com/ablab/spades/releases/download/v${PV}/${P}.tar.gz
-	http://cab.spbu.ru/files/release${PV}/manual.html -> ${P}_manual.html
-	http://cab.spbu.ru/files/release${PV}/rnaspades_manual.html -> ${P}_rnaspades_manual.html
-	http://cab.spbu.ru/files/release${PV}/truspades_manual.html -> ${P}_truspades_manual.html
-	http://spades.bioinf.spbau.ru/release3.11.1/dipspades_manual.html -> ${P}_dipspades_manual.html"
-# DEPRECATED in 3.12.0: dipSPAdes pipeline for highly polymorphic diploid genomes
-#	(still present in the release but no longer supported)
-
-LICENSE="GPL-2"
-SLOT="0"
-KEYWORDS=""
-IUSE=""
-
-DEPEND="
-	sys-libs/zlib
-	app-arch/bzip2
-	dev-python/regex"
-RDEPEND="${DEPEND}"
-# BUG:
-# SPAdes uses bundled while modified copy of dev-libs/boost (only headers are used,
-# not *.so or *.a are even used)
-#
-# BUG: "${S}"/ext/src/ contains plenty of bundled 3rd-party tools. Drop them all and properly DEPEND on their
-#      existing packages
-# nlopt
-# llvm
-# python_libs
-# bamtools
-# ConsensusCore
-# ssw
-# jemalloc
-# htrie
-# getopt_pp
-# cppformat
-# cityhash
-# samtools
-# bwa
-
-# BUG: "${S}"/ext/tools/ contains even two version of bwa, being installed as bwa-spades binary?
-# bwa-0.7.12
-# bwa-0.6.2
-
-pkg_pretend() {
-	if [[ ${MERGE_TYPE} != binary ]]; then
-		if [[ $(tc-getCXX) == *g++ ]] ; then
-			if [[ $(gcc-major-version) == 4 && $(gcc-minor-version) -lt 7 || $(gcc-major-version) -lt 4 ]] ; then
-				eerror "You need at least sys-devel/gcc-4.7.0"
-				die "You need at least sys-devel/gcc-4.7.0"
-			fi
-		fi
-	fi
-}
-
-src_compile(){
-	PREFIX="${ED}"/usr ./spades_compile.sh || die
-}
-
-src_install(){
-	# BUG: move *.py files to standard site-packages/ subdirectories
-	insinto /usr/share/"${PN}"
-	dodoc "${DISTDIR}"/${P}_*manual.html
-}
diff --git a/sci-biology/SPAdes/SPAdes-3.15.5.ebuild b/sci-biology/SPAdes/SPAdes-3.15.5.ebuild
new file mode 100644
index 000000000..026dd0476
--- /dev/null
+++ b/sci-biology/SPAdes/SPAdes-3.15.5.ebuild
@@ -0,0 +1,42 @@
+# Copyright 1999-2022 Gentoo Authors
+# Distributed under the terms of the GNU General Public License v2
+
+EAPI=8
+
+PYTHON_COMPAT=( python3_{10..12} )
+inherit python-single-r1
+
+DESCRIPTION="De novo de Bruijn genome assembler overcoming uneven coverage"
+HOMEPAGE="https://cab.spbu.ru/software/spades"
+SRC_URI="
+	https://github.com/ablab/spades/releases/download/v${PV}/${P}.tar.gz
+	https://cab.spbu.ru/files/release${PV}/manual.html -> ${P}_manual.html
+	https://cab.spbu.ru/files/release${PV}/rnaspades_manual.html -> ${P}_rnaspades_manual.html
+	https://cab.spbu.ru/files/release${PV}/truspades_manual.html -> ${P}_truspades_manual.html
+"
+
+LICENSE="GPL-2"
+SLOT="0"
+KEYWORDS="~amd64"
+REQUIRED_USE="${PYTHON_REQUIRED_USE}"
+
+DEPEND="
+	sys-libs/zlib
+	app-arch/bzip2
+	dev-python/regex
+	${PYTHON_DEPS}
+"
+RDEPEND="${DEPEND}"
+BDEPEND="dev-build/cmake"
+
+# Remove for next release:
+# https://github.com/ablab/spades/issues/1238#issuecomment-1904427831
+PATCHES=(
+	"${FILESDIR}/${P}-gcc13.patch"
+)
+
+src_install(){
+	einstalldocs
+	# WORKAROUND: This script does both compile and install in one go
+	PREFIX="${ED}"/usr ./spades_compile.sh || die
+}
diff --git a/sci-biology/SPAdes/files/SPAdes-3.15.5-gcc13.patch b/sci-biology/SPAdes/files/SPAdes-3.15.5-gcc13.patch
new file mode 100644
index 000000000..3dd3f8c02
--- /dev/null
+++ b/sci-biology/SPAdes/files/SPAdes-3.15.5-gcc13.patch
@@ -0,0 +1,49 @@
+From 3e802fa51d156fc958c36e25d607f20bf756f0bf Mon Sep 17 00:00:00 2001
+From: Bo YU <tsu.yubo@gmail.com>
+Date: Wed, 19 Jul 2023 18:42:04 +0800
+Subject: [PATCH] fix build issues due to gcc-13
+
+Signed-off-by: Bo YU <tsu.yubo@gmail.com>
+---
+ ext/include/llvm/Support/Signals.h   | 1 +
+ src/common/pipeline/library_data.hpp | 1 +
+ src/common/sequence/nucl.hpp         | 2 ++
+ 3 files changed, 4 insertions(+)
+
+diff --git a/assembler/ext/include/llvm/Support/Signals.h b/assembler/ext/include/llvm/Support/Signals.h
+index e0a18e72f..148216b8f 100644
+--- a/ext/include/llvm/Support/Signals.h
++++ b/ext/include/llvm/Support/Signals.h
+@@ -14,6 +14,7 @@
+ #ifndef LLVM_SUPPORT_SIGNALS_H
+ #define LLVM_SUPPORT_SIGNALS_H
+ 
++#include <cstdint>
+ #include <string>
+ 
+ namespace llvm {
+diff --git a/assembler/src/common/pipeline/library_data.hpp b/assembler/src/common/pipeline/library_data.hpp
+index 3cbaf0adb..1ffaa7b37 100644
+--- a/src/common/pipeline/library_data.hpp
++++ b/src/common/pipeline/library_data.hpp
+@@ -8,6 +8,7 @@
+ 
+ #include <map>
+ #include <string>
++#include <cstdint>
+ 
+ // Forward decls for LLVM YAML API
+ namespace llvm { namespace yaml { class IO; template<typename T> struct MappingTraits; } }
+diff --git a/assembler/src/common/sequence/nucl.hpp b/assembler/src/common/sequence/nucl.hpp
+index 9c7d6de13..e10e7f583 100755
+--- a/src/common/sequence/nucl.hpp
++++ b/src/common/sequence/nucl.hpp
+@@ -8,6 +8,8 @@
+ #ifndef NUCL_HPP_
+ #define NUCL_HPP_
+ 
++#include <cstdint>
++
+ #include "utils/verify.hpp"
+ 
+ /**
diff --git a/sci-biology/SPAdes/metadata.xml b/sci-biology/SPAdes/metadata.xml
index 0845ad7a4..5f573393e 100644
--- a/sci-biology/SPAdes/metadata.xml
+++ b/sci-biology/SPAdes/metadata.xml
@@ -10,8 +10,11 @@
 		<name>Gentoo Biology Project</name>
 	</maintainer>
 	<longdescription>
-truSPAdes includes support for Illumina TruSeq Synthetic Long Read technology reads.
-hammer and ionhammer are read error correcting modules for Illumina /IonTorrent reads, resp.
-dipspades is assembly module for highly polymorphic diploid genomes
-</longdescription>
+		truSPAdes includes support for Illumina TruSeq Synthetic Long Read technology reads.
+		hammer and ionhammer are read error correcting modules for Illumina /IonTorrent reads, resp.
+		dipspades is assembly module for highly polymorphic diploid genomes
+	</longdescription>
+	<upstream>
+		<remote-id type="github">ablab/spades</remote-id>
+	</upstream>
 </pkgmetadata>
diff --git a/sci-biology/SSAKE/SSAKE-3.8.2.ebuild b/sci-biology/SSAKE/SSAKE-3.8.2.ebuild
index 719887d8e..556b71596 100644
--- a/sci-biology/SSAKE/SSAKE-3.8.2.ebuild
+++ b/sci-biology/SSAKE/SSAKE-3.8.2.ebuild
@@ -1,22 +1,21 @@
-# Copyright 1999-2015 Gentoo Foundation
+# Copyright 1999-2021 Gentoo Authors
 # Distributed under the terms of the GNU General Public License v2
 
-EAPI=5
+EAPI=7
 
 DESCRIPTION="Short-read trimmer, OLC assembler, scaffolder in PERL using the 3'-most k-mers"
 HOMEPAGE="http://www.bcgsc.ca/platform/bioinfo/software/ssake"
-SRC_URI="http://www.bcgsc.ca/platform/bioinfo/software/ssake/releases/${PV}/ssake_v3-8-2.tar.gz"
+SRC_URI="http://www.bcgsc.ca/platform/bioinfo/software/ssake/releases/${PV}/ssake_v${PV//./-}.tar.gz"
 
 LICENSE="GPL-2+"
 SLOT="0"
 KEYWORDS="~amd64"
-IUSE=""
 
 # pure perl
 DEPEND="dev-lang/perl"
 RDEPEND="${DEPEND}"
 
-S=${WORKDIR}/ssake_v3-8-2
+S="${WORKDIR}/ssake_v${PV//./-}"
 
 src_install(){
 	dobin SSAKE
diff --git a/sci-biology/STAR/STAR-9999.ebuild b/sci-biology/STAR/STAR-9999.ebuild
deleted file mode 100644
index 787583b66..000000000
--- a/sci-biology/STAR/STAR-9999.ebuild
+++ /dev/null
@@ -1,36 +0,0 @@
-# Copyright 1999-2015 Gentoo Foundation
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=5
-
-inherit git-r3 toolchain-funcs
-
-DESCRIPTION="STAR aligner: align RNA-seq reads to reference genome uncompressed suffix arrays"
-HOMEPAGE="http://code.google.com/p/rna-star/"
-EGIT_REPO_URI="https://github.com/alexdobin/STAR.git"
-# http://rna-star.googlecode.com/files/STARmanual_2.3.0.1.pdf
-
-LICENSE="GPL-3"
-SLOT="0"
-KEYWORDS=""
-IUSE=""
-
-# contains bundled version sci-biology/htslib-0.0.1
-DEPEND=""
-RDEPEND="${DEPEND}"
-
-# contains bundled STAR-Fusion
-src_prepare(){
-	sed -e "s/= gcc/= $(tc-getCC)/;s/-O2/${CFLAGS}/g" -i source/htslib/Makefile || die
-	sed -e "s/-O3/${CFLAGS}/g" -i source/Makefile || die
-}
-
-src_compile(){
-	cd source || die
-	emake STAR
-}
-
-src_install(){
-	dobin source/STAR
-	dodoc doc/STARmanual.pdf
-}
diff --git a/sci-biology/STAR/metadata.xml b/sci-biology/STAR/metadata.xml
deleted file mode 100644
index 1f2f45f25..000000000
--- a/sci-biology/STAR/metadata.xml
+++ /dev/null
@@ -1,15 +0,0 @@
-<?xml version="1.0" encoding="UTF-8"?>
-<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
-<pkgmetadata>
-	<maintainer type="person">
-		<email>mmokrejs@fold.natur.cuni.cz</email>
-		<name>Martin Mokrejs</name>
-	</maintainer>
-	<maintainer type="project">
-		<email>sci-biology@gentoo.org</email>
-		<name>Gentoo Biology Project</name>
-	</maintainer>
-	<upstream>
-		<remote-id type="github">alexdobin/STAR</remote-id>
-	</upstream>
-</pkgmetadata>
diff --git a/sci-biology/Scaffolder-evaluation/Scaffolder-evaluation-9999.ebuild b/sci-biology/Scaffolder-evaluation/Scaffolder-evaluation-9999.ebuild
deleted file mode 100644
index 298dc7b22..000000000
--- a/sci-biology/Scaffolder-evaluation/Scaffolder-evaluation-9999.ebuild
+++ /dev/null
@@ -1,33 +0,0 @@
-# Copyright 1999-2016 Gentoo Foundation
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=6
-
-inherit git-r3
-
-DESCRIPTION="Scripts to run genome assembly scaffolding tools and analyse output for accuracy"
-HOMEPAGE="https://github.com/martinghunt/Scaffolder-evaluation
-	http://genomebiology.com/2014/15/3/R42"
-EGIT_REPO_URI="https://github.com/martinghunt/Scaffolder-evaluation.git"
-
-LICENSE="GPL-3"
-SLOT="0"
-KEYWORDS=""
-IUSE=""
-
-DEPEND=""
-RDEPEND="${DEPEND}
-	dev-lang/perl
-	dev-lang/python
-	dev-lang/R
-	media-gfx/graphviz
-	sci-biology/mummer
-	sci-biology/bowtie
-	sci-biology/samtools
-	sci-biology/ncbi-tools
-	sci-biology/Fastaq"
-
-src_install(){
-	dobin Analysis-scripts/* Wrapper-scripts/*
-	dodoc README.md
-}
diff --git a/sci-biology/Scaffolder-evaluation/metadata.xml b/sci-biology/Scaffolder-evaluation/metadata.xml
deleted file mode 100644
index 337db209e..000000000
--- a/sci-biology/Scaffolder-evaluation/metadata.xml
+++ /dev/null
@@ -1,15 +0,0 @@
-<?xml version="1.0" encoding="UTF-8"?>
-<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
-<pkgmetadata>
-	<maintainer type="person">
-		<email>mmokrejs@fold.natur.cuni.cz</email>
-		<name>Martin Mokrejs</name>
-	</maintainer>
-	<maintainer type="project">
-		<email>sci-biology@gentoo.org</email>
-		<name>Gentoo Biology Project</name>
-	</maintainer>
-	<upstream>
-		<remote-id type="github">martinghunt/Scaffolder-evaluation</remote-id>
-	</upstream>
-</pkgmetadata>
diff --git a/sci-biology/Sibelia/Sibelia-9999.ebuild b/sci-biology/Sibelia/Sibelia-9999.ebuild
deleted file mode 100644
index b173755c4..000000000
--- a/sci-biology/Sibelia/Sibelia-9999.ebuild
+++ /dev/null
@@ -1,35 +0,0 @@
-# Copyright 1999-2018 Gentoo Foundation
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=6
-
-PYTHON_COMPAT=( python2_7 )
-
-inherit cmake-utils git-r3
-
-DESCRIPTION="Draw synteny plots using circos"
-HOMEPAGE="http://bioinf.spbau.ru/en/sibelia"
-EGIT_REPO_URI="https://github.com/bioinf/Sibelia.git"
-
-LICENSE="GPL-2"
-SLOT="0"
-KEYWORDS=""
-IUSE=""
-
-DEPEND="
-	dev-lang/perl
-	dev-libs/boost:0
-	dev-cpp/tclap
-	>=dev-libs/libdivsufsort-2.0.1
-	sci-biology/seqan:*
-	sci-biology/lagan
-	>=sci-biology/SnpEff-3.3"
-# https://github.com/bioinf/Sibelia/issues/181
-# it contains bundled copies of all the above
-# we would need to create also a Gentoo package for D3.js
-#   (BSD License) http://d3js.org
-# it links using bundled libdivsufsort-2.0.1/lib/libdivsufsort.a
-# it install stuff into /usr/lib/Sibelia/{lagan,snpEff}/
-RDEPEND="${DEPEND}"
-
-S="${WORKDIR}"/"${P}"/src
diff --git a/sci-biology/Sibelia/metadata.xml b/sci-biology/Sibelia/metadata.xml
deleted file mode 100644
index 138cb7705..000000000
--- a/sci-biology/Sibelia/metadata.xml
+++ /dev/null
@@ -1,12 +0,0 @@
-<?xml version="1.0" encoding="UTF-8"?>
-<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
-<pkgmetadata>
-	<maintainer type="person">
-		<email>mmokrejs@fold.natur.cuni.cz</email>
-		<name>Martin Mokrejs</name>
-	</maintainer>
-	<maintainer type="project">
-		<email>sci-biology@gentoo.org</email>
-		<name>Gentoo Biology Project</name>
-	</maintainer>
-</pkgmetadata>
diff --git a/sci-biology/SnpEff/Manifest b/sci-biology/SnpEff/Manifest
index 9bec29d19..183a71158 100644
--- a/sci-biology/SnpEff/Manifest
+++ b/sci-biology/SnpEff/Manifest
@@ -1,2 +1,2 @@
-DIST SnpEff-4.3i.html 101923 SHA256 10e365b8567ecc11453eb123ab24a483a682223baeb269fbe66e7c81320e80c6 SHA512 ecf6c56508dff0abaec9dbc05677e958e10ad1df97ae0a29007b0748598de8f0982c298ea9a7e5d8692c5abe4adacd4afc1307137a92ea81e793577bc1e7ecaf WHIRLPOOL f503346a51461de107b05b047b5472b6739e264db1718afbf38c501ea2dc0ccb7a609eec38d383112790e1b4a6ac36680d5e198cd0d11f91b0f9d028c098fcf2
-DIST snpEff_v4_3i_core.zip 48456135 BLAKE2B ee5f77119883d2fb6f118f9de523dda76f0fc5ba742b2873e1affdae025a9d6121775aa760435caf2b0fcc3550873e198c20b0e2030bcd387d88a4cc4bc32114 SHA512 6eb90afe125022da48a0d70c445c362ea8f9138d7dcecbf5fff1bf4f2d6bdbba812591416669481890a0d8bc89518023c2e0d1ef2d91d5efa7cce61cdbb02676
+DIST SnpEff-4.3t.html 10041 BLAKE2B fe3f9b3cf2198af8690bd1f7fdda0a718c354f69343280d29b3021aa00a426653079aec738f8e0d0be0856d789526678481c8a255f0d77463e7e7dc2b4aec7a5 SHA512 fba76ce6e9414a610e2ee4247c6fa34601d0b2925cce1c35ffa7fc865ad80684c28e2a23c0f551cf5ee47057f847c5e2ebfaca18d5c47f41722951b192b1fbfb
+DIST snpEff_v4_3t_core.zip 69708122 BLAKE2B c64c68c9923951f086df447b93adf55e5555e545c59e30a2ce2fdef7e9690cf5219aaab112a6dce23ce6ea72d80772f686a7eb5f000d11b28503f792e0df09a7 SHA512 dfb48c2ae6b9b6dc07b02d44ae0b6ee09d235f1abce8e4df9e9bafbe8e9cd00f914f6e83dee7e67fcd7db0369e00c9dbb8f39575a956ddf3c611298d9c8e062f
diff --git a/sci-biology/SnpEff/SnpEff-4.3i.ebuild b/sci-biology/SnpEff/SnpEff-4.3i.ebuild
deleted file mode 100644
index 9921b3394..000000000
--- a/sci-biology/SnpEff/SnpEff-4.3i.ebuild
+++ /dev/null
@@ -1,62 +0,0 @@
-# Copyright 1999-2017 Gentoo Foundation
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=6
-
-inherit java-pkg-2 java-ant-2
-
-MY_PV=${PV/./_}
-
-DESCRIPTION="SnpEff, SnpSift: Annotate SNP changes and predict effect in HGVS-compliant VCF"
-HOMEPAGE="http://snpeff.sourceforge.net"
-SRC_URI="
-	http://sourceforge.net/projects/snpeff/files/snpEff_v${MY_PV}_core.zip
-	http://snpeff.sourceforge.net/SnpSift.html -> ${P}.html"
-
-LICENSE="LGPL-3"
-SLOT="0"
-KEYWORDS="~amd64 ~x86"
-IUSE=""
-
-# https://github.com/pcingola/SnpEff/blob/master/README_release.txt
-RDEPEND="
-	>=virtual/jre-1.7:*
-	dev-java/maven-bin:*
-	dev-java/antlr:*"
-DEPEND="${RDEPEND}
-	>=virtual/jdk-1.7:*
-	dev-java/ant-core"
-
-S="${WORKDIR}"
-
-#src_compile(){
-#	mvn || die
-#}
-
-src_install(){
-	cd .. || die
-	mkdir -p "${ED}"/usr/share || die
-	# but portage does not install the .* files and subdirs, grr!
-	unzip \
-		"${DISTDIR}"/snpEff_v"${MY_PV}"_core.zip -d "${ED}"/usr/share \
-		|| die "failed to unzip ${DISTDIR}/snpEff_v${MY_PV}_core.zip"
-	sed \
-		-e "s#$HOME/tools/picard/#${ED}/usr/share/picard/lib/#" \
-		-i "${ED}"/usr/share/snpEff/scripts/annotate_demo_GATK.sh || die
-	sed \
-		-e "s#$HOME/tools/gatk/#${ED}/usr/share/gatk/lib/#" \
-		-i "${ED}"/usr/share/snpEff/scripts/annotate_demo_GATK.sh || die
-	sed \
-		-e "s#$HOME/snpEff/#${ED}/usr/share/snpEff/#" \
-		-i "${ED}"/usr/share/snpEff/scripts/annotate_demo_GATK.sh || die
-	sed \
-	-e "s#$HOME/snpEff/snpEff.config#${ED}/usr/share/snpEff/snpEff.config#" \
-	-i "${ED}"/usr/share/snpEff/scripts/annotate_demo_GATK.sh || die
-}
-
-# now fetch the version-specific databases from http://sourceforge.net/projects/snpeff/files/databases/v4_1/
-# it also automagically fetches them but into /tmp/ unlike $CWD
-#
-# java -Xmx4g path/to/snpEff/snpEff.jar -c path/to/snpEff/snpEff.config GRCh37.75 path/to/snps.vcf
-#
-# It is best to just unpack the tarball locally and not use portage at all.
diff --git a/sci-biology/SnpEff/SnpEff-4.3t.ebuild b/sci-biology/SnpEff/SnpEff-4.3t.ebuild
new file mode 100644
index 000000000..843c00356
--- /dev/null
+++ b/sci-biology/SnpEff/SnpEff-4.3t.ebuild
@@ -0,0 +1,55 @@
+# Copyright 1999-2021 Gentoo Authors
+# Distributed under the terms of the GNU General Public License v2
+
+EAPI=7
+
+inherit java-pkg-2 java-ant-2
+
+DESCRIPTION="SnpEff, SnpSift: Annotate SNP changes and predict effect in HGVS-compliant VCF"
+HOMEPAGE="https://pcingola.github.io/SnpEff/"
+SRC_URI="
+	https://downloads.sourceforge.net/project/snpeff/snpEff_v${PV//./_}_core.zip
+	https://pcingola.github.io/SnpEff/index.html -> ${P}.html"
+
+LICENSE="LGPL-3"
+SLOT="0"
+KEYWORDS="~amd64"
+
+RDEPEND="
+	>=virtual/jre-1.7:*
+	dev-java/maven-bin:*
+	dev-java/antlr:*"
+DEPEND="${RDEPEND}
+	>=virtual/jdk-1.7:*
+	dev-java/ant-core"
+BDEPEND="app-arch/unzip"
+
+S="${WORKDIR}"
+
+src_install(){
+	cd .. || die
+	mkdir -p "${ED}"/usr/share || die
+	# but portage does not install the .* files and subdirs, grr!
+	unzip \
+		"${DISTDIR}"/snpEff_v"${PV//./_}"_core.zip -d "${ED}"/usr/share \
+		|| die "failed to unzip ${DISTDIR}/snpEff_v${PV//./_}_core.zip"
+	sed \
+		-e "s#$HOME/tools/picard/#${ED}/usr/share/picard/lib/#" \
+		-i "${ED}"/usr/share/snpEff/scripts/annotate_demo_GATK.sh || die
+	sed \
+		-e "s#$HOME/tools/gatk/#${ED}/usr/share/gatk/lib/#" \
+		-i "${ED}"/usr/share/snpEff/scripts/annotate_demo_GATK.sh || die
+	sed \
+		-e "s#$HOME/snpEff/#${ED}/usr/share/snpEff/#" \
+		-i "${ED}"/usr/share/snpEff/scripts/annotate_demo_GATK.sh || die
+	sed \
+	-e "s#$HOME/snpEff/snpEff.config#${ED}/usr/share/snpEff/snpEff.config#" \
+	-i "${ED}"/usr/share/snpEff/scripts/annotate_demo_GATK.sh || die
+}
+
+# now fetch the version-specific databases from http://sourceforge.net/projects/snpeff/files/databases/v4_1/
+# it also automagically fetches them but into /tmp/ unlike $CWD
+#
+# java -Xmx4g path/to/snpEff/snpEff.jar -c path/to/snpEff/snpEff.config GRCh37.75 path/to/snps.vcf
+#
+# It is best to just unpack the tarball locally and not use portage at all.
diff --git a/sci-biology/SolexaQA/Manifest b/sci-biology/SolexaQA/Manifest
index 228498d8e..acaa1c9e5 100644
--- a/sci-biology/SolexaQA/Manifest
+++ b/sci-biology/SolexaQA/Manifest
@@ -1 +1 @@
-DIST SolexaQA_v.2.2.zip 40266 BLAKE2B 8823500f354f0d08ec01b52a97bcddc503a0c88def8038c48b5a0365eee4e827b4af08b9c3e6e8ae4c404d7aa336be250e96eec47462bc31e11ef27f06c27021 SHA512 e1aef383ff891106479ee0f35bbcf973de8d65f4be4822f406378ceae7178e5c370583c966b14660ac205e82a57de495bd0f26eeed190b5018564de5b119e209
+DIST SolexaQA++_v3.1.7.1.zip 2915171 BLAKE2B 9fe9c76c33a4513c347aeb4c4c57dd02e7dc40c00b0769ecb10cc1c93f5e6908849cbee13b4a7af4a648a8ab16767420f1a0589e45c11b8f28f9784ae8baab18 SHA512 cd799e6f0b878ac614dfe9af737f2f4641610c4a5dc11ede4a15b5ba7300eabb2e7e17808c07ebc4be19f6cf9965061a7c2156a6f0b1e1efaa37c28ae2a1aea6
diff --git a/sci-biology/SolexaQA/SolexaQA-2.2.ebuild b/sci-biology/SolexaQA/SolexaQA-2.2.ebuild
deleted file mode 100644
index 62fc3dc8b..000000000
--- a/sci-biology/SolexaQA/SolexaQA-2.2.ebuild
+++ /dev/null
@@ -1,24 +0,0 @@
-# Copyright 1999-2015 Gentoo Foundation
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=5
-
-DESCRIPTION="Analyze and trim single-end and paired-end reads, show quality statistics"
-HOMEPAGE="http://sourceforge.net/projects/clview"
-SRC_URI="http://sourceforge.net/projects/solexaqa/files/src/SolexaQA_v.2.2.zip"
-
-LICENSE="GPL-3"
-SLOT="0"
-KEYWORDS="~amd64"
-IUSE=""
-
-DEPEND="
-	dev-lang/perl
-	dev-lang/R"
-RDEPEND="${DEPEND}"
-
-S=${WORKDIR}/"${PN}"_v."${PV}"
-
-src_install(){
-	dobin *.pl
-}
diff --git a/sci-biology/SolexaQA/SolexaQA-3.1.7.1.ebuild b/sci-biology/SolexaQA/SolexaQA-3.1.7.1.ebuild
new file mode 100644
index 000000000..81258a0ef
--- /dev/null
+++ b/sci-biology/SolexaQA/SolexaQA-3.1.7.1.ebuild
@@ -0,0 +1,31 @@
+# Copyright 1999-2021 Gentoo Authors
+# Distributed under the terms of the GNU General Public License v2
+
+EAPI=7
+
+DESCRIPTION="Analyze and trim single-end and paired-end reads, show quality statistics"
+HOMEPAGE="https://sourceforge.net/projects/solexaqa"
+SRC_URI="https://sourceforge.net/projects/solexaqa/files/src/SolexaQA++_v${PV}.zip"
+
+LICENSE="GPL-3"
+SLOT="0"
+KEYWORDS="~amd64"
+
+DEPEND="
+	sys-libs/zlib
+	dev-libs/boost
+"
+BDEPEND="app-arch/unzip"
+RDEPEND="${DEPEND}"
+
+S="${WORKDIR}/source"
+
+src_prepare() {
+	default
+	sed -i -e "s/\/lib/$(get_libdir)/g" -e "s/\/include/include\/boost/g" -e 's/-static//' makefile || die
+}
+
+src_install() {
+	newbin SolexaQA++ "${PN}"
+	einstalldocs
+}
diff --git a/sci-biology/StarORF/StarORF-9999.ebuild b/sci-biology/StarORF/StarORF-9999.ebuild
deleted file mode 100644
index 2dc2663f7..000000000
--- a/sci-biology/StarORF/StarORF-9999.ebuild
+++ /dev/null
@@ -1,29 +0,0 @@
-# Copyright 1999-2016 Gentoo Foundation
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=6
-
-inherit java-pkg-2 java-ant-2 git-r3
-
-DESCRIPTION="Java-based utility to show ORFs in a sequence"
-HOMEPAGE="http://star.mit.edu/orf"
-EGIT_REPO_URI="https://github.com/starteam/starorf_java.git"
-
-LICENSE="BSD-2"
-SLOT="0"
-KEYWORDS=""
-IUSE=""
-
-DEPEND="
-	>=virtual/jdk-1.5:*
-	dev-java/jreleaseinfo"
-RDEPEND="${DEPEND}
-	>=virtual/jre-1.5:*"
-
-#src_compile() {
-#	ant compile || die
-#}
-
-src_install() {
-	java-pkg_dojar StarORF.jar
-}
diff --git a/sci-biology/StarORF/metadata.xml b/sci-biology/StarORF/metadata.xml
deleted file mode 100644
index 138cb7705..000000000
--- a/sci-biology/StarORF/metadata.xml
+++ /dev/null
@@ -1,12 +0,0 @@
-<?xml version="1.0" encoding="UTF-8"?>
-<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
-<pkgmetadata>
-	<maintainer type="person">
-		<email>mmokrejs@fold.natur.cuni.cz</email>
-		<name>Martin Mokrejs</name>
-	</maintainer>
-	<maintainer type="project">
-		<email>sci-biology@gentoo.org</email>
-		<name>Gentoo Biology Project</name>
-	</maintainer>
-</pkgmetadata>
diff --git a/sci-biology/TransDecoder/Manifest b/sci-biology/TransDecoder/Manifest
index 90ba20194..8be75a508 100644
--- a/sci-biology/TransDecoder/Manifest
+++ b/sci-biology/TransDecoder/Manifest
@@ -1 +1 @@
-DIST TransDecoder-2.1.0.tar.gz 11500688 BLAKE2B 83d12acf0a80e3e5b696bed5433749d995e03973a8293921f8052526bfc744b2ab606d1f99e24b4ff491a4cedd5f48f150606fafa4bc99be0c84bfb68cf29fd2 SHA512 4635a544ef56718db3fbfbe84ab47dfd7af605df73ead69c98e79dca64649c91d6d5139f0b5540d307f23fce5d0d75289c4fd1bedffc393721ccd9b863b7b043
+DIST TransDecoder-v5.5.0.tar.gz 15748671 BLAKE2B e6c3fa38f562689ff5ab880d893beec65d9c1d30ce4f53b9fa003f8cba1ae92ff451515d234e0349b9d514fba27431b558f3dfda83f5481799f0ae74819e192a SHA512 a262397b7b81207c70bf03a78a5c6a03eb83034e02b070f64e9b929b53b68860df883477d6256a81efa1a64853510a206deaef697f3fee6a9ae75bf7a041737f
diff --git a/sci-biology/TransDecoder/TransDecoder-2.1.0.ebuild b/sci-biology/TransDecoder/TransDecoder-2.1.0.ebuild
deleted file mode 100644
index 6b462ff90..000000000
--- a/sci-biology/TransDecoder/TransDecoder-2.1.0.ebuild
+++ /dev/null
@@ -1,76 +0,0 @@
-# Copyright 1999-2017 Gentoo Foundation
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=6
-
-inherit perl-functions toolchain-funcs
-
-DESCRIPTION="Extract ORF/CDS regions from FASTA sequences"
-HOMEPAGE="http://transdecoder.github.io"
-
-if [[ ${PV} == *9999 ]]; then
-	inherit git-r3
-	EGIT_REPO_URI="https://github.com/TransDecoder/TransDecoder.git"
-else
-	SRC_URI="https://github.com/TransDecoder/TransDecoder/archive/v${PV}.tar.gz -> ${P}.tar.gz"
-	KEYWORDS="~amd64"
-fi
-
-LICENSE="BSD-BroadInstitute"
-SLOT="0"
-IUSE=""
-
-DEPEND="dev-lang/perl:="
-RDEPEND="${DEPEND}
-	sci-biology/cd-hit
-	sci-biology/parafly
-	sci-biology/ffindex"
-
-src_prepare() {
-	rm -rf transdecoder_plugins/cd-hit || die
-	local f p
-	for f in PerlLib/*.pm; do
-		p=$(basename $f .pm)
-
-		sed -e "s#use $p;#use TransDecoder::$p;#" \
-			-i PerlLib/*.pm util/*.pl TransDecoder.LongOrfs TransDecoder.Predict || die
-	done
-	eapply "${FILESDIR}"/"${P}"__fix_paths.patch
-	eapply "${FILESDIR}"/pfam_runner.pl.patch
-
-	eapply_user
-}
-
-src_compile() {
-	einfo "Skipping compilation of bundled cd-hit code, nothing else to do"
-}
-
-# avoid fetching 1.5TB "${S}"/pfam/Pfam-AB.hmm.bin, see
-# "Re: [Transdecoder-users] Announcement: Transdecoder release r20140704"
-# thread in archives. You can get it from
-# http://downloads.sourceforge.net/project/transdecoder/Pfam-AB.hmm.bin
-
-src_install() {
-	dobin TransDecoder.Predict TransDecoder.LongOrfs
-
-	insinto /usr/share/${PN}/util
-	doins util/*.pl
-
-	chmod -R a+rx "${ED%/}"/usr/share/${PN}/util || die
-	# zap the bundled cdhit binaries copied from transdecoder_plugins/cdhit/ to util/bin
-	rm -rf util/bin || die
-
-	perl_domodule -C ${PN} PerlLib/*.pm
-
-	# dodoc Release.Notes
-	einfo "Fetch your own Pfam-A.hmm (Pfam-AB.hmm is discontinued since 05/2015):"
-	einfo "wget --mirror -nH -nd ftp://ftp.ebi.ac.uk/pub/databases/Pfam/current_release/Pfam-A.hmm.gz"
-	einfo "hmmpress Pfam-A.hmm.bin"
-}
-
-pkg_postinst() {
-	einfo "It is recommended to use TransDecoder with sci-biology/hmmer-3 or"
-	einfo "at least with NCBI blast from either:"
-	einfo "    sci-biology/ncbi-blast+ (released more often) or from"
-	einfo "    sci-biology/ncbi-toolkit++ (a huge bundle with releases and less frequent bugfixes)"
-}
diff --git a/sci-biology/TransDecoder/TransDecoder-5.5.0.ebuild b/sci-biology/TransDecoder/TransDecoder-5.5.0.ebuild
new file mode 100644
index 000000000..c9181641f
--- /dev/null
+++ b/sci-biology/TransDecoder/TransDecoder-5.5.0.ebuild
@@ -0,0 +1,77 @@
+# Copyright 1999-2021 Gentoo Authors
+# Distributed under the terms of the GNU General Public License v2
+
+EAPI=7
+
+inherit perl-functions
+
+DESCRIPTION="Extract ORF/CDS regions from FASTA sequences"
+HOMEPAGE="https://github.com/TransDecoder/TransDecoder/wiki"
+
+if [[ ${PV} == *9999 ]]; then
+	inherit git-r3
+	EGIT_REPO_URI="https://github.com/TransDecoder/TransDecoder.git"
+else
+	SRC_URI="https://github.com/TransDecoder/TransDecoder/archive/TransDecoder-v${PV}.tar.gz"
+	KEYWORDS="~amd64"
+	S="${WORKDIR}/${PN}-${PN}-v${PV}"
+fi
+
+LICENSE="BSD-BroadInstitute"
+SLOT="0"
+
+RESTRICT="test"
+
+DEPEND="dev-lang/perl:="
+RDEPEND="${DEPEND}
+	sci-biology/cd-hit
+	sci-biology/parafly
+	sci-biology/ffindex"
+
+src_prepare() {
+	rm -rf transdecoder_plugins/cd-hit || die
+	local f p
+	for f in PerlLib/*.pm; do
+		p=$(basename $f .pm)
+
+		sed -e "s#use $p;#use TransDecoder::$p;#" \
+			-i PerlLib/*.pm util/*.pl TransDecoder.LongOrfs TransDecoder.Predict || die
+	done
+	eapply "${FILESDIR}"/pfam_runner.pl.patch
+
+	eapply_user
+}
+
+src_compile() {
+	einfo "Skipping compilation of bundled cd-hit code, nothing else to do"
+}
+
+# avoid fetching 1.5TB "${S}"/pfam/Pfam-AB.hmm.bin, see
+# "Re: [Transdecoder-users] Announcement: Transdecoder release r20140704"
+# thread in archives. You can get it from
+# http://downloads.sourceforge.net/project/transdecoder/Pfam-AB.hmm.bin
+
+src_install() {
+	dobin TransDecoder.Predict TransDecoder.LongOrfs
+
+	insinto /usr/share/${PN}/util
+	doins util/*.pl
+
+	chmod -R a+rx "${ED}"/usr/share/${PN}/util || die
+	# zap the bundled cdhit binaries copied from transdecoder_plugins/cdhit/ to util/bin
+	rm -rf util/bin || die
+
+	perl_domodule -C ${PN} PerlLib/*.pm
+
+	# dodoc Release.Notes
+	einfo "Fetch your own Pfam-A.hmm (Pfam-AB.hmm is discontinued since 05/2015):"
+	einfo "wget --mirror -nH -nd ftp://ftp.ebi.ac.uk/pub/databases/Pfam/current_release/Pfam-A.hmm.gz"
+	einfo "hmmpress Pfam-A.hmm.bin"
+}
+
+pkg_postinst() {
+	einfo "It is recommended to use TransDecoder with sci-biology/hmmer-3 or"
+	einfo "at least with NCBI blast from either:"
+	einfo "    sci-biology/ncbi-blast+ (released more often) or from"
+	einfo "    sci-biology/ncbi-toolkit++ (a huge bundle with releases and less frequent bugfixes)"
+}
diff --git a/sci-biology/TransDecoder/files/TransDecoder-2.1.0__fix_paths.patch b/sci-biology/TransDecoder/files/TransDecoder-2.1.0__fix_paths.patch
deleted file mode 100644
index 0a6fca050..000000000
--- a/sci-biology/TransDecoder/files/TransDecoder-2.1.0__fix_paths.patch
+++ /dev/null
@@ -1,22 +0,0 @@
---- TransDecoder-2.0.1/TransDecoder.LongOrfs.ori	2015-11-19 21:05:53.340219051 +0100
-+++ TransDecoder-2.0.1/TransDecoder.LongOrfs	2015-11-19 21:20:44.870221380 +0100
-@@ -64,7 +64,7 @@
- use TransDecoder::Fasta_reader;
- use TransDecoder::Longest_orf;
- 
--my $UTIL_DIR = "$FindBin::RealBin/util";
-+my $UTIL_DIR = "/usr/share/TransDecoder/util/";
- $ENV{PATH} = "$UTIL_DIR/bin:$ENV{PATH}";
- 
- 
---- TransDecoder-2.0.1/TransDecoder.Predict.ori	2015-11-19 21:06:04.280219080 +0100
-+++ TransDecoder-2.0.1/TransDecoder.Predict	2015-11-19 21:21:22.560221479 +0100
-@@ -52,7 +52,7 @@
- use TransDecoder::Fasta_reader;
- use TransDecoder::Longest_orf;
- 
--my $UTIL_DIR = "$FindBin::RealBin/util";
-+my $UTIL_DIR = "/usr/share/TransDecoder/util/";
- $ENV{PATH} = "$UTIL_DIR/bin:$ENV{PATH}";
- 
- 
diff --git a/sci-biology/Trinotate/Manifest b/sci-biology/Trinotate/Manifest
deleted file mode 100644
index 0433c4ad9..000000000
--- a/sci-biology/Trinotate/Manifest
+++ /dev/null
@@ -1 +0,0 @@
-DIST v2.0.1.tar.gz 29226683 BLAKE2B 427b9deb88729b870bca2b617af5cc14a4e2cfcee0e300eef35013e851c58009e1ac6ca3f5d699ea133aec2ab6a2b0de98df09d763a349c58d3fd8990db37a40 SHA512 389ae53c53910b26cc78578cd3803cf14925964e2209e1baabdce78f3a2a73d064f6484e0355cc9597f4cd13ec09ba93da97b19cdc5646fb9f8f4ab91fbc98db
diff --git a/sci-biology/Trinotate/Trinotate-2.0.1.ebuild b/sci-biology/Trinotate/Trinotate-2.0.1.ebuild
deleted file mode 100644
index 61d7e233e..000000000
--- a/sci-biology/Trinotate/Trinotate-2.0.1.ebuild
+++ /dev/null
@@ -1,44 +0,0 @@
-# Copyright 1999-2016 Gentoo Foundation
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=5
-
-PERL_EXPORT_PHASE_FUNCTIONS=no
-inherit perl-module eutils toolchain-funcs
-
-DESCRIPTION="Annotation and analysis pipeline for de novo assembled transcriptomes"
-HOMEPAGE="http://trinotate.github.io"
-SRC_URI="https://github.com/Trinotate/Trinotate/archive/v${PV}.tar.gz"
-
-LICENSE="BSD-BroadInstitute"
-SLOT="0"
-KEYWORDS=""
-IUSE=""
-
-DEPEND=""
-RDEPEND="${DEPEND}
-	sci-biology/ncbi-tools++
-	sci-biology/trinityrnaseq
-	sci-biology/TransDecoder"
-
-# http://www.cbs.dtu.dk/cgi-bin/sw_request?rnammer
-# >=sci-biology/rnammer-2.3.2
-#
-# http://www.cbs.dtu.dk/cgi-bin/nph-sw_request?signalp
-# >=sci-biology/signalp-4
-#
-# http://www.cbs.dtu.dk/cgi-bin/nph-sw_request?tmhmm
-
-# We suggest you rename this version of hmmsearch from hmmer-2 package to 'hmmsearch2'.
-# In the 'rnammer' software configuration, edit the rnammer script to point
-# $HMMSEARCH_BINARY = "/path/to/hmmsearch2";
-
-src_install(){
-	perl_set_version
-	dobin Trinotate
-	insinto /usr/share/"${PN}"
-	doins -r admin java sample_data util TrinotateWeb
-	insinto ${VENDOR_LIB}/${PN}
-	doins -r PerlLib/*
-	dodoc Release.Notes
-}
diff --git a/sci-biology/Trinotate/metadata.xml b/sci-biology/Trinotate/metadata.xml
deleted file mode 100644
index eaf731f09..000000000
--- a/sci-biology/Trinotate/metadata.xml
+++ /dev/null
@@ -1,15 +0,0 @@
-<?xml version="1.0" encoding="UTF-8"?>
-<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
-<pkgmetadata>
-	<maintainer type="person">
-		<email>mmokrejs@fold.natur.cuni.cz</email>
-		<name>Martin Mokrejs</name>
-	</maintainer>
-	<maintainer type="project">
-		<email>sci-biology@gentoo.org</email>
-		<name>Gentoo Biology Project</name>
-	</maintainer>
-	<upstream>
-		<remote-id type="github">Trinotate/Trinotate</remote-id>
-	</upstream>
-</pkgmetadata>
diff --git a/sci-biology/VarScan-bin/Manifest b/sci-biology/VarScan-bin/Manifest
index 0e3460d6d..94cdb837b 100644
--- a/sci-biology/VarScan-bin/Manifest
+++ b/sci-biology/VarScan-bin/Manifest
@@ -1,2 +1 @@
-DIST VarScan.v2.4.2.jar 114840 BLAKE2B 3e788d185bb02f6e5f35ba31cf1e8ecb084c7edf6010bb9500171f6998035b9b5eea6c5c4bd3eddff300bff4334a0a0091f9f0fe4fa01fe033b0f8ad8a3f63f2 SHA512 a58c35412a3fb5a3750a4f3fea834e92bde3e0b98c6bbf48e677589a3d99dcd82a01d864ab0c5d19d2089cad1174ea9f70c8081fbc02fddfb3723c8c9af6de68
-DIST VarScan.v2.4.3.jar 115272 BLAKE2B b7eaa043bcd69863d9b98b861daed86886b0229a97aa98cc650fbff4d271c29cc01ff38e4f7028d4548012cabf171cc6c2f1a4d4f6dd96e573e047ebfbe0d892 SHA512 4ac1b35796923261e0273f8e761b391090b2bb6ca8555bd87ef2ba8386f72ad840e84380202516cf332e5efffe2bbb71c97b1f504933e46579ed0f7a48d55091
+DIST VarScan.v2.4.4.jar 116249 BLAKE2B d59a4c37ce497a357f39a9a0bfb4ae27f12ae577a3d2edf0b1cf2bf261c35d9649b712612ed06ef9093eac6e56780f4f6e5d1ec355664055fe5d23ec8f8a1fbb SHA512 9a2eb8b917743bd798efb2285e9f7fee3b342ced8d7096066b9273a5a32ef9567b5f715a37ec517c2d799e095e386edb1b3825e83d73f06fe16122d77b4933a5
diff --git a/sci-biology/VarScan-bin/VarScan-bin-2.4.2.ebuild b/sci-biology/VarScan-bin/VarScan-bin-2.4.2.ebuild
deleted file mode 100644
index d2902cb7f..000000000
--- a/sci-biology/VarScan-bin/VarScan-bin-2.4.2.ebuild
+++ /dev/null
@@ -1,31 +0,0 @@
-# Copyright 1999-2016 Gentoo Foundation
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=5
-
-inherit java-pkg-2
-
-MY_PN="VarScan"
-DESCRIPTION="Variant detection (germline, multi-sample, somatic mut., CNA), SNP"
-HOMEPAGE="http://dkoboldt.github.io/varscan"
-
-# binary
-#http://downloads.sourceforge.net/project/varscan/VarScan.v2.3.7.jar
-#SRC_URI="http://downloads.sourceforge.net/project/varscan/${PN}.v${PV}.jar"
-SRC_URI="https://github.com/dkoboldt/varscan/blob/master/${MY_PN}.v${PV}.jar?raw=true -> ${MY_PN}.v${PV}.jar"
-
-LICENSE="Non-profit-OSL-3.0"
-SLOT="0"
-KEYWORDS="~amd64"
-IUSE=""
-
-DEPEND="
-	>=virtual/jdk-1.5:*"
-RDEPEND=">=virtual/jre-1.5:*"
-
-S="${WORKDIR}"/net/sf/varscan
-
-src_install(){
-	java-pkg_newjar "${DISTDIR}"/${MY_PN}.v${PV}.jar ${MY_PN}.jar
-	java-pkg_dolauncher VarScan
-}
diff --git a/sci-biology/VarScan-bin/VarScan-bin-2.4.3.ebuild b/sci-biology/VarScan-bin/VarScan-bin-2.4.3.ebuild
deleted file mode 100644
index d76eccfdb..000000000
--- a/sci-biology/VarScan-bin/VarScan-bin-2.4.3.ebuild
+++ /dev/null
@@ -1,31 +0,0 @@
-# Copyright 1999-2017 Gentoo Foundation
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=5
-
-inherit java-pkg-2
-
-MY_PN="VarScan"
-DESCRIPTION="Variant detection (germline, multi-sample, somatic mut., CNA), SNP"
-HOMEPAGE="http://dkoboldt.github.io/varscan"
-
-# binary
-#http://downloads.sourceforge.net/project/varscan/VarScan.v2.3.7.jar
-#SRC_URI="http://downloads.sourceforge.net/project/varscan/${PN}.v${PV}.jar"
-SRC_URI="https://github.com/dkoboldt/varscan/blob/master/${MY_PN}.v${PV}.jar?raw=true -> ${MY_PN}.v${PV}.jar"
-
-LICENSE="Non-profit-OSL-3.0"
-SLOT="0"
-KEYWORDS="~amd64"
-IUSE=""
-
-DEPEND="
-	>=virtual/jdk-1.5:*"
-RDEPEND=">=virtual/jre-1.5:*"
-
-S="${WORKDIR}"/net/sf/varscan
-
-src_install(){
-	java-pkg_newjar "${DISTDIR}"/${MY_PN}.v${PV}.jar ${MY_PN}.jar
-	java-pkg_dolauncher VarScan
-}
diff --git a/sci-biology/VarScan-bin/VarScan-bin-2.4.4.ebuild b/sci-biology/VarScan-bin/VarScan-bin-2.4.4.ebuild
new file mode 100644
index 000000000..5b06676c0
--- /dev/null
+++ b/sci-biology/VarScan-bin/VarScan-bin-2.4.4.ebuild
@@ -0,0 +1,30 @@
+# Copyright 1999-2021 Gentoo Authors
+# Distributed under the terms of the GNU General Public License v2
+
+EAPI=7
+
+inherit java-pkg-2
+
+MY_PN="VarScan"
+DESCRIPTION="Variant detection (germline, multi-sample, somatic mut., CNA), SNP"
+HOMEPAGE="http://dkoboldt.github.io/varscan"
+
+# binary
+#http://downloads.sourceforge.net/project/varscan/VarScan.v2.3.7.jar
+#SRC_URI="http://downloads.sourceforge.net/project/varscan/${PN}.v${PV}.jar"
+SRC_URI="https://github.com/dkoboldt/varscan/blob/master/${MY_PN}.v${PV}.jar?raw=true -> ${MY_PN}.v${PV}.jar"
+
+LICENSE="Non-profit-OSL-3.0"
+SLOT="0"
+KEYWORDS="~amd64"
+
+DEPEND=">=virtual/jdk-1.5:*"
+RDEPEND=">=virtual/jre-1.5:*
+	!sci-biology/VarScan"
+
+S="${WORKDIR}"/net/sf/varscan
+
+src_install(){
+	java-pkg_newjar "${DISTDIR}"/${MY_PN}.v${PV}.jar ${MY_PN}.jar
+	java-pkg_dolauncher VarScan
+}
diff --git a/sci-biology/VarScan/Manifest b/sci-biology/VarScan/Manifest
index 08287bf59..f5e3e9abe 100644
--- a/sci-biology/VarScan/Manifest
+++ b/sci-biology/VarScan/Manifest
@@ -1,2 +1 @@
-DIST VarScan.v2.4.2.source.jar 205503 SHA256 d65c3a761ef3ed25544a62b0885373628d3f4f644dde165cd47448e5c175c791 SHA512 92a31b22574144fdb9800b6b3bf016d151119f7e147b47fb9063d1f772a817867265057cd7895fd5a450ef998956e0871d52fb929acf00866f4224586efdce4c WHIRLPOOL a6e3336a55109744dd307556909f105ac4ea6a6a7c9c6a28b657b2a38a0f6da0152519275f6078c667fe4c03fe56c4b86e452a3cbcd5170ff55855d9a859770c
-DIST VarScan.v2.4.3.source.jar 206397 BLAKE2B da6834f57954faf6c3db4fe8adb2e278e709569165a202efc9ac5994d6755a975890c91f3430621afac65c0081cd2ee4443a1a16d5efa3125b3701d7f586f001 SHA512 620a3a41b1e99fe7e1d6ca629287de26bff517efb70a42610abbc66092c935775dc4b2ad10a68c38e69b3063cdadb5794355219f6bf20809761804038713117c
+DIST VarScan.v2.4.4.source.jar 208377 BLAKE2B 1e9205e3ea5b962562ff94ed40aa7d0d2f1a800cb427c402f99cdea87fe56e2e4e3ee1f3e74321a7ccf122ab2b7c47cd0bc2e6d99a1d5ea487c4d76e9add514e SHA512 980a80627a0dd91c5d16b8bab59ad51f6a528eb7b0e427eab6949ae12f4fa3fe2d5d4edba15f1e8b4fd607126b60acbbca87f5c31e6480e6ccb7aa21fd6936a8
diff --git a/sci-biology/VarScan/VarScan-2.4.2.ebuild b/sci-biology/VarScan/VarScan-2.4.2.ebuild
deleted file mode 100644
index 4add5f679..000000000
--- a/sci-biology/VarScan/VarScan-2.4.2.ebuild
+++ /dev/null
@@ -1,36 +0,0 @@
-# Copyright 1999-2017 Gentoo Foundation
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=5
-
-inherit java-pkg-2
-
-DESCRIPTION="Variant detection (germline, multi-sample, somatic mutations, CNA, SNP calls)"
-HOMEPAGE="http://varscan.sourceforge.net/"
-
-# binary
-#http://downloads.sourceforge.net/project/varscan/VarScan.v2.3.7.jar
-#SRC_URI="http://downloads.sourceforge.net/project/varscan/${PN}.v${PV}.jar"
-SRC_URI="http://downloads.sourceforge.net/project/varscan/${PN}.v${PV}.source.jar"
-
-LICENSE="Non-profit-OSL-3.0"
-SLOT="0"
-KEYWORDS="~amd64"
-IUSE=""
-
-DEPEND="
-	>=virtual/jdk-1.5:*
-	!sci-biology/VarScan-bin"
-RDEPEND=">=virtual/jre-1.5:*
-	sci-biology/bam-readcount"
-
-S="${WORKDIR}"/net/sf/varscan
-
-src_compile(){
-	javac *.java
-}
-
-src_install(){
-	java-pkg_newjar "${DISTDIR}"/${PN}.v${PV}.source.jar ${PN}.source.jar
-	java-pkg_dolauncher VarScan
-}
diff --git a/sci-biology/VarScan/VarScan-2.4.3.ebuild b/sci-biology/VarScan/VarScan-2.4.3.ebuild
deleted file mode 100644
index 0b3fc2ad5..000000000
--- a/sci-biology/VarScan/VarScan-2.4.3.ebuild
+++ /dev/null
@@ -1,35 +0,0 @@
-# Copyright 1999-2017 Gentoo Foundation
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=5
-
-inherit java-pkg-2
-
-DESCRIPTION="Variant detection (germline, multi-sample, somatic mutations, CNA, SNP calls)"
-HOMEPAGE="http://varscan.sourceforge.net/"
-
-# binary
-#https://github.com/dkoboldt/varscan/blob/master/VarScan.v2.4.3.jar
-SRC_URI="https://github.com/dkoboldt/varscan/blob/master/VarScan.v2.4.3.source.jar?raw=true -> ${PN}.v${PV}.source.jar"
-
-LICENSE="Non-profit-OSL-3.0"
-SLOT="0"
-KEYWORDS="~amd64"
-IUSE=""
-
-DEPEND="
-	>=virtual/jdk-1.5:*
-	!sci-biology/VarScan-bin"
-RDEPEND=">=virtual/jre-1.5:*
-	sci-biology/bam-readcount"
-
-S="${WORKDIR}"/net/sf/varscan
-
-src_compile(){
-	javac *.java
-}
-
-src_install(){
-	java-pkg_newjar "${DISTDIR}"/${PN}.v${PV}.source.jar ${PN}.source.jar
-	java-pkg_dolauncher VarScan
-}
diff --git a/sci-biology/VarScan/VarScan-2.4.4.ebuild b/sci-biology/VarScan/VarScan-2.4.4.ebuild
new file mode 100644
index 000000000..039a68f06
--- /dev/null
+++ b/sci-biology/VarScan/VarScan-2.4.4.ebuild
@@ -0,0 +1,36 @@
+# Copyright 1999-2021 Gentoo Authors
+# Distributed under the terms of the GNU General Public License v2
+
+EAPI=7
+
+inherit java-pkg-2
+
+DESCRIPTION="Variant detection (germline, multi-sample, somatic mutations, CNA, SNP calls)"
+HOMEPAGE="http://varscan.sourceforge.net/"
+
+# binary
+#https://github.com/dkoboldt/varscan/blob/master/VarScan.v2.4.3.jar
+SRC_URI="https://github.com/dkoboldt/varscan/blob/master/VarScan.v${PV}.source.jar?raw=true -> ${PN}.v${PV}.source.jar"
+
+LICENSE="Non-profit-OSL-3.0"
+SLOT="0"
+KEYWORDS="~amd64"
+
+DEPEND="
+	>=virtual/jdk-1.5:*
+"
+RDEPEND=">=virtual/jre-1.5:*
+	sci-biology/bam-readcount
+	!sci-biology/VarScan-bin
+"
+
+S="${WORKDIR}"/net/sf/varscan
+
+src_compile(){
+	javac *.java
+}
+
+src_install(){
+	java-pkg_newjar "${DISTDIR}"/${PN}.v${PV}.source.jar ${PN}.source.jar
+	java-pkg_dolauncher VarScan
+}
diff --git a/sci-biology/VelvetOptimiser/Manifest b/sci-biology/VelvetOptimiser/Manifest
index 08a93b8d3..78c2c554a 100644
--- a/sci-biology/VelvetOptimiser/Manifest
+++ b/sci-biology/VelvetOptimiser/Manifest
@@ -1 +1 @@
-DIST VelvetOptimiser-2.2.5.tar.gz 28786 BLAKE2B 4ed429bed3ed65a14886a02afadf80789b636967c05187338cd23c5adfa7cec4bfaabbbc8a724c73f3a0c4838de13d7b95dd28399c8f13c0e02748dce5e5b830 SHA512 27a19c360ce6c469cbb9d9025c14954b98f6b91680402a32f29843694be7f193113161bf89e98ed42d2bd70a400e9dd729ba51bee5e50f7b953789943ac83f68
+DIST VelvetOptimiser-2.2.6.tar.gz 5885844 BLAKE2B 388f4232242b8ed1e207d20d755c81127d46ca3364c833a9712e87176a513237cb756bfb0f60d14cedf361ef980235e8e612de63832f2f876d12e6014ca961f9 SHA512 2bf97afecbe70682ce6653b8b0170f9f1bea9f43ade8f0a071abf7b5fa35adf249dbbe3e58b0e6bfd1cb7d5c5e946eecbde9bbacbe9a705ce02db0d35270fc83
diff --git a/sci-biology/VelvetOptimiser/VelvetOptimiser-2.2.5.ebuild b/sci-biology/VelvetOptimiser/VelvetOptimiser-2.2.5.ebuild
deleted file mode 100644
index f5ad6e636..000000000
--- a/sci-biology/VelvetOptimiser/VelvetOptimiser-2.2.5.ebuild
+++ /dev/null
@@ -1,29 +0,0 @@
-# Copyright 1999-2017 Gentoo Foundation
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=6
-
-inherit perl-functions
-
-DESCRIPTION="Optimise Velvet sequence assembler"
-HOMEPAGE="http://www.vicbioinformatics.com/software.velvetoptimiser.shtml"
-SRC_URI="http://www.vicbioinformatics.com/"${P}".tar.gz"
-
-LICENSE="GPL-2"
-SLOT="0"
-KEYWORDS="~amd64"
-IUSE=""
-
-DEPEND=""
-RDEPEND="${DEPEND}
-	>=sci-biology/bioperl-1.4
-	>=sci-biology/velvet-0.7.5.1
-	dev-lang/perl[ithreads]" # actually >=5.8 but make sure 5.16 is recognized as > 5.8, heh
-
-src_install(){
-	dobin VelvetOptimiser.pl
-	perl_set_version
-	insinto ${VENDOR_LIB}/VelvetOpt
-	doins VelvetOpt/*.pm
-	dodoc README INSTALL CHANGELOG
-}
diff --git a/sci-biology/VelvetOptimiser/VelvetOptimiser-2.2.6.ebuild b/sci-biology/VelvetOptimiser/VelvetOptimiser-2.2.6.ebuild
new file mode 100644
index 000000000..49f2b6d9f
--- /dev/null
+++ b/sci-biology/VelvetOptimiser/VelvetOptimiser-2.2.6.ebuild
@@ -0,0 +1,26 @@
+# Copyright 1999-2021 Gentoo Authors
+# Distributed under the terms of the GNU General Public License v2
+
+EAPI=7
+
+inherit perl-functions
+
+DESCRIPTION="Optimise Velvet sequence assembler"
+HOMEPAGE="https://vicbioinformatics.com/software.velvetoptimiser.shtml"
+SRC_URI="https://github.com/tseemann/VelvetOptimiser/archive/${PV}.tar.gz -> ${P}.tar.gz"
+
+LICENSE="GPL-2"
+SLOT="0"
+KEYWORDS="~amd64"
+
+RDEPEND="
+	>=sci-biology/bioperl-1.4
+	>=sci-biology/velvet-0.7.5.1
+	dev-lang/perl[ithreads]" # actually >=5.8 but make sure 5.16 is recognized as > 5.8, heh
+
+src_install(){
+	dobin VelvetOptimiser.pl
+	perl_set_version
+	perl_domodule VelvetOpt/*.pm
+	einstalldocs
+}
diff --git a/sci-biology/VelvetOptimiser/metadata.xml b/sci-biology/VelvetOptimiser/metadata.xml
index 138cb7705..cc34f33b5 100644
--- a/sci-biology/VelvetOptimiser/metadata.xml
+++ b/sci-biology/VelvetOptimiser/metadata.xml
@@ -9,4 +9,7 @@
 		<email>sci-biology@gentoo.org</email>
 		<name>Gentoo Biology Project</name>
 	</maintainer>
+	<upstream>
+		<remote-id type="github">tseemann/VelvetOptimiser</remote-id>
+	</upstream>
 </pkgmetadata>
diff --git a/sci-biology/YASRA/YASRA-2.33.ebuild b/sci-biology/YASRA/YASRA-2.33.ebuild
index 77ca724dc..58e6da2b0 100644
--- a/sci-biology/YASRA/YASRA-2.33.ebuild
+++ b/sci-biology/YASRA/YASRA-2.33.ebuild
@@ -1,7 +1,7 @@
-# Copyright 1999-2014 Gentoo Foundation
+# Copyright 1999-2020 Gentoo Authors
 # Distributed under the terms of the GNU General Public License v2
 
-EAPI=5
+EAPI=7
 
 DESCRIPTION="Yet Another Short Read Assembler aligning to a reference using LASTZ"
 HOMEPAGE="http://www.bx.psu.edu/miller_lab/"
diff --git a/sci-biology/abacas/abacas-1.3.1.ebuild b/sci-biology/abacas/abacas-1.3.1.ebuild
index 4112bb8df..c347b508b 100644
--- a/sci-biology/abacas/abacas-1.3.1.ebuild
+++ b/sci-biology/abacas/abacas-1.3.1.ebuild
@@ -1,18 +1,17 @@
-# Copyright 1999-2017 Gentoo Foundation
+# Copyright 1999-2021 Gentoo Authors
 # Distributed under the terms of the GNU General Public License v2
 
-EAPI=6
+EAPI=7
 
-inherit eutils
+inherit optfeature
 
 DESCRIPTION="Order and orientate DNA contigs even via 6-frame protein alignments"
-HOMEPAGE="http://abacas.sourceforge.net"
-SRC_URI="http://downloads.sourceforge.net/project/abacas/abacas.1.3.1.pl"
+HOMEPAGE="https://abacas.sourceforge.net"
+SRC_URI="https://downloads.sourceforge.net/project/abacas/abacas.${PV}.pl"
 
 LICENSE="GPL-2+"
 SLOT="0"
 KEYWORDS="~amd64"
-IUSE=""
 
 DEPEND=""
 RDEPEND="${DEPEND}
@@ -22,11 +21,11 @@ RDEPEND="${DEPEND}
 S="${WORKDIR}"
 
 src_prepare(){
-	cp -p "${DISTDIR}"/abacas.1.3.1.pl abacas.pl || die
+	cp -p "${DISTDIR}"/abacas.${PV}.pl abacas.pl || die
 	sed \
 		-i 's#/usr/local/bin/perl#/usr/bin/perl#' \
 		-i abacas.pl || die
-	eapply_user
+	default
 }
 src_install(){
 	dobin abacas.pl
diff --git a/sci-biology/abacas/metadata.xml b/sci-biology/abacas/metadata.xml
index 0f267b755..0bb7ca029 100644
--- a/sci-biology/abacas/metadata.xml
+++ b/sci-biology/abacas/metadata.xml
@@ -10,6 +10,6 @@
 		<name>Gentoo Biology Project</name>
 	</maintainer>
 	<upstream>
-		<remote-id type="sourceforge">downloads</remote-id>
+		<remote-id type="sourceforge">abacas</remote-id>
 	</upstream>
 </pkgmetadata>
diff --git a/sci-biology/abyss/Manifest b/sci-biology/abyss/Manifest
deleted file mode 100644
index ca35373a8..000000000
--- a/sci-biology/abyss/Manifest
+++ /dev/null
@@ -1 +0,0 @@
-DIST abyss-2.1.5.tar.gz 1063069 BLAKE2B d934b116ff61c9227c64377d45a09f31c7b9be8d3ffb04a7338603d53d79e2d9313278cc3ea083c855a1f49d59fa588791d7729e6fa2fa24c5275790a586f32c SHA512 79a952a247ff3732cdbb5ee11525ad11d48e113b05a2810caf6fdba1bd7672e5623047b269e6737a22ad1384a8dbc1a6e601e023668fe56b11a78577c1ee021e
diff --git a/sci-biology/abyss/abyss-2.1.5.ebuild b/sci-biology/abyss/abyss-2.1.5.ebuild
deleted file mode 100644
index 66c216fab..000000000
--- a/sci-biology/abyss/abyss-2.1.5.ebuild
+++ /dev/null
@@ -1,54 +0,0 @@
-# Copyright 1999-2018 Gentoo Authors
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=6
-
-inherit autotools toolchain-funcs
-
-DESCRIPTION="Assembly By Short Sequences - a de novo, parallel, paired-end sequence assembler"
-HOMEPAGE="http://www.bcgsc.ca/platform/bioinfo/software/abyss/"
-SRC_URI="https://github.com/bcgsc/abyss/archive/${PV}.tar.gz -> ${P}.tar.gz"
-
-LICENSE="abyss"
-SLOT="0"
-IUSE="+mpi openmp misc-haskell"
-KEYWORDS="~amd64 ~x86"
-
-RDEPEND="
-	dev-cpp/sparsehash
-	dev-libs/boost:=
-	misc-haskell? (
-		dev-libs/gmp:0=
-		virtual/libffi:0=
-	)
-	mpi? ( sys-cluster/openmpi )"
-DEPEND="${RDEPEND}
-	misc-haskell? (
-		dev-lang/ghc
-	)"
-
-# todo: --enable-maxk=N configure option
-# todo: fix automagic mpi toggling
-
-pkg_pretend() {
-	[[ ${MERGE_TYPE} != binary ]] && use openmp && tc-check-openmp
-}
-
-pkg_setup() {
-	[[ ${MERGE_TYPE} != binary ]] && use openmp && tc-check-openmp
-}
-
-src_prepare() {
-	default
-	sed -i -e "s/-Werror//" configure.ac || die #365195
-	sed -i -e "/dist_pkgdoc_DATA/d" Makefile.am || die
-	eautoreconf
-}
-
-src_configure() {
-	# disable building haskell tool Misc/samtobreak
-	# unless request by user: bug #534412
-	use misc-haskell || export ac_cv_prog_ac_ct_GHC=
-
-	econf $(use_enable openmp) --enable-maxk=256
-}
diff --git a/sci-biology/abyss/metadata.xml b/sci-biology/abyss/metadata.xml
deleted file mode 100644
index 47116e507..000000000
--- a/sci-biology/abyss/metadata.xml
+++ /dev/null
@@ -1,18 +0,0 @@
-<?xml version='1.0' encoding='UTF-8'?>
-<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
-<pkgmetadata>
-  <maintainer type="project">
-    <email>sci-biology@gentoo.org</email>
-    <name>Gentoo Biology Project</name>
-  </maintainer>
-  <maintainer type="project">
-    <email>haskell@gentoo.org</email>
-    <name>Gentoo Haskell</name>
-  </maintainer>
-  <use>
-    <flag name="misc-haskell">build abyss-samtobreak tool, pull in haskell toolchain</flag>
-  </use>
-  <upstream>
-    <remote-id type="github">bcgsc/abyss</remote-id>
-  </upstream>
-</pkgmetadata>
diff --git a/sci-biology/act-bin/act-bin-17.0.1.ebuild b/sci-biology/act-bin/act-bin-17.0.1.ebuild
index c61df75f3..31bad30bb 100644
--- a/sci-biology/act-bin/act-bin-17.0.1.ebuild
+++ b/sci-biology/act-bin/act-bin-17.0.1.ebuild
@@ -1,12 +1,12 @@
-# Copyright 1999-2018 Gentoo Foundation
+# Copyright 1999-2021 Gentoo Authors
 # Distributed under the terms of the GNU General Public License v2
 
-EAPI=6
+EAPI=7
 
 inherit java-pkg-2
 
 DESCRIPTION="DNA contig sequence comparison tool supplementing Artemis"
-HOMEPAGE="http://www.sanger.ac.uk/science/tools/artemis-comparison-tool-act"
+HOMEPAGE="https://www.sanger.ac.uk/science/tools/artemis-comparison-tool-act"
 SRC_URI="ftp://ftp.sanger.ac.uk/pub/resources/software/act/v17/v${PV}/sact-v${PV}.jar
 	ftp://ftp.sanger.ac.uk/pub/resources/software/act/v17/v${PV}/act-v${PV}.jar
 	ftp://ftp.sanger.ac.uk/pub/resources/software/act/v13/act_manual_complete.pdf -> ${P}.manual.pdf
@@ -16,10 +16,8 @@ SRC_URI="ftp://ftp.sanger.ac.uk/pub/resources/software/act/v17/v${PV}/sact-v${PV
 LICENSE="GPL-2"
 SLOT="0"
 KEYWORDS="~amd64"
-IUSE=""
 
-DEPEND="
-	!sci-biology/artemis"
+BDEPEND="app-arch/unzip"
 RDEPEND="${DEPEND}
 	>=virtual/jre-1.8:*"
 
@@ -38,8 +36,8 @@ src_prepare(){
 src_install(){
 	java-pkg_dojar "${DISTDIR}"/*.jar
 	dodoc "${DISTDIR}"/${P}.manual.pdf "${DISTDIR}"/release_notes.txt
-	insinto /usr/share/doc/"${PN}"/html
-	doins act_html_build/*
+	docinto html
+	dodoc act_html_build/*
 }
 
 pkg_postinst(){
diff --git a/sci-biology/afni/Manifest b/sci-biology/afni/Manifest
index 7a32c9376..d1e783ff1 100644
--- a/sci-biology/afni/Manifest
+++ b/sci-biology/afni/Manifest
@@ -1,2 +1,4 @@
-DIST afni-18.1.04.tar.gz 196776384 BLAKE2B 389c2dcf11bf3e3d067cbe1cce772a299b6f9096e21936616893041f72b2d3f490b3bed6ef10d94dd5f7c08436206379339a05384ac005349f55d40bb241e695 SHA512 16151d2512d115a2e4531932cbfd50cb1cf6c2e5c809d91fb439495d7d62f2d50f05f5f411395af0cc24e9a34bf8e98efd389b9e50bc75f783e051e7ab3db121
-DIST afni-19.0.21.tar.gz 38228297 BLAKE2B 2d04b1d27c39bfbdfe9319a464920604b21f646e0f68d3d06d9ffffd7415e7c299fff983316834b84417a303229731abd2799a6f20e1edab56188726124ed436 SHA512 fbc01ca2acb5f6d64f539942661e9500407ccf5f6d583c7685eac85b81326414e3d9959372c49ed6f6b95f5b0fca2e936207a47313b753ffd3190dc8c474b78a
+DIST afni-24.0.04.gh.tar.gz 52888143 BLAKE2B db414b9ac9489aaab824e6f99cae54a1982e600d3b6d93a01cf3f175220ab76923a53ce6da647e4d8be87d3b50699c1b9603f8f0de43d812d34ceb1a65bde19d SHA512 aff673b63453a18c1f687775a6316614ee7495ff583e86c341aa0eed40d5f99b15cb599dea79baf05f8f8b77fea292436e3adc51b906dc13589968a8bdffa3d8
+DIST afni-24.0.08.gh.tar.gz 52917832 BLAKE2B 4cf61f3474c2c69d8373fbf9413c2236fbda77408535b142e6860effbf49ebcc6007ef9fb18943c07299b4815be6692477cc79423d7ac5a09bfe3d125565058c SHA512 90a9c8a48e1084dcc19d90e62b313057f0e71e87740f6ac63a305d19a4ded8ee01722b55546d2aaa2d4dfbfd0a206d4a9d25969592646c101cabe4743b8962c6
+DIST gifti-d3e873d8539d9b469daf7db04093da1d7e73d4f7.tar.gz 107745 BLAKE2B b8162fe08446d5c934762e8dce051e93c8c90fd574dca55757988ccc45be20bfdd07b7a401ef6c536afbe097e6bc05fd3b7f09c4404af4fad4e21fbada7109de SHA512 c458074c6976245cffc48c1e1e57811ec3c0cc5959345bdbc8d674eed6c8a8f93e9f9762bf3acce7142e004dc37930d14bed8cfb97c5b7e92b3f39598da924e2
+DIST nifti-da476fd27f46098f37f5c9c4c1baee01e559572c.tar.gz 451578 BLAKE2B 6bb92ae3ab48dba435b067f7ec0b6d417658ee1a46efe05070bf18fd6d46b8339eaffd09c2fea4971d2685f211496a700b36c255ffb164994636e535b64fe4f5 SHA512 df92345ed580e8bf0579f2ea3ed55a4c4c678a0fe3bfad1e62379e5bf16961272bb2d3e7fda89b96b503cda51c1bf2fb8eb74adba6aad9c73b6830d7d884d1f5
diff --git a/sci-biology/afni/afni-18.1.04.ebuild b/sci-biology/afni/afni-18.1.04.ebuild
deleted file mode 100644
index ba1a0bcd9..000000000
--- a/sci-biology/afni/afni-18.1.04.ebuild
+++ /dev/null
@@ -1,68 +0,0 @@
-# Copyright 1999-2018 Gentoo Foundation
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=7
-
-inherit eutils multilib pax-utils toolchain-funcs
-
-DESCRIPTION="An open-source environment for processing and displaying functional MRI data"
-HOMEPAGE="http://afni.nimh.nih.gov/"
-SRC_URI="https://github.com/afni/afni/archive/AFNI_${PV}.tar.gz -> ${P}.tar.gz"
-
-LICENSE="GPL-3+"
-SLOT="0"
-KEYWORDS="~amd64 ~x86"
-IUSE=""
-
-RDEPEND="dev-libs/expat
-	media-libs/netpbm
-	media-libs/qhull
-	media-video/mpeg-tools
-	sci-libs/gsl
-	sys-devel/llvm:*
-	virtual/jpeg:0
-	x11-libs/libGLw
-	x11-libs/libXft
-	x11-libs/libXi
-	x11-libs/libXpm
-	x11-libs/motif[-static-libs]"
-
-# x11-libs/motif[static-libs] breaks the build.
-# See upstream discussion
-# http://afni.nimh.nih.gov/afni/community/board/read.php?1,85348,85348#msg-85348
-
-DEPEND="${RDEPEND}
-	app-shells/tcsh"
-
-S="${WORKDIR}/${PN}-AFNI_${PV}/src"
-BUILD="linux_fedora_19_64"
-BIN_CONFLICTS=(qdelaunay whirlgif djpeg cjpeg qhull rbox count mpeg_encode)
-
-src_prepare() {
-	find -type f -exec sed -i -e "s/-lXp //g" {} +
-	cp other_builds/Makefile.${BUILD} Makefile || die "Could not copy Makefile"
-	sed -e "s~CC     = /usr/bin/gcc -O2 -m64~CC     = $(tc-getCC) \$(CFLAGS)~" \
-		-e "s~CCMIN  = /usr/bin/gcc -m64~CCMIN  = $(tc-getCC) \$(CFLAGS)~" \
-		-e "s~LD     = /usr/bin/gcc~LD     = $(tc-getCC)~" \
-		-e "s~AR     = /usr/bin/ar~AR     = $(tc-getAR)~" \
-		-e "s~RANLIB = /usr/bin/ranlib~RANLIB = $(tc-getRANLIB)~" \
-		-i Makefile || die "Could not edit Makefile"
-		# they provide somewhat problematic makefiles :(
-	sed -e "s~ifeq ($(CC),gcc)~ifeq (1,1)~"\
-		-i SUMA/SUMA_Makefile || die "Could not edit SUMA/SUMA_Makefile"
-		# upstream checks if $CC is EXACTLY gcc, else sets variables for Mac
-	find "${S}" -iname "*Makefile*" | xargs sed -e "s~/usr/~${EROOT}/usr/~g;" -i
-	eapply_user
-}
-
-src_compile() {
-	emake -j1 all plugins suma_exec
-}
-
-src_install() {
-	emake INSTALLDIR="${ED}/usr/bin" -j1 install install_plugins
-	emake INSTALLDIR="${ED}/usr/$(get_libdir)" -j1 install_lib
-	for CONFLICT in ${BIN_CONFLICTS[@]}; do
-		rm "${ED}/usr/bin/${CONFLICT}"
-	done
-}
diff --git a/sci-biology/afni/afni-19.0.21.ebuild b/sci-biology/afni/afni-19.0.21.ebuild
deleted file mode 100644
index 104015772..000000000
--- a/sci-biology/afni/afni-19.0.21.ebuild
+++ /dev/null
@@ -1,68 +0,0 @@
-# Copyright 1999-2019 Gentoo Authors
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=7
-
-inherit eutils multilib pax-utils toolchain-funcs
-
-DESCRIPTION="An open-source environment for processing and displaying functional MRI data"
-HOMEPAGE="http://afni.nimh.nih.gov/"
-SRC_URI="https://github.com/afni/afni/archive/AFNI_${PV}.tar.gz -> ${P}.tar.gz"
-
-LICENSE="GPL-3+"
-SLOT="0"
-KEYWORDS="~amd64 ~x86"
-IUSE=""
-
-RDEPEND="dev-libs/expat
-	media-libs/netpbm
-	media-libs/qhull
-	media-video/mpeg-tools
-	sci-libs/gsl
-	sys-devel/llvm:*
-	virtual/jpeg:0
-	x11-libs/libGLw
-	x11-libs/libXft
-	x11-libs/libXi
-	x11-libs/libXpm
-	x11-libs/motif[-static-libs]"
-
-# x11-libs/motif[static-libs] breaks the build.
-# See upstream discussion
-# http://afni.nimh.nih.gov/afni/community/board/read.php?1,85348,85348#msg-85348
-
-DEPEND="${RDEPEND}
-	app-shells/tcsh"
-
-S="${WORKDIR}/${PN}-AFNI_${PV}/src"
-BUILD="linux_fedora_19_64"
-BIN_CONFLICTS=(qdelaunay whirlgif djpeg cjpeg qhull rbox count mpeg_encode)
-
-src_prepare() {
-	find -type f -exec sed -i -e "s/-lXp //g" {} +
-	cp other_builds/Makefile.${BUILD} Makefile || die "Could not copy Makefile"
-	sed -e "s~CC     = /usr/bin/gcc -O2 -m64~CC     = $(tc-getCC) \$(CFLAGS)~" \
-		-e "s~CCMIN  = /usr/bin/gcc -m64~CCMIN  = $(tc-getCC) \$(CFLAGS)~" \
-		-e "s~LD     = /usr/bin/gcc~LD     = $(tc-getCC)~" \
-		-e "s~AR     = /usr/bin/ar~AR     = $(tc-getAR)~" \
-		-e "s~RANLIB = /usr/bin/ranlib~RANLIB = $(tc-getRANLIB)~" \
-		-i Makefile || die "Could not edit Makefile"
-		# they provide somewhat problematic makefiles :(
-	sed -e "s~ifeq ($(CC),gcc)~ifeq (1,1)~"\
-		-i SUMA/SUMA_Makefile || die "Could not edit SUMA/SUMA_Makefile"
-		# upstream checks if $CC is EXACTLY gcc, else sets variables for Mac
-	find "${S}" -iname "*Makefile*" | xargs sed -e "s~/usr/~${EROOT}/usr/~g;" -i
-	eapply_user
-}
-
-src_compile() {
-	emake -j1 all plugins suma_exec
-}
-
-src_install() {
-	emake INSTALLDIR="${ED}/usr/bin" -j1 install install_plugins
-	emake INSTALLDIR="${ED}/usr/$(get_libdir)" -j1 install_lib
-	for CONFLICT in ${BIN_CONFLICTS[@]}; do
-		rm "${ED}/usr/bin/${CONFLICT}"
-	done
-}
diff --git a/sci-biology/afni/afni-24.0.04-r1.ebuild b/sci-biology/afni/afni-24.0.04-r1.ebuild
new file mode 100644
index 000000000..557fbd579
--- /dev/null
+++ b/sci-biology/afni/afni-24.0.04-r1.ebuild
@@ -0,0 +1,110 @@
+# Copyright 1999-2021 Gentoo Authors
+# Distributed under the terms of the GNU General Public License v2
+
+EAPI=8
+
+PYTHON_COMPAT=( python3_{10..12} )
+
+DISTUTILS_USE_PEP517=setuptools
+inherit cmake distutils-r1 toolchain-funcs
+
+GTS_HASH="962155a01f5a1b87bd64e3e3d880b4dbc2347ac7"
+NIFTI_HASH="da476fd27f46098f37f5c9c4c1baee01e559572c"
+GIFTI_HASH="d3e873d8539d9b469daf7db04093da1d7e73d4f7"
+
+DESCRIPTION="Advanced Normalitazion Tools for neuroimaging"
+HOMEPAGE="http://stnava.github.io/ANTs/"
+SRC_URI="
+	https://github.com/afni/afni/archive/refs/tags/AFNI_${PV}.tar.gz -> ${P}.gh.tar.gz
+	https://github.com/NIFTI-Imaging/nifti_clib/archive/${NIFTI_HASH}.tar.gz -> nifti-${NIFTI_HASH}.tar.gz
+	https://github.com/NIFTI-Imaging/gifti_clib/archive/${GIFTI_HASH}.tar.gz -> gifti-${GIFTI_HASH}.tar.gz
+	"
+
+SLOT="0"
+LICENSE="GPL-3+"
+KEYWORDS="~amd64 ~x86"
+IUSE="test whirlgif"
+RESTRICT="!test? ( test )"
+
+RDEPEND="
+	dev-libs/glib:2
+	dev-libs/libf2c
+	dev-libs/expat
+	dev-build/ninja
+	media-libs/freeglut
+	media-libs/glu
+	media-libs/netpbm
+	media-libs/qhull
+	media-video/mpeg-tools
+	sci-libs/gsl
+	sci-libs/gts
+	sys-devel/llvm:*
+	sys-libs/libomp
+	virtual/jpeg-compat:62
+	x11-libs/libGLw
+	x11-libs/libXft
+	x11-libs/libXi
+	x11-libs/libXmu
+	x11-libs/libXpm
+	x11-libs/libXt
+	x11-libs/motif[-static-libs]
+	"
+DEPEND="
+	${RDEPEND}
+	app-shells/tcsh
+	"
+
+S="${WORKDIR}/afni-AFNI_${PV}"
+
+src_prepare() {
+	tar xf "${DISTDIR}/nifti-${NIFTI_HASH}.tar.gz" || die
+	tar xf "${DISTDIR}/gifti-${GIFTI_HASH}.tar.gz" || die
+	cmake_src_prepare
+	default
+	}
+
+src_configure() {
+	if use !whirlgif; then
+		eapply "${FILESDIR}/${P}-whirlgif.patch"
+	fi
+	export CFLAGS="-pthread ${CFLAGS}"
+	export GIT_REPO_VERSION=3.0.1.1
+	local mycmakeargs=(
+		-DLIBDIR=/usr/$(get_libdir)
+		-DNIFTI_INSTALL_LIBRARY_DIR=/usr/$(get_libdir)
+		-DGIFTI_INSTALL_LIBRARY_DIR=/usr/$(get_libdir)
+		-DGIFTI_INSTALL_LIB_DIR=/usr/$(get_libdir)
+		-DAFNI_INSTALL_LIBRARY_DIR=/usr/$(get_libdir)
+		-DCMAKE_INSTALL_LIBDIR=/usr/$(get_libdir)
+		-DCOMP_COREBINARIES=ON
+		-DUSE_SYSTEM_NIFTI=OFF
+		-DUSE_SYSTEM_GIFTI=OFF
+		-DUSE_SYSTEM_XMHTML=OFF
+		-DUSE_SYSTEM_GTS=ON
+		-DFETCHCONTENT_SOURCE_DIR_NIFTI_CLIB="${WORKDIR}/nifti_clib-${NIFTI_HASH}"
+		-DFETCHCONTENT_SOURCE_DIR_GIFTI_CLIB="${WORKDIR}/gifti_clib-${GIFTI_HASH}"
+		-DCOMP_GUI=ON
+		-DCOMP_PLUGINS=ON
+		-DUSE_OMP=ON
+		-DCOMP_PYTHON=OFF
+		-DUSE_SYSTEM_F2C=ON
+	)
+	tc-export CC
+	cmake_src_configure
+}
+
+src_compile() {
+	cmake_src_compile
+	pushd src/python_scripts
+		distutils-r1_src_compile
+	popd
+}
+
+src_install() {
+	cmake_src_install
+	pushd src/python_scripts
+		distutils-r1_src_install
+	popd
+	cd "${D}"
+	rm usr/bin/mpeg_encode
+}
diff --git a/sci-biology/afni/afni-24.0.08-r1.ebuild b/sci-biology/afni/afni-24.0.08-r1.ebuild
new file mode 100644
index 000000000..20293877f
--- /dev/null
+++ b/sci-biology/afni/afni-24.0.08-r1.ebuild
@@ -0,0 +1,114 @@
+# Copyright 1999-2021 Gentoo Authors
+# Distributed under the terms of the GNU General Public License v2
+
+EAPI=8
+
+PYTHON_COMPAT=( python3_{10..12} )
+
+DISTUTILS_USE_PEP517=setuptools
+inherit cmake distutils-r1 toolchain-funcs
+
+GTS_HASH="962155a01f5a1b87bd64e3e3d880b4dbc2347ac7"
+NIFTI_HASH="da476fd27f46098f37f5c9c4c1baee01e559572c"
+GIFTI_HASH="d3e873d8539d9b469daf7db04093da1d7e73d4f7"
+
+DESCRIPTION="Advanced Normalitazion Tools for neuroimaging"
+HOMEPAGE="http://stnava.github.io/ANTs/"
+SRC_URI="
+	https://github.com/afni/afni/archive/refs/tags/AFNI_${PV}.tar.gz -> ${P}.gh.tar.gz
+	https://github.com/NIFTI-Imaging/nifti_clib/archive/${NIFTI_HASH}.tar.gz -> nifti-${NIFTI_HASH}.tar.gz
+	https://github.com/NIFTI-Imaging/gifti_clib/archive/${GIFTI_HASH}.tar.gz -> gifti-${GIFTI_HASH}.tar.gz
+	"
+
+SLOT="0"
+LICENSE="GPL-3+"
+KEYWORDS="~amd64 ~x86"
+IUSE="test whirlgif"
+RESTRICT="!test? ( test )"
+
+RDEPEND="
+	dev-libs/glib:2
+	dev-libs/libf2c
+	dev-libs/expat
+	dev-build/ninja
+	media-libs/freeglut
+	media-libs/glu
+	media-libs/netpbm
+	media-libs/qhull
+	media-video/mpeg-tools
+	sci-libs/gsl
+	sci-libs/gts
+	sys-devel/llvm:*
+	sys-libs/libomp
+	virtual/jpeg-compat:62
+	x11-libs/libGLw
+	x11-libs/libXft
+	x11-libs/libXi
+	x11-libs/libXmu
+	x11-libs/libXpm
+	x11-libs/libXt
+	x11-libs/motif[-static-libs]
+	"
+DEPEND="
+	${RDEPEND}
+	app-shells/tcsh
+	"
+# Prospectively:
+#Update jpeg-compat to virtual/jpeg:0
+# look for xmhtlm
+
+S="${WORKDIR}/afni-AFNI_${PV}"
+
+	#tar xf "${DISTDIR}/${GTS_HASH}.tar.gz" || die
+src_prepare() {
+	tar xf "${DISTDIR}/nifti-${NIFTI_HASH}.tar.gz" || die
+	tar xf "${DISTDIR}/gifti-${GIFTI_HASH}.tar.gz" || die
+	cmake_src_prepare
+	default
+	}
+
+src_configure() {
+	if use !whirlgif; then
+		eapply "${FILESDIR}/${PN}-24.0.04-whirlgif.patch"
+	fi
+	export CFLAGS="-pthread ${CFLAGS}"
+	export GIT_REPO_VERSION=3.0.1.1
+	local mycmakeargs=(
+		-DLIBDIR=/usr/$(get_libdir)
+		-DNIFTI_INSTALL_LIBRARY_DIR=/usr/$(get_libdir)
+		-DGIFTI_INSTALL_LIBRARY_DIR=/usr/$(get_libdir)
+		-DGIFTI_INSTALL_LIB_DIR=/usr/$(get_libdir)
+		-DAFNI_INSTALL_LIBRARY_DIR=/usr/$(get_libdir)
+		-DCMAKE_INSTALL_LIBDIR=/usr/$(get_libdir)
+		-DCOMP_COREBINARIES=ON
+		-DUSE_SYSTEM_NIFTI=OFF
+		-DUSE_SYSTEM_GIFTI=OFF
+		-DUSE_SYSTEM_XMHTML=OFF
+		-DUSE_SYSTEM_GTS=ON
+		-DFETCHCONTENT_SOURCE_DIR_NIFTI_CLIB="${WORKDIR}/nifti_clib-${NIFTI_HASH}"
+		-DFETCHCONTENT_SOURCE_DIR_GIFTI_CLIB="${WORKDIR}/gifti_clib-${GIFTI_HASH}"
+		-DCOMP_GUI=ON
+		-DCOMP_PLUGINS=ON
+		-DUSE_OMP=ON
+		-DCOMP_PYTHON=OFF
+		-DUSE_SYSTEM_F2C=ON
+	)
+	tc-export CC
+	cmake_src_configure
+}
+
+src_compile() {
+	cmake_src_compile
+	pushd src/python_scripts
+		distutils-r1_src_compile
+	popd
+}
+
+src_install() {
+	cmake_src_install
+	pushd src/python_scripts
+		distutils-r1_src_install
+	popd
+	cd "${D}"
+	rm usr/bin/mpeg_encode
+}
diff --git a/sci-biology/afni/afni-9999.ebuild b/sci-biology/afni/afni-9999.ebuild
deleted file mode 100644
index e73bef8cc..000000000
--- a/sci-biology/afni/afni-9999.ebuild
+++ /dev/null
@@ -1,69 +0,0 @@
-# Copyright 1999-2018 Gentoo Foundation
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=7
-
-inherit eutils multilib pax-utils git-r3 toolchain-funcs
-
-DESCRIPTION="An open-source environment for processing and displaying functional MRI data"
-HOMEPAGE="http://afni.nimh.nih.gov/"
-SRC_URI=""
-EGIT_REPO_URI="https://github.com/AFNI/AFNI"
-
-LICENSE="GPL-3+"
-SLOT="0"
-KEYWORDS=""
-IUSE=""
-
-RDEPEND="dev-libs/expat
-	media-libs/netpbm
-	media-libs/qhull
-	media-video/mpeg-tools
-	sci-libs/gsl
-	sys-devel/llvm:*
-	virtual/jpeg:0
-	x11-libs/libGLw
-	x11-libs/libXft
-	x11-libs/libXi
-	x11-libs/libXpm
-	x11-libs/motif[-static-libs]"
-
-# x11-libs/motif[static-libs] breaks the build.
-# See upstream discussion
-# http://afni.nimh.nih.gov/afni/community/board/read.php?1,85348,85348#msg-85348
-
-DEPEND="${RDEPEND}
-	app-shells/tcsh"
-
-S="${WORKDIR}/${P}/src"
-BUILD="linux_fedora_19_64"
-BIN_CONFLICTS=(qdelaunay whirlgif djpeg cjpeg qhull rbox count mpeg_encode)
-
-src_prepare() {
-	find -type f -exec sed -i -e "s/-lXp //g" {} +
-	cp other_builds/Makefile.${BUILD} Makefile || die "Could not copy Makefile"
-	sed -e "s~CC     = /usr/bin/gcc -O2 -m64~CC     = $(tc-getCC) \$(CFLAGS)~" \
-		-e "s~CCMIN  = /usr/bin/gcc -m64~CCMIN  = $(tc-getCC) \$(CFLAGS)~" \
-		-e "s~LD     = /usr/bin/gcc~LD     = $(tc-getCC)~" \
-		-e "s~AR     = /usr/bin/ar~AR     = $(tc-getAR)~" \
-		-e "s~RANLIB = /usr/bin/ranlib~RANLIB = $(tc-getRANLIB)~" \
-		-i Makefile || die "Could not edit Makefile"
-		# they provide somewhat problematic makefiles :(
-	sed -e "s~ifeq ($(CC),gcc)~ifeq (1,1)~"\
-		-i SUMA/SUMA_Makefile || die "Could not edit SUMA/SUMA_Makefile"
-		# upstream checks if $CC is EXACTLY gcc, else sets variables for Mac
-	find "${S}" -iname "*Makefile*" | xargs sed -e "s~/usr/~${EROOT}/usr/~g;" -i
-	eapply_user
-}
-
-src_compile() {
-	emake -j1 all plugins suma_exec
-}
-
-src_install() {
-	emake INSTALLDIR="${ED}/usr/bin" -j1 install install_plugins
-	emake INSTALLDIR="${ED}/usr/$(get_libdir)" -j1 install_lib
-	for CONFLICT in ${BIN_CONFLICTS[@]}; do
-		rm "${ED}/usr/bin/${CONFLICT}"
-	done
-}
diff --git a/sci-biology/afni/files/afni-24.0.04-whirlgif.patch b/sci-biology/afni/files/afni-24.0.04-whirlgif.patch
new file mode 100644
index 000000000..a357799e6
--- /dev/null
+++ b/sci-biology/afni/files/afni-24.0.04-whirlgif.patch
@@ -0,0 +1,39 @@
+diff --git a/packaging/installation_components.txt b/packaging/installation_components.txt
+index 127193338..ba8825a7b 100644
+--- a/packaging/installation_components.txt
++++ b/packaging/installation_components.txt
+@@ -347,7 +347,6 @@ uniq_images, corebinaries
+ unu, corebinaries
+ waver, corebinaries
+ whereami, corebinaries
+-whirlgif, corebinaries
+ 3dMax, tcsh
+ 3dPAR2AFNI.pl, tcsh
+ @1dDiffMag, tcsh
+diff --git a/src/CMakeLists_binaries.txt b/src/CMakeLists_binaries.txt
+index d53368390..8c8e9e1fb 100644
+--- a/src/CMakeLists_binaries.txt
++++ b/src/CMakeLists_binaries.txt
+@@ -209,7 +209,6 @@ foreach(
+   uniq_images
+   unu
+   whereami
+-  whirlgif
+ )
+
+   add_afni_executable(${target} ${target}.c)
+diff --git a/src/Makefile.INCLUDE b/src/Makefile.INCLUDE
+index f44103def..7ac08a87d 100644
+--- a/src/Makefile.INCLUDE
++++ b/src/Makefile.INCLUDE
+@@ -3495,11 +3495,6 @@ help_format:help_format.o
+ ibinom:ibinom.o
+ 	$(CC) -o ibinom ibinom.o $(LFLAGS) $(LLIBS)
+
+-## GIF animation
+-
+-whirlgif:whirlgif.h whirlgif.c
+-	$(CC) -o whirlgif whirlgif.c $(INFLAGS) $(LFLAGS) $(LLIBS)
+-
+ extor.o:extor.c
+ 	$(CCFAST) -c extor.c $(INFLAGS)
diff --git a/sci-biology/afni/metadata.xml b/sci-biology/afni/metadata.xml
index 0923769c1..39ec69d08 100644
--- a/sci-biology/afni/metadata.xml
+++ b/sci-biology/afni/metadata.xml
@@ -2,7 +2,7 @@
 <!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
 <pkgmetadata>
 	<maintainer type="person">
-		<email>horea.christ@gmail.com</email>
+		<email>gentoo@chymera.eu</email>
 		<name>Horea Christian</name>
 	</maintainer>
 	<maintainer type="project">
@@ -13,4 +13,10 @@
 		Analysis of Functional NeuroImages (AFNI) is an open-source environment for processing and displaying 
 		functional MRI data—a technique for mapping human brain activity.
 	</longdescription>
+	<use>
+		<flag name="whirlgif">Build optional whirlgif binary</flag>
+	</use>
+	<upstream>
+		<remote-id type="github">afni/afni</remote-id>
+	</upstream>
 </pkgmetadata>
diff --git a/sci-biology/aghermann/aghermann-1.1.2-r2.ebuild b/sci-biology/aghermann/aghermann-1.1.2-r2.ebuild
new file mode 100644
index 000000000..b0ac5fe00
--- /dev/null
+++ b/sci-biology/aghermann/aghermann-1.1.2-r2.ebuild
@@ -0,0 +1,36 @@
+# Copyright 1999-2022 Gentoo Authors
+# Distributed under the terms of the GNU General Public License v2
+
+EAPI=7
+
+LUA_COMPAT=( lua5-{1..3} )
+
+inherit lua
+
+DESCRIPTION="A sleep-research experiment manager, EDF viewer & Process S simulator"
+HOMEPAGE="http://johnhommer.com/academic/code/aghermann"
+SRC_URI="http://johnhommer.com/code/aghermann/source/${P}.tar.xz"
+
+LICENSE="GPL-2+"
+SLOT="0"
+KEYWORDS="~amd64"
+
+REQUIRED_USE="${LUA_REQUIRED_USE}"
+
+RDEPEND="${LUA_DEPS}
+	dev-libs/libconfig
+	media-libs/libsamplerate
+	sci-libs/itpp
+	sci-libs/fftw:3.0
+	sci-libs/gsl
+	sci-libs/itpp
+	x11-libs/gtk+:3
+	x11-libs/vte:2.91
+"
+
+DEPEND="${RDEPEND}"
+BDEPEND="virtual/pkgconfig"
+
+src_configure() {
+	ITPP_LIBS="/usr/$(get_libdir)/libitpp.so" ITPP_CFLAGS="/usr/include/itpp/" econf --bindir="${EPREFIX}"/usr/bin
+}
diff --git a/sci-biology/aghermann/aghermann-1.1.2.ebuild b/sci-biology/aghermann/aghermann-1.1.2.ebuild
deleted file mode 100644
index a9eb6cbe7..000000000
--- a/sci-biology/aghermann/aghermann-1.1.2.ebuild
+++ /dev/null
@@ -1,28 +0,0 @@
-# Copyright 1999-2017 Gentoo Foundation
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=6
-
-DESCRIPTION="A sleep-research experiment manager, EDF viewer & Process S simulator"
-HOMEPAGE="http://johnhommer.com/academic/code/aghermann"
-SRC_URI="http://alfinston.dlinkddns.com/johnhommer.com/code/aghermann/source/${P}.tar.xz"
-
-LICENSE="GPL-2+"
-SLOT="0"
-KEYWORDS="~amd64 ~x86"
-
-RDEPEND="dev-lang/lua:*
-	dev-libs/libconfig
-	media-libs/libsamplerate
-	sci-libs/fftw:3.0
-	sci-libs/gsl
-	sci-libs/itpp
-	x11-libs/gtk+:3
-	x11-libs/vte:2.91"
-
-DEPEND="${RDEPEND}
-	virtual/pkgconfig"
-
-src_configure() {
-	econf --bindir="${EPREFIX}"/usr/bin
-}
diff --git a/sci-biology/align_to_scf/align_to_scf-1.06.ebuild b/sci-biology/align_to_scf/align_to_scf-1.06.ebuild
index f9564900c..86ce20a83 100644
--- a/sci-biology/align_to_scf/align_to_scf-1.06.ebuild
+++ b/sci-biology/align_to_scf/align_to_scf-1.06.ebuild
@@ -1,22 +1,18 @@
-# Copyright 1999-2015 Gentoo Foundation
+# Copyright 1999-2021 Gentoo Authors
 # Distributed under the terms of the GNU General Public License v2
 
-EAPI=5
-
-inherit eutils
+EAPI=7
 
 DESCRIPTION="View trace information at a given position missing from Roche .ace files"
 HOMEPAGE="http://genome.imb-jena.de/software/roche454ace2caf"
-SRC_URI="http://genome.imb-jena.de/software/roche454ace2caf/download/src/align_to_scf-1.06.tgz"
+SRC_URI="http://genome.imb-jena.de/software/roche454ace2caf/download/src/align_to_scf-${PV}.tgz"
 
 LICENSE="FLI-Jena"
 SLOT="0"
 KEYWORDS="~amd64 ~x86"
-IUSE=""
 
 src_prepare(){
-	sed -i "s:^CC :CC=$(tc-getCC) #:" Makefile || die "sed failed"
-	sed -i "s:^LD :LD=$(tc-getCC) #:" Makefile || die "sed failed"
+	default
 	sed -i 's:^CFLAGS.*:CFLAGS+= -D__LINUX__ -Wcast-align:' Makefile || die "sed failed"
 	sed -i 's:^LDFLAGS =:#LDFLAGS =:' Makefile || die "sed failed"
 }
diff --git a/sci-biology/amos/Manifest b/sci-biology/amos/Manifest
deleted file mode 100644
index f7c93a72f..000000000
--- a/sci-biology/amos/Manifest
+++ /dev/null
@@ -1 +0,0 @@
-DIST amos-3.1.0.tar.gz 2094268 BLAKE2B b9fb80d4e7b7e9e7769081c2680a3cba26591f00a4d9fdb17ad602e581dea5e8e2add4b0d9d3821a7f8a4ec1a45dfd867037baf35ecd401584f030c86b2b0f83 SHA512 7a416b9a0438b47425355383b709491a58f38c8d834df29e43c942170e710c6ea7e3bc8c509a58421b1340ad6eece9ea2da357ce5cd1d41ce08375676ee30491
diff --git a/sci-biology/amos/amos-3.1.0-r2.ebuild b/sci-biology/amos/amos-3.1.0-r2.ebuild
deleted file mode 100644
index 951f12c1b..000000000
--- a/sci-biology/amos/amos-3.1.0-r2.ebuild
+++ /dev/null
@@ -1,76 +0,0 @@
-# Copyright 1999-2018 Gentoo Foundation
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=5
-
-PYTHON_COMPAT=( python2_7 )
-inherit eutils python-r1
-
-PERL_EXPORT_PHASE_FUNCTIONS=no
-inherit perl-module eutils toolchain-funcs
-
-DESCRIPTION="Whole genome assembler, Hawkeye and AMOScmp to compare multiple assemblies"
-HOMEPAGE="http://amos.sourceforge.net/"
-SRC_URI="mirror://sourceforge/${PN}/${P}.tar.gz"
-
-LICENSE="Artistic"
-SLOT="0"
-KEYWORDS="~amd64 ~x86"
-IUSE="mpi qt5"
-
-DEPEND="
-	mpi? ( virtual/mpi )
-	dev-libs/boost
-	qt5? ( dev-qt/qtcore:5 )
-	sci-biology/blat
-	sci-biology/jellyfish:1"
-RDEPEND="${DEPEND}
-	dev-lang/perl
-	dev-perl/DBI
-	dev-perl/Statistics-Descriptive
-	sci-biology/mummer"
-
-MAKEOPTS+=" -j1"
-
-src_prepare() {
-	epatch \
-		"${FILESDIR}"/${P}-gcc-4.7.patch \
-		"${FILESDIR}"/${P}-goBambus2.py-indent-and-cleanup.patch \
-		"${FILESDIR}"/${P}-rename_to_jellyfish1.patch
-	# $ gap-links
-	# ERROR:  Could not open file  LIBGUESTFS_PATH=/usr/share/guestfs/appliance/
-	# $
-	sh ./bootstrap || die
-	default
-	eautoreconf
-	# prevent GCC 6 log pollution due to hash_map deprecation in C++11
-	# shutdown gcc-8.2.0 messages too
-	append-cxxflags -Wno-cpp -Wno-narrowing
-}
-
-src_configure() {
-	local myconf
-	use X && myconf+=( --with-x )
-	econf ${myconf[@]} --with-jellyfish="${EPREFIX}"/usr/include --with-Boost-dir="${EPREFIX}"/usr/include --with-qmake-qt4=qmake --enable-all
-}
-
-src_install() {
-	default
-	python_replicate_script "${ED}"/usr/bin/goBambus2
-	# bambus needs TIGR::FASTAreader.pm and others
-	# configure --libdir sadly copies both *.a files and *.pm into /usr/lib64/AMOS/ and /usr/lib64/TIGR/, work around it
-	perl_set_version
-	insinto ${VENDOR_LIB}/AMOS
-	doins "${D}"/usr/lib64/AMOS/*.pm
-	insinto ${VENDOR_LIB}/TIGR
-	doins "${D}"/usr/lib64/TIGR/*.pm
-	# move also /usr/lib64/AMOS/AMOS.py to /usr/bin
-	mv "${D}"/usr/lib64/AMOS/*.py "${D}"/usr/bin || die
-	# zap the mis-placed files ('make install' is at fault)
-	rm -f "${D}"/usr/lib64/AMOS/*.pm
-	rm -rf "${D}"/usr/lib64/TIGR
-	echo AMOSCONF="${EPREFIX}"/etc/amos.acf > "${S}"/99amos || die
-	mkdir -p "${ED}"/etc || die
-	touch "${ED}"/etc/amos.acf || die
-	doenvd "${S}/99amos"
-}
diff --git a/sci-biology/amos/amos-9999.ebuild b/sci-biology/amos/amos-9999.ebuild
deleted file mode 100644
index 923ac5978..000000000
--- a/sci-biology/amos/amos-9999.ebuild
+++ /dev/null
@@ -1,76 +0,0 @@
-# Copyright 1999-2018 Gentoo Foundation
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=5
-
-PYTHON_COMPAT=( python2_7 )
-
-PERL_EXPORT_PHASE_FUNCTIONS=no
-inherit perl-module eutils toolchain-funcs autotools flag-o-matic python-single-r1 qmake-utils
-
-AUTOTOOLS_AUTORECONF=true
-inherit autotools-utils git-r3
-
-DESCRIPTION="Whole genome assembler, Hawkeye and AMOScmp to compare multiple assemblies"
-HOMEPAGE="http://sourceforge.net/projects/amos"
-SRC_URI=""
-EGIT_REPO_URI="git://amos.git.sourceforge.net/gitroot/amos/amos"
-
-LICENSE="Artistic"
-SLOT="0"
-KEYWORDS=""
-IUSE="mpi qt5 X"
-
-DEPEND="
-	mpi? ( virtual/mpi )
-	dev-libs/boost
-	qt5? ( dev-qt/qtcore:5 )
-	sci-biology/blat
-	sci-biology/jellyfish:1"
-RDEPEND="${DEPEND}
-	dev-perl/DBI
-	dev-perl/Statistics-Descriptive
-	sci-biology/mummer"
-
-# $ gap-links
-# ERROR:  Could not open file  LIBGUESTFS_PATH=/usr/share/guestfs/appliance/
-# $
-
-src_prepare() {
-	epatch "${FILESDIR}"/"${P}"-fix-include-paths.patch
-	epatch "${FILESDIR}"/amos-3.1.0-rename_to_jellyfish1.patch
-	sh ./bootstrap || die
-	default
-	eautoreconf
-
-	# prevent GCC 6 log pollution due to hash_map deprecation in C++11
-	# shutdown gcc-8.2.0 messages too
-	append-cxxflags -Wno-cpp -Wno-narrowing
-}
-
-src_configure() {
-	local myconf
-	use X && myconf+=( --with-x )
-	econf ${myconf[@]} --with-jellyfish="${EPREFIX}"/usr/include --with-Boost-dir="${EPREFIX}"/usr/include --with-qmake-qt4=qmake --enable-all
-}
-
-src_install() {
-	default
-	python_replicate_script "${ED}"/usr/bin/goBambus2
-	# bambus needs TIGR::FASTAreader.pm and others
-	# configure --libdir sadly copies both *.a files and *.pm into /usr/lib64/AMOS/ and /usr/lib64/TIGR/, work around it
-	perl_set_version
-	insinto ${VENDOR_LIB}/AMOS
-	doins "${D}"/usr/lib64/AMOS/*.pm
-	insinto ${VENDOR_LIB}/TIGR
-	doins "${D}"/usr/lib64/TIGR/*.pm
-	# move also /usr/lib64/AMOS/AMOS.py to /usr/bin
-	mv "${D}"/usr/lib64/AMOS/*.py "${D}"/usr/bin || die
-	# zap the mis-placed files ('make install' is at fault)
-	rm -f "${D}"/usr/lib64/AMOS/*.pm
-	rm -rf "${D}"/usr/lib64/TIGR
-	echo AMOSCONF="${EPREFIX}"/etc/amos.acf > "${S}"/99amos || die
-	mkdir -p "${ED}"/etc || die
-	touch "${ED}"/etc/amos.acf || die
-	doenvd "${S}/99amos"
-}
diff --git a/sci-biology/amos/files/amos-3.1.0-gcc-4.7.patch b/sci-biology/amos/files/amos-3.1.0-gcc-4.7.patch
deleted file mode 100644
index de2a41184..000000000
--- a/sci-biology/amos/files/amos-3.1.0-gcc-4.7.patch
+++ /dev/null
@@ -1,15 +0,0 @@
- src/Align/find-tandem.cc |    1 +
- 1 files changed, 1 insertions(+), 0 deletions(-)
-
-diff --git a/src/Align/find-tandem.cc b/src/Align/find-tandem.cc
-index ddf1cab..a29e21e 100644
---- a/src/Align/find-tandem.cc
-+++ b/src/Align/find-tandem.cc
-@@ -7,6 +7,7 @@
- #include <vector>
- #include <ctime>
- #include <sys/time.h>
-+#include <unistd.h>
- using namespace std;
- 
- const int OFFSET_TABLE_SIZE = 100;
diff --git a/sci-biology/amos/files/amos-3.1.0-goBambus2.py-indent-and-cleanup.patch b/sci-biology/amos/files/amos-3.1.0-goBambus2.py-indent-and-cleanup.patch
deleted file mode 100644
index 97a8f59d0..000000000
--- a/sci-biology/amos/files/amos-3.1.0-goBambus2.py-indent-and-cleanup.patch
+++ /dev/null
@@ -1,25 +0,0 @@
---- amos-3.1.0/src/Pipeline/goBambus2.py.orig	2013-09-11 01:05:29.850090457 +0200
-+++ amos-3.1.0/src/Pipeline/goBambus2.py	2013-09-11 01:07:03.250090701 +0200
-@@ -1,7 +1,7 @@
- #pipeline script for assembly + Bambus 2
- #contributed by Todd J Treangen
- 
--import string, sys, os, subprocess#, spincursor
-+import sys, os, subprocess#, spincursor
- 
- RED =    "\033[0;31m"
- GREEN =  "\033[0;32m"
-@@ -360,7 +360,7 @@
-                 print "\t\t%s...failed%s"%(RED,NONE)
-                 sys.exit(1)
- 
--       p = subprocess.Popen(AMOSDIR+"OutputResults -b %s -prefix %s %s"%(amosbank, prefix+".scaff.linear"), shell=True, stdin=subprocess.PIPE, stdout=vtext, stderr=logfile)
-+        p = subprocess.Popen(AMOSDIR+"OutputResults -b %s -prefix %s %s"%(amosbank, prefix+".scaff.linear"), shell=True, stdin=subprocess.PIPE, stdout=vtext, stderr=logfile)
- 
-         if xopt_dict["verbose"] == 1:
-             print "10) running OutputResults"
-@@ -388,4 +388,3 @@
-             else:
-                 print "\t\t%s...failed%s"%(RED,NONE)
-                 sys.exit(1)
--)
diff --git a/sci-biology/amos/files/amos-3.1.0-rename_to_jellyfish1.patch b/sci-biology/amos/files/amos-3.1.0-rename_to_jellyfish1.patch
deleted file mode 100644
index 4b52c5640..000000000
--- a/sci-biology/amos/files/amos-3.1.0-rename_to_jellyfish1.patch
+++ /dev/null
@@ -1,43 +0,0 @@
---- config/amos.m4	2018-09-11 13:23:14.478444129 +0200
-+++ config/amos.m4	2018-09-11 13:36:36.697612245 +0200
-@@ -695,15 +695,15 @@
- else
- 	jellyfish_unspecified=no
- fi
--if ! test -f "$jellyfish_dir/jellyfish/mer_counting.hpp"; then
-+if ! test -f "$jellyfish_dir/jellyfish1/mer_counting.hpp"; then
- 	if test $jellyfish_unspecified = no; then
--		AC_MSG_ERROR([Could not find the file "$jellyfish_dir/jellyfish/compacted_hash.hpp"])
-+		AC_MSG_ERROR([Could not find the file "$jellyfish_dir/jellyfish1/compacted_hash.hpp"])
- 	fi
- 	JELLYFISH_LDADD=
- 	JELLYFISH_CPPFLAGS=
- 	AC_MSG_RESULT([not found])
- else
--	JELLYFISH_LDADD="-ljellyfish -lpthread"
-+	JELLYFISH_LDADD="-ljellyfish-1.1 -lpthread"
- 	JELLYFISH_CPPFLAGS="-I $jellyfish_dir"
- 	AC_DEFINE([WITH_JELLYFISH], [1], [Define to 1 if using Jellyfish])
- 	cppflags_save="$CPPFLAGS"
-@@ -715,7 +715,7 @@
- 	AC_LANG_PUSH([C++])
- 	AC_LINK_IFELSE([
- 		AC_LANG_PROGRAM([
--#include <jellyfish/mer_counting.hpp>
-+#include <jellyfish1/mer_counting.hpp>
- #include <string>
- 	], [
- std::string s;
---- src/Align/kmer-cov-plot.cc	2018-09-11 13:23:15.079443556 +0200
-+++ src/Align/kmer-cov-plot.cc	2018-09-11 13:36:36.831612096 +0200
-@@ -388,8 +388,8 @@
- 
- #ifdef WITH_JELLYFISH
- 
--#include <jellyfish/compacted_hash.hpp>
--#include <jellyfish/mer_counting.hpp>
-+#include <jellyfish1/compacted_hash.hpp>
-+#include <jellyfish1/mer_counting.hpp>
- 
- // Assert that jellyfish is using the expected kmer representation
- static void jellyfish_check()
diff --git a/sci-biology/amos/files/amos-9999-fix-include-paths.patch b/sci-biology/amos/files/amos-9999-fix-include-paths.patch
deleted file mode 100644
index a6e8dc9f0..000000000
--- a/sci-biology/amos/files/amos-9999-fix-include-paths.patch
+++ /dev/null
@@ -1,13 +0,0 @@
---- src/Bambus/Bundler/Makefile.am.old	2018-07-03 12:52:17.306095693 +0200
-+++ src/Bambus/Bundler/Makefile.am	2018-07-03 12:52:19.506101530 +0200
-@@ -78,8 +78,8 @@
- ##-- libBundler.a
- libBundler_a_CPPFLAGS = \
- 	$(BOOST_CXXFLAGS)  \
--	-I$(top_builddir)/src/GNU \
--	-I$(top_builddir)/src/AMOS
-+	-I$(top_srcdir)/src/GNU \
-+	-I$(top_srcdir)/src/AMOS
- 	## because some system headers will be built if necessary
- libBundler_a_LIBADD = \
- 	$(LIBOBJS:%=$(top_builddir)/src/GNU/%) \
diff --git a/sci-biology/amos/metadata.xml b/sci-biology/amos/metadata.xml
deleted file mode 100644
index ddba4784f..000000000
--- a/sci-biology/amos/metadata.xml
+++ /dev/null
@@ -1,21 +0,0 @@
-<?xml version="1.0" encoding="UTF-8"?>
-<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
-<pkgmetadata>
-	<maintainer type="person">
-		<email>mmokrejs@fold.natur.cuni.cz</email>
-		<name>Martin Mokrejs</name>
-	</maintainer>
-	<maintainer type="project">
-		<email>sci-biology@gentoo.org</email>
-		<name>Gentoo Biology Project</name>
-	</maintainer>
-	<longdescription>
-AMOS is collection of tools and class interfaces for the assembly of DNA 
-sequencing reads. The package includes a robust infrastructure, modular assembly
-pipelines, and tools for overlapping, consensus generation, contigging, and 
-assembly manipulation
-</longdescription>
-	<upstream>
-		<remote-id type="sourceforge">amos</remote-id>
-	</upstream>
-</pkgmetadata>
diff --git a/sci-biology/ampliconnoise/Manifest b/sci-biology/ampliconnoise/Manifest
deleted file mode 100644
index 6b910f882..000000000
--- a/sci-biology/ampliconnoise/Manifest
+++ /dev/null
@@ -1,3 +0,0 @@
-DIST AmpliconNoiseV1.27.tar.gz 1379908 BLAKE2B 2f02b031902488e5af144203602d515ef2a8659375db923f6d9961c670c20fb7a9683e65a7765c05a2d45f14d6f56fd791eea627a3713c1cef530cb3d23c0a0a SHA512 71d1f3c7cd890844b0109f35e5f299b41245e4cd0b7026f4a062d378706942537214979b208e5c25e00d6fb60111c5b1f17a21bd3cb8128a6a2c5854cc5d83a5
-DIST DiversityEstimates.tar.gz 35625 BLAKE2B 7d4afc13917643e5c15cf7bfeb496fc0f22c037948744f7504e8d67fc46ebab2994c1af443ad8907cf5e9737092192058658e1eec9d000b2b0a1b4b45ffc64a6 SHA512 81cd24ac3533a982555f8e4a0dfdc61c5fe6340892bbfad44babd801fe502f90ba68dedb938d881fc38d8e809cbe4a300d2218583f5e495c28c572726c777165
-DIST TutorialV1.22.tar.gz 31274115 BLAKE2B 2d6a7b3b47d7093021de4fb1fd5f47429e3059cb4770f352cc56b8beb23c6d310b4b6524820f3e76b5af8994f2ffebbc803c061554d9ec5f8da4848cbf78cd93 SHA512 73f67df1f0f2e6f0fc95a626ef4cbc002449aba62a1b1c0f1058347c48ccd39619fd6748fc109f2541a7e87b595e88ec491289dfba8e8b23c5fa06821bf3d660
diff --git a/sci-biology/ampliconnoise/ampliconnoise-1.27.ebuild b/sci-biology/ampliconnoise/ampliconnoise-1.27.ebuild
deleted file mode 100644
index 5555cf4c6..000000000
--- a/sci-biology/ampliconnoise/ampliconnoise-1.27.ebuild
+++ /dev/null
@@ -1,43 +0,0 @@
-# Copyright 1999-2016 Gentoo Foundation
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=6
-
-DESCRIPTION="Noise removal from pyrosequenced amplicons"
-HOMEPAGE="http://code.google.com/p/ampliconnoise/"
-SRC_URI="
-	http://ampliconnoise.googlecode.com/files/AmpliconNoiseV${PV}.tar.gz
-	http://ampliconnoise.googlecode.com/files/TutorialV1.22.tar.gz
-	http://ampliconnoise.googlecode.com/files/DiversityEstimates.tar.gz"
-
-LICENSE="LGPL-3"
-SLOT="0"
-KEYWORDS=""
-IUSE="mpi"
-RDEPEND="
-	mpi? ( virtual/mpi )
-	sci-libs/gsl
-	sci-biology/mafft
-	sci-biology/usearch-bin
-	dev-haskell/biosff || ( sci-biology/flower )"
-	# sci-biology/flower::haskell installs renamed binaries to avoid file collision
-	# unfortunately flower executable from the two packages
-	# dev-haskell/biosff::science vs. sci-biology/flower::haskell
-	# do not offer same cmdline options (upstream did not sync the two packages)
-
-S="${WORKDIR}/AmpliconNoiseV1.27"
-
-src_compile(){
-	# FIXME: the Makefile forcibly calls 'mpicc'
-	emake
-	cd ../DiversityEstimates || die
-	emake
-}
-
-src_install(){
-	default
-	dodoc "${WORKDIR}"/TutorialV1.22/Tutorial.ppt "${WORKDIR}"/TutorialV1.22/SmallTwins.* Doc.pdf
-	mv bin "${DESTDIR}/${EPREFIX}"/usr/ || die
-	insinto /usr/share/"${PN}"/scripts
-	doins Scripts/*.pl Scripts/*.sh
-}
diff --git a/sci-biology/ampliconnoise/metadata.xml b/sci-biology/ampliconnoise/metadata.xml
deleted file mode 100644
index 138cb7705..000000000
--- a/sci-biology/ampliconnoise/metadata.xml
+++ /dev/null
@@ -1,12 +0,0 @@
-<?xml version="1.0" encoding="UTF-8"?>
-<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
-<pkgmetadata>
-	<maintainer type="person">
-		<email>mmokrejs@fold.natur.cuni.cz</email>
-		<name>Martin Mokrejs</name>
-	</maintainer>
-	<maintainer type="project">
-		<email>sci-biology@gentoo.org</email>
-		<name>Gentoo Biology Project</name>
-	</maintainer>
-</pkgmetadata>
diff --git a/sci-biology/angsd/Manifest b/sci-biology/angsd/Manifest
new file mode 100644
index 000000000..8d9a2c42f
--- /dev/null
+++ b/sci-biology/angsd/Manifest
@@ -0,0 +1 @@
+DIST angsd-0.933.tar.gz 10566370 BLAKE2B 0955214ea4094df22f997f2721fe743c5e8f739261b1781d5622d0a6fadf99a77a24cbb84ab540bf93f088cb92cbb443da7a1393293a3c7595bfdd2541712a05 SHA512 3cc42ccd4cf8c3b03fe2da3226459a766b484a2810b5055fbed1c73d734bbc915efe75616841680065fc65101dd6f3229bdb1a3125b9ed0805e0c93e81fa8d7c
diff --git a/sci-biology/angsd/angsd-0.933.ebuild b/sci-biology/angsd/angsd-0.933.ebuild
new file mode 100644
index 000000000..9a37d2af6
--- /dev/null
+++ b/sci-biology/angsd/angsd-0.933.ebuild
@@ -0,0 +1,47 @@
+# Copyright 1999-2021 Gentoo Authors
+# Distributed under the terms of the GNU General Public License v2
+
+EAPI=7
+
+DESCRIPTION="Population genetics analysis package"
+HOMEPAGE="http://www.popgen.dk/angsd"
+SRC_URI="https://github.com/ANGSD/angsd/archive/${PV}.tar.gz -> ${P}.tar.gz"
+
+LICENSE="GPL-2"
+SLOT="0"
+KEYWORDS="~amd64"
+
+DEPEND="
+	dev-lang/R
+	sci-libs/htslib:0="
+RDEPEND="${DEPEND}"
+
+# https://github.com/ANGSD/angsd/issues/9
+src_prepare(){
+	default
+	sed \
+		-e 's@FLAGS=-O3@FLAGS=@' \
+		-e 's@HTSLIB = .*@HTSLIB = -lhts@' \
+		-e 's@all: htshook angsd misc@all: angsd misc@' \
+		-i Makefile || die
+	sed \
+		-e 's@HTSLIB = .*@HTSLIB = -lhts@' \
+		-e 's@HTSDIR = .*@HTSDIR = /usr/include@' \
+		-i misc/Makefile || die
+	sed \
+		-e 's@include "../htslib/bgzf.h@include "bgzf.h@' \
+		-i misc/thetaStat.cpp || die
+}
+
+src_compile(){
+	emake HTS=/usr/include
+}
+
+src_install(){
+	einstalldocs
+	dobin angsd
+	cd misc || die
+	dobin \
+		supersim haploToPlink ibs thetaStat realSFS msToGlf msHOT2glf smartCount \
+		printIcounts splitgl contamination contamination2 NGSadmix ngsPSMC scounts
+}
diff --git a/sci-biology/angsd/angsd-9999.ebuild b/sci-biology/angsd/angsd-9999.ebuild
deleted file mode 100644
index a4711d244..000000000
--- a/sci-biology/angsd/angsd-9999.ebuild
+++ /dev/null
@@ -1,50 +0,0 @@
-# Copyright 1999-2017 Gentoo Foundation
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=6
-
-inherit git-r3
-
-DESCRIPTION="Population genetics analysis package"
-HOMEPAGE="http://www.popgen.dk/angsd"
-EGIT_REPO_URI="https://github.com/ANGSD/angsd.git"
-
-LICENSE="GPL-2"
-SLOT="0"
-KEYWORDS=""
-IUSE=""
-
-DEPEND="
-	dev-lang/R
-	sci-libs/htslib:0="
-RDEPEND="${DEPEND}"
-
-# https://github.com/ANGSD/angsd/issues/9
-src_prepare(){
-	default
-	sed \
-		-e 's@FLAGS=-O3@FLAGS=@' \
-		-e 's@HTSLIB = .*@HTSLIB = -lhts@' \
-		-e 's@all: htshook angsd misc@all: angsd misc@' \
-		-i Makefile || die
-	sed \
-		-e 's@HTSLIB = .*@HTSLIB = -lhts@' \
-		-e 's@HTSDIR = .*@HTSDIR = /usr/include@' \
-		-i misc/Makefile || die
-	sed \
-		-e 's@include "../htslib/bgzf.h@include "bgzf.h@' \
-		-i misc/thetaStat.cpp || die
-}
-
-src_compile(){
-	emake HTS=/usr/include
-}
-
-src_install(){
-	dobin angsd
-	dodoc README.md
-	cd misc || die
-	dobin \
-		supersim thetaStat realSFS emOptim2 msToGlf smartCount \
-		printIcounts splitgl contamination NGSadmix
-}
diff --git a/sci-biology/angsd/metadata.xml b/sci-biology/angsd/metadata.xml
index 138cb7705..ed9e5b12d 100644
--- a/sci-biology/angsd/metadata.xml
+++ b/sci-biology/angsd/metadata.xml
@@ -9,4 +9,7 @@
 		<email>sci-biology@gentoo.org</email>
 		<name>Gentoo Biology Project</name>
 	</maintainer>
+	<upstream>
+		<remote-id type="github">ANGSD/angsd</remote-id>
+	</upstream>
 </pkgmetadata>
diff --git a/sci-biology/ants/Manifest b/sci-biology/ants/Manifest
index 5c411c55a..ef2d97caf 100644
--- a/sci-biology/ants/Manifest
+++ b/sci-biology/ants/Manifest
@@ -1 +1,2 @@
-DIST ants-2.3.1.tar.gz 2437950 BLAKE2B 60ffb1b017d066efd9cfc689af7877fb394c9828033c9d9e4542df723eb75e52ada490cbf8ecab0d7f149cc1b22a500791fdbe7872f7ae593a70fa1853c54d00 SHA512 c22af10b7aed1dc5c6b06d6b7d3b2c33ced382926ab5972dd55e4766ff0269330bf01e6975712d991e96c5d9d23f78c8081a3ff475ea92d539c695105b5cfe9a
+DIST ants-2.4.3.tar.gz 2474986 BLAKE2B 56a057673ff65e7ed3037ee34cea481e960122f32d2fd04b347644126793a2ba0a9249823b45e360abf2019136659b3ba4a24e49677458d69cc0b614266faca1 SHA512 50b42e30bec9077a00450253a39a8296ca841a3b3511f623a759071e6fbda9b6ab480b4f26566c621dc85107913f2782f2a1c4ecdeaa8361dc132209a432c544
+DIST ants_testdata-2.4.3.tar.xz 25058064 BLAKE2B ca3bb9998d7ded8fc9821a341a3a5b847a40fe93cccbc61458b5a6f9bab102a14fa297aad2425a5602b70c51e756edab2609213b01e06f7dc63eca2e67846351 SHA512 2689bdf1cb6bc4e608511efab574c8a0a5de839a376e9af91e277bae352744fa58463258ea604ea73041b7b596a3ab3a36e0f5a28c098ee5e7a1a9f8b8873779
diff --git a/sci-biology/ants/ants-2.3.1.ebuild b/sci-biology/ants/ants-2.3.1.ebuild
deleted file mode 100644
index e48e7892a..000000000
--- a/sci-biology/ants/ants-2.3.1.ebuild
+++ /dev/null
@@ -1,29 +0,0 @@
-# Copyright 1999-2018 Gentoo Foundation
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=6
-
-inherit cmake-utils multilib
-
-DESCRIPTION="Advanced Normalitazion Tools for neuroimaging"
-HOMEPAGE="http://stnava.github.io/ANTs/"
-SRC_URI="https://github.com/ANTsX/ANTs/archive/v${PV}.tar.gz -> ${P}.tar.gz"
-
-SLOT="0"
-LICENSE="BSD"
-KEYWORDS="~amd64 ~x86"
-
-DEPEND=">=dev-util/cmake-3.10.3"
-RDEPEND=""
-
-S="${WORKDIR}/ANTs-${PV}"
-
-src_install() {
-	cd "${WORKDIR}/${P}_build/ANTS-build" || die "build dir not found"
-	default
-	cd "${S}/Scripts" || die "scripts dir not found"
-	dobin *.sh
-	dodir /usr/$(get_libdir)/ants
-	install -t "${D}"usr/$(get_libdir)/ants *
-	doenvd "${FILESDIR}"/99ants
-}
diff --git a/sci-biology/ants/ants-2.4.3.ebuild b/sci-biology/ants/ants-2.4.3.ebuild
new file mode 100644
index 000000000..2dfa2a56d
--- /dev/null
+++ b/sci-biology/ants/ants-2.4.3.ebuild
@@ -0,0 +1,69 @@
+# Copyright 1999-2023 Gentoo Authors
+# Distributed under the terms of the GNU General Public License v2
+
+EAPI=8
+
+CMAKE_MAKEFILE_GENERATOR="emake"
+inherit cmake
+
+MY_PN="ANTs"
+
+DESCRIPTION="Advanced Normalitazion Tools for neuroimaging"
+HOMEPAGE="https://stnava.github.io/ANTs/"
+SRC_URI="
+	https://github.com/ANTsX/ANTs/archive/v${PV}.tar.gz ->  ${P}.tar.gz
+	test? (
+		https://resources.chymera.eu/distfiles/ants_testdata-${PV}.tar.xz
+	)
+"
+S="${WORKDIR}/${MY_PN}-${PV}"
+
+SLOT="0"
+LICENSE="BSD"
+KEYWORDS="~amd64 ~x86"
+IUSE="test vtk"
+RESTRICT="!test? ( test )"
+
+DEPEND="
+	!vtk? ( =sci-libs/itk-5.3*[fftw,-vtkglue] )
+	vtk? (
+		=sci-libs/itk-5.3*[fftw,vtkglue]
+		=sci-libs/vtk-9.2*
+	)
+"
+RDEPEND="${DEPEND}"
+
+src_unpack() {
+	default
+	if use test; then
+	    mkdir -p "${S}/.ExternalData/SHA512" || die "Could not create test data directory."
+	    tar xvf "${DISTDIR}/ants_testdata-${PV}.tar.xz" -C "${S}/.ExternalData/SHA512/" > /dev/null || die "Could not unpack test data."
+	fi
+}
+
+src_configure() {
+	local mycmakeargs=(
+		-DBUILD_EXAMPLES=OFF
+		-DUSE_SYSTEM_ITK=ON
+		-DITK_USE_SYSTEM_FFTW=ON
+		-DITK_DIR="${EPREFIX}/usr/include/ITK-5.3/"
+		-DBUILD_TESTING="$(usex test ON OFF)"
+		-DUSE_VTK=$(usex vtk ON OFF)
+		-DUSE_SYSTEM_VTK=$(usex vtk ON OFF)
+	)
+	use vtk && mycmakeargs+=(
+		-DVTK_DIR="${EPREFIX}/usr/include/vtk-9.2/"
+	)
+	cmake_src_configure
+}
+
+src_install() {
+	BUILD_DIR="${WORKDIR}/${MY_PN}-${PV}_build/ANTS-build"
+	cmake_src_install
+	cd "${S}/Scripts" || die "scripts dir not found"
+	dobin *.sh
+	dodir /usr/$(get_libdir)/ants
+	insinto "/usr/$(get_libdir)/ants"
+	doins *
+	doenvd "${FILESDIR}"/99ants
+}
diff --git a/sci-biology/ants/ants-9999.ebuild b/sci-biology/ants/ants-9999.ebuild
deleted file mode 100644
index da7514fca..000000000
--- a/sci-biology/ants/ants-9999.ebuild
+++ /dev/null
@@ -1,28 +0,0 @@
-# Copyright 1999-2018 Gentoo Foundation
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=6
-
-inherit cmake-utils git-r3 multilib
-
-DESCRIPTION="Advanced Normalitazion Tools for neuroimaging"
-HOMEPAGE="http://stnava.github.io/ANTs/"
-SRC_URI=""
-EGIT_REPO_URI="https://github.com/stnava/ANTs.git"
-
-SLOT="0"
-LICENSE="BSD"
-KEYWORDS=""
-
-DEPEND=">=dev-util/cmake-3.10.3"
-RDEPEND=""
-
-src_install() {
-	cd "${WORKDIR}/${P}_build/ANTS-build" || die "build dir not found"
-	default
-	cd "${WORKDIR}/ANTs-${PV}/Scripts" || die "scripts dir not found"
-	dobin *.sh
-	dodir /usr/$(get_libdir)/ants
-	install -t "${D}"usr/$(get_libdir)/ants *
-	doenvd "${FILESDIR}"/99ants
-}
diff --git a/sci-biology/ants/metadata.xml b/sci-biology/ants/metadata.xml
index 6d6b0d88a..e8372d21b 100644
--- a/sci-biology/ants/metadata.xml
+++ b/sci-biology/ants/metadata.xml
@@ -2,7 +2,7 @@
 <!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
 <pkgmetadata>
 	<maintainer type="person">
-		<email>horea.christ@gmail.com</email>
+		<email>gentoo@chymera.eu</email>
 		<name>Horea Christian</name>
 	</maintainer>
 	<maintainer type="project">
@@ -18,4 +18,10 @@
 		image analysis. ANTs depends on the Insight ToolKit (ITK), a widely used
 		medical image processing library to which ANTs developers contribute.
 	</longdescription>
+	<use>
+		<flag name="vtk">Optional support for a number of surface enabled tools (via sci-libs/vtk).</flag>
+	</use>
+	<upstream>
+		<remote-id type="github">ANTsX/ANTs</remote-id>
+	</upstream>
 </pkgmetadata>
diff --git a/sci-biology/apollo/apollo-9999.ebuild b/sci-biology/apollo/apollo-9999.ebuild
deleted file mode 100644
index 84f6eb69d..000000000
--- a/sci-biology/apollo/apollo-9999.ebuild
+++ /dev/null
@@ -1,40 +0,0 @@
-# Copyright 1999-2017 Gentoo Foundation
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=6
-
-inherit java-pkg-2 java-ant-2 subversion
-
-DESCRIPTION="Apollo genome editor"
-HOMEPAGE="http://gmod.org/wiki/Apollo"
-ESVN_REPO_URI="https://gmod.svn.sourceforge.net/svnroot/gmod/apollo/trunk"
-
-LICENSE="Artistic"
-SLOT="0"
-IUSE=""
-KEYWORDS=""
-
-RDEPEND="
-	>=virtual/jre-1.5:*
-	dev-lang/perl
-	"
-DEPEND="${RDEPEND}
-	>=virtual/jdk-1.5:*
-	dev-java/ant-core
-	"
-
-src_unpack() {
-	subversion_src_unpack
-}
-
-src_compile() {
-	cd src/java || die
-	ant compile || die
-}
-
-src_install() {
-	java-pkg_dojar jars/apollo.jar
-
-	echo "PATH=/opt/Apollo" > 99Apollo
-	doenvd 99Apollo
-}
diff --git a/sci-biology/apollo/metadata.xml b/sci-biology/apollo/metadata.xml
deleted file mode 100644
index 138cb7705..000000000
--- a/sci-biology/apollo/metadata.xml
+++ /dev/null
@@ -1,12 +0,0 @@
-<?xml version="1.0" encoding="UTF-8"?>
-<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
-<pkgmetadata>
-	<maintainer type="person">
-		<email>mmokrejs@fold.natur.cuni.cz</email>
-		<name>Martin Mokrejs</name>
-	</maintainer>
-	<maintainer type="project">
-		<email>sci-biology@gentoo.org</email>
-		<name>Gentoo Biology Project</name>
-	</maintainer>
-</pkgmetadata>
diff --git a/sci-biology/arachne/Manifest b/sci-biology/arachne/Manifest
deleted file mode 100644
index c70683996..000000000
--- a/sci-biology/arachne/Manifest
+++ /dev/null
@@ -1 +0,0 @@
-DIST arachne-46233.tar.gz 5161566 BLAKE2B dc9381fae80477e4a2439e24cbcf9bc462c7a4effb06c26a9f74ad1740f86a96273c3dae142d0065aad08d6340e9508528c35ee6914a8405b66327bfc4ec89da SHA512 4ab293e7f4477dd6aeba7c6bc1a78d168cbb811d7f67cbcbc1eea094a7b6bd180bdde6fb1b7c8256ff473dba3d748a43bd426d971575f1c0793289a0b200dc2b
diff --git a/sci-biology/arachne/arachne-46233.ebuild b/sci-biology/arachne/arachne-46233.ebuild
deleted file mode 100644
index 9efa4a5d4..000000000
--- a/sci-biology/arachne/arachne-46233.ebuild
+++ /dev/null
@@ -1,40 +0,0 @@
-# Copyright 1999-2016 Gentoo Foundation
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=5
-
-DESCRIPTION="Whole genome shotgun OLC assembler for Sanger reads (overlap-layout-contig)"
-HOMEPAGE="https://www.broadinstitute.org/crd/wiki
-	http://genome.cshlp.org/content/12/1/177.abstract"
-SRC_URI="ftp://ftp.broadinstitute.org/pub/crd/ARACHNE/latest_source_code/${P}.tar.gz"
-
-LICENSE="MIT" # not exactly MIT ... hence no KEYWORDS
-SLOT="0"
-KEYWORDS=""
-IUSE="doc openmp"
-
-DEPEND="dev-libs/xerces-c
-	doc? ( virtual/latex-base app-text/dvipsk )"
-RDEPEND="${DEPEND}"
-
-# needs >=g++-4.7 but does not compile with 5.3.0
-
-# --disable-openmp to disable requirement for OpenMP-capable compiler
-src_configure() {
-	local myconf=()
-	use openmp || myconf+=( --disable-openmp )
-	econf ${myconf[@]}
-}
-
-# set the following environment variables
-# http://www.broadinstitute.org/crd/wiki/index.php/Setup
-#
-# ARACHNE_PRE
-# ARACHNE_BIN_DIR
-# ARACHNE_PRETTY_HELP
-
-pkg_postinst(){
-	einfo "Please add these to your ~/.bashrc"
-	einfo "limit stacksize 100000"
-	einfo "limit datasize unlimited"
-}
diff --git a/sci-biology/arachne/metadata.xml b/sci-biology/arachne/metadata.xml
deleted file mode 100644
index 138cb7705..000000000
--- a/sci-biology/arachne/metadata.xml
+++ /dev/null
@@ -1,12 +0,0 @@
-<?xml version="1.0" encoding="UTF-8"?>
-<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
-<pkgmetadata>
-	<maintainer type="person">
-		<email>mmokrejs@fold.natur.cuni.cz</email>
-		<name>Martin Mokrejs</name>
-	</maintainer>
-	<maintainer type="project">
-		<email>sci-biology@gentoo.org</email>
-		<name>Gentoo Biology Project</name>
-	</maintainer>
-</pkgmetadata>
diff --git a/sci-biology/arcs/Manifest b/sci-biology/arcs/Manifest
new file mode 100644
index 000000000..af365300f
--- /dev/null
+++ b/sci-biology/arcs/Manifest
@@ -0,0 +1 @@
+DIST arcs-1.2.2.tar.gz 325997 BLAKE2B da03aa0533ad5dea2b736c97df09a5740bb05dfbf7dc9c35bab727212d18b29375433f44877fa98a5c8c317d497b78579cc0361490c4a7656bef5d639c59b1cb SHA512 07c5b2992859a77ee04c09134580888b7a5ec031fd2e864df781590a3c5a90eca3bf5026f7849d0aa66e51a779e5a01e555226320824d1dc148cb21e24daa017
diff --git a/sci-biology/arcs/arcs-1.2.2.ebuild b/sci-biology/arcs/arcs-1.2.2.ebuild
new file mode 100644
index 000000000..44a77c335
--- /dev/null
+++ b/sci-biology/arcs/arcs-1.2.2.ebuild
@@ -0,0 +1,35 @@
+# Copyright 1999-2021 Gentoo Authors
+# Distributed under the terms of the GNU General Public License v2
+
+EAPI=7
+
+DESCRIPTION="Scaffold genome sequence assemblies by Chromium/PacBio/Naopore reads"
+HOMEPAGE="https://github.com/bcgsc/arcs"
+SRC_URI="https://github.com/bcgsc/arcs/releases/download/v${PV}/${P}.tar.gz"
+
+LICENSE="GPL-3"
+SLOT="0"
+KEYWORDS="~amd64 ~x86"
+
+IUSE="minimal"
+
+# TODO: fix this
+# FileNotFoundError: [Errno 2] No such file or directory
+# happens even with --install
+RESTRICT="test"
+
+RDEPEND="
+	dev-libs/boost
+	dev-cpp/sparsehash
+	!minimal? (
+		sci-biology/abyss
+		sci-biology/tigmint
+	)
+"
+# !minimal? ( sci-biology/LINKS )
+
+src_install(){
+	default
+	insinto /usr/share/"${PN}"
+	doins -r Examples
+}
diff --git a/dev-perl/Bio-DB-HTS/metadata.xml b/sci-biology/arcs/metadata.xml
index 138cb7705..138cb7705 100644
--- a/dev-perl/Bio-DB-HTS/metadata.xml
+++ b/sci-biology/arcs/metadata.xml
diff --git a/sci-biology/argo-bin/Manifest b/sci-biology/argo-bin/Manifest
deleted file mode 100644
index fd419cbb2..000000000
--- a/sci-biology/argo-bin/Manifest
+++ /dev/null
@@ -1,2 +0,0 @@
-DIST argo.jar 26624770 BLAKE2B 2da6c978c5fa80c2a9026c4264cfafb2683dea1db0587a382480ba2d1f7d5af07e78672ca5cdfbd38ce8fb4dd49b1ecfdbadcafe4a17f1f801d05934f726dcd0 SHA512 fc1aaa39453502054d402386d3551014d71a81a73593420fe5073a462b3f605e00e8b32e21e54a4f669a3f09a25e8946db17928c65c17beea26ec4316e91458d
-DIST argo2.jar 27685069 BLAKE2B 402e4a837caaa2d31e2287c4946b89116e0b3dabe40b75ce15657fab605f4f92ed9178e457d11f74950dede3b2e1f51e7e0c08411077e5c29e9a571f7849b56e SHA512 8a03cfe6016ffa2d661dbf04ce9fde6e5474fcf111336399c934c481a4c71758b3007a20f3af931725c9e2f5f2bf3bc0c1d131cdda6e57992c10a6c0854207a8
diff --git a/sci-biology/argo-bin/argo-bin-1.0.31.ebuild b/sci-biology/argo-bin/argo-bin-1.0.31.ebuild
deleted file mode 100644
index 5f0fae0dc..000000000
--- a/sci-biology/argo-bin/argo-bin-1.0.31.ebuild
+++ /dev/null
@@ -1,29 +0,0 @@
-# Copyright 1999-2015 Gentoo Foundation
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=5
-
-inherit java-utils-2 toolchain-funcs
-
-DESCRIPTION="Visualization and manually annotating whole genomes"
-HOMEPAGE="http://www.broadinstitute.org/annotation/argo2
-	http://www.broadinstitute.org/annotation/argo"
-SRC_URI="http://www.broadinstitute.org/annotation/argo/argo.jar"
-#
-# Release Number: 1.0.31
-# Release Date:   2010-02-05
-
-LICENSE="LGPL-3"
-SLOT="0"
-KEYWORDS="~amd64 ~x86"
-IUSE=""
-
-DEPEND="!sci-biology/argo"
-RDEPEND="${DEPEND}
-		>=virtual/jre-1.5:*"
-S="${WORKDIR}"
-
-src_install() {
-	java-pkg_newjar "${DISTDIR}"/argo.jar argo.jar
-	java-pkg_dolauncher
-}
diff --git a/sci-biology/argo-bin/argo-bin-2.0.3.ebuild b/sci-biology/argo-bin/argo-bin-2.0.3.ebuild
deleted file mode 100644
index 7a6547fb8..000000000
--- a/sci-biology/argo-bin/argo-bin-2.0.3.ebuild
+++ /dev/null
@@ -1,29 +0,0 @@
-# Copyright 1999-2015 Gentoo Foundation
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=5
-
-inherit java-utils-2 toolchain-funcs
-
-DESCRIPTION="Visualization and manually annotating whole genomes"
-HOMEPAGE="http://www.broadinstitute.org/annotation/argo2
-	http://www.broadinstitute.org/annotation/argo"
-SRC_URI="http://www.broadinstitute.org/annotation/argo2/releases/argo2.jar"
-#
-# Release Number: 3
-# Release Date:   2010-06-23
-
-LICENSE="LGPL-3"
-SLOT="0"
-KEYWORDS="~amd64 ~x86"
-IUSE=""
-
-DEPEND="!sci-biology/argo"
-RDEPEND="${DEPEND}
-		>=virtual/jre-1.5:*"
-S="${WORKDIR}"
-
-src_install() {
-	java-pkg_newjar "${DISTDIR}"/argo2.jar argo2.jar
-	java-pkg_dolauncher
-}
diff --git a/sci-biology/argo-bin/metadata.xml b/sci-biology/argo-bin/metadata.xml
deleted file mode 100644
index 138cb7705..000000000
--- a/sci-biology/argo-bin/metadata.xml
+++ /dev/null
@@ -1,12 +0,0 @@
-<?xml version="1.0" encoding="UTF-8"?>
-<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
-<pkgmetadata>
-	<maintainer type="person">
-		<email>mmokrejs@fold.natur.cuni.cz</email>
-		<name>Martin Mokrejs</name>
-	</maintainer>
-	<maintainer type="project">
-		<email>sci-biology@gentoo.org</email>
-		<name>Gentoo Biology Project</name>
-	</maintainer>
-</pkgmetadata>
diff --git a/sci-biology/argo/Manifest b/sci-biology/argo/Manifest
deleted file mode 100644
index 59a49566f..000000000
--- a/sci-biology/argo/Manifest
+++ /dev/null
@@ -1 +0,0 @@
-DIST workspace-2008-03-11.tgz 109194467 BLAKE2B 8554b08770d4cf2ecb29a348de06d304f778623e1f253ceb28876620292aba7c34981f254cbfa7a13e9d6bfec35106316482aaeb137eb10e5eeb2da3e8bf4b59 SHA512 42696ac2a4dc0167d9fb84d8420254e4ba9256447ef320c1ca3906aac48944635397098962ee5a207b39afacc0faa2dc584e96c29ab1dead9892d6ff85228820
diff --git a/sci-biology/argo/argo-1.0.24.ebuild b/sci-biology/argo/argo-1.0.24.ebuild
deleted file mode 100644
index 218f74705..000000000
--- a/sci-biology/argo/argo-1.0.24.ebuild
+++ /dev/null
@@ -1,39 +0,0 @@
-# Copyright 1999-2015 Gentoo Foundation
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=5
-
-inherit java-pkg-2 java-ant-2 java-utils-2 toolchain-funcs
-
-DESCRIPTION="Production tool for visualizing and manually annotating whole genomes"
-HOMEPAGE="http://www.broadinstitute.org/annotation/argo2
-	http://www.broadinstitute.org/annotation/argo"
-SRC_URI="http://www.broadinstitute.org/annotation/argo/src/workspace-2008-03-11.tgz"
-#
-# cat workspace-2008-03-11/annotation/argo/version.txt
-# Gebo-1.0.17-build-1313
-
-LICENSE="LGPL-3"
-SLOT="0"
-KEYWORDS="~amd64 ~x86"
-IUSE=""
-
-DEPEND="
-	!sci-biology/argo-bin
-	>=virtual/jdk-1.5:*
-	dev-java/ant-core"
-RDEPEND=">=virtual/jre-1.5:*"
-
-S="${WORKDIR}"/workspace-2008-03-11
-
-src_compile(){
-	cd "${S}"/annotation/argo
-	ant build || die
-}
-
-src_install() {
-	java-pkg_dojar annotation/dist/argo/argo.jar
-	#java-pkg_dolauncher --jar argo.jar
-	java-pkg_dojar annotation/dist/argo/argo-applet-unproguarded.jar
-	#java-pkg_dolauncher --jar argo-applet-unproguarded.jar
-}
diff --git a/sci-biology/argo/metadata.xml b/sci-biology/argo/metadata.xml
deleted file mode 100644
index 138cb7705..000000000
--- a/sci-biology/argo/metadata.xml
+++ /dev/null
@@ -1,12 +0,0 @@
-<?xml version="1.0" encoding="UTF-8"?>
-<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
-<pkgmetadata>
-	<maintainer type="person">
-		<email>mmokrejs@fold.natur.cuni.cz</email>
-		<name>Martin Mokrejs</name>
-	</maintainer>
-	<maintainer type="project">
-		<email>sci-biology@gentoo.org</email>
-		<name>Gentoo Biology Project</name>
-	</maintainer>
-</pkgmetadata>
diff --git a/sci-biology/artemis/Manifest b/sci-biology/artemis/Manifest
deleted file mode 100644
index 230e664f0..000000000
--- a/sci-biology/artemis/Manifest
+++ /dev/null
@@ -1,2 +0,0 @@
-DIST artemis-9999.html_build.zip 2284822 BLAKE2B 4b29d2f503418e12433d9528bab618e1c98d3b6d54704dc8b7e443c9bbddd716a063810559a0680015ba396d76cedc4f76cc98bd822c97207ac17b9d98162631 SHA512 80c952fe20f98b647f38a08a469cb351bb44aa1b0a7d1a9b997fabbd37107d5d934a6d52fa2abfde243f90f4e752c99d418c4ad6b634d82de9744d089eb1cf8a
-DIST artemis-9999.manual.pdf 1149449 BLAKE2B 683583db0238bda801cd7fa3c915be41da53eb9d3b4e6e1fa1dfa5ce70585e483892263cd6d6a68ab6689d5663243897d6e6a758024a3a9644681ffe917bc972 SHA512 1c3056dab7239c3a68b2e76491d77612f22ac8f83eaf32e0ab0a3901e03d3c65d5ac02f5758d2d7728d94dd44c29517a498fa94a947d5d319ded43ddec4ba5fb
diff --git a/sci-biology/artemis/artemis-9999.ebuild b/sci-biology/artemis/artemis-9999.ebuild
deleted file mode 100644
index 162cc67e7..000000000
--- a/sci-biology/artemis/artemis-9999.ebuild
+++ /dev/null
@@ -1,70 +0,0 @@
-# Copyright 1999-2017 Gentoo Foundation
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=6
-
-inherit java-pkg-2 java-ant-2 git-r3
-
-DESCRIPTION="DNA sequence viewer/annotation (Artemis) and comparison (ACT) tool"
-HOMEPAGE="http://www.sanger.ac.uk/resources/software/artemis"
-SRC_URI="
-	ftp://ftp.sanger.ac.uk/pub/resources/software/artemis/artemis.pdf -> ${P}.manual.pdf
-	ftp://ftp.sanger.ac.uk/pub/resources/software/artemis/v16/art_html_build.zip -> ${P}.html_build.zip"
-EGIT_REPO_URI="https://github.com/sanger-pathogens/Artemis"
-
-LICENSE="GPL-2"
-SLOT="0"
-KEYWORDS=""
-IUSE=""
-
-# uses its own BamView
-RDEPEND="
-	sci-biology/samtools:0
-	>=virtual/jre-1.6:*"
-DEPEND="${RDEPEND}
-	!sci-biology/artemis-bin
-	dev-java/ant-core
-	>=virtual/jdk-1.6:*
-	dev-java/log4j
-	dev-java/jdbc-postgresql
-	dev-java/jakarta-regexp
-	dev-java/batik
-	dev-java/j2ssh
-	sci-biology/picard
-	dev-java/biojava"
-# some more dependencies extracted from /usr/bin/act
-# JacORB.jar, jemAlign.jar, macos.jar, chado-14-interface.jar, iBatis, biojava.jar,
-#
-
-# http://www.mail-archive.com/artemis-users@sanger.ac.uk/msg00551.html
-# http://www.mail-archive.com/artemis-users@sanger.ac.uk/msg00561.html
-# http://gmod.org/wiki/Artemis-Chado_Integration_Tutorial
-
-# BamView is at http://bamview.sourceforge.net/
-
-src_unpack(){
-	unzip "${DISTDIR}"/art_html_build.zip || die
-}
-
-src_compile(){
-	ant || die
-}
-
-src_install(){
-	dobin act act.command art dnaplotter gff2embl
-	java-pkg_dojar ant-build/artemis.jar
-	dodoc "${DISTDIR}"/"${P}".manual.pdf README
-	insinto /usr/share/doc/"${PN}"/html
-	doins art_html_build/*
-}
-
-# artemis_compiled_v16.0.11.tar.gz contains compiled binaries but also java *.class files
-# artemis_v16.0.11.jar and sartemis_v16.0.11.jar
-#   ftp://ftp.sanger.ac.uk/pub/resources/software/artemis/v16/v16.0.11/
-
-pkg_postinst(){
-	einfo "For BAM file support please install sci-biology/BamView"
-	einfo "You may find interesting the additional web resources:"
-	einfo "http://www.webact.org/WebACT"
-	einfo "http://www.hpa-bioinfotools.org.uk/pise/double_act.html"
-}
diff --git a/sci-biology/artemis/metadata.xml b/sci-biology/artemis/metadata.xml
deleted file mode 100644
index 138cb7705..000000000
--- a/sci-biology/artemis/metadata.xml
+++ /dev/null
@@ -1,12 +0,0 @@
-<?xml version="1.0" encoding="UTF-8"?>
-<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
-<pkgmetadata>
-	<maintainer type="person">
-		<email>mmokrejs@fold.natur.cuni.cz</email>
-		<name>Martin Mokrejs</name>
-	</maintainer>
-	<maintainer type="project">
-		<email>sci-biology@gentoo.org</email>
-		<name>Gentoo Biology Project</name>
-	</maintainer>
-</pkgmetadata>
diff --git a/sci-biology/assembly-stats/assembly-stats-9999.ebuild b/sci-biology/assembly-stats/assembly-stats-9999.ebuild
index 4245707f7..86727eab1 100644
--- a/sci-biology/assembly-stats/assembly-stats-9999.ebuild
+++ b/sci-biology/assembly-stats/assembly-stats-9999.ebuild
@@ -1,9 +1,9 @@
-# Copyright 1999-2016 Gentoo Foundation
+# Copyright 1999-2021 Gentoo Authors
 # Distributed under the terms of the GNU General Public License v2
 
-EAPI=5
+EAPI=7
 
-inherit git-r3 cmake-utils
+inherit git-r3 cmake
 
 DESCRIPTION="Assembly statistics (min, max, sum, N50, N90, count gaps and Ns)"
 HOMEPAGE="https://github.com/martinghunt/assembly-stats"
@@ -12,7 +12,6 @@ EGIT_REPO_URI="https://github.com/martinghunt/assembly-stats.git"
 LICENSE="GPL-3"
 SLOT="0"
 KEYWORDS=""
-IUSE=""
 
 DEPEND=">=dev-cpp/gtest-1.7.0"
 RDEPEND="${DEPEND}"
@@ -20,9 +19,5 @@ RDEPEND="${DEPEND}"
 # TODO: should not even try to compile bundled gtest
 src_prepare(){
 	sed -e "s#/usr/local/bin#${EPREFIX}/usr/bin#" -i CMakeLists.txt || die
-}
-
-src_install(){
-	dobin ../assembly-stats-9999_build/assembly-stats
-	dodoc README.md
+	cmake_src_prepare
 }
diff --git a/sci-biology/augustus/Manifest b/sci-biology/augustus/Manifest
deleted file mode 100644
index a36bf206c..000000000
--- a/sci-biology/augustus/Manifest
+++ /dev/null
@@ -1 +0,0 @@
-DIST augustus-3.3.tar.gz 125296783 BLAKE2B 37479eb1eb8cf702438e4c0da659bf43133fb8268960c3e4f0357c105b740447d903a198cb9de06cbbc4d237dd03daefd662afdc35615edefe5f36ddc832ed2c SHA512 c6acfc5cb358cac60b68da7e726a871ad898654e154ccb83d86f1a13aa45643b0e63f2af1017a8ab12616677818709abefb1df4b40b6f7b971c18dbc7519837f
diff --git a/sci-biology/augustus/augustus-3.3.ebuild b/sci-biology/augustus/augustus-3.3.ebuild
deleted file mode 100644
index b2b19a04e..000000000
--- a/sci-biology/augustus/augustus-3.3.ebuild
+++ /dev/null
@@ -1,70 +0,0 @@
-# Copyright 1999-2018 Gentoo Foundation
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=5
-
-inherit eutils toolchain-funcs
-
-DESCRIPTION="Eukaryotic gene predictor"
-HOMEPAGE="http://augustus.gobics.de/"
-SRC_URI="http://bioinf.uni-greifswald.de/augustus/binaries/${P}.tar.gz"
-
-LICENSE="GPL-3"
-# temporary drop in licensing scheme, see http://stubber.math-inf.uni-greifswald.de/bioinf/augustus/binaries/HISTORY.TXT
-# http://stubber.math-inf.uni-greifswald.de/bioinf/augustus/binaries/LICENCE.TXT
-# LICENSE="Artistic"
-SLOT="0"
-KEYWORDS="~amd64 ~x86"
-IUSE="examples"
-
-# TODO: provide USE for mysql and sqlite, edit src/Makefile to reflect paths
-#       and common.mk 
-RDEPEND="
-	sci-mathematics/lpsolve
-	sci-libs/gsl
-	dev-libs/boost
-	sys-libs/zlib"
-DEPEND="${RDEPEND}
-	sys-devel/flex"
-S="${WORKDIR}/${PN}"
-
-src_prepare() {
-	# TODO: do we need anything from the 2.5.5 patch?
-	# epatch "${FILESDIR}"/${P}-sane-build.patch
-	tc-export CC CXX
-	sed -e 's/ -O3//g' -i src/Makefile || die
-	# enable comparative gene prediction (needs c++11 compiler),
-	#    this needs sci-mathematics/lpsolve
-	sed -e 's/^# COMPGENEPRED/COMPGENEPRED/' -i common.mk || die
-	# respect $EPREFIX at src/Makefile, auxprogs/bam2hints/Makefile, more?
-	find . -name Makefile | while read f; do \
-		sed -s 's#/usr/include#${EPREFIX}/usr/include#' -i $f || die;
-	done
-}
-
-src_compile() {
-	emake clean && default
-}
-
-src_install() {
-	dobin bin/*
-#	dobin src/{augustus,etraining,consensusFinder,curve2hints,fastBlockSearch,prepareAlign}
-
-	exeinto /usr/libexec/${PN}
-	doexe scripts/*.p*
-	insinto /usr/libexec/${PN}
-	doins scripts/*.conf
-
-	insinto /usr/share/${PN}
-	doins -r config
-
-	echo "AUGUSTUS_CONFIG_PATH=\"/usr/share/${PN}/config\"" > "${S}/99${PN}"
-	doenvd "${S}/99${PN}"
-
-	dodoc -r README.TXT HISTORY.TXT docs/*.{pdf,txt}
-
-	if use examples; then
-		insinto /usr/share/${PN}/
-		doins -r docs/tutorial examples
-	fi
-}
diff --git a/sci-biology/autoeditor/Manifest b/sci-biology/autoeditor/Manifest
deleted file mode 100644
index 9ea148189..000000000
--- a/sci-biology/autoeditor/Manifest
+++ /dev/null
@@ -1,2 +0,0 @@
-DIST autoEditor-1.20-sample.tar.gz 71953287 BLAKE2B 531c524f70084d1b69fab801d4ab66c034dd25942c84af058cd6f3a2df3fabf88da0ea19c645e2de39be14c2054b4a36fd10a40d058862366b1d0843194152fc SHA512 4446f5f565621f51590db6ecd53c0c789a058756caf4be67cc15599c0054000487e10651f4b9f4ad03c6db6bcb9229c66e06b6217fbdb62ab51013669a4645a6
-DIST autoEditor-1.20.tar.gz 2438903 BLAKE2B 91b0c943fd3eb202188cd90cf290e2624ad5c27e9302bd93ecb2b4330a9dcc9b584c2023fb3ca2b9ccf6abf705bde0b3144f1ad48661113750d325969af631e2 SHA512 8599168296ead35621d1e6cd159852e7a05ce2f6de38d70058900e0a4d701f4aa146381221bcc0e7e63844f14141ff86c2d81c19d14a8e4a3e836186349dac5d
diff --git a/sci-biology/autoeditor/autoeditor-1.20.ebuild b/sci-biology/autoeditor/autoeditor-1.20.ebuild
deleted file mode 100644
index 5e4c631b7..000000000
--- a/sci-biology/autoeditor/autoeditor-1.20.ebuild
+++ /dev/null
@@ -1,40 +0,0 @@
-# Copyright 1999-2015 Gentoo Foundation
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=5
-
-inherit eutils
-
-DESCRIPTION="Automatic correct of discrepancies in multiple sequence alignments"
-HOMEPAGE="http://sourceforge.net/apps/mediawiki/amos/index.php?title=AutoEditor"
-SRC_URI="
-	ftp://ftp.cbcb.umd.edu/pub/software/autoEditor/autoEditor-1.20.tar.gz
-	test? ( ftp://ftp.cbcb.umd.edu/pub/software/autoEditor/autoEditor-1.20-sample.tar.gz )"
-
-LICENSE="Artistic"
-SLOT="0"
-KEYWORDS="~amd64 ~x86"
-IUSE="test"
-
-DEPEND="
-	>=sci-libs/io_lib-1.8.11
-	sci-biology/tigr-foundation-libs
-	sys-libs/zlib"
-RDEPEND="${DEPEND}"
-
-S="${WORKDIR}"/autoEditor-1.20
-
-src_prepare(){
-	epatch "${FILESDIR}"/Makefile.patch
-	rm -rf TigrFoundation-2.0 || die "Failed to drop TigrFoundation-2.0/"
-}
-
-# TODO:
-#  * QA Notice: Package has poor programming practices which may compile
-#  *            fine but exhibit random runtime failures.
-#  * getConsQV.c:1051: warning: implicit declaration of function 'memset'
-
-src_test(){
-	emake sample > sample.out
-	diff -u -w "${FILESDIR}"/sample_expected.out sample.out || die
-}
diff --git a/sci-biology/autoeditor/files/Makefile.patch b/sci-biology/autoeditor/files/Makefile.patch
deleted file mode 100644
index 643b1e452..000000000
--- a/sci-biology/autoeditor/files/Makefile.patch
+++ /dev/null
@@ -1,100 +0,0 @@
---- Makefile	2009-11-23 23:29:24.000000000 +0100
-+++ /tmp/Makefile	2010-12-05 15:06:53.000000000 +0100
-@@ -3,7 +3,7 @@
- 
- # $Id: Makefile,v 1.2 2009/11/23 22:29:24 mschatz Exp $
- 
--INSTALL_DIR = /usr/local/bin
-+INSTALL_DIR = $(DESTDIR)/bin
- 
- PROG_NAME = autoEditor
- all: $(PROG_NAME)
-@@ -56,10 +56,9 @@
- RAWCOBJS = $(SRCS:.c=.o)
- OBJS     = $(RAWCOBJS:.cc=.o)
- 
--TF_ROOT  = TigrFoundation-2.0
- LIBSLICE = libSlice-1.0
- 
--IOLIB      = ${PWD}/io_lib-1.8.11/install
-+IOLIB      = /usr
- IO_LIB_INC = $(IOLIB)/include/io_lib
- IO_LIB_LIB = $(IOLIB)/lib
- 
-@@ -68,8 +67,6 @@
- 
- DEFINES      = -DUSE_ZLIB -DUSE_CPP_FRONTEND
- 
--DEBUG = -O2 -g
--
- LFS=-D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE
- 
- ifeq ($(HOSTTYPE), alpha)
-@@ -96,32 +93,12 @@
- endif
- 
- CFLAGS   = -Wall $(DEBUG) $(DEFINES) $(INC) ${LFS}
--CPPFLAGS = $(CFLAGS) -I$(TF_ROOT) -L$(TF_ROOT) -D_HAS_GETOPT
--LDLIBS   = -lSlice -lTigrFoundation -lm -lread -lz 
--
-+CPPFLAGS = $(CFLAGS) -D_HAS_GETOPT
-+LDLIBS   = -lSlice -lTigrFoundation -lm -lstaden-read -lz 
- 
--${IOLIB}/lib/libread.la:
--	cd io_lib-1.8.11;                                             \
--  rm -Rf ${IOLIB};                                              \
--  if [ -e Makefile ] ; then make distclean; fi;                 \
--  ./configure --prefix=${IOLIB};                                \
--  make;                                                         \
--  make install;                                                 \
--  cp os.h ${IOLIB}/include/io_lib;                              \
--  cp config.h ${IOLIB}/include/io_lib;                          \
--  if [ -e ${IOLIB}/lib/libread.so ];                            \
--    then mv ${IOLIB}/lib/libread.so ${IOLIB}/lib/libread-so.so; \
--  fi;
- 
- libSlice-1.0/libSlice.a:
- 	cd libSlice-1.0; \
--	CXXFLAGS="-I../TigrFoundation-2.0 -L../TigrFoundation-2.0" \
--  CC=$(CC) \
--  CXX=$(CXX) \
--  make;
--
--TigrFoundation-2.0/libTigrFoundation.a:
--	cd TigrFoundation-2.0; \
-   CC=$(CC)   \
-   CXX=$(CXX) \
-   make;
-@@ -129,9 +106,7 @@
- 
- 
- # Rule for linking all of the objects into the program
--$(PROG_NAME): ${IOLIB}/lib/libread.la                \
--              TigrFoundation-2.0/libTigrFoundation.a \
--              libSlice-1.0/libSlice.a                \
-+$(PROG_NAME): libSlice-1.0/libSlice.a                \
-               $(OBJS)
- 	$(CXX) $(CPPFLAGS) -o $@ $(OBJS) $(LDLIBS);                 \
-   echo;                                                       \
-@@ -144,18 +119,13 @@
-   cd libSlice-1.0;            \
-   make clean;                 \
-   cd ..;                      \
--  cd TigrFoundation-2.0;      \
--  make clean;                 \
--  cd ..;                      \
--  cd io_lib-1.8.11;           \
--  rm -Rf install;             \
--  if [ -e Makefile ]; then make distclean; fi;
- 
- sample: ${PROG_NAME}
- 	./${PROG_NAME} -v -c sample/29713/chromo sample/29713/29713
- 
- install: ${PROG_NAME}
--	cp ${PROG_NAME} ${INSTALL_DIR}
-+	mkdir -p $(DESTDIR)/bin || exit
-+	cp ${PROG_NAME} $(DESTDIR)/bin/
- 
- uninstall:
--	rm ${INSTALL_DIR}/${PROG_NAME}
-+	rm ${DESTDIR}/${PROG_NAME}
diff --git a/sci-biology/autoeditor/files/sample_expected.out b/sci-biology/autoeditor/files/sample_expected.out
deleted file mode 100644
index e792b8455..000000000
--- a/sci-biology/autoeditor/files/sample_expected.out
+++ /dev/null
@@ -1,22 +0,0 @@
-./autoEditor -v -c sample/29713/chromo sample/29713/29713
-Creating index of offsets of seq_ids in sample/29713/29713.seq ... done
-Creating index of offsets of seq_ids in sample/29713/29713.qual ... done
-Creating index of offsets of seq_ids in sample/29713/29713.pos ... done
-ENTERING THE MAIN LOOP ... 
-Processing asmbl 29713  44 reads
-        Parsing sample/29713/29713.qual file ... done
-        Aligning sequences to the consensus sequence ... done
-        Parsing sample/29713/29713.seq file ... done
-        Parsing sample/29713/29713.pos file ... done
-        Correcting errors ... done
-        Freeing tiling data ... done
-        Aligning sequences to the consensus sequence ... done
-        Recalling consensus sequence values and their quality classes ... done
-        Correcting gap slices ... done
-        Freeing tiling data ... done
-        Aligning sequences to the consensus sequence ... done
-        Creating new contig, qual, and seq files ... done
-        Freeing tiling data ... done
-        Freeing sequence data ... done
-        Flushing Trace Cache ... done
-DONE WITH THE MAIN LOOP in 0min 1sec
diff --git a/sci-biology/autoeditor/metadata.xml b/sci-biology/autoeditor/metadata.xml
deleted file mode 100644
index a9237cbcc..000000000
--- a/sci-biology/autoeditor/metadata.xml
+++ /dev/null
@@ -1,25 +0,0 @@
-<?xml version="1.0" encoding="UTF-8"?>
-<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
-<pkgmetadata>
-	<maintainer type="person">
-		<email>mmokrejs@fold.natur.cuni.cz</email>
-		<name>Martin Mokrejs</name>
-	</maintainer>
-	<maintainer type="project">
-		<email>sci-biology@gentoo.org</email>
-		<name>Gentoo Biology Project</name>
-	</maintainer>
-	<longdescription>AutoEditor is a program that can automatically correct discrepancies in a
-multiple alignment by reanalyzing the chromatograms of the discrepant bases.
-The input to AutoEditor is the multiple alignment in contig form, the sequence
-and quality values in FASTA format, and the base call positions in
-"SEQNAME basecallpositions\n" format where the basecall positions are written
-in hex (4 nibbles per basecall position) concatentated together. The path
-to the chromatograms for the sequences should be specified with the -c option.
-More help is available with -h.
-
-The output is to a timestamped autoEditor directory that has the input files
-edited along with other TIGR specific file formats. Sample input data is
-provided with the distribution in the sample directory.
-</longdescription>
-</pkgmetadata>
diff --git a/sci-biology/bam-readcount/bam-readcount-0.8.0.ebuild b/sci-biology/bam-readcount/bam-readcount-0.8.0.ebuild
index 9c242afc1..1cdc8a5a3 100644
--- a/sci-biology/bam-readcount/bam-readcount-0.8.0.ebuild
+++ b/sci-biology/bam-readcount/bam-readcount-0.8.0.ebuild
@@ -1,9 +1,9 @@
-# Copyright 1999-2018 Gentoo Foundation
+# Copyright 1999-2021 Gentoo Authors
 # Distributed under the terms of the GNU General Public License v2
 
-EAPI=5
+EAPI=7
 
-inherit cmake-utils
+inherit cmake
 
 DESCRIPTION="Count DNA sequence reads in BAM files and other statistics calculations"
 HOMEPAGE="https://github.com/genome/bam-readcount"
@@ -12,7 +12,3 @@ SRC_URI="https://github.com/genome/bam-readcount/archive/v${PV}.tar.gz -> ${P}.t
 LICENSE="MIT"
 SLOT="0"
 KEYWORDS="~amd64 ~x86"
-IUSE=""
-
-DEPEND=""
-RDEPEND="${DEPEND}"
diff --git a/sci-biology/bam-readcount/bam-readcount-9999.ebuild b/sci-biology/bam-readcount/bam-readcount-9999.ebuild
index a9b8c4f0b..7dceb06e6 100644
--- a/sci-biology/bam-readcount/bam-readcount-9999.ebuild
+++ b/sci-biology/bam-readcount/bam-readcount-9999.ebuild
@@ -1,9 +1,9 @@
-# Copyright 1999-2017 Gentoo Foundation
+# Copyright 1999-2021 Gentoo Authors
 # Distributed under the terms of the GNU General Public License v2
 
-EAPI=5
+EAPI=7
 
-inherit git-r3 cmake-utils
+inherit git-r3 cmake
 
 DESCRIPTION="Count DNA sequence reads in BAM files and other statistics calculations"
 HOMEPAGE="https://github.com/genome/bam-readcount"
@@ -12,7 +12,3 @@ EGIT_REPO_URI="https://github.com/genome/bam-readcount.git"
 LICENSE="MIT"
 SLOT="0"
 KEYWORDS=""
-IUSE=""
-
-DEPEND=""
-RDEPEND="${DEPEND}"
diff --git a/sci-biology/bambino/Manifest b/sci-biology/bambino/Manifest
deleted file mode 100644
index e1a6f4d16..000000000
--- a/sci-biology/bambino/Manifest
+++ /dev/null
@@ -1,4 +0,0 @@
-DIST bambino_bundle_1.02.jar 1593449 SHA256 ae74319d78b55edf3c62877e77e93c4755a1d1bed589bba4980db096f891557b SHA512 947a3e99035523881671f34f4f5b567c84ffff4b95ab5df11ff6ce7c55805b769967b20b55aed8edf97bee4ba6e164c38cdc96546ef65edcc73b4e5941069da6 WHIRLPOOL c9bc342000080a552ab47f14ce4e38693ab748b13a4b76a20a538388f3480c9b9cf66574f01b82e03fe99af3bfe7d10aaa8027fec74b1d8e7122b46c2c7699fc
-DIST bambino_bundle_1.06.jar 615286 SHA256 31ec3858dbe1717c4460e3eaed107b23a2921a5d690626397b896a89ea40a75d SHA512 576af57ad252521d59f14a7603f2cb5c5dd4b14e7a2e4ff643b6739fa64cf7fddc644e38300f65a1e8ac4128f6ce013ee2115550443bc8555bc7a0e5c8cfad82 WHIRLPOOL 46eeaef912c93cc01d67a416cb0d12d95cafe6b63aeac2f13a47f85eeb9741f8a5eb291d835fe9a7c0709144e169e711e783b4783a2d97cd9e2f4275069d8288
-DIST bambino_core_1.02.jar 595652 SHA256 9a597afccb07341be916f2603097b7d4b5f983f8fc973a434660703ff0fa879a SHA512 cbdb9a719a4afc80d6c78bf8459171f6d53e31df81a74025cb9590eaa656669735d907457b6d52dd0d787eeec0225280b846248746db25808c3383e84b981f11 WHIRLPOOL 818d55f58f7c9744f081c767ab9e20924acc4738df7dc520f7c72b26647e0c0e98cdfa8d7f5ed4bd05b1b830a56f60896273e0ec15892074d4f22599f92bedc9
-DIST bambino_core_1.06.jar 1750284 SHA256 9f528d374eb04cb7e37a61484f85087dc5e8bf8346205f658e05efa43b8cb593 SHA512 bae8abdf5683945599a68ece9b8909e65e6ce3a5e24c20892865bee4d791672864caf1953a438ad2ea45805109159647d2bbfb45c77794084f0ae06332892f1d WHIRLPOOL b0e275595723cca5af7bd166eff47b8a5abbaa9f8e13b495cef57fcb6730b734ca8a85b963fbb84dc9388ec77010c03530176200702a000c342a31bed0fa1e4b
diff --git a/sci-biology/bambino/bambino-1.02.ebuild b/sci-biology/bambino/bambino-1.02.ebuild
deleted file mode 100644
index bfbf3c42d..000000000
--- a/sci-biology/bambino/bambino-1.02.ebuild
+++ /dev/null
@@ -1,36 +0,0 @@
-# Copyright 1999-2015 Gentoo Foundation
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=5
-
-inherit java-pkg-2 eutils
-
-DESCRIPTION="display SAM/BAM files and for SNP/indel detection, report coverage in .wig files"
-HOMEPAGE="https://cgwb.nci.nih.gov/goldenPath/bamview/documentation/index.html
-	https://cgwb.nci.nih.gov/goldenPath/bamview/documentation/bam_utils.html"
-
-# bug #377305
-SRC_URI="https://cgwb.nci.nih.gov/cgi-bin/bambino?download_bambino_jar=bundle -> bambino_core_1.02.jar
-		https://cgwb.nci.nih.gov/cgi-bin/bambino?download_bambino_jar=core -> bambino_bundle_1.02.jar"
-
-LICENSE="bambino"
-SLOT="0"
-KEYWORDS="~amd64 ~x86"
-IUSE=""
-
-DEPEND=">=virtual/jdk-1.6:*"
-RDEPEND="${DEPEND}
-	>=virtual/jre-1.6:*
-	sci-biology/picard
-	dev-java/jdbc-mysql"
-
-src_install(){
-	insinto "${DESTDIR}"/usr/share/"${PN}"/lib
-	doins "${DISTDIR}"/bambino_core_"${PV}".jar
-	doins "${DISTDIR}"/bambino_bundle_"${PV}".jar
-
-	einfo "bambino can be run using 'java -jar /usr/share/bambino/lib/bambino_bundle_1.02.jar'"
-	einfo "  or 'java -jar /usr/share/bambino/lib/bambino_core_1.02.jar'"
-	einfo "More info at "${HOMEPAGE}
-
-}
diff --git a/sci-biology/bambino/bambino-1.06.ebuild b/sci-biology/bambino/bambino-1.06.ebuild
deleted file mode 100644
index 7e51cf0b2..000000000
--- a/sci-biology/bambino/bambino-1.06.ebuild
+++ /dev/null
@@ -1,36 +0,0 @@
-# Copyright 1999-2015 Gentoo Foundation
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=5
-
-inherit java-pkg-2 eutils
-
-DESCRIPTION="display SAM/BAM files and for SNP/indel detection, report coverage in .wig files"
-HOMEPAGE="https://cgwb.nci.nih.gov/goldenPath/bamview/documentation/index.html
-	https://cgwb.nci.nih.gov/goldenPath/bamview/documentation/bam_utils.html"
-
-# bug #377305
-SRC_URI="https://cgwb.nci.nih.gov/cgi-bin/bambino?download_bambino_jar=bundle -> bambino_core_1.06.jar
-		https://cgwb.nci.nih.gov/cgi-bin/bambino?download_bambino_jar=core -> bambino_bundle_1.06.jar"
-
-LICENSE="bambino"
-SLOT="0"
-KEYWORDS="~amd64 ~x86"
-IUSE=""
-
-DEPEND=">=virtual/jdk-1.6:*"
-RDEPEND="${DEPEND}
-	>=virtual/jre-1.6:*
-	sci-biology/picard
-	dev-java/jdbc-mysql"
-
-src_install(){
-	insinto "${DESTDIR}"/usr/share/"${PN}"/lib
-	doins "${DISTDIR}"/bambino_core_"${PV}".jar
-	doins "${DISTDIR}"/bambino_bundle_"${PV}".jar
-
-	einfo "bambino can be run using 'java -jar /usr/share/bambino/lib/bambino_bundle_1.06.jar'"
-	einfo "  or 'java -jar /usr/share/bambino/lib/bambino_core_1.06.jar'"
-	einfo "More info at "${HOMEPAGE}
-
-}
diff --git a/sci-biology/bambino/metadata.xml b/sci-biology/bambino/metadata.xml
deleted file mode 100644
index 138cb7705..000000000
--- a/sci-biology/bambino/metadata.xml
+++ /dev/null
@@ -1,12 +0,0 @@
-<?xml version="1.0" encoding="UTF-8"?>
-<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
-<pkgmetadata>
-	<maintainer type="person">
-		<email>mmokrejs@fold.natur.cuni.cz</email>
-		<name>Martin Mokrejs</name>
-	</maintainer>
-	<maintainer type="project">
-		<email>sci-biology@gentoo.org</email>
-		<name>Gentoo Biology Project</name>
-	</maintainer>
-</pkgmetadata>
diff --git a/sci-biology/bambus/bambus-2.33-r2.ebuild b/sci-biology/bambus/bambus-2.33-r2.ebuild
new file mode 100644
index 000000000..1cb7aad1b
--- /dev/null
+++ b/sci-biology/bambus/bambus-2.33-r2.ebuild
@@ -0,0 +1,100 @@
+# Copyright 1999-2022 Gentoo Authors
+# Distributed under the terms of the GNU General Public License v2
+
+EAPI=8
+
+inherit perl-module toolchain-funcs
+
+DESCRIPTION="Scaffolding Polymorphic Genomes and Metagenomes, a part of AMOS bundle"
+HOMEPAGE="
+	https://sourceforge.net/apps/mediawiki/amos/index.php?title=AMOS
+	https://sourceforge.net/projects/amos/files/bambus"
+SRC_URI="
+	https://sourceforge.net/projects/amos/files/bambus/${PV}/${P}.tar.gz
+	https://mira-assembler.sourceforge.net/docs/scaffolding_MIRA_BAMBUS.pdf"
+
+LICENSE="Artistic"
+SLOT="0"
+KEYWORDS="~amd64 ~x86"
+
+RDEPEND="
+	sci-biology/tigr-foundation-libs
+	dev-perl/XML-Parser
+	dev-perl/Config-IniFiles
+	dev-perl/GraphViz"
+DEPEND="${RDEPEND}"
+
+PATCHES=(
+	"${FILESDIR}"/TigrFoundation-all-patches.patch
+)
+
+src_prepare() {
+	default
+#	eapply "${FILESDIR}"/amos-2.0.8-gcc44.patch
+	sed -e 's:BASEDIR = /usr/local/packages/bambus:BASEDIR = /usr:' -i Makefile || die
+	sed -e 's:PERL = /usr/local/bin/perl:PERL = /usr/bin/perl:' -i Makefile || die
+	sed \
+		-e 's:INSTDIR:DESTDIR:g' \
+			-i Makefile src/Makefile doc/Makefile || die
+	sed -e 's:make all;:make all || exit 255;:' -i src/Makefile || die
+	sed \
+		-e 's:INSTDIR:DESTDIR:g' \
+		-i src/IO/Makefile src/DotLib/Makefile src/grommit/Makefile || die
+	sed -e "s:^CC\t=:CC=$(tc-getCXX):" -i Makefile || die
+	sed -e "s:^CXX\t=:CXX=$(tc-getCXX):" -i Makefile || die
+	sed -e "s:^LD\t:LD=$(tc-getCXX):" -i Makefile || die
+	sed -e 's:^AR\t=:#AR=:' -i Makefile || die
+	sed -e 's:^export:#export:' -i Makefile || die
+	sed -e 's:-Wl::' -i src/grommit/Makefile || die
+	# sed -e 's:-L../TIGR_Foundation_CC/:-L../TIGR_Foundation_CC/:' -i src/grommit/Makefile || die
+	sed -e 's:make all:make all DESTDIR=$(DESTDIR):' -i Makefile || die
+	sed -e 's:make install:make install DESTDIR=$(DESTDIR):' -i Makefile || die
+	sed -e "s:# Main targets:LD=$(tc-getCXX):" -i src/grommit/Makefile || die
+	sed -e 's:^LDFLAGS =$(STATIC_$(OSTYPE)):LDFLAGS += $(STATIC_$(OSTYPE)):' -i src/grommit/Makefile || die
+	sed -e 's:CFLAGS = $(HEADERS) -g:CFLAGS += $(HEADERS) -fPIC:' -i src/grommit/Makefile || die
+	sed -e 's:^$ENV{PERLLIB}:$ENV{PERL5LIB}:' -i src/goBambus.pl || die
+	sed -e 's:^#!.*:#!/usr/bin/perl:' -i src/goBambus.pl || die
+	sed -e 's:^#!.*:#!/usr/bin/perl:' -i src/IO/*.pl || die
+	einfo "Argh, cannot delete src/TIGR_Foundation_CC/ because it has some extra files getopt.* not present"
+	einfo "in sci-biology/tigr-foundation-libs. It seems bambus-2.33/src/TIGR_Foundation_CC/ contains"
+	einfo "the following 3 files getopt.cc   getopt.hh   getopt1.cc which were possibly copied"
+	einfo "over from some old GNU libc and maybe could be completely dropped?"
+	einfo "Affected would be:"
+	einfo "bambus-2.33/src/grommit/newgrp.cc:#include <getopt.h>"
+	einfo "bambus-2.33/src/TIGR_Foundation_CC/Options.hh:#include <getopt.h>"
+	einfo "bambus-2.33/src/TIGR_Foundation_CC/Options.hh:#include \"getopt.hh\""
+	einfo "bambus-2.33/src/TIGR_Foundation_CC/OptionResult.cc:/*! Uses same syntax as getopt"
+	#rm -rf src/TIGR_Foundation_CC || die "Failed to rm -rf src/TIGR_Foundation_CC/, we use it from sci-biology/tigr-foundation-libs"
+	#sed -i 's:TIGR_Foundation_CC::' src/Makefile || die "Failed to zap last pointer to local copy of tigr-foundation-libs"
+}
+
+src_install() {
+	pushd src/TIGR_Foundation_CC || die
+	sed -e "s:/export/usr/local:${ED}/usr:g" -i Makefile || die
+	popd || die
+	emake DESTDIR="${ED}/usr" install
+	# cvs HEAD of amos now contains even more updated files: /usr/bin/printScaff /usr/bin/untangle /usr/lib/TIGR/AsmLib.pm
+	for f in FASTArecord.pm FASTAreader.pm Foundation.pm FASTAgrammar.pm AsmLib.pm; do rm "${ED}"/usr/lib/TIGR/$f; done || die
+	for f in printScaff untangle; do rm "${ED}"/usr/bin/$f; done || die
+
+	# we compiled using locally provided TIGR_Foundation_CC/{cc,.hh} files but
+	# link against the libTigrFoundation.a provided by sci-biology/tigr-foundation-libs package
+	for f in CategoryInformation.hh MessageLevel.hh ConfigFile.hh LogCategory.hh \
+			ConfigSection.hh TIGR_Foundation.hh OptionResult.hh Exceptions.hh \
+			LogMsg.hh Options.hh Logger.hh FileSystem.hh; do
+				rm "${ED}"/usr/include/$f || die
+	done
+	rm "${ED}"/usr/lib/libTigrFoundation.a || die
+
+	dodir /usr/share/doc/${PF}
+	mv "${ED}"/usr/doc/* "${ED}"/usr/share/doc/${PF} || die
+	rmdir "${ED}"/usr/doc || die
+
+	dobin "${FILESDIR}"/goBambus.pl
+	dodoc "${DISTDIR}"/scaffolding_MIRA_BAMBUS.pdf
+	rm -r "${ED}"/usr/lib || die
+}
+
+pkg_postinst(){
+	einfo "For manual see http://mira-assembler.sourceforge.net/docs/scaffolding_MIRA_BAMBUS.pdf"
+}
diff --git a/sci-biology/bambus/bambus-2.33.ebuild b/sci-biology/bambus/bambus-2.33.ebuild
deleted file mode 100644
index 71cc10aa5..000000000
--- a/sci-biology/bambus/bambus-2.33.ebuild
+++ /dev/null
@@ -1,115 +0,0 @@
-# Copyright 1999-2017 Gentoo Foundation
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=5
-
-PERL_EXPORT_PHASE_FUNCTIONS=no
-inherit perl-module eutils toolchain-funcs
-
-DESCRIPTION="Scaffolding Polymorphic Genomes and Metagenomes, a part of AMOS bundle"
-HOMEPAGE="
-	http://sourceforge.net/apps/mediawiki/amos/index.php?title=AMOS
-	http://sourceforge.net/projects/amos/files/bambus
-	http://www.tigr.org/software/bambus"
-SRC_URI="
-	http://sourceforge.net/projects/amos/files/bambus/${PV}/${P}.tar.gz
-	http://mira-assembler.sourceforge.net/docs/scaffolding_MIRA_BAMBUS.pdf"
-
-LICENSE="Artistic"
-SLOT="0"
-KEYWORDS="~amd64 ~x86"
-IUSE=""
-
-RDEPEND="
-	sci-biology/tigr-foundation-libs
-	dev-perl/XML-Parser
-	dev-perl/Config-IniFiles
-	dev-perl/GraphViz"
-DEPEND="${RDEPEND}"
-
-src_prepare() {
-#	epatch "${FILESDIR}"/amos-2.0.8-gcc44.patch
-	sed -e 's:BASEDIR = /usr/local/packages/bambus:BASEDIR = /usr:' -i Makefile || die
-	sed -e 's:PERL = /usr/local/bin/perl:PERL = /usr/bin/perl:' -i Makefile || die
-	sed \
-		-e 's:INSTDIR:DESTDIR:g' \
-			-i Makefile src/Makefile doc/Makefile || die
-	sed -e 's:make all;:make all || exit 255;:' -i src/Makefile || die
-	sed \
-		-e 's:INSTDIR:DESTDIR:g' \
-		-i src/IO/Makefile src/DotLib/Makefile src/grommit/Makefile || die
-	sed -e "s:^CC\t=:CC=$(tc-getCXX):" -i Makefile || die
-	sed -e "s:^CXX\t=:CXX=$(tc-getCXX):" -i Makefile || die
-	sed -e "s:^LD\t:LD=$(tc-getCXX):" -i Makefile || die
-	sed -e 's:^AR\t=:#AR=:' -i Makefile || die
-	sed -e 's:^export:#export:' -i Makefile || die
-	sed -e 's:-Wl::' -i src/grommit/Makefile || die
-	# sed -e 's:-L../TIGR_Foundation_CC/:-L../TIGR_Foundation_CC/:' -i src/grommit/Makefile || die
-	sed -e 's:make all:make all DESTDIR=$(DESTDIR):' -i Makefile || die
-	sed -e 's:make install:make install DESTDIR=$(DESTDIR):' -i Makefile || die
-	sed -e "s:# Main targets:LD=$(tc-getCXX):" -i src/grommit/Makefile || die
-	sed -e 's:^LDFLAGS =$(STATIC_$(OSTYPE)):LDFLAGS += $(STATIC_$(OSTYPE)):' -i src/grommit/Makefile || die
-	sed -e 's:CFLAGS = $(HEADERS) -g:CFLAGS += $(HEADERS) -fPIC:' -i src/grommit/Makefile || die
-	sed -e 's:^$ENV{PERLLIB}:$ENV{PERL5LIB}:' -i src/goBambus.pl || die
-	sed -e 's:^#!.*:#!/usr/bin/perl:' -i src/goBambus.pl || die
-	sed -e 's:^#!.*:#!/usr/bin/perl:' -i src/IO/*.pl || die
-	einfo "Argh, cannot delete src/TIGR_Foundation_CC/ because it has some extra files getopt.* not present"
-	einfo "in sci-biology/tigr-foundation-libs. It seems bambus-2.33/src/TIGR_Foundation_CC/ contains"
-	einfo "the following 3 files getopt.cc   getopt.hh   getopt1.cc which were possibly copied"
-	einfo "over from some old GNU libc and maybe could be completely dropped?"
-	einfo "Affected would be:"
-	einfo "bambus-2.33/src/grommit/newgrp.cc:#include <getopt.h>"
-	einfo "bambus-2.33/src/TIGR_Foundation_CC/Options.hh:#include <getopt.h>"
-	einfo "bambus-2.33/src/TIGR_Foundation_CC/Options.hh:#include \"getopt.hh\""
-	einfo "bambus-2.33/src/TIGR_Foundation_CC/OptionResult.cc:/*! Uses same syntax as getopt"
-	#rm -rf src/TIGR_Foundation_CC || die "Failed to rm -rf src/TIGR_Foundation_CC/, we use it from sci-biology/tigr-foundation-libs"
-	#sed -i 's:TIGR_Foundation_CC::' src/Makefile || die "Failed to zap last pointer to local copy of tigr-foundation-libs"
-	cd src/TIGR_Foundation_CC || die "Failed to cd src/TIGR_Foundation_CC/"
-	epatch "${FILESDIR}"/TigrFoundation-all-patches.patch || die
-	sed -e "s:/export/usr/local:${ED}/usr:g" -i Makefile || die
-}
-
-src_compile() {
-	emake DESTDIR="${ED}/usr"
-
-	# TODO:
-	#ld  -L../TIGR_Foundation_CC/ -shared -fPIC -o grommit grommit.o -L. -lgraph -lTigrFoundation
-	# ld: warning: creating a DT_TEXTREL in object.
-	#
-	# * QA Notice: The following files contain runtime text relocations
-	# *  Text relocations force the dynamic linker to perform extra
-	# *  work at startup, waste system resources, and may pose a security
-	# *  risk.  On some architectures, the code may not even function
-	# *  properly, if at all.
-	# *  For more information, see http://hardened.gentoo.org/pic-fix-guide.xml
-	# *  Please include the following list of files in your report:
-	# * TEXTREL usr/bin/grommit
-}
-
-src_install() {
-	emake DESTDIR="${ED}/usr" install
-	# cvs HEAD of amos now contains even more updated files: /usr/bin/printScaff /usr/bin/untangle /usr/lib/TIGR/AsmLib.pm
-	for f in FASTArecord.pm FASTAreader.pm Foundation.pm FASTAgrammar.pm AsmLib.pm; do rm "${ED}"/usr/lib/TIGR/$f; done || die
-	for f in printScaff untangle; do rm "${ED}"/usr/bin/$f; done || die
-
-	# we compiled using locally provided TIGR_Foundation_CC/{cc,.hh} files but
-	# link against the libTigrFoundation.a provided by sci-biology/tigr-foundation-libs package
-	for f in CategoryInformation.hh MessageLevel.hh ConfigFile.hh LogCategory.hh \
-			ConfigSection.hh TIGR_Foundation.hh OptionResult.hh Exceptions.hh \
-			LogMsg.hh Options.hh Logger.hh FileSystem.hh; do
-				rm "${ED}"/usr/include/$f || die
-	done
-	rm "${ED}"/usr/lib/libTigrFoundation.a || die
-
-	dodir /usr/share/doc/${P}
-	mv "${ED}"/usr/doc/* "${ED}"/usr/share/doc/${PF} || die
-	rmdir "${ED}"/usr/doc || die
-
-	dobin "${FILESDIR}"/goBambus.pl
-	dodoc "${DISTDIR}"/scaffolding_MIRA_BAMBUS.pdf
-	rm -rf "${ED}"/usr/lib || die
-}
-
-pkg_postinst(){
-	einfo "For manual see http://mira-assembler.sourceforge.net/docs/scaffolding_MIRA_BAMBUS.pdf"
-}
diff --git a/sci-biology/bambus/files/TigrFoundation-all-patches.patch b/sci-biology/bambus/files/TigrFoundation-all-patches.patch
index 57ad86e2e..11501494f 100644
--- a/sci-biology/bambus/files/TigrFoundation-all-patches.patch
+++ b/sci-biology/bambus/files/TigrFoundation-all-patches.patch
@@ -1,5 +1,5 @@
---- /tmp/autoEditor-1.20/TigrFoundation-2.0/ConfigFile.cc.old	2010-12-04 17:07:50.000000000 +0100
-+++ /tmp/autoEditor-1.20/TigrFoundation-2.0/ConfigFile.cc	2010-12-04 17:07:25.000000000 +0100
+--- a/src/TIGR_Foundation_CC/ConfigFile.cc	2010-12-04 17:07:50.000000000 +0100
++++ b/src/TIGR_Foundation_CC/ConfigFile.cc	2010-12-04 17:07:25.000000000 +0100
 @@ -33,6 +33,7 @@
   *  different values.
   */
@@ -8,8 +8,8 @@
  #include "ConfigFile.hh"
  
  //! Constructor
---- /tmp/autoEditor-1.20/TigrFoundation-2.0/Logger.hh.old	2010-12-04 17:20:19.000000000 +0100
-+++ /tmp/autoEditor-1.20/TigrFoundation-2.0/Logger.hh	2010-12-04 17:20:49.000000000 +0100
+--- a/src/TIGR_Foundation_CC/Logger.hh	2010-12-04 17:20:19.000000000 +0100
++++ b/src/TIGR_Foundation_CC/Logger.hh	2010-12-04 17:20:49.000000000 +0100
 @@ -15,6 +15,7 @@
  #include <list>
  #include <string>
@@ -18,8 +18,8 @@
  
  #include <time.h>
  #include <pwd.h>
---- /tmp/autoEditor-1.20/TigrFoundation-2.0/OptionResult.hh.old	2010-12-04 17:21:35.000000000 +0100
-+++ /tmp/autoEditor-1.20/TigrFoundation-2.0/OptionResult.hh	2010-12-04 17:22:02.000000000 +0100
+--- a/src/TIGR_Foundation_CC/OptionResult.hh	2010-12-04 17:21:35.000000000 +0100
++++ b/src/TIGR_Foundation_CC/OptionResult.hh	2010-12-04 17:22:02.000000000 +0100
 @@ -12,6 +12,7 @@
  #define OPTIONRESULT_HH 1
  
@@ -28,8 +28,8 @@
  #include <map>
  #include "Exceptions.hh"
  
---- /tmp/autoEditor-1.20/TigrFoundation-2.0/Options.hh.old	2010-12-04 17:22:37.000000000 +0100
-+++ /tmp/autoEditor-1.20/TigrFoundation-2.0/Options.hh	2010-12-04 17:23:01.000000000 +0100
+--- a/src/TIGR_Foundation_CC/Options.hh	2010-12-04 17:22:37.000000000 +0100
++++ b/src/TIGR_Foundation_CC/Options.hh	2010-12-04 17:23:01.000000000 +0100
 @@ -11,6 +11,7 @@
  #ifndef OPTIONS_HH
  #define OPTIONS_HH 1
@@ -38,8 +38,8 @@
  #include <list>
  #include <map>
  #include <set>
---- /tmp/autoEditor-1.20/TigrFoundation-2.0/FileSystem.cc.old	2010-12-04 17:24:02.000000000 +0100
-+++ /tmp/autoEditor-1.20/TigrFoundation-2.0/FileSystem.cc	2010-12-04 17:24:12.000000000 +0100
+--- a/src/TIGR_Foundation_CC/FileSystem.cc	2010-12-04 17:24:02.000000000 +0100
++++ b/src/TIGR_Foundation_CC/FileSystem.cc	2010-12-04 17:24:12.000000000 +0100
 @@ -55,7 +55,7 @@
    {
      // Check to see if path was given
@@ -49,8 +49,8 @@
      
      if (end_of_path)
      {
---- /tmp/autoEditor-1.20/TigrFoundation-2.0/Options.cc.old	2010-12-04 17:24:53.000000000 +0100
-+++ /tmp/autoEditor-1.20/TigrFoundation-2.0/Options.cc	2010-12-04 17:25:15.000000000 +0100
+--- a/src/TIGR_Foundation_CC/Options.cc	2010-12-04 17:24:53.000000000 +0100
++++ b/src/TIGR_Foundation_CC/Options.cc	2010-12-04 17:25:15.000000000 +0100
 @@ -25,6 +25,7 @@
   *  written to stderr is prefixed with (stderr).
   */
diff --git a/sci-biology/bamql/Manifest b/sci-biology/bamql/Manifest
index 984d254f7..12b0cf052 100644
--- a/sci-biology/bamql/Manifest
+++ b/sci-biology/bamql/Manifest
@@ -1 +1 @@
-DIST bamql-1.5.tar.gz 64857 BLAKE2B 264653e2caffb7d82bb765eb6bcc5c4b4d25f0abda7c0baf5cbf92f656bc2a46a0d615c503e60ab95fda27862ab1590f4c8314f9d796b41ce665d10833d921ac SHA512 f2c690f6ad91c28c5993d385038e355d4cffbf1ee783cbf81a8459c2786d4406de0f310cc5f9d4abe9dc59bdd7a41442597fd5b34e7cc8db1af7bc9bd0ef089f
+DIST bamql-1.6.1.tar.gz 63888 BLAKE2B 1be2c29f9bc7d4d10f2a9baa79b767e7a028eccbb3ae2de2101d8d53956efd8ed5628467aed46d8dd0329a375c2692bd41f784a143ca04f38c6cfea54e9370db SHA512 78ba7776327adac0a69d910e6753c8c9089ece98c743ef55713bb4bdef66bddcb06949822c05d8a240fc314bcb3b138d118810645af53b262d6868500f032420
diff --git a/sci-biology/bamql/bamql-1.5.ebuild b/sci-biology/bamql/bamql-1.5.ebuild
deleted file mode 100644
index ef78e3753..000000000
--- a/sci-biology/bamql/bamql-1.5.ebuild
+++ /dev/null
@@ -1,28 +0,0 @@
-# Copyright 1999-2018 Gentoo Foundation
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=6
-
-inherit autotools
-
-DESCRIPTION="Extract reads from BAM files"
-HOMEPAGE="https://github.com/BoutrosLaboratory/bamql
-	https://bmcbioinformatics.biomedcentral.com/articles/10.1186/s12859-016-1162-y"
-SRC_URI="https://github.com/BoutrosLaboratory/bamql/archive/v1.5.tar.gz -> ${P}.tar.gz"
-
-LICENSE="MIT"
-SLOT="0"
-KEYWORDS="~amd64 ~x86"
-IUSE=""
-
-DEPEND="
-	sys-devel/llvm:=
-	sys-apps/util-linux
-	sci-libs/htslib
-	dev-libs/libpcre"
-RDEPEND="${DEPEND}"
-
-src_prepare(){
-	eautoreconf
-	default
-}
diff --git a/sci-biology/bamql/bamql-1.6.1.ebuild b/sci-biology/bamql/bamql-1.6.1.ebuild
new file mode 100644
index 000000000..435a7b3a5
--- /dev/null
+++ b/sci-biology/bamql/bamql-1.6.1.ebuild
@@ -0,0 +1,35 @@
+# Copyright 1999-2021 Gentoo Authors
+# Distributed under the terms of the GNU General Public License v2
+
+EAPI=7
+
+inherit autotools
+
+DESCRIPTION="Extract reads from BAM files"
+HOMEPAGE="https://github.com/BoutrosLaboratory/bamql
+	https://bmcbioinformatics.biomedcentral.com/articles/10.1186/s12859-016-1162-y"
+SRC_URI="https://github.com/BoutrosLaboratory/${PN}/archive/v${PV}.tar.gz -> ${P}.tar.gz"
+
+LICENSE="MIT"
+SLOT="0"
+KEYWORDS="~amd64 ~x86"
+IUSE="static-libs"
+
+DEPEND="
+	sys-devel/llvm:=
+	sys-apps/util-linux
+	sci-libs/htslib
+	dev-libs/libpcre"
+RDEPEND="${DEPEND}"
+
+PATCHES=( "${FILESDIR}"/bamql-1.6.1_drop_enable_static_llvm.patch )
+
+src_prepare(){
+	default
+	eautoreconf
+}
+
+src_configure(){
+	econf \
+		$(use_enable static-libs static)
+}
diff --git a/sci-biology/bamql/bamql-9999.ebuild b/sci-biology/bamql/bamql-9999.ebuild
index 44a7d85f5..288aef6bc 100644
--- a/sci-biology/bamql/bamql-9999.ebuild
+++ b/sci-biology/bamql/bamql-9999.ebuild
@@ -1,7 +1,7 @@
-# Copyright 1999-2018 Gentoo Foundation
+# Copyright 1999-2019 Gentoo Authors
 # Distributed under the terms of the GNU General Public License v2
 
-EAPI=6
+EAPI=7
 
 inherit autotools git-r3
 
@@ -13,7 +13,7 @@ EGIT_REPO_URI="https://github.com/BoutrosLaboratory/bamql.git"
 LICENSE="MIT"
 SLOT="0"
 KEYWORDS=""
-IUSE=""
+IUSE="static-libs"
 
 DEPEND="
 	sys-devel/llvm:=
@@ -22,7 +22,14 @@ DEPEND="
 	dev-libs/libpcre"
 RDEPEND="${DEPEND}"
 
+PATCHES=( "${FILESDIR}"/bamql-1.6.1_drop_enable_static_llvm.patch )
+
 src_prepare(){
-	eautoreconf
 	default
+	eautoreconf
+}
+
+src_configure(){
+	econf \
+		$(use_enable static-libs static)
 }
diff --git a/sci-biology/bamql/files/bamql-1.6.1_drop_enable_static_llvm.patch b/sci-biology/bamql/files/bamql-1.6.1_drop_enable_static_llvm.patch
new file mode 100644
index 000000000..e76d245c8
--- /dev/null
+++ b/sci-biology/bamql/files/bamql-1.6.1_drop_enable_static_llvm.patch
@@ -0,0 +1,23 @@
+--- bamql-1.6.1/m4/ax_llvm.m4.old	2019-03-25 23:17:05.190272994 +0100
++++ bamql-1.6.1/m4/ax_llvm.m4	2019-03-25 23:16:10.698775171 +0100
+@@ -28,7 +28,6 @@
+ 
+ AC_DEFUN([AX_LLVM],
+ [
+-AC_ARG_ENABLE([static-llvm], AS_HELP_STRING([--enable-static-llvm], [compiled against the static LLVM libraries, instead of the shared library.]), [enable_static_llvm=yes])
+ AC_ARG_WITH([llvm-config],
+ 	AS_HELP_STRING([--with-llvm-config@<:@=FILE@:>@], [ the name or or complete path to the llvm-config script for llvm (optional)]),
+ 	[
+@@ -53,11 +52,7 @@
+ 		[$1]_LIBDIR="$($ac_llvm_config_path --libdir)"
+ 		LLVM_VERSION="$($ac_llvm_config_path --version | cut -f 1-2 -d .)"
+ 		LLVM_COMPONENTS="$2"
+-		if test "x$enable_static_llvm" != "xyes" ; then
+-			[$1]_LIBS="$($ac_llvm_config_path --libs --system-libs --link-static $LLVM_COMPONENTS | tr '\n' ' ')"
+-		else
+-			[$1]_LIBS="$($ac_llvm_config_path --libs --link-shared $LLVM_COMPONENTS | tr '\n' ' ')"
+-		fi
++		[$1]_LIBS="$($ac_llvm_config_path --libs $LLVM_COMPONENTS | tr '\n' ' ')"
+ 
+ 		AC_REQUIRE([AC_PROG_CXX])
+ 		CPPFLAGS_SAVED="$CPPFLAGS"
diff --git a/sci-biology/bamql/metadata.xml b/sci-biology/bamql/metadata.xml
index 138cb7705..927a160ba 100644
--- a/sci-biology/bamql/metadata.xml
+++ b/sci-biology/bamql/metadata.xml
@@ -9,4 +9,7 @@
 		<email>sci-biology@gentoo.org</email>
 		<name>Gentoo Biology Project</name>
 	</maintainer>
+	<upstream>
+		<remote-id type="github">BoutrosLaboratory/bamql</remote-id>
+	</upstream>
 </pkgmetadata>
diff --git a/sci-biology/barnacle/Manifest b/sci-biology/barnacle/Manifest
deleted file mode 100644
index 51ab4a364..000000000
--- a/sci-biology/barnacle/Manifest
+++ /dev/null
@@ -1 +0,0 @@
-DIST barnacle-1.0.4.tar.gz 519904 BLAKE2B a1ba1dccc82dc17755c6bfebf0bd00b104e1a7a7d739df91223191119934c855e672ec2d5790f5a273e8d66c35c2d9e5cc49ce2961fad242eb1e7eaef413d097 SHA512 1d6e52ae4f6a04c7816d098d92ccc54971a009d0a4b5ff780d69ec84a02e0ea05d692f09fdefb0a13d52b5bff6fcc65cd52f93d0a383ecfca268c1e6d2dafe5b
diff --git a/sci-biology/barnacle/barnacle-1.0.4.ebuild b/sci-biology/barnacle/barnacle-1.0.4.ebuild
deleted file mode 100644
index 970f127fd..000000000
--- a/sci-biology/barnacle/barnacle-1.0.4.ebuild
+++ /dev/null
@@ -1,39 +0,0 @@
-# Copyright 1999-2016 Gentoo Foundation
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=5
-
-PYTHON_COMPAT=( python2_7 )
-
-inherit distutils-r1
-
-DESCRIPTION="Check de novo assembly for chimeric contigs/transcripts"
-HOMEPAGE="http://www.bcgsc.ca/platform/bioinfo/software/barnacle"
-#SRC_URI="http://www.bcgsc.ca/platform/bioinfo/software/barnacle/releases/1.0.0/"${P}".tar.gz"
-SRC_URI="http://www.bcgsc.ca/platform/bioinfo/software/barnacle/releases/${PV}/${P}.tar.gz"
-# ftp://ftp.bcgsc.ca/supplementary/Barnacle_BMC_Genomics/aml_data.tar.gz
-# http://www.bcgsc.ca/platform/bioinfo/software/barnacle/releases/1.0.3
-
-LICENSE="bcca_2010"
-SLOT="0"
-KEYWORDS=""
-IUSE=""
-
-DEPEND=""
-RDEPEND="${DEPEND}"
-
-S="${S}"
-
-# follow README.txt
-src_compile(){
-	cd src || die
-	# Run setup.py to compile the portions of Barnacle that require compilation, and download and setup the default annotations
-	touch alignment_processing/gap_realigner_cluster || die # prevent compilation on a cluster
-	./setup.py localhost || die
-}
-
-src_install(){
-	dodoc README.txt
-	cd src || die
-	# do something
-}
diff --git a/sci-biology/barnacle/metadata.xml b/sci-biology/barnacle/metadata.xml
deleted file mode 100644
index 138cb7705..000000000
--- a/sci-biology/barnacle/metadata.xml
+++ /dev/null
@@ -1,12 +0,0 @@
-<?xml version="1.0" encoding="UTF-8"?>
-<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
-<pkgmetadata>
-	<maintainer type="person">
-		<email>mmokrejs@fold.natur.cuni.cz</email>
-		<name>Martin Mokrejs</name>
-	</maintainer>
-	<maintainer type="project">
-		<email>sci-biology@gentoo.org</email>
-		<name>Gentoo Biology Project</name>
-	</maintainer>
-</pkgmetadata>
diff --git a/sci-biology/barrnap/Manifest b/sci-biology/barrnap/Manifest
index 8f18d6c45..af109a6e0 100644
--- a/sci-biology/barrnap/Manifest
+++ b/sci-biology/barrnap/Manifest
@@ -1,2 +1 @@
-DIST barrnap-0.3.tar.gz 4102752 BLAKE2B d904f7207a22073de36dcab8d45cf2c5c9740af5f16883621b9989bd036376b8dc727f28f7d7412bebef3fb87c8d23c9e0cb1be274433187819cacd38ceae28b SHA512 4b67e995b335e9e8397481c60058bf3a21044e1829781f277027ce2b3e4836c17c30dc2453c6d7d3c00ef8c07394fc5cb46719bfd397e66db7d4ba3c5bfdd514
-DIST barrnap-0.4.tar.gz 8053614 BLAKE2B a0953ac21dbf7a762c0211433550f9b92ddea39192de3e77ba8ad1c6d3e1b09f08f5cf947a63ca6e67dc6cd5144481798b3ad04962b697c0dd54e0b30d1fb52d SHA512 77490398978df73cd2c5529403674cdb2142fa57506a997a95bd4c90a897756554a2d10598e28bac396b8b611b8c9b1c6eaf3bfb4e0d22724c4175d18c2e16ea
+DIST barrnap-0.9.tar.gz 11837541 BLAKE2B 72f404dbe7f7d01cf1bfffc2c8a6e33a9b3efed04b51179433343672f1296dd1009870ccabb2123382aab0dcd1d41293fdf25f59df515b752497decce0130565 SHA512 7824a8a5c1c383f2e85210c9d24d6aa7c69e5290d4ebb0fb18090def78719ed30e84179e460a47379a599e4736216f740ee38bfc6ca38259df2efde5cd63235c
diff --git a/sci-biology/barrnap/barrnap-0.3.ebuild b/sci-biology/barrnap/barrnap-0.3.ebuild
deleted file mode 100644
index be281351f..000000000
--- a/sci-biology/barrnap/barrnap-0.3.ebuild
+++ /dev/null
@@ -1,40 +0,0 @@
-# Copyright 1999-2017 Gentoo Foundation
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=5
-
-inherit perl-module
-
-DESCRIPTION="Predict Bacterial and Archaeal rRNA genes and output in GFF3 format"
-HOMEPAGE="http://www.vicbioinformatics.com/software.barrnap.shtml"
-SRC_URI="http://www.vicbioinformatics.com/"${P}".tar.gz"
-
-LICENSE="GPL-3"
-SLOT="0"
-KEYWORDS="~amd64"
-IUSE=""
-
-# contains bundled binaries of hmmer-3.1 (dev version)
-# needs >=perl-5.6
-
-DEPEND=""
-RDEPEND="${DEPEND}
-	dev-lang/perl:=
-	sci-biology/nesoni"
-
-src_install(){
-	# the below recreates the whole layout
-	insinto /usr/share/"${PN}"
-	doins barrnap
-	chmod a+rx "${ED}"/usr/share/"${PN}"/barrnap
-	insinto /usr/share/"${PN}"/binaries
-	doins binaries/nhmmer.linux
-	chmod a+rx "${ED}"/usr/share/"${PN}"/binaries/nhmmer.linux
-	insinto /usr/share/"${PN}"/db
-	doins db/*
-	insinto /usr/share/examples
-	doins examples/*
-
-	echo PATH=/usr/share/"${PN}":$PATH > "${S}"/99barrnap
-	doenvd "${S}"/99barrnap
-}
diff --git a/sci-biology/barrnap/barrnap-0.4.ebuild b/sci-biology/barrnap/barrnap-0.4.ebuild
deleted file mode 100644
index f4559fddc..000000000
--- a/sci-biology/barrnap/barrnap-0.4.ebuild
+++ /dev/null
@@ -1,42 +0,0 @@
-# Copyright 1999-2017 Gentoo Foundation
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=5
-
-inherit perl-module
-
-DESCRIPTION="Predict Bacterial and Archaeal rRNA genes and output in GFF3 format"
-HOMEPAGE="http://www.vicbioinformatics.com/software.barrnap.shtml"
-SRC_URI="http://www.vicbioinformatics.com/"${P}".tar.gz"
-
-LICENSE="GPL-3"
-SLOT="0"
-KEYWORDS="~amd64"
-IUSE=""
-
-# contains bundled binaries of hmmer-3.1 (dev version)
-# needs >=perl-5.6
-
-DEPEND=""
-RDEPEND="${DEPEND}
-	dev-lang/perl:=
-	sci-biology/nesoni"
-
-src_install(){
-	# the below recreates the whole layout
-	insinto /usr/share/"${PN}"/bin
-	doins bin/barrnap
-	chmod a+rx "${ED}"/usr/share/"${PN}"/bin/barrnap || die
-	insinto /usr/share/"${PN}"/binaries/linux
-	doins binaries/linux/nhmmer
-	chmod a+rx "${ED}"/usr/share/"${PN}"/binaries/linux/nhmmer || die
-	insinto /usr/share/"${PN}"/db
-	doins db/*
-	insinto /usr/share/"${PN}"/examples
-	doins examples/*
-
-	echo PATH=/usr/share/"${PN}"/bin:$PATH > "${S}"/99barrnap
-	doenvd "${S}"/99barrnap
-
-	dodoc README.md
-}
diff --git a/sci-biology/barrnap/barrnap-0.9.ebuild b/sci-biology/barrnap/barrnap-0.9.ebuild
new file mode 100644
index 000000000..6b7176e14
--- /dev/null
+++ b/sci-biology/barrnap/barrnap-0.9.ebuild
@@ -0,0 +1,42 @@
+# Copyright 1999-2021 Gentoo Authors
+# Distributed under the terms of the GNU General Public License v2
+
+EAPI=7
+
+inherit perl-module
+
+DESCRIPTION="Predict Bacterial and Archaeal rRNA genes and output in GFF3 format"
+HOMEPAGE="https://github.com/tseemann/barrnap"
+SRC_URI="https://github.com/tseemann/barrnap/archive/${PV}.tar.gz -> ${P}.tar.gz"
+
+LICENSE="GPL-3"
+SLOT="0"
+KEYWORDS="~amd64"
+IUSE=""
+
+# contains bundled binaries of hmmer-3.1 (dev version)
+# needs >=perl-5.6
+
+DEPEND=""
+RDEPEND="${DEPEND}
+	dev-lang/perl:=
+	"
+
+src_install(){
+	# the below recreates the whole layout
+	insinto /usr/share/"${PN}"/bin
+	doins bin/barrnap
+	chmod a+rx "${ED}"/usr/share/"${PN}"/bin/barrnap || die
+	insinto /usr/share/"${PN}"/binaries/linux
+	doins binaries/linux/nhmmer
+	chmod a+rx "${ED}"/usr/share/"${PN}"/binaries/linux/nhmmer || die
+	insinto /usr/share/"${PN}"/db
+	doins db/*
+	insinto /usr/share/"${PN}"/examples
+	doins examples/*
+
+	echo PATH=/usr/share/"${PN}"/bin:$PATH > "${S}"/99barrnap
+	doenvd "${S}"/99barrnap
+
+	dodoc README.md
+}
diff --git a/sci-biology/barrnap/metadata.xml b/sci-biology/barrnap/metadata.xml
index 138cb7705..9183ef1ec 100644
--- a/sci-biology/barrnap/metadata.xml
+++ b/sci-biology/barrnap/metadata.xml
@@ -9,4 +9,7 @@
 		<email>sci-biology@gentoo.org</email>
 		<name>Gentoo Biology Project</name>
 	</maintainer>
+	<upstream>
+		<remote-id type="github">tseemann/barrnap</remote-id>
+	</upstream>
 </pkgmetadata>
diff --git a/sci-biology/beagle/Manifest b/sci-biology/beagle/Manifest
index a4cb8d549..0b0fcc4be 100644
--- a/sci-biology/beagle/Manifest
+++ b/sci-biology/beagle/Manifest
@@ -1,4 +1,3 @@
 DIST beagle-example.sh 976 BLAKE2B 36b38e68f18f4b1a488176d61a863c6d7312a3a89146ea8a15994db6dcf05afc74b7d5a207c72f3d49891a72a8b7f7199e7e7bfd0be124408db109503b7186d2 SHA512 db07b8e7753b1fa7b314301227fd4da3f80e2f5ea47357cb7f17d1ab1ad11b498ff763d82dc034a3cdc914071285e8186dcc85d0e829b537a9407ce11a6e4e80
-DIST beagle-release_notes.txt 1208 BLAKE2B 79340af75cd37c8d589d5eccb16b450d43ea6db94303a8686c135c3e699426d6711596282e392c1e718d76087c0203975e738de346392c48e3468ecd73616dbc SHA512 fa347608eb76bea7ba65d8aa109a578ba43900e29b6854160b58acb2c78a19999542901e5f9ebe703d2feb5e46b60e318c23d78a5eb63ad6e7df1d9850902067
-DIST beagle.03Mar15.pdf 655574 BLAKE2B 05839803105d07fd0b1c29a678b11e47596b02888bb743edece06e3e2faf1cf9c9fff839989e460b2966e8b1fb46cd3a5b2fda3ce3ddb2532394c4e2b61304f1 SHA512 78dfcffae1bdb29b7a9741d9a3610905222030d91ab74b7be09f46c9fc3742333f1f26d330c9fe532d9127771de2c36ffda229d8603b082478b5b90528c7a649
-DIST beagle.r1399.src.zip 307214 BLAKE2B a9adb8265aaad3df723d372107d6417a06778261e4be819f1840002643c4be2b0d246e42f30309fff7d4a9d7df30807bc8b80e9c04278d7d7d363a3d3535142e SHA512 b22b6ba3c67e01cf3e7c332723af781d32c3b2b9dad15b2eb1e1f47a216ff89911f89617eb95214723554059314dc312271a5320677937df48c7c4f3bb889253
+DIST beagle.18May20.d20.jar 276715 BLAKE2B 21177856bd948536c0b22649f8e1c600814a5a2446a72e1c1608b848fb9ed9206660e4a3f57982a728d238d51804b85e9edac97482a55d42a97aaa48d729b49e SHA512 30210e594ce4dce48eb2482e593a01b2476946aefff267fb73a38fb39d4a198091a09a32444b089c678aa232b9369ca47ecedde41adf026e62714319dbcbc9de
+DIST beagle_5.1_08Nov19.pdf 701913 BLAKE2B fa2c7f5d54bd9353ae047d53dab3f6e8e32e6ad0ceb33d8b6e8da6bd795ae12dd51f10d28b6eaf357c6aa14d07a7800fa2ea8d159348996a58780a1dac76b7f7 SHA512 a1003bbf46cbe173c661b86cf7592e5b8861d65a729b8e7a3f11be56a4ece9e97156ee0c1624083bfc5ea658c9866b2286118d1eab31eeffe2d36850edf1d81b
diff --git a/sci-biology/beagle/beagle-4.0.ebuild b/sci-biology/beagle/beagle-4.0.ebuild
deleted file mode 100644
index 61a9463c6..000000000
--- a/sci-biology/beagle/beagle-4.0.ebuild
+++ /dev/null
@@ -1,22 +0,0 @@
-# Copyright 1999-2015 Gentoo Foundation
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=5
-
-inherit java-pkg-2 java-ant-2
-
-DESCRIPTION="Genotype calling/phasing, imputation of ungenotyped markers"
-HOMEPAGE="http://faculty.washington.edu/browning/beagle/beagle.html"
-SRC_URI="http://faculty.washington.edu/browning/beagle/beagle.r1399.src.zip
-	http://faculty.washington.edu/browning/beagle/beagle.03Mar15.pdf
-	http://faculty.washington.edu/browning/beagle/run.beagle.r1399.example -> ${PN}-example.sh
-	http://faculty.washington.edu/browning/beagle/release_notes -> ${PN}-release_notes.txt"
-
-LICENSE="GPL-3+"
-SLOT="0"
-KEYWORDS=""
-IUSE=""
-
-DEPEND=">=virtual/jdk-1.7:*"
-RDEPEND="${DEPEND}
-	sci-biology/conform-gt"
diff --git a/sci-biology/beagle/beagle-5.1.ebuild b/sci-biology/beagle/beagle-5.1.ebuild
new file mode 100644
index 000000000..38b04921c
--- /dev/null
+++ b/sci-biology/beagle/beagle-5.1.ebuild
@@ -0,0 +1,30 @@
+# Copyright 1999-2021 Gentoo Authors
+# Distributed under the terms of the GNU General Public License v2
+
+EAPI=7
+
+inherit java-pkg-2
+
+DESCRIPTION="Genotype calling/phasing, imputation of ungenotyped markers"
+HOMEPAGE="https://faculty.washington.edu/browning/beagle/beagle.html"
+SRC_URI="
+	https://faculty.washington.edu/browning/beagle/beagle.18May20.d20.jar
+	https://faculty.washington.edu/browning/beagle/beagle_${PV}_08Nov19.pdf
+	https://faculty.washington.edu/browning/beagle/run.beagle.18May20.d20.example -> ${PN}-example.sh
+"
+
+LICENSE="GPL-3+"
+SLOT="0"
+KEYWORDS="~amd64"
+
+DEPEND=">=virtual/jdk-1.8:*"
+RDEPEND="${DEPEND}
+	sci-biology/conform-gt"
+
+S="${WORKDIR}"
+
+src_install() {
+	java-pkg_newjar "${DISTDIR}/beagle.18May20.d20.jar" "${PN}.jar"
+	dodoc "${DISTDIR}/beagle_${PV}_08Nov19.pdf"
+	dodoc "${DISTDIR}/${PN}-example.sh"
+}
diff --git a/sci-biology/beaglecall/beaglecall-20101115.ebuild b/sci-biology/beaglecall/beaglecall-20101115.ebuild
index 7d358bedb..e564665b9 100644
--- a/sci-biology/beaglecall/beaglecall-20101115.ebuild
+++ b/sci-biology/beaglecall/beaglecall-20101115.ebuild
@@ -1,24 +1,23 @@
-# Copyright 1999-2015 Gentoo Foundation
+# Copyright 1999-2021 Gentoo Authors
 # Distributed under the terms of the GNU General Public License v2
 
-EAPI=5
+EAPI=7
 
-inherit java-pkg-2 java-ant-2
+inherit java-pkg-2 java-pkg-simple
 
 DESCRIPTION="Simultaneous genotype calling and haplotype phasing for unrelated individuals"
-HOMEPAGE="http://faculty.washington.edu/browning/beaglecall/beaglecall.html"
-SRC_URI="http://faculty.washington.edu/browning/beaglecall/beaglecall_1.0.1_15Nov10.src.zip
-	http://faculty.washington.edu/browning/beaglecall/beaglecall_1.0_15Nov10.pdf
-	http://faculty.washington.edu/browning/beaglecall/beaglecall_example.zip"
+HOMEPAGE="https://faculty.washington.edu/browning/beaglecall/beaglecall.html"
+SRC_URI="https://faculty.washington.edu/browning/beaglecall/beaglecall_1.0.1_15Nov10.src.zip
+	https://faculty.washington.edu/browning/beaglecall/beaglecall_1.0_15Nov10.pdf
+	https://faculty.washington.edu/browning/beaglecall/beaglecall_example.zip"
 
 LICENSE="Apache-2.0"
 SLOT="0"
-KEYWORDS=""
-IUSE=""
+KEYWORDS="~amd64"
 
-DEPEND=">=virtual/jdk-1.5:*"
+DEPEND=">=virtual/jdk-1.5:*
+	app-arch/unzip"
 RDEPEND="${DEPEND}
 	>=virtual/jre-1.5:*"
 
-# src/ contains *.java files only
-# example/
+S="${WORKDIR}/src"
diff --git a/sci-biology/bedops/Manifest b/sci-biology/bedops/Manifest
index 66623b67d..bfced61ea 100644
--- a/sci-biology/bedops/Manifest
+++ b/sci-biology/bedops/Manifest
@@ -1 +1,2 @@
 DIST bedops-2.4.26.tar.gz 27057360 BLAKE2B dc5152ac9ac22289c90c866556b6741a6591c3a857730e1bde481adca86c6d2e15e8491fb0a1580c0d29609676c678d660f3eb6cd27f5bb36eda7fdb39cbb356 SHA512 6c43ff4f42168da8e181e5d50e8d41a1c0a8c24bde3ca6ab81f9b2324d47b4f7d265e3031adf39ea7ad0e65773462d13ed59580774f5a0906b205b27648a8eaa
+DIST bedops-2.4.39.tar.gz 21781987 BLAKE2B e75fa5c0a14fe97b52e48f3c895076a4c9096918e1b2df0e338fdec91f46ef3e07b1361ff38635544c6f4e205ecc5a2ae014c20ee80875fb3eb5df7cdf1f6d3a SHA512 05036f3b5715de4d725fb96c2b9bda9aa1fd02f34154b57a9f734c06fccc64021edb0557ab93611acdd3b591841cbeb440f95e5d6e4bcdef9a889c15c2c0dd50
diff --git a/sci-biology/bedops/bedops-2.4.26.ebuild b/sci-biology/bedops/bedops-2.4.26.ebuild
index d281fbede..3746b4b8f 100644
--- a/sci-biology/bedops/bedops-2.4.26.ebuild
+++ b/sci-biology/bedops/bedops-2.4.26.ebuild
@@ -1,9 +1,7 @@
-# Copyright 1999-2017 Gentoo Foundation
+# Copyright 1999-2021 Gentoo Authors
 # Distributed under the terms of the GNU General Public License v2
 
-EAPI=6
-
-inherit toolchain-funcs eutils
+EAPI=7
 
 DESCRIPTION="Manipulate BED file (alternative to bedtools)"
 HOMEPAGE="http://bedops.readthedocs.io
@@ -13,13 +11,11 @@ SRC_URI="https://github.com/bedops/bedops/archive/v${PV}.tar.gz -> ${P}.tar.gz"
 LICENSE="GPL-2"
 SLOT="0"
 KEYWORDS="~amd64 ~x86"
-IUSE=""
 
-DEPEND=""
-RDEPEND="${DEPEND}"
+PATCHES=( "${FILESDIR}"/${P}-respect-cxxflags.patch )
 
-src_prepare(){
-	default
-	local PATCHES=("${FILESDIR}"/${P}-respect-cxxflags.patch)
-	epatch ${PATCHES[@]}
+src_install(){
+	emake install
+	dobin bin/*
+	dodoc README.md
 }
diff --git a/sci-biology/bedops/bedops-2.4.39.ebuild b/sci-biology/bedops/bedops-2.4.39.ebuild
new file mode 100644
index 000000000..348d53065
--- /dev/null
+++ b/sci-biology/bedops/bedops-2.4.39.ebuild
@@ -0,0 +1,22 @@
+# Copyright 1999-2021 Gentoo Authors
+# Distributed under the terms of the GNU General Public License v2
+
+EAPI=7
+
+DESCRIPTION="Manipulate BED file (alternative to bedtools)"
+HOMEPAGE="http://bedops.readthedocs.io
+	https://github.com/bedops/bedops"
+SRC_URI="https://github.com/bedops/bedops/archive/v${PV}.tar.gz -> ${P}.tar.gz"
+
+LICENSE="GPL-2"
+SLOT="0"
+KEYWORDS="~amd64 ~x86"
+
+DEPEND=""
+RDEPEND="${DEPEND}"
+
+src_install(){
+	emake install
+	dobin bin/*
+	dodoc README.md
+}
diff --git a/sci-biology/bfast/Manifest b/sci-biology/bfast/Manifest
deleted file mode 100644
index 43bf85bb0..000000000
--- a/sci-biology/bfast/Manifest
+++ /dev/null
@@ -1 +0,0 @@
-DIST bfast-0.7.0a.tar.gz 2456617 BLAKE2B a841e7651e731dbb3faf22eb03dce5d2008c84f9a6198204d3c41aea26626058e3a23375bc0e7e8fc142d4898e09ddbb168016c71a7b79527e602e06ec329151 SHA512 16e7ec5101c478f0dfc171016cbacb2b9240773e43b2d40eeb42d0e47afcee50a6dd5838e043a0326fc1ca9a87d3e55b42326a7f17b7c5654ef9825913860836
diff --git a/sci-biology/bfast/bfast-0.7.0_alpha.ebuild b/sci-biology/bfast/bfast-0.7.0_alpha.ebuild
deleted file mode 100644
index 3fed32f4c..000000000
--- a/sci-biology/bfast/bfast-0.7.0_alpha.ebuild
+++ /dev/null
@@ -1,19 +0,0 @@
-# Copyright 1999-2016 Gentoo Foundation
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=5
-
-DESCRIPTION="Blat-like Fast Accurate Search Tool (short read mapper)"
-HOMEPAGE="https://sourceforge.net/projects/bfast"
-SRC_URI="https://sourceforge.net/projects/bfast/files/bfast/0.7.0/bfast-0.7.0a.tar.gz"
-
-LICENSE="GPL-2"
-SLOT="0"
-KEYWORDS="~amd64"
-IUSE=""
-
-DEPEND=""
-RDEPEND="${DEPEND}
-	dev-lang/perl"
-
-S="${WORKDIR}"/bfast-0.7.0a
diff --git a/sci-biology/bfast/metadata.xml b/sci-biology/bfast/metadata.xml
deleted file mode 100644
index b60dfbcbc..000000000
--- a/sci-biology/bfast/metadata.xml
+++ /dev/null
@@ -1,15 +0,0 @@
-<?xml version="1.0" encoding="UTF-8"?>
-<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
-<pkgmetadata>
-	<maintainer type="person">
-		<email>mmokrejs@fold.natur.cuni.cz</email>
-		<name>Martin Mokrejs</name>
-	</maintainer>
-	<maintainer type="project">
-		<email>sci-biology@gentoo.org</email>
-		<name>Gentoo Biology Project</name>
-	</maintainer>
-	<upstream>
-		<remote-id type="sourceforge">bfast</remote-id>
-	</upstream>
-</pkgmetadata>
diff --git a/sci-biology/bidsschematools/Manifest b/sci-biology/bidsschematools/Manifest
new file mode 100644
index 000000000..283f2cedf
--- /dev/null
+++ b/sci-biology/bidsschematools/Manifest
@@ -0,0 +1,3 @@
+DIST bidsschematools-0.6.0.tar.gz 1162053 BLAKE2B b46ae2c19b96416908786347890db33aded14c0656b2af3f8396395a7decd9e74808b1ba54df3d049473eda038b706d7b0561f2e21c97ab5e9534f57c41a560a SHA512 32e2a679b85cb8c57e2a91783f315092b3e976e8cadc661a67822b499685b128a9f5abda70d2124ddcee42163a9357665474de6c3f96cf369c33cefe1586b7f1
+DIST bidsschematools-0.7.0.tar.gz 1227313 BLAKE2B 350621d8052ca8ee45be970c4f8973c34d5c7dfd9da0777758009d8f725691efaa665926d9f97723e2331f5511aedf3601fd1df520746b6ec4aebd6ef27a2cf6 SHA512 391e3ed1a96202bada1486de377ea4d96e8622cced132cbb014a697578dbd1c5fdfa3eb2ce6f44b5031136c987e2298a5bc702c1c5751e35479512cfe57a383b
+DIST bidsschematools-0.7.1.tar.gz 1226794 BLAKE2B 6bbc672ac047bd1475b5b79f5cb74b61f190207531be810018768a6cf62e2cae36ccef4893bee041a53ed546f8ae6f104bb64d2f0b89550c80c911d6a48fcee5 SHA512 8cf9e94496108c15360bcc25a1c8e5900350e1fb3da9886c2d089481ae69c94a634ea0cf67e2a1120a93c2982c07061cda8d0d8ecba9715f848c01388108517e
diff --git a/sci-biology/bidsschematools/bidsschematools-0.6.0.ebuild b/sci-biology/bidsschematools/bidsschematools-0.6.0.ebuild
new file mode 100644
index 000000000..96b6cd57f
--- /dev/null
+++ b/sci-biology/bidsschematools/bidsschematools-0.6.0.ebuild
@@ -0,0 +1,37 @@
+# Copyright 2022-2023 Gentoo Authors
+# Distributed under the terms of the GNU General Public License v2
+
+EAPI=8
+
+DISTUTILS_USE_PEP517=setuptools
+PYTHON_COMPAT=( python3_{10..11} )
+
+inherit distutils-r1 pypi
+
+DESCRIPTION="A Python library for working with the BIDS schema"
+HOMEPAGE="https://github.com/bids-standard/bids-specification"
+
+LICENSE="MIT"
+SLOT="0"
+KEYWORDS="~amd64 ~x86 ~amd64-linux ~x86-linux"
+IUSE="render"
+
+RDEPEND="
+	dev-python/pyyaml[${PYTHON_USEDEP}]
+	render? (
+		dev-python/markdown-it-py[${PYTHON_USEDEP}]
+		dev-python/pandas[${PYTHON_USEDEP}]
+		dev-python/tabulate[${PYTHON_USEDEP}]
+	)
+"
+DEPEND=""
+
+distutils_enable_tests pytest
+
+src_prepare() {
+	if ! use render; then
+		rm "${S}/bidsschematools/render.py"
+		rm "${S}/bidsschematools/tests/test_render.py"
+	fi
+	default
+}
diff --git a/sci-biology/bidsschematools/bidsschematools-0.7.0.ebuild b/sci-biology/bidsschematools/bidsschematools-0.7.0.ebuild
new file mode 100644
index 000000000..98b773243
--- /dev/null
+++ b/sci-biology/bidsschematools/bidsschematools-0.7.0.ebuild
@@ -0,0 +1,46 @@
+# Copyright 2023 Gentoo Authors
+# Distributed under the terms of the GNU General Public License v2
+
+EAPI=8
+
+DISTUTILS_USE_PEP517=setuptools
+PYTHON_COMPAT=( python3_{10..11} )
+
+inherit distutils-r1 pypi
+
+DESCRIPTION="A Python library for working with the BIDS schema"
+HOMEPAGE="https://github.com/bids-standard/bids-specification"
+
+LICENSE="MIT"
+SLOT="0"
+KEYWORDS="~amd64 ~x86 ~amd64-linux ~x86-linux"
+IUSE="render"
+# Documented upstream:
+# https://github.com/conda-forge/bidsschematools-feedstock/pull/2
+#RESTRICT="test"
+
+RDEPEND="
+	dev-python/pyyaml[${PYTHON_USEDEP}]
+	render? (
+		dev-python/markdown-it-py[${PYTHON_USEDEP}]
+		dev-python/pandas[${PYTHON_USEDEP}]
+		dev-python/tabulate[${PYTHON_USEDEP}]
+	)
+"
+DEPEND=""
+
+distutils_enable_tests pytest
+
+# Reported upstream:
+# https://github.com/bids-standard/bids-specification/issues/1500
+EPYTEST_DESELECT=(
+	"bidsschematools/tests/test_validator.py::test_bids_datasets[ds000248]"
+)
+
+src_prepare() {
+	if ! use render; then
+		rm "${S}/bidsschematools/render.py"
+		rm "${S}/bidsschematools/tests/test_render.py"
+	fi
+	default
+}
diff --git a/sci-biology/bidsschematools/bidsschematools-0.7.1.ebuild b/sci-biology/bidsschematools/bidsschematools-0.7.1.ebuild
new file mode 100644
index 000000000..b5b12165d
--- /dev/null
+++ b/sci-biology/bidsschematools/bidsschematools-0.7.1.ebuild
@@ -0,0 +1,37 @@
+# Copyright 2023 Gentoo Authors
+# Distributed under the terms of the GNU General Public License v2
+
+EAPI=8
+
+DISTUTILS_USE_PEP517=setuptools
+PYTHON_COMPAT=( python3_{10..11} )
+
+inherit distutils-r1 pypi
+
+DESCRIPTION="A Python library for working with the BIDS schema"
+HOMEPAGE="https://github.com/bids-standard/bids-specification"
+
+LICENSE="MIT"
+SLOT="0"
+KEYWORDS="~amd64 ~x86 ~amd64-linux ~x86-linux"
+IUSE="render"
+
+RDEPEND="
+	dev-python/pyyaml[${PYTHON_USEDEP}]
+	render? (
+		dev-python/markdown-it-py[${PYTHON_USEDEP}]
+		dev-python/pandas[${PYTHON_USEDEP}]
+		dev-python/tabulate[${PYTHON_USEDEP}]
+	)
+"
+DEPEND=""
+
+distutils_enable_tests pytest
+
+src_prepare() {
+	if ! use render; then
+		rm "${S}/bidsschematools/render.py"
+		rm "${S}/bidsschematools/tests/test_render.py"
+	fi
+	default
+}
diff --git a/sci-biology/bidsschematools/metadata.xml b/sci-biology/bidsschematools/metadata.xml
new file mode 100644
index 000000000..3fac5f14b
--- /dev/null
+++ b/sci-biology/bidsschematools/metadata.xml
@@ -0,0 +1,19 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
+<pkgmetadata>
+	<maintainer type="person">
+		<email>gentoo@chymera.eu</email>
+		<name>Horea Christian</name>
+	</maintainer>
+	<maintainer type="project">
+		<email>sci@gentoo.org</email>
+		<name>Gentoo Science Project</name>
+	</maintainer>
+	<upstream>
+		<remote-id type="github">bids-standard/bids-specification</remote-id>
+		<remote-id type="pypi">bidsschematools</remote-id>
+	</upstream>
+	<use>
+		<flag name="render">Support for schema table rendering</flag>
+	</use>
+</pkgmetadata>
diff --git a/sci-biology/bio-cd-hit-report/Manifest b/sci-biology/bio-cd-hit-report/Manifest
deleted file mode 100644
index b04456775..000000000
--- a/sci-biology/bio-cd-hit-report/Manifest
+++ /dev/null
@@ -1 +0,0 @@
-DIST bio-cd-hit-report-0.1.0.gem 8192 BLAKE2B 14a64c39e8ba3dbff1fcfe82e17e36c3eabd63efd6b8c1962f4cfca491e4d1dfb3cee3625fbc7c20ca5affdcfd7365d965843ab4fca1e394a8d5486c6847b207 SHA512 e4790d8d54688752538c39d5efa9c83c18990aeeebf6b66d1dd749f8d404e51b9f61b1f931e9a10025508c4bbc773380cdbd7d6130a42f32c5f30cc5ea069174
diff --git a/sci-biology/bio-cd-hit-report/bio-cd-hit-report-0.1.0.ebuild b/sci-biology/bio-cd-hit-report/bio-cd-hit-report-0.1.0.ebuild
deleted file mode 100644
index ad3ab1887..000000000
--- a/sci-biology/bio-cd-hit-report/bio-cd-hit-report-0.1.0.ebuild
+++ /dev/null
@@ -1,27 +0,0 @@
-# Copyright 1999-2017 Gentoo Foundation
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=6
-
-USE_RUBY="ruby22 ruby23 ruby24"
-
-RUBY_FAKEGEM_TASK_DOC=""
-RUBY_FAKEGEM_EXTRADOC="README.md"
-
-inherit ruby-fakegem
-
-DESCRIPTION="Ruby library for reading CD-HIT cluster reports"
-HOMEPAGE="https://rubygems.org/gems/bio-cd-hit-report"
-
-LICENSE="MIT"
-SLOT="0"
-KEYWORDS="~amd64"
-IUSE=""
-
-DEPEND="
-	>=dev-ruby/bundler-1.3.1
-	dev-ruby/jeweler
-	dev-ruby/minitest:*
-	dev-ruby/rdoc"
-RDEPEND="${DEPEND}
-	>=sci-biology/bioruby-1.4.3"
diff --git a/sci-biology/bio-cd-hit-report/metadata.xml b/sci-biology/bio-cd-hit-report/metadata.xml
deleted file mode 100644
index becca79c5..000000000
--- a/sci-biology/bio-cd-hit-report/metadata.xml
+++ /dev/null
@@ -1,15 +0,0 @@
-<?xml version="1.0" encoding="UTF-8"?>
-<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
-<pkgmetadata>
-	<maintainer type="person">
-		<email>mmokrejs@fold.natur.cuni.cz</email>
-		<name>Martin Mokrejs</name>
-	</maintainer>
-	<maintainer type="project">
-		<email>sci-biology@gentoo.org</email>
-		<name>Gentoo Biology Project</name>
-	</maintainer>
-	<upstream>
-		<remote-id type="rubygems">bio-cd-hit-report</remote-id>
-	</upstream>
-</pkgmetadata>
diff --git a/sci-biology/biobambam/Manifest b/sci-biology/biobambam/Manifest
deleted file mode 100644
index 562f6adcb..000000000
--- a/sci-biology/biobambam/Manifest
+++ /dev/null
@@ -1 +0,0 @@
-DIST 0.0.183-release-20141208165400.tar.gz 1100088 BLAKE2B f43e25c51c773b4ba5c086761758ddabd1b021efa51b0230fb60360845f4ed34f48004e9da0cec5d2a36586ca56f68732620bab3eb4d76c80a420fef867a1396 SHA512 64e05517754156c48116672e18d21ae59146a9544ae7bf3df115e6a6b475ec24d62043ac4e54417ce064d6e8acddba75698944865c6b407f64d40ff7e5dafa3c
diff --git a/sci-biology/biobambam/biobambam-0.0.183.ebuild b/sci-biology/biobambam/biobambam-0.0.183.ebuild
deleted file mode 100644
index 17a247d60..000000000
--- a/sci-biology/biobambam/biobambam-0.0.183.ebuild
+++ /dev/null
@@ -1,20 +0,0 @@
-# Copyright 1999-2014 Gentoo Foundation
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=5
-
-FULLVER=${PV}-release-20141208165400
-
-DESCRIPTION="Tools for bam file processing"
-HOMEPAGE="https://github.com/gt1/biobambam"
-SRC_URI="https://github.com/gt1/biobambam/archive/${FULLVER}.tar.gz"
-
-LICENSE="GPL-3"
-SLOT="0"
-KEYWORDS="~x86"
-IUSE=""
-
-DEPEND="sci-libs/libmaus"
-RDEPEND="${DEPEND}"
-
-S="${WORKDIR}"/${PN}-${FULLVER}
diff --git a/sci-biology/biobambam/metadata.xml b/sci-biology/biobambam/metadata.xml
deleted file mode 100644
index 782a697ab..000000000
--- a/sci-biology/biobambam/metadata.xml
+++ /dev/null
@@ -1,21 +0,0 @@
-<?xml version="1.0" encoding="UTF-8"?>
-<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
-<pkgmetadata>
-	<maintainer type="project">
-		<email>sci-biology@gentoo.org</email>
-		<name>Gentoo Biology Project</name>
-	</maintainer>
-	<longdescription lang="en">
-This package contains some tools for processing BAM files including
-
-bamcollate2: reads BAM and writes BAM reordered such that alignment or collated by query name
-bammarkduplicates: reads BAM and writes BAM with duplicate alignments marked using the BAM flags field
-bammaskflags: reads BAM and writes BAM while masking (removing) bits from the flags column
-bamrecompress: reads BAM and writes BAM with a defined compression setting. This tool is capable of multi-threading.
-bamsort: reads BAM and writes BAM resorted by coordinates or query name
-bamtofastq: reads BAM and writes FastQ; output can be collated or uncollated by query name
-</longdescription>
-	<upstream>
-		<remote-id type="github">gt1/biobambam</remote-id>
-	</upstream>
-</pkgmetadata>
diff --git a/sci-biology/biobambam2/Manifest b/sci-biology/biobambam2/Manifest
index c099c95e0..28b0d50e4 100644
--- a/sci-biology/biobambam2/Manifest
+++ b/sci-biology/biobambam2/Manifest
@@ -1 +1 @@
-DIST 2.0.89-release-20180518145034.tar.gz 1195105 BLAKE2B d8152e3f87c39096a4419829cb4c485a87c116d00aa5becdd221c3d1bc595f1c7e1b05a71099e66cceecd4e52e47a97e52f99ddaf0ae7a0a838f5ac696657ec8 SHA512 be53abfd74e6383815b4da6479770d5d9145127bc726c1b57c3464b3c3c8db79b0f0f29feb0232879bfad99f522985be80b9ec02ee369de023707404e77a74f3
+DIST biobambam2-2.0.146.tar.gz 1261153 BLAKE2B 604ea0a41849798a3c76674fe0fc9ebee2cf93fce852f4757d49aa7357efad3fd3c79159f49157729f7f10f594f5245b25ffe35be378160a3e97e66c7de3498c SHA512 996719f7d1fd188df21e9b9f9e9fcdf75fe57a3a9ab2c82fd2b7bef2b73bd9c375adc7a871d5f5d9fdf8bd0a9c0cf744593a114d7b5cd4ecae1f5ccb7e05fbe4
diff --git a/sci-biology/biobambam2/biobambam2-2.0.146.ebuild b/sci-biology/biobambam2/biobambam2-2.0.146.ebuild
new file mode 100644
index 000000000..ff7768d6d
--- /dev/null
+++ b/sci-biology/biobambam2/biobambam2-2.0.146.ebuild
@@ -0,0 +1,23 @@
+# Copyright 1999-2021 Gentoo Authors
+# Distributed under the terms of the GNU General Public License v2
+
+EAPI=7
+
+release_data="20191030105216"
+
+DESCRIPTION="Tools for bam file processing (libmaus2)"
+HOMEPAGE="https://gitlab.com/german.tischler/biobambam2"
+SRC_URI="https://gitlab.com/german.tischler/${PN}/-/archive/${PV}-release-${release_data}/${P}-release-${release_data}.tar.gz -> ${P}.tar.gz"
+
+LICENSE="GPL-3 MIT"
+SLOT="0"
+KEYWORDS="~amd64"
+
+DEPEND="sci-libs/libmaus2"
+RDEPEND="${DEPEND}"
+
+S="${WORKDIR}/${P}-release-${release_data}"
+
+src_configure(){
+	econf --with-libmaus2="${EPREFIX}"
+}
diff --git a/sci-biology/biobambam2/biobambam2-2.0.89.ebuild b/sci-biology/biobambam2/biobambam2-2.0.89.ebuild
deleted file mode 100644
index 3ebc9cae5..000000000
--- a/sci-biology/biobambam2/biobambam2-2.0.89.ebuild
+++ /dev/null
@@ -1,27 +0,0 @@
-# Copyright 1999-2019 Gentoo Authors
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=7
-
-inherit autotools
-
-DESCRIPTION="Tools for bam file processing (libmaus2)"
-HOMEPAGE="https://gitlab.com/german.tischler/biobambam2
-	https://github.com/gt1/biobambam2"
-SRC_URI="https://github.com/gt1/biobambam2/archive/2.0.89-release-20180518145034.tar.gz"
-
-LICENSE="GPL-3 MIT"
-SLOT="0"
-KEYWORDS=""
-IUSE=""
-
-DEPEND="
-	!sci-biology/biobambam
-	>=sci-libs/libmaus2-2.0.489"
-RDEPEND="${DEPEND}"
-
-S="${WORKDIR}"/biobambam2-2.0.89-release-20180518145034
-
-src_configure(){
-	econf --with-libmaus2="${EPREFIX}"
-}
diff --git a/sci-biology/biobambam2/biobambam2-9999.ebuild b/sci-biology/biobambam2/biobambam2-9999.ebuild
index 59774ca56..69f3ea31c 100644
--- a/sci-biology/biobambam2/biobambam2-9999.ebuild
+++ b/sci-biology/biobambam2/biobambam2-9999.ebuild
@@ -1,4 +1,4 @@
-# Copyright 1999-2019 Gentoo Authors
+# Copyright 1999-2020 Gentoo Authors
 # Distributed under the terms of the GNU General Public License v2
 
 EAPI=7
@@ -15,9 +15,7 @@ SLOT="0"
 KEYWORDS=""
 IUSE=""
 
-DEPEND="
-	!sci-biology/biobambam
-	>=sci-libs/libmaus2-2.0.555"
+DEPEND="sci-libs/libmaus2"
 RDEPEND="${DEPEND}"
 
 src_prepare() {
diff --git a/sci-biology/biopieces/biopieces-0.51.ebuild b/sci-biology/biopieces/biopieces-0.51.ebuild
deleted file mode 100644
index 03a9d78cc..000000000
--- a/sci-biology/biopieces/biopieces-0.51.ebuild
+++ /dev/null
@@ -1,71 +0,0 @@
-# Copyright 1999-2017 Gentoo Foundation
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=5
-
-PYTHON_COMPAT=( python2_7 )
-
-USE_RUBY="ruby22 ruby23 ruby24"
-
-if [ "$PV" == "9999" ]; then
-	ESVN_REPO_URI="http://biopieces.googlecode.com/svn/trunk"
-	KEYWORDS=""
-	inherit subversion
-else
-	SRC_URI="http://biopieces.googlecode.com/files/biopieces_installer-${PV}.sh"
-	KEYWORDS=""
-fi
-
-inherit ruby-fakegem python-single-r1
-
-DESCRIPTION="Trim adaptors, plot read lengths, qualities, map reads and submit to GenBank"
-HOMEPAGE="http://code.google.com/p/biopieces"
-SRC_URI=""
-
-LICENSE="GPL-2"
-SLOT="0"
-IUSE="test"
-
-REQUIRED_USE="${PYTHON_REQUIRED_USE}"
-
-#    Ruby terminal-table ?
-
-CDEPEND="${PYTHON_DEPS}
-	>=dev-lang/perl-5.8
-	dev-perl/libwww-perl
-	dev-perl/Bit-Vector
-	dev-perl/Carp-Clan
-	dev-perl/Class-Inspector
-	dev-perl/DBD-mysql
-	dev-perl/DBI
-	dev-perl/HTML-Parser
-	dev-perl/Inline
-	dev-perl/Parse-RecDescent
-	dev-perl/SOAP-Lite
-	dev-perl/SVG
-	dev-perl/TermReadKey
-	dev-perl/URI
-	dev-perl/XML-Parser
-	virtual/perl-version
-	virtual/perl-DB_File
-	virtual/perl-Time-HiRes"
-
-DEPEND="${CDEPEND}"
-
-ruby_add_bdepend "dev-ruby/RubyInline"
-ruby_add_rdepend "dev-ruby/gnuplot dev-ruby/narray"
-
-# sci-biology/vmatch # http://www.vmatch.de/ # fecth restrict
-# sci-biology/usearch-bin # http://www.drive5.com/usearch/ # fecth restrict
-
-RDEPEND="${CDEPEND}
-	sci-biology/ncbi-tools
-	sci-biology/muscle
-	sci-biology/mummer
-	sci-biology/blat
-	sci-biology/bowtie
-	sci-biology/bwa
-	sci-biology/velvet
-	sci-biology/Ray
-	sci-biology/scan_for_matches
-	sci-biology/idba"
diff --git a/sci-biology/biopieces/biopieces-9999.ebuild b/sci-biology/biopieces/biopieces-9999.ebuild
deleted file mode 100644
index 03a9d78cc..000000000
--- a/sci-biology/biopieces/biopieces-9999.ebuild
+++ /dev/null
@@ -1,71 +0,0 @@
-# Copyright 1999-2017 Gentoo Foundation
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=5
-
-PYTHON_COMPAT=( python2_7 )
-
-USE_RUBY="ruby22 ruby23 ruby24"
-
-if [ "$PV" == "9999" ]; then
-	ESVN_REPO_URI="http://biopieces.googlecode.com/svn/trunk"
-	KEYWORDS=""
-	inherit subversion
-else
-	SRC_URI="http://biopieces.googlecode.com/files/biopieces_installer-${PV}.sh"
-	KEYWORDS=""
-fi
-
-inherit ruby-fakegem python-single-r1
-
-DESCRIPTION="Trim adaptors, plot read lengths, qualities, map reads and submit to GenBank"
-HOMEPAGE="http://code.google.com/p/biopieces"
-SRC_URI=""
-
-LICENSE="GPL-2"
-SLOT="0"
-IUSE="test"
-
-REQUIRED_USE="${PYTHON_REQUIRED_USE}"
-
-#    Ruby terminal-table ?
-
-CDEPEND="${PYTHON_DEPS}
-	>=dev-lang/perl-5.8
-	dev-perl/libwww-perl
-	dev-perl/Bit-Vector
-	dev-perl/Carp-Clan
-	dev-perl/Class-Inspector
-	dev-perl/DBD-mysql
-	dev-perl/DBI
-	dev-perl/HTML-Parser
-	dev-perl/Inline
-	dev-perl/Parse-RecDescent
-	dev-perl/SOAP-Lite
-	dev-perl/SVG
-	dev-perl/TermReadKey
-	dev-perl/URI
-	dev-perl/XML-Parser
-	virtual/perl-version
-	virtual/perl-DB_File
-	virtual/perl-Time-HiRes"
-
-DEPEND="${CDEPEND}"
-
-ruby_add_bdepend "dev-ruby/RubyInline"
-ruby_add_rdepend "dev-ruby/gnuplot dev-ruby/narray"
-
-# sci-biology/vmatch # http://www.vmatch.de/ # fecth restrict
-# sci-biology/usearch-bin # http://www.drive5.com/usearch/ # fecth restrict
-
-RDEPEND="${CDEPEND}
-	sci-biology/ncbi-tools
-	sci-biology/muscle
-	sci-biology/mummer
-	sci-biology/blat
-	sci-biology/bowtie
-	sci-biology/bwa
-	sci-biology/velvet
-	sci-biology/Ray
-	sci-biology/scan_for_matches
-	sci-biology/idba"
diff --git a/sci-biology/biopieces/metadata.xml b/sci-biology/biopieces/metadata.xml
deleted file mode 100644
index 138cb7705..000000000
--- a/sci-biology/biopieces/metadata.xml
+++ /dev/null
@@ -1,12 +0,0 @@
-<?xml version="1.0" encoding="UTF-8"?>
-<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
-<pkgmetadata>
-	<maintainer type="person">
-		<email>mmokrejs@fold.natur.cuni.cz</email>
-		<name>Martin Mokrejs</name>
-	</maintainer>
-	<maintainer type="project">
-		<email>sci-biology@gentoo.org</email>
-		<name>Gentoo Biology Project</name>
-	</maintainer>
-</pkgmetadata>
diff --git a/sci-biology/bismark/Manifest b/sci-biology/bismark/Manifest
index c908dd10e..6c227f9d5 100644
--- a/sci-biology/bismark/Manifest
+++ b/sci-biology/bismark/Manifest
@@ -1 +1 @@
-DIST bismark_v0.13.0.tar.gz 1667188 BLAKE2B c72f59d35a91e6511a6f52d93547eaff9eba20688ec86c592019689625ce8f31a3ba802c62850421c185c03b285ed8a53549059c7e99779abc376523aff8b79a SHA512 5915e28a9647189d49c584cc0a90ee64ddd444e4acf9bc6c6ae25e1b01b18ab35ca1c3fa3b59834d641fa6c4a4b465d43f2908d3b23f1d45297d49323d3511c0
+DIST bismark-0.23.0.tar.gz 8802084 BLAKE2B fdd7cb13ac86ab99040dc6bd9baa5d8ab7f311b918298b9e8df327c54a7339e876e298354bded9a0f2280f9b069f0a64a588a9263a95663fb131e29d51536fd0 SHA512 1d0c9e62583a46e59431adec1acc6a3dfa39d4a306253d61a2d64ae44259650e2a6600bf67d8f6fb85ddb694949b3dccc47b18b3a18d74445ba7ea3ed0a2b3b0
diff --git a/sci-biology/bismark/bismark-0.13.0.ebuild b/sci-biology/bismark/bismark-0.13.0.ebuild
deleted file mode 100644
index 98aa75a61..000000000
--- a/sci-biology/bismark/bismark-0.13.0.ebuild
+++ /dev/null
@@ -1,31 +0,0 @@
-# Copyright 1999-2017 Gentoo Foundation
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=6
-
-inherit toolchain-funcs
-
-DESCRIPTION="Map bisulfite converted sequence reads and cytosine methylation states"
-HOMEPAGE="http://www.bioinformatics.babraham.ac.uk/projects/bismark/"
-SRC_URI="http://www.bioinformatics.babraham.ac.uk/projects/${PN}/${PN}_v${PV}.tar.gz"
-
-LICENSE="GPL-3+"
-SLOT="0"
-KEYWORDS="~amd64 ~x86"
-IUSE="+doc"
-
-DEPEND=""
-RDEPEND="sci-biology/bowtie"
-
-S="${WORKDIR}/${PN}_v${PV}"
-
-src_install() {
-	dobin \
-		bismark{,2bedGraph,2report,_genome_preparation,_methylation_extractor} \
-		coverage2cytosine deduplicate_bismark
-	insinto /usr/share/${P}
-	doins bismark_sitrep.tpl
-	dosym ../share/${P}/bismark_sitrep.tpl /usr/bin/bismark_sitrep.tpl
-	use doc \
-		dodoc Bismark_User_Guide.pdf RRBS_Guide.pdf license.txt RELEASE_NOTES.txt
-}
diff --git a/sci-biology/bismark/bismark-0.23.0.ebuild b/sci-biology/bismark/bismark-0.23.0.ebuild
new file mode 100644
index 000000000..121447992
--- /dev/null
+++ b/sci-biology/bismark/bismark-0.23.0.ebuild
@@ -0,0 +1,25 @@
+# Copyright 1999-2021 Gentoo Authors
+# Distributed under the terms of the GNU General Public License v2
+
+EAPI=7
+
+DESCRIPTION="Map bisulfite converted sequence reads and cytosine methylation states"
+HOMEPAGE="https://www.bioinformatics.babraham.ac.uk/projects/"
+SRC_URI="https://github.com/FelixKrueger/Bismark/archive/${PV}.tar.gz -> ${P}.tar.gz"
+
+LICENSE="GPL-3+"
+SLOT="0"
+KEYWORDS="~amd64 ~x86"
+
+DEPEND=""
+RDEPEND="sci-biology/bowtie"
+
+S="${WORKDIR}/${P^}"
+
+src_install() {
+	dobin \
+		bismark{,2bedGraph,2report,_genome_preparation,_methylation_extractor} \
+		coverage2cytosine deduplicate_bismark
+	einstalldocs
+	dodoc -r Docs
+}
diff --git a/sci-biology/bismark/metadata.xml b/sci-biology/bismark/metadata.xml
index 4c433a8ca..4ee13c559 100644
--- a/sci-biology/bismark/metadata.xml
+++ b/sci-biology/bismark/metadata.xml
@@ -20,4 +20,7 @@ and gapped alignments; (4) Alignment seed length, number of mismatches etc. are
 adjustable; (5) Output discriminates between cytosine methylation in CpG, CHG
 and CHH context.
 </longdescription>
+	<upstream>
+		<remote-id type="github">FelixKrueger/Bismark</remote-id>
+	</upstream>
 </pkgmetadata>
diff --git a/sci-biology/blasr/blasr-9999.ebuild b/sci-biology/blasr/blasr-9999.ebuild
deleted file mode 100644
index 3fe868450..000000000
--- a/sci-biology/blasr/blasr-9999.ebuild
+++ /dev/null
@@ -1,49 +0,0 @@
-# Copyright 1999-2019 Gentoo Authors
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=5
-
-inherit git-r3
-
-DESCRIPTION="The PacBio long read aligner"
-HOMEPAGE="http://www.smrtcommunity.com/SMRT-Analysis/Algorithms/BLASR"
-#SRC_URI="https://github.com/PacificBiosciences/blasr/tarball/${PV} -> ${P}.tar.gz"
-SRC_URI=""
-EGIT_REPO_URI="https://github.com/PacificBiosciences/blasr.git"
-
-LICENSE="blasr"
-SLOT="0"
-IUSE="hdf5"
-KEYWORDS=""
-
-CDEPEND="
-	dev-util/meson
-	dev-util/ninja
-	dev-util/cmake
-	dev-util/pkgconfig"
-# needs libblasr
-DEPEND="
-	sci-biology/pbbam
-	dev-libs/boost:=[threads]
-	hdf5? ( >=sci-libs/hdf5-1.8.12[cxx] )" # needs H5Cpp.h
-RDEPEND=""
-
-S="${WORKDIR}/blasr-9999"
-
-#src_configure(){
-#	if use hdf5; then \
-#		python ./configure.py --shared --sub --no-pbbam HDF5_INCLUDE="${EPREFIX}"/usr/include HDF5_LIB="${EPREFIX}"/usr/lib64 || die
-#	else
-#		python ./configure.py --shared --sub --no-pbbam || die
-#	fi
-#}
-
-src_compile(){
-	bash scripts/ci/build.sh || die
-	# BUG: meson.build:54:0: ERROR:  Dependency "pbbam" not found, tried pkgconfig and cmake
-}
-
-src_install() {
-	dodir /usr/bin
-	emake install ASSEMBLY_HOME="${ED}/usr"
-}
diff --git a/sci-biology/blasr/metadata.xml b/sci-biology/blasr/metadata.xml
deleted file mode 100644
index 8417d1580..000000000
--- a/sci-biology/blasr/metadata.xml
+++ /dev/null
@@ -1,8 +0,0 @@
-<?xml version="1.0" encoding="UTF-8"?>
-<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
-<pkgmetadata>
-	<maintainer type="project">
-		<email>sci-biology@gentoo.org</email>
-		<name>Gentoo Biology Project</name>
-	</maintainer>
-</pkgmetadata>
diff --git a/sci-biology/blat/Manifest b/sci-biology/blat/Manifest
deleted file mode 100644
index f37d442e9..000000000
--- a/sci-biology/blat/Manifest
+++ /dev/null
@@ -1 +0,0 @@
-DIST blatSrc36.zip 3227463 BLAKE2B a7cb55725ece7d08cebe0a4ba9b1d8498e2477032843ca7e7de35759bfa083f81d567a95865aa5c2c0b0f926c8087450caa2385bdda2e2d73edce307b1f7dc98 SHA512 18ebd1082aa3c44739ddbf31cba05aaf2d5e83bec0884ebd40dfb775fcf06b3b404192d8a63af062373a2f7fc0ce8844cbec6b7451d8576e21ddaa76750bbd7b
diff --git a/sci-biology/blat/blat-36.ebuild b/sci-biology/blat/blat-36.ebuild
deleted file mode 100644
index 086d60ffd..000000000
--- a/sci-biology/blat/blat-36.ebuild
+++ /dev/null
@@ -1,48 +0,0 @@
-# Copyright 1999-2017 Gentoo Foundation
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=6
-
-inherit eutils toolchain-funcs
-
-MY_PN="${PN}Src"
-
-DESCRIPTION="The BLAST-Like Alignment Tool, a fast genomic sequence aligner"
-HOMEPAGE="http://www.cse.ucsc.edu/~kent/"
-SRC_URI="http://hgwdev.cse.ucsc.edu/~kent/src/${MY_PN}${PV}.zip"
-
-SLOT="0"
-LICENSE="blat"
-KEYWORDS="~amd64 ~x86"
-IUSE=""
-
-S="${WORKDIR}/${MY_PN}"
-
-DEPEND="
-	app-arch/unzip
-	virtual/mysql
-	virtual/libmysqlclient"
-RDEPEND=""
-
-src_prepare() {
-	eapply_user
-	epatch "${FILESDIR}"/${PV}-gentoo.patch
-	sed \
-		-e "1i\CFLAGS=${CFLAGS}" \
-		-e "1i\LDFLAGS=${LDFLAGS}" \
-		-i inc/common.mk || die
-	tc-export CC
-}
-
-src_compile() {
-	MACHTYPE=$(tc-arch)
-	[[ ${MACHTYPE} == "x86" ]] && MACHTYPE="i386"
-	mkdir -p "${S}/bin/${MACHTYPE}"
-	emake MACHTYPE="${MACHTYPE}" HOME="${S}" LDFLAGS="${LDFLAGS}"
-}
-
-src_install() {
-	MACHTYPE=$(tc-arch)
-	[[ ${MACHTYPE} == "x86" ]] && MACHTYPE="i386"
-	dobin "${S}/bin/${MACHTYPE}/"*
-}
diff --git a/sci-biology/blat/files/36-gentoo.patch b/sci-biology/blat/files/36-gentoo.patch
deleted file mode 100644
index d05fe64c2..000000000
--- a/sci-biology/blat/files/36-gentoo.patch
+++ /dev/null
@@ -1,27 +0,0 @@
---- blatSrc/inc/userApp.mk.old	2014-11-06 04:19:54.000000000 +0100
-+++ blatSrc/inc/userApp.mk	2016-07-28 12:45:32.092378879 +0200
-@@ -28,11 +28,11 @@
- objects = ${O} ${extraObjects} ${externObjects}
- 
- ${DESTDIR}${BINDIR}/${A}${EXE}: ${DEPLIBS} ${O} ${extraObjects}
--	${CC} ${COPT} -o ${DESTDIR}${BINDIR}/${A}${EXE} ${objects} ${LINKLIBS} ${L} -lm
-+	${CC} ${COPT} ${CFLAGS} ${LDFLAGS} -o ${DESTDIR}${BINDIR}/${A}${EXE} ${objects} ${LINKLIBS} ${L} -lm
- 	${STRIP} ${DESTDIR}${BINDIR}/${A}${EXE}
- 
- compile:: ${DEPLIBS} ${O} ${extraObjects}
--	${CC} ${COPT} ${CFLAGS} -o ${A}${EXE} ${objects} ${LINKLIBS} ${L} -lm
-+	${CC} ${COPT} ${CFLAGS} ${LDFLAGS} -o ${A}${EXE} ${objects} ${LINKLIBS} ${L} -lm
- 
- install:: compile
- 	rm -f ${DESTDIR}${BINDIR}/${A}${EXE}
---- blatSrc/blat/makefile.old	2011-03-29 03:43:44.000000000 +0200
-+++ blatSrc/blat/makefile	2016-07-28 12:41:11.905261175 +0200
-@@ -7,7 +7,7 @@
- O = blat.o
- 
- blat: $O $(MYLIBS)
--	${CC} ${COPT} ${CFLAGS} -o ${DESTDIR}${BINDIR}/blat $O $(MYLIBS) $L
-+	${CC} ${COPT} ${CFLAGS} ${LDFLAGS} -o ${DESTDIR}${BINDIR}/blat $O $(MYLIBS) $L
- 	${STRIP} ${DESTDIR}${BINDIR}/blat${EXE}
- 
- all:
diff --git a/sci-biology/blat/metadata.xml b/sci-biology/blat/metadata.xml
deleted file mode 100644
index 8417d1580..000000000
--- a/sci-biology/blat/metadata.xml
+++ /dev/null
@@ -1,8 +0,0 @@
-<?xml version="1.0" encoding="UTF-8"?>
-<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
-<pkgmetadata>
-	<maintainer type="project">
-		<email>sci-biology@gentoo.org</email>
-		<name>Gentoo Biology Project</name>
-	</maintainer>
-</pkgmetadata>
diff --git a/sci-biology/blue/Manifest b/sci-biology/blue/Manifest
deleted file mode 100644
index 9130b6b5b..000000000
--- a/sci-biology/blue/Manifest
+++ /dev/null
@@ -1,6 +0,0 @@
-DIST blue-1.1.2-Changes_for_Blue_1.1.2.pdf 310372 BLAKE2B 4c3da1739a89d6b8b8b3b15d3244c65795269c6696d87c9c3e9ff32aa7e96de8cc44e1b929a3b03669d70dc78a476dfc067f903814b013c8dbf7d58e0cef549c SHA512 1f6d595018e880a9d10197816881fa88bbc1da9613fb83d0c3b77fe3ea22e614a9fc9783abfa7f649c242a4966a6929c53fcd1b845f98280d50c491b4cff8f73
-DIST blue-1.1.2-Correcting_reads_with_Blue.pdf 560129 BLAKE2B 19b58a7276ed0d2ae47caade89e4de94e9c085a7e3f5aa824d643e507e447393d5f56e89deeccf5e920d39f604adab059b6b7a74f9a9c792673b2b2b31289210 SHA512 1341a7f3d4c77b3a3f8d66f57b4cc976930bf7d28219d77a3a91efde0bc76f08bf0159c98df3227a2484dc0fe7d40904dbbde74dc03b6c110649285314a07585
-DIST blue-1.1.2.tar.gz 658544 SHA256 c038fa9fd76330cb70059cd47979327708368e2d6b6d7edae00825ba39dc23bd SHA512 933b2a8bb1e1f3fed241cff2eac9566d49d77c3f97b2f22f4a8194f3cdf25c09ae474b4d681ff65914d695598579fded6433f6a47ad06b78879c36d58402ea4b WHIRLPOOL 32c89ae39cfadab9beae038afd530cf85d8c8775a84bd5e2c29a2e67246d9b09d5c872492c1836dfab6fe20e9f59a1b0aaddc5dc051393030ccff39bb08fec8e
-DIST blue-1.1.3-Changes_for_Blue_1.1.3.pdf 310372 BLAKE2B 4c3da1739a89d6b8b8b3b15d3244c65795269c6696d87c9c3e9ff32aa7e96de8cc44e1b929a3b03669d70dc78a476dfc067f903814b013c8dbf7d58e0cef549c SHA512 1f6d595018e880a9d10197816881fa88bbc1da9613fb83d0c3b77fe3ea22e614a9fc9783abfa7f649c242a4966a6929c53fcd1b845f98280d50c491b4cff8f73
-DIST blue-1.1.3-Correcting_reads_with_Blue.pdf 560129 BLAKE2B 19b58a7276ed0d2ae47caade89e4de94e9c085a7e3f5aa824d643e507e447393d5f56e89deeccf5e920d39f604adab059b6b7a74f9a9c792673b2b2b31289210 SHA512 1341a7f3d4c77b3a3f8d66f57b4cc976930bf7d28219d77a3a91efde0bc76f08bf0159c98df3227a2484dc0fe7d40904dbbde74dc03b6c110649285314a07585
-DIST blue-1.1.3.tar.gz 717341 BLAKE2B 0be8bb8b8e30b7185cc01c8b9affe39521216cd3d487ad2952af28271d955eadd14f74cdaeb3ce47324845defadc1091fc230923ba30138a990003dff8f82105 SHA512 fc51965a063ced80304b3e59eb538742f6f4a2970d02cecc346aa8b15e961a242b6ce6cc3a847c8e4f478bee997ed5794f304d201554398130c1a16bceb84c30
diff --git a/sci-biology/blue/blue-1.1.2.ebuild b/sci-biology/blue/blue-1.1.2.ebuild
deleted file mode 100644
index 13c88494e..000000000
--- a/sci-biology/blue/blue-1.1.2.ebuild
+++ /dev/null
@@ -1,37 +0,0 @@
-# Copyright 1999-2015 Gentoo Foundation
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=5
-
-DESCRIPTION="Error corrector for Illummina and Roche/454, inculding insertions and deletions"
-HOMEPAGE="http://www.bioinformatics.csiro.au/blue"
-SRC_URI="
-	http://www.bioinformatics.csiro.au/public/files/Linux-${PV}.tar.gz -> ${P}.tar.gz
-	http://www.bioinformatics.csiro.au/public/files/Correcting_reads_with_Blue.pdf -> ${P}-Correcting_reads_with_Blue.pdf
-	http://www.bioinformatics.csiro.au/public/files/Changes_for_Blue_1.1.3.pdf -> ${P}-Changes_for_Blue_${PV}.pdf"
-LICENSE="GPL-2+"
-SLOT="0"
-KEYWORDS=""
-IUSE=""
-
-DEPEND="dev-lang/mono"
-RDEPEND="${DEPEND}"
-
-S="${WORKDIR}"/Linux
-
-src_compile(){
-	Blue/compile.sh || die
-	Tessel/compile.sh || die
-	GenerateMerPairs/compile.sh || die
-}
-
-src_install(){
-	dobin Tessel.exe GenerateMerPairs.exe Blue.exe
-	# one could install also the *.exe.so files for speedup into /usr/bin/
-
-	# The -hp option sets a flag that is checked when Blue is scanning along a read trying to find errors that could be corrected. There are a number of tests done at every base position, all based on depth of coverage. These tests will pick up random indel errors, but indels are so common at the end of homopolymer runs in 454 and IonTorrent data that multiple hp run lengths all look to be OK. For example, if our genome had AAAAAA then with Illumina data this is what we'd see almost all the time, with very rare indels at the end of the hp run resulting in runs of 5 or 7 As. With 454-like data, we'd probably get 5 As as frequently as 6 As so depth of coverage would say that neither of them are errors. The -hp flag looks out for the end of hp runs and forces an attempt at correction at that point. If the read wasn't in error, then no correction will be made.
-
-	# In general Blue will correct Ns - if a correct replacement can be found. The only time it doesn't do this is if there are too many consecutive Ns - as the process of finding likely replacements is combinatoric and the cost goes up exponentially with the number of consecutive Ns. In these cases, the read is abandoned and passed through uncorrected. Can you give an example of a read that you would like to see corrected differently?
-}
-
-# it's author uses 'mono-sgen /usr/bin/Blue.exe' to use the alternative garbage collector
diff --git a/sci-biology/blue/blue-1.1.3.ebuild b/sci-biology/blue/blue-1.1.3.ebuild
deleted file mode 100644
index cee0e8065..000000000
--- a/sci-biology/blue/blue-1.1.3.ebuild
+++ /dev/null
@@ -1,37 +0,0 @@
-# Copyright 1999-2015 Gentoo Foundation
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=5
-
-DESCRIPTION="Error corrector for Illummina and Roche/454, including insertions and deletions"
-HOMEPAGE="http://www.bioinformatics.csiro.au/blue"
-SRC_URI="
-	http://www.bioinformatics.csiro.au/public/files/Linux-${PV}.tar.gz -> ${P}.tar.gz
-	http://www.bioinformatics.csiro.au/public/files/Correcting_reads_with_Blue.pdf -> ${P}-Correcting_reads_with_Blue.pdf
-	http://www.bioinformatics.csiro.au/public/files/Changes_for_Blue_1.1.3.pdf -> ${P}-Changes_for_Blue_${PV}.pdf"
-LICENSE="GPL-2+"
-SLOT="0"
-KEYWORDS=""
-IUSE=""
-
-DEPEND="dev-lang/mono"
-RDEPEND="${DEPEND}"
-
-S="${WORKDIR}"/Linux
-
-src_compile(){
-	Blue/compile.sh || die
-	Tessel/compile.sh || die
-	GenerateMerPairs/compile.sh || die
-}
-
-src_install(){
-	dobin Tessel.exe GenerateMerPairs.exe Blue.exe
-	# one could install also the *.exe.so files for speedup into /usr/bin/
-
-	# The -hp option sets a flag that is checked when Blue is scanning along a read trying to find errors that could be corrected. There are a number of tests done at every base position, all based on depth of coverage. These tests will pick up random indel errors, but indels are so common at the end of homopolymer runs in 454 and IonTorrent data that multiple hp run lengths all look to be OK. For example, if our genome had AAAAAA then with Illumina data this is what we'd see almost all the time, with very rare indels at the end of the hp run resulting in runs of 5 or 7 As. With 454-like data, we'd probably get 5 As as frequently as 6 As so depth of coverage would say that neither of them are errors. The -hp flag looks out for the end of hp runs and forces an attempt at correction at that point. If the read wasn't in error, then no correction will be made.
-
-	# In general Blue will correct Ns - if a correct replacement can be found. The only time it doesn't do this is if there are too many consecutive Ns - as the process of finding likely replacements is combinatoric and the cost goes up exponentially with the number of consecutive Ns. In these cases, the read is abandoned and passed through uncorrected. Can you give an example of a read that you would like to see corrected differently?
-}
-
-# it's author uses 'mono-sgen /usr/bin/Blue.exe' to use the alternative garbage collector
diff --git a/sci-biology/blue/metadata.xml b/sci-biology/blue/metadata.xml
deleted file mode 100644
index 138cb7705..000000000
--- a/sci-biology/blue/metadata.xml
+++ /dev/null
@@ -1,12 +0,0 @@
-<?xml version="1.0" encoding="UTF-8"?>
-<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
-<pkgmetadata>
-	<maintainer type="person">
-		<email>mmokrejs@fold.natur.cuni.cz</email>
-		<name>Martin Mokrejs</name>
-	</maintainer>
-	<maintainer type="project">
-		<email>sci-biology@gentoo.org</email>
-		<name>Gentoo Biology Project</name>
-	</maintainer>
-</pkgmetadata>
diff --git a/sci-biology/bowtie/Manifest b/sci-biology/bowtie/Manifest
deleted file mode 100644
index 87beeab0c..000000000
--- a/sci-biology/bowtie/Manifest
+++ /dev/null
@@ -1 +0,0 @@
-DIST bowtie2-2.3.4.3-source.zip 17156180 BLAKE2B 4004aa417f318f5540b129eb97d7f14d31b087c77bb767d547b195d3b966ec272fe7df5888d60b5501330d2ac011f05bdc9b062fa34d5b96b2b29ea0b6167a5c SHA512 9e048c1a86a479c5fe728a492129372d2366d6c50530e05db3faad5ac055596d9f95ac0a9f50099ab3dd945893a587c02e8aaa9b62cc3ead75f6691c52413a2f
diff --git a/sci-biology/bowtie/bowtie-1.2.2_beta20190219.ebuild b/sci-biology/bowtie/bowtie-1.2.2_beta20190219.ebuild
deleted file mode 100644
index fcf0b4516..000000000
--- a/sci-biology/bowtie/bowtie-1.2.2_beta20190219.ebuild
+++ /dev/null
@@ -1,81 +0,0 @@
-# Copyright 1999-2019 Gentoo Authors
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=6
-
-inherit flag-o-matic toolchain-funcs git-r3
-
-DESCRIPTION="Popular short read aligner for Next-generation sequencing data"
-HOMEPAGE="http://bowtie-bio.sourceforge.net/"
-EGIT_REPO_URI="https://github.com/BenLangmead/bowtie.git"
-EGIT_BRANCH="bug_fixes"
-COMMIT="f253e204f5ba4565d14ae1b300ea6cb10dfe4660"
-
-LICENSE="Artistic"
-SLOT="1"
-KEYWORDS="~amd64 ~x86"
-
-IUSE="examples +tbb"
-
-RDEPEND="tbb? ( dev-cpp/tbb )"
-DEPEND="${RDEPEND}
-	app-arch/unzip"
-#	sci-biology/seqan:1.4"
-
-DOCS=( AUTHORS NEWS TUTORIAL doc/README )
-HTML_DOCS=( doc/{manual.html,style.css} )
-
-PATCHES=( "${FILESDIR}/bowtie-1.2.2-fix-isa-return-type.patch" )
-# not needed
-# "${FILESDIR}/${P}-fix-Intel-compilation.patch", obsoleted by https://github.com/BenLangmead/bowtie/commit/d8b661fb36c129cb9899fcd3689b3618036f8c7b
-#
-# still to be considered
-#PATCHES=(
-#	"${FILESDIR}/${P}-_ContextLss-1.1-1.4.patch"
-#	"${FILESDIR}/${P}-unbundle-seqan.patch"
-#	"${FILESDIR}/${P}-fix-setBegin-call.patch"
-#	"${FILESDIR}/${P}-seqan-popcount.patch"
-#	"${FILESDIR}/${P}-seqan-rename-ChunkPool.patch"
-#	"${FILESDIR}/${P}-seqan-rename-fill-to-resize.patch"
-#	"${FILESDIR}/${P}-spelling.patch"
-#	"${FILESDIR}/${P}-tbb-tinythread-missing.patch"
-#)
-
-src_prepare() {
-	default
-
-	# remove bundled library of headers, use system seqan 1.4
-	# rm -rf SeqAn-1.1/ third_party/ || die
-
-	# innocuous non-security flags, prevent log pollution
-	append-cxxflags \
-		-Wno-unused-local-typedefs \
-		-Wno-unused-but-set-variable \
-		-Wno-unused-variable
-}
-
-src_compile() {
-	emake \
-		CC="$(tc-getCC)" \
-		CPP="$(tc-getCXX)" \
-		CFLAGS="" \
-		CXXFLAGS="" \
-		EXTRA_FLAGS="${LDFLAGS}" \
-		RELEASE_FLAGS="${CXXFLAGS}" \
-		WITH_TBB="$(usex tbb 1 0)"
-}
-
-src_install() {
-	dobin ${PN} ${PN}-*
-
-	exeinto /usr/libexec/${PN}
-	doexe scripts/*
-
-	newman MANUAL ${PN}.1
-	einstalldocs
-
-	if use examples; then
-		insinto /usr/share/${PN}
-		doins -r genomes indexes
-	fi
-}
diff --git a/sci-biology/bowtie/bowtie-2.3.4.3.ebuild b/sci-biology/bowtie/bowtie-2.3.4.3.ebuild
deleted file mode 100644
index eea3059cf..000000000
--- a/sci-biology/bowtie/bowtie-2.3.4.3.ebuild
+++ /dev/null
@@ -1,62 +0,0 @@
-# Copyright 1999-2019 Gentoo Authors
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=6
-
-inherit toolchain-funcs
-
-DESCRIPTION="Popular short read aligner for Next-generation sequencing data"
-HOMEPAGE="http://bowtie-bio.sourceforge.net/bowtie2/"
-SRC_URI="mirror://sourceforge/project/${PN}-bio/${PN}2/${PV}/${PN}2-${PV}-source.zip"
-
-LICENSE="GPL-3"
-SLOT="2"
-KEYWORDS=""
-
-IUSE="examples cpu_flags_x86_sse2 +tbb"
-
-RDEPEND="dev-lang/perl
-	tbb? ( dev-cpp/tbb )"
-DEPEND="${RDEPEND}
-	app-arch/unzip
-	sys-libs/readline"
-
-S="${WORKDIR}/${PN}2-${PV}"
-
-DOCS=( AUTHORS NEWS TUTORIAL )
-HTML_DOCS=( doc/{manual.html,style.css} )
-#PATCHES=( "${FILESDIR}/${P}-fix-c++14.patch" ) # needs 2.3.4.3 update
-
-pkg_pretend() {
-	if ! use cpu_flags_x86_sse2 ; then
-		eerror "This package requires a CPU supporting the SSE2 instruction set."
-		die "SSE2 support missing"
-	fi
-}
-
-src_compile() {
-	emake \
-		CC="$(tc-getCC)" \
-		CPP="$(tc-getCXX)" \
-		CXX="$(tc-getCXX)" \
-		CFLAGS="" \
-		CXXFLAGS="" \
-		EXTRA_FLAGS="${LDFLAGS}" \
-		RELEASE_FLAGS="${CXXFLAGS} -msse2" \
-		WITH_TBB="$(usex tbb 1 0)"
-}
-
-src_install() {
-	dobin ${PN}2 ${PN}2-*
-
-	exeinto /usr/libexec/${PN}2
-	doexe scripts/*
-
-	newman MANUAL ${PN}2.1
-	einstalldocs
-
-	if use examples; then
-		insinto /usr/share/${PN}2
-		doins -r example
-	fi
-}
diff --git a/sci-biology/bowtie/files/bowtie-1.2.2-_ContextLss-1.1-1.4.patch b/sci-biology/bowtie/files/bowtie-1.2.2-_ContextLss-1.1-1.4.patch
deleted file mode 100644
index 4bcd61ba3..000000000
--- a/sci-biology/bowtie/files/bowtie-1.2.2-_ContextLss-1.1-1.4.patch
+++ /dev/null
@@ -1,17 +0,0 @@
-Description: Change class name of _Context_LSS
- New version 1.4 of SeQan uses a different name of the class. 
-Forwarded: no
-Author: Gert Wollny <gw.fossdev@gmail.com>
-Last-Update: 2014-100-06
-
---- bowtie-1.2.2/diff_sample.h	2017-11-03 01:25:56.000000000 +0100
-+++ bowtie-1.2.2/diff_sample.h	2019-02-18 12:50:37.894674282 +0100
-@@ -979,7 +979,7 @@
- 	{
- 		Timer timer(cout, "  Invoking Larsson-Sadakane on ranks time: ", this->verbose());
- 		VMSG_NL("  Invoking Larsson-Sadakane on ranks");
--		_Context_LSS<TIndexOff> c;
-+		ContextLss_<TIndexOff> c;
- 		c.suffixsort(
- 			(TIndexOff*)begin(_isaPrime, Standard()),
- 			(TIndexOff*)begin(sPrime, Standard()),
diff --git a/sci-biology/bowtie/files/bowtie-1.2.2-fix-Intel-compilation.patch b/sci-biology/bowtie/files/bowtie-1.2.2-fix-Intel-compilation.patch
deleted file mode 100644
index 75942efb5..000000000
--- a/sci-biology/bowtie/files/bowtie-1.2.2-fix-Intel-compilation.patch
+++ /dev/null
@@ -1,32 +0,0 @@
-fix compilation errors with Intel compilers:
-error: no operator "=" matches these operands
-author: Ward Poelmans
---- bowtie-1.2.2/hit.h	2018-01-24 12:57:47.135575442 +0100
-+++ bowtie-1.2.2/hit.h	2018-01-24 12:57:58.615869774 +0100
-@@ -640,10 +640,26 @@
- 			s.moveTo(btString);
- 		}
- 
-+		batch(const batch &other)
-+                {
-+                    batchId = other.batchId;
-+                    isWritten = other.isWritten;
-+                    btString = other.btString;
-+                }
-+
- 		bool operator<(const batch& other) const {
- 			return batchId < other.batchId;
- 		}
- 
-+		batch& operator=(batch&& other) {
-+			if (&other != this) {
-+				batchId = other.batchId;
-+				isWritten = other.isWritten;
-+				other.btString.moveTo(btString);
-+			}
-+			return *this;
-+		}
-+
- 		batch& operator=(batch& other) {
- 			if (&other != this) {
- 				batchId = other.batchId;
diff --git a/sci-biology/bowtie/files/bowtie-1.2.2-fix-isa-return-type.patch b/sci-biology/bowtie/files/bowtie-1.2.2-fix-isa-return-type.patch
deleted file mode 100644
index de19e42a8..000000000
--- a/sci-biology/bowtie/files/bowtie-1.2.2-fix-isa-return-type.patch
+++ /dev/null
@@ -1,22 +0,0 @@
-From 58c6ac97b1938909881877ef83167f5eff0e8ab1 Mon Sep 17 00:00:00 2001
-From: Rone Charles <rone_charles@fastmail.com>
-Date: Tue, 4 Sep 2018 21:06:39 -0400
-Subject: [PATCH] Fix isa return type
-
----
- ebwt.h | 2 +-
- 1 file changed, 1 insertion(+), 1 deletion(-)
-
-diff --git a/ebwt.h b/ebwt.h
-index fe6300cc..8f886b8d 100644
---- a/ebwt.h
-+++ b/ebwt.h
-@@ -862,7 +862,7 @@ class Ebwt {
- 	TIndexOffU*   ftab() const         { return _ftab; }
- 	TIndexOffU*   eftab() const        { return _eftab; }
- 	TIndexOffU*   offs() const         { return _offs; }
--	uint32_t*   isa() const          { return _isa; } /* check */
-+	TIndexOffU*   isa() const          { return _isa; } /* check */
- 	TIndexOffU*   plen() const         { return _plen; }
- 	TIndexOffU*   rstarts() const      { return _rstarts; }
- 	uint8_t*    ebwt() const         { return _ebwt; }
diff --git a/sci-biology/bowtie/files/bowtie-1.2.2-unbundle-seqan.patch b/sci-biology/bowtie/files/bowtie-1.2.2-unbundle-seqan.patch
deleted file mode 100644
index b1a5f98f5..000000000
--- a/sci-biology/bowtie/files/bowtie-1.2.2-unbundle-seqan.patch
+++ /dev/null
@@ -1,14 +0,0 @@
---- bowtie-1.2.2/Makefile	2019-02-18 13:26:29.490835084 +0100
-+++ bowtie-1.2.2/Makefile	2019-02-18 13:28:36.864742545 +0100
-@@ -5,10 +5,7 @@
- prefix = /usr/local
- bindir = $(prefix)/bin
- 
--SEQAN_DIR = ./SeqAn-1.1
--# treat SeqAn as a sysdir to suppress warnings
--SEQAN_INC = -isystem $(SEQAN_DIR)
--INC = $(if $(RELEASE_BUILD),-I$(CURDIR)/.include) $(SEQAN_INC) -I third_party
-+INC = $(if $(RELEASE_BUILD),-I$(CURDIR)/.include) `pkg-config --cflags seqan-1.4` -I third_party
- CPP = g++
- CXX = $(CPP)
- CC = gcc
diff --git a/sci-biology/bowtie/files/bowtie-1.2.2-void2int.patch b/sci-biology/bowtie/files/bowtie-1.2.2-void2int.patch
deleted file mode 100644
index 822b673ae..000000000
--- a/sci-biology/bowtie/files/bowtie-1.2.2-void2int.patch
+++ /dev/null
@@ -1,16 +0,0 @@
-#The latest Intel compiler (2016,2017) complains about the incompatibility of "void *" argument
-#being incompatible with parameter of type "int *"
-#M. Fujinaga (fujinaga@ualberta.ca)
---- processor_support.h	2017-02-02 21:48:42.436432756 +0000
-+++ processor_support.h	2017-02-02 21:48:54.419309743 +0000
-@@ -44,8 +44,8 @@
- 
-     try {
- #if ( defined(USING_INTEL_COMPILER) || defined(USING_MSC_COMPILER) )
--        __cpuid((void *) &regs,0); // test if __cpuid() works, if not catch the exception
--        __cpuid((void *) &regs,0x1); // POPCNT bit is bit 23 in ECX
-+        __cpuid((int *) &regs,0); // test if __cpuid() works, if not catch the exception
-+        __cpuid((int *) &regs,0x1); // POPCNT bit is bit 23 in ECX
- #elif defined(USING_GCC_COMPILER)
-         __get_cpuid(0x1, &regs.EAX, &regs.EBX, &regs.ECX, &regs.EDX);
- #else
diff --git a/sci-biology/bowtie/metadata.xml b/sci-biology/bowtie/metadata.xml
deleted file mode 100644
index 71e8d3bb8..000000000
--- a/sci-biology/bowtie/metadata.xml
+++ /dev/null
@@ -1,16 +0,0 @@
-<?xml version="1.0" encoding="UTF-8"?>
-<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
-<pkgmetadata>
-  <maintainer type="project">
-    <email>sci-biology@gentoo.org</email>
-    <name>Gentoo Biology Project</name>
-  </maintainer>
-  <upstream>
-    <remote-id type="sourceforge">bowtie-bio</remote-id>
-  </upstream>
-  <use>
-    <flag name="tbb">Enables building bowtie with the Intel
-      Threading Building Blocks from <pkg>dev-cpp/tbb</pkg>. This
-      flag is recommended.</flag>
-  </use>
-</pkgmetadata>
diff --git a/sci-biology/brat/brat-1.2.4.ebuild b/sci-biology/brat/brat-1.2.4.ebuild
index 39e29328d..2be8dcf0b 100644
--- a/sci-biology/brat/brat-1.2.4.ebuild
+++ b/sci-biology/brat/brat-1.2.4.ebuild
@@ -1,7 +1,7 @@
-# Copyright 1999-2016 Gentoo Foundation
+# Copyright 1999-2021 Gentoo Authors
 # Distributed under the terms of the GNU General Public License v2
 
-EAPI=5
+EAPI=7
 
 inherit toolchain-funcs
 
@@ -11,13 +11,10 @@ SRC_URI="http://compbio.cs.ucr.edu/${PN}/downloads/${P}.tar.gz"
 
 LICENSE="GPL-3"
 SLOT="0"
-IUSE=""
 KEYWORDS="~amd64 ~x86"
 
-DEPEND=""
-RDEPEND=""
-
 src_prepare() {
+	default
 	sed \
 		-e "s:g++:$(tc-getCXX):g" \
 		-e "s:-O3:${CFLAGS} ${LDFLAGS}:g" \
diff --git a/sci-biology/brat_bw/brat_bw-2.0.1.ebuild b/sci-biology/brat_bw/brat_bw-2.0.1.ebuild
index 6ffdaa7c0..d6daf3d1f 100644
--- a/sci-biology/brat_bw/brat_bw-2.0.1.ebuild
+++ b/sci-biology/brat_bw/brat_bw-2.0.1.ebuild
@@ -1,7 +1,7 @@
-# Copyright 1999-2016 Gentoo Foundation
+# Copyright 1999-2021 Gentoo Authors
 # Distributed under the terms of the GNU General Public License v2
 
-EAPI=5
+EAPI=7
 
 inherit toolchain-funcs
 
@@ -11,13 +11,13 @@ SRC_URI="http://compbio.cs.ucr.edu/brat/downloads/${P}.tar.gz"
 
 LICENSE="GPL-3"
 SLOT="0"
-IUSE=""
 KEYWORDS="~amd64 ~x86"
 
 DEPEND=""
 RDEPEND="!sci-biology/brat"
 
 src_prepare() {
+	default
 	sed \
 		-e "s:-Wl,-O1 : :g" \
 		-e "s:g++:$(tc-getCXX):g" \
diff --git a/sci-biology/brat_nova/brat_nova-20160103.ebuild b/sci-biology/brat_nova/brat_nova-20160103.ebuild
index d67acaeb6..6acb579a6 100644
--- a/sci-biology/brat_nova/brat_nova-20160103.ebuild
+++ b/sci-biology/brat_nova/brat_nova-20160103.ebuild
@@ -1,7 +1,7 @@
-# Copyright 1999-2016 Gentoo Foundation
+# Copyright 1999-2021 Gentoo Authors
 # Distributed under the terms of the GNU General Public License v2
 
-EAPI=5
+EAPI=7
 
 inherit toolchain-funcs
 
@@ -11,7 +11,6 @@ SRC_URI="http://compbio.cs.ucr.edu/brat/downloads/brat_nova.tar.gz -> ${P}.tar.g
 
 LICENSE="GPL-3"
 SLOT="0"
-IUSE=""
 KEYWORDS="~amd64 ~x86"
 
 DEPEND=""
@@ -21,6 +20,7 @@ RDEPEND="!sci-biology/brat
 S="${WORKDIR}"/"${PN}"
 
 src_prepare() {
+	default
 	sed \
 		-e "s:g++:$(tc-getCXX):g" \
 		-e "s:-O3 -w:${CFLAGS} ${LDFLAGS}:g" \
diff --git a/sci-biology/breakdancer/breakdancer-9999.ebuild b/sci-biology/breakdancer/breakdancer-9999.ebuild
deleted file mode 100644
index 9944acce4..000000000
--- a/sci-biology/breakdancer/breakdancer-9999.ebuild
+++ /dev/null
@@ -1,22 +0,0 @@
-# Copyright 1999-2017 Gentoo Foundation
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=6
-
-inherit cmake-utils git-r3 perl-functions
-
-DESCRIPTION="Genome-wide detection of structural variants from paired-end sequencing reads"
-HOMEPAGE="http://gmt.genome.wustl.edu/packages/breakdancer"
-EGIT_REPO_URI="https://github.com/genome/breakdancer.git"
-
-LICENSE="GPL-3"
-SLOT="0"
-IUSE=""
-KEYWORDS=""
-
-# http://search.cpan.org/~callahan/Math-CDF-0.1/CDF.pm
-DEPEND="
-	dev-lang/perl
-	dev-perl/Statistics-Descriptive
-	sci-biology/samtools:0"
-RDEPEND="${DEPEND}"
diff --git a/sci-biology/breakdancer/metadata.xml b/sci-biology/breakdancer/metadata.xml
deleted file mode 100644
index 138cb7705..000000000
--- a/sci-biology/breakdancer/metadata.xml
+++ /dev/null
@@ -1,12 +0,0 @@
-<?xml version="1.0" encoding="UTF-8"?>
-<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
-<pkgmetadata>
-	<maintainer type="person">
-		<email>mmokrejs@fold.natur.cuni.cz</email>
-		<name>Martin Mokrejs</name>
-	</maintainer>
-	<maintainer type="project">
-		<email>sci-biology@gentoo.org</email>
-		<name>Gentoo Biology Project</name>
-	</maintainer>
-</pkgmetadata>
diff --git a/sci-biology/brkraw/Manifest b/sci-biology/brkraw/Manifest
new file mode 100644
index 000000000..6bc79d823
--- /dev/null
+++ b/sci-biology/brkraw/Manifest
@@ -0,0 +1 @@
+DIST brkraw-0.3.11.gh.tar.gz 3919122 BLAKE2B 9881f53bb3fef038385eab4043f76d21c2e5391131c80daa49c909e7882359ed9d0b41b84fc82acd0432f4bac820a75061842de85b75cceff6f33d6f14988aea SHA512 a1e2725b6f50ff82ea6c4f9eacbd044ccb1c966aa26f2753c0872e3ee5e6469821dad336c9ef221dc6e15df2bed537ed9d31d5b09ff432694b757ab30af53631
diff --git a/sci-biology/brkraw/brkraw-0.3.11.ebuild b/sci-biology/brkraw/brkraw-0.3.11.ebuild
new file mode 100644
index 000000000..60a7767b1
--- /dev/null
+++ b/sci-biology/brkraw/brkraw-0.3.11.ebuild
@@ -0,0 +1,36 @@
+# Copyright 1999-2023 Gentoo Authors
+# Distributed under the terms of the GNU General Public License v2
+
+EAPI=8
+
+PYTHON_COMPAT=( python3_{10..11} )
+
+DISTUTILS_USE_PEP517=setuptools
+
+inherit distutils-r1 pypi
+
+DESCRIPTION="Fast and easy statistical learning on NeuroImaging data"
+HOMEPAGE="https://github.com/BrkRaw/brkraw"
+SRC_URI="https://github.com/BrkRaw/brkraw/archive/refs/tags/${PV}.tar.gz -> ${P}.gh.tar.gz"
+
+LICENSE="GPL-3"
+SLOT="0"
+KEYWORDS="~amd64 ~x86"
+IUSE="test"
+# Strange test infrastructure involving dynamic download via make:
+# https://github.com/BrkRaw/brkraw/blob/main/.github/workflows/test.yml
+RESTRICT="test"
+
+RDEPEND="
+	>=dev-python/numpy-1.18[${PYTHON_USEDEP}]
+	>=dev-python/pillow-7.1.1[${PYTHON_USEDEP}]
+	>=dev-python/tqdm-4.45.0[${PYTHON_USEDEP}]
+	>=dev-python/openpyxl-3.0.3[${PYTHON_USEDEP}]
+	>=dev-python/xlrd-1.1.0[${PYTHON_USEDEP}]
+	>=dev-python/pandas-1[${PYTHON_USEDEP}]
+	>=sci-libs/nibabel-3.0.2[${PYTHON_USEDEP}]
+"
+
+PATCHES=( "${FILESDIR}/${P}-testexclusion.patch" )
+
+distutils_enable_tests pytest
diff --git a/sci-biology/brkraw/files/brkraw-0.3.11-testexclusion.patch b/sci-biology/brkraw/files/brkraw-0.3.11-testexclusion.patch
new file mode 100644
index 000000000..40cc8fc4a
--- /dev/null
+++ b/sci-biology/brkraw/files/brkraw-0.3.11-testexclusion.patch
@@ -0,0 +1,11 @@
+--- a/setup.py	2023-07-05 17:09:42.000000000 -0400
++++ b/setup.py	2023-11-28 12:38:07.726369571 -0500
+@@ -24,7 +24,7 @@
+       author_email=__email__,
+       url=__url__,
+       license='GNLv3',
+-      packages=find_packages(),
++      packages=find_packages(exclude=["tests", "tests.*"]),
+       install_requires=['nibabel>=3.0.2',
+                         'numpy>=1.18.0',
+                         'pandas>=1.0.0',
diff --git a/sci-biology/brkraw/metadata.xml b/sci-biology/brkraw/metadata.xml
new file mode 100644
index 000000000..5c436db45
--- /dev/null
+++ b/sci-biology/brkraw/metadata.xml
@@ -0,0 +1,16 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
+<pkgmetadata>
+	<maintainer type="person">
+		<email>gentoo@chymera.eu</email>
+		<name>Horea Christian</name>
+	</maintainer>
+	<maintainer type="project">
+		<email>sci@gentoo.org</email>
+		<name>Gentoo Science Project</name>
+	</maintainer>
+	<upstream>
+		<remote-id type="github">BrkRaw/brkraw</remote-id>
+		<remote-id type="pypi">brkraw</remote-id>
+	</upstream>
+</pkgmetadata>
diff --git a/sci-biology/bru2nii/Manifest b/sci-biology/bru2nii/Manifest
index d540edffe..e9be6b129 100644
--- a/sci-biology/bru2nii/Manifest
+++ b/sci-biology/bru2nii/Manifest
@@ -1,2 +1 @@
-DIST bru2nii-1.0.20161212b.tar.gz 2604936 BLAKE2B 868540aab5e69d0f3e8e02d754b6df109c1d88cde3fef761f67d7b120d97543292258eb1ad8ff230dbcb0a4d769cf9d90049db3da6d7f51ce28b1277cb66a136 SHA512 d35a21a5b07c8d30043c2696369508d3440ead31206aabd79b259a5ec5b6ff0c05f92b748066b236ae08048b02683dc3af91983985e59fe4365f67f869bcd330
 DIST bru2nii-1.0.20180303.tar.gz 555129 BLAKE2B e64d1e98d306460cc63f7e8c3b7da7d41c80e084686a40b8446fe45344872b13a6db7eee285d5afa932c5e3e3cccd337673a0a9555666f9e5b0b676a44a55639 SHA512 96050f929d1d596d94d84ecfd2db704e48ca1d0922a63e1e06b5d6c297d0a2a14a78c18a58ae81b105af5d2d7c99d9d38a96d8734365045e11166bfc9f93ccac
diff --git a/sci-biology/bru2nii/bru2nii-1.0.20161212b.ebuild b/sci-biology/bru2nii/bru2nii-1.0.20161212b.ebuild
deleted file mode 100644
index 507aee256..000000000
--- a/sci-biology/bru2nii/bru2nii-1.0.20161212b.ebuild
+++ /dev/null
@@ -1,32 +0,0 @@
-# Copyright 1999-2016 Gentoo Foundation
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=6
-
-DESCRIPTION="Converts Bruker ParaVision MRI data to the NIfTI file format"
-HOMEPAGE="https://github.com/neurolabusc/Bru2Nii"
-SRC_URI="https://github.com/neurolabusc/Bru2Nii/archive/v${PV}.tar.gz -> ${P}.tar.gz"
-
-LICENSE="|| ( Artistic GPL-1+ )"
-SLOT="0"
-KEYWORDS="~amd64"
-IUSE="gui"
-
-RDEPEND=""
-DEPEND="dev-lang/fpc
-	gui? ( dev-lang/lazarus )"
-
-S="${WORKDIR}/Bru2Nii-${PV}"
-
-src_compile() {
-	fpc -Tlinux Bru2.lpr || die
-	if use gui ; then
-		lazbuild -B --lazarusdir="/usr/share/lazarus/" Bru2Nii.lpr || die
-	fi
-}
-
-src_install() {
-	dobin Bru2
-	use gui && dobin Bru2Nii
-	dodoc README.md
-}
diff --git a/sci-biology/bru2nii/bru2nii-1.0.20180303.ebuild b/sci-biology/bru2nii/bru2nii-1.0.20180303.ebuild
index 19ff47564..7ce360f79 100644
--- a/sci-biology/bru2nii/bru2nii-1.0.20180303.ebuild
+++ b/sci-biology/bru2nii/bru2nii-1.0.20180303.ebuild
@@ -1,7 +1,7 @@
-# Copyright 1999-2018 Gentoo Foundation
+# Copyright 1999-2020 Gentoo Authors
 # Distributed under the terms of the GNU General Public License v2
 
-EAPI=6
+EAPI=7
 
 DESCRIPTION="Converts Bruker ParaVision MRI data to the NIfTI file format"
 HOMEPAGE="https://github.com/neurolabusc/Bru2Nii"
diff --git a/sci-biology/bru2nii/bru2nii-9999.ebuild b/sci-biology/bru2nii/bru2nii-9999.ebuild
deleted file mode 100644
index 4a3297964..000000000
--- a/sci-biology/bru2nii/bru2nii-9999.ebuild
+++ /dev/null
@@ -1,32 +0,0 @@
-# Copyright 1999-2016 Gentoo Foundation
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=6
-
-inherit git-r3
-
-DESCRIPTION="Converts Bruker ParaVision MRI data to the NIfTI file format"
-HOMEPAGE="https://github.com/neurolabusc/Bru2Nii"
-SRC_URI=""
-EGIT_REPO_URI="https://github.com/neurolabusc/Bru2Nii.git"
-
-LICENSE="|| ( Artistic GPL-1+ )"
-SLOT="0"
-IUSE="gui"
-
-RDEPEND=""
-DEPEND="dev-lang/fpc
-	gui? ( dev-lang/lazarus )"
-
-src_compile() {
-	fpc -Tlinux Bru2.lpr || die
-	if use gui ; then
-		lazbuild -B --lazarusdir="/usr/share/lazarus/" Bru2Nii.lpr || die
-	fi
-}
-
-src_install() {
-	dobin Bru2
-	use gui && dobin Bru2Nii
-	dodoc README.md
-}
diff --git a/sci-biology/bru2nii/metadata.xml b/sci-biology/bru2nii/metadata.xml
index 30f63e57e..e4dfe274b 100644
--- a/sci-biology/bru2nii/metadata.xml
+++ b/sci-biology/bru2nii/metadata.xml
@@ -6,10 +6,10 @@
 		<name>Gentoo Science Project</name>
 	</maintainer>
 	<longdescription lang="en">
-This is a simple tool for converting Bruker ParaVision MRI data to
-the NIfTI file format. It includes both a drag-and-drop graphical
-interface (Bru2Nii) as well as a command line tool (Bru2).
-</longdescription>
+		This is a simple tool for converting Bruker ParaVision MRI data to
+		the NIfTI file format. It includes both a drag-and-drop graphical
+		interface (Bru2Nii) as well as a command line tool (Bru2).
+	</longdescription>
 	<upstream>
 		<remote-id type="github">neurolabusc/Bru2Nii</remote-id>
 	</upstream>
diff --git a/sci-biology/bruker2nifti/Manifest b/sci-biology/bruker2nifti/Manifest
new file mode 100644
index 000000000..689ee2686
--- /dev/null
+++ b/sci-biology/bruker2nifti/Manifest
@@ -0,0 +1 @@
+DIST bruker2nifti-1.0.4.tar.gz 1224995 BLAKE2B 034568e5184233a82ea5c027b76413c849d07e763ff56ca2c3a9fed7bb03975cd4fec5f0625850ca0d6bb4d0f866c0a15e5151b0a9263c319a7c5d236fe29ae1 SHA512 59c1996727f2bfe7f3f76dd47410e93f6fa9d0c6c4d93919861c841db41f717db5ed7e628fe930cccabc09caea467ea32de47f4889c61fbd4f6b7640d890e02d
diff --git a/sci-biology/bruker2nifti/bruker2nifti-1.0.4.ebuild b/sci-biology/bruker2nifti/bruker2nifti-1.0.4.ebuild
new file mode 100644
index 000000000..dc0c49e6f
--- /dev/null
+++ b/sci-biology/bruker2nifti/bruker2nifti-1.0.4.ebuild
@@ -0,0 +1,31 @@
+# Copyright 1999-2023 Gentoo Authors
+# Distributed under the terms of the GNU General Public License v2
+
+EAPI=8
+
+DISTUTILS_USE_SETUPTOOLS="rdepend"
+PYTHON_COMPAT=( python3_{10..11} )
+
+inherit distutils-r1
+
+DESCRIPTION="Medical image converter, from raw Bruker ParaVision to NIfTI"
+HOMEPAGE="https://github.com/SebastianoF/bruker2nifti"
+SRC_URI="https://github.com/SebastianoF/bruker2nifti/archive/v${PV}.tar.gz -> ${P}.tar.gz"
+
+LICENSE="MIT"
+SLOT="0"
+KEYWORDS="~amd64"
+
+RDEPEND="
+	dev-python/numpy[${PYTHON_USEDEP}]
+	sci-libs/nibabel[${PYTHON_USEDEP}]
+	"
+
+python_prepare_all() {
+	sed -i -e "s/packages=find_packages()/packages=find_packages(exclude=('test',))/g"\
+		setup.py || die
+	distutils-r1_python_prepare_all
+}
+
+distutils_enable_tests pytest
+distutils_enable_sphinx docs
diff --git a/sci-biology/bruker2nifti/metadata.xml b/sci-biology/bruker2nifti/metadata.xml
new file mode 100644
index 000000000..d67826b4d
--- /dev/null
+++ b/sci-biology/bruker2nifti/metadata.xml
@@ -0,0 +1,16 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
+<pkgmetadata>
+	<maintainer type="project">
+		<email>sci@gentoo.org</email>
+		<name>Gentoo Science Project</name>
+	</maintainer>
+	<longdescription lang="en">
+		Bruker2nifti is an open source medical image format converter from
+		raw Bruker ParaVision to NifTi, without any intermediate step through
+		the DICOM standard format.
+	</longdescription>
+	<upstream>
+		<remote-id type="github">SebastianoF/bruker2nifti</remote-id>
+	</upstream>
+</pkgmetadata>
diff --git a/sci-biology/btl_bloomfilter/Manifest b/sci-biology/btl_bloomfilter/Manifest
new file mode 100644
index 000000000..529f20ad7
--- /dev/null
+++ b/sci-biology/btl_bloomfilter/Manifest
@@ -0,0 +1 @@
+DIST btl_bloomfilter-1.2.1.tar.gz 134872 BLAKE2B b8b2ce0a643bb2f55b8e105497d463272b283dc17cae77e2dd091fe8274f8a1a661b46a065e5db625ba70a260e45bc95a43e3b87b096b22c38f6a3fe5f8e65ee SHA512 9fc4b59001ddea4d3f2e27032f7ec2a39e837a71b540efc5834f87c84532da10e8bec5916eb382ad21c32bbe93cf8ddeb2892fec700a37d83d539324c9aad304
diff --git a/sci-biology/btl_bloomfilter/btl_bloomfilter-1.2.1.ebuild b/sci-biology/btl_bloomfilter/btl_bloomfilter-1.2.1.ebuild
new file mode 100644
index 000000000..359a0941d
--- /dev/null
+++ b/sci-biology/btl_bloomfilter/btl_bloomfilter-1.2.1.ebuild
@@ -0,0 +1,31 @@
+# Copyright 2021 Gentoo Authors
+# Distributed under the terms of the GNU General Public License v2
+
+EAPI=7
+
+DESCRIPTION="BTL C/C common bloom filters"
+HOMEPAGE="https://github.com/bcgsc/btl_bloomfilter"
+SRC_URI="https://github.com/bcgsc/btl_bloomfilter/archive/refs/tags/${PV}.tar.gz -> ${P}.tar.gz"
+
+LICENSE="GPL-3"
+SLOT="0"
+KEYWORDS="~amd64 ~x86"
+
+DEPEND=""
+RDEPEND="${DEPEND}"
+BDEPEND=""
+
+src_prepare(){
+	sh ./autogen.sh || die
+	default
+}
+
+src_test(){
+	make check || die
+}
+
+src_install(){
+	default
+	insinto /usr/share/"${PN}"
+	doins -r swig pythonInterface Examples
+}
diff --git a/sci-biology/btl_bloomfilter/metadata.xml b/sci-biology/btl_bloomfilter/metadata.xml
new file mode 100644
index 000000000..1e02bb596
--- /dev/null
+++ b/sci-biology/btl_bloomfilter/metadata.xml
@@ -0,0 +1,15 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
+<pkgmetadata>
+	<maintainer type="person">
+		<email>mmokrejs@fold.natur.cuni.cz</email>
+		<name>Martin Mokrejs</name>
+	</maintainer>
+	<maintainer type="project">
+		<email>sci-biology@gentoo.org</email>
+		<name>Gentoo Biology Project</name>
+	</maintainer>
+	<upstream>
+		<remote-id type="github">bcgsc/btl_bloomfilter</remote-id>
+	</upstream>
+</pkgmetadata>
diff --git a/sci-biology/bwa/Manifest b/sci-biology/bwa/Manifest
deleted file mode 100644
index d5ec96afa..000000000
--- a/sci-biology/bwa/Manifest
+++ /dev/null
@@ -1 +0,0 @@
-DIST bwa-0.7.17.tar.bz2 190908 BLAKE2B d646352719a692d35d39ffcfbdbfdbda5d431f3b89b0d8dbc6abc21b64b249512322b123c95190ad35b65fbf3185ba86e8530d060c222d4b3a1787d338779419 SHA512 67cccfef1c7aa1b5aad6b59a49390e8d96f64320c414bfffacf232aeb08c15861e98be826c1b42b6222d6ff086eeb055b1318ea2e9eebfd87b2365d06fc89802
diff --git a/sci-biology/bwa/bwa-0.7.17.ebuild b/sci-biology/bwa/bwa-0.7.17.ebuild
deleted file mode 100644
index 429ba43e6..000000000
--- a/sci-biology/bwa/bwa-0.7.17.ebuild
+++ /dev/null
@@ -1,34 +0,0 @@
-# Copyright 1999-2018 Gentoo Foundation
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=6
-
-inherit toolchain-funcs
-
-DESCRIPTION="Burrows-Wheeler Alignment Tool, a fast short genomic sequence aligner"
-HOMEPAGE="http://bio-bwa.sourceforge.net/"
-SRC_URI="mirror://sourceforge/bio-bwa/${P}.tar.bz2"
-
-LICENSE="GPL-3"
-SLOT="0"
-IUSE=""
-KEYWORDS="~amd64 ~x86 ~x64-macos"
-
-RDEPEND="dev-lang/perl"
-
-PATCHES=( "${FILESDIR}"/${PN}-0.7.15-Makefile.patch )
-DOCS=( NEWS.md README-alt.md README.md )
-
-src_configure() {
-	tc-export CC AR
-}
-
-src_install() {
-	dobin bwa
-
-	exeinto /usr/libexec/${PN}
-	doexe qualfa2fq.pl xa2multi.pl
-
-	einstalldocs
-	doman bwa.1
-}
diff --git a/sci-biology/bwa/files/bwa-0.7.15-Makefile.patch b/sci-biology/bwa/files/bwa-0.7.15-Makefile.patch
deleted file mode 100644
index 39b437a02..000000000
--- a/sci-biology/bwa/files/bwa-0.7.15-Makefile.patch
+++ /dev/null
@@ -1,27 +0,0 @@
---- bwa-0.7.13/Makefile
-+++ bwa-0.7.13/Makefile
-@@ -1,8 +1,8 @@
--CC=			gcc
-+CC?=			gcc
- #CC=			clang --analyze
--CFLAGS=		-g -Wall -Wno-unused-function -O2
-+CFLAGS?=		-g -Wall -Wno-unused-function -O2
- WRAP_MALLOC=-DUSE_MALLOC_WRAPPERS
--AR=			ar
-+AR?=			ar
- DFLAGS=		-DHAVE_PTHREAD $(WRAP_MALLOC)
- LOBJS=		utils.o kthread.o kstring.o ksw.o bwt.o bntseq.o bwa.o bwamem.o bwamem_pair.o bwamem_extra.o malloc_wrap.o
- AOBJS=		QSufSort.o bwt_gen.o bwashm.o bwase.o bwaseqio.o bwtgap.o bwtaln.o bamlite.o \
-@@ -26,10 +26,10 @@
- all:$(PROG)
- 
- bwa:libbwa.a $(AOBJS) main.o
--		$(CC) $(CFLAGS) $(DFLAGS) $(AOBJS) main.o -o $@ -L. -lbwa $(LIBS)
-+		$(CC) $(CFLAGS) $(LDFLAGS) $(DFLAGS) $(AOBJS) main.o -o $@ -L. -lbwa $(LIBS)
- 
- bwamem-lite:libbwa.a example.o
--		$(CC) $(CFLAGS) $(DFLAGS) example.o -o $@ -L. -lbwa $(LIBS)
-+		$(CC) $(CFLAGS) $(LDFLAGS) $(DFLAGS) example.o -o $@ -L. -lbwa $(LIBS)
- 
- libbwa.a:$(LOBJS)
- 		$(AR) -csru $@ $(LOBJS)
diff --git a/sci-biology/bwa/metadata.xml b/sci-biology/bwa/metadata.xml
deleted file mode 100644
index ceb43ead2..000000000
--- a/sci-biology/bwa/metadata.xml
+++ /dev/null
@@ -1,11 +0,0 @@
-<?xml version="1.0" encoding="UTF-8"?>
-<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
-<pkgmetadata>
-  <maintainer type="project">
-    <email>sci-biology@gentoo.org</email>
-    <name>Gentoo Biology Project</name>
-  </maintainer>
-  <upstream>
-    <remote-id type="sourceforge">bio-bwa</remote-id>
-  </upstream>
-</pkgmetadata>
diff --git a/sci-biology/bx-python/Manifest b/sci-biology/bx-python/Manifest
index a55f1f0a3..90147dff7 100644
--- a/sci-biology/bx-python/Manifest
+++ b/sci-biology/bx-python/Manifest
@@ -1 +1,2 @@
-DIST bx-python-0.7.2.tar.gz 939454 BLAKE2B 2c1fbaa279a26951a7db3fe952296cfd0e3022124c51850521def385180ce2b8bde183ebba8b9029c11f1a6c729947464dacde8889748ae110d75ecb263d1d7d SHA512 6757250909be72daf61daef865b4c5ee29a823ca7444a70b17dd25db8cec22e39dd0b93186634a9ed9ac036fdb7054e225270141c9ffd63a231d82f0eee8c8cd
+DIST bx-python-0.8.9.gh.tar.gz 1651514 BLAKE2B ee75d08aaae8102c2af5be0175c75200382e157abc0c0c723a67b55d5542ab2d4b6ccd4e256975b0a2d00b39b2249d73df0c6f4324b3a74757c3e18e2aeb6c1a SHA512 37863c92258dc06a12b566b02697502f68bbf7e4d9decd8fc63af10ee58b614dd0e7cff35e9977ba1ddf913f176c49e7969728d8e64a9f78ac7100da4a3d70ea
+DIST bx-python-0.9.0.gh.tar.gz 1667445 BLAKE2B 0814792a2af8bfb7af5ef5fe1ddc184ed14a68df060a8286f4eba334388497363dc002f6c0de72836b5654452fe28f4cef67cd31b765a4a121c84f3af0634ea0 SHA512 955f396614d8e6d19a74e94a6612f7752a45f752a4a59c95853474dd363ed1960d20a340f17eb1815fda3aaf26d907dc30d37aa8c23608d718742b68864ca1bc
diff --git a/sci-biology/bx-python/bx-python-0.7.2.ebuild b/sci-biology/bx-python/bx-python-0.7.2.ebuild
deleted file mode 100644
index 1fa0ebbf6..000000000
--- a/sci-biology/bx-python/bx-python-0.7.2.ebuild
+++ /dev/null
@@ -1,23 +0,0 @@
-# Copyright 1999-2015 Gentoo Foundation
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=5
-
-PYTHON_COMPAT=( python2_7 )
-
-inherit distutils-r1
-
-DESCRIPTION="Library for rapid implementation of genome scale analyses"
-HOMEPAGE="https://bitbucket.org/james_taylor/bx-python/wiki/Home"
-SRC_URI="mirror://pypi/${PN:0:1}/${PN}/${P}.tar.gz"
-
-LICENSE="MIT"
-SLOT="0"
-KEYWORDS="~amd64 ~x86 ~amd64-linux ~x86-linux"
-IUSE=""
-
-RDEPEND="dev-python/numpy[${PYTHON_USEDEP}]"
-DEPEND="${RDEPEND}
-	dev-python/cython[${PYTHON_USEDEP}]"
-
-# has file collision with sci-biology/RSeQC
diff --git a/sci-biology/bx-python/bx-python-0.8.9.ebuild b/sci-biology/bx-python/bx-python-0.8.9.ebuild
new file mode 100644
index 000000000..6cffba1be
--- /dev/null
+++ b/sci-biology/bx-python/bx-python-0.8.9.ebuild
@@ -0,0 +1,35 @@
+# Copyright 1999-2023 Gentoo Authors
+# Distributed under the terms of the GNU General Public License v2
+
+EAPI=8
+
+PYTHON_COMPAT=( python3_{10..10} )
+
+inherit distutils-r1
+
+DESCRIPTION="Library for rapid implementation of genome scale analyses"
+HOMEPAGE="https://github.com/bxlab/bx-python"
+SRC_URI="https://github.com/bxlab/bx-python/archive/v${PV}.tar.gz -> ${P}.gh.tar.gz"
+
+LICENSE="MIT"
+SLOT="0"
+KEYWORDS="~amd64 ~x86"
+# Tests require dev-python/pytest-cython (currently not in ::gentoo or ::science)
+# (and might need some more work beyond that)
+RESTRICT=test
+
+RDEPEND="
+	dev-python/numpy[${PYTHON_USEDEP}]
+	dev-python/six[${PYTHON_USEDEP}]
+"
+BDEPEND="
+	dev-python/cython[${PYTHON_USEDEP}]
+"
+
+# has file collision with sci-biology/RSeQC
+
+# ToDo: fix doc building:
+# Reason: TemplateNotFound('i')
+#distutils_enable_sphinx doc/source
+
+distutils_enable_tests pytest
diff --git a/sci-biology/bx-python/bx-python-0.9.0.ebuild b/sci-biology/bx-python/bx-python-0.9.0.ebuild
new file mode 100644
index 000000000..6cffba1be
--- /dev/null
+++ b/sci-biology/bx-python/bx-python-0.9.0.ebuild
@@ -0,0 +1,35 @@
+# Copyright 1999-2023 Gentoo Authors
+# Distributed under the terms of the GNU General Public License v2
+
+EAPI=8
+
+PYTHON_COMPAT=( python3_{10..10} )
+
+inherit distutils-r1
+
+DESCRIPTION="Library for rapid implementation of genome scale analyses"
+HOMEPAGE="https://github.com/bxlab/bx-python"
+SRC_URI="https://github.com/bxlab/bx-python/archive/v${PV}.tar.gz -> ${P}.gh.tar.gz"
+
+LICENSE="MIT"
+SLOT="0"
+KEYWORDS="~amd64 ~x86"
+# Tests require dev-python/pytest-cython (currently not in ::gentoo or ::science)
+# (and might need some more work beyond that)
+RESTRICT=test
+
+RDEPEND="
+	dev-python/numpy[${PYTHON_USEDEP}]
+	dev-python/six[${PYTHON_USEDEP}]
+"
+BDEPEND="
+	dev-python/cython[${PYTHON_USEDEP}]
+"
+
+# has file collision with sci-biology/RSeQC
+
+# ToDo: fix doc building:
+# Reason: TemplateNotFound('i')
+#distutils_enable_sphinx doc/source
+
+distutils_enable_tests pytest
diff --git a/sci-biology/bx-python/bx-python-9999.ebuild b/sci-biology/bx-python/bx-python-9999.ebuild
index 10cbc8f5d..b29975b58 100644
--- a/sci-biology/bx-python/bx-python-9999.ebuild
+++ b/sci-biology/bx-python/bx-python-9999.ebuild
@@ -1,24 +1,35 @@
-# Copyright 1999-2015 Gentoo Foundation
+# Copyright 1999-2023 Gentoo Authors
 # Distributed under the terms of the GNU General Public License v2
 
-EAPI=5
+EAPI=8
 
-PYTHON_COMPAT=( python2_7 )
+PYTHON_COMPAT=( python3_{10..10} )
 
-inherit distutils-r1 mercurial
+inherit distutils-r1 git-r3
 
 DESCRIPTION="Library for rapid implementation of genome scale analyses"
-HOMEPAGE="https://bitbucket.org/james_taylor/bx-python/wiki/Home"
-SRC_URI=""
-EHG_REPO_URI="https://bitbucket.org/james_taylor/bx-python"
+HOMEPAGE="https://github.com/bxlab/bx-python"
+EGIT_REPO_URI="https://github.com/bxlab/bx-python"
 
 LICENSE="MIT"
 SLOT="0"
 KEYWORDS=""
-IUSE=""
+# Tests require dev-python/pytest-cython (currently not in ::gentoo or ::science)
+# (and might need some more work beyond that)
+RESTRICT=test
 
-RDEPEND="dev-python/numpy[${PYTHON_USEDEP}]"
-DEPEND="${RDEPEND}
-	dev-python/cython[${PYTHON_USEDEP}]"
+RDEPEND="
+	dev-python/numpy[${PYTHON_USEDEP}]
+	dev-python/six[${PYTHON_USEDEP}]
+"
+BDEPEND="
+	dev-python/cython[${PYTHON_USEDEP}]
+"
 
 # has file collision with sci-biology/RSeQC
+
+# ToDo: fix doc building:
+# Reason: TemplateNotFound('i')
+#distutils_enable_sphinx doc/source
+
+distutils_enable_tests pytest
diff --git a/sci-biology/bx-python/metadata.xml b/sci-biology/bx-python/metadata.xml
index 3e13342e3..f1fc4360e 100644
--- a/sci-biology/bx-python/metadata.xml
+++ b/sci-biology/bx-python/metadata.xml
@@ -10,7 +10,7 @@
 		<name>Gentoo Biology Project</name>
 	</maintainer>
 	<upstream>
-		<remote-id type="bitbucket">james_taylor/bx-python</remote-id>
+		<remote-id type="github">bxlab/bx-python</remote-id>
 		<remote-id type="pypi">bx-python</remote-id>
 	</upstream>
 </pkgmetadata>
diff --git a/sci-biology/caftools/Manifest b/sci-biology/caftools/Manifest
deleted file mode 100644
index 761665281..000000000
--- a/sci-biology/caftools/Manifest
+++ /dev/null
@@ -1,2 +0,0 @@
-DIST caftools-2.0.2.tar.gz 2645554 BLAKE2B a48d8fb71500b5dc07da37467a9dc8d5972dfd7f63ae19cf7ca016774c3a23c4a9cd0f4caa1bde8efe5ef74c2576b8143f8b7375f9bf34414edcb14ed34a17d2 SHA512 0c1a7f2127538ef932139cfee6bc6acb2411765d1006d508e65647ec74d1677a6ecd25b98cc37075bd8e5b0b1a245c11c1029cbbc51eefb46023bd121fdb2f1d
-DIST caftools-2.0.tar.gz 2644892 BLAKE2B 76aa90bf18d7543eb8f39de3e3be5fbca9a549e47341b032dd569394865ae02e269ea54a607acca2d88d404d271f78e1b97399bc8bdc1a107937163c89642323 SHA512 0b2b5d09d503b900b275efd61dfa1c5b01259e53c392d68626d9c5081add27ca87b324b5702ec18293415b788208c547eb31e461861f1244b759e28221244417
diff --git a/sci-biology/caftools/caftools-2.0.2.ebuild b/sci-biology/caftools/caftools-2.0.2.ebuild
deleted file mode 100644
index a722379b8..000000000
--- a/sci-biology/caftools/caftools-2.0.2.ebuild
+++ /dev/null
@@ -1,45 +0,0 @@
-# Copyright 1999-2015 Gentoo Foundation
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=5
-
-inherit eutils
-
-DESCRIPTION="Manipulate CAF files and convert to GAP4 format (not GAP5), ACE, PHRAP"
-HOMEPAGE="http://www.sanger.ac.uk/resources/software/caf
-	http://www.ncbi.nlm.nih.gov/pmc/articles/PMC310697"
-SRC_URI="
-	ftp://ftp.sanger.ac.uk/pub/PRODUCTION_SOFTWARE/src/${P}.tar.gz
-	ftp://ftp.sanger.ac.uk/pub/PRODUCTION_SOFTWARE/src/${PN}-2.0.tar.gz"
-
-LICENSE="GRL"
-SLOT="0"
-KEYWORDS="~amd64 ~x86"
-IUSE=""
-
-DEPEND="
-	sci-libs/io_lib
-	dev-lang/perl"
-RDEPEND="${DEPEND}"
-
-src_prepare(){
-	epatch "${FILESDIR}"/Makefile.in-"${PV}".patch
-	mv "${WORKDIR}"/caftools-2.0/man/*.{1,5} "${S}"/man/ || die
-}
-
-src_configure(){
-	default
-	sed \
-		-e 's:prefix = /usr:prefix = $(DESTDIR)/usr:' \
-		-i Makefile src/Makefile || die
-}
-
-# TODO: the 2.0.2 archive lacks manpages compared to 2.0, FIXME
-# The man/Makefile.in is screwed in 2.0.2 so we cannot use it to install the manpage files,
-# not even copying over whole caftools-2.0/man/ to caftools-2.0.2/man does not help.
-src_install(){
-	default
-	doman man/*.[1-5] || die
-	elog "Some usage info is at http://sarton.imb-jena.de/software/consed2gap/"
-	elog "for some reason caf_find_misassemblies is gone from 2.0.2 version"
-}
diff --git a/sci-biology/caftools/files/Makefile.in-2.0.2.patch b/sci-biology/caftools/files/Makefile.in-2.0.2.patch
deleted file mode 100644
index 1e5160487..000000000
--- a/sci-biology/caftools/files/Makefile.in-2.0.2.patch
+++ /dev/null
@@ -1,43 +0,0 @@
---- src/Makefile.in.ori	2010-12-05 22:59:40.000000000 +0100
-+++ src/Makefile.in	2010-12-05 23:01:19.000000000 +0100
-@@ -32,8 +32,6 @@
- includedir = @includedir@
- oldincludedir = /usr/include
- 
--DESTDIR =
--
- pkgdatadir = $(datadir)/@PACKAGE@
- pkglibdir = $(libdir)/@PACKAGE@
- pkgincludedir = $(includedir)/@PACKAGE@
-@@ -323,18 +321,18 @@
- 
- install-binPROGRAMS: $(bin_PROGRAMS)
- 	@$(NORMAL_INSTALL)
--	$(mkinstalldirs) $(DESTDIR)$(bindir)
-+	$(mkinstalldirs) $(bindir)
- 	@list='$(bin_PROGRAMS)'; for p in $$list; do \
- 	  if test -f $$p; then \
--	    echo "  $(INSTALL_PROGRAM) $$p $(DESTDIR)$(bindir)/`echo $$p|sed 's/$(EXEEXT)$$//'|sed '$(transform)'|sed 's/$$/$(EXEEXT)/'`"; \
--	     $(INSTALL_PROGRAM) $$p $(DESTDIR)$(bindir)/`echo $$p|sed 's/$(EXEEXT)$$//'|sed '$(transform)'|sed 's/$$/$(EXEEXT)/'`; \
-+	    echo "  $(INSTALL_PROGRAM) $$p $(bindir)/`echo $$p|sed 's/$(EXEEXT)$$//'|sed '$(transform)'|sed 's/$$/$(EXEEXT)/'`"; \
-+	     $(INSTALL_PROGRAM) $$p $(bindir)/`echo $$p|sed 's/$(EXEEXT)$$//'|sed '$(transform)'|sed 's/$$/$(EXEEXT)/'`; \
- 	  else :; fi; \
- 	done
- 
- uninstall-binPROGRAMS:
- 	@$(NORMAL_UNINSTALL)
- 	list='$(bin_PROGRAMS)'; for p in $$list; do \
--	  rm -f $(DESTDIR)$(bindir)/`echo $$p|sed 's/$(EXEEXT)$$//'|sed '$(transform)'|sed 's/$$/$(EXEEXT)/'`; \
-+	  rm -f $(bindir)/`echo $$p|sed 's/$(EXEEXT)$$//'|sed '$(transform)'|sed 's/$$/$(EXEEXT)/'`; \
- 	done
- 
- .c.o:
-@@ -579,7 +577,7 @@
- 	$(MAKE) $(AM_MAKEFLAGS) AM_INSTALL_PROGRAM_FLAGS=-s install
- installdirs: installdirs-recursive
- installdirs-am:
--	$(mkinstalldirs)  $(DESTDIR)$(bindir)
-+	$(mkinstalldirs)  $(bindir)
- 
- 
- mostlyclean-generic:
diff --git a/sci-biology/caftools/files/Makefile.in.patch b/sci-biology/caftools/files/Makefile.in.patch
deleted file mode 100644
index 4ddd9f628..000000000
--- a/sci-biology/caftools/files/Makefile.in.patch
+++ /dev/null
@@ -1,49 +0,0 @@
---- src/Makefile.in.ori	2010-12-05 22:08:50.000000000 +0100
-+++ src/Makefile.in	2010-12-05 22:10:07.000000000 +0100
-@@ -18,7 +18,7 @@
- srcdir = @srcdir@
- top_srcdir = @top_srcdir@
- VPATH = @srcdir@
--prefix = @prefix@
-+prefix = $(DESTDIR)/@prefix@
- exec_prefix = @exec_prefix@
- 
- bindir = @bindir@
-@@ -394,14 +394,14 @@
- binPROGRAMS_INSTALL = $(INSTALL_PROGRAM)
- install-binPROGRAMS: $(bin_PROGRAMS)
- 	@$(NORMAL_INSTALL)
--	$(mkinstalldirs) $(DESTDIR)$(bindir)
-+	$(mkinstalldirs) $(bindir)
- 	@list='$(bin_PROGRAMS)'; for p in $$list; do \
- 	  p1=`echo $$p|sed 's/$(EXEEXT)$$//'`; \
- 	  if test -f $$p \
- 	  ; then \
- 	    f=`echo "$$p1" | sed 's,^.*/,,;$(transform);s/$$/$(EXEEXT)/'`; \
--	   echo " $(INSTALL_PROGRAM_ENV) $(binPROGRAMS_INSTALL) $$p $(DESTDIR)$(bindir)/$$f"; \
--	   $(INSTALL_PROGRAM_ENV) $(binPROGRAMS_INSTALL) $$p $(DESTDIR)$(bindir)/$$f; \
-+	   echo " $(INSTALL_PROGRAM_ENV) $(binPROGRAMS_INSTALL) $$p $(bindir)/$$f"; \
-+	   $(INSTALL_PROGRAM_ENV) $(binPROGRAMS_INSTALL) $$p $(bindir)/$$f; \
- 	  else :; fi; \
- 	done
- 
-@@ -409,8 +409,8 @@
- 	@$(NORMAL_UNINSTALL)
- 	@list='$(bin_PROGRAMS)'; for p in $$list; do \
- 	  f=`echo "$$p" | sed 's,^.*/,,;s/$(EXEEXT)$$//;$(transform);s/$$/$(EXEEXT)/'`; \
--	  echo " rm -f $(DESTDIR)$(bindir)/$$f"; \
--	  rm -f $(DESTDIR)$(bindir)/$$f; \
-+	  echo " rm -f $(bindir)/$$f"; \
-+	  rm -f $(bindir)/$$f; \
- 	done
- 
- clean-binPROGRAMS:
-@@ -663,7 +663,7 @@
- all-am: Makefile $(PROGRAMS) config.h
- installdirs: installdirs-recursive
- installdirs-am:
--	$(mkinstalldirs) $(DESTDIR)$(bindir)
-+	$(mkinstalldirs) $(bindir)
- 
- install: install-recursive
- install-exec: install-exec-recursive
diff --git a/sci-biology/caftools/metadata.xml b/sci-biology/caftools/metadata.xml
deleted file mode 100644
index 224641279..000000000
--- a/sci-biology/caftools/metadata.xml
+++ /dev/null
@@ -1,17 +0,0 @@
-<?xml version="1.0" encoding="UTF-8"?>
-<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
-<pkgmetadata>
-	<maintainer type="person">
-		<email>mmokrejs@fold.natur.cuni.cz</email>
-		<name>Martin Mokrejs</name>
-	</maintainer>
-	<maintainer type="project">
-		<email>sci-biology@gentoo.org</email>
-		<name>Gentoo Biology Project</name>
-	</maintainer>
-	<longdescription>
-CAF is a text format for describing sequence assemblies. It is acedb-compliant
-and is an extension of the ace-file format used earlier, but with support for 
-base quality measures and a more extensive description of the Sequence data.
-</longdescription>
-</pkgmetadata>
diff --git a/sci-biology/canu/canu-9999.ebuild b/sci-biology/canu/canu-9999.ebuild
deleted file mode 100644
index 2233e284a..000000000
--- a/sci-biology/canu/canu-9999.ebuild
+++ /dev/null
@@ -1,77 +0,0 @@
-# Copyright 1999-2019 Gentoo Authors
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=5
-
-PYTHON_COMPAT=( python2_7 )
-PERL_EXPORT_PHASE_FUNCTIONS=no
-inherit eutils java-pkg-2 perl-module multilib git-r3
-
-DESCRIPTION="Fork of a wgs-assembler for Oxfordnanopore and PacBio sequences"
-HOMEPAGE="http://canu.readthedocs.io/en/latest"
-EGIT_REPO_URI="https://github.com/marbl/canu.git"
-
-LICENSE="GPL-2"
-SLOT="0"
-KEYWORDS=""
-IUSE=""
-
-REQUIRED_USE="${PYTHON_REQUIRED_USE}"
-
-RDEPEND="
-	>=virtual/jre-1.8:*
-	dev-lang/perl
-	virtual/perl-File-Path
-	sci-visualization/gnuplot
-	"
-# =sci-biology/mhap-2.1.3 if we unbundle it
-DEPEND="${RDEPEND}
-	>=virtual/jdk-1.8:*
-	dev-java/ant-core
-	!sci-biology/wgs-assembler
-	"
-
-# Detected file collision(s):
-#  * sci-biology/wgs-assembler-8.3_rc2:0::science
-#  * 	/usr/bin/bogart
-#  * 	/usr/bin/bogus
-#  * 	/usr/bin/fastqAnalyze
-#  * 	/usr/bin/fastqSample
-#  * 	/usr/bin/fastqSimulate
-#  * 	/usr/bin/fastqSimulate-sort
-#  * 	/usr/bin/meryl
-#  * 	/usr/bin/overlapInCore
-#  * 	/usr/bin/utgcns
-
-# Perl 5.12.0, or File::Path 2.08
-# Java SE 8
-# https://github.com/marbl/MHAP uses Apache maven
-S="${WORKDIR}"/"${P}"
-
-# contains bundled mhap-2.1.3.jar, kmer, pbutgcns, FALCON
-
-src_prepare(){
-	epatch "${FILESDIR}"/canu-1.8_respect_CXXFLAGS.patch
-}
-
-src_compile(){
-	cd src || die
-	emake
-}
-
-src_install(){
-	# installs
-	#  /usr/bin
-	#  /usr/lib/libcanu.a
-	#  /usr/lib64/perl5/vendor_perl/5.28.0/lib/site_perl/canu
-	#  /usr/share/java/classes/mhap-2.1.3.jar
-	rm -rf Linux-amd64/obj
-	insinto /usr
-	doins -r Linux-amd64/{bin,share}
-	insinto /usr/$(get_libdir)
-	dolib Linux-amd64/lib/libcanu.a
-	rm Linux-amd64/lib/libcanu.a || die
-	perl_set_version
-	insinto ${VENDOR_LIB}
-	doins -r Linux-amd64/lib
-}
diff --git a/sci-biology/canu/files/canu-1.8_respect_CXXFLAGS.patch b/sci-biology/canu/files/canu-1.8_respect_CXXFLAGS.patch
deleted file mode 100644
index ac46e0ddd..000000000
--- a/sci-biology/canu/files/canu-1.8_respect_CXXFLAGS.patch
+++ /dev/null
@@ -1,112 +0,0 @@
-diff --git a/src/Makefile b/src/Makefile
-index e2770f5a0..3cdb81a4c 100644
---- a/src/Makefile
-+++ b/src/Makefile
-@@ -388,6 +388,22 @@ endif
- #  and remove -fomit-frame-pointer from CXXFLAGS.  It added a bunch of complication and wasn't
- #  really used.
- 
-+ifeq ($(BUILDOPTIMIZED), 1)
-+else
-+  CXXFLAGS ?= -g3
-+endif
-+
-+ifeq ($(BUILDDEBUG), 1)
-+else
-+  ifeq (${OSTYPE}, FreeBSD)
-+  ifeq (${MACHINETYPE}, amd64)
-+    CXXFLAGS ?= -O3 -funroll-loops -fexpensive-optimizations -finline-functions -fomit-frame-pointer
-+  else
-+    CXXFLAGS ?= -O4 -funroll-loops -fexpensive-optimizations -finline-functions -fomit-frame-pointer
-+  endif
-+  endif
-+endif
-+
- ifeq (${OSTYPE}, Linux)
-   CC        ?= gcc
-   CXX       ?= g++
-@@ -398,16 +414,6 @@ ifeq (${OSTYPE}, Linux)
-   CXXFLAGS  += -Wall -Wextra -Wno-write-strings -Wno-unused -Wno-char-subscripts -Wno-sign-compare -Wformat
- 
-   BUILDSTACKTRACE ?= 1
--
--  ifeq ($(BUILDOPTIMIZED), 1)
--  else
--    CXXFLAGS += -g3
--  endif
--
--  ifeq ($(BUILDDEBUG), 1)
--  else
--    CXXFLAGS += -O4 -funroll-loops -fexpensive-optimizations -finline-functions -fomit-frame-pointer
--  endif
- endif
- 
- 
-@@ -479,16 +485,6 @@ ifeq (${OSTYPE}, Darwin)
- 
-   CXXFLAGS += -pthread -fPIC -m64 -Wall -Wextra -Wno-write-strings -Wno-unused -Wno-char-subscripts -Wno-sign-compare -Wno-format-truncation -Wformat
-   LDFLAGS  += -pthread -lm
--
--  ifeq ($(BUILDOPTIMIZED), 1)
--  else
--    CXXFLAGS += -g3
--  endif
--
--  ifeq ($(BUILDDEBUG), 1)
--  else
--    CXXFLAGS += -O4 -funroll-loops -fexpensive-optimizations -finline-functions -fomit-frame-pointer
--  endif
- endif
- 
- 
-@@ -519,16 +515,6 @@ ifeq (${MACHINETYPE}, amd64)
- 
-   #  callgrind
-   #CXXFLAGS  += -g3 -Wa,--gstabs -save-temps
--
--  ifeq ($(BUILDOPTIMIZED), 1)
--  else
--    CXXFLAGS += -g3
--  endif
--
--  ifeq ($(BUILDDEBUG), 1)
--  else
--    CXXFLAGS += -O3 -funroll-loops -fexpensive-optimizations -finline-functions -fomit-frame-pointer
--  endif
- endif
- endif
- 
-@@ -544,16 +530,6 @@ ifeq (${MACHINETYPE}, arm)
-   CXXFLAGS  += -Wall -Wextra -Wno-write-strings -Wno-unused -Wno-char-subscripts -Wno-sign-compare -Wformat -Wno-parentheses
-   CXXFLAGS  += -funroll-loops -fomit-frame-pointer
-   LDFLAGS   += 
--
--  ifeq ($(BUILDOPTIMIZED), 1)
--  else
--    CXXFLAGS += -g3
--  endif
--
--  ifeq ($(BUILDDEBUG), 1)
--  else
--    CXXFLAGS += -O4 -funroll-loops -fexpensive-optimizations -finline-functions -fomit-frame-pointer
--  endif
- endif
- endif
- 
-@@ -566,16 +542,6 @@ ifneq (,$(findstring CYGWIN, ${OSTYPE}))
-   LDFLAGS   := -fopenmp -pthread -lm
- 
-   CXXFLAGS  += -Wall -Wextra -Wno-write-strings -Wno-unused -Wno-char-subscripts -Wno-sign-compare -Wformat
--
--  ifeq ($(BUILDOPTIMIZED), 1)
--  else
--    CXXFLAGS += -g3
--  endif
--
--  ifeq ($(BUILDDEBUG), 1)
--  else
--    CXXFLAGS += -O4 -funroll-loops -fexpensive-optimizations -finline-functions -fomit-frame-pointer
--  endif
- endif
- 
- 
diff --git a/sci-biology/canu/metadata.xml b/sci-biology/canu/metadata.xml
deleted file mode 100644
index 138cb7705..000000000
--- a/sci-biology/canu/metadata.xml
+++ /dev/null
@@ -1,12 +0,0 @@
-<?xml version="1.0" encoding="UTF-8"?>
-<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
-<pkgmetadata>
-	<maintainer type="person">
-		<email>mmokrejs@fold.natur.cuni.cz</email>
-		<name>Martin Mokrejs</name>
-	</maintainer>
-	<maintainer type="project">
-		<email>sci-biology@gentoo.org</email>
-		<name>Gentoo Biology Project</name>
-	</maintainer>
-</pkgmetadata>
diff --git a/sci-biology/cast-bin/cast-bin-20080813.ebuild b/sci-biology/cast-bin/cast-bin-20080813.ebuild
index c0c8992c4..4628fe3f6 100644
--- a/sci-biology/cast-bin/cast-bin-20080813.ebuild
+++ b/sci-biology/cast-bin/cast-bin-20080813.ebuild
@@ -1,7 +1,7 @@
-# Copyright 1999-2016 Gentoo Foundation
+# Copyright 1999-2021 Gentoo Authors
 # Distributed under the terms of the GNU General Public License v2
 
-EAPI=5
+EAPI=7
 
 DESCRIPTION="Predict low-complexity regions in putative proteins"
 HOMEPAGE="http://bioinformatics.cenargen.embrapa.br/portrait/download"
@@ -18,7 +18,6 @@ SRC_URI="http://bioinformatics.cenargen.embrapa.br/portrait/download/cast-linux.
 LICENSE="GPL-2"
 SLOT="0"
 KEYWORDS="~amd64"
-IUSE=""
 
 DEPEND=""
 RDEPEND="${DEPEND}"
diff --git a/sci-biology/cd-hit-auxtools/Manifest b/sci-biology/cd-hit-auxtools/Manifest
deleted file mode 100644
index 703087663..000000000
--- a/sci-biology/cd-hit-auxtools/Manifest
+++ /dev/null
@@ -1,2 +0,0 @@
-DIST cd-hit-auxtools-manual.html 27123 SHA256 a17d1ff54f061ced8b3f797238ee5596330cb2fdb237d8fbfdff7e2c47c06d14 SHA512 8b7b646ac63cb4cc888a2b3db0ef2e1feb215189b9a52ed5a760ad5dd1af4f0a0f7722b3fa7b634f8a84e3154622c4336401dfefc45fe614770917ef1d59429a WHIRLPOOL 1b8149b66353ce58f074f412a33726b583497da2b204377e9b639eb2082e78c442e68af3b9d6bcba324373755b75a4b3aa51516f5f771e7d65d14675e76916f6
-DIST cd-hit-auxtools-v0.5-2012-03-07.tgz 97230 BLAKE2B cbc3032dcf02d4919a44d976f7fe2faa8f767e96149bd6eab9aeef1e0a7231e96cef7a87bca9ba8417b87d4b2f28d0a554d863b4efc65882eff1ee7b890c4bfe SHA512 5b00ff4951c9f2b85b23bad7eae484c060f05df8a20c35bf1cff0bae770a6552b7ed19c90bbc36204ea3ba1722490c8ba654c7ec1b1d55f743afbc82be53ef5b
diff --git a/sci-biology/cd-hit-auxtools/cd-hit-auxtools-0.5.ebuild b/sci-biology/cd-hit-auxtools/cd-hit-auxtools-0.5.ebuild
deleted file mode 100644
index 3c3de8097..000000000
--- a/sci-biology/cd-hit-auxtools/cd-hit-auxtools-0.5.ebuild
+++ /dev/null
@@ -1,43 +0,0 @@
-# Copyright 1999-2015 Gentoo Foundation
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=5
-
-inherit eutils flag-o-matic toolchain-funcs
-
-RELDATE="2012-03-07"
-RELEASE="${PN}-v${PV}-${RELDATE}"
-
-DESCRIPTION="Additional cd-hit itools: read-linker, cd-hit-lap and cd-hit-dup"
-HOMEPAGE="http://weizhong-lab.ucsd.edu/cd-hit/"
-SRC_URI="
-	http://cdhit.googlecode.com/files/${RELEASE}.tgz
-	http://weizhong-lab.ucsd.edu/cd-hit/wiki/doku.php?id=cd-hit-auxtools-manual -> cd-hit-auxtools-manual.html"
-
-SLOT="0"
-KEYWORDS="~amd64 ~x86 ~amd64-linux ~x86-linux"
-LICENSE="GPL-2"
-IUSE="doc openmp"
-
-S="${WORKDIR}"/${RELEASE}
-
-pkg_setup() {
-	 use openmp && ! tc-has-openmp && die "Please switch to an openmp compatible compiler"
-}
-
-src_prepare() {
-	tc-export CXX
-	use openmp || append-flags -DNO_OPENMP
-	epatch "${FILESDIR}"/${PV}-gentoo.patch
-}
-
-src_compile() {
-	local myconf=
-	use openmp && myconf="openmp=yes"
-	emake ${myconf}
-}
-
-src_install() {
-	dobin read-linker cd-hit-lap cd-hit-dup
-	use doc && dodoc "${DISTDIR}"/cd-hit-auxtools-manual.html
-}
diff --git a/sci-biology/cd-hit-auxtools/files/0.5-gentoo.patch b/sci-biology/cd-hit-auxtools/files/0.5-gentoo.patch
deleted file mode 100644
index 3977cbee3..000000000
--- a/sci-biology/cd-hit-auxtools/files/0.5-gentoo.patch
+++ /dev/null
@@ -1,47 +0,0 @@
---- Makefile.ori	2014-06-01 20:25:53.000000000 +0200
-+++ Makefile	2014-06-01 20:27:15.000000000 +0200
-@@ -1,8 +1,8 @@
- 
--CC = g++
-+CXX = g++
- 
--CFLAGS = -Wall -Wno-unused -I. -Imintlib
--LFLAGS = -fPIC
-+CXXFLAGS = -I. -Imintlib
-+LDFLAGS = -fPIC
- 
- 
- UNAME = $(shell uname)
-@@ -16,9 +16,9 @@
- endif
- 
- ifeq ($(debug),yes)
--CFLAGS += -ggdb
-+CiXXFLAGS +=
- else
--CFLAGS += -O2
-+CXXFLAGS +=
- endif
- 
- 
-@@ -32,16 +32,16 @@
- .SUFFIXES: .c .obj .cpp .cc .cxx .C
- 
- .cxx.o:
--	$(CC) -c $(CFLAGS) -o $@ $<
-+	$(CXX) -c $(CXXFLAGS) -o $@ $<
- 
- cd-hit-dup: $(OBJECTS) cdhit-dup.o
--	$(CC) $(LFLAGS) $(OBJECTS) cdhit-dup.o -o cd-hit-dup
-+	$(CXX) $(LDFLAGS) $(OBJECTS) cdhit-dup.o -o cd-hit-dup
- 
- cd-hit-lap: $(OBJECTS) cdhit-lap.o
--	$(CC) $(LFLAGS) $(OBJECTS) cdhit-lap.o -o cd-hit-lap
-+	$(CXX) $(LDFLAGS) $(OBJECTS) cdhit-lap.o -o cd-hit-lap
- 
- read-linker: $(OBJECTS) read-linker.o
--	$(CC) $(LFLAGS) $(OBJECTS) read-linker.o -o read-linker
-+	$(CXX) $(LDFLAGS) $(OBJECTS) read-linker.o -o read-linker
- 
- clean:
- 	rm $(OBJECTS) cdhit-dup.o cdhit-lap.o read-linker.o
diff --git a/sci-biology/cd-hit-auxtools/metadata.xml b/sci-biology/cd-hit-auxtools/metadata.xml
deleted file mode 100644
index 138cb7705..000000000
--- a/sci-biology/cd-hit-auxtools/metadata.xml
+++ /dev/null
@@ -1,12 +0,0 @@
-<?xml version="1.0" encoding="UTF-8"?>
-<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
-<pkgmetadata>
-	<maintainer type="person">
-		<email>mmokrejs@fold.natur.cuni.cz</email>
-		<name>Martin Mokrejs</name>
-	</maintainer>
-	<maintainer type="project">
-		<email>sci-biology@gentoo.org</email>
-		<name>Gentoo Biology Project</name>
-	</maintainer>
-</pkgmetadata>
diff --git a/sci-biology/cd-hit/Manifest b/sci-biology/cd-hit/Manifest
deleted file mode 100644
index 76a4f8ff6..000000000
--- a/sci-biology/cd-hit/Manifest
+++ /dev/null
@@ -1 +0,0 @@
-DIST cd-hit-4.6.5.tar.gz 1148585 BLAKE2B fdfb107957686bf23fab33e62a66c59c4f90106f22ef147b63d40e8cfba088293a979c58ff9909d436eb7fec7b33eee214a985b683038676ec631074d7f1e42c SHA512 d9dbcc61db36c67ccf4fc01f13c5a1a25d246ce60608ba1ac9eb8df4430c92fc70726b8adeaf5cc016025a07aa1d3f675a3636c5439cf3705992753497e319da
diff --git a/sci-biology/cd-hit/cd-hit-4.6.5.ebuild b/sci-biology/cd-hit/cd-hit-4.6.5.ebuild
deleted file mode 100644
index c7ba45f91..000000000
--- a/sci-biology/cd-hit/cd-hit-4.6.5.ebuild
+++ /dev/null
@@ -1,60 +0,0 @@
-# Copyright 1999-2015 Gentoo Foundation
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=5
-
-inherit eutils flag-o-matic toolchain-funcs
-
-RELDATE="2016-03-04"
-RELEASE="${PN}-v${PV}-${RELDATE}"
-
-DESCRIPTION="Clustering Database at High Identity with Tolerance"
-HOMEPAGE="http://weizhong-lab.ucsd.edu/cd-hit
-	http://weizhongli-lab.org/cd-hit"
-SRC_URI="https://github.com/weizhongli/cdhit/archive/V${PV}.tar.gz -> ${P}.tar.gz"
-
-SLOT="0"
-KEYWORDS="~amd64 ~x86 ~amd64-linux ~x86-linux"
-LICENSE="GPL-2"
-IUSE="doc openmp"
-
-DEPEND="!sci-biology/cd-hit-auxtools"
-
-S="${WORKDIR}"/cdhit-"${PV}"
-
-pkg_setup() {
-	 use openmp && ! tc-has-openmp && die "Please switch to an openmp compatible compiler"
-}
-
-src_prepare() {
-	tc-export CXX
-	use openmp || append-flags -DNO_OPENMP
-	epatch "${FILESDIR}"/${PV}-gentoo.patch
-}
-
-src_compile() {
-	local myconf=
-	use openmp && myconf="openmp=yes"
-	emake ${myconf}
-	cd cd-hit-auxtools || die
-	emake ${myconf}
-}
-
-src_install() {
-	dodir /usr/bin
-	emake PREFIX="${ED}/usr/bin" install
-	dobin psi-cd-hit/*.pl cd-hit-auxtools/*.pl cd-hit-auxtools/{cd-hit-lap,read-linker,cd-hit-dup}
-	dodoc ChangeLog psi-cd-hit/README.psi-cd-hit
-	use doc && dodoc doc/* psi-cd-hit/qsub-template "${FILESDIR}"/cd-hit-auxtools-manual.txt
-}
-
-pkg_postinst(){
-	einfo "From the original http://weizhong-lab.ucsd.edu/software/cdhit-454 package"
-	einfo "we still lack cdhit-cluster-consensus part. You may want to install yourself"
-	einfo "http://weizhong-lab.ucsd.edu/softwares/cd-hit-454/cdhit-cluster-consensus-2013-03-27.tgz"
-	einfo ""
-	einfo "The cd-hit-auxtools are no longer a separate package and belong to cd-hit since"
-	einfo "version 4.6.5. However, there is no manual for that in current cd-hit tree. Therefore"
-	einfo "see http://weizhong-lab.ucsd.edu/cd-hit/wiki/doku.php?id=cd-hit-auxtools-manual"
-	einfo "A local copy is is in /usr/share/doc/${PN}/cd-hit-auxtools-manual.txt"
-}
diff --git a/sci-biology/cd-hit/files/4.6.5-gentoo.patch b/sci-biology/cd-hit/files/4.6.5-gentoo.patch
deleted file mode 100644
index 5e989da40..000000000
--- a/sci-biology/cd-hit/files/4.6.5-gentoo.patch
+++ /dev/null
@@ -1,163 +0,0 @@
---- Makefile.ori	2016-02-12 01:58:32.000000000 +0100
-+++ Makefile	2016-03-15 16:55:53.726069350 +0100
-@@ -1,7 +1,4 @@
--
--CC = g++ -Wall -ggdb
--CC = g++ -pg
--CC = g++
-+CXX ?= g++
- 
- # without OpenMP
- 
-@@ -9,9 +6,9 @@
- # in command line: 
- # make openmp=yes
- ifeq ($(openmp),no)
--  CCFLAGS = -DNO_OPENMP
-+  CXXFLAGS += -DNO_OPENMP
- else
--  CCFLAGS = -fopenmp
-+  CXXFLAGS += -fopenmp
- endif
- 
- # support debugging
-@@ -19,13 +16,13 @@
- # make debug=yes
- # make openmp=yes debug=yes
- ifeq ($(debug),yes)
--CCFLAGS += -ggdb
-+CXXFLAGS += -ggdb
- else
--CCFLAGS += -O2
-+CXXFLAGS ?= -O2
- endif
- 
- ifdef MAX_SEQ
--CCFLAGS += -DMAX_SEQ=$(MAX_SEQ)
-+CXXFLAGS += -DMAX_SEQ=$(MAX_SEQ)
- endif
- 
- #LDFLAGS = -static -o
-@@ -34,10 +31,10 @@
- PROGS = cd-hit cd-hit-est cd-hit-2d cd-hit-est-2d cd-hit-div cd-hit-454
- 
- # Propagate hardening flags
--CCFLAGS := $(CPPFLAGS) $(CCFLAGS) $(CXXFLAGS)
-+CXXFLAGS := $(CPPFLAGS) $(CXXFLAGS)
- 
- .c++.o:
--	$(CC) $(CCFLAGS) -c $<
-+	$(CXX) $(CXXFLAGS) -c $<
- 
- all: $(PROGS)
- 
-@@ -47,49 +44,49 @@
- # programs
- 
- cd-hit: cdhit-common.o cdhit-utility.o cdhit.o
--	$(CC) $(CCFLAGS) cdhit.o cdhit-common.o cdhit-utility.o $(LDFLAGS) cd-hit
-+	$(CXX) $(CXXFLAGS) cdhit.o cdhit-common.o cdhit-utility.o $(LDFLAGS) cd-hit
- 
- cd-hit-2d: cdhit-common.o cdhit-utility.o cdhit-2d.o
--	$(CC) $(CCFLAGS) cdhit-2d.o cdhit-common.o cdhit-utility.o $(LDFLAGS) cd-hit-2d
-+	$(CXX) $(CXXFLAGS) cdhit-2d.o cdhit-common.o cdhit-utility.o $(LDFLAGS) cd-hit-2d
- 
- cd-hit-est: cdhit-common.o cdhit-utility.o cdhit-est.o
--	$(CC) $(CCFLAGS) cdhit-est.o cdhit-common.o cdhit-utility.o $(LDFLAGS) cd-hit-est
-+	$(CXX) $(CXXFLAGS) cdhit-est.o cdhit-common.o cdhit-utility.o $(LDFLAGS) cd-hit-est
- 
- cd-hit-est-2d: cdhit-common.o cdhit-utility.o cdhit-est-2d.o
--	$(CC) $(CCFLAGS) cdhit-est-2d.o cdhit-common.o cdhit-utility.o $(LDFLAGS) cd-hit-est-2d
-+	$(CXX) $(CXXFLAGS) cdhit-est-2d.o cdhit-common.o cdhit-utility.o $(LDFLAGS) cd-hit-est-2d
- 
- cd-hit-div: cdhit-common.o cdhit-utility.o cdhit-div.o
--	$(CC) $(CCFLAGS) cdhit-div.o cdhit-common.o cdhit-utility.o $(LDFLAGS) cd-hit-div
-+	$(CXX) $(CXXFLAGS) cdhit-div.o cdhit-common.o cdhit-utility.o $(LDFLAGS) cd-hit-div
- 
- cd-hit-454: cdhit-common.o cdhit-utility.o cdhit-454.o
--	$(CC) $(CCFLAGS) cdhit-454.o cdhit-common.o cdhit-utility.o $(LDFLAGS) cd-hit-454
-+	$(CXX) $(CXXFLAGS) cdhit-454.o cdhit-common.o cdhit-utility.o $(LDFLAGS) cd-hit-454
- 
- # objects
- cdhit-common.o: cdhit-common.c++ cdhit-common.h
--	$(CC) $(CCFLAGS) cdhit-common.c++ -c
-+	$(CXX) $(CXXFLAGS) cdhit-common.c++ -c
- 
- cdhit-utility.o: cdhit-utility.c++ cdhit-utility.h
--	$(CC) $(CCFLAGS) cdhit-utility.c++ -c
-+	$(CXX) $(CXXFLAGS) cdhit-utility.c++ -c
- 
- cdhit.o: cdhit.c++ cdhit-utility.h
--	$(CC) $(CCFLAGS) cdhit.c++ -c
-+	$(CXX) $(CXXFLAGS) cdhit.c++ -c
- 
- cdhit-2d.o: cdhit-2d.c++ cdhit-utility.h
--	$(CC) $(CCFLAGS) cdhit-2d.c++ -c
-+	$(CXX) $(CXXFLAGS) cdhit-2d.c++ -c
- 
- cdhit-est.o: cdhit-est.c++ cdhit-utility.h
--	$(CC) $(CCFLAGS) cdhit-est.c++ -c
-+	$(CXX) $(CXXFLAGS) cdhit-est.c++ -c
- 
- cdhit-est-2d.o: cdhit-est-2d.c++ cdhit-utility.h
--	$(CC) $(CCFLAGS) cdhit-est-2d.c++ -c
-+	$(CXX) $(CXXFLAGS) cdhit-est-2d.c++ -c
- 
- cdhit-div.o: cdhit-div.c++ cdhit-common.h
--	$(CC) $(CCFLAGS) cdhit-div.c++ -c
-+	$(CXX) $(CXXFLAGS) cdhit-div.c++ -c
- 
- cdhit-454.o: cdhit-454.c++ cdhit-common.h
--	$(CC) $(CCFLAGS) cdhit-454.c++ -c
-+	$(CXX) $(CXXFLAGS) cdhit-454.c++ -c
- 
--PREFIX ?= /usr/local/bin
-+PREFIX ?= $(DESTDIR)/usr/local/bin
- 
- install:
- 	for prog in $(PROGS); do \
---- cd-hit-auxtools/Makefile.ori	2016-03-15 17:02:39.986070411 +0100
-+++ cd-hit-auxtools/Makefile	2016-03-15 17:05:00.556070779 +0100
-@@ -1,9 +1,8 @@
-+CXX ?= g++
- 
--CC = g++
--
--CFLAGS = -Wall -Wno-unused -I. -Imintlib
-+CXXFLAGS ?= -Wall -Wno-unused
- LFLAGS = -fPIC
--
-+CPPFLAGS = -I. -Imintlib
- 
- UNAME = $(shell uname)
- 
-@@ -18,7 +17,7 @@
- ifeq ($(debug),yes)
- CXXFLAGS += -ggdb
- else
--CFLAGS += -O2
-+CXXFLAGS ?= -O2
- endif
- 
- 
-@@ -32,16 +31,16 @@
- .SUFFIXES: .c .obj .cpp .cc .cxx .C
- 
- .cxx.o:
--	$(CC) -c $(CFLAGS) -o $@ $<
-+	$(CXX) -c $(CXXFLAGS) $(CPPFLAGS) -o $@ $<
- 
- cd-hit-dup: $(OBJECTS) cdhit-dup.o
--	$(CC) $(LFLAGS) $(OBJECTS) cdhit-dup.o -o cd-hit-dup
-+	$(CXX) $(CXXFLAGS) $(LFLAGS) $(OBJECTS) cdhit-dup.o -o cd-hit-dup
- 
- cd-hit-lap: $(OBJECTS) cdhit-lap.o
--	$(CC) $(LFLAGS) $(OBJECTS) cdhit-lap.o -o cd-hit-lap
-+	$(CXX) $(CXXFLAGS) $(LFLAGS) $(OBJECTS) cdhit-lap.o -o cd-hit-lap
- 
- read-linker: $(OBJECTS) read-linker.o
--	$(CC) $(LFLAGS) $(OBJECTS) read-linker.o -o read-linker
-+	$(CXX) $(CXXFLAGS) $(LFLAGS) $(OBJECTS) read-linker.o -o read-linker
- 
- clean:
- 	rm $(OBJECTS) cdhit-dup.o cdhit-lap.o read-linker.o
diff --git a/sci-biology/cd-hit/files/cd-hit-auxtools-manual.txt b/sci-biology/cd-hit/files/cd-hit-auxtools-manual.txt
deleted file mode 100644
index 6e0ca68a9..000000000
--- a/sci-biology/cd-hit/files/cd-hit-auxtools-manual.txt
+++ /dev/null
@@ -1,212 +0,0 @@
-http://weizhong-lab.ucsd.edu/cd-hit/wiki/doku.php?id=cd-hit-auxtools-manual
-
-CD-HIT AuxTools: Manual
-
-Last updated: 2012/03/08 00:59
-
-http://cd-hit.org
-
-http://bioinformatics.org/cd-hit/
-
-Program developed by Weizhong Li's lab at UCSD http://weizhong-lab.ucsd.edu liwz@sdsc.edu
-Introduction
-
-CD-HIT AuxTools is a set of auxiliary programs that can be used to assist the analysis of the next generation sequencing data. It currently includes programs for removing read duplicates, finding pairs of overlapping reads or joining pair-end reads etc.
-cd-hit-dup
-
-cd-hit-dup is a simple tool for removing duplicates from sequencing reads, with optional step to detect and remove chimeric reads. A number of options are provided to tune how the duplicates are removed. Running the program without arguments should print out the list of available options, as the following:
-
-Options:
-    -i        Input file;
-    -i2       Second input file;
-    -o        Output file;
-    -d        Description length (default 0, truncate at the first whitespace character)
-    -u        Length of prefix to be used in the analysis (default 0, for full/maximum length);
-    -m        Match length (true/false, default true);
-    -e        Maximum number/percent of mismatches allowed;
-    -f        Filter out chimeric clusters (true/false, default false);
-    -s        Minimum length of common sequence shared between a chimeric read
-              and each of its parents (default 30, minimum 20);
-    -a        Abundance cutoff (default 1 without chimeric filtering, 2 with chimeric filtering);
-    -b        Abundance ratio between a parent read and a chimeric read (default 1);
-    -p        Dissimilarity control for chimeric filtering (default 1);
-
-Option details
-Common options
-
-Here are the more detailed description of the options.
-
-    -i        Input file;
-
-Input file that must be in fasta or fastq format.
-
-    -i2       Second input file;
-
-cd-hit-dup can take a pair of files as inputs, assuming they contain sequences of pair-end reads. �-i� can be used to specify the file for the first end; and �-i2� can be used to specify the file for the second end.
-
-When two files of pair-end reads are used as inputs, each pair of reads will be concatenated into a single one. And the following steps of duplicate and chimeric detection and removing.
-
-    -o        Output file;
-
-Output file which contains a list of reads without duplicates.
-
-    -d        Description length (default 0, truncate at the first whitespace character)
-
-The length of description line that should be written to the output.
-
-    -u        Length of prefix to be used in the analysis (default 0, for full/maximum length);
-
-For pair-end inputs, the program will take part (whole or prefix) of the first end and part (whole or prefix) of the second read, and join them together to form a single read to do the analysis. A positive value of this option specifies the length of the prefix to be taken from each read. If a read is shorter than this length, letter 'N's will be appended to the read to make up for the length. When this option is not used or is used with a non-positive value, the program will use the length of the longest read as the value of this option.
-
-For single input analysis, only a positive value of this option will be effective. It also allows the program to use only the prefix up to the specified length of each read to do the analysis. In case that a read is shorter than this length, no 'N' is appended to the read since it is not necessary.
-Options for duplicate detection
-
-    -m        Match length (true/false, default true);
-
-�-m� specifies whether the lengths of two reads should be exactly the same to be considered as duplicates.
-
-    -e        Maximum number/percent of mismatches allowed;
-
-Maximum number/percent of mismatches can be specified to control the similarity between two reads for duplicate and chimeric detection. For duplicate detection, any two reads with number of mismatches no greater than the specified value are considered to be duplicates. For chimeric detection, this option control how similar a read should be to either of its parents.
-Options for chimeric filtering
-
-    -f        Filter out chimeric clusters (true/false, default false);
-
-This option specifies whether or not to carry out an additional step to filter out chimeric clusters.
-
-    -s        Minimum length of common sequence shared between a chimeric read
-              and each of its parents (default 30, minimum 20);
-
-A read or cluster representative is considered as a potential chimeric only if it shares at least the number of bases specified by this option with either of its parents. This option is effective only if the option is set to true for filtering chimeric clusters.
-
-    -a        Abundance cutoff (default 1 without chimeric filtering, 2 with chimeric filtering);
-
-Each read is associated with an abundance number, which is the number of duplicates for the read. cd-hit-dup always assumes the input contains duplicates and perform the duplicate detection step. If no duplicate is found, the input is assumed to have duplicates remove in advance, and then, the program will try to obtain the abundance information from the descriptions of the reads, it interprets the number following “_abundance_� as the abundance number.
-
-The abundance cutoff is mainly used for chimeric filtering to skip chimeric checking on reads with abundance below this cutoff.
-
-    -b        Abundance ratio between a parent read and a chimeric read (default 1);
-
-This option specifies the abundance ratio between a parent read and a chimeric read. So for a read to be chimeric, either of its parents must have abundance at least as high as the ratio times the abundance of the chimeric read.
-
-    -p        Dissimilarity control for chimeric filtering (default 1);
-
-Internally dissimilarity is measured by percent of mismatches with ungapped alignments. By default the percentage cutoff is set to 0.01 (one percent). This option specifies a multiplier to this percentage cutoff. A higher value will increase the dissimilarity thresholds in chimeric filtering.
-Output files
-
-cd-hit-dup will output three files. Two of them are the same as the output files of CD-HIT: one (named exactly the same as the file name specified by the �-o� option) is the cluster (or duplicate) representatives, the other is the clustering file (xxx.clstr) relating each duplicate to its representative. The third file (xxx2.clstr) contains the chimeric clusters. In this file, the description for each chimeric cluster contains cluster ids of its parent clusters from the clustering file xxx.clstr.
-Examples
-Duplicate Detection
-
-Remove duplicates using default parameters:
-
-cd-hit-dup -i input.fa -o output
-
-By default, only reads that are identical are considered as duplicates. If �-m� is set to false, duplicates will be allowed to have different length, but the longer ones must have a prefix that is identical to the shorter ones.
-
-Remove duplicates with a few mismatches:
-
-cd-hit-dup -i input.fa -o output -e 2
-cd-hit-dup -i input.fa -o output -e 0.01
-
-The former will allow each duplicate read to have up to 2 mismatches when aligned to its representative; and the later will allow up to one percent mismatches.
-
-Remove duplicates from pair-end reads:
-
-cd-hit-dup -i pair-end1.fa -i2 pair-end2.fa -o output
-
-Each read from “pair-end1.fa� and “pair-end2.fa� will be joint to form a single read to detect duplicates. If they all are of the same length, the full length of each ends will be used in forming the single read; otherwise, the default value of option �-u� will be used to determine how the single read is created.
-
-Remove duplicates from pair-end reads with control on how the pair-ends are jointed:
-
-cd-hit-dup -i pair-end1.fa -i2 pair-end2.fa -o output -u 100
-
-With explicit �-u� options, any reads shorter than 100 will be padded with 'N's, and the longer ones will be cut down to 100 base long. Then each pair of the 100 base long reads will be jointed to form a single 200 base long read.
-Chimeric Filtering
-
-cd-hit-dup offers a very efficient way to detect chimeric reads. The basic idea is to find two parent reads whose cross-over is sufficient similar to the chimeric read, while each single parent is sufficiently dissimilar to it.
-
-Such dissimilarity is measured by the percent of mismatches for no-gapped alignments. For a given percentage “p� (from option �-p�), a chimeric read must share at least “p� percent mismatches with any other single read, namely, it much be sufficiently dissimilar to any single read.
-
-For more robust detection of chimeric reads, a background percentage “p_bg� is calculated as the mismatch percentage shared between the candidate chimeric read and the single read that is most similar to the candidate. If “p_bg� is greater than “1.5*p�, “1.5*p� will be used as “p_bg� instead.
-
-For a read to be classified as chimeric read, there must exist two reads/parents such that, the leading part of the read is sufficiently similar to one parent, and the rest is sufficiently similar to the other parent, with at most “p+p_bg� percent of mismatches in each part. And the crossover between the two parents must share at most “p_bg� mismatches with the chimeric read.
-
-Chimeric filtering with default parameters:
-
-cd-hit-dup -i input.fa -o output -f true
-
-Chimeric filtering with specified similarity level:
-
-cd-hit-dup -i input.fa -o output -f true -p 1.5
-
-Chimeric filtering with specified abundance difference:
-
-cd-hit-dup -i input.fa -o output -f true -a 2
-
-which means each parent of a chimeric read must be a least as twice abundant as the chimeric read.
-
-Chimeric filtering will produce a cluster file named like “xxx2.clstr�, in which each cluster entry is a chimeric read/cluster. For example,
-
-......
->Cluster 4 chimeric_parent1=2,chimeric_parent2=8
-0   256nt, >FV9NWLF01CRIR3_abundance_23... *
->Cluster 5 chimeric_parent1=2,chimeric_parent2=0
-0   250nt, >FV9NWLF01B4TBX_abundance_21... *
-......
-
-here “Cluster 5� contains a chimeric read “FV9NWLF01B4TBX�, whose parents are identified by cluster numbers “2� and “0� from the associated “xxx.clstr� file,
-
->Cluster 0
-0   252nt, >FV9NWLF01ANLX2_abundance_2239... *
->Cluster 1
-0   246nt, >FV9NWLF01C3KOB_abundance_1465... *
->Cluster 2
-0   260nt, >FV9NWLF01AQOWA_abundance_1284... *
-......
-
-So the parent reads of the chimeric read “FV9NWLF01B4TBX� are “FV9NWLF01AQOWA� and “FV9NWLF01ANLX2�.
-cd-hit-lap
-
-cd-hit-lap is program for extracting pairs of overlapping reads by clustering based on tail-head overlaps (with perfect matching). The basic clustering strategy is the same as that in standard CD-HIT programs. In this program, each read is clustered as either a “representative� or a “redundant� read. For each “redundant� read, it must have a prefix that is identical a suffix of its representative read.
-
-The options of this program can be obtained by running it it without any arguments:
-
-[compute-0-0 cdhit-dup]$ ./cd-hit-lap
-Options:
-    -i        Input file;
-    -o        Output file;
-    -m        Minimum length of overlapping part (default 20);
-    -p        Minimum percentage of overlapping part (default 0, any percentage);
-    -d        Description length (default 0, truncate at the first whitespace character)
-    -s        Random number seed for shuffling (default 0, no shuffling; shuffled before sorting by length);
-    -stdout   Standard output type (default "log", other options "rep", "clstr");
-
-The two options �-m� and �-p� can be used to control the minimum overlap that is required to classify them as overlapping reads. Each pair of overlapping reads must have overlap length no less than the threshold specified by �-m�, and must also not be less than the length threshold computed from the �-p� option.
-
-Since the overlapping reads are searched using a greedy strategy, so different sortings of reads may lead to different result. So it is advisable to run the program multiple times with read shuffling by different random number seeds, and then collect and merge the results.
-
-Sometimes it may be more convenient to pipe the results of this program as stdout directly to the stdin of other programs, to do this, the option �-stdout� can be used to choose which type (“log� for program console information, “rep� for representative reads in FASTA or FASTQ format, “clstr� for the clustering output in CD-HIT format) of results to be writen to the stdout.
-
-The output format of this program is the same as the standard CD-HIT. In the .clstr file, the alignment positions indicate how the reads are overlapped. For example,
-
->Cluster 0
-0   75nt, >1_lane2_624... *
-1   75nt, >1_lane2_7169... at 1:65:11:75/+/100.00%
-2   75nt, >1_lane2_36713... at 69:1:1:69/-/100.00%
-3   75nt, >1_lane2_141482... at 1:56:20:75/+/100.00%
-
-The cluster member #0 in cluster #0 is the representative of the cluster, and it overlaps with each of the other members in the cluster. For cluster member #1, “1:65:11:75/+� tells that the first 65 bases of member #1 overlaps with the last 65 bases of member #0; “69:1:1:69/-� indicates that the last 69 bases of member #2 overlaps with the first 69 bases of member #0.
-read-linker
-
-read-linker is a very simple program to concatenate pair-end reads into single ones. It support the following options:
-
-[compute-0-0 cdhit-dup]$ ./read-linker 
-Options:
-    -1 file       Input file, first end;
-    -2 file       Input file, second end;
-    -o file       Output file;
-    -l number     Minimum overlapping length (default 10);
-    -e number     Maximum number of errors (mismatches, default 1);
-
-Only the pairs of reads that share at least a minimum overlapping length with mismatched no more than the maximum number of errors, are jointed to form a single read.
diff --git a/sci-biology/cd-hit/metadata.xml b/sci-biology/cd-hit/metadata.xml
deleted file mode 100644
index 4112e9551..000000000
--- a/sci-biology/cd-hit/metadata.xml
+++ /dev/null
@@ -1,26 +0,0 @@
-<?xml version="1.0" encoding="UTF-8"?>
-<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
-<pkgmetadata>
-	<maintainer type="project">
-		<email>sci-biology@gentoo.org</email>
-		<name>Gentoo Biology Project</name>
-	</maintainer>
-	<longdescription>
-CD-HIT is a very widely used program for clustering and comparing large sets 
-of protein or nucleotide sequences. CD-HIT is very fast and can handle 
-extremely large databases. CD-HIT helps to significantly reduce the 
-computational and manual efforts in many sequence analysis tasks and aids in 
-understanding the data structure and correct the bias within a dataset.
-The CD-HIT package has CD-HIT, CD-HIT-2D, CD-HIT-EST, CD-HIT-EST-2D, 
-CD-HIT-454, CD-HIT-PARA, PSI-CD-HIT and over a dozen scripts. CD-HIT 
-(CD-HIT-EST) clusters similar proteins (DNAs) into clusters that meet a 
-user-defined similarity threshold. CD-HIT-2D (CD-HIT-EST-2D) compares 2 
-datasets and identifies the sequences in db2 that are similar to db1 above 
-a threshold. CD-HIT-454 is a program to identify natural and artificial 
-duplicates from pyrosequencing reads. The usage of other programs and 
-scripts can be found in CD-HIT user's guide.
-</longdescription>
-	<upstream>
-		<remote-id type="github">weizhongli/cdhit</remote-id>
-	</upstream>
-</pkgmetadata>
diff --git a/sci-biology/cdbfasta/Manifest b/sci-biology/cdbfasta/Manifest
index bac1bd267..a6fc6cfbe 100644
--- a/sci-biology/cdbfasta/Manifest
+++ b/sci-biology/cdbfasta/Manifest
@@ -1 +1 @@
-DIST cdbfasta.tar.gz 59735 BLAKE2B 69107a42e1b8069a70de9333891e050785cabaf6457245b4512c3725dc576ebfba54c43c3d1e356948061cf903a89a8aa0f011efbf36a4cda6b40a623f7019fe SHA512 500b3cdf4bf4e21c78a285739c6544e3f2bed377f8e3858c8ace240a9107d765c89cff8004ca2ea001860abc04fc48bc37c03569da5b16115f4419f5fd9bcd5e
+DIST cdbfasta-0.1.tar.gz 59735 BLAKE2B 69107a42e1b8069a70de9333891e050785cabaf6457245b4512c3725dc576ebfba54c43c3d1e356948061cf903a89a8aa0f011efbf36a4cda6b40a623f7019fe SHA512 500b3cdf4bf4e21c78a285739c6544e3f2bed377f8e3858c8ace240a9107d765c89cff8004ca2ea001860abc04fc48bc37c03569da5b16115f4419f5fd9bcd5e
diff --git a/sci-biology/cdbfasta/cdbfasta-0.1.ebuild b/sci-biology/cdbfasta/cdbfasta-0.1.ebuild
index f0f8918fa..c04ce4698 100644
--- a/sci-biology/cdbfasta/cdbfasta-0.1.ebuild
+++ b/sci-biology/cdbfasta/cdbfasta-0.1.ebuild
@@ -1,20 +1,20 @@
-# Copyright 1999-2015 Gentoo Foundation
+# Copyright 1999-2021 Gentoo Authors
 # Distributed under the terms of the GNU General Public License v2
 
-EAPI=5
+EAPI=7
 
 DESCRIPTION="FASTA record indexing/retrievieng utility"
-HOMEPAGE="http://compbio.dfci.harvard.edu/tgi/software"
-SRC_URI="ftp://occams.dfci.harvard.edu/pub/bio/tgi/software/cdbfasta/cdbfasta.tar.gz"
+HOMEPAGE="https://github.com/gpertea/cdbfasta"
+SRC_URI="ftp://occams.dfci.harvard.edu/pub/bio/tgi/software/cdbfasta/cdbfasta.tar.gz -> ${P}.tar.gz"
 
 LICENSE="Artistic"
 SLOT="0"
 KEYWORDS="~amd64 ~x86"
-IUSE=""
 
 S=${WORKDIR}/${PN}
 
 src_prepare() {
+	default
 	sed \
 		-e 's/CFLAGS[ ]*=/CFLAGS :=/; s/-D_REENTRANT/-D_REENTRANT \${CFLAGS}/; s/CFLAGS[ ]*:=[ ]*-O2$//' \
 		-i "${S}"/Makefile || die "Failed to patch Makefile"
diff --git a/sci-biology/cegma/Manifest b/sci-biology/cegma/Manifest
deleted file mode 100644
index 0c05b71b5..000000000
--- a/sci-biology/cegma/Manifest
+++ /dev/null
@@ -1 +0,0 @@
-DIST CEGMA_v2.5.tar.gz 12751140 BLAKE2B dbcd8e6f4a5b027b96e3fa6fa7ddee854d10b0d10b7b1428ef7cf5bf38971473c2b941e6d2e66b75e06c1c35f023beeb227675a871094e9312522bca1abf1f27 SHA512 b38772a80b40be08746d4d19e21f5a5c738baab14c496d9b024e3a248965f431669b90f3e811433a086021fcc5d364fd8fd87111d47f8764497093e1d8207c2c
diff --git a/sci-biology/cegma/cegma-2.5.ebuild b/sci-biology/cegma/cegma-2.5.ebuild
deleted file mode 100644
index 16e4fd3a7..000000000
--- a/sci-biology/cegma/cegma-2.5.ebuild
+++ /dev/null
@@ -1,38 +0,0 @@
-# Copyright 1999-2015 Gentoo Foundation
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=5
-
-PERL_EXPORT_PHASE_FUNCTIONS=no
-inherit perl-module eutils toolchain-funcs
-
-DESCRIPTION="Predict genes in a genome and use them for training to find all genes"
-HOMEPAGE="http://korflab.ucdavis.edu/datasets/cegma"
-SRC_URI="http://korflab.ucdavis.edu/datasets/cegma/CEGMA_v${PV}.tar.gz"
-
-LICENSE="GPL-2"
-SLOT="0"
-KEYWORDS="~amd64"
-IUSE=""
-
-DEPEND="
-	sci-biology/wise
-	sci-biology/geneid
-	sci-biology/ncbi-tools++"
-	# >=sci-biology/hmmer-3.0
-RDEPEND="${DEPEND}"
-
-S="${WORKDIR}"/CEGMA_v${PV}
-
-src_install(){
-	dobin bin/*
-	perl_set_version
-	insinto ${VENDOR_LIB}
-	doins lib/*.pm
-}
-
-pkg_postinst(){
-	ewarn "cegma needs >=sci-biology/hmmer-3.0 but sci-biology/wise uses sci-biology/hmmer-2.3"
-	ewarn "hmmer-3 is not backwards compatible and does not even have all its previous features"
-	ewarn "Therefore, we do not list hmmer in the list of DEPENDENCIES."
-}
diff --git a/sci-biology/cegma/metadata.xml b/sci-biology/cegma/metadata.xml
deleted file mode 100644
index 138cb7705..000000000
--- a/sci-biology/cegma/metadata.xml
+++ /dev/null
@@ -1,12 +0,0 @@
-<?xml version="1.0" encoding="UTF-8"?>
-<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
-<pkgmetadata>
-	<maintainer type="person">
-		<email>mmokrejs@fold.natur.cuni.cz</email>
-		<name>Martin Mokrejs</name>
-	</maintainer>
-	<maintainer type="project">
-		<email>sci-biology@gentoo.org</email>
-		<name>Gentoo Biology Project</name>
-	</maintainer>
-</pkgmetadata>
diff --git a/sci-biology/cg-cat/Manifest b/sci-biology/cg-cat/Manifest
deleted file mode 100644
index 2125e4476..000000000
--- a/sci-biology/cg-cat/Manifest
+++ /dev/null
@@ -1 +0,0 @@
-DIST r2cat.tar.gz 409067 BLAKE2B 18cffbc3ecf9655b3155a85495ee5be6f87735ebc9311588ee92b6e1c4130152c3f08d974854ceffe58201b9a232f70ae01fadcb388da20d222e156ce76f5bc5 SHA512 a837d216664fede82e147204e8f1ba07b2d5ad92ee3db6f3a1285ff4acc4fb5b70715ac272d727304901548d68cb4865c051ef24690226692c4c4d693c7988f1
diff --git a/sci-biology/cg-cat/cg-cat-20150130.ebuild b/sci-biology/cg-cat/cg-cat-20150130.ebuild
deleted file mode 100644
index b83ebd996..000000000
--- a/sci-biology/cg-cat/cg-cat-20150130.ebuild
+++ /dev/null
@@ -1,59 +0,0 @@
-# Copyright 1999-2016 Gentoo Foundation
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=5
-
-inherit java-pkg-2 java-ant-2
-
-DESCRIPTION="r2cat and treecat, scaffolding tools for ordering and orienting contigs"
-HOMEPAGE="http://bibiserv.techfak.uni-bielefeld.de/cgcat"
-SRC_URI="http://bibiserv.techfak.uni-bielefeld.de/applications/cgcat/resources/downloads/r2cat.tar.gz"
-# SRC_URI="http://bibiserv.techfak.uni-bielefeld.de/applications/cgcat/resources/downloads/r2cat.jar"
-
-LICENSE="GPL-3"
-SLOT="0"
-KEYWORDS="~amd64"
-IUSE=""
-
-RDEPEND="${DEPEND}
-	>=virtual/jre-1.6:*
-	dev-lang/perl
-	sci-biology/ncbi-tools"
-DEPEND="${RDEPEND}
-	>=virtual/jdk-1.6:*
-	dev-java/ant-core"
-
-S="${WORKDIR}"/r2cat
-
-src_prepare(){
-	sed -e "s#/vol/bioapps#"${D}"/usr#" -e "s#/vol/bibidev/r2cat#"${D}"/usr#" -i Makefile || die
-	sed -e "s#/vol/gnu#/usr#" -i de/bielefeld/uni/cebitec/r2cat/blast_to_r2cat.pl || die
-}
-
-src_compile(){
-	emake r2cat.jar
-}
-
-src_install(){
-	# emake install dies with:
-	# jarsigner -tsa https://timestamp.geotrust.com/tsa -keystore /homes/phuseman/.gnupg/jarsigner_keystore_cg-cat  cg-cat.jar cgcat
-	# Enter Passphrase for keystore: jarsigner: you must enter key password
-	# Makefile:44: recipe for target 'cg-cat.jar' failed
-	mkdir -p "${D}"/usr/share/r2cat
-	# emake install_cebitec
-	# emake install_bibiserv
-	# the blast_to_r2cat.pl script needs bioperl
-	dobin de/bielefeld/uni/cebitec/r2cat/blast_to_r2cat.pl
-	java-pkg_dojar r2cat.jar || die
-	dodoc README.md ReadmeLicenses.txt
-	insinto /usr/share/doc/"${PN}"/html
-	doins de/bielefeld/uni/cebitec/r2cat/help/*
-}
-
-# to start r2cat:
-# java -Xmx10240M -jar r2cat.jar de.bielefeld.uni.cebitec.r2cat.R2cat
-
-# to start treecat:
-# java -Xmx10240M -cp r2cat.jar de.bielefeld.uni.cebitec.treecat.Treecat -Xmx -d64
-
-# add -d64 on the java commandline if you need more than 4GB of memory and your system can handle it
diff --git a/sci-biology/cg-cat/metadata.xml b/sci-biology/cg-cat/metadata.xml
deleted file mode 100644
index 138cb7705..000000000
--- a/sci-biology/cg-cat/metadata.xml
+++ /dev/null
@@ -1,12 +0,0 @@
-<?xml version="1.0" encoding="UTF-8"?>
-<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
-<pkgmetadata>
-	<maintainer type="person">
-		<email>mmokrejs@fold.natur.cuni.cz</email>
-		<name>Martin Mokrejs</name>
-	</maintainer>
-	<maintainer type="project">
-		<email>sci-biology@gentoo.org</email>
-		<name>Gentoo Biology Project</name>
-	</maintainer>
-</pkgmetadata>
diff --git a/sci-biology/cgview-bin/Manifest b/sci-biology/cgview-bin/Manifest
deleted file mode 100644
index dd563c331..000000000
--- a/sci-biology/cgview-bin/Manifest
+++ /dev/null
@@ -1 +0,0 @@
-DIST cgview_comparison_tool.zip 140105113 SHA256 1ff6034cfc9791a890aadd7b5ee203c250fa19571b6d0338d1090364a633c273 SHA512 978a2eca3039ba2d7b244618249f1cdd70a16502ea9030cdfd3c139bcf50707e17cb2066e28df541a4d9bd5ed6decd425fd329d970c94ea2cbabecd7fb1eb1b1 WHIRLPOOL 165054be065d16f5b7dd1f05daff873cb2564882dafd395605a7f8f64477602684318a5c30f407d2e9d96aa6e80b6fa41e3f834bf9c5160a26509f5aa43add4b
diff --git a/sci-biology/cgview-bin/cgview-bin-20131130.ebuild b/sci-biology/cgview-bin/cgview-bin-20131130.ebuild
deleted file mode 100644
index 671466fc8..000000000
--- a/sci-biology/cgview-bin/cgview-bin-20131130.ebuild
+++ /dev/null
@@ -1,51 +0,0 @@
-# Copyright 1999-2015 Gentoo Foundation
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=5
-
-inherit java-pkg-2
-
-PERL_EXPORT_PHASE_FUNCTIONS=no
-inherit perl-module eutils toolchain-funcs
-
-DESCRIPTION="CGView Comparison Tool to compare genome sequences graphically (aka CCT)"
-HOMEPAGE="http://stothard.afns.ualberta.ca/downloads/CCT"
-SRC_URI="http://www.ualberta.ca/~stothard/downloads/cgview_comparison_tool.zip"
-
-LICENSE="GPL-2"
-SLOT="0"
-KEYWORDS=""
-IUSE=""
-
-DEPEND="
-	>=dev-lang/perl-5.8.8
-	>=sci-biology/ncbi-tools-2.2.15
-	>=virtual/jre-1.4.2:*
-	dev-java/xerces:2
-	dev-java/batik
-	dev-java/commons-lang:2.1
-	>=media-gfx/imagemagick-6
-	>=sci-biology/bioperl-1.4.0"
-RDEPEND="${DEPEND}"
-
-S="${WORKDIR}"/cgview_comparison_tool
-
-src_test(){
-	./update_cogs.sh || die
-	./test.sh || die
-}
-
-src_install() {
-	insinto /usr/share/${PN}/scripts
-	chmod a+x scripts/* # BUG: this does not work
-	doins scripts/*
-	echo 'CCT_HOME='${EPREFIX}'/usr/share/cgview' > "${S}/99cgview"
-	echo 'PATH="$PATH":"'${CCT_HOME}'/scripts"' >> "${S}/99cgview"
-	doenvd "${S}/99cgview"
-	perl_set_version
-	insinto ${VENDOR_LIB}/cgview
-	doins lib/perl_modules/Util/*.pm
-	#
-	# Exception in thread "main" java.lang.NoClassDefFoundError: org/apache/batik/svggen/SVGGraphics2DIOException
-	java-pkg_dojar bin/cgview.jar
-}
diff --git a/sci-biology/cgview-bin/metadata.xml b/sci-biology/cgview-bin/metadata.xml
deleted file mode 100644
index 138cb7705..000000000
--- a/sci-biology/cgview-bin/metadata.xml
+++ /dev/null
@@ -1,12 +0,0 @@
-<?xml version="1.0" encoding="UTF-8"?>
-<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
-<pkgmetadata>
-	<maintainer type="person">
-		<email>mmokrejs@fold.natur.cuni.cz</email>
-		<name>Martin Mokrejs</name>
-	</maintainer>
-	<maintainer type="project">
-		<email>sci-biology@gentoo.org</email>
-		<name>Gentoo Biology Project</name>
-	</maintainer>
-</pkgmetadata>
diff --git a/sci-biology/chiron/chiron-9999.ebuild b/sci-biology/chiron/chiron-9999.ebuild
deleted file mode 100644
index cd99cb976..000000000
--- a/sci-biology/chiron/chiron-9999.ebuild
+++ /dev/null
@@ -1,22 +0,0 @@
-# Copyright 1999-2018 Gentoo Foundation
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=6
-
-PYTHON_COMPAT=( python2_7 pypy )
-
-inherit distutils-r1 eutils git-r3
-
-DESCRIPTION="Basecaller for OxfordNanopore data using deep learning"
-HOMEPAGE="https://github.com/haotianteng/chiron
-	https://www.biorxiv.org/content/early/2017/09/12/179531"
-EGIT_REPO_URI="https://github.com/haotianteng/chiron"
-
-LICENSE="MPL-2.0"
-SLOT="0"
-KEYWORDS=""
-IUSE=""
-
-DEPEND="=sci-libs/tensorflow-1.0.1"
-RDEPEND="${DEPEND}
-	dev-python/h5py"
diff --git a/sci-biology/chiron/metadata.xml b/sci-biology/chiron/metadata.xml
deleted file mode 100644
index 138cb7705..000000000
--- a/sci-biology/chiron/metadata.xml
+++ /dev/null
@@ -1,12 +0,0 @@
-<?xml version="1.0" encoding="UTF-8"?>
-<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
-<pkgmetadata>
-	<maintainer type="person">
-		<email>mmokrejs@fold.natur.cuni.cz</email>
-		<name>Martin Mokrejs</name>
-	</maintainer>
-	<maintainer type="project">
-		<email>sci-biology@gentoo.org</email>
-		<name>Gentoo Biology Project</name>
-	</maintainer>
-</pkgmetadata>
diff --git a/sci-biology/clover/Manifest b/sci-biology/clover/Manifest
deleted file mode 100644
index 5134912e0..000000000
--- a/sci-biology/clover/Manifest
+++ /dev/null
@@ -1,2 +0,0 @@
-DIST clover-2011-10-24.tar.gz 15843 BLAKE2B 954817e40b49f63d7e3c1c98a82bcc5c56fb695e9428c16244f8c6f82f41cdf80584b933f01f6aec5b08bcfe8a15f193e63af90b9ac16071d57e7bbbbb4cffc5 SHA512 edf773943a33d58b07b7a47ca9e6c0fe08715d7f445ef1283848a14eb72d084b2113a911f23bc484b3229ec14b8eeb50d460c6b9fef89db2fa031ea059b36b93
-DIST jaspar2009core 54400 BLAKE2B 0260a968b212499ec287821dadc74bff908d4918668025639aa6528b6eb29b4a499762b25ed544ffab2938cbdcea645af23d7f50c8143ac6aa3dfa11388d25aa SHA512 621eac23fb0db78391d3d51471f03eccc791e1b348b23b5d9dae32b082c8301e847ee1eea4a76ac188796b639125a0970e5f0b3c0d3c673ae6f6634856c980a0
diff --git a/sci-biology/clover/clover-2011.10.24.ebuild b/sci-biology/clover/clover-2011.10.24.ebuild
deleted file mode 100644
index b8d395801..000000000
--- a/sci-biology/clover/clover-2011.10.24.ebuild
+++ /dev/null
@@ -1,39 +0,0 @@
-# Copyright 1999-2014 Gentoo Foundation
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=5
-
-inherit toolchain-funcs versionator
-
-MY_PV=$(replace_all_version_separators '-')
-
-DESCRIPTION="Cis-eLement OVERrepresentation: Detection of functional DNA motifs"
-HOMEPAGE="http://zlab.bu.edu/clover/"
-SRC_URI="
-	http://zlab.bu.edu/~mfrith/downloads/${PN}-${MY_PV}.tar.gz
-	http://zlab.bu.edu/clover/jaspar2009core"
-
-LICENSE="freedist"
-SLOT="0"
-IUSE=""
-KEYWORDS="~amd64 ~x86"
-
-S="${WORKDIR}/${PN}-${MY_PV}"
-
-src_prepare() {
-	sed \
-		-e "s:g++:$(tc-getCXX) \$(LDFLAGS):; s:-Wall -O3:${CFLAGS}:" \
-		-i Makefile || die "sed failed"
-}
-
-src_install() {
-	dobin clover
-	insinto /usr/share/${PN}
-	doins "${DISTDIR}/jaspar2009core"
-}
-
-pkg_postinst() {
-	einfo "The motif library jaspar2009core has been installed in"
-	einfo "    /usr/share/clover/jaspar2009core"
-	einfo "You can pass this library to clover for motif search, or use your own library."
-}
diff --git a/sci-biology/clover/metadata.xml b/sci-biology/clover/metadata.xml
deleted file mode 100644
index 770d40f6d..000000000
--- a/sci-biology/clover/metadata.xml
+++ /dev/null
@@ -1,11 +0,0 @@
-<?xml version="1.0" encoding="UTF-8"?>
-<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
-<pkgmetadata>
-	<maintainer type="project">
-		<email>maintainer-wanted@gentoo.org</email>
-	</maintainer>
-	<maintainer type="project">
-		<email>sci-biology@gentoo.org</email>
-		<name>Gentoo Biology Project</name>
-	</maintainer>
-</pkgmetadata>
diff --git a/sci-biology/cluster/Manifest b/sci-biology/cluster/Manifest
index 877b9b898..e6bd1df85 100644
--- a/sci-biology/cluster/Manifest
+++ b/sci-biology/cluster/Manifest
@@ -1 +1 @@
-DIST cluster-1.52a.tar.gz 872500 SHA256 e503a1b4680341a516b28804b3bfdbdefd7d8f01a0db659da7cb23f708ac1cd1 SHA512 37e17c179fd69af514b09ef98f1868c636803cd39c186c9a43e07ccbd0dbf0d1dad7334c859194724f0d5580dfa51107cc8ef72de117988ed415a70e17d6a683 WHIRLPOOL c7634fb1e1e802b40af8c28719fe9b81d6e3e1bd0edbfefc1b0048ffba714ef774166cf401e7dfd742d7f54de70b23310e03858e101f9d3737111e920f45043d
+DIST cluster-1.59.tar.gz 1420159 BLAKE2B 8eab9a30ca47c6e8578c23247353df212408dd5fdbf9f14017471318434df011b08f161596ea3460c68ae01e9b22b1f6727cf58418f2e4324907f4d261bd654b SHA512 3fff262ec355ade657639019d02902e97be9c698156fb6a619b659d4fe98e1d7943a9d14dcc564953eaa9e615b5f11d5641ff1fe5a11f283dd77076d82585e8b
diff --git a/sci-biology/cluster/cluster-1.52a.ebuild b/sci-biology/cluster/cluster-1.52a.ebuild
deleted file mode 100644
index b798e579b..000000000
--- a/sci-biology/cluster/cluster-1.52a.ebuild
+++ /dev/null
@@ -1,58 +0,0 @@
-# Copyright 1999-2015 Gentoo Foundation
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=5
-
-DESCRIPTION="Hierarchical, k-means, k-medians clustering for expression/microarray analysis"
-HOMEPAGE="http://bonsai.hgc.jp/~mdehoon/software/cluster
-	http://bonsai.hgc.jp/~mdehoon/software/cluster/software.htm#ctv"
-SRC_URI="${P}.tar.gz"
-
-LICENSE="Eisen"
-SLOT="0"
-KEYWORDS="~amd64 ~x86"
-IUSE="X"
-
-DEPEND="X? ( x11-libs/motif:0= )"
-RDEPEND="
-	X? (
-		x11-misc/xdg-utils
-		app-text/mupdf
-	)"
-
-RESTRICT="fetch"
-
-pkg_nofetch() {
-	einfo "Please obtain ${P}.tar.gz from ${HOMEPAGE} and place it in ${DISTDIR}"
-}
-
-src_prepare() {
-	sed -i \
-		-e 's:^docdir = .*$:docdir = @docdir@:' \
-		-e 's:^htmldir = .*$:htmldir = @htmldir@:' \
-		-e 's:^imagedir = .*$:imagedir = @htmldir@/images:' \
-		-e 's:^fileformatdir = .*$:fileformatdir = @docdir@:' \
-		X11/Makefile.in || die "sed failed"
-}
-
-src_configure() {
-	econf \
-		$(use_with X x) \
-		--docdir="/usr/share/doc/${P}" \
-		--htmldir="/usr/share/doc/${P}/html"
-}
-
-src_install() {
-	default
-
-	mv "${ED}"/usr/bin/cluster{,3} || die
-
-	insinto /usr/share/doc/${P}/examples
-	doins example/example.c example/README
-	insinto /usr/share/doc/${PR}
-	doins doc/cluster.pdf
-}
-
-pkg_postinst() {
-	elog "We renamed the cluster binary to cluster3"
-}
diff --git a/sci-biology/cluster/cluster-1.59.ebuild b/sci-biology/cluster/cluster-1.59.ebuild
new file mode 100644
index 000000000..8a1bf5d7f
--- /dev/null
+++ b/sci-biology/cluster/cluster-1.59.ebuild
@@ -0,0 +1,52 @@
+# Copyright 1999-2021 Gentoo Authors
+# Distributed under the terms of the GNU General Public License v2
+
+EAPI=7
+
+DESCRIPTION="Hierarchical, k-means, k-medians clustering for expression/microarray analysis"
+HOMEPAGE="http://bonsai.hgc.jp/~mdehoon/software/cluster
+	http://bonsai.hgc.jp/~mdehoon/software/cluster/software.htm#ctv"
+SRC_URI="http://bonsai.hgc.jp/~mdehoon/software/cluster/${P}.tar.gz"
+
+LICENSE="Eisen"
+SLOT="0"
+KEYWORDS="~amd64 ~x86"
+IUSE="X"
+
+DEPEND="X? ( x11-libs/motif:0= )"
+RDEPEND="
+	X? (
+		x11-misc/xdg-utils
+		app-text/mupdf
+	)"
+
+src_prepare() {
+	default
+	sed -i \
+		-e 's:^docdir = .*$:docdir = @docdir@:' \
+		-e 's:^htmldir = .*$:htmldir = @htmldir@:' \
+		-e 's:^imagedir = .*$:imagedir = @htmldir@/images:' \
+		-e 's:^fileformatdir = .*$:fileformatdir = @docdir@:' \
+		X11/Makefile.in || die "sed failed"
+}
+
+src_configure() {
+	econf \
+		$(use_with X x) \
+		--docdir="/usr/share/doc/${PF}" \
+		--htmldir="/usr/share/doc/${PF}/html"
+}
+
+src_install() {
+	default
+
+	mv "${ED}"/usr/bin/cluster{,3} || die
+
+	dodoc doc/cluster.pdf
+	docinto examples
+	dodoc example/example.c example/README
+}
+
+pkg_postinst() {
+	elog "We renamed the cluster binary to cluster3"
+}
diff --git a/sci-biology/cluster/files/cluster-1.38-helpmenu-fix.patch b/sci-biology/cluster/files/cluster-1.38-helpmenu-fix.patch
deleted file mode 100644
index 69f3a963e..000000000
--- a/sci-biology/cluster/files/cluster-1.38-helpmenu-fix.patch
+++ /dev/null
@@ -1,30 +0,0 @@
---- X11/gui.c	2007-05-05 00:21:30.000000000 -0500
-+++ X11/gui.c-new	2007-08-09 04:25:53.000000000 -0500
-@@ -1786,15 +1786,15 @@
- {   int item_no = (int) client_data;
-     switch (item_no)
-     {   case CMD_HELP_HTMLHELP:
--        {   system("netscape "PREFIX"/cluster/html/index.html &");
-+        {   system("xdg-open "PREFIX"/share/doc/cluster-1.36/html/index.html &");
- 	    break;
- 	}
-         case CMD_HELP_MANUAL:
--        {   system("acroread "PREFIX"/cluster/doc/cluster3.pdf &");
-+        {   system("xpdf "PREFIX"/share/doc/cluster-1.36/cluster3.pdf &");
- 	    break;
- 	}
-         case CMD_HELP_DOWNLOAD:
--        {   system("netscape http://bonsai.ims.u-tokyo.ac.jp/~mdehoon/software/cluster/manual/index.html &");
-+        {   system("xdg-open http://bonsai.ims.u-tokyo.ac.jp/~mdehoon/software/cluster/manual/index.html &");
- 	    break;
- 	}
-         case CMD_HELP_FILEFORMAT:
-@@ -1852,7 +1852,7 @@
- 	    XtManageChild(widget);
-             free(helptext);
- 	    n = 0;
--	    pixmap = XmGetPixmap(XtScreen(dialog),PREFIX"/cluster/format.xpm",0,0);
-+	    pixmap = XmGetPixmap(XtScreen(dialog),PREFIX"/share/doc/cluster-1.36/format.xpm",0,0);
- 	    XtSetArg(args[n], XmNx, 10); n++;
- 	    XtSetArg(args[n], XmNy, 410); n++;
- 	    XtSetArg(args[n],XmNlabelType, XmPIXMAP); n++;
diff --git a/sci-biology/cluster/metadata.xml b/sci-biology/cluster/metadata.xml
index dbca977f9..ef3a0ba7c 100644
--- a/sci-biology/cluster/metadata.xml
+++ b/sci-biology/cluster/metadata.xml
@@ -9,8 +9,4 @@
 		<email>sci-biology@gentoo.org</email>
 		<name>Gentoo Biology Project</name>
 	</maintainer>
-	<longdescription lang="en">
-Cluster provides an interface to access methods of gene expression data
-analysis.
-</longdescription>
 </pkgmetadata>
diff --git a/sci-biology/clview/Manifest b/sci-biology/clview/Manifest
deleted file mode 100644
index 271e4eb76..000000000
--- a/sci-biology/clview/Manifest
+++ /dev/null
@@ -1,2 +0,0 @@
-DIST clview_linux_i386.tar.gz 1050318 BLAKE2B c5c52662df29a0f70a5355c0f2f563e8fef0ec473a707aed0c51d79bd1f1d7e9555139a21bb0c83c509fbac549d8c532d2af8d9ecb9af77b329be581f255493f SHA512 2fbd5ed5ef7bb96a715537a1b1d8f0957e5733d2603aacc5a0dba5a5002a27483ca57dd53780204a98d5ce05ac1090e3d04a3b2784cec021f0afc545e98b35b1
-DIST clview_src.tar.gz 62178 BLAKE2B b116a03c6ddba0caf77168fdd9e39bb86f4b1eccc0535dcd9f81a1e7c2a9b81c1219a4786ae37944abeb4913633acd9cf6b94824adba9851359a955440d9f21f SHA512 24c115b76041981d6dba731180485108d92cccc4719fe6982a135d73c3d18deed2e89ebb6d7daeb8d79941084ec912be2c3333369ec0bf403f96a156932909b9
diff --git a/sci-biology/clview/clview-0.1.ebuild b/sci-biology/clview/clview-0.1.ebuild
deleted file mode 100644
index 8b5d9b34d..000000000
--- a/sci-biology/clview/clview-0.1.ebuild
+++ /dev/null
@@ -1,108 +0,0 @@
-# Copyright 1999-2015 Gentoo Foundation
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=5
-
-DESCRIPTION="clview is an assembly .ace file viewer from TIGR Gene Indices project tools"
-HOMEPAGE="http://sourceforge.net/projects/clview"
-SRC_URI="
-	http://sourceforge.net/projects/clview/files/source%20code/clview_src.tar.gz
-	ftp://occams.dfci.harvard.edu/pub/bio/tgi/software/clview/clview_src.tar.gz
-	ftp://occams.dfci.harvard.edu/pub/bio/tgi/software/clview/clview_linux_i386.tar.gz"
-
-# the ftp://occams.dfci.harvard.edu/pub/bio/tgi/software/tgicl/tgi_cpp_library.tar.gz
-# contain maybe an older but definitely larger set of .cpp files compared to clview/gcl/
-# contents. clview compiles against both versions with same warning messages from g++.
-#
-# mokrejs@vrapenec$ ls -la /var/tmp/portage/sci-biology/clview-0.1/work/gclib/
-# total 188
-# drwxr-xr-x 2 mmokrejs mmokrejs  4096 Dec  2 22:23 .
-# drwx------ 5 mmokrejs portage   4096 Dec  2 22:23 ..
-# -rw-r--r-- 1 mmokrejs mmokrejs 11632 Sep 17  2008 AceParser.cpp
-# -rw-r--r-- 1 mmokrejs mmokrejs   906 Sep 14  2008 AceParser.h
-# -rw-r--r-- 1 mmokrejs mmokrejs 32276 Dec  2 22:23 AceParser.o
-# -rw-r--r-- 1 mmokrejs mmokrejs 11012 Jan 22  2009 GBase.cpp
-# -rw-r--r-- 1 mmokrejs mmokrejs  9200 Dec 16  2008 GBase.h
-# -rw-r--r-- 1 mmokrejs mmokrejs  8844 Dec  2 22:23 GBase.o
-# -rw-r--r-- 1 mmokrejs mmokrejs 16813 Jul 29  2008 GHash.hh
-# -rw-r--r-- 1 mmokrejs mmokrejs 16516 Sep 10  2008 GList.hh
-# -rw-r--r-- 1 mmokrejs mmokrejs 11221 Jan 22  2009 LayoutParser.cpp
-# -rw-r--r-- 1 mmokrejs mmokrejs  6246 Sep 14  2008 LayoutParser.h
-# -rw-r--r-- 1 mmokrejs mmokrejs 32956 Dec  2 22:23 LayoutParser.o
-# mokrejs@vrapenec$ ls -la /var/tmp/portage/sci-biology/clview-0.1/work/tgi_cl/gcl/
-# total 268
-# drwxr-xr-x 2 mmokrejs mmokrejs  4096 Nov 18  2008 .
-# drwxr-xr-x 3 mmokrejs mmokrejs  4096 Oct 18  2006 ..
-# -rw-r--r-- 1 mmokrejs mmokrejs  9515 Nov  7  2005 AceParser.cpp
-# -rw-r--r-- 1 mmokrejs mmokrejs   886 Nov  7  2005 AceParser.h
-# -rw-r--r-- 1 mmokrejs mmokrejs 10768 Nov  7  2005 BitHash.hh
-# -rw-r--r-- 1 mmokrejs mmokrejs  7250 Nov  7  2005 GArgs.cpp
-# -rw-r--r-- 1 mmokrejs mmokrejs  2507 Nov  7  2005 GArgs.h
-# -rw-r--r-- 1 mmokrejs mmokrejs 10156 Nov 18  2008 GBase.cpp
-# -rw-r--r-- 1 mmokrejs mmokrejs  8142 Nov 18  2008 GBase.h
-# -rw-r--r-- 1 mmokrejs mmokrejs 14742 Nov  7  2005 GCdbYank.cpp
-# -rw-r--r-- 1 mmokrejs mmokrejs  1831 Nov  7  2005 GCdbYank.h
-# -rw-r--r-- 1 mmokrejs mmokrejs 16723 Nov  7  2005 GFastaFile.h
-# -rw-r--r-- 1 mmokrejs mmokrejs 16245 Nov  7  2005 GHash.hh
-# -rw-r--r-- 1 mmokrejs mmokrejs 15561 Nov  7  2005 GList.hh
-# -rw-r--r-- 1 mmokrejs mmokrejs    28 Nov  7  2005 GReadBuf.cpp
-# -rw-r--r-- 1 mmokrejs mmokrejs  4022 Nov  7  2005 GReadBuf.h
-# -rw-r--r-- 1 mmokrejs mmokrejs    48 Nov  7  2005 GShMem.cpp
-# -rw-r--r-- 1 mmokrejs mmokrejs  4012 Nov  7  2005 GShMem.h
-# -rw-r--r-- 1 mmokrejs mmokrejs 32875 Nov  7  2005 GString.cpp
-# -rw-r--r-- 1 mmokrejs mmokrejs  8453 Nov  7  2005 GString.h
-# -rw-r--r-- 1 mmokrejs mmokrejs 11157 Nov  7  2005 LayoutParser.cpp
-# -rw-r--r-- 1 mmokrejs mmokrejs  6063 Nov  7  2005 LayoutParser.h
-# -rw-r--r-- 1 mmokrejs mmokrejs 20253 Nov  7  2005 gcdb.cpp
-# -rw-r--r-- 1 mmokrejs mmokrejs  6941 Nov  7  2005 gcdb.h
-# -rw-r--r-- 1 mmokrejs mmokrejs  8998 Nov  7  2005 gcompress.cpp
-# -rw-r--r-- 1 mmokrejs mmokrejs  3670 Nov  7  2005 gcompress.h
-#
-
-LICENSE="Artistic"
-SLOT="0"
-KEYWORDS="~amd64 ~x86"
-IUSE=""
-
-DEPEND="=x11-libs/fox-1.6*"
-RDEPEND="${DEPEND}"
-
-S=${WORKDIR}
-
-src_unpack() {
-	unpack clview_src.tar.gz
-}
-
-src_prepare() {
-	# FIXME: we have to run `/usr/bin/fox-config --cflags' to yield
-	#        `-I/usr/include/fox-1.6'
-	# similarly `fox-config --libs' to yield e.g.
-	# `-lFOX-1.6 -lXext -lX11 -lXft -lXrender -lfontconfig -lfreetype -lz -lX11
-	# -lXcursor -lXrandr -ldl -lpthread -lrt -ljpeg -lpng -ltiff -lz -lbz2 -lm
-	# -lcups -lnsl -lGLU -lGL'
-	FOXVERSION=`WANT_FOX="1.6" fox-config --version`
-	FOXPREFIX=`WANT_FOX="1.6" fox-config --prefix`
-	FOXINCPATH=`WANT_FOX="1.6" fox-config --cflags`
-	FOXLIBS=`WANT_FOX="1.6" fox-config --libs`
-	einfo "Discovered path to fox ${FOXVERSION} files: ${FOXINCPATH}\n${FOXLIBS}"
-
-	sed -i "s#FOXPREFIX = /mylocal/geo#FOXPREFIX = ${FOXPREFIX}#" clview/Makefile || die "Failed to hack FOXPREFIX in clview/Makefile"
-	sed -i "s#FOXINCDIR := .*#FOXINCDIR := ${FOXINCPATH}#" clview/Makefile || die "Failed to hack FOXINCDIR in clview/Makefile"
-	sed -i "s#-I\${FOXINCDIR}#\${FOXINCDIR}#" clview/Makefile || die "Failed to revert the extra -I we introduced on a previous line to clview/Makefile"
-	sed -i "s#FOXLIBDIR := .*#FOXLIBDIR := ${FOXPREFIX}/lib#" clview/Makefile || die "Failed to hack FOXLIBDIR in clview/Makefile"
-	sed -i "s#LOADLIBS :=.*#LOADLIBS := ${FOXLIBS}#" clview/Makefile || die "Failed to hack LOADLIBS in clview/Makefile"
-	sed -i "s#-I-#-I #" clview/Makefile || die
-
-	# see tgi_cl/gcl/
-	sed -i "s#TGICLASSDIR := /tucan/geo/src/tgi_cl#TGICLASSDIR := ../gcl#" clview/Makefile || die
-}
-
-src_compile(){
-	cd "${S}"/clview || die
-	default
-}
-
-src_install() {
-	# install at least the binaries for clview when we cannot compile it
-	dobin clview/clview
-}
diff --git a/sci-biology/clview/metadata.xml b/sci-biology/clview/metadata.xml
deleted file mode 100644
index 7adf609cd..000000000
--- a/sci-biology/clview/metadata.xml
+++ /dev/null
@@ -1,15 +0,0 @@
-<?xml version="1.0" encoding="UTF-8"?>
-<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
-<pkgmetadata>
-	<maintainer type="person">
-		<email>mmokrejs@fold.natur.cuni.cz</email>
-		<name>Martin Mokrejs</name>
-	</maintainer>
-	<maintainer type="project">
-		<email>sci-biology@gentoo.org</email>
-		<name>Gentoo Biology Project</name>
-	</maintainer>
-	<upstream>
-		<remote-id type="sourceforge">clview</remote-id>
-	</upstream>
-</pkgmetadata>
diff --git a/sci-biology/cnrun/Manifest b/sci-biology/cnrun/Manifest
index 3d6c4e19a..fac2865b0 100644
--- a/sci-biology/cnrun/Manifest
+++ b/sci-biology/cnrun/Manifest
@@ -1 +1 @@
-DIST cnrun-2.1.0.tar.xz 385956 SHA256 983d9d09575f92bce7da93947383510957dd0ef2c016fde7fa7d8a18aabffe50 SHA512 fe8f2d5d357f323b8195b8991756f21797ac7f84ea07f403775ff7779ab52441b8dcf0bfe52f20e511d8ce6b1b3fb1121a06526b327b8e41de20b3b7fe073c51 WHIRLPOOL 3a9c80f82786999b5aa7b7b63e8e218fa894e21808986683f441be1c62e1226da9587b599cbf22456e90da2115cf3c2d4953ce60e0e112f70f297c3d7fd07a26
+DIST cnrun-2.1.0.tar.xz 386076 BLAKE2B 49418ed6037c9b0d4bed28682b58bc577782c4e637b64e12c6790732637085d690f898ba2794cded21b6eca7f04ef9725f9b2ce5895138a2495f5ce3d7dbcf75 SHA512 0510cc0189fb266f3bafd493cf0aed2e582e8b4a7e8605d14e652f05f394e722e245eb06348dfc664d137853835f6aa4779e5d6124f1e58496db4a4daf0f57bc
diff --git a/sci-biology/cnrun/cnrun-2.1.0-r2.ebuild b/sci-biology/cnrun/cnrun-2.1.0-r2.ebuild
new file mode 100644
index 000000000..44eed9cd2
--- /dev/null
+++ b/sci-biology/cnrun/cnrun-2.1.0-r2.ebuild
@@ -0,0 +1,36 @@
+# Copyright 1999-2021 Gentoo Authors
+# Distributed under the terms of the GNU General Public License v2
+
+EAPI=7
+
+LUA_COMPAT=( lua5-{1..3} )
+
+inherit autotools lua-single
+
+DESCRIPTION="A NeuroML-enabled, precise but slow neuronal network simulator"
+HOMEPAGE="http://johnhommer.com/academic/code/cnrun"
+SRC_URI="http://johnhommer.com/code/cnrun/source/${P}.tar.xz"
+
+LICENSE="GPL-2+"
+SLOT="0"
+KEYWORDS="~amd64 ~x86"
+
+REQUIRED_USE="${LUA_REQUIRED_USE}"
+
+RDEPEND="${LUA_DEPS}
+	dev-libs/libxml2
+	sci-libs/gsl"
+
+DEPEND="${RDEPEND}"
+
+src_prepare() {
+	default
+	# put docs in correct dir
+	sed -i -e "s#docdir=\${datarootdir}/doc/lua-cnrun#docdir=\${datarootdir}/doc/${PF}#g" doc/Makefile.am || die
+	eautoreconf
+
+}
+
+src_configure() {
+	econf --bindir="${EPREFIX}"/bin
+}
diff --git a/sci-biology/cnrun/cnrun-2.1.0.ebuild b/sci-biology/cnrun/cnrun-2.1.0.ebuild
deleted file mode 100644
index d9cf43c76..000000000
--- a/sci-biology/cnrun/cnrun-2.1.0.ebuild
+++ /dev/null
@@ -1,22 +0,0 @@
-# Copyright 1999-2017 Gentoo Foundation
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=6
-
-DESCRIPTION="A NeuroML-enabled, precise but slow neuronal network simulator"
-HOMEPAGE="http://johnhommer.com/academic/code/cnrun"
-SRC_URI="http://alfinston.dlinkddns.com/johnhommer.com/code/cnrun/source/${P}.tar.xz"
-
-LICENSE="GPL-2+"
-SLOT="0"
-KEYWORDS="~amd64 ~x86"
-
-RDEPEND="dev-libs/libxml2
-	 dev-lang/lua:*
-	 sci-libs/gsl"
-
-DEPEND="${RDEPEND}"
-
-src_configure() {
-	econf --bindir="${EPREFIX}"/bin
-}
diff --git a/sci-biology/codonw/codonw-1.4.4-r2.ebuild b/sci-biology/codonw/codonw-1.4.4-r2.ebuild
index a6c680eb5..56c76a408 100644
--- a/sci-biology/codonw/codonw-1.4.4-r2.ebuild
+++ b/sci-biology/codonw/codonw-1.4.4-r2.ebuild
@@ -1,29 +1,28 @@
-# Copyright 1999-2015 Gentoo Foundation
+# Copyright 1999-2021 Gentoo Authors
 # Distributed under the terms of the GNU General Public License v2
 
-EAPI=5
+EAPI=7
 
-inherit toolchain-funcs versionator
-
-MY_PV=$(replace_all_version_separators '_')
+inherit toolchain-funcs
 
 DESCRIPTION="Multivariate statistical analysis of codon and amino acid usage"
-HOMEPAGE="http://codonw.sourceforge.net/"
-SRC_URI="mirror://sourceforge/${PN}/CodonWSourceCode_${MY_PV}.tar.gz
-		http://codonw.sourceforge.net/JohnPedenThesisPressOpt_water.pdf"
+HOMEPAGE="https://codonw.sourceforge.net/"
+SRC_URI="https://downloads.sourceforge.net/${PN}/CodonWSourceCode_${PV//./_}.tar.gz
+		https://codonw.sourceforge.net/JohnPedenThesisPressOpt_water.pdf"
 
 LICENSE="GPL-2"
 SLOT="0"
 IUSE=""
 KEYWORDS="~amd64 ~x86"
 
-S=${WORKDIR}/codonW
+S="${WORKDIR}/codonW"
 
 src_prepare() {
 	sed \
 		-e 's/$(CC) -c/& -DBSD/' \
 		-e 's/$(CFLAGS)  $(objects)/$(CFLAGS) $(LDFLAGS) $(objects)/' \
 		-i Makefile || die
+	default
 }
 
 src_compile() {
diff --git a/sci-biology/conform-gt/Manifest b/sci-biology/conform-gt/Manifest
index 11bb1ffa0..efb9b49e9 100644
--- a/sci-biology/conform-gt/Manifest
+++ b/sci-biology/conform-gt/Manifest
@@ -1 +1 @@
-DIST conform-gt.r1174.zip 128608 BLAKE2B 54af005bdb32f76d6d255965bfda186c0b1fca9907d55a54d280eeaf7a26988efa7d7877400d62bb42f91dd73bea3f3ec913e29f7e2fcbaf877cff6eaf82241b SHA512 8547f122c4298e19d5284969ca7410d7a1581028e8155b554acedff16fed5d07ddb4f6f8e986279b8fec5012d7d95d278abd9af4049fa9d0ea08e5dfc775fffc
+DIST conform-gt.24May16.cee.jar 118655 BLAKE2B 9349ae8084724be365eba0dc248ff878436ef27d0d221f9a8df462ce42916417f29f3127b63aa380053039d96452792a82ac55928a36997362e51013fdf66e2a SHA512 c2588099190a15979d409bb6614aab9ccdd72f70fdd6faa9346cb288a0a1e9a34941925a4d1460b713d34baaf5fd484388e74c46f44b5befc2358eec42e361fa
diff --git a/sci-biology/conform-gt/conform-gt-1174.ebuild b/sci-biology/conform-gt/conform-gt-1174.ebuild
index 507c94c37..edd699ae1 100644
--- a/sci-biology/conform-gt/conform-gt-1174.ebuild
+++ b/sci-biology/conform-gt/conform-gt-1174.ebuild
@@ -1,21 +1,23 @@
-# Copyright 1999-2015 Gentoo Foundation
+# Copyright 1999-2021 Gentoo Authors
 # Distributed under the terms of the GNU General Public License v2
 
-EAPI=5
+EAPI=7
+
+inherit java-pkg-2
 
 DESCRIPTION="Modify your Variant Call Format file to be consistent with reference VCF"
-HOMEPAGE="http://faculty.washington.edu/browning/conform-gt.html"
-SRC_URI="http://faculty.washington.edu/browning/conform-gt/conform-gt.r1174.zip"
+HOMEPAGE="https://faculty.washington.edu/browning/conform-gt.html"
+SRC_URI="https://faculty.washington.edu/browning/conform-gt/conform-gt.24May16.cee.jar"
 
-LICENSE="Apache-2.0"
+LICENSE="Apache-2.0 MIT"
 SLOT="0"
-KEYWORDS=""
-IUSE=""
+KEYWORDS="~amd64 ~x86"
 
-DEPEND=""
+DEPEND=">=virtual/jre-1.7:*"
 RDEPEND="${DEPEND}"
-# Some source files in the net.sf.samtools package are licensed under the MIT License.
 
-# http://bochet.gcc.biostat.washington.edu/beagle/1000_Genomes_phase1_vcf/
+S="${WORKDIR}"
 
-S="${WORKDIR}"/src
+src_install() {
+	java-pkg_newjar "${DISTDIR}/conform-gt.24May16.cee.jar" "${PN}.jar"
+}
diff --git a/sci-biology/conifer/Manifest b/sci-biology/conifer/Manifest
deleted file mode 100644
index 6b6b76c59..000000000
--- a/sci-biology/conifer/Manifest
+++ /dev/null
@@ -1 +0,0 @@
-DIST conifer_v0.2.2.tar.gz 23105 BLAKE2B 66c60b294e268bcb08cd9feafcbc805627e6f9a96c555383a6485bdac09497ff8b787b23c81f7a34c11499371a48be778486892014c620c0c611008d2e53856b SHA512 deb2f1b3bbcbbd2911f6c8e2cae0ee6175782d0d3370fbca9b3b99b0f2e71fc92ddc9bf6e19bc83916e5a73800063ce05e20d488d12de6014148247e5c359838
diff --git a/sci-biology/conifer/conifer-0.2.2.ebuild b/sci-biology/conifer/conifer-0.2.2.ebuild
deleted file mode 100644
index ebfacd387..000000000
--- a/sci-biology/conifer/conifer-0.2.2.ebuild
+++ /dev/null
@@ -1,24 +0,0 @@
-# Copyright 1999-2014 Gentoo Foundation
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=5
-
-PYTHON_COMPAT=( python{2_6,2_7} )
-
-DESCRIPTION="Copy Number Inference/Variants (CNV) from exome reads"
-HOMEPAGE="http://conifer.sf.net"
-SRC_URI="http://downloads.sourceforge.net/project/conifer/CoNIFER%200.2.2/conifer_v0.2.2.tar.gz"
-
-LICENSE="GPL-3+"
-SLOT="0"
-KEYWORDS="~amd64"
-IUSE=""
-
-DEPEND=""
-RDEPEND="${DEPEND}"
-
-S="${WORKDIR}"/"${PN}"_v"${PV}"
-
-src_install(){
-	dobin *.py
-}
diff --git a/sci-biology/conifer/metadata.xml b/sci-biology/conifer/metadata.xml
deleted file mode 100644
index 0f267b755..000000000
--- a/sci-biology/conifer/metadata.xml
+++ /dev/null
@@ -1,15 +0,0 @@
-<?xml version="1.0" encoding="UTF-8"?>
-<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
-<pkgmetadata>
-	<maintainer type="person">
-		<email>mmokrejs@fold.natur.cuni.cz</email>
-		<name>Martin Mokrejs</name>
-	</maintainer>
-	<maintainer type="project">
-		<email>sci-biology@gentoo.org</email>
-		<name>Gentoo Biology Project</name>
-	</maintainer>
-	<upstream>
-		<remote-id type="sourceforge">downloads</remote-id>
-	</upstream>
-</pkgmetadata>
diff --git a/sci-biology/conrad/Manifest b/sci-biology/conrad/Manifest
deleted file mode 100644
index dbda934f8..000000000
--- a/sci-biology/conrad/Manifest
+++ /dev/null
@@ -1 +0,0 @@
-DIST conradSrcV1.zip 13315561 SHA256 fa978d5694d588f1047160f4cab2f8c8cdb613cda8c39a26f482e18e7e7dd742 SHA512 9a6cec2ecb601297e1055e2501c518156f6a4f8a3e30b77e8d2b83d347641f7f590595acdd3aa773296296b74826a3ad382bc538f90bcb439c5b135f83fb6b25 WHIRLPOOL 44712ed80c2e44628543373fe8791692ed8d8492983e3d9c1d70e59a77595a7b7cad2de93ec5a9163a621531739a4eeb9713e19be500d90c4dd631b5aa754461
diff --git a/sci-biology/conrad/conrad-1.ebuild b/sci-biology/conrad/conrad-1.ebuild
deleted file mode 100644
index 6de809361..000000000
--- a/sci-biology/conrad/conrad-1.ebuild
+++ /dev/null
@@ -1,55 +0,0 @@
-# Copyright 1999-2016 Gentoo Foundation
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=5
-
-inherit java-pkg-2 java-ant-2
-
-DESCRIPTION="Ab initio- and ad hoc evidence-based (RNA-Seq, BLAST) gene/ORF predictor"
-HOMEPAGE="http://www.broadinstitute.org/annotation/conrad
-	http://sourceforge.net/projects/conradcrf"
-SRC_URI="http://www.broadinstitute.org/annotation/conrad/conradSrcV1.zip"
-
-LICENSE="LGPL-2.1"
-SLOT="0"
-KEYWORDS=""
-IUSE=""
-
-# upstream binaries do not work with oracle-java-8
-RDEPEND="
-	>=virtual/jre-1.5:*
-	<=virtual/jre-1.7:*
-	dev-java/commons-logging
-	>=dev-java/commons-lang-2.1:*
-	dev-java/colt
-	dev-java/dom4j
-	"
-	# spring # see bug #97004
-	# dev-java/LBFGS # LBFGS is a numericla library we use internally for the solver
-DEPEND="${RDEPEND}
-	>=virtual/jdk-1.5:*
-	<=virtual/jdk-1.7:*
-	dev-java/ant-core
-	>=dev-java/jfreechart-1.0.3
-	>=dev-java/jcommon-1.0.6
-	>=dev-java/commons-math-1.1
-	"
-S="${WORKDIR}"
-
-src_prepare(){
-	sed -e s'#lib/conrad.jar#/usr/share/conrad/lib/conrad.jar#' -i bin/conrad.sh || die
-}
-
-src_compile(){
-	cd dev || die
-	ant compile || die
-}
-
-src_install() {
-	dobin bin/conrad.sh
-	java-pkg_newjar lib/conrad.jar
-	java-pkg_dojar lib/conrad.jar
-	java-pkg_dolauncher conrad --jar conrad.jar
-	insinto /usr/share/conrad
-	dodoc -r docs models samples trainingFiles
-}
diff --git a/sci-biology/conrad/metadata.xml b/sci-biology/conrad/metadata.xml
deleted file mode 100644
index 814dcabcc..000000000
--- a/sci-biology/conrad/metadata.xml
+++ /dev/null
@@ -1,15 +0,0 @@
-<?xml version="1.0" encoding="UTF-8"?>
-<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
-<pkgmetadata>
-	<maintainer type="person">
-		<email>mmokrejs@fold.natur.cuni.cz</email>
-		<name>Martin Mokrejs</name>
-	</maintainer>
-	<maintainer type="project">
-		<email>sci-biology@gentoo.org</email>
-		<name>Gentoo Biology Project</name>
-	</maintainer>
-	<upstream>
-		<remote-id type="sourceforge">conradcrf</remote-id>
-	</upstream>
-</pkgmetadata>
diff --git a/sci-biology/consed2gap/Manifest b/sci-biology/consed2gap/Manifest
deleted file mode 100644
index f7e07d291..000000000
--- a/sci-biology/consed2gap/Manifest
+++ /dev/null
@@ -1 +0,0 @@
-DIST consed2gap-20050520.tgz 2963585 BLAKE2B a5320f06e1879b8f59f8681b258081814cdf27508daa906f3790a5c24f6f2b145fd034cedcb414108333d1070ab2bd4be129528902338d0691be8fee59b2dd35 SHA512 be994e85c8e06fc1ea21187a206985c4deab0e3f34723df663959f553a007c836368f700e60c81a8f1bfc715d940025ec0347a6a6fefaffdd02a390bfba7541f
diff --git a/sci-biology/consed2gap/consed2gap-20050520.ebuild b/sci-biology/consed2gap/consed2gap-20050520.ebuild
deleted file mode 100644
index e8bf492df..000000000
--- a/sci-biology/consed2gap/consed2gap-20050520.ebuild
+++ /dev/null
@@ -1,37 +0,0 @@
-# Copyright 1999-2014 Gentoo Foundation
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=5
-
-inherit perl-module perl-app
-
-DESCRIPTION="Convert whole CONSED dataset to a GAP4 project"
-HOMEPAGE="http://genome.imb-jena.de/software/consed2gap/"
-SRC_URI="http://genome.imb-jena.de/software/consed2gap/consed2gap.tgz -> ${P}.tgz"
-
-LICENSE="FLI-Jena"
-SLOT="0"
-KEYWORDS="~amd64 ~x86"
-IUSE=""
-
-DEPEND=""
-RDEPEND="${DEPEND}
-	dev-lang/perl:=
-	sci-libs/io_lib
-	sci-biology/caftools
-	sci-biology/align_to_scf"
-
-S="${WORKDIR}/${PN}"
-
-src_prepare(){
-	sed -i 's#/usr/local/bin/perl#/usr/bin/env perl#' bin/phrap2caf || die
-	sed -i 's#/usr/local/bin/perl#/usr/bin/env perl#' bin/badgerGetOpt.pl || die
-}
-
-src_install(){
-	dobin bin/consed2gap bin/phrap2caf bin/badgerGetOpt.pl
-	dodir /usr/share/"${PN}"
-	mv example "${ED}"/usr/share/"${PN}"/ || die
-
-	cd bin && perl-module_src_install
-}
diff --git a/sci-biology/consed2gap/metadata.xml b/sci-biology/consed2gap/metadata.xml
deleted file mode 100644
index 138cb7705..000000000
--- a/sci-biology/consed2gap/metadata.xml
+++ /dev/null
@@ -1,12 +0,0 @@
-<?xml version="1.0" encoding="UTF-8"?>
-<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
-<pkgmetadata>
-	<maintainer type="person">
-		<email>mmokrejs@fold.natur.cuni.cz</email>
-		<name>Martin Mokrejs</name>
-	</maintainer>
-	<maintainer type="project">
-		<email>sci-biology@gentoo.org</email>
-		<name>Gentoo Biology Project</name>
-	</maintainer>
-</pkgmetadata>
diff --git a/sci-biology/coral/Manifest b/sci-biology/coral/Manifest
index 668cea338..d56dff68a 100644
--- a/sci-biology/coral/Manifest
+++ b/sci-biology/coral/Manifest
@@ -1 +1 @@
-DIST coral-1.4.tar.gz 34953 BLAKE2B 30e7417de2be7db84b712cf7863a08833446a8aab5697578861490582d9860442c08a667e9a985a314a6d058722098374aa40a828bffe4b02bd7890e0daf534c SHA512 eefc34a233b73a9eb1bfc0ba3836c7e736787c9774ca9716c3230379d31d37f3e2b3a0dcbc9bf396583461519d45e4bf0ac12db6d386b22b8d1f365e84305a0d
+DIST coral-1.4.1.tar.gz 35510 BLAKE2B 6396c96cca1cc5ba7fc615a3b392c85500b1b5a6ec4b43e1b1f86b759481610b940a99526142a52cef311841c7f60ac407c986479a455b12263958eeaa7ba2e5 SHA512 5ca9fecf39014422fafce90a38dcd7988edf0b4c9839f9ec7e5b1ed940030ad7bcfb7c492aa735adb1834fd315e64dbb41bb28e66126b79b0721445a42c8e51a
diff --git a/sci-biology/coral/coral-1.4.1.ebuild b/sci-biology/coral/coral-1.4.1.ebuild
new file mode 100644
index 000000000..0481e5e80
--- /dev/null
+++ b/sci-biology/coral/coral-1.4.1.ebuild
@@ -0,0 +1,27 @@
+# Copyright 1999-2021 Gentoo Authors
+# Distributed under the terms of the GNU General Public License v2
+
+EAPI=7
+
+inherit toolchain-funcs
+
+DESCRIPTION="Error corrector for Illumina and Roche/454 reads using multiple alignment info"
+HOMEPAGE="https://www.cs.helsinki.fi/u/lmsalmel/coral"
+SRC_URI="https://www.cs.helsinki.fi/u/lmsalmel/coral/${P}.tar.gz"
+
+LICENSE="GPL-3"
+SLOT="0"
+KEYWORDS="~amd64"
+
+DEPEND=""
+RDEPEND="${DEPEND}"
+
+src_prepare(){
+	default
+	sed -e "s#-O3 -Wall -g#${CXXFLAGS}#; s#g++#$(tc-getCXX)#" -i Makefile || die
+}
+
+src_install(){
+	dobin coral
+	dodoc README
+}
diff --git a/sci-biology/coral/coral-1.4.ebuild b/sci-biology/coral/coral-1.4.ebuild
deleted file mode 100644
index bbddff358..000000000
--- a/sci-biology/coral/coral-1.4.ebuild
+++ /dev/null
@@ -1,27 +0,0 @@
-# Copyright 1999-2015 Gentoo Foundation
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=5
-
-inherit eutils
-
-DESCRIPTION="Error corrector for Illumina and Roche/454 reads using multiple alignment info"
-HOMEPAGE="http://www.cs.helsinki.fi/u/lmsalmel/coral"
-SRC_URI="http://www.cs.helsinki.fi/u/lmsalmel/coral/coral-1.4.tar.gz"
-
-LICENSE="GPL-3"
-SLOT="0"
-KEYWORDS="~amd64"
-IUSE=""
-
-DEPEND=""
-RDEPEND="${DEPEND}"
-
-src_prepare(){
-	sed -e "s#-O3 -Wall -g#${CXXFLAGS}#; s#g++#$(tc-getCXX)#" -i Makefile || die
-}
-
-src_install(){
-	dobin coral
-	dodoc README
-}
diff --git a/sci-biology/cortex_var/Manifest b/sci-biology/cortex_var/Manifest
deleted file mode 100644
index 969e60d0a..000000000
--- a/sci-biology/cortex_var/Manifest
+++ /dev/null
@@ -1,2 +0,0 @@
-DIST CORTEX_release_v1.0.5.21.tgz 26902149 BLAKE2B 397d309fa941fd76ca51f58f20e036dd51548455ae2831738f03fed2293bb3f8dac7443282bba900b3f264a14e6bdacc23ff5460e713c05d4c5e5f11de021080 SHA512 92200cc1e886e519a8e54c9054a2901a03001091654a0534c7a92a5fa7a0ac43aba782b59731d588525902adf749cabca64cdb9cdb25c215be9afb01690215e3
-DIST cortex_var_user_manual.pdf 265899 BLAKE2B 83797183e88f0c17fe3a114c2912263bb84b4c2dca1a0a2a563c82fe377111d24a8ad726581f62b3e44a6cc714bcf58ffd8c18f9f5bd0eb9df6130bd49b296ee SHA512 e4ff442f9280e9eee384c2b82c75493bdb90589b354333fc8b2bee8cf9c9baa432ec09dce5325b2e12c1e1930971616065713858565d56f9a361c573ac0c4f65
diff --git a/sci-biology/cortex_var/cortex_var-1.0.5.21.ebuild b/sci-biology/cortex_var/cortex_var-1.0.5.21.ebuild
deleted file mode 100644
index b700de820..000000000
--- a/sci-biology/cortex_var/cortex_var-1.0.5.21.ebuild
+++ /dev/null
@@ -1,51 +0,0 @@
-# Copyright 1999-2017 Gentoo Foundation
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=6
-
-inherit perl-functions
-
-DESCRIPTION="Genotype variant discovery without reference sequence"
-HOMEPAGE="http://cortexassembler.sourceforge.net/index_cortex_var.html"
-SRC_URI="
-	http://sourceforge.net/projects/cortexassembler/files/cortex_var/latest/CORTEX_release_v1.0.5.21.tgz
-	http://cortexassembler.sourceforge.net/cortex_var_user_manual.pdf"
-
-LICENSE="GPL-3"
-SLOT="0"
-KEYWORDS=""
-IUSE=""
-
-# http://www.well.ox.ac.uk/project-stampy
-
-DEPEND="
-	sci-biology/vcftools
-	sci-libs/gsl
-	sci-libs/htslib:0=
-	dev-lang/perl"
-RDEPEND="${DEPEND}"
-
-S="${WORKDIR}"/CORTEX_release_v1.0.5.21
-
-src_prepare(){
-	default
-	sed -e "s/ -O3 / ${CFLAGS} /" Makefile || die
-	sed -e "s#libs/gsl-1.15#${EPREFIX}/usr/include/gsl#" Makefile || die
-}
-
-src_compile(){
-	rm -rf libs/htslib libs/gsl-1.15 || die
-	make NUM_COLS=1 MAXK=31 cortex_var || die
-}
-
-src_install(){
-	bash install.sh || die
-	perl_set_version
-	insinto ${VENDOR_LIB}
-	doins scripts/analyse_variants/bioinf-perl/lib/* scripts/calling/*
-	echo \
-		"PATH=${EPREFIX}/usr/share/${PN}/scripts/analyse_variants/needleman_wunsch" \
-		> "${T}/99${PN}" || die
-	doenvd "${T}/99${PN}"
-	dodoc "${DISTDIR}"/cortex_var_user_manual.pdf
-}
diff --git a/sci-biology/cortex_var/metadata.xml b/sci-biology/cortex_var/metadata.xml
deleted file mode 100644
index a2867d6fd..000000000
--- a/sci-biology/cortex_var/metadata.xml
+++ /dev/null
@@ -1,15 +0,0 @@
-<?xml version="1.0" encoding="UTF-8"?>
-<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
-<pkgmetadata>
-	<maintainer type="person">
-		<email>mmokrejs@fold.natur.cuni.cz</email>
-		<name>Martin Mokrejs</name>
-	</maintainer>
-	<maintainer type="project">
-		<email>sci-biology@gentoo.org</email>
-		<name>Gentoo Biology Project</name>
-	</maintainer>
-	<upstream>
-		<remote-id type="sourceforge">cortexassembler</remote-id>
-	</upstream>
-</pkgmetadata>
diff --git a/sci-biology/cramtools/Manifest b/sci-biology/cramtools/Manifest
deleted file mode 100644
index 7d81698d2..000000000
--- a/sci-biology/cramtools/Manifest
+++ /dev/null
@@ -1 +0,0 @@
-DIST cramtools-3.0.tar.gz 7394093 BLAKE2B dc0b21f94b1c3f256a55f4aa324106b6bfb3cd9548ce0aaf589c4da9f95fcbb0007a71c44ed6a915340d86c80555f91ebbf5864e38603f06a73aa132af23772e SHA512 077806ece2e0449f2245e4aefd5ebf5ae91e01f177575a3fed9f7458f8d0ba0a554c368ec56ba305f58ed7f3502a7ac1da1685fb38a19e3230564f4329ecb080
diff --git a/sci-biology/cramtools/cramtools-3.0.ebuild b/sci-biology/cramtools/cramtools-3.0.ebuild
deleted file mode 100644
index f0b8d7ac5..000000000
--- a/sci-biology/cramtools/cramtools-3.0.ebuild
+++ /dev/null
@@ -1,31 +0,0 @@
-# Copyright 1999-2016 Gentoo Foundation
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=5
-
-inherit java-pkg-2 java-ant-2
-
-DESCRIPTION="Java tools and APIs for efficient compression of sequence read data"
-HOMEPAGE="http://www.ebi.ac.uk/ena/software/cram-toolkit
-	https://github.com/enasequence/cramtools"
-SRC_URI="https://github.com/enasequence/cramtools/archive/v3.0.tar.gz -> ${P}.tar.gz"
-
-LICENSE="Apache-2.0"
-SLOT="0"
-KEYWORDS=""
-IUSE=""
-
-DEPEND="
-	>=virtual/jdk-1.7:*
-	dev-java/ant-core
-	dev-java/htsjdk"
-RDEPEND="
-	${DEPEND}
-	>=virtual/jre-1.7:*"
-
-# TODO: zap bundled htsjdk to ensure it uses dev-java/htsjdk?
-# https://github.com/enasequence/cramtools/issues/58
-# https://github.com/enasequence/cramtools/issues/59
-src_compile(){
-	ant -f build/build.xml runnable || die
-}
diff --git a/sci-biology/cramtools/metadata.xml b/sci-biology/cramtools/metadata.xml
deleted file mode 100644
index 5a55ad312..000000000
--- a/sci-biology/cramtools/metadata.xml
+++ /dev/null
@@ -1,15 +0,0 @@
-<?xml version="1.0" encoding="UTF-8"?>
-<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
-<pkgmetadata>
-	<maintainer type="person">
-		<email>mmokrejs@fold.natur.cuni.cz</email>
-		<name>Martin Mokrejs</name>
-	</maintainer>
-	<maintainer type="project">
-		<email>sci-biology@gentoo.org</email>
-		<name>Gentoo Biology Project</name>
-	</maintainer>
-	<upstream>
-		<remote-id type="github">enasequence/cramtools</remote-id>
-	</upstream>
-</pkgmetadata>
diff --git a/sci-biology/cross_genome/cross_genome-20140822.ebuild b/sci-biology/cross_genome/cross_genome-20140822.ebuild
index 9ea79067c..5b8ceea9e 100644
--- a/sci-biology/cross_genome/cross_genome-20140822.ebuild
+++ b/sci-biology/cross_genome/cross_genome-20140822.ebuild
@@ -1,16 +1,15 @@
-# Copyright 1999-2016 Gentoo Foundation
+# Copyright 1999-2021 Gentoo Authors
 # Distributed under the terms of the GNU General Public License v2
 
-EAPI=6
+EAPI=7
 
 DESCRIPTION="Genome scaffolding using cross-species synteny"
-HOMEPAGE="http://www.sanger.ac.uk/science/tools/crossgenome"
+HOMEPAGE="https://www.sanger.ac.uk/tool/crossgenome/"
 SRC_URI="https://sourceforge.net/projects/phusion2/files/cross_genome/cross_genome.tar.gz -> ${P}.tar.gz"
 
 LICENSE="GPL-3+"
 SLOT="0"
 KEYWORDS="~amd64"
-IUSE=""
 
 S="${WORKDIR}"
 
diff --git a/sci-biology/cutadapt/Manifest b/sci-biology/cutadapt/Manifest
deleted file mode 100644
index ed9f5f70f..000000000
--- a/sci-biology/cutadapt/Manifest
+++ /dev/null
@@ -1 +0,0 @@
-DIST cutadapt-1.9.1.tar.gz 595412 BLAKE2B 379f8c35f1d91b232d76b359187f6f708a0bb6c026a85a678ab49ce13aba2a536b81a181385cfe6e61a5c6b5bac4f5fa73ff5439fff2493966761eb708f0d207 SHA512 9611f3f12e2c99bf03cca2e921e030cafd91782b40e1204e5dc44e4f8b910e2248ddec7e8d394b40460348e8f195ed4fcebc48c018320ce2c3daa1d1722f39c5
diff --git a/sci-biology/cutadapt/cutadapt-1.9.1.ebuild b/sci-biology/cutadapt/cutadapt-1.9.1.ebuild
deleted file mode 100644
index 7570d57b0..000000000
--- a/sci-biology/cutadapt/cutadapt-1.9.1.ebuild
+++ /dev/null
@@ -1,19 +0,0 @@
-# Copyright 1999-2017 Gentoo Foundation
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=6
-
-PYTHON_COMPAT=( python2_7 )
-
-inherit distutils-r1
-
-DESCRIPTION="Remove adapter sequences from high-throughput sequencing data"
-HOMEPAGE="https://github.com/marcelm/cutadapt"
-SRC_URI="mirror://pypi/${PN:0:1}/${PN}/${P}.tar.gz"
-
-LICENSE="MIT"
-SLOT="0"
-KEYWORDS="~amd64 ~x86"
-IUSE=""
-
-DEPEND=">=dev-python/xopen-0.1.1[${PYTHON_USEDEP}]"
diff --git a/sci-biology/cutadapt/cutadapt-9999.ebuild b/sci-biology/cutadapt/cutadapt-9999.ebuild
deleted file mode 100644
index 4cbcb5a45..000000000
--- a/sci-biology/cutadapt/cutadapt-9999.ebuild
+++ /dev/null
@@ -1,19 +0,0 @@
-# Copyright 1999-2017 Gentoo Foundation
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=6
-
-PYTHON_COMPAT=( python2_7 )
-
-inherit distutils-r1 git-r3
-
-DESCRIPTION="Remove adapter sequences from high-throughput sequencing data"
-HOMEPAGE="https://github.com/marcelm/cutadapt"
-EGIT_REPO_URI="https://github.com/marcelm/cutadapt"
-
-LICENSE="MIT"
-SLOT="0"
-KEYWORDS=""
-IUSE=""
-
-DEPEND=">=dev-python/xopen-0.1.1[${PYTHON_USEDEP}]"
diff --git a/sci-biology/cutadapt/metadata.xml b/sci-biology/cutadapt/metadata.xml
deleted file mode 100644
index 6099a3fab..000000000
--- a/sci-biology/cutadapt/metadata.xml
+++ /dev/null
@@ -1,16 +0,0 @@
-<?xml version="1.0" encoding="UTF-8"?>
-<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
-<pkgmetadata>
-	<maintainer type="person">
-		<email>mmokrejs@fold.natur.cuni.cz</email>
-		<name>Martin Mokrejs</name>
-	</maintainer>
-	<maintainer type="project">
-		<email>sci-biology@gentoo.org</email>
-		<name>Gentoo Biology Project</name>
-	</maintainer>
-	<upstream>
-		<remote-id type="github">marcelm/cutadapt</remote-id>
-		<remote-id type="pypi">cutadapt</remote-id>
-	</upstream>
-</pkgmetadata>
diff --git a/sci-biology/dargcc_bidsdata/Manifest b/sci-biology/dargcc_bidsdata/Manifest
new file mode 100644
index 000000000..b02e57ecb
--- /dev/null
+++ b/sci-biology/dargcc_bidsdata/Manifest
@@ -0,0 +1 @@
+DIST dargcc_bidsdata-1.0.tar.xz 8664540260 BLAKE2B 6384bbba1eb68e3c43236ebe2b82bd372115219c7578390dd44f525a47b3ab31b128a2cab61f63785e9f0d60792f3a86b33304568e7ca8fb4f8c0200fd083e76 SHA512 1f3c84e2ef5deea7a86975e91ffd0f17f290c1e47cc1ae4f4fb5c62a8c7fa423192f7c917eae22f1e03d43c69bf6ca8072d9b213dec6c4340fe4f0d86b02158c
diff --git a/sci-biology/dargcc_bidsdata/dargcc_bidsdata-1.0.ebuild b/sci-biology/dargcc_bidsdata/dargcc_bidsdata-1.0.ebuild
new file mode 100644
index 000000000..0312eda29
--- /dev/null
+++ b/sci-biology/dargcc_bidsdata/dargcc_bidsdata-1.0.ebuild
@@ -0,0 +1,23 @@
+# Copyright 1999-2022 Gentoo Authors
+# Distributed under the terms of the GNU General Public License v2
+
+EAPI=7
+
+DESCRIPTION="BIDS data selection of wildtype animals from DARGCC article"
+HOMEPAGE="https://academic.oup.com/cercor/article/28/7/2495/4975475"
+SRC_URI="
+	https://zenodo.org/record/3885733/files/${P}.tar.xz
+	"
+
+LICENSE="GPL-3"
+SLOT="0"
+KEYWORDS="~amd64 ~x86 ~amd64-linux ~x86-linux"
+IUSE=""
+
+RDEPEND=""
+DEPEND=""
+
+src_install() {
+	insinto "/usr/share/${PN}"
+	doins -r *
+}
diff --git a/sci-biology/dargcc_bidsdata/metadata.xml b/sci-biology/dargcc_bidsdata/metadata.xml
new file mode 100644
index 000000000..174746f49
--- /dev/null
+++ b/sci-biology/dargcc_bidsdata/metadata.xml
@@ -0,0 +1,18 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
+<pkgmetadata>
+	<maintainer type="person">
+		<email>gentoo@chymera.eu</email>
+		<name>Horea Christian</name>
+	</maintainer>
+	<maintainer type="project">
+		<email>sci@gentoo.org</email>
+		<name>Gentoo Science Project</name>
+	</maintainer>
+	<longdescription lang="en">
+		BIDS data selection encompassing the wildtype mouse group form the
+		"Dysfunctional Autism Risk Genes Cause Circuit-Specific Connectivity
+		Deficits With Distinct Developmental Trajectories" publication, with
+		DOI: 10.1093/cercor/bhy046 .
+	</longdescription>
+</pkgmetadata>
diff --git a/sci-biology/dawg/Manifest b/sci-biology/dawg/Manifest
deleted file mode 100644
index 277fa1390..000000000
--- a/sci-biology/dawg/Manifest
+++ /dev/null
@@ -1 +0,0 @@
-DIST dawg-1.1.2-release.tar.gz 213666 BLAKE2B 3a2b9f0139a49b54285690fd718f4b3ffface6001ba5663f0ca53409741ee50ddedfbc420b852475ad6e99a9f596181b4171e22e74aac9ec6a54f9a889c1ff6f SHA512 e81ec3d3c2cac12ffc52f8af284c48a6741e8fe54fb9330da5aa760605c96ac286b36921032db068342d548a2f97d2d3bd5a4534d6b2431aa1571cf81aabb326
diff --git a/sci-biology/dawg/dawg-1.1.2.ebuild b/sci-biology/dawg/dawg-1.1.2.ebuild
deleted file mode 100644
index 920f3c1d8..000000000
--- a/sci-biology/dawg/dawg-1.1.2.ebuild
+++ /dev/null
@@ -1,21 +0,0 @@
-# Copyright 1999-2014 Gentoo Foundation
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=5
-
-inherit eutils
-
-DESCRIPTION="DNA Assembly With Gaps: Phylogenetic aligner for sequence evolution simulation"
-HOMEPAGE="http://scit.us/projects/dawg/"
-SRC_URI="http://scit.us/projects/files/dawg/Releases/${P}-release.tar.gz"
-
-LICENSE="GPL-2"
-SLOT="0"
-IUSE=""
-KEYWORDS="~amd64 ~x86"
-
-S="${WORKDIR}"/${P}-RELEASE
-
-src_prepare() {
-	epatch "${FILESDIR}"/${P}-gcc43.patch
-}
diff --git a/sci-biology/dawg/files/dawg-1.1.2-gcc43.patch b/sci-biology/dawg/files/dawg-1.1.2-gcc43.patch
deleted file mode 100644
index b9dda495d..000000000
--- a/sci-biology/dawg/files/dawg-1.1.2-gcc43.patch
+++ /dev/null
@@ -1,11 +0,0 @@
---- src/dawg.h.orig	2008-06-24 10:30:30.000000000 -0400
-+++ src/dawg.h	2008-06-24 10:30:41.000000000 -0400
-@@ -77,7 +77,7 @@
- 
- 
- #include <vector>
--#include <string>
-+#include <string.h>
- #include <fstream>
- #include <iostream>
- #include <algorithm>
diff --git a/sci-biology/dawg/metadata.xml b/sci-biology/dawg/metadata.xml
deleted file mode 100644
index 8417d1580..000000000
--- a/sci-biology/dawg/metadata.xml
+++ /dev/null
@@ -1,8 +0,0 @@
-<?xml version="1.0" encoding="UTF-8"?>
-<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
-<pkgmetadata>
-	<maintainer type="project">
-		<email>sci-biology@gentoo.org</email>
-		<name>Gentoo Biology Project</name>
-	</maintainer>
-</pkgmetadata>
diff --git a/sci-biology/dcm2niix/Manifest b/sci-biology/dcm2niix/Manifest
new file mode 100644
index 000000000..655b0c2b9
--- /dev/null
+++ b/sci-biology/dcm2niix/Manifest
@@ -0,0 +1,2 @@
+DIST dcm2niix-1.0.20201102.tar.gz 382906 BLAKE2B 066b8bb33408166a301fa128d2717b1bfe4a93908e0752368a5f559cda5ed542131c330d75d6eac78b743a4e0979bd3dd7390187e65f62b1b35912606f52fd7a SHA512 9cda7f82c1424cb9476113d7ddf7965d818d95350dfdbf71536748a117d0de2c070cebb2aed980208d6142c3eb9e3d2331210cffa900209fa4320195c92fd7f1
+DIST dcm2niix-1.0.20210317.tar.gz 389930 BLAKE2B fff5c5c15765f6400dce8eb40322b91bd33181ecf9fbc9c989f2b984d7dc9835bd3314df8eeffdd34ad867f79f3b730eaadd39c59fb8dd17d670bfdff350a226 SHA512 3a702784bb4de45218ae305eb0afb0e233341b0727bf13a13d263b6e6391d04e670e5cc314d66d456fccae1a3cf36a03d8919e3d393786625e9f5a13fd039e4a
diff --git a/sci-biology/dcm2niix/dcm2niix-1.0.20201102.ebuild b/sci-biology/dcm2niix/dcm2niix-1.0.20201102.ebuild
new file mode 100644
index 000000000..5ae682ea5
--- /dev/null
+++ b/sci-biology/dcm2niix/dcm2niix-1.0.20201102.ebuild
@@ -0,0 +1,41 @@
+# Copyright 1999-2021 Gentoo Authors
+# Distributed under the terms of the GNU General Public License v2
+
+EAPI=7
+
+inherit cmake optfeature
+
+DESCRIPTION="DICOM to NIfTI converter"
+HOMEPAGE="https://github.com/rordenlab/dcm2niix"
+SRC_URI="https://github.com/rordenlab/dcm2niix/archive/v${PV}.tar.gz -> ${P}.tar.gz"
+
+SLOT="0"
+LICENSE="BSD"
+KEYWORDS="~amd64 ~x86"
+IUSE="static system-jpeg +jpeg-ls jpeg2k"
+
+DEPEND="
+	system-jpeg? ( media-libs/libjpeg-turbo )
+	jpeg2k? ( media-libs/openjpeg )
+"
+RDEPEND="${DEPEND}"
+BDEPEND="virtual/pkgconfig"
+
+PATCHES=(
+	"${FILESDIR}"/${PN}-disable_find_git.patch
+)
+
+src_configure() {
+	local mycmakeargs=(
+		-DUSE_STATIC_RUNTIME=$(usex static)
+		-DUSE_TURBOJPEG=$(usex system-jpeg)
+		-DUSE_JPEGLS=$(usex jpeg-ls)
+		-DUSE_OPENJPEG=$(usex jpeg2k)
+	)
+
+	cmake_src_configure
+}
+
+pkg_postinst() {
+	optfeature "parallel gzip support" app-arch/pigz
+}
diff --git a/sci-biology/dcm2niix/dcm2niix-1.0.20210317.ebuild b/sci-biology/dcm2niix/dcm2niix-1.0.20210317.ebuild
new file mode 100644
index 000000000..5ae682ea5
--- /dev/null
+++ b/sci-biology/dcm2niix/dcm2niix-1.0.20210317.ebuild
@@ -0,0 +1,41 @@
+# Copyright 1999-2021 Gentoo Authors
+# Distributed under the terms of the GNU General Public License v2
+
+EAPI=7
+
+inherit cmake optfeature
+
+DESCRIPTION="DICOM to NIfTI converter"
+HOMEPAGE="https://github.com/rordenlab/dcm2niix"
+SRC_URI="https://github.com/rordenlab/dcm2niix/archive/v${PV}.tar.gz -> ${P}.tar.gz"
+
+SLOT="0"
+LICENSE="BSD"
+KEYWORDS="~amd64 ~x86"
+IUSE="static system-jpeg +jpeg-ls jpeg2k"
+
+DEPEND="
+	system-jpeg? ( media-libs/libjpeg-turbo )
+	jpeg2k? ( media-libs/openjpeg )
+"
+RDEPEND="${DEPEND}"
+BDEPEND="virtual/pkgconfig"
+
+PATCHES=(
+	"${FILESDIR}"/${PN}-disable_find_git.patch
+)
+
+src_configure() {
+	local mycmakeargs=(
+		-DUSE_STATIC_RUNTIME=$(usex static)
+		-DUSE_TURBOJPEG=$(usex system-jpeg)
+		-DUSE_JPEGLS=$(usex jpeg-ls)
+		-DUSE_OPENJPEG=$(usex jpeg2k)
+	)
+
+	cmake_src_configure
+}
+
+pkg_postinst() {
+	optfeature "parallel gzip support" app-arch/pigz
+}
diff --git a/sci-biology/dcm2niix/files/dcm2niix-disable_find_git.patch b/sci-biology/dcm2niix/files/dcm2niix-disable_find_git.patch
new file mode 100644
index 000000000..ba51997f2
--- /dev/null
+++ b/sci-biology/dcm2niix/files/dcm2niix-disable_find_git.patch
@@ -0,0 +1,19 @@
+disable finding git because it should not be used nor needed
+Written and tested by Lucas Mitrak.
+https://bugs.gentoo.org/755746
+
+--- a/SuperBuild/SuperBuild.cmake
++++ b/SuperBuild/SuperBuild.cmake
+@@ -1,8 +1,8 @@
+ # Check if git exists
+-find_package(Git)
+-if(NOT GIT_FOUND)
+-    message(FATAL_ERROR "Cannot find Git. Git is required for Superbuild")
+-endif()
++#find_package(Git)
++#if(NOT GIT_FOUND)
++#    message(FATAL_ERROR "Cannot find Git. Git is required for Superbuild")
++#endif()
+ 
+ # Use git protocol or not
+ option(USE_GIT_PROTOCOL "If behind a firewall turn this off to use http instead." ON)
diff --git a/sci-biology/dcm2niix/metadata.xml b/sci-biology/dcm2niix/metadata.xml
new file mode 100644
index 000000000..773e706a6
--- /dev/null
+++ b/sci-biology/dcm2niix/metadata.xml
@@ -0,0 +1,25 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
+<pkgmetadata>
+	<maintainer type="person">
+		<email>gentoo@chymera.eu</email>
+		<name>Horea Christian</name>
+	</maintainer>
+	<maintainer type="project">
+		<email>sci@gentoo.org</email>
+		<name>Gentoo Science Project</name>
+	</maintainer>
+	<use>
+	<flag name="system-jpeg">Use the system-wide <pkg>media-libs/libjpeg-turbo</pkg>
+		instead of bundled.</flag>
+	<flag name="jpeg-ls">Supprt for converting DICOM images compressed with the JPEG-LS transfer syntaxes using the bundled CharLS library</flag>
+	</use>
+	<longdescription>
+		dcm2niix is a designed to convert neuroimaging data from the DICOM
+		format to the NIfTI format. ICOM provides many ways to store/compress
+		image data, known as transfer syntaxes.
+	</longdescription>
+	<upstream>
+		<remote-id type="github">rordenlab/dcm2niix</remote-id>
+	</upstream>
+</pkgmetadata>
diff --git a/sci-biology/dcmstack/Manifest b/sci-biology/dcmstack/Manifest
new file mode 100644
index 000000000..ab8414c4e
--- /dev/null
+++ b/sci-biology/dcmstack/Manifest
@@ -0,0 +1 @@
+DIST dcmstack-0.9.gh.tar.gz 1739820 BLAKE2B 08b65589b1317ab7ac16a5ac126cf6fba7933941b0b929baa689fb72425f590fb98ae967908b358d5316f5009aa6443787e7077c13f22f156d3fae67a9b8396c SHA512 8061f55c0fa467c3fae94f8790f01331d377d8552cf7a896d705b3cf895340051aad7a4a79237cc225f587d2411be23255635970ab4067d1e5a37f82407b4b39
diff --git a/sci-biology/dcmstack/dcmstack-0.9.ebuild b/sci-biology/dcmstack/dcmstack-0.9.ebuild
new file mode 100644
index 000000000..d207526c0
--- /dev/null
+++ b/sci-biology/dcmstack/dcmstack-0.9.ebuild
@@ -0,0 +1,25 @@
+# Copyright 1999-2023 Gentoo Authors
+# Distributed under the terms of the GNU General Public License v2
+
+EAPI=8
+
+DISTUTILS_USE_PEP517=setuptools
+PYTHON_COMPAT=( python3_{10..11} )
+
+inherit distutils-r1
+
+DESCRIPTION="DICOM to Nifti coversion"
+HOMEPAGE="https://dcmstack.readthedocs.org/en/latest/"
+SRC_URI="https://github.com/moloney/dcmstack/archive/v${PV}.tar.gz -> ${P}.gh.tar.gz"
+
+LICENSE="MIT"
+SLOT="0"
+KEYWORDS="~amd64 ~x86"
+IUSE=""
+
+RDEPEND="
+	sci-libs/nibabel[${PYTHON_USEDEP}]
+	sci-libs/pydicom[${PYTHON_USEDEP}]
+"
+
+distutils_enable_tests pytest
diff --git a/sci-biology/dcmstack/dcmstack-9999.ebuild b/sci-biology/dcmstack/dcmstack-9999.ebuild
deleted file mode 100644
index d3d38dc2a..000000000
--- a/sci-biology/dcmstack/dcmstack-9999.ebuild
+++ /dev/null
@@ -1,23 +0,0 @@
-# Copyright 1999-2015 Gentoo Foundation
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=5
-
-PYTHON_COMPAT=( python2_7 )
-
-inherit distutils-r1 git-r3 multilib
-
-DESCRIPTION="DICOM to Nifti coversion"
-HOMEPAGE="https://dcmstack.readthedocs.org/en/latest/"
-SRC_URI=""
-EGIT_REPO_URI="https://github.com/moloney/dcmstack"
-
-LICENSE="MIT"
-SLOT="0"
-IUSE=""
-KEYWORDS=""
-
-DEPEND="
-	dev-python/setuptools[${PYTHON_USEDEP}]"
-RDEPEND="sci-libs/nibabel[${PYTHON_USEDEP}]
-	>=sci-libs/pydicom-0.9.7[${PYTHON_USEDEP}]"
diff --git a/sci-biology/dcmstack/metadata.xml b/sci-biology/dcmstack/metadata.xml
index ae9640ffb..0272cf14e 100644
--- a/sci-biology/dcmstack/metadata.xml
+++ b/sci-biology/dcmstack/metadata.xml
@@ -5,4 +5,7 @@
 		<email>sci@gentoo.org</email>
 		<name>Gentoo Science Project</name>
 	</maintainer>
+	<upstream>
+		<remote-id type="github">moloney/dcmstack</remote-id>
+	</upstream>
 </pkgmetadata>
diff --git a/sci-biology/deeptools-intervals/Manifest b/sci-biology/deeptools-intervals/Manifest
new file mode 100644
index 000000000..ad6745f3e
--- /dev/null
+++ b/sci-biology/deeptools-intervals/Manifest
@@ -0,0 +1 @@
+DIST deeptools-intervals-0.1.9.tar.gz 40839 BLAKE2B dcb86c054e8c9db6a466153860c0c41fd80c552571b5aa00084fd016051eacee0e9d8dad979edaa787d50ac25ca586128fe733956c4f5f0eb1ce02132a268754 SHA512 4e9a4dd2c392b13cd5084f1babc68098360429c81f2c7053a6b39fbd00812a7c57380ee2c3fef14c085e2bd2705d12e9970b4821984c91b008d0f7e02e42b16c
diff --git a/sci-biology/deeptools-intervals/deeptools-intervals-0.1.9.ebuild b/sci-biology/deeptools-intervals/deeptools-intervals-0.1.9.ebuild
new file mode 100644
index 000000000..38f9aea0f
--- /dev/null
+++ b/sci-biology/deeptools-intervals/deeptools-intervals-0.1.9.ebuild
@@ -0,0 +1,18 @@
+# Copyright 1999-2023 Gentoo Authors
+# Distributed under the terms of the GNU General Public License v2
+
+EAPI=8
+
+PYTHON_COMPAT=( python3_{10..11} )
+
+inherit distutils-r1
+
+DESCRIPTION="Constructing interval trees with associated exon/annotation information"
+HOMEPAGE="https://github.com/deeptools/deeptools_intervals"
+SRC_URI="https://github.com/deeptools/deeptools_intervals/archive/${PV}.tar.gz -> ${P}.tar.gz"
+
+LICENSE="MIT"
+SLOT="0"
+KEYWORDS="~amd64 ~x86"
+
+S="${WORKDIR}/${PN//-/_}-${PV}"
diff --git a/sci-biology/deeptools-intervals/metadata.xml b/sci-biology/deeptools-intervals/metadata.xml
new file mode 100644
index 000000000..853bd539c
--- /dev/null
+++ b/sci-biology/deeptools-intervals/metadata.xml
@@ -0,0 +1,11 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
+<pkgmetadata>
+	<maintainer type="project">
+		<email>sci-biology@gentoo.org</email>
+		<name>Gentoo Biology Project</name>
+	</maintainer>
+	<upstream>
+		<remote-id type="github">deeptools/deeptools_intervals</remote-id>
+	</upstream>
+</pkgmetadata>
diff --git a/sci-biology/deeptools/Manifest b/sci-biology/deeptools/Manifest
index eee64af33..649a31cdf 100644
--- a/sci-biology/deeptools/Manifest
+++ b/sci-biology/deeptools/Manifest
@@ -1 +1,2 @@
-DIST deeptools-2.5.0.tar.gz 59620916 BLAKE2B 83831449b71a72ce90b3d25fd6df6a73e5d786cf84e9e0420c888316867c1a1c8aaaddfc9d0682a459efc7bd9d0910f0a43aef488e8a86cfb9adb4cb0106e334 SHA512 5bd10d4c58cdd7b3318028eb28f6ca9252d42899dee8eb8ad6af1b372ad26fbcc605b712c3369ec45350600f2c822a17679062b9f536f454e5bfb0381715f98f
+DIST deeptools-3.5.0.tar.gz 62553343 BLAKE2B a8cd1520b96c50ad36667405677cf422a74376d88f0716f83cc0c6f58d01aefcf47ac1b862aa98b8801e61445d59831dbc9246660e2f41a5b3e0ed3d6573ad50 SHA512 699734c8a863ec76dfead728e3227bbe3ec04d62e91f447269a6aa8406d627ff618837b85ab2e31cc635c671e1d62230c4db0992106bbe921281b81164387b38
+DIST deeptools-3.5.1.tar.gz 62552044 BLAKE2B 3c785ba478b88fbbe7ba2617e2d05984b8a897f787e85d6f8f144f596af07b9e16ba920c8adee35efc4b1b067f255e81f66cf746aaea43e5ee61c23c4d15c9c3 SHA512 f7618f1a51b975d42712a38e13e9ab2ddfeafffe24d81fdab41f1ef7c2e44fd09da0351210670b0036bf72e7af11b679417275adce300ae9fabe4b5339ee9810
diff --git a/sci-biology/deeptools/deeptools-2.5.0.ebuild b/sci-biology/deeptools/deeptools-2.5.0.ebuild
deleted file mode 100644
index e69672942..000000000
--- a/sci-biology/deeptools/deeptools-2.5.0.ebuild
+++ /dev/null
@@ -1,32 +0,0 @@
-# Copyright 1999-2017 Gentoo Foundation
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=6
-
-PYTHON_COMPAT=( python2_7 python3_5 )
-
-inherit distutils-r1
-
-[ "$PV" == "9999" ] && inherit git-2
-
-DESCRIPTION="Extract reads from BAM files, normalize, draw figures, convert BAM to bigWig"
-HOMEPAGE="https://github.com/fidelram/deepTools"
-if [ "$PV" == "9999" ]; then
-	EGIT_REPO_URI="https://github.com/fidelram/deepTools"
-	KEYWORDS=""
-else
-	SRC_URI="https://github.com/fidelram/deepTools/archive/2.5.0.tar.gz -> ${P}.tar.gz"
-	KEYWORDS="~amd64"
-fi
-
-LICENSE="GPL-3"
-SLOT="0"
-IUSE=""
-
-DEPEND=">=dev-python/numpy-1.8.0
-		>=sci-libs/scipy-0.17.0
-		>=dev-python/py2bit-0.1.0
-		>=dev-python/pyBigWig-0.2.1
-		>=sci-biology/pysam-0.8
-		>=dev-python/matplotlib-1.4.0"
-RDEPEND="${DEPEND}"
diff --git a/sci-biology/deeptools/deeptools-3.5.0.ebuild b/sci-biology/deeptools/deeptools-3.5.0.ebuild
new file mode 100644
index 000000000..7c2eaa739
--- /dev/null
+++ b/sci-biology/deeptools/deeptools-3.5.0.ebuild
@@ -0,0 +1,37 @@
+# Copyright 1999-2023 Gentoo Authors
+# Distributed under the terms of the GNU General Public License v2
+
+EAPI=8
+
+DISTUTILS_USE_PEP517=setuptools
+PYTHON_COMPAT=( python3_{10..11} )
+
+inherit distutils-r1
+
+DESCRIPTION="Extract reads from BAM files, normalize, draw figures, convert BAM to bigWig"
+HOMEPAGE="https://github.com/deeptools/deepTools"
+SRC_URI="https://github.com/deeptools/deepTools/archive/${PV}.tar.gz -> ${P}.tar.gz"
+
+LICENSE="BSD"
+SLOT="0"
+KEYWORDS="~amd64"
+
+# TODO: fix this
+RESTRICT="test"
+
+RDEPEND="
+	>=sci-biology/deeptools-intervals-0.1.8[${PYTHON_USEDEP}]
+	>=dev-python/numpy-1.9.0[${PYTHON_USEDEP}]
+	>=dev-python/numpydoc-0.5[${PYTHON_USEDEP}]
+	>=dev-python/scipy-0.17.0[${PYTHON_USEDEP}]
+	dev-python/plotly[${PYTHON_USEDEP}]
+	>=dev-python/py2bit-0.2.0[${PYTHON_USEDEP}]
+	>=dev-python/pyBigWig-0.2.1[${PYTHON_USEDEP}]
+	>=sci-biology/pysam-0.14.0[${PYTHON_USEDEP}]
+	>=dev-python/matplotlib-3.1.0[${PYTHON_USEDEP}]
+"
+
+S="${WORKDIR}/deepTools-${PV}"
+
+distutils_enable_sphinx docs dev-python/sphinx-rtd-theme dev-python/sphinx-argparse
+#distutils_enable_tests nose
diff --git a/sci-biology/deeptools/deeptools-3.5.1.ebuild b/sci-biology/deeptools/deeptools-3.5.1.ebuild
new file mode 100644
index 000000000..7c2eaa739
--- /dev/null
+++ b/sci-biology/deeptools/deeptools-3.5.1.ebuild
@@ -0,0 +1,37 @@
+# Copyright 1999-2023 Gentoo Authors
+# Distributed under the terms of the GNU General Public License v2
+
+EAPI=8
+
+DISTUTILS_USE_PEP517=setuptools
+PYTHON_COMPAT=( python3_{10..11} )
+
+inherit distutils-r1
+
+DESCRIPTION="Extract reads from BAM files, normalize, draw figures, convert BAM to bigWig"
+HOMEPAGE="https://github.com/deeptools/deepTools"
+SRC_URI="https://github.com/deeptools/deepTools/archive/${PV}.tar.gz -> ${P}.tar.gz"
+
+LICENSE="BSD"
+SLOT="0"
+KEYWORDS="~amd64"
+
+# TODO: fix this
+RESTRICT="test"
+
+RDEPEND="
+	>=sci-biology/deeptools-intervals-0.1.8[${PYTHON_USEDEP}]
+	>=dev-python/numpy-1.9.0[${PYTHON_USEDEP}]
+	>=dev-python/numpydoc-0.5[${PYTHON_USEDEP}]
+	>=dev-python/scipy-0.17.0[${PYTHON_USEDEP}]
+	dev-python/plotly[${PYTHON_USEDEP}]
+	>=dev-python/py2bit-0.2.0[${PYTHON_USEDEP}]
+	>=dev-python/pyBigWig-0.2.1[${PYTHON_USEDEP}]
+	>=sci-biology/pysam-0.14.0[${PYTHON_USEDEP}]
+	>=dev-python/matplotlib-3.1.0[${PYTHON_USEDEP}]
+"
+
+S="${WORKDIR}/deepTools-${PV}"
+
+distutils_enable_sphinx docs dev-python/sphinx-rtd-theme dev-python/sphinx-argparse
+#distutils_enable_tests nose
diff --git a/sci-biology/deeptools/deeptools-9999.ebuild b/sci-biology/deeptools/deeptools-9999.ebuild
deleted file mode 100644
index a2c1fcfb9..000000000
--- a/sci-biology/deeptools/deeptools-9999.ebuild
+++ /dev/null
@@ -1,32 +0,0 @@
-# Copyright 1999-2017 Gentoo Foundation
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=5
-
-PYTHON_COMPAT=( python2_7 python3_5 )
-
-inherit distutils-r1
-
-[ "$PV" == "9999" ] && inherit git-2
-
-DESCRIPTION="Extract reads from BAM files, normalize, draw figures, convert BAM to bigWig"
-HOMEPAGE="https://github.com/fidelram/deepTools"
-if [ "$PV" == "9999" ]; then
-	EGIT_REPO_URI="https://github.com/fidelram/deepTools"
-	KEYWORDS=""
-else
-	SRC_URI="https://github.com/fidelram/deepTools/archive/2.5.0.tar.gz -> ${P}.tar.gz"
-	KEYWORDS="~amd64"
-fi
-
-LICENSE="GPL-3"
-SLOT="0"
-IUSE=""
-
-DEPEND=">=dev-python/numpy-1.8.0
-		>=sci-libs/scipy-0.17.0
-		>=dev-python/py2bit-0.1.0
-		>=dev-python/pyBigWig-0.2.1
-		>=sci-biology/pysam-0.8
-		>=dev-python/matplotlib-1.4.0"
-RDEPEND="${DEPEND}"
diff --git a/sci-biology/diamond/Manifest b/sci-biology/diamond/Manifest
index 6e784d485..accffad69 100644
--- a/sci-biology/diamond/Manifest
+++ b/sci-biology/diamond/Manifest
@@ -1 +1 @@
-DIST v0.9.19.tar.gz 402840 BLAKE2B 81d1586028f16fe01400da49322339fcb1da053d6291276d5b5821ea67ff16b2778f6779743cb783c08ad3d597f32b63382fcc84a60a07eea8f7b4882c3b9733 SHA512 a08dcf9148814cb8b9289813aa678a7cff5ee2703fe39dda8f792a56b96ea6dfd3153c16f8e5a73acbce0ff33ead26575da6cb8c298408427809ffcc5b2f1224
+DIST diamond-2.0.6.tar.gz 1405639 BLAKE2B dff5a9b959a42e49a1ef774174eb262ded6effd58cdbe4f212b82f867cd00d35c1932fa846cb01dd392ff18401fc08cd5d6008fba75a3485e710431f3bd0db34 SHA512 e4c932bfe3baaa808b0c3bb00354bf328103ce26a36483815b988b6a164c4a3d2648af227d82f526d452cb169cc3c78d343528f781fb262733d205fe50e8e98d
diff --git a/sci-biology/diamond/diamond-0.9.19.ebuild b/sci-biology/diamond/diamond-0.9.19.ebuild
deleted file mode 100644
index fde9b9080..000000000
--- a/sci-biology/diamond/diamond-0.9.19.ebuild
+++ /dev/null
@@ -1,27 +0,0 @@
-# Copyright 1999-2018 Gentoo Foundation
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=6
-
-inherit toolchain-funcs cmake-utils
-
-DESCRIPTION="Alternative of blastp/blastx searches using DNA short reads through protein db"
-HOMEPAGE="http://ab.inf.uni-tuebingen.de/software/diamond
-	https://github.com/bbuchfink/diamond"
-SRC_URI="https://github.com/bbuchfink/diamond/archive/v${PV}.tar.gz"
-# EGIT_REPO_URI="https://github.com/bbuchfink/diamond.git"
-
-LICENSE="AGPL-3" # diamond_manual.pdf says AGPL but src/COPYING used to say BSD?
-SLOT="0"
-KEYWORDS="~amd64 ~x86"
-IUSE=""
-# uses SSE instructions, SSSE3 and POPCNT
-
-DEPEND=""
-RDEPEND="${DEPEND}"
-
-# use cmake -DBUILD_STATIC=ON to create a statically linked binary
-src_install(){
-	cmake-utils_src_install
-	dodoc README.rst diamond_manual.pdf
-}
diff --git a/sci-biology/diamond/diamond-2.0.6.ebuild b/sci-biology/diamond/diamond-2.0.6.ebuild
new file mode 100644
index 000000000..1ec499917
--- /dev/null
+++ b/sci-biology/diamond/diamond-2.0.6.ebuild
@@ -0,0 +1,18 @@
+# Copyright 1999-2021 Gentoo Authors
+# Distributed under the terms of the GNU General Public License v2
+
+EAPI=7
+
+inherit cmake
+
+DESCRIPTION="Alternative of blastp/blastx searches using DNA short reads through protein db"
+HOMEPAGE="http://ab.inf.uni-tuebingen.de/software/diamond
+	https://github.com/bbuchfink/diamond"
+SRC_URI="https://github.com/bbuchfink/diamond/archive/v${PV}.tar.gz -> ${P}.tar.gz"
+
+LICENSE="AGPL-3" # diamond_manual.pdf says AGPL but src/COPYING used to say BSD?
+SLOT="0"
+KEYWORDS="~amd64 ~x86"
+
+# uses SSE instructions, SSSE3 and POPCNT
+# use cmake -DBUILD_STATIC=ON to create a statically linked binary
diff --git a/sci-biology/diamond/metadata.xml b/sci-biology/diamond/metadata.xml
index 138cb7705..ac7dfc24a 100644
--- a/sci-biology/diamond/metadata.xml
+++ b/sci-biology/diamond/metadata.xml
@@ -9,4 +9,7 @@
 		<email>sci-biology@gentoo.org</email>
 		<name>Gentoo Biology Project</name>
 	</maintainer>
+	<upstream>
+		<remote-id type="github">bbuchfink/diamond</remote-id>
+	</upstream>
 </pkgmetadata>
diff --git a/sci-biology/dipy/Manifest b/sci-biology/dipy/Manifest
index 168eef6f0..38863707e 100644
--- a/sci-biology/dipy/Manifest
+++ b/sci-biology/dipy/Manifest
@@ -1,2 +1 @@
-DIST dipy-0.11.0.tar.gz 4943339 SHA256 b9b7c19ccf9d5087f2bdea86478319a5355bb4d4c5cb23afd7d85b09048d1716 SHA512 012c043f6c555d7abf0e67598a129b9538af6e9c3b613356ed7e015d866e85a165f8d1d3f79efa2f79bc0e101a908c42778bbdec0244f1fa122e1ff828f93cda WHIRLPOOL 9b5a24355fd8eccd168c7583dab725cc2d4a398f15f1fc1b3b7609f253d461286bf41f2e80d2c2adc85f20659169307e3523c4c2c4ceab94c94e7096bec7d358
-DIST dipy-0.14.0.tar.gz 5768795 BLAKE2B c9003caf43a7054d59d6cdda8432cce7cbd61edbb21981e71dcbe85e5e659fe301184adcb777784687649f4fb49118799ba8b2e7aad021c32c44e561a28bd9eb SHA512 312c5ec997ceac3d43c4c0ad87e030dd6a7b9310ae31ae2ef2a0efc0286e576f862552800fc9d3a81fcc4ff5295c0dc90e2ac9c6b22924120b841378152d6882
+DIST dipy-1.1.1.tar.gz 6021111 BLAKE2B a235965e6bc68ac062b707ac804ed726c14cd15fd41eed8b361c91873ae8070bda8be00bee961d34546c0560b7874ed656e2efbe03c9d2bac8c9a6173838b151 SHA512 19049fd362d9ab44ad67369eb2eebf0149aaba76215beb96d298391d8d5baf4964d412546a3f28a1a83d07e643b2ce97ce911f22d2d4978a0316763839fdd6d0
diff --git a/sci-biology/dipy/dipy-0.11.0.ebuild b/sci-biology/dipy/dipy-0.11.0.ebuild
deleted file mode 100644
index fbbd4d519..000000000
--- a/sci-biology/dipy/dipy-0.11.0.ebuild
+++ /dev/null
@@ -1,34 +0,0 @@
-# Copyright 1999-2018 Gentoo Foundation
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=6
-
-PYTHON_COMPAT=( python2_7 python3_{4,5} )
-
-inherit distutils-r1
-
-DESCRIPTION="Computational neuroanatomy project focusing on diffusion MRI"
-HOMEPAGE="http://nipy.org/dipy"
-SRC_URI="https://github.com/nipy/dipy/archive/${PV}.tar.gz -> ${P}.tar.gz"
-
-LICENSE="BSD"
-SLOT="0"
-KEYWORDS="~amd64 ~x86"
-IUSE="test"
-
-RDEPEND="
-	dev-python/numpy[${PYTHON_USEDEP}]
-	sci-libs/scipy[${PYTHON_USEDEP}]
-	sci-libs/nibabel[${PYTHON_USEDEP}]
-"
-DEPEND="
-	test? ( ${RDEPEND} dev-python/nose[${PYTHON_USEDEP}] )
-	dev-python/setuptools[${PYTHON_USEDEP}]
-	dev-python/cython[${PYTHON_USEDEP}]
-"
-
-python_test() {
-	distutils_install_for_testing
-	cd "${TEST_DIR}"/lib || die
-	nosetests || die
-}
diff --git a/sci-biology/dipy/dipy-0.14.0.ebuild b/sci-biology/dipy/dipy-0.14.0.ebuild
deleted file mode 100644
index 2d76b74a2..000000000
--- a/sci-biology/dipy/dipy-0.14.0.ebuild
+++ /dev/null
@@ -1,38 +0,0 @@
-# Copyright 1999-2018 Gentoo Foundation
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=6
-
-PYTHON_COMPAT=( python2_7 python3_{4,5} )
-
-inherit distutils-r1
-
-DESCRIPTION="Computational neuroanatomy project focusing on diffusion MRI"
-HOMEPAGE="http://nipy.org/dipy"
-SRC_URI="https://github.com/nipy/dipy/archive/${PV}.tar.gz -> ${P}.tar.gz"
-
-LICENSE="BSD"
-SLOT="0"
-KEYWORDS="~amd64 ~x86"
-IUSE="test"
-
-RDEPEND="
-	sci-libs/nibabel[${PYTHON_USEDEP}]
-	dev-python/numpy[${PYTHON_USEDEP}]
-	sci-libs/scipy[${PYTHON_USEDEP}]
-"
-DEPEND="
-	dev-python/cython[${PYTHON_USEDEP}]
-	dev-python/h5py[${PYTHON_USEDEP}]
-	dev-python/setuptools[${PYTHON_USEDEP}]
-	test? ( dev-python/nose[${PYTHON_USEDEP}] )
-"
-
-# Tests for this release fail: https://github.com/nipy/dipy/issues/1531
-RESTRICT="test"
-
-python_test() {
-	distutils_install_for_testing
-	cd "${TEST_DIR}"/lib || die
-	nosetests || die
-}
diff --git a/sci-biology/dipy/dipy-1.1.1.ebuild b/sci-biology/dipy/dipy-1.1.1.ebuild
new file mode 100644
index 000000000..3656d6dc8
--- /dev/null
+++ b/sci-biology/dipy/dipy-1.1.1.ebuild
@@ -0,0 +1,39 @@
+# Copyright 1999-2022 Gentoo Authors
+# Distributed under the terms of the GNU General Public License v2
+
+EAPI=8
+
+PYTHON_COMPAT=( python3_10 )
+
+inherit distutils-r1
+
+DESCRIPTION="Computational neuroanatomy project focusing on diffusion MRI"
+HOMEPAGE="https://github.com/nipy/dipy"
+SRC_URI="https://github.com/nipy/dipy/archive/${PV}.tar.gz -> ${P}.tar.gz"
+
+LICENSE="BSD"
+SLOT="0"
+KEYWORDS="~amd64 ~x86"
+IUSE="test"
+
+RDEPEND="
+	sci-libs/nibabel[${PYTHON_USEDEP}]
+	dev-python/numpy[${PYTHON_USEDEP}]
+	dev-python/scipy[${PYTHON_USEDEP}]
+"
+DEPEND="
+	dev-python/packaging[${PYTHON_USEDEP}]
+	dev-python/cython[${PYTHON_USEDEP}]
+	dev-python/h5py[${PYTHON_USEDEP}]
+	test? ( dev-python/pytest[${PYTHON_USEDEP}] )
+"
+
+# Tests fail because they require data download:
+# https://github.com/dipy/dipy/issues/2092
+RESTRICT="test"
+
+python_test() {
+	distutils_install_for_testing
+	cd "${TEST_DIR}"/lib || die
+	pytest -m "not network" || die
+}
diff --git a/sci-biology/dipy/dipy-9999.ebuild b/sci-biology/dipy/dipy-9999.ebuild
deleted file mode 100644
index e9761d633..000000000
--- a/sci-biology/dipy/dipy-9999.ebuild
+++ /dev/null
@@ -1,36 +0,0 @@
-# Copyright 1999-2018 Gentoo Foundation
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=6
-
-PYTHON_COMPAT=( python2_7 python3_{4,5} )
-
-inherit distutils-r1 git-r3
-
-DESCRIPTION="Computational neuroanatomy project focusing on diffusion MRI"
-HOMEPAGE="http://nipy.org/dipy"
-SRC_URI=""
-EGIT_REPO_URI="https://github.com/nipy/dipy"
-
-LICENSE="BSD"
-SLOT="0"
-KEYWORDS=""
-IUSE="test"
-
-RDEPEND="
-	sci-libs/nibabel[${PYTHON_USEDEP}]
-	dev-python/numpy[${PYTHON_USEDEP}]
-	sci-libs/scipy[${PYTHON_USEDEP}]
-"
-DEPEND="
-	dev-python/cython[${PYTHON_USEDEP}]
-	dev-python/h5py[${PYTHON_USEDEP}]
-	dev-python/setuptools[${PYTHON_USEDEP}]
-	test? ( dev-python/nose[${PYTHON_USEDEP}] )
-"
-
-python_test() {
-	distutils_install_for_testing
-	cd "${TEST_DIR}"/lib || die
-	nosetests || die
-}
diff --git a/sci-biology/dipy/metadata.xml b/sci-biology/dipy/metadata.xml
index e198cb853..7dd1cbee8 100644
--- a/sci-biology/dipy/metadata.xml
+++ b/sci-biology/dipy/metadata.xml
@@ -2,7 +2,7 @@
 <!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
 <pkgmetadata>
 	<maintainer type="person">
-		<email>horea.christ@gmail.com</email>
+		<email>gentoo@chymera.eu</email>
 		<name>Horea Christian</name>
 	</maintainer>
 	<maintainer type="project">
@@ -10,11 +10,11 @@
 		<name>Gentoo Science Project</name>
 	</maintainer>
 	<longdescription lang="en">
-Dipy is a free and open source software project for computational neuroanatomy, focusing mainly on 
-diffusion magnetic resonance imaging (dMRI) analysis. It implements a broad range of algorithms for 
-denoising, registration, reconstruction, tracking, clustering, visualization, and statistical 
-analysis of MRI data.
-</longdescription>
+		Dipy is a free and open source software project for computational neuroanatomy, focusing mainly on 
+		diffusion magnetic resonance imaging (dMRI) analysis. It implements a broad range of algorithms for 
+		denoising, registration, reconstruction, tracking, clustering, visualization, and statistical 
+		analysis of MRI data.
+	</longdescription>
 	<upstream>
 		<remote-id type="github">nipy/dipy</remote-id>
 	</upstream>
diff --git a/sci-biology/discrover/Manifest b/sci-biology/discrover/Manifest
deleted file mode 100644
index a293b8424..000000000
--- a/sci-biology/discrover/Manifest
+++ /dev/null
@@ -1 +0,0 @@
-DIST discrover-1.6.0.tar.gz 251285 BLAKE2B dfbcf92ef8d76b8da9c03cdf1d932fb2c67d1361813d918212352fe814cae46391fc3606da69819b28f822ad7f894290bc8c12cadfc135d10b78d1a49750f375 SHA512 78215b8c05da214928934b63f78753d707fbbe5de8cf7dbd03ddededfaf8cedf232b6769755718748735ff504e129ce02bdef3b29d0ece2b57e3745ab2e1669b
diff --git a/sci-biology/discrover/discrover-1.6.0.ebuild b/sci-biology/discrover/discrover-1.6.0.ebuild
deleted file mode 100644
index 5840283fd..000000000
--- a/sci-biology/discrover/discrover-1.6.0.ebuild
+++ /dev/null
@@ -1,78 +0,0 @@
-# Copyright 1999-2015 Gentoo Foundation
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=5
-inherit cmake-utils
-
-DESCRIPTION="A sequence motif discovery tool that uses discriminative learning"
-HOMEPAGE="https://github.com/maaskola/discrover"
-SRC_URI="https://github.com/maaskola/discrover/archive/${PV}.tar.gz -> ${P}.tar.gz"
-
-LICENSE="GPL-3+"
-SLOT="0"
-KEYWORDS="~amd64 ~x86"
-IUSE="+cairo dreme doc +lto misc_scripts +rmathlib tcmalloc"
-
-RDEPEND="
-	dev-libs/boost
-	cairo? ( x11-libs/cairo )
-	dreme? ( sci-biology/meme )
-	rmathlib? ( dev-lang/R )
-	tcmalloc? ( dev-util/google-perftools )
-"
-DEPEND="${RDEPEND}
-	doc? (
-		dev-texlive/texlive-latex
-		dev-texlive/texlive-latexextra
-		dev-texlive/texlive-latexrecommended
-		media-gfx/imagemagick
-	)
-	lto? ( >=sys-devel/gcc-4.8:* )
-"
-pkg_pretend() {
-	if use lto; then
-		if [[ $(gcc-major-version) -lt 4 ]] || ( [[ $(gcc-major-version) -eq 4 && $(gcc-minor-version) -lt 8 ]] ) ; then
-			eerror "Compilation with link-time optimization and GCC older than 4.8 is not supported."
-			eerror "Please either disable the USE flag 'lto' or use >=sys-devel/gcc-4.8."
-			die "Compiling with USE flag 'lto' is not supported with <sys-devel/gcc-4.8."
-		fi
-	fi
-}
-src_configure() {
-	local mycmakeargs=(
-		$(cmake-utils_use_with cairo CAIRO)
-		$(cmake-utils_use_with dreme DREME)
-		$(cmake-utils_use_with doc DOC)
-		$(cmake-utils_use_with lto LTO)
-		$(cmake-utils_use_with misc_scripts MISC_SCRIPTS)
-		$(cmake-utils_use_with rmathlib RMATHLIB)
-		$(cmake-utils_use_with tcmalloc TCMALLOC)
-		-DDOC_DIR="${EPREFIX}${PREFIX}/share/doc/${PF}"
-	)
-
-	unset R_HOME
-
-	if use rmathlib ; then
-		echo
-		elog "Using statistical routines from standalone Rmathlib."
-		echo
-	fi
-	if use dreme ; then
-		echo
-		elog "Linking to DREME from the MEME suite."
-		echo
-	else
-		echo
-		elog "Not linking to DREME from the MEME suite (sci-biology/meme)."
-		elog "You will not be able to use DREME to find seeds."
-		echo
-	fi
-
-	if use doc ; then
-		echo
-		elog "User manual available at /usr/share/doc/discrover/discrover-manual.pdf"
-		echo
-	fi
-
-	cmake-utils_src_configure
-}
diff --git a/sci-biology/discrover/discrover-9999.ebuild b/sci-biology/discrover/discrover-9999.ebuild
deleted file mode 100644
index 627f32059..000000000
--- a/sci-biology/discrover/discrover-9999.ebuild
+++ /dev/null
@@ -1,79 +0,0 @@
-# Copyright 1999-2015 Gentoo Foundation
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=5
-inherit cmake-utils git-r3
-
-DESCRIPTION="A sequence motif discovery tool that uses discriminative learning"
-HOMEPAGE="https://github.com/maaskola/discrover"
-SRC_URI=""
-EGIT_REPO_URI="https://github.com/maaskola/${PN}"
-
-LICENSE="GPL-3+"
-SLOT="0"
-KEYWORDS="~amd64 ~x86"
-IUSE="+cairo dreme doc +lto misc_scripts +rmathlib tcmalloc"
-
-RDEPEND="
-	dev-libs/boost
-	cairo? ( x11-libs/cairo )
-	dreme? ( sci-biology/meme )
-	rmathlib? ( dev-lang/R )
-	tcmalloc? ( dev-util/google-perftools )
-"
-DEPEND="${RDEPEND}
-	doc? (
-		dev-texlive/texlive-latex
-		dev-texlive/texlive-latexextra
-		dev-texlive/texlive-latexrecommended
-		media-gfx/imagemagick
-	)
-	lto? ( >=sys-devel/gcc-4.8:* )
-"
-pkg_pretend() {
-	if use lto; then
-		if [[ $(gcc-major-version) -lt 4 ]] || ( [[ $(gcc-major-version) -eq 4 && $(gcc-minor-version) -lt 8 ]] ) ; then
-			eerror "Compilation with link-time optimization and GCC older than 4.8 is not supported."
-			eerror "Please either disable the USE flag 'lto' or use >=sys-devel/gcc-4.8."
-			die "Compiling with USE flag 'lto' is not supported with <sys-devel/gcc-4.8."
-		fi
-	fi
-}
-src_configure() {
-	local mycmakeargs=(
-		$(cmake-utils_use_with cairo CAIRO)
-		$(cmake-utils_use_with dreme DREME)
-		$(cmake-utils_use_with doc DOC)
-		$(cmake-utils_use_with lto LTO)
-		$(cmake-utils_use_with misc_scripts MISC_SCRIPTS)
-		$(cmake-utils_use_with rmathlib RMATHLIB)
-		$(cmake-utils_use_with tcmalloc TCMALLOC)
-		-DDOC_DIR="${EPREFIX}${PREFIX}/share/doc/${PF}"
-	)
-
-	unset R_HOME
-
-	if use rmathlib ; then
-		echo
-		elog "Using statistical routines from standalone Rmathlib."
-		echo
-	fi
-	if use dreme ; then
-		echo
-		elog "Linking to DREME from the MEME suite."
-		echo
-	else
-		echo
-		elog "Not linking to DREME from the MEME suite (sci-biology/meme)."
-		elog "You will not be able to use DREME to find seeds."
-		echo
-	fi
-
-	if use doc ; then
-		echo
-		elog "User manual available at /usr/share/doc/discrover/discrover-manual.pdf"
-		echo
-	fi
-
-	cmake-utils_src_configure
-}
diff --git a/sci-biology/discrover/metadata.xml b/sci-biology/discrover/metadata.xml
deleted file mode 100644
index 6f5916ea8..000000000
--- a/sci-biology/discrover/metadata.xml
+++ /dev/null
@@ -1,28 +0,0 @@
-<?xml version="1.0" encoding="UTF-8"?>
-<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
-<pkgmetadata>
-	<maintainer type="person">
-		<email>jonas@maaskola.de</email>
-		<name>Jonas Maaskola</name>
-	</maintainer>
-	<use>
-		<flag name="cairo">
-Use Cairo for sequence logo plotting capabilities
-</flag>
-		<flag name="dreme">
-Enable usage of DREME from the MEME package for seeding
-</flag>
-		<flag name="lto">
-Compile with link-time optimization (LTO)
-</flag>
-		<flag name="misc_scripts">
-Install miscellaneous scripts
-</flag>
-		<flag name="rmathlib">
-Link to the standalone Rmathlib for statistical routines
-</flag>
-	</use>
-	<upstream>
-		<remote-id type="github">maaskola/discrover</remote-id>
-	</upstream>
-</pkgmetadata>
diff --git a/sci-biology/dna2pep/Manifest b/sci-biology/dna2pep/Manifest
deleted file mode 100644
index 9f8f4cf84..000000000
--- a/sci-biology/dna2pep/Manifest
+++ /dev/null
@@ -1 +0,0 @@
-DIST dna2pep-1.1.tgz 13340 BLAKE2B 4a0096ac980b6950d7109bc469abae212953bbf9750b0eac97ef309493373d2ac25c231936b37a9dc2c8b23bad8be9d1fc800bc17437b943179c17eef41669dc SHA512 22016dafd190a9d72b8ba25fd42b96c2cf44f4aebba7b3c89ba86e543a4bffaca0e34581b79b31e4e0c48492911925e7740a0c60faf361fb52779c361c4f08db
diff --git a/sci-biology/dna2pep/dna2pep-1.1.ebuild b/sci-biology/dna2pep/dna2pep-1.1.ebuild
deleted file mode 100644
index 91aed370b..000000000
--- a/sci-biology/dna2pep/dna2pep-1.1.ebuild
+++ /dev/null
@@ -1,27 +0,0 @@
-# Copyright 1999-2016 Gentoo Foundation
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=5
-
-DESCRIPTION="Translate DNA sequence into protein (with STOP codon read-through)"
-HOMEPAGE="http://www.cbs.dtu.dk/services/VirtualRibosome/download.php"
-SRC_URI="http://www.cbs.dtu.dk/services/VirtualRibosome/releases/${P}.tgz"
-
-# source code does not explictly mention GPL version so I assume GPL-1
-LICENSE="GPL-1"
-SLOT="0"
-KEYWORDS="~amd64"
-IUSE=""
-
-DEPEND=""
-RDEPEND="${DEPEND}"
-
-src_prepare(){
-	sed -e 's@#!/usr/local/python/bin/python@#! /usr/bin/env python@' -i *.py || die
-}
-
-src_install(){
-	dobin *.py
-	insinto /usr/share/"${PN}"/
-	doins mtx/gcMitVertebrate.mtx
-}
diff --git a/sci-biology/dna2pep/metadata.xml b/sci-biology/dna2pep/metadata.xml
deleted file mode 100644
index 138cb7705..000000000
--- a/sci-biology/dna2pep/metadata.xml
+++ /dev/null
@@ -1,12 +0,0 @@
-<?xml version="1.0" encoding="UTF-8"?>
-<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
-<pkgmetadata>
-	<maintainer type="person">
-		<email>mmokrejs@fold.natur.cuni.cz</email>
-		<name>Martin Mokrejs</name>
-	</maintainer>
-	<maintainer type="project">
-		<email>sci-biology@gentoo.org</email>
-		<name>Gentoo Biology Project</name>
-	</maintainer>
-</pkgmetadata>
diff --git a/sci-biology/drlfom_bidsdata/Manifest b/sci-biology/drlfom_bidsdata/Manifest
new file mode 100644
index 000000000..0f214447d
--- /dev/null
+++ b/sci-biology/drlfom_bidsdata/Manifest
@@ -0,0 +1 @@
+DIST drlfom_bidsdata-1.1.tar.xz 22144796704 BLAKE2B e170247374eb2dc320591675606d49ed5d25547735600f312b3b23bbb6229af8a4e6feceafd2b2eb2a49e7e023e22a549ffa9712d927c7d9fd0d087380c78b8e SHA512 84e574cb6714060292d07cacb6ae84aed051100f966713db6b6ac0dd08d3c01e84da8afde66980eb9b0625e8de2f100444ab84d933d7a280af5a39b4b6eab531
diff --git a/sci-biology/drlfom_bidsdata/drlfom_bidsdata-1.1.ebuild b/sci-biology/drlfom_bidsdata/drlfom_bidsdata-1.1.ebuild
new file mode 100644
index 000000000..8ddd4007e
--- /dev/null
+++ b/sci-biology/drlfom_bidsdata/drlfom_bidsdata-1.1.ebuild
@@ -0,0 +1,29 @@
+# Copyright 1999-2023 Gentoo Authors
+# Distributed under the terms of the GNU General Public License v2
+
+EAPI=8
+
+inherit check-reqs
+
+DESCRIPTION="BIDS data files released with the DRLFOM publication"
+HOMEPAGE="https://chymera.eu/docs/focus/open-science/"
+SRC_URI="
+	https://zenodo.org/record/3598424/files/${P}.tar.xz
+"
+
+LICENSE="CC-BY-SA-4.0"
+SLOT="0"
+KEYWORDS="~amd64 ~x86 ~amd64-linux ~x86-linux"
+
+pkg_pretend() {
+	CHECKREQS_DISK_BUILD="21G"
+	check-reqs_pkg_pretend
+}
+
+# We disable this phase to not check requirements twice.
+pkg_setup() { :; }
+
+src_install() {
+	insinto "/usr/share/${PN}"
+	doins -r *
+}
diff --git a/sci-biology/drlfom_bidsdata/metadata.xml b/sci-biology/drlfom_bidsdata/metadata.xml
new file mode 100644
index 000000000..0275ce906
--- /dev/null
+++ b/sci-biology/drlfom_bidsdata/metadata.xml
@@ -0,0 +1,18 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
+<pkgmetadata>
+	<maintainer type="person">
+		<email>gentoo@chymera.eu</email>
+		<name>Horea Christian</name>
+	</maintainer>
+	<maintainer type="project">
+		<email>sci@gentoo.org</email>
+		<name>Gentoo Science Project</name>
+	</maintainer>
+	<longdescription lang="en">
+		BIDS-formatted MRI data recorded at the ETH/UZH Animal Imaging Center
+		and first associated with the DRLFOM publication. The data represents
+		optp-fMRI mouse brain scans with CBV contrast, tracking serotonergic
+		stimulation over the course of a fluoxetine drinking water treatment.
+	</longdescription>
+</pkgmetadata>
diff --git a/sci-biology/ePCR/Manifest b/sci-biology/ePCR/Manifest
deleted file mode 100644
index ff5ec5aa1..000000000
--- a/sci-biology/ePCR/Manifest
+++ /dev/null
@@ -1 +0,0 @@
-DIST e-PCR-2.3.12-src.tar.gz 76391 BLAKE2B b35be1614b5be3903850405b9abbadb6582f878cd1d87c1fc27853db1e3dee431035a9a76bab5352f6e5e32de4ff1183f8e95f20f1605b4d057c2f374cfb65d4 SHA512 d943b4f1f7173d517c09a98aa61649864b74362741192b52cbe9bbc40d12a7318bb9ce3753f99231cf953d8838c076378af187b4eb2404707669457709b5a412
diff --git a/sci-biology/ePCR/ePCR-2.3.12.ebuild b/sci-biology/ePCR/ePCR-2.3.12.ebuild
deleted file mode 100644
index ab91444bb..000000000
--- a/sci-biology/ePCR/ePCR-2.3.12.ebuild
+++ /dev/null
@@ -1,33 +0,0 @@
-# Copyright 1999-2015 Gentoo Foundation
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=5
-
-inherit eutils
-
-DESCRIPTION="Search for sub-sequences matching PCR primers"
-HOMEPAGE="http://www.ncbi.nlm.nih.gov/tools/epcr/"
-SRC_URI="ftp://ftp.ncbi.nlm.nih.gov/pub/schuler/e-PCR/e-PCR-"${PV}"-src.tar.gz"
-
-LICENSE="public-domain"
-SLOT="0"
-KEYWORDS=""
-IUSE=""
-
-DEPEND=""
-RDEPEND="${DEPEND}"
-
-S=${WORKDIR}"/e-PCR-"${PV}
-
-src_prepare(){
-	epatch "${FILESDIR}"/config.mk.patch
-}
-
-src_compile(){
-	emake -j1 srcdir="${S}" objdir="${S}"
-}
-
-src_install(){
-	dobin e-PCR famap fahash re-PCR
-	dodoc README.TXT
-}
diff --git a/sci-biology/ePCR/files/config.mk.patch b/sci-biology/ePCR/files/config.mk.patch
deleted file mode 100644
index 1960b43f7..000000000
--- a/sci-biology/ePCR/files/config.mk.patch
+++ /dev/null
@@ -1,18 +0,0 @@
---- stand/config.mk.ori	2012-01-16 17:38:11.000000000 +0100
-+++ stand/config.mk	2012-01-16 17:39:12.000000000 +0100
-@@ -52,11 +52,11 @@
- 
- #########################################################################
- # GNU compiler flags
--CC = gcc
--CXX = g++
--CXXFLAGS = -I$(srcdir) -I$(INCDIR) $(CC_FLAGS) $(PART_CXXFLAGS) \
-+#CC = gcc
-+#CXX = g++
-+CXXFLAGS = -I$(srcdir) -I$(INCDIR) -I`pwd` \
- 	-DDEALLOCATE=0 $(LF64CCFLAGS) $(VERSION_FLAGS) -DSTANDALONE=1
--LDFLAGS = $(LD_FLAGS) $(LF64LDFLAGS) -L$(tgtdir) -L$(LIBDIR) $(PART_LDFLAGS) 
-+LDFLAGS = $(LF64LDFLAGS) -L$(tgtdir) -L$(LIBDIR) 
- #	$(PART_PRELIBS) $(LIBS:%=-l%) $(PART_POSTLIBS)
- 
- LF64CCFLAGS = `getconf LFS_CFLAGS` 
diff --git a/sci-biology/ePCR/metadata.xml b/sci-biology/ePCR/metadata.xml
deleted file mode 100644
index 138cb7705..000000000
--- a/sci-biology/ePCR/metadata.xml
+++ /dev/null
@@ -1,12 +0,0 @@
-<?xml version="1.0" encoding="UTF-8"?>
-<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
-<pkgmetadata>
-	<maintainer type="person">
-		<email>mmokrejs@fold.natur.cuni.cz</email>
-		<name>Martin Mokrejs</name>
-	</maintainer>
-	<maintainer type="project">
-		<email>sci-biology@gentoo.org</email>
-		<name>Gentoo Biology Project</name>
-	</maintainer>
-</pkgmetadata>
diff --git a/sci-biology/edena/edena-3.131028.ebuild b/sci-biology/edena/edena-3.131028.ebuild
index c94db1bb7..c942377f3 100644
--- a/sci-biology/edena/edena-3.131028.ebuild
+++ b/sci-biology/edena/edena-3.131028.ebuild
@@ -1,7 +1,7 @@
-# Copyright 1999-2015 Gentoo Foundation
+# Copyright 1999-2021 Gentoo Authors
 # Distributed under the terms of the GNU General Public License v2
 
-EAPI=5
+EAPI=7
 
 inherit toolchain-funcs
 
@@ -12,19 +12,19 @@ SRC_URI="http://www.genomic.ch/edena/EdenaV"${PV}".tar.gz"
 LICENSE="GPL-3"
 SLOT="0"
 KEYWORDS="~amd64"
-IUSE=""
 
 DEPEND=""
 RDEPEND="${DEPEND}"
 
-S="${WORKDIR}"/EdenaV"${PV}"
+S="${WORKDIR}/EdenaV${PV}"
 
 src_prepare(){
-	sed -e "s@^CCC.*@CCC = $(tc-getCXX)@" -e "s@^CFLAGS.*@CFLAGS = ${CFLAGS} -pthread@" -i src/Makefile || die
+	default
+	sed -e "s@^CCC.*@CCC = $(tc-getCXX)@" -e "s@^CFLAGS.*@CFLAGS = ${CFLAGS} -ansi -pthread@" -i src/Makefile || die
 }
 
 src_compile(){
-	cd src
+	cd src || die
 	default
 }
 
diff --git a/sci-biology/ensembl-tools/Manifest b/sci-biology/ensembl-tools/Manifest
deleted file mode 100644
index c96d69a89..000000000
--- a/sci-biology/ensembl-tools/Manifest
+++ /dev/null
@@ -1 +0,0 @@
-DIST ensembl-tools-86.zip 193004 SHA256 55ce1578e6a927a21997342a07df9e4dbc1eddaf2fc5c99a0e72c04f1029811c SHA512 c897e0062d15b1c3f7e3b9f137c30ba2e65dc9b44da792250f4754c4c5570fe49990d4e206d605578fd9334b898fa9bfafc85c9f81d8f9e3b15b8663706d05c6 WHIRLPOOL 88e42734974422f429e0820c081275f4767ce7ff5622151a2ccd3e9f3dfde2f72a5a23a1d337f0cfb4dd3195db52312694eabe870acfd48b8dca03078db9b8df
diff --git a/sci-biology/ensembl-tools/ensembl-tools-86.ebuild b/sci-biology/ensembl-tools/ensembl-tools-86.ebuild
deleted file mode 100644
index 4c838f717..000000000
--- a/sci-biology/ensembl-tools/ensembl-tools-86.ebuild
+++ /dev/null
@@ -1,59 +0,0 @@
-# Copyright 1999-2016 Gentoo Foundation
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=5
-
-PERL_EXPORT_PHASE_FUNCTIONS=no
-inherit perl-module
-
-DESCRIPTION="Variant Effect Predictor (VEP), AssemblyMapper, IDMapper, RegionReporter tools"
-HOMEPAGE="http://www.ensembl.org/info/docs/tools/vep/script
-	http://www.ensembl.org/info/docs/tools/vep/script/vep_plugins.html"
-SRC_URI="https://github.com/Ensembl/ensembl-tools/archive/release/${PV}.zip -> ${P}.zip"
-
-LICENSE="Apache-2.0"
-SLOT="0"
-KEYWORDS=""
-IUSE=""
-
-DEPEND="dev-perl/File-Copy-Recursive
-	dev-perl/Archive-Extract
-	dev-perl/Bio-DB-HTS
-	dev-perl/Bio-EnsEMBL"
-#DEPEND="dev-perl/Perl-XS
-RDEPEND="${DEPEND}"
-
-S="${WORKDIR}/ensembl-tools-release-${PV}"
-
-src_install(){
-	perl_set_version
-	pushd scripts/variant_effect_predictor || die
-	# BUG1: the INSTALL.pl does not exit upon error with non-zero exit code
-	# BUG2: it complains if ${VENDOR_LIB}/${PN} is not in PERL5LIB
-	# perl INSTALL.pl --AUTO=acf --NO_HTSLIB --PLUGINS all --DESTDIR ${VENDOR_LIB}/${PN} || die
-	newdoc README.txt variant_effect_predictor.txt
-	dobin variant_effect_predictor.pl gtf2vep.pl filter_vep.pl convert_cache.pl
-	insinto /usr/share/"${PN}"/examples
-	doins example_*
-	popd
-	pushd scripts/region_reporter || die
-	dobin *.pl
-	newdoc README.txt region_reporter.txt
-	popd
-	pushd scripts/assembly_converter
-	dobin *.pl
-	doins assemblymapper.in
-	newdoc README.txt assembly_converter.txt
-	popd
-	pushd scripts/id_history_converter
-	dobin *.pl
-	newdoc README.txt id_history_converter.txt
-	doins idmapper.in
-	popd
-}
-
-pkg_postinst(){
-	einfo "Probably you want to download some of the files from ftp://ftp.ensembl.org/pub/release-86/variation/VEP/"
-}
-# TODO The INSTALL.pl fetches https://raw.githubusercontent.com/Ensembl/VEP_plugins/release/86/plugin_config.txt
-# and calls eval on its contents
diff --git a/sci-biology/ensembl-tools/metadata.xml b/sci-biology/ensembl-tools/metadata.xml
deleted file mode 100644
index 7cd2955fb..000000000
--- a/sci-biology/ensembl-tools/metadata.xml
+++ /dev/null
@@ -1,15 +0,0 @@
-<?xml version="1.0" encoding="UTF-8"?>
-<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
-<pkgmetadata>
-	<maintainer type="person">
-		<email>mmokrejs@fold.natur.cuni.cz</email>
-		<name>Martin Mokrejs</name>
-	</maintainer>
-	<maintainer type="project">
-		<email>sci-biology@gentoo.org</email>
-		<name>Gentoo Biology Project</name>
-	</maintainer>
-	<upstream>
-		<remote-id type="github">Ensembl/ensembl-tools</remote-id>
-	</upstream>
-</pkgmetadata>
diff --git a/sci-biology/epga/epga-9999.ebuild b/sci-biology/epga/epga-9999.ebuild
index 53d39a8ee..55b94d351 100644
--- a/sci-biology/epga/epga-9999.ebuild
+++ b/sci-biology/epga/epga-9999.ebuild
@@ -1,17 +1,15 @@
-# Copyright 1999-2015 Gentoo Foundation
+# Copyright 1999-2021 Gentoo Authors
 # Distributed under the terms of the GNU General Public License v2
 
-EAPI=5
-
-[ "$PV" == "9999" ] && inherit git-r3
+EAPI=7
 
 inherit toolchain-funcs
 
 DESCRIPTION="De novo assembler using distribution of reads and insert size"
 HOMEPAGE="https://github.com/bioinfomaticsCSU/EPGA"
 if [ "$PV" == "9999" ]; then
+	 inherit git-r3
 	EGIT_REPO_URI="https://github.com/bioinfomaticsCSU/EPGA.git"
-	KEYWORDS=""
 else
 	SRC_URI=""
 	KEYWORDS=""
diff --git a/sci-biology/erpin/erpin-5.5b.ebuild b/sci-biology/erpin/erpin-5.5b.ebuild
index a4cb3f487..3a471fa10 100644
--- a/sci-biology/erpin/erpin-5.5b.ebuild
+++ b/sci-biology/erpin/erpin-5.5b.ebuild
@@ -1,31 +1,30 @@
-# Copyright 1999-2014 Gentoo Foundation
+# Copyright 1999-2021 Gentoo Authors
 # Distributed under the terms of the GNU General Public License v2
 
-EAPI=5
+EAPI=7
 
 inherit toolchain-funcs
 
 ERPIN_BATCH_V=1.4
 
 DESCRIPTION="Easy RNA Profile IdentificatioN, an RNA motif search program"
-HOMEPAGE="http://tagc.univ-mrs.fr/erpin/"
+HOMEPAGE="http://rna.igmors.u-psud.fr"
 SRC_URI="
 	http://rna.igmors.u-psud.fr/download/Erpin/erpin${PV}.serv.tar.gz
 	http://rna.igmors.u-psud.fr/download/Erpin/ErpinBatch.${ERPIN_BATCH_V}.tar.gz"
 
 LICENSE="all-rights-reserved"
 SLOT="0"
-IUSE=""
 KEYWORDS="~amd64 ~x86"
 
-DEPEND="!sys-cluster/maui" # file collision
-RDEPEND=""
-
 S="${WORKDIR}"
 
+PATCHES=( "${FILESDIR}"/${P}-fno-common.patch )
+
 src_prepare() {
-	rm -f erpin${PV}.serv/{bin,lib}/* || die
-	rm -f ErpinBatch.${ERPIN_BATCH_V}/erpin* || die
+	default
+	rm erpin${PV}.serv/{bin,lib}/* || die
+	rm ErpinBatch.${ERPIN_BATCH_V}/erpin* || die
 	find -name '*.mk' | xargs sed -i \
 		-e 's/strip $@/echo skipping strip $@/' \
 		-e '/CFLAGS =/ d' \
@@ -44,6 +43,6 @@ src_install() {
 	insinto /usr/share/${PN}
 	doins -r erpin${PV}.serv/scripts ErpinBatch.${ERPIN_BATCH_V}
 	exeinto /usr/share/${PN}
-	newexe "${FILESDIR}/erpincommand-${PV}.pl" erpincommand
+	newexe "${FILESDIR}"/erpincommand-${PV}.pl erpincommand
 	dodoc erpin${PV}.serv/doc/doc*.pdf
 }
diff --git a/sci-biology/erpin/files/erpin-5.5b-fno-common.patch b/sci-biology/erpin/files/erpin-5.5b-fno-common.patch
new file mode 100644
index 000000000..bd38aacca
--- /dev/null
+++ b/sci-biology/erpin/files/erpin-5.5b-fno-common.patch
@@ -0,0 +1,55 @@
+--- a/erpin5.5b.serv/include/rnaIV.h
++++ b/erpin5.5b.serv/include/rnaIV.h
+@@ -178,10 +178,10 @@ typedef struct {
+   double  *vals;
+   } Histo;
+ 
+-Histo  MainMaskEvals;             /* histogramme des E-values des detections */
++extern Histo  MainMaskEvals;             /* histogramme des E-values des detections */
+                                                       /* du masque principal */
+-Histo  MainMaskDetects;    /* histogramme des detections du masque principal */
+-Map    MainMaskMap;       /* pour l'etalonnage de l'axe de 'MainMaskDetects' */
++extern Histo  MainMaskDetects;    /* histogramme des detections du masque principal */
++extern Map    MainMaskMap;       /* pour l'etalonnage de l'axe de 'MainMaskDetects' */
+ 
+ /*
+ -------------------------------------------------------------------------------
+--- a/erpin5.5b.serv/libsrc/dhisto.c
++++ b/erpin5.5b.serv/libsrc/dhisto.c
+@@ -36,6 +36,9 @@ void   AddToDetectsHisto(double x);
+ void   PrintHisto(Histo hist, char *filename);
+ Histo  ReadHisto(char *filename);
+ void   PrintScoresHisto(Context *ctxt);
++Histo MainMaskDetects;
++Histo MainMaskEvals;
++Map   MainMaskMap;
+ 
+ /*=============================================================================
+  InitDetectsHisto(): Initialise l'histogramme des detections gerees par 'ctxt'.
+@@ -44,9 +47,6 @@ void   PrintScoresHisto(Context *ctxt);
+ 
+ void InitDetectsHisto(Context *ctxt)
+ {
+-  extern Histo MainMaskDetects;
+-  extern Histo MainMaskEvals;
+-  extern Map   MainMaskMap;
+   
+   MainMaskDetects = SetupHist(ctxt->mask->threshold, MainMaskEvals.hmax,
+                               DELTA_H, 0);
+@@ -63,8 +63,6 @@ void InitDetectsHisto(Context *ctxt)
+ 
+ void AddToDetectsHisto(double x)
+ {
+-  extern Histo MainMaskDetects;
+-  extern Map   MainMaskMap;
+   int index;
+ 
+   if (x > MainMaskDetects.hmin && x < MainMaskDetects.hmax)
+@@ -132,7 +130,6 @@ Histo ReadHisto(char *filename)
+ 
+ void PrintScoresHisto(Context *ctxt)
+ {
+-  extern Histo MainMaskDetects;
+ 
+   if (ctxt->hist == ON)
+   {
diff --git a/sci-biology/est2assembly/Manifest b/sci-biology/est2assembly/Manifest
deleted file mode 100644
index 4c5a29069..000000000
--- a/sci-biology/est2assembly/Manifest
+++ /dev/null
@@ -1 +0,0 @@
-DIST est2assembly_1.08.tar.gz 5643052 BLAKE2B f5e289955d70d8031f30eb13df3fe86376d5de2f907761e2cf3a4b25a7337040c3a1cbe219988001553f2a9b066132a876e7cc9cb08b255ef760d36aef78054b SHA512 f58fd56df45bb9bffeec7d58a3a7b0b6ada6e52807d53f0d9bf36ae6f5e2fba19b0387c62f9f3712582b0e164f1360d08ad199e69b52d44d94e8226c56a592ac
diff --git a/sci-biology/est2assembly/est2assembly-1.08.ebuild b/sci-biology/est2assembly/est2assembly-1.08.ebuild
deleted file mode 100644
index a481a425c..000000000
--- a/sci-biology/est2assembly/est2assembly-1.08.ebuild
+++ /dev/null
@@ -1,27 +0,0 @@
-# Copyright 1999-2015 Gentoo Foundation
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=5
-
-DESCRIPTION="EST assembly and annotation pipeline for chado/gbrowse2 display"
-HOMEPAGE="http://code.google.com/p/est2assembly/"
-SRC_URI="http://est2assembly.googlecode.com/files/est2assembly_${PV}.tar.gz"
-
-LICENSE="GPL-3"
-SLOT="0"
-KEYWORDS="~amd64 ~x86"
-IUSE=""
-
-DEPEND="
-	app-arch/pbzip2
-	app-portage/g-cpan
-	dev-lang/perl
-	dev-perl/Time-Progress
-	sci-biology/fasta
-	sci-biology/ssaha2-bin
-	sci-biology/mira
-	sci-biology/emboss
-	sci-biology/bioperl"
-RDEPEND="${DEPEND}"
-
-S="${WORKDIR}"/"${PN}"
diff --git a/sci-biology/est2assembly/est2assembly-9999.ebuild b/sci-biology/est2assembly/est2assembly-9999.ebuild
deleted file mode 100644
index 5e71408a3..000000000
--- a/sci-biology/est2assembly/est2assembly-9999.ebuild
+++ /dev/null
@@ -1,47 +0,0 @@
-# Copyright 1999-2015 Gentoo Foundation
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=5
-
-PYTHON_COMPAT=( python2_7 )
-
-inherit eutils distutils-r1
-
-[ "$PV" == "9999" ] && inherit subversion
-
-DESCRIPTION="EST assembly and annotation pipeline for chado/gbrowse2 display"
-HOMEPAGE="http://code.google.com/p/est2assembly/"
-ESVN_REPO_URI="http://est2assembly.googlecode.com/svn/trunk"
-
-if [ "$PV" == "9999" ]; then
-	ESVN_REPO_URI="http://est2assembly.googlecode.com/svn/trunk"
-	KEYWORDS=""
-else
-	SRC_URI="http://est2assembly.googlecode.com/files/est2assembly_"${PV}".tar.gz"
-	KEYWORDS="~amd64 ~x86"
-fi
-
-LICENSE="GPL-3"
-SLOT="0"
-IUSE=""
-
-# still missing
-# annot8r  http://nematodes.org/bioinformatics/annot8r/index.shtml and http://nematodes.org/bioinformatics/Annot8r_physprop/
-# prot4EST http://nematodes.org/bioinformatics/prot4EST/
-
-DEPEND="
-	app-arch/pbzip2
-	dev-lang/perl
-	dev-perl/Time-Progress
-	sci-biology/fasta
-	sci-biology/ssaha2-bin
-	sci-biology/mira
-	sci-biology/emboss
-	sci-biology/bioperl"
-RDEPEND="${DEPEND}"
-
-# more install tricks in "${S}"/install.pl
-
-pkg_postinst(){
-	einfo "The package uses mira and newbler assemblers"
-}
diff --git a/sci-biology/est2assembly/metadata.xml b/sci-biology/est2assembly/metadata.xml
deleted file mode 100644
index 138cb7705..000000000
--- a/sci-biology/est2assembly/metadata.xml
+++ /dev/null
@@ -1,12 +0,0 @@
-<?xml version="1.0" encoding="UTF-8"?>
-<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
-<pkgmetadata>
-	<maintainer type="person">
-		<email>mmokrejs@fold.natur.cuni.cz</email>
-		<name>Martin Mokrejs</name>
-	</maintainer>
-	<maintainer type="project">
-		<email>sci-biology@gentoo.org</email>
-		<name>Gentoo Biology Project</name>
-	</maintainer>
-</pkgmetadata>
diff --git a/sci-biology/estscan/Manifest b/sci-biology/estscan/Manifest
deleted file mode 100644
index 79281bc74..000000000
--- a/sci-biology/estscan/Manifest
+++ /dev/null
@@ -1,9 +0,0 @@
-DIST At.smat.gz 32314 BLAKE2B c48c043fa7e7e26e406a677587380e0ade911aafb5878988668da9b9f09a978a369e636c931d2d4d65b6efc65398723e1a78c032805cfc71f2927a42d87788c4 SHA512 aeb3dec65b730570d70e8f49930bf85cc73fe39696d2ccc08e6a804cfe435ea43423f1f4a02b192c68da03727b628bb43ec0ba27bb4549e59f743eccd203df09
-DIST BTLib-0.19.tar.gz 36283 BLAKE2B 53d26fdc7fee3325104a7f2041617bbde464421c540b29c7d47381c60d8f837601e7274d9f0ef5694d1b86b3e2cc7e9a0b289090c3c957a343542e3e7305cd50 SHA512 00261daa7fab4d16dec9e9d4f9e382cc804a10c0ed6b813d6223902b53f6b260dc0a242acfab93897afa750e949ab3f21ecae537206d81eb712f06289387f7d2
-DIST Dm.smat.gz 31711 BLAKE2B 5e8da0668d0788ce2e70535605cb85ced4ec052c4e736b11d838919c0328c6978170aed8e6102d62c6f8770a99a7f49aad373492ddc79328df3238486b7ee703 SHA512 fe141598291fd1bead1f0918c2e52533db1f5c5f60d4c71838a16298ccf60a8a1857a02379f58979dbab3cfad4e0ac64556cf629fcb65d9a0e6861fe4ca163a4
-DIST Dr.smat.gz 8813 BLAKE2B 465d980cc9c1d61f8a83e4c3dd203852b2cfa4bde5730de268655d7a05db9d018f6cff6357246bbfc42002f3993aebf44c9fc27c2d31fa6657194600e5a364b0 SHA512 1880981db252ed08a762fdc8a321b27063ea2341cde56c40146cc7eeed0fdfa620e9b4c71c245fffee6521ae1efbc89b52e6558cd84aef89138e8b26b60460de
-DIST Hs.smat.gz 62935 BLAKE2B 4089dbcc54af5544071d9fc270a9048c758fef15e4846f92dc9c61abd5c60ba9d8ba4a25b9064f4d418cbe1a8a277c5bba49af9a85f51dd9f3bcaac30a7b568d SHA512 7ac3af9b018992014643fbbd83abc4128df4c8b9c516fb1b6b16e1fdc65b23df07811fa5b23ecec5ef2993de71e3efaec5bee3fc1626bcf2984794f13e343447
-DIST Mm.smat.gz 62711 BLAKE2B c65aeb6f8833e4effb360de29e3c25985184e4a9822272f370fc292ec2142843b78ac66485ec98b017aac3a18b7936fc45b510f58cb2db909d5230291573bdf3 SHA512 4ee5fac326bee7e4fe17ad9eab608a90007485a90b479557a181eb49628ff5fee22d04a3ef360b6bc29a76709723faa0a9df8ef1cdb40421d772a0b2dc9f3fc5
-DIST Rn.smat.gz 32388 BLAKE2B 06144cce26cd35eeb15d94db5f169a9cf6c6ab02b4c4f213e42140b2fe864473e7c107c910092620f255384eadd1e07a366e58a21d3df570e63e2843e537aaa3 SHA512 e517d95aa4d1928f766ac9cc885f277d9f980d27265dcc7a2c5d747b1023a5606bccb2dbce2fa9ff76fc0f0333fadd3bc0b7abe9ea4aa82396b57bb06b8dcf43
-DIST estscan-3.0.3.tar.gz 46412 BLAKE2B 998f4f117503e044492495d52e5b064fcb62c3800adb4ec4b357042ea90d8c6ce86902257e5b28ee119c2b332044389c8775101bad6875cba069db6961f73931 SHA512 d3ddb91a71a700a67807a63f7b9c9e2a1c45af847a7808afd757f60f276f7410e22adde6e0ffadbfef8e579890b79fe785b8a05e28cb3d67345464cd2035f69c
-DIST user_guide_fev_07.pdf 327005 BLAKE2B 5d66466c122c12618c5aadb2f12a404159b553b57e80fa421d707d8c3e70d795da7285a6976beacd67b7c6462297fde7843b89b48ed773752cdc0e00bfd1c36c SHA512 de1f046656c3e01a9b3e3930aadc7a91cb10d907a9d6af8fc1c2b0abe6ef0d1305baaeee463c80df0c700951a03b1c26a211fdd14e76fbf41ac5fca3467e49c1
diff --git a/sci-biology/estscan/estscan-3.0.3.ebuild b/sci-biology/estscan/estscan-3.0.3.ebuild
deleted file mode 100644
index e933c59b8..000000000
--- a/sci-biology/estscan/estscan-3.0.3.ebuild
+++ /dev/null
@@ -1,123 +0,0 @@
-# Copyright 1999-2014 Gentoo Foundation
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=5
-
-inherit eutils fortran-2 perl-module toolchain-funcs
-
-DESCRIPTION="Prediction of coding regions in DNA/RNA sequences"
-HOMEPAGE="http://sourceforge.net/projects/${PN}/"
-SRC_URI="
-	http://downloads.sourceforge.net/${PN}/${P}.tar.gz
-	http://downloads.sourceforge.net/${PN}/At.smat.gz
-	http://downloads.sourceforge.net/${PN}/Dm.smat.gz
-	http://downloads.sourceforge.net/${PN}/Dr.smat.gz
-	http://downloads.sourceforge.net/${PN}/Hs.smat.gz
-	http://downloads.sourceforge.net/${PN}/Mm.smat.gz
-	http://downloads.sourceforge.net/${PN}/Rn.smat.gz
-	http://downloads.sourceforge.net/${PN}/user_guide_fev_07.pdf
-	http://downloads.sourceforge.net/${PN}/BTLib-0.19.tar.gz"
-
-SLOT="0"
-LICENSE="estscan"
-KEYWORDS="~amd64 ~x86"
-IUSE="icc ifc"
-
-DEPEND="
-	dev-perl/BTLib
-	icc? ( dev-lang/icc )
-	ifc? ( dev-lang/ifc )"
-RDEPEND="${DEPEND}"
-
-S="${WORKDIR}"
-
-src_prepare() {
-	sed \
-		-e 's/\\rm -f/rm -rf/' \
-		-e 's/^ LDFLAGS = -lm/LDFLAGS = -lm/' \
-		-i "${P}"/Makefile || die "failed to edit Makefile"
-
-	# fix hard-coded paths
-	sed -e 's+/usr/molbio/share/ESTScan+/usr/share/ESTscan+' -i "${P}"/${PN}.c || die
-	sed -e 's+/usr/molbio/share/ESTScan+/usr/share/ESTscan+' -i "${P}"/${PN}.spec || die
-
-	if ! use icc; then
-		sed \
-			-e 's/^ CFLAGS = -O2/#CFLAGS = ${CFLAGS}/' -i "${P}"/Makefile || die
-	fi
-
-	if ! use ifc; then
-		sed \
-			-e 's/^ FFLAGS = -O2/#FFLAGS = ${FFLAGS}/' \
-			-e "s/^ F77 = g77/F77 = $(tc-getF77)/" -i "${P}"/Makefile \
-			|| die
-	fi
-
-	if use icc; then
-		# FIXME: I would use $(tc-getCC) instead of hard-coded icc but it gives
-		# me gcc instead, same for $(tc-getF77)
-		# Moreover, the if/else logic here should separate users having only icc
-		# while not ifort (and vice-versa) from those having only
-		# gcc/gfortran/g77
-		#
-		# FIXME: below as a dirty hack I force gfortran instead of ifort for
-		# my testing purposes. Didn't ebuild contain "PROVIDES" line?
-		# Same for FFLAGS.
-		sed \
-			-e "s:^# CC = icc:CC = icc:" \
-			-e "s:^# CFLAGS = -O3 -ipo -axP:#CFLAGS = -O3 -ipo -axP:" \
-			-e "s/^ CFLAGS = -O2/#CFLAGS = -O2/" \
-			-e "s/^ CC = gcc/# CC = gcc/" \
-			-i "${P}"/Makefile || die "sed failed to fix CFLAGS and CC"
-
-	fi
-
-	if use ifc; then
-		sed \
-			-e "s:^# FFLAGS = -O3 -ipo -axP:#FFLAGS = -O3 -ipo -axP:" \
-			-e "s/^# F77 = ifort/F77 = gfortran/" \
-			-e "s/^ FFLAGS = -O2/#FFLAGS = -O2/" \
-			-e "s/^ F77 = g77/# F77 = g77/" \
-			-i "${P}"/Makefile || die "sed failed to fix FFLAGS and F77"
-	fi
-}
-
-src_compile() {
-	emake -C ${P}
-}
-
-src_install() {
-	# FIXME: Some kind of documentation is in {P}/${PN}.spec
-	cd ${P} || die "Failed to chdir to ${P}"
-	dobin \
-		build_model ${PN} evaluate_model extract_EST extract_UG_EST \
-		extract_mRNA makesmat maskred prepare_data winsegshuffle
-	# the file build_model_utils.pl should go into some PERL site-packages dir
-	# see {P}/${PN}.spec
-
-	# install the doc (but is not in ${WORKDIR} because src_unpack() failed on it as it has .pdf extension
-	insinto /usr/share/doc/${PN}
-	# grab the file directly from ../distdir/
-	doins "${DISTDIR}"/user_guide_fev_07.pdf
-
-	# install the default precomputed matrices
-	cd "${WORKDIR}" || die "Failed to chdir to ${WORKDIR}"
-	insinto /usr/share/${PN}
-	doins *.smat
-
-	# install BTlib (in perl)
-	# dobin fetch indexer netfetch
-	insinto /usr/share/${PN}/
-	# install the config file which is packed inside the BTLib tarball while is not
-	# being installed by dev-perl/BTLib
-	doins "${WORKDIR}"/BTLib-0.19/fetch.conf
-
-	# FIXME: install the *.pm files from BTLib-0.19
-	# cd "${WORKDIR}"/BTLib-0.19 || die "Failed to chdir to "${WORKDIR}"/BTLib-0.19
-	# myinst="DESTDIR=${D}"
-	# perl-module_src_install
-
-	einfo "Please edit /usr/share/${PN}/fetch.conf to fit your local database layout."
-	einfo "Also create your own scoring matrices and place them into /usr/share/${PN}/."
-	einfo "You may follow the hints from http://${PN}.sourceforge.net/"
-}
diff --git a/sci-biology/estscan/metadata.xml b/sci-biology/estscan/metadata.xml
deleted file mode 100644
index c79c2d1b5..000000000
--- a/sci-biology/estscan/metadata.xml
+++ /dev/null
@@ -1,19 +0,0 @@
-<?xml version="1.0" encoding="UTF-8"?>
-<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
-<pkgmetadata>
-	<maintainer type="person">
-		<email>mmokrejs@fold.natur.cuni.cz</email>
-		<name>Martin Mokrejs</name>
-	</maintainer>
-	<maintainer type="project">
-		<email>sci-biology@gentoo.org</email>
-		<name>Gentoo Biology Project</name>
-	</maintainer>
-	<use>
-		<flag name="icc">Undocumented USE</flag>
-		<flag name="ifc">Undocumented USE</flag>
-	</use>
-	<upstream>
-		<remote-id type="sourceforge">downloads</remote-id>
-	</upstream>
-</pkgmetadata>
diff --git a/sci-biology/eugene/Manifest b/sci-biology/eugene/Manifest
deleted file mode 100644
index da51818cd..000000000
--- a/sci-biology/eugene/Manifest
+++ /dev/null
@@ -1 +0,0 @@
-DIST eugene-4.1d.tar.gz 7473965 BLAKE2B 537ba871b701a5c199791809f76ea883ff77fe768e27a69b95186ef82ab32cab9b5761405a9fadfeea9f58fe88cadce83bba4b1fa6cba5f4ede2347a516d1df0 SHA512 dab37930e211b3783954f6e4a762450760201b77e0b4214f16724516d9be583d0a7ec44a2f510e73f4370e9c2dc67a425456a057fdba8f51cb72386e16a26ef5
diff --git a/sci-biology/eugene/eugene-4.1d.ebuild b/sci-biology/eugene/eugene-4.1d.ebuild
deleted file mode 100644
index e90ec89b4..000000000
--- a/sci-biology/eugene/eugene-4.1d.ebuild
+++ /dev/null
@@ -1,36 +0,0 @@
-# Copyright 1999-2015 Gentoo Foundation
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=5
-
-inherit autotools eutils
-
-DESCRIPTION="Prokaryotic and Eukaryotic gene predictor"
-HOMEPAGE="http://www.inra.fr/mia/T/EuGene/"
-SRC_URI="https://mulcyber.toulouse.inra.fr/frs/download.php/1359/${P}.tar.gz"
-
-LICENSE="Artistic"
-SLOT="0"
-KEYWORDS="~amd64 ~x86"
-IUSE=""
-
-DEPEND="
-	media-libs/gd[png]
-	media-libs/libpng:0=
-	"
-RDEPEND="${DEPEND}"
-
-RESTRICT="test"
-
-src_prepare() {
-	# https://mulcyber.toulouse.inra.fr/tracker/index.php?func=detail&aid=1170
-	epatch \
-		"${FILESDIR}"/${PN}-3.6-overflow.patch \
-		"${FILESDIR}"/${PN}-3.6-plugins.patch \
-		"${FILESDIR}"/${PN}-4.1-format-security.patch
-	sed \
-		-e '/SUBDIRS/ s/doc//' \
-		-e '/INSTALL.*doc/ s/\(.*\)//' \
-		-i Makefile.am || die
-	eautoreconf
-}
diff --git a/sci-biology/eugene/files/eugene-3.6-overflow.patch b/sci-biology/eugene/files/eugene-3.6-overflow.patch
deleted file mode 100644
index 7222530ad..000000000
--- a/sci-biology/eugene/files/eugene-3.6-overflow.patch
+++ /dev/null
@@ -1,13 +0,0 @@
-http://bugs.gentoo.org/show_bug.cgi?id=336607
-
---- eugene-3.6/src/Sensor.cc
-+++ eugene-3.6/src/Sensor.cc
-@@ -224,7 +224,7 @@
- //--------------------------
- void Signals :: PrintS ()
- {
--  char t[7];
-+  char t[10];
-   char s = '+';
- 
-   switch (type) {
diff --git a/sci-biology/eugene/files/eugene-3.6-plugins.patch b/sci-biology/eugene/files/eugene-3.6-plugins.patch
deleted file mode 100644
index 1e910a13d..000000000
--- a/sci-biology/eugene/files/eugene-3.6-plugins.patch
+++ /dev/null
@@ -1,43 +0,0 @@
-http://bugs.gentoo.org/show_bug.cgi?id=297536
-
---- eugene-3.6/src/Makefile.am
-+++ eugene-3.6/src/Makefile.am
-@@ -20,7 +20,7 @@
- 
- SUBDIRS = Parametrization GDIF . SensorPlugins
- 
--AM_CXXFLAGS = $(eugene_cxxflags) -DDEFAULT_EUGENE_DIR=\"${pkgdatadir}\"
-+AM_CXXFLAGS = $(eugene_cxxflags) -DDEFAULT_EUGENE_DIR=\"${pkgdatadir}\" -DLIB_DIR=\"${libdir}\"
- AM_CFLAGS = 
- 
- bin_PROGRAMS = eugene
---- eugene-3.6/src/MSensor.cc
-+++ eugene-3.6/src/MSensor.cc
-@@ -97,7 +97,7 @@
-   std::string use_name;
- 
-   if (!IsInitialized) {
--    PluginsDir = (std::string)PAR.getC("eugene_dir")+"/"+PLUGINS_DIR+"/";
-+    PluginsDir = (std::string)LIB_DIR+"/eugene/"+PLUGINS_DIR+"/";
- 
-     // On récupère les couples nom de sensor/priorité du .par
-     PAR.ResetIter();
---- eugene-3.6/Makefile.am
-+++ eugene-3.6/Makefile.am
-@@ -125,7 +125,7 @@
- 	$(INSTALL) -d $(DESTDIR)/$(pkgdatadir)/web/Style
- 	$(INSTALL) -d $(DESTDIR)/$(pkgdatadir)/web/Javascripts
- 	$(INSTALL) -d $(DESTDIR)/$(pkgdatadir)/web/Images
--	$(INSTALL) -d $(DESTDIR)/$(pkgdatadir)/plugins
-+	$(INSTALL) -d $(DESTDIR)/$(libdir)/eugene/plugins
- 	$(INSTALL) -d $(DESTDIR)/$(pkgdatadir)/cfg
- 	$(INSTALL) -d $(DESTDIR)/$(pkgdatadir)/models
- 	$(INSTALL) -d $(DESTDIR)/$(pkgdatadir)/models/WAM
-@@ -144,6 +144,6 @@
- 	$(INSTALL) -m 644 $(srcdir)/web/Images/*jpg $(DESTDIR)/$(pkgdatadir)/web/Images
- 	$(INSTALL) -m 644 $(srcdir)/cfg/*.obo $(DESTDIR)/$(pkgdatadir)/cfg
- 	$(INSTALL) -m 644 $(srcdir)/cfg/*.par $(DESTDIR)/$(pkgdatadir)/cfg
--	$(INSTALL) src/SensorPlugins/*/*.so  $(DESTDIR)/$(pkgdatadir)/plugins
-+	$(INSTALL) src/SensorPlugins/*/*.so  $(DESTDIR)/$(libdir)/eugene/plugins
- 	$(INSTALL) $(srcdir)/Procedures/Eval/egn_* $(DESTDIR)/$(pkgdatadir)/Procedures/Eval
- 	$(INSTALL) $(srcdir)/Procedures/Get/egn_* $(DESTDIR)/$(pkgdatadir)/Procedures/Get
diff --git a/sci-biology/eugene/files/eugene-4.1-format-security.patch b/sci-biology/eugene/files/eugene-4.1-format-security.patch
deleted file mode 100644
index e6e4a6cc8..000000000
--- a/sci-biology/eugene/files/eugene-4.1-format-security.patch
+++ /dev/null
@@ -1,16 +0,0 @@
- src/Hits.cc | 2 +-
- 1 file changed, 1 insertion(+), 1 deletion(-)
-
-diff --git a/src/Hits.cc b/src/Hits.cc
-index edfe178..b228be6 100755
---- a/src/Hits.cc
-+++ b/src/Hits.cc
-@@ -166,7 +166,7 @@ Hits* Hits::ReadFromFile(FILE* HitFile, int *NumHits, int level, int margin, int
-     while ((read=fscanf(HitFile,"%d %d %d %lf %d %s %d %d %as\n", &deb, &fin,
-                         &poids, &evalue, &phase, HitId, &HSPDeb, &HSPFin,HSP)) >= 8)
-     {
--        if (HSP) fprintf(stderr,HSP);
-+        if (HSP) fprintf(stderr, "%s", HSP);
-         if (phase < 0  &&  deb > fin)
-         {
-             int tmp = deb;
diff --git a/sci-biology/eugene/metadata.xml b/sci-biology/eugene/metadata.xml
deleted file mode 100644
index 138cb7705..000000000
--- a/sci-biology/eugene/metadata.xml
+++ /dev/null
@@ -1,12 +0,0 @@
-<?xml version="1.0" encoding="UTF-8"?>
-<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
-<pkgmetadata>
-	<maintainer type="person">
-		<email>mmokrejs@fold.natur.cuni.cz</email>
-		<name>Martin Mokrejs</name>
-	</maintainer>
-	<maintainer type="project">
-		<email>sci-biology@gentoo.org</email>
-		<name>Gentoo Biology Project</name>
-	</maintainer>
-</pkgmetadata>
diff --git a/sci-biology/eval/Manifest b/sci-biology/eval/Manifest
deleted file mode 100644
index f8c424235..000000000
--- a/sci-biology/eval/Manifest
+++ /dev/null
@@ -1,2 +0,0 @@
-DIST eval-2.2.8.tar.gz 592357 BLAKE2B 1163122ac297505a9fd2dee081e899d419d7449380abc77f9ed0b47609d05184114dc7b4105f6af73537d0a70ec5e5efdb0c496f192f177b71ef209332c5e86b SHA512 ec9f72fa8cc1bb22544bf07964261fe0078cdfe204b0e6b262a648cb078fe31521286f106d7cb22f30ff7280c332d4a349b8689b361384f19342739795f8e76b
-DIST eval-documentation.pdf 548237 BLAKE2B 2332dfb9453c0c705d88804f48a724ab7009684633e9bf619596f17eee0254a41342162c82476c1bbe448083e3aa339f0e31f21ee60bbba90bc7a70ffc56f428 SHA512 b97ca2519b04e9f1222125d13593518cdf7a22c7660ca42ca8a539378526a82c409a3cb066a53ddd93c4501dd7c33242a868ee0fc184978df807bbd743475d2b
diff --git a/sci-biology/eval/eval-2.2.8.ebuild b/sci-biology/eval/eval-2.2.8.ebuild
deleted file mode 100644
index 074f39707..000000000
--- a/sci-biology/eval/eval-2.2.8.ebuild
+++ /dev/null
@@ -1,48 +0,0 @@
-# Copyright 1999-2017 Gentoo Foundation
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=5
-
-PYTHON_COMPAT=( python2_7 )
-PERL_EXPORT_PHASE_FUNCTIONS=no
-inherit perl-module eutils python-r1 toolchain-funcs
-
-DESCRIPTION="Validate, compare and draw summary statistics for GTF files"
-HOMEPAGE="http://mblab.wustl.edu/software.html"
-SRC_URI="
-	http://mblab.wustl.edu/software/download/${PN}-${PV}.tar.gz
-	http://mblab.wustl.edu/software/download/eval-documentation.pdf"
-
-LICENSE="GPL-2+"
-SLOT="0"
-KEYWORDS="~amd64"
-IUSE=""
-
-REQUIRED_USE="${PYTHON_REQUIRED_USE}"
-
-DEPEND="${PYTHON_DEPS}
-	dev-lang/tk:0=
-	sci-biology/vcftools
-	sci-visualization/gnuplot"
-RDEPEND="${DEPEND}"
-
-src_install(){
-	dobin *.pl
-	# TODO: prepend shebang lines to *.py files
-	# https://bugs.gentoo.org/show_bug.cgi?id=602580
-	sed -i -e "1i #!/usr/bin/env python" RangeFinder.py || die
-	python_foreach_impl python_doscript *.py
-	dodoc \
-		"${DISTDIR}"/eval-documentation.pdf \
-		help/*.ps
-	insinto /usr/share/${PN}
-	doins *.gtf
-	perl_set_version
-	insinto ${VENDOR_LIB}
-	doins *.pm
-}
-
-pkg_postinst(){
-	ewarn "The version of validate_gtf.pl bundled with eval differs a bit from"
-	ewarn "validate_gtf-1.0.pl from http://mblab.wustl.edu/software.html#validategtf"
-}
diff --git a/sci-biology/eval/metadata.xml b/sci-biology/eval/metadata.xml
deleted file mode 100644
index 138cb7705..000000000
--- a/sci-biology/eval/metadata.xml
+++ /dev/null
@@ -1,12 +0,0 @@
-<?xml version="1.0" encoding="UTF-8"?>
-<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
-<pkgmetadata>
-	<maintainer type="person">
-		<email>mmokrejs@fold.natur.cuni.cz</email>
-		<name>Martin Mokrejs</name>
-	</maintainer>
-	<maintainer type="project">
-		<email>sci-biology@gentoo.org</email>
-		<name>Gentoo Biology Project</name>
-	</maintainer>
-</pkgmetadata>
diff --git a/sci-biology/exomiser-bin/Manifest b/sci-biology/exomiser-bin/Manifest
deleted file mode 100644
index 67ae9e248..000000000
--- a/sci-biology/exomiser-bin/Manifest
+++ /dev/null
@@ -1,3 +0,0 @@
-DIST exomiser-bin.README 1445 SHA256 bf9b6ad3a0cd56fbe9d8155b5d671c1ce31b70742eef116a6158af4c9cebc488 SHA512 db27fbe1d7550ddde090b96928ff9c01049e2dbdee3927c73fff6810f5c5d921738866bf11424fddc14b5c955d79f7e9e6c6899191dc53e58d221388259800f8 WHIRLPOOL e0dff092281e5fae36c96f2af01d40e0a614acc4f638e80db2471743b0a61cff8629fa611a54271ba56db347ea416b6183a746294e29d7eb1f55db747f57942f
-DIST exomiser-bin.README.md 9604 SHA256 262565653c4c4ede6872b6f2b174266ef39f05b4ef72048028f939a7df0050d6 SHA512 e6f9eb9114ef875e6e471eda1cb9118d725bd9ec4c1fbcc2cd0ee63069768816a98a4de03529f10f865837c8b9efe4e4c525b5e2471e44440f355a814bb82891 WHIRLPOOL 0ada5a7663fb98bdf778aa0c85f2b4d70eb0250934556d3001c0545776c4e23a74400688205042b60a8c5c0d965f6f15159279a262949ce2c3e355d67719eec4
-DIST exomiser-cli-7.2.1-distribution.zip 51146162 SHA256 4a89fcfe7ce80fe057b4db1cbb07e9fadc8f05d57bd3e95756b4d6e2a3b9148e SHA512 1d523e6e8de4b03f1271ff9eb29397f43829e0930934447a77339d5934836a27aeee5c74aeb5e0c9c7acb98e7db07eecd8abb8b163bd845b69e015c784c8ba86 WHIRLPOOL b6031d0887125ed4d257ec855ae074610b6d362f24a88f4b8157282c3a90db9c28913091a2bf2482e304cef1443871321d2b2a2d6ebb818c26a33ff7a1645816
diff --git a/sci-biology/exomiser-bin/exomiser-bin-7.2.1.ebuild b/sci-biology/exomiser-bin/exomiser-bin-7.2.1.ebuild
deleted file mode 100644
index 87434fa8a..000000000
--- a/sci-biology/exomiser-bin/exomiser-bin-7.2.1.ebuild
+++ /dev/null
@@ -1,30 +0,0 @@
-# Copyright 1999-2016 Gentoo Foundation
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=5
-
-DESCRIPTION="Annotate VCF files and prioritize genome/exome mutations"
-HOMEPAGE="http://www.sanger.ac.uk/science/tools/exomiser"
-SRC_URI="ftp://ftp.sanger.ac.uk/pub/resources/software/exomiser/downloads/exomiser/exomiser-cli-${PV}-distribution.zip
-	ftp://ftp.sanger.ac.uk/pub/resources/software/exomiser/downloads/exomiser/GenomiserREADME -> ${PN}.README
-	ftp://ftp.sanger.ac.uk/pub/resources/software/exomiser/downloads/exomiser/README.md -> ${PN}.README.md"
-# 1.16GB !
-
-LICENSE="AGPL-3+"
-SLOT="0"
-KEYWORDS=""
-IUSE=""
-
-DEPEND="sci-biology/Jannovar-bin"
-RDEPEND="${DEPEND}"
-
-src_install(){
-	dodoc "${DISTDIR}"/${PN}.README "${DISTDIR}"/${PN}.README.md
-}
-
-pkg_postinst(){
-	einfo "Please download 3.7GB file from ftp://ftp.sanger.ac.uk/pub/resources/software/exomiser/downloads/exomiser/h2_db_dumps/exomiser-${PV}.BETA.h2.db.gz"
-	einfo "and follow README.md"
-	einfo "The is also 19GB file ftp://ftp.sanger.ac.uk/pub/resources/software/exomiser/downloads/exomiser/exomiser-cli-7.2.1-data.zip"
-	einfo "with test data"
-}
diff --git a/sci-biology/exomiser-bin/metadata.xml b/sci-biology/exomiser-bin/metadata.xml
deleted file mode 100644
index 138cb7705..000000000
--- a/sci-biology/exomiser-bin/metadata.xml
+++ /dev/null
@@ -1,12 +0,0 @@
-<?xml version="1.0" encoding="UTF-8"?>
-<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
-<pkgmetadata>
-	<maintainer type="person">
-		<email>mmokrejs@fold.natur.cuni.cz</email>
-		<name>Martin Mokrejs</name>
-	</maintainer>
-	<maintainer type="project">
-		<email>sci-biology@gentoo.org</email>
-		<name>Gentoo Biology Project</name>
-	</maintainer>
-</pkgmetadata>
diff --git a/sci-biology/exonerate-gff3/exonerate-gff3-9999.ebuild b/sci-biology/exonerate-gff3/exonerate-gff3-9999.ebuild
index 5800673ca..8820a11af 100644
--- a/sci-biology/exonerate-gff3/exonerate-gff3-9999.ebuild
+++ b/sci-biology/exonerate-gff3/exonerate-gff3-9999.ebuild
@@ -1,22 +1,20 @@
-# Copyright 1999-2015 Gentoo Foundation
+# Copyright 1999-2021 Gentoo Authors
 # Distributed under the terms of the GNU General Public License v2
 
-EAPI=5
+EAPI=7
 
-AUTOTOOLS_AUTORECONF=true
-
-inherit autotools-utils toolchain-funcs git-r3
+inherit toolchain-funcs git-r3
 
 DESCRIPTION="exonerate-2.2.0 with patches to add GFF3 formatted output"
 HOMEPAGE="https://github.com/hotdogee/exonerate-gff3"
-SRC_URI=""
 EGIT_REPO_URI="https://github.com/hotdogee/exonerate-gff3.git"
 
 LICENSE="GPL-3"
 SLOT="0"
 KEYWORDS=""
-IUSE="utils test threads"
 
+IUSE="utils test threads"
+RESTRICT="!test? ( test )"
 REQUIRED_USE="test? ( utils )"
 
 # block with sci-biology/exonerate , maybe the best would be to change SRC_URI in sci-biology/exonerate
@@ -25,10 +23,6 @@ DEPEND="
 	dev-libs/glib:2"
 RDEPEND="${DEPEND}"
 
-AUTOTOOLS_IN_SOURCE_BUILD=1
-
-PATCHES=( "${FILESDIR}"/${P}-asneeded.patch )
-
 src_prepare() {
 	tc-export CC
 	sed \
@@ -36,20 +30,18 @@ src_prepare() {
 		-i configure.in || die
 	# we patch the configure.in file like sci-biology/exonerate:gentoo does, though it is ugly hack
 	# mv configure.in configure.ac
-	autotools-utils_src_prepare
+	default
 }
 
 src_configure() {
-	local myeconfargs=(
-		$(use_enable utils utilities)
-		$(use_enable threads pthreads)
-		--enable-largefile
+	econf \
+		$(use_enable utils utilities) \
+		$(use_enable threads pthreads) \
+		--enable-largefile \
 		--enable-glib2
-	)
-	autotools-utils_src_configure
 }
 
 src_install() {
-	autotools-utils_src_install
+	default
 	doman doc/man/man1/*.1
 }
diff --git a/sci-biology/exonerate-gff3/files/exonerate-gff3-9999-asneeded.patch b/sci-biology/exonerate-gff3/files/exonerate-gff3-9999-asneeded.patch
deleted file mode 100644
index 3268055cd..000000000
--- a/sci-biology/exonerate-gff3/files/exonerate-gff3-9999-asneeded.patch
+++ /dev/null
@@ -1,15 +0,0 @@
-Fix build with --as-needed
-
-https://bugs.gentoo.org/268094
-
---- configure.in
-+++ configure.in
-@@ -289,7 +289,7 @@
- if test "$enable_pthreads" = yes; then
-     echo "Using PTHREADS"
-     CFLAGS="$CFLAGS -DUSE_PTHREADS"
--    LDFLAGS="$LDFLAGS -lpthread"
-+    LIBS="$LIBS -lpthread"
- elif test "$enable_pthreads" = no; then
-     echo "Not using pthreads"
- else
diff --git a/sci-biology/fastdnaml/fastdnaml-1.2.2_p10.ebuild b/sci-biology/fastdnaml/fastdnaml-1.2.2_p10.ebuild
index bf739d3c6..fe4bc2f25 100644
--- a/sci-biology/fastdnaml/fastdnaml-1.2.2_p10.ebuild
+++ b/sci-biology/fastdnaml/fastdnaml-1.2.2_p10.ebuild
@@ -1,29 +1,26 @@
-# Copyright 1999-2014 Gentoo Foundation
+# Copyright 1999-2021 Gentoo Authors
 # Distributed under the terms of the GNU General Public License v2
 
-EAPI=5
-
-inherit eutils
+EAPI=7
 
 DEB_PATCHLVL=10
 
 DESCRIPTION="Maximum likelihood phylogenetic tree builder for DNA sequences"
-HOMEPAGE="http://directory.fsf.org/project/fastDNAml/"
+HOMEPAGE="https://directory.fsf.org/wiki/FastDNAml"
 SRC_URI="
 	mirror://debian/pool/main/f/fastdnaml/${PN}_${PV%%_p${DEB_PATCHLVL}}.orig.tar.gz
 	mirror://debian/pool/main/f/fastdnaml/${PN}_${PV/_p/-}.debian.tar.gz"
 
 LICENSE="GPL-2"
 SLOT="0"
-IUSE=""
 KEYWORDS="~amd64 ~x86"
 
 S="${WORKDIR}"/fastDNAml_${PV%_p*}
 
 src_prepare() {
 	mv ../debian . || die
-	EPATCH_OPTS="-p1" \
-		epatch debian/patches/*patch
+	default
+	eapply debian/patches/*patch
 }
 
 src_install() {
diff --git a/sci-biology/fastp/Manifest b/sci-biology/fastp/Manifest
new file mode 100644
index 000000000..c158050fa
--- /dev/null
+++ b/sci-biology/fastp/Manifest
@@ -0,0 +1 @@
+DIST fastp-0.23.4.tar.gz 164071 BLAKE2B 58745d494b83bbf9ae34593159228dbef5c854ab856af91fea8770fef171ed7b3053a4cac8c31053af3dcd91d4298fddb7594670a32963f53f75bd5fa1ec3a68 SHA512 2c929e974708f8cd2d8cab95d59c0a5fd01bea912f6ba5d08841fd929f0f5019ef89e506c771057bd02b879836ae30564b8417271866b6bbcb4917fbeb387e76
diff --git a/sci-biology/fastp/fastp-0.23.4.ebuild b/sci-biology/fastp/fastp-0.23.4.ebuild
new file mode 100644
index 000000000..70d5ce330
--- /dev/null
+++ b/sci-biology/fastp/fastp-0.23.4.ebuild
@@ -0,0 +1,20 @@
+# Copyright 1999-2023 Gentoo Foundation
+# Distributed under the terms of the GNU General Public License v2
+
+EAPI=8
+
+DESCRIPTION="An ultra-fast all-in-one FASTQ preprocessor"
+HOMEPAGE="https://github.com/OpenGene/fastp"
+SRC_URI="https://github.com/OpenGene/fastp/archive/refs/tags/v${PV}.tar.gz -> ${P}.tar.gz"
+KEYWORDS="~amd64"
+
+LICENSE="MIT"
+SLOT="0"
+
+DEPEND="app-arch/libdeflate
+	dev-libs/isa-l"
+
+src_install() {
+	dodir /usr/bin
+	emake PREFIX="${ED}"/usr install
+}
diff --git a/sci-biology/fastp/metadata.xml b/sci-biology/fastp/metadata.xml
new file mode 100644
index 000000000..d51d87c5a
--- /dev/null
+++ b/sci-biology/fastp/metadata.xml
@@ -0,0 +1,11 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
+<pkgmetadata>
+	<maintainer type="person">
+		<email>mschu.dev@gmail.com</email>
+		<name>Michael Schubert</name>
+	</maintainer>
+	<upstream>
+		<remote-id type="github">OpenGene/fastp</remote-id>
+	</upstream>
+</pkgmetadata>
diff --git a/sci-biology/fastqc/Manifest b/sci-biology/fastqc/Manifest
index 470141cc1..91b60dbc9 100644
--- a/sci-biology/fastqc/Manifest
+++ b/sci-biology/fastqc/Manifest
@@ -1 +1 @@
-DIST fastqc_v0.11.3_source.zip 10073593 BLAKE2B 4b72d8c06c7495baa138a39f4f6140022c9d8a954dd284c3e66fdf547411315425995e72005eb6605559197b094ead9aab28918bf0f89b3a1d49fef00b02ce28 SHA512 bab27d6997ad6525b7804ba9a3a54eec1cdb835d548c2840ae882334902d12eea4bbff549370669176ade76633a5f1d7dc6f7ee865a25f1a41b525764660b471
+DIST fastqc-0.11.9.tar.gz 10077703 BLAKE2B 7922effe383801ae30a4f16cca06d893883af48a730f5640926bc83eedae4df78e956973f1985a5ff9bb83ff061314b80eeecaed738f0eafa7feb59ecfad6984 SHA512 20f46fd9b5608565b6da8ec3bedb1f173a3619b0004bc0987147b1e3240813ef6ebbb07b9bcf2c472272dfad8262ad6edf68055ccad3b81b5ffb63ddc5278a4a
diff --git a/sci-biology/fastqc/fastqc-0.11.3.ebuild b/sci-biology/fastqc/fastqc-0.11.3.ebuild
deleted file mode 100644
index f30dd8e2e..000000000
--- a/sci-biology/fastqc/fastqc-0.11.3.ebuild
+++ /dev/null
@@ -1,54 +0,0 @@
-# Copyright 1999-2015 Gentoo Foundation
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=5
-
-inherit java-pkg-2 eutils java-ant-2
-
-DESCRIPTION="Quality control FASTA/FASTQ sequence files"
-HOMEPAGE="http://www.bioinformatics.babraham.ac.uk/projects/fastqc/"
-SRC_URI="http://www.bioinformatics.babraham.ac.uk/projects/fastqc/fastqc_v"${PV}"_source.zip"
-
-LICENSE="GPL-3+"
-SLOT="0"
-KEYWORDS=""
-IUSE=""
-
-DEPEND="sci-biology/picard
-	sci-libs/jhdf5
-	>=virtual/jre-1.5:*"
-RDEPEND="${DEPEND}
-	dev-lang/perl
-	>=virtual/jdk-1.5:*
-	dev-java/ant-core"
-
-S="${WORKDIR}"/FastQC
-
-src_prepare(){
-	cp "${FILESDIR}"/build.xml . || die
-}
-
-src_compile(){
-	ant || die
-}
-
-src_install(){
-	dobin fastqc run_fastqc.bat
-	dodoc README.txt RELEASE_NOTES.txt
-
-	# There is no fastqc.jar.  The output from the compilation is the set of
-	# .class files (a jar file is just a zip file full of .class files).  All
-	# you need to copy out is the contents of the bin subdirectory, the rest of
-	# the download you can discard.
-	#
-	# jbzip2-0.9.jar comes from https://code.google.com/p/jbzip2
-	#
-	# ignore the sam-1.103.jar and rely on /usr/share/picard/lib/sam.jar from sci-biology/picard
-	# The sam-1.103.jar library comes from
-	# http://sourceforge.net/projects/picard/files/sam-jdk/.  Note that there is
-	# a newer version of this codebase at https://github.com/samtools/htsjdk but
-	# that FastQC is NOT yet compatible with the updated API (this will probably
-	# happen in a future release).  This library is needed to read SAM/BAM
-	# format files.
-	# cisd-jhdf5.jar should be provided by sci-libs/jhdf5
-}
diff --git a/sci-biology/fastqc/fastqc-0.11.9.ebuild b/sci-biology/fastqc/fastqc-0.11.9.ebuild
new file mode 100644
index 000000000..be2d3b340
--- /dev/null
+++ b/sci-biology/fastqc/fastqc-0.11.9.ebuild
@@ -0,0 +1,40 @@
+# Copyright 1999-2022 Gentoo Authors
+# Distributed under the terms of the GNU General Public License v2
+
+EAPI=8
+
+inherit desktop java-pkg-2 java-ant-2 xdg
+
+DESCRIPTION="Quality control FASTA/FASTQ sequence files"
+HOMEPAGE="https://www.bioinformatics.babraham.ac.uk/projects/fastqc/"
+SRC_URI="https://github.com/s-andrews/FastQC/archive/refs/tags/v${PV}.tar.gz -> ${P}.tar.gz"
+S="${WORKDIR}/FastQC-${PV}"
+
+LICENSE="GPL-3+"
+SLOT="0"
+KEYWORDS="~amd64"
+
+RDEPEND="
+	dev-lang/perl
+	>=virtual/jre-1.8:*
+"
+DEPEND="
+	dev-lang/perl
+	>=virtual/jdk-1.8:*
+"
+BDEPEND="media-gfx/imagemagick"
+
+EANT_BUILD_TARGET="build"
+
+src_install(){
+	insinto "opt/${PN}"
+	doins -r bin/*
+	chmod a+x "${ED}/opt/${PN}/fastqc"
+	# add convenience symlink
+	dosym ../${PN}/${PN} /opt/bin/${PN}
+
+	convert ${PN}_icon.ico ${PN}.png || die
+	doicon ${PN}.png
+	make_desktop_entry ${PN} FastQC ${PN}
+	einstalldocs
+}
diff --git a/sci-biology/fastqc/files/build.xml b/sci-biology/fastqc/files/build.xml
deleted file mode 100644
index c4a692096..000000000
--- a/sci-biology/fastqc/files/build.xml
+++ /dev/null
@@ -1,59 +0,0 @@
-<?xml version="1.0" encoding="UTF-8" standalone="no"?>
-<!-- WARNING: Eclipse auto-generated file.
-              Any modifications will be overwritten.
-              To include a user specific buildfile here, simply create one in the same
-              directory with the processing instruction <?eclipse.ant.import?>
-              as the first entry and export the buildfile again. -->
-<project basedir="." default="build" name="FastQC">
-    <property environment="env"/>
-    <property name="debuglevel" value="source,lines,vars"/>
-    <property name="target" value="1.5"/>
-    <property name="source" value="1.5"/>
-    <path id="FastQC.classpath">
-        <pathelement location="bin"/>
-        <pathelement location="jbzip2-0.9.jar"/>
-        <pathelement location="sam-1.103.jar"/>
-        <pathelement location="cisd-jhdf5.jar"/>
-    </path>
-    <target name="init">
-        <mkdir dir="bin"/>
-        <copy includeemptydirs="false" todir="bin">
-            <fileset dir=".">
-                <exclude name="**/*.launch"/>
-                <exclude name="**/*.java"/>
-            </fileset>
-        </copy>
-    </target>
-    <target name="clean">
-        <delete dir="bin"/>
-    </target>
-    <target depends="clean" name="cleanall"/>
-    <target depends="build-subprojects,build-project" name="build"/>
-    <target name="build-subprojects"/>
-    <target depends="init" name="build-project">
-        <echo message="${ant.project.name}: ${ant.file}"/>
-        <javac debug="true" debuglevel="${debuglevel}" destdir="bin" includeantruntime="false" source="${source}" target="${target}">
-            <src path="."/>
-            <classpath refid="FastQC.classpath"/>
-        </javac>
-    </target>
-    <target description="Build all projects which reference this project. Useful to propagate changes." name="build-refprojects"/>
-    <target description="copy Eclipse compiler jars to ant lib directory" name="init-eclipse-compiler">
-        <copy todir="${ant.library.dir}">
-            <fileset dir="${ECLIPSE_HOME}/plugins" includes="org.eclipse.jdt.core_*.jar"/>
-        </copy>
-        <unzip dest="${ant.library.dir}">
-            <patternset includes="jdtCompilerAdapter.jar"/>
-            <fileset dir="${ECLIPSE_HOME}/plugins" includes="org.eclipse.jdt.core_*.jar"/>
-        </unzip>
-    </target>
-    <target description="compile project with Eclipse compiler" name="build-eclipse-compiler">
-        <property name="build.compiler" value="org.eclipse.jdt.core.JDTCompilerAdapter"/>
-        <antcall target="build"/>
-    </target>
-    <target name="FastQCApplication">
-        <java classname="uk.ac.babraham.FastQC.FastQCApplication" failonerror="true" fork="yes">
-            <classpath refid="FastQC.classpath"/>
-        </java>
-    </target>
-</project>
diff --git a/sci-biology/fastqc/metadata.xml b/sci-biology/fastqc/metadata.xml
index 138cb7705..f13c6ccba 100644
--- a/sci-biology/fastqc/metadata.xml
+++ b/sci-biology/fastqc/metadata.xml
@@ -5,8 +5,15 @@
 		<email>mmokrejs@fold.natur.cuni.cz</email>
 		<name>Martin Mokrejs</name>
 	</maintainer>
+	<maintainer type="person">
+		<email>anton.stay.connected@gmail.com</email>
+		<name>Anton Molyboha</name>
+	</maintainer>
 	<maintainer type="project">
 		<email>sci-biology@gentoo.org</email>
 		<name>Gentoo Biology Project</name>
 	</maintainer>
+	<upstream>
+		<remote-id type="github">s-andrews/FastQC</remote-id>
+	</upstream>
 </pkgmetadata>
diff --git a/sci-biology/ffindex/Manifest b/sci-biology/ffindex/Manifest
index 28a5ef5d2..2c9643e66 100644
--- a/sci-biology/ffindex/Manifest
+++ b/sci-biology/ffindex/Manifest
@@ -1 +1 @@
-DIST ffindex-0.9.9.6.tar.gz 34833 BLAKE2B 356999066a5c702a67af55862e2318858e4693cc455460844f277633ec2e03127723ffc0d91274d3639a434214ac5b630ba08f4f27df70eed4015ec65e6884a7 SHA512 b7bbb0c560603922c03ecf6f4a112b246a1d09eb250846423e69ad7d4f15d538f050eaba879d69ad937ef02644aa96b475df93b861216ba5b189ea1fd5c57caf
+DIST ffindex-1.0.tar.gz 36658 BLAKE2B 854973a07c23a1e13d938296b1a8babd1de26084162b0bd8beccab6b89dc0179b7d53d94fc5873c0038cb5afac8292453ea0caf8f7171aa16344d18778679cdd SHA512 590f9bc544b36faf07515ce87f1cedd7ce990eccce5e9a033b9a56007bb3dc088deb12fb3f756b35d79cdc4a65108db0071b451265b3192b58de2ff09faeb58b
diff --git a/sci-biology/ffindex/ffindex-0.9.9.6.ebuild b/sci-biology/ffindex/ffindex-0.9.9.6.ebuild
deleted file mode 100644
index 8ea8a7633..000000000
--- a/sci-biology/ffindex/ffindex-0.9.9.6.ebuild
+++ /dev/null
@@ -1,50 +0,0 @@
-# Copyright 1999-2015 Gentoo Foundation
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=5
-
-DESCRIPTION="Simple index/database for huge amounts of small files"
-HOMEPAGE="http://www.splashground.de/~andy/programs/FFindex"
-#SRC_URI="http://downloads.sourceforge.net/project/transdecoder/TransDecoder_r20140704.tar.gz"
-SRC_URI="http://www.splashground.de/~andy/programs/FFindex/${P}.tar.gz"
-
-LICENSE="CC-BY-3.0"
-SLOT="0"
-KEYWORDS="~amd64"
-IUSE="mpi"
-
-DEPEND="mpi? ( virtual/mpi )"
-RDEPEND="${DEPEND}"
-
-#S="${WORKDIR}"/TransDecoder_r20140704/3rd_party/ffindex-0.9.9.3
-
-src_compile(){
-	if use mpi; then
-		emake HAVE_MPI=1
-	else
-		emake
-	fi
-}
-
-src_install(){
-	dodoc README
-	cd src || die
-	dobin ffindex_apply ffindex_unpack ffindex_modify ffindex_get ffindex_from_fasta ffindex_build
-	if use mpi; then
-		dobin ffindex_apply_mpi
-	fi
-
-	#  * QA Notice: The following files contain writable and executable sections
-	#  *  Files with such sections will not work properly (or at all!) on some
-	#  *  architectures/operating systems.  A bug should be filed at
-	#  *  http://bugs.gentoo.org/ to make sure the issue is fixed.
-	#  *  For more information, see http://hardened.gentoo.org/gnu-stack.xml
-	#  *  Please include the following list of files in your report:
-	#  *  Note: Bugs should be filed for the respective maintainers
-	#  *  of the package in question and not hardened@g.o.
-	#  * RWX --- --- usr/lib64/libffindex.so.0.1
-	#
-	dolib libffindex.so.0.1 libffindex.so
-
-	# make install INSTALL_DIR="${DESTDIR}" HAVE_MPI=1
-}
diff --git a/sci-biology/ffindex/ffindex-1.0.ebuild b/sci-biology/ffindex/ffindex-1.0.ebuild
new file mode 100644
index 000000000..ff1807353
--- /dev/null
+++ b/sci-biology/ffindex/ffindex-1.0.ebuild
@@ -0,0 +1,49 @@
+# Copyright 1999-2021 Gentoo Authors
+# Distributed under the terms of the GNU General Public License v2
+
+EAPI=7
+
+DESCRIPTION="Simple index/database for huge amounts of small files"
+HOMEPAGE="https://github.com/ahcm/ffindex"
+SRC_URI="https://github.com/ahcm/ffindex/archive/${P}.tar.gz"
+
+LICENSE="CC-BY-3.0"
+SLOT="0"
+KEYWORDS="~amd64"
+IUSE="mpi"
+
+DEPEND="mpi? ( virtual/mpi )"
+RDEPEND="${DEPEND}"
+
+S="${WORKDIR}/${PN}-${PN}-${PV}"
+
+src_compile(){
+	if use mpi; then
+		emake HAVE_MPI=1
+	else
+		emake
+	fi
+}
+
+src_install(){
+	dodoc README
+	cd src || die
+	dobin ffindex_apply ffindex_unpack ffindex_modify ffindex_get ffindex_from_fasta ffindex_build
+	if use mpi; then
+		dobin ffindex_apply_mpi
+	fi
+
+	#  * QA Notice: The following files contain writable and executable sections
+	#  *  Files with such sections will not work properly (or at all!) on some
+	#  *  architectures/operating systems.  A bug should be filed at
+	#  *  http://bugs.gentoo.org/ to make sure the issue is fixed.
+	#  *  For more information, see http://hardened.gentoo.org/gnu-stack.xml
+	#  *  Please include the following list of files in your report:
+	#  *  Note: Bugs should be filed for the respective maintainers
+	#  *  of the package in question and not hardened@g.o.
+	#  * RWX --- --- usr/lib64/libffindex.so.0.1
+	#
+	dolib.so libffindex.so.0.1 libffindex.so
+
+	# make install INSTALL_DIR="${DESTDIR}" HAVE_MPI=1
+}
diff --git a/sci-biology/ffindex/metadata.xml b/sci-biology/ffindex/metadata.xml
index 138cb7705..a9577a9c3 100644
--- a/sci-biology/ffindex/metadata.xml
+++ b/sci-biology/ffindex/metadata.xml
@@ -9,4 +9,7 @@
 		<email>sci-biology@gentoo.org</email>
 		<name>Gentoo Biology Project</name>
 	</maintainer>
+	<upstream>
+		<remote-id type="github">ahcm/ffindex</remote-id>
+	</upstream>
 </pkgmetadata>
diff --git a/sci-biology/fgap-bin/Manifest b/sci-biology/fgap-bin/Manifest
deleted file mode 100644
index 0e259aae3..000000000
--- a/sci-biology/fgap-bin/Manifest
+++ /dev/null
@@ -1 +0,0 @@
-DIST FGAP_1_8_1_LINUX64b.tar.gz 19403911 BLAKE2B 673558a57851542cc961083bc01ae2e95456222fd26c7db767a278c9170b2dbb521fb8167c15a864946c0a453615d566c3ff7c2d05619d60a8d3e17c3f0a8c78 SHA512 fc8d626d158ef362b5aa5d8ef5ffb8840b1496ecb2f4714441d74bc3fca5eacac3eab1e6d93e4344b175eece2b8228d98794493c7d5d300fbb30a8a3b6b8afd0
diff --git a/sci-biology/fgap-bin/fgap-bin-1.8.1.ebuild b/sci-biology/fgap-bin/fgap-bin-1.8.1.ebuild
deleted file mode 100644
index 40bd3b93c..000000000
--- a/sci-biology/fgap-bin/fgap-bin-1.8.1.ebuild
+++ /dev/null
@@ -1,34 +0,0 @@
-# Copyright 1999-2016 Gentoo Foundation
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=5
-
-DESCRIPTION="Tool to close gaps in de novo assembled contigs or scaffolds"
-HOMEPAGE="http://www.bioinfo.ufpr.br/fgap"
-SRC_URI="https://sourceforge.net/projects/fgap/files/FGAP_1_8_1_LINUX64b.tar.gz"
-# http://bmcresnotes.biomedcentral.com/articles/10.1186/1756-0500-7-371
-
-LICENSE="MIT"
-SLOT="0"
-KEYWORDS=""
-IUSE=""
-
-# Matlab (R2012a) or Octave (3.6.2)
-# fag from sci-biology/fgap-bin needs /usr/local/MATLAB/R2012a/bin/glnx86/libmwi18n.so, which comes from MATLAB
-# export LD_LIBRARY_PATH= /usr/local/MATLAB/R2012a/bin/glnx86
-#
-# Source code (Octave/Matlab): https://sourceforge.net/projects/fgap/files/fgap.m
-
-# MATLAB Component Runtime v7.17: https://sourceforge.net/projects/fgap/files/MCR_LINUX64b.tar.gz
-# http://www.mathworks.com/products/compiler/mcr/index.html
-DEPEND=""
-RDEPEND="${DEPEND}
-	sci-biology/ncbi-tools++"
-S="${WORKDIR}"/FGAP_1_8_1_LINUX64b
-
-src_install(){
-	dobin run_fgap.sh fgap
-	dodoc README
-	insinto /usr/share/"${PN}"/sample_data
-	doins sample_data/*.fasta
-}
diff --git a/sci-biology/fgap-bin/metadata.xml b/sci-biology/fgap-bin/metadata.xml
deleted file mode 100644
index b53e13d28..000000000
--- a/sci-biology/fgap-bin/metadata.xml
+++ /dev/null
@@ -1,15 +0,0 @@
-<?xml version="1.0" encoding="UTF-8"?>
-<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
-<pkgmetadata>
-	<maintainer type="person">
-		<email>mmokrejs@fold.natur.cuni.cz</email>
-		<name>Martin Mokrejs</name>
-	</maintainer>
-	<maintainer type="project">
-		<email>sci-biology@gentoo.org</email>
-		<name>Gentoo Biology Project</name>
-	</maintainer>
-	<upstream>
-		<remote-id type="sourceforge">fgap</remote-id>
-	</upstream>
-</pkgmetadata>
diff --git a/sci-biology/fgap/Manifest b/sci-biology/fgap/Manifest
deleted file mode 100644
index c6e88321a..000000000
--- a/sci-biology/fgap/Manifest
+++ /dev/null
@@ -1 +0,0 @@
-DIST fgap.m 66256 SHA256 9fdfeccb28ed8461696e05e5cdea32ee63eaead9f0d9c81cf8fe0dc6e59683b8 SHA512 05b0d46eb5a9b3a34e16c045966c58f52bdf09ee2f8c62198338b2d57835815a2ac034b596d6c180733b91edcc012fb77852c8bc0523174251a2c1b3c71b1e27 WHIRLPOOL 623df6b1d2b540fac5d5303e8c08d27128d44dbd678a4e85d49b5304ffde008562c3d4df1996f30d36a4da77f28a09f0c0ae47ee945bb3000fee7f1ffac70921
diff --git a/sci-biology/fgap/fgap-1.8.1.ebuild b/sci-biology/fgap/fgap-1.8.1.ebuild
deleted file mode 100644
index 9b34575db..000000000
--- a/sci-biology/fgap/fgap-1.8.1.ebuild
+++ /dev/null
@@ -1,25 +0,0 @@
-# Copyright 1999-2016 Gentoo Foundation
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=5
-
-DESCRIPTION="Tool to close gaps in de novo assembled contigs or scaffolds"
-HOMEPAGE="http://www.bioinfo.ufpr.br/fgap"
-SRC_URI="https://sourceforge.net/projects/fgap/files/fgap.m"
-# http://bmcresnotes.biomedcentral.com/articles/10.1186/1756-0500-7-371
-
-LICENSE="MIT"
-SLOT="0"
-KEYWORDS=""
-IUSE=""
-
-# Matlab (R2012a) or Octave (3.6.2)
-#
-# Source code (Octave/Matlab): https://sourceforge.net/projects/fgap/files/fgap.m
-
-# MATLAB Component Runtime v7.17: https://sourceforge.net/projects/fgap/files/MCR_LINUX64b.tar.gz
-# http://www.mathworks.com/products/compiler/mcr/index.html
-DEPEND=""
-RDEPEND="${DEPEND}
-	>=sci-biology/ncbi-tools-2.2.28
-	>=sci-mathematics/octave-3.6.2"
diff --git a/sci-biology/fgap/metadata.xml b/sci-biology/fgap/metadata.xml
deleted file mode 100644
index b53e13d28..000000000
--- a/sci-biology/fgap/metadata.xml
+++ /dev/null
@@ -1,15 +0,0 @@
-<?xml version="1.0" encoding="UTF-8"?>
-<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
-<pkgmetadata>
-	<maintainer type="person">
-		<email>mmokrejs@fold.natur.cuni.cz</email>
-		<name>Martin Mokrejs</name>
-	</maintainer>
-	<maintainer type="project">
-		<email>sci-biology@gentoo.org</email>
-		<name>Gentoo Biology Project</name>
-	</maintainer>
-	<upstream>
-		<remote-id type="sourceforge">fgap</remote-id>
-	</upstream>
-</pkgmetadata>
diff --git a/sci-biology/flexbar/Manifest b/sci-biology/flexbar/Manifest
index 92c682f14..a5f19fa17 100644
--- a/sci-biology/flexbar/Manifest
+++ b/sci-biology/flexbar/Manifest
@@ -1,2 +1 @@
-DIST flexbar-2.7.0.tar.gz 30033 BLAKE2B e8c8f8e9f2e44870c844b59d40cd7c6d4da599e1d59d5b5201e3b6e3dbc2d088680253e43c5c72b57a7a33401b0a2b4770c34700e415af6be4b250c6dda0806f SHA512 38dc40476dadd769977dd2428941928e839e107e719e9b595c2ba57e1d8764fb394c5960b809da99dc939a66cae9350ea607e393b9467e98d464d0e49bcdac47
-DIST flexbar-3.0.0.tar.gz 31292 BLAKE2B 43abf3cc9d58423f1a26d52d673fd08450b149de85af49aa35036abd2906e2648d844a83b5578be57a83b5636ae70d934c48891d64596260828ea638338e8bc0 SHA512 ccefb4d1342ce5353a64510f79f8b15c409eb68853eb98ed7c9b23cb53d926e5b6965b1a9d3d8a5b3699da2f18cf8a627d5ca3ed172e25693a80d878547d6d38
+DIST flexbar-3.5.0.tar.gz 44021 BLAKE2B 2d21b366f3da5ad5a4b3c73530af11c49a131453dc1588e7836fd2060f2a1aa5c21f109bfcdc362dab6d7aeecb0bed683e58b9d50e9ba808c98bef45b2510c57 SHA512 5df1e8cb2c713256945f9fe3ed5d5faca0f3776f5be24e01ba659973e373c45b87141331fd37ceb8f38483e1ee41762671157c55798da133cbca68608e25f409
diff --git a/sci-biology/flexbar/flexbar-2.7.0.ebuild b/sci-biology/flexbar/flexbar-2.7.0.ebuild
deleted file mode 100644
index 9fc465c10..000000000
--- a/sci-biology/flexbar/flexbar-2.7.0.ebuild
+++ /dev/null
@@ -1,33 +0,0 @@
-# Copyright 1999-2017 Gentoo Foundation
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=6
-
-inherit cmake-utils
-
-DESCRIPTION="Barcode, MID tag and adapter sequence removal"
-HOMEPAGE="https://github.com/seqan/flexbar"
-SRC_URI="https://github.com/seqan/flexbar/archive/v${PV}.tar.gz -> ${P}.tar.gz"
-
-LICENSE="GPL-3"
-SLOT="0"
-KEYWORDS=""
-IUSE=""
-
-CDEPEND="
-	dev-cpp/tbb
-	>=sci-biology/seqan-2.1.1:0"
-DEPEND="${CDEPEND}"
-RDEPEND="${CDEPEND}"
-
-# TODO: need to call 'pkg-config --cflags seqan-2.2' and pass it down
-src_configure() {
-	local CPPFLAGS=${CPPFLAGS}
-	append-cppflags `pkg-config --cflags seqan-2.2`
-	local CXXFLAGS="${CXXFLAGS}"
-	append-cxxflags "-std=c++14"
-	cmake-utils_src_configure
-}
-
-# SeqAn requires C++14! You must compile your application with -std=c++14, -std=gnu++14 or -std=c++1y
-# https://github.com/seqan/flexbar/issues/8
diff --git a/sci-biology/flexbar/flexbar-3.0.0.ebuild b/sci-biology/flexbar/flexbar-3.0.0.ebuild
deleted file mode 100644
index 65f5dd077..000000000
--- a/sci-biology/flexbar/flexbar-3.0.0.ebuild
+++ /dev/null
@@ -1,41 +0,0 @@
-# Copyright 1999-2017 Gentoo Foundation
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=6
-
-inherit cmake-utils
-
-DESCRIPTION="Barcode, MID tag and adapter sequence removal"
-HOMEPAGE="https://github.com/seqan/flexbar"
-SRC_URI="https://github.com/seqan/flexbar/archive/v${PV}.tar.gz -> ${P}.tar.gz"
-
-LICENSE="GPL-3"
-SLOT="0"
-KEYWORDS="~amd64 ~x86"
-IUSE=""
-
-CDEPEND="
-	dev-cpp/tbb
-	>=sci-biology/seqan-2.1.1:0
-	sys-libs/zlib
-	app-arch/bzip2"
-DEPEND="${CDEPEND}"
-RDEPEND="${CDEPEND}"
-
-# TODO: need to call 'pkg-config --cflags seqan-2.2' and pass it down
-src_configure() {
-	local CPPFLAGS=${CPPFLAGS}
-	append-cppflags `pkg-config --cflags seqan-2.2`
-	local CXXFLAGS="${CXXFLAGS}"
-	append-cxxflags "-std=c++14"
-	cmake-utils_src_configure
-}
-
-# SeqAn requires C++14! You must compile your application with -std=c++14, -std=gnu++14 or -std=c++1y
-# https://github.com/seqan/flexbar/issues/8
-
-src_install(){
-	elog `pwd`
-	dobin ../"${P}"_build/flexbar
-	dodoc ../"${P}"/README.md
-}
diff --git a/sci-biology/flexbar/flexbar-3.5.0.ebuild b/sci-biology/flexbar/flexbar-3.5.0.ebuild
new file mode 100644
index 000000000..49f67558b
--- /dev/null
+++ b/sci-biology/flexbar/flexbar-3.5.0.ebuild
@@ -0,0 +1,39 @@
+# Copyright 1999-2021 Gentoo Authors
+# Distributed under the terms of the GNU General Public License v2
+
+EAPI=7
+
+inherit cmake flag-o-matic
+
+DESCRIPTION="Barcode, MID tag and adapter sequence removal"
+HOMEPAGE="https://github.com/seqan/flexbar"
+SRC_URI="https://github.com/seqan/flexbar/archive/v${PV}.tar.gz -> ${P}.tar.gz"
+
+LICENSE="GPL-3"
+SLOT="0"
+KEYWORDS="~amd64 ~x86"
+
+CDEPEND="
+	dev-cpp/tbb
+	>=sci-biology/seqan-2.1.1:0
+	sys-libs/zlib
+	app-arch/bzip2"
+DEPEND="${CDEPEND}"
+RDEPEND="${CDEPEND}"
+
+# TODO: need to call 'pkg-config --cflags seqan-2.2' and pass it down
+src_configure() {
+	local CPPFLAGS=${CPPFLAGS}
+	append-cppflags `pkg-config --cflags seqan-2.2`
+	local CXXFLAGS="${CXXFLAGS}"
+	append-cxxflags "-std=c++14"
+	cmake_src_configure
+}
+
+# SeqAn requires C++14! You must compile your application with -std=c++14, -std=gnu++14 or -std=c++1y
+# https://github.com/seqan/flexbar/issues/8
+
+src_install(){
+	dobin ../"${P}"_build/flexbar
+	dodoc ../"${P}"/README.md
+}
diff --git a/sci-biology/freebayes/Manifest b/sci-biology/freebayes/Manifest
new file mode 100644
index 000000000..a08da1955
--- /dev/null
+++ b/sci-biology/freebayes/Manifest
@@ -0,0 +1 @@
+DIST freebayes-1.3.5-src.tar.gz 26889024 BLAKE2B 7f8d643610cf09ad5955a7b69b23a0a809d135ac0437165c4af089bd4529a2efe91b323cf519a65b2e037dec7d1488b12c76e4cb1dcdc61e281ca5a5e1fda7f8 SHA512 4b2005e00a714516bb9db01eb09e68881edb03bde113dea0440252e4779b67a563707692f5cf75128b7b63ff2513f5192b84a894dedb0b19a249691df7694f9d
diff --git a/sci-biology/freebayes/freebayes-1.3.5.ebuild b/sci-biology/freebayes/freebayes-1.3.5.ebuild
new file mode 100644
index 000000000..836508195
--- /dev/null
+++ b/sci-biology/freebayes/freebayes-1.3.5.ebuild
@@ -0,0 +1,25 @@
+# Copyright 1999-2021 Gentoo Authors
+# Distributed under the terms of the GNU General Public License v2
+
+EAPI=7
+
+inherit meson
+
+DESCRIPTION="Bayesian gen. variant detector to find short polymorphisms"
+HOMEPAGE="https://github.com/ekg/freebayes"
+SRC_URI="https://github.com/freebayes/freebayes/releases/download/v${PV}/${P}-src.tar.gz"
+
+LICENSE="MIT"
+SLOT="0"
+KEYWORDS="~amd64"
+
+# tests not included in release tarball?
+RESTRICT="test"
+
+DEPEND=""
+RDEPEND="${DEPEND}
+	sci-libs/htslib
+	sci-biology/bamtools
+	sci-biology/samtools:*"
+
+S="${WORKDIR}/${PN}"
diff --git a/sci-biology/freebayes/freebayes-9999.ebuild b/sci-biology/freebayes/freebayes-9999.ebuild
deleted file mode 100644
index 34b92b2ef..000000000
--- a/sci-biology/freebayes/freebayes-9999.ebuild
+++ /dev/null
@@ -1,110 +0,0 @@
-# Copyright 1999-2018 Gentoo Foundation
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=6
-
-inherit eutils git-r3 toolchain-funcs
-
-DESCRIPTION="Bayesian gen. variant detector to find short polymorphisms"
-HOMEPAGE="https://github.com/ekg/freebayes"
-EGIT_REPO_URI="https://github.com/ekg/freebayes.git"
-
-LICENSE="MIT"
-SLOT="0"
-KEYWORDS=""
-IUSE=""
-
-CDEPEND="dev-util/cmake"
-DEPEND=""
-RDEPEND="${DEPEND}
-	sci-libs/htslib
-	sci-biology/bamtools
-	sci-biology/samtools:*"
-
-# $ git clone --recursive https://github.com/ekg/freebayes.git
-# Cloning into 'freebayes'...
-# remote: Counting objects: 4942, done.
-# remote: Total 4942 (delta 0), reused 0 (delta 0), pack-reused 4942
-# Receiving objects: 100% (4942/4942), 5.93 MiB | 1.13 MiB/s, done.
-# Resolving deltas: 100% (3274/3274), done.
-# Submodule 'SeqLib' (https://github.com/walaj/SeqLib.git) registered for path 'SeqLib'
-# Submodule 'bamtools' (https://github.com/ekg/bamtools.git) registered for path 'bamtools'
-# Submodule 'intervaltree' (https://github.com/ekg/intervaltree.git) registered for path 'intervaltree'
-# Submodule 'bash-tap' (https://github.com/illusori/bash-tap.git) registered for path 'test/bash-tap'
-# Submodule 'test/test-simple-bash' (https://github.com/ingydotnet/test-simple-bash.git) registered for path 'test/test-simple-bash'
-# Submodule 'vcflib' (https://github.com/vcflib/vcflib.git) registered for path 'vcflib'
-# Cloning into '/home/mmokrejs/proj/sci/sci-biology/freebayes/a/freebayes/SeqLib'...
-# Cloning into '/home/mmokrejs/proj/sci/sci-biology/freebayes/a/freebayes/bamtools'...
-# Cloning into '/home/mmokrejs/proj/sci/sci-biology/freebayes/a/freebayes/intervaltree'...
-# Cloning into '/home/mmokrejs/proj/sci/sci-biology/freebayes/a/freebayes/test/bash-tap'...
-# Cloning into '/home/mmokrejs/proj/sci/sci-biology/freebayes/a/freebayes/test/test-simple-bash'...
-# Cloning into '/home/mmokrejs/proj/sci/sci-biology/freebayes/a/freebayes/vcflib'...
-# Submodule path 'SeqLib': checked out 'cce1e410ef6d2ac64972f5cacd8a0f9b86cecdd8'
-# Submodule 'bwa' (https://github.com/jwalabroad/bwa) registered for path 'SeqLib/bwa'
-# Submodule 'fermi-lite' (https://github.com/jwalabroad/fermi-lite) registered for path 'SeqLib/fermi-lite'
-# Submodule 'htslib' (https://github.com/samtools/htslib) registered for path 'SeqLib/htslib'
-# Cloning into '/home/mmokrejs/proj/sci/sci-biology/freebayes/a/freebayes/SeqLib/bwa'...
-# Cloning into '/home/mmokrejs/proj/sci/sci-biology/freebayes/a/freebayes/SeqLib/fermi-lite'...
-# Cloning into '/home/mmokrejs/proj/sci/sci-biology/freebayes/a/freebayes/SeqLib/htslib'...
-# Submodule path 'SeqLib/bwa': checked out 'fbd4dbc03904eccd71cdca8cac7aa48da749c19c'
-# Submodule path 'SeqLib/fermi-lite': checked out '5bc90f8d70e2b66184eccbd223a3be714c914365'
-# Submodule path 'SeqLib/htslib': checked out '0f298ce22c5c825c506129bf242348a31630c382'
-# Submodule path 'bamtools': checked out 'e77a43f5097ea7eee432ee765049c6b246d49baa'
-# Submodule path 'intervaltree': checked out 'dbb4c513d1ad3baac516fc1484c995daf9b42838'
-# Submodule path 'test/bash-tap': checked out 'c38fbfa401600cc81ccda66bfc0da3ea56288d03'
-# Submodule path 'test/test-simple-bash': checked out '124673ff204b01c8e96b7fc9f9b32ee35d898acc'
-# Submodule path 'vcflib': checked out '5e3ce04f758c6df16bc4d242b18a24d725d2e6e5'
-# Submodule 'fastahack' (https://github.com/ekg/fastahack.git) registered for path 'vcflib/fastahack'
-# Submodule 'filevercmp' (https://github.com/ekg/filevercmp.git) registered for path 'vcflib/filevercmp'
-# Submodule 'fsom' (https://github.com/ekg/fsom.git) registered for path 'vcflib/fsom'
-# Submodule 'googletest' (https://github.com/google/googletest.git) registered for path 'vcflib/googletest'
-# Submodule 'intervaltree' (https://github.com/ekg/intervaltree.git) registered for path 'vcflib/intervaltree'
-# Submodule 'multichoose' (https://github.com/ekg/multichoose.git) registered for path 'vcflib/multichoose'
-# Submodule 'smithwaterman' (https://github.com/ekg/smithwaterman.git) registered for path 'vcflib/smithwaterman'
-# Submodule 'tabixpp' (https://github.com/ekg/tabixpp.git) registered for path 'vcflib/tabixpp'
-# Cloning into '/home/mmokrejs/proj/sci/sci-biology/freebayes/a/freebayes/vcflib/fastahack'...
-# Cloning into '/home/mmokrejs/proj/sci/sci-biology/freebayes/a/freebayes/vcflib/filevercmp'...
-# Cloning into '/home/mmokrejs/proj/sci/sci-biology/freebayes/a/freebayes/vcflib/fsom'...
-# Cloning into '/home/mmokrejs/proj/sci/sci-biology/freebayes/a/freebayes/vcflib/googletest'...
-# Cloning into '/home/mmokrejs/proj/sci/sci-biology/freebayes/a/freebayes/vcflib/intervaltree'...
-# Cloning into '/home/mmokrejs/proj/sci/sci-biology/freebayes/a/freebayes/vcflib/multichoose'...
-# Cloning into '/home/mmokrejs/proj/sci/sci-biology/freebayes/a/freebayes/vcflib/smithwaterman'...
-# Cloning into '/home/mmokrejs/proj/sci/sci-biology/freebayes/a/freebayes/vcflib/tabixpp'...
-# Submodule path 'vcflib/fastahack': checked out 'c68cebb4f2e5d5d2b70cf08fbdf1944e9ab2c2dd'
-# Submodule path 'vcflib/filevercmp': checked out '1a9b779b93d0b244040274794d402106907b71b7'
-# Submodule path 'vcflib/fsom': checked out 'a6ef318fbd347c53189384aef7f670c0e6ce89a3'
-# Submodule path 'vcflib/googletest': checked out 'd225acc90bc3a8c420a9bcd1f033033c1ccd7fe0'
-# Submodule path 'vcflib/intervaltree': checked out 'b704f195e9b51d44dad68e33c209b06e63ebb353'
-# Submodule path 'vcflib/multichoose': checked out '73d35daa18bf35729b9ba758041a9247a72484a5'
-# Submodule path 'vcflib/smithwaterman': checked out '84c08d7eae7211d87fbcb1871dae20e6c2041e96'
-# Submodule path 'vcflib/tabixpp': checked out '80012f86dc22b13c75b73baf38195956db92473e'
-# Submodule 'htslib' (https://github.com/samtools/htslib.git) registered for path 'vcflib/tabixpp/htslib'
-# Cloning into '/home/mmokrejs/proj/sci/sci-biology/freebayes/a/freebayes/vcflib/tabixpp/htslib'...
-# Submodule path 'vcflib/tabixpp/htslib': checked out '0f298ce22c5c825c506129bf242348a31630c382'
-
-# g++ -O3 -D_FILE_OFFSET_BITS=64 -g -I../ttmath -I../bamtools/src/ -I../vcflib/src/ -I../vcflib/tabixpp/ -I../vcflib/smithwaterman/ -I../vcflib/multichoose/ -I../vcflib/filevercmp/ -I../vcflib/tabixpp/htslib -I../SeqLib -I../SeqLib/htslib -c freebayes.cpp
-
-src_prepare(){
-	find . -name Makefile | while read f; do \
-		sed -e "s/-O3 -D_FILE_OFFSET_BITS=64/${CFLAGS}/" -i $f || die
-		sed -e "s/^CFLAGS:= -O3/CFLAGS ?= ${CFLAGS}/" -i $f || die
-		sed -e "s/^CXX = g++/CXX = $(tc-getCXX)/;s/^CXX=g++/CXX = $(tc-getCXX)/" -i $f || die
-		sed -e "s/g++ /$(tc-getCXX) /" -i $f || die
-		sed -e "s/-O3/${CXXFLAGS}/" -i $f || die
-		sed -e "s/^CC[ 	]*=[ 	]gcc/CC = $(tc-getCC)/" -i $f || die
-		sed -e "s/-g -Wall -O2/${CFLAGS}/;s/-g -Wall -Wno-unused-function -O2/${CFLAGS}/" -i $f || die
-		sed -e "s/-O3 /${CFLAGS}/;s/ -O3/${CFLAGS}/" -i $f || die
-	done
-	sed -e "s/^C=gcc/C = $(tc-getCC)/" -i Makefile || die
-	sed -e "s/gcc/$(tc-getCC)/" -i SeqLib/bwa/Makefile SeqLib/fermi-lite/Makefile || die
-	sed -e "s/g++/$(tc-getCXX)/" -i SeqLib/src/Makefile.am || die
-	default
-}
-
-src_compile(){
-	emake -j1 # vcflib/smithwaterman/ sometimes does not compile
-}
-
-src_install(){
-	dobin bin/freebayes bin/bamleftalign
-}
diff --git a/sci-biology/fsa/fsa-1.15.9.ebuild b/sci-biology/fsa/fsa-1.15.9.ebuild
index e59c710c5..f77ae61aa 100644
--- a/sci-biology/fsa/fsa-1.15.9.ebuild
+++ b/sci-biology/fsa/fsa-1.15.9.ebuild
@@ -1,18 +1,15 @@
-# Copyright 1999-2016 Gentoo Foundation
+# Copyright 1999-2023 Gentoo Authors
 # Distributed under the terms of the GNU General Public License v2
 
-EAPI=5
-
-inherit eutils
+EAPI=8
 
 DESCRIPTION="Distance-based probabilistic multiple sequence alignment algo for DNA/RNA/prot"
-HOMEPAGE="http://fsa.sourceforge.net"
-SRC_URI="http://downloads.sourceforge.net/project/fsa/"${P}".tar.gz"
+HOMEPAGE="https://fsa.sourceforge.net"
+SRC_URI="https://downloads.sourceforge.net/project/fsa/${P}.tar.gz"
 
 LICENSE="GPL-3+"
 SLOT="0"
-KEYWORDS=""
-IUSE=""
+KEYWORDS="~amd64"
 
 DEPEND="dev-java/java-config"
 RDEPEND="${DEPEND}"
diff --git a/sci-biology/fsa/metadata.xml b/sci-biology/fsa/metadata.xml
index 0f267b755..e8c9d160f 100644
--- a/sci-biology/fsa/metadata.xml
+++ b/sci-biology/fsa/metadata.xml
@@ -10,6 +10,6 @@
 		<name>Gentoo Biology Project</name>
 	</maintainer>
 	<upstream>
-		<remote-id type="sourceforge">downloads</remote-id>
+		<remote-id type="sourceforge">fsa</remote-id>
 	</upstream>
 </pkgmetadata>
diff --git a/sci-biology/fsl/Manifest b/sci-biology/fsl/Manifest
index 4ba77f1e7..3a1d5a7d9 100644
--- a/sci-biology/fsl/Manifest
+++ b/sci-biology/fsl/Manifest
@@ -1,3 +1,2 @@
-DIST fsl-5.0.11.tar.gz 1507525689 BLAKE2B 212941aa6fb74c1c42f8b11d8e6803f1dfba50f1cdcb4092bfdf98d6832c552fcad59843a8db9e8887b98f86ce255fd9e80e3219a48286d7defe4544f0344225 SHA512 6f859723f8e4bd7e381761983f6423364180f5d3300cb165a3e57f3535d5301624ecb30c1796dae9579da5dd16e80a8a62d9994fec1caebf0835c2f6795ca055
-DIST fsl-5.0.8-sources.tar.gz 1420879532 BLAKE2B fab46d286b9c083f31408e885235a72a195f14a1e863264e8cbff2b6cfb8c70ef335cafe58dff38141b1d027aef301e94212da4c9b6d3f4306ba60c81e19cec7 SHA512 8dedf13d633d71fa28c5dd6591fab4adda4893b76467affa6f58aee917ee3fdc83da07d8f505feb61ac2733de1bfb84f7f9ff74589756946be21cdb9f057f0f0
-DIST fsl-5.0.9-sources.tar.gz 1491426239 BLAKE2B 310c4eb131856120f803d67f18e4d4e97df1ff22143bffa45be5f8abe31a01ce3df5a64abf5d065670b95394249a2f569a66a9cc22cd004b03e868e823d4555d SHA512 86a33084cf880ea1341ff8622eb13a364a462018a0fac55ee291dd8917e8453701db57f35529e144d419ea744397906b586b88acaf9a2dea0291fa3101ebb27d
+DIST fsl-6.0.4.tar.gz 2507673220 BLAKE2B 21e7437f8a3fde03ec6711b8022ee203ae159c07b5a3b998f37db768205d3335ffe9b28ad05b859e6bde4916933ea58e4e188012f147648f00fd6e6253ce1a12 SHA512 c65edcf5728920752e6dceea440dc2b528d007b7e4f56390a3d7eed91b1014457544563f699cae77f62c44cdfbdfcc5031265a5fd619fe0ecb99cad5653080d3
+DIST fsl-6.0.5.tar.gz 2509109593 BLAKE2B d1e5efbb6b73e2b40e7147dc4958584e057311084d2064335aae1c0a36cfab5e12061f3fac4f54118d840e66620b7e64a5dc4c32c0e0e3e6233c25cc3b48e6fd SHA512 e5124ae640f51002692de6ad9fdc3aec0e3caffc94dd18c16fadba686fa2a9bf37c7752e67affca53d9859cbab3e2e62ca28ef43c754c464bab5e182e55b02a1
diff --git a/sci-biology/fsl/files/fsl-5.0.11-no_xmlpp.patch b/sci-biology/fsl/files/fsl-5.0.11-no_xmlpp.patch
deleted file mode 100644
index bccf0e238..000000000
--- a/sci-biology/fsl/files/fsl-5.0.11-no_xmlpp.patch
+++ /dev/null
@@ -1,44 +0,0 @@
-diff --git a/src/flameo/Makefile b/src/flameo/Makefile
-index 5389e2f..52785c3 100644
---- a/src/flameo/Makefile
-+++ b/src/flameo/Makefile
-@@ -2,7 +2,7 @@ include ${FSLCONFDIR}/default.mk
- 
- PROJNAME = flame
- 
--USRINCFLAGS = -I${INC_NEWMAT} -I${INC_PROB} -I${INC_ZLIB} -DCIFTILIB_USE_XMLPP -I${FSLEXTINC} -I${INC_XML2} -I${INC_XML++} -I${INC_XML++CONF} -I${INC_BOOST} -I${FSLDIR}/include/ciftiio
-+USRINCFLAGS = -fPIC -I${INC_NEWMAT} -I${INC_PROB} -I${INC_ZLIB} -I${FSLEXTINC} ${CIFTICFLAGS} -I${INC_BOOST} -I${FSLDIR}/include/ciftiio
- USRLDFLAGS = -L${LIB_NEWMAT} -L${LIB_PROB} -L${LIB_ZLIB}
- 
- UNAME := $(shell uname)
-@@ -10,7 +10,7 @@ ifeq (${UNAME},Darwin)
-         LIBS = -liconv
- endif
- 
--LIBS += -lutils -lnewimage -lmiscmaths -lm -lnewmat -lfslio -lniftiio -lcifti -lxml++-2.6 -lxml2 -lboost_filesystem -lboost_system -lznz -lprob -lz 
-+LIBS += -lutils -lnewimage -lmiscmaths -lm -lnewmat -lfslio -lniftiio ${CIFTILIBS} -lboost_filesystem -lboost_system -lznz -lprob -lz 
- 
- XFILES = flameo
- 
-diff --git a/src/melodic/Makefile b/src/melodic/Makefile
-index 53b951a..803c39e 100644
---- a/src/melodic/Makefile
-+++ b/src/melodic/Makefile
-@@ -7,7 +7,7 @@ OPTFLAGS_alphaev6-dec-osf5.0-gcc2.95.2 = -O3 -mieee -mfp-trap-mode=sui
- 
- PROJNAME = melodic
- 
--USRINCFLAGS = -I${INC_NEWMAT} -I${INC_PROB} -I${INC_GD} -I${INC_GDC} -I${INC_PNG} -I${INC_ZLIB} -DCIFTILIB_USE_XMLPP -I${FSLEXTINC} -I${INC_XML2} -I${INC_XML++} -I${INC_XML++CONF} -I${INC_BOOST} -I${FSLDIR}/include/ciftiio
-+USRINCFLAGS = -fPIC -I${INC_NEWMAT} -I${INC_PROB} -I${INC_GD} -I${INC_GDC} -I${INC_PNG} -I${INC_ZLIB} -I${FSLEXTINC} ${CIFTICFLAGS} -I${INC_BOOST} -I${FSLDIR}/include/ciftiio
- USRLDFLAGS = -L${LIB_NEWMAT} -L${LIB_PROB} -L${LIB_GD} -L${LIB_GDC} -L${LIB_PNG} -L${LIB_ZLIB}
- 
- UNAME := $(shell uname)
-@@ -15,7 +15,7 @@ ifeq (${UNAME},Darwin)
-         LIBS = -liconv
- endif
- 
--LIBS += -lutils -lnewimage -lmiscplot -lmiscpic -lmiscmaths -lfslio -lniftiio -lcifti -lxml++-2.6 -lxml2 -lboost_filesystem -lboost_system -lznz -lnewmat -lprob -lm  -lgdc -lgd -lpng -lz
-+LIBS += -lutils -lnewimage -lmiscplot -lmiscpic -lmiscmaths -lfslio -lniftiio ${CIFTILIBS} -lboost_filesystem -lboost_system -lznz -lnewmat -lprob -lm  -lgdc -lgd -lpng -lz
- 
- TEST_OBJS = test.o 
- 
diff --git a/sci-biology/fsl/files/fsl-5.0.11-qstring_compat.patch b/sci-biology/fsl/files/fsl-5.0.11-qstring_compat.patch
deleted file mode 100644
index 78aa020c6..000000000
--- a/sci-biology/fsl/files/fsl-5.0.11-qstring_compat.patch
+++ /dev/null
@@ -1,63 +0,0 @@
-From bbd60f634cdcdfbbb3eb8f3b6d00f366d9f34bf9 Mon Sep 17 00:00:00 2001
-From: =?UTF-8?q?Fran=C3=A7ois=20Bissey?= <frp.bissey@gmail.com>
-Date: Thu, 18 Oct 2018 11:21:05 +1300
-Subject: [PATCH] Basic compatibility between for AString built with either
- glib ustring or QString
-
----
- src/flameo/gsa.cc      | 4 ++--
- src/melodic/meldata.cc | 2 +-
- src/melodic/meldata.h  | 2 +-
- 3 files changed, 4 insertions(+), 4 deletions(-)
-
-diff --git a/src/flameo/gsa.cc b/src/flameo/gsa.cc
-index 6a477f9..0860d46 100644
---- a/src/flameo/gsa.cc
-+++ b/src/flameo/gsa.cc
-@@ -74,7 +74,7 @@ namespace GSA {
-     sourceType=mode;
-     if ( sourceType.compare("CIFTI") == 0 ) {
-       cifti::CiftiFile inputCifti;
--      inputCifti.openFile(fslbasename(filename)+".nii");
-+      inputCifti.openFile((fslbasename(filename)+".nii").c_str());
-       ciftiExemplar=inputCifti.getCiftiXML();
-       cerr << "ndim " << ciftiExemplar.getNumberOfDimensions() << endl;
-       cerr << "type1 " << ciftiExemplar.getMappingType(0) << endl;
-@@ -194,7 +194,7 @@ namespace GSA {
-       scalarsMap.setLength(data.Nrows());
-       ciftiExemplar.setMap(0, scalarsMap);
-       CiftiFile outputFile;
--      outputFile.setWritingFile(fslbasename(filename)+extension+".nii");//sets up on-disk writing with default writing version
-+      outputFile.setWritingFile((fslbasename(filename)+extension+".nii").c_str());//sets up on-disk writing with default writing version
-       outputFile.setCiftiXML(ciftiExemplar,false);	    
-       vector<float> scratchRow(data.Nrows());//read/write a row at a time
-       for (int64_t row=0;row<data.Ncols();row++) {	    
-diff --git a/src/melodic/meldata.cc b/src/melodic/meldata.cc
-index f310dc7..5e9bc18 100644
---- a/src/melodic/meldata.cc
-+++ b/src/melodic/meldata.cc
-@@ -118,7 +118,7 @@ namespace Melodic{
-     	tmpData = RawData.matrix(Mask);
- 		memmsg(" after reshape ");	  
- 	} else { //Read in Cifti
--	  inputCifti.openFile(fname+".nii");
-+	  inputCifti.openFile((fname+".nii").c_str());
- 	  const vector<int64_t>& dims = inputCifti.getDimensions();
- 	  tmpData.ReSize(dims[0],dims[1]); //swapped compared to cifti
- 	  vector<float> scratchRow(dims[0]);//read/write a row at a time
-diff --git a/src/melodic/meldata.h b/src/melodic/meldata.h
-index 1e1adfc..d898152 100644
---- a/src/melodic/meldata.h
-+++ b/src/melodic/meldata.h
-@@ -109,7 +109,7 @@ namespace Melodic{
- 	  message("  " << logger.appendDir(fname) << endl);
- 	} else { //Process CIFTI save ICs as float
- 	  cifti::CiftiFile outputFile;
--	  outputFile.setWritingFile(logger.appendDir(fname)+".nii");//sets up on-disk writing with default writing version
-+	  outputFile.setWritingFile((logger.appendDir(fname)+".nii").c_str());//sets up on-disk writing with default writing version
- 	  cifti::CiftiXML xml(inputCifti.getCiftiXML());
- 	  cifti::CiftiScalarsMap scalarsMap;
- 	  std::vector<char> foo = xml.writeXMLToVector();
--- 
-2.18.1
-
diff --git a/sci-biology/fsl/files/fsl-5.0.11-setup.patch b/sci-biology/fsl/files/fsl-5.0.11-setup.patch
deleted file mode 100644
index cf9cb785d..000000000
--- a/sci-biology/fsl/files/fsl-5.0.11-setup.patch
+++ /dev/null
@@ -1,158 +0,0 @@
-diff --git a/build b/build
-index 6827443..19b2002 100755
---- a/build
-+++ b/build
-@@ -3,7 +3,7 @@
- if [ $# -ge 1 ] ; then
-   PROJECTS="$@";
- else
--  MASTERPROJECTS="CiftiLib-master utils znzlib NewNifti niftiio fslio giftiio miscmaths newimage libhfunc libvis first_lib \ 
-+  MASTERPROJECTS="utils znzlib NewNifti niftiio fslio giftiio miscmaths newimage libhfunc libvis first_lib \ 
- meshclass fslvtkio misc_tcl basisfield warpfns bint shapeModel MVdisc fslvtkconv fslsurface libmeshutils newmesh \
- DiscreteOpt FastPDlib MSMRegLib \
- misc_c avwutils basil bet2 cluster dpm copain tissue fast4 feat5 film filmbabe flirt fabber baycest \
-@@ -25,8 +25,8 @@ flameo oxford_asl relax qboot topup ptx2 lesions eddy dwssfp verbena MSM bianca
-   done
- fi
- 
--echo "Building projects - see build.log file for progress..."
--./config/common/buildproj $PROJECTS > ./build.log 2>&1
-+echo "Building projects"
-+./config/common/buildproj $PROJECTS
- finalStatus=$?
- if [ $finalStatus -eq 0 ]; then
-     echo "Build completed successfully.";
-diff --git a/config/common/buildproj b/config/common/buildproj
-index 3450bda..ec3edc1 100755
---- a/config/common/buildproj
-+++ b/config/common/buildproj
-@@ -11,10 +11,10 @@ if [ X$1 = X-strict ] ; then
- fi
- PROJECTS="$@" ; export PROJECTS ;
- 
--FSLDIR=`pwd`
-+#FSLDIR=`pwd`
- FSLDEVDIR=${FSLDIR}
- FSLCONFDIR=${FSLDIR}/config
--FSLMACHTYPE=`${FSLDIR}/etc/fslconf/fslmachtype.sh`
-+#FSLMACHTYPE=`${FSLDIR}/etc/fslconf/fslmachtype.sh`
- export FSLDIR FSLDEVDIR FSLCONFDIR FSLMACHTYPE
- 
- buildmessages="" ; export buildmessages ;
-@@ -66,7 +66,7 @@ for projname in $PROJECTS; do
- 	  if [ -x ./fslconfig ] ; then
- 	    . ./fslconfig ;
- 	  fi
--	  if ${MAKE} -k ${MAKEOPTIONS} ; then 
-+	  if ${MAKE} ${MAKEOPTIONS} ${MAKEOPTS} ; then 
- 	    if ${MAKE} ${MAKEOPTIONS} install ; then
- 	      installok=true;
- 	      # Clean up after ourselves
-@@ -81,6 +81,7 @@ for projname in $PROJECTS; do
- 	    if [ $installok = false ]  ; then
- 	      echo " "
- 	      echo "ERROR::Could not install $projname successfully" ;
-+	      exit 1
- 	    fi
- 	  else
- 	    echo " "
-@@ -89,6 +90,7 @@ for projname in $PROJECTS; do
- 	    echo " "
- 	    echo " "
- 	    errorprojs="$errorprojs $projname" ; export errorprojs ;
-+	    exit 1
- 	  fi
-     fi
- done
-diff --git a/config/common/vars.mk b/config/common/vars.mk
-index 53754be..ff7a117 100755
---- a/config/common/vars.mk
-+++ b/config/common/vars.mk
-@@ -24,15 +24,15 @@ USRINCFLAGS =
- USRCFLAGS = 
- USRCXXFLAGS =
- 
--LDFLAGS = ${ARCHLDFLAGS} ${USRLDFLAGS} -L. -L${DEVLIBDIR} -L${LIBDIR}
-+LDFLAGS = ${ARCHLDFLAGS} ${USRLDFLAGS} -L. -L${DEVLIBDIR} -L${LIBDIR} ${USERLDFLAGS}
- 
--AccumulatedIncFlags = -I${INC_BOOST} ${USRINCFLAGS} -I. -I${DEVINCDIR} -I${INCDIR}
-+AccumulatedIncFlags = ${USRINCFLAGS} -I. -I${DEVINCDIR} -I${INCDIR} ${CPPFLAGS}
- 
- CFLAGS = ${ANSI_FLAGS} ${ANSI_CFLAGS} ${DBGFLAGS} ${USEDCSTATICFLAGS} ${USRCFLAGS} ${ARCHFLAGS} ${OPTFLAGS}  \
--	${AccumulatedIncFlags}
-+	${AccumulatedIncFlags} ${USERCFLAGS}
- 
--CXXFLAGS = ${ANSI_FLAGS} ${ANSI_CXXFLAGS} ${DBGFLAGS} ${USEDCXXSTATICFLAGS} ${USRCXXFLAGS} ${ARCHFLAGS} ${OPTFLAGS}  \
--	${AccumulatedIncFlags}
-+CXXFLAGS = ${ANSI_CXXFLAGS} ${DBGFLAGS} ${USEDCXXSTATICFLAGS} ${USRCXXFLAGS} ${ARCHFLAGS} ${OPTFLAGS}  \
-+	${AccumulatedIncFlags} ${USERCXXFLAGS}
- 
- HFILES = *.h
- AFILES = *.a
-diff --git a/config/generic/systemvars.mk b/config/generic/systemvars.mk
-index e40e3d6..ddb5bfe 100755
---- a/config/generic/systemvars.mk
-+++ b/config/generic/systemvars.mk
-@@ -4,20 +4,20 @@ SHELL = /bin/sh
- 
- # System dependent commands (NB: the first two are the most platform dependent)
- 
--INSTALL = ginstall -p
--RANLIB = ranlib
-+INSTALL = install -p
-+RANLIB = @@GENTOO_RANLIB@@
- 
- RM = /bin/rm
- CP = /bin/cp
- MV = /bin/mv
- CHMOD = /bin/chmod
- MKDIR = /bin/mkdir
--TCLSH = ${FSLDIR}/bin/fsltclsh
-+TCLSH = tclsh
- 
- # Compiler dependent variables
- 
--CC = gcc
--CXX = c++
-+CC = @@GENTOO_CC@@
-+CXX = @@GENTOO_CXX@@
- CSTATICFLAGS = -static
- CXXSTATICFLAGS = -static
- 
-@@ -25,7 +25,7 @@ ARCHFLAGS =
- 
- DEPENDFLAGS = -MM
- 
--OPTFLAGS =  -O3 -fexpensive-optimizations ${ARCHFLAGS}
-+OPTFLAGS =
- MACHDBGFLAGS =
- GNU_ANSI_FLAGS = -Wall -ansi -pedantic
- SGI_ANSI_FLAGS = -ansi -fullwarn
-diff --git a/extras/build b/extras/build
-index 6133a1b..caeae2d 100755
---- a/extras/build
-+++ b/extras/build
-@@ -104,8 +104,8 @@ PROJECTS="${PROJECTS} libpng"
- if [ ${BUILDICONV} -eq 1 ]; then
-   PROJECTS="${PROJECTS} libiconv"
- fi
--PROJECTS="${PROJECTS} libgd libgdc libprob libcprob newmat cprob newran fftw"
--PROJECTS="${PROJECTS} boost libxml2-2.9.2 libxml++-2.34.0 libsqlite libnlopt ../include/armawrap/dummy_newmat"
-+PROJECTS="libgdc libprob libcprob newmat cprob newran"
-+PROJECTS="${PROJECTS} ../include/armawrap/dummy_newmat"
- for projname in $PROJECTS; do
-     if [ -d $FSLESRCDIR/$projname ] ; then
-        buildIt $FSLESRCDIR $projname 1 
-diff --git a/src/mist-clean/Makefile b/src/mist-clean/Makefile
-index b3a32fc..e949ba1 100755
---- a/src/mist-clean/Makefile
-+++ b/src/mist-clean/Makefile
-@@ -52,7 +52,7 @@ installpython:
- 		cp -r python/* ${DESTDIR}/python/mist
- 
- clean:
--			rm ${OBJS} mist/mist.o mist/mist
-+			rm -f ${OBJS} mist/mist.o mist/mist || echo "CLEAN could not locate some files scheduled for deletion."
- 
- .PHONY:		all clean installdata
- 
diff --git a/sci-biology/fsl/files/fsl-5.0.4-headers.patch b/sci-biology/fsl/files/fsl-5.0.4-headers.patch
deleted file mode 100644
index 803151bb7..000000000
--- a/sci-biology/fsl/files/fsl-5.0.4-headers.patch
+++ /dev/null
@@ -1,32 +0,0 @@
---- src/avwutils/fslmaths.cc.orig	2013-10-19 00:17:44.765129309 +1300
-+++ src/avwutils/fslmaths.cc	2013-10-19 00:18:02.975157728 +1300
-@@ -71,7 +71,7 @@
- #include "newimage/newimageall.h"
- #include "miscmaths/miscmaths.h"
- #include "utils/fsl_isfinite.h"
--#include "libprob/libprob.h"
-+#include "libprob.h"
- 
- using namespace MISCMATHS;
- using namespace NEWIMAGE;
---- src/miscvis/writepng.c.orig	2013-10-19 00:18:32.415203592 +1300
-+++ src/miscvis/writepng.c	2013-10-19 00:19:05.414255132 +1300
-@@ -32,6 +32,7 @@
- 
- #include <stdlib.h>     /* for exit() prototype */
- 
-+#include "zlib.h"
- #include "png.h"        /* libpng header; includes zlib.h and setjmp.h */
- #include "writepng.h"   /* typedefs, common macros, public prototypes */
- 
---- src/ptx2/surfmaths.cc.orig	2013-10-19 00:19:51.595327317 +1300
-+++ src/ptx2/surfmaths.cc	2013-10-19 00:20:09.284354805 +1300
-@@ -72,7 +72,7 @@
- #include "csv_mesh.h"
- #include "miscmaths/miscmaths.h"
- #include "utils/fsl_isfinite.h"
--#include "libprob/libprob.h"
-+#include "libprob.h"
- 
- using namespace MISCMATHS;
- 
diff --git a/sci-biology/fsl/files/fsl-5.0.4-setup.patch b/sci-biology/fsl/files/fsl-5.0.4-setup.patch
deleted file mode 100644
index 0b961492a..000000000
--- a/sci-biology/fsl/files/fsl-5.0.4-setup.patch
+++ /dev/null
@@ -1,110 +0,0 @@
---- extras/build.orig	2013-10-18 21:37:53.533939550 +1300
-+++ extras/build	2013-10-18 21:40:42.283158471 +1300
-@@ -41,7 +41,7 @@
- 
- errorprojs="" ; export errorprojs ;
- 
--PROJECTS="tcl tk zlib libpng libiconv libgd libgdc libprob libcprob newmat cprob newran cephes fftw"
-+PROJECTS="libgdc libprob libcprob newmat cprob newran cephes"
- 
- for projname in $PROJECTS; do
- 
---- build.orig	2013-10-18 22:24:22.312777248 +1300
-+++ build	2013-10-18 22:24:59.161835107 +1300
-@@ -11,8 +11,7 @@
- ifit load_varian load_dicom misc_scripts fdt first possum sgeutils flameo oxford_asl relax qboot topup ptx2 lesions eddy dwssfp";
- fi
- 
--echo "Building projects - see build.log file for progress..."
--./config/common/buildproj $PROJECTS > ./build.log 2>&1
--echo "Finished build : end of log file shows ..."
--tail -10 build.log
-+echo "Building projects"
-+./config/common/buildproj $PROJECTS
-+echo "Finished build"
- 
---- config/common/buildproj.orig	2013-10-18 22:28:40.683182435 +1300
-+++ config/common/buildproj	2013-10-18 22:29:09.612227825 +1300
-@@ -11,10 +11,10 @@
- fi
- PROJECTS="$@" ; export PROJECTS ;
- 
--FSLDIR=`pwd`
-+#FSLDIR=`pwd`
- FSLDEVDIR=${FSLDIR}
- FSLCONFDIR=${FSLDIR}/config
--FSLMACHTYPE=`${FSLDIR}/etc/fslconf/fslmachtype.sh`
-+#FSLMACHTYPE=`${FSLDIR}/etc/fslconf/fslmachtype.sh`
- export FSLDIR FSLDEVDIR FSLCONFDIR FSLMACHTYPE
- 
- buildmessages="" ; export buildmessages ;
---- config/generic/systemvars.mk.orig	2007-07-13 23:00:20.000000000 +1200
-+++ config/generic/systemvars.mk	2013-10-18 23:13:06.472693414 +1300
-@@ -4,20 +4,20 @@
- 
- # System dependent commands (NB: the first two are the most platform dependent)
- 
--INSTALL = ginstall -p
--RANLIB = ranlib
-+INSTALL = install -p
-+RANLIB = @@GENTOO_RANLIB@@
- 
- RM = /bin/rm
- CP = /bin/cp
- MV = /bin/mv
- CHMOD = /bin/chmod
- MKDIR = /bin/mkdir
--TCLSH = ${FSLDIR}/bin/fsltclsh
-+TCLSH = tclsh
- 
- # Compiler dependent variables
- 
--CC = gcc
--CXX = c++
-+CC = @@GENTOO_CC@@
-+CXX = @@GENTOO_CXX@@
- CSTATICFLAGS = -static
- CXXSTATICFLAGS = -static
- 
-@@ -25,7 +25,7 @@
- 
- DEPENDFLAGS = -MM
- 
--OPTFLAGS =  -O3 -fexpensive-optimizations ${ARCHFLAGS}
-+OPTFLAGS =
- MACHDBGFLAGS =
- GNU_ANSI_FLAGS = -Wall -ansi -pedantic
- SGI_ANSI_FLAGS = -ansi -fullwarn
---- config/common/vars.mk.orig	2013-10-18 23:39:26.384029157 +1300
-+++ config/common/vars.mk	2013-10-18 23:40:49.489145387 +1300
-@@ -24,15 +24,15 @@
- USRCFLAGS = 
- USRCXXFLAGS =
- 
--LDFLAGS = ${ARCHLDFLAGS} ${USRLDFLAGS} -L. -L${DEVLIBDIR} -L${LIBDIR}
-+LDFLAGS = ${ARCHLDFLAGS} ${USRLDFLAGS} -L. -L${DEVLIBDIR} -L${LIBDIR} ${USERLDFLAGS}
- 
--AccumulatedIncFlags = ${USRINCFLAGS} -I. -I${DEVINCDIR} -I${INCDIR}
-+AccumulatedIncFlags = ${USRINCFLAGS} -I. -I${DEVINCDIR} -I${INCDIR} ${CPPFLAGS}
- 
- CFLAGS = ${ANSI_FLAGS} ${DBGFLAGS} ${USEDCSTATICFLAGS} ${USRCFLAGS} ${ARCHFLAGS} ${OPTFLAGS}  \
--	${AccumulatedIncFlags}
-+	${AccumulatedIncFlags} ${USERCFLAGS}
- 
- CXXFLAGS = ${ANSI_FLAGS} ${DBGFLAGS} ${USEDCXXSTATICFLAGS} ${USRCXXFLAGS} ${ARCHFLAGS} ${OPTFLAGS}  \
--	${AccumulatedIncFlags}
-+	${AccumulatedIncFlags} ${USERCXXFLAGS}
- 
- HFILES = *.h
- AFILES = *.a
---- config/common/buildproj.orig	2013-10-19 23:27:10.477238469 +1300
-+++ config/common/buildproj	2013-10-19 23:28:32.207370622 +1300
-@@ -66,7 +66,7 @@
- 	  if [ -x fslconfig ] ; then
- 	    ./fslconfig ;
- 	  fi
--	  if ${MAKE} -k ${MAKEOPTIONS} ; then 
-+	  if ${MAKE} ${MAKEOPTIONS} ${MAKEOPTS} ; then 
- 	    if ${MAKE} install ; then
- 	      installok=true;
- 	      # Clean up after ourselves
diff --git a/sci-biology/fsl/files/fsl-5.0.6-fsldir_redux.patch b/sci-biology/fsl/files/fsl-5.0.6-fsldir_redux.patch
deleted file mode 100644
index a4fff260f..000000000
--- a/sci-biology/fsl/files/fsl-5.0.6-fsldir_redux.patch
+++ /dev/null
@@ -1,456 +0,0 @@
---- src/fast4/fast_two.cc.orig	2013-10-19 23:45:02.636971888 +1300
-+++ src/fast4/fast_two.cc	2013-10-19 23:46:45.436138299 +1300
-@@ -166,7 +166,7 @@
- string csfPriorName, grayPriorName, whitePriorName;
-   if(alternatePriors.unset())
-   {
--    string priorRootName=string(getenv("FSLDIR")) + "/data/standard/tissuepriors/avg152T1_";
-+    string priorRootName="@GENTOO_PORTAGE_EPREFIX@/usr/share/fsl/data/standard/tissuepriors/avg152T1_";
-     csfPriorName = priorRootName+"csf";
-     grayPriorName = priorRootName+"gray";
-     whitePriorName = priorRootName+"white";
-@@ -215,15 +215,15 @@
-     if(bapused>0)
-       {
- 	char reg[1024];
--	sprintf(reg, "%s/bin/flirt -ref %s -in %s -out %s -applyxfm -init %s", getenv("FSLDIR"), inname.c_str(), csfPriorName.c_str(), (main_prior_vol+"_csf_stdspace").c_str(),  bapriori.value().c_str());
-+	sprintf(reg, "flirt -ref %s -in %s -out %s -applyxfm -init %s", inname.c_str(), csfPriorName.c_str(), (main_prior_vol+"_csf_stdspace").c_str(),  bapriori.value().c_str());
-         if(verbose.value())
- 	  cout<<reg<<endl;
- 	system(reg);
--	sprintf(reg, "%s/bin/flirt -ref %s -in %s -out %s -applyxfm -init %s", getenv("FSLDIR"), inname.c_str(), grayPriorName.c_str(), (main_prior_vol+"_gm_stdspace").c_str(),  bapriori.value().c_str());
-+	sprintf(reg, "flirt -ref %s -in %s -out %s -applyxfm -init %s", inname.c_str(), grayPriorName.c_str(), (main_prior_vol+"_gm_stdspace").c_str(),  bapriori.value().c_str());
- 	if(verbose.value())
- 	  cout<<reg<<endl;
-         system(reg);
--	sprintf(reg, "%s/bin/flirt -ref %s -in %s -out %s -applyxfm -init %s", getenv("FSLDIR"), inname.c_str(), whitePriorName.c_str(), (main_prior_vol+"_wm_stdspace").c_str(),  bapriori.value().c_str());
-+	sprintf(reg, "flirt -ref %s -in %s -out %s -applyxfm -init %s", inname.c_str(), whitePriorName.c_str(), (main_prior_vol+"_wm_stdspace").c_str(),  bapriori.value().c_str());
- 	if(verbose.value())
- 	  cout << reg << endl;
- 	system(reg);
---- src/feat5/tsplot.cc.orig	2013-10-19 23:48:08.997273362 +1300
-+++ src/feat5/tsplot.cc	2013-10-19 23:50:59.376548902 +1300
-@@ -293,7 +293,7 @@
- ofstream     outputFile;
- int          numEVs, npts, numContrasts=1, nftests=0, GRPHSIZE(600), PSSIZE(600); 
- vector<double> normalisedContrasts, model, triggers;
-- string       fmriFileName, fslPath, featdir, vType, indexText;
-+ string       fmriFileName, featdir, vType, indexText;
- ColumnVector NewimageVoxCoord(4),NiftiVoxCoord(4);
- bool outputText(true), useCoordinate(false), prewhiten(false), useTriggers(false), customMask(false), modelFree(false), isHigherLevel(false), outputDataOnly(false);
- bool zWeightClusters(true);
-@@ -307,7 +307,6 @@
-   if (argc<2) usage("");
-   featdir=string(argv[1]);
-   fmriFileName=featdir+"/filtered_func_data";
--  fslPath=string(getenv("FSLDIR"));
- 
-   string outputName(featdir);
- 
-@@ -725,7 +724,7 @@
- 	cerr << "Can't open output report file " << outputName << endl;
- 	exit(1);
-       }
--      outputFile << "<HTML>\n<TITLE>"<< statType << num2str(i) <<"</TITLE>\n<BODY BACKGROUND=\"file:"<< fslPath <<"/doc/images/fsl-bg.jpg\">\n<hr><CENTER>\n<H1>FEAT Time Series Report - "<< statType << num2str(i) <<"</H1>\n</CENTER>\n<hr><b>Full plots</b><p>\n"<< graphText;
-+      outputFile << "<HTML>\n<TITLE>"<< statType << num2str(i) <<"</TITLE>\n<BODY BACKGROUND=\"file:"<< "@GENTOO_PORTAGE_EPREFIX@/usr/share/fsl/doc/images/fsl-bg.jpg\">\n<hr><CENTER>\n<H1>FEAT Time Series Report - "<< statType << num2str(i) <<"</H1>\n</CENTER>\n<hr><b>Full plots</b><p>\n"<< graphText;
-       if (useTriggers) outputFile << "\n<hr><b>Peristimulus plots</b><p>\n"<< peristimulusText <<"\n<HR></BODY></HTML>\n\n";
-       else outputFile << "\n</BODY></HTML>\n\n";
-       outputFile.close();
-@@ -740,7 +739,7 @@
-       cerr << "Can't open output report file " << outputName << endl;
-       exit(1);
-   }
--  outputFile << "<HTML>\n<TITLE>FEAT Time Series Report</TITLE>\n<BODY BACKGROUND=\"file:" << fslPath << "/doc/images/fsl-bg.jpg\">\n<hr><CENTER>\n<H1>FEAT Time Series Report</H1>\n</CENTER>\n<hr>" << indexText << "<HR></BODY></HTML>" << endl << endl;
-+  outputFile << "<HTML>\n<TITLE>FEAT Time Series Report</TITLE>\n<BODY BACKGROUND=\"file:" << "@GENTOO_PORTAGE_EPREFIX@/usr/share/fsl/doc/images/fsl-bg.jpg\">\n<hr><CENTER>\n<H1>FEAT Time Series Report</H1>\n</CENTER>\n<hr>" << indexText << "<HR></BODY></HTML>" << endl << endl;
-   outputFile.close();
- 
-   /* now output same thing without start and end, for inclusion in feat report */
---- src/feat5/feat_model.cc.orig	2013-10-19 23:52:13.456668655 +1300
-+++ src/feat5/feat_model.cc	2013-10-19 23:53:31.655795065 +1300
-@@ -734,7 +734,6 @@
-   vector<int> G;
-   vector<string> titles;
-   float  tr, mult, trmult, nltffwhm=0, maxconvwin=0;
--  char   fl[10000], *FSLDIR;
-   string fn, filename;
-   FONT_DATA *font_data = new FONT_DATA[1];
- 
-@@ -753,8 +752,6 @@
-   if (argc==3)
-     motionparams=remmean(read_ascii_matrix(argv[2]));
- 
--  FSLDIR=getenv("FSLDIR");
--
-   fn = string(argv[1])+".fsf";
- 
-   level      = atoi(find_line(fn, "fmri(level)", fl));
-@@ -1479,7 +1476,7 @@
-   writeCovarianceImage(string(argv[1])+"_cov.ppm", contrasts, F, nftests, realDesign, level, evs.eigenvals, font_data, contrasts.RE);
-   writeImagePreview(string(argv[1])+".ppm", contrasts, F, nftests, realDesign, level, evs, font_data, titles, tr, nltffwhm, nTimepoints, G);
- 
--  filename=string(getenv("FSLDIR"))+"/bin/wpng -q -overwrite  "+string(argv[1])+".ppm ";
-+  filename="wpng -q -overwrite  "+string(argv[1])+".ppm ";
-   system(filename.c_str());
- 
-   return(0);
-@@ -2122,6 +2119,6 @@
- 
-     fclose(outputfile);
- 
--    filename=string(getenv("FSLDIR")) + "/bin/wpng -q -overwrite  " + filename;
-+    filename="wpng -q -overwrite  " + filename;
-     system(filename.c_str());
- }
---- src/first/first_utils.cc.orig	2013-10-19 23:54:30.375890034 +1300
-+++ src/first/first_utils.cc	2013-10-19 23:59:11.706344887 +1300
-@@ -1954,8 +1954,8 @@
-     if (!surfaceVAout.value()) {
-       // do not output on the surface, instead do the new default of outputting a volume with the scalar normal dot product values (for use with randomise)
-       volume<float> refim;
--      if (useReconMNI.value()) { read_volume(refim,string(getenv("FSLDIR")) + "/data/standard/MNI152_T1_1mm"); } 
--      else { read_volume(refim,string(getenv("FSLDIR")) + "/data/standard/MNI152_T1_1mm"); } 
-+      if (useReconMNI.value()) { read_volume(refim,"@GENTOO_PORTAGE_EPREFIX@/usr/share/fsl/data/standard/MNI152_T1_1mm"); } 
-+      else { read_volume(refim,"@GENTOO_PORTAGE_EPREFIX@/usr/share/fsl/data/standard/MNI152_T1_1mm"); } 
-       volume<float> maskvol(refim);
-       maskvol=0.0f;
-       volume4D<float> volnormals;
---- src/fnirt/fnirtfns.cpp.orig	2013-10-20 00:00:18.106452166 +1300
-+++ src/fnirt/fnirtfns.cpp	2013-10-20 00:04:56.005901533 +1300
-@@ -1203,8 +1203,7 @@
-       return(string(ref_fname));
-     }
-     else {
--      const char *fsldir_ptr = getenv("FSLDIR");
--      string eref_fname = string(fsldir_ptr) + string("/data/standard/") + ref_fname;
-+      string eref_fname = string("@GENTOO_PORTAGE_EPREFIX@/usr/share/fsl/data/standard/") + ref_fname;
-       if (NEWIMAGE::fsl_imageexists(eref_fname)) return(eref_fname);
-       else return(string(""));
-     }
-@@ -1230,9 +1229,8 @@
-       NEWIMAGE::read_volume_hdr_only(vref,ref_fname); // Throws if file dont exist
-       eref_fname = ref_fname;
-     }
--    catch(...) { // Didn't exist in current directory, try in ${FSLDIR}/data/standard
--      const char *fsldir_ptr = getenv("FSLDIR");
--      eref_fname = string(fsldir_ptr) + string("/data/standard/") + ref_fname;
-+    catch(...) { // Didn't exist in current directory, try in .../data/standard
-+      eref_fname = string("@GENTOO_PORTAGE_EPREFIX@/usr/share/fsl/data/standard/") + ref_fname;
-       try {
-         cout << "Could not find " << ref_fname << ", now checking " << eref_fname << endl;
-         NEWIMAGE::read_volume_hdr_only(vref,eref_fname); // Throws if file dont exist
-@@ -1267,8 +1265,7 @@
-     if (check_exist(ecfname)) return(ecfname);
-   }
-   if (!FNIRT::path(cfname).length()) {              // If no path explicitly given
--    const char *fsldir_ptr = getenv("FSLDIR");
--    ecfname = string(fsldir_ptr) + string("/etc/flirtsch/") + cfname;
-+    ecfname = string("@GENTOO_PORTAGE_EPREFIX@/etc/flirtsch/") + cfname;
-     if (check_exist(ecfname)) return(ecfname);
-     else if (!FNIRT::extension(ecfname).length()) { // If no path _and_ no extension given
-       ecfname += string(".cnf");
---- src/fslsurface/fslsurface_first.cc.orig	2013-10-20 00:05:35.495965454 +1300
-+++ src/fslsurface/fslsurface_first.cc	2013-10-20 00:06:54.346092913 +1300
-@@ -500,8 +500,7 @@
-             
- 			volume<float>* immni = new volume<float>();
-             
--            char* fsldir = getenv("FSLDIR");
--            read_volume_hdr_only(*immni, string(fsldir) + "/data/standard/MNI152_T1_1mm");
-+            read_volume_hdr_only(*immni, "@GENTOO_PORTAGE_EPREFIX@/usr/share/fsl/data/standard/MNI152_T1_1mm");
-             
- 			//read_volume_hdr_only(*immni, template_name);
- 			
-@@ -699,8 +698,7 @@
-           
- 			volume<float>* immni = new volume<float>();
-             
--            char* fsldir = getenv("FSLDIR");
--            read_volume_hdr_only(*immni, string(fsldir) + "/data/standard/MNI152_T1_1mm");
-+            read_volume_hdr_only(*immni, "@GENTOO_PORTAGE_EPREFIX@/usr/share/fsl/data/standard/MNI152_T1_1mm");
-             
- 			//read_volume_hdr_only(*immni, template_name);
- 			
---- src/fslsurface/fslsurfacemaths.cpp.orig	2013-10-20 00:07:39.457165850 +1300
-+++ src/fslsurface/fslsurfacemaths.cpp	2013-10-20 00:09:28.396341998 +1300
-@@ -598,12 +598,6 @@
- 
-         }else if (command == "-reconFromBvars"){
-             cout<<"do recon "<<endl;
--            char* fsldir = getenv("FSLDIR");
--            if (fsldir == NULL)
--            {
--                cerr<<"FSLDIR has not been set. "<<endl;
--                exit(EXIT_FAILURE); 
--            }
-             //file.bvars,mni_template.nii.gz
-            // string mni = string(fsldir)+"/data/standard/MNI152_T1_1mm";
-             reconSurface_from_bvars( surf, string(argv[i_arg+1]));
-@@ -612,12 +606,6 @@
- 
-         }else if (command == "-reconAllFromBvarsAndSave"){
-             cout<<"do recon+save "<<argc<<" "<<i_arg<<endl;
--            char* fsldir = getenv("FSLDIR");
--            if (fsldir == NULL)
--            {
--                cerr<<"FSLDIR has not been set. "<<endl;
--                exit(EXIT_FAILURE); 
--            }
-             //file.bvars,mni_template.nii.gz
-             // string mni = string(fsldir)+"/data/standard/MNI152_T1_1mm";
-             cout<<"recon "<< string(argv[i_arg+1])<<endl;
---- src/libvis/miscpic.h.orig	2013-10-20 00:11:03.706496109 +1300
-+++ src/libvis/miscpic.h	2013-10-20 00:12:24.515626764 +1300
-@@ -89,12 +89,7 @@
- 	LR_label_flag = true;
- 	trans= -10;
- 	edgethresh = 0.0;
--	if(getenv("FSLDIR")!=0){
--	  lutbase = string(getenv("FSLDIR")) + "/etc/luts/";
--	}
--	else{
--	  lutbase = string("/");
--	}
-+	lutbase = "@GENTOO_PORTAGE_EPREFIX@/etc/luts/";
- 	title = string("");
- 	cbartype = string("");
- 	cbarptr = NULL;
---- src/melodic/melreport.cc.orig	2013-10-20 00:13:01.475686492 +1300
-+++ src/melodic/melreport.cc	2013-10-20 00:15:02.795882687 +1300
-@@ -85,7 +85,7 @@
- 
-       {//start IC page
- 				IChtml << "<HTML><HEAD><link REL=stylesheet TYPE=text/css href=file:" +
--					(string) getenv("FSLDIR") +"/doc/fsl.css>" << endl
-+					"@GENTOO_PORTAGE_EPREFIX@/usr/share/fsl/doc/fsl.css>" << endl
- 					<< "<style type=\"text/css\">OBJECT { width: 100% }</style>"
- 	       	<< "<TITLE>FSL</TITLE></HEAD>" << endl
- 	  			<< "<IFRAME  height=" << int(melodat.get_numfiles()/30 + 1)*50 
-@@ -488,7 +488,7 @@
-       {//start IC2 page
- 				IChtml2.setDir(report.getDir(),mmodel.get_prefix()+"_MM.html");
- 				IChtml2 << "<HTML><HEAD><link REL=stylesheet TYPE=text/css href=file:" +
--					(string) getenv("FSLDIR") +"/doc/fsl.css>" << endl
-+					"@GENTOO_PORTAGE_EPREFIX@/usr/share/fsl/doc/fsl.css>" << endl
- 					<< "<style type=\"text/css\">OBJECT { width: 100% }</style>"
- 	       	<< "<TITLE>FSL</TITLE></HEAD>" << endl
- 					<< "<IFRAME  height="<< int(melodat.get_numfiles()/30 + 1)*50 
-@@ -666,8 +666,8 @@
- 				IChtml << "<HTML> " << endl
- 	       	<< "<TITLE>MELODIC Component " << num2str(cnum)
- 	       	<< "</TITLE>" << endl
--	       	<< "<BODY BACKGROUND=\"file:" << getenv("FSLDIR") 
--	    		<< "/doc/images/fsl-bg.jpg\">" << endl 
-+	       	<< "<BODY BACKGROUND=\"file:"  
-+	    		<< "@GENTOO_PORTAGE_EPREFIX@/usr/share/fsl/doc/images/fsl-bg.jpg\">" << endl 
- 	     		<< "<hr><CENTER><H1>MELODIC Component " << num2str(cnum)
- 	       	<< "</H1>"<< endl;
- 	
---- src/melodic/meloptions.cc.orig	2013-10-20 00:15:46.755953769 +1300
-+++ src/melodic/meloptions.cc	2013-10-20 00:18:26.176211442 +1300
-@@ -93,14 +93,6 @@
-   		explicitnums = false;
-   		logfname = string("log.txt");
- 
--  		// work out the path to the $FSLDIR/bin directory
--  		if(getenv("FSLDIR")!=0){
--    		binpath = (string) getenv("FSLDIR") + "/bin/";
--  		} else{
--    		binpath = argv[0];
--    		binpath = binpath.substr(0,binpath.length()-7);
--  		}
--
-   		// parse once to establish log directory name
-   		for(int a = options.parse_command_line(argc, argv); a < argc; a++);
- 
---- src/melodic/meloptions.h.orig	2013-10-20 00:19:32.176318206 +1300
-+++ src/melodic/meloptions.h	2013-10-20 00:19:53.455352701 +1300
-@@ -93,7 +93,6 @@
-   	~MelodicOptions() { delete gopt; }
-   
-   	string version;
--  	string binpath;
-   	string logfname;
-   	bool   filtermode;
-   	bool   explicitnums;
---- src/melodic/meldata.cc.orig	2013-10-20 00:20:45.856437466 +1300
-+++ src/melodic/meldata.cc	2013-10-20 00:21:48.655538924 +1300
-@@ -921,7 +921,7 @@
-   void MelodicData::est_smoothness()
-   {
-     if(Resels == 0){
--      string SM_path = opts.binpath + "smoothest";
-+      string SM_path = "smoothest";
-       string Mask_fname = logger.appendDir("mask");
- 
-       if(opts.segment.value().length()>0){
-@@ -1086,7 +1086,7 @@
- 				// set up all strings
- 				string BET_outputfname = string(Mean_fname)+"_brain";
- 
--				string BET_path = opts.binpath + "bet";
-+				string BET_path = "bet";
- 				string BET_optarg = "-m -f 0.4"; // see man bet
- 				string Mask_fname = BET_outputfname+"_mask";
- 
---- src/melodic/melreport.h.orig	2013-10-20 00:22:41.816624872 +1300
-+++ src/melodic/melreport.h	2013-10-20 00:24:25.555792499 +1300
-@@ -105,20 +105,20 @@
- 		    		system(("mkdir "+ logger.appendDir("report") + " 2>/dev/null").c_str());
- 				report.setDir(logger.appendDir("report"),"00index.html",true,false,ios::out);
- 						report << "<HTML><HEAD><link REL=stylesheet TYPE=text/css href=file:" +
--							(string) getenv("FSLDIR") +"/doc/fsl.css>" 
-+							"@GENTOO_PORTAGE_EPREFIX@/usr/share/fsl/doc/fsl.css>" 
- 						  << "<TITLE>MELODIC report</TITLE></HEAD><BODY>"
- 							<< endl <<endl;
- 						loghtml.setDir(report.getDir(),"log.html");
- 						loghtml << "<HTML><HEAD><link REL=stylesheet TYPE=text/css href=file:" +
--							(string) getenv("FSLDIR") +"/doc/fsl.css>" 
-+							"@GENTOO_PORTAGE_EPREFIX@/usr/share/fsl/doc/fsl.css>" 
- 						  << "<TITLE>MELODIC report</TITLE></HEAD><BODY>"
- 							<< endl <<endl;						
- 						navigator.setDir(report.getDir(),"nav.html");
- 						head.setDir(report.getDir(),"head.html");
- 	  				navigator << "<link REL=stylesheet TYPE=text/css href=file:"+
--							(string) getenv("FSLDIR") +"/doc/fsl.css>"  << endl;
-+							"@GENTOO_PORTAGE_EPREFIX@/usr/share/fsl/doc/fsl.css>"  << endl;
- 						head << "<link REL=stylesheet TYPE=text/css href=file:"+
--							(string) getenv("FSLDIR") +"/doc/fsl.css>"  << endl;
-+							"@GENTOO_PORTAGE_EPREFIX@/usr/share/fsl/doc/fsl.css>"  << endl;
- 						head  <<"<TABLE BORDER=0><TR>" << endl
- 							<<" <TD ALIGN=CENTER WIDTH=100%>"<< endl
- 							<<"<TABLE BORDER=0>"<< endl
-@@ -130,8 +130,8 @@
- 							<< "</tr></table>" << endl
- 							<< "<TD ALIGN=RIGHT>" << endl
- 							<< "<a href=http://www.fmrib.ox.ac.uk/fsl target=_top>" << endl
--						  << "<IMG BORDER=0 SRC=file:"<< getenv("FSLDIR")
--							<< "/doc/images/fsl-logo-big.jpg WIDTH=165></a>" << endl
-+						  << "<IMG BORDER=0 SRC=file:"
-+							<< "@GENTOO_PORTAGE_EPREFIX@/usr/share/fsl/doc/images/fsl-logo-big.jpg WIDTH=165></a>" << endl
- 							<< "</TD>"<<endl<<"</TR></TABLE> <hr>"<<endl;
- 						if(opts.guireport.value()==""){
- 							report <<"<OBJECT data=head.html></OBJECT>" <<  endl;
---- src/mm/mixture_model.cc.orig	2013-10-20 00:25:00.355848878 +1300
-+++ src/mm/mixture_model.cc	2013-10-20 00:25:32.185900186 +1300
-@@ -2224,8 +2224,8 @@
- 
- 	htmllog << "<HTML> " << endl
- 		<< "<TITLE>Mixture Model fit for" << data_name << "</TITLE>" << endl
--		<< "<BODY BACKGROUND=\"file:" << getenv("FSLDIR") 
--		<< "/doc/images/fsl-bg.jpg\">" << endl 
-+		<< "<BODY BACKGROUND=\"file:"  
-+		<< "@GENTOO_PORTAGE_EPREFIX@/usr/share/fsl/doc/images/fsl-bg.jpg\">" << endl 
- 		<< "<hr><CENTER><H1>Mixture Model fit for<br>" << data_name << " </H1>"<< endl;
-      	
- 	htmllog << "<hr><p>" << endl;
---- src/siena/siena_diff.cc.orig	2013-10-20 00:26:13.215966685 +1300
-+++ src/siena/siena_diff.cc	2013-10-20 00:28:03.925145734 +1300
-@@ -107,7 +107,7 @@
- {
-   // {{{  vars
- 
--char   thestring[10000], segoptions[10000], fsldir[10000];
-+char   thestring[10000], segoptions[10000];
- int    x_size, y_size, z_size, size, x, y, z, i, count,
-   seg2=0, ignore_z=0, ignore_top_slices=0, //erode_mask=0, 
-   ignore_bottom_slices=0, debug=0, flow_output=1, edge_masking=0;
-@@ -124,8 +124,6 @@
- 
- string argv1(argv[1]), argv2(argv[2]);
- 
--sprintf(fsldir,"%s",getenv("FSLDIR"));
--
- for (i = 3; i < argc; i++) {
-   if (!strcmp(argv[i], "-i"))
-     ignore_z=1;
-@@ -209,26 +207,26 @@
- // }}}
-   // {{{  transform images and masks
- 
--sprintf(thestring,"%s/bin/flirt -o %s_halfwayto_%s -applyisoxfm 1 -paddingsize 0 -init %s_halfwayto_%s.mat -ref %s -in %s",
--	fsldir,argv[1],argv[2],argv[1],argv[2],argv[1],argv[1]);
-+sprintf(thestring,"flirt -o %s_halfwayto_%s -applyisoxfm 1 -paddingsize 0 -init %s_halfwayto_%s.mat -ref %s -in %s",
-+	argv[1],argv[2],argv[1],argv[2],argv[1],argv[1]);
- printf("%s\n",thestring); system(thestring);
- 
--sprintf(thestring,"%s/bin/flirt -o %s_halfwayto_%s -applyisoxfm 1 -paddingsize 0 -init %s_halfwayto_%s.mat -ref %s -in %s",
--	fsldir,argv[2],argv[1],argv[2],argv[1],argv[1],argv[2]);
-+sprintf(thestring,"flirt -o %s_halfwayto_%s -applyisoxfm 1 -paddingsize 0 -init %s_halfwayto_%s.mat -ref %s -in %s",
-+	argv[2],argv[1],argv[2],argv[1],argv[1],argv[2]);
- printf("%s\n",thestring); system(thestring);
- 
--sprintf(thestring,"%s/bin/flirt -o %s_halfwayto_%s_mask -applyisoxfm 1 -paddingsize 0 -init %s_halfwayto_%s.mat -ref %s -in %s_brain_mask",
--	fsldir,argv[1],argv[2],argv[1],argv[2],argv[1],argv[1]);
-+sprintf(thestring,"flirt -o %s_halfwayto_%s_mask -applyisoxfm 1 -paddingsize 0 -init %s_halfwayto_%s.mat -ref %s -in %s_brain_mask",
-+	argv[1],argv[2],argv[1],argv[2],argv[1],argv[1]);
- printf("%s\n",thestring); system(thestring);
- 
--sprintf(thestring,"%s/bin/flirt -o %s_halfwayto_%s_mask -applyisoxfm 1 -paddingsize 0 -init %s_halfwayto_%s.mat -ref %s -in %s_brain_mask",
--	fsldir,argv[2],argv[1],argv[2],argv[1],argv[1],argv[2]);
-+sprintf(thestring,"flirt -o %s_halfwayto_%s_mask -applyisoxfm 1 -paddingsize 0 -init %s_halfwayto_%s.mat -ref %s -in %s_brain_mask",
-+	argv[2],argv[1],argv[2],argv[1],argv[1],argv[2]);
- printf("%s\n",thestring); system(thestring);
- 
- if (edge_masking)
- {
--  sprintf(thestring,"%s/bin/flirt -o %s_halfwayto_%s_valid_mask -applyisoxfm 1 -paddingsize 0 -init %s_halfwayto_%s.mat -ref %s -in %s_valid_mask_with_%s",
--	  fsldir,argv[1],argv[2],argv[1],argv[2],argv[1],argv[1],argv[2]);
-+  sprintf(thestring,"flirt -o %s_halfwayto_%s_valid_mask -applyisoxfm 1 -paddingsize 0 -init %s_halfwayto_%s.mat -ref %s -in %s_valid_mask_with_%s",
-+	  argv[1],argv[2],argv[1],argv[2],argv[1],argv[1],argv[2]);
-   printf("%s\n",thestring); system(thestring);
- }
- 
-@@ -287,8 +285,8 @@
-     cout << "saving image 1 to disk prior to segmentation" << endl;
-     save_volume(in1,argv1+"_halfwayto_"+argv2+"_brain");
-     in1.destroy();
--    sprintf(thestring,"%s/bin/fast %s %s %s_halfwayto_%s_brain > %s_halfwayto_%s_brain.vol 2>&1",
--	    fsldir,segtype,segoptions,argv[1],argv[2],argv[1],argv[2]);
-+    sprintf(thestring,"fast %s %s %s_halfwayto_%s_brain > %s_halfwayto_%s_brain.vol 2>&1",
-+	    segtype,segoptions,argv[1],argv[2],argv[1],argv[2]);
-     cout << thestring << endl;
-     system(thestring);
-   }
---- src/topup/topupfns.cpp.orig	2013-10-20 00:28:36.456198320 +1300
-+++ src/topup/topupfns.cpp	2013-10-20 00:29:37.905297565 +1300
-@@ -463,8 +463,7 @@
-     if (TOPUP::check_exist(ecfname)) return(ecfname);
-   }
-   if (!TOPUP::path(cfname).length()) {              // If no path explicitly given
--    const char *fsldir_ptr = getenv("FSLDIR");
--    ecfname = string(fsldir_ptr) + string("/etc/flirtsch/") + cfname;
-+    ecfname = string("@GENTOO_PORTAGE_EPREFIX@/etc/flirtsch/") + cfname;
-     if (TOPUP::check_exist(ecfname)) return(ecfname);
-     else if (!TOPUP::extension(ecfname).length()) { // If no path _and_ no extension given
-       ecfname += string(".cnf");
---- etc/matlab/call_fsl.m.orig	2013-10-20 23:17:58.626045346 +1300
-+++ etc/matlab/call_fsl.m	2013-10-20 23:20:06.556252150 +1300
-@@ -8,7 +8,7 @@
- % Debian/Ubuntu users should uncomment as
- % indicated
- 
--fsldir=getenv('FSLDIR');
-+%fsldir=getenv('FSLDIR');
- 
- % Debian/Ubuntu - uncomment the following
- %fsllibdir=sprintf('%s/%s', fsldir, 'bin');
---- etc/js/label-div.html.orig	2013-10-20 23:22:04.906443685 +1300
-+++ etc/js/label-div.html	2013-10-20 23:23:35.006589232 +1300
-@@ -2,12 +2,12 @@
-   <head>
-     <title>label-div</title>
-     <!--[if IE]>
--    <script type="text/javascript" src="FSLDIR/etc/js/excanvas.js"></script>
-+    <script type="text/javascript" src="@GENTOO_PORTAGE_EPREFIX@/etc/js/excanvas.js"></script>
-     <![endif]-->
--    <script type="text/javascript" src="FSLDIR/etc/js/strftime-min.js"></script>
--    <script type="text/javascript" src="FSLDIR/etc/js/rgbcolor.js"></script>
--    <script type="text/javascript" src="FSLDIR/etc/js/dygraph-canvas.js"></script>
--    <script type="text/javascript" src="FSLDIR/etc/js/dygraph.js"></script>
-+    <script type="text/javascript" src="@GENTOO_PORTAGE_EPREFIX@/etc/js/strftime-min.js"></script>
-+    <script type="text/javascript" src="@GENTOO_PORTAGE_EPREFIX@/etc/js/rgbcolor.js"></script>
-+    <script type="text/javascript" src="@GENTOO_PORTAGE_EPREFIX@/etc/js/dygraph-canvas.js"></script>
-+    <script type="text/javascript" src="@GENTOO_PORTAGE_EPREFIX@/etc/js/dygraph.js"></script>
-     <script type="text/javascript" src="PNMDATA.js"></script>
-   </head>
-   <body>
diff --git a/sci-biology/fsl/files/fsl-5.0.8-fsldir_redux.patch b/sci-biology/fsl/files/fsl-5.0.8-fsldir_redux.patch
deleted file mode 100644
index 593c1c807..000000000
--- a/sci-biology/fsl/files/fsl-5.0.8-fsldir_redux.patch
+++ /dev/null
@@ -1,452 +0,0 @@
-diff -Naur src.orig/fast4/fast_two.cc src/fast4/fast_two.cc

---- src.orig/fast4/fast_two.cc	2015-03-30 11:54:10.522550233 +1300

-+++ src/fast4/fast_two.cc	2015-03-30 11:54:18.412569892 +1300

-@@ -166,7 +166,7 @@

- string csfPriorName, grayPriorName, whitePriorName;

-   if(alternatePriors.unset())

-   {

--    string priorRootName=string(getenv("FSLDIR")) + "/data/standard/tissuepriors/avg152T1_";

-+    string priorRootName="@GENTOO_PORTAGE_EPREFIX@/usr/share/fsl/data/standard/tissuepriors/avg152T1_";

-     csfPriorName = priorRootName+"csf";

-     grayPriorName = priorRootName+"gray";

-     whitePriorName = priorRootName+"white";

-@@ -215,15 +215,15 @@

-     if(bapused>0)

-       {

- 	char reg[1024];

--	sprintf(reg, "%s/bin/flirt -ref %s -in %s -out %s -applyxfm -init %s", getenv("FSLDIR"), inname.c_str(), csfPriorName.c_str(), (main_prior_vol+"_csf_stdspace").c_str(),  bapriori.value().c_str());

-+	sprintf(reg, "flirt -ref %s -in %s -out %s -applyxfm -init %s", inname.c_str(), csfPriorName.c_str(), (main_prior_vol+"_csf_stdspace").c_str(),  bapriori.value().c_str());

-         if(verbose.value())

- 	  cout<<reg<<endl;

- 	system(reg);

--	sprintf(reg, "%s/bin/flirt -ref %s -in %s -out %s -applyxfm -init %s", getenv("FSLDIR"), inname.c_str(), grayPriorName.c_str(), (main_prior_vol+"_gm_stdspace").c_str(),  bapriori.value().c_str());

-+	sprintf(reg, "flirt -ref %s -in %s -out %s -applyxfm -init %s", inname.c_str(), grayPriorName.c_str(), (main_prior_vol+"_gm_stdspace").c_str(),  bapriori.value().c_str());

- 	if(verbose.value())

- 	  cout<<reg<<endl;

-         system(reg);

--	sprintf(reg, "%s/bin/flirt -ref %s -in %s -out %s -applyxfm -init %s", getenv("FSLDIR"), inname.c_str(), whitePriorName.c_str(), (main_prior_vol+"_wm_stdspace").c_str(),  bapriori.value().c_str());

-+	sprintf(reg, "flirt -ref %s -in %s -out %s -applyxfm -init %s", inname.c_str(), whitePriorName.c_str(), (main_prior_vol+"_wm_stdspace").c_str(),  bapriori.value().c_str());

- 	if(verbose.value())

- 	  cout << reg << endl;

- 	system(reg);

-diff -Naur src.orig/feat5/feat_model.cc src/feat5/feat_model.cc

---- src.orig/feat5/feat_model.cc	2015-03-30 11:54:10.502550183 +1300

-+++ src/feat5/feat_model.cc	2015-03-30 11:54:18.412569892 +1300

-@@ -741,7 +741,7 @@

-   vector<int> G;

-   vector<string> titles;

-   float  tr, mult, trmult, nltffwhm=0, maxconvwin=0;

--  char   fl[10000], *FSLDIR;

-+  char   fl[10000];

-   string fn, filename;

-   FONT_DATA *font_data = new FONT_DATA[1];

- 

-@@ -760,8 +760,6 @@

-   if (argc==3)

-     motionparams=remmean(read_ascii_matrix(argv[2]));

- 

--  FSLDIR=getenv("FSLDIR");

--

-   fn = string(argv[1])+".fsf";

- 

-   level      = atoi(find_line(fn, "fmri(level)", fl));

-@@ -1491,7 +1489,7 @@

-   writeCovarianceImage(string(argv[1])+"_cov.ppm", contrasts, F, nftests, realDesign, level, evs.eigenvals, font_data, contrasts.RE);

-   writeImagePreview(string(argv[1])+".ppm", contrasts, F, nftests, realDesign, level, evs, font_data, titles, tr, nltffwhm, nTimepoints, G);

- 

--  filename=string(getenv("FSLDIR"))+"/bin/wpng -q -overwrite  "+string(argv[1])+".ppm ";

-+  filename="wpng -q -overwrite  "+string(argv[1])+".ppm ";

-   system(filename.c_str());

- 

-   return(0);

-@@ -2134,6 +2132,6 @@

- 

-     fclose(outputfile);

- 

--    filename=string(getenv("FSLDIR")) + "/bin/wpng -q -overwrite  " + filename;

-+    filename="wpng -q -overwrite  " + filename;

-     system(filename.c_str());

- }

-diff -Naur src.orig/feat5/tsplot.cc src/feat5/tsplot.cc

---- src.orig/feat5/tsplot.cc	2015-03-30 11:54:10.502550183 +1300

-+++ src/feat5/tsplot.cc	2015-03-30 11:54:18.412569892 +1300

-@@ -293,7 +293,7 @@

- ofstream     outputFile;

- int          numEVs, npts, numContrasts=1, nftests=0, GRPHSIZE(600), PSSIZE(600); 

- vector<double> normalisedContrasts, model, triggers;

-- string       fmriFileName, fslPath, featdir, vType, indexText;

-+ string       fmriFileName, featdir, vType, indexText;

- ColumnVector NewimageVoxCoord(4),NiftiVoxCoord(4);

- bool outputText(true), useCoordinate(false), prewhiten(false), useTriggers(false), customMask(false), modelFree(false), isHigherLevel(false), outputDataOnly(false);

- bool zWeightClusters(true);

-@@ -307,7 +307,6 @@

-   if (argc<2) usage("");

-   featdir=string(argv[1]);

-   fmriFileName=featdir+"/filtered_func_data";

--  fslPath=string(getenv("FSLDIR"));

- 

-   string outputName(featdir);

- 

-@@ -725,7 +724,7 @@

- 	cerr << "Can't open output report file " << outputName << endl;

- 	exit(1);

-       }

--      outputFile << "<HTML>\n<TITLE>"<< statType << num2str(i) <<"</TITLE>\n<BODY BACKGROUND=\"file:"<< fslPath <<"/doc/images/fsl-bg.jpg\">\n<hr><CENTER>\n<H1>FEAT Time Series Report - "<< statType << num2str(i) <<"</H1>\n</CENTER>\n<hr><b>Full plots</b><p>\n"<< graphText;

-+      outputFile << "<HTML>\n<TITLE>"<< statType << num2str(i) <<"</TITLE>\n<BODY BACKGROUND=\"file:"<< "@GENTOO_PORTAGE_EPREFIX@/usr/share/fsl/doc/images/fsl-bg.jpg\">\n<hr><CENTER>\n<H1>FEAT Time Series Report - "<< statType << num2str(i) <<"</H1>\n</CENTER>\n<hr><b>Full plots</b><p>\n"<< graphText;

-       if (useTriggers) outputFile << "\n<hr><b>Peristimulus plots</b><p>\n"<< peristimulusText <<"\n<HR></BODY></HTML>\n\n";

-       else outputFile << "\n</BODY></HTML>\n\n";

-       outputFile.close();

-@@ -740,7 +739,7 @@

-       cerr << "Can't open output report file " << outputName << endl;

-       exit(1);

-   }

--  outputFile << "<HTML>\n<TITLE>FEAT Time Series Report</TITLE>\n<BODY BACKGROUND=\"file:" << fslPath << "/doc/images/fsl-bg.jpg\">\n<hr><CENTER>\n<H1>FEAT Time Series Report</H1>\n</CENTER>\n<hr>" << indexText << "<HR></BODY></HTML>" << endl << endl;

-+  outputFile << "<HTML>\n<TITLE>FEAT Time Series Report</TITLE>\n<BODY BACKGROUND=\"file:" << "@GENTOO_PORTAGE_EPREFIX@/usr/share/fsl/doc/images/fsl-bg.jpg\">\n<hr><CENTER>\n<H1>FEAT Time Series Report</H1>\n</CENTER>\n<hr>" << indexText << "<HR></BODY></HTML>" << endl << endl;

-   outputFile.close();

- 

-   /* now output same thing without start and end, for inclusion in feat report */

-diff -Naur src.orig/first/first_utils.cc src/first/first_utils.cc

---- src.orig/first/first_utils.cc	2015-03-30 11:54:10.482550135 +1300

-+++ src/first/first_utils.cc	2015-03-30 11:54:18.412569892 +1300

-@@ -1954,8 +1954,8 @@

-     if (!surfaceVAout.value()) {

-       // do not output on the surface, instead do the new default of outputting a volume with the scalar normal dot product values (for use with randomise)

-       volume<float> refim;

--      if (useReconMNI.value()) { read_volume(refim,string(getenv("FSLDIR")) + "/data/standard/MNI152_T1_1mm"); } 

--      else { read_volume(refim,string(getenv("FSLDIR")) + "/data/standard/MNI152_T1_1mm"); } 

-+      if (useReconMNI.value()) { read_volume(refim,"@GENTOO_PORTAGE_EPREFIX@/usr/share/fsl/data/standard/MNI152_T1_1mm"); } 

-+      else { read_volume(refim,"@GENTOO_PORTAGE_EPREFIX@/usr/share/fsl/data/standard/MNI152_T1_1mm"); } 

-       volume<float> maskvol(refim);

-       maskvol=0.0f;

-       volume4D<float> volnormals;

-diff -Naur src.orig/fnirt/fnirtfns.cpp src/fnirt/fnirtfns.cpp

---- src.orig/fnirt/fnirtfns.cpp	2015-03-30 11:54:10.522550233 +1300

-+++ src/fnirt/fnirtfns.cpp	2015-03-30 11:54:18.412569892 +1300

-@@ -1203,8 +1203,7 @@

-       return(string(ref_fname));

-     }

-     else {

--      const char *fsldir_ptr = getenv("FSLDIR");

--      string eref_fname = string(fsldir_ptr) + string("/data/standard/") + ref_fname;

-+      string eref_fname = string("@GENTOO_PORTAGE_EPREFIX@/usr/share/fsl/data/standard/") + ref_fname;

-       if (NEWIMAGE::fsl_imageexists(eref_fname)) return(eref_fname);

-       else return(string(""));

-     }

-@@ -1230,9 +1229,8 @@

-       NEWIMAGE::read_volume_hdr_only(vref,ref_fname); // Throws if file dont exist

-       eref_fname = ref_fname;

-     }

--    catch(...) { // Didn't exist in current directory, try in ${FSLDIR}/data/standard

--      const char *fsldir_ptr = getenv("FSLDIR");

--      eref_fname = string(fsldir_ptr) + string("/data/standard/") + ref_fname;

-+    catch(...) { // Didn't exist in current directory, try in .../data/standard

-+      eref_fname = string("@GENTOO_PORTAGE_EPREFIX@/usr/share/fsl/data/standard/") + ref_fname;

-       try {

-         cout << "Could not find " << ref_fname << ", now checking " << eref_fname << endl;

-         NEWIMAGE::read_volume_hdr_only(vref,eref_fname); // Throws if file dont exist

-@@ -1267,8 +1265,7 @@

-     if (check_exist(ecfname)) return(ecfname);

-   }

-   if (!FNIRT::path(cfname).length()) {              // If no path explicitly given

--    const char *fsldir_ptr = getenv("FSLDIR");

--    ecfname = string(fsldir_ptr) + string("/etc/flirtsch/") + cfname;

-+    ecfname = string("@GENTOO_PORTAGE_EPREFIX@/etc/flirtsch/") + cfname;

-     if (check_exist(ecfname)) return(ecfname);

-     else if (!FNIRT::extension(ecfname).length()) { // If no path _and_ no extension given

-       ecfname += string(".cnf");

-diff -Naur src.orig/fslsurface/fslsurface_first.cc src/fslsurface/fslsurface_first.cc

---- src.orig/fslsurface/fslsurface_first.cc	2015-03-30 11:54:10.522550233 +1300

-+++ src/fslsurface/fslsurface_first.cc	2015-03-30 11:54:18.412569892 +1300

-@@ -500,8 +500,7 @@

-             

- 			volume<float>* immni = new volume<float>();

-             

--            char* fsldir = getenv("FSLDIR");

--            read_volume_hdr_only(*immni, string(fsldir) + "/data/standard/MNI152_T1_1mm");

-+            read_volume_hdr_only(*immni, "@GENTOO_PORTAGE_EPREFIX@/usr/share/fsl/data/standard/MNI152_T1_1mm");

-             

- 			//read_volume_hdr_only(*immni, template_name);

- 			

-@@ -699,8 +698,7 @@

-           

- 			volume<float>* immni = new volume<float>();

-             

--            char* fsldir = getenv("FSLDIR");

--            read_volume_hdr_only(*immni, string(fsldir) + "/data/standard/MNI152_T1_1mm");

-+            read_volume_hdr_only(*immni, "@GENTOO_PORTAGE_EPREFIX@/usr/share/fsl/data/standard/MNI152_T1_1mm");

-             

- 			//read_volume_hdr_only(*immni, template_name);

- 			

-diff -Naur src.orig/fslsurface/fslsurfacemaths.cpp src/fslsurface/fslsurfacemaths.cpp

---- src.orig/fslsurface/fslsurfacemaths.cpp	2015-03-30 11:54:10.522550233 +1300

-+++ src/fslsurface/fslsurfacemaths.cpp	2015-03-30 11:54:18.412569892 +1300

-@@ -598,12 +598,6 @@

- 

-         }else if (command == "-reconFromBvars"){

-             cout<<"do recon "<<endl;

--            char* fsldir = getenv("FSLDIR");

--            if (fsldir == NULL)

--            {

--                cerr<<"FSLDIR has not been set. "<<endl;

--                exit(EXIT_FAILURE); 

--            }

-             //file.bvars,mni_template.nii.gz

-            // string mni = string(fsldir)+"/data/standard/MNI152_T1_1mm";

-             reconSurface_from_bvars( surf, string(argv[i_arg+1]));

-@@ -612,12 +606,6 @@

- 

-         }else if (command == "-reconAllFromBvarsAndSave"){

-             cout<<"do recon+save "<<argc<<" "<<i_arg<<endl;

--            char* fsldir = getenv("FSLDIR");

--            if (fsldir == NULL)

--            {

--                cerr<<"FSLDIR has not been set. "<<endl;

--                exit(EXIT_FAILURE); 

--            }

-             //file.bvars,mni_template.nii.gz

-             // string mni = string(fsldir)+"/data/standard/MNI152_T1_1mm";

-             cout<<"recon "<< string(argv[i_arg+1])<<endl;

-diff -Naur src.orig/libvis/miscpic.h src/libvis/miscpic.h

---- src.orig/libvis/miscpic.h	2015-03-30 11:54:10.482550135 +1300

-+++ src/libvis/miscpic.h	2015-03-30 11:54:18.412569892 +1300

-@@ -89,12 +89,7 @@

- 	LR_label_flag = true;

- 	trans= -10;

- 	edgethresh = 0.0;

--	if(getenv("FSLDIR")!=0){

--	  lutbase = string(getenv("FSLDIR")) + "/etc/luts/";

--	}

--	else{

--	  lutbase = string("/");

--	}

-+	lutbase = "@GENTOO_PORTAGE_EPREFIX@/etc/luts/";

- 	title = string("");

- 	cbartype = string("");

- 	cbarptr = NULL;

-diff -Naur src.orig/melodic/meldata.cc src/melodic/meldata.cc

---- src.orig/melodic/meldata.cc	2015-03-30 11:54:10.502550183 +1300

-+++ src/melodic/meldata.cc	2015-03-30 11:54:18.412569892 +1300

-@@ -971,7 +971,7 @@

-   void MelodicData::est_smoothness()

-   {

-     if(Resels == 0){

--      string SM_path = opts.binpath + "smoothest";

-+      string SM_path = "smoothest";

-       string Mask_fname = logger.appendDir("mask");

- 

-       if(opts.segment.value().length()>0){

-@@ -1136,7 +1136,7 @@

- 				// set up all strings

- 				string BET_outputfname = string(Mean_fname)+"_brain";

- 

--				string BET_path = opts.binpath + "bet";

-+				string BET_path = "bet";

- 				string BET_optarg = "-m -f 0.4"; // see man bet

- 				string Mask_fname = BET_outputfname+"_mask";

- 

-diff -Naur src.orig/melodic/meloptions.cc src/melodic/meloptions.cc

---- src.orig/melodic/meloptions.cc	2015-03-30 11:54:10.502550183 +1300

-+++ src/melodic/meloptions.cc	2015-03-30 11:54:18.412569892 +1300

-@@ -93,14 +93,6 @@

-   		explicitnums = false;

-   		logfname = string("log.txt");

- 

--  		// work out the path to the $FSLDIR/bin directory

--  		if(getenv("FSLDIR")!=0){

--    		binpath = (string) getenv("FSLDIR") + "/bin/";

--  		} else{

--    		binpath = argv[0];

--    		binpath = binpath.substr(0,binpath.length()-7);

--  		}

--

-   		// parse once to establish log directory name

-   		for(int a = options.parse_command_line(argc, argv); a < argc; a++);

- 

-diff -Naur src.orig/melodic/meloptions.h src/melodic/meloptions.h

---- src.orig/melodic/meloptions.h	2015-03-30 11:54:10.502550183 +1300

-+++ src/melodic/meloptions.h	2015-03-30 11:54:18.412569892 +1300

-@@ -93,7 +93,6 @@

-   	~MelodicOptions() { delete gopt; }

-   

-   	string version;

--  	string binpath;

-   	string logfname;

-   	bool   filtermode;

-   	bool   explicitnums;

-diff -Naur src.orig/melodic/melreport.cc src/melodic/melreport.cc

---- src.orig/melodic/melreport.cc	2015-03-30 11:54:10.502550183 +1300

-+++ src/melodic/melreport.cc	2015-03-30 11:54:18.412569892 +1300

-@@ -84,8 +84,8 @@

- 			IChtml.setDir(report.getDir(),mmodel.get_prefix()+".html");

- 

-       {//start IC page

--				IChtml << "<HTML><HEAD><link REL=stylesheet TYPE=text/css href=file:" +

--					(string) getenv("FSLDIR") +"/doc/fsl.css>" << endl

-+				IChtml << "<HTML><HEAD><link REL=stylesheet TYPE=text/css href=file:"

-+				       << "@GENTOO_PORTAGE_EPREFIX@/usr/share/fsl/doc/fsl.css>" << endl

- 					<< "<style type=\"text/css\">OBJECT { width: 100% }</style>"

- 	       	<< "<TITLE>FSL</TITLE></HEAD>" << endl

- 	  			<< "<IFRAME  height=" << int(melodat.get_numfiles()/30 + 1)*50 

-@@ -487,8 +487,8 @@

- 

-       {//start IC2 page

- 				IChtml2.setDir(report.getDir(),mmodel.get_prefix()+"_MM.html");

--				IChtml2 << "<HTML><HEAD><link REL=stylesheet TYPE=text/css href=file:" +

--					(string) getenv("FSLDIR") +"/doc/fsl.css>" << endl

-+				IChtml2 << "<HTML><HEAD><link REL=stylesheet TYPE=text/css href=file:"

-+					<< "@GENTOO_PORTAGE_EPREFIX@/usr/share/fsl/doc/fsl.css>" << endl

- 					<< "<style type=\"text/css\">OBJECT { width: 100% }</style>"

- 	       	<< "<TITLE>FSL</TITLE></HEAD>" << endl

- 					<< "<IFRAME  height="<< int(melodat.get_numfiles()/30 + 1)*50 

-@@ -666,8 +666,8 @@

- 				IChtml << "<HTML> " << endl

- 	       	<< "<TITLE>MELODIC Component " << num2str(cnum)

- 	       	<< "</TITLE>" << endl

--	       	<< "<BODY BACKGROUND=\"file:" << getenv("FSLDIR") 

--	    		<< "/doc/images/fsl-bg.jpg\">" << endl 

-+	       	<< "<BODY BACKGROUND=\"file:"  

-+	    		<< "@GENTOO_PORTAGE_EPREFIX@/usr/share/fsl/doc/images/fsl-bg.jpg\">" << endl 

- 	     		<< "<hr><CENTER><H1>MELODIC Component " << num2str(cnum)

- 	       	<< "</H1>"<< endl;

- 	

-diff -Naur src.orig/melodic/melreport.h src/melodic/melreport.h

---- src.orig/melodic/melreport.h	2015-03-30 11:54:10.502550183 +1300

-+++ src/melodic/melreport.h	2015-03-30 12:11:17.995116883 +1300

-@@ -104,21 +104,21 @@

- 	  				const time_t tmptime = time(NULL);

- 		    		system(("mkdir "+ logger.appendDir("report") + " 2>/dev/null").c_str());

- 				report.setDir(logger.appendDir("report"),"00index.html",true,false,ios::out);

--						report << "<HTML><HEAD><link REL=stylesheet TYPE=text/css href=file:" +

--							(string) getenv("FSLDIR") +"/doc/fsl.css>" 

-+						report << "<HTML><HEAD><link REL=stylesheet TYPE=text/css href=file:"

-+							<< "@GENTOO_PORTAGE_EPREFIX@/usr/share/fsl/doc/fsl.css>" 

- 						  << "<TITLE>MELODIC report</TITLE></HEAD><BODY>"

- 							<< endl <<endl;

- 						loghtml.setDir(report.getDir(),"log.html");

--						loghtml << "<HTML><HEAD><link REL=stylesheet TYPE=text/css href=file:" +

--							(string) getenv("FSLDIR") +"/doc/fsl.css>" 

-+						loghtml << "<HTML><HEAD><link REL=stylesheet TYPE=text/css href=file:"

-+							<< "@GENTOO_PORTAGE_EPREFIX@/usr/share/fsl/doc/fsl.css>" 

- 						  << "<TITLE>MELODIC report</TITLE></HEAD><BODY>"

- 							<< endl <<endl;						

- 						navigator.setDir(report.getDir(),"nav.html");

- 						head.setDir(report.getDir(),"head.html");

--	  				navigator << "<link REL=stylesheet TYPE=text/css href=file:"+

--							(string) getenv("FSLDIR") +"/doc/fsl.css>"  << endl;

--						head << "<link REL=stylesheet TYPE=text/css href=file:"+

--							(string) getenv("FSLDIR") +"/doc/fsl.css>"  << endl;

-+	  				navigator << "<link REL=stylesheet TYPE=text/css href=file:"

-+						<< "@GENTOO_PORTAGE_EPREFIX@/usr/share/fsl/doc/fsl.css>"  << endl;

-+						head << "<link REL=stylesheet TYPE=text/css href=file:"

-+							<< "@GENTOO_PORTAGE_EPREFIX@/usr/share/fsl/doc/fsl.css>"  << endl;

- 						head  <<"<TABLE BORDER=0><TR>" << endl

- 							<<" <TD ALIGN=CENTER WIDTH=100%>"<< endl

- 							<<"<TABLE BORDER=0>"<< endl

-@@ -130,8 +130,8 @@

- 							<< "</tr></table>" << endl

- 							<< "<TD ALIGN=RIGHT>" << endl

- 							<< "<a href=http://www.fmrib.ox.ac.uk/fsl target=_top>" << endl

--						  << "<IMG BORDER=0 SRC=file:"<< getenv("FSLDIR")

--							<< "/doc/images/fsl-logo-big.jpg WIDTH=165></a>" << endl

-+						  << "<IMG BORDER=0 SRC=file:"

-+							<< "@GENTOO_PORTAGE_EPREFIX@/usr/share/fsl/doc/images/fsl-logo-big.jpg WIDTH=165></a>" << endl

- 							<< "</TD>"<<endl<<"</TR></TABLE> <hr>"<<endl;

- 						if(opts.guireport.value()==""){

- 							report <<"<OBJECT data=head.html></OBJECT>" <<  endl;

-diff -Naur src.orig/mm/mixture_model.cc src/mm/mixture_model.cc

---- src.orig/mm/mixture_model.cc	2015-03-30 11:54:10.522550233 +1300

-+++ src/mm/mixture_model.cc	2015-03-30 11:54:18.412569892 +1300

-@@ -2224,8 +2224,8 @@

- 

- 	htmllog << "<HTML> " << endl

- 		<< "<TITLE>Mixture Model fit for" << data_name << "</TITLE>" << endl

--		<< "<BODY BACKGROUND=\"file:" << getenv("FSLDIR") 

--		<< "/doc/images/fsl-bg.jpg\">" << endl 

-+		<< "<BODY BACKGROUND=\"file:"  

-+		<< "@GENTOO_PORTAGE_EPREFIX@/usr/share/fsl/doc/images/fsl-bg.jpg\">" << endl 

- 		<< "<hr><CENTER><H1>Mixture Model fit for<br>" << data_name << " </H1>"<< endl;

-      	

- 	htmllog << "<hr><p>" << endl;

-diff -Naur src.orig/siena/siena_diff.cc src/siena/siena_diff.cc

---- src.orig/siena/siena_diff.cc	2015-03-30 11:54:10.482550135 +1300

-+++ src/siena/siena_diff.cc	2015-03-30 11:54:18.412569892 +1300

-@@ -107,7 +107,7 @@

- {

-   // {{{  vars

- 

--char   thestring[10000], segoptions[10000], fsldir[10000];

-+char   thestring[10000], segoptions[10000];

- int    x_size, y_size, z_size, size, x, y, z, i, count,

-   seg2=0, ignore_z=0, ignore_top_slices=0, //erode_mask=0, 

-   ignore_bottom_slices=0, debug=0, flow_output=1, edge_masking=0;

-@@ -124,8 +124,6 @@

- 

- string argv1(argv[1]), argv2(argv[2]);

- 

--sprintf(fsldir,"%s",getenv("FSLDIR"));

--

- for (i = 3; i < argc; i++) {

-   if (!strcmp(argv[i], "-i"))

-     ignore_z=1;

-@@ -209,26 +207,26 @@

- // }}}

-   // {{{  transform images and masks

- 

--sprintf(thestring,"%s/bin/flirt -o %s_halfwayto_%s -applyisoxfm 1 -paddingsize 0 -init %s_halfwayto_%s.mat -ref %s -in %s",

--	fsldir,argv[1],argv[2],argv[1],argv[2],argv[1],argv[1]);

-+sprintf(thestring,"flirt -o %s_halfwayto_%s -applyisoxfm 1 -paddingsize 0 -init %s_halfwayto_%s.mat -ref %s -in %s",

-+	argv[1],argv[2],argv[1],argv[2],argv[1],argv[1]);

- printf("%s\n",thestring); system(thestring);

- 

--sprintf(thestring,"%s/bin/flirt -o %s_halfwayto_%s -applyisoxfm 1 -paddingsize 0 -init %s_halfwayto_%s.mat -ref %s -in %s",

--	fsldir,argv[2],argv[1],argv[2],argv[1],argv[1],argv[2]);

-+sprintf(thestring,"flirt -o %s_halfwayto_%s -applyisoxfm 1 -paddingsize 0 -init %s_halfwayto_%s.mat -ref %s -in %s",

-+	argv[2],argv[1],argv[2],argv[1],argv[1],argv[2]);

- printf("%s\n",thestring); system(thestring);

- 

--sprintf(thestring,"%s/bin/flirt -o %s_halfwayto_%s_mask -applyisoxfm 1 -paddingsize 0 -init %s_halfwayto_%s.mat -ref %s -in %s_brain_mask",

--	fsldir,argv[1],argv[2],argv[1],argv[2],argv[1],argv[1]);

-+sprintf(thestring,"flirt -o %s_halfwayto_%s_mask -applyisoxfm 1 -paddingsize 0 -init %s_halfwayto_%s.mat -ref %s -in %s_brain_mask",

-+	argv[1],argv[2],argv[1],argv[2],argv[1],argv[1]);

- printf("%s\n",thestring); system(thestring);

- 

--sprintf(thestring,"%s/bin/flirt -o %s_halfwayto_%s_mask -applyisoxfm 1 -paddingsize 0 -init %s_halfwayto_%s.mat -ref %s -in %s_brain_mask",

--	fsldir,argv[2],argv[1],argv[2],argv[1],argv[1],argv[2]);

-+sprintf(thestring,"flirt -o %s_halfwayto_%s_mask -applyisoxfm 1 -paddingsize 0 -init %s_halfwayto_%s.mat -ref %s -in %s_brain_mask",

-+	argv[2],argv[1],argv[2],argv[1],argv[1],argv[2]);

- printf("%s\n",thestring); system(thestring);

- 

- if (edge_masking)

- {

--  sprintf(thestring,"%s/bin/flirt -o %s_halfwayto_%s_valid_mask -applyisoxfm 1 -paddingsize 0 -init %s_halfwayto_%s.mat -ref %s -in %s_valid_mask_with_%s",

--	  fsldir,argv[1],argv[2],argv[1],argv[2],argv[1],argv[1],argv[2]);

-+  sprintf(thestring,"flirt -o %s_halfwayto_%s_valid_mask -applyisoxfm 1 -paddingsize 0 -init %s_halfwayto_%s.mat -ref %s -in %s_valid_mask_with_%s",

-+	  argv[1],argv[2],argv[1],argv[2],argv[1],argv[1],argv[2]);

-   printf("%s\n",thestring); system(thestring);

- }

- 

-@@ -287,8 +285,8 @@

-     cout << "saving image 1 to disk prior to segmentation" << endl;

-     save_volume(in1,argv1+"_halfwayto_"+argv2+"_brain");

-     in1.destroy();

--    sprintf(thestring,"%s/bin/fast %s %s %s_halfwayto_%s_brain > %s_halfwayto_%s_brain.vol 2>&1",

--	    fsldir,segtype,segoptions,argv[1],argv[2],argv[1],argv[2]);

-+    sprintf(thestring,"fast %s %s %s_halfwayto_%s_brain > %s_halfwayto_%s_brain.vol 2>&1",

-+	    segtype,segoptions,argv[1],argv[2],argv[1],argv[2]);

-     cout << thestring << endl;

-     system(thestring);

-   }

-diff -Naur src.orig/topup/topupfns.cpp src/topup/topupfns.cpp

---- src.orig/topup/topupfns.cpp	2015-03-30 11:54:10.522550233 +1300

-+++ src/topup/topupfns.cpp	2015-03-30 11:54:18.412569892 +1300

-@@ -463,8 +463,7 @@

-     if (TOPUP::check_exist(ecfname)) return(ecfname);

-   }

-   if (!TOPUP::path(cfname).length()) {              // If no path explicitly given

--    const char *fsldir_ptr = getenv("FSLDIR");

--    ecfname = string(fsldir_ptr) + string("/etc/flirtsch/") + cfname;

-+    ecfname = string("@GENTOO_PORTAGE_EPREFIX@/etc/flirtsch/") + cfname;

-     if (TOPUP::check_exist(ecfname)) return(ecfname);

-     else if (!TOPUP::extension(ecfname).length()) { // If no path _and_ no extension given

-       ecfname += string(".cnf");

-

diff --git a/sci-biology/fsl/files/fsl-5.0.8-headers.patch b/sci-biology/fsl/files/fsl-5.0.8-headers.patch
deleted file mode 100644
index ab2ab3da3..000000000
--- a/sci-biology/fsl/files/fsl-5.0.8-headers.patch
+++ /dev/null
@@ -1,21 +0,0 @@
---- src/miscvis/writepng.c.orig	2013-10-19 00:18:32.415203592 +1300
-+++ src/miscvis/writepng.c	2013-10-19 00:19:05.414255132 +1300
-@@ -32,6 +32,7 @@
- 
- #include <stdlib.h>     /* for exit() prototype */
- 
-+#include "zlib.h"
- #include "png.h"        /* libpng header; includes zlib.h and setjmp.h */
- #include "writepng.h"   /* typedefs, common macros, public prototypes */
- 
---- src/ptx2/surfmaths.cc.orig	2013-10-19 00:19:51.595327317 +1300
-+++ src/ptx2/surfmaths.cc	2013-10-19 00:20:09.284354805 +1300
-@@ -72,7 +72,7 @@
- #include "csv_mesh.h"
- #include "miscmaths/miscmaths.h"
- #include "utils/fsl_isfinite.h"
--#include "libprob/libprob.h"
-+#include "libprob.h"
- 
- using namespace MISCMATHS;
- 
diff --git a/sci-biology/fsl/files/fsl-5.0.8-setup.patch b/sci-biology/fsl/files/fsl-5.0.8-setup.patch
deleted file mode 100644
index 0cbda5d5c..000000000
--- a/sci-biology/fsl/files/fsl-5.0.8-setup.patch
+++ /dev/null
@@ -1,113 +0,0 @@
-diff -Naur fsl.orig/build fsl/build
---- fsl.orig/build	2015-03-29 00:10:39.845936000 +1300
-+++ fsl/build	2015-03-29 00:12:37.160487000 +1300
-@@ -11,8 +11,7 @@
- ifit load_varian load_dicom misc_scripts fdt first possum sgeutils flameo oxford_asl relax qboot topup ptx2 lesions eddy dwssfp";
- fi
- 
--echo "Building projects - see build.log file for progress..."
--./config/common/buildproj $PROJECTS > ./build.log 2>&1
--echo "Finished build : end of log file shows ..."
--tail -10 build.log
-+echo "Building projects"
-+./config/common/buildproj $PROJECTS
-+echo "Finished build"
- 
-diff -Naur fsl.orig/config/common/buildproj fsl/config/common/buildproj
---- fsl.orig/config/common/buildproj	2015-03-29 00:11:47.130998000 +1300
-+++ fsl/config/common/buildproj	2015-03-29 00:12:37.164319000 +1300
-@@ -11,10 +11,10 @@
- fi
- PROJECTS="$@" ; export PROJECTS ;
- 
--FSLDIR=`pwd`
-+#FSLDIR=`pwd`
- FSLDEVDIR=${FSLDIR}
- FSLCONFDIR=${FSLDIR}/config
--FSLMACHTYPE=`${FSLDIR}/etc/fslconf/fslmachtype.sh`
-+#FSLMACHTYPE=`${FSLDIR}/etc/fslconf/fslmachtype.sh`
- export FSLDIR FSLDEVDIR FSLCONFDIR FSLMACHTYPE
- 
- buildmessages="" ; export buildmessages ;
-@@ -66,7 +66,7 @@
- 	  if [ -x fslconfig ] ; then
- 	    ./fslconfig ;
- 	  fi
--	  if ${MAKE} -k ${MAKEOPTIONS} ; then 
-+	  if ${MAKE} ${MAKEOPTIONS} ${MAKEOPTS} ; then 
- 	    if ${MAKE} install ; then
- 	      installok=true;
- 	      # Clean up after ourselves
-diff -Naur fsl.orig/config/common/vars.mk fsl/config/common/vars.mk
---- fsl.orig/config/common/vars.mk	2015-03-29 00:11:47.183520000 +1300
-+++ fsl/config/common/vars.mk	2015-03-29 00:18:53.151222000 +1300
-@@ -24,15 +24,15 @@
- USRCFLAGS = 
- USRCXXFLAGS =
- 
--LDFLAGS = ${ARCHLDFLAGS} ${USRLDFLAGS} -L. -L${DEVLIBDIR} -L${LIBDIR}
-+LDFLAGS = ${ARCHLDFLAGS} ${USRLDFLAGS} -L. -L${DEVLIBDIR} -L${LIBDIR} ${USERLDFLAGS}
- 
--AccumulatedIncFlags = ${USRINCFLAGS} -I. -I${DEVINCDIR} -I${INCDIR}
-+AccumulatedIncFlags = ${USRINCFLAGS} -I. -I${DEVINCDIR} -I${INCDIR} ${CPPFLAGS}
- 
- CFLAGS = ${ANSI_FLAGS} ${ANSI_CFLAGS} ${DBGFLAGS} ${USEDCSTATICFLAGS} ${USRCFLAGS} ${ARCHFLAGS} ${OPTFLAGS}  \
--	${AccumulatedIncFlags}
-+	${AccumulatedIncFlags} ${USERCFLAGS}
- 
- CXXFLAGS = ${ANSI_FLAGS} ${ANSI_CXXFLAGS} ${DBGFLAGS} ${USEDCXXSTATICFLAGS} ${USRCXXFLAGS} ${ARCHFLAGS} ${OPTFLAGS}  \
--	${AccumulatedIncFlags}
-+	${AccumulatedIncFlags} ${USERCXXFLAGS}
- 
- HFILES = *.h
- AFILES = *.a
-diff -Naur fsl.orig/config/generic/systemvars.mk fsl/config/generic/systemvars.mk
---- fsl.orig/config/generic/systemvars.mk	2015-03-29 00:11:47.534246000 +1300
-+++ fsl/config/generic/systemvars.mk	2015-03-29 00:12:37.162129000 +1300
-@@ -4,20 +4,20 @@
- 
- # System dependent commands (NB: the first two are the most platform dependent)
- 
--INSTALL = ginstall -p
--RANLIB = ranlib
-+INSTALL = install -p
-+RANLIB = @@GENTOO_RANLIB@@
- 
- RM = /bin/rm
- CP = /bin/cp
- MV = /bin/mv
- CHMOD = /bin/chmod
- MKDIR = /bin/mkdir
--TCLSH = ${FSLDIR}/bin/fsltclsh
-+TCLSH = tclsh
- 
- # Compiler dependent variables
- 
--CC = gcc
--CXX = c++
-+CC = @@GENTOO_CC@@
-+CXX = @@GENTOO_CXX@@
- CSTATICFLAGS = -static
- CXXSTATICFLAGS = -static
- 
-@@ -25,7 +25,7 @@
- 
- DEPENDFLAGS = -MM
- 
--OPTFLAGS =  -O3 -fexpensive-optimizations ${ARCHFLAGS}
-+OPTFLAGS =
- MACHDBGFLAGS =
- GNU_ANSI_FLAGS = -Wall -ansi -pedantic
- SGI_ANSI_FLAGS = -ansi -fullwarn
-diff -Naur fsl.orig/extras/build fsl/extras/build
---- fsl.orig/extras/build	2015-03-29 00:11:15.080236000 +1300
-+++ fsl/extras/build	2015-03-29 00:15:53.170496000 +1300
-@@ -60,7 +60,7 @@
- if [ ${BUILDICONV} -eq 1 ]; then
-   PROJECTS="${PROJECTS} libiconv"
- fi
--PROJECTS="${PROJECTS} libgd libgdc libprob libcprob newmat cprob newran fftw"
-+PROJECTS="libgdc libprob libcprob newmat cprob newran"
- for projname in $PROJECTS; do
- 
-     if [ -d $FSLESRCDIR/$projname ] ; then
diff --git a/sci-biology/fsl/files/fsl-5.0.9-fsldir_redux.patch b/sci-biology/fsl/files/fsl-5.0.9-fsldir_redux.patch
deleted file mode 100644
index c28fabe42..000000000
--- a/sci-biology/fsl/files/fsl-5.0.9-fsldir_redux.patch
+++ /dev/null
@@ -1,456 +0,0 @@
-# Adapt hard-coded paths to the directory structure of Gentoo (including Prefix)

-# From: Francois Bissey <frp.bissey@gmail.com>

-# Signed-off-by: Horea Christian <horea.christ@gmail.com>

-

-diff -Naur fsl.orig/src/fast4/fast_two.cc fsl/src/fast4/fast_two.cc

---- fsl.orig/src/fast4/fast_two.cc	2015-03-30 11:54:10.522550233 +1300

-+++ fsl/src/fast4/fast_two.cc		2015-03-30 11:54:18.412569892 +1300

-@@ -166,7 +166,7 @@

- string csfPriorName, grayPriorName, whitePriorName;

-   if(alternatePriors.unset())

-   {

--    string priorRootName=string(getenv("FSLDIR")) + "/data/standard/tissuepriors/avg152T1_";

-+    string priorRootName="@GENTOO_PORTAGE_EPREFIX@/usr/share/fsl/data/standard/tissuepriors/avg152T1_";

-     csfPriorName = priorRootName+"csf";

-     grayPriorName = priorRootName+"gray";

-     whitePriorName = priorRootName+"white";

-@@ -215,15 +215,15 @@

-     if(bapused>0)

-       {

- 	char reg[1024];

--	sprintf(reg, "%s/bin/flirt -ref %s -in %s -out %s -applyxfm -init %s", getenv("FSLDIR"), inname.c_str(), csfPriorName.c_str(), (main_prior_vol+"_csf_stdspace").c_str(),  bapriori.value().c_str());

-+	sprintf(reg, "flirt -ref %s -in %s -out %s -applyxfm -init %s", inname.c_str(), csfPriorName.c_str(), (main_prior_vol+"_csf_stdspace").c_str(),  bapriori.value().c_str());

-         if(verbose.value())

- 	  cout<<reg<<endl;

- 	system(reg);

--	sprintf(reg, "%s/bin/flirt -ref %s -in %s -out %s -applyxfm -init %s", getenv("FSLDIR"), inname.c_str(), grayPriorName.c_str(), (main_prior_vol+"_gm_stdspace").c_str(),  bapriori.value().c_str());

-+	sprintf(reg, "flirt -ref %s -in %s -out %s -applyxfm -init %s", inname.c_str(), grayPriorName.c_str(), (main_prior_vol+"_gm_stdspace").c_str(),  bapriori.value().c_str());

- 	if(verbose.value())

- 	  cout<<reg<<endl;

-         system(reg);

--	sprintf(reg, "%s/bin/flirt -ref %s -in %s -out %s -applyxfm -init %s", getenv("FSLDIR"), inname.c_str(), whitePriorName.c_str(), (main_prior_vol+"_wm_stdspace").c_str(),  bapriori.value().c_str());

-+	sprintf(reg, "flirt -ref %s -in %s -out %s -applyxfm -init %s", inname.c_str(), whitePriorName.c_str(), (main_prior_vol+"_wm_stdspace").c_str(),  bapriori.value().c_str());

- 	if(verbose.value())

- 	  cout << reg << endl;

- 	system(reg);

-diff -Naur fsl.orig/src/feat5/feat_model.cc fsl/src/feat5/feat_model.cc

---- fsl.orig/src/feat5/feat_model.cc	2015-03-30 11:54:10.502550183 +1300

-+++ fsl/src/feat5/feat_model.cc		2015-03-30 11:54:18.412569892 +1300

-@@ -741,7 +741,7 @@

-   vector<int> G;

-   vector<string> titles;

-   float  tr, mult, trmult, nltffwhm=0, maxconvwin=0;

--  char   fl[10000], *FSLDIR;

-+  char   fl[10000];

-   string fn, filename;

-   FONT_DATA *font_data = new FONT_DATA[1];

- 

-@@ -760,8 +760,6 @@

-   if (argc==3)

-     motionparams=remmean(read_ascii_matrix(argv[2]));

- 

--  FSLDIR=getenv("FSLDIR");

--

-   fn = string(argv[1])+".fsf";

- 

-   level      = atoi(find_line(fn, "fmri(level)", fl));

-@@ -1491,7 +1489,7 @@

-   writeCovarianceImage(string(argv[1])+"_cov.ppm", contrasts, F, nftests, realDesign, level, evs.eigenvals, font_data, contrasts.RE);

-   writeImagePreview(string(argv[1])+".ppm", contrasts, F, nftests, realDesign, level, evs, font_data, titles, tr, nltffwhm, nTimepoints, G);

- 

--  filename=string(getenv("FSLDIR"))+"/bin/wpng -q -overwrite  "+string(argv[1])+".ppm ";

-+  filename="wpng -q -overwrite  "+string(argv[1])+".ppm ";

-   system(filename.c_str());

- 

-   return(0);

-@@ -2134,6 +2132,6 @@

- 

-     fclose(outputfile);

- 

--    filename=string(getenv("FSLDIR")) + "/bin/wpng -q -overwrite  " + filename;

-+    filename="wpng -q -overwrite  " + filename;

-     system(filename.c_str());

- }

-diff -Naur fsl.orig/src/feat5/tsplot.cc fsl/src/feat5/tsplot.cc

---- fsl.orig/src/feat5/tsplot.cc	2015-03-30 11:54:10.502550183 +1300

-+++ fsl/src/feat5/tsplot.cc		2015-03-30 11:54:18.412569892 +1300

-@@ -293,7 +293,7 @@

- ofstream     outputFile;

- int          numEVs, npts, numContrasts=1, nftests=0, GRPHSIZE(600), PSSIZE(600); 

- vector<double> normalisedContrasts, model, triggers;

-- string       fmriFileName, fslPath, featdir, vType, indexText;

-+ string       fmriFileName, featdir, vType, indexText;

- ColumnVector NewimageVoxCoord(4),NiftiVoxCoord(4);

- bool outputText(true), useCoordinate(false), prewhiten(false), useTriggers(false), customMask(false), modelFree(false), isHigherLevel(false), outputDataOnly(false);

- bool zWeightClusters(true);

-@@ -307,7 +307,6 @@

-   if (argc<2) usage("");

-   featdir=string(argv[1]);

-   fmriFileName=featdir+"/filtered_func_data";

--  fslPath=string(getenv("FSLDIR"));

- 

-   string outputName(featdir);

- 

-@@ -725,7 +724,7 @@

- 	cerr << "Can't open output report file " << outputName << endl;

- 	exit(1);

-       }

--      outputFile << "<HTML>\n<TITLE>"<< statType << num2str(i) <<"</TITLE>\n<BODY BACKGROUND=\"file:"<< fslPath <<"/doc/images/fsl-bg.jpg\">\n<hr><CENTER>\n<H1>FEAT Time Series Report - "<< statType << num2str(i) <<"</H1>\n</CENTER>\n<hr><b>Full plots</b><p>\n"<< graphText;

-+      outputFile << "<HTML>\n<TITLE>"<< statType << num2str(i) <<"</TITLE>\n<BODY BACKGROUND=\"file:"<< "@GENTOO_PORTAGE_EPREFIX@/usr/share/fsl/doc/images/fsl-bg.jpg\">\n<hr><CENTER>\n<H1>FEAT Time Series Report - "<< statType << num2str(i) <<"</H1>\n</CENTER>\n<hr><b>Full plots</b><p>\n"<< graphText;

-       if (useTriggers) outputFile << "\n<hr><b>Peristimulus plots</b><p>\n"<< peristimulusText <<"\n<HR></BODY></HTML>\n\n";

-       else outputFile << "\n</BODY></HTML>\n\n";

-       outputFile.close();

-@@ -740,7 +739,7 @@

-       cerr << "Can't open output report file " << outputName << endl;

-       exit(1);

-   }

--  outputFile << "<HTML>\n<TITLE>FEAT Time Series Report</TITLE>\n<BODY BACKGROUND=\"file:" << fslPath << "/doc/images/fsl-bg.jpg\">\n<hr><CENTER>\n<H1>FEAT Time Series Report</H1>\n</CENTER>\n<hr>" << indexText << "<HR></BODY></HTML>" << endl << endl;

-+  outputFile << "<HTML>\n<TITLE>FEAT Time Series Report</TITLE>\n<BODY BACKGROUND=\"file:" << "@GENTOO_PORTAGE_EPREFIX@/usr/share/fsl/doc/images/fsl-bg.jpg\">\n<hr><CENTER>\n<H1>FEAT Time Series Report</H1>\n</CENTER>\n<hr>" << indexText << "<HR></BODY></HTML>" << endl << endl;

-   outputFile.close();

- 

-   /* now output same thing without start and end, for inclusion in feat report */

-diff -Naur fsl.orig/src/first/first_utils.cc fsl/src/first/first_utils.cc

---- fsl.orig/src/first/first_utils.cc	2015-03-30 11:54:10.482550135 +1300

-+++ fsl/src/first/first_utils.cc	2015-03-30 11:54:18.412569892 +1300

-@@ -1954,8 +1954,8 @@

-     if (!surfaceVAout.value()) {

-       // do not output on the surface, instead do the new default of outputting a volume with the scalar normal dot product values (for use with randomise)

-       volume<float> refim;

--      if (useReconMNI.value()) { read_volume(refim,string(getenv("FSLDIR")) + "/data/standard/MNI152_T1_1mm"); } 

--      else { read_volume(refim,string(getenv("FSLDIR")) + "/data/standard/MNI152_T1_1mm"); } 

-+      if (useReconMNI.value()) { read_volume(refim,"@GENTOO_PORTAGE_EPREFIX@/usr/share/fsl/data/standard/MNI152_T1_1mm"); } 

-+      else { read_volume(refim,"@GENTOO_PORTAGE_EPREFIX@/usr/share/fsl/data/standard/MNI152_T1_1mm"); } 

-       volume<float> maskvol(refim);

-       maskvol=0.0f;

-       volume4D<float> volnormals;

-diff -Naur fsl.orig/src/fnirt/fnirtfns.cpp fsl/src/fnirt/fnirtfns.cpp

---- fsl.orig/src/fnirt/fnirtfns.cpp	2015-03-30 11:54:10.522550233 +1300

-+++ fsl/src/fnirt/fnirtfns.cpp		2015-03-30 11:54:18.412569892 +1300

-@@ -1203,8 +1203,7 @@

-       return(string(ref_fname));

-     }

-     else {

--      const char *fsldir_ptr = getenv("FSLDIR");

--      string eref_fname = string(fsldir_ptr) + string("/data/standard/") + ref_fname;

-+      string eref_fname = string("@GENTOO_PORTAGE_EPREFIX@/usr/share/fsl/data/standard/") + ref_fname;

-       if (NEWIMAGE::fsl_imageexists(eref_fname)) return(eref_fname);

-       else return(string(""));

-     }

-@@ -1230,9 +1229,8 @@

-       NEWIMAGE::read_volume_hdr_only(vref,ref_fname); // Throws if file dont exist

-       eref_fname = ref_fname;

-     }

--    catch(...) { // Didn't exist in current directory, try in ${FSLDIR}/data/standard

--      const char *fsldir_ptr = getenv("FSLDIR");

--      eref_fname = string(fsldir_ptr) + string("/data/standard/") + ref_fname;

-+    catch(...) { // Didn't exist in current directory, try in .../data/standard

-+      eref_fname = string("@GENTOO_PORTAGE_EPREFIX@/usr/share/fsl/data/standard/") + ref_fname;

-       try {

-         cout << "Could not find " << ref_fname << ", now checking " << eref_fname << endl;

-         NEWIMAGE::read_volume_hdr_only(vref,eref_fname); // Throws if file dont exist

-@@ -1267,8 +1265,7 @@

-     if (check_exist(ecfname)) return(ecfname);

-   }

-   if (!FNIRT::path(cfname).length()) {              // If no path explicitly given

--    const char *fsldir_ptr = getenv("FSLDIR");

--    ecfname = string(fsldir_ptr) + string("/etc/flirtsch/") + cfname;

-+    ecfname = string("@GENTOO_PORTAGE_EPREFIX@/etc/flirtsch/") + cfname;

-     if (check_exist(ecfname)) return(ecfname);

-     else if (!FNIRT::extension(ecfname).length()) { // If no path _and_ no extension given

-       ecfname += string(".cnf");

-diff -Naur fsl.orig/src/fslsurface/fslsurface_first.cc fsl/src/fslsurface/fslsurface_first.cc

---- fsl.orig/src/fslsurface/fslsurface_first.cc	2015-03-30 11:54:10.522550233 +1300

-+++ fsl/src/fslsurface/fslsurface_first.cc	2015-03-30 11:54:18.412569892 +1300

-@@ -500,8 +500,7 @@

-             

- 			volume<float>* immni = new volume<float>();

-             

--            char* fsldir = getenv("FSLDIR");

--            read_volume_hdr_only(*immni, string(fsldir) + "/data/standard/MNI152_T1_1mm");

-+            read_volume_hdr_only(*immni, "@GENTOO_PORTAGE_EPREFIX@/usr/share/fsl/data/standard/MNI152_T1_1mm");

-             

- 			//read_volume_hdr_only(*immni, template_name);

- 			

-@@ -699,8 +698,7 @@

-           

- 			volume<float>* immni = new volume<float>();

-             

--            char* fsldir = getenv("FSLDIR");

--            read_volume_hdr_only(*immni, string(fsldir) + "/data/standard/MNI152_T1_1mm");

-+            read_volume_hdr_only(*immni, "@GENTOO_PORTAGE_EPREFIX@/usr/share/fsl/data/standard/MNI152_T1_1mm");

-             

- 			//read_volume_hdr_only(*immni, template_name);

- 			

-diff -Naur fsl.orig/src/fslsurface/fslsurfacemaths.cpp fsl/src/fslsurface/fslsurfacemaths.cpp

---- fsl.orig/src/fslsurface/fslsurfacemaths.cpp	2015-03-30 11:54:10.522550233 +1300

-+++ fsl/src/fslsurface/fslsurfacemaths.cpp	2015-03-30 11:54:18.412569892 +1300

-@@ -598,12 +598,6 @@

- 

-         }else if (command == "-reconFromBvars"){

-             cout<<"do recon "<<endl;

--            char* fsldir = getenv("FSLDIR");

--            if (fsldir == NULL)

--            {

--                cerr<<"FSLDIR has not been set. "<<endl;

--                exit(EXIT_FAILURE); 

--            }

-             //file.bvars,mni_template.nii.gz

-            // string mni = string(fsldir)+"/data/standard/MNI152_T1_1mm";

-             reconSurface_from_bvars( surf, string(argv[i_arg+1]));

-@@ -612,12 +606,6 @@

- 

-         }else if (command == "-reconAllFromBvarsAndSave"){

-             cout<<"do recon+save "<<argc<<" "<<i_arg<<endl;

--            char* fsldir = getenv("FSLDIR");

--            if (fsldir == NULL)

--            {

--                cerr<<"FSLDIR has not been set. "<<endl;

--                exit(EXIT_FAILURE); 

--            }

-             //file.bvars,mni_template.nii.gz

-             // string mni = string(fsldir)+"/data/standard/MNI152_T1_1mm";

-             cout<<"recon "<< string(argv[i_arg+1])<<endl;

-diff -Naur fsl.orig/src/libvis/miscpic.h fsl/src/libvis/miscpic.h

---- fsl.orig/src/libvis/miscpic.h	2015-03-30 11:54:10.482550135 +1300

-+++ fsl/src/libvis/miscpic.h		2015-03-30 11:54:18.412569892 +1300

-@@ -89,12 +89,7 @@

- 	LR_label_flag = true;

- 	trans= -10;

- 	edgethresh = 0.0;

--	if(getenv("FSLDIR")!=0){

--	  lutbase = string(getenv("FSLDIR")) + "/etc/luts/";

--	}

--	else{

--	  lutbase = string("/");

--	}

-+	lutbase = "@GENTOO_PORTAGE_EPREFIX@/etc/luts/";

- 	title = string("");

- 	cbartype = string("");

- 	cbarptr = NULL;

-diff -Naur fsl.orig/src/melodic/meldata.cc fsl/src/melodic/meldata.cc

---- fsl.orig/src/melodic/meldata.cc	2015-03-30 11:54:10.502550183 +1300

-+++ fsl/src/melodic/meldata.cc		2015-03-30 11:54:18.412569892 +1300

-@@ -971,7 +971,7 @@

-   void MelodicData::est_smoothness()

-   {

-     if(Resels == 0){

--      string SM_path = opts.binpath + "smoothest";

-+      string SM_path = "smoothest";

-       string Mask_fname = logger.appendDir("mask");

- 

-       if(opts.segment.value().length()>0){

-@@ -1136,7 +1136,7 @@

- 				// set up all strings

- 				string BET_outputfname = string(Mean_fname)+"_brain";

- 

--				string BET_path = opts.binpath + "bet";

-+				string BET_path = "bet";

- 				string BET_optarg = "-m -f 0.4"; // see man bet

- 				string Mask_fname = BET_outputfname+"_mask";

- 

-diff -Naur fsl.orig/src/melodic/meloptions.cc fsl/src/melodic/meloptions.cc

---- fsl.orig/src/melodic/meloptions.cc	2015-03-30 11:54:10.502550183 +1300

-+++ fsl/src/melodic/meloptions.cc	2015-03-30 11:54:18.412569892 +1300

-@@ -93,14 +93,6 @@

-   		explicitnums = false;

-   		logfname = string("log.txt");

- 

--  		// work out the path to the $FSLDIR/bin directory

--  		if(getenv("FSLDIR")!=0){

--    		binpath = (string) getenv("FSLDIR") + "/bin/";

--  		} else{

--    		binpath = argv[0];

--    		binpath = binpath.substr(0,binpath.length()-7);

--  		}

--

-   		// parse once to establish log directory name

-   		for(int a = options.parse_command_line(argc, argv); a < argc; a++);

- 

-diff -Naur fsl.orig/src/melodic/meloptions.h fsl/src/melodic/meloptions.h

---- fsl.orig/src/melodic/meloptions.h	2015-03-30 11:54:10.502550183 +1300

-+++ fsl/src/melodic/meloptions.h	2015-03-30 11:54:18.412569892 +1300

-@@ -93,7 +93,6 @@

-   	~MelodicOptions() { delete gopt; }

-   

-   	string version;

--  	string binpath;

-   	string logfname;

-   	bool   filtermode;

-   	bool   explicitnums;

-diff -Naur fsl.orig/src/melodic/melreport.cc fsl/src/melodic/melreport.cc

---- fsl.orig/src/melodic/melreport.cc	2015-03-30 11:54:10.502550183 +1300

-+++ fsl/src/melodic/melreport.cc	2015-03-30 11:54:18.412569892 +1300

-@@ -84,8 +84,8 @@

- 			IChtml.setDir(report.getDir(),mmodel.get_prefix()+".html");

- 

-       {//start IC page

--				IChtml << "<HTML><HEAD><link REL=stylesheet TYPE=text/css href=file:" +

--					(string) getenv("FSLDIR") +"/doc/fsl.css>" << endl

-+				IChtml << "<HTML><HEAD><link REL=stylesheet TYPE=text/css href=file:"

-+				       << "@GENTOO_PORTAGE_EPREFIX@/usr/share/fsl/doc/fsl.css>" << endl

- 					<< "<style type=\"text/css\">OBJECT { width: 100% }</style>"

- 	       	<< "<TITLE>FSL</TITLE></HEAD>" << endl

- 	  			<< "<IFRAME  height=" << int(melodat.get_numfiles()/30 + 1)*50 

-@@ -487,8 +487,8 @@

- 

-       {//start IC2 page

- 				IChtml2.setDir(report.getDir(),mmodel.get_prefix()+"_MM.html");

--				IChtml2 << "<HTML><HEAD><link REL=stylesheet TYPE=text/css href=file:" +

--					(string) getenv("FSLDIR") +"/doc/fsl.css>" << endl

-+				IChtml2 << "<HTML><HEAD><link REL=stylesheet TYPE=text/css href=file:"

-+					<< "@GENTOO_PORTAGE_EPREFIX@/usr/share/fsl/doc/fsl.css>" << endl

- 					<< "<style type=\"text/css\">OBJECT { width: 100% }</style>"

- 	       	<< "<TITLE>FSL</TITLE></HEAD>" << endl

- 					<< "<IFRAME  height="<< int(melodat.get_numfiles()/30 + 1)*50 

-@@ -666,8 +666,8 @@

- 				IChtml << "<HTML> " << endl

- 	       	<< "<TITLE>MELODIC Component " << num2str(cnum)

- 	       	<< "</TITLE>" << endl

--	       	<< "<BODY BACKGROUND=\"file:" << getenv("FSLDIR") 

--	    		<< "/doc/images/fsl-bg.jpg\">" << endl 

-+	       	<< "<BODY BACKGROUND=\"file:"  

-+	    		<< "@GENTOO_PORTAGE_EPREFIX@/usr/share/fsl/doc/images/fsl-bg.jpg\">" << endl 

- 	     		<< "<hr><CENTER><H1>MELODIC Component " << num2str(cnum)

- 	       	<< "</H1>"<< endl;

- 	

-diff -Naur fsl.orig/src/melodic/melreport.h fsl/src/melodic/melreport.h

---- fsl.orig/src/melodic/melreport.h	2015-03-30 11:54:10.502550183 +1300

-+++ fsl/src/melodic/melreport.h		2015-03-30 12:11:17.995116883 +1300

-@@ -104,21 +104,21 @@

- 	  				const time_t tmptime = time(NULL);

- 		    		system(("mkdir "+ logger.appendDir("report") + " 2>/dev/null").c_str());

- 				report.setDir(logger.appendDir("report"),"00index.html",true,false,ios::out);

--						report << "<HTML><HEAD><link REL=stylesheet TYPE=text/css href=file:" +

--							(string) getenv("FSLDIR") +"/doc/fsl.css>" 

-+						report << "<HTML><HEAD><link REL=stylesheet TYPE=text/css href=file:"

-+							<< "@GENTOO_PORTAGE_EPREFIX@/usr/share/fsl/doc/fsl.css>" 

- 						  << "<TITLE>MELODIC report</TITLE></HEAD><BODY>"

- 							<< endl <<endl;

- 						loghtml.setDir(report.getDir(),"log.html");

--						loghtml << "<HTML><HEAD><link REL=stylesheet TYPE=text/css href=file:" +

--							(string) getenv("FSLDIR") +"/doc/fsl.css>" 

-+						loghtml << "<HTML><HEAD><link REL=stylesheet TYPE=text/css href=file:"

-+							<< "@GENTOO_PORTAGE_EPREFIX@/usr/share/fsl/doc/fsl.css>" 

- 						  << "<TITLE>MELODIC report</TITLE></HEAD><BODY>"

- 							<< endl <<endl;						

- 						navigator.setDir(report.getDir(),"nav.html");

- 						head.setDir(report.getDir(),"head.html");

--	  				navigator << "<link REL=stylesheet TYPE=text/css href=file:"+

--							(string) getenv("FSLDIR") +"/doc/fsl.css>"  << endl;

--						head << "<link REL=stylesheet TYPE=text/css href=file:"+

--							(string) getenv("FSLDIR") +"/doc/fsl.css>"  << endl;

-+	  				navigator << "<link REL=stylesheet TYPE=text/css href=file:"

-+						<< "@GENTOO_PORTAGE_EPREFIX@/usr/share/fsl/doc/fsl.css>"  << endl;

-+						head << "<link REL=stylesheet TYPE=text/css href=file:"

-+							<< "@GENTOO_PORTAGE_EPREFIX@/usr/share/fsl/doc/fsl.css>"  << endl;

- 						head  <<"<TABLE BORDER=0><TR>" << endl

- 							<<" <TD ALIGN=CENTER WIDTH=100%>"<< endl

- 							<<"<TABLE BORDER=0>"<< endl

-@@ -130,8 +130,8 @@

- 							<< "</tr></table>" << endl

- 							<< "<TD ALIGN=RIGHT>" << endl

- 							<< "<a href=http://www.fmrib.ox.ac.uk/fsl target=_top>" << endl

--						  << "<IMG BORDER=0 SRC=file:"<< getenv("FSLDIR")

--							<< "/doc/images/fsl-logo-big.jpg WIDTH=165></a>" << endl

-+						  << "<IMG BORDER=0 SRC=file:"

-+							<< "@GENTOO_PORTAGE_EPREFIX@/usr/share/fsl/doc/images/fsl-logo-big.jpg WIDTH=165></a>" << endl

- 							<< "</TD>"<<endl<<"</TR></TABLE> <hr>"<<endl;

- 						if(opts.guireport.value()==""){

- 							report <<"<OBJECT data=head.html></OBJECT>" <<  endl;

-diff -Naur fsl.orig/src/mm/mixture_model.cc fsl/src/mm/mixture_model.cc

---- fsl.orig/src/mm/mixture_model.cc	2015-03-30 11:54:10.522550233 +1300

-+++ fsl/src/mm/mixture_model.cc		2015-03-30 11:54:18.412569892 +1300

-@@ -2224,8 +2224,8 @@

- 

- 	htmllog << "<HTML> " << endl

- 		<< "<TITLE>Mixture Model fit for" << data_name << "</TITLE>" << endl

--		<< "<BODY BACKGROUND=\"file:" << getenv("FSLDIR") 

--		<< "/doc/images/fsl-bg.jpg\">" << endl 

-+		<< "<BODY BACKGROUND=\"file:"  

-+		<< "@GENTOO_PORTAGE_EPREFIX@/usr/share/fsl/doc/images/fsl-bg.jpg\">" << endl 

- 		<< "<hr><CENTER><H1>Mixture Model fit for<br>" << data_name << " </H1>"<< endl;

-      	

- 	htmllog << "<hr><p>" << endl;

-diff -Naur fsl.orig/src/siena/siena_diff.cc fsl/src/siena/siena_diff.cc

---- fsl.orig/src/siena/siena_diff.cc	2015-03-30 11:54:10.482550135 +1300

-+++ fsl/src/siena/siena_diff.cc		2015-03-30 11:54:18.412569892 +1300

-@@ -107,7 +107,7 @@

- {

-   // {{{  vars

- 

--char   thestring[10000], segoptions[10000], fsldir[10000];

-+char   thestring[10000], segoptions[10000];

- int    x_size, y_size, z_size, size, x, y, z, i, count,

-   seg2=0, ignore_z=0, ignore_top_slices=0, //erode_mask=0, 

-   ignore_bottom_slices=0, debug=0, flow_output=1, edge_masking=0;

-@@ -124,8 +124,6 @@

- 

- string argv1(argv[1]), argv2(argv[2]);

- 

--sprintf(fsldir,"%s",getenv("FSLDIR"));

--

- for (i = 3; i < argc; i++) {

-   if (!strcmp(argv[i], "-i"))

-     ignore_z=1;

-@@ -209,26 +207,26 @@

- // }}}

-   // {{{  transform images and masks

- 

--sprintf(thestring,"%s/bin/flirt -o %s_halfwayto_%s -applyisoxfm 1 -paddingsize 0 -init %s_halfwayto_%s.mat -ref %s -in %s",

--	fsldir,argv[1],argv[2],argv[1],argv[2],argv[1],argv[1]);

-+sprintf(thestring,"flirt -o %s_halfwayto_%s -applyisoxfm 1 -paddingsize 0 -init %s_halfwayto_%s.mat -ref %s -in %s",

-+	argv[1],argv[2],argv[1],argv[2],argv[1],argv[1]);

- printf("%s\n",thestring); system(thestring);

- 

--sprintf(thestring,"%s/bin/flirt -o %s_halfwayto_%s -applyisoxfm 1 -paddingsize 0 -init %s_halfwayto_%s.mat -ref %s -in %s",

--	fsldir,argv[2],argv[1],argv[2],argv[1],argv[1],argv[2]);

-+sprintf(thestring,"flirt -o %s_halfwayto_%s -applyisoxfm 1 -paddingsize 0 -init %s_halfwayto_%s.mat -ref %s -in %s",

-+	argv[2],argv[1],argv[2],argv[1],argv[1],argv[2]);

- printf("%s\n",thestring); system(thestring);

- 

--sprintf(thestring,"%s/bin/flirt -o %s_halfwayto_%s_mask -applyisoxfm 1 -paddingsize 0 -init %s_halfwayto_%s.mat -ref %s -in %s_brain_mask",

--	fsldir,argv[1],argv[2],argv[1],argv[2],argv[1],argv[1]);

-+sprintf(thestring,"flirt -o %s_halfwayto_%s_mask -applyisoxfm 1 -paddingsize 0 -init %s_halfwayto_%s.mat -ref %s -in %s_brain_mask",

-+	argv[1],argv[2],argv[1],argv[2],argv[1],argv[1]);

- printf("%s\n",thestring); system(thestring);

- 

--sprintf(thestring,"%s/bin/flirt -o %s_halfwayto_%s_mask -applyisoxfm 1 -paddingsize 0 -init %s_halfwayto_%s.mat -ref %s -in %s_brain_mask",

--	fsldir,argv[2],argv[1],argv[2],argv[1],argv[1],argv[2]);

-+sprintf(thestring,"flirt -o %s_halfwayto_%s_mask -applyisoxfm 1 -paddingsize 0 -init %s_halfwayto_%s.mat -ref %s -in %s_brain_mask",

-+	argv[2],argv[1],argv[2],argv[1],argv[1],argv[2]);

- printf("%s\n",thestring); system(thestring);

- 

- if (edge_masking)

- {

--  sprintf(thestring,"%s/bin/flirt -o %s_halfwayto_%s_valid_mask -applyisoxfm 1 -paddingsize 0 -init %s_halfwayto_%s.mat -ref %s -in %s_valid_mask_with_%s",

--	  fsldir,argv[1],argv[2],argv[1],argv[2],argv[1],argv[1],argv[2]);

-+  sprintf(thestring,"flirt -o %s_halfwayto_%s_valid_mask -applyisoxfm 1 -paddingsize 0 -init %s_halfwayto_%s.mat -ref %s -in %s_valid_mask_with_%s",

-+	  argv[1],argv[2],argv[1],argv[2],argv[1],argv[1],argv[2]);

-   printf("%s\n",thestring); system(thestring);

- }

- 

-@@ -287,8 +285,8 @@

-     cout << "saving image 1 to disk prior to segmentation" << endl;

-     save_volume(in1,argv1+"_halfwayto_"+argv2+"_brain");

-     in1.destroy();

--    sprintf(thestring,"%s/bin/fast %s %s %s_halfwayto_%s_brain > %s_halfwayto_%s_brain.vol 2>&1",

--	    fsldir,segtype,segoptions,argv[1],argv[2],argv[1],argv[2]);

-+    sprintf(thestring,"fast %s %s %s_halfwayto_%s_brain > %s_halfwayto_%s_brain.vol 2>&1",

-+	    segtype,segoptions,argv[1],argv[2],argv[1],argv[2]);

-     cout << thestring << endl;

-     system(thestring);

-   }

-diff -Naur fsl.orig/src/topup/topupfns.cpp fsl/src/topup/topupfns.cpp

---- fsl.orig/src/topup/topupfns.cpp	2015-03-30 11:54:10.522550233 +1300

-+++ fsl/src/topup/topupfns.cpp		2015-03-30 11:54:18.412569892 +1300

-@@ -463,8 +463,7 @@

-     if (TOPUP::check_exist(ecfname)) return(ecfname);

-   }

-   if (!TOPUP::path(cfname).length()) {              // If no path explicitly given

--    const char *fsldir_ptr = getenv("FSLDIR");

--    ecfname = string(fsldir_ptr) + string("/etc/flirtsch/") + cfname;

-+    ecfname = string("@GENTOO_PORTAGE_EPREFIX@/etc/flirtsch/") + cfname;

-     if (TOPUP::check_exist(ecfname)) return(ecfname);

-     else if (!TOPUP::extension(ecfname).length()) { // If no path _and_ no extension given

-       ecfname += string(".cnf");

-

diff --git a/sci-biology/fsl/files/fsl-5.0.9-headers.patch b/sci-biology/fsl/files/fsl-5.0.9-headers.patch
index 663dc565c..f4da2bb50 100644
--- a/sci-biology/fsl/files/fsl-5.0.9-headers.patch
+++ b/sci-biology/fsl/files/fsl-5.0.9-headers.patch
@@ -1,6 +1,6 @@
 # Include zlib header directly.
 # From: Francois Bissey <frp.bissey@gmail.com>
-# Signed-off-by: Horea Christian <horea.christ@gmail.com>
+# Signed-off-by: Horea Christian <gentoo@chymera.eu>
 # Submitted upstream: https://www.jiscmail.ac.uk/cgi-bin/webadmin?A2=ind1709&L=FSL&F=&S=&X=95C10F0B7D62EAAE7A&P=169254
 
 --- fsl/src/miscvis/writepng.c.orig	2013-10-19 00:18:32.415203592 +1300
diff --git a/sci-biology/fsl/files/fsl-5.0.9-setup.patch b/sci-biology/fsl/files/fsl-5.0.9-setup.patch
deleted file mode 100644
index c688cd6e8..000000000
--- a/sci-biology/fsl/files/fsl-5.0.9-setup.patch
+++ /dev/null
@@ -1,115 +0,0 @@
-diff -Naur fsl.orig/build fsl/build
---- fsl.orig/build	2015-03-29 00:10:39.845936000 +1300
-+++ fsl/build	2015-03-29 00:12:37.160487000 +1300
-@@ -11,9 +11,8 @@
- ifit load_varian load_dicom misc_scripts fdt first possum sgeutils \
- flameo oxford_asl relax qboot topup ptx2 lesions eddy dwssfp verbena";
- fi
- 
--echo "Building projects - see build.log file for progress..."
--./config/common/buildproj $PROJECTS > ./build.log 2>&1
--echo "Finished build : end of log file shows ..."
--tail -10 build.log
-+echo "Building projects"
-+./config/common/buildproj $PROJECTS
-+echo "Finished build"
- 
-diff -Naur fsl.orig/config/common/buildproj fsl/config/common/buildproj
---- fsl.orig/config/common/buildproj	2015-03-29 00:11:47.130998000 +1300
-+++ fsl/config/common/buildproj	2015-03-29 00:12:37.164319000 +1300
-@@ -11,10 +11,10 @@
- fi
- PROJECTS="$@" ; export PROJECTS ;
- 
--FSLDIR=`pwd`
-+#FSLDIR=`pwd`
- FSLDEVDIR=${FSLDIR}
- FSLCONFDIR=${FSLDIR}/config
--FSLMACHTYPE=`${FSLDIR}/etc/fslconf/fslmachtype.sh`
-+#FSLMACHTYPE=`${FSLDIR}/etc/fslconf/fslmachtype.sh`
- export FSLDIR FSLDEVDIR FSLCONFDIR FSLMACHTYPE
- 
- buildmessages="" ; export buildmessages ;
-@@ -66,7 +66,7 @@
- 	  if [ -x fslconfig ] ; then
- 	    ./fslconfig ;
- 	  fi
--	  if ${MAKE} -k ${MAKEOPTIONS} ; then 
-+	  if ${MAKE} ${MAKEOPTIONS} ${MAKEOPTS} ; then 
- 	    if ${MAKE} install ; then
- 	      installok=true;
- 	      # Clean up after ourselves
-diff -Naur fsl.orig/config/common/vars.mk fsl/config/common/vars.mk
---- fsl.orig/config/common/vars.mk	2015-03-29 00:11:47.183520000 +1300
-+++ fsl/config/common/vars.mk	2015-03-29 00:18:53.151222000 +1300
-@@ -24,15 +24,15 @@
- USRCFLAGS = 
- USRCXXFLAGS =
- 
--LDFLAGS = ${ARCHLDFLAGS} ${USRLDFLAGS} -L. -L${DEVLIBDIR} -L${LIBDIR}
-+LDFLAGS = ${ARCHLDFLAGS} ${USRLDFLAGS} -L. -L${DEVLIBDIR} -L${LIBDIR} ${USERLDFLAGS}
- 
--AccumulatedIncFlags = ${USRINCFLAGS} -I. -I${DEVINCDIR} -I${INCDIR}
-+AccumulatedIncFlags = ${USRINCFLAGS} -I. -I${DEVINCDIR} -I${INCDIR} ${CPPFLAGS}
- 
- CFLAGS = ${ANSI_FLAGS} ${ANSI_CFLAGS} ${DBGFLAGS} ${USEDCSTATICFLAGS} ${USRCFLAGS} ${ARCHFLAGS} ${OPTFLAGS}  \
--	${AccumulatedIncFlags}
-+	${AccumulatedIncFlags} ${USERCFLAGS}
- 
- CXXFLAGS = ${ANSI_FLAGS} ${ANSI_CXXFLAGS} ${DBGFLAGS} ${USEDCXXSTATICFLAGS} ${USRCXXFLAGS} ${ARCHFLAGS} ${OPTFLAGS}  \
--	${AccumulatedIncFlags}
-+	${AccumulatedIncFlags} ${USERCXXFLAGS}
- 
- HFILES = *.h
- AFILES = *.a
-diff -Naur fsl.orig/config/generic/systemvars.mk fsl/config/generic/systemvars.mk
---- fsl.orig/config/generic/systemvars.mk	2015-03-29 00:11:47.534246000 +1300
-+++ fsl/config/generic/systemvars.mk	2015-03-29 00:12:37.162129000 +1300
-@@ -4,20 +4,20 @@
- 
- # System dependent commands (NB: the first two are the most platform dependent)
- 
--INSTALL = ginstall -p
--RANLIB = ranlib
-+INSTALL = install -p
-+RANLIB = @@GENTOO_RANLIB@@
- 
- RM = /bin/rm
- CP = /bin/cp
- MV = /bin/mv
- CHMOD = /bin/chmod
- MKDIR = /bin/mkdir
--TCLSH = ${FSLDIR}/bin/fsltclsh
-+TCLSH = tclsh
- 
- # Compiler dependent variables
- 
--CC = gcc
--CXX = c++
-+CC = @@GENTOO_CC@@
-+CXX = @@GENTOO_CXX@@
- CSTATICFLAGS = -static
- CXXSTATICFLAGS = -static
- 
-@@ -25,7 +25,7 @@
- 
- DEPENDFLAGS = -MM
- 
--OPTFLAGS =  -O3 -fexpensive-optimizations ${ARCHFLAGS}
-+OPTFLAGS =
- MACHDBGFLAGS =
- GNU_ANSI_FLAGS = -Wall -ansi -pedantic
- SGI_ANSI_FLAGS = -ansi -fullwarn
-diff -Naur fsl.orig/extras/build fsl/extras/build
---- fsl.orig/extras/build	2015-03-29 00:11:15.080236000 +1300
-+++ fsl/extras/build	2015-03-29 00:15:53.170496000 +1300
-@@ -104,8 +104,8 @@
- if [ ${BUILDICONV} -eq 1 ]; then
-   PROJECTS="${PROJECTS} libiconv"
- fi
--PROJECTS="${PROJECTS} libgd libgdc libprob libcprob newmat cprob newran fftw"
-+PROJECTS="libgdc libprob libcprob newmat cprob newran"
- PROJECTS="${PROJECTS} boost libxml2-2.9.2 libxml++-2.34.0"
- for projname in $PROJECTS; do
- 
-     if [ -d $FSLESRCDIR/$projname ] ; then
diff --git a/sci-biology/fsl/files/fsl-6.0.2-no_xmlpp.patch b/sci-biology/fsl/files/fsl-6.0.2-no_xmlpp.patch
new file mode 100644
index 000000000..6eccc4370
--- /dev/null
+++ b/sci-biology/fsl/files/fsl-6.0.2-no_xmlpp.patch
@@ -0,0 +1,58 @@
+From 9de29e5141afa43c06f347ca158b67168fbb0031 Mon Sep 17 00:00:00 2001
+From: François Bissey <frp.bissey@gmail.com>
+Date: Mon, 20 Jan 2020 11:46:52 +1300
+Subject: [PATCH] Build without xmlpp since we use an external ciftilib that
+ doesnt require it. Replace it and other ciftilib flags with CIFTICFLAGS.
+
+---
+ src/flameo/Makefile  | 4 ++--
+ src/melodic/Makefile | 4 ++--
+ 2 files changed, 4 insertions(+), 4 deletions(-)
+
+diff --git a/src/flameo/Makefile b/src/flameo/Makefile
+index d22eb965..e967e682 100644
+--- a/src/flameo/Makefile
++++ b/src/flameo/Makefile
+@@ -2,7 +2,7 @@ include ${FSLCONFDIR}/default.mk
+ 
+ PROJNAME = flame
+ 
+-USRINCFLAGS = -I${INC_NEWMAT} -I${INC_PROB} -I${INC_ZLIB} -DCIFTILIB_USE_XMLPP -I${FSLEXTINC} -I${INC_XML2} -I${INC_XML++} -I${INC_XML++CONF} -I${INC_BOOST} -I${FSLDIR}/include/ciftiio
++USRINCFLAGS = -fPIC -I${INC_NEWMAT} -I${INC_PROB} -I${INC_ZLIB} -I${FSLEXTINC} ${CIFTICFLAGS} -I${INC_BOOST} -I${FSLDIR}/include/ciftiio
+ USRLDFLAGS = -L${LIB_NEWMAT} -L${LIB_PROB} -L${LIB_ZLIB}
+ 
+ UNAME := $(shell uname)
+@@ -10,7 +10,7 @@ ifeq (${UNAME},Darwin)
+         LIBS = -liconv
+ endif
+ 
+-LIBS += -lutils -lnewimage -lmiscmaths -lm -lnewmat -lNewNifti -lcifti -lxml++-2.6 -lxml2 -lboost_filesystem -lboost_system -lznz -lprob -lz 
++LIBS += -lutils -lnewimage -lmiscmaths -lm -lnewmat -lNewNifti ${CIFTILIBS} -lboost_filesystem -lboost_system -lznz -lprob -lz 
+ 
+ XFILES = flameo
+ 
+diff --git a/src/melodic/Makefile b/src/melodic/Makefile
+index 50666517..0c356a2d 100644
+--- a/src/melodic/Makefile
++++ b/src/melodic/Makefile
+@@ -7,7 +7,7 @@ OPTFLAGS_alphaev6-dec-osf5.0-gcc2.95.2 = -O3 -mieee -mfp-trap-mode=sui
+ 
+ PROJNAME = melodic
+ 
+-USRINCFLAGS = -I${INC_NEWMAT} -I${INC_PROB} -I${INC_GD} -I${INC_GDC} -I${INC_PNG} -I${INC_ZLIB} -DCIFTILIB_USE_XMLPP -I${FSLEXTINC} -I${INC_XML2} -I${INC_XML++} -I${INC_XML++CONF} -I${INC_BOOST} -I${FSLDIR}/include/ciftiio
++USRINCFLAGS = -fPIC -I${INC_NEWMAT} -I${INC_PROB} -I${INC_GD} -I${INC_GDC} -I${INC_PNG} -I${INC_ZLIB} -I${FSLEXTINC} ${CIFTICFLAGS} -I${INC_BOOST} -I${FSLDIR}/include/ciftiio
+ USRLDFLAGS = -L${LIB_NEWMAT} -L${LIB_PROB} -L${LIB_GD} -L${LIB_GDC} -L${LIB_PNG} -L${LIB_ZLIB}
+ 
+ UNAME := $(shell uname)
+@@ -15,7 +15,7 @@ ifeq (${UNAME},Darwin)
+         LIBS = -liconv
+ endif
+ 
+-LIBS += -lutils -lnewimage -lmiscplot -lmiscpic -lmiscmaths -lNewNifti -lcifti -lxml++-2.6 -lxml2 -lboost_filesystem -lboost_system -lznz -lnewmat -lprob -lm  -lgdc -lgd -lpng -lz
++LIBS += -lutils -lnewimage -lmiscplot -lmiscpic -lmiscmaths -lNewNifti ${CIFTILIBS} -lboost_filesystem -lboost_system -lznz -lnewmat -lprob -lm  -lgdc -lgd -lpng -lz
+ 
+ TEST_OBJS = test.o 
+ 
+-- 
+2.24.1
+
diff --git a/sci-biology/fsl/files/fsl-6.0.2-qstring_compat.patch b/sci-biology/fsl/files/fsl-6.0.2-qstring_compat.patch
new file mode 100644
index 000000000..9e6682a48
--- /dev/null
+++ b/sci-biology/fsl/files/fsl-6.0.2-qstring_compat.patch
@@ -0,0 +1,63 @@
+From 5a5ab3c80eaaea1fe9a43659e2ea5b773b587bb0 Mon Sep 17 00:00:00 2001
+From: François Bissey <frp.bissey@gmail.com>
+Date: Mon, 20 Jan 2020 11:51:52 +1300
+Subject: [PATCH] Because we use qstrings in ciftilib, calls to ciftilib file
+ function have to be made into compatible c strings.
+
+---
+ src/flameo/gsa.cc      | 4 ++--
+ src/melodic/meldata.cc | 2 +-
+ src/melodic/meldata.h  | 2 +-
+ 3 files changed, 4 insertions(+), 4 deletions(-)
+
+diff --git a/src/flameo/gsa.cc b/src/flameo/gsa.cc
+index 70f8f385..16167abe 100644
+--- a/src/flameo/gsa.cc
++++ b/src/flameo/gsa.cc
+@@ -74,7 +74,7 @@ namespace GSA {
+     sourceType=mode;
+     if ( sourceType.compare("CIFTI") == 0 ) {
+       cifti::CiftiFile inputCifti;
+-      inputCifti.openFile(make_basename(filename)+".nii");
++      inputCifti.openFile((make_basename(filename)+".nii").c_str());
+       ciftiExemplar=inputCifti.getCiftiXML();
+       cerr << "ndim " << ciftiExemplar.getNumberOfDimensions() << endl;
+       cerr << "type1 " << ciftiExemplar.getMappingType(0) << endl;
+@@ -194,7 +194,7 @@ namespace GSA {
+       scalarsMap.setLength(data.Nrows());
+       ciftiExemplar.setMap(0, scalarsMap);
+       CiftiFile outputFile;
+-      outputFile.setWritingFile(make_basename(filename)+extension+".nii");//sets up on-disk writing with default writing version
++      outputFile.setWritingFile((make_basename(filename)+extension+".nii").c_str());//sets up on-disk writing with default writing version
+       outputFile.setCiftiXML(ciftiExemplar,false);	    
+       vector<float> scratchRow(data.Nrows());//read/write a row at a time
+       for (int64_t row=0;row<data.Ncols();row++) {	    
+diff --git a/src/melodic/meldata.cc b/src/melodic/meldata.cc
+index c4ad2349..1515e702 100644
+--- a/src/melodic/meldata.cc
++++ b/src/melodic/meldata.cc
+@@ -118,7 +118,7 @@ namespace Melodic{
+     	tmpData = RawData.matrix(Mask);
+ 		memmsg(" after reshape ");	  
+ 	} else { //Read in Cifti
+-	  inputCifti.openFile(fname+".nii");
++	  inputCifti.openFile((fname+".nii").c_str());
+ 	  const vector<int64_t>& dims = inputCifti.getDimensions();
+ 	  tmpData.ReSize(dims[0],dims[1]); //swapped compared to cifti
+ 	  vector<float> scratchRow(dims[0]);//read/write a row at a time
+diff --git a/src/melodic/meldata.h b/src/melodic/meldata.h
+index 49774003..f5326bdd 100644
+--- a/src/melodic/meldata.h
++++ b/src/melodic/meldata.h
+@@ -109,7 +109,7 @@ namespace Melodic{
+ 	  message("  " << logger.appendDir(fname) << endl);
+ 	} else { //Process CIFTI save ICs as float
+ 	  cifti::CiftiFile outputFile;
+-	  outputFile.setWritingFile(logger.appendDir(fname)+".nii");//sets up on-disk writing with default writing version
++	  outputFile.setWritingFile((logger.appendDir(fname)+".nii").c_str());//sets up on-disk writing with default writing version
+ 	  cifti::CiftiXML xml(inputCifti.getCiftiXML());
+ 	  cifti::CiftiScalarsMap scalarsMap;
+ 	  std::vector<char> foo = xml.writeXMLToVector();
+-- 
+2.24.1
+
diff --git a/sci-biology/fsl/files/fsl-6.0.2-template.patch b/sci-biology/fsl/files/fsl-6.0.2-template.patch
new file mode 100644
index 000000000..597241a3b
--- /dev/null
+++ b/sci-biology/fsl/files/fsl-6.0.2-template.patch
@@ -0,0 +1,55 @@
+Subject: as discussed in https://github.com/gentoo/sci/issues/963
+
+--- a/src/newimage/generalio.cc	2019-09-11 09:24:32.000000000 -0400
++++ b/src/newimage/generalio.cc §2020-08-07 20:30:20.037494201 -0400
+@@ -308,6 +308,41 @@
+   return 0;
+ }
+
++template
++int readGeneralVolume<double>(volume<double>& target, const string& filename,
++		  short& dtype, const bool swap2radiological,
++		  int64_t x0, int64_t y0, int64_t z0, int64_t t0, int64_t d50, int64_t d60, int64_t d70,
++		  int64_t x1, int64_t y1, int64_t z1, int64_t t1, int64_t d51, int64_t d61, int64_t d71,
++		  const bool readAs4D);
++
++template
++int readGeneralVolume<float>(volume<float>& target, const string& filename,
++		  short& dtype, const bool swap2radiological,
++		  int64_t x0, int64_t y0, int64_t z0, int64_t t0, int64_t d50, int64_t d60, int64_t d70,
++		  int64_t x1, int64_t y1, int64_t z1, int64_t t1, int64_t d51, int64_t d61, int64_t d71,
++		  const bool readAs4D);
++
++template
++int readGeneralVolume<short>(volume<short>& target, const string& filename,
++		  short& dtype, const bool swap2radiological,
++		  int64_t x0, int64_t y0, int64_t z0, int64_t t0, int64_t d50, int64_t d60, int64_t d70,
++		  int64_t x1, int64_t y1, int64_t z1, int64_t t1, int64_t d51, int64_t d61, int64_t d71,
++		  const bool readAs4D);
++
++template
++int readGeneralVolume<char>(volume<char>& target, const string& filename,
++		  short& dtype, const bool swap2radiological,
++		  int64_t x0, int64_t y0, int64_t z0, int64_t t0, int64_t d50, int64_t d60, int64_t d70,
++		  int64_t x1, int64_t y1, int64_t z1, int64_t t1, int64_t d51, int64_t d61, int64_t d71,
++		  const bool readAs4D);
++
++template
++int readGeneralVolume<int>(volume<int>& target, const string& filename,
++		  short& dtype, const bool swap2radiological,
++		  int64_t x0, int64_t y0, int64_t z0, int64_t t0, int64_t d50, int64_t d60, int64_t d70,
++		  int64_t x1, int64_t y1, int64_t z1, int64_t t1, int64_t d51, int64_t d61, int64_t d71,
++		  const bool readAs4D);
++
+ template int read_volumeROI(volume<char>& target, const string& filename,
+ 			      short& dtype,
+ 			      int64_t x0, int64_t y0, int64_t z0, int64_t t0,
+
+--- a/src/fslsurface/fslsurfaceio.cc	2019-09-11 09:23:11.000000000 -0400
++++ b/src/fslsurface/fslsurfaceio.cc	2020-08-08 04:17:55.917387550 -0400
+@@ -1055,6 +1055,7 @@
+ 	  return 0;
+ 	}
+
++  template int readGIFTI<float, unsigned int>( fslSurface<float, unsigned int> & surf, const string & filename);
+   template int writeGIFTI<float, unsigned int>( const fslSurface<float, unsigned int> & surf, const std::string & filename, int enc);
diff --git a/sci-biology/fsl/files/fsl-6.0.4-cuda_buildsettings.patch b/sci-biology/fsl/files/fsl-6.0.4-cuda_buildsettings.patch
new file mode 100644
index 000000000..749e80623
--- /dev/null
+++ b/sci-biology/fsl/files/fsl-6.0.4-cuda_buildsettings.patch
@@ -0,0 +1,12 @@
+diff -Naur fsl.orig/config/buildSettings.mk fsl/config/buildSettings.mk
+--- fsl.orig/config/buildSettings.mk	2020-12-02 16:22:57.999912865 -0500
++++ fsl/config/buildSettings.mk	2020-12-02 16:24:15.332915270 -0500
+@@ -144,7 +144,7 @@
+ # CUDA development environment
+ CUDAVER := $(or $(CUDAVER),9.1)
+ #$(info $$CUDAVER is [${CUDAVER}])
+-CUDA_INSTALLATION = /opt/cuda-${CUDAVER}
++CUDA_INSTALLATION = /opt/cuda
+ ifdef SINGULARITY_NAME
+ CUDA_INSTALLATION = /usr/local/cuda-${CUDAVER}
+ endif
diff --git a/sci-biology/fsl/files/fsl-6.0.4-eddy_cuda.patch b/sci-biology/fsl/files/fsl-6.0.4-eddy_cuda.patch
new file mode 100644
index 000000000..ad118c39a
--- /dev/null
+++ b/sci-biology/fsl/files/fsl-6.0.4-eddy_cuda.patch
@@ -0,0 +1,21 @@
+diff -Naur fsl.orig/src/eddy/Makefile fsl/src/eddy/Makefile
+--- fsl.orig/src/eddy/Makefile	2020-12-02 16:07:47.327884548 -0500
++++ fsl/src/eddy/Makefile	2020-12-02 16:11:21.149891196 -0500
+@@ -29,6 +29,8 @@
+ TMPCXXFLAGS_2=
+ TMPNAME_1=
+ TMPNAME_2=
++cuda=1
++cpu=1
+ TOPUP_DIR=../topup
+ 
+ ifndef cuda
+@@ -74,7 +75,7 @@
+ ifdef NVCC11
+ 	NVCC=${NVCC11}
+ endif
+-NVCCFLAGS=-c -DCOMPILE_GPU -O3 -m 64 -std=c++11
++NVCCFLAGS=-c -DCOMPILE_GPU -O3 -m 64 -std=c++11 @@GENTOO_NVCC_FLAGS@@
+ ifeq ($(CLOBBER_CLANG),1)
+    NVCCFLAGS+= -DCLOBBER_CLANG
+ endif
diff --git a/sci-biology/fsl/files/fsl-6.0.4-fdt_cuda.patch b/sci-biology/fsl/files/fsl-6.0.4-fdt_cuda.patch
new file mode 100644
index 000000000..7f322027b
--- /dev/null
+++ b/sci-biology/fsl/files/fsl-6.0.4-fdt_cuda.patch
@@ -0,0 +1,14 @@
+diff -Naur fsl.orig/src/fdt/Makefile fsl/src/fdt/Makefile
+--- fsl.orig/src/fdt/Makefile	2020-12-02 19:06:55.826218772 -0500
++++ fsl/src/fdt/Makefile	2020-12-02 19:08:02.883220858 -0500
+@@ -6,7 +6,9 @@
+      $(eval $($(PROJNAME)_MASTERBUILD))
+ endif
+ 
+-ifeq ($(COMPILE_GPU), 1)
++# disable CUDA support for fdt
++#ifeq ($(COMPILE_GPU), 1)
++ifeq (0, 1)
+ 	COMPILE_WITH_GPU=libbedpostx_cuda.so merge_parts_gpu xfibres_gpu CUDA/split_parts_gpu
+ 	SCRIPTS_GPU=CUDA/bedpostx_gpu CUDA/bedpostx_postproc_gpu.sh
+ endif
diff --git a/sci-biology/fsl/files/fsl-6.0.4-flameo_std.patch b/sci-biology/fsl/files/fsl-6.0.4-flameo_std.patch
new file mode 100644
index 000000000..a991f1ed3
--- /dev/null
+++ b/sci-biology/fsl/files/fsl-6.0.4-flameo_std.patch
@@ -0,0 +1,11 @@
+diff -Naur fsl.orig/src/flameo/Makefile fsl/src/flameo/Makefile
+--- fsl.orig/src/flameo/Makefile	2021-01-06 14:04:35.728274475 -0500
++++ fsl/src/flameo/Makefile	2021-01-06 14:08:18.204269285 -0500
+@@ -4,6 +4,7 @@
+ 
+ USRINCFLAGS = -I${INC_NEWMAT} -I${INC_PROB} -I${INC_ZLIB} -DCIFTILIB_USE_XMLPP -I${FSLEXTINC} -I${INC_XML2} -I${INC_XML++} -I${INC_XML++CONF} -I${INC_BOOST} -I${FSLDIR}/include/ciftiio
+ USRLDFLAGS = -L${LIB_NEWMAT} -L${LIB_PROB} -L${LIB_ZLIB}
++USRCXXFLAGS = -std=c++11
+ 
+ UNAME := $(shell uname)
+ ifeq (${UNAME},Darwin)
diff --git a/sci-biology/fsl/files/fsl-6.0.4-fsldir_redux-p1.patch b/sci-biology/fsl/files/fsl-6.0.4-fsldir_redux-p1.patch
new file mode 100644
index 000000000..ca3945442
--- /dev/null
+++ b/sci-biology/fsl/files/fsl-6.0.4-fsldir_redux-p1.patch
@@ -0,0 +1,240 @@
+From 2bc4be1f55b27a733e1e624b34bc570187ba95e1 Mon Sep 17 00:00:00 2001
+From: François Bissey <frp.bissey@gmail.com>
+Date: Mon, 20 Jan 2020 11:40:53 +1300
+Subject: [PATCH] Making sure fsl code and executable can find other executable
+ and data in standard location.
+
+---
+ src/fast4/fast_two.cc              |  8 ++++----
+ src/feat5/feat_model.cc            |  8 +++-----
+ src/feat5/tsplot.cc                |  7 +++----
+ src/first/first_utils.cc           |  4 ++--
+ src/fnirt/fnirtfns.cpp             | 11 ++++-------
+ src/fslsurface/fslsurface_first.cc |  6 ++----
+ src/fslsurface/fslsurfacemaths.cpp | 12 ------------
+ src/libvis/miscpic.h               |  7 +------
+ src/melodic/meldata.cc             |  4 ++--
+ src/melodic/meloptions.cc          |  8 --------
+ src/melodic/meloptions.h           |  1 -
+ src/melodic/melreport.cc           | 12 ++++++------
+ src/melodic/melreport.h            | 20 ++++++++++----------
+ src/mm/mixture_model.cc            |  4 ++--
+ src/siena/siena_diff.cc            | 28 +++++++++++++---------------
+ src/topup/topupfns.cpp             |  3 +--
+ 16 files changed, 53 insertions(+), 90 deletions(-)
+
+diff --git a/src/fast4/fast_two.cc b/src/fast4/fast_two.cc
+index 592b5df..b525444 100644
+--- a/src/fast4/fast_two.cc
++++ b/src/fast4/fast_two.cc
+@@ -166,7 +166,7 @@ int prior_registration(string inname, string main_prior_vol, NEWIMAGE::volume<fl
+ string csfPriorName, grayPriorName, whitePriorName;
+   if(alternatePriors.unset())
+   {
+-    string priorRootName=string(getenv("FSLDIR")) + "/data/standard/tissuepriors/avg152T1_";
++    string priorRootName="@GENTOO_PORTAGE_EPREFIX@/usr/share/fsl/data/standard/tissuepriors/avg152T1_";
+     csfPriorName = priorRootName+"csf";
+     grayPriorName = priorRootName+"gray";
+     whitePriorName = priorRootName+"white";
+@@ -215,15 +215,15 @@ string csfPriorName, grayPriorName, whitePriorName;
+     if(bapused>0)
+       {
+ 	char reg[1024];
+-	sprintf(reg, "%s/bin/flirt -ref %s -in %s -out %s -applyxfm -init %s", getenv("FSLDIR"), inname.c_str(), csfPriorName.c_str(), (main_prior_vol+"_csf_stdspace").c_str(),  bapriori.value().c_str());
++	sprintf(reg, "flirt -ref %s -in %s -out %s -applyxfm -init %s", inname.c_str(), csfPriorName.c_str(), (main_prior_vol+"_csf_stdspace").c_str(),  bapriori.value().c_str());
+         if(verbose.value())
+ 	  cout<<reg<<endl;
+ 	system(reg);
+-	sprintf(reg, "%s/bin/flirt -ref %s -in %s -out %s -applyxfm -init %s", getenv("FSLDIR"), inname.c_str(), grayPriorName.c_str(), (main_prior_vol+"_gm_stdspace").c_str(),  bapriori.value().c_str());
++	sprintf(reg, "flirt -ref %s -in %s -out %s -applyxfm -init %s", inname.c_str(), grayPriorName.c_str(), (main_prior_vol+"_gm_stdspace").c_str(),  bapriori.value().c_str());
+ 	if(verbose.value())
+ 	  cout<<reg<<endl;
+         system(reg);
+-	sprintf(reg, "%s/bin/flirt -ref %s -in %s -out %s -applyxfm -init %s", getenv("FSLDIR"), inname.c_str(), whitePriorName.c_str(), (main_prior_vol+"_wm_stdspace").c_str(),  bapriori.value().c_str());
++	sprintf(reg, "flirt -ref %s -in %s -out %s -applyxfm -init %s", inname.c_str(), whitePriorName.c_str(), (main_prior_vol+"_wm_stdspace").c_str(),  bapriori.value().c_str());
+ 	if(verbose.value())
+ 	  cout << reg << endl;
+ 	system(reg);
+diff --git a/src/feat5/feat_model.cc b/src/feat5/feat_model.cc
+index 399a13e..e15e43c 100644
+--- a/src/feat5/feat_model.cc
++++ b/src/feat5/feat_model.cc
+@@ -744,7 +744,7 @@ int main(int argc, char **argv)
+   vector<int> G;
+   vector<string> titles;
+   float  tr, mult, trmult, nltffwhm=0, maxconvwin=0;
+-  char   fl[10000], *FSLDIR;
++  char   fl[10000];
+   string fn, filename;
+   FONT_DATA *font_data = new FONT_DATA[1];
+ 
+@@ -763,8 +763,6 @@ int main(int argc, char **argv)
+   if (argc==3)
+     motionparams=remmean(read_ascii_matrix(argv[2]));
+ 
+-  FSLDIR=getenv("FSLDIR");
+-
+   fn = string(argv[1])+".fsf";
+ 
+   level      = atoi(find_line(fn, "fmri(level)", fl));
+@@ -1510,7 +1508,7 @@ int main(int argc, char **argv)
+   writeCovarianceImage(string(argv[1])+"_cov.ppm", contrasts, F, nftests, realDesign, level, evs.eigenvals, font_data, contrasts.RE);
+   writeImagePreview(string(argv[1])+".ppm", contrasts, F, nftests, realDesign, level, evs, font_data, titles, tr, nltffwhm, nTimepoints, G);
+ 
+-  filename=string(getenv("FSLDIR"))+"/bin/wpng -q -overwrite  "+string(argv[1])+".ppm ";
++  filename="wpng -q -overwrite  "+string(argv[1])+".ppm ";
+   system(filename.c_str());
+ 
+   return(0);
+@@ -2161,6 +2159,6 @@ char the_string[10000];
+ 
+     fclose(outputfile);
+ 
+-    filename=string(getenv("FSLDIR")) + "/bin/wpng -q -overwrite  " + filename;
++    filename="wpng -q -overwrite  " + filename;
+     system(filename.c_str());
+ }
+diff --git a/src/feat5/tsplot.cc b/src/feat5/tsplot.cc
+index ae191fd..3a02b55 100644
+--- a/src/feat5/tsplot.cc
++++ b/src/feat5/tsplot.cc
+@@ -293,7 +293,7 @@ int main(int argc, char **argv)
+ ofstream     outputFile;
+ int          numEVs, npts, numContrasts=1, nftests=0, GRPHSIZE(600), PSSIZE(600); 
+ vector<double> normalisedContrasts, model, triggers;
+- string       fmriFileName, fslPath, featdir, vType, indexText;
++ string       fmriFileName, featdir, vType, indexText;
+ ColumnVector NewimageVoxCoord(4),NiftiVoxCoord(4);
+ bool outputText(true), useCoordinate(false), prewhiten(false), useTriggers(false), customMask(false), modelFree(false), isHigherLevel(false), outputDataOnly(false);
+ bool zWeightClusters(true);
+@@ -307,7 +307,6 @@ volume<float> immask;
+   if (argc<2) usage("");
+   featdir=string(argv[1]);
+   fmriFileName=featdir+"/filtered_func_data";
+-  fslPath=string(getenv("FSLDIR"));
+ 
+   string outputName(featdir);
+ 
+@@ -753,7 +752,7 @@ volume4D<float> acs;
+ 	cerr << "Can't open output report file " << outputName << endl;
+ 	exit(1);
+       }
+-      outputFile << "<HTML>\n<TITLE>"<< statType << num2str(i) <<"</TITLE>\n<BODY BACKGROUND=\"file:"<< fslPath <<"/doc/images/fsl-bg.jpg\">\n<hr><CENTER>\n<H1>FEAT Time Series Report - "<< statType << num2str(i) <<"</H1>\n</CENTER>\n<hr><b>Full plots</b><p>\n"<< graphText;
++      outputFile << "<HTML>\n<TITLE>"<< statType << num2str(i) <<"</TITLE>\n<BODY BACKGROUND=\"file:"<< "@GENTOO_PORTAGE_EPREFIX@/usr/share/fsl/doc/images/fsl-bg.jpg\">\n<hr><CENTER>\n<H1>FEAT Time Series Report - "<< statType << num2str(i) <<"</H1>\n</CENTER>\n<hr><b>Full plots</b><p>\n"<< graphText;
+       if (useTriggers) outputFile << "\n<hr><b>Peristimulus plots</b><p>\n"<< peristimulusText <<"\n<HR></BODY></HTML>\n\n";
+       else outputFile << "\n</BODY></HTML>\n\n";
+       outputFile.close();
+@@ -768,7 +767,7 @@ volume4D<float> acs;
+       cerr << "Can't open output report file " << outputName << endl;
+       exit(1);
+   }
+-  outputFile << "<HTML>\n<TITLE>FEAT Time Series Report</TITLE>\n<BODY BACKGROUND=\"file:" << fslPath << "/doc/images/fsl-bg.jpg\">\n<hr><CENTER>\n<H1>FEAT Time Series Report</H1>\n</CENTER>\n<hr>" << indexText << "<HR></BODY></HTML>" << endl << endl;
++  outputFile << "<HTML>\n<TITLE>FEAT Time Series Report</TITLE>\n<BODY BACKGROUND=\"file:" << "@GENTOO_PORTAGE_EPREFIX@/usr/share/fsl/doc/images/fsl-bg.jpg\">\n<hr><CENTER>\n<H1>FEAT Time Series Report</H1>\n</CENTER>\n<hr>" << indexText << "<HR></BODY></HTML>" << endl << endl;
+   outputFile.close();
+ 
+   /* now output same thing without start and end, for inclusion in feat report */
+diff --git a/src/first/first_utils.cc b/src/first/first_utils.cc
+index 68be44b..85960f4 100644
+--- a/src/first/first_utils.cc
++++ b/src/first/first_utils.cc
+@@ -1954,8 +1954,8 @@ void do_work_bvars(){
+     if (!surfaceVAout.value()) {
+       // do not output on the surface, instead do the new default of outputting a volume with the scalar normal dot product values (for use with randomise)
+       volume<float> refim;
+-      if (useReconMNI.value()) { read_volume(refim,string(getenv("FSLDIR")) + "/data/standard/MNI152_T1_1mm"); } 
+-      else { read_volume(refim,string(getenv("FSLDIR")) + "/data/standard/MNI152_T1_1mm"); } 
++      if (useReconMNI.value()) { read_volume(refim,"@GENTOO_PORTAGE_EPREFIX@/usr/share/fsl/data/standard/MNI152_T1_1mm"); } 
++      else { read_volume(refim,"@GENTOO_PORTAGE_EPREFIX@/usr/share/fsl/data/standard/MNI152_T1_1mm"); } 
+       volume<float> maskvol(refim);
+       maskvol=0.0f;
+       volume4D<float> volnormals;
+diff --git a/src/fnirt/fnirtfns.cpp b/src/fnirt/fnirtfns.cpp
+index 24e26fd..77899e7 100644
+--- a/src/fnirt/fnirtfns.cpp
++++ b/src/fnirt/fnirtfns.cpp
+@@ -1203,8 +1203,7 @@ string existing_ref_fname(const string& ref_fname)
+       return(string(ref_fname));
+     }
+     else {
+-      const char *fsldir_ptr = getenv("FSLDIR");
+-      string eref_fname = string(fsldir_ptr) + string("/data/standard/") + ref_fname;
++      string eref_fname = string("@GENTOO_PORTAGE_EPREFIX@/usr/share/fsl/data/standard/") + ref_fname;
+       if (NEWIMAGE::FslFileExists(eref_fname)) return(eref_fname);
+       else return(string(""));
+     }
+@@ -1230,9 +1229,8 @@ string existing_ref_fname(const string& ref_fname)
+       NEWIMAGE::read_volume_hdr_only(vref,ref_fname); // Throws if file dont exist
+       eref_fname = ref_fname;
+     }
+-    catch(...) { // Didn't exist in current directory, try in ${FSLDIR}/data/standard
+-      const char *fsldir_ptr = getenv("FSLDIR");
+-      eref_fname = string(fsldir_ptr) + string("/data/standard/") + ref_fname;
++    catch(...) { // Didn't exist in current directory, try in .../data/standard
++      eref_fname = string("@GENTOO_PORTAGE_EPREFIX@/usr/share/fsl/data/standard/") + ref_fname;
+       try {
+         cout << "Could not find " << ref_fname << ", now checking " << eref_fname << endl;
+         NEWIMAGE::read_volume_hdr_only(vref,eref_fname); // Throws if file dont exist
+@@ -1267,8 +1265,7 @@ string existing_conf_file(const string& cfname)
+     if (check_exist(ecfname)) return(ecfname);
+   }
+   if (!FNIRT::path(cfname).length()) {              // If no path explicitly given
+-    const char *fsldir_ptr = getenv("FSLDIR");
+-    ecfname = string(fsldir_ptr) + string("/etc/flirtsch/") + cfname;
++    ecfname = string("@GENTOO_PORTAGE_EPREFIX@/etc/flirtsch/") + cfname;
+     if (check_exist(ecfname)) return(ecfname);
+     else if (!FNIRT::extension(ecfname).length()) { // If no path _and_ no extension given
+       ecfname += string(".cnf");
+diff --git a/src/fslsurface/fslsurface_first.cc b/src/fslsurface/fslsurface_first.cc
+index faec642..b2ef794 100644
+--- a/src/fslsurface/fslsurface_first.cc
++++ b/src/fslsurface/fslsurface_first.cc
+@@ -500,8 +500,7 @@ namespace fslsurface_name {
+             
+ 			volume<float>* immni = new volume<float>();
+             
+-            char* fsldir = getenv("FSLDIR");
+-            read_volume_hdr_only(*immni, string(fsldir) + "/data/standard/MNI152_T1_1mm");
++            read_volume_hdr_only(*immni, "@GENTOO_PORTAGE_EPREFIX@/usr/share/fsl/data/standard/MNI152_T1_1mm");
+             
+ 			//read_volume_hdr_only(*immni, template_name);
+ 			
+@@ -699,8 +698,7 @@ namespace fslsurface_name {
+           
+ 			volume<float>* immni = new volume<float>();
+             
+-            char* fsldir = getenv("FSLDIR");
+-            read_volume_hdr_only(*immni, string(fsldir) + "/data/standard/MNI152_T1_1mm");
++            read_volume_hdr_only(*immni, "@GENTOO_PORTAGE_EPREFIX@/usr/share/fsl/data/standard/MNI152_T1_1mm");
+             
+ 			//read_volume_hdr_only(*immni, template_name);
+ 			
+diff --git a/src/fslsurface/fslsurfacemaths.cpp b/src/fslsurface/fslsurfacemaths.cpp
+index eaf55eb..3dc184d 100644
+--- a/src/fslsurface/fslsurfacemaths.cpp
++++ b/src/fslsurface/fslsurfacemaths.cpp
+@@ -598,12 +598,6 @@ int main (int argc, char * argv[])
+ 
+         }else if (command == "-reconFromBvars"){
+             cout<<"do recon "<<endl;
+-            char* fsldir = getenv("FSLDIR");
+-            if (fsldir == NULL)
+-            {
+-                cerr<<"FSLDIR has not been set. "<<endl;
+-                exit(EXIT_FAILURE); 
+-            }
+             //file.bvars,mni_template.nii.gz
+            // string mni = string(fsldir)+"/data/standard/MNI152_T1_1mm";
+             reconSurface_from_bvars( surf, string(argv[i_arg+1]));
+@@ -612,12 +606,6 @@ int main (int argc, char * argv[])
+ 
+         }else if (command == "-reconAllFromBvarsAndSave"){
+             cout<<"do recon+save "<<argc<<" "<<i_arg<<endl;
+-            char* fsldir = getenv("FSLDIR");
+-            if (fsldir == NULL)
+-            {
+-                cerr<<"FSLDIR has not been set. "<<endl;
+-                exit(EXIT_FAILURE); 
+-            }
+             //file.bvars,mni_template.nii.gz
+             // string mni = string(fsldir)+"/data/standard/MNI152_T1_1mm";
+             cout<<"recon "<< string(argv[i_arg+1])<<endl;
diff --git a/sci-biology/fsl/files/fsl-6.0.4-fsldir_redux-p2.patch b/sci-biology/fsl/files/fsl-6.0.4-fsldir_redux-p2.patch
new file mode 100644
index 000000000..af498b400
--- /dev/null
+++ b/sci-biology/fsl/files/fsl-6.0.4-fsldir_redux-p2.patch
@@ -0,0 +1,254 @@
+diff --git a/src/libvis/miscpic.h b/src/libvis/miscpic.h
+index a2f3855..5f440f2 100644
+--- a/src/libvis/miscpic.h
++++ b/src/libvis/miscpic.h
+@@ -90,12 +90,7 @@ namespace MISCPIC{
+ 	markRight=false;
+ 	trans= -10;
+ 	edgethresh = 0.0;
+-	if(getenv("FSLDIR")!=0){
+-	  lutbase = string(getenv("FSLDIR")) + "/etc/luts/";
+-	}
+-	else{
+-	  lutbase = string("/");
+-	}
++	lutbase = "@GENTOO_PORTAGE_EPREFIX@/etc/luts/";
+ 	title = string("");
+ 	cbartype = string("");
+ 	cbarptr = NULL;
+diff --git a/src/melodic/meldata.cc b/src/melodic/meldata.cc
+index 1749a45..c4ad234 100644
+--- a/src/melodic/meldata.cc
++++ b/src/melodic/meldata.cc
+@@ -992,7 +992,7 @@ namespace Melodic{
+   void MelodicData::est_smoothness()
+   {
+     if(Resels == 0){
+-      string SM_path = opts.binpath + "smoothest";
++      string SM_path = "smoothest";
+       string Mask_fname = logger.appendDir("mask");
+ 
+       if(opts.segment.value().length()>0){
+@@ -1157,7 +1157,7 @@ namespace Melodic{
+ 				// set up all strings
+ 				string BET_outputfname = string(Mean_fname)+"_brain";
+ 
+-				string BET_path = opts.binpath + "bet";
++				string BET_path = "bet";
+ 				string BET_optarg = "-m -f 0.4"; // see man bet
+ 				string Mask_fname = BET_outputfname+"_mask";
+ 
+diff --git a/src/melodic/meloptions.cc b/src/melodic/meloptions.cc
+index 08170c7..252e72b 100644
+--- a/src/melodic/meloptions.cc
++++ b/src/melodic/meloptions.cc
+@@ -93,14 +93,6 @@ MelodicOptions* MelodicOptions::gopt = NULL;
+   		explicitnums = false;
+   		logfname = string("log.txt");
+ 
+-  		// work out the path to the $FSLDIR/bin directory
+-  		if(getenv("FSLDIR")!=0){
+-    		binpath = (string) getenv("FSLDIR") + "/bin/";
+-  		} else{
+-    		binpath = argv[0];
+-    		binpath = binpath.substr(0,binpath.length()-7);
+-  		}
+-
+   		// parse once to establish log directory name
+   		for(int a = options.parse_command_line(argc, argv); a < argc; a++);
+ 
+diff --git a/src/melodic/meloptions.h b/src/melodic/meloptions.h
+index f546125..b964b7d 100644
+--- a/src/melodic/meloptions.h
++++ b/src/melodic/meloptions.h
+@@ -93,7 +93,6 @@ class MelodicOptions {
+   	~MelodicOptions() { delete gopt; }
+ 
+   	string version;
+-  	string binpath;
+   	string logfname;
+   	bool   filtermode;
+   	bool   explicitnums;
+diff --git a/src/melodic/melreport.cc b/src/melodic/melreport.cc
+index 141b6c2..2625059 100644
+--- a/src/melodic/melreport.cc
++++ b/src/melodic/melreport.cc
+@@ -84,8 +84,8 @@ namespace Melodic{
+ 			IChtml.setDir(report.getDir(),mmodel.get_prefix()+".html");
+ 
+       {//start IC page
+-				IChtml << "<HTML><HEAD><link REL=stylesheet TYPE=text/css href=file:" +
+-					(string) getenv("FSLDIR") +"/doc/fsl.css>" << endl
++				IChtml << "<HTML><HEAD><link REL=stylesheet TYPE=text/css href=file:"
++				       << "@GENTOO_PORTAGE_EPREFIX@/usr/share/fsl/doc/fsl.css>" << endl
+ 					<< "<style type=\"text/css\">OBJECT { width: 100% }</style>"
+ 	       	<< "<TITLE>FSL</TITLE></HEAD>" << endl
+ 	  			<< "<IFRAME  height=" << int(melodat.get_numfiles()/30 + 1)*50 
+@@ -486,8 +486,8 @@ namespace Melodic{
+ 
+       {//start IC2 page
+ 				IChtml2.setDir(report.getDir(),mmodel.get_prefix()+"_MM.html");
+-				IChtml2 << "<HTML><HEAD><link REL=stylesheet TYPE=text/css href=file:" +
+-					(string) getenv("FSLDIR") +"/doc/fsl.css>" << endl
++				IChtml2 << "<HTML><HEAD><link REL=stylesheet TYPE=text/css href=file:"
++					<< "@GENTOO_PORTAGE_EPREFIX@/usr/share/fsl/doc/fsl.css>" << endl
+ 					<< "<style type=\"text/css\">OBJECT { width: 100% }</style>"
+ 	       	<< "<TITLE>FSL</TITLE></HEAD>" << endl
+ 					<< "<IFRAME  height="<< int(melodat.get_numfiles()/30 + 1)*50 
+@@ -665,8 +665,8 @@ namespace Melodic{
+ 				IChtml << "<HTML> " << endl
+ 	       	<< "<TITLE>MELODIC Component " << num2str(cnum)
+ 	       	<< "</TITLE>" << endl
+-	       	<< "<BODY BACKGROUND=\"file:" << getenv("FSLDIR") 
+-	    		<< "/doc/images/fsl-bg.jpg\">" << endl 
++	       	<< "<BODY BACKGROUND=\"file:"  
++	    		<< "@GENTOO_PORTAGE_EPREFIX@/usr/share/fsl/doc/images/fsl-bg.jpg\">" << endl 
+ 	     		<< "<hr><CENTER><H1>MELODIC Component " << num2str(cnum)
+ 	       	<< "</H1>"<< endl;
+ 	
+diff --git a/src/melodic/melreport.h b/src/melodic/melreport.h
+index 574fc4c..e444681 100644
+--- a/src/melodic/melreport.h
++++ b/src/melodic/melreport.h
+@@ -104,21 +104,21 @@ namespace Melodic{
+ 	  				const time_t tmptime = time(NULL);
+ 		    		system(("mkdir "+ logger.appendDir("report") + " 2>/dev/null").c_str());
+ 				report.setDir(logger.appendDir("report"),"00index.html",true,false,ios::out);
+-						report << "<HTML><HEAD><link REL=stylesheet TYPE=text/css href=file:" +
+-							(string) getenv("FSLDIR") +"/doc/fsl.css>" 
++						report << "<HTML><HEAD><link REL=stylesheet TYPE=text/css href=file:"
++							<< "@GENTOO_PORTAGE_EPREFIX@/usr/share/fsl/doc/fsl.css>" 
+ 						  << "<TITLE>MELODIC report</TITLE></HEAD><BODY>"
+ 							<< endl <<endl;
+ 						loghtml.setDir(report.getDir(),"log.html");
+-						loghtml << "<HTML><HEAD><link REL=stylesheet TYPE=text/css href=file:" +
+-							(string) getenv("FSLDIR") +"/doc/fsl.css>" 
++						loghtml << "<HTML><HEAD><link REL=stylesheet TYPE=text/css href=file:"
++							<< "@GENTOO_PORTAGE_EPREFIX@/usr/share/fsl/doc/fsl.css>" 
+ 						  << "<TITLE>MELODIC report</TITLE></HEAD><BODY>"
+ 							<< endl <<endl;						
+ 						navigator.setDir(report.getDir(),"nav.html");
+ 						head.setDir(report.getDir(),"head.html");
+-	  				navigator << "<link REL=stylesheet TYPE=text/css href=file:"+
+-							(string) getenv("FSLDIR") +"/doc/fsl.css>"  << endl;
+-						head << "<link REL=stylesheet TYPE=text/css href=file:"+
+-							(string) getenv("FSLDIR") +"/doc/fsl.css>"  << endl;
++	  				navigator << "<link REL=stylesheet TYPE=text/css href=file:"
++						<< "@GENTOO_PORTAGE_EPREFIX@/usr/share/fsl/doc/fsl.css>"  << endl;
++						head << "<link REL=stylesheet TYPE=text/css href=file:"
++							<< "@GENTOO_PORTAGE_EPREFIX@/usr/share/fsl/doc/fsl.css>"  << endl;
+ 						head  <<"<TABLE BORDER=0><TR>" << endl
+ 							<<" <TD ALIGN=CENTER WIDTH=100%>"<< endl
+ 							<<"<TABLE BORDER=0>"<< endl
+@@ -130,8 +130,8 @@ namespace Melodic{
+ 							<< "</tr></table>" << endl
+ 							<< "<TD ALIGN=RIGHT>" << endl
+ 							<< "<a href=http://www.fmrib.ox.ac.uk/fsl target=_top>" << endl
+-						  << "<IMG BORDER=0 SRC=file:"<< getenv("FSLDIR")
+-							<< "/doc/images/fsl-logo-big.jpg WIDTH=165></a>" << endl
++						  << "<IMG BORDER=0 SRC=file:"
++							<< "@GENTOO_PORTAGE_EPREFIX@/usr/share/fsl/doc/images/fsl-logo-big.jpg WIDTH=165></a>" << endl
+ 							<< "</TD>"<<endl<<"</TR></TABLE> <hr>"<<endl;
+ 						if(opts.guireport.value()==""){
+ 							report <<"<OBJECT data=head.html></OBJECT>" <<  endl;
+diff --git a/src/mm/mixture_model.cc b/src/mm/mixture_model.cc
+index b8e6167..5f00693 100644
+--- a/src/mm/mixture_model.cc
++++ b/src/mm/mixture_model.cc
+@@ -2224,8 +2224,8 @@ namespace Mm {
+ 
+ 	htmllog << "<HTML> " << endl
+ 		<< "<TITLE>Mixture Model fit for" << data_name << "</TITLE>" << endl
+-		<< "<BODY BACKGROUND=\"file:" << getenv("FSLDIR") 
+-		<< "/doc/images/fsl-bg.jpg\">" << endl 
++		<< "<BODY BACKGROUND=\"file:"  
++		<< "@GENTOO_PORTAGE_EPREFIX@/usr/share/fsl/doc/images/fsl-bg.jpg\">" << endl 
+ 		<< "<hr><CENTER><H1>Mixture Model fit for<br>" << data_name << " </H1>"<< endl;
+      	
+ 	htmllog << "<hr><p>" << endl;
+diff -Naur fsl.orig/src/siena/siena_diff.cc fsl/src/siena/siena_diff.cc
+--- fsl.orig/src/siena/siena_diff.cc	2020-12-02 15:52:50.359856656 -0500
++++ fsl/src/siena/siena_diff.cc	2020-12-02 16:03:25.699876412 -0500
+@@ -107,7 +107,7 @@
+ {
+   // {{{  vars
+ 
+-char   thestring[10000], segoptions[10000], fsldir[10000];
++char   thestring[10000], segoptions[10000];
+ int    x_size, y_size, z_size, size, x, y, z, i, count,
+   seg2=0, ignore_z=0, ignore_top_slices=0, //erode_mask=0, 
+   ignore_bottom_slices=0, debug=0, flow_output=1, edge_masking=0;
+@@ -124,8 +124,6 @@
+ 
+ string argv1(argv[1]), argv2(argv[2]);
+ 
+-sprintf(fsldir,"%s",getenv("FSLDIR"));
+-
+ for (i = 3; i < argc; i++)
+   {
+     if (!strcmp(argv[i], "-i"))
+@@ -206,26 +204,26 @@
+ // }}}
+   // {{{  transform images and masks
+ 
+-sprintf(thestring,"%s/bin/flirt -o %s_halfwayto_%s -applyisoxfm 1 -paddingsize 0 -init %s_halfwayto_%s.mat -ref %s -in %s",
+-  fsldir,argv[1],argv[2],argv[1],argv[2],argv[1],argv[1]);
++sprintf(thestring,"flirt -o %s_halfwayto_%s -applyisoxfm 1 -paddingsize 0 -init %s_halfwayto_%s.mat -ref %s -in %s",
++	argv[1],argv[2],argv[1],argv[2],argv[1],argv[1]);
+ printf("%s\n",thestring); system(thestring);
+ 
+-sprintf(thestring,"%s/bin/flirt -o %s_halfwayto_%s -applyisoxfm 1 -paddingsize 0 -init %s_halfwayto_%s.mat -ref %s -in %s",
+-  fsldir,argv[2],argv[1],argv[2],argv[1],argv[1],argv[2]);
++sprintf(thestring,"flirt -o %s_halfwayto_%s -applyisoxfm 1 -paddingsize 0 -init %s_halfwayto_%s.mat -ref %s -in %s",
++	argv[2],argv[1],argv[2],argv[1],argv[1],argv[2]);
+ printf("%s\n",thestring); system(thestring);
+ 
+-sprintf(thestring,"%s/bin/flirt -o %s_halfwayto_%s_mask -applyisoxfm 1 -paddingsize 0 -init %s_halfwayto_%s.mat -ref %s -in %s_brain_mask",
+-  fsldir,argv[1],argv[2],argv[1],argv[2],argv[1],argv[1]);
++sprintf(thestring,"flirt -o %s_halfwayto_%s_mask -applyisoxfm 1 -paddingsize 0 -init %s_halfwayto_%s.mat -ref %s -in %s_brain_mask",
++	argv[1],argv[2],argv[1],argv[2],argv[1],argv[1]);
+ printf("%s\n",thestring); system(thestring);
+ 
+-sprintf(thestring,"%s/bin/flirt -o %s_halfwayto_%s_mask -applyisoxfm 1 -paddingsize 0 -init %s_halfwayto_%s.mat -ref %s -in %s_brain_mask",
+-  fsldir,argv[2],argv[1],argv[2],argv[1],argv[1],argv[2]);
++sprintf(thestring,"flirt -o %s_halfwayto_%s_mask -applyisoxfm 1 -paddingsize 0 -init %s_halfwayto_%s.mat -ref %s -in %s_brain_mask",
++	argv[2],argv[1],argv[2],argv[1],argv[1],argv[2]);
+ printf("%s\n",thestring); system(thestring);
+ 
+ if (edge_masking)
+ {
+-  sprintf(thestring,"%s/bin/flirt -o %s_halfwayto_%s_valid_mask -applyisoxfm 1 -paddingsize 0 -init %s_halfwayto_%s.mat -ref %s -in %s_valid_mask_with_%s",
+-    fsldir,argv[1],argv[2],argv[1],argv[2],argv[1],argv[1],argv[2]);
++  sprintf(thestring,"flirt -o %s_halfwayto_%s_valid_mask -applyisoxfm 1 -paddingsize 0 -init %s_halfwayto_%s.mat -ref %s -in %s_valid_mask_with_%s",
++	  argv[1],argv[2],argv[1],argv[2],argv[1],argv[1],argv[2]);
+   printf("%s\n",thestring); system(thestring);
+ }
+ 
+@@ -284,8 +282,8 @@
+     cout << "saving image 1 to disk prior to segmentation" << endl;
+     save_volume(in1,argv1+"_halfwayto_"+argv2+"_brain");
+     in1.destroy();
+-    sprintf(thestring,"%s/bin/fast %s %s %s_halfwayto_%s_brain > %s_halfwayto_%s_brain.vol 2>&1",
+-      fsldir,segtype,segoptions,argv[1],argv[2],argv[1],argv[2]);
++    sprintf(thestring,"fast %s %s %s_halfwayto_%s_brain > %s_halfwayto_%s_brain.vol 2>&1",
++	    segtype,segoptions,argv[1],argv[2],argv[1],argv[2]);
+     cout << thestring << endl;
+     system(thestring);
+   }
+diff --git a/src/topup/topupfns.cpp b/src/topup/topupfns.cpp
+index 6873758..9e8b956 100644
+--- a/src/topup/topupfns.cpp
++++ b/src/topup/topupfns.cpp
+@@ -463,8 +463,7 @@ string existing_conf_file(const string& cfname)
+     if (TOPUP::check_exist(ecfname)) return(ecfname);
+   }
+   if (!TOPUP::path(cfname).length()) {              // If no path explicitly given
+-    const char *fsldir_ptr = getenv("FSLDIR");
+-    ecfname = string(fsldir_ptr) + string("/etc/flirtsch/") + cfname;
++    ecfname = string("@GENTOO_PORTAGE_EPREFIX@/etc/flirtsch/") + cfname;
+     if (TOPUP::check_exist(ecfname)) return(ecfname);
+     else if (!TOPUP::extension(ecfname).length()) { // If no path _and_ no extension given
+       ecfname += string(".cnf");
+-- 
+2.24.1
+
diff --git a/sci-biology/fsl/files/fsl-6.0.4-gcc10_include.patch b/sci-biology/fsl/files/fsl-6.0.4-gcc10_include.patch
new file mode 100644
index 000000000..ae836c065
--- /dev/null
+++ b/sci-biology/fsl/files/fsl-6.0.4-gcc10_include.patch
@@ -0,0 +1,11 @@
+diff -Naur fsl.orig/src/newimage/newimageio.h fsl/src/newimage/newimageio.h
+--- fsl.orig/src/newimage/newimageio.h	2020-12-02 15:15:27.012786899 -0500
++++ fsl/src/newimage/newimageio.h	2020-12-02 15:19:51.046795110 -0500
+@@ -75,6 +75,7 @@
+ #include <iostream>
+ #include <fstream>
+ #include <sstream>
++#include <stdexcept>
+ #include "NewNifti/NewNifti.h"
+ #include "newmatio.h"
+ #include "newimage.h"
diff --git a/sci-biology/fsl/files/fsl-6.0.4-melodic_std.patch b/sci-biology/fsl/files/fsl-6.0.4-melodic_std.patch
new file mode 100644
index 000000000..83b5b9932
--- /dev/null
+++ b/sci-biology/fsl/files/fsl-6.0.4-melodic_std.patch
@@ -0,0 +1,11 @@
+diff -Naur fsl.orig/src/melodic/Makefile fsl/src/melodic/Makefile
+--- fsl.orig/src/melodic/Makefile	2021-01-06 14:04:35.743274475 -0500
++++ fsl/src/melodic/Makefile	2021-01-06 14:11:27.924264859 -0500
+@@ -9,6 +9,7 @@
+ 
+ USRINCFLAGS = -I${INC_NEWMAT} -I${INC_PROB} -I${INC_GD} -I${INC_GDC} -I${INC_PNG} -I${INC_ZLIB} -DCIFTILIB_USE_XMLPP -I${FSLEXTINC} -I${INC_XML2} -I${INC_XML++} -I${INC_XML++CONF} -I${INC_BOOST} -I${FSLDIR}/include/ciftiio
+ USRLDFLAGS = -L${LIB_NEWMAT} -L${LIB_PROB} -L${LIB_GD} -L${LIB_GDC} -L${LIB_PNG} -L${LIB_ZLIB}
++USRCXXFLAGS = -std=c++11
+ 
+ UNAME := $(shell uname)
+ ifeq (${UNAME},Darwin)
diff --git a/sci-biology/fsl/files/fsl-6.0.4-remove_fslpy_collisions-p1.patch b/sci-biology/fsl/files/fsl-6.0.4-remove_fslpy_collisions-p1.patch
new file mode 100644
index 000000000..434dc9cf6
--- /dev/null
+++ b/sci-biology/fsl/files/fsl-6.0.4-remove_fslpy_collisions-p1.patch
@@ -0,0 +1,303 @@
+diff -Naur fsl.orig/src/fslio/imln fsl/src/fslio/imln
+--- fsl.orig/src/fslio/imln	2021-02-01 15:29:34.842752994 -0500
++++ fsl/src/fslio/imln	1969-12-31 19:00:00.000000000 -0500
+@@ -1,90 +0,0 @@
+-#!/bin/sh
+-
+-#   imln - make symbolic link(s) to image file(s)
+-#
+-#   Stephen Smith and Mark Jenkinson, FMRIB Image Analysis Group
+-#
+-#   Copyright (C) 1999-2004 University of Oxford
+-#
+-#   Part of FSL - FMRIB's Software Library
+-#   http://www.fmrib.ox.ac.uk/fsl
+-#   fsl@fmrib.ox.ac.uk
+-#
+-#   Developed at FMRIB (Oxford Centre for Functional Magnetic Resonance
+-#   Imaging of the Brain), Department of Clinical Neurology, Oxford
+-#   University, Oxford, UK
+-#
+-#
+-#   LICENCE
+-#
+-#   FMRIB Software Library, Release 6.0 (c) 2018, The University of
+-#   Oxford (the "Software")
+-#
+-#   The Software remains the property of the Oxford University Innovation
+-#   ("the University").
+-#
+-#   The Software is distributed "AS IS" under this Licence solely for
+-#   non-commercial use in the hope that it will be useful, but in order
+-#   that the University as a charitable foundation protects its assets for
+-#   the benefit of its educational and research purposes, the University
+-#   makes clear that no condition is made or to be implied, nor is any
+-#   warranty given or to be implied, as to the accuracy of the Software,
+-#   or that it will be suitable for any particular purpose or for use
+-#   under any specific conditions. Furthermore, the University disclaims
+-#   all responsibility for the use which is made of the Software. It
+-#   further disclaims any liability for the outcomes arising from using
+-#   the Software.
+-#
+-#   The Licensee agrees to indemnify the University and hold the
+-#   University harmless from and against any and all claims, damages and
+-#   liabilities asserted by third parties (including claims for
+-#   negligence) which arise directly or indirectly from the use of the
+-#   Software or the sale of any products based on the Software.
+-#
+-#   No part of the Software may be reproduced, modified, transmitted or
+-#   transferred in any form or by any means, electronic or mechanical,
+-#   without the express permission of the University. The permission of
+-#   the University is not required if the said reproduction, modification,
+-#   transmission or transference is done without financial return, the
+-#   conditions of this Licence are imposed upon the receiver of the
+-#   product, and all original and amended source code is included in any
+-#   transmitted product. You may be held legally responsible for any
+-#   copyright infringement that is caused or encouraged by your failure to
+-#   abide by these terms and conditions.
+-#
+-#   You are not permitted under this Licence to use this Software
+-#   commercially. Use for which any financial return is received shall be
+-#   defined as commercial use, and includes (1) integration of all or part
+-#   of the source code or the Software into a product for sale or license
+-#   by or on behalf of Licensee to third parties or (2) use of the
+-#   Software or any derivative of it for research with the final aim of
+-#   developing software products for sale or license to a third party or
+-#   (3) use of the Software or any derivative of it for research with the
+-#   final aim of developing non-software products for sale or license to a
+-#   third party, or (4) use of the Software to provide any service to an
+-#   external organisation for which payment is received. If you are
+-#   interested in using the Software commercially, please contact Oxford
+-#   University Innovation ("OUI"), the technology transfer company of the
+-#   University, to negotiate a licence. Contact details are:
+-#   fsl@innovation.ox.ac.uk quoting Reference Project 9564, FSL.
+-export LC_ALL=C
+-
+-if [ $# -lt 2 ] ; then
+-  echo "Usage: $0 <file1> <file2>"
+-  echo "  Makes a link (called file2) to file1"
+-  echo "  NB: filenames can be basenames or include an extension"
+-  exit 1;
+-fi
+-
+-f1=`${FSLDIR}/bin/remove_ext $1`;
+-f2=`${FSLDIR}/bin/remove_ext $2`;
+-
+-if [ -f ${f1}.hdr ] ; then ln -fs ${f1}.hdr ${f2}.hdr ; fi
+-if [ -f ${f1}.hdr.gz ] ; then ln -fs ${f1}.hdr.gz ${f2}.hdr.gz ; fi 
+-if [ -f ${f1}.img ] ; then ln -fs ${f1}.img ${f2}.img ; fi 
+-if [ -f ${f1}.img.gz ] ; then ln -fs ${f1}.img.gz ${f2}.img.gz ; fi 
+-if [ -f ${f1}.nii ] ; then ln -fs ${f1}.nii ${f2}.nii ; fi 
+-if [ -f ${f1}.nii.gz ] ; then ln -fs ${f1}.nii.gz ${f2}.nii.gz ; fi 
+-if [ -f ${f1}.mnc ] ; then ln -fs ${f1}.mnc ${f2}.mnc ; fi 
+-if [ -f ${f1}.mnc.gz ] ; then ln -fs ${f1}.mnc.gz ${f2}.mnc.gz ; fi 
+-
+diff -Naur fsl.orig/src/fslio/imrm fsl/src/fslio/imrm
+--- fsl.orig/src/fslio/imrm	2021-02-01 15:29:34.842752994 -0500
++++ fsl/src/fslio/imrm	1969-12-31 19:00:00.000000000 -0500
+@@ -1,83 +0,0 @@
+-#!/bin/sh
+-
+-#   imrm - remove image files
+-#
+-#   Stephen Smith and Mark Jenkinson, FMRIB Image Analysis Group
+-#
+-#   Copyright (C) 1999-2004 University of Oxford
+-#
+-#   Part of FSL - FMRIB's Software Library
+-#   http://www.fmrib.ox.ac.uk/fsl
+-#   fsl@fmrib.ox.ac.uk
+-#
+-#   Developed at FMRIB (Oxford Centre for Functional Magnetic Resonance
+-#   Imaging of the Brain), Department of Clinical Neurology, Oxford
+-#   University, Oxford, UK
+-#
+-#
+-#   LICENCE
+-#
+-#   FMRIB Software Library, Release 6.0 (c) 2018, The University of
+-#   Oxford (the "Software")
+-#
+-#   The Software remains the property of the Oxford University Innovation
+-#   ("the University").
+-#
+-#   The Software is distributed "AS IS" under this Licence solely for
+-#   non-commercial use in the hope that it will be useful, but in order
+-#   that the University as a charitable foundation protects its assets for
+-#   the benefit of its educational and research purposes, the University
+-#   makes clear that no condition is made or to be implied, nor is any
+-#   warranty given or to be implied, as to the accuracy of the Software,
+-#   or that it will be suitable for any particular purpose or for use
+-#   under any specific conditions. Furthermore, the University disclaims
+-#   all responsibility for the use which is made of the Software. It
+-#   further disclaims any liability for the outcomes arising from using
+-#   the Software.
+-#
+-#   The Licensee agrees to indemnify the University and hold the
+-#   University harmless from and against any and all claims, damages and
+-#   liabilities asserted by third parties (including claims for
+-#   negligence) which arise directly or indirectly from the use of the
+-#   Software or the sale of any products based on the Software.
+-#
+-#   No part of the Software may be reproduced, modified, transmitted or
+-#   transferred in any form or by any means, electronic or mechanical,
+-#   without the express permission of the University. The permission of
+-#   the University is not required if the said reproduction, modification,
+-#   transmission or transference is done without financial return, the
+-#   conditions of this Licence are imposed upon the receiver of the
+-#   product, and all original and amended source code is included in any
+-#   transmitted product. You may be held legally responsible for any
+-#   copyright infringement that is caused or encouraged by your failure to
+-#   abide by these terms and conditions.
+-#
+-#   You are not permitted under this Licence to use this Software
+-#   commercially. Use for which any financial return is received shall be
+-#   defined as commercial use, and includes (1) integration of all or part
+-#   of the source code or the Software into a product for sale or license
+-#   by or on behalf of Licensee to third parties or (2) use of the
+-#   Software or any derivative of it for research with the final aim of
+-#   developing software products for sale or license to a third party or
+-#   (3) use of the Software or any derivative of it for research with the
+-#   final aim of developing non-software products for sale or license to a
+-#   third party, or (4) use of the Software to provide any service to an
+-#   external organisation for which payment is received. If you are
+-#   interested in using the Software commercially, please contact Oxford
+-#   University Innovation ("OUI"), the technology transfer company of the
+-#   University, to negotiate a licence. Contact details are:
+-#   fsl@innovation.ox.ac.uk quoting Reference Project 9564, FSL.
+-export LC_ALL=C
+-
+-if [ $# -lt 1 ] ; then
+-  echo "Usage: $0 <list of image names to remove>"
+-  echo "NB: filenames can be basenames or not"
+-  exit 1;
+-fi
+-
+-for f in $@ ; do
+-  fn=`${FSLDIR}/bin/remove_ext $f`;
+-  # do the rm silently
+-  /bin/rm -f ${fn}.img ${fn}.hdr ${fn}.hdr.gz ${fn}.img.gz ${fn}.nii ${fn}.nii.gz ${fn}.mnc ${fn}.mnc.gz
+-done
+-
+diff -Naur fsl.orig/src/fslio/imtest fsl/src/fslio/imtest
+--- fsl.orig/src/fslio/imtest	2021-02-01 15:29:34.842752994 -0500
++++ fsl/src/fslio/imtest	1969-12-31 19:00:00.000000000 -0500
+@@ -1,118 +0,0 @@
+-#!/bin/sh
+-
+-#   imtest - test to see if a valid image file exists with this name (root)
+-#
+-#   Stephen Smith and Mark Jenkinson, FMRIB Image Analysis Group
+-#
+-#   Copyright (C) 1999-2004 University of Oxford
+-#
+-#   Part of FSL - FMRIB's Software Library
+-#   http://www.fmrib.ox.ac.uk/fsl
+-#   fsl@fmrib.ox.ac.uk
+-#
+-#   Developed at FMRIB (Oxford Centre for Functional Magnetic Resonance
+-#   Imaging of the Brain), Department of Clinical Neurology, Oxford
+-#   University, Oxford, UK
+-#
+-#
+-#   LICENCE
+-#
+-#   FMRIB Software Library, Release 6.0 (c) 2018, The University of
+-#   Oxford (the "Software")
+-#
+-#   The Software remains the property of the Oxford University Innovation
+-#   ("the University").
+-#
+-#   The Software is distributed "AS IS" under this Licence solely for
+-#   non-commercial use in the hope that it will be useful, but in order
+-#   that the University as a charitable foundation protects its assets for
+-#   the benefit of its educational and research purposes, the University
+-#   makes clear that no condition is made or to be implied, nor is any
+-#   warranty given or to be implied, as to the accuracy of the Software,
+-#   or that it will be suitable for any particular purpose or for use
+-#   under any specific conditions. Furthermore, the University disclaims
+-#   all responsibility for the use which is made of the Software. It
+-#   further disclaims any liability for the outcomes arising from using
+-#   the Software.
+-#
+-#   The Licensee agrees to indemnify the University and hold the
+-#   University harmless from and against any and all claims, damages and
+-#   liabilities asserted by third parties (including claims for
+-#   negligence) which arise directly or indirectly from the use of the
+-#   Software or the sale of any products based on the Software.
+-#
+-#   No part of the Software may be reproduced, modified, transmitted or
+-#   transferred in any form or by any means, electronic or mechanical,
+-#   without the express permission of the University. The permission of
+-#   the University is not required if the said reproduction, modification,
+-#   transmission or transference is done without financial return, the
+-#   conditions of this Licence are imposed upon the receiver of the
+-#   product, and all original and amended source code is included in any
+-#   transmitted product. You may be held legally responsible for any
+-#   copyright infringement that is caused or encouraged by your failure to
+-#   abide by these terms and conditions.
+-#
+-#   You are not permitted under this Licence to use this Software
+-#   commercially. Use for which any financial return is received shall be
+-#   defined as commercial use, and includes (1) integration of all or part
+-#   of the source code or the Software into a product for sale or license
+-#   by or on behalf of Licensee to third parties or (2) use of the
+-#   Software or any derivative of it for research with the final aim of
+-#   developing software products for sale or license to a third party or
+-#   (3) use of the Software or any derivative of it for research with the
+-#   final aim of developing non-software products for sale or license to a
+-#   third party, or (4) use of the Software to provide any service to an
+-#   external organisation for which payment is received. If you are
+-#   interested in using the Software commercially, please contact Oxford
+-#   University Innovation ("OUI"), the technology transfer company of the
+-#   University, to negotiate a licence. Contact details are:
+-#   fsl@innovation.ox.ac.uk quoting Reference Project 9564, FSL.
+-export LC_ALL=C
+-
+-# return 0 if no image exists or 1 if the image exists
+-
+-if [ $# -lt 1 ] ; then
+- echo "0";
+- exit;
+-fi
+-
+-inputfile=$1
+-
+-
+-
+-for i in 1 2 3 4 5 6 7 8 9 10 11 12
+-do
+-if [ -h $inputfile ] ; then 
+-inputfile=`readlink $inputfile`;
+-fi
+-done
+-
+-filename=`${FSLDIR}/bin/remove_ext $inputfile`;
+-
+-if [ -r ${filename}.nii ] || [ -r ${filename}.nii.gz ] ; then
+-  echo "1";
+-  exit;
+-fi
+-
+-if [ -r ${filename}.mnc ] || [ -r ${filename}.mnc.gz ] ; then
+-  echo "1";
+-  exit;
+-fi
+-
+-if [ ! -r ${filename}.hdr ] && [ ! -r ${filename}.hdr.gz ] ; then
+-  # return 0 here as no header exists and no single image means no image!
+-  echo "0";
+-  exit;
+-fi
+-
+-if [ ! -r ${filename}.img ] && [ ! -r ${filename}.img.gz ] ; then
+-  # return 0 here as no img file exists and no single image means no image!
+-  echo "0";
+-  exit;
+-fi
+-
+-# only gets to here if there was a hdr and an img file
+-
+-echo "1";
+-exit;
+-
diff --git a/sci-biology/fsl/files/fsl-6.0.4-remove_fslpy_collisions-p2.patch b/sci-biology/fsl/files/fsl-6.0.4-remove_fslpy_collisions-p2.patch
new file mode 100644
index 000000000..ddb7cfb67
--- /dev/null
+++ b/sci-biology/fsl/files/fsl-6.0.4-remove_fslpy_collisions-p2.patch
@@ -0,0 +1,348 @@
+diff -Naur fsl.orig/src/fslio/Makefile fsl/src/fslio/Makefile
+--- fsl.orig/src/fslio/Makefile	2021-02-01 15:29:34.842752994 -0500
++++ fsl/src/fslio/Makefile	2021-02-01 15:32:19.723761859 -0500
+@@ -6,7 +6,7 @@
+ 
+ OBJS=fslio.o
+ 
+-SCRIPTS = remove_ext fsloutputtype imtest imglob imcp imln imrm immv
++SCRIPTS = fsloutputtype imglob imcp immv
+ 
+ all: 
+ 
+diff -Naur fsl.orig/src/fslio/remove_ext fsl/src/fslio/remove_ext
+--- fsl.orig/src/fslio/remove_ext	2021-02-01 15:29:34.842752994 -0500
++++ fsl/src/fslio/remove_ext	1969-12-31 19:00:00.000000000 -0500
+@@ -1,87 +0,0 @@
+-#!/bin/sh
+-
+-#   remove_ext - remove extension from image filename
+-#
+-#   Stephen Smith and Mark Jenkinson, FMRIB Image Analysis Group
+-#
+-#   Copyright (C) 1999-2004 University of Oxford
+-#
+-#   Part of FSL - FMRIB's Software Library
+-#   http://www.fmrib.ox.ac.uk/fsl
+-#   fsl@fmrib.ox.ac.uk
+-#
+-#   Developed at FMRIB (Oxford Centre for Functional Magnetic Resonance
+-#   Imaging of the Brain), Department of Clinical Neurology, Oxford
+-#   University, Oxford, UK
+-#
+-#
+-#   LICENCE
+-#
+-#   FMRIB Software Library, Release 6.0 (c) 2018, The University of
+-#   Oxford (the "Software")
+-#
+-#   The Software remains the property of the Oxford University Innovation
+-#   ("the University").
+-#
+-#   The Software is distributed "AS IS" under this Licence solely for
+-#   non-commercial use in the hope that it will be useful, but in order
+-#   that the University as a charitable foundation protects its assets for
+-#   the benefit of its educational and research purposes, the University
+-#   makes clear that no condition is made or to be implied, nor is any
+-#   warranty given or to be implied, as to the accuracy of the Software,
+-#   or that it will be suitable for any particular purpose or for use
+-#   under any specific conditions. Furthermore, the University disclaims
+-#   all responsibility for the use which is made of the Software. It
+-#   further disclaims any liability for the outcomes arising from using
+-#   the Software.
+-#
+-#   The Licensee agrees to indemnify the University and hold the
+-#   University harmless from and against any and all claims, damages and
+-#   liabilities asserted by third parties (including claims for
+-#   negligence) which arise directly or indirectly from the use of the
+-#   Software or the sale of any products based on the Software.
+-#
+-#   No part of the Software may be reproduced, modified, transmitted or
+-#   transferred in any form or by any means, electronic or mechanical,
+-#   without the express permission of the University. The permission of
+-#   the University is not required if the said reproduction, modification,
+-#   transmission or transference is done without financial return, the
+-#   conditions of this Licence are imposed upon the receiver of the
+-#   product, and all original and amended source code is included in any
+-#   transmitted product. You may be held legally responsible for any
+-#   copyright infringement that is caused or encouraged by your failure to
+-#   abide by these terms and conditions.
+-#
+-#   You are not permitted under this Licence to use this Software
+-#   commercially. Use for which any financial return is received shall be
+-#   defined as commercial use, and includes (1) integration of all or part
+-#   of the source code or the Software into a product for sale or license
+-#   by or on behalf of Licensee to third parties or (2) use of the
+-#   Software or any derivative of it for research with the final aim of
+-#   developing software products for sale or license to a third party or
+-#   (3) use of the Software or any derivative of it for research with the
+-#   final aim of developing non-software products for sale or license to a
+-#   third party, or (4) use of the Software to provide any service to an
+-#   external organisation for which payment is received. If you are
+-#   interested in using the Software commercially, please contact Oxford
+-#   University Innovation ("OUI"), the technology transfer company of the
+-#   University, to negotiate a licence. Contact details are:
+-#   fsl@innovation.ox.ac.uk quoting Reference Project 9564, FSL.
+-export LC_ALL=C
+-
+-
+-if [ $# -lt 1 ] ; then
+-  exit 1
+-fi
+-
+-lst="";
+-for fn in $@ ; do
+-    # for the ones at the end of the line
+-  f=`echo "$fn" | sed 's/\.hdr\.gz$//' | sed 's/\.img\.gz$//' | sed 's/\.hdr$//' | sed 's/\.img$//' | sed 's/\.nii.gz$//' | sed 's/\.nii$//' | sed 's/\.mnc.gz$//' | sed 's/\.mnc$//' | sed 's/\.$//'`;
+-    # for the ones in the middle of the line
+-  f=`echo "$f" | sed 's/\.hdr\.gz[ 	]/ /g' | sed 's/\.img\.gz[ 	]/ /g' | sed 's/\.hdr[ 	]/ /g' | sed 's/\.img[ 	]/ /g' | sed 's/\.nii\.gz[ 	]/ /g' | sed 's/\.nii[ 	]/ /g' | sed 's/\.mnc\.gz[ 	]/ /g' | sed 's/\.mnc[ 	]/ /g' |sed 's/\.[ 	]/ /g'`;
+-  lst="$lst $f";
+-done
+-echo $lst;
+-
+-
+diff -Naur fsl.orig/src/misc_scripts/fsl_abspath fsl/src/misc_scripts/fsl_abspath
+--- fsl.orig/src/misc_scripts/fsl_abspath	2021-02-01 15:29:34.828752994 -0500
++++ fsl/src/misc_scripts/fsl_abspath	1969-12-31 19:00:00.000000000 -0500
+@@ -1,71 +0,0 @@
+-#!/usr/bin/env fslpython
+-#   fsl_abspath - return true file path
+-#   Matthew Webster FMRIB Image Analysis Group
+-#   Copyright (C) 2009 University of Oxford 
+-#   Part of FSL - FMRIB's Software Library
+-#   http://www.fmrib.ox.ac.uk/fsl
+-#   fsl@fmrib.ox.ac.uk
+-#
+-#   Developed at FMRIB (Oxford Centre for Functional Magnetic Resonance
+-#   Imaging of the Brain), Department of Clinical Neurology, Oxford
+-#   University, Oxford, UK
+-#
+-#
+-#   LICENCE
+-#
+-#   FMRIB Software Library, Release 6.0 (c) 2018, The University of
+-#   Oxford (the "Software")
+-#
+-#   The Software remains the property of the Oxford University Innovation
+-#   ("the University").
+-#
+-#   The Software is distributed "AS IS" under this Licence solely for
+-#   non-commercial use in the hope that it will be useful, but in order
+-#   that the University as a charitable foundation protects its assets for
+-#   the benefit of its educational and research purposes, the University
+-#   makes clear that no condition is made or to be implied, nor is any
+-#   warranty given or to be implied, as to the accuracy of the Software,
+-#   or that it will be suitable for any particular purpose or for use
+-#   under any specific conditions. Furthermore, the University disclaims
+-#   all responsibility for the use which is made of the Software. It
+-#   further disclaims any liability for the outcomes arising from using
+-#   the Software.
+-#
+-#   The Licensee agrees to indemnify the University and hold the
+-#   University harmless from and against any and all claims, damages and
+-#   liabilities asserted by third parties (including claims for
+-#   negligence) which arise directly or indirectly from the use of the
+-#   Software or the sale of any products based on the Software.
+-#
+-#   No part of the Software may be reproduced, modified, transmitted or
+-#   transferred in any form or by any means, electronic or mechanical,
+-#   without the express permission of the University. The permission of
+-#   the University is not required if the said reproduction, modification,
+-#   transmission or transference is done without financial return, the
+-#   conditions of this Licence are imposed upon the receiver of the
+-#   product, and all original and amended source code is included in any
+-#   transmitted product. You may be held legally responsible for any
+-#   copyright infringement that is caused or encouraged by your failure to
+-#   abide by these terms and conditions.
+-#
+-#   You are not permitted under this Licence to use this Software
+-#   commercially. Use for which any financial return is received shall be
+-#   defined as commercial use, and includes (1) integration of all or part
+-#   of the source code or the Software into a product for sale or license
+-#   by or on behalf of Licensee to third parties or (2) use of the
+-#   Software or any derivative of it for research with the final aim of
+-#   developing software products for sale or license to a third party or
+-#   (3) use of the Software or any derivative of it for research with the
+-#   final aim of developing non-software products for sale or license to a
+-#   third party, or (4) use of the Software to provide any service to an
+-#   external organisation for which payment is received. If you are
+-#   interested in using the Software commercially, please contact Oxford
+-#   University Innovation ("OUI"), the technology transfer company of the
+-#   University, to negotiate a licence. Contact details are:
+-#   fsl@innovation.ox.ac.uk quoting Reference Project 9564, FSL.
+-from __future__ import print_function
+-import sys
+-import os
+-
+-print (os.path.realpath(sys.argv[1]))
+-sys.exit(0)
+diff -Naur fsl.orig/src/misc_scripts/Makefile fsl/src/misc_scripts/Makefile
+--- fsl.orig/src/misc_scripts/Makefile	2021-02-01 15:29:34.828752994 -0500
++++ fsl/src/misc_scripts/Makefile	2021-02-01 15:32:56.027763811 -0500
+@@ -2,6 +2,6 @@
+ 
+ PROJNAME = misc_scripts
+ 
+-SCRIPTS = fslecho regscript remove_vols replace_and_average_fmrib linkbedpost ocmr_preproc correct_and_average eddy_correct Text2Vest Vest2Text AnatomicalAverage fsl_abspath fsl_anat fslFixText
++SCRIPTS = fslecho regscript remove_vols replace_and_average_fmrib linkbedpost ocmr_preproc correct_and_average eddy_correct AnatomicalAverage fsl_anat fslFixText
+ 
+ all:
+diff -Naur fsl.orig/src/misc_scripts/Text2Vest fsl/src/misc_scripts/Text2Vest
+--- fsl.orig/src/misc_scripts/Text2Vest	2021-02-01 15:29:34.828752994 -0500
++++ fsl/src/misc_scripts/Text2Vest	1969-12-31 19:00:00.000000000 -0500
+@@ -1,80 +0,0 @@
+-#!/bin/sh
+-#   Copyright (C) 2012 University of Oxford
+-#
+-#   Part of FSL - FMRIB's Software Library
+-#   http://www.fmrib.ox.ac.uk/fsl
+-#   fsl@fmrib.ox.ac.uk
+-#
+-#   Developed at FMRIB (Oxford Centre for Functional Magnetic Resonance
+-#   Imaging of the Brain), Department of Clinical Neurology, Oxford
+-#   University, Oxford, UK
+-#
+-#
+-#   LICENCE
+-#
+-#   FMRIB Software Library, Release 6.0 (c) 2018, The University of
+-#   Oxford (the "Software")
+-#
+-#   The Software remains the property of the Oxford University Innovation
+-#   ("the University").
+-#
+-#   The Software is distributed "AS IS" under this Licence solely for
+-#   non-commercial use in the hope that it will be useful, but in order
+-#   that the University as a charitable foundation protects its assets for
+-#   the benefit of its educational and research purposes, the University
+-#   makes clear that no condition is made or to be implied, nor is any
+-#   warranty given or to be implied, as to the accuracy of the Software,
+-#   or that it will be suitable for any particular purpose or for use
+-#   under any specific conditions. Furthermore, the University disclaims
+-#   all responsibility for the use which is made of the Software. It
+-#   further disclaims any liability for the outcomes arising from using
+-#   the Software.
+-#
+-#   The Licensee agrees to indemnify the University and hold the
+-#   University harmless from and against any and all claims, damages and
+-#   liabilities asserted by third parties (including claims for
+-#   negligence) which arise directly or indirectly from the use of the
+-#   Software or the sale of any products based on the Software.
+-#
+-#   No part of the Software may be reproduced, modified, transmitted or
+-#   transferred in any form or by any means, electronic or mechanical,
+-#   without the express permission of the University. The permission of
+-#   the University is not required if the said reproduction, modification,
+-#   transmission or transference is done without financial return, the
+-#   conditions of this Licence are imposed upon the receiver of the
+-#   product, and all original and amended source code is included in any
+-#   transmitted product. You may be held legally responsible for any
+-#   copyright infringement that is caused or encouraged by your failure to
+-#   abide by these terms and conditions.
+-#
+-#   You are not permitted under this Licence to use this Software
+-#   commercially. Use for which any financial return is received shall be
+-#   defined as commercial use, and includes (1) integration of all or part
+-#   of the source code or the Software into a product for sale or license
+-#   by or on behalf of Licensee to third parties or (2) use of the
+-#   Software or any derivative of it for research with the final aim of
+-#   developing software products for sale or license to a third party or
+-#   (3) use of the Software or any derivative of it for research with the
+-#   final aim of developing non-software products for sale or license to a
+-#   third party, or (4) use of the Software to provide any service to an
+-#   external organisation for which payment is received. If you are
+-#   interested in using the Software commercially, please contact Oxford
+-#   University Innovation ("OUI"), the technology transfer company of the
+-#   University, to negotiate a licence. Contact details are:
+-#   fsl@innovation.ox.ac.uk quoting Reference Project 9564, FSL.
+-export LC_ALL=C
+-if [ $# -lt 2 ] ; then 
+-  echo "`basename $0` <text file> <vest file>"
+-  exit 0
+-fi
+-
+-NumPoints=`grep -cve '^\s*$' $1`
+-NumWaves=`wc $1 | awk '{ print $2 }'`
+-NumWaves=`expr $NumWaves / $NumPoints`
+-
+-echo /NumWaves $NumWaves    > $2
+-echo /NumPoints $NumPoints >> $2
+-echo /Matrix               >> $2
+-
+-cat $1 >> $2
+-
+diff -Naur fsl.orig/src/misc_scripts/Vest2Text fsl/src/misc_scripts/Vest2Text
+--- fsl.orig/src/misc_scripts/Vest2Text	2021-02-01 15:29:34.828752994 -0500
++++ fsl/src/misc_scripts/Vest2Text	1969-12-31 19:00:00.000000000 -0500
+@@ -1,71 +0,0 @@
+-#!/bin/sh
+-#   Copyright (C) 2012 University of Oxford
+-#
+-#   Part of FSL - FMRIB's Software Library
+-#   http://www.fmrib.ox.ac.uk/fsl
+-#   fsl@fmrib.ox.ac.uk
+-#
+-#   Developed at FMRIB (Oxford Centre for Functional Magnetic Resonance
+-#   Imaging of the Brain), Department of Clinical Neurology, Oxford
+-#   University, Oxford, UK
+-#
+-#
+-#   LICENCE
+-#
+-#   FMRIB Software Library, Release 6.0 (c) 2018, The University of
+-#   Oxford (the "Software")
+-#
+-#   The Software remains the property of the Oxford University Innovation
+-#   ("the University").
+-#
+-#   The Software is distributed "AS IS" under this Licence solely for
+-#   non-commercial use in the hope that it will be useful, but in order
+-#   that the University as a charitable foundation protects its assets for
+-#   the benefit of its educational and research purposes, the University
+-#   makes clear that no condition is made or to be implied, nor is any
+-#   warranty given or to be implied, as to the accuracy of the Software,
+-#   or that it will be suitable for any particular purpose or for use
+-#   under any specific conditions. Furthermore, the University disclaims
+-#   all responsibility for the use which is made of the Software. It
+-#   further disclaims any liability for the outcomes arising from using
+-#   the Software.
+-#
+-#   The Licensee agrees to indemnify the University and hold the
+-#   University harmless from and against any and all claims, damages and
+-#   liabilities asserted by third parties (including claims for
+-#   negligence) which arise directly or indirectly from the use of the
+-#   Software or the sale of any products based on the Software.
+-#
+-#   No part of the Software may be reproduced, modified, transmitted or
+-#   transferred in any form or by any means, electronic or mechanical,
+-#   without the express permission of the University. The permission of
+-#   the University is not required if the said reproduction, modification,
+-#   transmission or transference is done without financial return, the
+-#   conditions of this Licence are imposed upon the receiver of the
+-#   product, and all original and amended source code is included in any
+-#   transmitted product. You may be held legally responsible for any
+-#   copyright infringement that is caused or encouraged by your failure to
+-#   abide by these terms and conditions.
+-#
+-#   You are not permitted under this Licence to use this Software
+-#   commercially. Use for which any financial return is received shall be
+-#   defined as commercial use, and includes (1) integration of all or part
+-#   of the source code or the Software into a product for sale or license
+-#   by or on behalf of Licensee to third parties or (2) use of the
+-#   Software or any derivative of it for research with the final aim of
+-#   developing software products for sale or license to a third party or
+-#   (3) use of the Software or any derivative of it for research with the
+-#   final aim of developing non-software products for sale or license to a
+-#   third party, or (4) use of the Software to provide any service to an
+-#   external organisation for which payment is received. If you are
+-#   interested in using the Software commercially, please contact Oxford
+-#   University Innovation ("OUI"), the technology transfer company of the
+-#   University, to negotiate a licence. Contact details are:
+-#   fsl@innovation.ox.ac.uk quoting Reference Project 9564, FSL.
+-export LC_ALL=C
+-if [ $# -lt 2 ] ; then 
+-  echo "`basename $0` <vest file> <text file>"
+-  exit 0
+-fi
+-sed -e "/\//d" $1 | sed '/^$/d' > $2
+-
diff --git a/sci-biology/fsl/files/fsl-6.0.4-setup.patch b/sci-biology/fsl/files/fsl-6.0.4-setup.patch
new file mode 100644
index 000000000..061e1a22a
--- /dev/null
+++ b/sci-biology/fsl/files/fsl-6.0.4-setup.patch
@@ -0,0 +1,174 @@
+diff -Naur fsl.orig/build fsl/build
+--- fsl.orig/build	2020-12-02 15:29:12.180812558 -0500
++++ fsl/build	2020-12-02 15:34:03.854821628 -0500
+@@ -28,7 +28,6 @@
+     # The build order for MASTERLIBS is very important, and should not be modified unless you know what
+     # you are doing. 
+     MASTERLIBS="
+-    CiftiLib-master \
+     utils \
+     znzlib \
+     NewNifti \
+@@ -157,8 +156,8 @@
+     done #project (MASTERPROJECTS)
+ fi #full build
+ 
+-echo "Building projects - see build.log file for progress..."
+-./config/common/buildproj $PROJECTS > ./build.log 2>&1
++echo "Building projects"
++./config/common/buildproj $PROJECTS
+ finalStatus=$?
+ if [ $finalStatus -eq 0 ]; then
+     echo "Build completed successfully.";
+diff -Naur fsl.orig/config/buildSettings.mk fsl/config/buildSettings.mk
+--- fsl.orig/config/buildSettings.mk	2020-12-02 15:29:11.993812552 -0500
++++ fsl/config/buildSettings.mk	2020-12-02 15:39:37.269831995 -0500
+@@ -18,7 +18,7 @@
+ CHMOD = /bin/chmod
+ MKDIR = /bin/mkdir
+ INSTALL = install -p
+-TCLSH = ${FSLDIR}/bin/fsltclsh
++TCLSH = tclsh
+ DEPENDFLAGS = -MM
+ MACHDBGFLAGS = -g
+ #####################################################################
+@@ -127,19 +127,19 @@
+ #####################################################################
+ ifeq ($(SYSTYPE), Linux)
+ ###############   System Vars   #####################################
+-CC = gcc
+-CXX = c++
+-CXX11 = c++
++CC = @@GENTOO_CC@@
++CXX = @@GENTOO_CXX@@
++CXX11 = @@GENTOO_CXX@@
+ CSTATICFLAGS = -static
+ CXXSTATICFLAGS = -static
+-ARCHFLAGS = -m64
+-ARCHLDFLAGS = -Wl,-rpath,'$$ORIGIN/../lib'
++ARCHFLAGS =
++ARCHLDFLAGS =
+ PARALLELFLAGS = -fopenmp
+-OPTFLAGS = -g -O3 -fexpensive-optimizations ${ARCHFLAGS}
++OPTFLAGS =
+ GNU_ANSI_FLAGS = -Wall -ansi -pedantic -Wno-long-long
+ SGI_ANSI_FLAGS = -ansi -fullwarn
+ ANSI_FLAGS = ${GNU_ANSI_FLAGS}
+-RANLIB = echo
++RANLIB = @@GENTOO_RANLIB@@
+ FSLML = ${FSLDIR}/bin/fslml
+ # CUDA development environment
+ CUDAVER := $(or $(CUDAVER),9.1)
+@@ -158,8 +158,8 @@
+ NVCC = ${CUDA_INSTALLATION}/bin/nvcc
+ ###############   External Libs   #####################################
+ # ZLIB library
+-LIB_ZLIB = ${FSLEXTLIB}
+-INC_ZLIB = ${FSLEXTINC}
++#LIB_ZLIB = ${FSLEXTLIB}
++#INC_ZLIB = ${FSLEXTINC}
+ # QT library
+ QTDIR = /usr/lib/qt3
+ LIB_QT = ${QTDIR}/lib
+diff -Naur fsl.orig/config/common/buildproj fsl/config/common/buildproj
+--- fsl.orig/config/common/buildproj	2020-12-02 15:29:11.993812552 -0500
++++ fsl/config/common/buildproj	2020-12-02 15:41:25.579835363 -0500
+@@ -11,10 +11,10 @@
+ fi
+ PROJECTS="$@" ; export PROJECTS ;
+ 
+-FSLDIR=`pwd`
++#FSLDIR=`pwd`
+ FSLDEVDIR=${FSLDIR}
+ FSLCONFDIR=${FSLDIR}/config
+-FSLMACHTYPE=`${FSLDIR}/etc/fslconf/fslmachtype.sh`
++#FSLMACHTYPE=`${FSLDIR}/etc/fslconf/fslmachtype.sh`
+ FSLMASTERBUILD=1
+ export FSLDIR FSLDEVDIR FSLCONFDIR FSLMACHTYPE FSLMASTERBUILD
+ 
+@@ -67,7 +67,7 @@
+ 	  if [ -x ./fslconfig ] ; then
+ 	    . ./fslconfig ;
+ 	  fi
+-	  if ${MAKE} -k ${MAKEOPTIONS} ; then 
++	  if ${MAKE} ${MAKEOPTIONS} ; then 
+ 	    if ${MAKE} ${MAKEOPTIONS} install ; then
+ 	      installok=true;
+ 	      # Clean up after ourselves
+@@ -82,6 +82,7 @@
+ 	    if [ $installok = false ]  ; then
+ 	      echo " "
+ 	      echo "ERROR::Could not install $projname successfully" ;
++          exit 1
+ 	    fi
+ 	  else
+ 	    echo " "
+@@ -90,6 +91,7 @@
+ 	    echo " "
+ 	    echo " "
+ 	    errorprojs="$errorprojs $projname" ; export errorprojs ;
++        exit 1
+ 	  fi
+     fi
+ done
+diff -Naur fsl.orig/config/common/vars.mk fsl/config/common/vars.mk
+--- fsl.orig/config/common/vars.mk	2020-12-02 15:29:11.993812552 -0500
++++ fsl/config/common/vars.mk	2020-12-02 15:43:00.602838318 -0500
+@@ -24,15 +24,15 @@
+ USRCFLAGS = 
+ USRCXXFLAGS =
+ 
+-LDFLAGS = ${ARCHLDFLAGS} ${USRLDFLAGS} -L. -L${DEVLIBDIR} -L${LIBDIR}
++LDFLAGS = ${ARCHLDFLAGS} ${USRLDFLAGS} -L. -L${DEVLIBDIR} -L${LIBDIR} ${USERLDFLAGS}
+ 
+-AccumulatedIncFlags = -I${INC_BOOST} ${USRINCFLAGS} -I. -I${DEVINCDIR} -I${INCDIR}
++AccumulatedIncFlags = ${USRINCFLAGS} -I. -I${DEVINCDIR} -I${INCDIR} ${CPPFLAGS}
+ 
+ CFLAGS = ${ANSI_FLAGS} ${ANSI_CFLAGS} ${DBGFLAGS} ${USEDCSTATICFLAGS} ${USRCFLAGS} ${ARCHFLAGS} ${OPTFLAGS}  \
+-	${AccumulatedIncFlags}
++	${AccumulatedIncFlags} ${USERCFLAGS}
+ 
+-CXXFLAGS = ${ANSI_FLAGS} ${ANSI_CXXFLAGS} ${DBGFLAGS} ${USEDCXXSTATICFLAGS} ${USRCXXFLAGS} ${ARCHFLAGS} ${OPTFLAGS}  \
+-	${AccumulatedIncFlags}
++CXXFLAGS = ${ANSI_CXXFLAGS} ${DBGFLAGS} ${USEDCXXSTATICFLAGS} ${USRCXXFLAGS} ${ARCHFLAGS} ${OPTFLAGS}  \
++	${AccumulatedIncFlags} ${USERCXXFLAGS}
+ 
+ HFILES = *.h
+ AFILES = *.a
+diff -Naur fsl.orig/extras/build fsl/extras/build
+--- fsl.orig/extras/build	2020-12-02 15:29:12.404812565 -0500
++++ fsl/extras/build	2020-12-02 15:44:06.906840380 -0500
+@@ -96,16 +96,16 @@
+ 	BUILDICONV=1
+     fi
+ fi
+-PROJECTS="tcl tk"
++#PROJECTS="tcl tk"
+ if [ ${BUILDZLIB} -eq 1 ]; then
+   PROJECTS="${PROJECTS} zlib"
+ fi
+-PROJECTS="${PROJECTS} libpng"
++#PROJECTS="${PROJECTS} libpng"
+ if [ ${BUILDICONV} -eq 1 ]; then
+   PROJECTS="${PROJECTS} libiconv"
+ fi
+-PROJECTS="${PROJECTS} libgd libgdc libprob libcprob newmat cprob newran fftw"
+-PROJECTS="${PROJECTS} boost libxml2-2.9.2 libxmlpp libsqlite libnlopt ../include/armawrap/dummy_newmat"
++PROJECTS="${PROJECTS} libgdc libprob libcprob newmat cprob newran"
++PROJECTS="${PROJECTS} ../include/armawrap/dummy_newmat"
+ for projname in $PROJECTS; do
+     if [ -d $FSLESRCDIR/$projname ] ; then
+        buildIt $FSLESRCDIR $projname 1
+diff -Naur fsl.orig/src/mist/Makefile fsl/src/mist/Makefile
+--- fsl.orig/src/mist/Makefile	2020-12-02 15:29:12.875812580 -0500
++++ fsl/src/mist/Makefile	2020-12-02 15:45:09.805842335 -0500
+@@ -52,6 +52,8 @@
+ 		cp -r python/* ${DESTDIR}/python/mist
+ 
+ clean:
+-			rm -f ${OBJS} mist/mist.o mist/mist
++			rm -f ${OBJS} mist/mist.o mist/mist || echo "CLEAN could not locate some files scheduled for deletion."
++ 
++
+ 
+ .PHONY:		all clean installdata
diff --git a/sci-biology/fsl/fsl-5.0.11.ebuild b/sci-biology/fsl/fsl-5.0.11.ebuild
deleted file mode 100644
index d3985072d..000000000
--- a/sci-biology/fsl/fsl-5.0.11.ebuild
+++ /dev/null
@@ -1,157 +0,0 @@
-# Copyright 1999-2018 Gentoo Authors
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=6
-
-inherit flag-o-matic toolchain-funcs prefix
-
-DESCRIPTION="Analysis of functional, structural, and diffusion MRI brain imaging data"
-HOMEPAGE="http://www.fmrib.ox.ac.uk/fsl"
-SRC_URI="https://fsl.fmrib.ox.ac.uk/fsldownloads/${P}-sources.tar.gz -> ${P}.tar.gz"
-
-LICENSE="FSL BSD-2 newmat"
-SLOT="0"
-KEYWORDS="~amd64"
-IUSE=""
-
-COMMON_DEPEND="
-	dev-libs/boost
-	media-gfx/graphviz
-	media-libs/gd
-	media-libs/glu
-	media-libs/libpng:0=
-	sci-libs/ciftilib
-	sci-libs/nlopt
-	sys-libs/zlib
-	"
-DEPEND="${COMMON_DEPEND}"
-RDEPEND="${COMMON_DEPEND}
-	dev-lang/tcl:0=
-	dev-lang/tk:0=
-	"
-
-S=${WORKDIR}/${PN}
-UPSTREAM_FSLDIR="/usr/share/fsl"
-
-PATCHES=(
-	"${FILESDIR}/${PN}"-5.0.11-setup.patch
-	"${FILESDIR}/${PN}"-5.0.11-no_xmlpp.patch
-	"${FILESDIR}/${PN}"-5.0.11-niftiio_var_fix.patch
-	"${FILESDIR}/${PN}"-5.0.11-ifstream_use.patch
-	"${FILESDIR}/${PN}"-5.0.11-fslsurface_parallel_make.patch
-	"${FILESDIR}/${PN}"-5.0.11-qstring_compat.patch
-	"${FILESDIR}/${PN}"-5.0.9-headers.patch
-	"${FILESDIR}/${PN}"-5.0.9-fsldir_redux.patch
-)
-
-src_prepare(){
-	default
-
-	sed -i \
-		-e "s:@@GENTOO_RANLIB@@:$(tc-getRANLIB):" \
-		-e "s:@@GENTOO_CC@@:$(tc-getCC):" \
-		-e "s:@@GENTOO_CXX@@:$(tc-getCXX):" \
-		config/generic/systemvars.mk || die
-
-	eprefixify $(grep -rl GENTOO_PORTAGE_EPREFIX src/*) \
-		etc/js/label-div.html
-
-	makefilelist=$(find src/ -name Makefile)
-
-	sed -i \
-		-e "s:-I\${INC_BOOST}::" \
-		-e "s:-I\${INC_ZLIB}::" \
-		-e "s:-I\${INC_GD}::" \
-		-e "s:-I\${INC_PNG}::" \
-		-e "s:-L\${LIB_GD}::" \
-		-e "s:-L\${LIB_PNG}::" \
-		-e "s:-L\${LIB_ZLIB}::" \
-		${makefilelist} || die
-
-	sed -e "s:\${FSLDIR}/bin/::g" \
-		-e "s:\$FSLDIR/bin/::g" \
-		-i $(grep -rl "\${FSLDIR}/bin" src/*) \
-		$(grep -rl "\${FSLDIR}/bin" etc/matlab/*) || die
-
-	sed -e "s:\$FSLDIR/data:${EPREFIX}/usr/share/fsl/data:g" \
-		-e "s:\${FSLDIR}/data:${EPREFIX}/usr/share/fsl/data:g" \
-		-i $(grep -rl "\$FSLDIR/data" src/*) \
-		$(grep -rl "\${FSLDIR}/data" src/*) || die
-
-	sed -e "s:\$FSLDIR/doc:${EPREFIX}/usr/share/fsl/doc:g" \
-		-e "s:\${FSLDIR}/doc:${EPREFIX}/usr/share/fsl/doc:g" \
-		-i $(grep -rl "\$FSLDIR/doc" src/*) \
-		$(grep -rl "\${FSLDIR}/doc" src/*) || die
-
-	sed -e "s:/usr/share/fsl/doc:${EPREFIX}/usr/share/fsl/doc:g" \
-		-i $(grep -rl "/usr/share/fsl/doc" src/*) || die
-
-	sed -e "s:\$FSLDIR/etc:${EPREFIX}/etc:g" \
-		-e "s:\${FSLDIR}/etc:${EPREFIX}/etc:g" \
-		-i $(grep -rlI "\$FSLDIR/etc" *) \
-		-i $(grep -rlI "\${FSLDIR}/etc" *) || die
-
-	# script wanting to have access to flsversion at buildtime
-	sed -e "s:/etc/fslversion:${S}/etc/fslversion:g" \
-		-i ${makefilelist} || die
-}
-
-src_compile() {
-	export FSLDIR=${WORKDIR}/${PN}
-	export FSLCONDIR=${WORKDIR}/${PN}/config
-	export FSLMACHTYPE=generic
-
-	export USERLDFLAGS="${LDFLAGS}"
-	export USERCFLAGS="${CFLAGS}"
-	export USERCXXFLAGS="${CXXFLAGS}"
-
-	export CIFTICFLAGS="$($(tc-getPKG_CONFIG) --cflags CiftiLib)"
-	export CIFTILIBS="$($(tc-getPKG_CONFIG) --libs-only-l CiftiLib)"
-
-	./build || die
-}
-
-src_install() {
-	sed -i "s:\${FSLDIR}/tcl:/usr/libexec/fsl:g" \
-		$(grep -lI "\${FSLDIR}/tcl" bin/*) \
-		$(grep -l "\${FSLDIR}/tcl"  tcl/*) || die
-	sed -i "s:\$FSLDIR/tcl:/usr/libexec/fsl:g" \
-		$(grep -l "\$FSLDIR/tcl" tcl/*) || die
-
-	dobin bin/*
-
-	insinto /usr/share/${PN}
-	doins -r data
-	dodoc -r doc/. refdoc
-
-	insinto /usr/libexec/fsl
-	doins -r tcl/*
-
-	insinto /etc/fslconf
-	doins etc/fslconf/fsl.sh
-
-	insinto /etc
-	doins etc/fslversion
-	doins -r etc/default_flobs.flobs etc/flirtsch etc/js etc/luts
-	#if use matlab; then
-	#	doins etc/matlab
-	#fi
-
-	#the following is needed for FSL and depending programs to be able
-	#to find its files, since FSL uses an uncommon installation path:
-	#https://github.com/gentoo-science/sci/pull/612#r60289295
-	dosym ../../../etc ${UPSTREAM_FSLDIR}/etc
-	dosym ../doc/${PF} ${UPSTREAM_FSLDIR}/doc
-	dosym ../../bin ${UPSTREAM_FSLDIR}/bin
-
-	doenvd "$(prefixify_ro "${FILESDIR}"/99fsl)"
-	mv "${ED}"/usr/bin/{,fsl_}cluster || die
-}
-
-pkg_postinst() {
-	echo
-	einfo "Please run the following commands if you"
-	einfo "intend to use fsl from an existing shell:"
-	einfo "env-update && source /etc/profile"
-	echo
-}
diff --git a/sci-biology/fsl/fsl-5.0.8.ebuild b/sci-biology/fsl/fsl-5.0.8.ebuild
deleted file mode 100644
index d420bbacc..000000000
--- a/sci-biology/fsl/fsl-5.0.8.ebuild
+++ /dev/null
@@ -1,148 +0,0 @@
-# Copyright 1999-2017 Gentoo Foundation
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=6
-
-inherit eutils toolchain-funcs prefix
-
-DESCRIPTION="Analysis of functional, structural, and diffusion MRI brain imaging data"
-HOMEPAGE="http://www.fmrib.ox.ac.uk/fsl"
-SRC_URI="https://dev.gentoo.org/~jlec/distfiles/${P}-sources.tar.gz"
-
-LICENSE="FSL BSD-2 newmat"
-SLOT="0"
-KEYWORDS="~amd64"
-IUSE=""
-
-COMMON_DEPEND="
-	dev-libs/boost
-	media-gfx/graphviz
-	media-libs/gd
-	media-libs/glu
-	media-libs/libpng:0=
-	sys-libs/zlib
-	"
-DEPEND="${COMMON_DEPEND}"
-RDEPEND="${COMMON_DEPEND}
-	dev-lang/tcl:0=
-	dev-lang/tk:0=
-	"
-
-S=${WORKDIR}/${PN}
-
-src_prepare(){
-	epatch \
-		"${FILESDIR}/${PN}"-5.0.8-setup.patch \
-		"${FILESDIR}/${PN}"-5.0.8-headers.patch \
-		"${FILESDIR}/${PN}"-5.0.8-fsldir_redux.patch
-
-	sed -i \
-		-e "s:@@GENTOO_RANLIB@@:$(tc-getRANLIB):" \
-		-e "s:@@GENTOO_CC@@:$(tc-getCC):" \
-		-e "s:@@GENTOO_CXX@@:$(tc-getCXX):" \
-		config/generic/systemvars.mk || die
-
-	eprefixify $(grep -rl GENTOO_PORTAGE_EPREFIX src/*) \
-		etc/js/label-div.html
-
-	makefilelist=$(find src/ -name Makefile)
-
-	sed -i \
-		-e "s:-I\${INC_BOOST}::" \
-		-e "s:-I\${INC_ZLIB}::" \
-		-e "s:-I\${INC_GD}::" \
-		-e "s:-I\${INC_PNG}::" \
-		-e "s:-L\${LIB_GD}::" \
-		-e "s:-L\${LIB_PNG}::" \
-		-e "s:-L\${LIB_ZLIB}::" \
-		${makefilelist} || die
-
-	sed -i "s:\${FSLDIR}/bin/::g" \
-		$(grep -rl "\${FSLDIR}/bin" src/*) \
-		$(grep -rl "\${FSLDIR}/bin" etc/matlab/*)
-	sed -i "s:\$FSLDIR/bin/::g" \
-		$(grep -rl "\$FSLDIR/bin" src/*) \
-		$(grep -rl "\$FSLDIR/bin" etc/matlab/*)
-
-	sed -i "s:\$FSLDIR/data:${EPREFIX}/usr/share/fsl/data:g" \
-		$(grep -rl "\$FSLDIR/data" src/*)
-
-	sed -i "s:\${FSLDIR}/data:${EPREFIX}/usr/share/fsl/data:g" \
-		$(grep -rl "\${FSLDIR}/data" src/*)
-
-	sed -i "s:\$FSLDIR/etc:${EPREFIX}/etc:g" \
-		$(grep -rl "\$FSLDIR/etc" src/*)
-
-	sed -i "s:\${FSLDIR}/etc:${EPREFIX}/etc:g" \
-		$(grep -rl "\${FSLDIR}/etc" src/*)
-
-	sed -i "s:\$FSLDIR/doc:${EPREFIX}/usr/share/fsl/doc:g" \
-		$(grep -rl "\$FSLDIR/doc" src/*)
-
-	sed -i "s:\${FSLDIR}/doc:${EPREFIX}/usr/share/fsl/doc:g" \
-		$(grep -rl "\${FSLDIR}/doc" src/*)
-
-	sed -i "s:\'\${FSLDIR}\'/doc:${EPREFIX}/usr/share/fsl/doc:g" \
-		$(grep -rl "\'\${FSLDIR}\'/doc" src/*)
-
-	sed -i -e "s:\$FSLDIR/etc:/etc:g" `grep -rlI \$FSLDIR/etc *`
-	default
-}
-
-src_compile() {
-	export FSLDIR=${WORKDIR}/${PN}
-	export FSLCONDIR=${WORKDIR}/${PN}/config
-	export FSLMACHTYPE=generic
-
-	export USERLDFLAGS="${LDFLAGS}"
-	export USERCFLAGS="${CFLAGS}"
-	export USERCXXFLAGS="${CXXFLAGS}"
-
-	./build || die
-}
-
-src_install() {
-	sed -i "s:\${FSLDIR}/tcl:/usr/libexec/fsl:g" \
-		$(grep -lI "\${FSLDIR}/tcl" bin/*) \
-		$(grep -l "\${FSLDIR}/tcl"  tcl/*) || die
-	sed -i "s:\$FSLDIR/tcl:/usr/libexec/fsl:g" \
-		$(grep -l "\$FSLDIR/tcl" tcl/*) || die
-
-	dobin bin/*
-
-	insinto /usr/share/${PN}
-	doins -r data
-	dodoc -r doc/. refdoc
-
-	insinto /usr/libexec/fsl
-	doins -r tcl/*
-
-	insinto /etc/fslconf
-	doins etc/fslconf/fsl.sh
-
-	insinto /etc
-	doins etc/fslversion
-	doins -r etc/default_flobs.flobs etc/flirtsch etc/js etc/luts
-	#if use matlab; then
-	#	doins etc/matlab
-	#fi
-
-	#the following is needed for FSL and depending programs to be able
-	#to find its files, since FSL uses an uncommon:
-	#https://github.com/gentoo-science/sci/pull/612#r60289295
-	dosym ../../../etc /usr/share/fsl/etc
-	dosym ../doc/${P} /usr/share/fsl/doc
-
-	cp "${FILESDIR}"/99fsl "${TMPDIR}"/99fsl || die
-	eprefixify "${TMPDIR}"/99fsl
-	doenvd "${TMPDIR}"/99fsl
-	mv "${ED}"/usr/bin/{,fsl_}cluster || die
-}
-
-pkg_postinst() {
-	echo
-	einfo "Please run the following commands if you"
-	einfo "intend to use fsl from an existing shell:"
-	einfo "env-update && source /etc/profile"
-	echo
-}
diff --git a/sci-biology/fsl/fsl-5.0.9.ebuild b/sci-biology/fsl/fsl-5.0.9.ebuild
deleted file mode 100644
index 6e9ff6233..000000000
--- a/sci-biology/fsl/fsl-5.0.9.ebuild
+++ /dev/null
@@ -1,142 +0,0 @@
-# Copyright 1999-2017 Gentoo Foundation
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=6
-
-inherit toolchain-funcs prefix
-
-DESCRIPTION="Analysis of functional, structural, and diffusion MRI brain imaging data"
-HOMEPAGE="http://www.fmrib.ox.ac.uk/fsl"
-SRC_URI="https://dev.gentoo.org/~jlec/distfiles/${P}-sources.tar.gz"
-
-LICENSE="FSL BSD-2 newmat"
-SLOT="0"
-KEYWORDS="~amd64"
-IUSE=""
-
-COMMON_DEPEND="
-	dev-libs/boost
-	media-gfx/graphviz
-	media-libs/gd
-	media-libs/glu
-	media-libs/libpng:0=
-	sys-libs/zlib
-	"
-DEPEND="${COMMON_DEPEND}"
-RDEPEND="${COMMON_DEPEND}
-	dev-lang/tcl:0=
-	dev-lang/tk:0=
-	"
-
-S=${WORKDIR}/${PN}
-UPSTREAM_FSLDIR="/usr/share/fsl"
-
-PATCHES=(
-	"${FILESDIR}/${PN}"-5.0.9-setup.patch
-	"${FILESDIR}/${PN}"-5.0.9-headers.patch
-	"${FILESDIR}/${PN}"-5.0.9-fsldir_redux.patch
-)
-
-src_prepare(){
-	default
-	sed -i \
-		-e "s:@@GENTOO_RANLIB@@:$(tc-getRANLIB):" \
-		-e "s:@@GENTOO_CC@@:$(tc-getCC):" \
-		-e "s:@@GENTOO_CXX@@:$(tc-getCXX):" \
-		config/generic/systemvars.mk || die
-
-	eprefixify $(grep -rl GENTOO_PORTAGE_EPREFIX src/*) \
-		etc/js/label-div.html
-
-	makefilelist=$(find src/ -name Makefile)
-
-	sed -i \
-		-e "s:-I\${INC_BOOST}::" \
-		-e "s:-I\${INC_ZLIB}::" \
-		-e "s:-I\${INC_GD}::" \
-		-e "s:-I\${INC_PNG}::" \
-		-e "s:-L\${LIB_GD}::" \
-		-e "s:-L\${LIB_PNG}::" \
-		-e "s:-L\${LIB_ZLIB}::" \
-		${makefilelist} || die
-
-	sed -e "s:\${FSLDIR}/bin/::g" \
-		-e "s:\$FSLDIR/bin/::g" \
-		-i $(grep -rl "\${FSLDIR}/bin" src/*) \
-		$(grep -rl "\${FSLDIR}/bin" etc/matlab/*) || die
-
-	sed -e "s:\$FSLDIR/data:${EPREFIX}/usr/share/fsl/data:g" \
-		-e "s:\${FSLDIR}/data:${EPREFIX}/usr/share/fsl/data:g" \
-		-i $(grep -rl "\$FSLDIR/data" src/*) \
-		$(grep -rl "\${FSLDIR}/data" src/*) || die
-
-	sed -e "s:\$FSLDIR/doc:${EPREFIX}/usr/share/fsl/doc:g" \
-		-e "s:\${FSLDIR}/doc:${EPREFIX}/usr/share/fsl/doc:g" \
-		-i $(grep -rl "\$FSLDIR/doc" src/*) \
-		$(grep -rl "\${FSLDIR}/doc" src/*) || die
-
-	sed -e "s:/usr/share/fsl/doc:${EPREFIX}/usr/share/fsl/doc:g" \
-		$(grep -rl "/usr/share/fsl/doc" src/*) || die
-
-	sed -e "s:\$FSLDIR/etc:${EPREFIX}/etc:g" \
-		-e "s:\${FSLDIR}/etc:${EPREFIX}/etc:g" \
-		-i $(grep -rlI "\$FSLDIR/etc" *) \
-		-i $(grep -rlI "\${FSLDIR}/etc" *) || die
-}
-
-src_compile() {
-	export FSLDIR=${WORKDIR}/${PN}
-	export FSLCONDIR=${WORKDIR}/${PN}/config
-	export FSLMACHTYPE=generic
-
-	export USERLDFLAGS="${LDFLAGS}"
-	export USERCFLAGS="${CFLAGS}"
-	export USERCXXFLAGS="${CXXFLAGS}"
-
-	./build || die
-}
-
-src_install() {
-	sed -i "s:\${FSLDIR}/tcl:/usr/libexec/fsl:g" \
-		$(grep -lI "\${FSLDIR}/tcl" bin/*) \
-		$(grep -l "\${FSLDIR}/tcl"  tcl/*) || die
-	sed -i "s:\$FSLDIR/tcl:/usr/libexec/fsl:g" \
-		$(grep -l "\$FSLDIR/tcl" tcl/*) || die
-
-	dobin bin/*
-
-	insinto /usr/share/${PN}
-	doins -r data
-	dodoc -r doc/. refdoc
-
-	insinto /usr/libexec/fsl
-	doins -r tcl/*
-
-	insinto /etc/fslconf
-	doins etc/fslconf/fsl.sh
-
-	insinto /etc
-	doins etc/fslversion
-	doins -r etc/default_flobs.flobs etc/flirtsch etc/js etc/luts
-	#if use matlab; then
-	#	doins etc/matlab
-	#fi
-
-	#the following is needed for FSL and depending programs to be able
-	#to find its files, since FSL uses an uncommon installation path:
-	#https://github.com/gentoo-science/sci/pull/612#r60289295
-	dosym ../../../etc ${UPSTREAM_FSLDIR}/etc
-	dosym ../doc/${PF} ${UPSTREAM_FSLDIR}/doc
-	dosym ../../bin ${UPSTREAM_FSLDIR}/bin
-
-	doenvd "$(prefixify_ro "${FILESDIR}"/99fsl)"
-	mv "${ED}"/usr/bin/{,fsl_}cluster || die
-}
-
-pkg_postinst() {
-	echo
-	einfo "Please run the following commands if you"
-	einfo "intend to use fsl from an existing shell:"
-	einfo "env-update && source /etc/profile"
-	echo
-}
diff --git a/sci-biology/fsl/fsl-6.0.4.ebuild b/sci-biology/fsl/fsl-6.0.4.ebuild
new file mode 100644
index 000000000..6e5d6e779
--- /dev/null
+++ b/sci-biology/fsl/fsl-6.0.4.ebuild
@@ -0,0 +1,213 @@
+# Copyright 1999-2021 Gentoo Authors
+# Distributed under the terms of the GNU General Public License v2
+
+EAPI=7
+
+inherit cuda toolchain-funcs prefix
+
+DESCRIPTION="Analysis of functional, structural, and diffusion MRI brain imaging data"
+HOMEPAGE="https://www.fmrib.ox.ac.uk/fsl"
+SRC_URI="https://fsl.fmrib.ox.ac.uk/fsldownloads/${P}-sources.tar.gz -> ${P}.tar.gz"
+
+LICENSE="FSL BSD-2 newmat"
+SLOT="0"
+KEYWORDS="~amd64"
+IUSE="cuda"
+
+DEPEND="
+	dev-libs/boost
+	>=dev-python/fslpy-3
+	media-gfx/graphviz
+	media-libs/gd
+	media-libs/glu
+	media-libs/libpng:0=
+	sci-libs/ciftilib
+	sci-libs/nlopt
+	sys-libs/zlib
+	dev-lang/tcl:0=
+	dev-lang/tk:0=
+	>=virtual/lapack-3.8
+	>=virtual/blas-3.8
+	cuda? (
+		=dev-util/nvidia-cuda-toolkit-11* =sys-devel/gcc-9*:*
+	)
+	"
+RDEPEND="${DEPEND}"
+
+S=${WORKDIR}/${PN}
+UPSTREAM_FSLDIR="/usr/share/fsl"
+
+PATCHES=(
+	"${FILESDIR}/${P}"-gcc10_include.patch
+	"${FILESDIR}/${P}"-setup.patch
+	"${FILESDIR}/${PN}"-6.0.2-template.patch
+	"${FILESDIR}/${PN}"-6.0.2-no_xmlpp.patch
+	"${FILESDIR}/${PN}"-5.0.11-niftiio_var_fix.patch
+	"${FILESDIR}/${PN}"-5.0.11-ifstream_use.patch
+	"${FILESDIR}/${PN}"-5.0.11-fslsurface_parallel_make.patch
+	"${FILESDIR}/${PN}"-6.0.2-qstring_compat.patch
+	"${FILESDIR}/${PN}"-5.0.9-headers.patch
+	"${FILESDIR}/${P}"-fsldir_redux-p1.patch
+	"${FILESDIR}/${P}"-fsldir_redux-p2.patch
+	"${FILESDIR}/${P}"-flameo_std.patch
+	"${FILESDIR}/${P}"-melodic_std.patch
+	"${FILESDIR}/${P}"-remove_fslpy_collisions-p1.patch
+	"${FILESDIR}/${P}"-remove_fslpy_collisions-p2.patch
+	"${FILESDIR}/${P}"-fdt_cuda.patch
+)
+
+src_prepare() {
+	default
+
+	sed -i \
+		-e "s:@@GENTOO_RANLIB@@:$(tc-getRANLIB):" \
+		-e "s:@@GENTOO_CC@@:$(tc-getCC):" \
+		-e "s:@@GENTOO_CXX@@:$(tc-getCXX):" \
+		config/buildSettings.mk || die
+
+	eprefixify $(grep -rl GENTOO_PORTAGE_EPREFIX src/*) \
+		etc/js/label-div.html
+
+	# Disable mist the hard way for now.
+	rm -r src/mist || die
+
+	# Disable ptx2 for now
+	rm -r src/ptx2 || die
+
+	makefilelist=$(find src/ -name Makefile)
+
+	sed -i \
+		-e "s:-I\${INC_BOOST}::" \
+		-e "s:-I\${INC_ZLIB}::" \
+		-e "s:-I\${INC_GD}::" \
+		-e "s:-I\${INC_PNG}::" \
+		-e "s:-L\${LIB_GD}::" \
+		-e "s:-L\${LIB_PNG}::" \
+		-e "s:-L\${LIB_ZLIB}::" \
+		${makefilelist} || die
+
+	sed -e "s:\${FSLDIR}/bin/::g" \
+		-e "s:\$FSLDIR/bin/::g" \
+		-i $(grep -rl "\${FSLDIR}/bin" src/*) \
+		-i $(grep -rl "\$FSLDIR/bin" src/*) \
+		$(grep -rl "\${FSLDIR}/bin" etc/matlab/*)\
+		$(grep -rl "\$FSLDIR/bin" etc/matlab/*) || die
+
+	sed -e "s:\$FSLDIR/data:${EPREFIX}/usr/share/fsl/data:g" \
+		-e "s:\${FSLDIR}/data:${EPREFIX}/usr/share/fsl/data:g" \
+		-i $(grep -rl "\$FSLDIR/data" src/*) \
+		$(grep -rl "\${FSLDIR}/data" src/*) || die
+
+	sed -e "s:\$FSLDIR/doc:${EPREFIX}/usr/share/fsl/doc:g" \
+		-e "s:\${FSLDIR}/doc:${EPREFIX}/usr/share/fsl/doc:g" \
+		-i $(grep -rl "\$FSLDIR/doc" src/*) \
+		$(grep -rl "\${FSLDIR}/doc" src/*) || die
+
+	sed -e "s:/usr/share/fsl/doc:${EPREFIX}/usr/share/fsl/doc:g" \
+		-i $(grep -rl "/usr/share/fsl/doc" src/*) || die
+
+	sed -e "s:\$FSLDIR/etc:${EPREFIX}/etc:g" \
+		-e "s:\${FSLDIR}/etc:${EPREFIX}/etc:g" \
+		-i $(grep -rlI "\$FSLDIR/etc" *) \
+		-i $(grep -rlI "\${FSLDIR}/etc" *) || die
+
+	# Use generic blas/lapack rather than openblas
+	sed -e "s:-lopenblas:-llapack -lblas:g" \
+		-i $(grep -rlI lopenblas *) || die
+
+	# script wanting to have access to fslversion at buildtime
+	sed -e "s:/etc/fslversion:${S}/etc/fslversion:g" \
+		-i ${makefilelist} || die
+
+	if use cuda; then
+		einfo
+
+		gcc_ver=`gcc-fullversion`
+		einfo "GCC version: ${gcc_ver}"
+
+		cuda_gcc=`cuda_gccdir`
+		cuda_NVCC_flags=`cuda_gccdir -f`
+		einfo "CUDA GCC path: ${cuda_gcc}"
+		einfo "  ${cuda_NVCC_flags}"
+
+		CUDA_INSTALLATION="/opt/cuda"
+		CUDAVER=`cuda_toolkit_version`
+
+		eapply "${FILESDIR}/${P}-eddy_cuda.patch"
+		eapply "${FILESDIR}/${P}-cuda_buildsettings.patch"
+
+		sed -i \
+			-e "s:@@GENTOO_NVCC_FLAGS@@:${cuda_NVCC_flags}:" \
+			src/eddy/Makefile || die
+
+		cuda_sanitize
+	fi
+}
+
+src_compile() {
+	export FSLDIR=${WORKDIR}/${PN}
+	export FSLCONDIR=${WORKDIR}/${PN}/config
+	export FSLMACHTYPE=generic
+
+	# define the default build system to match upstream official standard
+	#  -> individual projects may overwrite the '-std=' flag
+	export ANSI_CFLAGS="-std=c11"
+	export ANSI_CXXFLAGS="-std=c++11"
+
+	export USERLDFLAGS="${LDFLAGS}"
+	export USERCFLAGS="${CFLAGS}"
+	export USERCPPFLAGS="${CPPFLAGS}"
+	export USERCXXFLAGS="${CXXFLAGS}"
+
+	export CIFTICFLAGS="$($(tc-getPKG_CONFIG) --cflags CiftiLib)"
+	export CIFTILIBS="$($(tc-getPKG_CONFIG) --libs-only-l CiftiLib)"
+
+	if use cuda; then
+		einfo "CUDA_INSTALLATION: ${CUDA_INSTALLATION}"
+		einfo "CUDAVER: ${CUDAVER}"
+	fi
+
+	./build || die
+}
+
+src_install() {
+	sed -i "s:\${FSLDIR}/tcl:/usr/libexec/fsl:g" \
+		$(grep -lI "\${FSLDIR}/tcl" bin/*) \
+		$(grep -l "\${FSLDIR}/tcl"  tcl/*) || die
+	sed -i "s:\$FSLDIR/tcl:/usr/libexec/fsl:g" \
+		$(grep -l "\$FSLDIR/tcl" tcl/*) || die
+
+	dobin bin/*
+
+	insinto /usr/share/${PN}
+	doins -r data
+	dodoc -r doc/. refdoc
+
+	insinto /usr/libexec/fsl
+	doins -r tcl/*
+
+	insinto /etc/fslconf
+	doins etc/fslconf/fsl.sh
+
+	insinto /etc
+	doins etc/fslversion
+	doins -r etc/default_flobs.flobs etc/flirtsch etc/js etc/luts
+
+	#the following is needed for FSL and depending programs to be able
+	#to find its files, since FSL uses an uncommon installation path:
+	#https://github.com/gentoo-science/sci/pull/612#r60289295
+	dosym ../../../etc ${UPSTREAM_FSLDIR}/etc
+	dosym ../doc/${PF} ${UPSTREAM_FSLDIR}/doc
+	dosym ../../bin ${UPSTREAM_FSLDIR}/bin
+
+	doenvd "$(prefixify_ro "${FILESDIR}"/99fsl)"
+	mv "${ED}"/usr/bin/{,fsl_}cluster || die
+}
+
+pkg_postinst() {
+	echo
+	einfo "Please run the following commands if you"
+	einfo "intend to use fsl from an existing shell:"
+	einfo "env-update && source /etc/profile"
+	echo
+}
diff --git a/sci-biology/fsl/fsl-6.0.5.ebuild b/sci-biology/fsl/fsl-6.0.5.ebuild
new file mode 100644
index 000000000..d3ec1de1d
--- /dev/null
+++ b/sci-biology/fsl/fsl-6.0.5.ebuild
@@ -0,0 +1,218 @@
+# Copyright 1999-2022 Gentoo Authors
+# Distributed under the terms of the GNU General Public License v2
+
+EAPI=8
+
+inherit cuda toolchain-funcs prefix
+
+DESCRIPTION="Analysis of functional, structural, and diffusion MRI brain imaging data"
+HOMEPAGE="https://www.fmrib.ox.ac.uk/fsl"
+SRC_URI="https://fsl.fmrib.ox.ac.uk/fsldownloads/${P}-sources.tar.gz -> ${P}.tar.gz"
+S="${WORKDIR}/${PN}"
+
+LICENSE="FSL BSD-2 newmat"
+SLOT="0"
+KEYWORDS=""
+IUSE="cuda"
+
+DEPEND="
+	dev-cpp/libxmlpp:=
+	dev-cpp/tbb
+	dev-db/sqlite
+	dev-libs/boost
+	dev-libs/libfmt
+	dev-libs/libxml2
+	dev-libs/pugixml
+	>=dev-python/fslpy-3.7.0
+	media-gfx/graphviz
+	media-libs/gd
+	media-libs/glu
+	media-libs/libpng:0=
+	sci-libs/gsl
+	sci-libs/ciftilib
+	sci-libs/fftw
+	sci-libs/nlopt
+	sci-libs/vtk
+	sys-libs/zlib
+	dev-lang/tcl:0=
+	dev-lang/tk:0=
+	>=virtual/lapack-3.8
+	>=virtual/blas-3.8
+	cuda? (
+		=dev-util/nvidia-cuda-toolkit-11* =sys-devel/gcc-9*:*
+	)
+	"
+RDEPEND="${DEPEND}"
+
+UPSTREAM_FSLDIR="/usr/share/fsl"
+
+PATCHES=(
+#	"${FILESDIR}/${PN}"-6.0.4-gcc10_include.patch
+	"${FILESDIR}/${PN}"-6.0.4-setup.patch
+# 	"${FILESDIR}/${PN}"-6.0.2-no_xmlpp.patch
+# 	"${FILESDIR}/${PN}"-5.0.11-niftiio_var_fix.patch
+# 	"${FILESDIR}/${PN}"-5.0.11-fslsurface_parallel_make.patch
+# 	"${FILESDIR}/${PN}"-6.0.2-qstring_compat.patch
+# 	"${FILESDIR}/${PN}"-5.0.9-headers.patch
+	"${FILESDIR}/${PN}"-6.0.4-flameo_std.patch
+	"${FILESDIR}/${PN}"-6.0.4-melodic_std.patch
+	"${FILESDIR}/${PN}"-6.0.4-remove_fslpy_collisions-p1.patch
+	"${FILESDIR}/${PN}"-6.0.4-remove_fslpy_collisions-p2.patch
+# 	"${FILESDIR}/${PN}"-6.0.4-fdt_cuda.patch
+)
+
+src_prepare() {
+	default
+
+	sed -i \
+		-e "s:@@GENTOO_RANLIB@@:$(tc-getRANLIB):" \
+		-e "s:@@GENTOO_CC@@:$(tc-getCC):" \
+		-e "s:@@GENTOO_CXX@@:$(tc-getCXX):" \
+		config/buildSettings.mk || die
+
+	eprefixify $(grep -rl GENTOO_PORTAGE_EPREFIX src/*) \
+		etc/js/label-div.html
+
+# 	# Disable mist the hard way for now.
+# 	rm -r src/mist || die
+#
+# 	# Disable ptx2 for now
+# 	rm -r src/ptx2 || die
+#
+	makefilelist=$(find src/ -name Makefile)
+
+# 	sed -i \
+# 		-e "s:-I\${INC_BOOST}::" \
+# 		-e "s:-I\${INC_ZLIB}::" \
+# 		-e "s:-I\${INC_GD}::" \
+# 		-e "s:-I\${INC_PNG}::" \
+# 		-e "s:-L\${LIB_GD}::" \
+# 		-e "s:-L\${LIB_PNG}::" \
+# 		-e "s:-L\${LIB_ZLIB}::" \
+# 		${makefilelist} || die
+
+	sed -e "s:\${FSLDIR}/bin/::g" \
+		-e "s:\$FSLDIR/bin/::g" \
+		-i $(grep -rl "\${FSLDIR}/bin" src/*) \
+		-i $(grep -rl "\$FSLDIR/bin" src/*) \
+		$(grep -rl "\${FSLDIR}/bin" etc/matlab/*)\
+		$(grep -rl "\$FSLDIR/bin" etc/matlab/*) || die
+
+	sed -e "s:\$FSLDIR/data:${EPREFIX}/usr/share/fsl/data:g" \
+		-e "s:\${FSLDIR}/data:${EPREFIX}/usr/share/fsl/data:g" \
+		-i $(grep -rl "\$FSLDIR/data" src/*) \
+		$(grep -rl "\${FSLDIR}/data" src/*) || die
+
+	sed -e "s:\$FSLDIR/doc:${EPREFIX}/usr/share/fsl/doc:g" \
+		-e "s:\${FSLDIR}/doc:${EPREFIX}/usr/share/fsl/doc:g" \
+		-i $(grep -rl "\$FSLDIR/doc" src/*) \
+		$(grep -rl "\${FSLDIR}/doc" src/*) || die
+
+	sed -e "s:/usr/share/fsl/doc:${EPREFIX}/usr/share/fsl/doc:g" \
+		-i $(grep -rl "/usr/share/fsl/doc" src/*) || die
+
+	sed -e "s:\$FSLDIR/etc:${EPREFIX}/etc:g" \
+		-e "s:\${FSLDIR}/etc:${EPREFIX}/etc:g" \
+		-i $(grep -rlI "\$FSLDIR/etc" *) \
+		-i $(grep -rlI "\${FSLDIR}/etc" *) || die
+
+	# Use generic blas/lapack rather than openblas
+	sed -e "s:-lopenblas:-llapack -lblas:g" \
+		-i $(grep -rlI lopenblas *) || die
+
+	# script wanting to have access to fslversion at buildtime
+	sed -e "s:/etc/fslversion:${S}/etc/fslversion:g" \
+		-i ${makefilelist} || die
+
+	if use cuda; then
+		einfo
+
+		gcc_ver=`gcc-fullversion`
+		einfo "GCC version: ${gcc_ver}"
+
+		cuda_gcc=`cuda_gccdir`
+		cuda_NVCC_flags=`cuda_gccdir -f`
+		einfo "CUDA GCC path: ${cuda_gcc}"
+		einfo "  ${cuda_NVCC_flags}"
+
+		CUDA_INSTALLATION="/opt/cuda"
+		CUDAVER=`cuda_toolkit_version`
+
+		eapply "${FILESDIR}/${PN}-6.0.4-eddy_cuda.patch"
+		eapply "${FILESDIR}/${PN}-6.0.4-cuda_buildsettings.patch"
+
+		sed -i \
+			-e "s:@@GENTOO_NVCC_FLAGS@@:${cuda_NVCC_flags}:" \
+			src/eddy/Makefile || die
+
+		cuda_sanitize
+	fi
+}
+
+src_compile() {
+	export FSLDIR=${WORKDIR}/${PN}
+	export FSLCONDIR=${WORKDIR}/${PN}/config
+	export FSLMACHTYPE=generic
+
+	# define the default build system to match upstream official standard
+	#  -> individual projects may overwrite the '-std=' flag
+	export ANSI_CFLAGS="-std=c99"
+	export ANSI_CXXFLAGS="-std=c++98"
+
+	export USERLDFLAGS="${LDFLAGS}"
+	export USERCFLAGS="${CFLAGS}"
+	export USERCPPFLAGS="${CPPFLAGS}"
+	export USERCXXFLAGS="${CXXFLAGS}"
+
+	export CIFTICFLAGS="$($(tc-getPKG_CONFIG) --cflags CiftiLib)"
+	export CIFTILIBS="$($(tc-getPKG_CONFIG) --libs-only-l CiftiLib)"
+
+	if use cuda; then
+		einfo "CUDA_INSTALLATION: ${CUDA_INSTALLATION}"
+		einfo "CUDAVER: ${CUDAVER}"
+	fi
+
+	./build || die
+}
+
+src_install() {
+	sed -i "s:\${FSLDIR}/tcl:/usr/libexec/fsl:g" \
+		$(grep -lI "\${FSLDIR}/tcl" bin/*) \
+		$(grep -l "\${FSLDIR}/tcl"  tcl/*) || die
+	sed -i "s:\$FSLDIR/tcl:/usr/libexec/fsl:g" \
+		$(grep -l "\$FSLDIR/tcl" tcl/*) || die
+
+	dobin bin/*
+
+	insinto /usr/share/${PN}
+	doins -r data
+	dodoc -r doc/. refdoc
+
+	insinto /usr/libexec/fsl
+	doins -r tcl/*
+
+	insinto /etc/fslconf
+	doins etc/fslconf/fsl.sh
+
+	insinto /etc
+	doins etc/fslversion
+	doins -r etc/default_flobs.flobs etc/flirtsch etc/js etc/luts
+
+	#the following is needed for FSL and depending programs to be able
+	#to find its files, since FSL uses an uncommon installation path:
+	#https://github.com/gentoo-science/sci/pull/612#r60289295
+	dosym ../../../etc ${UPSTREAM_FSLDIR}/etc
+	dosym ../doc/${PF} ${UPSTREAM_FSLDIR}/doc
+	dosym ../../bin ${UPSTREAM_FSLDIR}/bin
+
+	doenvd "$(prefixify_ro "${FILESDIR}"/99fsl)"
+	mv "${ED}"/usr/bin/{,fsl_}cluster || die
+}
+
+pkg_postinst() {
+	echo
+	einfo "Please run the following commands if you"
+	einfo "intend to use fsl from an existing shell:"
+	einfo "env-update && source /etc/profile"
+	echo
+}
diff --git a/sci-biology/fsl/metadata.xml b/sci-biology/fsl/metadata.xml
index d3788686e..e171f1431 100644
--- a/sci-biology/fsl/metadata.xml
+++ b/sci-biology/fsl/metadata.xml
@@ -5,7 +5,7 @@
 		<email>sci-biology@gentoo.org</email>
 		<name>Gentoo Biology Project</name>
 	</maintainer>
-	<longdescription>
-FSL is a comprehensive library of analysis tools for FMRI, MRI and DTI brain imaging data.
-</longdescription>
+	<use>
+		<flag name="cuda">Add support for CUDA</flag>
+	</use>
 </pkgmetadata>
diff --git a/sci-biology/full_lengther_next/Manifest b/sci-biology/full_lengther_next/Manifest
deleted file mode 100644
index fc5927852..000000000
--- a/sci-biology/full_lengther_next/Manifest
+++ /dev/null
@@ -1 +0,0 @@
-DIST full_lengther_next-0.6.2.gem 2039296 BLAKE2B f81a420f404d94b772b3140caca80d737c3d5fea0d58642dfd997b3d0525da74558133e86451232184a5319fb022c6eba6039850a400770798f46ce52c26a800 SHA512 19b2608137cb8129da08cbd064d2667290f8d0693f8471dcb3a7ab194de1d02b940b58c16abda8cfba5bf9e803b948f8da21c3a82c5e1b73c30346cbeb12191f
diff --git a/sci-biology/full_lengther_next/full_lengther_next-0.6.2.ebuild b/sci-biology/full_lengther_next/full_lengther_next-0.6.2.ebuild
deleted file mode 100644
index c333d2990..000000000
--- a/sci-biology/full_lengther_next/full_lengther_next-0.6.2.ebuild
+++ /dev/null
@@ -1,39 +0,0 @@
-# Copyright 1999-2017 Gentoo Foundation
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=6
-
-USE_RUBY="ruby22 ruby23 ruby24"
-
-RUBY_FAKEGEM_TASK_DOC=""
-RUBY_FAKEGEM_EXTRADOC="README.rdoc History.txt"
-
-inherit ruby-fakegem
-
-DESCRIPTION="Classify assembled transcripts and fix frameshifts in ORFs"
-HOMEPAGE="http://www.rubydoc.info/gems/full_lengther_next
-	http://www.scbi.uma.es/site/scbi/downloads/313-full-lengthernext"
-# https://rubygems.org/gems/full_lengther_next/versions/0.0.8
-# http://www.rubydoc.info/gems/full_lengther_next
-# https://www.omniref.com/ruby/gems/full_lengther_next/0.0.8/symbols/FullLengtherNext
-
-LICENSE="MIT"
-SLOT="0"
-KEYWORDS="~amd64"
-IUSE=""
-
-DEPEND="
-	>=dev-ruby/hoe-2.8.0
-	>=dev-ruby/rdoc-3.10
-	dev-ruby/bundler"
-	# >=dev-ruby/newgem-1.5.3
-RDEPEND="${DEPEND}
-	sci-biology/bioruby
-	>=sci-biology/bio-cd-hit-report-0.1.0
-	>=sci-biology/scbi_blast-0.0.37
-	>=sci-biology/scbi_fasta-0.1.7
-	>=sci-biology/scbi_zcat-0.0.2
-	>=sci-biology/scbi_mapreduce-0.0.29
-	>=sci-biology/scbi_plot-0.0.6
-	>=dev-ruby/xml-simple-1.0.12
-	>=dev-ruby/gnuplot-2.3.0"
diff --git a/sci-biology/full_lengther_next/metadata.xml b/sci-biology/full_lengther_next/metadata.xml
deleted file mode 100644
index 138cb7705..000000000
--- a/sci-biology/full_lengther_next/metadata.xml
+++ /dev/null
@@ -1,12 +0,0 @@
-<?xml version="1.0" encoding="UTF-8"?>
-<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
-<pkgmetadata>
-	<maintainer type="person">
-		<email>mmokrejs@fold.natur.cuni.cz</email>
-		<name>Martin Mokrejs</name>
-	</maintainer>
-	<maintainer type="project">
-		<email>sci-biology@gentoo.org</email>
-		<name>Gentoo Biology Project</name>
-	</maintainer>
-</pkgmetadata>
diff --git a/sci-biology/gap2caf/Manifest b/sci-biology/gap2caf/Manifest
deleted file mode 100644
index 48d2d68d2..000000000
--- a/sci-biology/gap2caf/Manifest
+++ /dev/null
@@ -1,2 +0,0 @@
-DIST gap2caf-2.1.0.tar.gz 92905 BLAKE2B 3d02b94a33047c00a42923204f6748e3903fe1609cc5ce6b31faee152882c665c8edba02e8d6b233e266efa1e994a0be6e2b8bf5078c0428f98343329cc02e51 SHA512 2a843d861b7be6d656793f4876953596b91a93c3da7d23ee8edc10c4620e33fc96a16beaeaaf4f66c1f5c5084eb8a9a255d4fa8e1ca6e87e96372f2459167c90
-DIST staden-2.0.0b8.tar.gz 4312143 BLAKE2B 318dffff9f40daae0d5c5de23f710bbf43440e0854bd15b5b0af07afc48bfac166dd95a91a2b27fccd19468b087f68bf6028a636147904090dfe6076335e6c74 SHA512 ddd273d281557595c90b93304cd03205adbe1367845ef43763a8c75d06c2729d99ca8622439ff5c31217595481a9ac4ccedf87c5948821aeaeb73c96133dc411
diff --git a/sci-biology/gap2caf/gap2caf-2.1.0.ebuild b/sci-biology/gap2caf/gap2caf-2.1.0.ebuild
deleted file mode 100644
index 90a117a8c..000000000
--- a/sci-biology/gap2caf/gap2caf-2.1.0.ebuild
+++ /dev/null
@@ -1,77 +0,0 @@
-# Copyright 1999-2016 Gentoo Foundation
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=5
-
-inherit autotools eutils
-
-DESCRIPTION="GAP4 file format to CAF v2 format converter for genomic assembly data"
-HOMEPAGE="http://www.sanger.ac.uk/resources/software/caf/"
-SRC_URI="
-	ftp://ftp.sanger.ac.uk/pub/PRODUCTION_SOFTWARE/src/gap2caf-2.1.0.tar.gz
-	http://downloads.sourceforge.net/staden/staden-2.0.0b8.tar.gz"
-
-LICENSE="GRL staden"
-SLOT="0"
-KEYWORDS=""
-IUSE=""
-
-DEPEND="
-	sci-biology/staden
-	>=dev-lang/tcl-8.5:0="
-RDEPEND="${DEPEND}"
-
-#src_prepare(){
-#	epatch "${FILESDIR}"/Makefile.in-"${PV}".patch || die
-#}
-
-src_prepare(){
-	sed -i 's:/include/tcl8.4:/include:' configure.ac || die
-	sed -i 's:libtcl8.4:libtcl:' configure.ac || die
-	sed \
-		-e 's:tcl8.4:tcl:' \
-		-e 's:pkglib_PROGRAMS:pkglibexec_PROGRAMS:g' \
-		-i src/Makefile.am || die
-	eautoreconf
-	sed -i 's:/include/tcl8.4:/include:' configure || die
-	sed -i 's:libtcl8.4:libtcl:' configure || die
-}
-
-src_configure(){
-	# STADENROOT=/usr is used to find $STADENROOT/lib/staden/staden.profile and staden_config.h
-	# STADENSRC is used to locate gap4/IO.h
-	#CPPFLAGS="$CPPFLAGS -I/home/mmokrejs/proj/staden/staden/trunk/src" \
-	#LDFLAGS="$LDFLAGS -L/usr/lib/staden -lmutlib -lprimer3 -lg -lmisc" \
-	# STADENROOT=/usr/share/staden \
-	# STADENSRC="${WORKDIR}"/staden-2.0.0b8-src \
-	econf \
-		--with-stadenroot=/usr \
-		--with-tcl=/usr \
-		--with-stadensrc="${WORKDIR}"/staden-2.0.0b8-src
-	#sed -i 's:prefix = /usr:prefix = $(DESTDIR)/usr:' Makefile || die
-	#sed -i 's:prefix = /usr:prefix = $(DESTDIR)/usr:' src/Makefile || die
-	sed -i 's:tcl8.4:tcl:' src/Makefile || die
-
-	# The below tricks in overall do not help, only for -ltk_utils somehow
-	sed -i 's:-ltk_utils:-Wl,--enable-new-dtags -Wl,-rpath,/usr/lib/staden -ltk_utils -rpath-link:' src/Makefile || die
-	sed -i 's:-lgap:-Wl,--enable-new-dtags -Wl,-rpath,/usr/lib/staden -lgap:' src/Makefile || die
-	sed -i 's:-lseq_utils:-Wl,--enable-new-dtags -Wl,-rpath,/usr/lib/staden -lseq_utils:' src/Makefile || die
-	sed -i 's:-rpath-link::' src/Makefile || die
-}
-
-# TODO: the 2.0.2 archive lacks manpages compared to 2.0, FIXME
-# The man/Makefile.in is screwed in 2.0.2 so we cannot use it to install the manpage files,
-# not even copying over whole caftools-2.0/man/ to caftools-2.0.2/man does not help.
-src_install(){
-	# do not use upstream's install it just install shell wrapper into /usr/bin/gap2caf
-	# calling "LD_LIBRARY_PATH=/usr/lib/staden /usr/lib/gap2caf/gap2caf $@"
-	# emake install DESTDIR="${D}" || die
-	#
-	# Instead, we rely on sci-biology/staden providind /etc/env.d/99staden file providing LDPATH=/usr/lib/staden
-	dobin src/gap2caf
-	dodoc README
-}
-
-# BUG #259848
-# A working ebuild which needs some files from staden source tree. That is ugly,
-# am sorting out with upstream how to get around in a clean way.
diff --git a/sci-biology/gap2caf/metadata.xml b/sci-biology/gap2caf/metadata.xml
deleted file mode 100644
index 0f267b755..000000000
--- a/sci-biology/gap2caf/metadata.xml
+++ /dev/null
@@ -1,15 +0,0 @@
-<?xml version="1.0" encoding="UTF-8"?>
-<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
-<pkgmetadata>
-	<maintainer type="person">
-		<email>mmokrejs@fold.natur.cuni.cz</email>
-		<name>Martin Mokrejs</name>
-	</maintainer>
-	<maintainer type="project">
-		<email>sci-biology@gentoo.org</email>
-		<name>Gentoo Biology Project</name>
-	</maintainer>
-	<upstream>
-		<remote-id type="sourceforge">downloads</remote-id>
-	</upstream>
-</pkgmetadata>
diff --git a/sci-biology/gatk/files/settings.xml b/sci-biology/gatk/files/settings.xml
deleted file mode 100644
index 9527ec0b7..000000000
--- a/sci-biology/gatk/files/settings.xml
+++ /dev/null
@@ -1,9 +0,0 @@
-<settings xmlns="http://maven.apache.org/SETTINGS/1.0.0"
-  xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance"
-  xsi:schemaLocation="http://maven.apache.org/SETTINGS/1.0.0
-                      https://maven.apache.org/xsd/settings-1.0.0.xsd">
-  <localRepository>${user.home}/.m2/repository</localRepository>
-  <interactiveMode>false</interactiveMode>
-  <usePluginRegistry>false</usePluginRegistry>
-  <offline>true</offline>
-</settings>
diff --git a/sci-biology/gatk/gatk-3.8.1.ebuild b/sci-biology/gatk/gatk-3.8.1.ebuild
deleted file mode 100644
index f46c1d322..000000000
--- a/sci-biology/gatk/gatk-3.8.1.ebuild
+++ /dev/null
@@ -1,104 +0,0 @@
-# Copyright 1999-2018 Gentoo Foundation
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=5
-
-inherit java-pkg-2 git-r3 # building from tar.gz snapshots is unsupported
-
-MY_PV=${PV/.1/-1} # convert 3.8.1 to 3.8-1
-DESCRIPTION="The Genome Analysis Toolkit"
-HOMEPAGE="http://www.broadinstitute.org/gsa/wiki/index.php/The_Genome_Analysis_Toolkit"
-EGIT_REPO_URI="https://github.com/broadgsa/gatk.git" # git tree for <=gatk-3
-# check out 3.8-1 branch but using a proper commit, not ${MY_PV}
-# https://github.com/broadinstitute/gatk/issues/4685#issuecomment-383188772
-EGIT_COMMIT="41147a655594c2aae6e2cad8462bd1648570b32b"
-# building outside of git is not possible,
-# see https://github.com/broadinstitute/picard/issues/605
-
-LICENSE="MIT"
-SLOT="0"
-IUSE=""
-KEYWORDS="~amd64" # 608.21 MiB git download and 134MB "${W}"/.m2 download
-
-COMMON_DEPS=""
-DEPEND="
-	>=virtual/jdk-1.6
-	dev-java/maven-bin:* || ( dev-java/netbeans-java )
-	dev-java/cofoja
-	${COMMON_DEPS}"
-RDEPEND="
-	>=virtual/jre-1.6
-	>=sci-biology/SnpEff-2.0.5
-	${COMMON_DEPS}"
-
-#S="${WORKDIR}/${PN}-${MY_PV}"
-
-# https://maven.apache.org/settings.html
-# The two settings files are located at:
-#   The Maven installation directory: $M2_HOME/conf/settings.xml
-#   The user's home directory: ${user.home}/.m2/settings.xml
-#
-# localRepository: This value is the path of this build system's local repository. 
-#    The default value is ${user.home}/.m2/repository. This element is especially
-#    useful for a main build server allowing all logged-in users to build from a
-#    common local repository.
-# interactiveMode: true if Maven should attempt to interact with the user for input,
-#    false if not. Defaults to true.
-# usePluginRegistry: true if Maven should use the ${user.home}/.m2/plugin-registry.xml
-#    file to manage plugin versions, defaults to false. Note that for the current version
-#    of Maven 2.0, the plugin-registry.xml file should not be depended upon. Consider it
-#    dormant for now.
-# offline: true if this build system should operate in offline mode, defaults to false.
-#    This element is useful for build servers which cannot connect to a remote repository,
-#    either because of network setup or security reasons.
-
-src_prepare() {
-	mvn clean -Dmaven.repo.local="${WORKDIR}"/.m2/repository || die
-	sed -e 's#mvn_args="#mvn_args="-Dmaven.repo.local=${WORKDIR}/.m2/repository #' -i ant-bridge.sh || die
-	mkdir -p "${WORKDIR}"/.m2/repository || die
-	cp "${FILESDIR}"/settings.xml "${WORKDIR}"/.m2/repository/ || die
-	#export M2_HOME="${EPREFIX}"/usr/share/maven-bin-3.3
-	#export MAVEN_HOME="${EPREFIX}"/usr/share/maven-bin-3.3
-	export M2="${WORKDIR}"/.m2/repository # not recognized?
-	#export MAVEN_OPTS="-Xms256m -Xmx512m" # works but not needed actually
-	sh ant-bridge.sh || die # BUG: this downloads and compiles lot of stuff
-	java-pkg-2_src_prepare
-}
-
-src_install() {
-	mvn install -Dmaven.repo.local="${WORKDIR}"/.m2/repository || die
-	# Java QA Notice: installing versioned jar 'gatk-tools-public-3.8-1.jar'
-	# Java QA Notice: installing versioned jar 'gatk-queue-extensions-generator-3.8-1.jar'
-	# Java QA Notice: installing versioned jar 'gatk-engine-3.8-1.jar'
-	# Java QA Notice: installing versioned jar 'gatk-queue-extensions-public-3.8-1.jar'
-	# Java QA Notice: installing versioned jar 'gatk-utils-3.8-1.jar'
-	# Java QA Notice: installing versioned jar 'gatk-queue-3.8-1.jar'
-	find public -name \*.jar | grep -v tests | grep -v cofoja | while read f; do \
-		java-pkg_dojar $f
-	done
-}
-
-pkg_postinst(){
-	einfo "The ebuild also installs bundled SnpEff-2.0.5.jar file until the"
-	einfo "installation layout gets more testing"
-}
-
-# TODO: adjust the build system to output GenomeAnalysisTK.jar file like in an official
-#       binary release
-# # equery files gatk
-#   * Searching for gatk ...
-#   * Contents of sci-biology/gatk-3.8.1:
-#  /usr
-#  /usr/share
-#  /usr/share/gatk
-#  /usr/share/gatk/lib
-#  /usr/share/gatk/lib/external-example-1.0-SNAPSHOT.jar
-#  /usr/share/gatk/lib/gatk-engine-3.8-1.jar
-#  /usr/share/gatk/lib/gatk-queue-3.8-1.jar
-#  /usr/share/gatk/lib/gatk-queue-extensions-generator-3.8-1.jar
-#  /usr/share/gatk/lib/gatk-queue-extensions-public-3.8-1.jar
-#  /usr/share/gatk/lib/gatk-tools-public-3.8-1.jar
-#  /usr/share/gatk/lib/gatk-utils-3.8-1.jar
-#  /usr/share/gatk/lib/original-external-example-1.0-SNAPSHOT.jar
-#  /usr/share/gatk/lib/snpeff-2.0.5.jar
-#  /usr/share/gatk/package.env
diff --git a/sci-biology/gatk/gatk-9999.ebuild b/sci-biology/gatk/gatk-9999.ebuild
deleted file mode 100644
index fc9db8986..000000000
--- a/sci-biology/gatk/gatk-9999.ebuild
+++ /dev/null
@@ -1,85 +0,0 @@
-# Copyright 1999-2018 Gentoo Foundation
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=5
-
-PYTHON_COMPAT=( python2_7 python3_{4,5,6} )
-
-inherit java-pkg-2 git-r3 # building from tar.gz snapshots is unsupported
-
-DESCRIPTION="The Genome Analysis Toolkit"
-HOMEPAGE="http://www.broadinstitute.org/gsa/wiki/index.php/The_Genome_Analysis_Toolkit"
-EGIT_REPO_URI="https://github.com/broadinstitute/gatk.git" # git tree for >=gatk-4
-EGIT_CLONE_TYPE="mirror"
-# building outside of git is not possible,
-# see https://github.com/broadinstitute/picard/issues/605
-#
-# 
-# must run 'git clone https://github.com/broadinstitute/gatk.git gatk'
-# see https://github.com/broadinstitute/gatk/issues/4687
-
-LICENSE="BSD-3" # since gatk-4
-SLOT="0"
-IUSE=""
-KEYWORDS="" # 148.19 MB git download and 134MB "${W}"/.m2 download
-
-COMMON_DEPS=""
-# gatk-4 needs java-1.8
-DEPEND="
-	>=virtual/jdk-1.8
-	>=dev-vcs/git-2.5
-	>=dev-vcs/git-lfs-1.1.0
-	>=dev-java/maven-bin-3.1:* || ( dev-java/netbeans-java )
-	dev-java/cofoja
-	${COMMON_DEPS}"
-RDEPEND="
-	>=virtual/jre-1.8
-	>=sci-biology/SnpEff-2.0.5
-	>=dev-lang/R-3.2.5
-	${COMMON_DEPS}"
-
-#S="${WORKDIR}/${PN}-${MY_PV}"
-
-# https://maven.apache.org/settings.html
-# The two settings files are located at:
-#   The Maven installation directory: $M2_HOME/conf/settings.xml
-#   The user's home directory: ${user.home}/.m2/settings.xml
-#
-# localRepository: This value is the path of this build system's local repository. 
-#    The default value is ${user.home}/.m2/repository. This element is especially
-#    useful for a main build server allowing all logged-in users to build from a
-#    common local repository.
-# interactiveMode: true if Maven should attempt to interact with the user for input,
-#    false if not. Defaults to true.
-# usePluginRegistry: true if Maven should use the ${user.home}/.m2/plugin-registry.xml
-#    file to manage plugin versions, defaults to false. Note that for the current version
-#    of Maven 2.0, the plugin-registry.xml file should not be depended upon. Consider it
-#    dormant for now.
-# offline: true if this build system should operate in offline mode, defaults to false.
-#    This element is useful for build servers which cannot connect to a remote repository,
-#    either because of network setup or security reasons.
-
-src_prepare() {
-	default
-}
-
-src_compile(){
-	# work around gradle writing $HOME/.gradle, requiring $HOME/.git and $HOME/.m2/
-	# https://github.com/samtools/htsjdk/issues/660#issuecomment-232155965
-	# make jure SDK-1.8 is available, JRE-1.8 is not enough
-	#
-	# https://github.com/broadinstitute/gatk#building
-	# gradlew tragets are bundle, localJar, sparkJar, ...
-	GRADLE_USER_HOME="${WORKDIR}" ./gradlew --stacktrace --debug bundle || die
-}
-
-src_install() {
-	cd build/libs || die
-	java-pkg_dojar "${PN}".jar
-	java-pkg_dojar "${PN}"-*-SNAPSHOT.jar
-	#java-pkg_dolauncher ${PN} --main picard.cmdline.PicardCommandLine
-	#use source && java-pkg_dosrc "${S}"/src/java/*
-	#use doc && java-pkg_dojavadoc "${S}"/javadoc
-	#
-	# install a bash-completion script gatk-completion.sh into proper place
-}
diff --git a/sci-biology/gatk/metadata.xml b/sci-biology/gatk/metadata.xml
deleted file mode 100644
index 5a54c7fec..000000000
--- a/sci-biology/gatk/metadata.xml
+++ /dev/null
@@ -1,11 +0,0 @@
-<?xml version="1.0" encoding="UTF-8"?>
-<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
-<pkgmetadata>
-	<maintainer type="project">
-		<email>sci-biology@gentoo.org</email>
-		<name>Gentoo Biology Project</name>
-	</maintainer>
-	<upstream>
-		<remote-id type="github">broadgsa/gatk</remote-id>
-	</upstream>
-</pkgmetadata>
diff --git a/sci-biology/gemini/gemini-9999.ebuild b/sci-biology/gemini/gemini-9999.ebuild
deleted file mode 100644
index b6d4ce1af..000000000
--- a/sci-biology/gemini/gemini-9999.ebuild
+++ /dev/null
@@ -1,36 +0,0 @@
-# Copyright 1999-2017 Gentoo Foundation
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=6
-
-PYTHON_COMPAT=( python2_7 )
-
-inherit git-r3 distutils-r1
-
-DESCRIPTION="Lightweight VCF to DB framework for disease and population genetics"
-HOMEPAGE="https://github.com/arq5x/gemini
-	http://gemini.readthedocs.org/en/latest"
-# https://media.readthedocs.org/pdf/gemini/latest/gemini.pdf
-# http://www.ploscompbiol.org/article/info%3Adoi%2F10.1371%2Fjournal.pcbi.1003153
-# http://quinlanlab.org/pdf/Gemini-Quinlan-Stroke-UVA.pdf
-EGIT_REPO_URI="https://github.com/arq5x/gemini.git"
-
-LICENSE="MIT" # see note below!
-SLOT="0"
-KEYWORDS=""
-IUSE=""
-
-DEPEND=""
-RDEPEND="dev-python/sqlalchemy
-	sci-biology/grabix
-	sci-libs/htslib
-	sci-biology/bedtools
-	sci-biology/pybedtools
-	${DEPEND}"
-
-# GEMINI includes CADD scores (PMID: 24487276) for annotating variants.
-#
-# CADD scores (http://cadd.gs.washington.edu/) are Copyright 2013 University of
-# Washington and Hudson-Alpha Institute for Biotechnology (all rights reserved)
-# but are freely available for all academic, non-commercial applications.
-# For commercial licensing information contact Jennifer McCullar
diff --git a/sci-biology/gemini/metadata.xml b/sci-biology/gemini/metadata.xml
deleted file mode 100644
index 260a8b4ae..000000000
--- a/sci-biology/gemini/metadata.xml
+++ /dev/null
@@ -1,15 +0,0 @@
-<?xml version="1.0" encoding="UTF-8"?>
-<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
-<pkgmetadata>
-	<maintainer type="person">
-		<email>mmokrejs@fold.natur.cuni.cz</email>
-		<name>Martin Mokrejs</name>
-	</maintainer>
-	<maintainer type="project">
-		<email>sci-biology@gentoo.org</email>
-		<name>Gentoo Biology Project</name>
-	</maintainer>
-	<upstream>
-		<remote-id type="github">arq5x/gemini</remote-id>
-	</upstream>
-</pkgmetadata>
diff --git a/sci-biology/geneid/Manifest b/sci-biology/geneid/Manifest
deleted file mode 100644
index 7ccc65fbc..000000000
--- a/sci-biology/geneid/Manifest
+++ /dev/null
@@ -1 +0,0 @@
-DIST geneid_v1.4.4.Jan_13_2011.tar.gz 2722565 BLAKE2B f81530271eb4258b3a4841f81d541cd01fdf49132733e32ea9f2b1c187571ab9be7588927981b354379883fae04f24564e3d2f6078b3447ce983931001117b87 SHA512 d44297da1dfe426640a90ac94f41d439b8d7a9a192c9368a8c43cc232e8a7044a16ec16b632f67a0a8010a86ea1b23da106f1ae3dc1d40243abb929bb33024a7
diff --git a/sci-biology/geneid/files/Makefile.patch b/sci-biology/geneid/files/Makefile.patch
deleted file mode 100644
index bd6a8667a..000000000
--- a/sci-biology/geneid/files/Makefile.patch
+++ /dev/null
@@ -1,11 +0,0 @@
---- geneid/Makefile	2014-06-17 11:37:07.000000000 +0200
-+++ geneid/Makefile	2014-06-17 11:37:27.000000000 +0200
-@@ -13,7 +13,7 @@
- PROGRAM= geneid
- PRODUCT= $(BIN)/$(PROGRAM)
- CC=gcc
--OPTS=-I$(INCLUDE) -Wall -O3
-+OPTS=$(CFLAGS) -I$(INCLUDE)
- #OPTS=-I$(INCLUDE) -Wall -g
- #######
- 
diff --git a/sci-biology/geneid/geneid-1.4.4.ebuild b/sci-biology/geneid/geneid-1.4.4.ebuild
deleted file mode 100644
index 2ee9478ca..000000000
--- a/sci-biology/geneid/geneid-1.4.4.ebuild
+++ /dev/null
@@ -1,31 +0,0 @@
-# Copyright 1999-2014 Gentoo Foundation
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=5
-
-inherit eutils
-
-DESCRIPTION="An ab initio exon/gene finding program"
-HOMEPAGE="http://genome.crg.es/software/geneid"
-SRC_URI="ftp://genome.crg.es/pub/software/geneid/geneid_v1.4.4.Jan_13_2011.tar.gz"
-
-LICENSE="GPL-2"
-SLOT="0"
-KEYWORDS="~amd64 ~x86"
-IUSE=""
-
-DEPEND=""
-RDEPEND="${DEPEND}"
-
-S="${WORKDIR}"/"${PN}"
-
-src_prepare() {
-	epatch "${FILESDIR}"/Makefile.patch
-}
-
-src_install() {
-	dobin bin/geneid
-	dohtml docs/*.html
-	dohtml -r docs/chapter*
-	dohtml -r docs/images
-}
diff --git a/sci-biology/geneid/metadata.xml b/sci-biology/geneid/metadata.xml
deleted file mode 100644
index 138cb7705..000000000
--- a/sci-biology/geneid/metadata.xml
+++ /dev/null
@@ -1,12 +0,0 @@
-<?xml version="1.0" encoding="UTF-8"?>
-<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
-<pkgmetadata>
-	<maintainer type="person">
-		<email>mmokrejs@fold.natur.cuni.cz</email>
-		<name>Martin Mokrejs</name>
-	</maintainer>
-	<maintainer type="project">
-		<email>sci-biology@gentoo.org</email>
-		<name>Gentoo Biology Project</name>
-	</maintainer>
-</pkgmetadata>
diff --git a/sci-biology/genepop/Manifest b/sci-biology/genepop/Manifest
index f78004fea..eb43f768f 100644
--- a/sci-biology/genepop/Manifest
+++ b/sci-biology/genepop/Manifest
@@ -1,2 +1 @@
-DIST genepop-4.2.1.tar.gz 136675 BLAKE2B 9ffc4e24bda4c739762c4790145c099455c65700ac51f6f8890fa57ac71a99f0f87e5b4d432cd5aa4d27ec73b2738605f5522309fc69e49b383310730de5d4ff SHA512 f658f6ab82c1ef21bf15a9bd03335ea792e670ce7cf8f2eb3e1c4d75ae24ff099bde5580b310fdcd552dfb1dbb6df55352a8c06fedeeb7d46434a58767233882
-DIST genepop-4.7.tar.gz 2034202 BLAKE2B caee5a069ad31ae7975fa6508e118983a5efcde4ccd2879d126815d72ce6da455e0440e3d8be2d48890d6fc6ed191c989e1e8579136c1c8bb08d392f0e9257d6 SHA512 95eb7e36d59d5278a77c420216f65e44475c98f93ec166dfb13f01c5f4ad93c80caff9f62d549f8ccb8a0af1a0196a257a5825681e5f27e3c1c26aa8d699d593
+DIST genepop-4.7.tar.gz 2038733 BLAKE2B b71139709a6a6f34fcf4e216178420f6deaeb0dc2c984a9f8f440706d213afa0819f7a8382b470270c9d125dfc9a37fb6038d4f142b2790cc7c42ba1ea0a7add SHA512 176ba767ab1d3d4be0c86a69b33efaa88c5e3940d92a819eda3be295398ce91781c283864c4507b90b857b6011cf1253cf9ec5ae193b20e6a9aea330d5b09ca5
diff --git a/sci-biology/genepop/genepop-4.2.1.ebuild b/sci-biology/genepop/genepop-4.2.1.ebuild
deleted file mode 100644
index 7119b9936..000000000
--- a/sci-biology/genepop/genepop-4.2.1.ebuild
+++ /dev/null
@@ -1,30 +0,0 @@
-# Copyright 1999-2015 Gentoo Foundation
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=5
-
-inherit cmake-utils
-
-DESCRIPTION="Population genetics analysis"
-HOMEPAGE="http://genepop.curtin.edu.au/ http://kimura.univ-montp2.fr/~rousset/Genepop.htm"
-SRC_URI="http://dev.gentoo.org/~jlec/distfiles/${P}.tar.gz"
-
-LICENSE="CeCILL-2"
-SLOT="0"
-IUSE=""
-KEYWORDS="~amd64 ~x86"
-
-S="${WORKDIR}"
-
-src_prepare() {
-	cat >> CMakeLists.txt <<- EOF
-	cmake_minimum_required (VERSION 2.6)
-	project (${PN} CXX)
-
-	set(CMAKE_CXX_FLAGS "\${CMAKE_CXX_FLAGS} -DNO_MODULES")
-
-	add_executable(Genepop GenepopS.cpp)
-	install(TARGETS Genepop DESTINATION bin)
-	EOF
-	cmake-utils_src_prepare
-}
diff --git a/sci-biology/genepop/genepop-4.7.ebuild b/sci-biology/genepop/genepop-4.7.ebuild
index 9430e7987..b3ed5bfc3 100644
--- a/sci-biology/genepop/genepop-4.7.ebuild
+++ b/sci-biology/genepop/genepop-4.7.ebuild
@@ -1,9 +1,9 @@
-# Copyright 1999-2018 Gentoo Foundation
+# Copyright 1999-2021 Gentoo Authors
 # Distributed under the terms of the GNU General Public License v2
 
-EAPI=6
+EAPI=7
 
-inherit cmake-utils
+inherit cmake
 
 DESCRIPTION="Population genetics analysis"
 HOMEPAGE="https://genepop.curtin.edu.au/ https://kimura.univ-montp2.fr/~rousset/Genepop.htm"
@@ -28,12 +28,11 @@ src_prepare() {
 	add_executable(Genepop GenepopS.cpp)
 	install(TARGETS Genepop DESTINATION bin)
 	EOF
-	cmake-utils_src_prepare
-	default
+	cmake_src_prepare
 }
 
 src_install(){
-	cmake-utils_src_install
+	cmake_src_install
 	mv "${ED}"/usr/bin/Genepop "${ED}"/usr/bin/genepop || die
 	newdoc Genepop.pdf genepop.pdf
 	insinto /usr/share/"${PN}"
diff --git a/sci-biology/generecon/Manifest b/sci-biology/generecon/Manifest
deleted file mode 100644
index 10f7613c1..000000000
--- a/sci-biology/generecon/Manifest
+++ /dev/null
@@ -1 +0,0 @@
-DIST generecon-1.2.1.tar.gz 239507 BLAKE2B b5eeaf94c8488e32b60180875c6baf6fb7b12792678f331a65166db758866ada87f97155fb35a3a011de387f93c6e08fc38951d4e7c73046f05395bc2b4770bb SHA512 59a3a7a54ce1086c8c4424aa8a2661e39c72b1896c2ac3af6147f8234ef8cfd4db9af69b709131e5ea63463fe4d8ab93109cd73cda8b59d2dc061a674af7bd4d
diff --git a/sci-biology/generecon/files/1.2.1-flags.patch b/sci-biology/generecon/files/1.2.1-flags.patch
deleted file mode 100644
index 7dd9a372e..000000000
--- a/sci-biology/generecon/files/1.2.1-flags.patch
+++ /dev/null
@@ -1,30 +0,0 @@
-diff --git a/Makefile.am b/Makefile.am
-index 37df12b..4ff621e 100644
---- a/Makefile.am
-+++ b/Makefile.am
-@@ -1,10 +1,10 @@
- 
--CXXFLAGS =
-+#CXXFLAGS =
- AM_CXXFLAGS =
--CXXFLAGS += -Wall
--AM_CXXFLAGS += -Wall
-+#CXXFLAGS += -Wall
-+#AM_CXXFLAGS += -Wall
- 
--LDFLAGS = -Wl,-rpath,/usr/local/lib
-+#LDFLAGS = -Wl,-rpath,/usr/local/lib
- 
- # for testing
- #CXXFLAGS += -g -O -lefence
-@@ -14,8 +14,8 @@ LDFLAGS = -Wl,-rpath,/usr/local/lib
- #AM_CXXFLAGS += -O3 -g -pg
- 
- # for production
--CXXFLAGS    += -O3 -fexpensive-optimizations
--AM_CXXFLAGS += -O3 -fexpensive-optimizations
-+#CXXFLAGS    += -O3 -fexpensive-optimizations
-+#AM_CXXFLAGS += -O3 -fexpensive-optimizations
- 
- #CXXFLAGS    += -O3 -fexpensive-optimizations -DNDEBUG
- #AM_CXXFLAGS += -O3 -fexpensive-optimizations -DNDEBUG
diff --git a/sci-biology/generecon/files/1.2.1-gcc4.patch b/sci-biology/generecon/files/1.2.1-gcc4.patch
deleted file mode 100644
index 6b71713c3..000000000
--- a/sci-biology/generecon/files/1.2.1-gcc4.patch
+++ /dev/null
@@ -1,368 +0,0 @@
-diff --git a/affected_unaffected_genotype_cluster_test.cc b/affected_unaffected_genotype_cluster_test.cc
-index 646af06..4e5fbde 100644
---- a/affected_unaffected_genotype_cluster_test.cc
-+++ b/affected_unaffected_genotype_cluster_test.cc
-@@ -32,6 +32,7 @@
- # include "random_tree_builder.hh"
- #endif
- 
-+#include <cstring>
- 
- void test_tree(const CoalescentTree &tree,
- 	       const Haplotype &h0, const Haplotype &h1,
-diff --git a/affected_unaffected_genotype_set_test.cc b/affected_unaffected_genotype_set_test.cc
-index 07fa122..5f333f5 100644
---- a/affected_unaffected_genotype_set_test.cc
-+++ b/affected_unaffected_genotype_set_test.cc
-@@ -19,6 +19,8 @@
- # include "region.hh"
- #endif
- 
-+#include <cstring>
-+
- int main(int argc, const char *argv[])
- {
-     HANDLE_TEST_OPTIONS;
-diff --git a/affected_unaffected_haplotype_cluster_test.cc b/affected_unaffected_haplotype_cluster_test.cc
-index 145e05f..b5dddaa 100644
---- a/affected_unaffected_haplotype_cluster_test.cc
-+++ b/affected_unaffected_haplotype_cluster_test.cc
-@@ -32,6 +32,7 @@
- # include "random_tree_builder.hh"
- #endif
- 
-+#include <cstring>
- 
- void test_tree(const CoalescentTree &tree,
- 	       const Haplotype &h0, const Haplotype &h1,
-diff --git a/affected_unaffected_haplotype_set_test.cc b/affected_unaffected_haplotype_set_test.cc
-index fda6173..8489c54 100644
---- a/affected_unaffected_haplotype_set_test.cc
-+++ b/affected_unaffected_haplotype_set_test.cc
-@@ -19,6 +19,8 @@
- # include "region.hh"
- #endif
- 
-+#include <cstring>
-+
- int main(int argc, const char *argv[])
- {
-     HANDLE_TEST_OPTIONS;
-diff --git a/au_random_tree_builder_test.cc b/au_random_tree_builder_test.cc
-index a2d4daa..d6689e0 100644
---- a/au_random_tree_builder_test.cc
-+++ b/au_random_tree_builder_test.cc
-@@ -30,6 +30,7 @@
- # include "test_random.hh"
- #endif
- 
-+#include <cstring>
- 
- void test_tree(const CoalescentTree *tree,
- 	       const Haplotype &h0, const Haplotype &h1,
-diff --git a/change_selector_test.cc b/change_selector_test.cc
-index 5f655d1..9004bef 100644
---- a/change_selector_test.cc
-+++ b/change_selector_test.cc
-@@ -23,6 +23,8 @@
- # include "change.hh"
- #endif
- 
-+#include <cstring>
-+
- // dummy class for testing
- struct DummyChange : public Change {
-     DummyChange() : Change("Dummy change") {}
-diff --git a/coalescent_tree.cc b/coalescent_tree.cc
-index eb937e5..9e54a2b 100644
---- a/coalescent_tree.cc
-+++ b/coalescent_tree.cc
-@@ -7,6 +7,7 @@
- 
- #include "coalescent_tree.hh"
- 
-+#include <algorithm>
- 
- /** \file
-  * \brief Implementation of the coalescent tree.
-diff --git a/coalescent_tree_test.cc b/coalescent_tree_test.cc
-index 20059e9..2971ead 100644
---- a/coalescent_tree_test.cc
-+++ b/coalescent_tree_test.cc
-@@ -30,6 +30,8 @@
- # define CMATH_INCLUDED
- #endif
- 
-+#include <cstring>
-+
- namespace {
- 
-     CoalescentTree *test_tree(HaplotypePool &pool)
-diff --git a/distance_matrix_test.cc b/distance_matrix_test.cc
-index e2e8435..9d367ee 100644
---- a/distance_matrix_test.cc
-+++ b/distance_matrix_test.cc
-@@ -15,6 +15,8 @@
- # include "haplotype_pool.hh"
- #endif
- 
-+#include <cstring>
-+
- namespace {
-     int distance(const Haplotype &h1, const Haplotype &h2)
-     {
-diff --git a/distance_tree_builder_test.cc b/distance_tree_builder_test.cc
-index e252c3e..3f589f4 100644
---- a/distance_tree_builder_test.cc
-+++ b/distance_tree_builder_test.cc
-@@ -15,6 +15,8 @@
- # include "test_random.hh"
- #endif
- 
-+#include <cstring>
-+
- int main(int argc, const char *argv[])
- {
-     HANDLE_TEST_OPTIONS;
-diff --git a/filter_iterator_test.cc b/filter_iterator_test.cc
-index bf5097b..e74a29f 100644
---- a/filter_iterator_test.cc
-+++ b/filter_iterator_test.cc
-@@ -21,6 +21,8 @@
- # define FUNCTIONAL_INCLUDED
- #endif
- 
-+#include <cstring>
-+
- namespace {
-   struct even : public std::unary_function<int,bool> {
-     bool operator () (int i) const { return i % 2 == 0; }
-diff --git a/genotype_pool_test.cc b/genotype_pool_test.cc
-index e62a03f..9a2badb 100644
---- a/genotype_pool_test.cc
-+++ b/genotype_pool_test.cc
-@@ -22,6 +22,8 @@
- # include "genotype.hh"
- #endif
- 
-+#include <cstring>
-+
- int main(int argc, const char *argv[])
- {
-     HANDLE_TEST_OPTIONS;
-diff --git a/genotype_test.cc b/genotype_test.cc
-index 3d704e4..64b3343 100644
---- a/genotype_test.cc
-+++ b/genotype_test.cc
-@@ -22,6 +22,8 @@
- # include "haplotype.hh"
- #endif
- 
-+#include <cstring>
-+
- int main(int argc, const char *argv[])
- {
-     HANDLE_TEST_OPTIONS;
-diff --git a/guile_sampler.cc b/guile_sampler.cc
-index b0d19f1..ffbec86 100644
---- a/guile_sampler.cc
-+++ b/guile_sampler.cc
-@@ -26,6 +26,7 @@
- # define CASSERT_INCLUDED
- #endif
- 
-+#include <memory>
- 
- /** \file
-  * \brief Implementation of the guile sampler wrapper.
-diff --git a/haplotype.cc b/haplotype.cc
-index a38541f..7810642 100644
---- a/haplotype.cc
-+++ b/haplotype.cc
-@@ -12,6 +12,8 @@
- # define SSTREAM_INCLUDED
- #endif
- 
-+#include <algorithm>
-+
- /** \file
-  * \brief Implementation of haplotype functionality.
-  */
-diff --git a/haplotype_pool.cc b/haplotype_pool.cc
-index ceef1b9..42c6125 100644
---- a/haplotype_pool.cc
-+++ b/haplotype_pool.cc
-@@ -7,6 +7,8 @@
- 
- #include "haplotype_pool.hh"
- 
-+#include <algorithm>
-+
- /** \file
-  * \brief Implementation of haplotype pool functionality.
-  */
-diff --git a/haplotype_pool_test.cc b/haplotype_pool_test.cc
-index a774809..4527d23 100644
---- a/haplotype_pool_test.cc
-+++ b/haplotype_pool_test.cc
-@@ -19,6 +19,8 @@
- # include "region.hh"
- #endif
- 
-+#include <cstring>
-+
- int main(int argc, const char *argv[])
- {
-     HANDLE_TEST_OPTIONS;
-diff --git a/haplotype_test.cc b/haplotype_test.cc
-index 134a601..b7f5b63 100644
---- a/haplotype_test.cc
-+++ b/haplotype_test.cc
-@@ -19,6 +19,8 @@
- # include "region.hh"
- #endif
- 
-+#include <cstring>
-+
- int main(int argc, const char *argv[])
- {
-     HANDLE_TEST_OPTIONS;
-diff --git a/marker_test.cc b/marker_test.cc
-index ff34d7c..317385d 100644
---- a/marker_test.cc
-+++ b/marker_test.cc
-@@ -13,6 +13,7 @@
- #include "testing.hh"
- 
- #include <cmath>
-+#include <cstring>
- 
- int main(int argc, const char *argv[])
- {
-diff --git a/markov_region_test.cc b/markov_region_test.cc
-index 58e0278..db0f9ba 100644
---- a/markov_region_test.cc
-+++ b/markov_region_test.cc
-@@ -11,7 +11,7 @@
- 
- #include "region.hh"
- #include "testing.hh"
--
-+#include <cstring>
- int main(int argc, const char *argv[])
- {
-     HANDLE_TEST_OPTIONS;
-diff --git a/qtl_haplotype_pool_test.cc b/qtl_haplotype_pool_test.cc
-index 72f763d..8c058af 100644
---- a/qtl_haplotype_pool_test.cc
-+++ b/qtl_haplotype_pool_test.cc
-@@ -19,6 +19,8 @@
- # include "region.hh"
- #endif
- 
-+#include <cstring>
-+
- int main(int argc, const char *argv[])
- {
-     HANDLE_TEST_OPTIONS;
-diff --git a/random_set_test.cc b/random_set_test.cc
-index 7eae435..b7a3451 100644
---- a/random_set_test.cc
-+++ b/random_set_test.cc
-@@ -15,6 +15,8 @@
- # include "test_random.hh"
- #endif
- 
-+#include <cstring>
-+
- int main(int argc, const char *argv[])
- {
-     HANDLE_TEST_OPTIONS;
-diff --git a/random_tree_builder_test.cc b/random_tree_builder_test.cc
-index e8c5957..7c95519 100644
---- a/random_tree_builder_test.cc
-+++ b/random_tree_builder_test.cc
-@@ -28,6 +28,7 @@
- # include "test_random.hh"
- #endif
- 
-+#include <cstring>
- 
- void test_tree(const CoalescentTree *tree,
- 	       const Haplotype &h0, const Haplotype &h1,
-diff --git a/region.cc b/region.cc
-index df22885..94bce6f 100644
---- a/region.cc
-+++ b/region.cc
-@@ -22,6 +22,8 @@
- # define CMATH_INCLUDED
- #endif
- 
-+#include <algorithm>
-+
- 
- /** \file
-  * \brief Implementation of region functionality.
-diff --git a/region_test.cc b/region_test.cc
-index 25f6cf0..e21084f 100644
---- a/region_test.cc
-+++ b/region_test.cc
-@@ -11,6 +11,7 @@
- 
- #include "region.hh"
- #include "testing.hh"
-+#include <cstring>
- 
- int main(int argc, const char *argv[])
- {
-diff --git a/selection_if_test.cc b/selection_if_test.cc
-index a9a6377..0fb8052 100644
---- a/selection_if_test.cc
-+++ b/selection_if_test.cc
-@@ -24,6 +24,8 @@
- # define VECTOR_INCLUDED
- #endif
- 
-+#include <cstring>
-+
- namespace {
-   struct even : public std::unary_function<int,bool> {
-     bool operator () (int i) const { return i % 2 == 0; }
-diff --git a/selection_test.cc b/selection_test.cc
-index 3bf673a..579931c 100644
---- a/selection_test.cc
-+++ b/selection_test.cc
-@@ -28,6 +28,8 @@
- # define LIST_INCLUDED
- #endif
- 
-+#include <cstring>
-+
- int main(int argc, const char *argv[])
- {
-     HANDLE_TEST_OPTIONS;
-diff --git a/testing.hh b/testing.hh
-index fbdcd87..c86dbc6 100644
---- a/testing.hh
-+++ b/testing.hh
-@@ -23,6 +23,8 @@
- # define CSTDLIB_INCLUDED
- #endif
- 
-+#include <cstring>
-+
- /// \brief Verboseness flag for running tests.
- ///
- /// If set, the test will report the failed tests, otherwise it will
-diff --git a/tree_builder.hh b/tree_builder.hh
-index 4b0ec01..c0bdc5a 100644
---- a/tree_builder.hh
-+++ b/tree_builder.hh
-@@ -34,6 +34,7 @@
- # include "meta_programming.hh"
- #endif
- 
-+#include <limits>
- 
- /**
-  * \brief Abstract class for tree builders.
diff --git a/sci-biology/generecon/files/generecon-docfiles.patch b/sci-biology/generecon/files/generecon-docfiles.patch
deleted file mode 100644
index 79d63e73f..000000000
--- a/sci-biology/generecon/files/generecon-docfiles.patch
+++ /dev/null
@@ -1,12 +0,0 @@
-diff -Nuar generecon-1.2.1.orig/Makefile.am generecon-1.2.1/Makefile.am
---- generecon-1.2.1.orig/Makefile.am	2006-04-19 12:52:18.000000000 -0300
-+++ generecon-1.2.1/Makefile.am	2006-04-19 12:55:53.000000000 -0300
-@@ -31,7 +31,7 @@
- bin_PROGRAMS     = generecon
- 
- 
--docdir = ${prefix}/share/generecon/doc
-+docdir = ${prefix}/share/doc/#PF#
- dist_doc_DATA =
- test_inputdir = ${prefix}/share/generecon/test-input
- dist_test_input_DATA =
diff --git a/sci-biology/generecon/generecon-1.2.1-r1.ebuild b/sci-biology/generecon/generecon-1.2.1-r1.ebuild
deleted file mode 100644
index eed5ce825..000000000
--- a/sci-biology/generecon/generecon-1.2.1-r1.ebuild
+++ /dev/null
@@ -1,31 +0,0 @@
-# Copyright 1999-2015 Gentoo Foundation
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=5
-
-inherit autotools eutils
-
-DESCRIPTION="Disequilibrium gene mapping based on coalescent theory using Bayesian MC methods"
-HOMEPAGE="http://www.daimi.au.dk/~mailund/GeneRecon/"
-SRC_URI="http://www.daimi.au.dk/~mailund/GeneRecon/download/${P}.tar.gz"
-
-SLOT="0"
-LICENSE="GPL-2"
-KEYWORDS="~amd64 ~x86"
-IUSE=""
-
-RDEPEND="
-	dev-libs/popt
-	dev-scheme/guile:12
-	sci-libs/gsl"
-DEPEND="${DEPEND}"
-
-src_prepare() {
-	sed 's|#PF#|'${PF}'|g' "${FILESDIR}"/${PN}-docfiles.patch > ${PN}-docfiles.patch
-
-	epatch \
-		${PN}-docfiles.patch \
-		"${FILESDIR}"/${PV}-gcc4.patch \
-		"${FILESDIR}"/${PV}-flags.patch
-	eautoreconf
-}
diff --git a/sci-biology/generecon/metadata.xml b/sci-biology/generecon/metadata.xml
deleted file mode 100644
index de97c87f7..000000000
--- a/sci-biology/generecon/metadata.xml
+++ /dev/null
@@ -1,12 +0,0 @@
-<?xml version="1.0" encoding="UTF-8"?>
-<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
-<pkgmetadata>
-	<maintainer type="person">
-		<email>lucas.chiesa@gmail.com</email>
-		<name>Lucas Chiesa</name>
-	</maintainer>
-	<maintainer type="project">
-		<email>sci-biology@gentoo.org</email>
-		<name>Gentoo Biology Project</name>
-	</maintainer>
-</pkgmetadata>
diff --git a/sci-biology/genometools/Manifest b/sci-biology/genometools/Manifest
deleted file mode 100644
index 64902c5ad..000000000
--- a/sci-biology/genometools/Manifest
+++ /dev/null
@@ -1 +0,0 @@
-DIST genometools-1.5.10.tar.gz 13621729 BLAKE2B ba102a3b7503d2ea6507b3d9cf05ee6801f8638252ec9d373db1fddb6a615330946a81c9099097bc1e13151f57590a49055a1a41035b355f45ae99583b12af66 SHA512 4b1fa67a27f172b644e8b97b5e454ac715b9cefcfa5fb2e901e3ae06fe0ff22262c156c3ac2ffa576b198fd7f2550e6da3321b72d1a9ae34f5ddfd76499a7233
diff --git a/sci-biology/genometools/genometools-1.5.10.ebuild b/sci-biology/genometools/genometools-1.5.10.ebuild
deleted file mode 100644
index 9e69302c6..000000000
--- a/sci-biology/genometools/genometools-1.5.10.ebuild
+++ /dev/null
@@ -1,41 +0,0 @@
-# Copyright 1999-2018 Gentoo Foundation
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=6
-
-DESCRIPTION="Tools for bioinformatics (Tallymer, Readjoiner, gff3validator, ...)"
-HOMEPAGE="http://genometools.org"
-SRC_URI="http://genometools.org/pub/${P}.tar.gz"
-
-LICENSE="ICS"
-SLOT="0"
-KEYWORDS=""
-IUSE="cairo"
-
-DEPEND="
-	dev-libs/glib
-	cairo? ( x11-libs/cairo x11-libs/pango )
-	sci-biology/samtools:0.1-legacy
-	dev-db/sqlite:3
-	>=dev-lang/lua-5.1:=
-	dev-lua/lpeg
-	dev-lua/luafilesystem
-	dev-lua/lua-md5
-	dev-lang/luajit
-	dev-libs/tre"
-RDEPEND="${DEPEND}"
-
-src_prepare(){
-	sed -e "s#/usr/local#"${EPREFIX}"/usr#g" -i Makefile || die
-	sed -e "s#/usr/include/bam#${EPREFIX}/usr/include/bam-0.1-legacy#" -i Makefile || die
-	sed -e "s#-lbam#-lbam-0.1-legacy#" -i Makefile || die
-	eapply_user
-}
-
-src_compile(){
-	local myemakeargs=( useshared=yes )
-	! use cairo && myemakeargs+=( cairo=no )
-	use x86 && myemakeargs+=( 32bit=yes )
-	use amd64 && myemakeargs+=( 64bit=yes )
-	emake ${myemakeargs}
-}
diff --git a/sci-biology/genometools/metadata.xml b/sci-biology/genometools/metadata.xml
deleted file mode 100644
index 138cb7705..000000000
--- a/sci-biology/genometools/metadata.xml
+++ /dev/null
@@ -1,12 +0,0 @@
-<?xml version="1.0" encoding="UTF-8"?>
-<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
-<pkgmetadata>
-	<maintainer type="person">
-		<email>mmokrejs@fold.natur.cuni.cz</email>
-		<name>Martin Mokrejs</name>
-	</maintainer>
-	<maintainer type="project">
-		<email>sci-biology@gentoo.org</email>
-		<name>Gentoo Biology Project</name>
-	</maintainer>
-</pkgmetadata>
diff --git a/sci-biology/genomeview-bin/genomeview-bin-2450.ebuild b/sci-biology/genomeview-bin/genomeview-bin-2450.ebuild
index 59aefc3ef..9d4480272 100644
--- a/sci-biology/genomeview-bin/genomeview-bin-2450.ebuild
+++ b/sci-biology/genomeview-bin/genomeview-bin-2450.ebuild
@@ -1,21 +1,24 @@
-# Copyright 1999-2014 Gentoo Foundation
+# Copyright 1999-2021 Gentoo Authors
 # Distributed under the terms of the GNU General Public License v2
 
-EAPI=5
+EAPI=7
 
-inherit java-pkg-opt-2 java-ant-2 eutils
+inherit java-pkg-opt-2 java-ant-2
 
 DESCRIPTION="Genome browser and annotation tool"
-HOMEPAGE="http://genomeview.sourceforge.net"
-SRC_URI="http://downloads.sourceforge.net/project/genomeview/GenomeView/genomeview-2450.zip"
+HOMEPAGE="https://genomeview.sourceforge.net"
+SRC_URI="https://downloads.sourceforge.net/project/genomeview/GenomeView/genomeview-2450.zip"
 
 LICENSE="GPL-2"
 SLOT="0"
-KEYWORDS=""
-IUSE=""
+KEYWORDS="~amd64"
 
-DEPEND="virtual/jdk
-	${COMMON_DEPS}"
-RDEPEND="virtual/jre"
+DEPEND=">=virtual/jdk-1.7:*"
+RDEPEND=">=virtual/jre-1.7:*"
+BDEPEND="app-arch/unzip"
 
-S="${WORKDIR}"/genomeview-"${PV}"
+S="${WORKDIR}/genomeview-${PV}"
+
+src_install() {
+	java-pkg_dojar *.jar lib/*.jar
+}
diff --git a/sci-biology/genomeview-bin/metadata.xml b/sci-biology/genomeview-bin/metadata.xml
index 0f267b755..b6476ca7b 100644
--- a/sci-biology/genomeview-bin/metadata.xml
+++ b/sci-biology/genomeview-bin/metadata.xml
@@ -10,6 +10,6 @@
 		<name>Gentoo Biology Project</name>
 	</maintainer>
 	<upstream>
-		<remote-id type="sourceforge">downloads</remote-id>
+		<remote-id type="sourceforge">genomeview</remote-id>
 	</upstream>
 </pkgmetadata>
diff --git a/sci-biology/germline/Manifest b/sci-biology/germline/Manifest
index 0ed52ba5e..7dde29082 100644
--- a/sci-biology/germline/Manifest
+++ b/sci-biology/germline/Manifest
@@ -1,2 +1 @@
-DIST germline-1-5-1.tar.gz 853549 BLAKE2B ecbad3acdedf897da412e3c3bed016fb3118972d5a6d2e5fd2bbc62cf83ed7227cc68609b879b6896f76fe8348a2ccccaa5f9f21276fd321f653006b410c3cad SHA512 d274106a332016f11abaa6aaedf5ca46743647b9074a55e593a3779b965a9cce0607edb06f79e0b380ea81fb0a7112b3fe7518a45c96586dbf4172ed8e820f3e
-DIST germline-1-5-2.tar.gz 854243 SHA256 24cd5dca659639d7a64feb2f1d96f38ba261c703f3a711d9154f5ad554d81821 SHA512 a30fd07beda057288a0651f764a92971b8cbf2d802aba7b8216ad3931a9330631e8007dcb74b4be1ac21b3460ba4e67cf08afe7a6689f3fe90f57577c7bf8c0e WHIRLPOOL 051547329162922831ba562a8e0ce443e389346cab604ae3199be57ab0107d0b6db27f3aa1e01a8593625bb39c5411dbc2260f82daf72b94f196f4c65acb2e0f
+DIST germline-1-5-3.tar.gz 928699 BLAKE2B 4aa170eb1c5c48e52cd8bd1f3933efe410272bebcbd0eee5aa07f0115dabc07f953299599c6a35019f53bfb4c6a585d5f79fb32f93eb1058ee7d428a148091b6 SHA512 3882ad1315aad374c2e344271ec02d14c15501fdae1924e9608c2128be7d0be6d60e7c58ab80a7f13981fa54e1fd01b2c5d43fbfc72de36f09d4b8312cbfeed0
diff --git a/sci-biology/germline/germline-1.5.1.ebuild b/sci-biology/germline/germline-1.5.1.ebuild
deleted file mode 100644
index 1a9063ee5..000000000
--- a/sci-biology/germline/germline-1.5.1.ebuild
+++ /dev/null
@@ -1,34 +0,0 @@
-# Copyright 1999-2016 Gentoo Foundation
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=6
-
-inherit versionator toolchain-funcs
-
-MY_PV=$(replace_all_version_separators '-')
-
-DESCRIPTION="Find shared segments of Identity by Descent (IBD) between pairs of individuals"
-HOMEPAGE="http://www.cs.columbia.edu/~gusev/germline
-	http://genome.cshlp.org/content/19/2/318.full"
-SRC_URI="http://www.cs.columbia.edu/~gusev/${PN}/${PN}-${MY_PV}.tar.gz"
-
-LICENSE="GPL-2"
-SLOT="0"
-KEYWORDS="~amd64 ~x86"
-IUSE=""
-
-DEPEND="dev-libs/boost"
-RDEPEND="${DEPEND}"
-
-S="${WORKDIR}"/${PN}-${MY_PV}
-
-src_prepare(){
-	sed -e "s/-O3 /${CXXFLAGS} /;s/g++/$(tc-getCXX)/" -i Makefile || die
-	sed -e "s#diff -q -s test/expected.match test/generated.match#diff -q -s test/expected.match test/generated.match || cat test/generated.err#" -i Makefile || die
-	sed -e "s/^all: clean germline bmatch test/all: clean germline bmatch/" -i Makefile || die
-	default
-}
-
-src_install(){
-	dobin germline parse_bmatch
-}
diff --git a/sci-biology/germline/germline-1.5.2.ebuild b/sci-biology/germline/germline-1.5.2.ebuild
deleted file mode 100644
index c7c5f8396..000000000
--- a/sci-biology/germline/germline-1.5.2.ebuild
+++ /dev/null
@@ -1,35 +0,0 @@
-# Copyright 1999-2016 Gentoo Foundation
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=6
-
-inherit versionator toolchain-funcs
-
-MY_PV=$(replace_all_version_separators '-')
-
-DESCRIPTION="Find shared segments of Identity by Descent (IBD) between pairs of individuals"
-HOMEPAGE="http://www.cs.columbia.edu/~gusev/germline
-	http://genome.cshlp.org/content/19/2/318.full"
-SRC_URI="http://www.cs.columbia.edu/~gusev/${PN}/${PN}-${MY_PV}.tar.gz"
-
-LICENSE="GPL-2"
-SLOT="0"
-KEYWORDS="~amd64 ~x86"
-IUSE=""
-
-DEPEND="dev-libs/boost"
-RDEPEND="${DEPEND}"
-
-S="${WORKDIR}"/${PN}-${MY_PV}
-
-src_prepare(){
-	sed -e "s/-O3 /${CXXFLAGS} /;s/g++/$(tc-getCXX)/" -i Makefile || die
-	sed -e "s#diff -q -s test/expected.match test/generated.match#diff -q -s test/expected.match test/generated.match || cat test/generated.err#" -i Makefile || die
-	sed -e "s/^all: clean germline bmatch test/all: clean germline bmatch/" -i Makefile || die
-	default
-}
-
-src_install(){
-	dobin germline parse_bmatch
-	dodoc README
-}
diff --git a/sci-biology/germline/germline-1.5.3.ebuild b/sci-biology/germline/germline-1.5.3.ebuild
new file mode 100644
index 000000000..0363b8fa8
--- /dev/null
+++ b/sci-biology/germline/germline-1.5.3.ebuild
@@ -0,0 +1,32 @@
+# Copyright 1999-2021 Gentoo Authors
+# Distributed under the terms of the GNU General Public License v2
+
+EAPI=7
+
+inherit toolchain-funcs
+
+DESCRIPTION="Find shared segments of Identity by Descent (IBD) between pairs of individuals"
+HOMEPAGE="http://gusevlab.org/projects/germline/
+	http://genome.cshlp.org/content/19/2/318.full"
+SRC_URI="http://gusevlab.org/projects/${PN}/release/${PN}-${PV//./-}.tar.gz"
+
+LICENSE="GPL-2"
+SLOT="0"
+KEYWORDS="~amd64 ~x86"
+
+DEPEND="dev-libs/boost"
+RDEPEND="${DEPEND}"
+
+S="${WORKDIR}"/${PN}-${PV//./-}
+
+src_prepare(){
+	sed -e "s/-O3 /${CXXFLAGS} /;s/g++/$(tc-getCXX)/" -i Makefile || die
+	sed -e "s#diff -q -s test/expected.match test/generated.match#diff -q -s test/expected.match test/generated.match || cat test/generated.err#" -i Makefile || die
+	sed -e "s/^all: clean germline bmatch test/all: clean germline bmatch/" -i Makefile || die
+	default
+}
+
+src_install(){
+	dobin germline parse_bmatch
+	dodoc README
+}
diff --git a/sci-biology/gffcompare/Manifest b/sci-biology/gffcompare/Manifest
index 33a4105eb..5a5d8c798 100644
--- a/sci-biology/gffcompare/Manifest
+++ b/sci-biology/gffcompare/Manifest
@@ -1,2 +1 @@
-DIST gclib-0.10.2.tar.gz 169370 BLAKE2B 21f50ce5c6b4f5e703243ce96ee983a20c37a4bedcc11aa5ac8c29eed659b88a040d36172fcabe0ac9da5f85cb7593181ada538c5a9f16e6efb0ecdb1987d501 SHA512 6ba8ce4abdc373c17e81e65b280d09f4452e19f3207a8d8be44f3c98a611ea589393a4d6c9d4acb8c465c3703d3f9bafca432a0b58568ea1927c25da9654f87e
-DIST gffcompare-0.10.5.tar.gz 51308 BLAKE2B 866d828dc2e7e3d980fc129e8d6f89fd52acc1e12f391c7d4ad27ae88c34381f7182e801fce5cfbb8adf7cbb4717c1f7bbb4b201b141d06211c65a169926f6e9 SHA512 ac57c51f241d9c6125b3ed8934753bc4f29f3363a727e891a03ae98f8d135eb537a8ce2f072c500f87baa0e04c46499186ab35f48d04c86c00276704e7565d6c
+DIST gffcompare-0.12.2.tar.gz 213658 BLAKE2B 9390534cc1c9b89f77a7943748f613cfa71d6ddbf302829999f635fb5cbe51e8dcd266ec4002638585396446077cf34a468b2f58e9253767344d42a528a9f899 SHA512 3fba0fb080494fcd787337331b38528163f4b00164ff403f3f7d305b2ba978ff88f35ee4d37394b2945d5a31dc50f23679d9993c32fd381f017f0300969ec0aa
diff --git a/sci-biology/gffcompare/files/Makefile.patch b/sci-biology/gffcompare/files/Makefile.patch
deleted file mode 100644
index afb52b2e1..000000000
--- a/sci-biology/gffcompare/files/Makefile.patch
+++ /dev/null
@@ -1,79 +0,0 @@
---- gffcompare-0.10.5/Makefile	2018-06-26 09:24:06.058542487 +0200
-+++ gffcompare-0.10.5/Makefile	2018-06-26 09:28:08.045119603 +0200
-@@ -16,7 +16,7 @@
- endif    
- 
- # CVS checked in
--CC      := g++
-+CXX      ?= g++
- BASEFLAGS  = -Wall -Wextra ${INCDIRS} $(MARCH) \
-  -fno-exceptions -fno-rtti -D_REENTRANT
- 
-@@ -24,7 +24,8 @@
- 
- ifneq (,$(filter %release %static, $(MAKECMDGOALS)))
-   # -- release build
--  CFLAGS = -O3 -DNDEBUG $(BASEFLAGS)
-+  CXXFLAGS ?= -O3 -g
-+  CXXFLAGS += -DNDEBUG $(BASEFLAGS)
-   LDFLAGS = 
-   LIBS = 
-   ifneq (,$(findstring static,$(MAKECMDGOALS)))
-@@ -37,16 +38,16 @@
-      ifeq "$(GCCVER49)" "0"
-        $(error gcc version 4.9 or greater is required for this build target)
-      endif
--     CFLAGS := -fno-omit-frame-pointer -fsanitize=undefined -fsanitize=address
-+     CXXFLAGS += -fno-omit-frame-pointer -fsanitize=undefined -fsanitize=address
-      GCCVER5 := $(shell expr `g++ -dumpversion | cut -f1 -d.` \>= 5)
-      ifeq "$(GCCVER5)" "1"
--       CFLAGS += -fsanitize=bounds -fsanitize=float-divide-by-zero -fsanitize=vptr
--       CFLAGS += -fsanitize=float-cast-overflow -fsanitize=object-size
--       #CFLAGS += -fcheck-pointer-bounds -mmpx
-+       CXXFLAGS += -fsanitize=bounds -fsanitize=float-divide-by-zero -fsanitize=vptr
-+       CXXFLAGS += -fsanitize=float-cast-overflow -fsanitize=object-size
-+       #CXXFLAGS += -fcheck-pointer-bounds -mmpx
-      endif
--     CFLAGS += $(BASEFLAGS)
--     CFLAGS := -g -DDEBUG -D_DEBUG -DGDEBUG -fno-common -fstack-protector $(CFLAGS)
--     LDFLAGS := -g
-+     CXXFLAGS += $(BASEFLAGS)
-+     CXXFLAGS += -DDEBUG -D_DEBUG -DGDEBUG -fno-common -fstack-protector
-+     LDFLAGS ?= -g
-      #LIBS := -Wl,-Bstatic -lasan -lubsan -Wl,-Bdynamic -ldl $(LIBS)
-      LIBS := -lasan -lubsan -ldl $(LIBS)
-   else
-@@ -55,26 +56,26 @@
-     #   GMEMTRACE=1
-     #endif
-     #--- just plain debug build ---
--     CFLAGS = -g -DDEBUG -D_DEBUG -DGDEBUG $(BASEFLAGS)
--     LDFLAGS = -g
-+     CXXFLAGS += -DDEBUG -D_DEBUG -DGDEBUG $(BASEFLAGS)
-+     LDFLAGS += -g
-      LIBS = 
-   endif
- endif
- 
- %.o : %.c
--	${CC} ${CFLAGS} -c $< -o $@
-+	${CXX} ${CXXFLAGS} -c $< -o $@
- 
- %.o : %.cc
--	${CC} ${CFLAGS} -c $< -o $@
-+	${CXX} ${CXXFLAGS} -c $< -o $@
- 
- %.o : %.C
--	${CC} ${CFLAGS} -c $< -o $@
-+	${CXX} ${CXXFLAGS} -c $< -o $@
- 
- %.o : %.cpp
--	${CC} ${CFLAGS} -c $< -o $@
-+	${CXX} ${CXXFLAGS} -c $< -o $@
- 
- %.o : %.cxx
--	${CC} ${CFLAGS} -c $< -o $@
-+	${CXX} ${CXXFLAGS} -c $< -o $@
- 
- # C/C++ linker
- 
diff --git a/sci-biology/gffcompare/gffcompare-0.10.5.ebuild b/sci-biology/gffcompare/gffcompare-0.10.5.ebuild
deleted file mode 100644
index 0b842d240..000000000
--- a/sci-biology/gffcompare/gffcompare-0.10.5.ebuild
+++ /dev/null
@@ -1,31 +0,0 @@
-# Copyright 1999-2018 Gentoo Foundation
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=6
-
-DESCRIPTION="Compare, classify, merge, track, annotate GFF files"
-HOMEPAGE="http://ccb.jhu.edu/software/stringtie/gff.shtml
-	https://github.com/gpertea/gffcompare"
-SRC_URI="https://github.com/gpertea/${PN}/archive/v${PV}.tar.gz -> ${P}.tar.gz
-	https://github.com/gpertea/gclib/archive/v0.10.2.tar.gz -> gclib-0.10.2.tar.gz"
-
-LICENSE="MIT Artistic-2"
-SLOT="0"
-KEYWORDS="~amd64 ~x86"
-IUSE=""
-
-# this cannot just depend on sci-biology/gclib (headers), the code inside
-# gclib needs to be compiled and objects get included inside gffcompare
-DEPEND=""
-RDEPEND="${DEPEND}"
-
-PATCHES=( "${FILESDIR}"/Makefile.patch )
-
-src_compile(){
-	GCLIB=../gclib-0.10.2 emake
-}
-
-src_install(){
-	dobin gffcompare
-	dodoc README.md
-}
diff --git a/sci-biology/gffcompare/gffcompare-0.12.2.ebuild b/sci-biology/gffcompare/gffcompare-0.12.2.ebuild
new file mode 100644
index 000000000..af8e58c00
--- /dev/null
+++ b/sci-biology/gffcompare/gffcompare-0.12.2.ebuild
@@ -0,0 +1,21 @@
+# Copyright 1999-2021 Gentoo Authors
+# Distributed under the terms of the GNU General Public License v2
+
+EAPI=7
+
+DESCRIPTION="Compare, classify, merge, track, annotate GFF files"
+HOMEPAGE="http://ccb.jhu.edu/software/stringtie/gff.shtml
+	https://github.com/gpertea/gffcompare"
+SRC_URI="https://github.com/gpertea/gffcompare/releases/download/v${PV}/${P}.tar.gz"
+
+LICENSE="MIT Artistic-2"
+SLOT="0"
+KEYWORDS="~amd64 ~x86"
+
+DEPEND=""
+RDEPEND="${DEPEND}"
+
+src_install(){
+	dobin gffcompare
+	dodoc README.md
+}
diff --git a/sci-biology/gffread/Manifest b/sci-biology/gffread/Manifest
index d27690e24..999049e10 100644
--- a/sci-biology/gffread/Manifest
+++ b/sci-biology/gffread/Manifest
@@ -1,2 +1,2 @@
-DIST gclib-0.10.2.tar.gz 169370 BLAKE2B 21f50ce5c6b4f5e703243ce96ee983a20c37a4bedcc11aa5ac8c29eed659b88a040d36172fcabe0ac9da5f85cb7593181ada538c5a9f16e6efb0ecdb1987d501 SHA512 6ba8ce4abdc373c17e81e65b280d09f4452e19f3207a8d8be44f3c98a611ea589393a4d6c9d4acb8c465c3703d3f9bafca432a0b58568ea1927c25da9654f87e
-DIST gffread-0.9.12.tar.gz 27010 BLAKE2B 5da01f7d595b42277cc372326bdb4d538d7edeee8e2c80b62cfc0691d43594feda4404e6b05884d42b07396924b16c3f45436919c06023a07e11ef04c7f854c8 SHA512 5107ccfd14455970ea555d25288c8097fc562c33bc9c477500e43b0beb2163db44552d6b61dc499902806495cac576d557237653c58cf8410ace062c180181e8
+DIST gclib-0.12.7.tar.gz 259314 BLAKE2B 9e3d4b535a7bbeb4b03360801a4ce4c81055d49525857cce306009e18f78709808732e24cb3dc3efa050b293c863d6f045f5fc3a5d3c14f3c6a2566acbc1f6f4 SHA512 2ff7be21f8ae002afdd7e34b6200e308f87077331c174dbea863972a01a0b6758062accda431bb73ef45ae91db44871f9eb0f5ae4bd564252599236282e57f90
+DIST gffread-0.12.7.tar.gz 403734 BLAKE2B e925518fad8e1047d7e4a785338e51cd0317d8e26545587024ee2617a2e432426e80172c62b9d4103ec9da0d33d758105d8803cc82b4f74cf5dba07009aab477 SHA512 33a2308caecd3e891788a76c6b68b79569afd8d0d749bf57a8c528550d26f7a7b61b8ca77e8a37e05a7dfaeac600470c255a22314ea94f63e2b2cac45674f97b
diff --git a/sci-biology/gffread/files/Makefile.patch b/sci-biology/gffread/files/Makefile.patch
deleted file mode 100644
index 35e6b088e..000000000
--- a/sci-biology/gffread/files/Makefile.patch
+++ /dev/null
@@ -1,39 +0,0 @@
---- gffread-0.9.12/Makefile	2018-06-26 09:52:26.024747027 +0200
-+++ gffread-0.9.12/Makefile	2018-06-26 09:52:41.845177021 +0200
-@@ -1,4 +1,4 @@
--GCLDIR := ../gclib
-+GCLDIR := ../gclib-0.10.2
- SEARCHDIRS := -I. -I${GCLDIR}
- 
- SYSTYPE :=     $(shell uname)
-@@ -10,7 +10,7 @@
-     MARCH = 
- endif    
- 
--CC      := g++
-+CXX      ?= g++
- 
- BASEFLAGS  := -Wall -Wextra ${SEARCHDIRS} $(MARCH) -D_FILE_OFFSET_BITS=64 \
- -D_LARGEFILE_SOURCE -D_REENTRANT -fno-strict-aliasing -fno-exceptions -fno-rtti
-@@ -26,15 +26,17 @@
- GCC45OPTMAIN :=
- 
- ifeq ($(findstring release,$(MAKECMDGOALS)),release)
--  CFLAGS := -O2 -DNDEBUG $(BASEFLAGS)
-+  CXXFLAGS ?= -O2
-+  CXXFLAGS += -DNDEBUG $(BASEFLAGS)
-   LDFLAGS :=
- else
--  CFLAGS := -g -DDEBUG $(BASEFLAGS)
--  LDFLAGS := -g
-+  CXXFLAGS ?= -g
-+  CXXFLAGS += -DDEBUG $(BASEFLAGS)
-+  LDFLAGS ?= -g
- endif
- 
- %.o : %.cpp
--	${CC} ${CFLAGS} -c $< -o $@
-+	${CXX} ${CXXFLAGS} -c $< -o $@
- 
- # C/C++ linker
- 
diff --git a/sci-biology/gffread/gffread-0.12.7.ebuild b/sci-biology/gffread/gffread-0.12.7.ebuild
new file mode 100644
index 000000000..9758ccef0
--- /dev/null
+++ b/sci-biology/gffread/gffread-0.12.7.ebuild
@@ -0,0 +1,29 @@
+# Copyright 1999-2022 Gentoo Authors
+# Distributed under the terms of the GNU General Public License v2
+
+EAPI=8
+
+DESCRIPTION="GFF/GTF utility providing format conversions, filter/extract regions from FASTA"
+HOMEPAGE="http://ccb.jhu.edu/software/stringtie/gff.shtml
+	https://github.com/gpertea/gffread"
+SRC_URI="https://github.com/gpertea/${PN}/archive/v${PV}.tar.gz -> ${P}.tar.gz
+	https://github.com/gpertea/gclib/archive/v${PV}.tar.gz -> gclib-${PV}.tar.gz"
+
+LICENSE="MIT"
+SLOT="0"
+KEYWORDS="~amd64 ~x86"
+
+src_prepare(){
+	default
+	sed -e "s/-g -O3/${CXXFLAGS}/" -i Makefile || die
+	cd .. && ln -s gclib-"${PV}" gclib || die
+}
+
+src_compile(){
+	emake release
+}
+
+src_install(){
+	dobin gffread
+	einstalldocs
+}
diff --git a/sci-biology/gffread/gffread-0.9.12.ebuild b/sci-biology/gffread/gffread-0.9.12.ebuild
deleted file mode 100644
index fc60b9a81..000000000
--- a/sci-biology/gffread/gffread-0.9.12.ebuild
+++ /dev/null
@@ -1,20 +0,0 @@
-# Copyright 1999-2018 Gentoo Foundation
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=6
-
-DESCRIPTION="GFF/GTF utility providing format conversions, filter/extract regions from FASTA"
-HOMEPAGE="http://ccb.jhu.edu/software/stringtie/gff.shtml
-	https://github.com/gpertea/gffread"
-SRC_URI="https://github.com/gpertea/${PN}/archive/v${PV}.tar.gz -> ${P}.tar.gz
-	https://github.com/gpertea/gclib/archive/v0.10.2.tar.gz -> gclib-0.10.2.tar.gz"
-
-LICENSE="MIT"
-SLOT="0"
-KEYWORDS=""
-IUSE=""
-
-DEPEND=""
-RDEPEND="${DEPEND}"
-
-PATCHES=( "${FILESDIR}"/Makefile.patch )
diff --git a/sci-biology/gfftools/Manifest b/sci-biology/gfftools/Manifest
deleted file mode 100644
index 2a3ab712a..000000000
--- a/sci-biology/gfftools/Manifest
+++ /dev/null
@@ -1,2 +0,0 @@
-DIST MANUAL_GFF2PS_v0.96.ps.gz 139407 BLAKE2B 0d0ddb96b56ef767392041cd52d08f74423ea74f89dc9ce09bc28cce1a4d8fb51835444bb9baec9f71f62b4f91ede4bbd73c6b86a335fce7220e76b130dddfe8 SHA512 3f11586b481b90f874898f5f18e6220a2cf7e6a9917455a3b5d6db3601e52604e139e5abdf2c7e9e14a87ae79cd47b81b7e46b42805a017b8586b280777b84bb
-DIST gff2ps_v0.98d.gz 45329 BLAKE2B 6219c9920dd91bec38169d0eed3cb28b5f769accb29593cafea3f7c88a2ed7be2f3eb9291c03c749ec19aa03e2c213905c0d0c03f5a37306c3018c8b41371cc6 SHA512 a1c219ac14afb94c6da331179e306197805b2930e5291b20509ea1a979c4c645af8aade4a030f2ce364cba561e90fb5161bfb3ac3259503dc07937ce924033d4
diff --git a/sci-biology/gfftools/gfftools-0.98d.ebuild b/sci-biology/gfftools/gfftools-0.98d.ebuild
deleted file mode 100644
index 7b5d1972b..000000000
--- a/sci-biology/gfftools/gfftools-0.98d.ebuild
+++ /dev/null
@@ -1,25 +0,0 @@
-# Copyright 1999-2015 Gentoo Foundation
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=5
-
-DESCRIPTION="gff2ps can render features annotated in GFF file format into PostScript figures"
-HOMEPAGE="http://genome.crg.es/software/gfftools/GFF2PS.html"
-SRC_URI="ftp://genome.imim.es/pub/gff_tools/gff2ps/gff2ps_v0.98d.gz
-	http://genome.imim.es/software/gfftools/gff2ps_docs/manual/MANUAL_GFF2PS_v0.96.ps.gz"
-
-LICENSE="GPL-2"
-SLOT="0"
-KEYWORDS="~amd64"
-IUSE=""
-
-DEPEND=""
-RDEPEND="${DEPEND}"
-
-S="${WORKDIR}"
-
-src_install(){
-	mv gff2ps_v0.98d gff2ps
-	dobin gff2ps
-	dodoc MANUAL_GFF2PS_v0.96.ps
-}
diff --git a/sci-biology/gfftools/metadata.xml b/sci-biology/gfftools/metadata.xml
deleted file mode 100644
index 138cb7705..000000000
--- a/sci-biology/gfftools/metadata.xml
+++ /dev/null
@@ -1,12 +0,0 @@
-<?xml version="1.0" encoding="UTF-8"?>
-<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
-<pkgmetadata>
-	<maintainer type="person">
-		<email>mmokrejs@fold.natur.cuni.cz</email>
-		<name>Martin Mokrejs</name>
-	</maintainer>
-	<maintainer type="project">
-		<email>sci-biology@gentoo.org</email>
-		<name>Gentoo Biology Project</name>
-	</maintainer>
-</pkgmetadata>
diff --git a/sci-biology/gffutils/Manifest b/sci-biology/gffutils/Manifest
index dbac0ec54..e8b006cbf 100644
--- a/sci-biology/gffutils/Manifest
+++ b/sci-biology/gffutils/Manifest
@@ -1 +1 @@
-DIST gffutils-0.8.7.1.tar.gz 1541112 BLAKE2B 65676cf0b910ad0fee478315409dba808a13d11922d0ab254694939ebd01f10b62c2237ae517d941999c6cf9bcb08d903bde8b9055bcf7a67116e14439ec4cca SHA512 4739dd402963d402f34a5e3da9cca7ba9586dcbbe62efbad89bf85c5dbb0feff0e260eea20563340911756e6817289c1556c261ef973a61f4e66e50efdfc8aa8
+DIST gffutils-0.11.1.tar.gz 1646787 BLAKE2B 96e573cf366844c8a348aff062362aeaea1a46360c74ae75a2d8d730d37cd69f0e6c658d1d0f348ca8f8e8c49d9a7c923c52619341e8d2dabd92a329fb43b677 SHA512 1844e9d7626a800549def2ba09b4d97e60c8a1a0fce2da60d7841cf4c4347da50aea850e8c1a67b07de08d4e6cf737b0d5c2bf8eb5fc87900427866282e82bdb
diff --git a/sci-biology/gffutils/gffutils-0.11.1.ebuild b/sci-biology/gffutils/gffutils-0.11.1.ebuild
new file mode 100644
index 000000000..8ee8fd4b5
--- /dev/null
+++ b/sci-biology/gffutils/gffutils-0.11.1.ebuild
@@ -0,0 +1,42 @@
+# Copyright 1999-2023 Gentoo Authors
+# Distributed under the terms of the GNU General Public License v2
+
+EAPI=8
+
+PYTHON_COMPAT=( python3_{10..11} )
+
+inherit distutils-r1
+
+DESCRIPTION="GFF and GTF file manipulation and interconversion"
+HOMEPAGE="https://gffutils.readthedocs.io/en/latest/"
+SRC_URI="https://github.com/daler/gffutils/archive/v${PV}.tar.gz -> ${P}.tar.gz"
+
+LICENSE="MIT"
+SLOT="0"
+KEYWORDS="~amd64 ~x86"
+IUSE="test"
+# Nose tests no longer supported, migration on next release
+#RESTRICT="test"
+RESTRICT="!test? ( test )"
+
+RDEPEND="
+	dev-python/simplejson[${PYTHON_USEDEP}]
+	dev-python/argh[${PYTHON_USEDEP}]
+	dev-python/argcomplete[${PYTHON_USEDEP}]
+	sci-biology/biopython[${PYTHON_USEDEP}]
+	sci-biology/pybedtools[${PYTHON_USEDEP}]
+	sci-biology/pyfaidx[${PYTHON_USEDEP}]
+"
+DEPEND="${RDEPEND}"
+
+python_prepare_all() {
+	if use test; then
+		sed -i -e "s:/tmp/gffutils-test:${T}:g" gffutils/test/test.py || die
+	fi
+	distutils-r1_python_prepare_all
+}
+
+python_test() {
+	distutils_install_for_testing
+	nosetests -v -x --with-doctest -a '!slow' || die
+}
diff --git a/sci-biology/gffutils/gffutils-0.8.7.1.ebuild b/sci-biology/gffutils/gffutils-0.8.7.1.ebuild
deleted file mode 100644
index 787a5668a..000000000
--- a/sci-biology/gffutils/gffutils-0.8.7.1.ebuild
+++ /dev/null
@@ -1,24 +0,0 @@
-# Copyright 1999-2017 Gentoo Foundation
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=5
-
-PYTHON_COMPAT=( python2_7 )
-
-inherit distutils-r1
-
-DESCRIPTION="GFF and GTF file manipulation and interconversion"
-HOMEPAGE="https://pythonhosted.org/gffutils/"
-SRC_URI="https://github.com/daler/gffutils/archive/v${PV}.tar.gz -> ${P}.tar.gz"
-
-LICENSE="MIT"
-SLOT="0"
-KEYWORDS="~amd64 ~x86 ~amd64-linux ~x86-linux"
-IUSE=""
-
-RDEPEND="
-	sci-biology/pyfaidx[${PYTHON_USEDEP}]
-	dev-python/simplejson[${PYTHON_USEDEP}]
-	dev-python/argh[${PYTHON_USEDEP}]
-	dev-python/argcomplete[${PYTHON_USEDEP}]"
-DEPEND="${RDEPEND}"
diff --git a/sci-biology/glean/glean-1.0.1.ebuild b/sci-biology/glean/glean-1.0.1.ebuild
index 48b4238f4..507f76900 100644
--- a/sci-biology/glean/glean-1.0.1.ebuild
+++ b/sci-biology/glean/glean-1.0.1.ebuild
@@ -1,14 +1,13 @@
-# Copyright 1999-2015 Gentoo Foundation
+# Copyright 1999-2021 Gentoo Authors
 # Distributed under the terms of the GNU General Public License v2
 
-EAPI=5
+EAPI=7
 
-PERL_EXPORT_PHASE_FUNCTIONS=no
-inherit perl-module eutils toolchain-funcs
+inherit perl-module
 
 DESCRIPTION="Merge various gene prediction into one (unsupervised learning system)"
-HOMEPAGE="http://sourceforge.net/projects/glean-gene"
-SRC_URI="http://downloads.sourceforge.net/project/glean-gene/GLEAN/glean-1-0-1/glean-1-0-1.tar.gz"
+HOMEPAGE="https://sourceforge.net/projects/glean-gene/"
+SRC_URI="https://downloads.sourceforge.net/project/glean-gene/GLEAN/glean-${PV//./-}/glean-${PV//./-}.tar.gz"
 
 LICENSE="Artistic"
 SLOT="0"
@@ -33,6 +32,5 @@ src_install(){
 	dobin bin/*
 	dodoc README
 	perl_set_version
-	insinto ${VENDOR_LIB}
-	doins -r lib/Glean
+	perl_domodule -r lib/Glean
 }
diff --git a/sci-biology/glean/metadata.xml b/sci-biology/glean/metadata.xml
index 0f267b755..26831499b 100644
--- a/sci-biology/glean/metadata.xml
+++ b/sci-biology/glean/metadata.xml
@@ -10,6 +10,6 @@
 		<name>Gentoo Biology Project</name>
 	</maintainer>
 	<upstream>
-		<remote-id type="sourceforge">downloads</remote-id>
+		<remote-id type="sourceforge">glean-gene</remote-id>
 	</upstream>
 </pkgmetadata>
diff --git a/sci-biology/gmap/Manifest b/sci-biology/gmap/Manifest
deleted file mode 100644
index cf02625ae..000000000
--- a/sci-biology/gmap/Manifest
+++ /dev/null
@@ -1 +0,0 @@
-DIST gmap-gsnap-2016-11-07.tar.gz 4541657 BLAKE2B f322aa78302dc7849b7ad3b51f2a76e1034f79d04648cd4a7bc9f8fab869d34243315a41164f2bb2ab63404fb3de6fd8b1bfe4de2e8b8239d2c4f25cdef3bc72 SHA512 3affb06417d654fb050b94006d123e3be9635b4e65a48346dd988a86b7db9d536853c6656b075f6fc06fbc8dd08692e662134b984d2f58b2f06504441d266f49
diff --git a/sci-biology/gmap/gmap-2016.11.07.ebuild b/sci-biology/gmap/gmap-2016.11.07.ebuild
deleted file mode 100644
index d04c40e6a..000000000
--- a/sci-biology/gmap/gmap-2016.11.07.ebuild
+++ /dev/null
@@ -1,22 +0,0 @@
-# Copyright 1999-2016 Gentoo Foundation
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=6
-
-inherit versionator
-
-MY_BASE_PV="$(replace_all_version_separators '-' $(get_version_component_range 1-3))"
-MY_PV="${MY_BASE_PV}"
-
-DESCRIPTION="DNA and splice-aware RNA/cDNA read aligners/mappers (gmap and gsnap)"
-HOMEPAGE="http://research-pub.gene.com/gmap/"
-SRC_URI="http://research-pub.gene.com/gmap/src/gmap-gsnap-${MY_PV}.tar.gz"
-
-LICENSE="gmap"
-SLOT="0"
-IUSE=""
-KEYWORDS="~amd64 ~x86"
-
-S="${WORKDIR}/gmap-${MY_BASE_PV}"
-
-# TODO: respect avx2
diff --git a/sci-biology/gmap/metadata.xml b/sci-biology/gmap/metadata.xml
deleted file mode 100644
index 8417d1580..000000000
--- a/sci-biology/gmap/metadata.xml
+++ /dev/null
@@ -1,8 +0,0 @@
-<?xml version="1.0" encoding="UTF-8"?>
-<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
-<pkgmetadata>
-	<maintainer type="project">
-		<email>sci-biology@gentoo.org</email>
-		<name>Gentoo Biology Project</name>
-	</maintainer>
-</pkgmetadata>
diff --git a/sci-biology/grabix/grabix-9999.ebuild b/sci-biology/grabix/grabix-9999.ebuild
index d32f4971b..db99ec960 100644
--- a/sci-biology/grabix/grabix-9999.ebuild
+++ b/sci-biology/grabix/grabix-9999.ebuild
@@ -1,7 +1,7 @@
-# Copyright 1999-2017 Gentoo Foundation
+# Copyright 1999-2021 Gentoo Authors
 # Distributed under the terms of the GNU General Public License v2
 
-EAPI=6
+EAPI=7
 
 inherit git-r3 toolchain-funcs
 
@@ -12,7 +12,6 @@ EGIT_REPO_URI="https://github.com/arq5x/grabix.git"
 LICENSE="MIT"
 SLOT="0"
 KEYWORDS=""
-IUSE=""
 
 DEPEND=""
 RDEPEND="${DEPEND}"
diff --git a/sci-biology/graf-bin/Manifest b/sci-biology/graf-bin/Manifest
index ab1a2df60..bb29de079 100644
--- a/sci-biology/graf-bin/Manifest
+++ b/sci-biology/graf-bin/Manifest
@@ -1 +1 @@
-DIST graf-bin-20171212.tar.gz 11295484 BLAKE2B 2529522104a94bafa050c36454eee383417f660c6245f2499da2ba73f6df82177748bfae652ef508e887a7b5f825ec595d3f2639c45099e8f46b4abb1e401c09 SHA512 0628014c6a343f79a6cf68b63cc50069ac502c2efed97841853ccc990f6f1ba91e7f7670016eb26b0d5b76ede08e1979637d236e80b79517391ef72359f00c1d
+DIST graf-bin-2.4.tar.gz 10526977 BLAKE2B 467b7d9e0a735c625121595ad4b3be37212d2b872d94ff7ac7c2af84b485dab6967d0738ca7ab9556b055f741a4f690dad324805b37df875e79d42aaa9d7270a SHA512 0e26ac12510454998672cfd5074ef5be691c943bc4e7f42524c80afeb8b17d9444f4addb0bab3521402ce9e64c94184b860a35b488192ecce16efdd5c53ca160
diff --git a/sci-biology/graf-bin/graf-bin-2.4.ebuild b/sci-biology/graf-bin/graf-bin-2.4.ebuild
new file mode 100644
index 000000000..8f73e8121
--- /dev/null
+++ b/sci-biology/graf-bin/graf-bin-2.4.ebuild
@@ -0,0 +1,31 @@
+# Copyright 1999-2021 Gentoo Authors
+# Distributed under the terms of the GNU General Public License v2
+
+EAPI=7
+
+inherit perl-module
+
+DESCRIPTION="Find closely related subjects using SNP genotype data, validate pedigree file"
+HOMEPAGE="https://www.ncbi.nlm.nih.gov/projects/gap/cgi-bin/Software.cgi"
+SRC_URI="https://www.ncbi.nlm.nih.gov/projects/gap/cgi-bin/GetZip.cgi?zip_name=GRAF_files.zip -> ${P}.tar.gz"
+
+LICENSE="public-domain"
+SLOT="0"
+KEYWORDS="~amd64"
+
+S="${WORKDIR}"
+
+src_prepare(){
+	default
+	sed -e 's#/usr/local/bin/perl#/usr/bin/env perl#' -i *.pl || die # there is not perl_fix_shebang
+}
+
+src_install(){
+	dobin graf graf_dups
+	perl_domodule *.pl
+}
+
+pkg_postinst(){
+	einfo "Probably you will use this program with sci-biology/plink and"
+	einfo "sci-biology/plinkseq outputs"
+}
diff --git a/sci-biology/graf-bin/graf-bin-20171212.ebuild b/sci-biology/graf-bin/graf-bin-20171212.ebuild
deleted file mode 100644
index 93d554892..000000000
--- a/sci-biology/graf-bin/graf-bin-20171212.ebuild
+++ /dev/null
@@ -1,37 +0,0 @@
-# Copyright 1999-2018 Gentoo Foundation
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=5
-
-inherit perl-module
-
-DESCRIPTION="Find closely related subjects using SNP genotype data, validate pedigree file"
-HOMEPAGE="http://www.ncbi.nlm.nih.gov/projects/gap/cgi-bin/Software.cgi"
-SRC_URI="http://www.ncbi.nlm.nih.gov/projects/gap/cgi-bin/GetZip.cgi?zip_name=GRAF_files.zip -> ${P}.tar.gz"
-# the .zip is indeed .tar.gz
-
-LICENSE="public-domain"
-SLOT="0"
-KEYWORDS="~amd64" # 64bit exe only
-IUSE=""
-
-DEPEND=""
-RDEPEND="${DEPEND}"
-
-S="${WORKDIR}"
-
-src_prepare(){
-	sed -e 's#/usr/local/bin/perl#/usr/bin/env perl#' -i *.pl || die # there is not perl_fix_shebang
-}
-
-src_install(){
-	dobin graf graf_dups *.pl
-	dodoc GRAF_ReadMe_*.docx GRAF-popDocumentation*.docx
-	insinto /usr/share/"${PN}"
-	doins *.txt *.bed *.bim *.fam
-}
-
-pkg_postinst(){
-	einfo "Probably you will use this program with sci-biology/plink and"
-	einfo "sci-biology/plinkseq outputs"
-}
diff --git a/sci-biology/grappa/files/grappa-2.0-inline.patch b/sci-biology/grappa/files/grappa-2.0-inline.patch
new file mode 100644
index 000000000..a78f394e6
--- /dev/null
+++ b/sci-biology/grappa/files/grappa-2.0-inline.patch
@@ -0,0 +1,18 @@
+--- a/greedy_median.c
++++ b/greedy_median.c
+@@ -7,7 +7,6 @@
+    chosen, including the original */
+ 
+ /* i->succ1[i] is the chosen adjacency */
+-INLINE int
+ finish1 ( int i, int *count, int *degree, int *succ1, int *succ2,
+           int *pred1, int *pred2, int *tour, int *otherEnd, int num_genes )
+ {
+@@ -82,7 +81,6 @@ finish1 ( int i, int *count, int *degree, int *succ1, int *succ2,
+ 
+ 
+ /* i->succ2[i] is the chosen adjacency */
+-INLINE int
+ finish2 ( int i, int *count, int *degree, int *succ1, int *succ2,
+           int *pred1, int *pred2, int *tour, int *otherEnd, int num_genes )
+ {
diff --git a/sci-biology/grappa/grappa-2.0.ebuild b/sci-biology/grappa/grappa-2.0.ebuild
index a60e024a7..df0392717 100644
--- a/sci-biology/grappa/grappa-2.0.ebuild
+++ b/sci-biology/grappa/grappa-2.0.ebuild
@@ -1,13 +1,15 @@
-# Copyright 1999-2015 Gentoo Foundation
+# Copyright 1999-2021 Gentoo Authors
 # Distributed under the terms of the GNU General Public License v2
 
-EAPI=5
+EAPI=7
+
+inherit flag-o-matic
 
 MY_P="GRAPPA20"
 
 DESCRIPTION="Genome Rearrangements Analysis under Parsimony and other Phylogenetic Algorithms"
-HOMEPAGE="http://www.cs.unm.edu/~moret/GRAPPA/"
-SRC_URI="http://www.cs.unm.edu/~moret/GRAPPA/${MY_P}.tar.gz"
+HOMEPAGE="https://www.cs.unm.edu/~moret/GRAPPA/"
+SRC_URI="https://www.cs.unm.edu/~moret/GRAPPA/${MY_P}.tar.gz"
 
 LICENSE="GPL-2"
 SLOT="0"
@@ -15,10 +17,18 @@ KEYWORDS="~amd64 ~x86"
 
 S="${WORKDIR}/${MY_P}"
 
+PATCHES=( "${FILESDIR}"/${P}-inline.patch )
+
 src_prepare() {
+	default
 	sed -i -e '/CFLAGS := -mcpu/ d' -e 's/\(CFLAGS := -D${OS}\)/\1 ${CFLAGS}/' "${S}/Makefile" || die
 }
 
+src_configure() {
+	append-cflags -fcommon
+	default
+}
+
 src_install() {
 	dobin grappa
 	dosym grappa /usr/bin/invdist
diff --git a/sci-biology/grass/files/fix_Makefile_variablenames.patch b/sci-biology/grass/files/fix_Makefile_variablenames.patch
deleted file mode 100644
index 5eaf5da0f..000000000
--- a/sci-biology/grass/files/fix_Makefile_variablenames.patch
+++ /dev/null
@@ -1,267 +0,0 @@
-diff --git a/Common/Makefile b/Common/Makefile
-index bc63a66..f83906a 100644
---- a/Common/Makefile
-+++ b/Common/Makefile
-@@ -14,7 +14,7 @@ $(ODIR) :
- 	$(MD) -p $(ODIR)
- 
- $(ODIR)/%.o : %.cpp %.h | $(ODIR) 
--	$(CCC) -c $(CCCFLAGS) $(CCCINC) -o $@ $<
-+	$(CXX) -c $(CXXFLAGS) $(CXXINC) -o $@ $<
- 
- clean :
- 	$(RM) -rf $(ODIR)
-diff --git a/Makefile.config b/Makefile.config
-index c589af5..73b88d2 100644
---- a/Makefile.config
-+++ b/Makefile.config
-@@ -1,16 +1,23 @@
- # C++ compiler
--CCC = g++
-+CXX ?= g++
- # Compiler flags (you probably don't need to change anything here)
--CCCFLAGS = -O2 -m64 -std=gnu++0x -Wall
-+CXXFLAGS += -std=gnu++0x -Wall
-+#
-+BAMTOOLS_INC ?= -I/usr/include/bamtools
-+BAMTOOLS_LIB ?= -lbamtools
-+NCBI_TOOLS_PLUSPLUS_INC ?= -I/usr/include/ncbi-tools++
-+NCBI_TOOLS_PLUSPLUS_LIBS ?= -lxalgoalignnw -lxobjmgr -lgenome_collection -lseqset -lseqedit -lseq -lseqcode -lsequtil -lpub -lmedline -lbiblio -lgeneral -lxser -lxutil -lxncbi -ltables
-+CPLEX_INC ?= -I/data/bio/alexeygritsenk/apps/ILOG/cplex/include
-+CPLEX_LIB ?= -L/data/bio/alexeygritsenk/apps/ILOG/cplex/lib/x86-64_sles10_4.1/static_pic -lilocplex -lcplex -L/data/bio/alexeygritsenk/apps/ILOG/concert/lib/x86-64_sles10_4.1/static_pic -lconcert
- # include directory
--CCCINC = -I../Common/ -I/usr/include/bamtools
-+CXXINC = -I../Common/ $(BAMTOOLS_INC)
- # library directory and libraries
--CCCLIB = -lbamtools
-+CXXLIB = $(BAMTOOLS_LIB)
- 
- # Extra flags. Used for compiling scaffoldOptimizer (it uses the NCBI C++ Toolkit and CPLEX API)
- CCEFLAGS = -fPIC -fexceptions -fopenmp -DNDEBUG -DIL_STD
--CCEINC = -I/data/bio/alexeygritsenk/apps/ILOG/cplex/include -I/data/bio/alexeygritsenk/apps/ILOG/concert/include -I/usr/include/ncbi-tools++
--CCELIB = -lxalgoalignnw -lxobjmgr -lgenome_collection -lseqset -lseqedit -lseq -lseqcode -lsequtil -lpub -lmedline -lbiblio -lgeneral -lxser -lxutil -lxncbi -ltables -L/data/bio/alexeygritsenk/apps/ILOG/cplex/lib/x86-64_sles10_4.1/static_pic -lilocplex -lcplex -L/data/bio/alexeygritsenk/apps/ILOG/concert/lib/x86-64_sles10_4.1/static_pic -lconcert -lm -pthread
-+CCEINC = $(CPLEX_INC) -I/data/bio/alexeygritsenk/apps/ILOG/concert/include $(NCBI_TOOLS_PLUSPLUS_INC)
-+CCELIB = $(NCBI_TOOLS_PLUSPLUS_LIBS) $(CPLEX_LIB) -lm -pthread
- 
- # Do not change anything below unless (you think) you know what you're doing.
- MAKE = make
-diff --git a/breakpointCounter/Makefile b/breakpointCounter/Makefile
-index f042f5d..879528f 100644
---- a/breakpointCounter/Makefile
-+++ b/breakpointCounter/Makefile
-@@ -13,7 +13,7 @@ _COBJ = $(patsubst %,$(CDIR)/$(ODIR)/%,$(COBJ))
- main : Common $(BDIR)/$(BNAME)
- 
- $(BDIR)/$(BNAME) : $(_OBJ) | $(BDIR)
--	$(CCC) $(CCCFLAGS) $(CCCINC) -o $(BDIR)/$(BNAME) $(_OBJ) $(_COBJ) $(CCCLIB)
-+	$(CXX) $(CXXFLAGS) $(CXXINC) -o $(BDIR)/$(BNAME) $(_OBJ) $(_COBJ) $(CXXLIB)
- 
- dirs : | $(ODIR) $(BDIR)
- 
-@@ -27,7 +27,7 @@ Common :
- 	$(MAKE) -C $(CDIR) $(_COBJ)
- 
- $(ODIR)/%.o : %.cpp | $(ODIR)
--	$(CCC) -c $(CCCFLAGS) $(CCCINC) -o $@ $<
-+	$(CXX) -c $(CXXFLAGS) $(CXXINC) -o $@ $<
- 
- clean :
- 	rm -f $(BDIR)/$(BNAME)
-diff --git a/coverageUtil/Makefile b/coverageUtil/Makefile
-index c9768ce..b81b1f9 100644
---- a/coverageUtil/Makefile
-+++ b/coverageUtil/Makefile
-@@ -13,7 +13,7 @@ _COBJ = $(patsubst %,$(CDIR)/$(ODIR)/%,$(COBJ))
- main : Common $(BDIR)/$(BNAME)
- 
- $(BDIR)/$(BNAME) : $(_OBJ) | $(BDIR)
--	$(CCC) $(CCCFLAGS) $(CCCINC) -o $(BDIR)/$(BNAME) $(_OBJ) $(_COBJ) $(CCCLIB)
-+	$(CXX) $(CXXFLAGS) $(CXXINC) -o $(BDIR)/$(BNAME) $(_OBJ) $(_COBJ) $(CXXLIB)
- 
- dirs : | $(ODIR) $(BDIR)
- 
-@@ -27,7 +27,7 @@ Common :
- 	$(MAKE) -C $(CDIR) $(_COBJ)
- 
- $(ODIR)/%.o : %.cpp | $(ODIR)
--	$(CCC) -c $(CCCFLAGS) $(CCCINC) -o $@ $<
-+	$(CXX) -c $(CXXFLAGS) $(CXXINC) -o $@ $<
- 
- clean :
- 	rm -f $(BDIR)/$(BNAME)
-diff --git a/dataFilter/Makefile b/dataFilter/Makefile
-index 86885a0..aac1281 100644
---- a/dataFilter/Makefile
-+++ b/dataFilter/Makefile
-@@ -13,7 +13,7 @@ _COBJ = $(patsubst %,$(CDIR)/$(ODIR)/%,$(COBJ))
- main : Common $(BDIR)/$(BNAME)
- 
- $(BDIR)/$(BNAME) : $(_OBJ) | $(BDIR)
--	$(CCC) $(CCCFLAGS) $(CCCINC) -o $(BDIR)/$(BNAME) $(_OBJ) $(_COBJ) $(CCCLIB)
-+	$(CXX) $(CXXFLAGS) $(CXXINC) -o $(BDIR)/$(BNAME) $(_OBJ) $(_COBJ) $(CXXLIB)
- 
- dirs : | $(ODIR) $(BDIR)
- 
-@@ -27,7 +27,7 @@ Common :
- 	$(MAKE) -C $(CDIR) $(_COBJ)
- 
- $(ODIR)/%.o : %.cpp | $(ODIR)
--	$(CCC) -c $(CCCFLAGS) $(CCCINC) -o $@ $<
-+	$(CXX) -c $(CXXFLAGS) $(CXXINC) -o $@ $<
- 
- clean :
- 	rm -f $(BDIR)/$(BNAME)
-diff --git a/dataLinker/Makefile b/dataLinker/Makefile
-index bb22310..8846d09 100644
---- a/dataLinker/Makefile
-+++ b/dataLinker/Makefile
-@@ -13,7 +13,7 @@ _COBJ = $(patsubst %,$(CDIR)/$(ODIR)/%,$(COBJ))
- main : Common $(BDIR)/$(BNAME)
- 
- $(BDIR)/$(BNAME) : $(_OBJ) | $(BDIR)
--	$(CCC) $(CCCFLAGS) $(CCCINC) -o $(BDIR)/$(BNAME) $(_OBJ) $(_COBJ) $(CCCLIB)
-+	$(CXX) $(CXXFLAGS) $(CXXINC) -o $(BDIR)/$(BNAME) $(_OBJ) $(_COBJ) $(CXXLIB)
- 
- dirs : | $(ODIR) $(BDIR)
- 
-@@ -27,7 +27,7 @@ Common :
- 	$(MAKE) -C $(CDIR) $(_COBJ)
- 
- $(ODIR)/%.o : %.cpp | $(ODIR)
--	$(CCC) -c $(CCCFLAGS) $(CCCINC) -o $@ $<
-+	$(CXX) -c $(CXXFLAGS) $(CXXINC) -o $@ $<
- 
- clean :
- 	rm -f $(BDIR)/$(BNAME)
-diff --git a/dataSelector/Makefile b/dataSelector/Makefile
-index 79be6fc..54e45c6 100644
---- a/dataSelector/Makefile
-+++ b/dataSelector/Makefile
-@@ -13,7 +13,7 @@ _COBJ = $(patsubst %,$(CDIR)/$(ODIR)/%,$(COBJ))
- main : Common $(BDIR)/$(BNAME)
- 
- $(BDIR)/$(BNAME) : $(_OBJ) | $(BDIR)
--	$(CCC) $(CCCFLAGS) $(CCCINC) -o $(BDIR)/$(BNAME) $(_OBJ) $(_COBJ) $(CCCLIB)
-+	$(CXX) $(CXXFLAGS) $(CXXINC) -o $(BDIR)/$(BNAME) $(_OBJ) $(_COBJ) $(CXXLIB)
- 
- dirs : | $(ODIR) $(BDIR)
- 
-@@ -27,7 +27,7 @@ Common :
- 	$(MAKE) -C $(CDIR) $(_COBJ)
- 
- $(ODIR)/%.o : %.cpp | $(ODIR)
--	$(CCC) -c $(CCCFLAGS) $(CCCINC) -o $@ $<
-+	$(CXX) -c $(CXXFLAGS) $(CXXINC) -o $@ $<
- 
- clean :
- 	rm -f $(BDIR)/$(BNAME)
-diff --git a/dataSimulator/Makefile b/dataSimulator/Makefile
-index 4151efc..a8d4cb6 100644
---- a/dataSimulator/Makefile
-+++ b/dataSimulator/Makefile
-@@ -13,7 +13,7 @@ _COBJ = $(patsubst %,$(CDIR)/$(ODIR)/%,$(COBJ))
- main : Common $(BDIR)/$(BNAME)
- 
- $(BDIR)/$(BNAME) : $(_OBJ) | $(BDIR)
--	$(CCC) $(CCCFLAGS) $(CCCINC) -o $(BDIR)/$(BNAME) $(_OBJ) $(_COBJ) $(CCCLIB)
-+	$(CXX) $(CXXFLAGS) $(CXXINC) -o $(BDIR)/$(BNAME) $(_OBJ) $(_COBJ) $(CXXLIB)
- 
- dirs : | $(ODIR) $(BDIR)
- 
-@@ -27,7 +27,7 @@ Common :
- 	$(MAKE) -C $(CDIR) $(_COBJ)
- 
- $(ODIR)/%.o : %.cpp | $(ODIR)
--	$(CCC) -c $(CCCFLAGS) $(CCCINC) -o $@ $<
-+	$(CXX) -c $(CXXFLAGS) $(CXXINC) -o $@ $<
- 
- clean :
- 	rm -f $(BDIR)/$(BNAME)
-diff --git a/kmer/Makefile b/kmer/Makefile
-index 733a007..04bf766 100644
---- a/kmer/Makefile
-+++ b/kmer/Makefile
-@@ -13,7 +13,7 @@ _COBJ = $(patsubst %,$(CDIR)/$(ODIR)/%,$(COBJ))
- main : Common $(BDIR)/$(BNAME)
- 
- $(BDIR)/$(BNAME) : $(_OBJ) | $(BDIR)
--	$(CCC) $(CCCFLAGS) $(CCCINC) -o $(BDIR)/$(BNAME) $(_OBJ) $(_COBJ) $(CCCLIB)
-+	$(CXX) $(CXXFLAGS) $(CXXINC) -o $(BDIR)/$(BNAME) $(_OBJ) $(_COBJ) $(CXXLIB)
- 
- dirs : | $(ODIR) $(BDIR)
- 
-@@ -27,7 +27,7 @@ Common :
- 	$(MAKE) -C $(CDIR) $(_COBJ)
- 
- $(ODIR)/%.o : %.cpp | $(ODIR)
--	$(CCC) -c $(CCCFLAGS) $(CCCINC) -o $@ $<
-+	$(CXX) -c $(CXXFLAGS) $(CXXINC) -o $@ $<
- 
- clean :
- 	rm -f $(BDIR)/$(BNAME)
-diff --git a/readCleaner/Makefile b/readCleaner/Makefile
-index d011432..b17c334 100644
---- a/readCleaner/Makefile
-+++ b/readCleaner/Makefile
-@@ -13,7 +13,7 @@ _COBJ = $(patsubst %,$(CDIR)/$(ODIR)/%,$(COBJ))
- main : Common $(BDIR)/$(BNAME)
- 
- $(BDIR)/$(BNAME) : $(_OBJ) | $(BDIR)
--	$(CCC) $(CCCFLAGS) $(CCCINC) -o $(BDIR)/$(BNAME) $(_OBJ) $(_COBJ) $(CCCLIB)
-+	$(CXX) $(CXXFLAGS) $(CXXINC) -o $(BDIR)/$(BNAME) $(_OBJ) $(_COBJ) $(CXXLIB)
- 
- dirs : | $(ODIR) $(BDIR)
- 
-@@ -27,7 +27,7 @@ Common :
- 	$(MAKE) -C $(CDIR) $(_COBJ)
- 
- $(ODIR)/%.o : %.cpp | $(ODIR)
--	$(CCC) -c $(CCCFLAGS) $(CCCINC) -o $@ $<
-+	$(CXX) -c $(CXXFLAGS) $(CXXINC) -o $@ $<
- 
- clean :
- 	rm -f $(BDIR)/$(BNAME)
-diff --git a/readDiff/Makefile b/readDiff/Makefile
-index 2d703c0..f1b184e 100644
---- a/readDiff/Makefile
-+++ b/readDiff/Makefile
-@@ -13,7 +13,7 @@ _COBJ = $(patsubst %,$(CDIR)/$(ODIR)/%,$(COBJ))
- main : Common $(BDIR)/$(BNAME)
- 
- $(BDIR)/$(BNAME) : $(_OBJ) | $(BDIR)
--	$(CCC) $(CCCFLAGS) $(CCCINC) -o $(BDIR)/$(BNAME) $(_OBJ) $(_COBJ) $(CCCLIB)
-+	$(CXX) $(CXXFLAGS) $(CXXINC) -o $(BDIR)/$(BNAME) $(_OBJ) $(_COBJ) $(CXXLIB)
- 
- dirs : | $(ODIR) $(BDIR)
- 
-@@ -27,7 +27,7 @@ Common :
- 	$(MAKE) -C $(CDIR) $(_COBJ)
- 
- $(ODIR)/%.o : %.cpp | $(ODIR)
--	$(CCC) -c $(CCCFLAGS) $(CCCINC) -o $@ $<
-+	$(CXX) -c $(CXXFLAGS) $(CXXINC) -o $@ $<
- 
- clean :
- 	rm -f $(BDIR)/$(BNAME)
-diff --git a/scaffoldOptimizer/Makefile b/scaffoldOptimizer/Makefile
-index 635cdd4..244c5ff 100644
---- a/scaffoldOptimizer/Makefile
-+++ b/scaffoldOptimizer/Makefile
-@@ -13,7 +13,7 @@ _COBJ = $(patsubst %,$(CDIR)/$(ODIR)/%,$(COBJ))
- main : Common $(BDIR)/$(BNAME)
- 
- $(BDIR)/$(BNAME) : $(_OBJ) | $(BDIR)
--	$(CCC) $(CCCFLAGS) $(CCEFLAGS) $(CCCINC) $(CCEINC) -o $(BDIR)/$(BNAME) $(_OBJ) $(_COBJ) $(CCCLIB) $(CCELIB)
-+	$(CXX) $(CXXFLAGS) $(CCEFLAGS) $(CXXINC) $(CCEINC) -o $(BDIR)/$(BNAME) $(_OBJ) $(_COBJ) $(CXXLIB) $(CCELIB)
- 
- dirs : | $(ODIR) $(BDIR)
- 
-@@ -27,7 +27,7 @@ Common :
- 	$(MAKE) -C $(CDIR) $(_COBJ)
- 
- $(ODIR)/%.o : %.cpp | $(ODIR)
--	$(CCC) -c $(CCCFLAGS) $(CCEFLAGS) $(CCCINC) $(CCEINC) -o $@ $<
-+	$(CXX) -c $(CXXFLAGS) $(CCEFLAGS) $(CXXINC) $(CCEINC) -o $@ $<
- 
- clean :
- 	rm -f $(BDIR)/$(BNAME)
diff --git a/sci-biology/grass/grass-9999.ebuild b/sci-biology/grass/grass-9999.ebuild
deleted file mode 100644
index 6d60c4427..000000000
--- a/sci-biology/grass/grass-9999.ebuild
+++ /dev/null
@@ -1,41 +0,0 @@
-# Copyright 1999-2016 Gentoo Foundation
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=5
-
-inherit git-r3 eutils
-
-DESCRIPTION="Scaffold next-generation sequencing assemblies"
-HOMEPAGE="https://github.com/AlexeyG/GRASS"
-#SRC_URI="https://github.com/AlexeyG/GRASS/archive/master.zip -> grass-20130628.zip
-#	https://tud-scaffolding.googlecode.com/files/GRASS%20manual.pdf -> grass_manual.pdf"
-EGIT_REPO_URI="https://github.com/AlexeyG/GRASS.git"
-
-LICENSE="GPL-3"
-SLOT="0"
-KEYWORDS=""
-IUSE=""
-
-# some IBM development CPLEX library?
-# ilcplex/ilocplex.h: No such file or directory
-# https://github.com/AlexeyG/GRASS/issues/6
-DEPEND="sci-biology/bamtools
-	sci-biology/ncbi-tools++
-	sys-cluster/openmpi"
-RDEPEND="${DEPEND}"
-
-src_prepare(){
-	epatch "${FILESDIR}"/fix_Makefile_variablenames.patch
-#	sed -e 's#/data/bio/alexeygritsenk/apps/include/ncbi-tools++#/usr/include/ncbi-tools++#' -i Makefile.config || die
-#	sed -e 's#/data/bio/alexeygritsenk/apps/include/#/usr/include/bamtools#' -i Makefile.config || die
-#	sed -e 's#/data/bio/alexeygritsenk/apps/lib#/usr/lib64#' -i Makefile.config || die
-}
-
-src_compile(){
-	emake all
-}
-
-src_install(){
-	newdoc manual/manual.pdf grass_manual.pdf
-	dobin bin/*
-}
diff --git a/sci-biology/grass/metadata.xml b/sci-biology/grass/metadata.xml
deleted file mode 100644
index b4153fae5..000000000
--- a/sci-biology/grass/metadata.xml
+++ /dev/null
@@ -1,15 +0,0 @@
-<?xml version="1.0" encoding="UTF-8"?>
-<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
-<pkgmetadata>
-	<maintainer type="person">
-		<email>mmokrejs@fold.natur.cuni.cz</email>
-		<name>Martin Mokrejs</name>
-	</maintainer>
-	<maintainer type="project">
-		<email>sci-biology@gentoo.org</email>
-		<name>Gentoo Biology Project</name>
-	</maintainer>
-	<upstream>
-		<remote-id type="github">AlexeyG/GRASS</remote-id>
-	</upstream>
-</pkgmetadata>
diff --git a/sci-biology/hexamer/hexamer-19990330.ebuild b/sci-biology/hexamer/hexamer-19990330.ebuild
index f8c94e98a..9124e22ad 100644
--- a/sci-biology/hexamer/hexamer-19990330.ebuild
+++ b/sci-biology/hexamer/hexamer-19990330.ebuild
@@ -1,18 +1,17 @@
-# Copyright 1999-2015 Gentoo Foundation
+# Copyright 1999-2021 Gentoo Authors
 # Distributed under the terms of the GNU General Public License v2
 
-EAPI=5
+EAPI=7
 
 inherit toolchain-funcs
 
 DESCRIPTION="Predict CDS using 6mers without deriving information from base composition"
 HOMEPAGE="http://www.sanger.ac.uk/resources/software"
-SRC_URI="ftp://ftp.sanger.ac.uk/pub/users/rd/hexamer.tar.gz -> hexamer-19990330.tar.gz"
+SRC_URI="ftp://ftp.sanger.ac.uk/pub/users/rd/${PN}.tar.gz -> ${P}.tar.gz"
 
 LICENSE="all-rights-reserved"
 SLOT="0"
 KEYWORDS="~amd64"
-IUSE=""
 
 DEPEND=""
 RDEPEND="${DEPEND}"
@@ -20,6 +19,7 @@ RDEPEND="${DEPEND}"
 S="${WORKDIR}"/hexamer
 
 src_prepare(){
+	default
 	sed -e "s#cc -g#$(tc-getCC) ${CFLAGS}#" -i Makefile || die
 }
 
diff --git a/sci-biology/hisat2/Manifest b/sci-biology/hisat2/Manifest
index 70929dffa..3d6bdba90 100644
--- a/sci-biology/hisat2/Manifest
+++ b/sci-biology/hisat2/Manifest
@@ -1 +1 @@
-DIST hisat2-2.0.5-source.zip 3914703 BLAKE2B 3da01db5ea2acef3d9c8afd14f8efc93ee6c71f68d97b06e4a20e5ab72a7d39babf8dba9e74488aa3fc8a7062a0554b356d555703d49496de71248027ff76a6c SHA512 a626ebf8bb2682bdd69ffde55d1f53c6926ef6172a2d852aadc7fb02c08ab7b1b25158e046a6e07acb4f406549c37a329e5354402eaa5e93612568c7c58b2559
+DIST hisat2-2.2.1.tar.gz 6761242 BLAKE2B 61d2bbab028b21715199a05a584375b5473898918d5e2c630b9eb5a8a044c593adccb3616d9fd84e003891bd1704b767f154c5b31c094006b1994f0737001fc3 SHA512 a5a688ad0ccfaf326b3ec6dc97206995306aa6f5b6e58223c2113adbca2745f1e8205b436fdf8e01f42da7a38718f9f3bf214b951fb5360d53247d99a0bdbf46
diff --git a/sci-biology/hisat2/files/hisat2-2.0.5-respect_CXXFLAGS.patch b/sci-biology/hisat2/files/hisat2-2.0.5-respect_CXXFLAGS.patch
deleted file mode 100644
index 26db123c8..000000000
--- a/sci-biology/hisat2/files/hisat2-2.0.5-respect_CXXFLAGS.patch
+++ /dev/null
@@ -1,53 +0,0 @@
---- hisat2-2.0.5/Makefile.ori	2017-03-01 11:35:36.430368298 +0100
-+++ hisat2-2.0.5/Makefile	2017-03-01 11:43:42.974034697 +0100
-@@ -23,9 +23,8 @@
- INC =
- GCC_PREFIX = $(shell dirname `which gcc`)
- GCC_SUFFIX =
--CC = $(GCC_PREFIX)/gcc$(GCC_SUFFIX)
--CPP = $(GCC_PREFIX)/g++$(GCC_SUFFIX)
--CXX = $(CPP)
-+CXX ?= $(GCC_PREFIX)/g++$(GCC_SUFFIX)
-+CXXFLAGS ?= "-O3"
- HEADERS = $(wildcard *.h)
- BOWTIE_MM = 1
- BOWTIE_SHARED_MEM = 0
-@@ -134,30 +133,30 @@
- VERSION = $(shell cat VERSION)
- 
- # Convert BITS=?? to a -m flag
--BITS=32
-+BITS?=32
- ifeq (x86_64,$(shell uname -m))
--BITS=64
-+BITS?=64
- endif
- # msys will always be 32 bit so look at the cpu arch instead.
- ifneq (,$(findstring AMD64,$(PROCESSOR_ARCHITEW6432)))
- 	ifeq (1,$(MINGW))
--		BITS=64
-+		BITS?=64
- 	endif
- endif
- BITS_FLAG =
- 
- ifeq (32,$(BITS))
--	BITS_FLAG = -m32
-+	BITS_FLAG ?= -m32
- endif
- 
- ifeq (64,$(BITS))
--	BITS_FLAG = -m64
-+	BITS_FLAG ?= -m64
- endif
--SSE_FLAG=-msse2
-+SSE_FLAG?=-msse2
- 
--DEBUG_FLAGS    = -O0 -g3 $(BIToS_FLAG) $(SSE_FLAG)
-+DEBUG_FLAGS    = -g3 -O0 $(CXXFLAGS) $(BIToS_FLAG) $(SSE_FLAG)
- DEBUG_DEFS     = -DCOMPILER_OPTIONS="\"$(DEBUG_FLAGS) $(EXTRA_FLAGS)\""
--RELEASE_FLAGS  = -O3 $(BITS_FLAG) $(SSE_FLAG) -funroll-loops -g3
-+RELEASE_FLAGS  = $(CXXFLAGS) $(BITS_FLAG) $(SSE_FLAG) -funroll-loops
- RELEASE_DEFS   = -DCOMPILER_OPTIONS="\"$(RELEASE_FLAGS) $(EXTRA_FLAGS)\""
- NOASSERT_FLAGS = -DNDEBUG
- FILE_FLAGS     = -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_GNU_SOURCE
diff --git a/sci-biology/hisat2/files/hisat2-2.2.1-respect_CXXFLAGS.patch b/sci-biology/hisat2/files/hisat2-2.2.1-respect_CXXFLAGS.patch
new file mode 100644
index 000000000..4ca550c66
--- /dev/null
+++ b/sci-biology/hisat2/files/hisat2-2.2.1-respect_CXXFLAGS.patch
@@ -0,0 +1,41 @@
+--- hisat2-2.2.1/Makefile.ori	2020-08-07 13:12:25.393396171 +0200
++++ hisat2-2.2.1/Makefile	2020-08-07 13:15:56.845080223 +0200
+@@ -152,30 +152,30 @@
+ VERSION = $(shell cat VERSION)
+ 
+ # Convert BITS=?? to a -m flag
+-BITS=32
++BITS?=32
+ ifeq (x86_64,$(shell uname -m))
+-BITS=64
++BITS?=64
+ endif
+ # msys will always be 32 bit so look at the cpu arch instead.
+ ifneq (,$(findstring AMD64,$(PROCESSOR_ARCHITEW6432)))
+ 	ifeq (1,$(MINGW))
+-		BITS=64
++		BITS?=64
+ 	endif
+ endif
+ BITS_FLAG =
+ 
+ ifeq (32,$(BITS))
+-	BITS_FLAG = -m32
++	BITS_FLAG ?= -m32
+ endif
+ 
+ ifeq (64,$(BITS))
+-	BITS_FLAG = -m64
++	BITS_FLAG ?= -m64
+ endif
+-SSE_FLAG=-msse2
++SSE_FLAG?=-msse2
+ 
+-DEBUG_FLAGS    = -O0 -g3 $(BITS_FLAG) $(SSE_FLAG)
++DEBUG_FLAGS    = -g3 -O0 $(CXXFLAGS) $(BITS_FLAG) $(SSE_FLAG)
+ DEBUG_DEFS     = -DCOMPILER_OPTIONS="\"$(DEBUG_FLAGS) $(EXTRA_FLAGS)\""
+-RELEASE_FLAGS  = -O3 $(BITS_FLAG) $(SSE_FLAG) -funroll-loops -g3
++RELEASE_FLAGS  = $(CXXFLAGS) $(BITS_FLAG) $(SSE_FLAG) -funroll-loops
+ RELEASE_DEFS   = -DCOMPILER_OPTIONS="\"$(RELEASE_FLAGS) $(EXTRA_FLAGS)\""
+ NOASSERT_FLAGS = -DNDEBUG
+ FILE_FLAGS     = -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_GNU_SOURCE
diff --git a/sci-biology/hisat2/hisat2-2.0.5.ebuild b/sci-biology/hisat2/hisat2-2.0.5.ebuild
deleted file mode 100644
index d200a57ac..000000000
--- a/sci-biology/hisat2/hisat2-2.0.5.ebuild
+++ /dev/null
@@ -1,54 +0,0 @@
-# Copyright 1999-2017 Gentoo Foundation
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=6
-
-PYTHON_COMPAT=( python2_7 )
-
-inherit python-r1
-
-DESCRIPTION="Align DNA reads to a population of genomes"
-HOMEPAGE="
-	https://ccb.jhu.edu/software/hisat2
-	https://github.com/infphilo/hisat2"
-SRC_URI="ftp://ftp.ccb.jhu.edu/pub/infphilo/hisat2/downloads/${P}-source.zip"
-
-LICENSE="GPL-3+"
-SLOT="0"
-KEYWORDS="~amd64 ~x86"
-IUSE="cpu_flags_x86_sse2"
-
-DEPEND="${PYTHON_DEPS}"
-RDEPEND="${DEPEND}"
-
-PATCHES=( "${FILESDIR}"/${P}-respect_CXXFLAGS.patch )
-
-# TODO: could depend on sci-biology/ncbi-tools++ or sra_sdk containing ncbi-vdb
-# For the support of SRA data access in HISAT2, please download and install the [NCBI-NGS] toolkit.
-# When running `make`, specify additional variables as follow.
-# `make USE_SRA=1 NCBI_NGS_DIR=/path/to/NCBI-NGS-directory NCBI_VDB_DIR=/path/to/NCBI-NGS-directory`,
-# where `NCBI_NGS_DIR` and `NCBI_VDB_DIR` will be used in Makefile for -I and -L compilation options.
-# For example, $(NCBI_NGS_DIR)/include and $(NCBI_NGS_DIR)/lib64 will be used.
-
-src_configure(){
-	if use cpu_flags_x86_sse2; then
-		SSE_FLAGS='-msse2'
-	fi
-	if [ "$ARCH" = "amd64" ] || [ "$ARCH" = "ia64" ] || [ "$ARCH" = "ppc64" ]; then
-		BITS='-m64'
-	else
-		BITS='-32'
-	fi
-}
-
-src_compile(){
-	emake SSE_FLAG="${SSE_FLAGS}" BITS="${BITS}"
-}
-
-src_install(){
-	dobin hisat2{,-build,-inspect,-build-s,-build-l,-align-s,-align-l,-inspect-s,-inspect-l}
-	python_foreach_impl python_doscript *.py
-	insinto /usr/share/"${PN}"/scripts
-	doins scripts/*.sh
-	dodoc MANUAL TUTORIAL
-}
diff --git a/sci-biology/hisat2/hisat2-2.2.1.ebuild b/sci-biology/hisat2/hisat2-2.2.1.ebuild
new file mode 100644
index 000000000..9a30d7aef
--- /dev/null
+++ b/sci-biology/hisat2/hisat2-2.2.1.ebuild
@@ -0,0 +1,56 @@
+# Copyright 1999-2023 Gentoo Authors
+# Distributed under the terms of the GNU General Public License v2
+
+EAPI=8
+
+PYTHON_COMPAT=( python3_{10..11} )
+
+inherit python-r1
+
+DESCRIPTION="Align DNA reads to a population of genomes"
+HOMEPAGE="
+	https://daehwankimlab.github.io/hisat2
+	https://github.com/DaehwanKimLab/hisat2"
+SRC_URI="https://github.com/DaehwanKimLab/hisat2/archive/v${PV}.tar.gz -> ${P}.tar.gz"
+
+LICENSE="GPL-3+"
+SLOT="0"
+KEYWORDS="~amd64 ~x86"
+
+IUSE="cpu_flags_x86_sse2"
+REQUIRED_USE="${PYTHON_REQUIRED_USE}"
+
+DEPEND="${PYTHON_DEPS}"
+RDEPEND="${DEPEND}"
+
+PATCHES=( "${FILESDIR}"/${P}-respect_CXXFLAGS.patch )
+
+# TODO: could depend on sci-biology/ncbi-tools++ or sra_sdk containing ncbi-vdb
+# For the support of SRA data access in HISAT2, please download and install the [NCBI-NGS] toolkit.
+# When running `make`, specify additional variables as follow.
+# `make USE_SRA=1 NCBI_NGS_DIR=/path/to/NCBI-NGS-directory NCBI_VDB_DIR=/path/to/NCBI-NGS-directory`,
+# where `NCBI_NGS_DIR` and `NCBI_VDB_DIR` will be used in Makefile for -I and -L compilation options.
+# For example, $(NCBI_NGS_DIR)/include and $(NCBI_NGS_DIR)/lib64 will be used.
+
+src_configure(){
+	if use cpu_flags_x86_sse2; then
+		SSE_FLAGS='-msse2'
+	fi
+	if [ "$ARCH" = "amd64" ] || [ "$ARCH" = "ia64" ] || [ "$ARCH" = "ppc64" ]; then
+		BITS='-m64'
+	else
+		BITS='-32'
+	fi
+}
+
+src_compile(){
+	emake SSE_FLAG="${SSE_FLAGS}" BITS="${BITS}"
+}
+
+src_install(){
+	dobin hisat2{,-build,-inspect,-build-s,-build-l,-align-s,-align-l,-inspect-s,-inspect-l}
+	python_foreach_impl python_doscript *.py
+	insinto /usr/share/"${PN}"/scripts
+	doins scripts/*.sh
+	dodoc MANUAL TUTORIAL
+}
diff --git a/sci-biology/hisat2/metadata.xml b/sci-biology/hisat2/metadata.xml
index 2a70cba7e..7954bc741 100644
--- a/sci-biology/hisat2/metadata.xml
+++ b/sci-biology/hisat2/metadata.xml
@@ -10,6 +10,6 @@
 		<name>Gentoo Biology Project</name>
 	</maintainer>
 	<upstream>
-		<remote-id type="github">infphilo/hisat2</remote-id>
+		<remote-id type="github">DaehwanKimLab/hisat2</remote-id>
 	</upstream>
 </pkgmetadata>
diff --git a/sci-biology/hts-python/hts-python-9999.ebuild b/sci-biology/hts-python/hts-python-9999.ebuild
deleted file mode 100644
index ba6779ab3..000000000
--- a/sci-biology/hts-python/hts-python-9999.ebuild
+++ /dev/null
@@ -1,21 +0,0 @@
-# Copyright 1999-2016 Gentoo Foundation
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=6
-
-PYTHON_COMPAT=( python2_7 )
-
-inherit distutils-r1 git-r3
-
-DESCRIPTION="Pythonic wrapper for htslib C-API using python cffi (unlike pysam)"
-HOMEPAGE="https://github.com/brentp/hts-python"
-EGIT_REPO_URI="https://github.com/brentp/hts-python.git"
-
-LICENSE="MIT"
-SLOT="0"
-KEYWORDS=""
-IUSE=""
-
-DEPEND=""
-RDEPEND="${DEPEND}
-	dev-python/cffi[${PYTHON_USEDEP}]"
diff --git a/sci-biology/hts-python/metadata.xml b/sci-biology/hts-python/metadata.xml
deleted file mode 100644
index ac270e09b..000000000
--- a/sci-biology/hts-python/metadata.xml
+++ /dev/null
@@ -1,15 +0,0 @@
-<?xml version="1.0" encoding="UTF-8"?>
-<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
-<pkgmetadata>
-	<maintainer type="person">
-		<email>mmokrejs@fold.natur.cuni.cz</email>
-		<name>Martin Mokrejs</name>
-	</maintainer>
-	<maintainer type="project">
-		<email>sci-biology@gentoo.org</email>
-		<name>Gentoo Biology Project</name>
-	</maintainer>
-	<upstream>
-		<remote-id type="github">brentp/hts-python</remote-id>
-	</upstream>
-</pkgmetadata>
diff --git a/sci-biology/hydra-sv/Manifest b/sci-biology/hydra-sv/Manifest
deleted file mode 100644
index 9278708af..000000000
--- a/sci-biology/hydra-sv/Manifest
+++ /dev/null
@@ -1 +0,0 @@
-DIST Hydra.v0.5.3.tar.gz 228772 BLAKE2B ea95810cf384a42d13df635fb1bc3c3bd8d606a78bf8e640dacf0db262b9c6ee84bf2d4b3357f3f5ff3bf0a0152dfb02bb520256076f73abb0f36f99c0f76075 SHA512 9d3421d97d58a4fab1631ab799d5be3c693f5664c96172e5e1ab14f200eb07e2ee07745afa87b77f566e99fd5148718b7a960d6ed6ce3611b600b4c21011f36f
diff --git a/sci-biology/hydra-sv/hydra-sv-0.5.3.ebuild b/sci-biology/hydra-sv/hydra-sv-0.5.3.ebuild
deleted file mode 100644
index ec74337e5..000000000
--- a/sci-biology/hydra-sv/hydra-sv-0.5.3.ebuild
+++ /dev/null
@@ -1,24 +0,0 @@
-# Copyright 1999-2014 Gentoo Foundation
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=5
-
-DESCRIPTION="Detection of structural variation breakpoints"
-HOMEPAGE="http://code.google.com/p/hydra-sv/"
-SRC_URI="http://hydra-sv.googlecode.com/files/Hydra.v${PV}.tar.gz"
-
-LICENSE="MIT"
-SLOT="0"
-IUSE=""
-KEYWORDS="~amd64 ~x86"
-
-S="${WORKDIR}/Hydra-Version-${PV}"
-
-src_compile() {
-	emake clean
-	default
-}
-
-src_install() {
-	dobin bin/* scripts/*
-}
diff --git a/sci-biology/hydra-sv/metadata.xml b/sci-biology/hydra-sv/metadata.xml
deleted file mode 100644
index ae9640ffb..000000000
--- a/sci-biology/hydra-sv/metadata.xml
+++ /dev/null
@@ -1,8 +0,0 @@
-<?xml version="1.0" encoding="UTF-8"?>
-<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
-<pkgmetadata>
-	<maintainer type="project">
-		<email>sci@gentoo.org</email>
-		<name>Gentoo Science Project</name>
-	</maintainer>
-</pkgmetadata>
diff --git a/sci-biology/idba/Manifest b/sci-biology/idba/Manifest
index b2840dd9b..d23decd54 100644
--- a/sci-biology/idba/Manifest
+++ b/sci-biology/idba/Manifest
@@ -1 +1 @@
-DIST idba-1.1.1.tar.gz 209382 BLAKE2B d87835418340500e2e9ff43c0335d813b537e64e3f2ade9b7661ab04ca2dbcd3d0a2ebfbe8856b672eb654d0911da37444e26df8d7173a6ca9d8bbeafccc82ab SHA512 4657c67809152c07dbdbfcf572532f4e88fb1dc8180e777eabd8ebda626bfeb7a318894eb9ce46dea6673bdf9e7ab1a5e99dc0d4c33c736d67152394e4d1521f
+DIST idba-1.1.3.tar.gz 446227 BLAKE2B 5f395c4294f8aaa4f85985ae42182524652f8474e0f5ce8e28f84283f89eca8ea1d08d89ca88af2e166d07ec67dc498125a6188cfb36bd583307fa58e38b9fbf SHA512 e974a62f9768100656f874b1113f84228f19ff54abff1310480cb2253e6e4deac6d7b1e1111d520596d9a285dc4b26d4c33d4711dedd4a73fc7981487b5448b5
diff --git a/sci-biology/idba/idba-1.1.1.ebuild b/sci-biology/idba/idba-1.1.1.ebuild
deleted file mode 100644
index 5054d3363..000000000
--- a/sci-biology/idba/idba-1.1.1.ebuild
+++ /dev/null
@@ -1,53 +0,0 @@
-# Copyright 1999-2017 Gentoo Foundation
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=6
-
-DESCRIPTION="De novo De Bruijn graph assembler iteratively using multimple k-mers"
-HOMEPAGE="http://i.cs.hku.hk/~alse/hkubrg/projects/idba
-	https://code.google.com/archive/p/hku-idba"
-SRC_URI="https://storage.googleapis.com/google-code-archive-downloads/v2/code.google.com/hku-idba/${P}.tar.gz"
-
-LICENSE="GPL-2+"
-SLOT="0"
-KEYWORDS="~amd64 ~x86"
-IUSE="openmp"
-
-DEPEND=""
-RDEPEND="${DEPEND}"
-
-pkg_setup() {
-	use openmp && ! tc-has-openmp && die "Please switch to an openmp compatible compiler"
-}
-
-src_prepare(){
-	# Makefile.am also forces '-fopenmp -pthread', do we care?
-	#code stolen from velvet-1.2.10.ebuild
-	if [[ $(tc-getCC) =~ gcc ]]; then
-		local eopenmp=-fopenmp
-	elif [[ $(tc-getCC) =~ icc ]]; then
-		local eopenmp=-openmp
-		sed -e 's/-fopenmp/-openmp/' -i BUILD || die
-	else
-		elog "Cannot detect compiler type so not setting openmp support"
-	fi
-	find . -name Makefile.in | while read f; do \
-		sed -e "s/-Wall -O3//" -i $f || die
-	done || die
-	sed -e 's/"-Wall", "-O3", //' -i BUILD || die
-	default
-}
-
-src_compile(){
-	sh build.sh || die
-}
-
-src_install(){
-	default
-	mkdir -p "${ED}"/usr/bin || die
-	mv "${D}"/usr/local/bin/* "${ED}"/usr/bin/ || die "Move to EPREFIX-compliant place"
-	rm "${ED}"/usr/bin/scan.py "${ED}"/usr/bin/run-unittest.py || die
-	rm bin/test bin/*.o bin/Makefile* || die # avoid file collision
-	dobin bin/* # https://github.com/loneknightpy/idba/issues/23
-	if [ ! -z "${EPREFIX}" ]; then rm -rf "${D}"/usr || die "Failed to zap empty non-EPREFIXED dirs"; fi
-}
diff --git a/sci-biology/idba/idba-1.1.3.ebuild b/sci-biology/idba/idba-1.1.3.ebuild
new file mode 100644
index 000000000..fb4583346
--- /dev/null
+++ b/sci-biology/idba/idba-1.1.3.ebuild
@@ -0,0 +1,39 @@
+# Copyright 1999-2021 Gentoo Authors
+# Distributed under the terms of the GNU General Public License v2
+
+EAPI=7
+
+inherit toolchain-funcs
+
+DESCRIPTION="De novo De Bruijn graph assembler iteratively using multimple k-mers"
+HOMEPAGE="https://i.cs.hku.hk/~alse/hkubrg/projects/idba_ud/"
+SRC_URI="https://github.com/loneknightpy/idba/releases/download/${PV}/${P}.tar.gz"
+
+LICENSE="GPL-2+"
+SLOT="0"
+KEYWORDS="~amd64 ~x86"
+IUSE="openmp"
+
+DEPEND=""
+RDEPEND="${DEPEND}"
+
+pkg_setup() {
+	use openmp && ! tc-has-openmp && die "Please switch to an openmp compatible compiler"
+}
+
+src_prepare(){
+	# Makefile.am also forces '-fopenmp -pthread', do we care?
+	#code stolen from velvet-1.2.10.ebuild
+	if [[ $(tc-getCC) =~ gcc ]]; then
+		local eopenmp=-fopenmp
+	elif [[ $(tc-getCC) =~ icc ]]; then
+		local eopenmp=-openmp
+		sed -e 's/-fopenmp/-openmp/' -i BUILD || die
+	else
+		elog "Cannot detect compiler type so not setting openmp support"
+	fi
+	find . -name Makefile.in | while read f; do \
+		sed -e "s/-Wall -O3//" -i $f || die
+	done || die
+	default
+}
diff --git a/sci-biology/idba/idba-9999.ebuild b/sci-biology/idba/idba-9999.ebuild
index 5810e7506..b90f44141 100644
--- a/sci-biology/idba/idba-9999.ebuild
+++ b/sci-biology/idba/idba-9999.ebuild
@@ -1,12 +1,12 @@
-# Copyright 1999-2017 Gentoo Foundation
+# Copyright 1999-2021 Gentoo Authors
 # Distributed under the terms of the GNU General Public License v2
 
-EAPI=6
+EAPI=7
 
 inherit git-r3 toolchain-funcs
 
 DESCRIPTION="De novo De Bruijn graph assembler iteratively using multimple k-mers"
-HOMEPAGE="http://i.cs.hku.hk/~alse/hkubrg/projects/idba_ud"
+HOMEPAGE="https://i.cs.hku.hk/~alse/hkubrg/projects/idba_ud/"
 EGIT_REPO_URI="https://github.com/loneknightpy/idba.git"
 
 LICENSE="GPL-2+"
diff --git a/sci-biology/igv/Manifest b/sci-biology/igv/Manifest
deleted file mode 100644
index 87f80e6ac..000000000
--- a/sci-biology/igv/Manifest
+++ /dev/null
@@ -1,4 +0,0 @@
-DIST igv-2.3.47.zip 146891756 SHA256 1a9e0f56c1dfde2bdcd3823ad196ac4e4deb983500152667e761560c34d9b91d SHA512 24eea8215db8eaa92d4562f5867d3d5cf4cdde5f0e65cd2dae63493c02a47fa27bd30765c7ce87ef4d5106dfb92106f3abca2471d077311bc1bb6de2a71d2d2c WHIRLPOOL 0dd2b6a542832d9f769ca47c7e969fd8cc7b7fdbebd57d63b4e3e8c9e80a175840255c2a7a8496415117ee58a65fa4a7f7aebfec18168223ac0232d7bd428e89
-DIST igv-2.3.81.zip 148743869 BLAKE2B 2828e543675b6fdded7079979783e8eed1ad8f224964e0eff2b6c33d90f7a9e370c2a9781d7be772486b3d647badf069dc721904f791eca05c5b2b15a524a341 SHA512 5f6fb29ac73ff87deb7987a535666bb7cd1c3c40144cd92185d2e81403cddee2aa66cbfa1e43bf4a4167f1884c42ab670598dfd1a5e680690953dc5831143bb7
-DIST igv-2.3.88.zip 150339120 BLAKE2B 217d85f83d19de34184b64cd2971d27fd227a6533ed825cb255f97211ec64937f9e4447491c54bb9b97e48f6c7ef932c7c1a7809750ff061fef4f6476e9f0bcd SHA512 f647f7c115dfbd24303744319ab7d4ab7e25624d82a664fb1aa9df2840a1246a833919d79747b793db466380c1e6091079992d7702295029b6abce924ce6782b
-DIST igv-2.3.92.zip 150354074 BLAKE2B 0d6e6658efe768ac1a407c69c92a04e76dc7f1020e36a3c533ab4a80a7a4c4bbe25d64f4180a9b424f571a45e784d5974793ccfcd76457dd1bfad36fc5eeaef7 SHA512 a10b7ec75bcb044929fcaf1ace9088436691a131af332f1dcf9a9ebb6349a78b06800cbeb2c1fc290a9db6308cde623f44a928d7c0a75a2d55e153bcad056a4a
diff --git a/sci-biology/igv/files/2.3.52-remove-oracle.jdbc.patch b/sci-biology/igv/files/2.3.52-remove-oracle.jdbc.patch
deleted file mode 100644
index 7d2274833..000000000
--- a/sci-biology/igv/files/2.3.52-remove-oracle.jdbc.patch
+++ /dev/null
@@ -1,21 +0,0 @@
-diff --git a/src/org/broad/igv/lists/GeneListEditDialog.java b/src/org/broad/igv/lists/GeneListEditDialog.java
-index f1aff7d..87d2dd1 100644
---- a/src/org/broad/igv/lists/GeneListEditDialog.java
-+++ b/src/org/broad/igv/lists/GeneListEditDialog.java
-@@ -22,15 +22,12 @@
- 
- package org.broad.igv.lists;
- 
--import oracle.jdbc.proxy.annotation.Pre;
--import org.broad.igv.Globals;
- import org.broad.igv.PreferenceManager;
- import org.broad.igv.ui.util.MessageUtils;
- 
- import java.awt.*;
- import java.awt.event.*;
- import java.io.*;
--import java.net.URLEncoder;
- import java.util.ArrayList;
- import java.util.Arrays;
- import javax.swing.*;
-
diff --git a/sci-biology/igv/igv-2.3.47.ebuild b/sci-biology/igv/igv-2.3.47.ebuild
deleted file mode 100644
index 751ad3943..000000000
--- a/sci-biology/igv/igv-2.3.47.ebuild
+++ /dev/null
@@ -1,82 +0,0 @@
-# Copyright 1999-2017 Gentoo Foundation
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=5
-
-inherit java-pkg-2 java-ant-2
-
-[ "$PV" == "9999" ] && inherit git-r3
-
-if [ "$PV" == "9999" ]; then
-	#ESVN_REPO_URI="http://igv.googlecode.com/svn/trunk"
-	#ESVN_REPO_URI="http://igv.googlecode.com/svn/tags/Version_${PV}"
-	EGIT_REPO_URI="https://github.com/broadinstitute/IGV.git"
-	KEYWORDS=""
-else
-	SRC_URI="https://github.com/broadinstitute/IGV/archive/v${PV}.zip -> ${P}.zip"
-	KEYWORDS=""
-	# binaries
-	# http://www.broadinstitute.org/igv/projects/downloads/IGV_2.3.40.zip
-	# http://www.broadinstitute.org/igv/projects/downloads/igvtools_2.3.40.zip
-fi
-
-DESCRIPTION="Integrative Genomics Viewer"
-HOMEPAGE="http://www.broadinstitute.org/igv/"
-
-LICENSE="LGPL-2.1"
-SLOT="0"
-IUSE=""
-KEYWORDS="~amd64"
-
-COMMON_DEPS="
-	dev-java/absolutelayout
-	dev-java/jama:0
-	dev-java/commons-logging:0
-	>=dev-java/commons-io-2.1:1
-	dev-java/commons-math:2
-	dev-java/commons-jexl:2
-	dev-java/jcommon:1.0
-	dev-java/jfreechart:1.0
-	dev-java/jlfgr:0
-	dev-java/log4j:0
-	dev-java/gson:2.2.2
-	dev-java/guava:20
-	dev-java/swing-layout:1
-	dev-java/jgrapht:0
-	dev-java/junit:4"
-
-DEPEND=">=virtual/jdk-1.7
-	app-arch/unzip
-	${COMMON_DEPS}"
-RDEPEND=">=virtual/jre-1.7
-	${COMMON_DEPS}"
-
-S="${WORKDIR}/IGV-${PV}"
-
-EANT_BUILD_TARGET="all"
-JAVA_ANT_REWRITE_CLASSPATH="true"
-EANT_NEEDS_TOOLS="true"
-EANT_EXTRA_ARGS="-Dnotests=true"
-
-EANT_GENTOO_CLASSPATH="absolutelayout,jama,commons-logging,commons-math-2,commons-jexl-2,jfreechart-1.0,jlfgr,log4j,commons-io-1,"
-EANT_GENTOO_CLASSPATH+="gson-2.2.2,guava-20,swing-layout-1,jgrapht,junit-4"
-
-java_prepare() {
-	mv lib oldlib || die
-	mkdir lib || die
-
-	mv -v oldlib/{htsjdk-1.124.jar,bcprov-debug-jdk15on-147.jar,jide-oss-3.5.5.jar,goby-io-igv__V1.0.jar,jargs.jar,mongo-java-driver-2.11.3.jar,na12878kb-utils.jar,picard-lib.jar} lib || die
-	mv -v oldlib/batik* lib || die
-
-	rm -rvf oldlib/* || die
-
-	epatch "${FILESDIR}"/"${PV}"-remove-oracle.jdbc.patch
-}
-
-src_install() {
-	java-pkg_newjar igv.jar
-
-	for i in lib/*.jar; do java-pkg_dojar $i; done
-
-	java-pkg_dolauncher igv --jar igv.jar --main org.broad.igv.ui.Main
-}
diff --git a/sci-biology/igv/igv-2.3.81.ebuild b/sci-biology/igv/igv-2.3.81.ebuild
deleted file mode 100644
index 5fabefeb3..000000000
--- a/sci-biology/igv/igv-2.3.81.ebuild
+++ /dev/null
@@ -1,87 +0,0 @@
-# Copyright 1999-2017 Gentoo Foundation
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=5
-
-inherit java-pkg-2 java-ant-2
-
-[ "$PV" == "9999" ] && inherit git-r3
-
-if [ "$PV" == "9999" ]; then
-	#ESVN_REPO_URI="http://igv.googlecode.com/svn/trunk"
-	#ESVN_REPO_URI="http://igv.googlecode.com/svn/tags/Version_${PV}"
-	EGIT_REPO_URI="https://github.com/broadinstitute/IGV.git"
-	KEYWORDS=""
-else
-	SRC_URI="https://github.com/broadinstitute/IGV/archive/v${PV}.zip -> ${P}.zip"
-	KEYWORDS=""
-	# binaries
-	# http://www.broadinstitute.org/igv/projects/downloads/IGV_2.3.40.zip
-	# http://www.broadinstitute.org/igv/projects/downloads/igvtools_2.3.40.zip
-fi
-
-DESCRIPTION="Integrative Genomics Viewer"
-HOMEPAGE="http://www.broadinstitute.org/igv/"
-
-LICENSE="LGPL-2.1"
-SLOT="0"
-IUSE=""
-KEYWORDS="" # igv-2.3.81/src/com/iontorrent/views/FlowSignalDistributionPanel.java:222: error: cannot access PublicCloneable
-
-# actually more exactly the COMMON_DEPS should contain:
-#   >=dev-java/commons-compress-1.11 # use bundled library until dev-java/commons-compress is bumped, see bug #591696
-COMMON_DEPS="
-	dev-java/absolutelayout:0
-	dev-java/jama:0
-	dev-java/commons-compress
-	dev-java/commons-logging:0
-	>=dev-java/commons-io-2.1:1
-	dev-java/commons-math:2
-	dev-java/commons-jexl:2
-	dev-java/jcommon:*
-	dev-java/jfreechart:1.0
-	dev-java/jlfgr:0
-	dev-java/log4j:0
-	dev-java/gson:2.2.2
-	dev-java/guava:20
-	dev-java/swing-layout:1
-	dev-java/jgrapht:0
-	dev-java/junit:4"
-
-DEPEND=">=virtual/jdk-1.7
-	app-arch/unzip
-	${COMMON_DEPS}"
-RDEPEND=">=virtual/jre-1.7
-	${COMMON_DEPS}"
-
-S="${WORKDIR}/igv-${PV}" # if the file unpacks into IGV_"${PV}" then you fetched wrong file with the precompiled jar
-
-EANT_BUILD_TARGET="all"
-JAVA_ANT_REWRITE_CLASSPATH="true"
-EANT_NEEDS_TOOLS="true"
-EANT_EXTRA_ARGS="-Dnotests=true"
-
-EANT_GENTOO_CLASSPATH="absolutelayout,jama,commons-logging,commons-math-2,commons-jexl-2,jfreechart-1.0,jlfgr,log4j,commons-io-1,"
-EANT_GENTOO_CLASSPATH+="gson-2.2.2,guava-20,swing-layout-1,jgrapht,junit-4"
-
-java_prepare() {
-	mv lib oldlib || die
-	mkdir lib || die
-
-	mv -v oldlib/{htsjdk-1.139-patched.jar,jide-oss-3.5.5.jar,goby-io-igv__V1.0.jar,jargs.jar,mongo-java-driver-2.11.3.jar,na12878kb-utils.jar,picard-lib.jar,mysql-connector-java-3.1.14-bin.jar} lib || die
-	mv -v oldlib/batik* lib || die
-
-	rm -rvf oldlib/* || die
-}
-
-src_install() {
-	java-pkg_newjar igv.jar
-
-	for i in lib/*.jar; do java-pkg_dojar $i; done
-
-	java-pkg_dolauncher igv --jar igv.jar --main org.broad.igv.ui.Main
-}
-
-pkg_postinst(){
-	einfo "You may want to install sci-biology/blat for easy sequence searches inside igv"
-}
diff --git a/sci-biology/igv/igv-2.3.88.ebuild b/sci-biology/igv/igv-2.3.88.ebuild
deleted file mode 100644
index 8011ea888..000000000
--- a/sci-biology/igv/igv-2.3.88.ebuild
+++ /dev/null
@@ -1,87 +0,0 @@
-# Copyright 1999-2017 Gentoo Foundation
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=5
-
-inherit java-pkg-2 java-ant-2
-
-[ "$PV" == "9999" ] && inherit git-r3
-
-if [ "$PV" == "9999" ]; then
-	#ESVN_REPO_URI="http://igv.googlecode.com/svn/trunk"
-	#ESVN_REPO_URI="http://igv.googlecode.com/svn/tags/Version_${PV}"
-	EGIT_REPO_URI="https://github.com/broadinstitute/IGV.git"
-	KEYWORDS=""
-else
-	SRC_URI="https://github.com/broadinstitute/IGV/archive/v${PV}.zip -> ${P}.zip"
-	KEYWORDS=""
-	# binaries
-	# http://www.broadinstitute.org/igv/projects/downloads/IGV_2.3.40.zip
-	# http://www.broadinstitute.org/igv/projects/downloads/igvtools_2.3.40.zip
-fi
-
-DESCRIPTION="Integrative Genomics Viewer"
-HOMEPAGE="http://www.broadinstitute.org/igv/"
-
-LICENSE="LGPL-2.1"
-SLOT="0"
-IUSE=""
-KEYWORDS="" # see upstream issue #332
-
-# actually more exactly the COMMON_DEPS should contain:
-#   >=dev-java/commons-compress-1.11 # use bundled library until dev-java/commons-compress is bumped, see bug #591696
-COMMON_DEPS="
-	dev-java/absolutelayout:0
-	dev-java/jama:0
-	dev-java/commons-compress
-	dev-java/commons-logging:0
-	>=dev-java/commons-io-2.1:1
-	dev-java/commons-math:2
-	dev-java/commons-jexl:2
-	dev-java/jcommon:*
-	dev-java/jfreechart:1.0
-	dev-java/jlfgr:0
-	dev-java/log4j:0
-	dev-java/gson:2.2.2
-	dev-java/guava:20
-	dev-java/swing-layout:1
-	dev-java/jgrapht:0
-	dev-java/junit:4"
-
-DEPEND=">=virtual/jdk-1.7
-	app-arch/unzip
-	${COMMON_DEPS}"
-RDEPEND=">=virtual/jre-1.7
-	${COMMON_DEPS}"
-
-S="${WORKDIR}/igv-${PV}" # if the file unpacks into IGV_"${PV}" then you fetched wrong file with the precompiled jar
-
-EANT_BUILD_TARGET="all"
-JAVA_ANT_REWRITE_CLASSPATH="true"
-EANT_NEEDS_TOOLS="true"
-EANT_EXTRA_ARGS="-Dnotests=true"
-
-EANT_GENTOO_CLASSPATH="absolutelayout,jama,commons-logging,commons-math-2,commons-jexl-2,jfreechart-1.0,jlfgr,log4j,commons-io-1,"
-EANT_GENTOO_CLASSPATH+="gson-2.2.2,guava-20,swing-layout-1,jgrapht,junit-4"
-
-java_prepare() {
-	mv lib oldlib || die
-	mkdir lib || die
-
-	mv -v oldlib/{htsjdk-1.139-patched.jar,jide-oss-3.5.5.jar,goby-io-igv__V1.0.jar,jargs.jar,mongo-java-driver-2.11.3.jar,na12878kb-utils.jar,picard-lib.jar,mysql-connector-java-3.1.14-bin.jar} lib || die
-	mv -v oldlib/batik* lib || die
-
-	rm -rvf oldlib/* || die
-}
-
-src_install() {
-	java-pkg_newjar igv.jar
-
-	for i in lib/*.jar; do java-pkg_dojar $i; done
-
-	java-pkg_dolauncher igv --jar igv.jar --main org.broad.igv.ui.Main
-}
-
-pkg_postinst(){
-	einfo "You may want to install sci-biology/blat for easy sequence searches inside igv"
-}
diff --git a/sci-biology/igv/igv-2.3.92.ebuild b/sci-biology/igv/igv-2.3.92.ebuild
deleted file mode 100644
index 8011ea888..000000000
--- a/sci-biology/igv/igv-2.3.92.ebuild
+++ /dev/null
@@ -1,87 +0,0 @@
-# Copyright 1999-2017 Gentoo Foundation
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=5
-
-inherit java-pkg-2 java-ant-2
-
-[ "$PV" == "9999" ] && inherit git-r3
-
-if [ "$PV" == "9999" ]; then
-	#ESVN_REPO_URI="http://igv.googlecode.com/svn/trunk"
-	#ESVN_REPO_URI="http://igv.googlecode.com/svn/tags/Version_${PV}"
-	EGIT_REPO_URI="https://github.com/broadinstitute/IGV.git"
-	KEYWORDS=""
-else
-	SRC_URI="https://github.com/broadinstitute/IGV/archive/v${PV}.zip -> ${P}.zip"
-	KEYWORDS=""
-	# binaries
-	# http://www.broadinstitute.org/igv/projects/downloads/IGV_2.3.40.zip
-	# http://www.broadinstitute.org/igv/projects/downloads/igvtools_2.3.40.zip
-fi
-
-DESCRIPTION="Integrative Genomics Viewer"
-HOMEPAGE="http://www.broadinstitute.org/igv/"
-
-LICENSE="LGPL-2.1"
-SLOT="0"
-IUSE=""
-KEYWORDS="" # see upstream issue #332
-
-# actually more exactly the COMMON_DEPS should contain:
-#   >=dev-java/commons-compress-1.11 # use bundled library until dev-java/commons-compress is bumped, see bug #591696
-COMMON_DEPS="
-	dev-java/absolutelayout:0
-	dev-java/jama:0
-	dev-java/commons-compress
-	dev-java/commons-logging:0
-	>=dev-java/commons-io-2.1:1
-	dev-java/commons-math:2
-	dev-java/commons-jexl:2
-	dev-java/jcommon:*
-	dev-java/jfreechart:1.0
-	dev-java/jlfgr:0
-	dev-java/log4j:0
-	dev-java/gson:2.2.2
-	dev-java/guava:20
-	dev-java/swing-layout:1
-	dev-java/jgrapht:0
-	dev-java/junit:4"
-
-DEPEND=">=virtual/jdk-1.7
-	app-arch/unzip
-	${COMMON_DEPS}"
-RDEPEND=">=virtual/jre-1.7
-	${COMMON_DEPS}"
-
-S="${WORKDIR}/igv-${PV}" # if the file unpacks into IGV_"${PV}" then you fetched wrong file with the precompiled jar
-
-EANT_BUILD_TARGET="all"
-JAVA_ANT_REWRITE_CLASSPATH="true"
-EANT_NEEDS_TOOLS="true"
-EANT_EXTRA_ARGS="-Dnotests=true"
-
-EANT_GENTOO_CLASSPATH="absolutelayout,jama,commons-logging,commons-math-2,commons-jexl-2,jfreechart-1.0,jlfgr,log4j,commons-io-1,"
-EANT_GENTOO_CLASSPATH+="gson-2.2.2,guava-20,swing-layout-1,jgrapht,junit-4"
-
-java_prepare() {
-	mv lib oldlib || die
-	mkdir lib || die
-
-	mv -v oldlib/{htsjdk-1.139-patched.jar,jide-oss-3.5.5.jar,goby-io-igv__V1.0.jar,jargs.jar,mongo-java-driver-2.11.3.jar,na12878kb-utils.jar,picard-lib.jar,mysql-connector-java-3.1.14-bin.jar} lib || die
-	mv -v oldlib/batik* lib || die
-
-	rm -rvf oldlib/* || die
-}
-
-src_install() {
-	java-pkg_newjar igv.jar
-
-	for i in lib/*.jar; do java-pkg_dojar $i; done
-
-	java-pkg_dolauncher igv --jar igv.jar --main org.broad.igv.ui.Main
-}
-
-pkg_postinst(){
-	einfo "You may want to install sci-biology/blat for easy sequence searches inside igv"
-}
diff --git a/sci-biology/igv/metadata.xml b/sci-biology/igv/metadata.xml
deleted file mode 100644
index 8b6e6434a..000000000
--- a/sci-biology/igv/metadata.xml
+++ /dev/null
@@ -1,11 +0,0 @@
-<?xml version="1.0" encoding="UTF-8"?>
-<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
-<pkgmetadata>
-	<maintainer type="project">
-		<email>sci-biology@gentoo.org</email>
-		<name>Gentoo Biology Project</name>
-	</maintainer>
-	<upstream>
-		<remote-id type="github">broadinstitute/IGV</remote-id>
-	</upstream>
-</pkgmetadata>
diff --git a/sci-biology/imagej/Manifest b/sci-biology/imagej/Manifest
index 60773ac92..4c5068f0a 100644
--- a/sci-biology/imagej/Manifest
+++ b/sci-biology/imagej/Manifest
@@ -1,3 +1,3 @@
 DIST ImageJ.png 13012 BLAKE2B b42ee855e6214b275cbdcc722f6c7b095fe83de477a151714c4afec8e23abe12b2d0bf62ae81a4f9c4ccefc9245a9e144085b844ee3f92121a88f7d27106acf5 SHA512 60c2ff73bcfc668931c59b0dfb299723a369b741601bdd591a407302e30fc58c6c626525b3f08b955a5dab37729d3f704db689317b42a94e7a3ccbfb72abc9b3
-DIST ij150.zip 4179316 SHA256 97aba6fc5eb908f5160243aebcdc4965726693cb1353d9c0d71b8f5dd832cb7b SHA512 a6aae1813c9144692d7e11a82199cfc1d52e5f99d5716de890b58456c303eadc047a01e37822cdbd0c610bae944954d9e2ae46c8961710c63311f649976930e9 WHIRLPOOL 6df690327c54a5809b4e0b3f4e7c52998265de2685b4fb901702e12cb52936a685eed3f9db9610b4ed6c2e778b87ae8e73cb09d770955aac4d87f0327a3e4fa3
-DIST ij151k-src.zip 1580015 BLAKE2B 143fca57d38457f8264f59517890b9541ebc2838f56ccc07fdc0fec114bdc02042dc74a0c9560e7ed47e8d5e3c91f83dd725c860f823f4956c55636c30025bfc SHA512 93249fb1c186e757dde78231d3064a1179f5c10d94dc02b9b0535febd5db78cb2666e9e952380de8847339c840d4e46e857eaa982340c6e5084d1003c44791e6
+DIST ij154.zip 6677151 BLAKE2B acd99e95c8123461710e3565a31121e475ac9bd1bb993649dc9569c1e17a055e6e0aad9a3fa482b4a021f39cd3467e779529a1512be557a370277c6091fa7b08 SHA512 92c9f13335e9d2cc111bf08851a6fb747d1d1eac8f3088563f42669e225cff6fd2ffbfd4ea474e7baaa266656c4a433107a3264539f9744412aa6400094cb2c9
+DIST imagej-1.54h.gh.tar.gz 5822723 BLAKE2B a293a4b3c2f5f998822c61e67586124491c0b902c5c91538d7ab7eb7d84f6f8ce79759eaa5f4e5de60731566923cc4b837277539c9522c2efe7bc079c6c13455 SHA512 6061fad8c11b26cdf7537f945abc26f9e4a10f34ed151701f6f89e794028be646dc8013437605c6889073acf803ea6784457f47e3cd645c54265fef24bfeb615
diff --git a/sci-biology/imagej/files/AutoThresholder.java.patch b/sci-biology/imagej/files/AutoThresholder.java.patch
deleted file mode 100644
index 97c893244..000000000
--- a/sci-biology/imagej/files/AutoThresholder.java.patch
+++ /dev/null
@@ -1,10 +0,0 @@
---- imagej-1.51k/work/source/ij/process/AutoThresholder.java.ori	2017-03-15 22:33:45.843801175 +0100
-+++ imagej-1.51k/work/source/ij/process/AutoThresholder.java	2017-03-15 22:33:55.104053480 +0100
-@@ -650,7 +650,6 @@
- 		}
- 		// The threshold is the minimum between the two peaks.
- 		for (int i=1; i<255; i++) {
--			//IJ.log(" "+i+"  "+iHisto[i]);
- 			if (iHisto[i-1] > iHisto[i] && iHisto[i+1] >= iHisto[i]) {
- 				threshold = i;
- 				break;
diff --git a/sci-biology/imagej/imagej-1.51k.ebuild b/sci-biology/imagej/imagej-1.51k.ebuild
deleted file mode 100644
index 931aef0bc..000000000
--- a/sci-biology/imagej/imagej-1.51k.ebuild
+++ /dev/null
@@ -1,132 +0,0 @@
-# Copyright 1999-2017 Gentoo Foundation
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=6
-
-inherit java-pkg-2 java-ant-2 eutils versionator
-
-MY_PN="ij"
-MY_PV=$(delete_all_version_separators)
-
-# NOTE:
-# as plugins are regularly lagging behind, we use the pack released for previous
-# version instead. Change to present version locally if you are sure proper
-# version has been released.
-# see https://bugs.gentoo.org/show_bug.cgi?id=112275
-# https://github.com/imagej/imagej1/issues/28
-IJ_PV=$((${MY_PV::3}-1))
-
-DESCRIPTION="Image Processing and Analysis in Java"
-HOMEPAGE="http://rsb.info.nih.gov/ij/"
-
-SRC_URI="http://imagej.nih.gov/ij/download/src/${MY_PN}${MY_PV}-src.zip
-	http://rsb.info.nih.gov/ij/images/ImageJ.png
-	plugins? ( http://wsr.imagej.net/distros/cross-platform/${MY_PN}${IJ_PV}.zip )"
-# plugins are under a different licenses and can be installed into user's $IJ_HOME/plugins
-#	plugins? ( http://rsb.info.nih.gov/ij/download/zips/${MY_PN}${IJ_PV}.zip )"
-
-RESTRICT=""
-LICENSE="public-domain" # http://imagej.net/disclaimer.html
-SLOT="0"
-
-KEYWORDS=""
-
-IUSE="doc plugins debug"
-
-RDEPEND=">=virtual/jre-1.6:*
-	dev-java/java-config
-	dev-java/jython"
-DEPEND=">=virtual/jdk-1.6:*
-	dev-java/ant-core
-	${RDEPEND}"
-
-S=${WORKDIR}/source
-IJ_S=${WORKDIR}/ImageJ
-
-src_prepare() {
-	cp "${DISTDIR}"/ImageJ.png "${WORKDIR}/${PN}.png" || die
-
-	if ! use debug ; then
-		sed -i 's: debug="on">: debug="off">:' "${S}"/build.xml || die
-	fi
-	epatch "${FILESDIR}"/AutoThresholder.java.patch
-	eapply_user
-}
-
-# in src_compile we get: !!! ERROR: Package jython was not found!
-# TODO: overwrite calls to jython ? See
-#   ij/plugin/frame/Editor.java
-#   plugin/PlugInInterpreter.java
-#   plugin/Macro_Runner.java
-
-src_compile() {
-	local antflags="build"
-	use doc && antflags="${antflags} javadocs"
-
-	ant ${antflags} || die  "ant build failed"
-
-	# Max memory usage depends on available memory and CPU type
-	MEM=$(grep MemTotal /proc/meminfo | cut -d':' -f2 | grep -o [0-9]*)
-	IJ_MAX_MEM=$(expr ${MEM} / 1024)
-	if use x86 && $IJ_MAX_MEM -gt 2048 ; then
-		IJ_MAX_MEM=2048
-	fi
-	# build finished, generate startup wrapper
-	cat <<EOF > "${T}/${PN}"
-#!${EPREFIX}/bin/bash
-IJ_LIB=${EPREFIX}/usr/share/${PN}/lib
-if !([ "\${IJ_HOME}" ]) ; then
-	IJ_HOME=\${HOME}/.imagej
-fi
-if [ -d \${IJ_HOME}/plugins ] ; then
-	IJ_PLG=\${IJ_HOME}
-else
-	IJ_PLG=${EPREFIX}/usr/share/${PN}/lib
-fi
-if !([ "\$IJ_MEM" ]) ; then
-	IJ_MEM=${IJ_MAX_MEM}
-fi
-if !([ "\$IJ_CP" ]) ; then
-	IJ_CP=\$(java-config -p imagej):\$(java-config -O)/lib/tools.jar
-else
-	IJ_CP=\$(java-config -p imagej):\$(java-config -O)/lib/tools.jar:\${IJ_CP}
-fi
-\$(java-config --java) \\
-	-Xmx\${IJ_MEM}m -Dswing.aatext=true \\
-	-Dawt.useSystemAAFontSettings=on\\
-	-cp \${IJ_CP} \\
-	-Duser.home=\${IJ_HOME} \\
-	-Dplugins.dir=\${IJ_PLG} \\
-	ij.ImageJ "\$@"
-EOF
-}
-
-src_install() {
-	java-pkg_dojar *.jar
-	dobin "${T}/${PN}"
-
-	if use plugins ; then
-		cp -R "${IJ_S}"/plugins "${ED}"/usr/share/"${PN}"/lib/
-		cp -R "${IJ_S}"/macros "${ED}"/usr/share/"${PN}"/lib/
-	fi
-
-	use doc && java-pkg_dohtml -r "${WORKDIR}"/api
-
-	insinto /usr/share/pixmaps
-	doins "${WORKDIR}/${PN}".png
-	make_desktop_entry "${PN}" ImageJ "${PN}".png Graphics
-}
-
-pkg_postinst() {
-	einfo ""
-	einfo "You can configure the path of a folder, which contains \"plugins\" directory and IJ_Prefs.txt,"
-	einfo "by setting the environmental variable, \$IJ_HOME."
-	einfo "Default setting is \$IJ_HOME=\${HOME}/.imagej, i.e. \${HOME}/.imagej/plugins and \${HOME}/.imagej/IJ_Prefs.txt."
-	einfo ""
-	einfo "You can also configure the memory size by setting the environmental variable, \$IJ_MEM,"
-	einfo "and the class path by setting the environmental variable, \$IJ_CP."
-	einfo ""
-	einfo "If you want to use much more plugins, please see http://rsb.info.nih.gov/ij/plugins/index.html"
-	einfo "and add *.class files to \$IJ_HOME/plugins folder"
-	einfo ""
-}
diff --git a/sci-biology/imagej/imagej-1.54h-r1.ebuild b/sci-biology/imagej/imagej-1.54h-r1.ebuild
new file mode 100644
index 000000000..0252d6613
--- /dev/null
+++ b/sci-biology/imagej/imagej-1.54h-r1.ebuild
@@ -0,0 +1,144 @@
+# Copyright 1999-2023 Gentoo Authors
+# Distributed under the terms of the GNU General Public License v2
+
+EAPI=8
+
+inherit java-pkg-2 java-ant-2 desktop
+
+MY_PN="ij"
+IJ_PV="154" #plugins now available for 154
+
+DESCRIPTION="Image Processing and Analysis in Java"
+
+HOMEPAGE="
+	https://imagej.nih.gov/ij/
+	https://github.com/imagej
+"
+
+SRC_URI="
+	https://imagej.nih.gov/ij/images/ImageJ.png
+	plugins? ( https://wsr.imagej.net/distros/cross-platform/${MY_PN}${IJ_PV}.zip )"
+# plugins are under a different licenses and can be installed into user's $IJ_HOME/plugins
+
+if [[ ${PV} == 9999 ]]; then
+	inherit git-r3
+	EGIT_REPO_URI="https://github.com/imagej/ImageJ"
+	IJ_S="${S}/ImageJ"
+else
+	SRC_URI+="
+		https://github.com/imagej/ImageJ/archive/refs/tags/v${PV}.tar.gz -> ${P}.gh.tar.gz
+	"
+	S="${WORKDIR}/ImageJ-${PV}"
+	IJ_S="${WORKDIR}/ImageJ"
+	KEYWORDS="~amd64"
+fi
+
+LICENSE="public-domain"
+
+SLOT="0"
+
+IUSE="doc plugins debug"
+
+RDEPEND="
+	>=virtual/jre-1.7:*
+	dev-java/java-config
+"
+
+DEPEND="
+	${RDEPEND}
+	>=virtual/jdk-1.7:*
+"
+
+BDEPEND="
+	dev-java/ant-core
+	app-arch/unzip
+"
+
+src_prepare() {
+	cp "${DISTDIR}"/ImageJ.png "${WORKDIR}/${PN}.png" || die
+
+	if [[ ${PV} == 9999 ]]; then
+	   if use plugins ; then
+		  unpack "${MY_PN}${IJ_PV}.zip"
+	   fi
+	fi
+
+	if ! use debug ; then
+		sed -i 's: debug="on">: debug="off">:' "${S}"/build.xml || die
+	fi
+	default
+}
+
+src_compile() {
+	local antflags="build"
+	use doc && antflags="${antflags} javadocs"
+
+	ant ${antflags} || die  "ant build failed"
+
+	# Max memory usage depends on available memory and CPU type
+	MEM=$(grep MemTotal /proc/meminfo | cut -d':' -f2 | grep -o [0-9]*)
+	IJ_MAX_MEM=$(expr ${MEM} / 1024)
+
+	if use x86 && $IJ_MAX_MEM -gt 2048 ; then
+	   IJ_MAX_MEM=2048
+	fi
+
+	# build finished, generate startup wrapper
+	cat <<EOF > "${T}/${PN}"
+#!${EPREFIX}/bin/bash
+IJ_LIB=${EPREFIX}/usr/share/${PN}/lib
+if !([ "\${IJ_HOME}" ]) ; then
+	IJ_HOME=\${HOME}/.imagej
+fi
+if [ -d \${IJ_HOME}/plugins ] ; then
+	IJ_PLG=\${IJ_HOME}
+else
+	IJ_PLG=${EPREFIX}/usr/share/${PN}/lib
+fi
+if !([ "\$IJ_MEM" ]) ; then
+	IJ_MEM=${IJ_MAX_MEM}
+fi
+if !([ "\$IJ_CP" ]) ; then
+	IJ_CP=\$(java-config -p imagej):\$(java-config -O)/lib/tools.jar
+else
+	IJ_CP=\$(java-config -p imagej):\$(java-config -O)/lib/tools.jar:\${IJ_CP}
+fi
+\$(java-config --java) \\
+	-Xmx\${IJ_MEM}m -Dswing.aatext=true \\
+	-Dawt.useSystemAAFontSettings=on\\
+	-cp \${IJ_CP} \\
+	-Duser.home=\${IJ_HOME} \\
+	-Dplugins.dir=\${IJ_PLG} \\
+	ij.ImageJ "\$@"
+EOF
+}
+
+src_install() {
+	java-pkg_dojar *.jar
+	dobin "${T}/${PN}"
+
+	if use plugins ; then
+		cp -R "${IJ_S}"/plugins "${ED}"/usr/share/"${PN}"/lib/
+		cp -R "${IJ_S}"/macros "${ED}"/usr/share/"${PN}"/lib/
+	fi
+
+	use doc && java-pkg_dohtml -r "${WORKDIR}"/api
+
+	insinto /usr/share/pixmaps
+	doins "${WORKDIR}/${PN}".png
+	make_desktop_entry "${PN}" ImageJ "${PN}" Graphics
+}
+
+pkg_postinst() {
+	einfo ""
+	einfo "You can configure the path of a folder, which contains \"plugins\" directory and IJ_Prefs.txt,"
+	einfo "by setting the environmental variable, \$IJ_HOME."
+	einfo "Default setting is \$IJ_HOME=\${HOME}/.imagej, i.e. \${HOME}/.imagej/plugins and \${HOME}/.imagej/IJ_Prefs.txt."
+	einfo ""
+	einfo "You can also configure the memory size by setting the environmental variable, \$IJ_MEM,"
+	einfo "and the class path by setting the environmental variable, \$IJ_CP."
+	einfo ""
+	einfo "If you want to use much more plugins, please see http://rsb.info.nih.gov/ij/plugins/index.html"
+	einfo "and add *.class files to \$IJ_HOME/plugins folder"
+	einfo ""
+}
diff --git a/sci-biology/imagej/imagej-9999.ebuild b/sci-biology/imagej/imagej-9999.ebuild
new file mode 100644
index 000000000..0252d6613
--- /dev/null
+++ b/sci-biology/imagej/imagej-9999.ebuild
@@ -0,0 +1,144 @@
+# Copyright 1999-2023 Gentoo Authors
+# Distributed under the terms of the GNU General Public License v2
+
+EAPI=8
+
+inherit java-pkg-2 java-ant-2 desktop
+
+MY_PN="ij"
+IJ_PV="154" #plugins now available for 154
+
+DESCRIPTION="Image Processing and Analysis in Java"
+
+HOMEPAGE="
+	https://imagej.nih.gov/ij/
+	https://github.com/imagej
+"
+
+SRC_URI="
+	https://imagej.nih.gov/ij/images/ImageJ.png
+	plugins? ( https://wsr.imagej.net/distros/cross-platform/${MY_PN}${IJ_PV}.zip )"
+# plugins are under a different licenses and can be installed into user's $IJ_HOME/plugins
+
+if [[ ${PV} == 9999 ]]; then
+	inherit git-r3
+	EGIT_REPO_URI="https://github.com/imagej/ImageJ"
+	IJ_S="${S}/ImageJ"
+else
+	SRC_URI+="
+		https://github.com/imagej/ImageJ/archive/refs/tags/v${PV}.tar.gz -> ${P}.gh.tar.gz
+	"
+	S="${WORKDIR}/ImageJ-${PV}"
+	IJ_S="${WORKDIR}/ImageJ"
+	KEYWORDS="~amd64"
+fi
+
+LICENSE="public-domain"
+
+SLOT="0"
+
+IUSE="doc plugins debug"
+
+RDEPEND="
+	>=virtual/jre-1.7:*
+	dev-java/java-config
+"
+
+DEPEND="
+	${RDEPEND}
+	>=virtual/jdk-1.7:*
+"
+
+BDEPEND="
+	dev-java/ant-core
+	app-arch/unzip
+"
+
+src_prepare() {
+	cp "${DISTDIR}"/ImageJ.png "${WORKDIR}/${PN}.png" || die
+
+	if [[ ${PV} == 9999 ]]; then
+	   if use plugins ; then
+		  unpack "${MY_PN}${IJ_PV}.zip"
+	   fi
+	fi
+
+	if ! use debug ; then
+		sed -i 's: debug="on">: debug="off">:' "${S}"/build.xml || die
+	fi
+	default
+}
+
+src_compile() {
+	local antflags="build"
+	use doc && antflags="${antflags} javadocs"
+
+	ant ${antflags} || die  "ant build failed"
+
+	# Max memory usage depends on available memory and CPU type
+	MEM=$(grep MemTotal /proc/meminfo | cut -d':' -f2 | grep -o [0-9]*)
+	IJ_MAX_MEM=$(expr ${MEM} / 1024)
+
+	if use x86 && $IJ_MAX_MEM -gt 2048 ; then
+	   IJ_MAX_MEM=2048
+	fi
+
+	# build finished, generate startup wrapper
+	cat <<EOF > "${T}/${PN}"
+#!${EPREFIX}/bin/bash
+IJ_LIB=${EPREFIX}/usr/share/${PN}/lib
+if !([ "\${IJ_HOME}" ]) ; then
+	IJ_HOME=\${HOME}/.imagej
+fi
+if [ -d \${IJ_HOME}/plugins ] ; then
+	IJ_PLG=\${IJ_HOME}
+else
+	IJ_PLG=${EPREFIX}/usr/share/${PN}/lib
+fi
+if !([ "\$IJ_MEM" ]) ; then
+	IJ_MEM=${IJ_MAX_MEM}
+fi
+if !([ "\$IJ_CP" ]) ; then
+	IJ_CP=\$(java-config -p imagej):\$(java-config -O)/lib/tools.jar
+else
+	IJ_CP=\$(java-config -p imagej):\$(java-config -O)/lib/tools.jar:\${IJ_CP}
+fi
+\$(java-config --java) \\
+	-Xmx\${IJ_MEM}m -Dswing.aatext=true \\
+	-Dawt.useSystemAAFontSettings=on\\
+	-cp \${IJ_CP} \\
+	-Duser.home=\${IJ_HOME} \\
+	-Dplugins.dir=\${IJ_PLG} \\
+	ij.ImageJ "\$@"
+EOF
+}
+
+src_install() {
+	java-pkg_dojar *.jar
+	dobin "${T}/${PN}"
+
+	if use plugins ; then
+		cp -R "${IJ_S}"/plugins "${ED}"/usr/share/"${PN}"/lib/
+		cp -R "${IJ_S}"/macros "${ED}"/usr/share/"${PN}"/lib/
+	fi
+
+	use doc && java-pkg_dohtml -r "${WORKDIR}"/api
+
+	insinto /usr/share/pixmaps
+	doins "${WORKDIR}/${PN}".png
+	make_desktop_entry "${PN}" ImageJ "${PN}" Graphics
+}
+
+pkg_postinst() {
+	einfo ""
+	einfo "You can configure the path of a folder, which contains \"plugins\" directory and IJ_Prefs.txt,"
+	einfo "by setting the environmental variable, \$IJ_HOME."
+	einfo "Default setting is \$IJ_HOME=\${HOME}/.imagej, i.e. \${HOME}/.imagej/plugins and \${HOME}/.imagej/IJ_Prefs.txt."
+	einfo ""
+	einfo "You can also configure the memory size by setting the environmental variable, \$IJ_MEM,"
+	einfo "and the class path by setting the environmental variable, \$IJ_CP."
+	einfo ""
+	einfo "If you want to use much more plugins, please see http://rsb.info.nih.gov/ij/plugins/index.html"
+	einfo "and add *.class files to \$IJ_HOME/plugins folder"
+	einfo ""
+}
diff --git a/sci-biology/imagej/metadata.xml b/sci-biology/imagej/metadata.xml
index ca2867d8c..8b8ebd7d9 100644
--- a/sci-biology/imagej/metadata.xml
+++ b/sci-biology/imagej/metadata.xml
@@ -12,4 +12,7 @@
 	<use>
 		<flag name="plugins">Install additional plugins</flag>
 	</use>
+	<upstream>
+		<remote-id type="github">imagej/ImageJ</remote-id>
+	</upstream>
 </pkgmetadata>
diff --git a/sci-biology/irsabi_bidsdata/ChangeLog b/sci-biology/irsabi_bidsdata/ChangeLog
deleted file mode 100644
index b50647328..000000000
--- a/sci-biology/irsabi_bidsdata/ChangeLog
+++ /dev/null
@@ -1,5 +0,0 @@
-*irsabi_bidsdata-1.0 (06 Jan 2019)
-
-  06 Jan 2019; Horea Christian <h.chr@mail.ru> +irsabi_bidsdata-1.0.ebuild,
-  +metadata.xml:
-  sci-biology/irsabi_bidsdata: new package ahead of Gentoo Science
diff --git a/sci-biology/irsabi_bidsdata/Manifest b/sci-biology/irsabi_bidsdata/Manifest
index 8b3b2dbf4..2ac34de55 100644
--- a/sci-biology/irsabi_bidsdata/Manifest
+++ b/sci-biology/irsabi_bidsdata/Manifest
@@ -1 +1 @@
-DIST irsabi_bidsdata-1.0.tar.xz 4503366188 BLAKE2B 7c0946b2287c082a35c832ee00b353b361abc1325d48414ae99f9f73c52f7e1d14f061781cc2627fe030930fb45f7f0e177d9cef35fb1f2fd2e1680937f503a5 SHA512 3fbb08c50ffc52eb64a5205753fbe0da17fcc2ff87eb6283b7db1462e9143431e1263eae1ce75b0f5960cd987e6d33b9e8a2829608931996b32f8a6c63100f0e
+DIST irsabi_bidsdata-1.4.tar.xz 4503367352 BLAKE2B 4d0b3fa9f508a002c1e6d1c6d7a897d36788d120a0361f22decc944c1230542a119020d808f2e1d808ff2edb566ea06d57d25ffc3c863913b61b995fbb2f7310 SHA512 20a6e486d74ca57b3a8cced87db7fc110ae7ad2e466bd76cfd3ad46ec317c30597a4569005696c509dc2f9fc40dd1d0dbee0c0bf174e5ae8cab53058ce980b10
diff --git a/sci-biology/irsabi_bidsdata/irsabi_bidsdata-1.0.ebuild b/sci-biology/irsabi_bidsdata/irsabi_bidsdata-1.0.ebuild
deleted file mode 100644
index 7cf730e8e..000000000
--- a/sci-biology/irsabi_bidsdata/irsabi_bidsdata-1.0.ebuild
+++ /dev/null
@@ -1,30 +0,0 @@
-# Copyright 1999-2019 Gentoo Authors
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=7
-
-inherit check-reqs
-
-DESCRIPTION="BIDS data files released with the IRSABI publication"
-HOMEPAGE="http://www.aic-fmi.ethz.ch/"
-SRC_URI="http://chymera.eu/distfiles/${P}.tar.xz"
-
-LICENSE="CC-BY-SA-4.0"
-SLOT="0"
-KEYWORDS="~amd64 ~x86 ~amd64-linux ~x86-linux"
-
-RDEPEND=""
-DEPEND=""
-
-pkg_pretend() {
-	CHECKREQS_DISK_BUILD="10G"
-	check-reqs_pkg_pretend
-}
-
-# We disable this phase to not check requirements twice.
-pkg_setup() { :; }
-
-src_install() {
-	insinto "/usr/share/${PN}"
-	doins -r *
-}
diff --git a/sci-biology/irsabi_bidsdata/irsabi_bidsdata-1.4.ebuild b/sci-biology/irsabi_bidsdata/irsabi_bidsdata-1.4.ebuild
new file mode 100644
index 000000000..021929bad
--- /dev/null
+++ b/sci-biology/irsabi_bidsdata/irsabi_bidsdata-1.4.ebuild
@@ -0,0 +1,32 @@
+# Copyright 1999-2022 Gentoo Authors
+# Distributed under the terms of the GNU General Public License v2
+
+EAPI=7
+
+inherit check-reqs
+
+DESCRIPTION="BIDS data files released with the IRSABI publication"
+HOMEPAGE="https://chymera.eu/docs/focus/open-science/"
+SRC_URI="
+	https://zenodo.org/record/3601531/files/${P}.tar.xz
+"
+
+LICENSE="CC-BY-SA-4.0"
+SLOT="0"
+KEYWORDS="~amd64 ~x86 ~amd64-linux ~x86-linux"
+
+RDEPEND=""
+DEPEND=""
+
+pkg_pretend() {
+	CHECKREQS_DISK_BUILD="10G"
+	check-reqs_pkg_pretend
+}
+
+# We disable this phase to not check requirements twice.
+pkg_setup() { :; }
+
+src_install() {
+	insinto "/usr/share/${PN}"
+	doins -r *
+}
diff --git a/sci-biology/irsabi_bidsdata/metadata.xml b/sci-biology/irsabi_bidsdata/metadata.xml
index 9c6323c0a..b4cb59969 100644
--- a/sci-biology/irsabi_bidsdata/metadata.xml
+++ b/sci-biology/irsabi_bidsdata/metadata.xml
@@ -2,7 +2,7 @@
 <!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
 <pkgmetadata>
 	<maintainer type="person">
-		<email>horea.christ@gmail.com</email>
+		<email>gentoo@chymera.eu</email>
 		<name>Horea Christian</name>
 	</maintainer>
 	<maintainer type="project">
diff --git a/sci-biology/jannovar-bin/Manifest b/sci-biology/jannovar-bin/Manifest
index 784120abf..29a2a696f 100644
--- a/sci-biology/jannovar-bin/Manifest
+++ b/sci-biology/jannovar-bin/Manifest
@@ -1,6 +1,5 @@
-DIST jannovar-cli-0.17.jar 8540135 BLAKE2B 1f286e61ae85e3d097a47043687d042c7a66f2e3a9617bb11a872bedd3388fab2a379381478da9fc1e28824ce9c64070da7db59ccd1a2c833de9d9ce9b37fb79 SHA512 bef201e98176269b2b0069e08aae8c6cdb687d8e0342a53a08b5c00c28d0afbe5c3230dbf57deaea6b0f332d81b7639a5f25a9f25722b756a951d9699fdd9bf9
-DIST jannovar-core-0.17.jar 284035 BLAKE2B 82e334b0e76f20dc8fbd2890206b0839187a52af1c805ebde6a1c229a4e989f8d8fc2ded0b53a8833149608b1f7bd0af9fb6723817170e35a4527dbe133a395f SHA512 78eff3bd16abc3053546b7a14c00b597f17c3b58c2c17e11be033b22b2452c2e3ad0de56cc76387321c00db6cda70219f627022905bdd81354bb45baca5d3c02
-DIST jannovar-hgvs-0.17.jar 198023 BLAKE2B 283719aec622f7bc2f8fca98c1bbe85ccfa986b04e27cde604d147c2e4d71d2aa4e8f407822cdc4b5afb972c4a3d278e144cd50ba2650e80155a8a5f1b47bc61 SHA512 2cd750dccae52bcd6a255feacd26729ff001e7561a3f49eb99f68012f5e0d4948450def8e22e189e3364a509ee7899189a3ba7c94fb9f784d94bea06277a3616
-DIST jannovar-htsjdk-0.17.jar 66149 BLAKE2B 7bd91c8f544d4071556ead47f513cc7abbe09ac3f36935b945ae912301e9af6be8e259510a26e60505d5fa2f2c9ac3bab39f6e7b812e564d81fa183aff8e8e2f SHA512 0605fd7bd53607ba79427a9f7c9e0d30789b6e6d33528bb9d3aa35b876503c8524751c58e38fa3f5d97c2b9b95521d6057eb20ea4fc3c9b378f9df82aa419082
-DIST jannovar-inheritance-checker-0.17.jar 34815 BLAKE2B 367aece2ed477e9f9d47d7e0f1c9930069141f12d05344336b61fcf0bfb4cb80f62c9ecb4f696c1c81676ea5b0e8e0214d1a9e20cf102763ecd23a8a6eef9efe SHA512 777397ff2d0d4d8327eb4a120f3f8fdba6b371c574e6c7c65186c4c7717c6d6a2f41e6246ad3ce741f3022d0a8daaa407dac75988b0c53ea5fa26e2a08c389bf
-DIST jannovar-vardbs-0.17.jar 73655 BLAKE2B d9b7ce562902c688e04252d5e3b4e029f181b338908f2c67347d2e40f7374097c7f92d6e2303c610f82c43c54fd6734126f4a9d591dd17d3b2c66cc2d3bbe087 SHA512 f6d837d9f6fa6ac1b71fe478d76b877fc394fecd95f050704d9d42fddf02b5c059d70351611af6788c4380fd125c46703a4573111671a48b53ff16d31e8ed15d
+DIST jannovar-cli-0.35.jar 15561583 BLAKE2B d1b8f40635beb5b12a33fc1a218878849e18989cd0315e7bfac032bb71920974789f22f361697467b3fa42a3bc6e00003fade3a2940ec08d3b97d9d2b1a6fd8c SHA512 e0615c7982627a57750bc243078002712d92c827fa2b8e264bcc4141768251cde91206e61896f9939aaeee3d8e061ca99ab6d5ed575ec0e28ac377ad6f2c5daf
+DIST jannovar-core-0.35.jar 381491 BLAKE2B 24514d0f6cce77f79724e06bc736a18f1ee94625230a53abc098a728a2003dfdf7a82dc516de8f1c841eda7916a257cf1b91353680f4bafdbf2dbb0576cf7584 SHA512 9da6f681e88fa05837f74d9029dfdcbaf83fc246f395345f982c47098fe9609c8904a5300bb4a9d11b95f026b670f2c6a76f015f5a3774553ccbc6c956d2e662
+DIST jannovar-hgvs-0.35.jar 201027 BLAKE2B 9b91276accfa1d593db181caf6bc51387d133b14e2d4a60cc8b02b3ba26ef8477f962180913586c2a192ab1e869b2d2f6ef4211bd7928884537830fc0b393b62 SHA512 527614f3fc603df76f93895bc7852d6e4adadc4a51f583b0d30c23e4730617d6392fb3d5b7eb684bc4b749d4f77bca2e79c105581ed98f9407b08da4abc40df2
+DIST jannovar-htsjdk-0.35.jar 81035 BLAKE2B f601e0c7c2c8cbcbee4850a39db4131ec512f28d791ebf1e7e43ed96e23560006cf9b98cfa5a2534d0780abff704c4428b5440d3d9076a3612b7206de75c2068 SHA512 342289d848f45d18354862f21e084f391044dd45e7b7398b464d5c309e580c286e34a71db2c3afa62fdb94c36458c1ccaa467e09add0567a4251ce1df2f0c748
+DIST jannovar-vardbs-0.35.jar 198351 BLAKE2B e2e16a2dd1867325c02bfe75fee9c5bf2a34352f19f560057a646015227f412815559637bce8e403fd5aef56d1b841a3eed2ef0d284eab236f5e56a6ca25bf98 SHA512 b393acc88ef580188624c6fa6172c14c648e2c6b9a95b60c6aac24a6324d610e71a5f11f2143cd11b4c717e3ca93cd09958b546991ae8c0bc5f5b4dd61a7b7ff
diff --git a/sci-biology/jannovar-bin/jannovar-bin-0.17.ebuild b/sci-biology/jannovar-bin/jannovar-bin-0.17.ebuild
deleted file mode 100644
index 4544eaab8..000000000
--- a/sci-biology/jannovar-bin/jannovar-bin-0.17.ebuild
+++ /dev/null
@@ -1,36 +0,0 @@
-# Copyright 1999-2016 Gentoo Foundation
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=5
-
-inherit java-pkg-2
-
-DESCRIPTION="Exome annotation tool (upstream jar binaries)"
-HOMEPAGE="http://compbio.charite.de
-	https://github.com/charite/jannovar"
-SRC_URI="https://search.maven.org/remotecontent?filepath=de/charite/compbio/jannovar-cli/${PV}/jannovar-cli-${PV}.jar
-	https://search.maven.org/remotecontent?filepath=de/charite/compbio/jannovar-vardbs/${PV}/jannovar-vardbs-${PV}.jar
-	https://search.maven.org/remotecontent?filepath=de/charite/compbio/jannovar-htsjdk/${PV}/jannovar-htsjdk-${PV}.jar
-	https://search.maven.org/remotecontent?filepath=de/charite/compbio/jannovar-inheritance-checker/${PV}/jannovar-inheritance-checker-${PV}.jar
-	https://search.maven.org/remotecontent?filepath=de/charite/compbio/jannovar-core/${PV}/jannovar-core-${PV}.jar
-	https://search.maven.org/remotecontent?filepath=de/charite/compbio/jannovar-hgvs/${PV}/jannovar-hgvs-${PV}.jar"
-
-LICENSE="BSD-2"
-SLOT="0"
-KEYWORDS="~amd64 ~x86"
-IUSE=""
-
-DEPEND=">=virtual/jdk-1.6"
-RDEPEND=">=virtual/jre-1.6"
-
-S="${WORKDIR}"
-
-src_install(){
-	java-pkg_newjar "${DISTDIR}"/jannovar-cli-"${PV}".jar jannovar-cli.jar
-	java-pkg_dolauncher jannovar-cli-bin --jar jannovar-cli.jar
-	java-pkg_newjar "${DISTDIR}"/jannovar-vardbs-"${PV}".jar jannovar-vardbs.jar
-	java-pkg_newjar "${DISTDIR}"/jannovar-htsjdk-"${PV}".jar jannovar-htsjdk.jar
-	java-pkg_newjar "${DISTDIR}"/jannovar-inheritance-checker-"${PV}".jar jannovar-inheritance-checker.jar
-	java-pkg_newjar "${DISTDIR}"/jannovar-core-${PV}.jar jannovar-core.jar
-	java-pkg_newjar "${DISTDIR}"/jannovar-hgvs-${PV}.jar jannovar-hgvs.jar
-}
diff --git a/sci-biology/jannovar-bin/jannovar-bin-0.35.ebuild b/sci-biology/jannovar-bin/jannovar-bin-0.35.ebuild
new file mode 100644
index 000000000..1b3a90297
--- /dev/null
+++ b/sci-biology/jannovar-bin/jannovar-bin-0.35.ebuild
@@ -0,0 +1,33 @@
+# Copyright 1999-2021 Gentoo Authors
+# Distributed under the terms of the GNU General Public License v2
+
+EAPI=7
+
+inherit java-pkg-2
+
+DESCRIPTION="Exome annotation tool (upstream jar binaries)"
+HOMEPAGE="https://jannovar.readthedocs.io/en/master/"
+SRC_URI="
+	https://search.maven.org/remotecontent?filepath=de/charite/compbio/jannovar-cli/${PV}/jannovar-cli-${PV}.jar
+	https://search.maven.org/remotecontent?filepath=de/charite/compbio/jannovar-vardbs/${PV}/jannovar-vardbs-${PV}.jar
+	https://search.maven.org/remotecontent?filepath=de/charite/compbio/jannovar-htsjdk/${PV}/jannovar-htsjdk-${PV}.jar
+	https://search.maven.org/remotecontent?filepath=de/charite/compbio/jannovar-core/${PV}/jannovar-core-${PV}.jar
+	https://search.maven.org/remotecontent?filepath=de/charite/compbio/jannovar-hgvs/${PV}/jannovar-hgvs-${PV}.jar"
+
+LICENSE="BSD-2"
+SLOT="0"
+KEYWORDS="~amd64 ~x86"
+
+DEPEND=">=virtual/jdk-1.7"
+RDEPEND=">=virtual/jre-1.7"
+
+S="${WORKDIR}"
+
+src_install(){
+	java-pkg_newjar "${DISTDIR}"/jannovar-cli-"${PV}".jar jannovar-cli.jar
+	java-pkg_dolauncher jannovar-cli-bin --jar jannovar-cli.jar
+	java-pkg_newjar "${DISTDIR}"/jannovar-vardbs-"${PV}".jar jannovar-vardbs.jar
+	java-pkg_newjar "${DISTDIR}"/jannovar-htsjdk-"${PV}".jar jannovar-htsjdk.jar
+	java-pkg_newjar "${DISTDIR}"/jannovar-core-${PV}.jar jannovar-core.jar
+	java-pkg_newjar "${DISTDIR}"/jannovar-hgvs-${PV}.jar jannovar-hgvs.jar
+}
diff --git a/sci-biology/jannovar/Manifest b/sci-biology/jannovar/Manifest
deleted file mode 100644
index 9166ee546..000000000
--- a/sci-biology/jannovar/Manifest
+++ /dev/null
@@ -1 +0,0 @@
-DIST jannovar-0.17.tar.gz 1143413 SHA256 f6437916115e207718e996f4d6d95a6f895009ce926b56c76cd6d00c53f6a2ff SHA512 4c746ba71c3d79dff2798c2cfe8bfdb762b106bf1c838c59e64871fc2aac7adec62146c11eb210fdd5dd190b6a88a7d611fcf42235e84c9d7352fd4006e0ffd7 WHIRLPOOL d3396bffd75c5da5e22bc8858af8684393990a90c1a86b368baa29afc1c44f380756520380ef8253e73741a3d737297e8c6aadff9f762076b7b258d8b8708961
diff --git a/sci-biology/jannovar/jannovar-0.17.ebuild b/sci-biology/jannovar/jannovar-0.17.ebuild
deleted file mode 100644
index 7337adbc2..000000000
--- a/sci-biology/jannovar/jannovar-0.17.ebuild
+++ /dev/null
@@ -1,58 +0,0 @@
-# Copyright 1999-2016 Gentoo Foundation
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=5
-
-inherit java-pkg-2
-
-DESCRIPTION="Exome annotation tool"
-HOMEPAGE="http://compbio.charite.de/contao/index.php/jannovar.html"
-SRC_URI="https://github.com/charite/jannovar/archive/v"${PV}".tar.gz -> ${P}.tar.gz"
-
-# https://github.com/charite/jannovar
-LICENSE="BSD-2"
-SLOT="0"
-KEYWORDS=""
-IUSE=""
-
-COMMON_DEPS="
-	dev-java/commons-compress
-	dev-java/commons-io
-	dev-java/commons-jexl:*
-	dev-java/commons-logging:0
-	dev-java/commons-net
-	dev-java/guava:*
-	dev-java/hamcrest-core:*
-	dev-java/htsjdk
-	dev-java/ini4j
-	dev-java/junit:*
-	dev-java/log4j:0"
-DEPEND=">=virtual/jdk-1.6
-	dev-java/maven-bin:*
-	${COMMON_DEPS}"
-RDEPEND=">=virtual/jre-1.6
-	${COMMON_DEPS}"
-
-# TODO: set a proxy because it downloads data during compile step
-# http://jannovar.readthedocs.io/en/master/install.html
-# see https://github.com/charite/jannovar/issues/218
-# https://maven.apache.org/settings.html#Proxies
-src_compile(){
-	mvn package -Dmaven.test.skip.exec=true -DskipTests=true -Duser.home="${HOME}" || die
-}
-
-src_install(){
-	# maven download 95MB from the network into "${PORTAGE_BUILDDIR}/homedir/"
-	export M2="${HOME}"
-	mvn install -Dmaven.test.skip.exec=true -Duser.home="${HOME}" || die
-	# jannovar-cli-${PV}.jar includes all libraries (jannovar and others like htsjdk)
-	java-pkg_dojar jannovar-cli/target/jannovar-cli-"${PV}".jar
-	java-pkg_dolauncher jannovar-cli --jar jannovar-cli-"${PV}".jar
-	# original-jannovar-cli-0.17.jar contains only the source files of the specific package
-	java-pkg_dojar jannovar-cli/target/original-jannovar-cli-"${PV}".jar
-	java-pkg_dojar jannovar-hgvs/target/jannovar-hgvs-"${PV}".jar
-	java-pkg_dojar jannovar-htsjdk/target/jannovar-htsjdk-"${PV}".jar
-	java-pkg_dojar jannovar-core/target/jannovar-core-"${PV}".jar
-	java-pkg_dojar jannovar-vardbs/target/jannovar-vardbs-"${PV}".jar
-	java-pkg_dojar jannovar-inheritance-checker/target/jannovar-inheritance-checker-"${PV}".jar
-}
diff --git a/sci-biology/jannovar/metadata.xml b/sci-biology/jannovar/metadata.xml
deleted file mode 100644
index 5e4e28811..000000000
--- a/sci-biology/jannovar/metadata.xml
+++ /dev/null
@@ -1,15 +0,0 @@
-<?xml version="1.0" encoding="UTF-8"?>
-<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
-<pkgmetadata>
-	<maintainer type="person">
-		<email>mmokrejs@fold.natur.cuni.cz</email>
-		<name>Martin Mokrejs</name>
-	</maintainer>
-	<maintainer type="project">
-		<email>sci-biology@gentoo.org</email>
-		<name>Gentoo Biology Project</name>
-	</maintainer>
-	<upstream>
-		<remote-id type="github">charite/jannovar</remote-id>
-	</upstream>
-</pkgmetadata>
diff --git a/sci-biology/jellyfish/Manifest b/sci-biology/jellyfish/Manifest
index 40acba1ff..810ff5a35 100644
--- a/sci-biology/jellyfish/Manifest
+++ b/sci-biology/jellyfish/Manifest
@@ -1,6 +1,2 @@
-DIST JellyfishUserGuide.pdf 142367 BLAKE2B 371d04c920a6e4d25ba74238c5262a9f8c182645b73468d0bed9f519da25d8c886cb9895a8e9334169caa247ebe9f8aa4738ed2e8d7d14cd5ecfb35ede7403a8 SHA512 a9d65be7591d4b9b275b9f76ab79806d31bf7ef36b297b67b1802a302687aa8d49d4c491c3bb9201aec58268bcfc8c703940c72991b9080bbd1bde95bbda5b8a
 DIST jellyfish-1.1.12.tar.gz 1097948 BLAKE2B c1394527c0645d1ac14045691d0c7defc080dbdc2d33c64cb12462d0f3e4c08bd5e65e4f8276741e67595b6d942b211a088ed4981fb419fffb5afbed9316dc11 SHA512 95739117a9090f6338c388ee3b4a3d2a3df32f1311d11f1b23fabd873efed19f7beaf2da1385c0fd78ada3684bf8c7282608292c642f5f35e201676fb87953bf
-DIST jellyfish-2.1.3.tar.gz 955773 BLAKE2B f01891238aa819ddeb2ca3b45276f23fe209cb0015bc5874adbed6355bce44ab23c19020fd5a10779a93c29ca3d241e36fe72fb5b4ffee4a37b954980cb6b217 SHA512 2b6fea6c2686de7b568988543d5a9466676eb17252ecce3243b0dc7e3c833aed02ae6570749df58c2921289db0167b39848ccd80eb3cc568cdbaa0045114b702
-DIST jellyfish-2.1.4.tar.gz 958038 BLAKE2B 8cb3fa50858f8cc4fbb3e5e9c64f76e2d3ff4453767411a36fab1188673cbfd12f52270ee7f4269c606931f34e9805c878a05c6dcd3370b7b0de65f25ad7a1fb SHA512 28bbaf6ed5c69caec24a09ceb2dfa99b160f3a9c2764d3f30ab205374a6f17dfc5c6d7405e75fd5161882350db160442a91568dd65ea9851e8cb74eb71f25742
-DIST jellyfish-2.2.10.tar.gz 1123173 BLAKE2B 9a30d4dce8189b199842abe9ffd1efba7a60240786898deb38af6b67365311eff38d60c886c4c290747d413e4a03a9bbb0060282b12025fa81e507533f062bb7 SHA512 241f151981c840f8c68b39465d19db2c2199183908e7de337ccb1bf0fb107a088c2ea116f8a023ca6eab338a6a63c46d6b7915ce508577d8a5bc1d5537f8de19
-DIST jellyfish-2.2.6.tar.gz 1082535 BLAKE2B 8ad044c470245132c843f93c639f9c0e502bcf41031a7a561b9c2bbfb46763d91651de5af51bf9d42bf560dbb7de9be5595aa00b9cf3a060db731a5087494780 SHA512 c3320facbbad1c6f2aede2edd7d2574bbff0e5a7f655d8b0224e511f07a319c4682adc1576a189367a546011c43d79f7b01474580dcc9c44f8e087397b475056
+DIST jellyfish-2.3.0.tar.gz 1151287 BLAKE2B adf91b15a5bdfdd9bcc8fa0b1274ac016051712630e31e7203e7ab27620d575172bbd01ae1e4a3fce97f897bfcf436fc1e0c3c4ac38e6c29b580d3f767bdf979 SHA512 5bd2b458bbd05f62dc36e4e7e81d13e1ae3207a4c063e95ede1678af9c0fdb9155a2452b272d1a6b5a60f0672ac01e70853b6ab2e5ae021c83f60d50527f94c7
diff --git a/sci-biology/jellyfish/jellyfish-1.1.12.ebuild b/sci-biology/jellyfish/jellyfish-1.1.12.ebuild
index d39fb6104..a6989c2bf 100644
--- a/sci-biology/jellyfish/jellyfish-1.1.12.ebuild
+++ b/sci-biology/jellyfish/jellyfish-1.1.12.ebuild
@@ -1,12 +1,10 @@
-# Copyright 1999-2018 Gentoo Foundation
+# Copyright 1999-2023 Gentoo Authors
 # Distributed under the terms of the GNU General Public License v2
 
-EAPI=6
-
-inherit eutils flag-o-matic
+EAPI=8
 
 DESCRIPTION="k-mer counter within reads for assemblies"
-HOMEPAGE="http://www.cbcb.umd.edu/software/jellyfish"
+HOMEPAGE="https://genome.umd.edu/jellyfish.html"
 SRC_URI="https://github.com/gmarcais/Jellyfish/releases/download/v${PV}/${P}.tar.gz"
 
 # older version is hidden in trinityrnaseq_r20140413p1/trinity-plugins/jellyfish-1.1.11
@@ -18,21 +16,18 @@ SLOT="1"
 KEYWORDS="~amd64 ~x86"
 IUSE="cpu_flags_x86_sse"
 
-DEPEND=""
-DEPEND="${RDEPEND}
-	virtual/pkgconfig"
+BDEPEND="virtual/pkgconfig"
 
-src_prepare(){
+src_configure() {
 	#  --with-sse              enable SSE
 	#  --with-half             enable half float (16 bits)
 	#  --with-int128           enable int128
 	local myconf
 	use cpu_flags_x86_sse && myconf+=( --with-sse )
 	econf ${myconf[@]}
-	eapply_user
 }
 
-src_install(){
+src_install() {
 	default
 	# install the binary under jellyfish1 name like Debian/Ubuntu to avoid name clash with jellyfish2 and allow simultaneous installs
 	mv "${ED}"/usr/bin/jellyfish "${ED}"/usr/bin/jellyfish1 || die
diff --git a/sci-biology/jellyfish/jellyfish-2.1.3-r1.ebuild b/sci-biology/jellyfish/jellyfish-2.1.3-r1.ebuild
deleted file mode 100644
index 5404d6bfb..000000000
--- a/sci-biology/jellyfish/jellyfish-2.1.3-r1.ebuild
+++ /dev/null
@@ -1,45 +0,0 @@
-# Copyright 1999-2018 Gentoo Foundation
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=6
-
-inherit eutils flag-o-matic
-
-DESCRIPTION="k-mer counter within reads for assemblies"
-HOMEPAGE="http://www.genome.umd.edu/jellyfish.html"
-SRC_URI="ftp://ftp.genome.umd.edu/pub/${PN}/${P}.tar.gz
-	ftp://ftp.genome.umd.edu/pub/jellyfish/JellyfishUserGuide.pdf"
-
-# older version is hidden in trinityrnaseq_r20140413p1/trinity-plugins/jellyfish-1.1.11
-
-LICENSE="GPL-3+ BSD"
-SLOT="2"
-KEYWORDS="~amd64 ~x86"
-IUSE="cpu_flags_x86_sse"
-
-DEPEND=""
-DEPEND="${RDEPEND}
-	virtual/pkgconfig"
-
-src_prepare(){
-	#  --with-sse              enable SSE
-	#  --with-half             enable half float (16 bits)
-	#  --with-int128           enable int128
-	local myconf
-	use cpu_flags_x86_sse && myconf+=( --with-sse )
-	econf ${myconf[@]}
-	eapply_user
-}
-
-src_install(){
-	default
-	mv "${ED}"/usr/bin/jellyfish "${ED}"/usr/bin/jellyfish2 || die
-	sed -e "s#jellyfish-${PV}#jellyfish#" -i "${ED}/usr/$(get_libdir)"/pkgconfig/jellyfish-2.0.pc || die
-	find "${ED}"/usr/include/"${P}"/"${PN}" -type f | while read f; do
-	sed -e "s#include <jellyfish/#include <jellyfish${SLOT}/#" -i $f || die
-	done
-	mkdir -p "${ED}/usr/include/${PN}${SLOT}" || die
-	mv "${ED}"/usr/include/"${P}"/"${PN}"/* "${ED}/usr/include/${PN}${SLOT}/" || die
-	rm -r "${ED}/usr/include/${P}" || die
-	mv "${ED}"/usr/share/man/man1/jellyfish.1 "${ED}"/usr/share/man/man1/jellyfish"${SLOT}".1 || die
-}
diff --git a/sci-biology/jellyfish/jellyfish-2.1.4-r1.ebuild b/sci-biology/jellyfish/jellyfish-2.1.4-r1.ebuild
deleted file mode 100644
index 11a4a4805..000000000
--- a/sci-biology/jellyfish/jellyfish-2.1.4-r1.ebuild
+++ /dev/null
@@ -1,45 +0,0 @@
-# Copyright 1999-2018 Gentoo Foundation
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=6
-
-inherit eutils flag-o-matic
-
-DESCRIPTION="k-mer counter within reads for assemblies"
-HOMEPAGE="http://www.genome.umd.edu/jellyfish.html"
-SRC_URI="ftp://ftp.genome.umd.edu/pub/${PN}/${P}.tar.gz
-	ftp://ftp.genome.umd.edu/pub/jellyfish/JellyfishUserGuide.pdf"
-
-# older version is hidden in trinityrnaseq_r20140413p1/trinity-plugins/jellyfish-1.1.11
-
-LICENSE="GPL-3+ BSD"
-SLOT="2"
-KEYWORDS="~amd64 ~x86"
-IUSE="cpu_flags_x86_sse"
-
-DEPEND=""
-DEPEND="${RDEPEND}
-	virtual/pkgconfig"
-
-src_prepare(){
-	#  --with-sse              enable SSE
-	#  --with-half             enable half float (16 bits)
-	#  --with-int128           enable int128
-	local myconf
-	use cpu_flags_x86_sse && myconf+=( --with-sse )
-	econf ${myconf[@]}
-	eapply_user
-}
-
-src_install(){
-	default
-	mv "${ED}"/usr/bin/jellyfish "${ED}"/usr/bin/jellyfish2 || die
-	sed -e "s#jellyfish-${PV}#jellyfish#" -i "${ED}/usr/$(get_libdir)"/pkgconfig/jellyfish-2.0.pc || die
-	find "${ED}"/usr/include/"${P}"/"${PN}" -type f | while read f; do
-		sed -e "s#include <jellyfish/#include <jellyfish${SLOT}/#" -i $f || die
-	done
-	mkdir -p "${ED}/usr/include/${PN}${SLOT}" || die
-	mv "${ED}"/usr/include/"${P}"/"${PN}"/* "${ED}/usr/include/${PN}${SLOT}/" || die
-	rm -r "${ED}/usr/include/${P}" || die
-	mv "${ED}"/usr/share/man/man1/jellyfish.1 "${ED}"/usr/share/man/man1/jellyfish"${SLOT}".1 || die
-}
diff --git a/sci-biology/jellyfish/jellyfish-2.2.10.ebuild b/sci-biology/jellyfish/jellyfish-2.2.10.ebuild
deleted file mode 100644
index 89f9fa231..000000000
--- a/sci-biology/jellyfish/jellyfish-2.2.10.ebuild
+++ /dev/null
@@ -1,51 +0,0 @@
-# Copyright 1999-2018 Gentoo Foundation
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=6
-
-inherit eutils flag-o-matic autotools
-
-DESCRIPTION="k-mer counter within reads for assemblies"
-HOMEPAGE="http://www.genome.umd.edu/jellyfish.html"
-SRC_URI="https://github.com/gmarcais/Jellyfish/releases/download/v${PV}/${P}.tar.gz"
-
-# older version is hidden in trinityrnaseq_r20140413p1/trinity-plugins/jellyfish-1.1.11
-
-LICENSE="GPL-3+ BSD"
-SLOT="2"
-KEYWORDS="~amd64 ~x86"
-IUSE="cpu_flags_x86_sse"
-
-RDEPEND=""
-DEPEND="${RDEPEND}
-	virtual/pkgconfig"
-
-src_prepare(){
-	eautoreconf
-	default
-}
-
-# TODO: enable compilation of Bindings to Ruby, Python and Perl
-# '--enable-ruby-binding', '--enable-python-binding' or '--enable-perl-binding',  '--enable-swig'
-src_configure(){
-	#  --with-sse              enable SSE
-	#  --with-half             enable half float (16 bits)
-	#  --with-int128           enable int128
-	local myconf
-	use cpu_flags_x86_sse && myconf+=( --with-sse )
-	econf ${myconf[@]}
-}
-
-src_install(){
-	default
-	mv "${ED}"/usr/bin/jellyfish "${ED}"/usr/bin/jellyfish2 || die
-	sed -e "s#jellyfish-${PV}#jellyfish#" -i "${ED}/usr/$(get_libdir)"/pkgconfig/jellyfish-2.0.pc || die
-	find "${ED}"/usr/include/"${P}"/"${PN}" -type f | while read f; do
-		sed -e "s#include <jellyfish/#include <jellyfish${SLOT}/#" -i $f || die
-	done
-	mkdir -p "${ED}/usr/include/${PN}${SLOT}" || die
-	mv "${ED}"/usr/include/"${P}"/"${PN}"/* "${ED}/usr/include/${PN}${SLOT}/" || die
-	rm -r "${ED}/usr/include/${P}" || die
-	mv "${ED}"/usr/share/man/man1/jellyfish.1 "${ED}"/usr/share/man/man1/jellyfish"${SLOT}".1 || die
-	dodoc doc/jellyfish.pdf
-}
diff --git a/sci-biology/jellyfish/jellyfish-2.2.6-r1.ebuild b/sci-biology/jellyfish/jellyfish-2.2.6-r1.ebuild
deleted file mode 100644
index 89f9fa231..000000000
--- a/sci-biology/jellyfish/jellyfish-2.2.6-r1.ebuild
+++ /dev/null
@@ -1,51 +0,0 @@
-# Copyright 1999-2018 Gentoo Foundation
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=6
-
-inherit eutils flag-o-matic autotools
-
-DESCRIPTION="k-mer counter within reads for assemblies"
-HOMEPAGE="http://www.genome.umd.edu/jellyfish.html"
-SRC_URI="https://github.com/gmarcais/Jellyfish/releases/download/v${PV}/${P}.tar.gz"
-
-# older version is hidden in trinityrnaseq_r20140413p1/trinity-plugins/jellyfish-1.1.11
-
-LICENSE="GPL-3+ BSD"
-SLOT="2"
-KEYWORDS="~amd64 ~x86"
-IUSE="cpu_flags_x86_sse"
-
-RDEPEND=""
-DEPEND="${RDEPEND}
-	virtual/pkgconfig"
-
-src_prepare(){
-	eautoreconf
-	default
-}
-
-# TODO: enable compilation of Bindings to Ruby, Python and Perl
-# '--enable-ruby-binding', '--enable-python-binding' or '--enable-perl-binding',  '--enable-swig'
-src_configure(){
-	#  --with-sse              enable SSE
-	#  --with-half             enable half float (16 bits)
-	#  --with-int128           enable int128
-	local myconf
-	use cpu_flags_x86_sse && myconf+=( --with-sse )
-	econf ${myconf[@]}
-}
-
-src_install(){
-	default
-	mv "${ED}"/usr/bin/jellyfish "${ED}"/usr/bin/jellyfish2 || die
-	sed -e "s#jellyfish-${PV}#jellyfish#" -i "${ED}/usr/$(get_libdir)"/pkgconfig/jellyfish-2.0.pc || die
-	find "${ED}"/usr/include/"${P}"/"${PN}" -type f | while read f; do
-		sed -e "s#include <jellyfish/#include <jellyfish${SLOT}/#" -i $f || die
-	done
-	mkdir -p "${ED}/usr/include/${PN}${SLOT}" || die
-	mv "${ED}"/usr/include/"${P}"/"${PN}"/* "${ED}/usr/include/${PN}${SLOT}/" || die
-	rm -r "${ED}/usr/include/${P}" || die
-	mv "${ED}"/usr/share/man/man1/jellyfish.1 "${ED}"/usr/share/man/man1/jellyfish"${SLOT}".1 || die
-	dodoc doc/jellyfish.pdf
-}
diff --git a/sci-biology/jellyfish/jellyfish-2.3.0.ebuild b/sci-biology/jellyfish/jellyfish-2.3.0.ebuild
new file mode 100644
index 000000000..2237173e0
--- /dev/null
+++ b/sci-biology/jellyfish/jellyfish-2.3.0.ebuild
@@ -0,0 +1,47 @@
+# Copyright 1999-2023 Gentoo Authors
+# Distributed under the terms of the GNU General Public License v2
+
+EAPI=8
+
+DESCRIPTION="k-mer counter within reads for assemblies"
+HOMEPAGE="https://genome.umd.edu/jellyfish.html"
+SRC_URI="https://github.com/gmarcais/Jellyfish/releases/download/v${PV}/${P}.tar.gz"
+
+# older version is hidden in trinityrnaseq_r20140413p1/trinity-plugins/jellyfish-1.1.11
+
+LICENSE="GPL-3+ BSD"
+SLOT="2"
+KEYWORDS="~amd64 ~x86"
+IUSE="cpu_flags_x86_sse"
+
+RDEPEND="
+	sci-biology/samtools:0
+	sci-libs/htslib
+"
+DEPEND="${RDEPEND}"
+BDEPEND="virtual/pkgconfig"
+
+# TODO: enable compilation of Bindings to Ruby, Python and Perl
+# '--enable-ruby-binding', '--enable-python-binding' or '--enable-perl-binding',  '--enable-swig'
+src_configure(){
+	#  --with-sse              enable SSE
+	#  --with-half             enable half float (16 bits)
+	#  --with-int128           enable int128
+	local myconf
+	use cpu_flags_x86_sse && myconf+=( --with-sse )
+	econf ${myconf[@]}
+}
+
+src_install(){
+	default
+	mv "${ED}"/usr/bin/jellyfish "${ED}"/usr/bin/jellyfish2 || die
+	sed -e "s#jellyfish-${PV}#jellyfish#" -i "${ED}/usr/$(get_libdir)"/pkgconfig/jellyfish-2.0.pc || die
+	find "${ED}"/usr/include/"${P}"/"${PN}" -type f | while read f; do
+		sed -e "s#include <jellyfish/#include <jellyfish${SLOT}/#" -i $f || die
+	done
+	mkdir -p "${ED}/usr/include/${PN}${SLOT}" || die
+	mv "${ED}"/usr/include/"${P}"/"${PN}"/* "${ED}/usr/include/${PN}${SLOT}/" || die
+	rm -r "${ED}/usr/include/${P}" || die
+	mv "${ED}"/usr/share/man/man1/jellyfish.1 "${ED}"/usr/share/man/man1/jellyfish"${SLOT}".1 || die
+	dodoc doc/jellyfish.pdf
+}
diff --git a/sci-biology/jellyfish/metadata.xml b/sci-biology/jellyfish/metadata.xml
index 138cb7705..f2c1cd819 100644
--- a/sci-biology/jellyfish/metadata.xml
+++ b/sci-biology/jellyfish/metadata.xml
@@ -9,4 +9,7 @@
 		<email>sci-biology@gentoo.org</email>
 		<name>Gentoo Biology Project</name>
 	</maintainer>
+	<upstream>
+		<remote-id type="github">gmarcais/Jellyfish</remote-id>
+	</upstream>
 </pkgmetadata>
diff --git a/sci-biology/jigsaw/Manifest b/sci-biology/jigsaw/Manifest
deleted file mode 100644
index 6f8a181f3..000000000
--- a/sci-biology/jigsaw/Manifest
+++ /dev/null
@@ -1 +0,0 @@
-DIST jigsaw-3.2.10.tar.gz 1033424 BLAKE2B 9a254e47f32629e3613938aa0430b844ecefedf375e5a6585870f9b3a452842a7445234e190a59df2f65a2d2123c0973ba9b48ba3f0fea071f42fd2e01e683f4 SHA512 dfce29afd91603e328da6dcbb65851674f7c396746c8091e3bd81bfb06433404b1d87778f75dfaf683eafc9736e6bd7d91e48ac4c51198bf6bdcae68457ba05f
diff --git a/sci-biology/jigsaw/jigsaw-3.2.10.ebuild b/sci-biology/jigsaw/jigsaw-3.2.10.ebuild
deleted file mode 100644
index 47ef93f7f..000000000
--- a/sci-biology/jigsaw/jigsaw-3.2.10.ebuild
+++ /dev/null
@@ -1,13 +0,0 @@
-# Copyright 1999-2015 Gentoo Foundation
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=5
-
-DESCRIPTION="Combine results from external gene predictors into final gene models"
-HOMEPAGE="http://www.cbcb.umd.edu/software/jigsaw"
-SRC_URI="http://cbcb.umd.edu/software/jigsaw/${P}.tar.gz"
-
-LICENSE="Artistic"
-SLOT="0"
-KEYWORDS=""
-IUSE=""
diff --git a/sci-biology/jigsaw/metadata.xml b/sci-biology/jigsaw/metadata.xml
deleted file mode 100644
index 138cb7705..000000000
--- a/sci-biology/jigsaw/metadata.xml
+++ /dev/null
@@ -1,12 +0,0 @@
-<?xml version="1.0" encoding="UTF-8"?>
-<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
-<pkgmetadata>
-	<maintainer type="person">
-		<email>mmokrejs@fold.natur.cuni.cz</email>
-		<name>Martin Mokrejs</name>
-	</maintainer>
-	<maintainer type="project">
-		<email>sci-biology@gentoo.org</email>
-		<name>Gentoo Biology Project</name>
-	</maintainer>
-</pkgmetadata>
diff --git a/sci-biology/jtreeview-bin/Manifest b/sci-biology/jtreeview-bin/Manifest
index 77ecdad39..a8d59a199 100644
--- a/sci-biology/jtreeview-bin/Manifest
+++ b/sci-biology/jtreeview-bin/Manifest
@@ -1,2 +1,2 @@
-DIST TreeView-1.1.6r4-bin.tar.gz 1491322 BLAKE2B ca4cee83a4abc0f718a854e6c281e9a4627ce61a39d514b123c3f6badd04ac0eac1ea730b3a3c7988b4e4c8f5946e5892b5a47601e7456659445eecdb4037b4e SHA512 b60046d9f8669c9c7ad9679a7e3325ef9c937182fd9dea8f089add4845b02f9e68b6ac716745a29dd7ba342275984fa2f9efb730d188186cbfc816f649dd3d7d
+DIST TreeView-1.2.0-bin.tar.gz 1516223 BLAKE2B 4d521b4e6c4126a6ba9f204dcd0346a2c33cd8c1aba5f2ffbcdfa64be936371097ebf66c710bed2719e436beee5a84eb1935721da18f9cfc3547b7d1c26fee34 SHA512 2a2a46912b5cdc58da5192336cd1ce52c72a23ee5a788644b5cdb82f451496e9bd22265e4423ba4aa8215d53400cbe90820d79abb42043e87644693594fda545
 DIST helper-scripts-0.0.2.tar.gz 18260 BLAKE2B 2f794063fa2f9263b92465b48a891efc5ae65ab3a64ade7250aa3a9f166873d9a6f9c5ad69387caa6d9f15affb907cd2b3587e7c261b862337319c0e7d7be9d6 SHA512 6d335ffa4da7db2d5b2d0009e8db87145cc9b3b85772059f6afde55f544de1ee1348a8450e69393ea59313268549204be3d26931dc43085d843ff3c6c3c27d88
diff --git a/sci-biology/jtreeview-bin/jtreeview-bin-1.1.6.4.ebuild b/sci-biology/jtreeview-bin/jtreeview-bin-1.1.6.4.ebuild
deleted file mode 100644
index 365c534bf..000000000
--- a/sci-biology/jtreeview-bin/jtreeview-bin-1.1.6.4.ebuild
+++ /dev/null
@@ -1,43 +0,0 @@
-# Copyright 1999-2017 Gentoo Foundation
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=5
-
-PERL_EXPORT_PHASE_FUNCTIONS=no
-inherit java-pkg-2 java-ant-2 eutils perl-module
-
-S="${WORKDIR}"/TreeView-1.1.6r4-bin
-
-DESCRIPTION="Viewer for Microarray Data in PCL or CDT formats"
-HOMEPAGE="http://jtreeview.sourceforge.net/"
-SRC_URI="
-	http://sourceforge.net/projects/jtreeview/files/jtreeview/1.1.6r4/TreeView-1.1.6r4-bin.tar.gz
-	http://sourceforge.net/projects/jtreeview/files/helper-scripts/0.0.2/helper-scripts-0.0.2.tar.gz"
-
-LICENSE="GPL-2"
-SLOT="0"
-KEYWORDS="" # src_install is wrong somehow, TreeView.jar does not start
-IUSE=""
-
-DEPEND="
-	>virtual/jdk-1.5:*
-	!sci-biology/jtreeview"
-RDEPEND="${DEPEND}
-	>=virtual/jre-1.5:*"
-
-# TODO: use xltproc to create docs following TreeView-1.1.6r4-src/doc/README
-
-src_install(){
-	java-pkg_dojar TreeView.jar
-	java-pkg_dolauncher ${PN} TreeView.jar
-	insinto /usr/share/"${PN}"/lib/plugins
-	doins plugins/*.jar
-	cd ../helper-scripts-0.0.2 || die
-	perl_set_version
-	insinto "${VENDOR_LIB}"
-	doins *.pm
-	dobin *.pl
-	insinto /usr/share/"${PN}"/examples
-	doins blues.color
-	newdoc README README.helper-scripts
-}
diff --git a/sci-biology/jtreeview-bin/jtreeview-bin-1.2.0.ebuild b/sci-biology/jtreeview-bin/jtreeview-bin-1.2.0.ebuild
new file mode 100644
index 000000000..63ec84d2f
--- /dev/null
+++ b/sci-biology/jtreeview-bin/jtreeview-bin-1.2.0.ebuild
@@ -0,0 +1,43 @@
+# Copyright 1999-2022 Gentoo Authors
+# Distributed under the terms of the GNU General Public License v2
+
+EAPI=7
+
+inherit java-pkg-2 java-ant-2 perl-module
+
+S="${WORKDIR}"/TreeView-1.1.6r4-bin
+
+DESCRIPTION="Viewer for Microarray Data in PCL or CDT formats"
+HOMEPAGE="https://jtreeview.sourceforge.net/"
+SRC_URI="
+	https://sourceforge.net/projects/jtreeview/files/jtreeview/${PV}/TreeView-${PV}-bin.tar.gz
+	https://sourceforge.net/projects/jtreeview/files/helper-scripts/0.0.2/helper-scripts-0.0.2.tar.gz
+"
+S="${WORKDIR}/TreeView-${PV}-bin"
+
+LICENSE="GPL-2"
+SLOT="0"
+KEYWORDS="~amd64"
+
+DEPEND="
+	>virtual/jdk-1.5:*
+"
+RDEPEND="${DEPEND}
+	>=virtual/jre-1.5:*
+"
+
+# TODO: use xltproc to create docs following TreeView-1.1.6r4-src/doc/README
+
+src_install(){
+	java-pkg_dojar TreeView.jar
+	java-pkg_dolauncher ${PN} TreeView.jar
+	insinto /usr/share/"${PN}"/lib/plugins
+	doins plugins/*.jar
+	cd ../helper-scripts-0.0.2 || die
+	perl_set_version
+	perl_domodule *.pm
+	perl_domodule *.pl
+	insinto /usr/share/"${PN}"/examples
+	doins blues.color
+	newdoc README README.helper-scripts
+}
diff --git a/sci-biology/jtreeview/Manifest b/sci-biology/jtreeview/Manifest
deleted file mode 100644
index 53e7ff11f..000000000
--- a/sci-biology/jtreeview/Manifest
+++ /dev/null
@@ -1,2 +0,0 @@
-DIST TreeView-1.1.6r4-src.tar.gz 3148856 BLAKE2B 6d6c4007cb8e6a2245050e64c6b97ab8e28be02159089b3904ed7ba58605933c42ac8ff3dfa792186fb945ab5d1649027cdf6d49eab8c406734af0eaf1de38a8 SHA512 a83962c4c37e3e4536ad549b5e24f69ad9cab8ba67af550d37d16bccef1926ac5b2ddf23a6e95262f02723009a336937fd49bf6786dd983ae26c85d94d78c37d
-DIST helper-scripts-0.0.2.tar.gz 18260 BLAKE2B 2f794063fa2f9263b92465b48a891efc5ae65ab3a64ade7250aa3a9f166873d9a6f9c5ad69387caa6d9f15affb907cd2b3587e7c261b862337319c0e7d7be9d6 SHA512 6d335ffa4da7db2d5b2d0009e8db87145cc9b3b85772059f6afde55f544de1ee1348a8450e69393ea59313268549204be3d26931dc43085d843ff3c6c3c27d88
diff --git a/sci-biology/jtreeview/jtreeview-1.1.6.4.ebuild b/sci-biology/jtreeview/jtreeview-1.1.6.4.ebuild
deleted file mode 100644
index f1e58af01..000000000
--- a/sci-biology/jtreeview/jtreeview-1.1.6.4.ebuild
+++ /dev/null
@@ -1,41 +0,0 @@
-# Copyright 1999-2017 Gentoo Foundation
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=5
-
-PERL_EXPORT_PHASE_FUNCTIONS=no
-inherit java-pkg-2 java-ant-2 eutils perl-module
-
-S="${WORKDIR}"/TreeView-1.1.6r4-src
-
-DESCRIPTION="Viewer for Microarray Data in PCL or CDT formats"
-HOMEPAGE="http://jtreeview.sourceforge.net/"
-SRC_URI="
-	http://sourceforge.net/projects/jtreeview/files/jtreeview/1.1.6r4/TreeView-1.1.6r4-src.tar.gz
-	http://sourceforge.net/projects/jtreeview/files/helper-scripts/0.0.2/helper-scripts-0.0.2.tar.gz"
-#http://sourceforge.net/projects/jtreeview/files/jtreeview/1.1.6r4/TreeView-1.1.6r4-bin.tar.gz
-
-LICENSE="GPL-2"
-SLOT="0"
-KEYWORDS="" # resulting java binary does not execute for me
-IUSE=""
-
-DEPEND=">virtual/jdk-1.5:*
-	dev-java/nanoxml"
-RDEPEND="${DEPEND}
-	>=virtual/jre-1.5:*"
-
-# TODO: use xltproc to create docs following TreeView-1.1.6r4-src/doc/README
-
-src_install(){
-	java-pkg_dojar TreeView.jar
-	java-pkg_dolauncher ${PN} TreeView.jar
-	cd ../helper-scripts-0.0.2 || die
-	perl_set_version
-	insinto "${VENDOR_LIB}"
-	doins *.pm
-	dobin *.pl
-	insinto /usr/share/"${PN}"/examples
-	doins blues.color
-	newdoc README README.helper-scripts
-}
diff --git a/sci-biology/jtreeview/jtreeview-9999.ebuild b/sci-biology/jtreeview/jtreeview-9999.ebuild
deleted file mode 100644
index 0d7a1be51..000000000
--- a/sci-biology/jtreeview/jtreeview-9999.ebuild
+++ /dev/null
@@ -1,38 +0,0 @@
-# Copyright 1999-2017 Gentoo Foundation
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=6
-
-inherit java-pkg-2 git-r3
-
-DESCRIPTION="Viewer for Microarray Data in PCL or CDT formats"
-HOMEPAGE="http://jtreeview.sourceforge.net
-	https://bitbucket.org/TreeView3Dev/treeview3"
-EGIT_REPO_URI="https://bitbucket.org/TreeView3Dev/treeview3.git"
-
-LICENSE="MIT"
-SLOT="0"
-KEYWORDS="" # builds and executes fines
-IUSE=""
-
-DEPEND=">virtual/jdk-1.7:*"
-RDEPEND="${DEPEND}
-	>=virtual/jre-1.7:*"
-
-src_prepare(){
-	chmod u+x ./gradle* || die
-	eapply_user
-}
-
-src_compile(){
-	# work around gradle writing $HOME/.gradle, requiring $HOME/.git and $HOME/.m2/
-	# https://github.com/samtools/htsjdk/issues/660#issuecomment-232155965
-	# make jure SDK-1.8 is available, JRE-1.8 is not enough
-	GRADLE_USER_HOME="${WORKDIR}" ./gradlew || die
-}
-
-src_install(){
-	cd build/libs || die
-	java-pkg_dojar *.jar
-	java-pkg_dolauncher ${PN}
-}
diff --git a/sci-biology/jtreeview/metadata.xml b/sci-biology/jtreeview/metadata.xml
deleted file mode 100644
index 5139daeeb..000000000
--- a/sci-biology/jtreeview/metadata.xml
+++ /dev/null
@@ -1,16 +0,0 @@
-<?xml version="1.0" encoding="UTF-8"?>
-<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
-<pkgmetadata>
-	<maintainer type="person">
-		<email>mmokrejs@fold.natur.cuni.cz</email>
-		<name>Martin Mokrejs</name>
-	</maintainer>
-	<maintainer type="project">
-		<email>sci-biology@gentoo.org</email>
-		<name>Gentoo Biology Project</name>
-	</maintainer>
-	<upstream>
-		<remote-id type="bitbucket">TreeView3Dev/treeview3</remote-id>
-		<remote-id type="sourceforge">jtreeview</remote-id>
-	</upstream>
-</pkgmetadata>
diff --git a/sci-biology/karect/Manifest b/sci-biology/karect/Manifest
index 243eea561..dcb263550 100644
--- a/sci-biology/karect/Manifest
+++ b/sci-biology/karect/Manifest
@@ -1 +1 @@
-DIST karect-1.0.0.tar.gz 239445 BLAKE2B be9c5b00a68a96b59a97e9c6aeef71388faaf4dedb41313ba1e6981a8f8bde84baef86c000a291d4063a9a92e66d25344b81e25202bf7aea13c92dddbbf8b7dc SHA512 c833a862c15027eaf84eff7ddf1cf36a369fbd94bd44ab596fcee89e402e1517ba3ef2646591365d273f98f1e3f13b6ad990f73660e440f0a45c87b84a08491c
+DIST karect-1.0.tar.gz 239390 BLAKE2B 449b519aace8c4c78dad89b57fcbc2b737805ca78e1906ffb610ad500974acecbeefe47ef2289fab1a41e09b7e3635b1557ac206112138374942c1e676732a04 SHA512 19e8957a3fbc2ce725e80c72ad14f4f73632950927063201b09efa7d8bbce37b6b6f57ad3c12eb7cbe601654933f1a5906bdbf034d0e8db5a6c9bf99199f821a
diff --git a/sci-biology/karect/karect-1.0.0.ebuild b/sci-biology/karect/karect-1.0.0.ebuild
deleted file mode 100644
index ddb015dbc..000000000
--- a/sci-biology/karect/karect-1.0.0.ebuild
+++ /dev/null
@@ -1,32 +0,0 @@
-# Copyright 1999-2017 Gentoo Foundation
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=5
-
-inherit toolchain-funcs
-
-DESCRIPTION="Error-correct mismatches and InDels of raw reads incl. paired-end"
-HOMEPAGE="https://github.com/aminallam/karect
-	http://bioinformatics.oxfordjournals.org/content/31/21/3421.abstract"
-SRC_URI="https://codeload.github.com/aminallam/karect/legacy.tar.gz/master -> karect-1.0.0.tar.gz"
-# actually fetches aminallam-karect-v1.0-0-gba3ad54.tar.gz
-# https://github.com/aminallam/karect.git
-
-LICENSE="GPL-2"
-SLOT="0"
-KEYWORDS="~amd64"
-IUSE=""
-
-DEPEND=""
-RDEPEND="${DEPEND}"
-
-S="${WORKDIR}"/aminallam-karect-ba3ad54/
-
-src_compile(){
-	$(tc-getCXX) ${CXXFLAGS} -pthread -lpthread karect.cpp -o karect || die
-}
-
-src_install(){
-	dobin karect
-	dodoc karect_manual.pdf README README.md
-}
diff --git a/sci-biology/karect/karect-1.0.ebuild b/sci-biology/karect/karect-1.0.ebuild
new file mode 100644
index 000000000..2360395ba
--- /dev/null
+++ b/sci-biology/karect/karect-1.0.ebuild
@@ -0,0 +1,29 @@
+# Copyright 1999-2021 Gentoo Authors
+# Distributed under the terms of the GNU General Public License v2
+
+EAPI=7
+
+inherit toolchain-funcs
+
+DESCRIPTION="Error-correct mismatches and InDels of raw reads incl. paired-end"
+HOMEPAGE="https://github.com/aminallam/karect
+	http://bioinformatics.oxfordjournals.org/content/31/21/3421.abstract"
+SRC_URI="https://github.com/aminallam/karect/archive/v${PV}.tar.gz -> ${P}.tar.gz"
+# actually fetches aminallam-karect-v1.0-0-gba3ad54.tar.gz
+# https://github.com/aminallam/karect.git
+
+LICENSE="GPL-2"
+SLOT="0"
+KEYWORDS="~amd64"
+
+DEPEND=""
+RDEPEND="${DEPEND}"
+
+src_compile(){
+	$(tc-getCXX) ${CXXFLAGS} -pthread -lpthread karect.cpp -o karect || die
+}
+
+src_install(){
+	dobin karect
+	dodoc karect_manual.pdf README README.md
+}
diff --git a/sci-biology/kat/Manifest b/sci-biology/kat/Manifest
deleted file mode 100644
index 0bdd2dd15..000000000
--- a/sci-biology/kat/Manifest
+++ /dev/null
@@ -1 +0,0 @@
-DIST kat-2.4.2.tar.gz 21829118 BLAKE2B 52a0056f322dfb405c005b31a0cb182c739a6af05173123dc1cef1d986f515a8318c1481f1ed0f8c247c01c6b460c951147d81f904709f4e27a7d3d1f47bda3d SHA512 696e3b9ed307ed17085790b24d617195f47fbdb7180be13ee644718c2464c429ffd964959857fc8d1317a451d57b74f6d7b2857fe3764573d9605d58a53b2a0c
diff --git a/sci-biology/kat/files/kat-2.4.2-ignore-bundled-deps.patch b/sci-biology/kat/files/kat-2.4.2-ignore-bundled-deps.patch
deleted file mode 100644
index 46d343294..000000000
--- a/sci-biology/kat/files/kat-2.4.2-ignore-bundled-deps.patch
+++ /dev/null
@@ -1,79 +0,0 @@
-diff --git a/lib/Makefile.am b/lib/Makefile.am
-index ac23917..0ca4be9 100644
---- a/lib/Makefile.am
-+++ b/lib/Makefile.am
-@@ -6,7 +6,6 @@ pkgconfig_DATA = kat.pc
- lib_LTLIBRARIES = libkat.la
- 
- libkat_la_LDFLAGS = \
--	-L$(top_builddir)/deps/boost/build/lib/ \
- 	-version-info 2:4:2
- 
- LIBS = \
-@@ -41,7 +40,6 @@ library_include_HEADERS =   $(KI)/distance_metrics.hpp \
- 
- libkat_la_CPPFLAGS = \
- 	-I$(top_srcdir)/deps/jellyfish-2.2.0/include \
--	-I$(top_srcdir)/deps/boost/build/include \
- 	-I$(top_srcdir)/lib/include \
- 	-DKAT_SITE_PKGS='"$(prefix)/lib/python$(PYTHON_VERSION)/site-packages"' \
- 	@AM_CPPFLAGS@
-diff --git a/src/Makefile.am b/src/Makefile.am
-index 1cdf7e0..dfa878b 100644
---- a/src/Makefile.am
-+++ b/src/Makefile.am
-@@ -14,7 +14,6 @@ kat_CXXFLAGS = \
- kat_CPPFLAGS = \
- 	-I$(top_srcdir)/deps/seqan-library-2.0.0/include \
- 	-I$(top_srcdir)/deps/jellyfish-2.2.0/include \
--	-I$(top_srcdir)/deps/boost/build/include \
- 	-I$(top_srcdir)/lib/include \
- 	-DKAT_SCRIPTS='"$(datarootdir)/scripts"' \
- 	-DKAT_SITE_PKGS='"$(prefix)/lib/python$(PYTHON_VERSION)/site-packages"' \
-@@ -25,13 +24,13 @@ kat_LDFLAGS = \
- 	@AM_LDFLAGS@
- 
- kat_LDADD = \
--	$(top_builddir)/deps/boost/build/lib/libboost_timer.a \
--	$(top_builddir)/deps/boost/build/lib/libboost_chrono.a \
--	$(top_builddir)/deps/boost/build/lib/libboost_filesystem.a \
--	$(top_builddir)/deps/boost/build/lib/libboost_program_options.a \
--	$(top_builddir)/deps/boost/build/lib/libboost_system.a \
--	$(top_builddir)/deps/jellyfish-2.2.0/.libs/libkat_jellyfish.la \
- 	$(top_builddir)/lib/libkat.la \
-+	$(top_builddir)/deps/jellyfish-2.2.0/.libs/libkat_jellyfish.la \
-+	-lboost_timer \
-+	-lboost_chrono \
-+	-lboost_filesystem \
-+	-lboost_program_options \
-+	-lboost_system \
- 	@AM_LIBS@
- 
- noinst_HEADERS = \
-diff --git a/tests/Makefile.am b/tests/Makefile.am
-index eee4e8b..dec2a5f 100644
---- a/tests/Makefile.am
-+++ b/tests/Makefile.am
-@@ -31,7 +31,6 @@ AM_CPPFLAGS = \
- 	-I$(top_srcdir)/lib/include \
- 	-I$(top_srcdir)/deps/seqan-library-2.0.0/include \
- 	-I$(top_srcdir)/deps/jellyfish-2.2.0/include \
--	-I$(top_srcdir)/deps/boost/build/include \
- 	-DDATADIR=\"$(srcdir)/data\" \
- 	-DKAT_SITE_PKGS='"$(prefix)/lib/python$(PYTHON_VERSION)/site-packages"' \
- 	@AM_CPPFLAGS@
-@@ -58,13 +57,11 @@ check_unit_tests_SOURCES = \
- 
- check_unit_tests_LDFLAGS = \
- 	-static \
--	-L$(top_builddir)/deps/boost/build/lib \
--	-Wl,-rpath $(top_builddir)/deps/boost/build/lib \
- 	@AM_LDFLAGS@
- 
- check_unit_tests_LDADD = \
- 	libgtest.la \
--    $(top_builddir)/lib/libkat.la \
-+	$(top_builddir)/lib/libkat.la \
- 	-lboost_timer \
- 	-lboost_chrono \
- 	-lboost_filesystem \
diff --git a/sci-biology/kat/files/kat-2.4.2-no_static_build.patch b/sci-biology/kat/files/kat-2.4.2-no_static_build.patch
deleted file mode 100644
index 48ad6d562..000000000
--- a/sci-biology/kat/files/kat-2.4.2-no_static_build.patch
+++ /dev/null
@@ -1,56 +0,0 @@
-diff --git a/configure.ac b/configure.ac
-index 9acc141..24a4b14 100644
---- a/configure.ac
-+++ b/configure.ac
-@@ -178,8 +178,6 @@ define([PC_FILE], lib/kat-2.2.pc)
- 
- AM_CXXFLAGS="-g -O2 -std=c++11"
- AC_SUBST([AM_CXXFLAGS])
--AM_LDFLAGS="-static-libstdc++"
--AC_SUBST([AM_LDFLAGS])
- 
- if [[ "${make_pykat}" == "yes" ]]; then
-     AM_CPPFLAGS="${PYTHON_CPPFLAGS}"
-diff --git a/deps/jellyfish-2.2.0/Makefile.am b/deps/jellyfish-2.2.0/Makefile.am
-index 83192d9..e3b1694 100644
---- a/deps/jellyfish-2.2.0/Makefile.am
-+++ b/deps/jellyfish-2.2.0/Makefile.am
-@@ -7,7 +7,7 @@ man1_MANS = doc/kat_jellyfish.man
- pkgconfigdir = $(libdir)/pkgconfig
- pkgconfig_DATA = kat_jellyfish.pc
- 
--AM_LDFLAGS = -lz -lpthread -static-libstdc++ # $(VALGRIND_LIBS)
-+AM_LDFLAGS = -lz -lpthread # $(VALGRIND_LIBS)
- AM_CPPFLAGS = -I$(top_srcdir) -I$(top_srcdir)/include # $(VALGRIND_CFLAGS)
- AM_CXXFLAGS = $(ALL_CXXFLAGS) -Wall -Wnon-virtual-dtor -Wno-deprecated-declarations
- 
-diff --git a/src/Makefile.am b/src/Makefile.am
-index 2d5cd72..cb5cb0e 100644
---- a/src/Makefile.am
-+++ b/src/Makefile.am
-@@ -18,10 +18,6 @@ kat_CPPFLAGS = \
- 	-DKAT_SCRIPTS='"$(datadir)/scripts"' \
- 	@AM_CPPFLAGS@
- 
--kat_LDFLAGS = \
--	-static \
--	@AM_LDFLAGS@
--
- kat_LDADD = \
- 	$(top_builddir)/lib/libkat.la \
- 	$(top_builddir)/deps/jellyfish-2.2.0/.libs/libkat_jellyfish.la \
-diff --git a/tests/Makefile.am b/tests/Makefile.am
-index d96363a..90e4f61 100644
---- a/tests/Makefile.am
-+++ b/tests/Makefile.am
-@@ -54,10 +54,6 @@ check_unit_tests_SOURCES = \
- 	check_compcounters.cc \
- 	check_main.cc
- 
--check_unit_tests_LDFLAGS = \
--	-static \
--	@AM_LDFLAGS@
--
- check_unit_tests_LDADD = \
- 	libgtest.la \
- 	$(top_builddir)/lib/libkat.la \
diff --git a/sci-biology/kat/kat-2.4.2.ebuild b/sci-biology/kat/kat-2.4.2.ebuild
deleted file mode 100644
index 9d3981439..000000000
--- a/sci-biology/kat/kat-2.4.2.ebuild
+++ /dev/null
@@ -1,78 +0,0 @@
-# Copyright 1999-2018 Gentoo Foundation
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=6
-
-PYTHON_COMPAT=( python3_{5,6} )
-# https://github.com/Ensembl/Bio-DB-HTS/issues/30
-
-inherit flag-o-matic autotools distutils-r1
-
-DESCRIPTION="K-mer Analysis Toolkit (histogram, filter, compare sets, plot)"
-HOMEPAGE="https://github.com/TGAC/KAT"
-SRC_URI="https://github.com/TGAC/KAT/archive/Release-${PV}.tar.gz -> ${P}.tar.gz"
-
-LICENSE="GPL-3+"
-SLOT="0"
-KEYWORDS="~amd64 ~x86"
-IUSE="cpu_flags_x86_sse static-libs test"
-
-CDEPEND="
-	>=dev-libs/boost-1.52[${PYTHON_USEDEP}]
-	sys-libs/zlib
-	dev-python/tabulate[${PYTHON_USEDEP}]
-	dev-python/matplotlib[${PYTHON_USEDEP}]
-	dev-python/numpy[${PYTHON_USEDEP}]
-	sci-libs/scipy[${PYTHON_USEDEP}]"
-DEPEND="${CDEPEND}
-	dev-python/sphinx
-	test? ( sys-process/time )"
-RDEPEND="${CDEPEND}"
-# contains bundled and *modified* version of jellyfish-2.2.0
-#   (libkat_jellyfish.{a,so} and "kat_" prefixes are added to all binaries)
-#   https://github.com/TGAC/KAT/issues/93#issuecomment-383377666
-# contains embedded sci-biology/seqan headers
-
-PATCHES=(
-	"${FILESDIR}"/kat-2.4.2-ignore-bundled-deps.patch
-	"${FILESDIR}"/kat-2.4.2-no_static_build.patch
-	)
-
-S="${WORKDIR}"/KAT-Release-"${PV}"
-
-src_prepare(){
-	default
-	rm -rf deps/boost || die "Failed to zap bundled boost"
-	eautoreconf
-}
-
-src_configure(){
-	python_setup
-	local myconf=()
-	myconf+=(
-		--disable-gnuplot
-		--disable-pykat-install
-		$(use_enable static-libs static)
-		) # python3 does better image rendering, no need for gnuplot
-	# pass down to jellyfish-2.2.0/configure
-	use cpu_flags_x86_sse && myconf+=( $(use_with cpu_flags_x86_sse sse) )
-	econf ${myconf[@]}
-}
-
-src_compile(){
-	default
-	pushd scripts >/dev/null || die
-	distutils-r1_src_compile
-	popd > /dev/null || die
-}
-
-src_install(){
-	default
-	pushd scripts >/dev/null || die
-	distutils-r1_src_install
-	popd > /dev/null || die
-}
-
-src_test(){
-	default
-}
diff --git a/sci-biology/kat/kat-9999.ebuild b/sci-biology/kat/kat-9999.ebuild
deleted file mode 100644
index aaf8842ba..000000000
--- a/sci-biology/kat/kat-9999.ebuild
+++ /dev/null
@@ -1,79 +0,0 @@
-# Copyright 1999-2018 Gentoo Foundation
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=6
-
-PYTHON_COMPAT=( python3_{5,6} )
-# https://github.com/Ensembl/Bio-DB-HTS/issues/30
-
-inherit flag-o-matic autotools distutils-r1 git-r3
-
-DESCRIPTION="K-mer Analysis Toolkit (histogram, filter, compare sets, plot)"
-HOMEPAGE="https://github.com/TGAC/KAT"
-EGIT_REPO_URI="https://github.com/TGAC/KAT.git"
-EGIT_CHECKOUT_DIR="${WORKDIR}"/KAT-Release-"${PV}"
-
-LICENSE="GPL-3+"
-SLOT="0"
-KEYWORDS="~amd64 ~x86"
-IUSE="cpu_flags_x86_sse static-libs test"
-
-CDEPEND="
-	>=dev-libs/boost-1.52[${PYTHON_USEDEP}]
-	sys-libs/zlib
-	dev-python/tabulate[${PYTHON_USEDEP}]
-	dev-python/matplotlib[${PYTHON_USEDEP}]
-	dev-python/numpy[${PYTHON_USEDEP}]
-	sci-libs/scipy[${PYTHON_USEDEP}]"
-DEPEND="${CDEPEND}
-	dev-python/sphinx
-	test? ( sys-process/time )"
-RDEPEND="${CDEPEND}"
-# contains bundled and *modified* version of jellyfish-2.2.0
-#   (libkat_jellyfish.{a,so} and "kat_" prefixes are added to all binaries)
-#   https://github.com/TGAC/KAT/issues/93#issuecomment-383377666
-# contains embedded sci-biology/seqan headers
-
-PATCHES=(
-	"${FILESDIR}"/kat-2.4.2-ignore-bundled-deps.patch
-	"${FILESDIR}"/kat-2.4.2-no_static_build.patch
-	)
-
-S="${WORKDIR}"/KAT-Release-"${PV}"
-
-src_prepare(){
-	default
-	rm -rf deps/boost || die "Failed to zap bundled boost"
-	eautoreconf
-}
-
-src_configure(){
-	python_setup
-	local myconf=()
-	myconf+=(
-		--disable-gnuplot
-		--disable-pykat-install
-		$(use_enable static-libs static)
-		) # python3 does better image rendering, no need for gnuplot
-	# pass down to jellyfish-2.2.0/configure
-	use cpu_flags_x86_sse && myconf+=( $(use_with cpu_flags_x86_sse sse) )
-	econf ${myconf[@]}
-}
-
-src_compile(){
-	default
-	pushd scripts >/dev/null || die
-	distutils-r1_src_compile
-	popd > /dev/null || die
-}
-
-src_install(){
-	default
-	pushd scripts >/dev/null || die
-	distutils-r1_src_install
-	popd > /dev/null || die
-}
-
-src_test(){
-	default
-}
diff --git a/sci-biology/kat/metadata.xml b/sci-biology/kat/metadata.xml
deleted file mode 100644
index 6810aabae..000000000
--- a/sci-biology/kat/metadata.xml
+++ /dev/null
@@ -1,15 +0,0 @@
-<?xml version="1.0" encoding="UTF-8"?>
-<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
-<pkgmetadata>
-	<maintainer type="person">
-		<email>mmokrejs@fold.natur.cuni.cz</email>
-		<name>Martin Mokrejs</name>
-	</maintainer>
-	<maintainer type="project">
-		<email>sci-biology@gentoo.org</email>
-		<name>Gentoo Biology Project</name>
-	</maintainer>
-	<upstream>
-		<remote-id type="github">TGAC/KAT</remote-id>
-	</upstream>
-</pkgmetadata>
diff --git a/sci-biology/khmer/Manifest b/sci-biology/khmer/Manifest
deleted file mode 100644
index 83beb745a..000000000
--- a/sci-biology/khmer/Manifest
+++ /dev/null
@@ -1,2 +0,0 @@
-DIST khmer-0.8.tar.gz 18924997 BLAKE2B d1996f40f14875bad7712ee7711b3dd67561da212c5c0d61c166218800108a1181d5b767272aa3d4cbd8a0bf243309dd113d6a32a672a90b7b654df785450822 SHA512 712c0879f686fc279c34be371b1926b42322ba1f2cc679fbc61bf682096cc15c4170d30cf7280d8153af61a23fcc34412b8833112d046de4225bb64808bd37a4
-DIST khmer-1.0.1.tar.gz 18975505 BLAKE2B 352452cff425ca9b497d94933844c1ee89cbc7a41118625e797ccee367322348e7d58efb1d15c657265a374a03301b967a1f497982b250d58fe21549b72e620e SHA512 930dd3795a2921794a9f67da6352752fc8bd6baff15292f8b354d821883b429c422bda4f03501442bce65dfce3cc50eebdb2773056fb6049659536831f8929fd
diff --git a/sci-biology/khmer/khmer-0.8.ebuild b/sci-biology/khmer/khmer-0.8.ebuild
deleted file mode 100644
index e19d27e9b..000000000
--- a/sci-biology/khmer/khmer-0.8.ebuild
+++ /dev/null
@@ -1,39 +0,0 @@
-# Copyright 1999-2014 Gentoo Foundation
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=5
-
-PYTHON_COMPAT=( python2_7 )
-
-inherit distutils-r1
-
-DESCRIPTION="In-memory K-mer counting in DNA/RNA/protein sequences"
-HOMEPAGE="https://github.com/ged-lab/khmer"
-SRC_URI="mirror://pypi/${PN:0:1}/${PN}/${P}.tar.gz"
-
-LICENSE="BSD"
-SLOT="0"
-KEYWORDS="~amd64 ~x86 ~amd64-linux ~x86-linux"
-IUSE=""
-
-DEPEND=""
-RDEPEND="sci-biology/screed"
-
-python_prepare_all(){
-	rm -rf lib/{bzip2,zlib} || die
-
-	sed \
-		-e 's:zlib/zlib.h:zlib.h:g' \
-		-e 's:bzip2/bzlib.h:bzlib.h:g' \
-		-i lib/read_parsers.hh lib/counting.cc || die
-
-	sed \
-		-e "/extra_objects/d" \
-		-e "s:'nose >= 1.0', ::g" \
-		-e "s:'sphinx',::g" \
-		-e '/libraries/s:, ]:, "z", "bz2", ]:g' \
-		-e "s:'-O3',::g" \
-		-i setup.py || die
-
-	distutils-r1_python_prepare_all
-}
diff --git a/sci-biology/khmer/khmer-1.0.1.ebuild b/sci-biology/khmer/khmer-1.0.1.ebuild
deleted file mode 100644
index 7ace41d54..000000000
--- a/sci-biology/khmer/khmer-1.0.1.ebuild
+++ /dev/null
@@ -1,62 +0,0 @@
-# Copyright 1999-2014 Gentoo Foundation
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=5
-
-PYTHON_COMPAT=( python2_7 )
-
-inherit distutils-r1
-
-DESCRIPTION="In-memory K-mer counting in DNA/RNA/protein sequences"
-HOMEPAGE="https://github.com/ged-lab/khmer"
-SRC_URI="mirror://pypi/${PN:0:1}/${PN}/${P}.tar.gz"
-
-LICENSE="BSD"
-SLOT="0"
-KEYWORDS="~amd64 ~x86 ~amd64-linux ~x86-linux"
-IUSE=""
-
-DEPEND=""
-RDEPEND="sci-biology/screed"
-
-python_prepare_all(){
-	rm -rf lib/{bzip2,zlib} || die
-
-	sed \
-		-e 's:zlib/zlib.h:zlib.h:g' \
-		-e 's:bzip2/bzlib.h:bzlib.h:g' \
-		-i lib/read_parsers.hh lib/counting.cc || die
-
-	sed \
-		-e "/^EXTRA_COMPILE_ARGS/s:=.*:=[]:g" \
-		-i setup.py || die
-
-	cat > setup.cfg <<- EOF
-	[nosetests]
-	verbosity = 2
-	stop = TRUE
-	attr = !known_failing
-
-	[build_ext]
-	undef = NO_UNIQUE_RC
-	libraries = z,bz2
-	## if using system libraries
-	include-dirs = lib:lib/zlib:lib/bzip2
-	# include-dirs = lib
-	## if using system libraries (broken)
-
-	define = NDEBUG
-	# is not needed for most Linux installs
-	# see the OPT line in /usr/lib/python2.7/config/Makefile which gets included
-	# in distutils version of CFLAGS
-
-	[easy_install]
-
-	EOF
-
-	distutils-r1_python_prepare_all
-}
-
-python_test() {
-	esetup.py nosetests || die
-}
diff --git a/sci-biology/khmer/khmer-9999.ebuild b/sci-biology/khmer/khmer-9999.ebuild
deleted file mode 100644
index 7855665e1..000000000
--- a/sci-biology/khmer/khmer-9999.ebuild
+++ /dev/null
@@ -1,42 +0,0 @@
-# Copyright 1999-2018 Gentoo Foundation
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=5
-
-PYTHON_COMPAT=( python2_7 )
-
-inherit distutils-r1 git-r3
-
-DESCRIPTION="In-memory K-mer counting in DNA/RNA/protein sequences"
-HOMEPAGE="https://github.com/ged-lab/khmer"
-#SRC_URI=""
-EGIT_REPO_URI="https://github.com/ged-lab/khmer"
-
-LICENSE="BSD"
-SLOT="0"
-KEYWORDS=""
-IUSE=""
-
-DEPEND=""
-RDEPEND="sci-biology/screed"
-
-#python_prepare_all(){
-#	rm -rf lib/{bzip2,zlib} || die
-#
-#	sed \
-#		-e 's:zlib/zlib.h:zlib.h:g' \
-#		-e 's:bzip2/bzlib.h:bzlib.h:g' \
-#		-i lib/read_parsers.hh lib/counting.cc || die
-#
-#	sed \
-#		-e "/extra_objects/d" \
-#		-e "s:'nose >= 1.0', ::g" \
-#		-e "s:'sphinx',::g" \
-#		-e '/libraries/s:, ]:, "z", "bz2", ]:g' \
-#		-e "s:'-O3',::g" \
-#		-i setup.py || die
-#
-#	distutils-r1_python_prepare_all
-#}
-
-# setup.py --libraries z,bz2 || die
diff --git a/sci-biology/khmer/metadata.xml b/sci-biology/khmer/metadata.xml
deleted file mode 100644
index 91ed395d8..000000000
--- a/sci-biology/khmer/metadata.xml
+++ /dev/null
@@ -1,16 +0,0 @@
-<?xml version="1.0" encoding="UTF-8"?>
-<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
-<pkgmetadata>
-	<maintainer type="person">
-		<email>mmokrejs@fold.natur.cuni.cz</email>
-		<name>Martin Mokrejs</name>
-	</maintainer>
-	<maintainer type="project">
-		<email>sci-biology@gentoo.org</email>
-		<name>Gentoo Biology Project</name>
-	</maintainer>
-	<upstream>
-		<remote-id type="github">ged-lab/khmer</remote-id>
-		<remote-id type="pypi">khmer</remote-id>
-	</upstream>
-</pkgmetadata>
diff --git a/sci-biology/kmergenie/Manifest b/sci-biology/kmergenie/Manifest
deleted file mode 100644
index 8403e72d3..000000000
--- a/sci-biology/kmergenie/Manifest
+++ /dev/null
@@ -1 +0,0 @@
-DIST kmergenie-1.6971.tar.gz 422649 BLAKE2B 8eeb2fc8d0518c38aca7bd127410c016ec6e1f2a6f10b03045a21ccd5800ca3f627d083762d3aec5beeb073577cd2cc5f98e8c267833b79071ae354716ab7962 SHA512 43dad36b461444023c0f730bd8097f2481e958e58db9fbe32ce6e38414438a946d3e648ec719bda63215661457ff1d3ce805631203f2ef69e3ffb8aa2075325d
diff --git a/sci-biology/kmergenie/kmergenie-1.6971.ebuild b/sci-biology/kmergenie/kmergenie-1.6971.ebuild
deleted file mode 100644
index a451dc8c6..000000000
--- a/sci-biology/kmergenie/kmergenie-1.6971.ebuild
+++ /dev/null
@@ -1,44 +0,0 @@
-# Copyright 1999-2015 Gentoo Foundation
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=5
-
-inherit eutils
-
-PYTHON_COMPAT=( python{2_6,2_7} )
-
-DESCRIPTION="Estimate best k-mer length to be used in novo assemblies"
-HOMEPAGE="http://kmergenie.bx.psu.edu/"
-SRC_URI="http://kmergenie.bx.psu.edu/"${P}".tar.gz"
-
-LICENSE="CeCILL-1.1"
-SLOT="0"
-KEYWORDS="~amd64"
-IUSE=""
-
-# dev-python/docopt[${PYTHON_USEDEP}]
-DEPEND="dev-python/docopt
-	dev-lang/R"
-RDEPEND="${DEPEND}"
-
-# Type `make` in the KmerGenie directory
-# To enable larger values of k, e.g. 200, type `make clean ; make k=200`.
-#
-# usage: ./kmergenie reads_file
-
-src_prepare(){
-	sed -e 's#-O4##' -i makefile || die
-	sed -e 's#third_party.##' -i kmergenie || die
-}
-
-src_compile(){
-	make -j 1 || die
-}
-
-src_install(){
-	dobin kmergenie specialk
-	dodoc README
-	# TODO: install also the python files
-	insinto /usr/share/${PN}/R
-	doins scripts/*
-}
diff --git a/sci-biology/kmergenie/metadata.xml b/sci-biology/kmergenie/metadata.xml
deleted file mode 100644
index 138cb7705..000000000
--- a/sci-biology/kmergenie/metadata.xml
+++ /dev/null
@@ -1,12 +0,0 @@
-<?xml version="1.0" encoding="UTF-8"?>
-<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
-<pkgmetadata>
-	<maintainer type="person">
-		<email>mmokrejs@fold.natur.cuni.cz</email>
-		<name>Martin Mokrejs</name>
-	</maintainer>
-	<maintainer type="project">
-		<email>sci-biology@gentoo.org</email>
-		<name>Gentoo Biology Project</name>
-	</maintainer>
-</pkgmetadata>
diff --git a/sci-biology/kraken/Manifest b/sci-biology/kraken/Manifest
deleted file mode 100644
index d27cdc56a..000000000
--- a/sci-biology/kraken/Manifest
+++ /dev/null
@@ -1,2 +0,0 @@
-DIST kraken-1.0.tar.gz 407131 BLAKE2B 948d64b14432f0d7327fa98a0f3a647b8a5e08d4979c6636d6a9924a83adcb5e3c96925815db41513ebbb7d398920e23ae059f2ee33725e2edece77edb1477d5 SHA512 3916890132e5573e72b0b4101ed5cb5e4c99bf9e5c799635002c6c4b23c266ea390fbd641916661ffc31f4e673c0a9d762be01c5094ba9b2241891b3aa5f49f6
-DIST kraken-1.0_MANUAL.html 46202 BLAKE2B 8dc02ba8eb1ee156ce0476511f34b152e4bbc73e970806e03c69bcf896b6027f75b9c4ff7d6e4df5fc517c8f53c135f78e8094a3c3c36dc98554b47ffa3f2bea SHA512 cfd0ac55ad662b8568683ee0fe96ed6c57a6c34b0804f120b2189e25408a9ae4e0740f58ab9314ad4a6677fb3808ad54a8a3bd410df7761b6e94529df1ee697b
diff --git a/sci-biology/kraken/kraken-1.0.ebuild b/sci-biology/kraken/kraken-1.0.ebuild
deleted file mode 100644
index efad890ce..000000000
--- a/sci-biology/kraken/kraken-1.0.ebuild
+++ /dev/null
@@ -1,53 +0,0 @@
-# Copyright 1999-2018 Gentoo Foundation
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=5
-
-PERL_EXPORT_PHASE_FUNCTIONS=no
-inherit perl-module
-
-DESCRIPTION="Detect sequencing project contaminants by mapping reads to taxonomic groups"
-HOMEPAGE="http://ccb.jhu.edu/software/kraken
-	http://genomebiology.com/2014/15/3/R46"
-SRC_URI="https://github.com/DerrickWood/kraken/archive/v1.0.tar.gz -> ${P}.tar.gz
-	http://ccb.jhu.edu/software/kraken/MANUAL.html -> ${P}_MANUAL.html"
-
-LICENSE="GPL-3"
-SLOT="0"
-KEYWORDS="~amd64"
-IUSE=""
-
-DEPEND=""
-RDEPEND="${DEPEND}
-	dev-lang/perl
-	net-misc/wget
-	sci-biology/jellyfish:1"
-
-src_prepare(){
-	sed -e 's/^CXX = /CXX ?= /' -e 's/^CXXFLAGS = /CXXFLAGS ?= /' -i src/Makefile || die
-	echo "exit 0" >> install_kraken.sh || die
-}
-
-src_compile(){
-	./install_kraken.sh destdir || die
-}
-
-src_install(){
-	dodoc "${DISTDIR}"/${P}_MANUAL.html
-	perl_set_version
-	insinto ${VENDOR_LIB}/${PN}
-	doins destdir/*.pm
-	insinto /usr/share/${PN}/util
-	doins destdir/*.pl
-	chmod -R a+rx "${D}"/"${EPREFIX}"/usr/share/${PN}/util
-	rm -f destdir/krakenlib.pm
-	dobin destdir/*
-}
-
-pkg_postinst(){
-	ewarn "Kraken may optionally need <=sci-biology/jellyfish-2 if you want to build your own dbs"
-	ewarn "Kraken needs high network bandwidth for its huge downloads, be sure to read"
-	ewarn "http://ccb.jhu.edu/software/kraken and prepare at least 160GB of disk space"
-	ewarn "Consider placing the db files in ramfs (needs root permissions) taking >75GB RAM"
-	ewarn "Results can be visualized with http://sourceforge.net/p/krona/home/krona"
-}
diff --git a/sci-biology/kraken/metadata.xml b/sci-biology/kraken/metadata.xml
deleted file mode 100644
index 138cb7705..000000000
--- a/sci-biology/kraken/metadata.xml
+++ /dev/null
@@ -1,12 +0,0 @@
-<?xml version="1.0" encoding="UTF-8"?>
-<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
-<pkgmetadata>
-	<maintainer type="person">
-		<email>mmokrejs@fold.natur.cuni.cz</email>
-		<name>Martin Mokrejs</name>
-	</maintainer>
-	<maintainer type="project">
-		<email>sci-biology@gentoo.org</email>
-		<name>Gentoo Biology Project</name>
-	</maintainer>
-</pkgmetadata>
diff --git a/sci-biology/last/Manifest b/sci-biology/last/Manifest
deleted file mode 100644
index eadb2539b..000000000
--- a/sci-biology/last/Manifest
+++ /dev/null
@@ -1 +0,0 @@
-DIST last-852.zip 721683 BLAKE2B e2a8d1c59d369f580e46723c2153ffc406f781502c7d7fa60dbc50556ac14703122d76c1a2ec8d938c6dcf0954d02347ee3d4beef60515839c248fa7e6467e18 SHA512 9945967efb5025b72507dfeb28531e1595d9691096dc2d074711fd1f5cce92714341a387577b7c6054f3b2605084528817381ed6f39bd32e828341f4a06380b9
diff --git a/sci-biology/last/files/last-852-fix-build-system.patch b/sci-biology/last/files/last-852-fix-build-system.patch
deleted file mode 100644
index 6ee4f5a67..000000000
--- a/sci-biology/last/files/last-852-fix-build-system.patch
+++ /dev/null
@@ -1,54 +0,0 @@
---- last-852/makefile.ori	2016-12-13 07:22:11.000000000 +0100
-+++ last-852/makefile	2017-05-10 11:04:14.610665834 +0200
-@@ -1,6 +1,7 @@
--CXXFLAGS = -O3 -std=c++11 -pthread -DHAS_CXX_THREADS
-+CXXFLAGS ?= -O3
-+CXXFLAGS += -std=c++11 -pthread -DHAS_CXX_THREADS
- all:
--	@cd src && $(MAKE) CXXFLAGS="$(CXXFLAGS)"
-+	$(MAKE) -C src
- 
- progs = src/lastdb src/lastal src/last-split src/last-merge-batches	\
- src/last-pair-probs src/lastdb8 src/lastal8 src/last-split8
-@@ -13,17 +14,17 @@
- 	cp $(progs) scripts/* $(bindir)
- 
- clean:
--	@cd src && $(MAKE) clean
-+	$(MAKE) -C src clean
- 
- html:
--	@cd doc && $(MAKE)
-+	$(MAKE) -C doc
- 
- distdir = last-`hg id -n`
- 
- RSYNCFLAGS = -aC --exclude '*8' --exclude 'last??' --exclude last-split --exclude last-merge-batches --exclude last-pair-probs
- 
- dist: log html
--	@cd src && $(MAKE) version.hh CyclicSubsetSeedData.hh ScoreMatrixData.hh
-+	$(MAKE) -C src version.hh CyclicSubsetSeedData.hh ScoreMatrixData.hh
- 	rsync $(RSYNCFLAGS) build doc examples makefile scripts src data *.txt $(distdir)
- 	zip -qrm $(distdir) $(distdir)
- 
---- last-852/src/makefile.ori	2016-12-13 06:53:24.000000000 +0100
-+++ last-852/src/makefile	2017-05-10 11:05:22.792501835 +0200
-@@ -1,12 +1,13 @@
--CXX = g++
--CC  = gcc
-+CXX ?= g++
-+CC  ?= gcc
- 
--CXXFLAGS = -O3 -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef	\
---Wcast-align -pedantic -g -std=c++11 -pthread -DHAS_CXX_THREADS
-+CXXFLAGS ?= -O3 -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef	\
-+-Wcast-align -pedantic -g
-+CXXFLAGS += -std=c++11 -pthread -DHAS_CXX_THREADS
- # -Wconversion
- # -fomit-frame-pointer ?
- 
--CFLAGS = -Wall -O2
-+CFLAGS ?= -Wall -O2
- 
- alpObj = alp/sls_alignment_evaluer.o alp/sls_pvalues.o		\
- alp/sls_alp_sim.o alp/sls_alp_regression.o alp/sls_alp_data.o	\
diff --git a/sci-biology/last/files/last-852-portable-shebangs.patch b/sci-biology/last/files/last-852-portable-shebangs.patch
deleted file mode 100644
index c2131da63..000000000
--- a/sci-biology/last/files/last-852-portable-shebangs.patch
+++ /dev/null
@@ -1,56 +0,0 @@
---- last-852/scripts/last-dotplot.ori	2017-05-10 11:14:05.206748593 +0200
-+++ last-852/scripts/last-dotplot	2017-05-10 11:15:31.009058957 +0200
-@@ -1,4 +1,4 @@
--#! /usr/bin/env python
-+#! /usr/bin/env python2
- 
- # Read pair-wise alignments in MAF or LAST tabular format: write an
- # "Oxford grid", a.k.a. dotplot.
---- last-852/scripts/last-map-probs.ori	2017-05-10 11:14:11.856927669 +0200
-+++ last-852/scripts/last-map-probs	2017-05-10 11:15:35.139288498 +0200
-@@ -1,4 +1,4 @@
--#! /usr/bin/env python
-+#! /usr/bin/env python2
- 
- # Copyright 2010, 2011, 2012, 2014 Martin C. Frith
- 
---- last-852/scripts/last-postmask.ori	2017-05-10 11:14:19.817142021 +0200
-+++ last-852/scripts/last-postmask	2017-05-10 11:15:44.939556158 +0200
-@@ -1,4 +1,4 @@
--#! /usr/bin/env python
-+#! /usr/bin/env python2
- 
- # Copyright 2014 Martin C. Frith
- 
---- last-852/scripts/last-train.ori	2017-05-10 11:14:27.687353953 +0200
-+++ last-852/scripts/last-train	2017-05-10 11:15:48.679658384 +0200
-@@ -1,4 +1,4 @@
--#! /usr/bin/env python
-+#! /usr/bin/env python2
- # Copyright 2015 Martin C. Frith
- 
- import math, optparse, os, random, signal, subprocess, sys, tempfile
---- last-852/scripts/maf-convert.ori	2017-05-10 11:14:34.267531142 +0200
-+++ last-852/scripts/maf-convert	2017-05-10 11:15:52.439761157 +0200
-@@ -1,4 +1,4 @@
--#! /usr/bin/env python
-+#! /usr/bin/env python2
- # Copyright 2010, 2011, 2013, 2014 Martin C. Frith
- # Read MAF-format alignments: write them in other formats.
- # Seems to work with Python 2.x, x>=6
---- last-852/scripts/maf-join.ori	2017-05-10 11:14:41.407723414 +0200
-+++ last-852/scripts/maf-join	2017-05-10 11:15:56.699877600 +0200
-@@ -1,4 +1,4 @@
--#! /usr/bin/env python
-+#! /usr/bin/env python2
- 
- # Copyright 2009, 2010, 2011 Martin C. Frith
- 
---- last-852/scripts/maf-swap.ori	2017-05-10 11:14:48.417912185 +0200
-+++ last-852/scripts/maf-swap	2017-05-10 11:16:02.300030669 +0200
-@@ -1,4 +1,4 @@
--#! /usr/bin/env python
-+#! /usr/bin/env python2
- 
- # Read MAF-format alignments, and write them, after moving the Nth
- # sequence to the top in each alignment.
diff --git a/sci-biology/last/last-852.ebuild b/sci-biology/last/last-852.ebuild
deleted file mode 100644
index b063550b3..000000000
--- a/sci-biology/last/last-852.ebuild
+++ /dev/null
@@ -1,42 +0,0 @@
-# Copyright 1999-2017 Gentoo Foundation
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=6
-
-PYTHON_COMPAT=( python2_7 )
-
-inherit toolchain-funcs python-single-r1
-
-DESCRIPTION="Genome-scale comparison of biological sequences"
-HOMEPAGE="http://last.cbrc.jp/"
-SRC_URI="http://last.cbrc.jp/${P}.zip"
-
-LICENSE="GPL-3"
-SLOT="0"
-KEYWORDS="~amd64 ~x86"
-IUSE=""
-REQUIRED_USE="${PYTHON_REQUIRED_USE}"
-
-RDEPEND="${PYTHON_DEPS}"
-DEPEND="app-arch/unzip"
-
-PATCHES=(
-	"${FILESDIR}"/${PN}-${PV}-fix-build-system.patch
-	"${FILESDIR}"/${PN}-${PV}-portable-shebangs.patch
-)
-
-src_configure() {
-	tc-export CC CXX
-}
-
-src_install() {
-	local DOCS=( doc/*.txt ChangeLog.txt README.txt )
-	local HTML_DOCS=( doc/*html )
-	einstalldocs
-
-	dobin src/lastdb src/lastal src/last-split src/last-merge-batches \
-		src/last-pair-probs src/lastdb8 src/lastal8 src/last-split8
-
-	cd scripts || die
-	dobin *
-}
diff --git a/sci-biology/last/metadata.xml b/sci-biology/last/metadata.xml
deleted file mode 100644
index 8417d1580..000000000
--- a/sci-biology/last/metadata.xml
+++ /dev/null
@@ -1,8 +0,0 @@
-<?xml version="1.0" encoding="UTF-8"?>
-<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
-<pkgmetadata>
-	<maintainer type="project">
-		<email>sci-biology@gentoo.org</email>
-		<name>Gentoo Biology Project</name>
-	</maintainer>
-</pkgmetadata>
diff --git a/sci-biology/lastz/Manifest b/sci-biology/lastz/Manifest
index 200d02449..de7bc8e13 100644
--- a/sci-biology/lastz/Manifest
+++ b/sci-biology/lastz/Manifest
@@ -1 +1 @@
-DIST lastz-1.04.00.tar.gz 734145 BLAKE2B cb738d2be8c30fc10a56a360042db768317d9adbd296523b13d5ea75044716653291b53df4645e847901e5c40b348c3c45aaa3dee40fa6b2942c9c49d6de5fe6 SHA512 fa027141d8c797e9c425755b928bd40616ea193bfbd99ebbabc7bc44042edb894eafc493e9953a48cda94702109a9ec295d12c334f3db225e9880d51488e7972
+DIST lastz-1.04.03.tar.gz 5080263 BLAKE2B 74814342f8c973a231d7e736a3854ac685b0d4992511924484223c3c75dd7e89b78e2645304063c92012570e059607931e228ed56c8afb5a2c31d7e268b22cb5 SHA512 f5085dcfa3f8ce817be08dc2130d4bf5bd07dafef6629b6d28c7eeff65ea871bd6da1b16dd12cbe864a448a0d10e0479d69a4b4ba97708eb183a4104d6a51a40
diff --git a/sci-biology/lastz/files/lastz-1.04.00-build.patch b/sci-biology/lastz/files/lastz-1.04.00-build.patch
deleted file mode 100644
index d3705c514..000000000
--- a/sci-biology/lastz/files/lastz-1.04.00-build.patch
+++ /dev/null
@@ -1,49 +0,0 @@
---- lastz-distrib-1.04.00/src/Makefile.ori	2017-11-16 16:09:47.232140878 +0100
-+++ lastz-distrib-1.04.00/src/Makefile	2017-11-16 16:14:12.589271305 +0100
-@@ -1,7 +1,7 @@
- include ../make-include.mak
- include version.mak
- 
--CC=gcc
-+CC?=gcc
- 
- # default targets
- 
-@@ -54,7 +54,8 @@
- #
- #---------
- 
--definedForAll = -Wall -Wextra -Werror -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE
-+mycflags = -O3 -Wall -Wextra -Werror
-+definedForAll = -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE
- flagsFor32    = -Dmax_sequence_index=32 -Dmax_malloc_index=40 -Ddiag_hash_size=4194304
- 
- allowBackToBackGaps ?= 0                       # by default allowBackToBackGaps
-@@ -70,8 +71,8 @@
- 	-DREVISION_DATE="\"${REVISION_DATE}"\" \
- 	-DSUBVERSION_REV="\"${SUBVERSION_REV}"\"
- 
--
--CFLAGS = -O3 ${definedForAll} ${VERSION_FLAGS}
-+CFLAGS ?= ${mycflags}
-+CFLAGS += ${definedForAll} ${VERSION_FLAGS}
- 
- 
- srcFiles = lastz infer_scores \
-@@ -101,13 +102,13 @@
- 
- 
- lastz: $(foreach part,${srcFiles},${part}.o)
--	${CC} $(foreach part,${srcFiles},${part}.o) -lm -o $@
-+	${CC} $(LDFLAGS) $(foreach part,${srcFiles},${part}.o) -lm -o $@
- 
- lastz_D: $(foreach part,${srcFiles},${part}_D.o)
--	${CC} $(foreach part,${srcFiles},${part}_D.o) -lm -o $@
-+	${CC} $(LDFLAGS) $(foreach part,${srcFiles},${part}_D.o) -lm -o $@
- 
- lastz_32: $(foreach part,${srcFiles},${part}_32.o)
--	${CC} $(foreach part,${srcFiles},${part}_32.o) -lm -o $@
-+	${CC} $(LDFLAGS) $(foreach part,${srcFiles},${part}_32.o) -lm -o $@
- 
- # cleanup
- 
diff --git a/sci-biology/lastz/files/lastz-1.04.03-build.patch b/sci-biology/lastz/files/lastz-1.04.03-build.patch
new file mode 100644
index 000000000..b18eed269
--- /dev/null
+++ b/sci-biology/lastz/files/lastz-1.04.03-build.patch
@@ -0,0 +1,49 @@
+--- a/src/Makefile	2017-11-16 16:09:47.232140878 +0100
++++ b/src/Makefile	2017-11-16 16:14:12.589271305 +0100
+@@ -1,7 +1,7 @@
+ include ../make-include.mak
+ include version.mak
+ 
+-CC=gcc
++CC?=gcc
+ 
+ # default targets
+ 
+@@ -54,7 +54,8 @@
+ #
+ #---------
+ 
+-definedForAll = -Wall -Wextra -Werror -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE
++mycflags = -O3 -Wall -Wextra -Werror
++definedForAll = -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE
+ flagsFor32    = -Dmax_sequence_index=32 -Dmax_malloc_index=40 -Ddiag_hash_size=4194304
+ 
+ allowBackToBackGaps ?= 0                       # by default allowBackToBackGaps
+@@ -70,8 +71,8 @@
+ 	-DREVISION_DATE="\"${REVISION_DATE}"\" \
+ 	-DSUBVERSION_REV="\"${SUBVERSION_REV}"\"
+ 
+-
+-CFLAGS = -O3 ${definedForAll} ${VERSION_FLAGS}
++CFLAGS ?= ${mycflags}
++CFLAGS += ${definedForAll} ${VERSION_FLAGS}
+ 
+ 
+ srcFiles = lastz infer_scores \
+@@ -101,13 +102,13 @@
+ 
+ 
+ lastz: $(foreach part,${srcFiles},${part}.o)
+-	${CC} $(foreach part,${srcFiles},${part}.o) -lm -o $@
++	${CC} $(LDFLAGS) $(foreach part,${srcFiles},${part}.o) -lm -o $@
+ 
+ lastz_D: $(foreach part,${srcFiles},${part}_D.o)
+-	${CC} $(foreach part,${srcFiles},${part}_D.o) -lm -o $@
++	${CC} $(LDFLAGS) $(foreach part,${srcFiles},${part}_D.o) -lm -o $@
+ 
+ lastz_32: $(foreach part,${srcFiles},${part}_32.o)
+-	${CC} $(foreach part,${srcFiles},${part}_32.o) -lm -o $@
++	${CC} $(LDFLAGS) $(foreach part,${srcFiles},${part}_32.o) -lm -o $@
+ 
+ # cleanup
+ 
diff --git a/sci-biology/lastz/lastz-1.04.00.ebuild b/sci-biology/lastz/lastz-1.04.00.ebuild
deleted file mode 100644
index 6acd3d39c..000000000
--- a/sci-biology/lastz/lastz-1.04.00.ebuild
+++ /dev/null
@@ -1,39 +0,0 @@
-# Copyright 1999-2017 Gentoo Foundation
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=5
-
-inherit eutils flag-o-matic toolchain-funcs
-
-DESCRIPTION="A pairwise DNA sequence aligner, a BLASTZ replacement"
-HOMEPAGE="http://www.bx.psu.edu/~rsharris/lastz/"
-SRC_URI="http://www.bx.psu.edu/~rsharris/lastz/newer/${P}.tar.gz"
-
-SLOT="0"
-LICENSE="all-rights-reserved"
-KEYWORDS="~amd64 ~x86"
-IUSE=""
-
-S="${WORKDIR}"/lastz-distrib-"${PV}"
-
-RESTRICT="mirror"
-
-src_prepare() {
-	append-lfs-flags
-	epatch "${FILESDIR}"/${P}-build.patch
-
-	tc-export CC
-}
-
-src_compile(){
-	emake
-	emake lastz_32
-}
-
-src_install(){
-	emake install
-	emake install_32
-	dobin src/lastz src/lastz_D src/lastz_32
-	dodoc README.lastz.html
-	dohtml lav_format.html
-}
diff --git a/sci-biology/lastz/lastz-1.04.03.ebuild b/sci-biology/lastz/lastz-1.04.03.ebuild
new file mode 100644
index 000000000..667b2b7ba
--- /dev/null
+++ b/sci-biology/lastz/lastz-1.04.03.ebuild
@@ -0,0 +1,41 @@
+# Copyright 1999-2021 Gentoo Authors
+# Distributed under the terms of the GNU General Public License v2
+
+EAPI=7
+
+inherit flag-o-matic toolchain-funcs
+
+DESCRIPTION="A pairwise DNA sequence aligner, a BLASTZ replacement"
+HOMEPAGE="http://www.bx.psu.edu/~rsharris/lastz/"
+SRC_URI="http://www.bx.psu.edu/~rsharris/lastz/newer/${P}.tar.gz"
+
+SLOT="0"
+LICENSE="all-rights-reserved"
+KEYWORDS="~amd64 ~x86 ~amd64-linux ~x86-linux"
+
+S="${WORKDIR}"/lastz-distrib-"${PV}"
+
+RESTRICT="mirror"
+
+PATCHES=(
+	"${FILESDIR}"/${P}-build.patch
+)
+
+src_prepare() {
+	default
+	append-lfs-flags
+
+	tc-export CC
+}
+
+src_compile(){
+	emake
+	emake lastz_32
+}
+
+src_install(){
+	emake install
+	emake install_32
+	dobin src/lastz src/lastz_D src/lastz_32
+	dodoc README.lastz.html lav_format.html
+}
diff --git a/sci-biology/lemur-brain-atlas/Manifest b/sci-biology/lemur-brain-atlas/Manifest
new file mode 100644
index 000000000..5e589cac5
--- /dev/null
+++ b/sci-biology/lemur-brain-atlas/Manifest
@@ -0,0 +1 @@
+DIST lemur-brain-atlas-0.1.tar.gz 79871940 BLAKE2B fee879d1d8b87ef72e23ec5fc32d79679414986ec54869fb50d9911968d55d5d27440432f71981fbda76f8584960640a89c5c082a7427e147a17a39e13bdd5a0 SHA512 a54b55b93b52b69eabc870ac157e9e01ae5c6e56cdca516e61546eb2e78c032ac51088b11ab12b708844c93a4179a556a670550fc7a1a7ec60de81cba8e40b33
diff --git a/sci-biology/lemur-brain-atlas/lemur-brain-atlas-0.1.ebuild b/sci-biology/lemur-brain-atlas/lemur-brain-atlas-0.1.ebuild
new file mode 100644
index 000000000..6c6d80a44
--- /dev/null
+++ b/sci-biology/lemur-brain-atlas/lemur-brain-atlas-0.1.ebuild
@@ -0,0 +1,23 @@
+# Copyright 1999-2019 Gentoo Authors
+# Distributed under the terms of the GNU General Public License v2
+
+EAPI=7
+
+DESCRIPTION="MRI Brain Template and Atlas of the Mouse Lemur"
+HOMEPAGE="https://www.nitrc.org/projects/mouselemuratlas"
+SRC_URI="https://www.nitrc.org/frs/downloadlink.php/10867 -> ${P}.tar.gz"
+
+LICENSE="CeCILL-2"
+SLOT="0"
+KEYWORDS="~amd64 ~x86 ~amd64-linux ~x86-linux"
+IUSE=""
+
+RDEPEND=""
+DEPEND=""
+
+S="${WORKDIR}/MIRCen-MouseLemurAtlas_V0.01"
+
+src_install() {
+	insinto "/usr/share/${PN}"
+	doins *
+}
diff --git a/sci-biology/lemur-brain-atlas/metadata.xml b/sci-biology/lemur-brain-atlas/metadata.xml
new file mode 100644
index 000000000..aab44690d
--- /dev/null
+++ b/sci-biology/lemur-brain-atlas/metadata.xml
@@ -0,0 +1,20 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
+<pkgmetadata>
+	<maintainer type="person">
+		<email>gentoo@chymera.eu</email>
+		<name>Horea Christian</name>
+	</maintainer>
+	<maintainer type="project">
+		<email>sci@gentoo.org</email>
+		<name>Gentoo Science Project</name>
+	</maintainer>
+	<longdescription lang="en">
+		MRI template and 120-region atlas for the mouse lemur primate Microcebus
+		murinus. Generated from 34 animals aged 15-58 months old scanned at 7T
+		using a T2-weighted sequence, resolution 115 × 115 × 230 µm. The template
+		was up-sampled to 91 µm isotropic for hand-segmentation of structures,
+		and also used to create probability maps of grey matter, white matter and
+		cerebro-spinal fluid.
+	</longdescription>
+</pkgmetadata>
diff --git a/sci-biology/libBigWig/Manifest b/sci-biology/libBigWig/Manifest
index d7a42d43b..249395f6f 100644
--- a/sci-biology/libBigWig/Manifest
+++ b/sci-biology/libBigWig/Manifest
@@ -1 +1,2 @@
-DIST libBigWig-0.4.0.tar.gz 268726 BLAKE2B 7cd3153d5979b2c038e47c5cd99d855e23898c95f983a7883cb26be398f87cb918fa5f7ef2323245e48f180a01222d6988c5c2311b02add429cf7142308a895f SHA512 9849264b21b2c000acd31bc82137e4342ef866c9ac7d65b5fe5794df7ff4e1e35a190f970135071044df787bd6f4041fd1f6e14773266966a0623e8c5e979466
+DIST libBigWig-0.4.4.tar.gz 272926 BLAKE2B ffde5fced9991b28cf1fdb8b296a88744d949ea6f044d3bc6f5bbcb3405bc8a08906d94a614d489758fbfc625361b910bbbdcf9ea721fa22dee0edf2f286fc08 SHA512 85e0b60e4ce541eb1328528d834f54ea827cc79b5890093688661dfc9bc72e417c8d293cfe5b93987973b4584b042f10a6edd77adca6ea6b1e57ed3741edba71
+DIST libBigWig-0.4.7.tar.gz 302341 BLAKE2B 667aff6153dc11a3491362e19673b64ff72a0779f5c722508d21f2af8ce4c5e9fb410c9685fc2ecfc3a1fade85454f40ada8d2969948eb1d3336b13ed3a816be SHA512 52f1b7c8e21e16238b3bb07baef6aa3611797b1b5ff44d912c874f8f4527c516a0676877fad21c103b8b25a733e84bef48530f28dc224a79d43f7764eae7ed40
diff --git a/sci-biology/libBigWig/libBigWig-0.4.0.ebuild b/sci-biology/libBigWig/libBigWig-0.4.0.ebuild
deleted file mode 100644
index bd71899f7..000000000
--- a/sci-biology/libBigWig/libBigWig-0.4.0.ebuild
+++ /dev/null
@@ -1,25 +0,0 @@
-# Copyright 1999-2017 Gentoo Foundation
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=6
-
-DESCRIPTION="C library for handling bigWig files (functionally replacing Jim Kent's lib)"
-HOMEPAGE="https://github.com/dpryan79/libBigWig"
-SRC_URI="https://github.com/dpryan79/libBigWig/archive/${PV}.tar.gz -> ${P}.tar.gz"
-
-LICENSE="MIT"
-SLOT="0"
-KEYWORDS="~amd64 ~x86" # https://github.com/dpryan79/libBigWig/issues/30
-IUSE=""
-
-DEPEND="net-misc/curl"
-RDEPEND="${DEPEND}"
-
-src_prepare(){
-	default
-	sed -e 's#/usr/local#$(DESTDIR)/usr#' -i Makefile || die
-}
-
-src_install(){
-	emake install DESTDIR="${ED}"
-}
diff --git a/sci-biology/libBigWig/libBigWig-0.4.4.ebuild b/sci-biology/libBigWig/libBigWig-0.4.4.ebuild
new file mode 100644
index 000000000..0d95f6972
--- /dev/null
+++ b/sci-biology/libBigWig/libBigWig-0.4.4.ebuild
@@ -0,0 +1,31 @@
+# Copyright 1999-2020 Gentoo Authors
+# Distributed under the terms of the GNU General Public License v2
+
+EAPI=7
+
+DESCRIPTION="C library for handling bigWig files (functionally replacing Jim Kent's lib)"
+HOMEPAGE="https://github.com/dpryan79/libBigWig"
+
+if [[ ${PV} == 9999 ]] ; then
+	inherit git-r3
+	EGIT_REPO_URI="https://github.com/dpryan79/libBigWig"
+else
+	SRC_URI="https://github.com/dpryan79/libBigWig/archive/${PV}.tar.gz -> ${P}.tar.gz"
+	KEYWORDS="~amd64 ~x86"
+fi
+
+LICENSE="MIT"
+SLOT="0"
+
+DEPEND="net-misc/curl"
+RDEPEND="${DEPEND}"
+
+src_prepare(){
+	default
+	sed -e 's#/usr/local#$(DESTDIR)/usr#' -i Makefile || die
+	sed -e "s:/lib:/$(get_libdir):" -i Makefile || die
+}
+
+src_install(){
+	emake install DESTDIR="${ED}"
+}
diff --git a/sci-biology/libBigWig/libBigWig-0.4.7.ebuild b/sci-biology/libBigWig/libBigWig-0.4.7.ebuild
new file mode 100644
index 000000000..7dc83ceed
--- /dev/null
+++ b/sci-biology/libBigWig/libBigWig-0.4.7.ebuild
@@ -0,0 +1,31 @@
+# Copyright 1999-2020 Gentoo Authors
+# Distributed under the terms of the GNU General Public License v2
+
+EAPI=8
+
+DESCRIPTION="C library for handling bigWig files (functionally replacing Jim Kent's lib)"
+HOMEPAGE="https://github.com/dpryan79/libBigWig"
+
+if [[ ${PV} == 9999 ]] ; then
+	inherit git-r3
+	EGIT_REPO_URI="https://github.com/dpryan79/libBigWig"
+else
+	SRC_URI="https://github.com/dpryan79/libBigWig/archive/${PV}.tar.gz -> ${P}.tar.gz"
+	KEYWORDS="~amd64 ~x86"
+fi
+
+LICENSE="MIT"
+SLOT="0"
+
+DEPEND="net-misc/curl"
+RDEPEND="${DEPEND}"
+
+src_prepare(){
+	default
+	sed -e 's#/usr/local#$(DESTDIR)/usr#' -i Makefile || die
+	sed -e "s:/lib:/$(get_libdir):" -i Makefile || die
+}
+
+src_install(){
+	emake install DESTDIR="${ED}"
+}
diff --git a/sci-biology/libBigWig/libBigWig-9999.ebuild b/sci-biology/libBigWig/libBigWig-9999.ebuild
index d470de250..0d95f6972 100644
--- a/sci-biology/libBigWig/libBigWig-9999.ebuild
+++ b/sci-biology/libBigWig/libBigWig-9999.ebuild
@@ -1,18 +1,21 @@
-# Copyright 1999-2017 Gentoo Foundation
+# Copyright 1999-2020 Gentoo Authors
 # Distributed under the terms of the GNU General Public License v2
 
-EAPI=5
-
-inherit git-r3
+EAPI=7
 
 DESCRIPTION="C library for handling bigWig files (functionally replacing Jim Kent's lib)"
 HOMEPAGE="https://github.com/dpryan79/libBigWig"
-EGIT_REPO_URI="https://github.com/dpryan79/libBigWig.git"
+
+if [[ ${PV} == 9999 ]] ; then
+	inherit git-r3
+	EGIT_REPO_URI="https://github.com/dpryan79/libBigWig"
+else
+	SRC_URI="https://github.com/dpryan79/libBigWig/archive/${PV}.tar.gz -> ${P}.tar.gz"
+	KEYWORDS="~amd64 ~x86"
+fi
 
 LICENSE="MIT"
 SLOT="0"
-KEYWORDS="" # https://github.com/dpryan79/libBigWig/issues/30
-IUSE=""
 
 DEPEND="net-misc/curl"
 RDEPEND="${DEPEND}"
@@ -20,6 +23,7 @@ RDEPEND="${DEPEND}"
 src_prepare(){
 	default
 	sed -e 's#/usr/local#$(DESTDIR)/usr#' -i Makefile || die
+	sed -e "s:/lib:/$(get_libdir):" -i Makefile || die
 }
 
 src_install(){
diff --git a/sci-biology/lighter/Manifest b/sci-biology/lighter/Manifest
new file mode 100644
index 000000000..f6c604f55
--- /dev/null
+++ b/sci-biology/lighter/Manifest
@@ -0,0 +1 @@
+DIST lighter-1.1.2.tar.gz 48529 BLAKE2B 6249e849d83e304969f010f0438f3e9252c92d5f53f8b228ca61465faa8182f5e4a4f3aac66ce9e234f51dc9fdd60518c37e042b08411e41a7b0591af4ae3bbc SHA512 8dc96621758a29e5e582b322a3e3ce7a27c5e88096a6c81c89fe37289698e354e627e9d3d119d170ca4e946b12a5b4bdc594920269868cf5fa0cc8aee81ea54f
diff --git a/sci-biology/lighter/lighter-1.1.2.ebuild b/sci-biology/lighter/lighter-1.1.2.ebuild
new file mode 100644
index 000000000..2d08c45c4
--- /dev/null
+++ b/sci-biology/lighter/lighter-1.1.2.ebuild
@@ -0,0 +1,26 @@
+# Copyright 1999-2021 Gentoo Authors
+# Distributed under the terms of the GNU General Public License v2
+
+EAPI=7
+
+DESCRIPTION="NGS reads corrector"
+HOMEPAGE="https://github.com/mourisl/Lighter"
+if [ "$PV" == "9999" ]; then
+	inherit git-r3
+	EGIT_REPO_URI="https://github.com/mourisl/Lighter.git"
+else
+	SRC_URI="https://github.com/mourisl/Lighter/archive/v${PV}.tar.gz -> ${P}.tar.gz"
+	KEYWORDS="~amd64"
+	S="${WORKDIR}/Lighter-${PV}"
+fi
+
+LICENSE="GPL-2+"
+SLOT="0"
+
+DEPEND="sys-libs/zlib"
+RDEPEND="${DEPEND}"
+
+src_install(){
+	dobin lighter
+	dodoc README.md
+}
diff --git a/sci-biology/lighter/lighter-9999.ebuild b/sci-biology/lighter/lighter-9999.ebuild
index 87f6fb390..2d08c45c4 100644
--- a/sci-biology/lighter/lighter-9999.ebuild
+++ b/sci-biology/lighter/lighter-9999.ebuild
@@ -1,34 +1,25 @@
-# Copyright 1999-2015 Gentoo Foundation
+# Copyright 1999-2021 Gentoo Authors
 # Distributed under the terms of the GNU General Public License v2
 
-EAPI=5
-
-inherit toolchain-funcs
-
-[ "$PV" == "9999" ] && inherit git-r3
+EAPI=7
 
 DESCRIPTION="NGS reads corrector"
 HOMEPAGE="https://github.com/mourisl/Lighter"
 if [ "$PV" == "9999" ]; then
+	inherit git-r3
 	EGIT_REPO_URI="https://github.com/mourisl/Lighter.git"
-	KEYWORDS=""
 else
-	SRC_URI=""
-	KEYWORDS=""
+	SRC_URI="https://github.com/mourisl/Lighter/archive/v${PV}.tar.gz -> ${P}.tar.gz"
+	KEYWORDS="~amd64"
+	S="${WORKDIR}/Lighter-${PV}"
 fi
 
 LICENSE="GPL-2+"
 SLOT="0"
-IUSE="threads"
 
-DEPEND="sys-libs/zlib
-	sci-libs/bloom"
+DEPEND="sys-libs/zlib"
 RDEPEND="${DEPEND}"
 
-src_prepare(){
-	sed -e "s#g++#$(tc-getCC)#;s#-Wall -O3#${CXXFLAGS}#" -i Makefile || die
-}
-
 src_install(){
 	dobin lighter
 	dodoc README.md
diff --git a/sci-biology/longstitch/Manifest b/sci-biology/longstitch/Manifest
new file mode 100644
index 000000000..2327cd7d4
--- /dev/null
+++ b/sci-biology/longstitch/Manifest
@@ -0,0 +1 @@
+DIST longstitch-1.0.1.tar.gz 7190631 BLAKE2B 29ea35de8ccebc1b5525edd483ac19dca217424b101f5b80b87d52947fb8ec401d6aa1ad9cb4650dbacfaf3f1a00ae79ab8070de3b624cc6bcf5ce721852bec8 SHA512 da2f3837e9be6dee5fffe29b99665c456607d69aa405069fe3a977e55b9063108871b99b8a2a8f017597e7fa3553084694170f5b6bf301c37218ed1dabfd3ee3
diff --git a/sci-biology/longstitch/longstitch-1.0.1.ebuild b/sci-biology/longstitch/longstitch-1.0.1.ebuild
new file mode 100644
index 000000000..b14bdee87
--- /dev/null
+++ b/sci-biology/longstitch/longstitch-1.0.1.ebuild
@@ -0,0 +1,27 @@
+# Copyright 1999-2022 Gentoo Authors
+# Distributed under the terms of the GNU General Public License v2
+
+EAPI=8
+
+DESCRIPTION="Scaffold genome assemblies by Chromium/PacBio/Nanopore reads"
+HOMEPAGE="https://github.com/bcgsc/LongStitch"
+SRC_URI="https://github.com/bcgsc/LongStitch/archive/refs/tags/v${PV}.tar.gz -> ${P}.tar.gz"
+S="${WORKDIR}/LongStitch-${PV}"
+
+LICENSE="GPL-3"
+SLOT="0"
+KEYWORDS="~amd64"
+
+RESTRICT="test"
+
+RDEPEND="
+	sci-biology/abyss
+	sci-biology/tigmint
+	sci-biology/LINKS
+	sci-biology/samtools
+"
+
+src_install(){
+	dobin longstitch
+	dodoc README.md LongStitch_overview.pdf
+}
diff --git a/sci-biology/longstitch/metadata.xml b/sci-biology/longstitch/metadata.xml
new file mode 100644
index 000000000..b25087121
--- /dev/null
+++ b/sci-biology/longstitch/metadata.xml
@@ -0,0 +1,15 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
+<pkgmetadata>
+	<maintainer type="person">
+		<email>mmokrejs@fold.natur.cuni.cz</email>
+		<name>Martin Mokrejs</name>
+	</maintainer>
+	<maintainer type="project">
+		<email>sci-biology@gentoo.org</email>
+		<name>Gentoo Biology Project</name>
+	</maintainer>
+	<upstream>
+		<remote-id type="github">bcgsc/LongStitch</remote-id>
+	</upstream>
+</pkgmetadata>
diff --git a/sci-biology/lucy/lucy-1.20.ebuild b/sci-biology/lucy/lucy-1.20.ebuild
index 8f4ed8edd..a47e5fcf8 100644
--- a/sci-biology/lucy/lucy-1.20.ebuild
+++ b/sci-biology/lucy/lucy-1.20.ebuild
@@ -1,20 +1,20 @@
-# Copyright 1999-2015 Gentoo Foundation
+# Copyright 1999-2021 Gentoo Authors
 # Distributed under the terms of the GNU General Public License v2
 
-EAPI=5
+EAPI=7
 
 DESCRIPTION="DNA sequence quality and vector trimming tool"
-HOMEPAGE="http://lucy.sourceforge.net/"
-SRC_URI="http://sourceforge.net/projects/lucy/files/lucy/lucy%201.20/lucy1.20.tar.gz"
+HOMEPAGE="https://lucy.sourceforge.net/"
+SRC_URI="https://sourceforge.net/projects/lucy/files/lucy/lucy%201.20/lucy${PV}.tar.gz"
 
 LICENSE="Artistic"
 SLOT="0"
 KEYWORDS="~amd64 ~x86"
-IUSE=""
 
-S="${WORKDIR}"/lucy-1.20p
+S="${WORKDIR}/lucy-${PV}p"
 
 src_prepare(){
+	default
 	sed -i 's/^CC = cc/#CC = cc/' Makefile || die
 	sed -i 's/^CFLAGS = -O/#CFLAGS = -O/' Makefile || die
 }
diff --git a/sci-biology/lumpy-sv/Manifest b/sci-biology/lumpy-sv/Manifest
new file mode 100644
index 000000000..df35426fc
--- /dev/null
+++ b/sci-biology/lumpy-sv/Manifest
@@ -0,0 +1 @@
+DIST lumpy-sv-0.3.1.tar.gz 56671785 BLAKE2B d3878f66a5f001c11b4e78fc015102f6b357e72403545bc9c4c8e2104dbcb692fb2d9a53eb9be996ccfa788bac5b03c72be8a591636abb84731b4bab702ceea3 SHA512 efa6992f94005464b49f01c350855ead1b8d5f1006305c09634adee33e0621b0b19b55eaa2ad57583b2b9dc5365e70663892591de85a156eb08d6f14aa0f7c11
diff --git a/sci-biology/lumpy-sv/lumpy-sv-0.3.1.ebuild b/sci-biology/lumpy-sv/lumpy-sv-0.3.1.ebuild
new file mode 100644
index 000000000..f98892b95
--- /dev/null
+++ b/sci-biology/lumpy-sv/lumpy-sv-0.3.1.ebuild
@@ -0,0 +1,41 @@
+# Copyright 1999-2021 Gentoo Authors
+# Distributed under the terms of the GNU General Public License v2
+
+EAPI=7
+
+DESCRIPTION="Probabilistic framework for structural variant discovery"
+HOMEPAGE="https://github.com/arq5x/lumpy-sv"
+SRC_URI="https://github.com/arq5x/lumpy-sv/archive/v${PV}.tar.gz -> ${P}.tar.gz"
+
+LICENSE="MIT"
+SLOT="0"
+KEYWORDS="~amd64"
+
+DEPEND="sci-libs/htslib"
+RDEPEND="${DEPEND}"
+
+src_prepare() {
+	default
+	# do not build bundled htslib, link to system lib
+	sed -i -e 's/lumpy_filter: htslib/lumpy_filter:/g' Makefile || die
+	sed -i -e 's/-I..\/..\/lib\/htslib\///' -e 's/..\/..\/lib\/htslib\/libhts.a/-lhts/g' src/filter/Makefile || die
+}
+
+src_install(){
+	cat > "${T}"/99lumpy-sv <<- EOF
+	LUMPY_HOME=${EPREFIX}/usr/share/lumpy-sv
+	PAIREND_DISTRO=${EPREFIX}/usr/share/lumpy-sv/scripts/pairend_distro.py
+	BAMGROUPREADS=${EPREFIX}/usr/share/lumpy-sv/scripts/bamkit/bamgroupreads.py
+	BAMFILTERRG=${EPREFIX}/usr/share/lumpy-sv/scripts/bamkit/bamfilterrg.py
+	BAMLIBS=${EPREFIX}/usr/share/lumpy-sv/scripts/bamkit/bamlibs.py
+	EOF
+	doenvd "${T}"/99lumpy-sv
+	rm -f bin/lumpyexpress.config
+	dobin bin/*
+	insinto /usr/share/lumpy-sv/scripts
+	for f in lumpyexpress lumpyexpress.config; do
+		rm scripts/"$f" || die
+	done
+	doins scripts/*
+	einstalldocs
+}
diff --git a/sci-biology/lumpy-sv/lumpy-sv-9999.ebuild b/sci-biology/lumpy-sv/lumpy-sv-9999.ebuild
deleted file mode 100644
index 4c565c0c0..000000000
--- a/sci-biology/lumpy-sv/lumpy-sv-9999.ebuild
+++ /dev/null
@@ -1,43 +0,0 @@
-# Copyright 1999-2017 Gentoo Foundation
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=6
-
-inherit git-r3
-
-DESCRIPTION="Probabilistic framework for structural variant discovery"
-HOMEPAGE="https://github.com/arq5x/lumpy-sv"
-EGIT_REPO_URI="https://github.com/arq5x/lumpy-sv.git"
-
-LICENSE="MIT"
-SLOT="0"
-KEYWORDS=""
-IUSE=""
-
-# contains bundled htslib
-CDEPEND="dev-util/cmake"
-DEPEND=""
-RDEPEND="${DEPEND}"
-
-src_install(){
-	cat > "${T}"/99lumpy-sv <<- EOF
-	LUMPY_HOME=${EPREFIX}/usr/share/lumpy-sv
-	PAIREND_DISTRO=${EPREFIX}/usr/share/lumpy-sv/scripts/pairend_distro.py
-	BAMGROUPREADS=${EPREFIX}/usr/share/lumpy-sv/scripts/bamkit/bamgroupreads.py
-	BAMFILTERRG=${EPREFIX}/usr/share/lumpy-sv/scripts/bamkit/bamfilterrg.py
-	BAMLIBS=${EPREFIX}/usr/share/lumpy-sv/scripts/bamkit/bamlibs.py
-	EOF
-	doenvd "${T}"/99lumpy-sv
-	rm -f bin/lumpyexpress.config
-	dobin bin/*
-	insinto /usr/share/lumpy-sv/scripts
-	for f in lumpyexpress lumpyexpress.config; do
-		rm scripts/"$f" || die
-	done
-	doins scripts/*
-	dodoc README.md
-	insinto /usr/share/lumpy-sv/scripts/bamkit
-	cd scripts/bamkit || die
-	doins *.py sectosupp
-	newdoc README.md README_bamkit.md
-}
diff --git a/sci-biology/mRNAmarkup/Manifest b/sci-biology/mRNAmarkup/Manifest
deleted file mode 100644
index f14ab8b9e..000000000
--- a/sci-biology/mRNAmarkup/Manifest
+++ /dev/null
@@ -1,2 +0,0 @@
-DIST mRNAmarkup-10-3-2013.tar.gz 225283371 SHA256 4fce294745dde0e55c0dda71c9c186d2372c28850d26cc7f4db68b23278f84a1 SHA512 bf752ed2459bb01ddb6d982a7aee4417634a52c42be5eda56f680aaf77e5e37c6feb3199f03784e754d95a417b9cda3eff83e47c31a733365f25e93a4c412303 WHIRLPOOL a3905f30aeda2980b803a50734529d4eca8b216398eb6db1b9d38bc372b5470971e50b87cfffa59c7d84c64333c5b6422facbe4574947f2f170ad28291b31f14
-DIST mRNAmarkup-4-8-2015.tar.gz 192523324 BLAKE2B 5a327c1cef195bb637eb5cf22f030f1e18c4a7374630dee0f777e68b86888b558a07766aef374c9c1373154ad04e728c105c803372707321c0ec0cabae55f143 SHA512 caf537f98bf3a11e28e47a6e6833eb70e1f810cd1ad3033d30f7a941fb136f08e243abb373a105a86191ba939fc56537967ef598f714d1a8f40f6ee9967732b3
diff --git a/sci-biology/mRNAmarkup/mRNAmarkup-1.0.ebuild b/sci-biology/mRNAmarkup/mRNAmarkup-1.0.ebuild
deleted file mode 100644
index dbdc3e368..000000000
--- a/sci-biology/mRNAmarkup/mRNAmarkup-1.0.ebuild
+++ /dev/null
@@ -1,57 +0,0 @@
-# Copyright 1999-2016 Gentoo Foundation
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=5
-
-DESCRIPTION="Transcript annotation workflow"
-HOMEPAGE="http://brendelgroup.org/bioinformatics2go/mRNAmarkup.php"
-SRC_URI="http://www.brendelgroup.org/bioinformatics2go/Download/mRNAmarkup-10-3-2013.tar.gz" # 215MB
-
-# 0README in version 20131003 says it is 1.0
-
-LICENSE="mRNAmarkup"
-SLOT="0"
-KEYWORDS="~amd64"
-IUSE=""
-
-DEPEND="
-	sci-biology/ncbi-tools++
-	sci-biology/estscan"
-# sci-biology/MuSeqBox has fetch-restrict and probably only works with old BLAST plaintex output
-# but, mRNAmarkup/INSTALL says:
-# 'For convenience, a copy of the MuSeqBox code distribution is included in directory src/contributed
-#
-# has a slightly modified estscan copy in src/contributed
-RDEPEND="${DEPEND}"
-
-S="${WORKDIR}"/"${PN}"
-
-src_prepare(){
-	sed -e \
-		"s#configfile=$installdir/mRNAmarkup.conf#configfile=/usr/share/mRNAmarkup/etc/mRNAmarkup.conf#" \
-		-i bin/mRNAmarkup.orig || die
-	sed -e \
-		"s#$installdir/bin/ESTScan.conf#/usr/share/mRNAmarkup/etc/ESTScan.conf#" \
-		-i bin/mRNAmarkup.orig
-}
-
-src_compile(){
-	cd src
-	emake
-}
-
-src_install(){
-	mv bin/mRNAmarkup.orig bin/mRNAmarkup
-	sed -e 's#INSTALLDIR#/usr/share/mRNAmarkup/etc/#' -i bin/mRNAmarkup
-	dobin bin/mRNAmarkup bin/*.pl bin/dnatopro bin/genestat
-	# TODO: there are some more files in bin/ , sigh!
-	insinto /usr/share/mRNAmarkup/etc
-	mv mRNAmarkup.conf.orig mRNAmarkup.conf
-	doins mRNAmarkup.conf
-	doins bin/ESTScan.conf
-	dodoc 0README INSTALL
-}
-
-pkg_postinst(){
-	einfo "Please obtain a local copy of NCBI CDD dastabase"
-}
diff --git a/sci-biology/mRNAmarkup/mRNAmarkup-1.1.ebuild b/sci-biology/mRNAmarkup/mRNAmarkup-1.1.ebuild
deleted file mode 100644
index f68f0d335..000000000
--- a/sci-biology/mRNAmarkup/mRNAmarkup-1.1.ebuild
+++ /dev/null
@@ -1,57 +0,0 @@
-# Copyright 1999-2016 Gentoo Foundation
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=5
-
-DESCRIPTION="Transcript annotation workflow"
-HOMEPAGE="http://brendelgroup.org/bioinformatics2go/mRNAmarkup.php"
-SRC_URI="http://www.brendelgroup.org/bioinformatics2go/Download/mRNAmarkup-4-8-2015.tar.gz" # 184MB
-
-# mRNAmarkup-4-8-2015.tar.gz is 1.1 version
-
-LICENSE="mRNAmarkup"
-SLOT="0"
-KEYWORDS="~amd64"
-IUSE=""
-
-DEPEND="
-	sci-biology/ncbi-tools++
-	sci-biology/estscan"
-# sci-biology/MuSeqBox has fetch-restrict and probably only works with old BLAST plaintex output
-# but, mRNAmarkup/INSTALL says:
-# 'For convenience, a copy of the MuSeqBox code distribution is included in directory src/contributed
-#
-# has a slightly modified estscan copy in src/contributed
-RDEPEND="${DEPEND}"
-
-S="${WORKDIR}"/"${PN}"
-
-src_prepare(){
-	sed -e \
-		"s#configfile=$installdir/mRNAmarkup.conf#configfile=/usr/share/mRNAmarkup/etc/mRNAmarkup.conf#" \
-		-i bin/mRNAmarkup.orig || die
-	sed -e \
-		"s#$installdir/bin/ESTScan.conf#/usr/share/mRNAmarkup/etc/ESTScan.conf#" \
-		-i bin/mRNAmarkup.orig
-}
-
-src_compile(){
-	cd src
-	emake
-}
-
-src_install(){
-	mv bin/mRNAmarkup.orig bin/mRNAmarkup
-	sed -e 's#INSTALLDIR#/usr/share/mRNAmarkup/etc/#' -i bin/mRNAmarkup
-	dobin bin/mRNAmarkup bin/*.pl bin/dnatopro bin/genestat
-	# TODO: there are some more files in bin/ , sigh!
-	insinto /usr/share/mRNAmarkup/etc
-	mv mRNAmarkup.conf.orig mRNAmarkup.conf
-	doins mRNAmarkup.conf
-	doins bin/ESTScan.conf
-	dodoc 0README INSTALL
-}
-
-pkg_postinst(){
-	einfo "Please obtain a local copy of NCBI CDD dastabase"
-}
diff --git a/sci-biology/mRNAmarkup/metadata.xml b/sci-biology/mRNAmarkup/metadata.xml
deleted file mode 100644
index 138cb7705..000000000
--- a/sci-biology/mRNAmarkup/metadata.xml
+++ /dev/null
@@ -1,12 +0,0 @@
-<?xml version="1.0" encoding="UTF-8"?>
-<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
-<pkgmetadata>
-	<maintainer type="person">
-		<email>mmokrejs@fold.natur.cuni.cz</email>
-		<name>Martin Mokrejs</name>
-	</maintainer>
-	<maintainer type="project">
-		<email>sci-biology@gentoo.org</email>
-		<name>Gentoo Biology Project</name>
-	</maintainer>
-</pkgmetadata>
diff --git a/sci-biology/maker/Manifest b/sci-biology/maker/Manifest
deleted file mode 100644
index 8b2a8d085..000000000
--- a/sci-biology/maker/Manifest
+++ /dev/null
@@ -1 +0,0 @@
-DIST maker-2.31.8.tgz 13607357 SHA256 a99c7e433638979808ea3f4bcd2b6b69f4474bd898807aba4520debd58717420 SHA512 1533888c4960a74395f4bfdd26a4f86ba33d93764b1e40094fcd2d8e7e355495464619820b0c805061f467c20d979ddf17bdb2979a7f17117c1a721032ee538d WHIRLPOOL 2df90ae76891160ed08fc3a703d3d8a982e737fa23c3f65d197bd900816588a2e8d8ec364e1122af4be289f01b5c704414487eb19ece8a8fedd9c9aac11e40e2
diff --git a/sci-biology/maker/maker-2.31.8.ebuild b/sci-biology/maker/maker-2.31.8.ebuild
deleted file mode 100644
index e5c791ab2..000000000
--- a/sci-biology/maker/maker-2.31.8.ebuild
+++ /dev/null
@@ -1,134 +0,0 @@
-# Copyright 1999-2016 Gentoo Foundation
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=5
-
-PERL_EXPORT_PHASE_FUNCTIONS=no
-inherit eutils perl-module
-
-DESCRIPTION="A genome annotation viewer and pipeline for small eukaryota and prokaryota"
-HOMEPAGE="http://www.yandell-lab.org/software/maker.html"
-SRC_URI="maker-"${PV}".tgz"
-
-RESTRICT="fetch"
-
-# for academia: GPL-v2 or Artistic-2
-# for commercial: ask
-LICENSE="|| ( GPL-2 Artistic-2 )"
-SLOT="0"
-KEYWORDS=""
-IUSE="mpi"
-
-# http://search.cpan.org/~rybskej/forks-0.36/lib/forks.pm             # bug #566360
-# http://search.cpan.org/~rybskej/forks-0.36/lib/forks/shared.pm
-DEPEND="
-	mpi? ( sys-cluster/mpich2 || ( sys-cluster/openmpi ) )
-	dev-perl/DBI
-	dev-perl/DBD-SQLite
-	dev-perl/File-Which
-	dev-perl/Bit-Vector
-	dev-perl/Inline-C
-	dev-perl/IO-All
-	dev-perl/libwww-perl
-	dev-perl/DBD-Pg
-	dev-perl/Module-Build
-	dev-perl/Want
-	dev-perl/IO-Prompt
-	dev-perl/Perl-Unsafe-Signals
-	dev-perl/forks
-	>=sci-biology/GAL-0.2.1
-	>=sci-biology/bioperl-1.6
-	sci-biology/ncbi-tools || ( sci-biology/ncbi-tools++ )
-	sci-biology/snap
-	sci-biology/exonerate
-	>=sci-biology/augustus-2.0
-	sci-biology/repeatmasker"
-	#sci-biology/GeneMark_ES-bin
-	#sci-biology/GeneMark_S-bin
-	#>=sci-biology/FGENESH-bin-2.4 (not in gentoo yet)
-RDEPEND="${DEPEND}"
-# dev-perl/forks-shared ?
-
-# ==============================================================================
-# STATUS MAKER v2.31.8
-# ==============================================================================
-# PERL Dependencies:      MISSING
-#                   !  Perl::Unsafe::Signals
-#                   !  Want
-#                   !  forks
-#                   !  forks::shared
-#
-# External Programs:      MISSING
-#                   !  RepeatMasker
-#
-# External C Libraries:   VERIFIED
-# MPI SUPPORT:            DISABLED
-# MWAS Web Interface:     DISABLED
-# MAKER PACKAGE:          MISSING PREREQUISITES
-#
-#
-# Important Commands:
-#         ./Build installdeps     #installs missing PERL dependencies
-#         ./Build installexes     #installs all missing external programs
-#         ./Build install         #installs MAKER
-#         ./Build status          #Shows this status menu
-#
-# Other Commands:
-#         ./Build repeatmasker    #installs RepeatMasker (asks for RepBase)
-#         ./Build blast           #installs BLAST (NCBI BLAST+)
-#         ./Build exonerate       #installs Exonerate (v2 on UNIX / v1 on Mac OSX)
-#         ./Build snap            #installs SNAP
-#         ./Build augustus        #installs Augustus
-#         ./Build apollo          #installs Apollo
-#         ./Build gbrowse         #installs GBrowse (must be root)
-#         ./Build jbrowse         #installs JBrowse (MAKER copy, not web accecible)
-#         ./Build webapollo       #installs WebApollo (use maker2wap to create DBs)
-#         ./Build mpich2          #installs MPICH2 (but manual install recommended)
-# Building MAKER
-#
-# * MISSING MAKER PREREQUISITES - CANNOT CONTINUE!!
-
-S="${WORKDIR}"/maker/src
-
-pkg_nofetch() {
-	einfo "Please visit ${HOMEPAGE} and obtain the file"
-	einfo "maker-"${PV}".tgz and place it into ${DISTDIR}"
-	einfo "You must also install sci-biology/repeatmasker otherwise"
-	einfo "MAKER install process will stop."
-	einfo "That in turn requires you to register at http://www.girinst.org/server/RepBase"
-	einfo "to obtain sci-biology/repeatmasker-libraries data file"
-	einfo "For execution through openmpi or mpich please read INSTALL file"
-	einfo "Customization typically go into maker_opts.ctl file"
-}
-
-src_compile(){
-	perl Build.PL || die
-	./Build install || die
-}
-
-# If you move it, then the executables won’t be able to locate dependencies in the …/maker/data,
-# …/maker/lib, and …/maker/perl directories. You should really either add the location of
-# …/maker/bin to you PATH environmental variable or at most soft link the executables somewhere
-# else using the ‘ln -s’ command.
-src_install(){
-	cd "${WORKDIR}"/maker || die
-	rm -f bin/fasta_tool # is part of sci-biology/GAL
-	# drop development related accessory script requiring Parallel/MPIcar.pm
-	find . -name mpi_evaluator | xargs rm || die
-	mv bin/compare bin/compare_gff3_to_chado # rename as agreed by upstream, will be in maker-3 as well
-	dobin bin/*
-	perl_set_version
-	insinto "${VENDOR_LIB}"/MAKER # uppercase, not "${PN}"
-	doins perl/lib/MAKER/*.pm
-	doman perl/man/*.3pm
-	insinto "${VENDOR_LIB}"/Parallel/Application
-	doins perl/lib/Parallel/Application/*.pm
-	insinto /usr/share/"${PN}"/data
-	doins data/*
-	# FIXME: find equivalent perl packages for lib/* contents, for example lib/GI.pm
-	dodoc README INSTALL
-	insinto /usr/share/"${PN}"/GMOD/Apollo
-	doins GMOD/Apollo/gff3.tiers
-	insinto /usr/share/"${PN}"/GMOD/JBrowse
-	doins GMOD/JBrowse/maker.css
-}
diff --git a/sci-biology/maker/metadata.xml b/sci-biology/maker/metadata.xml
deleted file mode 100644
index 138cb7705..000000000
--- a/sci-biology/maker/metadata.xml
+++ /dev/null
@@ -1,12 +0,0 @@
-<?xml version="1.0" encoding="UTF-8"?>
-<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
-<pkgmetadata>
-	<maintainer type="person">
-		<email>mmokrejs@fold.natur.cuni.cz</email>
-		<name>Martin Mokrejs</name>
-	</maintainer>
-	<maintainer type="project">
-		<email>sci-biology@gentoo.org</email>
-		<name>Gentoo Biology Project</name>
-	</maintainer>
-</pkgmetadata>
diff --git a/sci-biology/manatee-igs/Manifest b/sci-biology/manatee-igs/Manifest
deleted file mode 100644
index 05b1077e2..000000000
--- a/sci-biology/manatee-igs/Manifest
+++ /dev/null
@@ -1,2 +0,0 @@
-DIST README_Linux.txt 9628 BLAKE2B c44cb04313f30726b5d7a1943de3ff39651e3b869fe664ac570063958dc75210dedaff9c5c4e3feedb3e05bec4eb3c149600c8188dde00291570b3695cd3116b SHA512 7cfb666c1bf066595a6f0fae8a9cff1e6a7150382c33e5ea717b9e09bb91ee2e8eb9bae0fd9e93a0a790a39fb2d66ba83029e5ab55755e56ee85958a5df8a99a
-DIST manatee-2.23.1_linux.tgz 19879146 BLAKE2B bd69d0d701c92ad4e4c8bbfdf8c9cb23184fa2778a924f71dd83e01901a8054296fb32adb58c5bb66d442b29c564c31c8690398479d214e020697726fc413a59 SHA512 50a76d36f69e3b8b80bcdf7fe28e1c9eb7c15bd8889bd8d130bc65f879ec99aa0caec6d0df495d7ab5804e6414599fc316073c9c55ecd1d370c5dd72aadd65ba
diff --git a/sci-biology/manatee-igs/manatee-igs-2.23.1.ebuild b/sci-biology/manatee-igs/manatee-igs-2.23.1.ebuild
deleted file mode 100644
index 774224625..000000000
--- a/sci-biology/manatee-igs/manatee-igs-2.23.1.ebuild
+++ /dev/null
@@ -1,78 +0,0 @@
-# Copyright 1999-2016 Gentoo Foundation
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=6
-
-DESCRIPTION="IGS-modified version of the genome annotation tool using Chado database schema"
-HOMEPAGE="http://manatee.sourceforge.net/igs"
-SRC_URI="
-	http://sourceforge.net/projects/manatee/files/igs_manatee/"${PV}"/manatee-"${PV}"_linux.tgz
-	http://manatee.sourceforge.net/igs/docs/README_Linux.txt"
-
-LICENSE="Artistic-Manatee"
-SLOT="0"
-KEYWORDS="~amd64 ~x86"
-IUSE=""
-
-DEPEND="
-	>=dev-libs/expat-1.95.8
-	>=media-libs/gd-2.0.34
-	dev-perl/CGI
-	dev-perl/Bio-DB-Das-Chado
-	dev-perl/DBI
-	dev-perl/DBD-mysql
-	dev-perl/XML-Parser
-	dev-perl/XML-Twig
-	dev-perl/XML-Simple
-	dev-perl/XML-Writer
-	dev-perl/HTML-Template
-	dev-perl/Tree-DAG_Node
-	virtual/perl-File-Spec
-	virtual/perl-Data-Dumper
-	dev-perl/GD
-	dev-perl/GDTextUtil
-	dev-perl/GDGraph
-	virtual/perl-Storable
-	dev-perl/Log-Log4perl
-	dev-perl/Log-Cabin
-	dev-perl/Date-Manip
-	dev-perl/IO-Tee
-	dev-perl/MLDBM
-	dev-perl/JSON
-	dev-perl/JSON-Any
-	sci-biology/bioperl"
-RDEPEND="${DEPEND}
-	>=virtual/mysql-5:*
-	>=www-servers/apache-2.2"
-
-S="${WORKDIR}"/manatee-"${PV}"_linux
-
-src_prepare(){
-	find "${S}" -name \*.cgi | while read f; do sed -e 's|#!/usr/local/bin/perl|#!/usr/bin/perl|' -i $f; done
-	find "${S}" -name \*.pl | while read f; do sed -e 's|#!/usr/local/bin/perl|#!/usr/bin/perl|' -i $f; done
-	find "${S}" -name \*.pm | while read f; do sed -e 's|#!/usr/local/bin/perl|#!/usr/bin/perl|' -i $f; done
-}
-
-#src_configure(){
-#	there used to be manateee-="${PV}".tgz file which contained configure script in the past
-#	now the layout is different, temporarily commenting out untill we find the current full sources back again
-#	econf HTTPD=/usr/sbin/httpd HTTPD_SCRIPT_HOME=/var/www/cgi-bin HTTPD_DOC_HOME=/var/www/htdocs MYSQLD=/usr/sbin/mysqld || die
-#}
-#
-#src_compile(){
-#	default
-#}
-
-src_install(){
-	dodoc ${DISTDIR}"/README_Linux.txt"
-	dodir /var/www/localhost/cgi-bin
-	cp -r src/cgi-bin/chado_prok_manatee "${D}"/var/www/localhost/cgi-bin
-	dodir /var/www/localhost/htdocs/manatee
-	cp -r src/htdocs/tdb "${D}"/var/www/localhost/htdocs/manatee
-
-	einfo "Please read the "${S}"/databases/Makefile.PL and import the databases into your MySQL database"
-
-	einfo "You have to fetch the 1.1 GB large file from http://sourceforge.net/projects/manatee/files/igs_manatee/"${PV}"/lookups-"${PV}"_linux.tgz"
-	einfo "You need to update it regularly."
-	einfo "Also fetch http://sourceforge.net/projects/manatee/files/igs_manatee/"${PV}"/blastdb-"${PV}".tgz (about 2MB in size)"
-}
diff --git a/sci-biology/manatee-igs/metadata.xml b/sci-biology/manatee-igs/metadata.xml
deleted file mode 100644
index 8a3d26043..000000000
--- a/sci-biology/manatee-igs/metadata.xml
+++ /dev/null
@@ -1,15 +0,0 @@
-<?xml version="1.0" encoding="UTF-8"?>
-<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
-<pkgmetadata>
-	<maintainer type="person">
-		<email>mmokrejs@fold.natur.cuni.cz</email>
-		<name>Martin Mokrejs</name>
-	</maintainer>
-	<maintainer type="project">
-		<email>sci-biology@gentoo.org</email>
-		<name>Gentoo Biology Project</name>
-	</maintainer>
-	<upstream>
-		<remote-id type="sourceforge">manatee</remote-id>
-	</upstream>
-</pkgmetadata>
diff --git a/sci-biology/manatee-jcvi/Manifest b/sci-biology/manatee-jcvi/Manifest
deleted file mode 100644
index 9efd473f9..000000000
--- a/sci-biology/manatee-jcvi/Manifest
+++ /dev/null
@@ -1 +0,0 @@
-DIST manatee-2.4.3.tgz 1840410 BLAKE2B e80b499e4a9a6fddc60851e1da126dc48356d675df36938f1ed1a920f19a5f76708fc4be295164ae69330d1978cebbf6e6b9c1f7c098e8049710a3e48eeee0d3 SHA512 0bfb9dff8bdaec1e602fdaa1ec6e2939cba1813ac639b95b9e2679e3473719ad74bb383ba54c56cf4dc0553eac002ea3955ae05a1bc87215c7553b9edb9f9fcf
diff --git a/sci-biology/manatee-jcvi/manatee-jcvi-2.4.3.ebuild b/sci-biology/manatee-jcvi/manatee-jcvi-2.4.3.ebuild
deleted file mode 100644
index 344f3b59b..000000000
--- a/sci-biology/manatee-jcvi/manatee-jcvi-2.4.3.ebuild
+++ /dev/null
@@ -1,52 +0,0 @@
-# Copyright 1999-2015 Gentoo Foundation
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=5
-
-DESCRIPTION="Genome annotation tool"
-HOMEPAGE="http://manatee.sourceforge.net/jcvi/downloads.shtml"
-SRC_URI="http://downloads.sourceforge.net/project/manatee/manatee/manatee-2.4.3/manatee-2.4.3.tgz"
-
-LICENSE="Artistic-Manatee"
-SLOT="0"
-KEYWORDS=""
-#KEYWORDS="~amd64 ~x86"
-IUSE=""
-
-DEPEND=">=dev-libs/expat-1.95.8
-		>=media-libs/gd-2.0.34
-		dev-perl/DBI
-		dev-perl/DBD-mysql
-		dev-perl/XML-Parser
-		dev-perl/XML-Twig
-		dev-perl/XML-Simple
-		dev-perl/XML-Writer
-		dev-perl/HTML-Template
-		dev-perl/Tree-DAG_Node
-		virtual/perl-File-Spec
-		virtual/perl-Data-Dumper
-		dev-perl/GD
-		virtual/perl-Storable
-		dev-perl/Log-Log4perl
-		dev-perl/Log-Cabin
-		dev-perl/IO-Tee
-		dev-perl/MLDBM"
-		#dev-perl/CGI
-		#dev-perl/CGI-Carp
-		#dev-perl/CGI-Cookie
-		#dev-perl/GD-Text
-		#dev-perl/GD-Graph
-		#dev-perl/Date-Manip
-RDEPEND="${DEPEND}
-		>=virtual/mysql-5:*
-		>=www-servers/apache-2.2"
-
-S="${WORKDIR}"/manatee-"${PV}"
-
-src_configure(){
-	econf HTTPD=/usr/sbin/httpd HTTPD_SCRIPT_HOME=/var/www/cgi-bin HTTPD_DOC_HOME=/var/www/htdocs MYSQLD=/usr/sbin/mysqld
-}
-
-src_compile(){
-	default
-}
diff --git a/sci-biology/manatee-jcvi/metadata.xml b/sci-biology/manatee-jcvi/metadata.xml
deleted file mode 100644
index 0f267b755..000000000
--- a/sci-biology/manatee-jcvi/metadata.xml
+++ /dev/null
@@ -1,15 +0,0 @@
-<?xml version="1.0" encoding="UTF-8"?>
-<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
-<pkgmetadata>
-	<maintainer type="person">
-		<email>mmokrejs@fold.natur.cuni.cz</email>
-		<name>Martin Mokrejs</name>
-	</maintainer>
-	<maintainer type="project">
-		<email>sci-biology@gentoo.org</email>
-		<name>Gentoo Biology Project</name>
-	</maintainer>
-	<upstream>
-		<remote-id type="sourceforge">downloads</remote-id>
-	</upstream>
-</pkgmetadata>
diff --git a/sci-biology/mappy/Manifest b/sci-biology/mappy/Manifest
new file mode 100644
index 000000000..ff114e6ea
--- /dev/null
+++ b/sci-biology/mappy/Manifest
@@ -0,0 +1,2 @@
+DIST mappy-2.24.tar.gz 140859 BLAKE2B af8ecf8f00c33951b2c7e81bec1e45fe39b7b41da1692fc8c4804b3ad5465320f453e2d53f771c09ce88fa681ad60c0c3706334ace8a682eee8b6f4ebccb02fc SHA512 5500b76ffb0f530aa8f1433c01f1805f5b95e329445ab103847e6ec6e0977a54e5c0dabe405869c7dd8d9103646db0b3cff0ef13b79d7021752ed266002a1dd4
+DIST mappy-2.26.tar.gz 135105 BLAKE2B 26c4c94eae3b719cfaadf2fe31a84faeaef4894b8b8c9ad6bbba46dbb17f609c62c61ecfd42e3be07a7eace38545d029ab03d1fee611868ac6839b3d3362698d SHA512 75949b705561455c317713bfb4bca2de24368881e6c0bb3bf2d11841db9f9e792c7eef0e46f00a7b27e38fe143db5b00be5f281fe058dca32130b745057dcb75
diff --git a/sci-biology/mappy/mappy-2.24.ebuild b/sci-biology/mappy/mappy-2.24.ebuild
new file mode 100644
index 000000000..0fa703188
--- /dev/null
+++ b/sci-biology/mappy/mappy-2.24.ebuild
@@ -0,0 +1,16 @@
+# Copyright 1999-2023 Gentoo Authors
+# Distributed under the terms of the GNU General Public License v2
+
+EAPI=8
+
+DISTUTILS_USE_PEP517=setuptools
+PYTHON_COMPAT=( python3_{10..11} )
+
+inherit distutils-r1 pypi
+
+DESCRIPTION="Minimap2 python binding"
+HOMEPAGE="https://github.com/haotianteng/chiron"
+
+LICENSE="MIT"
+SLOT="0"
+KEYWORDS="~amd64 ~x86"
diff --git a/sci-biology/mappy/mappy-2.26.ebuild b/sci-biology/mappy/mappy-2.26.ebuild
new file mode 100644
index 000000000..0fa703188
--- /dev/null
+++ b/sci-biology/mappy/mappy-2.26.ebuild
@@ -0,0 +1,16 @@
+# Copyright 1999-2023 Gentoo Authors
+# Distributed under the terms of the GNU General Public License v2
+
+EAPI=8
+
+DISTUTILS_USE_PEP517=setuptools
+PYTHON_COMPAT=( python3_{10..11} )
+
+inherit distutils-r1 pypi
+
+DESCRIPTION="Minimap2 python binding"
+HOMEPAGE="https://github.com/haotianteng/chiron"
+
+LICENSE="MIT"
+SLOT="0"
+KEYWORDS="~amd64 ~x86"
diff --git a/sci-biology/mappy/metadata.xml b/sci-biology/mappy/metadata.xml
new file mode 100644
index 000000000..2b83a776c
--- /dev/null
+++ b/sci-biology/mappy/metadata.xml
@@ -0,0 +1,12 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
+<pkgmetadata>
+	<maintainer type="project">
+		<email>sci-biology@gentoo.org</email>
+		<name>Gentoo Biology Project</name>
+	</maintainer>
+	<upstream>
+		<remote-id type="github">haotianteng/chiron</remote-id>
+		<remote-id type="pypi">mappy</remote-id>
+	</upstream>
+</pkgmetadata>
diff --git a/sci-biology/mavid/Manifest b/sci-biology/mavid/Manifest
deleted file mode 100644
index 232b32ab5..000000000
--- a/sci-biology/mavid/Manifest
+++ /dev/null
@@ -1 +0,0 @@
-DIST mavid-package-2.0.4.tar.gz 85863 BLAKE2B 3ff4a914e8796faefb7799bef597638e2581885338dfe8c841290cbf4560da95c57495c2c9a7f93ce8270292f440e6ad78f41ad9eb5ee6553f4872c342baa823 SHA512 6c64e51df3069859bb0226efc078c488c0b5602e9fcd5fa7f596a29f07c279ccdfca580c947fbd4efdac66cbc86669f5d2388a68f3e861d45c8979d710e65e00
diff --git a/sci-biology/mavid/mavid-2.0.4.ebuild b/sci-biology/mavid/mavid-2.0.4.ebuild
deleted file mode 100644
index c75e28111..000000000
--- a/sci-biology/mavid/mavid-2.0.4.ebuild
+++ /dev/null
@@ -1,48 +0,0 @@
-# Copyright 1999-2014 Gentoo Foundation
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=5
-
-inherit toolchain-funcs
-
-DESCRIPTION="Multiple alignment of large DNA sequences"
-HOMEPAGE="http://baboon.math.berkeley.edu/mavid/"
-SRC_URI="http://bio.math.berkeley.edu/mavid/download/mavid-package-${PV}.tar.gz"
-
-LICENSE="mavid"
-SLOT="0"
-IUSE=""
-KEYWORDS="~amd64 ~x86"
-
-DEPEND=""
-RDEPEND="
-	sci-biology/clustalw
-	sci-biology/fastdnaml"
-
-S="${WORKDIR}"/${PN}-package-${PV}
-
-src_prepare() {
-	sed \
-		-e 's:OPT_CPP_OPTIONS =:OPT_CPP_OPTIONS ?=:g' \
-		-e 's:DEBUG_CPP_OPTIONS =:DEBUG_CPP_OPTIONS ?=:g' \
-		-i $(find -type f -name Makefile) || die
-}
-
-src_compile() {
-	emake \
-		CPP=$(tc-getCXX) \
-		BASE_CPP_OPTIONS="${CXXFLAGS}" \
-		DEBUG_CPP_OPTIONS="${CXXFLAGS}" \
-		OPT_CPP_OPTIONS="${CXXFLAGS}"
-
-}
-
-src_install() {
-	local i
-	dobin mavid/{mavid,mavid.pl}
-	for i in checkfasta cut_alignment extract_seq extract_tree fasta2phylip phylip2fasta project_alignment randtree root_tree tree_dists; do
-		dobin utils/$i/$i
-	done
-	dodoc examples/*
-	newdoc mavid/README README.mavid
-}
diff --git a/sci-biology/mavid/metadata.xml b/sci-biology/mavid/metadata.xml
deleted file mode 100644
index 8417d1580..000000000
--- a/sci-biology/mavid/metadata.xml
+++ /dev/null
@@ -1,8 +0,0 @@
-<?xml version="1.0" encoding="UTF-8"?>
-<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
-<pkgmetadata>
-	<maintainer type="project">
-		<email>sci-biology@gentoo.org</email>
-		<name>Gentoo Biology Project</name>
-	</maintainer>
-</pkgmetadata>
diff --git a/sci-biology/megahit/Manifest b/sci-biology/megahit/Manifest
new file mode 100644
index 000000000..34e1f60a0
--- /dev/null
+++ b/sci-biology/megahit/Manifest
@@ -0,0 +1 @@
+DIST megahit-1.2.9.tar.gz 268591 BLAKE2B 5c6fb5a8104516beb6e43fd58e7438ac746cd0314180cc0d085ac303de5b2fbd9d63e00263f9fc86b994dff798964e0f8aa0891857b1a18940a17e9269eb100d SHA512 b4e306414e46d8d7c0844fdedfb9b47a5774afb347ff7e949fb17bdab070f06ca6b48ddd193da284ca4ceb352296008d4533633274f3b7a7a46c7aca34a98168
diff --git a/sci-biology/megahit/megahit-1.2.9.ebuild b/sci-biology/megahit/megahit-1.2.9.ebuild
new file mode 100644
index 000000000..3e1766259
--- /dev/null
+++ b/sci-biology/megahit/megahit-1.2.9.ebuild
@@ -0,0 +1,32 @@
+# Copyright 1999-2021 Gentoo Authors
+# Distributed under the terms of the GNU General Public License v2
+
+EAPI=7
+
+inherit toolchain-funcs cmake
+
+DESCRIPTION="Metagenome assembler using succinct de Bruijn graph approach with CUDA"
+HOMEPAGE="https://github.com/voutcn/megahit
+	http://bioinformatics.oxfordjournals.org/content/31/10/1674.abstract"
+SRC_URI="https://github.com/voutcn/megahit/archive/v${PV}.tar.gz -> ${P}.tar.gz"
+
+LICENSE="GPL-3"
+SLOT="0"
+KEYWORDS="~amd64"
+IUSE="+openmp cuda"
+
+DEPEND=""
+RDEPEND="${DEPEND}
+	sys-libs/zlib
+	cuda? ( >=dev-util/nvidia-cuda-toolkit-5 dev-libs/cudnn )"
+# contains bundled copy og idba from https://github.com/loneknightpy/idba
+
+pkg_setup() {
+	use openmp && ! tc-has-openmp && die "Please switch to an openmp compatible compiler"
+}
+
+pkg_postinst(){
+	einfo "The maximum k-mer size is 255. You can edit kMaxK in definitions.h"
+	einfo "and recompile, eventually"
+	einfo "If you enabled GPU then use 'megahit --use-gpu' to activate it."
+}
diff --git a/sci-biology/megahit/megahit-9999.ebuild b/sci-biology/megahit/megahit-9999.ebuild
deleted file mode 100644
index e403604ca..000000000
--- a/sci-biology/megahit/megahit-9999.ebuild
+++ /dev/null
@@ -1,60 +0,0 @@
-# Copyright 1999-2018 Gentoo Foundation
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=6
-
-inherit git-r3 toolchain-funcs eutils
-
-DESCRIPTION="Metagenome assembler using succinct de Bruijn graph approach with CUDA"
-HOMEPAGE="https://github.com/voutcn/megahit
-	http://bioinformatics.oxfordjournals.org/content/31/10/1674.abstract"
-EGIT_REPO_URI="https://github.com/voutcn/megahit.git"
-
-LICENSE="GPL-3"
-SLOT="0"
-KEYWORDS=""
-IUSE="+openmp cuda"
-
-DEPEND=""
-RDEPEND="${DEPEND}
-	sys-libs/zlib
-	cuda? ( >=dev-util/nvidia-cuda-toolkit-5 dev-libs/cudnn )"
-# >=gcc-4.4
-# contains bundled copy og idba from https://github.com/loneknightpy/idba
-
-pkg_setup() {
-	use openmp && ! tc-has-openmp && die "Please switch to an openmp compatible compiler"
-}
-
-src_prepare(){
-	default
-	if [[ $(tc-getCXX) =~ g++ ]]; then
-		local eopenmp=-fopenmp
-	elif [[ $(tc-getCXX) =~ cxx ]]; then
-		local eopenmp=-openmp
-		sed -e "s#-fopenmp#-openmp#" -i Makefile || die
-	else
-		elog "Cannot detect compiler type so not setting openmp support"
-	fi
-	if use cuda; then
-		local makeopts="use_gpu=1"
-	else
-		local makeopts=""
-	fi
-	sed -e "s#^CXXFLAGS = -g -O2#CXXFLAGS = ${CFLAGS}#" -i Makefile || die
-}
-
-src_compile(){
-	emake $makeopts
-}
-
-src_install(){
-	dobin megahit megahit_toolkit megahit_sdbg_build megahit_asm_core
-	dodoc README.md
-}
-
-pkg_postinst(){
-	einfo "The maximum k-mer size is 255. You can edit kMaxK in definitions.h"
-	einfo "and recompile, eventually"
-	einfo "If you enabled GPU then use 'megahit --use-gpu' to activate it."
-}
diff --git a/sci-biology/merlin/merlin-1.1.2.ebuild b/sci-biology/merlin/merlin-1.1.2.ebuild
index 63ab49359..9151564d5 100644
--- a/sci-biology/merlin/merlin-1.1.2.ebuild
+++ b/sci-biology/merlin/merlin-1.1.2.ebuild
@@ -1,20 +1,20 @@
-# Copyright 1999-2015 Gentoo Foundation
+# Copyright 1999-2021 Gentoo Authors
 # Distributed under the terms of the GNU General Public License v2
 
-EAPI=5
+EAPI=7
 
 inherit toolchain-funcs
 
 DESCRIPTION="Statistical analysis of gene flow in pedigrees"
-HOMEPAGE="http://www.sph.umich.edu/csg/abecasis/Merlin/"
-SRC_URI="http://www.sph.umich.edu/csg/abecasis/Merlin/download/${P}.tar.gz"
+HOMEPAGE="https://csg.sph.umich.edu/abecasis/Merlin/"
+SRC_URI="https://www.sph.umich.edu/csg/abecasis/Merlin/download/${P}.tar.gz"
 
 LICENSE="merlin"
 SLOT="0"
-IUSE=""
 KEYWORDS="~amd64 ~x86"
 
 src_prepare() {
+	default
 	sed -i -e 's/CXX=g++/CXX='$(tc-getCXX)'/' -e 's/CFLAGS=/CFLAGS+= /' "${S}/Makefile" || die
 }
 
diff --git a/sci-biology/metaseq/Manifest b/sci-biology/metaseq/Manifest
deleted file mode 100644
index 8abf162d1..000000000
--- a/sci-biology/metaseq/Manifest
+++ /dev/null
@@ -1 +0,0 @@
-DIST metaseq-0.5.3.tar.gz 5233997 BLAKE2B a3af67882efbcb497a7eadf78d50538887d4db18a92b3bf0d5613f16e3ca5335026546ba0663e1231439979c2c557e07790f0681591689137b9b040fefb4eda5 SHA512 18e9aa7260d076c0332674dd99e189964f49a5af689858905f43b8ef4168923c50cc9a42ce53cd0865329663d76863c95eb1c4fb125c62b2e03026bd6f0bccac
diff --git a/sci-biology/metaseq/metadata.xml b/sci-biology/metaseq/metadata.xml
deleted file mode 100644
index 64cf80c39..000000000
--- a/sci-biology/metaseq/metadata.xml
+++ /dev/null
@@ -1,15 +0,0 @@
-<?xml version="1.0" encoding="UTF-8"?>
-<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
-<pkgmetadata>
-	<maintainer type="person">
-		<email>mschu.dev@gmail.com</email>
-		<name>Michael Schubert</name>
-	</maintainer>
-	<maintainer type="project">
-		<email>sci-biology@gentoo.org</email>
-		<name>Gentoo Biology Project</name>
-	</maintainer>
-	<upstream>
-		<remote-id type="github">daler/metaseq</remote-id>
-	</upstream>
-</pkgmetadata>
diff --git a/sci-biology/metaseq/metaseq-0.5.3.ebuild b/sci-biology/metaseq/metaseq-0.5.3.ebuild
deleted file mode 100644
index 7b57483e7..000000000
--- a/sci-biology/metaseq/metaseq-0.5.3.ebuild
+++ /dev/null
@@ -1,31 +0,0 @@
-# Copyright 1999-2017 Gentoo Foundation
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=6
-
-PYTHON_COMPAT=( python2_7 )
-
-inherit distutils-r1
-
-DESCRIPTION="Framework for integrated analysis and plotting of ChIP/RIP/RNA/*-seq data"
-HOMEPAGE="http://pythonhosted.org/metaseq/"
-SRC_URI="https://github.com/daler/metaseq/archive/v${PV}.tar.gz -> ${P}.tar.gz"
-
-LICENSE="MIT"
-SLOT="0"
-KEYWORDS="~amd64 ~x86 ~amd64-linux ~x86-linux"
-IUSE=""
-
-RDEPEND="
-	dev-python/matplotlib[${PYTHON_USEDEP}]
-	dev-python/numpy[${PYTHON_USEDEP}]
-	dev-python/pandas[${PYTHON_USEDEP}]
-	dev-python/pyyaml[${PYTHON_USEDEP}]
-	sci-biology/bx-python[${PYTHON_USEDEP}]
-	sci-biology/gffutils[${PYTHON_USEDEP}]
-	sci-biology/pysam[${PYTHON_USEDEP}]
-	sci-biology/pybedtools[${PYTHON_USEDEP}]
-	sci-biology/samtools:0[${PYTHON_USEDEP}]
-	sci-libs/scipy[${PYTHON_USEDEP}]
-	"
-DEPEND="${RDEPEND}"
diff --git a/sci-biology/mgblast/Manifest b/sci-biology/mgblast/Manifest
deleted file mode 100644
index 67b6fdaf4..000000000
--- a/sci-biology/mgblast/Manifest
+++ /dev/null
@@ -1 +0,0 @@
-DIST mgblast.tar.gz 22904 BLAKE2B b56d16ef878e32ffb2673889c55c658156620f89753205fb013578b04caea175d67c41fba830c3cb8bce6ac90cafa4de13c7229d5f47972946060b3e3f247261 SHA512 64e36e7bcfd013c85d7b7a79a0728dc2e3aee476772550147680ea2bdd2d3255d4ee9e20a26f886e459e34b42f47082fc34581a60112d99774d291664f45819f
diff --git a/sci-biology/mgblast/metadata.xml b/sci-biology/mgblast/metadata.xml
deleted file mode 100644
index 138cb7705..000000000
--- a/sci-biology/mgblast/metadata.xml
+++ /dev/null
@@ -1,12 +0,0 @@
-<?xml version="1.0" encoding="UTF-8"?>
-<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
-<pkgmetadata>
-	<maintainer type="person">
-		<email>mmokrejs@fold.natur.cuni.cz</email>
-		<name>Martin Mokrejs</name>
-	</maintainer>
-	<maintainer type="project">
-		<email>sci-biology@gentoo.org</email>
-		<name>Gentoo Biology Project</name>
-	</maintainer>
-</pkgmetadata>
diff --git a/sci-biology/mgblast/mgblast-0.1.ebuild b/sci-biology/mgblast/mgblast-0.1.ebuild
deleted file mode 100644
index 1f7a63ec8..000000000
--- a/sci-biology/mgblast/mgblast-0.1.ebuild
+++ /dev/null
@@ -1,45 +0,0 @@
-# Copyright 1999-2014 Gentoo Foundation
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=5
-
-DESCRIPTION="Customized version of megablast from TIGR Gene Indices project"
-HOMEPAGE="http://compbio.dfci.harvard.edu/tgi/software/"
-SRC_URI="ftp://occams.dfci.harvard.edu/pub/bio/tgi/software/tgicl/mgblast.tar.gz"
-
-LICENSE="Artistic"
-SLOT="0"
-KEYWORDS="" # upstream binary is provided by sci-biology/tgicl currently
-#KEYWORDS="~amd64 ~x86"
-IUSE=""
-
-DEPEND="sci-biology/ncbi-tools"
-RDEPEND="${DEPEND}"
-
-S="${WORKDIR}"
-
-# mgblast needs old version of ncbi-tools unpacked and compiled during its own compilation
-# from newer tools you need to include blfmtutl.h but the next error is no go for me:
-#   mgblast.c:2205: error: too few arguments to function ‘BXMLBuildOneQueryIteration’
-
-# Quoting from mgblast/README: the present package was built and tested only with the release 20060507
-
-src_prepare(){
-	# mgblast cannot be compiled against newer ncbi-tools but let's try
-	mv mgblast/makefile mgblast/Makefile 2>/dev/null || true
-	sed -i 's#/usr/local/projects/tgi/ncbitoolkit/ncbi#/usr#' mgblast/Makefile || die
-	sed -i 's#NCBIDIR = /mylocal/src/ncbi#NCBIDIR = /usr#' mgblast/Makefile || die
-	sed -i 's#NCBI_INCDIR = .*#NCBI_INCDIR = /usr/include/ncbi#' mgblast/Makefile || die
-	sed -i 's#NCBI_LIBDIR = .*#NCBI_LIBDIR = /usr/lib#' mgblast/Makefile || die # a PATH to NCBI-TOOLKIT (/usr/lib) while NOT /usr/lib/ncbi-tools++ !
-	sed -i "s#-I-#-iquote#" mgblast/Makefile || die
-}
-
-src_compile(){
-	cd "${S}"/mgblast || die
-	default
-}
-
-src_install(){
-	cd "${S}"/mgblast || die
-	dobin mgblast
-}
diff --git a/sci-biology/minced/Manifest b/sci-biology/minced/Manifest
new file mode 100644
index 000000000..1014985f6
--- /dev/null
+++ b/sci-biology/minced/Manifest
@@ -0,0 +1 @@
+DIST minced-0.4.2.tar.gz 510282 BLAKE2B 4ff935d8d5ecea900f3a702603a5ce83031d99e9c3bef7414307b4d631eef67632bc600a5bd4ed3e750b77a0e952e152ef310746ad79bf66e3b28487bcca7150 SHA512 6e88ecf8ab8af1aeb53582c5e901bc5b890570ec74c9bfdf1b5f6d3e60775ed5e30fd010a6b885a9f1fdd9c3f802c55c535a7e673b23027630711f8d5565a52b
diff --git a/sci-biology/minced/minced-0.4.2.ebuild b/sci-biology/minced/minced-0.4.2.ebuild
new file mode 100644
index 000000000..b9845e859
--- /dev/null
+++ b/sci-biology/minced/minced-0.4.2.ebuild
@@ -0,0 +1,23 @@
+# Copyright 1999-2021 Gentoo Authors
+# Distributed under the terms of the GNU General Public License v2
+
+EAPI=7
+
+inherit java-pkg-2 java-pkg-simple
+
+DESCRIPTION="Short Palindromic Repeat finder tool (for CRISPRs)"
+HOMEPAGE="https://github.com/ctSkennerton/minced"
+SRC_URI="https://github.com/ctSkennerton/minced/archive/${PV}.tar.gz -> ${P}.tar.gz"
+
+LICENSE="GPL-3"
+SLOT="0"
+KEYWORDS="~amd64"
+
+DEPEND=">=virtual/jdk-1.7"
+RDEPEND=">=virtual/jre-1.7"
+
+src_install(){
+	java-pkg_dojar minced.jar
+	java-pkg_dolauncher
+	einstalldocs
+}
diff --git a/sci-biology/minced/minced-9999.ebuild b/sci-biology/minced/minced-9999.ebuild
deleted file mode 100644
index e9884583e..000000000
--- a/sci-biology/minced/minced-9999.ebuild
+++ /dev/null
@@ -1,28 +0,0 @@
-# Copyright 1999-2015 Gentoo Foundation
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=5
-
-inherit git-r3 java-pkg-2
-
-DESCRIPTION="Short Palindromic Repeat finder tool (for CRISPRs)"
-HOMEPAGE="https://github.com/ctSkennerton/minced/tree/master"
-EGIT_REPO_URI="https://github.com/ctSkennerton/minced.git"
-
-LICENSE="GPL-3"
-SLOT="0"
-KEYWORDS=""
-IUSE=""
-
-DEPEND=">=virtual/jdk-1.7"
-RDEPEND=">=virtual/jre-1.7"
-
-src_compile(){
-	default
-}
-
-src_install(){
-	java-pkg_dojar minced.jar
-	java-pkg_dolauncher
-	dodoc README
-}
diff --git a/sci-biology/minimap2/Manifest b/sci-biology/minimap2/Manifest
new file mode 100644
index 000000000..54585ee56
--- /dev/null
+++ b/sci-biology/minimap2/Manifest
@@ -0,0 +1 @@
+DIST minimap2-2.24.tar.bz2 169939 BLAKE2B 0e16e144b748c291990c1d076157939ec773643659201ba84cf24587b910e8e56d0d90c28bdeccfcfd120c388a3df495282ade0d1454567910471fd897472a34 SHA512 0f16cfbafd7c5aa2e554052d82384aba14dd83cf60fe425526f7e0d093670d105e5c5c1051bc465113202e026bb320bbb36fc174dc50ed15aabf14f7bfa68859
diff --git a/sci-biology/minimap2/metadata.xml b/sci-biology/minimap2/metadata.xml
new file mode 100644
index 000000000..604410dd8
--- /dev/null
+++ b/sci-biology/minimap2/metadata.xml
@@ -0,0 +1,15 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
+<pkgmetadata>
+	<maintainer type="person">
+		<email>mmokrejs@fold.natur.cuni.cz</email>
+		<name>Martin Mokrejs</name>
+	</maintainer>
+	<maintainer type="project">
+		<email>sci-biology@gentoo.org</email>
+		<name>Gentoo Biology Project</name>
+	</maintainer>
+	<upstream>
+		<remote-id type="github">lh3/minimap2</remote-id>
+	</upstream>
+</pkgmetadata>
diff --git a/sci-biology/minimap2/minimap2-2.24.ebuild b/sci-biology/minimap2/minimap2-2.24.ebuild
new file mode 100644
index 000000000..6934f2a74
--- /dev/null
+++ b/sci-biology/minimap2/minimap2-2.24.ebuild
@@ -0,0 +1,63 @@
+# Copyright 2021-2022 Gentoo Authors
+# Distributed under the terms of the GNU General Public License v2
+
+EAPI=8
+
+PYTHON_COMPAT=( python3_10 )
+DISTUTILS_OPTIONAL=1
+inherit distutils-r1
+
+DESCRIPTION="splice-aware sequence aligner with SSE2 and SSE4.1"
+HOMEPAGE="https://github.com/lh3/minimap2"
+SRC_URI="https://github.com/lh3/${PN}/releases/download/v${PV}/${P}.tar.bz2"
+
+LICENSE="MIT"
+SLOT="0"
+KEYWORDS="~amd64 ~x86"
+IUSE="python cpu_flags_x86_sse4_1"
+REQUIRED_USE="${PYTHON_REQUIRED_USE}"
+
+DEPEND="sys-libs/zlib
+	python? (
+		${PYTHON_DEPS}
+	)"
+RDEPEND="${DEPEND}"
+BDEPEND="python? ( dev-python/cython[${PYTHON_USEDEP}] )"
+
+src_prepare(){
+	sed -e 's/-O2 //' -e 's/^CFLAGS=/CFLAGS+=/' -i Makefile || die
+	if ! use cpu_flags_x86_sse4_1; then
+		sed -i -e "/extra_compile_args.append('-msse4.1')/d" setup.py || die
+	fi
+	if use python; then
+		distutils-r1_src_prepare
+	fi
+	default
+}
+
+src_configure() {
+	if use python; then
+		distutils-r1_src_configure
+	fi
+	default
+}
+
+src_compile() {
+	if use python; then
+		distutils-r1_src_compile
+	fi
+	default
+}
+
+src_install() {
+	if use python; then
+		distutils-r1_src_install
+	fi
+	dobin "${PN}"
+	insinto /usr/include
+	doins minimap.h mmpriv.h
+	insinto /usr/share/"${PN}"/examples
+	doins example.c
+	doman minimap2.1
+	einstalldocs
+}
diff --git a/sci-biology/mip-scaffolder/mip-scaffolder-0.6.ebuild b/sci-biology/mip-scaffolder/mip-scaffolder-0.6.ebuild
index cb1da348f..aa2c6b3e7 100644
--- a/sci-biology/mip-scaffolder/mip-scaffolder-0.6.ebuild
+++ b/sci-biology/mip-scaffolder/mip-scaffolder-0.6.ebuild
@@ -1,18 +1,17 @@
-# Copyright 1999-2015 Gentoo Foundation
+# Copyright 1999-2021 Gentoo Authors
 # Distributed under the terms of the GNU General Public License v2
 
-EAPI=5
+EAPI=7
 
 inherit toolchain-funcs
 
 DESCRIPTION="Scaffold contigs using ABI Solid or Illumina mate pair info"
 HOMEPAGE="http://www.cs.helsinki.fi/u/lmsalmel/mip-scaffolder"
-SRC_URI="http://www.cs.helsinki.fi/u/lmsalmel/mip-scaffolder/"${P}".tar.gz"
+SRC_URI="http://www.cs.helsinki.fi/u/lmsalmel/mip-scaffolder/${P}.tar.gz"
 
 LICENSE="BSD-2"
 SLOT="0"
 KEYWORDS="~amd64"
-IUSE=""
 
 DEPEND="sci-libs/lemon
 	sci-mathematics/lpsolve
@@ -20,6 +19,7 @@ DEPEND="sci-libs/lemon
 RDEPEND="${DEPEND}"
 
 src_prepare(){
+	default
 	sed -e 's:/home/user/lp-solve/:/usr/include/lpsolve/:; s:/home/user/lemon/:/usr/include/lemon:; s:/home/user/mip-scaffolder-0.6/:/usr/bin:' -i Makefile
 	find . -name Makefile | while read f; do sed -e "s:CC=g++:CC=$(tc-getCXX):; s:CFLAGS=-Wall -g -O9:CFLAGS=${CXXFLAGS}:" -i $f; done
 	sed -e 's:$(LPSOLVEROOT)/liblpsolve55.a:-llpsolve55:' -i split-scaffold/Makefile
diff --git a/sci-biology/mira/Manifest b/sci-biology/mira/Manifest
deleted file mode 100644
index 7f796dec8..000000000
--- a/sci-biology/mira/Manifest
+++ /dev/null
@@ -1,2 +0,0 @@
-DIST mira-4.9.5.tar.bz2 10444005 BLAKE2B aa4d342cedf3a9545250ce1bad45397b7e73592359984a216ef7081a7a53747113da5662990258d94493d492d1695b52ebb7373752408e901820cf569f79c511 SHA512 f56bd9e1c6982b501534bc8c64fed0ed81f20505546d6e79b48cfed3d82780a43691e985f5be3910af55adf12a955dbf1901cb1da1f182636d5e1357d8129cf8
-DIST mira_3rdparty_06-07-2012.tar.bz2 31656 BLAKE2B 7e952d96e9073acd8ab1d1fc7c51c37f6526287d31698c5090500d421147285b535e8cab7e49f4e51a5634c901d1cd969206b1727e683d3fcebdc195399e3589 SHA512 4d4dbdf7ab5126f9d47160bee8bc127b6a225de8087f6b9914c754324a74d966333207c86a3f38cf0ea9f91408707e2a24086dbe1318fdfa2870b0c39bc5033b
diff --git a/sci-biology/mira/files/mira-3.4.0.2-boost-1.50.patch b/sci-biology/mira/files/mira-3.4.0.2-boost-1.50.patch
deleted file mode 100644
index 427192294..000000000
--- a/sci-biology/mira/files/mira-3.4.0.2-boost-1.50.patch
+++ /dev/null
@@ -1,24 +0,0 @@
- config/m4/ax_boost_regex.m4 | 4 ++--
- 1 file changed, 2 insertions(+), 2 deletions(-)
-
-diff --git a/config/m4/ax_boost_regex.m4 b/config/m4/ax_boost_regex.m4
-index 1ac06af..5b7be93 100644
---- a/config/m4/ax_boost_regex.m4
-+++ b/config/m4/ax_boost_regex.m4
-@@ -78,14 +78,14 @@ AC_DEFUN([AX_BOOST_REGEX],
-                 for libextension in `ls $BOOSTLIBDIR/libboost_regex*.so* $BOOSTLIBDIR/libboost_regex*.a* 2>/dev/null | sed 's,.*/,,' | sed -e 's;^lib\(boost_regex.*\)\.so.*$;\1;' -e 's;^lib\(boost_regex.*\)\.a*$;\1;'` ; do
-                      ax_lib=${libextension}
- 				    AC_CHECK_LIB($ax_lib, exit,
--                                 [BOOST_REGEX_LIB="-l$ax_lib"; AC_SUBST(BOOST_REGEX_LIB) link_regex="yes"; break],
-+                                 [BOOST_REGEX_LIB="-l$ax_lib -lboost_system"; AC_SUBST(BOOST_REGEX_LIB) link_regex="yes"; break],
-                                  [link_regex="no"])
- 				done
-                 if test "x$link_regex" != "xyes"; then
-                 for libextension in `ls $BOOSTLIBDIR/boost_regex*.{dll,a}* 2>/dev/null | sed 's,.*/,,' | sed -e 's;^\(boost_regex.*\)\.dll.*$;\1;' -e 's;^\(boost_regex.*\)\.a*$;\1;'` ; do
-                      ax_lib=${libextension}
- 				    AC_CHECK_LIB($ax_lib, exit,
--                                 [BOOST_REGEX_LIB="-l$ax_lib"; AC_SUBST(BOOST_REGEX_LIB) link_regex="yes"; break],
-+                                 [BOOST_REGEX_LIB="-l$ax_lib -lboost_system"; AC_SUBST(BOOST_REGEX_LIB) link_regex="yes"; break],
-                                  [link_regex="no"])
- 				done
-                 fi
diff --git a/sci-biology/mira/files/mira-4.9.5-cout.patch b/sci-biology/mira/files/mira-4.9.5-cout.patch
deleted file mode 100644
index 14feb0284..000000000
--- a/sci-biology/mira/files/mira-4.9.5-cout.patch
+++ /dev/null
@@ -1,16 +0,0 @@
- src/progs/quirks.C | 2 ++
- 1 file changed, 2 insertions(+)
-
-diff --git a/src/progs/quirks.C b/src/progs/quirks.C
-index 47e5ee8..060b6f3 100644
---- a/src/progs/quirks.C
-+++ b/src/progs/quirks.C
-@@ -25,6 +25,8 @@
- 
- #include <boost/filesystem.hpp>
- 
-+#include <iostream>
-+
- // make the "tcmalloc: large alloc" messages from TCMallom disappear
- // by setting the reporting environment variable to a very large value
- // see: http://groups.google.com/group/google-perftools/browse_thread/thread/24a003fc35f3d470?pli=1
diff --git a/sci-biology/mira/files/mira-4.9.5-fix-miramer-symlink-error.patch b/sci-biology/mira/files/mira-4.9.5-fix-miramer-symlink-error.patch
deleted file mode 100644
index 6bdda946a..000000000
--- a/sci-biology/mira/files/mira-4.9.5-fix-miramer-symlink-error.patch
+++ /dev/null
@@ -1,22 +0,0 @@
---- mira-4.9.5/src/progs/Makefile.in.ori	2015-07-21 00:55:09.860884698 +0200
-+++ mira-4.9.5/src/progs/Makefile.in	2015-07-21 00:55:29.660884750 +0200
-@@ -717,7 +717,7 @@
- 	rm -f mirabait$(EXEEXT) && \
- 	$(LN_S) mira$(EXEEXT) mirabait$(EXEEXT) &&\
- 	rm -f miraconvert$(EXEEXT) && \
--	$(LN_S) mira$(EXEEXT) miraconvert$(EXEEXT) \
-+	$(LN_S) mira$(EXEEXT) miraconvert$(EXEEXT) && \
- 	rm -f miramer$(EXEEXT) && \
- 	$(LN_S) mira$(EXEEXT) miramer$(EXEEXT)
- 
---- mira-4.9.5/src/progs/Makefile.am.ori	2015-07-21 01:30:09.580890184 +0200
-+++ mira-4.9.5/src/progs/Makefile.am	2015-07-21 01:30:24.590890223 +0200
-@@ -51,7 +51,7 @@
- 	rm -f mirabait$(EXEEXT) && \
- 	$(LN_S) mira$(EXEEXT) mirabait$(EXEEXT) &&\
- 	rm -f miraconvert$(EXEEXT) && \
--	$(LN_S) mira$(EXEEXT) miraconvert$(EXEEXT) \
-+	$(LN_S) mira$(EXEEXT) miraconvert$(EXEEXT) && \
- 	rm -f miramer$(EXEEXT) && \
- 	$(LN_S) mira$(EXEEXT) miramer$(EXEEXT)
- 
diff --git a/sci-biology/mira/metadata.xml b/sci-biology/mira/metadata.xml
deleted file mode 100644
index 65cad0432..000000000
--- a/sci-biology/mira/metadata.xml
+++ /dev/null
@@ -1,11 +0,0 @@
-<?xml version="1.0" encoding="UTF-8"?>
-<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
-<pkgmetadata>
-	<maintainer type="project">
-		<email>sci-biology@gentoo.org</email>
-		<name>Gentoo Biology Project</name>
-	</maintainer>
-	<upstream>
-		<remote-id type="sourceforge">mira-assembler</remote-id>
-	</upstream>
-</pkgmetadata>
diff --git a/sci-biology/mira/mira-4.9.5.ebuild b/sci-biology/mira/mira-4.9.5.ebuild
deleted file mode 100644
index 7c888a5e7..000000000
--- a/sci-biology/mira/mira-4.9.5.ebuild
+++ /dev/null
@@ -1,92 +0,0 @@
-# Copyright 1999-2015 Gentoo Foundation
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=5
-
-MIRA_3RDPARTY_PV="06-07-2012"
-MY_PV="${PV/_}" # convert from mira-4.0_rc2 (Gentoo ebuild filename derived) to mira-4.0rc2 (upstream fromat)
-
-inherit autotools eutils multilib
-
-DESCRIPTION="Whole Genome Shotgun and EST Sequence Assembler"
-HOMEPAGE="http://www.chevreux.org/projects_mira.html"
-SRC_URI="
-	http://sourceforge.net/projects/mira-assembler/files/MIRA/development/"${PN}"-"${MY_PV}".tar.bz2
-	mirror://sourceforge/mira-assembler/mira_3rdparty_${MIRA_3RDPARTY_PV}.tar.bz2"
-# 	http://sourceforge.net/projects/mira-assembler/files/MIRA/stable/"${PN}"-"${MY_PV}".tar.bz2
-#	http://sourceforge.net/projects/mira-assembler/files/MIRA/development/${P}.tar.bz2
-#	mirror://sourceforge/mira-assembler/mira_3rdparty_${MIRA_3RDPARTY_PV}.tar.bz2"
-
-S="${WORKDIR}"/"${PN}"-"${MY_PV}"
-
-SLOT="0"
-LICENSE="GPL-2"
-KEYWORDS="~amd64 ~x86 ~amd64-linux ~x86-linux ~x86-macos"
-IUSE="doc"
-
-CDEPEND="
-	dev-libs/boost
-	dev-util/google-perftools"
-DEPEND="${CDEPEND}
-	app-editors/vim-core
-	dev-libs/expat"
-RDEPEND="${CDEPEND}"
-
-#DOCS=( AUTHORS GETTING_STARTED NEWS README HELP_WANTED
-#	THANKS doc/3rdparty/scaffolding_MIRA_BAMBUS.pdf )
-DOCS=( AUTHORS GETTING_STARTED NEWS README HELP_WANTED THANKS )
-
-# mira 4.9.x requires C++14 standard compliant compiler, so >=gcc-4.9.1
-src_prepare() {
-	find -name 'configure*' -or -name 'Makefile*' | xargs sed -i 's/flex++/flex -+/' || die
-	epatch \
-		"${FILESDIR}"/${PN}-3.4.0.2-boost-1.50.patch \
-		"${FILESDIR}"/${P}-cout.patch \
-		"${FILESDIR}"/${P}-fix-miramer-symlink-error.patch
-
-	sed \
-		-e "s:-O[23]::g" \
-		-e "s:-funroll-loops::g" \
-		-i configure.ac || die
-
-	eautoreconf
-}
-
-src_configure() {
-	econf \
-		--with-boost="${EPREFIX}/usr/$(get_libdir)" \
-		--with-boost-libdir="${EPREFIX}/usr/$(get_libdir)" \
-		--with-boost-thread=boost_thread-mt
-}
-
-#src_compile() {
-#	base_src_compile
-#	# TODO: resolve docbook incompatibility for building docs
-#	if use doc; then emake -C doc clean docs || die; fi
-#}
-
-src_install() {
-	default
-	dodoc ${DOCS[@]}
-
-	dobin "${WORKDIR}"/3rdparty/{sff_extract,qual2ball,*.pl}
-	dodoc "${WORKDIR}"/3rdparty/{README.txt,midi_screen.fasta}
-
-	# if sci-biology/staden is installed, ideally use configprotect?
-	if [ -e "${ED}"/usr/share/staden/etc/GTAGDB ]; then
-		if [ `grep -c HAF "${ED}"/usr/share/staden/etc/GTAGDB` -eq 0 ]; then
-			cat "${ED}"/usr/share/staden/etc/GTAGDB "${S}"/src/support/GTAGDB > "${WORKDIR}"/GTAGDB || die
-			insinto /usr/share/staden/etc/
-			doins "${WORKDIR}"/GTAGDB
-		fi
-	fi
-	if [ -e "/etc/consedrc/" ]; then
-		insinto /etc/consedrc
-		doins "${S}"/src/support/consedtaglib.txt
-	fi
-}
-
-pkg_postinst() {
-	einfo "Documentation is no longer built, you can find it at:"
-	einfo "http://mira-assembler.sourceforge.net/docs/DefinitiveGuideToMIRA.html"
-}
diff --git a/sci-biology/miranda/miranda-3.3a.ebuild b/sci-biology/miranda/miranda-3.3a.ebuild
index 1bf1c058c..941aeeec3 100644
--- a/sci-biology/miranda/miranda-3.3a.ebuild
+++ b/sci-biology/miranda/miranda-3.3a.ebuild
@@ -1,20 +1,24 @@
-# Copyright 1999-2014 Gentoo Foundation
+# Copyright 1999-2021 Gentoo Authors
 # Distributed under the terms of the GNU General Public License v2
 
-EAPI=5
+EAPI=7
+
+inherit flag-o-matic
 
 MY_PN=miRanda
 MY_P=${MY_PN}-${PV}
 
 DESCRIPTION="An algorithm for finding genomic targets for microRNAs"
-HOMEPAGE="http://www.microrna.org/"
+HOMEPAGE="https://www.mskcc.org/research/ski/programs/computational-biology"
 SRC_URI="http://cbio.mskcc.org/microrna_data/${MY_PN}-aug2010.tar.gz"
 
 LICENSE="GPL-2"
 SLOT="0"
-IUSE=""
 KEYWORDS="~amd64 ~x86"
 
-S=${WORKDIR}/${MY_P}
+S="${WORKDIR}/${MY_P}"
 
-DOCS=( AUTHORS ChangeLog NEWS README THANKS )
+src_configure() {
+	append-cflags -fcommon
+	default
+}
diff --git a/sci-biology/mmseqs2/Manifest b/sci-biology/mmseqs2/Manifest
new file mode 100644
index 000000000..dbfe85988
--- /dev/null
+++ b/sci-biology/mmseqs2/Manifest
@@ -0,0 +1 @@
+DIST mmseqs2-13.0.tar.gz 10199551 BLAKE2B 282d270c2b63a186d7534add93f6c23d625c5011392dc2cdff3cf11572ff23cb527726c19f5e9b092830216fa70a788faa46b1a4a2daafee05a513bff37a8a14 SHA512 90904392edd8a619577f79d75b44461b1bb647133850cc384caddb39bcfa3de0793392521edef0e86436ea0f76c9626298bd7975aba961ac7e846786eaf2e919
diff --git a/sci-biology/mmseqs2/files/mmseqs2-13.0-properly-handle-cpuflags.patch b/sci-biology/mmseqs2/files/mmseqs2-13.0-properly-handle-cpuflags.patch
new file mode 100644
index 000000000..10884765c
--- /dev/null
+++ b/sci-biology/mmseqs2/files/mmseqs2-13.0-properly-handle-cpuflags.patch
@@ -0,0 +1,40 @@
+diff --git a/CMakeLists.txt b/CMakeLists.txt
+index 1a677e3..df1d765 100644
+--- a/CMakeLists.txt
++++ b/CMakeLists.txt
+@@ -56,23 +56,29 @@ if (HAVE_AVX2)
+         set(MMSEQS_ARCH "${MMSEQS_ARCH} -mavx2 -mcx16 -Wa,-q")
+     endif ()
+     set(X64 1)
+-elseif (HAVE_SSE4_1)
++endif ()
++if (HAVE_SSE4_1)
+     set(MMSEQS_ARCH "${MMSEQS_ARCH} -msse4.1 -mcx16")
+     set(X64 1)
+-elseif (HAVE_SSE2)
++endif ()
++if (HAVE_SSE2)
+     set(MMSEQS_ARCH "${MMSEQS_ARCH} -msse2")
+     set(DISABLE_IPS4O 1)
+     set(X64 1)
+-elseif (HAVE_POWER9)
++endif ()
++if (HAVE_POWER9)
+     set(MMSEQS_ARCH "${MMSEQS_ARCH} -mcpu=power9 -mvsx")
+     set(PPC64 1)
+-elseif (HAVE_POWER8)
++endif ()
++if (HAVE_POWER8)
+     set(MMSEQS_ARCH "${MMSEQS_ARCH} -mcpu=power8 -mvsx")
+     set(PPC64 1)
+-elseif (HAVE_ARM8)
++endif ()
++if (HAVE_ARM8)
+     set(MMSEQS_ARCH "${MMSEQS_ARCH} -march=armv8-a+simd")
+     set(ARM 1)
+-elseif (HAVE_S390X)
++endif ()
++if (HAVE_S390X)
+     set(MMSEQS_ARCH "${MMSEQS_ARCH} -mzarch -march=z14")
+     set(ZARCH 1)
+ endif ()
diff --git a/sci-biology/mmseqs2/metadata.xml b/sci-biology/mmseqs2/metadata.xml
new file mode 100644
index 000000000..c957d777e
--- /dev/null
+++ b/sci-biology/mmseqs2/metadata.xml
@@ -0,0 +1,22 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
+<pkgmetadata>
+    <upstream>
+        <remote-id type="github">soedinglab/mmseqs2</remote-id>
+        <doc>https://github.com/soedinglab/mmseqs2/wiki</doc>
+    </upstream>
+    <maintainer type="person">
+        <email>joel@generisbio.com</email>
+        <name>Joel Berendzen</name>
+    </maintainer>
+    <longdescription>
+        MMseqs2 (Many-against-Many sequence searching) is a software suite toi
+        search and cluster huge protein and nucleotide sequence sets.
+        MMseqs2 is open source GPL-licensed software implemented in C++.
+        The software is designed to run on multiple cores and servers
+        and exhibits very good scalability. MMseqs2 can run 10000 times
+        faster than BLAST. At 100 times its speed it achieves almost the
+        same sensitivity. It can perform profile searches with the same
+        sensitivity as PSI-BLAST at over 400 times its speed.
+    </longdescription>
+</pkgmetadata>
diff --git a/sci-biology/mmseqs2/mmseqs2-13.0-r1.ebuild b/sci-biology/mmseqs2/mmseqs2-13.0-r1.ebuild
new file mode 100644
index 000000000..6cbd139d8
--- /dev/null
+++ b/sci-biology/mmseqs2/mmseqs2-13.0-r1.ebuild
@@ -0,0 +1,55 @@
+# Copyright 2021-2022 Gentoo Authors
+# Distributed under the terms of the GNU General Public License v2
+
+EAPI=8
+
+inherit bash-completion-r1 cmake
+
+MY_PN="MMseqs2"
+
+# Must be manually updated with each release
+COMMIT="45111b641859ed0ddd875b94d6fd1aef1a675b7e"
+
+DESCRIPTION="Fast and sensitive sequence search and clustering"
+HOMEPAGE="https://github.com/soedinglab/MMseqs2"
+SRC_URI="https://github.com/soedinglab/${MY_PN}/archive/${COMMIT}.tar.gz -> ${P}.tar.gz"
+S="${WORKDIR}/${MY_PN}-${COMMIT}"
+
+LICENSE="GPL-3"
+SLOT="0"
+KEYWORDS="~amd64"
+IUSE="cpu_flags_x86_sse4_1 cpu_flags_x86_sse2 cpu_flags_x86_avx2"
+
+RDEPEND="
+	app-arch/zstd[static-libs]
+	sys-libs/zlib
+	app-arch/bzip2
+"
+DEPEND="${RDEPEND}"
+
+PATCHES=(
+	"${FILESDIR}/${P}-properly-handle-cpuflags.patch"
+)
+
+src_configure() {
+	local mycmakeargs=(
+		# Need static libs: https://github.com/soedinglab/MMseqs2/issues/411
+		-DBUILD_SHARED_LIBS=OFF
+		-DUSE_SYSTEM_ZSTD=ON
+		# Disable auto detection, build respecting cpu flags instead
+		-DNATIVE_ARCH=OFF
+		-DHAVE_AVX2="$(usex cpu_flags_x86_avx2)"
+		-DHAVE_SSE4_1="$(usex cpu_flags_x86_sse4_1)"
+		-DHAVE_SSE2="$(usex cpu_flags_x86_sse2)"
+		# We also have cpu flags for ppc/arm/s390x
+		-DVERSION_OVERRIDE=${PV}
+	)
+	cmake_src_configure
+}
+
+src_install(){
+	cmake_src_install
+	# move the bashcomp to correct dir
+	newbashcomp "${ED}/usr/util/bash-completion.sh" "${PN}"
+	rm -r "${ED}/usr/util/" || die
+}
diff --git a/sci-biology/mne-python/Manifest b/sci-biology/mne-python/Manifest
deleted file mode 100644
index 38d6e3b27..000000000
--- a/sci-biology/mne-python/Manifest
+++ /dev/null
@@ -1 +0,0 @@
-DIST v0.7.zip 58120981 SHA256 26711803c8068adc7f3c06997b6bd1e076fea170e9f87af3b488c51eb6e3caa9 SHA512 1221038daa9687e358c7b51aed969c0174e5ea979e35c2e2663a5d2795b751f837bb8e1f45fd12251f713b6b69a5c5086e8f07d417e23abfa4302562f271f774 WHIRLPOOL a44c067c02270285103ad978d2d1afbf46972ad39eeec77548d78bb1515bd4a22fca713c2e814d5b462b09ce3caad2696deda1b09f67ed9f3c8f0a74de3fdaee
diff --git a/sci-biology/mne-python/metadata.xml b/sci-biology/mne-python/metadata.xml
deleted file mode 100644
index d9ac16118..000000000
--- a/sci-biology/mne-python/metadata.xml
+++ /dev/null
@@ -1,11 +0,0 @@
-<?xml version="1.0" encoding="UTF-8"?>
-<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
-<pkgmetadata>
-	<maintainer type="project">
-		<email>sci@gentoo.org</email>
-		<name>Gentoo Science Project</name>
-	</maintainer>
-	<upstream>
-		<remote-id type="github">mne-tools/mne-python</remote-id>
-	</upstream>
-</pkgmetadata>
diff --git a/sci-biology/mne-python/mne-python-0.7.ebuild b/sci-biology/mne-python/mne-python-0.7.ebuild
deleted file mode 100644
index ed1648fca..000000000
--- a/sci-biology/mne-python/mne-python-0.7.ebuild
+++ /dev/null
@@ -1,56 +0,0 @@
-# Copyright 1999-2014 Gentoo Foundation
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=5
-
-PYTHON_COMPAT=( python2_7 )
-
-inherit distutils-r1 virtualx
-
-DESCRIPTION="Python package for MEG and EEG data analysis"
-HOMEPAGE="http://martinos.org/mne/mne-python.html"
-SRC_URI="https://github.com/mne-tools/mne-python/archive/v${PV}.zip"
-
-LICENSE="BSD"
-SLOT="0"
-IUSE="test"
-#IUSE="cuda test"
-KEYWORDS="~amd64 ~x86"
-
-RDEPEND="
-	dev-python/numpy[${PYTHON_USEDEP}]
-	sci-libs/scipy[${PYTHON_USEDEP}]
-	sci-libs/scikits_learn[${PYTHON_USEDEP}]
-	dev-python/joblib[${PYTHON_USEDEP}]
-	sci-libs/nibabel[${PYTHON_USEDEP}]
-	sci-biology/pysurfer[${PYTHON_USEDEP}]
-	sci-visualization/mayavi
-	dev-python/matplotlib[${PYTHON_USEDEP}]"
-
-#	cuda? (
-#		dev-python/pycuda[${PYTHON_USEDEP}]
-#		dev-python/scikits-cuda[${PYTHON_USEDEP}]
-#	)
-#"
-
-DEPEND="
-	test? ( dev-python/nose ${RDEPEND} )
-"
-
-S="${WORKDIR}/mne-python-${PV}"
-
-run_test() {
-	PYTHONPATH=. MNE_SKIP_SAMPLE_DATASET_TESTS=1 nosetests -v mne
-}
-
-python_test() {
-	distutils_install_for_testing
-	esetup.py install --root="${T}/test-${EPYTHON}" --no-compile
-	# Link to test data that won't be included in the final installation
-	local TEST_DIR="${T}/test-${EPYTHON}/$(python_get_sitedir)"
-	cd "${S}" || die
-	find . -type d -name data -exec ln -s "${S}"/{} ${TEST_DIR}/{} \; || die
-	cd ${TEST_DIR} || die
-	VIRTUALX_COMMAND="run_test"
-	virtualmake
-}
diff --git a/sci-biology/mne-python/mne-python-9999.ebuild b/sci-biology/mne-python/mne-python-9999.ebuild
deleted file mode 100644
index 8dbe304d9..000000000
--- a/sci-biology/mne-python/mne-python-9999.ebuild
+++ /dev/null
@@ -1,54 +0,0 @@
-# Copyright 1999-2014 Gentoo Foundation
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=5
-
-PYTHON_COMPAT=( python2_7 )
-
-inherit distutils-r1 git-r3 virtualx
-
-DESCRIPTION="Python package for MEG and EEG data analysis"
-HOMEPAGE="http://martinos.org/mne/mne-python.html"
-EGIT_REPO_URI="https://github.com/mne-tools/mne-python.git"
-
-LICENSE="BSD"
-SLOT="0"
-IUSE="test"
-#IUSE="cuda test"
-KEYWORDS=""
-
-RDEPEND="
-	dev-python/numpy[${PYTHON_USEDEP}]
-	sci-libs/scipy[${PYTHON_USEDEP}]
-	sci-libs/scikits_learn[${PYTHON_USEDEP}]
-	dev-python/joblib[${PYTHON_USEDEP}]
-	sci-libs/nibabel[${PYTHON_USEDEP}]
-	sci-biology/pysurfer[${PYTHON_USEDEP}]
-	sci-visualization/mayavi
-	dev-python/matplotlib[${PYTHON_USEDEP}]"
-
-#	cuda? (
-#		dev-python/pycuda[${PYTHON_USEDEP}]
-#		dev-python/scikits-cuda[${PYTHON_USEDEP}]
-#	)
-#"
-
-DEPEND="
-	test? ( dev-python/nose ${RDEPEND} )
-"
-
-run_test() {
-	PYTHONPATH=. MNE_SKIP_SAMPLE_DATASET_TESTS=1 nosetests -v mne
-}
-
-python_test() {
-	distutils_install_for_testing
-	esetup.py install --root="${T}/test-${EPYTHON}" --no-compile
-	# Link to test data that won't be included in the final installation
-	local TEST_DIR="${T}/test-${EPYTHON}/$(python_get_sitedir)"
-	cd "${S}" || die
-	find . -type d -name data -exec ln -s "${S}"/{} ${TEST_DIR}/{} \; || die
-	cd ${TEST_DIR} || die
-	VIRTUALX_COMMAND="run_test"
-	virtualmake
-}
diff --git a/sci-biology/mothur/Manifest b/sci-biology/mothur/Manifest
deleted file mode 100644
index a4c1e3b43..000000000
--- a/sci-biology/mothur/Manifest
+++ /dev/null
@@ -1 +0,0 @@
-DIST mothur-1.36.1.tar.gz 1785450 BLAKE2B a57e0e460548ca60a6214c22e94e453403387fc67e4ea46768662a9905aacefe7977b2d936d9bea2837b1e5b14c333e8936632d3414ece74e01e417994b12cde SHA512 c745efabbdc859f470b07d22266a3ad97fa81c011bc7ff1b705aa76d4d118ea81dfa58754f96e3172a393a29625e0aaa253252f76e442572fca869ccdc34b2ff
diff --git a/sci-biology/mothur/files/mothur-1.36.1-makefile.patch b/sci-biology/mothur/files/mothur-1.36.1-makefile.patch
deleted file mode 100644
index 08e0b7b3b..000000000
--- a/sci-biology/mothur/files/mothur-1.36.1-makefile.patch
+++ /dev/null
@@ -1,61 +0,0 @@
---- mothur-1.36.1/makefile.ori	2015-11-30 18:38:40.511576683 +0100
-+++ mothur-1.36.1/makefile	2015-11-30 18:41:24.261579412 +0100
-@@ -9,7 +9,7 @@
- #
- 
- USEMPI ?= no
--64BIT_VERSION ?= yes
-+64BIT_VERSION ?= no
- USEREADLINE ?= yes
- USECOMPRESSION ?= no
- USEBOOST ?= yes
-@@ -18,7 +18,7 @@
- VERSION = "\"1.36.1\""
- 
- # Optimize to level 3:
--CXXFLAGS += -O3
-+# CXXFLAGS += -O3
- 
- 
- ifeq  ($(strip $(64BIT_VERSION)),yes)
-@@ -58,7 +58,7 @@
- 
- 
- ifeq  ($(strip $(USEMPI)),yes)
--    CXX = mpic++
-+#    CXX = mpic++
-     CXXFLAGS += -DUSE_MPI
- endif
- 
-@@ -106,10 +106,8 @@
-     OBJECTS+=$(patsubst %.cpp,%.o,$(wildcard *.cpp))
-     OBJECTS+=$(patsubst %.c,%.o,$(wildcard *.c))
- 
--mothur : $(OBJECTS) uchime
-+mothur : $(OBJECTS)
- 	$(CXX) $(LDFLAGS) $(TARGET_ARCH) -o $@ $(OBJECTS) $(LIBS)
--	strip mothur
--
- 
- uchime:
- 	cd source/uchime_src && ./mk && mv uchime ../../ && cd ..
---- mothur-1.36.1/makefile.ori	2015-11-30 18:46:41.411584697 +0100
-+++ mothur-1.36.1/makefile	2015-11-30 19:15:18.531613315 +0100
-@@ -64,14 +64,12 @@
- 
- #The boost libraries allow you to read gz files.
- ifeq  ($(strip $(USEBOOST)),yes)
--    BOOST_INCLUDE_DIR="/usr/local/include"
--    BOOST_LIBRARY_DIR="/usr/local/lib"
-+    BOOST_INCLUDE_DIR="/usr/include"
-+    BOOST_LIBRARY_DIR="/usr/lib"
- 
-     CXXFLAGS += -DUSE_BOOST
- 
--    LIBS += \
--    ${BOOST_LIBRARY_DIR}/libboost_iostreams.a \
--    ${BOOST_LIBRARY_DIR}/zlib.a
-+    LIBS += -lboost_iostreams -lz
- 
-     #if linux or windows then ${BOOST_LIBRARY_DIR}/libz.a
- endif
diff --git a/sci-biology/mothur/metadata.xml b/sci-biology/mothur/metadata.xml
deleted file mode 100644
index e29003407..000000000
--- a/sci-biology/mothur/metadata.xml
+++ /dev/null
@@ -1,11 +0,0 @@
-<?xml version="1.0" encoding="UTF-8"?>
-<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
-<pkgmetadata>
-	<maintainer type="project">
-		<email>sci-biology@gentoo.org</email>
-		<name>Gentoo Biology Project</name>
-	</maintainer>
-	<upstream>
-		<remote-id type="github">mothur/mothur</remote-id>
-	</upstream>
-</pkgmetadata>
diff --git a/sci-biology/mothur/mothur-1.36.1.ebuild b/sci-biology/mothur/mothur-1.36.1.ebuild
deleted file mode 100644
index 7f3d0cc91..000000000
--- a/sci-biology/mothur/mothur-1.36.1.ebuild
+++ /dev/null
@@ -1,48 +0,0 @@
-# Copyright 1999-2016 Gentoo Foundation
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=5
-
-inherit eutils flag-o-matic fortran-2 toolchain-funcs
-
-DESCRIPTION="A suite of algorithms for ecological bioinformatics"
-HOMEPAGE="http://www.mothur.org/"
-SRC_URI="https://github.com/mothur/mothur/archive/v${PV}.tar.gz -> ${P}.tar.gz"
-
-LICENSE="GPL-3"
-SLOT="0"
-IUSE="mpi readline zlib"
-KEYWORDS="~amd64 ~x86"
-
-CDEPEND="dev-libs/boost"
-RDEPEND="
-	readline? ( sys-libs/readline:= )
-	sci-biology/uchime
-	mpi? ( virtual/mpi )"
-DEPEND="${RDEPEND}
-	app-arch/unzip"
-
-pkg_setup() {
-	fortran-2_pkg_setup
-	use mpi && export CXX=mpicxx || export CXX=$(tc-getCXX)
-	use amd64 && append-cppflags -DBIT_VERSION
-	use readline && export USEREADLINE=yes || export USEREADLINE=no
-	export USEBOOST=yes
-	use zlib && export USECOMPRESSION=yes || export USECOMPRESSION=no
-}
-
-src_prepare() {
-	epatch \
-		"${FILESDIR}"/${P}-makefile.patch \
-#		"${FILESDIR}"/${PN}-1.27.0-overflows.patch
-}
-
-src_compile() {
-	# USEBOOST should be set already in pkg_setup
-	emake USEMPI=$(usex mpi) USEREADLINE=$(usex readline) USECOMPRESSION=$(usex zlib)
-}
-
-src_install() {
-	dobin ${PN}
-	dodoc README.md
-}
diff --git a/sci-biology/mouse-brain-atlases/Manifest b/sci-biology/mouse-brain-atlases/Manifest
deleted file mode 100644
index adac082a6..000000000
--- a/sci-biology/mouse-brain-atlases/Manifest
+++ /dev/null
@@ -1,12 +0,0 @@
-DIST mouse-brain-atlases-0.3.tar.xz 571379296 BLAKE2B 4bddcb130471e271dc1dbd5003ba1e15a62554163b50d6f9d8e76b3ae4c64c5c3ee76305bb3e3da28e5b532872b975b78b442cd53ca2c12d08157b6c54580050 SHA512 304883e309d22db552a2617b05aafa642008d0eef65c87510d9f62f85c25f10e8995549bcbd16ed5187cf307216fd5d514b230d7b8f89fcbab7c6aa001230a7e
-DIST mouse-brain-atlases-0.4.tar.xz 571520524 BLAKE2B 7980055d8debfdbe159397a22d569369811adb7497af8a06b2a1fd88d7f35c6ce80315021294dd7ffe7dc1eb24197292943b3d7f05d07284716ebf9d8cce8c4b SHA512 ec20fd7ade690ea8e3197ef6b7bee8b3db85631d7da93dcd9de790313e47ecdbbaa1dc2f1bf4fad78a521cdd19fb8d507029dfe86b1638e24d2b04d67d036e50
-DIST mouse-brain-atlases-0.5.1.tar.xz 591874684 BLAKE2B 0ab84eddfc0bbe9b4850a632fc2b66964f78bcee78dafbab2e7c5846170035fb221e4c8dcf286f87a6cc9b03a52d2effcc26adf2b34bf8f3bf79855358b794d4 SHA512 7dc62a2114452f617394b6191a2d5c5ccfebfbe4e6152809d63ca7f7c6a6a3ea2a399279265c2dc7688f7d6c1a3eaa3592003436e785047a0bbfb5cc2324aa9a
-DIST mouse-brain-atlases-0.5.2.tar.xz 592054648 BLAKE2B a888705a4889894327413851ca6dfaa6fec03e2005e671a6b8d005439992a5d6d9637d339f7810748e74c77796a224bae46039d887a53efef6d79b77078ac0d9 SHA512 a8b9ccf6b893e1211bde9cf52d0274a940e12facaee65f835225fb29a74a5f7fcbd3678190772729de667a8bc3adbd125d02c5b03c9ebfe61e484eb38417aea5
-DIST mouse-brain-atlases-0.5.3.tar.xz 591935168 BLAKE2B ceabe728d65b9a73afc9ec18dde14146e26c8465a71b53fdb607ad05ff4626a748ac8cc3d56c2876a2dabf53015db9da0caa66dc48ce83fbaddffcd19c0becce SHA512 7d7ca79f99d03e4a9a97ccf6517fc6570770bee0cea80c2b31e7c4fb4500b8eb49ffb7df5579901c12dd982fd3efb6fc93490dcf53da715c167d47939ea44bdb
-DIST mouse-brain-atlases-0.5.tar.xz 592024784 BLAKE2B 725563a947e1c6c3efd2a8bafab3726f9d4b8f78527bd701d829568f7c8e267db916f216f4a82b28423988244c2b59b34baed24b55349cfda17db9da4c982dc7 SHA512 b09b3482a025640dee31be3991e2b08394af389664fbb6e3f2faac26de65053f3ee1abe78de1ce7a92dd7b6f4fb43c017320895ce63d7cb3e8b936525dac30f8
-DIST mouse-brain-atlasesHD-0.3.tar.xz 914450112 BLAKE2B 04d6d05fd728260e6f5d07b19d6bfaf030b4e6742a94525fa1d0a46cfae48f340d40886cbe61e5a52da656bf61c22688dc8d14c0c37d210b7aaeb3e4f687ae0f SHA512 784e798285750ede30872e04b9397bfc3fc6807b3482ee40f90c96e971bf5ab4c33bd6aad1afa5ff837084a605b2d54ffcedb866d25a181c5658c7cfe2db9ea0
-DIST mouse-brain-atlasesHD-0.4.tar.xz 914324752 BLAKE2B 095a58b7204c6993a4c7411cdf972c0ffdb7ae0837ec258450cf9a9922838447077a839afb56708ca68f869f5c6854be7fe22998724e10ce09fe8c01d77d94a3 SHA512 98b6510a248be40070c48d1b4171ba6100a7fccf85bb689d73e6876c660b738af78089c7a077e6580b116a285726fb01e66dc1227a52eb4a98a01f9cd0d6427f
-DIST mouse-brain-atlasesHD-0.5.1.tar.xz 914332600 BLAKE2B 0a9cce258c419648ecdac9b2407a4d3fd6ee9606b1e187722f23e0d30272234b876c2b093fb1f3bf6d2fe1a64ab0d61c919bc46ae1406c31f752955c3f94cdb8 SHA512 e8f4e5ba89dc0e36f6728f2cf31209f5e3aca097e902727b74608aa450cd5ac3ec197c9aade59b5c20de6d67d3ffb3e9c63fbe193335ae495c2021c5c9c5a123
-DIST mouse-brain-atlasesHD-0.5.2.tar.xz 914406936 BLAKE2B d0a0afb980dcf04f357ea20f0982840e98a4856e6c2761b8986a5eee73bfd1a823c2dcaf40066372a1a08e634d14fd742f23047f349bb20c8baca3dc37a7ddc2 SHA512 587c3a2aa996eb2d4a8a476e38240dcd1cb8e3f2239f5817ae7809639da0a74a970fa456a6e69819134fb51169f930bb96144689cd796e0207e26ac0ea64efbf
-DIST mouse-brain-atlasesHD-0.5.3.tar.xz 915990788 BLAKE2B 3be900c9421849a32473a9f1fb1188f73b9fffd36f1e4edc7b6ead91b485bde3cfe211d03f73c4e09cfe194debdc92aad8639e72a64f66036d9a45f08a29cf47 SHA512 46c74d41d323d4cdd7cdf5e8c8ceec03eecf5e7b5c83bb95b7ad4814e55dc32ada7f781710dc40145ffd751d650d35eb5727c460920b831135ab706f5e136718
-DIST mouse-brain-atlasesHD-0.5.tar.xz 914324344 BLAKE2B 2046e57c183acb14fe2fdf5d5ed14c5100201061445b2cc42df5793c87146e0f8ce385783631e7fb79d7d0ac747bf125c9ad4a4615c8db9b50c894906cbd81b6 SHA512 4d11fb4cce3af23a0f318bc6e24411da727a43e95a337c798a940d235beef2c48e6d385822847823d27a6fc7dde1a6b412cc0c35e19ce15bb419d89272ffa65b
diff --git a/sci-biology/mouse-brain-atlases/metadata.xml b/sci-biology/mouse-brain-atlases/metadata.xml
deleted file mode 100644
index a8c20f15c..000000000
--- a/sci-biology/mouse-brain-atlases/metadata.xml
+++ /dev/null
@@ -1,19 +0,0 @@
-<?xml version="1.0" encoding="UTF-8"?>
-<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
-<pkgmetadata>
-	<maintainer type="person">
-		<email>horea.christ@gmail.com</email>
-		<name>Horea Christian</name>
-	</maintainer>
-	<maintainer type="project">
-		<email>sci@gentoo.org</email>
-		<name>Gentoo Science Project</name>
-	</maintainer>
-	<longdescription lang="en">
-		Digital mouse brain atlases in NIfTI format for use in magnetic
-		resonance mouse brain imaging.
-	</longdescription>
-	<use>
-		<flag name="hires">Also install high-resolution atlases.</flag>
-	</use>
-</pkgmetadata>
diff --git a/sci-biology/mouse-brain-atlases/mouse-brain-atlases-0.3.ebuild b/sci-biology/mouse-brain-atlases/mouse-brain-atlases-0.3.ebuild
deleted file mode 100644
index 65963d55a..000000000
--- a/sci-biology/mouse-brain-atlases/mouse-brain-atlases-0.3.ebuild
+++ /dev/null
@@ -1,44 +0,0 @@
-# Copyright 1999-2018 Gentoo Authors
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=7
-
-inherit check-reqs
-
-DESCRIPTION="A collection of mouse brain atlases in NIfTI format"
-HOMEPAGE="https://github.com/IBT-FMI/mouse-brain-atlases"
-SRC_URI="
-	http://chymera.eu/distfiles/${P}.tar.xz
-	hires? ( http://chymera.eu/distfiles/${PN}HD-${PV}.tar.xz )
-	"
-
-LICENSE="fairuse"
-SLOT="0"
-KEYWORDS="~amd64 ~x86 ~amd64-linux ~x86-linux"
-IUSE="hires"
-
-RDEPEND=""
-DEPEND=""
-
-pkg_pretend() {
-	if use hires; then
-		CHECKREQS_DISK_BUILD="4G"
-		CHECKREQS_DISK_USR="4G"
-		CHECKREQS_DISK_VAR="8G"
-	else
-		CHECKREQS_DISK_BUILD="500M"
-	fi
-	check-reqs_pkg_pretend
-}
-
-# We disable this phase to not check requirements twice.
-pkg_setup() { :; }
-
-src_install() {
-	insinto "/usr/share/${PN}"
-	doins *
-	if use hires; then
-		cd "../${PN}HD-${PV}"
-		doins *
-	fi
-}
diff --git a/sci-biology/mouse-brain-atlases/mouse-brain-atlases-0.4.ebuild b/sci-biology/mouse-brain-atlases/mouse-brain-atlases-0.4.ebuild
deleted file mode 100644
index 65963d55a..000000000
--- a/sci-biology/mouse-brain-atlases/mouse-brain-atlases-0.4.ebuild
+++ /dev/null
@@ -1,44 +0,0 @@
-# Copyright 1999-2018 Gentoo Authors
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=7
-
-inherit check-reqs
-
-DESCRIPTION="A collection of mouse brain atlases in NIfTI format"
-HOMEPAGE="https://github.com/IBT-FMI/mouse-brain-atlases"
-SRC_URI="
-	http://chymera.eu/distfiles/${P}.tar.xz
-	hires? ( http://chymera.eu/distfiles/${PN}HD-${PV}.tar.xz )
-	"
-
-LICENSE="fairuse"
-SLOT="0"
-KEYWORDS="~amd64 ~x86 ~amd64-linux ~x86-linux"
-IUSE="hires"
-
-RDEPEND=""
-DEPEND=""
-
-pkg_pretend() {
-	if use hires; then
-		CHECKREQS_DISK_BUILD="4G"
-		CHECKREQS_DISK_USR="4G"
-		CHECKREQS_DISK_VAR="8G"
-	else
-		CHECKREQS_DISK_BUILD="500M"
-	fi
-	check-reqs_pkg_pretend
-}
-
-# We disable this phase to not check requirements twice.
-pkg_setup() { :; }
-
-src_install() {
-	insinto "/usr/share/${PN}"
-	doins *
-	if use hires; then
-		cd "../${PN}HD-${PV}"
-		doins *
-	fi
-}
diff --git a/sci-biology/mouse-brain-atlases/mouse-brain-atlases-0.5.1.ebuild b/sci-biology/mouse-brain-atlases/mouse-brain-atlases-0.5.1.ebuild
deleted file mode 100644
index 65963d55a..000000000
--- a/sci-biology/mouse-brain-atlases/mouse-brain-atlases-0.5.1.ebuild
+++ /dev/null
@@ -1,44 +0,0 @@
-# Copyright 1999-2018 Gentoo Authors
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=7
-
-inherit check-reqs
-
-DESCRIPTION="A collection of mouse brain atlases in NIfTI format"
-HOMEPAGE="https://github.com/IBT-FMI/mouse-brain-atlases"
-SRC_URI="
-	http://chymera.eu/distfiles/${P}.tar.xz
-	hires? ( http://chymera.eu/distfiles/${PN}HD-${PV}.tar.xz )
-	"
-
-LICENSE="fairuse"
-SLOT="0"
-KEYWORDS="~amd64 ~x86 ~amd64-linux ~x86-linux"
-IUSE="hires"
-
-RDEPEND=""
-DEPEND=""
-
-pkg_pretend() {
-	if use hires; then
-		CHECKREQS_DISK_BUILD="4G"
-		CHECKREQS_DISK_USR="4G"
-		CHECKREQS_DISK_VAR="8G"
-	else
-		CHECKREQS_DISK_BUILD="500M"
-	fi
-	check-reqs_pkg_pretend
-}
-
-# We disable this phase to not check requirements twice.
-pkg_setup() { :; }
-
-src_install() {
-	insinto "/usr/share/${PN}"
-	doins *
-	if use hires; then
-		cd "../${PN}HD-${PV}"
-		doins *
-	fi
-}
diff --git a/sci-biology/mouse-brain-atlases/mouse-brain-atlases-0.5.2.ebuild b/sci-biology/mouse-brain-atlases/mouse-brain-atlases-0.5.2.ebuild
deleted file mode 100644
index 65963d55a..000000000
--- a/sci-biology/mouse-brain-atlases/mouse-brain-atlases-0.5.2.ebuild
+++ /dev/null
@@ -1,44 +0,0 @@
-# Copyright 1999-2018 Gentoo Authors
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=7
-
-inherit check-reqs
-
-DESCRIPTION="A collection of mouse brain atlases in NIfTI format"
-HOMEPAGE="https://github.com/IBT-FMI/mouse-brain-atlases"
-SRC_URI="
-	http://chymera.eu/distfiles/${P}.tar.xz
-	hires? ( http://chymera.eu/distfiles/${PN}HD-${PV}.tar.xz )
-	"
-
-LICENSE="fairuse"
-SLOT="0"
-KEYWORDS="~amd64 ~x86 ~amd64-linux ~x86-linux"
-IUSE="hires"
-
-RDEPEND=""
-DEPEND=""
-
-pkg_pretend() {
-	if use hires; then
-		CHECKREQS_DISK_BUILD="4G"
-		CHECKREQS_DISK_USR="4G"
-		CHECKREQS_DISK_VAR="8G"
-	else
-		CHECKREQS_DISK_BUILD="500M"
-	fi
-	check-reqs_pkg_pretend
-}
-
-# We disable this phase to not check requirements twice.
-pkg_setup() { :; }
-
-src_install() {
-	insinto "/usr/share/${PN}"
-	doins *
-	if use hires; then
-		cd "../${PN}HD-${PV}"
-		doins *
-	fi
-}
diff --git a/sci-biology/mouse-brain-atlases/mouse-brain-atlases-0.5.3.ebuild b/sci-biology/mouse-brain-atlases/mouse-brain-atlases-0.5.3.ebuild
deleted file mode 100644
index 65963d55a..000000000
--- a/sci-biology/mouse-brain-atlases/mouse-brain-atlases-0.5.3.ebuild
+++ /dev/null
@@ -1,44 +0,0 @@
-# Copyright 1999-2018 Gentoo Authors
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=7
-
-inherit check-reqs
-
-DESCRIPTION="A collection of mouse brain atlases in NIfTI format"
-HOMEPAGE="https://github.com/IBT-FMI/mouse-brain-atlases"
-SRC_URI="
-	http://chymera.eu/distfiles/${P}.tar.xz
-	hires? ( http://chymera.eu/distfiles/${PN}HD-${PV}.tar.xz )
-	"
-
-LICENSE="fairuse"
-SLOT="0"
-KEYWORDS="~amd64 ~x86 ~amd64-linux ~x86-linux"
-IUSE="hires"
-
-RDEPEND=""
-DEPEND=""
-
-pkg_pretend() {
-	if use hires; then
-		CHECKREQS_DISK_BUILD="4G"
-		CHECKREQS_DISK_USR="4G"
-		CHECKREQS_DISK_VAR="8G"
-	else
-		CHECKREQS_DISK_BUILD="500M"
-	fi
-	check-reqs_pkg_pretend
-}
-
-# We disable this phase to not check requirements twice.
-pkg_setup() { :; }
-
-src_install() {
-	insinto "/usr/share/${PN}"
-	doins *
-	if use hires; then
-		cd "../${PN}HD-${PV}"
-		doins *
-	fi
-}
diff --git a/sci-biology/mouse-brain-atlases/mouse-brain-atlases-0.5.ebuild b/sci-biology/mouse-brain-atlases/mouse-brain-atlases-0.5.ebuild
deleted file mode 100644
index 65963d55a..000000000
--- a/sci-biology/mouse-brain-atlases/mouse-brain-atlases-0.5.ebuild
+++ /dev/null
@@ -1,44 +0,0 @@
-# Copyright 1999-2018 Gentoo Authors
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=7
-
-inherit check-reqs
-
-DESCRIPTION="A collection of mouse brain atlases in NIfTI format"
-HOMEPAGE="https://github.com/IBT-FMI/mouse-brain-atlases"
-SRC_URI="
-	http://chymera.eu/distfiles/${P}.tar.xz
-	hires? ( http://chymera.eu/distfiles/${PN}HD-${PV}.tar.xz )
-	"
-
-LICENSE="fairuse"
-SLOT="0"
-KEYWORDS="~amd64 ~x86 ~amd64-linux ~x86-linux"
-IUSE="hires"
-
-RDEPEND=""
-DEPEND=""
-
-pkg_pretend() {
-	if use hires; then
-		CHECKREQS_DISK_BUILD="4G"
-		CHECKREQS_DISK_USR="4G"
-		CHECKREQS_DISK_VAR="8G"
-	else
-		CHECKREQS_DISK_BUILD="500M"
-	fi
-	check-reqs_pkg_pretend
-}
-
-# We disable this phase to not check requirements twice.
-pkg_setup() { :; }
-
-src_install() {
-	insinto "/usr/share/${PN}"
-	doins *
-	if use hires; then
-		cd "../${PN}HD-${PV}"
-		doins *
-	fi
-}
diff --git a/sci-biology/mouse-brain-templates/Manifest b/sci-biology/mouse-brain-templates/Manifest
new file mode 100644
index 000000000..efee14737
--- /dev/null
+++ b/sci-biology/mouse-brain-templates/Manifest
@@ -0,0 +1,2 @@
+DIST mouse-brain-templates-0.5.3.tar.xz 592329680 BLAKE2B 22d73f87fa1d44990d5514653233ac05e3cbf845cd3c677910f13bfb2c87952d4a76823e73e2553f9fba372237a6c4759bcf2f26dbb50934f31bd4b1ce57548e SHA512 1dc20fc6db723e18b54c9b401ed7f677fadc2d9c27b8da7e43b4a02330f01a6553ee88c86883821387742518a6d51891c3f3136521a4502d7daa29ed3fc04576
+DIST mouse-brain-templatesHD-0.5.3.tar.xz 914229640 BLAKE2B 833f9cd74d70d8db29a443afc1bd6a37dff094d10f43502186aaa31d2df4750bdf67a1f2935571d1f694993631ea71955033a89181b2cc8b13db30cb81e246e0 SHA512 6c836dc65a99b3c20ab1a648deb9be7f6a6827cf263b178f0939d33c06fe8dfc4f20e2c487b3d78182ae0ae7332550f19d496190ff260b1b213f25a71d3745dd
diff --git a/sci-biology/mouse-brain-templates/metadata.xml b/sci-biology/mouse-brain-templates/metadata.xml
new file mode 100644
index 000000000..97fbbcbf2
--- /dev/null
+++ b/sci-biology/mouse-brain-templates/metadata.xml
@@ -0,0 +1,18 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
+<pkgmetadata>
+	<maintainer type="person">
+		<email>gentoo@chymera.eu</email>
+		<name>Horea Christian</name>
+	</maintainer>
+	<maintainer type="project">
+		<email>sci@gentoo.org</email>
+		<name>Gentoo Science Project</name>
+	</maintainer>
+	<use>
+		<flag name="hires">Also install high-resolution atlases.</flag>
+	</use>
+	<upstream>
+		<remote-id type="github">IBT-FMI/mouse-brain-templates_generator</remote-id>
+	</upstream>
+</pkgmetadata>
diff --git a/sci-biology/mouse-brain-templates/mouse-brain-templates-0.5.3.ebuild b/sci-biology/mouse-brain-templates/mouse-brain-templates-0.5.3.ebuild
new file mode 100644
index 000000000..60d06f934
--- /dev/null
+++ b/sci-biology/mouse-brain-templates/mouse-brain-templates-0.5.3.ebuild
@@ -0,0 +1,44 @@
+# Copyright 1999-2023 Gentoo Authors
+# Distributed under the terms of the GNU General Public License v2
+
+EAPI=7
+
+inherit check-reqs
+
+DESCRIPTION="A collection of mouse brain templates in NIfTI format"
+HOMEPAGE="https://github.com/IBT-FMI/mouse-brain-templates_generator"
+SRC_URI="
+	https://resources.chymera.eu/distfiles/${P}.tar.xz
+	hires? ( https://resources.chymera.eu/distfiles/${PN}HD-${PV}.tar.xz )
+	"
+
+LICENSE="fairuse"
+SLOT="0"
+KEYWORDS="~amd64 ~x86 ~amd64-linux ~x86-linux"
+IUSE="hires"
+
+RDEPEND=""
+DEPEND=""
+
+pkg_pretend() {
+	if use hires; then
+		CHECKREQS_DISK_BUILD="4G"
+		CHECKREQS_DISK_USR="4G"
+		CHECKREQS_DISK_VAR="8G"
+	else
+		CHECKREQS_DISK_BUILD="500M"
+	fi
+	check-reqs_pkg_pretend
+}
+
+# We disable this phase to not check requirements twice.
+pkg_setup() { :; }
+
+src_install() {
+	insinto "/usr/share/${PN}"
+	doins *
+	if use hires; then
+		cd "../${PN}HD-${PV}"
+		doins *
+	fi
+}
diff --git a/sci-biology/mreps/Manifest b/sci-biology/mreps/Manifest
index 23c8e069f..c471e480c 100644
--- a/sci-biology/mreps/Manifest
+++ b/sci-biology/mreps/Manifest
@@ -1 +1 @@
-DIST mreps-2.5.tar.gz 28084 BLAKE2B eed5b7b3d04f611ed4d889caa4654a67242e776221017f969e0d90b7a7c7e1e0cee8bc32537455eb396297165f3d9fbfbe0d3bc645bd714c8ccf92640b1fff9e SHA512 6a7a4ea48d497e5c71a7702b30e133758ec84465ad20df4307212b8e15e320ed9a2bd1e45faa1a5dca00d22499ee72bfc11e268acaf2ed836d341482b17ac3ef
+DIST mreps-2.6.01.tar.gz 37981 BLAKE2B 3d8bad49776c66e57f86de9ed24c7b6f120fbcca3a74ac7d5898bb5e525439f3f22447480626da13b3a3f62aaed69c2744881ea7bc0d97b04991ea5228180bc3 SHA512 6d8874a7e480fc1108c496fdadd6e31fe9a1e3d5a07664e38e12b4095ada49f195b458e52579ee2f150dcc6cabfde85a8bd1a0b137c61d4da807e7f8232e8e20
diff --git a/sci-biology/mreps/metadata.xml b/sci-biology/mreps/metadata.xml
index 8417d1580..a60e8c1b5 100644
--- a/sci-biology/mreps/metadata.xml
+++ b/sci-biology/mreps/metadata.xml
@@ -5,4 +5,7 @@
 		<email>sci-biology@gentoo.org</email>
 		<name>Gentoo Biology Project</name>
 	</maintainer>
+	<upstream>
+		<remote-id type="github">gregorykucherov/mreps</remote-id>
+	</upstream>
 </pkgmetadata>
diff --git a/sci-biology/mreps/mreps-2.5.ebuild b/sci-biology/mreps/mreps-2.5.ebuild
deleted file mode 100644
index 86926cad7..000000000
--- a/sci-biology/mreps/mreps-2.5.ebuild
+++ /dev/null
@@ -1,27 +0,0 @@
-# Copyright 1999-2014 Gentoo Foundation
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=5
-
-inherit toolchain-funcs
-
-DESCRIPTION="Identification of serial/tandem repeats in DNA sequences"
-HOMEPAGE="http://bioinfo.lifl.fr/mreps/"
-SRC_URI="http://bioinfo.lifl.fr/mreps/${P}.tar.gz"
-
-LICENSE="GPL-2"
-SLOT="0"
-IUSE=""
-KEYWORDS="~amd64 ~x86"
-
-src_prepare() {
-	sed \
-		-e 's/CC\s*=\s*gcc/CC := ${CC} ${CFLAGS}/' \
-		-e 's:-O3::g' \
-		-i "${S}"/Makefile || die
-	tc-export CC
-}
-
-src_install() {
-	dobin mreps
-}
diff --git a/sci-biology/mreps/mreps-2.6.01.ebuild b/sci-biology/mreps/mreps-2.6.01.ebuild
new file mode 100644
index 000000000..2a58610c9
--- /dev/null
+++ b/sci-biology/mreps/mreps-2.6.01.ebuild
@@ -0,0 +1,27 @@
+# Copyright 1999-2021 Gentoo Authors
+# Distributed under the terms of the GNU General Public License v2
+
+EAPI=7
+
+inherit toolchain-funcs
+
+DESCRIPTION="Identification of serial/tandem repeats in DNA sequences"
+HOMEPAGE="https://mreps.univ-mlv.fr/"
+SRC_URI="https://github.com/gregorykucherov/mreps/archive/${PV}.tar.gz -> ${P}.tar.gz"
+
+LICENSE="GPL-2"
+SLOT="0"
+KEYWORDS="~amd64 ~x86"
+
+src_prepare() {
+	default
+	sed \
+		-e 's/CC\s*=\s*gcc/CC := ${CC} ${CFLAGS}/' \
+		-e 's:-O3::g' \
+		-i "${S}"/Makefile || die
+	tc-export CC
+}
+
+src_install() {
+	dobin mreps
+}
diff --git a/sci-biology/mrfast/mrfast-2.6.0.1.ebuild b/sci-biology/mrfast/mrfast-2.6.0.1.ebuild
index 3c81f7281..42fc0b62d 100644
--- a/sci-biology/mrfast/mrfast-2.6.0.1.ebuild
+++ b/sci-biology/mrfast/mrfast-2.6.0.1.ebuild
@@ -1,20 +1,20 @@
-# Copyright 1999-2014 Gentoo Foundation
+# Copyright 1999-2021 Gentoo Authors
 # Distributed under the terms of the GNU General Public License v2
 
-EAPI=5
+EAPI=7
 
-inherit eutils toolchain-funcs
+inherit flag-o-matic toolchain-funcs
 
 DESCRIPTION="Micro Read Fast Alignment Search Tool"
 HOMEPAGE="http://mrfast.sourceforge.net/"
-SRC_URI="mirror://sourceforge/${PN}/${P}.tar.gz"
+SRC_URI="https://downloads.sourceforge.net/${PN}/${P}.tar.gz"
 
 LICENSE="BSD"
 SLOT="0"
-IUSE=""
 KEYWORDS="~amd64"
 
 src_prepare() {
+	default
 	sed \
 		-e '/^CC/s:=:?=:g' \
 		-e 's/CFLAGS =/CFLAGS +=/' \
@@ -22,7 +22,12 @@ src_prepare() {
 		-e 's:-O3.*::g' \
 		-e 's:$(CC) $(OBJECTS):$(CC) $(LDFLAGS) $(OBJECTS):g' \
 		-i Makefile || die
+}
+
+src_configure() {
 	tc-export CC
+	append-cflags -fcommon
+	default
 }
 
 src_install() {
diff --git a/sci-biology/mrsfast/Manifest b/sci-biology/mrsfast/Manifest
deleted file mode 100644
index 0a8a14be2..000000000
--- a/sci-biology/mrsfast/Manifest
+++ /dev/null
@@ -1 +0,0 @@
-DIST mrsfast-2.6.0.4.zip 38384 SHA256 695f65788096098259fd86e1269b32918cf9d717a7ba722c99fbdcc5270924c5 SHA512 df14dfb4c5d0d4ad2da26f47f7d10ff94e2857519aace4f11914dc9be09cc937168e63396b5523f992ff49b826a6ec565998eb220f840982febbc26f32345ab9 WHIRLPOOL aa4570bfac2708e910cce778a6ba74c27dc41be7ec49702d73cfd63e17c780be28d245c57de63a9f355549e08a23878ec1157c4d08119073d0805567ec6a0a2d
diff --git a/sci-biology/mrsfast/metadata.xml b/sci-biology/mrsfast/metadata.xml
deleted file mode 100644
index 309390097..000000000
--- a/sci-biology/mrsfast/metadata.xml
+++ /dev/null
@@ -1,11 +0,0 @@
-<?xml version="1.0" encoding="UTF-8"?>
-<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
-<pkgmetadata>
-	<maintainer type="project">
-		<email>sci-biology@gentoo.org</email>
-		<name>Gentoo Biology Project</name>
-	</maintainer>
-	<upstream>
-		<remote-id type="sourceforge">mrsfast</remote-id>
-	</upstream>
-</pkgmetadata>
diff --git a/sci-biology/mrsfast/mrsfast-2.6.0.4.ebuild b/sci-biology/mrsfast/mrsfast-2.6.0.4.ebuild
deleted file mode 100644
index bdd86b273..000000000
--- a/sci-biology/mrsfast/mrsfast-2.6.0.4.ebuild
+++ /dev/null
@@ -1,28 +0,0 @@
-# Copyright 1999-2014 Gentoo Foundation
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=5
-
-inherit eutils toolchain-funcs
-
-DESCRIPTION="Micro Read Fast Alignment Search Tool"
-HOMEPAGE="http://mrsfast.sourceforge.net/Home"
-SRC_URI="mirror://sourceforge/mrsfast/${PV}/${P}.zip"
-
-LICENSE="BSD"
-SLOT="0"
-IUSE=""
-KEYWORDS="~amd64"
-
-src_prepare() {
-	sed \
-		-e "s:gcc:$(tc-getCC) ${LDFLAGS}:g" \
-		-e '/^CFLAGS/d' \
-		-e '/^LDFLAGS/d' \
-		-i Makefile || die
-	tc-export CC
-}
-
-src_install() {
-	dobin ${PN}
-}
diff --git a/sci-biology/msautil/msautil-1.1-r1.ebuild b/sci-biology/msautil/msautil-1.1-r1.ebuild
index b30b38490..572d8abe5 100644
--- a/sci-biology/msautil/msautil-1.1-r1.ebuild
+++ b/sci-biology/msautil/msautil-1.1-r1.ebuild
@@ -1,7 +1,7 @@
-# Copyright 1999-2017 Gentoo Foundation
+# Copyright 1999-2021 Gentoo Authors
 # Distributed under the terms of the GNU General Public License v2
 
-EAPI=6
+EAPI=7
 
 inherit toolchain-funcs
 
@@ -11,8 +11,7 @@ SRC_URI="http://bioresearch.byu.edu/msa/${P}.tgz"
 
 LICENSE="all-rights-reserved"
 SLOT="0"
-KEYWORDS=""
-IUSE=""
+KEYWORDS="~amd64"
 
 src_prepare(){
 	sed \
diff --git a/sci-biology/multiqc/Manifest b/sci-biology/multiqc/Manifest
new file mode 100644
index 000000000..3585038a3
--- /dev/null
+++ b/sci-biology/multiqc/Manifest
@@ -0,0 +1 @@
+DIST multiqc-1.19.tar.gz 1159781 BLAKE2B 32d592dba5675f8cb673c8fced9f8ed32977ecd2baf1407aff4ef16b88d8bdad6a9541748717b90d5ab755f6354166e2de62cb1abd282d0e5ce9d1c89529d249 SHA512 75ef5a1b6c6433d68b878e2a1d51b6f420b8c77831cb1279a0b87aff5d6dee7a65bcca5d1f4deb04d4957feef0f27a1155198e244bd165404b08a23bfc8a9354
diff --git a/sci-biology/multiqc/metadata.xml b/sci-biology/multiqc/metadata.xml
new file mode 100644
index 000000000..09bd2b6e6
--- /dev/null
+++ b/sci-biology/multiqc/metadata.xml
@@ -0,0 +1,12 @@
+<?xml version='1.0' encoding='UTF-8'?>
+<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
+<pkgmetadata>
+	<maintainer type="person">
+		<email>mschu.dev@gmail.com</email>
+		<name>Michael Schubert</name>
+	</maintainer>
+	<upstream>
+		<remote-id type="github">ewels/MultiQC</remote-id>
+		<remote-id type="pypi">multiqc</remote-id>
+	</upstream>
+</pkgmetadata>
diff --git a/sci-biology/multiqc/multiqc-1.19.ebuild b/sci-biology/multiqc/multiqc-1.19.ebuild
new file mode 100644
index 000000000..187f06c22
--- /dev/null
+++ b/sci-biology/multiqc/multiqc-1.19.ebuild
@@ -0,0 +1,40 @@
+# Copyright 1999-2023 Gentoo Authors
+# Distributed under the terms of the GNU General Public License v2
+
+EAPI=8
+
+DISTUTILS_USE_PEP517=setuptools
+PYTHON_COMPAT=( python3_{10..11} )
+
+inherit pypi distutils-r1
+
+DESCRIPTION="Aggregate bioinformatics results across many samples into a single report"
+HOMEPAGE="https://multiqc.info/"
+
+LICENSE="GPL-3"
+SLOT="0"
+KEYWORDS="~amd64 ~amd64-linux"
+
+RDEPEND="dev-python/matplotlib[${PYTHON_USEDEP}]
+	dev-python/networkx[${PYTHON_USEDEP}]
+	dev-python/numpy[${PYTHON_USEDEP}]
+	dev-python/click[${PYTHON_USEDEP}]
+	dev-python/coloredlogs[${PYTHON_USEDEP}]
+	dev-python/future[${PYTHON_USEDEP}]
+	dev-python/jinja[${PYTHON_USEDEP}]
+	dev-python/lzstring[${PYTHON_USEDEP}]
+	dev-python/markdown[${PYTHON_USEDEP}]
+	dev-python/packaging[${PYTHON_USEDEP}]
+	dev-python/pyyaml[${PYTHON_USEDEP}]
+	dev-python/requests[${PYTHON_USEDEP}]
+	dev-python/rich[${PYTHON_USEDEP}]
+	dev-python/rich-click[${PYTHON_USEDEP}]
+	dev-python/simplejson[${PYTHON_USEDEP}]
+	dev-python/spectra[${PYTHON_USEDEP}]
+	dev-python/importlib-metadata[$PYTHON_USEDEP]
+	dev-python/humanize[$PYTHON_USEDEP]
+	dev-python/pyaml-env[$PYTHON_USEDEP]"
+
+# pypi tarball does not include tests
+RESTRICT="test"
+#distutils_enable_tests pytest
diff --git a/sci-biology/nanopolish/nanopolish-9999.ebuild b/sci-biology/nanopolish/nanopolish-9999.ebuild
index cea5cce27..5ca92904f 100644
--- a/sci-biology/nanopolish/nanopolish-9999.ebuild
+++ b/sci-biology/nanopolish/nanopolish-9999.ebuild
@@ -1,7 +1,7 @@
-# Copyright 1999-2018 Gentoo Foundation
+# Copyright 1999-2021 Gentoo Authors
 # Distributed under the terms of the GNU General Public License v2
 
-EAPI=6
+EAPI=7
 
 inherit git-r3
 
@@ -12,7 +12,6 @@ EGIT_REPO_URI="https://github.com/jts/nanopolish.git"
 LICENSE="MIT"
 SLOT="0"
 KEYWORDS=""
-IUSE=""
 
 # HDF5 is not thread safe by default and nanopolish currently requires a threadsafe HDF5.
 # This is one reason we download the compile it ourself (the main reason is to make it
@@ -32,8 +31,6 @@ src_prepare(){
 }
 
 src_compile(){
-	# >=gcc-4.8 but <gcc-7 is needed
-	# https://github.com/jts/nanopolish/issues/145
 	emake HDF5="noinstall" EIGEN="noinstall" HTS="noinstall" HTS_LIB=-lhts HTS_INCLUDE=-I/usr/include/htslib EIGEN_INCLUDE=-I/usr/include/eigen3 # TODO: FAST5_INCLUDE=-I/usr/include/fast5
 }
 
@@ -42,7 +39,3 @@ src_install(){
 	dobin nanopolish
 	# add scripts/ subdirectory to PATH
 }
-
-src_test(){
-	nanopolish_test || die
-}
diff --git a/sci-biology/ncbi-blast+/Manifest b/sci-biology/ncbi-blast+/Manifest
deleted file mode 100644
index 2fc318de7..000000000
--- a/sci-biology/ncbi-blast+/Manifest
+++ /dev/null
@@ -1,3 +0,0 @@
-DIST ncbi-blast-2.2.30+-src.tar.gz 18985378 BLAKE2B 59e749964ee5c6e30ac0286fc928fa8806abfd01aa70d937751642929de4d4e8ebc2109061f5dc82baf7e517a8718e1e11b9372c84f8be3b4140f55708ab264b SHA512 501727486aaa384ee5c40368332243ec2e19f22ab88f50c9396b4d33738bde4dbb5d3a1025ae599c1b5f4b4dd3d065ba4d0eb30305f42bfc781c95bbc4140a17
-DIST ncbi-blast-2.2.31+-src.tar.gz 18971327 BLAKE2B 4f6b124ddf6c892a0be36cbdcb00fe20a15b6f7a49af3f022e31a757ebd48d95c52219ecb2d56fa7787f936dbc08853affe07250ddf5461aff2f7fa5a9742be7 SHA512 2681a4394cc250d1ee545cd85dc962d73b1dbbdd987790a029bf51a58e74cbb08b5c8cf4a02b9b7c95916e3fb0d1613e2ed8631bb7ad683156759421081bb4ca
-DIST ncbi-blast-2.6.0+-src.tar.gz 20025526 BLAKE2B d97d1245e3f2030025e99323d67d889e6cecaa719fe525dbe1574a916e5f8b7b620880d44efe51851d64b9d1cdd0538f13161bfea8e233dcca6a223548d5090d SHA512 ea6444892a0b10459193d33d243b5960ad206b702e01e94a554a5ebda0291ff45e1ce43479713c23a96eba676b40bb8c57a7ef9dd2118729feef6b2cd98560c6
diff --git a/sci-biology/ncbi-blast+/files/disable-testsuite-compilation.txt b/sci-biology/ncbi-blast+/files/disable-testsuite-compilation.txt
deleted file mode 100644
index aeaf75e45..000000000
--- a/sci-biology/ncbi-blast+/files/disable-testsuite-compilation.txt
+++ /dev/null
@@ -1,3 +0,0 @@
-.*
--.*/test
--.*/unit_test
diff --git a/sci-biology/ncbi-blast+/files/ncbi-blast+-2.2.30__fix_lib_deps.patch b/sci-biology/ncbi-blast+/files/ncbi-blast+-2.2.30__fix_lib_deps.patch
deleted file mode 100644
index 13dffeee7..000000000
--- a/sci-biology/ncbi-blast+/files/ncbi-blast+-2.2.30__fix_lib_deps.patch
+++ /dev/null
@@ -1,668 +0,0 @@
-Subject: ensure that all libraries link against all direct dependencies

-

- * src/**/Makefile.*.lib: set DLL_(D)LIB correctly.  Break the dependency

-   loop between libxblast and libxalgoblastdbindex by having the former

-   provide only the C++ BLAST API, leaving the C core only in libblast.

- * src/build-system/library_relations.txt: Change xblast's

-   relationship to blast from includes to needs, accordingly.

- * src/algo/blast/dbindex*/*/Makefile.*.app: Link against libxconnect

-   rather than libconnect for consistency with libblast, which uses the

-   former to keep the aforementioned cycle-breaking from causing

-   inconsistency elsewhere.

-

-Debian-Bug: 633567.

-Author: Aaron M. Ucko <ucko@debian.org>

-Last-Update: 2014-12-02

---- a/c++/src/algo/blast/core/Makefile.blast.lib

-+++ b/c++/src/algo/blast/core/Makefile.blast.lib

-@@ -21,6 +21,7 @@ LIB = blast

- CFLAGS  = $(FAST_CFLAGS)  

- LDFLAGS = $(FAST_LDFLAGS) 

- 

-+DLL_LIB = composition_adjustment xconnect tables

- 

- WATCHERS = madden camacho

- 

---- a/c++/src/algo/blast/dbindex/Makefile.xalgoblastdbindex.lib

-+++ b/c++/src/algo/blast/dbindex/Makefile.xalgoblastdbindex.lib

-@@ -11,6 +11,8 @@ SRC = sequence_istream_fasta \

- CXXFLAGS = -DDO_INLINE $(FAST_CXXFLAGS)

- LDFLAGS  = $(FAST_LDFLAGS)

- 

-+DLL_LIB = blast seqdb xobjread xobjutil xobjmgr seqset seq xser xutil xncbi

-+

- ASN_DEP = seqset

- 

- WATCHERS = morgulis

---- a/c++/src/algo/blast/format/Makefile.xblastformat.lib

-+++ b/c++/src/algo/blast/format/Makefile.xblastformat.lib

-@@ -7,7 +7,8 @@ SRC = blastfmtutil blastxml_format blast

- 

- CPPFLAGS = -DNCBI_MODULE=BLASTFORMAT $(ORIG_CPPFLAGS)

- 

--DLL_LIB = align_format blastxml blastxml2 xhtml xcgi

-+DLL_LIB = xblast align_format xalnmgr xobjmgr xnetblast scoremat blastxml \

-+          seq general xser tables xncbi blastxml2

- 

- WATCHERS = jianye zaretska madden camacho fongah2

- 

---- a/c++/src/algo/winmask/Makefile.xalgowinmask.lib

-+++ b/c++/src/algo/winmask/Makefile.xalgowinmask.lib

-@@ -21,7 +21,7 @@ SRC = seq_masker seq_masker_score_mean s

- CXXFLAGS = $(FAST_CXXFLAGS)

- LDFLAGS  = $(FAST_LDFLAGS)

- 

--

-+DLL_LIB = seqmasks_io xobjread xobjutil xobjmgr seq xncbi

- 

- USES_LIBRARIES =  \

-     seqmasks_io

---- a/c++/src/cgi/Makefile.cgi.lib

-+++ b/c++/src/cgi/Makefile.cgi.lib

-@@ -9,6 +9,8 @@ SRC = ncbicgi cgiapp cgictx ncbicgir ncb

-       user_agent

- LIB = xcgi

- 

-+DLL_LIB = xutil xncbi

-+

- CPPFLAGS = $(ORIG_CPPFLAGS) $(FASTCGI_INCLUDE)

- 

- WATCHERS = vakatov

---- a/c++/src/html/Makefile.html.lib

-+++ b/c++/src/html/Makefile.html.lib

-@@ -7,6 +7,8 @@ SRC = node html htmlhelper page pager se

-       commentdiag indentstream html_exception writer_htmlenc

- LIB = xhtml

- 

-+DLL_LIB = xncbi

-+

- WATCHERS = ivanov

- 

- 

---- a/c++/src/objects/blast/Makefile.xnetblastcli.lib

-+++ b/c++/src/objects/blast/Makefile.xnetblastcli.lib

-@@ -3,6 +3,7 @@ ASN_DEP = xnetblast

- LIB = xnetblastcli

- SRC = blastclient blastclient_

- 

-+DLL_LIB = xnetblast xser xconnect xutil xncbi

- 

- USES_LIBRARIES =  \

-     xconnect xnetblast

---- a/c++/src/objtools/align_format/Makefile.align_format.lib

-+++ b/c++/src/objtools/align_format/Makefile.align_format.lib

-@@ -13,6 +13,10 @@ SRC = format_flags align_format_util sho

- 

- CPPFLAGS = -DNCBI_MODULE=BLASTFORMAT $(ORIG_CPPFLAGS)

- 

-+DLL_LIB = xalnmgr ncbi_xloader_genbank seqdb blast_services xobjread xobjutil \

-+          xobjmgr xnetblast blastdb gene_info seqset seq general xser \

-+          xcgi xhtml tables xncbi

-+

- ###  EXAMPLES OF OTHER SETTINGS THAT MIGHT BE OF INTEREST

- # CFLAGS   = $(FAST_CFLAGS)

- # CXXFLAGS = $(FAST_CXXFLAGS)

---- a/c++/src/objtools/alnmgr/Makefile.alnmgr.lib

-+++ b/c++/src/objtools/alnmgr/Makefile.alnmgr.lib

-@@ -12,7 +12,7 @@ SRC = aln_builders aln_converters aln_ge

- 

- WATCHERS = todorov dicuccio grichenk

- 

--

-+DLL_LIB = xobjmgr seqset seq xser tables xncbi

- 

- USES_LIBRARIES =  \

-     tables xobjutil

---- a/c++/src/objtools/readers/Makefile.xobjread.lib

-+++ b/c++/src/objtools/readers/Makefile.xobjread.lib

-@@ -21,7 +21,7 @@ SRC = read_util format_guess_ex \

-       message_listener line_error

- 

- 

--DLL_LIB = creaders

-+DLL_LIB = submit seqset seq pub general xser creaders sequtil xutil xncbi

- 

- 

- 

---- a/c++/src/objtools/seqmasks_io/Makefile.seqmasks_io.lib

-+++ b/c++/src/objtools/seqmasks_io/Makefile.seqmasks_io.lib

-@@ -12,7 +12,7 @@ mask_writer_seqloc \

- mask_writer_blastdb_maskinfo

- 

- ASN_DEP = seqset

--DLL_LIB = seqdb blastdb

-+DLL_LIB = seqdb xobjread xobjutil xobjmgr blastdb seqset seq xser xncbi

- 

- WATCHERS = morgulis camacho

- 

---- a/c++/src/objtools/simple/Makefile.xobjsimple.lib

-+++ b/c++/src/objtools/simple/Makefile.xobjsimple.lib

-@@ -7,6 +7,8 @@ WATCHERS =  jcherry

- 

- ASN_DEP = seqset

- 

-+DLL_LIB = ncbi_xloader_genbank xobjmgr seq xncbi

-+

- LIB = xobjsimple

- SRC = simple_om

- 

---- a/c++/src/objtools/blast/seqdb_reader/Makefile.seqdb.lib

-+++ b/c++/src/objtools/blast/seqdb_reader/Makefile.seqdb.lib

-@@ -24,6 +24,8 @@ seqdbobj

- 

- LIB = seqdb

- 

-+DLL_LIB = blastdb xobjmgr seq general xser sequtil xncbi

-+

- CFLAGS   = $(FAST_CFLAGS)

- CPPFLAGS = -DNCBI_MODULE=BLASTDB $(ORIG_CPPFLAGS)

- CXXFLAGS = $(FAST_CXXFLAGS)

---- a/c++/src/objtools/data_loaders/blastdb/Makefile.ncbi_xloader_blastdb.lib

-+++ b/c++/src/objtools/data_loaders/blastdb/Makefile.ncbi_xloader_blastdb.lib

-@@ -7,6 +7,8 @@ CPPFLAGS = -DNCBI_MODULE=BLASTDB $(ORIG_

- 

- ASN_DEP = blastdb seqset

- 

-+DLL_LIB = seqdb xobjmgr seqset seq xncbi

-+

- WATCHERS = camacho

- 

- 

---- a/c++/src/objtools/data_loaders/blastdb/Makefile.ncbi_xloader_blastdb_rmt.lib

-+++ b/c++/src/objtools/data_loaders/blastdb/Makefile.ncbi_xloader_blastdb_rmt.lib

-@@ -5,6 +5,8 @@ SRC = bdbloader_rmt remote_blastdb_adapt

- 

- CPPFLAGS = -DNCBI_MODULE=BLASTDB $(ORIG_CPPFLAGS)

- 

-+DLL_LIB = ncbi_xloader_blastdb blast_services xobjmgr seq xncbi

-+

- ASN_DEP = blastdb xnetblast

- 

- WATCHERS = camacho

---- a/c++/src/algo/blast/api/Makefile.xblast.lib

-+++ b/c++/src/algo/blast/api/Makefile.xblast.lib

-@@ -74,14 +74,15 @@ cdd_pssm_input \

- deltablast_options \

- deltablast

- 

--SRC  = $(SRC_C:%=.core_%) $(SRC_CXX)

-+SRC  = $(SRC_CXX) # $(SRC_C:%=.core_%)

- 

- LIB = xblast

- 

- DLL_LIB = xalgoblastdbindex composition_adjustment xalgowinmask \

- 	xalgodustmask seqmasks_io seqdb $(OBJREAD_LIBS) xobjutil \

- 	blastdb xnetblastcli xnetblast scoremat xconnect tables \

--	$(SOBJMGR_LIBS)

-+        $(SOBJMGR_LIBS) blast seqdb seqset seq general \

-+        xser xconnect sequtil tables xutil xncbi

- 

- CFLAGS   = $(FAST_CFLAGS) 

- CPPFLAGS = -DNCBI_MODULE=BLAST $(ORIG_CPPFLAGS)

---- a/c++/src/algo/blast/blastinput/Makefile.blastinput.lib

-+++ b/c++/src/algo/blast/blastinput/Makefile.blastinput.lib

-@@ -24,7 +24,9 @@ SRC  = $(SRC_CXX)

- 

- LIB = blastinput

- 

--DLL_LIB = xblast align_format ncbi_xloader_blastdb_rmt ncbi_xloader_blastdb seqdb $(OBJREAD_LIBS) $(OBJMGR_LIBS) xutil

-+    DLL_LIB = xblast align_format ncbi_xloader_blastdb_rmt ncbi_xloader_blastdb seqdb xobjread \

-+              $(OBJREAD_LIBS) $(OBJMGR_LIBS) xutil ncbi_xloader_genbank ncbi_xreader_id2 ncbi_xreader \

-+              scoremat seqset seq xser xutil xncbi

- 

- # should be redundant, given the above :-/

- ASN_DEP = seqset xnetblast

---- a/c++/src/algo/dustmask/Makefile.xalgodustmask.lib

-+++ b/c++/src/algo/dustmask/Makefile.xalgodustmask.lib

-@@ -8,6 +8,8 @@ LIB = xalgodustmask

- 

- SRC = symdust

- 

-+DLL_LIB = xobjmgr seq xncbi

-+

- CXXFLAGS = $(FAST_CXXFLAGS)

- LDFLAGS  = $(FAST_LDFLAGS)

- 

---- a/c++/src/connect/Makefile.xconnect.lib

-+++ b/c++/src/connect/Makefile.xconnect.lib

-@@ -14,6 +14,8 @@ UNIX_SRC = $(LOCAL_LBSM)

- LIB  = xconnect

- PROJ_TAG = core

- 

-+DLL_LIB = xncbi

-+

- LIBS = $(NETWORK_LIBS) $(ORIG_LIBS)

- 

- WATCHERS = lavr

---- a/c++/src/connect/ext/Makefile.xconnext.lib

-+++ b/c++/src/connect/ext/Makefile.xconnext.lib

-@@ -6,6 +6,8 @@ SRC      = $(SRC_C) ncbi_dblb_svcmapper

- 

- LIB      = xconnext

- 

-+DLL_LIB = xconnect xncbi

-+

- WATCHERS = lavr

- 

- 

---- a/c++/src/objects/blast/Makefile.blast.lib

-+++ b/c++/src/objects/blast/Makefile.blast.lib

-@@ -1,6 +1,8 @@

- LIB = xnetblast

- SRC = blast__ blast___ names

- 

-+DLL_LIB = scoremat seqset seq xser xncbi

-+

- WATCHERS = camacho

- 

- 

---- a/c++/src/objects/blastxml/Makefile.blastxml.lib

-+++ b/c++/src/objects/blastxml/Makefile.blastxml.lib

-@@ -1,6 +1,8 @@

- LIB = blastxml

- SRC = blastxml__ blastxml___

- 

-+DLL_LIB = xser xncbi

-+

- 

- USES_LIBRARIES =  \

-     xser

---- a/c++/src/objects/scoremat/Makefile.scoremat.lib

-+++ b/c++/src/objects/scoremat/Makefile.scoremat.lib

-@@ -1,6 +1,8 @@

- LIB = scoremat

- SRC = scoremat__ scoremat___

- 

-+DLL_LIB = seqset seq general xser xncbi

-+

- 

- USES_LIBRARIES =  \

-     seqset

---- a/c++/src/objects/seqedit/Makefile.seqedit.lib

-+++ b/c++/src/objects/seqedit/Makefile.seqedit.lib

-@@ -1,6 +1,7 @@

- LIB = seqedit

- SRC = seqedit__ seqedit___

-- 

-+

-+DLL_LIB = seqset seq general xser xncbi

- 

- 

- USES_LIBRARIES =  \

---- a/c++/src/objects/submit/Makefile.submit.lib

-+++ b/c++/src/objects/submit/Makefile.submit.lib

-@@ -1,6 +1,8 @@

- LIB = submit

- SRC = submit__ submit___

- 

-+DLL_LIB = seqset seq biblio general xser xncbi

-+

- 

- USES_LIBRARIES =  \

-     seqset

---- a/c++/src/objmgr/util/Makefile.util.lib

-+++ b/c++/src/objmgr/util/Makefile.util.lib

-@@ -8,6 +8,8 @@ ASN_DEP = submit

- SRC = weight sequence feature seqtitle create_defline obj_sniff seq_loc_util seq_align_util seq_trimmer bioseqgaps_ci

- LIB = xobjutil

- 

-+DLL_LIB = xobjmgr seqset seq pub biblio general xser sequtil xutil xncbi

-+

- WATCHERS = ucko vasilche kornbluh

- 

- 

---- a/c++/src/objtools/blast/blastdb_format/Makefile.blastdb_format.lib

-+++ b/c++/src/objtools/blast/blastdb_format/Makefile.blastdb_format.lib

-@@ -11,6 +11,7 @@ SRC = seq_writer blastdb_dataextract bla

- 

- CPPFLAGS = -DNCBI_MODULE=BLASTDB $(ORIG_CPPFLAGS)

- 

-+DLL_LIB = seqdb xobjutil xobjmgr seq xser sequtil xutil xncbi

- 

- ###  EXAMPLES OF OTHER SETTINGS THAT MIGHT BE OF INTEREST

- # CFLAGS   = $(FAST_CFLAGS)

---- a/c++/src/objtools/blast/services/Makefile.blast_services.lib

-+++ b/c++/src/objtools/blast/services/Makefile.blast_services.lib

-@@ -8,6 +8,8 @@ SRC = blast_services

- 

- LIB = blast_services

- 

-+DLL_LIB = xnetblastcli xnetblast xser xconnect xutil xncbi

-+

- CFLAGS   = $(FAST_CFLAGS)

- CPPFLAGS = -DNCBI_MODULE=NETBLAST $(ORIG_CPPFLAGS)

- CXXFLAGS = $(FAST_CXXFLAGS)

---- a/c++/src/objtools/data_loaders/genbank/Makefile.ncbi_xloader_genbank.lib

-+++ b/c++/src/objtools/data_loaders/genbank/Makefile.ncbi_xloader_genbank.lib

-@@ -12,6 +12,9 @@ LIB_OR_DLL = both

- # Dependencies for shared library

- DLL_LIB = ncbi_xreader$(DLL)

- 

-+DLL_DLIB = ncbi_xreader_cache ncbi_xreader_id1 ncbi_xreader_id2 \

-+           id2 id1 ncbi_xreader xobjmgr seq xutil xncbi

-+

- WATCHERS = vasilche

- 

- 

---- a/c++/src/objtools/data_loaders/genbank/Makefile.ncbi_xreader.lib

-+++ b/c++/src/objtools/data_loaders/genbank/Makefile.ncbi_xreader.lib

-@@ -15,6 +15,9 @@ LIB_OR_DLL = both

- DLL_LIB = 

- DLL_DLIB = $(GENBANK_READER_LDEP)

- 

-+DLL_DLIB = xobjmgr id2 seqsplit id1 seqset seq general \

-+           xser xconnect xcompress xutil xncbi

-+

- WATCHERS = vasilche

- 

- 

---- a/c++/src/objtools/data_loaders/genbank/cache/Makefile.ncbi_xreader_cache.lib

-+++ b/c++/src/objtools/data_loaders/genbank/cache/Makefile.ncbi_xreader_cache.lib

-@@ -12,6 +12,8 @@ LIB_OR_DLL = both

- # Dependencies for shared library

- DLL_LIB = ncbi_xreader$(DLL)

- 

-+DLL_DLIB = ncbi_xreader xobjmgr seq xser xncbi

-+

- CPPFLAGS = $(ORIG_CPPFLAGS) $(CMPRS_INCLUDE)

- 

- WATCHERS = vasilche

---- a/c++/src/objtools/data_loaders/genbank/id1/Makefile.ncbi_xreader_id1.lib

-+++ b/c++/src/objtools/data_loaders/genbank/id1/Makefile.ncbi_xreader_id1.lib

-@@ -12,6 +12,8 @@ LIB_OR_DLL = both

- # Dependencies for shared library

- DLL_LIB = xconnect ncbi_xreader$(DLL)

- 

-+DLL_DLIB = ncbi_xreader xobjmgr id1 seq general xser xconnect xutil xncbi

-+

- CPPFLAGS = $(ORIG_CPPFLAGS) $(CMPRS_INCLUDE)

- 

- WATCHERS = vasilche

---- a/c++/src/objtools/data_loaders/genbank/id2/Makefile.ncbi_xreader_id2.lib

-+++ b/c++/src/objtools/data_loaders/genbank/id2/Makefile.ncbi_xreader_id2.lib

-@@ -12,7 +12,10 @@ LIB_OR_DLL = both

- CPPFLAGS = $(ORIG_CPPFLAGS) $(Z_INCLUDE)

- 

- # Dependencies for shared library (disabled due to problems on Darwin)

--# DLL_LIB = xconnect ncbi_xreader$(DLL)

-+DLL_LIB = xconnect ncbi_xreader$(DLL)

-+

-+DLL_DLIB = ncbi_xreader xobjmgr id2 seqsplit seq xser xconnect xncbi

-+

- 

- WATCHERS = vasilche

- 

---- a/c++/src/util/compress/api/Makefile.compress.lib

-+++ b/c++/src/util/compress/api/Makefile.compress.lib

-@@ -7,7 +7,7 @@ LIB = xcompress

- 

- CPPFLAGS = $(ORIG_CPPFLAGS) $(CMPRS_INCLUDE)

- 

--DLL_LIB =  $(BZ2_LIB)  $(Z_LIB)  $(LZO_LIB)

-+DLL_LIB =  $(BZ2_LIB)  $(Z_LIB)  $(LZO_LIB) xutil xncbi

- LIBS    =  $(BZ2_LIBS) $(Z_LIBS) $(LZO_LIBS) $(ORIG_LIBS)

- 

- WATCHERS = ivanov

---- a/c++/src/util/sequtil/Makefile.sequtil.lib

-+++ b/c++/src/util/sequtil/Makefile.sequtil.lib

-@@ -3,6 +3,8 @@

- LIB = sequtil

- SRC = sequtil sequtil_convert sequtil_convert_imp sequtil_manip sequtil_tables sequtil_shared

- 

-+DLL_LIB = xncbi

-+

- WATCHERS = shomrat

- 

- 

---- a/c++/src/corelib/Makefile.test_boost.lib

-+++ b/c++/src/corelib/Makefile.test_boost.lib

-@@ -3,6 +3,8 @@

- SRC = test_boost teamcity_messages

- LIB = test_boost

- 

-+DLL_LIB = xncbi

-+

- CPPFLAGS = $(ORIG_CPPFLAGS) $(BOOST_INCLUDE)

- 

- REQUIRES = Boost.Test.Included

---- a/c++/src/corelib/Makefile.test_mt.lib

-+++ b/c++/src/corelib/Makefile.test_mt.lib

-@@ -3,6 +3,8 @@

- SRC = test_mt

- LIB    = test_mt

- 

-+DLL_LIB = xncbi

-+

- # REQUIRES = MT

- 

- USE_PCH = no

---- a/c++/src/objects/biblio/Makefile.biblio.lib

-+++ b/c++/src/objects/biblio/Makefile.biblio.lib

-@@ -1,6 +1,8 @@

- LIB = biblio

- SRC = biblio__ biblio___ citation_base

- 

-+DLL_LIB = general xser xncbi

-+

- 

- USES_LIBRARIES =  \

-     general

---- a/c++/src/objects/blastdb/Makefile.blastdb.lib

-+++ b/c++/src/objects/blastdb/Makefile.blastdb.lib

-@@ -1,5 +1,7 @@

- # $Id: Makefile.blastdb.lib 427424 2014-02-20 13:38:50Z gouriano $

- 

-+

-+DLL_LIB = seq xser xncbi

- LIB = blastdb

- SRC = blastdb__ blastdb___

- 

---- a/c++/src/objects/general/Makefile.general.lib

-+++ b/c++/src/objects/general/Makefile.general.lib

-@@ -1,6 +1,8 @@

- LIB = general

- SRC = general__ general___ uoconv

- 

-+DLL_LIB = xser xncbi

-+

- 

- USES_LIBRARIES =  \

-     xser

---- a/c++/src/objects/genomecoll/Makefile.genome_collection.lib

-+++ b/c++/src/objects/genomecoll/Makefile.genome_collection.lib

-@@ -3,6 +3,8 @@

- LIB = genome_collection

- SRC = genome_collection__ genome_collection___

- 

-+DLL_LIB = seq general xser xncbi

-+

- WATCHERS = dicuccio

- 

- 

---- a/c++/src/objects/id1/Makefile.id1.lib

-+++ b/c++/src/objects/id1/Makefile.id1.lib

-@@ -3,6 +3,8 @@ ASN_DEP = seq

- LIB = id1

- SRC = id1__ id1___

- 

-+DLL_LIB = seqset seq xser xncbi

-+

- WATCHERS = vasilche

- 

- 

---- a/c++/src/objects/id2/Makefile.id2.lib

-+++ b/c++/src/objects/id2/Makefile.id2.lib

-@@ -1,6 +1,8 @@

- LIB = id2

- SRC = id2__ id2___

- 

-+DLL_LIB = seqsplit seq xser xncbi

-+

- WATCHERS = vasilche

- 

- 

---- a/c++/src/objects/medline/Makefile.medline.lib

-+++ b/c++/src/objects/medline/Makefile.medline.lib

-@@ -1,6 +1,8 @@

- LIB = medline

- SRC = medline__ medline___

- 

-+DLL_LIB = biblio general xser xncbi

-+

- 

- USES_LIBRARIES =  \

-     biblio

---- a/c++/src/objects/pub/Makefile.pub.lib

-+++ b/c++/src/objects/pub/Makefile.pub.lib

-@@ -1,6 +1,8 @@

- LIB = pub

- SRC = pub__ pub___

- 

-+DLL_LIB = medline biblio xser xncbi

-+

- 

- USES_LIBRARIES =  \

-     medline

---- a/c++/src/objects/seq/Makefile.seq.lib

-+++ b/c++/src/objects/seq/Makefile.seq.lib

-@@ -12,6 +12,8 @@ SRC = $(ASN:%=%__) $(ASN:%=%___) seqport

-       seq_loc_mapper_base seq_align_mapper_base seqlocinfo sofa_map \

-       seq_loc_from_string seq_loc_reverse_complementer

- 

-+DLL_LIB = seqcode pub biblio general xser sequtil xutil xncbi

-+

- WATCHERS = vasilche grichenk

- 

- 

---- a/c++/src/objects/seqcode/Makefile.seqcode.lib

-+++ b/c++/src/objects/seqcode/Makefile.seqcode.lib

-@@ -1,6 +1,8 @@

- LIB = seqcode

- SRC = seqcode__ seqcode___

- 

-+DLL_LIB = xser xncbi

-+

- 

- USES_LIBRARIES =  \

-     xser

---- a/c++/src/objects/seqset/Makefile.seqset.lib

-+++ b/c++/src/objects/seqset/Makefile.seqset.lib

-@@ -1,6 +1,8 @@

- LIB = seqset

- SRC = seqset__ seqset___ gb_release_file

- 

-+DLL_LIB = seq general xser xncbi

-+

- 

- USES_LIBRARIES =  \

-     $(SEQ_LIBS) pub

---- a/c++/src/objects/seqsplit/Makefile.seqsplit.lib

-+++ b/c++/src/objects/seqsplit/Makefile.seqsplit.lib

-@@ -1,6 +1,8 @@

- LIB = seqsplit

- SRC = seqsplit__ seqsplit___

- 

-+DLL_LIB = seqset seq xser xncbi

-+

- WATCHERS = vasilche

- 

- 

---- a/c++/src/serial/Makefile.serial.lib

-+++ b/c++/src/serial/Makefile.serial.lib

-@@ -18,6 +18,8 @@ SRC = \

- 

- LIB    = xser

- 

-+DLL_LIB = xutil xncbi

-+

- WATCHERS = gouriano

- 

- 

---- a/c++/src/util/Makefile.util.lib

-+++ b/c++/src/util/Makefile.util.lib

-@@ -12,6 +12,7 @@ SRC = random_gen utf8 checksum bytesrc s

- LIB = xutil

- PROJ_TAG = core

- 

-+DLL_LIB = xncbi

- LIBS = $(ORIG_LIBS)

- 

- WATCHERS = vakatov kornbluh

---- a/c++/src/util/xregexp/Makefile.xregexp.lib

-+++ b/c++/src/util/xregexp/Makefile.xregexp.lib

-@@ -6,7 +6,7 @@ LIB = xregexp

- 

- CPPFLAGS = $(ORIG_CPPFLAGS) $(PCRE_INCLUDE)

- 

--DLL_LIB = $(PCRE_LIB)

-+DLL_LIB = $(PCRE_LIB) xncbi

- LIBS    = $(PCRE_LIBS)

- 

- WATCHERS = ivanov

---- a/c++/src/algo/segmask/Makefile.xalgosegmask.lib

-+++ b/c++/src/algo/segmask/Makefile.xalgosegmask.lib

-@@ -8,6 +8,8 @@ LIB = xalgosegmask

- 

- SRC = segmask

- 

-+DLL_LIB = blast xobjmgr xncbi

-+

- CXXFLAGS = $(FAST_CXXFLAGS)

- LDFLAGS  = $(FAST_LDFLAGS)

- 

---- a/c++/src/objmgr/split/Makefile.id2_split.lib

-+++ b/c++/src/objmgr/split/Makefile.id2_split.lib

-@@ -17,7 +17,7 @@ LIB = id2_split

- 

- CPPFLAGS = $(ORIG_CPPFLAGS) $(CMPRS_INCLUDE)

- 

--DLL_LIB = $(SOBJMGR_LIBS)

-+DLL_LIB = xobjmgr seqsplit seqset seq general xser xcompress xncbi

- 

- WATCHERS = vasilche

- 

---- a/c++/src/objtools/blast/seqdb_writer/Makefile.writedb.lib

-+++ b/c++/src/objtools/blast/seqdb_writer/Makefile.writedb.lib

-@@ -8,6 +8,9 @@ SRC = writedb writedb_impl writedb_volum

- 

- LIB = writedb

- 

-+DLL_LIB = seqdb xobjread xobjmgr blastdb seqset seq general \

-+          xser sequtil xutil xncbi

-+

- CFLAGS   = $(FAST_CFLAGS)

- CPPFLAGS = -DNCBI_MODULE=BLASTDB $(ORIG_CPPFLAGS)

- CXXFLAGS = $(FAST_CXXFLAGS)

---- a/c++/src/algo/blast/Makefile.blast_macros.mk

-+++ b/c++/src/algo/blast/Makefile.blast_macros.mk

-@@ -18,7 +18,7 @@ BLAST_INPUT_LIBS = blastinput \

- BLAST_SRA_LIBS=blast_sra $(SRAXF_LIBS) vxf $(SRA_LIBS)

- 

- # BLAST_FORMATTER_LIBS and BLAST_INPUT_LIBS need $BLAST_LIBS

--BLAST_LIBS = xblast xalgoblastdbindex composition_adjustment \

-+BLAST_LIBS = xblast xalgoblastdbindex blast composition_adjustment \

- 		xalgodustmask xalgowinmask seqmasks_io seqdb blast_services xobjutil \

- 		$(OBJREAD_LIBS) xnetblastcli xnetblast blastdb scoremat tables xalnmgr

- # BLAST additionally needs xconnect $(SOBJMGR_LIBS) or $(OBJMGR_LIBS)

---- a/c++/src/algo/blast/dbindex/makeindex/Makefile.makeindex.app

-+++ b/c++/src/algo/blast/dbindex/makeindex/Makefile.makeindex.app

-@@ -2,7 +2,7 @@ APP = makembindex

- SRC = main mkindex_app

- 

- LIB_ = xalgoblastdbindex blast composition_adjustment seqdb blastdb \

--      $(OBJREAD_LIBS) xobjutil tables connect $(SOBJMGR_LIBS)

-+      $(OBJREAD_LIBS) xobjutil tables xconnect $(SOBJMGR_LIBS)

- LIB = $(LIB_:%=%$(STATIC))

- 

- CXXFLAGS = $(FAST_CXXFLAGS)

---- a/c++/src/build-system/library_relations.txt

-+++ b/c++/src/build-system/library_relations.txt

-@@ -1189,7 +1189,7 @@ xasmcompare needs $(SEQ_LIBS)

- xasmcompare needs pub

- xasn needs xhtml

- xasn needs3party $(NCBI_C_ncbi)

--xblast includes blast

-+xblast needs blast

- xblast needs xalgoblastdbindex

- xblast needs xalgodustmask

- xblast needs xalgowinmask

diff --git a/sci-biology/ncbi-blast+/metadata.xml b/sci-biology/ncbi-blast+/metadata.xml
deleted file mode 100644
index 93556eaa7..000000000
--- a/sci-biology/ncbi-blast+/metadata.xml
+++ /dev/null
@@ -1,23 +0,0 @@
-<?xml version="1.0" encoding="UTF-8"?>
-<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
-<pkgmetadata>
-	<maintainer type="person">
-		<email>mmokrejs@fold.natur.cuni.cz</email>
-		<name>Martin Mokrejs</name>
-	</maintainer>
-	<maintainer type="project">
-		<email>sci-biology@gentoo.org</email>
-		<name>Gentoo Biology Project</name>
-	</maintainer>
-	<use>
-		<flag name="boost">Undocumented USE</flag>
-		<flag name="cppunit">Undocumented USE</flag>
-		<flag name="freetype">Undocumented USE</flag>
-		<flag name="mesa">Undocumented USE</flag>
-		<flag name="muparser">Undocumented USE</flag>
-		<flag name="sablotron">Undocumented USE</flag>
-		<flag name="xerces">Undocumented USE</flag>
-		<flag name="xalan">Undocumented USE</flag>
-		<flag name="xslt">Undocumented USE</flag>
-	</use>
-</pkgmetadata>
diff --git a/sci-biology/ncbi-blast+/ncbi-blast+-2.2.30.ebuild b/sci-biology/ncbi-blast+/ncbi-blast+-2.2.30.ebuild
deleted file mode 100644
index dd6f3444f..000000000
--- a/sci-biology/ncbi-blast+/ncbi-blast+-2.2.30.ebuild
+++ /dev/null
@@ -1,351 +0,0 @@
-# Copyright 1999-2016 Gentoo Foundation
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=5
-
-PYTHON_COMPAT=( python2_7 )
-
-inherit eutils flag-o-matic multilib python-single-r1 toolchain-funcs
-
-MY_PV="2.2.30"
-MY_P="ncbi-blast-${PV}+-src"
-# workdir/ncbi-blast-2.2.30+-src
-# ftp://ftp.ncbi.nlm.nih.gov/blast/executables/blast+/2.2.30/ncbi-blast-2.2.30+-src.tar.gz
-
-DESCRIPTION="A subset of NCBI C++ Toolkit containing just the NCBI BLAST+"
-HOMEPAGE="http://www.ncbi.nlm.nih.gov/books/bv.fcgi?rid=toolkit"
-SRC_URI="
-	ftp://ftp.ncbi.nih.gov/blast/executables/blast+/${PV}/${MY_P}.tar.gz"
-#	http://dev.gentoo.org/~jlec/distfiles/${PN}-${PV#0.}-asneeded.patch.xz"
-
-# should also install ftp://ftp.ncbi.nlm.nih.gov/blast/db/taxdb.tar.gz
-# see http://www.biostars.org/p/76551/ and http://blastedbio.blogspot.cz/2012/05/blast-tabular-missing-descriptions.html
-LICENSE="public-domain"
-SLOT="0"
-IUSE="
-	debug static-libs static threads pch
-	test wxwidgets odbc
-	berkdb boost bzip2 cppunit curl expat fltk freetype gif
-	glut gnutls hdf5 icu jpeg lzo mesa mysql muparser opengl pcre png python
-	sablotron sqlite tiff xerces xalan xml xpm xslt X"
-KEYWORDS="~amd64 ~x86 ~amd64-linux ~x86-linux"
-#KEYWORDS=""
-
-REQUIRED_USE="${PYTHON_REQUIRED_USE}"
-
-# sys-libs/db should be compiled with USE=cxx
-DEPEND="
-	!sci-biology/ncbi-tools++
-	!sci-biology/sra_sdk
-	berkdb? ( sys-libs/db:4.3[cxx] )
-	boost? ( dev-libs/boost )
-	curl? ( net-misc/curl )
-	sqlite? ( dev-db/sqlite:3 )
-	mysql? ( virtual/mysql )
-	fltk? ( x11-libs/fltk )
-	opengl? ( virtual/opengl media-libs/glew:0= )
-	mesa? ( media-libs/mesa[osmesa] )
-	glut? ( media-libs/freeglut )
-	freetype? ( media-libs/freetype )
-	gnutls? ( net-libs/gnutls )
-	python? ( ${PYTHON_DEPS} )
-	cppunit? ( dev-util/cppunit )
-	icu? ( dev-libs/icu )
-	expat? ( dev-libs/expat )
-	sablotron? ( app-text/sablotron )
-	xml? ( dev-libs/libxml2 )
-	xslt? ( dev-libs/libxslt )
-	xerces? ( dev-libs/xerces-c )
-	xalan? ( dev-libs/xalan-c )
-	muparser? ( dev-cpp/muParser )
-	hdf5? ( sci-libs/hdf5[cxx] )
-	gif? ( media-libs/giflib )
-	jpeg? ( virtual/jpeg:0= )
-	png? ( media-libs/libpng:0= )
-	tiff? ( media-libs/tiff:0= )
-	xpm? ( x11-libs/libXpm )
-	dev-libs/lzo
-	app-arch/bzip2
-	dev-libs/libpcre"
-# USE flags which should be added somehow: wxWindows wxWidgets SP ORBacus ODBC OEChem sge
-# Intentionally omitted USE flags:
-#   ftds? ( dev-db/freetds ) # support for outside FreeTDS installations is currently broken.
-#                              The default (heavily patched) embedded copy should work, or you can
-#                              leave it off altogether -- the only public apps that make use of it are
-#                              samples and tests, since NCBI's database servers are of course firewalled.
-
-# seems muParser is required, also glew is required. configure exits otherwise if these are explicitly passed to it (due to USE flag enabled)
-
-RDEPEND="${DEPEND}"
-
-S="${WORKDIR}/${MY_P}/c++"
-# ncbi-blast-2.2.30+-src/c++
-
-src_prepare() {
-#	filter-ldflags -Wl,--as-needed
-#	append-ldflags -Wl,--no-undefined
-#	sed -i -e 's/-print-file-name=libstdc++.a//' \
-#		-e '/sed/ s/\([gO]\[0-9\]\)\*/\1\\+/' \
-#		src/build-system/configure || die
-#	epatch \
-#		"${FILESDIR}"/${PN}-${PV#0.}-fix-order-of-libs.patch \
-#		"${FILESDIR}"/curl-types.patch \
-#		"${FILESDIR}"/malloc_initialize_upstream_fix.patch \
-#		"${FILESDIR}"/respect_CXXFLAGS_configure.ac.patch \
-#		"${FILESDIR}"/respect_CXXFLAGS_configure.patch \
-#		"${FILESDIR}"/report_project_settings_configure.ac.patch \
-#		"${FILESDIR}"/report_project_settings_configure.patch \
-#		"${FILESDIR}"/make_install.patch
-
-#		"${FILESDIR}"/${PN}-${PV#0.}-disable_test_compress.patch
-
-#		"${FILESDIR}"/${PN}-${PV#0.}-gcc46.patch \
-#		"${FILESDIR}"/${PN}-${PV#0.}-gcc47.patch \
-#		"${WORKDIR}"/${PN}-${PV#0.}-asneeded.patch \
-#		"${FILESDIR}"/${PN}-${PV#0.}-libpng15.patch \
-#		"${FILESDIR}"/${PN}-${PV#0.}-glibc-214.patch
-
-#	use prefix && append-ldflags -Wl,-rpath,"${EPREFIX}/usr/$(get_libdir)/${PN}"
-
-# The conf-opts.patch and as-needed.patch need to be adjusted for 12.0.0 line numbers
-##	local PATCHES=(
-##		"${FILESDIR}"/${P}-conf-opts.patch
-##		"${FILESDIR}"/${P}-fix-svn-URL-upstream.patch
-##		"${FILESDIR}"/${P}-linkage-tuneups.patch
-##		"${FILESDIR}"/${P}-more-patches.patch
-##		"${FILESDIR}"/${P}-linkage-tuneups-addons.patch
-##		"${FILESDIR}"/${P}-configure.patch
-##		"${FILESDIR}"/${P}-drop-STATIC-from-LIB.patch
-##		"${FILESDIR}"/${P}-fix-install.patch
-##		)
-		# "${FILESDIR}"/${P}-support-autoconf-2.60.patch
-##	epatch ${PATCHES[@]}
-
-	# use a Debian patch from http://anonscm.debian.org/viewvc/debian-med/trunk/packages/ncbi-blast%2B/trunk/debian/patches/fix_lib_deps?revision=18535&view=markup
-	epatch "${FILESDIR}"/"${P}"__fix_lib_deps.patch
-	# make sure this one is the last one and contains the actual patches applied unless we can have autoconf-2.59 or 2.60
-	# https://bugs.gentoo.org/show_bug.cgi?id=514706
-
-	tc-export CXX CC
-
-##	cd src/build-system || die
-#	eautoreconf
-
-	# Temporarily disabling eautoconf because we patch configure via ${P}-support-autoconf-2.60.patch
-	# eautoconf # keep it disabled until we can ensure 2.59 is installed
-	# beware 12.0.0. and previous required autoconf-2.59, a patch for 12.0.0 brings autoconf-2.60 support
-}
-
-# possibly place modified contents of ${W}/src/build-system/config.site.ncbi and {W}/src/build-system/config.site.ex into ${W}/src/build-system/config.site
-src_configure() {
-	local myconf=()
-	#--without-optimization  turn off optimization flags in non-debug mode
-	#--with-profiling        build profiled versions of libs and apps
-	#--with-tcheck(=DIR)     build for Intel Thread Checker (in DIR)
-	#--with-plugin-auto-load always enable the plugin manager by default
-	#--with-bundles          build bundles in addition to dylibs on Mac OS X
-	#--with-bin-release      build executables suitable for public release
-	#	no dll and such
-	#--with-64               compile to 64-bit code
-	#--with-universal        build universal binaries on Mac OS X
-	#--with-universal=CPUs   build universal binaries targeting the given CPUs
-	#--without-exe           do not build executables
-	#--with-relative-runpath=P specify an executable-relative DLL search path
-	#--with-hard-runpath     hard-code runtime path, ignoring LD_LIBRARY_PATH
-	#--with-limited-linker   don't attempt to build especially large projects
-	#--with-extra-action=    script to call after the configuration is complete
-	#--with-autodep          automatic generation of dependencies (GNU make)
-	#--with-fake-root=DIR    appear to have been built under DIR
-	#--with-build-root-sfx=X add a user-specified suffix to the build dir name
-	#--without-execopy       do not copy built executables to the BIN area
-	#--with-lib-rebuilds     ensure that apps use up-to-date libraries
-	#--with-lib-rebuilds=ask ask whether to update each app's libraries
-	#--without-deactivation  keep old copies of libraries that no longer build
-	#--without-makefile-auto-update  do not auto-update generated makefiles
-	#--with-projects=FILE    build projects listed in FILE by default
-	#--without-flat-makefile do not generate an all-encompassing flat makefile
-	#--with-configure-dialog allow interactive flat makefile project selection
-	#--with-saved-settings=F load configuration settings from the file F
-	#--with-check-tools=...  use the specified tools for testing
-	#--with-ncbi-public      ensure compatibility for all in-house platforms
-	#--with-sybase-local=DIR use local SYBASE install (DIR is optional)
-	#--with-sybase-new       use newer SYBASE install (12.5 rather than 12.0)
-	#--without-sp            do not use SP libraries
-	#--without-orbacus       do not use ORBacus CORBA libraries
-	#--with-orbacus=DIR      use ORBacus installation in DIR
-	#--with-jni(=JDK-DIR)    build Java bindings (against the JDK in JDK-DIR)
-	#--with-sablot=DIR       use Sablotron installation in DIR
-	#--without-sablot,       do not use Sablotron
-	#--with-oechem=DIR       use OpenEye OEChem installation in DIR
-	#--without-oechem        do not use OEChem
-	#--with-sge=DIR          use Sun Grid Engine installation in DIR
-	#--without-sge           do not use Sun Grid Engine
-	#--with-magic=DIR        use libmagic installation in DIR
-	#--without-magic         do not use libmagic
-	#--without-local-lbsm    turn off support for IPC with locally running LBSMD
-	#--without-ncbi-crypt    use a dummy stubbed-out version of ncbi_crypt
-	#--without-connext       do not build non-public CONNECT library extensions
-	#--without-serial        do not build the serialization library and tools
-	#--without-objects       do not generate/build serializeable objects from ASNs
-	#--without-dbapi         do not build database connectivity libraries
-	#--without-app           do not build standalone applications like ID1_FETCH
-	#--without-gui           do not build most graphical projects
-	#--without-algo          do not build CPU-intensive algorithms
-	#--without-internal      do not build internal projects
-	#--with-gbench           ensure that Genome Workbench can be built
-	#--without-gbench        do not build Genome Workbench
-	myconf+=(
-	--with-dll
-	--with-lfs
-	--with-build-root="${S}"_build
-	--without-suffix
-	--without-hostspec
-	--without-version
-	--with-bincopy
-	--without-strip
-	--without-ccache
-	--without-distcc
-#	--with-ncbi-c
-	--without-ctools
-#	--with-sss
-#	--with-sssutils
-#	--with-sssdb
-#	--with-included-sss
-	--with-z="${EPREFIX}/usr"
-	--with-bz2="${EPREFIX}/usr"
-	--without-sybase
-	--with-autodep
-#	--with-3psw=std:netopt favor standard (system) builds of the above pkgs
-	$(use_with debug)
-	$(use_with debug max-debug)
-	$(use_with debug symbols)
-	$(use_with static-libs static)
-	$(use_with static static-exe)
-	$(use_with threads mt)
-	$(use_with prefix runpath "${EPREFIX}/usr/$(get_libdir)/${PN}")
-	$(use_with test check)
-	$(use_with pch)
-	$(use_with lzo lzo "${EPREFIX}/usr")
-	$(use_with pcre pcre "${EPREFIX}/usr")
-	$(use_with gnutls gnutls "${EPREFIX}/usr")
-	$(use_with mysql mysql "${EPREFIX}/usr")
-	$(use_with muparser muparser "${EPREFIX}/usr")
-	$(usex fltk --with-fltk="${EPREFIX}/usr" "")
-	$(use_with opengl opengl "${EPREFIX}/usr")
-	$(use_with mesa mesa "${EPREFIX}/usr")
-	$(use_with opengl glut "${EPREFIX}/usr")
-	$(use_with opengl glew "${EPREFIX}/usr")
-	$(use_with opengl glew-mx)
-	$(use_with wxwidgets wxwidgets "${EPREFIX}/usr")
-	$(use_with wxwidgets wxwidgets-ucs)
-	$(use_with freetype freetype "${EPREFIX}/usr")
-#	$(use_with berkdb bdb "${EPREFIX}/usr") # not in ncbi-blast+
-	$(usex odbc --with-odbc="${EPREFIX}/usr" "")
-	$(use_with python python "${EPREFIX}/usr")
-	$(use_with boost boost "${EPREFIX}/usr")
-	$(use_with sqlite sqlite3 "${EPREFIX}/usr")
-	$(use_with icu icu "${EPREFIX}/usr")
-	$(use_with expat expat "${EPREFIX}/usr")
-	$(use_with xml libxml "${EPREFIX}/usr")
-	$(use_with xml libxslt "${EPREFIX}/usr")
-	$(use_with xerces xerces "${EPREFIX}/usr")
-	$(use_with hdf5 hdf5 "${EPREFIX}/usr")
-	$(use_with xalan xalan "${EPREFIX}/usr")
-#	$(use_with gif gif "${EPREFIX}/usr") # prevent compilation failure in "ncbi-tools++-12.0.0/src/util/image/image_io_gif.cpp:351: error: 'QuantizeBuffer' was not declared in this scope"
-	--without-gif
-	$(use_with jpeg jpeg "${EPREFIX}/usr")
-	$(use_with tiff tiff "${EPREFIX}/usr")
-	$(use_with png png "${EPREFIX}/usr")
-	$(use_with xpm xpm "${EPREFIX}/usr")
-	$(use_with curl curl "${EPREFIX}/usr")
-#	$(use_with X x "${EPREFIX}/usr")
-#	$(use_with X x) # there is no --with-x option
-	)
-
-	# http://www.ncbi.nlm.nih.gov/books/NBK7167/
-	use test ||	myconf+=( --with-projects="${FILESDIR}"/disable-testsuite-compilation.txt )
-
-	# TODO
-	# copy optimization -O options from CXXFLAGS to DEF_FAST_FLAGS and pass that also to configure
-	# otherwise your -O2 will be dropped in some subdirectories and replaced by e.g. -O9
-
-	einfo "bash ./src/build-system/configure --srcdir="${S}" --prefix="${EPREFIX}/usr" --libdir=/usr/lib64 ${myconf[@]}"
-
-#	ECONF_SOURCE="src/build-system" \
-#		econf \
-	bash \
-		./src/build-system/configure \
-		--srcdir="${S}" \
-		--prefix="${EPREFIX}/usr" \
-		--libdir=/usr/lib64 \
-		--with-flat-makefile \
-		${myconf[@]} || die
-#--without-debug \
-#		--with-bin-release \
-#		--with-bincopy \
-#		--without-static \
-#		--with-dll \
-#		--with-mt \
-#		--with-openmp \
-#		--with-lfs \
-#		--prefix="${ED}"/usr \
-#		--libdir="${ED}"/usr/$(get_libdir)/"${PN}" \
-#		${myconf} LDFLAGS="-Wl,--no-as-needed" \
-#		|| die
-#	econf ${myconf[@]}
-}
-
-src_compile() {
-	## all_r would ignore the --with-projects contents and build more
-	## emake all_r -C GCC*-Release*/build || die
-	## all_p with compile only selected/required components
-	##cd "${S}"_build &&\
-	##emake all_p -C GCC*-Release*/build || die "gcc-4.5.3 crashes at src/objects/valerr/ValidError.cpp:226:1: internal compiler error: Segmentation fault, right?"
-	#emake all_p -C "${S}"_build/build
-
-	#
-	# Re: /usr/lib64/ncbi-tools++/libdbapi_driver.so: undefined reference to `ncbi::NcbiGetlineEOL(std::istream&, std::string&)'
-	#
-	# The next release should automatically address such underlinking, albeit
-	# only in --with-flat-makefile configurations.  For now (12.0.0), you'll need to
-	# add or extend more DLL_LIB settings, to which end you may find the
-	# resources at http://www.ncbi.nlm.nih.gov/IEB/ToolBox/CPP_DOC/depgraphs/
-	# helpful.  For instance,
-	#
-	# http://www.ncbi.nlm.nih.gov/IEB/ToolBox/CPP_DOC/depgraphs/dbapi_driver.html
-	#
-	# indicates that src/dbapi/driver/Makefile.dbapi_driver.lib should set
-	#
-	# DLL_LIB = xncbi
-	#
-	# (You can find the path to that makefile by examining
-	# .../status/.dbapi_driver.dep or .../build/Makefile.flat.)
-	#
-	# To take full advantage of --with-flat-makefile, you'll need the following (instead of 'emake all_p -C "${S}"_build/build') and call configure --with-flat-makefile:
-	emake -C "${S}"_build/build -f Makefile.flat
-}
-
-src_install() {
-	rm -rvf "${S}"_build/lib/ncbi || die
-	emake install prefix="${ED}/usr" libdir="${ED}/usr/$(get_libdir)/${PN}"
-
-#	dobin "${S}"_build/bin/*
-#	dolib.so "${S}"_build/lib/*so*
-#	dolib.a "${S}"_build/lib/*.a
-#	doheader "${S}"_build/inc/*
-
-	# File collisions with sci-biology/ncbi-tools
-	mv "${ED}"/usr/bin/asn2asn "${ED}"/usr/bin/asn2asn+
-	mv "${ED}"/usr/bin/rpsblast "${ED}"/usr/bin/rpsblast+
-	mv -f "${ED}"/usr/bin/test_regexp "${ED}"/usr/bin/test_regexp+ # drop the eventually mistakenly compiled binaries
-	mv "${ED}"/usr/bin/vecscreen "${ED}"/usr/bin/vecscreen+
-	mv "${ED}"/usr/bin/seedtop "${ED}"/usr/bin/seedtop+
-
-	echo "LDPATH=${EPREFIX}/usr/$(get_libdir)/${PN}" > ${S}/99${PN}
-	doenvd "${S}/99${PN}"
-}
-
-pkg_postinst() {
-	einfo 'Please run "source /etc/profile" before using this package in the current shell.'
-	einfo 'Documentation is at http://www.ncbi.nlm.nih.gov/books/NBK7167/'
-}
diff --git a/sci-biology/ncbi-blast+/ncbi-blast+-2.2.31.ebuild b/sci-biology/ncbi-blast+/ncbi-blast+-2.2.31.ebuild
deleted file mode 100644
index 4622ac976..000000000
--- a/sci-biology/ncbi-blast+/ncbi-blast+-2.2.31.ebuild
+++ /dev/null
@@ -1,354 +0,0 @@
-# Copyright 1999-2016 Gentoo Foundation
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=5
-
-PYTHON_COMPAT=( python2_7 )
-
-inherit eutils flag-o-matic multilib python-single-r1 toolchain-funcs
-
-MY_PV="2.2.30"
-MY_P="ncbi-blast-${PV}+-src"
-# workdir/ncbi-blast-2.2.30+-src
-# ftp://ftp.ncbi.nlm.nih.gov/blast/executables/blast+/2.2.30/ncbi-blast-2.2.30+-src.tar.gz
-
-DESCRIPTION="A subset of NCBI C++ Toolkit containing just the NCBI BLAST+"
-HOMEPAGE="http://www.ncbi.nlm.nih.gov/books/bv.fcgi?rid=toolkit"
-SRC_URI="
-	ftp://ftp.ncbi.nih.gov/blast/executables/blast+/${PV}/${MY_P}.tar.gz"
-#	http://dev.gentoo.org/~jlec/distfiles/${PN}-${PV#0.}-asneeded.patch.xz"
-
-# should also install ftp://ftp.ncbi.nlm.nih.gov/blast/db/taxdb.tar.gz
-# see http://www.biostars.org/p/76551/ and http://blastedbio.blogspot.cz/2012/05/blast-tabular-missing-descriptions.html
-LICENSE="public-domain"
-SLOT="0"
-IUSE="
-	debug static-libs static threads pch
-	test wxwidgets odbc
-	berkdb boost bzip2 cppunit curl expat fltk freetype gif
-	glut gnutls hdf5 icu jpeg lzo mesa mysql muparser opengl pcre png python
-	sablotron sqlite tiff xerces xalan xml xpm xslt X"
-KEYWORDS="~amd64 ~x86 ~amd64-linux ~x86-linux"
-#KEYWORDS=""
-
-REQUIRED_USE="${PYTHON_REQUIRED_USE}"
-
-# sys-libs/db should be compiled with USE=cxx
-DEPEND="
-	!sci-biology/ncbi-tools++
-	!sci-biology/sra_sdk
-	berkdb? ( sys-libs/db:4.3[cxx] )
-	boost? ( dev-libs/boost )
-	curl? ( net-misc/curl )
-	sqlite? ( dev-db/sqlite:3 )
-	mysql? ( virtual/mysql )
-	fltk? ( x11-libs/fltk )
-	opengl? ( virtual/opengl media-libs/glew:0= )
-	mesa? ( media-libs/mesa[osmesa] )
-	glut? ( media-libs/freeglut )
-	freetype? ( media-libs/freetype )
-	gnutls? ( net-libs/gnutls )
-	python? ( ${PYTHON_DEPS} )
-	cppunit? ( dev-util/cppunit )
-	icu? ( dev-libs/icu )
-	expat? ( dev-libs/expat )
-	sablotron? ( app-text/sablotron )
-	xml? ( dev-libs/libxml2 )
-	xslt? ( dev-libs/libxslt )
-	xerces? ( dev-libs/xerces-c )
-	xalan? ( dev-libs/xalan-c )
-	muparser? ( dev-cpp/muParser )
-	hdf5? ( sci-libs/hdf5[cxx] )
-	gif? ( media-libs/giflib )
-	jpeg? ( virtual/jpeg:0= )
-	png? ( media-libs/libpng:0= )
-	tiff? ( media-libs/tiff:0= )
-	xpm? ( x11-libs/libXpm )
-	dev-libs/lzo
-	app-arch/bzip2
-	dev-libs/libpcre"
-# USE flags which should be added somehow: wxWindows wxWidgets SP ORBacus ODBC OEChem sge
-# Intentionally omitted USE flags:
-#   ftds? ( dev-db/freetds ) # support for outside FreeTDS installations is currently broken.
-#                              The default (heavily patched) embedded copy should work, or you can
-#                              leave it off altogether -- the only public apps that make use of it are
-#                              samples and tests, since NCBI's database servers are of course firewalled.
-
-# seems muParser is required, also glew is required. configure exits otherwise if these are explicitly passed to it (due to USE flag enabled)
-
-RDEPEND="${DEPEND}"
-
-S="${WORKDIR}/${MY_P}/c++"
-# ncbi-blast-2.2.30+-src/c++
-
-src_prepare() {
-#	filter-ldflags -Wl,--as-needed
-#	append-ldflags -Wl,--no-undefined
-#	sed -i -e 's/-print-file-name=libstdc++.a//' \
-#		-e '/sed/ s/\([gO]\[0-9\]\)\*/\1\\+/' \
-#		src/build-system/configure || die
-#	epatch \
-#		"${FILESDIR}"/${PN}-${PV#0.}-fix-order-of-libs.patch \
-#		"${FILESDIR}"/curl-types.patch \
-#		"${FILESDIR}"/malloc_initialize_upstream_fix.patch \
-#		"${FILESDIR}"/respect_CXXFLAGS_configure.ac.patch \
-#		"${FILESDIR}"/respect_CXXFLAGS_configure.patch \
-#		"${FILESDIR}"/report_project_settings_configure.ac.patch \
-#		"${FILESDIR}"/report_project_settings_configure.patch \
-#		"${FILESDIR}"/make_install.patch
-
-#		"${FILESDIR}"/${PN}-${PV#0.}-disable_test_compress.patch
-
-#		"${FILESDIR}"/${PN}-${PV#0.}-gcc46.patch \
-#		"${FILESDIR}"/${PN}-${PV#0.}-gcc47.patch \
-#		"${WORKDIR}"/${PN}-${PV#0.}-asneeded.patch \
-#		"${FILESDIR}"/${PN}-${PV#0.}-libpng15.patch \
-#		"${FILESDIR}"/${PN}-${PV#0.}-glibc-214.patch
-
-#	use prefix && append-ldflags -Wl,-rpath,"${EPREFIX}/usr/$(get_libdir)/${PN}"
-
-# The conf-opts.patch and as-needed.patch need to be adjusted for 12.0.0 line numbers
-##	local PATCHES=(
-##		"${FILESDIR}"/${P}-conf-opts.patch
-##		"${FILESDIR}"/${P}-fix-svn-URL-upstream.patch
-##		"${FILESDIR}"/${P}-linkage-tuneups.patch
-##		"${FILESDIR}"/${P}-more-patches.patch
-##		"${FILESDIR}"/${P}-linkage-tuneups-addons.patch
-##		"${FILESDIR}"/${P}-configure.patch
-##		"${FILESDIR}"/${P}-drop-STATIC-from-LIB.patch
-##		"${FILESDIR}"/${P}-fix-install.patch
-##		)
-		# "${FILESDIR}"/${P}-support-autoconf-2.60.patch
-##	epatch ${PATCHES[@]}
-
-	# use a Debian patch from http://anonscm.debian.org/viewvc/debian-med/trunk/packages/ncbi-blast%2B/trunk/debian/patches/fix_lib_deps?revision=18535&view=markup
-	# the patches for 2.2.30+ do not apply to 2.2.31, mostly DLL_LIB is gone but somewhere
-	# it is still present, plus in a few places was something else patched
-	# staying without any patches for now and lets see is it works on Gentoo
-	# epatch "${FILESDIR}"/fix_lib_deps.patch
-	# make sure this one is the last one and contains the actual patches applied unless we can have autoconf-2.59 or 2.60
-	# https://bugs.gentoo.org/show_bug.cgi?id=514706
-
-	tc-export CXX CC
-
-##	cd src/build-system || die
-#	eautoreconf
-
-	# Temporarily disabling eautoconf because we patch configure via ${P}-support-autoconf-2.60.patch
-	# eautoconf # keep it disabled until we can ensure 2.59 is installed
-	# beware 12.0.0. and previous required autoconf-2.59, a patch for 12.0.0 brings autoconf-2.60 support
-}
-
-# possibly place modified contents of ${W}/src/build-system/config.site.ncbi and {W}/src/build-system/config.site.ex into ${W}/src/build-system/config.site
-src_configure() {
-	local myconf=()
-	#--without-optimization  turn off optimization flags in non-debug mode
-	#--with-profiling        build profiled versions of libs and apps
-	#--with-tcheck(=DIR)     build for Intel Thread Checker (in DIR)
-	#--with-plugin-auto-load always enable the plugin manager by default
-	#--with-bundles          build bundles in addition to dylibs on Mac OS X
-	#--with-bin-release      build executables suitable for public release
-	#	no dll and such
-	#--with-64               compile to 64-bit code
-	#--with-universal        build universal binaries on Mac OS X
-	#--with-universal=CPUs   build universal binaries targeting the given CPUs
-	#--without-exe           do not build executables
-	#--with-relative-runpath=P specify an executable-relative DLL search path
-	#--with-hard-runpath     hard-code runtime path, ignoring LD_LIBRARY_PATH
-	#--with-limited-linker   don't attempt to build especially large projects
-	#--with-extra-action=    script to call after the configuration is complete
-	#--with-autodep          automatic generation of dependencies (GNU make)
-	#--with-fake-root=DIR    appear to have been built under DIR
-	#--with-build-root-sfx=X add a user-specified suffix to the build dir name
-	#--without-execopy       do not copy built executables to the BIN area
-	#--with-lib-rebuilds     ensure that apps use up-to-date libraries
-	#--with-lib-rebuilds=ask ask whether to update each app's libraries
-	#--without-deactivation  keep old copies of libraries that no longer build
-	#--without-makefile-auto-update  do not auto-update generated makefiles
-	#--with-projects=FILE    build projects listed in FILE by default
-	#--without-flat-makefile do not generate an all-encompassing flat makefile
-	#--with-configure-dialog allow interactive flat makefile project selection
-	#--with-saved-settings=F load configuration settings from the file F
-	#--with-check-tools=...  use the specified tools for testing
-	#--with-ncbi-public      ensure compatibility for all in-house platforms
-	#--with-sybase-local=DIR use local SYBASE install (DIR is optional)
-	#--with-sybase-new       use newer SYBASE install (12.5 rather than 12.0)
-	#--without-sp            do not use SP libraries
-	#--without-orbacus       do not use ORBacus CORBA libraries
-	#--with-orbacus=DIR      use ORBacus installation in DIR
-	#--with-jni(=JDK-DIR)    build Java bindings (against the JDK in JDK-DIR)
-	#--with-sablot=DIR       use Sablotron installation in DIR
-	#--without-sablot,       do not use Sablotron
-	#--with-oechem=DIR       use OpenEye OEChem installation in DIR
-	#--without-oechem        do not use OEChem
-	#--with-sge=DIR          use Sun Grid Engine installation in DIR
-	#--without-sge           do not use Sun Grid Engine
-	#--with-magic=DIR        use libmagic installation in DIR
-	#--without-magic         do not use libmagic
-	#--without-local-lbsm    turn off support for IPC with locally running LBSMD
-	#--without-ncbi-crypt    use a dummy stubbed-out version of ncbi_crypt
-	#--without-connext       do not build non-public CONNECT library extensions
-	#--without-serial        do not build the serialization library and tools
-	#--without-objects       do not generate/build serializeable objects from ASNs
-	#--without-dbapi         do not build database connectivity libraries
-	#--without-app           do not build standalone applications like ID1_FETCH
-	#--without-gui           do not build most graphical projects
-	#--without-algo          do not build CPU-intensive algorithms
-	#--without-internal      do not build internal projects
-	#--with-gbench           ensure that Genome Workbench can be built
-	#--without-gbench        do not build Genome Workbench
-	myconf+=(
-	--with-dll
-	--with-lfs
-	--with-build-root="${S}"_build
-	--without-suffix
-	--without-hostspec
-	--without-version
-	--with-bincopy
-	--without-strip
-	--without-ccache
-	--without-distcc
-#	--with-ncbi-c
-	--without-ctools
-#	--with-sss
-#	--with-sssutils
-#	--with-sssdb
-#	--with-included-sss
-	--with-z="${EPREFIX}/usr"
-	--with-bz2="${EPREFIX}/usr"
-	--without-sybase
-	--with-autodep
-#	--with-3psw=std:netopt favor standard (system) builds of the above pkgs
-	$(use_with debug)
-	$(use_with debug max-debug)
-	$(use_with debug symbols)
-	$(use_with static-libs static)
-	$(use_with static static-exe)
-	$(use_with threads mt)
-	$(use_with prefix runpath "${EPREFIX}/usr/$(get_libdir)/${PN}")
-	$(use_with test check)
-	$(use_with pch)
-	$(use_with lzo lzo "${EPREFIX}/usr")
-	$(use_with pcre pcre "${EPREFIX}/usr")
-	$(use_with gnutls gnutls "${EPREFIX}/usr")
-	$(use_with mysql mysql "${EPREFIX}/usr")
-	$(use_with muparser muparser "${EPREFIX}/usr")
-	$(usex fltk --with-fltk="${EPREFIX}/usr" "")
-	$(use_with opengl opengl "${EPREFIX}/usr")
-	$(use_with mesa mesa "${EPREFIX}/usr")
-	$(use_with opengl glut "${EPREFIX}/usr")
-	$(use_with opengl glew "${EPREFIX}/usr")
-	$(use_with opengl glew-mx)
-	$(use_with wxwidgets wxwidgets "${EPREFIX}/usr")
-	$(use_with wxwidgets wxwidgets-ucs)
-	$(use_with freetype freetype "${EPREFIX}/usr")
-#	$(use_with berkdb bdb "${EPREFIX}/usr") # not in ncbi-blast+
-	$(usex odbc --with-odbc="${EPREFIX}/usr" "")
-	$(use_with python python "${EPREFIX}/usr")
-	$(use_with boost boost "${EPREFIX}/usr")
-	$(use_with sqlite sqlite3 "${EPREFIX}/usr")
-	$(use_with icu icu "${EPREFIX}/usr")
-	$(use_with expat expat "${EPREFIX}/usr")
-	$(use_with xml libxml "${EPREFIX}/usr")
-	$(use_with xml libxslt "${EPREFIX}/usr")
-	$(use_with xerces xerces "${EPREFIX}/usr")
-	$(use_with hdf5 hdf5 "${EPREFIX}/usr")
-	$(use_with xalan xalan "${EPREFIX}/usr")
-#	$(use_with gif gif "${EPREFIX}/usr") # prevent compilation failure in "ncbi-tools++-12.0.0/src/util/image/image_io_gif.cpp:351: error: 'QuantizeBuffer' was not declared in this scope"
-	--without-gif
-	$(use_with jpeg jpeg "${EPREFIX}/usr")
-	$(use_with tiff tiff "${EPREFIX}/usr")
-	$(use_with png png "${EPREFIX}/usr")
-	$(use_with xpm xpm "${EPREFIX}/usr")
-	$(use_with curl curl "${EPREFIX}/usr")
-#	$(use_with X x "${EPREFIX}/usr")
-#	$(use_with X x) # there is no --with-x option
-	)
-
-	# http://www.ncbi.nlm.nih.gov/books/NBK7167/
-	use test ||	myconf+=( --with-projects="${FILESDIR}"/disable-testsuite-compilation.txt )
-
-	# TODO
-	# copy optimization -O options from CXXFLAGS to DEF_FAST_FLAGS and pass that also to configure
-	# otherwise your -O2 will be dropped in some subdirectories and replaced by e.g. -O9
-
-	einfo "bash ./src/build-system/configure --srcdir="${S}" --prefix="${EPREFIX}/usr" --libdir=/usr/lib64 ${myconf[@]}"
-
-#	ECONF_SOURCE="src/build-system" \
-#		econf \
-	bash \
-		./src/build-system/configure \
-		--srcdir="${S}" \
-		--prefix="${EPREFIX}/usr" \
-		--libdir=/usr/lib64 \
-		--with-flat-makefile \
-		${myconf[@]} || die
-#--without-debug \
-#		--with-bin-release \
-#		--with-bincopy \
-#		--without-static \
-#		--with-dll \
-#		--with-mt \
-#		--with-openmp \
-#		--with-lfs \
-#		--prefix="${ED}"/usr \
-#		--libdir="${ED}"/usr/$(get_libdir)/"${PN}" \
-#		${myconf} LDFLAGS="-Wl,--no-as-needed" \
-#		|| die
-#	econf ${myconf[@]}
-}
-
-src_compile() {
-	## all_r would ignore the --with-projects contents and build more
-	## emake all_r -C GCC*-Release*/build || die
-	## all_p with compile only selected/required components
-	##cd "${S}"_build &&\
-	##emake all_p -C GCC*-Release*/build || die "gcc-4.5.3 crashes at src/objects/valerr/ValidError.cpp:226:1: internal compiler error: Segmentation fault, right?"
-	#emake all_p -C "${S}"_build/build
-
-	#
-	# Re: /usr/lib64/ncbi-tools++/libdbapi_driver.so: undefined reference to `ncbi::NcbiGetlineEOL(std::istream&, std::string&)'
-	#
-	# The next release should automatically address such underlinking, albeit
-	# only in --with-flat-makefile configurations.  For now (12.0.0), you'll need to
-	# add or extend more DLL_LIB settings, to which end you may find the
-	# resources at http://www.ncbi.nlm.nih.gov/IEB/ToolBox/CPP_DOC/depgraphs/
-	# helpful.  For instance,
-	#
-	# http://www.ncbi.nlm.nih.gov/IEB/ToolBox/CPP_DOC/depgraphs/dbapi_driver.html
-	#
-	# indicates that src/dbapi/driver/Makefile.dbapi_driver.lib should set
-	#
-	# DLL_LIB = xncbi
-	#
-	# (You can find the path to that makefile by examining
-	# .../status/.dbapi_driver.dep or .../build/Makefile.flat.)
-	#
-	# To take full advantage of --with-flat-makefile, you'll need the following (instead of 'emake all_p -C "${S}"_build/build') and call configure --with-flat-makefile:
-	emake -C "${S}"_build/build -f Makefile.flat
-}
-
-src_install() {
-	rm -rvf "${S}"_build/lib/ncbi || die
-	emake install prefix="${ED}/usr" libdir="${ED}/usr/$(get_libdir)/${PN}"
-
-#	dobin "${S}"_build/bin/*
-#	dolib.so "${S}"_build/lib/*so*
-#	dolib.a "${S}"_build/lib/*.a
-#	doheader "${S}"_build/inc/*
-
-	# File collisions with sci-biology/ncbi-tools
-	mv "${ED}"/usr/bin/asn2asn "${ED}"/usr/bin/asn2asn+
-	mv "${ED}"/usr/bin/rpsblast "${ED}"/usr/bin/rpsblast+
-	mv -f "${ED}"/usr/bin/test_regexp "${ED}"/usr/bin/test_regexp+ # drop the eventually mistakenly compiled binaries
-	mv "${ED}"/usr/bin/vecscreen "${ED}"/usr/bin/vecscreen+
-	mv "${ED}"/usr/bin/seedtop "${ED}"/usr/bin/seedtop+
-
-	echo "LDPATH=${EPREFIX}/usr/$(get_libdir)/${PN}" > ${S}/99${PN}
-	doenvd "${S}/99${PN}"
-}
-
-pkg_postinst() {
-	einfo 'Please run "source /etc/profile" before using this package in the current shell.'
-	einfo 'Documentation is at http://www.ncbi.nlm.nih.gov/books/NBK7167/'
-}
diff --git a/sci-biology/ncbi-blast+/ncbi-blast+-2.6.0.ebuild b/sci-biology/ncbi-blast+/ncbi-blast+-2.6.0.ebuild
deleted file mode 100644
index 6adbefad3..000000000
--- a/sci-biology/ncbi-blast+/ncbi-blast+-2.6.0.ebuild
+++ /dev/null
@@ -1,359 +0,0 @@
-# Copyright 1999-2017 Gentoo Foundation
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=5
-
-PYTHON_COMPAT=( python2_7 )
-
-inherit eutils flag-o-matic multilib python-single-r1 toolchain-funcs
-
-MY_PV="2.3.0"
-MY_P="ncbi-blast-${PV}+-src"
-# workdir/ncbi-blast-2.2.30+-src
-# ftp://ftp.ncbi.nlm.nih.gov/blast/executables/blast+/2.2.30/ncbi-blast-2.2.30+-src.tar.gz
-# ftp://ftp.ncbi.nlm.nih.gov/blast/executables/blast+/LATEST/ncbi-blast-2.3.0+-src.tar.gz
-
-DESCRIPTION="A subset of NCBI C++ Toolkit containing just the NCBI BLAST+"
-HOMEPAGE="http://www.ncbi.nlm.nih.gov/books/bv.fcgi?rid=toolkit"
-SRC_URI="
-	ftp://ftp.ncbi.nih.gov/blast/executables/blast+/${PV}/${MY_P}.tar.gz"
-#	http://dev.gentoo.org/~jlec/distfiles/${PN}-${PV#0.}-asneeded.patch.xz"
-
-# should also install ftp://ftp.ncbi.nlm.nih.gov/blast/db/taxdb.tar.gz
-# see http://www.biostars.org/p/76551/ and http://blastedbio.blogspot.cz/2012/05/blast-tabular-missing-descriptions.html
-LICENSE="public-domain"
-SLOT="0"
-IUSE="
-	debug static-libs static threads pch
-	test wxwidgets odbc
-	berkdb boost bzip2 cppunit curl expat fltk freetype gif
-	glut gnutls hdf5 icu jpeg lzo mesa mysql muparser opengl pcre png python
-	sablotron sqlite tiff xerces xalan xml xpm xslt X"
-KEYWORDS="~amd64 ~x86 ~amd64-linux ~x86-linux"
-#KEYWORDS=""
-
-REQUIRED_USE="${PYTHON_REQUIRED_USE}"
-
-# sys-libs/db should be compiled with USE=cxx
-DEPEND="
-	!sci-biology/ncbi-tools++
-	!sci-biology/sra_sdk
-	berkdb? ( sys-libs/db:4.3[cxx] )
-	boost? ( dev-libs/boost )
-	curl? ( net-misc/curl )
-	sqlite? ( dev-db/sqlite:3 )
-	mysql? ( virtual/mysql )
-	fltk? ( x11-libs/fltk )
-	opengl? ( virtual/opengl media-libs/glew:0= )
-	mesa? ( media-libs/mesa[osmesa] )
-	glut? ( media-libs/freeglut )
-	freetype? ( media-libs/freetype )
-	gnutls? ( net-libs/gnutls )
-	python? ( ${PYTHON_DEPS} )
-	cppunit? ( dev-util/cppunit )
-	icu? ( dev-libs/icu )
-	expat? ( dev-libs/expat )
-	sablotron? ( app-text/sablotron )
-	xml? ( dev-libs/libxml2 )
-	xslt? ( dev-libs/libxslt )
-	xerces? ( dev-libs/xerces-c )
-	xalan? ( dev-libs/xalan-c )
-	muparser? ( dev-cpp/muParser )
-	hdf5? ( sci-libs/hdf5[cxx] )
-	gif? ( media-libs/giflib )
-	jpeg? ( virtual/jpeg:0= )
-	png? ( media-libs/libpng:0= )
-	tiff? ( media-libs/tiff:0= )
-	xpm? ( x11-libs/libXpm )
-	dev-libs/lzo
-	app-arch/bzip2
-	dev-libs/libpcre"
-# USE flags which should be added somehow: wxWindows wxWidgets SP ORBacus ODBC OEChem sge
-# Intentionally omitted USE flags:
-#   ftds? ( dev-db/freetds ) # support for outside FreeTDS installations is currently broken.
-#                              The default (heavily patched) embedded copy should work, or you can
-#                              leave it off altogether -- the only public apps that make use of it are
-#                              samples and tests, since NCBI's database servers are of course firewalled.
-
-# seems muParser is required, also glew is required. configure exits otherwise if these are explicitly passed to it (due to USE flag enabled)
-
-RDEPEND="${DEPEND}"
-
-S="${WORKDIR}/${MY_P}/c++"
-# ncbi-blast-2.2.30+-src/c++
-
-src_prepare() {
-#	filter-ldflags -Wl,--as-needed
-#	append-ldflags -Wl,--no-undefined
-#	sed -i -e 's/-print-file-name=libstdc++.a//' \
-#		-e '/sed/ s/\([gO]\[0-9\]\)\*/\1\\+/' \
-#		src/build-system/configure || die
-#	epatch \
-#		"${FILESDIR}"/${PN}-${PV#0.}-fix-order-of-libs.patch \
-#		"${FILESDIR}"/curl-types.patch \
-#		"${FILESDIR}"/malloc_initialize_upstream_fix.patch \
-#		"${FILESDIR}"/respect_CXXFLAGS_configure.ac.patch \
-#		"${FILESDIR}"/respect_CXXFLAGS_configure.patch \
-#		"${FILESDIR}"/report_project_settings_configure.ac.patch \
-#		"${FILESDIR}"/report_project_settings_configure.patch \
-#		"${FILESDIR}"/make_install.patch
-
-#		"${FILESDIR}"/${PN}-${PV#0.}-disable_test_compress.patch
-
-#		"${FILESDIR}"/${PN}-${PV#0.}-gcc46.patch \
-#		"${FILESDIR}"/${PN}-${PV#0.}-gcc47.patch \
-#		"${WORKDIR}"/${PN}-${PV#0.}-asneeded.patch \
-#		"${FILESDIR}"/${PN}-${PV#0.}-libpng15.patch \
-#		"${FILESDIR}"/${PN}-${PV#0.}-glibc-214.patch
-
-#	use prefix && append-ldflags -Wl,-rpath,"${EPREFIX}/usr/$(get_libdir)/${PN}"
-
-# The conf-opts.patch and as-needed.patch need to be adjusted for 12.0.0 line numbers
-##	local PATCHES=(
-##		"${FILESDIR}"/${P}-conf-opts.patch
-##		"${FILESDIR}"/${P}-fix-svn-URL-upstream.patch
-##		"${FILESDIR}"/${P}-linkage-tuneups.patch
-##		"${FILESDIR}"/${P}-more-patches.patch
-##		"${FILESDIR}"/${P}-linkage-tuneups-addons.patch
-##		"${FILESDIR}"/${P}-configure.patch
-##		"${FILESDIR}"/${P}-drop-STATIC-from-LIB.patch
-##		"${FILESDIR}"/${P}-fix-install.patch
-##		)
-		# "${FILESDIR}"/${P}-support-autoconf-2.60.patch
-##	epatch ${PATCHES[@]}
-
-	# use a Debian patch from http://anonscm.debian.org/viewvc/debian-med/trunk/packages/ncbi-blast%2B/trunk/debian/patches/fix_lib_deps?revision=18535&view=markup
-	# the patches for 2.2.30+ do not apply to 2.2.31, mostly DLL_LIB is gone but somewhere
-	# it is still present, plus in a few places was something else patched
-	# staying without any patches for now and lets see is it works on Gentoo
-	# epatch "${FILESDIR}"/fix_lib_deps.patch
-	# make sure this one is the last one and contains the actual patches applied unless we can have autoconf-2.59 or 2.60
-	# https://bugs.gentoo.org/show_bug.cgi?id=514706
-
-	tc-export CXX CC
-
-##	cd src/build-system || die
-#	eautoreconf
-
-	# Temporarily disabling eautoconf because we patch configure via ${P}-support-autoconf-2.60.patch
-	# eautoconf # keep it disabled until we can ensure 2.59 is installed
-	# beware 12.0.0. and previous required autoconf-2.59, a patch for 12.0.0 brings autoconf-2.60 support
-}
-
-# possibly place modified contents of ${W}/src/build-system/config.site.ncbi and {W}/src/build-system/config.site.ex into ${W}/src/build-system/config.site
-src_configure() {
-	local myconf=()
-	#--without-optimization  turn off optimization flags in non-debug mode
-	#--with-profiling        build profiled versions of libs and apps
-	#--with-tcheck(=DIR)     build for Intel Thread Checker (in DIR)
-	#--with-plugin-auto-load always enable the plugin manager by default
-	#--with-bundles          build bundles in addition to dylibs on Mac OS X
-	#--with-bin-release      build executables suitable for public release
-	#	no dll and such
-	#--with-64               compile to 64-bit code
-	#--with-universal        build universal binaries on Mac OS X
-	#--with-universal=CPUs   build universal binaries targeting the given CPUs
-	#--without-exe           do not build executables
-	#--with-relative-runpath=P specify an executable-relative DLL search path
-	#--with-hard-runpath     hard-code runtime path, ignoring LD_LIBRARY_PATH
-	#--with-limited-linker   don't attempt to build especially large projects
-	#--with-extra-action=    script to call after the configuration is complete
-	#--with-autodep          automatic generation of dependencies (GNU make)
-	#--with-fake-root=DIR    appear to have been built under DIR
-	#--with-build-root-sfx=X add a user-specified suffix to the build dir name
-	#--without-execopy       do not copy built executables to the BIN area
-	#--with-lib-rebuilds     ensure that apps use up-to-date libraries
-	#--with-lib-rebuilds=ask ask whether to update each app's libraries
-	#--without-deactivation  keep old copies of libraries that no longer build
-	#--without-makefile-auto-update  do not auto-update generated makefiles
-	#--with-projects=FILE    build projects listed in FILE by default
-	#--without-flat-makefile do not generate an all-encompassing flat makefile
-	#--with-configure-dialog allow interactive flat makefile project selection
-	#--with-saved-settings=F load configuration settings from the file F
-	#--with-check-tools=...  use the specified tools for testing
-	#--with-ncbi-public      ensure compatibility for all in-house platforms
-	#--with-sybase-local=DIR use local SYBASE install (DIR is optional)
-	#--with-sybase-new       use newer SYBASE install (12.5 rather than 12.0)
-	#--without-sp            do not use SP libraries
-	#--without-orbacus       do not use ORBacus CORBA libraries
-	#--with-orbacus=DIR      use ORBacus installation in DIR
-	#--with-jni(=JDK-DIR)    build Java bindings (against the JDK in JDK-DIR)
-	#--with-sablot=DIR       use Sablotron installation in DIR
-	#--without-sablot,       do not use Sablotron
-	#--with-oechem=DIR       use OpenEye OEChem installation in DIR
-	#--without-oechem        do not use OEChem
-	#--with-sge=DIR          use Sun Grid Engine installation in DIR
-	#--without-sge           do not use Sun Grid Engine
-	#--with-magic=DIR        use libmagic installation in DIR
-	#--without-magic         do not use libmagic
-	#--without-local-lbsm    turn off support for IPC with locally running LBSMD
-	#--without-ncbi-crypt    use a dummy stubbed-out version of ncbi_crypt
-	#--without-connext       do not build non-public CONNECT library extensions
-	#--without-serial        do not build the serialization library and tools
-	#--without-objects       do not generate/build serializeable objects from ASNs
-	#--without-dbapi         do not build database connectivity libraries
-	#--without-app           do not build standalone applications like ID1_FETCH
-	#--without-gui           do not build most graphical projects
-	#--without-algo          do not build CPU-intensive algorithms
-	#--without-internal      do not build internal projects
-	#--with-gbench           ensure that Genome Workbench can be built
-	#--without-gbench        do not build Genome Workbench
-	myconf+=(
-	--with-dll
-	--with-lfs
-	--with-build-root="${S}"_build
-	--without-suffix
-	--without-hostspec
-	--without-version
-	--with-bincopy
-	--without-strip
-	--without-ccache
-	--without-distcc
-#	--with-ncbi-c
-	--without-ctools
-#	--with-sss
-#	--with-sssutils
-#	--with-sssdb
-#	--with-included-sss
-	--with-z="${EPREFIX}/usr"
-	--with-bz2="${EPREFIX}/usr"
-	--without-sybase
-	--with-autodep
-#	--with-3psw=std:netopt favor standard (system) builds of the above pkgs
-	$(use_with debug)
-	$(use_with debug max-debug)
-	$(use_with debug symbols)
-	$(use_with static-libs static)
-	$(use_with static static-exe)
-	$(use_with threads mt)
-	$(use_with prefix runpath "${EPREFIX}/usr/$(get_libdir)/${PN}")
-	$(use_with test check)
-	$(use_with pch)
-	$(use_with lzo lzo "${EPREFIX}/usr")
-	$(use_with pcre pcre "${EPREFIX}/usr")
-	$(use_with gnutls gnutls "${EPREFIX}/usr")
-	$(use_with mysql mysql "${EPREFIX}/usr")
-	$(use_with muparser muparser "${EPREFIX}/usr")
-	$(usex fltk --with-fltk="${EPREFIX}/usr" "")
-	$(use_with opengl opengl "${EPREFIX}/usr")
-	$(use_with mesa mesa "${EPREFIX}/usr")
-	$(use_with opengl glut "${EPREFIX}/usr")
-	$(use_with opengl glew "${EPREFIX}/usr")
-	#
-	# GLEW 2.0 dropped support for this, see https://bugs.gentoo.org/show_bug.cgi?id=611302
-	# $(use_with opengl glew-mx)
-	$(use_with wxwidgets wxwidgets "${EPREFIX}/usr")
-	$(use_with wxwidgets wxwidgets-ucs)
-	$(use_with freetype freetype "${EPREFIX}/usr")
-#	$(use_with berkdb bdb "${EPREFIX}/usr") # not in ncbi-blast+
-	$(usex odbc --with-odbc="${EPREFIX}/usr" "")
-	$(use_with python python "${EPREFIX}/usr")
-	$(use_with boost boost "${EPREFIX}/usr")
-	$(use_with sqlite sqlite3 "${EPREFIX}/usr")
-	$(use_with icu icu "${EPREFIX}/usr")
-	$(use_with expat expat "${EPREFIX}/usr")
-	$(use_with xml libxml "${EPREFIX}/usr")
-	$(use_with xml libxslt "${EPREFIX}/usr")
-	$(use_with xerces xerces "${EPREFIX}/usr")
-	$(use_with hdf5 hdf5 "${EPREFIX}/usr")
-	$(use_with xalan xalan "${EPREFIX}/usr")
-#	$(use_with gif gif "${EPREFIX}/usr") # prevent compilation failure in "ncbi-tools++-12.0.0/src/util/image/image_io_gif.cpp:351: error: 'QuantizeBuffer' was not declared in this scope"
-	--without-gif
-	$(use_with jpeg jpeg "${EPREFIX}/usr")
-	$(use_with tiff tiff "${EPREFIX}/usr")
-	$(use_with png png "${EPREFIX}/usr")
-	$(use_with xpm xpm "${EPREFIX}/usr")
-	$(use_with curl curl "${EPREFIX}/usr")
-#	$(use_with X x "${EPREFIX}/usr")
-#	$(use_with X x) # there is no --with-x option
-	# prevent downloading VDB sources from https://github.com/ncbi/ncbi-vdb.git during configure execution
-	--without-vdb
-	)
-
-	# http://www.ncbi.nlm.nih.gov/books/NBK7167/
-	use test ||	myconf+=( --with-projects="${FILESDIR}"/disable-testsuite-compilation.txt )
-
-	# TODO
-	# copy optimization -O options from CXXFLAGS to DEF_FAST_FLAGS and pass that also to configure
-	# otherwise your -O2 will be dropped in some subdirectories and replaced by e.g. -O9
-
-	einfo "bash ./src/build-system/configure --srcdir="${S}" --prefix="${EPREFIX}/usr" --libdir=/usr/lib64 ${myconf[@]}"
-
-#	ECONF_SOURCE="src/build-system" \
-#		econf \
-	bash \
-		./src/build-system/configure \
-		--srcdir="${S}" \
-		--prefix="${EPREFIX}/usr" \
-		--libdir=/usr/lib64 \
-		--with-flat-makefile \
-		${myconf[@]} || die
-#--without-debug \
-#		--with-bin-release \
-#		--with-bincopy \
-#		--without-static \
-#		--with-dll \
-#		--with-mt \
-#		--with-openmp \
-#		--with-lfs \
-#		--prefix="${ED}"/usr \
-#		--libdir="${ED}"/usr/$(get_libdir)/"${PN}" \
-#		${myconf} LDFLAGS="-Wl,--no-as-needed" \
-#		|| die
-#	econf ${myconf[@]}
-}
-
-src_compile() {
-	## all_r would ignore the --with-projects contents and build more
-	## emake all_r -C GCC*-Release*/build || die
-	## all_p with compile only selected/required components
-	##cd "${S}"_build &&\
-	##emake all_p -C GCC*-Release*/build || die "gcc-4.5.3 crashes at src/objects/valerr/ValidError.cpp:226:1: internal compiler error: Segmentation fault, right?"
-	#emake all_p -C "${S}"_build/build
-
-	#
-	# Re: /usr/lib64/ncbi-tools++/libdbapi_driver.so: undefined reference to `ncbi::NcbiGetlineEOL(std::istream&, std::string&)'
-	#
-	# The next release should automatically address such underlinking, albeit
-	# only in --with-flat-makefile configurations.  For now (12.0.0), you'll need to
-	# add or extend more DLL_LIB settings, to which end you may find the
-	# resources at http://www.ncbi.nlm.nih.gov/IEB/ToolBox/CPP_DOC/depgraphs/
-	# helpful.  For instance,
-	#
-	# http://www.ncbi.nlm.nih.gov/IEB/ToolBox/CPP_DOC/depgraphs/dbapi_driver.html
-	#
-	# indicates that src/dbapi/driver/Makefile.dbapi_driver.lib should set
-	#
-	# DLL_LIB = xncbi
-	#
-	# (You can find the path to that makefile by examining
-	# .../status/.dbapi_driver.dep or .../build/Makefile.flat.)
-	#
-	# To take full advantage of --with-flat-makefile, you'll need the following (instead of 'emake all_p -C "${S}"_build/build') and call configure --with-flat-makefile:
-	emake -C "${S}"_build/build -f Makefile.flat
-}
-
-src_install() {
-	rm -rvf "${S}"_build/lib/ncbi || die
-	emake install prefix="${ED}/usr" libdir="${ED}/usr/$(get_libdir)/${PN}"
-
-#	dobin "${S}"_build/bin/*
-#	dolib.so "${S}"_build/lib/*so*
-#	dolib.a "${S}"_build/lib/*.a
-#	doheader "${S}"_build/inc/*
-
-	# File collisions with sci-biology/ncbi-tools
-	mv "${ED}"/usr/bin/asn2asn "${ED}"/usr/bin/asn2asn+
-	mv "${ED}"/usr/bin/rpsblast "${ED}"/usr/bin/rpsblast+
-	mv -f "${ED}"/usr/bin/test_regexp "${ED}"/usr/bin/test_regexp+ # drop the eventually mistakenly compiled binaries
-	mv "${ED}"/usr/bin/vecscreen "${ED}"/usr/bin/vecscreen+
-	mv "${ED}"/usr/bin/seedtop "${ED}"/usr/bin/seedtop+
-
-	echo "LDPATH=${EPREFIX}/usr/$(get_libdir)/${PN}" > ${S}/99${PN}
-	doenvd "${S}/99${PN}"
-}
-
-pkg_postinst() {
-	einfo 'Please run "source /etc/profile" before using this package in the current shell.'
-	einfo 'Documentation is at http://www.ncbi.nlm.nih.gov/books/NBK7167/'
-}
diff --git a/sci-biology/ncbi-genome-download/Manifest b/sci-biology/ncbi-genome-download/Manifest
deleted file mode 100644
index 93f87bdd3..000000000
--- a/sci-biology/ncbi-genome-download/Manifest
+++ /dev/null
@@ -1 +0,0 @@
-DIST ncbi-genome-download-0.2.2.tar.gz 17601 BLAKE2B fd3b132d67d6e81429b2d6f1078a588ed2efb71d847bd5ca6cc5b934cf136b18d93e2afa25393f8c4e296ea7f8c13e7bf0c95700480f899fbbbc377863896594 SHA512 da5ccc00d02db272b647e89f27caea1c396776b3a548882bb04b7385cece6105abcc8bb15cfed07a155d59d9442cb8e925697f814ada78a5c68be2ca042e186f
diff --git a/sci-biology/ncbi-genome-download/metadata.xml b/sci-biology/ncbi-genome-download/metadata.xml
deleted file mode 100644
index 0bd027def..000000000
--- a/sci-biology/ncbi-genome-download/metadata.xml
+++ /dev/null
@@ -1,12 +0,0 @@
-<?xml version="1.0" encoding="UTF-8"?>
-<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
-<pkgmetadata>
-	<maintainer type="person">
-		<email>freeh4cker@gmail.com</email>
-		<name>Bertrand Néron</name>
-	</maintainer>
-	<longdescription>Scripts to download genomes from the NCBI FTP servers.</longdescription>
-	<upstream>
-		<remote-id type="github">kblin/ncbi-genome-download</remote-id>
-	</upstream>
-</pkgmetadata>
diff --git a/sci-biology/ncbi-genome-download/ncbi-genome-download-0.2.2.ebuild b/sci-biology/ncbi-genome-download/ncbi-genome-download-0.2.2.ebuild
deleted file mode 100644
index fe3d0f2d4..000000000
--- a/sci-biology/ncbi-genome-download/ncbi-genome-download-0.2.2.ebuild
+++ /dev/null
@@ -1,20 +0,0 @@
-# Copyright 1999-2016 Gentoo Foundation
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=6
-
-PYTHON_COMPAT=( python2_7 python3_{4,5} )
-
-inherit distutils-r1 python-r1
-
-DESCRIPTION="Download genomes from the NCBI FTP servers"
-HOMEPAGE="https://github.com/kblin/ncbi-genome-download"
-SRC_URI="https://github.com/kblin/${PN}/archive/${PV}.tar.gz  -> ${P}.tar.gz"
-
-LICENSE="Apache-2.0"
-SLOT="0"
-KEYWORDS="~amd64 ~x86"
-IUSE=""
-
-DEPEND=""
-RDEPEND="${DEPEND}"
diff --git a/sci-biology/ncbi-tools++/Manifest b/sci-biology/ncbi-tools++/Manifest
deleted file mode 100644
index 0bf4ddb07..000000000
--- a/sci-biology/ncbi-tools++/Manifest
+++ /dev/null
@@ -1,2 +0,0 @@
-DIST ncbi_cxx--12_0_0.tar.gz 37925914 BLAKE2B 45490961293d8b3ace24c21602f4039041003f9b45d9f1763957c97ba1e55d6d336c33b6116262b2e774cc26b9366cc3d61bead0c0c7fbd4c461cad2921d80d4 SHA512 1a79f2d95960efde6263289814102499460ec235dad36337dd398d668665e44015e06e40fd0e66a8fb16f526d326949adcaadcb667debeba5d8570b1a92e30ed
-DIST ncbi_cxx--18_0_0.tar.gz 69807228 BLAKE2B 2221232e4ab38845708a9ec5601a94f1dd25c5dd6fff265bde3c3d64b9108eec00b8480a1888d2517881f25abe9127e547ba88528b95398480ecd09d133482a7 SHA512 70dd07597aafa3f48881640530bf2aeebcac6fa13843fada4c590ca101cb8fdfa1aabf240ed0177d371a1fc36c6d231d667125279096006cd1eba119ea9514f5
diff --git a/sci-biology/ncbi-tools++/files/curl-types.patch b/sci-biology/ncbi-tools++/files/curl-types.patch
deleted file mode 100644
index 3e6079057..000000000
--- a/sci-biology/ncbi-tools++/files/curl-types.patch
+++ /dev/null
@@ -1,24 +0,0 @@
-Index: libs/kns/url-fetcher-curl.c
-===================================================================
---- src/sra/sdk/libs/kns/url-fetcher-curl.c (revision 11878)
-+++ src/sra/sdk/libs/kns/url-fetcher-curl.c (revision 11880)
-@@ -38,7 +38,6 @@
- #include <string.h>
- 
- #include <curl/curl.h>
--#include <curl/types.h>
- #include <curl/easy.h>
- 
- /*--------------------------------------------------------------------------
-Index: tools/refseq-load/refseq-load.c
-===================================================================
---- src/sra/sdk/tools/refseq-load/refseq-load.c     (revision 11878)
-+++ src/sra/sdk/tools/refseq-load/refseq-load.c     (revision 11880)
-@@ -41,7 +41,6 @@
- #include <sysalloc.h>
- 
- #include <curl/curl.h>
--#include <curl/types.h>
- #include <curl/easy.h>
- 
- #include <stdlib.h>
diff --git a/sci-biology/ncbi-tools++/files/disable-testsuite-compilation.txt b/sci-biology/ncbi-tools++/files/disable-testsuite-compilation.txt
deleted file mode 100644
index 8df346f64..000000000
--- a/sci-biology/ncbi-tools++/files/disable-testsuite-compilation.txt
+++ /dev/null
@@ -1,4 +0,0 @@
-.*
--.*/test
--.*/unit_test
--.*/unit_tests
diff --git a/sci-biology/ncbi-tools++/files/make_install.patch b/sci-biology/ncbi-tools++/files/make_install.patch
deleted file mode 100644
index e98f1110d..000000000
--- a/sci-biology/ncbi-tools++/files/make_install.patch
+++ /dev/null
@@ -1,14 +0,0 @@
---- src/build-system/Makefile.in.top.old	2013-01-07 23:07:29.970141951 +0100
-+++ src/build-system/Makefile.in.top	2013-01-07 23:08:37.940990190 +0100
-@@ -39,7 +39,10 @@
- 	-$(RMDIR) $(pincludedir)
- 	$(INSTALL) -d $(bindir) $(libdir) $(pincludedir)
- 	$(INSTALL) $(lbindir)/* $(bindir)
--	$(INSTALL) -m 644 $(llibdir)/* $(libdir)
-+	$(INSTALL) -m 644 $(llibdir)/*.* $(libdir)
-+	if test -d $(llibdir)/ncbi; then \
-+	    cp -pPR $(llibdir)/ncbi $(libdir)/; \
-+	fi
- 	-rm -f $(libdir)/lib*-static.a
- 	cd $(libdir)  && \
- 	    for x in *.a; do ln -s "$$x" "`basename \"$$x\" .a`-static.a"; done
diff --git a/sci-biology/ncbi-tools++/files/malloc_initialize_upstream_fix.patch b/sci-biology/ncbi-tools++/files/malloc_initialize_upstream_fix.patch
deleted file mode 100644
index 4900e529a..000000000
--- a/sci-biology/ncbi-tools++/files/malloc_initialize_upstream_fix.patch
+++ /dev/null
@@ -1,100 +0,0 @@
---- trunk/c++/src/app/netcache/nc_memory.cpp    2011/12/16 17:42:54     52330
-+++ trunk/c++/src/app/netcache/nc_memory.cpp    2012/02/27 14:38:30     53136
-@@ -360,7 +360,7 @@
-     m_ObjLock.Lock();
-     ++m_SysFrees;
-     m_SystemMem -= alloced_size;
--    m_LostMem   -= alloced_size -= asked_size;
-+    m_LostMem   -= alloced_size - asked_size;
-     m_ObjLock.Unlock();
- }
- 
-@@ -2539,7 +2539,7 @@
- bool
- CNCMemManager::InitializeApp(void)
- {
--    try {
-+    /*try {
-         CSQLITE_Global::SetCustomMallocFuncs(&s_NCMallocMethods);
-     }
-     catch (CSQLITE_Exception& ex) {
-@@ -2547,13 +2547,15 @@
-         return false;
-     }
- 
--    return CNCMMCentral::RunLateInit();
-+    return CNCMMCentral::RunLateInit();*/
-+    g_InitNCThreadIndexes();
-+    return true;
- }
- 
- void
- CNCMemManager::FinalizeApp(void)
- {
--    CNCMMCentral::PrepareToStop();
-+    //CNCMMCentral::PrepareToStop();
- }
- 
- void
-@@ -2571,28 +2573,29 @@
- void
- CNCMemManager::PrintStats(CPrintTextProxy& proxy)
- {
--    CNCMMStats stats_sum;
-+    /*CNCMMStats stats_sum;
-     CNCMMStats::CollectAllStats(&stats_sum);
--    stats_sum.Print(proxy);
-+    stats_sum.Print(proxy);*/
- }
- 
- size_t
- CNCMemManager::GetMemoryLimit(void)
- {
--    return CNCMMCentral::GetMemLimit();
-+    return 0;//CNCMMCentral::GetMemLimit();
- }
- 
- size_t
- CNCMemManager::GetMemoryUsed(void)
- {
--    CNCMMStats stat;
-+    /*CNCMMStats stat;
-     CNCMMStats::CollectAllStats(&stat);
--    return stat.GetSystemMem();
-+    return stat.GetSystemMem();*/
-+    return 0;
- }
- 
- END_NCBI_SCOPE
- 
--
-+/*
- void*
- operator new (size_t size)
- #ifndef NCBI_COMPILER_MSVC
-@@ -2626,13 +2629,13 @@
- {
-     NCBI_NS_NCBI::CNCMMCentral::DeallocMemory(ptr);
- }
--
-+*/
- #ifdef __GLIBC__
- // glibc has special method of overriding C library allocation functions.
- 
- #include <malloc.h>
- 
--
-+/*
- void* s_NCMallocHook(size_t size, const void* caller)
- {
-     return NCBI_NS_NCBI::CNCMMCentral::AllocMemory(size);
-@@ -2656,7 +2659,7 @@
- }
- 
- void (*__malloc_initialize_hook) (void) = s_NCInitMallocHook;
--
-+*/
- #elif !defined(NCBI_OS_MSWIN)
- // Changing of C library allocation functions on Windows is very tricky (if
- // possible at all) and NetCache will never run in production on Windows. So
-
diff --git a/sci-biology/ncbi-tools++/files/ncbi-tools++-12.0.0-bdb6.patch b/sci-biology/ncbi-tools++/files/ncbi-tools++-12.0.0-bdb6.patch
deleted file mode 100644
index 9589481d4..000000000
--- a/sci-biology/ncbi-tools++/files/ncbi-tools++-12.0.0-bdb6.patch
+++ /dev/null
@@ -1,114 +0,0 @@
-Index: include/db/bdb/bdb_file.hpp
-===================================================================
---- include/db/bdb/bdb_file.hpp	(revision 470126)
-+++ include/db/bdb/bdb_file.hpp	(working copy)
-@@ -660,6 +660,9 @@
-     void x_ConstructKeyBuf();
-     void x_ConstructDataBuf();
- 
-+    static int x_CompareShim(DB* db, const DBT* dbt1, const DBT* dbt2,
-+                             size_t* locp);
-+
- private:
-     auto_ptr<CBDB_BufferManager>   m_KeyBuf;
-     auto_ptr<CBDB_BufferManager>   m_DataBuf;
-Index: src/db/bdb/bdb_blob.cpp
-===================================================================
---- src/db/bdb/bdb_blob.cpp	(revision 470126)
-+++ src/db/bdb/bdb_blob.cpp	(working copy)
-@@ -583,12 +583,31 @@
-     return m_DBT_Data->size;
- }
- 
-+#if DB_VERSION_MAJOR >= 6
-+extern "C" {
-+    typedef int (*BDB_CompareFunction_V6)(DB*, const DBT*, const DBT*,
-+                                          size_t*);
-+    int BDB_Uint4Compare_V6(DB* db, const DBT* dbt1, const DBT* dbt2, size_t*)
-+        { return BDB_Uint4Compare(db, dbt1, dbt2); }
-+    int BDB_ByteSwap_Uint4Compare_V6(DB* db, const DBT* dbt1, const DBT* dbt2,
-+                                    size_t*)
-+        { return BDB_ByteSwap_Uint4Compare(db, dbt1, dbt2); }
-+}
-+#endif
-+
- void CBDB_LobFile::SetCmp(DB*)
- {
-+#if DB_VERSION_MAJOR >= 6
-+    BDB_CompareFunction_V6 func = BDB_Uint4Compare_V6;
-+    if (IsByteSwapped()) {
-+        func = BDB_ByteSwap_Uint4Compare_V6;
-+    }
-+#else
-     BDB_CompareFunction func = BDB_Uint4Compare;
-     if (IsByteSwapped()) {
-         func = BDB_ByteSwap_Uint4Compare;
-     }
-+#endif
- 
-     _ASSERT(func);
-     int ret = m_DB->set_bt_compare(m_DB, func);
-Index: src/db/bdb/bdb_file.cpp
-===================================================================
---- src/db/bdb/bdb_file.cpp	(revision 470126)
-+++ src/db/bdb/bdb_file.cpp	(working copy)
-@@ -1535,12 +1535,27 @@
- }
- 
- 
-+#if DB_VERSION_MAJOR >= 6
-+int CBDB_File::x_CompareShim(DB* db, const DBT* dbt1, const DBT* dbt2, size_t*)
-+{
-+    const CBDB_BufferManager* key_buf
-+        = static_cast<const CBDB_BufferManager*>(db->app_private);
-+    _ASSERT(key_buf);
-+    return (key_buf->GetCompareFunction())(db, dbt1, dbt2);
-+}
-+#endif
-+
-+
- void CBDB_File::SetCmp(DB* db)
- {
-     _ASSERT(m_DB_Type == eBtree);
-+#if DB_VERSION_MAJOR >= 6
-+    int ret = db->set_bt_compare(db, x_CompareShim);
-+#else
-     BDB_CompareFunction func = m_KeyBuf->GetCompareFunction();
-     _ASSERT(func);
-     int ret = db->set_bt_compare(db, func);
-+#endif
-     BDB_CHECK(ret, 0);
- 
-     if (m_PrefixCompress) {
-@@ -2056,12 +2071,31 @@
-     BindKey("id", &IdKey);
- }
- 
-+#if DB_VERSION_MAJOR >= 6
-+extern "C" {
-+    typedef int (*BDB_CompareFunction_V6)(DB*, const DBT*, const DBT*,
-+                                          size_t*);
-+    int BDB_Int4Compare_V6(DB* db, const DBT* dbt1, const DBT* dbt2, size_t*)
-+        { return BDB_Int4Compare(db, dbt1, dbt2); }
-+    int BDB_ByteSwap_Int4Compare_V6(DB* db, const DBT* dbt1, const DBT* dbt2,
-+                                    size_t*)
-+        { return BDB_ByteSwap_Int4Compare(db, dbt1, dbt2); }
-+}
-+#endif
-+
- void CBDB_IdFile::SetCmp(DB* /* db */)
- {
-+#if DB_VERSION_MAJOR >= 6
-+    BDB_CompareFunction_V6 func = BDB_Int4Compare_V6;
-+    if (IsByteSwapped()) {
-+        func = BDB_ByteSwap_Int4Compare_V6;
-+    }
-+#else
-     BDB_CompareFunction func = BDB_Int4Compare;
-     if (IsByteSwapped()) {
-         func = BDB_ByteSwap_Int4Compare;
-     }
-+#endif
- 
-     _ASSERT(func);
-     int ret = m_DB->set_bt_compare(m_DB, func);
diff --git a/sci-biology/ncbi-tools++/files/ncbi-tools++-12.0.0-conf-opts.patch b/sci-biology/ncbi-tools++/files/ncbi-tools++-12.0.0-conf-opts.patch
deleted file mode 100644
index 3ed3e7d5f..000000000
--- a/sci-biology/ncbi-tools++/files/ncbi-tools++-12.0.0-conf-opts.patch
+++ /dev/null
@@ -1,64 +0,0 @@
- src/build-system/configure.ac | 17 ++++++++++++++---
- 1 file changed, 14 insertions(+), 3 deletions(-)
-
-diff --git a/src/build-system/configure.ac b/src/build-system/configure.ac
-index 03e34b4..336453d 100644
---- a/src/build-system/configure.ac
-+++ b/src/build-system/configure.ac
-@@ -224,7 +224,7 @@ AC_ARG_WITH(ncbi-c,
- AC_ARG_WITH(sss,
-    [ --without-sss           do not use NCBI SSS libraries])
- AC_ARG_WITH(sssutils,
--   [ --without-utils         do not use NCBI SSS UTIL library])
-+   [ --without-sssutils      do not use NCBI SSS UTIL library])
- AC_ARG_WITH(sssdb,
-    [ --without-sssdb         do not use NCBI SSS DB library])
- AC_ARG_WITH(included-sss,
-@@ -490,13 +490,13 @@ check ncbi-public strip pch caution ccache distcc \
- ncbi-c wxwidgets wxwidgets-ucs fastcgi sss sssdb sssutils included-sss \
- geo included-geo \
- z bz2 lzo pcre gcrypt gnutls openssl krb5 sybase sybase-local sybase-new \
--ftds mysql orbacus freetype ftgl opengl mesa glut glew glew-mx \
-+ftds mysql orbacus odbc freetype ftgl opengl mesa glut glew glew-mx \
- bdb python perl jni sqlite3 icu boost boost-tag \
- sp expat sablot libxml libxslt libexslt xerces xalan zorba \
- oechem sge muparser hdf5 \
- gif jpeg tiff png xpm magic curl mimetic 3psw \
- local-lbsm ncbi-crypt connext \
--serial objects dbapi app ctools gui algo internal gbench"
-+serial objects dbapi app ctools gui algo internal gbench x"
- 
- changequote(, )dnl
- x_with_list=`echo "$x_with_list" | sed 's/\([^ ][^ ]*\)/--with-\1 --without-\1/g'`
-@@ -522,6 +522,7 @@ for x_arg in "$@" ; do
-    case "$x_arg" in
-       --with-extra-action= | --exec-prefix= | --with-projects= | --srcdir= \
-       | --cache-file= | --build= | --host= | --target= | --with-runpath= \
-+      | --mandir= | --infodir= | --datadir= | --sysconfdir= | --localstatedir= \
-       | --with-relative-runpath= | --x-includes= | --x-libraries= )
-       AC_MSG_ERROR([$x_arg:  requires value;  use --help to show usage])
-       ;;
-@@ -532,6 +533,7 @@ for x_arg in "$@" ; do
-       | --with-universal=* | --with-tcheck=* \
-       | --cache-file=* | --build=* | --host=* | --prefix=* | --exec-prefix=* \
-       | --libdir=* | --bindir=* | --includedir=* | --srcdir=* \
-+      | --mandir=* | --infodir=* | --datadir=* | --sysconfdir=* | --localstatedir=* \
-       | [[A-Z]*=*] \
-       | --with-z=* | --with-bz2=* | --with-lzo=* \
-       | --with-pcre=* \
-@@ -647,6 +649,15 @@ if test -z "${DEF_FAST_FLAGS}${FAST_CXXFLAGS}"; then
-       *\ -O* | *\ -xO* ) skip_fast_flags=yes ;;
-    esac
- fi
-+if test -n "$with_projects"; then
-+   case "$with_projects" in
-+      /* ) abs_projects=$with_projects         ;;
-+      yes) abs_projects=$srcdir/projects       ;;
-+      *  ) abs_projects=$srcdir/$with_projects ;;
-+   esac
-+   test -r "$abs_projects"  ||  \
-+      AC_MSG_ERROR([unable to read requested projects file "$abs_projects".])
-+fi
- 
- #### Always define this
- AC_DEFINE(NCBI_CXX_TOOLKIT, 1, [This is the NCBI C++ Toolkit.])
diff --git a/sci-biology/ncbi-tools++/files/ncbi-tools++-12.0.0-configure.patch b/sci-biology/ncbi-tools++/files/ncbi-tools++-12.0.0-configure.patch
deleted file mode 100644
index d44993da2..000000000
--- a/sci-biology/ncbi-tools++/files/ncbi-tools++-12.0.0-configure.patch
+++ /dev/null
@@ -1,216 +0,0 @@
---- ncbi_cxx--12_0_0/src/build-system/configure.ori	2014-06-25 23:47:05.000000000 +0200
-+++ ncbi_cxx--12_0_0/src/build-system/configure	2014-06-25 23:52:35.000000000 +0200
-@@ -927,7 +927,7 @@
-  --without-distcc        do not automatically use distcc if available
-  --without-ncbi-c        do not use NCBI C Toolkit
-  --without-sss           do not use NCBI SSS libraries
-- --without-utils         do not use NCBI SSS UTIL library
-+ --without-sssutils      do not use NCBI SSS UTIL library
-  --without-sssdb         do not use NCBI SSS DB library
-  --with-included-sss     use the in-tree copy of SSS
-  --with-z=DIR            use zlib installation in DIR
-@@ -2965,13 +2965,13 @@
- ncbi-c wxwidgets wxwidgets-ucs fastcgi sss sssdb sssutils included-sss \
- geo included-geo \
- z bz2 lzo pcre gcrypt gnutls openssl krb5 sybase sybase-local sybase-new \
--ftds mysql orbacus freetype ftgl opengl mesa glut glew glew-mx \
-+ftds mysql orbacus odbc freetype ftgl opengl mesa glut glew glew-mx \
- bdb python perl jni sqlite3 icu boost boost-tag \
- sp expat sablot libxml libxslt libexslt xerces xalan zorba \
- oechem sge muparser hdf5 \
- gif jpeg tiff png xpm magic curl mimetic 3psw \
- local-lbsm ncbi-crypt connext \
--serial objects dbapi app ctools gui algo internal gbench"
-+serial objects dbapi app ctools gui algo internal gbench x"
- 
- x_with_list=`echo "$x_with_list" | sed 's/\([^ ][^ ]*\)/--with-\1 --without-\1/g'`
- 
-@@ -2995,6 +2995,7 @@
-    case "$x_arg" in
-       --with-extra-action= | --exec-prefix= | --with-projects= | --srcdir= \
-       | --cache-file= | --build= | --host= | --target= | --with-runpath= \
-+      | --mandir= | --infodir= | --datadir= | --sysconfdir= | --localstatedir= \
-       | --with-relative-runpath= | --x-includes= | --x-libraries= )
-       { { echo "$as_me:$LINENO: error: $x_arg:  requires value;  use --help to show usage" >&5
- echo "$as_me: error: $x_arg:  requires value;  use --help to show usage" >&2;}
-@@ -3007,6 +3008,7 @@
-       | --with-universal=* | --with-tcheck=* \
-       | --cache-file=* | --build=* | --host=* | --prefix=* | --exec-prefix=* \
-       | --libdir=* | --bindir=* | --includedir=* | --srcdir=* \
-+      | --mandir=* | --infodir=* | --datadir=* | --sysconfdir=* | --localstatedir=* \
-       | [A-Z]*=* \
-       | --with-z=* | --with-bz2=* | --with-lzo=* \
-       | --with-pcre=* \
-@@ -3201,6 +3203,17 @@
-       *\ -O* | *\ -xO* ) skip_fast_flags=yes ;;
-    esac
- fi
-+if test -n "$with_projects"; then
-+   case "$with_projects" in
-+      /* ) abs_projects=$with_projects         ;;
-+      yes) abs_projects=$srcdir/projects       ;;
-+      *  ) abs_projects=$srcdir/$with_projects ;;
-+   esac
-+   test -r "$abs_projects"  ||  \
-+      { { echo "$as_me:$LINENO: error: unable to read requested projects file \"$abs_projects\"." >&5
-+echo "$as_me: error: unable to read requested projects file \"$abs_projects\"." >&2;}
-+   { (exit 1); exit 1; }; }
-+fi
- 
- #### Always define this
- 
-@@ -17878,68 +17891,6 @@
- fi
- 
- 
--echo "$as_me:$LINENO: checking for std::is_sorted<> in <algorithm>" >&5
--echo $ECHO_N "checking for std::is_sorted<> in <algorithm>... $ECHO_C" >&6
--if test "${ncbi_cv_func_is_sorted+set}" = set; then
--  echo $ECHO_N "(cached) $ECHO_C" >&6
--else
--  cat >conftest.$ac_ext <<_ACEOF
--/* confdefs.h.  */
--_ACEOF
--cat confdefs.h >>conftest.$ac_ext
--cat >>conftest.$ac_ext <<_ACEOF
--/* end confdefs.h.  */
--#include <algorithm>
--int
--main ()
--{
--int a[2]; return std::is_sorted(a, a+2) ? 0 : 1;
--  ;
--  return 0;
--}
--_ACEOF
--rm -f conftest.$ac_objext
--if { (eval echo "$as_me:$LINENO: \"$ac_compile\"") >&5
--  (eval $ac_compile) 2>conftest.er1
--  ac_status=$?
--  grep -v '^ *+' conftest.er1 >conftest.err
--  rm -f conftest.er1
--  cat conftest.err >&5
--  echo "$as_me:$LINENO: \$? = $ac_status" >&5
--  (exit $ac_status); } &&
--	 { ac_try='test -z "$ac_cxx_werror_flag"
--			 || test ! -s conftest.err'
--  { (eval echo "$as_me:$LINENO: \"$ac_try\"") >&5
--  (eval $ac_try) 2>&5
--  ac_status=$?
--  echo "$as_me:$LINENO: \$? = $ac_status" >&5
--  (exit $ac_status); }; } &&
--	 { ac_try='test -s conftest.$ac_objext'
--  { (eval echo "$as_me:$LINENO: \"$ac_try\"") >&5
--  (eval $ac_try) 2>&5
--  ac_status=$?
--  echo "$as_me:$LINENO: \$? = $ac_status" >&5
--  (exit $ac_status); }; }; then
--  ncbi_cv_func_is_sorted=yes
--else
--  echo "$as_me: failed program was:" >&5
--sed 's/^/| /' conftest.$ac_ext >&5
--
--ncbi_cv_func_is_sorted=no
--fi
--rm -f conftest.err conftest.$ac_objext conftest.$ac_ext
--fi
--echo "$as_me:$LINENO: result: $ncbi_cv_func_is_sorted" >&5
--echo "${ECHO_T}$ncbi_cv_func_is_sorted" >&6
--if test "$ncbi_cv_func_is_sorted" = yes; then
--
--cat >>confdefs.h <<\_ACEOF
--#define HAVE_IS_SORTED 1
--_ACEOF
--
--fi
--
--
- 
- echo "$as_me:$LINENO: checking for SysV semaphores" >&5
- echo $ECHO_N "checking for SysV semaphores... $ECHO_C" >&6
-@@ -18550,7 +18501,7 @@
-   echo $ECHO_N "(cached) $ECHO_C" >&6
- else
-   ncbi_cv_c_restrict=no
--    for restrict in restrict __restrict__ __restrict; do
-+    for restrict in __restrict__ __restrict restrict; do
-        test "$ncbi_cv_c_restrict" = "no" || break
-        cat >conftest.$ac_ext <<_ACEOF
- /* confdefs.h.  */
-@@ -18620,7 +18571,7 @@
-   echo $ECHO_N "(cached) $ECHO_C" >&6
- else
-   ncbi_cv_cxx_restrict=no
--    for restrict in restrict __restrict__ __restrict; do
-+    for restrict in __restrict__ __restrict restrict; do
-        test "$ncbi_cv_cxx_restrict" = "no" || break
-        cat >conftest.$ac_ext <<_ACEOF
- /* confdefs.h.  */
-@@ -19046,67 +18997,6 @@
- _ACEOF
- 
- fi
--
--echo "$as_me:$LINENO: checking whether $CXX supports C++0x nullptr" >&5
--echo $ECHO_N "checking whether $CXX supports C++0x nullptr... $ECHO_C" >&6
--if test "${ncbi_cv_cxx_nullptr+set}" = set; then
--  echo $ECHO_N "(cached) $ECHO_C" >&6
--else
--  cat >conftest.$ac_ext <<_ACEOF
--/* confdefs.h.  */
--_ACEOF
--cat confdefs.h >>conftest.$ac_ext
--cat >>conftest.$ac_ext <<_ACEOF
--/* end confdefs.h.  */
--
--int
--main ()
--{
--void * p = nullptr;
--  ;
--  return 0;
--}
--_ACEOF
--rm -f conftest.$ac_objext
--if { (eval echo "$as_me:$LINENO: \"$ac_compile\"") >&5
--  (eval $ac_compile) 2>conftest.er1
--  ac_status=$?
--  grep -v '^ *+' conftest.er1 >conftest.err
--  rm -f conftest.er1
--  cat conftest.err >&5
--  echo "$as_me:$LINENO: \$? = $ac_status" >&5
--  (exit $ac_status); } &&
--	 { ac_try='test -z "$ac_cxx_werror_flag"
--			 || test ! -s conftest.err'
--  { (eval echo "$as_me:$LINENO: \"$ac_try\"") >&5
--  (eval $ac_try) 2>&5
--  ac_status=$?
--  echo "$as_me:$LINENO: \$? = $ac_status" >&5
--  (exit $ac_status); }; } &&
--	 { ac_try='test -s conftest.$ac_objext'
--  { (eval echo "$as_me:$LINENO: \"$ac_try\"") >&5
--  (eval $ac_try) 2>&5
--  ac_status=$?
--  echo "$as_me:$LINENO: \$? = $ac_status" >&5
--  (exit $ac_status); }; }; then
--  ncbi_cv_cxx_nullptr=yes
--else
--  echo "$as_me: failed program was:" >&5
--sed 's/^/| /' conftest.$ac_ext >&5
--
--ncbi_cv_cxx_nullptr=no
--fi
--rm -f conftest.err conftest.$ac_objext conftest.$ac_ext
--fi
--echo "$as_me:$LINENO: result: $ncbi_cv_cxx_nullptr" >&5
--echo "${ECHO_T}$ncbi_cv_cxx_nullptr" >&6
--if test "$ncbi_cv_cxx_nullptr" = yes; then
--
--cat >>confdefs.h <<\_ACEOF
--#define HAVE_NULLPTR 1
--_ACEOF
--
--fi
- 
- ### Check for the availability of other packages
- ### --------------------------------------------
diff --git a/sci-biology/ncbi-tools++/files/ncbi-tools++-12.0.0-drop-STATIC-from-LIB.patch b/sci-biology/ncbi-tools++/files/ncbi-tools++-12.0.0-drop-STATIC-from-LIB.patch
deleted file mode 100644
index fad02c38e..000000000
--- a/sci-biology/ncbi-tools++/files/ncbi-tools++-12.0.0-drop-STATIC-from-LIB.patch
+++ /dev/null
@@ -1,44 +0,0 @@
---- ncbi_cxx--12_0_0/src/app/speedtest/Makefile.speedtest.app.ori	2014-06-26 16:46:27.000000000 +0200
-+++ ncbi_cxx--12_0_0/src/app/speedtest/Makefile.speedtest.app	2014-06-26 16:47:26.000000000 +0200
-@@ -9,7 +9,7 @@
- APP = speedtest
- SRC = speedtest
- LIB = prosplign xalgoalignutil xalgoseq xcleanup taxon1 submit $(BLAST_LIBS) \
--      xqueryparse xregexp $(PCRE_LIB) $(OBJMGR_LIBS:%=%$(STATIC))
-+      xqueryparse xregexp $(PCRE_LIB) $(OBJMGR_LIBS)
- 
- LIBS = $(CMPRS_LIBS) $(DL_LIBS) $(PCRE_LIBS) $(ORIG_LIBS)
- 
---- ncbi_cxx--12_0_0/src/app/compart/Makefile.compart.app.ori	2014-06-26 16:47:53.000000000 +0200
-+++ ncbi_cxx--12_0_0/src/app/compart/Makefile.compart.app	2014-06-26 16:48:07.000000000 +0200
-@@ -7,7 +7,7 @@
- 
- LIB =  xalgoalignutil xalgoalignsplign xalgoalignnw xalgoseq \
-        taxon1 xalnmgr xqueryparse xregexp $(PCRE_LIB) \
--       $(BLAST_LIBS:%=%$(STATIC)) $(OBJMGR_LIBS:%=%$(STATIC))
-+       $(BLAST_LIBS) $(OBJMGR_LIBS)
- 
- LIBS = $(PCRE_LIBS) $(CMPRS_LIBS) $(NETWORK_LIBS) $(DL_LIBS) $(ORIG_LIBS)
-
---- ncbi_cxx--12_0_0/src/app/igblast/Makefile.igblastp.app.ori	2014-06-26 17:45:11.000000000 +0200
-+++ ncbi_cxx--12_0_0/src/app/igblast/Makefile.igblastp.app	2014-06-26 17:48:26.000000000 +0200
-@@ -3,7 +3,7 @@
- APP = igblastp
- SRC = igblastp_app
- LIB_ = $(BLAST_INPUT_LIBS) $(BLAST_LIBS) $(OBJMGR_LIBS)
--LIB = blast_app_util igblast $(LIB_:%=%$(STATIC))
-+LIB = blast_app_util igblast $(LIB_)
- 
- # De-universalize Mac builds to work around a PPC toolchain limitation
- CFLAGS   = $(FAST_CFLAGS:ppc=i386)
---- ncbi_cxx--12_0_0/src/app/igblast/Makefile.igblastn.app.ori	2014-06-26 17:47:53.000000000 +0200
-+++ ncbi_cxx--12_0_0/src/app/igblast/Makefile.igblastn.app	2014-06-26 17:49:31.000000000 +0200
-@@ -3,7 +3,7 @@
- APP = igblastn
- SRC = igblastn_app
- LIB_ = $(BLAST_INPUT_LIBS)  xalgoalignutil xqueryparse $(BLAST_LIBS) $(OBJMGR_LIBS) 
--LIB = blast_app_util igblast $(LIB_:%=%$(STATIC))
-+LIB = blast_app_util igblast $(LIB_)
- 
- # De-universalize Mac builds to work around a PPC toolchain limitation
- CFLAGS   = $(FAST_CFLAGS:ppc=i386)
diff --git a/sci-biology/ncbi-tools++/files/ncbi-tools++-12.0.0-fix-FreeTDS-upstream.patch b/sci-biology/ncbi-tools++/files/ncbi-tools++-12.0.0-fix-FreeTDS-upstream.patch
deleted file mode 100644
index fede70e51..000000000
--- a/sci-biology/ncbi-tools++/files/ncbi-tools++-12.0.0-fix-FreeTDS-upstream.patch
+++ /dev/null
@@ -1,19 +0,0 @@
---- src/app/agpconvert/Makefile.agpconvert.app.ori	2013-09-13 23:56:22.660032261 +0200
-+++ src/app/agpconvert/Makefile.agpconvert.app	2013-09-13 23:57:31.340032441 +0200
-@@ -6,13 +6,12 @@
- APP = agpconvert
- SRC = agpconvert
- 
--LIB  = xalgoseq xobjedit $(OBJREAD_LIBS) taxon1 xalnmgr xobjutil submit \
--    ncbi_xdbapi_ftds $(FTDS_LIB) tables xregexp $(PCRE_LIB) $(OBJMGR_LIBS)
--LIBS = $(FTDS_LIBS) $(CMPRS_LIBS) $(PCRE_LIBS) $(NETWORK_LIBS) $(DL_LIBS) $(ORIG_LIBS)
-+LIB  = $(OBJREAD_LIBS) taxon1 xregexp $(PCRE_LIB) $(OBJMGR_LIBS)
-+LIBS = $(CMPRS_LIBS) $(PCRE_LIBS) $(NETWORK_LIBS) $(DL_LIBS) $(ORIG_LIBS)
- 
- CXXFLAGS = $(FAST_CXXFLAGS)
- LDFLAGS  = $(FAST_LDFLAGS)
- 
--REQUIRES = objects algo
-+REQUIRES = objects
- 
- WATCHERS = xiangcha
diff --git a/sci-biology/ncbi-tools++/files/ncbi-tools++-12.0.0-fix-creaders-linking.patch b/sci-biology/ncbi-tools++/files/ncbi-tools++-12.0.0-fix-creaders-linking.patch
deleted file mode 100644
index 46c2e83fb..000000000
--- a/sci-biology/ncbi-tools++/files/ncbi-tools++-12.0.0-fix-creaders-linking.patch
+++ /dev/null
@@ -1,11 +0,0 @@
---- src/objtools/alnmgr/demo/Makefile.alnmrg.app.ori	2013-09-13 23:51:34.340031508 +0200
-+++ src/objtools/alnmgr/demo/Makefile.alnmrg.app	2013-09-13 23:51:36.660031514 +0200
-@@ -5,7 +5,7 @@
- SRC = alnmrg
- 
- LIB = xalnmgr $(OBJREAD_LIBS) ncbi_xloader_blastdb seqdb xobjutil submit blastdb \
--      tables $(OBJMGR_LIBS)
-+      tables creaders $(OBJMGR_LIBS)
- 
- LIBS = $(CMPRS_LIBS) $(DL_LIBS) $(NETWORK_LIBS) $(ORIG_LIBS)
- 
diff --git a/sci-biology/ncbi-tools++/files/ncbi-tools++-12.0.0-fix-install.patch b/sci-biology/ncbi-tools++/files/ncbi-tools++-12.0.0-fix-install.patch
deleted file mode 100644
index 97e845fdb..000000000
--- a/sci-biology/ncbi-tools++/files/ncbi-tools++-12.0.0-fix-install.patch
+++ /dev/null
@@ -1,11 +0,0 @@
---- ncbi_cxx--12_0_0/src/build-system/Makefile.in.top.ori	2014-06-26 22:49:49.000000000 +0200
-+++ ncbi_cxx--12_0_0/src/build-system/Makefile.in.top	2014-06-26 22:50:57.000000000 +0200
-@@ -48,7 +48,7 @@
- 	    for x in *.a; do ln -s "$$x" "`basename \"$$x\" .a`-static.a"; done
- 	cd $(includedir0) && find * -name CVS -prune -o -print |\
-             cpio -pd $(pincludedir)
--	$(INSTALL) -m 644 $(incdir)/* $(pincludedir)
-+	$(INSTALL) -m 644 $(incdir)/*.* $(pincludedir)
- ## set up appropriate build and status directories somewhere under $(libdir)?
- 
- install-gbench:
diff --git a/sci-biology/ncbi-tools++/files/ncbi-tools++-12.0.0-fix-svn-URL-upstream.patch b/sci-biology/ncbi-tools++/files/ncbi-tools++-12.0.0-fix-svn-URL-upstream.patch
deleted file mode 100644
index 8bba91f1d..000000000
--- a/sci-biology/ncbi-tools++/files/ncbi-tools++-12.0.0-fix-svn-URL-upstream.patch
+++ /dev/null
@@ -1,10 +0,0 @@
---- scripts/common/new_project.sh      (revision 408264)
-+++ scripts/common/new_project.sh      (working copy)
-@@ -6,7 +6,7 @@
- svn_revision=`echo '$Revision$' | sed "s%\\$[R]evision: *\\([^$][^$]*\\) \\$.*%\\1%"`
- def_builddir="$NCBI/c++/Debug/build"
- 
--repository_url='https://svn.ncbi.nlm.nih.gov/repos/toolkit'
-+repository_url='http://anonsvn.ncbi.nlm.nih.gov/repos/v1'
- tmp_app_checkout_dir='tmp_app_sample'
- stem='sample/app'
diff --git a/sci-biology/ncbi-tools++/files/ncbi-tools++-12.0.0-linkage-tuneups-addons.patch b/sci-biology/ncbi-tools++/files/ncbi-tools++-12.0.0-linkage-tuneups-addons.patch
deleted file mode 100644
index 553e41d29..000000000
--- a/sci-biology/ncbi-tools++/files/ncbi-tools++-12.0.0-linkage-tuneups-addons.patch
+++ /dev/null
@@ -1,13 +0,0 @@
---- ncbi_cxx--12_0_0/src/app/agpconvert/Makefile.agpconvert.app.ori     (revision 439078)
-+++ ncbi_cxx--12_0_0/src/app/agpconvert/Makefile.agpconvert.app     (working copy)
-@@ -7,8 +7,8 @@
- SRC = agpconvert
- 
- LIB  = xalgoseq xobjedit $(OBJREAD_LIBS) taxon1 xalnmgr xobjutil submit \
--    ncbi_xdbapi_ftds $(FTDS_LIB) tables xregexp $(PCRE_LIB) $(OBJMGR_LIBS)
--LIBS = $(FTDS_LIBS) $(CMPRS_LIBS) $(PCRE_LIBS) $(NETWORK_LIBS) $(DL_LIBS) $(ORIG_LIBS)
-+       tables xregexp $(PCRE_LIB) $(OBJMGR_LIBS)
-+LIBS = $(CMPRS_LIBS) $(PCRE_LIBS) $(NETWORK_LIBS) $(DL_LIBS) $(ORIG_LIBS)
- 
- CXXFLAGS = $(FAST_CXXFLAGS)
- LDFLAGS  = $(FAST_LDFLAGS)
diff --git a/sci-biology/ncbi-tools++/files/ncbi-tools++-12.0.0-linkage-tuneups.patch b/sci-biology/ncbi-tools++/files/ncbi-tools++-12.0.0-linkage-tuneups.patch
deleted file mode 100644
index 86e96b865..000000000
--- a/sci-biology/ncbi-tools++/files/ncbi-tools++-12.0.0-linkage-tuneups.patch
+++ /dev/null
@@ -1,421 +0,0 @@
-Index: src/algo/blast/format/Makefile.xblastformat.lib
-===================================================================
---- src/algo/blast/format/Makefile.xblastformat.lib	(revision 439078)
-+++ src/algo/blast/format/Makefile.xblastformat.lib	(working copy)
-@@ -7,6 +7,6 @@
- 
- CPPFLAGS = -DNCBI_MODULE=BLASTFORMAT $(ORIG_CPPFLAGS)
- 
--DLL_LIB = align_format blastxml xhtml xcgi
-+DLL_LIB = align_format xblast xnetblast blastxml xhtml xcgi
- 
- WATCHERS = jianye zaretska madden camacho fongah2
-Index: src/app/compart/Makefile.compart.app
-===================================================================
---- src/app/compart/Makefile.compart.app	(revision 439078)
-+++ src/app/compart/Makefile.compart.app	(working copy)
-@@ -5,11 +5,11 @@
- APP = compart
- SRC = compart
- 
--LIB =  xalgoalignutil xalgoalignsplign xalgoalignnw xqueryparse xalnmgr \
--       $(BLAST_LIBS:%=%$(STATIC)) \
--       $(OBJMGR_LIBS:%=%$(STATIC))
-+LIB =  xalgoalignutil xalgoalignsplign xalgoalignnw xalgoseq \
-+       taxon1 xalnmgr xqueryparse xregexp $(PCRE_LIB) \
-+       $(BLAST_LIBS:%=%$(STATIC)) $(OBJMGR_LIBS:%=%$(STATIC))
- 
--LIBS = $(CMPRS_LIBS) $(NETWORK_LIBS) $(DL_LIBS) $(ORIG_LIBS)
-+LIBS = $(PCRE_LIBS) $(CMPRS_LIBS) $(NETWORK_LIBS) $(DL_LIBS) $(ORIG_LIBS)
- 
- CXXFLAGS = $(FAST_CXXFLAGS)
- LDFLAGS  = $(FAST_LDFLAGS)
-Index: src/app/compart/Makefile.compartp.app
-===================================================================
---- src/app/compart/Makefile.compartp.app	(revision 439078)
-+++ src/app/compart/Makefile.compartp.app	(working copy)
-@@ -5,7 +5,8 @@
- APP = compartp
- SRC = compartp
- 
--LIB = prosplign  xalgoalignutil $(BLAST_LIBS)  xqueryparse $(OBJMGR_LIBS)
-+LIB = prosplign xalgoalignutil xalgoseq taxon1 $(BLAST_LIBS) \
-+      xqueryparse xregexp $(PCRE_LIB) $(OBJMGR_LIBS)
- 
- LIBS = $(CMPRS_LIBS) $(PCRE_LIBS) $(NETWORK_LIBS) $(DL_LIBS) $(ORIG_LIBS)
- 
-Index: src/app/grid/util/Makefile.ncfetch.app
-===================================================================
---- src/app/grid/util/Makefile.ncfetch.app	(revision 439078)
-+++ src/app/grid/util/Makefile.ncfetch.app	(working copy)
-@@ -5,7 +5,7 @@
- APP = ncfetch.cgi
- SRC = ncfetch
- 
--LIB = xcgi xconnserv xconnect xutil xncbi
-+LIB = xcgi xconnserv xthrserv xconnect xutil xncbi
- LIBS = $(NETWORK_LIBS) $(DL_LIBS) $(ORIG_LIBS)
- 
- WATCHERS = kazimird
-Index: src/app/hfilter/Makefile.hfilter.app
-===================================================================
---- src/app/hfilter/Makefile.hfilter.app	(revision 439078)
-+++ src/app/hfilter/Makefile.hfilter.app	(working copy)
-@@ -5,9 +5,10 @@
- APP = hfilter
- SRC = hitfilter_app
- 
--LIB = xalgoalignutil $(BLAST_LIBS) xqueryparse $(OBJMGR_LIBS)
-+LIB = xalgoalignutil xalgoseq taxon1 $(BLAST_LIBS) xqueryparse \
-+      xregexp $(PCRE_LIB) $(OBJMGR_LIBS)
- 
--LIBS = $(CMPRS_LIBS) $(NETWORK_LIBS) $(DL_LIBS) $(ORIG_LIBS)
-+LIBS = $(PCRE_LIBS) $(CMPRS_LIBS) $(NETWORK_LIBS) $(DL_LIBS) $(ORIG_LIBS)
- 
- CXXFLAGS = $(FAST_CXXFLAGS)
- LDFLAGS  = $(FAST_LDFLAGS)
-Index: src/app/speedtest/Makefile.speedtest.app
-===================================================================
---- src/app/speedtest/Makefile.speedtest.app	(revision 439078)
-+++ src/app/speedtest/Makefile.speedtest.app	(working copy)
-@@ -8,7 +8,7 @@
- 
- APP = speedtest
- SRC = speedtest
--LIB = prosplign xalgoalignutil xcleanup submit $(BLAST_LIBS) \
-+LIB = prosplign xalgoalignutil xalgoseq xcleanup taxon1 submit $(BLAST_LIBS) \
-       xqueryparse xregexp $(PCRE_LIB) $(OBJMGR_LIBS:%=%$(STATIC))
- 
- LIBS = $(CMPRS_LIBS) $(DL_LIBS) $(PCRE_LIBS) $(ORIG_LIBS)
-Index: src/app/splign/Makefile.splign.app
-===================================================================
---- src/app/splign/Makefile.splign.app	(revision 439078)
-+++ src/app/splign/Makefile.splign.app	(working copy)
-@@ -12,7 +12,7 @@
- LIB = xalgoalignsplign xalgoalignutil xalgoalignnw \
-       $(BLAST_DB_DATA_LOADER_LIBS) \
-       ncbi_xloader_lds2 lds2 sqlitewrapp \
--      xqueryparse xalgoseq $(PCRE_LIB) \
-+      xqueryparse xalgoseq taxon1 xregexp $(PCRE_LIB) \
-       $(BLAST_LIBS:%=%$(STATIC)) submit \
-       $(OBJMGR_LIBS:%=%$(STATIC))
- 
-Index: src/connect/services/test/Makefile.test_nsstorage.app
-===================================================================
---- src/connect/services/test/Makefile.test_nsstorage.app	(revision 439078)
-+++ src/connect/services/test/Makefile.test_nsstorage.app	(working copy)
-@@ -2,7 +2,7 @@
- 
- APP = test_nsstorage
- SRC = test_nsstorage
--LIB = xconnserv xconnect xutil xncbi
-+LIB = xconnserv xthrserv xconnect xutil xncbi
- 
- LIBS = $(NETWORK_LIBS) $(DL_LIBS) $(ORIG_LIBS)
- 
-Index: src/misc/hgvs/test/Makefile.hgvs2variation.app
-===================================================================
---- src/misc/hgvs/test/Makefile.hgvs2variation.app	(revision 439078)
-+++ src/misc/hgvs/test/Makefile.hgvs2variation.app	(working copy)
-@@ -6,7 +6,7 @@
- 
- CPPFLAGS = $(ORIG_CPPFLAGS) $(BOOST_INCLUDE)
- 
--LIB_ = hgvs variation \
-+LIB_ = hgvs objcoords variation \
-        entrez2cli entrez2 xregexp $(PCRE_LIB) xobjutil $(OBJMGR_LIBS)
- LIB = $(LIB_:%=%$(STATIC))
- 
-Index: src/misc/hgvs/test/Makefile.test_hgvs_parser.app
-===================================================================
---- src/misc/hgvs/test/Makefile.test_hgvs_parser.app	(revision 439078)
-+++ src/misc/hgvs/test/Makefile.test_hgvs_parser.app	(working copy)
-@@ -5,7 +5,7 @@
- 
- CPPFLAGS = $(ORIG_CPPFLAGS) $(BOOST_INCLUDE)
- 
--LIB_ = hgvs variation test_boost xregexp $(PCRE_LIB) xobjutil \
-+LIB_ = hgvs objcoords variation test_boost xregexp $(PCRE_LIB) xobjutil \
-        entrez2cli entrez2 $(OBJMGR_LIBS)
- 
- LIB = $(LIB_:%=%$(STATIC))
-Index: src/objects/biblio/Makefile.biblio.lib
-===================================================================
---- src/objects/biblio/Makefile.biblio.lib	(revision 439078)
-+++ src/objects/biblio/Makefile.biblio.lib	(working copy)
-@@ -1,2 +1,4 @@
- LIB = biblio
- SRC = biblio__ biblio___ citation_base
-+
-+DLL_LIB = general
-Index: src/objects/blast/Makefile.blast.lib
-===================================================================
---- src/objects/blast/Makefile.blast.lib	(revision 439078)
-+++ src/objects/blast/Makefile.blast.lib	(working copy)
-@@ -1,4 +1,6 @@
- LIB = xnetblast
- SRC = blast__ blast___ names
- 
-+DLL_LIB = scoremat seqset
-+
- WATCHERS = camacho
-Index: src/objects/blast/Makefile.xnetblastcli.lib
-===================================================================
---- src/objects/blast/Makefile.xnetblastcli.lib	(revision 439078)
-+++ src/objects/blast/Makefile.xnetblastcli.lib	(working copy)
-@@ -2,3 +2,5 @@
- 
- LIB = xnetblastcli
- SRC = blastclient blastclient_
-+
-+DLL_LIB = xnetblast xconnect
-Index: src/objects/blastdb/Makefile.blastdb.lib
-===================================================================
---- src/objects/blastdb/Makefile.blastdb.lib	(revision 439078)
-+++ src/objects/blastdb/Makefile.blastdb.lib	(working copy)
-@@ -1,2 +1,4 @@
- LIB = blastdb
- SRC = blastdb__ blastdb___
-+
-+DLL_LIB = seq
-Index: src/objects/general/Makefile.general.lib
-===================================================================
---- src/objects/general/Makefile.general.lib	(revision 439078)
-+++ src/objects/general/Makefile.general.lib	(working copy)
-@@ -1,2 +1,4 @@
- LIB = general
- SRC = general__ general___ uoconv
-+
-+DLL_LIB = xser
-Index: src/objects/medline/Makefile.medline.lib
-===================================================================
---- src/objects/medline/Makefile.medline.lib	(revision 439078)
-+++ src/objects/medline/Makefile.medline.lib	(working copy)
-@@ -1,2 +1,4 @@
- LIB = medline
- SRC = medline__ medline___
-+
-+DLL_LIB = biblio general
-Index: src/objects/pub/Makefile.pub.lib
-===================================================================
---- src/objects/pub/Makefile.pub.lib	(revision 439078)
-+++ src/objects/pub/Makefile.pub.lib	(working copy)
-@@ -1,2 +1,4 @@
- LIB = pub
- SRC = pub__ pub___
-+
-+DLL_LIB = medline biblio
-Index: src/objects/scoremat/Makefile.scoremat.lib
-===================================================================
---- src/objects/scoremat/Makefile.scoremat.lib	(revision 439078)
-+++ src/objects/scoremat/Makefile.scoremat.lib	(working copy)
-@@ -1,2 +1,4 @@
- LIB = scoremat
- SRC = scoremat__ scoremat___
-+
-+DLL_LIB = seqset
-Index: src/objects/seq/Makefile.seq.lib
-===================================================================
---- src/objects/seq/Makefile.seq.lib	(revision 439078)
-+++ src/objects/seq/Makefile.seq.lib	(working copy)
-@@ -13,3 +13,5 @@
-       seq_loc_from_string seq_loc_reverse_complementer
- 
- WATCHERS = vasilche grichenk
-+
-+DLL_LIB = seqcode pub biblio general xser sequtil
-Index: src/objects/seqset/Makefile.seqset.lib
-===================================================================
---- src/objects/seqset/Makefile.seqset.lib	(revision 439078)
-+++ src/objects/seqset/Makefile.seqset.lib	(working copy)
-@@ -1,2 +1,4 @@
- LIB = seqset
- SRC = seqset__ seqset___ gb_release_file
-+
-+DLL_LIB = xser
-Index: src/objects/taxon1/Makefile.taxon1.lib
-===================================================================
---- src/objects/taxon1/Makefile.taxon1.lib	(revision 439078)
-+++ src/objects/taxon1/Makefile.taxon1.lib	(working copy)
-@@ -3,4 +3,6 @@
- LIB = taxon1
- SRC = taxon1__ taxon1___ taxon1 cache utils ctreecont
- 
-+DLL_LIB = xconnect
-+
- WATCHERS = domrach
-Index: src/objmgr/util/Makefile.util.lib
-===================================================================
---- src/objmgr/util/Makefile.util.lib	(revision 439078)
-+++ src/objmgr/util/Makefile.util.lib	(working copy)
-@@ -8,5 +8,7 @@
- SRC = weight sequence feature seqtitle create_defline obj_sniff seq_loc_util seq_align_util
- LIB = xobjutil
- 
-+DLL_LIB = xobjmgr
-+
- WATCHERS = ucko vasilche
- 
-Index: src/objtools/blast/seqdb_reader/Makefile.seqdb.lib
-===================================================================
---- src/objtools/blast/seqdb_reader/Makefile.seqdb.lib	(revision 439078)
-+++ src/objtools/blast/seqdb_reader/Makefile.seqdb.lib	(working copy)
-@@ -29,4 +29,6 @@
- CXXFLAGS = $(FAST_CXXFLAGS)
- LDFLAGS  = $(FAST_LDFLAGS)
- 
-+DLL_LIB = xobjmgr blastdb
-+
- WATCHERS = maning camacho
-Index: src/objtools/blast/services/Makefile.blast_services.lib
-===================================================================
---- src/objtools/blast/services/Makefile.blast_services.lib	(revision 439078)
-+++ src/objtools/blast/services/Makefile.blast_services.lib	(working copy)
-@@ -13,3 +13,4 @@
- CXXFLAGS = $(FAST_CXXFLAGS)
- LDFLAGS  = $(FAST_LDFLAGS)
- 
-+DLL_LIB = xnetblastcli xconnect
-Index: src/objtools/data_loaders/blastdb/Makefile.ncbi_xloader_blastdb.lib
-===================================================================
---- src/objtools/data_loaders/blastdb/Makefile.ncbi_xloader_blastdb.lib	(revision 439078)
-+++ src/objtools/data_loaders/blastdb/Makefile.ncbi_xloader_blastdb.lib	(working copy)
-@@ -7,4 +7,6 @@
- 
- ASN_DEP = blastdb seqset
- 
-+DLL_LIB = seqdb
-+
- WATCHERS = camacho
-Index: src/objtools/data_loaders/blastdb/Makefile.ncbi_xloader_blastdb_rmt.lib
-===================================================================
---- src/objtools/data_loaders/blastdb/Makefile.ncbi_xloader_blastdb_rmt.lib	(revision 439078)
-+++ src/objtools/data_loaders/blastdb/Makefile.ncbi_xloader_blastdb_rmt.lib	(working copy)
-@@ -7,4 +7,6 @@
- 
- ASN_DEP = blastdb xnetblast
- 
-+DLL_LIB = blast_services
-+
- WATCHERS = camacho
-Index: src/objtools/lds2/Makefile.lds2.lib
-===================================================================
---- src/objtools/lds2/Makefile.lds2.lib	(revision 439078)
-+++ src/objtools/lds2/Makefile.lds2.lib	(working copy)
-@@ -8,9 +8,9 @@
- SRC = lds2 lds2_db lds2_handlers
- 
- # Dependencies for shared library
--#DLL_LIB = sqlitewrapp
-+DLL_LIB = sqlitewrapp $(COMPRESS_LIBS)
- 
--LIBS = $(CMPRS_LIBS) $(ORIG_LIBS)
-+LIBS = $(SQLITE3_LIBS) $(CMPRS_LIBS) $(ORIG_LIBS)
- 
- CPPFLAGS = $(SQLITE3_INCLUDE) $(CMPRS_INCLUDE) $(ORIG_CPPFLAGS)
- 
-Index: src/objtools/readers/Makefile.xobjread.lib
-===================================================================
---- src/objtools/readers/Makefile.xobjread.lib	(revision 439078)
-+++ src/objtools/readers/Makefile.xobjread.lib	(working copy)
-@@ -19,5 +19,6 @@
-       best_feat_finder source_mod_parser fasta_exception
- 
- 
--DLL_LIB = creaders
-+DLL_LIB = seqset $(SEQ_LIBS) pub general creaders xutil
- 
-+
-Index: src/sample/app/cgi/Makefile.cgi_session_sample.app
-===================================================================
---- src/sample/app/cgi/Makefile.cgi_session_sample.app	(revision 439078)
-+++ src/sample/app/cgi/Makefile.cgi_session_sample.app	(working copy)
-@@ -11,7 +11,7 @@
- # the lines reading "### BEGIN/END COPIED SETTINGS" in any way.
- 
- ### BEGIN COPIED SETTINGS
--LIB = xgridcgi xcgi xhtml xconnserv xconnect xutil xncbi
-+LIB = xgridcgi xcgi xhtml xconnserv xthrserv xconnect xutil xncbi
- 
- LIBS = $(NETWORK_LIBS) $(DL_LIBS) $(ORIG_LIBS)
- 
-Index: src/sample/app/netcache/Makefile.netcache_cgi_sample.app
-===================================================================
---- src/sample/app/netcache/Makefile.netcache_cgi_sample.app	(revision 439078)
-+++ src/sample/app/netcache/Makefile.netcache_cgi_sample.app	(working copy)
-@@ -4,7 +4,7 @@
- SRC = netcache_cgi_sample
- 
- ### BEGIN COPIED SETTINGS
--LIB = xconnserv xconnect xcgi xhtml xutil xncbi
-+LIB = xconnserv xthrserv xconnect xcgi xhtml xutil xncbi
- 
- LIBS = $(NETWORK_LIBS) $(DL_LIBS) $(ORIG_LIBS)
- ### END COPIED SETTINGS
-Index: src/serial/Makefile.serial.lib
-===================================================================
---- src/serial/Makefile.serial.lib	(revision 439078)
-+++ src/serial/Makefile.serial.lib	(working copy)
-@@ -19,3 +19,5 @@
- LIB    = xser
- 
- WATCHERS = gouriano
-+
-+DLL_LIB = xutil xncbi
-Index: src/sra/data_loaders/bam/test/Makefile.test_bam_loader.app
-===================================================================
---- src/sra/data_loaders/bam/test/Makefile.test_bam_loader.app	(revision 439078)
-+++ src/sra/data_loaders/bam/test/Makefile.test_bam_loader.app	(working copy)
-@@ -7,7 +7,8 @@
- 
- CPPFLAGS = $(ORIG_CPPFLAGS) $(BOOST_INCLUDE)
- 
--LIB = ncbi_xloader_bam bamread $(BAM_LIBS) xobjreadex xobjutil test_boost $(OBJMGR_LIBS)
-+LIB = ncbi_xloader_bam bamread $(BAM_LIBS) \
-+      xobjreadex $(OBJREAD_LIBS) xobjutil test_boost $(OBJMGR_LIBS)
- 
- LIBS = $(SRA_SDK_SYSLIBS) $(CMPRS_LIBS) $(NETWORK_LIBS) $(ORIG_LIBS)
- 
-Index: src/sra/data_loaders/csra/test/Makefile.test_csra_loader.app
-===================================================================
---- src/sra/data_loaders/csra/test/Makefile.test_csra_loader.app	(revision 439078)
-+++ src/sra/data_loaders/csra/test/Makefile.test_csra_loader.app	(working copy)
-@@ -5,7 +5,8 @@
- 
- CPPFLAGS = $(ORIG_CPPFLAGS) $(BOOST_INCLUDE)
- 
--LIB = ncbi_xloader_csra $(SRAREAD_LIBS) xobjreadex xobjutil test_boost $(OBJMGR_LIBS)
-+LIB = ncbi_xloader_csra $(SRAREAD_LIBS) xobjreadex $(OBJREAD_LIBS) xobjutil \
-+      test_boost $(OBJMGR_LIBS)
- 
- LIBS = $(SRA_SDK_SYSLIBS) $(CMPRS_LIBS) $(NETWORK_LIBS) $(ORIG_LIBS)
- 
-Index: src/sra/readers/bam/test/Makefile.bam_test.app
-===================================================================
---- src/sra/readers/bam/test/Makefile.bam_test.app	(revision 439078)
-+++ src/sra/readers/bam/test/Makefile.bam_test.app	(working copy)
-@@ -9,7 +9,8 @@
- APP = bam_test
- SRC = bam_test
- 
--LIB =   bamread xobjreadex xobjutil xobjsimple $(OBJMGR_LIBS) $(BAM_LIBS)
-+LIB =   bamread $(BAM_LIBS) xobjreadex $(OBJREAD_LIBS) xobjutil xobjsimple \
-+        $(OBJMGR_LIBS)
- LIBS =  $(SRA_SDK_SYSLIBS) $(CMPRS_LIBS) $(NETWORK_LIBS) $(ORIG_LIBS)
- 
- REQUIRES = objects
-Index: src/sra/sdk/libs/vfs/Makefile.vfs.lib
-===================================================================
---- src/sra/sdk/libs/vfs/Makefile.vfs.lib	(revision 16076)
-+++ src/sra/sdk/libs/vfs/Makefile.vfs.lib	(working copy)
-@@ -8,6 +8,9 @@
- CPPFLAGS = -I$(srcdir) $(SRA_INCLUDE) $(Z_INCLUDE) $(BZ2_INCLUDE) \
-            $(SRA_INTERNAL_CPPFLAGS) -D_LIBRARY -DALWAYS_ADD_EXE $(ORIG_CPPFLAGS)
- 
--DLL_LIB = srapath$(DLL) kurl$(DLL) krypto$(DLL) kfg$(DLL) kfs$(DLL) klib$(DLL)
-+DLL_LIB = srapath$(FORCE_STATIC) kurl$(FORCE_STATIC) \
-+          krypto$(DLL) kfg$(DLL) kfs$(DLL) klib$(DLL)
- 
-+LIBS = $(SRA_SDK_SYSLIBS)
-+
- LIB_OR_DLL = both
diff --git a/sci-biology/ncbi-tools++/files/ncbi-tools++-12.0.0-more-patches.patch b/sci-biology/ncbi-tools++/files/ncbi-tools++-12.0.0-more-patches.patch
deleted file mode 100644
index 449bbc5a9..000000000
--- a/sci-biology/ncbi-tools++/files/ncbi-tools++-12.0.0-more-patches.patch
+++ /dev/null
@@ -1,136 +0,0 @@
---- ncbi_cxx--12_0_0/include/common/config/ncbiconf_msvc.h.ori     2013/09/30 13:46:04     59961
-+++ ncbi_cxx--12_0_0/include/common/config/ncbiconf_msvc.h     2013/09/30 14:10:44     59962
-@@ -62,10 +62,6 @@
- #define HAVE_SYS_TYPES_H 1
- #define HAVE_VSNPRINTF   1
- 
--#if _MSC_VER >= 1600
--#  define HAVE_IS_SORTED   1
--#endif
--
- #if _MSC_VER < 1500
- #  define vsnprintf        _vsnprintf
- #endif
-@@ -136,10 +132,6 @@
- 
- #endif
- 
--#if _MSC_VER >= 1600
--#  define HAVE_NULLPTR  1
--#endif
--
- /* Windows XP and above */
- #define NCBI_WIN32_WINNT 0x0501
- #if !defined(_WIN32_WINNT)
---- ncbi_cxx--12_0_0/include/common/config/ncbiconf_xcode.h.ori    2013/09/30 13:46:04     59961
-+++ ncbi_cxx--12_0_0/include/common/config/ncbiconf_xcode.h    2013/09/30 14:10:44     59962
-@@ -258,9 +258,6 @@
- /* Define to 1 if you have `ios(_base)::register_callback'. */
- #define HAVE_IOS_REGISTER_CALLBACK 1
- 
--/* Define to 1 if <algorithm> supplies `std::is_sorted<>'. */
--/* #undef HAVE_IS_SORTED */
--
- /* Define to 1 if you have the `lchown' function. */
- /* #undef HAVE_LCHOWN */
- 
-@@ -595,9 +592,6 @@
- /* Define to 1 if wxWidgets is available. */
- /* #undef HAVE_WXWIDGETS */
- 
--/* Define to 1 if nullptr keyword is available. */
--/* #undef HAVE_NULLPTR */
--
- /* Define as const if the declaration of iconv() needs const. */
- #if MAC_OS_X_VERSION_MIN_REQUIRED >= 1050 /* MAC_OS_X_VERSION_10_5 */
- #  define ICONV_CONST
---- ncbi_cxx--12_0_0/include/common/ncbiconf_impl.h.ori    2013/09/30 13:46:04     59961
-+++ ncbi_cxx--12_0_0/include/common/ncbiconf_impl.h    2013/09/30 14:10:44     59962
-@@ -115,6 +115,11 @@
-       || defined(__GXX_EXPERIMENTAL_CPP0X__)
- #    define NCBI_HAVE_CXX11 1
- #  endif
-+#  if defined(NCBI_HAVE_CXX11) \
-+      ||  (defined(NCBI_COMPILER_MSVC)  &&  _MSC_VER >= 1600)
-+#    define HAVE_IS_SORTED 1
-+#    define HAVE_NULLPTR 1
-+#  endif
- #endif
- 
- #include <common/ncbi_skew_guard.h>
---- ncbi_cxx--12_0_0/src/build-system/config.h.in.ori      2013/09/30 13:46:04     59961
-+++ ncbi_cxx--12_0_0/src/build-system/config.h.in      2013/09/30 14:10:44     59962
-@@ -179,9 +179,6 @@
- /* Define to 1 if you have `ios(_base)::register_callback'. */
- #undef HAVE_IOS_REGISTER_CALLBACK
- 
--/* Define to 1 if <algorithm> supplies `std::is_sorted<>'. */
--#undef HAVE_IS_SORTED
--
- /* Define to 1 if you have the `lchown' function. */
- #undef HAVE_LCHOWN
- 
-@@ -391,9 +388,6 @@
- /* Define to 1 if `min'/`max' templates are not implemented. */
- #undef HAVE_NO_MINMAX_TEMPLATE
- 
--/* Define to 1 if your C++ compiler supports the C++0x `nullptr' keyword. */
--#undef HAVE_NULLPTR
--
- /* Define to 1 if ODBC libraries are available. */
- #undef HAVE_ODBC
- 
---- ncbi_cxx--12_0_0/src/build-system/configure.ac.ori     2013/09/30 13:46:04     59961
-+++ ncbi_cxx--12_0_0/src/build-system/configure.ac     2013/09/30 14:10:44     59962
-@@ -3351,17 +3351,6 @@
- fi
- 
- 
--AC_CACHE_CHECK([for std::is_sorted<> in <algorithm>], ncbi_cv_func_is_sorted,
--   [AC_COMPILE_IFELSE([AC_LANG_PROGRAM(
--       [[#include <algorithm>]],
--       [[int a[2]; return std::is_sorted(a, a+2) ? 0 : 1;]])],
--       [ncbi_cv_func_is_sorted=yes], [ncbi_cv_func_is_sorted=no])])
--if test "$ncbi_cv_func_is_sorted" = yes; then
--   AC_DEFINE(HAVE_IS_SORTED, 1,
--             [Define to 1 if <algorithm> supplies `std::is_sorted<>'.])
--fi
--
--
- 
- AC_CACHE_CHECK([for SysV semaphores], ncbi_cv_sys_semaphores,
-    AC_LINK_IFELSE([AC_LANG_PROGRAM([#include <sys/types.h>
-@@ -3498,7 +3487,7 @@
- AC_CACHE_CHECK([whether the C compiler supports C99 restrict],
-    ncbi_cv_c_restrict,
-    [ncbi_cv_c_restrict=no
--    for restrict in restrict __restrict__ __restrict; do
-+    for restrict in __restrict__ __restrict restrict; do
-        test "$ncbi_cv_c_restrict" = "no" || break
-        AC_COMPILE_IFELSE([AC_LANG_SOURCE([void f(int * $restrict p);])],
-           [ncbi_cv_c_restrict=$restrict], [])
-@@ -3518,7 +3507,7 @@
- AC_CACHE_CHECK([whether the C++ compiler supports C99 restrict],
-    ncbi_cv_cxx_restrict,
-    [ncbi_cv_cxx_restrict=no
--    for restrict in restrict __restrict__ __restrict; do
-+    for restrict in __restrict__ __restrict restrict; do
-        test "$ncbi_cv_cxx_restrict" = "no" || break
-        AC_COMPILE_IFELSE([AC_LANG_SOURCE([void f(int * $restrict p);])],
-           [ncbi_cv_cxx_restrict=$restrict], [])
-@@ -3623,14 +3612,6 @@
-               unaligned addresses.])
- fi
- 
--AC_CACHE_CHECK([whether $CXX supports C++0x nullptr], ncbi_cv_cxx_nullptr,
--   [AC_COMPILE_IFELSE([AC_LANG_PROGRAM([], [[void * p = nullptr;]])],
--       [ncbi_cv_cxx_nullptr=yes], [ncbi_cv_cxx_nullptr=no])])
--if test "$ncbi_cv_cxx_nullptr" = yes; then
--   AC_DEFINE(HAVE_NULLPTR, 1,
--      [Define to 1 if your C++ compiler supports the C++0x `nullptr' keyword.])
--fi
--
- ### Check for the availability of other packages
- ### --------------------------------------------
- 
-
diff --git a/sci-biology/ncbi-tools++/files/ncbi-tools++-12.0.0-never_build_test_boost.patch b/sci-biology/ncbi-tools++/files/ncbi-tools++-12.0.0-never_build_test_boost.patch
deleted file mode 100644
index 68baea046..000000000
--- a/sci-biology/ncbi-tools++/files/ncbi-tools++-12.0.0-never_build_test_boost.patch
+++ /dev/null
@@ -1,11 +0,0 @@
---- ncbi_cxx--12_0_0/src/corelib/Makefile.in.ori	2016-12-01 20:28:33.239758102 +0100
-+++ ncbi_cxx--12_0_0/src/corelib/Makefile.in	2016-12-01 20:28:46.330110659 +0100
-@@ -7,7 +7,7 @@
- #################################
- 
- USR_PROJ = precompile
--LIB_PROJ = corelib test_mt test_boost
-+LIB_PROJ = corelib test_mt
- SUB_PROJ = test
- PROJ_TAG = core
- 
diff --git a/sci-biology/ncbi-tools++/files/ncbi-tools++-12.0.0-support-autoconf-2.60.patch b/sci-biology/ncbi-tools++/files/ncbi-tools++-12.0.0-support-autoconf-2.60.patch
deleted file mode 100644
index 9047c3384..000000000
--- a/sci-biology/ncbi-tools++/files/ncbi-tools++-12.0.0-support-autoconf-2.60.patch
+++ /dev/null
@@ -1,296 +0,0 @@
---- ncbi_cxx--12_0_0/src/build-system/aclocal.m4.ori       2014/05/05 12:38:59     62744
-+++ ncbi_cxx--12_0_0/src/build-system/aclocal.m4       2014/05/05 13:59:33     62745
-@@ -1,126 +1,44 @@
--# Hacked up in various ways, since Autoconf's version doesn't quite
--# suit our (unusual) conventions.  (Originally from status.m4)
--m4_define([_AC_SRCPATHS],
--[#ac_builddir=. # Useless!
--ac_builddir=$builddir
--dnl Base source directories on path to *input* file.
--if test -n "$ac_file_in"; then
--   ac_dir_in=`AS_DIRNAME(["$ac_file_in"])`
-+# Autoconf's _AC_SRCDIRS (from status.m4; historically _AC_SRCPATHS)
-+# doesn't quite suit the C++ Toolkit's conventions; tweak it accordingly.
-+m4_copy([_AC_SRCDIRS], [NCBI_ORIG__AC_SRCDIRS])
-+m4_define([_AC_SRCDIRS],
-+[# Base source directories on path to *input* file.
-+if test -n "$ac_f"; then
-+   ac_dir_in=`AS_DIRNAME(["$ac_f"])`
- else
-    ac_dir_in=$1
- fi
- 
--if test $ac_dir_in != .; then
--  ac_dir_suffix=`echo $ac_dir_in | sed 's,^\.[[\\/]],,'`
--  # A "../" for each directory in $ac_dir_suffix.
--  ac_top_builddir=../`echo "$ac_dir_suffix" | sed 's,/[[^\\/]]*,../,g'`
--else
--  ac_dir_suffix= ac_top_builddir=
--fi
-+NCBI_ORIG__AC_SRCDIRS(["$ac_dir_in"])
- 
--case $srcdir in
--  .)  # No --srcdir option.  We are building in place.
--    ac_srcdir=.
--    if test -z "$ac_top_builddir"; then
--       ac_top_srcdir=.
--    else
--       ac_top_srcdir=`echo $ac_top_builddir | sed 's,/$,,'`
--    fi ;;
--  [[\\/]]* | ?:[[\\/]]* )  # Absolute path.
--    ac_srcdir=$srcdir/$ac_dir_suffix;
--    ac_top_srcdir=$srcdir ;;
--  *) # Relative path.
--    ac_srcdir=$ac_top_builddir$srcdir/$ac_dir_suffix
--    ac_top_srcdir=$ac_top_builddir$srcdir ;;
--esac
--# Do not use `cd foo && pwd` to compute absolute paths, because
--# the directories may not exist.
--AS_SET_CATFILE([ac_abs_builddir],   [$builddir],        [$1])
--AS_SET_CATFILE([ac_abs_top_builddir],
--                                    [$ac_abs_builddir], [${ac_top_builddir}.])
--AS_SET_CATFILE([ac_abs_top_srcdir], [$ac_dir_in],       [$real_srcdir])
--AS_SET_CATFILE([ac_abs_srcdir],     [$ac_abs_top_srcdir], [$ac_dir_suffix])
--])# _AC_SRCPATHS
--
--
--# Copied from autoconf 2.59 (m4sh.m4), but rearranged to make bash a
--# last resort due to issues with sourcing .bashrc.
--m4_define([_AS_LINENO_PREPARE],
--[_AS_LINENO_WORKS || {
--  # Find who we are.  Look in the path if we contain no path at all
--  # relative or not.
--  case $[0] in
--    *[[\\/]]* ) as_myself=$[0] ;;
--    *) _AS_PATH_WALK([],
--                   [test -r "$as_dir/$[0]" && as_myself=$as_dir/$[0] && break])
--       ;;
--  esac
--  # We did not find ourselves, most probably we were run as `sh COMMAND'
--  # in which case we are not to be found in the path.
--  if test "x$as_myself" = x; then
--    as_myself=$[0]
--  fi
--  if test ! -f "$as_myself"; then
--    AS_ERROR([cannot find myself; rerun with an absolute path])
--  fi
--  case $CONFIG_SHELL in
--  '')
--    AS_UNSET(ZSH_VERSION)
--    for as_base in sh ksh sh5 bash; do
--      _AS_PATH_WALK([/bin$PATH_SEPARATOR/usr/bin$PATH_SEPARATOR$PATH],
--         [case $as_dir in
--         /*)
--           if ("$as_dir/$as_base" -c \
--                 'test -z "$ZSH_VERSION" && { _AS_LINENO_WORKS; }') 2>/dev/null
--           then
--             AS_UNSET(BASH_ENV)
--             AS_UNSET(ENV)
--             CONFIG_SHELL=$as_dir/$as_base
--             export CONFIG_SHELL
--             exec "$CONFIG_SHELL" "$[0]" ${1+"$[@]"}
--           fi;;
--         esac
--       done]);;
--  esac
--
--  # Create $as_me.lineno as a copy of $as_myself, but with $LINENO
--  # uniformly replaced by the line number.  The first 'sed' inserts a
--  # line-number line before each line; the second 'sed' does the real
--  # work.  The second script uses 'N' to pair each line-number line
--  # with the numbered line, and appends trailing '-' during
--  # substitution so that $LINENO is not a special case at line end.
--  # (Raja R Harinath suggested sed '=', and Paul Eggert wrote the
--  # second 'sed' script.  Blame Lee E. McMahon for sed's syntax.  :-)
--  sed '=' <$as_myself |
--    sed '
--      N
--      s,$,-,
--      : loop
--      s,^\([['$as_cr_digits']]*\)\(.*\)[[$]]LINENO\([[^'$as_cr_alnum'_]]\),\1\2\1\3,
--      t loop
--      s,-$,,
--      s,^[['$as_cr_digits']]*\n,,
--    ' >$as_me.lineno &&
--  chmod +x $as_me.lineno ||
--    AS_ERROR([cannot create $as_me.lineno; rerun with a POSIX shell])
--
--  # Don't try to exec as it changes $[0], causing all sort of problems
--  # (the dirname of $[0] is not the place where we might find the
--  # original and so on.  Autoconf is especially sensible to this).
--  . ./$as_me.lineno
--  # Exit status is that of the last command.
--  exit
--}
--])# _AS_LINENO_PREPARE
-+ac_builddir=$builddir
-+])
-+
-+
-+# _AS_DETECT_BETTER_SHELL and its helper _AS_RUN (from m4sh.m4; both
-+# historically part of _AS_LINENO_PREPARE) also need tweaking, to make
-+# bash a last resort due to issues with sourcing .bashrc while entirely
-+# avoiding zsh, which passes itself off as ksh on some systems but runs
-+# parent shells' exit handlers from subshells, resulting in premature
-+# cleanup of temporary files (notably confdefs.h).
-+m4_copy([_AS_DETECT_BETTER_SHELL], [NCBI_ORIG__AS_DETECT_BETTER_SHELL])
-+m4_copy([_AS_RUN], [NCBI_ORIG___AS_RUN])
-+
-+m4_define([_AS_DETECT_BETTER_SHELL],
-+  [patsubst(m4_defn([NCBI_ORIG__AS_DETECT_BETTER_SHELL]),
-+     [sh bash ksh sh5], [sh ksh sh5 bash])])
-+m4_define([_AS_RUN],
-+[m4_divert_once([M4SH-SANITIZE], [AS_UNSET(ZSH_VERSION)])dnl
-+NCBI_ORIG___AS_RUN([test -z "${ZSH_VERSION+set}" || exit $?; $1], [$2])])
- 
- 
- # One more hack: suppress PACKAGE_*, as we don't use them and some
- # third-party libraries expose their corresponding settings, leading
- # to preprocessor warnings.
--m4_define([NCBI_ORIG_ACDU], m4_defn([AC_DEFINE_UNQUOTED]))
-+m4_copy([AC_DEFINE_UNQUOTED], [NCBI_ORIG_AC_DEFINE_UNQUOTED])
- m4_define([AC_DEFINE_UNQUOTED],
-    [ifelse(m4_substr([$1], 0, 8), [PACKAGE_], [],
--       [NCBI_ORIG_ACDU($@)])])
-+       [NCBI_ORIG_AC_DEFINE_UNQUOTED($@)])])
- 
- 
- AC_DEFUN(NCBI_FIX_DIR,
-@@ -158,7 +76,7 @@
-        AC_MSG_WARN([Proceeding without questions per --without-caution]) ;;
-     * )
-        echo "$1 [[y/N]]"
--       read answer
-+       read answer <& AS_ORIGINAL_STDIN_FD
-        case "$answer" in
-          [[Yy]]* )  AC_MSG_WARN([Proceeding at your own risk...]) ;;
-          *       )  AC_MSG_ERROR([Configuration has been canceled by user.]) ;;
---- ncbi_cxx--12_0_0/src/build-system/configure.ac.ori     2014/05/05 12:38:59     62744
-+++ ncbi_cxx--12_0_0/src/build-system/configure.ac     2014/05/05 13:59:33     62745
-@@ -38,7 +38,7 @@
- #
- #############################################################################
- 
--AC_PREREQ(2.59)
-+AC_PREREQ(2.60)
- 
- dnl Early setup, most crucially for locking.  The diversion magic lets
- dnl this occur before AC_INIT, which already interferes with other
-@@ -493,6 +493,10 @@
-    [***** See also HTML documentation in ./doc/index.html *****])
- 
- 
-+AC_DIVERT_PUSH(PARSE_ARGS)
-+dnl As of Autoconf 2.60, this needs to run too early for config.log,
-+dnl to which AC_MSG_ERROR normally copies its output, to be available.
-+m4_rename([AS_MESSAGE_LOG_FD], [NCBI_ORIG_ASMLFD])
- #### Check the passed arguments against the list of available ones
- x_with_list="\
- debug max-debug symbols optimization profiling tcheck dll static static-exe \
-@@ -564,7 +568,7 @@
-       | --with-muparser=* | --with-hdf5=* | --with-jni=* | --with-magic=* \
-       | --x-includes=* | --x-libraries=* | --with-3psw=* \
-       | --target=* | --with-runpath=* | --with-relative-runpath=* \
--      | --no-create | --no-recursion)
-+      | --help | --no-create | --no-recursion)
-       ;;
- 
-       * )
-@@ -572,6 +576,8 @@
-       ;;
-    esac
- done
-+m4_rename([NCBI_ORIG_ASMLFD], [AS_MESSAGE_LOG_FD])
-+AC_DIVERT_POP
- 
- 
- if test "$with_gbench" = "yes" ; then
-@@ -2176,7 +2182,7 @@
- fi
- 
- AC_PATH_PROG(TOUCH, touch, [], /bin:/usr/bin:$PATH)
--AC_PATH_PROG(GREP, grep)
-+dnl AC_PATH_PROG(GREP, grep)
- AC_PROG_EGREP
- AC_MSG_CHECKING([how to run $EGREP quietly])
- if test -z "`echo foo | $EGREP -q fo+ 2>>config.log || echo $?`"; then
---- ncbi_cxx--12_0_0/include/common/config/ncbiconf_xcode.h.ori    2014/05/05 14:10:55     62749
-+++ ncbi_cxx--12_0_0/include/common/config/ncbiconf_xcode.h    2014/05/05 14:23:49     62750
-@@ -694,7 +694,7 @@
- /* Define to empty if `const' does not conform to ANSI C. */
- /* #undef const */
- 
--/* Define to `unsigned' if <sys/types.h> does not define. */
-+/* Define to `unsigned int' if <sys/types.h> does not define. */
- /* #undef size_t */
- 
- /*
---- ncbi_cxx--12_0_0/src/build-system/config.h.in.ori      2014/05/05 14:10:55     62749
-+++ ncbi_cxx--12_0_0/src/build-system/config.h.in      2014/05/05 14:23:49     62750
-@@ -802,37 +802,37 @@
-    by a signal. */
- #undef SELECT_UPDATES_TIMEOUT
- 
--/* The size of a `char', as computed by sizeof. */
-+/* The size of `char', as computed by sizeof. */
- #undef SIZEOF_CHAR
- 
--/* The size of a `double', as computed by sizeof. */
-+/* The size of `double', as computed by sizeof. */
- #undef SIZEOF_DOUBLE
- 
--/* The size of a `float', as computed by sizeof. */
-+/* The size of `float', as computed by sizeof. */
- #undef SIZEOF_FLOAT
- 
--/* The size of a `int', as computed by sizeof. */
-+/* The size of `int', as computed by sizeof. */
- #undef SIZEOF_INT
- 
--/* The size of a `long', as computed by sizeof. */
-+/* The size of `long', as computed by sizeof. */
- #undef SIZEOF_LONG
- 
--/* The size of a `long double', as computed by sizeof. */
-+/* The size of `long double', as computed by sizeof. */
- #undef SIZEOF_LONG_DOUBLE
- 
--/* The size of a `long long', as computed by sizeof. */
-+/* The size of `long long', as computed by sizeof. */
- #undef SIZEOF_LONG_LONG
- 
--/* The size of a `short', as computed by sizeof. */
-+/* The size of `short', as computed by sizeof. */
- #undef SIZEOF_SHORT
- 
--/* The size of a `size_t', as computed by sizeof. */
-+/* The size of `size_t', as computed by sizeof. */
- #undef SIZEOF_SIZE_T
- 
--/* The size of a `void*', as computed by sizeof. */
-+/* The size of `void*', as computed by sizeof. */
- #undef SIZEOF_VOIDP
- 
--/* The size of a `__int64', as computed by sizeof. */
-+/* The size of `__int64', as computed by sizeof. */
- #undef SIZEOF___INT64
- 
- /* Define to 1 if the stack grows down. */
-@@ -873,5 +873,5 @@
- /* Define to empty if `const' does not conform to ANSI C. */
- #undef const
- 
--/* Define to `unsigned' if <sys/types.h> does not define. */
-+/* Define to `unsigned int' if <sys/types.h> does not define. */
- #undef size_t
---- ncbi_cxx--12_0_0/src/build-system/aclocal.m4.ori       2014/05/06 13:12:18     62759
-+++ ncbi_cxx--12_0_0/src/build-system/aclocal.m4       2014/05/06 13:42:48     62760
-@@ -11,6 +11,7 @@
- 
- NCBI_ORIG__AC_SRCDIRS(["$ac_dir_in"])
- 
-+AS_SET_CATFILE([ac_abs_top_srcdir], [$ac_dir_in], [$real_srcdir])
- ac_builddir=$builddir
- ])
- 
-
diff --git a/sci-biology/ncbi-tools++/files/ncbi-tools++-18.0.0-configure.patch b/sci-biology/ncbi-tools++/files/ncbi-tools++-18.0.0-configure.patch
deleted file mode 100644
index b2d887c92..000000000
--- a/sci-biology/ncbi-tools++/files/ncbi-tools++-18.0.0-configure.patch
+++ /dev/null
@@ -1,20 +0,0 @@
---- ncbi_cxx--12_0_0/src/build-system/configure.ori	2014-06-25 23:47:05.000000000 +0200
-+++ ncbi_cxx--12_0_0/src/build-system/configure	2014-06-25 23:52:35.000000000 +0200
-@@ -3201,6 +3203,17 @@
-       *\ -O* | *\ -xO* ) skip_fast_flags=yes ;;
-    esac
- fi
-+if test -n "$with_projects"; then
-+   case "$with_projects" in
-+      /* ) abs_projects=$with_projects         ;;
-+      yes) abs_projects=$srcdir/projects       ;;
-+      *  ) abs_projects=$srcdir/$with_projects ;;
-+   esac
-+   test -r "$abs_projects"  ||  \
-+      { { echo "$as_me:$LINENO: error: unable to read requested projects file \"$abs_projects\"." >&5
-+echo "$as_me: error: unable to read requested projects file \"$abs_projects\"." >&2;}
-+   { (exit 1); exit 1; }; }
-+fi
- 
- #### Always define this
- 
diff --git a/sci-biology/ncbi-tools++/files/ncbi-tools++-18.0.0-fix-annotwriter-linking.patch b/sci-biology/ncbi-tools++/files/ncbi-tools++-18.0.0-fix-annotwriter-linking.patch
deleted file mode 100644
index c9428084d..000000000
--- a/sci-biology/ncbi-tools++/files/ncbi-tools++-18.0.0-fix-annotwriter-linking.patch
+++ /dev/null
@@ -1,15 +0,0 @@
-Index: c++.18.0.0/src/app/annotwriter/Makefile.annotwriter.app
-===================================================================
---- c++.18.0.0/src/app/annotwriter/Makefile.annotwriter.app	(revision 523253)
-+++ c++.18.0.0/src/app/annotwriter/Makefile.annotwriter.app	(working copy)
-@@ -8,8 +8,8 @@
- 
- APP = annotwriter
- SRC = annotwriter
--LIB = xobjwrite variation_utils $(OBJREAD_LIBS) xalnmgr xobjutil \
--      gbseq entrez2cli entrez2 tables $(OBJMGR_LIBS)
-+LIB = xobjwrite $(XFORMAT_LIBS) variation_utils $(OBJREAD_LIBS) xalnmgr \
-+      xobjutil entrez2cli entrez2 tables xregexp $(PCRE_LIB) $(OBJMGR_LIBS)
- 
- LIBS = $(CMPRS_LIBS) $(NETWORK_LIBS) $(DL_LIBS) $(ORIG_LIBS)
- 
diff --git a/sci-biology/ncbi-tools++/files/ncbi-tools++-18.0.0-fix-app-blast_sample-linking.patch b/sci-biology/ncbi-tools++/files/ncbi-tools++-18.0.0-fix-app-blast_sample-linking.patch
deleted file mode 100644
index 7a158dc5c..000000000
--- a/sci-biology/ncbi-tools++/files/ncbi-tools++-18.0.0-fix-app-blast_sample-linking.patch
+++ /dev/null
@@ -1,26 +0,0 @@
-Index: c++.18.0.0/src/sample/app/blast/Makefile.blast_sample.app
-===================================================================
---- c++.18.0.0/src/sample/app/blast/Makefile.blast_sample.app	(revision 523253)
-+++ c++.18.0.0/src/sample/app/blast/Makefile.blast_sample.app	(working copy)
-@@ -12,7 +12,7 @@
- # the lines reading "### BEGIN/END COPIED SETTINGS" in any way.
- 
- ### BEGIN COPIED SETTINGS
--LIB_ = xobjsimple $(BLAST_LIBS) $(OBJMGR_LIBS)
-+LIB_ = xobjsimple $(BLAST_LIBS) xregexp $(PCRE_LIB) $(OBJMGR_LIBS)
- LIB = $(LIB_:%=%$(STATIC))
- LIBS = $(CMPRS_LIBS) $(NETWORK_LIBS) $(DL_LIBS) $(ORIG_LIBS)
- 
-Index: c++.18.0.0/src/sample/app/blast/Makefile.vsrun_sample.app
-===================================================================
---- c++.18.0.0/src/sample/app/blast/Makefile.vsrun_sample.app	(revision 523253)
-+++ c++.18.0.0/src/sample/app/blast/Makefile.vsrun_sample.app	(working copy)
-@@ -12,7 +12,7 @@
- # the lines reading "### BEGIN/END COPIED SETTINGS" in any way.
- 
- ### BEGIN COPIED SETTINGS
--LIB_ = xobjsimple $(BLAST_INPUT_LIBS) $(BLAST_LIBS) $(OBJMGR_LIBS)
-+LIB_ = xobjsimple $(BLAST_INPUT_LIBS) $(BLAST_LIBS) xregexp $(PCRE_LIB) $(OBJMGR_LIBS)
- LIB = $(LIB_:%=%$(STATIC))
- LIBS = $(CMPRS_LIBS) $(NETWORK_LIBS) $(DL_LIBS) $(ORIG_LIBS)
- 
diff --git a/sci-biology/ncbi-tools++/files/ncbi-tools++-18.0.0-fix-app-compartp-linking.patch b/sci-biology/ncbi-tools++/files/ncbi-tools++-18.0.0-fix-app-compartp-linking.patch
deleted file mode 100644
index 749c2e57f..000000000
--- a/sci-biology/ncbi-tools++/files/ncbi-tools++-18.0.0-fix-app-compartp-linking.patch
+++ /dev/null
@@ -1,29 +0,0 @@
-Index: c++.18.0.0/src/app/compart/Makefile.compart.app
-===================================================================
---- c++.18.0.0/src/app/compart/Makefile.compart.app	(revision 523253)
-+++ c++.18.0.0/src/app/compart/Makefile.compart.app	(working copy)
-@@ -5,8 +5,8 @@
- APP = compart
- SRC = compart
- 
--LIB =  xalgoalignsplign xalgoalignutil xalgoalignnw xqueryparse \
--       $(BLAST_LIBS:%=%$(STATIC)) \
-+LIB =  xalgoalignsplign xalgoalignutil xalgoalignnw xalgoseq taxon1 \
-+       $(BLAST_LIBS:%=%$(STATIC)) xqueryparse xregexp $(PCRE_LIB) \
-        $(OBJMGR_LIBS:%=%$(STATIC))
- 
- LIBS = $(CMPRS_LIBS) $(NETWORK_LIBS) $(DL_LIBS) $(ORIG_LIBS)
-Index: c++.18.0.0/src/app/compart/Makefile.compartp.app
-===================================================================
---- c++.18.0.0/src/app/compart/Makefile.compartp.app	(revision 523253)
-+++ c++.18.0.0/src/app/compart/Makefile.compartp.app	(working copy)
-@@ -5,7 +5,8 @@
- APP = compartp
- SRC = compartp
- 
--LIB = prosplign  xalgoalignutil $(BLAST_LIBS)  xqueryparse $(OBJMGR_LIBS)
-+LIB = prosplign xalgoalignutil xalgoseq taxon1 $(BLAST_LIBS) xqueryparse \
-+      xregexp $(PCRE_LIB) $(OBJMGR_LIBS)
- 
- LIBS = $(CMPRS_LIBS) $(PCRE_LIBS) $(NETWORK_LIBS) $(DL_LIBS) $(ORIG_LIBS)
- 
diff --git a/sci-biology/ncbi-tools++/files/ncbi-tools++-18.0.0-fix-app-convert_seq-linking.patch b/sci-biology/ncbi-tools++/files/ncbi-tools++-18.0.0-fix-app-convert_seq-linking.patch
deleted file mode 100644
index e495c9645..000000000
--- a/sci-biology/ncbi-tools++/files/ncbi-tools++-18.0.0-fix-app-convert_seq-linking.patch
+++ /dev/null
@@ -1,11 +0,0 @@
---- ncbi_cxx--18_0_0/src/app/convert_seq/Makefile.convert_seq.app.ori	2017-03-23 19:24:31.534280319 +0100
-+++ ncbi_cxx--18_0_0/src/app/convert_seq/Makefile.convert_seq.app	2017-03-23 19:25:14.395360214 +0100
-@@ -2,7 +2,7 @@
- 
- APP = convert_seq
- SRC = convert_seq
--LIB = $(ncbi_xloader_wgs) $(SRAREAD_LIBS) xobjwrite \
-+LIB = $(ncbi_xloader_wgs) $(SRAREAD_LIBS) xobjwrite variation_utils \
-       $(OBJREAD_LIBS) $(XFORMAT_LIBS) xalnmgr xobjutil tables xregexp \
-       $(PCRE_LIB) $(OBJMGR_LIBS)
- 
diff --git a/sci-biology/ncbi-tools++/files/ncbi-tools++-18.0.0-fix-app-hfilter-linking.patch b/sci-biology/ncbi-tools++/files/ncbi-tools++-18.0.0-fix-app-hfilter-linking.patch
deleted file mode 100644
index 63bbcc45a..000000000
--- a/sci-biology/ncbi-tools++/files/ncbi-tools++-18.0.0-fix-app-hfilter-linking.patch
+++ /dev/null
@@ -1,14 +0,0 @@
-Index: c++.18.0.0/src/app/hfilter/Makefile.hfilter.app
-===================================================================
---- c++.18.0.0/src/app/hfilter/Makefile.hfilter.app	(revision 523253)
-+++ c++.18.0.0/src/app/hfilter/Makefile.hfilter.app	(working copy)
-@@ -5,7 +5,8 @@
- APP = hfilter
- SRC = hitfilter_app
- 
--LIB = xalgoalignutil $(BLAST_LIBS) xqueryparse $(OBJMGR_LIBS)
-+LIB = xalgoalignutil xalgoseq taxon1 $(BLAST_LIBS) \
-+	xqueryparse xregexp $(PCRE_LIB) $(OBJMGR_LIBS)
- 
- LIBS = $(CMPRS_LIBS) $(NETWORK_LIBS) $(DL_LIBS) $(ORIG_LIBS)
- 
diff --git a/sci-biology/ncbi-tools++/files/ncbi-tools++-18.0.0-fix-app-igblast-linking.patch b/sci-biology/ncbi-tools++/files/ncbi-tools++-18.0.0-fix-app-igblast-linking.patch
deleted file mode 100644
index ffd3f897f..000000000
--- a/sci-biology/ncbi-tools++/files/ncbi-tools++-18.0.0-fix-app-igblast-linking.patch
+++ /dev/null
@@ -1,28 +0,0 @@
-Index: c++.18.0.0/src/app/igblast/Makefile.igblastn.app
-===================================================================
---- c++.18.0.0/src/app/igblast/Makefile.igblastn.app	(revision 523253)
-+++ c++.18.0.0/src/app/igblast/Makefile.igblastn.app	(working copy)
-@@ -2,7 +2,8 @@
- 
- APP = igblastn
- SRC = igblastn_app
--LIB_ = xalgoalignutil $(BLAST_INPUT_LIBS) xqueryparse $(BLAST_LIBS) $(OBJMGR_LIBS)
-+LIB_ = xalgoalignutil $(BLAST_INPUT_LIBS) xqueryparse $(BLAST_LIBS) \
-+	xregexp $(PCRE_LIB) $(OBJMGR_LIBS)
- LIB = blast_app_util igblast $(LIB_:%=%$(STATIC))
- 
- # De-universalize Mac builds to work around a PPC toolchain limitation
-Index: c++.18.0.0/src/app/igblast/Makefile.igblastp.app
-===================================================================
---- c++.18.0.0/src/app/igblast/Makefile.igblastp.app	(revision 523253)
-+++ c++.18.0.0/src/app/igblast/Makefile.igblastp.app	(working copy)
-@@ -2,7 +2,8 @@
- 
- APP = igblastp
- SRC = igblastp_app
--LIB_ = $(BLAST_INPUT_LIBS) $(BLAST_LIBS) $(OBJMGR_LIBS)
-+LIB_ = xalgoalignutil $(BLAST_INPUT_LIBS) xqueryparse $(BLAST_LIBS) \
-+	xregexp $(PCRE_LIB) $(OBJMGR_LIBS)
- LIB = blast_app_util igblast $(LIB_:%=%$(STATIC))
- 
- # De-universalize Mac builds to work around a PPC toolchain limitation
diff --git a/sci-biology/ncbi-tools++/files/ncbi-tools++-18.0.0-fix-app-rmblastn-linking.patch b/sci-biology/ncbi-tools++/files/ncbi-tools++-18.0.0-fix-app-rmblastn-linking.patch
deleted file mode 100644
index fce7263b2..000000000
--- a/sci-biology/ncbi-tools++/files/ncbi-tools++-18.0.0-fix-app-rmblastn-linking.patch
+++ /dev/null
@@ -1,11 +0,0 @@
---- ncbi_cxx--18_0_0/src/app/rmblastn/Makefile.rmblastn.app.ori	2017-03-26 18:49:50.431994978 +0200
-+++ ncbi_cxx--18_0_0/src/app/rmblastn/Makefile.rmblastn.app	2017-03-26 18:50:11.222552131 +0200
-@@ -2,7 +2,7 @@
- 
- APP = rmblastn
- SRC = rmblastn_app
--LIB_ = $(BLAST_INPUT_LIBS) $(BLAST_LIBS) $(OBJMGR_LIBS)
-+LIB_ = $(BLAST_INPUT_LIBS) $(BLAST_LIBS) xregexp $(PCRE_LIB) $(OBJMGR_LIBS)
- LIB = blast_app_util $(LIB_:%=%$(STATIC))
- 
- # De-universalize Mac builds to work around a PPC toolchain limitation
diff --git a/sci-biology/ncbi-tools++/files/ncbi-tools++-18.0.0-fix-app-table2asn-linking.patch b/sci-biology/ncbi-tools++/files/ncbi-tools++-18.0.0-fix-app-table2asn-linking.patch
deleted file mode 100644
index 222cb2c06..000000000
--- a/sci-biology/ncbi-tools++/files/ncbi-tools++-18.0.0-fix-app-table2asn-linking.patch
+++ /dev/null
@@ -1,13 +0,0 @@
---- ncbi_cxx--18_0_0/src/app/table2asn/Makefile.table2asn.app.ori	2017-03-27 00:41:58.742206850 +0200
-+++ ncbi_cxx--18_0_0/src/app/table2asn/Makefile.table2asn.app	2017-03-27 00:43:13.142206236 +0200
-@@ -12,8 +12,8 @@
- 
- LIB  = xdiscrepancy xalgophytree fastme prosplign xalgoalignutil xalgoseq xmlwrapp \
-        xvalidate xobjwrite xobjreadex valerr biotree macro \
--       $(OBJEDIT_LIBS) $(XFORMAT_LIBS) $(BLAST_LIBS) id2cli \
--       xregexp $(PCRE_LIB) $(SRAREAD_LIBS) $(DATA_LOADERS_UTIL_LIB) $(OBJMGR_LIBS)
-+       $(OBJEDIT_LIBS) $(XFORMAT_LIBS) $(BLAST_LIBS) taxon1 id2cli \
-+       xregexp $(PCRE_LIB) xqueryparse $(DATA_LOADERS_UTIL_LIB) $(OBJMGR_LIBS)
- 
- LIBS = $(LIBXSLT_LIBS) $(DATA_LOADERS_UTIL_LIBS) $(LIBXML_LIBS) $(CMPRS_LIBS) $(PCRE_LIBS) \
-        $(SRA_SDK_SYSLIBS) \
diff --git a/sci-biology/ncbi-tools++/files/ncbi-tools++-18.0.0-fix-app-tls-linking.patch b/sci-biology/ncbi-tools++/files/ncbi-tools++-18.0.0-fix-app-tls-linking.patch
deleted file mode 100644
index 541dc2514..000000000
--- a/sci-biology/ncbi-tools++/files/ncbi-tools++-18.0.0-fix-app-tls-linking.patch
+++ /dev/null
@@ -1,11 +0,0 @@
---- ncbi_cxx--18_0_0/src/app/tls/Makefile.tls.app.ori	2017-03-27 02:33:36.312151540 +0200
-+++ ncbi_cxx--18_0_0/src/app/tls/Makefile.tls.app	2017-03-27 02:34:19.372151184 +0200
-@@ -10,7 +10,7 @@
- SRC = tls
- 
- LIB = $(OBJEDIT_LIBS) $(XFORMAT_LIBS) xalnmgr xobjutil \
--       xregexp $(PCRE_LIB) $(OBJMGR_LIBS)
-+       xregexp $(PCRE_LIB) tables $(OBJMGR_LIBS)
- 
- LIBS = $(PCRE_LIBS) \
-        $(NETWORK_LIBS) $(CMPRS_LIBS) $(ORIG_LIBS)
diff --git a/sci-biology/ncbi-tools++/files/ncbi-tools++-18.0.0-fix-app-vecscreen-linking.patch b/sci-biology/ncbi-tools++/files/ncbi-tools++-18.0.0-fix-app-vecscreen-linking.patch
deleted file mode 100644
index 898e3a70b..000000000
--- a/sci-biology/ncbi-tools++/files/ncbi-tools++-18.0.0-fix-app-vecscreen-linking.patch
+++ /dev/null
@@ -1,13 +0,0 @@
-Index: c++.18.0.0/src/app/vecscreen/Makefile.vecscreen.app
-===================================================================
---- c++.18.0.0/src/app/vecscreen/Makefile.vecscreen.app	(revision 523253)
-+++ c++.18.0.0/src/app/vecscreen/Makefile.vecscreen.app	(working copy)
-@@ -4,7 +4,7 @@
- 
- APP = vecscreen
- SRC = vecscreen_app
--LIB_ = $(BLAST_INPUT_LIBS) $(BLAST_LIBS) $(OBJMGR_LIBS)
-+LIB_ = $(BLAST_INPUT_LIBS) $(BLAST_LIBS) xregexp $(PCRE_LIB) $(OBJMGR_LIBS)
- LIB = $(LIB_:%=%$(STATIC))
- # FIXME: do we need blast_app_util
- #LIB = blast_app_util $(LIB_:%=%$(STATIC))
diff --git a/sci-biology/ncbi-tools++/files/ncbi-tools++-18.0.0-fix-apps-blast-linking.patch b/sci-biology/ncbi-tools++/files/ncbi-tools++-18.0.0-fix-apps-blast-linking.patch
deleted file mode 100644
index e9dd1f710..000000000
--- a/sci-biology/ncbi-tools++/files/ncbi-tools++-18.0.0-fix-apps-blast-linking.patch
+++ /dev/null
@@ -1,130 +0,0 @@
-Index: c++.18.0.0/src/app/blast/Makefile.blast_formatter.app
-===================================================================
---- c++.18.0.0/src/app/blast/Makefile.blast_formatter.app	(revision 523253)
-+++ c++.18.0.0/src/app/blast/Makefile.blast_formatter.app	(working copy)
-@@ -2,7 +2,7 @@
- 
- APP = blast_formatter
- SRC = blast_formatter
--LIB_ = $(BLAST_INPUT_LIBS) $(BLAST_LIBS) $(OBJMGR_LIBS)
-+LIB_ = $(BLAST_INPUT_LIBS) $(BLAST_LIBS) xregexp $(PCRE_LIB) $(OBJMGR_LIBS)
- LIB = blast_app_util $(LIB_:%=%$(STATIC))
- 
- # De-universalize Mac builds to work around a PPC toolchain limitation
-Index: c++.18.0.0/src/app/blast/Makefile.blastp.app
-===================================================================
---- c++.18.0.0/src/app/blast/Makefile.blastp.app	(revision 523253)
-+++ c++.18.0.0/src/app/blast/Makefile.blastp.app	(working copy)
-@@ -4,7 +4,7 @@
- 
- APP = blastp
- SRC = blastp_app
--LIB_ = $(BLAST_INPUT_LIBS) $(BLAST_LIBS) $(OBJMGR_LIBS)
-+LIB_ = $(BLAST_INPUT_LIBS) $(BLAST_LIBS) xregexp $(PCRE_LIB) $(OBJMGR_LIBS)
- LIB = blast_app_util $(LIB_:%=%$(STATIC))
- 
- # De-universalize Mac builds to work around a PPC toolchain limitation
-Index: c++.18.0.0/src/app/blast/Makefile.blastx.app
-===================================================================
---- c++.18.0.0/src/app/blast/Makefile.blastx.app	(revision 523253)
-+++ c++.18.0.0/src/app/blast/Makefile.blastx.app	(working copy)
-@@ -4,7 +4,7 @@
- 
- APP = blastx
- SRC = blastx_app
--LIB_ = $(BLAST_INPUT_LIBS) $(BLAST_LIBS) $(OBJMGR_LIBS)
-+LIB_ = $(BLAST_INPUT_LIBS) $(BLAST_LIBS) xregexp $(PCRE_LIB) $(OBJMGR_LIBS)
- LIB = blast_app_util $(LIB_:%=%$(STATIC))
- 
- # De-universalize Mac builds to work around a PPC toolchain limitation
-Index: c++.18.0.0/src/app/blast/Makefile.deltablast.app
-===================================================================
---- c++.18.0.0/src/app/blast/Makefile.deltablast.app	(revision 523253)
-+++ c++.18.0.0/src/app/blast/Makefile.deltablast.app	(working copy)
-@@ -1,7 +1,7 @@
- 
- APP = deltablast
- SRC = deltablast_app
--LIB_ = $(BLAST_INPUT_LIBS) $(BLAST_LIBS) $(OBJMGR_LIBS)
-+LIB_ = $(BLAST_INPUT_LIBS) $(BLAST_LIBS) xregexp $(PCRE_LIB) $(OBJMGR_LIBS)
- LIB = blast_app_util $(LIB_:%=%$(STATIC))
- 
- # De-universalize Mac builds to work around a PPC toolchain limitation
-Index: c++.18.0.0/src/app/blast/Makefile.psiblast.app
-===================================================================
---- c++.18.0.0/src/app/blast/Makefile.psiblast.app	(revision 523253)
-+++ c++.18.0.0/src/app/blast/Makefile.psiblast.app	(working copy)
-@@ -2,7 +2,7 @@
- 
- APP = psiblast
- SRC = psiblast_app
--LIB_ = $(BLAST_INPUT_LIBS) $(BLAST_LIBS) $(OBJMGR_LIBS)
-+LIB_ = $(BLAST_INPUT_LIBS) $(BLAST_LIBS) xregexp $(PCRE_LIB) $(OBJMGR_LIBS)
- LIB = blast_app_util $(LIB_:%=%$(STATIC))
- 
- # De-universalize Mac builds to work around a PPC toolchain limitation
-Index: c++.18.0.0/src/app/blast/Makefile.rpsblast.app
-===================================================================
---- c++.18.0.0/src/app/blast/Makefile.rpsblast.app	(revision 523253)
-+++ c++.18.0.0/src/app/blast/Makefile.rpsblast.app	(working copy)
-@@ -2,7 +2,7 @@
- 
- APP = rpsblast
- SRC = rpsblast_app
--LIB_ = $(BLAST_INPUT_LIBS) $(BLAST_LIBS) $(OBJMGR_LIBS)
-+LIB_ = $(BLAST_INPUT_LIBS) $(BLAST_LIBS) xregexp $(PCRE_LIB) $(OBJMGR_LIBS)
- LIB = blast_app_util $(LIB_:%=%$(STATIC))
- 
- # De-universalize Mac builds to work around a PPC toolchain limitation
-Index: c++.18.0.0/src/app/blast/Makefile.rpstblastn.app
-===================================================================
---- c++.18.0.0/src/app/blast/Makefile.rpstblastn.app	(revision 523253)
-+++ c++.18.0.0/src/app/blast/Makefile.rpstblastn.app	(working copy)
-@@ -2,7 +2,7 @@
- 
- APP = rpstblastn
- SRC = rpstblastn_app
--LIB_ = $(BLAST_INPUT_LIBS) $(BLAST_LIBS) $(OBJMGR_LIBS)
-+LIB_ = $(BLAST_INPUT_LIBS) $(BLAST_LIBS) xregexp $(PCRE_LIB) $(OBJMGR_LIBS)
- LIB = blast_app_util $(LIB_:%=%$(STATIC))
- 
- # De-universalize Mac builds to work around a PPC toolchain limitation
-Index: c++.18.0.0/src/app/blast/Makefile.seedtop.app
-===================================================================
---- c++.18.0.0/src/app/blast/Makefile.seedtop.app	(revision 523253)
-+++ c++.18.0.0/src/app/blast/Makefile.seedtop.app	(working copy)
-@@ -2,7 +2,7 @@
- 
- APP = seedtop
- SRC = seedtop_app
--LIB_ = $(BLAST_INPUT_LIBS) $(BLAST_LIBS) $(OBJMGR_LIBS)
-+LIB_ = $(BLAST_INPUT_LIBS) $(BLAST_LIBS) xregexp $(PCRE_LIB) $(OBJMGR_LIBS)
- LIB = blast_app_util $(LIB_:%=%$(STATIC))
- 
- # De-universalize Mac builds to work around a PPC toolchain limitation
-Index: c++.18.0.0/src/app/blast/Makefile.tblastn.app
-===================================================================
---- c++.18.0.0/src/app/blast/Makefile.tblastn.app	(revision 523253)
-+++ c++.18.0.0/src/app/blast/Makefile.tblastn.app	(working copy)
-@@ -4,7 +4,7 @@
- 
- APP = tblastn
- SRC = tblastn_app
--LIB_ = $(BLAST_INPUT_LIBS) $(BLAST_LIBS) $(OBJMGR_LIBS)
-+LIB_ = $(BLAST_INPUT_LIBS) $(BLAST_LIBS) xregexp $(PCRE_LIB) $(OBJMGR_LIBS)
- LIB = blast_app_util $(LIB_:%=%$(STATIC))
- 
- # De-universalize Mac builds to work around a PPC toolchain limitation
-Index: c++.18.0.0/src/app/blast/Makefile.tblastx.app
-===================================================================
---- c++.18.0.0/src/app/blast/Makefile.tblastx.app	(revision 523253)
-+++ c++.18.0.0/src/app/blast/Makefile.tblastx.app	(working copy)
-@@ -4,7 +4,7 @@
- 
- APP = tblastx
- SRC = tblastx_app
--LIB_ = $(BLAST_INPUT_LIBS) $(BLAST_LIBS) $(OBJMGR_LIBS)
-+LIB_ = $(BLAST_INPUT_LIBS) $(BLAST_LIBS) xregexp $(PCRE_LIB) $(OBJMGR_LIBS)
- LIB = blast_app_util $(LIB_:%=%$(STATIC))
- 
- # De-universalize Mac builds to work around a PPC toolchain limitation
diff --git a/sci-biology/ncbi-tools++/files/ncbi-tools++-18.0.0-fix-install.patch b/sci-biology/ncbi-tools++/files/ncbi-tools++-18.0.0-fix-install.patch
deleted file mode 100644
index 97e845fdb..000000000
--- a/sci-biology/ncbi-tools++/files/ncbi-tools++-18.0.0-fix-install.patch
+++ /dev/null
@@ -1,11 +0,0 @@
---- ncbi_cxx--12_0_0/src/build-system/Makefile.in.top.ori	2014-06-26 22:49:49.000000000 +0200
-+++ ncbi_cxx--12_0_0/src/build-system/Makefile.in.top	2014-06-26 22:50:57.000000000 +0200
-@@ -48,7 +48,7 @@
- 	    for x in *.a; do ln -s "$$x" "`basename \"$$x\" .a`-static.a"; done
- 	cd $(includedir0) && find * -name CVS -prune -o -print |\
-             cpio -pd $(pincludedir)
--	$(INSTALL) -m 644 $(incdir)/* $(pincludedir)
-+	$(INSTALL) -m 644 $(incdir)/*.* $(pincludedir)
- ## set up appropriate build and status directories somewhere under $(libdir)?
- 
- install-gbench:
diff --git a/sci-biology/ncbi-tools++/files/ncbi-tools++-18.0.0-fix-ncfetch-linking.patch b/sci-biology/ncbi-tools++/files/ncbi-tools++-18.0.0-fix-ncfetch-linking.patch
deleted file mode 100644
index aacb20a6c..000000000
--- a/sci-biology/ncbi-tools++/files/ncbi-tools++-18.0.0-fix-ncfetch-linking.patch
+++ /dev/null
@@ -1,11 +0,0 @@
---- ncbi_cxx--18_0_0/src/app/grid/util/Makefile.ncfetch.app.ori	2017-03-23 21:12:52.028724998 +0100
-+++ ncbi_cxx--18_0_0/src/app/grid/util/Makefile.ncfetch.app	2017-03-23 21:13:30.079737366 +0100
-@@ -5,7 +5,7 @@
- APP = ncfetch.cgi
- SRC = ncfetch
- 
--LIB = xcgi xconnserv xconnect xutil xncbi
-+LIB = xcgi xconnserv xthrserv xconnect xutil xncbi
- LIBS = $(NETWORK_LIBS) $(DL_LIBS) $(ORIG_LIBS)
- 
- WATCHERS = sadyrovr
diff --git a/sci-biology/ncbi-tools++/files/ncbi-tools++-18.0.0-fix-netcache_cgi_sample-linking.patch b/sci-biology/ncbi-tools++/files/ncbi-tools++-18.0.0-fix-netcache_cgi_sample-linking.patch
deleted file mode 100644
index e074046cf..000000000
--- a/sci-biology/ncbi-tools++/files/ncbi-tools++-18.0.0-fix-netcache_cgi_sample-linking.patch
+++ /dev/null
@@ -1,11 +0,0 @@
---- ncbi_cxx--18_0_0/src/sample/app/netcache/Makefile.netcache_cgi_sample.app.ori	2017-03-23 21:16:18.824226906 +0100
-+++ ncbi_cxx--18_0_0/src/sample/app/netcache/Makefile.netcache_cgi_sample.app	2017-03-23 21:16:50.085058615 +0100
-@@ -4,7 +4,7 @@
- SRC = netcache_cgi_sample
- 
- ### BEGIN COPIED SETTINGS
--LIB = xconnserv xconnect xcgi xhtml xutil xncbi
-+LIB = xconnserv xthrserv xconnect xcgi xhtml xutil xncbi
- 
- LIBS = $(NETWORK_LIBS) $(DL_LIBS) $(ORIG_LIBS)
- ### END COPIED SETTINGS
diff --git a/sci-biology/ncbi-tools++/files/ncbi-tools++-18.0.0-fix-netstorage_gc-linking.patch b/sci-biology/ncbi-tools++/files/ncbi-tools++-18.0.0-fix-netstorage_gc-linking.patch
deleted file mode 100644
index f237a86d8..000000000
--- a/sci-biology/ncbi-tools++/files/ncbi-tools++-18.0.0-fix-netstorage_gc-linking.patch
+++ /dev/null
@@ -1,11 +0,0 @@
---- ncbi_cxx--18_0_0/src/app/netstorage/utils/Makefile.netstorage_gc.app.ori	2017-03-23 21:22:14.463688886 +0100
-+++ ncbi_cxx--18_0_0/src/app/netstorage/utils/Makefile.netstorage_gc.app	2017-03-23 21:22:48.854603873 +0100
-@@ -10,7 +10,7 @@
- REQUIRES = MT Linux
- 
- 
--LIB =  netstorage ncbi_xcache_netcache xconnserv \
-+LIB =  netstorage ncbi_xcache_netcache xconnserv xthrserv \
-        $(SDBAPI_LIB) xconnect connssl xutil xncbi
- LIBS = $(SDBAPI_LIBS) $(NETWORK_LIBS) $(GNUTLS_LIBS) $(CMPRS_LIBS) $(DL_LIBS) $(ORIG_LIBS)
- 
diff --git a/sci-biology/ncbi-tools++/files/ncbi-tools++-18.0.0-fix-sample-app-cgi-linking.patch b/sci-biology/ncbi-tools++/files/ncbi-tools++-18.0.0-fix-sample-app-cgi-linking.patch
deleted file mode 100644
index c45d4ad96..000000000
--- a/sci-biology/ncbi-tools++/files/ncbi-tools++-18.0.0-fix-sample-app-cgi-linking.patch
+++ /dev/null
@@ -1,11 +0,0 @@
---- ncbi_cxx--18_0_0/src/sample/app/cgi/Makefile.cgi_session_sample.app.ori	2017-03-22 23:52:58.984696074 +0100
-+++ ncbi_cxx--18_0_0/src/sample/app/cgi/Makefile.cgi_session_sample.app	2017-03-22 23:53:54.746258126 +0100
-@@ -11,7 +11,7 @@
- # the lines reading "### BEGIN/END COPIED SETTINGS" in any way.
- 
- ### BEGIN COPIED SETTINGS
--LIB = xgridcgi xcgi xhtml xconnserv xconnect xutil xncbi
-+LIB = xgridcgi xcgi xhtml xconnserv xthrserv xconnect xutil xncbi
- 
- LIBS = $(NETWORK_LIBS) $(DL_LIBS) $(ORIG_LIBS)
- 
diff --git a/sci-biology/ncbi-tools++/files/ncbi-tools++-18.0.0-fix-speedtest-linking.patch b/sci-biology/ncbi-tools++/files/ncbi-tools++-18.0.0-fix-speedtest-linking.patch
deleted file mode 100644
index 9435e8b6a..000000000
--- a/sci-biology/ncbi-tools++/files/ncbi-tools++-18.0.0-fix-speedtest-linking.patch
+++ /dev/null
@@ -1,11 +0,0 @@
---- ncbi_cxx--18_0_0/src/app/speedtest/Makefile.speedtest.app.ori	2017-03-23 21:41:31.084603405 +0100
-+++ ncbi_cxx--18_0_0/src/app/speedtest/Makefile.speedtest.app	2017-03-23 21:45:47.601428174 +0100
-@@ -8,7 +8,7 @@
- 
- APP = speedtest
- SRC = speedtest
--LIB = prosplign xalgoalignutil xcleanup taxon3 valid valerr $(BLAST_LIBS) \
-+LIB = prosplign xalgoalignutil taxon1 xalgoseq xcleanup taxon3 valid valerr $(BLAST_LIBS) \
-       xqueryparse xregexp $(PCRE_LIB) $(OBJMGR_LIBS:%=%$(STATIC))
- 
- LIBS = $(CMPRS_LIBS) $(NETWORK_LIBS) $(DL_LIBS) $(PCRE_LIBS) $(ORIG_LIBS)
diff --git a/sci-biology/ncbi-tools++/files/ncbi-tools++-18.0.0-fix-splign-linking.patch b/sci-biology/ncbi-tools++/files/ncbi-tools++-18.0.0-fix-splign-linking.patch
deleted file mode 100644
index 56f213f08..000000000
--- a/sci-biology/ncbi-tools++/files/ncbi-tools++-18.0.0-fix-splign-linking.patch
+++ /dev/null
@@ -1,11 +0,0 @@
---- ncbi_cxx--18_0_0/src/app/splign/Makefile.splign.app.ori	2017-03-23 22:08:16.937327984 +0100
-+++ ncbi_cxx--18_0_0/src/app/splign/Makefile.splign.app	2017-03-23 22:09:19.208984755 +0100
-@@ -12,7 +12,7 @@
- LIB = xalgoalignsplign xalgoalignutil xalgoalignnw \
-       $(BLAST_DB_DATA_LOADER_LIBS) \
-       ncbi_xloader_lds2 lds2 sqlitewrapp \
--      xqueryparse xalgoseq $(PCRE_LIB) \
-+      xqueryparse xalgoseq taxon1 xregexp $(PCRE_LIB) \
-       $(BLAST_LIBS:%=%$(STATIC)) \
-       $(OBJMGR_LIBS:%=%$(STATIC))
- 
diff --git a/sci-biology/ncbi-tools++/files/ncbi-tools++-18.0.0-fix-srcchk-linking.patch b/sci-biology/ncbi-tools++/files/ncbi-tools++-18.0.0-fix-srcchk-linking.patch
deleted file mode 100644
index 49a4adb4e..000000000
--- a/sci-biology/ncbi-tools++/files/ncbi-tools++-18.0.0-fix-srcchk-linking.patch
+++ /dev/null
@@ -1,15 +0,0 @@
-Index: c++.18.0.0/src/app/srcchk/Makefile.srcchk.app
-===================================================================
---- c++.18.0.0/src/app/srcchk/Makefile.srcchk.app	(revision 523253)
-+++ c++.18.0.0/src/app/srcchk/Makefile.srcchk.app	(working copy)
-@@ -8,8 +8,8 @@
- 
- APP = srcchk
- SRC = srcchk
--LIB = xobjwrite variation_utils $(OBJREAD_LIBS) xalnmgr xobjutil \
--      gbseq entrez2cli entrez2 tables $(OBJMGR_LIBS)
-+LIB = xobjwrite $(XFORMAT_LIBS) variation_utils $(OBJREAD_LIBS) xalnmgr \
-+      xobjutil entrez2cli entrez2 tables xregexp $(PCRE_LIB) $(OBJMGR_LIBS)
- 
- LIBS = $(CMPRS_LIBS) $(NETWORK_LIBS) $(DL_LIBS) $(ORIG_LIBS)
- 
diff --git a/sci-biology/ncbi-tools++/files/ncbi-tools++-18.0.0-fix-undefined-lxncbi.patch b/sci-biology/ncbi-tools++/files/ncbi-tools++-18.0.0-fix-undefined-lxncbi.patch
deleted file mode 100644
index f0a27d85a..000000000
--- a/sci-biology/ncbi-tools++/files/ncbi-tools++-18.0.0-fix-undefined-lxncbi.patch
+++ /dev/null
@@ -1,10 +0,0 @@
---- work/ncbi_cxx--18_0_0/src/connect/Makefile.xthrserv.lib.ori	2017-03-17 22:33:51.569635396 +0100
-+++ ncbi_cxx--18_0_0/src/connect/Makefile.xthrserv.lib	2017-03-17 22:33:58.349811199 +0100
-@@ -4,6 +4,6 @@
- LIB      = xthrserv
- PROJ_TAG = core
- LIBS     = $(NETWORK_LIBS)
--DLL_LIB  = xutil xconnect
-+DLL_LIB  = xncbi xutil xconnect
- 
- WATCHERS = vakatov
diff --git a/sci-biology/ncbi-tools++/files/ncbi-tools++-18.0.0-fix-undefined-xobjread.patch b/sci-biology/ncbi-tools++/files/ncbi-tools++-18.0.0-fix-undefined-xobjread.patch
deleted file mode 100644
index 3c1cb0a9e..000000000
--- a/sci-biology/ncbi-tools++/files/ncbi-tools++-18.0.0-fix-undefined-xobjread.patch
+++ /dev/null
@@ -1,11 +0,0 @@
---- ncbi_cxx--18_0_0/src/app/asn2fasta/Makefile.asn2fasta.app.ori	2016-06-24 16:55:25.000000000 +0200
-+++ ncbi_cxx--18_0_0/src/app/asn2fasta/Makefile.asn2fasta.app	2017-03-21 14:07:31.070364301 +0100
-@@ -9,7 +9,7 @@
- APP = asn2fasta
- SRC = asn2fasta
- LIB = $(ncbi_xloader_wgs) $(SRAREAD_LIBS) \
--          xobjwrite xobjread $(XFORMAT_LIBS) xalnmgr xobjutil valerr xregexp \
-+          xobjwrite variation_utils $(OBJREAD_LIBS) $(XFORMAT_LIBS) xalnmgr xobjutil valerr xregexp \
- 	  ncbi_xdbapi_ftds dbapi $(ncbi_xreader_pubseqos2) $(FTDS_LIB) \
- 	  entrez2cli entrez2 tables $(OBJMGR_LIBS) $(PCRE_LIB)
- 
diff --git a/sci-biology/ncbi-tools++/files/ncbi-tools++-18.0.0-never_build_test_boost.patch b/sci-biology/ncbi-tools++/files/ncbi-tools++-18.0.0-never_build_test_boost.patch
deleted file mode 100644
index 68baea046..000000000
--- a/sci-biology/ncbi-tools++/files/ncbi-tools++-18.0.0-never_build_test_boost.patch
+++ /dev/null
@@ -1,11 +0,0 @@
---- ncbi_cxx--12_0_0/src/corelib/Makefile.in.ori	2016-12-01 20:28:33.239758102 +0100
-+++ ncbi_cxx--12_0_0/src/corelib/Makefile.in	2016-12-01 20:28:46.330110659 +0100
-@@ -7,7 +7,7 @@
- #################################
- 
- USR_PROJ = precompile
--LIB_PROJ = corelib test_mt test_boost
-+LIB_PROJ = corelib test_mt
- SUB_PROJ = test
- PROJ_TAG = core
- 
diff --git a/sci-biology/ncbi-tools++/files/ncbi-tools++-18.0.0-remove-old-symlinks.patch b/sci-biology/ncbi-tools++/files/ncbi-tools++-18.0.0-remove-old-symlinks.patch
deleted file mode 100644
index 098a9ad1e..000000000
--- a/sci-biology/ncbi-tools++/files/ncbi-tools++-18.0.0-remove-old-symlinks.patch
+++ /dev/null
@@ -1,10 +0,0 @@
---- ncbi_cxx--18_0_0/src/dbapi/lang_bind/python/tests/Makefile.symlink.in.old	2017-03-26 19:01:58.101495278 +0200
-+++ ncbi_cxx--18_0_0/src/dbapi/lang_bind/python/tests/Makefile.symlink.in	2017-03-26 19:02:16.581990522 +0200
-@@ -13,6 +13,7 @@
- 	     -a ! -d $(libdir)/64 ]; then \
- 	    cd $(libdir)  &&  $(LN_S) . 64; \
- 	fi
-+	$(RM) $(LINK)
- 	cd $(libdir)  &&  $(LN_S) libpython_ncbi_dbapi$(loadable_ext) $(LINK)
- 
- clean:;
diff --git a/sci-biology/ncbi-tools++/files/report_project_settings_configure.ac.patch b/sci-biology/ncbi-tools++/files/report_project_settings_configure.ac.patch
deleted file mode 100644
index 41240c330..000000000
--- a/sci-biology/ncbi-tools++/files/report_project_settings_configure.ac.patch
+++ /dev/null
@@ -1,64 +0,0 @@
---- trunk/c++/src/build-system/configure.ac     2012/12/27 15:43:29     56694
-+++ trunk/c++/src/build-system/configure.ac     2013/01/03 03:16:14     56754
-@@ -605,7 +605,8 @@
- fi
- 
- case "$with_projects" in
-- "") if test -r projects; then
-+ ""|yes)
-+     if test -r projects; then
-         AC_MSG_NOTICE([using default projects file "projects".])
-         with_projects=projects
-         AC_SUBST(PROJECTS, "\$(top_srcdir)/projects")
-@@ -623,6 +624,16 @@
-  * ) AC_SUBST(PROJECTS, "\$(top_srcdir)/$with_projects") ;;
- esac
- 
-+if test -n "$with_projects"; then
-+   case "$with_projects" in
-+      /* ) abs_projects=$with_projects         ;;
-+      yes) abs_projects=$srcdir/projects       ;;
-+      *  ) abs_projects=$srcdir/$with_projects ;;
-+   esac
-+   test -r "$abs_projects"  ||  \
-+      AC_MSG_ERROR([unable to read requested projects file "$abs_projects".])
-+fi
-+
- # Check for custom optimization flags before potentially going with defaults.
- skip_fast_flags=no
- if test -z "${DEF_FAST_FLAGS}${FAST_CXXFLAGS}"; then
-@@ -6379,7 +6390,7 @@
-      sep=", "
-    fi
-    if test -n "$reason" -a "$with_internal" = "yes"; then
--      if test -z "$with_projects"  -o  "$with_projects" = "no"; then
-+      if test -z "$with_projects"; then
-          AC_MSG_ERROR([--with-internal:  Cannot build INTERNAL projects: missing $reason])
-       else
-          AC_MSG_WARN([--with-internal:  Cannot build all INTERNAL projects: missing $reason])
-@@ -6982,11 +6993,9 @@
-    else
-       cfm_flags='-remoteptb'
-    fi
--   case "$with_projects" in
--      yes     ) cfm_flags="$cfm_flags -p projects" ;;
--      no | '' ) ;;
--      *       ) cfm_flags="$cfm_flags -p $with_projects" ;;
--   esac
-+   if test -n "$with_projects"; then
-+      cfm_flags="$cfm_flags -p $with_projects"
-+   fi
-    if test "$with_configure_dialog" = yes; then
-       cfm_flags="$cfm_flags -cfg"
-    fi
-@@ -7029,7 +7038,8 @@
- esac
- 
- if test -n "$with_projects"; then
--    build_proj="To build selected projects:  cd $builddir && make all_p"
-+    build_proj="To build selected projects (as listed in \"$with_projects\"):
-+  cd $builddir && make all_p"
- fi
- 
- cat << EOCONF
-
diff --git a/sci-biology/ncbi-tools++/files/report_project_settings_configure.patch b/sci-biology/ncbi-tools++/files/report_project_settings_configure.patch
deleted file mode 100644
index 0c1b2d227..000000000
--- a/sci-biology/ncbi-tools++/files/report_project_settings_configure.patch
+++ /dev/null
@@ -1,66 +0,0 @@
--- trunk/c++/src/build-system/configure 2012/12/27 15:43:29     56694
-+++ trunk/c++/src/build-system/configure        2013/01/03 03:16:14     56754
-@@ -3125,7 +3125,8 @@
- fi
- 
- case "$with_projects" in
-- "") if test -r projects; then
-+ ""|yes)
-+     if test -r projects; then
-         { echo "$as_me:$LINENO: using default projects file \"projects\"." >&5
- echo "$as_me: using default projects file \"projects\"." >&6;}
-         with_projects=projects
-@@ -3151,6 +3152,18 @@
-  ;;
- esac
- 
-+if test -n "$with_projects"; then
-+   case "$with_projects" in
-+      /* ) abs_projects=$with_projects         ;;
-+      yes) abs_projects=$srcdir/projects       ;;
-+      *  ) abs_projects=$srcdir/$with_projects ;;
-+   esac
-+   test -r "$abs_projects"  ||  \
-+      { { echo "$as_me:$LINENO: error: unable to read requested projects file \"$abs_projects\"." >&5
-+echo "$as_me: error: unable to read requested projects file \"$abs_projects\"." >&2;}
-+   { (exit 1); exit 1; }; }
-+fi
-+
- # Check for custom optimization flags before potentially going with defaults.
- skip_fast_flags=no
- if test -z "${DEF_FAST_FLAGS}${FAST_CXXFLAGS}"; then
-@@ -33825,7 +33838,7 @@
-      sep=", "
-    fi
-    if test -n "$reason" -a "$with_internal" = "yes"; then
--      if test -z "$with_projects"  -o  "$with_projects" = "no"; then
-+      if test -z "$with_projects"; then
-          { { echo "$as_me:$LINENO: error: --with-internal:  Cannot build INTERNAL projects: missing $reason" >&5
- echo "$as_me: error: --with-internal:  Cannot build INTERNAL projects: missing $reason" >&2;}
-    { (exit 1); exit 1; }; }
-@@ -36062,11 +36075,9 @@
-    else
-       cfm_flags='-remoteptb'
-    fi
--   case "$with_projects" in
--      yes     ) cfm_flags="$cfm_flags -p projects" ;;
--      no | '' ) ;;
--      *       ) cfm_flags="$cfm_flags -p $with_projects" ;;
--   esac
-+   if test -n "$with_projects"; then
-+      cfm_flags="$cfm_flags -p $with_projects"
-+   fi
-    if test "$with_configure_dialog" = yes; then
-       cfm_flags="$cfm_flags -cfg"
-    fi
-@@ -36110,7 +36121,8 @@
- esac
- 
- if test -n "$with_projects"; then
--    build_proj="To build selected projects:  cd $builddir && make all_p"
-+    build_proj="To build selected projects (as listed in \"$with_projects\"):
-+  cd $builddir && make all_p"
- fi
- 
- cat << EOCONF
-
diff --git a/sci-biology/ncbi-tools++/files/respect_CXXFLAGS_configure.ac.patch b/sci-biology/ncbi-tools++/files/respect_CXXFLAGS_configure.ac.patch
deleted file mode 100644
index 89dae23ad..000000000
--- a/sci-biology/ncbi-tools++/files/respect_CXXFLAGS_configure.ac.patch
+++ /dev/null
@@ -1,54 +0,0 @@
---- trunk/c++/src/build-system/configure.ac     2012/12/21 15:12:14     56664
-+++ trunk/c++/src/build-system/configure.ac     2012/12/27 15:43:29     56694
-@@ -623,6 +623,13 @@
-  * ) AC_SUBST(PROJECTS, "\$(top_srcdir)/$with_projects") ;;
- esac
- 
-+# Check for custom optimization flags before potentially going with defaults.
-+skip_fast_flags=no
-+if test -z "${DEF_FAST_FLAGS}${FAST_CXXFLAGS}"; then
-+   case " $CFLAGS $CXXFLAGS" in
-+      *\ -O* | *\ -xO* ) skip_fast_flags=yes ;;
-+   esac
-+fi
- 
- #### Always define this
- AC_DEFINE(NCBI_CXX_TOOLKIT, 1, [This is the NCBI C++ Toolkit.])
-@@ -1431,7 +1438,7 @@
- wsrx="[[$wschars]]"
- 
- #### Flags to enable (potentially unsafe) extra optimization.
--if test -z "$DEF_FAST_FLAGS"  -o  -z "$FAST_CXXFLAGS" ; then
-+if test "$skip_fast_flags" = no -a -z "$DEF_FAST_FLAGS" ; then
-    case "$compiler:$compiler_version" in
-       GCC:2* | GCC:344 )
-         # GCC 2.9x sometimes experiences internal errors at high optimization;
-@@ -1502,8 +1509,6 @@
-         DEF_FAST_FLAGS="-O"
-         ;;
-    esac
--else
--   DEF_FAST_FLAGS="-O"
- fi
- 
- : ${FAST_CFLAGS="$DEF_FAST_FLAGS"}
-@@ -2608,9 +2613,15 @@
-          CXXFLAGS="$CXXFLAGS -O" ; fi
-       if echo " $LDFLAGS "  | grep -v "$optrx" >/dev/null ; then
-          LDFLAGS="$LDFLAGS -O" ; fi
--      FAST_CFLAGS="$NOPT_CFLAGS $FAST_CFLAGS"
--      FAST_CXXFLAGS="$NOPT_CXXFLAGS $FAST_CXXFLAGS"
--      FAST_LDFLAGS="$NOPT_LDFLAGS $FAST_LDFLAGS"
-+      if test "$skip_fast_flags" = yes ; then
-+         FAST_CFLAGS="$CFLAGS"
-+         FAST_CXXFLAGS="$CXXFLAGS"
-+         FAST_LDFLAGS="$LDFLAGS"
-+      else
-+         FAST_CFLAGS="$NOPT_CFLAGS $FAST_CFLAGS"
-+         FAST_CXXFLAGS="$NOPT_CXXFLAGS $FAST_CXXFLAGS"
-+         FAST_LDFLAGS="$NOPT_LDFLAGS $FAST_LDFLAGS"
-+      fi
-    fi
- changequote([, ])dnl
- fi
-
diff --git a/sci-biology/ncbi-tools++/files/respect_CXXFLAGS_configure.patch b/sci-biology/ncbi-tools++/files/respect_CXXFLAGS_configure.patch
deleted file mode 100644
index 669b31722..000000000
--- a/sci-biology/ncbi-tools++/files/respect_CXXFLAGS_configure.patch
+++ /dev/null
@@ -1,53 +0,0 @@
---- trunk/c++/src/build-system/configure        2012/12/21 15:12:14     56664
-+++ trunk/c++/src/build-system/configure        2012/12/27 15:43:29     56694
-@@ -3151,6 +3151,13 @@
-  ;;
- esac
- 
-+# Check for custom optimization flags before potentially going with defaults.
-+skip_fast_flags=no
-+if test -z "${DEF_FAST_FLAGS}${FAST_CXXFLAGS}"; then
-+   case " $CFLAGS $CXXFLAGS" in
-+      *\ -O* | *\ -xO* ) skip_fast_flags=yes ;;
-+   esac
-+fi
- 
- #### Always define this
- 
-@@ -5715,7 +5722,7 @@
- wsrx="[$wschars]"
- 
- #### Flags to enable (potentially unsafe) extra optimization.
--if test -z "$DEF_FAST_FLAGS"  -o  -z "$FAST_CXXFLAGS" ; then
-+if test "$skip_fast_flags" = no -a -z "$DEF_FAST_FLAGS" ; then
-    case "$compiler:$compiler_version" in
-       GCC:2* | GCC:344 )
-         # GCC 2.9x sometimes experiences internal errors at high optimization;
-@@ -5786,8 +5793,6 @@
-         DEF_FAST_FLAGS="-O"
-         ;;
-    esac
--else
--   DEF_FAST_FLAGS="-O"
- fi
- 
- : ${FAST_CFLAGS="$DEF_FAST_FLAGS"}
-@@ -8936,9 +8941,15 @@
-          CXXFLAGS="$CXXFLAGS -O" ; fi
-       if echo " $LDFLAGS "  | grep -v "$optrx" >/dev/null ; then
-          LDFLAGS="$LDFLAGS -O" ; fi
--      FAST_CFLAGS="$NOPT_CFLAGS $FAST_CFLAGS"
--      FAST_CXXFLAGS="$NOPT_CXXFLAGS $FAST_CXXFLAGS"
--      FAST_LDFLAGS="$NOPT_LDFLAGS $FAST_LDFLAGS"
-+      if test "$skip_fast_flags" = yes ; then
-+         FAST_CFLAGS="$CFLAGS"
-+         FAST_CXXFLAGS="$CXXFLAGS"
-+         FAST_LDFLAGS="$LDFLAGS"
-+      else
-+         FAST_CFLAGS="$NOPT_CFLAGS $FAST_CFLAGS"
-+         FAST_CXXFLAGS="$NOPT_CXXFLAGS $FAST_CXXFLAGS"
-+         FAST_LDFLAGS="$NOPT_LDFLAGS $FAST_LDFLAGS"
-+      fi
-    fi
- fi
- 
diff --git a/sci-biology/ncbi-tools++/metadata.xml b/sci-biology/ncbi-tools++/metadata.xml
deleted file mode 100644
index fbf79d9b7..000000000
--- a/sci-biology/ncbi-tools++/metadata.xml
+++ /dev/null
@@ -1,19 +0,0 @@
-<?xml version="1.0" encoding="UTF-8"?>
-<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
-<pkgmetadata>
-	<maintainer type="project">
-		<email>sci-biology@gentoo.org</email>
-		<name>Gentoo Biology Project</name>
-	</maintainer>
-	<use>
-		<flag name="boost">Undocumented USE</flag>
-		<flag name="cppunit">Undocumented USE</flag>
-		<flag name="freetype">Undocumented USE</flag>
-		<flag name="mesa">Undocumented USE</flag>
-		<flag name="muparser">Undocumented USE</flag>
-		<flag name="sablotron">Undocumented USE</flag>
-		<flag name="xerces">Undocumented USE</flag>
-		<flag name="xalan">Undocumented USE</flag>
-		<flag name="xslt">Undocumented USE</flag>
-	</use>
-</pkgmetadata>
diff --git a/sci-biology/ncbi-tools++/ncbi-tools++-12.0.0.ebuild b/sci-biology/ncbi-tools++/ncbi-tools++-12.0.0.ebuild
deleted file mode 100644
index 14e1fabda..000000000
--- a/sci-biology/ncbi-tools++/ncbi-tools++-12.0.0.ebuild
+++ /dev/null
@@ -1,365 +0,0 @@
-# Copyright 1999-2017 Gentoo Foundation
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=5
-
-PYTHON_COMPAT=( python2_7 )
-
-inherit eutils flag-o-matic multilib python-single-r1 toolchain-funcs
-
-MY_TAG="Jun_15_2010"
-MY_Y="${MY_TAG/*_/}"
-MY_PV="12_0_0"
-MY_P="ncbi_cxx--${MY_PV}"
-#ftp://ftp.ncbi.nlm.nih.gov/toolbox/ncbi_tools++/ARCHIVE/9_0_0/ncbi_cxx--9_0_0.tar.gz
-
-# for example sci-biology/ncbi-tools++-12.0.0 contains blastn-2.2.28+
-DESCRIPTION="NCBI C++ Toolkit, including NCBI BLAST+"
-HOMEPAGE="http://www.ncbi.nlm.nih.gov/books/bv.fcgi?rid=toolkit"
-SRC_URI="
-	ftp://ftp.ncbi.nih.gov/toolbox/ncbi_tools++/ARCHIVE/${MY_PV}/ncbi_cxx--${MY_PV}.tar.gz"
-#	http://dev.gentoo.org/~jlec/distfiles/${PN}-${PV#0.}-asneeded.patch.xz"
-
-# should also install ftp://ftp.ncbi.nlm.nih.gov/blast/db/taxdb.tar.gz
-# see http://www.biostars.org/p/76551/ and http://blastedbio.blogspot.cz/2012/05/blast-tabular-missing-descriptions.html
-LICENSE="public-domain"
-SLOT="0"
-IUSE="
-	debug static-libs static threads pch
-	test wxwidgets odbc
-	berkdb boost bzip2 cppunit curl expat fastcgi fltk freetype gif
-	glut gnutls hdf5 icu jpeg lzo mesa mysql muparser opengl pcre png python
-	sablotron sqlite tiff xerces xalan xml xpm xslt X"
-#KEYWORDS="~amd64 ~x86 ~amd64-linux ~x86-linux"
-KEYWORDS="~amd64"
-
-REQUIRED_USE="${PYTHON_REQUIRED_USE}"
-
-# sys-libs/db should be compiled with USE=cxx
-DEPEND="
-	!sci-biology/sra_sdk
-	app-arch/cpio
-	berkdb? ( sys-libs/db:4.3[cxx] )
-	boost? ( dev-libs/boost )
-	curl? ( net-misc/curl )
-	sqlite? ( dev-db/sqlite:3 )
-	mysql? ( virtual/mysql )
-	fltk? ( x11-libs/fltk )
-	opengl? ( virtual/opengl media-libs/glew:0= )
-	mesa? ( media-libs/mesa[osmesa] )
-	glut? ( media-libs/freeglut )
-	freetype? ( media-libs/freetype )
-	gnutls? ( net-libs/gnutls )
-	python? ( ${PYTHON_DEPS} )
-	cppunit? ( dev-util/cppunit )
-	icu? ( dev-libs/icu )
-	expat? ( dev-libs/expat )
-	sablotron? ( app-text/sablotron )
-	xml? ( dev-libs/libxml2 )
-	xslt? ( dev-libs/libxslt )
-	xerces? ( dev-libs/xerces-c )
-	xalan? ( dev-libs/xalan-c )
-	muparser? ( dev-cpp/muParser )
-	hdf5? ( sci-libs/hdf5[cxx] )
-	gif? ( media-libs/giflib )
-	jpeg? ( virtual/jpeg:0= )
-	png? ( media-libs/libpng:0= )
-	tiff? ( media-libs/tiff:0= )
-	xpm? ( x11-libs/libXpm )
-	dev-libs/lzo
-	app-arch/bzip2
-	dev-libs/libpcre"
-# USE flags which should be added somehow: wxWindows wxWidgets SP ORBacus ODBC OEChem sge
-# Intentionally omitted USE flags:
-#   ftds? ( dev-db/freetds ) # support for outside FreeTDS installations is currently broken.
-#                              The default (heavily patched) embedded copy should work, or you can
-#                              leave it off altogether -- the only public apps that make use of it are
-#                              samples and tests, since NCBI's database servers are of course firewalled.
-
-# seems muParser is required, also glew is required. configure exits otherwise if these are explicitly passed to it (due to USE flag enabled)
-
-RDEPEND="${DEPEND}"
-
-S="${WORKDIR}/${MY_P}"
-
-src_prepare() {
-#	filter-ldflags -Wl,--as-needed
-#	append-ldflags -Wl,--no-undefined
-#	sed -i -e 's/-print-file-name=libstdc++.a//' \
-#		-e '/sed/ s/\([gO]\[0-9\]\)\*/\1\\+/' \
-#		src/build-system/configure || die
-#	epatch \
-#		"${FILESDIR}"/${PN}-${PV#0.}-fix-order-of-libs.patch \
-#		"${FILESDIR}"/curl-types.patch \
-#		"${FILESDIR}"/malloc_initialize_upstream_fix.patch \
-#		"${FILESDIR}"/respect_CXXFLAGS_configure.ac.patch \
-#		"${FILESDIR}"/respect_CXXFLAGS_configure.patch \
-#		"${FILESDIR}"/report_project_settings_configure.ac.patch \
-#		"${FILESDIR}"/report_project_settings_configure.patch \
-#		"${FILESDIR}"/make_install.patch
-
-#		"${FILESDIR}"/${PN}-${PV#0.}-disable_test_compress.patch
-
-#		"${FILESDIR}"/${PN}-${PV#0.}-gcc46.patch \
-#		"${FILESDIR}"/${PN}-${PV#0.}-gcc47.patch \
-#		"${WORKDIR}"/${PN}-${PV#0.}-asneeded.patch \
-#		"${FILESDIR}"/${PN}-${PV#0.}-libpng15.patch \
-#		"${FILESDIR}"/${PN}-${PV#0.}-glibc-214.patch
-
-#	use prefix && append-ldflags -Wl,-rpath,"${EPREFIX}/usr/$(get_libdir)/${PN}"
-
-# The conf-opts.patch and as-needed.patch need to be adjusted for 12.0.0 line numbers
-	local PATCHES=(
-		"${FILESDIR}"/${P}-conf-opts.patch
-		"${FILESDIR}"/${P}-fix-svn-URL-upstream.patch
-		"${FILESDIR}"/${P}-linkage-tuneups.patch
-		"${FILESDIR}"/${P}-more-patches.patch
-		"${FILESDIR}"/${P}-linkage-tuneups-addons.patch
-		"${FILESDIR}"/${P}-configure.patch
-		"${FILESDIR}"/${P}-drop-STATIC-from-LIB.patch
-		"${FILESDIR}"/${P}-fix-install.patch
-		"${FILESDIR}"/${P}-bdb6.patch
-		"${FILESDIR}"/${P}-never_build_test_boost.patch # bug #579248
-		)
-#       "${FILESDIR}"/${P}-as-needed.patch
-#       "${FILESDIR}"/${P}-fix-creaders-linking.patch
-#       "${FILESDIR}"/${P}-fix-FreeTDS-upstream.patch
-#		)
-		# "${FILESDIR}"/${P}-support-autoconf-2.60.patch
-	epatch ${PATCHES[@]}
-	# make sure this one is the last one and contains the actual patches applied unless we can have autoconf-2.59 or 2.60
-	# https://bugs.gentoo.org/show_bug.cgi?id=514706
-
-	tc-export CXX CC
-
-	cd src/build-system || die
-#	eautoreconf
-
-	# Temporarily disabling eautoconf because we patch configure via ${P}-support-autoconf-2.60.patch
-	# eautoconf # keep it disabled until we can ensure 2.59 is installed
-	# beware 12.0.0. and previous required autoconf-2.59, a patch for 12.0.0 brings autoconf-2.60 support
-}
-
-# possibly place modified contents of ${W}/src/build-system/config.site.ncbi and {W}/src/build-system/config.site.ex into ${W}/src/build-system/config.site
-src_configure() {
-	local myconf=()
-	#--without-optimization  turn off optimization flags in non-debug mode
-	#--with-profiling        build profiled versions of libs and apps
-	#--with-tcheck(=DIR)     build for Intel Thread Checker (in DIR)
-	#--with-plugin-auto-load always enable the plugin manager by default
-	#--with-bundles          build bundles in addition to dylibs on Mac OS X
-	#--with-bin-release      build executables suitable for public release
-	#	no dll and such
-	#--with-64               compile to 64-bit code
-	#--with-universal        build universal binaries on Mac OS X
-	#--with-universal=CPUs   build universal binaries targeting the given CPUs
-	#--without-exe           do not build executables
-	#--with-relative-runpath=P specify an executable-relative DLL search path
-	#--with-hard-runpath     hard-code runtime path, ignoring LD_LIBRARY_PATH
-	#--with-limited-linker   don't attempt to build especially large projects
-	#--with-extra-action=    script to call after the configuration is complete
-	#--with-autodep          automatic generation of dependencies (GNU make)
-	#--with-fake-root=DIR    appear to have been built under DIR
-	#--with-build-root-sfx=X add a user-specified suffix to the build dir name
-	#--without-execopy       do not copy built executables to the BIN area
-	#--with-lib-rebuilds     ensure that apps use up-to-date libraries
-	#--with-lib-rebuilds=ask ask whether to update each app's libraries
-	#--without-deactivation  keep old copies of libraries that no longer build
-	#--without-makefile-auto-update  do not auto-update generated makefiles
-	#--with-projects=FILE    build projects listed in FILE by default
-	#--without-flat-makefile do not generate an all-encompassing flat makefile
-	#--with-configure-dialog allow interactive flat makefile project selection
-	#--with-saved-settings=F load configuration settings from the file F
-	#--with-check-tools=...  use the specified tools for testing
-	#--with-ncbi-public      ensure compatibility for all in-house platforms
-	#--with-sybase-local=DIR use local SYBASE install (DIR is optional)
-	#--with-sybase-new       use newer SYBASE install (12.5 rather than 12.0)
-	#--without-sp            do not use SP libraries
-	#--without-orbacus       do not use ORBacus CORBA libraries
-	#--with-orbacus=DIR      use ORBacus installation in DIR
-	#--with-jni(=JDK-DIR)    build Java bindings (against the JDK in JDK-DIR)
-	#--with-sablot=DIR       use Sablotron installation in DIR
-	#--without-sablot,       do not use Sablotron
-	#--with-oechem=DIR       use OpenEye OEChem installation in DIR
-	#--without-oechem        do not use OEChem
-	#--with-sge=DIR          use Sun Grid Engine installation in DIR
-	#--without-sge           do not use Sun Grid Engine
-	#--with-magic=DIR        use libmagic installation in DIR
-	#--without-magic         do not use libmagic
-	#--without-local-lbsm    turn off support for IPC with locally running LBSMD
-	#--without-ncbi-crypt    use a dummy stubbed-out version of ncbi_crypt
-	#--without-connext       do not build non-public CONNECT library extensions
-	#--without-serial        do not build the serialization library and tools
-	#--without-objects       do not generate/build serializeable objects from ASNs
-	#--without-dbapi         do not build database connectivity libraries
-	#--without-app           do not build standalone applications like ID1_FETCH
-	#--without-gui           do not build most graphical projects
-	#--without-algo          do not build CPU-intensive algorithms
-	#--without-internal      do not build internal projects
-	#--with-gbench           ensure that Genome Workbench can be built
-	#--without-gbench        do not build Genome Workbench
-	myconf+=(
-	--with-dll
-	--with-lfs
-	--with-build-root="${S}"_build
-	--without-suffix
-	--without-hostspec
-	--without-version
-	--with-bincopy
-	--without-strip
-	--without-ccache
-	--without-distcc
-#	--with-ncbi-c
-	--without-ctools
-#	--with-sss
-#	--with-sssutils
-#	--with-sssdb
-#	--with-included-sss
-	--with-z="${EPREFIX}/usr"
-	--with-bz2="${EPREFIX}/usr"
-	--without-sybase
-	--with-autodep
-#	--with-3psw=std:netopt favor standard (system) builds of the above pkgs
-	# --without-downloaded-vdb is not available in 12.0.0 release yet
-	# preventing executing git to checkout during configure phase ncbi-vdb sources
-	# resulting in 'checking for ncbi-vdb... no' and
-	# '^PACKAGES:'
-	# '^  disabled: ... VDB'
-	# --without-downloaded-vdb
-	$(use_with debug)
-	$(use_with debug max-debug)
-	$(use_with debug symbols)
-	$(use_with static-libs static)
-	$(use_with static static-exe)
-	$(use_with threads mt)
-	$(use_with prefix runpath "${EPREFIX}/usr/$(get_libdir)/${PN}")
-	$(use_with test check)
-	$(use_with pch)
-	$(use_with lzo lzo "${EPREFIX}/usr")
-	$(use_with pcre pcre "${EPREFIX}/usr")
-	$(use_with gnutls gnutls "${EPREFIX}/usr")
-	$(use_with mysql mysql "${EPREFIX}/usr")
-	$(use_with muparser muparser "${EPREFIX}/usr")
-	$(usex fltk --with-fltk="${EPREFIX}/usr" "")
-	$(use_with opengl opengl "${EPREFIX}/usr")
-	$(use_with mesa mesa "${EPREFIX}/usr")
-	$(use_with opengl glut "${EPREFIX}/usr")
-	$(use_with opengl glew "${EPREFIX}/usr")
-	$(use_with opengl glew-mx)
-	$(use_with wxwidgets wxwidgets "${EPREFIX}/usr")
-	$(use_with wxwidgets wxwidgets-ucs)
-	$(use_with freetype freetype "${EPREFIX}/usr")
-	$(use_with fastcgi fastcgi "${EPREFIX}/usr")
-	$(use_with berkdb bdb "${EPREFIX}/usr")
-	$(usex odbc --with-odbc="${EPREFIX}/usr" "")
-	$(use_with python python "${EPREFIX}/usr")
-	$(use_with boost boost "${EPREFIX}/usr")
-	$(use_with sqlite sqlite3 "${EPREFIX}/usr")
-	$(use_with icu icu "${EPREFIX}/usr")
-	$(use_with expat expat "${EPREFIX}/usr")
-	$(use_with xml libxml "${EPREFIX}/usr")
-	$(use_with xml libxslt "${EPREFIX}/usr")
-	$(use_with xerces xerces "${EPREFIX}/usr")
-	$(use_with hdf5 hdf5 "${EPREFIX}/usr")
-	$(use_with xalan xalan "${EPREFIX}/usr")
-#	$(use_with gif gif "${EPREFIX}/usr") # prevent compilation failure in "ncbi-tools++-12.0.0/src/util/image/image_io_gif.cpp:351: error: 'QuantizeBuffer' was not declared in this scope"
-	--without-gif
-	$(use_with jpeg jpeg "${EPREFIX}/usr")
-	$(use_with tiff tiff "${EPREFIX}/usr")
-	$(use_with png png "${EPREFIX}/usr")
-	$(use_with xpm xpm "${EPREFIX}/usr")
-	$(use_with curl curl "${EPREFIX}/usr")
-#	$(use_with X x "${EPREFIX}/usr")
-#	$(use_with X x) # there is no --with-x option
-	)
-
-	# http://www.ncbi.nlm.nih.gov/books/NBK7167/
-	use test ||	myconf+=( --with-projects="${FILESDIR}"/disable-testsuite-compilation.txt )
-
-	# TODO
-	# copy optimization -O options from CXXFLAGS to DEF_FAST_FLAGS and pass that also to configure
-	# otherwise your -O2 will be dropped in some subdirectories and replaced by e.g. -O9
-
-	einfo "bash ./src/build-system/configure --srcdir="${S}" --prefix="${EPREFIX}/usr" --libdir=/usr/lib64 ${myconf[@]}"
-
-#	ECONF_SOURCE="src/build-system" \
-#		econf \
-	bash \
-		./src/build-system/configure \
-		--srcdir="${S}" \
-		--prefix="${EPREFIX}/usr" \
-		--libdir=/usr/lib64 \
-		--with-flat-makefile \
-		${myconf[@]} || die
-#--without-debug \
-#		--with-bin-release \
-#		--with-bincopy \
-#		--without-static \
-#		--with-dll \
-#		--with-mt \
-#		--with-openmp \
-#		--with-lfs \
-#		--prefix="${ED}"/usr \
-#		--libdir="${ED}"/usr/$(get_libdir)/"${PN}" \
-#		${myconf} LDFLAGS="-Wl,--no-as-needed" \
-#		|| die
-#	econf ${myconf[@]}
-}
-
-src_compile() {
-	## all_r would ignore the --with-projects contents and build more
-	## emake all_r -C GCC*-Release*/build || die
-	## all_p with compile only selected/required components
-	##cd "${S}"_build &&\
-	##emake all_p -C GCC*-Release*/build || die "gcc-4.5.3 crashes at src/objects/valerr/ValidError.cpp:226:1: internal compiler error: Segmentation fault, right?"
-	#emake all_p -C "${S}"_build/build
-
-	#
-	# Re: /usr/lib64/ncbi-tools++/libdbapi_driver.so: undefined reference to `ncbi::NcbiGetlineEOL(std::istream&, std::string&)'
-	#
-	# The next release should automatically address such underlinking, albeit
-	# only in --with-flat-makefile configurations.  For now (12.0.0), you'll need to
-	# add or extend more DLL_LIB settings, to which end you may find the
-	# resources at http://www.ncbi.nlm.nih.gov/IEB/ToolBox/CPP_DOC/depgraphs/
-	# helpful.  For instance,
-	#
-	# http://www.ncbi.nlm.nih.gov/IEB/ToolBox/CPP_DOC/depgraphs/dbapi_driver.html
-	#
-	# indicates that src/dbapi/driver/Makefile.dbapi_driver.lib should set
-	#
-	# DLL_LIB = xncbi
-	#
-	# (You can find the path to that makefile by examining
-	# .../status/.dbapi_driver.dep or .../build/Makefile.flat.)
-	#
-	# To take full advantage of --with-flat-makefile, you'll need the following (instead of 'emake all_p -C "${S}"_build/build') and call configure --with-flat-makefile:
-	emake -C "${S}"_build/build -f Makefile.flat
-	#
-	# >=gcc-5.3.0 is not supported, see also bug #579248#c8
-	# configure: error: Do not know how to build MT-safe with compiler /usr/bin/x86_64-pc-linux-gnu-g++  5.3.0
-}
-
-src_install() {
-	rm -rvf "${S}"_build/lib/ncbi || die
-	emake install prefix="${ED}/usr" libdir="${ED}/usr/$(get_libdir)/${PN}"
-
-#	dobin "${S}"_build/bin/*
-#	dolib.so "${S}"_build/lib/*so*
-#	dolib.a "${S}"_build/lib/*.a
-#	doheader "${S}"_build/inc/*
-
-	# File collisions with sci-biology/ncbi-tools
-	mv "${ED}"/usr/bin/asn2asn "${ED}"/usr/bin/asn2asn+
-	mv "${ED}"/usr/bin/rpsblast "${ED}"/usr/bin/rpsblast+
-	mv -f "${ED}"/usr/bin/test_regexp "${ED}"/usr/bin/test_regexp+ # drop the eventually mistakenly compiled binaries
-	mv "${ED}"/usr/bin/vecscreen "${ED}"/usr/bin/vecscreen+
-	mv "${ED}"/usr/bin/seedtop "${ED}"/usr/bin/seedtop+
-
-	echo "LDPATH=${EPREFIX}/usr/$(get_libdir)/${PN}" > ${S}/99${PN}
-	doenvd "${S}/99${PN}"
-}
-
-pkg_postinst() {
-	einfo 'Please run "source /etc/profile" before using this package in the current shell.'
-	einfo 'Documentation is at http://www.ncbi.nlm.nih.gov/books/NBK7167/'
-}
diff --git a/sci-biology/ncbi-tools++/ncbi-tools++-18.0.0.ebuild b/sci-biology/ncbi-tools++/ncbi-tools++-18.0.0.ebuild
deleted file mode 100644
index 3f1fc7bd1..000000000
--- a/sci-biology/ncbi-tools++/ncbi-tools++-18.0.0.ebuild
+++ /dev/null
@@ -1,380 +0,0 @@
-# Copyright 1999-2017 Gentoo Foundation
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=5
-
-PYTHON_COMPAT=( python2_7 )
-
-inherit eutils flag-o-matic multilib python-single-r1 toolchain-funcs
-
-MY_TAG="Jun_15_2010"
-MY_Y="${MY_TAG/*_/}"
-MY_PV="18_0_0"
-MY_P="ncbi_cxx--${MY_PV}"
-#ftp://ftp.ncbi.nlm.nih.gov/toolbox/ncbi_tools++/ARCHIVE/9_0_0/ncbi_cxx--9_0_0.tar.gz
-
-# for example sci-biology/ncbi-tools++-12.0.0 contains blastn-2.2.28+
-DESCRIPTION="NCBI C++ Toolkit, including NCBI BLAST+"
-HOMEPAGE="http://www.ncbi.nlm.nih.gov/books/bv.fcgi?rid=toolkit"
-SRC_URI="
-	ftp://ftp.ncbi.nih.gov/toolbox/ncbi_tools++/ARCHIVE/2017/Jan_10_2017/ncbi_cxx--${MY_PV}.tar.gz"
-#	http://dev.gentoo.org/~jlec/distfiles/${PN}-${PV#0.}-asneeded.patch.xz"
-
-# should also install ftp://ftp.ncbi.nlm.nih.gov/blast/db/taxdb.tar.gz
-# see http://www.biostars.org/p/76551/ and http://blastedbio.blogspot.cz/2012/05/blast-tabular-missing-descriptions.html
-LICENSE="public-domain"
-SLOT="0"
-IUSE="
-	debug static-libs static threads pch
-	test wxwidgets odbc
-	berkdb boost bzip2 cppunit curl expat fastcgi fltk freetype gif
-	glut gnutls hdf5 icu jpeg lzo mesa mysql muparser opengl pcre png python
-	sablotron sqlite tiff xerces xalan xml xpm xslt X"
-KEYWORDS="~amd64 ~x86 ~amd64-linux ~x86-linux"
-
-REQUIRED_USE="${PYTHON_REQUIRED_USE}"
-
-# sys-libs/db should be compiled with USE=cxx
-DEPEND="
-	!sci-biology/sra_sdk
-	app-arch/cpio
-	berkdb? ( sys-libs/db:4.3[cxx] )
-	boost? ( dev-libs/boost )
-	curl? ( net-misc/curl )
-	sqlite? ( dev-db/sqlite:3 )
-	mysql? ( virtual/mysql )
-	fltk? ( x11-libs/fltk )
-	opengl? ( virtual/opengl media-libs/glew:0= )
-	mesa? ( media-libs/mesa[osmesa] )
-	glut? ( media-libs/freeglut )
-	freetype? ( media-libs/freetype )
-	gnutls? ( net-libs/gnutls )
-	python? ( ${PYTHON_DEPS} )
-	cppunit? ( dev-util/cppunit )
-	icu? ( dev-libs/icu )
-	expat? ( dev-libs/expat )
-	sablotron? ( app-text/sablotron )
-	xml? ( dev-libs/libxml2 )
-	xslt? ( dev-libs/libxslt )
-	xerces? ( dev-libs/xerces-c )
-	xalan? ( dev-libs/xalan-c )
-	muparser? ( dev-cpp/muParser )
-	hdf5? ( sci-libs/hdf5[cxx] )
-	gif? ( media-libs/giflib )
-	jpeg? ( virtual/jpeg:0= )
-	png? ( media-libs/libpng:0= )
-	tiff? ( media-libs/tiff:0= )
-	xpm? ( x11-libs/libXpm )
-	dev-libs/lzo
-	app-arch/bzip2
-	dev-libs/libpcre"
-# USE flags which should be added somehow: wxWindows wxWidgets SP ORBacus ODBC OEChem sge
-# Intentionally omitted USE flags:
-#   ftds? ( dev-db/freetds ) # support for outside FreeTDS installations is currently broken.
-#                              The default (heavily patched) embedded copy should work, or you can
-#                              leave it off altogether -- the only public apps that make use of it are
-#                              samples and tests, since NCBI's database servers are of course firewalled.
-
-# seems muParser is required, also glew is required. configure exits otherwise if these are explicitly passed to it (due to USE flag enabled)
-
-RDEPEND="${DEPEND}"
-
-S="${WORKDIR}/${MY_P}"
-
-src_prepare() {
-#	filter-ldflags -Wl,--as-needed
-#	append-ldflags -Wl,--no-undefined
-#	sed -i -e 's/-print-file-name=libstdc++.a//' \
-#		-e '/sed/ s/\([gO]\[0-9\]\)\*/\1\\+/' \
-#		src/build-system/configure || die
-#	epatch \
-#		"${FILESDIR}"/${PN}-${PV#0.}-fix-order-of-libs.patch \
-#		"${FILESDIR}"/curl-types.patch \
-#		"${FILESDIR}"/malloc_initialize_upstream_fix.patch \
-#		"${FILESDIR}"/respect_CXXFLAGS_configure.ac.patch \
-#		"${FILESDIR}"/respect_CXXFLAGS_configure.patch \
-#		"${FILESDIR}"/report_project_settings_configure.ac.patch \
-#		"${FILESDIR}"/report_project_settings_configure.patch \
-#		"${FILESDIR}"/make_install.patch
-
-#		"${FILESDIR}"/${PN}-${PV#0.}-disable_test_compress.patch
-
-#		"${FILESDIR}"/${PN}-${PV#0.}-gcc46.patch \
-#		"${FILESDIR}"/${PN}-${PV#0.}-gcc47.patch \
-#		"${WORKDIR}"/${PN}-${PV#0.}-asneeded.patch \
-#		"${FILESDIR}"/${PN}-${PV#0.}-libpng15.patch \
-#		"${FILESDIR}"/${PN}-${PV#0.}-glibc-214.patch
-
-#	use prefix && append-ldflags -Wl,-rpath,"${EPREFIX}/usr/$(get_libdir)/${PN}"
-
-# The conf-opts.patch and as-needed.patch need to be adjusted for 12.0.0 line numbers
-	local PATCHES=(
-		"${FILESDIR}"/${P}-configure.patch
-		"${FILESDIR}"/${P}-fix-install.patch
-		"${FILESDIR}"/${P}-never_build_test_boost.patch # bug #579248
-		"${FILESDIR}"/${P}-fix-annotwriter-linking.patch
-		"${FILESDIR}"/${P}-fix-undefined-xobjread.patch
-		"${FILESDIR}"/${P}-fix-apps-blast-linking.patch
-		"${FILESDIR}"/${P}-fix-sample-app-cgi-linking.patch
-		"${FILESDIR}"/${P}-fix-app-compartp-linking.patch
-		"${FILESDIR}"/${P}-fix-app-convert_seq-linking.patch
-		"${FILESDIR}"/${P}-fix-app-hfilter-linking.patch
-		"${FILESDIR}"/${P}-fix-app-igblast-linking.patch
-		"${FILESDIR}"/${P}-fix-ncfetch-linking.patch
-		"${FILESDIR}"/${P}-fix-netcache_cgi_sample-linking.patch
-		"${FILESDIR}"/${P}-fix-netstorage_gc-linking.patch
-		"${FILESDIR}"/${P}-fix-speedtest-linking.patch
-		"${FILESDIR}"/${P}-fix-splign-linking.patch
-		"${FILESDIR}"/${P}-fix-srcchk-linking.patch
-		"${FILESDIR}"/${P}-fix-app-rmblastn-linking.patch
-		"${FILESDIR}"/${P}-remove-old-symlinks.patch
-		"${FILESDIR}"/${P}-fix-app-table2asn-linking.patch
-		"${FILESDIR}"/${P}-fix-app-tls-linking.patch
-		"${FILESDIR}"/${P}-fix-app-vecscreen-linking.patch
-		"${FILESDIR}"/${P}-fix-app-blast_sample-linking.patch
-		)
-	#ncbi-tools++-18.0.0-fix-undefined-lxncbi.patch
-	epatch ${PATCHES[@]}
-	# make sure this one is the last one and contains the actual patches applied unless we can have autoconf-2.59 or 2.60
-	# https://bugs.gentoo.org/show_bug.cgi?id=514706
-
-	tc-export CXX CC
-
-	cd src/build-system || die
-#	eautoreconf
-
-	# Temporarily disabling eautoconf because we patch configure via ${P}-support-autoconf-2.60.patch
-	# eautoconf # keep it disabled until we can ensure 2.59 is installed
-	# beware 12.0.0. and previous required autoconf-2.59, a patch for 12.0.0 brings autoconf-2.60 support
-}
-
-# possibly place modified contents of ${W}/src/build-system/config.site.ncbi and {W}/src/build-system/config.site.ex into ${W}/src/build-system/config.site
-src_configure() {
-	local myconf=()
-	#--without-optimization  turn off optimization flags in non-debug mode
-	#--with-profiling        build profiled versions of libs and apps
-	#--with-tcheck(=DIR)     build for Intel Thread Checker (in DIR)
-	#--with-plugin-auto-load always enable the plugin manager by default
-	#--with-bundles          build bundles in addition to dylibs on Mac OS X
-	#--with-bin-release      build executables suitable for public release
-	#	no dll and such
-	#--with-64               compile to 64-bit code
-	#--with-universal        build universal binaries on Mac OS X
-	#--with-universal=CPUs   build universal binaries targeting the given CPUs
-	#--without-exe           do not build executables
-	#--with-relative-runpath=P specify an executable-relative DLL search path
-	#--with-hard-runpath     hard-code runtime path, ignoring LD_LIBRARY_PATH
-	#--with-limited-linker   don't attempt to build especially large projects
-	#--with-extra-action=    script to call after the configuration is complete
-	#--with-autodep          automatic generation of dependencies (GNU make)
-	#--with-fake-root=DIR    appear to have been built under DIR
-	#--with-build-root-sfx=X add a user-specified suffix to the build dir name
-	#--without-execopy       do not copy built executables to the BIN area
-	#--with-lib-rebuilds     ensure that apps use up-to-date libraries
-	#--with-lib-rebuilds=ask ask whether to update each app's libraries
-	#--without-deactivation  keep old copies of libraries that no longer build
-	#--without-makefile-auto-update  do not auto-update generated makefiles
-	#--with-projects=FILE    build projects listed in FILE by default
-	#--without-flat-makefile do not generate an all-encompassing flat makefile
-	#--with-configure-dialog allow interactive flat makefile project selection
-	#--with-saved-settings=F load configuration settings from the file F
-	#--with-check-tools=...  use the specified tools for testing
-	#--with-ncbi-public      ensure compatibility for all in-house platforms
-	#--with-sybase-local=DIR use local SYBASE install (DIR is optional)
-	#--with-sybase-new       use newer SYBASE install (12.5 rather than 12.0)
-	#--without-sp            do not use SP libraries
-	#--without-orbacus       do not use ORBacus CORBA libraries
-	#--with-orbacus=DIR      use ORBacus installation in DIR
-	#--with-jni(=JDK-DIR)    build Java bindings (against the JDK in JDK-DIR)
-	#--with-sablot=DIR       use Sablotron installation in DIR
-	#--without-sablot,       do not use Sablotron
-	#--with-oechem=DIR       use OpenEye OEChem installation in DIR
-	#--without-oechem        do not use OEChem
-	#--with-sge=DIR          use Sun Grid Engine installation in DIR
-	#--without-sge           do not use Sun Grid Engine
-	#--with-magic=DIR        use libmagic installation in DIR
-	#--without-magic         do not use libmagic
-	#--without-local-lbsm    turn off support for IPC with locally running LBSMD
-	#--without-ncbi-crypt    use a dummy stubbed-out version of ncbi_crypt
-	#--without-connext       do not build non-public CONNECT library extensions
-	#--without-serial        do not build the serialization library and tools
-	#--without-objects       do not generate/build serializeable objects from ASNs
-	#--without-dbapi         do not build database connectivity libraries
-	#--without-app           do not build standalone applications like ID1_FETCH
-	#--without-gui           do not build most graphical projects
-	#--without-algo          do not build CPU-intensive algorithms
-	#--without-internal      do not build internal projects
-	#--with-gbench           ensure that Genome Workbench can be built
-	#--without-gbench        do not build Genome Workbench
-	myconf+=(
-	--with-dll
-	--with-lfs
-	--with-build-root="${S}"_build
-	--without-suffix
-	--without-hostspec
-	--without-version
-	--with-bincopy
-	--without-strip
-	--without-ccache
-	--without-distcc
-#	--with-ncbi-c
-	--without-ctools
-#	--with-sss
-#	--with-sssutils
-#	--with-sssdb
-#	--with-included-sss
-	--with-z="${EPREFIX}/usr"
-	--with-bz2="${EPREFIX}/usr"
-	--without-sybase
-	--with-autodep
-#	--with-3psw=std:netopt favor standard (system) builds of the above pkgs
-	# --without-downloaded-vdb is not available in 12.0.0 release yet
-	# preventing executing git to checkout during configure phase ncbi-vdb sources
-	# resulting in 'checking for ncbi-vdb... no' and
-	# '^PACKAGES:'
-	# '^  disabled: ... VDB'
-	--without-downloaded-vdb
-	$(use_with debug)
-	$(use_with debug max-debug)
-	$(use_with debug symbols)
-	$(use_with static-libs static)
-	$(use_with static static-exe)
-	$(use_with threads mt)
-	$(use_with prefix runpath "${EPREFIX}/usr/$(get_libdir)/${PN}")
-	$(use_with test check)
-	$(use_with pch)
-	$(use_with lzo lzo "${EPREFIX}/usr")
-	$(use_with pcre pcre "${EPREFIX}/usr")
-	$(use_with gnutls gnutls "${EPREFIX}/usr")
-	$(use_with mysql mysql "${EPREFIX}/usr")
-	$(use_with muparser muparser "${EPREFIX}/usr")
-	$(usex fltk --with-fltk="${EPREFIX}/usr" "")
-	$(use_with opengl opengl "${EPREFIX}/usr")
-	$(use_with mesa mesa "${EPREFIX}/usr")
-	$(use_with opengl glut "${EPREFIX}/usr")
-	$(use_with opengl glew "${EPREFIX}/usr")
-	$(use_with opengl glew-mx)
-	$(use_with wxwidgets wxwidgets "${EPREFIX}/usr")
-	$(use_with wxwidgets wxwidgets-ucs)
-	$(use_with freetype freetype "${EPREFIX}/usr")
-	$(use_with fastcgi fastcgi "${EPREFIX}/usr")
-	$(use_with berkdb bdb "${EPREFIX}/usr")
-	$(usex odbc --with-odbc="${EPREFIX}/usr" "")
-	$(use_with python python "${EPREFIX}/usr")
-	$(use_with boost boost "${EPREFIX}/usr")
-	$(use_with sqlite sqlite3 "${EPREFIX}/usr")
-	$(use_with icu icu "${EPREFIX}/usr")
-	$(use_with expat expat "${EPREFIX}/usr")
-	$(use_with xml libxml "${EPREFIX}/usr")
-	$(use_with xml libxslt "${EPREFIX}/usr")
-	$(use_with xerces xerces "${EPREFIX}/usr")
-	$(use_with hdf5 hdf5 "${EPREFIX}/usr")
-	$(use_with xalan xalan "${EPREFIX}/usr")
-#	$(use_with gif gif "${EPREFIX}/usr") # prevent compilation failure in "ncbi-tools++-12.0.0/src/util/image/image_io_gif.cpp:351: error: 'QuantizeBuffer' was not declared in this scope"
-	--without-gif
-	$(use_with jpeg jpeg "${EPREFIX}/usr")
-	$(use_with tiff tiff "${EPREFIX}/usr")
-	$(use_with png png "${EPREFIX}/usr")
-	$(use_with xpm xpm "${EPREFIX}/usr")
-	$(use_with curl curl "${EPREFIX}/usr")
-#	$(use_with X x "${EPREFIX}/usr")
-#	$(use_with X x) # there is no --with-x option
-	)
-
-	# http://www.ncbi.nlm.nih.gov/books/NBK7167/
-	use test ||	myconf+=( --with-projects="${FILESDIR}"/disable-testsuite-compilation.txt )
-
-	# TODO
-	# copy optimization -O options from CXXFLAGS to DEF_FAST_FLAGS and pass that also to configure
-	# otherwise your -O2 will be dropped in some subdirectories and replaced by e.g. -O9
-
-	einfo "bash ./src/build-system/configure --srcdir="${S}" --prefix="${EPREFIX}/usr" --libdir=/usr/lib64 ${myconf[@]}"
-
-#	ECONF_SOURCE="src/build-system" \
-#		econf \
-	bash \
-		./src/build-system/configure \
-		--srcdir="${S}" \
-		--prefix="${EPREFIX}/usr" \
-		--libdir=/usr/lib64 \
-		--with-flat-makefile \
-		${myconf[@]} || die
-#--without-debug \
-#		--with-bin-release \
-#		--with-bincopy \
-#		--without-static \
-#		--with-dll \
-#		--with-mt \
-#		--with-openmp \
-#		--with-lfs \
-#		--prefix="${ED}"/usr \
-#		--libdir="${ED}"/usr/$(get_libdir)/"${PN}" \
-#		${myconf} LDFLAGS="-Wl,--no-as-needed" \
-#		|| die
-#	econf ${myconf[@]}
-}
-
-src_compile() {
-	## all_r would ignore the --with-projects contents and build more
-	## emake all_r -C GCC*-Release*/build || die
-	## all_p with compile only selected/required components
-	##cd "${S}"_build &&\
-	##emake all_p -C GCC*-Release*/build || die "gcc-4.5.3 crashes at src/objects/valerr/ValidError.cpp:226:1: internal compiler error: Segmentation fault, right?"
-	#emake all_p -C "${S}"_build/build
-
-	#
-	# Re: /usr/lib64/ncbi-tools++/libdbapi_driver.so: undefined reference to `ncbi::NcbiGetlineEOL(std::istream&, std::string&)'
-	#
-	# The next release should automatically address such underlinking, albeit
-	# only in --with-flat-makefile configurations.  For now (12.0.0), you'll need to
-	# add or extend more DLL_LIB settings, to which end you may find the
-	# resources at http://www.ncbi.nlm.nih.gov/IEB/ToolBox/CPP_DOC/depgraphs/
-	# helpful.  For instance,
-	#
-	# http://www.ncbi.nlm.nih.gov/IEB/ToolBox/CPP_DOC/depgraphs/dbapi_driver.html
-	#
-	# indicates that src/dbapi/driver/Makefile.dbapi_driver.lib should set
-	#
-	# DLL_LIB = xncbi
-	#
-	# (You can find the path to that makefile by examining
-	# .../status/.dbapi_driver.dep or .../build/Makefile.flat.)
-	#
-	# To take full advantage of --with-flat-makefile, you'll need the following (instead of 'emake all_p -C "${S}"_build/build') and call configure --with-flat-makefile:
-	emake -C "${S}"_build/build -f Makefile.flat
-	#
-	# >=gcc-5.3.0 is not supported, see also bug #579248#c8
-	# configure: error: Do not know how to build MT-safe with compiler /usr/bin/x86_64-pc-linux-gnu-g++  5.3.0
-}
-
-src_install() {
-	rm -rvf "${S}"_build/lib/ncbi || die
-	emake install prefix="${ED}/usr" libdir="${ED}/usr/$(get_libdir)/${PN}"
-
-#	dobin "${S}"_build/bin/*
-#	dolib.so "${S}"_build/lib/*so*
-#	dolib.a "${S}"_build/lib/*.a
-#	doheader "${S}"_build/inc/*
-
-	# File collisions with sci-biology/ncbi-tools
-	mv "${ED}"/usr/bin/asn2asn "${ED}"/usr/bin/asn2asn+
-	mv "${ED}"/usr/bin/rpsblast "${ED}"/usr/bin/rpsblast+
-	mv -f "${ED}"/usr/bin/test_regexp "${ED}"/usr/bin/test_regexp+ # drop the eventually mistakenly compiled binaries
-	mv "${ED}"/usr/bin/vecscreen "${ED}"/usr/bin/vecscreen+
-	mv "${ED}"/usr/bin/seedtop "${ED}"/usr/bin/seedtop+
-	#
-	# idfetch collides with idfetch from ncbi-tools-2.2.26
-	# Although the two idfetch implementations do deliberately have several
-	# options in common, the C++ version is not yet a full drop-in replacement
-	# for the C version (and will never entirely be, due to fundamental
-	# differences between the two toolkits' argument-parsing conventions).
-	mv "${ED}"/usr/bin/idfetch "${ED}"/usr/bin/idfetch+ # new in ncbi-tools++-18.0.0
-
-	echo "LDPATH=${EPREFIX}/usr/$(get_libdir)/${PN}" > ${S}/99${PN}
-	doenvd "${S}/99${PN}"
-}
-
-pkg_postinst() {
-	einfo 'Please run "source /etc/profile" before using this package in the current shell.'
-	einfo 'Documentation is at http://www.ncbi.nlm.nih.gov/books/NBK7167/'
-}
diff --git a/sci-biology/ncbi-vdb/Manifest b/sci-biology/ncbi-vdb/Manifest
new file mode 100644
index 000000000..6e69589e6
--- /dev/null
+++ b/sci-biology/ncbi-vdb/Manifest
@@ -0,0 +1 @@
+DIST ncbi-vdb-2.11.2.tar.gz 26543426 BLAKE2B a0acdeefa5e4fadfcc304d33b29be5ae937630fb74b13674e1e7ea8dd4cd71048a1374803fcc6e2248fa4ecb9be93945fcd567f40159748eb86f0fdc98bf6aff SHA512 c3b9e582c9faccd637d5718bbaac49603c993be9234c7bd561ab84cabb9a2d60508822211871c9cd2d3bd42fbb059e5f72194d9e28e126c21ccf70ea8ab6b5b0
diff --git a/dev-perl/Bio-EnsEMBL/metadata.xml b/sci-biology/ncbi-vdb/metadata.xml
index 138cb7705..138cb7705 100644
--- a/dev-perl/Bio-EnsEMBL/metadata.xml
+++ b/sci-biology/ncbi-vdb/metadata.xml
diff --git a/sci-biology/ncbi-vdb/ncbi-vdb-2.11.2.ebuild b/sci-biology/ncbi-vdb/ncbi-vdb-2.11.2.ebuild
new file mode 100644
index 000000000..15f83b00c
--- /dev/null
+++ b/sci-biology/ncbi-vdb/ncbi-vdb-2.11.2.ebuild
@@ -0,0 +1,45 @@
+# Copyright 1999-2022 Gentoo Authors
+# Distributed under the terms of the GNU General Public License v2
+
+EAPI=8
+
+PYTHON_COMPAT=( python3_10 )
+inherit python-single-r1
+
+DESCRIPTION=" NCBI SRA ( Sequence Read Archive )"
+HOMEPAGE="https://github.com/ncbi/ncbi-vdb"
+SRC_URI="https://github.com/ncbi/ncbi-vdb/archive/${PV}.tar.gz -> ${P}.tar.gz"
+
+LICENSE="public-domain"
+SLOT="0"
+# Sandbox error: tries to access files from within deleted dir in compile phase
+KEYWORDS=""
+REQUIRED_USE="${PYTHON_REQUIRED_USE}"
+
+DEPEND="${PYTHON_DEPS}
+	sci-libs/hdf5
+	sci-biology/ngs
+"
+RDEPEND="${DEPEND}"
+
+src_configure() {
+	# this is some non-standard configure script
+	./configure \
+		--with-ngs-sdk-prefix=/usr/ngs/ngs-sdk \
+		--with-hdf5-prefix=/usr \
+		|| die
+}
+
+src_install() {
+	dodir /usr/include
+	dodir /etc/profile.d
+	# Hard way around hard coded paths
+	find . -type f -exec sed -i \
+		-e "s:/usr/local:${ED}/usr:g" \
+		-e "s:/etc:${ED}/etc:g" \
+		-e "s:/usr/lib:${ED}/usr/lib:g" \
+		-e "s:/usr/include:${ED}/usr/include:g" \
+		-e "s:setup.py -q install:setup.py install --root="${D}":g" \
+		{} \; || die
+	default
+}
diff --git a/sci-biology/nesoni/Manifest b/sci-biology/nesoni/Manifest
deleted file mode 100644
index 1b00acdce..000000000
--- a/sci-biology/nesoni/Manifest
+++ /dev/null
@@ -1 +0,0 @@
-DIST nesoni-0.128.tar.gz 252773 BLAKE2B 79807e456fac3b0826ec3485d3f67ad13154c5d24a8ec7807cf3fa1765edd3c467d27ff5cbd2dac77a28444b0b3802f055c091b1ff64c29ebac460189d4c9f7d SHA512 8df36b11b0371c5895d690b7497a298a34154f7c14f05d340f9fa5d6352d96e49e4a1b1e4e2089bce0a652bbc3911c8d6b361055263ffd573274b62955df0462
diff --git a/sci-biology/nesoni/metadata.xml b/sci-biology/nesoni/metadata.xml
deleted file mode 100644
index 138cb7705..000000000
--- a/sci-biology/nesoni/metadata.xml
+++ /dev/null
@@ -1,12 +0,0 @@
-<?xml version="1.0" encoding="UTF-8"?>
-<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
-<pkgmetadata>
-	<maintainer type="person">
-		<email>mmokrejs@fold.natur.cuni.cz</email>
-		<name>Martin Mokrejs</name>
-	</maintainer>
-	<maintainer type="project">
-		<email>sci-biology@gentoo.org</email>
-		<name>Gentoo Biology Project</name>
-	</maintainer>
-</pkgmetadata>
diff --git a/sci-biology/nesoni/nesoni-0.128.ebuild b/sci-biology/nesoni/nesoni-0.128.ebuild
deleted file mode 100644
index 096214e35..000000000
--- a/sci-biology/nesoni/nesoni-0.128.ebuild
+++ /dev/null
@@ -1,32 +0,0 @@
-# Copyright 1999-2015 Gentoo Foundation
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=5
-
-PYTHON_COMPAT=( python2_7 )
-
-inherit distutils-r1 eutils
-
-DESCRIPTION="Analysis package for next-generation sequencing data and prepare for IGV display"
-HOMEPAGE="http://www.vicbioinformatics.com/software.nesoni.shtml"
-SRC_URI="http://www.vicbioinformatics.com/"${P}".tar.gz"
-
-LICENSE="GPL-2"
-SLOT="0"
-KEYWORDS="~amd64"
-IUSE=""
-
-DEPEND=""
-RDEPEND="${DEPEND}
-	sci-biology/shrimp
-	sci-biology/bowtie
-	sci-biology/mummer
-	sci-biology/biopython
-	sci-biology/picard
-	dev-lang/R"
-
-	# sci-biology/freebayes
-	# SplitsTree4 http://www.splitstree.org/
-	# BioConductor (limma, edgeR, goseq)
-	# seriation
-	# NMF
diff --git a/sci-biology/neuroconv/Manifest b/sci-biology/neuroconv/Manifest
new file mode 100644
index 000000000..35c461b92
--- /dev/null
+++ b/sci-biology/neuroconv/Manifest
@@ -0,0 +1 @@
+DIST neuroconv-0.4.8.gh.tar.gz 1020546 BLAKE2B 880d7c4bdce3faf3bc969c9a0fd4206e1fd9d57254e40aa1181cf2d8f48abd72491b8b66d8ccc1988a623f8b2a8be160f2575f59ea69080a8bb6ed501c389881 SHA512 d06a625823a71f21a5eac957e452ab80b6fb847fc5f8c8e68fb6c46360402c4bc338f7fc611537272e72c0b72555a2951c346d38aa89c8ac8b209921ea7af72d
diff --git a/sci-biology/neuroconv/metadata.xml b/sci-biology/neuroconv/metadata.xml
new file mode 100644
index 000000000..efd00647e
--- /dev/null
+++ b/sci-biology/neuroconv/metadata.xml
@@ -0,0 +1,21 @@
+<?xml version='1.0' encoding='UTF-8'?>
+<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
+<pkgmetadata>
+	<maintainer type="person">
+		<email>gentoo@chymera.eu</email>
+		<name>Horea Christian</name>
+	</maintainer>
+	<maintainer type="project">
+		<email>sci@gentoo.org</email>
+		<name>Gentoo Science Project</name>
+	</maintainer>
+	<use>
+		<flag name="ecephys">Extracellular electrophysiology interfaces</flag>
+		<flag name="icephys">Intracellular electrophysiology interfaces</flag>
+		<flag name="ophys">Optical physiology interfaces</flag>
+	</use>
+	<upstream>
+		<remote-id type="github">catalystneuro/roiextractors</remote-id>
+		<remote-id type="pypi">roiextractors</remote-id>
+	</upstream>
+</pkgmetadata>
diff --git a/sci-biology/neuroconv/neuroconv-0.4.8-r1.ebuild b/sci-biology/neuroconv/neuroconv-0.4.8-r1.ebuild
new file mode 100644
index 000000000..b21c2fd8e
--- /dev/null
+++ b/sci-biology/neuroconv/neuroconv-0.4.8-r1.ebuild
@@ -0,0 +1,66 @@
+# Copyright 2021-2023 Gentoo Authors
+# Distributed under the terms of the GNU General Public License v2
+
+EAPI=8
+
+PYTHON_COMPAT=( python3_{10..11} )
+DISTUTILS_USE_PEP517=setuptools
+inherit distutils-r1
+
+DESCRIPTION="Create NWB files from proprietary formats."
+HOMEPAGE="https://github.com/catalystneuro/neuroconv"
+SRC_URI="https://github.com/catalystneuro/neuroconv/archive/refs/tags/v${PV}.tar.gz -> ${P}.gh.tar.gz"
+
+LICENSE="BSD"
+SLOT="0"
+KEYWORDS="~amd64"
+IUSE="+ecephys +icephys +ophys"
+
+RDEPEND="
+	dev-python/docstring-parser[${PYTHON_USEDEP}]
+	dev-python/h5py[${PYTHON_USEDEP}]
+	dev-python/hdmf-zarr[${PYTHON_USEDEP}]
+	dev-python/hdmf[${PYTHON_USEDEP}]
+	dev-python/jsonschema[${PYTHON_USEDEP}]
+	dev-python/numpy[${PYTHON_USEDEP}]
+	dev-python/nwbinspector[${PYTHON_USEDEP}]
+	dev-python/pandas[${PYTHON_USEDEP}]
+	dev-python/parse[${PYTHON_USEDEP}]
+	dev-python/psutil[${PYTHON_USEDEP}]
+	dev-python/pydantic[${PYTHON_USEDEP}]
+	dev-python/pynwb[${PYTHON_USEDEP}]
+	dev-python/pyyaml[${PYTHON_USEDEP}]
+	dev-python/scipy[${PYTHON_USEDEP}]
+	dev-python/tqdm[${PYTHON_USEDEP}]
+	ecephys? (
+		dev-python/spikeinterface[${PYTHON_USEDEP}]
+	)
+	icephys? (
+		dev-python/neo[${PYTHON_USEDEP}]
+	)
+	ophys? (
+		sci-biology/roiextractors[${PYTHON_USEDEP}]
+	)
+"
+BDEPEND="
+	test? (
+		dev-python/parameterized[${PYTHON_USEDEP}]
+	)
+"
+
+distutils_enable_tests pytest
+
+# Reported upstream:
+# https://github.com/catalystneuro/neuroconv/issues/785
+EPYTEST_DESELECT=(
+	tests/test_ecephys/test_mock_recording_interface.py::TestMockRecordingInterface::test_conversion_as_lone_interface
+)
+
+python_test() {
+	# Additional tests require complex data getting infrastructure, ophys tests still have issues:
+	# https://github.com/catalystneuro/neuroconv/issues/305
+	local my_tests=( "tests/test_minimal" )
+	use ecephys && my_tests+=( "tests/test_ecephys" )
+	#use ophys && my_tests+=( "tests/test_ophys" )
+	epytest ${my_tests[*]// /|}
+}
diff --git a/sci-biology/nextclip/metadata.xml b/sci-biology/nextclip/metadata.xml
index 138cb7705..b0874714e 100644
--- a/sci-biology/nextclip/metadata.xml
+++ b/sci-biology/nextclip/metadata.xml
@@ -9,4 +9,7 @@
 		<email>sci-biology@gentoo.org</email>
 		<name>Gentoo Biology Project</name>
 	</maintainer>
+	<upstream>
+		<remote-id type="github">richardmleggett/nextclip</remote-id>
+	</upstream>
 </pkgmetadata>
diff --git a/sci-biology/nextclip/nextclip-1.3.1.ebuild b/sci-biology/nextclip/nextclip-1.3.1.ebuild
index 3efbb61c6..3f0741815 100644
--- a/sci-biology/nextclip/nextclip-1.3.1.ebuild
+++ b/sci-biology/nextclip/nextclip-1.3.1.ebuild
@@ -1,9 +1,9 @@
-# Copyright 1999-2018 Gentoo Foundation
+# Copyright 1999-2021 Gentoo Authors
 # Distributed under the terms of the GNU General Public License v2
 
-EAPI=6
+EAPI=7
 
-inherit flag-o-matic toolchain-funcs
+inherit toolchain-funcs
 
 DESCRIPTION="Split Illumina Nextera long mate-pairs"
 HOMEPAGE="https://github.com/richardmleggett/nextclip
@@ -13,7 +13,6 @@ SRC_URI="https://github.com/richardmleggett/nextclip/archive/NextClip_v1.3.1.tar
 LICENSE="GPL-3+"
 SLOT="0"
 KEYWORDS="~amd64 ~x86"
-IUSE=""
 
 DEPEND=""
 RDEPEND="${DEPEND}
diff --git a/sci-biology/ngs/Manifest b/sci-biology/ngs/Manifest
new file mode 100644
index 000000000..1941b3421
--- /dev/null
+++ b/sci-biology/ngs/Manifest
@@ -0,0 +1 @@
+DIST ngs-2.11.2.tar.gz 1101119 BLAKE2B efa877540b8df1fbaad5550ba17ee17bd01a692a30536bd4d172b8189f7e35a88d3cd55050b676653531d1bf4655950a25a3c65a8555ef89fbcb6b503a0d3b21 SHA512 708d3b20d4aa26f44a04e103dc4fd0621acda3c07ff70911aba406e869285612879329ffb06f4f7fa69d5216c503d4118114247c9d5e851a2c400b79a01c5921
diff --git a/sci-biology/ngs/metadata.xml b/sci-biology/ngs/metadata.xml
new file mode 100644
index 000000000..f165e6cbc
--- /dev/null
+++ b/sci-biology/ngs/metadata.xml
@@ -0,0 +1,15 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
+<pkgmetadata>
+	<maintainer type="person">
+		<email>mmokrejs@fold.natur.cuni.cz</email>
+		<name>Martin Mokrejs</name>
+	</maintainer>
+	<maintainer type="project">
+		<email>sci-biology@gentoo.org</email>
+		<name>Gentoo Biology Project</name>
+	</maintainer>
+	<upstream>
+		<remote-id type="github">ncbi/ngs</remote-id>
+	</upstream>
+</pkgmetadata>
diff --git a/sci-biology/ngs/ngs-2.11.2.ebuild b/sci-biology/ngs/ngs-2.11.2.ebuild
new file mode 100644
index 000000000..0574c5076
--- /dev/null
+++ b/sci-biology/ngs/ngs-2.11.2.ebuild
@@ -0,0 +1,43 @@
+# Copyright 1999-2022 Gentoo Authors
+# Distributed under the terms of the GNU General Public License v2
+
+EAPI=8
+
+PYTHON_COMPAT=( python3_10 )
+inherit python-single-r1 java-pkg-2
+
+DESCRIPTION="NGS Language Bindings "
+HOMEPAGE="https://github.com/ncbi/ngs"
+SRC_URI="https://github.com/ncbi/ngs/archive/${PV}.tar.gz -> ${P}.tar.gz"
+
+LICENSE="public-domain"
+SLOT="0"
+KEYWORDS="~amd64"
+REQUIRED_USE="${PYTHON_REQUIRED_USE}"
+
+DEPEND="${PYTHON_DEPS}
+	sci-biology/bamtools
+	virtual/jdk:1.8
+"
+RDEPEND="${DEPEND}
+	virtual/jre:1.8
+"
+
+src_configure() {
+	# this is some non-standard configure script
+	./configure || die
+}
+
+src_install() {
+	dodir /usr/include
+	dodir /etc/profile.d
+	# Hard way around hard coded paths
+	find . -type f -exec sed -i \
+		-e "s:/usr/local:${ED}/usr:g" \
+		-e "s:/etc:${ED}/etc:g" \
+		-e "s:/usr/lib:${ED}/usr/lib:g" \
+		-e "s:/usr/include:${ED}/usr/include:g" \
+		-e "s:setup.py -q install:setup.py install --root="${D}":g" \
+		{} \; || die
+	default
+}
diff --git a/sci-biology/ngs_backbone/Manifest b/sci-biology/ngs_backbone/Manifest
deleted file mode 100644
index 800d7e67b..000000000
--- a/sci-biology/ngs_backbone/Manifest
+++ /dev/null
@@ -1 +0,0 @@
-DIST ngs_backbone-1.4.0.tar.gz 143619961 SHA256 d388f57ee9b5636a1475c8e345d0ad2ed433773bf3b69c2928f26680412ea8cf SHA512 518283341114ae7af5ab5e9f9ba0bf5147c7a0d8e57020b158d643be73afb144eb13a777e23c7e7601149ff023f52daa51a749c39facc31a88e10cf754652138 WHIRLPOOL 260254e6a170c042cc054990b836cee79a38e23024bd0bfc9b91c0a7a739185cd9913c59e59cf09668ad59734444ec78da1e799bf3383b061d903d7f0e8cfcb6
diff --git a/sci-biology/ngs_backbone/metadata.xml b/sci-biology/ngs_backbone/metadata.xml
deleted file mode 100644
index 138cb7705..000000000
--- a/sci-biology/ngs_backbone/metadata.xml
+++ /dev/null
@@ -1,12 +0,0 @@
-<?xml version="1.0" encoding="UTF-8"?>
-<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
-<pkgmetadata>
-	<maintainer type="person">
-		<email>mmokrejs@fold.natur.cuni.cz</email>
-		<name>Martin Mokrejs</name>
-	</maintainer>
-	<maintainer type="project">
-		<email>sci-biology@gentoo.org</email>
-		<name>Gentoo Biology Project</name>
-	</maintainer>
-</pkgmetadata>
diff --git a/sci-biology/ngs_backbone/ngs_backbone-1.4.0.ebuild b/sci-biology/ngs_backbone/ngs_backbone-1.4.0.ebuild
deleted file mode 100644
index 6ea39e0ad..000000000
--- a/sci-biology/ngs_backbone/ngs_backbone-1.4.0.ebuild
+++ /dev/null
@@ -1,148 +0,0 @@
-# Copyright 1999-2016 Gentoo Foundation
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=6
-
-PYTHON_COMPAT=( python2_7 )
-
-inherit distutils-r1
-
-DESCRIPTION="Assembly & annotation pipeline with web interface for EST/chromosomal sequences"
-HOMEPAGE="http://bioinf.comav.upv.es/ngs_backbone/index.html"
-SRC_URI="http://bioinf.comav.upv.es/_downloads/"${P}".tar.gz"
-
-LICENSE="GPL-3"
-SLOT="0"
-KEYWORDS="~amd64"
-IUSE=""
-
-DEPEND=""
-RDEPEND="${DEPEND}
-	sci-biology/biopython[${PYTHON_USEDEP}]
-	sci-biology/samtools[${PYTHON_USEDEP}]
-	sci-biology/picard
-	sci-biology/mira
-	sci-biology/bwa
-	sci-biology/gatk
-	sci-biology/pysam[${PYTHON_USEDEP}]
-	sci-biology/estscan
-	sci-biology/ncbi-tools
-	sci-biology/lucy
-	sci-biology/gmap
-	sci-biology/emboss
-	dev-python/matplotlib[${PYTHON_USEDEP}]
-	dev-python/psubprocess[${PYTHON_USEDEP}]
-	dev-python/configobj[${PYTHON_USEDEP}]"
-	# ( blast2GO || b2g4pipe )
-	# sci-biology/sputnik
-	# sci-biology/gsnap
-
-# blast2GO is http://www.blast2go.org/home
-# a non-GUI pipeline is called b2g4pipe, see https://sites.google.com/a/brown.edu/bioinformatics-in-biomed/b2g4pipe-2-5
-
-# TODO: drop the bundled binaries but ...
-# 1. the QA check did not find all bundled binaries, e.g. sputnik, lucy, trimpoly
-# 2. until we have them all, maybe keep the installed
-#
-# * QA Notice: The following files contain writable and executable sections
-# *  Files with such sections will not work properly (or at all!) on some
-# *  architectures/operating systems.  A bug should be filed at
-# *  http://bugs.gentoo.org/ to make sure the issue is fixed.
-# *  For more information, see http://hardened.gentoo.org/gnu-stack.xml
-# *  Please include the following list of files in your report:
-# *  Note: Bugs should be filed for the respective maintainers
-# *  of the package in question and not hardened@g.o.
-# * RWX --- --- usr/lib64/python2.7/site-packages/ext/bin/linux/32bit/tblastx
-# * RWX --- --- usr/lib64/python2.7/site-packages/ext/bin/linux/32bit/makeblastdb
-# * RWX --- --- usr/lib64/python2.7/site-packages/ext/bin/linux/32bit/blastx
-# * RWX --- --- usr/lib64/python2.7/site-packages/ext/bin/linux/32bit/blastp
-# * RWX --- --- usr/lib64/python2.7/site-packages/ext/bin/linux/32bit/tblastn
-# * RWX --- --- usr/lib64/python2.7/site-packages/ext/bin/linux/32bit/blastn
-# * RWX --- --- usr/lib64/python2.7/site-packages/ext/bin/linux/64bit/tblastx
-# * RWX --- --- usr/lib64/python2.7/site-packages/ext/bin/linux/64bit/makeblastdb
-# * RWX --- --- usr/lib64/python2.7/site-packages/ext/bin/linux/64bit/blastx
-# * RWX --- --- usr/lib64/python2.7/site-packages/ext/bin/linux/64bit/blastp
-# * RWX --- --- usr/lib64/python2.7/site-packages/ext/bin/linux/64bit/tblastn
-# * RWX --- --- usr/lib64/python2.7/site-packages/ext/bin/linux/64bit/blastn
-
-#/usr/lib64/python2.7/site-packages/ext/bin/linux/32bit
-#/usr/lib64/python2.7/site-packages/ext/bin/linux/32bit/bgzip
-#/usr/lib64/python2.7/site-packages/ext/bin/linux/32bit/blastn
-#/usr/lib64/python2.7/site-packages/ext/bin/linux/32bit/blastp
-#/usr/lib64/python2.7/site-packages/ext/bin/linux/32bit/blastx
-#/usr/lib64/python2.7/site-packages/ext/bin/linux/32bit/bwa
-#/usr/lib64/python2.7/site-packages/ext/bin/linux/32bit/emboss_data
-#/usr/lib64/python2.7/site-packages/ext/bin/linux/32bit/emboss_data/EBLOSUM62
-#/usr/lib64/python2.7/site-packages/ext/bin/linux/32bit/emboss_data/EDNAFULL
-#/usr/lib64/python2.7/site-packages/ext/bin/linux/32bit/emboss_data/codes.english
-#/usr/lib64/python2.7/site-packages/ext/bin/linux/32bit/emboss_data/est2genome.acd
-#/usr/lib64/python2.7/site-packages/ext/bin/linux/32bit/emboss_data/knowntypes.standard
-#/usr/lib64/python2.7/site-packages/ext/bin/linux/32bit/emboss_data/water.acd
-#/usr/lib64/python2.7/site-packages/ext/bin/linux/32bit/est2genome
-#/usr/lib64/python2.7/site-packages/ext/bin/linux/32bit/estscan
-#/usr/lib64/python2.7/site-packages/ext/bin/linux/32bit/fa_coords
-#/usr/lib64/python2.7/site-packages/ext/bin/linux/32bit/gmap
-#/usr/lib64/python2.7/site-packages/ext/bin/linux/32bit/gmap_build
-#/usr/lib64/python2.7/site-packages/ext/bin/linux/32bit/gmap_compress
-#/usr/lib64/python2.7/site-packages/ext/bin/linux/32bit/gmap_process
-#/usr/lib64/python2.7/site-packages/ext/bin/linux/32bit/gmap_reassemble
-#/usr/lib64/python2.7/site-packages/ext/bin/linux/32bit/gmap_setup
-#/usr/lib64/python2.7/site-packages/ext/bin/linux/32bit/gmap_uncompress
-#/usr/lib64/python2.7/site-packages/ext/bin/linux/32bit/gmapindex
-#/usr/lib64/python2.7/site-packages/ext/bin/linux/32bit/gsnap
-#/usr/lib64/python2.7/site-packages/ext/bin/linux/32bit/gsnap_tally
-#/usr/lib64/python2.7/site-packages/ext/bin/linux/32bit/lucy
-#/usr/lib64/python2.7/site-packages/ext/bin/linux/32bit/makeblastdb
-#/usr/lib64/python2.7/site-packages/ext/bin/linux/32bit/md_coords
-#/usr/lib64/python2.7/site-packages/ext/bin/linux/32bit/mdust
-#/usr/lib64/python2.7/site-packages/ext/bin/linux/32bit/samtools
-#/usr/lib64/python2.7/site-packages/ext/bin/linux/32bit/sputnik
-#/usr/lib64/python2.7/site-packages/ext/bin/linux/32bit/tabix
-#/usr/lib64/python2.7/site-packages/ext/bin/linux/32bit/tblastn
-#/usr/lib64/python2.7/site-packages/ext/bin/linux/32bit/tblastx
-#/usr/lib64/python2.7/site-packages/ext/bin/linux/32bit/trimpoly
-#/usr/lib64/python2.7/site-packages/ext/bin/linux/32bit/water
-#/usr/lib64/python2.7/site-packages/ext/bin/linux/64bit
-#/usr/lib64/python2.7/site-packages/ext/bin/linux/64bit/bgzip
-#/usr/lib64/python2.7/site-packages/ext/bin/linux/64bit/blastn
-#/usr/lib64/python2.7/site-packages/ext/bin/linux/64bit/blastp
-#/usr/lib64/python2.7/site-packages/ext/bin/linux/64bit/blastx
-#/usr/lib64/python2.7/site-packages/ext/bin/linux/64bit/bwa
-#/usr/lib64/python2.7/site-packages/ext/bin/linux/64bit/emboss_data
-#/usr/lib64/python2.7/site-packages/ext/bin/linux/64bit/emboss_data/EBLOSUM62
-#/usr/lib64/python2.7/site-packages/ext/bin/linux/64bit/emboss_data/EDNAFULL
-#/usr/lib64/python2.7/site-packages/ext/bin/linux/64bit/emboss_data/codes.english
-#/usr/lib64/python2.7/site-packages/ext/bin/linux/64bit/emboss_data/est2genome.acd
-#/usr/lib64/python2.7/site-packages/ext/bin/linux/64bit/emboss_data/knowntypes.standard
-#/usr/lib64/python2.7/site-packages/ext/bin/linux/64bit/emboss_data/water.acd
-#/usr/lib64/python2.7/site-packages/ext/bin/linux/64bit/est2genome
-#/usr/lib64/python2.7/site-packages/ext/bin/linux/64bit/estscan
-#/usr/lib64/python2.7/site-packages/ext/bin/linux/64bit/fa_coords
-#/usr/lib64/python2.7/site-packages/ext/bin/linux/64bit/gmap
-#/usr/lib64/python2.7/site-packages/ext/bin/linux/64bit/gmap_build
-#/usr/lib64/python2.7/site-packages/ext/bin/linux/64bit/gmap_compress
-#/usr/lib64/python2.7/site-packages/ext/bin/linux/64bit/gmap_process
-#/usr/lib64/python2.7/site-packages/ext/bin/linux/64bit/gmap_reassemble
-#/usr/lib64/python2.7/site-packages/ext/bin/linux/64bit/gmap_setup
-#/usr/lib64/python2.7/site-packages/ext/bin/linux/64bit/gmap_uncompress
-#/usr/lib64/python2.7/site-packages/ext/bin/linux/64bit/gmapindex
-#/usr/lib64/python2.7/site-packages/ext/bin/linux/64bit/gsnap
-#/usr/lib64/python2.7/site-packages/ext/bin/linux/64bit/gsnap_tally
-#/usr/lib64/python2.7/site-packages/ext/bin/linux/64bit/lucy
-#/usr/lib64/python2.7/site-packages/ext/bin/linux/64bit/makeblastdb
-#/usr/lib64/python2.7/site-packages/ext/bin/linux/64bit/md_coords
-#/usr/lib64/python2.7/site-packages/ext/bin/linux/64bit/mdust
-#/usr/lib64/python2.7/site-packages/ext/bin/linux/64bit/samtools
-#/usr/lib64/python2.7/site-packages/ext/bin/linux/64bit/sputnik
-#/usr/lib64/python2.7/site-packages/ext/bin/linux/64bit/tabix
-#/usr/lib64/python2.7/site-packages/ext/bin/linux/64bit/tblastn
-#/usr/lib64/python2.7/site-packages/ext/bin/linux/64bit/tblastx
-#/usr/lib64/python2.7/site-packages/ext/bin/linux/64bit/trimpoly
-#/usr/lib64/python2.7/site-packages/ext/bin/linux/64bit/water
-
-pkg_postinst(){
-	einfo "It is highly recommended to install blast2GO. Either the commercial version with GUI"
-	einfo "   or a non-GUI version called b2g4pipe. Either way, refer to http://www.blast2go.org"
-	einfo "   Brief installation process is at http://bioinf.comav.upv.es/ngs_backbone/install.html"
-	einfo "Alternatively, a VirtualBox image with ngs_bakbone is at http://bioinf.comav.upv.es/_downloads/ngs_machine_v3.tar.gz"
-}
diff --git a/sci-biology/ngs_backbone/ngs_backbone-9999.ebuild b/sci-biology/ngs_backbone/ngs_backbone-9999.ebuild
deleted file mode 100644
index 03f606c31..000000000
--- a/sci-biology/ngs_backbone/ngs_backbone-9999.ebuild
+++ /dev/null
@@ -1,148 +0,0 @@
-# Copyright 1999-2016 Gentoo Foundation
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=6
-
-PYTHON_COMPAT=( python2_7 )
-
-inherit distutils-r1 git-r3
-
-DESCRIPTION="Assembly & annotation pipeline with web interface for EST/chromosomal sequences"
-HOMEPAGE="http://bioinf.comav.upv.es/ngs_backbone/index.html"
-EGIT_REPO_URI="https://github.com/JoseBlanca/franklin"
-
-LICENSE="GPL-3"
-SLOT="0"
-KEYWORDS=""
-IUSE=""
-
-DEPEND=""
-RDEPEND="${DEPEND}
-	sci-biology/biopython[${PYTHON_USEDEP}]
-	sci-biology/samtools[${PYTHON_USEDEP}]
-	sci-biology/picard
-	sci-biology/mira
-	sci-biology/bwa
-	sci-biology/gatk
-	sci-biology/pysam[${PYTHON_USEDEP}]
-	sci-biology/estscan
-	sci-biology/ncbi-tools
-	sci-biology/lucy
-	sci-biology/gmap
-	sci-biology/emboss
-	dev-python/matplotlib[${PYTHON_USEDEP}]
-	dev-python/psubprocess[${PYTHON_USEDEP}]
-	dev-python/configobj[${PYTHON_USEDEP}]"
-	# ( blast2GO || b2g4pipe )
-	# sci-biology/sputnik
-	# sci-biology/gsnap
-
-# blast2GO is http://www.blast2go.org/home
-# a non-GUI pipeline is called b2g4pipe, see https://sites.google.com/a/brown.edu/bioinformatics-in-biomed/b2g4pipe-2-5
-
-# TODO: drop the bundled binaries but ...
-# 1. the QA check did not find all bundled binaries, e.g. sputnik, lucy, trimpoly
-# 2. until we have them all, maybe keep the installed
-#
-# * QA Notice: The following files contain writable and executable sections
-# *  Files with such sections will not work properly (or at all!) on some
-# *  architectures/operating systems.  A bug should be filed at
-# *  http://bugs.gentoo.org/ to make sure the issue is fixed.
-# *  For more information, see http://hardened.gentoo.org/gnu-stack.xml
-# *  Please include the following list of files in your report:
-# *  Note: Bugs should be filed for the respective maintainers
-# *  of the package in question and not hardened@g.o.
-# * RWX --- --- usr/lib64/python2.7/site-packages/ext/bin/linux/32bit/tblastx
-# * RWX --- --- usr/lib64/python2.7/site-packages/ext/bin/linux/32bit/makeblastdb
-# * RWX --- --- usr/lib64/python2.7/site-packages/ext/bin/linux/32bit/blastx
-# * RWX --- --- usr/lib64/python2.7/site-packages/ext/bin/linux/32bit/blastp
-# * RWX --- --- usr/lib64/python2.7/site-packages/ext/bin/linux/32bit/tblastn
-# * RWX --- --- usr/lib64/python2.7/site-packages/ext/bin/linux/32bit/blastn
-# * RWX --- --- usr/lib64/python2.7/site-packages/ext/bin/linux/64bit/tblastx
-# * RWX --- --- usr/lib64/python2.7/site-packages/ext/bin/linux/64bit/makeblastdb
-# * RWX --- --- usr/lib64/python2.7/site-packages/ext/bin/linux/64bit/blastx
-# * RWX --- --- usr/lib64/python2.7/site-packages/ext/bin/linux/64bit/blastp
-# * RWX --- --- usr/lib64/python2.7/site-packages/ext/bin/linux/64bit/tblastn
-# * RWX --- --- usr/lib64/python2.7/site-packages/ext/bin/linux/64bit/blastn
-
-#/usr/lib64/python2.7/site-packages/ext/bin/linux/32bit
-#/usr/lib64/python2.7/site-packages/ext/bin/linux/32bit/bgzip
-#/usr/lib64/python2.7/site-packages/ext/bin/linux/32bit/blastn
-#/usr/lib64/python2.7/site-packages/ext/bin/linux/32bit/blastp
-#/usr/lib64/python2.7/site-packages/ext/bin/linux/32bit/blastx
-#/usr/lib64/python2.7/site-packages/ext/bin/linux/32bit/bwa
-#/usr/lib64/python2.7/site-packages/ext/bin/linux/32bit/emboss_data
-#/usr/lib64/python2.7/site-packages/ext/bin/linux/32bit/emboss_data/EBLOSUM62
-#/usr/lib64/python2.7/site-packages/ext/bin/linux/32bit/emboss_data/EDNAFULL
-#/usr/lib64/python2.7/site-packages/ext/bin/linux/32bit/emboss_data/codes.english
-#/usr/lib64/python2.7/site-packages/ext/bin/linux/32bit/emboss_data/est2genome.acd
-#/usr/lib64/python2.7/site-packages/ext/bin/linux/32bit/emboss_data/knowntypes.standard
-#/usr/lib64/python2.7/site-packages/ext/bin/linux/32bit/emboss_data/water.acd
-#/usr/lib64/python2.7/site-packages/ext/bin/linux/32bit/est2genome
-#/usr/lib64/python2.7/site-packages/ext/bin/linux/32bit/estscan
-#/usr/lib64/python2.7/site-packages/ext/bin/linux/32bit/fa_coords
-#/usr/lib64/python2.7/site-packages/ext/bin/linux/32bit/gmap
-#/usr/lib64/python2.7/site-packages/ext/bin/linux/32bit/gmap_build
-#/usr/lib64/python2.7/site-packages/ext/bin/linux/32bit/gmap_compress
-#/usr/lib64/python2.7/site-packages/ext/bin/linux/32bit/gmap_process
-#/usr/lib64/python2.7/site-packages/ext/bin/linux/32bit/gmap_reassemble
-#/usr/lib64/python2.7/site-packages/ext/bin/linux/32bit/gmap_setup
-#/usr/lib64/python2.7/site-packages/ext/bin/linux/32bit/gmap_uncompress
-#/usr/lib64/python2.7/site-packages/ext/bin/linux/32bit/gmapindex
-#/usr/lib64/python2.7/site-packages/ext/bin/linux/32bit/gsnap
-#/usr/lib64/python2.7/site-packages/ext/bin/linux/32bit/gsnap_tally
-#/usr/lib64/python2.7/site-packages/ext/bin/linux/32bit/lucy
-#/usr/lib64/python2.7/site-packages/ext/bin/linux/32bit/makeblastdb
-#/usr/lib64/python2.7/site-packages/ext/bin/linux/32bit/md_coords
-#/usr/lib64/python2.7/site-packages/ext/bin/linux/32bit/mdust
-#/usr/lib64/python2.7/site-packages/ext/bin/linux/32bit/samtools
-#/usr/lib64/python2.7/site-packages/ext/bin/linux/32bit/sputnik
-#/usr/lib64/python2.7/site-packages/ext/bin/linux/32bit/tabix
-#/usr/lib64/python2.7/site-packages/ext/bin/linux/32bit/tblastn
-#/usr/lib64/python2.7/site-packages/ext/bin/linux/32bit/tblastx
-#/usr/lib64/python2.7/site-packages/ext/bin/linux/32bit/trimpoly
-#/usr/lib64/python2.7/site-packages/ext/bin/linux/32bit/water
-#/usr/lib64/python2.7/site-packages/ext/bin/linux/64bit
-#/usr/lib64/python2.7/site-packages/ext/bin/linux/64bit/bgzip
-#/usr/lib64/python2.7/site-packages/ext/bin/linux/64bit/blastn
-#/usr/lib64/python2.7/site-packages/ext/bin/linux/64bit/blastp
-#/usr/lib64/python2.7/site-packages/ext/bin/linux/64bit/blastx
-#/usr/lib64/python2.7/site-packages/ext/bin/linux/64bit/bwa
-#/usr/lib64/python2.7/site-packages/ext/bin/linux/64bit/emboss_data
-#/usr/lib64/python2.7/site-packages/ext/bin/linux/64bit/emboss_data/EBLOSUM62
-#/usr/lib64/python2.7/site-packages/ext/bin/linux/64bit/emboss_data/EDNAFULL
-#/usr/lib64/python2.7/site-packages/ext/bin/linux/64bit/emboss_data/codes.english
-#/usr/lib64/python2.7/site-packages/ext/bin/linux/64bit/emboss_data/est2genome.acd
-#/usr/lib64/python2.7/site-packages/ext/bin/linux/64bit/emboss_data/knowntypes.standard
-#/usr/lib64/python2.7/site-packages/ext/bin/linux/64bit/emboss_data/water.acd
-#/usr/lib64/python2.7/site-packages/ext/bin/linux/64bit/est2genome
-#/usr/lib64/python2.7/site-packages/ext/bin/linux/64bit/estscan
-#/usr/lib64/python2.7/site-packages/ext/bin/linux/64bit/fa_coords
-#/usr/lib64/python2.7/site-packages/ext/bin/linux/64bit/gmap
-#/usr/lib64/python2.7/site-packages/ext/bin/linux/64bit/gmap_build
-#/usr/lib64/python2.7/site-packages/ext/bin/linux/64bit/gmap_compress
-#/usr/lib64/python2.7/site-packages/ext/bin/linux/64bit/gmap_process
-#/usr/lib64/python2.7/site-packages/ext/bin/linux/64bit/gmap_reassemble
-#/usr/lib64/python2.7/site-packages/ext/bin/linux/64bit/gmap_setup
-#/usr/lib64/python2.7/site-packages/ext/bin/linux/64bit/gmap_uncompress
-#/usr/lib64/python2.7/site-packages/ext/bin/linux/64bit/gmapindex
-#/usr/lib64/python2.7/site-packages/ext/bin/linux/64bit/gsnap
-#/usr/lib64/python2.7/site-packages/ext/bin/linux/64bit/gsnap_tally
-#/usr/lib64/python2.7/site-packages/ext/bin/linux/64bit/lucy
-#/usr/lib64/python2.7/site-packages/ext/bin/linux/64bit/makeblastdb
-#/usr/lib64/python2.7/site-packages/ext/bin/linux/64bit/md_coords
-#/usr/lib64/python2.7/site-packages/ext/bin/linux/64bit/mdust
-#/usr/lib64/python2.7/site-packages/ext/bin/linux/64bit/samtools
-#/usr/lib64/python2.7/site-packages/ext/bin/linux/64bit/sputnik
-#/usr/lib64/python2.7/site-packages/ext/bin/linux/64bit/tabix
-#/usr/lib64/python2.7/site-packages/ext/bin/linux/64bit/tblastn
-#/usr/lib64/python2.7/site-packages/ext/bin/linux/64bit/tblastx
-#/usr/lib64/python2.7/site-packages/ext/bin/linux/64bit/trimpoly
-#/usr/lib64/python2.7/site-packages/ext/bin/linux/64bit/water
-
-pkg_postinst(){
-	einfo "It is highly recommended to install blast2GO. Either the commercial version with GUI"
-	einfo "   or a non-GUI version called b2g4pipe. Either way, refer to http://www.blast2go.org"
-	einfo "   Brief installation process is at http://bioinf.comav.upv.es/ngs_backbone/install.html"
-	einfo "Alternatively, a VirtualBox image with ngs_bakbone is at http://bioinf.comav.upv.es/_downloads/ngs_machine_v3.tar.gz"
-}
diff --git a/sci-biology/nilearn/Manifest b/sci-biology/nilearn/Manifest
index cda3b1922..550ed1f0f 100644
--- a/sci-biology/nilearn/Manifest
+++ b/sci-biology/nilearn/Manifest
@@ -1,4 +1,2 @@
-DIST nilearn-0.3.1.tar.gz 2793233 BLAKE2B 55054fdcb21f5a80283a2ba958510aa8a22a73882a324a22e37ee0c5292745658f6f7dd16042ba2e3eb91e7145650961c71de979716cd17af18842763c66223c SHA512 e222d868c2fff4dbe94a8e81498b4e3c4628a77e7f5d7ca77f9a28486f6e993b9ac20c55cf16f06b93cb3ffb577e9e0a87756b089f83c3387ab515e7991d8654
-DIST nilearn-0.4.1.tar.gz 2835584 BLAKE2B c3e8a06b410b087abc8a3e05cbac65397e558de43da0af7d6776fb4817fa190da422b9b085977998cad52bca266799b3bcc285e8ccdef6b9f8cdb6840b934064 SHA512 b5849d49170d5d2a7488d9632162db4922f7edc093182dff2814fd661a6177b8b3f1a459626be0294075fab82d4bfa06485b03bb6b6e290ea230651515982c87
-DIST nilearn-0.4.2.tar.gz 2837042 BLAKE2B 8cf9e37e6b51b423b13b796a0ff4150a1c5d36b4b09150298f82e55e1690cd0e21e2e9393467470e804c66a9c437c7650a665c2a34d74d40bfea31341c990ebd SHA512 13acce019c903885caaadd3c0ce103ef2450b475e3297e08008c66a35777d7615dae264bd78507cc4117f87a3dd0d417cc9e1653f2186ee5c959b54ad9b6e577
-DIST nilearn-0.5.0.tar.gz 5654672 BLAKE2B f109c768aace07b2d22883dff7c1d6a855f5b951952be8d56cbe509fb582dddd6e6602d1a41612e361d7708bc19ee43fb7478a0a91c9337444942f28a79739f8 SHA512 de1b9a3aa0d3cb546ccaa5969e362f7a1720dfddf7625cb3e572eb3da676667e2f8a2a4307f3c911e444531b996d6ad213f2ef13b43b39dc658663f9b5e78a86
+DIST nilearn-0.8.1.gh.tar.gz 11305317 BLAKE2B adefde80f5bce5ef115299326d212a7771a6ca1fc1ed7afc20fdd5b099882cfe37cc2d163807677450328916704d44e8f4044229b1470f764c75ee12d2e72b63 SHA512 4de95caa5c2080665e827310de28efb48a8b2e8161ac62f9e799984dbcd364f45ce486fcd21e9f30ef1fc41f48d2e41e477846acec5f89caf3cc1489373293d4
+DIST nilearn-0.9.1.gh.tar.gz 11660100 BLAKE2B f2031b531faf2b7f77a6128ce2c41d4d8c4c9d5fab79df453ca127228f7ec4784b319107a9e9988b3d3a9ce87358d251e500a88dfb8226a6d4510ae5fe9f3a0c SHA512 f824fc563fd56b25508ee5803963fc98c2048fbab8823a6a6bde39e4b428a871588211649b4ce939f65173f6d4afd019e9fe1445b5cfdd00fba7823d9e23a571
diff --git a/sci-biology/nilearn/files/0.4.1-bundled_joblib_test.patch b/sci-biology/nilearn/files/0.4.1-bundled_joblib_test.patch
deleted file mode 100755
index e229d25fb..000000000
--- a/sci-biology/nilearn/files/0.4.1-bundled_joblib_test.patch
+++ /dev/null
@@ -1,39 +0,0 @@
---- a/nilearn/input_data/tests/test_nifti_masker.py	2018-08-02 18:57:07.700111595 +0200
-+++ b/nilearn/input_data/tests/test_nifti_masker.py	2018-08-02 18:57:29.453556439 +0200
-@@ -219,36 +219,6 @@
-     assert_raises(ValueError, masker.fit_transform, data_img)
- 
- 
--def test_joblib_cache():
--    from sklearn.externals.joblib import hash, Memory
--    mask = np.zeros((40, 40, 40))
--    mask[20, 20, 20] = 1
--    mask_img = Nifti1Image(mask, np.eye(4))
--
--    with testing.write_tmp_imgs(mask_img, create_files=True) as filename:
--        masker = NiftiMasker(mask_img=filename)
--        masker.fit()
--        mask_hash = hash(masker.mask_img_)
--        masker.mask_img_.get_data()
--        assert_true(mask_hash == hash(masker.mask_img_))
--
--        # Test a tricky issue with memmapped joblib.memory that makes
--        # imgs return by inverse_transform impossible to save
--        cachedir = mkdtemp()
--        try:
--            masker.memory = Memory(cachedir=cachedir, mmap_mode='r',
--                                   verbose=0)
--            X = masker.transform(mask_img)
--            # inverse_transform a first time, so that the result is cached
--            out_img = masker.inverse_transform(X)
--            out_img = masker.inverse_transform(X)
--            out_img.to_filename(os.path.join(cachedir, 'test.nii'))
--        finally:
--            # enables to delete "filename" on windows
--            del masker
--            shutil.rmtree(cachedir, ignore_errors=True)
--
--
- def test_mask_init_errors():
-     # Errors that are caught in init
-     mask = NiftiMasker(mask_strategy='oops')
diff --git a/sci-biology/nilearn/files/nilearn-0.9.1-tests.patch b/sci-biology/nilearn/files/nilearn-0.9.1-tests.patch
new file mode 100644
index 000000000..6d13b76b1
--- /dev/null
+++ b/sci-biology/nilearn/files/nilearn-0.9.1-tests.patch
@@ -0,0 +1,10 @@
+--- a/setup.cfg
++++ b/setup.cfg
+@@ -78,7 +78,6 @@
+ doctest_optionflags = NORMALIZE_WHITESPACE ELLIPSIS
+ junit_family = xunit2
+ addopts =
+-	--doctest-modules
+ 	-s
+ 	-vv
+ 	--durations=0
diff --git a/sci-biology/nilearn/metadata.xml b/sci-biology/nilearn/metadata.xml
index 2010f6625..9da61e484 100644
--- a/sci-biology/nilearn/metadata.xml
+++ b/sci-biology/nilearn/metadata.xml
@@ -2,7 +2,7 @@
 <!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
 <pkgmetadata>
 	<maintainer type="person">
-		<email>horea.christ@gmail.com</email>
+		<email>gentoo@chymera.eu</email>
 		<name>Horea Christian</name>
 	</maintainer>
 	<maintainer type="project">
@@ -14,9 +14,6 @@ Nilearn is a Python module for fast and easy statistical learning on NeuroImagin
 It leverages the scikit-learn Python toolbox for multivariate statistics with applications
 such as predictive modelling, classification, decoding, or connectivity analysis.
 </longdescription>
-	<use>
-		<flag name="plot">Adds optional dependency needed for plotting function subset.</flag>
-	</use>
 	<upstream>
 		<remote-id type="github">nilearn/nilearn</remote-id>
 		<remote-id type="pypi">nilearn</remote-id>
diff --git a/sci-biology/nilearn/nilearn-0.3.1.ebuild b/sci-biology/nilearn/nilearn-0.3.1.ebuild
deleted file mode 100644
index 49f7a1a33..000000000
--- a/sci-biology/nilearn/nilearn-0.3.1.ebuild
+++ /dev/null
@@ -1,51 +0,0 @@
-# Copyright 1999-2018 Gentoo Foundation
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=6
-
-PYTHON_COMPAT=( python{2_7,3_4,3_5} )
-
-inherit distutils-r1
-
-DESCRIPTION="Fast and easy statistical learning on NeuroImaging data"
-HOMEPAGE="http://nilearn.github.io/"
-SRC_URI="https://github.com/nilearn/nilearn/archive/${PV}.tar.gz -> ${P}.tar.gz"
-
-LICENSE="BSD"
-SLOT="0"
-KEYWORDS="~amd64 ~x86"
-IUSE="+plot test"
-
-DEPEND="
-	test? (
-		${RDEPEND}
-		dev-python/nose[${PYTHON_USEDEP}]
-		)
-	dev-python/setuptools[${PYTHON_USEDEP}]
-	"
-RDEPEND="
-	dev-python/joblib[${PYTHON_USEDEP}]
-	dev-python/numpy[${PYTHON_USEDEP}]
-	sci-libs/scikits_learn[${PYTHON_USEDEP}]
-	sci-libs/scipy[${PYTHON_USEDEP}]
-	sci-libs/nibabel[${PYTHON_USEDEP}]
-	plot? ( dev-python/matplotlib[${PYTHON_USEDEP}] )"
-
-# upstream is reluctant to *not* depend on bundled scikits_learn:
-# https://github.com/nilearn/nilearn/pull/1398
-python_prepare_all() {
-	local f
-	for f in nilearn/{*/*/,*/,}*.py; do
-		sed -r \
-			-e '/^from/s/(sklearn|\.|)\.externals\.joblib/joblib/' \
-			-e 's/from (sklearn|\.|)\.externals import/import/' \
-		-i $f || die
-	done
-
-	distutils-r1_python_prepare_all
-}
-
-python_test() {
-	echo "backend: Agg" > matplotlibrc
-	MPLCONFIGDIR=. nosetests -v || die
-}
diff --git a/sci-biology/nilearn/nilearn-0.4.1.ebuild b/sci-biology/nilearn/nilearn-0.4.1.ebuild
deleted file mode 100644
index 80d3e2910..000000000
--- a/sci-biology/nilearn/nilearn-0.4.1.ebuild
+++ /dev/null
@@ -1,53 +0,0 @@
-# Copyright 1999-2018 Gentoo Foundation
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=7
-
-PYTHON_COMPAT=( python{2_7,3_4,3_5,3_6} )
-
-inherit distutils-r1
-
-DESCRIPTION="Fast and easy statistical learning on NeuroImaging data"
-HOMEPAGE="http://nilearn.github.io/"
-SRC_URI="https://github.com/nilearn/nilearn/archive/${PV}.tar.gz -> ${P}.tar.gz"
-
-LICENSE="BSD"
-SLOT="0"
-KEYWORDS="~amd64 ~x86"
-IUSE="+plot test"
-
-DEPEND="
-	test? (
-		${RDEPEND}
-		dev-python/nose[${PYTHON_USEDEP}]
-		)
-	dev-python/setuptools[${PYTHON_USEDEP}]
-	"
-RDEPEND="
-	dev-python/joblib[${PYTHON_USEDEP}]
-	dev-python/numpy[${PYTHON_USEDEP}]
-	sci-libs/scikits_learn[${PYTHON_USEDEP}]
-	sci-libs/scipy[${PYTHON_USEDEP}]
-	sci-libs/nibabel[${PYTHON_USEDEP}]
-	plot? ( dev-python/matplotlib[${PYTHON_USEDEP}] )"
-
-PATCHES=( "${FILESDIR}/${PV}-bundled_joblib_test.patch" )
-
-python_prepare_all() {
-	# upstream is reluctant to *not* depend on bundled scikits_learn:
-	# https://github.com/nilearn/nilearn/pull/1398
-	local f
-	for f in nilearn/{*/*/,*/,}*.py; do
-		sed -r \
-			-e '/^from/s/(sklearn|\.|)\.externals\.joblib/joblib/' \
-			-e 's/from (sklearn|\.|)\.externals import/import/' \
-		-i $f || die
-	done
-
-	distutils-r1_python_prepare_all
-}
-
-python_test() {
-	echo "backend: Agg" > matplotlibrc
-	MPLCONFIGDIR=. nosetests -v || die
-}
diff --git a/sci-biology/nilearn/nilearn-0.4.2.ebuild b/sci-biology/nilearn/nilearn-0.4.2.ebuild
deleted file mode 100644
index 4b4d429bb..000000000
--- a/sci-biology/nilearn/nilearn-0.4.2.ebuild
+++ /dev/null
@@ -1,53 +0,0 @@
-# Copyright 1999-2018 Gentoo Foundation
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=7
-
-PYTHON_COMPAT=( python{2_7,3_4,3_5,3_6} )
-
-inherit distutils-r1
-
-DESCRIPTION="Fast and easy statistical learning on NeuroImaging data"
-HOMEPAGE="http://nilearn.github.io/"
-SRC_URI="https://github.com/nilearn/nilearn/archive/${PV}.tar.gz -> ${P}.tar.gz"
-
-LICENSE="BSD"
-SLOT="0"
-KEYWORDS="~amd64 ~x86"
-IUSE="+plot test"
-
-DEPEND="
-	test? (
-		${RDEPEND}
-		dev-python/nose[${PYTHON_USEDEP}]
-		)
-	dev-python/setuptools[${PYTHON_USEDEP}]
-	"
-RDEPEND="
-	dev-python/joblib[${PYTHON_USEDEP}]
-	dev-python/numpy[${PYTHON_USEDEP}]
-	sci-libs/scikits_learn[${PYTHON_USEDEP}]
-	sci-libs/scipy[${PYTHON_USEDEP}]
-	sci-libs/nibabel[${PYTHON_USEDEP}]
-	plot? ( dev-python/matplotlib[${PYTHON_USEDEP}] )"
-
-PATCHES=( "${FILESDIR}/0.4.1-bundled_joblib_test.patch" )
-
-python_prepare_all() {
-	# upstream is reluctant to *not* depend on bundled scikits_learn:
-	# https://github.com/nilearn/nilearn/pull/1398
-	local f
-	for f in nilearn/{*/*/,*/,}*.py; do
-		sed -r \
-			-e '/^from/s/(sklearn|\.|)\.externals\.joblib/joblib/' \
-			-e 's/from (sklearn|\.|)\.externals import/import/' \
-		-i $f || die
-	done
-
-	distutils-r1_python_prepare_all
-}
-
-python_test() {
-	echo "backend: Agg" > matplotlibrc
-	MPLCONFIGDIR=. nosetests -v || die
-}
diff --git a/sci-biology/nilearn/nilearn-0.5.0.ebuild b/sci-biology/nilearn/nilearn-0.5.0.ebuild
deleted file mode 100644
index 3380e73c6..000000000
--- a/sci-biology/nilearn/nilearn-0.5.0.ebuild
+++ /dev/null
@@ -1,57 +0,0 @@
-# Copyright 1999-2018 Gentoo Authors
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=7
-
-PYTHON_COMPAT=( python{2_7,3_4,3_5,3_6} )
-
-inherit distutils-r1
-
-DESCRIPTION="Fast and easy statistical learning on NeuroImaging data"
-HOMEPAGE="http://nilearn.github.io/"
-SRC_URI="https://github.com/nilearn/nilearn/archive/${PV}.tar.gz -> ${P}.tar.gz"
-
-LICENSE="BSD"
-SLOT="0"
-KEYWORDS="~amd64 ~x86"
-IUSE="+plot test"
-
-DEPEND="
-	test? (
-		${RDEPEND}
-		dev-python/nose[${PYTHON_USEDEP}]
-		)
-	dev-python/setuptools[${PYTHON_USEDEP}]
-	"
-RDEPEND="
-	dev-python/joblib[${PYTHON_USEDEP}]
-	dev-python/numpy[${PYTHON_USEDEP}]
-	sci-libs/scikits_learn[${PYTHON_USEDEP}]
-	sci-libs/scipy[${PYTHON_USEDEP}]
-	sci-libs/nibabel[${PYTHON_USEDEP}]
-	plot? ( dev-python/matplotlib[${PYTHON_USEDEP}] )"
-
-# (Temporarily) commented out, since Gentoo sci-libs/scikits_learn decided it
-# is a mess to maintain system joblib usage
-#PATCHES=( "${FILESDIR}/0.4.1-bundled_joblib_test.patch" )
-
-python_prepare_all() {
-	# upstream is reluctant to *not* depend on bundled scikits_learn:
-	# https://github.com/nilearn/nilearn/pull/1398
-	# (Temporarily) commented out, since Gentoo sci-libs/scikits_learn decided it
-	# is a mess to maintain system joblib usage
-	#local f
-	#for f in nilearn/{*/*/,*/,}*.py; do
-	#	sed -r \
-	#		-e '/^from/s/(sklearn|\.|)\.externals\.joblib/joblib/' \
-	#		-e 's/from (sklearn|\.|)\.externals import/import/' \
-	#	-i $f || die
-	#done
-
-	distutils-r1_python_prepare_all
-}
-
-python_test() {
-	echo "backend: Agg" > matplotlibrc
-	MPLCONFIGDIR=. nosetests -v || die
-}
diff --git a/sci-biology/nilearn/nilearn-0.8.1.ebuild b/sci-biology/nilearn/nilearn-0.8.1.ebuild
new file mode 100644
index 000000000..3064c0ba5
--- /dev/null
+++ b/sci-biology/nilearn/nilearn-0.8.1.ebuild
@@ -0,0 +1,42 @@
+# Copyright 1999-2023 Gentoo Authors
+# Distributed under the terms of the GNU General Public License v2
+
+EAPI=8
+
+PYTHON_COMPAT=( python3_{10..11} )
+
+inherit distutils-r1
+
+DESCRIPTION="Fast and easy statistical learning on NeuroImaging data"
+HOMEPAGE="http://nilearn.github.io/"
+SRC_URI="https://github.com/nilearn/nilearn/archive/${PV}.tar.gz -> ${P}.gh.tar.gz"
+
+LICENSE="BSD"
+SLOT="0"
+KEYWORDS="~amd64 ~x86"
+
+# Tests attempt to download external data.
+RESTRICT="test"
+
+BDEPEND="
+	test? (
+		dev-python/matplotlib[${PYTHON_USEDEP}]
+	)
+"
+
+RDEPEND="
+	>=dev-python/joblib-0.12[${PYTHON_USEDEP}]
+	>=dev-python/numpy-1.16[${PYTHON_USEDEP}]
+	>=sci-libs/scikit-learn-0.21[${PYTHON_USEDEP}]
+	>=dev-python/scipy-1.2[${PYTHON_USEDEP}]
+	>=sci-libs/nibabel-2.5[${PYTHON_USEDEP}]
+	>=dev-python/pandas-0.24.0[${PYTHON_USEDEP}]
+	>=dev-python/requests-2[${PYTHON_USEDEP}]
+"
+
+distutils_enable_tests pytest
+
+python_test() {
+	echo "backend: Agg" > matplotlibrc
+	MPLCONFIGDIR=. epytest
+}
diff --git a/sci-biology/nilearn/nilearn-0.9.1.ebuild b/sci-biology/nilearn/nilearn-0.9.1.ebuild
new file mode 100644
index 000000000..425e79444
--- /dev/null
+++ b/sci-biology/nilearn/nilearn-0.9.1.ebuild
@@ -0,0 +1,53 @@
+# Copyright 1999-2023 Gentoo Authors
+# Distributed under the terms of the GNU General Public License v2
+
+EAPI=8
+
+PYTHON_COMPAT=( python3_{10..11} )
+
+inherit distutils-r1
+
+DESCRIPTION="Fast and easy statistical learning on NeuroImaging data"
+HOMEPAGE="http://nilearn.github.io/"
+SRC_URI="https://github.com/nilearn/nilearn/archive/${PV}.tar.gz -> ${P}.gh.tar.gz"
+
+LICENSE="BSD"
+SLOT="0"
+KEYWORDS="~amd64 ~x86"
+IUSE="test"
+
+RDEPEND="
+	>=dev-python/joblib-0.15[${PYTHON_USEDEP}]
+	dev-python/lxml[${PYTHON_USEDEP}]
+	>=dev-python/matplotlib-3[${PYTHON_USEDEP}]
+	>=dev-python/numpy-1.18[${PYTHON_USEDEP}]
+	>=dev-python/pandas-1[${PYTHON_USEDEP}]
+	>=dev-python/requests-2[${PYTHON_USEDEP}]
+	>=dev-python/scipy-1.5[${PYTHON_USEDEP}]
+	>=sci-libs/nibabel-3[${PYTHON_USEDEP}]
+	>=sci-libs/scikit-learn-0.22[${PYTHON_USEDEP}]
+"
+
+PATCHES=( "${FILESDIR}/${P}-tests.patch" )
+
+distutils_enable_tests pytest
+
+EPYTEST_IGNORE=(
+	"examples/05_glm_second_level/plot_second_level_association_test.py"
+	"examples/05_glm_second_level/plot_second_level_one_sample_test.py"
+	"examples/05_glm_second_level/plot_second_level_two_sample_test.py"
+)
+# Reported upstream:
+# https://github.com/nilearn/nilearn/issues/3232
+EPYTEST_DESELECT=(
+	"nilearn/decoding/tests/test_decoder.py::test_decoder_dummy_classifier"
+	"nilearn/interfaces/fmriprep/tests/test_load_confounds.py::test_nilearn_standardize[False-True-zscore]"
+	"nilearn/interfaces/fmriprep/tests/test_load_confounds.py::test_nilearn_standardize[False-True-psc]"
+	"nilearn/interfaces/fmriprep/tests/test_load_confounds.py::test_nilearn_standardize[True-True-zscore]"
+	"nilearn/interfaces/fmriprep/tests/test_load_confounds.py::test_nilearn_standardize[True-True-psc]"
+)
+
+python_test() {
+	echo "backend: Agg" > matplotlibrc
+	MPLCONFIGDIR=. epytest
+}
diff --git a/sci-biology/nilearn/nilearn-9999.ebuild b/sci-biology/nilearn/nilearn-9999.ebuild
deleted file mode 100644
index 345f604b4..000000000
--- a/sci-biology/nilearn/nilearn-9999.ebuild
+++ /dev/null
@@ -1,54 +0,0 @@
-# Copyright 1999-2018 Gentoo Foundation
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=7
-
-PYTHON_COMPAT=( python{2_7,3_4,3_5,3_6} )
-
-inherit distutils-r1 git-r3
-
-DESCRIPTION="Fast and easy statistical learning on NeuroImaging data"
-HOMEPAGE="http://nilearn.github.io/"
-SRC_URI=""
-EGIT_REPO_URI="https://github.com/nilearn/nilearn"
-
-LICENSE="BSD"
-SLOT="0"
-KEYWORDS=""
-IUSE="+plot test"
-
-DEPEND="
-	test? (
-		${RDEPEND}
-		dev-python/nose[${PYTHON_USEDEP}]
-		)
-	dev-python/setuptools[${PYTHON_USEDEP}]
-	"
-RDEPEND="
-	dev-python/joblib[${PYTHON_USEDEP}]
-	dev-python/numpy[${PYTHON_USEDEP}]
-	sci-libs/scikits_learn[${PYTHON_USEDEP}]
-	sci-libs/scipy[${PYTHON_USEDEP}]
-	sci-libs/nibabel[${PYTHON_USEDEP}]
-	plot? ( dev-python/matplotlib[${PYTHON_USEDEP}] )"
-
-PATCHES=( "${FILESDIR}/0.4.1-bundled_joblib_test.patch" )
-
-python_prepare_all() {
-	# upstream is reluctant to *not* depend on bundled scikits_learn:
-	# https://github.com/nilearn/nilearn/pull/1398
-	local f
-	for f in nilearn/{*/*/,*/,}*.py; do
-		sed -r \
-			-e '/^from/s/(sklearn|\.|)\.externals\.joblib/joblib/' \
-			-e 's/from (sklearn|\.|)\.externals import/import/' \
-		-i $f || die
-	done
-
-	distutils-r1_python_prepare_all
-}
-
-python_test() {
-	echo "backend: Agg" > matplotlibrc
-	MPLCONFIGDIR=. nosetests -v || die
-}
diff --git a/sci-biology/nireg/metadata.xml b/sci-biology/nireg/metadata.xml
deleted file mode 100644
index d6592a893..000000000
--- a/sci-biology/nireg/metadata.xml
+++ /dev/null
@@ -1,15 +0,0 @@
-<?xml version="1.0" encoding="UTF-8"?>
-<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
-<pkgmetadata>
-	<maintainer type="person">
-		<email>horea.christ@gmail.com</email>
-		<name>Horea Christian</name>
-	</maintainer>
-	<maintainer type="project">
-		<email>sci@gentoo.org</email>
-		<name>Gentoo Science Project</name>
-	</maintainer>
-	<longdescription lang="en">
-Nireg is a package for nytive-python image registration.
-</longdescription>
-</pkgmetadata>
diff --git a/sci-biology/nireg/nireg-9999.ebuild b/sci-biology/nireg/nireg-9999.ebuild
deleted file mode 100644
index 980307fff..000000000
--- a/sci-biology/nireg/nireg-9999.ebuild
+++ /dev/null
@@ -1,32 +0,0 @@
-# Copyright 1999-2016 Gentoo Foundation
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=6
-
-PYTHON_COMPAT=( python{2_7,3_4,3_5} )
-
-inherit distutils-r1 git-r3
-
-DESCRIPTION="Image registration package for Python"
-HOMEPAGE="http://nipy.org/"
-SRC_URI=""
-EGIT_REPO_URI="https://github.com/nipy/${PN}"
-
-LICENSE="BSD"
-SLOT="0"
-IUSE="test"
-KEYWORDS=""
-
-COMMONDEPEND="dev-python/numpy[${PYTHON_USEDEP}]"
-DEPEND="${COMMONDEPEND}
-	dev-python/setuptools[${PYTHON_USEDEP}]
-	test? ( dev-python/nose[${PYTHON_USEDEP}] )"
-RDEPEND="${COMMONDEPEND}
-	sci-libs/scipy[${PYTHON_USEDEP}]
-	sci-libs/nibabel[${PYTHON_USEDEP}]
-	"
-
-python_test() {
-	#nosetests -v || die
-	python -c "import nireg; nireg.test()" || die
-}
diff --git a/sci-biology/nistats/metadata.xml b/sci-biology/nistats/metadata.xml
deleted file mode 100644
index 5b04d23d9..000000000
--- a/sci-biology/nistats/metadata.xml
+++ /dev/null
@@ -1,16 +0,0 @@
-<?xml version="1.0" encoding="UTF-8"?>
-<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
-<pkgmetadata>
-	<maintainer type="person">
-		<email>horea.christ@gmail.com</email>
-		<name>Horea Christian</name>
-	</maintainer>
-	<maintainer type="project">
-		<email>sci@gentoo.org</email>
-		<name>Gentoo Science Project</name>
-	</maintainer>
-	<longdescription lang="en">
-Nistats is a Python module for fast and easy modeling and statistical analysis of 
-functional Magnetic Resonance Imaging data.
-</longdescription>
-</pkgmetadata>
diff --git a/sci-biology/nistats/nistats-9999.ebuild b/sci-biology/nistats/nistats-9999.ebuild
deleted file mode 100644
index 30ef606c9..000000000
--- a/sci-biology/nistats/nistats-9999.ebuild
+++ /dev/null
@@ -1,33 +0,0 @@
-# Copyright 1999-2016 Gentoo Foundation
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=6
-
-PYTHON_COMPAT=( python{2_7,3_4} )
-
-inherit distutils-r1 git-r3
-
-DESCRIPTION="Neuroimaging tools for Python"
-HOMEPAGE="http://nipy.org/"
-SRC_URI=""
-EGIT_REPO_URI="https://github.com/nistats/${PN}"
-
-LICENSE="BSD"
-SLOT="0"
-IUSE=""
-KEYWORDS=""
-
-COMMONDEPEND="
-	dev-python/numpy[${PYTHON_USEDEP}]
-	dev-python/patsy[${PYTHON_USEDEP}]
-	"
-DEPEND="${COMMONDEPEND}
-	dev-python/setuptools[${PYTHON_USEDEP}]
-	"
-RDEPEND="${COMMONDEPEND}
-	sci-libs/scipy[${PYTHON_USEDEP}]
-	dev-python/sympy[${PYTHON_USEDEP}]
-	sci-libs/nibabel[${PYTHON_USEDEP}]
-	dev-python/pandas[${PYTHON_USEDEP}]
-	sci-biology/nilearn[${PYTHON_USEDEP}]
-	"
diff --git a/sci-biology/nitime/Manifest b/sci-biology/nitime/Manifest
index cb4790f33..4a9a85cc0 100644
--- a/sci-biology/nitime/Manifest
+++ b/sci-biology/nitime/Manifest
@@ -1 +1,2 @@
-DIST nitime-0.6.tar.gz 6205960 BLAKE2B 0ba316aea962d40f042586962420d08e3ef3b452f6431f51bd6f58c253e6c33b0af6cb3dc06ca3ba598d9c1c5c4cbc1844d0ccf3684ef2085fdc5747b70a7ff1 SHA512 ab91845ad1a29fbb8bf0a442668fb54976fe21d49ecfa57ec40f1596c10baf8684fd52aa3276a58d59faea4051621327cb50d5da8239ea8605365203cc009ae6
+DIST nitime-0.10.2.tar.gz 6231004 BLAKE2B 2214eb4fcb29567ebb4e819451bf7401ae6b467c0a2d196904c08bc44343e5c1ea840770f72d37df5e6642df455d895bfc9453b9389d8ef96cc88f3abc0d586e SHA512 c8c687f6c5e189e48bbe5cba4bbe3f19f34e6d087b43e3b0aa42d587f46081d3727867dbe07fa6d945381119086e12c98cdf12798055529a484152a4c04eae21
+DIST nitime-0.9.tar.gz 6222979 BLAKE2B 45dbf34fd89b805f97ae5d4f88264f47ff88fa1f89b7ef05527477270bfa588a79fd1b356b2e7206919ed675936207accc02ad5b9a4be27e916a1dcf0561147e SHA512 cd8af7c3463143ac1765c472c1274915adfaf85508c334008c703ef72961e0a5e9ccbbd9321aaf62f7a58d9534934386baf1c7269a1d8f2d41b678707cd69406
diff --git a/sci-biology/nitime/metadata.xml b/sci-biology/nitime/metadata.xml
index a09589ab6..606822ddb 100644
--- a/sci-biology/nitime/metadata.xml
+++ b/sci-biology/nitime/metadata.xml
@@ -2,7 +2,7 @@
 <!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
 <pkgmetadata>
 	<maintainer type="person">
-		<email>horea.christ@gmail.com</email>
+		<email>gentoo@chymera.eu</email>
 		<name>Horea Christian</name>
 	</maintainer>
 	<maintainer type="project">
@@ -10,10 +10,11 @@
 		<name>Gentoo Science Project</name>
 	</maintainer>
 	<longdescription lang="en">
-Nitime is a library for time-series analysis of data from neuroscience experiments
-in both the time and spectral domains.
-</longdescription>
+		Nitime is a library for time-series analysis of data from neuroscience experiments
+		in both the time and spectral domains.
+	</longdescription>
 	<upstream>
 		<remote-id type="github">nipy/nitime</remote-id>
+		<remote-id type="pypi">nitime</remote-id>
 	</upstream>
 </pkgmetadata>
diff --git a/sci-biology/nitime/nitime-0.10.2.ebuild b/sci-biology/nitime/nitime-0.10.2.ebuild
new file mode 100644
index 000000000..7e47d7288
--- /dev/null
+++ b/sci-biology/nitime/nitime-0.10.2.ebuild
@@ -0,0 +1,33 @@
+# Copyright 1999-2023 Gentoo Authors
+# Distributed under the terms of the GNU General Public License v2
+
+EAPI=8
+
+DISTUTILS_USE_PEP517=setuptools
+PYTHON_COMPAT=( python3_{10..11} )
+
+inherit distutils-r1 pypi
+
+DESCRIPTION="Time-series analysis of neuroscience data"
+HOMEPAGE="http://nipy.org/nitime/index.html"
+
+LICENSE="BSD"
+SLOT="0"
+KEYWORDS="~amd64 ~x86"
+
+COMMON_DEPEND="
+	dev-python/numpy[${PYTHON_USEDEP}]
+	dev-python/matplotlib[${PYTHON_USEDEP}]
+	dev-python/scipy[${PYTHON_USEDEP}]
+	"
+BDEPEND="${COMMON_DEPEND}
+	dev-python/cython[${PYTHON_USEDEP}]
+	"
+RDEPEND="
+	${COMMON_DEPEND}
+	dev-python/networkx[${PYTHON_USEDEP}]
+	sci-libs/nibabel[${PYTHON_USEDEP}]
+	"
+
+distutils_enable_tests pytest
+distutils_enable_sphinx doc
diff --git a/sci-biology/nitime/nitime-0.6.ebuild b/sci-biology/nitime/nitime-0.6.ebuild
deleted file mode 100644
index 6435b792b..000000000
--- a/sci-biology/nitime/nitime-0.6.ebuild
+++ /dev/null
@@ -1,38 +0,0 @@
-# Copyright 1999-2016 Gentoo Foundation
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=6
-
-PYTHON_COMPAT=( python{2_7,3_4,3_5} )
-
-inherit distutils-r1
-
-DESCRIPTION="Time-series analysis of neuroscience data"
-HOMEPAGE="http://nipy.org/nitime/index.html"
-SRC_URI="https://github.com/nipy/nitime/archive/rel/${PV}.tar.gz -> ${P}.tar.gz"
-
-LICENSE="BSD"
-SLOT="0"
-KEYWORDS="~amd64 ~x86"
-IUSE="test"
-
-COMMON_DEPEND="
-	dev-python/numpy[${PYTHON_USEDEP}]
-	dev-python/matplotlib[${PYTHON_USEDEP}]
-	sci-libs/scipy[${PYTHON_USEDEP}]
-	"
-DEPEND="
-	test? ( dev-python/nose[${PYTHON_USEDEP}] )
-	dev-python/setuptools[${PYTHON_USEDEP}]
-	"
-RDEPEND="
-	${COMMON_DEPEND}
-	dev-python/networkx[${PYTHON_USEDEP}]
-	sci-libs/nibabel[${PYTHON_USEDEP}]
-	"
-
-S="${WORKDIR}/${PN}-rel-${PV}"
-
-python_test() {
-	nosetests -v || die
-}
diff --git a/sci-biology/nitime/nitime-0.9.ebuild b/sci-biology/nitime/nitime-0.9.ebuild
new file mode 100644
index 000000000..cae7fdfea
--- /dev/null
+++ b/sci-biology/nitime/nitime-0.9.ebuild
@@ -0,0 +1,39 @@
+# Copyright 1999-2023 Gentoo Authors
+# Distributed under the terms of the GNU General Public License v2
+
+EAPI=8
+
+PYTHON_COMPAT=( python3_{10..11} )
+
+inherit distutils-r1 pypi virtualx
+
+DESCRIPTION="Time-series analysis of neuroscience data"
+HOMEPAGE="http://nipy.org/nitime/index.html"
+
+LICENSE="BSD"
+SLOT="0"
+KEYWORDS="~amd64 ~x86"
+
+# import file mismatch:
+RESTRICT="test"
+
+COMMON_DEPEND="
+	dev-python/numpy[${PYTHON_USEDEP}]
+	dev-python/matplotlib[${PYTHON_USEDEP}]
+	dev-python/scipy[${PYTHON_USEDEP}]
+	"
+BDEPEND="${COMMON_DEPEND}
+	dev-python/cython[${PYTHON_USEDEP}]
+	"
+RDEPEND="
+	${COMMON_DEPEND}
+	dev-python/networkx[${PYTHON_USEDEP}]
+	sci-libs/nibabel[${PYTHON_USEDEP}]
+	"
+
+distutils_enable_tests pytest
+distutils_enable_sphinx doc
+
+python_test() {
+	virtx pytest -v || die
+}
diff --git a/sci-biology/nitime/nitime-9999.ebuild b/sci-biology/nitime/nitime-9999.ebuild
index 539bc1ee5..ee81c01dc 100644
--- a/sci-biology/nitime/nitime-9999.ebuild
+++ b/sci-biology/nitime/nitime-9999.ebuild
@@ -1,9 +1,10 @@
-# Copyright 1999-2018 Gentoo Foundation
+# Copyright 1999-2023 Gentoo Authors
 # Distributed under the terms of the GNU General Public License v2
 
-EAPI=6
+EAPI=8
 
-PYTHON_COMPAT=( python{2_7,3_4,3_5} )
+DISTUTILS_USE_PEP517=setuptools
+PYTHON_COMPAT=( python3_{10..11} )
 
 inherit distutils-r1 git-r3
 
@@ -15,16 +16,14 @@ EGIT_REPO_URI="https://github.com/nipy/nitime"
 LICENSE="BSD"
 SLOT="0"
 KEYWORDS=""
-IUSE="test"
 
 COMMON_DEPEND="
 	dev-python/numpy[${PYTHON_USEDEP}]
 	dev-python/matplotlib[${PYTHON_USEDEP}]
-	sci-libs/scipy[${PYTHON_USEDEP}]
+	dev-python/scipy[${PYTHON_USEDEP}]
 	"
-DEPEND="
-	test? ( dev-python/nose[${PYTHON_USEDEP}] )
-	dev-python/setuptools[${PYTHON_USEDEP}]
+BDEPEND="${COMMON_DEPEND}
+	dev-python/cython[${PYTHON_USEDEP}]
 	"
 RDEPEND="
 	${COMMON_DEPEND}
@@ -32,6 +31,5 @@ RDEPEND="
 	sci-libs/nibabel[${PYTHON_USEDEP}]
 	"
 
-python_test() {
-	nosetests -v || die
-}
+distutils_enable_tests pytest
+distutils_enable_sphinx doc
diff --git a/sci-biology/nrcl/nrcl-110625.ebuild b/sci-biology/nrcl/nrcl-110625.ebuild
index 7d6fbf2d2..2538beab6 100644
--- a/sci-biology/nrcl/nrcl-110625.ebuild
+++ b/sci-biology/nrcl/nrcl-110625.ebuild
@@ -1,25 +1,28 @@
-# Copyright 1999-2015 Gentoo Foundation
+# Copyright 1999-2021 Gentoo Authors
 # Distributed under the terms of the GNU General Public License v2
 
-EAPI=5
+EAPI=7
 
-inherit eutils toolchain-funcs
+inherit toolchain-funcs
 
 DESCRIPTION="Containment clustering and layout utility for processing pairwise alignments"
-HOMEPAGE="http://compbio.dfci.harvard.edu/tgi/software/"
+HOMEPAGE="https://web.archive.org/web/20140726030702/http://compbio.dfci.harvard.edu/tgi/software/"
 SRC_URI="
 	ftp://occams.dfci.harvard.edu/pub/bio/tgi/software/tgicl/${PN}.tar.gz -> ${P}.tar.gz
-	ftp://occams.dfci.harvard.edu/pub/bio/tgi/software/tgicl/gclib.tar.gz -> gclib.tar.gz"
+	ftp://occams.dfci.harvard.edu/pub/bio/tgi/software/tgicl/gclib.tar.gz"
 
 LICENSE="Artistic"
 SLOT="0"
 KEYWORDS="~amd64 ~x86"
-IUSE=""
 
-S="${WORKDIR}"/${PN}
+S="${WORKDIR}/${PN}"
+
+PATCHES=(
+	"${FILESDIR}/${PV}-build.patch"
+)
 
 src_prepare() {
-	epatch "${FILESDIR}"/${PV}-build.patch
+	default
 	tc-export CXX
 }
 
diff --git a/sci-biology/ntCard/Manifest b/sci-biology/ntCard/Manifest
index ca6ebf5e3..6eac0789e 100644
--- a/sci-biology/ntCard/Manifest
+++ b/sci-biology/ntCard/Manifest
@@ -1 +1 @@
-DIST ntCard-1.1.0.tar.gz 14516 BLAKE2B 496d25c608db3332809aba2a05ca2942356204055eaf953adab1fb24915547aaef6a261f16925d3739c12fff9b8e6e213ad358d7415215e6ab36f8f2dcd99b00 SHA512 edeeaa73c4685c8efa50ad9b6c7d4899c46630038de9a5d70b7a628eadd1d5c85e7bfdf1185062fea18c8e5efd2147f338c6b3aaeab83e9428c41d4aea5472df
+DIST ntCard-1.2.2.tar.gz 160979 BLAKE2B c603d2b39845cf03615f9041ac8c1f24c25f8e8bc033cf89cbfcd9af02242b954651a7a1f330dadf0e181ef2bd2de899a62ce0574073261a5aa75dc9959159a8 SHA512 53a70ba3e260f64a18d8e9ccc6102f726a31557302173fcd327b6841e849df77c380b34bc640cb47d02dc755006e8f66df1c2f2597bef3129b38423373fee759
diff --git a/sci-biology/ntCard/metadata.xml b/sci-biology/ntCard/metadata.xml
index 138cb7705..fb03df79c 100644
--- a/sci-biology/ntCard/metadata.xml
+++ b/sci-biology/ntCard/metadata.xml
@@ -9,4 +9,7 @@
 		<email>sci-biology@gentoo.org</email>
 		<name>Gentoo Biology Project</name>
 	</maintainer>
+	<upstream>
+		<remote-id type="github">bcgsc/ntCard</remote-id>
+	</upstream>
 </pkgmetadata>
diff --git a/sci-biology/ntCard/ntCard-1.1.0.ebuild b/sci-biology/ntCard/ntCard-1.1.0.ebuild
deleted file mode 100644
index 580b91962..000000000
--- a/sci-biology/ntCard/ntCard-1.1.0.ebuild
+++ /dev/null
@@ -1,29 +0,0 @@
-# Copyright 1999-2018 Gentoo Authors
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=6
-
-inherit eutils
-
-DESCRIPTION="Estimate k-mer coverage histogram of genomics data"
-HOMEPAGE="https://github.com/bcgsc/ntCard"
-SRC_URI="https://github.com/bcgsc/${PN}/archive/v${PV}.tar.gz -> ${P}.tar.gz"
-
-LICENSE="MIT"
-SLOT="0"
-KEYWORDS="~amd64 ~x86"
-IUSE="openmp"
-
-DEPEND=""
-RDEPEND="${DEPEND}"
-
-src_prepare(){
-	sh ./autogen.sh || die
-	default
-}
-
-src_configure() {
-	local myconf=()
-	use openmp || myconf+=( --disable-openmp )
-	econf ${myconf[@]}
-}
diff --git a/sci-biology/ntCard/ntCard-1.2.2.ebuild b/sci-biology/ntCard/ntCard-1.2.2.ebuild
new file mode 100644
index 000000000..20a9d495a
--- /dev/null
+++ b/sci-biology/ntCard/ntCard-1.2.2.ebuild
@@ -0,0 +1,30 @@
+# Copyright 1999-2021 Gentoo Authors
+# Distributed under the terms of the GNU General Public License v2
+
+EAPI=7
+
+DESCRIPTION="Estimate k-mer coverage histogram of genomics data"
+HOMEPAGE="https://github.com/bcgsc/ntCard"
+SRC_URI="https://github.com/bcgsc/${PN}/archive/${PV}.tar.gz -> ${P}.tar.gz"
+
+LICENSE="MIT"
+SLOT="0"
+KEYWORDS="~amd64 ~x86"
+
+IUSE="openmp"
+# requires network
+RESTRICT="test"
+
+DEPEND=""
+RDEPEND="${DEPEND}"
+
+src_prepare(){
+	sh ./autogen.sh || die
+	default
+}
+
+src_configure() {
+	local myconf=()
+	use openmp || myconf+=( --disable-openmp )
+	econf ${myconf[@]}
+}
diff --git a/sci-biology/ntCard/ntCard-9999.ebuild b/sci-biology/ntCard/ntCard-9999.ebuild
index e6dff7db4..72d44fd87 100644
--- a/sci-biology/ntCard/ntCard-9999.ebuild
+++ b/sci-biology/ntCard/ntCard-9999.ebuild
@@ -1,9 +1,9 @@
-# Copyright 1999-2018 Gentoo Foundation
+# Copyright 1999-2021 Gentoo Authors
 # Distributed under the terms of the GNU General Public License v2
 
-EAPI=6
+EAPI=7
 
-inherit eutils git-r3
+inherit git-r3
 
 DESCRIPTION="Estimate k-mer coverage histogram of genomics data"
 HOMEPAGE="https://github.com/bcgsc/ntCard"
@@ -12,7 +12,10 @@ EGIT_REPO_URI="https://github.com/bcgsc/ntCard.git"
 LICENSE="MIT"
 SLOT="0"
 KEYWORDS=""
+
 IUSE="openmp"
+# requires network
+RESTRICT="test"
 
 DEPEND=""
 RDEPEND="${DEPEND}"
diff --git a/sci-biology/nwalign/Manifest b/sci-biology/nwalign/Manifest
deleted file mode 100644
index 9b1fa975e..000000000
--- a/sci-biology/nwalign/Manifest
+++ /dev/null
@@ -1 +0,0 @@
-DIST nwalign-0.3.1.tar.gz 50228 BLAKE2B 7791acfdc846b2048ae7d7f52c3ce763c53e878871deee00e3da5e1aa027c12d253c61d799981ffb9b3359bb6132ec110360992df61985582fbcdc90b60ddf17 SHA512 78e98743a016cc247831364eb9f44b320592013aaeed001db86ef560df4824e5872a722a780511dfec6970007d84483512f54e52ccc444fdd08e8854de46b1da
diff --git a/sci-biology/nwalign/metadata.xml b/sci-biology/nwalign/metadata.xml
deleted file mode 100644
index e593c9312..000000000
--- a/sci-biology/nwalign/metadata.xml
+++ /dev/null
@@ -1,15 +0,0 @@
-<?xml version="1.0" encoding="UTF-8"?>
-<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
-<pkgmetadata>
-	<maintainer type="person">
-		<email>mmokrejs@fold.natur.cuni.cz</email>
-		<name>Martin Mokrejs</name>
-	</maintainer>
-	<maintainer type="project">
-		<email>sci-biology@gentoo.org</email>
-		<name>Gentoo Biology Project</name>
-	</maintainer>
-	<upstream>
-		<remote-id type="pypi">nwalign</remote-id>
-	</upstream>
-</pkgmetadata>
diff --git a/sci-biology/nwalign/nwalign-0.3.1.ebuild b/sci-biology/nwalign/nwalign-0.3.1.ebuild
deleted file mode 100644
index d419002fd..000000000
--- a/sci-biology/nwalign/nwalign-0.3.1.ebuild
+++ /dev/null
@@ -1,20 +0,0 @@
-# Copyright 1999-2016 Gentoo Foundation
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=5
-
-PYTHON_COMPAT=( python2_7 )
-
-inherit python-single-r1
-
-DESCRIPTION="Needleman-Wunsch global sequence alignment in python/cython"
-HOMEPAGE="https://pypi.python.org/pypi/nwalign"
-SRC_URI="mirror://pypi/n/${PN}/${P}.tar.gz"
-
-LICENSE="BSD"
-SLOT="0"
-KEYWORDS="~amd64"
-IUSE=""
-
-DEPEND=""
-RDEPEND="${DEPEND}"
diff --git a/sci-biology/nxtrim/Manifest b/sci-biology/nxtrim/Manifest
new file mode 100644
index 000000000..e2ccfb8d6
--- /dev/null
+++ b/sci-biology/nxtrim/Manifest
@@ -0,0 +1 @@
+DIST nxtrim-0.4.3.tar.gz 785990 BLAKE2B 379e2214f80e7ad0a461656e9c78a99c2467467e4f1318a67c7d691a466be0d01c0be5b0c1052bc3180acfbdf684920f4bdfc4e1c880d35eef484d59f16c060c SHA512 f5660478b82d8d05fe70efca3e6dd6f7775700ee052d44b1f57c92634e840d88142b408378094c3d261fce28ec9354e68afa880eae87dcc9d75c6c0ba6391b66
diff --git a/sci-biology/nxtrim/nxtrim-0.4.3.ebuild b/sci-biology/nxtrim/nxtrim-0.4.3.ebuild
new file mode 100644
index 000000000..6ccd90101
--- /dev/null
+++ b/sci-biology/nxtrim/nxtrim-0.4.3.ebuild
@@ -0,0 +1,23 @@
+# Copyright 1999-2021 Gentoo Authors
+# Distributed under the terms of the GNU General Public License v2
+
+EAPI=7
+
+DESCRIPTION="Trim Illumina TruSeq adapters and split reads by Nextera MatePair linker"
+HOMEPAGE="https://github.com/sequencing/NxTrim"
+SRC_URI="https://github.com/sequencing/NxTrim/archive/v${PV}.tar.gz -> ${P}.tar.gz"
+
+LICENSE="BSD-2"
+SLOT="0"
+KEYWORDS="~amd64"
+
+DEPEND=""
+RDEPEND="${DEPEND}"
+
+S="${WORKDIR}/NxTrim-${PV}"
+
+src_install(){
+	dobin nxtrim scripts/*
+	einstalldocs
+	dodoc -r docs/*
+}
diff --git a/sci-biology/nxtrim/nxtrim-9999.ebuild b/sci-biology/nxtrim/nxtrim-9999.ebuild
deleted file mode 100644
index 9a12a0226..000000000
--- a/sci-biology/nxtrim/nxtrim-9999.ebuild
+++ /dev/null
@@ -1,23 +0,0 @@
-# Copyright 1999-2017 Gentoo Foundation
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=6
-
-inherit git-r3 eutils
-
-DESCRIPTION="Trim Illumina TruSeq adapters and split reads by Nextera MatePair linker"
-HOMEPAGE="https://github.com/sequencing/NxTrim"
-EGIT_REPO_URI="https://github.com/sequencing/NxTrim.git"
-
-LICENSE="BSD-2"
-SLOT="0"
-KEYWORDS="" # https://github.com/sequencing/NxTrim/issues/32
-IUSE=""
-
-DEPEND=""
-RDEPEND="${DEPEND}"
-
-src_install(){
-	dobin nxtrim mergeReads
-	dodoc README.md
-}
diff --git a/sci-biology/oases/Manifest b/sci-biology/oases/Manifest
deleted file mode 100644
index 031a5ff34..000000000
--- a/sci-biology/oases/Manifest
+++ /dev/null
@@ -1,2 +0,0 @@
-DIST OasesManual.pdf 113886 BLAKE2B aa8492887cea64e67966238e620b24aa5f90a8622a6de9bc4d4e1f56554f624c9ae7a19e0c46d83478849ec5d2ecb758fd8e253d8327d4d2bdcdda9db2e114a7 SHA512 c710a62cd1982060f723918f5f4de91adff12870d1682d0729035a3588ed37d26898c399c07b1b81b4b399c7ea1a14509784a6dbb9de6004bcadf6677cd5859f
-DIST oases_0.2.08.tgz 92037 BLAKE2B ff9762264d18c42e20b2208a057b073a2a960dab1ca17372db2fbf6f09094d3446ccd29a6038e17ee59b5adee9afe23cd59bbc4b640f57ce04141d2990b32b90 SHA512 e9a73a9227ce13995fcac7f456534a650099d8160d48d2d9831f3f05e482353c29dd76bbc74b0b451154eb5061ddb473649d21442941360f0e8c7623f6fe586c
diff --git a/sci-biology/oases/files/Makefile.patch b/sci-biology/oases/files/Makefile.patch
deleted file mode 100644
index 58652b00e..000000000
--- a/sci-biology/oases/files/Makefile.patch
+++ /dev/null
@@ -1,15 +0,0 @@
---- Makefile.ori	2016-04-10 22:34:31.976222662 +0200
-+++ Makefile	2016-04-10 22:37:49.636225327 +0200
-@@ -1,8 +1,8 @@
--CC = gcc
--CFLAGS = -Wall
--DEBUG = -g
-+CC ?= gcc
-+CFLAGS ?= -Wall
-+DEBUG ?= -g
- LIBS = -lm
--OPT = -O3
-+#OPT = -O3
- export MAXKMERLENGTH = 64
- export CATEGORIES = 2
- DEF = -D MAXKMERLENGTH=$(MAXKMERLENGTH) -D CATEGORIES=$(CATEGORIES)
diff --git a/sci-biology/oases/metadata.xml b/sci-biology/oases/metadata.xml
deleted file mode 100644
index 138cb7705..000000000
--- a/sci-biology/oases/metadata.xml
+++ /dev/null
@@ -1,12 +0,0 @@
-<?xml version="1.0" encoding="UTF-8"?>
-<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
-<pkgmetadata>
-	<maintainer type="person">
-		<email>mmokrejs@fold.natur.cuni.cz</email>
-		<name>Martin Mokrejs</name>
-	</maintainer>
-	<maintainer type="project">
-		<email>sci-biology@gentoo.org</email>
-		<name>Gentoo Biology Project</name>
-	</maintainer>
-</pkgmetadata>
diff --git a/sci-biology/oases/oases-0.2.08.ebuild b/sci-biology/oases/oases-0.2.08.ebuild
deleted file mode 100644
index dcd1e83ab..000000000
--- a/sci-biology/oases/oases-0.2.08.ebuild
+++ /dev/null
@@ -1,33 +0,0 @@
-# Copyright 1999-2016 Gentoo Foundation
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=5
-
-inherit eutils
-
-DESCRIPTION="De novo transcriptome assembler"
-HOMEPAGE="http://www.ebi.ac.uk/~zerbino/oases"
-SRC_URI="http://www.ebi.ac.uk/~zerbino/oases/oases_0.2.08.tgz
-	http://www.ebi.ac.uk/~zerbino/oases/OasesManual.pdf"
-KEYWORDS=""
-
-LICENSE="GPL-3"
-SLOT="0"
-IUSE=""
-
-DEPEND=""
-RDEPEND="${DEPEND}
-	>=sci-biology/velvet-1.2.08"
-
-S="${WORKDIR}"/oases_0.2.8
-
-src_prepare(){
-	epatch "${FILESDIR}"/Makefile.patch
-	sed -e 's#cleanobj velvet oases doc#oases#' -i Makefile || die
-}
-
-src_install(){
-	dobin oases
-	dodoc README.md
-	dodoc "${DISTDIR}"/OasesManual.pdf
-}
diff --git a/sci-biology/oases/oases-9999.ebuild b/sci-biology/oases/oases-9999.ebuild
deleted file mode 100644
index fbbe6e6dd..000000000
--- a/sci-biology/oases/oases-9999.ebuild
+++ /dev/null
@@ -1,38 +0,0 @@
-# Copyright 1999-2018 Gentoo Foundation
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=5
-
-[ "$PV" == "9999" ] && inherit git-r3
-
-inherit eutils
-
-DESCRIPTION="De novo transcriptome assembler"
-HOMEPAGE="http://www.ebi.ac.uk/~zerbino/oases"
-if [ "$PV" == "9999" ]; then
-	EGIT_REPO_URI="https://github.com/dzerbino/oases.git"
-	SRC_URI="http://www.ebi.ac.uk/~zerbino/oases/OasesManual.pdf"
-	KEYWORDS=""
-else
-	SRC_URI="http://www.ebi.ac.uk/~zerbino/oases/oases_0.2.08.tgz
-	http://www.ebi.ac.uk/~zerbino/oases/OasesManual.pdf"
-	KEYWORDS="~amd64"
-fi
-
-LICENSE="GPL-3"
-SLOT="0"
-IUSE=""
-
-DEPEND=""
-RDEPEND="${DEPEND}
-	>=sci-biology/velvet-1.2.08"
-
-src_prepare(){
-	epatch "${FILESDIR}"/Makefile.patch
-}
-
-src_install(){
-	dobin oases
-	dodoc README.md
-	dodoc "${DISTDIR}"/OasesManual.pdf
-}
diff --git a/sci-biology/oncotator/Manifest b/sci-biology/oncotator/Manifest
deleted file mode 100644
index de90530e9..000000000
--- a/sci-biology/oncotator/Manifest
+++ /dev/null
@@ -1 +0,0 @@
-DIST oncotator-1.9.2.0.tar.gz 12020766 SHA256 47b79c4a0cba098f0e39c10d5fc5a39bcfdd0e02689bf1f4e6ec3f04b06bd7b4 SHA512 a912081dc0d8ebf64b955e417ef88282ff2342e5e71f7edb955abc92c638acf1fd3d7bf9811909953a14639f4d3acdb6b5d522fe7bd75e9107742b1e1ed4ffcb WHIRLPOOL 3589ad6748b37447f99d803d38b2baf124afaf99c9c52e98b7e2277c5a742002d8ab10de229ce4feda85eebdf6c8be26d9799c140af10d17879b0c75457fc775
diff --git a/sci-biology/oncotator/metadata.xml b/sci-biology/oncotator/metadata.xml
deleted file mode 100644
index 7b9024751..000000000
--- a/sci-biology/oncotator/metadata.xml
+++ /dev/null
@@ -1,15 +0,0 @@
-<?xml version="1.0" encoding="UTF-8"?>
-<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
-<pkgmetadata>
-	<maintainer type="person">
-		<email>mmokrejs@fold.natur.cuni.cz</email>
-		<name>Martin Mokrejs</name>
-	</maintainer>
-	<maintainer type="project">
-		<email>sci-biology@gentoo.org</email>
-		<name>Gentoo Biology Project</name>
-	</maintainer>
-	<upstream>
-		<remote-id type="github">broadinstitute/oncotator</remote-id>
-	</upstream>
-</pkgmetadata>
diff --git a/sci-biology/oncotator/oncotator-1.9.2.0.ebuild b/sci-biology/oncotator/oncotator-1.9.2.0.ebuild
deleted file mode 100644
index 77f439b6d..000000000
--- a/sci-biology/oncotator/oncotator-1.9.2.0.ebuild
+++ /dev/null
@@ -1,36 +0,0 @@
-# Copyright 1999-2017 Gentoo Foundation
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=6
-
-PYTHON_COMPAT=( python2_7 ) # no python3+, issue #364
-inherit distutils-r1
-
-DESCRIPTION="Annotate genetic variants in VCF"
-HOMEPAGE="https://github.com/broadinstitute/oncotator"
-SRC_URI="https://github.com/broadinstitute/oncotator/archive/v${PV}.tar.gz -> ${P}.tar.gz"
-
-LICENSE="oncotator"
-SLOT="0"
-KEYWORDS="~amd64 ~x86" # breaks silently during install because of python syntax errors
-IUSE=""
-
-RESTRICT="fetch"
-
-DEPEND="
-	>=sci-biology/pysam-0.9.0
-	>=dev-python/bcbio-gff-0.6.2
-	>=dev-python/pyvcf-0.6.8
-	>=dev-python/pandas-0.18.0
-	>=sci-biology/biopython-1.66
-	>=dev-python/numpy-1.11.0
-	>=dev-python/cython-0.24
-	>=dev-python/shove-0.6.6
-	>=dev-python/sqlalchemy-1.0.12
-	>=dev-python/nose-1.3.7
-	>=dev-python/python-memcached-1.57
-	>=dev-python/natsort-4.0.4
-	>=dev-python/more-itertools-2.2
-	>=dev-python/enum34-1.1.2
-	dev-python/ngslib"
-RDEPEND="${DEPEND}"
diff --git a/sci-biology/open-ephys-gui/Manifest b/sci-biology/open-ephys-gui/Manifest
new file mode 100644
index 000000000..5863b7945
--- /dev/null
+++ b/sci-biology/open-ephys-gui/Manifest
@@ -0,0 +1,3 @@
+DIST open-ephys-gui-0.5.5.tar.gz 63347783 BLAKE2B 8f3ab3c20e23dd4f613e2ed47dca1827ddbcc5e95be5ca12dfeefdc84611653d531d629b78049397fd4951d558f63531ea2265d13e629c8da793fc20090d1075 SHA512 b835a7f8bb3eeb08ec77f6d14f988d6278b2f5b1966fbf8bec55d429c9cee36050cf574dd78a2ebad4adc5c681bcec5b64dcfb1ec87e548c55e2bf1bff2eb2dc
+DIST open-ephys-gui-0.6.1.tar.gz 44674639 BLAKE2B 10113418c41ccc62064bd8b993aab5402691259702c53c580e39371bd5034bc3b65babfa0adcaa7e2aadb8a86758e52cc4a86fee83db05614c849ed4c2b76ff4 SHA512 00ef7e5fd1242c84948e8eaf0479337365de21a28cb77252bf2baf806b186b9c8b7a424d756a4b6a883ecac48aefd6d2a532a8cadaa910e295b474d38056547e
+DIST open-ephys-gui-0.6.4.tar.gz 44686737 BLAKE2B 839e33679cc14ffa9e2da99622e7a18f6c4f17d6a45a6c07b1136372126e2c05ad4804bc3bdf5412c7e74d00242d61d0a084574d619ea7acad4485a4aa150795 SHA512 5ac81076731d0b325ea9267d52c702c4fbb972a9c73ab156ccf9752b14cc842d7fdbca2ba292277c9127f124ca2fa73c555a51219bd3e1c95c63f40837f7eff2
diff --git a/sci-biology/open-ephys-gui/files/open-ephys-gui-0.5.5.patch b/sci-biology/open-ephys-gui/files/open-ephys-gui-0.5.5.patch
new file mode 100644
index 000000000..77e401639
--- /dev/null
+++ b/sci-biology/open-ephys-gui/files/open-ephys-gui-0.5.5.patch
@@ -0,0 +1,12 @@
+# Add 'Gentoo' build type
+
+--- ../CMakeLists.txt	2019-12-02 22:29:24.021065669 -0300
++++ ../CMakeLists.txt	2019-12-02 22:29:11.251065418 -0300
+@@ -123,6 +123,7 @@
+ 	if(${CMAKE_BUILD_TYPE} STREQUAL "Debug")
+ 
+ 	elseif (${CMAKE_BUILD_TYPE} STREQUAL "Release")
++	elseif (${CMAKE_BUILD_TYPE} STREQUAL "Gentoo")
+ 	else()
+ 		message(FATAL_ERROR "Invalid build type")
+ 	endif()
diff --git a/sci-biology/open-ephys-gui/files/open-ephys-gui-0.6.1.patch b/sci-biology/open-ephys-gui/files/open-ephys-gui-0.6.1.patch
new file mode 100644
index 000000000..0992f2241
--- /dev/null
+++ b/sci-biology/open-ephys-gui/files/open-ephys-gui-0.6.1.patch
@@ -0,0 +1,15 @@
+# Add 'Gentoo' build type
+
+--- ../CMakeLists.txt	2022-08-24 15:27:32.871426442 -0300
++++ ../CMakeLists.txt	2022-08-24 15:31:03.438087613 -0300
+@@ -171,8 +171,8 @@
+ 		target_compile_options(open-ephys PRIVATE -O0) #enable optimization for linux debug
+ 	elseif (${CMAKE_BUILD_TYPE} STREQUAL "Release")
+ 		target_compile_options(open-ephys PRIVATE -O3) #enable optimization for linux release
+-	else()
+-		message(FATAL_ERROR "Invalid build type")
++    # else()
++    # 	message(FATAL_ERROR "Invalid build type")
+ 	endif()
+ 	find_package(CURL REQUIRED)
+ 	find_package(PkgConfig REQUIRED)
diff --git a/sci-biology/open-ephys-gui/files/open-ephys-gui-0.6.4.patch b/sci-biology/open-ephys-gui/files/open-ephys-gui-0.6.4.patch
new file mode 100644
index 000000000..5c0c6526e
--- /dev/null
+++ b/sci-biology/open-ephys-gui/files/open-ephys-gui-0.6.4.patch
@@ -0,0 +1,15 @@
+# Add 'Gentoo' build type
+
+--- ../CMakeLists.txt	2022-08-24 15:27:32.871426442 -0300
++++ ../CMakeLists.txt	2022-08-24 15:31:03.438087613 -0300
+@@ -173,8 +173,8 @@
+ 		target_compile_options(open-ephys PRIVATE -O0) #enable optimization for linux debug
+ 	elseif (${CMAKE_BUILD_TYPE} STREQUAL "Release")
+ 		target_compile_options(open-ephys PRIVATE -O3) #enable optimization for linux release
+-	else()
+-		message(FATAL_ERROR "Invalid build type")
++    # else()
++    # 	message(FATAL_ERROR "Invalid build type")
+ 	endif()
+ 	find_package(CURL REQUIRED)
+ 	find_package(PkgConfig REQUIRED)
diff --git a/sci-biology/open-ephys-gui/metadata.xml b/sci-biology/open-ephys-gui/metadata.xml
new file mode 100644
index 000000000..2c9af77a9
--- /dev/null
+++ b/sci-biology/open-ephys-gui/metadata.xml
@@ -0,0 +1,15 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
+<pkgmetadata>
+	<maintainer type="person">
+		<email>malfatti@disroot.org</email>
+		<name>T Malfatti</name>
+	</maintainer>
+	<maintainer type="project">
+		<email>sci@gentoo.org</email>
+		<name>Gentoo Science Project</name>
+	</maintainer>
+	<upstream>
+		<remote-id type="github">open-ephys/plugin-GUI</remote-id>
+	</upstream>
+</pkgmetadata>
diff --git a/sci-biology/open-ephys-gui/open-ephys-gui-0.5.5.ebuild b/sci-biology/open-ephys-gui/open-ephys-gui-0.5.5.ebuild
new file mode 100644
index 000000000..1c2b20e24
--- /dev/null
+++ b/sci-biology/open-ephys-gui/open-ephys-gui-0.5.5.ebuild
@@ -0,0 +1,80 @@
+# Copyright 2019-2021 Gentoo Authors
+# Distributed under the terms of the GNU General Public License v2
+
+EAPI=7
+inherit cmake udev
+
+DESCRIPTION="Processing, recording, and visualizing multichannel ephys data"
+HOMEPAGE="https://open-ephys.org/gui/"
+LICENSE="GPL-3"
+
+if [[ ${PV} == "9999" ]] ; then
+	inherit git-r3
+	EGIT_REPO_URI="https://github.com/open-ephys/plugin-GUI"
+	EGIT_BRANCH="master"
+	Suffix=${EGIT_BRANCH}
+	SubDir=${P}
+elif [[ ${PV} == "99999999" ]] ; then
+	inherit git-r3
+	EGIT_REPO_URI="https://github.com/open-ephys/plugin-GUI"
+	EGIT_BRANCH="development"
+	Suffix=${EGIT_BRANCH}
+	SubDir=${P}
+else
+	SRC_URI="https://github.com/open-ephys/plugin-GUI/archive/v${PV}.tar.gz -> ${P}.tar.gz"
+	Suffix=${PV}
+	SubDir="plugin-GUI-${PV}"
+	S="${WORKDIR}/${SubDir}"
+	KEYWORDS="~amd64 ~x86"
+fi
+
+SLOT="${PV}"
+IUSE="jack"
+
+DEPEND="
+	media-libs/alsa-lib
+	media-libs/freeglut
+	media-libs/freetype
+	x11-libs/libXrandr
+	x11-libs/libXcursor
+	x11-libs/libXinerama
+	jack? ( || ( media-sound/jack-audio-connection-kit media-sound/jack2 ) )
+"
+RDEPEND="${DEPEND}"
+
+BUILD_DIR="${S}/Build"
+PATCHES=( "${FILESDIR}"/${P}.patch )
+
+QA_PREBUILT="opt/open-ephys-*/shared/*.so"
+QA_PRESTRIPPED="
+	opt/open-ephys-*/plugins/*.so
+	opt/open-ephys-*/open-ephys
+"
+
+src_prepare() {
+	cmake_src_prepare
+
+	if use jack; then
+		sed -i 's/JUCE_APP_VERSION=/JUCE_JACK=1\n    JUCE_APP_VERSION=/' "${WORKDIR}/${SubDir}/CMakeLists.txt" || die "Sed failed!"
+	fi
+}
+
+src_configure() {
+	local mycmakeargs=( -DCMAKE_SKIP_RPATH=ON )
+	cmake_src_configure
+}
+
+src_install() {
+	dodir opt/open-ephys-"${Suffix}"/ lib/udev/rules.d/
+	cp -R "${BUILD_DIR}"/Gentoo/* "${ED}"/opt/open-ephys-"${Suffix}"/
+	udev_newrules "${WORKDIR}"/"${SubDir}"/Resources/Scripts/40-open-ephys.rules 40-open-ephys-"${Suffix}".rules
+	dosym ../../opt/open-ephys-"${Suffix}"/open-ephys usr/bin/open-ephys-"${Suffix}"
+}
+
+pkg_postinst() {
+	udev_reload
+}
+
+pkg_postrm() {
+	udev_reload
+}
diff --git a/sci-biology/open-ephys-gui/open-ephys-gui-0.6.1.ebuild b/sci-biology/open-ephys-gui/open-ephys-gui-0.6.1.ebuild
new file mode 100644
index 000000000..fe6791a2d
--- /dev/null
+++ b/sci-biology/open-ephys-gui/open-ephys-gui-0.6.1.ebuild
@@ -0,0 +1,83 @@
+# Copyright 2019-2022 Gentoo Authors
+# Distributed under the terms of the GNU General Public License v2
+
+EAPI=8
+inherit cmake udev
+
+DESCRIPTION="Processing, recording, and visualizing multichannel ephys data"
+HOMEPAGE="https://open-ephys.org/gui/"
+LICENSE="GPL-3"
+
+if [[ ${PV} == "9999" ]] ; then
+	inherit git-r3
+	EGIT_REPO_URI="https://github.com/open-ephys/plugin-GUI"
+	EGIT_BRANCH="main"
+	Suffix=${EGIT_BRANCH}
+	SubDir=${P}
+elif [[ ${PV} == "99999999" ]] ; then
+	inherit git-r3
+	EGIT_REPO_URI="https://github.com/open-ephys/plugin-GUI"
+	EGIT_BRANCH="development"
+	Suffix=${EGIT_BRANCH}
+	SubDir=${P}
+else
+	SRC_URI="https://github.com/open-ephys/plugin-GUI/archive/v${PV}.tar.gz -> ${P}.tar.gz"
+	Suffix=${PV}
+	SubDir="plugin-GUI-${PV}"
+	S="${WORKDIR}/${SubDir}"
+	KEYWORDS="~amd64 ~x86"
+fi
+
+SLOT="${PV}"
+IUSE="jack"
+
+DEPEND="
+	dev-libs/openssl
+	media-libs/alsa-lib
+	media-libs/freeglut
+	media-libs/freetype
+	net-libs/webkit-gtk
+	net-misc/curl
+	x11-libs/libXrandr
+	x11-libs/libXcursor
+	x11-libs/libXinerama
+	jack? ( || ( media-sound/jack-audio-connection-kit media-sound/jack2 ) )
+"
+RDEPEND="${DEPEND}"
+
+BUILD_DIR="${S}/Build"
+PATCHES=( "${FILESDIR}"/${P}.patch )
+
+QA_PREBUILT="opt/open-ephys-*/shared/*.so"
+QA_PRESTRIPPED="
+	opt/open-ephys-*/plugins/*.so
+	opt/open-ephys-*/open-ephys
+"
+
+src_prepare() {
+	cmake_src_prepare
+
+	if use jack; then
+		sed -i 's/JUCE_APP_VERSION=/JUCE_JACK=1\n    JUCE_APP_VERSION=/' "${WORKDIR}/${SubDir}/CMakeLists.txt" || die "Sed failed!"
+	fi
+}
+
+src_configure() {
+	local mycmakeargs=( -DCMAKE_SKIP_RPATH=ON )
+	cmake_src_configure
+}
+
+src_install() {
+	dodir opt/open-ephys-"${Suffix}"/ lib/udev/rules.d/
+	cp -R "${BUILD_DIR}"/RelWithDebInfo/* "${ED}"/opt/open-ephys-"${Suffix}"/ || die
+	udev_newrules "${WORKDIR}"/"${SubDir}"/Resources/Scripts/40-open-ephys.rules 40-open-ephys-"${Suffix}".rules
+	dosym ../../opt/open-ephys-"${Suffix}"/open-ephys usr/bin/open-ephys-"${Suffix}"
+}
+
+pkg_postinst() {
+	udev_reload
+}
+
+pkg_postrm() {
+	udev_reload
+}
diff --git a/sci-biology/open-ephys-gui/open-ephys-gui-0.6.4.ebuild b/sci-biology/open-ephys-gui/open-ephys-gui-0.6.4.ebuild
new file mode 100644
index 000000000..cae41e773
--- /dev/null
+++ b/sci-biology/open-ephys-gui/open-ephys-gui-0.6.4.ebuild
@@ -0,0 +1,83 @@
+# Copyright 2019-2023 Gentoo Authors
+# Distributed under the terms of the GNU General Public License v2
+
+EAPI=8
+inherit cmake udev
+
+DESCRIPTION="Processing, recording, and visualizing multichannel ephys data"
+HOMEPAGE="https://open-ephys.org/gui/"
+LICENSE="GPL-3"
+
+if [[ ${PV} == "9999" ]] ; then
+	inherit git-r3
+	EGIT_REPO_URI="https://github.com/open-ephys/plugin-GUI"
+	EGIT_BRANCH="main"
+	Suffix=${EGIT_BRANCH}
+	SubDir=${P}
+elif [[ ${PV} == "99999999" ]] ; then
+	inherit git-r3
+	EGIT_REPO_URI="https://github.com/open-ephys/plugin-GUI"
+	EGIT_BRANCH="development"
+	Suffix=${EGIT_BRANCH}
+	SubDir=${P}
+else
+	SRC_URI="https://github.com/open-ephys/plugin-GUI/archive/v${PV}.tar.gz -> ${P}.tar.gz"
+	Suffix=${PV}
+	SubDir="plugin-GUI-${PV}"
+	S="${WORKDIR}/${SubDir}"
+	KEYWORDS="~amd64 ~x86"
+fi
+
+SLOT="${PV}"
+IUSE="jack"
+
+DEPEND="
+	dev-libs/openssl
+	media-libs/alsa-lib
+	media-libs/freeglut
+	media-libs/freetype
+	net-libs/webkit-gtk:4
+	net-misc/curl
+	x11-libs/libXrandr
+	x11-libs/libXcursor
+	x11-libs/libXinerama
+	jack? ( || ( media-sound/jack-audio-connection-kit media-sound/jack2 ) )
+"
+RDEPEND="${DEPEND}"
+
+BUILD_DIR="${S}/Build"
+PATCHES=( "${FILESDIR}"/${P}.patch )
+
+QA_PREBUILT="opt/open-ephys-*/shared/*.so"
+QA_PRESTRIPPED="
+	opt/open-ephys-*/plugins/*.so
+	opt/open-ephys-*/open-ephys
+"
+
+src_prepare() {
+	cmake_src_prepare
+
+	if use jack; then
+		sed -i 's/JUCE_APP_VERSION=/JUCE_JACK=1\n    JUCE_APP_VERSION=/' "${WORKDIR}/${SubDir}/CMakeLists.txt" || die "Sed failed!"
+	fi
+}
+
+src_configure() {
+	local mycmakeargs=( -DCMAKE_SKIP_RPATH=ON )
+	cmake_src_configure
+}
+
+src_install() {
+	dodir opt/open-ephys-"${Suffix}"/ lib/udev/rules.d/
+	cp -R "${BUILD_DIR}"/RelWithDebInfo/* "${ED}"/opt/open-ephys-"${Suffix}"/ || die
+	udev_newrules "${WORKDIR}"/"${SubDir}"/Resources/Scripts/40-open-ephys.rules 40-open-ephys-"${Suffix}".rules
+	dosym ../../opt/open-ephys-"${Suffix}"/open-ephys usr/bin/open-ephys-"${Suffix}"
+}
+
+pkg_postinst() {
+	udev_reload
+}
+
+pkg_postrm() {
+	udev_reload
+}
diff --git a/sci-biology/open-ephys-gui/open-ephys-gui-9999.ebuild b/sci-biology/open-ephys-gui/open-ephys-gui-9999.ebuild
new file mode 100644
index 000000000..2ab957f40
--- /dev/null
+++ b/sci-biology/open-ephys-gui/open-ephys-gui-9999.ebuild
@@ -0,0 +1,83 @@
+# Copyright 2019-2023 Gentoo Authors
+# Distributed under the terms of the GNU General Public License v2
+
+EAPI=8
+inherit cmake udev
+
+DESCRIPTION="Processing, recording, and visualizing multichannel ephys data"
+HOMEPAGE="https://open-ephys.org/gui/"
+LICENSE="GPL-3"
+
+if [[ ${PV} == "9999" ]] ; then
+	inherit git-r3
+	EGIT_REPO_URI="https://github.com/open-ephys/plugin-GUI"
+	EGIT_BRANCH="main"
+	Suffix=${EGIT_BRANCH}
+	SubDir=${P}
+elif [[ ${PV} == "99999999" ]] ; then
+	inherit git-r3
+	EGIT_REPO_URI="https://github.com/open-ephys/plugin-GUI"
+	EGIT_BRANCH="development"
+	Suffix=${EGIT_BRANCH}
+	SubDir=${P}
+else
+	SRC_URI="https://github.com/open-ephys/plugin-GUI/archive/v${PV}.tar.gz -> ${P}.tar.gz"
+	Suffix=${PV}
+	SubDir="plugin-GUI-${PV}"
+	S="${WORKDIR}/${SubDir}"
+	KEYWORDS="~amd64 ~x86"
+fi
+
+SLOT="${PV}"
+IUSE="jack"
+
+DEPEND="
+	dev-libs/openssl
+	media-libs/alsa-lib
+	media-libs/freeglut
+	media-libs/freetype
+	net-libs/webkit-gtk:4
+	net-misc/curl
+	x11-libs/libXrandr
+	x11-libs/libXcursor
+	x11-libs/libXinerama
+	jack? ( || ( media-sound/jack-audio-connection-kit media-sound/jack2 ) )
+"
+RDEPEND="${DEPEND}"
+
+BUILD_DIR="${S}/Build"
+PATCHES=( "${FILESDIR}"/"${PN}"-0.6.4.patch )
+
+QA_PREBUILT="opt/open-ephys-*/shared/*.so"
+QA_PRESTRIPPED="
+	opt/open-ephys-*/plugins/*.so
+	opt/open-ephys-*/open-ephys
+"
+
+src_prepare() {
+	cmake_src_prepare
+
+	if use jack; then
+		sed -i 's/JUCE_APP_VERSION=/JUCE_JACK=1\n    JUCE_APP_VERSION=/' "${WORKDIR}/${SubDir}/CMakeLists.txt" || die "Sed failed!"
+	fi
+}
+
+src_configure() {
+	local mycmakeargs=( -DCMAKE_SKIP_RPATH=ON )
+	cmake_src_configure
+}
+
+src_install() {
+	dodir opt/open-ephys-"${Suffix}"/ lib/udev/rules.d/
+	cp -R "${BUILD_DIR}"/RelWithDebInfo/* "${ED}"/opt/open-ephys-"${Suffix}"/ || die
+	udev_newrules "${WORKDIR}"/"${SubDir}"/Resources/Scripts/40-open-ephys.rules 40-open-ephys-"${Suffix}".rules
+	dosym ../../opt/open-ephys-"${Suffix}"/open-ephys usr/bin/open-ephys-"${Suffix}"
+}
+
+pkg_postinst() {
+	udev_reload
+}
+
+pkg_postrm() {
+	udev_reload
+}
diff --git a/sci-biology/open-ephys-gui/open-ephys-gui-99999999.ebuild b/sci-biology/open-ephys-gui/open-ephys-gui-99999999.ebuild
new file mode 100644
index 000000000..2ab957f40
--- /dev/null
+++ b/sci-biology/open-ephys-gui/open-ephys-gui-99999999.ebuild
@@ -0,0 +1,83 @@
+# Copyright 2019-2023 Gentoo Authors
+# Distributed under the terms of the GNU General Public License v2
+
+EAPI=8
+inherit cmake udev
+
+DESCRIPTION="Processing, recording, and visualizing multichannel ephys data"
+HOMEPAGE="https://open-ephys.org/gui/"
+LICENSE="GPL-3"
+
+if [[ ${PV} == "9999" ]] ; then
+	inherit git-r3
+	EGIT_REPO_URI="https://github.com/open-ephys/plugin-GUI"
+	EGIT_BRANCH="main"
+	Suffix=${EGIT_BRANCH}
+	SubDir=${P}
+elif [[ ${PV} == "99999999" ]] ; then
+	inherit git-r3
+	EGIT_REPO_URI="https://github.com/open-ephys/plugin-GUI"
+	EGIT_BRANCH="development"
+	Suffix=${EGIT_BRANCH}
+	SubDir=${P}
+else
+	SRC_URI="https://github.com/open-ephys/plugin-GUI/archive/v${PV}.tar.gz -> ${P}.tar.gz"
+	Suffix=${PV}
+	SubDir="plugin-GUI-${PV}"
+	S="${WORKDIR}/${SubDir}"
+	KEYWORDS="~amd64 ~x86"
+fi
+
+SLOT="${PV}"
+IUSE="jack"
+
+DEPEND="
+	dev-libs/openssl
+	media-libs/alsa-lib
+	media-libs/freeglut
+	media-libs/freetype
+	net-libs/webkit-gtk:4
+	net-misc/curl
+	x11-libs/libXrandr
+	x11-libs/libXcursor
+	x11-libs/libXinerama
+	jack? ( || ( media-sound/jack-audio-connection-kit media-sound/jack2 ) )
+"
+RDEPEND="${DEPEND}"
+
+BUILD_DIR="${S}/Build"
+PATCHES=( "${FILESDIR}"/"${PN}"-0.6.4.patch )
+
+QA_PREBUILT="opt/open-ephys-*/shared/*.so"
+QA_PRESTRIPPED="
+	opt/open-ephys-*/plugins/*.so
+	opt/open-ephys-*/open-ephys
+"
+
+src_prepare() {
+	cmake_src_prepare
+
+	if use jack; then
+		sed -i 's/JUCE_APP_VERSION=/JUCE_JACK=1\n    JUCE_APP_VERSION=/' "${WORKDIR}/${SubDir}/CMakeLists.txt" || die "Sed failed!"
+	fi
+}
+
+src_configure() {
+	local mycmakeargs=( -DCMAKE_SKIP_RPATH=ON )
+	cmake_src_configure
+}
+
+src_install() {
+	dodir opt/open-ephys-"${Suffix}"/ lib/udev/rules.d/
+	cp -R "${BUILD_DIR}"/RelWithDebInfo/* "${ED}"/opt/open-ephys-"${Suffix}"/ || die
+	udev_newrules "${WORKDIR}"/"${SubDir}"/Resources/Scripts/40-open-ephys.rules 40-open-ephys-"${Suffix}".rules
+	dosym ../../opt/open-ephys-"${Suffix}"/open-ephys usr/bin/open-ephys-"${Suffix}"
+}
+
+pkg_postinst() {
+	udev_reload
+}
+
+pkg_postrm() {
+	udev_reload
+}
diff --git a/sci-biology/opfvta_bidsdata/Manifest b/sci-biology/opfvta_bidsdata/Manifest
new file mode 100644
index 000000000..acda17fc8
--- /dev/null
+++ b/sci-biology/opfvta_bidsdata/Manifest
@@ -0,0 +1 @@
+DIST opfvta_bidsdata-2.0.tar.xz 12372152444 BLAKE2B 55e247a1cdc337a178776436240f88d2d4d631b165c9d08bff9023549c7ea5a0078b2a4751dfb6812a3b06caca61b8f32dc365957147ebacd97c66282849f020 SHA512 4e8769e358a8f0e2c25b46db094d0cbf375bf4aa83365834be5ee6a1db012d6be6174f0416f0158354a17e9616863a459f9d89ea3df8694bf23d4ecd75b289fc
diff --git a/sci-biology/opfvta_bidsdata/metadata.xml b/sci-biology/opfvta_bidsdata/metadata.xml
new file mode 100644
index 000000000..56b97ddfe
--- /dev/null
+++ b/sci-biology/opfvta_bidsdata/metadata.xml
@@ -0,0 +1,20 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
+<pkgmetadata>
+	<maintainer type="person">
+		<email>gentoo@chymera.eu</email>
+		<name>Horea Christian</name>
+	</maintainer>
+	<maintainer type="project">
+		<email>sci@gentoo.org</email>
+		<name>Gentoo Science Project</name>
+	</maintainer>
+	<longdescription lang="en">
+		BIDS-formatted MRI data recorded at the ETH/UZH Animal Imaging Center
+		and first associated with the OPFVTA publication. The data represents
+		f/MRI mouse brain scans with both BOLD and CBV contrasts, using block
+		and phasic stimulation protocols delivered via a laser to the VTA,
+		which is rendered sensitive by channelrhodopsin expression under
+		the dopamine transporter promoter.
+	</longdescription>
+</pkgmetadata>
diff --git a/sci-biology/opfvta_bidsdata/opfvta_bidsdata-2.0.ebuild b/sci-biology/opfvta_bidsdata/opfvta_bidsdata-2.0.ebuild
new file mode 100644
index 000000000..d21f85f8c
--- /dev/null
+++ b/sci-biology/opfvta_bidsdata/opfvta_bidsdata-2.0.ebuild
@@ -0,0 +1,32 @@
+# Copyright 1999-2022 Gentoo Authors
+# Distributed under the terms of the GNU General Public License v2
+
+EAPI=7
+
+inherit check-reqs
+
+DESCRIPTION="BIDS data files released with the OPFVTA publication"
+HOMEPAGE="http://chymera.eu/docs/focus/open-science/"
+SRC_URI="
+	https://zenodo.org/record/3575149/files/${P}.tar.xz
+	"
+
+LICENSE="CC-BY-SA-4.0"
+SLOT="0"
+KEYWORDS="~amd64 ~x86 ~amd64-linux ~x86-linux"
+
+RDEPEND=""
+DEPEND=""
+
+pkg_pretend() {
+	CHECKREQS_DISK_BUILD="33G"
+	check-reqs_pkg_pretend
+}
+
+# We disable this phase to not check requirements twice.
+pkg_setup() { :; }
+
+src_install() {
+	insinto "/usr/share/${PN}"
+	doins -r *
+}
diff --git a/sci-biology/pairagon/pairagon-1.1.ebuild b/sci-biology/pairagon/pairagon-1.1.ebuild
index 843198232..71f68463b 100644
--- a/sci-biology/pairagon/pairagon-1.1.ebuild
+++ b/sci-biology/pairagon/pairagon-1.1.ebuild
@@ -1,18 +1,22 @@
-# Copyright 1999-2017 Gentoo Foundation
+# Copyright 1999-2021 Gentoo Authors
 # Distributed under the terms of the GNU General Public License v2
 
-EAPI=6
+EAPI=7
 
-inherit perl-functions toolchain-funcs
+inherit perl-functions
 
 DESCRIPTION="HMM-based cDNA to genome aligner"
-HOMEPAGE="http://mblab.wustl.edu/software.html"
-SRC_URI="http://mblab.wustl.edu/software/download/pairagon_.tar"
+HOMEPAGE="https://mblab.wustl.edu/software.html"
+#SRC_URI="http://mblab.wustl.edu/software/download/pairagon_.tar"
+# ERROR: cannot verify mblab.wustl.edu's certificate, issued by ‘CN=InCommon RSA Server CA,OU=InCommon,O=Internet2,L=Ann Arbor,ST=MI,C=US’:
+# Unable to locally verify the issuer's authority.
+# To connect to mblab.wustl.edu insecurely, use `--no-check-certificate'.
+RESTRICT="fetch"
+SRC_URI="pairagon_.tar"
 
 LICENSE="BSD-2"
 SLOT="0"
 KEYWORDS="~amd64"
-IUSE=""
 
 DEPEND="dev-lang/perl:="
 RDEPEND="${DEPEND}"
diff --git a/sci-biology/parafly/Manifest b/sci-biology/parafly/Manifest
index b70d01fe5..4818dac2c 100644
--- a/sci-biology/parafly/Manifest
+++ b/sci-biology/parafly/Manifest
@@ -1 +1 @@
-DIST TransDecoder_r20140704.tar.gz 21189681 BLAKE2B 9d6602cb9ef9f05dcfbc7f04aa07c0fad067d04af454f9d6a31baeb62e883cf9eb20a29ea0cc5505968c05143738c308fca7bfda00f689d7639f88c2baa02a1c SHA512 fa70e440c3f8b8d11da780858ff6433adf9065b126b29eb047983b17913e382c677a272881ee78be8e30867bbd447eb9bda71bd11abda5203d6a3abfb5316e90
+DIST parafly-0.1.0.tar.gz 233214 BLAKE2B 7f98ea21e9970bee227f4b2525dd1b3c514ac063ff0733ea36f98153d5a58b6a75a5ae3d57ead3fde6f88a2a5874911c607655458f48b1aea94e0bbe78ecddb4 SHA512 087385025d70c07472ccce86ca9027d5cc6c0df477b50abbb6757e21b5f95569176b982c2de05b51a80d58efdf27913fd8f7f0bb51cc9727267d9552e463138f
diff --git a/sci-biology/parafly/parafly-0.1.0.ebuild b/sci-biology/parafly/parafly-0.1.0.ebuild
new file mode 100644
index 000000000..ce1084020
--- /dev/null
+++ b/sci-biology/parafly/parafly-0.1.0.ebuild
@@ -0,0 +1,21 @@
+# Copyright 1999-2021 Gentoo Authors
+# Distributed under the terms of the GNU General Public License v2
+
+EAPI=7
+
+DESCRIPTION="Parallel cmd processing utility"
+HOMEPAGE="https://github.com/ParaFly/ParaFly"
+SRC_URI="https://github.com/ParaFly/ParaFly/archive/v${PV}.tar.gz -> ${P}.tar.gz"
+
+LICENSE="BSD-BroadInstitute"
+SLOT="0"
+KEYWORDS="~amd64"
+
+DEPEND=""
+RDEPEND="${DEPEND}"
+
+S="${WORKDIR}/ParaFly-${PV}"
+
+src_configure(){
+	./configure --prefix="${EPREFIX}"/usr
+}
diff --git a/sci-biology/parafly/parafly-20130121.ebuild b/sci-biology/parafly/parafly-20130121.ebuild
deleted file mode 100644
index 4df553a85..000000000
--- a/sci-biology/parafly/parafly-20130121.ebuild
+++ /dev/null
@@ -1,26 +0,0 @@
-# Copyright 1999-2016 Gentoo Foundation
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=5
-
-DESCRIPTION="Some dependency for transdecoder"
-HOMEPAGE="http://sourceforge.net/projects/transdecoder/"
-SRC_URI="http://sourceforge.net/projects/transdecoder/files/OLDER/TransDecoder_r20140704.tar.gz"
-# are current sources available only from here?
-# https://github.com/trinityrnaseq/trinityrnaseq/tree/f81f0497a211c84ba4299063086604760933e6e3/trinity-plugins/parafly-code
-
-LICENSE="BSD-BroadInstitute"
-SLOT="0"
-KEYWORDS="~amd64"
-IUSE=""
-
-DEPEND=""
-RDEPEND="${DEPEND}"
-
-S="${WORKDIR}"/TransDecoder_r20140704/3rd_party/parafly-r2013-01-21
-
-# maybe we once the CXXFLAGS and LDFLAGS mentioned
-#   in https://github.com/trinityrnaseq/trinityrnaseq/issues/65 ?
-src_configure(){
-	./configure --prefix="${EPREFIX}"/usr
-}
diff --git a/sci-biology/pb-honey/Manifest b/sci-biology/pb-honey/Manifest
deleted file mode 100644
index 897d384b2..000000000
--- a/sci-biology/pb-honey/Manifest
+++ /dev/null
@@ -1 +0,0 @@
-DIST PBHoney_14.1.15.tgz 1277165 SHA256 5b709ec9a4951abf2c9df6b01fb9856e4bc4e1b50c7c10f5c777779657cb2a8f SHA512 05214e3299ec508523cdb63ecc17f518f493bf809a23febee5dec1ebe44c46c086c92c9633de9ad48d57ca8e062f09ccf8e97a064d73fd9ffd7d9163af2c3294 WHIRLPOOL 6ab0ef2ad8fa05e5cc96ab6509262a812969d54c768f9ed1f0ffc909a92416e533ecef48b729345424a72f97df1b9a1e7806128b1aabf06c5cf1b643c547736a
diff --git a/sci-biology/pb-honey/metadata.xml b/sci-biology/pb-honey/metadata.xml
deleted file mode 100644
index 1b533d8a5..000000000
--- a/sci-biology/pb-honey/metadata.xml
+++ /dev/null
@@ -1,15 +0,0 @@
-<?xml version="1.0" encoding="UTF-8"?>
-<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
-<pkgmetadata>
-	<maintainer type="person">
-		<email>mmokrejs@fold.natur.cuni.cz</email>
-		<name>Martin Mokrejs</name>
-	</maintainer>
-	<maintainer type="project">
-		<email>sci-biology@gentoo.org</email>
-		<name>Gentoo Biology Project</name>
-	</maintainer>
-	<upstream>
-		<remote-id type="sourceforge">pb-jelly</remote-id>
-	</upstream>
-</pkgmetadata>
diff --git a/sci-biology/pb-honey/pb-honey-14.1.15.ebuild b/sci-biology/pb-honey/pb-honey-14.1.15.ebuild
deleted file mode 100644
index 1a4e10778..000000000
--- a/sci-biology/pb-honey/pb-honey-14.1.15.ebuild
+++ /dev/null
@@ -1,25 +0,0 @@
-# Copyright 1999-2017 Gentoo Foundation
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=6
-
-PYTHON_COMPAT=( python2_7 )
-
-inherit distutils-r1
-
-DESCRIPTION="Structural variant identification (SNV) using long reads (over 10kbp)"
-HOMEPAGE="https://www.hgsc.bcm.edu/software/honey"
-SRC_URI="http://sourceforge.net/projects/pb-jelly/files/PBHoney/PBHoney_14.1.15.tgz"
-
-LICENSE="BSD-2"
-SLOT="0"
-KEYWORDS=""
-IUSE=""
-
-DEPEND="
-	sci-biology/blasr
-	sci-biology/pysam[${PYTHON_USEDEP}]
-	sci-biology/samtools:0[${PYTHON_USEDEP}]
-	dev-python/h5py[${PYTHON_USEDEP}]
-	dev-python/numpy[${PYTHON_USEDEP}]"
-RDEPEND="${DEPEND}"
diff --git a/sci-biology/pb-jelly/Manifest b/sci-biology/pb-jelly/Manifest
deleted file mode 100644
index 44cad9c3e..000000000
--- a/sci-biology/pb-jelly/Manifest
+++ /dev/null
@@ -1 +0,0 @@
-DIST pb-jelly-14.9.9.tgz 2571636 BLAKE2B e857251b293a662ca309e16d396ff0c96750ecc921e439cfabf4e4cbd5233a64f86f571ed34fd0ed1d33ee697b5547eb8adea03c73e50ff2a4058600bc327313 SHA512 2cc578f6e01d2a3b59ada049ad9967204bc91e7e56b53517b9aef07d6163e5cea5c30b5d83b42ad86e45f80a0a9b67282c2a6af417374270b9e395a3e1e70dc4
diff --git a/sci-biology/pb-jelly/metadata.xml b/sci-biology/pb-jelly/metadata.xml
deleted file mode 100644
index 1b533d8a5..000000000
--- a/sci-biology/pb-jelly/metadata.xml
+++ /dev/null
@@ -1,15 +0,0 @@
-<?xml version="1.0" encoding="UTF-8"?>
-<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
-<pkgmetadata>
-	<maintainer type="person">
-		<email>mmokrejs@fold.natur.cuni.cz</email>
-		<name>Martin Mokrejs</name>
-	</maintainer>
-	<maintainer type="project">
-		<email>sci-biology@gentoo.org</email>
-		<name>Gentoo Biology Project</name>
-	</maintainer>
-	<upstream>
-		<remote-id type="sourceforge">pb-jelly</remote-id>
-	</upstream>
-</pkgmetadata>
diff --git a/sci-biology/pb-jelly/pb-jelly-14.9.9.ebuild b/sci-biology/pb-jelly/pb-jelly-14.9.9.ebuild
deleted file mode 100644
index 32c52e9d0..000000000
--- a/sci-biology/pb-jelly/pb-jelly-14.9.9.ebuild
+++ /dev/null
@@ -1,22 +0,0 @@
-# Copyright 1999-2015 Gentoo Foundation
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=5
-
-PYTHON_COMPAT=( python2_7 )
-
-inherit distutils-r1
-
-DESCRIPTION="Close gaps using PacBio RS or 454 FLX+ reads"
-HOMEPAGE="https://www.hgsc.bcm.edu/software/jelly"
-SRC_URI="http://sourceforge.net/projects/pb-jelly/files/PBSuite_14.9.9.tgz -> pb-jelly-14.9.9.tgz"
-
-LICENSE="BSD-2"
-SLOT="0"
-KEYWORDS=""
-IUSE=""
-
-DEPEND="
-	sci-biology/blasr
-	<=dev-python/networkx-1.1[${PYTHON_USEDEP}]" # upstream says "Versions past v1.1 have been shown to have many issues."
-RDEPEND="${DEPEND}"
diff --git a/sci-biology/pbbam/Manifest b/sci-biology/pbbam/Manifest
new file mode 100644
index 000000000..1bb2b2625
--- /dev/null
+++ b/sci-biology/pbbam/Manifest
@@ -0,0 +1 @@
+DIST pbbam-2.1.0.tar.gz 10405332 BLAKE2B c91122afcc8fae747fbf1e40274aeb7f2fbc5a02789945798899c6ae87ff01beaae994a80a356a71a788e8626ee5a3595537d8bd6468ac30a874733fa9e9d883 SHA512 5f606620d1a6eb7c31c36db4d6fd125e397c4b81d9f695dc8756535074ce98c4b05e04d86077ed33e0ba1e503e766b1b59e08bb73e8f8129af7789024f308094
diff --git a/sci-biology/pbbam/metadata.xml b/sci-biology/pbbam/metadata.xml
index 138cb7705..e12f3579e 100644
--- a/sci-biology/pbbam/metadata.xml
+++ b/sci-biology/pbbam/metadata.xml
@@ -9,4 +9,7 @@
 		<email>sci-biology@gentoo.org</email>
 		<name>Gentoo Biology Project</name>
 	</maintainer>
+	<upstream>
+		<remote-id type="github">PacificBiosciences/pbbam</remote-id>
+	</upstream>
 </pkgmetadata>
diff --git a/sci-biology/pbbam/pbbam-2.1.0.ebuild b/sci-biology/pbbam/pbbam-2.1.0.ebuild
new file mode 100644
index 000000000..a114da0fc
--- /dev/null
+++ b/sci-biology/pbbam/pbbam-2.1.0.ebuild
@@ -0,0 +1,27 @@
+# Copyright 1999-2022 Gentoo Authors
+# Distributed under the terms of the GNU General Public License v2
+
+EAPI=8
+
+inherit meson
+
+DESCRIPTION="PacBio modified BAM file format"
+HOMEPAGE="https://pbbam.readthedocs.io/en/latest/index.html"
+SRC_URI="https://github.com/PacificBiosciences/pbbam/archive/v${PV}.tar.gz -> ${P}.tar.gz"
+
+LICENSE="blasr"
+SLOT="0"
+KEYWORDS="~amd64 ~x86"
+
+BDEPEND="
+	virtual/pkgconfig
+	>=dev-cpp/gtest-1.8.1
+	>=dev-lang/swig-3.0.5
+"
+DEPEND="
+	sci-biology/pbcopper
+	sci-biology/samtools:0
+	>=sci-libs/htslib-1.3.1:=
+	>=dev-libs/boost-1.55:=
+"
+RDEPEND="${DEPEND}"
diff --git a/sci-biology/pbbam/pbbam-9999.ebuild b/sci-biology/pbbam/pbbam-9999.ebuild
deleted file mode 100644
index 5593b4072..000000000
--- a/sci-biology/pbbam/pbbam-9999.ebuild
+++ /dev/null
@@ -1,49 +0,0 @@
-# Copyright 1999-2019 Gentoo Authors
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=5
-
-inherit git-r3 multilib
-
-DESCRIPTION="PacBio modified BAM file format"
-HOMEPAGE="https://pbbam.readthedocs.io/en/latest/index.html"
-EGIT_REPO_URI="https://github.com/PacificBiosciences/pbbam.git"
-
-LICENSE="blasr"
-SLOT="0"
-IUSE="hdf5 doc"
-KEYWORDS=""
-# https://github.com/PacificBiosciences/pbbam/issues/25
-
-CDEPEND="
-	dev-util/meson
-	dev-util/ninja
-	dev-util/pkgconfig
-	>=dev-cpp/gtest-1.8.1
-	>=dev-lang/swig-3.0.5
-	doc? ( app-doc/doxygen )"
-DEPEND="
-	>=sci-libs/htslib-1.3.1:=
-	>=dev-libs/boost-1.55:=[threads]
-	hdf5? ( >=sci-libs/hdf5-1.8.12[cxx] )" # needs H5Cpp.h
-RDEPEND=""
-
-#S="${WORKDIR}/${PN}"
-
-src_compile(){
-	mkdir -p build || die
-	cd build || die
-	meson --prefix "${ED}/usr" || die
-	ninja || die
-	use doc && ( ninja doc )
-}
-
-src_install() {
-	cd build || die
-	ninja install || die
-	#dobin bin/*
-	#insinto /usr/include
-	#doins include/*
-	#insinto /usr/$(get_libdir)/${P}
-	#doins lib/*
-}
diff --git a/sci-biology/pbcopper/Manifest b/sci-biology/pbcopper/Manifest
new file mode 100644
index 000000000..93e0659d5
--- /dev/null
+++ b/sci-biology/pbcopper/Manifest
@@ -0,0 +1 @@
+DIST pbcopper-1.9.5.tar.gz 3386984 BLAKE2B d38b6dfa7c5f0a9ed7fc9b89f9ee71bcd0e2248a36e593cea82ce214411b0e16bac6aff289805bcafb38ad69abe38805fbd4d7c5c0bdb7b197691ee0514c397b SHA512 006470f318341c311f600e12495b9e72a47a0fb1795dcd4d13b06c02e4872f7cde077d98bebc32ac29bb41d410d0bc7b73eead4da4ac6cf3c110e896c15df8c6
diff --git a/sci-biology/augustus/metadata.xml b/sci-biology/pbcopper/metadata.xml
index 8417d1580..8417d1580 100644
--- a/sci-biology/augustus/metadata.xml
+++ b/sci-biology/pbcopper/metadata.xml
diff --git a/sci-biology/pbcopper/pbcopper-1.9.5.ebuild b/sci-biology/pbcopper/pbcopper-1.9.5.ebuild
new file mode 100644
index 000000000..79307d839
--- /dev/null
+++ b/sci-biology/pbcopper/pbcopper-1.9.5.ebuild
@@ -0,0 +1,26 @@
+# Copyright 1999-2022 Gentoo Authors
+# Distributed under the terms of the GNU General Public License v2
+
+EAPI=8
+
+inherit meson
+
+DESCRIPTION="Core C++ library for data structures, algorithms, and utilities"
+HOMEPAGE="https://github.com/PacificBiosciences/pbcopper"
+SRC_URI="https://github.com/PacificBiosciences/pbcopper/archive/v${PV}.tar.gz -> ${P}.tar.gz"
+
+LICENSE="blasr"
+SLOT="0"
+KEYWORDS="~amd64 ~x86"
+
+BDEPEND="
+	virtual/pkgconfig
+	>=dev-lang/swig-3.0.5
+	>=dev-cpp/gtest-1.8.1
+"
+
+DEPEND="
+	>=sci-libs/htslib-1.3.1:=
+	>=dev-libs/boost-1.55:=
+"
+RDEPEND="${DEPEND}"
diff --git a/sci-biology/perga/perga-9999.ebuild b/sci-biology/perga/perga-9999.ebuild
index aeb6e2630..267b31ce4 100644
--- a/sci-biology/perga/perga-9999.ebuild
+++ b/sci-biology/perga/perga-9999.ebuild
@@ -1,9 +1,9 @@
-# Copyright 1999-2016 Gentoo Foundation
+# Copyright 1999-2021 Gentoo Authors
 # Distributed under the terms of the GNU General Public License v2
 
-EAPI=5
+EAPI=7
 
-inherit git-r3 eutils toolchain-funcs
+inherit flag-o-matic git-r3 toolchain-funcs
 
 DESCRIPTION="Paired End Reads Guided Assembler"
 HOMEPAGE="https://github.com/hitbio/PERGA
@@ -13,17 +13,18 @@ EGIT_REPO_URI="https://github.com/hitbio/PERGA.git"
 LICENSE="all-rights-reserved"
 SLOT="0"
 KEYWORDS=""
-IUSE=""
 
 DEPEND=""
 RDEPEND="${DEPEND}"
 
 src_prepare(){
+	default
+	# needed for newer gcc versions
+	append-cflags -Wl,--unresolved-symbols=ignore-in-object-files
 	sed -e "s/gcc -g /$(tc-getCC) ${CFLAGS} ${LDFLAGS} /" -i src/Makefile || die
 	sed -e 's/-Wl,-O1//' -i src/Makefile || die
 }
 
-# does not compile with gcc-5.3.0 but 4.9.3 works
 src_compile(){
 	cd src || die
 	emake
@@ -31,5 +32,5 @@ src_compile(){
 
 src_install(){
 	dobin src/perga
-	dodoc README
+	einstalldocs
 }
diff --git a/sci-biology/perlprimer/perlprimer-1.1.21.ebuild b/sci-biology/perlprimer/perlprimer-1.1.21.ebuild
index ce5f4de15..bc15bb8f4 100644
--- a/sci-biology/perlprimer/perlprimer-1.1.21.ebuild
+++ b/sci-biology/perlprimer/perlprimer-1.1.21.ebuild
@@ -1,16 +1,15 @@
-# Copyright 1999-2014 Gentoo Foundation
+# Copyright 1999-2021 Gentoo Authors
 # Distributed under the terms of the GNU General Public License v2
 
-EAPI=5
+EAPI=7
 
 DESCRIPTION="Primers design for standard PCR, bisulphite PCR and Real-time PCR"
 HOMEPAGE="http://perlprimer.sourceforge.net/"
-SRC_URI="mirror://sourceforge/${PN}/${P}.tar.bz2"
+SRC_URI="https://downloads.sourceforge.net/${PN}/${P}.tar.bz2"
 
 LICENSE="GPL-2"
 SLOT="0"
 KEYWORDS="~amd64 ~x86"
-IUSE=""
 
 DEPEND=""
 RDEPEND="
@@ -19,6 +18,7 @@ RDEPEND="
 	>=sci-biology/rebase-904"
 
 src_prepare() {
+	default
 	sed \
 		-e "s:\(\"\$HOME\".\"gcg.*\"\):\"/usr/share/rebase/gcg.*\":g" \
 		-i perlprimer.pl || die "Sed failed!"
diff --git a/sci-biology/phusion/Manifest b/sci-biology/phusion/Manifest
deleted file mode 100644
index 9bfe37e62..000000000
--- a/sci-biology/phusion/Manifest
+++ /dev/null
@@ -1 +0,0 @@
-DIST phusion_pipeline_v2.1c.tar.gz 12029104 BLAKE2B 75cb94be34815d78d404e67630767640306bab958bf5f214a8d12d0c0ea9ee4ac12ab9b84277b3fa2e4ab1b968e645606ac1dcdea6a780210398b2d5e03d4afa SHA512 b5ed5b2b893fa3d4cdbb6ae96acf515894b1df65ba2536f3a47829f383eca1e157f1b7b117e0d1bf0f763328e8bc2ffddac9a570dbec757c057040c3fb66a765
diff --git a/sci-biology/phusion/metadata.xml b/sci-biology/phusion/metadata.xml
deleted file mode 100644
index 138cb7705..000000000
--- a/sci-biology/phusion/metadata.xml
+++ /dev/null
@@ -1,12 +0,0 @@
-<?xml version="1.0" encoding="UTF-8"?>
-<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
-<pkgmetadata>
-	<maintainer type="person">
-		<email>mmokrejs@fold.natur.cuni.cz</email>
-		<name>Martin Mokrejs</name>
-	</maintainer>
-	<maintainer type="project">
-		<email>sci-biology@gentoo.org</email>
-		<name>Gentoo Biology Project</name>
-	</maintainer>
-</pkgmetadata>
diff --git a/sci-biology/phusion/phusion-2.1c.ebuild b/sci-biology/phusion/phusion-2.1c.ebuild
deleted file mode 100644
index 7c72e31fd..000000000
--- a/sci-biology/phusion/phusion-2.1c.ebuild
+++ /dev/null
@@ -1,59 +0,0 @@
-# Copyright 1999-2017 Gentoo Foundation
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=5
-
-inherit eutils flag-o-matic toolchain-funcs
-
-DESCRIPTION="Whole genome shotgun assembler using phrap (for Sanger-based reads)"
-HOMEPAGE="http://www.sanger.ac.uk/resources/software/phusion/"
-SRC_URI="ftp://ftp.sanger.ac.uk/pub/resources/software/phusion/phusion_pipeline_v2.1c.tar.gz"
-
-LICENSE="all-rights-reserved" # temporarily placed value
-# from http://genome.cshlp.org/content/13/1/81.full
-# Availability
-# Phusion is undergoing a rewrite of the code to make this a portable package. It will be made available free of charge to academic sites, but requires licensing for commercial use. For more information please contact the authors.
-SLOT="0"
-KEYWORDS="" # compile process does not exit upon errors
-# one file does not compile
-# x86_64-pc-linux-gnu-gcc  -O2 -pipe -maes -mpclmul -mpopcnt -mavx -march=native  -o contigoverlap  contigoverlap.o  -lm
-# contigoverlap.o: In function `HashFasta':
-# contigoverlap.c:(.text+0xbb1): relocation truncated to fit: R_X86_64_PC32 against symbol `n_Entry' defined in COMMON section in contigoverlap.o
-# contigoverlap.o: In function `Reads_Overlap':
-# contigoverlap.c:(.text+0x2637): relocation truncated to fit: R_X86_64_32S against symbol `qinfo' defined in COMMON section in contigoverlap.o
-IUSE=""
-
-DEPEND="app-shells/tcsh"
-RDEPEND="${DEPEND}
-	sci-biology/phrap
-	dev-lang/perl"
-
-# contains bundled ssaha
-# file collision with sci-biology/shrimp on /usr/bin/fasta2fastq
-
-S="${WORKDIR}"/"phusion_pipeline_v2.1c"
-
-src_prepare(){
-	cp -pf "${EPREFIX}"/usr/bin/phrap src/phrap/phrap.manylong || die
-	# prevent file collision with sci-biology/shrimp-2.2.3 and sci-biology/phusion2-3.0
-	sed -e "s#fasta2fastq#fasta2fastq_"${PN}"#" -i src/fasta2fastq/fasta2fastq.c \
-		src/fasta2fastq/Makefile || die
-	sed -e "s#ctgreads.pl#ctgreads_"${PN}".pl#" -i src/Tcsh_scripts/*.csh || die
-	mv src/fasta2fastq/fasta2fastq.c src/fasta2fastq/fasta2fastq_"${PN}".c || die
-	mv src/Perl_scripts/ctgreads.pl src/Perl_scripts/ctgreads_"${PN}".pl || die
-	find . -name Makefile | while read f; do
-		sed -e "s/^CC =/CC = $(tc-getCC) #/" -i "$f" || die
-		sed -e "s/^ CFLAGS2 =/ CFLAGS2 = ${CFLAGS} #/" -i "$f" || die
-		sed -e "s/^CFLAGS =/CFLAGS = ${CFLAGS} #/" -i "$f" || die
-		sed -e "s/^ CFLAGS =/ CFLAGS = ${CFLAGS} #/" -i "$f" || die
-	done
-}
-
-src_compile(){
-	tcsh install.csh || csh install.csh || die
-}
-
-src_install(){
-	dobin bin/*
-	dodoc README.1st releaseNote_v2.1c doc/*
-}
diff --git a/sci-biology/phusion2/Manifest b/sci-biology/phusion2/Manifest
deleted file mode 100644
index fce8afa2a..000000000
--- a/sci-biology/phusion2/Manifest
+++ /dev/null
@@ -1 +0,0 @@
-DIST phusion2-3.0.tar.gz 136875 BLAKE2B 8338df1865ac8f684ba3a2a2fc15520fe167a1ace02e8f64db17f6acf07ea8cde2da18fd6f18a958e53b00dd02e7e8138305e2a762a84c6bf8d7cfbd2cb9b999 SHA512 a29e4102806d404a7bc78c1611d702f9c6415bc04ca518416632bf8d9d3e570324add907c43e627f645a5281b807ccf169908637121f66883c4e878080345eca
diff --git a/sci-biology/phusion2/metadata.xml b/sci-biology/phusion2/metadata.xml
deleted file mode 100644
index 0f267b755..000000000
--- a/sci-biology/phusion2/metadata.xml
+++ /dev/null
@@ -1,15 +0,0 @@
-<?xml version="1.0" encoding="UTF-8"?>
-<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
-<pkgmetadata>
-	<maintainer type="person">
-		<email>mmokrejs@fold.natur.cuni.cz</email>
-		<name>Martin Mokrejs</name>
-	</maintainer>
-	<maintainer type="project">
-		<email>sci-biology@gentoo.org</email>
-		<name>Gentoo Biology Project</name>
-	</maintainer>
-	<upstream>
-		<remote-id type="sourceforge">downloads</remote-id>
-	</upstream>
-</pkgmetadata>
diff --git a/sci-biology/phusion2/phusion2-3.0.ebuild b/sci-biology/phusion2/phusion2-3.0.ebuild
deleted file mode 100644
index 105224531..000000000
--- a/sci-biology/phusion2/phusion2-3.0.ebuild
+++ /dev/null
@@ -1,39 +0,0 @@
-# Copyright 1999-2015 Gentoo Foundation
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=5
-
-inherit eutils
-
-DESCRIPTION="Whole genome shotgun assembler using phrap (for Sanger-based reads)"
-HOMEPAGE="http://www.sanger.ac.uk/resources/software/phusion/"
-SRC_URI="http://downloads.sourceforge.net/project/${PN}/${P}.tar.gz"
-
-LICENSE="all-rights-reserved" # temporarily placed value
-# from http://genome.cshlp.org/content/13/1/81.full
-# Availability
-# Phusion is undergoing a rewrite of the code to make this a portable package. It will be made available free of charge to academic sites, but requires licensing for commercial use. For more information please contact the authors.
-SLOT="0"
-KEYWORDS=""
-IUSE=""
-
-DEPEND="app-shells/tcsh
-	sys-cluster/openmpi"
-RDEPEND="${DEPEND}
-	sci-biology/phrap
-	dev-lang/perl"
-
-# contains bundled ssaha
-# file collision with sci-biology/shrimp on /usr/bin/fasta2fastq
-
-S="${WORKDIR}"
-
-src_prepare(){
-	rm -f phusion2 *.o
-	sed -e 's/^CFLAGS =/# CFLAGS =/' -i Makefile || die
-}
-
-src_install(){
-	dobin ctgreads.pl phusion2
-	dodoc how_to_make_mates
-}
diff --git a/sci-biology/picard/Manifest b/sci-biology/picard/Manifest
deleted file mode 100644
index 2f14e87a2..000000000
--- a/sci-biology/picard/Manifest
+++ /dev/null
@@ -1,2 +0,0 @@
-DIST picard-1.141.tar.gz 5692255 BLAKE2B 26bb6edd32b75895a52c549e61e5873b6b5d1127fa1458e671b24a2b792c86bb3db5f9f8b8f24f9419a4ce1680f6bbad98da8dc7da4bf9b14178e901a28d803e SHA512 5fed8ff0076ec5f096a5138b95ae07805f8f4d68db33b65f2e21325f49493c50f235519768823c2db981b2e543fbf05f55be7939d75cbd5d257ac84e633b9bf4
-DIST picard-2.2.2.tar.gz 6565857 BLAKE2B e18bd45c9422b97e129418804bb063806614a707dbb9bafd42ae77a0899328cbade45a3b9d8a91f6a07e3508b6b8b3e4b964ee0c9b838a0d6d9cd5eef04d83f6 SHA512 4ee97443397b45236a2481fa64c80edbd7761d6562cc134d65f1d95fa101ccc82402bbf21ed6b186e15324f2c189737790066e18cd0143bb50768c20ee4b156b
diff --git a/sci-biology/picard/files/2.2.2-build.xml.patch b/sci-biology/picard/files/2.2.2-build.xml.patch
deleted file mode 100644
index 278c4a1a4..000000000
--- a/sci-biology/picard/files/2.2.2-build.xml.patch
+++ /dev/null
@@ -1,115 +0,0 @@
-diff --git a/build.xml b/build.xml
-index f0b98ab..14ff7f7 100755
---- a/build.xml
-+++ b/build.xml
-@@ -83,15 +83,6 @@
-     <!-- INIT -->
-     <target name="init">
-         <path id="classpath">
--            <fileset dir="${htsjdk_lib_dir}">
--                <include name="*.jar"/>
--                <include name="**/*.jar"/>
--            </fileset>
--            <!-- for the specific HTSJDK library JARs -->
--            <fileset dir="${htsjdk}/lib">
--                <include name="*.jar"/>
--                <include name="**/*.jar"/>
--            </fileset>
-             <fileset dir="${lib}">
-                 <include name="**/*.jar"/>
-             </fileset>
-@@ -117,53 +108,21 @@
- 
-     <!-- HTS-JDK -->
-     <target name="set-htsjdk-version">
--        <!-- set the htsjdk version -->
--        <ant antfile="build.xml" dir="${htsjdk}" target="write-version-property" inheritall="false"/>
--        <loadfile property="htsjdk-version" srcFile="${htsjdk}/htsjdk.version.properties">
--            <filterchain>
--                <linecontains>
--                    <contains value="htsjdk-version="/>
--                </linecontains>
--                <tokenfilter>
--                    <replacestring from="htsjdk-version=" to=""/>
--                </tokenfilter>
--                <striplinebreaks/>
--            </filterchain>
--        </loadfile>
-     </target>
- 
-     <target name="clone-htsjdk" description="Clone HTS-JDK sources from Sourceforge">
--        <exec executable="git" failonerror="true">
--            <arg value="clone"/>
--            <arg value="${htsjdk_git_url}"/>
--            <arg value="${htsjdk}"/>
--        </exec>
-     </target>
- 
-     <target name="compile-htsjdk" depends="set-htsjdk-version" description="Build HTS-JDK, and grab build jars">
--        <ant antfile="build.xml" dir="${htsjdk}" target="clean" inheritall="false"/>
--        <ant antfile="build.xml" dir="${htsjdk}" target="all" inheritall="false"/>
--        <copy todir="${htsjdk_lib_dir}">
--            <fileset dir="${htsjdk}/dist" includes="**/*-*.jar"/>
--            <fileset dir="${htsjdk}/lib" includes="*.jar"/>
--        </copy>
--        <copy todir="${dist}">
--            <fileset dir="${htsjdk}/dist" includes="**/*.jar" excludes="**/*-*.jar"/>
--        </copy>
--        <!-- set the htsjdk version -->
--        <ant antfile="build.xml" dir="${htsjdk}" target="write-version-property" inheritall="false"/>
-     </target>
- 
-     <target name="clean-htsjdk" description="Clean HTS-JDK">
--        <ant antfile="build.xml" dir="${htsjdk}" target="clean" inheritall="false"/>
-     </target>
- 
-     <target name="test-htsjdk" description="Test HTS-JDK">
--        <ant antfile="build.xml" dir="${htsjdk}" target="test" inheritall="false"/>
-     </target>
- 
-     <target name="compile-htsjdk-tests" description="Compile HTS-JDK Tests">
--        <ant antfile="build.xml" dir="${htsjdk}" target="compile-tests" inheritall="false"/>
-     </target>
- 
-     <!-- COMPILE -->
-@@ -292,15 +251,11 @@
-             <fileset dir="${lib}">
-                 <exclude name="**/jacocoant.jar"/> <!-- must exclude this jar from packing into picard - this is only used for testing -->
-             </fileset>
--            <fileset dir="${htsjdk_lib_dir}">
--                <include name="*.jar"/>
--            </fileset>
-         </unjar>
- 
-         <jar destfile="${dist}/picard.jar" compress="no">
-             <fileset dir="${classes}" includes="picard/**/*.*, META-INF/**/*"/>
-             <fileset dir="${src.scripts}" includes="**/*.R"/>
--            <fileset dir="${htsjdk-classes}" includes ="${htsjdk}/*/**/*.*"/>
-             <fileset dir="${dist.tmp}" includes="**/*"/>
-             <fileset dir="${jar_opt}" includes="**/*"/>
- 
-@@ -396,13 +351,9 @@
-                 <fileset dir="${lib}">
-                     <include name="**/*.jar"/>
-                 </fileset>
--                <fileset dir="${htsjdk}/dist">
--                    <include name="**/*.jar"/>
--                </fileset>
-             </classpath>
-             <fileset dir=".">
-                 <include name="${src}/**/*.java"/>
--                <include name="${htsjdk_src}/**/*.java"/>
-             </fileset>
-             <arg line="-f ${command-line-html-dir}/picard-metric-definitions.html"/>
-         </javadoc>
-@@ -508,10 +459,8 @@
-             description="Default build target">
-         <zip zipfile="${dist}/picard-tools-${picard-version}.zip">
-             <zipfileset dir="${dist}" includes="*.jar" prefix="picard-tools-${picard-version}"/>
--            <zipfileset dir="${htsjdk_lib_dir}" includes="htsjdk-*.jar" prefix="picard-tools-${picard-version}"/>
-             <zipfileset dir="${lib}" includes="snappy*.jar"/>
-             <!-- distribute libJniDeflater.so in same directory as jarfiles-->
--            <zipfileset dir="${htsjdk}/lib/jni" includes="*" prefix="picard-tools-${picard-version}"/>
-         </zip>
-     </target>
- 
diff --git a/sci-biology/picard/metadata.xml b/sci-biology/picard/metadata.xml
deleted file mode 100644
index 1d81f108f..000000000
--- a/sci-biology/picard/metadata.xml
+++ /dev/null
@@ -1,16 +0,0 @@
-<?xml version="1.0" encoding="UTF-8"?>
-<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
-<pkgmetadata>
-	<maintainer type="person">
-		<email>ercpe@gentoo.org</email>
-		<name>Johann Schmitz (ercpe)</name>
-	</maintainer>
-	<maintainer type="project">
-		<email>sci-biology@gentoo.org</email>
-		<name>Gentoo Biology Project</name>
-	</maintainer>
-	<upstream>
-		<remote-id type="github">broadinstitute/picard</remote-id>
-		<remote-id type="sourceforge">picard</remote-id>
-	</upstream>
-</pkgmetadata>
diff --git a/sci-biology/picard/picard-1.141.ebuild b/sci-biology/picard/picard-1.141.ebuild
deleted file mode 100644
index 68b10a73d..000000000
--- a/sci-biology/picard/picard-1.141.ebuild
+++ /dev/null
@@ -1,72 +0,0 @@
-# Copyright 1999-2017 Gentoo Foundation
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=5
-
-JAVA_PKG_IUSE="doc source test"
-WANT_ANT_TASKS="ant-apache-bcel dev-java/testng:0 ant-junit4"
-
-inherit java-pkg-2 java-ant-2
-
-DESCRIPTION="Java-based command-line utilities that manipulate SAM/BAM/CRAM/VCF files"
-HOMEPAGE="http://picard.sourceforge.net
-	http://broadinstitute.github.io/picard"
-#SRC_URI="https://dev.gentoo.org/~ercpe/distfiles/${CATEGORY}/${PN}/${P}.tar.bz2"
-SRC_URI="https://github.com/broadinstitute/picard/archive/${PV}.tar.gz -> ${P}.tar.gz"
-
-LICENSE="Apache-2.0" # 2.2.2 is MIT instead, not sure when it changed away from Apache
-SLOT="0"
-IUSE=""
-KEYWORDS=""
-
-CDEPEND="dev-java/snappy:1.0
-	dev-java/cofoja:0
-	dev-java/commons-jexl:2
-	dev-java/ant-core:0"
-
-DEPEND=">=virtual/jdk-1.7
-	dev-java/ant-apache-bcel:0
-	test? (
-		dev-java/testng:0
-		dev-lang/R
-	)
-	${CDEPEND}"
-RDEPEND=">=virtual/jre-1.7
-	${CDEPEND}"
-
-EANT_BUILD_TARGET="all"
-EANT_TEST_TARGET="test"
-EANT_NEEDS_TOOLS="true"
-JAVA_ANT_REWRITE_CLASSPATH="true"
-EANT_GENTOO_CLASSPATH="snappy-1.0,cofoja,commons-jexl-2,ant-core"
-EANT_TEST_GENTOO_CLASSPATH="${EANT_GENTOO_CLASSPATH},testng"
-
-java_prepare() {
-	mkdir -p "${S}"/lib || die
-
-	# TODO: update the patch
-	#epatch "${FILESDIR}"/${PV}-gentoo.patch
-
-	mv "${S}"/src/java/net/sf/samtools/SAMTestUtil.java "${S}"/src/tests/java/net/sf/samtools || die
-}
-
-src_install() {
-	cd dist || die
-
-	for i in *-${PV}.jar; do
-		java-pkg_newjar $i ${i/-${PV}/}
-		rm $i || die
-	done
-
-	java-pkg_dojar *.jar
-	for i in *.jar; do
-		java-pkg_dolauncher ${i/.jar/} --jar $i;
-	done
-
-	use source && java-pkg_dosrc "${S}"/src/java/*
-	use doc && java-pkg_dojavadoc "${S}"/javadoc
-}
-
-src_test() {
-	java-pkg-2_src_test
-}
diff --git a/sci-biology/picard/picard-2.18.2.ebuild b/sci-biology/picard/picard-2.18.2.ebuild
deleted file mode 100644
index 9292b1e19..000000000
--- a/sci-biology/picard/picard-2.18.2.ebuild
+++ /dev/null
@@ -1,62 +0,0 @@
-# Copyright 1999-2018 Gentoo Foundation
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=6
-
-#JAVA_PKG_IUSE="doc source"
-JAVA_PKG_IUSE=""
-
-inherit git-r3 java-pkg-2
-
-DESCRIPTION="Java-based command-line utilities that manipulate SAM/BAM/CRAM/VCF files"
-HOMEPAGE="http://picard.sourceforge.net
-	http://broadinstitute.github.io/picard"
-EGIT_REPO_URI="https://github.com/broadinstitute/picard.git"
-EGIT_COMMIT="${PV}"
-# building outside of git is not possible,
-# see https://github.com/broadinstitute/picard/issues/605
-#SRC_URI="https://github.com/broadinstitute/picard/archive/${PV}.tar.gz -> ${P}.tar.gz"
-
-LICENSE="MIT"
-SLOT="0"
-IUSE=""
-KEYWORDS=""
-
-CDEPEND="dev-java/snappy:1.1
-	dev-java/cofoja:0
-	dev-java/commons-jexl:2
-	dev-java/htsjdk:0"
-
-DEPEND=">=virtual/jdk-1.8
-	${CDEPEND}"
-
-RDEPEND=">=virtual/jre-1.8
-	${CDEPEND}"
-
-EANT_BUILD_TARGET="all"
-EANT_NEEDS_TOOLS="true"
-JAVA_ANT_REWRITE_CLASSPATH="true"
-EANT_GENTOO_CLASSPATH="snappy-1.1,cofoja,commons-jexl-2,htsjdk"
-
-src_prepare() {
-	default
-}
-
-src_compile(){
-	# work around gradle writing $HOME/.gradle, requiring $HOME/.git and $HOME/.m2/
-	# https://github.com/samtools/htsjdk/issues/660#issuecomment-232155965
-	# make jure SDK-1.8 is available, JRE-1.8 is not enough
-	# see more gradlew arg options in build.xml, especially jar versus shadowJar
-	GRADLE_USER_HOME="${WORKDIR}" ./gradlew --stacktrace --debug compileJava jar || die
-}
-
-src_install() {
-	cd build/libs || die
-	java-pkg_dojar "${PN}".jar
-	java-pkg_dojar "${PN}"-*-SNAPSHOT.jar
-
-	java-pkg_dolauncher ${PN} --main picard.cmdline.PicardCommandLine
-
-	#use source && java-pkg_dosrc "${S}"/src/java/*
-	#use doc && java-pkg_dojavadoc "${S}"/javadoc
-}
diff --git a/sci-biology/picard/picard-2.2.2.ebuild b/sci-biology/picard/picard-2.2.2.ebuild
deleted file mode 100644
index c2bfb0503..000000000
--- a/sci-biology/picard/picard-2.2.2.ebuild
+++ /dev/null
@@ -1,53 +0,0 @@
-# Copyright 1999-2017 Gentoo Foundation
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=6
-
-JAVA_PKG_IUSE="doc source"
-
-inherit java-pkg-2 java-ant-2
-
-DESCRIPTION="Java-based command-line utilities that manipulate SAM/BAM/CRAM/VCF files"
-HOMEPAGE="http://picard.sourceforge.net
-	http://broadinstitute.github.io/picard"
-SRC_URI="https://github.com/broadinstitute/picard/archive/${PV}.tar.gz -> ${P}.tar.gz"
-
-LICENSE="MIT"
-SLOT="0"
-IUSE=""
-KEYWORDS="~amd64 ~x86"
-
-CDEPEND="dev-java/snappy:1.1
-	dev-java/cofoja:0
-	dev-java/commons-jexl:2
-	dev-java/ant-core:0
-	dev-java/htsjdk:0"
-
-DEPEND=">=virtual/jdk-1.8
-	${CDEPEND}"
-
-RDEPEND=">=virtual/jre-1.8
-	${CDEPEND}"
-
-EANT_BUILD_TARGET="all"
-EANT_NEEDS_TOOLS="true"
-JAVA_ANT_REWRITE_CLASSPATH="true"
-EANT_GENTOO_CLASSPATH="snappy-1.1,cofoja,commons-jexl-2,ant-core,htsjdk"
-
-java_prepare() {
-	default
-	rm -r src/java/picard/util/TestNGUtil.java src/tests/java/* || die
-	epatch "${FILESDIR}"/${PV}-build.xml.patch
-}
-
-src_install() {
-	cd dist || die
-
-	java-pkg_dojar ${PN}.jar
-	java-pkg_dojar ${PN}-lib.jar
-
-	java-pkg_dolauncher ${PN} --main picard.cmdline.PicardCommandLine
-
-	use source && java-pkg_dosrc "${S}"/src/java/*
-	use doc && java-pkg_dojavadoc "${S}"/javadoc
-}
diff --git a/sci-biology/picard/picard-9999.ebuild b/sci-biology/picard/picard-9999.ebuild
deleted file mode 100644
index 57bbfdb9f..000000000
--- a/sci-biology/picard/picard-9999.ebuild
+++ /dev/null
@@ -1,57 +0,0 @@
-# Copyright 1999-2018 Gentoo Foundation
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=6
-
-#JAVA_PKG_IUSE="doc source"
-JAVA_PKG_IUSE=""
-
-inherit git-r3 java-pkg-2
-
-DESCRIPTION="Java-based command-line utilities that manipulate SAM/BAM/CRAM/VCF files"
-HOMEPAGE="http://picard.sourceforge.net
-	http://broadinstitute.github.io/picard"
-EGIT_REPO_URI="https://github.com/broadinstitute/picard.git"
-
-LICENSE="MIT"
-SLOT="0"
-IUSE=""
-KEYWORDS=""
-
-CDEPEND="dev-java/snappy:1.1
-	dev-java/cofoja:0
-	dev-java/commons-jexl:2
-	dev-java/htsjdk:0"
-
-DEPEND=">=virtual/jdk-1.8
-	${CDEPEND}"
-
-RDEPEND=">=virtual/jre-1.8
-	${CDEPEND}"
-
-EANT_BUILD_TARGET="all"
-EANT_NEEDS_TOOLS="true"
-JAVA_ANT_REWRITE_CLASSPATH="true"
-EANT_GENTOO_CLASSPATH="snappy-1.1,cofoja,commons-jexl-2,htsjdk"
-
-src_prepare() {
-	default
-}
-
-src_compile(){
-	# work around gradle writing $HOME/.gradle, requiring $HOME/.git and $HOME/.m2/
-	# https://github.com/samtools/htsjdk/issues/660#issuecomment-232155965
-	# make jure SDK-1.8 is available, JRE-1.8 is not enough
-	GRADLE_USER_HOME="${WORKDIR}" ./gradlew || die
-}
-
-src_install() {
-	cd build/libs || die
-	java-pkg_dojar "${PN}".jar
-	java-pkg_dojar "${PN}"-*-SNAPSHOT.jar
-
-	java-pkg_dolauncher ${PN} --main picard.cmdline.PicardCommandLine
-
-	#use source && java-pkg_dosrc "${S}"/src/java/*
-	#use doc && java-pkg_dojavadoc "${S}"/javadoc
-}
diff --git a/sci-biology/pileup/Manifest b/sci-biology/pileup/Manifest
index 84c8730b9..2085f9d14 100644
--- a/sci-biology/pileup/Manifest
+++ b/sci-biology/pileup/Manifest
@@ -1 +1 @@
-DIST pileup.tgz 685778 BLAKE2B edc1de01855fc1617be96a54aca505d83f967b77ca5326137da80cc0c4a570da8b98f101d47484108c0c3ee06e1a340c408b20facd99c2b9fa00a9c615e47663 SHA512 d65a3bc3bc43f17c74033808ea4d536d3ca46b971101275240261bd0f97c54855566e7254d8244501427f1dbab9f1cef5cd7c853a00d253aad2a0dbdab1488ab
+DIST pileup-0.6.tgz 685778 BLAKE2B edc1de01855fc1617be96a54aca505d83f967b77ca5326137da80cc0c4a570da8b98f101d47484108c0c3ee06e1a340c408b20facd99c2b9fa00a9c615e47663 SHA512 d65a3bc3bc43f17c74033808ea4d536d3ca46b971101275240261bd0f97c54855566e7254d8244501427f1dbab9f1cef5cd7c853a00d253aad2a0dbdab1488ab
diff --git a/sci-biology/pileup/pileup-0.6.ebuild b/sci-biology/pileup/pileup-0.6.ebuild
index ac9359081..ad978f70f 100644
--- a/sci-biology/pileup/pileup-0.6.ebuild
+++ b/sci-biology/pileup/pileup-0.6.ebuild
@@ -1,36 +1,36 @@
-# Copyright 1999-2014 Gentoo Foundation
+# Copyright 1999-2021 Gentoo Authors
 # Distributed under the terms of the GNU General Public License v2
 
-EAPI=5
+EAPI=7
 
 DESCRIPTION="SSAHA2-based pipeline to align reads"
-HOMEPAGE="http://www.sanger.ac.uk/resources/software/ssaha2/"
-SRC_URI="ftp://ftp.sanger.ac.uk/pub4/resources/software/ssaha2/pileup.tgz"
+HOMEPAGE="https://www.sanger.ac.uk/resources/software/ssaha2/"
+SRC_URI="ftp://ftp.sanger.ac.uk/pub4/resources/software/ssaha2/pileup.tgz -> ${P}.tgz"
 
 # http://samtools.sourceforge.net/pileup.shtml
 #
 LICENSE="GRL"
 SLOT="0"
-KEYWORDS=""
-IUSE=""
+KEYWORDS="~amd64"
 
-DEPEND=""
-RDEPEND="${DEPEND}"
-
-S="${WORKDIR}"/pileup_v"${PV}"
+S="${WORKDIR}/pileup_v${PV}"
 
 src_prepare(){
-	sed -i "s/^CC= gcc/#CC= gcc/" ssaha_pileup/ssaha_pileup/makefile || die "sed failed to fix makefile"
-	sed -i "s/^CFLAGS= -O2/#CFLAGS= -O2/" ssaha_pileup/ssaha_pileup/makefile || die "sed failed to fix makefile"
+	default
+	sed -i -e "s/^CC= gcc/#CC= gcc/" \
+		-e "s/^CFLAGS= -O2/#CFLAGS= -O2/" \
+		ssaha_pileup/ssaha_pileup/makefile || die "sed failed to fix makefile"
 
 	for d in get_seqreads ssaha_split; do
-		sed -i "s/^CC = cc/#CC = cc/" ssaha_pileup/other_codes/$d/Makefile || die "sed failed to fix Makefile"
-		sed -i "s/^CFLAGS = -O4/#CFLAGS = -O4/" ssaha_pileup/other_codes/$d/Makefile || die "sed failed to fix Makefile"
+		sed -i -e "s/^CC = cc/#CC = cc/" \
+			-e "s/^CFLAGS = -O4/#CFLAGS = -O4/" \
+			ssaha_pileup/other_codes/$d/Makefile || die "sed failed to fix Makefile"
 	done
 
 	for d in search_read ssaha_parseSNP; do
-		sed -i "s/^CC = gcc/#CC = gcc/" ssaha_pileup/other_codes/$d/Makefile || die "sed failed to fix Makefile"
-		sed -i "s/^CFLAGS = -Wall -O4/#CFLAGS = -Wall -O4/" ssaha_pileup/other_codes/$d/Makefile || die "sed failed to fix Makefile"
+		sed -i -e "s/^CC = gcc/#CC = gcc/" \
+			-e "s/^CFLAGS = -Wall -O4/#CFLAGS = -Wall -O4/" \
+		ssaha_pileup/other_codes/$d/Makefile || die "sed failed to fix Makefile"
 	done
 }
 
@@ -40,22 +40,17 @@ src_compile(){
 
 	for d in get_seqreads ssaha_split ssaha_parseSNP search_read; do
 		cd "${S}"/ssaha_pileup/other_codes/$d  || die "Cannot cd to "${S}"ssaha_pileup/other_codes/"$d
-		make clean
+		emake clean
 		default
 	done
 }
 
 src_install(){
 	cd ssaha_pileup/ssaha_pileup || die "Cannot cd to "${S}"ssaha_pileup/ssaha_pileup"
-	dobin ssaha_pileup ssaha_solexa ssaha_pairs ssaha_clean ssaha_mates ssaha_cigar ssaha_indel view_pileup ssaha_reads ssaha_merge ssaha_check-cigar "dobin failed"
+	dobin ssaha_pileup ssaha_solexa ssaha_pairs ssaha_clean ssaha_mates ssaha_cigar ssaha_indel view_pileup ssaha_reads ssaha_merge ssaha_check-cigar
 
-	cd "${S}" || die
-	for f in ssaha_pileup/other_codes/get_seqreads/get_seqreads \
-		ssaha_pileup/other_codes/ssaha_split/ssaha_split \
-		ssaha_pileup/other_codes/ssaha_parseSNP/ssaha_parseSNP \
-		ssaha_pileup/other_codes/search_read/search_read; do
-			dobin $f "dobin failed"
-	done
+	cd "${S}/ssaha_pileup/other_codes" || die
+	dobin get_seqreads/get_seqreads ssaha_split/ssaha_split ssaha_parseSNP/ssaha_parseSNP search_read/search_read
 
 	# TODO:
 	# pileup_v0.6/ssaha_pileup/tag.pl
diff --git a/sci-biology/pilon-bin/Manifest b/sci-biology/pilon-bin/Manifest
deleted file mode 100644
index a60543190..000000000
--- a/sci-biology/pilon-bin/Manifest
+++ /dev/null
@@ -1 +0,0 @@
-DIST pilon-1.23.jar 7387440 BLAKE2B 76d40a62280a13ebbdd0119b167b9d082e9388ade8f08acdf257dc46ba6352618bf2895136be1182c255cbcd38c834e64d09ce2a67d451522331ab9e08ee69fe SHA512 e328cf06187743c7b24966aa72123ddd001bf1be3c3fd20feb2aa2347cdb87ffe0762075286d19169b076a1bfa066a330339c457d631e2db17a1a968cc97d7c4
diff --git a/sci-biology/pilon-bin/metadata.xml b/sci-biology/pilon-bin/metadata.xml
deleted file mode 100644
index 138cb7705..000000000
--- a/sci-biology/pilon-bin/metadata.xml
+++ /dev/null
@@ -1,12 +0,0 @@
-<?xml version="1.0" encoding="UTF-8"?>
-<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
-<pkgmetadata>
-	<maintainer type="person">
-		<email>mmokrejs@fold.natur.cuni.cz</email>
-		<name>Martin Mokrejs</name>
-	</maintainer>
-	<maintainer type="project">
-		<email>sci-biology@gentoo.org</email>
-		<name>Gentoo Biology Project</name>
-	</maintainer>
-</pkgmetadata>
diff --git a/sci-biology/pilon-bin/pilon-bin-1.23.ebuild b/sci-biology/pilon-bin/pilon-bin-1.23.ebuild
deleted file mode 100644
index de401bd21..000000000
--- a/sci-biology/pilon-bin/pilon-bin-1.23.ebuild
+++ /dev/null
@@ -1,30 +0,0 @@
-# Copyright 1999-2018 Gentoo Authors
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=6
-
-inherit java-pkg-2
-
-DESCRIPTION="Fix assembled reference using BAM-aligned reads, call SNPs"
-HOMEPAGE="
-	https://github.com/broadinstitute/pilon
-	https://github.com/broadinstitute/pilon/wiki"
-SRC_URI="https://github.com/broadinstitute/pilon/releases/download/v${PV}/pilon-${PV}.jar"
-
-LICENSE="GPL-2"
-SLOT="0"
-KEYWORDS="~amd64"
-IUSE=""
-
-# contains bundled sbt-assembly module
-DEPEND=">=virtual/jdk-1.7:*"
-RDEPEND="${DEPEND}
-	>=virtual/jre-1.7:*
-	>=dev-java/htsjdk-1.130"
-
-S="${WORKDIR}"
-
-src_install(){
-	cp -p "${DISTDIR}"/pilon-${PV}.jar . || die
-	java-pkg_dojar pilon-${PV}.jar
-}
diff --git a/sci-biology/plink/Manifest b/sci-biology/plink/Manifest
deleted file mode 100644
index c93526052..000000000
--- a/sci-biology/plink/Manifest
+++ /dev/null
@@ -1 +0,0 @@
-DIST plink-1.90_pre160731.zip 1069338 SHA256 9cda19d4a4812d2c91f7407bcfd1d76106bce8b4899745c0139a92baf84b9c0a SHA512 184a3da42e514a8478de1da637d0f2d22bd9c178113d0096b937b6e2e0a8372897f2dba013be36ab518fa9b801fa6de0a410fea41d8673af612f53b36b98c79b WHIRLPOOL bdc290a9d0bd7778c68b1fa963b770082b9043392a5e81dfc666fd07f00a72ddd5ef307c451e522b489a0c5421d4cfc06b5fc2abed3549eeade0e86760cdd6fd
diff --git a/sci-biology/plink/metadata.xml b/sci-biology/plink/metadata.xml
deleted file mode 100644
index 8417d1580..000000000
--- a/sci-biology/plink/metadata.xml
+++ /dev/null
@@ -1,8 +0,0 @@
-<?xml version="1.0" encoding="UTF-8"?>
-<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
-<pkgmetadata>
-	<maintainer type="project">
-		<email>sci-biology@gentoo.org</email>
-		<name>Gentoo Biology Project</name>
-	</maintainer>
-</pkgmetadata>
diff --git a/sci-biology/plink/plink-1.90_pre160731.ebuild b/sci-biology/plink/plink-1.90_pre160731.ebuild
deleted file mode 100644
index 525cfbcbb..000000000
--- a/sci-biology/plink/plink-1.90_pre160731.ebuild
+++ /dev/null
@@ -1,65 +0,0 @@
-# Copyright 1999-2016 Gentoo Foundation
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=5
-
-inherit eutils toolchain-funcs
-
-DESCRIPTION="Whole genome association analysis toolset"
-HOMEPAGE="http://pngu.mgh.harvard.edu/~purcell/plink
-	https://www.cog-genomics.org/plink2/"
-SRC_URI="https://www.cog-genomics.org/static/bin/plink160731/plink_src.zip -> ${P}.zip"
-
-LICENSE="GPL-3+"
-SLOT="0"
-KEYWORDS="~amd64 ~x86"
-IUSE="lapack"
-
-DEPEND="
-	app-arch/unzip
-	virtual/pkgconfig"
-RDEPEND="
-	sys-libs/zlib
-	lapack? ( virtual/lapack
-		virtual/cblas )"
-
-S="${WORKDIR}/"
-
-# Package collides with net-misc/putty. Renamed to p-link following discussion with Debian.
-# Package contains bytecode-only jar gPLINK.jar. Ignored, notified upstream.
-
-src_prepare() {
-	rm -rf zlib-1.2.8 || die
-	sed \
-		-e 's:zlib-1.2.8/zlib.h:zlib.h:g' \
-		-i *.{c,h} || die
-
-	sed \
-		-e 's:g++:$(CXX):g' \
-		-e 's:gcc:$(CC):g' \
-		-e 's:gfortran:$(FC):g' \
-		-i Makefile || die
-	if ! use lapack; then
-		sed -e 's/^NO_LAPACK =/NO_LAPACK = 1/' -i Makefile || die
-		sed -e 's@^// #define NOLAPACK@#define NOLAPACK@' -i plink_common.h || die
-	fi
-	tc-export PKG_CONFIG
-}
-
-src_compile() {
-	local blasflags
-	use lapack && blasflags="$($(tc-getPKG_CONFIG) --libs lapack cblas)"
-	emake \
-		CXX=$(tc-getCXX) \
-		CFLAGS="${CFLAGS}" \
-		ZLIB="$($(tc-getPKG_CONFIG) --libs zlib)" \
-		BLASFLAGS="$blasflags"
-}
-
-src_install() {
-	newbin plink p-link
-}
-
-pkg_postinst(){
-	einfo "plink binary is now renamed to p-link to avoid file collision"
-}
diff --git a/sci-biology/plinkseq/Manifest b/sci-biology/plinkseq/Manifest
deleted file mode 100644
index fdf7b1f9d..000000000
--- a/sci-biology/plinkseq/Manifest
+++ /dev/null
@@ -1 +0,0 @@
-DIST plinkseq-0.10.tgz 6090698 BLAKE2B 86ddc1952c742f024fefdd8e3dec7af73bbe1be3231dc9a795650f3470b9b641ce86f6fa8157f6090943bf6cb53eb262204e2d4872b5cad14fa078b3cf27c514 SHA512 b8fa0a0b42a5f67612b1549d1f2fbed67333abb57ef024d4be683cd326e53a8ef08c6c0acae8ed3195fad619c8aea9005e315f937d76cd990a7ffff1d808af41
diff --git a/sci-biology/plinkseq/metadata.xml b/sci-biology/plinkseq/metadata.xml
deleted file mode 100644
index 138cb7705..000000000
--- a/sci-biology/plinkseq/metadata.xml
+++ /dev/null
@@ -1,12 +0,0 @@
-<?xml version="1.0" encoding="UTF-8"?>
-<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
-<pkgmetadata>
-	<maintainer type="person">
-		<email>mmokrejs@fold.natur.cuni.cz</email>
-		<name>Martin Mokrejs</name>
-	</maintainer>
-	<maintainer type="project">
-		<email>sci-biology@gentoo.org</email>
-		<name>Gentoo Biology Project</name>
-	</maintainer>
-</pkgmetadata>
diff --git a/sci-biology/plinkseq/plinkseq-0.10.ebuild b/sci-biology/plinkseq/plinkseq-0.10.ebuild
deleted file mode 100644
index b1e4937d7..000000000
--- a/sci-biology/plinkseq/plinkseq-0.10.ebuild
+++ /dev/null
@@ -1,51 +0,0 @@
-# Copyright 1999-2017 Gentoo Foundation
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=5
-
-AUTOTOOLS_AUTORECONF=yes
-
-inherit toolchain-funcs autotools-utils
-
-DESCRIPTION="C/C++ library for working with human genetic variation data"
-HOMEPAGE="http://atgu.mgh.harvard.edu/plinkseq"
-SRC_URI="http://psychgen.u.hpc.mssm.edu/plinkseq_downloads/plinkseq-src-latest.tgz -> ${P}.tgz"
-# https://bitbucket.org/statgen/plinkseq.git
-# http://pngu.mgh.harvard.edu/~purcell/plink/download.shtml
-
-LICENSE="GPL-2"
-SLOT="0"
-KEYWORDS=""
-IUSE=""
-
-DEPEND="sys-libs/zlib
-	dev-libs/protobuf
-	!sci-biology/fsl" # file collision on /usr/bin/mm
-RDEPEND="${DEPEND}"
-
-src_prepare(){
-	sed -e "s/gcc/$(tc-getCC)/g;s/g++/$(tc-getCXX)/g;s/-O3/${CFLAGS}/g" -i config_defs.Makefile || die
-	sed -e "s/= -static/=/g" -i config_defs.Makefile || die
-	rm -rf sources/ext/protobuf-* || die
-	rm sources/ext/protobuf sources/ext/sources/include/google || die
-	rm -rf sources/mongoose || die
-	sed -e 's@^all:.*@all: # skipping compilation of bundled dev-libs/protobuf@' -i sources/ext/Makefile || die
-	# TODO: fix also sources/ext/sources/include/DUMMY/include/google/protobuf/compiler/plugin.proto causing:
-	# plugin.proto: Import "google/protobuf/descriptor.proto" was not found or had errors.
-	# plugin.proto:74:12: "FileDescriptorProto" is not defined.
-	find . -name \*.proto | while read f; do \
-		d=`dirname $f`; \
-		pushd $d; \
-		protoc --cpp_out=. *.proto || exit 255; \
-		popd; \
-	done || die
-	autotools-utils_src_prepare
-}
-
-src_install(){
-	cd build/execs || die
-	# TODO: avoid file collision with sci-biology/fsl
-	# https://bitbucket.org/statgen/plinkseq/issue/9/rename-mm-filename-to-plinkseq_mm
-	# TODO: avoid file collision with www-servers/mongoose
-	dobin gcol browser pseq behead mm smp tab2vcf pdas
-}
diff --git a/sci-biology/plinkseq/plinkseq-9999.ebuild b/sci-biology/plinkseq/plinkseq-9999.ebuild
deleted file mode 100644
index cffdaff97..000000000
--- a/sci-biology/plinkseq/plinkseq-9999.ebuild
+++ /dev/null
@@ -1,63 +0,0 @@
-# Copyright 1999-2017 Gentoo Foundation
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=5
-
-AUTOTOOLS_AUTORECONF=yes
-
-inherit toolchain-funcs git-r3
-
-DESCRIPTION="C/C++ library for working with human genetic variation data"
-HOMEPAGE="http://atgu.mgh.harvard.edu/plinkseq"
-EGIT_REPO_URI="https://bitbucket.org/statgen/plinkseq.git"
-# https://bitbucket.org/statgen/plinkseq/commits/all
-# http://pngu.mgh.harvard.edu/~purcell/plink/download.shtml
-
-LICENSE="GPL-2"
-SLOT="0"
-KEYWORDS=""
-IUSE=""
-
-DEPEND="sys-libs/zlib
-	dev-libs/protobuf
-	!sci-biology/fsl" # file collision on /usr/bin/mm
-RDEPEND="${DEPEND}"
-
-src_prepare(){
-	sed -e "s/gcc/$(tc-getCC)/g;s/g++/$(tc-getCXX)/g;s/-O3/${CFLAGS}/g" -i config_defs.Makefile || die
-	sed -e "s/= -static/=/g" -i config_defs.Makefile || die
-	rm -rf sources/ext/protobuf-* || die
-	rm sources/ext/protobuf sources/ext/sources/include/google || die
-	# we cannot zap calls to bundled mongoose because www-servers/mongoose does not build a library at all
-	# rm -rf sources/mongoose || die
-	# sed -e "s@$(MONGOOSE_LIB_DIR) @@;s@$(MONGOOSE_INC) @@;s@$(MONGOOSE_LIB_BASE_DIR) @@" - Makefile || die
-	sed -e 's@^all:.*@all: # skipping compilation of bundled dev-libs/protobuf@' -i sources/ext/Makefile || die
-	find . -name \*.proto | while read f; do \
-		d=`dirname $f`; \
-		pushd $d; \
-		protoc --cpp_out=. *.proto || exit 255; \
-		popd; \
-	done || die
-	#
-	# recopy the updated files
-	cp -p sources/plinkseq/sources/lib/matrix.pb.h sources/plinkseq/sources/include/plinkseq/matrix.pb.h || die
-	cp -p sources/plinkseq/sources/lib/variant.pb.h sources/plinkseq/sources/include/plinkseq/variant.pb.h || die
-	sed -e 's/google::protobuf::internal::kEmptyString/google::protobuf::internal::GetEmptyStringAlreadyInited()/g' -i sources/plinkseq/sources/lib/matrix.pb.cpp || die
-	sed -e 's/google::protobuf::internal::kEmptyString/google::protobuf::internal::GetEmptyStringAlreadyInited()/g' -i sources/plinkseq/sources/lib/variant.pb.cpp || die
-	local myinc=`pkg-config protobuf --variable=includedir`
-	sed -e 's@$(PROTOBUF_LIB_BASE_DIR)/$(INC_DIR)/@'"${myinc}@" -i Makefile || die
-	local mylib=`pkg-config protobuf --variable=libdir`
-	sed -e 's@$(PROTOBUF_LIB_BASE_DIR)/$(BLD_LIB_DIR)/@'"-L${mylib} @" -i Makefile || die # note the trailing space as it get prepended to PROTOBUF_LIBS
-	# anyway $(PROTOBUF_LIB_FULL_PATH) is a necessary build target, just drop it
-	sed -e 's@^PROTOBUF_LIB_FULL_PATH =.*/@PROTOBUF_LIB_FULL_PATH =@' -i Makefile || die
-	local mylibs=`pkg-config protobuf --libs`
-	sed -e "s@libprotobuf.a@ ${mylibs}@ " -i Makefile || die
-}
-
-src_install(){
-	cd build/execs || die
-	# TODO: avoid file collision with sci-biology/fsl
-	# https://bitbucket.org/statgen/plinkseq/issue/9/rename-mm-filename-to-plinkseq_mm
-	# TODO: avoid file collision with www-servers/mongoose
-	dobin gcol browser pseq behead mm smp tab2vcf pdas
-}
diff --git a/sci-biology/polyphen/Manifest b/sci-biology/polyphen/Manifest
deleted file mode 100644
index 60d0df7bb..000000000
--- a/sci-biology/polyphen/Manifest
+++ /dev/null
@@ -1 +0,0 @@
-DIST polyphen-2.2.2r405b.tar.gz 2189910 SHA256 25415a0dcc1149968d116fe5ffc8663c939bc4533a9fb660431a12a7ca4b4859 SHA512 0dfcce2bc1670416520149cc5d8544fd59a1586ac41bf96eb90d0425fdc60b19503acef196793b72cfaa9a7165d2d97c4868a7383eb7d7f17ec4b63cb92447d9 WHIRLPOOL be6b649536bb993eff5674ac09c2e2ad8ef3ea0d6e7d1eb72dd084167e103e8697530a0ee47cda7098bf97989937e55ef87de86da027d894f0c571f25e62ff50
diff --git a/sci-biology/polyphen/metadata.xml b/sci-biology/polyphen/metadata.xml
deleted file mode 100644
index 138cb7705..000000000
--- a/sci-biology/polyphen/metadata.xml
+++ /dev/null
@@ -1,12 +0,0 @@
-<?xml version="1.0" encoding="UTF-8"?>
-<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
-<pkgmetadata>
-	<maintainer type="person">
-		<email>mmokrejs@fold.natur.cuni.cz</email>
-		<name>Martin Mokrejs</name>
-	</maintainer>
-	<maintainer type="project">
-		<email>sci-biology@gentoo.org</email>
-		<name>Gentoo Biology Project</name>
-	</maintainer>
-</pkgmetadata>
diff --git a/sci-biology/polyphen/polyphen-2.2.2.ebuild b/sci-biology/polyphen/polyphen-2.2.2.ebuild
deleted file mode 100644
index 2bd569632..000000000
--- a/sci-biology/polyphen/polyphen-2.2.2.ebuild
+++ /dev/null
@@ -1,22 +0,0 @@
-# Copyright 1999-2015 Gentoo Foundation
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=5
-
-DESCRIPTION="Predict effect of aminoacid substitution on human protein function"
-HOMEPAGE="http://genetics.bwh.harvard.edu/pph2/dokuwiki/start"
-SRC_URI="http://genetics.bwh.harvard.edu/pph2/dokuwiki/_media/polyphen-2.2.2r405b.tar.gz"
-
-LICENSE="polyphen" # for non-commercial use only
-SLOT="0"
-KEYWORDS=""
-IUSE=""
-
-# 3.7GB
-# ftp://genetics.bwh.harvard.edu/pph2/bundled/polyphen-2.2.2-databases-2011_12.tar.bz2
-
-# 2.4GB
-# ftp://genetics.bwh.harvard.edu/pph2/bundled/polyphen-2.2.2-alignments-mlc-2011_12.tar.bz2
-
-# 895MB
-# ftp://genetics.bwh.harvard.edu/pph2/bundled/polyphen-2.2.2-alignments-multiz-2009_10.tar.bz2
diff --git a/sci-biology/poretools/Manifest b/sci-biology/poretools/Manifest
deleted file mode 100644
index eb69d6213..000000000
--- a/sci-biology/poretools/Manifest
+++ /dev/null
@@ -1 +0,0 @@
-DIST poretools-0.6.0.tar.gz 68959206 BLAKE2B f1a7259b141d1e6d7b3052a5b451967b71c755abd2ba694f3af4e949a8a4bdce92277deb85b657bca8a9942f675cb58005db77dc28b208c977627b25793a4ef8 SHA512 4d624c498199a8d968b6b379053c62f569e8278649c1ac944fbf6a83b198289e1e0dd89700daf54d7ad397dbe87a9819bec8852bb63feec69116985755427181
diff --git a/sci-biology/poretools/metadata.xml b/sci-biology/poretools/metadata.xml
deleted file mode 100644
index 138cb7705..000000000
--- a/sci-biology/poretools/metadata.xml
+++ /dev/null
@@ -1,12 +0,0 @@
-<?xml version="1.0" encoding="UTF-8"?>
-<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
-<pkgmetadata>
-	<maintainer type="person">
-		<email>mmokrejs@fold.natur.cuni.cz</email>
-		<name>Martin Mokrejs</name>
-	</maintainer>
-	<maintainer type="project">
-		<email>sci-biology@gentoo.org</email>
-		<name>Gentoo Biology Project</name>
-	</maintainer>
-</pkgmetadata>
diff --git a/sci-biology/poretools/poretools-0.6.0.ebuild b/sci-biology/poretools/poretools-0.6.0.ebuild
deleted file mode 100644
index 158c10a9d..000000000
--- a/sci-biology/poretools/poretools-0.6.0.ebuild
+++ /dev/null
@@ -1,27 +0,0 @@
-# Copyright 1999-2018 Gentoo Foundation
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=6
-
-PYTHON_COMPAT=( python2_7 )
-
-inherit distutils-r1
-
-DESCRIPTION="Tools for sequencing FAST5 data from Oxford Nanopore"
-HOMEPAGE="https://poretools.readthedocs.io
-	https://github.com/arq5x/poretools"
-SRC_URI="https://github.com/arq5x/poretools/archive/v0.6.0.tar.gz -> ${P}.tar.gz"
-
-LICENSE="MIT"
-SLOT="0"
-KEYWORDS="~amd64 ~x86"
-IUSE=""
-
-DEPEND=""
-RDEPEND="${DEPEND}
-	>=sci-libs/hdf5-1.8.7
-	>=dev-python/h5py-2.2[${PYTHON_USEDEP}]
-	dev-python/matplotlib[${PYTHON_USEDEP}]
-	dev-python/seaborn[${PYTHON_USEDEP}]
-	dev-python/pandas[${PYTHON_USEDEP}]
-	dev-python/python-dateutil[${PYTHON_USEDEP}]"
diff --git a/sci-biology/portrait/Manifest b/sci-biology/portrait/Manifest
index e89dc573b..42f67f850 100644
--- a/sci-biology/portrait/Manifest
+++ b/sci-biology/portrait/Manifest
@@ -1 +1 @@
-DIST portrait.tar.gz 12102665 BLAKE2B 9e270e9d78df541342582188794d1df1e3e7fe7da6e8262a898abc31e5bd70a2e8dbdd42da460653cf909a4ae22207f5885a5ff89350bac8cc623e37a9752cba SHA512 724abe0f7afbca22ee422095498033501e136530db51314f28538a72734e7b591fda4f557ecb47781f2b7408fb35586a33c9a214ad40e23bcc8912cdc16bbb1f
+DIST portrait-1.1.tar.gz 12102665 BLAKE2B 9e270e9d78df541342582188794d1df1e3e7fe7da6e8262a898abc31e5bd70a2e8dbdd42da460653cf909a4ae22207f5885a5ff89350bac8cc623e37a9752cba SHA512 724abe0f7afbca22ee422095498033501e136530db51314f28538a72734e7b591fda4f557ecb47781f2b7408fb35586a33c9a214ad40e23bcc8912cdc16bbb1f
diff --git a/sci-biology/portrait/portrait-1.1.ebuild b/sci-biology/portrait/portrait-1.1.ebuild
index 424ccfcd6..81da03922 100644
--- a/sci-biology/portrait/portrait-1.1.ebuild
+++ b/sci-biology/portrait/portrait-1.1.ebuild
@@ -1,16 +1,15 @@
-# Copyright 1999-2016 Gentoo Foundation
+# Copyright 1999-2021 Gentoo Authors
 # Distributed under the terms of the GNU General Public License v2
 
-EAPI=5
+EAPI=7
 
 DESCRIPTION="Ab initio ncRNA prediction"
 HOMEPAGE="http://bioinformatics.cenargen.embrapa.br/portrait"
-SRC_URI="http://bioinformatics.cenargen.embrapa.br/portrait/download/portrait.tar.gz"
+SRC_URI="http://bioinformatics.cenargen.embrapa.br/portrait/download/portrait.tar.gz -> ${P}.tar.gz"
 
 LICENSE="GPL-3+"
 SLOT="0"
-KEYWORDS=""
-IUSE=""
+KEYWORDS="~amd64"
 
 DEPEND=""
 RDEPEND="
@@ -22,7 +21,7 @@ RDEPEND="
 # was only tested with sci-libs/libsvm-2.84
 
 src_install(){
-	sed -e 's/
//' -i *.pl || die "Failed to convert from DOS line endings to Unix"
+	sed -e 's/\r//' -i *.pl || die "Failed to convert from DOS line endings to Unix"
 	sed -e 's#/home/rtarrial/prog#/usr/bin#' -i *.pl
 	dobin *.pl
 	dodoc README.txt
diff --git a/sci-biology/primerD/Manifest b/sci-biology/primerD/Manifest
deleted file mode 100644
index c63bc73c2..000000000
--- a/sci-biology/primerD/Manifest
+++ /dev/null
@@ -1 +0,0 @@
-DIST primerD-1.0.tar.gz 58132 BLAKE2B 4fdf1126649ba3bddb92852dacd14a4e4bf652715166f7c6d9ba23aa3ebe8ab7419cf939131e6bde09190c65e5ed04222172757ff642d7af9eb34bfadd9875eb SHA512 9f70ccb2a8304fe9e3a3885f2607969ca00483c1f3bb70ea3b5da709db0c43979cdd6bbf2b9ef805c13d215000afab2053fdeda66dc48006cb50f536886b86b2
diff --git a/sci-biology/primerD/metadata.xml b/sci-biology/primerD/metadata.xml
deleted file mode 100644
index 138cb7705..000000000
--- a/sci-biology/primerD/metadata.xml
+++ /dev/null
@@ -1,12 +0,0 @@
-<?xml version="1.0" encoding="UTF-8"?>
-<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
-<pkgmetadata>
-	<maintainer type="person">
-		<email>mmokrejs@fold.natur.cuni.cz</email>
-		<name>Martin Mokrejs</name>
-	</maintainer>
-	<maintainer type="project">
-		<email>sci-biology@gentoo.org</email>
-		<name>Gentoo Biology Project</name>
-	</maintainer>
-</pkgmetadata>
diff --git a/sci-biology/primerD/primerD-1.0.0.ebuild b/sci-biology/primerD/primerD-1.0.0.ebuild
deleted file mode 100644
index 7752926c3..000000000
--- a/sci-biology/primerD/primerD-1.0.0.ebuild
+++ /dev/null
@@ -1,26 +0,0 @@
-# Copyright 1999-2015 Gentoo Foundation
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=5
-
-inherit toolchain-funcs
-
-DESCRIPTION="Design degenerate primers"
-HOMEPAGE="http://mblab.wustl.edu/software.html"
-SRC_URI="http://mblab.wustl.edu/software/download/primerD.tar.gz -> primerD-1.0.tar.gz"
-
-LICENSE="LGPL-2.1"
-SLOT="0"
-KEYWORDS=""
-IUSE=""
-
-S="${WORKDIR}"/primerD
-
-src_prepare(){
-	sed -e "s:CC=g++:CC=$(tc-getCXX):; s:-Wall -g:${CFLAGS}:" -i Makefile || die
-}
-
-src_install(){
-	dodoc README
-	dobin primerD
-}
diff --git a/sci-biology/prinseq-lite/prinseq-lite-0.20.4.ebuild b/sci-biology/prinseq-lite/prinseq-lite-0.20.4.ebuild
index 6b4ca0b30..034fd86a5 100644
--- a/sci-biology/prinseq-lite/prinseq-lite-0.20.4.ebuild
+++ b/sci-biology/prinseq-lite/prinseq-lite-0.20.4.ebuild
@@ -1,7 +1,7 @@
-# Copyright 1999-2016 Gentoo Foundation
+# Copyright 1999-2021 Gentoo Authors
 # Distributed under the terms of the GNU General Public License v2
 
-EAPI=6
+EAPI=7
 
 DESCRIPTION="Describe, trim, reformat and convert to or form FASTA/FASTQ files"
 HOMEPAGE="http://prinseq.sourceforge.net/"
@@ -9,8 +9,7 @@ SRC_URI="https://sourceforge.net/projects/prinseq/files/standalone/${P}.tar.gz"
 
 LICENSE="GPL-3+"
 SLOT="0"
-KEYWORDS=""
-IUSE=""
+KEYWORDS="~amd64"
 
 DEPEND=""
 RDEPEND="${DEPEND}
diff --git a/sci-biology/proda/proda-1.0.ebuild b/sci-biology/proda/proda-1.0.ebuild
index 67def6a7e..0723b9512 100644
--- a/sci-biology/proda/proda-1.0.ebuild
+++ b/sci-biology/proda/proda-1.0.ebuild
@@ -1,11 +1,11 @@
-# Copyright 1999-2014 Gentoo Foundation
+# Copyright 1999-2021 Gentoo Authors
 # Distributed under the terms of the GNU General Public License v2
 
-EAPI=5
+EAPI=7
 
-inherit eutils flag-o-matic toolchain-funcs versionator
+inherit flag-o-matic toolchain-funcs
 
-MY_PV=$(replace_all_version_separators '_')
+MY_PV=${PV//./_}
 
 DESCRIPTION="Multiple alignment of protein sequences with repeated and shuffled elements"
 HOMEPAGE="http://proda.stanford.edu/"
@@ -13,7 +13,8 @@ SRC_URI="http://proda.stanford.edu/proda_${MY_PV}.tar.gz"
 
 LICENSE="public-domain"
 SLOT="0"
-IUSE="debug "
+IUSE="debug"
+
 KEYWORDS="~amd64 ~x86"
 
 S="${WORKDIR}"/${PN}
@@ -24,7 +25,7 @@ PATCHES=(
 	)
 
 src_prepare() {
-	epatch ${PATCHES[@]}
+	default
 	use debug || append-flags -DNDEBUG
 	tc-export CXX
 }
diff --git a/sci-biology/prokka/Manifest b/sci-biology/prokka/Manifest
deleted file mode 100644
index 0e683ece1..000000000
--- a/sci-biology/prokka/Manifest
+++ /dev/null
@@ -1 +0,0 @@
-DIST prokka-1.11.tar.gz 359226217 BLAKE2B 233c5234b839c0c18f03dcded2f89f2ad0bf8ccaceec1387fd6e5c9add4ab71698220031ed1d6cf6b38425bae924cd774fce5f622ea5e3fb01bf03fb30134692 SHA512 7b35d340ca07685886ff9ef97f0d40a28f05bc378a407a0349b06c8be9df005c4030b205a93985ec691fac4b6442a607f8723f3ca8f2066704f15b8667476034
diff --git a/sci-biology/prokka/metadata.xml b/sci-biology/prokka/metadata.xml
deleted file mode 100644
index 138cb7705..000000000
--- a/sci-biology/prokka/metadata.xml
+++ /dev/null
@@ -1,12 +0,0 @@
-<?xml version="1.0" encoding="UTF-8"?>
-<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
-<pkgmetadata>
-	<maintainer type="person">
-		<email>mmokrejs@fold.natur.cuni.cz</email>
-		<name>Martin Mokrejs</name>
-	</maintainer>
-	<maintainer type="project">
-		<email>sci-biology@gentoo.org</email>
-		<name>Gentoo Biology Project</name>
-	</maintainer>
-</pkgmetadata>
diff --git a/sci-biology/prokka/prokka-1.11.ebuild b/sci-biology/prokka/prokka-1.11.ebuild
deleted file mode 100644
index 06cc2a630..000000000
--- a/sci-biology/prokka/prokka-1.11.ebuild
+++ /dev/null
@@ -1,33 +0,0 @@
-# Copyright 1999-2015 Gentoo Foundation
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=5
-
-DESCRIPTION="Prokaryotic whole genome annotation pipeline"
-HOMEPAGE="http://www.bioinformatics.net.au/software.prokka.shtml"
-SRC_URI="http://www.vicbioinformatics.com/prokka-"${PV}".tar.gz"
-# 360MB
-
-LICENSE="GPL-2"
-SLOT="0"
-KEYWORDS="~amd64"
-IUSE=""
-
-DEPEND=""
-RDEPEND="${DEPEND}
-	sys-process/parallel
-	sci-biology/bioperl
-	sci-biology/prodigal
-	|| ( sci-biology/ncbi-tools++ sci-biology/ncbi-blast+ )
-	sci-biology/hmmer
-	sci-biology/infernal
-	sci-biology/exonerate
-	sci-biology/barrnap"
-# sci-biology/minced
-# >=sci-biolohy/hmmer-3.1
-# Aragorn
-# >=RNAmmer-1.2
-# >=HMMmmer-2.0 (that is not sci-biology/hmmer)
-# SignalP >= 3.0
-# sequin
-# tbl2asn >= 23.0 from wget --mirror -nH -nd ftp://ftp.ncbi.nih.gov/toolbox/ncbi_tools/converters/by_program/tbl2asn/linux64.tbl2asn.gz
diff --git a/sci-biology/proovread/metadata.xml b/sci-biology/proovread/metadata.xml
deleted file mode 100644
index 138cb7705..000000000
--- a/sci-biology/proovread/metadata.xml
+++ /dev/null
@@ -1,12 +0,0 @@
-<?xml version="1.0" encoding="UTF-8"?>
-<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
-<pkgmetadata>
-	<maintainer type="person">
-		<email>mmokrejs@fold.natur.cuni.cz</email>
-		<name>Martin Mokrejs</name>
-	</maintainer>
-	<maintainer type="project">
-		<email>sci-biology@gentoo.org</email>
-		<name>Gentoo Biology Project</name>
-	</maintainer>
-</pkgmetadata>
diff --git a/sci-biology/proovread/proovread-9999.ebuild b/sci-biology/proovread/proovread-9999.ebuild
deleted file mode 100644
index d8d3dc913..000000000
--- a/sci-biology/proovread/proovread-9999.ebuild
+++ /dev/null
@@ -1,54 +0,0 @@
-# Copyright 1999-2018 Gentoo Foundation
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=6
-
-[ "$PV" == "9999" ] && inherit git-r3
-
-inherit perl-functions toolchain-funcs
-
-DESCRIPTION="Error correct PacBio subreads using Illumina reads"
-HOMEPAGE="https://github.com/BioInf-Wuerzburg/proovread"
-if [ "$PV" == "9999" ]; then
-	EGIT_REPO_URI="https://github.com/BioInf-Wuerzburg/proovread"
-	KEYWORDS=""
-else
-	SRC_URI=""
-	KEYWORDS="~amd64 ~x86" # issue #125
-fi
-
-LICENSE="Artistic-2 GPL-3"
-SLOT="0"
-IUSE=""
-
-# needs Fasta::Parser
-RDEPEND="
-	>=dev-lang/perl-5.10
-	dev-perl/Log-Log4perl
-	dev-perl/File-Which
-	>=sci-biology/ncbi-tools++-2.2.24
-	>=sci-biology/samtools-1.1"
-DEPEND="${RDEPEND}
-	>=sci-biology/shrimp-2
-	sci-biology/blasr"
-
-src_install(){
-	cd bin || die
-	dobin ChimeraToSeqFilter.pl dazz2sam ccseq bam2cns test_cfg.pl siamaera samfilter sam2cns proovread-flex proovread
-	cd ../util/bwa || die
-	dobin bwa-proovread # xa2multi.pl qualfa2fq.pl libbwa.a bwa.1
-	cd ../../util/SeqFilter || die
-	dobin bin/SeqFilter
-	cd ../../util/SeqChunker || die
-	dobin bin/*
-	cd ../../lib || die
-	perl_domodule -r -C ${PN} *
-	# cd ../util/blasr-1.3.1 || die
-	# dobin blasr
-	# dodoc LICENSE.txt
-}
-
-pkg_postinst(){
-	einfo "Proovread uses its own, modified version of bwa as bwa-proovread"
-	einfo "with linked in libbwa.a. It also bundles shrimp2 and blasr"
-}
diff --git a/sci-biology/prot4EST/Manifest b/sci-biology/prot4EST/Manifest
deleted file mode 100644
index b010efd0e..000000000
--- a/sci-biology/prot4EST/Manifest
+++ /dev/null
@@ -1 +0,0 @@
-DIST prot4EST_rl3.1b.tgz 21869514 BLAKE2B eeafdd97482ff397c54d85195069471756b7dca685c9e066038aa78fbd76a84a907e2b0b16b4912c445644aedf2bea7117eb4ebd857a644c337154bdbfb8bf98 SHA512 0768d36066c9d0f88ce53100ffaf71cdb27bb75ab2e36cc0f5950ac5995292bb31c3226033b17acbaf43f002474df4ddafed7bc2cf4e454bcd3282e85656ff78
diff --git a/sci-biology/prot4EST/metadata.xml b/sci-biology/prot4EST/metadata.xml
deleted file mode 100644
index 138cb7705..000000000
--- a/sci-biology/prot4EST/metadata.xml
+++ /dev/null
@@ -1,12 +0,0 @@
-<?xml version="1.0" encoding="UTF-8"?>
-<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
-<pkgmetadata>
-	<maintainer type="person">
-		<email>mmokrejs@fold.natur.cuni.cz</email>
-		<name>Martin Mokrejs</name>
-	</maintainer>
-	<maintainer type="project">
-		<email>sci-biology@gentoo.org</email>
-		<name>Gentoo Biology Project</name>
-	</maintainer>
-</pkgmetadata>
diff --git a/sci-biology/prot4EST/prot4EST-3.1b.ebuild b/sci-biology/prot4EST/prot4EST-3.1b.ebuild
deleted file mode 100644
index 344a0b383..000000000
--- a/sci-biology/prot4EST/prot4EST-3.1b.ebuild
+++ /dev/null
@@ -1,38 +0,0 @@
-# Copyright 1999-2016 Gentoo Foundation
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=5
-
-inherit perl-module
-
-DESCRIPTION="Predict proteins from EST sequences overcoming frameshifts"
-HOMEPAGE="http://www.compsysbio.org/lab/?q=prot4EST
-	http://www.biomedcentral.com/1471-2105/5/187"
-SRC_URI="http://www.compsysbio.org/lab/james/prot4EST_rl3.1b.tgz"
-
-LICENSE="GPL-1"
-SLOT="0"
-KEYWORDS=""
-IUSE=""
-
-DEPEND="sci-biology/emboss
-	sci-biology/estscan
-	sci-biology/bioperl
-	sci-biology/ncbi-tools
-	virtual/perl-File-Path
-	virtual/perl-Getopt-Long
-	dev-perl/Statistics-Descriptive
-	dev-perl/Tie-IxHash
-	dev-perl/Algorithm-Loops"
-	# sci-biology/DECODER
-RDEPEND="${DEPEND}"
-
-S="${WORKDIR}"/"p4e3.1b"
-
-src_install(){
-	mydoc="README INSTALL"
-	perl-module_src_install
-	mv bin/prot4EST*.pl bin/prot4EST.pl
-	dobin bin/*.pl
-	dodoc doc/*
-}
diff --git a/sci-biology/psx/Manifest b/sci-biology/psx/Manifest
index f60969934..2d1c14e4e 100644
--- a/sci-biology/psx/Manifest
+++ b/sci-biology/psx/Manifest
@@ -1 +1 @@
-DIST psx.tar.gz 7797 BLAKE2B db6d67b8e68b98f6e01c7a10bd1d5e11c6b67f82bb454bb25b9c2a44e2698a7ff535fd6a4306895a869456e8e5883b6d33977966ded02d80e38419a009ed654e SHA512 3a5adc6bf73cb8c2090d2c579171508058e097dabb5565ba27be221181e5298a66c1e58980549dfd84daadf2439205954e85aebf32862f48cf048463560b64f4
+DIST psx-0.1.tar.gz 7797 BLAKE2B db6d67b8e68b98f6e01c7a10bd1d5e11c6b67f82bb454bb25b9c2a44e2698a7ff535fd6a4306895a869456e8e5883b6d33977966ded02d80e38419a009ed654e SHA512 3a5adc6bf73cb8c2090d2c579171508058e097dabb5565ba27be221181e5298a66c1e58980549dfd84daadf2439205954e85aebf32862f48cf048463560b64f4
diff --git a/sci-biology/psx/psx-0.1.ebuild b/sci-biology/psx/psx-0.1.ebuild
index d9ebb989c..2595fb697 100644
--- a/sci-biology/psx/psx-0.1.ebuild
+++ b/sci-biology/psx/psx-0.1.ebuild
@@ -1,20 +1,19 @@
-# Copyright 1999-2015 Gentoo Foundation
+# Copyright 1999-2021 Gentoo Authors
 # Distributed under the terms of the GNU General Public License v2
 
-EAPI=5
+EAPI=7
 
 inherit toolchain-funcs
 
 DESCRIPTION="parallel multi-FASTA file processing tool from TIGR Gene Indices project tools"
-HOMEPAGE="http://compbio.dfci.harvard.edu/tgi/software/"
-SRC_URI="ftp://occams.dfci.harvard.edu/pub/bio/tgi/software/tgicl/${PN}.tar.gz"
+HOMEPAGE="https://web.archive.org/web/20140726030702/http://compbio.dfci.harvard.edu/tgi/software/"
+SRC_URI="ftp://occams.dfci.harvard.edu/pub/bio/tgi/software/tgicl/${PN}.tar.gz -> ${P}.tar.gz"
 
 LICENSE="Artistic"
 SLOT="0"
 KEYWORDS="~amd64 ~x86"
-IUSE=""
 
-S=${WORKDIR}
+S="${WORKDIR}"
 
 src_compile() {
 	emake \
diff --git a/sci-biology/psychopy/Manifest b/sci-biology/psychopy/Manifest
deleted file mode 100644
index a856f1c06..000000000
--- a/sci-biology/psychopy/Manifest
+++ /dev/null
@@ -1,3 +0,0 @@
-DIST psychopy-1.84.0.tar.gz 15370622 BLAKE2B 33da59a906437e2d6507076fa329e90a22a2ee55df66c79a3b0b62a92bebacb91d38bab2025d4f64d3283b6684c8b3ebfd249f9f92fc4e0b5f99d3d01fa58179 SHA512 24199ad0d680e7dbafa9328510d5cf405c5fd664767e7f9e5e497f8fd87a7ce7bd3fcf80cf9f833884e9adcf5cf5c3c0b654994bfcfe8148b987a475133235c6
-DIST psychopy-1.84.1.tar.gz 15371195 BLAKE2B 08428183c508c07bfed88063f845afcc2e3b8109094838e20db92d1e491de4e765c3210d751cafbb496ffc97a920be8831f7373503ad290854172d50190fa808 SHA512 1d9f114c89e10c8ea6d080e2d0245e7ee505301eb3f9326f03f118f12898c441b1afecd46455e206d35218b122db5411b901356ff8fb1e0d568ed2318b7bd961
-DIST psychopy-1.84.2.tar.gz 15373437 BLAKE2B 213cbb533a223ab82688f778f2f21fafd9a78f727ec0e5d48bbd7085cb6a12c0eb0fe0ee1e738df38a806999ad2353ba5b140e3e08f02c3e650a070266df1a5f SHA512 edc74507c60e3d3fe98bdca85bc2010e945d500df819a067024141fa5d19f5a42e5bac81bf61d0f237d8e8783b2b5686346ade4de3066378248bfd9496fe5b17
diff --git a/sci-biology/psychopy/metadata.xml b/sci-biology/psychopy/metadata.xml
deleted file mode 100644
index 2c3fbd8bb..000000000
--- a/sci-biology/psychopy/metadata.xml
+++ /dev/null
@@ -1,11 +0,0 @@
-<?xml version="1.0" encoding="UTF-8"?>
-<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
-<pkgmetadata>
-	<maintainer type="person">
-		<email>horea.christ@gmail.com</email>
-		<name>Horea Christian</name>
-	</maintainer>
-	<upstream>
-		<remote-id type="github">psychopy/psychopy</remote-id>
-	</upstream>
-</pkgmetadata>
diff --git a/sci-biology/psychopy/psychopy-1.84.0.ebuild b/sci-biology/psychopy/psychopy-1.84.0.ebuild
deleted file mode 100644
index 3ae39347a..000000000
--- a/sci-biology/psychopy/psychopy-1.84.0.ebuild
+++ /dev/null
@@ -1,49 +0,0 @@
-# Copyright 1999-2016 Gentoo Foundation
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=6
-
-PYTHON_COMPAT=( python2_7 )
-PYTHON_REQ_USE="threads(+)"
-
-inherit eutils gnome2-utils distutils-r1
-
-DESCRIPTION="Python experimental psychology toolkit"
-HOMEPAGE="http://www.psychopy.org/"
-SRC_URI="https://github.com/psychopy/psychopy/archive/v${PV}.tar.gz -> ${P}.tar.gz"
-
-LICENSE="GPL-3+"
-SLOT="0"
-KEYWORDS="~amd64 ~x86"
-
-DEPEND="
-	dev-python/setuptools[${PYTHON_USEDEP}]
-	"
-RDEPEND="
-	dev-python/configobj[${PYTHON_USEDEP}]
-	dev-python/lxml[${PYTHON_USEDEP}]
-	dev-python/matplotlib[${PYTHON_USEDEP}]
-	dev-python/moviepy[${PYTHON_USEDEP}]
-	dev-python/numpy[lapack,${PYTHON_USEDEP}]
-	dev-python/pillow[${PYTHON_USEDEP}]
-	dev-python/pygame[${PYTHON_USEDEP}]
-	dev-python/pyglet[${PYTHON_USEDEP}]
-	dev-python/pyopengl[${PYTHON_USEDEP}]
-	dev-python/wxpython:*[${PYTHON_USEDEP}]
-	media-libs/avbin-bin
-	media-libs/opencv[python,${PYTHON_USEDEP}]
-	sci-libs/scipy[${PYTHON_USEDEP}]
-	"
-
-python_install_all() {
-	distutils-r1_python_install_all
-	newicon -s scalable psychopy/monitors/psychopy-icon.svg psychopy.svg
-	make_desktop_entry psychopyApp.py PsychoPy psychopy
-}
-
-pkg_postinst() {
-	gnome2_icon_cache_update
-}
-pkg_postrm() {
-	gnome2_icon_cache_update
-}
diff --git a/sci-biology/psychopy/psychopy-1.84.1.ebuild b/sci-biology/psychopy/psychopy-1.84.1.ebuild
deleted file mode 100644
index fd51715ff..000000000
--- a/sci-biology/psychopy/psychopy-1.84.1.ebuild
+++ /dev/null
@@ -1,49 +0,0 @@
-# Copyright 1999-2016 Gentoo Foundation
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=6
-
-PYTHON_COMPAT=( python2_7 )
-PYTHON_REQ_USE="threads(+)"
-
-inherit eutils gnome2-utils distutils-r1
-
-DESCRIPTION="Python experimental psychology toolkit"
-HOMEPAGE="http://www.psychopy.org/"
-SRC_URI="https://github.com/psychopy/psychopy/archive/${PV}.tar.gz -> ${P}.tar.gz"
-
-LICENSE="GPL-3+"
-SLOT="0"
-KEYWORDS="~amd64 ~x86"
-
-DEPEND="
-	dev-python/setuptools[${PYTHON_USEDEP}]
-	"
-RDEPEND="
-	dev-python/configobj[${PYTHON_USEDEP}]
-	dev-python/lxml[${PYTHON_USEDEP}]
-	dev-python/matplotlib[${PYTHON_USEDEP}]
-	dev-python/moviepy[${PYTHON_USEDEP}]
-	dev-python/numpy[lapack,${PYTHON_USEDEP}]
-	dev-python/pillow[${PYTHON_USEDEP}]
-	dev-python/pygame[${PYTHON_USEDEP}]
-	dev-python/pyglet[${PYTHON_USEDEP}]
-	dev-python/pyopengl[${PYTHON_USEDEP}]
-	dev-python/wxpython:*[${PYTHON_USEDEP}]
-	media-libs/avbin-bin
-	media-libs/opencv[python,${PYTHON_USEDEP}]
-	sci-libs/scipy[${PYTHON_USEDEP}]
-	"
-
-python_install_all() {
-	distutils-r1_python_install_all
-	newicon -s scalable psychopy/monitors/psychopy-icon.svg psychopy.svg
-	make_desktop_entry psychopyApp.py PsychoPy psychopy
-}
-
-pkg_postinst() {
-	gnome2_icon_cache_update
-}
-pkg_postrm() {
-	gnome2_icon_cache_update
-}
diff --git a/sci-biology/psychopy/psychopy-1.84.2.ebuild b/sci-biology/psychopy/psychopy-1.84.2.ebuild
deleted file mode 100644
index fd51715ff..000000000
--- a/sci-biology/psychopy/psychopy-1.84.2.ebuild
+++ /dev/null
@@ -1,49 +0,0 @@
-# Copyright 1999-2016 Gentoo Foundation
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=6
-
-PYTHON_COMPAT=( python2_7 )
-PYTHON_REQ_USE="threads(+)"
-
-inherit eutils gnome2-utils distutils-r1
-
-DESCRIPTION="Python experimental psychology toolkit"
-HOMEPAGE="http://www.psychopy.org/"
-SRC_URI="https://github.com/psychopy/psychopy/archive/${PV}.tar.gz -> ${P}.tar.gz"
-
-LICENSE="GPL-3+"
-SLOT="0"
-KEYWORDS="~amd64 ~x86"
-
-DEPEND="
-	dev-python/setuptools[${PYTHON_USEDEP}]
-	"
-RDEPEND="
-	dev-python/configobj[${PYTHON_USEDEP}]
-	dev-python/lxml[${PYTHON_USEDEP}]
-	dev-python/matplotlib[${PYTHON_USEDEP}]
-	dev-python/moviepy[${PYTHON_USEDEP}]
-	dev-python/numpy[lapack,${PYTHON_USEDEP}]
-	dev-python/pillow[${PYTHON_USEDEP}]
-	dev-python/pygame[${PYTHON_USEDEP}]
-	dev-python/pyglet[${PYTHON_USEDEP}]
-	dev-python/pyopengl[${PYTHON_USEDEP}]
-	dev-python/wxpython:*[${PYTHON_USEDEP}]
-	media-libs/avbin-bin
-	media-libs/opencv[python,${PYTHON_USEDEP}]
-	sci-libs/scipy[${PYTHON_USEDEP}]
-	"
-
-python_install_all() {
-	distutils-r1_python_install_all
-	newicon -s scalable psychopy/monitors/psychopy-icon.svg psychopy.svg
-	make_desktop_entry psychopyApp.py PsychoPy psychopy
-}
-
-pkg_postinst() {
-	gnome2_icon_cache_update
-}
-pkg_postrm() {
-	gnome2_icon_cache_update
-}
diff --git a/sci-biology/psychopy/psychopy-9999.ebuild b/sci-biology/psychopy/psychopy-9999.ebuild
deleted file mode 100644
index e15f3ac38..000000000
--- a/sci-biology/psychopy/psychopy-9999.ebuild
+++ /dev/null
@@ -1,50 +0,0 @@
-# Copyright 1999-2016 Gentoo Foundation
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=6
-
-PYTHON_COMPAT=( python2_7 )
-PYTHON_REQ_USE="threads(+)"
-
-inherit eutils gnome2-utils distutils-r1 git-r3
-
-DESCRIPTION="Python experimental psychology toolkit"
-HOMEPAGE="http://www.psychopy.org/"
-SRC_URI=""
-EGIT_REPO_URI="https://github.com/psychopy/psychopy.git"
-
-LICENSE="GPL-3+"
-SLOT="0"
-KEYWORDS=""
-
-DEPEND="
-	dev-python/setuptools[${PYTHON_USEDEP}]
-	"
-RDEPEND="
-	dev-python/configobj[${PYTHON_USEDEP}]
-	dev-python/lxml[${PYTHON_USEDEP}]
-	dev-python/matplotlib[${PYTHON_USEDEP}]
-	dev-python/moviepy[${PYTHON_USEDEP}]
-	dev-python/numpy[lapack,${PYTHON_USEDEP}]
-	dev-python/pillow[${PYTHON_USEDEP}]
-	dev-python/pygame[${PYTHON_USEDEP}]
-	dev-python/pyglet[${PYTHON_USEDEP}]
-	dev-python/pyopengl[${PYTHON_USEDEP}]
-	dev-python/wxpython:*[${PYTHON_USEDEP}]
-	media-libs/avbin-bin
-	media-libs/opencv[python,${PYTHON_USEDEP}]
-	sci-libs/scipy[${PYTHON_USEDEP}]
-	"
-
-python_install_all() {
-	distutils-r1_python_install_all
-	newicon -s scalable psychopy/monitors/psychopy-icon.svg psychopy.svg
-	make_desktop_entry psychopyApp.py PsychoPy psychopy
-}
-
-pkg_postinst() {
-	gnome2_icon_cache_update
-}
-pkg_postrm() {
-	gnome2_icon_cache_update
-}
diff --git a/sci-biology/pvmsx/Manifest b/sci-biology/pvmsx/Manifest
deleted file mode 100644
index e9dcc9384..000000000
--- a/sci-biology/pvmsx/Manifest
+++ /dev/null
@@ -1,2 +0,0 @@
-DIST cdbfasta.tar.gz 59735 BLAKE2B 69107a42e1b8069a70de9333891e050785cabaf6457245b4512c3725dc576ebfba54c43c3d1e356948061cf903a89a8aa0f011efbf36a4cda6b40a623f7019fe SHA512 500b3cdf4bf4e21c78a285739c6544e3f2bed377f8e3858c8ace240a9107d765c89cff8004ca2ea001860abc04fc48bc37c03569da5b16115f4419f5fd9bcd5e
-DIST pvmsx.tar.gz 10963 BLAKE2B 0ff27593754534e670b442270e4796f79570de44e9a7200b301ee60ab71bb9ce20dd7f8154d9ee7a6af1cf3540488f48eea0ed96d7471c7c7ee3f85842a5a056 SHA512 065bc0047e76e1fc4d7b368c53e285d312798fdb283b06aa689a4be593cebaa8086126bf996faefb9d582418603c8379eaf4f7551289e35bf33b2916fc79bb7c
diff --git a/sci-biology/pvmsx/metadata.xml b/sci-biology/pvmsx/metadata.xml
deleted file mode 100644
index 138cb7705..000000000
--- a/sci-biology/pvmsx/metadata.xml
+++ /dev/null
@@ -1,12 +0,0 @@
-<?xml version="1.0" encoding="UTF-8"?>
-<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
-<pkgmetadata>
-	<maintainer type="person">
-		<email>mmokrejs@fold.natur.cuni.cz</email>
-		<name>Martin Mokrejs</name>
-	</maintainer>
-	<maintainer type="project">
-		<email>sci-biology@gentoo.org</email>
-		<name>Gentoo Biology Project</name>
-	</maintainer>
-</pkgmetadata>
diff --git a/sci-biology/pvmsx/pvmsx-0.1.ebuild b/sci-biology/pvmsx/pvmsx-0.1.ebuild
deleted file mode 100644
index b88863a45..000000000
--- a/sci-biology/pvmsx/pvmsx-0.1.ebuild
+++ /dev/null
@@ -1,43 +0,0 @@
-# Copyright 1999-2015 Gentoo Foundation
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=5
-
-DESCRIPTION="Parallel multi-FASTA file processing tool"
-HOMEPAGE="http://compbio.dfci.harvard.edu/tgi/software/"
-SRC_URI="
-	ftp://occams.dfci.harvard.edu/pub/bio/tgi/software/tgicl/${PN}.tar.gz
-	ftp://occams.dfci.harvard.edu/pub/bio/tgi/software/tgicl/cdbfasta.tar.gz"
-
-LICENSE="Artistic"
-SLOT="0"
-KEYWORDS="~amd64 ~x86"
-IUSE=""
-
-#DEPEND="sys-cluster/pvm"
-#RDEPEND="${DEPEND}"
-
-S=${WORKDIR}
-
-src_prepare() {
-	# we need gclib from cdbfasta.tar.gz bundle which has fewer files than tgi_cpp_library.tar.gz wbut has e.g. GStr.h
-	sed \
-		-e 's/CFLAGS[ ]*=/CFLAGS :=/; s/-D_REENTRANT/-D_REENTRANT \${CFLAGS}/; s/CFLAGS[ ]*:=[ ]*-O2$//' \
-		-i "${S}"/Makefile || die "Failed to run sed"
-	sed \
-		-e 's#GCLDIR := ../gclib#GCLDIR := ../cdbfasta/gclib#' \
-		-i "${S}"/Makefile || die
-	sed \
-		-e "s#-I-#-iquote#" \
-		-i "${S}"/Makefile || die
-	ln -s ../cdbfasta/gcl . || die "Cannot make a softlink"
-}
-
-src_compile() {
-	default
-}
-
-src_install() {
-	dobin ${PN}
-	newdoc README README.${PN}
-}
diff --git a/sci-biology/pybedtools/Manifest b/sci-biology/pybedtools/Manifest
index 60c219413..a952ac4b8 100644
--- a/sci-biology/pybedtools/Manifest
+++ b/sci-biology/pybedtools/Manifest
@@ -1 +1,2 @@
-DIST pybedtools-0.6.9.tar.gz 18738115 BLAKE2B 81f9057129d65b92106b254b9ae6c74d59e359a28847af45e26d25090d8787003038cc93db552d6b9ce4c9588efd48f2d0b7155591f6f305222cbfff7154cadc SHA512 64d54145899db947499b706310941980c75b515cb8d88f67708153b625d782e62021826b9615dd4fe225f4435d9c9d4aa8583538109308625f703883599aeb79
+DIST pybedtools-0.8.2.tar.gz 12496355 BLAKE2B f1ff67f524a5a51a6f6a5450bb72ecd6602fe41232c77a38838b9b4051c528abadaa65d561bbef69cb595624a7f2edee8b98927ca0e7a55d5352e56e17f81d64 SHA512 4534c0ff4eeebbe8e3b1f126563700e4ba2b212581a76106d89fa8c61e043974b76649bf68d0b78f45923d66eb63c44bc69994de1f5a42e5069a761a93b8acbe
+DIST pybedtools-0.9.0.tar.gz 12497249 BLAKE2B f43c94a7dae773b2ca46c0105d4de57f4e93a095f168b67771a568b64bc088b517e160da27ef68d81fea3df75689cad1a3db2b25dda36a37ed688e4e426fe43a SHA512 aa0cca035d560bd4e4d39f6eac74e677e3bac3266af5b69ceca1c4878742220d576d0db9ebf9c8da490d24259b1153e9999a78d2a5c46f1acb544fa3dba73a18
diff --git a/sci-biology/pybedtools/pybedtools-0.6.9.ebuild b/sci-biology/pybedtools/pybedtools-0.6.9.ebuild
deleted file mode 100644
index f0d497802..000000000
--- a/sci-biology/pybedtools/pybedtools-0.6.9.ebuild
+++ /dev/null
@@ -1,21 +0,0 @@
-# Copyright 1999-2015 Gentoo Foundation
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=5
-
-PYTHON_COMPAT=( python2_7 )
-
-inherit distutils-r1
-
-DESCRIPTION="Wrapper for Aaron Quinlan's BEDtools, plus other useful methods for working"
-HOMEPAGE="http://pythonhosted.org/pybedtools/"
-SRC_URI="https://github.com/daler/pybedtools/archive/v${PV}.tar.gz -> ${P}.tar.gz"
-
-LICENSE="MIT"
-SLOT="0"
-KEYWORDS="~amd64 ~x86 ~amd64-linux ~x86-linux"
-IUSE=""
-
-RDEPEND="sci-biology/bedtools"
-DEPEND="${RDEPEND}
-	dev-python/cython[${PYTHON_USEDEP}]"
diff --git a/sci-biology/pybedtools/pybedtools-0.8.2.ebuild b/sci-biology/pybedtools/pybedtools-0.8.2.ebuild
new file mode 100644
index 000000000..bc02bda6f
--- /dev/null
+++ b/sci-biology/pybedtools/pybedtools-0.8.2.ebuild
@@ -0,0 +1,43 @@
+# Copyright 1999-2023 Gentoo Authors
+# Distributed under the terms of the GNU General Public License v2
+
+EAPI=8
+
+PYTHON_COMPAT=( python3_{10..11} )
+DISTUTILS_USE_PEP517=setuptools
+
+inherit distutils-r1
+
+DESCRIPTION="Use BED and GFF files from python using BEDtools"
+HOMEPAGE="https://daler.github.io/pybedtools"
+SRC_URI="https://github.com/daler/pybedtools/archive/v${PV}.tar.gz -> ${P}.tar.gz"
+
+LICENSE="MIT"
+SLOT="0"
+KEYWORDS="~amd64 ~x86"
+
+RDEPEND="
+	sci-biology/bedtools
+	sci-biology/pysam[${PYTHON_USEDEP}]
+	dev-python/six[${PYTHON_USEDEP}]
+	dev-python/numpy[${PYTHON_USEDEP}]
+	dev-python/pandas[${PYTHON_USEDEP}]
+	dev-python/matplotlib[${PYTHON_USEDEP}]
+"
+
+BDEPEND="dev-python/cython[${PYTHON_USEDEP}]"
+
+# TODO: fix docs building
+# ModuleNotFoundError: No module named 'pybedtools.cbedtools'
+# even if pybedtools is installed
+#distutils_enable_sphinx docs/source
+distutils_enable_tests pytest
+
+python_test() {
+	# Requires network
+	local EPYTEST_DESELECT=(
+		test/test_helpers.py::test_chromsizes
+	)
+	cd "${T}" || die
+	epytest --pyargs pybedtools
+}
diff --git a/sci-biology/pybedtools/pybedtools-0.9.0.ebuild b/sci-biology/pybedtools/pybedtools-0.9.0.ebuild
new file mode 100644
index 000000000..bc02bda6f
--- /dev/null
+++ b/sci-biology/pybedtools/pybedtools-0.9.0.ebuild
@@ -0,0 +1,43 @@
+# Copyright 1999-2023 Gentoo Authors
+# Distributed under the terms of the GNU General Public License v2
+
+EAPI=8
+
+PYTHON_COMPAT=( python3_{10..11} )
+DISTUTILS_USE_PEP517=setuptools
+
+inherit distutils-r1
+
+DESCRIPTION="Use BED and GFF files from python using BEDtools"
+HOMEPAGE="https://daler.github.io/pybedtools"
+SRC_URI="https://github.com/daler/pybedtools/archive/v${PV}.tar.gz -> ${P}.tar.gz"
+
+LICENSE="MIT"
+SLOT="0"
+KEYWORDS="~amd64 ~x86"
+
+RDEPEND="
+	sci-biology/bedtools
+	sci-biology/pysam[${PYTHON_USEDEP}]
+	dev-python/six[${PYTHON_USEDEP}]
+	dev-python/numpy[${PYTHON_USEDEP}]
+	dev-python/pandas[${PYTHON_USEDEP}]
+	dev-python/matplotlib[${PYTHON_USEDEP}]
+"
+
+BDEPEND="dev-python/cython[${PYTHON_USEDEP}]"
+
+# TODO: fix docs building
+# ModuleNotFoundError: No module named 'pybedtools.cbedtools'
+# even if pybedtools is installed
+#distutils_enable_sphinx docs/source
+distutils_enable_tests pytest
+
+python_test() {
+	# Requires network
+	local EPYTEST_DESELECT=(
+		test/test_helpers.py::test_chromsizes
+	)
+	cd "${T}" || die
+	epytest --pyargs pybedtools
+}
diff --git a/sci-biology/pybrain/Manifest b/sci-biology/pybrain/Manifest
deleted file mode 100644
index 9acb5c6de..000000000
--- a/sci-biology/pybrain/Manifest
+++ /dev/null
@@ -1 +0,0 @@
-DIST pybrain-0.3.3.tar.gz 1179157 BLAKE2B 0bd96a4e0dc1626f50e9970a7d3dacc569a3fe63ec8fd7412e662eb347356ec2422ee4e1957025232078b097ee9a048cdcacd6e1156803cc25bf27aa771ece70 SHA512 d0b0401b083cf62260b65c833a12e71ac8d5d3079f24cce3eccccb7109a68493b1795b38603cf64251cc1653bec3ea00308fa6bc792d73c265d7cb4da0970ab1
diff --git a/sci-biology/pybrain/metadata.xml b/sci-biology/pybrain/metadata.xml
deleted file mode 100644
index a5d6d4bfc..000000000
--- a/sci-biology/pybrain/metadata.xml
+++ /dev/null
@@ -1,11 +0,0 @@
-<?xml version="1.0" encoding="UTF-8"?>
-<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
-<pkgmetadata>
-	<maintainer type="project">
-		<email>sci@gentoo.org</email>
-		<name>Gentoo Science Project</name>
-	</maintainer>
-	<upstream>
-		<remote-id type="github">pybrain/pybrain</remote-id>
-	</upstream>
-</pkgmetadata>
diff --git a/sci-biology/pybrain/pybrain-0.3.3.ebuild b/sci-biology/pybrain/pybrain-0.3.3.ebuild
deleted file mode 100644
index 56715c985..000000000
--- a/sci-biology/pybrain/pybrain-0.3.3.ebuild
+++ /dev/null
@@ -1,27 +0,0 @@
-# Copyright 1999-2016 Gentoo Foundation
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=6
-
-PYTHON_COMPAT=( python{2_7,3_4,3_5} )
-
-inherit distutils-r1
-
-DESCRIPTION="The Python Machine Learning Library"
-HOMEPAGE="http://pybrain.org/"
-SRC_URI="https://github.com/pybrain/pybrain/archive/${PV}.tar.gz -> ${P}.tar.gz"
-
-LICENSE="BSD"
-SLOT="0"
-KEYWORDS="~amd64 ~x86"
-IUSE="test"
-
-RDEPEND="sci-libs/scipy[${PYTHON_USEDEP}]"
-DEPEND="
-	dev-python/setuptools[${PYTHON_USEDEP}]
-	test? (	${RDEPEND} )
-	"
-
-python_test() {
-	python pybrain/tests/runtests.py || die
-}
diff --git a/sci-biology/pybrain/pybrain-9999.ebuild b/sci-biology/pybrain/pybrain-9999.ebuild
deleted file mode 100644
index a0322e505..000000000
--- a/sci-biology/pybrain/pybrain-9999.ebuild
+++ /dev/null
@@ -1,28 +0,0 @@
-# Copyright 1999-2018 Gentoo Foundation
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=6
-
-PYTHON_COMPAT=( python{2_7,3_4,3_5} )
-
-inherit distutils-r1 git-r3
-
-DESCRIPTION="The Python Machine Learning Library"
-HOMEPAGE="http://pybrain.org/"
-SRC_URI=""
-EGIT_REPO_URI="https://github.com/pybrain/pybrain.git"
-
-LICENSE="BSD"
-SLOT="0"
-KEYWORDS=""
-IUSE="test"
-
-RDEPEND="sci-libs/scipy[${PYTHON_USEDEP}]"
-DEPEND="
-	dev-python/setuptools[${PYTHON_USEDEP}]
-	test? ( ${RDEPEND} )
-	"
-
-python_test() {
-	python pybrain/tests/runtests.py || die
-}
diff --git a/sci-biology/pyfaidx/Manifest b/sci-biology/pyfaidx/Manifest
index da863afee..0bb3b35f4 100644
--- a/sci-biology/pyfaidx/Manifest
+++ b/sci-biology/pyfaidx/Manifest
@@ -1 +1,2 @@
-DIST pyfaidx-0.4.8.1.tar.gz 22154 BLAKE2B af1840e86624facf3bfdfd0a09e9f48becd36adb4342db942238fa1a2976a3092c09f8631690acafeb3295dead5cbf23ba7969ff7fcb08287fb843680223f81c SHA512 1fc13bc40885b44eaa6846f3cbc119f52dc2e06c3d35736095678dc8db987412ea3693572ad837729039a643eba1b07a5db33dfde4acd4e92a43e156c1d523c3
+DIST pyfaidx-0.5.9.2.tar.gz 93438 BLAKE2B 3d3d225907f8bd04fdf4b20d608d02cd0e5a723f2a73df24b732992f139102e2a9042c37c5a73f762256fd007dd7e14bace910c0961e60870926c2ce1dca3ac3 SHA512 57b94421d6858fa2bd7b867b386d47d53d3afd75878b08e6e32fb7d8f4942f2a051e0123e6c4b4395abe656d639fa4f47afadbd8c4b2cbc001c5113cbbf96af4
+DIST pyfaidx-0.7.2.1.tar.gz 102951 BLAKE2B d8c76bb9f817a7f4a0f3aa58ef20344c1d5aa5e99a181f1171145264baab4603d772d7c37f8286654442ee0f6bf3b62f8d94d6e0495a65f54495e084403c0b92 SHA512 20833c2e11f942aa69b524170a0203ca4d035d058d1d8029c2fab50c4b60a4e947cbbdc0dc954e4ecdefbf07d095f861a86dbebdfdac4bdbecf65a691226e25c
diff --git a/sci-biology/pyfaidx/metadata.xml b/sci-biology/pyfaidx/metadata.xml
index fd0f24633..47cc39d79 100644
--- a/sci-biology/pyfaidx/metadata.xml
+++ b/sci-biology/pyfaidx/metadata.xml
@@ -11,5 +11,6 @@
 	</maintainer>
 	<upstream>
 		<remote-id type="pypi">pyfaidx</remote-id>
+		<remote-id type="github">mdshw5/pyfaidx</remote-id>
 	</upstream>
 </pkgmetadata>
diff --git a/sci-biology/pyfaidx/pyfaidx-0.4.8.1.ebuild b/sci-biology/pyfaidx/pyfaidx-0.4.8.1.ebuild
deleted file mode 100644
index abea85b56..000000000
--- a/sci-biology/pyfaidx/pyfaidx-0.4.8.1.ebuild
+++ /dev/null
@@ -1,17 +0,0 @@
-# Copyright 1999-2017 Gentoo Foundation
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=5
-
-PYTHON_COMPAT=( python2_7 )
-
-inherit distutils-r1
-
-DESCRIPTION="Efficient pythonic random access to fasta subsequences"
-HOMEPAGE="https://pypi.python.org/pypi/pyfaidx"
-SRC_URI="mirror://pypi/${PN:0:1}/${PN}/${P}.tar.gz"
-
-LICENSE="MIT"
-SLOT="0"
-KEYWORDS="~amd64 ~x86 ~amd64-linux ~x86-linux"
-IUSE=""
diff --git a/sci-biology/pyfaidx/pyfaidx-0.5.9.2.ebuild b/sci-biology/pyfaidx/pyfaidx-0.5.9.2.ebuild
new file mode 100644
index 000000000..bec223f6c
--- /dev/null
+++ b/sci-biology/pyfaidx/pyfaidx-0.5.9.2.ebuild
@@ -0,0 +1,22 @@
+# Copyright 1999-2023 Gentoo Authors
+# Distributed under the terms of the GNU General Public License v2
+
+EAPI=8
+
+PYTHON_COMPAT=( python3_{10..11} )
+DISTUTILS_USE_SETUPTOOLS=rdepend
+
+inherit distutils-r1
+
+DESCRIPTION="Efficient pythonic random access to fasta subsequences"
+HOMEPAGE="https://pypi.python.org/pypi/pyfaidx https://github.com/mdshw5/pyfaidx"
+SRC_URI="https://github.com/mdshw5/pyfaidx/archive/v${PV}.tar.gz -> ${P}.tar.gz"
+
+LICENSE="MIT"
+SLOT="0"
+KEYWORDS="~amd64 ~x86"
+IUSE=""
+
+REPEND="dev-python/six[${PYTHON_USEDEP}]"
+
+#distutils_enable_tests nose
diff --git a/sci-biology/pyfaidx/pyfaidx-0.7.2.1.ebuild b/sci-biology/pyfaidx/pyfaidx-0.7.2.1.ebuild
new file mode 100644
index 000000000..14f557869
--- /dev/null
+++ b/sci-biology/pyfaidx/pyfaidx-0.7.2.1.ebuild
@@ -0,0 +1,24 @@
+# Copyright 1999-2023 Gentoo Authors
+# Distributed under the terms of the GNU General Public License v2
+
+EAPI=8
+
+PYTHON_COMPAT=( python3_{10..11} )
+DISTUTILS_USE_PEP517=setuptools
+
+inherit distutils-r1 pypi
+
+DESCRIPTION="Efficient pythonic random access to fasta subsequences"
+HOMEPAGE="https://pypi.python.org/pypi/pyfaidx https://github.com/mdshw5/pyfaidx"
+
+LICENSE="MIT"
+SLOT="0"
+KEYWORDS="~amd64 ~x86"
+IUSE=""
+# Test issues reported upstream:
+# https://github.com/mdshw5/pyfaidx/issues/208
+RESTRICT="test"
+
+REPEND="dev-python/six[${PYTHON_USEDEP}]"
+
+distutils_enable_tests pytest
diff --git a/sci-biology/pysamstats/Manifest b/sci-biology/pysamstats/Manifest
deleted file mode 100644
index 1b3419190..000000000
--- a/sci-biology/pysamstats/Manifest
+++ /dev/null
@@ -1 +0,0 @@
-DIST pysamstats-0.24.2.tar.gz 269977 BLAKE2B 45abe9a869955b3b611965f3d9e9364c67fe35b1a5b96ea7ff0d015df4720e3925ccc825ed4c8983b39e1d8d570f500e707c61e7d904209025e811c79bc66e7c SHA512 a22a929d2f4d762256563e270c781a37bfe7e7f0aa3ad263d4f0c82d09003ae644cce658d02480e8b6d6506898ef062a5a7ad1612f2bb6819fcb6fe02b00bcfe
diff --git a/sci-biology/pysamstats/metadata.xml b/sci-biology/pysamstats/metadata.xml
deleted file mode 100644
index cc923c1df..000000000
--- a/sci-biology/pysamstats/metadata.xml
+++ /dev/null
@@ -1,16 +0,0 @@
-<?xml version="1.0" encoding="UTF-8"?>
-<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
-<pkgmetadata>
-	<maintainer type="person">
-		<email>mmokrejs@fold.natur.cuni.cz</email>
-		<name>Martin Mokrejs</name>
-	</maintainer>
-	<maintainer type="project">
-		<email>sci-biology@gentoo.org</email>
-		<name>Gentoo Biology Project</name>
-	</maintainer>
-	<upstream>
-		<remote-id type="github">alimanfoo/pysamstats</remote-id>
-		<remote-id type="pypi">pysamstats</remote-id>
-	</upstream>
-</pkgmetadata>
diff --git a/sci-biology/pysamstats/pysamstats-0.24.2.ebuild b/sci-biology/pysamstats/pysamstats-0.24.2.ebuild
deleted file mode 100644
index d6e1350a4..000000000
--- a/sci-biology/pysamstats/pysamstats-0.24.2.ebuild
+++ /dev/null
@@ -1,22 +0,0 @@
-# Copyright 1999-2018 Gentoo Foundation
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=6
-
-PYTHON_COMPAT=( python2_7 python3_4 )
-
-inherit distutils-r1
-
-DESCRIPTION="Calculate stats against genome positions from SAM/BAM/CRAM file"
-HOMEPAGE="https://github.com/alimanfoo/pysamstats
-	https://pypi.python.org/pypi/pysamstats"
-SRC_URI="mirror://pypi/p/${PN}/${P}.tar.gz"
-
-LICENSE="MIT"
-SLOT="0"
-KEYWORDS="" # needs working pysam, see bug #645060
-IUSE=""
-
-DEPEND="dev-python/cython
-	>=sci-biology/pysam-0.8.4"
-RDEPEND="${DEPEND}"
diff --git a/sci-biology/pysurfer/Manifest b/sci-biology/pysurfer/Manifest
deleted file mode 100644
index c7d62837d..000000000
--- a/sci-biology/pysurfer/Manifest
+++ /dev/null
@@ -1,2 +0,0 @@
-DIST pysurfer-0.4.zip 1900346 BLAKE2B 63212cb734e6bb970e2d102289d927eca1987ef33619b0d0b340050a478a6f8b2300d477e9a1389b580cb00b16c2c8b7b3913e5777abcfce3d8185d1dbd0d6f7 SHA512 74ea0dcb8d432431c200caff9ea72f7bc5ec22b4234079177e0f114e652b34efefc06c1ca6fb6b05c0ee50176513917d8f7c447093c94c1bd1180d59cee36798
-DIST pysurfer-0.6.zip 11911071 BLAKE2B 2a32125e533645251f3aeee33d0562dc1da76b66fa85dfdf7cb4857fef856751a14b03d5f7b322c2440aaac1f4b811cec858c3f177292059f2818138122a46de SHA512 1667acf0ce9a6d6f7b4eb2a46a2f9a5c17296fa01104c78f5be0f085e2b8a77acb63eb8fda36f27464f94bc376782ae0f94f84e34648bdf43a934fd1ca128ef3
diff --git a/sci-biology/pysurfer/files/0.4-headless_build.patch b/sci-biology/pysurfer/files/0.4-headless_build.patch
deleted file mode 100644
index 0cebc112a..000000000
--- a/sci-biology/pysurfer/files/0.4-headless_build.patch
+++ /dev/null
@@ -1,22 +0,0 @@
-diff --git a/setup.py b/setup.py
-index c8681c2..41c21a5 100644
---- a/setup.py
-+++ b/setup.py
-@@ -10,8 +10,6 @@ import os
- # deal with MPL sandbox violations during easy_install
- os.environ['MPLCONFIGDIR'] = '.'
- 
--import surfer
--
- DISTNAME = 'pysurfer'
- DESCRIPTION = descr
- LONG_DESCRIPTION = descr
-@@ -20,7 +18,7 @@ MAINTAINER_EMAIL = 'mwaskom@stanford.edu'
- URL = 'http://pysurfer.github.com'
- LICENSE = 'BSD (3-clause)'
- DOWNLOAD_URL = 'https://github.com/nipy/PySurfer'
--VERSION = surfer.__version__
-+VERSION = "0.4"
- 
- import setuptools  # we are using a setuptools namespace
- from numpy.distutils.core import setup
diff --git a/sci-biology/pysurfer/files/0.6-headless_build.patch b/sci-biology/pysurfer/files/0.6-headless_build.patch
deleted file mode 100644
index e75def095..000000000
--- a/sci-biology/pysurfer/files/0.6-headless_build.patch
+++ /dev/null
@@ -1,13 +0,0 @@
-diff --git a/setup.py b/setup.py
-index c8681c2..41c21a5 100644
---- a/setup.py
-+++ b/setup.py
-@@ -20,7 +18,7 @@ MAINTAINER_EMAIL = 'mwaskom@stanford.edu'
- URL = 'http://pysurfer.github.com'
- LICENSE = 'BSD (3-clause)'
- DOWNLOAD_URL = 'https://github.com/nipy/PySurfer'
--VERSION = version
-+VERSION = "0.6"
- 
- import setuptools  # we are using a setuptools namespace
- from numpy.distutils.core import setup
diff --git a/sci-biology/pysurfer/metadata.xml b/sci-biology/pysurfer/metadata.xml
deleted file mode 100644
index e4897b79c..000000000
--- a/sci-biology/pysurfer/metadata.xml
+++ /dev/null
@@ -1,11 +0,0 @@
-<?xml version="1.0" encoding="UTF-8"?>
-<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
-<pkgmetadata>
-	<maintainer type="project">
-		<email>sci@gentoo.org</email>
-		<name>Gentoo Science Project</name>
-	</maintainer>
-	<upstream>
-		<remote-id type="github">nipy/PySurfer</remote-id>
-	</upstream>
-</pkgmetadata>
diff --git a/sci-biology/pysurfer/pysurfer-0.4.ebuild b/sci-biology/pysurfer/pysurfer-0.4.ebuild
deleted file mode 100644
index 400b8bcdc..000000000
--- a/sci-biology/pysurfer/pysurfer-0.4.ebuild
+++ /dev/null
@@ -1,28 +0,0 @@
-# Copyright 1999-2015 Gentoo Foundation
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=5
-
-PYTHON_COMPAT=( python2_7 )
-
-inherit distutils-r1
-
-DESCRIPTION="Python based program for visualization of data from Freesurfer"
-HOMEPAGE="http://pysurfer.github.com"
-SRC_URI="https://github.com/nipy/PySurfer/archive/${PV}.zip -> ${P}.zip"
-
-LICENSE="BSD"
-SLOT="0"
-KEYWORDS="~amd64 ~x86"
-
-RDEPEND="
-	sci-visualization/mayavi[${PYTHON_USEDEP}]
-	dev-python/matplotlib[${PYTHON_USEDEP}]
-	sci-libs/nibabel[${PYTHON_USEDEP}]
-	dev-python/numpy[${PYTHON_USEDEP}]
-	sci-libs/scipy[${PYTHON_USEDEP}]"
-DEPEND=""
-
-S="${WORKDIR}/PySurfer-${PV}"
-
-PATCHES=( "${FILESDIR}/${PV}-headless_build.patch" )
diff --git a/sci-biology/pysurfer/pysurfer-0.6.ebuild b/sci-biology/pysurfer/pysurfer-0.6.ebuild
deleted file mode 100644
index 400b8bcdc..000000000
--- a/sci-biology/pysurfer/pysurfer-0.6.ebuild
+++ /dev/null
@@ -1,28 +0,0 @@
-# Copyright 1999-2015 Gentoo Foundation
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=5
-
-PYTHON_COMPAT=( python2_7 )
-
-inherit distutils-r1
-
-DESCRIPTION="Python based program for visualization of data from Freesurfer"
-HOMEPAGE="http://pysurfer.github.com"
-SRC_URI="https://github.com/nipy/PySurfer/archive/${PV}.zip -> ${P}.zip"
-
-LICENSE="BSD"
-SLOT="0"
-KEYWORDS="~amd64 ~x86"
-
-RDEPEND="
-	sci-visualization/mayavi[${PYTHON_USEDEP}]
-	dev-python/matplotlib[${PYTHON_USEDEP}]
-	sci-libs/nibabel[${PYTHON_USEDEP}]
-	dev-python/numpy[${PYTHON_USEDEP}]
-	sci-libs/scipy[${PYTHON_USEDEP}]"
-DEPEND=""
-
-S="${WORKDIR}/PySurfer-${PV}"
-
-PATCHES=( "${FILESDIR}/${PV}-headless_build.patch" )
diff --git a/sci-biology/pysurfer/pysurfer-9999.ebuild b/sci-biology/pysurfer/pysurfer-9999.ebuild
deleted file mode 100644
index faa5dd437..000000000
--- a/sci-biology/pysurfer/pysurfer-9999.ebuild
+++ /dev/null
@@ -1,26 +0,0 @@
-# Copyright 1999-2014 Gentoo Foundation
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=5
-
-PYTHON_COMPAT=( python2_7 )
-
-inherit distutils-r1 git-r3
-
-DESCRIPTION="Python based program for visualization of data from Freesurfer"
-HOMEPAGE="http://pysurfer.github.com"
-SRC_URI=""
-EGIT_REPO_URI="https://github.com/nipy/PySurfer.git"
-
-LICENSE="BSD"
-SLOT="0"
-
-RDEPEND="
-	sci-visualization/mayavi[${PYTHON_USEDEP}]
-	dev-python/matplotlib[${PYTHON_USEDEP}]
-	sci-libs/nibabel[${PYTHON_USEDEP}]
-	dev-python/numpy[${PYTHON_USEDEP}]
-	sci-libs/scipy[${PYTHON_USEDEP}]"
-DEPEND=""
-
-S="${WORKDIR}/PySurfer-${PV}"
diff --git a/sci-biology/quast/Manifest b/sci-biology/quast/Manifest
deleted file mode 100644
index 6a16099d1..000000000
--- a/sci-biology/quast/Manifest
+++ /dev/null
@@ -1 +0,0 @@
-DIST quast-4.4.tar.gz 29635321 BLAKE2B 4f7e6de19ced81299ee2b79161212aaa5c1b5188c421599942170ed58c7922e01af2cf0f2d66781e6eb6e5f74a6bc87ed67282f87fd248eef86b1e2b7f8f838a SHA512 3ec1cf367f69493d89132f23c3bdfa5c648ebcad4f0bc5e5c3828b43f58fc79f8d51661589f6cd66c835d58ad3a4d1073da2061ee6785c2c0790aded2f670fc9
diff --git a/sci-biology/quast/metadata.xml b/sci-biology/quast/metadata.xml
deleted file mode 100644
index c821b722e..000000000
--- a/sci-biology/quast/metadata.xml
+++ /dev/null
@@ -1,15 +0,0 @@
-<?xml version="1.0" encoding="UTF-8"?>
-<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
-<pkgmetadata>
-	<maintainer type="person">
-		<email>mmokrejs@fold.natur.cuni.cz</email>
-		<name>Martin Mokrejs</name>
-	</maintainer>
-	<maintainer type="project">
-		<email>sci-biology@gentoo.org</email>
-		<name>Gentoo Biology Project</name>
-	</maintainer>
-	<upstream>
-		<remote-id type="sourceforge">quast</remote-id>
-	</upstream>
-</pkgmetadata>
diff --git a/sci-biology/quast/quast-4.4.ebuild b/sci-biology/quast/quast-4.4.ebuild
deleted file mode 100644
index 8a566b7e0..000000000
--- a/sci-biology/quast/quast-4.4.ebuild
+++ /dev/null
@@ -1,44 +0,0 @@
-# Copyright 1999-2017 Gentoo Foundation
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=5
-
-PYTHON_COMPAT=( python2_7 )
-
-inherit python-r1
-
-DESCRIPTION="Compare quality of multiple genome assemblies to each other"
-HOMEPAGE="http://bioinf.spbau.ru/QUAST"
-SRC_URI="http://sourceforge.net/projects/quast/files/${P}.tar.gz"
-
-LICENSE="GPL-2" # and some other for the bundled copies, see http://quast.bioinf.spbau.ru/LICENSE
-SLOT="0"
-KEYWORDS=""
-IUSE=""
-
-DEPEND="
-	dev-python/matplotlib[${PYTHON_USEDEP}]
-	sci-biology/mummer
-	sci-biology/glimmerhmm"
-#	sci-biology/GAGE
-#	sci-biology/GeneMarkS
-#   sci-biology/GeneMarkES
-#	sci-biology/MetaGeneMark
-#   sci-biology/ncbi-tools++
-#
-# comes with bundled executables in ./quast_libs
-
-# the above packages need to be created first
-
-RDEPEND="${DEPEND}"
-
-src_install(){
-	python_foreach_impl python_newscript quast.py quast
-	python_foreach_impl python_newscript metaquast.py metaquast
-	python_foreach_impl python_newscript icarus.py icarus
-
-	dodoc manual.html
-
-	# TODO: install quast_libs/ subdirectory contents into some PATH and PYTHON_PATH
-	# TODO: unbundle bundled executables
-}
diff --git a/sci-biology/quicktree/Manifest b/sci-biology/quicktree/Manifest
index ad1fb6b71..87bf992c7 100644
--- a/sci-biology/quicktree/Manifest
+++ b/sci-biology/quicktree/Manifest
@@ -1 +1 @@
-DIST quicktree-1.1.tar.gz 39035 BLAKE2B e6a3c4e1ae7f2b7af65ffd5f71c00902cea51605895572c134c2fd999cf0d87d3f05b1cc1b6c43811d82a3abb1f82dc0987bef57f5dce6fae25c5d3a38fd51fa SHA512 1b58b786a5f0c96d7a86280e0349eb48b9a1f11160e0266e6b837dfde20a159de1393ec46bc4cdcaae09ffa59c68e8bbc5a985286133b67d6ab8fa6e248823fb
+DIST quicktree-2.5.tar.gz 39784 BLAKE2B e4914a2722ccdd466b58190a46b9a92f8fae01d9a7688d617a6e1a5217334a03d56d5527ca8e6e1963a76e8eb2a47aecbfb8600c7c81c0fa6ff35fbd620acb62 SHA512 351587e54e71e3a79c43370e7f11401c869e0f02aedd98b329923674b68e32e81db688a169a2b4f69dd6957144d448f12e533011c7f228ea038f760c4e9eb2de
diff --git a/sci-biology/quicktree/metadata.xml b/sci-biology/quicktree/metadata.xml
index 8417d1580..e3ce321ed 100644
--- a/sci-biology/quicktree/metadata.xml
+++ b/sci-biology/quicktree/metadata.xml
@@ -5,4 +5,7 @@
 		<email>sci-biology@gentoo.org</email>
 		<name>Gentoo Biology Project</name>
 	</maintainer>
+	<upstream>
+		<remote-id type="github">khowe/quicktree</remote-id>
+	</upstream>
 </pkgmetadata>
diff --git a/sci-biology/quicktree/quicktree-1.1-r1.ebuild b/sci-biology/quicktree/quicktree-1.1-r1.ebuild
deleted file mode 100644
index 552831110..000000000
--- a/sci-biology/quicktree/quicktree-1.1-r1.ebuild
+++ /dev/null
@@ -1,32 +0,0 @@
-# Copyright 1999-2015 Gentoo Foundation
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=5
-
-inherit toolchain-funcs
-
-DESCRIPTION="Rapid reconstruction of phylogenies by the Neighbor-Joining method"
-HOMEPAGE="http://www.sanger.ac.uk/Software/analysis/quicktree/"
-SRC_URI="ftp://ftp.sanger.ac.uk/pub4/resources/software/${PN}/${PN}.tar.gz -> ${P}.tar.gz"
-
-LICENSE="GRL"
-SLOT="0"
-IUSE=""
-KEYWORDS="~amd64 ~x86"
-
-S=${WORKDIR}/${PN}_${PV}
-
-src_prepare() {
-	sed \
-		-e "s/\-O2 \-Wall/${CFLAGS}/" \
-		-i Makefile || die
-}
-
-src_compile() {
-	emake CC="$(tc-getCC)" LFLAGS="${LDFLAGS}"
-}
-
-src_install() {
-	dobin bin/quicktree
-	dodoc README
-}
diff --git a/sci-biology/quicktree/quicktree-2.5.ebuild b/sci-biology/quicktree/quicktree-2.5.ebuild
new file mode 100644
index 000000000..c2fd315f9
--- /dev/null
+++ b/sci-biology/quicktree/quicktree-2.5.ebuild
@@ -0,0 +1,31 @@
+# Copyright 1999-2021 Gentoo Authors
+# Distributed under the terms of the GNU General Public License v2
+
+EAPI=7
+
+inherit toolchain-funcs
+
+DESCRIPTION="Rapid reconstruction of phylogenies by the Neighbor-Joining method"
+HOMEPAGE="https://github.com/khowe/quicktree/"
+SRC_URI="https://github.com/khowe/quicktree/archive/v${PV}.tar.gz -> ${P}.tar.gz"
+
+LICENSE="Apache-2.0"
+SLOT="0"
+KEYWORDS="~amd64 ~x86"
+
+#S=${WORKDIR}/${PN}_${PV}
+
+src_prepare() {
+	default
+	sed -e "s/\-O2/${CFLAGS}/" \
+	    -i Makefile || die
+}
+
+src_compile() {
+	emake CC="$(tc-getCC)" LFLAGS="${LDFLAGS}"
+}
+
+src_install() {
+	dobin quicktree
+	einstalldocs
+}
diff --git a/sci-biology/quorum/Manifest b/sci-biology/quorum/Manifest
deleted file mode 100644
index 68b3dd9c6..000000000
--- a/sci-biology/quorum/Manifest
+++ /dev/null
@@ -1 +0,0 @@
-DIST quorum-1.1.1.tar.gz 659218 BLAKE2B 26710674e12115b3d218c113eaa6b36d9694f85c65bb5e1a8b8e2b4405b585115b2e3ded34c84bdb24d680ae5a1d6e4c387689bdde8bc63824d8eb254d0894da SHA512 12d7a03ffa45dd358f52c55226e6888fc92bff8e361e1c5eca7b4f8545d70243793dd963602932b895702284f89cd77361b2b5636c062d86b467b538df0b9f16
diff --git a/sci-biology/quorum/files/quorum-0.2.1-use-jellyfish1.patch b/sci-biology/quorum/files/quorum-0.2.1-use-jellyfish1.patch
deleted file mode 100644
index b5b68a8fb..000000000
--- a/sci-biology/quorum/files/quorum-0.2.1-use-jellyfish1.patch
+++ /dev/null
@@ -1,74 +0,0 @@
---- src/error_correct_reads.cc	2018-04-21 14:25:41.310473159 +0200
-+++ src/error_correct_reads.cc	2018-04-21 14:26:58.262493179 +0200
-@@ -25,9 +25,9 @@
- #endif
- 
- //#define DEBUG 1
--#include <jellyfish/dbg.hpp>
--#include <jellyfish/atomic_gcc.hpp>
--#include <jellyfish/mer_counting.hpp>
-+#include <jellyfish1/dbg.hpp>
-+#include <jellyfish1/atomic_gcc.hpp>
-+#include <jellyfish1/mer_counting.hpp>
- 
- #include <jflib/multiplexed_io.hpp>
- #include <gzip_stream.hpp>
---- src/combine_jf_dbs.cc	2018-04-21 14:25:50.220707057 +0200
-+++ src/combine_jf_dbs.cc	2018-04-21 14:27:04.652660923 +0200
-@@ -1,9 +1,9 @@
--#include <jellyfish/err.hpp>
--#include <jellyfish/misc.hpp>
--#include <jellyfish/mer_counting.hpp>
--#include <jellyfish/compacted_hash.hpp>
--#include <jellyfish/thread_exec.hpp>
--#include <jellyfish/misc.hpp>
-+#include <jellyfish1/err.hpp>
-+#include <jellyfish1/misc.hpp>
-+#include <jellyfish1/mer_counting.hpp>
-+#include <jellyfish1/compacted_hash.hpp>
-+#include <jellyfish1/thread_exec.hpp>
-+#include <jellyfish1/misc.hpp>
- #include <src/combine_jf_dbs.hpp>
- 
- int main(int argc, char *argv[])
---- src/error_correct_reads.hpp	2018-04-21 14:26:10.091228666 +0200
-+++ src/error_correct_reads.hpp	2018-04-21 14:27:09.792795853 +0200
-@@ -2,12 +2,12 @@
- #define __ERROR_CORRECT_READS_HPP__
- 
- #include <config.h>
--#include <jellyfish/err.hpp>
--#include <jellyfish/mapped_file.hpp>
--#include <jellyfish/invertible_hash_array.hpp>
--#include <jellyfish/allocators_mmap.hpp>
--#include <jellyfish/parse_read.hpp>
--#include <jellyfish/thread_exec.hpp>
-+#include <jellyfish1/err.hpp>
-+#include <jellyfish1/mapped_file.hpp>
-+#include <jellyfish1/invertible_hash_array.hpp>
-+#include <jellyfish1/allocators_mmap.hpp>
-+#include <jellyfish1/parse_read.hpp>
-+#include <jellyfish1/thread_exec.hpp>
- #include <iostream>
- #include <fstream>
- #include <assert.h>
---- configure.ac.ori	2018-04-21 15:00:35.225439196 +0200
-+++ configure.ac	2018-04-21 15:01:37.977086449 +0200
-@@ -28,7 +28,7 @@
- JELLYFISH_VERSION=$(pkg-config --modversion jellyfish-1.1)
- AC_SUBST([JELLYFISH_VERSION])
- AC_ARG_VAR([JELLYFISH], [Jellyfish executable absolute path (default to looking in PATH)])
--AS_IF([test "x$JELLYFISH" = "x"], [AC_PATH_PROG([JELLYFISH], [jellyfish], [false])])
-+AS_IF([test "x$JELLYFISH" = "x"], [AC_PATH_PROG([JELLYFISH], [jellyfish1], [false])])
- 
- AC_ARG_VAR([JF_LIB_PATH], [Append this path to LD_LIBRARY_PATH in quorum])
- 
-@@ -47,7 +47,7 @@
- # --with-relative-jf-path
- AC_ARG_WITH([relative-jf-path],
-             [AC_HELP_STRING([--with-relative-jf-path], [relative path from quorum to jellyfish (use an absolute path if not given. default to "." if given with no argument)])],
--            [case "$withval" in (yes) with_relative_jf_path="jellyfish" ;; (no) with_relative_jf_path= ;; (*) with_relative_jf_path=$withval/jellyfish ;; esac],
-+            [case "$withval" in (yes) with_relative_jf_path="jellyfish1" ;; (no) with_relative_jf_path= ;; (*) with_relative_jf_path=$withval/jellyfish1 ;; esac],
-             [with_relative_jf_path= ])
- AC_SUBST([RELATIVE_JF_PATH], $with_relative_jf_path)
- AM_CONDITIONAL([HAVE_RELATIVE_JF_PATH], [test x$with_relative_jf_path != x])
diff --git a/sci-biology/quorum/metadata.xml b/sci-biology/quorum/metadata.xml
deleted file mode 100644
index 138cb7705..000000000
--- a/sci-biology/quorum/metadata.xml
+++ /dev/null
@@ -1,12 +0,0 @@
-<?xml version="1.0" encoding="UTF-8"?>
-<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
-<pkgmetadata>
-	<maintainer type="person">
-		<email>mmokrejs@fold.natur.cuni.cz</email>
-		<name>Martin Mokrejs</name>
-	</maintainer>
-	<maintainer type="project">
-		<email>sci-biology@gentoo.org</email>
-		<name>Gentoo Biology Project</name>
-	</maintainer>
-</pkgmetadata>
diff --git a/sci-biology/quorum/quorum-1.1.1.ebuild b/sci-biology/quorum/quorum-1.1.1.ebuild
deleted file mode 100644
index 6fa222ff7..000000000
--- a/sci-biology/quorum/quorum-1.1.1.ebuild
+++ /dev/null
@@ -1,22 +0,0 @@
-# Copyright 1999-2018 Gentoo Foundation
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=6
-
-DESCRIPTION="Correct substitution errors in Illumina reads"
-HOMEPAGE="http://www.genome.umd.edu/quorum.html
-	https://github.com/gmarcais/Quorum"
-SRC_URI="https://github.com/gmarcais/Quorum/releases/download/v${PV}/${P}.tar.gz"
-
-LICENSE="GPL-3"
-SLOT="0"
-KEYWORDS="~amd64 ~x86"
-IUSE=""
-
-DEPEND=">=sci-biology/jellyfish-2.1.4:2"
-RDEPEND="${DEPEND}"
-
-src_configure(){
-	econf --enable-relative-paths --with-relative-jf-path
-	default
-}
diff --git a/sci-biology/rat-brain-templates/Manifest b/sci-biology/rat-brain-templates/Manifest
new file mode 100644
index 000000000..cd4db2757
--- /dev/null
+++ b/sci-biology/rat-brain-templates/Manifest
@@ -0,0 +1 @@
+DIST rat-brain-templates-0.2.tar.xz 5557236924 BLAKE2B a2a5715eb4a28983a2aca6828966cca032132d7827452da2669e48df73dd4ef3bde20e4f028d7ede54ff552dcdf64152ebc59a49a16a2c10f80ae35a9af1d885 SHA512 b3317ade2d7016efe683f95503beb2aac6619a28a665b3ad6bfe27d78e3f87a9b3a63b9aeed191b6485706d80065afedc32a56df58e195836da435d74a9189e5
diff --git a/sci-biology/rat-brain-templates/metadata.xml b/sci-biology/rat-brain-templates/metadata.xml
new file mode 100644
index 000000000..5dacf4476
--- /dev/null
+++ b/sci-biology/rat-brain-templates/metadata.xml
@@ -0,0 +1,20 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
+<pkgmetadata>
+	<maintainer type="person">
+		<email>horea.christ@gmail.com</email>
+		<name>Horea Christian</name>
+	</maintainer>
+	<maintainer type="project">
+		<email>sci@gentoo.org</email>
+		<name>Gentoo Science Project</name>
+	</maintainer>
+	<longdescription lang="en">
+		Digital rat brain template collection containing data files in NIfTI
+		format oriented in the standard RAS space, with origin at bregma for
+		use in magnetic resonance rat brain imaging.
+	</longdescription>
+	<upstream>
+		<remote-id type="gitlab">FOS-FMI/rat-brain-templates_generator</remote-id>
+	</upstream>
+</pkgmetadata>
diff --git a/sci-biology/rat-brain-templates/rat-brain-templates-0.2.ebuild b/sci-biology/rat-brain-templates/rat-brain-templates-0.2.ebuild
new file mode 100644
index 000000000..cab3dec4f
--- /dev/null
+++ b/sci-biology/rat-brain-templates/rat-brain-templates-0.2.ebuild
@@ -0,0 +1,27 @@
+# Copyright 2021 Gentoo Authors
+# Distributed under the terms of the GNU General Public License v2
+
+EAPI=7
+
+inherit check-reqs
+
+DESCRIPTION="A collection of rat brain templates in NIfTI format"
+HOMEPAGE="https://gitlab.com/FOS-FMI/rat-brain-templates_generator"
+SRC_URI="https://resources.chymera.eu/distfiles/${P}.tar.xz"
+
+LICENSE="fairuse"
+SLOT="0"
+KEYWORDS="~amd64 ~x86 ~amd64-linux ~x86-linux"
+
+pkg_pretend() {
+	CHECKREQS_DISK_BUILD="16G"
+	check-reqs_pkg_pretend
+}
+
+# We disable this phase to not check requirements twice.
+pkg_setup() { :; }
+
+src_install() {
+	insinto "/usr/share/${PN}"
+	doins *
+}
diff --git a/sci-biology/reaper/Manifest b/sci-biology/reaper/Manifest
deleted file mode 100644
index 157b6934d..000000000
--- a/sci-biology/reaper/Manifest
+++ /dev/null
@@ -1 +0,0 @@
-DIST reaper-15-348.tgz 143739 BLAKE2B 0b2fe464df4c823bf60a429e91215b5d793f8a66274b87611e7cf10ffa95ed9fc27c6d5a34b8e240eff99e1acb5377bfddabe77d1135b84983ceee4b6e9ed4e4 SHA512 ac8186af07da26d5835e70dab878884daa4744ff3c5a13f5d8ec432881d579ca9b3585c89d232158d2b95af2533c9f79cb5185ab67819236d00d1cf9f576dbca
diff --git a/sci-biology/reaper/metadata.xml b/sci-biology/reaper/metadata.xml
deleted file mode 100644
index 138cb7705..000000000
--- a/sci-biology/reaper/metadata.xml
+++ /dev/null
@@ -1,12 +0,0 @@
-<?xml version="1.0" encoding="UTF-8"?>
-<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
-<pkgmetadata>
-	<maintainer type="person">
-		<email>mmokrejs@fold.natur.cuni.cz</email>
-		<name>Martin Mokrejs</name>
-	</maintainer>
-	<maintainer type="project">
-		<email>sci-biology@gentoo.org</email>
-		<name>Gentoo Biology Project</name>
-	</maintainer>
-</pkgmetadata>
diff --git a/sci-biology/reaper/reaper-15348.ebuild b/sci-biology/reaper/reaper-15348.ebuild
deleted file mode 100644
index 6609bc06f..000000000
--- a/sci-biology/reaper/reaper-15348.ebuild
+++ /dev/null
@@ -1,33 +0,0 @@
-# Copyright 1999-2016 Gentoo Foundation
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=5
-
-MY_PV="15-348"
-
-DESCRIPTION="Demultiplex, trim 3'-adapter/polyA and filter short read DNA sequences"
-HOMEPAGE="http://www.ebi.ac.uk/~stijn/reaper"
-SRC_URI="http://www.ebi.ac.uk/~stijn/reaper/src/${PN}-${MY_PV}.tgz"
-
-LICENSE="GPL-3"
-SLOT="0"
-KEYWORDS="~amd64"
-IUSE=""
-
-DEPEND="sys-libs/zlib"
-RDEPEND="${DEPEND}"
-
-S="${WORKDIR}"/"${PN}"-"${MY_PV}"/src
-
-src_prepare(){
-	sed -e 's/ -O3 / ${CFLAGS} /' -i Makefile || die
-}
-
-src_compile(){
-	emake
-}
-
-src_install(){
-	dobin reaper tally minion swan
-	dodoc ../doc/*.html
-}
diff --git a/sci-biology/reapr/Manifest b/sci-biology/reapr/Manifest
deleted file mode 100644
index 9bf4825be..000000000
--- a/sci-biology/reapr/Manifest
+++ /dev/null
@@ -1,2 +0,0 @@
-DIST Reapr_1.0.18.manual.pdf 325751 BLAKE2B 67f44d91b312d1fed27b74ee80506fc86fa73b06df18cb2312228d46500c4e77388ec7e93e8d13b6e98c967ebf9cac87209852a551637584e84c081b8a450984 SHA512 2960d93a330bd6a0aeda749213a83dc4fcbc5128be9c6bd1917ec2abea2def9406bbedad764d48d83b7f95c2da6207a027f98b341299d85c6ed898c5ca7b370f
-DIST Reapr_1.0.18.tar.gz 7966110 BLAKE2B a6537757d62bcf0255fd18204df8f7a6678fb526eb4a5f92dee296f83c44433e0f55c781a78602ad1ad46136b54cce0d83b148dbda34bd2f0527a82ea8e8738b SHA512 12f1e97da6b6a3d080df29d9055aaf4ab2d02eb19a6c9eecb9d1e7268bf13bbe531feda6496d4b74c63ab53db0d1be15ed72f3391c47f9b1a23c34ed6a6c5fcb
diff --git a/sci-biology/reapr/files/fix_sort_samtools13.patch b/sci-biology/reapr/files/fix_sort_samtools13.patch
deleted file mode 100644
index f009223ce..000000000
--- a/sci-biology/reapr/files/fix_sort_samtools13.patch
+++ /dev/null
@@ -1,16 +0,0 @@
-Description: adapt samtools sort usage to 1.3 syntax 
- Samtools 1.3 changed the syntax of the 'samtools sort' command, breaking
- REAPR's smaltmap command in the process.
- Discussed and forwarded to upstream in person, hence no URL.
-Author: Sascha Steinbiss <sascha@steinbiss.name>
---- a/src/task_smaltmap.pl
-+++ b/src/task_smaltmap.pl
-@@ -155,7 +155,7 @@
-                . " | $samtools view -S -T $assembly -b - > $raw_bam";
- 
- # sort the bam by coordinate
--push @commands, "$samtools sort $raw_bam $raw_bam.sort";
-+push @commands, "$samtools sort $raw_bam -O bam -o $raw_bam.sort.bam";
- 
- # remove duplicates
- push @commands, "$samtools rmdup $raw_bam.sort.bam $rmdup_bam";
diff --git a/sci-biology/reapr/files/use_shared_libs.patch b/sci-biology/reapr/files/use_shared_libs.patch
deleted file mode 100644
index b748c7e6d..000000000
--- a/sci-biology/reapr/files/use_shared_libs.patch
+++ /dev/null
@@ -1,252 +0,0 @@
-Description: Use_shared_libs
---- a/src/Makefile
-+++ b/src/Makefile
-@@ -1,7 +1,6 @@
--BAMTOOLS_ROOT = $(CURDIR)/bamtools
- CC = g++
--CFLAGS = -Wl,-rpath,$(BAMTOOLS_ROOT)/lib  -Wall -O3  -I $(BAMTOOLS_ROOT)/include -L $(BAMTOOLS_ROOT)/lib
--TABIX = tabix/tabix.o  -L./tabix -ltabix -lz
-+CFLAGS = -Wall -O3  -I /usr/include/bamtools -I /usr/include
-+TABIX = -ltabix -lhts -lz
- STATS_OBJS =  trianglePlot.o coveragePlot.o fasta.o histogram.o utils.o
- SCORE_OBJS = errorWindow.o utils.o histogram.o
- BREAK_OBJS = fasta.o utils.o
-@@ -35,46 +34,46 @@
- 	$(CC) $(CFLAGS) -c histogram.cpp
- 
- utils.o: utils.cpp
--	$(CC) $(CFLAGS) -lbamtools -c utils.cpp
-+	$(CC) $(CFLAGS) -c utils.cpp
- 
- task_stats: task_stats.o $(STATS_OBJS)
--	$(CC) $(CFLAGS) task_stats.o $(STATS_OBJS) -lbamtools -o task_stats $(TABIX)
-+	$(CC) $(CFLAGS) task_stats.o  $(STATS_OBJS)  -lbamtools $(TABIX) -o task_stats
- 
- task_stats.o: task_stats.cpp $(STATS_OBJS)
- 	$(CC) $(CFLAGS) -c task_stats.cpp
- 
- task_score: task_score.o $(SCORE_OBJS)
--	$(CC) $(CFLAGS) task_score.o $(SCORE_OBJS) -lbamtools -o task_score $(TABIX)
-+	$(CC) -o task_score $(CFLAGS) task_score.o $(SCORE_OBJS) -lbamtools $(TABIX)
- 
- task_score.o: task_score.cpp $(SCORE_OBJS)
- 	$(CC) $(CFLAGS) -c task_score.cpp
- 
- task_break: task_break.o $(BREAK_OBJS)
--	$(CC) $(CFLAGS) task_break.o $(BREAK_OBJS) -lbamtools -o task_break $(TABIX)
-+	$(CC) $(CFLAGS) task_break.o $(BREAK_OBJS) -lbamtools $(TABIX) -o task_break
- 
- task_break.o: task_break.cpp $(BREAK_OBJS)
- 	$(CC) $(CFLAGS) -c task_break.cpp
- 
- bam2fragCov: bam2fragCov.o $(BAM2COV_OBJS)
--	$(CC) $(CFLAGS) bam2fragCov.o $(BAM2COV_OBJS) -lbamtools -o bam2fragCov $(TABIX)
-+	$(CC) $(CFLAGS) bam2fragCov.o $(BAM2COV_OBJS) $(TABIX) -lbamtools -o bam2fragCov
- 
- bam2fragCov.o: bam2fragCov.cpp $(BAM2COV_OBJS)
- 	$(CC) $(CFLAGS) -c bam2fragCov.cpp
- 
- bam2insert: bam2insert.o $(BAM2INSERT_OBJS)
--	$(CC) $(CFLAGS) bam2insert.o $(BAM2INSERT_OBJS) -lbamtools -o bam2insert $(TABIX)
-+	$(CC) $(CFLAGS) bam2insert.o $(BAM2INSERT_OBJS) $(TABIX) -lbamtools -o bam2insert
- 
- bam2insert.o: bam2insert.cpp $(BAM2INSERT_OBJS)
- 	$(CC) $(CFLAGS) -c bam2insert.cpp
- 
- bam2perfect: bam2perfect.o $(BAM2PERFECT_OBJS)
--	$(CC) $(CFLAGS) bam2perfect.o $(BAM2PERFECT_OBJS) -lbamtools -o bam2perfect $(TABIX)
-+	$(CC) $(CFLAGS) bam2perfect.o $(BAM2PERFECT_OBJS) $(TABIX) -lbamtools -o bam2perfect
- 
- bam2perfect.o: bam2perfect.cpp $(BAM2PERFECT_OBJS)
- 	$(CC) $(CFLAGS) -c bam2perfect.cpp
- 
- bam2fcdEstimate: bam2fcdEstimate.o $(BAM2FCDESTIMATE_OBJS)
--	$(CC) $(CFLAGS) bam2fcdEstimate.o $(BAM2FCDESTIMATE_OBJS) -lbamtools -o bam2fcdEstimate $(TABIX)
-+	$(CC) $(CFLAGS) bam2fcdEstimate.o $(TABIX) $(BAM2FCDESTIMATE_OBJS) -o bam2fcdEstimate
- 
- bam2fcdEstimate.o: bam2fcdEstimate.cpp $(BAM2FCDESTIMATE_OBJS)
- 	$(CC) $(CFLAGS) -c bam2fcdEstimate.cpp
-@@ -110,13 +109,13 @@
- 	$(CC) $(CFLAGS) -c scaff2contig.cpp
- 
- task_gapresize: task_gapresize.o $(GAPRESIZE_OBJS)
--	$(CC) $(CFLAGS) task_gapresize.o $(GAPRESIZE_OBJS) -lbamtools -o task_gapresize $(TABIX)
-+	$(CC) $(CFLAGS) task_gapresize.o $(TABIX) $(GAPRESIZE_OBJS) -o task_gapresize
- 
- task_gapresize.o: task_gapresize.cpp $(GAPRESIZE_OBJS)
- 	$(CC) $(CFLAGS) -c task_gapresize.cpp
- 
- task_fcdrate: task_fcdrate.o $(FCDRATE_OBJS)
--	$(CC) $(CFLAGS) task_fcdrate.o $(FCDRATE_OBJS) -lbamtools -o task_fcdrate $(TABIX)
-+	$(CC) $(CFLAGS) task_fcdrate.o $(TABIX) $(FCDRATE_OBJS) -o task_fcdrate
- 
- task_fcdrate.o: task_fcdrate.cpp $(FCDRATE_OBJS)
- 	$(CC) $(CFLAGS) -c task_fcdrate.cpp
---- a/src/task_break.cpp
-+++ b/src/task_break.cpp
-@@ -10,7 +10,6 @@
- #include <assert.h>
- #include "fasta.h"
- #include "utils.h"
--#include "tabix/tabix.hpp"
- 
- using namespace std;
- 
---- a/src/task_score.cpp
-+++ b/src/task_score.cpp
-@@ -18,7 +18,6 @@
- #include "histogram.h"
- #include "api/BamMultiReader.h"
- #include "api/BamReader.h"
--#include "tabix/tabix.hpp"
- 
- using namespace BamTools;
- using namespace std;
---- a/src/task_stats.cpp
-+++ b/src/task_stats.cpp
-@@ -18,7 +18,6 @@
- #include "utils.h"
- #include "api/BamMultiReader.h"
- #include "api/BamReader.h"
--#include "tabix/tabix.hpp"
- 
- using namespace BamTools;
- using namespace std;
---- a/src/utils.h
-+++ b/src/utils.h
-@@ -11,7 +11,7 @@
- 
- #include "api/BamMultiReader.h"
- #include "api/BamReader.h"
--#include "tabix/tabix.hpp"
-+#include "tabix.hpp"
- 
- const short INNIE = 1;
- const short OUTTIE = 2;
---- a/src/task_fcdrate.cpp
-+++ b/src/task_fcdrate.cpp
-@@ -9,7 +9,6 @@
- 
- #include "utils.h"
- #include "histogram.h"
--#include "tabix/tabix.hpp"
- 
- using namespace std;
- 
---- a/src/reapr.pl
-+++ b/src/reapr.pl
-@@ -12,8 +12,8 @@
- $this_script = File::Spec->rel2abs($this_script);
- my ($scriptname, $scriptdir) = fileparse($this_script);
- $scriptdir = File::Spec->rel2abs($scriptdir);
--my $tabix = File::Spec->catfile($scriptdir, 'tabix/tabix');
--my $bgzip = File::Spec->catfile($scriptdir, 'tabix/bgzip');
-+my $tabix = 'tabix';
-+my $bgzip = 'bgzip';
- my $version = '1.0.18';
- 
- if ($#ARGV == -1) {
---- a/src/task_preprocess.pl
-+++ b/src/task_preprocess.pl
-@@ -52,9 +52,9 @@
- my $ideal_fcd_file = File::Spec->catfile($sample_dir, 'ideal_fcd.txt');
- my $lowess_prefix = File::Spec->catfile($sample_dir, 'gc_vs_cov.lowess');
- my $r_script = File::Spec->catfile($sample_dir, 'gc_vs_cov.R');
--my $tabix = File::Spec->catfile($scriptdir, 'tabix/tabix');
--my $bgzip = File::Spec->catfile($scriptdir, 'tabix/bgzip');
--my $samtools = File::Spec->catfile($scriptdir, 'samtools');
-+my $tabix = 'tabix';
-+my $bgzip = 'bgzip';
-+my $samtools = 'samtools';
- 
- # make directory and soft links to required files
- $fasta_in = File::Spec->rel2abs($fasta_in);
---- a/src/task_perfectfrombam.pl
-+++ b/src/task_perfectfrombam.pl
-@@ -57,12 +57,12 @@
- my $min_perfect_map_qual = $ARGV[5];
- my $min_align_score = $ARGV[6];
- my $bam2perfect = File::Spec->catfile($scriptdir, 'bam2perfect');
--my $bgzip = File::Spec->catfile($scriptdir, 'tabix/bgzip');
--my $tabix = File::Spec->catfile($scriptdir, 'tabix/tabix');
-+my $bgzip = 'bgzip';
-+my $tabix = 'tabix';
- my $ERROR_PREFIX = '[REAPR perfectfrombam]';
- my $perfect_bam = "$out_prefix.tmp.perfect.bam";
- my $repetitive_bam = "$out_prefix.tmp.repetitive.bam";
--my $samtools = File::Spec->catfile($scriptdir, 'samtools');
-+my $samtools = 'samtools';
- my %seq_lengths;
- my %used_seqs;
- my $hist_file = "$out_prefix.hist";
---- a/src/task_perfectmap.pl
-+++ b/src/task_perfectmap.pl
-@@ -38,14 +38,14 @@
- my $reads_2 = $ARGV[2];
- my $fragsize = $ARGV[3];
- my $preout = $ARGV[4];
--my $findknownsnps = File::Spec->catfile($scriptdir, 'findknownsnps');
-+my $findknownsnps = 'findknownsnps';
- my $ERROR_PREFIX = '[REAPR perfect_map]';
- my $raw_coverage_file = "$preout.tmp.cov.txt";
- my $tmp_bin = "$preout.tmp.bin";
- my $tmp_bin_single_match = "$tmp_bin\_single_match.fastq";
--my $tabix = File::Spec->catfile($scriptdir, 'tabix/tabix');
--my $bgzip = File::Spec->catfile($scriptdir, 'tabix/bgzip');
--my $samtools = File::Spec->catfile($scriptdir, 'samtools');
-+my $tabix = 'tabix';
-+my $bgzip = 'bgzip';
-+my $samtools = 'samtools';
- my $all_bases_outfile = "$preout.perfect_cov.gz";
- my $hist_outfile = "$preout.hist";
- my @coverage = (0) x 101;
---- a/src/task_plots.pl
-+++ b/src/task_plots.pl
-@@ -50,9 +50,9 @@
- }
- 
- 
--my $tabix = File::Spec->catfile($scriptdir, 'tabix/tabix');
--my $bgzip = File::Spec->catfile($scriptdir, 'tabix/bgzip');
--my $samtools = File::Spec->catfile($scriptdir, 'samtools');
-+my $tabix = 'tabix';
-+my $bgzip = 'bgzip';
-+my $samtools = 'samtools';
- my @plot_list = ('frag_cov', 'frag_cov_cor', 'read_cov', 'read_ratio_f', 'read_ratio_r', 'clip', 'FCD_err');
- my @file_list;
- my $fa_out = "$outprefix.ref.fa";
---- a/src/task_pipeline.pl
-+++ b/src/task_pipeline.pl
-@@ -9,7 +9,7 @@
- 
- my ($scriptname, $scriptdir) = fileparse($0);
- my $reapr_dir = abs_path(File::Spec->catfile($scriptdir, File::Spec->updir()));
--my $reapr = File::Spec->catfile($reapr_dir, 'reapr');
-+my $reapr = 'reapr';
- 
- my %options = (fcdcut => 0);
- 
---- a/src/task_seqrename.pl
-+++ b/src/task_seqrename.pl
-@@ -7,7 +7,7 @@
- use Getopt::Long;
- 
- my ($scriptname, $scriptdir) = fileparse($0);
--my $samtools = File::Spec->catfile($scriptdir, 'samtools');
-+my $samtools = 'samtools';
- my %options;
- my $usage = qq/<rename file> <in.bam> <out.bam>
- 
---- a/src/task_smaltmap.pl
-+++ b/src/task_smaltmap.pl
-@@ -77,8 +77,8 @@
- my $reads_2 = $ARGV[2];
- my $final_bam = $ARGV[3];
- my $ERROR_PREFIX = '[REAPR smaltmap]';
--my $samtools = File::Spec->catfile($scriptdir, 'samtools');
--my $smalt = File::Spec->catfile($scriptdir, 'smalt');
-+my $samtools = 'samtools';
-+my $smalt = 'smalt';
- my $tmp_prefix = "$final_bam.tmp.$$.smaltmap";
- my $smalt_index = "$tmp_prefix.smalt_index";
- my $smalt_sample = "$tmp_prefix.smalt_sample";
diff --git a/sci-biology/reapr/metadata.xml b/sci-biology/reapr/metadata.xml
deleted file mode 100644
index 138cb7705..000000000
--- a/sci-biology/reapr/metadata.xml
+++ /dev/null
@@ -1,12 +0,0 @@
-<?xml version="1.0" encoding="UTF-8"?>
-<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
-<pkgmetadata>
-	<maintainer type="person">
-		<email>mmokrejs@fold.natur.cuni.cz</email>
-		<name>Martin Mokrejs</name>
-	</maintainer>
-	<maintainer type="project">
-		<email>sci-biology@gentoo.org</email>
-		<name>Gentoo Biology Project</name>
-	</maintainer>
-</pkgmetadata>
diff --git a/sci-biology/reapr/reapr-1.0.18.ebuild b/sci-biology/reapr/reapr-1.0.18.ebuild
deleted file mode 100644
index a8c226c9d..000000000
--- a/sci-biology/reapr/reapr-1.0.18.ebuild
+++ /dev/null
@@ -1,61 +0,0 @@
-# Copyright 1999-2016 Gentoo Foundation
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=6
-
-inherit eutils
-
-DESCRIPTION="Verify and correct genome assembly scaffolds using paired-end reads"
-HOMEPAGE="http://www.sanger.ac.uk/science/tools/reapr"
-SRC_URI="ftp://ftp.sanger.ac.uk/pub/resources/software/reapr/Reapr_${PV}.tar.gz
-	ftp://ftp.sanger.ac.uk/pub/resources/software/reapr/Reapr_1.0.18.manual.pdf"
-
-LICENSE="GPL-3"
-SLOT="0"
-KEYWORDS=""
-IUSE=""
-
-# tested smalt versions 0.6.4 to 0.7.0.1 only
-DEPEND="sci-biology/bamtools
-	=sci-biology/samtools-0.1.19-r2" # actually bundled is 0.1.18
-RDEPEND="${DEPEND}"
-#	sci-biology/smalt
-#	dev-perl/File-Basename
-#	dev-perl/File-Copy
-#	dev-perl/File-Spec
-#	perl-core/Getopt-Long
-#	dev-perl/List-Util
-#	dev-lang/R"
-
-S="${WORKDIR}"/Reapr_"${PV}"
-
-# we use temporarily patches from https://anonscm.debian.org/cgit/debian-med/reapr.git/tree/debian/patches
-
-src_prepare(){
-	default
-	for f in "${FILESDIR}"/*.patch; do epatch $f || die; done
-	sed -e 's#^CC = g++#CXX ?= g++#' -i src/Makefile || die
-	sed -e 's#$(CC)#$(CXX)#' -i src/Makefile || die
-	sed -e 's#-O3##' -i src/Makefile || die
-	sed -e 's#^CFLAGS =#CXXFLAGS += -I../third_party/tabix -L../third_party/tabix -I../third_party/bamtools/src -L../third_party/bamtools/src#' -i src/Makefile || die
-	#sed -e 's#-lbamtools#../third_party/bamtools/src/libbamtools.so#' -i src/Makefile || die
-	sed -e 's#-ltabix#../third_party/tabix/libtabix.a#' -i src/Makefile || die
-	sed -e 's#CFLAGS#CXXFLAGS#' -i src/Makefile || die
-}
-
-src_compile(){
-	cd third_party/tabix || die
-	emake # to yield tabix.o object
-	cd ../.. || die
-	cd src || die
-	emake # link directly tabix.o but elsewhere also ../third_party/tabix/libtabix.a
-}
-
-src_install(){
-	dodoc "${DISTDIR}"/Reapr_"${PV}".manual.pdf
-}
-
-pkg_postinst(){
-	einfo "There are test data at ftp://ftp.sanger.ac.uk/pub/resources/software/reapr/Reapr_${PV}.test_data.tar.gz"
-	einfo "You can view results with >=sci-biology/artemis*-15.0.0"
-}
diff --git a/sci-biology/repeatmasker-libraries/Manifest b/sci-biology/repeatmasker-libraries/Manifest
deleted file mode 100644
index 8c96926fc..000000000
--- a/sci-biology/repeatmasker-libraries/Manifest
+++ /dev/null
@@ -1,3 +0,0 @@
-DIST RepBaseRepeatMaskerEdition-20181026.tar.gz 56076961 BLAKE2B b7bc61764c5b888c429685dd90a525f080efa6ab933f56aa263ac4adaab0d76de32c28a50a158a7a579ae1e2534eb28043444fe4437d384da69bc528cced7064 SHA512 e4d345b4785f6d1124e4f01b16e21b538fb07feab418a45ac710e8911dedae4f7e6698088da8214198f27b2b30cd21b8ef9aa27d801191f8760dcbfd6b33a803
-DIST repeatmaskerlibraries-20150807.tar.gz 62891642 BLAKE2B 80badbcdfb9ff5c326d5d8c2030d006780dfd7b8de2b1eeaf61890a3502459f596c27d6c08032ab32f13f61e2f88cd7e9c06325ed9da8e3c6f4225493ea5ddc9 SHA512 ac5486af92a38ce1964dd0dd025663729f99050a12a4c0499a4337353e97a1d2f550fddb6e8d0821c4b3a955f5e4fb6201b10251062966f43bd93968bcfac766
-DIST repeatmaskerlibraries-20160829.tar.gz 73076493 BLAKE2B 9aa88dddf8d1caad237d2965c1d80938a3247bc8602e8cd69a8cfb1cc620facd1bfda2a9b7519e76276fee48514571e1ab281bbd6a2395482414b230e95b82ff SHA512 fea99ec5983e12a321af9c007271e08012498450988d412ab00cc8450fd43f45037f7d4ba09a79d0eb08e8eead322f9f4c96ef8b581472a0d3302addaad96d26
diff --git a/sci-biology/repeatmasker-libraries/metadata.xml b/sci-biology/repeatmasker-libraries/metadata.xml
deleted file mode 100644
index 8417d1580..000000000
--- a/sci-biology/repeatmasker-libraries/metadata.xml
+++ /dev/null
@@ -1,8 +0,0 @@
-<?xml version="1.0" encoding="UTF-8"?>
-<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
-<pkgmetadata>
-	<maintainer type="project">
-		<email>sci-biology@gentoo.org</email>
-		<name>Gentoo Biology Project</name>
-	</maintainer>
-</pkgmetadata>
diff --git a/sci-biology/repeatmasker-libraries/repeatmasker-libraries-20150807.ebuild b/sci-biology/repeatmasker-libraries/repeatmasker-libraries-20150807.ebuild
deleted file mode 100644
index ff9bbd89d..000000000
--- a/sci-biology/repeatmasker-libraries/repeatmasker-libraries-20150807.ebuild
+++ /dev/null
@@ -1,37 +0,0 @@
-# Copyright 1999-2018 Gentoo Authors
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=5
-
-DESCRIPTION="A special version of RepBase used by RepeatMasker"
-HOMEPAGE="http://repeatmasker.org/"
-SRC_URI="repeatmaskerlibraries-${PV}.tar.gz"
-
-LICENSE="all-rights-reserved"
-SLOT="0"
-KEYWORDS="~amd64 ~x86"
-IUSE=""
-
-DEPEND=""
-RDEPEND=""
-
-S="${WORKDIR}/Libraries"
-
-RESTRICT="fetch"
-
-pkg_nofetch() {
-	einfo "Please register at http://www.girinst.org/ and go to"
-	einfo '"Repbase Update - RepeatMasker edition" link'
-	einfo 'which should take you to http://www.girinst.org/server/RepBase).'
-	einfo "Download repeatmaskerlibraries-${PV}.tar.gz and place it in '${DISTDIR}"
-	einfo "Older releases can be found in archive:"
-	einfo "https://www.girinst.org/repbase/update"
-	einfo "This one at https://www.girinst.org/server/archive/RepBase20.08"
-}
-
-src_install() {
-	insinto /usr/share/repeatmasker/Libraries
-	doins "${S}"/RepeatMaskerLib.embl
-	dodoc README
-	dohtml README.html
-}
diff --git a/sci-biology/repeatmasker-libraries/repeatmasker-libraries-20160829.ebuild b/sci-biology/repeatmasker-libraries/repeatmasker-libraries-20160829.ebuild
deleted file mode 100644
index a30389e54..000000000
--- a/sci-biology/repeatmasker-libraries/repeatmasker-libraries-20160829.ebuild
+++ /dev/null
@@ -1,37 +0,0 @@
-# Copyright 1999-2018 Gentoo Authors
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=5
-
-DESCRIPTION="A special version of RepBase used by RepeatMasker"
-HOMEPAGE="http://repeatmasker.org/"
-SRC_URI="repeatmaskerlibraries-${PV}.tar.gz"
-
-LICENSE="all-rights-reserved"
-SLOT="0"
-KEYWORDS="~amd64 ~x86"
-IUSE=""
-
-DEPEND=""
-RDEPEND=""
-
-S="${WORKDIR}/Libraries"
-
-RESTRICT="fetch"
-
-pkg_nofetch() {
-	einfo "Please register at http://www.girinst.org/ and go to"
-	einfo '"Repbase Update - RepeatMasker edition" link'
-	einfo 'which should take you to http://www.girinst.org/server/RepBase).'
-	einfo "Download repeatmaskerlibraries-${PV}.tar.gz and place it in '${DISTDIR}"
-	einfo "Older releases can be found in archive:"
-	einfo "https://www.girinst.org/repbase/update"
-	einfo "This one at https://www.girinst.org/server/archive/RepBase21.12"
-}
-
-src_install() {
-	insinto /usr/share/repeatmasker/Libraries
-	doins "${S}"/RepeatMaskerLib.embl
-	dodoc README
-	dohtml README.html
-}
diff --git a/sci-biology/repeatmasker-libraries/repeatmasker-libraries-20181026.ebuild b/sci-biology/repeatmasker-libraries/repeatmasker-libraries-20181026.ebuild
deleted file mode 100644
index d7b1821bd..000000000
--- a/sci-biology/repeatmasker-libraries/repeatmasker-libraries-20181026.ebuild
+++ /dev/null
@@ -1,36 +0,0 @@
-# Copyright 1999-2018 Gentoo Authors
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=5
-
-DESCRIPTION="A special version of RepBase used by RepeatMasker"
-HOMEPAGE="http://repeatmasker.org/"
-SRC_URI="RepBaseRepeatMaskerEdition-${PV}.tar.gz"
-
-LICENSE="all-rights-reserved"
-SLOT="0"
-KEYWORDS=""
-IUSE=""
-
-DEPEND=""
-RDEPEND=""
-
-S="${WORKDIR}/Libraries"
-
-RESTRICT="fetch"
-
-pkg_nofetch() {
-	einfo "Please register at http://www.girinst.org/ and go to"
-	einfo '"Repbase Update - RepeatMasker edition" link'
-	einfo 'which should take you to http://www.girinst.org/server/RepBase).'
-	einfo "Download RepBaseRepeatMaskerEdition-${PV}.tar.gz and place it in '${DISTDIR}"
-	einfo "Older releases can be found in archive:"
-	einfo "https://www.girinst.org/repbase/update"
-	einfo "This one at https://www.girinst.org/server/archive/RepBase23.10"
-}
-
-src_install() {
-	insinto /usr/share/repeatmasker/Libraries
-	doins "${S}"/RMRBSeqs.embl
-	dodoc README.RMRBSeqs
-}
diff --git a/sci-biology/repeatmasker/Manifest b/sci-biology/repeatmasker/Manifest
deleted file mode 100644
index fce5af28f..000000000
--- a/sci-biology/repeatmasker/Manifest
+++ /dev/null
@@ -1,2 +0,0 @@
-DIST RepeatMasker-open-4-0-6.tar.gz 266192837 BLAKE2B 1c46cb8dfa48a42093b72b3e61aba2a8c566617ca049064224b4fe8a080a6f75ff2e01d2f53cd9d26e5dfe39aaa8596b051fb1f2ff8dcdc74bab3a574b33f16a SHA512 3ca3593a736ab3741c01cfc79e6bdce0ff069cdd12e7e98864b4feeabf93422247aebaf0305d2121b99fd08166be2f7cc443080a2966331dc7f4c45b800a8a97
-DIST RepeatMasker-open-4-0-8.tar.gz 284258491 BLAKE2B 3a01fa951b4ac285ea5313b2c7dc679b22e265ab6475bc7a0eedbe87eb1c372b02fccd12b3b857ca47ba5d11ed0faa6a6c051ce52abc8f4cd4ab34a2c34a26f9 SHA512 7517bad308c331d2b6b4dbb65d4d425983da2e335fcf19ea4ff1e4618668adf7b5941ecf6f1e65205b307dbd0b67e1feb4b03a27a93abe2346f40d0fc443217a
diff --git a/sci-biology/repeatmasker/files/repeatmasker-4.0.6__configure.patch b/sci-biology/repeatmasker/files/repeatmasker-4.0.6__configure.patch
deleted file mode 100644
index e4042190f..000000000
--- a/sci-biology/repeatmasker/files/repeatmasker-4.0.6__configure.patch
+++ /dev/null
@@ -1,106 +0,0 @@
---- configure.ori	2015-11-24 20:56:46.000000000 +0100
-+++ configure	2015-11-24 20:59:58.000000000 +0100
-@@ -253,17 +253,16 @@
-   close INVERS;
- }
- else {
--  print "\nYour RepeatMasker installation is missing a library file.\n"
-+  die "\nYour RepeatMasker installation is missing a library file.\n"
-       . "RepeatMasker requires a minimal set of library sequences to run\n"
-       . "properly.  Please check that all files were extracted from the\n"
-       . "distribution before re-running the configure program.\n\n";
--  exit;
- }
- 
- print "\n  -- Building monolithic RM database...";
- system(
- "$rmLocation/util/buildRMLibFromEMBL.pl $rmLocation/Libraries/RepeatMaskerLib.embl > $rmLocation/Libraries/RepeatMasker.lib 2>/dev/null"
--);
-+) and die "$rmLocation/util/buildRMLibFromEMBL.pl $rmLocation/Libraries/RepeatMaskerLib.embl command filed with: $!";
- 
- ##
- ## TRF location
-@@ -475,7 +474,7 @@
-     }
-     close IN;
-     close OUT;
--    system( "mv $configFile.tmp $configFile" );
-+    system( "mv $configFile.tmp $configFile" ) and die "mv $configFile.tmp $configFile failed with: $!";
-   }
- 
- }
-@@ -607,15 +606,15 @@
-   }
-   close IN;
-   close OUT;
--  system( "mv $configFile.tmp $configFile" );
-+  system( "mv $configFile.tmp $configFile" ) and die "Faled to mv $configFile.tmp $configFile: $!";
- 
-   # Freeze RM and RMPep libraries for RepeatModeler use among others
-   my $rmLocation = "$FindBin::Bin";
-   print "Building RMBlast frozen libraries..\n";
-   system(   "$pgLocation/makeblastdb -dbtype nucl -in "
--          . "$rmLocation/Libraries/RepeatMasker.lib > /dev/null 2>&1" );
-+          . "$rmLocation/Libraries/RepeatMasker.lib > /dev/null 2>&1" ) and die "$pgLocation/makeblastdb -dbtype nucl -in $rmLocation/Libraries/RepeatMasker.lib failed: $!";
-   system(   "$pgLocation/makeblastdb -dbtype prot -in "
--          . "$rmLocation/Libraries/RepeatPeps.lib > /dev/null 2>&1" );
-+          . "$rmLocation/Libraries/RepeatPeps.lib > /dev/null 2>&1" ) and die "$pgLocation/makeblastdb -dbtype prot -in $rmLocation/Libraries/RepeatPeps.lib failed with: $!";
- 
-   my $pgDefault = &promptScreen(
-     "",
-@@ -682,15 +681,15 @@
-   }
-   close IN;
-   close OUT;
--  system( "mv $configFile.tmp $configFile" );
-+  system( "mv $configFile.tmp $configFile" ) and die "mv $configFile.tmp $configFile failed with: $!";
- 
-   # Freeze RM and RMPep libraries
-   my $rmLocation = "$FindBin::Bin";
-   print "Building WUBlast/ABBlast frozen libraries..\n";
-   system(   "$wuLocation/xdformat -n -I "
--          . "$rmLocation/Libraries/RepeatMasker.lib > /dev/null 2>&1" );
-+          . "$rmLocation/Libraries/RepeatMasker.lib > /dev/null 2>&1" ) and die "$wuLocation/xdformat -n -I $rmLocation/Libraries/RepeatMasker.lib failed with: $!";
-   system(   "$wuLocation/xdformat -p -I "
--          . "$rmLocation/Libraries/RepeatPeps.lib > /dev/null 2>&1" );
-+          . "$rmLocation/Libraries/RepeatPeps.lib > /dev/null 2>&1" ) and die "$wuLocation/xdformat -p -I $rmLocation/Libraries/RepeatPeps.lib failed with: $!";
- 
-   my $wuDefault = &promptScreen(
-     "",
-@@ -756,7 +755,7 @@
-       }
-     }
-     else {
--      print "ERROR: Could not find nhmmer program in this directory!\n";
-+      print "ERROR: Could not find nhmmer program in '$location' directory!\n";
-     }
-   }
- 
-@@ -776,7 +775,7 @@
-   }
-   close IN;
-   close OUT;
--  system( "mv $configFile.tmp $configFile" );
-+  system( "mv $configFile.tmp $configFile" ) and die "mv $configFile.tmp $configFile failed with: $!";
- 
-   my $default = &promptScreen(
-     "",
-@@ -830,7 +829,7 @@
-   }
-   close IN;
-   close OUT;
--  system( "mv $configFile.tmp $configFile" );
-+  system( "mv $configFile.tmp $configFile" ) and die "mv $configFile.tmp $configFile failed with: $!";
- 
-   my $deDefault = &promptScreen(
-     "",
-@@ -866,9 +865,6 @@
- 
-   my $answer = undef;
- 
--  # Clear the screen
--  system( "clear" );
--
-   print "\n\n\n";
-   print $screenText;
-   my $numLines = ( $screenText =~ s/(\n)/$1/g );
diff --git a/sci-biology/repeatmasker/files/repeatmasker-4.0.8__configure.patch b/sci-biology/repeatmasker/files/repeatmasker-4.0.8__configure.patch
deleted file mode 100644
index 728bb75b1..000000000
--- a/sci-biology/repeatmasker/files/repeatmasker-4.0.8__configure.patch
+++ /dev/null
@@ -1,118 +0,0 @@
---- RepeatMasker/configure.ori	2018-11-30 16:50:39.918872258 +0100
-+++ RepeatMasker/configure	2018-11-30 17:00:33.255400144 +0100
-@@ -78,11 +78,10 @@
- ## unqualified from another installation directory.
- ##
- if ( cwd() ne $FindBin::RealBin ) {
--  print "\n    The RepeatMasker configure script must be run from\n"
-+  die "\n    The RepeatMasker configure script must be run from\n"
-       . "    inside the RepeatMasker installation directory:\n\n"
-       . "       $FindBin::RealBin\n\n"
-       . "    Perhaps this is not the \"configure\" you are looking for?\n\n";
--  exit;
- }
- 
- ##
-@@ -228,12 +227,12 @@
- print "\n  -- Building FASTA database...";
- system(
- "$rmLocation/util/buildRMLibFromEMBL.pl $rmLocation/Libraries/RepeatMaskerLib.embl > $rmLocation/Libraries/RepeatMasker.lib 2>/dev/null"
--);
-+) and die "$rmLocation/util/buildRMLibFromEMBL.pl $rmLocation/Libraries/RepeatMaskerLib.embl command filed with: $!";
- 
- ## Uncompress taxonomy.dat
- if ( -s "$rmLocation/Libraries/taxonomy.dat.gz" ) {
-   print "\n  -- Uncompressing taxonomy.dat...";
--  system( "gunzip $rmLocation/Libraries/taxonomy.dat.gz" );
-+  system( "gunzip $rmLocation/Libraries/taxonomy.dat.gz" ) and die "gunzip $rmLocation/Libraries/taxonomy.dat.gz failed with: $!";
- }
- 
- ##
-@@ -278,7 +277,7 @@
- } while ( $goodParam != 1 );
- 
- # Initialize config from template.
--system( "cp RepeatMaskerConfig.tmpl RepeatMaskerConfig.pm" );
-+system( "cp RepeatMaskerConfig.tmpl RepeatMaskerConfig.pm" ) and die "cp RepeatMaskerConfig.tmpl RepeatMaskerConfig.pm failed with: $!";
- 
- # Make changes to file.
- my $configFile = "RepeatMaskerConfig.pm";
-@@ -290,7 +289,7 @@
- }
- close IN;
- close OUT;
--system( "mv $configFile.tmp $configFile" );
-+system( "mv $configFile.tmp $configFile" ) and die "mv $configFile.tmp $configFile failed with: $!";
- 
- ##
- ## Search Engine Configuration
-@@ -452,7 +451,7 @@
-     }
-     close IN;
-     close OUT;
--    system( "mv $configFile.tmp $configFile" );
-+    system( "mv $configFile.tmp $configFile" ) and die "mv $configFile.tmp $configFile failed with: $!";
-   }
- 
- }
-@@ -590,9 +589,9 @@
-   my $rmLocation = "$FindBin::Bin";
-   print "Building RMBlast frozen libraries..\n";
-   system(   "$pgLocation/makeblastdb -dbtype nucl -in "
--          . "$rmLocation/Libraries/RepeatMasker.lib > /dev/null 2>&1" );
-+          . "$rmLocation/Libraries/RepeatMasker.lib > /dev/null 2>&1" ) and die "$pgLocation/makeblastdb -dbtype nucl -in $rmLocation/Libraries/RepeatMasker.lib failed: $!";
-   system(   "$pgLocation/makeblastdb -dbtype prot -in "
--          . "$rmLocation/Libraries/RepeatPeps.lib > /dev/null 2>&1" );
-+          . "$rmLocation/Libraries/RepeatPeps.lib > /dev/null 2>&1" ) and die "$pgLocation/makeblastdb -dbtype prot -in $rmLocation/Libraries/RepeatPeps.lib failed with: $!";
- 
-   my $pgDefault = &promptScreen(
-     "",
-@@ -665,9 +664,9 @@
-   my $rmLocation = "$FindBin::Bin";
-   print "Building WUBlast/ABBlast frozen libraries..\n";
-   system(   "$wuLocation/xdformat -n -I "
--          . "$rmLocation/Libraries/RepeatMasker.lib > /dev/null 2>&1" );
-+          . "$rmLocation/Libraries/RepeatMasker.lib > /dev/null 2>&1" ) and die "$wuLocation/xdformat -n -I $rmLocation/Libraries/RepeatMasker.lib failed with: $!";
-   system(   "$wuLocation/xdformat -p -I "
--          . "$rmLocation/Libraries/RepeatPeps.lib > /dev/null 2>&1" );
-+          . "$rmLocation/Libraries/RepeatPeps.lib > /dev/null 2>&1" ) and die "$wuLocation/xdformat -p -I $rmLocation/Libraries/RepeatPeps.lib failed with: $!";
- 
-   my $wuDefault = &promptScreen(
-     "",
-@@ -733,7 +732,7 @@
-       }
-     }
-     else {
--      print "ERROR: Could not find nhmmer program in this directory!\n";
-+      print "ERROR: Could not find nhmmer program in '$location' directory!\n";
-     }
-   }
- 
-@@ -753,7 +752,7 @@
-   }
-   close IN;
-   close OUT;
--  system( "mv $configFile.tmp $configFile" );
-+  system( "mv $configFile.tmp $configFile" ) and die "mv $configFile.tmp $configFile failed with: $!";
- 
-   my $default = &promptScreen(
-     "",
-@@ -807,7 +806,7 @@
-   }
-   close IN;
-   close OUT;
--  system( "mv $configFile.tmp $configFile" );
-+  system( "mv $configFile.tmp $configFile" ) and die "mv $configFile.tmp $configFile failed with: $!";
- 
-   my $deDefault = &promptScreen(
-     "",
-@@ -843,9 +842,6 @@
- 
-   my $answer = undef;
- 
--  # Clear the screen
--  system( "clear" );
--
-   print "\n\n\n";
-   print $screenText;
-   my $numLines = ( $screenText =~ s/(\n)/$1/g );
diff --git a/sci-biology/repeatmasker/metadata.xml b/sci-biology/repeatmasker/metadata.xml
deleted file mode 100644
index 8417d1580..000000000
--- a/sci-biology/repeatmasker/metadata.xml
+++ /dev/null
@@ -1,8 +0,0 @@
-<?xml version="1.0" encoding="UTF-8"?>
-<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
-<pkgmetadata>
-	<maintainer type="project">
-		<email>sci-biology@gentoo.org</email>
-		<name>Gentoo Biology Project</name>
-	</maintainer>
-</pkgmetadata>
diff --git a/sci-biology/repeatmasker/repeatmasker-4.0.6-r3.ebuild b/sci-biology/repeatmasker/repeatmasker-4.0.6-r3.ebuild
deleted file mode 100644
index d41784eb7..000000000
--- a/sci-biology/repeatmasker/repeatmasker-4.0.6-r3.ebuild
+++ /dev/null
@@ -1,111 +0,0 @@
-# Copyright 1999-2018 Gentoo Authors
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=6
-
-inherit eutils perl-module
-
-MY_PV=${PV//\./-}
-
-DESCRIPTION="Screen DNA sequences for interspersed repeats and low complexity DNA"
-HOMEPAGE="http://repeatmasker.org/"
-SRC_URI="http://www.repeatmasker.org/RepeatMasker-open-${MY_PV}.tar.gz"
-
-LICENSE="OSL-2.1"
-SLOT="0"
-KEYWORDS="~amd64 ~x86"
-IUSE=""
-
-DEPEND=">=dev-lang/perl-5.8"
-RDEPEND="
-	dev-perl/Text-Soundex
-	sci-biology/phrap
-	<=sci-biology/repeatmasker-libraries-20160829
-	sci-biology/rmblast
-	!sci-biology/trf
-	>=sci-biology/trf-bin-4.0.4
-"
-
-S="${WORKDIR}/RepeatMasker"
-
-PATCHES=( "${FILESDIR}"/"${P}"__configure.patch )
-
-src_configure() {
-	sed \
-		-e "s#/usr/bin/which#which#g" \
-		-e "s#/usr/bin/perl#perl#g" \
-		-i "${S}"/configure || die
-	perl_set_version
-	insinto ${VENDOR_LIB}
-	sed -e "s#/usr/perl5/lib/#${VENDOR_LIB}/#g" -i "${S}"/configure || die
-	# The below is wrong as it causes:
-	# Enter path [ /var/tmp/portage/sci-biology/repeatmasker-4.0.1-r1/work/RepeatMasker ]:
-	#  -- Building monolithic RM database...sh: /var/tmp/portage/sci-biology/repeatmasker-4.0.1-r1/image///usr/share/repeatmasker/Libraries/RepeatMasker.lib: No such file or directory
-	# -e 's|> \($rmLocation/Libraries/RepeatMasker.lib\)|> '${D}'/\1|'
-	sed -i -e 's/system( "clear" );//' "${S}/configure" || die
-	mkdir -p "${ED}"/usr/share/repeatmasker/Libraries/ || die
-	#
-	# the below files is actually overwritten by buildRMLibFromEMBL.pl so the 'blah'
-	# item does not get installed
-	echo ">blah\natgc" > "${ED}"/usr/share/repeatmasker/Libraries/RepeatMasker.lib || die
-	# below try to define paths to trf, cross_match, rmblast and nhmmer as search tools
-	echo "
-env
-${S}
-${EPREFIX}/opt/trf/bin
-1
-${EPREFIX}/usr/bin
-Y
-2
-${EPREFIX}/usr/bin
-Y
-4
-${EPREFIX}/usr/bin
-Y
-5" | "${S}"/configure || die "configure failed"
-	sed -i -e "s|use lib $FindBin::RealBin;|use lib ${EPREFIX}/usr/share/${PN}/lib;|" \
-		-e "s|.*\(taxonomy.dat\)|${EPREFIX}/usr/share/${PN}/Libraries/\1|" \
-		-e "/$REPEATMASKER_DIR/ s|$FindBin::RealBin|${EPREFIX}/usr/share/${PN}|" \
-		"${S}"/{DateRepeats,ProcessRepeats,RepeatMasker,DupMasker,RepeatProteinMask,RepeatMaskerConfig.pm,Taxonomy.pm} || die
-}
-# configure failed to 'cp RepeatMaskerConfig.tmpl RepeatMaskerConfig.pm'
-# replace also /u1/local/bin/perl with proper Gentoo PATH
-
-src_install() {
-	exeinto /usr/share/${PN}
-	for i in DateRepeats ProcessRepeats RepeatMasker DupMasker RepeatProteinMask; do
-		doexe $i
-		dosym ../share/${PN}/$i /usr/bin/$i
-	done
-
-	perl_set_version
-	insinto "${VENDOR_LIB}"
-	doins "${S}"/*.pm "${S}"/Libraries/*.pm
-	# zap the supposedly misplaced RepeatAnnotationData.pm file
-	rm -r "${S}"/Libraries/*.pm || die
-
-	# if sci-biology/repeatmasker-libraries is installed prevent file collision
-	# and do NOT install Libraries/RepeatMaskerLib.embl file which contains
-	# a limited version of the file: 20110419-min
-	rm -r Libraries/RepeatMaskerLib.embl || die
-	insinto /usr/share/${PN}
-	doins -r util Matrices Libraries *.help
-	keepdir /usr/share/${PN}/Libraries
-
-	dodoc README INSTALL *.help
-}
-
-pkg_postinst(){
-	einfo "RepeatMasker provides bundled human repeats database"
-	einfo "from Dfam-1.0 database www.dfam.org"
-	einfo "You can configure which search search engine is to be used and"
-	einfo "PATHs to the search binaries are defined in"
-	einfo "${EPREFIX}/usr/share/${PN}/lib/RepeatMaskerConfig.pm"
-	einfo "Supported search engines are:"
-	optfeature "cross_match" sci-biology/phrap
-	optfeature "rmblast" sci-biology/rmblast
-	optfeature "nhmmer" \>=sci-biology/hmmer-3.1
-	einfo "abblast/wublast from http://blast.advbiocomp.com/licensing"
-	einfo "repeatmasker-libraries-20160829 (RepBase 21.12) is the last"
-	einfo "version compatible with <repeatmasker-4.0.7"
-}
diff --git a/sci-biology/repeatmasker/repeatmasker-4.0.8-r1.ebuild b/sci-biology/repeatmasker/repeatmasker-4.0.8-r1.ebuild
deleted file mode 100644
index 9b4af2312..000000000
--- a/sci-biology/repeatmasker/repeatmasker-4.0.8-r1.ebuild
+++ /dev/null
@@ -1,111 +0,0 @@
-# Copyright 1999-2018 Gentoo Authors
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=6
-
-inherit eutils perl-module
-
-MY_PV=${PV//\./-}
-
-DESCRIPTION="Screen DNA sequences for interspersed repeats and low complexity DNA"
-HOMEPAGE="http://repeatmasker.org/"
-SRC_URI="http://www.repeatmasker.org/RepeatMasker-open-${MY_PV}.tar.gz"
-
-LICENSE="OSL-2.1"
-SLOT="0"
-KEYWORDS="~amd64 ~x86"
-IUSE=""
-
-DEPEND=">=dev-lang/perl-5.8"
-RDEPEND="
-	dev-perl/Text-Soundex
-	sci-biology/phrap
-	>sci-biology/repeatmasker-libraries-20160829
-	sci-biology/rmblast
-	!sci-biology/trf
-	>=sci-biology/trf-bin-4.0.4
-"
-
-S="${WORKDIR}/RepeatMasker"
-
-PATCHES=( "${FILESDIR}"/"${P}"__configure.patch )
-
-src_configure() {
-	sed \
-		-e "s#/usr/bin/which#which#g" \
-		-e "s#/usr/bin/perl#perl#g" \
-		-i "${S}"/configure || die
-	perl_set_version
-	insinto ${VENDOR_LIB}
-	sed -e "s#/usr/perl5/lib/#${VENDOR_LIB}/#g" -i "${S}"/configure || die
-	# The below is wrong as it causes:
-	# Enter path [ /var/tmp/portage/sci-biology/repeatmasker-4.0.1-r1/work/RepeatMasker ]:
-	#  -- Building monolithic RM database...sh: /var/tmp/portage/sci-biology/repeatmasker-4.0.1-r1/image///usr/share/repeatmasker/Libraries/RepeatMasker.lib: No such file or directory
-	# -e 's|> \($rmLocation/Libraries/RepeatMasker.lib\)|> '${D}'/\1|'
-	sed -i -e 's/system( "clear" );//' "${S}/configure" || die
-	mkdir -p "${ED}"/usr/share/repeatmasker/Libraries/ || die
-	#
-	# the below files is actually overwritten by buildRMLibFromEMBL.pl so the 'blah'
-	# item does not get installed
-	echo ">blah\natgc" > "${ED}"/usr/share/repeatmasker/Libraries/RepeatMasker.lib || die
-	# below try to define paths to trf, cross_match, rmblast and nhmmer as search tools
-	echo "
-env
-${S}
-${EPREFIX}/opt/trf/bin
-1
-${EPREFIX}/usr/bin
-Y
-2
-${EPREFIX}/usr/bin
-Y
-4
-${EPREFIX}/usr/bin
-Y
-5" | "${S}"/configure || die "configure failed"
-	sed -i -e "s|use lib $FindBin::RealBin;|use lib ${EPREFIX}/usr/share/${PN}/lib;|" \
-		-e "s|.*\(taxonomy.dat\)|${EPREFIX}/usr/share/${PN}/Libraries/\1|" \
-		-e "/$REPEATMASKER_DIR/ s|$FindBin::RealBin|${EPREFIX}/usr/share/${PN}|" \
-		"${S}"/{DateRepeats,ProcessRepeats,RepeatMasker,DupMasker,RepeatProteinMask,RepeatMaskerConfig.pm,Taxonomy.pm} || die
-}
-# configure failed to 'cp RepeatMaskerConfig.tmpl RepeatMaskerConfig.pm'
-# replace also /u1/local/bin/perl with proper Gentoo PATH
-
-src_install() {
-	exeinto /usr/share/${PN}
-	for i in DateRepeats ProcessRepeats RepeatMasker DupMasker RepeatProteinMask; do
-		doexe $i
-		dosym ../share/${PN}/$i /usr/bin/$i
-	done
-
-	perl_set_version
-	insinto "${VENDOR_LIB}"
-	doins "${S}"/*.pm "${S}"/Libraries/*.pm
-	# zap the supposedly misplaced RepeatAnnotationData.pm file
-	rm -r "${S}"/Libraries/*.pm || die
-
-	# if sci-biology/repeatmasker-libraries is installed prevent file collision
-	# and do NOT install Libraries/RepeatMaskerLib.embl file which contains
-	# a limited version of the file: 20110419-min
-	rm -r Libraries/RepeatMaskerLib.embl || die
-	insinto /usr/share/${PN}
-	doins -r util Matrices Libraries *.help
-	keepdir /usr/share/${PN}/Libraries
-
-	dodoc README.md INSTALL *.help
-}
-
-pkg_postinst(){
-	einfo "RepeatMasker provides bundled human repeats database"
-	einfo "from Dfam-1.0 database www.dfam.org"
-	einfo "You can configure which search search engine is to be used and"
-	einfo "PATHs to the search binaries are defined in"
-	einfo "${EPREFIX}/usr/share/${PN}/lib/RepeatMaskerConfig.pm"
-	einfo "Supported search engines are:"
-	optfeature "cross_match" sci-biology/phrap
-	optfeature "rmblast" sci-biology/rmblast
-	optfeature "nhmmer" \>=sci-biology/hmmer-3.1
-	einfo "abblast/wublast from http://blast.advbiocomp.com/licensing"
-	einfo "repeatmasker-libraries-20160829 (RepBase 21.12) was the last"
-	einfo "version compatible with <repeatmasker-4.0.7"
-}
diff --git a/sci-biology/reptile/Manifest b/sci-biology/reptile/Manifest
deleted file mode 100644
index ff7626ba7..000000000
--- a/sci-biology/reptile/Manifest
+++ /dev/null
@@ -1 +0,0 @@
-DIST reptile-v1.1.zip 79227 BLAKE2B 23be3768918eb5a9c15b2958a5a067ddff2d1cab978eb537a447ea38eeb8c360d2d66e1095666f854f4fc7efadf20cb54408f5a159182384766100568f453abd SHA512 ca397671d16e718926f61f8671920cff06f0ec458c63987361dc4c1b8b0742ee94759b22786ab3c8176238078a0d571d5b33edf805b176d8967a331a505c6d0e
diff --git a/sci-biology/reptile/metadata.xml b/sci-biology/reptile/metadata.xml
deleted file mode 100644
index 138cb7705..000000000
--- a/sci-biology/reptile/metadata.xml
+++ /dev/null
@@ -1,12 +0,0 @@
-<?xml version="1.0" encoding="UTF-8"?>
-<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
-<pkgmetadata>
-	<maintainer type="person">
-		<email>mmokrejs@fold.natur.cuni.cz</email>
-		<name>Martin Mokrejs</name>
-	</maintainer>
-	<maintainer type="project">
-		<email>sci-biology@gentoo.org</email>
-		<name>Gentoo Biology Project</name>
-	</maintainer>
-</pkgmetadata>
diff --git a/sci-biology/reptile/reptile-1.1.ebuild b/sci-biology/reptile/reptile-1.1.ebuild
deleted file mode 100644
index f9e9de522..000000000
--- a/sci-biology/reptile/reptile-1.1.ebuild
+++ /dev/null
@@ -1,40 +0,0 @@
-# Copyright 1999-2015 Gentoo Foundation
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=5
-
-DESCRIPTION="Illumina read corrector"
-HOMEPAGE="http://aluru-sun.ece.iastate.edu/doku.php?id=reptile"
-SRC_URI="http://aluru-sun.ece.iastate.edu/lib/exe/fetch.php?media=source:reptile-v${PV}.zip -> "${PN}"-v"${PV}".zip"
-
-LICENSE="LGPL-3 GPL-3 Boost-1.0"
-SLOT="0"
-KEYWORDS="~amd64"
-IUSE=""
-
-DEPEND=""
-RDEPEND="${DEPEND}
-	dev-lang/perl"
-
-S="${WORKDIR}"/"${PN}"-v"${PV}"
-
-src_prepare(){
-	sed -e 's#-Wall -O3#$(CXXFLAGS)#' -i src/makefile || die
-	sed -e 's#-Wall -O3#$(CXXFLAGS)#' -i utils/reptile_merger/makefile || die
-	sed -e 's#-Wall -O3#$(CXXFLAGS)#' -i utils/seq-analy/makefile || die
-}
-
-src_compile(){
-	cd src || die
-	emake all
-	cd ../utils/reptile_merger || die
-	emake all
-	cd ../seq-analy || die
-	emake all
-}
-
-src_install(){
-	newbin src/reptile-v1.1 reptile
-	dobin utils/reptile_merger/reptile_merger
-	dobin utils/fastq-converter-v2.0.pl
-}
diff --git a/sci-biology/rmblast/Manifest b/sci-biology/rmblast/Manifest
deleted file mode 100644
index 2282ca6fd..000000000
--- a/sci-biology/rmblast/Manifest
+++ /dev/null
@@ -1 +0,0 @@
-DIST rmblast-1.2-ncbi-blast-2.2.23+-src.tar.gz 10744076 BLAKE2B 6539ec8fcd345bcc1c3ecede6acec233cdc343c3df18748e195dc525f4a65fefeee8398471a26dc671bfed8612e010c26b7a8a66a3c7198f142c2e068ff72751 SHA512 e7c2ebd114aee045ea3f3f462cf2658440e13a2d1eb777648386e1c5eeda9f8083af383c019f9b5802d935d6eb2367eef20822afc45233ddb44a426b4dd7ddb6
diff --git a/sci-biology/rmblast/files/disable-testsuite-compilation.txt b/sci-biology/rmblast/files/disable-testsuite-compilation.txt
deleted file mode 100644
index 8df346f64..000000000
--- a/sci-biology/rmblast/files/disable-testsuite-compilation.txt
+++ /dev/null
@@ -1,4 +0,0 @@
-.*
--.*/test
--.*/unit_test
--.*/unit_tests
diff --git a/sci-biology/rmblast/files/rmblast-1.2-gcc47.patch b/sci-biology/rmblast/files/rmblast-1.2-gcc47.patch
deleted file mode 100644
index 70200d59e..000000000
--- a/sci-biology/rmblast/files/rmblast-1.2-gcc47.patch
+++ /dev/null
@@ -1,865 +0,0 @@
- c++/include/corelib/ncbiexpt.hpp                   |   4 +-
- c++/include/corelib/ncbimisc.hpp                   |   2 +
- c++/include/corelib/ncbiobj.hpp                    |   2 +-
- c++/include/corelib/ncbistl.hpp                    |   6 +-
- c++/include/corelib/ncbistr.hpp                    |   2 +-
- c++/include/corelib/test_boost.hpp                 |  44 +++++-
- c++/include/dbapi/driver/dbapi_object_convert.hpp  |   8 +-
- .../dbapi/driver/impl/dbapi_driver_utils.hpp       |   2 +-
- c++/include/serial/impl/stltypes.hpp               |  16 ++-
- c++/include/serial/iterator.hpp                    |   6 +-
- c++/include/serial/serialbase.hpp                  |   8 +-
- c++/include/util/bitset/bmfunc.h                   |   7 +
- c++/include/util/linkedset.hpp                     |  16 +--
- c++/include/util/rangemap.hpp                      |   4 +-
- c++/src/connect/ncbi_gnutls.c                      |  19 ++-
- c++/src/corelib/ncbifile.cpp                       |   2 +-
- c++/src/corelib/test_boost.cpp                     | 156 ++++++++++++++++++++-
- c++/src/objtools/blast/seqdb_reader/seqdbimpl.hpp  |   2 +-
- c++/src/serial/stdtypes.cpp                        |   8 +-
- 19 files changed, 269 insertions(+), 45 deletions(-)
-
-diff --git a/c++/include/corelib/ncbiexpt.hpp b/c++/include/corelib/ncbiexpt.hpp
-index a9cf850..6d90e74 100644
---- a/c++/include/corelib/ncbiexpt.hpp
-+++ b/c++/include/corelib/ncbiexpt.hpp
-@@ -831,7 +831,7 @@ const TTo* UppermostCast(const TFrom& from)
-     exception_class(const exception_class& other) \
-        : base_class(other) \
-     { \
--        x_Assign(other); \
-+        this->x_Assign(other); \
-     } \
- public: \
-     virtual ~exception_class(void) throw() {} \
-@@ -1154,7 +1154,7 @@ public:
-         : TBase( other)
-     {
-         m_Errno = other.m_Errno;
--        x_Assign(other);
-+        this->x_Assign(other);
-     }
- 
-     /// Destructor.
-diff --git a/c++/include/corelib/ncbimisc.hpp b/c++/include/corelib/ncbimisc.hpp
-index f45d280..f0c030d 100644
---- a/c++/include/corelib/ncbimisc.hpp
-+++ b/c++/include/corelib/ncbimisc.hpp
-@@ -57,6 +57,8 @@
-  * @{
-  */
- 
-+#include <stdlib.h>
-+
- #ifndef NCBI_ESWITCH_DEFINED
- #define NCBI_ESWITCH_DEFINED
- 
-diff --git a/c++/include/corelib/ncbiobj.hpp b/c++/include/corelib/ncbiobj.hpp
-index 4f83db4..815c188 100644
---- a/c++/include/corelib/ncbiobj.hpp
-+++ b/c++/include/corelib/ncbiobj.hpp
-@@ -2128,7 +2128,7 @@ public:
-         CIRef<Interface, TThisType> ref(
-                    dynamic_cast<Interface*>(proxy->GetLockedObject()), *this);
-         if (ref.NotNull()) {
--            Unlock(ref.GetPointer());
-+            this->Unlock(ref.GetPointer());
-         }
-         return ref;
-     }
-diff --git a/c++/include/corelib/ncbistl.hpp b/c++/include/corelib/ncbistl.hpp
-index 0bf465a..0618d9d 100644
---- a/c++/include/corelib/ncbistl.hpp
-+++ b/c++/include/corelib/ncbistl.hpp
-@@ -37,7 +37,6 @@
- 
- #include <common/ncbi_export.h>
- 
--
- // Get rid of some warnings in MSVC++ 6.00
- #if (_MSC_VER >= 1200)
- // too long identificator name in the debug info;  truncated
-@@ -162,6 +161,9 @@ typedef int NCBI_NAME2(T_EAT_SEMICOLON_,UniqueName)
- #endif
- 
- #if defined(NCBI_COMPILER_GCC) || defined(NCBI_COMPILER_WORKSHOP)
-+#  if defined(NCBI_COMPILER_GCC)  &&  NCBI_COMPILER_VERSION >= 400
-+#    include <algorithm>
-+#  endif
- // This template is used by some stl algorithms (sort, reverse...)
- // We need to have our own implementation because some C++ Compiler vendors 
- // implemented it by using a temporary variable and an assignment operator 
-@@ -174,7 +176,7 @@ template<typename Iter>
- inline
- void iter_swap( Iter it1, Iter it2 )
- {
--    swap( *it1, * it2 );
-+    swap( *it1, *it2 );
- }
- 
- END_STD_SCOPE
-diff --git a/c++/include/corelib/ncbistr.hpp b/c++/include/corelib/ncbistr.hpp
-index db7054f..63e3299 100644
---- a/c++/include/corelib/ncbistr.hpp
-+++ b/c++/include/corelib/ncbistr.hpp
-@@ -2583,7 +2583,7 @@ public:
-         : TBase(other)
-     {
-         m_Pos = other.m_Pos;
--        x_Assign(other);
-+        this->x_Assign(other);
-     }
- 
-     /// Destructor.
-diff --git a/c++/include/corelib/test_boost.hpp b/c++/include/corelib/test_boost.hpp
-index 69c41f3..4cd77d3 100644
---- a/c++/include/corelib/test_boost.hpp
-+++ b/c++/include/corelib/test_boost.hpp
-@@ -56,10 +56,18 @@
- #  undef BOOST_AUTO_TEST_MAIN
- #endif
- 
-+#ifdef NCBI_COMPILER_MSVC
-+#  pragma warning(push)
-+// 'class' : class has virtual functions, but destructor is not virtual
-+#  pragma warning(disable: 4265)
-+#endif
-+
-+#include <boost/version.hpp>
- #include <boost/test/auto_unit_test.hpp>
- #include <boost/test/floating_point_comparison.hpp>
- #include <boost/test/framework.hpp>
- #include <boost/test/execution_monitor.hpp>
-+#include <boost/test/parameterized_test.hpp>
- 
- #include <boost/preprocessor/tuple/rem.hpp>
- #include <boost/preprocessor/repeat.hpp>
-@@ -72,6 +80,7 @@
- #undef BOOST_CHECK_THROW_IMPL
- #undef BOOST_CHECK_NO_THROW_IMPL
- #undef BOOST_FIXTURE_TEST_CASE
-+#undef BOOST_PARAM_TEST_CASE
- 
- #define BOOST_CHECK_THROW_IMPL( S, E, P, prefix, TL )                    \
- try {                                                                    \
-@@ -109,6 +118,12 @@ catch( ... ) {                                                               \
- }                                                                            \
- /**/
- 
-+#if BOOST_VERSION >= 104200
-+#  define NCBI_BOOST_LOCATION()  , boost::execution_exception::location()
-+#else
-+#  define NCBI_BOOST_LOCATION()
-+#endif
-+
- #define BOOST_FIXTURE_TEST_CASE( test_name, F )                         \
- struct test_name : public F { void test_method(); };                    \
-                                                                         \
-@@ -124,7 +139,8 @@ static void BOOST_AUTO_TC_INVOKER( test_name )()                        \
-                          ::framework::current_test_case().p_name        \
-                  << "\"" << ex);                                        \
-         throw boost::execution_exception(                               \
--                boost::execution_exception::cpp_exception_error, "");   \
-+                boost::execution_exception::cpp_exception_error, ""     \
-+                NCBI_BOOST_LOCATION() );                                \
-     }                                                                   \
- }                                                                       \
-                                                                         \
-@@ -142,6 +158,12 @@ BOOST_JOIN( BOOST_JOIN( test_name, _registrar ), __LINE__ ) (           \
- void test_name::test_method()                                           \
- /**/
- 
-+#define BOOST_PARAM_TEST_CASE( function, begin, end )                       \
-+    ::NCBI_NS_NCBI::NcbiTestGenTestCases( function,                         \
-+                                          BOOST_TEST_STRINGIZE( function ), \
-+                                          (begin), (end) )                  \
-+/**/
-+
- /// Set timeout value for the test case created using auto-registration
- /// facility.
- #define BOOST_AUTO_TEST_CASE_TIMEOUT(test_name, n)                      \
-@@ -158,6 +180,26 @@ static struct BOOST_JOIN( test_name, _timeout_spec )                    \
- } BOOST_JOIN( test_name, _timeout_spec_inst );                          \
- /**/
- 
-+/// Automatic registration of the set of test cases based on some function
-+/// accepting one parameter. Set of parameters used to call that function is
-+/// taken from iterator 'begin' which is incremented until it reaches 'end'.
-+///
-+/// @sa BOOST_PARAM_TEST_CASE
-+#define BOOST_AUTO_PARAM_TEST_CASE( function, begin, end )               \
-+    BOOST_AUTO_TU_REGISTRAR(function) (                                  \
-+                            BOOST_PARAM_TEST_CASE(function, begin, end)) \
-+/**/
-+
-+#define BOOST_TIMEOUT(M)                                        \
-+    do {                                                        \
-+        static string s(M);                                     \
-+        throw boost::execution_exception(                       \
-+                boost::execution_exception::timeout_error, s    \
-+                NCBI_BOOST_LOCATION());                         \
-+    } while (0)                                                 \
-+/**/
-+
-+
- 
- #define NCBITEST_CHECK_IMPL(P, check_descr, TL, CT)                          \
-     BOOST_CHECK_NO_THROW_IMPL(BOOST_CHECK_IMPL(P, check_descr, TL, CT), TL)
-diff --git a/c++/include/dbapi/driver/dbapi_object_convert.hpp b/c++/include/dbapi/driver/dbapi_object_convert.hpp
-index 6fcde61..eddde81 100644
---- a/c++/include/dbapi/driver/dbapi_object_convert.hpp
-+++ b/c++/include/dbapi/driver/dbapi_object_convert.hpp
-@@ -67,7 +67,7 @@ public:
-     operator const CTime&(void) const;
- 
- private:
--    mutable obj_type& m_Value; 
-+    obj_type& m_Value; 
- };
- 
- ////////////////////////////////////////////////////////////////////////////////
-@@ -92,7 +92,7 @@ public:
-     operator const CTime&(void) const;
- 
- private:
--    mutable obj_type& m_Value; 
-+    obj_type& m_Value; 
- };
- 
- ////////////////////////////////////////////////////////////////////////////////
-@@ -133,7 +133,7 @@ public:
-     operator const CTime&(void) const;
- 
- private:
--    mutable obj_type& m_Value; 
-+    obj_type& m_Value; 
- };
- 
- ////////////////////////////////////////////////////////////////////////////////
-@@ -174,7 +174,7 @@ public:
-     operator const CTime&(void) const;
- 
- private:
--    mutable obj_type& m_Value; 
-+    obj_type& m_Value; 
- };
- 
- ////////////////////////////////////////////////////////////////////////////////
-diff --git a/c++/include/dbapi/driver/impl/dbapi_driver_utils.hpp b/c++/include/dbapi/driver/impl/dbapi_driver_utils.hpp
-index 0792a6d..b6bd64b 100644
---- a/c++/include/dbapi/driver/impl/dbapi_driver_utils.hpp
-+++ b/c++/include/dbapi/driver/impl/dbapi_driver_utils.hpp
-@@ -231,7 +231,7 @@ protected:
- 
- private:
-     const string& m_SPName;
--    mutable impl::CConnection& m_Conn;
-+    impl::CConnection& m_Conn;
- };
- 
- 
-diff --git a/c++/include/serial/impl/stltypes.hpp b/c++/include/serial/impl/stltypes.hpp
-index d41ab94..7d9e3ce 100644
---- a/c++/include/serial/impl/stltypes.hpp
-+++ b/c++/include/serial/impl/stltypes.hpp
-@@ -412,6 +412,7 @@ public:
-     typedef StlIterator TStlIterator;
-     typedef TypeInfoIterator TTypeInfoIterator;
-     typedef typename TTypeInfoIterator::TObjectPtr TObjectPtr;
-+    typedef CStlClassInfoFunctions<Container> CParent;
- 
-     static TStlIterator& It(TTypeInfoIterator& iter)
-         {
-@@ -437,7 +438,8 @@ public:
-         }
-     static bool InitIterator(TTypeInfoIterator& iter)
-         {
--            TStlIterator stl_iter = Get(iter.GetContainerPtr()).begin();
-+            TStlIterator stl_iter
-+                = CParent::Get(iter.GetContainerPtr()).begin();
-             if ( sizeof(TStlIterator) <= sizeof(iter.m_IteratorData) ) {
-                 void* data = &iter.m_IteratorData;
-                 new (data) TStlIterator(stl_iter);
-@@ -445,7 +447,7 @@ public:
-             else {
-                 iter.m_IteratorData = new TStlIterator(stl_iter);
-             }
--            return stl_iter != Get(iter.GetContainerPtr()).end();
-+            return stl_iter != CParent::Get(iter.GetContainerPtr()).end();
-         }
-     static void ReleaseIterator(TTypeInfoIterator& iter)
-         {
-@@ -466,7 +468,7 @@ public:
- 
-     static bool NextElement(TTypeInfoIterator& iter)
-         {
--            return ++It(iter) != Get(iter.GetContainerPtr()).end();
-+            return ++It(iter) != CParent::Get(iter.GetContainerPtr()).end();
-         }
-     static TObjectPtr GetElementPtr(const TTypeInfoIterator& iter)
-         {
-@@ -503,7 +505,7 @@ public:
-     
-     static bool EraseElement(TTypeInfoIterator& iter)
-         {
--            TStlIterator& it = It(iter);
-+            TStlIterator& it = CParent::It(iter);
-             Container* c = static_cast<Container*>(iter.GetContainerPtr());
-             it = c->erase(it);
-             return it != c->end();
-@@ -511,7 +513,7 @@ public:
-     static void EraseAllElements(TTypeInfoIterator& iter)
-         {
-             Container* c = static_cast<Container*>(iter.GetContainerPtr());
--            c->erase(It(iter), c->end());
-+            c->erase(CParent::It(iter), c->end());
-         }
- 
-     static void SetIteratorFunctions(CStlOneArgTemplate* info)
-@@ -542,7 +544,7 @@ public:
-         }
-     static bool EraseElement(TTypeInfoIterator& iter)
-         {
--            TStlIterator& it = It(iter);
-+            TStlIterator& it = CParent::It(iter);
-             Container* c = static_cast<Container*>(iter.GetContainerPtr());
-             TStlIterator erase = it++;
-             c->erase(erase);
-@@ -551,7 +553,7 @@ public:
-     static void EraseAllElements(TTypeInfoIterator& iter)
-         {
-             Container* c = static_cast<Container*>(iter.GetContainerPtr());
--            c->erase(It(iter), c->end());
-+            c->erase(CParent::It(iter), c->end());
-         }
- 
-     static void SetIteratorFunctions(CStlOneArgTemplate* info)
-diff --git a/c++/include/serial/iterator.hpp b/c++/include/serial/iterator.hpp
-index 25e1193..cddb046 100644
---- a/c++/include/serial/iterator.hpp
-+++ b/c++/include/serial/iterator.hpp
-@@ -491,13 +491,13 @@ protected:
-     CTypeIteratorBase(TTypeInfo needType, const TBeginInfo& beginInfo)
-         : m_NeedType(needType)
-         {
--            Init(beginInfo);
-+            this->Init(beginInfo);
-         }
-     CTypeIteratorBase(TTypeInfo needType, const TBeginInfo& beginInfo,
-                       const string& filter)
-         : m_NeedType(needType)
-         {
--            Init(beginInfo, filter);
-+            this->Init(beginInfo, filter);
-         }
- 
-     virtual bool CanSelect(const CConstObjectInfo& object)
-@@ -599,7 +599,7 @@ public:
- 
-     CTypesIteratorBase<Parent>& operator=(const TBeginInfo& beginInfo)
-         {
--            Init(beginInfo);
-+            this->Init(beginInfo);
-             return *this;
-         }
- 
-diff --git a/c++/include/serial/serialbase.hpp b/c++/include/serial/serialbase.hpp
-index be6a4f9..d59fb25 100644
---- a/c++/include/serial/serialbase.hpp
-+++ b/c++/include/serial/serialbase.hpp
-@@ -364,11 +364,15 @@ public:
-     // cast to object type
-     TObject& operator*(void)
-         {
--            return *reinterpret_cast<TObject*>(m_Buffer);
-+            TObject* ptr = static_cast<TObject*>
-+                (static_cast<void*>(m_Buffer));
-+            return *ptr;
-         }
-     const TObject& operator*(void) const
-         {
--            return *reinterpret_cast<const TObject*>(m_Buffer);
-+            const TObject* ptr = static_cast<const TObject*>
-+                (static_cast<const void*>(m_Buffer));
-+            return *ptr;
-         }
- 
-     // construct/destruct object
-diff --git a/c++/include/util/bitset/bmfunc.h b/c++/include/util/bitset/bmfunc.h
-index 5917ee5..a8c204b 100644
---- a/c++/include/util/bitset/bmfunc.h
-+++ b/c++/include/util/bitset/bmfunc.h
-@@ -37,6 +37,13 @@ For more information please visit:  http://bmagic.sourceforge.net
- namespace bm
- {
- 
-+bm::id_t bit_block_any_range(const bm::word_t* block,
-+                             bm::word_t left,
-+                             bm::word_t right);
-+
-+bm::id_t bit_block_calc_count_range(const bm::word_t* block,
-+                                    bm::word_t left,
-+                                    bm::word_t right);
- 
- /*!
-     @brief Structure with statistical information about bitset's memory 
-diff --git a/c++/include/util/linkedset.hpp b/c++/include/util/linkedset.hpp
-index e8bbe6e..364164b 100644
---- a/c++/include/util/linkedset.hpp
-+++ b/c++/include/util/linkedset.hpp
-@@ -268,10 +268,10 @@ public:
-             pair<iterator, bool> ins = m_Container.insert(value);
-             if ( ins.second ) {
-                 if ( ins.first == begin() )
--                    insertToStart(*ins.first);
-+                    this->insertToStart(*ins.first);
-                 else {
-                     iterator prev = ins.first;
--                    insertAfter(*--prev, *ins.first);
-+                    this->insertAfter(*--prev, *ins.first);
-                 }
-             }
-             return ins;
-@@ -280,10 +280,10 @@ public:
-     void erase(iterator iter)
-         {
-             if ( iter == begin() )
--                removeFromStart(*iter);
-+                this->removeFromStart(*iter);
-             else {
-                 iterator prev = iter;
--                removeAfter(*--prev, *iter);
-+                this->removeAfter(*--prev, *iter);
-             }
-             m_Container.erase(iter);
-         }
-@@ -422,10 +422,10 @@ public:
-         {
-             iterator iter = m_Container.insert(value);
-             if ( iter == begin() )
--                insertToStart(get(iter));
-+                this->insertToStart(get(iter));
-             else {
-                 iterator prev = iter;
--                insertAfter(get(--prev), get(iter));
-+                this->insertAfter(get(--prev), get(iter));
-             }
-             return iter;
-         }
-@@ -433,10 +433,10 @@ public:
-     void erase(iterator iter)
-         {
-             if ( iter == begin() )
--                removeFromStart(get(iter));
-+                this->removeFromStart(get(iter));
-             else {
-                 iterator prev = iter;
--                removeAfter(get(--prev), get(iter));
-+                this->removeAfter(get(--prev), get(iter));
-             }
-             m_Container.erase(iter);
-         }
-diff --git a/c++/include/util/rangemap.hpp b/c++/include/util/rangemap.hpp
-index c4f5f37..56e267d 100644
---- a/c++/include/util/rangemap.hpp
-+++ b/c++/include/util/rangemap.hpp
-@@ -578,7 +578,7 @@ public:
-             // get level
- 
-             // insert element
--            TSelectMapI selectIter = insertLevel(selectKey);
-+            TSelectMapI selectIter = this->insertLevel(selectKey);
-             pair<TLevelMapI, bool> levelIns = selectIter->second.insert(value);
-             
-             pair<iterator, bool> ret;
-@@ -640,7 +640,7 @@ public:
-             // insert element
-             iterator ret;
-             ret.m_Range = range_type::GetWhole();
--            ret.m_SelectIter = insertLevel(selectKey);
-+            ret.m_SelectIter = this->insertLevel(selectKey);
-             ret.m_SelectIterEnd = this->m_SelectMap.end();
-             ret.m_LevelIter = ret.m_SelectIter->second.insert(value);
-             return ret;
-diff --git a/c++/src/connect/ncbi_gnutls.c b/c++/src/connect/ncbi_gnutls.c
-index f0242b7..8b13713 100644
---- a/c++/src/connect/ncbi_gnutls.c
-+++ b/c++/src/connect/ncbi_gnutls.c
-@@ -98,7 +98,6 @@ static const int kGnuTlsCertPrio[] = {
-     0
- };
- static const int kGnuTlsCompPrio[] = {
--    GNUTLS_COMP_LZO,
-     GNUTLS_COMP_ZLIB,
-     GNUTLS_COMP_NULL,
-     0
-@@ -254,6 +253,24 @@ static EIO_Status s_GnuTlsOpen(void* session, int* error)
- }
- 
- 
-+/*ARGSUSED*/
-+static void x_set_errno(gnutls_session_t session, int error)
-+{
-+#  ifdef LIBGNUTLS_VERSION_NUMBER
-+#    if                                         \
-+    LIBGNUTLS_VERSION_MAJOR > 1  ||             \
-+    LIBGNUTLS_VERSION_MINOR > 5  ||             \
-+    LIBGNUTLS_VERSION_PATCH > 3
-+    gnutls_transport_set_errno(session, error);
-+    return;
-+#    endif /*LIBGNUTLS_VERSION >= 1.5.4*/
-+#  endif /*LIBGNUTLS_VERSION_NUMBER*/
-+    /*NOTREACHED*/
-+    if (error)
-+        errno = error;
-+}
-+
-+
- static ssize_t x_GnuTlsPull(gnutls_transport_ptr_t ptr,
-                             void* buf, size_t size)
- {
-diff --git a/c++/src/corelib/ncbifile.cpp b/c++/src/corelib/ncbifile.cpp
-index d751e62..fdc81c7 100644
---- a/c++/src/corelib/ncbifile.cpp
-+++ b/c++/src/corelib/ncbifile.cpp
-@@ -51,8 +51,8 @@
- #  include <dirent.h>
- #  include <pwd.h>
- #  include <fcntl.h>
--#  include <sys/time.h>
- #  include <sys/mman.h>
-+#  include <sys/time.h>
- #  ifdef HAVE_SYS_STATVFS_H
- #    include <sys/statvfs.h>
- #  endif
-diff --git a/c++/src/corelib/test_boost.cpp b/c++/src/corelib/test_boost.cpp
-index dfd9cc8..f93d2ca 100644
---- a/c++/src/corelib/test_boost.cpp
-+++ b/c++/src/corelib/test_boost.cpp
-@@ -41,6 +41,7 @@
- #ifndef BOOST_TEST_NO_LIB
- #  define BOOST_TEST_NO_LIB
- #endif
-+#define BOOST_TEST_NO_MAIN
- #include <corelib/test_boost.hpp>
- 
- #include <boost/preprocessor/cat.hpp>
-@@ -95,6 +96,7 @@ const char* kTestResultTimeout     = "timeout";
- const char* kTestResultAborted     = "aborted";
- const char* kTestResultSkipped     = "skipped";
- const char* kTestResultDisabled    = "disabled";
-+const char* kTestResultToFix       = "tofix";
- 
- 
- typedef but::results_reporter::format   TBoostRepFormatter;
-@@ -168,14 +170,24 @@ public:
-                                           unsigned long elapsed);
-     virtual
-     void test_unit_skipped(ostream& ostr, but::test_unit const& tu);
-+#if BOOST_VERSION >= 104200
-+    virtual
-+    void log_exception    (ostream& ostr, but::log_checkpoint_data const& lcd,
-+                                          boost::execution_exception const& ex);
-+    // Next line is necessary for compiling with ICC and Boost 1.41.0 and up
-+    using TBoostLogFormatter::log_exception;
-+#else
-     virtual
-     void log_exception    (ostream& ostr, but::log_checkpoint_data const& lcd,
-                                           but::const_string explanation);
-+#endif
-     virtual
-     void log_entry_start  (ostream& ostr, but::log_entry_data const& led,
-                                           log_entry_types let);
-     virtual
-     void log_entry_value  (ostream& ostr, but::const_string value);
-+    // Next line is necessary for compiling with ICC and Boost 1.41.0 and up
-+    using TBoostLogFormatter::log_entry_value;
-     virtual
-     void log_entry_finish (ostream& ostr);
- 
-@@ -402,10 +414,15 @@ public:
- 
-     /// Mark test case as failed due to hit of the timeout
-     void SetTestTimedOut(but::test_case* tc);
-+    /// Register the fact of test failure
-+    void SetTestErrored(but::test_case* tc);
-+    /// Check if given test is marked as requiring fixing in the future
-+    bool IsTestToFix(const but::test_unit* tu);
- 
-     /// Get number of actually executed tests
-     int GetRanTestsCount(void);
--
-+    /// Get number of tests that were failed but are marked to be fixed
-+    int GetToFixTestsCount(void);
-     /// Get string representation of result of test execution
-     string GetTestResultString(but::test_unit* tu);
- 
-@@ -415,6 +432,11 @@ public:
-     /// Check if user initialization functions failed
-     bool IsInitFailed(void);
- 
-+    /// Check if there were any test errors
-+    bool HasTestErrors(void);
-+    /// Check if there were any timeouted tests
-+    bool HasTestTimeouts(void);
-+
- private:
-     typedef list<TNcbiTestUserFunction> TUserFuncsList;
- 
-@@ -493,6 +515,8 @@ private:
-     TUnitsSet                 m_DisabledTests;
-     /// List of all tests which result is a timeout
-     TUnitsSet                 m_TimedOutTests;
-+    /// List of all tests marked as in need of fixing in the future
-+    TUnitsSet                 m_ToFixTests;
-     /// List of all dependencies for each test having dependencies
-     TUnitToManyMap            m_TestDeps;
-     /// Observer to make test dependencies and look for unit's timeouts
-@@ -512,12 +536,18 @@ private:
-     /// String representation for whole test timeout (real value taken from
-     /// CHECK_TIMEOUT in Makefile).
-     string                    m_TimeoutStr;
-+    /// Multiplicator for timeouts
-+    double                    m_TimeMult;
-     /// Timer measuring elapsed time for the whole test
-     CStopWatch                m_Timer;
-     /// Timeout that was set in currently executing unit before adjustment
-     ///
-     /// @sa AdjustTestTimeout()
-     unsigned int              m_CurUnitTimeout;
-+    /// Flag showing if there were some test errors
-+    bool                      m_HasTestErrors;
-+    /// Flag showing if there were some timeouted tests
-+    bool                      m_HasTestTimeouts;
- };
- 
- 
-@@ -794,7 +824,10 @@ CNcbiTestApplication::CNcbiTestApplication(void)
-       m_RunMode  (0),
-       m_DummyTest(NULL),
-       m_Timeout  (0),
--      m_Timer    (CStopWatch::eStart)
-+      m_TimeMult (1),
-+      m_Timer    (CStopWatch::eStart),
-+      m_HasTestErrors(false),
-+      m_HasTestTimeouts(false)
- {
-     m_Reporter = new CNcbiBoostReporter();
-     m_Logger   = new CNcbiBoostLogger();
-@@ -1244,6 +1277,24 @@ CNcbiTestApplication::GetRanTestsCount(void)
-     return result;
- }
- 
-+int
-+CNcbiTestApplication::GetToFixTestsCount(void)
-+{
-+    int result = 0;
-+    ITERATE(TUnitsSet, it, m_ToFixTests) {
-+        if (!but::results_collector.results((*it)->p_id).passed())
-+            ++result;
-+    }
-+    return result;
-+}
-+
-+inline bool
-+CNcbiTestApplication::IsTestToFix(const but::test_unit* tu)
-+{
-+    return m_ToFixTests.find(const_cast<but::test_unit*>(tu))
-+                                                        != m_ToFixTests.end();
-+}
-+
- inline void
- CNcbiTestApplication::x_SetupBoostReporters(void)
- {
-@@ -1391,6 +1442,18 @@ CNcbiTestApplication::InitTestFramework(int argc, char* argv[])
-     return NULL;
- }
- 
-+inline bool
-+CNcbiTestApplication::HasTestErrors(void)
-+{
-+    return m_HasTestErrors;
-+}
-+
-+inline bool
-+CNcbiTestApplication::HasTestTimeouts(void)
-+{
-+    return m_HasTestTimeouts;
-+}
-+
- void
- CNcbiTestsCollector::visit(but::test_case const& test)
- {
-@@ -1431,9 +1494,20 @@ CNcbiTestsObserver::test_unit_finish(but::test_unit const& tu,
-     // elapsed comes in microseconds
-     if (timeout != 0  &&  timeout < elapsed / 1000000) {
-         boost::execution_exception ex(
--               boost::execution_exception::timeout_error, "Timeout exceeded");
-+               boost::execution_exception::timeout_error, "Timeout exceeded"
-+               NCBI_BOOST_LOCATION());
-         but::framework::exception_caught(ex);
-     }
-+
-+    but::test_results& tr = but::s_rc_impl().m_results_store[tu.p_id];
-+    if (!tr.passed()  &&  s_GetTestApp().IsTestToFix(&tu)) {
-+        static_cast<but::readwrite_property<bool>& >(
-+            static_cast<but::class_property<bool>& >(
-+                                            tr.p_skipped)).set(true);
-+        static_cast<but::readwrite_property<but::counter_t>& >(
-+            static_cast<but::class_property<but::counter_t>& >(
-+                                            tr.p_assertions_failed)).set(0);
-+    }
- }
- 
- void
-@@ -1551,12 +1625,21 @@ CNcbiBoostLogger::test_unit_skipped(ostream& ostr, but::test_unit const& tu)
-     m_Upper->test_unit_skipped(ostr, tu);
- }
- 
-+#if BOOST_VERSION >= 104200
-+void
-+CNcbiBoostLogger::log_exception(ostream& ostr, but::log_checkpoint_data const& lcd,
-+                                boost::execution_exception const& ex)
-+{
-+    m_Upper->log_exception(ostr, lcd, ex);
-+}
-+#else
- void
- CNcbiBoostLogger::log_exception(ostream& ostr, but::log_checkpoint_data const& lcd,
-                                 but::const_string explanation)
- {
-     m_Upper->log_exception(ostr, lcd, explanation);
- }
-+#endif
- 
- void
- CNcbiBoostLogger::log_entry_start(ostream& ostr, but::log_entry_data const& led,
-@@ -1631,9 +1714,74 @@ NcbiTestGetUnit(CTempString test_name)
- END_NCBI_SCOPE
- 
- 
-+using namespace but;
-+
- /// Global initialization function called from Boost framework
--but::test_suite*
-+test_suite*
- init_unit_test_suite(int argc, char* argv[])
- {
-     return NCBI_NS_NCBI::s_GetTestApp().InitTestFramework(argc, argv);
- }
-+
-+// This main() is mostly a copy from Boost's unit_test_main.ipp
-+int
-+main(int argc, char* argv[])
-+{
-+    int result = boost::exit_success;
-+
-+    try {
-+        framework::init( &init_unit_test_suite, argc, argv );
-+
-+        if( !runtime_config::test_to_run().is_empty() ) {
-+            test_case_filter filter( runtime_config::test_to_run() );
-+
-+            traverse_test_tree( framework::master_test_suite().p_id, filter );
-+        }
-+
-+        framework::run();
-+
-+        // Let's try to make report in case of any error after all catches.
-+        //results_reporter::make_report();
-+
-+        if (!runtime_config::no_result_code()) {
-+            result = results_collector.results( framework::master_test_suite().p_id ).result_code();
-+            if (!NCBI_NS_NCBI::s_GetTestApp().HasTestErrors()
-+                &&  NCBI_NS_NCBI::s_GetTestApp().HasTestTimeouts())
-+            {
-+                // This should certainly go to the output. So we can use only
-+                // printf, nothing else.
-+                printf("There were no test failures, only timeouts.\n"
-+                       " (for autobuild scripts: NCBI_UNITTEST_TIMEOUTS_BUT_NO_ERRORS)\n");
-+            }
-+        }
-+    }
-+#if BOOST_VERSION >= 104200
-+    catch( framework::nothing_to_test const& ) {
-+        result = boost::exit_success;
-+    }
-+#endif
-+    catch( framework::internal_error const& ex ) {
-+        results_reporter::get_stream() << "Boost.Test framework internal error: " << ex.what() << std::endl;
-+        
-+        result = boost::exit_exception_failure;
-+    }
-+    catch( framework::setup_error const& ex ) {
-+        results_reporter::get_stream() << "Test setup error: " << ex.what() << std::endl;
-+        
-+        result = boost::exit_exception_failure;
-+    }
-+    catch( std::exception const& ex ) {
-+        results_reporter::get_stream() << "Test framework error: " << ex.what() << std::endl;
-+
-+        result = boost::exit_exception_failure;
-+    }
-+    catch( ... ) {
-+        results_reporter::get_stream() << "Boost.Test framework internal error: unknown reason" << std::endl;
-+        
-+        result = boost::exit_exception_failure;
-+    }
-+
-+    results_reporter::make_report();
-+
-+    return result;
-+}
-diff --git a/c++/src/objtools/blast/seqdb_reader/seqdbimpl.hpp b/c++/src/objtools/blast/seqdb_reader/seqdbimpl.hpp
-index 92e817f..cfab8ab 100644
---- a/c++/src/objtools/blast/seqdb_reader/seqdbimpl.hpp
-+++ b/c++/src/objtools/blast/seqdb_reader/seqdbimpl.hpp
-@@ -1199,7 +1199,7 @@ private:
-     CSeqDBAtlasHolder m_AtlasHolder;
-     
-     /// Reference to memory management layer.
--    mutable CSeqDBAtlas & m_Atlas;
-+    CSeqDBAtlas & m_Atlas;
-     
-     /// The list of database names provided to the constructor.
-     string m_DBNames;
-diff --git a/c++/src/serial/stdtypes.cpp b/c++/src/serial/stdtypes.cpp
-index f6fa651..d6e8f80 100644
---- a/c++/src/serial/stdtypes.cpp
-+++ b/c++/src/serial/stdtypes.cpp
-@@ -720,7 +720,7 @@ public:
-             if ( IsSigned() ) {
-                 // signed -> unsigned
-                 // check for negative value
--                if ( IsNegative(value) )
-+                if ( CParent::IsNegative(value) )
-                     ThrowIntegerOverflow();
-             }
-             if ( sizeof(value) > sizeof(result) ) {
-@@ -751,7 +751,7 @@ public:
-                 // unsigned -> signed
-                 if ( sizeof(value) == sizeof(result) ) {
-                     // same size - check for sign change only
--                    if ( IsNegative(result) )
-+                    if ( CParent::IsNegative(result) )
-                         ThrowIntegerOverflow();
-                 }
-             }
-@@ -786,7 +786,7 @@ public:
-             if ( IsSigned() ) {
-                 // signed -> unsigned
-                 // check for negative value
--                if ( IsNegative(value) )
-+                if ( CParent::IsNegative(value) )
-                     ThrowIntegerOverflow();
-             }
-             if ( sizeof(value) > sizeof(result) ) {
-@@ -817,7 +817,7 @@ public:
-                 // unsigned -> signed
-                 if ( sizeof(value) == sizeof(result) ) {
-                     // same size - check for sign change only
--                    if ( IsNegative(result) )
-+                    if ( CParent::IsNegative(result) )
-                         ThrowIntegerOverflow();
-                 }
-             }
diff --git a/sci-biology/rmblast/files/rmblast-1.2-never_build_test_boost.patch b/sci-biology/rmblast/files/rmblast-1.2-never_build_test_boost.patch
deleted file mode 100644
index 9303b35f4..000000000
--- a/sci-biology/rmblast/files/rmblast-1.2-never_build_test_boost.patch
+++ /dev/null
@@ -1,11 +0,0 @@
---- c++/src/corelib/Makefile.in.old	2016-12-19 17:30:15.284886605 +0100
-+++ c++/src/corelib/Makefile.in	2016-12-19 17:30:22.994886600 +0100
-@@ -7,7 +7,7 @@
- #################################
- 
- USR_PROJ = precompile
--LIB_PROJ = corelib test_mt test_boost
-+LIB_PROJ = corelib test_mt
- SUB_PROJ = test
- 
- EXTRA_CONFIGURABLES = Makefile.precompile ncbicfg.c
diff --git a/sci-biology/rmblast/metadata.xml b/sci-biology/rmblast/metadata.xml
deleted file mode 100644
index 8417d1580..000000000
--- a/sci-biology/rmblast/metadata.xml
+++ /dev/null
@@ -1,8 +0,0 @@
-<?xml version="1.0" encoding="UTF-8"?>
-<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
-<pkgmetadata>
-	<maintainer type="project">
-		<email>sci-biology@gentoo.org</email>
-		<name>Gentoo Biology Project</name>
-	</maintainer>
-</pkgmetadata>
diff --git a/sci-biology/rmblast/rmblast-1.2-r2.ebuild b/sci-biology/rmblast/rmblast-1.2-r2.ebuild
deleted file mode 100644
index 8dd036436..000000000
--- a/sci-biology/rmblast/rmblast-1.2-r2.ebuild
+++ /dev/null
@@ -1,49 +0,0 @@
-# Copyright 1999-2016 Gentoo Foundation
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=5
-
-inherit eutils flag-o-matic toolchain-funcs
-
-MY_NCBI_BLAST_V=2.2.23+
-
-DESCRIPTION="RepeatMasker compatible version of NCBI BLAST+ ${MY_NCBI_BLAST_V}"
-HOMEPAGE="http://www.repeatmasker.org/RMBlast.html"
-SRC_URI="http://www.repeatmasker.org/rmblast-${PV}-ncbi-blast-${MY_NCBI_BLAST_V}-src.tar.gz"
-
-LICENSE="OSL-2.1"
-SLOT="0"
-IUSE="test"
-KEYWORDS="~amd64 ~x86"
-
-RDEPEND="dev-libs/boost"
-DEPEND="${RDEPEND}
-	app-arch/cpio"
-
-S="${WORKDIR}/${P}-ncbi-blast-${MY_NCBI_BLAST_V}-src/c++"
-
-src_prepare() {
-	filter-ldflags -Wl,--as-needed
-	sed \
-		-e 's/-print-file-name=libstdc++.a//' \
-		-e '/sed/ s/\([gO]\[0-9\]\)\*/\1\\+/' \
-		-e "/DEF_FAST_FLAGS=/s:=\".*\":=\"${CFLAGS}\":g" \
-		-e 's/2.95\* | 2.96\* | 3\.\* | 4\.\* )/2.95\* | 2.96\* | \[3-9\]\.\* )/g' \
-		-i src/build-system/configure || die
-	epatch "${FILESDIR}"/${P}-gcc47.patch
-	epatch "${FILESDIR}"/${P}-never_build_test_boost.patch
-}
-
-src_configure() {
-	tc-export CXX CC
-	local myconf
-	use test || myconf+=( --with-projects="${FILESDIR}"/disable-testsuite-compilation.txt )
-
-	"${S}"/configure --without-debug \
-		--with-mt \
-		--without-static \
-		--with-dll \
-		--prefix="${ED}"/opt/${PN} \
-		--with-boost="${EPREFIX}"/usr/include/boost ${myconf[@]} \
-		|| die
-}
diff --git a/sci-biology/rnaplex/files/rnaplex-0.2-inline.patch b/sci-biology/rnaplex/files/rnaplex-0.2-inline.patch
new file mode 100644
index 000000000..30d05cd97
--- /dev/null
+++ b/sci-biology/rnaplex/files/rnaplex-0.2-inline.patch
@@ -0,0 +1,14 @@
+--- a/lib/fold.c
++++ b/lib/fold.c
+@@ -64,9 +64,9 @@ PRIVATE void backtrack(const char *sequence, int s);
+ PRIVATE int fill_arrays(const char *sequence);
+ /*@unused@*/
+ INLINE PRIVATE  int oldLoopEnergy(int i, int j, int p, int q, int type, int type_2);
+-INLINE int  LoopEnergy(int n1, int n2, int type, int type_2,
++int  LoopEnergy(int n1, int n2, int type, int type_2,
+ 			 int si1, int sj1, int sp1, int sq1);
+-INLINE int  HairpinE(int size, int type, int si1, int sj1, const char *string);
++int  HairpinE(int size, int type, int si1, int sj1, const char *string);
+ 
+ #define MAXSECTORS      500     /* dimension for a backtrack array */
+ #define LOCALITY        0.      /* locality parameter for base-pairs */
diff --git a/sci-biology/rnaplex/rnaplex-0.2.ebuild b/sci-biology/rnaplex/rnaplex-0.2.ebuild
index 11de0007c..5892f4676 100644
--- a/sci-biology/rnaplex/rnaplex-0.2.ebuild
+++ b/sci-biology/rnaplex/rnaplex-0.2.ebuild
@@ -1,17 +1,24 @@
-# Copyright 1999-2015 Gentoo Foundation
+# Copyright 1999-2021 Gentoo Authors
 # Distributed under the terms of the GNU General Public License v2
 
-EAPI=5
+EAPI=7
 
-MY_P=RNAplex-${PV}
+inherit flag-o-matic
 
+MY_P=RNAplex-${PV}
 DESCRIPTION="RNA-RNA interaction search"
 HOMEPAGE="http://www.bioinf.uni-leipzig.de/Software/RNAplex/"
 SRC_URI="http://www.bioinf.uni-leipzig.de/Software/RNAplex/${MY_P}.tar.gz"
 
 LICENSE="GPL-2"
 SLOT="0"
-IUSE=""
 KEYWORDS="~amd64 ~x86"
 
-S=${WORKDIR}/${MY_P}
+S="${WORKDIR}/${MY_P}"
+
+PATCHES=( "${FILESDIR}"/${P}-inline.patch )
+
+src_configure() {
+	append-cflags -fcommon
+	default
+}
diff --git a/sci-biology/roche454ace2caf/Manifest b/sci-biology/roche454ace2caf/Manifest
deleted file mode 100644
index 6711cecd3..000000000
--- a/sci-biology/roche454ace2caf/Manifest
+++ /dev/null
@@ -1 +0,0 @@
-DIST roche454ace2gap-2010-12-08.tgz 261317 BLAKE2B e00ba3b1d19c9856447c74d3943854e2c6556c14ef19a1abe73a6e0375b8e889c57b4c00beda2f9f9adf6cb76f6f89a12bfe9c9782b5668c0f883e914fa68204 SHA512 ce477ab88c45e947764d0dcb667f76de195db8f1ebc53ca6892f74017a79e231f77c458564a9ac682679bb6b486493ee6692157628401351de5a732894e5a732
diff --git a/sci-biology/roche454ace2caf/metadata.xml b/sci-biology/roche454ace2caf/metadata.xml
deleted file mode 100644
index 138cb7705..000000000
--- a/sci-biology/roche454ace2caf/metadata.xml
+++ /dev/null
@@ -1,12 +0,0 @@
-<?xml version="1.0" encoding="UTF-8"?>
-<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
-<pkgmetadata>
-	<maintainer type="person">
-		<email>mmokrejs@fold.natur.cuni.cz</email>
-		<name>Martin Mokrejs</name>
-	</maintainer>
-	<maintainer type="project">
-		<email>sci-biology@gentoo.org</email>
-		<name>Gentoo Biology Project</name>
-	</maintainer>
-</pkgmetadata>
diff --git a/sci-biology/roche454ace2caf/roche454ace2caf-20100812.ebuild b/sci-biology/roche454ace2caf/roche454ace2caf-20100812.ebuild
deleted file mode 100644
index dc93a2bec..000000000
--- a/sci-biology/roche454ace2caf/roche454ace2caf-20100812.ebuild
+++ /dev/null
@@ -1,29 +0,0 @@
-# Copyright 1999-2016 Gentoo Foundation
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=6
-
-DESCRIPTION="ace to gap4 converter"
-HOMEPAGE="http://genome.imb-jena.de/software/roche454ace2caf"
-SRC_URI="http://genome.imb-jena.de/software/roche454ace2caf/download/src/roche454ace2gap-2010-12-08.tgz"
-
-LICENSE="FLI-Jena"
-SLOT="0"
-KEYWORDS=""
-IUSE=""
-
-DEPEND=""
-RDEPEND="${DEPEND}
-	sci-biology/align_to_scf
-	sci-biology/sff_dump
-	sci-biology/caftools
-	sci-biology/staden
-	dev-lang/perl
-	app-shells/ksh"
-
-S="${WORKDIR}"/roche2gap
-
-src_install(){
-	dobin bin/*.pl bin/roche454ace2gap
-	dosym bin/roche454ace2gap roche2gap # claims to require ksh, have not tested bash
-}
diff --git a/sci-biology/roiextractors/Manifest b/sci-biology/roiextractors/Manifest
new file mode 100644
index 000000000..4db78b7b8
--- /dev/null
+++ b/sci-biology/roiextractors/Manifest
@@ -0,0 +1 @@
+DIST roiextractors-0.5.1.gh.tar.gz 288765 BLAKE2B 5e1b1931f3da8c1157fc2668c203e3ea9812b94246b85e97848d25ff880b1b6d9433637b9847a28dc53c9d88746d1eaa472c7beffd2593d461a24f98eaddd997 SHA512 6f02decfca12f45c8e18ad9ee07931a5891a2099b046e56a7c415d179d93bc6b9a47a320e4ce500217b1f02abdbbdb59c7e85b4f0a773cbd44ba983f5b7595d6
diff --git a/sci-biology/roiextractors/metadata.xml b/sci-biology/roiextractors/metadata.xml
new file mode 100644
index 000000000..000a44418
--- /dev/null
+++ b/sci-biology/roiextractors/metadata.xml
@@ -0,0 +1,16 @@
+<?xml version='1.0' encoding='UTF-8'?>
+<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
+<pkgmetadata>
+	<maintainer type="person">
+		<email>gentoo@chymera.eu</email>
+		<name>Horea Christian</name>
+	</maintainer>
+	<maintainer type="project">
+		<email>sci@gentoo.org</email>
+		<name>Gentoo Science Project</name>
+	</maintainer>
+	<upstream>
+		<remote-id type="github">catalystneuro/roiextractors</remote-id>
+		<remote-id type="pypi">roiextractors</remote-id>
+	</upstream>
+</pkgmetadata>
diff --git a/sci-biology/roiextractors/roiextractors-0.5.1.ebuild b/sci-biology/roiextractors/roiextractors-0.5.1.ebuild
new file mode 100644
index 000000000..1c2fba6ea
--- /dev/null
+++ b/sci-biology/roiextractors/roiextractors-0.5.1.ebuild
@@ -0,0 +1,40 @@
+# Copyright 2021-2023 Gentoo Authors
+# Distributed under the terms of the GNU General Public License v2
+
+EAPI=8
+
+PYTHON_COMPAT=( python3_{10..11} )
+DISTUTILS_USE_PEP517=setuptools
+inherit distutils-r1
+
+DESCRIPTION="Optical imaging data handling from several file formats"
+HOMEPAGE="https://github.com/catalystneuro/roiextractors"
+SRC_URI="https://github.com/catalystneuro/roiextractors/archive/refs/tags/v${PV}.tar.gz -> ${P}.gh.tar.gz"
+
+LICENSE="BSD"
+SLOT="0"
+KEYWORDS="~amd64"
+IUSE=""
+
+RDEPEND="
+	dev-python/dill[${PYTHON_USEDEP}]
+	dev-python/h5py[${PYTHON_USEDEP}]
+	dev-python/lazy_ops[${PYTHON_USEDEP}]
+	dev-python/psutil[${PYTHON_USEDEP}]
+	dev-python/pynwb[${PYTHON_USEDEP}]
+	dev-python/pyyaml[${PYTHON_USEDEP}]
+	dev-python/scipy[${PYTHON_USEDEP}]
+	dev-python/tqdm[${PYTHON_USEDEP}]
+"
+BDEPEND="
+	test? (
+		dev-python/parameterized[${PYTHON_USEDEP}]
+		dev-python/spikeinterface[${PYTHON_USEDEP}]
+	)
+"
+
+distutils_enable_tests pytest
+
+python_test() {
+	epytest tests/test_internals
+}
diff --git a/sci-biology/rtg-tools/metadata.xml b/sci-biology/rtg-tools/metadata.xml
deleted file mode 100644
index 138cb7705..000000000
--- a/sci-biology/rtg-tools/metadata.xml
+++ /dev/null
@@ -1,12 +0,0 @@
-<?xml version="1.0" encoding="UTF-8"?>
-<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
-<pkgmetadata>
-	<maintainer type="person">
-		<email>mmokrejs@fold.natur.cuni.cz</email>
-		<name>Martin Mokrejs</name>
-	</maintainer>
-	<maintainer type="project">
-		<email>sci-biology@gentoo.org</email>
-		<name>Gentoo Biology Project</name>
-	</maintainer>
-</pkgmetadata>
diff --git a/sci-biology/rtg-tools/rtg-tools-9999.ebuild b/sci-biology/rtg-tools/rtg-tools-9999.ebuild
deleted file mode 100644
index b658f7c17..000000000
--- a/sci-biology/rtg-tools/rtg-tools-9999.ebuild
+++ /dev/null
@@ -1,44 +0,0 @@
-# Copyright 1999-2018 Gentoo Foundation
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=6
-
-inherit java-pkg-2 java-ant-2 eutils git-r3
-
-DESCRIPTION="Manipulate and analyze VCF files"
-HOMEPAGE="https://github.com/RealTimeGenomics/rtg-tools"
-EGIT_REPO_URI="https://github.com/RealTimeGenomics/rtg-tools.git"
-
-LICENSE="BSD-2"
-SLOT="0"
-KEYWORDS=""
-IUSE=""
-
-DEPEND="
-		>=virtual/jdk-1.8:*
-		dev-java/ant-core
-		dev-java/jython"
-RDEPEND="${DEPEND}
-		>=virtual/jre-1.8:*"
-
-src_compile(){
-	ant runalltests || die
-}
-
-# "${S}"/lib/sam-2.9.1.jar
-# "${S}"/lib/findbugs-annotations.jar
-# "${S}"/lib/findbugs-jsr305.jar
-# "${S}"/lib/velocity-tools-generic.jar
-# "${S}"/lib/RPlot.jar
-# "${S}"/lib/commons-collections-3.2.1.jar
-# "${S}"/lib/velocity-1.7.jar
-# "${S}"/lib/commons-compress-1.4.1.jar
-# "${S}"/lib/commons-lang-2.4.jar
-# "${S}"/lib/jumble-annotations.jar
-# "${S}"/lib/sam-2.9.1-src.jar
-# "${S}"/lib/gzipfix.jar
-# "${S}"/buildLib/ant-contrib-1.0b3.jar
-# "${S}"/buildLib/handlechecker.jar
-# "${S}"/testLib/hamcrest-core-1.3.jar
-# "${S}"/testLib/junit.jar
-# "${S}"/testLib/spelling.jar
diff --git a/sci-biology/ruffus/Manifest b/sci-biology/ruffus/Manifest
deleted file mode 100644
index 25c7b46c7..000000000
--- a/sci-biology/ruffus/Manifest
+++ /dev/null
@@ -1 +0,0 @@
-DIST ruffus-2.6.3.tar.gz 36863807 BLAKE2B 7862e42968b9e4af9daa89d13270a3b1472510e60252d46065fea5a977507a492070df4e17fa8a785417f1c220edcde8e3c8c0083b066b333d61be1401b9ece8 SHA512 47d9090d51bda9bb8a14b1c874fd5980e52380cff707719760b1ce4c81f6ed6b7eceb8c37530ede7725bdec12e0a958e8f4a95f7acc1d6a75d907260c5f42d81
diff --git a/sci-biology/ruffus/metadata.xml b/sci-biology/ruffus/metadata.xml
deleted file mode 100644
index 1a91c19c5..000000000
--- a/sci-biology/ruffus/metadata.xml
+++ /dev/null
@@ -1,15 +0,0 @@
-<?xml version="1.0" encoding="UTF-8"?>
-<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
-<pkgmetadata>
-	<maintainer type="person">
-		<email>mmokrejs@fold.natur.cuni.cz</email>
-		<name>Martin Mokrejs</name>
-	</maintainer>
-	<maintainer type="project">
-		<email>sci-biology@gentoo.org</email>
-		<name>Gentoo Biology Project</name>
-	</maintainer>
-	<upstream>
-		<remote-id type="pypi">ruffus</remote-id>
-	</upstream>
-</pkgmetadata>
diff --git a/sci-biology/ruffus/ruffus-2.6.3.ebuild b/sci-biology/ruffus/ruffus-2.6.3.ebuild
deleted file mode 100644
index b4417d29c..000000000
--- a/sci-biology/ruffus/ruffus-2.6.3.ebuild
+++ /dev/null
@@ -1,22 +0,0 @@
-# Copyright 1999-2017 Gentoo Foundation
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=5
-
-PYTHON_COMPAT=( python2_7 )
-
-inherit distutils-r1
-
-DESCRIPTION="Python module to support computational pipelines"
-HOMEPAGE="http://www.ruffus.org.uk"
-SRC_URI="mirror://pypi/${PN:0:1}/${PN}/${P}.tar.gz"
-# git@github.com:bunbun/ruffus.git
-
-LICENSE="MIT"
-SLOT="0"
-KEYWORDS="~amd64 ~x86"
-IUSE=""
-
-DEPEND="dev-python/setuptools[${PYTHON_USEDEP}]
-		media-gfx/graphviz"
-RDEPEND="${DEPEND}"
diff --git a/sci-biology/ruffus/ruffus-9999.ebuild b/sci-biology/ruffus/ruffus-9999.ebuild
deleted file mode 100644
index 9c12d9170..000000000
--- a/sci-biology/ruffus/ruffus-9999.ebuild
+++ /dev/null
@@ -1,23 +0,0 @@
-# Copyright 1999-2017 Gentoo Foundation
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=5
-
-PYTHON_COMPAT=( python2_7 )
-
-inherit distutils-r1 git-r3
-
-DESCRIPTION="Python module to support computational pipelines"
-HOMEPAGE="http://www.ruffus.org.uk"
-# SRC_URI="http://code.google.com/p/ruffus/downloads/detail?name=ruffus-2.4beta3.tar.gz"
-EGIT_REPO_URI="https://code.google.com/archive/p/ruffus"
-# git@github.com:bunbun/ruffus.git
-
-LICENSE="MIT"
-SLOT="0"
-KEYWORDS=""
-IUSE=""
-
-DEPEND="dev-python/setuptools[${PYTHON_USEDEP}]
-		media-gfx/graphviz"
-RDEPEND="${DEPEND}"
diff --git a/sci-biology/rum/Manifest b/sci-biology/rum/Manifest
deleted file mode 100644
index 4fdb9270f..000000000
--- a/sci-biology/rum/Manifest
+++ /dev/null
@@ -1 +0,0 @@
-DIST rum-2.0.5.5.tar.gz 5420665 BLAKE2B 76fdb44b468e493c34be766aaaf62c2670f926a2c11b43f73e386db4d8bf7a05d5a33bfe03a3a314446c515fd60ef1b8e53982b33de7cbc081e0fe000209dbcd SHA512 7a6600e7d98fa4649a281b161eaaaa2fbfd337b7b26b0d054e23974aa555a383d476b5464183b259812330c4e00a36be44a5efe210950e2ad24ab867375cb9be
diff --git a/sci-biology/rum/metadata.xml b/sci-biology/rum/metadata.xml
deleted file mode 100644
index 032147c48..000000000
--- a/sci-biology/rum/metadata.xml
+++ /dev/null
@@ -1,15 +0,0 @@
-<?xml version="1.0" encoding="UTF-8"?>
-<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
-<pkgmetadata>
-	<maintainer type="person">
-		<email>mmokrejs@fold.natur.cuni.cz</email>
-		<name>Martin Mokrejs</name>
-	</maintainer>
-	<maintainer type="project">
-		<email>sci-biology@gentoo.org</email>
-		<name>Gentoo Biology Project</name>
-	</maintainer>
-	<upstream>
-		<remote-id type="github">itmat/rum</remote-id>
-	</upstream>
-</pkgmetadata>
diff --git a/sci-biology/rum/rum-2.0.5.5.ebuild b/sci-biology/rum/rum-2.0.5.5.ebuild
deleted file mode 100644
index 015bb1499..000000000
--- a/sci-biology/rum/rum-2.0.5.5.ebuild
+++ /dev/null
@@ -1,37 +0,0 @@
-# Copyright 1999-2015 Gentoo Foundation
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=5
-
-inherit perl-module eutils
-
-DESCRIPTION="RNA-Seq Unified Mapper (digital normalization)"
-HOMEPAGE="https://github.com/itmat/rum/wiki"
-SRC_URI="https://github.com/itmat/rum/archive/v2.0.5_05.tar.gz -> ${P}.tar.gz"
-
-# stable
-#EGIT_REPO_URI="https://github.com/PGFI/rum/tags"
-
-# dev
-#EGIT_REPO_URI="https://github.com/PGFI/rum"
-
-LICENSE="UPennState"
-SLOT="0"
-KEYWORDS="~amd64 ~x86"
-IUSE=""
-
-DEPEND="
-	dev-perl/Log-Log4perl
-	virtual/perl-autodie"
-RDEPEND="${DEPEND}
-	sci-biology/seqclean
-	sci-biology/blat
-	sci-biology/bowtie
-	sci-biology/seqclean"
-
-S="${WORKDIR}/${PN}-2.0.5_05"
-
-src_install(){
-	default
-	rm "${ED}"/usr/lib64/perl5/vendor_perl/*/RUM/{bowtie,blat,mdust} ]] die
-}
diff --git a/sci-biology/sabre/sabre-9999.ebuild b/sci-biology/sabre/sabre-9999.ebuild
index bfa4bde63..222fcac9a 100644
--- a/sci-biology/sabre/sabre-9999.ebuild
+++ b/sci-biology/sabre/sabre-9999.ebuild
@@ -1,17 +1,15 @@
-# Copyright 1999-2015 Gentoo Foundation
+# Copyright 1999-2021 Gentoo Authors
 # Distributed under the terms of the GNU General Public License v2
 
-EAPI=5
-
-[ "$PV" == "9999" ] && inherit git-r3
+EAPI=7
 
 inherit toolchain-funcs
 
 DESCRIPTION="Barcode demultiplexing and trimming tool for Illumina FastQ files"
 HOMEPAGE="https://github.com/najoshi/sabre"
 if [ "$PV" == "9999" ]; then
+	inherit git-r3
 	EGIT_REPO_URI="https://github.com/najoshi/sabre.git"
-	KEYWORDS=""
 else
 	SRC_URI=""
 	KEYWORDS=""
@@ -23,9 +21,8 @@ SLOT="0"
 DEPEND="sys-libs/zlib"
 RDEPEND="${DEPEND}"
 
-S="${S}"/src
-
 src_prepare(){
+	default
 	sed -e "s#OPT = -O3#OPT = ${CFLAGS}#" \
 		-e "s#CC = gcc#CC = $(tc-getCC)#" -i Makefile || die
 }
diff --git a/sci-biology/sailfish/Manifest b/sci-biology/sailfish/Manifest
deleted file mode 100644
index cb996531b..000000000
--- a/sci-biology/sailfish/Manifest
+++ /dev/null
@@ -1 +0,0 @@
-DIST sailfish-0.10.0.tar.gz 1621862 BLAKE2B d04d8db99e1d191ad1bea690bf43f31d23d6505bc3e80399cfafbbf4e1404edf8a4bbe0532e2c47ec59a5a26f50509342a7143bc0b0c41c3a8723ec0f6e53bd4 SHA512 ec66cff89dac037b84deaf997b7769802f594e69820d42915fb830bfcd527786c9c466a9476bdf2b29b9f7481e98905acf580f4a766765bccaa1b0ced22c4bb2
diff --git a/sci-biology/sailfish/files/sailfish-0.9.2-no-boost-static.patch b/sci-biology/sailfish/files/sailfish-0.9.2-no-boost-static.patch
deleted file mode 100644
index 7ac3d0882..000000000
--- a/sci-biology/sailfish/files/sailfish-0.9.2-no-boost-static.patch
+++ /dev/null
@@ -1,20 +0,0 @@
-Do not force static and multithreaded boost libs, use what is available
-
-Patch by Michael Schubert
-
---- a/CMakeLists.txt
-+++ b/CMakeLists.txt
-@@ -162,13 +162,6 @@ if ( DEFINED CUSTOM_BOOST_PATH )
-     set (CMAKE_LIBRARY_PATH ${CUSTOM_BOOST_PATH}/lib ${CMAKE_LIBRARY_PATH})
- endif ( DEFINED CUSTOM_BOOST_PATH )
- 
--##
--# We want static, multithreaded boost libraries
--##
--set (Boost_USE_STATIC_LIBS ON)
--set (Boost_USE_MULTITHREADED ON)
--#set (Boost_USE_STATIC_RUNTIME OFF)
--
- find_package (ZLIB)
- if (NOT ZLIB_FOUND)
- 	message (FATAL_ERROR "zlib must be installed before configuration & building can proceed")
diff --git a/sci-biology/sailfish/metadata.xml b/sci-biology/sailfish/metadata.xml
deleted file mode 100644
index 530333987..000000000
--- a/sci-biology/sailfish/metadata.xml
+++ /dev/null
@@ -1,15 +0,0 @@
-<?xml version="1.0" encoding="UTF-8"?>
-<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
-<pkgmetadata>
-	<maintainer type="project">
-		<email>sci-biology@gentoo.org</email>
-		<name>Gentoo Biology Project</name>
-	</maintainer>
-	<maintainer type="person">
-		<email>mschu.dev@gmail.com</email>
-		<name>Michael Schubert</name>
-	</maintainer>
-	<upstream>
-		<remote-id type="github">kingsfordgroup/sailfish</remote-id>
-	</upstream>
-</pkgmetadata>
diff --git a/sci-biology/sailfish/sailfish-0.10.0.ebuild b/sci-biology/sailfish/sailfish-0.10.0.ebuild
deleted file mode 100644
index 228fcfdbb..000000000
--- a/sci-biology/sailfish/sailfish-0.10.0.ebuild
+++ /dev/null
@@ -1,38 +0,0 @@
-# Copyright 1999-2018 Gentoo Foundation
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=6
-
-inherit cmake-utils multilib
-
-DESCRIPTION="Rapid Mapping-based Isoform Quantification from RNA-Seq Reads"
-HOMEPAGE="http://www.cs.cmu.edu/~ckingsf/software/sailfish/"
-SRC_URI="https://github.com/kingsfordgroup/${PN}/archive/v${PV}.tar.gz -> ${P}.tar.gz"
-
-LICENSE="GPL-3+"
-SLOT="0"
-KEYWORDS=""
-IUSE=""
-
-PATCHES=( "${FILESDIR}"/${PN}-0.9.2-no-boost-static.patch )
-
-DEPEND="dev-libs/boost:0
-		dev-libs/jemalloc
-		dev-cpp/tbb
-		sci-biology/jellyfish:2"
-RDEPEND="${DEPEND}"
-# a C++-11 compliant compiler is needs, aka >=gcc-4.7
-
-# TODO: disable running wget/curl during src_compile
-# https://github.com/kingsfordgroup/sailfish/issues/80
-# contains bundled RapMap https://github.com/COMBINE-lab/RapMap
-# contains bundled libdivsufsort
-# contains bundled libgff https://github.com/COMBINE-lab/libgff
-# contains bundled jellyfish-2.2.5
-# contains bundled sparsehash-2.0.2
-
-src_install() {
-	cmake-utils_src_install
-	rm -r "${ED}"/usr/tests || die
-	rm -f "${ED}"/usr/bin/jellyfish "${ED}"/usr/$(get_libdir)/libjellyfish || die
-}
diff --git a/sci-biology/sailfish/sailfish-9999.ebuild b/sci-biology/sailfish/sailfish-9999.ebuild
deleted file mode 100644
index 29a967af8..000000000
--- a/sci-biology/sailfish/sailfish-9999.ebuild
+++ /dev/null
@@ -1,37 +0,0 @@
-# Copyright 1999-2018 Gentoo Foundation
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=6
-
-inherit cmake-utils git-r3 multilib
-
-DESCRIPTION="Rapid Mapping-based Isoform Quantification from RNA-Seq Reads"
-HOMEPAGE="http://www.cs.cmu.edu/~ckingsf/software/sailfish/"
-SRC_URI=""
-EGIT_REPO_URI="https://github.com/kingsfordgroup/sailfish.git"
-
-LICENSE="GPL-3"
-SLOT="0"
-IUSE=""
-
-PATCHES=( "${FILESDIR}"/${PN}-0.9.2-no-boost-static.patch )
-
-DEPEND="dev-libs/boost:0
-		dev-libs/jemalloc
-		dev-cpp/tbb
-		sci-biology/jellyfish:2"
-RDEPEND="${DEPEND}"
-
-# TODO: disable running wget/curl during src_compile
-# https://github.com/kingsfordgroup/sailfish/issues/80
-# contains bundled RapMap https://github.com/COMBINE-lab/RapMap
-# contains bundled libdivsufsort
-# contains bundled libgff https://github.com/COMBINE-lab/libgff
-# contains bundled jellyfish-2.2.5
-# contains bundled sparsehash-2.0.2
-
-src_install() {
-	cmake-utils_src_install
-	rm -r "${ED}"/usr/tests || die
-	rm -f "${ED}"/usr/bin/jellyfish "${ED}"/usr/$(get_libdir)/libjellyfish || die
-}
diff --git a/sci-biology/salmon/Manifest b/sci-biology/salmon/Manifest
deleted file mode 100644
index 8a357c311..000000000
--- a/sci-biology/salmon/Manifest
+++ /dev/null
@@ -1,7 +0,0 @@
-DIST bwa-0.7.12.5.tar.gz 224584 BLAKE2B af273aa6751d73e82ce1891acdd42c7cbb0f332312157e1bcaf3f6175417f7358f1d73fd900ede7bddc4071b62f68ea8c79d1e0eb04f02ee618130bd0c33579f SHA512 c56a08c115fd15ca017f5ca5a2e053aef4df9fdf7b3a8f575646b2443cb38853dcd17e72588750dc0c8acdd7accca173d84894220d6cd06959ba0d994851f6c9
-DIST cereal-1.2.2.tar.gz 335759 BLAKE2B 6804b9aabb235a546758c70554502208f1b7b6bcab9b602fa075123335331f0522191a83027fdbac4ee947881c6866f24f48223a00b9490fca5ca961f3e4b260 SHA512 9567b2e19add9446b24f8afd122eea09ba6ecd1a090335cf0ab31fdc8f64c6c97daa3d9eaf0801c36a770737488e0eebf81d96d7b7a65deed30da6130f2d47eb
-DIST libgff-1.1.tgz 79006 BLAKE2B 626a62614c4c52d823104eae78e4f04e0976eb43cd2ea7b820ac6549535771fb2ecccbcf4476a22f53a66b5d8bea4fd260c6d3cee864a2c1b264c6f223744dac SHA512 af797fdc753c21a61a817f0b57da55c523220a9c831a71b73328a49ec66b667a503f1fcbddab714826f802a4e2becf310265535276973e2978d5ad73525fa0bb
-DIST salmon-0.10.2.tar.gz 10766806 BLAKE2B f9ba6f208a72a11f37c44a056e9b464f4bf018db88c13e67ce84fcdecee98d878046b2018b144dd48a152300f1ba0a178cf03c5c541b16358e210a5013fdfdce SHA512 828c3d5f3f8f42181bf4b563a49f789bdb82843cbdc9aec4555e7623642e2c663a2552ea7bfd1967cc4f8033e6f0678f8f6f82ce776bc2312bc0b4b8ab7ed19f
-DIST salmon-0.10.2_RapMap.zip 1141708 BLAKE2B 397341693e0388093af8ffe620fa91941c584de0887a648d219a3f5662ffd6f9af22179f205bfb83927bc8913756b4d68cbc9179cbfb11f9b329c6aed32220a1 SHA512 8aa593feb61a45d25cc757f39b907e6e0cc108831bad69857268f3ac19614d76cf88de6d8679e52d3eea43bcf5b603bfd55135ececf39acb1700a23408fca573
-DIST spdlog-0.16.1.tar.gz 162408 BLAKE2B c90b94bac128f8b143d85522d224223b1361f7d552d9caa8b253e494dd72de56a2149cbd8d568eb4305224d7caf80d8067fbce606a1071bd94f74c43b3245782 SHA512 0ef741f2abcae7c925808b44bba7d2e55aa8bd3b07a77ab6e785068beb505cdbcd7835d7d103e8e96094235e262954969a176d9f4977e9d373f1bee8e2716ff2
-DIST staden-io_lib-1.14.8.tar.gz 2506985 BLAKE2B 0d64847d0958e0efc763e87bf0600e3af90d30b67c77908b2effa20b18ce43a0d5ad1b213747c46f9e9000a75c4f1260759b3c90cd632be821e039870a26eb4b SHA512 535c6701e61a1786ceb7b22905afe702d277e0383816fba82f69af553dd22ca497bf00766f9768fd9173621632483a02ea9919437e1786008b2236c1c2c8c69f
diff --git a/sci-biology/salmon/files/salmon-0.10.2-no-boost-static.patch b/sci-biology/salmon/files/salmon-0.10.2-no-boost-static.patch
deleted file mode 100644
index ac561d793..000000000
--- a/sci-biology/salmon/files/salmon-0.10.2-no-boost-static.patch
+++ /dev/null
@@ -1,18 +0,0 @@
---- salmon-0.10.2/CMakeLists.txt	2018-06-25 10:51:47.179712781 +0200
-+++ salmon-0.10.2/CMakeLists.txt	2018-06-25 10:52:47.951289159 +0200
-@@ -213,15 +213,6 @@
-     set (CMAKE_LIBRARY_PATH ${CUSTOM_BOOST_PATH}/lib ${CMAKE_LIBRARY_PATH})
- endif ( DEFINED CUSTOM_BOOST_PATH )
- 
--##
--# We want static, multithreaded boost libraries
--##
--if(CONDA_BUILD)
--  set (Boost_USE_STATIC_LIBS OFF)
--else ()
--  set (Boost_USE_STATIC_LIBS ON)
--endif(CONDA_BUILD)
--
- set (Boost_USE_MULTITHREADED ON)
- #set (Boost_USE_STATIC_RUNTIME OFF)
- 
diff --git a/sci-biology/salmon/files/salmon-0.10.2_TestSalmonQuasi.cmake.patch b/sci-biology/salmon/files/salmon-0.10.2_TestSalmonQuasi.cmake.patch
deleted file mode 100644
index 81edf96f5..000000000
--- a/sci-biology/salmon/files/salmon-0.10.2_TestSalmonQuasi.cmake.patch
+++ /dev/null
@@ -1,11 +0,0 @@
---- salmon-0.10.2/cmake/TestSalmonQuasi.cmake	2018-06-26 10:39:51.061971241 +0200
-+++ salmon-0.10.2/cmake/TestSalmonQuasi.cmake	2018-06-26 10:40:22.372822258 +0200
-@@ -5,7 +5,7 @@
-                 )
- 
- if (SALMON_QUASI_INDEX_RESULT)
--    message(FATAL_ERROR "Error running ${SALMON_QUASI_INDEX_COMMAND}")
-+    message(FATAL_ERROR "Error running ${SALMON_QUASI_INDEX_CMD}")
- endif()
- 
- set(SALMON_QUANT_COMMAND ${CMAKE_BINARY_DIR}/salmon quant -i sample_salmon_quasi_index -l IU -1 reads_1.fastq -2 reads_2.fastq -o sample_salmon_quasi_quant)
diff --git a/sci-biology/salmon/files/salmon-0.10.2_fix_lib_dir.patch b/sci-biology/salmon/files/salmon-0.10.2_fix_lib_dir.patch
deleted file mode 100644
index eb606c00c..000000000
--- a/sci-biology/salmon/files/salmon-0.10.2_fix_lib_dir.patch
+++ /dev/null
@@ -1,22 +0,0 @@
---- salmon-0.10.2/src/CMakeLists.txt	2018-06-25 13:35:45.723519730 +0200
-+++ salmon-0.10.2/src/CMakeLists.txt	2018-06-25 13:44:01.326139539 +0200
-@@ -296,6 +296,8 @@
-     )
- ENDIF(CMAKE_INSTALL_PREFIX_INITIALIZED_TO_DEFAULT)
- 
-+include(GNUInstallDirs)
-+
- set(INSTALL_LIB_DIR lib )
- set(INSTALL_BIN_DIR bin )
- set(INSTALL_INCLUDE_DIR include )
-@@ -311,8 +313,8 @@
- 
- install(TARGETS salmon salmon_core
-                 RUNTIME DESTINATION bin
--                LIBRARY DESTINATION lib
--                ARCHIVE DESTINATION lib
-+                LIBRARY DESTINATION "${CMAKE_INSTALL_FULL_LIBDIR}"
-+                ARCHIVE DESTINATION "${CMAKE_INSTALL_FULL_LIBDIR}"
-         )
- 
- add_custom_command(TARGET unitTests POST_BUILD
diff --git a/sci-biology/salmon/files/salmon-0.10.2_fix_tests.patch b/sci-biology/salmon/files/salmon-0.10.2_fix_tests.patch
deleted file mode 100644
index 0a95757a8..000000000
--- a/sci-biology/salmon/files/salmon-0.10.2_fix_tests.patch
+++ /dev/null
@@ -1,10 +0,0 @@
---- salmon-0.10.2/src/CMakeLists.txt.ori	2018-06-26 10:34:29.293225671 +0200
-+++ salmon-0.10.2/src/CMakeLists.txt	2018-06-26 10:35:24.674730920 +0200
-@@ -335,6 +335,6 @@
- )
- 
- include(InstallRequiredSystemLibraries)
--add_test( NAME unit_tests COMMAND ${CMAKE_COMMAND} -DTOPLEVEL_DIR=${CMAKE_INSTALL_PREFIX} -P ${GAT_SOURCE_DIR}/cmake/UnitTests.cmake )
-+add_test( NAME unit_tests COMMAND ${CMAKE_COMMAND} -DTOPLEVEL_DIR=${GAT_SOURCE_DIR} -P ${GAT_SOURCE_DIR}/cmake/UnitTests.cmake )
- add_test( NAME salmon_read_test_fmd COMMAND ${CMAKE_COMMAND} -DTOPLEVEL_DIR=${GAT_SOURCE_DIR} -P ${GAT_SOURCE_DIR}/cmake/TestSalmonFMD.cmake )
- add_test( NAME salmon_read_test_quasi COMMAND ${CMAKE_COMMAND} -DTOPLEVEL_DIR=${GAT_SOURCE_DIR} -P ${GAT_SOURCE_DIR}/cmake/TestSalmonQuasi.cmake )
diff --git a/sci-biology/salmon/files/salmon-0.10.2_remove_curl_call.patch b/sci-biology/salmon/files/salmon-0.10.2_remove_curl_call.patch
deleted file mode 100644
index 8eddc6e3a..000000000
--- a/sci-biology/salmon/files/salmon-0.10.2_remove_curl_call.patch
+++ /dev/null
@@ -1,12 +0,0 @@
---- salmon-9999/scripts/fetchRapMap.sh	2018-06-25 11:11:07.019798309 +0200
-+++ salmon-9999/scripts/fetchRapMap.sh	2018-06-25 11:12:25.131824486 +0200
-@@ -29,7 +29,8 @@
- EXPECTED_SHA256=c4ca27de299bee395b404d117d9d98ad9f0d6ee256ea1deb2890ea402893e688
- 
- mkdir -p ${EXTERNAL_DIR}
--curl -k -L https://github.com/COMBINE-lab/RapMap/archive/${SVER}.zip -o ${EXTERNAL_DIR}/rapmap.zip
-+# curl -k -L https://github.com/COMBINE-lab/RapMap/archive/${SVER}.zip -o ${EXTERNAL_DIR}/rapmap.zip
-+cp ../../distdir/salmon-0.10.2_RapMap.zip ${EXTERNAL_DIR}/rapmap.zip
- 
- hashcheck=""
- if exists sha256sum; then
diff --git a/sci-biology/salmon/files/salmon-0.10.2_remove_curl_calls.patch b/sci-biology/salmon/files/salmon-0.10.2_remove_curl_calls.patch
deleted file mode 100644
index 438763960..000000000
--- a/sci-biology/salmon/files/salmon-0.10.2_remove_curl_calls.patch
+++ /dev/null
@@ -1,200 +0,0 @@
---- salmon-0.10.2/CMakeLists.txt	2018-06-25 13:12:49.275828719 +0200
-+++ salmon-0.10.2/CMakeLists.txt	2018-06-25 13:12:38.945565690 +0200
-@@ -235,31 +235,7 @@
- 
- find_package (LibLZMA)
- if (NOT LIBLZMA_FOUND)
--    message ("Will attempt to fetch and build liblzma")
--    message ("=======================================")
--ExternalProject_Add(liblzma
--    DOWNLOAD_DIR ${CMAKE_CURRENT_SOURCE_DIR}/external
--    ##
--    DOWNLOAD_COMMAND curl -k -L http://tukaani.org/xz/xz-5.2.2.tar.gz -o xz-5.2.2.tar.gz &&
--                     ${SHASUM} 73df4d5d34f0468bd57d09f2d8af363e95ed6cc3a4a86129d2f2c366259902a2 xz-5.2.2.tar.gz &&
--                     tar -xzvf xz-5.2.2.tar.gz
--    #URL http://tukaani.org/xz/xz-5.2.2.tar.gz
--    #URL_HASH SHA1=14663612422ab61386673be78fbb2556f50a1f08
--    ##
--    SOURCE_DIR ${CMAKE_CURRENT_SOURCE_DIR}/external/xz-5.2.2
--    INSTALL_DIR ${CMAKE_CURRENT_SOURCE_DIR}/external/install
--    BUILD_IN_SOURCE TRUE
--    CONFIGURE_COMMAND ${CMAKE_CURRENT_SOURCE_DIR}/external/xz-5.2.2/configure --prefix=<INSTALL_DIR> CC=${CMAKE_C_COMPILER} CXX=${CMAKE_CXX_COMPILER} CFLAGS=${EXTRA_CMAKE_INCLUDE_FLAGS} CPPFLAGS=${EXTRA_CMAKE_INCLUDE_FLAGS} LDFLAGS=${EXTRA_CMAKE_LIBRARY_FLAGS}
--    BUILD_COMMAND make ${QUIET_MAKE}
--    INSTALL_COMMAND make ${QUIET_MAKE} install
--)
--
--# Tell cmake that the external project generated a library so we can
--# add dependencies here instead of later
--set (LIBLZMA_LIBRARIES ${GAT_SOURCE_DIR}/external/install/lib/liblzma.a)
--set (LIBSTADEN_LDFLAGS "-L${GAT_SOURCE_DIR}/external/install/lib")
--set (LIBSTADEN_CFLAGS "-I${GAT_SOURCE_DIR}/external/install/include")
--set (FETCHED_LIBLZMA TRUE)
-+    message (FATAL_ERROR "liblzma must be installed before configuration & building can proceed")
- else()
-     message("Found liblzma library: ${LIBLZMA_LIBRARIES}")
-     message("===========================================")
-@@ -267,28 +243,7 @@
- 
- find_package (BZip2)
- if (NOT BZIP2_FOUND)
--    message ("Will attempt to fetch and build libbz2")
--    message ("=======================================")
--ExternalProject_Add(libbz2
--    DOWNLOAD_DIR ${CMAKE_CURRENT_SOURCE_DIR}/external
--    DOWNLOAD_COMMAND curl -k -L http://www.bzip.org/1.0.6/bzip2-1.0.6.tar.gz -o bzip2-1.0.6.tar.gz &&
--                     ${SHASUM} a2848f34fcd5d6cf47def00461fcb528a0484d8edef8208d6d2e2909dc61d9cd bzip2-1.0.6.tar.gz &&
--                     tar -xzvf  bzip2-1.0.6.tar.gz
--    #URL http://www.bzip.org/1.0.6/bzip2-1.0.6.tar.gz
--    #URL_HASH SHA1=3f89f861209ce81a6bab1fd1998c0ef311712002
--    SOURCE_DIR ${CMAKE_CURRENT_SOURCE_DIR}/external/bzip2-1.0.6
--    INSTALL_DIR ${CMAKE_CURRENT_SOURCE_DIR}/external/install
--    BUILD_IN_SOURCE TRUE
--    CONFIGURE_COMMAND ""
--    BUILD_COMMAND make ${QUIET_MAKE} CC=${CMAKE_C_COMPILER} CXX=${CMAKE_CXX_COMPILER}
--    INSTALL_COMMAND make ${QUIET_MAKE} install PREFIX=<INSTALL_DIR>
--)
--# Tell cmake that the external project generated a library so we can
--# add dependencies here instead of later
--set (BZIP2_LIBRARIES ${GAT_SOURCE_DIR}/external/install/lib/libbz2.a)
--set (LIBSTADEN_LDFLAGS "-L${GAT_SOURCE_DIR}/external/install/lib -I${GAT_SOURCE_DIR}/external/install/include")
--set (LIBSTADEN_CFLAGS "-I${GAT_SOURCE_DIR}/external/install/include")
--set (FETCHED_LIBBZ2 TRUE)
-+    message (FATAL_ERROR "libbz2 must be installed before configuration & building can proceed")
- else()
-     message("Found libbz2 library: ${BZIP2_LIBRARIES}")
-     message("===========================================")
-@@ -333,61 +288,15 @@
- # Either inform the user of how to obtain Boost, or, if they passed in the FETCH_BOOST
- # option, go and grab it for them.
- ##
--if ((NOT Boost_FOUND) AND (NOT FETCH_BOOST))
-+if (NOT Boost_FOUND)
- 	message(FATAL_ERROR
-         "Salmon cannot be compiled without Boost.\n"
-         "It is recommended to visit http://www.boost.org/ and install Boost according to those instructions.\n"
-         "This build system can also download and install a local version of boost for you (this takes a lot of time).\n"
-         "To fetch and build boost locally, call cmake with -DFETCH_BOOST=TRUE"
-     )
--elseif(FETCH_BOOST)
--    ## Let the rest of the build process know we're going to be fetching boost
--    set (BOOST_LIB_SUBSET --with-iostreams --with-atomic --with-chrono --with-container --with-date_time --with-exception
--                          --with-filesystem --with-graph --with-graph_parallel --with-math
--                          --with-program_options --with-system --with-thread
--                          --with-timer)
--    set (BOOST_WILL_RECONFIGURE TRUE)
--    set (FETCH_BOOST FALSE)
--    message("Build system will fetch and build Boost")
--    message("==================================================================")
--    ExternalProject_Add(libboost
--        DOWNLOAD_DIR ${CMAKE_CURRENT_SOURCE_DIR}/external
--        DOWNLOAD_COMMAND curl -k -L  http://downloads.sourceforge.net/project/boost/boost/1.66.0/boost_1_66_0.tar.gz -o boost_1_66_0.tar.gz &&
--                         ${SHASUM} bd0df411efd9a585e5a2212275f8762079fed8842264954675a4fddc46cfcf60 boost_1_66_0.tar.gz &&
--                         tar xzf boost_1_66_0.tar.gz
--        SOURCE_DIR ${CMAKE_CURRENT_SOURCE_DIR}/external/boost_1_66_0
--        INSTALL_DIR ${CMAKE_CURRENT_SOURCE_DIR}/external/install
--        #PATCH_COMMAND patch -p2 < ${CMAKE_CURRENT_SOURCE_DIR}/external/boost156.patch
--	CONFIGURE_COMMAND CC=${CMAKE_C_COMPILER} CXX=${CMAKE_CXX_COMPILER} ${CMAKE_CURRENT_SOURCE_DIR}/external/boost_1_66_0/bootstrap.sh ${BOOST_CONFIGURE_TOOLSET} ${BOOST_BUILD_LIBS} --prefix=<INSTALL_DIR>
--	BUILD_COMMAND CC=${CMAKE_C_COMPILER} CXX=${CMAKE_CXX_COMPILER} ${CMAKE_CURRENT_SOURCE_DIR}/external/boost_1_66_0/b2 -d0 -j2 ${BOOST_LIB_SUBSET} toolset=${BOOST_TOOLSET} ${BOOST_EXTRA_FLAGS} cxxflags=${BOOST_CXX_FLAGS} link=static install
--        BUILD_IN_SOURCE 1
--        INSTALL_COMMAND ""
--    )
--
--    ##
--    # After we've installed boost,
--    ##
--    SET( RECONFIG_FLAGS ${RECONFIG_FLAGS} -DBOOST_WILL_RECONFIGURE=FALSE -DBOOST_RECONFIGURE=TRUE -DFETCH_BOOST=FALSE)
--    ExternalProject_Add_Step(libboost reconfigure
--        COMMAND ${CMAKE_COMMAND} ${CMAKE_CURRENT_SOURCE_DIR} ${RECONFIG_FLAGS}
--        DEPENDEES install
--    )
--    set (FETCHED_BOOST TRUE)
- endif()
- 
--##
--# If we're fetching boost and we need to have dummy paths for these variables
--# so that CMake won't complain
--##
--if (BOOST_WILL_RECONFIGURE)
--    message("Setting Temporary Boost paths")
--    set(Boost_INCLUDE_DIR ${CMAKE_CURRENT_SOURCE_DIR}/external/install/include)
--    set(Boost_INCLUDE_DIRS ${CMAKE_CURRENT_SOURCE_DIR}/external/install/include)
--    set(Boost_LIBRARY_DIRS ${CMAKE_CURRENT_SOURCE_DIR}/external/install/lib)
--    set(Boost_FOUND TRUE)
--endif()
--
--
- message("BOOST INCLUDE DIR = ${Boost_INCLUDE_DIR}")
- message("BOOST INCLUDE DIRS = ${Boost_INCLUDE_DIRS}")
- message("BOOST LIB DIR = ${Boost_LIBRARY_DIRS}")
-@@ -422,9 +331,9 @@
- include(ExternalProject)
- ExternalProject_Add(libcereal
-     DOWNLOAD_DIR ${CMAKE_CURRENT_SOURCE_DIR}/external
--    DOWNLOAD_COMMAND curl -k -L https://github.com/USCiLab/cereal/archive/v1.2.2.tar.gz -o cereal-v1.2.2.tar.gz &&		 
--                     ${SHASUM} 1921f26d2e1daf9132da3c432e2fd02093ecaedf846e65d7679ddf868c7289c4  cereal-v1.2.2.tar.gz &&
--                     tar -xzvf cereal-v1.2.2.tar.gz
-+    DOWNLOAD_COMMAND cp ../../../distdir/cereal-1.2.2.tar.gz . &&		 
-+                     ${SHASUM} 1921f26d2e1daf9132da3c432e2fd02093ecaedf846e65d7679ddf868c7289c4  cereal-1.2.2.tar.gz &&
-+                     tar -xzvf cereal-1.2.2.tar.gz
- 
-     ##
-     #URL https://github.com/USCiLab/cereal/archive/v1.2.2.tar.gz
-@@ -455,12 +364,12 @@
- ExternalProject_Add(libbwa
-     DOWNLOAD_DIR ${CMAKE_CURRENT_SOURCE_DIR}/external
-     #URL https://github.com/COMBINE-lab/bwa/archive/0.7.12.3.tar.gz
--    #DOWNLOAD_NAME bwa-master.tar.gz
--    DOWNLOAD_COMMAND curl -k -L https://github.com/COMBINE-lab/bwa/archive/v0.7.12.5.tar.gz -o bwa-master.tar.gz &&
--                    ${SHASUM} 1ac5661d9e12e9017a47f0264201a75d9128f28dbd9a26952925f7745ddf6036 bwa-master.tar.gz &&
--                    mkdir -p bwa-master &&
--                    tar -xzvf bwa-master.tar.gz --strip-components=1 -C bwa-master
--    SOURCE_DIR ${CMAKE_CURRENT_SOURCE_DIR}/external/bwa-master
-+    #DOWNLOAD_NAME bwa-0.7.12.5.tar.gz
-+    DOWNLOAD_COMMAND cp ../../../distdir/bwa-0.7.12.5.tar.gz . &&
-+                    ${SHASUM} 1ac5661d9e12e9017a47f0264201a75d9128f28dbd9a26952925f7745ddf6036 bwa-0.7.12.5.tar.gz &&
-+                    mkdir -p bwa-0.7.12.5 &&
-+                    tar -xzvf bwa-0.7.12.5.tar.gz --strip-components=1 -C bwa-0.7.12.5
-+    SOURCE_DIR ${CMAKE_CURRENT_SOURCE_DIR}/external/bwa-0.7.12.5
-     INSTALL_DIR ${CMAKE_CURRENT_SOURCE_DIR}/external/install
-     CONFIGURE_COMMAND ""
-     BUILD_COMMAND sh -c "make ${QUIET_MAKE} CC=${CMAKE_C_COMPILER} CXX=${CMAKE_CXX_COMPILER}"
-@@ -562,9 +471,9 @@
- message("==================================================================")
- ExternalProject_Add(libgff
-     DOWNLOAD_DIR ${CMAKE_CURRENT_SOURCE_DIR}/external
--    DOWNLOAD_COMMAND curl -k -L https://github.com/COMBINE-lab/libgff/archive/v1.1.tar.gz -o libgff.tgz &&
--                     ${SHASUM} 34597ecd3718e6d6e7a1dd4350220664be2c1cd992070d1218564a20d7aa5697  libgff.tgz &&
--                     tar -xzvf libgff.tgz 
-+    DOWNLOAD_COMMAND cp ../../../distdir/libgff-1.1.tgz . &&
-+                     ${SHASUM} 34597ecd3718e6d6e7a1dd4350220664be2c1cd992070d1218564a20d7aa5697 libgff-1.1.tgz &&
-+                     tar -xzvf libgff-1.1.tgz
-     ##
-     #URL https://github.com/COMBINE-lab/libgff/archive/v1.1.tar.gz
-     #DOWNLOAD_NAME libff.tgz
-@@ -600,10 +509,10 @@
- message("==================================================================")
- ExternalProject_Add(libstadenio
-     DOWNLOAD_DIR ${CMAKE_CURRENT_SOURCE_DIR}/external
--    DOWNLOAD_COMMAND curl -k -L https://github.com/COMBINE-lab/staden-io_lib/archive/v1.14.8.1.tar.gz -o staden-io_lib-v1.14.8.tar.gz &&
--                     ${SHASUM} f6f30eefa478cfb708f3109a35fb6ffa0e24951d9d971985df2cef5919dd0bc3 staden-io_lib-v1.14.8.tar.gz &&
-+    DOWNLOAD_COMMAND cp ../../../distdir/staden-io_lib-1.14.8.tar.gz . &&
-+                     ${SHASUM} f6f30eefa478cfb708f3109a35fb6ffa0e24951d9d971985df2cef5919dd0bc3 staden-io_lib-1.14.8.tar.gz &&
-                      mkdir -p staden-io_lib-1.14.8 &&
--                     tar -xzf staden-io_lib-v1.14.8.tar.gz --strip-components=1 -C staden-io_lib-1.14.8 &&
-+                     tar -xzf staden-io_lib-1.14.8.tar.gz --strip-components=1 -C staden-io_lib-1.14.8 &&
-                      rm -fr staden-io_lib &&
-                      mv -f staden-io_lib-1.14.8 staden-io_lib
-     SOURCE_DIR ${CMAKE_CURRENT_SOURCE_DIR}/external/staden-io_lib
-@@ -620,9 +529,9 @@
- message("==================================================================")
- ExternalProject_Add(libspdlog
-     DOWNLOAD_DIR ${CMAKE_CURRENT_SOURCE_DIR}/external
--    DOWNLOAD_COMMAND curl -k -L https://github.com/COMBINE-lab/spdlog/archive/v0.16.1.tar.gz -o spdlog-v0.16.1.tar.gz &&
--                     ${SHASUM} 733260e1fbdcf1b3dc307fc585e4476240026de8be28eb905731d2ab0942deae spdlog-v0.16.1.tar.gz &&
--                     tar -xzf spdlog-v0.16.1.tar.gz 
-+    DOWNLOAD_COMMAND cp ../../../distdir/spdlog-0.16.1.tar.gz . &&
-+                     ${SHASUM} 733260e1fbdcf1b3dc307fc585e4476240026de8be28eb905731d2ab0942deae spdlog-0.16.1.tar.gz &&
-+                     tar -xzf spdlog-0.16.1.tar.gz 
-     ##
-     #URL https://github.com/COMBINE-lab/spdlog/archive/v0.12.0.tar.gz
-     #DOWNLOAD_NAME spdlog-v0.12.0.tar.gz
diff --git a/sci-biology/salmon/metadata.xml b/sci-biology/salmon/metadata.xml
deleted file mode 100644
index 1907254d6..000000000
--- a/sci-biology/salmon/metadata.xml
+++ /dev/null
@@ -1,15 +0,0 @@
-<?xml version="1.0" encoding="UTF-8"?>
-<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
-<pkgmetadata>
-	<maintainer type="project">
-		<email>sci-biology@gentoo.org</email>
-		<name>Gentoo Biology Project</name>
-	</maintainer>
-	<maintainer type="person">
-		<email>mschu.dev@gmail.com</email>
-		<name>Michael Schubert</name>
-	</maintainer>
-	<upstream>
-		<remote-id type="github">COMBINE-lab/salmon</remote-id>
-	</upstream>
-</pkgmetadata>
diff --git a/sci-biology/salmon/salmon-0.10.2.ebuild b/sci-biology/salmon/salmon-0.10.2.ebuild
deleted file mode 100644
index 088fea331..000000000
--- a/sci-biology/salmon/salmon-0.10.2.ebuild
+++ /dev/null
@@ -1,55 +0,0 @@
-# Copyright 1999-2018 Gentoo Foundation
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=6
-
-inherit cmake-utils
-
-DESCRIPTION="Transcript-level quantification from RNA-seq reads using lightweight alignments"
-HOMEPAGE="https://github.com/COMBINE-lab/salmon"
-SRC_URI="https://github.com/COMBINE-lab/${PN}/archive/v${PV}.tar.gz -> ${P}.tar.gz
-	https://github.com/COMBINE-lab/RapMap/archive/salmon-v0.10.2.zip -> ${P}_RapMap.zip
-	https://github.com/USCiLab/cereal/archive/v1.2.2.tar.gz -> cereal-1.2.2.tar.gz
-	https://github.com/COMBINE-lab/bwa/archive/v0.7.12.5.tar.gz -> bwa-0.7.12.5.tar.gz
-	https://github.com/COMBINE-lab/libgff/archive/v1.1.tar.gz -> libgff-1.1.tgz
-	https://github.com/COMBINE-lab/staden-io_lib/archive/v1.14.8.1.tar.gz -> staden-io_lib-1.14.8.tar.gz
-	https://github.com/COMBINE-lab/spdlog/archive/v0.16.1.tar.gz -> spdlog-0.16.1.tar.gz"
-
-LICENSE="GPL-3"
-SLOT="0"
-KEYWORDS="~amd64 ~x86 ~amd64-linux ~x86-linux"
-IUSE=""
-
-PATCHES=( "${FILESDIR}"/${P}-no-boost-static.patch
-		"${FILESDIR}"/salmon-0.10.2_remove_curl_call.patch
-		"${FILESDIR}"/salmon-0.10.2_remove_curl_calls.patch
-		"${FILESDIR}"/salmon-0.10.2_fix_lib_dir.patch
-		"${FILESDIR}"/salmon-0.10.2_fix_tests.patch
-		"${FILESDIR}"/salmon-0.10.2_TestSalmonQuasi.cmake.patch )
-
-RDEPEND="${DEPEND}"
-# budled copies of:
-# sci-biology/bwa-0.7.12.5
-# sci-biology/jellyfish
-# sci-biology/staden-1.14.8.1
-# sci-biology/gfftools
-#
-# libgff-1.1 from https://github.com/Kingsford-Group/libgff
-#    actually unreleased version from https://github.com/COMBINE-lab/libgff/archive/v1.1.tar.gz
-#    https://github.com/Kingsford-Group/libgff/issues/1
-#
-# dev-libs/spdlog-0.16.1
-# cereal-1.2.2
-
-# see the many curl executions:
-# salmon-0.10.2$ find . -type f | xargs grep curl 2>/dev/null
-#
-DEPEND="net-misc/curl
-		app-arch/unzip
-		sys-libs/zlib
-		app-arch/bzip2
-		app-arch/xz-utils
-		dev-libs/boost:0[threads]
-		>=dev-libs/jemalloc-5.0.1
-		>=dev-cpp/tbb-2018.20180312"
-RDEPEND="${DEPEND}"
diff --git a/sci-biology/salmon/salmon-9999.ebuild b/sci-biology/salmon/salmon-9999.ebuild
deleted file mode 100644
index 8862ff790..000000000
--- a/sci-biology/salmon/salmon-9999.ebuild
+++ /dev/null
@@ -1,69 +0,0 @@
-# Copyright 1999-2018 Gentoo Foundation
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=6
-
-inherit multilib cmake-utils git-r3
-
-DESCRIPTION="Transcript-level quantification from RNA-seq reads using lightweight alignments"
-HOMEPAGE="https://github.com/COMBINE-lab/salmon"
-EGIT_REPO_URI="https://github.com/COMBINE-lab/salmon.git"
-#SRC_URI="https://github.com/COMBINE-lab/RapMap/archive/salmon-v0.10.2.zip -> ${P}_RapMap.zip
-#    https://github.com/USCiLab/cereal/archive/v1.2.2.tar.gz -> cereal-1.2.2.tar.gz
-#    https://github.com/COMBINE-lab/bwa/archive/v0.7.12.5.tar.gz -> bwa-0.7.12.5.tar.gz
-#    https://github.com/COMBINE-lab/libgff/archive/v1.1.tar.gz -> libgff-1.1.tgz
-#    https://github.com/COMBINE-lab/staden-io_lib/archive/v1.14.8.1.tar.gz -> staden-io_lib-1.14.8.tar.gz
-#    https://github.com/COMBINE-lab/spdlog/archive/v0.16.1.tar.gz -> spdlog-0.16.1.tar.gz"
-
-LICENSE="GPL-3"
-SLOT="0"
-IUSE=""
-
-PATCHES=( "${FILESDIR}"/salmon-0.10.2-no-boost-static.patch
-	"${FILESDIR}"/salmon-0.10.2_remove_curl_call.patch
-	"${FILESDIR}"/salmon-0.10.2_remove_curl_calls.patch
-	"${FILESDIR}"/salmon-0.10.2_fix_lib_dir.patch
-	"${FILESDIR}"/salmon-0.10.2_fix_tests.patch
-	"${FILESDIR}"/salmon-0.10.2_TestSalmonQuasi.cmake.patch )
-
-# budled copies of:
-# sci-biology/bwa-0.7.12.5
-# sci-biology/jellyfish
-# sci-biology/staden-1.14.8.1
-# sci-biology/gfftools
-#
-# libgff-1.1 from https://github.com/Kingsford-Group/libgff
-#    actually unreleased version from https://github.com/COMBINE-lab/libgff/archive/v1.1.tar.gz
-#    https://github.com/Kingsford-Group/libgff/issues/1
-#
-# dev-libs/spdlog-0.16.1
-# cereal-1.2.2
-DEPEND="net-misc/curl
-		app-arch/unzip
-		sys-libs/zlib
-		app-arch/bzip2
-		app-arch/xz-utils
-		dev-libs/boost:0[threads]
-		>=dev-libs/jemalloc-5.0.1
-		>=dev-cpp/tbb-2018.20180312"
-RDEPEND="${DEPEND}"
-
-# https://github.com/COMBINE-lab/salmon/issues/19
-#
-# contains bundled copies of https://github.com/jemalloc/jemalloc
-# https://github.com/gabime/spdlog
-# https://github.com/efficient/libcuckoo
-# https://github.com/greg7mdp/sparsepp
-# https://github.com/COMBINE-lab/RapMap , actually runs curl to fetch it
-# https://github.com/Kingsford-Group/libgff
-# sci-libs/io_lib
-#
-# https://github.com/COMBINE-lab/salmon/issues/19#issuecomment-144721158
-# modified bwa copy
-#
-# and maybe more
-
-# See https://github.com/COMBINE-lab/salmon/issues/236 for Cmake tweaks needed by Debian
-
-# see the many curl executions:
-# salmon-0.10.2$ find . -type f | xargs grep curl 2>/dev/null
diff --git a/sci-biology/sambamba/Manifest b/sci-biology/sambamba/Manifest
deleted file mode 100644
index c8fbec14b..000000000
--- a/sci-biology/sambamba/Manifest
+++ /dev/null
@@ -1 +0,0 @@
-DIST sambamba-0.6.5.tar.gz 249275 BLAKE2B a01b2863053838c1fe7151e7baf3041c1396ad547ec962d495b8c486cc6f0cdfcbd1cc5c6963795017dfd77e27a605462aa11fb7043dcf2f6ad666e64ad8bbef SHA512 a0353523bb921a32e4f7601d9c5552b2103567cfa23fb622b213170028122f49cb6929942e9a630890ddd93b7ebf00f048344edb75d5f2d10b1c86bae018497c
diff --git a/sci-biology/sambamba/metadata.xml b/sci-biology/sambamba/metadata.xml
deleted file mode 100644
index 3c6df6245..000000000
--- a/sci-biology/sambamba/metadata.xml
+++ /dev/null
@@ -1,15 +0,0 @@
-<?xml version="1.0" encoding="UTF-8"?>
-<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
-<pkgmetadata>
-	<maintainer type="person">
-		<email>mmokrejs@fold.natur.cuni.cz</email>
-		<name>Martin Mokrejs</name>
-	</maintainer>
-	<maintainer type="project">
-		<email>sci-biology@gentoo.org</email>
-		<name>Gentoo Biology Project</name>
-	</maintainer>
-	<upstream>
-		<remote-id type="github">lomereiter/sambamba</remote-id>
-	</upstream>
-</pkgmetadata>
diff --git a/sci-biology/sambamba/sambamba-0.6.5.ebuild b/sci-biology/sambamba/sambamba-0.6.5.ebuild
deleted file mode 100644
index ab2fb990e..000000000
--- a/sci-biology/sambamba/sambamba-0.6.5.ebuild
+++ /dev/null
@@ -1,27 +0,0 @@
-# Copyright 1999-2017 Gentoo Foundation
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=6
-
-DESCRIPTION="Parallell process SAM/BAM/CRAM files faster than samtools"
-HOMEPAGE="http://lomereiter.github.io/sambamba"
-SRC_URI="https://github.com/lomereiter/sambamba/archive/v0.6.5.tar.gz -> ${P}.tar.gz"
-
-LICENSE="GPL-2+"
-SLOT="0"
-KEYWORDS=""
-IUSE="debug"
-
-# https://github.com/ldc-developers/gentoo-overlay/tree/master/dev-lang/ldc2
-#
-# contains bundled htslib
-DEPEND=""
-RDEPEND="${DEPEND}"
-
-src_compile(){
-	if use debug ; then
-		emake sambamba-ldmd2-debug
-	else
-		emake sambamba-ldmd2-64
-	fi
-}
diff --git a/sci-biology/sambamba/sambamba-9999.ebuild b/sci-biology/sambamba/sambamba-9999.ebuild
deleted file mode 100644
index 8cd4c3ba2..000000000
--- a/sci-biology/sambamba/sambamba-9999.ebuild
+++ /dev/null
@@ -1,28 +0,0 @@
-# Copyright 1999-2017 Gentoo Foundation
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=6
-
-inherit git-r3
-
-DESCRIPTION="Parallell process SAM/BAM/CRAM files faster than samtools"
-HOMEPAGE="http://lomereiter.github.io/sambamba"
-EGIT_REPO_URI="https://github.com/lomereiter/sambamba.git"
-
-LICENSE="GPL-2+"
-SLOT="0"
-KEYWORDS=""
-IUSE="debug"
-
-DEPEND=""
-RDEPEND="${DEPEND}"
-
-# https://github.com/ldc-developers/gentoo-overlay/tree/master/dev-lang/ldc2
-
-src_compile(){
-	if use debug ; then
-		emake sambamba-ldmd2-debug
-	else
-		emake sambamba-ldmd2-64
-	fi
-}
diff --git a/sci-biology/samri/Manifest b/sci-biology/samri/Manifest
index 8e2af4995..26d7dd5ed 100644
--- a/sci-biology/samri/Manifest
+++ b/sci-biology/samri/Manifest
@@ -1,2 +1,2 @@
-DIST samri-0.1.tar.gz 1767390 BLAKE2B 65fd268949b5e0e64d4f3aa9eef0fc7016a9404a468865634e1add74f4b8915f86bb7ee5ec9b8383b48ce0ab51624928cf4a6a65fda4595da67098cb72b00fdc SHA512 2d79a06455fae56edc1324a34186cfce2be4999733c502bbafcf6b310848ef4042012fd8f915f9a3ee7bf26f55398af19da93548d8d96453ba33a2ea22bfe775
-DIST samri-0.2.tar.gz 4091362 BLAKE2B 60cf74873027a0e033af946b48a3a3fe56462d3b7305a9a02bdded022af98bca50eb77b851b4d624816e90a18c18ed4ab17ddae22734de9ff404f5e26ed894b0 SHA512 85d0728bf44c62040d4d05736048a8a8d93ed580db763b07db65546de2891bbbb3036a661309cf37ac8ff256b0dcc28b47d4ce84a5a57bc95f3bcc3c24a5d989
+DIST samri-0.5.3.tar.gz 4122035 BLAKE2B 343dc6de7acf74b5fc169c1f07a4a7209483bee1d050021045a9582d13ea9ae2b8bd4dba0f7f876548e218863cd01bf6d12e571e2d83860366e88ceec7f8441c SHA512 fb9c98843477a35ec313d9284c1c23777af7c6c29fbaa3672b6aa7f7357a81ef874883e0f09f97f52a75febed11deb714343bdadc06708f3a5dcb12fea121a06
+DIST samri-0.5.4.tar.gz 4122057 BLAKE2B 3afdfe6198bc61697cac9ab80560d438d3c488b182d0da9b4a8321efca99d733c964bde000ef8a6a8b849df753f3369d8ea3ba984c8a9736fef466fe196dc003 SHA512 c783156b4eb66b146d039338381867d5683c2f90214d4451448da631609e1e0113f803851a04965b9e400ca5bc69910ec8cbaa1af4b023a89ded0ba6b38901b8
diff --git a/sci-biology/samri/metadata.xml b/sci-biology/samri/metadata.xml
index a98f0b857..51e342e68 100644
--- a/sci-biology/samri/metadata.xml
+++ b/sci-biology/samri/metadata.xml
@@ -2,7 +2,7 @@
 <!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
 <pkgmetadata>
 	<maintainer type="person">
-		<email>horea.christ@gmail.com</email>
+		<email>gentoo@chymera.eu</email>
 		<name>Horea Christian</name>
 	</maintainer>
 	<longdescription lang="en">
diff --git a/sci-biology/samri/samri-0.1.ebuild b/sci-biology/samri/samri-0.1.ebuild
deleted file mode 100644
index 94598cb7c..000000000
--- a/sci-biology/samri/samri-0.1.ebuild
+++ /dev/null
@@ -1,58 +0,0 @@
-# Copyright 1999-2018 Gentoo Foundation
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=7
-
-PYTHON_COMPAT=( python{2_7,3_4,3_5} )
-
-inherit distutils-r1
-
-DESCRIPTION="Small Animal Magnetic Resonance Imaging"
-HOMEPAGE="https://github.com/IBT-FMI/SAMRI"
-SRC_URI="https://github.com/IBT-FMI/SAMRI/archive/${PV}.tar.gz -> ${P}.tar.gz"
-
-LICENSE="GPL-3"
-SLOT="0"
-IUSE="atlases labbookdb test"
-KEYWORDS="~amd64 ~x86"
-
-# Numpy dependency to circumvent scikits_learn dependency bug:
-# https://bugs.gentoo.org/653052
-DEPEND="test? ( sci-biology/samri_bindata )"
-RDEPEND="
-	dev-python/argh[${PYTHON_USEDEP}]
-	dev-python/joblib[${PYTHON_USEDEP}]
-	>=dev-python/matplotlib-2.0.2[${PYTHON_USEDEP}]
-	>=dev-python/numpy-1.13.3[${PYTHON_USEDEP}]
-	dev-python/pandas[${PYTHON_USEDEP}]
-	dev-python/seaborn[${PYTHON_USEDEP}]
-	dev-python/sqlalchemy[${PYTHON_USEDEP}]
-	dev-python/statsmodels[${PYTHON_USEDEP}]
-	>=sci-biology/fsl-5.0.9
-	sci-biology/bru2nii
-	atlases? ( sci-biology/mouse-brain-atlases )
-	labbookdb? ( sci-libs/labbookdb[${PYTHON_USEDEP}] )
-	sci-libs/nibabel[${PYTHON_USEDEP}]
-	>=sci-libs/nipy-0.4.1[${PYTHON_USEDEP}]
-	>=sci-libs/nipype-0.14.0_pre20170830[${PYTHON_USEDEP}]
-	sci-libs/pybids[${PYTHON_USEDEP}]
-	sci-libs/scipy[${PYTHON_USEDEP}]
-	sci-biology/ants
-	sci-biology/afni
-	sci-biology/nilearn[${PYTHON_USEDEP}]
-	"
-
-S="${WORKDIR}/SAMRI-${PV}"
-
-python_test() {
-	distutils_install_for_testing
-	export MPLBACKEND="agg"
-	export PATH=${TEST_DIR}/scripts:$PATH
-	export PYTHONIOENCODING=utf-8
-	pytest || die
-	for i in samri/examples/*.py; do
-		echo "Executing ${EPYTHON} ${i}"
-		${EPYTHON} "$i" || die "Example Python script $i failed with ${EPYTHON}"
-	done
-	./test_scripts.sh || die "Test scripts failed."
-}
diff --git a/sci-biology/samri/samri-0.2.ebuild b/sci-biology/samri/samri-0.2.ebuild
deleted file mode 100644
index 12c8d5e01..000000000
--- a/sci-biology/samri/samri-0.2.ebuild
+++ /dev/null
@@ -1,64 +0,0 @@
-# Copyright 1999-2019 Gentoo Authors
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=7
-
-PYTHON_COMPAT=( python{2_7,3_4,3_5,3_6} )
-
-inherit distutils-r1
-
-DESCRIPTION="Small Animal Magnetic Resonance Imaging"
-HOMEPAGE="https://github.com/IBT-FMI/SAMRI"
-SRC_URI="https://github.com/IBT-FMI/SAMRI/archive/${PV}.tar.gz -> ${P}.tar.gz"
-
-LICENSE="GPL-3"
-SLOT="0"
-IUSE="+atlases labbookdb test"
-KEYWORDS="~amd64 ~x86"
-
-# Numpy dependency to circumvent scikits_learn dependency bug:
-# https://bugs.gentoo.org/653052
-DEPEND="
-	test? (
-		dev-python/pytest[${PYTHON_USEDEP}]
-		sci-biology/samri_bidsdata
-		sci-biology/samri_bindata
-		)
-	"
-RDEPEND="
-	dev-python/argh[${PYTHON_USEDEP}]
-	dev-python/joblib[${PYTHON_USEDEP}]
-	>=dev-python/matplotlib-2.0.2[${PYTHON_USEDEP}]
-	>=dev-python/numpy-1.13.3[${PYTHON_USEDEP}]
-	dev-python/pandas[${PYTHON_USEDEP}]
-	dev-python/seaborn[${PYTHON_USEDEP}]
-	dev-python/statsmodels[${PYTHON_USEDEP}]
-	>=sci-biology/fsl-5.0.9
-	sci-biology/bru2nii
-	atlases? ( sci-biology/mouse-brain-atlases )
-	labbookdb? ( sci-libs/labbookdb[${PYTHON_USEDEP}] )
-	sci-libs/nibabel[${PYTHON_USEDEP}]
-	>=sci-libs/nipy-0.4.1[${PYTHON_USEDEP}]
-	>=sci-libs/nipype-0.14.0_pre20170830[${PYTHON_USEDEP}]
-	sci-libs/pybids[${PYTHON_USEDEP}]
-	sci-libs/scipy[${PYTHON_USEDEP}]
-	sci-biology/ants
-	sci-biology/afni
-	sci-biology/nilearn[${PYTHON_USEDEP}]
-	"
-
-REQUIRED_USE="test? ( atlases )"
-
-S="${WORKDIR}/SAMRI-${PV}"
-
-python_test() {
-	distutils_install_for_testing
-	export MPLBACKEND="agg"
-	export PATH=${TEST_DIR}/scripts:$PATH
-	export PYTHONIOENCODING=utf-8
-	./test_scripts.sh || die "Test scripts failed."
-	sed -i -e \
-		"/def test_bru2bids():/i@pytest.mark.skip('Removed in full test suite, as this is already tested in `test_scripts.sh`')" \
-		samri/pipelines/tests/test_repos.py || die
-	pytest -vv || die
-}
diff --git a/sci-biology/samri/samri-0.5.3.ebuild b/sci-biology/samri/samri-0.5.3.ebuild
new file mode 100644
index 000000000..f632f83a8
--- /dev/null
+++ b/sci-biology/samri/samri-0.5.3.ebuild
@@ -0,0 +1,77 @@
+# Copyright 1999-2023 Gentoo Authors
+# Distributed under the terms of the GNU General Public License v2
+
+EAPI=8
+
+PYTHON_COMPAT=( python3_{10..11} )
+DISTUTILS_USE_PEP517=setuptools
+
+inherit distutils-r1 prefix
+
+DESCRIPTION="Small Animal Magnetic Resonance Imaging"
+HOMEPAGE="https://github.com/IBT-FMI/SAMRI"
+if [ "$PV" == "9999" ]; then
+		inherit git-r3
+		EGIT_REPO_URI="https://github.com/IBT-FMI/SAMRI.git"
+else
+		SRC_URI="https://github.com/IBT-FMI/SAMRI/archive/${PV}.tar.gz -> ${P}.tar.gz"
+		KEYWORDS="~amd64"
+		S="${WORKDIR}/SAMRI-${PV}"
+fi
+
+LICENSE="GPL-3"
+SLOT="0"
+IUSE="+atlases labbookdb"
+REQUIRED_USE="test? ( atlases )"
+
+DEPEND="
+	test? (
+		sci-biology/samri_bidsdata
+		sci-biology/samri_bindata
+		)
+	"
+RDEPEND="
+	dev-python/argh[${PYTHON_USEDEP}]
+	dev-python/joblib[${PYTHON_USEDEP}]
+	>=dev-python/matplotlib-2.0.2[${PYTHON_USEDEP}]
+	>=dev-python/numpy-1.13.3[${PYTHON_USEDEP}]
+	dev-python/pandas[${PYTHON_USEDEP}]
+	dev-python/scipy[${PYTHON_USEDEP}]
+	dev-python/seaborn[${PYTHON_USEDEP}]
+	dev-python/statsmodels[${PYTHON_USEDEP}]
+	>=media-gfx/blender-2.83.4
+	>=sci-biology/fsl-5.0.9
+	sci-biology/bru2nii
+	atlases? ( sci-biology/mouse-brain-templates )
+	labbookdb? ( sci-libs/labbookdb[${PYTHON_USEDEP}] )
+	sci-libs/nibabel[${PYTHON_USEDEP}]
+	>=sci-libs/nipy-0.4.1[${PYTHON_USEDEP}]
+	>=sci-libs/nipype-1.0.0[${PYTHON_USEDEP}]
+	<sci-libs/pybids-0.10.2[${PYTHON_USEDEP}]
+	dev-python/scikit-image[${PYTHON_USEDEP}]
+	sci-biology/ants
+	sci-biology/afni
+	sci-biology/nilearn[${PYTHON_USEDEP}]
+"
+
+distutils_enable_tests pytest
+distutils_enable_sphinx doc/source dev-python/sphinxcontrib-napoleon
+
+src_prepare() {
+	distutils-r1_src_prepare
+	sed -i -e "s:/usr:@GENTOO_PORTAGE_EPREFIX@/usr:g" `grep -rlI \'/usr/ samri` || die
+	sed -i -e "s:/usr:@GENTOO_PORTAGE_EPREFIX@/usr:g" `grep -rlI /usr/ test_scripts.sh` || die
+	eprefixify $(grep -rl GENTOO_PORTAGE_EPREFIX samri/* test_scripts.sh)
+}
+
+python_test() {
+	distutils_install_for_testing
+	export MPLBACKEND="agg"
+	export PATH=${TEST_DIR}/scripts:$PATH
+	export PYTHONIOENCODING=utf-8
+	./test_scripts.sh || die "Test scripts failed."
+	sed -i -e \
+		"/def test_bru2bids():/i@pytest.mark.skip('Removed in full test suite, as this is already tested in `test_scripts.sh`')" \
+		samri/pipelines/tests/test_repos.py || die
+	epytest -k "not longtime"
+}
diff --git a/sci-biology/samri/samri-0.5.4.ebuild b/sci-biology/samri/samri-0.5.4.ebuild
new file mode 100644
index 000000000..f632f83a8
--- /dev/null
+++ b/sci-biology/samri/samri-0.5.4.ebuild
@@ -0,0 +1,77 @@
+# Copyright 1999-2023 Gentoo Authors
+# Distributed under the terms of the GNU General Public License v2
+
+EAPI=8
+
+PYTHON_COMPAT=( python3_{10..11} )
+DISTUTILS_USE_PEP517=setuptools
+
+inherit distutils-r1 prefix
+
+DESCRIPTION="Small Animal Magnetic Resonance Imaging"
+HOMEPAGE="https://github.com/IBT-FMI/SAMRI"
+if [ "$PV" == "9999" ]; then
+		inherit git-r3
+		EGIT_REPO_URI="https://github.com/IBT-FMI/SAMRI.git"
+else
+		SRC_URI="https://github.com/IBT-FMI/SAMRI/archive/${PV}.tar.gz -> ${P}.tar.gz"
+		KEYWORDS="~amd64"
+		S="${WORKDIR}/SAMRI-${PV}"
+fi
+
+LICENSE="GPL-3"
+SLOT="0"
+IUSE="+atlases labbookdb"
+REQUIRED_USE="test? ( atlases )"
+
+DEPEND="
+	test? (
+		sci-biology/samri_bidsdata
+		sci-biology/samri_bindata
+		)
+	"
+RDEPEND="
+	dev-python/argh[${PYTHON_USEDEP}]
+	dev-python/joblib[${PYTHON_USEDEP}]
+	>=dev-python/matplotlib-2.0.2[${PYTHON_USEDEP}]
+	>=dev-python/numpy-1.13.3[${PYTHON_USEDEP}]
+	dev-python/pandas[${PYTHON_USEDEP}]
+	dev-python/scipy[${PYTHON_USEDEP}]
+	dev-python/seaborn[${PYTHON_USEDEP}]
+	dev-python/statsmodels[${PYTHON_USEDEP}]
+	>=media-gfx/blender-2.83.4
+	>=sci-biology/fsl-5.0.9
+	sci-biology/bru2nii
+	atlases? ( sci-biology/mouse-brain-templates )
+	labbookdb? ( sci-libs/labbookdb[${PYTHON_USEDEP}] )
+	sci-libs/nibabel[${PYTHON_USEDEP}]
+	>=sci-libs/nipy-0.4.1[${PYTHON_USEDEP}]
+	>=sci-libs/nipype-1.0.0[${PYTHON_USEDEP}]
+	<sci-libs/pybids-0.10.2[${PYTHON_USEDEP}]
+	dev-python/scikit-image[${PYTHON_USEDEP}]
+	sci-biology/ants
+	sci-biology/afni
+	sci-biology/nilearn[${PYTHON_USEDEP}]
+"
+
+distutils_enable_tests pytest
+distutils_enable_sphinx doc/source dev-python/sphinxcontrib-napoleon
+
+src_prepare() {
+	distutils-r1_src_prepare
+	sed -i -e "s:/usr:@GENTOO_PORTAGE_EPREFIX@/usr:g" `grep -rlI \'/usr/ samri` || die
+	sed -i -e "s:/usr:@GENTOO_PORTAGE_EPREFIX@/usr:g" `grep -rlI /usr/ test_scripts.sh` || die
+	eprefixify $(grep -rl GENTOO_PORTAGE_EPREFIX samri/* test_scripts.sh)
+}
+
+python_test() {
+	distutils_install_for_testing
+	export MPLBACKEND="agg"
+	export PATH=${TEST_DIR}/scripts:$PATH
+	export PYTHONIOENCODING=utf-8
+	./test_scripts.sh || die "Test scripts failed."
+	sed -i -e \
+		"/def test_bru2bids():/i@pytest.mark.skip('Removed in full test suite, as this is already tested in `test_scripts.sh`')" \
+		samri/pipelines/tests/test_repos.py || die
+	epytest -k "not longtime"
+}
diff --git a/sci-biology/samri/samri-9999.ebuild b/sci-biology/samri/samri-9999.ebuild
index 758eed180..f632f83a8 100644
--- a/sci-biology/samri/samri-9999.ebuild
+++ b/sci-biology/samri/samri-9999.ebuild
@@ -1,27 +1,31 @@
-# Copyright 1999-2019 Gentoo Authors
+# Copyright 1999-2023 Gentoo Authors
 # Distributed under the terms of the GNU General Public License v2
 
-EAPI=7
+EAPI=8
 
-PYTHON_COMPAT=( python{3_4,3_5,3_6} )
+PYTHON_COMPAT=( python3_{10..11} )
+DISTUTILS_USE_PEP517=setuptools
 
-inherit distutils-r1 git-r3 prefix
+inherit distutils-r1 prefix
 
 DESCRIPTION="Small Animal Magnetic Resonance Imaging"
 HOMEPAGE="https://github.com/IBT-FMI/SAMRI"
-SRC_URI=""
-EGIT_REPO_URI="https://github.com/IBT-FMI/SAMRI"
+if [ "$PV" == "9999" ]; then
+		inherit git-r3
+		EGIT_REPO_URI="https://github.com/IBT-FMI/SAMRI.git"
+else
+		SRC_URI="https://github.com/IBT-FMI/SAMRI/archive/${PV}.tar.gz -> ${P}.tar.gz"
+		KEYWORDS="~amd64"
+		S="${WORKDIR}/SAMRI-${PV}"
+fi
 
 LICENSE="GPL-3"
 SLOT="0"
-IUSE="+atlases labbookdb test"
-KEYWORDS=""
+IUSE="+atlases labbookdb"
+REQUIRED_USE="test? ( atlases )"
 
-# Numpy dependency to circumvent scikits_learn dependency bug:
-# https://bugs.gentoo.org/653052
 DEPEND="
 	test? (
-		dev-python/pytest[${PYTHON_USEDEP}]
 		sci-biology/samri_bidsdata
 		sci-biology/samri_bindata
 		)
@@ -32,29 +36,31 @@ RDEPEND="
 	>=dev-python/matplotlib-2.0.2[${PYTHON_USEDEP}]
 	>=dev-python/numpy-1.13.3[${PYTHON_USEDEP}]
 	dev-python/pandas[${PYTHON_USEDEP}]
+	dev-python/scipy[${PYTHON_USEDEP}]
 	dev-python/seaborn[${PYTHON_USEDEP}]
 	dev-python/statsmodels[${PYTHON_USEDEP}]
+	>=media-gfx/blender-2.83.4
 	>=sci-biology/fsl-5.0.9
 	sci-biology/bru2nii
-	atlases? ( sci-biology/mouse-brain-atlases )
+	atlases? ( sci-biology/mouse-brain-templates )
 	labbookdb? ( sci-libs/labbookdb[${PYTHON_USEDEP}] )
 	sci-libs/nibabel[${PYTHON_USEDEP}]
 	>=sci-libs/nipy-0.4.1[${PYTHON_USEDEP}]
-	>=sci-libs/nipype-0.14.0_pre20170830[${PYTHON_USEDEP}]
-	sci-libs/pybids[${PYTHON_USEDEP}]
-	sci-libs/scipy[${PYTHON_USEDEP}]
+	>=sci-libs/nipype-1.0.0[${PYTHON_USEDEP}]
+	<sci-libs/pybids-0.10.2[${PYTHON_USEDEP}]
+	dev-python/scikit-image[${PYTHON_USEDEP}]
 	sci-biology/ants
 	sci-biology/afni
 	sci-biology/nilearn[${PYTHON_USEDEP}]
-	"
+"
 
-REQUIRED_USE="test? ( atlases )"
+distutils_enable_tests pytest
+distutils_enable_sphinx doc/source dev-python/sphinxcontrib-napoleon
 
 src_prepare() {
 	distutils-r1_src_prepare
-	sed -i -e "s:/usr:@GENTOO_PORTAGE_EPREFIX@/usr:g" `grep -rlI \'/usr/ *`
-	sed -i -e "s:/usr:@GENTOO_PORTAGE_EPREFIX@/usr:g" `grep -rlI \"/usr/ *`
-	sed -i -e "s:/usr:@GENTOO_PORTAGE_EPREFIX@/usr:g" `grep -rlI /usr/ test_scripts.sh`
+	sed -i -e "s:/usr:@GENTOO_PORTAGE_EPREFIX@/usr:g" `grep -rlI \'/usr/ samri` || die
+	sed -i -e "s:/usr:@GENTOO_PORTAGE_EPREFIX@/usr:g" `grep -rlI /usr/ test_scripts.sh` || die
 	eprefixify $(grep -rl GENTOO_PORTAGE_EPREFIX samri/* test_scripts.sh)
 }
 
@@ -64,10 +70,8 @@ python_test() {
 	export PATH=${TEST_DIR}/scripts:$PATH
 	export PYTHONIOENCODING=utf-8
 	./test_scripts.sh || die "Test scripts failed."
-	sed -i \
-		-e '1s/^/import pytest \n/' \
-		-e "/def test_bru2bids():/i@pytest.mark.skip('Skipped by Portage, as this was already tested in test_scripts.sh')" \
-		samri/pipelines/tests/test_reposit.py || die
-	cd "${BUILD_DIR}" || die
-	pytest -vv || die
+	sed -i -e \
+		"/def test_bru2bids():/i@pytest.mark.skip('Removed in full test suite, as this is already tested in `test_scripts.sh`')" \
+		samri/pipelines/tests/test_repos.py || die
+	epytest -k "not longtime"
 }
diff --git a/sci-biology/samri_bidsdata/Manifest b/sci-biology/samri_bidsdata/Manifest
index 4eb51d0c0..e9a3374e1 100644
--- a/sci-biology/samri_bidsdata/Manifest
+++ b/sci-biology/samri_bidsdata/Manifest
@@ -1,2 +1 @@
-DIST samri_bidsdata-0.2.1.tar.xz 11498379580 BLAKE2B 96497a8482ea2274686b2c50ebaaa73dc6ddaab63ebbf6d8e4b26db3bb16df6c587636fbd5d44c0eff840f3cde96ddb6c8e1d77af971ff189428bf6710723d70 SHA512 798ad9405dba3d9ce6c21b04bac62dfc01b3ddea95808cae5867d4e805b23359eaed88b3c99abcfa1a4ce3a2037ceaf3a6804d7b218ce10c37e44a82b48eebf2
-DIST samri_bidsdata-0.2.tar.xz 11450737688 BLAKE2B fc4ecf3faf97cbcebb7ddf7dd5b0c16b0e33ef6a7861d0919913cffb9f5b7a320a25f3e9644710cfa32e7252679c27ea8efca99cc04404d87be3161bf01ebfab SHA512 d9f16055f029dd5517b796e6211c9d4ce0a43bc881affe6453341c0b6a6712423cbf6bd41ceb721e7124d671d642ff2658a1ccce9278c07de946731ecb7b0367
+DIST samri_bidsdata-0.3.tar.xz 11498387144 BLAKE2B d09541ed212a33201d47932110ad9a18b514f043dd225c05537546e44eca491da58b40af6a59413aaf484c0664bf52c818aa6d9aa565d660f7d1ba4405f57f40 SHA512 bed72df1e5288c0597168f3100b4e839cee869173217df0f3cbdc47ea5b5167d4fcd7f1e8efa681a723bd47d017e6a502a2acf4ce2b225487fff7b8911aa0ff1
diff --git a/sci-biology/samri_bidsdata/metadata.xml b/sci-biology/samri_bidsdata/metadata.xml
index 5d9ef7d5b..cb6710311 100644
--- a/sci-biology/samri_bidsdata/metadata.xml
+++ b/sci-biology/samri_bidsdata/metadata.xml
@@ -2,14 +2,11 @@
 <!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
 <pkgmetadata>
 	<maintainer type="person">
-		<email>horea.christ@gmail.com</email>
+		<email>gentoo@chymera.eu</email>
 		<name>Horea Christian</name>
 	</maintainer>
 	<maintainer type="project">
 		<email>sci@gentoo.org</email>
 		<name>Gentoo Science Project</name>
 	</maintainer>
-	<longdescription lang="en">
-		Larger BIDS example data package for sci-biology/samri.
-	</longdescription>
 </pkgmetadata>
diff --git a/sci-biology/samri_bidsdata/samri_bidsdata-0.2.1.ebuild b/sci-biology/samri_bidsdata/samri_bidsdata-0.2.1.ebuild
deleted file mode 100644
index 3b5cf1a1c..000000000
--- a/sci-biology/samri_bidsdata/samri_bidsdata-0.2.1.ebuild
+++ /dev/null
@@ -1,21 +0,0 @@
-# Copyright 1999-2019 Gentoo Authors
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=7
-
-DESCRIPTION="BIDS-formatted example mouse brain data for SAMRI."
-HOMEPAGE="https://github.com/IBT-FMI/SAMRI"
-SRC_URI="http://chymera.eu/distfiles/${P}.tar.xz"
-
-LICENSE="GPL-3"
-SLOT="0"
-KEYWORDS="~amd64 ~x86 ~amd64-linux ~x86-linux"
-IUSE=""
-
-RDEPEND=""
-DEPEND=""
-
-src_install() {
-	insinto "/usr/share/${PN}"
-	doins -r *
-}
diff --git a/sci-biology/samri_bidsdata/samri_bidsdata-0.2.ebuild b/sci-biology/samri_bidsdata/samri_bidsdata-0.2.ebuild
deleted file mode 100644
index 9ab76ec84..000000000
--- a/sci-biology/samri_bidsdata/samri_bidsdata-0.2.ebuild
+++ /dev/null
@@ -1,23 +0,0 @@
-# Copyright 1999-2018 Gentoo Authors
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=7
-
-DESCRIPTION="BIDS-formatted example mouse brain data for SAMRI."
-HOMEPAGE="https://github.com/IBT-FMI/SAMRI"
-SRC_URI="http://chymera.eu/distfiles/${P}.tar.xz"
-
-LICENSE="GPL-3"
-SLOT="0"
-KEYWORDS="~amd64 ~x86 ~amd64-linux ~x86-linux"
-IUSE=""
-
-RDEPEND=""
-DEPEND=""
-
-src_install() {
-	insinto "/usr/share/${PN}"
-	doins -r *
-}
-
-S=${WORKDIR}/${PN}
diff --git a/sci-biology/samri_bidsdata/samri_bidsdata-0.3.ebuild b/sci-biology/samri_bidsdata/samri_bidsdata-0.3.ebuild
new file mode 100644
index 000000000..8e47fb775
--- /dev/null
+++ b/sci-biology/samri_bidsdata/samri_bidsdata-0.3.ebuild
@@ -0,0 +1,23 @@
+# Copyright 1999-2022 Gentoo Authors
+# Distributed under the terms of the GNU General Public License v2
+
+EAPI=7
+
+DESCRIPTION="BIDS-formatted example mouse brain data for SAMRI"
+HOMEPAGE="https://github.com/IBT-FMI/SAMRI"
+SRC_URI="
+	https://zenodo.org/record/3831124/files/${P}.tar.xz
+	"
+
+LICENSE="GPL-3"
+SLOT="0"
+KEYWORDS="~amd64 ~x86 ~amd64-linux ~x86-linux"
+IUSE=""
+
+RDEPEND=""
+DEPEND=""
+
+src_install() {
+	insinto "/usr/share/${PN}"
+	doins -r *
+}
diff --git a/sci-biology/samri_bindata/Manifest b/sci-biology/samri_bindata/Manifest
index 9e753b7ad..bb327170a 100644
--- a/sci-biology/samri_bindata/Manifest
+++ b/sci-biology/samri_bindata/Manifest
@@ -1,2 +1 @@
-DIST samri_bindata-0.1.1.zip 1012370776 BLAKE2B f171e2f81cf96359de00ee0bc0f1f4206fe34b4efb7c8a32f953e573705f089f91fdbfbac49540e27fc151fc7f81615fdc7f0ce23b3cd3f25fc15834ddc96c3d SHA512 7d7d654aa52a8c7fae2dd0893e9840c6e132487f4ff84f647f69ac7caf3bf77252c9817735c157d3fa2e9cb6432add00b170843ec3caa553dfdff4347e9fc571
-DIST samri_bindata-0.1.2.tar.xz 863086064 BLAKE2B adb9c4558bdeb2bf8dfc8579105eb5caaeb6988f1588ff84d4ec81e458309063d05720060e504184871830ce11a6c40f9003605775f8a072c3e3ab00d27e5e66 SHA512 9e4a10d41dceee1a806c8942f585688fd642fc129fbddce9822323462fa7c8222c192b94f7acae0ecf2f4c3a9da3db750245684a0eb8af4be3fd2d912e851d00
+DIST samri_bindata-0.4.tar.xz 2349556936 BLAKE2B c6996cdb927453c5fe54fd9bc1b7e03b38afff0449ed9d8249abf69da81d2f589a01bad881d00e7acbf2a7a820d549c65ed238cee9f31f409187843960556f2a SHA512 18a16e9e3bd75497f50923f2e304364dff78fa66308290350ca72717e01217e24b2fdeedfda56a5ba07a436d3643ceebc104bc802025ddd776b07986f45d53e0
diff --git a/sci-biology/samri_bindata/metadata.xml b/sci-biology/samri_bindata/metadata.xml
index 32dc63d5f..cb6710311 100644
--- a/sci-biology/samri_bindata/metadata.xml
+++ b/sci-biology/samri_bindata/metadata.xml
@@ -2,14 +2,11 @@
 <!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
 <pkgmetadata>
 	<maintainer type="person">
-		<email>horea.christ@gmail.com</email>
+		<email>gentoo@chymera.eu</email>
 		<name>Horea Christian</name>
 	</maintainer>
 	<maintainer type="project">
 		<email>sci@gentoo.org</email>
 		<name>Gentoo Science Project</name>
 	</maintainer>
-	<longdescription lang="en">
-		Larger binary testing data package for sci-biology/samri.
-	</longdescription>
 </pkgmetadata>
diff --git a/sci-biology/samri_bindata/samri_bindata-0.1.1.ebuild b/sci-biology/samri_bindata/samri_bindata-0.1.1.ebuild
deleted file mode 100644
index fb5f5e074..000000000
--- a/sci-biology/samri_bindata/samri_bindata-0.1.1.ebuild
+++ /dev/null
@@ -1,21 +0,0 @@
-# Copyright 1999-2018 Gentoo Foundation
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=7
-
-DESCRIPTION="Mouse brain atlasses for SAMRI."
-HOMEPAGE="https://github.com/IBT-FMI/SAMRI"
-SRC_URI="http://chymera.eu/distfiles/${P}.zip"
-
-LICENSE="GPL-3"
-SLOT="0"
-KEYWORDS="~amd64 ~x86 ~amd64-linux ~x86-linux"
-IUSE=""
-
-RDEPEND=""
-DEPEND=""
-
-src_install() {
-	insinto "/usr/share/${PN}"
-	doins -r *
-}
diff --git a/sci-biology/samri_bindata/samri_bindata-0.1.2.ebuild b/sci-biology/samri_bindata/samri_bindata-0.1.2.ebuild
deleted file mode 100644
index a6baa0b09..000000000
--- a/sci-biology/samri_bindata/samri_bindata-0.1.2.ebuild
+++ /dev/null
@@ -1,21 +0,0 @@
-# Copyright 1999-2018 Gentoo Foundation
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=7
-
-DESCRIPTION="Mouse brain atlasses for SAMRI."
-HOMEPAGE="https://github.com/IBT-FMI/SAMRI"
-SRC_URI="http://chymera.eu/distfiles/${P}.tar.xz"
-
-LICENSE="GPL-3"
-SLOT="0"
-KEYWORDS="~amd64 ~x86 ~amd64-linux ~x86-linux"
-IUSE=""
-
-RDEPEND=""
-DEPEND=""
-
-src_install() {
-	insinto "/usr/share/${PN}"
-	doins -r *
-}
diff --git a/sci-biology/samri_bindata/samri_bindata-0.4.ebuild b/sci-biology/samri_bindata/samri_bindata-0.4.ebuild
new file mode 100644
index 000000000..9ab92211a
--- /dev/null
+++ b/sci-biology/samri_bindata/samri_bindata-0.4.ebuild
@@ -0,0 +1,23 @@
+# Copyright 1999-2022 Gentoo Authors
+# Distributed under the terms of the GNU General Public License v2
+
+EAPI=7
+
+DESCRIPTION="ParaVision Mouse, Rat, and Lemur Testing Data for SAMRI"
+HOMEPAGE="https://github.com/IBT-FMI/SAMRI"
+SRC_URI="
+	https://zenodo.org/record/3823441/files/${P}.tar.xz
+	"
+
+LICENSE="GPL-3"
+SLOT="0"
+KEYWORDS="~amd64 ~x86 ~amd64-linux ~x86-linux"
+IUSE=""
+
+RDEPEND=""
+DEPEND=""
+
+src_install() {
+	insinto "/usr/share/${PN}"
+	doins -r *
+}
diff --git a/sci-biology/samstat/files/samstat-1.5.1-fno-common.patch b/sci-biology/samstat/files/samstat-1.5.1-fno-common.patch
new file mode 100644
index 000000000..d5bed9ed6
--- /dev/null
+++ b/sci-biology/samstat/files/samstat-1.5.1-fno-common.patch
@@ -0,0 +1,31 @@
+--- a/src/nuc_code.c
++++ b/src/nuc_code.c
+@@ -29,6 +29,9 @@
+ #include <stdlib.h>
+ #include "nuc_code.h"
+ 
++unsigned int rev_nuc_code[5];
++unsigned int nuc_code[256];
++
+ 
+ /** \fn void init_nuc_code()
+  \brief Initializes nucleotide conversion arrays. 
+--- a/src/nuc_code.h
++++ b/src/nuc_code.h
+@@ -32,14 +32,14 @@
+  *
+  *
+  */
+-unsigned int nuc_code[256];
++extern unsigned int nuc_code[256];
+ 
+ /**
+  * @brief Converts 0-5 nucleotides into printable ASCII to.
+  *
+  *
+  */
+-unsigned int rev_nuc_code[5];
++extern unsigned int rev_nuc_code[5];
+ 
+ void init_nuc_code(void);
+ 
diff --git a/sci-biology/samstat/samstat-1.5.1.ebuild b/sci-biology/samstat/samstat-1.5.1.ebuild
index 1ea4ffdde..5f1922467 100644
--- a/sci-biology/samstat/samstat-1.5.1.ebuild
+++ b/sci-biology/samstat/samstat-1.5.1.ebuild
@@ -1,18 +1,17 @@
-# Copyright 1999-2018 Gentoo Foundation
+# Copyright 1999-2021 Gentoo Authors
 # Distributed under the terms of the GNU General Public License v2
 
-EAPI=6
-
-inherit eutils
+EAPI=7
 
 DESCRIPTION="Statistics of BAM/SAM files"
-HOMEPAGE="http://samstat.sourceforge.net"
-SRC_URI="http://sourceforge.net/projects/samstat/files/${P}.tar.gz"
+HOMEPAGE="http://samstat.sourceforge.net" # no https
+SRC_URI="https://sourceforge.net/projects/samstat/files/${P}.tar.gz"
 
 LICENSE="GPL-3"
 SLOT="0"
 KEYWORDS="~amd64"
-IUSE=""
 
-DEPEND=""
+DEPEND="sci-biology/samtools:="
 RDEPEND="${DEPEND}"
+
+PATCHES=( "${FILESDIR}"/${P}-fno-common.patch )
diff --git a/sci-biology/scaffold_builder/Manifest b/sci-biology/scaffold_builder/Manifest
deleted file mode 100644
index 8bd2afc78..000000000
--- a/sci-biology/scaffold_builder/Manifest
+++ /dev/null
@@ -1,3 +0,0 @@
-DIST Manual_v2.1.pdf 25897 BLAKE2B 8a5a54609554904e8c29102df6588c7b4ea50e69bebf286ebb0e6c7fcca497ab4f0d7642e36458b3776ac0d2df50f9ad8ae6838a47f21eda79c53c12d0f273c1 SHA512 48ba5fcd33ba7585c970d29df477686afe19ed0d0d30184661cab3ac10e39fdbce6174ec85a126c18eac038c62464068b5c012a70ca256c9ec5c7ef4032710ab
-DIST scaffold_builder_v2.1.zip 20864 BLAKE2B 318f7b02de49acdc29ff7e10f882b9ea8f8c8437eb561e1c7d7462008e6dbbfaf79075d71863affe694142e42aaeff59ccf1fc2b4c7ea2982af9ad9d1a335d99 SHA512 9d092ac0275cc3cfecdc0172bb0817fa3d404efb3acd7b3b3316db3787817869dac20cae245806b6e086f0d4c5cbf757fd665f38f09478ea207c9a11af6acf16
-DIST scaffold_builder_v2_help.doc 50176 BLAKE2B 2b49f43a89c58045f67adc48b8ba3b91325e9d8bf9bb22b4048d60dfebb39a5d3acea54813fe84bce78fa91dbeb2898923cc67e7acdf3aaff7bdb32ef1cc4758 SHA512 1c3fdf085864a9a1cf684578af468166e4034c55a5576ab3d190443c323272152dcc19678d509cb2cccb3aac15570861f7483f4400638c8ef5af7aa1a6689ff2
diff --git a/sci-biology/scaffold_builder/metadata.xml b/sci-biology/scaffold_builder/metadata.xml
deleted file mode 100644
index 0f267b755..000000000
--- a/sci-biology/scaffold_builder/metadata.xml
+++ /dev/null
@@ -1,15 +0,0 @@
-<?xml version="1.0" encoding="UTF-8"?>
-<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
-<pkgmetadata>
-	<maintainer type="person">
-		<email>mmokrejs@fold.natur.cuni.cz</email>
-		<name>Martin Mokrejs</name>
-	</maintainer>
-	<maintainer type="project">
-		<email>sci-biology@gentoo.org</email>
-		<name>Gentoo Biology Project</name>
-	</maintainer>
-	<upstream>
-		<remote-id type="sourceforge">downloads</remote-id>
-	</upstream>
-</pkgmetadata>
diff --git a/sci-biology/scaffold_builder/scaffold_builder-20131122-r1.ebuild b/sci-biology/scaffold_builder/scaffold_builder-20131122-r1.ebuild
deleted file mode 100644
index ab9a50360..000000000
--- a/sci-biology/scaffold_builder/scaffold_builder-20131122-r1.ebuild
+++ /dev/null
@@ -1,40 +0,0 @@
-# Copyright 1999-2015 Gentoo Foundation
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=5
-
-PYTHON_COMPAT=( python2_7 )
-
-inherit python-r1
-
-DESCRIPTION="Combine FASTA contigs from a de novo assembly into scaffolds"
-HOMEPAGE="
-	http://sourceforge.net/projects/scaffold-b
-	http://edwards.sdsu.edu/scaffold_builder"
-SRC_URI="
-	http://sourceforge.net/projects/scaffold-b/files/scaffold_builder_v2.1.zip
-	http://sourceforge.net/projects/scaffold-b/files/scaffold_builder_v2_help.doc
-	http://downloads.sourceforge.net/project/scaffold-b/Manual_v2.1.pdf"
-
-#http://www.scfbm.org/content/8/1/23
-LICENSE="GPL-3"
-SLOT="0"
-KEYWORDS="~amd64"
-IUSE=""
-
-REQUIRED_USE="${PYTHON_REQUIRED_USE}"
-
-RDEPEND="${PYTHON_DEPS}
-	sci-biology/mummer"
-DEPEND="${RDEPEND}"
-
-S="${WORKDIR}"
-
-src_install(){
-	echo "#! /usr/bin/env python" > scaffold_builder.pyy || die
-	cat scaffold_builder.py >> scaffold_builder.pyy || die
-	mv scaffold_builder.pyy scaffold_builder.py || die
-	python_foreach_impl python_doscript scaffold_builder.py
-	dodoc "${DISTDIR}"/scaffold_builder_v2_help.doc
-	newdoc "${DISTDIR}"/Manual_v2.1.pdf scaffold_builder.pdf
-}
diff --git a/sci-biology/scan_for_matches/Manifest b/sci-biology/scan_for_matches/Manifest
index efc48e7bc..ab6862110 100644
--- a/sci-biology/scan_for_matches/Manifest
+++ b/sci-biology/scan_for_matches/Manifest
@@ -1 +1 @@
-DIST scan_for_matches.tgz 83918 BLAKE2B f9e16be3b061967f72b18c92c6701b32b6a5f62c8e37b74a836e2db813bee9876bca78477249239a12af6d0e2278a6f743d6410557d326b8032516aa005352cb SHA512 faa525bfcf72225b35eb8ac2e7404adb5b172f6f94e39d2173d73713cb98ee59260bf057bfb25ebe5ed0f39311be4032fee86e350d8f7174289926df6c4eab27
+DIST scan_for_matches-20121220.tgz 83918 BLAKE2B f9e16be3b061967f72b18c92c6701b32b6a5f62c8e37b74a836e2db813bee9876bca78477249239a12af6d0e2278a6f743d6410557d326b8032516aa005352cb SHA512 faa525bfcf72225b35eb8ac2e7404adb5b172f6f94e39d2173d73713cb98ee59260bf057bfb25ebe5ed0f39311be4032fee86e350d8f7174289926df6c4eab27
diff --git a/sci-biology/scan_for_matches/scan_for_matches-20121220.ebuild b/sci-biology/scan_for_matches/scan_for_matches-20121220.ebuild
index 1f562eee3..6d7d8cdc0 100644
--- a/sci-biology/scan_for_matches/scan_for_matches-20121220.ebuild
+++ b/sci-biology/scan_for_matches/scan_for_matches-20121220.ebuild
@@ -1,24 +1,21 @@
-# Copyright 1999-2014 Gentoo Foundation
+# Copyright 1999-2021 Gentoo Authors
 # Distributed under the terms of the GNU General Public License v2
 
-EAPI=5
-
-inherit eutils
-
-S="${WORKDIR}"/scan_for_matches
+EAPI=7
 
 DESCRIPTION="Pattern search through DNA sequences (aka patscan)"
-HOMEPAGE="http://blog.theseed.org/servers/2010/07/scan-for-matches.html"
-SRC_URI="http://www.theseed.org/servers/downloads/scan_for_matches.tgz"
+HOMEPAGE="https://blog.theseed.org/servers/2010/07/scan-for-matches.html"
+SRC_URI="https://www.theseed.org/servers/downloads/scan_for_matches.tgz -> ${P}.tgz"
 
 LICENSE="public-domain"
 SLOT="0"
 KEYWORDS="~amd64"
-IUSE=""
 
 DEPEND=""
 RDEPEND="${DEPEND}"
 
+S="${WORKDIR}/scan_for_matches"
+
 src_install(){
 	dobin scan_for_matches
 	dodoc README
diff --git a/sci-biology/scbi_blast/Manifest b/sci-biology/scbi_blast/Manifest
deleted file mode 100644
index 6feefc4d0..000000000
--- a/sci-biology/scbi_blast/Manifest
+++ /dev/null
@@ -1 +0,0 @@
-DIST scbi_blast-0.0.43.gem 22528 BLAKE2B b93d2bba19d3e3e13dfdc8f9e97eed6feabdd5fea61193f0b88ae7a83aac0a9ee018d064d511126d42917dfed76b2ab53982bc86a0db5043edfa11a81d9b576b SHA512 e2456146ee5f2bdf06135d0a588d347e90dae2bf61eaee5a044f74be6a3604a0226df45a72074f809ad81694afd2db37f0dd208b2675c29063b691f5a8a77692
diff --git a/sci-biology/scbi_blast/metadata.xml b/sci-biology/scbi_blast/metadata.xml
deleted file mode 100644
index 4e1fea2dd..000000000
--- a/sci-biology/scbi_blast/metadata.xml
+++ /dev/null
@@ -1,15 +0,0 @@
-<?xml version="1.0" encoding="UTF-8"?>
-<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
-<pkgmetadata>
-	<maintainer type="person">
-		<email>mmokrejs@fold.natur.cuni.cz</email>
-		<name>Martin Mokrejs</name>
-	</maintainer>
-	<maintainer type="project">
-		<email>sci-biology@gentoo.org</email>
-		<name>Gentoo Biology Project</name>
-	</maintainer>
-	<upstream>
-		<remote-id type="rubygems">scbi_blast</remote-id>
-	</upstream>
-</pkgmetadata>
diff --git a/sci-biology/scbi_blast/scbi_blast-0.0.43.ebuild b/sci-biology/scbi_blast/scbi_blast-0.0.43.ebuild
deleted file mode 100644
index f5e447265..000000000
--- a/sci-biology/scbi_blast/scbi_blast-0.0.43.ebuild
+++ /dev/null
@@ -1,26 +0,0 @@
-# Copyright 1999-2017 Gentoo Foundation
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=6
-
-USE_RUBY="ruby22 ruby23 ruby24"
-
-RUBY_FAKEGEM_TASK_DOC=""
-RUBY_FAKEGEM_EXTRADOC="README.rdoc"
-
-inherit ruby-fakegem
-
-DESCRIPTION="Handle blast+ executions using pipes instead of files"
-HOMEPAGE="https://rubygems.org/gems/scbi_blast"
-
-LICENSE="MIT"
-SLOT="0"
-KEYWORDS="~amd64"
-IUSE=""
-
-DEPEND="
-	>=dev-ruby/hoe-2.8.0
-	>=dev-ruby/rdoc-4.0"
-	#>=dev-ruby/newgem-1.5.3"
-RDEPEND="${DEPEND}
-	>=dev-ruby/xml-simple-1.0.12"
diff --git a/sci-biology/scbi_fasta/Manifest b/sci-biology/scbi_fasta/Manifest
deleted file mode 100644
index 2093e4af1..000000000
--- a/sci-biology/scbi_fasta/Manifest
+++ /dev/null
@@ -1 +0,0 @@
-DIST scbi_fasta-0.1.9.gem 9216 BLAKE2B 6c49b8c619f103f010cfc60670c9a1b121ef33b3b7b69eee326e941fa83add51eac70e51ab0361d0bd57618df373020b68b94eddef2310d7b3c6d1d54c84dbef SHA512 1a5c71fb3224a6b202bd0fd5098696f73eb22a5ed3ceeafcaeff01326fce5aa1c3856876bc6e1bde9610fc8429e364135080dde69eb9a125f1f770a27239bdd0
diff --git a/sci-biology/scbi_fasta/metadata.xml b/sci-biology/scbi_fasta/metadata.xml
deleted file mode 100644
index bedbad038..000000000
--- a/sci-biology/scbi_fasta/metadata.xml
+++ /dev/null
@@ -1,15 +0,0 @@
-<?xml version="1.0" encoding="UTF-8"?>
-<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
-<pkgmetadata>
-	<maintainer type="person">
-		<email>mmokrejs@fold.natur.cuni.cz</email>
-		<name>Martin Mokrejs</name>
-	</maintainer>
-	<maintainer type="project">
-		<email>sci-biology@gentoo.org</email>
-		<name>Gentoo Biology Project</name>
-	</maintainer>
-	<upstream>
-		<remote-id type="rubygems">scbi_fasta</remote-id>
-	</upstream>
-</pkgmetadata>
diff --git a/sci-biology/scbi_fasta/scbi_fasta-0.1.9.ebuild b/sci-biology/scbi_fasta/scbi_fasta-0.1.9.ebuild
deleted file mode 100644
index 0595b48ea..000000000
--- a/sci-biology/scbi_fasta/scbi_fasta-0.1.9.ebuild
+++ /dev/null
@@ -1,22 +0,0 @@
-# Copyright 1999-2017 Gentoo Foundation
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=6
-
-USE_RUBY="ruby22 ruby23 ruby24"
-
-RUBY_FAKEGEM_TASK_DOC=""
-RUBY_FAKEGEM_EXTRADOC="README.rdoc History.txt"
-
-inherit ruby-fakegem
-
-DESCRIPTION="Read FASTA and QUAL files"
-HOMEPAGE="https://rubygems.org/gems/scbi_fasta"
-
-LICENSE="MIT"
-SLOT="0"
-KEYWORDS="~amd64"
-IUSE=""
-
-DEPEND=">=dev-ruby/hoe-2.8.0"
-RDEPEND="${DEPEND}"
diff --git a/sci-biology/scbi_fastq/Manifest b/sci-biology/scbi_fastq/Manifest
deleted file mode 100644
index 0e0e7ac07..000000000
--- a/sci-biology/scbi_fastq/Manifest
+++ /dev/null
@@ -1 +0,0 @@
-DIST scbi_fastq-0.0.22.gem 666112 BLAKE2B 23a9dc35876ffcba0327668f8ebcfb8054a858a822ddbe7350dccbb9ad1812703bebc2eeebf4223eddd8a795c464e0ab4198a5e7fa33cdb611a6609ed5c5be47 SHA512 84ac0b947b9c28114137208bec4f666004559cda38114cba6dc8dde8304f56c60dd2a54ea36fb09b320bc3ceb9261569008c8a9bcac1777192a2f5cd5f61c090
diff --git a/sci-biology/scbi_fastq/metadata.xml b/sci-biology/scbi_fastq/metadata.xml
deleted file mode 100644
index 6468736c1..000000000
--- a/sci-biology/scbi_fastq/metadata.xml
+++ /dev/null
@@ -1,15 +0,0 @@
-<?xml version="1.0" encoding="UTF-8"?>
-<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
-<pkgmetadata>
-	<maintainer type="person">
-		<email>mmokrejs@fold.natur.cuni.cz</email>
-		<name>Martin Mokrejs</name>
-	</maintainer>
-	<maintainer type="project">
-		<email>sci-biology@gentoo.org</email>
-		<name>Gentoo Biology Project</name>
-	</maintainer>
-	<upstream>
-		<remote-id type="rubygems">scbi_fastq</remote-id>
-	</upstream>
-</pkgmetadata>
diff --git a/sci-biology/scbi_fastq/scbi_fastq-0.0.22.ebuild b/sci-biology/scbi_fastq/scbi_fastq-0.0.22.ebuild
deleted file mode 100644
index a9ea0d90b..000000000
--- a/sci-biology/scbi_fastq/scbi_fastq-0.0.22.ebuild
+++ /dev/null
@@ -1,25 +0,0 @@
-# Copyright 1999-2017 Gentoo Foundation
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=6
-
-USE_RUBY="ruby22 ruby23 ruby24"
-
-RUBY_FAKEGEM_TASK_DOC=""
-RUBY_FAKEGEM_EXTRADOC="README.md"
-
-inherit ruby-fakegem
-
-DESCRIPTION="Read/write FASTQ files"
-HOMEPAGE="https://rubygems.org/gems/scbi_fastq"
-
-LICENSE="MIT"
-SLOT="0"
-KEYWORDS="~amd64"
-IUSE=""
-
-DEPEND="
-	>=dev-ruby/bundler-1.7
-	>=dev-ruby/rake-10.0"
-RDEPEND="${DEPEND}
-	>=sci-biology/scbi_zcat-0.0.2"
diff --git a/sci-biology/scbi_mapreduce/Manifest b/sci-biology/scbi_mapreduce/Manifest
deleted file mode 100644
index a8a6fe376..000000000
--- a/sci-biology/scbi_mapreduce/Manifest
+++ /dev/null
@@ -1 +0,0 @@
-DIST scbi_mapreduce-0.0.45.gem 765440 BLAKE2B 6dc4ea3dd79d365a992caa8c290dea87b6f9e65046fcac2e607c03b3ad2ca059be8030c98b108e7c66a3831dd9596dd82741ab78801ce6ed45734c70d925e062 SHA512 77de3fdd5f34669e8ea881c244dd69e6ecc6beab560ea4e7132f00dc77d85e6e77793f2fdf0de2d951dce05b481b71d31960b2c447f9ff91f5b250cd83833ba4
diff --git a/sci-biology/scbi_mapreduce/metadata.xml b/sci-biology/scbi_mapreduce/metadata.xml
deleted file mode 100644
index fec60e6f5..000000000
--- a/sci-biology/scbi_mapreduce/metadata.xml
+++ /dev/null
@@ -1,15 +0,0 @@
-<?xml version="1.0" encoding="UTF-8"?>
-<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
-<pkgmetadata>
-	<maintainer type="person">
-		<email>mmokrejs@fold.natur.cuni.cz</email>
-		<name>Martin Mokrejs</name>
-	</maintainer>
-	<maintainer type="project">
-		<email>sci-biology@gentoo.org</email>
-		<name>Gentoo Biology Project</name>
-	</maintainer>
-	<upstream>
-		<remote-id type="rubygems">scbi_mapreduce</remote-id>
-	</upstream>
-</pkgmetadata>
diff --git a/sci-biology/scbi_mapreduce/scbi_mapreduce-0.0.45.ebuild b/sci-biology/scbi_mapreduce/scbi_mapreduce-0.0.45.ebuild
deleted file mode 100644
index 2e4527061..000000000
--- a/sci-biology/scbi_mapreduce/scbi_mapreduce-0.0.45.ebuild
+++ /dev/null
@@ -1,26 +0,0 @@
-# Copyright 1999-2017 Gentoo Foundation
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=6
-
-USE_RUBY="ruby22 ruby23 ruby24"
-
-RUBY_FAKEGEM_TASK_DOC=""
-RUBY_FAKEGEM_EXTRADOC="README.md"
-
-inherit ruby-fakegem
-
-DESCRIPTION="Run parallel and distributed computing jobs"
-HOMEPAGE="https://rubygems.org/gems/scbi_mapreduce"
-
-LICENSE="MIT"
-SLOT="0"
-KEYWORDS="~amd64"
-IUSE=""
-
-DEPEND="
-	>=dev-ruby/hoe-3.6
-	>=dev-ruby/rdoc-4.0"
-RDEPEND="${DEPEND}
-	>=dev-ruby/eventmachine-0.12.0
-	dev-ruby/json"
diff --git a/sci-biology/scbi_plot/Manifest b/sci-biology/scbi_plot/Manifest
deleted file mode 100644
index 3463d9eb7..000000000
--- a/sci-biology/scbi_plot/Manifest
+++ /dev/null
@@ -1 +0,0 @@
-DIST scbi_plot-0.0.7.gem 9216 BLAKE2B f3c0f7c79bc2fef47bc37097fb6f3ab1f9068505c66240ba0527e142a8c2dec2651910d76f83ab162fc744cfa0216d5281972f9cf260d642a3ca88fe157a8ff0 SHA512 be27448fb0c73e184d395d139a26b9c82c8726bf0879e6ade22002d4cdd004098293cc33c8780768408af338cf6fdf506869adc56e583db5538b266bb0e8f54e
diff --git a/sci-biology/scbi_plot/metadata.xml b/sci-biology/scbi_plot/metadata.xml
deleted file mode 100644
index f94206d02..000000000
--- a/sci-biology/scbi_plot/metadata.xml
+++ /dev/null
@@ -1,15 +0,0 @@
-<?xml version="1.0" encoding="UTF-8"?>
-<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
-<pkgmetadata>
-	<maintainer type="person">
-		<email>mmokrejs@fold.natur.cuni.cz</email>
-		<name>Martin Mokrejs</name>
-	</maintainer>
-	<maintainer type="project">
-		<email>sci-biology@gentoo.org</email>
-		<name>Gentoo Biology Project</name>
-	</maintainer>
-	<upstream>
-		<remote-id type="rubygems">scbi_plot</remote-id>
-	</upstream>
-</pkgmetadata>
diff --git a/sci-biology/scbi_plot/scbi_plot-0.0.7.ebuild b/sci-biology/scbi_plot/scbi_plot-0.0.7.ebuild
deleted file mode 100644
index e51b6d0aa..000000000
--- a/sci-biology/scbi_plot/scbi_plot-0.0.7.ebuild
+++ /dev/null
@@ -1,25 +0,0 @@
-# Copyright 1999-2017 Gentoo Foundation
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=6
-
-USE_RUBY="ruby22 ruby23 ruby24"
-
-RUBY_FAKEGEM_TASK_DOC=""
-RUBY_FAKEGEM_EXTRADOC="README.rdoc History.txt"
-
-inherit ruby-fakegem
-
-DESCRIPTION="Wrapper to create plots with gnuplot"
-HOMEPAGE="https://rubygems.org/gems/scbi_plot"
-
-LICENSE="MIT"
-SLOT="0"
-KEYWORDS="~amd64"
-IUSE=""
-
-DEPEND="
-	>=dev-ruby/hoe-2.8.0
-	>=dev-ruby/rdoc-4.0"
-RDEPEND="${DEPEND}
-	>=sci-visualization/gnuplot-2.3.0"
diff --git a/sci-biology/scbi_zcat/Manifest b/sci-biology/scbi_zcat/Manifest
deleted file mode 100644
index 562b759b7..000000000
--- a/sci-biology/scbi_zcat/Manifest
+++ /dev/null
@@ -1 +0,0 @@
-DIST scbi_zcat-0.0.2.gem 7680 BLAKE2B 2d27c1d970d7ee680504fc463e4a706bb25558194158c8c735cde454f952b27d26819a5123c3fb413d30c126050e7f56385e26a3c317e320802d34e40aa16389 SHA512 b37433fe26cabaf8702be4ce9c4282e0c094f637e739bc51b6b760e10531f559acbebd50cc8f7aadb22c78cb4dbed15297fa595c3cd460d8aecde51587407f48
diff --git a/sci-biology/scbi_zcat/metadata.xml b/sci-biology/scbi_zcat/metadata.xml
deleted file mode 100644
index aaf119d8f..000000000
--- a/sci-biology/scbi_zcat/metadata.xml
+++ /dev/null
@@ -1,15 +0,0 @@
-<?xml version="1.0" encoding="UTF-8"?>
-<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
-<pkgmetadata>
-	<maintainer type="person">
-		<email>mmokrejs@fold.natur.cuni.cz</email>
-		<name>Martin Mokrejs</name>
-	</maintainer>
-	<maintainer type="project">
-		<email>sci-biology@gentoo.org</email>
-		<name>Gentoo Biology Project</name>
-	</maintainer>
-	<upstream>
-		<remote-id type="rubygems">scbi_zcat</remote-id>
-	</upstream>
-</pkgmetadata>
diff --git a/sci-biology/scbi_zcat/scbi_zcat-0.0.2.ebuild b/sci-biology/scbi_zcat/scbi_zcat-0.0.2.ebuild
deleted file mode 100644
index 27bb17da9..000000000
--- a/sci-biology/scbi_zcat/scbi_zcat-0.0.2.ebuild
+++ /dev/null
@@ -1,24 +0,0 @@
-# Copyright 1999-2017 Gentoo Foundation
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=6
-
-USE_RUBY="ruby22 ruby23 ruby24"
-
-RUBY_FAKEGEM_TASK_DOC=""
-RUBY_FAKEGEM_EXTRADOC="README.md"
-
-inherit ruby-fakegem
-
-DESCRIPTION="Read files from a zcat pipe of a gz file"
-HOMEPAGE="https://rubygems.org/gems/scbi_zcat"
-
-LICENSE="MIT"
-SLOT="0"
-KEYWORDS="~amd64"
-IUSE=""
-
-DEPEND="
-	>=dev-ruby/bundler-1.7
-	>=dev-ruby/rake-10.0"
-RDEPEND="${DEPEND}"
diff --git a/sci-biology/sclust/Manifest b/sci-biology/sclust/Manifest
deleted file mode 100644
index 4524ce986..000000000
--- a/sci-biology/sclust/Manifest
+++ /dev/null
@@ -1,2 +0,0 @@
-DIST cdbfasta.tar.gz 59735 BLAKE2B 69107a42e1b8069a70de9333891e050785cabaf6457245b4512c3725dc576ebfba54c43c3d1e356948061cf903a89a8aa0f011efbf36a4cda6b40a623f7019fe SHA512 500b3cdf4bf4e21c78a285739c6544e3f2bed377f8e3858c8ace240a9107d765c89cff8004ca2ea001860abc04fc48bc37c03569da5b16115f4419f5fd9bcd5e
-DIST sclust.tar.gz 13467 BLAKE2B 8e50ae561da3665728dca8f055a60194577b93c537a84af5a9595d28110743e13e7c3f5c52855946ad4990f83ee5febc570e96ed2b4a82b2851d7b4bd3e52ad6 SHA512 5cfee8b142f1fd6f7f289407b80dfa91fcb71d94c1cf3ebc979d000b31690c88dc544bab830a30e783e4e17232bd141b4d6f45a6e1ee4e75ae85bdef07fb6650
diff --git a/sci-biology/sclust/metadata.xml b/sci-biology/sclust/metadata.xml
deleted file mode 100644
index 138cb7705..000000000
--- a/sci-biology/sclust/metadata.xml
+++ /dev/null
@@ -1,12 +0,0 @@
-<?xml version="1.0" encoding="UTF-8"?>
-<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
-<pkgmetadata>
-	<maintainer type="person">
-		<email>mmokrejs@fold.natur.cuni.cz</email>
-		<name>Martin Mokrejs</name>
-	</maintainer>
-	<maintainer type="project">
-		<email>sci-biology@gentoo.org</email>
-		<name>Gentoo Biology Project</name>
-	</maintainer>
-</pkgmetadata>
diff --git a/sci-biology/sclust/sclust-0.1.ebuild b/sci-biology/sclust/sclust-0.1.ebuild
deleted file mode 100644
index a4c16f997..000000000
--- a/sci-biology/sclust/sclust-0.1.ebuild
+++ /dev/null
@@ -1,36 +0,0 @@
-# Copyright 1999-2015 Gentoo Foundation
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=5
-
-DESCRIPTION="Seeded clustering tool by processing pairwise alignments"
-HOMEPAGE="http://compbio.dfci.harvard.edu/tgi/software/"
-SRC_URI="
-	ftp://occams.dfci.harvard.edu/pub/bio/tgi/software/tgicl/${PN}.tar.gz
-	ftp://occams.dfci.harvard.edu/pub/bio/tgi/software/tgicl/cdbfasta.tar.gz"
-
-LICENSE="Artistic"
-SLOT="0"
-KEYWORDS="~amd64 ~x86"
-IUSE=""
-
-S=${WORKDIR}
-
-src_prepare() {
-	# we need gclib from cdbfasta.tar.gz bundle which has fewer files than tgi_cpp_library.tar.gz wbut has e.g. GStr.h
-	sed -i 's/CFLAGS[ ]*=/CFLAGS :=/; s/-D_REENTRANT/-D_REENTRANT \${CFLAGS}/; s/CFLAGS[ ]*:=[ ]*-O2$//' "${S}"/${PN}/Makefile || die "Failed to run sed"
-	sed -i 's#GCLDIR := ../gclib#GCLDIR := ../cdbfasta/gclib#' "${S}"/"${PN}"/Makefile || die
-	cd ${PN} || die
-	ln -s ../cdbfasta/gcl . || die "Cannot make a softlink"
-}
-
-src_compile() {
-	cd ${PN} || die
-	default
-}
-
-src_install() {
-	cd ${PN} || die
-	dobin ${PN}
-	newdoc README README.${PN}
-}
diff --git a/sci-biology/screed/Manifest b/sci-biology/screed/Manifest
deleted file mode 100644
index 90079a017..000000000
--- a/sci-biology/screed/Manifest
+++ /dev/null
@@ -1 +0,0 @@
-DIST screed-0.9.tar.gz 115709 BLAKE2B a8eb4ee02ea0038624d3c6e2537194e8c605c7599fe0848c85adcb97ed5d3b11087d7266d33a5b3435d411cc22e829b04c7e33eea002e797aa904af8fa5d971c SHA512 204fc0f7a62954a21f4fd0f6801abb8fe404e9e29bf00da07d28cfce0506c13971370963bf4c5749e05640a7a1f402b0404219bccdfb02b6070a386bc41105b1
diff --git a/sci-biology/screed/metadata.xml b/sci-biology/screed/metadata.xml
deleted file mode 100644
index 297401f3d..000000000
--- a/sci-biology/screed/metadata.xml
+++ /dev/null
@@ -1,12 +0,0 @@
-<?xml version="1.0" encoding="UTF-8"?>
-<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
-<pkgmetadata>
-	<maintainer type="project">
-		<email>sci-biology@gentoo.org</email>
-		<name>Gentoo Biology Project</name>
-	</maintainer>
-	<upstream>
-		<remote-id type="github">ged-lab/screed</remote-id>
-		<remote-id type="pypi">screed</remote-id>
-	</upstream>
-</pkgmetadata>
diff --git a/sci-biology/screed/screed-0.9.ebuild b/sci-biology/screed/screed-0.9.ebuild
deleted file mode 100644
index 017ff4376..000000000
--- a/sci-biology/screed/screed-0.9.ebuild
+++ /dev/null
@@ -1,17 +0,0 @@
-# Copyright 1999-2016 Gentoo Foundation
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=5
-
-PYTHON_COMPAT=( python2_7 python3_3 python3_4 python3_5 )
-
-inherit distutils-r1
-
-DESCRIPTION="Short read sequence utilities"
-HOMEPAGE="https://pypi.python.org/pypi/screed http://github.com/ged-lab/screed/"
-SRC_URI="mirror://pypi/${PN:0:1}/${PN}/${P}.tar.gz"
-
-SLOT="0"
-LICENSE="BSD"
-KEYWORDS="~amd64 ~x86 ~amd64-linux ~x86-linux"
-IUSE=""
diff --git a/sci-biology/scythe/scythe-0.992.ebuild b/sci-biology/scythe/scythe-0.992.ebuild
deleted file mode 100644
index 1ae6fddf7..000000000
--- a/sci-biology/scythe/scythe-0.992.ebuild
+++ /dev/null
@@ -1,25 +0,0 @@
-# Copyright 1999-2014 Gentoo Foundation
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=5
-
-inherit eutils git-r3
-
-DESCRIPTION="Bayesian 3'-end adapter (only) trimmer for Illumina/Solexa"
-HOMEPAGE="https://github.com/vsbuffalo/scythe"
-EGIT_REPO_URI="https://github.com/vsbuffalo/scythe"
-
-LICENSE="MIT"
-SLOT="0"
-KEYWORDS="~amd64"
-IUSE=""
-
-DEPEND=""
-RDEPEND="${DEPEND}
-	sys-libs/zlib"
-
-src_install(){
-	dobin scythe
-	dodoc README.md
-	dodoc illumina_adapters.fa
-}
diff --git a/sci-biology/scythe/scythe-9999.ebuild b/sci-biology/scythe/scythe-9999.ebuild
new file mode 100644
index 000000000..d2f051ef1
--- /dev/null
+++ b/sci-biology/scythe/scythe-9999.ebuild
@@ -0,0 +1,25 @@
+# Copyright 1999-2021 Gentoo Authors
+# Distributed under the terms of the GNU General Public License v2
+
+EAPI=7
+
+inherit git-r3
+
+DESCRIPTION="Bayesian 3'-end adapter (only) trimmer for Illumina/Solexa"
+HOMEPAGE="https://github.com/vsbuffalo/scythe"
+EGIT_REPO_URI="https://github.com/vsbuffalo/scythe"
+
+LICENSE="MIT"
+SLOT="0"
+KEYWORDS=""
+
+RESTRICT="test"
+
+DEPEND="sys-libs/zlib"
+RDEPEND="${DEPEND}"
+
+src_install(){
+	dobin scythe
+	dodoc README.md
+	dodoc illumina_adapters.fa
+}
diff --git a/sci-biology/seq_crumbs/Manifest b/sci-biology/seq_crumbs/Manifest
deleted file mode 100644
index 192c5b2f4..000000000
--- a/sci-biology/seq_crumbs/Manifest
+++ /dev/null
@@ -1 +0,0 @@
-DIST v0.1.9.tar.gz 2172379 BLAKE2B 121055a96181b5a94ef847965f4cf4be9b5e429765981d733781eb454f2f539577decf2be6923496cd8da5e8a4e3dd5cca630dbb742b940091bd0d67e0ed41d6 SHA512 075be693ce712e9b5bd6e72b02a5a0822ace9ee0363696f8fca6d07f266c99c81b5d9d099db3ad5f70548b5a98e4f2d85cc6cd4dc2fd7c06dece6c6e50d287d5
diff --git a/sci-biology/seq_crumbs/metadata.xml b/sci-biology/seq_crumbs/metadata.xml
deleted file mode 100644
index f68a1b6fa..000000000
--- a/sci-biology/seq_crumbs/metadata.xml
+++ /dev/null
@@ -1,12 +0,0 @@
-<?xml version="1.0" encoding="UTF-8"?>
-<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
-<pkgmetadata>
-  <maintainer type="person">
-    <email>mmokrejs@fold.natur.cuni.cz</email>
-    <name>Martin Mokrejs</name>
-  </maintainer>
-  <maintainer type="project">
-    <email>sci-biology@gentoo.org</email>
-    <name>Gentoo Biology Project</name>
-  </maintainer>
-</pkgmetadata>
diff --git a/sci-biology/seq_crumbs/seq_crumbs-0.1.9.ebuild b/sci-biology/seq_crumbs/seq_crumbs-0.1.9.ebuild
deleted file mode 100644
index 94ce00a94..000000000
--- a/sci-biology/seq_crumbs/seq_crumbs-0.1.9.ebuild
+++ /dev/null
@@ -1,46 +0,0 @@
-# Copyright 1999-2018 Gentoo Foundation
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=6
-
-PYTHON_COMPAT=( python2_7 )
-
-inherit distutils-r1 eutils
-
-DESCRIPTION="Filter, split and trim NGS sequence data"
-HOMEPAGE="https://github.com/JoseBlanca/seq_crumbs"
-SRC_URI="https://github.com/JoseBlanca/"${PN}"/archive/v"${PV}".tar.gz"
-
-LICENSE="GPL-3"
-SLOT="0"
-KEYWORDS=""
-IUSE=""
-
-DEPEND="
-	>=sci-biology/biopython-1.60
-	>=sci-biology/pysam-0.8
-	>=dev-python/rpy-2
-	dev-python/matplotlib
-	dev-python/configobj
-	dev-python/toolz"
-RDEPEND="${DEPEND}"
-
-# TODO fix file collisions
-#  * Detected file collision(s):
-#  * 
-#  * 	/usr/share/man/man1/index.1.bz2
-#  * 	/usr/share/man/man1/install.1.bz2
-#  * 
-#  * Searching all installed packages for file collisions...
-#  * 
-#  * Press Ctrl-C to Stop
-#  * 
-#  * sys-apps/coreutils-8.29:0::gentoo
-#  * 	/usr/share/man/man1/install.1.bz2
-#  * 
-#  * media-libs/netpbm-10.76.00:0::gentoo
-#  * 	/usr/share/man/man1/index.1.bz2
-src_prepare(){
-	sed -e "s#sys.prefix#os.getenv('ED')+'/usr/'#" -i setup.py || die
-	default
-}
diff --git a/sci-biology/seqclean/Manifest b/sci-biology/seqclean/Manifest
deleted file mode 100644
index 5a742c218..000000000
--- a/sci-biology/seqclean/Manifest
+++ /dev/null
@@ -1,3 +0,0 @@
-DIST mdust-110625.tar.gz 7526 BLAKE2B 9d2f91025d6cfccb8c75b8f2d6c9f3df9b76469ef7b77a74c3bbd3e37c2d2ba0ce737eaca518200246e1c302d7862af4929bad4bffb6c53692fbfaa586dbf4d7 SHA512 349446115d3b778d28a184eb118ada112476b2c51a058dd7467ff539678f7550dab675a731c452f9aa002fda9a54f13576db02302df935946d034eb9e0d4566e
-DIST seqcl_scripts-110625.tar.gz 14840 BLAKE2B 107ac1d966870f976c5b8f2bd74beb95f49cc1d57975c686e730ad4f519378c3435a626c086244f04e3e075d9f63d1f6541a9bf8dbae1c141ccc3bbd8c613fb5 SHA512 84cca02165856f51614b05e3fb416765695ca3442a8f9d47ee341946a375b6fc9ec6b77e5f18b58d21d5a6e93e21010a866efd2940dc60771f9e6e97722d5a96
-DIST trimpoly-110625.tar.gz 12747 BLAKE2B e395c19549e376b373028c9ca22197021dcf7a7465f2528e1b9051d5e9bbd27c8180103a0a849c3aa8de98eef0edeb71db18b457a62bd3a07e6fe68e083d4062 SHA512 74e7ed6169cbe5f9e9bdcaaffed8ceb74c4ea1ccce912fc656dc29f5ddf8bbeee2975814c97691a8b5eb419c202e332ba79634feb11ffac9a3ab3341db61076f
diff --git a/sci-biology/seqclean/files/seqclean-110625-build.patch b/sci-biology/seqclean/files/seqclean-110625-build.patch
deleted file mode 100644
index b5797618f..000000000
--- a/sci-biology/seqclean/files/seqclean-110625-build.patch
+++ /dev/null
@@ -1,135 +0,0 @@
- mdust/Makefile    |   18 +++++++++---------
- mdust/fastafile.c |    3 ++-
- mdust/mdust.c     |    1 +
- trimpoly/Makefile |   16 ++++++++--------
- 4 files changed, 20 insertions(+), 18 deletions(-)
-
-diff --git a/mdust/Makefile b/mdust/Makefile
-index 81bf4e9..0c75e69 100644
---- a/mdust/Makefile
-+++ b/mdust/Makefile
-@@ -1,40 +1,40 @@
- # Useful directories
- 
- # Directories to search for header files
--SEARCHDIRS := -I. -I- 
-+SEARCHDIRS := -I. -iquote
- 
- 
- #SYSTYPE :=     $(shell uname)
- 
--CC      := gcc
--CFLAGS  = -O2 -Wall ${SEARCHDIRS} -D_REENTRANT
-+CC      ?= gcc
-+CFLAGS  += ${SEARCHDIRS} -D_REENTRANT
-+CXXFLAGS  += ${SEARCHDIRS} -D_REENTRANT
- 
- %.o : %.c
- 	${CC} ${CFLAGS} -c $< -o $@
- 
- %.o : %.cc
--	${CC} ${CFLAGS} -c $< -o $@
-+	${CXX} ${CXXFLAGS} -c $< -o $@
- 
- %.o : %.C
--	${CC} ${CFLAGS} -c $< -o $@
-+	${CXX} ${CXXFLAGS} -c $< -o $@
- 
- %.o : %.cpp
--	${CC} ${CFLAGS} -c $< -o $@
-+	${CXX} ${CXXFLAGS} -c $< -o $@
- 
- %.o : %.cxx
--	${CC} ${CFLAGS} -c $< -o $@
-+	${CXX} ${CXXFLAGS} -c $< -o $@
- 
- # C/C++ linker
- 
- LINKER    := gcc
--LDFLAGS    =
- LOADLIBES := 
- 
- .PHONY : all
- all:    mdust
- 
- mdust:  ./mdust.o ./dust.o ./fastafile.o
--	${LINKER} ${LDFLAGS} -o $@ ${filter-out %.a %.so, $^} ${LOADLIBES}
-+	${CXX} ${LDFLAGS} -o $@ ${filter-out %.a %.so, $^} ${LOADLIBES}
- 
- # target for removing all object files
- 
-diff --git a/mdust/fastafile.c b/mdust/fastafile.c
-index 6c14b99..5f70f14 100644
---- a/mdust/fastafile.c
-+++ b/mdust/fastafile.c
-@@ -1,7 +1,8 @@
- #include <stdio.h>
- #include <ctype.h>
- #include <malloc.h>
--
-+#include <string.h>
-+#include <stdlib.h>
- #include "fastafile.h"
- 
- 
-diff --git a/mdust/mdust.c b/mdust/mdust.c
-index f2bae99..c3ee686 100644
---- a/mdust/mdust.c
-+++ b/mdust/mdust.c
-@@ -1,6 +1,7 @@
- #include <stdlib.h>
- #include <stdio.h>
- #include <ctype.h>
-+#include <string.h>
- #include "dust.h"
- #include "fastafile.h"
- 
-diff --git a/trimpoly/Makefile b/trimpoly/Makefile
-index 84db22d..71145c2 100644
---- a/trimpoly/Makefile
-+++ b/trimpoly/Makefile
-@@ -3,28 +3,28 @@
- # Directories to search for header files
- SEARCHDIRS := -I.
- 
--CC      := gcc
--CFLAGS  = -O2 -Wall ${SEARCHDIRS} -D_REENTRANT
-+CC      ?= gcc
-+CFLAGS  += ${SEARCHDIRS} -D_REENTRANT
-+CXXFLAGS  += ${SEARCHDIRS} -D_REENTRANT
- 
- %.o : %.c
- 	${CC} ${CFLAGS} -c $< -o $@
- 
- %.o : %.cc
--	${CC} ${CFLAGS} -c $< -o $@
-+	${CXX} ${CXXFLAGS} -c $< -o $@
- 
- %.o : %.C
--	${CC} ${CFLAGS} -c $< -o $@
-+	${CXX} ${CXXFLAGS} -c $< -o $@
- 
- %.o : %.cpp
--	${CC} ${CFLAGS} -c $< -o $@
-+	${CXX} ${CXXFLAGS} -c $< -o $@
- 
- %.o : %.cxx
--	${CC} ${CFLAGS} -c $< -o $@
-+	${CXX} ${CXXFLAGS} -c $< -o $@
- 
- # C/C++ linker
- 
- LINKER    := gcc
--LDFLAGS    = 
- LOADLIBES =
- SYSTYPE :=     $(shell uname)
- #ifeq ($(SYSTYPE), Linux)
-@@ -37,7 +37,7 @@ SYSTYPE :=     $(shell uname)
- all:    trimpoly
- 
- trimpoly:  ./trimpoly.o color_c.o
--	${LINKER} ${LDFLAGS} -o $@ ${filter-out %.a %.so, $^} ${LOADLIBES}
-+	${CXX} ${LDFLAGS} -o $@ ${filter-out %.a %.so, $^} ${LOADLIBES}
- 
- # target for removing all object files
- 
diff --git a/sci-biology/seqclean/metadata.xml b/sci-biology/seqclean/metadata.xml
deleted file mode 100644
index 138cb7705..000000000
--- a/sci-biology/seqclean/metadata.xml
+++ /dev/null
@@ -1,12 +0,0 @@
-<?xml version="1.0" encoding="UTF-8"?>
-<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
-<pkgmetadata>
-	<maintainer type="person">
-		<email>mmokrejs@fold.natur.cuni.cz</email>
-		<name>Martin Mokrejs</name>
-	</maintainer>
-	<maintainer type="project">
-		<email>sci-biology@gentoo.org</email>
-		<name>Gentoo Biology Project</name>
-	</maintainer>
-</pkgmetadata>
diff --git a/sci-biology/seqclean/seqclean-110625.ebuild b/sci-biology/seqclean/seqclean-110625.ebuild
deleted file mode 100644
index 575cab9a6..000000000
--- a/sci-biology/seqclean/seqclean-110625.ebuild
+++ /dev/null
@@ -1,53 +0,0 @@
-# Copyright 1999-2015 Gentoo Foundation
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=5
-
-inherit eutils toolchain-funcs
-
-DESCRIPTION="Trimpoly and mdust for trimming and validation of ESTs/DNA sequences"
-HOMEPAGE="http://compbio.dfci.harvard.edu/tgi/software/"
-for i in seqcl_scripts mdust trimpoly; do
-	SRC_URI="${SRC_URI} ftp://occams.dfci.harvard.edu/pub/bio/tgi/software/seqclean/${i}.tar.gz -> ${i}-${PV}.tar.gz"
-done
-
-LICENSE="Artistic"
-SLOT="0"
-KEYWORDS="~amd64 ~x86"
-IUSE=""
-
-DEPEND="
-	dev-lang/perl
-	sci-biology/ncbi-tools"
-RDEPEND="${DEPEND}"
-
-S=${WORKDIR}
-
-src_prepare() {
-	# disable the necessity to install Mailer.pm with this tool
-	einfo "Disabling mailer feature within seqclean"
-	sed -i 's/use Mailer;/#use Mailer;/' "${S}"/"${PN}"/"${PN}" || die
-
-	epatch "${FILESDIR}"/${P}-build.patch
-
-	tc-export CC CXX
-}
-
-src_compile() {
-	for i in mdust trimpoly; do
-		LDLFAGS="${LDFLAGS}" \
-			emake -C "${S}"/${i}
-	done
-}
-
-src_install() {
-	dobin seqclean/{seqclean,cln2qual,bin/seqclean.psx}
-	newdoc seqclean/README README.seqclean
-	for i in mdust trimpoly; do
-		dobin ${i}/${i}
-	done
-
-	einfo "Optionally, you may want to download UniVec from NCBI if you do not have your own"
-	einfo "fasta file with vector sequences you want to remove from sequencing"
-	einfo "reads. See http://www.ncbi.nlm.nih.gov/VecScreen/UniVec.html"
-}
diff --git a/sci-biology/seqtk/metadata.xml b/sci-biology/seqtk/metadata.xml
index 138cb7705..a2d91d1c4 100644
--- a/sci-biology/seqtk/metadata.xml
+++ b/sci-biology/seqtk/metadata.xml
@@ -9,4 +9,7 @@
 		<email>sci-biology@gentoo.org</email>
 		<name>Gentoo Biology Project</name>
 	</maintainer>
+	<upstream>
+		<remote-id type="github">lh3/seqtk</remote-id>
+	</upstream>
 </pkgmetadata>
diff --git a/sci-biology/seqtools/seqtools-4.44.1.ebuild b/sci-biology/seqtools/seqtools-4.44.1.ebuild
index 7416d9fab..fc4bca4ba 100644
--- a/sci-biology/seqtools/seqtools-4.44.1.ebuild
+++ b/sci-biology/seqtools/seqtools-4.44.1.ebuild
@@ -1,7 +1,7 @@
-# Copyright 1999-2018 Gentoo Foundation
+# Copyright 1999-2021 Gentoo Authors
 # Distributed under the terms of the GNU General Public License v2
 
-EAPI=6
+EAPI=7
 
 DESCRIPTION="Display alignments and GFF files, matrix dot plots (blixem, dotter, belvu)"
 HOMEPAGE="http://www.sanger.ac.uk/resources/software/seqtools"
@@ -10,7 +10,6 @@ SRC_URI="ftp://ftp.sanger.ac.uk/pub/resources/software/${PN}/PRODUCTION/${P}.tar
 LICENSE="GPL-3"
 SLOT="0"
 KEYWORDS="~amd64 ~x86"
-IUSE=""
 
 DEPEND="
 	sys-libs/readline:*
diff --git a/sci-biology/sff_dump/sff_dump-1.04.ebuild b/sci-biology/sff_dump/sff_dump-1.04.ebuild
index 8ae736155..3f434a1ea 100644
--- a/sci-biology/sff_dump/sff_dump-1.04.ebuild
+++ b/sci-biology/sff_dump/sff_dump-1.04.ebuild
@@ -1,7 +1,7 @@
-# Copyright 1999-2015 Gentoo Foundation
+# Copyright 1999-2021 Gentoo Authors
 # Distributed under the terms of the GNU General Public License v2
 
-EAPI=5
+EAPI=7
 
 inherit toolchain-funcs
 
@@ -12,9 +12,9 @@ SRC_URI="http://genome.imb-jena.de/software/roche454ace2caf/download/src/${P}.tg
 LICENSE="FLI-Jena"
 SLOT="0"
 KEYWORDS="~amd64 ~x86"
-IUSE=""
 
 src_prepare(){
+	default
 	sed \
 		-e 's:^CC :#CC :' \
 		-e 's:^LD :#LD :' \
diff --git a/sci-biology/sga/sga-9999.ebuild b/sci-biology/sga/sga-9999.ebuild
index 8ec029f94..7519b3e2a 100644
--- a/sci-biology/sga/sga-9999.ebuild
+++ b/sci-biology/sga/sga-9999.ebuild
@@ -1,9 +1,9 @@
-# Copyright 1999-2018 Gentoo Foundation
+# Copyright 1999-2021 Gentoo Authors
 # Distributed under the terms of the GNU General Public License v2
 
-EAPI=5
+EAPI=7
 
-inherit eutils git-r3
+inherit git-r3 autotools
 
 DESCRIPTION="String Graph OLC Assembler for short reads (overlap-layout-consensus)"
 HOMEPAGE="https://github.com/jts/sga"
@@ -14,20 +14,27 @@ SLOT="0"
 KEYWORDS=""
 IUSE="jemalloc python"
 
-DEPEND="dev-cpp/sparsehash
+DEPEND="
+	dev-cpp/sparsehash
 	sci-biology/bamtools
 	sys-libs/zlib
-	jemalloc? ( dev-libs/jemalloc )"
+	jemalloc? ( dev-libs/jemalloc )
+"
 RDEPEND="${DEPEND}
 	sci-biology/abyss
 	python? ( sci-biology/pysam
 			sci-biology/ruffus )"
 
+S="${WORKDIR}/${P}/src"
+
+src_prepare() {
+	default
+	eautoreconf
+}
+
 # http://www.vcru.wisc.edu/simonlab/bioinformatics/programs/install/sga.htm
 src_configure(){
-	cd src || die
-	./autogen.sh || die
-	econf --with-bamtools="${EPREFIX}"/usr
+	econf --with-bamtools="${EPREFIX}"/usr --with-sparsehash="${EPREFIX}"/usr
 }
 
 src_compile(){
@@ -38,12 +45,10 @@ src_compile(){
 	#
 	# other unreviewed patches:
 	# https://github.com/jts/sga/issues/96
-	cd src || die "Try -atd=g++-98, try gcc-5 or -std=c++03"
 	default
 }
 
 src_install(){
-	cd src || die
 	dodoc README
 	emake install DESTDIR="${D}"
 	insinto /usr/share/sga/examples
diff --git a/sci-biology/sgp2/Manifest b/sci-biology/sgp2/Manifest
deleted file mode 100644
index be53bd01c..000000000
--- a/sci-biology/sgp2/Manifest
+++ /dev/null
@@ -1 +0,0 @@
-DIST sgp2_v1.1.May_8_2012.tar.gz 3941100 BLAKE2B a6310ff9ca17540ace02b3bd9f379654a0e7ce6cd0e1b7b2af18e7e1648b42f101baa82815a92d2574476d2d4f8db2e6325150ba9c73ef7f21394ece69c71c2e SHA512 f32fcbb84fbcd67e0e4e7189bb73376232f2d5ff84ff453153adaa81b78b78b65657a1ac6102a180ec5f96bad22589a18ce1461237612f5e62a1a1ad576f4eca
diff --git a/sci-biology/sgp2/files/Makefile.patch b/sci-biology/sgp2/files/Makefile.patch
deleted file mode 100644
index c1d64bdc8..000000000
--- a/sci-biology/sgp2/files/Makefile.patch
+++ /dev/null
@@ -1,88 +0,0 @@
---- Makefile.ori	2014-06-17 12:24:40.000000000 +0200
-+++ Makefile	2014-06-17 12:26:47.000000000 +0200
-@@ -39,12 +39,12 @@
- #
- ### PATHS
- 
--       BBIN = /bin
--       UBIN = /usr/bin
--       LBIN = /usr/local/bin
-+       BBIN = $(DESTDIR)/bin
-+       UBIN = $(DESTDIR)/usr/bin
-+       LBIN = $(DESTDIR)/usr/local/bin
-  #%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
-  #  REMEMBER: INSTALLDIR is the only variable that should be modified
-- INSTALLDIR = $(LBIN)
-+ INSTALLDIR = $(UBIN)
-  #%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
- 
- #
-@@ -97,19 +97,19 @@
- 
-        SGP2 = sgp2
-  PARSEBLAST = parseblast
--     GENEID = geneid
-+#     GENEID = geneid
-    #  HSP2SR = blast2gff
- 
- 
--     GENEIDD = $(SRC)/geneid
-+#     GENEIDD = $(SRC)/geneid
-  #    HSP2SRD = $(SRC)/blast2gff
- 
--   GENEIDSRC = $(wildcard $(addprefix $(GENEIDD)/src/, *.c)) \
--               $(wildcard $(addprefix $(GENEIDD)/include/, *.h))
-+#   GENEIDSRC = $(wildcard $(addprefix $(GENEIDD)/src/, *.c)) \
-+#               $(wildcard $(addprefix $(GENEIDD)/include/, *.h))
- #   HSP2SRSRC = $(wildcard $(addprefix $(HSP2SRD)/src/, *.c)) \
-  #              $(wildcard $(addprefix $(HSP2SRD)/include/, *.h))
- 
--     SRCCODE = $(GENEID)-sgp  $(PARSEBLAST) \
-+     SRCCODE = $(PARSEBLAST) \
-                $(SGP2)
- #    SRCCODE = $(GENEID)-sgp  $(PARSEBLAST) \
- #              $(HSP2SR) $(SGP2)
-@@ -134,9 +134,9 @@
- cleanbin :
- 	-@$(RM) -f $(wildcard $(BIN)/*);
- 	rmdir $(BIN);
--	@echo "### Cleaning GENEID..."
--	@cd $(GENEIDD); \
--	 $(MAKE) clean;
-+#	@echo "### Cleaning GENEID..."
-+#	@cd $(GENEIDD); \
-+#	 $(MAKE) clean;
- #	@echo "### Cleaning HSP2SR..."
- #	@cd $(HSP2SRD); \
- #	 $(MAKE) clean;
-@@ -147,6 +147,7 @@
- 
- installbin : $(BINCODE)
- 	@echo "### COPYING BIN FILES TO $(INSTALLDIR)...";
-+	mkdir -p $(INSTALLDIR);
- 	@$(CP) -p $^ $(INSTALLDIR)/;
- 
- #
-@@ -155,14 +156,14 @@
- $(BIN) :
- 	mkdir $(BIN);
- 
--$(addprefix $(BIN)/, $(GENEID)-sgp) : $(addprefix $(GENEIDD)/bin/, $(GENEID))
--	@${CP} $(addprefix $(GENEIDD)/bin/, $(GENEID)) \
--           $(addprefix $(BIN)/, $(GENEID)-sgp)
--
--$(addprefix $(GENEIDD)/bin/, $(GENEID)) : $(GENEIDSRC)
--	@echo "### Making GENEID..."
--	@cd $(GENEIDD); \
--	 $(MAKE) -f ./Makefile;
-+#$(addprefix $(BIN)/, $(GENEID)-sgp) : $(addprefix $(GENEIDD)/bin/, $(GENEID))
-+#	@${CP} $(addprefix $(GENEIDD)/bin/, $(GENEID)) \
-+#           $(addprefix $(BIN)/, $(GENEID)-sgp)
-+
-+#$(addprefix $(GENEIDD)/bin/, $(GENEID)) : $(GENEIDSRC)
-+#	@echo "### Making GENEID..."
-+#	@cd $(GENEIDD); \
-+#	 $(MAKE) -f ./Makefile;
- 
- #$(addprefix $(BIN)/, $(HSP2SR)) : $(addprefix $(HSP2SRD)/bin/, $(HSP2SR))
- #	@${CP} $(addprefix $(HSP2SRD)/bin/, $(HSP2SR)) \
diff --git a/sci-biology/sgp2/metadata.xml b/sci-biology/sgp2/metadata.xml
deleted file mode 100644
index 138cb7705..000000000
--- a/sci-biology/sgp2/metadata.xml
+++ /dev/null
@@ -1,12 +0,0 @@
-<?xml version="1.0" encoding="UTF-8"?>
-<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
-<pkgmetadata>
-	<maintainer type="person">
-		<email>mmokrejs@fold.natur.cuni.cz</email>
-		<name>Martin Mokrejs</name>
-	</maintainer>
-	<maintainer type="project">
-		<email>sci-biology@gentoo.org</email>
-		<name>Gentoo Biology Project</name>
-	</maintainer>
-</pkgmetadata>
diff --git a/sci-biology/sgp2/sgp2-1.1.ebuild b/sci-biology/sgp2/sgp2-1.1.ebuild
deleted file mode 100644
index 58620bbdb..000000000
--- a/sci-biology/sgp2/sgp2-1.1.ebuild
+++ /dev/null
@@ -1,34 +0,0 @@
-# Copyright 1999-2015 Gentoo Foundation
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=5
-
-inherit eutils
-
-DESCRIPTION="Find ORFs by comparing two genomic/EST sequences"
-HOMEPAGE="http://genome.crg.es/software/sgp2/"
-SRC_URI="ftp://genome.crg.es/pub/software/sgp2/sgp2_v1.1.May_8_2012.tar.gz"
-
-LICENSE="GPL-2"
-SLOT="0"
-KEYWORDS="~amd64 ~x86"
-IUSE=""
-
-DEPEND="dev-lang/perl"
-RDEPEND="${DEPEND}
-	sci-biology/geneid"
-
-S="${WORKDIR}"/"${PN}"
-
-src_prepare() {
-	# disable bundled geneid sources
-	epatch "${FILESDIR}"/Makefile.patch
-	# do not look for renamed geneid-sgp binary
-	sed -i -e 's#geneid-sgp#geneid#g' src/sgp2.pl
-}
-
-src_install() {
-	dobin bin/sgp2 bin/parseblast
-	insinto /usr/share/"${PN}"
-	doins -r param samples
-}
diff --git a/sci-biology/sickle/Manifest b/sci-biology/sickle/Manifest
index f257e6e54..61fb84aa7 100644
--- a/sci-biology/sickle/Manifest
+++ b/sci-biology/sickle/Manifest
@@ -1 +1 @@
-DIST v1.33.tar.gz 631275 BLAKE2B 81ede2a0e6cfb64a0cc4754f094526cc516683845d1835afdcde9bcff90c2b98cac6c9fb74ead17495e7b80ff959ea4cb27d241259133b7cfa1a39ed658fa058 SHA512 94d9794861655c9d8688a4c71757ba93166f167ae529c5661998d287b93c6ccc9755d9e3db8d481bbd5dca4cf047f6266880a5fc1f8099e597bc857954404dcb
+DIST sickle-1.33.tar.gz 631275 BLAKE2B 81ede2a0e6cfb64a0cc4754f094526cc516683845d1835afdcde9bcff90c2b98cac6c9fb74ead17495e7b80ff959ea4cb27d241259133b7cfa1a39ed658fa058 SHA512 94d9794861655c9d8688a4c71757ba93166f167ae529c5661998d287b93c6ccc9755d9e3db8d481bbd5dca4cf047f6266880a5fc1f8099e597bc857954404dcb
diff --git a/sci-biology/sickle/sickle-1.33.ebuild b/sci-biology/sickle/sickle-1.33.ebuild
index 4069e75f9..e2ebdb3a3 100644
--- a/sci-biology/sickle/sickle-1.33.ebuild
+++ b/sci-biology/sickle/sickle-1.33.ebuild
@@ -1,33 +1,23 @@
-# Copyright 1999-2015 Gentoo Foundation
+# Copyright 1999-2021 Gentoo Authors
 # Distributed under the terms of the GNU General Public License v2
 
-EAPI=5
-
-inherit eutils eutils toolchain-funcs
-
-[ "$PV" == "9999" ] && inherit git-r3
+EAPI=7
 
 DESCRIPTION="Windowed adaptive quality-based trimming tool for FASTQ data"
 HOMEPAGE="https://github.com/najoshi/sickle"
 if [ "$PV" == "9999" ]; then
+	inherit git-r3
 	EGIT_REPO_URI="https://github.com/najoshi/sickle"
-	KEYWORDS=""
 else
-	SRC_URI="https://github.com/najoshi/sickle/archive/v"${PV}".tar.gz"
+	SRC_URI="https://github.com/najoshi/sickle/archive/v${PV}.tar.gz -> ${P}.tar.gz"
 	KEYWORDS="~amd64"
 fi
 
 LICENSE="MIT"
 SLOT="0"
-IUSE=""
 
-DEPEND=""
-RDEPEND="${DEPEND}
-	sys-libs/zlib"
-
-src_prepare(){
-	sed -e "s#-pedantic#-pedantic ${CFLAGS}#;s#gcc#"$(tc-getCC)"#" -i Makefile || die
-}
+DEPEND="sys-libs/zlib"
+RDEPEND="${DEPEND}"
 
 src_install(){
 	dobin sickle
diff --git a/sci-biology/sickle/sickle-9999.ebuild b/sci-biology/sickle/sickle-9999.ebuild
index 4069e75f9..e2ebdb3a3 100644
--- a/sci-biology/sickle/sickle-9999.ebuild
+++ b/sci-biology/sickle/sickle-9999.ebuild
@@ -1,33 +1,23 @@
-# Copyright 1999-2015 Gentoo Foundation
+# Copyright 1999-2021 Gentoo Authors
 # Distributed under the terms of the GNU General Public License v2
 
-EAPI=5
-
-inherit eutils eutils toolchain-funcs
-
-[ "$PV" == "9999" ] && inherit git-r3
+EAPI=7
 
 DESCRIPTION="Windowed adaptive quality-based trimming tool for FASTQ data"
 HOMEPAGE="https://github.com/najoshi/sickle"
 if [ "$PV" == "9999" ]; then
+	inherit git-r3
 	EGIT_REPO_URI="https://github.com/najoshi/sickle"
-	KEYWORDS=""
 else
-	SRC_URI="https://github.com/najoshi/sickle/archive/v"${PV}".tar.gz"
+	SRC_URI="https://github.com/najoshi/sickle/archive/v${PV}.tar.gz -> ${P}.tar.gz"
 	KEYWORDS="~amd64"
 fi
 
 LICENSE="MIT"
 SLOT="0"
-IUSE=""
 
-DEPEND=""
-RDEPEND="${DEPEND}
-	sys-libs/zlib"
-
-src_prepare(){
-	sed -e "s#-pedantic#-pedantic ${CFLAGS}#;s#gcc#"$(tc-getCC)"#" -i Makefile || die
-}
+DEPEND="sys-libs/zlib"
+RDEPEND="${DEPEND}"
 
 src_install(){
 	dobin sickle
diff --git a/sci-biology/signalp/Manifest b/sci-biology/signalp/Manifest
deleted file mode 100644
index 4f4d96631..000000000
--- a/sci-biology/signalp/Manifest
+++ /dev/null
@@ -1 +0,0 @@
-DIST signalp-3.0.Linux.tar.Z 1216617 SHA256 260c2e5bd945b386e833a7b7326cff6d7332302868e99c0aeae306212047c0c2
diff --git a/sci-biology/signalp/metadata.xml b/sci-biology/signalp/metadata.xml
deleted file mode 100644
index 8417d1580..000000000
--- a/sci-biology/signalp/metadata.xml
+++ /dev/null
@@ -1,8 +0,0 @@
-<?xml version="1.0" encoding="UTF-8"?>
-<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
-<pkgmetadata>
-	<maintainer type="project">
-		<email>sci-biology@gentoo.org</email>
-		<name>Gentoo Biology Project</name>
-	</maintainer>
-</pkgmetadata>
diff --git a/sci-biology/signalp/signalp-3.0.ebuild b/sci-biology/signalp/signalp-3.0.ebuild
deleted file mode 100644
index be10dcdbb..000000000
--- a/sci-biology/signalp/signalp-3.0.ebuild
+++ /dev/null
@@ -1,45 +0,0 @@
-# Copyright 1999-2015 Gentoo Foundation
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=5
-
-DESCRIPTION="Prediction of signal peptide cleavage sites in amino acid sequences"
-HOMEPAGE="http://www.cbs.dtu.dk/services/SignalP/"
-SRC_URI="${P}.Linux.tar.Z"
-
-LICENSE="signalp"
-SLOT="0"
-IUSE="gnuplot"
-KEYWORDS="~amd64 ~x86"
-
-DEPEND=""
-RDEPEND="gnuplot? (
-	sci-visualization/gnuplot
-	media-libs/netpbm )"
-
-RESTRICT="fetch strip"
-
-pkg_nofetch() {
-	einfo "Please visit ${HOMEPAGE} and obtain the file"
-	einfo "\"${SRC_URI}\", then place it in ${DISTDIR}"
-}
-
-src_prepare() {
-	sed -i -e '/SIGNALP=/ s/\/usr//' \
-		-e '/TMPDIR=/ s/$SIGNALP//' "${S}/signalp" || die
-	sed -i 's/nawk/gawk/' "${S}"/bin/* || die
-}
-
-src_install() {
-	dobin signalp
-	insinto /opt/${P}
-	doins -r bin hmm how mod syn* test
-	exeinto /opt/${P}/bin
-	doexe bin/*
-	exeinto /opt/${P}/hmm
-	doexe hmm/*
-	exeinto /opt/${P}/how
-	doexe how/*
-	doman signalp.1
-	dodoc *readme
-}
diff --git a/sci-biology/skewer-bin/Manifest b/sci-biology/skewer-bin/Manifest
index d9a0196fb..2913b23d3 100644
--- a/sci-biology/skewer-bin/Manifest
+++ b/sci-biology/skewer-bin/Manifest
@@ -1,2 +1,2 @@
-DIST skewer-0.1.104-linux-x86_64 97877 BLAKE2B a0c5bc4f675fa9c1688b06216d9e00af81d77d2f13dcc87cf7a66ee2cbcda79be8691c284b10bd559a61cac3fdbe22d533894b66ed6fe05ede8e98e667a28251 SHA512 c2a4b73c4a4c87528e9a33c16d839aa2a20771c34b38e0593ab3caf654fee47463c8eb63ceb29c6eee13ffc75657d3e69da5afc3c9fd86479f74a1888652fd05
+DIST skewer-0.2.2-linux-x86_64 182796 BLAKE2B 08c2ef3180dc3d6754477ba7c08fdb3aa1dbc3388d823db689cb8c62cb09ddb7fcfcb4e3fa8a0636867bf057249589e5a5b8313718ab9d904893660c300048ec SHA512 e75caa1122ebbbbd6f6d2cf14c63aa2619e0522fab60e90e00d3bfbed6a2cbf73da4b626e23f369e968a1fe152d82ec2aae29026e9951d77393bcac1241007ff
 DIST srna-scripts-0.1.2.tar.gz 3811 BLAKE2B e0dbed1bd81deaed675b5b60af165bb3f1906c91f11b90e725977cf12af8ed57f2fcbc5e83a37425980f6efc3fd3174e844e02470a2a637706f1c1d4c7f43a68 SHA512 18b65c182cbd054a5ffada386cbeeb7ea26bab27e98e9586b9b30d68b028fc139f74df88a42d8b7142485e18b72d5275cde2dc3e0567a7567c514cb5459eeea0
diff --git a/sci-biology/skewer-bin/skewer-bin-0.1.104.ebuild b/sci-biology/skewer-bin/skewer-bin-0.1.104.ebuild
deleted file mode 100644
index 3de2417b9..000000000
--- a/sci-biology/skewer-bin/skewer-bin-0.1.104.ebuild
+++ /dev/null
@@ -1,24 +0,0 @@
-# Copyright 1999-2015 Gentoo Foundation
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=5
-
-DESCRIPTION="Adaptor and MID removal / trimming tool"
-HOMEPAGE="http://sourceforge.net/projects/skewer"
-SRC_URI="
-	http://sourceforge.net/projects/skewer/files/Binaries/skewer-0.1.104-linux-x86_64
-	http://sourceforge.net/projects/skewer/files/Scripts/srna-scripts-0.1.2.tar.gz"
-
-LICENSE="Artistic"
-SLOT="0"
-KEYWORDS="~amd64"
-IUSE=""
-
-DEPEND=""
-RDEPEND="${DEPEND}
-	dev-lang/perl"
-
-src_install() {
-	cp "${DISTDIR}"/skewer-* skewer || die
-	dobin *.pl skewer
-}
diff --git a/sci-biology/skewer-bin/skewer-bin-0.2.2.ebuild b/sci-biology/skewer-bin/skewer-bin-0.2.2.ebuild
new file mode 100644
index 000000000..de542ea04
--- /dev/null
+++ b/sci-biology/skewer-bin/skewer-bin-0.2.2.ebuild
@@ -0,0 +1,24 @@
+# Copyright 1999-2021 Gentoo Authors
+# Distributed under the terms of the GNU General Public License v2
+
+EAPI=7
+
+DESCRIPTION="Adaptor and MID removal / trimming tool"
+HOMEPAGE="https://sourceforge.net/projects/skewer"
+SRC_URI="
+	https://sourceforge.net/projects/skewer/files/Binaries/skewer-${PV}-linux-x86_64
+	https://sourceforge.net/projects/skewer/files/Scripts/srna-scripts-0.1.2.tar.gz"
+
+LICENSE="Artistic"
+SLOT="0"
+KEYWORDS="~amd64"
+
+RDEPEND="${DEPEND}
+	dev-lang/perl"
+
+S="${WORKDIR}"
+
+src_install() {
+	cp "${DISTDIR}"/skewer-* skewer || die
+	dobin *.pl skewer
+}
diff --git a/sci-biology/smalt-bin/Manifest b/sci-biology/smalt-bin/Manifest
index efd02e592..2ef859b3c 100644
--- a/sci-biology/smalt-bin/Manifest
+++ b/sci-biology/smalt-bin/Manifest
@@ -1 +1 @@
-DIST smalt-0.7.4.tgz 1437480 BLAKE2B 72f94cc403a1fd364bed8a170e6a2dde6b679482b6845569fc2a3e9fa342e32fb84713b8a1de843d355539d046772ac055a33d0b3ba6a017a81953d71ce91086 SHA512 9c31f358ef4094566bdc67f92b2576e6cf15a010bbf7dc1eb4a66afb2107253dfe4947a529c10c579484ccd7aff6aaae048ea8b17fd468804b08d88fb6588e39
+DIST smalt-0.7.6-bin.tar.gz 1526694 BLAKE2B 7d5ab259e192366e66bd495b3e8a13d51ce4800f621e358f133b8936f9607218e7c2842942a7c50a1b60a1f125e26f2df8f1ed4fea74a3dda1535c50c28146b6 SHA512 ee463bf9448159446d158a9114cf6fcbfe6eae0a4fe0f5f487e1d00547da5908d3f5c01f997552a9a5b173a8045d2940cef60aeb7cdfb0469e91fe9f03d3e752
diff --git a/sci-biology/smalt-bin/smalt-bin-0.7.4.ebuild b/sci-biology/smalt-bin/smalt-bin-0.7.4.ebuild
deleted file mode 100644
index 2059abad6..000000000
--- a/sci-biology/smalt-bin/smalt-bin-0.7.4.ebuild
+++ /dev/null
@@ -1,30 +0,0 @@
-# Copyright 1999-2014 Gentoo Foundation
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=5
-
-MY_PN="${PN%-bin}"
-MY_P="${MY_PN}-${PV}"
-
-DESCRIPTION="Pairwise sequence alignment mapping DNA reads onto genomic reference"
-HOMEPAGE="http://www.sanger.ac.uk/resources/software/smalt/"
-SRC_URI="ftp://ftp.sanger.ac.uk/pub4/resources/software/${MY_PN}/${MY_P}.tgz"
-
-LICENSE="all-rights-reserved"
-SLOT="0"
-KEYWORDS="~amd64 ~x86"
-IUSE=""
-
-S="${WORKDIR}"/${MY_P}
-
-QA_PREBUILT="/opt/.*"
-
-src_install(){
-	exeinto /opt/bin
-	use x86 && newexe ${MY_PN}_i386 ${MY_PN}
-	use amd64 && newexe ${MY_PN}_x86_64 ${MY_PN}
-	use ia64 && newexe ${MY_PN}_ia64 ${MY_PN}
-
-	dodoc NEWS ${MY_PN}_manual.pdf
-	doman ${MY_PN}.1
-}
diff --git a/sci-biology/smalt-bin/smalt-bin-0.7.6.ebuild b/sci-biology/smalt-bin/smalt-bin-0.7.6.ebuild
new file mode 100644
index 000000000..780bf4210
--- /dev/null
+++ b/sci-biology/smalt-bin/smalt-bin-0.7.6.ebuild
@@ -0,0 +1,29 @@
+# Copyright 1999-2021 Gentoo Authors
+# Distributed under the terms of the GNU General Public License v2
+
+EAPI=7
+
+MY_PN="${PN%-bin}"
+MY_P="${MY_PN}-${PV}"
+
+DESCRIPTION="Pairwise sequence alignment mapping DNA reads onto genomic reference"
+HOMEPAGE="https://sourceforge.net/projects/smalt/"
+SRC_URI="https://sourceforge.net/projects/${MY_PN}/files/${MY_P}-bin.tar.gz"
+
+LICENSE="all-rights-reserved"
+SLOT="0"
+KEYWORDS="~amd64 ~x86"
+
+S="${WORKDIR}/${MY_P}-bin"
+
+QA_PREBUILT="/opt/.*"
+
+src_install(){
+	exeinto /opt/bin
+	use x86 && newexe ${MY_PN}_i386 ${MY_PN}
+	use amd64 && newexe ${MY_PN}_x86_64 ${MY_PN}
+	use ia64 && newexe ${MY_PN}_ia64 ${MY_PN}
+
+	dodoc NEWS ${MY_PN}_manual.pdf
+	doman ${MY_PN}.1
+}
diff --git a/sci-biology/smalt/smalt-0.7.6.ebuild b/sci-biology/smalt/smalt-0.7.6.ebuild
index 141269ae4..f140481bf 100644
--- a/sci-biology/smalt/smalt-0.7.6.ebuild
+++ b/sci-biology/smalt/smalt-0.7.6.ebuild
@@ -1,19 +1,18 @@
-# Copyright 1999-2016 Gentoo Foundation
+# Copyright 1999-2021 Gentoo Authors
 # Distributed under the terms of the GNU General Public License v2
 
-EAPI=5
+EAPI=7
 
 MY_PN="${PN%-bin}"
 MY_P="${MY_PN}-${PV}"
 
 DESCRIPTION="DNA read mapper using k=20 (successor of ssaha2)"
-HOMEPAGE="http://www.sanger.ac.uk/resources/software/smalt/"
-SRC_URI="http://sourceforge.net/projects/${PN}/files/${P}.tar.gz"
+HOMEPAGE="https://sourceforge.net/projects/smalt/"
+SRC_URI="https://sourceforge.net/projects/${PN}/files/${P}.tar.gz"
 
 LICENSE="GPL-3"
 SLOT="0"
 KEYWORDS="~amd64"
-IUSE=""
 
 DEPEND=""
 RDEPEND="${DEPEND}"
diff --git a/sci-biology/snap/files/snap-20131129-fno-common.patch b/sci-biology/snap/files/snap-20131129-fno-common.patch
new file mode 100644
index 000000000..4b3b1b587
--- /dev/null
+++ b/sci-biology/snap/files/snap-20131129-fno-common.patch
@@ -0,0 +1,15 @@
+--- a/Zoe/zoeTools.h
++++ b/Zoe/zoeTools.h
+@@ -40,9 +40,9 @@ The MIT License (MIT) - opensource.org/licenses/MIT
+ #include <stdlib.h>
+ #include <string.h>
+ 
+-const char * zoeFunction;
+-const char * zoeConstructor;
+-const char * zoeMethod;
++extern char * zoeFunction;
++extern char * zoeConstructor;
++extern char * zoeMethod;
+ 
+ void   zoeLibInfo (void);
+ void   zoeSetProgramName (const char*);
diff --git a/sci-biology/snap/snap-20131129.ebuild b/sci-biology/snap/snap-20131129.ebuild
index 84305c131..bc92eff18 100644
--- a/sci-biology/snap/snap-20131129.ebuild
+++ b/sci-biology/snap/snap-20131129.ebuild
@@ -1,9 +1,9 @@
-# Copyright 1999-2015 Gentoo Foundation
+# Copyright 1999-2021 Gentoo Authors
 # Distributed under the terms of the GNU General Public License v2
 
-EAPI=5
+EAPI=7
 
-inherit eutils toolchain-funcs
+inherit toolchain-funcs
 
 DESCRIPTION="HMM-based prokaryotic and eukaryotic gene prediction tool"
 HOMEPAGE="http://korflab.ucdavis.edu/software.html"
@@ -12,14 +12,13 @@ SRC_URI="http://korflab.ucdavis.edu/Software/snap-2013-11-29.tar.gz"
 LICENSE="MIT"
 SLOT="0"
 KEYWORDS="~amd64"
-IUSE=""
-
-DEPEND=""
-RDEPEND="${DEPEND}"
 
 S="${WORKDIR}"/snap
 
+PATCHES=( "${FILESDIR}"/${P}-fno-common.patch )
+
 src_prepare(){
+	default
 	sed -e "s#CC=\"gcc.*#CC=$(tc-getCC)#" -i Zoe/Makefile || die
 	sed -e "s#CC=\"gcc.*#CC=$(tc-getCC)#" -i Makefile || die
 }
@@ -31,4 +30,5 @@ src_install(){
 	doins HMM/[a-zA-Z]*.hmm
 	dobin snap fathom forge *.pl
 	dodoc 00README
+	einstalldocs
 }
diff --git a/sci-biology/snapgene-viewer/Manifest b/sci-biology/snapgene-viewer/Manifest
new file mode 100644
index 000000000..2e6582002
--- /dev/null
+++ b/sci-biology/snapgene-viewer/Manifest
@@ -0,0 +1 @@
+DIST snapgene_7.0.3_linux.deb 129706720 BLAKE2B 539257921cc36c8770f5786e3af37502a6e958636ed32f861dcb2fd4621dfbac19d39c9a0772e0d08a532226f9b1875964bf657638917b52c606ff448a03b6f3 SHA512 b902d2bc229e697c4409b09b4f8e2a0ef6583a1958e7a38ef8321b453cdda687e33bc42adb14133d7320cc18791ec1b79409701efbfc5f6be0bbcce2f4e6e87f
diff --git a/sci-biology/snapgene-viewer/metadata.xml b/sci-biology/snapgene-viewer/metadata.xml
new file mode 100644
index 000000000..5c83ce208
--- /dev/null
+++ b/sci-biology/snapgene-viewer/metadata.xml
@@ -0,0 +1,12 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
+<pkgmetadata>
+	<maintainer type="person">
+		<email>pacho@gentoo.org</email>
+		<name>Pacho Ramos</name>
+	</maintainer>
+	<maintainer type="project">
+		<email>sci-chemistry@gentoo.org</email>
+		<name>Gentoo Chemistry Project</name>
+	</maintainer>
+</pkgmetadata>
diff --git a/sci-biology/snapgene-viewer/snapgene-viewer-7.0.3.ebuild b/sci-biology/snapgene-viewer/snapgene-viewer-7.0.3.ebuild
new file mode 100644
index 000000000..d117fbc14
--- /dev/null
+++ b/sci-biology/snapgene-viewer/snapgene-viewer-7.0.3.ebuild
@@ -0,0 +1,65 @@
+# Copyright 2023 Gentoo Authors
+# Distributed under the terms of the GNU General Public License v2
+
+EAPI=8
+inherit unpacker wrapper xdg
+
+DESCRIPTION="Software for plasmid mapping, primer design, and restriction site analysis"
+HOMEPAGE="https://www.snapgene.com/features"
+SRC_URI="snapgene_${PV}_linux.deb"
+SNAPGENE_DOWNLOAD="https://www.snapgene.com/local/targets/download.php?os=linux_deb&variant=paid&release=${PV}"
+RESTRICT="fetch"
+
+LICENSE="GSL"
+SLOT="0"
+KEYWORDS="~amd64"
+
+DEPEND=""
+# ldd /opt/gslbiotech/snapgene/snapgene
+RDEPEND="${DEPEND}
+	app-arch/bzip2
+	app-arch/xz-utils
+	app-crypt/qca[qt6]
+	dev-libs/openssl-compat:1.1.1
+	dev-qt/qt5compat:6
+	dev-qt/qtbase:6[concurrent,gui,network,opengl,sql,widgets,xml]
+	dev-qt/qtdeclarative:6
+	dev-qt/qtpositioning:6
+	dev-qt/qtwebchannel:6
+	dev-qt/qtwebengine:6
+	media-libs/libglvnd
+	media-libs/tiff-compat:4
+	sci-libs/htslib:0/3
+	sys-devel/gcc
+	sys-libs/glibc
+	sys-libs/libcxx[libcxxabi]
+	sys-libs/libunwind:0/8
+	x11-libs/libX11
+	x11-libs/libXau
+	x11-libs/libXdmcp
+	x11-libs/libxcb
+"
+BDEPEND=">=dev-util/patchelf-0.10"
+
+S="${WORKDIR}"
+QA_PREBUILT="*"
+
+pkg_nofetch() {
+	elog "Please download ${SRC_URI} from"
+	elog "${SNAPGENE_DOWNLOAD}"
+	elog "and place it into your DISTDIR directory."
+}
+
+src_install() {
+	patchelf --replace-needed libunwind.so.1 libunwind.so.8 \
+		opt/gslbiotech/snapgene/snapgene || die
+
+	mv usr/share/doc/snapgene usr/share/doc/${PF} || die
+	gzip -d usr/share/doc/${PF}/changelog.Debian.gz || die
+
+	insinto /
+	doins -r *
+
+	fperms +x /opt/gslbiotech/snapgene/snapgene{,.sh}
+	make_wrapper ${PN} ./snapgene.sh /opt/gslbiotech/snapgene/
+}
diff --git a/sci-biology/snphylo/Manifest b/sci-biology/snphylo/Manifest
deleted file mode 100644
index e373a86f0..000000000
--- a/sci-biology/snphylo/Manifest
+++ /dev/null
@@ -1 +0,0 @@
-DIST snphylo-20140701.tar.gz 19522 BLAKE2B 9355ba532e30eaeb45e8a5e9f569d281eb0c4064b9d84efa3faadc26fc463ea83af4202d17f650f380e793ba5900d9b783d3ddb1013ad22862c6efe51de8c26a SHA512 575c97caf01126dea194007494c783de69653b468964c8f0a004a93c8b33deefd9d79a0e02841814bcceda69bed29fd3343ca492c7f71b46c55139acf4f0a3c6
diff --git a/sci-biology/snphylo/metadata.xml b/sci-biology/snphylo/metadata.xml
deleted file mode 100644
index 138cb7705..000000000
--- a/sci-biology/snphylo/metadata.xml
+++ /dev/null
@@ -1,12 +0,0 @@
-<?xml version="1.0" encoding="UTF-8"?>
-<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
-<pkgmetadata>
-	<maintainer type="person">
-		<email>mmokrejs@fold.natur.cuni.cz</email>
-		<name>Martin Mokrejs</name>
-	</maintainer>
-	<maintainer type="project">
-		<email>sci-biology@gentoo.org</email>
-		<name>Gentoo Biology Project</name>
-	</maintainer>
-</pkgmetadata>
diff --git a/sci-biology/snphylo/snphylo-20140701.ebuild b/sci-biology/snphylo/snphylo-20140701.ebuild
deleted file mode 100644
index c10401184..000000000
--- a/sci-biology/snphylo/snphylo-20140701.ebuild
+++ /dev/null
@@ -1,34 +0,0 @@
-# Copyright 1999-2015 Gentoo Foundation
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=5
-
-DESCRIPTION="Pipeline to generate phylogenetic tree from SNP data"
-HOMEPAGE="http://chibba.pgml.uga.edu/snphylo"
-SRC_URI="http://chibba.pgml.uga.edu/snphylo/snphylo.tar.gz -> ${P}.tar.gz"
-# http://github.com/thlee/SNPhylo
-# http://www.biomedcentral.com/1471-2164/15/162
-
-LICENSE="GPL-2"
-SLOT="0"
-KEYWORDS=""
-IUSE=""
-
-DEPEND=""
-RDEPEND="${DEPEND}
-	sci-biology/fastdnaml
-	sci-biology/muscle
-	sci-biology/phylip"
-# http://chibba.pgml.uga.edu/snphylo/install_on_linux.html
-# R packages (phangorn, gdsfmt, SNPRelate and getopt)
-# $ apt-get -y install r-base-dev r-cran-getopt r-cran-rgl
-
-S="${WORKDIR}"/"${PN}"
-
-src_compile(){
-	bash setup.sh || die
-}
-
-src_install(){
-	dobin snphylo.sh
-}
diff --git a/sci-biology/snpomatic/Manifest b/sci-biology/snpomatic/Manifest
new file mode 100644
index 000000000..28de8c730
--- /dev/null
+++ b/sci-biology/snpomatic/Manifest
@@ -0,0 +1 @@
+DIST snpomatic-1.0.tar.gz 66546 BLAKE2B 6638c0ff0fc976d7de230736994813e03a58b410012cdd4176680222b43c18eb3be9c51a8b4053059cf6985aa56f163f96ea007251b1f0fc87501fec32df3862 SHA512 18ea42a19c47b21dc7923ee2bb6dcf06c0107df77bd01702a5085a8a1ed61fed85407c78e45e7558d9f530180101c10d2a1a1572eb51ee279a9a8815c1bc70c0
diff --git a/sci-biology/snpomatic/snpomatic-1.0.ebuild b/sci-biology/snpomatic/snpomatic-1.0.ebuild
new file mode 100644
index 000000000..e33271b2e
--- /dev/null
+++ b/sci-biology/snpomatic/snpomatic-1.0.ebuild
@@ -0,0 +1,30 @@
+# Copyright 1999-2021 Gentoo Authors
+# Distributed under the terms of the GNU General Public License v2
+
+EAPI=7
+
+DESCRIPTION="Stringent short-read aligner supporting filters and various output formats"
+HOMEPAGE="https://github.com/magnusmanske/snpomatic"
+if [ "$PV" == "9999" ]; then
+	inherit git-r3
+	EGIT_REPO_URI="https://github.com/magnusmanske/snpomatic.git"
+else
+	SRC_URI="https://github.com/magnusmanske/snpomatic/archive/v${PV}.tar.gz -> ${P}.tar.gz"
+	KEYWORDS="~amd64"
+fi
+
+LICENSE="GPL-3"
+SLOT="0"
+
+DEPEND=""
+RDEPEND="${DEPEND}"
+
+src_prepare(){
+	default
+	sed -e 's/^CXX=/#CXX=/;s/^CXXFLAGS=/#CXXFLAGS=/' -i Makefile || die
+}
+
+src_install(){
+	dobin findknownsnps
+	dodoc doc/Manual.doc
+}
diff --git a/sci-biology/snpomatic/snpomatic-9999.ebuild b/sci-biology/snpomatic/snpomatic-9999.ebuild
deleted file mode 100644
index 15b8e3e4b..000000000
--- a/sci-biology/snpomatic/snpomatic-9999.ebuild
+++ /dev/null
@@ -1,33 +0,0 @@
-# Copyright 1999-2016 Gentoo Foundation
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=5
-
-[ "$PV" == "9999" ] && inherit git-r3
-
-DESCRIPTION="Stringent short-read aligner supporting filters and various output formats"
-HOMEPAGE="https://github.com/magnusmanske/snpomatic"
-# http://snpomatic.sourceforge.net/snpomatic_manual.pdf
-if [ "$PV" == "9999" ]; then
-	EGIT_REPO_URI="https://github.com/magnusmanske/snpomatic.git"
-	KEYWORDS=""
-else
-	SRC_URI=""
-	KEYWORDS=""
-fi
-
-LICENSE="GPL-3"
-SLOT="0"
-IUSE=""
-
-DEPEND=""
-RDEPEND="${DEPEND}"
-
-src_prepare(){
-	sed -e 's/^CXX=/#CXX=/;s/^CXXFLAGS=/#CXXFLAGS=/' -i Makefile || die
-}
-
-src_install(){
-	dobin findknownsnps
-	dodoc doc/Manual.doc
-}
diff --git a/sci-biology/somatic-sniper/Manifest b/sci-biology/somatic-sniper/Manifest
deleted file mode 100644
index 699c88287..000000000
--- a/sci-biology/somatic-sniper/Manifest
+++ /dev/null
@@ -1 +0,0 @@
-DIST somatic-sniper-1.0.4.tar.gz 1985061 BLAKE2B e721656fc6429d66dd2dbd9d27ae9a1f75df7a54d302f6583c664c99950882ab6ad14e5338ab6b39aa879421cc7ba0247e9d3e159d63ed65560c9dfd2ee48748 SHA512 ce6093ba5d853f6ed597cf7c707a52dce7121c7b0b5f6c18ecf3c9850ae41c1df062465390085411669f528c2a85c106a8cb60c0bc39b8d3e3a6ebd644800445
diff --git a/sci-biology/somatic-sniper/metadata.xml b/sci-biology/somatic-sniper/metadata.xml
deleted file mode 100644
index ff905cc3e..000000000
--- a/sci-biology/somatic-sniper/metadata.xml
+++ /dev/null
@@ -1,15 +0,0 @@
-<?xml version="1.0" encoding="UTF-8"?>
-<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
-<pkgmetadata>
-	<maintainer type="person">
-		<email>mmokrejs@fold.natur.cuni.cz</email>
-		<name>Martin Mokrejs</name>
-	</maintainer>
-	<maintainer type="project">
-		<email>sci-biology@gentoo.org</email>
-		<name>Gentoo Biology Project</name>
-	</maintainer>
-	<upstream>
-		<remote-id type="github">genome/somatic-sniper</remote-id>
-	</upstream>
-</pkgmetadata>
diff --git a/sci-biology/somatic-sniper/somatic-sniper-1.0.4.ebuild b/sci-biology/somatic-sniper/somatic-sniper-1.0.4.ebuild
deleted file mode 100644
index 51a4b9db8..000000000
--- a/sci-biology/somatic-sniper/somatic-sniper-1.0.4.ebuild
+++ /dev/null
@@ -1,28 +0,0 @@
-# Copyright 1999-2018 Gentoo Foundation
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=5
-
-inherit cmake-utils
-
-DESCRIPTION="Compare BAM files from normal and tumor samples and report somatic SNPs"
-HOMEPAGE="http://gmt.genome.wustl.edu"
-SRC_URI="https://github.com/genome/somatic-sniper/archive/v${PV}.tar.gz -> ${P}.tar.gz"
-# git clone https://github.com/genome/somatic-sniper.git
-
-LICENSE="MIT"
-SLOT="0"
-KEYWORDS="~amd64"
-IUSE=""
-
-DEPEND="
-	sys-libs/zlib
-	sys-libs/ncurses:*
-	sci-biology/samtools:0.1-legacy"
-RDEPEND="${DEPEND}"
-
-# contains bundled copy of samtools-0.1.6 but links using a static version
-# cd /var/tmp/portage/sci-biology/somatic-sniper-1.0.4/work/somatic-sniper-1.0.4_build/build/src/exe/bam-somaticsniper && /usr/bin/cmake -E cmake_link_script CMakeFiles/bam-somaticsniper.dir/link.txt --verbose=1
-# /usr/bin/x86_64-pc-linux-gnu-gcc  -Wall   -Wl,-O1 -Wl,--as-needed CMakeFiles/bam-somaticsniper.dir/main.c.o  -o ../../../../bin/bam-somaticsniper -rdynamic -lpthread -lpthread ../../lib/sniper/libsniper.a -lpthread -lm ../../../../vendor/samtools/libbam.a -lz
-
-# contains build-common from git tree
diff --git a/sci-biology/spm/Manifest b/sci-biology/spm/Manifest
index 81b930322..6d40dd923 100644
--- a/sci-biology/spm/Manifest
+++ b/sci-biology/spm/Manifest
@@ -1,4 +1 @@
-DIST spm-12_p6470.tar.gz 94904848 BLAKE2B 51ba79b721e7a3518b546edd3fca647fd1e12fc80d1bc942d6ca208831ddcf82c2b37b6f2b158978add4e60ddea53eb6d712c6d2817f37b86c3d96c69976ed63 SHA512 7cc2cfed5aa69ea9846cb36f5e489255340e8c27f2e404372a474923d9c4fee6b6ee2dc5dd7f31362b6d2f95eeb281f24008b8b3e174ae3702e6cb040f06c4f2
-DIST spm-12_p7219.tar.gz 97358283 BLAKE2B 70c174f0a7f8f0005f8217d01fb01f45877f7b8d608f5a3ab933b48fae7a7f79d7f4a64f363dae918819688172958e1d503b52408564eb182a5e0dcec155afe4 SHA512 7312c0e74abb65eb211f920f8787e7582fe3269e272920283a5e4ebf6760baf12f2d4223e19696bcf1040c01242513fae2f0ab6241ddcba7de057c2adb33880a
-DIST spm12.0.zip 93842449 BLAKE2B 3b942fc17f9b584ee4a7a0f09d6435a635a718f217e84c8775b0ad9b50b632aa964b07ee96313a235bae62ad6fe0f81d41292181383b79fd9defb3d1eccaa5c6 SHA512 d09267360c3d67ae0b462f47c9b4445c4970524c60cf80e96afc035087e2212050ab7422957525aeb67f6853dd9ba3b9ee5cfe2e26afcec2e1ea7bc2f5828e4b
-DIST spm8.zip 92048821 BLAKE2B 97059a284b7eba4c063ef97bedf877237f8afea4fdc1aa3a877d8b73bde743dcfab2ec687c0841910f8a363f50c567bdc381a0e0ab8315d9c6aaeaa7afcbe1a0 SHA512 da942841bbac74461950639648aeb4f8aef1c6229f3b30a47713c158bf9751dcec0d825b7d6349c03eab1ee91467f86e0c504c761ac1094343718a373effb451
+DIST spm-12_p7771.tar.gz 113583785 BLAKE2B e3c011206569ad66af4ca4475a224751622c760760bd02f27ef18b1cbbde63592da633ca6a880a42a7cf22857eb40bf8d8bba6a6cb92ba53cb1b73bec25534af SHA512 063adac233d28d6912ab6e0a1bc4bda56f011bf0349855eb45ae5e2f63ee6b6a459829ed5a7145ee6744d1afa7c7d9ca8acfe8783784876f048e88d7ee287adb
diff --git a/sci-biology/spm/metadata.xml b/sci-biology/spm/metadata.xml
index ae9640ffb..d888971d1 100644
--- a/sci-biology/spm/metadata.xml
+++ b/sci-biology/spm/metadata.xml
@@ -5,4 +5,7 @@
 		<email>sci@gentoo.org</email>
 		<name>Gentoo Science Project</name>
 	</maintainer>
+	<upstream>
+		<remote-id type="github">spm/spm12</remote-id>
+	</upstream>
 </pkgmetadata>
diff --git a/sci-biology/spm/spm-12.ebuild b/sci-biology/spm/spm-12.ebuild
deleted file mode 100644
index a46cbff23..000000000
--- a/sci-biology/spm/spm-12.ebuild
+++ /dev/null
@@ -1,33 +0,0 @@
-# Copyright 1999-2015 Gentoo Foundation
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=5
-
-DESCRIPTION="Analysis of brain imaging data sequences for Octave or Matlab"
-HOMEPAGE="http://www.fil.ion.ucl.ac.uk/spm/"
-SRC_URI="http://www.fil.ion.ucl.ac.uk/spm/download/restricted/eldorado/${PN}${PV}.0.zip"
-
-LICENSE="GPL-2+"
-SLOT="0"
-KEYWORDS="~amd64"
-
-RDEPEND=">=sci-mathematics/octave-3.8"
-DEPEND="${RDEPEND}
-	app-arch/unzip
-"
-
-S="${WORKDIR}/${PN}${PV}/src"
-
-src_prepare() {
-	emake distclean PLATFORM=octave
-}
-
-src_compile() {
-	emake -j1 PLATFORM=octave
-}
-
-src_install() {
-	emake install PLATFORM=octave
-	insinto "$(octave-config --m-site-dir)/${P}"
-	doins -r "${WORKDIR}/${PN}${PV}"/*
-}
diff --git a/sci-biology/spm/spm-12_p6470.ebuild b/sci-biology/spm/spm-12_p6470.ebuild
deleted file mode 100644
index 0f8e8ec54..000000000
--- a/sci-biology/spm/spm-12_p6470.ebuild
+++ /dev/null
@@ -1,36 +0,0 @@
-# Copyright 1999-2018 Gentoo Foundation
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=7
-
-MY_PV_MAJ=$(ver_cut 1)
-MY_PV_REL=$(ver_cut 3)
-DESCRIPTION="Analysis of brain imaging data sequences for Octave or Matlab"
-HOMEPAGE="http://www.fil.ion.ucl.ac.uk/spm/"
-SRC_URI="https://github.com/${PN}/${PN}${MY_PV_MAJ}/archive/r${MY_PV_REL}.tar.gz -> ${P}.tar.gz"
-LICENSE="GPL-2+"
-SLOT="0"
-KEYWORDS="~amd64"
-
-RDEPEND=">=sci-mathematics/octave-3.8"
-DEPEND="${RDEPEND}
-	app-arch/unzip
-"
-
-MY_PN="${PN}${MY_PV_MAJ}-r${MY_PV_REL}"
-S="${WORKDIR}/${MY_PN}/src"
-
-src_prepare() {
-	default
-	emake distclean PLATFORM=octave
-}
-
-src_compile() {
-	emake PLATFORM=octave
-}
-
-src_install() {
-	emake install PLATFORM=octave
-	insinto "$(octave-config --m-site-dir)/${P}"
-	doins -r "${WORKDIR}/${MY_PN}"/*
-}
diff --git a/sci-biology/spm/spm-12_p7219.ebuild b/sci-biology/spm/spm-12_p7219.ebuild
deleted file mode 100644
index 1e8d15bbe..000000000
--- a/sci-biology/spm/spm-12_p7219.ebuild
+++ /dev/null
@@ -1,36 +0,0 @@
-# Copyright 1999-2018 Gentoo Authors
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=7
-
-MY_PV_MAJ=$(ver_cut 1)
-MY_PV_REL=$(ver_cut 3)
-DESCRIPTION="Analysis of brain imaging data sequences for Octave or Matlab"
-HOMEPAGE="http://www.fil.ion.ucl.ac.uk/spm/"
-SRC_URI="https://github.com/${PN}/${PN}${MY_PV_MAJ}/archive/r${MY_PV_REL}.tar.gz -> ${P}.tar.gz"
-LICENSE="GPL-2+"
-SLOT="0"
-KEYWORDS="~amd64"
-
-RDEPEND=">=sci-mathematics/octave-3.8"
-DEPEND="${RDEPEND}
-	app-arch/unzip
-"
-
-MY_PN="${PN}${MY_PV_MAJ}-r${MY_PV_REL}"
-S="${WORKDIR}/${MY_PN}/src"
-
-src_prepare() {
-	default
-	emake distclean PLATFORM=octave
-}
-
-src_compile() {
-	emake PLATFORM=octave
-}
-
-src_install() {
-	emake install PLATFORM=octave
-	insinto "$(octave-config --m-site-dir)/${P}"
-	doins -r "${WORKDIR}/${MY_PN}"/*
-}
diff --git a/sci-biology/spm/spm-12_p7771.ebuild b/sci-biology/spm/spm-12_p7771.ebuild
new file mode 100644
index 000000000..86e2d5a0d
--- /dev/null
+++ b/sci-biology/spm/spm-12_p7771.ebuild
@@ -0,0 +1,37 @@
+# Copyright 1999-2021 Gentoo Authors
+# Distributed under the terms of the GNU General Public License v2
+
+EAPI=7
+
+MY_PV_MAJ=$(ver_cut 1)
+MY_PV_REL=$(ver_cut 3)
+DESCRIPTION="Analysis of brain imaging data sequences for Octave or Matlab"
+HOMEPAGE="https://www.fil.ion.ucl.ac.uk/spm/"
+SRC_URI="https://github.com/${PN}/${PN}${MY_PV_MAJ}/archive/r${MY_PV_REL}.tar.gz -> ${P}.tar.gz"
+
+LICENSE="GPL-2+"
+SLOT="0"
+KEYWORDS="~amd64"
+
+RDEPEND=">=sci-mathematics/octave-3.8"
+DEPEND="${RDEPEND}
+	app-arch/unzip
+"
+
+MY_PN="${PN}${MY_PV_MAJ}-r${MY_PV_REL}"
+S="${WORKDIR}/${MY_PN}/src"
+
+src_prepare() {
+	default
+	emake distclean PLATFORM=octave
+}
+
+src_compile() {
+	emake PLATFORM=octave
+}
+
+src_install() {
+	emake install PLATFORM=octave
+	insinto "$(octave-config --m-site-dir)/${P}"
+	doins -r "${WORKDIR}/${MY_PN}"/*
+}
diff --git a/sci-biology/spm/spm-8.ebuild b/sci-biology/spm/spm-8.ebuild
deleted file mode 100644
index 55376a7f0..000000000
--- a/sci-biology/spm/spm-8.ebuild
+++ /dev/null
@@ -1,39 +0,0 @@
-# Copyright 1999-2015 Gentoo Foundation
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=5
-
-DESCRIPTION="Analysis of brain imaging data sequences for Octave or Matlab"
-HOMEPAGE="http://www.fil.ion.ucl.ac.uk/spm/"
-SRC_URI="http://www.fil.ion.ucl.ac.uk/spm/download/restricted/idyll/${PN}${PV}.zip"
-
-LICENSE="GPL-2+"
-SLOT="0"
-KEYWORDS="~amd64"
-
-RDEPEND=">=sci-mathematics/octave-3.6.4
-	"
-
-DEPEND="${RDEPEND}
-	app-arch/unzip
-	"
-
-S="${WORKDIR}/${PN}${PV}"
-
-src_prepare() {
-	echo "MEXOPTS += -v" >> src/Makefile.var
-	emake -C src distclean PLATFORM=octave
-	emake -C src toolbox-distclean PLATFORM=octave
-}
-
-src_compile() {
-	emake -C src -j1 PLATFORM=octave
-	emake -C src toolbox PLATFORM=octave
-}
-
-src_install() {
-	emake -C src -j1 install PLATFORM=octave
-	emake -C src -j1 toolbox-install PLATFORM=octave
-	insinto $(octave-config --m-site-dir)
-	doins -r "${S}"/*.m
-}
diff --git a/sci-biology/sra-tools/Manifest b/sci-biology/sra-tools/Manifest
new file mode 100644
index 000000000..1ece174af
--- /dev/null
+++ b/sci-biology/sra-tools/Manifest
@@ -0,0 +1 @@
+DIST sra-tools-2.11.3.tar.gz 9098150 BLAKE2B 852db3b1d1409b37e3a8f36d0a64f5480ba8c85b86efa8f1d9524a5a8a4c2763aa6970739aa06a0821be576b920946784ab9a9ce1af3e6ceaa54da9b743a0434 SHA512 070ab552df1789d37e970e1c9ac2ce7ac6b39ce7833a999aabee4baef553a29a4bfcbdb21be00f4b5d8a55013bcf88b46c839a124dde704b4a371b234c05609f
diff --git a/dev-perl/Data-Types/metadata.xml b/sci-biology/sra-tools/metadata.xml
index 138cb7705..138cb7705 100644
--- a/dev-perl/Data-Types/metadata.xml
+++ b/sci-biology/sra-tools/metadata.xml
diff --git a/sci-biology/sra-tools/sra-tools-2.11.3.ebuild b/sci-biology/sra-tools/sra-tools-2.11.3.ebuild
new file mode 100644
index 000000000..57c5b881e
--- /dev/null
+++ b/sci-biology/sra-tools/sra-tools-2.11.3.ebuild
@@ -0,0 +1,48 @@
+# Copyright 1999-2022 Gentoo Authors
+# Distributed under the terms of the GNU General Public License v2
+
+EAPI=8
+
+DESCRIPTION="NCBI Sequence Read Archive (SRA) sratoolkit"
+HOMEPAGE="https://trace.ncbi.nlm.nih.gov/Traces/sra/sra.cgi https://github.com/ncbi/sra-tools"
+SRC_URI="https://github.com/ncbi/sra-tools/archive/${PV}.tar.gz -> ${P}.tar.gz"
+
+LICENSE="public-domain"
+SLOT="0"
+# Fix ncbi-vdb first
+KEYWORDS=""
+
+DEPEND="
+	sys-libs/zlib
+	app-arch/bzip2
+	dev-libs/libxml2:2=
+	sci-libs/hdf5
+	sci-biology/ngs
+	sci-biology/ncbi-vdb
+"
+
+RDEPEND="${DEPEND}"
+
+S="${WORKDIR}/sra-tools-${PV}"
+
+src_configure() {
+	# this is some non-standard configure script
+	./configure \
+		--with-ngs-sdk-prefix=/usr/ngs/ngs-sdk \
+		--with-hdf5-prefix=/usr \
+		|| die
+}
+
+src_install() {
+	dodir /usr/include
+	dodir /etc/profile.d
+	# Hard way around hard coded paths
+	find . -type f -exec sed -i \
+		-e "s:/usr/local:${ED}/usr:g" \
+		-e "s:/etc:${ED}/etc:g" \
+		-e "s:/usr/lib:${ED}/usr/lib:g" \
+		-e "s:/usr/include:${ED}/usr/include:g" \
+		-e "s:setup.py -q install:setup.py install --root="${D}":g" \
+		{} \; || die
+	default
+}
diff --git a/sci-biology/sra_sdk/Manifest b/sci-biology/sra_sdk/Manifest
deleted file mode 100644
index c334775e0..000000000
--- a/sci-biology/sra_sdk/Manifest
+++ /dev/null
@@ -1 +0,0 @@
-DIST sra_sdk-2.2.2a.tar.gz 5105408 BLAKE2B b124251d0172831199697a043f53059f35dcd20757632542a92d10c15dad66ee7ab8b24f55f8a58b0edf81bf93d409db5ef159c93ca5f69cb7b6066802c5eb7d SHA512 748b4892383255da424f50d6757e87e1bea4bc07e2b0dce4ea34fc143b660ad35f06955d75ba439f17223965db93f32f1163118bc68f4fe955c98dd9f5be4c6e
diff --git a/sci-biology/sra_sdk/files/libs_sra_Makefile.patch b/sci-biology/sra_sdk/files/libs_sra_Makefile.patch
deleted file mode 100644
index 44acc42b0..000000000
--- a/sci-biology/sra_sdk/files/libs_sra_Makefile.patch
+++ /dev/null
@@ -1,77 +0,0 @@
-diff -u -w sra_sdk-2.1.9/work/sra_sdk-2.1.9/libs/sra/Makefile sra_sdk-2.1.9/work/sra_sdk-2.1.9/libs/sra/Makefile
---- sra_sdk-2.1.9/work/sra_sdk-2.1.9/libs/sra/Makefile	2011-12-02 21:30:12.000000000 +0100
-+++ sra_sdk-2.1.9/work/sra_sdk-2.1.9/libs/sra/Makefile	2012-02-06 18:38:45.000000000 +0100
-@@ -100,7 +100,7 @@
- 	$(addsuffix .$(LOBX),$(SRAPATH_SRC))
- 
- $(LIBDIR)/libsrapath.$(LIBX): $(SRAPATH_OBJ)
--	$(LD) --slib -o $@ $^
-+	$(LD) --slib -o $(DESTDIR)$@ $^
- 
- libsrapath.vers.h:
- 	@ true
-@@ -138,10 +138,10 @@
- 	-dklib
- 
- $(LIBDIR)/libsra-schema.$(SHLX): $(SRA_SCHEMA_OBJ)
--	$(LD) --dlib --vers $(SRCDIR) -o $@ $^ $(SRA_SCHEMA_LIB)
-+	$(LD) --dlib --vers $(SRCDIR) -o $(DESTDIR)$@ $^ $(SRA_SCHEMA_LIB)
- 
- $(LIBDIR)/libwsra-schema.$(SHLX): $(WSRA_SCHEMA_OBJ)
--	$(LD) --dlib --vers $(SRCDIR) -o $@ $^ $(WSRA_SCHEMA_LIB)
-+	$(LD) --dlib --vers $(SRCDIR) -o $(DESTDIR)$@ $^ $(WSRA_SCHEMA_LIB)
- 
- SRASCHEMA_SRC = \
- 	sraschema-stub
-@@ -168,10 +168,10 @@
- 	$(addsuffix .$(LOBX),$(WSRASCHEMA_SRC))
- 
- $(LIBDIR)/libsraschema.$(LIBX): $(SRASCHEMA_OBJ) $(SRASCHEMA_DEPS)
--	$(LD) --slib -o $@ $(SRASCHEMA_OBJ) $(SRA_SCHEMA_LIB)
-+	$(LD) --slib -o $(DESTDIR)$@ $(SRASCHEMA_OBJ) $(SRA_SCHEMA_LIB)
- 
- $(LIBDIR)/libwsraschema.$(LIBX): $(WSRASCHEMA_OBJ) $(WSRASCHEMA_DEPS)
--	$(LD) --slib -o $@ $(WSRASCHEMA_OBJ) $(WSRA_SCHEMA_LIB)
-+	$(LD) --slib -o $(DESTDIR)$@ $(WSRASCHEMA_OBJ) $(WSRA_SCHEMA_LIB)
- 
- libsraschema_tag:
- 	@ $(TOP)/build/tag-module.sh $(MODULE) libsraschema $(SRASCHEMA_OBJ)
-@@ -205,10 +205,10 @@
- 	-dklib
- 
- $(LIBDIR)/libsradb.$(SHLX): $(SRADB_OBJ)
--	$(LD) --dlib --vers $(SRCDIR) -o $@ $^ $(SRADB_LIB)
-+	$(LD) --dlib --vers $(SRCDIR) -o $(DESTDIR)$@ $^ $(SRADB_LIB)
- 
- $(LIBDIR)/libsradb.$(LIBX): $(SRADB_OBJ)
--	$(LD) --slib --vers $(SRCDIR) -o $@ $^ $(SRADB_LIB)
-+	$(LD) --slib --vers $(SRCDIR) -o $(DESTDIR)$@ $^ $(SRADB_LIB)
- 
- libsradb_tag: $(SRADB_TAGS)
- 	@ $(TOP)/build/tag-module.sh $(MODULE) libsradb $(SRADB_OBJ)
-@@ -236,10 +236,10 @@
- 	-dklib
- 
- $(LIBDIR)/libwsradb.$(SHLX): $(WSRADB_OBJ)
--	$(LD) --dlib --vers $(SRCDIR) -o $@ $^ $(WSRADB_LIB)
-+	$(LD) --dlib --vers $(SRCDIR) -o $(DESTDIR)$@ $^ $(WSRADB_LIB)
- 
- $(LIBDIR)/libwsradb.$(LIBX): $(WSRADB_OBJ)
--	$(LD) --slib --vers $(SRCDIR) -o $@ $^ $(WSRADB_LIB)
-+	$(LD) --slib --vers $(SRCDIR) -o $(DESTDIR)$@ $^ $(WSRADB_LIB)
- 
- libwsradb_tag: $(WSRADB_TAGS)
- 	@ $(TOP)/build/tag-module.sh $(MODULE) libwsradb $(WSRADB_OBJ)
-@@ -266,10 +266,10 @@
- 	-dklib
- 
- $(LIBDIR)/libsrareader.$(SHLX): $(SRAREADER_OBJ)
--	$(LD) --dlib --vers $(SRCDIR) -o $@ $^ $(SRAREADER_LIB)
-+	$(LD) --dlib --vers $(SRCDIR) -o $(DESTDIR)$@ $^ $(SRAREADER_LIB)
- 
- $(LIBDIR)/libsrareader.$(LIBX): $(SRAREADER_OBJ)
--	$(LD) --slib --vers $(SRCDIR) -o $@ $^ $(SRAREADER_LIB)
-+	$(LD) --slib --vers $(SRCDIR) -o $(DESTDIR)$@ $^ $(SRAREADER_LIB)
- 
- libsrareader_tag:
- 	@ $(TOP)/build/tag-module.sh $(MODULE) libsrareader $(SRAREADER_OBJ)
diff --git a/sci-biology/sra_sdk/files/sra_sdk-destdir.patch b/sci-biology/sra_sdk/files/sra_sdk-destdir.patch
deleted file mode 100644
index bf66c6e46..000000000
--- a/sci-biology/sra_sdk/files/sra_sdk-destdir.patch
+++ /dev/null
@@ -1,76 +0,0 @@
-diff -r -u -w sra_sdk-2.1.9/work/sra_sdk-2.1.9/build/Makefile.env sra_sdk-2.1.9-/work/sra_sdk-2.1.9/build/Makefile.env
---- sra_sdk-2.1.9/work/sra_sdk-2.1.9/build/Makefile.env	2011-08-31 21:46:21.000000000 +0200
-+++ sra_sdk-2.1.9-/work/sra_sdk-2.1.9/build/Makefile.env	2012-02-06 02:02:38.000000000 +0100
-@@ -141,7 +141,7 @@
- 
- # create all required output directories
- makedirs:
--	@ mkdir -p $(addprefix $(TARGDIR)/,$(SUBDIRS) obj/$(MODULE)) $(NCBIDIR)
-+	@ mkdir -p $(addprefix $(TARGDIR)/,$(SUBDIRS) obj/$(MODULE)) $(DESTDIR)/$(NCBIDIR)
- 
- ifeq (win,$(OS))
- 
-diff -r -u -w sra_sdk-2.1.9/work/sra_sdk-2.1.9/build/ld.linux.gcc.sh sra_sdk-2.1.9-/work/sra_sdk-2.1.9/build/ld.linux.gcc.sh
---- sra_sdk-2.1.9/work/sra_sdk-2.1.9/build/ld.linux.gcc.sh	2010-12-28 22:46:39.000000000 +0100
-+++ sra_sdk-2.1.9-/work/sra_sdk-2.1.9/build/ld.linux.gcc.sh	2012-02-06 02:23:07.000000000 +0100
-@@ -38,10 +38,10 @@
- # versioned output
- if [ "$VERS" = "" ]
- then
--    DLIB_CMD="$DLIB_CMD -o $TARG"
--    EXE_CMD="$EXE_CMD -o $TARG"
-+    DLIB_CMD="$DLIB_CMD -o $DESTDIR$TARG"
-+    EXE_CMD="$EXE_CMD -o $TARG"
- else
-     set-vers $(echo $VERS | tr '.' ' ')
--    DLIB_CMD="$DLIB_CMD -o $OUTDIR/$NAME$DBGAP.so.$VERS -Wl,-soname,$NAME.so.$MAJ"
--    EXE_CMD="$EXE_CMD -o $OUTDIR/$NAME$DBGAP.$VERS"
-+    DLIB_CMD="$DLIB_CMD -o $DESTDIR$OUTDIR/$NAME$DBGAP.so.$VERS -Wl,-soname,$NAME.so.$MAJ"
-+    EXE_CMD="$EXE_CMD -o $DESTDIR$OUTDIR/$NAME$DBGAP.$VERS"
- fi
-diff -r -u -w sra_sdk-2.1.9/work/sra_sdk-2.1.9/build/ld.linux.ln.sh sra_sdk-2.1.9-/work/sra_sdk-2.1.9/build/ld.linux.ln.sh
---- sra_sdk-2.1.9/work/sra_sdk-2.1.9/build/ld.linux.ln.sh	2010-12-28 22:46:39.000000000 +0100
-+++ sra_sdk-2.1.9-/work/sra_sdk-2.1.9/build/ld.linux.ln.sh	2012-02-06 02:34:46.000000000 +0100
-@@ -52,12 +52,12 @@
- 
- set-vers $(echo $VERS | tr '.' ' ')
- 
--cd "$OUTDIR" || exit 5
-+cd $DESTDIR$OUTDIR || exit 5
- 
- # create link
- create-link ()
- {
--    rm -f "$2"
-+    rm -f $DESTDIR"$2"
-     local CMD="ln -s $1 $2"
-     echo $CMD
-     $CMD
---- sra_sdk-2.1.9/work/sra_sdk-2.1.9/build/ld.linux.slib.sh        2012-02-06 04:05:16.000000000 +0100
-+++ sra_sdk-2.1.9-/work/sra_sdk-2.1.9/build/ld.linux.slib.sh	2012-02-06 04:05:29.000000000 +0100
-@@ -77,7 +77,7 @@
-     CMD="$CMD $TARG"
- else
-     set-vers $(echo $VERS | tr '.' ' ')
--    CMD="$CMD $OUTDIR/$NAME$DBGAP.a.$VERS"
-+    CMD="$CMD $DESTDIR/$OUTDIR/$NAME$DBGAP.a.$VERS"
- fi
- 
- # tack on object files
---- sra_sdk-2.1.9/work/sra_sdk-2.1.9/build/Makefile.gcc.ori	2012-02-06 04:24:39.000000000 +0100
-+++ sra_sdk-2.1.9/work/sra_sdk-2.1.9/build/Makefile.gcc	2012-02-06 04:22:57.000000000 +0100
-@@ -36,12 +36,12 @@
- LD = @ $(TOP)/build/ld.sh $(OS) $(ARCH) gcc \
- 	--build $(BUILD) --ldflags "$(LDFLAGS)" $(STATIC) \
- 	$(STATICSYSLIBS) $(CHECKSUM) --objx $(OBJX) --shlx $(SHLX) --libx $(LIBX) \
--	-MD --srcdir $(SRCDIR) --bindir $(BINDIR) -L$(LIBDIR):$(ILIBDIR)
-+	-MD --srcdir $(SRCDIR) --bindir $(BINDIR) -L$(DESTDIR)$(LIBDIR):$(ILIBDIR)
- 
- LP = @ $(TOP)/build/ld.sh $(OS) $(ARCH) g++ \
- 	--build $(BUILD) --ldflags "$(LDFLAGS)" $(STATIC) \
- 	$(STATICSYSLIBS) $(CHECKSUM) --objx $(OBJX) --shlx $(SHLX) --libx $(LIBX) \
--	-MD --srcdir $(SRCDIR) --bindir $(BINDIR) -L$(LIBDIR):$(ILIBDIR)
-+	-MD --srcdir $(SRCDIR) --bindir $(BINDIR) -L$(DESTDIR)$(LIBDIR):$(ILIBDIR)
- 
- # tool options
- WARN = -Wall -Wno-variadic-macros # -Wconversion
diff --git a/sci-biology/sra_sdk/files/tools_vdb-vcopy_Makefile.patch b/sci-biology/sra_sdk/files/tools_vdb-vcopy_Makefile.patch
deleted file mode 100644
index 738d67cbd..000000000
--- a/sci-biology/sra_sdk/files/tools_vdb-vcopy_Makefile.patch
+++ /dev/null
@@ -1,12 +0,0 @@
-diff -u -w sra_sdk-2.1.9/work/sra_sdk-2.1.9/tools/vdb-copy/Makefile sra_sdk-2.1.9/work/sra_sdk-2.1.9/tools/vdb-copy/Makefile
---- sra_sdk-2.1.9/work/sra_sdk-2.1.9/tools/vdb-copy/Makefile	2011-12-02 22:00:36.000000000 +0100
-+++ sra_sdk-2.1.9/work/sra_sdk-2.1.9/tools/vdb-copy/Makefile	2012-02-06 18:39:05.000000000 +0100
-@@ -89,7 +89,7 @@
- $(BINDIR)/vdb-copy: $(NCBIDIR)/vdb-copy.kfg 
- 
- $(NCBIDIR)/vdb-copy.kfg: $(SRCDIR)/vdb-copy.kfg
--	cp $^ $@
-+	cp $^ $(DESTDIR)$@
- 
- VDB_COPY_SRC = \
- 	num-gen \
diff --git a/sci-biology/sra_sdk/metadata.xml b/sci-biology/sra_sdk/metadata.xml
deleted file mode 100644
index 138cb7705..000000000
--- a/sci-biology/sra_sdk/metadata.xml
+++ /dev/null
@@ -1,12 +0,0 @@
-<?xml version="1.0" encoding="UTF-8"?>
-<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
-<pkgmetadata>
-	<maintainer type="person">
-		<email>mmokrejs@fold.natur.cuni.cz</email>
-		<name>Martin Mokrejs</name>
-	</maintainer>
-	<maintainer type="project">
-		<email>sci-biology@gentoo.org</email>
-		<name>Gentoo Biology Project</name>
-	</maintainer>
-</pkgmetadata>
diff --git a/sci-biology/sra_sdk/sra_sdk-2.2.2a.ebuild b/sci-biology/sra_sdk/sra_sdk-2.2.2a.ebuild
deleted file mode 100644
index fd420bf88..000000000
--- a/sci-biology/sra_sdk/sra_sdk-2.2.2a.ebuild
+++ /dev/null
@@ -1,100 +0,0 @@
-# Copyright 1999-2015 Gentoo Foundation
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=5
-
-inherit eutils
-
-W="${WORKDIR}"/"${P}"
-
-DESCRIPTION="NCBI Sequence Read Archive (SRA) sratoolkit"
-HOMEPAGE="http://trace.ncbi.nlm.nih.gov/Traces/sra/sra.cgi?cmd=show&f=faspftp_runs_v1&m=downloads&s=download_sra"
-SRC_URI="http://ftp-private.ncbi.nlm.nih.gov/sra/sdk/2.2.2a/sra_sdk-"${PV}".tar.gz"
-# http://ftp-private.ncbi.nlm.nih.gov/sra/sdk/2.2.2a/sratoolkit.2.2.2a-centos_linux64.tar.gz
-
-LICENSE="public-domain"
-SLOT="0"
-#KEYWORDS=""
-KEYWORDS="~amd64 ~x86"
-IUSE="static"
-
-DEPEND="
-	app-shells/bash:*
-	sys-libs/zlib
-	app-arch/bzip2
-	dev-libs/libxml2:2="
-RDEPEND="${DEPEND}"
-
-# upstream says:
-# icc, icpc are supported: tested with 11.0 (64-bit) and 10.1 (32-bit), 32-bit 11.0 does not work
-
-#src_prepare(){
-	# epatch "${FILESDIR}"/sra_sdk-destdir.patch || die
-	# epatch "${FILESDIR}"/tools_vdb-vcopy_Makefile.patch || die
-	# epatch "${FILESDIR}"/libs_sra_Makefile.patch || die
-	# mkdir -p /var/tmp/portage/sci-biology/"${P}"/image//var/tmp/portage/sci-biology/
-	# ln -s /var/tmp/portage/sci-biology/"${P}" /var/tmp/portage/sci-biology/"${P}"/image//var/tmp/portage/sci-biology/"${P}"
-
-#}
-
-src_compile(){
-	# # COMP env variable may have 'GCC' or 'ICC' values
-	#if use static; then
-	#	emake static LIBDIR=/usr/lib64 DESTDIR="${D}"
-	#else
-	#	emake dynamic LIBDIR=/usr/lib64 DESTDIR="${D}"
-	#fi
-
-	#LIBXML_INCLUDES="/usr/include/libxml2" make -j1 OUTDIR="${WORKDIR}"/objdir out LIBDIR=/usr/lib64 DESTDIR="${D}" || die
-	#LIBXML_INCLUDES="/usr/include/libxml2" make -j1 OUTDIR="${WORKDIR}"/objdir LIBDIR=/usr/lib64 DESTDIR="${D}" || die
-
-	# preserve the libs written directly into $DESTDIR by ar/ld/gcc
-	#mkdir -p "${WORKDIR}"/objdir/linux/rel/gcc/x86_64/lib
-	#mv "${D}"/usr/lib64/* "${WORKDIR}"/objdir/linux/rel/gcc/x86_64/lib/
-	emake OUTDIR="${WORKDIR}"/objdir out
-	emake dynamic
-	emake release
-	default
-}
-
-src_install(){
-	rm -rf  /var/tmp/portage/sci-biology/"${P}"/image/var
-	# BUG: at the moment every binary is installed three times, e.g.:
-	# -rwxr-xr-x 1 root root 1797720 Sep 23 01:31 abi-dump
-	# -rwxr-xr-x 1 root root 1797720 Sep 23 01:31 abi-dump.2
-	# -rwxr-xr-x 1 root root 1797720 Sep 23 01:31 abi-dump.2.1.6
-	if use amd64; then
-		builddir="x86_64"
-	elif use x86; then
-		builddir="i386"
-	fi
-	dodir /usr/bin /usr/lib/ncbi /usr/ncbi/schema
-
-	OBJDIR="${WORKDIR}"/objdir/linux/gcc/dyn/"${builddir}"/rel
-
-	# BUG: neither 'doins -r' nor cp --preserve=all work
-	#insinto /usr/bin
-	#doins -r "${WORKDIR}"/objdir/linux/rel/gcc/"${builddir}"/bin/*
-	for f in "${OBJDIR}"/bin/*; do cp --preserve=all "$f" "${D}"/usr/bin/ || die "$f copying failed" ; done
-
-	# install the main libs and the ncbi/vdb-copy.kfg file
-	insinto /usr/lib/ncbi
-	doins "${OBJDIR}"/lib/ncbi/*
-
-	# zap the subdirectory so that copying below does not fail
-	rm -rf "${OBJDIR}"/lib/ncbi || die
-
-	# BUG: neither the dolib nor cp --preserve=all work
-	#insinto /usr/lib64
-	#dolib "${WORKDIR}"/objdir/linux/rel/gcc/"${builddir}"/lib/*
-	mkdir -p "${D}"/usr/lib64
-	for f in "${OBJDIR}"/lib/*; do cp --preserve=all "$f" "${D}"/usr/lib64/ || die "$f copying failed" ; done
-
-	insinto /usr/ncbi/schema
-	doins \
-		"${W}"/interfaces/align/*.vschema \
-		"${W}"/interfaces/sra/*.vschema \
-		"${W}"/interfaces/vdb/*.vschema \
-		"${W}"/interfaces/ncbi/*.vschema \
-		"${W}"/interfaces/insdc/*.vschema
-}
diff --git a/sci-biology/ssaha2-bin/ssaha2-bin-2.5.5-r1.ebuild b/sci-biology/ssaha2-bin/ssaha2-bin-2.5.5-r1.ebuild
new file mode 100644
index 000000000..2c0d5f63d
--- /dev/null
+++ b/sci-biology/ssaha2-bin/ssaha2-bin-2.5.5-r1.ebuild
@@ -0,0 +1,38 @@
+# Copyright 1999-2022 Gentoo Authors
+# Distributed under the terms of the GNU General Public License v2
+
+EAPI=8
+
+inherit toolchain-funcs
+
+MY_PN="${PN%-bin}"
+MY_P="${MY_PN}_v${PV}"
+
+DESCRIPTION="SSAHA2: Sequence Search and Alignment by Hashing Algorithm"
+HOMEPAGE="https://www.sanger.ac.uk/tool/ssaha2-0/"
+SRC_URI="
+	x86? ( ftp://ftp.sanger.ac.uk/pub4/resources/software/${MY_PN}/${MY_P}_i686.tgz )
+	amd64? ( ftp://ftp.sanger.ac.uk/pub4/resources/software/${MY_PN}/${MY_P}_x86_64.tgz )
+	ftp://ftp.sanger.ac.uk/pub4/resources/software/ssaha2/samflag.c
+	ftp://ftp.sanger.ac.uk/pub4/resources/software/ssaha2/ssaha2-manual.pdf"
+
+LICENSE="all-rights-reserved"
+SLOT="0"
+KEYWORDS="~amd64 ~x86"
+
+QA_PREBUILT="*"
+
+src_unpack() {
+	default
+	use x86 && export S="${WORKDIR}"/${MY_P}_i686
+	use amd64 && export S="${WORKDIR}"/${MY_P}_x86_64
+}
+src_compile() {
+	$(tc-getCC) ${CFLAGS} ${LDFLAGS} -o samflag "${DISTDIR}"/samflag.c || die "Failed to compile samflags"
+}
+
+src_install() {
+	dobin samflag ssaha2 ssaha2Build ssahaSNP
+	dodoc README "${DISTDIR}"/ssaha2-manual.pdf
+	einstalldocs
+}
diff --git a/sci-biology/ssaha2-bin/ssaha2-bin-2.5.5.ebuild b/sci-biology/ssaha2-bin/ssaha2-bin-2.5.5.ebuild
deleted file mode 100644
index 34f157b23..000000000
--- a/sci-biology/ssaha2-bin/ssaha2-bin-2.5.5.ebuild
+++ /dev/null
@@ -1,39 +0,0 @@
-# Copyright 1999-2014 Gentoo Foundation
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=5
-
-inherit toolchain-funcs
-
-MY_PN="${PN%-bin}"
-MY_P="${MY_PN}_v${PV}"
-
-DESCRIPTION="SSAHA2: Sequence Search and Alignment by Hashing Algorithm"
-HOMEPAGE="http://www.sanger.ac.uk/resources/software/ssaha2"
-SRC_URI="
-	x86? ( ftp://ftp.sanger.ac.uk/pub4/resources/software/${MY_PN}/${MY_P}_i686.tgz )
-	amd64? ( ftp://ftp.sanger.ac.uk/pub4/resources/software/${MY_PN}/${MY_P}_x86_64.tgz )
-	ftp://ftp.sanger.ac.uk/pub4/resources/software/ssaha2/samflag.c
-	ftp://ftp.sanger.ac.uk/pub4/resources/software/ssaha2/ssaha2-manual.pdf"
-
-LICENSE="all-rights-reserved"
-SLOT="0"
-KEYWORDS="~amd64 ~x86"
-IUSE=""
-
-QA_PREBUILT="/opt/.*"
-
-pkg_setup() {
-	use x86 && export S="${WORKDIR}"/${MY_P}_i686
-	use amd64 && export S="${WORKDIR}"/${MY_P}_x86_64
-}
-src_compile() {
-	$(tc-getCC) ${CFLAGS} ${LDFLAGS} -o samflag "${DISTDIR}"/samflag.c || die "Failed to compile samflags"
-}
-
-src_install() {
-	dobin samflag
-	exeinto /opt/bin
-	doexe ssaha2 ssaha2Build ssahaSNP
-	dodoc README "${DISTDIR}"/ssaha2-manual.pdf
-}
diff --git a/sci-biology/stacks/Manifest b/sci-biology/stacks/Manifest
index a71ef0cc2..06b5c03ad 100644
--- a/sci-biology/stacks/Manifest
+++ b/sci-biology/stacks/Manifest
@@ -1 +1 @@
-DIST stacks-1.44.tar.gz 904141 BLAKE2B 787bfdc3ab44519dfb5372f13de9f629b8d5b67b999b0a4d4555b3071ffc392682ad4afd2fcbf1fba96ee491930901379ae8063cfc46278df613c20b76a92341 SHA512 fd89b8fab3519e9b7c6387574cc13e46800a97627f580e5d5a9841e8d09327ff1de2b91d4e6de78748febcdd9314c0f4ac827f8cbcacdd17aca347e1541eb867
+DIST stacks-2.60.tar.gz 12135281 BLAKE2B 8d529ba75af4c78710bc36230ef7c564551cd2f2cb9c2ff2cfdc9372f5721bcb463b959b67b7082cdc95f88c772b4e6146cd0c48c25a7b4a6f21d8cdb3045b8e SHA512 9bb2bf730ab5a35cb732107b989ca5068c1e2a8d7a647423d62195ab2049f61409e5ad5b9f16444c10791196f322d677aa7f0e0e73bcfccb9b7c4c00ec40ad32
diff --git a/sci-biology/stacks/files/stacks-make-install.patch b/sci-biology/stacks/files/stacks-make-install.patch
new file mode 100644
index 000000000..e5011dfcf
--- /dev/null
+++ b/sci-biology/stacks/files/stacks-make-install.patch
@@ -0,0 +1,83 @@
+diff --git a/Makefile.am b/Makefile.am
+index 7ff8a2b..e6e4682 100644
+--- a/Makefile.am
++++ b/Makefile.am
+@@ -104,19 +104,20 @@ debug:
+ 	$(MAKE) all "CXXFLAGS=-g -Wall -DDEBUG -Og"
+ 
+ install-data-hook:
+-	sed -e 's,_VERSION_,$(VERSION),' -e 's,_BINDIR_,$(bindir)/,g' -e 's,_PKGDATADIR_,$(pkgdatadir)/,g' $(DESTDIR)$(bindir)/denovo_map.pl > $(DESTDIR)$(bindir)/denovo_map.pl.subst
+-	mv $(DESTDIR)$(bindir)/denovo_map.pl.subst $(DESTDIR)$(bindir)/denovo_map.pl
+-	chmod +x $(DESTDIR)$(bindir)/denovo_map.pl
+-	sed -e 's,_VERSION_,$(VERSION),' -e 's,_BINDIR_,$(bindir)/,g' -e 's,_PKGDATADIR_,$(pkgdatadir)/,g' $(DESTDIR)$(bindir)/ref_map.pl > $(DESTDIR)$(bindir)/ref_map.pl.subst
+-	mv $(DESTDIR)$(bindir)/ref_map.pl.subst $(DESTDIR)$(bindir)/ref_map.pl
+-	chmod +x $(DESTDIR)$(bindir)/ref_map.pl
+-	sed -i.bkp -e 's,_VERSION_,$(VERSION),' $(DESTDIR)$(bindir)/stacks-integrate-alignments
+-	sed -i.bkp -e 's,_VERSION_,$(VERSION),' $(DESTDIR)$(bindir)/stacks-samtools-tview
+-	rm -f $(DESTDIR)$(bindir)/stacks-integrate-alignments.bkp
+-	rm -f $(DESTDIR)$(bindir)/stacks-samtools-tview.bkp
+-	chmod +x $(DESTDIR)$(bindir)/stacks-integrate-alignments
+-	chmod +x $(DESTDIR)$(bindir)/stacks-dist-extract
+-	chmod +x $(DESTDIR)$(bindir)/stacks-gdb
++	echo "Skipped"
++	##sed -e 's,_VERSION_,$(VERSION),' -e 's,_BINDIR_,$(bindir)/,g' -e 's,_PKGDATADIR_,$(pkgdatadir)/,g' $(DESTDIR)$(bindir)/denovo_map.pl > $(DESTDIR)$(bindir)/denovo_map.pl.subst
++	##mv $(DESTDIR)$(bindir)/denovo_map.pl.subst $(DESTDIR)$(bindir)/denovo_map.pl
++	##chmod +x $(DESTDIR)$(bindir)/denovo_map.pl
++	##sed -e 's,_VERSION_,$(VERSION),' -e 's,_BINDIR_,$(bindir)/,g' -e 's,_PKGDATADIR_,$(pkgdatadir)/,g' $(DESTDIR)$(bindir)/ref_map.pl > $(DESTDIR)$(bindir)/ref_map.pl.subst
++	##mv $(DESTDIR)$(bindir)/ref_map.pl.subst $(DESTDIR)$(bindir)/ref_map.pl
++	##chmod +x $(DESTDIR)$(bindir)/ref_map.pl
++	##sed -i.bkp -e 's,_VERSION_,$(VERSION),' $(DESTDIR)$(bindir)/stacks-integrate-alignments
++	##sed -i.bkp -e 's,_VERSION_,$(VERSION),' $(DESTDIR)$(bindir)/stacks-samtools-tview
++	##rm -f $(DESTDIR)$(bindir)/stacks-integrate-alignments.bkp
++	##rm -f $(DESTDIR)$(bindir)/stacks-samtools-tview.bkp
++	##chmod +x $(DESTDIR)$(bindir)/stacks-integrate-alignments
++	##chmod +x $(DESTDIR)$(bindir)/stacks-dist-extract
++	##chmod +x $(DESTDIR)$(bindir)/stacks-gdb
+ 	##sed -e 's,_VERSION_,$(VERSION),' -e 's,_BINDIR_,$(DESTDIR)$(bindir)/,g' -e 's,_PKGDATADIR_,$(pkgdatadir)/,g' $(DESTDIR)$(bindir)/denovo_map.py > $(DESTDIR)$(bindir)/denovo_map.py.subst
+ 	##mv $(DESTDIR)$(bindir)/denovo_map.py.subst $(DESTDIR)$(bindir)/denovo_map.py
+ 	##chmod +x $(DESTDIR)$(bindir)/denovo_map.py
+diff --git a/Makefile.in b/Makefile.in
+index ca1c64f..2c85268 100644
+--- a/Makefile.in
++++ b/Makefile.in
+@@ -819,10 +819,7 @@ install-binPROGRAMS: $(bin_PROGRAMS)
+ 	  END { for (d in files) print "f", d, files[d] }' | \
+ 	while read type dir files; do \
+ 	    if test "$$dir" = .; then dir=; else dir=/$$dir; fi; \
+-	    test -z "$$files" || { \
+-	      echo " $(INSTALL_PROGRAM_ENV) $(INSTALL_PROGRAM) $$files '$(DESTDIR)$(bindir)$$dir'"; \
+-	      $(INSTALL_PROGRAM_ENV) $(INSTALL_PROGRAM) $$files "$(DESTDIR)$(bindir)$$dir" || exit $$?; \
+-	    } \
++	    test -z "$$files" || { echo "Skipped" } \
+ 	; done
+ 
+ uninstall-binPROGRAMS:
+@@ -1006,10 +1003,7 @@ install-dist_binSCRIPTS: $(dist_bin_SCRIPTS)
+ 	  END { for (d in files) print "f", d, files[d] }' | \
+ 	while read type dir files; do \
+ 	     if test "$$dir" = .; then dir=; else dir=/$$dir; fi; \
+-	     test -z "$$files" || { \
+-	       echo " $(INSTALL_SCRIPT) $$files '$(DESTDIR)$(bindir)$$dir'"; \
+-	       $(INSTALL_SCRIPT) $$files "$(DESTDIR)$(bindir)$$dir" || exit $$?; \
+-	     } \
++	     test -z "$$files" || { echo "Skipped" } \
+ 	; done
+ 
+ uninstall-dist_binSCRIPTS:
+@@ -1600,15 +1594,7 @@ install-am: all-am
+ 
+ installcheck: installcheck-recursive
+ install-strip:
+-	if test -z '$(STRIP)'; then \
+-	  $(MAKE) $(AM_MAKEFLAGS) INSTALL_PROGRAM="$(INSTALL_STRIP_PROGRAM)" \
+-	    install_sh_PROGRAM="$(INSTALL_STRIP_PROGRAM)" INSTALL_STRIP_FLAG=-s \
+-	      install; \
+-	else \
+-	  $(MAKE) $(AM_MAKEFLAGS) INSTALL_PROGRAM="$(INSTALL_STRIP_PROGRAM)" \
+-	    install_sh_PROGRAM="$(INSTALL_STRIP_PROGRAM)" INSTALL_STRIP_FLAG=-s \
+-	    "INSTALL_PROGRAM_ENV=STRIPPROG='$(STRIP)'" install; \
+-	fi
++	echo "Skipped"
+ mostlyclean-generic:
+ 	-test -z "$(TEST_LOGS)" || rm -f $(TEST_LOGS)
+ 	-test -z "$(TEST_LOGS:.log=.trs)" || rm -f $(TEST_LOGS:.log=.trs)
diff --git a/sci-biology/stacks/stacks-1.44.ebuild b/sci-biology/stacks/stacks-1.44.ebuild
deleted file mode 100644
index 3106657e9..000000000
--- a/sci-biology/stacks/stacks-1.44.ebuild
+++ /dev/null
@@ -1,58 +0,0 @@
-# Copyright 1999-2017 Gentoo Foundation
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=5
-
-AUTOTOOLS_AUTORECONF=yes
-
-inherit flag-o-matic eutils perl-module webapp autotools
-
-DESCRIPTION="Analyze restriction enzyme data, draw gen. maps, population genomics"
-HOMEPAGE="http://creskolab.uoregon.edu/stacks"
-SRC_URI="http://creskolab.uoregon.edu/stacks/source/${P}.tar.gz"
-
-LICENSE="GPL-3"
-# SLOT="0" # webapp ebuilds do not set SLOT
-KEYWORDS=""
-IUSE=""
-
-DEPEND="
-	>=sci-libs/htslib-1.3.1:0
-	dev-cpp/sparsehash
-	sci-biology/samtools:*
-	sci-biology/bamtools
-	sci-biology/gmap" # Source code for both GMAP and GSNAP
-RDEPEND="${DEPEND}
-	dev-lang/perl
-	>=dev-lang/php-5
-	dev-perl/DBD-mysql"
-
-src_prepare(){
-	sed -e 's/SUBDIRS = htslib/SUBDIRS = /' -i Makefile.am || die
-	#mycppflags=`pkg-config --cflags htslib` # is blocked by bug #601366
-	if [ -z "$mycppflags" ]; then mycppflags="."; fi
-	sed -e "s#-I./htslib/htslib#-I/usr/include/bam -I${mycppflags}#" -i configure.ac || die
-	eautoreconf
-}
-
-src_configure() {
-	econf --enable-bam --enable-sparsehash
-	webapp_src_preinst
-	sed -i 's#/usr/lib/libbam.a#-lbam#;#./htslib/libhts.a#-lhts#' Makefile || die
-}
-
-src_compile(){
-	rm -rf htslib # zap bundled htslib-1.3.1
-	emake DESTDIR="${D}"
-}
-
-src_install() {
-	emake install DESTDIR="${D}"
-	mydoc="Changes README TODO INSTALL"
-	perl-module_src_install DESTDIR="${D}"
-	webapp_src_install || die "Failed running webapp_src_install"
-}
-
-pkg_postinst() {
-	webapp_pkg_postinst || die "webapp_pkg_postinst failed"
-}
diff --git a/sci-biology/stacks/stacks-2.60.ebuild b/sci-biology/stacks/stacks-2.60.ebuild
new file mode 100644
index 000000000..4de3f8da8
--- /dev/null
+++ b/sci-biology/stacks/stacks-2.60.ebuild
@@ -0,0 +1,54 @@
+# Copyright 1999-2022 Gentoo Authors
+# Distributed under the terms of the GNU General Public License v2
+
+EAPI=8
+
+inherit perl-module webapp autotools
+
+DESCRIPTION="Analyze restriction enzyme data, draw gen. maps, population genomics"
+HOMEPAGE="http://creskolab.uoregon.edu/stacks"
+SRC_URI="http://creskolab.uoregon.edu/stacks/source/${P}.tar.gz"
+
+LICENSE="GPL-3"
+KEYWORDS="~amd64"
+
+RESTRICT="test"
+
+DEPEND="
+	>=sci-libs/htslib-1.3.1:0
+	dev-cpp/sparsehash
+	sci-biology/samtools:*
+	sci-biology/bamtools
+	sci-biology/gmap
+"
+
+RDEPEND="${DEPEND}
+	dev-lang/perl
+	>=dev-lang/php-5:*
+	dev-perl/DBD-mysql
+"
+
+PATCHES=(
+	"${FILESDIR}/${PN}-make-install.patch"
+)
+
+src_prepare(){
+	default
+	#mycppflags=`pkg-config --cflags htslib` # is blocked by bug #601366
+	if [ -z "$mycppflags" ]; then mycppflags="."; fi
+	sed -e "s#-I./htslib/htslib#-I/usr/include/bam -I${mycppflags}#" -i configure.ac || die
+	eautoreconf
+}
+
+src_configure() {
+	econf
+	sed -e 's#/usr/lib/libbam.a#-lbam#;#./htslib/libhts.a#-lhts#' -i Makefile || die
+}
+
+src_install() {
+	webapp_src_preinst
+	DESTDIR="${ED}" default
+	DESTDIR="${ED}" perl-module_src_install
+	dodir /usr/share/webapps/${PN}/${PV}
+	webapp_src_install
+}
diff --git a/sci-biology/staden/Manifest b/sci-biology/staden/Manifest
deleted file mode 100644
index 6800d9339..000000000
--- a/sci-biology/staden/Manifest
+++ /dev/null
@@ -1,2 +0,0 @@
-DIST staden-2.0.0_beta11-src.tar.gz 4754651 BLAKE2B d55dcff2192a5f6c505d141960f624ad30afb358e481c438d285a267bb116f8e26e1b7d6562c222b4c7392729bacd14524ee9275ada5201b7d8bcefbd244112f SHA512 6f85cc3aa3b909431333a4998566b267f1d344b3160603604306caf41504cc36c05980790bf5a8f2b4a53f7aea2a369ffafbce163b41c3ea94605f7fee07a26a
-DIST staden-2.0.0b10-src.tar.gz 4616845 BLAKE2B b1a401d28e14d2a480eecf8b9d016a3b87fb0552c7533bccc127ae0436d96f52fba8ac43980f73e02deb9b2ec72d80d5be37b8b1438f93baff9978eb001a1997 SHA512 6ed8316a4cd9631b1aa632dbb51c190044470898404c0cf6dadba9acd4d36f8ecc36babce00ca44d0987b9e69a457f9a333a6711d4e2cec8a9917037deda72fa
diff --git a/sci-biology/staden/files/staden-2.0.0_beta10-ldflags.patch b/sci-biology/staden/files/staden-2.0.0_beta10-ldflags.patch
deleted file mode 100644
index 735feb315..000000000
--- a/sci-biology/staden/files/staden-2.0.0_beta10-ldflags.patch
+++ /dev/null
@@ -1,30 +0,0 @@
- abi/Makefile | 2 +-
- alf/Makefile | 2 +-
- 2 files changed, 2 insertions(+), 2 deletions(-)
-
-diff --git a/abi/Makefile b/abi/Makefile
-index 3c1f8fb..58b4353 100644
---- a/abi/Makefile
-+++ b/abi/Makefile
-@@ -23,7 +23,7 @@ getABISampleName: $(OBJSSN)
- 	$(CLD) $(LDEXEFLAG)$@$(EXE_SUFFIX) $(SUBSYSTEMCONSOLE) $(OBJSSN) $(LIBS) $(LIBSC)
- 
- getABIdate: $(OBJSD)
--	$(CLD) $(LDEXEFLAG)$@$(EXE_SUFFIX) $(SUBSYSTEMCONSOLE) $(OBJSD) $(IOUTILS_LIB) $(MISC_LIB) $(LIBSC)
-+	$(CLD) $(LDFLAGS) $(LDEXEFLAG)$@$(EXE_SUFFIX) $(SUBSYSTEMCONSOLE) $(OBJSD) $(IOUTILS_LIB) $(MISC_LIB) $(LIBSC)
- 
- getABIcomment: $(OBJSC)
- 	$(CLD) $(LDEXEFLAG)$@$(EXE_SUFFIX) $(SUBSYSTEMCONSOLE) $(OBJSC) $(LIBS) $(LIBSC)
-diff --git a/alf/Makefile b/alf/Makefile
-index 94b7480..ef41a26 100644
---- a/alf/Makefile
-+++ b/alf/Makefile
-@@ -16,7 +16,7 @@ INCLUDES_E += $(MISC_INC)
- ALFOBJ = alfsplit.o
- 
- alfsplit: $(ALFOBJ)
--	$(CLD) $(LDEXEFLAG)$@$(EXE_SUFFIX) $(SUBSYSTEMCONSOLE) $(ALFOBJ) $(LIBSC)
-+	$(CLD) $(LDFLAGS) $(LDEXEFLAG)$@$(EXE_SUFFIX) $(SUBSYSTEMCONSOLE) $(ALFOBJ) $(LIBSC)
- 
- RSOBJ = $(ALFBIN)/2rs.o
- 
diff --git a/sci-biology/staden/files/staden-2.0.0_beta10-zlib.patch b/sci-biology/staden/files/staden-2.0.0_beta10-zlib.patch
deleted file mode 100644
index 39537604e..000000000
--- a/sci-biology/staden/files/staden-2.0.0_beta10-zlib.patch
+++ /dev/null
@@ -1,16 +0,0 @@
- gap5/zfio.c | 2 +-
- 1 file changed, 1 insertion(+), 1 deletion(-)
-
-diff --git a/gap5/zfio.c b/gap5/zfio.c
-index 35da12a..1b628e4 100644
---- a/gap5/zfio.c
-+++ b/gap5/zfio.c
-@@ -51,7 +51,7 @@ int zfpeek(zfp *zf) {
- 	if (c != EOF)
- 	    ungetc(c, zf->fp);
-     } else {
--	c = gzgetc(zf->gz);
-+	c = gzgetc((gzFile)zf->gz);
- 	if (c != EOF)
- 	    gzungetc(c, zf->gz);
-     }
diff --git a/sci-biology/staden/files/staden-2.0.0_beta11-ldflags.patch b/sci-biology/staden/files/staden-2.0.0_beta11-ldflags.patch
deleted file mode 100644
index 735feb315..000000000
--- a/sci-biology/staden/files/staden-2.0.0_beta11-ldflags.patch
+++ /dev/null
@@ -1,30 +0,0 @@
- abi/Makefile | 2 +-
- alf/Makefile | 2 +-
- 2 files changed, 2 insertions(+), 2 deletions(-)
-
-diff --git a/abi/Makefile b/abi/Makefile
-index 3c1f8fb..58b4353 100644
---- a/abi/Makefile
-+++ b/abi/Makefile
-@@ -23,7 +23,7 @@ getABISampleName: $(OBJSSN)
- 	$(CLD) $(LDEXEFLAG)$@$(EXE_SUFFIX) $(SUBSYSTEMCONSOLE) $(OBJSSN) $(LIBS) $(LIBSC)
- 
- getABIdate: $(OBJSD)
--	$(CLD) $(LDEXEFLAG)$@$(EXE_SUFFIX) $(SUBSYSTEMCONSOLE) $(OBJSD) $(IOUTILS_LIB) $(MISC_LIB) $(LIBSC)
-+	$(CLD) $(LDFLAGS) $(LDEXEFLAG)$@$(EXE_SUFFIX) $(SUBSYSTEMCONSOLE) $(OBJSD) $(IOUTILS_LIB) $(MISC_LIB) $(LIBSC)
- 
- getABIcomment: $(OBJSC)
- 	$(CLD) $(LDEXEFLAG)$@$(EXE_SUFFIX) $(SUBSYSTEMCONSOLE) $(OBJSC) $(LIBS) $(LIBSC)
-diff --git a/alf/Makefile b/alf/Makefile
-index 94b7480..ef41a26 100644
---- a/alf/Makefile
-+++ b/alf/Makefile
-@@ -16,7 +16,7 @@ INCLUDES_E += $(MISC_INC)
- ALFOBJ = alfsplit.o
- 
- alfsplit: $(ALFOBJ)
--	$(CLD) $(LDEXEFLAG)$@$(EXE_SUFFIX) $(SUBSYSTEMCONSOLE) $(ALFOBJ) $(LIBSC)
-+	$(CLD) $(LDFLAGS) $(LDEXEFLAG)$@$(EXE_SUFFIX) $(SUBSYSTEMCONSOLE) $(ALFOBJ) $(LIBSC)
- 
- RSOBJ = $(ALFBIN)/2rs.o
- 
diff --git a/sci-biology/staden/metadata.xml b/sci-biology/staden/metadata.xml
deleted file mode 100644
index 1ed1820a4..000000000
--- a/sci-biology/staden/metadata.xml
+++ /dev/null
@@ -1,15 +0,0 @@
-<?xml version="1.0" encoding="UTF-8"?>
-<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
-<pkgmetadata>
-	<maintainer type="person">
-		<email>mmokrejs@fold.natur.cuni.cz</email>
-		<name>Martin Mokrejs</name>
-	</maintainer>
-	<maintainer type="project">
-		<email>sci-biology@gentoo.org</email>
-		<name>Gentoo Biology Project</name>
-	</maintainer>
-	<upstream>
-		<remote-id type="sourceforge">staden</remote-id>
-	</upstream>
-</pkgmetadata>
diff --git a/sci-biology/staden/staden-2.0.0_beta10.ebuild b/sci-biology/staden/staden-2.0.0_beta10.ebuild
deleted file mode 100644
index e2fb8bf37..000000000
--- a/sci-biology/staden/staden-2.0.0_beta10.ebuild
+++ /dev/null
@@ -1,84 +0,0 @@
-# Copyright 1999-2016 Gentoo Foundation
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=5
-
-AUTOTOOLS_AUTORECONF=yes
-
-inherit autotools-utils eutils flag-o-matic fortran-2 multilib
-
-DESCRIPTION="DNA sequence assembly (gap4, gap5), editing and analysis tools (Spin)"
-HOMEPAGE="http://sourceforge.net/projects/staden"
-SRC_URI="http://downloads.sourceforge.net/staden/staden-${PV/_beta/b}-src.tar.gz"
-
-LICENSE="staden"
-SLOT="0"
-KEYWORDS=""
-IUSE="debug doc fortran png tcl tk X zlib"
-
-# either g77 or gfortran must be available
-# edit src/mk/linux.mk accordingly
-#
-# this is a glibc-2.9 issue, see https://sourceforge.net/tracker/index.php?func=detail&aid=2629155&group_id=100316&atid=627058
-#
-#
-#
-
-DEPEND="
-	app-arch/xz-utils
-	dev-lang/tk:0=
-	dev-tcltk/tklib
-	media-libs/libpng:0
-	sci-biology/samtools:0
-	>=sci-libs/io_lib-1.13.8
-	sys-libs/zlib"
-RDEPEND="${DEPEND}
-	>=dev-tcltk/iwidgets-4.0
-	tcl? ( >=dev-tcltk/itcl-3.2 )
-	tk? ( >=dev-tcltk/itk-3.2 )
-	net-misc/curl
-	doc? ( sci-biology/staden_doc )"
-
-S="${WORKDIR}"/staden-${PV/_beta/b}-src
-
-AUTOTOOLS_IN_SOURCE_BUILD=1
-
-PATCHES=(
-	"${FILESDIR}"/${P}-ldflags.patch
-	"${FILESDIR}"/${P}-zlib.patch )
-
-src_prepare() {
-	sed \
-		-e 's:svnversion:false:' \
-		-i configure.in || die
-
-	AT_M4DIR=ac_stubs autotools-utils_src_prepare
-}
-
-src_configure(){
-	local myeconfargs=()
-	use X && myeconfargs+=( --with-x )
-	myeconfargs+=(
-		--with-tklib=/usr/$(get_libdir)/tklib
-		)
-	use amd64 && myeconfargs+=( --enable-64bit )
-	use debug && append-cflags "-DCACHE_REF_DEBUG"
-	autotools-utils_src_configure
-}
-
-src_install() {
-	autotools-utils_src_install
-	# install the LDPATH so that it appears in /etc/ld.so.conf after env-update
-	# subsequently, apps linked against /usr/lib/staden can be run because
-	# loader can find the library (I failed to use '-Wl,-rpath,/usr/lib/staden'
-	# somehow for gap2caf, for example
-	cat >> "${T}"/99staden <<- EOF
-	STADENROOT="${EPREFIX}"/usr/share/staden
-	LDPATH="${EPREFIX}/usr/$(get_libdir)/staden"
-	EOF
-	doenvd "${T}"/99staden
-}
-
-pkg_postinst(){
-	einfo "There is a tutorial at https://sourceforge.net/projects/staden/files/tutorials/1.1/course-1.1.tar.gz"
-}
diff --git a/sci-biology/staden/staden-2.0.0_beta11.ebuild b/sci-biology/staden/staden-2.0.0_beta11.ebuild
deleted file mode 100644
index a84e6c178..000000000
--- a/sci-biology/staden/staden-2.0.0_beta11.ebuild
+++ /dev/null
@@ -1,82 +0,0 @@
-# Copyright 1999-2016 Gentoo Foundation
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=5
-
-AUTOTOOLS_AUTORECONF=yes
-
-inherit autotools-utils eutils flag-o-matic fortran-2 multilib
-
-DESCRIPTION="DNA sequence assembly (gap4, gap5), editing and analysis tools (Spin)"
-HOMEPAGE="http://sourceforge.net/projects/staden"
-SRC_URI="http://downloads.sourceforge.net/staden/staden-${PV/_beta/b}-2016-src.tar.gz -> ${P}-src.tar.gz"
-
-LICENSE="staden"
-SLOT="0"
-KEYWORDS=""
-IUSE="debug doc fortran png tcl tk X zlib"
-
-# either g77 or gfortran must be available
-# edit src/mk/linux.mk accordingly
-#
-# this is a glibc-2.9 issue, see https://sourceforge.net/tracker/index.php?func=detail&aid=2629155&group_id=100316&atid=627058
-#
-#
-#
-
-DEPEND="
-	app-arch/xz-utils
-	dev-lang/tk:0=
-	dev-tcltk/tklib
-	media-libs/libpng:0
-	sci-biology/samtools:0
-	>=sci-libs/io_lib-1.13.8
-	sys-libs/zlib"
-RDEPEND="${DEPEND}
-	>=dev-tcltk/iwidgets-4.0
-	tcl? ( >=dev-tcltk/itcl-3.2 )
-	tk? ( >=dev-tcltk/itk-3.2 )
-	net-misc/curl
-	doc? ( sci-biology/staden_doc )"
-
-S="${WORKDIR}"/staden-${PV/_beta/b}-2016-src
-
-AUTOTOOLS_IN_SOURCE_BUILD=1
-
-PATCHES=("${FILESDIR}"/${P}-ldflags.patch)
-
-src_prepare() {
-	sed \
-		-e 's:svnversion:false:' \
-		-i configure.in || die
-
-	AT_M4DIR=ac_stubs autotools-utils_src_prepare
-}
-
-src_configure(){
-	local myeconfargs=()
-	use X && myeconfargs+=( --with-x )
-	myeconfargs+=(
-		--with-tklib=/usr/$(get_libdir)/tklib
-		)
-	use amd64 && myeconfargs+=( --enable-64bit )
-	use debug && append-cflags "-DCACHE_REF_DEBUG"
-	autotools-utils_src_configure
-}
-
-src_install() {
-	autotools-utils_src_install
-	# install the LDPATH so that it appears in /etc/ld.so.conf after env-update
-	# subsequently, apps linked against /usr/lib/staden can be run because
-	# loader can find the library (I failed to use '-Wl,-rpath,/usr/lib/staden'
-	# somehow for gap2caf, for example
-	cat >> "${T}"/99staden <<- EOF
-	STADENROOT="${EPREFIX}"/usr/share/staden
-	LDPATH="${EPREFIX}/usr/$(get_libdir)/staden"
-	EOF
-	doenvd "${T}"/99staden
-}
-
-pkg_postinst(){
-	einfo "There is a tutorial at https://sourceforge.net/projects/staden/files/tutorials/1.1/course-1.1.tar.gz"
-}
diff --git a/sci-biology/staden/staden-9999.ebuild b/sci-biology/staden/staden-9999.ebuild
deleted file mode 100644
index 0253c9eb5..000000000
--- a/sci-biology/staden/staden-9999.ebuild
+++ /dev/null
@@ -1,76 +0,0 @@
-# Copyright 1999-2016 Gentoo Foundation
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=5
-
-AUTOTOOLS_AUTORECONF=yes
-
-inherit autotools-utils flag-o-matic fortran-2 multilib subversion
-
-DESCRIPTION="DNA sequence assembly (gap4, gap5), editing and analysis tools (Spin)"
-HOMEPAGE="http://sourceforge.net/projects/staden/"
-SRC_URI=""
-ESVN_REPO_URI="https://staden.svn.sourceforge.net/svnroot/staden/staden/trunk/src"
-
-LICENSE="staden"
-SLOT="0"
-KEYWORDS=""
-IUSE="debug doc fortran png tcl tk X zlib"
-
-# either g77 or gfortran must be available
-# edit src/mk/linux.mk accordingly
-#
-# this is a glibc-2.9 issue, see https://sourceforge.net/tracker/index.php?func=detail&aid=2629155&group_id=100316&atid=627058
-#
-#
-#
-DEPEND="
-	app-arch/xz-utils
-	dev-lang/tk:0=
-	dev-tcltk/tklib
-	media-libs/libpng:0
-	sci-biology/samtools:0
-	>=sci-libs/io_lib-1.13.8
-	sys-libs/zlib"
-RDEPEND="${DEPEND}
-	>=dev-tcltk/iwidgets-4.0
-	tcl? ( >=dev-tcltk/itcl-3.2 )
-	tk? ( >=dev-tcltk/itk-3.2 )
-	net-misc/curl
-	doc? ( sci-biology/staden_doc )"
-
-AUTOTOOLS_IN_SOURCE_BUILD=1
-
-src_prepare() {
-	sed \
-		-e 's:svnversion:false:' \
-		-i configure.in || die
-
-	AT_M4DIR=ac_stubs autotools-utils_src_prepare
-}
-
-src_configure() {
-	local myeconfargs=()
-	use X && myeconfargs+=( --with-x )
-	myeconfargs+=(
-		--with-tklib=/usr/$(get_libdir)/tklib
-		)
-	use amd64 && myeconfargs+=( --enable-64bit )
-	use debug && append-cflags "-DCACHE_REF_DEBUG"
-		autotools-utils_src_configure
-	# edit system.mk to place there proper version number of the svn-controlled checkout
-	sed -e "s/^SVNVERS.*/SVNVERS = "${ESVN_REVISION}"/" -i system.mk || die
-}
-
-src_install() {
-	autotools-utils_src_install SVN_VERSION="${ESVN_REVISION}"
-	cat >> "${T}"/99staden <<- EOF
-	STADENROOT="${EPREFIX}"/usr/share/staden
-	LDPATH="${EPREFIX}/usr/$(get_libdir)/staden"
-	EOF
-	doenvd "${T}"/99staden
-}
-
-pkg_postinst(){
-	einfo "There is a tutorial at https://sourceforge.net/projects/staden/files/tutorials/1.1/course-1.1.tar.gz"
-}
diff --git a/sci-biology/staden_doc/Manifest b/sci-biology/staden_doc/Manifest
deleted file mode 100644
index c991e8f5f..000000000
--- a/sci-biology/staden_doc/Manifest
+++ /dev/null
@@ -1,2 +0,0 @@
-DIST staden_doc-2.0.0b11-src.tar.gz 3184526 BLAKE2B cf67f702efd0743899b0f955434b815bdb695d28641069a4da981e5fe5de9091980b997e55d10897ff21fca1928f1afb787aa9a89d66ab658b14f8db9b35d110 SHA512 ca8aad2ab3ec660dbd8631bb65df95b10fa64e20d5d509925a03e277896ed8a2eebef89f6b170fe2acd0dd10e0075585620dd162b7b5c9153b248ee6dedd6ef1
-DIST staden_doc-2.0.0b9-src.tar.gz 3181687 BLAKE2B 97127dfd01737ac27aedb99b3d07cf6fcd65ebc9c0c0747fb115a55fdacaf0c2dd886f4ed0a845acf6801f32c12e15ec8cf514c5edad013fd5c97de152acc2d6 SHA512 9f1d1ec7f8301058574ec7da604274d1767258293c88f6cde6426ad361a8543833fa4b755e5f0109ca4dd88ea41cd7fa94f2f7e14a4d9a516ec06ae49540c15f
diff --git a/sci-biology/staden_doc/metadata.xml b/sci-biology/staden_doc/metadata.xml
deleted file mode 100644
index 1ed1820a4..000000000
--- a/sci-biology/staden_doc/metadata.xml
+++ /dev/null
@@ -1,15 +0,0 @@
-<?xml version="1.0" encoding="UTF-8"?>
-<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
-<pkgmetadata>
-	<maintainer type="person">
-		<email>mmokrejs@fold.natur.cuni.cz</email>
-		<name>Martin Mokrejs</name>
-	</maintainer>
-	<maintainer type="project">
-		<email>sci-biology@gentoo.org</email>
-		<name>Gentoo Biology Project</name>
-	</maintainer>
-	<upstream>
-		<remote-id type="sourceforge">staden</remote-id>
-	</upstream>
-</pkgmetadata>
diff --git a/sci-biology/staden_doc/staden_doc-2.0.0_beta11.ebuild b/sci-biology/staden_doc/staden_doc-2.0.0_beta11.ebuild
deleted file mode 100644
index cc58b4334..000000000
--- a/sci-biology/staden_doc/staden_doc-2.0.0_beta11.ebuild
+++ /dev/null
@@ -1,43 +0,0 @@
-# Copyright 1999-2016 Gentoo Foundation
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=5
-
-inherit eutils
-
-DESCRIPTION="Documentation files for the staden package"
-HOMEPAGE="http://sourceforge.net/projects/staden"
-SRC_URI="http://sourceforge.net/projects/staden/files/staden/${PV/_beta/b}/staden_doc-${PV/_beta/b}-src.tar.gz"
-# https://sourceforge.net/p/staden/code/HEAD/tree/staden/trunk/doc/
-
-LICENSE="staden"
-SLOT="0"
-KEYWORDS=""
-IUSE=""
-
-DEPEND="dev-lang/perl
-	app-text/texlive
-	app-text/texi2html"
-RDEPEND="${DEPEND}"
-
-S="${WORKDIR}"/staden_doc-${PV/_beta/b}-src
-
-# do not use texi2html-5 because it fails with:
-# texi2html -menu -verbose -split_chapter -index_chars interface.htmlinfo
-# Unknown option: index_char
-# src_prepare(){
-# 	# avoid running bundled texi2html code
-# 	sed -e "s#./tools/texi2html#texi2html#" -i manual/Makefile || die
-# }
-
-src_compile(){
-	cd manual || die
-	make -j 1 spotless || die
-	cd .. || die
-	emake -j 1 unix PAPER=A4
-}
-
-src_install(){
-	emake -j 1 install prefix="${D}"/usr
-	dodoc gkb547_gml.pdf
-}
diff --git a/sci-biology/staden_doc/staden_doc-2.0.0_beta9.ebuild b/sci-biology/staden_doc/staden_doc-2.0.0_beta9.ebuild
deleted file mode 100644
index cc58b4334..000000000
--- a/sci-biology/staden_doc/staden_doc-2.0.0_beta9.ebuild
+++ /dev/null
@@ -1,43 +0,0 @@
-# Copyright 1999-2016 Gentoo Foundation
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=5
-
-inherit eutils
-
-DESCRIPTION="Documentation files for the staden package"
-HOMEPAGE="http://sourceforge.net/projects/staden"
-SRC_URI="http://sourceforge.net/projects/staden/files/staden/${PV/_beta/b}/staden_doc-${PV/_beta/b}-src.tar.gz"
-# https://sourceforge.net/p/staden/code/HEAD/tree/staden/trunk/doc/
-
-LICENSE="staden"
-SLOT="0"
-KEYWORDS=""
-IUSE=""
-
-DEPEND="dev-lang/perl
-	app-text/texlive
-	app-text/texi2html"
-RDEPEND="${DEPEND}"
-
-S="${WORKDIR}"/staden_doc-${PV/_beta/b}-src
-
-# do not use texi2html-5 because it fails with:
-# texi2html -menu -verbose -split_chapter -index_chars interface.htmlinfo
-# Unknown option: index_char
-# src_prepare(){
-# 	# avoid running bundled texi2html code
-# 	sed -e "s#./tools/texi2html#texi2html#" -i manual/Makefile || die
-# }
-
-src_compile(){
-	cd manual || die
-	make -j 1 spotless || die
-	cd .. || die
-	emake -j 1 unix PAPER=A4
-}
-
-src_install(){
-	emake -j 1 install prefix="${D}"/usr
-	dodoc gkb547_gml.pdf
-}
diff --git a/sci-biology/stampy-bin/Manifest b/sci-biology/stampy-bin/Manifest
deleted file mode 100644
index de0e30879..000000000
--- a/sci-biology/stampy-bin/Manifest
+++ /dev/null
@@ -1 +0,0 @@
-DIST stampy-1.0.28.tar.gz 2410675 SHA256 d842179bab0e80689f79700fc39aac4acd707f3a5195d09bec33844bf19bc1d6 SHA512 f520b12699d082677c2cd0297eda9a0518a06df81c9ae696a5548a8f527c4fe4e6d58855d7093f0f35e72e378ff273b7b8baf4c95a168552ecffa308cf2f8b38 WHIRLPOOL 3f7e1da98bb975972c0009946aa749654e23944b957f2f7f16b3513eed7a03611373e53035b76d15f5128bde089b84d909f637c446565b23ded51044af05df99
diff --git a/sci-biology/stampy-bin/metadata.xml b/sci-biology/stampy-bin/metadata.xml
deleted file mode 100644
index 138cb7705..000000000
--- a/sci-biology/stampy-bin/metadata.xml
+++ /dev/null
@@ -1,12 +0,0 @@
-<?xml version="1.0" encoding="UTF-8"?>
-<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
-<pkgmetadata>
-	<maintainer type="person">
-		<email>mmokrejs@fold.natur.cuni.cz</email>
-		<name>Martin Mokrejs</name>
-	</maintainer>
-	<maintainer type="project">
-		<email>sci-biology@gentoo.org</email>
-		<name>Gentoo Biology Project</name>
-	</maintainer>
-</pkgmetadata>
diff --git a/sci-biology/stampy-bin/stampy-bin-1.0.28.ebuild b/sci-biology/stampy-bin/stampy-bin-1.0.28.ebuild
deleted file mode 100644
index 178b5539d..000000000
--- a/sci-biology/stampy-bin/stampy-bin-1.0.28.ebuild
+++ /dev/null
@@ -1,42 +0,0 @@
-# Copyright 1999-2016 Gentoo Foundation
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=5
-PYTHON_COMPAT=( python2_7 )
-
-inherit toolchain-funcs python-r1 python-utils-r1
-
-DESCRIPTION="Map highly divergent short reads to a reference"
-HOMEPAGE="http://www.well.ox.ac.uk/project-stampy"
-SRC_URI="stampy-${PV}.tar.gz"
-
-LICENSE="stampy-academic"
-SLOT="0"
-KEYWORDS="~amd64 ~x86"
-IUSE=""
-
-RESTRICT="fetch"
-
-DEPEND=""
-RDEPEND="${DEPEND}"
-
-S="${WORKDIR}"/stampy-${PV}
-
-# FIXME: the makefile calls python but fails if that is under python-3.4, 2.7 works
-# FIXME: respect CC and CXX
-
-src_prepare(){
-	sed -e 's/-O2 -Wall/$(CFLAGS)/' -i makefile || die
-}
-
-src_install(){
-	dobin *.py
-	python_foreach_impl python_domodule maptools.so
-	python_moduleinto Stampy
-	python_foreach_impl python_domodule build/python2.7/Stampy/*.pyc # only *.pyc files available
-	python_moduleinto ext
-	python_foreach_impl python_domodule build/python2.7/ext/*.pyc # only *.pyc files available
-	python_moduleinto plugins
-	python_foreach_impl python_domodule build/python2.7/plugins/*.py*
-	dodoc README.txt
-}
diff --git a/sci-biology/stringtie/Manifest b/sci-biology/stringtie/Manifest
index 1e23e3aa7..0541b973f 100644
--- a/sci-biology/stringtie/Manifest
+++ b/sci-biology/stringtie/Manifest
@@ -1 +1 @@
-DIST stringtie-1.3.4d.tar.gz 438025 BLAKE2B e9ea21f9d42cc90cb1fba200f13e840061bb8b34e1c3217aeaaee16edc2e2ededd5bae93d9575a7e198590d8ac8c4ba2d85f282a829d53296fd3edcd221a2d9a SHA512 450790af11536f1d9ac90e45af719b25bf7bd3a3123dcf8173b31e64446e650acb89bc9c9424c6fd0d527722fe204f510955308123f167ebd1c4334368fa2a4f
+DIST stringtie-2.1.5.tar.gz 2031196 BLAKE2B 9a064d9c666006e2207354f992d2291701bbc6a90e3487fc87c8ba59e0edc72727aba70e9785bb06ed997bb5f65f07c08c03e20553646a1eea5fa1c7ac92986a SHA512 882b0782695b967c1f234e9dd3ed5b25b9d64b9bba7a2508345db8e7e2c29d11362f0222ee2f39203f0a294fc3f1be65f09bec49b31fcd70bde2ab8ccbb0e016
diff --git a/sci-biology/stringtie/files/Makefile.patch b/sci-biology/stringtie/files/Makefile.patch
deleted file mode 100644
index b7efa605c..000000000
--- a/sci-biology/stringtie/files/Makefile.patch
+++ /dev/null
@@ -1,112 +0,0 @@
---- stringtie-1.3.4d/Makefile	2018-06-26 00:36:17.119583211 +0200
-+++ stringtie-1.3.4d/Makefile	2018-06-26 00:46:43.406712302 +0200
-@@ -1,28 +1,32 @@
--BAM := ./samtools-0.1.18
--#path to the directory where the samtools package was built (in place)
--#so libbam.a and *.h files MUST be in here
-+#-- for now these MUST point to the included samtools-0.x.x and gclib subdirectories
-+BAM  := ./samtools-0.1.18
-+GDIR := ./gclib
-+#--
- 
--GDIR      :=./gclib
-+INCDIRS := -I. -I${GDIR} -I${BAM}
- 
--INCDIRS   := -I. -I${GDIR} -I${BAM}
--
--CC        := g++
-+#CXX  ?= g++
-+CXX   := $(if $(CXX),$(CXX),g++)
- 
- BASEFLAGS := -Wall -Wextra ${INCDIRS} -fsigned-char -D_FILE_OFFSET_BITS=64 \
- -D_LARGEFILE_SOURCE -fno-strict-aliasing -fno-exceptions -fno-rtti
-+#for gcc 8+ add: -Wno-class-memaccess
-+
-+
-+LINKER  := $(if $(LINKER),$(LINKER),g++)
- 
--LINKER    := g++
-+LDFLAGS := $(if $(LDFLAGS),$(LDFLAGS),-g)
- 
--LDFLAGS   := -g -L${BAM} $(LDFLAGS)
-+LDFLAGS += -L${BAM}
- 
--LIBS      := -lbam -lz
-+LIBS    := -lbam -lz
- 
- ifneq (,$(findstring nothreads,$(MAKECMDGOALS)))
-  NOTHREADS=1
- endif
- 
- #detect MinGW (Windows environment)
--ifneq (,$(findstring mingw,$(shell ${CC} -dumpmachine)))
-+ifneq (,$(findstring mingw,$(shell ${CXX} -dumpmachine)))
-  WINDOWS=1
- endif
- 
-@@ -63,7 +67,8 @@ endif
- ifneq (,$(filter %release %static, $(MAKECMDGOALS)))
-   # -- release build
-   RELEASE_BUILD=1
--  CFLAGS := -DNDEBUG -g $(BASEFLAGS) $(CFLAGS) -O3
-+  CXXFLAGS := $(if $(CXXFLAGS),$(CXXFLAGS),-g -O3)
-+  CXXFLAGS += -DNDEBUG $(BASEFLAGS)
- else
-   ifneq (,$(filter %memcheck %memdebug, $(MAKECMDGOALS)))
-      #use sanitizer in gcc 4.9+
-@@ -72,21 +77,21 @@ else
-      ifeq "$(GCCVER49)" "0"
-        $(error gcc version 4.9 or greater is required for this build target)
-      endif
--     CFLAGS := -fno-omit-frame-pointer -fsanitize=undefined -fsanitize=address $(BASEFLAGS)
-+     CXXFLAGS := $(if $(CXXFLAGS),$(CXXFLAGS),-g -O0)
-+     CXXFLAGS += -fno-omit-frame-pointer -fsanitize=undefined -fsanitize=address $(BASEFLAGS)
-      GCCVER5 := $(shell expr `g++ -dumpversion | cut -f1 -d.` \>= 5)
-      ifeq "$(GCCVER5)" "1"
--       CFLAGS += -fsanitize=bounds -fsanitize=float-divide-by-zero -fsanitize=vptr
--       CFLAGS += -fsanitize=float-cast-overflow -fsanitize=object-size
--       #CFLAGS += -fcheck-pointer-bounds -mmpx
-+       CXXFLAGS += -fsanitize=bounds -fsanitize=float-divide-by-zero -fsanitize=vptr
-+       CXXFLAGS += -fsanitize=float-cast-overflow -fsanitize=object-size
-+       #CXXFLAGS += -fcheck-pointer-bounds -mmpx
-      endif
--     CFLAGS := -g -DDEBUG -D_DEBUG -DGDEBUG -fno-common -fstack-protector $(CFLAGS)
-+     CXXFLAGS += -DDEBUG -D_DEBUG -DGDEBUG -fno-common -fstack-protector
-      LIBS := -lasan -lubsan -ldl $(LIBS)
-   else
--    ifeq (,$(findstring clean,$(MAKECMDGOALS)))
-      #just plain debug build
-      DEBUG_BUILD=1
--     CFLAGS := -g -DDEBUG -D_DEBUG -DGDEBUG $(BASEFLAGS)
--    endif
-+     CXXFLAGS := $(if $(CXXFLAGS),$(CXXFLAGS),-g -O0)
-+     CXXFLAGS += -DDEBUG -D_DEBUG -DGDEBUG $(BASEFLAGS)
-   endif
- endif
- 
-@@ -106,23 +111,20 @@ ifdef DEBUG_BUILD
-   DBG_WARN+='WARNING: built DEBUG version [much slower], use "make clean release" for a faster, optimized version of the program.'
- endif
- 
--
- OBJS := ${GDIR}/GBase.o ${GDIR}/GArgs.o ${GDIR}/GStr.o ${GDIR}/GBam.o \
-  ${GDIR}/gdna.o ${GDIR}/codons.o ${GDIR}/GFaSeqGet.o ${GDIR}/gff.o 
- 
--
- ifneq (,$(filter %memtrace %memusage %memuse, $(MAKECMDGOALS)))
--    CFLAGS += -DGMEMTRACE
-+    CXXFLAGS += -DGMEMTRACE
-     OBJS += ${GDIR}/proc_mem.o
- endif
- 
- ifndef NOTHREADS
-  OBJS += ${GDIR}/GThreads.o 
- endif
- 
--
- %.o : %.cpp
--	${CC} ${CFLAGS} -c $< -o $@
-+	${CXX} ${CXXFLAGS} -c $< -o $@
- 
- OBJS += rlink.o tablemaker.o tmerge.o
- 
diff --git a/sci-biology/stringtie/stringtie-1.3.4d.ebuild b/sci-biology/stringtie/stringtie-1.3.4d.ebuild
deleted file mode 100644
index 953999e87..000000000
--- a/sci-biology/stringtie/stringtie-1.3.4d.ebuild
+++ /dev/null
@@ -1,33 +0,0 @@
-# Copyright 1999-2018 Gentoo Foundation
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=6
-
-DESCRIPTION="Transcriptome assembler and RNA-Seq analysis on BAM files aka cufflinks"
-HOMEPAGE="https://ccb.jhu.edu/software/stringtie
-	https://github.com/gpertea/stringtie"
-SRC_URI="http://ccb.jhu.edu/software/stringtie/dl/${P}.tar.gz"
-
-LICENSE="Artistic-2 MIT" # MIT from bundled samtools-0.1.18
-SLOT="0"
-KEYWORDS="~amd64 ~x86"
-IUSE=""
-
-# contains bundled and modified samtools-0.1.18
-# https://github.com/gpertea/stringtie/issues/185#issuecomment-400128090
-#
-# contains bundled gclib (0.9.8?), a modified version?
-# https://github.com/gpertea/stringtie/issues/186#issuecomment-400131844
-DEPEND=""
-RDEPEND="${DEPEND}"
-
-PATCHES=( "${FILESDIR}"/Makefile.patch )
-
-src_compile(){
-	emake release
-}
-
-src_install(){
-	dobin stringtie
-	dodoc README
-}
diff --git a/sci-biology/stringtie/stringtie-2.1.5.ebuild b/sci-biology/stringtie/stringtie-2.1.5.ebuild
new file mode 100644
index 000000000..9b1e205da
--- /dev/null
+++ b/sci-biology/stringtie/stringtie-2.1.5.ebuild
@@ -0,0 +1,29 @@
+# Copyright 1999-2021 Gentoo Authors
+# Distributed under the terms of the GNU General Public License v2
+
+EAPI=7
+
+DESCRIPTION="Transcriptome assembler and RNA-Seq analysis on BAM files aka cufflinks"
+HOMEPAGE="https://ccb.jhu.edu/software/stringtie
+	https://github.com/gpertea/stringtie"
+SRC_URI="https://github.com/gpertea/stringtie/releases/download/v${PV}/${P}.tar.gz"
+
+LICENSE="Artistic-2 MIT" # MIT from bundled samtools-0.1.18
+SLOT="0"
+KEYWORDS="~amd64 ~x86"
+
+# requires network
+RESTRICT="test"
+
+# contains bundled and modified samtools-0.1.18
+# https://github.com/gpertea/stringtie/issues/185#issuecomment-400128090
+#
+# contains bundled gclib (0.9.8?), a modified version?
+# https://github.com/gpertea/stringtie/issues/186#issuecomment-400131844
+DEPEND=""
+RDEPEND="${DEPEND}"
+
+src_install(){
+	dobin stringtie
+	einstalldocs
+}
diff --git a/sci-biology/subread/Manifest b/sci-biology/subread/Manifest
index dc31ef636..8b4dcee7c 100644
--- a/sci-biology/subread/Manifest
+++ b/sci-biology/subread/Manifest
@@ -1 +1 @@
-DIST subread-1.4.6-source.tar.gz 20173034 BLAKE2B 28bac4ae6b2aad2b765f2849f18dd9cfc9dbe8541b5c05943f313c01fc7b5ed5dcf10e6ed6bdb4738814b86a5273dc1a55d23638c47cc407c76de45110ff8813 SHA512 48636244d814ac985ba7ca2d1e54882b59c47145392958faab5680104ec2b35c7106d6351dfac675bfb5c5b8372e43585c603f76d830e3ddb25b6747a28b0132
+DIST subread-2.0.3-source.tar.gz 23304665 BLAKE2B 715907360f477a8ef69ba0465d6de1f23224da0c2095a21141f597a9cfe5c787cbafaa5d3c9cb04175f4d73cc4d184e13628541072d164596ee0b9b24175b501 SHA512 085d436d933c317555f36cbfb8e8c200ca15f20e56e48ae5427a673a74017dca7818320143a4841b78946685839931d48ae563b8b8e3ee6074581536cd0ff13b
diff --git a/sci-biology/subread/subread-1.4.6.ebuild b/sci-biology/subread/subread-1.4.6.ebuild
deleted file mode 100644
index 7b6cff913..000000000
--- a/sci-biology/subread/subread-1.4.6.ebuild
+++ /dev/null
@@ -1,41 +0,0 @@
-# Copyright 1999-2015 Gentoo Foundation
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=5
-
-[ "$PV" == "9999" ] && inherit subversion
-
-DESCRIPTION="NGS suite for analysis of mapped reads, summary of exon/intron/gene counts"
-HOMEPAGE="http://bioinf.wehi.edu.au/featureCounts/"
-if [ "$PV" == "9999" ]; then
-	ESVN_REPO_URI="https://subread.svn.sourceforge.net/svnroot/subread/trunk"
-	#KEYWORDS="~amd64 ~x86"
-else
-	SRC_URI="http://sourceforge.net/projects/subread/files/"${P}"/"${P}"-source.tar.gz"
-	KEYWORDS="~amd64 ~x86"
-fi
-
-LICENSE="GPL-3"
-SLOT="0"
-IUSE=""
-
-DEPEND="sys-libs/zlib"
-RDEPEND="${DEPEND}"
-
-S="${S}"-source
-
-src_prepare(){
-	sed -e "s/-mtune=core2//g" -e "s/-O9//g" -i src/Makefile.Linux || die
-}
-
-src_compile(){
-	cd src || die
-	emake -f Makefile.Linux
-}
-
-src_install(){
-	dobin bin/[a-s]* bin/utilities/*
-	dodoc README.txt doc/SubreadUsersGuide.pdf
-	insinto  /usr/share/subread
-	doins annotation/*.txt
-}
diff --git a/sci-biology/subread/subread-2.0.3.ebuild b/sci-biology/subread/subread-2.0.3.ebuild
new file mode 100644
index 000000000..624509aa5
--- /dev/null
+++ b/sci-biology/subread/subread-2.0.3.ebuild
@@ -0,0 +1,33 @@
+# Copyright 1999-2022 Gentoo Authors
+# Distributed under the terms of the GNU General Public License v2
+
+EAPI=8
+
+DESCRIPTION="NGS suite for analysis of mapped reads, summary of exon/intron/gene counts"
+HOMEPAGE="http://bioinf.wehi.edu.au/featureCounts/" # no https
+SRC_URI="https://sourceforge.net/projects/subread/files/${P}/${P}-source.tar.gz"
+S="${S}-source"
+
+LICENSE="GPL-3"
+SLOT="0"
+KEYWORDS="~amd64"
+
+DEPEND="sys-libs/zlib"
+RDEPEND="${DEPEND}"
+
+src_prepare(){
+	default
+	sed -e "s/-mtune=core2//g" -e "s/-O9//g" -i src/Makefile.Linux || die
+}
+
+src_compile(){
+	cd src || die
+	emake -f Makefile.Linux
+}
+
+src_install(){
+	dobin bin/[a-s]* bin/utilities/*
+	dodoc README.txt doc/SubreadUsersGuide.pdf
+	insinto  /usr/share/subread
+	doins annotation/*.txt
+}
diff --git a/sci-biology/swissknife/Manifest b/sci-biology/swissknife/Manifest
index bb9f2ec6d..098e05282 100644
--- a/sci-biology/swissknife/Manifest
+++ b/sci-biology/swissknife/Manifest
@@ -1 +1 @@
-DIST Swissknife_1.73.tar.gz 1644057 BLAKE2B 263a6ea2c572852e16fbc3f4694bd0132e4b50d8820a9a042d74946c33fe211a1277c00b59fe8b756eb1bfc8b497e0dde2ec1994034020bed593df51c6b00d35 SHA512 eddcdde093c73de3c3d0fc4c4f02eab77728b782843ac06cb29c39e58e76cc70e0a7cc622a8bbaa89abdd74ecb3c804b6594b849c23e576e0d129c5c360f605f
+DIST swissknife_1.80.tar.gz 1617939 BLAKE2B c2f6c3d83ecda02d6417301cf8d0b2ce9495e08d0d5817eb2e0c06771740f56ba13d6806c3c6030ba3eb2f44b7dea38a2eb90aecf3768acc70030367e4d0ab2a SHA512 b6577263b601843e1ef1399886459c61d7d18d3d18ff4ef117284f5aa592c54804846ba903647dc95273f71190c87997a902df0cf7b7adeb71e3c7bdfd8f3135
diff --git a/sci-biology/swissknife/swissknife-1.73.ebuild b/sci-biology/swissknife/swissknife-1.73.ebuild
deleted file mode 100644
index be1a921a5..000000000
--- a/sci-biology/swissknife/swissknife-1.73.ebuild
+++ /dev/null
@@ -1,25 +0,0 @@
-# Copyright 1999-2017 Gentoo Foundation
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=5
-
-inherit perl-module
-
-DESCRIPTION="Perl library of modules to manipulate SwissProt flatfiles"
-HOMEPAGE="http://swissknife.sourceforge.net/"
-SRC_URI="ftp://ftp.ebi.ac.uk/pub/software/swissprot/Swissknife/Swissknife_${PV}.tar.gz"
-
-SLOT="0"
-KEYWORDS="~amd64 ~x86"
-IUSE=""
-
-DEPEND="dev-perl/Module-Build"
-RDEPEND="${DEPEND}
-	>=dev-lang/perl-5.002:="
-	#dev-perl/Carp
-	#dev-perl/Data-Dumper
-	#dev-perl/Exporter"
-
-SRC_TEST=no
-
-S="${WORKDIR}"/Swissknife_${PV}
diff --git a/sci-biology/swissknife/swissknife-1.80.ebuild b/sci-biology/swissknife/swissknife-1.80.ebuild
new file mode 100644
index 000000000..46c3a32d2
--- /dev/null
+++ b/sci-biology/swissknife/swissknife-1.80.ebuild
@@ -0,0 +1,25 @@
+# Copyright 1999-2021 Gentoo Authors
+# Distributed under the terms of the GNU General Public License v2
+
+EAPI=7
+
+inherit perl-module
+
+DESCRIPTION="Perl library of modules to manipulate SwissProt flatfiles"
+HOMEPAGE="http://swissknife.sourceforge.net/"
+SRC_URI="https://downloads.sourceforge.net/project/${PN}/${PN}/${PV}/${PN}_${PV}.tar.gz"
+
+LICENSE="GPL-2+"
+SLOT="0"
+KEYWORDS="~amd64 ~x86"
+
+RESTRICT="test"
+
+DEPEND="dev-perl/Module-Build"
+RDEPEND="${DEPEND}
+	>=dev-lang/perl-5.002:="
+	#dev-perl/Carp
+	#dev-perl/Data-Dumper
+	#dev-perl/Exporter"
+
+S="${WORKDIR}"/swissknife_${PV}
diff --git a/sci-biology/symap/Manifest b/sci-biology/symap/Manifest
deleted file mode 100644
index 2d625ad38..000000000
--- a/sci-biology/symap/Manifest
+++ /dev/null
@@ -1 +0,0 @@
-DIST symap_40.tar.gz 115283449 SHA256 9fe4b3c456a62cbf177b6e894f549530c4561eeb7c31c4d1c8d4bb2a87f6399e SHA512 8b6e608a01637e13511223ce2cf67660c9d4ae20857b7fa11596d5278e11bd985f7b109b2de531d14c3fa1d8dcca2d50624095794abba9a33f539d7eca9883cc WHIRLPOOL 2d759a272625b3cc6cfa299fb94dcb9691749907484ae087eb7f026e8d603c7d9d6f1c5e21471d1f703bdb2970c7ac5ce984bc2d6ff2af90bd34806e63fb7ea7
diff --git a/sci-biology/symap/metadata.xml b/sci-biology/symap/metadata.xml
deleted file mode 100644
index ae9640ffb..000000000
--- a/sci-biology/symap/metadata.xml
+++ /dev/null
@@ -1,8 +0,0 @@
-<?xml version="1.0" encoding="UTF-8"?>
-<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
-<pkgmetadata>
-	<maintainer type="project">
-		<email>sci@gentoo.org</email>
-		<name>Gentoo Science Project</name>
-	</maintainer>
-</pkgmetadata>
diff --git a/sci-biology/symap/symap-4.0.ebuild b/sci-biology/symap/symap-4.0.ebuild
deleted file mode 100644
index bc485ff04..000000000
--- a/sci-biology/symap/symap-4.0.ebuild
+++ /dev/null
@@ -1,29 +0,0 @@
-# Copyright 1999-2014 Gentoo Foundation
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=5
-
-DESCRIPTION="Synteny Mapping and Analysis Program"
-HOMEPAGE="http://www.agcol.arizona.edu/software/symap/"
-SRC_URI="symap_40.tar.gz"
-
-LICENSE="GPL-2"
-SLOT="0"
-KEYWORDS=""
-#KEYWORDS="~x86 ~amd64"
-IUSE=""
-
-RESTRICT="fetch"
-
-pkg_nofetch() {
-	elog "Please register and download symap_${PV}.tar.gz (110MB)"
-	elog "at http://www.agcol.arizona.edu/software/symap/v${PV}/download/"
-	elog "and place it in ${DISTDIR}"
-}
-
-DEPEND="
-	sci-biology/blat
-	sci-biology/mummer
-	sci-biology/muscle"
-RDEPEND="${DEPEND}
-	virtual/jre"
diff --git a/sci-biology/tabixpp/Manifest b/sci-biology/tabixpp/Manifest
new file mode 100644
index 000000000..330d29178
--- /dev/null
+++ b/sci-biology/tabixpp/Manifest
@@ -0,0 +1 @@
+DIST tabixpp-1.1.0.tar.gz 3741 BLAKE2B 7a539a8d807a7ae6d3a3a317287f3231799717a7f4681a1093eb324efc316a8d050a8a91a7db5da6b56b5ca8c973c5c7fb1b6aea5b897070180358e7764f332c SHA512 6a69c1405dd9212d00a8a24860748d83492c3a3ca35aee18aae05093f0fbcec42fcec3e40dbf4560f735ffa263d59137ca564d0be17dbcfee1faeaa015ceca9b
diff --git a/sci-biology/tabixpp/metadata.xml b/sci-biology/tabixpp/metadata.xml
new file mode 100644
index 000000000..6a36d8a92
--- /dev/null
+++ b/sci-biology/tabixpp/metadata.xml
@@ -0,0 +1,11 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
+<pkgmetadata>
+	<maintainer type="project">
+		<email>sci-biology@gentoo.org</email>
+		<name>Gentoo Biology Project</name>
+	</maintainer>
+	<upstream>
+		<remote-id type="github">vcflib/vcflib</remote-id>
+	</upstream>
+</pkgmetadata>
diff --git a/sci-biology/tabixpp/tabixpp-1.1.0.ebuild b/sci-biology/tabixpp/tabixpp-1.1.0.ebuild
new file mode 100644
index 000000000..d3e69f914
--- /dev/null
+++ b/sci-biology/tabixpp/tabixpp-1.1.0.ebuild
@@ -0,0 +1,27 @@
+# Copyright 1999-2021 Gentoo Authors
+# Distributed under the terms of the GNU General Public License v2
+
+EAPI=7
+
+DESCRIPTION="C++ wrapper to tabix indexer "
+HOMEPAGE="https://github.com/ekg/tabixpp"
+SRC_URI="https://github.com/ekg/tabixpp/archive/v${PV}.tar.gz -> ${P}.tar.gz"
+
+LICENSE="MIT"
+SLOT="0"
+KEYWORDS="~amd64"
+
+DEPEND="sci-biology/samtools:0"
+RDEPEND="${DEPEND}"
+
+src_prepare(){
+	default
+	sed -e 's@HTS_HEADERS?=	htslib/htslib/bgzf.h htslib/htslib/tbx.h@HTS_HEADERS?=	/usr/include/htslib/bgzf.h /usr/include/htslib/tbx.h@g' -i Makefile || die
+	sed -e 's@HTS_LIB?=	htslib/libhts.a@HTS_LIB?=	/usr/'"$(get_libdir)"'/libhts.so@g' -i Makefile || die
+}
+
+src_install() {
+	einstalldocs
+	dobin tabix++
+	doheader tabix.hpp
+}
diff --git a/sci-biology/tablet-bin/Manifest b/sci-biology/tablet-bin/Manifest
deleted file mode 100644
index 912a58142..000000000
--- a/sci-biology/tablet-bin/Manifest
+++ /dev/null
@@ -1,2 +0,0 @@
-DIST coveragestats.py 4800 BLAKE2B 58f3c1e6b08d77b261aaa7462a840d9be77ee129ec3ddc410c89d560063e3d85fffe65f2c96a7dbca6be38cc5d1e4568d8d9711876f2b2f0fc41cb5b40261f82 SHA512 d5688832c13dc9c2e2e015df0b5c50113f72e2eeae076d479c43b65a4b028f8dcfa5f0fb833b4341d76d3956ea27707c55a51389b73a2efed6abd2b96ccdc3cd
-DIST tablet-bin-1.16.09.06.sh 53992010 SHA256 52a8d9a47d8f3bafdafedecaef48d67e21b7bb08b714de16dd39b964cd2d7b90 SHA512 da57de45ad2f9a5f1fcef625a67db435114186e5375cbb7bd69de1f243aa6281ec7caf0d6ddb361fab655b4c335fb34f5bdbe3f285c0df90cbf167bf13b9586d WHIRLPOOL 5c554c7ae9e511eb924017f637803e4350df672f0743fbe381c858c8ea9e67fce1a54b06b18d6b06926cc3d1fe3fbfd6edb3056449e40302732844be990284d1
diff --git a/sci-biology/tablet-bin/files/response.varfile b/sci-biology/tablet-bin/files/response.varfile
deleted file mode 100644
index cfa2e6808..000000000
--- a/sci-biology/tablet-bin/files/response.varfile
+++ /dev/null
@@ -1,11 +0,0 @@
-#install4j response file for Tablet x.xx.xx.xx
-#Mon Jan 24 11:35:29 GMT 2011
-executeLauncherAction$Boolean=false
-sys.programGroupDisabled$Boolean=true
-# somehow, this happens: ln -s /scratch/var/tmp/portage/sci-biology/tablet-bin-1.11.02.18/image/opt/Tablet/tablet /usr/local/bin/tablet
-# # that happens because /scratch/var/tmp/portage/sci-biology/tablet-bin-1.11.02.18/image/opt/Tablet/.install4j/response.varfile does not reflect our values
-sys.symlinkDir="${D}"usr/bin
-#sys.symlinkDir=/scratch/var/tmp/portage/sci-biology/tablet-bin-1.11.02.18/image/usr/bin
-sys.languageId=en
-sys.userHome="${D}"/../temp
-sys.installationDir="${D}"opt/Tablet
diff --git a/sci-biology/tablet-bin/metadata.xml b/sci-biology/tablet-bin/metadata.xml
deleted file mode 100644
index 138cb7705..000000000
--- a/sci-biology/tablet-bin/metadata.xml
+++ /dev/null
@@ -1,12 +0,0 @@
-<?xml version="1.0" encoding="UTF-8"?>
-<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
-<pkgmetadata>
-	<maintainer type="person">
-		<email>mmokrejs@fold.natur.cuni.cz</email>
-		<name>Martin Mokrejs</name>
-	</maintainer>
-	<maintainer type="project">
-		<email>sci-biology@gentoo.org</email>
-		<name>Gentoo Biology Project</name>
-	</maintainer>
-</pkgmetadata>
diff --git a/sci-biology/tablet-bin/tablet-bin-1.16.09.06.ebuild b/sci-biology/tablet-bin/tablet-bin-1.16.09.06.ebuild
deleted file mode 100644
index 401515e00..000000000
--- a/sci-biology/tablet-bin/tablet-bin-1.16.09.06.ebuild
+++ /dev/null
@@ -1,117 +0,0 @@
-# Copyright 1999-2018 Gentoo Foundation
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=6
-
-PYTHON_COMPAT=( python2_7 )
-
-inherit java-pkg-2 python-r1
-
-DESCRIPTION="Viewer of next generation sequence assemblies and alignments"
-HOMEPAGE="http://ics.hutton.ac.uk/tablet/"
-SRC_URI="
-	x86? ( http://bioinf.hutton.ac.uk/tablet/installers/tablet_linux_x86_$(replace_all_version_separators _).sh -> ${P}.sh )
-	amd64? ( http://bioinf.hutton.ac.uk/tablet/installers/tablet_linux_x64_$(replace_all_version_separators _).sh -> ${P}.sh )
-	http://bioinf.hutton.ac.uk/tablet/additional/coveragestats.py"
-
-# Upstream says regarding source code unavailability:
-# Tablet uses a modified version of the BSD License which has been edited to
-# remove references to distribution and use in source forms. This means that
-# we are happy for you to distribute and use Tablet however you please, but we
-# do not (yet) want to make the source code publicly available.
-
-# The licence file itself is in the installer, and ends up on disk after
-# installation at /opt/Tablet/docs/tablet.html
-# The original BSD licence was modified to remove references to distribution
-# and use in source forms, because we cannot make the source code available
-# for Tablet.
-
-LICENSE="Tablet"
-SLOT="0"
-KEYWORDS="~amd64 ~x86"
-IUSE=""
-
-REQUIRED_USE="${PYTHON_REQUIRED_USE}"
-
-DEPEND="${PYTHON_DEPS}
-	app-text/dos2unix
-	>=virtual/jdk-1.8:*"
-RDEPEND="${DEPEND}"
-# contains bundled sqlite-jdbc-3.8.6.jar, samtools-linux64.jar, picard.jar
-# sqlite-jdbc-3.8.6.jar is not dev-db/sqlite:3 and samtools-linux64.jar is not sci-biology/samtools either
-# replacing picard.jar with a symlink to picard.jar from sci-biology.picard does not help either
-
-S="${WORKDIR}"
-
-src_unpack() {
-	local file
-	for file in ${A}; do
-		cp "${DISTDIR}"/${file} "${WORKDIR}" || die
-	done
-}
-
-src_install() {
-	# In theory it seems this binary package could be installed through ant
-	# instead of the install4j package which is not easy to be forced
-	# non-interactive. The below approach via install4j is not ideal but works.
-	sed "s#\"\${D}\"#\"${D}\"#g" "${FILESDIR}"/response.varfile > "${WORKDIR}"/response.varfile || die "sed failed"
-
-	# the intallation script somehow does not pickup
-	# -varfile="${DISTDIR}"/response.varfile from the commandline and therefore
-	# we place the file rather directly into the place where it should reside.
-	# In the file you can read details how the variables were mangled. For
-	# example, the trick with sys.symlinkDir in the response.varfile is to
-	# disable the installation process to symlink from /usr/local/bin/table to
-	# /opt/Tablet/tablet. That was logged in that file with the following line:
-	#
-	# /var/tmp/portage/sci-biology/tablet-bin-1.11.02.18/image/opt/Tablet/.install4j/installation.log:
-	#	Variable changed: sys.symlinkDir=/usr/local/bin[class java.lang.String]
-	#
-	# The file is then left on the installed system in "${D}"/opt/Tablet/.install4j/response.varfile
-	dodir /opt/Tablet/.install4j
-	cat "${WORKDIR}"/response.varfile > "${ED}"/opt/Tablet/.install4j/response.varfile || die
-
-	# make sure we force java to point a to $HOME which is inside our sanbox
-	# directory area. We force -Duser.home . It seems also -Dinstall4j.userHome
-	# could be done based on the figure shown at http://resources.ej-technologies.com/install4j/help/doc/
-	if [ -z "${EPREFIX}" ]; then
-		sed \
-		-e "s#/bin/java\" -Dinstall4j.jvmDir#/bin/java\" -Duser.home=${TMPDIR} -Dinstall4j.jvmDir -Djava.util.prefs.systemRoot=${TMPDIR}#" -i "${WORKDIR}"/${P}.sh || die
-	else
-		sed \
-			-e 's#"$app_java_home/bin/java" -Dinstall4j.jvmDir# '"${EPREFIX}""/usr/bin/java -Duser.home=${TMPDIR} -Dinstall4j.jvmDir -Djava.util.prefs.systemRoot=${TMPDIR}#" -i "${WORKDIR}"/${P}.sh || die
-	fi
-	sh \
-		"${WORKDIR}"/${P}.sh \
-		-q -overwrite \
-		-varfile="${DISTDIR}"/response.varfile \
-		--destination="${ED}"/opt/Tablet \
-		-dir "${ED}"/opt/Tablet || die
-
-	rm -rf "${ED}"/opt/Tablet/jre "${ED}"/opt/Tablet/.install4j || die
-
-	# zap bundled jars
-	# do not zap even picard.jar because tablet does not start then with an error:
-	#   java.lang.NoClassDefFoundError: net/sf/samtools/SAMReadGroupRecord
-	# not even a symlink to "${EPREFIX}"/usr/share/picard/lib/picard.jar helps
-	#
-	# for f in picard.jar; do
-	# 	rm -f "${ED}"/opt/Tablet/lib/"$f" || die
-	# done
-
-	# this dies with tablet-bin-1.14.04.10 with
-	#  * python2_7: running python_doscript /mnt/1TB/var/tmp/portage/sci-biology/tablet-bin-1.14.04.10/work/coveragestats.py
-	#  * The file has incompatible shebang:
-	#  *   file: /usr/lib/python-exec/python2.7/coveragestats.py
-	#  *   current shebang: #!/usr/bin/env python
-	#  *   requested impl: python2.7
-	#
-	# python_foreach_impl python_doscript "${WORKDIR}"/coveragestats.py
-	dos2unix "${WORKDIR}"/coveragestats.py coveragestats.py || die
-	insinto /opt/Tablet/utils
-	doins coveragestats.py
-
-	# do not use 99Tablet to avoid file collision with sci-biology/tablet
-	echo "PATH=${EPREFIX}/opt/Tablet" > 99Tablet-bin
-	doenvd 99Tablet-bin
-}
diff --git a/sci-biology/tablet/files/response.varfile b/sci-biology/tablet/files/response.varfile
deleted file mode 100644
index cfa2e6808..000000000
--- a/sci-biology/tablet/files/response.varfile
+++ /dev/null
@@ -1,11 +0,0 @@
-#install4j response file for Tablet x.xx.xx.xx
-#Mon Jan 24 11:35:29 GMT 2011
-executeLauncherAction$Boolean=false
-sys.programGroupDisabled$Boolean=true
-# somehow, this happens: ln -s /scratch/var/tmp/portage/sci-biology/tablet-bin-1.11.02.18/image/opt/Tablet/tablet /usr/local/bin/tablet
-# # that happens because /scratch/var/tmp/portage/sci-biology/tablet-bin-1.11.02.18/image/opt/Tablet/.install4j/response.varfile does not reflect our values
-sys.symlinkDir="${D}"usr/bin
-#sys.symlinkDir=/scratch/var/tmp/portage/sci-biology/tablet-bin-1.11.02.18/image/usr/bin
-sys.languageId=en
-sys.userHome="${D}"/../temp
-sys.installationDir="${D}"opt/Tablet
diff --git a/sci-biology/tablet/metadata.xml b/sci-biology/tablet/metadata.xml
deleted file mode 100644
index 138cb7705..000000000
--- a/sci-biology/tablet/metadata.xml
+++ /dev/null
@@ -1,12 +0,0 @@
-<?xml version="1.0" encoding="UTF-8"?>
-<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
-<pkgmetadata>
-	<maintainer type="person">
-		<email>mmokrejs@fold.natur.cuni.cz</email>
-		<name>Martin Mokrejs</name>
-	</maintainer>
-	<maintainer type="project">
-		<email>sci-biology@gentoo.org</email>
-		<name>Gentoo Biology Project</name>
-	</maintainer>
-</pkgmetadata>
diff --git a/sci-biology/tablet/tablet-1.15.09.01.ebuild b/sci-biology/tablet/tablet-1.15.09.01.ebuild
deleted file mode 100644
index c0b67d139..000000000
--- a/sci-biology/tablet/tablet-1.15.09.01.ebuild
+++ /dev/null
@@ -1,51 +0,0 @@
-# Copyright 1999-2017 Gentoo Foundation
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=5
-
-PYTHON_COMPAT=( python2_7 )
-
-inherit java-pkg-2 java-ant-2 python-r1
-
-# [ "$PV" == "9999" ] && inherit subversion
-inherit subversion
-
-DESCRIPTION="Viewer of next generation sequence assemblies and alignments"
-HOMEPAGE="http://bioinf.scri.ac.uk/tablet/"
-if [ "$PV" == "9999" ]; then
-	ESVN_REPO_URI="http://ics.hutton.ac.uk/svn/tablet/trunk/"
-	KEYWORDS=""
-else
-	ESVN_REPO_URI="http://ics.hutton.ac.uk/svn/tablet/tags/${PV}"
-	KEYWORDS="~amd64 ~x86"
-fi
-
-LICENSE="Tablet"
-SLOT="0"
-IUSE=""
-
-REQUIRED_USE="${PYTHON_REQUIRED_USE}"
-
-DEPEND="${PYTHON_DEPS}
-	>=virtual/jdk-1.8:*"
-RDEPEND="${PYTHON_DEPS}
-	>=virtual/jre-1.8:*"
-# contains bundled sqlite-jdbc-3.8.6.jar, samtools-linux64.jar, picard.jar
-# sqlite-jdbc-3.8.6.jar is not dev-db/sqlite:3 and samtools-linux64.jar is not sci-biology/samtools either
-# replacing picard.jar with a symlink to picard.jar from sci-biology.picard does not help either
-
-S="${WORKDIR}"
-
-src_install() {
-	java-pkg_dojar lib/tablet.jar
-	java-pkg_dolauncher ${PN}
-	java-pkg_dojar lib/tablet-resources.jar
-	java-pkg_dojar lib/flamingo.jar
-	java-pkg_dojar lib/scri-commons.jar
-	java-pkg_dojar lib/samtools*.jar
-	java-pkg_dojar lib/picard*.jar
-	java-pkg_dojar lib/sqlite-jdbc*.jar
-
-	echo "PATH=${EPREFIX}/usr/share/${PN}/" > 99Tablet
-	doenvd 99Tablet
-}
diff --git a/sci-biology/tablet/tablet-1.16.09.06.ebuild b/sci-biology/tablet/tablet-1.16.09.06.ebuild
deleted file mode 100644
index e72339d61..000000000
--- a/sci-biology/tablet/tablet-1.16.09.06.ebuild
+++ /dev/null
@@ -1,51 +0,0 @@
-# Copyright 1999-2017 Gentoo Foundation
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=5
-
-PYTHON_COMPAT=( python2_7 )
-
-inherit java-pkg-2 java-ant-2 python-r1
-
-# [ "$PV" == "9999" ] && inherit subversion
-inherit subversion
-
-DESCRIPTION="Viewer of next generation sequence assemblies and alignments"
-HOMEPAGE="http://bioinf.scri.ac.uk/tablet/"
-if [ "$PV" == "9999" ]; then
-	ESVN_REPO_URI="http://ics.hutton.ac.uk/svn/tablet/trunk/"
-	KEYWORDS=""
-else
-	ESVN_REPO_URI="http://ics.hutton.ac.uk/svn/tablet/tags/${PV}"
-	KEYWORDS="~amd64 ~x86"
-fi
-
-LICENSE="Tablet"
-SLOT="0"
-IUSE=""
-
-REQUIRED_USE="${PYTHON_REQUIRED_USE}"
-
-DEPEND="${PYTHON_DEPS}
-	>=virtual/jdk-1.8:*"
-RDEPEND="${PYTHON_DEPS}
-	>=virtual/jre-1.8:*"
-# contains bundled sqlite-jdbc-3.8.6.jar, samtools-linux64.jar, picard.jar
-# sqlite-jdbc-3.8.6.jar is not dev-db/sqlite:3 and samtools-linux64.jar is not sci-biology/samtools either
-# replacing picard.jar with a symlink to picard.jar from sci-biology.picard does not help either
-
-S="${WORKDIR}"
-
-src_install() {
-	java-pkg_dojar lib/tablet.jar
-	java-pkg_dolauncher ${PN}
-	java-pkg_dojar lib/tablet-resources.jar
-	java-pkg_dojar lib/flamingo.jar
-	java-pkg_dojar lib/scri-commons.jar
-	java-pkg_dojar lib/samtools*.jar
-	java-pkg_dojar lib/picard*.jar # is picard-1.113 in tablet-1.16.09.06
-	java-pkg_dojar lib/sqlite-jdbc*.jar
-
-	echo "PATH=${EPREFIX}/opt/Tablet" > 99Tablet
-	doenvd 99Tablet
-}
diff --git a/sci-biology/tablet/tablet-9999.ebuild b/sci-biology/tablet/tablet-9999.ebuild
deleted file mode 100644
index 467895e5d..000000000
--- a/sci-biology/tablet/tablet-9999.ebuild
+++ /dev/null
@@ -1,51 +0,0 @@
-# Copyright 1999-2017 Gentoo Foundation
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=5
-
-PYTHON_COMPAT=( python2_7 )
-
-inherit java-pkg-2 java-ant-2 python-r1
-
-# [ "$PV" == "9999" ] && inherit subversion
-inherit subversion
-
-DESCRIPTION="Viewer of next generation sequence assemblies and alignments"
-HOMEPAGE="http://bioinf.scri.ac.uk/tablet/"
-if [ "$PV" == "9999" ]; then
-	ESVN_REPO_URI="http://ics.hutton.ac.uk/svn/tablet/trunk/"
-	KEYWORDS=""
-else
-	ESVN_REPO_URI="http://ics.hutton.ac.uk/svn/tablet/tags/${PV}"
-	KEYWORDS=""
-fi
-
-LICENSE="Tablet"
-SLOT="0"
-IUSE=""
-
-REQUIRED_USE="${PYTHON_REQUIRED_USE}"
-
-DEPEND="${PYTHON_DEPS}
-	>=virtual/jdk-1.8:*"
-RDEPEND="${PYTHON_DEPS}
-	>=virtual/jre-1.8:*"
-# contains bundled sqlite-jdbc-3.8.6.jar, samtools-linux64.jar, picard.jar
-# sqlite-jdbc-3.8.6.jar is not dev-db/sqlite:3 and samtools-linux64.jar is not sci-biology/samtools either
-# replacing picard.jar with a symlink to picard.jar from sci-biology.picard does not help either
-
-S="${WORKDIR}"
-
-src_install() {
-	java-pkg_dojar lib/tablet.jar
-	java-pkg_dolauncher ${PN}
-	java-pkg_dojar lib/tablet-resources.jar
-	java-pkg_dojar lib/flamingo.jar
-	java-pkg_dojar lib/scri-commons.jar
-	java-pkg_dojar lib/samtools*.jar
-	java-pkg_dojar lib/picard*.jar
-	java-pkg_dojar lib/sqlite-jdbc*.jar
-
-	echo "PATH=${EPREFIX}/usr/share/${PN}" > 99Tablet
-	doenvd 99Tablet
-}
diff --git a/sci-biology/tagdust/Manifest b/sci-biology/tagdust/Manifest
index f9a18f2b1..34ad38a8e 100644
--- a/sci-biology/tagdust/Manifest
+++ b/sci-biology/tagdust/Manifest
@@ -1 +1 @@
-DIST tagdust.tgz 313456 BLAKE2B 63f7fb2a122664dd230f74bf000fec27458e3559538a1abef5d79a6c18fa9a53c42c629c2ed8179fd306f1c89537c73e4f534772688ae5dd0f6f7975fdd8658f SHA512 c792c241e702a33d851f0897b98494277441247973df84e90c1ac730b75a656d147960dc5619ba78a8e4f87953c64d9ce0067cbb83c0b19438bf4889b07a2c36
+DIST tagdust-20101028.tgz 313456 BLAKE2B 63f7fb2a122664dd230f74bf000fec27458e3559538a1abef5d79a6c18fa9a53c42c629c2ed8179fd306f1c89537c73e4f534772688ae5dd0f6f7975fdd8658f SHA512 c792c241e702a33d851f0897b98494277441247973df84e90c1ac730b75a656d147960dc5619ba78a8e4f87953c64d9ce0067cbb83c0b19438bf4889b07a2c36
diff --git a/sci-biology/tagdust/files/tagdust-20101028-fno-common.patch b/sci-biology/tagdust/files/tagdust-20101028-fno-common.patch
new file mode 100644
index 000000000..01fd2d274
--- /dev/null
+++ b/sci-biology/tagdust/files/tagdust-20101028-fno-common.patch
@@ -0,0 +1,77 @@
+--- a/background.c
++++ b/background.c
+@@ -28,6 +28,9 @@
+ #include <ctype.h>
+ #define MIN(a, b) (a > b ? b : a)
+ 
++extern int *seed;
++extern int nuc_code[255];
++
+ /*
+  
+  Collects length and nucleotide composition of the input reads. Simultaneously counts how many sequences are covered by x,x+1 ... percent library sequences
+--- a/detect.h
++++ b/detect.h
+@@ -70,11 +70,11 @@ struct stats_dat{
+ 	int *p_counts;
+ };
+ 
+-int nuc_code[255]; 
++extern int nuc_code[255]; 
+ 
+-int *seed;
++extern int *seed;
+ 
+-int linewrap;
++extern int linewrap;
+ 
+ void init_nuc_code();
+ 
+--- a/input.c
++++ b/input.c
+@@ -28,6 +28,10 @@
+ #include <ctype.h>
+ 
+ static int numseq = 0;
++extern int linewrap;
++extern int *seed;
++extern int nuc_code[255];
++
+ 
+ 
+ int compare(const void* a, const void* b)
+--- a/interface.c
++++ b/interface.c
+@@ -33,6 +33,8 @@
+ #define OPT_FASTA 5
+ #define OPT_MODEL 6
+ 
++extern int linewrap;
++
+ struct parameters* interface(struct parameters* param,int argc, char **argv)
+ {
+ 	int c;
+--- a/main.c
++++ b/main.c
+@@ -27,6 +27,10 @@
+ #include "detect.h"
+ #include "sys/time.h"
+ 
++int linewrap;
++int *seed;
++int nuc_code[255];
++
+ 
+ int main (int argc, char * argv[]) {
+ 	struct parameters* param = 0;
+--- a/test_sequence.c
++++ b/test_sequence.c
+@@ -26,6 +26,8 @@
+ 
+ #include "detect.h"
+ 
++extern int *seed;
++
+ /* 
+  Checks if a sequence is covered by library sequences. Return the fraction of residues covered by library sequences.  
+ */
diff --git a/sci-biology/tagdust/tagdust-20101028.ebuild b/sci-biology/tagdust/tagdust-20101028.ebuild
index 61a2c3838..2f5a1777e 100644
--- a/sci-biology/tagdust/tagdust-20101028.ebuild
+++ b/sci-biology/tagdust/tagdust-20101028.ebuild
@@ -1,32 +1,31 @@
-# Copyright 1999-2015 Gentoo Foundation
+# Copyright 1999-2021 Gentoo Authors
 # Distributed under the terms of the GNU General Public License v2
 
-EAPI=5
+EAPI=7
 
 DESCRIPTION="Trim multimers of various primers/adapter from Illumina datasets"
 HOMEPAGE="http://genome.gsc.riken.jp/osc/english/dataresource"
-SRC_URI="http://genome.gsc.riken.jp/osc/english/software/src/tagdust.tgz"
+SRC_URI="http://genome.gsc.riken.jp/osc/english/software/src/tagdust.tgz -> ${P}.tgz"
 
 LICENSE="GPL-3"
 SLOT="0"
 KEYWORDS="~amd64"
-IUSE=""
 
-DEPEND=""
-RDEPEND="${DEPEND}"
+S="${WORKDIR}/tagdust"
 
-S="${WORKDIR}"/tagdust
+PATCHES=( "${FILESDIR}"/${P}-fno-common.patch )
 
 src_prepare(){
+	default
 	sed -e "s/^CFLAGS/#CFLAGS/" -e "s#/usr/local/bin#\$(DESTDIR)/usr/bin#" \
-		-e "s#/usr/share/man/#\$(DESTDIR)/usr/share/man/#" -i Makefile
+		-e "s#/usr/share/man/#\$(DESTDIR)/usr/share/man/#" -i Makefile || die
 }
 
-src_install(){
+src_install() {
 	doman tagdust.1
 	dobin tagdust
 	insinto /usr/share/tagdust/Illumina
-	doins "test/"solexa*.fa
+	doins test/solexa*.fa
 	insinto /usr/share/tagdust
-	doins "test/"protocol.txt README
+	doins test/protocol.txt README
 }
diff --git a/sci-biology/tclust/Manifest b/sci-biology/tclust/Manifest
deleted file mode 100644
index 2ad5e841b..000000000
--- a/sci-biology/tclust/Manifest
+++ /dev/null
@@ -1,2 +0,0 @@
-DIST gclib-110625.tar.gz 82727 BLAKE2B b99a89d39ed76c643a9e379cb7294c63ec0d186a106c331f6ff4df6a40fcc5585f81e4c9d6015af434e2a75ea46e0e3783dda627abae32276ce9204c719bef2f SHA512 a6819e6dcb092c13b4f5da7eca6c82a9a46b512aeff2596cb4b921aeb8088c40bf2283be66862ab4d2195062b8126169e02945bcf4c8d4f118fa1e34bccba197
-DIST tclust-110625.tar.gz 9521 BLAKE2B a37acdb940f8666c53e357fa653c61c074afb82a71b120afd0fa9e4e90591144964edeab3ecfb5cb3be29fb7474b438f0fddd961f7a702ab3e4ba3011f622327 SHA512 b61497340c3bac08de2b5db4c16e9c2bd616651a1d1ae8ebfd9d2c3e2c4a436aba094e179e669d18cf4069c29c6ea5f75fca45fdc84660bc75ade9c5c5cef451
diff --git a/sci-biology/tclust/files/tclust-110625-build.patch b/sci-biology/tclust/files/tclust-110625-build.patch
deleted file mode 100644
index 9474916af..000000000
--- a/sci-biology/tclust/files/tclust-110625-build.patch
+++ /dev/null
@@ -1,43 +0,0 @@
- Makefile |    9 ++++-----
- 1 files changed, 4 insertions(+), 5 deletions(-)
-
-diff --git a/Makefile b/Makefile
-index f4f69f1..30ba16e 100644
---- a/Makefile
-+++ b/Makefile
-@@ -11,8 +11,8 @@ SYSTYPE :=     $(shell uname)
- 
- # C compiler
- 
--CC      := g++
--CFLAGS  = -O2 -Wall ${SEARCHDIRS} -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_REENTRANT -fno-exceptions -fno-rtti -fno-strict-aliasing
-+CC      ?= g++
-+CXXFLAGS  += -Wall ${SEARCHDIRS} -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_REENTRANT -fno-exceptions -fno-rtti -fno-strict-aliasing
- 
- %.o : %.c
- 	${CC} ${CFLAGS} -c $< -o $@
-@@ -24,7 +24,7 @@ CFLAGS  = -O2 -Wall ${SEARCHDIRS} -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_
- 	${CC} ${CFLAGS} -c $< -o $@
- 
- %.o : %.cpp
--	${CC} ${CFLAGS} -c $< -o $@
-+	${CXX} ${CXXFLAGS} -c $< -o $@
- 
- %.o : %.cxx
- 	${CC} ${CFLAGS} -c $< -o $@
-@@ -32,14 +32,13 @@ CFLAGS  = -O2 -Wall ${SEARCHDIRS} -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_
- # C/C++ linker
- 
- LINKER    := g++
--LDFLAGS    =
- LOADLIBES := 
- 
- .PHONY : all
- all:    tclust
- 
- tclust:  ./tclust.o ${GCLDIR}/GBase.o ${GCLDIR}/GStr.o ${GCLDIR}/GArgs.o
--	${LINKER} ${LDFLAGS} -o $@ ${filter-out %.a %.so, $^} ${LOADLIBES}
-+	${CXX} ${LDFLAGS} -o $@ ${filter-out %.a %.so, $^} ${LOADLIBES}
- 
- # target for removing all object files
- 
diff --git a/sci-biology/tclust/metadata.xml b/sci-biology/tclust/metadata.xml
deleted file mode 100644
index 138cb7705..000000000
--- a/sci-biology/tclust/metadata.xml
+++ /dev/null
@@ -1,12 +0,0 @@
-<?xml version="1.0" encoding="UTF-8"?>
-<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
-<pkgmetadata>
-	<maintainer type="person">
-		<email>mmokrejs@fold.natur.cuni.cz</email>
-		<name>Martin Mokrejs</name>
-	</maintainer>
-	<maintainer type="project">
-		<email>sci-biology@gentoo.org</email>
-		<name>Gentoo Biology Project</name>
-	</maintainer>
-</pkgmetadata>
diff --git a/sci-biology/tclust/tclust-110625.ebuild b/sci-biology/tclust/tclust-110625.ebuild
deleted file mode 100644
index b5b26ca7a..000000000
--- a/sci-biology/tclust/tclust-110625.ebuild
+++ /dev/null
@@ -1,29 +0,0 @@
-# Copyright 1999-2015 Gentoo Foundation
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=5
-
-inherit eutils toolchain-funcs
-
-DESCRIPTION="Transitive closure clustering tool with overlap filtering options"
-HOMEPAGE="http://compbio.dfci.harvard.edu/tgi/software/"
-SRC_URI="
-	ftp://occams.dfci.harvard.edu/pub/bio/tgi/software/tgicl/${PN}.tar.gz -> ${P}.tar.gz
-	ftp://occams.dfci.harvard.edu/pub/bio/tgi/software/tgicl/gclib.tar.gz -> gclib-${PV}.tar.gz"
-
-LICENSE="Artistic"
-SLOT="0"
-KEYWORDS="~amd64 ~x86"
-IUSE=""
-
-S=${WORKDIR}/${PN}
-
-src_prepare() {
-	epatch "${FILESDIR}"/${P}-build.patch
-	tc-export CC CXX
-}
-
-src_install() {
-	dobin ${PN}
-	dodoc README
-}
diff --git a/sci-biology/tigmint/Manifest b/sci-biology/tigmint/Manifest
index 5032ee1eb..4c87774b6 100644
--- a/sci-biology/tigmint/Manifest
+++ b/sci-biology/tigmint/Manifest
@@ -1 +1 @@
-DIST tigmint-1.1.0.tar.gz 330542 BLAKE2B 01159031c132b0dbf5089f3e31970362d816443b9a29aa7d664f6ec97fe126c3afbc4fe4765a27554726c0b73816843b1e017722d45ec43f61eed7e82050f110 SHA512 dc14adcf2bde135770aa9beb99d750770e4ea891d4eaa1ad607431c321c414f66ca7befc246647cc98ad23cdff008604b254fda429fcabf90b173554ea41a81b
+DIST tigmint-1.2.4.tar.gz 7691928 BLAKE2B 77a42d11f696f340267d5746cb6682a29b2adb5350d9237b5f4fc4ce7d69448157db719d32cd9fc689909faffb2913fa2f4dd783403c954c45614ed0fcfb7c5d SHA512 3ba214cd60396439ecca5e04c458c59a804598729fb28c18adc397eebad3a32c170cfcd6ad59c3226ba181d71f02002fec9c1ed0fd2f21f76825afc20773e853
diff --git a/sci-biology/tigmint/tigmint-1.1.0.ebuild b/sci-biology/tigmint/tigmint-1.1.0.ebuild
deleted file mode 100644
index 66a1f3460..000000000
--- a/sci-biology/tigmint/tigmint-1.1.0.ebuild
+++ /dev/null
@@ -1,31 +0,0 @@
-# Copyright 1999-2018 Gentoo Foundation
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=6
-
-DESCRIPTION="Correct misassemblies using linked reads from 10x Genomics Chromium"
-HOMEPAGE="https://github.com/bcgsc/tigmint"
-SRC_URI="https://github.com/bcgsc/tigmint/archive/1.1.0.tar.gz -> ${P}.tar.gz"
-
-LICENSE="GPL-3"
-SLOT="0"
-KEYWORDS=""
-IUSE=""
-
-DEPEND="
-	dev-python/intervaltree
-	sci-biology/pybedtools
-	sci-biology/pysam
-	dev-python/statistics"
-RDEPEND="${DEPEND}
-	sci-biology/bwa
-	sci-biology/bedtools
-	sci-biology/samtools:0
-	sci-biology/seqtools
-	dev-util/makefile2graph
-	media-gfx/graphviz
-	dev-vcs/git
-	dev-libs/libxslt
-	net-misc/curl"
-# for full features also sci-biology/abyss should be installed but it addition here
-# would create circular dependency
diff --git a/sci-biology/tigmint/tigmint-1.2.4-r1.ebuild b/sci-biology/tigmint/tigmint-1.2.4-r1.ebuild
new file mode 100644
index 000000000..c5f630a96
--- /dev/null
+++ b/sci-biology/tigmint/tigmint-1.2.4-r1.ebuild
@@ -0,0 +1,69 @@
+# Copyright 1999-2023 Gentoo Authors
+# Distributed under the terms of the GNU General Public License v2
+
+EAPI=8
+
+PYTHON_COMPAT=( python3_{10..10} )
+DISTUTILS_USE_SETUPTOOLS=no
+
+inherit distutils-r1
+
+DESCRIPTION="Correct misassemblies using linked reads from 10x Genomics Chromium"
+HOMEPAGE="https://github.com/bcgsc/tigmint https://bcgsc.github.io/tigmint/"
+SRC_URI="https://github.com/bcgsc/tigmint/releases/download/v${PV}/${P}.tar.gz"
+
+LICENSE="GPL-3"
+SLOT="0"
+KEYWORDS="~amd64 ~x86"
+
+RESTRICT="test"
+PROPERTIES="test_network"
+
+RDEPEND="
+	dev-python/intervaltree[${PYTHON_USEDEP}]
+	sci-biology/pybedtools[${PYTHON_USEDEP}]
+	sci-biology/pysam[${PYTHON_USEDEP}]
+	app-arch/pigz
+	app-shells/zsh
+	sci-biology/samtools
+	sci-biology/minimap2
+	sci-biology/seqtk
+"
+
+distutils_enable_tests pytest
+
+src_prepare(){
+	# install the executable into /usr/bin
+	sed -i Makefile -e 's#prefix=/usr/local#prefix=/usr#'
+	default
+}
+
+src_configure(){
+	python_setup
+	default
+}
+
+# do not run src_compile step as it runs git, makefile2graph, gsed, tred
+
+python_install() {
+	# This is a bit unorthodox, but it allows us to get both a symlink from
+	# /usr/bin to our script using the correct python implementation
+	# *and* to import it from the python shell
+	python_domodule bin/*.py
+	python_domodule bin/tigmint-arcs-tsv
+	python_domodule bin/tigmint-cut
+
+	python_doscript bin/*.py
+	python_doscript bin/tigmint-arcs-tsv
+	python_doscript bin/tigmint-cut
+}
+
+python_install_all() {
+	dobin bin/tigmint
+	dobin bin/tigmint-make
+}
+
+src_test(){
+	default
+	distutils-r1_src_test
+}
diff --git a/sci-biology/tigr-foundation-libs/files/TigrFoundation-all-patches.patch b/sci-biology/tigr-foundation-libs/files/TigrFoundation-all-patches.patch
index 57ad86e2e..459ae96d1 100644
--- a/sci-biology/tigr-foundation-libs/files/TigrFoundation-all-patches.patch
+++ b/sci-biology/tigr-foundation-libs/files/TigrFoundation-all-patches.patch
@@ -1,5 +1,5 @@
---- /tmp/autoEditor-1.20/TigrFoundation-2.0/ConfigFile.cc.old	2010-12-04 17:07:50.000000000 +0100
-+++ /tmp/autoEditor-1.20/TigrFoundation-2.0/ConfigFile.cc	2010-12-04 17:07:25.000000000 +0100
+--- a/ConfigFile.cc	2010-12-04 17:07:50.000000000 +0100
++++ b/ConfigFile.cc	2010-12-04 17:07:25.000000000 +0100
 @@ -33,6 +33,7 @@
   *  different values.
   */
@@ -8,8 +8,8 @@
  #include "ConfigFile.hh"
  
  //! Constructor
---- /tmp/autoEditor-1.20/TigrFoundation-2.0/Logger.hh.old	2010-12-04 17:20:19.000000000 +0100
-+++ /tmp/autoEditor-1.20/TigrFoundation-2.0/Logger.hh	2010-12-04 17:20:49.000000000 +0100
+--- a/Logger.hh	2010-12-04 17:20:19.000000000 +0100
++++ b/Logger.hh	2010-12-04 17:20:49.000000000 +0100
 @@ -15,6 +15,7 @@
  #include <list>
  #include <string>
@@ -18,8 +18,8 @@
  
  #include <time.h>
  #include <pwd.h>
---- /tmp/autoEditor-1.20/TigrFoundation-2.0/OptionResult.hh.old	2010-12-04 17:21:35.000000000 +0100
-+++ /tmp/autoEditor-1.20/TigrFoundation-2.0/OptionResult.hh	2010-12-04 17:22:02.000000000 +0100
+--- a/OptionResult.hh	2010-12-04 17:21:35.000000000 +0100
++++ b/OptionResult.hh	2010-12-04 17:22:02.000000000 +0100
 @@ -12,6 +12,7 @@
  #define OPTIONRESULT_HH 1
  
@@ -28,8 +28,8 @@
  #include <map>
  #include "Exceptions.hh"
  
---- /tmp/autoEditor-1.20/TigrFoundation-2.0/Options.hh.old	2010-12-04 17:22:37.000000000 +0100
-+++ /tmp/autoEditor-1.20/TigrFoundation-2.0/Options.hh	2010-12-04 17:23:01.000000000 +0100
+--- a/Options.hh	2010-12-04 17:22:37.000000000 +0100
++++ b/Options.hh	2010-12-04 17:23:01.000000000 +0100
 @@ -11,6 +11,7 @@
  #ifndef OPTIONS_HH
  #define OPTIONS_HH 1
@@ -38,8 +38,8 @@
  #include <list>
  #include <map>
  #include <set>
---- /tmp/autoEditor-1.20/TigrFoundation-2.0/FileSystem.cc.old	2010-12-04 17:24:02.000000000 +0100
-+++ /tmp/autoEditor-1.20/TigrFoundation-2.0/FileSystem.cc	2010-12-04 17:24:12.000000000 +0100
+--- a/FileSystem.cc	2010-12-04 17:24:02.000000000 +0100
++++ b/FileSystem.cc	2010-12-04 17:24:12.000000000 +0100
 @@ -55,7 +55,7 @@
    {
      // Check to see if path was given
@@ -49,8 +49,8 @@
      
      if (end_of_path)
      {
---- /tmp/autoEditor-1.20/TigrFoundation-2.0/Options.cc.old	2010-12-04 17:24:53.000000000 +0100
-+++ /tmp/autoEditor-1.20/TigrFoundation-2.0/Options.cc	2010-12-04 17:25:15.000000000 +0100
+--- a/Options.cc	2010-12-04 17:24:53.000000000 +0100
++++ b/Options.cc	2010-12-04 17:25:15.000000000 +0100
 @@ -25,6 +25,7 @@
   *  written to stderr is prefixed with (stderr).
   */
diff --git a/sci-biology/tigr-foundation-libs/tigr-foundation-libs-2.0-r1.ebuild b/sci-biology/tigr-foundation-libs/tigr-foundation-libs-2.0-r1.ebuild
deleted file mode 100644
index 330e67f3d..000000000
--- a/sci-biology/tigr-foundation-libs/tigr-foundation-libs-2.0-r1.ebuild
+++ /dev/null
@@ -1,30 +0,0 @@
-# Copyright 1999-2017 Gentoo Foundation
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=6
-
-inherit eutils
-
-DESCRIPTION="TIGR Foundation for C++"
-HOMEPAGE="http://sourceforge.net/apps/mediawiki/amos/index.php?title=AutoEditor"
-SRC_URI="ftp://ftp.cbcb.umd.edu/pub/software/autoEditor/autoEditor-1.20.tar.gz"
-
-# the one bundled in autoEditor-1.20/TigrFoundation-2.0/ is same with the one in bambus
-# but in bambus-2.33/src/TIGR_Foundation_CC/ there are 3 getopt.* files in addition
-
-LICENSE="Artistic"
-SLOT="0"
-KEYWORDS="~amd64 ~x86"
-IUSE=""
-
-S="${WORKDIR}"/autoEditor-1.20/TigrFoundation-2.0
-
-src_prepare(){
-	epatch "${FILESDIR}"/TigrFoundation-all-patches.patch
-	sed -i "s:/export/usr/local:${ED}/usr:g" Makefile || die
-	default
-}
-
-src_install(){
-	emake install DESTDIR="${D}/${EPREFIX}"/usr # Makefile does not respect DESTDIR
-}
diff --git a/sci-biology/tigr-foundation-libs/tigr-foundation-libs-2.0-r2.ebuild b/sci-biology/tigr-foundation-libs/tigr-foundation-libs-2.0-r2.ebuild
new file mode 100644
index 000000000..18eec4e53
--- /dev/null
+++ b/sci-biology/tigr-foundation-libs/tigr-foundation-libs-2.0-r2.ebuild
@@ -0,0 +1,26 @@
+# Copyright 1999-2022 Gentoo Authors
+# Distributed under the terms of the GNU General Public License v2
+
+EAPI=8
+
+DESCRIPTION="TIGR Foundation for C++"
+HOMEPAGE="https://sourceforge.net/projects/amos/"
+SRC_URI="ftp://ftp.cbcb.umd.edu/pub/software/autoEditor/autoEditor-1.20.tar.gz"
+
+# the one bundled in autoEditor-1.20/TigrFoundation-2.0/ is same with the one in bambus
+# but in bambus-2.33/src/TIGR_Foundation_CC/ there are 3 getopt.* files in addition
+
+LICENSE="Artistic"
+SLOT="0"
+KEYWORDS="~amd64 ~x86"
+
+S="${WORKDIR}/autoEditor-1.20/TigrFoundation-2.0"
+
+PATCHES=(
+	"${FILESDIR}/TigrFoundation-all-patches.patch"
+)
+
+src_install(){
+	sed -i "s:/export/usr/local:${ED}/usr:g" Makefile || die
+	DESTDIR="${ED}/usr" emake install # Makefile does not respect DESTDIR
+}
diff --git a/sci-biology/tmhmm/Manifest b/sci-biology/tmhmm/Manifest
deleted file mode 100644
index 875ce562e..000000000
--- a/sci-biology/tmhmm/Manifest
+++ /dev/null
@@ -1 +0,0 @@
-DIST tmhmm-2.0c.Linux.tar.gz 191561 SHA256 761a87ca82c174e0e6660c5065f257ef0b201fab98f934e1342291e4e673ca40
diff --git a/sci-biology/tmhmm/metadata.xml b/sci-biology/tmhmm/metadata.xml
deleted file mode 100644
index 8417d1580..000000000
--- a/sci-biology/tmhmm/metadata.xml
+++ /dev/null
@@ -1,8 +0,0 @@
-<?xml version="1.0" encoding="UTF-8"?>
-<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
-<pkgmetadata>
-	<maintainer type="project">
-		<email>sci-biology@gentoo.org</email>
-		<name>Gentoo Biology Project</name>
-	</maintainer>
-</pkgmetadata>
diff --git a/sci-biology/tmhmm/tmhmm-2.0c.ebuild b/sci-biology/tmhmm/tmhmm-2.0c.ebuild
deleted file mode 100644
index bdb57e464..000000000
--- a/sci-biology/tmhmm/tmhmm-2.0c.ebuild
+++ /dev/null
@@ -1,38 +0,0 @@
-# Copyright 1999-2017 Gentoo Foundation
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=6
-
-DESCRIPTION="Prediction of transmembrane helices in proteins"
-HOMEPAGE="http://www.cbs.dtu.dk/services/TMHMM/"
-SRC_URI="${P}.Linux.tar.gz"
-
-LICENSE="tmhmm"
-SLOT="0"
-KEYWORDS="~amd64 ~x86"
-
-RESTRICT="fetch"
-
-S="TMHMM${PV}"
-
-pkg_nofetch() {
-	einfo "Please visit ${HOMEPAGE} and obtain the file"
-	einfo "\"${SRC_URI}\", then place it in ${DISTDIR}"
-}
-
-src_prepare() {
-	sed -i '1 i #!/usr/bin/env perl' "${S}"/bin/tmhmm* || die
-	sed -i '1 a $opt_basedir = "/opt/tmhmm";' "${S}"/bin/tmhmm || die
-}
-
-src_install() {
-	exeinto /opt/${PN}/bin
-	doexe bin/*
-
-	insinto /opt/${PN}/lib
-	doins lib/*
-
-	dosym ../${PN}/bin/tmhmm /opt/bin/tmhmm
-
-	dodoc README TMHMM2.0.html
-}
diff --git a/sci-biology/trans-abyss/Manifest b/sci-biology/trans-abyss/Manifest
deleted file mode 100644
index 647c12f67..000000000
--- a/sci-biology/trans-abyss/Manifest
+++ /dev/null
@@ -1 +0,0 @@
-DIST trans-ABySS-v1.4.8_20130916.tar.gz 1861658 BLAKE2B 922a23bcbbfc1570c229e70e272f779f344f7307c00913f36d7fd427a049007e1069fa4cf11a9c85c87bb16c881822f5e8eeea383a0a920a29bd772ed508e9d1 SHA512 ad4c72401097385c6c80830bc4d43ccbbc634101ed1e6e397d710d5d0a24ec19d2239739bd5b8c2591a8d8a889c46cf05d013dfe015b0a0fcf32223200d8c4b3
diff --git a/sci-biology/trans-abyss/metadata.xml b/sci-biology/trans-abyss/metadata.xml
deleted file mode 100644
index 138cb7705..000000000
--- a/sci-biology/trans-abyss/metadata.xml
+++ /dev/null
@@ -1,12 +0,0 @@
-<?xml version="1.0" encoding="UTF-8"?>
-<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
-<pkgmetadata>
-	<maintainer type="person">
-		<email>mmokrejs@fold.natur.cuni.cz</email>
-		<name>Martin Mokrejs</name>
-	</maintainer>
-	<maintainer type="project">
-		<email>sci-biology@gentoo.org</email>
-		<name>Gentoo Biology Project</name>
-	</maintainer>
-</pkgmetadata>
diff --git a/sci-biology/trans-abyss/trans-abyss-1.4.8.ebuild b/sci-biology/trans-abyss/trans-abyss-1.4.8.ebuild
deleted file mode 100644
index dbb2d668f..000000000
--- a/sci-biology/trans-abyss/trans-abyss-1.4.8.ebuild
+++ /dev/null
@@ -1,24 +0,0 @@
-# Copyright 1999-2015 Gentoo Foundation
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=5
-
-DESCRIPTION="Analyze and combine multiple assemblies from abyss"
-HOMEPAGE="http://www.bcgsc.ca/platform/bioinfo/software/trans-abyss"
-SRC_URI="http://www.bcgsc.ca/platform/bioinfo/software/trans-abyss/releases/${PV}/trans-ABySS-v${PV}_20130916.tar.gz"
-
-# http://www.bcgsc.ca/platform/bioinfo/license/bcca_2010
-LICENSE="bcca_2010"
-SLOT="0"
-KEYWORDS="~amd64 ~x86"
-IUSE=""
-
-# perl and python
-DEPEND=""
-RDEPEND="${DEPEND}"
-
-S="${WORKDIR}"/trans-ABySS-v"${PV}"
-
-# TODO
-#src_install(){
-#}
diff --git a/sci-biology/trf-bin/Manifest b/sci-biology/trf-bin/Manifest
index a02d742dd..648e780ba 100644
--- a/sci-biology/trf-bin/Manifest
+++ b/sci-biology/trf-bin/Manifest
@@ -1,2 +1,2 @@
-DIST trf409.linux32 116944 SHA256 09da272ea67fbfac67e65050d2c95f3f739b73cb8087ad569654f326988bda3c SHA512 41397d9973b93b58532d2a16d4fa19f21863da233abc17073a52909676f7a45a7bf3dbbbc58b934de9428b1067d9fadc825a6a6d1d99aa93ebe6d3d4b0da81fb WHIRLPOOL f6c315363bde49b79e4f02a65c38d197621f3ae1de1ee22a6e813cbafa60043858993b0eaac1ae7e5360ba75a4b3282cef09ad1c603235dc3f86fb332a875585
+DIST trf409.linux32 116944 BLAKE2B ad12d52bc91c68afdc5b867de19d54c334bcd3e947738989b0fe9786a5ae4cf2b69d188fb900000d366cfcc2a04105b27190852424786f16d483ea5f50a6b221 SHA512 41397d9973b93b58532d2a16d4fa19f21863da233abc17073a52909676f7a45a7bf3dbbbc58b934de9428b1067d9fadc825a6a6d1d99aa93ebe6d3d4b0da81fb
 DIST trf409.linux64 116192 BLAKE2B 5fe1b0199adb70a1729576b55d18fc777ae4f2020d5aae120abdd234e8ff0dea77d01863c89acd04f6fed50ecf55a1e66a319e1aae7308f98442f13d3981f822 SHA512 1d90c7901e4487ab12ac99669278740d2ab3bc640298ef371cb302f4de51caaa048971666a034df1304a0292716c2c29ce7e40b8a5b2a145ce4133f99aecc86d
diff --git a/sci-biology/trf-bin/trf-bin-4.09.ebuild b/sci-biology/trf-bin/trf-bin-4.09.ebuild
index 896f7fb7c..7d3a9a8b5 100644
--- a/sci-biology/trf-bin/trf-bin-4.09.ebuild
+++ b/sci-biology/trf-bin/trf-bin-4.09.ebuild
@@ -1,9 +1,7 @@
-# Copyright 1999-2017 Gentoo Foundation
+# Copyright 1999-2021 Gentoo Authors
 # Distributed under the terms of the GNU General Public License v2
 
-EAPI=6
-
-inherit eutils
+EAPI=7
 
 MY_PV="${PV/.}" # drop the dot
 MY_PN="trf"
diff --git a/sci-biology/trf/Manifest b/sci-biology/trf/Manifest
deleted file mode 100644
index ac58bc510..000000000
--- a/sci-biology/trf/Manifest
+++ /dev/null
@@ -1,4 +0,0 @@
-DIST trf.definitions.html 7108 BLAKE2B f01da2ad7328721f28b7d643e98110843dd2d65f2bf634a0146796f3136814e32e5e748921f24a1a63d46cac325f61c4f862462399ae1337cb828853a28cda64 SHA512 69b333ba8da97216350102dd054bf97679e36563a9371e9872bcd4d279519cd6179c7d8580b84564ff4dde2b89dc1803c4868ead5a8781efa39a7be27653d1ab
-DIST trf.unix.help.html 8258 SHA256 635961550fbef3083e9d318617c3d1ff743636275a8077dd5d58766c2c2a5353 SHA512 fa274dc2eef227fdb1e0ce661d73b397188921a3ea2f7bd3d8d8af787ccd3b8b8534d7c284b24157786a244ead55cdec89315785b01abd7d9f8d94e843e788a7 WHIRLPOOL 6e8ca9b6a09acbcce1f799a844a68b4c8e77e6e849df596b7746a31c4b370bb8bc4168370c0ce0d79bb676191c7c64805e42414705420b30409781fb0e0626c5
-DIST trf.whatnew.html 11945 BLAKE2B be44f5dd637250220b75fa41a20a74c3c00ae932de1a0d000aade391bb2163021bfd17b591329b5b3565adfee1da52ff7925c964bacffe9c38c3860270de653d SHA512 bacdcae046107de57fb73b0ba62be5e3eb47b4293b94a87b8f5984ad83635ffef6e74f950dbe20540118a26909e01b3621ee71ba8ba5a3b263fba6550aab6531
-DIST trf404.linux 89853 BLAKE2B 36abf95c88a5b8793e875a276f1494af4df48ff3b3f095e07683589d84eaadfb54099c1764dcd437158c356dcd9d55dd274e7e41515ef098ee2a929493cc0d83 SHA512 c1aa05e394d47ea153df3082258f9a089aa59976963e9ac5d5816ef9dcd95c47e2e46861d1b2aae52b5ea9950a823a2449dd0d8426b04f2b738f5552c319393e
diff --git a/sci-biology/trf/metadata.xml b/sci-biology/trf/metadata.xml
deleted file mode 100644
index 8417d1580..000000000
--- a/sci-biology/trf/metadata.xml
+++ /dev/null
@@ -1,8 +0,0 @@
-<?xml version="1.0" encoding="UTF-8"?>
-<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
-<pkgmetadata>
-	<maintainer type="project">
-		<email>sci-biology@gentoo.org</email>
-		<name>Gentoo Biology Project</name>
-	</maintainer>
-</pkgmetadata>
diff --git a/sci-biology/trf/trf-4.07b.ebuild b/sci-biology/trf/trf-4.07b.ebuild
deleted file mode 100644
index ecfb560b1..000000000
--- a/sci-biology/trf/trf-4.07b.ebuild
+++ /dev/null
@@ -1,42 +0,0 @@
-# Copyright 1999-2017 Gentoo Foundation
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=6
-
-MY_P="${PN}404"
-
-DESCRIPTION="Tandem Repeats Finder"
-HOMEPAGE="http://tandem.bu.edu/trf/trf.html"
-SRC_URI="
-	http://tandem.bu.edu/trf/downloads/${MY_P}.linux
-	http://tandem.bu.edu/trf/trf.unix.help.html
-	http://tandem.bu.edu/trf/trf.definitions.html
-	http://tandem.bu.edu/trf/trf.whatnew.html"
-
-LICENSE="trf"	# http://tandem.bu.edu/trf/trf.license.html
-SLOT="0"
-KEYWORDS="~amd64 ~x86"
-RESTRICT="mirror bindist"
-
-S="${WORKDIR}"
-
-QA_PREBUILT="opt/${PN}/.*"
-
-src_unpack() {
-	cp "${DISTDIR}/${MY_P}.linux" "${S}/${MY_P}.linux.exe" || die
-}
-
-src_install() {
-	exeinto /opt/${PN}
-	doexe trf404.linux.exe
-	dosym ../${PN}/${MY_P}.linux.exe /opt/bin/trf
-	# GTK version (http://tandem.bu.edu/trf/downloads/trf400.linuxgtk.exe) has broken linking
-	#if use gtk; then
-	#	doexe trf400.linuxgtk.exe
-	#	make_desktop_entry /opt/${PN}/trf400.linuxgtk.exe "Tandem Repeats Finder" || die
-	#fi
-	dodoc \
-		"${DISTDIR}/"trf.unix.help.html \
-		"${DISTDIR}/"trf.definitions.html \
-		"${DISTDIR}/"trf.whatnew.html
-}
diff --git a/sci-biology/trim_galore/Manifest b/sci-biology/trim_galore/Manifest
deleted file mode 100644
index 3f46bbb6e..000000000
--- a/sci-biology/trim_galore/Manifest
+++ /dev/null
@@ -1 +0,0 @@
-DIST trim_galore_v0.4.0.zip 1271343 SHA256 b7146c4a3c541910925ab4b490b754c467d4641bfd53e304884d837f95e859ba SHA512 71a742fe0f5d851f46bd21c3da2fdea5f6b048462179fb4784e49e7fd82fca51a521eda97f18844f6edbcf7e222189cef995c05d0433139b931dc8a351ce2924 WHIRLPOOL 40b40ff3032632083e7c2ce876eb116a05896b0500e981120b32acc93063499bc520aac4d7059fb6e8fa67ffdf0c5736f13717a3522dfa5e4099114b3a16d752
diff --git a/sci-biology/trim_galore/metadata.xml b/sci-biology/trim_galore/metadata.xml
deleted file mode 100644
index 138cb7705..000000000
--- a/sci-biology/trim_galore/metadata.xml
+++ /dev/null
@@ -1,12 +0,0 @@
-<?xml version="1.0" encoding="UTF-8"?>
-<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
-<pkgmetadata>
-	<maintainer type="person">
-		<email>mmokrejs@fold.natur.cuni.cz</email>
-		<name>Martin Mokrejs</name>
-	</maintainer>
-	<maintainer type="project">
-		<email>sci-biology@gentoo.org</email>
-		<name>Gentoo Biology Project</name>
-	</maintainer>
-</pkgmetadata>
diff --git a/sci-biology/trim_galore/trim_galore-0.4.0.ebuild b/sci-biology/trim_galore/trim_galore-0.4.0.ebuild
deleted file mode 100644
index 2ef6d591e..000000000
--- a/sci-biology/trim_galore/trim_galore-0.4.0.ebuild
+++ /dev/null
@@ -1,26 +0,0 @@
-# Copyright 1999-2015 Gentoo Foundation
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=5
-
-DESCRIPTION="Perl wrapper around Cutadapt and FastQC to adapter and quality trimming"
-HOMEPAGE="http://www.bioinformatics.babraham.ac.uk/projects/trim_galore"
-SRC_URI="http://www.bioinformatics.babraham.ac.uk/projects/trim_galore/trim_galore_v${PV}.zip"
-LICENSE="GPL-3"
-SLOT="0"
-KEYWORDS=""
-IUSE=""
-
-DEPEND=""
-RDEPEND="
-	dev-lang/perl
-	sci-biology/cutadapt
-	sci-biology/fastqc
-	${DEPEND}"
-
-S="${WORKDIR}"
-
-src_install(){
-	dobin trim_galore
-	dodoc *.pdf
-}
diff --git a/sci-biology/trimmomatic/Manifest b/sci-biology/trimmomatic/Manifest
index ca56aa644..d46449f08 100644
--- a/sci-biology/trimmomatic/Manifest
+++ b/sci-biology/trimmomatic/Manifest
@@ -1,2 +1,2 @@
-DIST Trimmomatic-Src-0.38.zip 108472 BLAKE2B c0f3f48000103544715d1259d276ccb1ab9e5460fad3011faafbbfac9d6c49c3b0507e0024bff1e89b0dc1c7a19751765932f080c57d71faabe4779a0aa3bf90 SHA512 79e25bd83d2cdb145fbefe3a23cfcf6de758c2ec0565bd03a7af2deb2f62deb24ac7f8a169507ba1e219bb36b70e814c081232e62a31c8200ceecbb2bdcd9d8a
-DIST trimmomatic-0.38_manual.pdf 338248 BLAKE2B 846833b9e263e2bdeca29a4d2474248ff7eb1d65434314bd21dc401b00ca38208a2747474d8ac49be07c45bd48d23e3ecebbd46abe85dd5db2dddd3c935b7670 SHA512 a306ce82f5f67c51f3ce62be9758c3c49cb6363932e1d55bb171d102b6f400a1fd3518263bf74c7ba3bac596630c6654ec7de6b055566d182eb6c9ae68e3ed38
+DIST Trimmomatic-Src-0.39.zip 108940 BLAKE2B cf4ec487409f678f5350fc1ca51b26722a6421171a74c8972f97a873317ba82d818ecb6bc1411faca4155b3f2849f439a42cd6638986acd349cc3eb301b4131f SHA512 ded529706b9bdbfc5c1c6b3ab02afa841e4aabb68ff924b0b153d0cff6c576fc27db057a3e08999ae8596fae9e275e41525bc5796edc3fa52e489973fa547fae
+DIST trimmomatic-0.39_manual.pdf 338248 BLAKE2B 846833b9e263e2bdeca29a4d2474248ff7eb1d65434314bd21dc401b00ca38208a2747474d8ac49be07c45bd48d23e3ecebbd46abe85dd5db2dddd3c935b7670 SHA512 a306ce82f5f67c51f3ce62be9758c3c49cb6363932e1d55bb171d102b6f400a1fd3518263bf74c7ba3bac596630c6654ec7de6b055566d182eb6c9ae68e3ed38
diff --git a/sci-biology/trimmomatic/trimmomatic-0.38.ebuild b/sci-biology/trimmomatic/trimmomatic-0.38.ebuild
deleted file mode 100644
index bf01fd874..000000000
--- a/sci-biology/trimmomatic/trimmomatic-0.38.ebuild
+++ /dev/null
@@ -1,35 +0,0 @@
-# Copyright 1999-2018 Gentoo Foundation
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=6
-
-inherit java-pkg-2 java-ant-2
-
-DESCRIPTION="Illumina adapter trimming tool"
-HOMEPAGE="http://www.usadellab.org/cms/?page=trimmomatic"
-SRC_URI="
-	http://www.usadellab.org/cms/uploads/supplementary/Trimmomatic/Trimmomatic-Src-${PV}.zip
-	http://www.usadellab.org/cms/uploads/supplementary/Trimmomatic/TrimmomaticManual_V0.32.pdf -> "${P}"_manual.pdf"
-
-# http://www.usadellab.org/cms/uploads/supplementary/Trimmomatic/Trimmomatic-0.32.zip
-
-LICENSE="GPL-3"
-SLOT="0"
-KEYWORDS="~amd64 ~x86"
-IUSE=""
-
-DEPEND=">=virtual/jdk-1.6:*
-	dev-java/ant-core"
-RDEPEND=">=virtual/jre-1.6:*"
-
-# somehow fails to build with oracle-jdk-bin-1.7 while ibm-jdk-bin-1.6 works
-
-EANT_BUILD_TARGET="dist"
-
-src_install() {
-	java-pkg_newjar "dist/jar/${P}.jar" "${PN}.jar"
-	insinto /usr/share/${PN}/Illumina
-	doins adapters/*.fa
-	insinto /usr/share/doc/${P}
-	dodoc "${DISTDIR}"/${P}_manual.pdf
-}
diff --git a/sci-biology/trimmomatic/trimmomatic-0.39.ebuild b/sci-biology/trimmomatic/trimmomatic-0.39.ebuild
new file mode 100644
index 000000000..331ab5cd8
--- /dev/null
+++ b/sci-biology/trimmomatic/trimmomatic-0.39.ebuild
@@ -0,0 +1,34 @@
+# Copyright 1999-2021 Gentoo Authors
+# Distributed under the terms of the GNU General Public License v2
+
+EAPI=7
+
+inherit java-pkg-2 java-ant-2
+
+DESCRIPTION="Illumina adapter trimming tool"
+HOMEPAGE="http://www.usadellab.org/cms/?page=trimmomatic"
+SRC_URI="
+	http://www.usadellab.org/cms/uploads/supplementary/Trimmomatic/Trimmomatic-Src-${PV}.zip
+	http://www.usadellab.org/cms/uploads/supplementary/Trimmomatic/TrimmomaticManual_V0.32.pdf -> "${P}"_manual.pdf"
+
+# http://www.usadellab.org/cms/uploads/supplementary/Trimmomatic/Trimmomatic-0.32.zip
+
+LICENSE="GPL-3"
+SLOT="0"
+KEYWORDS="~amd64 ~x86"
+
+DEPEND=">=virtual/jdk-1.6:*
+	dev-java/ant-core
+	app-arch/unzip"
+RDEPEND=">=virtual/jre-1.6:*"
+
+# somehow fails to build with oracle-jdk-bin-1.7 while ibm-jdk-bin-1.6 works
+
+EANT_BUILD_TARGET="dist"
+
+src_install() {
+	java-pkg_newjar "dist/jar/${P}.jar" "${PN}.jar"
+	insinto /usr/share/${PN}/Illumina
+	doins adapters/*.fa
+	dodoc "${DISTDIR}"/${P}_manual.pdf
+}
diff --git a/sci-biology/trinityrnaseq/Manifest b/sci-biology/trinityrnaseq/Manifest
index c8bda9d39..153f208fd 100644
--- a/sci-biology/trinityrnaseq/Manifest
+++ b/sci-biology/trinityrnaseq/Manifest
@@ -1,4 +1 @@
-DIST trinityrnaseq-2.0.6.tar.gz 158619106 BLAKE2B 9be82099f8c563ac6520462feffcdcb1d0cec7fde4b5d3a430abde987bc419f6011642c1a2548de27734493ac8728e9c24d8a67bd8201108a9b1e26020aca2d6 SHA512 459461db38e42d0b77b9cb84b1ecc4ccb03bbe0fe6e970915d5df58e8c98368a07fab7a157679b0d4247b729b49966b1f3927abee11059e5e3a3406e8e598d45
-DIST trinityrnaseq-2.1.1.tar.gz 137541420 SHA256 012ccb42e1eab8a5b14c4e78becf3e7e69964d76c17fcca8110db6ffe63d3e0b SHA512 36b67211902871c6dbba31a074c4e92d2e925c57fe54bf59418874282e283693d2d9b4e14333385a7adcef3edbf928bc1001df105b56412841662c45a9a74f3f WHIRLPOOL 73869a3f2dbc72011723429d6ac3acb3fde8c7ccfe4122510afbea9fdfc732a457c8f5d16573190448c4e0d2c5dcc437e2f9cfe96f4239368c95b2da79fd52bd
-DIST trinityrnaseq-2.2.0.tar.gz 174159736 SHA256 f34603e56ac76a81447dd230b31248d5890ecffee8ef264104d4f1fa7fe46c9e SHA512 87ba299df990d066ae6aa8a870c3a27647da0d78cf0a48c5084967865d4e278ce383b3f6e54541d4626654f0638f12c739aaed04ed770bc99ed84b94c2e6e5c3 WHIRLPOOL 027ccd958288991c4871cfa6b370d14bc2bf586bc1ffc3247795aaf305368caac373343682f11cde6d72a65422c95718b89fee65ac77c04a21c7c3aaa4c8112d
-DIST trinityrnaseq-2.6.6.tar.gz 21796945 BLAKE2B 0d5ff2d7e2ba11d231695c19e0125d507a5f510a944fc3ab68c3e5073b6bb4ef0973bc02b207b79ea6adbc58a469eeb894610bd765c11ccf3963deaeebe3ff00 SHA512 2e4438010cc987706b8f7dd343cdd84024318f2e7370bce40be6d54b07b17bfd6a4a28c27400250384e4ffd560386fde3b9c51987f86b376e11c4daa10d6b7cb
+DIST trinityrnaseq-2.13.2.tar.gz 310355363 BLAKE2B 63055e11976a8d70b2c10b4859b25c8a27f23c05d1f5196eca137f281812aa54558b7eda343498a61af0c5aaa0e8d255e5d0a81e53c906859b455e0725180f95 SHA512 8399e12516d6d3cfde6803323b3bfb9ae249528fc79c08a6b290f42e7498783e6b300b89f9890570b28b2847ebe0f7894f59a888bf47d51190aad9e7c1ce54b7
diff --git a/sci-biology/trinityrnaseq/files/trinityrnaseq-2.1.1-disable_some_plugins.patch b/sci-biology/trinityrnaseq/files/trinityrnaseq-2.1.1-disable_some_plugins.patch
deleted file mode 100644
index 43a06ae53..000000000
--- a/sci-biology/trinityrnaseq/files/trinityrnaseq-2.1.1-disable_some_plugins.patch
+++ /dev/null
@@ -1,20 +0,0 @@
---- trinityrnaseq-2.1.1/trinity-plugins/Makefile.ori	2015-11-21 00:34:52.310075544 +0100
-+++ trinityrnaseq-2.1.1/trinity-plugins/Makefile	2015-11-21 00:37:16.260075920 +0100
-@@ -10,7 +10,7 @@
- PARAFLY_CODE=parafly-code
- TRIMMOMATIC_CODE=Trimmomatic-0.32
- 
--trinity_essentials: jellyfish scaffold_iworm_contigs_target fastool_target parafly_target trimmomatic_target samtools
-+trinity_essentials: scaffold_iworm_contigs_target fastool_target parafly_target
- 
- trimmomatic_target:
- 	ln -sf ${TRIMMOMATIC_CODE} Trimmomatic
-@@ -31,7 +31,7 @@
- #	cd htslib-1.2.1 && ./configure && $(MAKE)
- 	tar xvf ${HTSLIB_CODE} && cd htslib && $(MAKE)
- 
--scaffold_iworm_contigs_target: htslib_target
-+scaffold_iworm_contigs_target:
- 	cd scaffold_iworm_contigs && $(MAKE)
- 
- fastool_target:
diff --git a/sci-biology/trinityrnaseq/files/trinityrnaseq-2.11.0-fix-compilation.patch b/sci-biology/trinityrnaseq/files/trinityrnaseq-2.11.0-fix-compilation.patch
new file mode 100644
index 000000000..8647aad3a
--- /dev/null
+++ b/sci-biology/trinityrnaseq/files/trinityrnaseq-2.11.0-fix-compilation.patch
@@ -0,0 +1,12 @@
+diff --git a/trinity-plugins/bamsifter/sift_bam_max_cov.cpp b/trinity-plugins/bamsifter/sift_bam_max_cov.cpp
+index e8ecbcf..ccdbd27 100644
+--- a/trinity-plugins/bamsifter/sift_bam_max_cov.cpp
++++ b/trinity-plugins/bamsifter/sift_bam_max_cov.cpp
+@@ -10,6 +10,7 @@
+ #include <set>
+ #include <utility>
+ #include <vector>
++#include <string>
+ 
+ #include "htslib/sam.h"
+ #include "htslib/bgzf.h"
diff --git a/sci-biology/trinityrnaseq/files/trinityrnaseq-2.6.6-disable_some_plugins.patch b/sci-biology/trinityrnaseq/files/trinityrnaseq-2.6.6-disable_some_plugins.patch
deleted file mode 100644
index 02f4d5d8a..000000000
--- a/sci-biology/trinityrnaseq/files/trinityrnaseq-2.6.6-disable_some_plugins.patch
+++ /dev/null
@@ -1,23 +0,0 @@
---- trinity-plugins/Makefile	2018-04-21 20:01:58.389880915 +0200
-+++ trinity-plugins/Makefile	2018-04-21 20:03:31.752684954 +0200
-@@ -7,7 +7,7 @@
- 
- 
- 
--trinity_essentials: seqtk_target parafly_target trimmomatic_target
-+trinity_essentials: parafly_target
- 
- trimmomatic_target:
- 	ln -sf ${TRIMMOMATIC_CODE} Trimmomatic
-@@ -39,11 +39,9 @@
- 	cd COLLECTL && tar xvf ${COLLECTL_CODE}.src.tar.gz && ln -sf ${COLLECTL_CODE} collectl
- 
- clean:
--	rm -rf ./seqtk-trinity-0.0.2
- 	cd scaffold_iworm_contigs && $(MAKE) clean
- 	cd parafly-code && $(MAKE) clean
- 	rm -f ./parafly # rm symlink
--	rm -f ./Trimmomatic # rm symlink
- 	cd slclust && $(MAKE) clean
- 	cd COLLECTL && rm -rf ${COLLECTL_CODE} && rm -f collectl
- 	@echo "\n\n** Done cleaning plugins area **"
diff --git a/sci-biology/trinityrnaseq/trinityrnaseq-2.0.6.ebuild b/sci-biology/trinityrnaseq/trinityrnaseq-2.0.6.ebuild
deleted file mode 100644
index 1941db22a..000000000
--- a/sci-biology/trinityrnaseq/trinityrnaseq-2.0.6.ebuild
+++ /dev/null
@@ -1,66 +0,0 @@
-# Copyright 1999-2018 Gentoo Foundation
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=5
-
-PERL_EXPORT_PHASE_FUNCTIONS=no
-inherit perl-module eutils toolchain-funcs
-
-# Butterfly should not require any special compilation, as its written in Java and already provided as portable precompiled software ...
-# There is bundled jellyfish-1.1.11 source tree
-
-DESCRIPTION="Transcriptome assembler for RNA-seq reads"
-HOMEPAGE="http://trinityrnaseq.github.io/"
-SRC_URI="https://github.com/${PN}/${PN}/archive/v${PV}.tar.gz -> ${P}.tar.gz"
-
-LICENSE="BSD-BroadInstitute"
-SLOT="0"
-KEYWORDS=""
-IUSE=""
-
-DEPEND=""
-RDEPEND="${DEPEND}
-	sci-biology/parafly
-	>=sci-biology/jellyfish-2.1.4:2
-	sci-biology/samtools:0.1-legacy
-	>=sci-biology/GAL-0.2.1
-	dev-perl/IO-All"
-# ReleaseNotes mentions that <sci-biology/samtools-1.1 is needed
-# version of bundled jellyfish is 2.1.4
-
-# optionally install https://github.com/HpcGridRunner/HpcGridRunner/releases
-
-#src_compile(){
-#	emake all
-#	emake plugins # bundled copies of TransDecoder, trimmomatic, fastool, parafly
-#}
-
-src_install(){
-	perl_set_version
-	dobin Trinity util/*.pl
-	# should become a new package depending on dev-perl/IO-All
-	dobin trinity-plugins/fstrozzi-Fastool-7c3e034f05/fastool
-	dodoc trinity-plugins/fstrozzi-Fastool-7c3e034f05/README.md
-	#
-	insinto /usr/share/"${PN}"/util
-	rm -rf trinity-plugins/GAL_0.2.1 util/fasta_tool
-	doins -r util/*
-	#
-	dobin Inchworm/bin/*
-	cd Chrysalis || die
-	dobin MakeDepend checkLock BreakTransByPairs Chrysalis GraphFromFasta IsoformAugment JoinTransByPairs QuantifyGraph ReadsToTranscripts RunButterfly TranscriptomeFromVaryK analysis/ReadsToComponents.pl
-	cd "${S}" || die
-	insinto "${VENDOR_LIB}/${PN}"
-	doins util/misc/PerlLib/*.pm PerlLib/*.pm
-	insinto "${VENDOR_LIB}/${PN}"/KmerGraphLib
-	doins PerlLib/KmerGraphLib/*.pm
-	insinto "${VENDOR_LIB}/${PN}"/CDNA
-	doins PerlLib/CDNA/*.pm
-	insinto "${VENDOR_LIB}/${PN}"/HPC
-	doins PerlLib/HPC/*.pm
-	insinto "${VENDOR_LIB}/${PN}"/Simulate
-	doins PerlLib/Simulate/*.pm
-	insinto "${VENDOR_LIB}/${PN}"/CanvasXpress
-	doins PerlLib/CanvasXpress/*.pm
-	chmod a+rx -R "${ED}/${VENDOR_LIB}/${PN}"
-}
diff --git a/sci-biology/trinityrnaseq/trinityrnaseq-2.1.1.ebuild b/sci-biology/trinityrnaseq/trinityrnaseq-2.1.1.ebuild
deleted file mode 100644
index 05759d02d..000000000
--- a/sci-biology/trinityrnaseq/trinityrnaseq-2.1.1.ebuild
+++ /dev/null
@@ -1,75 +0,0 @@
-# Copyright 1999-2018 Gentoo Foundation
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=5
-
-PERL_EXPORT_PHASE_FUNCTIONS=no
-inherit perl-module eutils toolchain-funcs
-
-# Butterfly should not require any special compilation, as its written in Java and already provided as portable precompiled software ...
-
-DESCRIPTION="Transcriptome assembler for RNA-seq reads"
-HOMEPAGE="http://trinityrnaseq.github.io/"
-SRC_URI="https://github.com/${PN}/${PN}/archive/v${PV}.tar.gz -> ${P}.tar.gz"
-
-LICENSE="BSD-BroadInstitute"
-SLOT="0"
-KEYWORDS=""
-IUSE=""
-
-DEPEND=""
-RDEPEND="${DEPEND}
-	sci-biology/parafly
-	>=sci-biology/jellyfish-2.1.4:2
-	>=sci-libs/htslib-1.2.1
-	sci-biology/samtools:0.1-legacy
-	>=sci-biology/trimmomatic-0.32
-	>=sci-biology/GAL-0.2.1
-	dev-perl/IO-All"
-# ReleaseNotes mentions that <sci-biology/samtools-1.1 is needed
-# version of bundled jellyfish is 2.1.4
-# version of bundled samtools is 0.1.19
-# version of bundled htslib is 1.2.1
-# version of bundled GAL is 0.2.1
-# version of bundled trimmomatic is 0.32
-
-# optionally install https://github.com/HpcGridRunner/HpcGridRunner/releases
-
-src_prepare(){
-	epatch "${FILESDIR}"/trinityrnaseq-2.1.1-disable_some_plugins.patch
-}
-
-#src_compile(){
-#	emake all
-#	emake plugins # bundled copies of TransDecoder, trimmomatic, fastool, parafly
-#}
-
-src_install(){
-	perl_set_version
-	dobin Trinity util/*.pl
-	# should become a new package depending on dev-perl/IO-All
-	dobin trinity-plugins/fstrozzi-Fastool-7c3e034f05/fastool
-	dodoc trinity-plugins/fstrozzi-Fastool-7c3e034f05/README.md
-	#
-	insinto /usr/share/"${PN}"/util
-	rm -rf trinity-plugins/GAL_0.2.1 util/fasta_tool
-	doins -r util/*
-	#
-	dobin Inchworm/bin/*
-	cd Chrysalis  || die
-	dobin MakeDepend checkLock BreakTransByPairs Chrysalis GraphFromFasta IsoformAugment JoinTransByPairs QuantifyGraph ReadsToTranscripts RunButterfly TranscriptomeFromVaryK analysis/ReadsToComponents.pl
-	cd "${S}" || die
-	insinto "${VENDOR_LIB}/${PN}"
-	doins util/misc/PerlLib/*.pm PerlLib/*.pm
-	insinto "${VENDOR_LIB}/${PN}"/KmerGraphLib
-	doins PerlLib/KmerGraphLib/*.pm
-	insinto "${VENDOR_LIB}/${PN}"/CDNA
-	doins PerlLib/CDNA/*.pm
-	insinto "${VENDOR_LIB}/${PN}"/HPC
-	doins PerlLib/HPC/*.pm
-	insinto "${VENDOR_LIB}/${PN}"/Simulate
-	doins PerlLib/Simulate/*.pm
-	insinto "${VENDOR_LIB}/${PN}"/CanvasXpress
-	doins PerlLib/CanvasXpress/*.pm
-	chmod a+rx -R "${ED}/${VENDOR_LIB}/${PN}"
-}
diff --git a/sci-biology/trinityrnaseq/trinityrnaseq-2.13.2.ebuild b/sci-biology/trinityrnaseq/trinityrnaseq-2.13.2.ebuild
new file mode 100644
index 000000000..3b94d9713
--- /dev/null
+++ b/sci-biology/trinityrnaseq/trinityrnaseq-2.13.2.ebuild
@@ -0,0 +1,45 @@
+# Copyright 1999-2022 Gentoo Authors
+# Distributed under the terms of the GNU General Public License v2
+
+EAPI=8
+
+inherit perl-module
+
+DESCRIPTION="Transcriptome assembler for RNA-seq reads"
+HOMEPAGE="https://github.com/Trinotate/Trinotate.github.io/wiki"
+SRC_URI="https://github.com/${PN}/${PN}/releases/download/Trinity-v${PV}/${PN}-v${PV}.FULL_with_extendedTestData.tar.gz -> ${P}.tar.gz"
+S="${WORKDIR}/${PN}-v${PV}"
+
+LICENSE="BSD-BroadInstitute"
+SLOT="0"
+KEYWORDS="~amd64"
+
+DEPEND=""
+RDEPEND="${DEPEND}
+	sci-biology/parafly
+	>=sci-biology/jellyfish-2.2.6:2
+	>=sci-libs/htslib-1.2.1
+	>=sci-biology/samtools-1.3:0
+	>=sci-biology/trimmomatic-0.36
+	>=sci-biology/GAL-0.2.1
+	dev-perl/IO-All
+	sci-biology/seqtools
+"
+
+PATCHES=(
+	"${FILESDIR}/${PN}-2.11.0-fix-compilation.patch"
+)
+
+src_compile(){
+	# missing submodule for bamsifter
+	emake no_bamsifter
+	emake plugins
+}
+
+src_install(){
+	# fix the install path
+	sed -e "s:/usr/local/bin:${ED}/usr/bin:g" \
+		-i util/support_scripts/trinity_installer.py || die
+	dodir /usr/bin
+	default
+}
diff --git a/sci-biology/trinityrnaseq/trinityrnaseq-2.2.0.ebuild b/sci-biology/trinityrnaseq/trinityrnaseq-2.2.0.ebuild
deleted file mode 100644
index 6d8da6ab9..000000000
--- a/sci-biology/trinityrnaseq/trinityrnaseq-2.2.0.ebuild
+++ /dev/null
@@ -1,76 +0,0 @@
-# Copyright 1999-2018 Gentoo Foundation
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=5
-
-PERL_EXPORT_PHASE_FUNCTIONS=no
-inherit perl-module eutils toolchain-funcs
-
-# Butterfly should not require any special compilation, as its written in Java and already provided as portable precompiled software ...
-
-DESCRIPTION="Transcriptome assembler for RNA-seq reads"
-HOMEPAGE="http://trinityrnaseq.github.io/"
-SRC_URI="https://github.com/${PN}/${PN}/archive/v${PV}.tar.gz -> ${P}.tar.gz"
-
-LICENSE="BSD-BroadInstitute"
-SLOT="0"
-KEYWORDS=""
-IUSE=""
-
-DEPEND=""
-RDEPEND="${DEPEND}
-	sci-biology/parafly
-	>=sci-biology/jellyfish-2.1.4:2
-	>=sci-libs/htslib-1.2.1
-	sci-biology/samtools:0.1-legacy
-	>=sci-biology/trimmomatic-0.32
-	>=sci-biology/GAL-0.2.1
-	dev-perl/IO-All"
-# ReleaseNotes mentions that <sci-biology/samtools-1.1 is needed
-# version of bundled jellyfish is 2.1.4
-# version of bundled samtools is 0.1.19
-# version of bundled htslib is 1.2.1
-# version of bundled GAL is 0.2.1
-# version of bundled trimmomatic is 0.32
-
-# optionally install https://github.com/HpcGridRunner/HpcGridRunner/releases
-
-src_prepare(){
-	epatch "${FILESDIR}"/trinityrnaseq-2.1.1-disable_some_plugins.patch
-}
-
-#src_compile(){
-#	emake all
-#	emake plugins # bundled copies of TransDecoder, trimmomatic, fastool, parafly
-#}
-
-src_install(){
-	perl_set_version
-	dobin Trinity util/*.pl
-	# should become a new package depending on dev-perl/IO-All
-	dobin trinity-plugins/fstrozzi-Fastool-7c3e034f05/fastool
-	dodoc trinity-plugins/fstrozzi-Fastool-7c3e034f05/README.md
-	#
-	# https://github.com/trinityrnaseq/trinityrnaseq/issues/126
-	insinto /usr/share/"${PN}"/util
-	rm -rf trinity-plugins/GAL_0.2.1 util/fasta_tool
-	doins -r util/*
-	#
-	dobin Inchworm/bin/*
-	cd Chrysalis  || die
-	dobin MakeDepend checkLock BreakTransByPairs Chrysalis GraphFromFasta IsoformAugment JoinTransByPairs QuantifyGraph ReadsToTranscripts RunButterfly TranscriptomeFromVaryK analysis/ReadsToComponents.pl
-	cd "${S}" || die
-	insinto "${VENDOR_LIB}/${PN}"
-	doins util/misc/PerlLib/*.pm PerlLib/*.pm
-	insinto "${VENDOR_LIB}/${PN}"/KmerGraphLib
-	doins PerlLib/KmerGraphLib/*.pm
-	insinto "${VENDOR_LIB}/${PN}"/CDNA
-	doins PerlLib/CDNA/*.pm
-	insinto "${VENDOR_LIB}/${PN}"/HPC
-	doins PerlLib/HPC/*.pm
-	insinto "${VENDOR_LIB}/${PN}"/Simulate
-	doins PerlLib/Simulate/*.pm
-	insinto "${VENDOR_LIB}/${PN}"/CanvasXpress
-	doins PerlLib/CanvasXpress/*.pm
-	chmod a+rx -R "${ED}/${VENDOR_LIB}/${PN}"
-}
diff --git a/sci-biology/trinityrnaseq/trinityrnaseq-2.6.6.ebuild b/sci-biology/trinityrnaseq/trinityrnaseq-2.6.6.ebuild
deleted file mode 100644
index 238766eed..000000000
--- a/sci-biology/trinityrnaseq/trinityrnaseq-2.6.6.ebuild
+++ /dev/null
@@ -1,76 +0,0 @@
-# Copyright 1999-2018 Gentoo Foundation
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=5
-
-PERL_EXPORT_PHASE_FUNCTIONS=no
-inherit perl-module eutils toolchain-funcs
-
-# Butterfly should not require any special compilation, as its written in Java and already provided as portable precompiled software ...
-
-DESCRIPTION="Transcriptome assembler for RNA-seq reads"
-HOMEPAGE="http://trinityrnaseq.github.io/"
-SRC_URI="https://github.com/trinityrnaseq/trinityrnaseq/archive/Trinity-v${PV}.tar.gz -> ${P}.tar.gz"
-
-LICENSE="BSD-BroadInstitute"
-SLOT="0"
-KEYWORDS="" # PERL5INC path is wrong when /usr/bin/Trinity is executed
-IUSE=""
-
-DEPEND=""
-RDEPEND="${DEPEND}
-	sci-biology/parafly
-	>=sci-biology/jellyfish-2.2.6:2
-	>=sci-libs/htslib-1.2.1
-	>=sci-biology/samtools-1.3:0
-	>=sci-biology/trimmomatic-0.36
-	>=sci-biology/GAL-0.2.1
-	dev-perl/IO-All
-	sci-biology/seqtools"
-# optionally install https://github.com/HpcGridRunner/HpcGridRunner/releases
-# has the following "plugins" (aka bundled 3rd-party code)
-# slclust
-# DEXseq_util
-# COLLECTL
-# ParaFly-0.1.0
-
-S="${WORKDIR}"/trinityrnaseq-Trinity-v"${PV}"
-
-src_prepare(){
-	epatch "${FILESDIR}"/"${P}"-disable_some_plugins.patch
-}
-
-#src_compile(){
-#	emake all
-#	emake plugins # bundled copies of TransDecoder, trimmomatic, fastool, parafly
-#}
-
-src_install(){
-	dodoc Chrysalis/chrysalis.notes
-	dodoc Changelog.txt
-	perl_set_version
-	dobin Trinity util/*.pl
-	dobin Inchworm/bin/*
-	cd Chrysalis  || die
-	dobin MakeDepend checkLock BreakTransByPairs BubbleUpClustering Chrysalis CreateIwormFastaBundle GraphFromFasta GraphFromFasta_MPI IsoformAugment JoinTransByPairs QuantifyGraph ReadsToTranscripts ReadsToTranscripts_MPI ReadsToTranscripts_MPI_chang RunButterfly TranscriptomeFromVaryK analysis/ReadsToComponents.pl
-	cd ../util/R || die
-	insinto /usr/share/"${PN}"/R
-	doins *.R
-	cd ../PBS || die
-	insinto /usr/share/"${PN}"/PBS
-	doins *
-	cd .. || die
-	cp -rp support_scripts misc "${ED}"/usr/share/"${PN}"/ || die
-	cd "${S}" || die
-	insinto "${VENDOR_LIB}/${PN}"
-	doins util/misc/PerlLib/*.pm PerlLib/*.pm
-	insinto "${VENDOR_LIB}/${PN}"/KmerGraphLib
-	doins PerlLib/KmerGraphLib/*.pm
-	insinto "${VENDOR_LIB}/${PN}"/CDNA
-	doins PerlLib/CDNA/*.pm
-	insinto "${VENDOR_LIB}/${PN}"/Simulate
-	doins PerlLib/Simulate/*.pm
-	insinto "${VENDOR_LIB}/${PN}"/CanvasXpress
-	doins PerlLib/CanvasXpress/*.pm
-	chmod a+rx -R "${ED}/${VENDOR_LIB}/${PN}"
-}
diff --git a/sci-biology/trowel/Manifest b/sci-biology/trowel/Manifest
deleted file mode 100644
index 0f559502e..000000000
--- a/sci-biology/trowel/Manifest
+++ /dev/null
@@ -1 +0,0 @@
-DIST trowel.0.1.4.1.src.tar.gz 298643 BLAKE2B 10ef63713ed7fd9cec772d0786b8262a9ebffb363a3f310a5dfabe1229428eee6158398f4f5d4426795bab9093d308d9bfa03e09f13a8fdc2755998fea8fcb26 SHA512 1b2951cfbda73affeefa514ca43af245bca68347d404ee6081327b5214f0f6649612a8dbd26a137c6f1fef6a5c0194e7e79864e5733f18944fca9086ae3c6a07
diff --git a/sci-biology/trowel/metadata.xml b/sci-biology/trowel/metadata.xml
deleted file mode 100644
index 0f267b755..000000000
--- a/sci-biology/trowel/metadata.xml
+++ /dev/null
@@ -1,15 +0,0 @@
-<?xml version="1.0" encoding="UTF-8"?>
-<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
-<pkgmetadata>
-	<maintainer type="person">
-		<email>mmokrejs@fold.natur.cuni.cz</email>
-		<name>Martin Mokrejs</name>
-	</maintainer>
-	<maintainer type="project">
-		<email>sci-biology@gentoo.org</email>
-		<name>Gentoo Biology Project</name>
-	</maintainer>
-	<upstream>
-		<remote-id type="sourceforge">downloads</remote-id>
-	</upstream>
-</pkgmetadata>
diff --git a/sci-biology/trowel/trowel-0.1.4.1.ebuild b/sci-biology/trowel/trowel-0.1.4.1.ebuild
deleted file mode 100644
index 4f4e5283e..000000000
--- a/sci-biology/trowel/trowel-0.1.4.1.ebuild
+++ /dev/null
@@ -1,19 +0,0 @@
-# Copyright 1999-2015 Gentoo Foundation
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=5
-
-DESCRIPTION="Error corrector for genomic Illumina FASTQ reads"
-HOMEPAGE="http://sourceforge.net/projects/trowel-ec"
-SRC_URI="http://downloads.sourceforge.net/project/trowel-ec/src/trowel.0.1.4.1.src.tar.gz"
-
-LICENSE="GPL-3"
-SLOT="0"
-KEYWORDS="~amd64"
-IUSE=""
-
-DEPEND=">=dev-libs/boost-1.53.0
-	>=dev-cpp/sparsehash-2.0.2"
-RDEPEND="${DEPEND}"
-
-S="${WORKDIR}"/trowel.0.1.4.1.src
diff --git a/sci-biology/twinscan/Manifest b/sci-biology/twinscan/Manifest
index ecf54c4a0..81f4d8d86 100644
--- a/sci-biology/twinscan/Manifest
+++ b/sci-biology/twinscan/Manifest
@@ -1 +1 @@
-DIST twinscan-4.1.2.tar.gz 5894833 BLAKE2B 5d8b14694961eca181d8b7aeb0387f31b6f9eac77674a919df2d3c2aec1d65f845f4dd4ed937deb6c3d338389e545d9692d6f6b57db6cc7bac5ccadfb74c8714 SHA512 d216f790f6d0f35a070575d1aa4b5e1866c00132168b381b9177b076b1b2a16f2ecd7a88aa443d7ba6b8f62c3ec2595ba33c4608a674e09d94e9f7dc6a181327
+DIST iscan-4.1.2.tar.gz 5894833 BLAKE2B 5d8b14694961eca181d8b7aeb0387f31b6f9eac77674a919df2d3c2aec1d65f845f4dd4ed937deb6c3d338389e545d9692d6f6b57db6cc7bac5ccadfb74c8714 SHA512 d216f790f6d0f35a070575d1aa4b5e1866c00132168b381b9177b076b1b2a16f2ecd7a88aa443d7ba6b8f62c3ec2595ba33c4608a674e09d94e9f7dc6a181327
diff --git a/sci-biology/twinscan/twinscan-4.1.2-r1.ebuild b/sci-biology/twinscan/twinscan-4.1.2-r1.ebuild
index 7c8993f9f..ce3651f3d 100644
--- a/sci-biology/twinscan/twinscan-4.1.2-r1.ebuild
+++ b/sci-biology/twinscan/twinscan-4.1.2-r1.ebuild
@@ -1,26 +1,30 @@
-# Copyright 1999-2016 Gentoo Foundation
+# Copyright 1999-2021 Gentoo Authors
 # Distributed under the terms of the GNU General Public License v2
 
-EAPI=5
+EAPI=7
 
-PERL_EXPORT_PHASE_FUNCTIONS=no
-inherit perl-module eutils toolchain-funcs
+inherit perl-module toolchain-funcs
 
 DESCRIPTION="iscan (aka twinscan and N-SCAN), Pairagon wrapper: Gene structure pred. pipeline"
-HOMEPAGE="http://mblab.wustl.edu/software/twinscan"
-SRC_URI="http://mblab.wustl.edu/software/download/iscan-${PV}.tar_.gz -> ${P}.tar.gz"
+HOMEPAGE="https://mblab.wustl.edu/software.html"
+#SRC_URI="https://mblab.wustl.edu/software/download/iscan-${PV}.tar_.gz -> ${P}.tar.gz"
+# ERROR: cannot verify mblab.wustl.edu's certificate, issued by ‘CN=InCommon RSA Server CA,OU=InCommon,O=Internet2,L=Ann Arbor,ST=MI,C=US’:
+# Unable to locally verify the issuer's authority.
+# To connect to mblab.wustl.edu insecurely, use `--no-check-certificate'.
+SRC_URI="iscan-${PV}.tar.gz"
 
 LICENSE="all-rights-reserved"
 SLOT="0"
-IUSE=""
 KEYWORDS="~amd64 ~x86"
 
 DEPEND="dev-libs/glib:2"
 RDEPEND="${DEPEND}"
 
 S="${WORKDIR}/N-SCAN"
+RESTRICT="test fetch"
 
 src_prepare() {
+	default
 	sed "1 a use lib '/usr/share/${PN}/lib/perl5';" -i "${S}"/bin/*.pl || die
 	sed '/my $blast_param/ s/#//' -i "${S}/bin/runTwinscan2.pl" || die
 	tc-export CC AR RANLIB
@@ -42,14 +46,13 @@ src_install() {
 	# also fix a Genscan++ToZoe.pl Nscan_driver.pl runTwinscan2.pl run_iscan.pl run_iscan_cons.pl run_iscan_cons_list.pl test.pl
 	rm src/test.pl || die
 	dobin bin/iscan bin/zoe2gtf bin/*.pl src/*.pl
-	dolib lib/libzoe.a
+	dolib.so lib/libzoe.a
 	insinto /usr/share/${PN}
 	doins -r parameters
 	insinto /usr/share/${PN}/src
 	doins src/*.zhmm
 	perl_set_version
-	insinto ${VENDOR_LIB}/${PN}
-	doins lib/perl5/*.pm
+	perl_domodule lib/perl5/*.pm
 	echo "TWINSCAN=/usr" > "${S}"/99${PN}
 	doenvd "${S}"/99${PN}
 	rm -rf examples/tmp
diff --git a/sci-biology/ugene/Manifest b/sci-biology/ugene/Manifest
index 1288bb2e7..46f39c632 100644
--- a/sci-biology/ugene/Manifest
+++ b/sci-biology/ugene/Manifest
@@ -1 +1 @@
-DIST ugene-1.20.0.tar.gz 21194907 SHA256 618987aa599d8880b53fd6bf1938b2b57d7a6112c909b8cce9b21b05e7a36c5f SHA512 063d15de5ddd39876ac5364d7ec4313080bf2816fb5d0b78b9b8de9b5ae9b473019c6ee3f5494acba8391a6a052344d4737dbc968c6f307ce449d46717a1293a WHIRLPOOL 5c084b8a2bcbc583443d9406ad5c6fc612bf31959e84361af9f7112470fc8af22bdc02828e4bdbf160399fc661b2aaf4bbb8478ec882d7c25d6a41c757b90ec6
+DIST ugene-40.1.tar.gz 28791083 BLAKE2B 85cb0fdbd10c68e8e6933f5131744d21011febfaa2d96b07d3b5a53e69dfc6ee0de14d8b63dcf4e11ea83edd2724af4ca6e76344ed6961d294fac5d010d8e771 SHA512 b2e056532a2ecf2a396d9bdd7a44f3af1e3e49d1ab2d95169be5583a4e59b43773d02224987b096fdd48f91568c65dc9fa575702a881b40fdabfdc776cd16af1
diff --git a/sci-biology/ugene/metadata.xml b/sci-biology/ugene/metadata.xml
index a3daeebd2..36e8936e5 100644
--- a/sci-biology/ugene/metadata.xml
+++ b/sci-biology/ugene/metadata.xml
@@ -9,4 +9,7 @@
 		<email>sci@gentoo.org</email>
 		<name>Gentoo Science Project</name>
 	</maintainer>
+	<upstream>
+		<remote-id type="github">ugeneunipro/ugene</remote-id>
+	</upstream>
 </pkgmetadata>
diff --git a/sci-biology/ugene/ugene-1.20.0.ebuild b/sci-biology/ugene/ugene-1.20.0.ebuild
deleted file mode 100644
index 3aa9dfebe..000000000
--- a/sci-biology/ugene/ugene-1.20.0.ebuild
+++ /dev/null
@@ -1,42 +0,0 @@
-# Copyright 1999-2016 Gentoo Foundation
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=5
-
-inherit qmake-utils
-
-DESCRIPTION="A free open-source cross-platform bioinformatics software"
-HOMEPAGE="http://ugene.unipro.ru"
-SRC_URI="http://${PN}.unipro.ru/downloads/${P}.tar.gz"
-
-LICENSE="GPL-2"
-SLOT="0"
-KEYWORDS="~amd64"
-IUSE="cpu_flags_x86_sse2"
-
-# http://ugene.net/download.html states Qt5.4 and QtWebkit but:
-#   Project MESSAGE: Cannot build Unipro UGENE with Qt version 4.8.7
-#   Project ERROR: Use at least Qt 5.2.1.
-DEPEND="
-	>=dev-qt/qtgui-5.2.1
-	>=dev-qt/qtscript-5.2.1[scripttools]"
-RDEPEND="${DEPEND}"
-
-LANGS="cs en ru zh"
-
-src_configure() {
-	local CONFIG_OPTS
-	if use amd64; then
-		CONFIG_OPTS+=( CONFIG+="x64" )
-	elif use ppc; then
-		CONFIG_OPTS+=( CONFIG+="ppc" )
-	fi
-
-	use cpu_flags_x86_sse2 && CONFIG_OPTS+=( use_sse2 )
-
-	eqmake5 $CONFIG_OPTS || die
-}
-
-src_install() {
-	emake DESTDIR="${D}" INSTALL_ROOT="${ED}" install
-}
diff --git a/sci-biology/ugene/ugene-40.1.ebuild b/sci-biology/ugene/ugene-40.1.ebuild
new file mode 100644
index 000000000..ab96355c4
--- /dev/null
+++ b/sci-biology/ugene/ugene-40.1.ebuild
@@ -0,0 +1,48 @@
+# Copyright 1999-2021 Gentoo Authors
+# Distributed under the terms of the GNU General Public License v2
+
+EAPI=7
+
+inherit qmake-utils xdg
+
+DESCRIPTION="A free open-source cross-platform bioinformatics software"
+HOMEPAGE="http://ugene.unipro.ru"
+SRC_URI="https://github.com/ugeneunipro/ugene/archive/${PV}.tar.gz -> ${P}.tar.gz"
+
+LICENSE="GPL-2"
+SLOT="0"
+KEYWORDS="~amd64"
+
+IUSE="cpu_flags_x86_sse2"
+
+DEPEND="
+	>=dev-qt/qtgui-5.4.2
+	>=dev-qt/qtsvg-5.4.2
+	>=dev-qt/qtscript-5.4.2[scripttools]
+"
+RDEPEND="${DEPEND}"
+
+src_prepare() {
+	default
+	# remove Werror
+	sed -i -e '/-Werror=/d' CMakeLists.txt || die
+	sed -i -e '/-Werror=/d' src/ugene_globals.pri || die
+}
+
+src_configure() {
+	local CONFIG_OPTS
+	if use amd64; then
+		CONFIG_OPTS+=( CONFIG+="x64" )
+	elif use ppc; then
+		CONFIG_OPTS+=( CONFIG+="ppc" )
+	fi
+
+	use cpu_flags_x86_sse2 && CONFIG_OPTS+=( use_sse2 )
+
+	eqmake5 $CONFIG_OPTS || die
+}
+
+src_install() {
+	einstalldocs
+	emake DESTDIR="${D}" INSTALL_ROOT="${ED}" install
+}
diff --git a/sci-biology/vague-bin/vague-bin-1.0.5.ebuild b/sci-biology/vague-bin/vague-bin-1.0.5.ebuild
index bbb594948..79ed9fc48 100644
--- a/sci-biology/vague-bin/vague-bin-1.0.5.ebuild
+++ b/sci-biology/vague-bin/vague-bin-1.0.5.ebuild
@@ -1,20 +1,18 @@
-# Copyright 1999-2018 Gentoo Foundation
+# Copyright 1999-2021 Gentoo Authors
 # Distributed under the terms of the GNU General Public License v2
 
-EAPI=5
+EAPI=7
 
 inherit java-pkg-2
 
-[ "$PV" == "9999" ] && inherit git-r3
-
 DESCRIPTION="GUI for Velvet de novo assembler"
-HOMEPAGE="http://www.vicbioinformatics.com/software.vague.shtml"
+HOMEPAGE="https://vicbioinformatics.com/software.vague.shtml"
 
 if [ "$PV" == "9999" ]; then
+	inherit git-r3
 	EGIT_REPO_URI="https://github.com/Victorian-Bioinformatics-Consortium/vague"
-	KEYWORDS=""
 else
-	SRC_URI="http://www.vicbioinformatics.com/vague-${PV}.tar.gz"
+	SRC_URI="https://vicbioinformatics.com/vague-${PV}.tar.gz"
 	KEYWORDS="~amd64"
 fi
 
@@ -23,14 +21,17 @@ SLOT="0"
 
 RDEPEND="
 	>=virtual/jre-1.5:*
-	sci-biology/velvet
-	sci-biology/velvetk"
+	sci-biology/velvet"
 DEPEND=">=virtual/jdk-1.5:*"
 
 S="${WORKDIR}"/vague-${PV}
 
+PATCHES=(
+	"${FILESDIR}"/vague.patch
+)
+
 src_prepare(){
-	epatch "${FILESDIR}"/vague.patch
+	default
 	sed -e "s#-jar /usr/share#-jar ${EPREFIX}/usr/share#" -i vague || die
 }
 
diff --git a/sci-biology/vcflib/Manifest b/sci-biology/vcflib/Manifest
new file mode 100644
index 000000000..a535ea547
--- /dev/null
+++ b/sci-biology/vcflib/Manifest
@@ -0,0 +1 @@
+DIST vcflib-1.0.3.tar.gz 19213097 BLAKE2B 142685d494759d61e7b0ed40e9d91b78d7856038b6fb73f7f26f80152b0a85006bd6f3e9b5e7422e74841eb9a21e3a86efc3f63545e3fea7545fb91a7475b409 SHA512 16c7b3932fd4e6a985adbc1131dd0b48028501be3023d85fd57b4efccaf071a11ba6f49219df723f6eacc2787218e8f3f2b318e016633ce3e829139b698154a2
diff --git a/sci-biology/vcflib/vcflib-1.0.3.ebuild b/sci-biology/vcflib/vcflib-1.0.3.ebuild
new file mode 100644
index 000000000..d4cf1e02f
--- /dev/null
+++ b/sci-biology/vcflib/vcflib-1.0.3.ebuild
@@ -0,0 +1,54 @@
+# Copyright 1999-2022 Gentoo Authors
+# Distributed under the terms of the GNU General Public License v2
+
+EAPI=8
+
+inherit cmake toolchain-funcs
+
+DESCRIPTION="VCF/BED utils, Genotype Phenotype Association Toolkit (GPAT++)"
+HOMEPAGE="https://github.com/vcflib/vcflib"
+SRC_URI="https://github.com/vcflib/vcflib/archive/refs/tags/v${PV}.tar.gz -> ${P}.tar.gz"
+
+LICENSE="MIT-with-advertising"
+SLOT="0"
+# No proper release tarball for this release yet
+KEYWORDS=""
+IUSE="openmp"
+
+DEPEND="
+	sys-libs/zlib
+	sci-libs/htslib
+	sci-biology/tabixpp
+"
+RDEPEND="${DEPEND}"
+
+src_prepare(){
+	cmake_src_prepare
+	sed -e "s/^CXX = g++/CXX = $(tc-getCXX)/" -i Makefile || die
+	sed -e "s/^CXXFLAGS = -O3/CXXFLAGS = ${CXXFLAGS}/" -i Makefile || die
+	# openmp detection stolen from velvet-1.2.10.ebuild
+	if use openmp; then
+		if [[ $(tc-getCXX) =~ g++ ]]; then
+			local eopenmp=-fopenmp
+		elif [[ $(tc-getCXX) =~ cxx ]]; then
+			local eopenmp=-openmp
+			sed -e "s/-fopenmp/${eopenmp}/" -i Makefile || die
+		else
+			elog "Cannot detect compiler type so not setting openmp support"
+		fi
+	fi
+}
+
+src_compile(){
+	mycmakeargs=(
+		-DOPENMP="$(use_enable openmp)"
+		-DHTSLIB_LOCAL=ON
+	)
+	cmake_src_compile
+}
+#
+# src_install(){
+# 	dobin bin/*
+# 	dolib lib/* # install libvcflib.a
+# 	dodoc README.md
+# }
diff --git a/sci-biology/vcflib/vcflib-9999.ebuild b/sci-biology/vcflib/vcflib-9999.ebuild
deleted file mode 100644
index 91a14eca3..000000000
--- a/sci-biology/vcflib/vcflib-9999.ebuild
+++ /dev/null
@@ -1,53 +0,0 @@
-# Copyright 1999-2017 Gentoo Foundation
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=6
-
-inherit git-r3 toolchain-funcs
-
-DESCRIPTION="VCF/BED utils, Genotype Phenotype Association Toolkit (GPAT++)"
-HOMEPAGE="https://github.com/vcflib/vcflib"
-EGIT_REPO_URI="https://github.com/vcflib/vcflib.git"
-
-# vcflib is incorporated into several projects, such as freebayes
-
-LICENSE="MIT-with-advertising"
-SLOT="0"
-KEYWORDS=""
-IUSE="openmp"
-
-DEPEND=""
-RDEPEND="${DEPEND}"
-# contains bundled sci-biology/htslib ?
-# see also ./include for possible traces of other bundled sw
-
-src_prepare(){
-	default
-	sed -e "s/^CXX = g++/CXX = $(tc-getCXX)/" -i Makefile || die
-	sed -e "s/^CXXFLAGS = -O3/CXXFLAGS = ${CXXFLAGS}/" -i Makefile || die
-	# openmp detection stolen from velvet-1.2.10.ebuild
-	if use openmp; then
-		if [[ $(tc-getCXX) =~ g++ ]]; then
-			local eopenmp=-fopenmp
-		elif [[ $(tc-getCXX) =~ cxx ]]; then
-			local eopenmp=-openmp
-			sed -e "s/-fopenmp/${eopenmp}/" -i Makefile || die
-		else
-			elog "Cannot detect compiler type so not setting openmp support"
-		fi
-	fi
-}
-
-src_compile(){
-	if use openmp ; then
-		emake openmp
-	else
-		emake
-	fi
-}
-
-src_install(){
-	dobin bin/*
-	dolib lib/* # install libvcflib.a
-	dodoc README.md
-}
diff --git a/sci-biology/vcftools/Manifest b/sci-biology/vcftools/Manifest
deleted file mode 100644
index 90b2bb4ad..000000000
--- a/sci-biology/vcftools/Manifest
+++ /dev/null
@@ -1 +0,0 @@
-DIST vcftools-0.1.15.tar.gz 481398 BLAKE2B c6a2578d35f02b4bd33a4dfc6c356228e0c59617440f03ec48a13ac4eb13135ea1dbd3119937a65734cad3d3144c901a05f6de97de505fd4f39b24046c67e17a SHA512 9ef5688202b263139c7e6f3ff0d6f2565f08bc7b5a67dba7b5f6845791b34ae23515e65b2b294502fe8a8343d061612fa9c5f11742323cd70c2f8409609e0366
diff --git a/sci-biology/vcftools/metadata.xml b/sci-biology/vcftools/metadata.xml
deleted file mode 100644
index 0253c16be..000000000
--- a/sci-biology/vcftools/metadata.xml
+++ /dev/null
@@ -1,12 +0,0 @@
-<?xml version="1.0" encoding="UTF-8"?>
-<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
-<pkgmetadata>
-	<maintainer type="project">
-		<email>sci-biology@gentoo.org</email>
-		<name>Gentoo Biology Project</name>
-	</maintainer>
-	<upstream>
-		<remote-id type="github">vcftools/vcftools</remote-id>
-		<remote-id type="sourceforge">vcftools</remote-id>
-	</upstream>
-</pkgmetadata>
diff --git a/sci-biology/vcftools/vcftools-0.1.15.ebuild b/sci-biology/vcftools/vcftools-0.1.15.ebuild
deleted file mode 100644
index 3748c67f0..000000000
--- a/sci-biology/vcftools/vcftools-0.1.15.ebuild
+++ /dev/null
@@ -1,36 +0,0 @@
-# Copyright 1999-2017 Gentoo Foundation
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=6
-
-inherit flag-o-matic perl-functions toolchain-funcs
-
-MY_PV=${PV/_pre/}
-S="${WORKDIR}/${PN}-${MY_PV}"
-
-DESCRIPTION="Tools for working with VCF (Variant Call Format) files"
-HOMEPAGE="http://vcftools.sourceforge.net/"
-SRC_URI="https://github.com/${PN}/${PN}/releases/download/v${PV}/${PN}-${PV}.tar.gz"
-
-LICENSE="LGPL-3"
-SLOT="0"
-KEYWORDS="~amd64 ~x86"
-IUSE="lapack"
-
-RDEPEND="
-	sys-libs/zlib
-	dev-lang/perl:=
-	lapack? ( virtual/lapack )"
-DEPEND="${RDEPEND}
-	virtual/pkgconfig"
-
-src_configure() {
-	perl_set_version
-
-	append-flags $($(tc-getPKG_CONFIG) --cflags lapack)
-	append-libs $($(tc-getPKG_CONFIG) --libs lapack)
-
-	econf \
-		$(use_enable lapack pca) \
-		--with-pmdir="${VENDOR_LIB#${EPREFIX}/usr}"
-}
diff --git a/sci-biology/velvetk/Manifest b/sci-biology/velvetk/Manifest
deleted file mode 100644
index 56070ef2f..000000000
--- a/sci-biology/velvetk/Manifest
+++ /dev/null
@@ -1 +0,0 @@
-DIST velvetk.pl 5862 BLAKE2B adae9add735093b4b4424c26fad82d205cbfe4eb50efc7297fb6bec1b8b67d39adbf80c03e9488be9ab7c5fa84d4d4a1c5a4e3a84eedfb8a75fe42d991511629 SHA512 2f89964888730ffa0fc1fee043af0f050ff856e059ca541f664637d27c88c0fc306bec5d078683641863c0e17c09c76dfaf5e7ebe2eed42714cca3725239af51
diff --git a/sci-biology/velvetk/metadata.xml b/sci-biology/velvetk/metadata.xml
deleted file mode 100644
index 138cb7705..000000000
--- a/sci-biology/velvetk/metadata.xml
+++ /dev/null
@@ -1,12 +0,0 @@
-<?xml version="1.0" encoding="UTF-8"?>
-<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
-<pkgmetadata>
-	<maintainer type="person">
-		<email>mmokrejs@fold.natur.cuni.cz</email>
-		<name>Martin Mokrejs</name>
-	</maintainer>
-	<maintainer type="project">
-		<email>sci-biology@gentoo.org</email>
-		<name>Gentoo Biology Project</name>
-	</maintainer>
-</pkgmetadata>
diff --git a/sci-biology/velvetk/velvetk-20120606.ebuild b/sci-biology/velvetk/velvetk-20120606.ebuild
deleted file mode 100644
index a2fdb7c25..000000000
--- a/sci-biology/velvetk/velvetk-20120606.ebuild
+++ /dev/null
@@ -1,24 +0,0 @@
-# Copyright 1999-2015 Gentoo Foundation
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=5
-
-inherit perl-module
-
-DESCRIPTION="Estimate the best k-mer size to use for your Velvet de novo assembly"
-HOMEPAGE="http://www.vicbioinformatics.com/software.velvetk.shtml"
-SRC_URI="http://www.vicbioinformatics.com/velvetk.pl"
-
-LICENSE="GPL-2"
-SLOT="0"
-KEYWORDS="~amd64"
-IUSE=""
-
-DEPEND="dev-lang/perl"
-RDEPEND="${DEPEND}"
-
-S="${WORKDIR}"
-
-src_install(){
-	dobin "${DISTDIR}"/velvetk.pl
-}
diff --git a/sci-biology/verifyBamID/Manifest b/sci-biology/verifyBamID/Manifest
index 0dc22078a..b8d84bf7f 100644
--- a/sci-biology/verifyBamID/Manifest
+++ b/sci-biology/verifyBamID/Manifest
@@ -1,2 +1,2 @@
-DIST libStatGen-1.0.13.tar.gz 558682 BLAKE2B 8e9308c698110e2e3a735e14171954c2bf1e7ac7f05d6c86072389aa697246d69033a0844f4bfccce1dc74623e847c551e388e19b00469274d5ef945e080811c SHA512 bcce3dd2f343e5941857d5bca0f2960d69b3e1083da6312e018a96bb92fb8dbc91ac511e062b024720c45508aa805d3f4f6511f60201438176a898ab789e746f
+DIST libStatGen-1.0.15.tar.gz 560782 BLAKE2B e605adc37291aa3b6563698bbad0990239d71dd2ac6c4e1f70232f58a75ae2cc328f7e27c799c41caf6214c25d125083fdb6f4b77663a5a6e34d94ec199a9864 SHA512 6408ab47b9781df7fdf65302d47e90acc6fd58985680a0c5ef794d8dd2bba343cacb39b32774d60f931d98b99cd156cf7059c9af87cde5b672739bac5bda0569
 DIST verifyBamID-1.1.3.tar.gz 68447 BLAKE2B 411511edf45dd6ddd9f882f894a133fb7734c5bbab0a6b34e3b20849c25719b2566de93a4e9bc2dc119782bfe0089a772baeb53b52fad237d7c89ad98991b897 SHA512 1b39b1f7b8a40f3c6c08af5a4ad24b8aebe5dc0dc3b1bf4401632fa6cac56dc8d5e17c18f142caa5cc00c7c654f43737b2550149f4c4416166f439688634235e
diff --git a/sci-biology/verifyBamID/verifyBamID-1.1.3.ebuild b/sci-biology/verifyBamID/verifyBamID-1.1.3.ebuild
index 040816a76..a528aef5a 100644
--- a/sci-biology/verifyBamID/verifyBamID-1.1.3.ebuild
+++ b/sci-biology/verifyBamID/verifyBamID-1.1.3.ebuild
@@ -1,19 +1,16 @@
-# Copyright 1999-2017 Gentoo Foundation
+# Copyright 1999-2021 Gentoo Authors
 # Distributed under the terms of the GNU General Public License v2
 
-EAPI=6
-
-inherit toolchain-funcs
+EAPI=7
 
 DESCRIPTION="Verify sample identity/mix and genotype concordance"
 HOMEPAGE="http://genome.sph.umich.edu/wiki/VerifyBamID"
-SRC_URI="https://github.com/statgen/verifyBamID/archive/v1.1.3.tar.gz -> ${P}.tar.gz
-	https://github.com/statgen/libStatGen/archive/v1.0.13.tar.gz -> libStatGen-1.0.13.tar.gz"
+SRC_URI="https://github.com/statgen/verifyBamID/archive/v${PV}.tar.gz -> ${P}.tar.gz
+	https://github.com/statgen/libStatGen/archive/v1.0.15.tar.gz -> libStatGen-1.0.15.tar.gz"
 
 LICENSE="GPL-3+"
 SLOT="0"
 KEYWORDS="~amd64 ~x86"
-IUSE=""
 
 # DEPEND="sci-libs/libStatGen" # TODO: currently it uses its own bundled copy
 DEPEND=""
@@ -21,18 +18,18 @@ RDEPEND="${DEPEND}"
 
 src_prepare(){
 	# unpack ./libStatGen-1.0.13/ contents
-	gzip -dc "${DISTDIR}"/libStatGen-1.0.13.tar.gz | tar xf - || die
-	ln -s libStatGen-1.0.13 libStatGen || die
+	gzip -dc "${DISTDIR}"/libStatGen-1.0.15.tar.gz | tar xf - || die
+	ln -s libStatGen-1.0.15 libStatGen || die
 	cd "${WORKDIR}" || die
-	ln -s libStatGen-1.0.13 libStatGen || die
+	ln -s libStatGen-1.0.15 libStatGen || die
 	sed -e 's/-Werror//' -i verifyBamID-1.1.3/src/Makefile || die
-	sed -e 's/-Werror//' -i verifyBamID-1.1.3/libStatGen-1.0.13/general/Makefile || die
-	eapply_user
+	sed -e 's/-Werror//' -i verifyBamID-1.1.3/libStatGen-1.0.15/general/Makefile || die
+	default
 }
 
 src_compile(){
 	# LIB_PATH_GENERAL="${EPREFIX}"/usr/"$(get_libdir)" emake
-	LIB_PATH_GENERAL="../libStatGen-1.0.13" emake USER_WARNINGS=' '
+	LIB_PATH_GENERAL="../libStatGen-1.0.15" emake USER_WARNINGS=' '
 }
 
 src_install(){
diff --git a/sci-biology/vt/vt-9999.ebuild b/sci-biology/vt/vt-9999.ebuild
index 59b45030c..fbc2d7a5e 100644
--- a/sci-biology/vt/vt-9999.ebuild
+++ b/sci-biology/vt/vt-9999.ebuild
@@ -1,7 +1,7 @@
-# Copyright 1999-2017 Gentoo Foundation
+# Copyright 1999-2021 Gentoo Authors
 # Distributed under the terms of the GNU General Public License v2
 
-EAPI=5
+EAPI=7
 
 inherit git-r3 toolchain-funcs
 
@@ -31,6 +31,7 @@ RDEPEND="${DEPEND}
 
 # Compiles statically bundled version of htslib and Rmath, only libpcre2 is dynamically linked
 src_prepare(){
+	default
 	sed -e "s/= -O3/= ${CFLAGS}/" -i Makefile || die
 	sed -e 's/^CXX = /CXX ?= /' -i Makefile || die
 	sed -e "s/-g -Wall -O2/${CFLAGS}/" -i lib/htslib/Makefile || die
diff --git a/sci-biology/wcd/Manifest b/sci-biology/wcd/Manifest
deleted file mode 100644
index 82794c9c1..000000000
--- a/sci-biology/wcd/Manifest
+++ /dev/null
@@ -1,3 +0,0 @@
-DIST wcd-0.6.3.tar.gz 825166 BLAKE2B 163ae4c0dbae68630dc2424b2b5abcc8ebcb5929c41c76eb7c09fb29fb9161de064a7c064ed931771b7991b270c8c8f3bc085802a178b0dc558b63d15836ae93 SHA512 6c9a93636c201bad33b38d405ac56e8c12dbc59b0b0752bc1bf40420db2a188c76741d51d60cb13de52a0393a0d120c86862bf5d8794ef2a3892773c3d0505d8
-DIST wcd.html 8448 BLAKE2B d1561925a0f299d12c177f499a95fbc314d558c18106642c49852bd96a104bdef5271b5ea1b4312e70936db6726ea3ea54e3a942d9c9c52e806b48137321cf05 SHA512 11156d4811b7716632fbd7b0330d918ae30b6dcc9ebbd59c95d445ba465504aa68d0fa9863b3ad4b5743c929f4558d1698af03c124fd02299ef13479a80555c2
-DIST wcd.pdf 275513 BLAKE2B 049d0d8b9d6db0e2754322f69903c5680a62c007a9abf5466b21a96f778a9f537a8ec91344d729961317ff6a8b484ca870f5ee0a78fa7cec8ae4ba2d7c5f1939 SHA512 ef2e0e8bbe49a5c5b304a305d8948b253ba2bf789790941600c5d5ba74351fe41e54a66dd189a33846304a8f2a8fa4c70025e516f3b73643da71030cbded63a2
diff --git a/sci-biology/wcd/files/wcd-0.6.3-impl-decl.patch b/sci-biology/wcd/files/wcd-0.6.3-impl-decl.patch
deleted file mode 100644
index 15d851577..000000000
--- a/sci-biology/wcd/files/wcd-0.6.3-impl-decl.patch
+++ /dev/null
@@ -1,15 +0,0 @@
- src/auxcluster.c | 1 +
- 1 file changed, 1 insertion(+)
-
-diff --git a/src/auxcluster.c b/src/auxcluster.c
-index ac00a0f..e98f19f 100644
---- a/src/auxcluster.c
-+++ b/src/auxcluster.c
-@@ -2,6 +2,7 @@
- 
- #include "common.h"
- #include "strings.h"
-+#include <string.h>
- #include "assert.h"
- 
- extern SeqInfoPtr seqInfo;
diff --git a/sci-biology/wcd/files/wcd-0.6.3-ldflags.patch b/sci-biology/wcd/files/wcd-0.6.3-ldflags.patch
deleted file mode 100644
index d697d00b7..000000000
--- a/sci-biology/wcd/files/wcd-0.6.3-ldflags.patch
+++ /dev/null
@@ -1,16 +0,0 @@
- src/Makefile.am | 2 +-
- 1 file changed, 1 insertion(+), 1 deletion(-)
-
-diff --git a/src/Makefile.am b/src/Makefile.am
-index e986a91..ff87e29 100644
---- a/src/Makefile.am
-+++ b/src/Makefile.am
-@@ -7,7 +7,7 @@ wcd_CFLAGS += -DMPI
- endif
- if PTHREADS
- wcd_CFLAGS += -DPTHREADS
--wcd_LDFLAGS += -lpthread
-+wcd_LDADD = -lpthread
- endif
- if !COMPILER
- wcd_CFLAGS += -DNOINLINE 
diff --git a/sci-biology/wcd/metadata.xml b/sci-biology/wcd/metadata.xml
deleted file mode 100644
index 138cb7705..000000000
--- a/sci-biology/wcd/metadata.xml
+++ /dev/null
@@ -1,12 +0,0 @@
-<?xml version="1.0" encoding="UTF-8"?>
-<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
-<pkgmetadata>
-	<maintainer type="person">
-		<email>mmokrejs@fold.natur.cuni.cz</email>
-		<name>Martin Mokrejs</name>
-	</maintainer>
-	<maintainer type="project">
-		<email>sci-biology@gentoo.org</email>
-		<name>Gentoo Biology Project</name>
-	</maintainer>
-</pkgmetadata>
diff --git a/sci-biology/wcd/wcd-0.6.3.ebuild b/sci-biology/wcd/wcd-0.6.3.ebuild
deleted file mode 100644
index d4b797608..000000000
--- a/sci-biology/wcd/wcd-0.6.3.ebuild
+++ /dev/null
@@ -1,62 +0,0 @@
-# Copyright 1999-2015 Gentoo Foundation
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=5
-
-AUTOTOOLS_AUTORECONF=true
-
-inherit autotools-utils flag-o-matic multilib
-
-DESCRIPTION="EST sequence clustering: d2 function, edit distance, common word heuristics"
-HOMEPAGE="http://code.google.com/p/wcdest/"
-SRC_URI="http://wcdest.googlecode.com/files/wcd-express-${PV}.tar.gz -> ${P}.tar.gz
-	http://www.bioinf.wits.ac.za/~scott/wcd.html
-	http://www.bioinf.wits.ac.za/~scott/wcd.pdf"
-
-S="${WORKDIR}"/wcd-express-"${PV}"
-
-LICENSE="GPL-2"
-SLOT="0"
-KEYWORDS="~amd64 ~x86"
-IUSE="doc mpi threads"
-
-# This code (0.4.1 at least) has been tested using LAMMPI (RedHat, Suse,
-# MacOS X), MPICH (Ubuntu) and MVAPICH (Suse)
-DEPEND="mpi? ( sys-cluster/mpich2 )"
-RDEPEND=""
-
-PATCHES=(
-	"${FILESDIR}"/${P}-ldflags.patch
-	"${FILESDIR}"/${P}-impl-decl.patch
-	)
-
-src_prepare() {
-	rm -r src/*o src/.deps || die
-	autotools-utils_src_prepare
-}
-
-src_configure(){
-	local myeconfargs=()
-	use mpi && myeconfargs+=( --enable-mpi )
-
-	use threads && myeconfargs+=( --enable-pthreads )
-
-	autotools-utils_src_configure
-}
-
-src_compile() {
-	autotools-utils_src_compile
-	use doc && autotools-utils_src_compile pdf info html
-}
-
-src_install() {
-	use doc && HTML_DOCS=( doc/wcd.html doc/wcd.pdf doc/wcd.texi )
-	autotools-utils_src_install PREFIX=/usr LIBDIR="${D}"usr/$(get_libdir)
-	dodoc "${DISTDIR}"/wcd.*
-}
-
-# consider providing the EMBOSS wrapper for wcd
-# https://code.google.com/p/wcdest/downloads/detail?name=wcd_emboss_wrap_001.tar.gz
-
-# also consider ESTsim
-# https://code.google.com/p/wcdest/downloads/detail?name=estsim_distrib.tar.gz&can=2&q=
diff --git a/sci-biology/weblogo/Manifest b/sci-biology/weblogo/Manifest
deleted file mode 100644
index eb9181eff..000000000
--- a/sci-biology/weblogo/Manifest
+++ /dev/null
@@ -1 +0,0 @@
-DIST weblogo.2.8.2.tar.gz 303971 BLAKE2B fd3dd23e94a534d8a0e62331053913ca9558270a3d55484c9e9ff49bc88f3f9cd6b44a6c4dfdfdd6163327be7579b43c02722830892576ef309542fb42cd59fc SHA512 05fe94db1c82d78913141dde650d2f6c7e851e88c5b4a7707253103e562d44f9cac318a8037f14dbe605c0f5ec3a89bb806a0c199d4c43eb018ed66a980e535d
diff --git a/sci-biology/weblogo/metadata.xml b/sci-biology/weblogo/metadata.xml
deleted file mode 100644
index 138cb7705..000000000
--- a/sci-biology/weblogo/metadata.xml
+++ /dev/null
@@ -1,12 +0,0 @@
-<?xml version="1.0" encoding="UTF-8"?>
-<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
-<pkgmetadata>
-	<maintainer type="person">
-		<email>mmokrejs@fold.natur.cuni.cz</email>
-		<name>Martin Mokrejs</name>
-	</maintainer>
-	<maintainer type="project">
-		<email>sci-biology@gentoo.org</email>
-		<name>Gentoo Biology Project</name>
-	</maintainer>
-</pkgmetadata>
diff --git a/sci-biology/weblogo/weblogo-2.8.2.ebuild b/sci-biology/weblogo/weblogo-2.8.2.ebuild
deleted file mode 100644
index 09bd31ac1..000000000
--- a/sci-biology/weblogo/weblogo-2.8.2.ebuild
+++ /dev/null
@@ -1,36 +0,0 @@
-# Copyright 1999-2015 Gentoo Foundation
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=5
-
-PERL_EXPORT_PHASE_FUNCTIONS=no
-inherit eutils perl-module
-
-DESCRIPTION="generate consensus sequence logo figures"
-HOMEPAGE="http://weblogo.berkeley.edu/"
-SRC_URI="http://weblogo.berkeley.edu/release/weblogo.2.8.2.tar.gz"
-
-LICENSE="MIT"
-SLOT="0"
-KEYWORDS="~amd64 ~x86"
-IUSE=""
-
-DEPEND=""
-RDEPEND="${DEPEND}
-	app-text/ghostscript-gpl
-	media-gfx/imagemagick"
-
-S="${WORKDIR}/${PN}"
-
-src_install(){
-	perl_set_version
-	dobin seqlogo
-	insinto /usr/share/"${PN}"
-	doins logo.css logo.xml template.eps logo.conf.init clustal.dat globin.fasta test.html logo.cgi info.html README
-	doins -r img
-	insinto ${VENDOR_LIB}
-	doins *.pm
-	HTML_DOCS=( examples.html )
-	DOCS=( Crooks-2004-GR-WebLogo.pdf )
-	einstalldocs
-}
diff --git a/sci-biology/wgs-assembler/Manifest b/sci-biology/wgs-assembler/Manifest
deleted file mode 100644
index eb30e2759..000000000
--- a/sci-biology/wgs-assembler/Manifest
+++ /dev/null
@@ -1 +0,0 @@
-DIST wgs-8.3rc2.tar.bz2 24603412 BLAKE2B ac6ae82289df6f9c79ed1438459135b6ecd0b75ddd9b319d3305c06f661f1478b58b5ae9ed4587cd21c9b33497048936205a533d6a2d06a83c3b8bfc3eb15736 SHA512 10646ce59c3d557b744287b63f8f0ff494fd6919c61974389b9a3870a03b19067d58ba3f545afbc1e1dfda85cac76ea0e84474911442ae2097660cc6ea73fc44
diff --git a/sci-biology/wgs-assembler/files/wgs-assembler-8.3_rc2-rename-jellyfish.patch b/sci-biology/wgs-assembler/files/wgs-assembler-8.3_rc2-rename-jellyfish.patch
deleted file mode 100644
index d98ba7b52..000000000
--- a/sci-biology/wgs-assembler/files/wgs-assembler-8.3_rc2-rename-jellyfish.patch
+++ /dev/null
@@ -1,69 +0,0 @@
---- src/AS_PBR/PBcR.pl.ori	2015-05-20 23:28:27.000000000 +0200
-+++ src/AS_PBR/PBcR.pl	2018-04-21 16:24:14.189313208 +0200
-@@ -1259,12 +1259,12 @@
-   setGlobal("mhap", undef);
- }
- 
--if (! -e "$JELLYFISH/jellyfish") {
--   if (-e "$CA/jellyfish") {
-+if (! -e "$JELLYFISH/jellyfish2") {
-+   if (-e "$CA/jellyfish2") {
-       $JELLYFISH = $CA;
-    } else {
-       # try to use path
--      my $amosPath = `which jellyfish`;
-+      my $amosPath = `which jellyfish2`;
-       chomp $amosPath;
-       my @t = split '/', "$amosPath";
-       pop @t;                      #  blasr
-@@ -1698,7 +1698,7 @@
- }
-  
- my $ignore = "";
--if (!defined(getGlobal("bowtie")) && $cutoffSpecified == 0 && !(defined(getGlobal("mhap")) && -e "$JELLYFISH/jellyfish")) {
-+if (!defined(getGlobal("bowtie")) && $cutoffSpecified == 0 && !(defined(getGlobal("mhap")) && -e "$JELLYFISH/jellyfish2")) {
-    # run correction up thorough meryl
-    if (! -e "$wrk/temp$libraryname/0-mercounts/$asm.nmers.ovl.fasta") {
-       $cmd  = "$CA/runCA ";
-@@ -1740,20 +1740,20 @@
-     $inFile = `ls $wrk/*.$inMer.ignore |wc -l |awk '{print \$1}'`;
- }
- chomp $inFile;
--if ($inFile == 0 && !-e "$wrk/temp$libraryname/$asm.ignore" &&  -e "$JELLYFISH/jellyfish" && defined(getGlobal("mhap"))) {
-+if ($inFile == 0 && !-e "$wrk/temp$libraryname/$asm.ignore" &&  -e "$JELLYFISH/jellyfish2" && defined(getGlobal("mhap"))) {
-    my $f = makeAbsolute($fastqFile);
-    if ($f =~ /\.bz2$/i || $f =~ /\.zip$/i || $f =~ /\.gz$/i) {
-       die "Input fastq file $f is compressed. This is currently not supported, please uncompress the file and try again.";
-    }
--   $cmd  = "$JELLYFISH/jellyfish count ";
-+   $cmd  = "$JELLYFISH/jellyfish2 count ";
-    $cmd .= " -m " . getGlobal("merSize") . " -s 120000000 -t " . getGlobal("merylThreads") . " -o $wrk/temp$libraryname/$asm.mers " . makeAbsolute($fastqFile);
-    runCommand("$wrk/temp$libraryname", $cmd);
-    if ( -e "$wrk/temp$libraryname/$asm.mers_0") {
--      $cmd = "$JELLYFISH/jellyfish merge -s 120000000 -o $wrk/temp$libraryname/$asm.mers $wrk/temp$libraryname/$asm.mers_*";
-+      $cmd = "$JELLYFISH/jellyfish2 merge -s 120000000 -o $wrk/temp$libraryname/$asm.mers $wrk/temp$libraryname/$asm.mers_*";
-       runCommand("$wrk/temp$libraryname", $cmd);
-    } 
- 
--   $cmd =  "$JELLYFISH/jellyfish histo -t " . getGlobal("merylThreads") . " -f $wrk/temp$libraryname/$asm.mers > $wrk/temp$libraryname/$asm.hist";
-+   $cmd =  "$JELLYFISH/jellyfish2 histo -t " . getGlobal("merylThreads") . " -f $wrk/temp$libraryname/$asm.mers > $wrk/temp$libraryname/$asm.hist";
-    runCommand("$wrk/temp$libraryname", $cmd);
-    my $total = 0;
-    my $runningSum = 0;
-@@ -1763,7 +1763,7 @@
-    chomp $cut;
-    $cut++;
- 
--   $cmd = "$JELLYFISH/jellyfish dump -c -t -L $cut $wrk/temp$libraryname/$asm.mers |awk -v TOTAL=$sum '{printf(\"\%s\\t\%0.10f\\t\%d\\t\%d\\n\", \$1, \$2/TOTAL, \$2, TOTAL)}' |sort -T . -rnk2> $wrk/temp$libraryname/$asm.ignore";
-+   $cmd = "$JELLYFISH/jellyfish2 dump -c -t -L $cut $wrk/temp$libraryname/$asm.mers |awk -v TOTAL=$sum '{printf(\"\%s\\t\%0.10f\\t\%d\\t\%d\\n\", \$1, \$2/TOTAL, \$2, TOTAL)}' |sort -T . -rnk2> $wrk/temp$libraryname/$asm.ignore";
-    runCommand("$wrk/temp$libraryname", $cmd);
-    runCommand("$wrk/temp$libraryname", "rm $wrk/temp$libraryname/$asm.mers*");
- } elsif (!-e "$wrk/temp$libraryname/$asm.ignore" &&  defined(getGlobal("mhap"))) {
---- src/AS_PBR/Makefile.ori	2015-02-20 23:54:49.000000000 +0100
-+++ src/AS_PBR/Makefile	2018-04-21 16:24:50.730272421 +0200
-@@ -222,4 +222,4 @@
- 	@echo "!!!!!!! WARNING pbutgcns     not supplied for $(LOCAL_NAME).  Please add to your PATH if installed."
- 
- jellyfish_missing:
--	@echo "!!!!!!! WARNING jellyfish    not supplied for $(LOCAL_NAME).  Please add to your PATH if installed."
-+	@echo "!!!!!!! WARNING jellyfish2    not supplied for $(LOCAL_NAME).  Please add to your PATH if installed."
diff --git a/sci-biology/wgs-assembler/metadata.xml b/sci-biology/wgs-assembler/metadata.xml
deleted file mode 100644
index 530c31d3e..000000000
--- a/sci-biology/wgs-assembler/metadata.xml
+++ /dev/null
@@ -1,11 +0,0 @@
-<?xml version="1.0" encoding="UTF-8"?>
-<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
-<pkgmetadata>
-	<maintainer type="project">
-		<email>sci-biology@gentoo.org</email>
-		<name>Gentoo Biology Project</name>
-	</maintainer>
-	<upstream>
-		<remote-id type="sourceforge">wgs-assembler</remote-id>
-	</upstream>
-</pkgmetadata>
diff --git a/sci-biology/wgs-assembler/wgs-assembler-8.3_rc2.ebuild b/sci-biology/wgs-assembler/wgs-assembler-8.3_rc2.ebuild
deleted file mode 100644
index ce6d289c4..000000000
--- a/sci-biology/wgs-assembler/wgs-assembler-8.3_rc2.ebuild
+++ /dev/null
@@ -1,74 +0,0 @@
-# Copyright 1999-2018 Gentoo Foundation
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=5
-
-PYTHON_COMPAT=( python2_7 )
-
-inherit eutils python-single-r1 toolchain-funcs
-
-MY_PV="${PV/_}" # convert from _rc2 to rc2
-
-DESCRIPTION="De novo whole-genome shotgun DNA sequence OLC assembler"
-HOMEPAGE="http://sourceforge.net/projects/wgs-assembler/"
-SRC_URI="http://sourceforge.net/projects/${PN}/files/${PN}/wgs-8.3/wgs-${MY_PV}.tar.bz2"
-
-LICENSE="GPL-2"
-SLOT="0"
-KEYWORDS="~amd64 ~x86"
-IUSE="static-libs"
-
-DEPEND="
-	x11-libs/libXt
-	!x11-terms/terminator"
-RDEPEND="${DEPEND}
-	app-shells/tcsh
-	dev-perl/Log-Log4perl
-	sci-biology/jellyfish:2"
-
-S="${WORKDIR}/wgs-${MY_PV}"
-
-src_prepare() {
-	epatch "${FILESDIR}"/${P}-rename-jellyfish.patch
-	tc-export CC CXX
-}
-
-src_configure() {
-	cd "${S}/kmer" || die
-	./configure.sh || die
-}
-
-src_compile() {
-	# not really an install target
-	emake -C kmer -j1 install
-	emake -C src -j1 SITE_NAME=LOCAL
-}
-
-src_install() {
-	OSTYPE=$(uname)
-	MACHTYPE=$(uname -m)
-	MACHTYPE=${MACHTYPE/x86_64/amd64}
-	MY_S="${OSTYPE}-${MACHTYPE}"
-	sed -i 's|#!/usr/local/bin/|#!/usr/bin/env |' $(find $MY_S -type f) || die
-
-	sed -i '/sub getBinDirectory ()/ a return "/usr/bin";' ${MY_S}/bin/runCA* || die
-	sed -i '/sub getBinDirectoryShellCode ()/ a return "bin=/usr/bin\n";' ${MY_S}/bin/runCA* || die
-	sed -i '1 a use lib "/usr/share/'${PN}'/lib";' $(find $MY_S -name '*.p*') || die
-
-	dobin kmer/"${MY_S}"/bin/*
-	insinto /usr/$(get_libdir)/"${PN}"
-	use static-libs && doins kmer/"${MY_S}"/lib/*
-
-	insinto /usr/include/"${PN}"
-	doins kmer/"${MY_S}"/include/*
-
-	insinto /usr/share/${PN}/lib
-	doins -r "${MY_S}"/bin/TIGR
-	rm -rf "${MY_S}"/bin/TIGR || die
-	dobin "${MY_S}"/bin/*
-	use static-libs && dolib.a ${MY_S}/lib/*
-	dodoc README
-
-	# drop bundled jellyfish-2.0.0
-	rm "${ED}"/usr/bin/jellyfish || die
-}
diff --git a/sci-biology/wgs_tools/Manifest b/sci-biology/wgs_tools/Manifest
index 26de9f371..de085ffd5 100644
--- a/sci-biology/wgs_tools/Manifest
+++ b/sci-biology/wgs_tools/Manifest
@@ -1,2 +1,2 @@
-DIST taxid2tsa.pl 3125 SHA256 aecf00bf36cc60fba16e8102ba3f9b1b8a229afbcb8c081bf29d427eb2458ff9 SHA512 4272be49bf4669506fa7a65e31769b1dd3e6e1a1556872c3a7c4261a54ee162011b931b918b3308b2c558da3766d0822e69bfb75850781f5e5a3500f3eaaa10a WHIRLPOOL d910b6fcf33ce2e52b9634246f422cb35b0c7b7a07fe24de6219c1f30a7f29ee65c5d20481339b6ec065097e28ff87dbe1e26a37ba93060b639a6786ae29d288
-DIST taxid2wgs.pl 3126 SHA256 877e7ee33dc0fd1c412ac57d17461b4cce5e73dc176ea987437fb5ce26e1d232 SHA512 75b26481909f8a37b6ec44c16acc964618253db744501d6a402ee1ed68132cd62a928bdd40aaf34f0b8f7b01800be14d5e2cd2f3e828bf5f70a0d833fd49f621 WHIRLPOOL de5455fbf267fcfc1f0d34870c862587b7fd7365e513d87161283ab043930ea4bd9667e9eed6c529934b46d07c578a675a67027f87d1259175f6b52691a00b92
+DIST taxid2tsa.pl 3577 BLAKE2B 294925bde54ceebe3fd0d48f3774feaf869e8d170fea917297ba078debc1580abe6b6e4a74559c8008ae73ce3b845b54f5ea88805586ca7de5389968d51906d9 SHA512 9bccb65e071a1bd6717f39c7ef977c796ea4a9886ff352aeb768e50227fb705a0fe849ebfede9e0abeb6be96a0e8524a622af3485c73d22f2e70eb46b31acb65
+DIST taxid2wgs.pl 3577 BLAKE2B 37c6b75461a33e7a812c1d8594e103574c8bd816a0229d48ec7d3ad92c808d421e2ceb74412594a8c61e155cc825cd25606569f85a7d2386042b5a611b0cb32a SHA512 b7cb5840b6b8b6fe8aa6bd3f33c6317ab66a5b676365e3bcdda0e5a03dc8d76ead13608668b27523467a7a7b6b0776980438a902664d73d571387d5ea360fa5f
diff --git a/sci-biology/wgs_tools/wgs_tools-9999.ebuild b/sci-biology/wgs_tools/wgs_tools-9999.ebuild
index 94a2d9648..8ea3959ea 100644
--- a/sci-biology/wgs_tools/wgs_tools-9999.ebuild
+++ b/sci-biology/wgs_tools/wgs_tools-9999.ebuild
@@ -1,25 +1,22 @@
-# Copyright 1999-2017 Gentoo Foundation
+# Copyright 1999-2021 Gentoo Authors
 # Distributed under the terms of the GNU General Public License v2
 
-EAPI=5
+EAPI=7
 
 DESCRIPTION="Scripts for ncbi-tools++ and SRA postprocessing using taxonomy"
 HOMEPAGE="ftp://ftp.ncbi.nih.gov/blast/WGS_TOOLS
-	http://www.ncbi.nlm.nih.gov/books/NBK279690/
-	http://www.ncbi.nlm.nih.gov/genbank/wgs"
+	https://www.ncbi.nlm.nih.gov/books/NBK279690/
+	https://www.ncbi.nlm.nih.gov/genbank/wgs"
 SRC_URI="ftp://ftp.ncbi.nih.gov/blast/WGS_TOOLS/taxid2tsa.pl
 	ftp://ftp.ncbi.nih.gov/blast/WGS_TOOLS/taxid2wgs.pl"
 
 LICENSE="all-rights-reserved"
 SLOT="0"
 KEYWORDS="~amd64 ~x86"
-IUSE=""
 
-DEPEND=""
-RDEPEND="${DEPEND}
-	dev-lang/perl"
+RDEPEND="dev-lang/perl"
 
-S="${W}/"
+S="${WORKDIR}"
 
 src_install(){
 	cd "${DISTDIR}" || die
diff --git a/sci-biology/wise/Manifest b/sci-biology/wise/Manifest
deleted file mode 100644
index e0adc951a..000000000
--- a/sci-biology/wise/Manifest
+++ /dev/null
@@ -1 +0,0 @@
-DIST wise2.4.1.tar.gz 3193910 BLAKE2B 45e33b1a4c8ffcb73ad1d2c50be4baeb3a0958a94c2c057db163b33ae33edd5e7159d7fd818725fd13c9ccb2440f61a747e2535b68e0eb25bc09c907d0b4da4d SHA512 aca14bf4fb1ab6070847cfd857d5b3c518695a020fc85b67e1f34b69b5cdb7b28b68c5779eca9af84679d56ca98f7caf1f8c2596ff02b5dd304cd9235aeb2f61
diff --git a/sci-biology/wise/files/01_welcome-csh.patch b/sci-biology/wise/files/01_welcome-csh.patch
deleted file mode 100644
index 3a9057e06..000000000
--- a/sci-biology/wise/files/01_welcome-csh.patch
+++ /dev/null
@@ -1,22 +0,0 @@
-Author: Philipp Benner <mail@philipp-benner.de>
-Description: Avoid dependency from csh
-
---- wise-2.4.1.orig/src/makefile
-+++ wise-2.4.1/src/makefile
-@@ -109,7 +109,7 @@
- bin : 
- 	mkdir bin
- 	cp models/pswdb models/psw models/genewisedb models/estwisedb models/estwise models/genewise models/dba models/dnal models/promoterwise network/scanwise_server models/scanwise ./bin
--	csh welcome.csh
-+	./welcome.csh
- 
- libs : 
- 	(cd base   ; $(MAKE) CC="$(CC)" CFLAGS="$(CFLAGS)" libwisebase.a )
---- wise-2.4.1.orig/src/welcome.csh
-+++ wise-2.4.1/src/welcome.csh
-@@ -1,4 +1,4 @@
--#!/bin/tcsh -f
-+#!/bin/sh
- 
- echo ""
- echo "Welcome to Wise2.4"
diff --git a/sci-biology/wise/files/02_isnumber.patch b/sci-biology/wise/files/02_isnumber.patch
deleted file mode 100644
index a6ae90856..000000000
--- a/sci-biology/wise/files/02_isnumber.patch
+++ /dev/null
@@ -1,14 +0,0 @@
-Author: Philipp Benner <mail@philipp-benner.de>
-Description: Replace isnumber() (which does not exist on linux) by isdigit().
-
---- wise-2.4.1.orig/src/models/phasemodel.c
-+++ wise-2.4.1/src/models/phasemodel.c
-@@ -20,7 +20,7 @@
-     if( line[0] == '#' ) {
-       continue;
-     }
--    if( !isnumber(line[0]) ) {
-+    if( !isdigit(line[0]) ) {
-       warn("Bad looking line in intron file, %s",line);
-       continue;
-     }
diff --git a/sci-biology/wise/files/03_doc-nodycache.patch b/sci-biology/wise/files/03_doc-nodycache.patch
deleted file mode 100644
index 6fe7b1893..000000000
--- a/sci-biology/wise/files/03_doc-nodycache.patch
+++ /dev/null
@@ -1,15 +0,0 @@
-Author Philipp Benner <mail@philipp-benner.de>
-Description: Documentation bugfix.
-
---- wise-2.4.1.orig/docs/wise2.tex
-+++ wise-2.4.1/docs/wise2.tex
-@@ -1617,7 +1617,8 @@
- \item[-hithelp]   more detailed help on hitlist formats
- \item[-dymem]      memory style [default/linear/explicit]
- \item[-kbyte]       memory amount to use [4000]
--\item[-\[no\]dycache] implicitly cache dy matrix usage (default yes)
-+\item[-dycache] implicitly cache dy matrix usage (default)
-+\item[-nodycache] do not implicitly cache dy matrix usage
- \item[-dydebug]     drop into dynamite dp matrix debugger
- \item[-paldebug]    print PackAln after debugger run if used
- \item[-help]      show help options
diff --git a/sci-biology/wise/files/04_wise2-pdflatex-update.patch b/sci-biology/wise/files/04_wise2-pdflatex-update.patch
deleted file mode 100644
index bbaf2861d..000000000
--- a/sci-biology/wise/files/04_wise2-pdflatex-update.patch
+++ /dev/null
@@ -1,38 +0,0 @@
-Author Philipp Benner <mail@philipp-benner.de>
-Description: Make wise2.tex pdflatex compatible.
-
---- wise-2.4.1.orig/docs/wise2.tex
-+++ wise-2.4.1/docs/wise2.tex
-@@ -1,6 +1,7 @@
- 
- \documentclass{article}
--\usepackage{epsfig}
-+%\usepackage{epsfig}
-+\usepackage{graphicx}
- 
- \begin{document}
- \newcommand{\programtext}[1]{{\tt #1}}
-@@ -707,8 +708,9 @@
- \begin{figure}
- \begin{center}
- \leavevmode  
--\epsfxsize 300pt
--\epsfbox{genewise21.eps}
-+%\epsfxsize 300pt
-+%\epsfbox{genewise21.eps}
-+%\includegraphics[scale=0.75]{genewise21.pdf}
- \newline     
- \caption{GeneWise21:93 Algorithm. The dark circles represent states, and the
- arrows between them transitions. Black transitions are standard
-@@ -898,8 +900,9 @@
- \begin{figure}
- \begin{center}
- \leavevmode  
--\epsfxsize 300pt
--\epsfbox{genewise6.eps}
-+%\epsfxsize 300pt
-+%\epsfbox{genewise6.eps}
-+%\includegraphics[scale=0.75]{genewise6.pdf}
- \newline     
- \caption{GeneWise6:23}
- \label{Figure:genewise623}
diff --git a/sci-biology/wise/files/06_getline.patch b/sci-biology/wise/files/06_getline.patch
deleted file mode 100644
index 341cdae82..000000000
--- a/sci-biology/wise/files/06_getline.patch
+++ /dev/null
@@ -1,305 +0,0 @@
-Author: Philipp Benner <philipp@debian.org>
-Last-Update: Sat, 31 Oct 2009 21:25:52 +0000
-Bug-Debian: http://bugs.debian.org/552821
-Description: Fixed conflicting definitions of getline().
-
---- wise-2.4.1.orig/src/HMMer2/sqio.c
-+++ wise-2.4.1/src/HMMer2/sqio.c
-@@ -213,7 +213,7 @@
-     }
- }
- 
--/* Function: getline()
-+/* Function: getline_()
-  * Date:     SRE, Tue Mar  3 08:30:01 1998 [St. Louis]
-  *
-  * Purpose:  read a line from a sequence file into V->sbuffer.
-@@ -229,7 +229,7 @@
-  * Returns:  (void)
-  */
- static void 
--getline(struct ReadSeqVars *V)
-+getline_(struct ReadSeqVars *V)
- {
-   char *cp;
-   
-@@ -299,7 +299,7 @@
-   V->seqlen = 0;
-   if (addfirst) addseq(V->sbuffer, V);
-   do {
--    getline(V);
-+    getline_(V);
- 	/* feof() alone is a bug; files not necessarily \n terminated */
-     if (*(V->sbuffer) == '\0' && feof(V->f))
-       done = TRUE;
-@@ -327,7 +327,7 @@
-   char *sptr;
- 				/* load first line of entry  */
-   while (!feof(V->f) && strncmp(V->sbuffer, "ENTRY", 5) != 0)
--    getline(V);
-+    getline_(V);
-   if (feof(V->f)) return;
- 
-   if ((sptr = strtok(V->sbuffer + 15, "\n\t ")) != NULL)
-@@ -336,7 +336,7 @@
-       SetSeqinfoString(V->sqinfo, sptr, SQINFO_ID);
-     }
-   do {
--    getline(V);
-+    getline_(V);
-     if (!feof(V->f) && strncmp(V->sbuffer, "TITLE", 5) == 0)
-       SetSeqinfoString(V->sqinfo, V->sbuffer+15, SQINFO_DESC);
-     else if (!feof(V->f) && strncmp(V->sbuffer, "ACCESSION", 9) == 0)
-@@ -345,7 +345,7 @@
- 	  SetSeqinfoString(V->sqinfo, sptr, SQINFO_ACC);
-       }
-   } while (! feof(V->f) && (strncmp(V->sbuffer,"SEQUENCE", 8) != 0));
--  getline(V);			/* skip next line, coords */
-+  getline_(V);			/* skip next line, coords */
- 
-   readLoop(0, endPIR, V);
- 
-@@ -359,7 +359,7 @@
-   /* get next line
-    */
-   while (!feof(V->f) && strncmp(V->sbuffer, "ENTRY", 5) != 0)
--    getline(V);
-+    getline_(V);
- }
- 
- 
-@@ -377,7 +377,7 @@
-   char *nm;
- 				/* position past ';' comments */
-   do {
--    getline(V);
-+    getline_(V);
-   } while (! (feof(V->f) || ((*V->sbuffer != 0) && (*V->sbuffer != ';')) ));
- 
-   if (!feof(V->f))
-@@ -389,7 +389,7 @@
-     }
-   
-   while (!(feof(V->f) || ((*V->sbuffer != '\0') && (*V->sbuffer == ';'))))
--    getline(V);
-+    getline_(V);
- }
- 
- static int 
-@@ -411,7 +411,7 @@
- 	  if ((nm = strtok(V->sbuffer+16, ",\n\t ")) != NULL)
- 	    SetSeqinfoString(V->sqinfo, nm, SQINFO_NAME);
- 	}
--      getline(V);
-+      getline_(V);
-     }
- 
-   if (! feof(V->f))
-@@ -420,7 +420,7 @@
-   /* load next line
-    */
-   while ((!feof(V->f)) && (*V->sbuffer != ';')) 
--    getline(V);
-+    getline_(V);
- }
- 
- 
-@@ -438,7 +438,7 @@
-   int   in_definition;
- 
-   while (strncmp(V->sbuffer, "LOCUS", 5) != 0)
--    getline(V);
-+    getline_(V);
- 
-   if ((sptr = strtok(V->sbuffer+12, "\n\t ")) != NULL)
-     {
-@@ -449,7 +449,7 @@
-   in_definition = FALSE;
-   while (! feof(V->f))
-     {
--      getline(V);
-+      getline_(V);
-       if (! feof(V->f) && strstr(V->sbuffer, "DEFINITION") == V->sbuffer)
- 	{
- 	  if ((sptr = strtok(V->sbuffer+12, "\n")) != NULL)
-@@ -482,11 +482,11 @@
- 
- 
-   while (!(feof(V->f) || ((*V->sbuffer!=0) && (strstr(V->sbuffer,"LOCUS") == V->sbuffer))))
--    getline(V);
-+    getline_(V);
- 				/* SRE: V->s now holds "//", so sequential
- 				   reads are wedged: fixed Tue Jul 13 1993 */
-   while (!feof(V->f) && strstr(V->sbuffer, "LOCUS  ") != V->sbuffer)
--    getline(V);
-+    getline_(V);
- }
- 
- static int
-@@ -515,7 +515,7 @@
-     Die("bogus GCGdata format? %s", V->sbuffer);
- 
- 				/* second line contains free text description */
--  getline(V);
-+  getline_(V);
-   SetSeqinfoString(V->sqinfo, V->sbuffer, SQINFO_DESC);
- 
-   if (binary) {
-@@ -535,7 +535,7 @@
-   else readLoop(0, endGCGdata, V);
-   
-   while (!(feof(V->f) || ((*V->sbuffer != 0) && (*V->sbuffer == '>'))))
--    getline(V);
-+    getline_(V);
- }
- 
- static int
-@@ -555,12 +555,12 @@
-   if ((sptr = strtok(NULL, "\n")) != NULL)
-     SetSeqinfoString(V->sqinfo, sptr, SQINFO_DESC);
- 				/* workaround for long NCBI NR lines */
--  while (V->longline && ! feof(V->f)) getline(V);
-+  while (V->longline && ! feof(V->f)) getline_(V);
- 
-   readLoop(0, endPearson, V);
- 
-   while (!(feof(V->f) || ((*V->sbuffer != 0) && (*V->sbuffer == '>'))))
--    getline(V);
-+    getline_(V);
- }
- 
- 
-@@ -587,7 +587,7 @@
- 
- 				/* make sure we have first line */
-   while (!feof(V->f) && strncmp(V->sbuffer, "ID  ", 4) != 0)
--    getline(V);
-+    getline_(V);
- 
-   if ((sptr = strtok(V->sbuffer+5, "\n\t ")) != NULL)
-     {
-@@ -596,7 +596,7 @@
-     }
- 
-   do {
--    getline(V);
-+    getline_(V);
-     if (!feof(V->f) && strstr(V->sbuffer, "AC  ") == V->sbuffer)
-       {
- 	if ((sptr = strtok(V->sbuffer+5, ";  \t\n")) != NULL)
-@@ -620,7 +620,7 @@
- 
- 				/* load next record's ID line */
-   while (!feof(V->f) && strncmp(V->sbuffer, "ID  ", 4) != 0)
--    getline(V);
-+    getline_(V);
- }
- 
- 
-@@ -636,7 +636,7 @@
- {
-   char *sptr;
- 
--  getline(V);  /*s == "seqLen seqid string..."*/
-+  getline_(V);  /*s == "seqLen seqid string..."*/
- 
-   if ((sptr = strtok(V->sbuffer+6, " \t\n")) != NULL)
-     SetSeqinfoString(V->sqinfo, sptr, SQINFO_NAME);
-@@ -647,7 +647,7 @@
-   readLoop(0, endZuker, V);
- 
-   while (!(feof(V->f) | ((*V->sbuffer != '\0') & (*V->sbuffer == '('))))
--    getline(V);
-+    getline_(V);
- }
- 
- static void 
-@@ -669,7 +669,7 @@
- 
-   do {
-     done = feof(V->f);
--    getline(V);
-+    getline_(V);
-     if (! done) addseq(V->sbuffer, V);
-   } while (!done);
- }
-@@ -681,7 +681,7 @@
-   char *sptr;
-   int   dostruc = FALSE;
- 
--  while (strncmp(V->sbuffer, "NAM ", 4) != 0) getline(V);
-+  while (strncmp(V->sbuffer, "NAM ", 4) != 0) getline_(V);
- 
-   if ((sptr = strtok(V->sbuffer+4, "\n\t ")) != NULL)
-     SetSeqinfoString(V->sqinfo, sptr, SQINFO_NAME);
-@@ -689,7 +689,7 @@
-   /*CONSTCOND*/
-   while (1)
-     {
--      getline(V);
-+      getline_(V);
-       if (feof(V->f)) {squid_errno = SQERR_FORMAT; return; }
- 
-       if (strncmp(V->sbuffer, "SRC ", 4) == 0)
-@@ -721,14 +721,14 @@
-   while (1)
-     {
- 				/* sequence line */
--      getline(V);
-+      getline_(V);
-       if (feof(V->f) || strncmp(V->sbuffer, "++", 2) == 0) 
- 	break;
-       addseq(V->sbuffer, V);
- 				/* structure line */
-       if (dostruc)
- 	{
--	  getline(V);
-+	  getline_(V);
- 	  if (feof(V->f)) { squid_errno = SQERR_FORMAT; return; }
- 	  addstruc(V->sbuffer, V);
- 	}
-@@ -736,7 +736,7 @@
- 
- 
-   while (!feof(V->f) && strncmp(V->sbuffer, "NAM ", 4) != 0)
--    getline(V);
-+    getline_(V);
- }
- 
- 
-@@ -816,7 +816,7 @@
- 
-   /* Load the first line.
-    */
--  getline(dbfp);
-+  getline_(dbfp);
- 
-   return dbfp;
- }
-@@ -833,7 +833,7 @@
-     Die("SeqfilePosition() failed: in a nonrewindable data file or stream");
- 
-   fseek(sqfp->f, offset, SEEK_SET);
--  getline(sqfp);
-+  getline_(sqfp);
- }
- 
- 
-@@ -853,7 +853,7 @@
-   if (sqfp->ali_aseqs != NULL) sqfp->ali_curridx = 0;
-   else {
-     rewind(sqfp->f);
--    getline(sqfp);
-+    getline_(sqfp);
-   }
- }
- 
-@@ -949,7 +949,7 @@
-       do {			/* skip leading comments on GCG file */
- 	gotuw = (strstr(V->sbuffer,"..") != NULL);
- 	if (gotuw) readUWGCG(V);
--	getline(V);
-+	getline_(V);
-       } while (! feof(V->f));
-       break;
- 
diff --git a/sci-biology/wise/files/07_ld--as-needed.patch b/sci-biology/wise/files/07_ld--as-needed.patch
deleted file mode 100644
index 51ee25437..000000000
--- a/sci-biology/wise/files/07_ld--as-needed.patch
+++ /dev/null
@@ -1,52 +0,0 @@
-Description: Fix FTBFS with ld --as-needed.
-Bug-Ubuntu: https://bugs.launchpad.net/ubuntu/+source/wise/+bug/832935
-
---- wise-2.4.1.orig/src/models/makefile
-+++ wise-2.4.1/src/models/makefile
-@@ -215,7 +215,7 @@
- 	$(CC)  $(CFLAGS) $(INCFLAGS)  -o scanwisep_wiseserver.o -DSCAN_WISESERVER -I../network -I../socket -I../external/mott scanwisep.c 
- 
- scanwise : scanwisep_wiseserver.o seqaligndisplay.o proteinsw.o sw_wrap.o abc.o pba.o hsp2aln_sw.o
--	$(CC) -o scanwise scanwisep_wiseserver.o sw_wrap.o seqaligndisplay.o proteinsw.o abc.o pba.o hsp2aln_sw.o   ../network/net_hspscan.o ../network/client_multihspscan.o  $(LDFLAGS) -L../external/mott -L../socket -lmott -ldyna_glib -ldyna -lwisesocket -lwisebase  $(EXTRALIBS) -lpthread 
-+	$(CC) -o scanwise scanwisep_wiseserver.o sw_wrap.o seqaligndisplay.o proteinsw.o abc.o pba.o hsp2aln_sw.o   ../network/net_hspscan.o ../network/client_multihspscan.o  $(LDFLAGS) -L../external/mott -L../socket -lmott -ldyna_glib -ldyna -lwisesocket -lwisebase  $(EXTRALIBS) -lpthread $(LDFLAGS)
- 
- scanwisep_compress.o : scanwisep.c
- 	$(CC)  $(CFLAGS) -DSCAN_COMPRESS -I../dnaindex -I../network -I../socket -I../external/mott scanwisep.c 
-@@ -275,7 +275,7 @@
- 	$(CC) -o makerandomdb makerandomdb.o $(LDFLAGS) -ldyna_glib -ldyna -lwisebase  $(EXTRALIBS)
- 
- genewise : genewise.o $(NEWG) 
--	$(CC) -o genewise genewise.o $(NEWG) $(LDFLAGS) -lhmmer -ldyna_glib -ldyna_glib -ldyna_glib -ldyna -lwisebase  $(EXTRALIBS)
-+	$(CC) -o genewise genewise.o $(NEWG) $(LDFLAGS) -lhmmer -ldyna_glib -ldyna_glib -ldyna_glib -ldyna -lwisebase  $(EXTRALIBS) $(LDFLAGS)
- 
- cdnawise : cdnawise.o $(NEWG) cdnawise10.o 
- 	$(CC) -g -o cdnawise cdnawise.o cdnawise10.o $(NEWG) $(LDFLAGS) -lhmmer -ldyna_glib -ldyna -lwisebase  $(EXTRALIBS)
-@@ -300,16 +300,16 @@
- 
- 
- genewisedb : genewisedb.o $(NEWG) 
--	$(CC) -g -o genewisedb genewisedb.o  $(NEWG)  $(LDFLAGS) -lhmmer -ldyna_glib -ldyna -lwisebase  $(EXTRALIBS) 
-+	$(CC) -g -o genewisedb genewisedb.o  $(NEWG)  $(LDFLAGS) -lhmmer -ldyna_glib -ldyna -lwisebase  $(EXTRALIBS)  $(LDFLAGS)
- 
- estwisedb : estwisedb.o $(NEWG) 
--	$(CC) -g -o estwisedb estwisedb.o $(NEWG)  $(LDFLAGS) -lhmmer -ldyna_glib -ldyna -lwisebase  $(EXTRALIBS)
-+	$(CC) -g -o estwisedb estwisedb.o $(NEWG)  $(LDFLAGS) -lhmmer -ldyna_glib -ldyna -lwisebase  $(EXTRALIBS) $(LDFLAGS)
- 
- edb : estwisedb.o $(NEWG) 
- 	$(CC) -g -o estwisedb estwisedb.o $(NEWG)  $(LDFLAGS) -lhmmer -ldyna_glib -ldyna -lwisebase  $(EXTRALIBS) -lefence
- 
- estwise : estwise.o $(NEWG) 
--	$(CC) -g -o estwise estwise.o  $(NEWG) $(LDFLAGS) -lhmmer -ldyna_glib -ldyna -lwisebase  $(EXTRALIBS)
-+	$(CC) -g -o estwise estwise.o  $(NEWG) $(LDFLAGS) -lhmmer -ldyna_glib -ldyna -lwisebase  $(EXTRALIBS) $(LDFLAGS)
- 
- 
- amplimer_resolver : amplimer_resolver.o dnaalign.o dnamatcher.o 
-@@ -331,7 +331,7 @@
- 	$(CC) -g -o statwise statwise.o statwise10.o syexonmodel.o genestats.o pwmdna.o geneutil.o $(LDFLAGS) -ldyna_glib -ldyna -lwisebase  $(EXTRALIBS)
- 
- pseudowise : pseudowise.o pseudowise7.o $(NEWG) 
--	$(CC) -g -o pseudowise pseudowise.o pseudowise7.o $(NEWG) $(LDFLAGS) -lhmmer -ldyna_glib -ldyna -lwisebase  $(EXTRALIBS)
-+	$(CC) -g -o pseudowise pseudowise.o pseudowise7.o $(NEWG) $(LDFLAGS) -lhmmer -ldyna_glib -ldyna -lwisebase  $(EXTRALIBS) $(LDFLAGS)
- 
- clonewise : clonewise.o clonewisedp.o localclonewisedp.o mapstruct.o
- 	$(CC) -g -o clonewise clonewise.o clonewisedp.o localclonewisedp.o mapstruct.o $(LDFLAGS) -ldyna_glib -ldyna -lwisebase  $(EXTRALIBS)
diff --git a/sci-biology/wise/files/08_mayhem.patch b/sci-biology/wise/files/08_mayhem.patch
deleted file mode 100644
index c54c7c66a..000000000
--- a/sci-biology/wise/files/08_mayhem.patch
+++ /dev/null
@@ -1,103 +0,0 @@
-Author: Philipp Benner <philipp@debian.org>
-Last-Update: Sun, 07 Jul 2013 13:33:01 +0200
-Description: Fix run time errors detected by Mayhem
-
---- wise-2.4.1.orig/src/models/dbac.c
-+++ wise-2.4.1/src/models/dbac.c
-@@ -535,8 +535,12 @@
-    *  
-    */  
-   
--  one = read_fasta_file_Sequence(*argv++);  
--  two = read_fasta_file_Sequence(*argv++);  
-+  if( (one = read_fasta_file_Sequence(*argv++)) == NULL ) {
-+    fatal("Unable to read the sequence in file");
-+  }
-+  if( (two = read_fasta_file_Sequence(*argv++)) == NULL ) {
-+    fatal("Unable to read the sequence in file");
-+  }
-   
-   uppercase_Sequence(one);  
-   uppercase_Sequence(two);  
---- wise-2.4.1.orig/src/models/estwise.c
-+++ wise-2.4.1/src/models/estwise.c
-@@ -313,7 +313,7 @@
-     }
-   }
- 
--  if( reverse == TRUE ) {
-+  if( cdna && reverse == TRUE ) {
-     if( tstart > tend ) {
-       warn("You have already reversed the DNA by using %d - %d truncation. Re-reversing",tstart,tend);
-     }
-@@ -323,7 +323,7 @@
-     cdna = cdna_temp;
-   }
- 
--  if( target_abs == TRUE ) {
-+  if( cdna && target_abs == TRUE ) {
-     cdna->baseseq->offset = 1;
-     cdna->baseseq->end  = strlen(cdna->baseseq->seq);
-   }
-@@ -472,8 +472,11 @@
-   }
- 
-   cp = flat_cDNAParser(indel_error);
--  cm = flat_CodonMapper(ct);
--  sprinkle_errors_over_CodonMapper(cm,subs_error);
-+
-+  if( ct ) {
-+    cm = flat_CodonMapper(ct);
-+    sprinkle_errors_over_CodonMapper(cm,subs_error);
-+  }
- 
-   return ret;
- 
---- wise-2.4.1.orig/src/models/genewise.c
-+++ wise-2.4.1/src/models/genewise.c
-@@ -550,8 +550,10 @@
-       ret =  FALSE;
-     }
- 
--    gen->baseseq->offset = 1;
--    gen->baseseq->end  = strlen(gen->baseseq->seq);
-+    if ( gen ) {
-+      gen->baseseq->offset = 1;
-+      gen->baseseq->end  = strlen(gen->baseseq->seq);
-+    }
-   }
- 
-   if( alg_str != NULL ) {
---- wise-2.4.1.orig/src/models/estwisedb.c
-+++ wise-2.4.1/src/models/estwisedb.c
-@@ -688,8 +688,11 @@
- 
- 
-   cps = flat_cDNAParser(indel_error);
--  cm = flat_CodonMapper(ct);
--  sprinkle_errors_over_CodonMapper(cm,subs_error);
-+
-+  if( ct ) {
-+    cm = flat_CodonMapper(ct);
-+    sprinkle_errors_over_CodonMapper(cm,subs_error);
-+  }
- 
-   return ret;
- 
---- wise-2.4.1.orig/src/models/promoterwise.c
-+++ wise-2.4.1/src/models/promoterwise.c
-@@ -147,8 +147,12 @@
- 
-   lchs = standard_LocalCisHitScore(NMaskType_VARIABLE);
- 
--  query = read_fasta_file_Sequence(argv[1]);
--  target = read_fasta_file_Sequence(argv[2]);
-+  if( (query = read_fasta_file_Sequence(argv[1])) == NULL ) {
-+    fatal("Unable to read the sequence in query file");
-+  }
-+  if( (target = read_fasta_file_Sequence(argv[2])) == NULL ) {
-+    fatal("Unable to read the sequence in target file");
-+  }
- 
-   for(i=0;i<query->len;i++) {
-     query->seq[i] = toupper(query->seq[i]);
diff --git a/sci-biology/wise/files/09_dnal-add-return-statement.patch b/sci-biology/wise/files/09_dnal-add-return-statement.patch
deleted file mode 100644
index 237e59688..000000000
--- a/sci-biology/wise/files/09_dnal-add-return-statement.patch
+++ /dev/null
@@ -1,17 +0,0 @@
-Author: Dejan Latinovic <Dejan.Latinovic@imgtec.com>
-Last-Update: Mon, 4 Aug 2014 17:10:38 +0000
-Bug-Debian: http://bugs.debian.org/751277
-Desription: Make sure dnal has a valid return value
- This affects a bug reported against python-biopython.
-
---- wise-2.4.1.orig/src/models/dnal.c
-+++ wise-2.4.1/src/models/dnal.c
-@@ -75,6 +75,8 @@
- 
-   if( show_alb == TRUE )
-     dump_ascii_AlnBlock(alb,stdout);
-+
-+  return 0;
- }
- 
- 
diff --git a/sci-biology/wise/files/11_consistent_manual_dates.patch b/sci-biology/wise/files/11_consistent_manual_dates.patch
deleted file mode 100644
index eaea1eec9..000000000
--- a/sci-biology/wise/files/11_consistent_manual_dates.patch
+++ /dev/null
@@ -1,53 +0,0 @@
-Description: Use fixed dates for manuals.
- These make the build reproducible. I have picked the file modificatin dates of
- the corresponding source .tex files.
-Author: Sascha Steinbiss <sascha@steinbiss.name>
---- a/docs/dynamite.tex
-+++ b/docs/dynamite.tex
-@@ -1,4 +1,5 @@
- \documentstyle{article}
-+\pdftrailerid{}
- \begin{document}
- 
- \newcommand{\programtext}[1]{{\tt #1}}
-@@ -10,6 +11,7 @@
- Hinxton, Cambridge CB10 1SA,\\
- England.\\
- Email: birney@sanger.ac.uk}
-+\date{18/6/2001}
- 
- \maketitle
-  
---- a/docs/wise2.tex
-+++ b/docs/wise2.tex
-@@ -1,5 +1,6 @@
- 
- \documentclass{article}
-+\pdftrailerid{}
- %\usepackage{epsfig}
- \usepackage{graphicx}
- 
-@@ -13,6 +14,7 @@
- Hinxton, Cambridge CB10 1SD,\\
- England.\\
- Email: birney@ebi.ac.uk}
-+\date{18/6/2001}
- 
- \maketitle
-  
---- a/docs/wise2api.tex
-+++ b/docs/wise2api.tex
-@@ -1,4 +1,5 @@
- \documentstyle{article}
-+\pdftrailerid{}
- \begin{document}
- 
- \newcommand{\programtext}[1]{{\tt #1}}
-@@ -10,6 +11,7 @@
- Hinxton, Cambridge CB10 1SA,\\
- England.\\
- Email: birney@sanger.ac.uk}
-+\date{18/6/2001}
- 
- \maketitle
-  
diff --git a/sci-biology/wise/files/wise-2.2.0-glibc-2.10.patch b/sci-biology/wise/files/wise-2.2.0-glibc-2.10.patch
deleted file mode 100644
index 1ec433f19..000000000
--- a/sci-biology/wise/files/wise-2.2.0-glibc-2.10.patch
+++ /dev/null
@@ -1,301 +0,0 @@
-diff -ur wise2.2.0.orig/src/HMMer2/sqio.c wise2.2.0/src/HMMer2/sqio.c
---- wise2.2.0.orig/src/HMMer2/sqio.c	2001-06-18 16:59:51.000000000 +0300
-+++ wise2.2.0/src/HMMer2/sqio.c	2009-08-05 22:39:04.000000000 +0300
-@@ -213,7 +213,7 @@
-     }
- }
- 
--/* Function: getline()
-+/* Function: get_line()
-  * Date:     SRE, Tue Mar  3 08:30:01 1998 [St. Louis]
-  *
-  * Purpose:  read a line from a sequence file into V->sbuffer.
-@@ -229,7 +229,7 @@
-  * Returns:  (void)
-  */
- static void 
--getline(struct ReadSeqVars *V)
-+get_line(struct ReadSeqVars *V)
- {
-   char *cp;
-   
-@@ -299,7 +299,7 @@
-   V->seqlen = 0;
-   if (addfirst) addseq(V->sbuffer, V);
-   do {
--    getline(V);
-+    get_line(V);
- 	/* feof() alone is a bug; files not necessarily \n terminated */
-     if (*(V->sbuffer) == '\0' && feof(V->f))
-       done = TRUE;
-@@ -327,7 +327,7 @@
-   char *sptr;
- 				/* load first line of entry  */
-   while (!feof(V->f) && strncmp(V->sbuffer, "ENTRY", 5) != 0)
--    getline(V);
-+    get_line(V);
-   if (feof(V->f)) return;
- 
-   if ((sptr = strtok(V->sbuffer + 15, "\n\t ")) != NULL)
-@@ -336,7 +336,7 @@
-       SetSeqinfoString(V->sqinfo, sptr, SQINFO_ID);
-     }
-   do {
--    getline(V);
-+    get_line(V);
-     if (!feof(V->f) && strncmp(V->sbuffer, "TITLE", 5) == 0)
-       SetSeqinfoString(V->sqinfo, V->sbuffer+15, SQINFO_DESC);
-     else if (!feof(V->f) && strncmp(V->sbuffer, "ACCESSION", 9) == 0)
-@@ -345,7 +345,7 @@
- 	  SetSeqinfoString(V->sqinfo, sptr, SQINFO_ACC);
-       }
-   } while (! feof(V->f) && (strncmp(V->sbuffer,"SEQUENCE", 8) != 0));
--  getline(V);			/* skip next line, coords */
-+  get_line(V);			/* skip next line, coords */
- 
-   readLoop(0, endPIR, V);
- 
-@@ -359,7 +359,7 @@
-   /* get next line
-    */
-   while (!feof(V->f) && strncmp(V->sbuffer, "ENTRY", 5) != 0)
--    getline(V);
-+    get_line(V);
- }
- 
- 
-@@ -377,7 +377,7 @@
-   char *nm;
- 				/* position past ';' comments */
-   do {
--    getline(V);
-+    get_line(V);
-   } while (! (feof(V->f) || ((*V->sbuffer != 0) && (*V->sbuffer != ';')) ));
- 
-   if (!feof(V->f))
-@@ -389,7 +389,7 @@
-     }
-   
-   while (!(feof(V->f) || ((*V->sbuffer != '\0') && (*V->sbuffer == ';'))))
--    getline(V);
-+    get_line(V);
- }
- 
- static int 
-@@ -411,7 +411,7 @@
- 	  if ((nm = strtok(V->sbuffer+16, ",\n\t ")) != NULL)
- 	    SetSeqinfoString(V->sqinfo, nm, SQINFO_NAME);
- 	}
--      getline(V);
-+      get_line(V);
-     }
- 
-   if (! feof(V->f))
-@@ -420,7 +420,7 @@
-   /* load next line
-    */
-   while ((!feof(V->f)) && (*V->sbuffer != ';')) 
--    getline(V);
-+    get_line(V);
- }
- 
- 
-@@ -438,7 +438,7 @@
-   int   in_definition;
- 
-   while (strncmp(V->sbuffer, "LOCUS", 5) != 0)
--    getline(V);
-+    get_line(V);
- 
-   if ((sptr = strtok(V->sbuffer+12, "\n\t ")) != NULL)
-     {
-@@ -449,7 +449,7 @@
-   in_definition = FALSE;
-   while (! feof(V->f))
-     {
--      getline(V);
-+      get_line(V);
-       if (! feof(V->f) && strstr(V->sbuffer, "DEFINITION") == V->sbuffer)
- 	{
- 	  if ((sptr = strtok(V->sbuffer+12, "\n")) != NULL)
-@@ -482,11 +482,11 @@
- 
- 
-   while (!(feof(V->f) || ((*V->sbuffer!=0) && (strstr(V->sbuffer,"LOCUS") == V->sbuffer))))
--    getline(V);
-+    get_line(V);
- 				/* SRE: V->s now holds "//", so sequential
- 				   reads are wedged: fixed Tue Jul 13 1993 */
-   while (!feof(V->f) && strstr(V->sbuffer, "LOCUS  ") != V->sbuffer)
--    getline(V);
-+    get_line(V);
- }
- 
- static int
-@@ -515,7 +515,7 @@
-     Die("bogus GCGdata format? %s", V->sbuffer);
- 
- 				/* second line contains free text description */
--  getline(V);
-+  get_line(V);
-   SetSeqinfoString(V->sqinfo, V->sbuffer, SQINFO_DESC);
- 
-   if (binary) {
-@@ -535,7 +535,7 @@
-   else readLoop(0, endGCGdata, V);
-   
-   while (!(feof(V->f) || ((*V->sbuffer != 0) && (*V->sbuffer == '>'))))
--    getline(V);
-+    get_line(V);
- }
- 
- static int
-@@ -555,12 +555,12 @@
-   if ((sptr = strtok(NULL, "\n")) != NULL)
-     SetSeqinfoString(V->sqinfo, sptr, SQINFO_DESC);
- 				/* workaround for long NCBI NR lines */
--  while (V->longline && ! feof(V->f)) getline(V);
-+  while (V->longline && ! feof(V->f)) get_line(V);
- 
-   readLoop(0, endPearson, V);
- 
-   while (!(feof(V->f) || ((*V->sbuffer != 0) && (*V->sbuffer == '>'))))
--    getline(V);
-+    get_line(V);
- }
- 
- 
-@@ -587,7 +587,7 @@
- 
- 				/* make sure we have first line */
-   while (!feof(V->f) && strncmp(V->sbuffer, "ID  ", 4) != 0)
--    getline(V);
-+    get_line(V);
- 
-   if ((sptr = strtok(V->sbuffer+5, "\n\t ")) != NULL)
-     {
-@@ -596,7 +596,7 @@
-     }
- 
-   do {
--    getline(V);
-+    get_line(V);
-     if (!feof(V->f) && strstr(V->sbuffer, "AC  ") == V->sbuffer)
-       {
- 	if ((sptr = strtok(V->sbuffer+5, ";  \t\n")) != NULL)
-@@ -620,7 +620,7 @@
- 
- 				/* load next record's ID line */
-   while (!feof(V->f) && strncmp(V->sbuffer, "ID  ", 4) != 0)
--    getline(V);
-+    get_line(V);
- }
- 
- 
-@@ -636,7 +636,7 @@
- {
-   char *sptr;
- 
--  getline(V);  /*s == "seqLen seqid string..."*/
-+  get_line(V);  /*s == "seqLen seqid string..."*/
- 
-   if ((sptr = strtok(V->sbuffer+6, " \t\n")) != NULL)
-     SetSeqinfoString(V->sqinfo, sptr, SQINFO_NAME);
-@@ -647,7 +647,7 @@
-   readLoop(0, endZuker, V);
- 
-   while (!(feof(V->f) | ((*V->sbuffer != '\0') & (*V->sbuffer == '('))))
--    getline(V);
-+    get_line(V);
- }
- 
- static void 
-@@ -669,7 +669,7 @@
- 
-   do {
-     done = feof(V->f);
--    getline(V);
-+    get_line(V);
-     if (! done) addseq(V->sbuffer, V);
-   } while (!done);
- }
-@@ -681,7 +681,7 @@
-   char *sptr;
-   int   dostruc = FALSE;
- 
--  while (strncmp(V->sbuffer, "NAM ", 4) != 0) getline(V);
-+  while (strncmp(V->sbuffer, "NAM ", 4) != 0) get_line(V);
- 
-   if ((sptr = strtok(V->sbuffer+4, "\n\t ")) != NULL)
-     SetSeqinfoString(V->sqinfo, sptr, SQINFO_NAME);
-@@ -689,7 +689,7 @@
-   /*CONSTCOND*/
-   while (1)
-     {
--      getline(V);
-+      get_line(V);
-       if (feof(V->f)) {squid_errno = SQERR_FORMAT; return; }
- 
-       if (strncmp(V->sbuffer, "SRC ", 4) == 0)
-@@ -721,14 +721,14 @@
-   while (1)
-     {
- 				/* sequence line */
--      getline(V);
-+      get_line(V);
-       if (feof(V->f) || strncmp(V->sbuffer, "++", 2) == 0) 
- 	break;
-       addseq(V->sbuffer, V);
- 				/* structure line */
-       if (dostruc)
- 	{
--	  getline(V);
-+	  get_line(V);
- 	  if (feof(V->f)) { squid_errno = SQERR_FORMAT; return; }
- 	  addstruc(V->sbuffer, V);
- 	}
-@@ -736,7 +736,7 @@
- 
- 
-   while (!feof(V->f) && strncmp(V->sbuffer, "NAM ", 4) != 0)
--    getline(V);
-+    get_line(V);
- }
- 
- 
-@@ -816,7 +816,7 @@
- 
-   /* Load the first line.
-    */
--  getline(dbfp);
-+  get_line(dbfp);
- 
-   return dbfp;
- }
-@@ -833,7 +833,7 @@
-     Die("SeqfilePosition() failed: in a nonrewindable data file or stream");
- 
-   fseek(sqfp->f, offset, SEEK_SET);
--  getline(sqfp);
-+  get_line(sqfp);
- }
- 
- 
-@@ -853,7 +853,7 @@
-   if (sqfp->ali_aseqs != NULL) sqfp->ali_curridx = 0;
-   else {
-     rewind(sqfp->f);
--    getline(sqfp);
-+    get_line(sqfp);
-   }
- }
- 
-@@ -949,7 +949,7 @@
-       do {			/* skip leading comments on GCG file */
- 	gotuw = (strstr(V->sbuffer,"..") != NULL);
- 	if (gotuw) readUWGCG(V);
--	getline(V);
-+	get_line(V);
-       } while (! feof(V->f));
-       break;
- 
diff --git a/sci-biology/wise/files/wise-2.4.1-cflags.patch b/sci-biology/wise/files/wise-2.4.1-cflags.patch
deleted file mode 100644
index 705ada853..000000000
--- a/sci-biology/wise/files/wise-2.4.1-cflags.patch
+++ /dev/null
@@ -1,407 +0,0 @@
---- wise2.4.1/src/makefile.old	2017-01-10 15:22:43.545646202 +0000
-+++ wise2.4.1/src/makefile	2017-01-10 15:23:58.484888011 +0000
-@@ -22,7 +22,7 @@
- # Change the cc line to gcc if you get compiler errors
- # Most likely you have a non ANSI C compiler
- # CC =  /opt/intel_cc_80/bin/icc
--CC = cc
-+CC += gcc
- 
- # These are the CFLAGS to use. These days Wise2 is inherently
- # pthreaded, and everything is compiled with threads. However
-@@ -31,13 +31,13 @@
- 
- 
- # Intel icc flags
--# CFLAGS = -c  -O3 -axWK -ipo `glib-config --cflags`
-+# CFLAGS = -c  -O3 -axWK -ipo `pkg-config glib-2.0 --cflags`
- 
- # alpha flags (-pthread)
--# CFLAGS = -c -O3 -pthread `glib-config --cflags`
-+# CFLAGS = -c -O3 -pthread `pkg-config glib-2.0 --cflags`
- 
- # normal linux/bsd/mac flags
--CFLAGS = -c -O3  `glib-config --cflags`
-+CFLAGS += -c `pkg-config glib-2.0 --cflags`
- 
- 
- EXTRALIBS = -lm
---- wise2.4.1/src/base/makefile.old	2017-01-10 15:11:43.396368920 +0000
-+++ wise2.4.1/src/base/makefile	2017-01-10 15:12:30.590885552 +0000
-@@ -20,8 +20,8 @@
- 
- 
- #CFLAGS = -c  -g -DUNIX -DWISE_MEMORY_WATCH
--CFLAGS = -c  -O2 -DUNIX -pthread
--LFLAGS =  -g  -lm 
-+CFLAGS += -c  -DUNIX -pthread
-+LFLAGS =  -lm 
- DFLAGS = -n Wise2_ -a _api.h -b _api.t -l -D
- AR_OPTIONS = ru
- 
---- wise2.4.1/src/corba/makefile.old	2017-01-10 15:12:43.086757650 +0000
-+++ wise2.4.1/src/corba/makefile	2017-01-10 15:17:24.179888689 +0000
-@@ -1,10 +1,10 @@
- 
- 
--CC = cc
-+CC += gcc
- INCFLAGS = -I../base/ -I../dynlibsrc
- #gCFLAGS = -Wall -g -pedantic -c  -DUNIX -I../base/
--#CFLAGS =  -O2 -c  -DUNIX  -I../base/ `glib-config --cflags` -I/usr/local/include/orbit-1.0/
--CFLAGS =  -pthread -c  -DUNIX  -I../base/ -I../dynlibsrc `orbit-config --cflags client`
-+#CFLAGS =  -O2 -c  -DUNIX  -I../base/ `pkg-config glib-2.0 --cflags` -I/usr/local/include/orbit-1.0/
-+CFLAGS +=  -pthread -c  -DUNIX  -I../base/ -I../dynlibsrc `pkg-config ORBit-2.0 --cflags`
- LFLAGS =   -L../base/ -lm -lpthread
- AR_OPTIONS = ru
- 
-@@ -14,18 +14,18 @@
- 	orbit-idl hspscan_corba.idl
- 
- test_server : test_server.o hspscan_server_impl.o hspscan_corba-common.o hspscan_corba-skels.o hspscan_corba-stubs.o corba_singleton.o 
--	cc -g -o test_server  test_server.o hspscan_server_impl.o  hspscan_corba-common.o hspscan_corba-skels.o hspscan_corba-stubs.o  corba_singleton.o ../dynlibsrc/libdyna.a ../base/libwisebase.a ../dynlibsrc/hsp.o ../dynlibsrc/subseqhash.o ../dynlibsrc/linkedlist_lookpos.o   ../dynlibsrc/libdyna_glib.a `glib-config --libs` -lm -lORBit -lIIOP -lORBitutil -lpthread
-+	$(CC) $(CFLAGS) $(LDFLAGS) -o test_server  test_server.o hspscan_server_impl.o  hspscan_corba-common.o hspscan_corba-skels.o hspscan_corba-stubs.o  corba_singleton.o ../dynlibsrc/libdyna.a ../base/libwisebase.a ../dynlibsrc/hsp.o ../dynlibsrc/subseqhash.o ../dynlibsrc/linkedlist_lookpos.o   ../dynlibsrc/libdyna_glib.a `pkg-config glib-2.0 --libs` -lm -lORBit -lIIOP -lORBitutil -lpthread
- 
- scanwise_protein_index : scanwise_protein_index.o hspscan_server_impl.o hspscan_corba-common.o hspscan_corba-skels.o hspscan_corba-stubs.o corba_singleton.o 
--	cc -o scanwise_protein_index  scanwise_protein_index.o hspscan_server_impl.o  hspscan_corba-common.o hspscan_corba-skels.o hspscan_corba-stubs.o  corba_singleton.o  ../dynlibsrc/libdyna_glib.a ../dynlibsrc/libdyna.a ../base/libwisebase.a `glib-config --libs` -lm -lORBit -lIIOP -lORBitutil -lpthread
-+	$(CC) $(CFLAGS) $(LDFLAGS) -o scanwise_protein_index  scanwise_protein_index.o hspscan_server_impl.o  hspscan_corba-common.o hspscan_corba-skels.o hspscan_corba-stubs.o  corba_singleton.o  ../dynlibsrc/libdyna_glib.a ../dynlibsrc/libdyna.a ../base/libwisebase.a `pkg-config glib-2.0 --libs` -lm -lORBit -lIIOP -lORBitutil -lpthread
- 
- 
- test_client : test_client.o hspscan_corba-common.o hspscan_corba-stubs.o 
--	cc -g -o test_client  test_client.o  hspscan_corba-common.o hspscan_corba-stubs.o ../dynlibsrc/libdyna.a ../base/libwisebase.a `glib-config --libs` -lm -lORBit -lIIOP -lORBitutil -lpthread
-+	$(CC) $(CFLAGS) $(LDFLAGS) -o test_client  test_client.o  hspscan_corba-common.o hspscan_corba-stubs.o ../dynlibsrc/libdyna.a ../base/libwisebase.a `pkg-config glib-2.0 --libs` -lm -lORBit -lIIOP -lORBitutil -lpthread
- 
- 
- test_wrapper : test_wrapper.o hspscan_corba-common.o hspscan_corba-stubs.o hspscan_corba_wrapper.o corba_singleton.o 
--	cc -g -o test_wrapper test_wrapper.o  hspscan_corba-common.o hspscan_corba-stubs.o   corba_singleton.o hspscan_corba_wrapper.o ../dynlibsrc/hsp.o ../dynlibsrc/libdyna.a ../base/libwisebase.a  `glib-config --libs` -lm -lORBit -lIIOP -lORBitutil -lpthread
-+	$(CC) $(CFLAGS) $(LDFLAGS) -o test_wrapper test_wrapper.o  hspscan_corba-common.o hspscan_corba-stubs.o   corba_singleton.o hspscan_corba_wrapper.o ../dynlibsrc/hsp.o ../dynlibsrc/libdyna.a ../base/libwisebase.a  `pkg-config glib-2.0 --libs` -lm -lORBit -lIIOP -lORBitutil -lpthread
- 
- .c.o :
- 	$(CC) $(CFLAGS) $(INCFLAGS) $?
---- wise2.4.1/src/dnaindex/assembly/makefile.old	2017-01-10 15:17:42.238704557 +0000
-+++ wise2.4.1/src/dnaindex/assembly/makefile	2017-01-10 15:19:04.599866950 +0000
-@@ -25,11 +25,11 @@
- 
- 
- 
--CC = cc
--CFLAGS = -Wall -pthread -c  -DHAS_PTHREAD_SETSCOPE -g -DUNIX -I../../base/ -I../../dynlibsrc/ -I../ -I../../models/ `glib-config --cflags`
-+CC += gcc
-+CFLAGS += -Wall -pthread -c  -DHAS_PTHREAD_SETSCOPE -g -DUNIX -I../../base/ -I../../dynlibsrc/ -I../ -I../../models/ `pkg-config glib-2.0 --cflags`
- 
- 
--LFLAGS =  -g -L../../base/ -L../../dynlibsrc/ -lpthread `glib-config --libs` -lm
-+LFLAGS =  -g -L../../base/ -L../../dynlibsrc/ -lpthread `pkg-config glib-2.0 --libs` -lm
- 
- 
- .c.o :
---- wise2.4.1/src/dnaindex/makefile.old	2017-01-10 15:19:16.053750635 +0000
-+++ wise2.4.1/src/dnaindex/makefile	2017-01-10 15:19:50.679398862 +0000
-@@ -27,14 +27,14 @@
- 
- 
- kwise : kwise.o $(ASSEMBLY_OBJ)
--	$(CC) -o kwise kwise.o $(ASSEMBLY_OBJ)  -ldyna -lwisebase $(LFLAGS) `glib-config --libs`
-+	$(CC) -o kwise kwise.o $(ASSEMBLY_OBJ)  -ldyna -lwisebase $(LFLAGS) `pkg-config glib-2.0 --libs`
- 
- arraymatcher : arraymatcher.o $(ASSEMBLY_OBJ) 
--	$(CC) -o arraymatcher arraymatcher.o $(ASSEMBLY_OBJ)  -ldyna -lwisebase $(LFLAGS) `glib-config --libs`
-+	$(CC) -o arraymatcher arraymatcher.o $(ASSEMBLY_OBJ)  -ldyna -lwisebase $(LFLAGS) `pkg-config glib-2.0 --libs`
- 
- 
- findbad_kmer : findbad_kmer.o $(ASSEMBLY_OBJ)
--	$(CC) -o findbad_kmer findbad_kmer.o $(ASSEMBLY_OBJ)  -ldyna -lwisebase $(LFLAGS) `glib-config --libs`
-+	$(CC) -o findbad_kmer findbad_kmer.o $(ASSEMBLY_OBJ)  -ldyna -lwisebase $(LFLAGS) `pkg-config glib-2.0 --libs`
- 
- make_shotgun : make_shotgun.o shotgun.o
- 	$(CC) -o make_shotgun make_shotgun.o shotgun.o -ldyna -lwisebase $(LFLAGS)
-@@ -69,11 +69,11 @@
- show_euler : show_euler.o eulerindex.o singleseqspace.o
- 	$(CC) -o show_euler show_euler.o eulerindex.o singleseqspace.o -ldyna -lwisebase $(LFLAGS)
- 
--CC = cc
--CFLAGS = -pthread -c  -DHAS_PTHREAD_SETSCOPE -g -DUNIX -I../base/ -I../dynlibsrc/ `glib-config --cflags`
-+CC += gcc
-+CFLAGS += -pthread -c  -DHAS_PTHREAD_SETSCOPE -g -DUNIX -I../base/ -I../dynlibsrc/ `pkg-config glib-2.0 --cflags`
- 
- 
--LFLAGS =  -g -L../base/ -L../dynlibsrc/ -lpthread `glib-config --libs` -lm
-+LFLAGS =  -g -L../base/ -L../dynlibsrc/ -lpthread `pkg-config glib-2.0 --libs` -lm
- 
- 
- .c.o :
---- wise2.4.1/src/dynlibsrc/makefile.old	2017-01-10 15:20:08.159221406 +0000
-+++ wise2.4.1/src/dynlibsrc/makefile	2017-01-10 15:21:22.739464830 +0000
-@@ -81,12 +81,12 @@
- 
- 
- 
--CC = cc
-+CC += gcc
- INCFLAGS = -I../base/
- #CFLAGS = -Wall -g -pedantic -c  -DUNIX -I../base/
--CFLAGS =  -Wall -pthread -g3 -DCOMPILE_VERBOSITY -DPTHREAD -O2 -c  -DUNIX -I../base/ `glib-config --cflags`
--#CFLAGS =  -Wall -g3 -pg -DPTHREAD -O2  -c  -DUNIX -I../base/ `glib-config --cflags`
--#CFLAGS =   -O2 -c -pthread  -DUNIX  -I../base/ `glib-config --cflags`
-+CFLAGS +=  -pthread -DCOMPILE_VERBOSITY -DPTHREAD -c -DUNIX -I../base/ `pkg-config glib-2.0 --cflags`
-+#CFLAGS =  -Wall -g3 -pg -DPTHREAD -O2  -c  -DUNIX -I../base/ `pkg-config glib-2.0 --cflags`
-+#CFLAGS =   -O2 -c -pthread  -DUNIX  -I../base/ `pkg-config glib-2.0 --cflags`
- #CFLAGS =   -O -c -DUNIX -DNOERROR -I../base/
- LFLAGS =  -g -L../base/ -lm 
- AR_OPTIONS = ru
-@@ -148,13 +148,13 @@
- 	$(CC) -g -o test_shadowindex test_shadowindex.o shadowseqindex.o shadowseq.o ./libdyna.a ../base/libwisebase.a -lm
- 
- test_seqhash : test_seqhash.o subseqhash.o hsp.o hitlist.o hspscaninterface.o hsplookupscan.o libdyna.a
--	$(CC) -g -o test_seqhash `glib-config --libs` test_seqhash.o subseqhash.o hsp.o  hitlist.o hspscaninterface.o hsplookupscan.o libdyna.a ../base/libwisebase.a -lm  
-+	$(CC) -o test_seqhash `pkg-config glib-2.0 --libs` test_seqhash.o subseqhash.o hsp.o  hitlist.o hspscaninterface.o hsplookupscan.o libdyna.a ../base/libwisebase.a -lm  
- 
- test_hsp : test_hsp.o codon.o sequence.o hsp.o compmat.o probability.o 
--	$(CC) -g -o test_hsp test_hsp.o codon.o sequence.o hsp.o compmat.o probability.o  ../base/libwisebase.a -lm `glib-config --libs`
-+	$(CC) -o test_hsp test_hsp.o codon.o sequence.o hsp.o compmat.o probability.o  ../base/libwisebase.a -lm `pkg-config glib-2.0 --libs`
- 
- test_topscore : test_topscore.o codon.o sequence.o hsp.o compmat.o probability.o 
--	$(CC) -g -o test_topscore test_topscore.o codon.o sequence.o hsp.o compmat.o probability.o  ../base/libwisebase.a -lm `glib-config --libs`
-+	$(CC) -o test_topscore test_topscore.o codon.o sequence.o hsp.o compmat.o probability.o  ../base/libwisebase.a -lm `pkg-config glib-2.0 --libs`
- 
- 
- testgendb : probability.o genomicdb.o genomic.o testgendb.o sequence.o codon.o sequencedb.o complexsequence.o complexevalset.o
---- wise2.4.1/src/external/mott/makefile.old	2017-01-10 15:21:45.914229629 +0000
-+++ wise2.4.1/src/external/mott/makefile	2017-01-10 15:22:13.528950163 +0000
-@@ -14,10 +14,10 @@
- wise2_mott_bridge.o : wise2_mott_bridge.c
- 	$(CC) $(CFLAGS) -I../../dynlibsrc -I../../base wise2_mott_bridge.c
- 
--CC = cc
-+CC += gcc
- 
--CFLAGS =  -Wall -g3 -DPTHREAD -O2 -c 
--LFLAGS =  -g -L../base/ -lm 
-+CFLAGS =  -DPTHREAD -c 
-+LFLAGS =  -L../base/ -lm 
- AR_OPTIONS = ru
- 
- 
---- wise2.4.1/src/models/makefile.old	2017-01-10 15:24:11.908752314 +0000
-+++ wise2.4.1/src/models/makefile	2017-01-10 15:34:14.159658724 +0000
-@@ -50,6 +50,8 @@
- 	proteinsw.o \
- 	estquick3.o 
- 
-+EXTRALIBS += `pkg-config glib-2.0 --libs`
-+
- all : dnal psw pswdb dba estwise genewise genewisedb estwisedb genomewise sywise pseudowise promoterwise scanwise libmodel.a
- 
- libmodel.a : $(NEWG) 
-@@ -180,7 +182,7 @@
- 	$(CC) $(CFLAGS) fivestarscan.c -I../base/ -I../dynlibsrc/ -I../HMMer2/ -I.
- 
- oldpostwise : oldpostwise.o $(NEWG) 
--	$(CC) -g -o oldpostwise oldpostwise.o $(NEWG) $(LFLAGS) -lhmmer -ldyna_glib -ldyna -lwisebase  
-+	$(CC) $(LDFLAGS) -o oldpostwise oldpostwise.o $(NEWG) $(LFLAGS) -lhmmer -ldyna_glib -ldyna -lwisebase  
- 
- testdna : testdna.o dnaalign.o seqaligndisplay.o 
- 	$(CC) -o testdna testdna.o dnaalign.o seqaligndisplay.o $(LFLAGS) -ldyna_glib -ldyna -lwisebase  $(EXTRALIBS)
-@@ -192,10 +194,10 @@
- 	$(CC) -o psw psw.o sw_wrap.o seqaligndisplay.o proteinsw.o abc.o pba.o   $(LFLAGS) -ldyna_glib -ldyna -lwisebase  $(EXTRALIBS)
- 
- scanwisep.o : scanwisep.c
--	$(CC) $(CFLAGS) $(INCFLAGS) -I../external/mott `glib-config --cflags` $?
-+	$(CC) $(CFLAGS) $(INCFLAGS) -I../external/mott `pkg-config glib-2.0 --cflags` $?
- 
- hsp2aln_sw.o : hsp2aln_sw.c
--	$(CC) $(CFLAGS) $(INCFLAGS) `glib-config --cflags` $?
-+	$(CC) $(CFLAGS) $(INCFLAGS) `pkg-config glib-2.0 --cflags` $?
- 
- scanwisep_mysql.o : scanwisep.c
- 	$(CC)  $(CFLAGS) -DSCAN_MYSQL -I../corba -I../external/mott -I../mysql/protein_index/ -I/usr/local/mysql/include scanwisep.c 
-@@ -212,10 +214,10 @@
- 
- 
- scanwisep_wiseserver.o : scanwisep.c
--	$(CC)  $(CFLAGS) $(INCFLAGS)  -o scanwisep_wiseserver.o -DSCAN_WISESERVER -I../network -I../socket -I../external/mott scanwisep.c 
-+	$(CC)  $(CFLAGS) $(INCFLAGS)  -o scanwisep_wiseserver.o -DSCAN_WISESERVER -I../network -I../socket -I../external/mott scanwisep.c `pkg-config glib-2.0 --libs`
- 
- scanwise : scanwisep_wiseserver.o seqaligndisplay.o proteinsw.o sw_wrap.o abc.o pba.o hsp2aln_sw.o
--	$(CC) -o scanwise scanwisep_wiseserver.o sw_wrap.o seqaligndisplay.o proteinsw.o abc.o pba.o hsp2aln_sw.o   ../network/net_hspscan.o ../network/client_multihspscan.o  $(LFLAGS) -L../external/mott -L../socket -lmott -ldyna_glib -ldyna -lwisesocket -lwisebase  $(EXTRALIBS) -lpthread 
-+	$(CC) -o scanwise scanwisep_wiseserver.o sw_wrap.o seqaligndisplay.o proteinsw.o abc.o pba.o hsp2aln_sw.o   ../network/net_hspscan.o ../network/client_multihspscan.o  $(LFLAGS) -L../external/mott -L../socket -lmott -ldyna_glib -ldyna -lwisesocket -lwisebase  $(EXTRALIBS) -lpthread `pkg-config glib-2.0 --libs`
- 
- scanwisep_compress.o : scanwisep.c
- 	$(CC)  $(CFLAGS) -DSCAN_COMPRESS -I../dnaindex -I../network -I../socket -I../external/mott scanwisep.c 
-@@ -226,25 +228,25 @@
- 
- 
- scanwisep : scanwisep.o seqaligndisplay.o proteinsw.o sw_wrap.o abc.o pba.o hsp2aln_sw.o
--	$(CC) -o scanwisep scanwisep.o sw_wrap.o seqaligndisplay.o proteinsw.o abc.o pba.o hsp2aln_sw.o   $(LFLAGS)  -L../external/mott -lmott -ldyna_glib -ldyna  -lwisebase  $(EXTRALIBS) `glib-config --libs` -lpthread
-+	$(CC) -o scanwisep scanwisep.o sw_wrap.o seqaligndisplay.o proteinsw.o abc.o pba.o hsp2aln_sw.o   $(LFLAGS)  -L../external/mott -lmott -ldyna_glib -ldyna  -lwisebase  $(EXTRALIBS) `pkg-config glib-2.0 --libs` -lpthread
- 
- test_gwhsp : test_gwhsp.o genewisehsp.o
--	$(CC) -o test_gwhsp test_gwhsp.o genewisehsp.o $(LFLAGS) -ldyna_glib -ldyna_glib -ldyna_glib -ldyna -lwisebase  $(EXTRALIBS) `glib-config --libs` -lpthread
-+	$(CC) -o test_gwhsp test_gwhsp.o genewisehsp.o $(LFLAGS) -ldyna_glib -ldyna_glib -ldyna_glib -ldyna -lwisebase  $(EXTRALIBS) `pkg-config glib-2.0 --libs` -lpthread
- 
- localcishit.o : localcishit.c
--	$(CC) $(CFLAGS) $(INCFLAGS) `glib-config --cflags` $?
-+	$(CC) $(CFLAGS) $(INCFLAGS) `pkg-config glib-2.0 --cflags` $?
- 
- promoterwise.o : promoterwise.c  
--	$(CC) $(CFLAGS) $(INCFLAGS) `glib-config --cflags` $?
-+	$(CC) $(CFLAGS) $(INCFLAGS) `pkg-config glib-2.0 --cflags` $?
- 
- promoterwise : promoterwise.o localdba.o localcishit.o localcispara.o dbadisplay.o motifmatrix.o motifmatrixdp.o transfactor.o pwmdna.o pairwiseshortdna.o
--	$(CC) -g -o promoterwise promoterwise.o localdba.o  localcishit.o localcispara.o dbadisplay.o  motifmatrix.o motifmatrixdp.o transfactor.o pwmdna.o  pairwiseshortdna.o $(LFLAGS) -ldyna_glib -ldyna -lwisebase  $(EXTRALIBS) `glib-config --libs` -lpthread
-+	$(CC) -g -o promoterwise promoterwise.o localdba.o  localcishit.o localcispara.o dbadisplay.o  motifmatrix.o motifmatrixdp.o transfactor.o pwmdna.o  pairwiseshortdna.o $(LFLAGS) -ldyna_glib -ldyna -lwisebase  $(EXTRALIBS) `pkg-config glib-2.0 --libs` -lpthread
- 
- test_deng : test_deng.o localdba.o localcishit.o localcispara.o dbadisplay.o motifmatrix.o motifmatrixdp.o transfactor.o pwmdna.o pairwiseshortdna.o dnaprofile.o dnaprofiledp.o dnaprofileengine.o
--	$(CC) -o test_deng test_deng.o  localdba.o localcishit.o localcispara.o dbadisplay.o motifmatrix.o motifmatrixdp.o transfactor.o pwmdna.o pairwiseshortdna.o dnaprofile.o dnaprofiledp.o dnaprofileengine.o $(LFLAGS) -ldyna_glib -ldyna -lwisebase  $(EXTRALIBS) `glib-config --libs` -lpthread
-+	$(CC) -o test_deng test_deng.o  localdba.o localcishit.o localcispara.o dbadisplay.o motifmatrix.o motifmatrixdp.o transfactor.o pwmdna.o pairwiseshortdna.o dnaprofile.o dnaprofiledp.o dnaprofileengine.o $(LFLAGS) -ldyna_glib -ldyna -lwisebase  $(EXTRALIBS) `pkg-config glib-2.0 --libs` -lpthread
- 
- promotercluster : promotercluster.o localdba.o localcishit.o localcispara.o dbadisplay.o motifmatrix.o motifmatrixdp.o transfactor.o pwmdna.o pairwiseshortdna.o dnaprofile.o dnaprofiledp.o dnaprofileengine.o
--	$(CC) -o promotercluster promotercluster.o  localdba.o localcishit.o localcispara.o dbadisplay.o motifmatrix.o motifmatrixdp.o transfactor.o pwmdna.o pairwiseshortdna.o dnaprofile.o dnaprofiledp.o dnaprofileengine.o $(LFLAGS) -ldyna_glib -ldyna -lwisebase  $(EXTRALIBS) `glib-config --libs` -lpthread
-+	$(CC) -o promotercluster promotercluster.o  localdba.o localcishit.o localcispara.o dbadisplay.o motifmatrix.o motifmatrixdp.o transfactor.o pwmdna.o pairwiseshortdna.o dnaprofile.o dnaprofiledp.o dnaprofileengine.o $(LFLAGS) -ldyna_glib -ldyna -lwisebase  $(EXTRALIBS) `pkg-config glib-2.0 --libs` -lpthread
- 
- dnawise : dnawise.o dnahmm.o dnahmmdp.o seqaligndisplay.o 
- 	$(CC) -o dnawise dnawise.o dnahmm.o dnahmmdp.o  seqaligndisplay.o $(LFLAGS) -ldyna_glib -ldyna -lwisebase  -lpthread
-@@ -275,35 +277,35 @@
- 	$(CC) -o makerandomdb makerandomdb.o $(LFLAGS) -ldyna_glib -ldyna -lwisebase  $(EXTRALIBS)
- 
- genewise : genewise.o $(NEWG) 
--	$(CC) -o genewise genewise.o $(NEWG) $(LFLAGS) -lhmmer -ldyna_glib -ldyna_glib -ldyna_glib -ldyna -lwisebase  $(EXTRALIBS)
-+	$(CC) $(LDFLAGS) -o genewise genewise.o $(NEWG) $(LFLAGS) -lhmmer -ldyna_glib -ldyna_glib -ldyna_glib -ldyna -lwisebase  $(EXTRALIBS) `pkg-config glib-2.0 --libs`
- 
- cdnawise : cdnawise.o $(NEWG) cdnawise10.o 
--	$(CC) -g -o cdnawise cdnawise.o cdnawise10.o $(NEWG) $(LFLAGS) -lhmmer -ldyna_glib -ldyna -lwisebase  $(EXTRALIBS)
-+	$(CC) $(LDFLAGS) -o cdnawise cdnawise.o cdnawise10.o $(NEWG) $(LFLAGS) -lhmmer -ldyna_glib -ldyna -lwisebase  $(EXTRALIBS)
- 
- fivestar : fivestar.o fivestatemodel.o fivestate.o threestatemodel.o threestatedb.o pfamhmmer1db.o wise2xhmmer2.o seqaligndisplay.o standardout.o threestatedp.o
--	$(CC) -g -o fivestar fivestar.o fivestatemodel.o fivestate.o threestatedb.o threestatemodel.o pfamhmmer1db.o wise2xhmmer2.o seqaligndisplay.o standardout.o  threestatedp.o $(LFLAGS) -lhmmer -ldyna_glib -ldyna -lwisebase  $(EXTRALIBS)
-+	$(CC) $(LDFLAGS) -o fivestar fivestar.o fivestatemodel.o fivestate.o threestatedb.o threestatemodel.o pfamhmmer1db.o wise2xhmmer2.o seqaligndisplay.o standardout.o  threestatedp.o $(LFLAGS) -lhmmer -ldyna_glib -ldyna -lwisebase  $(EXTRALIBS)
- 
- 
- fivestarsearch : fivestarsearch.o fivestatemodel.o fivestate.o threestatemodel.o threestatedb.o pfamhmmer1db.o wise2xhmmer2.o seqaligndisplay.o standardout.o threestatedp.o
--	$(CC) -g -o fivestarsearch fivestarsearch.o fivestatemodel.o fivestate.o threestatedb.o threestatemodel.o pfamhmmer1db.o wise2xhmmer2.o seqaligndisplay.o standardout.o  threestatedp.o $(LFLAGS) -lhmmer -ldyna_glib -ldyna -lwisebase  $(EXTRALIBS)
-+	$(CC) $(LDFLAGS) -o fivestarsearch fivestarsearch.o fivestatemodel.o fivestate.o threestatedb.o threestatemodel.o pfamhmmer1db.o wise2xhmmer2.o seqaligndisplay.o standardout.o  threestatedp.o $(LFLAGS) -lhmmer -ldyna_glib -ldyna -lwisebase  $(EXTRALIBS)
- 
- fivestarscan : fivestarscan.o fivestatemodel.o fivestate.o threestatemodel.o threestatedb.o pfamhmmer1db.o wise2xhmmer2.o seqaligndisplay.o standardout.o threestatedp.o
--	$(CC) -g -o fivestarscan fivestarscan.o fivestatemodel.o fivestate.o threestatedb.o threestatemodel.o pfamhmmer1db.o wise2xhmmer2.o seqaligndisplay.o standardout.o  threestatedp.o $(LFLAGS) -lhmmer -ldyna_glib -ldyna -lwisebase  $(EXTRALIBS)
-+	$(CC) $(LDFLAGS) -o fivestarscan fivestarscan.o fivestatemodel.o fivestate.o threestatedb.o threestatemodel.o pfamhmmer1db.o wise2xhmmer2.o seqaligndisplay.o standardout.o  threestatedp.o $(LFLAGS) -lhmmer -ldyna_glib -ldyna -lwisebase  $(EXTRALIBS)
- 
- 
- editdist : editdist.o editdistdp.o standardout.o seqaligndisplay.o 
--	$(CC) -g -o editdist editdist.o editdistdp.o standardout.o seqaligndisplay.o $(LFLAGS) -ldyna_glib -ldyna -lwisebase 
-+	$(CC) $(LDFLAGS) -o editdist editdist.o editdistdp.o standardout.o seqaligndisplay.o $(LFLAGS) -ldyna_glib -ldyna -lwisebase 
- 
- 
- efgw   : genewise.o $(NEWG) 
--	$(CC) -g -o genewise genewise.o  $(NEWG)  $(LFLAGS) -lhmmer -ldyna_glib -ldyna -lwisebase  $(EXTRALIBS) -lefence
-+	$(CC) $(LDFLAGS) -o genewise genewise.o  $(NEWG)  $(LFLAGS) -lhmmer -ldyna_glib -ldyna -lwisebase  $(EXTRALIBS) -lefence
- 
- 
- genewisedb : genewisedb.o $(NEWG) 
--	$(CC) -g -o genewisedb genewisedb.o  $(NEWG)  $(LFLAGS) -lhmmer -ldyna_glib -ldyna -lwisebase  $(EXTRALIBS) 
-+	$(CC) $(LDFLAGS) -o genewisedb genewisedb.o  $(NEWG)  $(LFLAGS) -lhmmer -ldyna_glib -ldyna -lwisebase  $(EXTRALIBS) `pkg-config glib-2.0 --libs`
- 
- estwisedb : estwisedb.o $(NEWG) 
--	$(CC) -g -o estwisedb estwisedb.o $(NEWG)  $(LFLAGS) -lhmmer -ldyna_glib -ldyna -lwisebase  $(EXTRALIBS)
-+	$(CC) $(LDFLAGS) -o estwisedb estwisedb.o $(NEWG)  $(LFLAGS) -lhmmer -ldyna_glib -ldyna -lwisebase  $(EXTRALIBS) `pkg-config glib-2.0 --libs`
- 
- edb : estwisedb.o $(NEWG) 
- 	$(CC) -g -o estwisedb estwisedb.o $(NEWG)  $(LFLAGS) -lhmmer -ldyna_glib -ldyna -lwisebase  $(EXTRALIBS) -lefence
-@@ -313,28 +315,28 @@
- 
- 
- amplimer_resolver : amplimer_resolver.o dnaalign.o dnamatcher.o 
--	$(CC) -g -o amplimer_resolver amplimer_resolver.o dnamatcher.o dnaalign.o $(LFLAGS) -ldyna_glib -ldyna -lwisebase  $(EXTRALIBS)
-+	$(CC) $(LDFLAGS) -o amplimer_resolver amplimer_resolver.o dnamatcher.o dnaalign.o $(LFLAGS) -ldyna_glib -ldyna -lwisebase  $(EXTRALIBS)
- 
- genomewise : genomewise.o genomewise9.o genome_evidence.o est_evidence.o geneutil.o geneoutput.o
--	$(CC) -g -o genomewise genomewise.o genomewise9.o genome_evidence.o est_evidence.o geneoutput.o geneutil.o $(LFLAGS) -ldyna_glib -ldyna -lwisebase  $(EXTRALIBS)
-+	$(CC) $(LDFLAGS) -o genomewise genomewise.o genomewise9.o genome_evidence.o est_evidence.o geneoutput.o geneutil.o $(LFLAGS) -ldyna_glib -ldyna -lwisebase  $(EXTRALIBS)
- 
- sywise : sywise.o sywise20.o syexonmodel.o genestats.o pwmdna.o geneutil.o standardout.o
--	$(CC) -g -o sywise sywise.o sywise20.o syexonmodel.o genestats.o pwmdna.o  standardout.o geneutil.o $(LFLAGS) -ldyna_glib -ldyna -lwisebase  $(EXTRALIBS)
-+	$(CC) $(LDFLAGS) -o sywise sywise.o sywise20.o syexonmodel.o genestats.o pwmdna.o  standardout.o geneutil.o $(LFLAGS) -ldyna_glib -ldyna -lwisebase  $(EXTRALIBS)
- 
- alignwise : alignwise.o alignwisedp.o aligngenemodel.o genestats.o pwmdna.o geneutil.o standardout.o geneoutput.o
--	$(CC) -g -o alignwise alignwise.o alignwisedp.o aligngenemodel.o genestats.o pwmdna.o geneutil.o standardout.o geneoutput.o $(LFLAGS) -ldyna_glib -ldyna -lwisebase  $(EXTRALIBS)
-+	$(CC) $(LDFLAGS) -o alignwise alignwise.o alignwisedp.o aligngenemodel.o genestats.o pwmdna.o geneutil.o standardout.o geneoutput.o $(LFLAGS) -ldyna_glib -ldyna -lwisebase  $(EXTRALIBS)
- 
- test_splice : test_splice.o  aligngenemodel.o genestats.o pwmdna.o geneutil.o standardout.o
--	$(CC) -g -o test_splice test_splice.o aligngenemodel.o genestats.o pwmdna.o geneutil.o standardout.o $(LFLAGS) -ldyna_glib -ldyna -lwisebase  $(EXTRALIBS)
-+	$(CC) $(LDFLAGS) -o test_splice test_splice.o aligngenemodel.o genestats.o pwmdna.o geneutil.o standardout.o $(LFLAGS) -ldyna_glib -ldyna -lwisebase  $(EXTRALIBS)
- 
- statwise : statwise.o statwise10.o syexonmodel.o genestats.o pwmdna.o geneutil.o
--	$(CC) -g -o statwise statwise.o statwise10.o syexonmodel.o genestats.o pwmdna.o geneutil.o $(LFLAGS) -ldyna_glib -ldyna -lwisebase  $(EXTRALIBS)
-+	$(CC) $(LDFLAGS) -o statwise statwise.o statwise10.o syexonmodel.o genestats.o pwmdna.o geneutil.o $(LFLAGS) -ldyna_glib -ldyna -lwisebase  $(EXTRALIBS)
- 
- pseudowise : pseudowise.o pseudowise7.o $(NEWG) 
--	$(CC) -g -o pseudowise pseudowise.o pseudowise7.o $(NEWG) $(LFLAGS) -lhmmer -ldyna_glib -ldyna -lwisebase  $(EXTRALIBS)
-+	$(CC) $(LDFLAGS) -o pseudowise pseudowise.o pseudowise7.o $(NEWG) $(LFLAGS) -lhmmer -ldyna_glib -ldyna -lwisebase  $(EXTRALIBS) `pkg-config glib-2.0 --libs`
- 
- clonewise : clonewise.o clonewisedp.o localclonewisedp.o mapstruct.o
--	$(CC) -g -o clonewise clonewise.o clonewisedp.o localclonewisedp.o mapstruct.o $(LFLAGS) -ldyna_glib -ldyna -lwisebase  $(EXTRALIBS)
-+	$(CC) $(LDFLAGS) -o clonewise clonewise.o clonewisedp.o localclonewisedp.o mapstruct.o $(LFLAGS) -ldyna_glib -ldyna -lwisebase  $(EXTRALIBS)
- 
- 
- HMMER_LIBS = ../HMMer2/
-@@ -342,14 +344,14 @@
- HMMER_DEFINE = 
- 
- 
--CC = cc
-+CC += gcc
- #CFLAGS = -c -O2  -pg -I../base/ -I../dynlibsrc/
- #CFLAGS = -c -O2 -DPTHREAD -DHAS_PTHREAD_SETSCOPE  -DUNIX  -I../base/ -I../dynlibsrc/ -I.
--CFLAGS = -c -g3 -O2  -DUNIX  -I../base/ -I../dynlibsrc/ -I. -pthread `glib-config --cflags`
--#CFLAGS = -c  -g -DHAS_PTHREAD_SETSCOPE -DUNIX -I../base/ -I../dynlibsrc/ `glib-config --cflags`
-+CFLAGS = -c -DUNIX  -I../base/ -I../dynlibsrc/ -I. -pthread `pkg-config glib-2.0 --cflags`
-+#CFLAGS = -c  -g -DHAS_PTHREAD_SETSCOPE -DUNIX -I../base/ -I../dynlibsrc/ `pkg-config glib-2.0 --cflags`
- #LFLAGS =  -L../base/ -L../dynlibsrc/ -L../HMMer2/  
- 
--LFLAGS =  -L../base/ -L../dynlibsrc/ -L$(HMMER_LIBS) -lpthread `glib-config --libs`
-+LFLAGS =  -L../base/ -L../dynlibsrc/ -L$(HMMER_LIBS) -lpthread `pkg-config glib-2.0 --libs`
- AR_OPTIONS = ru
- 
- RANLIB_NEEDED = 0
---- wise2.4.1/src/network/makefile.old	2017-01-10 15:34:31.649482055 +0000
-+++ wise2.4.1/src/network/makefile	2017-01-10 15:35:11.545079297 +0000
-@@ -1,10 +1,10 @@
- 
- .SUFFIXES :  .dy
- 
--CC = cc
-+CC += gcc
- INCFLAGS = -I../base/  -I../socket -I../dynlibsrc -I../dnaindex
--CFLAGS =    -O2  -c -pthread  -DUNIX  -I../base/ -I../socket -I../dynlibsrc -I../dnaindex `glib-config --cflags`
--LFLAGS =  -g -L../base/ -L../socket -L../dynlibsrc -L../dnaindex -lm `glib-config --libs`
-+CFLAGS += -c -pthread  -DUNIX  -I../base/ -I../socket -I../dynlibsrc -I../dnaindex `pkg-config glib-2.0 --cflags`
-+LFLAGS =  -g -L../base/ -L../socket -L../dynlibsrc -L../dnaindex -lm `pkg-config glib-2.0 --libs`
- AR_OPTIONS = ru
- 
- RANLIB_NEEDED = 0
---- wise2.4.1/src/snp/makefile.old	2017-01-10 15:35:18.714006953 +0000
-+++ wise2.4.1/src/snp/makefile	2017-01-10 15:36:14.330445965 +0000
-@@ -2,12 +2,12 @@
- .SUFFIXES :  .dy
- 
- 
--CC = cc
-+CC += gcc
- #CFLAGS = -c -O2  -pg -I../base/ -I../dynlibsrc/
- #CFLAGS = -c -O2 -DPTHREAD -DHAS_PTHREAD_SETSCOPE  -DUNIX  -I../base/ -I../dynlibsrc/ -I.
--CFLAGS = -c -g3 -O2  -DUNIX  -I../base/ -I../dynlibsrc/ -I. -pthread `glib-config --cflags`
-+CFLAGS += -c -DUNIX  -I../base/ -I../dynlibsrc/ -I. -pthread `pkg-config glib-2.0 --cflags`
- 
--LFLAGS =  -g -L../base/ -L../dynlibsrc/ -lpthread `glib-config --libs` -lpthread -lm
-+LFLAGS =  -g -L../base/ -L../dynlibsrc/ -lpthread `pkg-config glib-2.0 --libs` -lpthread -lm
- AR_OPTIONS = ru
- 
- RANLIB_NEEDED = 0
-@@ -16,7 +16,7 @@
- 	$(CC) $(CFLAGS) $(INCFLAGS) $?
- 
- test_est : test_est.o genotype.o person.o locus_framework.o locus_model_estimators.o frequency_count.o 
--	$(CC) -o test_est test_est.o genotype.o person.o locus_framework.o locus_model_estimators.o frequency_count.o ../dynlibsrc/libdyna.a ../base/libwisebase.a $(LFLAGS)
-+	$(CC) $(LDFLAGS) -o test_est test_est.o genotype.o person.o locus_framework.o locus_model_estimators.o frequency_count.o ../dynlibsrc/libdyna.a ../base/libwisebase.a $(LFLAGS)
- 
- INCFLAGS = -I../base/ -I../dynlibsrc/
- DFLAGS = -l -D -n Wise2_ -a _api.h -b _api.t -pthreads -dbtrace 5 -nocwarn
diff --git a/sci-biology/wise/files/wise-env b/sci-biology/wise/files/wise-env
deleted file mode 100644
index 3f781c808..000000000
--- a/sci-biology/wise/files/wise-env
+++ /dev/null
@@ -1 +0,0 @@
-WISECONFIGDIR="/usr/share/wise/wisecfg"
diff --git a/sci-biology/wise/metadata.xml b/sci-biology/wise/metadata.xml
deleted file mode 100644
index 8417d1580..000000000
--- a/sci-biology/wise/metadata.xml
+++ /dev/null
@@ -1,8 +0,0 @@
-<?xml version="1.0" encoding="UTF-8"?>
-<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
-<pkgmetadata>
-	<maintainer type="project">
-		<email>sci-biology@gentoo.org</email>
-		<name>Gentoo Biology Project</name>
-	</maintainer>
-</pkgmetadata>
diff --git a/sci-biology/wise/wise-2.4.1.ebuild b/sci-biology/wise/wise-2.4.1.ebuild
deleted file mode 100644
index 4ea9cb90a..000000000
--- a/sci-biology/wise/wise-2.4.1.ebuild
+++ /dev/null
@@ -1,96 +0,0 @@
-# Copyright 1999-2017 Gentoo Foundation
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=5
-
-inherit eutils toolchain-funcs versionator
-
-DESCRIPTION="Genewise, promoterwise: align protein HMMs to DNA for CDS predictions"
-HOMEPAGE="http://www.ebi.ac.uk/~birney/wise2"
-SRC_URI="http://www.ebi.ac.uk/~birney/${PN}2/${PN}$(delete_version_separator 3).tar.gz"
-#SRC_URI="ftp://ftp.ebi.ac.uk/pub/software/${PN}2/${PN}$(delete_version_separator 3).tar.gz"
-
-LICENSE="BSD"
-SLOT="0"
-KEYWORDS="~amd64 ~x86"
-IUSE="doc static-libs"
-
-RDEPEND="sci-biology/hmmer:2"
-DEPEND="
-	${RDEPEND}
-	dev-lang/perl
-	virtual/latex-base
-	dev-libs/glib"
-
-S="${WORKDIR}"/${PN}$(delete_version_separator 3)
-
-src_prepare() {
-	epatch "${FILESDIR}"/wise-2.2.0-glibc-2.10.patch
-	epatch "${FILESDIR}"/wise-2.4.1-cflags.patch
-	epatch "${FILESDIR}"/01_welcome-csh.patch
-	epatch "${FILESDIR}"/02_isnumber.patch
-	epatch "${FILESDIR}"/03_doc-nodycache.patch
-	epatch "${FILESDIR}"/04_wise2-pdflatex-update.patch
-	# the two below are already in wise-2.2.0-glibc-2.10.patch wise-2.4.1-cflags.patch
-	#epatch "${FILESDIR}"/06_getline.patch
-	#epatch "${FILESDIR}"/07_ld--as-needed.patch
-	epatch "${FILESDIR}"/08_mayhem.patch
-	epatch "${FILESDIR}"/09_dnal-add-return-statement.patch
-	epatch "${FILESDIR}"/11_consistent_manual_dates.patch
-#	cd "${S}"/docs || die
-#	cat "${S}"/src/models/*.tex "${S}"/src/dynlibsrc/*.tex | perl gettex.pl > temp.tex || die
-#	cat wise2api.tex temp.tex apiend.tex > api.tex || die
-#	epatch "${FILESDIR}"/${PN}-api.tex.patch
-	#
-	# eventually, zap bundled but modified version of hmmer-2?
-	# This is not recommended, because sean and I diverged a while back on indexing
-	# strategies. At some point I will need to port the later HMMer into Wise2.
-	# rm -rf src/HMMer2 || die "Cannot zap bundled hmmer-2 sources"
-	# sed -e "s#HMMER_INCLUDE = ../HMMer2/#HMMER_INCLUDE = ${EPREFIX}/usr/include/hmmer2#" -i src/makefile || die
-	# sed -e "s#HMMER_LIBS.* = ../HMMer2/#HMMER_LIBS = ${EPREFIX}/usr/$(get_libdir)"#" -i src/makefile || die
-	# TODO: change eventual callers of the hmmer-2 binaries?
-	# ./test_data/*.{HMM,hmm}
-	# ./src/test/*.{HMM,hmm}
-	# ./src/perl/makelib.pl
-	#for e in hmmalign hmmbuild hmmcalibrate hmmconvert hmmemit hmmpfam hmmsearch; do \
-	#	# append '2' to the filename in "$e"
-	#done
-}
-
-src_compile() {
-	emake \
-		-C src \
-		CC="$(tc-getCC)" \
-		all
-	if use doc; then
-		cd "${S}"/docs || die
-		for i in api appendix dynamite wise2 wise3arch; do
-			latex ${i} || die
-			latex ${i} || die
-			dvips ${i}.dvi -o || die
-		done
-	fi
-}
-
-src_test() {
-	cd "${S}"/src || die
-	WISECONFIGDIR="${S}/wisecfg" emake test
-}
-
-src_install() {
-	dobin "${S}"/src/bin/* "${S}"/src/dynlibsrc/testgendb
-	use static-libs && \
-		dolib.a \
-			"${S}"/src/base/libwisebase.a \
-			"${S}"/src/dynlibsrc/libdyna.a \
-			"${S}"/src/models/libmodel.a
-
-	insinto /usr/share/${PN}
-	doins -r "${S}"/wisecfg
-
-	if use doc; then
-		insinto /usr/share/doc/${PF}
-		doins "${S}"/docs/*.ps
-	fi
-	newenvd "${FILESDIR}"/${PN}-env 24wise || die "Failed to install env file"
-}
diff --git a/sci-biology/yaha/yaha-9999.ebuild b/sci-biology/yaha/yaha-9999.ebuild
index 88a6dcfa6..f24827d3a 100644
--- a/sci-biology/yaha/yaha-9999.ebuild
+++ b/sci-biology/yaha/yaha-9999.ebuild
@@ -1,7 +1,7 @@
-# Copyright 1999-2018 Gentoo Foundation
+# Copyright 1999-2021 Gentoo Authors
 # Distributed under the terms of the GNU General Public License v2
 
-EAPI=6
+EAPI=7
 
 inherit flag-o-matic git-r3 toolchain-funcs
 
@@ -12,7 +12,6 @@ EGIT_REPO_URI="https://github.com/GregoryFaust/yaha.git"
 LICENSE="MIT"
 SLOT="0"
 KEYWORDS=""
-IUSE=""
 
 PATCHES=(
 	"${FILESDIR}"/${P}-fpermissive.patch
diff --git a/sci-biology/zmap/zmap-2.12.0.ebuild b/sci-biology/zmap/zmap-2.12.0.ebuild
index 4b52b3ebf..b4cb2e9b4 100644
--- a/sci-biology/zmap/zmap-2.12.0.ebuild
+++ b/sci-biology/zmap/zmap-2.12.0.ebuild
@@ -1,10 +1,10 @@
-# Copyright 1999-2018 Gentoo Authors
+# Copyright 1999-2021 Gentoo Authors
 # Distributed under the terms of the GNU General Public License v2
 
 EAPI=7
 
 DESCRIPTION="A desktop genome browser using GFF inputs"
-HOMEPAGE="http://www.sanger.ac.uk/science/tools/zmap"
+HOMEPAGE="https://www.sanger.ac.uk/science/tools/zmap"
 SRC_URI="ftp://ftp.sanger.ac.uk/pub/resources/software/zmap/production/zmap-${PV}.tar.gz
 	ftp://ftp.sanger.ac.uk/pub/resources/software/zmap/ZMap_User_Manual.pdf"
 
diff --git a/sci-biology/zmsort/zmsort-110625.ebuild b/sci-biology/zmsort/zmsort-110625.ebuild
index 3a46da4f9..773a80cc5 100644
--- a/sci-biology/zmsort/zmsort-110625.ebuild
+++ b/sci-biology/zmsort/zmsort-110625.ebuild
@@ -6,7 +6,7 @@ EAPI=7
 inherit toolchain-funcs
 
 DESCRIPTION="Merge-sort utility for compressed alignment files, with multi-file output"
-HOMEPAGE="http://compbio.dfci.harvard.edu/tgi/software/"
+HOMEPAGE="https://web.archive.org/web/20140726030702/http://compbio.dfci.harvard.edu/tgi/software/"
 SRC_URI="
 	ftp://occams.dfci.harvard.edu/pub/bio/tgi/software/tgicl/${PN}.tar.gz -> ${P}.tar.gz
 	ftp://occams.dfci.harvard.edu/pub/bio/tgi/software/tgicl/gclib.tar.gz -> gclib-${PV}.tar.gz"
diff --git a/sci-chemistry/GromacsWrapper/GromacsWrapper-9999.ebuild b/sci-chemistry/GromacsWrapper/GromacsWrapper-9999.ebuild
deleted file mode 100644
index b51f80273..000000000
--- a/sci-chemistry/GromacsWrapper/GromacsWrapper-9999.ebuild
+++ /dev/null
@@ -1,40 +0,0 @@
-# Copyright 1999-2014 Gentoo Foundation
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=5
-
-PYTHON_COMPAT=( python2_7 )
-
-if [[ $PV = *9999* ]]; then
-	scm_eclass=git-r3
-	EGIT_REPO_URI="
-		git://github.com/orbeckst/${PN}.git
-		https://github.com/orbeckst/${PN}.git"
-	EGIT_BRANCH="develop"
-	SRC_URI=""
-	KEYWORDS=""
-else
-	scm_eclass=vcs-snapshot
-	SRC_URI="https://github.com/orbeckst/${PN}/archive/release-${PV}.tar.gz -> ${P}.tar.gz"
-	KEYWORDS="~amd64 ~x86"
-fi
-
-inherit eutils distutils-r1 ${scm_eclass}
-
-DESCRIPTION="Python framework for Gromacs"
-HOMEPAGE="http://orbeckst.github.com/GromacsWrapper/"
-
-LICENSE="GPL-3 LGPL-3"
-SLOT="0"
-IUSE=""
-
-DEPEND="
-	>=dev-python/matplotlib-0.91.3[${PYTHON_USEDEP}]
-	>=dev-python/RecSQL-0.3[${PYTHON_USEDEP}]
-	>=sci-libs/scipy-0.9[${PYTHON_USEDEP}]
-		"
-RDEPEND="${DEPEND}"
-
-PATCHES=(
-	"${FILESDIR}/0001-Drop-chmod-hack.patch"
-)
diff --git a/sci-chemistry/GromacsWrapper/files/0001-Drop-chmod-hack.patch b/sci-chemistry/GromacsWrapper/files/0001-Drop-chmod-hack.patch
deleted file mode 100644
index 8645df77b..000000000
--- a/sci-chemistry/GromacsWrapper/files/0001-Drop-chmod-hack.patch
+++ /dev/null
@@ -1,28 +0,0 @@
-From 49b8d9662365e0e9b0725682b8a8479de402b272 Mon Sep 17 00:00:00 2001
-From: Alexey Shvetsov <alexxy@gentoo.org>
-Date: Sat, 23 Mar 2013 16:40:04 +0400
-Subject: [PATCH] Drop chmod hack.
-
-It doesnt work if wrapper installed system-wide
-
-Signed-off-by: Alexey Shvetsov <alexxy@gentoo.org>
----
- gromacs/config.py | 2 --
- 1 file changed, 2 deletions(-)
-
-diff --git a/gromacs/config.py b/gromacs/config.py
-index cece6fc..2e686e7 100644
---- a/gromacs/config.py
-+++ b/gromacs/config.py
-@@ -619,8 +619,6 @@ del g
- # Must extract because it is part of a zipped python egg;
- # see http://peak.telecommunity.com/DevCenter/PythonEggs#accessing-package-resources
- GridMAT_MD = resource_filename(__name__,'external/GridMAT-MD_v1.0.2/GridMAT-MD.pl')
--os.chmod(GridMAT_MD, 0755)
--
- 
- #: 3rd party bundled analysis scripts and tools; this is a list of triplets of
- #:
--- 
-1.8.1.5
-
diff --git a/sci-chemistry/GromacsWrapper/metadata.xml b/sci-chemistry/GromacsWrapper/metadata.xml
deleted file mode 100644
index 7daa2ce7e..000000000
--- a/sci-chemistry/GromacsWrapper/metadata.xml
+++ /dev/null
@@ -1,12 +0,0 @@
-<?xml version="1.0" encoding="UTF-8"?>
-<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
-<pkgmetadata>
-	<maintainer type="person">
-		<email>alexxy@gentoo.org</email>
-		<name>Alexey Shvetsov</name>
-	</maintainer>
-	<maintainer type="project">
-		<email>sci-chemistry@gentoo.org</email>
-		<name>Gentoo Chemistry Project</name>
-	</maintainer>
-</pkgmetadata>
diff --git a/sci-chemistry/MotionCor2/Manifest b/sci-chemistry/MotionCor2/Manifest
new file mode 100644
index 000000000..8dc156cba
--- /dev/null
+++ b/sci-chemistry/MotionCor2/Manifest
@@ -0,0 +1 @@
+DIST MotionCor2_1.4.0.zip 3514692 BLAKE2B b2204dbb6d241890be362076cda641b6ccfe6fa7f1d89e5a26c3725b7b82148e45a56c778d8172a3d81bea039ed866cb0a402d6d5ca47d0e11c5357d9de2bfb8 SHA512 69b3ae237f85fb5759ce36f30670f3313d273d8fdac0143c665a22878f84f1b7679e155c1f1ec3a648ce2a2adc0ada2787afb2df3cefd8679004017f45646529
diff --git a/sci-chemistry/MotionCor2/MotionCor2-1.4.0.ebuild b/sci-chemistry/MotionCor2/MotionCor2-1.4.0.ebuild
new file mode 100644
index 000000000..1f08bd4ac
--- /dev/null
+++ b/sci-chemistry/MotionCor2/MotionCor2-1.4.0.ebuild
@@ -0,0 +1,37 @@
+# Copyright 2019-2021 Gentoo Authors
+# Distributed under the terms of the GNU General Public License v2
+
+EAPI=7
+
+DESCRIPTION="Correction of electron beam-induced sample motion"
+HOMEPAGE="https://emcore.ucsf.edu/ucsf-motioncor2"
+SRC_URI="${PN}_${PV}.zip"
+S="${WORKDIR}"/${PN}_${PV}
+
+LICENSE="UCSF-Motioncor2"
+SLOT="0"
+KEYWORDS="~amd64"
+RESTRICT="fetch"
+
+RDEPEND="
+	media-libs/tiff
+	app-arch/xz-utils
+	media-libs/libjpeg-turbo
+"
+BDEPEND="app-arch/unzip"
+
+pkg_nofetch() {
+	elog "Please download ${PN}_${PV}.zip from:"
+	elog "\t ${HOMEPAGE}"
+	elog "and place it into your DISTDIR folder"
+}
+
+src_install() {
+	dodoc MotionCor2-UserManual-10-08-2020.pdf \
+	      MotionCor2_1.4.0_ReleaseIntro-10-14-2020.docx
+	docompress -x /usr/share/doc/${PF}
+
+	local mcbin
+	dobin "${mcbin}"
+	dosym "${mcbin}" /usr/bin/MotionCor2
+}
diff --git a/sci-chemistry/MotionCor2/metadata.xml b/sci-chemistry/MotionCor2/metadata.xml
new file mode 100644
index 000000000..7e9e870fd
--- /dev/null
+++ b/sci-chemistry/MotionCor2/metadata.xml
@@ -0,0 +1,12 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
+<pkgmetadata>
+	<maintainer type="project">
+		<email>sci-chemistry@gentoo.org</email>
+		<name>Gentoo Chemistry Project</name>
+	</maintainer>
+	<maintainer type="person">
+		<email>alexxy@gentoo.org</email>
+		<name>Alexey Shvetsov</name>
+	</maintainer>
+</pkgmetadata>
diff --git a/sci-chemistry/acpype/Manifest b/sci-chemistry/acpype/Manifest
deleted file mode 100644
index 16db05919..000000000
--- a/sci-chemistry/acpype/Manifest
+++ /dev/null
@@ -1 +0,0 @@
-DIST acpype-0.1.0.tar.gz 1187249 BLAKE2B 6fc18b1b293c5b7bf14c5be9ee63d281deee83aa381dd1f71af5b27bb8d4a3f4c2b6f646b652befd28c674f72996b45aa31d110e01754b9e51d7f9bdf8840b38 SHA512 4edfd17a4d474d00a086ff59c4d4423bed9e0c39d2e762d6667792332dff0c121d37e18e9693f6d6a45967e06d0ce17597d62f5754c187ea19fb6750b5310fe0
diff --git a/sci-chemistry/acpype/acpype-0.1.0.ebuild b/sci-chemistry/acpype/acpype-0.1.0.ebuild
deleted file mode 100644
index 30b496f31..000000000
--- a/sci-chemistry/acpype/acpype-0.1.0.ebuild
+++ /dev/null
@@ -1,32 +0,0 @@
-# Copyright 1999-2017 Gentoo Foundation
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=6
-
-PYTHON_COMPAT=( python2_7 )
-
-inherit distutils-r1
-
-DESCRIPTION="AnteChamber PYthon Parser interfacE"
-HOMEPAGE="https://github.com/llazzaro"
-SRC_URI="https://github.com/llazzaro/${PN}/archive/${PV}.tar.gz -> ${P}.tar.gz"
-
-LICENSE="MIT"
-SLOT="0"
-KEYWORDS="~amd64 ~x86 ~amd64-linux"
-IUSE=""
-
-REQUIRED_USE="${PYTHON_REQUIRED_USE}"
-
-DEPEND="
-	${PYTHON_DEPS}
-	sci-chemistry/openbabel
-	sci-chemistry/ambertools"
-RDEPEND="${DEPEND}"
-
-src_prepare() {
-	sed \
-		-e '1s:^:#!/usr/bin/python\n\n:g' \
-		-i acpype/CcpnToAcpype.py || die
-	default
-}
diff --git a/sci-chemistry/acpype/metadata.xml b/sci-chemistry/acpype/metadata.xml
deleted file mode 100644
index 9528200f2..000000000
--- a/sci-chemistry/acpype/metadata.xml
+++ /dev/null
@@ -1,9 +0,0 @@
-<?xml version="1.0" encoding="UTF-8"?>
-<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
-<pkgmetadata>
-	<maintainer type="person">
-		<email>alexxy@gentoo.org</email>
-		<name>Alexey Shvetsov</name>
-		<description>AnteChamber PYthon Parser interfacE</description>
-	</maintainer>
-</pkgmetadata>
diff --git a/sci-chemistry/ambertools/Manifest b/sci-chemistry/ambertools/Manifest
deleted file mode 100644
index be7b142b3..000000000
--- a/sci-chemistry/ambertools/Manifest
+++ /dev/null
@@ -1,3 +0,0 @@
-DIST AmberTools12.tar.bz2 89175545 BLAKE2B cbcdadc0e207606ff4a67e31d715ac4f1113d0d72a6f7b17243d448ced788ab75fd7ed93a299e7be120b15fae187697838d6799db02e8efc25c37c207ae3eaca SHA512 4c34d460fdedf00ade847040856d4bf7df65e7370d4a696dd858fdd3612c192ddc13dabde559bc1a7ae4068ba8040ee159479e247b2c1e59ed976a5aa6344970
-DIST AmberTools15.tar.bz2 231809206 SHA256 f0ed40998d0dc8ce5487aaa673827b8cf29bed2b6a09dbdec22e90236a614ec8 SHA512 f91ec69a0f0c632aea9152d36c63dc1ce67a6aaa7b77715fb3b12cadcbcc687ec2a142bd6a0e600cfb8715ae25c33fe90ad8bee3d5bbe94359e91c9e62c1dbd0 WHIRLPOOL 20565fbf1959ce994c590a9f97818a847974f4fabddf4c1719eb85b4ae39f7f52acd5eaddbb5e2c5871454cede066f0f21a69f01ae0ecba4dee0b45f28dd4437
-DIST ambertools-bugfixes-12_p38.tar.xz 88340 BLAKE2B 2bf4e6159a8ad3b064e4abb42e87b0340030400d79497a998009d9680b2e54816071162ad675c4e08dc12b7ce65e831cf9045a046d6f86282e4752cd796399ee SHA512 485123d81e689e06f2a1affc9f17d99e9ba18f92e464beb8fb9c835897693a1bd7d330a8bf9d3526c91eadb32a9b58692185e218c61002f0eeab22ff6efbbb08
diff --git a/sci-chemistry/ambertools/ambertools-12_p38-r1.ebuild b/sci-chemistry/ambertools/ambertools-12_p38-r1.ebuild
deleted file mode 100644
index e8fe18256..000000000
--- a/sci-chemistry/ambertools/ambertools-12_p38-r1.ebuild
+++ /dev/null
@@ -1,164 +0,0 @@
-# Copyright 1999-2016 Gentoo Foundation
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=5
-
-inherit eutils fortran-2 multilib multiprocessing toolchain-funcs
-
-DESCRIPTION="A suite for carrying out complete molecular mechanics investigations"
-HOMEPAGE="http://ambermd.org/#AmberTools"
-SRC_URI="
-	AmberTools${PV%_p*}.tar.bz2
-	http://dev.gentoo.org/~jlec/distfiles/${PN}-bugfixes-${PV}.tar.xz"
-
-LICENSE="GPL-2"
-SLOT="0"
-KEYWORDS="~amd64 ~x86 ~amd64-linux"
-IUSE="openmp X"
-
-RESTRICT="fetch"
-
-RDEPEND="
-	virtual/cblas
-	virtual/lapack
-	sci-libs/clapack
-	sci-libs/arpack
-	sci-libs/cifparse-obj
-	sci-chemistry/mopac7
-	sci-libs/netcdf
-	>=sci-libs/fftw-3.3:3.0
-	sci-chemistry/reduce"
-DEPEND="${RDEPEND}
-	app-shells/tcsh
-	dev-util/byacc
-	dev-libs/libf2c
-	sys-devel/ucpp"
-
-S="${WORKDIR}/amber12"
-
-pkg_nofetch() {
-	einfo "Go to ${HOMEPAGE} and get AmberTools${PV%_p*}.tar.bz2"
-	einfo "and download http://dev.gentoo.org/~jlec/distfiles/${PN}-bugfixes-${PV}.tar.xz"
-	einfo "Place both into ${DISTDIR}"
-}
-
-pkg_setup() {
-	fortran-2_pkg_setup
-	if use openmp; then
-		tc-has-openmp || \
-			die "Please select an openmp capable compiler like gcc[openmp]"
-	fi
-	export AMBERHOME="${S}"
-}
-
-src_prepare() {
-	epatch \
-		"${FILESDIR}"/${P}-gcc5.patch \
-		"${FILESDIR}"/${P}-format-security.patch \
-		"${FILESDIR}"/${PN}-12-gentoo.patch \
-		"${WORKDIR}"/bugfixes/bugfix.{14..38}
-	cd "${S}"/AmberTools/src || die
-	rm -r \
-		arpack \
-		blas \
-		byacc \
-		lapack \
-		fftw-3.3 \
-		c9x-complex \
-		cifparse \
-		netcdf \
-		reduce \
-		ucpp-1.3 \
-		|| die
-
-	cd "${S}"/AmberTools/src || die
-	sed \
-		-e "s:\\\\\$(LIBDIR)/arpack.a:-larpack:g" \
-		-e "s:\\\\\$(LIBDIR)/lapack.a:$($(tc-getPKG_CONFIG) lapack --libs) -lclapack:g" \
-		-e "s:-llapack:$($(tc-getPKG_CONFIG) lapack --libs) -lclapack:g" \
-		-e "s:\\\\\$(LIBDIR)/blas.a:$($(tc-getPKG_CONFIG) blas cblas --libs):g" \
-		-e "s:-lblas:$($(tc-getPKG_CONFIG) blas cblas --libs):g" \
-		-e "s:GENTOO_CFLAGS:${CFLAGS} -DBINTRAJ :g" \
-		-e "s:GENTOO_CXXFLAGS:${CXXFLAGS}:g" \
-		-e "s:GENTOO_FFLAGS:${FFLAGS}:g" \
-		-e "s:GENTOO_LDFLAGS:${LDFLAGS}:g" \
-		-e "s:GENTOO_INCLUDE:${EPREFIX}/usr/include:g" \
-		-e "s:GENTOO_FFTW3_LIBS:$($(tc-getPKG_CONFIG) fftw3 --libs):" \
-		-e "s:fc=g77:fc=$(tc-getFC):g" \
-		-e "s:\$netcdfflag:$($(tc-getPKG_CONFIG) netcdf --libs):g" \
-		-e "s:NETCDF=\$netcdf:NETCDF=netcdf.mod:g" \
-		-i configure2 || die
-
-	sed \
-		-e "s:arsecond_:arscnd_:g" \
-		-i sff/time.c sff/sff.h sff/sff.c || die
-
-}
-
-src_configure() {
-	local myconf="--no-updates"
-
-	use X || myconf="${myconf} -noX11"
-
-	use openmp && myconf="${myconf} -openmp"
-
-	cd "${S}" || die
-
-	sed \
-		-e '/patch_amber.py/d' \
-		-i configure || die
-
-	./configure \
-		${myconf} \
-		-nobintraj \
-		-nomtkpp \
-		gnu || die
-}
-
-src_test() {
-	use openmp && export OMP_NUM_THREADS=$(makeopts_jobs)
-
-	emake test
-}
-
-src_compile() {
-	emake \
-		CC=$(tc-getCC) \
-		FC=$(tc-getFC)
-}
-
-src_install() {
-	rm bin/*.py || die
-
-	for x in bin/*
-	do
-		[ ! -d ${x} ] && dobin ${x}
-	done
-
-	dobin AmberTools/src/antechamber/mopac.sh
-	sed \
-		-e "s:\$AMBERHOME/bin/mopac:mopac7:g" \
-		-i "${ED}/usr/bin/mopac.sh" || die
-
-	# Make symlinks untill binpath for amber will be fixed
-	dodir /usr/share/${PN}/bin
-	cd "${ED}/usr/bin" || die
-	for x in *; do
-		dosym ../../../bin/${x} /usr/share/${PN}/bin/${x}
-	done
-	cd "${S}" || die
-
-	dodoc doc/AmberTools12.pdf
-	dolib.a lib/*
-	insinto /usr/include/${PN}
-	doins include/*
-	insinto /usr/share/${PN}
-	doins -r dat
-	cd AmberTools || die
-	doins -r benchmarks examples test
-
-	cat >> "${T}"/99ambertools <<- EOF
-	AMBERHOME="${EPREFIX}/usr/share/ambertools"
-	EOF
-	doenvd "${T}"/99ambertools
-}
diff --git a/sci-chemistry/ambertools/ambertools-15_p6.ebuild b/sci-chemistry/ambertools/ambertools-15_p6.ebuild
deleted file mode 100644
index 8aa759071..000000000
--- a/sci-chemistry/ambertools/ambertools-15_p6.ebuild
+++ /dev/null
@@ -1,190 +0,0 @@
-# Copyright 1999-2016 Gentoo Foundation
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=6
-
-PYTHON_COMPAT=( python2_7 )
-
-inherit fortran-2 python-r1 toolchain-funcs
-
-DESCRIPTION="A suite for carrying out complete molecular mechanics investigations"
-HOMEPAGE="http://ambermd.org/#AmberTools"
-SRC_URI="
-	AmberTools${PV%_p*}.tar.bz2"
-
-LICENSE="GPL-2"
-SLOT="0"
-KEYWORDS="~amd64 ~x86 ~amd64-linux"
-IUSE="X"
-
-RESTRICT="fetch"
-
-RDEPEND="${PYTHON_DEPS}
-	virtual/cblas
-	virtual/lapack
-	sci-libs/clapack
-	sci-libs/arpack
-	sci-chemistry/mopac7
-	sci-libs/netcdf
-	sci-libs/netcdf-fortran
-	>=sci-libs/fftw-3.3:3.0
-	sci-chemistry/reduce"
-DEPEND="${RDEPEND}
-	app-shells/tcsh
-	dev-util/byacc
-	dev-libs/libf2c
-	sys-devel/ucpp"
-
-S="${WORKDIR}/amber14"
-
-pkg_nofetch() {
-	einfo "Go to ${HOMEPAGE} and get AmberTools${PV%_p*}.tar.bz2"
-	einfo "Place it into ${DISTDIR}"
-}
-
-pkg_setup() {
-	fortran-2_pkg_setup
-	export AMBERHOME="${S}"
-}
-
-src_prepare() {
-	eapply \
-		"${FILESDIR}"/${PN}-15-gentoo.patch
-	eapply -p0 \
-		"${FILESDIR}"/${PN}-15-update.{1..6}.patch
-
-	eapply_user
-
-	cd "${S}"/AmberTools/src || die
-	rm -r \
-		arpack \
-		blas \
-		byacc \
-		lapack \
-		fftw-3.3 \
-		c9x-complex \
-		netcdf-fortran-4.2 \
-		netcdf-4.3.0 \
-		reduce \
-		ucpp-1.3 \
-		|| die
-
-	cd "${S}"/AmberTools/src || die
-	sed \
-		-e "s:\\\\\$(LIBDIR)/arpack.a:-larpack:g" \
-		-e "s:\\\\\$(LIBDIR)/lapack.a:$($(tc-getPKG_CONFIG) lapack --libs) -lclapack:g" \
-		-e "s:-llapack:$($(tc-getPKG_CONFIG) lapack --libs) -lclapack:g" \
-		-e "s:\\\\\$(LIBDIR)/blas.a:$($(tc-getPKG_CONFIG) blas cblas --libs):g" \
-		-e "s:-lblas:$($(tc-getPKG_CONFIG) blas cblas --libs):g" \
-		-e "s:GENTOO_CFLAGS:${CFLAGS}:g" \
-		-e "s:GENTOO_CXXFLAGS:${CXXFLAGS}:g" \
-		-e "s:GENTOO_FFLAGS:${FFLAGS}:g" \
-		-e "s:GENTOO_LDFLAGS:${LDFLAGS}:g" \
-		-e "s:GENTOO_INCLUDE:${EPREFIX}/usr/include:g" \
-		-e "s:GENTOO_FFTW3_LIBS:$($(tc-getPKG_CONFIG) fftw3 --libs):" \
-		-e "s:fc=g77:fc=$(tc-getFC):g" \
-		-e "s:NETCDF=\$netcdf:NETCDF=netcdf.mod:g" \
-		-e "s:\$netcdf_flag:$($(tc-getPKG_CONFIG) netcdf --libs):g" \
-		-e "s:\$netcdfflagc:$($(tc-getPKG_CONFIG) netcdf --libs):g" \
-		-e "s:\$netcdfflagf:$($(tc-getPKG_CONFIG) netcdf-fortran --libs):g" \
-		-i configure2 || die
-
-	sed \
-		-e "s:arsecond_:arscnd_:g" \
-		-i sff/time.c sff/sff.h sff/sff.c || die
-
-}
-
-src_configure() {
-	python_setup
-
-	local myconf="--no-updates"
-
-	use X || myconf="${myconf} -noX11"
-
-	cd "${S}" || die
-
-	sed \
-		-e '/patch_amber.py/d' \
-		-i configure || die
-
-	./configure \
-		${myconf} \
-		-nomtkpp \
-		--with-python ${PYTHON} \
-		--with-netcdf /usr \
-		gnu || die
-}
-
-src_compile() {
-	emake \
-		CC=$(tc-getCC) \
-		FC=$(tc-getFC)
-}
-
-src_test() {
-	source ${AMBERHOME}/amber.sh
-
-	emake test
-}
-
-src_install() {
-	local x
-	for x in bin/*
-	do
-		[ ! -d ${x} ] && dobin ${x}
-	done
-
-	dobin AmberTools/src/antechamber/mopac.sh
-	sed \
-		-e "s:\$AMBERHOME/bin/mopac:mopac7:g" \
-		-i "${ED}/usr/bin/mopac.sh" || die
-
-	# Make symlinks untill binpath for amber will be fixed
-	dodir /usr/share/${PN}/bin
-	cd "${ED}/usr/bin" || die
-	for x in *
-	do
-		dosym ../../../bin/${x} /usr/share/${PN}/bin/${x}
-	done
-	cd "${S}" || die
-
-	dodoc doc/Amber15.pdf
-
-	dolib.a  lib/*.a
-	dolib.so lib/*.so
-
-	local m=(
-		chemistry
-		compat24.py
-		cpinutils
-		fortranformat
-		interface
-		mcpb
-		mdoutanalyzer
-		MMPBSA_mods
-		ParmedTools
-		pymsmtexp.py
-		pymsmtlib
-		pymsmtmol
-		sander
-		sanderles
-	)
-	for x in ${m[@]}
-	do
-		python_domodule lib/${EPYTHON}/site-packages/${x}
-	done
-
-	insinto /usr/include/${PN}
-	doins include/*
-
-	insinto /usr/share/${PN}
-	doins -r dat
-	cd AmberTools || die
-	doins -r benchmarks examples test
-
-	cat >> "${T}"/99ambertools <<- EOF
-	AMBERHOME="${EPREFIX}/usr/share/ambertools"
-	EOF
-	doenvd "${T}"/99ambertools
-}
diff --git a/sci-chemistry/ambertools/files/ambertools-12-gentoo.patch b/sci-chemistry/ambertools/files/ambertools-12-gentoo.patch
deleted file mode 100644
index 110343e22..000000000
--- a/sci-chemistry/ambertools/files/ambertools-12-gentoo.patch
+++ /dev/null
@@ -1,1345 +0,0 @@
- AmberTools/src/Makefile                            |  42 +-
- AmberTools/src/configure2                          |  63 +-
- AmberTools/src/cpptraj/src/Makefile_at             |  14 +-
- AmberTools/src/mdgx/Makefile                       |   9 +-
- AmberTools/src/mdgx/Trajectory.c                   |   2 +-
- .../src/mmpbsa_py/MMPBSA_mods/amber_outputs.py     |   4 +-
- AmberTools/src/nab/database.c                      |   2 +-
- AmberTools/src/nab/nab.c                           |   4 +-
- AmberTools/src/pbsa/Makefile                       |  44 +-
- AmberTools/src/ptraj/Makefile                      |   9 +-
- AmberTools/src/ptraj/trajectory.c                  |   2 +-
- AmberTools/src/sff/Makefile                        |   4 +-
- AmberTools/src/sff/dsarpack.f                      | 654 +++++++++++++++++++++
- AmberTools/src/sqm/Makefile                        |   7 +-
- AmberTools/test/Makefile                           |   4 +-
- .../01_Generalized_Born/energies.csv.save          |   8 +-
- AmberTools/test/nab/Makefile                       |   2 +
- AmberTools/test/nab/Run.rism_sp                    |   2 +-
- AmberTools/test/nab/Run.rism_sp2                   |   2 +-
- AmberTools/test/test_at_serial.sh                  |   6 +
- Makefile                                           |   2 +-
- 21 files changed, 725 insertions(+), 161 deletions(-)
-
-diff --git a/AmberTools/src/Makefile b/AmberTools/src/Makefile
-index e5c0ded..ce8f883 100644
---- a/AmberTools/src/Makefile
-+++ b/AmberTools/src/Makefile
-@@ -13,12 +13,6 @@ install: $(INSTALLTYPE)
- serial: configured_serial THIRDPARTY $(MTKPP)
- 	@echo "Starting installation of ${AMBERTOOLS} serial at `date`".
- #	utility routines and libraries:
--	(cd ucpp-1.3 && $(MAKE) $(UCPP) )
--	(cd byacc && $(MAKE) install )
--	(cd arpack && $(MAKE) install );
--	(cd lapack && $(MAKE) $(LAPACK) )
--	(cd blas && $(MAKE) $(BLAS) )
--	(cd c9x-complex && $(MAKE) $(C9XCOMPLEX) )
- 	(cd etc && $(MAKE) install )
- 	(cd chamber && $(MAKE) install )
- 	(cd pbsa && $(MAKE) install )
-@@ -34,13 +28,11 @@ serial: configured_serial THIRDPARTY $(MTKPP)
- 	(cd cpptraj && $(MAKE) install)
- 
- #   miscellaneous:
--	(cd reduce && $(MAKE) install )
- 
- #   leap
- 	(cd leap && $(MAKE) install )
- 
- #   nab:
--	(cd cifparse && $(MAKE) install )
- 	(cd sff && $(MAKE) install )
- 	(cd pbsa && $(MAKE) libinstall )
- 	(cd rism && $(MAKE) $(RISM) )
-@@ -77,17 +69,10 @@ serial: configured_serial THIRDPARTY $(MTKPP)
- 	@echo "Installation of ${AMBERTOOLS} serial is complete at `date`."
- 	@echo ""
- 
--nabonly: $(NETCDF) $(XBLAS)  
-+nabonly: $(XBLAS)
- #	utility routines and libraries:
--	(cd ucpp-1.3 && $(MAKE) $(UCPP) )
--	(cd byacc && $(MAKE) install )
--	(cd arpack && $(MAKE) install );
--	(cd lapack && $(MAKE) $(LAPACK) )
--	(cd blas && $(MAKE) $(BLAS) )
--	(cd c9x-complex && $(MAKE) $(C9XCOMPLEX) )
- 	(cd pbsa && $(MAKE) libinstall )
- 	(cd rism && $(MAKE) $(RISM) )
--	(cd cifparse && $(MAKE) install )
- 	(cd sff && $(MAKE) install )
- 	(cd nab && $(MAKE) install )
- 	(cd nss && $(MAKE) install )
-@@ -119,8 +104,6 @@ parallel: configured_parallel THIRDPARTY
- 	(cd sff && $(MAKE) libsff_mpi )
- #	(cd pbsa && $(MAKE) clean && $(MAKE) install.parallel )
- 	(cd pbsa && $(MAKE) libinstall )
--	(cd byacc && $(MAKE) install )
--	(cd ucpp-1.3 && $(MAKE) $(UCPP) )
- #	(cd mdgx && $(MAKE) parallel )
- 	(if [ "$(RISM)" = "yes" ]; then \
- 		cd rism && $(MAKE) install_mpi ; \
-@@ -162,18 +145,11 @@ configured_parallel: configured
- 	)
- 
- clean::  netcdf_clean
--	-(cd ucpp-1.3 && $(MAKE) clean )
--	-(cd byacc && $(MAKE) clean )
--	-(cd cifparse && $(MAKE) clean )
- 	-(cd nab && $(MAKE) clean )
- 	-(cd sff && $(MAKE) clean )
- 	-(cd nss && $(MAKE) clean )
- 	-(cd leap && $(MAKE) clean )
--	-(cd arpack && $(MAKE) clean )
--	-(cd blas && $(MAKE) clean )
- 	-(cd xblas && $(MAKE) clean )
--	-(cd lapack && $(MAKE) clean )
--	-(cd c9x-complex && $(MAKE) clean )
- 	-(cd etc && $(MAKE) clean )
- 	-(cd chamber && $(MAKE) clean )
- 	-(cd pbsa && $(MAKE) clean )
-@@ -182,15 +158,12 @@ clean::  netcdf_clean
- 	-(cd lib && $(MAKE) clean )
- 	-(cd ptraj && $(MAKE) clean )
- 	-(cd cpptraj && $(MAKE) clean)
--	-(cd reduce && $(MAKE) clean )
- 	-(cd mtkpp && $(MAKE) clean )
- 	-(cd mdgx && $(MAKE) clean )
- 	-(cd xtalutil/CPrograms && $(MAKE) clean )
- 	-(cd xray && $(MAKE) clean )
- 	-(cd paramfit && $(MAKE) clean )
- 	-(cd rism && $(MAKE) clean )
--	-(cd fftw-3.3 && $(MAKE) clean )
--	-($(RM) -f fftw-3.3/mpi/fftw3-mpi.f03 )
- 	-(cd mmpbsa_py && $(MAKE) clean )
- 	-(cd parmed && $(MAKE) clean )
- 
-@@ -201,18 +174,11 @@ netcdf_clean:
- 	-(cd netcdf/bin && rm -f *)
- 
- uninstall:
--	-(cd ucpp-1.3 && $(MAKE) uninstall )
--	-(cd byacc && $(MAKE) uninstall )
--	-(cd cifparse && $(MAKE) uninstall )
- 	-(cd nab && $(MAKE) uninstall )
- 	-(cd sff && $(MAKE) uninstall )
- 	-(cd nss && $(MAKE) uninstall )
- 	-(cd leap && $(MAKE) uninstall )
--	-(cd arpack && $(MAKE) uninstall )
--	-(cd blas && $(MAKE) uninstall )
- 	-($(RM) -f $(LIBDIR)/libxblas.a )
--	-(cd lapack && $(MAKE) uninstall )
--	-(cd c9x-complex && $(MAKE) uninstall )
- 	-(cd etc && $(MAKE) uninstall )
- 	-(cd chamber && $(MAKE) uninstall )
- 	-(cd pbsa && $(MAKE) uninstall )
-@@ -220,7 +186,6 @@ uninstall:
- 	-(cd sqm && $(MAKE) uninstall )
- 	-(cd lib && $(MAKE) uninstall )
- 	-(cd ptraj && $(MAKE) uninstall )
--	-(cd reduce && $(MAKE) uninstall )
- 	-(cd mdgx && $(MAKE) uninstall )
- 	-(cd xtalutil/CPrograms && $(MAKE) uninstall )
- 	-(cd xray && $(MAKE) uninstall )
-@@ -228,15 +193,12 @@ uninstall:
- 	-(cd paramfit && $(MAKE) uninstall )
- 	-(cd rism && $(MAKE) uninstall )
- 	-(cd netcdf/src && $(MAKE) uninstall)
--	-(cd fftw-3.3 && $(MAKE) uninstall)
- 	-(cd cpptraj && $(MAKE) uninstall)
- 	-(cd mmpbsa_py && $(MAKE) uninstall )
- 	-(cd parmed && $(MAKE) uninstall )
- 	-(cd amberlite && $(MAKE) uninstall )
- 	-/bin/rm -f ../test/numprocs
- 	-/bin/rm -fr $(BINDIR)/ncmpidump $(BINDIR)/ncmpigen $(BINDIR)/ncvalid $(LIBDIR)/libnetcdf.a $(INCDIR)/mtkpp
--	-(cd $(LIBDIR) && /bin/rm -f libxblas-amb.a libfftw3_mpi.a libfftw3_mpi.la)
--	-(cd $(INCDIR) && /bin/rm -f fftw3-mpi.f03 fftw3-mpi.h)
- 
- $(INCDIR)/netcdf.mod:
- 	cd netcdf/src && $(MAKE) && $(MAKE) -j 1 install
-@@ -247,7 +209,7 @@ $(LIBDIR)/libxblas-amb.a:
- $(LIBDIR)/libfftw3.a $(LIBDIR)/libfftw3_mpi.a: 
- 	cd fftw-3.3 && $(MAKE) && $(MAKE) -j 1 install;
- 
--THIRDPARTY: $(NETCDF) $(XBLAS) $(FFTW3)
-+THIRDPARTY: $(XBLAS)
- 
- cuda:
- 	@echo "$(AMBERTOOLS) has no CUDA-enabled components"
-diff --git a/AmberTools/src/configure2 b/AmberTools/src/configure2
-index 25d3f0a..1ad86e6 100755
---- a/AmberTools/src/configure2
-+++ b/AmberTools/src/configure2
-@@ -387,11 +387,11 @@ omp_flag=
- mpi_flag=
- lex=flex
- flibs_mkl=
--lapack=install
--blas=install
-+lapack=skip
-+blas=skip
- f2c=skip
--ucpp=install
--cpp="ucpp -l"
-+ucpp=skip
-+cpp="\$(EPREFIX)/usr/bin/ucpp -l"
- 
- #-----------------------------------
- # skip building of xleap?
-@@ -618,13 +618,14 @@ gnu)
-     flibs_arch="-lgfortran -w"
-     flibsf_arch=
-     cc=gcc
--    cflags=
-+    cflags="GENTOO_CFLAGS"
-     ambercflags=""
-     cplusplus=g++
--    cxxflags=
-+    cxxflags="GENTOO_CXXFLAGS"
-     ambercxxflags=""
-     fc=gfortran
--    fflags=
-+    fflags="GENTOO_FFLAGS"
-+    ldflags="GENTOO_LDFLAGS"
-     staticflag='-static'
-     
-     # If -noopt has been requested, force lack of optimisation;
-@@ -645,11 +646,11 @@ gnu)
-       foptflags=""
-     else
-       cnooptflags=
--      coptflags="-O3"
-+      coptflags="GENTOO_CFLAGS"
-       cxxnooptflags=
--      cxxoptflags="-O3"
-+      cxxoptflags="GENTOO_CXXFLAGS"
-       fnooptflags="-O0"
--      foptflags="-O3"
-+      foptflags="GENTOO_FFLAGS"
-     fi
-     
-     # Debugging options
-@@ -2026,26 +2027,26 @@ EOF
-       if [ "$sse" = "yes" ]; then
-           enable_sse="--enable-sse2=yes" # --enable-avx=yes"
-       fi
--      cd fftw-3.3 && \
--	  ./configure --prefix=$AMBERHOME --libdir=$AMBERHOME/lib \
--          --enable-static=yes \
--          $enable_mpi $enable_debug $enable_sse\
--	  CC="$cc" CFLAGS="$cflags $coptflags" \
--          F77="$fc" FFLAGS="$fflags $foptflags" \
--          FLIBS="$flibs_arch" \
--	  > ../fftw3_config.log 2>&1
--      ncerror=$?
--      if [ $ncerror -gt 0 ]; then
--          echo "    Error: FFTW configure returned $ncerror"
--          echo "    FFTW configure failed! Check the fftw3_config.log file"
--          echo "    in the $AMBERHOME/AmberTools/src diretory."
--          exit 1
--      else
--          echo "    fftw-3.3 configure succeeded."
--      fi
--      cd ..
-+#      cd fftw-3.3 && \
-+#	  ./configure --prefix=$AMBERHOME --libdir=$AMBERHOME/lib \
-+#          --enable-static=yes \
-+#          $enable_mpi $enable_debug $enable_sse\
-+#	  CC="$cc" CFLAGS="$cflags $coptflags" \
-+#          F77="$fc" FFLAGS="$fflags $foptflags" \
-+#          FLIBS="$flibs_arch" \
-+#	  > ../fftw3_config.log 2>&1
-+#      ncerror=$?
-+#      if [ $ncerror -gt 0 ]; then
-+#          echo "    Error: FFTW configure returned $ncerror"
-+#          echo "    FFTW configure failed! Check the fftw3_config.log file"
-+#          echo "    in the $AMBERHOME/AmberTools/src diretory."
-+#          exit 1
-+#      else
-+#          echo "    fftw-3.3 configure succeeded."
-+#      fi
-+#      cd ..
-       fftw3="FFTW3"
--      flibs_fftw3="-lfftw3"
-+      flibs_fftw3="GENTOO_FFTW3_LIBS"
-       fftw3="\$(LIBDIR)/libfftw3.a"
-       if [ "$mpi" = 'yes' ]; then
-           flibs_fftw3="-lfftw3_mpi $flibs_fftw3"
-@@ -2282,7 +2283,7 @@ LDFLAGS=$ldflags \$(CUSTOMBUILDFLAGS)
- AMBERLDFLAGS=\$(AMBERBUILDFLAGS)
- 
- LEX=   $lex
--YACC=  \$(BINDIR)/yacc
-+YACC=  byacc
- AR=    ar rv
- M4=    $m4
- RANLIB=$ranlib
-@@ -2319,7 +2320,7 @@ CP=$localcp
- #  Information about Fortran compilation:
- 
- FC=$fc
--FFLAGS= $fflags \$(LOCALFLAGS) \$(CUSTOMBUILDFLAGS) -I\$(INCDIR) \$(NETCDFINC) $mklinc
-+FFLAGS= $fflags \$(LOCALFLAGS) \$(CUSTOMBUILDFLAGS) -IGENTOO_INCLUDE \$(NETCDFINC) $mklinc
- FNOOPTFLAGS= $fnooptflags
- FOPTFLAGS= $foptflags
- AMBERFFLAGS=\$(AMBERBUILDFLAGS)
-diff --git a/AmberTools/src/cpptraj/src/Makefile_at b/AmberTools/src/cpptraj/src/Makefile_at
-index 822b451..0684b0c 100644
---- a/AmberTools/src/cpptraj/src/Makefile_at
-+++ b/AmberTools/src/cpptraj/src/Makefile_at
-@@ -29,22 +29,10 @@ dependclean:
- 	-/bin/rm FindDepend.o
- 	-/bin/rm findDepend
- 
--cpptraj$(SFX): $(NETCDF) $(OBJECTS) $(PTRAJ_OBJECTS) $(EXTERNAL_LIBS) 
-+cpptraj$(SFX): $(OBJECTS) $(PTRAJ_OBJECTS)
- 	$(CXX) $(LDFLAGS) -o cpptraj$(SFX) $(OBJECTS) $(PTRAJ_OBJECTS) \
-                -L$(LIBDIR) $(NETCDFLIB) $(ZLIB) $(BZLIB) $(FLIBS_PTRAJ)
- 
--$(INCDIR)/netcdf.mod: ../../netcdf_config.log
--	cd ../../netcdf/src && $(MAKE) install
--
--$(LIBDIR)/libarpack.a:
--	cd ../../arpack && $(MAKE) install
--
--$(LIBDIR)/liblapack.a:
--	cd ../../lapack && $(MAKE) $(LAPACK)
--
--$(LIBDIR)/libblas.a:
--	cd ../../blas && $(MAKE) $(BLAS)
--
- thermo.o:  ../../ptraj/thermo.F90
- 	$(FC) $(FPPFLAGS) -c $(FREEFORMAT_FLAG) $(FOPTFLAGS) $(FFLAGS) $(AMBERFFLAGS) -o $@ ../../ptraj/thermo.F90
- 
-diff --git a/AmberTools/src/mdgx/Makefile b/AmberTools/src/mdgx/Makefile
-index 7bad950..b7a560b 100644
---- a/AmberTools/src/mdgx/Makefile
-+++ b/AmberTools/src/mdgx/Makefile
-@@ -132,19 +132,16 @@ MDGX_HEADERS = \
- 	       ptrajmask.h \
- 	       ../sff/AmberNetcdf.h 
- 
--mdgx$(SFX) : $(MDGX_OBJS) $(LIBDIR)/libfftw3.a
-+mdgx$(SFX) : $(MDGX_OBJS)
- 	$(CC) $(COPTFLAGS) $(CFLAGS) $(AMBERCFLAGS) $(LDFLAGS) \
- 	-o $@ $(MDGX_OBJS) $(FFTWLIB) -L$(LIBDIR) $(NETCDFLIB) $(LM)
- 
--mdgx.MPI$(SFX) : $(MDGX_OBJS) $(LIBDIR)/libfftw3.a
-+mdgx.MPI$(SFX) : $(MDGX_OBJS)
- 	$(CC) $(COPTFLAGS) $(CFLAGS) $(AMBERCFLAGS) $(LDFLAGS) \
- 	-o $@ $(MDGX_OBJS) $(FFTWLIB) -L$(LIBDIR) $(NETCDFLIB) $(LM)
- 
--$(LIBDIR)/fftw3.a: ../fftw-3.3/config.log
--	cd ../fftw-3.3 && $(MAKE) && $(MAKE) -j 1 install;
--
- .c.o:
--	$(CC) -c $(COPTFLAGS) $(CFLAGS) $(AMBERCFLAGS) -I$(INCDIR) -I../fftw-3.3/api -o $@ $<
-+	$(CC) -c $(COPTFLAGS) $(CFLAGS) $(AMBERCFLAGS) -I$(INCDIR) -o $@ $<
- 
- clean:
- 	/bin/rm -f $(MDGX_OBJS) mdgx$(SFX)
-diff --git a/AmberTools/src/mdgx/Trajectory.c b/AmberTools/src/mdgx/Trajectory.c
-index 524dad8..5df64c6 100644
---- a/AmberTools/src/mdgx/Trajectory.c
-+++ b/AmberTools/src/mdgx/Trajectory.c
-@@ -214,7 +214,7 @@ void ExtendCoordinates(coord *tc, prmtop *tp)
- coord ReadRst(prmtop *tp, char* source)
- {
-   int i, rsttype;
--  char line[128];
-+  char line[MAXLINE];
-   FILE *inp;
-   coord tc;
- 
-diff --git a/AmberTools/src/mmpbsa_py/MMPBSA_mods/amber_outputs.py b/AmberTools/src/mmpbsa_py/MMPBSA_mods/amber_outputs.py
-index b01b891..24ea20f 100644
---- a/AmberTools/src/mmpbsa_py/MMPBSA_mods/amber_outputs.py
-+++ b/AmberTools/src/mmpbsa_py/MMPBSA_mods/amber_outputs.py
-@@ -210,7 +210,7 @@ class AmberOutput(object):
- 
-       # write out each frame
-       for i in range(len(self.data[print_keys[0]])):
--         csvwriter.writerow([i] + [self.data[key][i] for key in print_keys])
-+         csvwriter.writerow([i] + ["%.4f" % self.data[key][i] for key in print_keys])
- 
-    #==================================================
- 
-@@ -1003,7 +1003,7 @@ class BindingStatistics(object):
- 
-          # write out each frame
-          for i in range(len(self.data[print_keys[0]])):
--            csvwriter.writerow([i]+[self.data[key][i] for key in print_keys])
-+            csvwriter.writerow([i]+["%.4f" % self.data[key][i] for key in print_keys])
-          csvwriter.writerow([])
- 
-    #==================================================
-diff --git a/AmberTools/src/nab/database.c b/AmberTools/src/nab/database.c
-index 0b98d35..9aad62a 100644
---- a/AmberTools/src/nab/database.c
-+++ b/AmberTools/src/nab/database.c
-@@ -1135,7 +1135,7 @@ int*		iPLines;
- char*           PBuffer;
- int             iBufferInc;
- {
--String          sLine;
-+String          sLine[MAXDATALINELEN];
- 
- 
- 
-diff --git a/AmberTools/src/nab/nab.c b/AmberTools/src/nab/nab.c
-index 84e03ef..d49b711 100644
---- a/AmberTools/src/nab/nab.c
-+++ b/AmberTools/src/nab/nab.c
-@@ -161,8 +161,8 @@ char	*cppstring;
-                fprintf( stderr, "AMBERHOME is not set!\n" );
-                exit(1);
-             }
--			sprintf( cmd, "%s/bin/%s %s -I%s/include %s ",
--				amberhome, CPP, cppstring, amberhome,
-+			sprintf( cmd, "%s %s -I%s/include %s ",
-+				CPP, cppstring, amberhome,
- 				argv[ ac ] ? argv[ ac ] : "" );
- 			if( cgdopt ) fprintf( stderr, "cpp cmd: %s\n", cmd );
- 			nfields = split( cmd, fields, " " );
-diff --git a/AmberTools/src/pbsa/Makefile b/AmberTools/src/pbsa/Makefile
-index 0a3f12f..2105b00 100644
---- a/AmberTools/src/pbsa/Makefile
-+++ b/AmberTools/src/pbsa/Makefile
-@@ -144,23 +144,23 @@ configured_parallel: configured
- 	)
- 
- #---------------------------------------------------------------------------
--pbsa$(SFX): FFTW3 $(OBJ) syslib netlib c9x-complex configured_serial 
-+pbsa$(SFX): $(OBJ) syslib configured_serial 
- 	$(FC) $(PBSAFLAG) $(FPPFLAGS) $(FFLAGS) $(AMBERFFLAGS) -o pbsa$(SFX) $(OBJ) \
- 	        ../lib/nxtsec.o ../lib/random.o $(FLIBS_FFTW3) \
- 	        -L$(LIBDIR) $(FLIBSF) $(LDFLAGS) $(AMBERLDFLAGS)
- 
--pbsa.MPI$(SFX): FFTW3.MPI $(OBJ) syslib netlib c9x-complex configured_parallel 
-+pbsa.MPI$(SFX): $(OBJ) syslib configured_parallel 
- 	$(FC) $(PBSAFLAG) $(FPPFLAGS) $(FFLAGS) $(AMBERFFLAGS) -o pbsa.MPI$(SFX) $(OBJ) \
- 	        ../lib/nxtsec.o ../lib/random.o $(FLIBS_FFTW3) \
- 	        -L$(LIBDIR) $(FLIBSF) $(LDFLAGS) $(AMBERLDFLAGS)
- 
--simplepbsa$(SFX): simplepbsa.o gopt.o libpbsa.a sfflib syslib netlib c9x-complex
-+simplepbsa$(SFX): simplepbsa.o gopt.o libpbsa.a sfflib syslib
- 	$(FC) $(PBSAFLAG) $(FPPFLAGS) $(FFLAGS) $(AMBERFFLAGS) -o simplepbsa$(SFX) simplepbsa.o gopt.o \
- 		libpbsa.a $(LIBDIR)/libsff.a ../lib/nxtsec.o -L$(LIBDIR) $(FLIBSF) \
- 		$(LDFLAGS) $(AMBERLDFLAGS)
- 	/bin/mv simplepbsa$(SFX) $(BINDIR)
- 
--libpbsa.a: FFTW3 $(LIBPBSAOBJS) syslib
-+libpbsa.a: $(LIBPBSAOBJS) syslib
- 	-rm -f libpbsa.a
- 	$(AR) libpbsa.a $(LIBPBSAOBJS) ../lib/random.o
- 	$(RANLIB) libpbsa.a
-@@ -188,48 +188,12 @@ libFpbsa.parallel: $(SANDERPBSAOBJS)
- 	$(RANLIB) libFpbsa.a
- 	/bin/mv libFpbsa.a $(LIBDIR)
- 
--FFTW3:
--	@if [ "$(PBSAFLAG)" = "-DFFTW" ]; then \
--	if [ "$(FLIBS_FFTW3)" = '-lfftw3xf_$(COMPILER)' ]; then\
--		cd $(MKL)/interfaces/fftw3xf && $(MAKE) lib$(MKL_PROCESSOR) \
--		compiler=$(COMPILER) PRECISION=MKL_DOUBLE \
--		INSTALL_DIR=$(LIBDIR); \
--	else \
--	    if [ ! -f $(INCDIR)/fftw3.f03 ]; then\
--		cd ../fftw-3.3 && $(MAKE) && $(MAKE) -j 1 install; \
--	    fi \
--	fi \
--	fi
--
--FFTW3.MPI:
--	@if [ "$(PBSAFLAG)" = "-DFFTW" ]; then \
--	if [ "$(FLIBS_FFTW3)" = '-lfftw3xf_$(COMPILER)' ]; then\
--		cd $(MKL)/interfaces/fftw3xf && $(MAKE) lib$(MKL_PROCESSOR) \
--		compiler=$(COMPILER) PRECISION=MKL_DOUBLE \
--		INSTALL_DIR=$(LIBDIR); \
--	else \
--	    if [ ! -f $(INCDIR)/fftw3-mpi.f03 ]; then\
--		cd ../fftw-3.3 && $(MAKE) && $(MAKE) -j 1 install; \
--	    fi \
--	fi \
--	fi
--
- syslib:
- 	cd ../lib && $(MAKE) nxtsec.o random.o
- 
- sfflib:
- 	cd ../sff && $(MAKE) install
- 
--netlib: 
--	cd ../lapack && $(MAKE) $(LAPACK)
--	cd ../blas && $(MAKE) $(BLAS)
--	cd ../arpack && $(MAKE) install
--
--c9x-complex:
--	@if test $(C9XCOMPLEX) != "skip"; then \
--	   cd ../c9x-complex && $(MAKE) libmc.a; \
--	 fi
--
- pb_init.o: pb_init.F90
- 	$(FC) $(PBSAFLAG) $(FPPFLAGS) -c -O0 $(FFLAGS) $(AMBERFFLAGS) -o $@ $<
- 
-diff --git a/AmberTools/src/ptraj/Makefile b/AmberTools/src/ptraj/Makefile
-index 3e643b9..b3089f1 100644
---- a/AmberTools/src/ptraj/Makefile
-+++ b/AmberTools/src/ptraj/Makefile
-@@ -61,21 +61,16 @@ rdparm$(SFX): libs $(OBJECTS)
- 	$(CC) $(CFLAGS) $(AMBERCFLAGS) $(LDFLAGS) $(AMBERLDFLAGS) \
- 		-o rdparm$(SFX) $(OBJECTS) $(LIBS) $(NETCDFLIB) $(LM)
- 
--ptraj$(SFX): libs netlib $(OBJECTS)
-+ptraj$(SFX): libs $(OBJECTS)
- 	$(CC) $(CFLAGS) $(AMBERCFLAGS) $(LDFLAGS) $(AMBERLDFLAGS) \
- 		-o ptraj$(SFX) $(OBJECTS) $(LIBS) $(NETCDFLIB) $(LM)
- 
--ptraj.MPI$(SFX): libs netlib $(OBJECTS)
-+ptraj.MPI$(SFX): libs $(OBJECTS)
- 	$(CC) $(CFLAGS) $(AMBERCFLAGS) $(LDFLAGS) $(AMBERLDFLAGS) \
- 		-o ptraj.MPI$(SFX) $(OBJECTS) $(LIBS) $(PNETCDFLIB) $(LM)
- 
- libs: 
- 	cd pdb && $(MAKE) 
--	cd ../arpack && $(MAKE)
--
--netlib:
--	cd ../lapack && $(MAKE) $(LAPACK)
--	cd ../blas && $(MAKE) $(BLAS)
- 
- clean:
- 	cd pdb && $(MAKE) clean
-diff --git a/AmberTools/src/ptraj/trajectory.c b/AmberTools/src/ptraj/trajectory.c
-index 110ffce..49bdf1a 100644
---- a/AmberTools/src/ptraj/trajectory.c
-+++ b/AmberTools/src/ptraj/trajectory.c
-@@ -1315,7 +1315,7 @@ readAmberTrajectory_nobuffer(FILE *fpin, int natoms,
- {
-   fpos_t fileMarker;         /* marker for current file postition */
-   char *junk;
--  char buffer[120];
-+  char buffer[BUFFER_SIZE];
-   char coords[26];    /* room for 24 characters (3f8.3) + \n + (char) 0  */
-   char c;     
-   int j,ret;
-diff --git a/AmberTools/src/sff/Makefile b/AmberTools/src/sff/Makefile
-index 83f362c..13efc78 100644
---- a/AmberTools/src/sff/Makefile
-+++ b/AmberTools/src/sff/Makefile
-@@ -3,7 +3,7 @@ include ../config.h
- .c.o:
- 	$(CC) -c -Dflex $(COPTFLAGS) $(CFLAGS) $(AMBERCFLAGS) $(RISMSFF) $(NETCDFINC) -o $@ $<
- 
--OBJS = binpos.o conjgrad.o lmodC.o memutil.o nblist.o newton.o nmode.o \
-+OBJS = binpos.o conjgrad.o dsarpack.o lmodC.o memutil.o nblist.o newton.o nmode.o \
- 	prm.o rand2.o sasad.o sff.o time.o xminC.o AmberNetcdf.o $(SFF_RISM_INTERFACE)
- 
- 
-@@ -63,7 +63,7 @@ xminC.o:  sff.h
- AmberNetcdf.o:  AmberNetcdf.h
- 
- hcp_getpdb: hcp_getpdb.c
--	$(CC) -o $(BINDIR)/hcp_getpdb hcp_getpdb.c
-+	$(CC) $(CFLAGS) $(LDFLAGS) -o $(BINDIR)/hcp_getpdb hcp_getpdb.c
- 
- .PHONY: ../rism/amber_rism_interface.NAB.o
- ../rism/amber_rism_interface.NAB.o:
-diff --git a/AmberTools/src/sff/dsarpack.f b/AmberTools/src/sff/dsarpack.f
-new file mode 100644
-index 0000000..5544df9
---- /dev/null
-+++ b/AmberTools/src/sff/dsarpack.f
-@@ -0,0 +1,654 @@
-+      subroutine dsarpack(n_dim,n_eig_in,n_eig_out,ncv_in,itr_in,
-+     &                    eigval_tol,eigvals,eigvecs,spectrum,
-+     &                    need_eigvecs,ierr,debug_arpack,
-+     &                    v,workl,workd,d,resid,ax,select,
-+     &                    xyz,grad,return_flag,label)
-+c
-+      implicit none
-+c
-+c     %-----------------%
-+c     | Dummy Arguments |
-+c     %-----------------%
-+c
-+      integer n_dim,n_eig_in,n_eig_out,ncv_in,itr_in,spectrum,
-+     &        need_eigvecs,ierr,debug_arpack,return_flag,label
-+      Double precision eigval_tol
-+      Double precision eigvals(n_eig_in),eigvecs(n_dim * n_eig_in)
-+      Double precision v(n_dim,ncv_in),
-+     &                 workl(ncv_in*(ncv_in+8)),workd(3*n_dim),
-+     &                 d(ncv_in,2),resid(n_dim),ax(n_dim),
-+     &                 xyz(n_dim),grad(n_dim)
-+      logical select(ncv_in)
-+c
-+      save
-+c
-+c     %---------------%
-+c     | Include Files |
-+c     %---------------%
-+c
-+c     include 'debug.h'
-+c
-+c\SCCS Information: @(#) 
-+c FILE: debug.h   SID: 2.3   DATE OF SID: 11/16/95   RELEASE: 2 
-+c
-+c     %---------------------------------%
-+c     | See debug.doc for documentation |
-+c     %---------------------------------%
-+      integer  logfil, ndigit, mgetv0,
-+     &         msaupd, msaup2, msaitr, mseigt, msapps, msgets, mseupd,
-+     &         mnaupd, mnaup2, mnaitr, mneigh, mnapps, mngets, mneupd,
-+     &         mcaupd, mcaup2, mcaitr, mceigh, mcapps, mcgets, mceupd
-+      common /debug/ 
-+     &         logfil, ndigit, mgetv0,
-+     &         msaupd, msaup2, msaitr, mseigt, msapps, msgets, mseupd,
-+     &         mnaupd, mnaup2, mnaitr, mneigh, mnapps, mngets, mneupd,
-+     &         mcaupd, mcaup2, mcaitr, mceigh, mcapps, mcgets, mceupd
-+c
-+c     This code shows how to use ARPACK to find a few eigenvalues 
-+c     (lambda) and corresponding eigenvectors (x) for the standard 
-+c     eigenvalue problem:
-+c          
-+c                        A*x = lambda*x
-+c 
-+c     where A is an n by n real symmetric matrix.
-+c
-+c     The main points illustrated here are 
-+c
-+c        1) How to declare sufficient memory to find NEV 
-+c           eigenvalues of largest magnitude.  Other options
-+c           are available.
-+c
-+c        2) Illustration of the reverse communication interface 
-+c           needed to utilize the top level ARPACK routine DSAUPD 
-+c           that computes the quantities needed to construct
-+c           the desired eigenvalues and eigenvectors(if requested).
-+c
-+c        3) How to extract the desired eigenvalues and eigenvectors
-+c           using the ARPACK routine DSEUPD.
-+c
-+c     The only thing that must be supplied in order to use this
-+c     routine on your problem is to change the array dimensions 
-+c     appropriately, to specify WHICH eigenvalues you want to compute 
-+c     and to supply a matrix-vector product
-+c
-+c                         w <-  Av
-+c
-+c     in place of the call to AV( ) below.
-+c
-+c     Once usage of this routine is understood, you may wish to explore
-+c     the other available options to improve convergence, to solve generalized
-+c     problems, etc.  Look at the file ex-sym.doc in DOCUMENTS directory.
-+c     This codes implements  
-+c
-+c\Example-1
-+c     ... Suppose we want to solve A*x = lambda*x in regular mode,
-+c         where A is derived from the central difference discretization
-+c         of the 2-dimensional Laplacian on the unit square with
-+c         zero Dirichlet boundary condition.
-+c     ... OP = A  and  B = I.
-+c     ... Assume "call av (n,x,y)" computes y = A*x
-+c     ... Use mode 1 of DSAUPD.
-+c
-+c\BeginLib
-+c
-+c\Routines called:
-+c     dsaupd  ARPACK reverse communication interface routine.
-+c     dseupd  ARPACK routine that returns Ritz values and (optionally)
-+c             Ritz vectors.
-+c     dnrm2   Level 1 BLAS that computes the norm of a vector.
-+c     daxpy   Level 1 BLAS that computes y <- alpha*x+y.
-+c
-+c\Author
-+c     Richard Lehoucq
-+c     Danny Sorensen
-+c     Chao Yang
-+c     Dept. of Computational &
-+c     Applied Mathematics
-+c     Rice University
-+c     Houston, Texas
-+c
-+c\SCCS Information: %Z%
-+c FILE: %M%   SID: %I%   DATE OF SID: %G%   RELEASE: %R%
-+c
-+c\Remarks
-+c     1. None
-+c
-+c\EndLib
-+c
-+c-----------------------------------------------------------------------
-+c
-+c     %-------------------------------------------------------%
-+c     | Storage Declarations:                                 |
-+c     |                                                       |
-+c     | The maximum dimensions for all arrays are             |
-+c     | set here to accommodate a problem size of             |
-+c     | N .le. MAXN                                           |
-+c     |                                                       |
-+c     | NEV is the number of eigenvalues requested.           |
-+c     |     See specifications for ARPACK usage below.        |
-+c     |                                                       |
-+c     | NCV is the largest number of basis vectors that will  |
-+c     |     be used in the Implicitly Restarted Arnoldi       |
-+c     |     Process.  Work per major iteration is             |
-+c     |     proportional to N*NCV*NCV.                        |
-+c     |                                                       |
-+c     | You must set:                                         |
-+c     |                                                       |
-+c     | MAXN:   Maximum dimension of the A allowed. (dynamic) |
-+c     | MAXNEV: Maximum NEV allowed. (dynamic)                |
-+c     | MAXNCV: Maximum NCV allowed. (dynamic)                |
-+c     %-------------------------------------------------------%
-+c
-+C     %--------------------------------------%
-+C     | F90 Allocatable Arrays (on the heap) |
-+C     %--------------------------------------%
-+c
-+C     Double precision,allocatable,save :: v(:,:)
-+C     integer,save :: v_row_allocated = 0, v_col_allocated = 0
-+c
-+c     %----------------------------------------------%
-+c     | Originally, as F77 parameters, the following |
-+c     | integers were used to dimension work arrays. |
-+c     | They are replaced by dummy arguments used to |
-+c     | dimension the work arrays as F90 automatic   |
-+c     | arrays, but the integers are still used for  |
-+c     | passing the dimensions to lower level ARPACK |
-+c     | routines dsaupd, dseupd and dmout.           |
-+c     %----------------------------------------------%
-+c
-+      integer          maxn, maxnev, maxncv, ldv
-+c
-+c     %-------------------------------------------%
-+c     | Local F90 Automatic Arrays (on the stack) |
-+c     %-------------------------------------------%
-+c
-+      Double precision
-+C    &                 workl(ncv_in*(ncv_in+8)),
-+C    &                 workd(3*n_dim), d(ncv_in,2), resid(n_dim),
-+C    &                 ax(n_dim),
-+     &                 cg_dstat(4)
-+C     logical          select(ncv_in)
-+      integer          iparam(11), ipntr(11),
-+     &                 cg_istat(4)
-+c
-+c     %---------------%
-+c     | Local Scalars |
-+c     %---------------%
-+c
-+      character        bmat*1, which*2
-+      integer          ido, n, nev, ncv, lworkl, info,
-+     &                 i, j, nx, ishfts, maxitr, mode1, nconv
-+      integer          L12, L18, ARPACK_ERROR, status_flag
-+      data             L12, L18, ARPACK_ERROR /1, 2, -2/
-+C     integer          v_row_needed, v_col_needed
-+      logical          rvec
-+      Double precision      
-+     &                 tol, sigma
-+c
-+c     %------------%
-+c     | Parameters |
-+c     %------------%
-+c
-+      Double precision
-+     &                 zero
-+      parameter        (zero = 0.0D+0)
-+c  
-+c     %-----------------------------%
-+c     | BLAS & LAPACK routines used |
-+c     %-----------------------------%
-+c
-+      Double precision           
-+     &                 dnrm2
-+      external         dnrm2, daxpy, hessvec
-+c
-+c     %--------------------%
-+c     | Intrinsic function |
-+c     %--------------------%
-+c
-+      intrinsic        abs
-+c
-+c     %-----------------------%
-+c     | Executable Statements |
-+c     %-----------------------%
-+c
-+      if ( label.eq.0 ) go to 1
-+      go to (12,18) label
-+  1   continue
-+c
-+c     %------------------------------------------------%
-+c     | Values used to calculate work array dimensions |
-+c     %------------------------------------------------%
-+c
-+      maxn = n_dim
-+      maxnev = n_eig_in
-+      maxncv = ncv_in
-+      ldv = maxn
-+c
-+c     %---------------------------------------------------%
-+c     | The include debug.h statement above and           |
-+c     | assignments here initiate trace output from the   |
-+c     | internal actions of ARPACK.  See debug.doc in the |
-+c     | DOCUMENTS directory for usage.  Initially, the    |
-+c     | most useful information will be a breakdown of    |
-+c     | time spent in the various stages of computation   |
-+c     | given by setting msaupd = 1.                      |
-+c     %---------------------------------------------------%
-+c
-+      ndigit = -5
-+      logfil = 6
-+      msgets = 0
-+      msaitr = 0 
-+      msapps = 0
-+      if ( debug_arpack.eq.1 ) then
-+        msaupd = 1
-+      else
-+        msaupd = 0
-+      endif
-+      msaup2 = 0
-+      mseigt = 0
-+      mseupd = 0
-+c     
-+c   *** Allocatable array v will be allowed to grow to its largest size;
-+c   ***  it is never deallocated:
-+C     v_row_needed = n_dim        !!! ldv
-+C     v_col_needed = ncv_in       !!! maxncv
-+C     if( allocated(v) )then
-+C       if( (v_row_needed .gt. v_row_allocated)
-+C    & .or. (v_col_needed .gt. v_col_allocated) )then
-+C         deallocate(v,stat=ierr)
-+C         if( ierr .ne. 0 )then
-+C           write( logfil, '(a,i16,1x,i8)' )
-+C    &       'ARPACK: could not deallocate v'
-+C           go to 9000
-+C         endif
-+C       endif
-+C     endif
-+C     if( .not. allocated(v) )then
-+C       allocate( v(v_row_needed,v_col_needed), stat=ierr )
-+C       if( ierr .ne. 0 )then
-+C         write( logfil, '(a,2i10)' )
-+C    &     'ARPACK: could not allocate v'
-+C         go to 9000
-+C       endif
-+C       v_row_allocated = v_row_needed
-+C       v_col_allocated = v_col_needed
-+C     endif
-+C     v = zero !!! zero out entire v array
-+c     
-+c     %-------------------------------------------------%
-+c     | The following sets dimensions for this problem. |
-+c     %-------------------------------------------------%
-+c
-+      n = n_dim
-+c
-+c     %----------------------------------------------%
-+c     |                                              | 
-+c     | Specifications for ARPACK usage are set      | 
-+c     | below:                                       |
-+c     |                                              |
-+c     |    1) NEV = N_EIG_IN  asks for N_EIG_IN      |  
-+c     |       eigenvalues to be computed.            | 
-+c     |                                              |
-+c     |    2) NCV = NCV_IN sets the length of the    |
-+c     |       Arnoldi factorization                  |
-+c     |                                              |
-+c     |    3) This is a standard problem             |
-+c     |         (indicated by bmat  = 'I')           |
-+c     |                                              |
-+c     |    4) Ask for the NEV eigenvalues of         |
-+c     |       smallest magnitude                     |
-+c     |         (indicated by which = 'SM')          |
-+c     |       See documentation in SSAUPD for the    |
-+c     |       other options SA, LA, LM, BE.          | 
-+c     |                                              |
-+c     | Note: NEV and NCV must satisfy the following |
-+c     | conditions:                                  |
-+c     |              NEV <= MAXNEV                   |
-+c     |          NEV + 1 <= NCV <= MAXNCV            |
-+c     %----------------------------------------------%
-+c
-+      nev   = n_eig_in
-+      ncv   = ncv_in 
-+      bmat  = 'I'
-+      if ( spectrum .eq. 1 ) then
-+         which = 'SM'
-+      else if ( spectrum .eq. 2 ) then
-+         which = 'SA'
-+      else if ( spectrum .eq. 3 ) then
-+         which = 'LM'
-+      else if ( spectrum .eq. 4 ) then
-+         which = 'LA'
-+      else if ( spectrum .eq. 5 ) then
-+         which = 'BE'
-+      else
-+          print *, ' ERROR with _SSIMP: Spectrum .NE. (SM|SA|LA|LM|BE)'
-+         go to 9000
-+      end if
-+c
-+      if ( n .gt. maxn ) then
-+         print *, ' ERROR with _SSIMP: N is greater than MAXN '
-+         go to 9000
-+      else if ( nev .gt. maxnev ) then
-+         print *, ' ERROR with _SSIMP: NEV is greater than MAXNEV '
-+         go to 9000
-+      else if ( ncv .gt. maxncv ) then
-+         print *, ' ERROR with _SSIMP: NCV is greater than MAXNCV '
-+         go to 9000
-+      end if
-+c
-+c     %-----------------------------------------------------%
-+c     |                                                     |
-+c     | Specification of stopping rules and initial         |
-+c     | conditions before calling DSAUPD                    |
-+c     |                                                     |
-+c     | TOL  determines the stopping criterion.             |
-+c     |                                                     |
-+c     |      Expect                                         |
-+c     |           abs(lambdaC - lambdaT) < TOL*abs(lambdaC) |
-+c     |               computed   true                       |
-+c     |                                                     |
-+c     |      If TOL .le. 0,  then TOL <- macheps            |
-+c     |           (machine precision) is used.              |
-+c     |                                                     |
-+c     | IDO  is the REVERSE COMMUNICATION parameter         |
-+c     |      used to specify actions to be taken on return  |
-+c     |      from DSAUPD. (See usage below.)                |
-+c     |                                                     |
-+c     |      It MUST initially be set to 0 before the first |
-+c     |      call to DSAUPD.                                | 
-+c     |                                                     |
-+c     | INFO on entry specifies starting vector information |
-+c     |      and on return indicates error codes            |
-+c     |                                                     |
-+c     |      Initially, setting INFO=0 indicates that a     | 
-+c     |      random starting vector is requested to         |
-+c     |      start the ARNOLDI iteration.  Setting INFO to  |
-+c     |      a nonzero value on the initial call is used    |
-+c     |      if you want to specify your own starting       |
-+c     |      vector (This vector must be placed in RESID.)  | 
-+c     |                                                     |
-+c     | The work array WORKL is used in DSAUPD as           | 
-+c     | workspace.  Its dimension LWORKL is set as          |
-+c     | illustrated below.                                  |
-+c     |                                                     |
-+c     %-----------------------------------------------------%
-+c
-+      lworkl = ncv*(ncv+8)
-+      tol = eigval_tol 
-+      info = 0
-+      ido = 0
-+c
-+c     %---------------------------------------------------%
-+c     | Specification of Algorithm Mode:                  |
-+c     |                                                   |
-+c     | This program uses the exact shift strategy        |
-+c     | (indicated by setting PARAM(1) = 1).              |
-+c     | IPARAM(3) specifies the maximum number of Arnoldi |
-+c     | iterations allowed.  Mode 1 of DSAUPD is used     |
-+c     | (IPARAM(7) = 1). All these options can be changed |
-+c     | by the user. For details see the documentation in |
-+c     | DSAUPD.                                           |
-+c     %---------------------------------------------------%
-+c
-+      ishfts = 1
-+      maxitr = itr_in 
-+      mode1 = 1
-+c
-+      iparam(1) = ishfts
-+c                
-+      iparam(3) = maxitr
-+c                  
-+      iparam(7) = mode1
-+c
-+c     %------------------------------------------------%
-+c     | M A I N   L O O P (Reverse communication loop) |
-+c     %------------------------------------------------%
-+c
-+ 10   continue
-+c
-+c        %---------------------------------------------%
-+c        | Repeatedly call the routine DSAUPD and take | 
-+c        | actions indicated by parameter IDO until    |
-+c        | either convergence is indicated or maxitr   |
-+c        | has been exceeded.                          |
-+c        %---------------------------------------------%
-+c
-+         call dsaupd ( ido, bmat, n, which, nev, tol, resid, 
-+     &                 ncv, v, ldv, iparam, ipntr, workd, workl,
-+     &                 lworkl, info )
-+c
-+         if (ido .eq. -1 .or. ido .eq. 1) then
-+c
-+c           %--------------------------------------%
-+c           | Perform matrix vector multiplication |
-+c           |              y <--- OP*x             |
-+c           | The user should supply his/her own   |
-+c           | matrix vector multiplication routine |
-+c           | here that takes workd(ipntr(1)) as   |
-+c           | the input, and return the result to  |
-+c           | workd(ipntr(2)).                     |
-+c           %--------------------------------------%
-+c
-+            status_flag = 0
-+ 11         continue
-+               call hessvec ( n, workd(ipntr(1)), workd(ipntr(2)),
-+     &                        xyz, grad, return_flag, status_flag )
-+               if ( status_flag.eq.0 ) go to 13
-+               if ( status_flag.lt.0 ) go to 9000
-+               label = L12
-+               return
-+ 12         go to 11
-+ 13         continue
-+c
-+c           %-----------------------------------------%
-+c           | L O O P   B A C K to call DSAUPD again. |
-+c           %-----------------------------------------%
-+c
-+            go to 10
-+c
-+         end if 
-+c
-+c     %----------------------------------------%
-+c     | Either we have convergence or there is |
-+c     | an error.                              |
-+c     %----------------------------------------%
-+c
-+      if ( info .lt. 0 ) then
-+c
-+c        %--------------------------%
-+c        | Error message. Check the |
-+c        | documentation in DSAUPD. |
-+c        %--------------------------%
-+c
-+         print *, ' '
-+         print *, ' Error with _saupd, info = ', info
-+         print *, ' Check documentation in _saupd '
-+         print *, ' '
-+         go to 9000
-+c
-+      else 
-+c
-+c        %-------------------------------------------%
-+c        | No fatal errors occurred.                 |
-+c        | Post-Process using DSEUPD.                |
-+c        |                                           |
-+c        | Computed eigenvalues may be extracted.    |  
-+c        |                                           |
-+c        | Eigenvectors may be also computed now if  |
-+c        | desired.  (indicated by rvec = .true.)    | 
-+c        |                                           |
-+c        | The routine DSEUPD now called to do this  |
-+c        | post processing (Other modes may require  |
-+c        | more complicated post processing than     |
-+c        | mode1.)                                   |
-+c        |                                           |
-+c        %-------------------------------------------%
-+c           
-+         if ( need_eigvecs .eq. 1 ) then
-+            rvec = .true.
-+         else
-+            rvec = .false.
-+         end if
-+c
-+         call dseupd ( rvec, 'All', select, d, v, ldv, sigma, 
-+     &        bmat, n, which, nev, tol, resid, ncv, v, ldv, 
-+     &        iparam, ipntr, workd, workl, lworkl, ierr )
-+c
-+c        %----------------------------------------------%
-+c        | Eigenvalues are returned in the first column |
-+c        | of the two dimensional array D and the       |
-+c        | corresponding eigenvectors are returned in   |
-+c        | the first NCONV (=IPARAM(5)) columns of the  |
-+c        | two dimensional array V if requested.        |
-+c        | Otherwise, an orthogonal basis for the       |
-+c        | invariant subspace corresponding to the      |
-+c        | eigenvalues in D is returned in V.           |
-+c        %----------------------------------------------%
-+c
-+         if ( ierr .ne. 0) then
-+c
-+c           %------------------------------------%
-+c           | Error condition:                   |
-+c           | Check the documentation of DSEUPD. |
-+c           %------------------------------------%
-+c
-+            print *, ' '
-+            print *, ' Error with _seupd, info = ', ierr
-+            print *, ' Check the documentation of _seupd. '
-+            print *, ' '
-+            go to 9000
-+c
-+         else if ( debug_arpack.eq.1 ) then
-+c
-+            nconv =  iparam(5)
-+            n_eig_out = nconv
-+            if ( nconv .le. 0 ) then
-+               print *, ' '
-+               print *, ' ARPACK: Not a single mode converged.'
-+               print *, ' '
-+               go to 9000
-+            endif
-+c
-+C           %--------------------------------------------%
-+C           | "UnDO" DO 20 j=1,nconv loop, because it is |
-+C           | illegal to jump in and out from a DO loop. |
-+C           %--------------------------------------------%
-+c
-+            j = 1
-+ 16         continue
-+c
-+c              %---------------------------%
-+c              | Compute the residual norm |
-+c              |                           |
-+c              |   ||  A*x - lambda*x ||   |
-+c              |                           |
-+c              | for the NCONV accurately  |
-+c              | computed eigenvalues and  |
-+c              | eigenvectors.  (iparam(5) |
-+c              | indicates how many are    |
-+c              | accurate to the requested |
-+c              | tolerance)                |
-+c              %---------------------------%
-+c
-+               status_flag = 0
-+ 17            continue
-+                  call hessvec ( n, v(1,j), ax, xyz, grad,
-+     &                           return_flag, status_flag )
-+                  if ( status_flag.eq.0 ) go to 19
-+                  if ( status_flag.lt.0 ) go to 9000
-+                  label = L18
-+                  return
-+ 18            go to 17
-+ 19            continue
-+c
-+               call daxpy(n, -d(j,1), v(1,j), 1, ax, 1)
-+               d(j,2) = dnrm2(n, ax, 1)
-+               d(j,2) = d(j,2) / abs(d(j,1))
-+c
-+               j = j + 1
-+               if ( j .gt. nconv ) go to 20
-+c
-+               go to 16
-+c
-+ 20         continue
-+c
-+c           %-----------------------------%
-+c           | Display computed residuals. |
-+c           %-----------------------------%
-+c
-+            call dmout(6, nconv, 2, d, maxncv, -6,
-+     &           'Ritz values and relative residuals')
-+c
-+c           %-------------------------------------------%
-+c           | Print additional convergence information. |
-+c           %-------------------------------------------%
-+c
-+            if ( info .eq. 1) then
-+               print *, ' '
-+               print *, ' Maximum number of iterations reached.'
-+               print *, ' '
-+            else if ( info .eq. 3) then
-+               print *, ' '
-+               print *, ' No shifts could be applied during implicit',
-+     &                  ' Arnoldi update, try increasing NCV.'
-+               print *, ' '
-+            end if
-+c
-+            print *, ' '
-+            print *, ' _SSIMP '
-+            print *, ' ====== '
-+            print *, ' '
-+            print *, ' Size of the matrix is ', n
-+            print *, ' The number of Ritz values requested is ', nev
-+            print *, ' The number of Arnoldi vectors generated',
-+     &               ' (NCV) is ', ncv
-+            print *, ' What portion of the spectrum: ', which
-+            print *, ' The number of converged Ritz values is ',
-+     &                 nconv
-+            print *, ' The number of Implicit Arnoldi update',
-+     &               ' iterations taken is ', iparam(3)
-+            print *, ' The number of OP*x is ', iparam(9)
-+            print *, ' The convergence criterion is ', tol
-+            print *, ' '
-+         end if
-+c
-+c        %----------------------------%
-+c        | Return eigvals and eigvecs |
-+c        %----------------------------%
-+c
-+         nconv =  iparam(5)
-+         n_eig_out = nconv
-+         if ( nconv .le. 0 ) then
-+            print *, ' '
-+            print *, ' ARPACK: Not a single mode converged.'
-+            print *, ' '
-+            go to 9000
-+         endif
-+c
-+         do 40 j=1, nconv
-+             eigvals(j) = d(j,1)
-+c
-+             do 30 i=1, n
-+                eigvecs((j-1)*n+i) = v(i,j)
-+ 30          continue
-+ 40      continue
-+c
-+      end if
-+c
-+c     %--------------------------------%
-+c     | Done with subroutine dsarpack. |
-+c     %--------------------------------%
-+c
-+      label = 0
-+      return
-+c
-+ 9000 continue !!! Error
-+c
-+      if( status_flag.eq.0 ) status_flag = ARPACK_ERROR
-+c
-+      label = status_flag
-+      return
-+c
-+      end
-+c 
-+c ------------------------------------------------------------------
-diff --git a/AmberTools/src/sqm/Makefile b/AmberTools/src/sqm/Makefile
-index 3b49c55..61d0dc3 100644
---- a/AmberTools/src/sqm/Makefile
-+++ b/AmberTools/src/sqm/Makefile
-@@ -82,7 +82,7 @@ QMOBJ = qm2_allocate_e_repul.o qm2_calc_charges.o qm2_calc_dipole.o \
- install: sqm$(SFX)
- 	mv sqm$(SFX) $(BINDIR)
- 
--sqm$(SFX): $(SQMOBJ) $(QMOBJ) netlib sys
-+sqm$(SFX): $(SQMOBJ) $(QMOBJ) sys
- 	$(FC) $(FPPFLAGS) $(FFLAGS) $(AMBERFFLAGS) -o sqm$(SFX) $(SQMOBJ) $(QMOBJ) \
- 		-L$(LIBDIR) $(FLIBSF) ../lib/sys.a $(LDFLAGS) $(AMBERLDFLAGS)
- 
-@@ -101,11 +101,6 @@ $(LIBDIR)/libsqm.a: $(QMOBJ) $(LIBQMOBJ)
- sys:
- 	cd ../lib; $(MAKE) sys.a
- 
--netlib:
--	cd ../lapack; $(MAKE) $(LAPACK)
--	cd ../blas; $(MAKE) $(BLAS)
--	cd ../arpack && $(MAKE) install
--
- clean:
- 	/bin/rm -f *.o  *.mod *.d sqm$(SFX)
- 
-diff --git a/AmberTools/test/Makefile b/AmberTools/test/Makefile
-index 27afe24..4796250 100644
---- a/AmberTools/test/Makefile
-+++ b/AmberTools/test/Makefile
-@@ -3,14 +3,14 @@ include ../src/config.h
- ######    Top-level targets, for general use:    ############################
- 
- test:
--	./test_at_serial.sh
-+	+./test_at_serial.sh
- 
- test.parallel:
- 	./test_at_parallel.sh
- 
- ######    Intermediate-level targets:    ############################
- 
--test.serial: clean is_amberhome_defined \
-+test.serial: is_amberhome_defined \
- 	test.nab test.ptraj test.cpptraj test.antechamber \
- 	test.leap test.resp test.pbsa test.mmpbsa test.parmed \
- 	test.ambpdb test.elsize test.chamber test.sqm test.rism1d \
-diff --git a/AmberTools/test/mmpbsa_py/01_Generalized_Born/energies.csv.save b/AmberTools/test/mmpbsa_py/01_Generalized_Born/energies.csv.save
-index 3595375..1a0be46 100644
---- a/AmberTools/test/mmpbsa_py/01_Generalized_Born/energies.csv.save
-+++ b/AmberTools/test/mmpbsa_py/01_Generalized_Born/energies.csv.save
-@@ -7,16 +7,16 @@ Frame #,VDWAALS,EEL,EGB,ESURF,G gas,G solv,TOTAL
- Receptor Energy Terms

- Frame #,VDWAALS,EEL,EGB,ESURF,G gas,G solv,TOTAL

- 0,-1969.4265,-17103.7958,-3027.0953,101.7772,-19073.2223,-2925.3181,-21998.5404

--1,-1956.6674,-17020.9923,-3062.954,102.3918,-18977.6597,-2960.5622,-21938.2219

-+1,-1956.6674,-17020.9923,-3062.9540,102.3918,-18977.6597,-2960.5622,-21938.2219

- 

- Ligand Energy Terms

- Frame #,VDWAALS,EEL,EGB,ESURF,G gas,G solv,TOTAL

--0,-1.2566,-5.6263,-28.5797,4.4486,-6.8829,-24.1311,-31.014

-+0,-1.2566,-5.6263,-28.5797,4.4486,-6.8829,-24.1311,-31.0140

- 1,-3.1118,-6.1548,-29.3738,4.4016,-9.2666,-24.9722,-34.2388

- 

- DELTA Energy Terms

- Frame #,VDWAALS,EEL,EGB,ESURF,DELTA G gas,DELTA G solv,DELTA TOTAL

--0,-63.4582,-32.3518,35.2679,-8.3751,-95.81,26.8928,-68.9172

--1,-60.9966,-35.1045,41.6205,-8.465,-96.1011,33.1555,-62.9456

-+0,-63.4582,-32.3518,35.2679,-8.3751,-95.8100,26.8928,-68.9172

-+1,-60.9966,-35.1045,41.6205,-8.4650,-96.1011,33.1555,-62.9456

- 

- 

-diff --git a/AmberTools/test/nab/Makefile b/AmberTools/test/nab/Makefile
-index 1bb2505..7459a15 100644
---- a/AmberTools/test/nab/Makefile
-+++ b/AmberTools/test/nab/Makefile
-@@ -12,6 +12,8 @@ testrism:  \
- 	rism_ion-noasymp rism_ion_pse1 rism_ion_pse3 rism_mdiis0 rism_mdiis1 \
- 	rism_sp rism_sp2
- 
-+.NOTPARALLEL:
-+
- duplex_test::
- 	@./Run.duplex
- 
-diff --git a/AmberTools/test/nab/Run.rism_sp b/AmberTools/test/nab/Run.rism_sp
-index bd8471d..a88bf58 100755
---- a/AmberTools/test/nab/Run.rism_sp
-+++ b/AmberTools/test/nab/Run.rism_sp
-@@ -47,7 +47,7 @@ $DO_PARALLEL $cmd --pdb ala.pdb --prmtop ala.parm7 --traj ala.nc \
-                   --polarDecomp\
-                   --noprogress > rism3d.snglpnt.out || error
- 
--checkrism3d -err 1e-6 rism3d.snglpnt.out.check rism3d.snglpnt.out
-+./checkrism3d -err 1e-6 rism3d.snglpnt.out.check rism3d.snglpnt.out
- 
- awk '{if (NR % 10 == 0) print $0}' quv.1.xyzv > quv.1.xyzv.trunc
- ../dacdif -r 1e-6 quv.1.xyzv.trunc.check quv.1.xyzv.trunc
-diff --git a/AmberTools/test/nab/Run.rism_sp2 b/AmberTools/test/nab/Run.rism_sp2
-index a2b9521..11da8de 100755
---- a/AmberTools/test/nab/Run.rism_sp2
-+++ b/AmberTools/test/nab/Run.rism_sp2
-@@ -38,7 +38,7 @@ $DO_PARALLEL $cmd --pdb ala.pdb --prmtop ala.parm7 --traj ala.crd \
-                   --buffer 10 --guv guv.2\
-                   --noprogress > rism3d.snglpnt.2.out || error
- 
--checkrism3d -err 1e-6 rism3d.snglpnt.2.out.check rism3d.snglpnt.2.out
-+./checkrism3d -err 1e-6 rism3d.snglpnt.2.out.check rism3d.snglpnt.2.out
- ../dacdif -a 1e-6 guv.2.O.1.dx.check guv.2.O.1.dx
- ../dacdif -a 1e-6 guv.2.H1.2.dx.check guv.2.H1.2.dx
- ../dacdif -a 1e-6 guv.2.O.3.dx.check guv.2.O.3.dx
-diff --git a/AmberTools/test/test_at_serial.sh b/AmberTools/test/test_at_serial.sh
-index 15bb590..8fa52e3 100755
---- a/AmberTools/test/test_at_serial.sh
-+++ b/AmberTools/test/test_at_serial.sh
-@@ -39,3 +39,9 @@ fi
- 
- # save summary for later reporting:
- tail -5 ${logfile} > ${logdir}/at_summary
-+
-+if [ "${questionable_count}" -ne 0 -o "${error_count}" -ne 0 ]
-+then
-+  # Tests failed
-+  exit 1
-+fi
-diff --git a/Makefile b/Makefile
-index 54ddfcb..643ba15 100644
---- a/Makefile
-+++ b/Makefile
-@@ -30,7 +30,7 @@ clean.test:
- test::  test.$(INSTALLTYPE)
- 
- test.serial:
--	-(cd AmberTools/test && $(MAKE) test)
-+	(cd AmberTools/test && $(MAKE) test)
- 	-@(if [ -n "$(BUILDAMBER)" ] ; then \
- 	    cd test && $(MAKE) test; \
- 	    echo "" ; \
diff --git a/sci-chemistry/ambertools/files/ambertools-12_p38-format-security.patch b/sci-chemistry/ambertools/files/ambertools-12_p38-format-security.patch
deleted file mode 100644
index bb22a627a..000000000
--- a/sci-chemistry/ambertools/files/ambertools-12_p38-format-security.patch
+++ /dev/null
@@ -1,100 +0,0 @@
- AmberTools/src/mdgx/ChargeFit.c  | 4 ++--
- AmberTools/src/nab/cgen.c        | 2 +-
- AmberTools/src/nab/traceback.c   | 2 +-
- AmberTools/src/ptraj/cluster.c   | 2 +-
- AmberTools/src/ptraj/interface.c | 6 +++---
- AmberTools/src/semantics/parse.c | 2 +-
- 6 files changed, 9 insertions(+), 9 deletions(-)
-
-diff --git a/AmberTools/src/mdgx/ChargeFit.c b/AmberTools/src/mdgx/ChargeFit.c
-index fccf5d0..fe4afac 100644
---- a/AmberTools/src/mdgx/ChargeFit.c
-+++ b/AmberTools/src/mdgx/ChargeFit.c
-@@ -77,9 +77,9 @@ static void AssignGridTopologies(fset *myfit, prmtop *tp)
-   }
-   for (i = 0; i < myfit->ngrd; i++) {
-     if (myfit->tpname.map[i][0] == '\0') {
--      sprintf(myfit->tpname.map[i], tp->source);
-+      sprintf(myfit->tpname.map[i], "%s", tp->source);
-       if (myfit->eprule.map[i][0] == '\0' && tp->eprulesource[0] != '\0') {
--	sprintf(myfit->eprule.map[i], tp->eprulesource);
-+	sprintf(myfit->eprule.map[i], "%s", tp->eprulesource);
-       }
-     }
-   }
-diff --git a/AmberTools/src/nab/cgen.c b/AmberTools/src/nab/cgen.c
-index 6254d44..e206879 100644
---- a/AmberTools/src/nab/cgen.c
-+++ b/AmberTools/src/nab/cgen.c
-@@ -1642,7 +1642,7 @@ static	char	*CG_gentype( char *csp, NODE_T *npt )
- 		strcpy( csp, tname );
- 		csp += strlen( csp );
- 	}else
--		fprintf( cg_cfp, tname );
-+		fprintf( cg_cfp, "%s", tname );
- 	needspace = TRUE;
- 	return( csp );
- }
-diff --git a/AmberTools/src/nab/traceback.c b/AmberTools/src/nab/traceback.c
-index f916474..e376552 100644
---- a/AmberTools/src/nab/traceback.c
-+++ b/AmberTools/src/nab/traceback.c
-@@ -6,7 +6,7 @@
- int	rt_errormsg( int fatal, char msg[] )
- {
- 
--	fprintf( stderr, msg );
-+	fprintf( stderr, "%s", msg );
- 	if( fatal )
- 		exit( 1 );
- 	return(0);
-diff --git a/AmberTools/src/ptraj/cluster.c b/AmberTools/src/ptraj/cluster.c
-index 2cb60f0..5e0f33d 100644
---- a/AmberTools/src/ptraj/cluster.c
-+++ b/AmberTools/src/ptraj/cluster.c
-@@ -1240,7 +1240,7 @@ void ClusteringMergeNames(PtrajClustering* This, ClusterNode* MergeNodeA, Cluste
-   {
-     return;
-   }
--  sprintf(Temp, ClusterB->Name);
-+  sprintf(Temp, "%s", ClusterB->Name);
-   sprintf(ClusterB->Name, "(%s,%s)", ClusterA->Name, Temp);
- 
- }
-diff --git a/AmberTools/src/ptraj/interface.c b/AmberTools/src/ptraj/interface.c
-index 4087fa7..1ee4273 100644
---- a/AmberTools/src/ptraj/interface.c
-+++ b/AmberTools/src/ptraj/interface.c
-@@ -97,8 +97,8 @@ interface(interfaceMode mode, char *filename)
- 
-     tokenlist = (Token *) &rdparmTokenlist;
- 
--    fprintf(stdout, rdparm_header);
--    fprintf(stdout, rdparm_prompt);
-+    fprintf(stdout, "%s", rdparm_header);
-+    fprintf(stdout, "%s", rdparm_prompt);
-     while (1) {
- 
-       fflush(stdout);
-@@ -112,7 +112,7 @@ interface(interfaceMode mode, char *filename)
- 
-       }
-     
--      fprintf(stdout, rdparm_prompt);
-+      fprintf(stdout, "%s", rdparm_prompt);
-     }
-   }
- }
-diff --git a/AmberTools/src/semantics/parse.c b/AmberTools/src/semantics/parse.c
-index 55c724c..68f23da 100644
---- a/AmberTools/src/semantics/parse.c
-+++ b/AmberTools/src/semantics/parse.c
-@@ -2039,7 +2039,7 @@ int	n_tab;
- DEF_T	tab[];	
- {
- 
--	fprintf( fp, oval );
-+	fprintf( fp, "%s", oval );
- 		
- }
- 
diff --git a/sci-chemistry/ambertools/files/ambertools-12_p38-gcc5.patch b/sci-chemistry/ambertools/files/ambertools-12_p38-gcc5.patch
deleted file mode 100644
index 92e64954f..000000000
--- a/sci-chemistry/ambertools/files/ambertools-12_p38-gcc5.patch
+++ /dev/null
@@ -1,28 +0,0 @@
- AmberTools/src/configure2 | 14 ++++++++------
- 1 file changed, 8 insertions(+), 6 deletions(-)
-
-diff --git a/AmberTools/src/configure2 b/AmberTools/src/configure2
-index 913c50d..1232f6a 100755
---- a/AmberTools/src/configure2
-+++ b/AmberTools/src/configure2
-@@ -703,12 +703,14 @@ gnu)
-     # if gcc <= 4.2, fftw3 is not compiled and pbsa fft solver and rism
-     #   are disabled
-     if [ "$rism" != 'no' -o -n "$pbsaflag" ]; then
--        if ( [ $gnu_majorversion -ge 4 ] && [ $gnu_minorversion -le 2 ] ) \
--            || [ $gnu_majorversion -le 3 ]; then
--            echo "ERROR: RISM and PBSA FFT solver require version 4.3 or higher of the GNU compiler."
--            echo "       Please re-run configure with the '-nofftw3' flag to use this compiler:"
--            echo "            `mod_command_args '-rism' '-nofftw3'`"
--            exit 1
-+        if  [ $gnu_majorversion -lt 5 ]; then
-+            if ( [ $gnu_majorversion -ge 4 ] && [ $gnu_minorversion -le 2 ] ) \
-+                || [ $gnu_majorversion -le 3 ]; then
-+                echo "ERROR: RISM and PBSA FFT solver require version 4.3 or higher of the GNU compiler."
-+                echo "       Please re-run configure with the '-nofftw3' flag to use this compiler:"
-+                echo "            `mod_command_args '-rism' '-nofftw3'`"
-+                exit 1
-+            fi
-         fi
-     fi
- 
diff --git a/sci-chemistry/ambertools/files/ambertools-15-gentoo.patch b/sci-chemistry/ambertools/files/ambertools-15-gentoo.patch
deleted file mode 100644
index 76be4f8af..000000000
--- a/sci-chemistry/ambertools/files/ambertools-15-gentoo.patch
+++ /dev/null
@@ -1,1428 +0,0 @@
-diff --git a/AmberTools/src/Makefile b/AmberTools/src/Makefile
-index 3d69773..71c794c 100644
---- a/AmberTools/src/Makefile
-+++ b/AmberTools/src/Makefile
-@@ -15,12 +15,6 @@ install: $(INSTALLTYPE)
- serial: configured_serial THIRDPARTY $(MTKPP)
- 	@echo "Starting installation of ${AMBERTOOLS} serial at `date`".
- #	utility routines and libraries:
--	(cd ucpp-1.3 && $(MAKE) $(UCPP) )
--	(cd byacc && $(MAKE) install )
--	(cd arpack && $(MAKE) install );
--	(cd lapack && $(MAKE) $(LAPACK) )
--	(cd blas && $(MAKE) $(BLAS) )
--	(cd c9x-complex && $(MAKE) $(C9XCOMPLEX) )
- 	(cd pbsa && $(MAKE) install )
- 	(cd gbnsr6 && $(MAKE) install )
- 	(cd cifparse && $(MAKE) install )
-@@ -33,7 +27,6 @@ serial: configured_serial THIRDPARTY $(MTKPP)
- 	$(MAKE) cpptraj
- 
- #   miscellaneous:
--	(cd reduce && $(MAKE) install )
- 
- #   leap
- 	(cd leap && $(MAKE) install )
-@@ -103,12 +96,6 @@ serial: configured_serial THIRDPARTY $(MTKPP)
- 
- nabonly: configured_serial $(XBLAS)  
- #	utility routines and libraries:
--	(cd ucpp-1.3 && $(MAKE) $(UCPP) )
--	(cd byacc && $(MAKE) install )
--	(cd arpack && $(MAKE) install );
--	(cd lapack && $(MAKE) $(LAPACK) )
--	(cd blas && $(MAKE) $(BLAS) )
--	(cd c9x-complex && $(MAKE) $(C9XCOMPLEX) )
- 	(cd pbsa && $(MAKE) libinstall )
- 	(cd rism && $(MAKE) $(RISM) )
- 	(cd cifparse && $(MAKE) install )
-@@ -144,12 +131,7 @@ parallel: configured_parallel THIRDPARTY
- #	(cd pbsa && $(MAKE) clean && $(MAKE) install.parallel )
- 	(cd pbsa && $(MAKE) libinstall )
- 	$(MAKE) cpptraj
--	(cd byacc && $(MAKE) install )
--	(cd ucpp-1.3 && $(MAKE) $(UCPP) )
- 	(cd cifparse && $(MAKE) install )
--	(cd arpack && $(MAKE) install );
--	(cd lapack && $(MAKE) $(LAPACK) )
--	(cd blas && $(MAKE) $(BLAS) )
- 	(cd mdgx && $(MAKE) $(MDGX) )
- 	(if [ "$(RISM)" = "yes" ]; then \
- 		cd rism && $(MAKE) install_mpi ; \
-@@ -215,18 +197,12 @@ netcdf_uninstall:
- 	-/bin/rm -f netcdf_config.log ../lib/libnetcdf* ../include/netcdf.*
- 
- clean::
--	-(cd ucpp-1.3 && $(MAKE) clean )
--	-(cd byacc && $(MAKE) clean )
- 	-(cd cifparse && $(MAKE) clean )
- 	-(cd nab && $(MAKE) clean )
- 	-(cd sff && $(MAKE) clean )
- 	-(cd nss && $(MAKE) clean )
- 	-(cd leap && $(MAKE) clean )
--	-(cd arpack && $(MAKE) clean )
--	-(cd blas && $(MAKE) clean )
- 	-(cd xblas && $(MAKE) clean )
--	-(cd lapack && $(MAKE) clean )
--	-(cd c9x-complex && $(MAKE) clean )
- 	-(cd etc && $(MAKE) clean )
- 	-(cd chamber && $(MAKE) clean )
- 	-(cd pbsa && $(MAKE) clean )
-@@ -236,15 +212,12 @@ clean::
- 	-(cd lib && $(MAKE) clean )
- 	-(cd ptraj && $(MAKE) clean )
- 	-(cd cpptraj && $(MAKE) clean)
--	-(cd reduce && $(MAKE) clean )
- 	-(cd mtkpp && $(MAKE) clean )
- 	-(cd mdgx && $(MAKE) clean )
- 	-(cd xtalutil/CPrograms && $(MAKE) clean )
- 	-(cd saxs && $(MAKE) clean )
- 	-(cd paramfit && $(MAKE) clean )
- 	-(cd rism && $(MAKE) clean )
--	-(cd fftw-3.3 && $(MAKE) clean )
--	-($(RM) -f fftw-3.3/mpi/fftw3-mpi.f03 )
- 	-(cd mmpbsa_py && /bin/rm -fr MMPBSA.py.MPI build/ mpi4py-1.2.2/)
- 	-(cd mm_pbsa && $(MAKE) clean )
- 	-(cd FEW && $(MAKE) clean )
-@@ -315,7 +288,7 @@ $(LIBDIR)/libxblas-amb.a:
- $(LIBDIR)/libfftw3.a $(LIBDIR)/libfftw3_mpi.a: 
- 	cd fftw-3.3 && $(MAKE) && $(MAKE) -j 1 install;
- 
--THIRDPARTY: $(XBLAS) $(FFTW3)
-+THIRDPARTY: $(XBLAS)
- 
- cuda:
- 	@echo "$(AMBERTOOLS) has no CUDA-enabled components"
-diff --git a/AmberTools/src/configure2 b/AmberTools/src/configure2
-index f1a3cff..4b07fa5 100755
---- a/AmberTools/src/configure2
-+++ b/AmberTools/src/configure2
-@@ -318,7 +318,7 @@ fi
- #------------------------------------------------------------------------------
- #  Define variables that are currently constants:
- #------------------------------------------------------------------------------
--bintraj='yes'
-+bintraj='no'
- ldout=' -o '
- localcp='cp'
- localmv='mv'
-@@ -358,7 +358,7 @@ cygwin='no'
- debug='no'
- dragonegg=''
- fpp="cpp -traditional -P"
--fppflags=''
-+fppflags='-DBINTRAJ'
- freeformat_flag=''
- fwarnflag=''
- g95='no'
-@@ -370,7 +370,7 @@ installtype='serial'
- intel_compiler_flag_mkl='no'
- intelmpi='no'
- is_mac='no'
--ldflags=''
-+ldflags='GENTOO_LDFLAGS'
- ld='ld '
- lfs='yes'
- lm='-lm'
-@@ -599,11 +599,11 @@ omp_flag=
- mpi_flag=
- lex=flex
- flibs_mkl=
--lapack=install
--blas=install
-+lapack=skip
-+blas=skip
- f2c=skip
--ucpp=install
--cpp="ucpp -l"
-+ucpp=skip
-+cpp="\$(EPREFIX)/usr/bin/ucpp -l"
- 
- #-----------------------------------
- # skip building of xleap?
-@@ -907,7 +907,7 @@ gnu)
-     flibs_arch="-lgfortran -w"
-     flibsf_arch=
-     cc=gcc
--    cflags="-fPIC"
-+    cflags="-fPIC -DBINTRAJ"
-     ambercflags=""
-     cplusplus=g++
-     cxxflags="-fPIC"
-@@ -937,11 +937,11 @@ gnu)
-       foptflags=""
-     else
-       cnooptflags=
--      coptflags="-O3"
-+      coptflags="GENTOO_CFLAGS"
-       cxxnooptflags=
--      cxxoptflags="-fPIC -O3"
-+      cxxoptflags="-fPIC GENTOO_CXXFLAGS"
-       fnooptflags="-O0"
--      foptflags="-O3"
-+      foptflags="GENTOO_FFLAGS"
-     fi
-     
-     # Debugging options
-@@ -957,11 +957,11 @@ gnu)
-       if [ $sse = 'yes' ]; then
-         if [ $x86_64 = 'yes' ]; then
-           #-mfpmath=sse is default for x86_64, no need to specific it
--          coptflags="$coptflags -mtune=native"
--          foptflags="$foptflags -mtune=native"
-+          coptflags="$coptflags"
-+          foptflags="$foptflags"
-         else # i386 needs to be told to use sse prior to using -mfpmath=sse
--          coptflags="$coptflags -mtune=native -msse -mfpmath=sse"
--          foptflags="$foptflags -mtune=native -msse -mfpmath=sse"
-+          coptflags="$coptflags"
-+          foptflags="$foptflags"
-         fi
-       fi
-       fcreal8="-fdefault-real-8"
-@@ -1032,7 +1032,7 @@ gnu)
- #       pmemd_fpp_flags='-DFFTW_FFT'
- #   fi
-     pmemd_foptflags="$foptflags"
--    pmemd_coptflags="$coptflags"
-+    pmemd_coptflags="$coptflags -DBINTRAJ"
-     if [ ! -z $dragonegg ]; then
-         pmemd_foptflags="-fplugin=$dragonegg $fflags $pmemd_foptflags"
-         pmemd_coptflags="-fplugin=$dragonegg $pmemd_coptflags"
-@@ -1062,7 +1062,7 @@ gnu)
-         fi
-         pmemd_cu_includes="$pmemd_cu_includes $mpi_inc"
-         pmemd_cu_defines="$pmemd_cu_defines -DMPI  -DMPICH_IGNORE_CXX_SEEK"
--        pmemd_coptflags="$coptflags -DMPICH_IGNORE_CXX_SEEK"
-+        pmemd_coptflags="$coptflags -DMPICH_IGNORE_CXX_SEEK -DBINTRAJ"
-       fi
-     fi
-     if [ "$cuda_SPFP" = 'yes' ]; then
-@@ -2649,40 +2649,40 @@ if [ "$has_fftw3" = 'yes' ]; then
-     if [ "$sse" = "yes" ]; then
-         enable_sse="--enable-sse2=yes" # --enable-avx=yes"
-     fi
--    if [ "$mic" = 'yes' ]; then
--      echo "   --configuring for mic (native mode)..."        
--      echo
--      cd fftw-3.3 && \
--      ./configure --prefix=$AMBERHOME --libdir=$AMBERHOME/lib \
--        --enable-static --enable-shared --host=x86_64-k1om-linux \
--      --build=x86_64-unknown-linux \
--       $enable_mpi $mpicc $enable_debug \
--        CC="$cc -mmic" CFLAGS="$cflags $coptflags " \
--        F77="$fc -mmic" FFLAGS="$fflags $foptflags " \
--        FLIBS="$flibs_arch" \
--        > ../fftw3_config.log 2>&1
--      ncerror=$?
--    else
--      cd fftw-3.3 && \
--        ./configure --prefix=$AMBERHOME --libdir=$AMBERHOME/lib \
--        --enable-static --enable-shared \
--        $enable_mpi $mpicc $enable_debug $enable_sse\
--        CC="$cc" CFLAGS="$cflags $coptflags" \
--        F77="$fc" FFLAGS="$fflags $foptflags" \
--        FLIBS="$flibs_arch" \
--        > ../fftw3_config.log 2>&1
--      ncerror=$?
--    fi
--    if [ $ncerror -gt 0 ]; then
--        echo "Error: FFTW configure returned $ncerror"
--        echo "       FFTW configure failed! Check the fftw3_config.log file"
--        echo "       in the $AMBERHOME/AmberTools/src directory."
--        exit 1
--    else
--        echo "    fftw-3.3 configure succeeded."
--    fi
--    cd ..
--    flibs_fftw3="-lfftw3"
-+#    if [ "$mic" = 'yes' ]; then
-+#      echo "   --configuring for mic (native mode)..."        
-+#      echo
-+#      cd fftw-3.3 && \
-+#      ./configure --prefix=$AMBERHOME --libdir=$AMBERHOME/lib \
-+#        --enable-static --enable-shared --host=x86_64-k1om-linux \
-+#      --build=x86_64-unknown-linux \
-+#       $enable_mpi $mpicc $enable_debug \
-+#        CC="$cc -mmic" CFLAGS="$cflags $coptflags " \
-+#        F77="$fc -mmic" FFLAGS="$fflags $foptflags " \
-+#        FLIBS="$flibs_arch" \
-+#        > ../fftw3_config.log 2>&1
-+#      ncerror=$?
-+#    else
-+#      cd fftw-3.3 && \
-+#        ./configure --prefix=$AMBERHOME --libdir=$AMBERHOME/lib \
-+#        --enable-static --enable-shared \
-+#        $enable_mpi $mpicc $enable_debug $enable_sse\
-+#        CC="$cc" CFLAGS="$cflags $coptflags" \
-+#        F77="$fc" FFLAGS="$fflags $foptflags" \
-+#        FLIBS="$flibs_arch" \
-+#        > ../fftw3_config.log 2>&1
-+#      ncerror=$?
-+#    fi
-+#    if [ $ncerror -gt 0 ]; then
-+#        echo "Error: FFTW configure returned $ncerror"
-+#        echo "       FFTW configure failed! Check the fftw3_config.log file"
-+#        echo "       in the $AMBERHOME/AmberTools/src directory."
-+#        exit 1
-+#    else
-+#        echo "    fftw-3.3 configure succeeded."
-+#    fi
-+#    cd ..
-+    flibs_fftw3="GENTOO_FFTW3_LIBS"
-     fftw3="\$(LIBDIR)/libfftw3.a"
-     if [ "$mpi" = 'yes' -a "$intelmpi" = 'no' ]; then
-         flibs_fftw3="-lfftw3_mpi $flibs_fftw3"
-@@ -2701,23 +2701,23 @@ elif [ "$mdgx" = 'yes' ]; then
-     if [ "$sse" = "yes" ]; then
-         enable_sse="--enable-sse2=yes" # --enable-avx=yes"
-     fi
--    cd fftw-3.3 && \
--        ./configure --prefix=$AMBERHOME --libdir=$AMBERHOME/lib \
--        --enable-static --enable-shared --disable-fortran \
--        $enable_debug $enable_sse\
--        CC="$cc" CFLAGS="$cflags $coptflags" \
--        > ../fftw3_config.log 2>&1
--    ncerror=$?
--    if [ $ncerror -gt 0 ]; then
--        echo "Error: FFTW configure returned $ncerror"
--        echo "       FFTW configure failed! Check the fftw3_config.log file"
--        echo "       in the $AMBERHOME/AmberTools/src directory."
--        exit 1
--    else
--        echo "    fftw-3.3 configure succeeded."
--    fi
--    cd ..
--    flibs_fftw3="-lfftw3"
-+#    cd fftw-3.3 && \
-+#        ./configure --prefix=$AMBERHOME --libdir=$AMBERHOME/lib \
-+#        --enable-static --enable-shared --disable-fortran \
-+#        $enable_debug $enable_sse\
-+#        CC="$cc" CFLAGS="$cflags $coptflags" \
-+#        > ../fftw3_config.log 2>&1
-+#    ncerror=$?
-+#    if [ $ncerror -gt 0 ]; then
-+#        echo "Error: FFTW configure returned $ncerror"
-+#        echo "       FFTW configure failed! Check the fftw3_config.log file"
-+#        echo "       in the $AMBERHOME/AmberTools/src directory."
-+#        exit 1
-+#    else
-+#        echo "    fftw-3.3 configure succeeded."
-+#    fi
-+#    cd ..
-+    flibs_fftw3="GENTOO_FFTW3_LIBS"
-     fftw3="\$(LIBDIR)/libfftw3.a"
- else
-     echo "" 
-@@ -3162,7 +3162,7 @@ LDFLAGS=$ldflags \$(CUSTOMBUILDFLAGS) \$(AMBERBUILDFLAGS)
- AMBERLDFLAGS=\$(AMBERBUILDFLAGS)
- 
- LEX=   $lex
--YACC=  \$(BINDIR)/yacc
-+YACC=  byacc
- AR=    ar rv
- M4=    $m4
- RANLIB=$ranlib
-@@ -3198,7 +3198,7 @@ CP=$localcp
- #  Information about Fortran compilation:
- 
- FC=$fc
--FFLAGS= $fflags \$(LOCALFLAGS) \$(CUSTOMBUILDFLAGS) -I\$(INCDIR) \$(NETCDFINC) $mklinc \$(AMBERBUILDFLAGS)
-+FFLAGS= $fflags \$(LOCALFLAGS) \$(CUSTOMBUILDFLAGS) -IGENTOO_INCLUDE \$(NETCDFINC) $mklinc \$(AMBERBUILDFLAGS)
- FNOOPTFLAGS= $fnooptflags
- FOPTFLAGS= $foptflags
- AMBERFFLAGS=\$(AMBERBUILDFLAGS)
-diff --git a/AmberTools/src/cpptraj/src/Makefile_at b/AmberTools/src/cpptraj/src/Makefile_at
-index 977439f..4bf25c8 100644
---- a/AmberTools/src/cpptraj/src/Makefile_at
-+++ b/AmberTools/src/cpptraj/src/Makefile_at
-@@ -10,7 +10,7 @@ CPPTRAJ_FLAGS= -I$(INCDIR) $(COPTFLAGS) $(CFLAGS) $(NETCDFINC)
- # NOTE: Since -nobintraj is possible and the dependency for netcdf is not
- #       set correctly by configure there is no way this can work for netcdf
- READLINE_HOME=readline
--READLINE=$(READLINE_HOME)/libreadline.a
-+READLINE=-lreadline
- EXTERNAL_LIBS=$(LIBDIR)/libarpack.a $(LIBDIR)/liblapack.a $(LIBDIR)/libblas.a $(READLINE)
- 
- include cpptrajfiles
-@@ -45,7 +45,7 @@ depend: findDepend
- dependclean:
- 	/bin/rm -f FindDepend.o findDepend
- 
--cpptraj$(SFX): $(OBJECTS) pub_fft.o $(EXTERNAL_LIBS) 
-+cpptraj$(SFX): $(OBJECTS) pub_fft.o
- 	$(CXX) $(WARNFLAGS) $(LDFLAGS) -o cpptraj$(SFX) $(OBJECTS) pub_fft.o \
-                -L$(LIBDIR) $(NETCDFLIB) $(ZLIB) $(BZLIB) $(FLIBS_PTRAJ) $(READLINE)
- 
-@@ -53,12 +53,12 @@ ambpdb$(SFX): $(AMBPDB_OBJECTS)
- 	$(CXX) $(WARNFLAGS) $(LDFLAGS) -o ambpdb$(SFX) $(AMBPDB_OBJECTS) \
-                -L$(LIBDIR) $(NETCDFLIB) $(ZLIB) $(BZLIB)
- 
--cpptraj.sander$(SFX): $(OBJECTS) pub_fft.o $(EXTERNAL_LIBS) $(LIBDIR)/libsander.so
-+cpptraj.sander$(SFX): $(OBJECTS) pub_fft.o $(LIBDIR)/libsander.so
- 	$(CXX) $(WARNFLAGS) $(LDFLAGS) -o cpptraj.sander$(SFX) $(OBJECTS) pub_fft.o \
- 	       -L$(LIBDIR) $(NETCDFLIB) $(ZLIB) $(BZLIB) $(FLIBS_PTRAJ) $(READLINE)  \
- 	       -lsander
- 
--libcpptraj$(SHARED_SUFFIX): $(OBJECTS) pub_fft.o $(EXTERNAL_LIBS)
-+libcpptraj$(SHARED_SUFFIX): $(OBJECTS) pub_fft.o
- 	$(CXX) $(MAKE_SHARED) $(WARNFLAGS) $(LDFLAGS) -o $@ $(OBJECTS) pub_fft.o \
- 		-L$(LIBDIR) $(NETCDFLIB) $(ZLIB) $(BZLIB) $(FLIBS_PTRAJ) $(READLINE)
- 
-diff --git a/AmberTools/src/gbnsr6/Makefile b/AmberTools/src/gbnsr6/Makefile
-index 0d704cb..85042d4 100644
---- a/AmberTools/src/gbnsr6/Makefile
-+++ b/AmberTools/src/gbnsr6/Makefile
-@@ -66,7 +66,7 @@ configured_serial: configured
- 	)
- 
- #---------------------------------------------------------------------------
--gbnsr6$(SFX): $(OBJ) syslib netlib c9x-complex configured_serial 
-+gbnsr6$(SFX): $(OBJ) syslib configured_serial 
- 	$(FC) $(PBSAFLAG) $(FPPFLAGS) $(FFLAGS) $(AMBERFFLAGS) -o gbnsr6$(SFX) $(OBJ) \
- 	        ../lib/nxtsec.o ../lib/random.o  \
- 	        -L$(LIBDIR) $(FLIBSF) $(LDFLAGS) $(AMBERLDFLAGS)
-diff --git a/AmberTools/src/mdgx/Makefile b/AmberTools/src/mdgx/Makefile
-index 5751142..04e8e1c 100644
---- a/AmberTools/src/mdgx/Makefile
-+++ b/AmberTools/src/mdgx/Makefile
-@@ -151,7 +151,7 @@ MDGX_HEADERS = \
- 	       ptrajmask.h \
- 	       AmberNetcdf.h 
- 
--$(BINDIR)/mdgx$(SFX) : $(FFTW3) $(MDGX_OBJS)
-+$(BINDIR)/mdgx$(SFX) : $(MDGX_OBJS)
- 	$(CC) $(COPTFLAGS) $(CFLAGS) $(AMBERCFLAGS) $(LDFLAGS) \
- 	-o $@ $(MDGX_OBJS) -L$(LIBDIR) $(FLIBS_FFTW3) $(NETCDFLIB) $(LM)
- 
-@@ -159,7 +159,7 @@ $(BINDIR)/mdgx.MPI$(SFX) : $(MDGX_OBJS)
- 	$(CC) $(COPTFLAGS) $(CFLAGS) $(AMBERCFLAGS) $(LDFLAGS) \
- 	-o $@ $(MDGX_OBJS) -L$(LIBDIR) $(FLIBSF) $(FLIBS_FFTW3) $(NETCDFLIB) $(LM)
- 
--$(LIBDIR)/libmdgx$(SHARED_SUFFIX): $(MDGX_OBJS) $(MDGXWRAP_OBJS) $(BINDIR)/ucpp
-+$(LIBDIR)/libmdgx$(SHARED_SUFFIX): $(MDGX_OBJS) $(MDGXWRAP_OBJS)
- 	$(CC) $(MAKE_SHARED) -o $@ $(CFLAGS) $(COPTFLAGS) -L$(LIBDIR) $(FLIBSF) \
- 		$(FLIBS_FFTW3) $(NETCDFLIB) $(LM) $(MDGX_OBJS) $(MDGXWRAP_OBJS)
- 	cp -p mdgxapi.h $(INCDIR)/mdgx.h
-diff --git a/AmberTools/src/nab/nab.c b/AmberTools/src/nab/nab.c
-index 2e90068..cf83aaa 100644
---- a/AmberTools/src/nab/nab.c
-+++ b/AmberTools/src/nab/nab.c
-@@ -161,8 +161,8 @@ char	*cppstring;
-                fprintf( stderr, "AMBERHOME is not set!\n" );
-                exit(1);
-             }
--			sprintf( cmd, "%s/bin/%s %s -I%s/include %s ",
--				amberhome, CPP, cppstring, amberhome,
-+			sprintf( cmd, "%s %s -I%s/include %s ",
-+				CPP, cppstring, amberhome,
- 				argv[ ac ] ? argv[ ac ] : "" );
- 			if( cgdopt ) fprintf( stderr, "cpp cmd: %s\n", cmd );
- 			nfields = split( cmd, fields, " " );
-diff --git a/AmberTools/src/nmode/Makefile b/AmberTools/src/nmode/Makefile
-index 12acf35..4f26593 100644
---- a/AmberTools/src/nmode/Makefile
-+++ b/AmberTools/src/nmode/Makefile
-@@ -87,12 +87,12 @@ LIBOBJ= ../lib/rfree.o   ../lib/matinv.o ../lib/nxtsec.o \
- LIBOBJNOPATH= rfree.o   matinv.o nxtsec.o \
- 	amopen.o rgroup.o
- 
--$(BINDIR)/nmode$(SFX):	$(OBJ) libobj syslib netlib
-+$(BINDIR)/nmode$(SFX):	$(OBJ) libobj syslib
- 	$(FC) $(FPPFLAGS) $(FFLAGS) $(AMBERFFLAGS) -o $(BINDIR)/nmode$(SFX) \
- 		$(OBJ) $(LIBOBJ) \
- 		../lib/sys.a -L$(LIBDIR) $(FLIBSF) $(LDFLAGS) $(AMBERLDFLAGS)
- 
--nmanal$(SFX):	$(OBJ1) libobj netlib binpos.o
-+nmanal$(SFX):	$(OBJ1) libobj binpos.o
- 	$(FC) $(FPPFLAGS) $(FFLAGS) $(AMBERFFLAGS) -o nmanal$(SFX) \
- 		$(OBJ1) $(LIBOBJ) binpos.o \
- 		-L$(LIBDIR) $(FLIBSF) $(LDFLAGS) $(AMBERLDFLAGS)
-@@ -103,7 +103,7 @@ lmanal$(SFX):	$(OBJ2) libobj binpos.o
-         -L$(LIBDIR) $(FLIBSF) $(LDFLAGS) $(AMBERLDFLAGS)
- 
- quasih$(SFX):     quasih.o fileio.o thermo.o mexit.o \
--				syslib netlib libobj binpos.o
-+				syslib libobj binpos.o
- 	$(FC) $(FPPFLAGS) $(FFLAGS) $(AMBERFFLAGS) -o quasih$(SFX) \
- 		quasih.o fileio.o thermo.o mexit.o \
- 		$(LIBOBJ) binpos.o ../lib/sys.a -L$(LIBDIR) $(FLIBSF) \
-diff --git a/AmberTools/src/pbsa/Makefile b/AmberTools/src/pbsa/Makefile
-index 1b2c09a..6dc65a6 100644
---- a/AmberTools/src/pbsa/Makefile
-+++ b/AmberTools/src/pbsa/Makefile
-@@ -148,23 +148,23 @@ configured_parallel: configured
- 	)
- 
- #---------------------------------------------------------------------------
--pbsa$(SFX): FFTW3 $(OBJ) syslib netlib c9x-complex configured_serial 
-+pbsa$(SFX): $(OBJ) syslib configured_serial 
- 	$(FC) $(PBSAFLAG) $(FPPFLAGS) $(FFLAGS) $(AMBERFFLAGS) -o pbsa$(SFX) $(OBJ) \
- 	        ../lib/nxtsec.o ../lib/random.o $(FLIBS_FFTW3) \
- 	        -L$(LIBDIR) $(FLIBSF) $(LDFLAGS) $(AMBERLDFLAGS)
- 
--pbsa.MPI$(SFX): FFTW3.MPI $(OBJ) syslib netlib c9x-complex configured_parallel 
-+pbsa.MPI$(SFX): $(OBJ) syslib configured_parallel 
- 	$(FC) $(PBSAFLAG) $(FPPFLAGS) $(FFLAGS) $(AMBERFFLAGS) -o pbsa.MPI$(SFX) $(OBJ) \
- 	        ../lib/nxtsec.o ../lib/random.o $(FLIBS_FFTW3) \
- 	        -L$(LIBDIR) $(FLIBSF) $(LDFLAGS) $(AMBERLDFLAGS)
- 
--simplepbsa$(SFX): simplepbsa.o gopt.o libpbsa.a sfflib syslib netlib c9x-complex
-+simplepbsa$(SFX): simplepbsa.o gopt.o libpbsa.a sfflib syslib
- 	$(FC) $(PBSAFLAG) $(FPPFLAGS) $(FFLAGS) $(AMBERFFLAGS) -o simplepbsa$(SFX) simplepbsa.o gopt.o \
- 		libpbsa.a $(LIBDIR)/libsff.a ../lib/nxtsec.o -L$(LIBDIR) $(FLIBSF) \
- 		$(LDFLAGS) $(AMBERLDFLAGS)
- 	/bin/mv simplepbsa$(SFX) $(BINDIR)
- 
--libpbsa.a: FFTW3 $(LIBPBSAOBJS) syslib
-+libpbsa.a: $(LIBPBSAOBJS) syslib
- 	-rm -f libpbsa.a
- 	$(AR) libpbsa.a $(LIBPBSAOBJS) ../lib/random.o
- 	$(RANLIB) libpbsa.a
-diff --git a/AmberTools/src/ptraj/Makefile b/AmberTools/src/ptraj/Makefile
-index df789e8..48227d5 100644
---- a/AmberTools/src/ptraj/Makefile
-+++ b/AmberTools/src/ptraj/Makefile
-@@ -61,17 +61,16 @@ rdparm$(SFX): libs $(OBJECTS)
- 	$(CC) $(CFLAGS) $(AMBERCFLAGS) $(LDFLAGS) $(AMBERLDFLAGS) \
- 		-o rdparm$(SFX) $(OBJECTS) $(LIBS) $(NETCDFLIB) $(LM)
- 
--ptraj$(SFX): libs netlib $(OBJECTS)
-+ptraj$(SFX): libs $(OBJECTS)
- 	$(CC) $(CFLAGS) $(AMBERCFLAGS) $(LDFLAGS) $(AMBERLDFLAGS) \
- 		-o ptraj$(SFX) $(OBJECTS) $(LIBS) $(NETCDFLIB) $(LM)
- 
--ptraj.MPI$(SFX): libs netlib $(OBJECTS) 
-+ptraj.MPI$(SFX): libs $(OBJECTS) 
- 	$(CC) $(CFLAGS) $(AMBERCFLAGS) $(LDFLAGS) $(AMBERLDFLAGS) \
- 		-o ptraj.MPI$(SFX) $(OBJECTS) $(LIBS) $(PNETCDFLIB) $(LM)
- 
- libs: 
- 	cd pdb && $(MAKE) 
--	cd ../arpack && $(MAKE)
- 
- netlib:
- 	cd ../lapack && $(MAKE) $(LAPACK)
-diff --git a/AmberTools/src/sander/Makefile b/AmberTools/src/sander/Makefile
-index 9b9488c..de25fc7 100644
---- a/AmberTools/src/sander/Makefile
-+++ b/AmberTools/src/sander/Makefile
-@@ -90,7 +90,7 @@ APBSOBJ= \
-     file_io_dat.APBS.o apbs_vars.APBS.o apbs.APBS.o \
-     constants.o state.o memory_module.o stack.o \
-     nose_hoover.o nose_hoover_init.o \
--    trace.o rmsgrd.o lmod.o rand2.o lmodC.o xminC.o decomp.o \
-+    trace.o rmsgrd.o lmod.o rand2.o dsarpack.o lmodC.o xminC.o decomp.o \
-     icosasurf.o egb.o remd.o findmask.o \
-     relax_mat.o nmr.o multitmd.o \
-     multisander.o sander.APBS.o trajene.o cshf.o nmrcal.o mtmdcall.o pearsn.o \
-@@ -138,7 +138,7 @@ SEBOMDLIB = ../sebomd/sebomd.a
- 
- MMOBJ=  file_io_dat.o constants.o state.o memory_module.o stack.o \
-     nose_hoover.o nose_hoover_init.o \
--    trace.o rmsgrd.o lmod.o rand2.o lmodC.o xminC.o decomp.o \
-+    trace.o rmsgrd.o lmod.o rand2.o dsarpack.o lmodC.o xminC.o decomp.o \
-     icosasurf.o egb.o remd.o findmask.o \
-     relax_mat.o nmr.o multitmd.o \
-     multisander.o sander.o trajene.o cshf.o nmrcal.o mtmdcall.o pearsn.o \
-@@ -159,7 +159,7 @@ MMOBJ=  file_io_dat.o constants.o state.o memory_module.o stack.o \
- 
- APIOBJ=  file_io_dat.o constants.o state.o memory_module.o stack.o \
-     nose_hoover.o nose_hoover_init.o \
--    trace.o rmsgrd.o lmod.o rand2.o lmodC.o xminC.o decomp.o \
-+    trace.o rmsgrd.o lmod.o rand2.o dsarpack.o lmodC.o xminC.o decomp.o \
-     icosasurf.o egb.o remd.o findmask.o \
-     relax_mat.o nmr.o multitmd.o \
-     trajene.o cshf.o nmrcal.o mtmdcall.o pearsn.o \
-@@ -180,7 +180,7 @@ APIOBJ=  file_io_dat.o constants.o state.o memory_module.o stack.o \
- 
- LESAPIOBJ= memory_module.o stack.o file_io_dat.o les.o \
-     constants.o state.o nose_hoover.o nose_hoover_init_LES.o \
--    trace.o rmsgrd.o rand2.o lmodC.o xminC.o decomp.o icosasurf.o \
-+    trace.o rmsgrd.o rand2.o dsarpack.o lmodC.o xminC.o decomp.o icosasurf.o \
-     egb.LES.o remd.LES.o findmask.o relax_mat.o nmr.LES.o multitmd.o \
-     cshf.o nmrcal.o mtmdcall.o pearsn.o cpparm.LES.o \
-     printe.o runmin.o nonbond_list.LESAPI.o force.LES.o rdparm.LESAPI.o \
-@@ -209,7 +209,7 @@ PARTPIMDOBJ = pimd_vars.o pimd_force.LES.o pimd_init.LES.o cmd_vars.o cmd_matrix
- 
- PUPILOBJ= file_io_dat.o constants.o state.o memory_module.o stack.o \
- 	nose_hoover.o nose_hoover_init.o \
--	trace.o rmsgrd.o lmod.o rand2.o lmodC.o xminC.o decomp.o \
-+	trace.o rmsgrd.o lmod.o rand2.o dsarpack.o lmodC.o xminC.o decomp.o \
- 	pupildata.o icosasurf.o egb.o findmask.o \
- 	relax_mat.o nmr.o multitmd.o \
- 	multisander.o sander.PUPIL.o trajene.o cshf.o nmrcal.o mtmdcall.o pearsn.o \
-@@ -233,7 +233,7 @@ LSCIVROBJ = lscivr_vars.o lsc_init.o lsc_xp.o
- 
- LESOBJ= memory_module.o stack.o file_io_dat.o \
-     constants.o state.o nose_hoover.o nose_hoover_init_LES.o \
--    trace.o rmsgrd.o rand2.o lmodC.o xminC.o decomp.o icosasurf.o \
-+    trace.o rmsgrd.o rand2.o dsarpack.o lmodC.o xminC.o decomp.o icosasurf.o \
-     egb.LES.o remd.LES.o findmask.o \
-     relax_mat.o nmr.LES.o multitmd.o \
-     multisander.LES.o sander.LES.o  cshf.o nmrcal.o mtmdcall.o pearsn.o \
-@@ -293,7 +293,7 @@ all_serial_programs: $(SERIALPROGS)
- $(BINDIR)/sander$(SFX): libsqm $(MMOBJ) $(QMOBJ) $(FULLPIMDOBJ) $(EMIL) \
-               $(SEBOMDOBJ) sebomd \
-               $(LSCIVROBJ) force.o syslib \
--              ../lib/nxtsec.o netlib configured_serial \
-+              ../lib/nxtsec.o configured_serial \
-               $(NCSU_OBJECTS) $(XRAY_OBJS) libpbsa librism $(PLUMED_DEPENDENCIES)
- 	$(FC) $(FPPFLAGS) $(FFLAGS) $(AMBERFFLAGS) -o $@  $(MMOBJ) $(QMOBJ) $(SEBOMDOBJ) \
- 	      $(FULLPIMDOBJ) $(LSCIVROBJ) force.o -L$(LIBDIR) -lsqm \
-@@ -308,7 +308,7 @@ $(BINDIR)/sander$(SFX): libsqm $(MMOBJ) $(QMOBJ) $(FULLPIMDOBJ) $(EMIL) \
- $(BINDIR)/sander.MPI$(SFX): libsqm $(MMOBJ) $(QMOBJ) $(FULLPIMDOBJ) $(EMIL) \
-               $(LSCIVROBJ) $(EVBOBJ) force.o \
-               $(SEBOMDOBJ) sebomd $(XRAY_OBJS) \
--              syslib ../lib/nxtsec.o netlib libpbsa librism_mpi configured_parallel $(NCSU_OBJECTS) \
-+              syslib ../lib/nxtsec.o libpbsa librism_mpi configured_parallel $(NCSU_OBJECTS) \
-               $(PLUMED_DEPENDENCIES)
- 	$(FC) $(FPPFLAGS) $(FFLAGS) $(AMBERFFLAGS) -o $@  $(MMOBJ) $(QMOBJ) $(SEBOMDOBJ) \
-               $(FULLPIMDOBJ) $(LSCIVROBJ) $(EVBOBJ) force.o \
-@@ -323,7 +323,7 @@ $(BINDIR)/sander.MPI$(SFX): libsqm $(MMOBJ) $(QMOBJ) $(FULLPIMDOBJ) $(EMIL) \
- $(BINDIR)/sander.PUPIL$(SFX): libsqm $(PUPILOBJ) $(QMOBJ) $(FULLPIMDOBJ) $(EMIL) \
- 		$(LSCIVROBJ)  syslib $(XRAY_OBJS) \
-                 $(SEBOMDOBJ) sebomd \
--		../lib/nxtsec.o netlib libpbsa librism configured_serial $(NCSU_OBJECTS) \
-+		../lib/nxtsec.o libpbsa librism configured_serial $(NCSU_OBJECTS) \
-                 $(PLUMED_DEPENDENCIES)
- 	$(FC) $(FPPFLAGS) $(FFLAGS) $(AMBERFFLAGS) -o $@ $(PUPILOBJ) $(QMOBJ) $(SEBOMDOBJ) $(FULLPIMDOBJ) \
- 		$(LSCIVROBJ) -L$(LIBDIR) -lsqm -lFpbsa \
-@@ -335,7 +335,7 @@ $(BINDIR)/sander.PUPIL$(SFX): libsqm $(PUPILOBJ) $(QMOBJ) $(FULLPIMDOBJ) $(EMIL)
- 
- #---------------------------------------------------------------------------
- $(BINDIR)/sander.LES$(SFX): libsqm $(LESOBJ) $(PARTPIMDOBJ) syslib \
--        ../lib/nxtsec.o netlib \
-+        ../lib/nxtsec.o \
- 		$(LSCIVROBJ) $(NCSU_OBJECTS) $(XRAY_OBJS) configured_serial \
- 		libpbsa librism $(EMIL) sebomd $(PLUMED_DEPENDENCIES)
- 	$(FC) $(FPPFLAGS) $(FFLAGS) $(AMBERFFLAGS) -o $@ $(LESOBJ) $(PARTPIMDOBJ) $(LSCIVROBJ) \
-@@ -348,7 +348,7 @@ $(BINDIR)/sander.LES$(SFX): libsqm $(LESOBJ) $(PARTPIMDOBJ) syslib \
- #---------------------------------------------------------------------------
- $(BINDIR)/sander.LES.MPI$(SFX): libsqm $(LESOBJ) $(EVBPIMD) \
-         $(PARTPIMDOBJ) syslib ../lib/nxtsec.o \
--	    netlib libpbsa librism_mpi $(EMIL) $(XRAY_OBJS) \
-+	    libpbsa librism_mpi $(EMIL) $(XRAY_OBJS) \
- 		$(LSCIVROBJ) $(NCSU_OBJECTS) sebomd configured_parallel $(PLUMED_DEPENDENCIES)
- 	$(FC) $(FPPFLAGS) $(FFLAGS) $(AMBERFFLAGS) -o $@ $(LESOBJ) $(EVBPIMD) \
-         $(PARTPIMDOBJ) $(LSCIVROBJ) $(XRAY_OBJS) \
-@@ -363,7 +363,7 @@ $(BINDIR)/sander.APBS$(SFX): libsqm $(APBSOBJ) $(QMOBJ) \
-               $(LSCIVROBJ) $(FULLPIMDOBJ) $(NCSU_OBJECTS) \
-               force.APBS.o syslib librism $(EMIL) \
-               $(SEBOMDOBJ) sebomd $(XRAY_OBJS) \
--              ../lib/nxtsec.o netlib configured_serial $(PLUMED_DEPENDENCIES)
-+              ../lib/nxtsec.o configured_serial $(PLUMED_DEPENDENCIES)
- 	$(FC) $(FPPFLAGS) $(FFLAGS) $(AMBERFFLAGS) -o $@  $(APBSOBJ) $(QMOBJ) $(SEBOMDOBJ) \
-               $(FULLPIMDOBJ) $(LSCIVROBJ) force.APBS.o \
-               -L$(APBS_LIBDIR) $(APBS_LIBS) \
-@@ -386,7 +386,7 @@ $(BINDIR)/ambmask$(SFX): 	ambmask.o findmask.o amopen.o parms.o \
- $(LIBDIR)/libsander$(SHARED_SUFFIX): libsqm $(APIOBJ) $(QMAPIOBJ) $(FULLPIMDOBJ) $(EMIL) \
-               $(SEBOMDOBJ) sebomd $(INCDIR)/sander_api.mod \
-               $(LSCIVROBJ) force.o syslib $(PLUMED_DEPENDENCIES) \
--              ../lib/nxtsec.o netlib configured_serial \
-+              ../lib/nxtsec.o configured_serial \
-               $(NCSU_OBJECTS) $(XRAY_OBJS) libpbsa librism
- 	$(FC) $(MAKE_SHARED) $(FPPFLAGS) $(FFLAGS) $(AMBERFFLAGS) -o $@  $(APIOBJ) \
- 		  $(QMAPIOBJ) $(SEBOMDOBJ) $(FULLPIMDOBJ) $(LSCIVROBJ) force.o \
-@@ -399,7 +399,7 @@ $(LIBDIR)/libsander$(SHARED_SUFFIX): libsqm $(APIOBJ) $(QMAPIOBJ) $(FULLPIMDOBJ)
- 	      $(LIOLIBS) $(PLUMED_LOAD)
- 
- $(LIBDIR)/libsanderles$(SHARED_SUFFIX): libsqm $(LESAPIOBJ) $(PARTPIMDOBJ) $(QMAPIOBJ) syslib \
--        ../lib/nxtsec.o netlib $(INCDIR)/sanderles_api.mod \
-+        ../lib/nxtsec.o $(INCDIR)/sanderles_api.mod \
- 		$(LSCIVROBJ) $(NCSU_OBJECTS) $(XRAY_OBJS) configured_serial \
- 		libpbsa librism $(EMIL) sebomd $(PLUMED_DEPENDENCIES)
- 	$(FC) $(MAKE_SHARED) $(FPPFLAGS) $(FFLAGS) $(AMBERFFLAGS) \
-@@ -452,6 +452,10 @@ rand2.o:  ../sff/rand2.c
- 	$(CC) -c $(CNOOPTFLAGS) $(CFLAGS) $(AMBERCFLAGS) \
- 		-o rand2.o ../sff/rand2.c
- 
-+dsarpack.o:  ../sff/dsarpack.f
-+	$(FC) -c $(FPPFLAGS) $(CFLAGS) $(AMBERFFLAGS) \
-+	        -o dsarpack.o ../sff/dsarpack.f
-+
- lmodC.o:  ../sff/lmodC.c
- 	$(CC) -c -DSQM $(CNOOPTFLAGS) $(CFLAGS) $(AMBERCFLAGS) \
- 		-o lmodC.o ../sff/lmodC.c
-diff --git a/AmberTools/src/sander/depend b/AmberTools/src/sander/depend
-index 67cc33b..b8667d7 100644
---- a/AmberTools/src/sander/depend
-+++ b/AmberTools/src/sander/depend
-@@ -5774,7 +5774,7 @@ yammpnb.o: \
- yammpnb.o:   yammpnb.F90
- 	$(FC) $(FWARNFLAGS) $(FPPFLAGS) -c $(FOPTFLAGS) $(FFLAGS) $(AMBERFFLAGS) $(RISMSANDER) -o $@ yammpnb.F90
- 
--netcdf.o:  $(NETCDF)
-+netcdf.o:
- 	test -e $@ || touch netcdf.o
- 
- AmberNetcdf.o: ../lib/AmberNetcdf.F90
-diff --git a/AmberTools/src/sander/makedepend b/AmberTools/src/sander/makedepend
-index 05c04c4..a18d979 100755
---- a/AmberTools/src/sander/makedepend
-+++ b/AmberTools/src/sander/makedepend
-@@ -232,7 +232,7 @@ foreach $file ( <*.F90> ){
- }
- 
- # special "compilation rule" for netcdf.o
--printf "netcdf.o:  \$(NETCDF)\n\ttest -e \$\@ || touch netcdf.o\n\n";
-+printf "netcdf.o:\n\ttest -e \$\@ || touch netcdf.o\n\n";
- 
- # special compilation rule for AmberNetcdf.o, random.o, and constants.o
- printf "AmberNetcdf.o: ../lib/AmberNetcdf.F90\n";
-diff --git a/AmberTools/src/sander/sander.h b/AmberTools/src/sander/sander.h
-index e4ca7e3..23cb216 100644
---- a/AmberTools/src/sander/sander.h
-+++ b/AmberTools/src/sander/sander.h
-@@ -47,7 +47,7 @@
- // Workaround for strange behavior of clang compiler -- clang C doesn't seem to
- // like the inline specifier on any of these functions, but clang++ handles it
- // just fine.
--#if defined(__cplusplus) || !defined(__clang__)
-+#if defined(__cplusplus)
- #   define INLINE inline
- #else
- #   define INLINE
-diff --git a/AmberTools/src/sff/Makefile b/AmberTools/src/sff/Makefile
-index 228625a..88d5531 100644
---- a/AmberTools/src/sff/Makefile
-+++ b/AmberTools/src/sff/Makefile
-@@ -3,7 +3,7 @@ include ../config.h
- .c.o:
- 	$(CC) -c -Dflex $(COPTFLAGS) $(CFLAGS) $(AMBERCFLAGS) $(RISMSFF) $(NETCDFINC) -o $@ $<
- 
--OBJS = binpos.o conjgrad.o lmodC.o memutil.o nblist.o newton.o nmode.o \
-+OBJS = binpos.o conjgrad.o dsarpack.o lmodC.o memutil.o nblist.o newton.o nmode.o \
- 	prm.o rand2.o sasad.o sff.o time.o xminC.o AmberNetcdf.o atomic_number.o $(SFF_RISM_INTERFACE)
- 
- 
-@@ -65,7 +65,7 @@ xminC.o:  sff.h
- AmberNetcdf.o:  AmberNetcdf.h
- 
- hcp_getpdb: hcp_getpdb.c
--	$(CC) -o $(BINDIR)/hcp_getpdb hcp_getpdb.c
-+	$(CC) $(CFLAGS) $(LDFLAGS) -o $(BINDIR)/hcp_getpdb hcp_getpdb.c
- 
- .PHONY: ../rism/amber_rism_interface.NAB.o
- ../rism/amber_rism_interface.NAB.o:
-diff --git a/AmberTools/src/sff/dsarpack.f b/AmberTools/src/sff/dsarpack.f
-new file mode 100644
-index 0000000..5544df9
---- /dev/null
-+++ b/AmberTools/src/sff/dsarpack.f
-@@ -0,0 +1,654 @@
-+      subroutine dsarpack(n_dim,n_eig_in,n_eig_out,ncv_in,itr_in,
-+     &                    eigval_tol,eigvals,eigvecs,spectrum,
-+     &                    need_eigvecs,ierr,debug_arpack,
-+     &                    v,workl,workd,d,resid,ax,select,
-+     &                    xyz,grad,return_flag,label)
-+c
-+      implicit none
-+c
-+c     %-----------------%
-+c     | Dummy Arguments |
-+c     %-----------------%
-+c
-+      integer n_dim,n_eig_in,n_eig_out,ncv_in,itr_in,spectrum,
-+     &        need_eigvecs,ierr,debug_arpack,return_flag,label
-+      Double precision eigval_tol
-+      Double precision eigvals(n_eig_in),eigvecs(n_dim * n_eig_in)
-+      Double precision v(n_dim,ncv_in),
-+     &                 workl(ncv_in*(ncv_in+8)),workd(3*n_dim),
-+     &                 d(ncv_in,2),resid(n_dim),ax(n_dim),
-+     &                 xyz(n_dim),grad(n_dim)
-+      logical select(ncv_in)
-+c
-+      save
-+c
-+c     %---------------%
-+c     | Include Files |
-+c     %---------------%
-+c
-+c     include 'debug.h'
-+c
-+c\SCCS Information: @(#) 
-+c FILE: debug.h   SID: 2.3   DATE OF SID: 11/16/95   RELEASE: 2 
-+c
-+c     %---------------------------------%
-+c     | See debug.doc for documentation |
-+c     %---------------------------------%
-+      integer  logfil, ndigit, mgetv0,
-+     &         msaupd, msaup2, msaitr, mseigt, msapps, msgets, mseupd,
-+     &         mnaupd, mnaup2, mnaitr, mneigh, mnapps, mngets, mneupd,
-+     &         mcaupd, mcaup2, mcaitr, mceigh, mcapps, mcgets, mceupd
-+      common /debug/ 
-+     &         logfil, ndigit, mgetv0,
-+     &         msaupd, msaup2, msaitr, mseigt, msapps, msgets, mseupd,
-+     &         mnaupd, mnaup2, mnaitr, mneigh, mnapps, mngets, mneupd,
-+     &         mcaupd, mcaup2, mcaitr, mceigh, mcapps, mcgets, mceupd
-+c
-+c     This code shows how to use ARPACK to find a few eigenvalues 
-+c     (lambda) and corresponding eigenvectors (x) for the standard 
-+c     eigenvalue problem:
-+c          
-+c                        A*x = lambda*x
-+c 
-+c     where A is an n by n real symmetric matrix.
-+c
-+c     The main points illustrated here are 
-+c
-+c        1) How to declare sufficient memory to find NEV 
-+c           eigenvalues of largest magnitude.  Other options
-+c           are available.
-+c
-+c        2) Illustration of the reverse communication interface 
-+c           needed to utilize the top level ARPACK routine DSAUPD 
-+c           that computes the quantities needed to construct
-+c           the desired eigenvalues and eigenvectors(if requested).
-+c
-+c        3) How to extract the desired eigenvalues and eigenvectors
-+c           using the ARPACK routine DSEUPD.
-+c
-+c     The only thing that must be supplied in order to use this
-+c     routine on your problem is to change the array dimensions 
-+c     appropriately, to specify WHICH eigenvalues you want to compute 
-+c     and to supply a matrix-vector product
-+c
-+c                         w <-  Av
-+c
-+c     in place of the call to AV( ) below.
-+c
-+c     Once usage of this routine is understood, you may wish to explore
-+c     the other available options to improve convergence, to solve generalized
-+c     problems, etc.  Look at the file ex-sym.doc in DOCUMENTS directory.
-+c     This codes implements  
-+c
-+c\Example-1
-+c     ... Suppose we want to solve A*x = lambda*x in regular mode,
-+c         where A is derived from the central difference discretization
-+c         of the 2-dimensional Laplacian on the unit square with
-+c         zero Dirichlet boundary condition.
-+c     ... OP = A  and  B = I.
-+c     ... Assume "call av (n,x,y)" computes y = A*x
-+c     ... Use mode 1 of DSAUPD.
-+c
-+c\BeginLib
-+c
-+c\Routines called:
-+c     dsaupd  ARPACK reverse communication interface routine.
-+c     dseupd  ARPACK routine that returns Ritz values and (optionally)
-+c             Ritz vectors.
-+c     dnrm2   Level 1 BLAS that computes the norm of a vector.
-+c     daxpy   Level 1 BLAS that computes y <- alpha*x+y.
-+c
-+c\Author
-+c     Richard Lehoucq
-+c     Danny Sorensen
-+c     Chao Yang
-+c     Dept. of Computational &
-+c     Applied Mathematics
-+c     Rice University
-+c     Houston, Texas
-+c
-+c\SCCS Information: %Z%
-+c FILE: %M%   SID: %I%   DATE OF SID: %G%   RELEASE: %R%
-+c
-+c\Remarks
-+c     1. None
-+c
-+c\EndLib
-+c
-+c-----------------------------------------------------------------------
-+c
-+c     %-------------------------------------------------------%
-+c     | Storage Declarations:                                 |
-+c     |                                                       |
-+c     | The maximum dimensions for all arrays are             |
-+c     | set here to accommodate a problem size of             |
-+c     | N .le. MAXN                                           |
-+c     |                                                       |
-+c     | NEV is the number of eigenvalues requested.           |
-+c     |     See specifications for ARPACK usage below.        |
-+c     |                                                       |
-+c     | NCV is the largest number of basis vectors that will  |
-+c     |     be used in the Implicitly Restarted Arnoldi       |
-+c     |     Process.  Work per major iteration is             |
-+c     |     proportional to N*NCV*NCV.                        |
-+c     |                                                       |
-+c     | You must set:                                         |
-+c     |                                                       |
-+c     | MAXN:   Maximum dimension of the A allowed. (dynamic) |
-+c     | MAXNEV: Maximum NEV allowed. (dynamic)                |
-+c     | MAXNCV: Maximum NCV allowed. (dynamic)                |
-+c     %-------------------------------------------------------%
-+c
-+C     %--------------------------------------%
-+C     | F90 Allocatable Arrays (on the heap) |
-+C     %--------------------------------------%
-+c
-+C     Double precision,allocatable,save :: v(:,:)
-+C     integer,save :: v_row_allocated = 0, v_col_allocated = 0
-+c
-+c     %----------------------------------------------%
-+c     | Originally, as F77 parameters, the following |
-+c     | integers were used to dimension work arrays. |
-+c     | They are replaced by dummy arguments used to |
-+c     | dimension the work arrays as F90 automatic   |
-+c     | arrays, but the integers are still used for  |
-+c     | passing the dimensions to lower level ARPACK |
-+c     | routines dsaupd, dseupd and dmout.           |
-+c     %----------------------------------------------%
-+c
-+      integer          maxn, maxnev, maxncv, ldv
-+c
-+c     %-------------------------------------------%
-+c     | Local F90 Automatic Arrays (on the stack) |
-+c     %-------------------------------------------%
-+c
-+      Double precision
-+C    &                 workl(ncv_in*(ncv_in+8)),
-+C    &                 workd(3*n_dim), d(ncv_in,2), resid(n_dim),
-+C    &                 ax(n_dim),
-+     &                 cg_dstat(4)
-+C     logical          select(ncv_in)
-+      integer          iparam(11), ipntr(11),
-+     &                 cg_istat(4)
-+c
-+c     %---------------%
-+c     | Local Scalars |
-+c     %---------------%
-+c
-+      character        bmat*1, which*2
-+      integer          ido, n, nev, ncv, lworkl, info,
-+     &                 i, j, nx, ishfts, maxitr, mode1, nconv
-+      integer          L12, L18, ARPACK_ERROR, status_flag
-+      data             L12, L18, ARPACK_ERROR /1, 2, -2/
-+C     integer          v_row_needed, v_col_needed
-+      logical          rvec
-+      Double precision      
-+     &                 tol, sigma
-+c
-+c     %------------%
-+c     | Parameters |
-+c     %------------%
-+c
-+      Double precision
-+     &                 zero
-+      parameter        (zero = 0.0D+0)
-+c  
-+c     %-----------------------------%
-+c     | BLAS & LAPACK routines used |
-+c     %-----------------------------%
-+c
-+      Double precision           
-+     &                 dnrm2
-+      external         dnrm2, daxpy, hessvec
-+c
-+c     %--------------------%
-+c     | Intrinsic function |
-+c     %--------------------%
-+c
-+      intrinsic        abs
-+c
-+c     %-----------------------%
-+c     | Executable Statements |
-+c     %-----------------------%
-+c
-+      if ( label.eq.0 ) go to 1
-+      go to (12,18) label
-+  1   continue
-+c
-+c     %------------------------------------------------%
-+c     | Values used to calculate work array dimensions |
-+c     %------------------------------------------------%
-+c
-+      maxn = n_dim
-+      maxnev = n_eig_in
-+      maxncv = ncv_in
-+      ldv = maxn
-+c
-+c     %---------------------------------------------------%
-+c     | The include debug.h statement above and           |
-+c     | assignments here initiate trace output from the   |
-+c     | internal actions of ARPACK.  See debug.doc in the |
-+c     | DOCUMENTS directory for usage.  Initially, the    |
-+c     | most useful information will be a breakdown of    |
-+c     | time spent in the various stages of computation   |
-+c     | given by setting msaupd = 1.                      |
-+c     %---------------------------------------------------%
-+c
-+      ndigit = -5
-+      logfil = 6
-+      msgets = 0
-+      msaitr = 0 
-+      msapps = 0
-+      if ( debug_arpack.eq.1 ) then
-+        msaupd = 1
-+      else
-+        msaupd = 0
-+      endif
-+      msaup2 = 0
-+      mseigt = 0
-+      mseupd = 0
-+c     
-+c   *** Allocatable array v will be allowed to grow to its largest size;
-+c   ***  it is never deallocated:
-+C     v_row_needed = n_dim        !!! ldv
-+C     v_col_needed = ncv_in       !!! maxncv
-+C     if( allocated(v) )then
-+C       if( (v_row_needed .gt. v_row_allocated)
-+C    & .or. (v_col_needed .gt. v_col_allocated) )then
-+C         deallocate(v,stat=ierr)
-+C         if( ierr .ne. 0 )then
-+C           write( logfil, '(a,i16,1x,i8)' )
-+C    &       'ARPACK: could not deallocate v'
-+C           go to 9000
-+C         endif
-+C       endif
-+C     endif
-+C     if( .not. allocated(v) )then
-+C       allocate( v(v_row_needed,v_col_needed), stat=ierr )
-+C       if( ierr .ne. 0 )then
-+C         write( logfil, '(a,2i10)' )
-+C    &     'ARPACK: could not allocate v'
-+C         go to 9000
-+C       endif
-+C       v_row_allocated = v_row_needed
-+C       v_col_allocated = v_col_needed
-+C     endif
-+C     v = zero !!! zero out entire v array
-+c     
-+c     %-------------------------------------------------%
-+c     | The following sets dimensions for this problem. |
-+c     %-------------------------------------------------%
-+c
-+      n = n_dim
-+c
-+c     %----------------------------------------------%
-+c     |                                              | 
-+c     | Specifications for ARPACK usage are set      | 
-+c     | below:                                       |
-+c     |                                              |
-+c     |    1) NEV = N_EIG_IN  asks for N_EIG_IN      |  
-+c     |       eigenvalues to be computed.            | 
-+c     |                                              |
-+c     |    2) NCV = NCV_IN sets the length of the    |
-+c     |       Arnoldi factorization                  |
-+c     |                                              |
-+c     |    3) This is a standard problem             |
-+c     |         (indicated by bmat  = 'I')           |
-+c     |                                              |
-+c     |    4) Ask for the NEV eigenvalues of         |
-+c     |       smallest magnitude                     |
-+c     |         (indicated by which = 'SM')          |
-+c     |       See documentation in SSAUPD for the    |
-+c     |       other options SA, LA, LM, BE.          | 
-+c     |                                              |
-+c     | Note: NEV and NCV must satisfy the following |
-+c     | conditions:                                  |
-+c     |              NEV <= MAXNEV                   |
-+c     |          NEV + 1 <= NCV <= MAXNCV            |
-+c     %----------------------------------------------%
-+c
-+      nev   = n_eig_in
-+      ncv   = ncv_in 
-+      bmat  = 'I'
-+      if ( spectrum .eq. 1 ) then
-+         which = 'SM'
-+      else if ( spectrum .eq. 2 ) then
-+         which = 'SA'
-+      else if ( spectrum .eq. 3 ) then
-+         which = 'LM'
-+      else if ( spectrum .eq. 4 ) then
-+         which = 'LA'
-+      else if ( spectrum .eq. 5 ) then
-+         which = 'BE'
-+      else
-+          print *, ' ERROR with _SSIMP: Spectrum .NE. (SM|SA|LA|LM|BE)'
-+         go to 9000
-+      end if
-+c
-+      if ( n .gt. maxn ) then
-+         print *, ' ERROR with _SSIMP: N is greater than MAXN '
-+         go to 9000
-+      else if ( nev .gt. maxnev ) then
-+         print *, ' ERROR with _SSIMP: NEV is greater than MAXNEV '
-+         go to 9000
-+      else if ( ncv .gt. maxncv ) then
-+         print *, ' ERROR with _SSIMP: NCV is greater than MAXNCV '
-+         go to 9000
-+      end if
-+c
-+c     %-----------------------------------------------------%
-+c     |                                                     |
-+c     | Specification of stopping rules and initial         |
-+c     | conditions before calling DSAUPD                    |
-+c     |                                                     |
-+c     | TOL  determines the stopping criterion.             |
-+c     |                                                     |
-+c     |      Expect                                         |
-+c     |           abs(lambdaC - lambdaT) < TOL*abs(lambdaC) |
-+c     |               computed   true                       |
-+c     |                                                     |
-+c     |      If TOL .le. 0,  then TOL <- macheps            |
-+c     |           (machine precision) is used.              |
-+c     |                                                     |
-+c     | IDO  is the REVERSE COMMUNICATION parameter         |
-+c     |      used to specify actions to be taken on return  |
-+c     |      from DSAUPD. (See usage below.)                |
-+c     |                                                     |
-+c     |      It MUST initially be set to 0 before the first |
-+c     |      call to DSAUPD.                                | 
-+c     |                                                     |
-+c     | INFO on entry specifies starting vector information |
-+c     |      and on return indicates error codes            |
-+c     |                                                     |
-+c     |      Initially, setting INFO=0 indicates that a     | 
-+c     |      random starting vector is requested to         |
-+c     |      start the ARNOLDI iteration.  Setting INFO to  |
-+c     |      a nonzero value on the initial call is used    |
-+c     |      if you want to specify your own starting       |
-+c     |      vector (This vector must be placed in RESID.)  | 
-+c     |                                                     |
-+c     | The work array WORKL is used in DSAUPD as           | 
-+c     | workspace.  Its dimension LWORKL is set as          |
-+c     | illustrated below.                                  |
-+c     |                                                     |
-+c     %-----------------------------------------------------%
-+c
-+      lworkl = ncv*(ncv+8)
-+      tol = eigval_tol 
-+      info = 0
-+      ido = 0
-+c
-+c     %---------------------------------------------------%
-+c     | Specification of Algorithm Mode:                  |
-+c     |                                                   |
-+c     | This program uses the exact shift strategy        |
-+c     | (indicated by setting PARAM(1) = 1).              |
-+c     | IPARAM(3) specifies the maximum number of Arnoldi |
-+c     | iterations allowed.  Mode 1 of DSAUPD is used     |
-+c     | (IPARAM(7) = 1). All these options can be changed |
-+c     | by the user. For details see the documentation in |
-+c     | DSAUPD.                                           |
-+c     %---------------------------------------------------%
-+c
-+      ishfts = 1
-+      maxitr = itr_in 
-+      mode1 = 1
-+c
-+      iparam(1) = ishfts
-+c                
-+      iparam(3) = maxitr
-+c                  
-+      iparam(7) = mode1
-+c
-+c     %------------------------------------------------%
-+c     | M A I N   L O O P (Reverse communication loop) |
-+c     %------------------------------------------------%
-+c
-+ 10   continue
-+c
-+c        %---------------------------------------------%
-+c        | Repeatedly call the routine DSAUPD and take | 
-+c        | actions indicated by parameter IDO until    |
-+c        | either convergence is indicated or maxitr   |
-+c        | has been exceeded.                          |
-+c        %---------------------------------------------%
-+c
-+         call dsaupd ( ido, bmat, n, which, nev, tol, resid, 
-+     &                 ncv, v, ldv, iparam, ipntr, workd, workl,
-+     &                 lworkl, info )
-+c
-+         if (ido .eq. -1 .or. ido .eq. 1) then
-+c
-+c           %--------------------------------------%
-+c           | Perform matrix vector multiplication |
-+c           |              y <--- OP*x             |
-+c           | The user should supply his/her own   |
-+c           | matrix vector multiplication routine |
-+c           | here that takes workd(ipntr(1)) as   |
-+c           | the input, and return the result to  |
-+c           | workd(ipntr(2)).                     |
-+c           %--------------------------------------%
-+c
-+            status_flag = 0
-+ 11         continue
-+               call hessvec ( n, workd(ipntr(1)), workd(ipntr(2)),
-+     &                        xyz, grad, return_flag, status_flag )
-+               if ( status_flag.eq.0 ) go to 13
-+               if ( status_flag.lt.0 ) go to 9000
-+               label = L12
-+               return
-+ 12         go to 11
-+ 13         continue
-+c
-+c           %-----------------------------------------%
-+c           | L O O P   B A C K to call DSAUPD again. |
-+c           %-----------------------------------------%
-+c
-+            go to 10
-+c
-+         end if 
-+c
-+c     %----------------------------------------%
-+c     | Either we have convergence or there is |
-+c     | an error.                              |
-+c     %----------------------------------------%
-+c
-+      if ( info .lt. 0 ) then
-+c
-+c        %--------------------------%
-+c        | Error message. Check the |
-+c        | documentation in DSAUPD. |
-+c        %--------------------------%
-+c
-+         print *, ' '
-+         print *, ' Error with _saupd, info = ', info
-+         print *, ' Check documentation in _saupd '
-+         print *, ' '
-+         go to 9000
-+c
-+      else 
-+c
-+c        %-------------------------------------------%
-+c        | No fatal errors occurred.                 |
-+c        | Post-Process using DSEUPD.                |
-+c        |                                           |
-+c        | Computed eigenvalues may be extracted.    |  
-+c        |                                           |
-+c        | Eigenvectors may be also computed now if  |
-+c        | desired.  (indicated by rvec = .true.)    | 
-+c        |                                           |
-+c        | The routine DSEUPD now called to do this  |
-+c        | post processing (Other modes may require  |
-+c        | more complicated post processing than     |
-+c        | mode1.)                                   |
-+c        |                                           |
-+c        %-------------------------------------------%
-+c           
-+         if ( need_eigvecs .eq. 1 ) then
-+            rvec = .true.
-+         else
-+            rvec = .false.
-+         end if
-+c
-+         call dseupd ( rvec, 'All', select, d, v, ldv, sigma, 
-+     &        bmat, n, which, nev, tol, resid, ncv, v, ldv, 
-+     &        iparam, ipntr, workd, workl, lworkl, ierr )
-+c
-+c        %----------------------------------------------%
-+c        | Eigenvalues are returned in the first column |
-+c        | of the two dimensional array D and the       |
-+c        | corresponding eigenvectors are returned in   |
-+c        | the first NCONV (=IPARAM(5)) columns of the  |
-+c        | two dimensional array V if requested.        |
-+c        | Otherwise, an orthogonal basis for the       |
-+c        | invariant subspace corresponding to the      |
-+c        | eigenvalues in D is returned in V.           |
-+c        %----------------------------------------------%
-+c
-+         if ( ierr .ne. 0) then
-+c
-+c           %------------------------------------%
-+c           | Error condition:                   |
-+c           | Check the documentation of DSEUPD. |
-+c           %------------------------------------%
-+c
-+            print *, ' '
-+            print *, ' Error with _seupd, info = ', ierr
-+            print *, ' Check the documentation of _seupd. '
-+            print *, ' '
-+            go to 9000
-+c
-+         else if ( debug_arpack.eq.1 ) then
-+c
-+            nconv =  iparam(5)
-+            n_eig_out = nconv
-+            if ( nconv .le. 0 ) then
-+               print *, ' '
-+               print *, ' ARPACK: Not a single mode converged.'
-+               print *, ' '
-+               go to 9000
-+            endif
-+c
-+C           %--------------------------------------------%
-+C           | "UnDO" DO 20 j=1,nconv loop, because it is |
-+C           | illegal to jump in and out from a DO loop. |
-+C           %--------------------------------------------%
-+c
-+            j = 1
-+ 16         continue
-+c
-+c              %---------------------------%
-+c              | Compute the residual norm |
-+c              |                           |
-+c              |   ||  A*x - lambda*x ||   |
-+c              |                           |
-+c              | for the NCONV accurately  |
-+c              | computed eigenvalues and  |
-+c              | eigenvectors.  (iparam(5) |
-+c              | indicates how many are    |
-+c              | accurate to the requested |
-+c              | tolerance)                |
-+c              %---------------------------%
-+c
-+               status_flag = 0
-+ 17            continue
-+                  call hessvec ( n, v(1,j), ax, xyz, grad,
-+     &                           return_flag, status_flag )
-+                  if ( status_flag.eq.0 ) go to 19
-+                  if ( status_flag.lt.0 ) go to 9000
-+                  label = L18
-+                  return
-+ 18            go to 17
-+ 19            continue
-+c
-+               call daxpy(n, -d(j,1), v(1,j), 1, ax, 1)
-+               d(j,2) = dnrm2(n, ax, 1)
-+               d(j,2) = d(j,2) / abs(d(j,1))
-+c
-+               j = j + 1
-+               if ( j .gt. nconv ) go to 20
-+c
-+               go to 16
-+c
-+ 20         continue
-+c
-+c           %-----------------------------%
-+c           | Display computed residuals. |
-+c           %-----------------------------%
-+c
-+            call dmout(6, nconv, 2, d, maxncv, -6,
-+     &           'Ritz values and relative residuals')
-+c
-+c           %-------------------------------------------%
-+c           | Print additional convergence information. |
-+c           %-------------------------------------------%
-+c
-+            if ( info .eq. 1) then
-+               print *, ' '
-+               print *, ' Maximum number of iterations reached.'
-+               print *, ' '
-+            else if ( info .eq. 3) then
-+               print *, ' '
-+               print *, ' No shifts could be applied during implicit',
-+     &                  ' Arnoldi update, try increasing NCV.'
-+               print *, ' '
-+            end if
-+c
-+            print *, ' '
-+            print *, ' _SSIMP '
-+            print *, ' ====== '
-+            print *, ' '
-+            print *, ' Size of the matrix is ', n
-+            print *, ' The number of Ritz values requested is ', nev
-+            print *, ' The number of Arnoldi vectors generated',
-+     &               ' (NCV) is ', ncv
-+            print *, ' What portion of the spectrum: ', which
-+            print *, ' The number of converged Ritz values is ',
-+     &                 nconv
-+            print *, ' The number of Implicit Arnoldi update',
-+     &               ' iterations taken is ', iparam(3)
-+            print *, ' The number of OP*x is ', iparam(9)
-+            print *, ' The convergence criterion is ', tol
-+            print *, ' '
-+         end if
-+c
-+c        %----------------------------%
-+c        | Return eigvals and eigvecs |
-+c        %----------------------------%
-+c
-+         nconv =  iparam(5)
-+         n_eig_out = nconv
-+         if ( nconv .le. 0 ) then
-+            print *, ' '
-+            print *, ' ARPACK: Not a single mode converged.'
-+            print *, ' '
-+            go to 9000
-+         endif
-+c
-+         do 40 j=1, nconv
-+             eigvals(j) = d(j,1)
-+c
-+             do 30 i=1, n
-+                eigvecs((j-1)*n+i) = v(i,j)
-+ 30          continue
-+ 40      continue
-+c
-+      end if
-+c
-+c     %--------------------------------%
-+c     | Done with subroutine dsarpack. |
-+c     %--------------------------------%
-+c
-+      label = 0
-+      return
-+c
-+ 9000 continue !!! Error
-+c
-+      if( status_flag.eq.0 ) status_flag = ARPACK_ERROR
-+c
-+      label = status_flag
-+      return
-+c
-+      end
-+c 
-+c ------------------------------------------------------------------
-diff --git a/AmberTools/src/sqm/Makefile b/AmberTools/src/sqm/Makefile
-index a0fa790..5983764 100644
---- a/AmberTools/src/sqm/Makefile
-+++ b/AmberTools/src/sqm/Makefile
-@@ -82,7 +82,7 @@ QMOBJ = qm2_allocate_e_repul.o qm2_calc_charges.o qm2_calc_dipole.o \
- install: sqm$(SFX)
- 	mv sqm$(SFX) $(BINDIR)
- 
--sqm$(SFX): $(SQMOBJ) $(QMOBJ) netlib sys
-+sqm$(SFX): $(SQMOBJ) $(QMOBJ) sys
- 	$(FC) $(FPPFLAGS) $(FFLAGS) $(AMBERFFLAGS) -o sqm$(SFX) $(SQMOBJ) $(QMOBJ) \
- 		-L$(LIBDIR) $(FLIBSF) ../lib/sys.a $(LDFLAGS) $(AMBERLDFLAGS)
- 
-diff --git a/AmberTools/test/Makefile b/AmberTools/test/Makefile
-index 8252d52..24b9272 100644
---- a/AmberTools/test/Makefile
-+++ b/AmberTools/test/Makefile
-@@ -3,14 +3,14 @@ include ../src/config.h
- ######    Top-level targets, for general use:    ############################
- 
- test::
--	./test_at_serial.sh
-+	+./test_at_serial.sh
- 
- test.parallel::
- 	./test_at_parallel.sh
- 
- ######    Intermediate-level targets:    ############################
- 
--test.serial: clean is_amberhome_defined \
-+test.serial: is_amberhome_defined \
- 	test.nab test.cpptraj test.antechamber test.mdgx \
- 	test.leap test.resp test.pbsa test.gbnsr6 test.mmpbsa test.parmed \
- 	test.elsize test.sqm test.rism1d test.amberlite \
-diff --git a/AmberTools/test/test_at_serial.sh b/AmberTools/test/test_at_serial.sh
-index a154c84..c092eb6 100755
---- a/AmberTools/test/test_at_serial.sh
-+++ b/AmberTools/test/test_at_serial.sh
-@@ -44,3 +44,9 @@ fi
- 
- # save summary for later reporting:
- tail -5 ${logfile} > ${logdir}/at_summary
-+
-+if [ "${questionable_count}" -ne 0 -o "${error_count}" -ne 0 ]
-+then
-+  # Tests failed
-+  exit 1
-+fi
-diff --git a/AmberTools/test/test_check.sh b/AmberTools/test/test_check.sh
-index 108c446..62c0b88 100644
---- a/AmberTools/test/test_check.sh
-+++ b/AmberTools/test/test_check.sh
-@@ -63,7 +63,7 @@ check_environment() {
-    # We are done here for Macs
-    test $is_mac = "yes" && return
- 
--   python << EOF
-+   python2 << EOF
- import os
- import sys
- ambhome = os.getenv('AMBERHOME')
diff --git a/sci-chemistry/ambertools/files/ambertools-15-update.1.patch b/sci-chemistry/ambertools/files/ambertools-15-update.1.patch
deleted file mode 100644
index 28d25e590..000000000
--- a/sci-chemistry/ambertools/files/ambertools-15-update.1.patch
+++ /dev/null
@@ -1,118 +0,0 @@
-*******> update.1
-
-Author: Jason Swails
-
-Date: June 1, 2015
-
-Programs: MMPBSA.py, ParmEd, cpptraj
-
-Description: This fixes a number of small issues:
-             1) Fix Python 2.4 and Python 2.5 support for ParmEd and MMPBSA.py
-             2) Fix the MMPBSA.py Python API
-             3) Scale charges correctly for LIE action in cpptraj with non-unity
-                dielectric constant
-
---------------------------------------------------------------------------------
-
- AmberTools/src/cpptraj/src/Action_LIE.cpp              |  2 +-
- AmberTools/src/mmpbsa_py/MMPBSA_mods/API.py            |  3 ++-
- AmberTools/src/mmpbsa_py/MMPBSA_mods/infofile.py       |  1 +
- AmberTools/src/parmed/chemistry/__init__.py            |  6 +++++-
- .../test/mmpbsa_py/07_Comprehensive/Run.comprehensive  | 18 ++++++++++++++++++
- 5 files changed, 27 insertions(+), 3 deletions(-)
-
-diff --git AmberTools/src/cpptraj/src/Action_LIE.cpp AmberTools/src/cpptraj/src/Action_LIE.cpp
-index 25825c1..716a04f 100644
---- AmberTools/src/cpptraj/src/Action_LIE.cpp
-+++ AmberTools/src/cpptraj/src/Action_LIE.cpp
-@@ -132,7 +132,7 @@ int Action_LIE::SetupParms(Topology const& ParmIn) {
-   atom_charge_.reserve( ParmIn.Natom() );
-   for (Topology::atom_iterator atom = ParmIn.begin();
-                                atom != ParmIn.end(); ++atom)
--    atom_charge_.push_back( atom->Charge() * Constants::ELECTOAMBER / dielc_ );
-+    atom_charge_.push_back( atom->Charge() * Constants::ELECTOAMBER / sqrt(dielc_) );
-   return 0;
- }
- 
-diff --git AmberTools/src/mmpbsa_py/MMPBSA_mods/API.py AmberTools/src/mmpbsa_py/MMPBSA_mods/API.py
-index e6c4fe9..d7cc7ec 100644
---- AmberTools/src/mmpbsa_py/MMPBSA_mods/API.py
-+++ AmberTools/src/mmpbsa_py/MMPBSA_mods/API.py
-@@ -63,7 +63,7 @@ class mmpbsa_data(dict):
-       self.stability = app.stability
-       # Now load the data
-       for key in app.calc_types:
--         if key == 'mutant':
-+         if key == 'mutant' or key =='qh':
-             has_mutant = True
-             continue
-          self[key] = {}
-@@ -86,6 +86,7 @@ class mmpbsa_data(dict):
-       if has_mutant:
-          self.mutant = {}
-          for key in app.calc_types['mutant']:
-+            if key == 'qh': continue
-             self.mutant[key] = {}
-             tmpdict = {}
-             for dkey in app.calc_types['mutant'][key]['complex'].data:
-diff --git AmberTools/src/mmpbsa_py/MMPBSA_mods/infofile.py AmberTools/src/mmpbsa_py/MMPBSA_mods/infofile.py
-index ecdc2f2..ecaa6c1 100644
---- AmberTools/src/mmpbsa_py/MMPBSA_mods/infofile.py
-+++ AmberTools/src/mmpbsa_py/MMPBSA_mods/infofile.py
-@@ -80,6 +80,7 @@ class InfoFile(object):
-       outfile.write('numframes = %d\n' % self.app.numframes)
-       outfile.write('numframes_nmode = %d\n' % self.app.numframes_nmode)
-       outfile.write("mut_str = '%s'\n" % self.app.mut_str)
-+      outfile.write('using_chamber = %s\n' % self.app.using_chamber)
-       outfile.write(self.app.input_file_text)
- 
-    def read_info(self, name=None):
-diff --git AmberTools/src/parmed/chemistry/__init__.py AmberTools/src/parmed/chemistry/__init__.py
-index 52f5245..544e016 100644
---- AmberTools/src/parmed/chemistry/__init__.py
-+++ AmberTools/src/parmed/chemistry/__init__.py
-@@ -11,10 +11,14 @@ from chemistry.structure import Structure
- from chemistry.topologyobjects import *
- from chemistry import unit
- from chemistry.residue import *
--from chemistry import amber, charmm, tinker, openmm
-+from chemistry import amber, charmm, tinker
- from chemistry import formats
- load_file = formats.load_file
- read_PDB = formats.PDBFile.parse
- read_CIF = formats.CIFFile.parse
- write_PDB = formats.PDBFile.write
- write_CIF = formats.CIFFile.write
-+try:
-+    from chemistry import openmm
-+except ImportError:
-+    pass
-diff --git AmberTools/test/mmpbsa_py/07_Comprehensive/Run.comprehensive AmberTools/test/mmpbsa_py/07_Comprehensive/Run.comprehensive
-index 268515e..aa7d9df 100755
---- AmberTools/test/mmpbsa_py/07_Comprehensive/Run.comprehensive
-+++ AmberTools/test/mmpbsa_py/07_Comprehensive/Run.comprehensive
-@@ -108,6 +108,24 @@ if [ -z "$DO_PARALLEL" ]; then
-    ../../dacdif -a 6.0 FINAL_RESULTS_MMPBSA_2.dat.save FINAL_RESULTS_MMPBSA_2.dat
- fi
- 
-+# Check the API
-+python << EOF
-+from __future__ import division
-+import MMPBSA_mods.API as API
-+
-+print('Checking the API')
-+try:
-+    stuff = API.load_mmpbsa_info('_MMPBSA_info')
-+    total_data = stuff['gb']['complex']['TOTAL']
-+    if abs((sum(total_data) / len(total_data)) + 466.7565) > 0.0002:
-+        print('possible FAILURE')
-+    else:
-+        print('PASSED')
-+except:
-+    print('Program error')
-+print('==============================================================')
-+EOF
-+
- $EXE --clean 2>&1 > /dev/null
- 
- rm -f mmpbsa.in mmpbsa.out FINAL_DECOMP_MMPBSA_2.csv-e FINAL_DECOMP_MMPBSA.dat
diff --git a/sci-chemistry/ambertools/files/ambertools-15-update.2.patch b/sci-chemistry/ambertools/files/ambertools-15-update.2.patch
deleted file mode 100644
index b0f1cd978..000000000
--- a/sci-chemistry/ambertools/files/ambertools-15-update.2.patch
+++ /dev/null
@@ -1,56 +0,0 @@
-*******> update.2
-
-Author: Jason Swails, Ross Walker
-
-Date: June 2, 2015
-
-Programs: AmberTools, CUDA
-
-Description: Adds support for CUDA 7. Also fixes an erroneous error report when
-             AmberTools is configured for *only* OpenMP, CUDA, or CUDA-MPI with
-             regards to missing Python modules.
-
---------------------------------------------------------------------------------
-
- AmberTools/src/configure2     | 4 ++--
- AmberTools/test/test_check.sh | 7 ++++---
- 2 files changed, 6 insertions(+), 5 deletions(-)
-
-diff --git AmberTools/src/configure2 AmberTools/src/configure2
-index f1a3cff..9a504b1 100755
---- AmberTools/src/configure2
-+++ AmberTools/src/configure2
-@@ -861,13 +861,13 @@ if [ "$cuda_SPFP" = 'yes' -o "$cuda_SPXP" = 'yes' -o "$cuda_DPFP" = 'yes' ]; the
-       echo "CUDA Version $cudaversion detected"
-       echo "Configuring for SM2.0 and SM3.0 - warning does not support Maxwell (GM200/GM204) cards [e.g. GTX970/980]"
-       nvccflags="$sm20flags $sm30flags"
--    elif [ "$cudaversion" = "6.5" ]; then
-+    elif [ "$cudaversion" = "6.5" -o  "$cudaversion" = "7.0" ]; then
-       echo "CUDA Version $cudaversion detected"
-       echo "Configuring for SM2.0, SM3.0 and SM5.0"
-       nvccflags="$sm20flags $sm30flags $sm50flags"
-     else
-       echo "Error: Unsupported CUDA version $cudaversion detected."
--      echo "       AMBER requires CUDA version == 5.0 .or. 5.5 .or. 6.0 .or. 6.5"
-+      echo "       AMBER requires CUDA version == 5.0 .or. 5.5 .or. 6.0 .or. 6.5 .or. 7.0"
-       exit 1
-     fi
-     nvcc="$nvcc $nvccflags"
-diff --git AmberTools/test/test_check.sh AmberTools/test/test_check.sh
-index 108c446..a5399d8 100644
---- AmberTools/test/test_check.sh
-+++ AmberTools/test/test_check.sh
-@@ -83,9 +83,10 @@ def error():
- try:
-     import chemistry
- except ImportError:
--    sys.stderr.write('Could not import Amber Python modules. This likely means\\n'
--        'that your Amber Python environment was not set up correctly\\n\\n')
--    error()
-+    if os.path.exists(os.path.join(ambhome, 'parmed.py')):
-+        sys.stderr.write('Could not import Amber Python modules. This likely means\\n'
-+            'that your Amber Python environment was not set up correctly\\n\\n')
-+        error()
- 
- if 'darwin' in sys.platform:
-     sys.exit(0) # Nothing to check here
diff --git a/sci-chemistry/ambertools/files/ambertools-15-update.3.patch b/sci-chemistry/ambertools/files/ambertools-15-update.3.patch
deleted file mode 100644
index a892ecefd..000000000
--- a/sci-chemistry/ambertools/files/ambertools-15-update.3.patch
+++ /dev/null
@@ -1,95 +0,0 @@
-********> update.3
-  Author: Istvan Kolossvary
-  Date:   15 June 2015
-
-  Programs: nab, sff
-
-  Description: Fix problem with lmod docking when fixed atoms are present
-
-  ---------------------------------------------------------------------------
-
-diff --git AmberTools/src/sff/lmodC.c AmberTools/src/sff/lmodC.c
-index 8a19dd8..45c8244 100644
---- AmberTools/src/sff/lmodC.c
-+++ AmberTools/src/sff/lmodC.c
-@@ -864,7 +864,7 @@ trans_ligand(double *xyz, int start, int end, double dx, double dy,
-              double dz)
- {
-    int i, x, y, z;
--   for (i = start - 1; i < end; i++) {
-+   for (i = start; i <= end; i++) {
-       x = 3 * i;
-       y = x + 1;
-       z = y + 1;
-@@ -900,7 +900,7 @@ rot_ligand(double *xyz, int start, int end, double cent_x, double cent_y,
- {
-    int i, x, y, z;
-    double temp_x, temp_y, temp_z;
--   for (i = start - 1; i < end; i++) {
-+   for (i = start; i <= end; i++) {
-       x = 3 * i;
-       y = x + 1;
-       z = y + 1;
-@@ -930,7 +930,7 @@ calc_centroid(double *xyz, int start, int end, double *cent_x,
- {
-    int i, x, y, z, n;
-    *cent_x = *cent_y = *cent_z = ZERO;
--   for (i = start - 1; i < end; i++) {
-+   for (i = start; i <= end; i++) {
-       x = 3 * i;
-       y = x + 1;
-       z = y + 1;
-@@ -1591,6 +1591,7 @@ lmodC(int *nlmodit, int *nmod, int *kmod, int *rotran, int *natm_ext,
-        i, j, k, kk, l, n, cnt;
-    static int barrier_crossing_test_on, do_all, do_ligs;
-    static int *index = NULL;
-+   static int ikk, lig_start_kk, lig_end_kk, lig_rot_cent_kk;
-    static double ref_energy, energy, energy_old, min_energy,
-        glob_min_energy, rad, sum, max_atmov, scale, lmod_step, rms,
-        rms_old, grad_rms;
-@@ -2554,7 +2555,19 @@ lmodC(int *nlmodit, int *nmod, int *kmod, int *rotran, int *natm_ext,
-                xtrans *= trscale / trnorm;
-                ytrans *= trscale / trnorm;
-                ztrans *= trscale / trnorm;
--               trans_ligand(xyz_local, lig_start[kk], lig_end[kk], xtrans,
-+               for (ikk = 0; ikk < natm_local; ikk++ ) {
-+                 if ( atm_indx[ikk] == (lig_start[kk] -1) ) {  /* lig_start[] contains external PDB atom numbers */
-+                   lig_start_kk = ikk;
-+                   break;
-+                 }
-+               }
-+               for (ikk = 0; ikk < natm_local; ikk++ ) {
-+                 if ( atm_indx[ikk] == (lig_end[kk] -1) ) {  /* lig_end[] contains external PDB atom numbers */
-+                   lig_end_kk = ikk;
-+                   break;
-+                 }
-+               }
-+               trans_ligand(xyz_local, lig_start_kk, lig_end_kk, xtrans,
-                             ytrans, ztrans);
-                do {
-                   xrot = 2 * rand2() - 1;
-@@ -2568,13 +2581,19 @@ lmodC(int *nlmodit, int *nmod, int *kmod, int *rotran, int *natm_ext,
-                rotang = angmin[kk] + (angmax[kk] - angmin[kk]) * rand2();
-                calc_rot_matrix(DEG2RAD * rotang, xrot, yrot, zrot, rotmat);
-                if (lig_rot_cent[kk]) {
--                  xcent = xyz_local[(lig_rot_cent[kk] - 1) * 3    ];
--                  ycent = xyz_local[(lig_rot_cent[kk] - 1) * 3 + 1];
--                  zcent = xyz_local[(lig_rot_cent[kk] - 1) * 3 + 2];
-+                 for (ikk = 0; ikk < natm_local; ikk++ ) {
-+                   if ( atm_indx[ikk] == (lig_rot_cent[kk] -1)   ) {  /* lig_rot_cent[] contains external PDB atom numbers */
-+                     lig_rot_cent_kk = ikk;
-+                     break;
-+                   }
-+                 }
-+                 xcent = xyz_local[ lig_rot_cent_kk * 3    ];
-+                 ycent = xyz_local[ lig_rot_cent_kk * 3 + 1];
-+                 zcent = xyz_local[ lig_rot_cent_kk * 3 + 2];
-                } else
--                  calc_centroid(xyz_local, lig_start[kk], lig_end[kk],
-+                  calc_centroid(xyz_local, lig_start_kk, lig_end_kk,
-                                 &xcent, &ycent, &zcent);
--               rot_ligand(xyz_local, lig_start[kk], lig_end[kk], xcent,
-+               rot_ligand(xyz_local, lig_start_kk, lig_end_kk, xcent,
-                           ycent, zcent, rotmat);
-             }
-             /* close pair separation operates on xyz_ext[]: */
diff --git a/sci-chemistry/ambertools/files/ambertools-15-update.4.patch b/sci-chemistry/ambertools/files/ambertools-15-update.4.patch
deleted file mode 100644
index 4176a583a..000000000
--- a/sci-chemistry/ambertools/files/ambertools-15-update.4.patch
+++ /dev/null
@@ -1,908 +0,0 @@
-*******> update.4
-Author: Benjamin D. Madej
-Date: October 19, 2015
-Programs: Leap, Lipid14 force field
-Description: Adds a parameter set for cholesterol to the Lipid14 force field.
-             Please reference:
-             Madej, B. D.; Gould, I.R.; Walker, R. C. A Parameterization of
-             Cholesterol for Mixed Lipid Bilayer Simulation within the Amber
-             Lipid14 Force Field. J. Phys. Chem. B 2015, 119 (38)
-             pp 12424-12435.
--------------------------------------------------------------------------------
- dat/leap/lib/lipid14.lib  | 480 ++++++++++++++++++++++++++++++++++++++++++++++
- dat/leap/parm/lipid11.dat |   2 +-
- dat/leap/parm/lipid14.dat | 291 ++++++++++++++++++----------
- 3 files changed, 666 insertions(+), 107 deletions(-)
-
-diff --git dat/leap/lib/lipid14.lib dat/leap/lib/lipid14.lib
-index 891937b..75c2f2b 100644
---- dat/leap/lib/lipid14.lib
-+++ dat/leap/lib/lipid14.lib
-@@ -1,10 +1,490 @@
- !!index array str
-+ "CHL"
-  "LA"
-  "MY"
-  "OL"
-  "PA"
-  "PC"
-  "PE"
-+!entry.CHL.unit.atoms table  str name  str type  int typex  int resx  int flags  int seq  int elmnt  dbl chg
-+ "C1" "cA" 0 1 131073 1 6 -0.031691
-+ "H11" "hA" 0 1 131073 2 1 0.009380
-+ "H12" "hA" 0 1 131073 3 1 0.009380
-+ "C2" "cA" 0 1 131073 4 6 -0.088130
-+ "H21" "hA" 0 1 131073 5 1 0.044625
-+ "H22" "hA" 0 1 131073 6 1 0.044625
-+ "C3" "cA" 0 1 131073 7 6 0.293553
-+ "H31" "hE" 0 1 131073 8 1 0.029611
-+ "C4" "cA" 0 1 131073 9 6 -0.162218
-+ "H41" "hA" 0 1 131073 10 1 0.090036
-+ "H42" "hA" 0 1 131073 11 1 0.090036
-+ "C5" "cB" 0 1 131073 12 6 -0.139495
-+ "C6" "cB" 0 1 131073 13 6 -0.208190
-+ "H61" "hB" 0 1 131073 14 1 0.122828
-+ "C7" "cA" 0 1 131073 15 6 -0.069897
-+ "H71" "hA" 0 1 131073 16 1 0.047919
-+ "H72" "hA" 0 1 131073 17 1 0.047919
-+ "C8" "cA" 0 1 131073 18 6 -0.011390
-+ "H81" "hA" 0 1 131073 19 1 0.072891
-+ "C9" "cA" 0 1 131073 20 6 0.019609
-+ "H91" "hA" 0 1 131073 21 1 0.029289
-+ "C10" "cA" 0 1 131073 22 6 0.079112
-+ "C11" "cA" 0 1 131073 23 6 -0.066365
-+ "H111" "hA" 0 1 131073 24 1 0.030085
-+ "H112" "hA" 0 1 131073 25 1 0.030085
-+ "C12" "cA" 0 1 131073 26 6 -0.064973
-+ "H121" "hA" 0 1 131073 27 1 0.010352
-+ "H122" "hA" 0 1 131073 28 1 0.010352
-+ "C13" "cA" 0 1 131073 29 6 0.057407
-+ "C14" "cA" 0 1 131073 30 6 0.005830
-+ "H141" "hA" 0 1 131073 31 1 0.031557
-+ "C15" "cA" 0 1 131073 32 6 -0.101977
-+ "H151" "hA" 0 1 131073 33 1 0.026458
-+ "H152" "hA" 0 1 131073 34 1 0.026458
-+ "C16" "cA" 0 1 131073 35 6 -0.092064
-+ "H161" "hA" 0 1 131073 36 1 0.033335
-+ "H162" "hA" 0 1 131073 37 1 0.033335
-+ "C17" "cA" 0 1 131073 38 6 0.032398
-+ "H171" "hA" 0 1 131073 39 1 0.016590
-+ "C18" "cA" 0 1 131073 40 6 -0.115049
-+ "H181" "hA" 0 1 131073 41 1 0.024541
-+ "H182" "hA" 0 1 131073 42 1 0.024541
-+ "H183" "hA" 0 1 131073 43 1 0.024541
-+ "C19" "cA" 0 1 131073 44 6 -0.108064
-+ "H191" "hA" 0 1 131073 45 1 0.033990
-+ "H192" "hA" 0 1 131073 46 1 0.033990
-+ "H193" "hA" 0 1 131073 47 1 0.033990
-+ "C20" "cD" 0 1 131075 48 6 0.044268
-+ "H201" "hL" 0 1 131075 49 1 0.020951
-+ "C21" "cD" 0 1 131075 50 6 -0.154621
-+ "H211" "hL" 0 1 131075 51 1 0.036274
-+ "H212" "hL" 0 1 131075 52 1 0.036274
-+ "H213" "hL" 0 1 131075 53 1 0.036274
-+ "C22" "cD" 0 1 131075 54 6 -0.039033
-+ "H221" "hL" 0 1 131075 55 1 0.008359
-+ "H222" "hL" 0 1 131075 56 1 0.008359
-+ "C23" "cD" 0 1 131075 57 6 -0.028460
-+ "H231" "hL" 0 1 131075 58 1 0.015742
-+ "H232" "hL" 0 1 131075 59 1 0.015742
-+ "C24" "cD" 0 1 131075 60 6 -0.125596
-+ "H241" "hL" 0 1 131075 61 1 0.040110
-+ "H242" "hL" 0 1 131075 62 1 0.040110
-+ "C25" "cD" 0 1 131075 63 6 0.212446
-+ "H251" "hL" 0 1 131075 64 1 -0.002466
-+ "C26" "cD" 0 1 131075 65 6 -0.257776
-+ "H261" "hL" 0 1 131075 66 1 0.057982
-+ "H262" "hL" 0 1 131075 67 1 0.057982
-+ "H263" "hL" 0 1 131075 68 1 0.057982
-+ "C27" "cD" 0 1 131075 69 6 -0.257776
-+ "H271" "hL" 0 1 131075 70 1 0.057982
-+ "H272" "hL" 0 1 131075 71 1 0.057982
-+ "H273" "hL" 0 1 131075 72 1 0.057982
-+ "O1" "oH" 0 1 131073 73 8 -0.703022
-+ "HO1" "hO" 0 1 131073 74 1 0.414804
-+!entry.CHL.unit.atomspertinfo table  str pname  str ptype  int ptypex  int pelmnt  dbl pchg
-+ "C1" "cA" 0 -1 0.0
-+ "H11" "hA" 0 -1 0.0
-+ "H12" "hA" 0 -1 0.0
-+ "C2" "cA" 0 -1 0.0
-+ "H21" "hA" 0 -1 0.0
-+ "H22" "hA" 0 -1 0.0
-+ "C3" "cA" 0 -1 0.0
-+ "H31" "hE" 0 -1 0.0
-+ "C4" "cA" 0 -1 0.0
-+ "H41" "hA" 0 -1 0.0
-+ "H42" "hA" 0 -1 0.0
-+ "C5" "cB" 0 -1 0.0
-+ "C6" "cB" 0 -1 0.0
-+ "H61" "hB" 0 -1 0.0
-+ "C7" "cA" 0 -1 0.0
-+ "H71" "hA" 0 -1 0.0
-+ "H72" "hA" 0 -1 0.0
-+ "C8" "cA" 0 -1 0.0
-+ "H81" "hA" 0 -1 0.0
-+ "C9" "cA" 0 -1 0.0
-+ "H91" "hA" 0 -1 0.0
-+ "C10" "cA" 0 -1 0.0
-+ "C11" "cA" 0 -1 0.0
-+ "H111" "hA" 0 -1 0.0
-+ "H112" "hA" 0 -1 0.0
-+ "C12" "cA" 0 -1 0.0
-+ "H121" "hA" 0 -1 0.0
-+ "H122" "hA" 0 -1 0.0
-+ "C13" "cA" 0 -1 0.0
-+ "C14" "cA" 0 -1 0.0
-+ "H141" "hA" 0 -1 0.0
-+ "C15" "cA" 0 -1 0.0
-+ "H151" "hA" 0 -1 0.0
-+ "H152" "hA" 0 -1 0.0
-+ "C16" "cA" 0 -1 0.0
-+ "H161" "hA" 0 -1 0.0
-+ "H162" "hA" 0 -1 0.0
-+ "C17" "cA" 0 -1 0.0
-+ "H171" "hA" 0 -1 0.0
-+ "C18" "cA" 0 -1 0.0
-+ "H181" "hA" 0 -1 0.0
-+ "H182" "hA" 0 -1 0.0
-+ "H183" "hA" 0 -1 0.0
-+ "C19" "cA" 0 -1 0.0
-+ "H191" "hA" 0 -1 0.0
-+ "H192" "hA" 0 -1 0.0
-+ "H193" "hA" 0 -1 0.0
-+ "C20" "cA" 0 -1 0.0
-+ "H201" "hA" 0 -1 0.0
-+ "C21" "cA" 0 -1 0.0
-+ "H211" "hA" 0 -1 0.0
-+ "H212" "hA" 0 -1 0.0
-+ "H213" "hA" 0 -1 0.0
-+ "C22" "cA" 0 -1 0.0
-+ "H221" "hA" 0 -1 0.0
-+ "H222" "hA" 0 -1 0.0
-+ "C23" "cA" 0 -1 0.0
-+ "H231" "hA" 0 -1 0.0
-+ "H232" "hA" 0 -1 0.0
-+ "C24" "cA" 0 -1 0.0
-+ "H241" "hA" 0 -1 0.0
-+ "H242" "hA" 0 -1 0.0
-+ "C25" "cA" 0 -1 0.0
-+ "H251" "hA" 0 -1 0.0
-+ "C26" "cA" 0 -1 0.0
-+ "H261" "hA" 0 -1 0.0
-+ "H262" "hA" 0 -1 0.0
-+ "H263" "hA" 0 -1 0.0
-+ "C27" "cA" 0 -1 0.0
-+ "H271" "hA" 0 -1 0.0
-+ "H272" "hA" 0 -1 0.0
-+ "H273" "hA" 0 -1 0.0
-+ "O1" "oH" 0 -1 0.0
-+ "HO1" "hO" 0 -1 0.0
-+!entry.CHL.unit.boundbox array dbl
-+ -1.000000
-+ 0.0
-+ 0.0
-+ 0.0
-+ 0.0
-+!entry.CHL.unit.childsequence single int
-+ 2
-+!entry.CHL.unit.connect array int
-+ 0
-+ 0
-+!entry.CHL.unit.connectivity table  int atom1x  int atom2x  int flags
-+ 1 2 1
-+ 1 3 1
-+ 1 4 1
-+ 1 22 1
-+ 4 5 1
-+ 4 6 1
-+ 4 7 1
-+ 7 8 1
-+ 7 9 1
-+ 7 73 1
-+ 9 10 1
-+ 9 11 1
-+ 9 12 1
-+ 12 13 2
-+ 12 22 1
-+ 13 14 1
-+ 13 15 1
-+ 15 16 1
-+ 15 17 1
-+ 15 18 1
-+ 18 19 1
-+ 18 20 1
-+ 18 30 1
-+ 20 21 1
-+ 20 22 1
-+ 20 23 1
-+ 22 44 1
-+ 23 24 1
-+ 23 25 1
-+ 23 26 1
-+ 26 27 1
-+ 26 28 1
-+ 26 29 1
-+ 29 30 1
-+ 29 38 1
-+ 29 40 1
-+ 30 31 1
-+ 30 32 1
-+ 32 33 1
-+ 32 34 1
-+ 32 35 1
-+ 35 36 1
-+ 35 37 1
-+ 35 38 1
-+ 38 39 1
-+ 38 48 1
-+ 40 41 1
-+ 40 42 1
-+ 40 43 1
-+ 44 45 1
-+ 44 46 1
-+ 44 47 1
-+ 48 49 1
-+ 48 50 1
-+ 48 54 1
-+ 50 51 1
-+ 50 52 1
-+ 50 53 1
-+ 54 55 1
-+ 54 56 1
-+ 54 57 1
-+ 57 58 1
-+ 57 59 1
-+ 57 60 1
-+ 60 61 1
-+ 60 62 1
-+ 60 63 1
-+ 63 64 1
-+ 63 65 1
-+ 63 69 1
-+ 65 66 1
-+ 65 67 1
-+ 65 68 1
-+ 69 70 1
-+ 69 71 1
-+ 69 72 1
-+ 73 74 1
-+!entry.CHL.unit.hierarchy table  str abovetype  int abovex  str belowtype  int belowx
-+ "U" 0 "R" 1
-+ "R" 1 "A" 1
-+ "R" 1 "A" 2
-+ "R" 1 "A" 3
-+ "R" 1 "A" 4
-+ "R" 1 "A" 5
-+ "R" 1 "A" 6
-+ "R" 1 "A" 7
-+ "R" 1 "A" 8
-+ "R" 1 "A" 9
-+ "R" 1 "A" 10
-+ "R" 1 "A" 11
-+ "R" 1 "A" 12
-+ "R" 1 "A" 13
-+ "R" 1 "A" 14
-+ "R" 1 "A" 15
-+ "R" 1 "A" 16
-+ "R" 1 "A" 17
-+ "R" 1 "A" 18
-+ "R" 1 "A" 19
-+ "R" 1 "A" 20
-+ "R" 1 "A" 21
-+ "R" 1 "A" 22
-+ "R" 1 "A" 23
-+ "R" 1 "A" 24
-+ "R" 1 "A" 25
-+ "R" 1 "A" 26
-+ "R" 1 "A" 27
-+ "R" 1 "A" 28
-+ "R" 1 "A" 29
-+ "R" 1 "A" 30
-+ "R" 1 "A" 31
-+ "R" 1 "A" 32
-+ "R" 1 "A" 33
-+ "R" 1 "A" 34
-+ "R" 1 "A" 35
-+ "R" 1 "A" 36
-+ "R" 1 "A" 37
-+ "R" 1 "A" 38
-+ "R" 1 "A" 39
-+ "R" 1 "A" 40
-+ "R" 1 "A" 41
-+ "R" 1 "A" 42
-+ "R" 1 "A" 43
-+ "R" 1 "A" 44
-+ "R" 1 "A" 45
-+ "R" 1 "A" 46
-+ "R" 1 "A" 47
-+ "R" 1 "A" 48
-+ "R" 1 "A" 49
-+ "R" 1 "A" 50
-+ "R" 1 "A" 51
-+ "R" 1 "A" 52
-+ "R" 1 "A" 53
-+ "R" 1 "A" 54
-+ "R" 1 "A" 55
-+ "R" 1 "A" 56
-+ "R" 1 "A" 57
-+ "R" 1 "A" 58
-+ "R" 1 "A" 59
-+ "R" 1 "A" 60
-+ "R" 1 "A" 61
-+ "R" 1 "A" 62
-+ "R" 1 "A" 63
-+ "R" 1 "A" 64
-+ "R" 1 "A" 65
-+ "R" 1 "A" 66
-+ "R" 1 "A" 67
-+ "R" 1 "A" 68
-+ "R" 1 "A" 69
-+ "R" 1 "A" 70
-+ "R" 1 "A" 71
-+ "R" 1 "A" 72
-+ "R" 1 "A" 73
-+ "R" 1 "A" 74
-+!entry.CHL.unit.name single str
-+ "CHL"
-+!entry.CHL.unit.positions table  dbl x  dbl y  dbl z
-+ 4.697000 -1.469000 -0.739000
-+ 4.428000 -1.214000 -1.762000
-+ 4.303000 -2.462000 -0.556000
-+ 6.224000 -1.517000 -0.642000
-+ 6.547000 -1.874000 0.331000
-+ 6.617000 -2.214000 -1.376000
-+ 6.830000 -0.145000 -0.877000
-+ 6.590000 0.176000 -1.891000
-+ 6.246000 0.863000 0.111000
-+ 6.601000 0.589000 1.102000
-+ 6.636000 1.856000 -0.095000
-+ 4.731000 0.895000 0.070000
-+ 4.091000 2.041000 -0.088000
-+ 4.668000 2.946000 -0.204000
-+ 2.599000 2.206000 -0.119000
-+ 2.323000 3.070000 0.480000
-+ 2.290000 2.443000 -1.137000
-+ 1.853000 0.964000 0.375000
-+ 1.922000 0.946000 1.460000
-+ 2.514000 -0.306000 -0.204000
-+ 2.518000 -0.165000 -1.285000
-+ 4.012000 -0.452000 0.214000
-+ 1.671000 -1.566000 0.076000
-+ 2.085000 -2.410000 -0.467000
-+ 1.730000 -1.829000 1.125000
-+ 0.190000 -1.429000 -0.312000
-+ 0.108000 -1.322000 -1.392000
-+ -0.312000 -2.355000 -0.056000
-+ -0.469000 -0.212000 0.358000
-+ 0.381000 1.015000 -0.041000
-+ 0.381000 1.020000 -1.132000
-+ -0.462000 2.215000 0.391000
-+ -0.304000 2.443000 1.442000
-+ -0.217000 3.115000 -0.163000
-+ -1.913000 1.751000 0.131000
-+ -2.537000 1.930000 1.001000
-+ -2.357000 2.309000 -0.684000
-+ -1.859000 0.228000 -0.203000
-+ -1.794000 0.127000 -1.286000
-+ -0.546000 -0.407000 1.886000
-+ -1.062000 0.412000 2.374000
-+ 0.431000 -0.485000 2.344000
-+ -1.086000 -1.316000 2.130000
-+ 4.156000 -0.937000 1.675000
-+ 3.579000 -0.319000 2.354000
-+ 5.185000 -0.898000 2.008000
-+ 3.826000 -1.963000 1.788000
-+ -3.141000 -0.519000 0.237000
-+ -3.267000 -0.372000 1.309000
-+ -3.080000 -2.029000 -0.029000
-+ -2.330000 -2.520000 0.577000
-+ -2.851000 -2.232000 -1.072000
-+ -4.025000 -2.508000 0.198000
-+ -4.375000 0.093000 -0.461000
-+ -4.324000 1.175000 -0.403000
-+ -4.337000 -0.153000 -1.522000
-+ -5.732000 -0.335000 0.111000
-+ -5.862000 -1.406000 0.010000
-+ -5.752000 -0.121000 1.179000
-+ -6.898000 0.389000 -0.569000
-+ -6.718000 1.461000 -0.516000
-+ -6.910000 0.137000 -1.629000
-+ -8.286000 0.104000 0.028000
-+ -8.244000 0.333000 1.092000
-+ -8.705000 -1.362000 -0.122000
-+ -8.034000 -2.035000 0.400000
-+ -8.723000 -1.655000 -1.169000
-+ -9.702000 -1.521000 0.280000
-+ -9.336000 1.023000 -0.605000
-+ -9.079000 2.069000 -0.470000
-+ -10.316000 0.862000 -0.166000
-+ -9.420000 0.839000 -1.674000
-+ 8.224000 -0.262000 -0.734000
-+ 8.633000 0.570000 -0.924000
-+!entry.CHL.unit.residueconnect table  int c1x  int c2x  int c3x  int c4x  int c5x  int c6x
-+ 0 0 0 0 0 0
-+!entry.CHL.unit.residues table  str name  int seq  int childseq  int startatomx  str restype  int imagingx
-+ "CHL" 1 75 1 "?" 0
-+!entry.CHL.unit.residuesPdbSequenceNumber array int
-+ 0
-+!entry.CHL.unit.solventcap array dbl
-+ -1.000000
-+ 0.0
-+ 0.0
-+ 0.0
-+ 0.0
-+!entry.CHL.unit.velocities table  dbl x  dbl y  dbl z
-+ 0.0 0.0 0.0
-+ 0.0 0.0 0.0
-+ 0.0 0.0 0.0
-+ 0.0 0.0 0.0
-+ 0.0 0.0 0.0
-+ 0.0 0.0 0.0
-+ 0.0 0.0 0.0
-+ 0.0 0.0 0.0
-+ 0.0 0.0 0.0
-+ 0.0 0.0 0.0
-+ 0.0 0.0 0.0
-+ 0.0 0.0 0.0
-+ 0.0 0.0 0.0
-+ 0.0 0.0 0.0
-+ 0.0 0.0 0.0
-+ 0.0 0.0 0.0
-+ 0.0 0.0 0.0
-+ 0.0 0.0 0.0
-+ 0.0 0.0 0.0
-+ 0.0 0.0 0.0
-+ 0.0 0.0 0.0
-+ 0.0 0.0 0.0
-+ 0.0 0.0 0.0
-+ 0.0 0.0 0.0
-+ 0.0 0.0 0.0
-+ 0.0 0.0 0.0
-+ 0.0 0.0 0.0
-+ 0.0 0.0 0.0
-+ 0.0 0.0 0.0
-+ 0.0 0.0 0.0
-+ 0.0 0.0 0.0
-+ 0.0 0.0 0.0
-+ 0.0 0.0 0.0
-+ 0.0 0.0 0.0
-+ 0.0 0.0 0.0
-+ 0.0 0.0 0.0
-+ 0.0 0.0 0.0
-+ 0.0 0.0 0.0
-+ 0.0 0.0 0.0
-+ 0.0 0.0 0.0
-+ 0.0 0.0 0.0
-+ 0.0 0.0 0.0
-+ 0.0 0.0 0.0
-+ 0.0 0.0 0.0
-+ 0.0 0.0 0.0
-+ 0.0 0.0 0.0
-+ 0.0 0.0 0.0
-+ 0.0 0.0 0.0
-+ 0.0 0.0 0.0
-+ 0.0 0.0 0.0
-+ 0.0 0.0 0.0
-+ 0.0 0.0 0.0
-+ 0.0 0.0 0.0
-+ 0.0 0.0 0.0
-+ 0.0 0.0 0.0
-+ 0.0 0.0 0.0
-+ 0.0 0.0 0.0
-+ 0.0 0.0 0.0
-+ 0.0 0.0 0.0
-+ 0.0 0.0 0.0
-+ 0.0 0.0 0.0
-+ 0.0 0.0 0.0
-+ 0.0 0.0 0.0
-+ 0.0 0.0 0.0
-+ 0.0 0.0 0.0
-+ 0.0 0.0 0.0
-+ 0.0 0.0 0.0
-+ 0.0 0.0 0.0
-+ 0.0 0.0 0.0
-+ 0.0 0.0 0.0
-+ 0.0 0.0 0.0
-+ 0.0 0.0 0.0
-+ 0.0 0.0 0.0
-+ 0.0 0.0 0.0
- !entry.LA.unit.atoms table  str name  str type  int typex  int resx  int flags  int seq  int elmnt  dbl chg
-  "H12T" "hL" 0 1 131073 1 1 0.025809
-  "C112" "cD" 0 1 131073 2 6 -0.118534
-diff --git dat/leap/parm/lipid11.dat dat/leap/parm/lipid11.dat
-index 0f8d83e..9c25f35 100644
---- dat/leap/parm/lipid11.dat
-+++ dat/leap/parm/lipid11.dat
-@@ -1,4 +1,4 @@
--AMBER Lipid 2011 Force Field (v1.0), A.Skjevik, B. Madej, K.Teigen & R.C.Walker
-+** Warning: Lipid11 is deprecated. Please refer to Amber Lipid14 for more information ** AMBER Lipid 2011 Force Field (v1.0), A.Skjevik, B. Madej, K.Teigen & R.C.Walker
- cC 12.01                             carbonyl sp2 carbon (GAFF c -)
- cB 12.01                             aliphatic sp2 carbon (GAFF c2-)  
- cA 12.01                             sp3 carbon (GAFF c3-)
-diff --git dat/leap/parm/lipid14.dat dat/leap/parm/lipid14.dat
-index 46da737..f102976 100644
---- dat/leap/parm/lipid14.dat
-+++ dat/leap/parm/lipid14.dat
-@@ -3,59 +3,81 @@ cA 12.01                             sp3 carbon (GAFF c3-head,glycerol)
- cB 12.01                             aliphatic sp2 carbon (GAFF c2-tail)  
- cC 12.01                             carbonyl sp2 carbon (GAFF c -head,glycerol)
- cD 12.010                            sp3 carbon (GAFFlipid a3-tail)
-+hA 1.008                             H bonded to aliphatic carbon without electrwd. group (GAFF hc-)
-+hB 1.008                             H bonded to aromatic carbon (GAFF ha-)
-+hE 1.008                             H bonded to aliphatic carbon with 1 electrwd. group (GAFF h1-)
-+hL 1.008                             H bonded to aliphatic carbon without electrwd. group (GAFFlipid hl-)
-+hN 1.008                             H bonded to nitrogen (GAFF hn-)
-+hO 1.008                             H in Hydroxyl group (GAFF ho-)
-+hX 1.008                             H bonded to C next to positively charged group (GAFF hx-)
-+nA 14.01                             sp3 N with four connected atoms (GAFF n4-)
- oC 16.00                             sp2 oxygen with one connected atom (e.g C=O, COO-) (GAFF o -)
--oS 16.00                             sp3 oxygen in ethers and esters (GAFF os-)
-+oH 16.00                             sp3 oxygen in hydroxyl group (GAFF oh-)
- oP 16.00                             sp2 oxygen with one connected atom (e.g P-O) in phosphate group (GAFF o -)
-+oS 16.00                             sp3 oxygen in ethers and esters (GAFF os-)
- oT 16.00                             sp3 oxygen bonded to carbon in phosphate group (GAFF os-)
--nA 14.01                             sp3 N with four connected atoms (GAFF n4-)
- pA 30.97                             phosphorus with four connected atoms, such as O=P(OH)3 (GAFF p5-)
--hE 1.008                             H bonded to aliphatic carbon with 1 electrwd. group (GAFF h1-)
--hX 1.008                             H bonded to C next to positively charged group (GAFF hx-)
--hB 1.008                             H bonded to aromatic carbon (GAFF ha-)
--hN 1.008                             H bonded to nitrogen (GAFF hn-)
--hL 1.008                             H bonded to aliphatic carbon without electrwd. group (GAFFlipid hl-)
- 
- cA cB cC cD oC oS oP oT nA pA hE hX hB hN hL
- cA-cA  303.1    1.5350       Lipid11  v1.0 (GAFF c3-c3)
-+cA-cB  328.3    1.5080       Lipid11  v1.0 (GAFF c3-c2)
-+cA-cD  303.1    1.5350       Lipid14  v2.14(GAFF c3-c3)
-+cA-hA  337.3    1.0920       Lipid11  v1.0 (GAFF c3-hc)
- cA-hE  335.9    1.0930       Lipid11  v1.0 (GAFF c3-h1)
- cA-hX  338.7    1.0910       Lipid11  v1.0 (GAFF c3-hx)
- cA-nA  293.6    1.4990       Lipid11  v1.0 (GAFF c3-n4)
-+cA-oH  314.1    1.4260       Lipid11  v1.0 (GAFF c3-oh)
- cA-oS  301.5    1.4390       Lipid11  v1.0 (GAFF c3-os)
- cA-oT  301.5    1.4390       Lipid11  v1.0 (GAFF c3-os)
- cB-cB  589.7    1.3240       Lipid11  v1.0 (GAFF c2-c2)
-+cB-cD  328.3    1.5080       Lipid14  v2.0 (GAFF c2-c3)
- cB-hB  344.3    1.0870       Lipid11  v1.0 (GAFF c2-ha)
-+cC-cD  328.3    1.5080       Lipid14  v2.0 (GAFF c -c3)
- cC-oC  648.0    1.2140       Lipid11  v1.0 (GAFF c -o )
- cC-oS  411.3    1.3430       Lipid11  v1.0 (GAFF c -os)
--cD-cB  328.3    1.5080       Lipid14  v2.0 (GAFF c3-c2)
--cD-cC  328.3    1.5080       Lipid14  v2.0 (GAFF c3-c )
- cD-cD  303.1    1.5350       Lipid14  v2.0 (GAFF c3-c3)
- cD-hL  337.3    1.0920       Lipid14  v2.0 (GAFF c3-hc)
- hN-nA  369.0    1.0330       Lipid11  v1.0 (GAFF hn-n4)
-+hO-oH  369.6    0.9740       Lipid11  v1.0 (GAFF ho-oh)
- oP-pA  487.7    1.4810       Lipid11  v1.0 (GAFF o -p5)
- oT-pA  342.5    1.6020       Lipid11  v1.0 (GAFF os-p5)
- 
- cA-cA-cA   63.210     110.630   Lipid11  v1.0 (GAFF c3-c3-c3)
-+cA-cA-cB   63.530     111.440   Lipid11  v1.0 (GAFF c3-c3-c2)
-+cA-cA-cD   63.210     110.630   Lipid14  v2.14(GAFF c3-c3-c3)
-+cA-cA-hA   46.370     110.050   Lipid11  v1.0 (GAFF c3-c3-hc)
- cA-cA-hE   46.360     110.070   Lipid11  v1.0 (GAFF c3-c3-h1)
- cA-cA-hX   46.020     111.740   Lipid11  v1.0 (GAFF c3-c3-hx)
- cA-cA-nA   64.450     114.320   Lipid11  v1.0 (GAFF c3-c3-n4)
-+cA-cA-oH   67.720     109.430   Lipid11  v1.0 (GAFF c3-c3-oh)
- cA-cA-oS   67.780     108.420   Lipid11  v1.0 (GAFF c3-c3-os)
- cA-cA-oT   67.780     108.420   Lipid11  v1.0 (GAFF c3-c3-os)
-+cA-cB-cA   62.700     116.520   Lipid11  v1.0 (GAFF c3-c2-c3)
-+cA-cB-cB   64.330     123.420   Lipid11  v1.0 (GAFF c3-c2-c2)
-+cA-cB-hB   45.660     117.300   Lipid11  v1.0 (GAFF c3-c2-ha)
-+cA-cD-cD   63.210     110.630   Lipid14  v2.14(GAFF c3-c3-c3)
-+cA-cD-hL   46.370     110.050   Lipid14  v2.14(GAFF c3-c3-hc)
- cA-nA-cA   62.840     110.640   Lipid11  v1.0 (GAFF c3-n4-c3)
- cA-nA-hN   46.190     110.110   Lipid11  v1.0 (GAFF c3-n4-hn)
-+cA-oH-hO   47.090     108.160   Lipid11  v1.0 (GAFF c3-oh-ho)
- cA-oS-cC   63.630     115.140   Lipid11  v1.0 (GAFF c3-os-c ) 
- cA-oT-pA   78.480     118.000   Lipid11  v1.0 (GAFF c3-os-p5)
-+cB-cA-hA   47.030     110.490   Lipid11  v1.0 (GAFF c2-c3-hc)
-+cB-cB-cD   64.330     123.420   Lipid14  v2.0 (GAFF c2-c2-c3)
- cB-cB-hB   50.040     120.940   Lipid11  v1.0 (GAFF c2-c2-ha)
-+cB-cD-cD   63.530     111.440   Lipid14  v2.0 (GAFF c2-c3-c3)
- cB-cD-hL   47.030     110.490   Lipid14  v2.0 (GAFF c2-c3-hc)
-+cC-cD-cD   63.790     110.530   Lipid14  v2.0 (GAFF c -c3-c3)
- cC-cD-hL   47.200     109.680   Lipid14  v2.0 (GAFF c -c3-hc)
--cD-cB-cB   64.330     123.420   Lipid14  v2.0 (GAFF c3-c2-c2)
-+cD-cA-hA   46.370     110.050   Lipid14  v2.14(GAFF c3-c3-hc)
- cD-cB-hB   45.660     117.300   Lipid14  v2.0 (GAFF c3-c2-ha)
- cD-cC-oC   68.030     123.110   Lipid14  v2.0 (GAFF c3-c -o )
- cD-cC-oS   69.260     111.960   Lipid14  v2.0 (GAFF c3-c -os)
--cD-cD-cB   63.530     111.440   Lipid14  v2.0 (GAFF c3-c3-c2)
--cD-cD-cC   63.790     110.530   Lipid14  v2.0 (GAFF c3-c3-c )
- cD-cD-cD   63.210     110.630   Lipid14  v2.0 (GAFF c3-c3-c3)
- cD-cD-hL   46.370     110.050   Lipid14  v2.0 (GAFF c3-c3-hc)
-+hA-cA-hA   39.430     108.350   Lipid11  v1.0 (GAFF hc-c3-hc)
- hE-cA-hE   39.180     109.550   Lipid11  v1.0 (GAFF h1-c3-h1)
-+hE-cA-oH   50.970     109.880   Lipid11  v1.0 (GAFF ha-c3-oh)
- hE-cA-oS   50.840     108.820   Lipid11  v1.0 (GAFF h1-c3-os)
- hE-cA-oT   50.840     108.820   Lipid11  v1.0 (GAFF h1-c3-os)
- hL-cD-hL   39.430     108.350   Lipid14  v2.0 (GAFF hc-c3-hc)
-@@ -67,86 +89,133 @@ oP-pA-oP   46.010     115.800   Lipid11  v1.0 (GAFF o -p5-o )
- oP-pA-oT   44.010     116.090   Lipid11  v1.0 (GAFF o -p5-os)
- oT-pA-oT   45.370     101.770   Lipid11  v1.0 (GAFF os-p5-os)
- 
--cA-cA-cA-hE   1    0.1556        0.0             3.000     SCEE=1.2 SCNB=2.0 Lipid11  v1.0 (GAFF X -c3-c3-X )
--cA-cA-cA-oS   1    0.1556        0.0             3.000     SCEE=1.2 SCNB=2.0 Lipid11  v1.0 (GAFF X -c3-c3-X )
--cA-cA-cA-oT   1    0.1556        0.0             3.000     SCEE=1.2 SCNB=2.0 Lipid11  v1.0 (GAFF X -c3-c3-X )
--cA-cA-nA-cA   1    0.1556        0.0             3.000     SCEE=1.2 SCNB=2.0 Lipid11  v1.0 (GAFF X -c3-n4-X )
--cA-cA-nA-hN   1    0.1556        0.0             3.000     SCEE=1.2 SCNB=2.0 Lipid11  v1.0 (GAFF X -c3-n4-X )
--cA-cA-oT-pA   1    0.3833        0.0             3.000     SCEE=1.2 SCNB=2.0 Lipid11  v1.0 (GAFF X -c3-os-X )
--cA-nA-cA-hX   1    0.1556        0.0             3.000     SCEE=1.2 SCNB=2.0 Lipid11  v1.0 (GAFF X -c3-n4-X )
--cA-oS-cC-oS   1    2.700       180.0             2.000     SCEE=1.2 SCNB=2.0 Lipid11  v1.0 (GAFF X -c -os-X )
--cA-oT-pA-oP   1    0.800         0.0             2.000     SCEE=1.2 SCNB=2.0 Lipid11  v1.0 (GAFF X -os-p5-X )
--cA-oT-pA-oP   1    0.800         0.0             2.000     SCEE=1.2 SCNB=2.0 Lipid11  v1.0 (GAFF X -os-p5-X )
--cA-oT-pA-oT   1    0.25          0.0            -3.000     SCEE=1.2 SCNB=2.0 Lipid11  v1.0 (GAFF c3-os-p5-os)
--cA-oT-pA-oT   1    1.20          0.0             2.000     SCEE=1.2 SCNB=2.0 Lipid11  v1.0 (GAFF c3-os-p5-os)
--cB-cB-cD-cD   1    0.3464        0.000           1.000     SCEE=1.2 SCNB=2.0 Lipid14  v2.10 (paramfit)
--cB-cB-cD-cD   1   -0.5577        0.000           2.000     SCEE=1.2 SCNB=2.0 Lipid14  v2.10 (paramfit)
--cB-cB-cD-cD   1   -0.2920        0.000           3.000     SCEE=1.2 SCNB=2.0 Lipid14  v2.10 (paramfit)
--cB-cB-cD-cD   1   -0.0943        0.000           4.000     SCEE=1.2 SCNB=2.0 Lipid14  v2.10 (paramfit)
--cB-cB-cD-cD   1    0.0226        0.000           5.000     SCEE=1.2 SCNB=2.0 Lipid14  v2.10 (paramfit)
--cB-cD-cD-cD   1    0.0251      180.000           1.000     SCEE=1.2 SCNB=2.0 Lipid14  v2.10 (paramfit)
--cB-cD-cD-cD   1    0.0054      180.000           2.000     SCEE=1.2 SCNB=2.0 Lipid14  v2.10 (paramfit)
--cB-cD-cD-cD   1    0.2007        0.000           3.000     SCEE=1.2 SCNB=2.0 Lipid14  v2.10 (paramfit)
--cB-cD-cD-cD   1    0.2103        0.000           4.000     SCEE=1.2 SCNB=2.0 Lipid14  v2.10 (paramfit)
--cB-cD-cD-cD   1    0.0811        0.000           5.000     SCEE=1.2 SCNB=2.0 Lipid14  v2.10 (paramfit)
--cB-cD-cD-hL   1    0.1556        0.0             3.000     SCEE=1.2 SCNB=2.0 Lipid14  v2.0 (GAFF X -c3-c3-X )
--cC-cD-cD-hL   1    0.1556        0.0             3.000     SCEE=1.2 SCNB=2.0 Lipid14  v2.0 (GAFF X -c3-c3-X )
--cC-oS-cA-cA   1    0.383         0.0            -3.000     SCEE=1.2 SCNB=2.0 Lipid11  v1.0 (GAFF c3-c3-os-c )
--cC-oS-cA-cA   1    0.80        180.0             1.000     SCEE=1.2 SCNB=2.0 Lipid11  v1.0 (GAFF c3-c3-os-c )
--cC-oS-cA-hE   1    0.3833        0.0             3.000     SCEE=1.2 SCNB=2.0 Lipid11  v1.0 (GAFF X -c3-os-X )
--cD-cB-cB-cD   1    0.3073      180.000           1.000     SCEE=1.2 SCNB=2.0 Lipid14  v2.10 (paramfit)
--cD-cB-cB-cD   1    4.0051      180.000           2.000     SCEE=1.2 SCNB=2.0 Lipid14  v2.10 (paramfit)
--cD-cB-cB-cD   1    0.1990        0.000           3.000     SCEE=1.2 SCNB=2.0 Lipid14  v2.10 (paramfit)
--cD-cB-cB-cD   1    0.3242        0.000           4.000     SCEE=1.2 SCNB=2.0 Lipid14  v2.10 (paramfit)
--cD-cB-cB-cD   1   -0.0415        0.000           5.000     SCEE=1.2 SCNB=2.0 Lipid14  v2.10 (paramfit)
--cD-cB-cB-hB   1    6.650       180.0             2.000     SCEE=1.2 SCNB=2.0 Lipid14  v2.0 (GAFF X -c2-c2-X )
--cD-cC-oS-cA   1    2.700       180.000           2.000     SCEE=1.2 SCNB=2.0 Lipid11  v1.0 (GAFF X -c -os-X )
--cD-cD-cC-oC   1   -0.9110      180.000           1.000     SCEE=1.2 SCNB=2.0 Lipid14  v2.10 (paramfit)
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-+cD-cD-cD-cD   1    0.2170        0.000           5.000     SCEE=1.2 SCNB=2.0 Lipid14 v2.10 (paramfit)
-+cD-cD-cD-hL   1    0.16          0.0             3.000     SCEE=1.2 SCNB=2.0 Lipid14 v2.0 (GAFF c3-c3-c3-hc)
-+hA-cA-cA-hA   1    0.15          0.0             3.000     SCEE=1.2 SCNB=2.0 Lipid11 v1.0 (GAFF hc-c3-c3-hc)
-+hA-cA-cA-hE   1    0.1556        0.0             3.000     SCEE=1.2 SCNB=2.0 Lipid11 v1.0 (GAFF X -c3-c3-X )
-+hA-cA-cA-oH   1    0.00          0.0            -3.000     SCEE=1.2 SCNB=2.0 Lipid11 v1.0 (GAFF hc-c3-c3-oh)
-+hA-cA-cA-oH   1    0.25          0.0             1.000     SCEE=1.2 SCNB=2.0 Lipid11 v1.0 (GAFF hc-c3-c3-oh)
-+hA-cA-cB-hB   1    0.000         0.0             2.000     SCEE=1.2 SCNB=2.0 Lipid11 v1.0 (GAFF X -c3-c2-X )
-+hA-cA-cD-hL   1    0.15          0.0             3.000     SCEE=1.2 SCNB=2.0 Lipid14 v2.14(GAFF hc-c3-c3-hc)
-+hB-cB-cB-hB   1    6.650       180.0             2.000     SCEE=1.2 SCNB=2.0 Lipid11 v1.0 (GAFF X -c2-c2-X )
-+hB-cB-cD-hL   1    0.000         0.0             2.000     SCEE=1.2 SCNB=2.0 Lipid14 v2.0 (GAFF X -c3-c2-X )
-+hE-cA-cA-hE   1    0.1556        0.0             3.000     SCEE=1.2 SCNB=2.0 Lipid11 v1.0 (GAFF X -c3-c3-X )
-+hE-cA-cA-hX   1    0.1556        0.0             3.000     SCEE=1.2 SCNB=2.0 Lipid11 v1.0 (GAFF X -c3-c3-X )
-+hE-cA-cA-nA   1    0.1556        0.0             3.000     SCEE=1.2 SCNB=2.0 Lipid11 v1.0 (GAFF X -c3-c3-X )
-+hE-cA-cA-oS   1    0.00          0.0            -3.000     SCEE=1.2 SCNB=2.0 Lipid11 v1.0 (GAFF h1-c3-c3-os)
-+hE-cA-cA-oS   1    0.25          0.0             1.000     SCEE=1.2 SCNB=2.0 Lipid11 v1.0 (GAFF h1-c3-c3-os)
-+hE-cA-cA-oT   1    0.00          0.0            -3.000     SCEE=1.2 SCNB=2.0 Lipid11 v1.0 (GAFF h1-c3-c3-os)
-+hE-cA-cA-oT   1    0.25          0.0             1.000     SCEE=1.2 SCNB=2.0 Lipid11 v1.0 (GAFF h1-c3-c3-os)
-+hE-cA-oH-hO   1    0.500         0.0             3.000     SCEE=1.2 SCNB=2.0 Lipid11 v1.0 (GAFF X -c3-oh-X )
-+hE-cA-oT-pA   1    0.3833        0.0             3.000     SCEE=1.2 SCNB=2.0 Lipid11 v1.0 (GAFF X -c3-os-X )
-+hL-cD-cC-oC   1    0.08        180.0            -3.000     SCEE=1.2 SCNB=2.0 Lipid14 v2.0 (GAFF hc-c3-c -o )
-+hL-cD-cC-oC   1    0.80          0.0             1.000     SCEE=1.2 SCNB=2.0 Lipid14 v2.0 (GAFF hc-c3-c -o )
-+hL-cD-cC-oS   1    0.000       180.0             2.000     SCEE=1.2 SCNB=2.0 Lipid14 v2.0 (GAFF X -c -c3-X )
-+hL-cD-cD-hL   1    0.15          0.0             3.000     SCEE=1.2 SCNB=2.0 Lipid14 v2.0 (GAFF hc-c3-c3-hc)
-+hN-nA-cA-hX   1    0.1556        0.0             3.000     SCEE=1.2 SCNB=2.0 Lipid11 v1.0 (GAFF X -c3-n4-X )
-+hX-cA-cA-oT   1    0.1556        0.0             3.000     SCEE=1.2 SCNB=2.0 Lipid11 v1.0 (GAFF X -c3-c3-X )
-+nA-cA-cA-oT   1    0.1556        0.0             3.000     SCEE=1.2 SCNB=2.0 Lipid11 v1.0 (GAFF X -c3-c3-X )
-+oS-cA-cA-oS   1    0.144         0.0            -3.000     SCEE=1.2 SCNB=2.0 Lipid11 v1.0 (GAFF os-c3-c3-os)
-+oS-cA-cA-oS   1    1.175         0.0             2.000     SCEE=1.2 SCNB=2.0 Lipid11 v1.0 (GAFF os-c3-c3-os)
-+oS-cA-cA-oT   1    0.144         0.0            -3.000     SCEE=1.2 SCNB=2.0 Lipid11 v1.0 (GAFF os-c3-c3-os)
-+oS-cA-cA-oT   1    1.175         0.0             2.000     SCEE=1.2 SCNB=2.0 Lipid11 v1.0 (GAFF os-c3-c3-os)
-+
-+cA-cB-cB-cA         1.1          180.          2.0         Lipid14 CHL (GAFF)
-+cB-cA-cB-hB         1.1          180.          2.0         Lipid14 CHL (GAFF)
-+cB-cD-cB-hB         1.1          180.0         2.0         Lipid14  v2.0 aliphatic improper (GAFF c2-c3-c2-ha)
- cD-oC-cC-oS         10.5         180.0         2.0         Lipid14  v2.0 ester improper (GAFF X -X -c -o )
--cB-cD-cB-hB         1.1          180.0         2.0         Lipid14  v2.0 aliphatic improper (GAFF c2-c3-c2-ha - default)
- 
-   hw  ow  0000.     0000.                                4.  flag for fast water - Hack for no 10-12 terms
- 
-@@ -156,17 +225,20 @@ MOD4      RE
-   cB          1.9080  0.0860             Lipid14 v2.10
-   cC          1.9080  0.0700             Lipid14 v2.10
-   cD          1.9080  0.1094             OPLS
-+  hA          1.4870  0.0157             OPLS
-+  hB          1.2500  0.0070             Lipid14 v2.10
-+  hE          1.3870  0.0157             Veenstra et al JCC,8,(1992),963
-+  hL          1.4600  0.0100             Lipid14 v2.10
-+  hN          0.6000  0.0157             !Ferguson base pair geom.
-+  hO          0.0000  0.0000             OPLS Jorgensen, JACS,110,(1988),1657 (RCW Needs fixing give radii)
-+  hX          1.1000  0.0157             Veenstra et al JCC,8,(1992),963
-+  nA          1.8240  0.1700             OPLS
-   oC          1.6500  0.1400             Lipid14 v2.10
-+  oH          1.7210  0.2104             OPLS
-+  oP          1.6500  0.1400             Lipid14 v2.10
-   oS          1.6500  0.1200             Lipid14 v2.10
-   oT          1.6500  0.1200             Lipid14 v2.10
--  oP          1.6500  0.1400             Lipid14 v2.10
--  nA          1.8240  0.1700             OPLS
-   pA          2.1000  0.2000             JCC,7,(1986),230; 
--  hE          1.3870  0.0157             Veenstra et al JCC,8,(1992),963
--  hX          1.1000  0.0157             Veenstra et al JCC,8,(1992),963
--  hB          1.2500  0.0070             Lipid14 v2.10
--  hN          0.6000  0.0157            !Ferguson base pair geom.
--  hL          1.4600  0.0100             Lipid14 v2.10
- 
- END
- 
-@@ -175,7 +247,7 @@ END
- 
- *** AMBER Lipid14 Force Field, C. Dickson, B. Madej, A.Skjevik, K. Teigen, I.R. Gould, R.C. Walker ***
- 
--Citation is - Released version 2.10: 
-+Citation is: 
- 
- Dickson, C.J., Madej, B.D., Skjevik, A.A., Betz, R.M., Teigen, K., Gould, I.R., Walker, R.C., "Lipid14: The Amber Lipid Force Field", J. Chem. Theory Comput., 2014, in press, DOI: 10.1021/ct4010307
- 
-@@ -241,24 +313,31 @@ Version 2.11 (February 2014)
- Version 2.12 (February 2014)
- - Replace angle force constants involving phosporus with the correct values from the update GAFF.dat file.
- 
-+Version 2.14 (September 2015)
-+- Reorder parameters so they are alphabetical.
-+- Add cholesterol parameters
-+
- Atom type mapping
- -----------------
- 
- GAFF     Lipid14    Description
- ----     -------    -----------
-- c3        cA       sp3 carbon
-- c2        cB       aliphatic sp2 carbon
-  c         cC       carbonyl sp2 carbon
-- o         oC       sp2 oxygen with one connected atom (e.g C=O, COO-)
-- os        oS       sp3 oxygen in ethers and esters
-- n4        nA       sp3 N with four connected atoms 
-- p5        pA       phosphorus with four connected atoms, such as O=P(OH)3
-+ c2        cB       aliphatic sp2 carbon
-+ c3        cA       sp3 carbon
-  h1        hE       H bonded to aliphatic carbon with 1 electrwd. group
-- hx        hX       H bonded to C next to positively charged group
-  ha        hB       H bonded to aromatic carbon
-+ hc        hA       H bonded to aliphatic carbon without electrwd. group
-  hn        hN       H bonded to nitrogen
-+ ho        hO       H in Hydroxyl group
-+ hx        hX       H bonded to C next to positively charged group
-+ n4        nA       sp3 N with four connected atoms 
-+ o         oC       sp2 oxygen with one connected atom (e.g C=O, COO-)
-  o         oP       sp2 oxygen with one connected atom (e.g P-O) in phosphate group
-+ oh        oH       sp3 oxygen in hydroxyl group
-+ os        oS       sp3 oxygen in ethers and esters
-  os        oT       sp3 oxygen bonded to carbon in phosphate group
-+ p5        pA       phosphorus with four connected atoms, such as O=P(OH)3
- 
- GAFFlipid Lipid14   Description
- --------- -------   -----------
diff --git a/sci-chemistry/ambertools/files/ambertools-15-update.5.patch b/sci-chemistry/ambertools/files/ambertools-15-update.5.patch
deleted file mode 100644
index 017cb8d6d..000000000
--- a/sci-chemistry/ambertools/files/ambertools-15-update.5.patch
+++ /dev/null
@@ -1,25 +0,0 @@
-**********> update.5
-
-Author: Jason Swails
-
-Date: Oct. 31, 2015
-
-Program: ParmEd
-
-Description: Fix Python 2.6-compatibility for ParmEd
-
---------------------------------------------------------------------------------
-
- AmberTools/src/parmed/chemistry/openmm/reporters.py | 2 +-
- 1 file changed, 1 insertion(+), 1 deletion(-)
-
-diff --git AmberTools/src/parmed/chemistry/openmm/reporters.py AmberTools/src/parmed/chemistry/openmm/reporters.py
-index d4e47d4..0f4c3ea 100644
---- AmberTools/src/parmed/chemistry/openmm/reporters.py
-+++ AmberTools/src/parmed/chemistry/openmm/reporters.py
-@@ -1,4 +1,4 @@
--from __future__ import division
-+from __future__ import division, with_statement
- 
- from chemistry.amber.asciicrd import AmberMdcrd
- from chemistry.geometry import box_vectors_to_lengths_and_angles
diff --git a/sci-chemistry/ambertools/files/ambertools-15-update.6.patch b/sci-chemistry/ambertools/files/ambertools-15-update.6.patch
deleted file mode 100644
index d7df551f5..000000000
--- a/sci-chemistry/ambertools/files/ambertools-15-update.6.patch
+++ /dev/null
@@ -1,59 +0,0 @@
-********> update.6
-
-Author: Charles Lin
-
-Date: November 10, 2015
-
-Programs: pmemd.cuda
-
-Description: This update gives support to cuda 7.5 and optional support for 7.0 (it is recommended to run cuda 6.5 or 7.5)
-
---------------------------------------------------------
-
- AmberTools/src/configure2 | 31 ++++++++++++++++++++++++++++++-
- 1 file changed, 30 insertions(+), 1 deletion(-)
-
-diff --git AmberTools/src/configure2 AmberTools/src/configure2
-index 9a504b1..6835c9c 100755
---- AmberTools/src/configure2
-+++ AmberTools/src/configure2
-@@ -865,9 +865,38 @@ if [ "$cuda_SPFP" = 'yes' -o "$cuda_SPXP" = 'yes' -o "$cuda_DPFP" = 'yes' ]; the
-       echo "CUDA Version $cudaversion detected"
-       echo "Configuring for SM2.0, SM3.0 and SM5.0"
-       nvccflags="$sm20flags $sm30flags $sm50flags"
-+    elif [ "$cudaversion" = "7.0" ]; then
-+      printf "\n"
-+      printf "Version 7.0 of the NVIDIA CUDA compiler has been detected.\n\
-+Support for version 7.0 has been deprecated and we recommend use\n\
-+of either 7.5 or 6.5 instead.  Version 7.0 introduced a performance\n\
-+regression over earlier compilers and also a bug in the way that GPUs are\n\
-+selected based on whether they are in use or not.  This bug causes AMBER to\n\
-+print a GPU selection error rather than auto selecting a free GPU.  These\n\
-+issues do not effect v6.5 and have been addressed in version 7.5."
-+      printf "\n"
-+      printf "If you still want to proceed with v7.0 on the\n\
-+understanding that it is considered deprecated from a support process please type\n\
-+'yes' to proceed.  Otherwise type 'no', switch to either 6.5 or 7.5\n\
-+and rerun configure."
-+      printf "\n"
-+      read answer
-+      ans=`echo $answer | awk '{print substr($1,1,1)}'`
-+ 
-+      if [ "$ans" = "y" -o "$ans" = "Y" ]; then
-+        echo "Configuring for SM2.0, SM3.0 and SM5.0"
-+        nvccflags="$sm20flags $sm30flags $sm50flags"
-+      else
-+        echo "Please set cuda version to 6.5 or 7.5!"
-+        exit 1
-+      fi
-+    elif [ "$cudaversion" = "7.5" ]; then
-+      echo "CUDA Version $cudaversion detected"
-+      echo "Configuring for SM2.0, SM3.0, SM5.0 and SM5.2"
-+      nvccflags="$sm20flags $sm30flags $sm50flags $sm52flags"
-     else
-       echo "Error: Unsupported CUDA version $cudaversion detected."
--      echo "       AMBER requires CUDA version == 5.0 .or. 5.5 .or. 6.0 .or. 6.5 .or. 7.0"
-+      echo "       AMBER requires CUDA version == 5.0 .or. 5.5 .or. 6.0 .or. 6.5 .or. 7.5"
-       exit 1
-     fi
-     nvcc="$nvcc $nvccflags"
diff --git a/sci-chemistry/ambertools/metadata.xml b/sci-chemistry/ambertools/metadata.xml
deleted file mode 100644
index 7daa2ce7e..000000000
--- a/sci-chemistry/ambertools/metadata.xml
+++ /dev/null
@@ -1,12 +0,0 @@
-<?xml version="1.0" encoding="UTF-8"?>
-<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
-<pkgmetadata>
-	<maintainer type="person">
-		<email>alexxy@gentoo.org</email>
-		<name>Alexey Shvetsov</name>
-	</maintainer>
-	<maintainer type="project">
-		<email>sci-chemistry@gentoo.org</email>
-		<name>Gentoo Chemistry Project</name>
-	</maintainer>
-</pkgmetadata>
diff --git a/sci-chemistry/burrow-owl/Manifest b/sci-chemistry/burrow-owl/Manifest
deleted file mode 100644
index 1931a9516..000000000
--- a/sci-chemistry/burrow-owl/Manifest
+++ /dev/null
@@ -1 +0,0 @@
-DIST burrow-demos.tar 80896000 BLAKE2B cafd01273887a30f3dadd3e0aba9b5dab22f865a2470ce779e8b94a1cd43ec34f3bea5d0909b3f106b97735c5abf3c0237490f0ecae0da2a0f81443dcc64c06a SHA512 76948846b4bff2f5c0814e41ee1745122580d6e28f8de217edbf42c4530bc64fb093dc9c96e9c0c083098755c525300b563ee1368caa12be791b2bea7015ee6b
diff --git a/sci-chemistry/burrow-owl/burrow-owl-9999.ebuild b/sci-chemistry/burrow-owl/burrow-owl-9999.ebuild
deleted file mode 100644
index 0e62aceee..000000000
--- a/sci-chemistry/burrow-owl/burrow-owl-9999.ebuild
+++ /dev/null
@@ -1,63 +0,0 @@
-# Copyright 1999-2015 Gentoo Foundation
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=5
-
-AUTOTOOLS_AUTORECONF="true"
-
-inherit autotools-utils git-r3 virtualx
-
-DESCRIPTION="Visualize multidimensional nuclear magnetic resonance (NMR) spectra"
-HOMEPAGE="http://burrow-owl.sourceforge.net/"
-SRC_URI="examples? ( mirror://sourceforge/${PN}/burrow-demos.tar )"
-EGIT_REPO_URI="git://burrow-owl.git.sourceforge.net/gitroot/burrow-owl/burrow-owl"
-
-LICENSE="GPL-2"
-SLOT="0"
-KEYWORDS=""
-IUSE="doc examples static-libs"
-
-RDEPEND="
-	dev-libs/g-wrap
-	dev-libs/glib:2
-	dev-scheme/guile:12=[networking,regex]
-	dev-scheme/guile-cairo
-	dev-scheme/guile-gnome-platform
-	sci-libs/starparse
-	x11-libs/gtk+:2"
-DEPEND="${RDEPEND}
-	dev-util/indent
-	virtual/pkgconfig
-	doc? ( app-doc/doxygen )
-"
-
-PATCHES=(
-	"${FILESDIR}"/${P}-prll.patch
-	"${FILESDIR}"/${P}-impl-dec.patch
-	)
-
-src_unpack() {
-	git-r3_src_unpack
-	use examples && unpack ${A}
-}
-
-src_configure() {
-	local myeconfargs=(
-		$(use_with doc doxygen doxygen)
-	)
-	autotools-utils_src_configure
-}
-
-src_test () {
-	VIRTUALX_COMMAND="autotools-utils_src_compile -C test-suite check"
-	virtualmake
-}
-
-src_install() {
-	use doc && HTML_DOCS=( "${AUTOTOOLS_BUILD_DIR}/doc/api/html/." )
-	autotools-utils_src_install
-
-	use examples && \
-		insinto /usr/share/${PN} && \
-		doins -r "${WORKDIR}"/burrow-demos/*
-}
diff --git a/sci-chemistry/burrow-owl/files/burrow-owl-9999-impl-dec.patch b/sci-chemistry/burrow-owl/files/burrow-owl-9999-impl-dec.patch
deleted file mode 100644
index 461e3e691..000000000
--- a/sci-chemistry/burrow-owl/files/burrow-owl-9999-impl-dec.patch
+++ /dev/null
@@ -1,15 +0,0 @@
- burrow/spectrum/spectrum.c |    2 +-
- 1 files changed, 1 insertions(+), 1 deletions(-)
-
-diff --git a/burrow/spectrum/spectrum.c b/burrow/spectrum/spectrum.c
-index 5e099d8..38040bb 100644
---- a/burrow/spectrum/spectrum.c
-+++ b/burrow/spectrum/spectrum.c
-@@ -35,6 +35,7 @@
- #include "spectrum_priv.h"
- #include "skiplist.h"
- #include "debug.h"
-+#include <stdlib.h>
- 
- /* for debugging purposes; make value available */
- static const gdouble datum_unknown_value_substitute=DATUM_UNKNOWN_VALUE_SUBSTITUTE;
diff --git a/sci-chemistry/burrow-owl/files/burrow-owl-9999-prll.patch b/sci-chemistry/burrow-owl/files/burrow-owl-9999-prll.patch
deleted file mode 100644
index 340ccd236..000000000
--- a/sci-chemistry/burrow-owl/files/burrow-owl-9999-prll.patch
+++ /dev/null
@@ -1,20 +0,0 @@
- burrow/canvas/gw/Makefile.am |    4 +++-
- 1 files changed, 3 insertions(+), 1 deletions(-)
-
-diff --git a/burrow/canvas/gw/Makefile.am b/burrow/canvas/gw/Makefile.am
-index da50ee3..2ed89bc 100644
---- a/burrow/canvas/gw/Makefile.am
-+++ b/burrow/canvas/gw/Makefile.am
-@@ -31,9 +31,11 @@ H2DEF=@top_srcdir@/utils/h2def.py
- canvas.defs: $(HEADERS_1)
- 	$(H2DEF) --all $(HEADERS_1) > $@
- 
--canvas-gw.c canvas-gw.h canvas-gw.scm: canvas.defs
-+canvas-gw.c canvas-gw.h: canvas.defs
- 	GUILE_LOAD_PATH=@srcdir@:@builddir@:@GUILE_GNOME_MODULE_DIR@:@G_WRAP_MODULE_DIR@:$$GUILE_LOAD_PATH $(GUILE) -s @srcdir@/run-g-wrap.scm
- 
-+BUILT_SOURCES=canvas-gw.c canvas-gw.h canvas.defs
-+
- INCLUDES=@GTK_CFLAGS@ @G_WRAP_CFLAGS@ @GUILE_GNOME_CFLAGS@ @GUILE_CAIRO_CFLAGS@ @GUILE_CFLAGS@ -I$(headers_dir) -I@top_srcdir@
- 
- moduledir=$(datadir)/guile/burrow
diff --git a/sci-chemistry/burrow-owl/metadata.xml b/sci-chemistry/burrow-owl/metadata.xml
deleted file mode 100644
index d78ba4b82..000000000
--- a/sci-chemistry/burrow-owl/metadata.xml
+++ /dev/null
@@ -1,11 +0,0 @@
-<?xml version="1.0" encoding="UTF-8"?>
-<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
-<pkgmetadata>
-	<maintainer type="project">
-		<email>sci-chemistry@gentoo.org</email>
-		<name>Gentoo Chemistry Project</name>
-	</maintainer>
-	<upstream>
-		<remote-id type="sourceforge">burrow-owl</remote-id>
-	</upstream>
-</pkgmetadata>
diff --git a/sci-chemistry/camshift/Manifest b/sci-chemistry/camshift/Manifest
deleted file mode 100644
index 24a81ef33..000000000
--- a/sci-chemistry/camshift/Manifest
+++ /dev/null
@@ -1 +0,0 @@
-DIST camshift-1.35.0.tar.gz 6297498 BLAKE2B 21ae317ceacaec7487312794653744fa4a0075ca088e438b1447c30987064e7aa152f931b37a2b580c9089252af4669f76c4dcaa1168dcc938c88387c52074ed SHA512 78cf5e257c00f0f025052fddd9066c6ef404765d106df72737ed360a269e1106c19ff25ec4962fc8faf2be9af935e0230506c55d2ff4e521c2ad955771b3396c
diff --git a/sci-chemistry/camshift/camshift-1.35.0.ebuild b/sci-chemistry/camshift/camshift-1.35.0.ebuild
deleted file mode 100644
index 3964d0400..000000000
--- a/sci-chemistry/camshift/camshift-1.35.0.ebuild
+++ /dev/null
@@ -1,51 +0,0 @@
-# Copyright 1999-2015 Gentoo Foundation
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=5
-
-AUTOTOOLS_AUTORECONF=true
-
-inherit autotools-utils flag-o-matic
-
-DESCRIPTION="Structure based prediction of protein chemical shifts"
-HOMEPAGE="http://www-vendruscolo.ch.cam.ac.uk/camshift/camshift.php"
-SRC_URI="http://www-vendruscolo.ch.cam.ac.uk/${PN}/${P}.tar.gz"
-
-LICENSE="GPL-2"
-SLOT="0"
-KEYWORDS="~amd64 ~x86 ~amd64-linux ~x86-linux"
-IUSE="cpu_flags_x86_sse"
-
-RDEPEND="
-	virtual/blas
-	virtual/lapack"
-DEPEND="${RDEPEND}
-	virtual/pkgconfig"
-
-PATCHES=(
-	"${FILESDIR}"/${PV}-gcc47.patch
-	"${FILESDIR}"/${PV}-gentoo.patch )
-
-src_configure(){
-	local myeconfargs=(
-		--with-lapack
-		--with-external-blas
-		$(use_enable cpu_flags_x86_sse mkasm)
-	)
-	autotools-utils_src_configure
-}
-
-src_compile() {
-	autotools-utils_src_compile \
-		CFLAGS="${CFLAGS}" \
-		CXXFLAGS="${CXXFLAGS}" \
-		LDFLAGS="${LDFLAGS}"
-}
-
-src_install() {
-	dobin "${BUILD_DIR}"/bin/${PN}
-
-	insinto /usr/share/${PN}
-	doins -r data
-	dodoc README NEWS ChangeLog AUTHORS
-}
diff --git a/sci-chemistry/camshift/files/1.35.0-gcc47.patch b/sci-chemistry/camshift/files/1.35.0-gcc47.patch
deleted file mode 100644
index 7e9d4b973..000000000
--- a/sci-chemistry/camshift/files/1.35.0-gcc47.patch
+++ /dev/null
@@ -1,148 +0,0 @@
- include/almost/forcefield/intern/angleenergy.h | 14 ++++-----
- include/almost/forcefield/intern/bondenergy.h  |  2 +-
- include/almost/kernel/molecule.h               |  2 +-
- include/almost/kernel/rmsd.h                   | 42 +++++++++++++-------------
- src/lib/io/formostream.cpp                     |  4 +--
- 5 files changed, 32 insertions(+), 32 deletions(-)
-
-diff --git a/include/almost/forcefield/intern/angleenergy.h b/include/almost/forcefield/intern/angleenergy.h
-index 75308ca..a9bc70c 100644
---- a/include/almost/forcefield/intern/angleenergy.h
-+++ b/include/almost/forcefield/intern/angleenergy.h
-@@ -419,7 +419,7 @@ namespace Almost {
- 	int f = Coor<float_type>::DIM*this->first_[i];
- 	int m = Coor<float_type>::DIM*this->middle_[i];
- 	int l = Coor<float_type>::DIM*this->last_[i];
--	dangle = angle(coor,f,m,l);
-+	dangle = this->angle(coor,f,m,l);
- 	ene += this->ka_[i]*(dangle-this->a0_[i])*(dangle-this->a0_[i]);
-       }
-       return ene;
-@@ -444,9 +444,9 @@ namespace Almost {
- 	vkj[2] = coor.coor[l+2]-coor.coor[m+2];
- 
- 	
--	float_type nij = norm(vij);
--	float_type nkj = norm(vkj);
--	float_type n   = scal(vij,vkj);
-+	float_type nij = this->norm(vij);
-+	float_type nkj = this->norm(vkj);
-+	float_type n   = this->scal(vij,vkj);
- 	float_type cosd = n/(nij*nkj);;
- 	float_type dangle = acos(cosd);
- 	float_type sind = sqrt(1-cosd*cosd);
-@@ -513,9 +513,9 @@ namespace Almost {
- 	vkj[2] = coor.coor[l+2]-coor.coor[m+2];
- 
- 	
--	float_type nij = norm(vij);
--	float_type nkj = norm(vkj);
--	float_type n   = scal(vij,vkj);
-+	float_type nij = this->norm(vij);
-+	float_type nkj = this->norm(vkj);
-+	float_type n   = this->scal(vij,vkj);
- 	float_type cosd = n/(nij*nkj);;
- 	float_type dangle = acos(cosd);
- 	float_type sind = sqrt(1-cosd*cosd);
-diff --git a/include/almost/forcefield/intern/bondenergy.h b/include/almost/forcefield/intern/bondenergy.h
-index f60d99c..d6977f2 100644
---- a/include/almost/forcefield/intern/bondenergy.h
-+++ b/include/almost/forcefield/intern/bondenergy.h
-@@ -242,7 +242,7 @@ namespace Almost {
- 	float_type d;
- 	int f = this->first_[i];
- 	int s = this->second_[i];
--	d = sqrt(distanceP2(coor.coor+Coor<float_type>::DIM*f,
-+	d = sqrt(this->distanceP2(coor.coor+Coor<float_type>::DIM*f,
- 			    coor.coor+Coor<float_type>::DIM*s));
- 	e +=this->kb_[i]*(d-this->b0_[i])*(d-this->b0_[i]);
-       }
-diff --git a/include/almost/kernel/molecule.h b/include/almost/kernel/molecule.h
-index e399d8d..0ea1d28 100644
---- a/include/almost/kernel/molecule.h
-+++ b/include/almost/kernel/molecule.h
-@@ -1100,7 +1100,7 @@ namespace Kernel {
- 	if(this->fragment_atoms_[i][j]>=gpos) ++this->fragment_atoms_[i][j];
- 
- 
--    return add_atom_(fd,atom,pos);
-+    return this->add_atom_(fd,atom,pos);
-   }
- 
- 
-diff --git a/include/almost/kernel/rmsd.h b/include/almost/kernel/rmsd.h
-index 0947666..210f53e 100644
---- a/include/almost/kernel/rmsd.h
-+++ b/include/almost/kernel/rmsd.h
-@@ -172,6 +172,27 @@ namespace Almost {
-     /*====================================================================*/
- 
-     template <typename float_type>
-+    float_type EPpythag(float_type a,float_type b)
-+    {
-+      /* finds sqrt(a*a+b*b) without overflow or destructive underflow */
-+
-+      float_type p,r,s,t,u;
-+
-+      p=(abs(a) > abs(b) ? abs(a) : abs(b));
-+      if (p>0) {
-+	r=(abs(a)<abs(b)?abs(a):abs(b))/p;
-+	r=r*r;
-+	for (t=4.0+r;t!=4.0;t=4.0+r) {
-+	  s=r/t;
-+	  u=1.0+2.0*s;
-+	  p=u*p;
-+	  r=(s/u)*(s/u)*r;
-+	}
-+      }
-+      return(p);
-+    }
-+
-+    template <typename float_type>
-     int EPimtql2(int n,float_type *d,float_type *e,float_type **z)
-     {
-       int i,j,k,l,m,ii,mml;
-@@ -316,27 +337,6 @@ namespace Almost {
- 
-     /*====================================================================*/
- 
--    template <typename float_type>
--    float_type EPpythag(float_type a,float_type b)
--    {
--      /* finds sqrt(a*a+b*b) without overflow or destructive underflow */
--
--      float_type p,r,s,t,u;
--
--      p=(abs(a) > abs(b) ? abs(a) : abs(b));
--      if (p>0) {
--	r=(abs(a)<abs(b)?abs(a):abs(b))/p;
--	r=r*r;
--	for (t=4.0+r;t!=4.0;t=4.0+r) {
--	  s=r/t;
--	  u=1.0+2.0*s;
--	  p=u*p;
--	  r=(s/u)*(s/u)*r;
--	}
--      }
--      return(p);
--    }
--
-     template<typename float_type>
-     inline float_type rmsd_dist(const Almost::Coor<float_type> & ref,
- 				const Almost::Coor<float_type> & to_move,
-diff --git a/src/lib/io/formostream.cpp b/src/lib/io/formostream.cpp
-index 9a98154..1469b8a 100644
---- a/src/lib/io/formostream.cpp
-+++ b/src/lib/io/formostream.cpp
-@@ -1572,9 +1572,9 @@ PDBOStream & operator<<(PDBOStream & pdb, const Molecules & molecules){
-     
-   for(int i=0;i<molecules.solvent_size();i++){
-     pdb<<molecules.solvent(i);
--    int i = molecules.solvent_size()-1;
-+    int j = molecules.solvent_size()-1;
-     sprintf(buff,
--	    "%-6s%5i\n","TER",molecules.solvent(i).atom_size()
-+	    "%-6s%5j\n","TER",molecules.solvent(i).atom_size()
- 	    +molecules.solvent(i).atom_offset());
-     pdb.stream()<<buff;
-       
diff --git a/sci-chemistry/camshift/files/1.35.0-gentoo.patch b/sci-chemistry/camshift/files/1.35.0-gentoo.patch
deleted file mode 100644
index 845325713..000000000
--- a/sci-chemistry/camshift/files/1.35.0-gentoo.patch
+++ /dev/null
@@ -1,85 +0,0 @@
- bin/Makefile.am            |  2 +-
- configure.in               | 18 +++---------------
- src/forcefield/Makefile.am |  4 ++--
- src/lib/Makefile.am        |  2 +-
- 4 files changed, 7 insertions(+), 19 deletions(-)
-
-diff --git a/bin/Makefile.am b/bin/Makefile.am
-index c9f5f40..0f1d790 100644
---- a/bin/Makefile.am
-+++ b/bin/Makefile.am
-@@ -1,4 +1,4 @@
--INCLUDES = -I../..  -I../include/almost
-+INCLUDES = -I$(top_srcdir)  -I$(top_srcdir)/include/almost
- bin_PROGRAMS=camshift
- 
- if LIBBZ2
-diff --git a/configure.in b/configure.in
-index e0d186d..9b15335 100644
---- a/configure.in
-+++ b/configure.in
-@@ -167,9 +167,6 @@ echo Constraint disabled value $
- fi
- 
- 
--#C and CPPFLAFS
--CFLAGS="-O9 -ffast-math -fomit-frame-pointer"
--CXXFLAGS="-O9 -ffast-math"
- 
- #alm_sse
- mkasm=false
-@@ -231,11 +228,6 @@ else
- echo OS ${host-os}
- fi
- 
--if test x$darwin = xtrue; then
--CFLAGS=$CFLAGS" -fast"
--CXXFLAGS=$CXXFLAGS" -fast"
--fi
--
- if test x$powerpc = xtrue; then
- AC_DEFINE([POWERPC],[],"PowerPC CPU")
- fi
-@@ -250,17 +242,13 @@ AM_CONDITIONAL(IX86, test x$ix86 = xtrue)
- 
- if test x$darwin = xtrue; then
- if test x$ix86 = xtrue; then
--CXXFLAGS=$CXXFLAGS" -msse -msse2 -mmmx"
--CFLAGS=$CFLAGS" -msse -msse2 -mmmx"
--fi
--fi
--
--if test x$darwin = xtrue; then
--if test x$ix86 = xtrue; then
- CCAS=$PWD/darwinas
- fi
- fi
- 
-+PKG_CHECK_MODULES(BLAS, blas)
-+PKG_CHECK_MODULES(LAPACK, lapack)
-+
- echo ${host} ${host-cpu}  ${host-vendor} ${host-os} $ix86 $powerpc
- AC_OUTPUT(
- 		almost.h 
-diff --git a/src/forcefield/Makefile.am b/src/forcefield/Makefile.am
-index 8d143ab..4b72814 100644
---- a/src/forcefield/Makefile.am
-+++ b/src/forcefield/Makefile.am
-@@ -1,4 +1,4 @@
--INCLUDES = -I../../include/almost
-+INCLUDES = -I$(top_srcdir)/include/almost
- 
- lib_LIBRARIES= libnbimpl.a
--libnbimpl_a_SOURCES=enefunc.c enefuncvdw.c pbcenefunc.c forcefunc.c forcefuncvdw.c pbcforcefunc.c sasaenefunc.c pbcsasaenefunc.c sasaforcefunc.c pbcsasaforcefunc.c eneforcefunc.c enefunchs.c  forcefunchs.c enefuncsoft.c forcefuncsoft.c qvdwfunc.c $(ASMF)
-\ No newline at end of file
-+libnbimpl_a_SOURCES=enefunc.c enefuncvdw.c pbcenefunc.c forcefunc.c forcefuncvdw.c pbcforcefunc.c sasaenefunc.c pbcsasaenefunc.c sasaforcefunc.c pbcsasaforcefunc.c eneforcefunc.c enefunchs.c  forcefunchs.c enefuncsoft.c forcefuncsoft.c qvdwfunc.c $(ASMF)
-diff --git a/src/lib/Makefile.am b/src/lib/Makefile.am
-index 02ee6ee..0e9001f 100644
---- a/src/lib/Makefile.am
-+++ b/src/lib/Makefile.am
-@@ -1,4 +1,4 @@
--INCLUDES=-I../../include/almost
-+INCLUDES=-I$(top_srcdir)/include/almost
- lib_LIBRARIES=libAlm.a
- PBDSOURCES = 	pdb/pdbatomline.cpp \
- 		pdb/pdbauthorline.cpp \
diff --git a/sci-chemistry/camshift/metadata.xml b/sci-chemistry/camshift/metadata.xml
deleted file mode 100644
index da36ecbfc..000000000
--- a/sci-chemistry/camshift/metadata.xml
+++ /dev/null
@@ -1,8 +0,0 @@
-<?xml version="1.0" encoding="UTF-8"?>
-<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
-<pkgmetadata>
-	<maintainer type="project">
-		<email>sci-chemistry@gentoo.org</email>
-		<name>Gentoo Chemistry Project</name>
-	</maintainer>
-</pkgmetadata>
diff --git a/sci-chemistry/chimera-bin/Manifest b/sci-chemistry/chimera-bin/Manifest
deleted file mode 100644
index 72c72bc43..000000000
--- a/sci-chemistry/chimera-bin/Manifest
+++ /dev/null
@@ -1,2 +0,0 @@
-DIST chimera-1.11.2-linux.bin 119741818 SHA256 b71e552f58f54e7881fcecae622f9bc7f1087230214ad6d4665a0aeb717e2f8e SHA512 d10ddc4ca2b2ead248cab09da4a45a4856992825e902d10f8d446960a413ebbc62d9ba6496482ca5af2c0e592fb0d02333d81721f00111db43c3de59337c9885 WHIRLPOOL 545ce9795a6bca66ccecfff6f9b9cfc7a04936fa26ae16710866a43c085d241ed72c0dc17869d81940322327ffb2cf91ed17d2151907b8469566864ad6d93787
-DIST chimera-1.11.2-linux_x86_64.bin 121926923 SHA256 d8bb4d0e049762e1b3fc1fab950478881464c9cdb318909269ac7a081e7b44bd SHA512 d9594bcf0812adbdf82c2706f9c14dba74286ed6c1390503c9af84d356531f97be85cc13cc8a9ffb500092e9356c285b93d19798ed066822d1a3c37fb5ae9197 WHIRLPOOL 387c0fce9d189adb13d2ae7de059aef54e61347ec35df9d799f2524c61c9b5e6d0172fdf3731e99e6c3dcbefef3a658912122501ab69eed6fbb4b748f5a203ef
diff --git a/sci-chemistry/chimera-bin/chimera-bin-1.11.2.ebuild b/sci-chemistry/chimera-bin/chimera-bin-1.11.2.ebuild
deleted file mode 100644
index 74176f329..000000000
--- a/sci-chemistry/chimera-bin/chimera-bin-1.11.2.ebuild
+++ /dev/null
@@ -1,95 +0,0 @@
-# Copyright 1999-2016 Gentoo Foundation
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=6
-
-inherit eutils
-
-DESCRIPTION="An extensible Molecular Modelling System"
-HOMEPAGE="http://www.cgl.ucsf.edu/chimera"
-SRC_URI="
-	amd64? ( chimera-${PV}-linux_x86_64.bin )
-	x86? ( chimera-${PV}-linux.bin )"
-
-SLOT="0"
-LICENSE="chimera"
-KEYWORDS="~amd64 ~x86 ~amd64-linux ~x86-linux"
-IUSE=""
-
-DEPEND="prefix? ( dev-util/patchelf )"
-RDEPEND="
-	dev-lang/tcl
-	dev-lang/tk
-	dev-libs/expat
-	dev-libs/libotf
-	dev-libs/openssl:0
-	dev-libs/libpcre
-	sys-libs/zlib
-	media-libs/fontconfig
-	media-libs/freetype
-	media-libs/ftgl
-	media-libs/libpng:1.2
-	media-libs/tiff
-	media-libs/tiff:3
-	sci-libs/hdf5
-	sci-libs/xdrfile
-	sys-devel/gcc[openmp,fortran]
-	virtual/jpeg
-	virtual/glu
-	virtual/opengl
-	x11-libs/libX11
-	x11-libs/libICE
-	x11-libs/libXext
-	x11-libs/libXft
-	x11-libs/libXmu
-	x11-libs/libXpm
-	x11-libs/libXrender
-	x11-libs/libSM
-	x11-libs/libXt
-	x11-libs/libGLw"
-
-S="${WORKDIR}"
-
-RESTRICT="fetch strip"
-
-QA_PREBUILT="opt/.*"
-
-pkg_nofetch() {
-	elog "Please visit"
-	elog "http://www.cgl.ucsf.edu/chimera/download.html"
-	elog "or"
-	elog "http://www.cgl.ucsf.edu/chimera/olddownload.html"
-	elog "and download ${A} into ${DISTDIR}"
-}
-
-src_unpack() {
-	cp "${DISTDIR}"/${A} ${A}.zip
-	unzip ${A}.zip || die
-}
-
-src_install() {
-	chmod +x ./chimera.bin
-	dodir /opt/
-	./chimera.bin -d foo || die
-	doicon foo/chimeraIcon.png
-	mv foo "${ED}/opt/${PN}" || die
-
-	cat >> "${T}"/chimera <<- EOF
-	#!${EPREFX}/bin/bash
-
-	export PATH="${EPREFIX}/opt/${PN}/bin:\${PATH}"
-	"${EPREFIX}/opt/${PN}/bin/chimera" \$@
-	EOF
-
-	exeinto /opt/bin/
-	doexe "${T}"/chimera
-
-	make_desktop_entry "${EPREFIX}/opt/bin/chimera" Chimera chimeraIcon
-
-	if use prefix; then
-		local i
-		for i in "${ED}"/opt/${PN}/bin/{tiffcp,povray,al2co} "${ED}"/opt/${PN}/lib/*.so; do
-			patchelf --set-rpath "${EPREFIX}/usr/lib:${EPREFIX}/opt/${PN}/lib" "${i}" || die
-		done
-	fi
-}
diff --git a/sci-chemistry/chimera-bin/metadata.xml b/sci-chemistry/chimera-bin/metadata.xml
deleted file mode 100644
index da36ecbfc..000000000
--- a/sci-chemistry/chimera-bin/metadata.xml
+++ /dev/null
@@ -1,8 +0,0 @@
-<?xml version="1.0" encoding="UTF-8"?>
-<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
-<pkgmetadata>
-	<maintainer type="project">
-		<email>sci-chemistry@gentoo.org</email>
-		<name>Gentoo Chemistry Project</name>
-	</maintainer>
-</pkgmetadata>
diff --git a/sci-chemistry/chimera/Manifest b/sci-chemistry/chimera/Manifest
new file mode 100644
index 000000000..953fae5f9
--- /dev/null
+++ b/sci-chemistry/chimera/Manifest
@@ -0,0 +1,3 @@
+DIST Chimera512.png 68464 BLAKE2B 51797728b8b9421ab6e42e57bb60881a706d17eed09cbef57506f706b7ebab6511397f90834d15efaea5e86a22fc2ff9e55cf42c7a87d6166716444252d18f49 SHA512 6ed0dd8bd1b5a6b164f80acc1d7e1a91629513b147d37472e1831b657201a3f25c1c0c9a1b44bf565afaa4aa99469910d1ac307a45a80b9a12d0554e1812e2c5
+DIST chimera-1.17.1-linux_x86_64.bin 149832020 BLAKE2B 01e78d09a3373a3d927c93daa03d0c17473c18079afd989a29afaad5c56aa57bbfeb968bcef42eb50924e1cde67e939c92a545080c0e7b55549c30e43aae564d SHA512 f6df3ad320f09b3f8d918660a4a7596505c2a97ac0d60a4f6ef9c414851a90bb59ccba9728d5a71df93404b8c6ecf99ab9dca84befcfa10e60285f3a33e3c3bc
+DIST chimera-1.17.3-linux_x86_64.bin 155528316 BLAKE2B 09caddbac9a518606b8065a19840fd2f5e3a57cbb529bea2e4b63cb83ecd91105c1de34dc3f1139382fc80f14e69b28c39152d9b15e16c39a08732ebcd374c51 SHA512 cfbf42dd3aa030db0619bf5750d08ba94acc53f54a890109d422a675394616afba9c85779e5d62bcd4ad83db4a7cfcf8190c2c42c84719c991061859c87288b7
diff --git a/sci-chemistry/chimera/chimera-1.17.1.ebuild b/sci-chemistry/chimera/chimera-1.17.1.ebuild
new file mode 100644
index 000000000..919350ac9
--- /dev/null
+++ b/sci-chemistry/chimera/chimera-1.17.1.ebuild
@@ -0,0 +1,93 @@
+# Copyright 1999-2021 Gentoo Authors
+# Distributed under the terms of the GNU General Public License v2
+
+EAPI=8
+inherit desktop xdg
+
+DESCRIPTION="Next generation molecular visualization program from RBVI"
+HOMEPAGE="https://www.cgl.ucsf.edu/chimera/"
+SRC_URI="chimera-${PV}-linux_x86_64.bin
+	fetch+http://svn.cgl.ucsf.edu/svn/chimera/trunk/icons/chimera/Chimera512.png"
+
+SLOT="0"
+LICENSE="chimera"
+KEYWORDS="~amd64 ~x86"
+
+RESTRICT="fetch mirror strip"
+QA_PREBUILT="*"
+
+DEPEND=""
+BDEPEND=""
+RDEPEND="
+	dev-lang/tcl
+	dev-lang/tk
+	dev-libs/expat
+	dev-libs/libotf
+	dev-libs/openssl:0
+	dev-libs/libpcre
+	sys-libs/zlib
+	media-libs/fontconfig
+	media-libs/freetype
+	media-libs/ftgl
+	media-libs/libpng
+	media-libs/tiff
+	sci-libs/hdf5
+	sys-devel/gcc[openmp,fortran]
+	media-libs/libjpeg-turbo
+	virtual/glu
+	virtual/opengl
+	x11-libs/libX11
+	x11-libs/libICE
+	x11-libs/libXext
+	x11-libs/libXft
+	x11-libs/libXmu
+	x11-libs/libXpm
+	x11-libs/libXrender
+	x11-libs/libSM
+	x11-libs/libXt
+	x11-libs/libGLw
+	virtual/libcrypt:=
+"
+
+S="${WORKDIR}"
+
+pkg_nofetch() {
+	elog "Please visit"
+	elog "https://www.cgl.ucsf.edu/chimera/download.html"
+	elog "and download chimera-${PV}-linux_x86_64.bin into your DISTDIR"
+}
+
+src_unpack() {
+	cp "${DISTDIR}"/chimera-${PV}-linux_x86_64.bin chimera-${PV}-linux_x86_64.bin.zip
+	unzip chimera-${PV}-linux_x86_64.bin.zip || die
+}
+
+src_install() {
+	chmod +x ./chimera.bin
+	dodir /opt/
+	./chimera.bin -d foo || die
+	newicon "${DISTDIR}"/Chimera512.png Chimera.png
+	make_desktop_entry "${EPREFIX}/opt/bin/chimera" Chimera Chimera
+	mv foo "${ED}/opt/${PN}" || die
+
+	cat >> "${T}"/chimera <<- EOF
+	#!${EPREFX}/bin/bash
+
+	export PATH="${EPREFIX}/opt/${PN}/bin:\${PATH}"
+	"${EPREFIX}/opt/${PN}/bin/chimera" \$@
+	EOF
+
+	exeinto /opt/bin/
+	doexe "${T}"/chimera
+
+	# point the symlink to the correct location
+	rm "${ED}/opt/chimera/include/ft2build.h" || die
+	dosym ../../../usr/include/freetype2/ft2build.h opt/chimera/include/ft2build.h
+
+	if use prefix; then
+		local i
+		for i in "${ED}"/opt/${PN}/bin/{tiffcp,povray,al2co} "${ED}"/opt/${PN}/lib/*.so; do
+			patchelf --set-rpath "${EPREFIX}/usr/lib:${EPREFIX}/opt/${PN}/lib" "${i}" || die
+		done
+	fi
+}
diff --git a/sci-chemistry/chimera/chimera-1.17.3.ebuild b/sci-chemistry/chimera/chimera-1.17.3.ebuild
new file mode 100644
index 000000000..4fdafd361
--- /dev/null
+++ b/sci-chemistry/chimera/chimera-1.17.3.ebuild
@@ -0,0 +1,93 @@
+# Copyright 1999-2021 Gentoo Authors
+# Distributed under the terms of the GNU General Public License v2
+
+EAPI=8
+inherit desktop xdg
+
+DESCRIPTION="Next generation molecular visualization program from RBVI"
+HOMEPAGE="https://www.cgl.ucsf.edu/chimera/"
+SRC_URI="${P}-linux_x86_64.bin
+	mirror+https://dev.gentoo.org/~pacho/${PN}/Chimera512.png"
+
+SLOT="0"
+LICENSE="chimera"
+KEYWORDS="~amd64 ~x86"
+
+RESTRICT="fetch mirror strip"
+QA_PREBUILT="*"
+
+DEPEND=""
+BDEPEND=""
+RDEPEND="
+	dev-lang/tcl
+	dev-lang/tk
+	dev-libs/expat
+	dev-libs/libotf
+	dev-libs/openssl:0
+	dev-libs/libpcre
+	sys-libs/zlib
+	media-libs/fontconfig
+	media-libs/freetype
+	media-libs/ftgl
+	media-libs/libpng
+	media-libs/tiff
+	sci-libs/hdf5
+	sys-devel/gcc[openmp,fortran]
+	media-libs/libjpeg-turbo
+	virtual/glu
+	virtual/opengl
+	x11-libs/libX11
+	x11-libs/libICE
+	x11-libs/libXext
+	x11-libs/libXft
+	x11-libs/libXmu
+	x11-libs/libXpm
+	x11-libs/libXrender
+	x11-libs/libSM
+	x11-libs/libXt
+	x11-libs/libGLw
+	virtual/libcrypt:=
+"
+
+S="${WORKDIR}"
+
+pkg_nofetch() {
+	elog "Please visit"
+	elog "https://www.cgl.ucsf.edu/chimera/download.html"
+	elog "and download ${P}-linux_x86_64.bin into your DISTDIR"
+}
+
+src_unpack() {
+	cp "${DISTDIR}"/${P}-linux_x86_64.bin ${P}-linux_x86_64.bin.zip
+	unzip ${P}-linux_x86_64.bin.zip || die
+}
+
+src_install() {
+	chmod +x ./chimera.bin
+	dodir /opt/
+	./chimera.bin -d foo || die
+	newicon "${DISTDIR}"/Chimera512.png Chimera.png
+	make_desktop_entry "${EPREFIX}/opt/bin/chimera" Chimera Chimera
+	mv foo "${ED}/opt/${PN}" || die
+
+	cat >> "${T}"/chimera <<- EOF
+	#!${EPREFX}/bin/bash
+
+	export PATH="${EPREFIX}/opt/${PN}/bin:\${PATH}"
+	"${EPREFIX}/opt/${PN}/bin/chimera" \$@
+	EOF
+
+	exeinto /opt/bin/
+	doexe "${T}"/chimera
+
+	# point the symlink to the correct location
+	rm "${ED}/opt/chimera/include/ft2build.h" || die
+	dosym ../../../usr/include/freetype2/ft2build.h opt/chimera/include/ft2build.h
+
+	if use prefix; then
+		local i
+		for i in "${ED}"/opt/${PN}/bin/{tiffcp,povray,al2co} "${ED}"/opt/${PN}/lib/*.so; do
+			patchelf --set-rpath "${EPREFIX}/usr/lib:${EPREFIX}/opt/${PN}/lib" "${i}" || die
+		done
+	fi
+}
diff --git a/sci-chemistry/chimera/metadata.xml b/sci-chemistry/chimera/metadata.xml
new file mode 100644
index 000000000..5c83ce208
--- /dev/null
+++ b/sci-chemistry/chimera/metadata.xml
@@ -0,0 +1,12 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
+<pkgmetadata>
+	<maintainer type="person">
+		<email>pacho@gentoo.org</email>
+		<name>Pacho Ramos</name>
+	</maintainer>
+	<maintainer type="project">
+		<email>sci-chemistry@gentoo.org</email>
+		<name>Gentoo Chemistry Project</name>
+	</maintainer>
+</pkgmetadata>
diff --git a/sci-chemistry/chooch/Manifest b/sci-chemistry/chooch/Manifest
deleted file mode 100644
index b57a4f17b..000000000
--- a/sci-chemistry/chooch/Manifest
+++ /dev/null
@@ -1 +0,0 @@
-DIST chooch-5.0.2.tar.gz 3057641 BLAKE2B 00dce8a0cf8aa2b057b4a0c7b69f5862b3030b824ec4a2ba3013667734e92c4f480601e5a1434180cdf3cd3bead3e44d7f98ebf428ad702f4d6d663ca78868dc SHA512 028d0b57e5f8e17a23e7573e9ce4d187cde6fc546ea83e43e3e497f769ac99b60a21ea811d3fa41180089b3bd05df535d536504f0ee677d09c385c37d97b0818
diff --git a/sci-chemistry/chooch/chooch-5.0.2-r1.ebuild b/sci-chemistry/chooch/chooch-5.0.2-r1.ebuild
deleted file mode 100644
index 227e947d5..000000000
--- a/sci-chemistry/chooch/chooch-5.0.2-r1.ebuild
+++ /dev/null
@@ -1,53 +0,0 @@
-# Copyright 1999-2014 Gentoo Foundation
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=5
-
-AUTOTOOLS_AUTORECONF=true
-
-inherit autotools-utils multilib toolchain-funcs
-
-DESCRIPTION="Automatically determine values of the anomalous scattering factors"
-HOMEPAGE="http://www.gwyndafevans.co.uk/id2.html"
-SRC_URI="ftp://ftp.ccp4.ac.uk/${PN}/${PV}/packed/${P}.tar.gz"
-
-SLOT="0"
-LICENSE="GPL-2"
-KEYWORDS="~amd64 ~x86"
-IUSE="examples"
-
-RDEPEND="
-	sci-libs/gsl
-	sci-libs/Cgraph
-	sci-libs/pgplot"
-DEPEND="${RDEPEND}"
-
-S="${WORKDIR}"/${PN}/${P}
-
-PATCHES=(
-	"${FILESDIR}"/${PV}-Makefile.am.patch
-	"${FILESDIR}"/${PV}-aclocal.patch
-)
-
-AT_M4DIR="${S}"
-
-DOCS=( doc/${PN}.pdf )
-
-src_configure() {
-	local myeconfargs=(
-		--with-pgplot-prefix="${EPREFIX}/usr"
-		--with-cgraph-prefix="${EPREFIX}/usr"
-		--with-gsl-prefix="${EPREFIX}/usr"
-		--disable-gsltest
-	)
-	autotools-utils_src_configure
-}
-
-src_install() {
-	autotools-utils_src_install
-
-	if	use examples; then
-		insinto /usr/share/${PN}
-		doins -r examples
-	fi
-}
diff --git a/sci-chemistry/chooch/files/5.0.2-Makefile.am.patch b/sci-chemistry/chooch/files/5.0.2-Makefile.am.patch
deleted file mode 100644
index ca6bcafb1..000000000
--- a/sci-chemistry/chooch/files/5.0.2-Makefile.am.patch
+++ /dev/null
@@ -1,30 +0,0 @@
---- Makefile.am	2004-10-20 14:47:12.000000000 +0200
-+++ Makefile.am.new	2009-05-13 12:14:09.000000000 +0200
-@@ -1,4 +1,4 @@
--bin_PROGRAMS = chooch
-+bin_PROGRAMS = chooch chooch-pg
- 
- chooch_SOURCES = main.c      fluread.c printbanner.c minmax.c  spline.c \
-         mucal.c     fdprime.c smooth.c      fits.c    normalize.c \
-@@ -12,4 +12,8 @@
- 
- chooch_LDADD = $(GSL_LIBS) $(PGPLOT_LIBS) $(CGRAPH_LIBS)
- 
-+chooch_pg_CFLAGS = -DPGPLOT $(GSL_CFLAGS) $(PGPLOT_CFLAGS) $(CGRAPH_CFLAGS)
-+
-+chooch_pg_LDADD = $(GSL_LIBS) $(PGPLOT_LIBS) $(CGRAPH_LIBS)
-+
- man_MANS = man/chooch.1
---- Makefile.am	2009-05-13 12:16:05.000000000 +0200
-+++ Makefile.am.new	2009-05-13 12:18:33.000000000 +0200
-@@ -1,5 +1,10 @@
- bin_PROGRAMS = chooch chooch-pg
- 
-+chooch_pg_SOURCES = main.c      fluread.c printbanner.c minmax.c  spline.c \
-+        mucal.c     fdprime.c smooth.c      fits.c    normalize.c \
-+        checks.c    usage.c   integrate.c   psplot.c  selwavel.c \
-+        copyright.c toplot.c  license.c
-+
- chooch_SOURCES = main.c      fluread.c printbanner.c minmax.c  spline.c \
-         mucal.c     fdprime.c smooth.c      fits.c    normalize.c \
-         checks.c    usage.c   integrate.c   psplot.c  selwavel.c \
diff --git a/sci-chemistry/chooch/files/5.0.2-Makefile.patch b/sci-chemistry/chooch/files/5.0.2-Makefile.patch
deleted file mode 100644
index 89eaf95ef..000000000
--- a/sci-chemistry/chooch/files/5.0.2-Makefile.patch
+++ /dev/null
@@ -1,45 +0,0 @@
---- Makefile	2004-10-13 15:17:38.000000000 +0200
-+++ Makefile.new	2009-05-12 21:24:48.000000000 +0200
-@@ -21,21 +21,21 @@
- #INCLUDE   = /users/opd14/Gwyndaf/include
- GSLDIR = /usr/local/lib
- CGRAPHDIR = /usr/local/lib
--BINDIR    = /home/ge73/bin
-+BINDIR    = /usr/bin
- INCLUDE   = /usr/local/pgplot
- #PGPLOTDIR = /home/sci/software/misc/pgplot
- X11LIBDIR  = /usr/X11R6/lib
- ######################################
- #
- CGRAPH = -lcgraph
--LIBS = -lgsl -lgslcblas -lX11
-+LIBS = -lgsl -lgslcblas -lX11 -L/usr/GENTOO_LIBDIR $(PGLIBS) $(CGRAPH) -lm -ldl -lpthread
- PGLIBS =  -lcpgplot -lpgplot
--EXE    = chooch-5.0.2.$(ARCH)
--EXEPG    = chooch-5.0.2-pg.$(ARCH)
-+EXE    = chooch
-+EXEPG    = chooch-pg
- #
- # How to compile and link
- #
--include Makefile.$(ARCH)
-+#include Makefile.$(ARCH)
- #
- # Basic definitions
- #
-@@ -51,13 +51,13 @@
- #
- #
- chooch : clean ${OBJECTS} Makefile
--	$(CC) -o ${EXE} ${OBJECTS} $(LDFLAGS)
-+	$(CC) $(LDFLAGS) -o ${EXE} ${OBJECTS} $(LIBS)
- 
- chooch-pg : 
- 	make chooch-with-pgplot "CFLAGS = $(CFLAGS) -DPGPLOT"
- 
- chooch-with-pgplot : clean ${OBJECTS} Makefile
--	$(FC) -v $(CFLAGS) -o ${EXEPG} ${OBJECTS} $(LDFLAGS)
-+	$(CC) $(CFLAGS) $(LDFLAGS) -o ${EXEPG} ${OBJECTS} $(LIBS)
- #
- all: chooch chooch-pg
- #
diff --git a/sci-chemistry/chooch/files/5.0.2-aclocal.patch b/sci-chemistry/chooch/files/5.0.2-aclocal.patch
deleted file mode 100644
index 84dbaed9b..000000000
--- a/sci-chemistry/chooch/files/5.0.2-aclocal.patch
+++ /dev/null
@@ -1,11 +0,0 @@
---- pgplot.m4	2004-10-18 13:13:21.000000000 +0200
-+++ pgplot.m4.new	2009-05-13 11:52:43.000000000 +0200
-@@ -15,7 +15,7 @@
- 
- if test "x$pgplot_prefix" != x ; then
-   PGPLOT_CFLAGS="-I$pgplot_prefix/include"
--  PGPLOT_LIBS="-L$pgplot_prefix/lib -lpgplot"
-+  PGPLOT_LIBS="-L$pgplot_prefix/lib -lpgplot -lcpgplot"
- fi
- 
- AC_MSG_CHECKING([for libpgplot])
diff --git a/sci-chemistry/chooch/metadata.xml b/sci-chemistry/chooch/metadata.xml
deleted file mode 100644
index da36ecbfc..000000000
--- a/sci-chemistry/chooch/metadata.xml
+++ /dev/null
@@ -1,8 +0,0 @@
-<?xml version="1.0" encoding="UTF-8"?>
-<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
-<pkgmetadata>
-	<maintainer type="project">
-		<email>sci-chemistry@gentoo.org</email>
-		<name>Gentoo Chemistry Project</name>
-	</maintainer>
-</pkgmetadata>
diff --git a/sci-chemistry/concoord/Manifest b/sci-chemistry/concoord/Manifest
index 5607cb51b..053b53267 100644
--- a/sci-chemistry/concoord/Manifest
+++ b/sci-chemistry/concoord/Manifest
@@ -1,4 +1,2 @@
-DIST concoord2.1_linux_i386.tgz 2948256 BLAKE2B 862de32d37a1680fbc3bdd7512127c2491e421ac63c716dc24ca43e58123ed3f1c00a6d4cb63f91a15d41a3ac0d885c08950de7896abc841167da65a99ce9d80 SHA512 2af10b14f24305dbea4ff12df86ca9bc5e8d2957873756b2f9b5ee57fc7b8db91a787ff09d70ce70a1c3d9278a142474c893250944aa3b8c83862311ed3e3cef
-DIST concoord2.1_linux_x86_64.tgz 3352731 BLAKE2B d3ed53866053474378b22bb186822a46c01be4506f09930d26476814591d8c6474d7eff6797c1738c240c1cd8fc840849b9150f30c73aa8f826e246460313251 SHA512 cfb30d7d0950e5978ea0a908a0e607b675333e267ee7da6103ead1b27ceb4dedde42daef3f7027c47e40e01cd247f3e57c5fa13eb76c0f3ac7fa1868f5fb8bf5
 DIST concoord_2.1.2_linux32.tgz 1193266 BLAKE2B 2adb51fdba074d608a2dc172556d5a0f37df2d8b7259b36da7d4330ded4a81f104b2c0ba1f18505141204d507f60b9bbfeffbc91eb2d129918fec9ad28ddde6c SHA512 d74f2fdbb6184f79d3c0770cfa01324dd52448f3a865f5fb379a51431024b843537b8de551aacd2b0117736f7cb2412379cf23e765716969c1ab3069e6e75ea2
 DIST concoord_2.1.2_linux64.tgz 1431558 BLAKE2B 6e8d8d42bd629a79e86e84874590a66dc8b30269bda18fb75b91e3dcb84b4e8c36d61177e10282b0421f68d3828cd407f0d81f976f8aa32f28bd9dfb34506fd1 SHA512 e625e10ebe2e5ef6a84af3fe665e792d59ffed3df009f19d66ec0972bd88ec91167e3ec0eee9a72b1c35ba0a85ec70fa5420a7718b83e238b167ad31d95303cf
diff --git a/sci-chemistry/concoord/concoord-2.1.2.ebuild b/sci-chemistry/concoord/concoord-2.1.2.ebuild
index 1a94efd6e..56de61279 100644
--- a/sci-chemistry/concoord/concoord-2.1.2.ebuild
+++ b/sci-chemistry/concoord/concoord-2.1.2.ebuild
@@ -1,18 +1,17 @@
-# Copyright 1999-2014 Gentoo Foundation
+# Copyright 1999-2021 Gentoo Authors
 # Distributed under the terms of the GNU General Public License v2
 
-EAPI=5
+EAPI=7
 
 DESCRIPTION="Protein conformations around a known structure based on geometric restrictions"
-HOMEPAGE="http://www.mpibpc.mpg.de/groups/de_groot/concoord/concoord.html"
+HOMEPAGE="https://www3.mpibpc.mpg.de/groups/de_groot/concoord/concoord.html"
 SRC_URI="
-	amd64? ( http://www3.mpibpc.mpg.de/groups/de_groot/${PN}/${PN}_${PV}_linux64.tgz )
-	x86? ( http://www3.mpibpc.mpg.de/groups/de_groot/${PN}/${PN}_${PV}_linux32.tgz )"
+	amd64? ( https://www3.mpibpc.mpg.de/groups/de_groot/${PN}/${PN}_${PV}_linux64.tgz )
+	x86? ( https://www3.mpibpc.mpg.de/groups/de_groot/${PN}/${PN}_${PV}_linux32.tgz )"
 
 SLOT="0"
 KEYWORDS="-* ~amd64 ~x86 ~amd64-linux ~x86-linux"
 LICENSE="all-rights-reserved"
-IUSE=""
 
 QA_PREBUILT="opt/${PN}/bin/*"
 
diff --git a/sci-chemistry/concoord/concoord-2.1.ebuild b/sci-chemistry/concoord/concoord-2.1.ebuild
deleted file mode 100644
index 1a7728ddd..000000000
--- a/sci-chemistry/concoord/concoord-2.1.ebuild
+++ /dev/null
@@ -1,33 +0,0 @@
-# Copyright 1999-2015 Gentoo Foundation
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=5
-
-DESCRIPTION="Protein conformations around a known structure based on geometric restrictions"
-HOMEPAGE="http://www.mpibpc.mpg.de/groups/de_groot/concoord/concoord.html"
-SRC_URI="
-	amd64? ( http://www.mpibpc.mpg.de/groups/de_groot/concoord/concoord2.1_linux_x86_64.tgz )
-	x86? ( http://www.mpibpc.mpg.de/groups/de_groot/concoord/concoord2.1_linux_i386.tgz )"
-
-SLOT="0"
-KEYWORDS="-* ~amd64 ~x86 ~amd64-linux ~x86-linux"
-LICENSE="all-rights-reserved"
-IUSE=""
-
-QA_PREBUILT="opt/${PN}/bin/*"
-
-S="${WORKDIR}"/${PN}${PV}
-
-src_install() {
-	insinto /opt/${PN}/
-	rm lib/*.a || die
-	doins -r lib
-	exeinto /opt/${PN}/bin
-	doexe bin/*
-	cat >> "${T}"/60${PN} <<- EOF
-	CONCOORDLIB="${EPREFIX}/opt/${PN}/lib"
-	CONCOORDBIN="${EPREFIX}/opt/${PN}/bin"
-	PATH="${EPREFIX}/opt/${PN}/bin"
-	EOF
-	doenvd "${T}"/60${PN}
-}
diff --git a/sci-chemistry/coot/Manifest b/sci-chemistry/coot/Manifest
deleted file mode 100644
index 20ba2aa9c..000000000
--- a/sci-chemistry/coot/Manifest
+++ /dev/null
@@ -1 +0,0 @@
-DIST greg-data.tar.gz 8677037 BLAKE2B bb2eac183598fed429c4977f9512e90335ccb988f154a3a29985668e6d3a90a19cb77ec61e0453e7294243b8dffd9b5ef6bb318bac2280b26eab37e2de25a18a SHA512 28396a5fa64af61e8932b565c6593ed27c4708e6a59158d62c94005bea9fa8c46562b6caba97011209a40705e5ec6711b949138dd8a23bb954df2ab4dfa9bb33
diff --git a/sci-chemistry/coot/coot-9999.ebuild b/sci-chemistry/coot/coot-9999.ebuild
deleted file mode 100644
index f13e9b681..000000000
--- a/sci-chemistry/coot/coot-9999.ebuild
+++ /dev/null
@@ -1,177 +0,0 @@
-# Copyright 1999-2018 Gentoo Authors
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=6
-
-PYTHON_COMPAT=( python2_7 )
-
-inherit autotools git-r3 python-single-r1 toolchain-funcs versionator
-
-MY_S2_PV=$(replace_version_separator 2 - ${PV})
-MY_S2_P=${PN}-${MY_S2_PV/pre1/pre-1}
-MY_S_P=${MY_S2_P}-${PR/r/revision-}
-MY_PV=${PV}
-MY_P=${PN}-${MY_PV}
-
-DESCRIPTION="Crystallographic Object-Oriented Toolkit"
-HOMEPAGE="https://www2.mrc-lmb.cam.ac.uk/Personal/pemsley/coot/"
-SRC_URI="test? ( https://www2.mrc-lmb.cam.ac.uk/Personal/pemsley/coot/data/greg-data.tar.gz )"
-EGIT_REPO_URI="https://github.com/pemsley/coot.git"
-
-SLOT="0"
-LICENSE="GPL-3"
-KEYWORDS=""
-IUSE="+openmp static-libs test"
-
-REQUIRED_USE="${PYTHON_REQUIRED_USE}"
-
-AUTOTOOLS_IN_SOURCE_BUILD=1
-
-SCIDEPS="
-	sci-libs/libccp4
-	sci-libs/clipper
-	>=sci-libs/coot-data-2
-	>=sci-libs/gsl-1.3
-	sci-libs/fftw:2.1=
-	sci-libs/mmdb:2
-	sci-libs/monomer-db
-	sci-libs/ssm
-	sci-chemistry/reduce
-	sci-chemistry/probe"
-
-XDEPS="
-	gnome-base/libgnomecanvas
-	gnome-base/librsvg:2
-	media-libs/libpng:0=
-	media-libs/freeglut
-	x11-libs/gtk+:2
-	x11-libs/goocanvas:0
-	x11-libs/gtkglext
-	virtual/opengl"
-
-SCHEMEDEPS="
-	dev-scheme/net-http
-	dev-scheme/guile-gui
-	>=dev-scheme/guile-lib-0.1.6
-	dev-scheme/guile-www
-	>=x11-libs/guile-gtk-2.1"
-
-RDEPEND="
-	${SCIDEPS}
-	${XDEPS}
-	${SCHEMEDEPS}
-	${PYTHON_DEPS}
-	dev-db/sqlite:3
-	dev-libs/boost:0=[python,${PYTHON_USEDEP}]
-	dev-libs/glib:2
-	>=dev-libs/gmp-4.2.2-r2:0=
-	dev-python/pygobject:2[${PYTHON_USEDEP}]
-	dev-python/pygtk:2[${PYTHON_USEDEP}]
-	>=net-misc/curl-7.19.6
-	net-dns/libidn:0
-	sys-libs/readline:0=
-	"
-DEPEND="${RDEPEND}
-	virtual/pkgconfig
-	>=sys-devel/libtool-2.4-r2
-	dev-lang/swig
-	sys-devel/bc
-	test? ( dev-scheme/greg )"
-
-pkg_setup() {
-	if use openmp; then
-		tc-has-openmp || die "Please use an OPENMP capable compiler"
-	fi
-	python-single-r1_pkg_setup
-}
-
-PATCHES=(
-	"${FILESDIR}"/${P}-desktop.patch
-	"${FILESDIR}"/${P}-sandbox-icons.patch
-	"${FILESDIR}"/${P}-libtool.patch
-	"${FILESDIR}"/${P}-libguile.patch
-)
-
-src_unpack() {
-	git-r3_src_unpack
-	if use test; then
-		cd "${S}" || die
-		unpack ${A}
-		ln -sf . "${S}"/coot-ccp4 || die
-	fi
-}
-
-src_prepare() {
-	sed \
-		-e '/export LD_LIBRARY/s:^:#:g' \
-		-i src/coot.in || die
-
-	sed \
-		-e "s:AM_COOT_SYS_BUILD_TYPE:COOT_SYS_BUILD_TYPE=Gentoo-Linux-${EPYTHON}-gtk2 ; AC_MSG_RESULT([\$COOT_SYS_BUILD_TYPE]); AC_SUBST(COOT_SYS_BUILD_TYPE):g" \
-		-i configure.ac || die
-
-	default
-	eautoreconf
-}
-
-src_configure() {
-	# All the --with's are used to activate various parts.
-	# Yes, this is broken behavior.
-	local myeconfargs=(
-		--with-goocanvas-prefix="${EPREFIX}/usr"
-		--with-guile="${EPREFIX}/usr"
-		--with-python="${EPREFIX}/usr"
-		--with-guile-gtk
-		--with-pygtk="${EPREFIX}/usr"
-		--with-sqlite3
-		--with-boost="${EPREFIX}/usr"
-		)
-	econf ${myeconfargs[@]}
-}
-
-src_test() {
-	source "${EPREFIX}/etc/profile.d/40ccp4.setup.sh"
-	mkdir "${T}"/coot_test || die
-
-	export COOT_STANDARD_RESIDUES="${S}/standard-residues.pdb"
-	export COOT_SCHEME_DIR="${S}/scheme/"
-	export COOT_RESOURCES_FILE="${S}/cootrc"
-	export COOT_PIXMAPS_DIR="${S}/pixmaps/"
-	export COOT_DATA_DIR="${S}/"
-	export COOT_PYTHON_DIR="${S}/python/"
-	export PYTHONPATH="${COOT_PYTHON_DIR}:${S}/src:${PYTHONPATH}"
-	export PYTHONHOME="${EPREFIX}"/usr/
-	export CCP4_SCR="${T}"/coot_test/
-	export CLIBD_MON="${EPREFIX}/usr/share/data/monomers/"
-	export COOT_REF_STRUCTS="${EPREFIX}/usr/share/data/monomers/"
-	export SYMINFO="${S}/syminfo.lib"
-
-	export COOT_TEST_DATA_DIR="${S}"/greg-data/
-
-	cat > command-line-greg.scm <<- EOF
-	(use-modules (ice-9 greg))
-		(set! greg-tools (list "greg-tests"))
-			(set! greg-debug #t)
-			(set! greg-verbose 5)
-			(let ((r (greg-test-run)))
-				(if r
-				(coot-real-exit 0)
-				(coot-real-exit 1)))
-	EOF
-
-	einfo "Running test with following paths ..."
-	einfo "COOT_STANDARD_RESIDUES $COOT_STANDARD_RESIDUES"
-	einfo "COOT_SCHEME_DIR $COOT_SCHEME_DIR"
-	einfo "COOT_RESOURCES_FILE $COOT_RESOURCES_FILE"
-	einfo "COOT_PIXMAPS_DIR $COOT_PIXMAPS_DIR"
-	einfo "COOT_DATA_DIR $COOT_DATA_DIR"
-	einfo "COOT_PYTHON_DIR $COOT_PYTHON_DIR"
-	einfo "PYTHONPATH $PYTHONPATH"
-	einfo "PYTHONHOME $PYTHONHOME"
-	einfo "CCP4_SCR ${CCP4_SCR}"
-	einfo "CLIBD_MON ${CLIBD_MON}"
-	einfo "SYMINFO ${SYMINFO}"
-
-	"${S}"/src/coot-bin --no-graphics --script command-line-greg.scm || die
-	"${S}"/src/coot-bin --no-graphics --script python-tests/coot_unittest.py || die
-}
diff --git a/sci-chemistry/coot/files/coot-9999-desktop.patch b/sci-chemistry/coot/files/coot-9999-desktop.patch
deleted file mode 100644
index c264dd5a7..000000000
--- a/sci-chemistry/coot/files/coot-9999-desktop.patch
+++ /dev/null
@@ -1,21 +0,0 @@
- coot.desktop | 7 +++----
- 1 file changed, 3 insertions(+), 4 deletions(-)
-
-diff --git a/coot.desktop b/coot.desktop
-index 74aecf3..8668018 100644
---- a/coot.desktop
-+++ b/coot.desktop
-@@ -1,10 +1,9 @@
- [Desktop Entry]
- Type=Application
--Encoding=UTF-8
- Name=Coot
- Comment=Macromolecular model builder
- Exec=coot
--Icon=coot.png
-+Icon=coot
- Terminal=true
--Categories=Science;Graphics
--MimeType=chemical/x-pdb;chemical/x-mmcif;chemical/x-mdl-molfile
-+Categories=Science;Graphics;
-+MimeType=chemical/x-pdb;chemical/x-mmcif;chemical/x-mdl-molfile;
diff --git a/sci-chemistry/coot/files/coot-9999-libguile.patch b/sci-chemistry/coot/files/coot-9999-libguile.patch
deleted file mode 100644
index cbaccefb2..000000000
--- a/sci-chemistry/coot/files/coot-9999-libguile.patch
+++ /dev/null
@@ -1,29 +0,0 @@
- src/graphics-info-modelling.cc | 1 +
- src/graphics-info.cc           | 2 ++
- 2 files changed, 3 insertions(+)
-
-diff --git a/src/graphics-info-modelling.cc b/src/graphics-info-modelling.cc
-index 05a63ad..4b7d129 100644
---- a/src/graphics-info-modelling.cc
-+++ b/src/graphics-info-modelling.cc
-@@ -102,6 +102,7 @@
- 
- #include "utils/coot-utils.hh"
- 
-+#include <libguile.h>
- 
- // Idealize the geometry without considering the map.
- //
-diff --git a/src/graphics-info.cc b/src/graphics-info.cc
-index e2f9d52..76b6769 100644
---- a/src/graphics-info.cc
-+++ b/src/graphics-info.cc
-@@ -92,6 +92,8 @@
- #include "cc-interface-scripting.hh"
- #endif
- 
-+#include <libguile.h>
-+
- // A few non-class members - should be somewhere else, I guess.
- // 
- void initialize_graphics_molecules() { 
diff --git a/sci-chemistry/coot/files/coot-9999-libtool.patch b/sci-chemistry/coot/files/coot-9999-libtool.patch
deleted file mode 100644
index 10c43ad55..000000000
--- a/sci-chemistry/coot/files/coot-9999-libtool.patch
+++ /dev/null
@@ -1,39 +0,0 @@
- configure.ac    |  2 +-
- lbg/Makefile.am | 11 -----------
- 2 files changed, 1 insertion(+), 12 deletions(-)
-
-diff --git a/configure.ac b/configure.ac
-index 73d6ed7..b04dcd6 100644
---- a/configure.ac
-+++ b/configure.ac
-@@ -69,7 +69,7 @@ AC_LIB_PREPARE_MULTILIB
- 
- AC_SUBST(COOT_STDTYPES)
- 
--EXPORT_DYNAMIC_FLAG_SPEC=$export_dynamic_flag_spec
-+eval EXPORT_DYNAMIC_FLAG_SPEC=\"$export_dynamic_flag_spec\"
- AC_SUBST(EXPORT_DYNAMIC_FLAG_SPEC)
- 
- 
-diff --git a/lbg/Makefile.am b/lbg/Makefile.am
-index 1277afe..a79ebe0 100644
---- a/lbg/Makefile.am
-+++ b/lbg/Makefile.am
-@@ -43,17 +43,6 @@ pkginclude_HEADERS = lbg.hh wmolecule.hh  flev-annotations.hh graphics-c-interfa
- 	lbg-drag-and-drop.hh qed-interface.hh alerts.hh pi-stacking.hh
- pkgincludedir = $(includedir)/coot/lbg
- 
--# 20140521
--# lidia_LDFLAGS = -Wl,--export-dynamic
--# 
--# Now we use EXPORT_DYNAMIC_FLAG_SPEC which usually evaluates to ${wl}--export-dynamic
--# (but not for MacOSX, where it Does The Right Thing (hopefully)).
--# We manually set the value of wl here, but maybe the Right Thing To Do for that is 
--# run (eval) $($LIBTOOL --config | grep ^wl).  How do I do that here though?  
--# I don't understand.  Maybe the setting of wl should be done in configure?  But then
--# I have to force the output of libtool.  Bleugh.  Hmm...
--# Anyway, thankyou Gary Vaughan.
--wl=-Wl,
- lidia_LDFLAGS = $(EXPORT_DYNAMIC_FLAG_SPEC)
- 
- # res spec output operator means we include libcoot-coord-utils
diff --git a/sci-chemistry/coot/files/coot-9999-sandbox-icons.patch b/sci-chemistry/coot/files/coot-9999-sandbox-icons.patch
deleted file mode 100644
index 2a9ff2d71..000000000
--- a/sci-chemistry/coot/files/coot-9999-sandbox-icons.patch
+++ /dev/null
@@ -1,16 +0,0 @@
- pixmaps/icons/Makefile.am | 4 ++--
- 1 file changed, 2 insertions(+), 2 deletions(-)
-
-diff --git a/pixmaps/icons/Makefile.am b/pixmaps/icons/Makefile.am
-index 0c183ae..dddc11a 100644
---- a/pixmaps/icons/Makefile.am
-+++ b/pixmaps/icons/Makefile.am
-@@ -11,6 +11,6 @@ install-data-local:
- 		CONTEXT=` echo $$icon | cut -d_ -f2`; \
- 		SIZE=`    echo $$icon | cut -d_ -f3`; \
- 		ICONFILE=`echo $$icon | cut -d_ -f4`; \
--		mkdir -p $(datadir)/icons/$$THEME/$$SIZE/$$CONTEXT; \
--		$(INSTALL_DATA) $(srcdir)/$$icon $(datadir)/icons/$$THEME/$$SIZE/$$CONTEXT/$$ICONFILE; \
-+		mkdir -p $(DESTDIR)$(datadir)/icons/$$THEME/$$SIZE/$$CONTEXT; \
-+		$(INSTALL_DATA) $(srcdir)/$$icon $(DESTDIR)$(datadir)/icons/$$THEME/$$SIZE/$$CONTEXT/$$ICONFILE; \
- 	done;
diff --git a/sci-chemistry/coot/metadata.xml b/sci-chemistry/coot/metadata.xml
deleted file mode 100644
index 79d42af98..000000000
--- a/sci-chemistry/coot/metadata.xml
+++ /dev/null
@@ -1,12 +0,0 @@
-<?xml version="1.0" encoding="UTF-8"?>
-<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
-<pkgmetadata>
-	<maintainer type="person">
-		<email>jlec@gentoo.org</email>
-		<name>Justin Lecher</name>
-	</maintainer>
-	<maintainer type="project">
-		<email>sci-chemistry@gentoo.org</email>
-		<name>Gentoo Chemistry Project</name>
-	</maintainer>
-</pkgmetadata>
diff --git a/sci-chemistry/cpmgfit/Manifest b/sci-chemistry/cpmgfit/Manifest
deleted file mode 100644
index aa09cd758..000000000
--- a/sci-chemistry/cpmgfit/Manifest
+++ /dev/null
@@ -1 +0,0 @@
-DIST cpmgfit-1.43.tar.gz 89002 BLAKE2B 0965c2f0915a117eb8469987133a46912bad9dbdee51682eb9bccd806152512701864ccbd071d50e378b153361b7216e9aca71e621c03a71ca2f5d1eddb274d3 SHA512 ad10ec8cde4eb13dd21f99ebca5552ec844b89785a0485df287e8fad7b63a2f99cd713d281904d2f83cc9485c5fc0a0b3f963d23af8785f0277cb1f7418051a3
diff --git a/sci-chemistry/cpmgfit/cpmgfit-1.43.ebuild b/sci-chemistry/cpmgfit/cpmgfit-1.43.ebuild
deleted file mode 100644
index 0339bc908..000000000
--- a/sci-chemistry/cpmgfit/cpmgfit-1.43.ebuild
+++ /dev/null
@@ -1,48 +0,0 @@
-# Copyright 1999-2015 Gentoo Foundation
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=5
-
-inherit fortran-2 multilib
-
-DESCRIPTION="non-linear least squares fitting of CPMG relaxation dispersion curves"
-HOMEPAGE="http://biochemistry.hs.columbia.edu/labs/palmer/software/cpmgfit.html"
-SRC_URI="http://biochemistry.hs.columbia.edu/labs/palmer/software/cpmgfit.linux.tar.gz -> ${P}.tar.gz"
-
-SLOT="0"
-LICENSE="GPL-2"
-KEYWORDS=""
-IUSE="examples"
-
-RDEPEND="
-	sci-libs/blas-reference
-	=sys-devel/gcc-4.1*"
-DEPEND="dev-util/patchelf"
-
-S="${WORKDIR}"/linux
-
-QA_PREBUILT="opt/bin/.*"
-
-src_install() {
-	local _exe
-
-	exeinto /opt/bin
-	if use x86; then
-		_exe=./linux_32/${PN}
-	elif use amd64; then
-		_exe=./linux_64/${PN}
-	fi
-
-	patchelf --set-rpath "${EPREFIX}/opt/${PN}:${EPREFIX}/usr/$(get_libdir)/gcc/x86_64-pc-linux-gnu/4.1.2/" ${_exe}
-
-	doexe ${_exe}
-
-	dosym ../../usr/$(get_libdir)/librefblas.so /opt/${PN}/libblas.so.3
-
-	dohtml ${PN}_manual.html
-
-	if use examples; then
-		insinto /usr/share/${PN}/examples/
-		doins sample*
-	fi
-}
diff --git a/sci-chemistry/cpmgfit/metadata.xml b/sci-chemistry/cpmgfit/metadata.xml
deleted file mode 100644
index da36ecbfc..000000000
--- a/sci-chemistry/cpmgfit/metadata.xml
+++ /dev/null
@@ -1,8 +0,0 @@
-<?xml version="1.0" encoding="UTF-8"?>
-<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
-<pkgmetadata>
-	<maintainer type="project">
-		<email>sci-chemistry@gentoo.org</email>
-		<name>Gentoo Chemistry Project</name>
-	</maintainer>
-</pkgmetadata>
diff --git a/sci-chemistry/cs-rosetta/Manifest b/sci-chemistry/cs-rosetta/Manifest
deleted file mode 100644
index 69a3f17b1..000000000
--- a/sci-chemistry/cs-rosetta/Manifest
+++ /dev/null
@@ -1,3 +0,0 @@
-DIST cs-rosetta-1.01.2009.1109.11-changelog 953 BLAKE2B ea99d07f24ce2bc4f9607ed3cff0f56a1eafad1611d02e8faf9a556077c81b84d66e10ce929221215072864477d845ec52114e6b0d1b0b1179027b507e65cc34 SHA512 dee6ffdb448dbd35f26f9fc1d1db4095fe445c833bd7c5d7a6aa37edc1ae526d6ba6e851aa83ee8204e5aa262b01c88684161f507f5db5eff6ac8d008dd09012
-DIST cs-rosetta-1.01.2009.1109.11-install.com 12420 BLAKE2B 46695218b5ac1a5cc5602c88de5097a80dfb3dc11fd50784e879771b4e386a13076ac51f2ae47489261228126f37abf607f6b68c6dd402c2fd8b4e7e90d71c79 SHA512 dc7ae15bef5fe591a5a11418c5eb203a39fba961da0a130ea6960e16a5c678af1b3a94cb7aef2c5ca3faa600fe9d1b8e31440b35b68b1f090597e261f8de76c9
-DIST cs-rosetta-1.01.2009.1109.11.tar.Z 15461998 BLAKE2B 1b81e2d8ca2298b174a4b5811f8cc2d7b110f4f15e4417be3fd6c82205095ab303a99b197fe063bc000b68d3d1abbb9f8508abcd9f32c7e81eb1d522530a9c57 SHA512 6c4872ca7e7fffa1de99b6c8447953bceaf226f24e02ceb4a2e6019aaaa52d6ae0393c55a8276b060e317980b051da19943879e5341020ec1ab2b42175e42aa1
diff --git a/sci-chemistry/cs-rosetta/cs-rosetta-1.01.2009.1109.11.ebuild b/sci-chemistry/cs-rosetta/cs-rosetta-1.01.2009.1109.11.ebuild
deleted file mode 100644
index 74cf932d8..000000000
--- a/sci-chemistry/cs-rosetta/cs-rosetta-1.01.2009.1109.11.ebuild
+++ /dev/null
@@ -1,103 +0,0 @@
-# Copyright 1999-2014 Gentoo Foundation
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=5
-
-inherit flag-o-matic fortran-2 toolchain-funcs
-
-DESCRIPTION="System for chemical shifts based protein structure prediction using ROSETTA"
-HOMEPAGE="http://spin.niddk.nih.gov/bax/software/CSROSETTA/"
-SRC_URI="
-	http://spin.niddk.nih.gov/bax/software/CSROSETTA/install.com -> ${P}-install.com
-	http://spin.niddk.nih.gov/bax/software/CSROSETTA/CSRosetta.tar.Z -> ${P}.tar.Z
-	http://spin.niddk.nih.gov/bax/software/CSROSETTA/changeLog -> ${P}-changelog"
-
-SLOT="0"
-LICENSE="all-rights-reserved"
-KEYWORDS=""
-IUSE="custom-cflags"
-
-RDEPEND="
-	dev-lang/perl
-	|| ( sci-biology/update-blastdb sci-biology/ncbi-tools++ )
-	sci-biology/profphd
-	sci-biology/psipred
-	sci-biology/samtools
-	~sci-libs/cs-rosetta-db-${PV}
-	sci-chemistry/nmrpipe
-	sci-chemistry/rosetta"
-DEPEND=""
-
-S="${WORKDIR}"
-
-src_unpack() {
-	unpack ${P}.tar.Z
-}
-
-src_prepare() {
-	cat >> "${T}"/39${PN} <<- EOF
-	rosetta3="${EPREFIX}/usr/bin/AbinitioRelax"
-	rosetta3_extpdbs="${EPREFIX}/usr/bin/extract_pdbs"
-	rosetta3DB="${EPREFIX}/usr/share/rosetta-db"
-	csrosettaDir="${EPREFIX}/opt/${PN}"
-	csrosettaCom="${EPREFIX}/opt/${PN}/com"
-	PATH="${EPREFIX}/opt/${PN}/com"
-	MFR="${EPREFIX}/opt/${PN}/com/mfr.tcl"
-	EOF
-
-	# needs more love
-	sed \
-		-e "s:CSROSETTA_DIR/src/nnmake/pNNMAKE.gnu:${EPREFIX}/opt/${PN}/src/nnmake/pNNMAKE:g" \
-		-i com/make_fragments_2000.pl || die
-
-	append-fflags -ffixed-line-length-132
-}
-
-src_compile() {
-	use custom-cflags || CXXFLAGS="-pipe -ffor-scope -fno-exceptions -O3 -ffast-math -funroll-loops -finline-functions -finline-limit=20000"
-
-	compilation() {
-		if [[ -f dipolar_nn.f ]]; then
-			sed \
-				-e '/write/s:(i,6f6.3):(i3,6(1x,f6.3)):g' \
-				-i dipolar_nn.f || die
-		fi
-
-		sed \
-			-e '/LDFLAGS/s: = : ?= :g' \
-			-e '/CCFLAGS/s: = : += :g' \
-			-e 's:$(OBJECT) $(LDFLAGS):$(LDFLAGS) $(OBJECT) -lm -o:g' \
-			-e 's:$(FFLAGS) -o:$(FFLAGS) $(LDFLAGS) -o:g' \
-			-e '/make.system/d' \
-			-i *akefile || die
-		emake \
-			CC=$(tc-getCXX) \
-			CCFLAGS="${CXXFLAGS}"
-
-		if [[ -f pNNMAKE. ]]; then
-			mv pNNMAKE{.,} || die
-			emake almostsuperclean
-		else
-			emake clean
-		fi
-	}
-
-	for i in src/{mfr2rosetta,SPARTA/src,pdbrms,TALOS,rosettaFrag2csFrag,nnmake}; do
-		pushd ${i} > /dev/null
-			compilation
-		popd > /dev/null
-	done
-}
-
-src_install() {
-	insinto /opt/${PN}/
-	doins -r *
-	chmod 755 \
-		"${ED}"/opt/${PN}/com/* \
-		"${ED}"/opt/${PN}/src/{mfr2rosetta/mfr2rosetta,SPARTA/src/SPARTA,pdbrms/pdbrms,TALOS/TALOS,rosettaFrag2csFrag/rosettaFrag2csFrag,nnmake/pNNMAKE} \
-		 || die
-
-	dosym make_fragments_2000.pl /opt/${PN}/com/make_fragment_2000.pl
-
-	doenvd "${T}"/39${PN}
-}
diff --git a/sci-chemistry/cs-rosetta/metadata.xml b/sci-chemistry/cs-rosetta/metadata.xml
deleted file mode 100644
index da36ecbfc..000000000
--- a/sci-chemistry/cs-rosetta/metadata.xml
+++ /dev/null
@@ -1,8 +0,0 @@
-<?xml version="1.0" encoding="UTF-8"?>
-<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
-<pkgmetadata>
-	<maintainer type="project">
-		<email>sci-chemistry@gentoo.org</email>
-		<name>Gentoo Chemistry Project</name>
-	</maintainer>
-</pkgmetadata>
diff --git a/sci-chemistry/ctffind/Manifest b/sci-chemistry/ctffind/Manifest
new file mode 100644
index 000000000..103ece6da
--- /dev/null
+++ b/sci-chemistry/ctffind/Manifest
@@ -0,0 +1,3 @@
+DIST ctffind-4.1.10.tar.gz 625495 BLAKE2B 29c16308005322f53de8e0e9e9c03bc4219f5499bdd303d08e6ee93debe022151fc6b4ea5a2dec3f5c155e26913ae678de98a9b8b37f10d391c284011399f36a SHA512 abaa94781a16b6a72d5ed461f89c1aa313540e4d982c75e81879df2e863bf3ff8ad9fb30d00df603bdc7b56565508e9caba31ef2af67a4a8b732df33b53ee4c6
+DIST ctffind-4.1.13.tar.gz 637267 BLAKE2B 89440d497c6cfe962fd6af14ebc78049ff7341f246bb794384337d7b69571e9123da2bb200f34bf6fdafd984e7f38a77ed1f11a2a4da30f1463b6cfdded0d247 SHA512 1523856b75431b1cdbc3d29336f7d59bf0e7ecee70573c79273a97661e75387aa78c91c3d337431a432e1b15760ca34ad2692832f2f57bdc37951d1bc03958eb
+DIST ctffind-4.1.14.tar.gz 662195 BLAKE2B cb81a971c74e8f2b38e87945aca9f34d4d9cf90770b149ddc5febaee9af4a7392e1d295b2146a14212ea7c820ebf51c5179811cd42875b8a0ef279f6a07e8642 SHA512 115d04ad1adce3f8a99b14e15844df8d6caa4b873faa24eed9d6999a48e88f5a35ffd0cffa6c50c38566cc0091e0de5baec4d0cc62719540a9cfe67bc7333d42
diff --git a/sci-chemistry/ctffind/ctffind-4.1.10.ebuild b/sci-chemistry/ctffind/ctffind-4.1.10.ebuild
new file mode 100644
index 000000000..a69a36308
--- /dev/null
+++ b/sci-chemistry/ctffind/ctffind-4.1.10.ebuild
@@ -0,0 +1,37 @@
+# Copyright 2019-2021 Gentoo Authors
+# Distributed under the terms of the GNU General Public License v2
+
+EAPI=7
+
+WX_GTK_VER="3.0-gtk3"
+inherit wxwidgets
+
+DESCRIPTION="CTF estimation (ctffind, ctftilt)"
+HOMEPAGE="https://grigoriefflab.umassmed.edu/"
+SRC_URI="https://grigoriefflab.umassmed.edu/system/tdf?path=ctffind-${PV}.tar.gz&file=1&type=node&id=26 -> ${P}.tar.gz"
+
+LICENSE="Janelia-1.2"
+SLOT="0"
+KEYWORDS="~amd64 ~x86"
+
+DEPEND="
+	sci-libs/fftw:3.0
+	media-libs/libjpeg-turbo
+	media-libs/tiff
+	x11-libs/wxGTK:*
+"
+RDEPEND="${DEPEND}"
+BDEPEND="
+	${DEPEND}
+	virtual/pkgconfig"
+
+src_prepare() {
+	default
+	sed /pdb/d -i src/core/core_headers.h || die "removing pdb.h failed"
+	sed /water/d -i src/core/core_headers.h || die "removing water.h failed"
+}
+
+src_configure() {
+	setup-wxwidgets
+	default
+}
diff --git a/sci-chemistry/ctffind/ctffind-4.1.13.ebuild b/sci-chemistry/ctffind/ctffind-4.1.13.ebuild
new file mode 100644
index 000000000..a69a36308
--- /dev/null
+++ b/sci-chemistry/ctffind/ctffind-4.1.13.ebuild
@@ -0,0 +1,37 @@
+# Copyright 2019-2021 Gentoo Authors
+# Distributed under the terms of the GNU General Public License v2
+
+EAPI=7
+
+WX_GTK_VER="3.0-gtk3"
+inherit wxwidgets
+
+DESCRIPTION="CTF estimation (ctffind, ctftilt)"
+HOMEPAGE="https://grigoriefflab.umassmed.edu/"
+SRC_URI="https://grigoriefflab.umassmed.edu/system/tdf?path=ctffind-${PV}.tar.gz&file=1&type=node&id=26 -> ${P}.tar.gz"
+
+LICENSE="Janelia-1.2"
+SLOT="0"
+KEYWORDS="~amd64 ~x86"
+
+DEPEND="
+	sci-libs/fftw:3.0
+	media-libs/libjpeg-turbo
+	media-libs/tiff
+	x11-libs/wxGTK:*
+"
+RDEPEND="${DEPEND}"
+BDEPEND="
+	${DEPEND}
+	virtual/pkgconfig"
+
+src_prepare() {
+	default
+	sed /pdb/d -i src/core/core_headers.h || die "removing pdb.h failed"
+	sed /water/d -i src/core/core_headers.h || die "removing water.h failed"
+}
+
+src_configure() {
+	setup-wxwidgets
+	default
+}
diff --git a/sci-chemistry/ctffind/ctffind-4.1.14.ebuild b/sci-chemistry/ctffind/ctffind-4.1.14.ebuild
new file mode 100644
index 000000000..a69a36308
--- /dev/null
+++ b/sci-chemistry/ctffind/ctffind-4.1.14.ebuild
@@ -0,0 +1,37 @@
+# Copyright 2019-2021 Gentoo Authors
+# Distributed under the terms of the GNU General Public License v2
+
+EAPI=7
+
+WX_GTK_VER="3.0-gtk3"
+inherit wxwidgets
+
+DESCRIPTION="CTF estimation (ctffind, ctftilt)"
+HOMEPAGE="https://grigoriefflab.umassmed.edu/"
+SRC_URI="https://grigoriefflab.umassmed.edu/system/tdf?path=ctffind-${PV}.tar.gz&file=1&type=node&id=26 -> ${P}.tar.gz"
+
+LICENSE="Janelia-1.2"
+SLOT="0"
+KEYWORDS="~amd64 ~x86"
+
+DEPEND="
+	sci-libs/fftw:3.0
+	media-libs/libjpeg-turbo
+	media-libs/tiff
+	x11-libs/wxGTK:*
+"
+RDEPEND="${DEPEND}"
+BDEPEND="
+	${DEPEND}
+	virtual/pkgconfig"
+
+src_prepare() {
+	default
+	sed /pdb/d -i src/core/core_headers.h || die "removing pdb.h failed"
+	sed /water/d -i src/core/core_headers.h || die "removing water.h failed"
+}
+
+src_configure() {
+	setup-wxwidgets
+	default
+}
diff --git a/sci-chemistry/ctffind/metadata.xml b/sci-chemistry/ctffind/metadata.xml
new file mode 100644
index 000000000..7e9e870fd
--- /dev/null
+++ b/sci-chemistry/ctffind/metadata.xml
@@ -0,0 +1,12 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
+<pkgmetadata>
+	<maintainer type="project">
+		<email>sci-chemistry@gentoo.org</email>
+		<name>Gentoo Chemistry Project</name>
+	</maintainer>
+	<maintainer type="person">
+		<email>alexxy@gentoo.org</email>
+		<name>Alexey Shvetsov</name>
+	</maintainer>
+</pkgmetadata>
diff --git a/sci-chemistry/curvefit/Manifest b/sci-chemistry/curvefit/Manifest
deleted file mode 100644
index 8da1a8f5a..000000000
--- a/sci-chemistry/curvefit/Manifest
+++ /dev/null
@@ -1 +0,0 @@
-DIST curvefit.linux.tar.gz 72480 BLAKE2B de88402dd9bbb9b5086662ceffff25b424917d890ce9c3b4605bde5f2cf77db4fcc6f2c2c1b78937d13f89fc960f673bb0cbd5c47d5ce0a7525531386c6dec6e SHA512 657c4a08d2278cfbcfbe890ba7488187c9962d01ede4d79758f5e46559889152a2fad354226c000628025757a2d11cf1d8f2622dcead60683136ac2e45e93898
diff --git a/sci-chemistry/curvefit/curvefit-1.40.ebuild b/sci-chemistry/curvefit/curvefit-1.40.ebuild
deleted file mode 100644
index 225325523..000000000
--- a/sci-chemistry/curvefit/curvefit-1.40.ebuild
+++ /dev/null
@@ -1,53 +0,0 @@
-# Copyright 1999-2015 Gentoo Foundation
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=5
-
-inherit fortran-2 multilib
-
-DESCRIPTION="Linear and non-linear least squares fitting"
-HOMEPAGE="http://cpmcnet.columbia.edu/dept/gsas/biochem/labs/palmer/software/curvefit.html"
-SRC_URI="http://cpmcnet.columbia.edu/dept/gsas/biochem/labs/palmer/software/curvefit.linux.tar.gz"
-
-SLOT="0"
-LICENSE="GPL-2"
-KEYWORDS=""
-IUSE="examples"
-
-RDEPEND="
-	sci-libs/blas-reference
-	=sys-devel/gcc-4.1*"
-DEPEND="dev-util/patchelf"
-
-S="${WORKDIR}"/linux
-
-QA_PREBUILT="opt/bin/.*"
-
-src_install() {
-	local _exe
-	sed \
-		-e 's: xmgr : xmgrace :g' \
-		-e "s: /bin/ls:${EPREFIX}/bin/ls:g" \
-		-i batch_curve curveplot || die
-
-	exeinto /opt/bin
-	if use x86; then
-		_exe=./linux_32/${PN}
-	elif use amd64; then
-		_exe=./linux_64/${PN}
-	fi
-
-	patchelf --set-rpath "${EPREFIX}/opt/${PN}:$(gcc-config -L):${EPREFIX}/usr/$(get_libdir)/gcc/x86_64-pc-linux-gnu/4.1.2/" ${_exe} || die
-
-	doexe batch_curve curveplot ${_exe}
-
-	dosym ../../usr/$(get_libdir)/librefblas.so /opt/${PN}/libblas.so.3
-
-	dodoc Versions
-	dohtml curvefit_manual.html
-
-	if use examples; then
-		insinto /usr/share/${PN}/examples/
-		doins sample*
-	fi
-}
diff --git a/sci-chemistry/curvefit/metadata.xml b/sci-chemistry/curvefit/metadata.xml
deleted file mode 100644
index da36ecbfc..000000000
--- a/sci-chemistry/curvefit/metadata.xml
+++ /dev/null
@@ -1,8 +0,0 @@
-<?xml version="1.0" encoding="UTF-8"?>
-<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
-<pkgmetadata>
-	<maintainer type="project">
-		<email>sci-chemistry@gentoo.org</email>
-		<name>Gentoo Chemistry Project</name>
-	</maintainer>
-</pkgmetadata>
diff --git a/sci-chemistry/dl_poly/Manifest b/sci-chemistry/dl_poly/Manifest
index 1d2781521..c0fef1a08 100644
--- a/sci-chemistry/dl_poly/Manifest
+++ b/sci-chemistry/dl_poly/Manifest
@@ -1,2 +1,2 @@
-DIST dl_class_1.9.tar.gz 3280421 SHA256 eac3d0de86bfc9cfec9ee3024ef46114e85c501aec025d61e22c2c6ffda1cae8 SHA512 c87537c71552f8e9f190bfe6d216a498c0d9d202b8aa2d0ade3bca3120d67eb6b880661320119fa98e9a791cb8fa3075d617657d15f311fdb327e07e3eee4106 WHIRLPOOL 9b2caadd1bee363bbae78d5325acc0366ac6cf4f9c3a107c805c4d0bb3d94257b56a5b11857fe446383aad9235999a709d96f366ccb2ee901b461f72a118f605
-DIST dl_poly_4.05.tar.gz 3133828 SHA256 ff3854a005148b55563d9994af4d449276ebb774a334ba9effb491bd3b13475d SHA512 926bb105537a70d7974a824872ca67edf1596896c01eecc2d6ca6c9cd10e828f2d33addcecceee72aa8e169c3813f8e8d2e5674d059f6f128bafcb1b63891fed WHIRLPOOL 8eff43198f24763b60de1eb6bf18e68609faf1649c1c0e3e408b2f12bf43c4bf2b39034d25db00ed0fdd003a7c806ce4f1551a301ecc47dc48014de42354a2c5
+DIST dl_poly-1.10.tar.gz 9158743 BLAKE2B 422c384c4dada15d1dd96f919ca8056152a9f718cba158e60b7037fbbe2d473b6b797dbe0d4b6820046a8239496ea26e11da73c3a10d35b2ea485e72d70e7999 SHA512 60b82bfe35de34353be465dad5a668ab4280913fa8171305f0f9c498e3d3233eca0641e1bf671d8213a74fe426d60504a95cde1589830f62551a77944c7cc1b8
+DIST dl_poly-5.0.0.tar.gz 3013573 BLAKE2B cde37b38d79d6216abb9becec3f30db3959e97e85c5491f5d95b3bd560db590b1b882b48827d4bfa494016f97c5389a8fe383d232ef55c2b2318b206aee2ded9 SHA512 1432867aa808f91d6dad4e109508b9d9e182bad52c38c423aa3dc37b5a81be344cb393a913d5416952a157986e9466f2b2d51ae32d2a523971930941c9e841dc
diff --git a/sci-chemistry/dl_poly/dl_poly-1.10.ebuild b/sci-chemistry/dl_poly/dl_poly-1.10.ebuild
new file mode 100644
index 000000000..d93ef8576
--- /dev/null
+++ b/sci-chemistry/dl_poly/dl_poly-1.10.ebuild
@@ -0,0 +1,35 @@
+# Copyright 1999-2021 Gentoo Authors
+# Distributed under the terms of the GNU General Public License v2
+
+EAPI=7
+
+inherit fortran-2 toolchain-funcs
+
+DESCRIPTION="a general purpose molecular dynamics simulation package"
+HOMEPAGE="http://www.ccp5.ac.uk/DL_POLY_CLASSIC/"
+SRC_URI="https://gitlab.com/DL_POLY_Classic/dl_poly/-/archive/RELEASE-${PV//./-}/${PN}-RELEASE-${PV//./-}.tar.gz -> ${P}.tar.gz"
+
+LICENSE="BSD"
+SLOT="0"
+KEYWORDS="~amd64"
+IUSE="doc"
+
+DEPEND="virtual/mpi[fortran]"
+RDEPEND="${DEPEND}"
+
+S="${WORKDIR}/${PN}-RELEASE-${PV//./-}/source"
+
+src_prepare() {
+	default
+	cp ../build/MakeSEQ Makefile || die
+}
+
+src_compile() {
+	emake -j1 FC=$(tc-getF77) FFLAGS="${FFLAGS} -c" LD="$(tc-getF77) -o" LDFLAGS="${LDFLAGS}" EXE="${PN}" seq
+}
+
+src_install() {
+	newbin "${PN}" DLPOLY.Z
+	dodoc ../README
+	use doc && dodoc ../manual/USRMAN.pdf
+}
diff --git a/sci-chemistry/dl_poly/dl_poly-1.9.ebuild b/sci-chemistry/dl_poly/dl_poly-1.9.ebuild
deleted file mode 100644
index 61056c7bc..000000000
--- a/sci-chemistry/dl_poly/dl_poly-1.9.ebuild
+++ /dev/null
@@ -1,34 +0,0 @@
-# Copyright 1999-2014 Gentoo Foundation
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=5
-
-inherit fortran-2 toolchain-funcs
-
-DESCRIPTION="a general purpose molecular dynamics simulation package"
-HOMEPAGE="http://www.ccp5.ac.uk/DL_POLY_CLASSIC/"
-SRC_URI="http://ccpforge.cse.rl.ac.uk/gf/download/frsrelease/255/2627/dl_class_1.9.tar.gz"
-
-LICENSE="BSD"
-SLOT="0"
-KEYWORDS="~amd64"
-IUSE="doc"
-
-DEPEND=""
-RDEPEND="${DEPEND}"
-
-S="${WORKDIR}/dl_class_1.9/source"
-
-src_prepare() {
-	cp ../build/MakeSEQ Makefile || die
-}
-
-src_compile() {
-	emake -j1 FC=$(tc-getF77) FFLAGS="${FFLAGS} -c" LD="$(tc-getF77) -o" LDFLAGS="${LDFLAGS}" EXE="${PN}" seq
-}
-
-src_install() {
-	newbin "${PN}" DLPOLY.Z
-	dodoc ../README
-	use doc && dodoc ../manual/USRMAN.pdf
-}
diff --git a/sci-chemistry/dl_poly/dl_poly-4.05.ebuild b/sci-chemistry/dl_poly/dl_poly-4.05.ebuild
deleted file mode 100644
index 330034af5..000000000
--- a/sci-chemistry/dl_poly/dl_poly-4.05.ebuild
+++ /dev/null
@@ -1,39 +0,0 @@
-# Copyright 1999-2015 Gentoo Foundation
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=5
-
-inherit fortran-2 multilib toolchain-funcs
-
-DESCRIPTION="a general purpose molecular dynamics simulation package"
-HOMEPAGE="http://www.ccp5.ac.uk/DL_POLY/"
-SRC_URI="dl_poly_4.05.tar.gz"
-
-LICENSE="STFC"
-SLOT="0"
-KEYWORDS="~amd64"
-IUSE="doc"
-RESTRICT="fetch"
-
-DEPEND="virtual/mpi[fortran]"
-RDEPEND="${DEPEND}"
-
-S="${WORKDIR}/${P//-/_}/source"
-
-pkg_nofetch() {
-	einfo "Go to ${HOMEPAGE} and download ${A}"
-	einfo "into ${DISTDIR}"
-}
-
-src_prepare() {
-	cp ../build/Makefile_MPI Makefile || die
-}
-
-src_compile() {
-	emake -j1 FC="mpif77 -c" FCFLAGS="${FFLAGS}" LD="mpif77 -o" LDFLAGS="${LDFLAGS}" EXE="${PN}" master
-}
-
-src_install() {
-	newbin "${PN}" DLPOLY.Z
-	use doc && dodoc ../manual/USRMAN*.pdf
-}
diff --git a/sci-chemistry/dl_poly/dl_poly-5.0.0.ebuild b/sci-chemistry/dl_poly/dl_poly-5.0.0.ebuild
new file mode 100644
index 000000000..313216aa7
--- /dev/null
+++ b/sci-chemistry/dl_poly/dl_poly-5.0.0.ebuild
@@ -0,0 +1,19 @@
+# Copyright 1999-2021 Gentoo Authors
+# Distributed under the terms of the GNU General Public License v2
+
+EAPI=7
+
+inherit cmake
+
+DESCRIPTION="a general purpose molecular dynamics simulation package"
+HOMEPAGE="http://www.ccp5.ac.uk/DL_POLY/"
+SRC_URI="https://gitlab.com/ccp5/dl-poly/-/archive/${PV}/${P}.tar.gz"
+
+LICENSE="STFC"
+SLOT="0"
+KEYWORDS="~amd64"
+
+DEPEND="virtual/mpi[fortran]"
+RDEPEND="${DEPEND}"
+
+S="${WORKDIR}/${P//_/-}-f8aaa10e91f07107c6cc2a0501a7c5064ec598d6"
diff --git a/sci-chemistry/drawxtl/drawxtl-45.ebuild b/sci-chemistry/drawxtl/drawxtl-45.ebuild
index 9558ffcef..e555eb352 100644
--- a/sci-chemistry/drawxtl/drawxtl-45.ebuild
+++ b/sci-chemistry/drawxtl/drawxtl-45.ebuild
@@ -1,9 +1,9 @@
-# Copyright 1999-2014 Gentoo Foundation
+# Copyright 1999-2021 Gentoo Authors
 # Distributed under the terms of the GNU General Public License v2
 
-EAPI=5
+EAPI=7
 
-inherit eutils toolchain-funcs
+inherit toolchain-funcs
 
 MY_PN="DRAWxtl"
 MY_P=${MY_PN}${PV}
@@ -27,8 +27,12 @@ RDEPEND="${DEPEND}"
 
 S="${WORKDIR}/${MY_PN}"
 
+PATCHES=(
+	"${FILESDIR}"/${P}-gentoo.patch
+)
+
 src_prepare() {
-	epatch "${FILESDIR}"/${P}-gentoo.patch
+	default
 	cd "${S}"/source || die
 	if ! use opengl; then
 		sed -i -e 's:define OPENGL 1:undef OPENGL:' ${MY_P}/drawxtl.h || die "sed failed"
@@ -59,8 +63,7 @@ src_install() {
 	fi
 
 	dodoc docs/readme.txt
-	insinto /usr/share/doc/${P}
-	doins docs/*.pdf
+	dodoc docs/*.pdf
 
 	if use examples; then
 		docinto examples
diff --git a/sci-chemistry/drawxtl/drawxtl-55.ebuild b/sci-chemistry/drawxtl/drawxtl-55.ebuild
index df7a16b53..c18fa4b2f 100644
--- a/sci-chemistry/drawxtl/drawxtl-55.ebuild
+++ b/sci-chemistry/drawxtl/drawxtl-55.ebuild
@@ -1,9 +1,9 @@
-# Copyright 1999-2014 Gentoo Foundation
+# Copyright 1999-2021 Gentoo Authors
 # Distributed under the terms of the GNU General Public License v2
 
-EAPI=5
+EAPI=7
 
-inherit eutils toolchain-funcs
+inherit toolchain-funcs
 
 MY_PN="DRAWxtl"
 MY_P=${MY_PN}${PV}
@@ -26,9 +26,9 @@ RDEPEND="${DEPEND}"
 
 S="${WORKDIR}/${MY_PN}"
 
-src_prepare() {
-	epatch "${FILESDIR}"/${P}-gentoo.patch
-}
+PATCHES=(
+	"${FILESDIR}"/${P}-gentoo.patch
+)
 
 src_compile() {
 	cd source/${MY_P} || die
@@ -41,8 +41,7 @@ src_install() {
 	dobin exe/${MY_P}
 
 	dodoc docs/readme.txt
-	insinto /usr/share/doc/${P}
-	doins docs/*.pdf
+	dodoc docs/*.pdf
 
 	if use examples; then
 		docinto examples
diff --git a/sci-chemistry/drawxtl/metadata.xml b/sci-chemistry/drawxtl/metadata.xml
index 37be5d841..da36ecbfc 100644
--- a/sci-chemistry/drawxtl/metadata.xml
+++ b/sci-chemistry/drawxtl/metadata.xml
@@ -5,8 +5,4 @@
 		<email>sci-chemistry@gentoo.org</email>
 		<name>Gentoo Chemistry Project</name>
 	</maintainer>
-	<longdescription lang="en">
-This software can be used to produce crystal structure drawings from structural
-data.
-</longdescription>
 </pkgmetadata>
diff --git a/sci-chemistry/dssp2pdb/Manifest b/sci-chemistry/dssp2pdb/Manifest
deleted file mode 100644
index d1d2701ea..000000000
--- a/sci-chemistry/dssp2pdb/Manifest
+++ /dev/null
@@ -1 +0,0 @@
-DIST dssp2pdb-0.03.tar 10240 BLAKE2B bcaf56243e9191b6dc3efcae94ad55e7802d7e0b13c4affab14ae6ef002f7bce98268c147a5438ac45438db46f8095f88eaa4e9aacf90bf9d38e4e36608216ce SHA512 010e243d0b98191afc761a5a6a02ce3f208b8cb3417c3db186e626d17890745db829debe9880b7aa2892babb50378741bb653589b3d3c9566c55f74fdcd43d65
diff --git a/sci-chemistry/dssp2pdb/dssp2pdb-0.03.ebuild b/sci-chemistry/dssp2pdb/dssp2pdb-0.03.ebuild
deleted file mode 100644
index 56280bf9c..000000000
--- a/sci-chemistry/dssp2pdb/dssp2pdb-0.03.ebuild
+++ /dev/null
@@ -1,24 +0,0 @@
-# Copyright 1999-2015 Gentoo Foundation
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=5
-
-DESCRIPTION="convert dssp to pdb"
-HOMEPAGE="http://structure.usc.edu/dssp2pdb/"
-SRC_URI="http://dev.gentooexperimental.org/~jlec/distfiles/${P}.tar"
-
-SLOT="0"
-KEYWORDS="~amd64 ~x86 ~amd64-linux ~x86-linux"
-LICENSE="GPL-2"
-IUSE=""
-
-RDEPEND="
-	dev-lang/perl
-	sci-chemistry/dssp"
-DEPEND=""
-
-S="${WORKDIR}"
-
-src_install() {
-	dobin ${PN}
-}
diff --git a/sci-chemistry/dssp2pdb/metadata.xml b/sci-chemistry/dssp2pdb/metadata.xml
deleted file mode 100644
index da36ecbfc..000000000
--- a/sci-chemistry/dssp2pdb/metadata.xml
+++ /dev/null
@@ -1,8 +0,0 @@
-<?xml version="1.0" encoding="UTF-8"?>
-<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
-<pkgmetadata>
-	<maintainer type="project">
-		<email>sci-chemistry@gentoo.org</email>
-		<name>Gentoo Chemistry Project</name>
-	</maintainer>
-</pkgmetadata>
diff --git a/sci-chemistry/erkale/Manifest b/sci-chemistry/erkale/Manifest
new file mode 100644
index 000000000..c7ee5eb6b
--- /dev/null
+++ b/sci-chemistry/erkale/Manifest
@@ -0,0 +1 @@
+DIST erkale-0_p20220106.tar.gz 45625969 BLAKE2B 038c504008c1023064426b39c6266e3e26c7a09a47c595a4d1c1ebd70e43a9c8acef527fd47079ca95f337e0ea8c81370a43fb24c7f87887d1f1637c162449fe SHA512 f41b8e82703d7a8d4b9728d04e9deed471af608368b27c2ab6a42073426c3ae5bab3151efbebef6c3baeb1de839472d4ed7b2df430eaafd7e47962cbc06de48f
diff --git a/sci-chemistry/erkale/erkale-0_p20220106.ebuild b/sci-chemistry/erkale/erkale-0_p20220106.ebuild
new file mode 100644
index 000000000..1ed7ab033
--- /dev/null
+++ b/sci-chemistry/erkale/erkale-0_p20220106.ebuild
@@ -0,0 +1,76 @@
+# Copyright 1999-2022 Gentoo Authors
+# Distributed under the terms of the GNU General Public License v2
+
+EAPI=8
+
+inherit cmake flag-o-matic multibuild toolchain-funcs
+
+COMMIT="bfb9d499a45e1da78b32a9fd52a06fd0dafc52f8"
+
+DESCRIPTION="Quantum chemistry program for atoms and molecules"
+HOMEPAGE="https://github.com/susilehtola/erkale"
+SRC_URI="https://github.com/susilehtola/${PN}/archive/${COMMIT}.tar.gz -> ${P}.tar.gz"
+S="${WORKDIR}/${PN}-${COMMIT}"
+
+SLOT="0"
+LICENSE="GPL-2"
+KEYWORDS="~amd64"
+IUSE="openmp"
+
+RDEPEND="
+	sci-libs/gsl
+	sci-libs/hdf5
+	sci-libs/libint:2
+	>=sci-libs/libxc-2.0.0
+"
+DEPEND="
+	>=sci-libs/armadillo-4[blas,lapack]
+	${RDEPEND}
+"
+BDEPEND="virtual/pkgconfig"
+
+MULTIBUILD_VARIANTS=( serial )
+
+src_prepare() {
+	use openmp && MULTIBUILD_VARIANTS+=( omp )
+	append-cxxflags "-DARMA_DONT_USE_ATLAS -DARMA_DONT_USE_WRAPPER"
+	cmake_src_prepare
+	# libint has renamed things
+	find -type f -name "*.h" -exec sed -i -e 's/#include <libint\/libint.h>/#include <libint2.h>/g' {} + || die
+	find -type f -name "*.h" -exec sed -i -e 's/#include <libderiv\/libderiv.h>/#include <libint2\/deriv_iter.h>/g' {} + || die
+}
+
+src_configure() {
+	my_configure() {
+		local OMP=OFF && [[ ${MULTIBUILD_VARIANT} == "omp" ]] && OMP=ON
+		local basis="${EPREFIX}/usr/share/${PN}/basis"
+		local mycmakeargs=(
+			-DUSE_OPENMP=${OMP}
+			-DBUILD_SHARED_LIBS=ON
+			-DERKALE_SYSTEM_LIBRARY="${basis/\/\///}"
+			-DLAPACK_INCLUDE_DIRS="$($(tc-getPKG_CONFIG) lapack --cflags-only-I | sed 's/-I//')"
+		)
+		cmake_src_configure
+	}
+	multibuild_foreach_variant my_configure
+}
+
+src_compile() {
+	multibuild_foreach_variant cmake_src_compile
+}
+
+src_test() {
+	my_test() {
+		cd "${BUILD_DIR}/src/test"
+		local OMP="" && [[ ${MULTIBUILD_VARIANT} == "omp" ]] && OMP="_omp"
+		ERKALE_LIBRARY="${S}/basis" ./erkale_tests${OMP} || eerror "Tests failed!"
+	}
+	multibuild_foreach_variant my_test
+}
+
+src_install() {
+	insinto "/usr/share/${PN}"
+	doins -r "${S}/basis"
+
+	multibuild_foreach_variant cmake_src_install
+}
diff --git a/sci-chemistry/erkale/erkale-9999.ebuild b/sci-chemistry/erkale/erkale-9999.ebuild
deleted file mode 100644
index 50fb53d02..000000000
--- a/sci-chemistry/erkale/erkale-9999.ebuild
+++ /dev/null
@@ -1,70 +0,0 @@
-# Copyright 1999-2017 Gentoo Foundation
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=6
-
-inherit cmake-utils flag-o-matic git-r3 multibuild toolchain-funcs
-
-DESCRIPTION="Quantum chemistry program for atoms and molecules"
-HOMEPAGE="https://code.google.com/p/erkale/"
-EGIT_REPO_URI="https://github.com/susilehtola/erkale.git"
-
-SLOT="0"
-LICENSE="GPL-2"
-KEYWORDS=""
-IUSE="openmp"
-
-RDEPEND="
-	sci-libs/gsl
-	sci-libs/hdf5
-	sci-libs/libint:2
-	>=sci-libs/libxc-2.0.0
-"
-DEPEND="
-	>=sci-libs/armadillo-4[blas,lapack]
-	virtual/pkgconfig
-	${RDEPEND}
-"
-
-MULTIBUILD_VARIANTS=( serial )
-
-src_prepare() {
-	use openmp && MULTIBUILD_VARIANTS+=( omp )
-	append-cxxflags "-DARMA_DONT_USE_ATLAS -DARMA_DONT_USE_WRAPPER"
-	cmake-utils_src_prepare
-}
-
-src_configure() {
-	my_configure() {
-		local OMP=OFF && [[ ${MULTIBUILD_VARIANT} == "omp" ]] && OMP=ON
-		local basis="${EROOT}/usr/share/${PN}/basis"
-		local mycmakeargs=(
-			-DUSE_OPENMP=${OMP}
-			-DBUILD_SHARED_LIBS=ON
-			-DERKALE_SYSTEM_LIBRARY="${basis/\/\///}"
-			-DLAPACK_INCLUDE_DIRS="$($(tc-getPKG_CONFIG) lapack --cflags-only-I | sed 's/-I//')"
-		)
-		cmake-utils_src_configure
-	}
-	multibuild_foreach_variant my_configure
-}
-
-src_compile() {
-	multibuild_foreach_variant cmake-utils_src_compile
-}
-
-src_test() {
-	my_test() {
-		cd "${BUILD_DIR}/src/test"
-		local OMP="" && [[ ${MULTIBUILD_VARIANT} == "omp" ]] && OMP="_omp"
-		ERKALE_LIBRARY="${S}/basis" ./erkale_tests${OMP} || eerror "Tests failed!"
-	}
-	multibuild_foreach_variant my_test
-}
-
-src_install() {
-	insinto "/usr/share/${PN}"
-	doins -r "${S}/basis"
-
-	multibuild_foreach_variant cmake-utils_src_install
-}
diff --git a/sci-chemistry/erkale/metadata.xml b/sci-chemistry/erkale/metadata.xml
index eea62e858..996e48735 100644
--- a/sci-chemistry/erkale/metadata.xml
+++ b/sci-chemistry/erkale/metadata.xml
@@ -18,4 +18,7 @@ ground-state electron momentum densities and Compton profiles, and core
 (x-ray absorption and x-ray Raman scattering) and valence electron
 excitation spectra of atoms and molecules.
 </longdescription>
+	<upstream>
+		<remote-id type="github">susilehtola/erkale</remote-id>
+	</upstream>
 </pkgmetadata>
diff --git a/sci-chemistry/freeon/freeon-9999.ebuild b/sci-chemistry/freeon/freeon-9999.ebuild
deleted file mode 100644
index 60a8af7cb..000000000
--- a/sci-chemistry/freeon/freeon-9999.ebuild
+++ /dev/null
@@ -1,47 +0,0 @@
-# Copyright 1999-2015 Gentoo Foundation
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=5
-
-AUTOTOOLS_AUTORECONF=1
-FORTRAN_STANDARD=90
-PYTHON_COMPAT=( python{2_7,3_4} )
-
-inherit autotools-utils fortran-2 git-r3 python-any-r1
-
-DESCRIPTION="An experimental suite of programs for linear scaling quantum chemistry"
-HOMEPAGE="http://www.freeon.org"
-SRC_URI=""
-EGIT_REPO_URI="https://github.com/FreeON/freeon.git"
-EGIT_BRANCH="master"
-
-LICENSE="GPL-3"
-SLOT="live"
-KEYWORDS=""
-IUSE=""
-
-RDEPEND="
-	sci-libs/hdf5
-	virtual/blas
-	virtual/lapack"
-DEPEND="${RDEPEND}
-	${PYTHON_DEPS}"
-
-src_prepare() {
-	bash fix_localversion.sh || die
-	autotools-utils_src_prepare
-}
-
-src_configure() {
-	local myeconfargs=(
-		"--enable-git-tag"
-		"--prefix=/opt/freeon"
-		"--mandir=/opt/freeon/share/man"
-		"--infodir=/opt/freeon/share/info"
-		"--datadir=/opt/freeon/share"
-		"--sysconfdir=/opt/freeon/etc"
-		"--libdir=/opt/freeon/lib64"
-		"--docdir=/opt/freeon/share/doc"
-	)
-	autotools-utils_src_configure
-}
diff --git a/sci-chemistry/freeon/metadata.xml b/sci-chemistry/freeon/metadata.xml
deleted file mode 100644
index 79f403367..000000000
--- a/sci-chemistry/freeon/metadata.xml
+++ /dev/null
@@ -1,15 +0,0 @@
-<?xml version="1.0" encoding="UTF-8"?>
-<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
-<pkgmetadata>
-	<longdescription lang="en">
-FreeON is an experimental, open source (GPL) suite of programs for linear scaling quantum chemistry.
-</longdescription>
-	<maintainer type="person">
-		<email>nicolasbock@gentoo.org</email>
-		<name>Nicolas Bock</name>
-	</maintainer>
-	<maintainer type="project">
-		<email>sci-chemistry@gentoo.org</email>
-		<name>Gentoo Chemistry Project</name>
-	</maintainer>
-</pkgmetadata>
diff --git a/sci-chemistry/gamess/gamess-20180930.3-r1.ebuild b/sci-chemistry/gamess/gamess-20180930.3-r1.ebuild
new file mode 100644
index 000000000..173e3513e
--- /dev/null
+++ b/sci-chemistry/gamess/gamess-20180930.3-r1.ebuild
@@ -0,0 +1,379 @@
+# Copyright 1999-2021 Gentoo Authors
+# Distributed under the terms of the GNU General Public License v2
+
+EAPI=7
+
+inherit check-reqs fortran-2 flag-o-matic pax-utils toolchain-funcs
+
+DESCRIPTION="A powerful quantum chemistry package"
+HOMEPAGE="https://www.msg.chem.iastate.edu/GAMESS/GAMESS.html"
+SRC_URI="
+	${P}.tar.gz
+	qmmm-tinker? ( tinker.tar.gz )"
+
+SLOT="0"
+LICENSE="gamess"
+# NOTE: PLEASE do not stabilize gamess. It does not make sense
+# since the tarball has fetch restrictions and upstream only
+# provides the latest version. In other words: As soon as a
+# new version comes out the stable version will be useless since
+# users can not get at the tarball any more.
+KEYWORDS="~amd64 ~x86"
+IUSE="mpi msucc neo openmp pax-kernel qmmm-tinker vb2000"
+
+CDEPEND="
+	app-shells/tcsh
+	mpi? ( virtual/mpi )
+	virtual/blas"
+DEPEND="${CDEPEND}"
+BDEPEND="virtual/pkgconfig"
+RDEPEND="${CDEPEND}
+	net-misc/openssh"
+
+REQUIRED_USE="( openmp? ( !neo !vb2000 ) )"
+
+S="${WORKDIR}/${PN}"
+
+RESTRICT="fetch"
+
+GAMESS_DOWNLOAD="http://www.msg.ameslab.gov/GAMESS/License_Agreement.html"
+GAMESS_VERSION="September 30, 2018 R3"
+
+pre_build_checks() {
+	if use msucc; then
+		CHECKREQS_MEMORY=6G
+		check-reqs_pkg_setup
+	fi
+}
+
+pkg_pretend() {
+	pre_build_checks
+}
+
+pkg_nofetch() {
+	echo
+	elog "Please download ${PN}-current.tar.gz from"
+	elog "${GAMESS_DOWNLOAD}."
+	elog "Be sure to select the version ${GAMESS_VERSION} tarball!!"
+	elog "Then move the tarball into your DISTDIR folder"
+	if use qmmm-tinker ; then
+		elog "Also download http://www.msg.ameslab.gov/GAMESS/tinker.tar.gz"
+		elog "and place tinker.tar.gz into your DISTDIR folder"
+	fi
+	echo
+}
+
+get_fcomp() {
+	case $(tc-getFC) in
+		*gfortran* )
+			FCOMP="gfortran" ;;
+		ifort )
+			FCOMP="ifc" ;;
+		* )
+			FCOMP=$(tc-getFC) ;;
+	esac
+}
+
+pkg_setup() {
+	pre_build_checks
+	use openmp && FORTRAN_NEED_OPENMP=1
+	fortran-2_pkg_setup
+	get_fcomp
+	# currently amd64 is only supported with gfortran
+	if [[ "${ARCH}" == "amd64" ]] && [[ ${FCOMP} != *gfortran* ]];
+		then die "You will need gfortran to compile gamess on amd64"
+	fi
+
+	# note about qmmm-tinker
+	if use qmmm-tinker; then
+			einfo "By default MM subsistem is restricted to 1000 atoms"
+			einfo "if you want larger MM subsystems then you should set"
+			einfo "QMMM_GAMESS_MAXMM variable to needed value in your make.conf"
+			einfo "By default maximum number of atom classes types and size of"
+			einfo "hessian are restricted to 250, 500 and 1000000 respectively"
+			einfo "If you want larger sizes set:"
+			einfo "QMMM_GAMESS_MAXCLASS"
+			einfo "QMMM_GAMESS_MAXCTYP"
+			einfo "QMMM_GAMESS_MAXHESS"
+			einfo "in your make.conf"
+	fi
+
+	#note about mpi
+	if use mpi; then
+		ewarn ""
+		ewarn "You should adjust rungms script for your mpi implentation"
+		ewarn "because deafult one will not work"
+		ewarn ""
+	fi
+}
+
+src_unpack() {
+	unpack ${A}
+
+	if use qmmm-tinker; then
+		mv tinker gamess/ || die "failed to move tinker directory"
+	fi
+}
+
+src_prepare() {
+	tc-export PKG_CONFIG
+	# apply LINUX-arch patches to gamess makesfiles
+	eapply "${FILESDIR}/${P}.gentoo.patch"
+	eapply_user
+	# select arch
+	# NOTE: please leave lked alone; it should be good as is!!
+	cd "${S}"
+	local active_arch;
+	if [[ "${ARCH}" == "amd64" ]]; then
+		active_arch="linux64";
+	else
+		active_arch="linux32";
+	fi
+
+	# fix "relocation truncated to fit" problem
+	append-flags -mcmodel=medium
+	append-ldflags -mcmodel=medium
+
+	# for hardened-gcc let't turn off ssp, since it breakes
+	# a few routines
+	if use pax-kernel && [[ ${FCOMP} == g77 ]]; then
+		FFLAGS="${FFLAGS} -fno-stack-protector-all"
+	fi
+
+	# Enable mpi stuff
+	if use mpi; then
+		sed -e "s:set COMM = sockets:set COMM = mpi:g" \
+			-i ddi/compddi || die "Enabling mpi build failed"
+		sed -e "s:MPI_INCLUDE_PATH = ' ':MPI_INCLUDE_PATH =	'-I/usr/include ':g" \
+			-i ddi/compddi || die "Enabling mpi build failed"
+		sed -e "s:MSG_LIBRARIES='../ddi/libddi.a -lpthread':MSG_LIBRARIES='../ddi/libddi.a -lmpi -lpthread':g" \
+			-i lked || die "Enabling mpi build failed"
+	fi
+
+	# enable NEO
+	if use neo; then
+		sed -e "s:NEO=false:NEO=true:" -i compall lked || \
+			die "Failed to enable NEO code"
+	else
+		sed -e "s:NEO=true:NEO=false:" -i compall lked || \
+			die "Failed to disable NEO code"
+	fi
+	# enable VB2000
+	if use vb2000; then
+		sed -e "s:VB2000=false:VB2000=true:" -i compall lked || \
+			die "Failed to enable VB2000 code"
+	else
+		sed -e "s:VB2000=true:VB2000=false:" -i compall lked || \
+			die "Failed to disable VB2000 code"
+	fi
+	# enable GAMESS-qmmm
+	if use qmmm-tinker; then
+		eapply "${FILESDIR}/${PN}-qmmm-tinker-fix-idate.patch"
+		sed -e "s:TINKER=false:TINKER=true:" -i compall lked || \
+			die "Failed to enable TINKER code"
+		if [ "x$QMMM_GAMESS_MAXMM" == "x" ]; then
+			einfo "No QMMM_GAMESS_MAXMM set. Using default value = 1000"
+		else
+			einfo "Setting QMMM_GAMESS_MAXMM to $QMMM_GAMESS_MAXMM"
+			sed -e "s:maxatm=1000:maxatm=$QMMM_GAMESS_MAXMM:g" \
+			 -i tinker/sizes.i \
+			 || die "Setting QMMM_GAMESS_MAXMM failed"
+			sed -e "s:MAXATM=1000:MAXATM=$QMMM_GAMESS_MAXMM:g" \
+			 -i source/inputb.src \
+			 || die "Setting QMMM_GAMESS_MAXMM failed"
+		fi
+		if [ "x$QMMM_GAMESS_MAXCLASS" == "x" ]; then
+			einfo "No QMMM_GAMESS_MAXMM set. Using default value = 250"
+		else
+			sed -e "s:maxclass=250:maxclass=$QMMM_GAMESS_MAXCLASS:g" \
+				-i tinker/sizes.i \
+				|| die "Setting QMMM_GAMESS_MAXCLASS failed"
+		fi
+		if [ "x$QMMM_GAMESS_MAXCTYP" == "x" ]; then
+			einfo "No QMMM_GAMESS_MAXCTYP set. Using default value = 500"
+		else
+			sed -e "s:maxtyp=500:maxtyp=$QMMM_GAMESS_MAXCTYP:g" \
+				-i tinker/sizes.i \
+				|| die "Setting QMMM_GAMESS_MAXCTYP failed"
+		fi
+		if [ "x$QMMM_GAMESS_MAXHESS" == "x" ]; then
+			einfo "No QMMM_GAMESS_MAXHESS set. Usingdefault value = 1000000"
+		else
+			sed -e "s:maxhess=1000000:maxhess=$QMMM_GAMESS_MAXHESS:g" \
+				-i tinker/sizes.i \
+				|| die "Setting QMMM_GAMESS_MAXHESS failed"
+		fi
+	fi
+	# create proper activate sourcefile
+	cp "./tools/actvte.code" "./tools/actvte.f" || \
+		die "Failed to create actvte.f"
+	sed -e "s/^\*UNX/    /" -i "./tools/actvte.f" || \
+		die "Failed to perform UNX substitutions in actvte.f"
+
+	# fix GAMESS' compall script to use proper CC
+	sed -e "s|\$CCOMP -c \$extraflags source/zunix.c|$(tc-getCC) -c \$extraflags source/zunix.c|" \
+		-i compall || die "Failed setting up compall script"
+
+	# insert proper FFLAGS into GAMESS' comp makefile
+	# in case we're using ifc let's strip all the gcc
+	# specific stuff
+	if [[ ${FCOMP} == "ifort" ]]; then
+		sed -e "s/gentoo-OPT = '-O2'/OPT = '${FFLAGS} -quiet'/" \
+			-i comp || die "Failed setting up comp script"
+	elif ! use x86; then
+		sed -e "s/-malign-double //" \
+			-e "s/gentoo-OPT='-O2'/OPT='${FFLAGS}'/" \
+			-i comp || die "Failed setting up comp script"
+	else
+		sed -e "s/gentoo-OPT = '-O2'/OPT = '${FFLAGS}'/" \
+			-i comp || die "Failed setting up comp script"
+	fi
+
+	# fix up GAMESS' linker script;
+	sed -e "s/gentoo-LDOPTS=' '/LDOPTS='${LDFLAGS}'/" \
+		-i lked || die "Failed setting up lked script"
+	# fix up GAMESS' ddi TCP/IP socket build
+	sed -e "s/gentoo-CC = 'gcc'/CC = '$(tc-getCC)'/" \
+		-i ddi/compddi || die "Failed setting up compddi script"
+	# Creating install.info
+	cat > install.info <<-EOF
+	#!/bin/csh
+	setenv GMS_PATH $WORKDIR/gamess
+	setenv GMS_BUILD_DIR $WORKDIR/gamess
+	setenv GMS_TARGET $active_arch
+	setenv GMS_FORTRAN $FCOMP
+	setenv GMS_GFORTRAN_VERNO $(gcc-major-version).$(gcc-minor-version)
+	setenv GMS_MATHLIB atlas
+	setenv GMS_MATHLIB_PATH  /usr/$(get_libdir)/atlas
+	setenv GMS_DDI_COMM sockets
+	setenv GMS_LIBCCHEM false
+	setenv GMS_PHI false
+	setenv GMS_SHMTYPE sysv
+	setenv GMS_OPENMP $(usex openmp true false)
+	setenv GMS_MSUCC $(usex msucc true false)
+	EOF
+
+}
+
+src_compile() {
+	# build actvte
+	cd "${S}"/tools
+	${FCOMP} -o actvte.x actvte.f || \
+		die "Failed to compile actvte.x"
+
+	# for hardened (PAX) users and ifc we need to turn
+	# MPROTECT off
+	if [[ ${FCOMP} == "ifort" ]] && use pax-kernel; then
+		pax-mark -PemRxS actvte.x
+	fi
+
+	# build gamess
+	cd "${S}"
+	./compall || die "compall failed"
+
+	# build the ddi TCP/IP socket stuff
+	cd "${S}/ddi"
+	./compddi || die "compddi failed"
+
+	# finally, link it all together
+	cd "${S}"
+	./lked || die "lked failed"
+
+	# for hardened (PAX) users and ifc we need to turn
+	# MPROTECT off
+	if [[ ${FCOMP} == "ifort" ]] && use pax-kernel; then
+		pax-mark -PemRxS ${PN}.00.x
+	fi
+}
+
+src_install() {
+	# the executables
+	dobin ${PN}.00.x rungms gms-files.csh \
+		|| die "Failed installing binaries"
+	if use !mpi; then
+		dobin ddi/ddikick.x \
+			|| die "Failed installing binaries"
+	fi
+
+	# the docs
+	dodoc *.DOC qmnuc/*.DOC
+
+	# install ericftm
+	insinto /usr/share/${PN}
+	doins auxdata/ericfmt.dat
+
+	# install mcpdata
+	insinto /usr/share/${PN}/MCP
+	doins auxdata/MCP/*
+
+	# install BASES
+	insinto /usr/share/${PN}/BASES
+	doins auxdata/BASES/*
+
+	# install QUANPOL
+	insinto /usr/share/${PN}/QUANPOL
+	doins auxdata/QUANPOL/*
+
+	# install tinker params in case of qmmm
+	if use qmmm-tinker ; then
+			dodoc tinker/simomm.doc
+			insinto /usr/share/${PN}
+			doins -r tinker/params51
+	fi
+
+	# install the tests the user should run, and
+	# fix up the runscript; also grab a copy of rungms
+	# so the user is ready to run the tests
+	insinto /usr/share/${PN}/tests
+	insopts -m0644
+	doins -r tests/*
+	insopts -m0744
+	doins runall
+	#doins tools/checktst/checktst tools/checktst/chkabs || \
+	#	die "Failed to install main test checker"
+	#doins tools/checktst/exam* || \
+	#	die "Failed to install individual test files"
+
+	insinto /usr/share/${PN}/neotests
+	insopts -m0644
+	doins -r qmnuc/neotests/*
+
+	if use vb2000; then
+		insinto /usr/share/${PN}/vb2000
+		insopts -m0644
+		doins -r vb2000/{MAP,VBOLIB,test_results,tests}
+		insopts -m0744
+		doins -r vb2000/{checktst,checkvbtst,runallvb}
+		docinto vb2000
+		dodoc vb2000/DOC/*
+	fi
+}
+
+pkg_postinst() {
+	echo
+	einfo "Before you use GAMESS for any serious work you HAVE"
+	einfo "to run the supplied test files located in"
+	einfo "/usr/share/gamess/tests and check them thoroughly."
+	einfo "Otherwise all scientific publications resulting from"
+	einfo "your GAMESS runs should be immediately rejected :)"
+	einfo "To do so copy the content of /usr/share/gamess/tests"
+	einfo "to some temporary location and execute './runall'. "
+	einfo "Then run the checktst script in the same directory to"
+	einfo "validate the tests."
+	einfo "Please consult TEST.DOC and the other docs!"
+
+	if [[ ${FCOMP} == "ifort" ]]; then
+		echo
+		ewarn "IMPORTANT NOTE: We STRONGLY recommend to stay away"
+		ewarn "from ifc-9.0 for now and use the ifc-8.1 series of"
+		ewarn "compilers UNLESS you can run through ALL of the "
+		ewarn "test cases (see above) successfully."
+	fi
+
+	echo
+	einfo "If you want to run on more than a single CPU"
+	einfo "you will have to acquaint yourself with the way GAMESS"
+	einfo "does multiprocessor runs and adjust rungms according to"
+	einfo "your target network architecture."
+	echo
+}
diff --git a/sci-chemistry/gamess/gamess-20180930.3.ebuild b/sci-chemistry/gamess/gamess-20180930.3.ebuild
deleted file mode 100644
index 44e7fa323..000000000
--- a/sci-chemistry/gamess/gamess-20180930.3.ebuild
+++ /dev/null
@@ -1,381 +0,0 @@
-# Copyright 1999-2018 Gentoo Authors
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=6
-
-inherit check-reqs fortran-2 flag-o-matic pax-utils toolchain-funcs
-
-DESCRIPTION="A powerful quantum chemistry package"
-HOMEPAGE="http://www.msg.chem.iastate.edu/GAMESS/GAMESS.html"
-SRC_URI="
-	${P}.tar.gz
-	qmmm-tinker? ( tinker.tar.gz )"
-
-SLOT="0"
-LICENSE="gamess"
-# NOTE: PLEASE do not stabilize gamess. It does not make sense
-# since the tarball has fetch restrictions and upstream only
-# provides the latest version. In other words: As soon as a
-# new version comes out the stable version will be useless since
-# users can not get at the tarball any more.
-KEYWORDS="~amd64 ~x86"
-IUSE="mpi msucc neo openmp pax_kernel qmmm-tinker vb2000"
-
-CDEPEND="
-	app-shells/tcsh
-	mpi? ( virtual/mpi )
-	virtual/blas"
-DEPEND="${CDEPEND}
-	virtual/pkgconfig"
-RDEPEND="${CDEPEND}
-	net-misc/openssh"
-
-REQUIRED_USE="(
-	openmp? ( !neo !vb2000 ) )"
-
-S="${WORKDIR}/${PN}"
-
-RESTRICT="fetch"
-
-GAMESS_DOWNLOAD="http://www.msg.ameslab.gov/GAMESS/License_Agreement.html"
-GAMESS_VERSION="September 30, 2018 R3"
-
-pre_build_checks() {
-	if use msucc; then
-		CHECKREQS_MEMORY=6G
-		check-reqs_pkg_setup
-	fi
-}
-
-pkg_pretend() {
-	pre_build_checks
-}
-
-pkg_nofetch() {
-	echo
-	elog "Please download ${PN}-current.tar.gz from"
-	elog "${GAMESS_DOWNLOAD}."
-	elog "Be sure to select the version ${GAMESS_VERSION} tarball!!"
-	elog "Then move the tarball to"
-	elog "${DISTDIR}/${P}.tar.gz"
-	if use qmmm-tinker ; then
-		elog "Also download http://www.msg.ameslab.gov/GAMESS/tinker.tar.gz"
-		elog "and place tinker.tar.gz to ${DISTDIR}"
-	fi
-	echo
-}
-
-get_fcomp() {
-	case $(tc-getFC) in
-		*gfortran* )
-			FCOMP="gfortran" ;;
-		ifort )
-			FCOMP="ifc" ;;
-		* )
-			FCOMP=$(tc-getFC) ;;
-	esac
-}
-
-pkg_setup() {
-	pre_build_checks
-	use openmp && FORTRAN_NEED_OPENMP=1
-	fortran-2_pkg_setup
-	get_fcomp
-	# currently amd64 is only supported with gfortran
-	if [[ "${ARCH}" == "amd64" ]] && [[ ${FCOMP} != *gfortran* ]];
-		then die "You will need gfortran to compile gamess on amd64"
-	fi
-
-	# note about qmmm-tinker
-	if use qmmm-tinker; then
-			einfo "By default MM subsistem is restricted to 1000 atoms"
-			einfo "if you want larger MM subsystems then you should set"
-			einfo "QMMM_GAMESS_MAXMM variable to needed value in your make.conf"
-			einfo "By default maximum number of atom classes types and size of"
-			einfo "hessian are restricted to 250, 500 and 1000000 respectively"
-			einfo "If you want larger sizes set:"
-			einfo "QMMM_GAMESS_MAXCLASS"
-			einfo "QMMM_GAMESS_MAXCTYP"
-			einfo "QMMM_GAMESS_MAXHESS"
-			einfo "in your make.conf"
-	fi
-
-	#note about mpi
-	if use mpi; then
-		ewarn ""
-		ewarn "You should adjust rungms script for your mpi implentation"
-		ewarn "because deafult one will not work"
-		ewarn ""
-	fi
-}
-
-src_unpack() {
-	unpack ${A}
-
-	if use qmmm-tinker; then
-		mv tinker gamess/ || die "failed to move tinker directory"
-	fi
-}
-
-src_prepare() {
-	tc-export PKG_CONFIG
-	# apply LINUX-arch patches to gamess makesfiles
-	eapply "${FILESDIR}/${P}.gentoo.patch"
-	eapply_user
-	# select arch
-	# NOTE: please leave lked alone; it should be good as is!!
-	cd "${S}"
-	local active_arch;
-	if [[ "${ARCH}" == "amd64" ]]; then
-		active_arch="linux64";
-	else
-		active_arch="linux32";
-	fi
-
-	# fix "relocation truncated to fit" problem
-	append-flags -mcmodel=medium
-	append-ldflags -mcmodel=medium
-
-	# for hardened-gcc let't turn off ssp, since it breakes
-	# a few routines
-	if use pax_kernel && [[ ${FCOMP} == g77 ]]; then
-		FFLAGS="${FFLAGS} -fno-stack-protector-all"
-	fi
-
-	# Enable mpi stuff
-	if use mpi; then
-		sed -e "s:set COMM = sockets:set COMM = mpi:g" \
-			-i ddi/compddi || die "Enabling mpi build failed"
-		sed -e "s:MPI_INCLUDE_PATH = ' ':MPI_INCLUDE_PATH =	'-I/usr/include ':g" \
-			-i ddi/compddi || die "Enabling mpi build failed"
-		sed -e "s:MSG_LIBRARIES='../ddi/libddi.a -lpthread':MSG_LIBRARIES='../ddi/libddi.a -lmpi -lpthread':g" \
-			-i lked || die "Enabling mpi build failed"
-	fi
-
-	# enable NEO
-	if use neo; then
-		sed -e "s:NEO=false:NEO=true:" -i compall lked || \
-			die "Failed to enable NEO code"
-	else
-		sed -e "s:NEO=true:NEO=false:" -i compall lked || \
-			die "Failed to disable NEO code"
-	fi
-	# enable VB2000
-	if use vb2000; then
-		sed -e "s:VB2000=false:VB2000=true:" -i compall lked || \
-			die "Failed to enable VB2000 code"
-	else
-		sed -e "s:VB2000=true:VB2000=false:" -i compall lked || \
-			die "Failed to disable VB2000 code"
-	fi
-	# enable GAMESS-qmmm
-	if use qmmm-tinker; then
-		eapply "${FILESDIR}/${PN}-qmmm-tinker-fix-idate.patch"
-		sed -e "s:TINKER=false:TINKER=true:" -i compall lked || \
-			die "Failed to enable TINKER code"
-		if [ "x$QMMM_GAMESS_MAXMM" == "x" ]; then
-			einfo "No QMMM_GAMESS_MAXMM set. Using default value = 1000"
-		else
-			einfo "Setting QMMM_GAMESS_MAXMM to $QMMM_GAMESS_MAXMM"
-			sed -e "s:maxatm=1000:maxatm=$QMMM_GAMESS_MAXMM:g" \
-			 -i tinker/sizes.i \
-			 || die "Setting QMMM_GAMESS_MAXMM failed"
-			sed -e "s:MAXATM=1000:MAXATM=$QMMM_GAMESS_MAXMM:g" \
-			 -i source/inputb.src \
-			 || die "Setting QMMM_GAMESS_MAXMM failed"
-		fi
-		if [ "x$QMMM_GAMESS_MAXCLASS" == "x" ]; then
-			einfo "No QMMM_GAMESS_MAXMM set. Using default value = 250"
-		else
-			sed -e "s:maxclass=250:maxclass=$QMMM_GAMESS_MAXCLASS:g" \
-				-i tinker/sizes.i \
-				|| die "Setting QMMM_GAMESS_MAXCLASS failed"
-		fi
-		if [ "x$QMMM_GAMESS_MAXCTYP" == "x" ]; then
-			einfo "No QMMM_GAMESS_MAXCTYP set. Using default value = 500"
-		else
-			sed -e "s:maxtyp=500:maxtyp=$QMMM_GAMESS_MAXCTYP:g" \
-				-i tinker/sizes.i \
-				|| die "Setting QMMM_GAMESS_MAXCTYP failed"
-		fi
-		if [ "x$QMMM_GAMESS_MAXHESS" == "x" ]; then
-			einfo "No QMMM_GAMESS_MAXHESS set. Usingdefault value = 1000000"
-		else
-			sed -e "s:maxhess=1000000:maxhess=$QMMM_GAMESS_MAXHESS:g" \
-				-i tinker/sizes.i \
-				|| die "Setting QMMM_GAMESS_MAXHESS failed"
-		fi
-	fi
-	# create proper activate sourcefile
-	cp "./tools/actvte.code" "./tools/actvte.f" || \
-		die "Failed to create actvte.f"
-	sed -e "s/^\*UNX/    /" -i "./tools/actvte.f" || \
-		die "Failed to perform UNX substitutions in actvte.f"
-
-	# fix GAMESS' compall script to use proper CC
-	sed -e "s|\$CCOMP -c \$extraflags source/zunix.c|$(tc-getCC) -c \$extraflags source/zunix.c|" \
-		-i compall || die "Failed setting up compall script"
-
-	# insert proper FFLAGS into GAMESS' comp makefile
-	# in case we're using ifc let's strip all the gcc
-	# specific stuff
-	if [[ ${FCOMP} == "ifort" ]]; then
-		sed -e "s/gentoo-OPT = '-O2'/OPT = '${FFLAGS} -quiet'/" \
-			-i comp || die "Failed setting up comp script"
-	elif ! use x86; then
-		sed -e "s/-malign-double //" \
-			-e "s/gentoo-OPT='-O2'/OPT='${FFLAGS}'/" \
-			-i comp || die "Failed setting up comp script"
-	else
-		sed -e "s/gentoo-OPT = '-O2'/OPT = '${FFLAGS}'/" \
-			-i comp || die "Failed setting up comp script"
-	fi
-
-	# fix up GAMESS' linker script;
-	sed -e "s/gentoo-LDOPTS=' '/LDOPTS='${LDFLAGS}'/" \
-		-i lked || die "Failed setting up lked script"
-	# fix up GAMESS' ddi TCP/IP socket build
-	sed -e "s/gentoo-CC = 'gcc'/CC = '$(tc-getCC)'/" \
-		-i ddi/compddi || die "Failed setting up compddi script"
-	# Creating install.info
-	cat > install.info <<-EOF
-	#!/bin/csh
-	setenv GMS_PATH $WORKDIR/gamess
-	setenv GMS_BUILD_DIR $WORKDIR/gamess
-	setenv GMS_TARGET $active_arch
-	setenv GMS_FORTRAN $FCOMP
-	setenv GMS_GFORTRAN_VERNO $(gcc-major-version).$(gcc-minor-version)
-	setenv GMS_MATHLIB atlas
-	setenv GMS_MATHLIB_PATH  /usr/$(get_libdir)/atlas
-	setenv GMS_DDI_COMM sockets
-	setenv GMS_LIBCCHEM false
-	setenv GMS_PHI false
-	setenv GMS_SHMTYPE sysv
-	setenv GMS_OPENMP $(usex openmp true false)
-	setenv GMS_MSUCC $(usex msucc true false)
-	EOF
-
-}
-
-src_compile() {
-	# build actvte
-	cd "${S}"/tools
-	${FCOMP} -o actvte.x actvte.f || \
-		die "Failed to compile actvte.x"
-
-	# for hardened (PAX) users and ifc we need to turn
-	# MPROTECT off
-	if [[ ${FCOMP} == "ifort" ]] && use pax_kernel; then
-		pax-mark -PemRxS actvte.x
-	fi
-
-	# build gamess
-	cd "${S}"
-	./compall || die "compall failed"
-
-	# build the ddi TCP/IP socket stuff
-	cd ${S}/"ddi"
-	./compddi || die "compddi failed"
-
-	# finally, link it all together
-	cd "${S}"
-	./lked || die "lked failed"
-
-	# for hardened (PAX) users and ifc we need to turn
-	# MPROTECT off
-	if [[ ${FCOMP} == "ifort" ]] && use pax_kernel; then
-		pax-mark -PemRxS ${PN}.00.x
-	fi
-}
-
-src_install() {
-	# the executables
-	dobin ${PN}.00.x rungms gms-files.csh \
-		|| die "Failed installing binaries"
-	if use !mpi; then
-		dobin ddi/ddikick.x \
-			|| die "Failed installing binaries"
-	fi
-
-	# the docs
-	dodoc *.DOC qmnuc/*.DOC
-
-	# install ericftm
-	insinto /usr/share/${PN}
-	doins auxdata/ericfmt.dat
-
-	# install mcpdata
-	insinto /usr/share/${PN}/MCP
-	doins auxdata/MCP/*
-
-	# install BASES
-	insinto /usr/share/${PN}/BASES
-	doins auxdata/BASES/*
-
-	# install QUANPOL
-	insinto /usr/share/${PN}/QUANPOL
-	doins auxdata/QUANPOL/*
-
-	# install tinker params in case of qmmm
-	if use qmmm-tinker ; then
-			dodoc tinker/simomm.doc
-			insinto /usr/share/${PN}
-			doins -r tinker/params51
-	fi
-
-	# install the tests the user should run, and
-	# fix up the runscript; also grab a copy of rungms
-	# so the user is ready to run the tests
-	insinto /usr/share/${PN}/tests
-	insopts -m0644
-	doins -r tests/*
-	insopts -m0744
-	doins runall
-	#doins tools/checktst/checktst tools/checktst/chkabs || \
-	#	die "Failed to install main test checker"
-	#doins tools/checktst/exam* || \
-	#	die "Failed to install individual test files"
-
-	insinto /usr/share/${PN}/neotests
-	insopts -m0644
-	doins -r qmnuc/neotests/*
-
-	if use vb2000; then
-		insinto /usr/share/${PN}/vb2000
-		insopts -m0644
-		doins -r vb2000/{MAP,VBOLIB,test_results,tests}
-		insopts -m0744
-		doins -r vb2000/{checktst,checkvbtst,runallvb}
-		docinto vb2000
-		dodoc vb2000/DOC/*
-	fi
-}
-
-pkg_postinst() {
-	echo
-	einfo "Before you use GAMESS for any serious work you HAVE"
-	einfo "to run the supplied test files located in"
-	einfo "/usr/share/gamess/tests and check them thoroughly."
-	einfo "Otherwise all scientific publications resulting from"
-	einfo "your GAMESS runs should be immediately rejected :)"
-	einfo "To do so copy the content of /usr/share/gamess/tests"
-	einfo "to some temporary location and execute './runall'. "
-	einfo "Then run the checktst script in the same directory to"
-	einfo "validate the tests."
-	einfo "Please consult TEST.DOC and the other docs!"
-
-	if [[ ${FCOMP} == "ifort" ]]; then
-		echo
-		ewarn "IMPORTANT NOTE: We STRONGLY recommend to stay away"
-		ewarn "from ifc-9.0 for now and use the ifc-8.1 series of"
-		ewarn "compilers UNLESS you can run through ALL of the "
-		ewarn "test cases (see above) successfully."
-	fi
-
-	echo
-	einfo "If you want to run on more than a single CPU"
-	einfo "you will have to acquaint yourself with the way GAMESS"
-	einfo "does multiprocessor runs and adjust rungms according to"
-	einfo "your target network architecture."
-	echo
-}
diff --git a/sci-chemistry/gamess/metadata.xml b/sci-chemistry/gamess/metadata.xml
index 7f7e33d86..5d367dd16 100644
--- a/sci-chemistry/gamess/metadata.xml
+++ b/sci-chemistry/gamess/metadata.xml
@@ -13,7 +13,7 @@
 		<flag name="msucc">Build Michigan State University CCT3 and CCSD3A methods.
 			This will increase build time and memory requirements by ~10 times</flag>
 		<flag name="neo">Enable NEO for nuclear basis support</flag>
-		<flag name="pax_kernel">Make this package work on PAX kernels</flag>
+		<flag name="pax-kernel">Make this package work on PAX kernels</flag>
 		<flag name="qmmm-tinker">Enable tinker qmmm code</flag>
 		<flag name="vb2000">Enable Valence Bond method using VB2000 code</flag>
 	</use>
diff --git a/sci-chemistry/gnome-chemistry-utils/Manifest b/sci-chemistry/gnome-chemistry-utils/Manifest
deleted file mode 100644
index 5895e4a91..000000000
--- a/sci-chemistry/gnome-chemistry-utils/Manifest
+++ /dev/null
@@ -1 +0,0 @@
-DIST gnome-chemistry-utils-0.14.2.tar.bz2 6348310 BLAKE2B 194fa8b3e8d95622620a076a6d51ce842d9ad74f9a36fad6c381ecd3212db0d9f4649a635b56c09fa2acb81773635fd0c175884d29f832c6d193a5107de7874c SHA512 61e76be0cf4277b542c550d01dcf27229b0844d280946fa7d2e420194e97f657582c892dc12b48546ad35df08c2c9c6ab5a2539e3984b1170a76a0fbb655e681
diff --git a/sci-chemistry/gnome-chemistry-utils/files/gnome-chemistry-utils-0.14.2-extern-c.patch b/sci-chemistry/gnome-chemistry-utils/files/gnome-chemistry-utils-0.14.2-extern-c.patch
deleted file mode 100644
index f505af970..000000000
--- a/sci-chemistry/gnome-chemistry-utils/files/gnome-chemistry-utils-0.14.2-extern-c.patch
+++ /dev/null
@@ -1,84 +0,0 @@
- goffice/gchemutils-priv.h | 2 +-
- goffice/gchemutils.cc     | 7 ++++---
- goffice/gchemutils.h      | 6 +++---
- goffice/gogcuapp.h        | 2 +-
- 4 files changed, 9 insertions(+), 8 deletions(-)
-
-diff --git a/goffice/gchemutils-priv.h b/goffice/gchemutils-priv.h
-index 480e1a5..deb9687 100644
---- a/goffice/gchemutils-priv.h
-+++ b/goffice/gchemutils-priv.h
-@@ -23,12 +23,12 @@
- #ifndef GOFFICE_GCHEMUTILS_PRIV_H
- #define GOFFICE_GCHEMUTILS_PRIV_H
- 
--#include "gchemutils.h"
- #include <gcu/chem3ddoc.h>
- #include <gcu/structs.h>
- #include <gogcuapp.h>
- #include <gcu/document.h>
- #include <gcugtk/window.h>
-+#include "gchemutils.h"
- 
- struct _GOGChemUtilsComponent
- {
-diff --git a/goffice/gchemutils.cc b/goffice/gchemutils.cc
-index 2aa85b5..a477b13 100644
---- a/goffice/gchemutils.cc
-+++ b/goffice/gchemutils.cc
-@@ -20,6 +20,10 @@
-  * USA
-  */
- 
-+#include <map>
-+#include <string>
-+#include <cstring>
-+
- #include "config.h"
- #include "gchemutils-priv.h"
- #include "gogcpapp.h"
-@@ -31,9 +35,6 @@
- #include <goffice/app/module-plugin-defs.h>
- #include <goffice/component/go-component-factory.h>
- #include <glib/gi18n-lib.h>
--#include <map>
--#include <string>
--#include <cstring>
- 
- //gcuGOfficeApplication *app;
- 
-diff --git a/goffice/gchemutils.h b/goffice/gchemutils.h
-index 2f62aa5..8e6acb9 100644
---- a/goffice/gchemutils.h
-+++ b/goffice/gchemutils.h
-@@ -23,12 +23,12 @@
- #ifndef GOFFICE_GCHEMPAINT_H
- #define GOFFICE_GCHEMPAINT_H
- 
--#include <goffice/component/goffice-component.h>
--#include <goffice/component/go-component.h>
--
- extern "C"
- {
- 
-+#include <goffice/component/goffice-component.h>
-+#include <goffice/component/go-component.h>
-+
- typedef struct _GOGChemUtilsComponent GOGChemUtilsComponent;
- 
- typedef GOComponentClass GOGChemUtilsComponentClass;
-diff --git a/goffice/gogcuapp.h b/goffice/gogcuapp.h
-index 0012931..0cad715 100644
---- a/goffice/gogcuapp.h
-+++ b/goffice/gogcuapp.h
-@@ -23,9 +23,9 @@
- #ifndef GO_GCU_APP_H
- #define GO_GCU_APP_H
- 
--#include "gchemutils.h"
- #include <gcu/structs.h>
- #include <string>
-+#include "gchemutils.h"
- 
- namespace gcu {
- 	class Document;
diff --git a/sci-chemistry/gnome-chemistry-utils/gnome-chemistry-utils-0.14.2-r1.ebuild b/sci-chemistry/gnome-chemistry-utils/gnome-chemistry-utils-0.14.2-r1.ebuild
deleted file mode 100644
index 74b6741ec..000000000
--- a/sci-chemistry/gnome-chemistry-utils/gnome-chemistry-utils-0.14.2-r1.ebuild
+++ /dev/null
@@ -1,45 +0,0 @@
-# Copyright 1999-2014 Gentoo Foundation
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=5
-
-GCONF_DEBUG="no"
-inherit eutils gnome2 versionator
-
-DESCRIPTION="Programs and library containing GTK widgets and C++ classes related to chemistry"
-HOMEPAGE="http://gchemutils.nongnu.org/"
-SRC_URI="http://download.savannah.gnu.org/releases/gchemutils/$(get_version_component_range 1-2)/${P}.tar.bz2"
-
-SLOT="0"
-KEYWORDS="~amd64 ~x86"
-LICENSE="GPL-3 FDL-1.3"
-IUSE="gnumeric nls"
-
-RDEPEND="
-	>=app-text/gnome-doc-utils-0.3.2
-	>=dev-libs/glib-2.26.0:2
-	>=dev-libs/libxml2-2.4.16:2
-	>=gnome-extra/libgsf-1.14.9
-	>=sci-chemistry/bodr-5
-	>=sci-chemistry/chemical-mime-data-0.1.94
-	>=sci-chemistry/openbabel-2.3.0
-	>=x11-libs/cairo-1.6.0
-	>=x11-libs/gdk-pixbuf-2.22.0
-	>=x11-libs/goffice-0.10.4
-	x11-libs/gtk+:3
-	>=x11-libs/libX11-1.0.0
-	gnumeric? ( >=app-office/gnumeric-1.11.6 )"
-DEPEND="
-	virtual/pkgconfig
-	app-doc/doxygen"
-
-RESTRICT="mirror"
-
-src_configure() {
-	local myeconfargs=(
-		$(use_enable nls)
-		--disable-mozilla-plugin
-		--disable-update-databases
-	)
-	gnome2_src_configure ${myeconfargs[@]}
-}
diff --git a/sci-chemistry/gnome-chemistry-utils/gnome-chemistry-utils-9999.ebuild b/sci-chemistry/gnome-chemistry-utils/gnome-chemistry-utils-9999.ebuild
deleted file mode 100644
index 98af45ada..000000000
--- a/sci-chemistry/gnome-chemistry-utils/gnome-chemistry-utils-9999.ebuild
+++ /dev/null
@@ -1,52 +0,0 @@
-# Copyright 1999-2014 Gentoo Foundation
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=5
-
-GCONF_DEBUG="no"
-inherit autotools flag-o-matic gnome2 versionator subversion
-
-DESCRIPTION="Programs and library containing GTK widgets and C++ classes related to chemistry"
-HOMEPAGE="http://gchemutils.nongnu.org/"
-SRC_URI=""
-ESVN_REPO_URI="svn://svn.savannah.nongnu.org/gchemutils/trunk/gchemutils"
-
-SLOT="0"
-KEYWORDS=""
-LICENSE="GPL-3 FDL-1.3"
-IUSE="gnumeric nls"
-
-RDEPEND="
-	>=dev-libs/glib-2.36.0:2
-	>=dev-libs/libxml2-2.4.16:2
-	>=gnome-extra/libgsf-1.14.9
-	>=sci-chemistry/bodr-5
-	>=sci-chemistry/chemical-mime-data-0.1.94
-	>=sci-chemistry/openbabel-2.3.0
-	>=x11-libs/cairo-1.6.0
-	>=x11-libs/gdk-pixbuf-2.22.0
-	>=x11-libs/goffice-0.10.4
-	x11-libs/gtk+:3
-	>=x11-libs/libX11-1.0.0
-	gnumeric? ( >=app-office/gnumeric-1.11.6 )"
-DEPEND="
-	virtual/pkgconfig
-	app-doc/doxygen"
-
-RESTRICT="mirror"
-
-ESVN_BOOTSTRAP="eautoreconf"
-
-src_prepare() {
-	subversion_src_prepare
-	gnome2_src_prepare
-}
-
-src_configure() {
-	local myeconfargs=(
-		$(use_enable nls)
-		--disable-mozilla-plugin
-		--disable-update-databases
-	)
-	gnome2_src_configure ${myeconfargs[@]}
-}
diff --git a/sci-chemistry/gnome-chemistry-utils/metadata.xml b/sci-chemistry/gnome-chemistry-utils/metadata.xml
deleted file mode 100644
index c6cbb8582..000000000
--- a/sci-chemistry/gnome-chemistry-utils/metadata.xml
+++ /dev/null
@@ -1,11 +0,0 @@
-<?xml version="1.0" encoding="UTF-8"?>
-<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
-<pkgmetadata>
-	<longdescription lang="en">
-The Gnome Chemistry Utils provide some programs and library containing
-GTK widgets and some C++ classes related to chemistry. 
-</longdescription>
-	<use>
-		<flag name="gnumeric">Build pluging for gnumeric</flag>
-	</use>
-</pkgmetadata>
diff --git a/sci-chemistry/hydronmr/Manifest b/sci-chemistry/hydronmr/Manifest
deleted file mode 100644
index 581a1e0aa..000000000
--- a/sci-chemistry/hydronmr/Manifest
+++ /dev/null
@@ -1,13 +0,0 @@
-DIST 6lyz.pdb 117590 BLAKE2B b56062b3aba0f463c2b42f40e91b44701ed8ef6cf9b6e130966e7ba68b404e516a0812a6bfee96fe1f113b5fea89a73bb306b59405c0b21a12cdb04e755b57ab SHA512 f1e6814528e290556ab31ec81ff14a42b3bca03b417b462fd43a5ed6c154eb278deb8bd79ffe6af474f07e43258b250e4a188625d27e7eac3cbcd653e0976db4
-DIST fast-hydronmr-1.pdf 80922 BLAKE2B 568586d2fc6b7aa30f55c6682897e7039809a3d1a165fd462410556f625377e14a56c7b8913084b391de756a54da629106f53299fb1e4903883cdbe6447ffe96 SHA512 9698d3f2ab0cab996e67cf5a3484e77ceeaacdaa89c0ad33ea76ace873c5f3f60ad2f2ff4f0af2811909a8bab92fd0bf40f98f3b0bba0f3d7286803368b802c0
-DIST fast-hydronmr-2.pdf 148950 BLAKE2B e3d77775beb884f2a69798e1fa51e45e4e82b0aefe9f58de59aba9872ca29d351928750830db043f61690bc6a5d015243d5d453d3ce8e37f778cb4c6c9deb996 SHA512 ff8ab25fbf90e8245fce039cf8ea866f77a0bf752ed9627c9f7fc008cdaa4ca313336467c01eb25323634e9ca2e5eaf24ffe8f1a4548b09488b0b85590c31ca8
-DIST fast-hydronmr7c2lnx.exe 418849 BLAKE2B a2eb49b91544c82ac4053ca369553af96f0d273cde4efb20302c130401136b175c3b9748432f080b9a0ca346cf3b57c96058a6f4fe9db95bbc8838d1b69ba6cc SHA512 47280c5f8eea689a12c1309a1e2039a6477cff68ba07a1398ed0a4a0be1848ae1427b54d26057f7781304ab8708b041a44f1ed675e624eaa41637f523c94206e
-DIST hydronmr.dat 898 BLAKE2B 5974555afddcc5153c2ca646b330c9ad1b08ea25c122dfd5aa34515b0e0627c8a9913ad442e6b7d73f441c1ada74eef28e06b4c306ed924b7627e052ec3c8f7f SHA512 bc37da9cd82fcb958bad3a38923732a7ae952d9780b5be13ace57a10aa4383e118bfc42594def1232e27f39687f9956feae3096709c36027042246b98f80726b
-DIST hydronmr.pdf 193769 BLAKE2B 84c40f7604e04695061734ae70ae275cd79ee8a80c82f97217d1a966fd83a874ce00ea4e456dbfa8e4730f530a79aa4a63e6e098d872de716b1d65f57ed3ed38 SHA512 33f5b3a01c988913bf28265054c6ada4660fa2071ecf8d0210bfaefc22ee4e265e5b41a72297127656f58cda9ca8cb4c783b0daf677a2bdf46d69d5cc254e17a
-DIST hydronmr7c.pdf 24524 BLAKE2B 0cc4f95d6b76e972fe6f8c8af84b10b708aabd3f0400d388e905d9c01d9225cf1d87c991689664965dc3289df3f7ffee2734430f47df9a2553e7b0d22c4b8c16 SHA512 cfba5db480973d525d3376a45e745407ef20d584b3d2146550035c47b32ca09229db586fb662e92925024752bdb9303939f9dd4bf311f89ca4d16c3d4e064716
-DIST hydronmr7c2lnx.exe 418847 BLAKE2B a90e88e3336b3c2b85c6f34f06ead99b2e882b815f470eda82472cd5b1747da23c9cb18f18b2eef604502b324d93d8bea5b5040f7607733455d592bfa980ef86 SHA512 f3d8be7cf4c1d0465247227af19fdc47c4ab7e9e84379ce93eb58f3b46823a5a265d2ba457d24227909894a7a1f047beea6a8b2e800a5335a9fb805d7a0c3588
-DIST lysozyme31-fast-nmr.res 76529 BLAKE2B b4daaa7f6a316aca0c6ef8d4d63dc8be7296ba38b374feb728f0135e5475f32978a85b7a985c889334f4ef5c8885b4b7e896058e0a137ca9c3c3e6341df86d3b SHA512 6d82d374e6d4bca773e47d7f9b8ef284e815fa0cb05bcb7f577c0f1f30b278a57a454bc5fe4f8a85bf334387190b8b61841e262b0e7e7a50c230e8486c7cac16
-DIST lysozyme31-fast-nmr.t12 12891 BLAKE2B b9179d3c44ff09e8a6340c32e1319c790497bf35ae2a401ec3c18e948e461658b293bc9fb5f3dfb977129e6d552d3f74f7bc319a84afd46e1debf1adb31fc418 SHA512 82bfea32955260e4bf87b71e0527ce979db7f263545904aa86ea6f1c4533a4fade586cafe5cd2e76708e9d15e27975de7012f45586ec789df1ec2b43a88accc9
-DIST lysozyme31-nmr-pri.bea 56056 BLAKE2B 8d12f76c6dfe454543309374a6578650eae663311ef976fd7004b461e16bba34f68e465acc78819f869c8728e34802d86c70eeafb00288a07b56257ad56ab25d SHA512 520cb607592be3dc4cd4a8c9ee75a82e50334fb42b00c6bcc2eae5e12e53fc231e29e7c7636fa845e4e6360aa9a7a976a0e509912993d80aeb6eb51b3f4204b2
-DIST lysozyme31-nmr.res 76828 BLAKE2B f96a63636f2ef775a75f55ade37fe502b9ed65e02d8f4944b6627437866520fbe1f63f0809ec9284d1c0133acbf6116a461c9c84ed1901ecc1f0008c3e87c1ae SHA512 0704b593a3cba5115dd00693750ddde7a79c842c68c1872f2d9b7f8279db89f7f93c229dd9e3e6bf280c7eec1f9d4818dfce9aefd2621f100cc882523cf4885c
-DIST lysozyme31-nmr.t12 12891 BLAKE2B 020dbde3a404ff306cc6e11aff1d1f2d1e28f0016faaf549a4e768fe84435afb76f60aa99254b68e6036a4a9b6d6ede47887bf635f72040eb515a053858e5ad4 SHA512 4e553201973f7f308b6eaaf7080775b202ab0dc188ea78b286adc09a694f6ae957edb252fd0fc0f61d6bd2d25b582566de4136157eeb7490c030cc8a1b623f78
diff --git a/sci-chemistry/hydronmr/hydronmr-7c.ebuild b/sci-chemistry/hydronmr/hydronmr-7c.ebuild
deleted file mode 100644
index afdc48581..000000000
--- a/sci-chemistry/hydronmr/hydronmr-7c.ebuild
+++ /dev/null
@@ -1,52 +0,0 @@
-# Copyright 1999-2014 Gentoo Foundation
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=5
-
-DESCRIPTION="Calculation of NMR relaxation of small, quasirigid macromolecules"
-HOMEPAGE="http://leonardo.inf.um.es/macromol/programs/hydronmr/hydronmr.htm"
-SRC_URI="
-	http://leonardo.inf.um.es/macromol/programs/hydronmr/hydronmr7c2lnx.exe
-	http://leonardo.inf.um.es/macromol/programs/hydronmr/fast-hydronmr7c2lnx.exe
-	http://leonardo.inf.um.es/macromol/programs/hydronmr/hydronmr.pdf
-	http://leonardo.inf.um.es/macromol/programs/hydronmr/hydronmr7c.pdf
-	http://leonardo.inf.um.es/macromol/programs/hydronmr/fast-hydronmr-1.pdf
-	http://leonardo.inf.um.es/macromol/programs/hydronmr/fast-hydronmr-2.pdf
-	examples? (
-		http://leonardo.inf.um.es/macromol/programs/hydronmr/hydronmr.dat
-		http://leonardo.inf.um.es/macromol/programs/hydronmr/6lyz.pdb
-		http://leonardo.inf.um.es/macromol/programs/hydronmr/lysozyme31-nmr.res
-		http://leonardo.inf.um.es/macromol/programs/hydronmr/lysozyme31-nmr.t12
-		http://leonardo.inf.um.es/macromol/programs/hydronmr/lysozyme31-nmr-pri.bea
-		http://leonardo.inf.um.es/macromol/programs/hydronmr/lysozyme31-fast-nmr.res
-		http://leonardo.inf.um.es/macromol/programs/hydronmr/lysozyme31-fast-nmr.t12
-	)"
-
-SLOT="0"
-LICENSE="all-rights-reserved"
-KEYWORDS="~amd64 ~x86 ~amd64-linux ~x86-linux"
-IUSE="examples"
-
-QA_PREBUILT="opt/bin/.*"
-
-src_unpack() {
-	mkdir -p "${S}" || die
-	cd "${S}" || die
-	cp "${DISTDIR}"/* . || die
-}
-
-src_install() {
-	local exe
-	for exe in *exe; do
-		into /opt
-		newbin ${exe} ${exe%7c2lnx.exe}
-		rm ${exe} || die
-	done
-	dodoc *pdf
-	rm -f *pdf || die
-
-	if use examples; then
-		insinto /usr/share/${PN}/examples
-		doins *
-	fi
-}
diff --git a/sci-chemistry/hydronmr/metadata.xml b/sci-chemistry/hydronmr/metadata.xml
deleted file mode 100644
index da36ecbfc..000000000
--- a/sci-chemistry/hydronmr/metadata.xml
+++ /dev/null
@@ -1,8 +0,0 @@
-<?xml version="1.0" encoding="UTF-8"?>
-<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
-<pkgmetadata>
-	<maintainer type="project">
-		<email>sci-chemistry@gentoo.org</email>
-		<name>Gentoo Chemistry Project</name>
-	</maintainer>
-</pkgmetadata>
diff --git a/sci-chemistry/jligand/jligand-1.0.40.ebuild b/sci-chemistry/jligand/jligand-1.0.40.ebuild
index 52ae2c0a1..879964bbf 100644
--- a/sci-chemistry/jligand/jligand-1.0.40.ebuild
+++ b/sci-chemistry/jligand/jligand-1.0.40.ebuild
@@ -1,9 +1,9 @@
-# Copyright 1999-2015 Gentoo Foundation
+# Copyright 1999-2021 Gentoo Authors
 # Distributed under the terms of the GNU General Public License v2
 
-EAPI=5
+EAPI=7
 
-inherit java-pkg-2 java-ant-2 multilib
+inherit java-pkg-2 java-ant-2
 
 MY_PN="JLigand"
 
@@ -13,13 +13,12 @@ SRC_URI="http://www.ysbl.york.ac.uk/mxstat/${MY_PN}/${MY_PN}.${PV}.tar.gz"
 
 LICENSE="ccp4"
 SLOT="0"
-KEYWORDS=""
-IUSE=""
+KEYWORDS="~amd64"
 
 RDEPEND=">=virtual/jre-1.5"
 DEPEND=">=virtual/jdk-1.5"
 
-S="${WORKDIR}"/${MY_PN}.${PV}
+S="${WORKDIR}/${MY_PN}.${PV}"
 
 src_compile() {
 	sed 's:makefile::g' -i Makefile || die
@@ -27,7 +26,7 @@ src_compile() {
 }
 
 src_install() {
-	java-pkg_dojar ${PN}.jar
-	java-pkg_dolauncher ${PN} \
-		--jar ${PN}.jar
+	java-pkg_newjar JLigand.jar "${PN}.jar"
+	java-pkg_dolauncher JLigand \
+		--jar "${PN}.jar"
 }
diff --git a/sci-chemistry/ligplot+/Manifest b/sci-chemistry/ligplot+/Manifest
deleted file mode 100644
index 996b438bb..000000000
--- a/sci-chemistry/ligplot+/Manifest
+++ /dev/null
@@ -1 +0,0 @@
-DIST LigPlus.zip 1937904 SHA256 5d47af05f1fb48b4c0a6dee4d8eacb0d2ffe90966b0419d954c9d0f7a6580b49 SHA512 fee1c9b54c895d26ebd81f283ab942b199db87d189a01f22aebf26d6ed90e801f53b64cf9abf870721a4b478e68bf390b0e1c9eb9b02a692a1011271611f7afd WHIRLPOOL d86822b5e4cd0bd429df912f3b60de11094a2e549841f59343c0435a329a5c1181e543e06af9eb760d3bbbc6a12414fc5477c87f192deb40304d7ce619b65f28
diff --git a/sci-chemistry/ligplot+/ligplot+-1.4.ebuild b/sci-chemistry/ligplot+/ligplot+-1.4.ebuild
deleted file mode 100644
index f880a31fa..000000000
--- a/sci-chemistry/ligplot+/ligplot+-1.4.ebuild
+++ /dev/null
@@ -1,42 +0,0 @@
-# Copyright 1999-2015 Gentoo Foundation
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=5
-
-inherit java-pkg-2
-
-DESCRIPTION="GUI-based version of LIGPLOT"
-HOMEPAGE="http://www.ebi.ac.uk/thornton-srv/software/LigPlus/"
-SRC_URI="LigPlus.zip"
-
-SLOT="0"
-LICENSE="ligplot+"
-KEYWORDS="~amd64 ~x86 ~amd64-linux ~x86-linux"
-IUSE=""
-
-RDEPEND="virtual/jre:*"
-DEPEND=""
-
-RESTRICT="fetch"
-
-S="${WORKDIR}"/LigPlus
-
-QA_PREBUILT="opt/${PN}/.*"
-
-pkg_nofetch() {
-	elog "Please visit"
-	elog "http://www.ebi.ac.uk/thornton-srv/software/LigPlus/applicence.html"
-	elog "download ${A}"
-	elog "and save in ${DISTDIR}"
-}
-
-src_prepare() {
-	rm -rf lib/*{win,mac} || die
-}
-
-src_install() {
-	insinto /opt/${PN}
-	doins -r lib LigPlus.jar
-
-	make_wrapper ${PN} "java -jar \"${EPREFIX}/opt/${PN}/LigPlus.jar\""
-}
diff --git a/sci-chemistry/ligplot+/metadata.xml b/sci-chemistry/ligplot+/metadata.xml
deleted file mode 100644
index da36ecbfc..000000000
--- a/sci-chemistry/ligplot+/metadata.xml
+++ /dev/null
@@ -1,8 +0,0 @@
-<?xml version="1.0" encoding="UTF-8"?>
-<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
-<pkgmetadata>
-	<maintainer type="project">
-		<email>sci-chemistry@gentoo.org</email>
-		<name>Gentoo Chemistry Project</name>
-	</maintainer>
-</pkgmetadata>
diff --git a/sci-chemistry/mage/Manifest b/sci-chemistry/mage/Manifest
deleted file mode 100644
index 72cb530fd..000000000
--- a/sci-chemistry/mage/Manifest
+++ /dev/null
@@ -1 +0,0 @@
-DIST mage.6.44.060606.src.tgz 726357 BLAKE2B e427bf0707b192653c6cafd392a6ceaf49ec45fcff5447c42b4dd7e0e75ff46bf78edd9b03260cfe0d465c6ae0c6b1ff6a6340fb4fdf34feec1dba13a971d3ca SHA512 dceb63cc9806690539d0838079c2b57d6e62164049ca178d158e9c7eae759988c28d7e911942fd50f1ea880e61b2e9d7a38cc64bc5c229a4e5d442357c1f9227
diff --git a/sci-chemistry/mage/files/6.44.060606-Makefile.patch b/sci-chemistry/mage/files/6.44.060606-Makefile.patch
deleted file mode 100644
index df4fa4e1a..000000000
--- a/sci-chemistry/mage/files/6.44.060606-Makefile.patch
+++ /dev/null
@@ -1,29 +0,0 @@
-diff --git a/Makefile b/Makefile
-index 62a2033..1722ba5 100644
---- a/Makefile
-+++ b/Makefile
-@@ -11,7 +11,7 @@
- #  and static compile fails for RH 7.2 and 7.3
- #
- ifeq ($(MAKECMDGOALS),dynamic)
--CFLAGS = -I/usr/X11R6/include    #for RH7.3
-+CFLAGS += -I/usr/X11R6/include    #for RH7.3
- # CFLAGS = -I/usr/X11R6/LessTif/Motif1.2/include/ #for RH7.1
- else  #for RH8.0
- CFLAGS = -D_STATIC_
-@@ -80,13 +80,13 @@ static: $(OBJS) dlstubs.o
- 	$(CC) -static -o mage $(OBJS) dlstubs.o $(LIBS) $(FIN)
- 
- dynamic: $(OBJS)
--	$(CC) -o mage $(OBJS) -L/usr/X11R6/lib $(LIBS) -ldl $(FIN)
-+	$(CC) $(CFLAGS) $(LDFLAGS) -o mage $(OBJS) -L/usr/X11R6/lib $(LIBS) -ldl $(FIN)
- #	$(CC) -o mage $(OBJS) -L/usr/X11R6/LessTif/Motif1.2/lib $(LIBS) -ldl $(FIN)
- # where RH7.1 needed explicit LessTif and could compile static
- # RH7.3 fails static in all tried cases, but has Xm libraries implicit
- 
- debug: $(OBJS)
--	$(CC) -o mage $(OBJS) -L/usr/X11R6/lib $(LIBS) -ldl $(FIN)
-+	$(CC) $(CFLAGS) $(LDFLAGS) -o mage $(OBJS) -L/usr/X11R6/lib $(LIBS) -ldl $(FIN)
- 
- debugs: $(OBJS) dlstubs.o
- 	$(CC) -static -o mage $(OBJS) dlstubs.o $(LIBS) $(FIN)
diff --git a/sci-chemistry/mage/files/digest-mage-6.44.060606 b/sci-chemistry/mage/files/digest-mage-6.44.060606
deleted file mode 100644
index a73fa1c02..000000000
--- a/sci-chemistry/mage/files/digest-mage-6.44.060606
+++ /dev/null
@@ -1,3 +0,0 @@
-MD5 aa49ae2cd466d718891391f593202f97 mage.6.44.060606.src.tgz 726357
-RMD160 08305d65dd61ed573c67e58975a611439235e9f5 mage.6.44.060606.src.tgz 726357
-SHA256 c812202138cfee6b6434c51206286d460e83a12828e694013ecb16f2d5e839b3 mage.6.44.060606.src.tgz 726357
diff --git a/sci-chemistry/mage/mage-6.44.060606.ebuild b/sci-chemistry/mage/mage-6.44.060606.ebuild
deleted file mode 100644
index fa919faf1..000000000
--- a/sci-chemistry/mage/mage-6.44.060606.ebuild
+++ /dev/null
@@ -1,35 +0,0 @@
-# Copyright 1999-2015 Gentoo Foundation
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=5
-
-inherit eutils toolchain-funcs
-
-MY_P="${PN}.${PV}"
-
-DESCRIPTION="Mage is a 3D vector display program which shows 'kinemage' graphics"
-HOMEPAGE="http://kinemage.biochem.duke.edu/software/mage.php"
-SRC_URI="http://kinemage.biochem.duke.edu/downloads/software/mage/${MY_P}.src.tgz"
-
-LICENSE="richardson"
-SLOT="0"
-KEYWORDS="~amd64 ~x86"
-
-RDEPEND="sci-chemistry/prekin"
-DEPEND="${RDEPEND}"
-
-S="${WORKDIR}/${MY_P}"
-
-src_prepare() {
-	epatch "${FILESDIR}"/${PV}-Makefile.patch
-}
-
-src_compile() {
-	emake \
-		CC="$(tc-getCC)" \
-		dynamic
-}
-
-src_install() {
-	dobin "${S}"/mage
-}
diff --git a/sci-chemistry/mage/metadata.xml b/sci-chemistry/mage/metadata.xml
deleted file mode 100644
index da36ecbfc..000000000
--- a/sci-chemistry/mage/metadata.xml
+++ /dev/null
@@ -1,8 +0,0 @@
-<?xml version="1.0" encoding="UTF-8"?>
-<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
-<pkgmetadata>
-	<maintainer type="project">
-		<email>sci-chemistry@gentoo.org</email>
-		<name>Gentoo Chemistry Project</name>
-	</maintainer>
-</pkgmetadata>
diff --git a/sci-chemistry/mddnmr/Manifest b/sci-chemistry/mddnmr/Manifest
deleted file mode 100644
index 0002e4dba..000000000
--- a/sci-chemistry/mddnmr/Manifest
+++ /dev/null
@@ -1 +0,0 @@
-DIST mddnmr2.4.tgz 16659141 BLAKE2B 15ced6f083c1b99e28035b74d10f12908833078f94b2c00afab68461f0a0d42019d66fe353ae17b44123c71d6868bb8d82680892c3a03f588757ca83828e7359 SHA512 2ace437d184c79f9ed43a54efe31e8af12b2f555f49de864de55454f35139df2018f0ccd37ac7223752abbf517d815051be30904f29265d77767814dd97a667f
diff --git a/sci-chemistry/mddnmr/mddnmr-2.4-r1.ebuild b/sci-chemistry/mddnmr/mddnmr-2.4-r1.ebuild
deleted file mode 100644
index f635e927b..000000000
--- a/sci-chemistry/mddnmr/mddnmr-2.4-r1.ebuild
+++ /dev/null
@@ -1,65 +0,0 @@
-# Copyright 1999-2014 Gentoo Foundation
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=5
-
-PYTHON_COMPAT=( python2_7 )
-
-inherit python-single-r1
-
-MY_P="${PN}${PV}"
-
-DESCRIPTION="Program for processing of NUS multidimensional NMR spectra"
-HOMEPAGE="http://www.nmr.gu.se/~mdd/"
-SRC_URI="http://pc8.nmr.gu.se/~mdd/Downloads/${MY_P}.tgz"
-
-SLOT="0"
-KEYWORDS=""
-LICENSE="mddnmr"
-IUSE=""
-
-REQUIRED_USE="${PYTHON_REQUIRED_USE}"
-
-RDEPEND="
-	${PYTHON_DEPS}
-	app-shells/tcsh
-	sci-chemistry/nmrpipe"
-DEPEND=""
-
-RESTRICT="mirror"
-
-S="${WORKDIR}"/${PN}
-
-QA_PREBUILT="opt/${PN}/.*"
-
-src_install() {
-	exeinto /opt/${PN}/com
-	doexe com/*
-
-	exeinto /opt/${PN}/bin
-	if use amd64; then
-		doexe binXeonE5mkl/*
-	elif use x86; then
-		doexe binUbuntu32Static/*
-	fi
-
-	insinto /opt/${PN}/
-	doins -r GUI
-
-	cat >> "${T}"/qMDD <<- EOF
-	#!${EPREFIX}/bin/csh
-
-	setenv LD_LIBRARY_PATH $(grep LDPATH "${EPREFIX}"/etc/env.d/35intelsdp | sed 's:LDAPATH=::g')"
-	setenv MDD_NMR "${EPREFIX}/opt/${PN}"
-	setenv MDD_NMRbin "${EPREFIX}/opt/${PN}/bin/"
-	set path=( . "\$MDD_NMRbin"  "\${MDD_NMR}/com" \$path )
-
-	csh "${EPREFIX}/opt/${PN}/GUI/qMDD"
-	EOF
-
-	dobin "${T}"/qMDD
-
-	dodoc *pdf
-
-	python_optimize "${ED}"
-}
diff --git a/sci-chemistry/mddnmr/metadata.xml b/sci-chemistry/mddnmr/metadata.xml
deleted file mode 100644
index da36ecbfc..000000000
--- a/sci-chemistry/mddnmr/metadata.xml
+++ /dev/null
@@ -1,8 +0,0 @@
-<?xml version="1.0" encoding="UTF-8"?>
-<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
-<pkgmetadata>
-	<maintainer type="project">
-		<email>sci-chemistry@gentoo.org</email>
-		<name>Gentoo Chemistry Project</name>
-	</maintainer>
-</pkgmetadata>
diff --git a/sci-chemistry/mdsctk/Manifest b/sci-chemistry/mdsctk/Manifest
deleted file mode 100644
index fd27777bf..000000000
--- a/sci-chemistry/mdsctk/Manifest
+++ /dev/null
@@ -1 +0,0 @@
-DIST mdsctk-1.2.0.tar.gz 4454304 BLAKE2B 9752649c13140ca312545b31c86ba4adeafd9e9f1f9b8ea5ba4a76e4a5a94a2d4904573ee5ed15fb7d0a5b9f94bf381db4f8dba5a42b09954d4909b6a8e46956 SHA512 e1a0895135fb83734e80dce19320016971c6dfc397f3ac5bcc44a6a23ae531c722f1e56bdebcfccf165bf1805ab2715f4ab5f9052b5513e9c4d6e4f6c0944cb6
diff --git a/sci-chemistry/mdsctk/mdsctk-1.2.0.ebuild b/sci-chemistry/mdsctk/mdsctk-1.2.0.ebuild
deleted file mode 100644
index 1a099e69c..000000000
--- a/sci-chemistry/mdsctk/mdsctk-1.2.0.ebuild
+++ /dev/null
@@ -1,43 +0,0 @@
-# Copyright 1999-2015 Gentoo Foundation
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=5
-
-inherit cmake-utils db-use toolchain-funcs
-
-DESCRIPTION="Molecular Dynamics Spectral Clustering Toolkit"
-HOMEPAGE="https://github.com/douradopalmares/mdsctk"
-SRC_URI="https://github.com/douradopalmares/${PN}/archive/${PV}.tar.gz -> ${P}.tar.gz"
-
-LICENSE="GPL-2"
-SLOT="0"
-KEYWORDS=""
-IUSE="examples R"
-
-DEPEND="
-	=sci-chemistry/gromacs-4.6*:=
-	sci-libs/gsl
-	sys-libs/db:=[cxx]
-	virtual/blas
-	virtual/lapack
-	sci-libs/arpack
-	R? ( dev-lang/R )
-	"
-RDEPEND="${DEPEND}"
-
-src_configure() {
-	echo 'include_directories(${DB_CXX_INCLUDE_PATH})' >> CMakeLists.txt
-	local mycmakeargs=( -DDB_CXX_INCLUDE_PATH="$(db_includedir)" )
-	cmake-utils_src_configure
-}
-
-src_install() {
-	dodoc AUTHORS README.md
-	use R && dobin clustering_nmi.r  clustering_pdf.r  density.r  entropy.r  kmeans.r  mdsctk.r  plot_pdf.r \
-		probability.r
-	insinto /usr/share/"${PN}"/examples
-	use examples && doins -r examples
-	cd "${BUILD_DIR}" || die
-	dobin auto_decomp_sparse auto_decomp_sparse_nystrom bb_xtc_to_phipsi check_xtc decomp_sparse decomp_sparse_nystrom \
-		knn_data knn_rms make_sysparse make_gesparse phipsi_to_sincos rms_test split_xtc
-}
diff --git a/sci-chemistry/mdsctk/metadata.xml b/sci-chemistry/mdsctk/metadata.xml
deleted file mode 100644
index 466c91299..000000000
--- a/sci-chemistry/mdsctk/metadata.xml
+++ /dev/null
@@ -1,18 +0,0 @@
-<?xml version="1.0" encoding="UTF-8"?>
-<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
-<pkgmetadata>
-	<maintainer type="person">
-		<email>ottxor@gentoo.org</email>
-		<name>Christoph Junghans</name>
-	</maintainer>
-	<maintainer type="project">
-		<email>sci-chemistry@gentoo.org</email>
-		<name>Gentoo Chemistry Project</name>
-	</maintainer>
-	<use>
-		<flag name="R">Install <pkg>dev-lang/R</pkg> scripts as well</flag>
-	</use>
-	<upstream>
-		<remote-id type="github">douradopalmares/mdsctk</remote-id>
-	</upstream>
-</pkgmetadata>
diff --git a/sci-chemistry/mgltools-autodocktools/Manifest b/sci-chemistry/mgltools-autodocktools/Manifest
deleted file mode 100644
index 366b14ae4..000000000
--- a/sci-chemistry/mgltools-autodocktools/Manifest
+++ /dev/null
@@ -1 +0,0 @@
-DIST mgltools_source_1.5.6.tar.gz 40275811 BLAKE2B 98a2d71f33fc92233f1082637b54d63a180b6cf1fa8cc052cb497380ba1ea4c8bb1af023d492acfcbf11e23c33f4af7d297eada113838cb6f0133a55684546f3 SHA512 4ed956197f08b7c3779f0bb39393b40cdaff3461071b48815200c6ad0dce2de87375cda96fe20d3ace4ab81ba6b8cdb50b58d82f5e5b54fe2c7751201ff2f63e
diff --git a/sci-chemistry/mgltools-autodocktools/metadata.xml b/sci-chemistry/mgltools-autodocktools/metadata.xml
deleted file mode 100644
index da36ecbfc..000000000
--- a/sci-chemistry/mgltools-autodocktools/metadata.xml
+++ /dev/null
@@ -1,8 +0,0 @@
-<?xml version="1.0" encoding="UTF-8"?>
-<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
-<pkgmetadata>
-	<maintainer type="project">
-		<email>sci-chemistry@gentoo.org</email>
-		<name>Gentoo Chemistry Project</name>
-	</maintainer>
-</pkgmetadata>
diff --git a/sci-chemistry/mgltools-autodocktools/mgltools-autodocktools-1.5.6.ebuild b/sci-chemistry/mgltools-autodocktools/mgltools-autodocktools-1.5.6.ebuild
deleted file mode 100644
index 7af92f5db..000000000
--- a/sci-chemistry/mgltools-autodocktools/mgltools-autodocktools-1.5.6.ebuild
+++ /dev/null
@@ -1,66 +0,0 @@
-# Copyright 1999-2015 Gentoo Foundation
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=5
-
-PYTHON_COMPAT=( python2_7 )
-PYTHON_REQ_USE="tk"
-
-inherit distutils-r1 eutils
-
-MY_PN="AutoDockTools"
-MY_P="${MY_PN}-${PV/_rc3/}"
-
-DESCRIPTION="MGLTools Plugin -- AutoDockTools"
-HOMEPAGE="http://mgltools.scripps.edu"
-SRC_URI="http://mgltools.scripps.edu/downloads/tars/releases/REL${PV}/mgltools_source_${PV}.tar.gz"
-
-LICENSE="MGLTOOLS MPL-1.1"
-SLOT="0"
-KEYWORDS="~amd64 ~x86"
-IUSE=""
-
-RDEPEND="
-	dev-python/zsi[${PYTHON_USEDEP}]
-	sci-chemistry/autodock
-	sci-chemistry/mgltools-dejavu[${PYTHON_USEDEP}]
-	sci-chemistry/mgltools-geomutils[${PYTHON_USEDEP}]
-	sci-chemistry/mgltools-mglutil[${PYTHON_USEDEP}]
-	sci-chemistry/mgltools-molkit[${PYTHON_USEDEP}]
-	sci-chemistry/mgltools-opengltk[${PYTHON_USEDEP}]
-	sci-chemistry/mgltools-pmv[${PYTHON_USEDEP}]
-	sci-chemistry/mgltools-pybabel[${PYTHON_USEDEP}]
-	sci-chemistry/mgltools-pyglf[${PYTHON_USEDEP}]
-	sci-chemistry/mgltools-support[${PYTHON_USEDEP}]
-	sci-chemistry/mgltools-viewer-framework[${PYTHON_USEDEP}]
-	dev-python/pillow[tk,${PYTHON_USEDEP}]
-"
-DEPEND="${RDEPEND}
-	dev-lang/swig"
-
-S="${WORKDIR}"/${MY_P}
-
-DOCS=( AutoDockTools/RELNOTES )
-
-src_unpack() {
-	tar xzpf "${DISTDIR}"/${A} mgltools_source_${PV/_/}/MGLPACKS/${MY_P}.tar.gz || die
-	tar xzpf mgltools_source_${PV/_/}/MGLPACKS/${MY_P}.tar.gz || die
-}
-
-python_prepare_all() {
-	ecvs_clean
-	find "${S}" -name LICENSE -type f -delete || die
-
-	sed  \
-		-e 's:^.*CVS:#&1:g' \
-		-e 's:^.*LICENSE:#&1:g' \
-		-i "${S}"/MANIFEST.in || die
-	distutils-r1_python_prepare_all
-}
-
-python_install_all() {
-	distutils-r1_python_install_all
-
-	sed '1s:^.*$:#!/usr/bin/python:g' -i AutoDockTools/bin/runAdt || die
-	python_foreach_impl python_doscript AutoDockTools/bin/runAdt
-}
diff --git a/sci-chemistry/mgltools-bhtree/Manifest b/sci-chemistry/mgltools-bhtree/Manifest
deleted file mode 100644
index 366b14ae4..000000000
--- a/sci-chemistry/mgltools-bhtree/Manifest
+++ /dev/null
@@ -1 +0,0 @@
-DIST mgltools_source_1.5.6.tar.gz 40275811 BLAKE2B 98a2d71f33fc92233f1082637b54d63a180b6cf1fa8cc052cb497380ba1ea4c8bb1af023d492acfcbf11e23c33f4af7d297eada113838cb6f0133a55684546f3 SHA512 4ed956197f08b7c3779f0bb39393b40cdaff3461071b48815200c6ad0dce2de87375cda96fe20d3ace4ab81ba6b8cdb50b58d82f5e5b54fe2c7751201ff2f63e
diff --git a/sci-chemistry/mgltools-bhtree/metadata.xml b/sci-chemistry/mgltools-bhtree/metadata.xml
deleted file mode 100644
index da36ecbfc..000000000
--- a/sci-chemistry/mgltools-bhtree/metadata.xml
+++ /dev/null
@@ -1,8 +0,0 @@
-<?xml version="1.0" encoding="UTF-8"?>
-<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
-<pkgmetadata>
-	<maintainer type="project">
-		<email>sci-chemistry@gentoo.org</email>
-		<name>Gentoo Chemistry Project</name>
-	</maintainer>
-</pkgmetadata>
diff --git a/sci-chemistry/mgltools-bhtree/mgltools-bhtree-1.5.6.ebuild b/sci-chemistry/mgltools-bhtree/mgltools-bhtree-1.5.6.ebuild
deleted file mode 100644
index da8462b7d..000000000
--- a/sci-chemistry/mgltools-bhtree/mgltools-bhtree-1.5.6.ebuild
+++ /dev/null
@@ -1,43 +0,0 @@
-# Copyright 1999-2015 Gentoo Foundation
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=5
-
-PYTHON_COMPAT=( python2_7 )
-PYTHON_REQ_USE="tk"
-
-inherit distutils-r1 eutils
-
-MY_PN="bhtree"
-MY_P="${MY_PN}-${PV/_rc3/}"
-
-DESCRIPTION="MGLTools Plugin -- bhtree"
-HOMEPAGE="http://mgltools.scripps.edu"
-SRC_URI="http://mgltools.scripps.edu/downloads/tars/releases/REL${PV}/mgltools_source_${PV}.tar.gz"
-
-LICENSE="MGLTOOLS MPL-1.1"
-SLOT="0"
-KEYWORDS="~amd64 ~x86"
-IUSE=""
-
-RDEPEND="dev-python/numpy[${PYTHON_USEDEP}]"
-DEPEND="${RDEPEND}
-	dev-lang/swig"
-
-S="${WORKDIR}"/${MY_P}
-
-src_unpack() {
-	tar xzpf "${DISTDIR}"/${A} mgltools_source_${PV/_/}/MGLPACKS/${MY_P}.tar.gz || die
-	tar xzpf mgltools_source_${PV/_/}/MGLPACKS/${MY_P}.tar.gz || die
-}
-
-python_prepare_all() {
-	ecvs_clean
-	find "${S}" -name LICENSE -type f -delete || die
-
-	sed  \
-		-e 's:^.*CVS:#&1:g' \
-		-e 's:^.*LICENSE:#&1:g' \
-		-i "${S}"/MANIFEST.in || die
-	distutils-r1_python_prepare_all
-}
diff --git a/sci-chemistry/mgltools-cadd/Manifest b/sci-chemistry/mgltools-cadd/Manifest
deleted file mode 100644
index 366b14ae4..000000000
--- a/sci-chemistry/mgltools-cadd/Manifest
+++ /dev/null
@@ -1 +0,0 @@
-DIST mgltools_source_1.5.6.tar.gz 40275811 BLAKE2B 98a2d71f33fc92233f1082637b54d63a180b6cf1fa8cc052cb497380ba1ea4c8bb1af023d492acfcbf11e23c33f4af7d297eada113838cb6f0133a55684546f3 SHA512 4ed956197f08b7c3779f0bb39393b40cdaff3461071b48815200c6ad0dce2de87375cda96fe20d3ace4ab81ba6b8cdb50b58d82f5e5b54fe2c7751201ff2f63e
diff --git a/sci-chemistry/mgltools-cadd/metadata.xml b/sci-chemistry/mgltools-cadd/metadata.xml
deleted file mode 100644
index da36ecbfc..000000000
--- a/sci-chemistry/mgltools-cadd/metadata.xml
+++ /dev/null
@@ -1,8 +0,0 @@
-<?xml version="1.0" encoding="UTF-8"?>
-<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
-<pkgmetadata>
-	<maintainer type="project">
-		<email>sci-chemistry@gentoo.org</email>
-		<name>Gentoo Chemistry Project</name>
-	</maintainer>
-</pkgmetadata>
diff --git a/sci-chemistry/mgltools-cadd/mgltools-cadd-1.5.6.ebuild b/sci-chemistry/mgltools-cadd/mgltools-cadd-1.5.6.ebuild
deleted file mode 100644
index 3f6ccc4ec..000000000
--- a/sci-chemistry/mgltools-cadd/mgltools-cadd-1.5.6.ebuild
+++ /dev/null
@@ -1,42 +0,0 @@
-# Copyright 1999-2015 Gentoo Foundation
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=5
-
-PYTHON_COMPAT=( python2_7 )
-
-inherit distutils-r1 eutils
-
-MY_PN="CADD"
-MY_P="${MY_PN}-${PV/_rc3/}"
-
-DESCRIPTION="MGLTools Plugin -- CADD"
-HOMEPAGE="http://mgltools.scripps.edu"
-SRC_URI="http://mgltools.scripps.edu/downloads/tars/releases/REL${PV}/mgltools_source_${PV}.tar.gz"
-
-LICENSE="MGLTOOLS MPL-1.1"
-SLOT="0"
-KEYWORDS="~amd64 ~x86"
-IUSE=""
-
-RDEPEND=""
-DEPEND="${RDEPEND}
-	dev-lang/swig"
-
-S="${WORKDIR}"/${MY_P}
-
-src_unpack() {
-	tar xzpf "${DISTDIR}"/${A} mgltools_source_${PV/_/}/MGLPACKS/${MY_P}.tar.gz || die
-	tar xzpf mgltools_source_${PV/_/}/MGLPACKS/${MY_P}.tar.gz || die
-}
-
-python_prepare_all() {
-	ecvs_clean
-	find "${S}" -name LICENSE -type f -delete || die
-
-	sed  \
-		-e 's:^.*CVS:#&1:g' \
-		-e 's:^.*LICENSE:#&1:g' \
-		-i "${S}"/MANIFEST.in || die
-	distutils-r1_python_prepare_all
-}
diff --git a/sci-chemistry/mgltools-cmolkit/Manifest b/sci-chemistry/mgltools-cmolkit/Manifest
deleted file mode 100644
index 366b14ae4..000000000
--- a/sci-chemistry/mgltools-cmolkit/Manifest
+++ /dev/null
@@ -1 +0,0 @@
-DIST mgltools_source_1.5.6.tar.gz 40275811 BLAKE2B 98a2d71f33fc92233f1082637b54d63a180b6cf1fa8cc052cb497380ba1ea4c8bb1af023d492acfcbf11e23c33f4af7d297eada113838cb6f0133a55684546f3 SHA512 4ed956197f08b7c3779f0bb39393b40cdaff3461071b48815200c6ad0dce2de87375cda96fe20d3ace4ab81ba6b8cdb50b58d82f5e5b54fe2c7751201ff2f63e
diff --git a/sci-chemistry/mgltools-cmolkit/metadata.xml b/sci-chemistry/mgltools-cmolkit/metadata.xml
deleted file mode 100644
index da36ecbfc..000000000
--- a/sci-chemistry/mgltools-cmolkit/metadata.xml
+++ /dev/null
@@ -1,8 +0,0 @@
-<?xml version="1.0" encoding="UTF-8"?>
-<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
-<pkgmetadata>
-	<maintainer type="project">
-		<email>sci-chemistry@gentoo.org</email>
-		<name>Gentoo Chemistry Project</name>
-	</maintainer>
-</pkgmetadata>
diff --git a/sci-chemistry/mgltools-cmolkit/mgltools-cmolkit-1.5.6.ebuild b/sci-chemistry/mgltools-cmolkit/mgltools-cmolkit-1.5.6.ebuild
deleted file mode 100644
index 0b1ee8975..000000000
--- a/sci-chemistry/mgltools-cmolkit/mgltools-cmolkit-1.5.6.ebuild
+++ /dev/null
@@ -1,42 +0,0 @@
-# Copyright 1999-2015 Gentoo Foundation
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=5
-
-PYTHON_COMPAT=( python2_7 )
-
-inherit distutils-r1 eutils
-
-MY_PN="cMolKit"
-MY_P="${MY_PN}-${PV/_rc3/}"
-
-DESCRIPTION="MGLTools Plugin -- cMolKit"
-HOMEPAGE="http://mgltools.scripps.edu"
-SRC_URI="http://mgltools.scripps.edu/downloads/tars/releases/REL${PV}/mgltools_source_${PV}.tar.gz"
-
-LICENSE="MGLTOOLS MPL-1.1"
-SLOT="0"
-KEYWORDS="~amd64 ~x86"
-IUSE=""
-
-RDEPEND=""
-DEPEND="${RDEPEND}
-	dev-lang/swig"
-
-S="${WORKDIR}"/${MY_P}
-
-src_unpack() {
-	tar xzpf "${DISTDIR}"/${A} mgltools_source_${PV/_/}/MGLPACKS/${MY_P}.tar.gz || die
-	tar xzpf mgltools_source_${PV/_/}/MGLPACKS/${MY_P}.tar.gz || die
-}
-
-python_prepare_all() {
-	ecvs_clean
-	find "${S}" -name LICENSE -type f -delete || die
-
-	sed  \
-		-e 's:^.*CVS:#&1:g' \
-		-e 's:^.*LICENSE:#&1:g' \
-		-i "${S}"/MANIFEST.in || die
-	distutils-r1_python_prepare_all
-}
diff --git a/sci-chemistry/mgltools-dejavu/Manifest b/sci-chemistry/mgltools-dejavu/Manifest
deleted file mode 100644
index 366b14ae4..000000000
--- a/sci-chemistry/mgltools-dejavu/Manifest
+++ /dev/null
@@ -1 +0,0 @@
-DIST mgltools_source_1.5.6.tar.gz 40275811 BLAKE2B 98a2d71f33fc92233f1082637b54d63a180b6cf1fa8cc052cb497380ba1ea4c8bb1af023d492acfcbf11e23c33f4af7d297eada113838cb6f0133a55684546f3 SHA512 4ed956197f08b7c3779f0bb39393b40cdaff3461071b48815200c6ad0dce2de87375cda96fe20d3ace4ab81ba6b8cdb50b58d82f5e5b54fe2c7751201ff2f63e
diff --git a/sci-chemistry/mgltools-dejavu/files/mgltools-dejavu-1.5.6-pil.patch b/sci-chemistry/mgltools-dejavu/files/mgltools-dejavu-1.5.6-pil.patch
deleted file mode 100644
index 0ac1abdea..000000000
--- a/sci-chemistry/mgltools-dejavu/files/mgltools-dejavu-1.5.6-pil.patch
+++ /dev/null
@@ -1,43 +0,0 @@
- DejaVu/Camera.py  | 12 +++++++++---
- DejaVu/Texture.py |  5 ++++-
- 2 files changed, 13 insertions(+), 4 deletions(-)
-
-diff --git a/DejaVu/Camera.py b/DejaVu/Camera.py
-index 9ecc0eb..555666a 100644
---- a/DejaVu/Camera.py
-+++ b/DejaVu/Camera.py
-@@ -38,9 +38,15 @@ This Module implements the Camera class and the Fog class.
- 
- import os, sys, warnings
- 
--import Image
--import ImageFilter
--import ImageChops
-+try:
-+    import Image
-+    import ImageFilter
-+    import ImageChops
-+except ImportError:
-+    from PIL import Image
-+    from PIL import ImageFilter
-+    from PIL import ImageChops
-+
- 
- import tkMessageBox
- 
-diff --git a/DejaVu/Texture.py b/DejaVu/Texture.py
-index dccc280..bcf16be 100644
---- a/DejaVu/Texture.py
-+++ b/DejaVu/Texture.py
-@@ -15,7 +15,10 @@
- #
- 
- import sys, os
--import Image
-+try:
-+    import Image
-+except ImportError:
-+    from PIL import Image
- import numpy.oldnumeric as Numeric
- import warnings
- 
diff --git a/sci-chemistry/mgltools-dejavu/metadata.xml b/sci-chemistry/mgltools-dejavu/metadata.xml
deleted file mode 100644
index da36ecbfc..000000000
--- a/sci-chemistry/mgltools-dejavu/metadata.xml
+++ /dev/null
@@ -1,8 +0,0 @@
-<?xml version="1.0" encoding="UTF-8"?>
-<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
-<pkgmetadata>
-	<maintainer type="project">
-		<email>sci-chemistry@gentoo.org</email>
-		<name>Gentoo Chemistry Project</name>
-	</maintainer>
-</pkgmetadata>
diff --git a/sci-chemistry/mgltools-dejavu/mgltools-dejavu-1.5.6-r1.ebuild b/sci-chemistry/mgltools-dejavu/mgltools-dejavu-1.5.6-r1.ebuild
deleted file mode 100644
index 01029173c..000000000
--- a/sci-chemistry/mgltools-dejavu/mgltools-dejavu-1.5.6-r1.ebuild
+++ /dev/null
@@ -1,47 +0,0 @@
-# Copyright 1999-2015 Gentoo Foundation
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=5
-
-PYTHON_COMPAT=( python2_7 )
-PYTHON_REQ_USE="tk"
-
-inherit distutils-r1 eutils
-
-MY_PN="DejaVu"
-MY_P="${MY_PN}-${PV/_rc3/}"
-
-DESCRIPTION="MGLTools Plugin -- DejaVu"
-HOMEPAGE="http://mgltools.scripps.edu"
-SRC_URI="http://mgltools.scripps.edu/downloads/tars/releases/REL${PV}/mgltools_source_${PV}.tar.gz"
-
-LICENSE="MGLTOOLS MPL-1.1"
-SLOT="0"
-KEYWORDS="~amd64 ~x86"
-IUSE=""
-
-RDEPEND=""
-DEPEND="${RDEPEND}
-	dev-lang/swig"
-
-S="${WORKDIR}"/${MY_P}
-
-DOCS=( DejaVu/RELNOTES )
-
-PATCHES=( "${FILESDIR}"/${P}-pil.patch )
-
-src_unpack() {
-	tar xzpf "${DISTDIR}"/${A} mgltools_source_${PV/_/}/MGLPACKS/${MY_P}.tar.gz || die
-	tar xzpf mgltools_source_${PV/_/}/MGLPACKS/${MY_P}.tar.gz || die
-}
-
-python_prepare_all() {
-	ecvs_clean
-	find "${S}" -name LICENSE -type f -delete || die
-
-	sed  \
-		-e 's:^.*CVS:#&1:g' \
-		-e 's:^.*LICENSE:#&1:g' \
-		-i "${S}"/MANIFEST.in || die
-	distutils-r1_python_prepare_all
-}
diff --git a/sci-chemistry/mgltools-geomutils/Manifest b/sci-chemistry/mgltools-geomutils/Manifest
deleted file mode 100644
index 366b14ae4..000000000
--- a/sci-chemistry/mgltools-geomutils/Manifest
+++ /dev/null
@@ -1 +0,0 @@
-DIST mgltools_source_1.5.6.tar.gz 40275811 BLAKE2B 98a2d71f33fc92233f1082637b54d63a180b6cf1fa8cc052cb497380ba1ea4c8bb1af023d492acfcbf11e23c33f4af7d297eada113838cb6f0133a55684546f3 SHA512 4ed956197f08b7c3779f0bb39393b40cdaff3461071b48815200c6ad0dce2de87375cda96fe20d3ace4ab81ba6b8cdb50b58d82f5e5b54fe2c7751201ff2f63e
diff --git a/sci-chemistry/mgltools-geomutils/files/1.5.4-gcc4.3.patch b/sci-chemistry/mgltools-geomutils/files/1.5.4-gcc4.3.patch
deleted file mode 100644
index ac7c2bdc0..000000000
--- a/sci-chemistry/mgltools-geomutils/files/1.5.4-gcc4.3.patch
+++ /dev/null
@@ -1,9 +0,0 @@
---- geomutils-1.5.4/src/geomAlgorithms/objfile.cpp	2007-06-26 01:04:34.000000000 +0200
-+++ geomutils-1.5.4/src/geomAlgorithms/objfile.cpp.new	2009-05-17 20:30:43.597472969 +0200
-@@ -1,5 +1,6 @@
- #include <assert.h>
- #include <fstream>
-+#include <cstring>
- 
- #include "objfile.h"
- 
diff --git a/sci-chemistry/mgltools-geomutils/files/1.5.4-impl-dec.patch b/sci-chemistry/mgltools-geomutils/files/1.5.4-impl-dec.patch
deleted file mode 100644
index 468d23544..000000000
--- a/sci-chemistry/mgltools-geomutils/files/1.5.4-impl-dec.patch
+++ /dev/null
@@ -1,12 +0,0 @@
-diff --git a/src/efit/efit.c b/src/efit/efit.c
-index cfdf7b4..ef71e37 100644
---- a/src/efit/efit.c
-+++ b/src/efit/efit.c
-@@ -6,6 +6,7 @@
- 
- #include <stdio.h>
- #include <math.h>
-+#include <string.h>
- 
- #define EFIT_MAIN 1
- 
diff --git a/sci-chemistry/mgltools-geomutils/metadata.xml b/sci-chemistry/mgltools-geomutils/metadata.xml
deleted file mode 100644
index da36ecbfc..000000000
--- a/sci-chemistry/mgltools-geomutils/metadata.xml
+++ /dev/null
@@ -1,8 +0,0 @@
-<?xml version="1.0" encoding="UTF-8"?>
-<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
-<pkgmetadata>
-	<maintainer type="project">
-		<email>sci-chemistry@gentoo.org</email>
-		<name>Gentoo Chemistry Project</name>
-	</maintainer>
-</pkgmetadata>
diff --git a/sci-chemistry/mgltools-geomutils/mgltools-geomutils-1.5.6.ebuild b/sci-chemistry/mgltools-geomutils/mgltools-geomutils-1.5.6.ebuild
deleted file mode 100644
index 53c34289b..000000000
--- a/sci-chemistry/mgltools-geomutils/mgltools-geomutils-1.5.6.ebuild
+++ /dev/null
@@ -1,42 +0,0 @@
-# Copyright 1999-2015 Gentoo Foundation
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=5
-
-PYTHON_COMPAT=( python2_7 )
-
-inherit distutils-r1 eutils
-
-MY_PN="geomutils"
-MY_P="${MY_PN}-${PV/_rc3/}"
-
-DESCRIPTION="MGLTools Plugin -- geomutils"
-HOMEPAGE="http://mgltools.scripps.edu"
-SRC_URI="http://mgltools.scripps.edu/downloads/tars/releases/REL${PV}/mgltools_source_${PV}.tar.gz"
-
-LICENSE="MGLTOOLS MPL-1.1"
-SLOT="0"
-KEYWORDS="~amd64 ~x86"
-IUSE=""
-
-RDEPEND="dev-python/numpy[${PYTHON_USEDEP}]"
-DEPEND="${RDEPEND}
-	dev-lang/swig"
-
-S="${WORKDIR}"/${MY_P}
-
-src_unpack() {
-	tar xzpf "${DISTDIR}"/${A} mgltools_source_${PV/_/}/MGLPACKS/${MY_P}.tar.gz || die
-	tar xzpf mgltools_source_${PV/_/}/MGLPACKS/${MY_P}.tar.gz || die
-}
-
-python_prepare_all() {
-	ecvs_clean
-	find "${S}" -name LICENSE -type f -delete || die
-
-	sed  \
-		-e 's:^.*CVS:#&1:g' \
-		-e 's:^.*LICENSE:#&1:g' \
-		-i "${S}"/MANIFEST.in || die
-	distutils-r1_python_prepare_all
-}
diff --git a/sci-chemistry/mgltools-gle/Manifest b/sci-chemistry/mgltools-gle/Manifest
deleted file mode 100644
index 366b14ae4..000000000
--- a/sci-chemistry/mgltools-gle/Manifest
+++ /dev/null
@@ -1 +0,0 @@
-DIST mgltools_source_1.5.6.tar.gz 40275811 BLAKE2B 98a2d71f33fc92233f1082637b54d63a180b6cf1fa8cc052cb497380ba1ea4c8bb1af023d492acfcbf11e23c33f4af7d297eada113838cb6f0133a55684546f3 SHA512 4ed956197f08b7c3779f0bb39393b40cdaff3461071b48815200c6ad0dce2de87375cda96fe20d3ace4ab81ba6b8cdb50b58d82f5e5b54fe2c7751201ff2f63e
diff --git a/sci-chemistry/mgltools-gle/files/mgltools-gle-1.5.6-swig.patch b/sci-chemistry/mgltools-gle/files/mgltools-gle-1.5.6-swig.patch
deleted file mode 100644
index 4b632df88..000000000
--- a/sci-chemistry/mgltools-gle/files/mgltools-gle-1.5.6-swig.patch
+++ /dev/null
@@ -1,43 +0,0 @@
- gle-1.5.6/gle/gle.i | 8 ++++----
- 1 file changed, 4 insertions(+), 4 deletions(-)
-
-diff --git a/gle-1.5.6/gle/gle.i b/gle-1.5.6/gle/gle.i
-index bc48694..76170f1 100644
---- a/gle-1.5.6/gle/gle.i
-+++ b/gle-1.5.6/gle/gle.i
-@@ -149,7 +149,7 @@ glePolyCone_c4f (int npoints,	 /* numpoints in poly-line */
-                    gleColor4f color_array[1],	/* colors at polyline verts */
-                    gleDouble radius_array[1]); /* cone radii at polyline verts */
- 
--#typemaps for Numeric arrays
-+/* typemaps for Numeric arrays */
- DOUBLE_ARRAY2D( contour, [1][2], ncp )
- %apply double ARRAY2D[ANY][ANY] { double cont_normal[1][2] };
- %apply double VECTOR_NULL[ANY] { double up[3] };
-@@ -172,7 +172,7 @@ gleExtrusion_c4f (int ncp,         /* number of contour points */
-                 gleDouble point_array[1][3], /* polyline vertices */
-                 gleColor4f color_array[1]); /* colors at polyline verts */
- 
--#typemaps for Numeric arrays
-+/* typemaps for Numeric arrays */
- %apply double VECTOR[ANY] { double twist_array[1] };
- 
- /* extrude 2D contour, specifying local rotations (twists) */
-@@ -195,7 +195,7 @@ gleTwistExtrusion_c4f (int ncp,         /* number of contour points */
-                 gleDouble twist_array[1]);   /* countour twists (in degrees) */
- 
- 
--#typemaps for Numeric arrays
-+/* typemaps for Numeric arrays */
- %apply double ARRAY3D_NULL[ANY][ANY][ANY] { double xform_array[1][2][3] };
- 
- /* extrude 2D contour, specifying local affine tranformations */
-@@ -218,7 +218,7 @@ gleSuperExtrusion_c4f (int ncp,  /* number of contour points */
-                 gleColor4f color_array[1],        /* color at polyline verts */
-                 gleDouble xform_array[1][2][3]);   /* 2D contour xforms */
- 
--#typemaps for Numeric arrays
-+/* typemaps for Numeric arrays */
- %apply double ARRAY2D_NULL[ANY][ANY] { double startXform[2][3] };
- %apply double ARRAY2D_NULL[ANY][ANY] { double dXformdTheta[2][3] };
- 
diff --git a/sci-chemistry/mgltools-gle/metadata.xml b/sci-chemistry/mgltools-gle/metadata.xml
deleted file mode 100644
index da36ecbfc..000000000
--- a/sci-chemistry/mgltools-gle/metadata.xml
+++ /dev/null
@@ -1,8 +0,0 @@
-<?xml version="1.0" encoding="UTF-8"?>
-<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
-<pkgmetadata>
-	<maintainer type="project">
-		<email>sci-chemistry@gentoo.org</email>
-		<name>Gentoo Chemistry Project</name>
-	</maintainer>
-</pkgmetadata>
diff --git a/sci-chemistry/mgltools-gle/mgltools-gle-1.5.6.ebuild b/sci-chemistry/mgltools-gle/mgltools-gle-1.5.6.ebuild
deleted file mode 100644
index b4a972135..000000000
--- a/sci-chemistry/mgltools-gle/mgltools-gle-1.5.6.ebuild
+++ /dev/null
@@ -1,44 +0,0 @@
-# Copyright 1999-2015 Gentoo Foundation
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=5
-
-PYTHON_COMPAT=( python2_7 )
-PYTHON_REQ_USE="tk"
-
-inherit distutils-r1 eutils
-
-MY_PN="gle"
-MY_P="${MY_PN}-${PV/_rc3/}"
-
-DESCRIPTION="MGLTools Plugin -- gle"
-HOMEPAGE="http://mgltools.scripps.edu"
-SRC_URI="http://mgltools.scripps.edu/downloads/tars/releases/REL${PV}/mgltools_source_${PV}.tar.gz"
-
-LICENSE="MGLTOOLS MPL-1.1"
-SLOT="0"
-KEYWORDS="~amd64 ~x86"
-IUSE=""
-
-RDEPEND="virtual/opengl"
-DEPEND="${RDEPEND}
-	dev-lang/swig"
-
-S="${WORKDIR}"/${MY_P}
-
-src_unpack() {
-	tar xzpf "${DISTDIR}"/${A} mgltools_source_${PV/_/}/MGLPACKS/${MY_P}.tar.gz || die
-	tar xzpf mgltools_source_${PV/_/}/MGLPACKS/${MY_P}.tar.gz || die
-}
-
-python_prepare_all() {
-	local PATCHES=( "${FILESDIR}"/${P}-swig.patch )
-	ecvs_clean
-	find "${S}" -name LICENSE -type f -delete || die
-
-	sed  \
-		-e 's:^.*CVS:#&1:g' \
-		-e 's:^.*LICENSE:#&1:g' \
-		-i "${S}"/MANIFEST.in || die
-	distutils-r1_python_prepare_all
-}
diff --git a/sci-chemistry/mgltools-mglutil/Manifest b/sci-chemistry/mgltools-mglutil/Manifest
deleted file mode 100644
index 366b14ae4..000000000
--- a/sci-chemistry/mgltools-mglutil/Manifest
+++ /dev/null
@@ -1 +0,0 @@
-DIST mgltools_source_1.5.6.tar.gz 40275811 BLAKE2B 98a2d71f33fc92233f1082637b54d63a180b6cf1fa8cc052cb497380ba1ea4c8bb1af023d492acfcbf11e23c33f4af7d297eada113838cb6f0133a55684546f3 SHA512 4ed956197f08b7c3779f0bb39393b40cdaff3461071b48815200c6ad0dce2de87375cda96fe20d3ace4ab81ba6b8cdb50b58d82f5e5b54fe2c7751201ff2f63e
diff --git a/sci-chemistry/mgltools-mglutil/files/1.5.4-python.patch b/sci-chemistry/mgltools-mglutil/files/1.5.4-python.patch
deleted file mode 100644
index c2fecf8f5..000000000
--- a/sci-chemistry/mgltools-mglutil/files/1.5.4-python.patch
+++ /dev/null
@@ -1,13 +0,0 @@
-diff --git a/mglutil/math/Tests/test_matToAxis.py b/mglutil/math/Tests/test_matToAxis.py
-index 25befa4..acf75f3 100644
---- a/mglutil/math/Tests/test_matToAxis.py
-+++ b/mglutil/math/Tests/test_matToAxis.py
-@@ -33,7 +33,7 @@ def rotateObject():
-     for i in range(len(m1)):
-         if fabs(m1[i]-m2[i]) > 1e-4:
-             bSame = False
--    assert (bSame, True)
-+    assert bSame, True
- 
- 
- def test_rotateObject():
diff --git a/sci-chemistry/mgltools-mglutil/files/mgltools-mglutil-1.5.6-tcltk86.patch b/sci-chemistry/mgltools-mglutil/files/mgltools-mglutil-1.5.6-tcltk86.patch
deleted file mode 100644
index dc926cf83..000000000
--- a/sci-chemistry/mgltools-mglutil/files/mgltools-mglutil-1.5.6-tcltk86.patch
+++ /dev/null
@@ -1,104 +0,0 @@
-Index: mglutil-1.5.7~rc1+cvs.20150324/mglutil/gui/BasicWidgets/Tk/thumbwheel.py
-===================================================================
---- mglutil-1.5.7~rc1+cvs.20150324.orig/mglutil/gui/BasicWidgets/Tk/thumbwheel.py
-+++ mglutil-1.5.7~rc1+cvs.20150324/mglutil/gui/BasicWidgets/Tk/thumbwheel.py
-@@ -88,7 +88,8 @@
- #            checkkeywords(kw)
-             
- 	Tkinter.Frame.__init__(self, master)
--	Tkinter.Pack.config(self, side='left', anchor='w')
-+	#Tkinter.Pack.config(self, side='left', anchor='w')
-+	Tkinter.Pack.config(master, side='left', anchor='w')
- 
-         #FIXME: nblines are not dynamically computed
-         self.nblines = 30
-Index: mglutil-1.5.7~rc1+cvs.20150324/mglutil/gui/BasicWidgets/Tk/vector3DGUI.py
-===================================================================
---- mglutil-1.5.7~rc1+cvs.20150324.orig/mglutil/gui/BasicWidgets/Tk/vector3DGUI.py
-+++ mglutil-1.5.7~rc1+cvs.20150324/mglutil/gui/BasicWidgets/Tk/vector3DGUI.py
-@@ -86,7 +86,7 @@
-              [  0.25      ,  0.25      ,  0.93541437,  0.        ],
-              [  0.        ,  0.        ,  0.        ,  1.        ]],'f')
-         self.viewingMat = Numeric.transpose(self.viewingMatInv)
--        self.createCanvas(master, size)
-+        self.createCanvas(self, size)
-         self.createEntries(self.frame)
- 	Tkinter.Widget.bind(self.canvas, "<ButtonPress-1>", self.mouseDown)
- 	Tkinter.Widget.bind(self.canvas, "<ButtonRelease-1>", self.mouseUp)
-@@ -357,19 +357,22 @@
- 
-     def createEntries(self, master):
-         self.f = Tkinter.Frame(master)
--	self.f.grid(column=3, rowspan=3)
-+        self.f.pack(side='top', expand=1)
-+        self.f.grid = Tkinter.Frame(self.f)
-+        self.f.grid.pack(side='top', expand=1)
-+	self.f.grid.grid(column=3, rowspan=3)
- 
-         def fX(): self.vector = [1.,0.,0.]; self.setEntries(); self.callbacks.CallCallbacks(self.vector)
-         def fY(): self.vector = [0.,1.,0.]; self.setEntries(); self.callbacks.CallCallbacks(self.vector)
-         def fZ(): self.vector = [0.,0.,1.]; self.setEntries(); self.callbacks.CallCallbacks(self.vector)
--        lX = Tkinter.Button(master=self.f, text='x', command=fX)
--        lY = Tkinter.Button(master=self.f, text='y', command=fY)
--        lZ = Tkinter.Button(master=self.f, text='z', command=fZ)
-+        lX = Tkinter.Button(master=self.f.grid, text='x', command=fX)
-+        lY = Tkinter.Button(master=self.f.grid, text='y', command=fY)
-+        lZ = Tkinter.Button(master=self.f.grid, text='z', command=fZ)
-         lX.grid(row=0, column=0)
-         lY.grid(row=1, column=0)
-         lZ.grid(row=2, column=0)
- 
--        self.thumbx = ThumbWheel(master=self.f, width=50,
-+        self.thumbx = ThumbWheel(master=self.f.grid, width=50,
-                                  height=20, labcfg={'text':'X:','side':'left'},
-                                  wheelPad=2, oneTurn=.1, min=-1, max=1,
-                                  showLabel=0, precision=5, type=float)
-@@ -378,7 +381,7 @@
-         self.thumbx.canvas.unbind("<Button-3>")
-         self.thumbx.grid(row=0, column=1)
- 
--        self.thumby = ThumbWheel(master=self.f, width=50,
-+        self.thumby = ThumbWheel(master=self.f.grid, width=50,
-                                  height=20, labcfg={'text':'Y:','side':'left'},
-                                  wheelPad=2, oneTurn=.1, min=-1, max=1,
-                                  showLabel=0, precision=5, type=float)
-@@ -387,7 +390,7 @@
-         self.thumby.canvas.unbind("<Button-3>")
-         self.thumby.grid(row=1, column=1)
- 
--        self.thumbz = ThumbWheel(master=self.f, width=50,
-+        self.thumbz = ThumbWheel(master=self.f.grid, width=50,
-                                  height=20, labcfg={'text':'Z:','side':'left'},
-                                  wheelPad=2, oneTurn=.1, min=-1, max=1,
-                                  showLabel=0, precision=5, type=float)
-@@ -397,19 +400,19 @@
-         self.thumbz.grid(row=2, column=1)
- 
-         self.entryXTk = Tkinter.StringVar()
--        self.entryX = Tkinter.Entry(master=self.f, textvariable=self.entryXTk,
-+        self.entryX = Tkinter.Entry(master=self.f.grid, textvariable=self.entryXTk,
-                                     width=8)
-         self.entryX.bind('<Return>', self.entryX_cb)
-         self.entryX.grid(row=0, column=2)
- 
-         self.entryYTk = Tkinter.StringVar()
--        self.entryY = Tkinter.Entry(master=self.f, textvariable=self.entryYTk,
-+        self.entryY = Tkinter.Entry(master=self.f.grid, textvariable=self.entryYTk,
-                                     width=8)
-         self.entryY.bind('<Return>', self.entryY_cb)
-         self.entryY.grid(row=1, column=2)
- 
-         self.entryZTk = Tkinter.StringVar()
--        self.entryZ = Tkinter.Entry(master=self.f, textvariable=self.entryZTk,
-+        self.entryZ = Tkinter.Entry(master=self.f.grid, textvariable=self.entryZTk,
-                                     width=8)
-         self.entryZ.bind('<Return>', self.entryZ_cb)
-         self.entryZ.grid(row=2, column=2)
-@@ -420,7 +423,6 @@
-         
-         self.entryV.bind('<Return>', self.entryV_cb)
-         
--        self.f.pack(side='top', expand=1)
- 
-         self.entryV.pack()
-         
diff --git a/sci-chemistry/mgltools-mglutil/metadata.xml b/sci-chemistry/mgltools-mglutil/metadata.xml
deleted file mode 100644
index da36ecbfc..000000000
--- a/sci-chemistry/mgltools-mglutil/metadata.xml
+++ /dev/null
@@ -1,8 +0,0 @@
-<?xml version="1.0" encoding="UTF-8"?>
-<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
-<pkgmetadata>
-	<maintainer type="project">
-		<email>sci-chemistry@gentoo.org</email>
-		<name>Gentoo Chemistry Project</name>
-	</maintainer>
-</pkgmetadata>
diff --git a/sci-chemistry/mgltools-mglutil/mgltools-mglutil-1.5.6-r1.ebuild b/sci-chemistry/mgltools-mglutil/mgltools-mglutil-1.5.6-r1.ebuild
deleted file mode 100644
index b15258435..000000000
--- a/sci-chemistry/mgltools-mglutil/mgltools-mglutil-1.5.6-r1.ebuild
+++ /dev/null
@@ -1,48 +0,0 @@
-# Copyright 1999-2015 Gentoo Foundation
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=5
-
-PYTHON_COMPAT=( python2_7 )
-
-inherit distutils-r1 eutils
-
-MY_PN="mglutil"
-MY_P="${MY_PN}-${PV/_rc3/}"
-
-DESCRIPTION="MGLTools Plugin -- mglutil"
-HOMEPAGE="http://mgltools.scripps.edu"
-SRC_URI="http://mgltools.scripps.edu/downloads/tars/releases/REL${PV}/mgltools_source_${PV}.tar.gz"
-
-LICENSE="MGLTOOLS MPL-1.1"
-SLOT="0"
-KEYWORDS="~amd64 ~x86"
-IUSE=""
-
-RDEPEND=""
-DEPEND="${RDEPEND}
-	dev-lang/swig"
-
-S="${WORKDIR}"/${MY_P}
-
-DOCS=( mglutil/RELNOTES )
-
-src_unpack() {
-	tar xzpf "${DISTDIR}"/${A} mgltools_source_${PV/_/}/MGLPACKS/${MY_P}.tar.gz || die
-	tar xzpf mgltools_source_${PV/_/}/MGLPACKS/${MY_P}.tar.gz || die
-}
-
-python_prepare_all() {
-	local PATCHES=(
-		"${FILESDIR}"/1.5.4-python.patch
-		"${FILESDIR}"/${P}-tcltk86.patch
-		)
-	ecvs_clean
-	find "${S}" -name LICENSE -type f -delete || die
-
-	sed  \
-		-e 's:^.*CVS:#&1:g' \
-		-e 's:^.*LICENSE:#&1:g' \
-		-i "${S}"/MANIFEST.in || die
-	distutils-r1_python_prepare_all
-}
diff --git a/sci-chemistry/mgltools-molkit/Manifest b/sci-chemistry/mgltools-molkit/Manifest
deleted file mode 100644
index 366b14ae4..000000000
--- a/sci-chemistry/mgltools-molkit/Manifest
+++ /dev/null
@@ -1 +0,0 @@
-DIST mgltools_source_1.5.6.tar.gz 40275811 BLAKE2B 98a2d71f33fc92233f1082637b54d63a180b6cf1fa8cc052cb497380ba1ea4c8bb1af023d492acfcbf11e23c33f4af7d297eada113838cb6f0133a55684546f3 SHA512 4ed956197f08b7c3779f0bb39393b40cdaff3461071b48815200c6ad0dce2de87375cda96fe20d3ace4ab81ba6b8cdb50b58d82f5e5b54fe2c7751201ff2f63e
diff --git a/sci-chemistry/mgltools-molkit/metadata.xml b/sci-chemistry/mgltools-molkit/metadata.xml
deleted file mode 100644
index da36ecbfc..000000000
--- a/sci-chemistry/mgltools-molkit/metadata.xml
+++ /dev/null
@@ -1,8 +0,0 @@
-<?xml version="1.0" encoding="UTF-8"?>
-<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
-<pkgmetadata>
-	<maintainer type="project">
-		<email>sci-chemistry@gentoo.org</email>
-		<name>Gentoo Chemistry Project</name>
-	</maintainer>
-</pkgmetadata>
diff --git a/sci-chemistry/mgltools-molkit/mgltools-molkit-1.5.6.ebuild b/sci-chemistry/mgltools-molkit/mgltools-molkit-1.5.6.ebuild
deleted file mode 100644
index dd79cf6ef..000000000
--- a/sci-chemistry/mgltools-molkit/mgltools-molkit-1.5.6.ebuild
+++ /dev/null
@@ -1,44 +0,0 @@
-# Copyright 1999-2015 Gentoo Foundation
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=5
-
-PYTHON_COMPAT=( python2_7 )
-
-inherit distutils-r1 eutils
-
-MY_PN="MolKit"
-MY_P="${MY_PN}-${PV/_rc3/}"
-
-DESCRIPTION="MGLTools Plugin -- MolKit"
-HOMEPAGE="http://mgltools.scripps.edu"
-SRC_URI="http://mgltools.scripps.edu/downloads/tars/releases/REL${PV}/mgltools_source_${PV}.tar.gz"
-
-LICENSE="MGLTOOLS MPL-1.1"
-SLOT="0"
-KEYWORDS="~amd64 ~x86"
-IUSE=""
-
-RDEPEND="sci-chemistry/pdb2pqr"
-DEPEND="${RDEPEND}
-	dev-lang/swig"
-
-S="${WORKDIR}"/${MY_P}
-
-DOCS=( MolKit/RELNOTES )
-
-src_unpack() {
-	tar xzpf "${DISTDIR}"/${A} mgltools_source_${PV/_/}/MGLPACKS/${MY_P}.tar.gz || die
-	tar xzpf mgltools_source_${PV/_/}/MGLPACKS/${MY_P}.tar.gz || die
-}
-
-python_prepare_all() {
-	ecvs_clean
-	find "${S}" -name LICENSE -type f -delete || die
-
-	sed  \
-		-e 's:^.*CVS:#&1:g' \
-		-e 's:^.*LICENSE:#&1:g' \
-		-i "${S}"/MANIFEST.in || die
-	distutils-r1_python_prepare_all
-}
diff --git a/sci-chemistry/mgltools-networkeditor/Manifest b/sci-chemistry/mgltools-networkeditor/Manifest
deleted file mode 100644
index 366b14ae4..000000000
--- a/sci-chemistry/mgltools-networkeditor/Manifest
+++ /dev/null
@@ -1 +0,0 @@
-DIST mgltools_source_1.5.6.tar.gz 40275811 BLAKE2B 98a2d71f33fc92233f1082637b54d63a180b6cf1fa8cc052cb497380ba1ea4c8bb1af023d492acfcbf11e23c33f4af7d297eada113838cb6f0133a55684546f3 SHA512 4ed956197f08b7c3779f0bb39393b40cdaff3461071b48815200c6ad0dce2de87375cda96fe20d3ace4ab81ba6b8cdb50b58d82f5e5b54fe2c7751201ff2f63e
diff --git a/sci-chemistry/mgltools-networkeditor/metadata.xml b/sci-chemistry/mgltools-networkeditor/metadata.xml
deleted file mode 100644
index da36ecbfc..000000000
--- a/sci-chemistry/mgltools-networkeditor/metadata.xml
+++ /dev/null
@@ -1,8 +0,0 @@
-<?xml version="1.0" encoding="UTF-8"?>
-<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
-<pkgmetadata>
-	<maintainer type="project">
-		<email>sci-chemistry@gentoo.org</email>
-		<name>Gentoo Chemistry Project</name>
-	</maintainer>
-</pkgmetadata>
diff --git a/sci-chemistry/mgltools-networkeditor/mgltools-networkeditor-1.5.6.ebuild b/sci-chemistry/mgltools-networkeditor/mgltools-networkeditor-1.5.6.ebuild
deleted file mode 100644
index 8b2630d7a..000000000
--- a/sci-chemistry/mgltools-networkeditor/mgltools-networkeditor-1.5.6.ebuild
+++ /dev/null
@@ -1,44 +0,0 @@
-# Copyright 1999-2015 Gentoo Foundation
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=5
-
-PYTHON_COMPAT=( python2_7 )
-
-inherit distutils-r1 eutils
-
-MY_PN="NetworkEditor"
-MY_P="${MY_PN}-${PV/_rc3/}"
-
-DESCRIPTION="MGLTools Plugin -- NetworkEditor"
-HOMEPAGE="http://mgltools.scripps.edu"
-SRC_URI="http://mgltools.scripps.edu/downloads/tars/releases/REL${PV}/mgltools_source_${PV}.tar.gz"
-
-LICENSE="MGLTOOLS MPL-1.1"
-SLOT="0"
-KEYWORDS="~amd64 ~x86"
-IUSE=""
-
-RDEPEND=""
-DEPEND="${RDEPEND}
-	dev-lang/swig"
-
-S="${WORKDIR}"/${MY_P}
-
-DOCS=( NetworkEditor/RELNOTES )
-
-src_unpack() {
-	tar xzpf "${DISTDIR}"/${A} mgltools_source_${PV/_/}/MGLPACKS/${MY_P}.tar.gz || die
-	tar xzpf mgltools_source_${PV/_/}/MGLPACKS/${MY_P}.tar.gz || die
-}
-
-python_prepare_all() {
-	ecvs_clean
-	find "${S}" -name LICENSE -type f -delete || die
-
-	sed  \
-		-e 's:^.*CVS:#&1:g' \
-		-e 's:^.*LICENSE:#&1:g' \
-		-i "${S}"/MANIFEST.in || die
-	distutils-r1_python_prepare_all
-}
diff --git a/sci-chemistry/mgltools-opengltk/Manifest b/sci-chemistry/mgltools-opengltk/Manifest
deleted file mode 100644
index 366b14ae4..000000000
--- a/sci-chemistry/mgltools-opengltk/Manifest
+++ /dev/null
@@ -1 +0,0 @@
-DIST mgltools_source_1.5.6.tar.gz 40275811 BLAKE2B 98a2d71f33fc92233f1082637b54d63a180b6cf1fa8cc052cb497380ba1ea4c8bb1af023d492acfcbf11e23c33f4af7d297eada113838cb6f0133a55684546f3 SHA512 4ed956197f08b7c3779f0bb39393b40cdaff3461071b48815200c6ad0dce2de87375cda96fe20d3ace4ab81ba6b8cdb50b58d82f5e5b54fe2c7751201ff2f63e
diff --git a/sci-chemistry/mgltools-opengltk/files/mgltools-opengltk-1.5.6_rc2-glew.patch b/sci-chemistry/mgltools-opengltk/files/mgltools-opengltk-1.5.6_rc2-glew.patch
deleted file mode 100644
index 8e62dbb1a..000000000
--- a/sci-chemistry/mgltools-opengltk/files/mgltools-opengltk-1.5.6_rc2-glew.patch
+++ /dev/null
@@ -1,16 +0,0 @@
- setup.py |    2 +-
- 1 files changed, 1 insertions(+), 1 deletions(-)
-
-diff --git a/setup.py b/setup.py
-index 21f893f..ca5ec85 100644
---- a/setup.py
-+++ b/setup.py
-@@ -615,7 +615,7 @@ elif platform == 'win32':
-     macros = [('WIN32', None)]
- else:
-     extra_link_args = ''
--    libraries = ''
-+    libraries = gl_libs
-     macros = []
- 
- glextlib_ext = MyExtension("extent._glextlib",
diff --git a/sci-chemistry/mgltools-opengltk/files/mgltools-opengltk-1.5.6_rc2-unbundle.patch b/sci-chemistry/mgltools-opengltk/files/mgltools-opengltk-1.5.6_rc2-unbundle.patch
deleted file mode 100644
index 3b03fc0c5..000000000
--- a/sci-chemistry/mgltools-opengltk/files/mgltools-opengltk-1.5.6_rc2-unbundle.patch
+++ /dev/null
@@ -1,28 +0,0 @@
- setup.py |    7 ++-----
- 1 files changed, 2 insertions(+), 5 deletions(-)
-
-diff --git a/setup.py b/setup.py
-index 0191ba2..bda3e41 100644
---- a/setup.py
-+++ b/setup.py
-@@ -268,9 +268,6 @@ class build_EXT(build_ext):
-                     if path.isfile(statlib1) and path.isfile(statlib2):
-                         self.spawn(["ranlib", "-s", statlib1])
-                         self.spawn(["ranlib", "-s", statlib2])
--            togl_build(self,self.include_dirs,
--                       self.library_dirs,
--                       togl_libs)
-         #if platform in ["linux2", "win32"]:
-         if os.name in ['nt']:
-             tkdnd_build(self)
-@@ -716,8 +713,8 @@ glxlib_ext = MyExtension("extent._glxlib",
-                            ], #sources
-                           define_macros = macros,
-                           include_dirs = glx_incldirs,
--                          library_dirs = glx_libdirs,
--                          libraries = ['X11'] + gl_libs,
-+                          library_dirs = glx_libdirs + ['@GENTOO_PORTAGE_EPREFIX@/usr/lib64/Togl2.0/'],
-+                          libraries = ['X11', 'GLEW', 'GLEWmx'] + gl_libs,
-                           headers = {
-                              'name': path.join("GL","glx.h"),
-                              'dir': h_dir,
diff --git a/sci-chemistry/mgltools-opengltk/metadata.xml b/sci-chemistry/mgltools-opengltk/metadata.xml
deleted file mode 100644
index da36ecbfc..000000000
--- a/sci-chemistry/mgltools-opengltk/metadata.xml
+++ /dev/null
@@ -1,8 +0,0 @@
-<?xml version="1.0" encoding="UTF-8"?>
-<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
-<pkgmetadata>
-	<maintainer type="project">
-		<email>sci-chemistry@gentoo.org</email>
-		<name>Gentoo Chemistry Project</name>
-	</maintainer>
-</pkgmetadata>
diff --git a/sci-chemistry/mgltools-opengltk/mgltools-opengltk-1.5.6.ebuild b/sci-chemistry/mgltools-opengltk/mgltools-opengltk-1.5.6.ebuild
deleted file mode 100644
index 598039d5a..000000000
--- a/sci-chemistry/mgltools-opengltk/mgltools-opengltk-1.5.6.ebuild
+++ /dev/null
@@ -1,60 +0,0 @@
-# Copyright 1999-2017 Gentoo Foundation
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=6
-
-PYTHON_COMPAT=( python2_7 )
-
-inherit distutils-r1 eutils prefix
-
-MY_PN="opengltk"
-MY_P="${MY_PN}-${PV/_rc3/}"
-
-DESCRIPTION="MGLTools Plugin -- opengltk"
-HOMEPAGE="http://mgltools.scripps.edu"
-SRC_URI="http://mgltools.scripps.edu/downloads/tars/releases/REL${PV}/mgltools_source_${PV}.tar.gz"
-
-LICENSE="MGLTOOLS MPL-1.1"
-SLOT="0"
-KEYWORDS="~amd64 ~x86"
-IUSE=""
-
-RDEPEND="
-	dev-lang/tk:0
-	dev-python/numpy[${PYTHON_USEDEP}]
-	dev-tcltk/tkdnd
-	dev-tcltk/togl:0
-	media-libs/glew:0=
-	virtual/opengl"
-DEPEND="${RDEPEND}
-	dev-lang/swig"
-
-S="${WORKDIR}"/${MY_P}
-
-src_unpack() {
-	tar xzpf "${DISTDIR}"/${A} mgltools_source_${PV/_/}/MGLPACKS/${MY_P}.tar.gz || die
-	tar xzpf mgltools_source_${PV/_/}/MGLPACKS/${MY_P}.tar.gz || die
-}
-
-python_prepare_all() {
-	local tcl_ver="$(best_version dev-lang/tcl | cut -d- -f3 | cut -d. -f1,2)"
-
-	local PATCHES=( "${FILESDIR}"/${PN}-1.5.6_rc2-unbundle.patch )
-
-	eprefixify setup.py
-
-	ecvs_clean
-	find "${S}" -name LICENSE -type f -delete || die
-	find Togl2.0 tkdnd2.0 include/tcltk84 -delete || die
-
-	sed  \
-		-e 's:^.*CVS:#&1:g' \
-		-e 's:^.*LICENSE:#&1:g' \
-		-i "${S}"/MANIFEST.in || die
-
-	sed \
-		-e "s:8.4:${tcl_ver}:g" \
-		-e "s:8.5:${tcl_ver}:g" \
-		-i setup.py || die
-	distutils-r1_python_prepare_all
-}
diff --git a/sci-chemistry/mgltools-pmv/Manifest b/sci-chemistry/mgltools-pmv/Manifest
deleted file mode 100644
index 366b14ae4..000000000
--- a/sci-chemistry/mgltools-pmv/Manifest
+++ /dev/null
@@ -1 +0,0 @@
-DIST mgltools_source_1.5.6.tar.gz 40275811 BLAKE2B 98a2d71f33fc92233f1082637b54d63a180b6cf1fa8cc052cb497380ba1ea4c8bb1af023d492acfcbf11e23c33f4af7d297eada113838cb6f0133a55684546f3 SHA512 4ed956197f08b7c3779f0bb39393b40cdaff3461071b48815200c6ad0dce2de87375cda96fe20d3ace4ab81ba6b8cdb50b58d82f5e5b54fe2c7751201ff2f63e
diff --git a/sci-chemistry/mgltools-pmv/files/mgltools-pmv-1.5.6_rc2-code-fix.patch b/sci-chemistry/mgltools-pmv/files/mgltools-pmv-1.5.6_rc2-code-fix.patch
deleted file mode 100644
index 10e2d3b96..000000000
--- a/sci-chemistry/mgltools-pmv/files/mgltools-pmv-1.5.6_rc2-code-fix.patch
+++ /dev/null
@@ -1,66 +0,0 @@
- .../blender/plugin/blenderPmvClientGUI.py          |    2 +-
- .../cinema4d/plugin/epmv_c4d_plugin.py             |    2 +-
- Pmv/hostappInterface/cinema4d/test/energy_test.py  |    4 ++--
- Pmv/styles/sessionToStyle.py                       |    3 +--
- 4 files changed, 5 insertions(+), 6 deletions(-)
-
-diff --git a/Pmv/hostappInterface/blender/plugin/blenderPmvClientGUI.py b/Pmv/hostappInterface/blender/plugin/blenderPmvClientGUI.py
-index 68e09c0..d52b17d 100644
---- a/Pmv/hostappInterface/blender/plugin/blenderPmvClientGUI.py
-+++ b/Pmv/hostappInterface/blender/plugin/blenderPmvClientGUI.py
-@@ -46,7 +46,7 @@ interface...
- import math
- import sys
- 
--MGL_ROOT=   #'/Library/MGLTools/1.5.6.csv'
-+MGL_ROOT= ""   #'/Library/MGLTools/1.5.6.csv'
- sys.path[0]=(MGL_ROOT+'/lib/python2.5/site-packages')
- sys.path.append(MGL_ROOT+'/lib/python2.5/site-packages/PIL')
- sys.path.append(MGL_ROOT+'/MGLToolsPckgs')
-diff --git a/Pmv/hostappInterface/cinema4d/plugin/epmv_c4d_plugin.py b/Pmv/hostappInterface/cinema4d/plugin/epmv_c4d_plugin.py
-index 42617e3..6087cd0 100644
---- a/Pmv/hostappInterface/cinema4d/plugin/epmv_c4d_plugin.py
-+++ b/Pmv/hostappInterface/cinema4d/plugin/epmv_c4d_plugin.py
-@@ -38,7 +38,7 @@ __version__="v0.1.1a"
- # ***** END GPL LICENCE BLOCK ***** 
- # -------------------------------------------------------------------------- 
-     
--MGL_ROOT=
-+MGL_ROOT= ""
- 
- #TODO:
- #make the pyrosetta extension
-diff --git a/Pmv/hostappInterface/cinema4d/test/energy_test.py b/Pmv/hostappInterface/cinema4d/test/energy_test.py
-index 9393e25..c5f83c9 100644
---- a/Pmv/hostappInterface/cinema4d/test/energy_test.py
-+++ b/Pmv/hostappInterface/cinema4d/test/energy_test.py
-@@ -56,7 +56,7 @@ c = self.md_Amber94
- #call md_Amber94 command
- #c('mdtest5', 349, callback=1, filename='0', log=0, callback_freq=10)
- import thread
--thread.start_new(c,('mdtest5', 349, callback=1, filename='0', log=0, callback_freq=10))
-+thread.start_new_thread(c,'mdtest5', 349, callback=1, filename='0', log=0, callback_freq=10)
- thr = MyThread()#c,'mdtest5', 349, callback=1, filename='0', log=0, callback_freq=10)
- thr.start(back=True)
- #do some other operations here
-@@ -101,4 +101,4 @@ for mode in modes:
- 
- 
- # Show animation of the first non-trivial mode 
--view(modes[6])
-\ No newline at end of file
-+view(modes[6])
-diff --git a/Pmv/styles/sessionToStyle.py b/Pmv/styles/sessionToStyle.py
-index 013bae1..4b0db48 100644
---- a/Pmv/styles/sessionToStyle.py
-+++ b/Pmv/styles/sessionToStyle.py
-@@ -14,8 +14,7 @@ name, ext = os.path.splitext(filename)
- f = open(name+'_style.py', 'w')
- f.write("numberOfMolecules = 1\n\n")
- 
--f.write("__doc__ = """Style_01: Applies to X molecules. It displays ..
--"""\n")
-+f.write('__doc__ = """Style_01: Applies to X molecules. It displays .."""\n')
- 
- f.write("def applyStyle(mv, molName):\n")
- f.write("    mode='both'\n")
diff --git a/sci-chemistry/mgltools-pmv/metadata.xml b/sci-chemistry/mgltools-pmv/metadata.xml
deleted file mode 100644
index da36ecbfc..000000000
--- a/sci-chemistry/mgltools-pmv/metadata.xml
+++ /dev/null
@@ -1,8 +0,0 @@
-<?xml version="1.0" encoding="UTF-8"?>
-<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
-<pkgmetadata>
-	<maintainer type="project">
-		<email>sci-chemistry@gentoo.org</email>
-		<name>Gentoo Chemistry Project</name>
-	</maintainer>
-</pkgmetadata>
diff --git a/sci-chemistry/mgltools-pmv/mgltools-pmv-1.5.6.ebuild b/sci-chemistry/mgltools-pmv/mgltools-pmv-1.5.6.ebuild
deleted file mode 100644
index 405ab74be..000000000
--- a/sci-chemistry/mgltools-pmv/mgltools-pmv-1.5.6.ebuild
+++ /dev/null
@@ -1,52 +0,0 @@
-# Copyright 1999-2015 Gentoo Foundation
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=5
-
-PYTHON_COMPAT=( python2_7 )
-
-inherit distutils-r1 eutils
-
-MY_PN="Pmv"
-MY_P="${MY_PN}-${PV/_rc3/}"
-
-DESCRIPTION="MGLTools Plugin -- Pmv"
-HOMEPAGE="http://mgltools.scripps.edu"
-SRC_URI="http://mgltools.scripps.edu/downloads/tars/releases/REL${PV}/mgltools_source_${PV}.tar.gz"
-
-LICENSE="MGLTOOLS MPL-1.1"
-SLOT="0"
-KEYWORDS="~amd64 ~x86"
-IUSE=""
-
-RDEPEND="
-	sci-chemistry/mgltools-dejavu[${PYTHON_USEDEP}]
-	sci-chemistry/mgltools-mglutil[${PYTHON_USEDEP}]
-	sci-chemistry/mgltools-molkit[${PYTHON_USEDEP}]
-	sci-chemistry/mgltools-opengltk[${PYTHON_USEDEP}]
-	sci-chemistry/mgltools-pybabel[${PYTHON_USEDEP}]
-	sci-chemistry/mgltools-support[${PYTHON_USEDEP}]
-	"
-DEPEND="${RDEPEND}
-	dev-lang/swig"
-
-S="${WORKDIR}"/${MY_P}
-
-DOCS=( Pmv/RELNOTES Pmv/doc )
-
-src_unpack() {
-	tar xzpf "${DISTDIR}"/${A} mgltools_source_${PV/_/}/MGLPACKS/${MY_P}.tar.gz || die
-	tar xzpf mgltools_source_${PV/_/}/MGLPACKS/${MY_P}.tar.gz || die
-}
-
-python_prepare_all() {
-	local PATCHES=( "${FILESDIR}"/${PN}-1.5.6_rc2-code-fix.patch )
-	ecvs_clean
-	find "${S}" -name LICENSE -type f -delete || die
-
-	sed  \
-		-e 's:^.*CVS:#&1:g' \
-		-e 's:^.*LICENSE:#&1:g' \
-		-i "${S}"/MANIFEST.in || die
-	distutils-r1_python_prepare_all
-}
diff --git a/sci-chemistry/mgltools-pyautodock/Manifest b/sci-chemistry/mgltools-pyautodock/Manifest
deleted file mode 100644
index 366b14ae4..000000000
--- a/sci-chemistry/mgltools-pyautodock/Manifest
+++ /dev/null
@@ -1 +0,0 @@
-DIST mgltools_source_1.5.6.tar.gz 40275811 BLAKE2B 98a2d71f33fc92233f1082637b54d63a180b6cf1fa8cc052cb497380ba1ea4c8bb1af023d492acfcbf11e23c33f4af7d297eada113838cb6f0133a55684546f3 SHA512 4ed956197f08b7c3779f0bb39393b40cdaff3461071b48815200c6ad0dce2de87375cda96fe20d3ace4ab81ba6b8cdb50b58d82f5e5b54fe2c7751201ff2f63e
diff --git a/sci-chemistry/mgltools-pyautodock/metadata.xml b/sci-chemistry/mgltools-pyautodock/metadata.xml
deleted file mode 100644
index da36ecbfc..000000000
--- a/sci-chemistry/mgltools-pyautodock/metadata.xml
+++ /dev/null
@@ -1,8 +0,0 @@
-<?xml version="1.0" encoding="UTF-8"?>
-<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
-<pkgmetadata>
-	<maintainer type="project">
-		<email>sci-chemistry@gentoo.org</email>
-		<name>Gentoo Chemistry Project</name>
-	</maintainer>
-</pkgmetadata>
diff --git a/sci-chemistry/mgltools-pyautodock/mgltools-pyautodock-1.5.6.ebuild b/sci-chemistry/mgltools-pyautodock/mgltools-pyautodock-1.5.6.ebuild
deleted file mode 100644
index 07f3dd8de..000000000
--- a/sci-chemistry/mgltools-pyautodock/mgltools-pyautodock-1.5.6.ebuild
+++ /dev/null
@@ -1,42 +0,0 @@
-# Copyright 1999-2015 Gentoo Foundation
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=5
-
-PYTHON_COMPAT=( python2_7 )
-
-inherit distutils-r1 eutils
-
-MY_PN="PyAutoDock"
-MY_P="${MY_PN}-${PV/_rc3/}"
-
-DESCRIPTION="MGLTools Plugin -- PyAutoDock"
-HOMEPAGE="http://mgltools.scripps.edu"
-SRC_URI="http://mgltools.scripps.edu/downloads/tars/releases/REL${PV}/mgltools_source_${PV}.tar.gz"
-
-LICENSE="MGLTOOLS MPL-1.1"
-SLOT="0"
-KEYWORDS="~amd64 ~x86"
-IUSE=""
-
-RDEPEND=""
-DEPEND="${RDEPEND}
-	dev-lang/swig"
-
-S="${WORKDIR}"/${MY_P}
-
-src_unpack() {
-	tar xzpf "${DISTDIR}"/${A} mgltools_source_${PV/_/}/MGLPACKS/${MY_P}.tar.gz || die
-	tar xzpf mgltools_source_${PV/_/}/MGLPACKS/${MY_P}.tar.gz || die
-}
-
-python_prepare_all() {
-	ecvs_clean
-	find "${S}" -name LICENSE -type f -delete || die
-
-	sed  \
-		-e 's:^.*CVS:#&1:g' \
-		-e 's:^.*LICENSE:#&1:g' \
-		-i "${S}"/MANIFEST.in || die
-	distutils-r1_python_prepare_all
-}
diff --git a/sci-chemistry/mgltools-pybabel/Manifest b/sci-chemistry/mgltools-pybabel/Manifest
deleted file mode 100644
index 366b14ae4..000000000
--- a/sci-chemistry/mgltools-pybabel/Manifest
+++ /dev/null
@@ -1 +0,0 @@
-DIST mgltools_source_1.5.6.tar.gz 40275811 BLAKE2B 98a2d71f33fc92233f1082637b54d63a180b6cf1fa8cc052cb497380ba1ea4c8bb1af023d492acfcbf11e23c33f4af7d297eada113838cb6f0133a55684546f3 SHA512 4ed956197f08b7c3779f0bb39393b40cdaff3461071b48815200c6ad0dce2de87375cda96fe20d3ace4ab81ba6b8cdb50b58d82f5e5b54fe2c7751201ff2f63e
diff --git a/sci-chemistry/mgltools-pybabel/metadata.xml b/sci-chemistry/mgltools-pybabel/metadata.xml
deleted file mode 100644
index da36ecbfc..000000000
--- a/sci-chemistry/mgltools-pybabel/metadata.xml
+++ /dev/null
@@ -1,8 +0,0 @@
-<?xml version="1.0" encoding="UTF-8"?>
-<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
-<pkgmetadata>
-	<maintainer type="project">
-		<email>sci-chemistry@gentoo.org</email>
-		<name>Gentoo Chemistry Project</name>
-	</maintainer>
-</pkgmetadata>
diff --git a/sci-chemistry/mgltools-pybabel/mgltools-pybabel-1.5.6.ebuild b/sci-chemistry/mgltools-pybabel/mgltools-pybabel-1.5.6.ebuild
deleted file mode 100644
index a619ad235..000000000
--- a/sci-chemistry/mgltools-pybabel/mgltools-pybabel-1.5.6.ebuild
+++ /dev/null
@@ -1,44 +0,0 @@
-# Copyright 1999-2015 Gentoo Foundation
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=5
-
-PYTHON_COMPAT=( python2_7 )
-
-inherit distutils-r1 eutils
-
-MY_PN="PyBabel"
-MY_P="${MY_PN}-${PV/_rc3/}"
-
-DESCRIPTION="MGLTools Plugin -- PyBabel"
-HOMEPAGE="http://mgltools.scripps.edu"
-SRC_URI="http://mgltools.scripps.edu/downloads/tars/releases/REL${PV}/mgltools_source_${PV}.tar.gz"
-
-LICENSE="MGLTOOLS MPL-1.1"
-SLOT="0"
-KEYWORDS="~amd64 ~x86"
-IUSE=""
-
-RDEPEND=""
-DEPEND="${RDEPEND}
-	dev-lang/swig"
-
-S="${WORKDIR}"/${MY_P}
-
-DOCS=( PyBabel/RELNOTES )
-
-src_unpack() {
-	tar xzpf "${DISTDIR}"/${A} mgltools_source_${PV/_/}/MGLPACKS/${MY_P}.tar.gz || die
-	tar xzpf mgltools_source_${PV/_/}/MGLPACKS/${MY_P}.tar.gz || die
-}
-
-python_prepare_all() {
-	ecvs_clean
-	find "${S}" -name LICENSE -type f -delete || die
-
-	sed  \
-		-e 's:^.*CVS:#&1:g' \
-		-e 's:^.*LICENSE:#&1:g' \
-		-i "${S}"/MANIFEST.in || die
-	distutils-r1_python_prepare_all
-}
diff --git a/sci-chemistry/mgltools-pyglf/Manifest b/sci-chemistry/mgltools-pyglf/Manifest
deleted file mode 100644
index 366b14ae4..000000000
--- a/sci-chemistry/mgltools-pyglf/Manifest
+++ /dev/null
@@ -1 +0,0 @@
-DIST mgltools_source_1.5.6.tar.gz 40275811 BLAKE2B 98a2d71f33fc92233f1082637b54d63a180b6cf1fa8cc052cb497380ba1ea4c8bb1af023d492acfcbf11e23c33f4af7d297eada113838cb6f0133a55684546f3 SHA512 4ed956197f08b7c3779f0bb39393b40cdaff3461071b48815200c6ad0dce2de87375cda96fe20d3ace4ab81ba6b8cdb50b58d82f5e5b54fe2c7751201ff2f63e
diff --git a/sci-chemistry/mgltools-pyglf/metadata.xml b/sci-chemistry/mgltools-pyglf/metadata.xml
deleted file mode 100644
index da36ecbfc..000000000
--- a/sci-chemistry/mgltools-pyglf/metadata.xml
+++ /dev/null
@@ -1,8 +0,0 @@
-<?xml version="1.0" encoding="UTF-8"?>
-<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
-<pkgmetadata>
-	<maintainer type="project">
-		<email>sci-chemistry@gentoo.org</email>
-		<name>Gentoo Chemistry Project</name>
-	</maintainer>
-</pkgmetadata>
diff --git a/sci-chemistry/mgltools-pyglf/mgltools-pyglf-1.5.6.ebuild b/sci-chemistry/mgltools-pyglf/mgltools-pyglf-1.5.6.ebuild
deleted file mode 100644
index ddf51d228..000000000
--- a/sci-chemistry/mgltools-pyglf/mgltools-pyglf-1.5.6.ebuild
+++ /dev/null
@@ -1,42 +0,0 @@
-# Copyright 1999-2015 Gentoo Foundation
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=5
-
-PYTHON_COMPAT=( python2_7 )
-
-inherit distutils-r1 eutils
-
-MY_PN="pyglf"
-MY_P="${MY_PN}-${PV/_rc3/}"
-
-DESCRIPTION="MGLTools Plugin -- pyglf"
-HOMEPAGE="http://mgltools.scripps.edu"
-SRC_URI="http://mgltools.scripps.edu/downloads/tars/releases/REL${PV}/mgltools_source_${PV}.tar.gz"
-
-LICENSE="MGLTOOLS MPL-1.1"
-SLOT="0"
-KEYWORDS="~amd64 ~x86"
-IUSE=""
-
-RDEPEND="dev-python/numpy[${PYTHON_USEDEP}]"
-DEPEND="${RDEPEND}
-	dev-lang/swig"
-
-S="${WORKDIR}"/${MY_P}
-
-src_unpack() {
-	tar xzpf "${DISTDIR}"/${A} mgltools_source_${PV/_/}/MGLPACKS/${MY_P}.tar.gz || die
-	tar xzpf mgltools_source_${PV/_/}/MGLPACKS/${MY_P}.tar.gz || die
-}
-
-python_prepare_all() {
-	ecvs_clean
-	find "${S}" -name LICENSE -type f -delete || die
-
-	sed  \
-		-e 's:^.*CVS:#&1:g' \
-		-e 's:^.*LICENSE:#&1:g' \
-		-i "${S}"/MANIFEST.in || die
-	distutils-r1_python_prepare_all
-}
diff --git a/sci-chemistry/mgltools-qslimlib/Manifest b/sci-chemistry/mgltools-qslimlib/Manifest
deleted file mode 100644
index 366b14ae4..000000000
--- a/sci-chemistry/mgltools-qslimlib/Manifest
+++ /dev/null
@@ -1 +0,0 @@
-DIST mgltools_source_1.5.6.tar.gz 40275811 BLAKE2B 98a2d71f33fc92233f1082637b54d63a180b6cf1fa8cc052cb497380ba1ea4c8bb1af023d492acfcbf11e23c33f4af7d297eada113838cb6f0133a55684546f3 SHA512 4ed956197f08b7c3779f0bb39393b40cdaff3461071b48815200c6ad0dce2de87375cda96fe20d3ace4ab81ba6b8cdb50b58d82f5e5b54fe2c7751201ff2f63e
diff --git a/sci-chemistry/mgltools-qslimlib/files/1.5.4-gcc4.3.patch b/sci-chemistry/mgltools-qslimlib/files/1.5.4-gcc4.3.patch
deleted file mode 100644
index 5305a9004..000000000
--- a/sci-chemistry/mgltools-qslimlib/files/1.5.4-gcc4.3.patch
+++ /dev/null
@@ -1,52 +0,0 @@
---- QSlimLib-1.5.4/src/mixkit/MxDynBlock.h	2009-05-18 22:04:02.783721647 +0200
-+++ QSlimLib-1.5.4/src/mixkit/MxDynBlock.h.new	2009-05-18 22:14:07.010554394 +0200
-@@ -35,7 +35,7 @@
- 
-     void room_for(int len)
-     {
--	if( length()<len ) resize(len);
-+	if( length()<len ) this->resize(len);
- 	fill = len;
-     }
- 
---- QSlimLib-1.5.4/src/mixkit/MxDynBlock.h	2009-05-18 22:20:40.238540252 +0200
-+++ QSlimLib-1.5.4/src/mixkit/MxDynBlock.h.new	2009-05-18 22:21:22.416124721 +0200
-@@ -62,8 +62,8 @@
-     //
-     int size() const { return length(); }
- 
--    typename MxBlock<T>::iterator end()       { return begin()+size(); }
--    typename MxBlock<T>::const_iterator end() const { return begin()+size(); }
-+    typename MxBlock<T>::iterator end()       { return this->begin()+size(); }
-+    typename MxBlock<T>::const_iterator end() const { return this->begin()+size(); }
- 
-     void push_back(const T& t) { add(t); }
- };
---- QSlimLib-1.5.4/src/mixkit/MxStack.h	2004-10-25 23:02:10.000000000 +0200
-+++ QSlimLib-1.5.4/src/mixkit/MxStack.h.new	2009-05-18 22:25:01.804175361 +0200
-@@ -26,12 +26,12 @@
-     MxStack(const T& val, unsigned int n) : MxDynBlock<T>(n)
- 	{ push(val); }
- 
--    T&       top()       { return last(); }
--    const T& top() const { return last(); }
-+    T&       top()       { return this->last(); }
-+    const T& top() const { return this->last(); }
- 
--    bool is_empty() { return length()==0; }
-+    bool is_empty() { return this->length()==0; }
- 
--    T& pop() { return drop(); }
-+    T& pop() { return this->drop(); }
- 
-     void push(const T& val) { add(val); }
-     //
-@@ -41,7 +41,7 @@
-     //       broken!  The top() will grab a pointer into the block,
-     //       but the add() may reallocate the block before doing the
-     //       assignment.  Thus, the pointer will become invalid.
--    void push() { add(); top() = (*this)[length()-2]; }
-+    void push() { this->add(); top() = (*this)[this->length()-2]; }
- };
- 
- // MXSTACK_INCLUDED
diff --git a/sci-chemistry/mgltools-qslimlib/files/1.5.4-gcc4.7.patch b/sci-chemistry/mgltools-qslimlib/files/1.5.4-gcc4.7.patch
deleted file mode 100644
index 5e94b74d1..000000000
--- a/sci-chemistry/mgltools-qslimlib/files/1.5.4-gcc4.7.patch
+++ /dev/null
@@ -1,30 +0,0 @@
- src/mixkit/MxDynBlock.h |    2 +-
- src/mixkit/MxStack.h    |    2 +-
- 2 files changed, 2 insertions(+), 2 deletions(-)
-
-diff --git a/src/mixkit/MxDynBlock.h b/src/mixkit/MxDynBlock.h
-index 51cc89b..4e313d2 100644
---- a/src/mixkit/MxDynBlock.h
-+++ b/src/mixkit/MxDynBlock.h
-@@ -41,7 +41,7 @@ public:
- 
-     T& add()
-     {
--	if( length()==total_space() )  resize(total_space() * 2);
-+	if( length()==total_space() )  this->resize(total_space() * 2);
- 	fill++;
- 	return last();
-     }
-diff --git a/src/mixkit/MxStack.h b/src/mixkit/MxStack.h
-index 9ed9a05..1275ddd 100644
---- a/src/mixkit/MxStack.h
-+++ b/src/mixkit/MxStack.h
-@@ -33,7 +33,7 @@ public:
- 
-     T& pop() { return this->drop(); }
- 
--    void push(const T& val) { add(val); }
-+    void push(const T& val) { this->add(val); }
-     //
-     // NOTE: In this code, it is *crucial* that we do the add() and
-     //       assignment in separate steps.  The obvious alternative
diff --git a/sci-chemistry/mgltools-qslimlib/metadata.xml b/sci-chemistry/mgltools-qslimlib/metadata.xml
deleted file mode 100644
index da36ecbfc..000000000
--- a/sci-chemistry/mgltools-qslimlib/metadata.xml
+++ /dev/null
@@ -1,8 +0,0 @@
-<?xml version="1.0" encoding="UTF-8"?>
-<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
-<pkgmetadata>
-	<maintainer type="project">
-		<email>sci-chemistry@gentoo.org</email>
-		<name>Gentoo Chemistry Project</name>
-	</maintainer>
-</pkgmetadata>
diff --git a/sci-chemistry/mgltools-qslimlib/mgltools-qslimlib-1.5.6.ebuild b/sci-chemistry/mgltools-qslimlib/mgltools-qslimlib-1.5.6.ebuild
deleted file mode 100644
index e33e5f6fb..000000000
--- a/sci-chemistry/mgltools-qslimlib/mgltools-qslimlib-1.5.6.ebuild
+++ /dev/null
@@ -1,46 +0,0 @@
-# Copyright 1999-2015 Gentoo Foundation
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=5
-
-PYTHON_COMPAT=( python2_7 )
-
-inherit distutils-r1 eutils
-
-MY_PN="QSlimLib"
-MY_P="${MY_PN}-${PV/_rc3/}"
-
-DESCRIPTION="MGLTools Plugin -- QSlimLib"
-HOMEPAGE="http://mgltools.scripps.edu"
-SRC_URI="http://mgltools.scripps.edu/downloads/tars/releases/REL${PV}/mgltools_source_${PV}.tar.gz"
-
-LICENSE="MGLTOOLS MPL-1.1"
-SLOT="0"
-KEYWORDS="~amd64 ~x86"
-IUSE=""
-
-RDEPEND="dev-python/numpy[${PYTHON_USEDEP}]"
-DEPEND="${RDEPEND}
-	dev-lang/swig"
-
-S="${WORKDIR}"/${MY_P}
-
-src_unpack() {
-	tar xzpf "${DISTDIR}"/${A} mgltools_source_${PV/_/}/MGLPACKS/${MY_P}.tar.gz || die
-	tar xzpf mgltools_source_${PV/_/}/MGLPACKS/${MY_P}.tar.gz || die
-}
-
-python_prepare_all() {
-	local PATCHES=(
-		"${FILESDIR}"/1.5.4-gcc4.3.patch
-		"${FILESDIR}"/1.5.4-gcc4.7.patch
-		)
-	ecvs_clean
-	find "${S}" -name LICENSE -type f -delete || die
-
-	sed  \
-		-e 's:^.*CVS:#&1:g' \
-		-e 's:^.*LICENSE:#&1:g' \
-		-i "${S}"/MANIFEST.in || die
-	distutils-r1_python_prepare_all
-}
diff --git a/sci-chemistry/mgltools-scenario2/Manifest b/sci-chemistry/mgltools-scenario2/Manifest
deleted file mode 100644
index 366b14ae4..000000000
--- a/sci-chemistry/mgltools-scenario2/Manifest
+++ /dev/null
@@ -1 +0,0 @@
-DIST mgltools_source_1.5.6.tar.gz 40275811 BLAKE2B 98a2d71f33fc92233f1082637b54d63a180b6cf1fa8cc052cb497380ba1ea4c8bb1af023d492acfcbf11e23c33f4af7d297eada113838cb6f0133a55684546f3 SHA512 4ed956197f08b7c3779f0bb39393b40cdaff3461071b48815200c6ad0dce2de87375cda96fe20d3ace4ab81ba6b8cdb50b58d82f5e5b54fe2c7751201ff2f63e
diff --git a/sci-chemistry/mgltools-scenario2/metadata.xml b/sci-chemistry/mgltools-scenario2/metadata.xml
deleted file mode 100644
index da36ecbfc..000000000
--- a/sci-chemistry/mgltools-scenario2/metadata.xml
+++ /dev/null
@@ -1,8 +0,0 @@
-<?xml version="1.0" encoding="UTF-8"?>
-<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
-<pkgmetadata>
-	<maintainer type="project">
-		<email>sci-chemistry@gentoo.org</email>
-		<name>Gentoo Chemistry Project</name>
-	</maintainer>
-</pkgmetadata>
diff --git a/sci-chemistry/mgltools-scenario2/mgltools-scenario2-1.5.6.ebuild b/sci-chemistry/mgltools-scenario2/mgltools-scenario2-1.5.6.ebuild
deleted file mode 100644
index 79d4c2583..000000000
--- a/sci-chemistry/mgltools-scenario2/mgltools-scenario2-1.5.6.ebuild
+++ /dev/null
@@ -1,45 +0,0 @@
-# Copyright 1999-2015 Gentoo Foundation
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=5
-
-PYTHON_COMPAT=( python2_7 )
-
-inherit distutils-r1 eutils
-
-MY_PN="Scenario2"
-MY_P="${MY_PN}-${PV/_rc3/}"
-
-DESCRIPTION="MGLTools Plugin -- Scenario2"
-HOMEPAGE="http://mgltools.scripps.edu"
-SRC_URI="http://mgltools.scripps.edu/downloads/tars/releases/REL${PV}/mgltools_source_${PV}.tar.gz"
-
-LICENSE="MGLTOOLS MPL-1.1"
-SLOT="0"
-KEYWORDS="~amd64 ~x86"
-IUSE=""
-
-RDEPEND="
-	dev-python/simpy[${PYTHON_USEDEP}]
-	virtual/python-pmw[${PYTHON_USEDEP}]
-	"
-DEPEND="${RDEPEND}
-	dev-lang/swig"
-
-S="${WORKDIR}"/${MY_P}
-
-src_unpack() {
-	tar xzpf "${DISTDIR}"/${A} mgltools_source_${PV/_/}/MGLPACKS/${MY_P}.tar.gz || die
-	tar xzpf mgltools_source_${PV/_/}/MGLPACKS/${MY_P}.tar.gz || die
-}
-
-python_prepare_all() {
-	ecvs_clean
-	find "${S}" -name LICENSE -type f -delete || die
-
-	sed  \
-		-e 's:^.*CVS:#&1:g' \
-		-e 's:^.*LICENSE:#&1:g' \
-		-i "${S}"/MANIFEST.in || die
-	distutils-r1_python_prepare_all
-}
diff --git a/sci-chemistry/mgltools-sff/Manifest b/sci-chemistry/mgltools-sff/Manifest
deleted file mode 100644
index 366b14ae4..000000000
--- a/sci-chemistry/mgltools-sff/Manifest
+++ /dev/null
@@ -1 +0,0 @@
-DIST mgltools_source_1.5.6.tar.gz 40275811 BLAKE2B 98a2d71f33fc92233f1082637b54d63a180b6cf1fa8cc052cb497380ba1ea4c8bb1af023d492acfcbf11e23c33f4af7d297eada113838cb6f0133a55684546f3 SHA512 4ed956197f08b7c3779f0bb39393b40cdaff3461071b48815200c6ad0dce2de87375cda96fe20d3ace4ab81ba6b8cdb50b58d82f5e5b54fe2c7751201ff2f63e
diff --git a/sci-chemistry/mgltools-sff/files/1.5.4-impl-dec.patch b/sci-chemistry/mgltools-sff/files/1.5.4-impl-dec.patch
deleted file mode 100644
index 253051992..000000000
--- a/sci-chemistry/mgltools-sff/files/1.5.4-impl-dec.patch
+++ /dev/null
@@ -1,12 +0,0 @@
-diff --git a/src/bhtree.c b/src/bhtree.c
-index 1db701a..cb16afb 100644
---- a/src/bhtree.c
-+++ b/src/bhtree.c
-@@ -38,6 +38,7 @@
- */
- #include <stdio.h>
- #include <math.h>
-+#include <stdlib.h>
- #include "bhtree.h"
- 
- /* Barnes - Hut Trees ? */
diff --git a/sci-chemistry/mgltools-sff/metadata.xml b/sci-chemistry/mgltools-sff/metadata.xml
deleted file mode 100644
index da36ecbfc..000000000
--- a/sci-chemistry/mgltools-sff/metadata.xml
+++ /dev/null
@@ -1,8 +0,0 @@
-<?xml version="1.0" encoding="UTF-8"?>
-<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
-<pkgmetadata>
-	<maintainer type="project">
-		<email>sci-chemistry@gentoo.org</email>
-		<name>Gentoo Chemistry Project</name>
-	</maintainer>
-</pkgmetadata>
diff --git a/sci-chemistry/mgltools-sff/mgltools-sff-1.5.6.ebuild b/sci-chemistry/mgltools-sff/mgltools-sff-1.5.6.ebuild
deleted file mode 100644
index 6b81d92dc..000000000
--- a/sci-chemistry/mgltools-sff/mgltools-sff-1.5.6.ebuild
+++ /dev/null
@@ -1,43 +0,0 @@
-# Copyright 1999-2015 Gentoo Foundation
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=5
-
-PYTHON_COMPAT=( python2_7 )
-
-inherit distutils-r1 eutils
-
-MY_PN="sff"
-MY_P="${MY_PN}-${PV/_rc3/}"
-
-DESCRIPTION="MGLTools Plugin -- sff"
-HOMEPAGE="http://mgltools.scripps.edu"
-SRC_URI="http://mgltools.scripps.edu/downloads/tars/releases/REL${PV}/mgltools_source_${PV}.tar.gz"
-
-LICENSE="MGLTOOLS MPL-1.1"
-SLOT="0"
-KEYWORDS="~amd64 ~x86"
-IUSE=""
-
-RDEPEND="dev-python/numpy[${PYTHON_USEDEP}]"
-DEPEND="${RDEPEND}
-	dev-lang/swig"
-
-S="${WORKDIR}"/${MY_P}
-
-src_unpack() {
-	tar xzpf "${DISTDIR}"/${A} mgltools_source_${PV/_/}/MGLPACKS/${MY_P}.tar.gz || die
-	tar xzpf mgltools_source_${PV/_/}/MGLPACKS/${MY_P}.tar.gz || die
-}
-
-python_prepare_all() {
-	local PATCHES=( "${FILESDIR}"/1.5.4-impl-dec.patch )
-	ecvs_clean
-	find "${S}" -name LICENSE -type f -delete || die
-
-	sed  \
-		-e 's:^.*CVS:#&1:g' \
-		-e 's:^.*LICENSE:#&1:g' \
-		-i "${S}"/MANIFEST.in || die
-	distutils-r1_python_prepare_all
-}
diff --git a/sci-chemistry/mgltools-support/Manifest b/sci-chemistry/mgltools-support/Manifest
deleted file mode 100644
index 366b14ae4..000000000
--- a/sci-chemistry/mgltools-support/Manifest
+++ /dev/null
@@ -1 +0,0 @@
-DIST mgltools_source_1.5.6.tar.gz 40275811 BLAKE2B 98a2d71f33fc92233f1082637b54d63a180b6cf1fa8cc052cb497380ba1ea4c8bb1af023d492acfcbf11e23c33f4af7d297eada113838cb6f0133a55684546f3 SHA512 4ed956197f08b7c3779f0bb39393b40cdaff3461071b48815200c6ad0dce2de87375cda96fe20d3ace4ab81ba6b8cdb50b58d82f5e5b54fe2c7751201ff2f63e
diff --git a/sci-chemistry/mgltools-support/metadata.xml b/sci-chemistry/mgltools-support/metadata.xml
deleted file mode 100644
index da36ecbfc..000000000
--- a/sci-chemistry/mgltools-support/metadata.xml
+++ /dev/null
@@ -1,8 +0,0 @@
-<?xml version="1.0" encoding="UTF-8"?>
-<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
-<pkgmetadata>
-	<maintainer type="project">
-		<email>sci-chemistry@gentoo.org</email>
-		<name>Gentoo Chemistry Project</name>
-	</maintainer>
-</pkgmetadata>
diff --git a/sci-chemistry/mgltools-support/mgltools-support-1.5.6.ebuild b/sci-chemistry/mgltools-support/mgltools-support-1.5.6.ebuild
deleted file mode 100644
index c25bf8a46..000000000
--- a/sci-chemistry/mgltools-support/mgltools-support-1.5.6.ebuild
+++ /dev/null
@@ -1,42 +0,0 @@
-# Copyright 1999-2015 Gentoo Foundation
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=5
-
-PYTHON_COMPAT=( python2_7 )
-
-inherit distutils-r1 eutils
-
-MY_PN="Support"
-MY_P="${MY_PN}-${PV/_rc3/}"
-
-DESCRIPTION="MGLTools Plugin -- Support"
-HOMEPAGE="http://mgltools.scripps.edu"
-SRC_URI="http://mgltools.scripps.edu/downloads/tars/releases/REL${PV}/mgltools_source_${PV}.tar.gz"
-
-LICENSE="MGLTOOLS MPL-1.1"
-SLOT="0"
-KEYWORDS="~amd64 ~x86"
-IUSE=""
-
-RDEPEND=""
-DEPEND="${RDEPEND}
-	dev-lang/swig"
-
-S="${WORKDIR}"/${MY_P}
-
-src_unpack() {
-	tar xzpf "${DISTDIR}"/${A} mgltools_source_${PV/_/}/MGLPACKS/${MY_P}.tar.gz || die
-	tar xzpf mgltools_source_${PV/_/}/MGLPACKS/${MY_P}.tar.gz || die
-}
-
-python_prepare_all() {
-	ecvs_clean
-	find "${S}" -name LICENSE -type f -delete || die
-
-	sed  \
-		-e 's:^.*CVS:#&1:g' \
-		-e 's:^.*LICENSE:#&1:g' \
-		-i "${S}"/MANIFEST.in || die
-	distutils-r1_python_prepare_all
-}
diff --git a/sci-chemistry/mgltools-symserv/Manifest b/sci-chemistry/mgltools-symserv/Manifest
deleted file mode 100644
index 366b14ae4..000000000
--- a/sci-chemistry/mgltools-symserv/Manifest
+++ /dev/null
@@ -1 +0,0 @@
-DIST mgltools_source_1.5.6.tar.gz 40275811 BLAKE2B 98a2d71f33fc92233f1082637b54d63a180b6cf1fa8cc052cb497380ba1ea4c8bb1af023d492acfcbf11e23c33f4af7d297eada113838cb6f0133a55684546f3 SHA512 4ed956197f08b7c3779f0bb39393b40cdaff3461071b48815200c6ad0dce2de87375cda96fe20d3ace4ab81ba6b8cdb50b58d82f5e5b54fe2c7751201ff2f63e
diff --git a/sci-chemistry/mgltools-symserv/metadata.xml b/sci-chemistry/mgltools-symserv/metadata.xml
deleted file mode 100644
index da36ecbfc..000000000
--- a/sci-chemistry/mgltools-symserv/metadata.xml
+++ /dev/null
@@ -1,8 +0,0 @@
-<?xml version="1.0" encoding="UTF-8"?>
-<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
-<pkgmetadata>
-	<maintainer type="project">
-		<email>sci-chemistry@gentoo.org</email>
-		<name>Gentoo Chemistry Project</name>
-	</maintainer>
-</pkgmetadata>
diff --git a/sci-chemistry/mgltools-symserv/mgltools-symserv-1.5.6.ebuild b/sci-chemistry/mgltools-symserv/mgltools-symserv-1.5.6.ebuild
deleted file mode 100644
index 9c1f2c8e2..000000000
--- a/sci-chemistry/mgltools-symserv/mgltools-symserv-1.5.6.ebuild
+++ /dev/null
@@ -1,42 +0,0 @@
-# Copyright 1999-2015 Gentoo Foundation
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=5
-
-PYTHON_COMPAT=( python2_7 )
-
-inherit distutils-r1 eutils
-
-MY_PN="symserv"
-MY_P="${MY_PN}-${PV/_rc3/}"
-
-DESCRIPTION="MGLTools Plugin -- symserv"
-HOMEPAGE="http://mgltools.scripps.edu"
-SRC_URI="http://mgltools.scripps.edu/downloads/tars/releases/REL${PV}/mgltools_source_${PV}.tar.gz"
-
-LICENSE="MGLTOOLS MPL-1.1"
-SLOT="0"
-KEYWORDS="~amd64 ~x86"
-IUSE=""
-
-RDEPEND=""
-DEPEND="${RDEPEND}
-	dev-lang/swig"
-
-S="${WORKDIR}"/${MY_P}
-
-src_unpack() {
-	tar xzpf "${DISTDIR}"/${A} mgltools_source_${PV/_/}/MGLPACKS/${MY_P}.tar.gz || die
-	tar xzpf mgltools_source_${PV/_/}/MGLPACKS/${MY_P}.tar.gz || die
-}
-
-python_prepare_all() {
-	ecvs_clean
-	find "${S}" -name LICENSE -type f -delete || die
-
-	sed  \
-		-e 's:^.*CVS:#&1:g' \
-		-e 's:^.*LICENSE:#&1:g' \
-		-i "${S}"/MANIFEST.in || die
-	distutils-r1_python_prepare_all
-}
diff --git a/sci-chemistry/mgltools-utpackages/Manifest b/sci-chemistry/mgltools-utpackages/Manifest
deleted file mode 100644
index 366b14ae4..000000000
--- a/sci-chemistry/mgltools-utpackages/Manifest
+++ /dev/null
@@ -1 +0,0 @@
-DIST mgltools_source_1.5.6.tar.gz 40275811 BLAKE2B 98a2d71f33fc92233f1082637b54d63a180b6cf1fa8cc052cb497380ba1ea4c8bb1af023d492acfcbf11e23c33f4af7d297eada113838cb6f0133a55684546f3 SHA512 4ed956197f08b7c3779f0bb39393b40cdaff3461071b48815200c6ad0dce2de87375cda96fe20d3ace4ab81ba6b8cdb50b58d82f5e5b54fe2c7751201ff2f63e
diff --git a/sci-chemistry/mgltools-utpackages/files/1.5.4-gcc4.3.patch b/sci-chemistry/mgltools-utpackages/files/1.5.4-gcc4.3.patch
deleted file mode 100644
index 24984b360..000000000
--- a/sci-chemistry/mgltools-utpackages/files/1.5.4-gcc4.3.patch
+++ /dev/null
@@ -1,11 +0,0 @@
---- UTpackages-1.5.4/UTisocontourDIST/src/queue.h	2004-06-16 21:46:53.000000000 +0200
-+++ UTpackages-1.5.4/UTisocontourDIST/src/queue.h.new	2009-05-28 21:40:02.000000000 +0200
-@@ -17,7 +17,7 @@
- #define __QUEUE_H
- 
- #include "utilities.h"
--
-+#include <algorithm>
- 
- //@ManMemo: A templated FIFO queue
- /*@Doc: Implementation of a FIFO queue based on a circular array.
diff --git a/sci-chemistry/mgltools-utpackages/metadata.xml b/sci-chemistry/mgltools-utpackages/metadata.xml
deleted file mode 100644
index da36ecbfc..000000000
--- a/sci-chemistry/mgltools-utpackages/metadata.xml
+++ /dev/null
@@ -1,8 +0,0 @@
-<?xml version="1.0" encoding="UTF-8"?>
-<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
-<pkgmetadata>
-	<maintainer type="project">
-		<email>sci-chemistry@gentoo.org</email>
-		<name>Gentoo Chemistry Project</name>
-	</maintainer>
-</pkgmetadata>
diff --git a/sci-chemistry/mgltools-utpackages/mgltools-utpackages-1.5.6.ebuild b/sci-chemistry/mgltools-utpackages/mgltools-utpackages-1.5.6.ebuild
deleted file mode 100644
index e8fbc41e6..000000000
--- a/sci-chemistry/mgltools-utpackages/mgltools-utpackages-1.5.6.ebuild
+++ /dev/null
@@ -1,42 +0,0 @@
-# Copyright 1999-2015 Gentoo Foundation
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=5
-
-PYTHON_COMPAT=( python2_7 )
-
-inherit distutils-r1 eutils
-
-MY_PN="UTpackages"
-MY_P="${MY_PN}-${PV/_rc3/}"
-
-DESCRIPTION="MGLTools Plugin -- UTpackages"
-HOMEPAGE="http://mgltools.scripps.edu"
-SRC_URI="http://mgltools.scripps.edu/downloads/tars/releases/REL${PV}/mgltools_source_${PV}.tar.gz"
-
-LICENSE="MGLTOOLS MPL-1.1 UTPackages"
-SLOT="0"
-KEYWORDS="~amd64 ~x86"
-IUSE=""
-
-RDEPEND="dev-python/numpy[${PYTHON_USEDEP}]"
-DEPEND="${RDEPEND}
-	dev-lang/swig"
-
-S="${WORKDIR}"/${MY_P}
-
-src_unpack() {
-	tar xzpf "${DISTDIR}"/${A} mgltools_source_${PV/_/}/MGLPACKS/${MY_P}.tar.gz || die
-	tar xzpf mgltools_source_${PV/_/}/MGLPACKS/${MY_P}.tar.gz || die
-}
-
-python_prepare_all() {
-	ecvs_clean
-	find "${S}" -name LICENSE -type f -delete || die
-
-	sed  \
-		-e 's:^.*CVS:#&1:g' \
-		-e 's:^.*LICENSE:#&1:g' \
-		-i "${S}"/MANIFEST.in || die
-	distutils-r1_python_prepare_all
-}
diff --git a/sci-chemistry/mgltools-viewer-framework/Manifest b/sci-chemistry/mgltools-viewer-framework/Manifest
deleted file mode 100644
index 366b14ae4..000000000
--- a/sci-chemistry/mgltools-viewer-framework/Manifest
+++ /dev/null
@@ -1 +0,0 @@
-DIST mgltools_source_1.5.6.tar.gz 40275811 BLAKE2B 98a2d71f33fc92233f1082637b54d63a180b6cf1fa8cc052cb497380ba1ea4c8bb1af023d492acfcbf11e23c33f4af7d297eada113838cb6f0133a55684546f3 SHA512 4ed956197f08b7c3779f0bb39393b40cdaff3461071b48815200c6ad0dce2de87375cda96fe20d3ace4ab81ba6b8cdb50b58d82f5e5b54fe2c7751201ff2f63e
diff --git a/sci-chemistry/mgltools-viewer-framework/metadata.xml b/sci-chemistry/mgltools-viewer-framework/metadata.xml
deleted file mode 100644
index da36ecbfc..000000000
--- a/sci-chemistry/mgltools-viewer-framework/metadata.xml
+++ /dev/null
@@ -1,8 +0,0 @@
-<?xml version="1.0" encoding="UTF-8"?>
-<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
-<pkgmetadata>
-	<maintainer type="project">
-		<email>sci-chemistry@gentoo.org</email>
-		<name>Gentoo Chemistry Project</name>
-	</maintainer>
-</pkgmetadata>
diff --git a/sci-chemistry/mgltools-viewer-framework/mgltools-viewer-framework-1.5.6.ebuild b/sci-chemistry/mgltools-viewer-framework/mgltools-viewer-framework-1.5.6.ebuild
deleted file mode 100644
index eabcc214f..000000000
--- a/sci-chemistry/mgltools-viewer-framework/mgltools-viewer-framework-1.5.6.ebuild
+++ /dev/null
@@ -1,47 +0,0 @@
-# Copyright 1999-2015 Gentoo Foundation
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=5
-
-PYTHON_COMPAT=( python2_7 )
-
-inherit distutils-r1 eutils
-
-MY_PN="ViewerFramework"
-MY_P="${MY_PN}-${PV/_rc3/}"
-
-DESCRIPTION="MGLTools Plugin -- ViewerFramework"
-HOMEPAGE="http://mgltools.scripps.edu"
-SRC_URI="http://mgltools.scripps.edu/downloads/tars/releases/REL${PV}/mgltools_source_${PV}.tar.gz"
-
-LICENSE="MGLTOOLS MPL-1.1"
-SLOT="0"
-KEYWORDS="~amd64 ~x86"
-IUSE=""
-
-RDEPEND=""
-DEPEND="${RDEPEND}
-	dev-lang/swig"
-
-S="${WORKDIR}"/${MY_P}
-
-DOCS=( ViewerFramework/RELNOTES )
-
-src_unpack() {
-	tar xzpf "${DISTDIR}"/${A} mgltools_source_${PV/_/}/MGLPACKS/${MY_P}.tar.gz || die
-	tar xzpf mgltools_source_${PV/_/}/MGLPACKS/${MY_P}.tar.gz || die
-}
-
-python_prepare_all() {
-	ecvs_clean
-	find "${S}" -name LICENSE -type f -delete || die
-
-	sed  \
-		-e 's:^.*CVS:#&1:g' \
-		-e 's:^.*LICENSE:#&1:g' \
-		-i "${S}"/MANIFEST.in || die
-	sed \
-		-e '/__debug__/d' \
-		-i ViewerFramework/VF.py || die
-	distutils-r1_python_prepare_all
-}
diff --git a/sci-chemistry/mgltools-vision/Manifest b/sci-chemistry/mgltools-vision/Manifest
deleted file mode 100644
index 366b14ae4..000000000
--- a/sci-chemistry/mgltools-vision/Manifest
+++ /dev/null
@@ -1 +0,0 @@
-DIST mgltools_source_1.5.6.tar.gz 40275811 BLAKE2B 98a2d71f33fc92233f1082637b54d63a180b6cf1fa8cc052cb497380ba1ea4c8bb1af023d492acfcbf11e23c33f4af7d297eada113838cb6f0133a55684546f3 SHA512 4ed956197f08b7c3779f0bb39393b40cdaff3461071b48815200c6ad0dce2de87375cda96fe20d3ace4ab81ba6b8cdb50b58d82f5e5b54fe2c7751201ff2f63e
diff --git a/sci-chemistry/mgltools-vision/metadata.xml b/sci-chemistry/mgltools-vision/metadata.xml
deleted file mode 100644
index da36ecbfc..000000000
--- a/sci-chemistry/mgltools-vision/metadata.xml
+++ /dev/null
@@ -1,8 +0,0 @@
-<?xml version="1.0" encoding="UTF-8"?>
-<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
-<pkgmetadata>
-	<maintainer type="project">
-		<email>sci-chemistry@gentoo.org</email>
-		<name>Gentoo Chemistry Project</name>
-	</maintainer>
-</pkgmetadata>
diff --git a/sci-chemistry/mgltools-vision/mgltools-vision-1.5.6.ebuild b/sci-chemistry/mgltools-vision/mgltools-vision-1.5.6.ebuild
deleted file mode 100644
index f50816ffd..000000000
--- a/sci-chemistry/mgltools-vision/mgltools-vision-1.5.6.ebuild
+++ /dev/null
@@ -1,53 +0,0 @@
-# Copyright 1999-2015 Gentoo Foundation
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=5
-
-PYTHON_COMPAT=( python2_7 )
-
-inherit distutils-r1 eutils
-
-MY_PN="Vision"
-MY_P="${MY_PN}-${PV/_rc3/}"
-
-DESCRIPTION="MGLTools Plugin -- Vision"
-HOMEPAGE="http://mgltools.scripps.edu"
-SRC_URI="http://mgltools.scripps.edu/downloads/tars/releases/REL${PV}/mgltools_source_${PV}.tar.gz"
-
-LICENSE="MGLTOOLS MPL-1.1"
-SLOT="0"
-KEYWORDS="~amd64 ~x86"
-IUSE=""
-
-RDEPEND="dev-python/matplotlib[tk,${PYTHON_USEDEP}]"
-DEPEND="${RDEPEND}
-	dev-lang/swig"
-
-S="${WORKDIR}"/${MY_P}
-
-DOCS=( Vision/FAQ.txt )
-
-src_unpack() {
-	tar xzpf "${DISTDIR}"/${A} mgltools_source_${PV/_/}/MGLPACKS/${MY_P}.tar.gz || die
-	tar xzpf mgltools_source_${PV/_/}/MGLPACKS/${MY_P}.tar.gz || die
-}
-
-python_prepare_all() {
-	ecvs_clean
-	find "${S}" -name LICENSE -type f -delete || die
-
-	sed  \
-		-e 's:^.*CVS:#&1:g' \
-		-e 's:^.*LICENSE:#&1:g' \
-		-i "${S}"/MANIFEST.in || die
-	distutils-r1_python_prepare_all
-}
-
-python_install_all() {
-	distutils-r1_python_install_all
-
-	sed '1s:^.*$:#!/usr/bin/python:g' -i Vision/bin/runVision || die
-	dobin Vision/bin/runVision
-
-	dohtml Vision/FAQ.html
-}
diff --git a/sci-chemistry/mgltools-visionlib/Manifest b/sci-chemistry/mgltools-visionlib/Manifest
deleted file mode 100644
index 366b14ae4..000000000
--- a/sci-chemistry/mgltools-visionlib/Manifest
+++ /dev/null
@@ -1 +0,0 @@
-DIST mgltools_source_1.5.6.tar.gz 40275811 BLAKE2B 98a2d71f33fc92233f1082637b54d63a180b6cf1fa8cc052cb497380ba1ea4c8bb1af023d492acfcbf11e23c33f4af7d297eada113838cb6f0133a55684546f3 SHA512 4ed956197f08b7c3779f0bb39393b40cdaff3461071b48815200c6ad0dce2de87375cda96fe20d3ace4ab81ba6b8cdb50b58d82f5e5b54fe2c7751201ff2f63e
diff --git a/sci-chemistry/mgltools-visionlib/metadata.xml b/sci-chemistry/mgltools-visionlib/metadata.xml
deleted file mode 100644
index da36ecbfc..000000000
--- a/sci-chemistry/mgltools-visionlib/metadata.xml
+++ /dev/null
@@ -1,8 +0,0 @@
-<?xml version="1.0" encoding="UTF-8"?>
-<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
-<pkgmetadata>
-	<maintainer type="project">
-		<email>sci-chemistry@gentoo.org</email>
-		<name>Gentoo Chemistry Project</name>
-	</maintainer>
-</pkgmetadata>
diff --git a/sci-chemistry/mgltools-visionlib/mgltools-visionlib-1.5.6.ebuild b/sci-chemistry/mgltools-visionlib/mgltools-visionlib-1.5.6.ebuild
deleted file mode 100644
index e141c98a9..000000000
--- a/sci-chemistry/mgltools-visionlib/mgltools-visionlib-1.5.6.ebuild
+++ /dev/null
@@ -1,42 +0,0 @@
-# Copyright 1999-2015 Gentoo Foundation
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=5
-
-PYTHON_COMPAT=( python2_7 )
-
-inherit distutils-r1 eutils
-
-MY_PN="VisionLibraries"
-MY_P="${MY_PN}-${PV/_rc3/}"
-
-DESCRIPTION="MGLTools Plugin -- VisionLibraries"
-HOMEPAGE="http://mgltools.scripps.edu"
-SRC_URI="http://mgltools.scripps.edu/downloads/tars/releases/REL${PV}/mgltools_source_${PV}.tar.gz"
-
-LICENSE="MGLTOOLS MPL-1.1"
-SLOT="0"
-KEYWORDS="~amd64 ~x86"
-IUSE=""
-
-RDEPEND=""
-DEPEND="${RDEPEND}
-	dev-lang/swig"
-
-S="${WORKDIR}"/${MY_P}
-
-src_unpack() {
-	tar xzpf "${DISTDIR}"/${A} mgltools_source_${PV/_/}/MGLPACKS/${MY_P}.tar.gz || die
-	tar xzpf mgltools_source_${PV/_/}/MGLPACKS/${MY_P}.tar.gz || die
-}
-
-python_prepare_all() {
-	ecvs_clean
-	find "${S}" -name LICENSE -type f -delete || die
-
-	sed  \
-		-e 's:^.*CVS:#&1:g' \
-		-e 's:^.*LICENSE:#&1:g' \
-		-i "${S}"/MANIFEST.in || die
-	distutils-r1_python_prepare_all
-}
diff --git a/sci-chemistry/mgltools-volume/Manifest b/sci-chemistry/mgltools-volume/Manifest
deleted file mode 100644
index 366b14ae4..000000000
--- a/sci-chemistry/mgltools-volume/Manifest
+++ /dev/null
@@ -1 +0,0 @@
-DIST mgltools_source_1.5.6.tar.gz 40275811 BLAKE2B 98a2d71f33fc92233f1082637b54d63a180b6cf1fa8cc052cb497380ba1ea4c8bb1af023d492acfcbf11e23c33f4af7d297eada113838cb6f0133a55684546f3 SHA512 4ed956197f08b7c3779f0bb39393b40cdaff3461071b48815200c6ad0dce2de87375cda96fe20d3ace4ab81ba6b8cdb50b58d82f5e5b54fe2c7751201ff2f63e
diff --git a/sci-chemistry/mgltools-volume/metadata.xml b/sci-chemistry/mgltools-volume/metadata.xml
deleted file mode 100644
index da36ecbfc..000000000
--- a/sci-chemistry/mgltools-volume/metadata.xml
+++ /dev/null
@@ -1,8 +0,0 @@
-<?xml version="1.0" encoding="UTF-8"?>
-<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
-<pkgmetadata>
-	<maintainer type="project">
-		<email>sci-chemistry@gentoo.org</email>
-		<name>Gentoo Chemistry Project</name>
-	</maintainer>
-</pkgmetadata>
diff --git a/sci-chemistry/mgltools-volume/mgltools-volume-1.5.6.ebuild b/sci-chemistry/mgltools-volume/mgltools-volume-1.5.6.ebuild
deleted file mode 100644
index 33dbaaac8..000000000
--- a/sci-chemistry/mgltools-volume/mgltools-volume-1.5.6.ebuild
+++ /dev/null
@@ -1,44 +0,0 @@
-# Copyright 1999-2015 Gentoo Foundation
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=5
-
-PYTHON_COMPAT=( python2_7 )
-
-inherit distutils-r1 eutils
-
-MY_PN="Volume"
-MY_P="${MY_PN}-${PV/_rc3/}"
-
-DESCRIPTION="MGLTools Plugin -- Volume"
-HOMEPAGE="http://mgltools.scripps.edu"
-SRC_URI="http://mgltools.scripps.edu/downloads/tars/releases/REL${PV}/mgltools_source_${PV}.tar.gz"
-
-LICENSE="MGLTOOLS MPL-1.1"
-SLOT="0"
-KEYWORDS="~amd64 ~x86"
-IUSE=""
-
-RDEPEND=""
-DEPEND="${RDEPEND}
-	dev-lang/swig"
-
-S="${WORKDIR}"/${MY_P}
-
-DOCS=( Volume/RELNOTES Volume/README Volume/TODO )
-
-src_unpack() {
-	tar xzpf "${DISTDIR}"/${A} mgltools_source_${PV/_/}/MGLPACKS/${MY_P}.tar.gz || die
-	tar xzpf mgltools_source_${PV/_/}/MGLPACKS/${MY_P}.tar.gz || die
-}
-
-python_prepare_all() {
-	ecvs_clean
-	find "${S}" -name LICENSE -type f -delete || die
-
-	sed  \
-		-e 's:^.*CVS:#&1:g' \
-		-e 's:^.*LICENSE:#&1:g' \
-		-i "${S}"/MANIFEST.in || die
-	distutils-r1_python_prepare_all
-}
diff --git a/sci-chemistry/mgltools-webservices/Manifest b/sci-chemistry/mgltools-webservices/Manifest
deleted file mode 100644
index 366b14ae4..000000000
--- a/sci-chemistry/mgltools-webservices/Manifest
+++ /dev/null
@@ -1 +0,0 @@
-DIST mgltools_source_1.5.6.tar.gz 40275811 BLAKE2B 98a2d71f33fc92233f1082637b54d63a180b6cf1fa8cc052cb497380ba1ea4c8bb1af023d492acfcbf11e23c33f4af7d297eada113838cb6f0133a55684546f3 SHA512 4ed956197f08b7c3779f0bb39393b40cdaff3461071b48815200c6ad0dce2de87375cda96fe20d3ace4ab81ba6b8cdb50b58d82f5e5b54fe2c7751201ff2f63e
diff --git a/sci-chemistry/mgltools-webservices/metadata.xml b/sci-chemistry/mgltools-webservices/metadata.xml
deleted file mode 100644
index da36ecbfc..000000000
--- a/sci-chemistry/mgltools-webservices/metadata.xml
+++ /dev/null
@@ -1,8 +0,0 @@
-<?xml version="1.0" encoding="UTF-8"?>
-<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
-<pkgmetadata>
-	<maintainer type="project">
-		<email>sci-chemistry@gentoo.org</email>
-		<name>Gentoo Chemistry Project</name>
-	</maintainer>
-</pkgmetadata>
diff --git a/sci-chemistry/mgltools-webservices/mgltools-webservices-1.5.6.ebuild b/sci-chemistry/mgltools-webservices/mgltools-webservices-1.5.6.ebuild
deleted file mode 100644
index 82aea5667..000000000
--- a/sci-chemistry/mgltools-webservices/mgltools-webservices-1.5.6.ebuild
+++ /dev/null
@@ -1,42 +0,0 @@
-# Copyright 1999-2015 Gentoo Foundation
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=5
-
-PYTHON_COMPAT=( python2_7 )
-
-inherit distutils-r1 eutils
-
-MY_PN="WebServices"
-MY_P="${MY_PN}-${PV/_rc3/}"
-
-DESCRIPTION="MGLTools Plugin -- WebServices"
-HOMEPAGE="http://mgltools.scripps.edu"
-SRC_URI="http://mgltools.scripps.edu/downloads/tars/releases/REL${PV}/mgltools_source_${PV}.tar.gz"
-
-LICENSE="MGLTOOLS MPL-1.1"
-SLOT="0"
-KEYWORDS="~amd64 ~x86"
-IUSE=""
-
-RDEPEND="dev-python/zsi[${PYTHON_USEDEP}]"
-DEPEND="${RDEPEND}
-	dev-lang/swig"
-
-S="${WORKDIR}"/${MY_P}
-
-src_unpack() {
-	tar xzpf "${DISTDIR}"/${A} mgltools_source_${PV/_/}/MGLPACKS/${MY_P}.tar.gz || die
-	tar xzpf mgltools_source_${PV/_/}/MGLPACKS/${MY_P}.tar.gz || die
-}
-
-python_prepare_all() {
-	ecvs_clean
-	find "${S}" -name LICENSE -type f -delete || die
-
-	sed  \
-		-e 's:^.*CVS:#&1:g' \
-		-e 's:^.*LICENSE:#&1:g' \
-		-i "${S}"/MANIFEST.in || die
-	distutils-r1_python_prepare_all
-}
diff --git a/sci-chemistry/mgltools/Manifest b/sci-chemistry/mgltools/Manifest
deleted file mode 100644
index 366b14ae4..000000000
--- a/sci-chemistry/mgltools/Manifest
+++ /dev/null
@@ -1 +0,0 @@
-DIST mgltools_source_1.5.6.tar.gz 40275811 BLAKE2B 98a2d71f33fc92233f1082637b54d63a180b6cf1fa8cc052cb497380ba1ea4c8bb1af023d492acfcbf11e23c33f4af7d297eada113838cb6f0133a55684546f3 SHA512 4ed956197f08b7c3779f0bb39393b40cdaff3461071b48815200c6ad0dce2de87375cda96fe20d3ace4ab81ba6b8cdb50b58d82f5e5b54fe2c7751201ff2f63e
diff --git a/sci-chemistry/mgltools/metadata.xml b/sci-chemistry/mgltools/metadata.xml
deleted file mode 100644
index da36ecbfc..000000000
--- a/sci-chemistry/mgltools/metadata.xml
+++ /dev/null
@@ -1,8 +0,0 @@
-<?xml version="1.0" encoding="UTF-8"?>
-<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
-<pkgmetadata>
-	<maintainer type="project">
-		<email>sci-chemistry@gentoo.org</email>
-		<name>Gentoo Chemistry Project</name>
-	</maintainer>
-</pkgmetadata>
diff --git a/sci-chemistry/mgltools/mgltools-1.5.6.ebuild b/sci-chemistry/mgltools/mgltools-1.5.6.ebuild
deleted file mode 100644
index 488d1553d..000000000
--- a/sci-chemistry/mgltools/mgltools-1.5.6.ebuild
+++ /dev/null
@@ -1,47 +0,0 @@
-# Copyright 1999-2015 Gentoo Foundation
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=5
-
-PYTHON_COMPAT=( python2_7 )
-
-inherit eutils python-r1
-
-PLUGINS="autodocktools bhtree cadd cmolkit dejavu geomutils gle mglutil molkit
-	networkeditor opengltk pmv pyautodock pybabel pyglf qslimlib scenario2 sff
-	support symserv utpackages viewer-framework vision visionlib volume
-	webservices"
-
-DESCRIPTION="Software to visualization and analysis of molecular structures"
-HOMEPAGE="http://mgltools.scripps.edu/"
-SRC_URI="http://mgltools.scripps.edu/downloads/downloads/tars/releases/REL${PV}/${PN}_source_${PV}.tar.gz"
-
-LICENSE="MGLTOOLS MPL-1.1"
-SLOT="0"
-KEYWORDS="~amd64 ~x86"
-IUSE=""
-
-REQUIRED_USE="${PYTHON_REQUIRED_USE}"
-
-S="${WORKDIR}"/${PN}_source_${PV/_/}
-
-for plug in ${PLUGINS}; do
-	PLUG_DEP="${PLUG_DEP} =sci-chemistry/mgltools-${plug}-${PV}*[${PYTHON_USEDEP}]"
-done
-
-RDEPEND="${PLUG_DEP}
-	${PYTHON_DEPS}
-	dev-lang/tk:0
-	dev-python/numpy[${PYTHON_USEDEP}]
-	dev-python/simpy[${PYTHON_USEDEP}]
-	sci-libs/msms
-	dev-python/pillow[tk,${PYTHON_USEDEP}]
-	virtual/python-pmw[${PYTHON_USEDEP}]
-"
-DEPEND="${RDEPEND}"
-
-src_install() {
-	ecvs_clean
-	insinto /usr/share/${PN}
-	doins -r Data
-}
diff --git a/sci-chemistry/mics/mics-1.00.2011.327.12.00.ebuild b/sci-chemistry/mics/mics-1.00.2011.327.12.00.ebuild
index 41d7ca76b..5be82db7b 100644
--- a/sci-chemistry/mics/mics-1.00.2011.327.12.00.ebuild
+++ b/sci-chemistry/mics/mics-1.00.2011.327.12.00.ebuild
@@ -1,13 +1,13 @@
-# Copyright 1999-2015 Gentoo Foundation
+# Copyright 1999-2021 Gentoo Authors
 # Distributed under the terms of the GNU General Public License v2
 
-EAPI=5
+EAPI=7
 
 inherit java-pkg-opt-2
 
 DESCRIPTION="Prediction of Protein Structural Motifs from NMR Chemical Shifts"
-HOMEPAGE="http://spin.niddk.nih.gov/bax/software/MICS/"
-SRC_URI="http://spin.niddk.nih.gov/bax/software/MICS/mics.tar.Z -> ${P}.tgz"
+HOMEPAGE="https://spin.niddk.nih.gov/bax/software/MICS/"
+SRC_URI="https://spin.niddk.nih.gov/bax/software/MICS/mics.tar.Z -> ${P}.tgz"
 
 SLOT="0"
 LICENSE="all-rights-reserved"
@@ -17,11 +17,12 @@ IUSE="examples"
 RDEPEND=">=virtual/jre-1.5:*"
 DEPEND="${RDEPEND}"
 
-S="${WORKDIR}"/MICS
+S="${WORKDIR}/MICS"
 
 QA_PREBUILT="/opt/.*"
 
 src_prepare() {
+	default
 	rm -f bin/MICS.{mac,static.*,exe} || die
 }
 
diff --git a/sci-chemistry/modelfree/Manifest b/sci-chemistry/modelfree/Manifest
deleted file mode 100644
index 367013fd9..000000000
--- a/sci-chemistry/modelfree/Manifest
+++ /dev/null
@@ -1 +0,0 @@
-DIST modelfree4_linux.tar.gz 1148228 BLAKE2B f0637aba667f0b4ccf99aef288310ea5b1279d759629ea7bcb2c087c3ae2097e965a84a9fe9e4223d019fe504530312033ee232ac6542d68da640c5e66ba8d19 SHA512 88a6521448481fd87bae261a4745926c53cfb970c45ba49985c909a95ddcf687dd8089a3aa0d7e5a6b486ed13b2682030bd5331ebc5ea93149095730c8562f90
diff --git a/sci-chemistry/modelfree/metadata.xml b/sci-chemistry/modelfree/metadata.xml
deleted file mode 100644
index 713d21566..000000000
--- a/sci-chemistry/modelfree/metadata.xml
+++ /dev/null
@@ -1,11 +0,0 @@
-<?xml version="1.0" encoding="UTF-8"?>
-<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
-<pkgmetadata>
-	<maintainer type="person">
-		<email>jlec@gentoo.org</email>
-	</maintainer>
-	<maintainer type="project">
-		<email>sci-chemistry@gentoo.org</email>
-		<name>Gentoo Chemistry Project</name>
-	</maintainer>
-</pkgmetadata>
diff --git a/sci-chemistry/modelfree/modelfree-4.20.ebuild b/sci-chemistry/modelfree/modelfree-4.20.ebuild
deleted file mode 100644
index 3f13a72c5..000000000
--- a/sci-chemistry/modelfree/modelfree-4.20.ebuild
+++ /dev/null
@@ -1,47 +0,0 @@
-# Copyright 1999-2015 Gentoo Foundation
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=5
-
-inherit fortran-2 multilib
-
-DESCRIPTION="Optimizing Lipari-Szabo model free parameters to heteronuclear relaxation data"
-HOMEPAGE="http://www.palmer.hs.columbia.edu/software/modelfree.html"
-SRC_URI="http://www.palmer.hs.columbia.edu/software/modelfree4_linux.tar.gz"
-
-SLOT="0"
-LICENSE="GPL-2"
-KEYWORDS=""
-IUSE="doc examples"
-
-RDEPEND="
-	sci-libs/blas-reference
-	=sys-devel/gcc-4.1*"
-DEPEND="dev-util/patchelf"
-
-S="${WORKDIR}"
-
-QA_PREBUILT="opt/bin/.*"
-
-src_install() {
-	local _exe
-	dosym ../../usr/$(get_libdir)/librefblas.so /opt/${PN}/libblas.so.3
-	dosym ../../usr/$(get_libdir)/libreflapack.so /opt/${PN}/liblapack.so.3
-
-	exeinto /opt/bin
-	if use x86; then
-		_exe=./linux_32/${PN}4
-	elif use amd64; then
-		_exe=./linux_64/${PN}4
-	fi
-
-	patchelf --set-rpath \
-		"${EPREFIX}/opt/${PN}:$(gcc-config -L | sed 's|:.*$||g'):${EPREFIX}/usr/$(get_libdir)/gcc/x86_64-pc-linux-gnu/4.1.2/" \
-		${_exe}
-
-	doexe ${_exe}
-	dosym ${PN}4 /opt/bin/${PN}
-
-	use doc && dodoc docs/{modelfree_manual.pdf,VERSIONS.README}
-	use examples && insinto /usr/share/${PN} && doins -r testing
-}
diff --git a/sci-chemistry/modeller/Manifest b/sci-chemistry/modeller/Manifest
deleted file mode 100644
index 8c5c6393b..000000000
--- a/sci-chemistry/modeller/Manifest
+++ /dev/null
@@ -1,2 +0,0 @@
-DIST modeller-9.12.tar.gz 29273842 BLAKE2B 06b4ba3ed918b7f4552ed4bfb358332e623402b92ba48c8def8b4a4f8fe2eba3f30a02b868746cde5a6d7109129f073851523676544bd749a58b86dc71e19198 SHA512 5c0acaf453771347a9de3a0c7240f7ce376244803748edb28923dbaefda779041211ef4b26af5a2774bdf6bc63d7c7d7e62e1354e1550a6742c9575076864352
-DIST modeller-9.19.tar.gz 34885366 BLAKE2B 46310bb7b26392aab2a68881ff666fe05e973ce85b59d16edcc1dab1b5c3f4a9396d991467d189656ac5b71b509049219e54ff246967f305671e57247bcf1f45 SHA512 04bf1195b58a337541e97fc9812b5c0887909a687e4a6004cc9deb89dd078dbc78148fd81552ba189c063b7373e35f4b4a0603e4638af4e2d40fa30625be4c63
diff --git a/sci-chemistry/modeller/files/9v5-setup.patch b/sci-chemistry/modeller/files/9v5-setup.patch
deleted file mode 100644
index 5fe460580..000000000
--- a/sci-chemistry/modeller/files/9v5-setup.patch
+++ /dev/null
@@ -1,12 +0,0 @@
-diff -Nu -Nu -uarN modeller-9v3.orig/src/swig/setup.py modeller-9v3/src/swig/setup.py
---- modeller-9v4.orig/src/swig/setup.py	2008-04-15 12:57:50.000000000 +0200
-+++ modeller-9v4/src/swig/setup.py	2008-04-15 12:57:59.000000000 +0200
-@@ -19,7 +19,7 @@
-                 include_dirs=['../include', '../include/%s' % exetype] + \
-                              glib['include_dirs'],
-                 libraries=['modeller'] + glib['libraries'],
--                library_dirs=['../../lib/%s' % exetype] + glib['library_dirs'])
-+                library_dirs=['../../lib/%s' % exetype])
- 
- setup(name='Modeller',
-       description='Protein structure modeling by satisfaction of ' \
diff --git a/sci-chemistry/modeller/metadata.xml b/sci-chemistry/modeller/metadata.xml
deleted file mode 100644
index da36ecbfc..000000000
--- a/sci-chemistry/modeller/metadata.xml
+++ /dev/null
@@ -1,8 +0,0 @@
-<?xml version="1.0" encoding="UTF-8"?>
-<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
-<pkgmetadata>
-	<maintainer type="project">
-		<email>sci-chemistry@gentoo.org</email>
-		<name>Gentoo Chemistry Project</name>
-	</maintainer>
-</pkgmetadata>
diff --git a/sci-chemistry/modeller/modeller-9.12-r3.ebuild b/sci-chemistry/modeller/modeller-9.12-r3.ebuild
deleted file mode 100644
index de64378e1..000000000
--- a/sci-chemistry/modeller/modeller-9.12-r3.ebuild
+++ /dev/null
@@ -1,145 +0,0 @@
-# Copyright 1999-2016 Gentoo Foundation
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=6
-
-PYTHON_COMPAT=( python2_7 )
-
-inherit distutils-r1 eutils multilib versionator
-
-DESCRIPTION="Homology or comparative modeling of protein three-dimensional structures"
-HOMEPAGE="http://salilab.org/modeller/"
-SRC_URI="http://salilab.org/${PN}/${PV}/${P}.tar.gz"
-
-LICENSE="modeller"
-KEYWORDS="~amd64 ~x86 ~amd64-linux ~x86-linux"
-IUSE="doc examples"
-SLOT="0"
-
-RESTRICT="mirror"
-
-DEPEND=">=dev-lang/swig-1.3"
-RDEPEND=""
-
-INPATH="${EPREFIX}"/opt/modeller${ver}
-
-QA_PREBUILT="/opt/*"
-
-pkg_setup() {
-	case ${ARCH} in
-		x86)
-			EXECTYPE="i386-intel8";;
-		amd64)
-			EXECTYPE="x86_64-intel8";;
-		*)
-			die "Your arch "${ARCH}" does not appear supported at this time.";;
-	esac
-}
-
-python_prepare_all(){
-	sed "s:i386-intel8:${EXECTYPE}:g" -i src/swig/setup.py || die
-	distutils-r1_python_prepare_all
-}
-
-python_compile(){
-	cd src/swig || die
-	swig -python -keyword -nodefaultctor -nodefaultdtor -noproxy modeller.i || die
-	distutils-r1_python_compile
-}
-
-python_install() {
-	cd src/swig || die
-	distutils-r1_python_install
-}
-
-python_install_all(){
-	cd "${S}" || die
-	sed \
-		-e "/^EXECUTABLE_TYPE/s:xxx:${EXECTYPE}:g" \
-		-e "/MODINSTALL/s:xxx:\"${INPATH}\":g" \
-		-i bin/modscript || die
-
-	sed -e "s;@TOPDIR\@;\"${INPATH}\";" \
-		-e "s;@EXETYPE\@;${EXECTYPE};" \
-		bin/modpy.sh.in > "${T}/modpy.sh"
-
-	insinto ${INPATH}
-	doins -r modlib
-	python_foreach_impl python_domodule modlib/modeller
-
-	insinto ${INPATH}/bin
-	doins -r bin/{lib,*top}
-
-	exeinto ${INPATH}/bin
-	doexe bin/{modscript,mod${PV}_${EXECTYPE}} "${T}"/modpy.sh
-
-	python_foreach_impl python_doscript bin/modslave.py
-	dosym ${INPATH}/bin/modscript /opt/bin/mod${PV}
-	dosym ${INPATH}/bin/modpy.sh /opt/bin/modpy.sh
-
-	exeinto ${INPATH}/lib/${EXECTYPE}/
-	doexe lib/${EXECTYPE}/lib*
-	dosym libmodeller.so.8 ${INPATH}/lib/${EXECTYPE}/libmodeller.so
-	dosym ../../${INPATH}/lib/${EXECTYPE}/libmodeller.so.8 /usr/$(get_libdir)/libmodeller.so.8
-
-	use doc && HTML_DOCS=( doc/. )
-	distutils-r1_python_install_all
-
-	if use examples; then
-		insinto /usr/share/${PN}/
-		doins -r examples
-	fi
-
-	insinto /etc/revdep-rebuild
-	cat >> "${T}"/40-${PN} <<- EOF
-	SEARCH_DIRS_MASK="${EPREFIX}/opt/modeller/lib/"
-	EOF
-	doins "${T}"/40-${PN}
-}
-
-pkg_postinst() {
-	if [[ ! -e "${INPATH}/modlib/modeller/config.py" ]]; then
-		echo install_dir = \"${INPATH}/\"> ${INPATH}/modlib/modeller/config.py
-	fi
-
-	if grep -q license ${INPATH}/modlib/modeller/config.py; then
-		einfo "A license key file is already present in ${IN_PATH}/modlib/modeller/config.py"
-	else
-		ewarn "Obtain a license Key from"
-		ewarn "http://salilab.org/modeller/registration.html"
-		ewarn "And run this before using modeller:"
-		ewarn "emerge --config =${CATEGORY}/${PF}"
-		ewarn "That way you can [re]enter your license key."
-	fi
-}
-
-pkg_postrm() {
-	ewarn "This package leaves a license Key file in ${INPATH}/modlib/modeller/config.py"
-	ewarn "that you need to remove to completely get rid of modeller."
-}
-
-pkg_config() {
-	ewarn "Your license key is NOT checked for validity here."
-	ewarn "  Make sure you type it in correctly."
-	eerror "If you CTRL+C out of this, modeller will not run!"
-	while true
-	do
-		einfo "Please enter your license key:"
-		read license_key1
-		einfo "Please re-enter your license key:"
-		read license_key2
-		if [[ "$license_key1" == "" ]]
-		then
-			echo "You entered a blank license key.  Try again."
-		else
-			if [[ "$license_key1" == "$license_key2" ]]
-			then
-				echo license = '"'$license_key1'"' >> "${INPATH}/modlib/modeller/config.py"
-				einfo "Thank you!"
-				break
-			else
-				eerror "Your license key entries do not match.  Try again."
-			fi
-		fi
-	done
-}
diff --git a/sci-chemistry/modeller/modeller-9.19.ebuild b/sci-chemistry/modeller/modeller-9.19.ebuild
deleted file mode 100644
index 0d29c3843..000000000
--- a/sci-chemistry/modeller/modeller-9.19.ebuild
+++ /dev/null
@@ -1,145 +0,0 @@
-# Copyright 1999-2018 Gentoo Foundation
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=6
-
-PYTHON_COMPAT=( python2_7 )
-
-inherit distutils-r1 eutils multilib versionator
-
-DESCRIPTION="Homology or comparative modeling of protein three-dimensional structures"
-HOMEPAGE="http://salilab.org/modeller/"
-SRC_URI="http://salilab.org/${PN}/${PV}/${P}.tar.gz"
-
-LICENSE="modeller"
-KEYWORDS="~amd64 ~x86 ~amd64-linux ~x86-linux"
-IUSE="doc examples"
-SLOT="0"
-
-RESTRICT="mirror"
-
-DEPEND=">=dev-lang/swig-1.3"
-RDEPEND=""
-
-INPATH="${EPREFIX}"/opt/modeller${ver}
-
-QA_PREBUILT="/opt/*"
-
-pkg_setup() {
-	case ${ARCH} in
-		x86)
-			EXECTYPE="i386-intel8";;
-		amd64)
-			EXECTYPE="x86_64-intel8";;
-		*)
-			die "Your arch "${ARCH}" does not appear supported at this time.";;
-	esac
-}
-
-python_prepare_all(){
-	sed "s:i386-intel8:${EXECTYPE}:g" -i src/swig/setup.py || die
-	distutils-r1_python_prepare_all
-}
-
-python_compile(){
-	cd src/swig || die
-	swig -python -keyword -nodefaultctor -nodefaultdtor -noproxy modeller.i || die
-	distutils-r1_python_compile
-}
-
-python_install() {
-	cd src/swig || die
-	distutils-r1_python_install
-}
-
-python_install_all(){
-	cd "${S}" || die
-	sed \
-		-e "/^EXECUTABLE_TYPE/s:xxx:${EXECTYPE}:g" \
-		-e "/MODINSTALL/s:xxx:\"${INPATH}\":g" \
-		-i bin/modscript || die
-
-	sed -e "s;@TOPDIR\@;\"${INPATH}\";" \
-		-e "s;@EXETYPE\@;${EXECTYPE};" \
-		bin/modpy.sh.in > "${T}/modpy.sh"
-
-	insinto ${INPATH}
-	doins -r modlib
-	python_foreach_impl python_domodule modlib/modeller
-
-	insinto ${INPATH}/bin
-	doins -r bin/{lib,*top}
-
-	exeinto ${INPATH}/bin
-	doexe bin/{modscript,mod${PV}_${EXECTYPE}} "${T}"/modpy.sh
-
-	python_foreach_impl python_doscript bin/modslave.py
-	dosym ${INPATH}/bin/modscript /opt/bin/mod${PV}
-	dosym ${INPATH}/bin/modpy.sh /opt/bin/modpy.sh
-
-	exeinto ${INPATH}/lib/${EXECTYPE}/
-	doexe lib/${EXECTYPE}/lib*
-	dosym libmodeller.so.8 ${INPATH}/lib/${EXECTYPE}/libmodeller.so
-	dosym ../../${INPATH}/lib/${EXECTYPE}/libmodeller.so.8 /usr/$(get_libdir)/libmodeller.so.8
-
-	use doc && HTML_DOCS=( doc/. )
-	distutils-r1_python_install_all
-
-	if use examples; then
-		insinto /usr/share/${PN}/
-		doins -r examples
-	fi
-
-	insinto /etc/revdep-rebuild
-	cat >> "${T}"/40-${PN} <<- EOF
-	SEARCH_DIRS_MASK="${EPREFIX}/opt/modeller/lib/"
-	EOF
-	doins "${T}"/40-${PN}
-}
-
-pkg_postinst() {
-	if [[ ! -e "${INPATH}/modlib/modeller/config.py" ]]; then
-		echo install_dir = \"${INPATH}/\"> ${INPATH}/modlib/modeller/config.py
-	fi
-
-	if grep -q license ${INPATH}/modlib/modeller/config.py; then
-		einfo "A license key file is already present in ${IN_PATH}/modlib/modeller/config.py"
-	else
-		ewarn "Obtain a license Key from"
-		ewarn "http://salilab.org/modeller/registration.html"
-		ewarn "And run this before using modeller:"
-		ewarn "emerge --config =${CATEGORY}/${PF}"
-		ewarn "That way you can [re]enter your license key."
-	fi
-}
-
-pkg_postrm() {
-	ewarn "This package leaves a license Key file in ${INPATH}/modlib/modeller/config.py"
-	ewarn "that you need to remove to completely get rid of modeller."
-}
-
-pkg_config() {
-	ewarn "Your license key is NOT checked for validity here."
-	ewarn "  Make sure you type it in correctly."
-	eerror "If you CTRL+C out of this, modeller will not run!"
-	while true
-	do
-		einfo "Please enter your license key:"
-		read license_key1
-		einfo "Please re-enter your license key:"
-		read license_key2
-		if [[ "$license_key1" == "" ]]
-		then
-			echo "You entered a blank license key.  Try again."
-		else
-			if [[ "$license_key1" == "$license_key2" ]]
-			then
-				echo license = '"'$license_key1'"' >> "${INPATH}/modlib/modeller/config.py"
-				einfo "Thank you!"
-				break
-			else
-				eerror "Your license key entries do not match.  Try again."
-			fi
-		fi
-	done
-}
diff --git a/sci-chemistry/module2/Manifest b/sci-chemistry/module2/Manifest
deleted file mode 100644
index 2bb0b7338..000000000
--- a/sci-chemistry/module2/Manifest
+++ /dev/null
@@ -1 +0,0 @@
-DIST MODULE2.tar.gz 1593965 SHA256 c98a32e2b9af109bf8cfc0670bff1350b97adf3ede4a44e33f6c977fb0348e48 SHA512 bae62229268affd7d9e059f4e7862ebe266d881d98b7a87b42c01591a6304be727bb516e3966666bd105341e131d739cc66f4352ecce69a13cce34fcf0baec39 WHIRLPOOL 77ada1b4e795f39a660a2b8edad98afa18bb31807a13c0005c9d7259e9c4a185c2f10d0bf7d65628217bb7a02d1ff2d97b51770f3b19875615001a5f517c3aee
diff --git a/sci-chemistry/module2/metadata.xml b/sci-chemistry/module2/metadata.xml
deleted file mode 100644
index 713d21566..000000000
--- a/sci-chemistry/module2/metadata.xml
+++ /dev/null
@@ -1,11 +0,0 @@
-<?xml version="1.0" encoding="UTF-8"?>
-<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
-<pkgmetadata>
-	<maintainer type="person">
-		<email>jlec@gentoo.org</email>
-	</maintainer>
-	<maintainer type="project">
-		<email>sci-chemistry@gentoo.org</email>
-		<name>Gentoo Chemistry Project</name>
-	</maintainer>
-</pkgmetadata>
diff --git a/sci-chemistry/module2/module2-0_pre20140717.ebuild b/sci-chemistry/module2/module2-0_pre20140717.ebuild
deleted file mode 100644
index 894de6662..000000000
--- a/sci-chemistry/module2/module2-0_pre20140717.ebuild
+++ /dev/null
@@ -1,50 +0,0 @@
-# Copyright 1999-2014 Gentoo Foundation
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=5
-
-# inherit
-
-DESCRIPTION="Residual dipolar coupling and residual chemical shift analysis software"
-HOMEPAGE="http://www.ibs.fr/science-213/scientific-output/software/module/?lang=en"
-SRC_URI="MODULE2.tar.gz"
-
-SLOT="0"
-LICENSE="all-rights-reserved"
-KEYWORDS=""
-IUSE=""
-
-RDEPEND="
-	x11-libs/motif:2.2[abi_x86_32(-)]
-	x11-libs/libX11[abi_x86_32(-)]
-	x11-libs/libXext[abi_x86_32(-)]
-	x11-libs/libXpm[abi_x86_32(-)]
-	x11-libs/libXt[abi_x86_32(-)]
-"
-DEPEND="${RDEPEND}
-"
-
-RESTRICT="fetch splitdebug"
-
-S="${WORKDIR}"/MODULE2
-
-QA_PREBUILT="opt/bin/.*"
-
-pkg_nofetch() {
-	elog "Please download ${A} from"
-	elog "${HOMEPAGE}"
-	elog "and place it in ${DISTDIR}"
-}
-
-src_install() {
-	use prefix && \
-		patchelf --set-rpath "${EPREFIX}"/usr/lib
-	exeinto /opt/bin
-	doexe module
-	dosym module /opt/bin/${PN}
-
-	dohtml -r MODULE2_manual_fichiers MODULE2_manual.htm
-
-	insinto /usr/share/${PN}
-	doins sample*
-}
diff --git a/sci-chemistry/mtz2hkl/Manifest b/sci-chemistry/mtz2hkl/Manifest
deleted file mode 100644
index 1798d374c..000000000
--- a/sci-chemistry/mtz2hkl/Manifest
+++ /dev/null
@@ -1 +0,0 @@
-DIST mtz2hkl_v0.3.tar.gz 11315 BLAKE2B d5b27a943730e85cd2af20972962ee04c53832068c97aa37487915223b11ccbca8a7543a22cd731ac6d76ae1d43d0da9004262e6a9633a31a88f475d535445a5 SHA512 ee003c7cefc9ba41846abd0826c418370930ded665bab76ba3b8118f301f31af83d0954e817354ff73ac48cf56cc980a150b889cadbaaeadca13d3192449bd3e
diff --git a/sci-chemistry/mtz2hkl/files/0.3-gentoo.patch b/sci-chemistry/mtz2hkl/files/0.3-gentoo.patch
deleted file mode 100644
index 6bb2f4a6b..000000000
--- a/sci-chemistry/mtz2hkl/files/0.3-gentoo.patch
+++ /dev/null
@@ -1,24 +0,0 @@
---- Makefile	2009-07-16 13:40:43.000000000 +0200
-+++ Makefile.new	2009-07-16 22:09:28.000000000 +0200
-@@ -1,9 +1,9 @@
- CXX=g++
- TARGET=mtz2hkl
- GPP4=/usr/local/crystallography/libs/gpp4-1.0.4
--INCL=-I${GPP4}/include/gpp4
--CFLAGS=-O3 -fPIC
--LIBS=-L${GPP4}/lib -lgpp4
-+INCL=-I/usr/include/cpp4
-+CFLAGS+=-fPIC
-+LIBS=-lccp4c
- 
- LDFLAGS=-static
- 
-@@ -16,7 +16,7 @@
- 		utils.o
- 		
- all:	${OBJS}
--		${CXX} ${CFLAG} ${OBJS} ${LIBS} ${LDFLAGS} -o ${TARGET}
-+		${CXX} ${CFLAGS} ${LDFLAGS} -o ${TARGET} ${OBJS} ${LIBS}
- 		
- %.o:	%.cpp %.h defines.h
- 		${CXX} ${CFLAGS} ${INCL} -c $<
diff --git a/sci-chemistry/mtz2hkl/metadata.xml b/sci-chemistry/mtz2hkl/metadata.xml
deleted file mode 100644
index da36ecbfc..000000000
--- a/sci-chemistry/mtz2hkl/metadata.xml
+++ /dev/null
@@ -1,8 +0,0 @@
-<?xml version="1.0" encoding="UTF-8"?>
-<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
-<pkgmetadata>
-	<maintainer type="project">
-		<email>sci-chemistry@gentoo.org</email>
-		<name>Gentoo Chemistry Project</name>
-	</maintainer>
-</pkgmetadata>
diff --git a/sci-chemistry/mtz2hkl/mtz2hkl-0.3.ebuild b/sci-chemistry/mtz2hkl/mtz2hkl-0.3.ebuild
deleted file mode 100644
index 097e9f4a6..000000000
--- a/sci-chemistry/mtz2hkl/mtz2hkl-0.3.ebuild
+++ /dev/null
@@ -1,35 +0,0 @@
-# Copyright 1999-2015 Gentoo Foundation
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=5
-
-inherit eutils toolchain-funcs
-
-DESCRIPTION="Facilitate the transition from refmac5 refinement to shelxh or shelxl refinement"
-HOMEPAGE="http://shelx.uni-ac.gwdg.de/~tg/research/programs/conv/mtz2x/mtz2hkl/"
-SRC_URI="http://shelx.uni-ac.gwdg.de/~tg/research/programs/conv/mtz2x/${PN}/downloads/${PV}/${PN}_v${PV}.tar.gz"
-
-LICENSE="GPL-3"
-SLOT="0"
-KEYWORDS="~amd64 ~x86"
-IUSE=""
-
-RDEPEND="sci-libs/libccp4"
-DEPEND="${RDEPEND}"
-
-S="${WORKDIR}"/${PN}
-
-src_prepare() {
-	epatch "${FILESDIR}"/${PV}-gentoo.patch
-}
-
-src_compile() {
-	emake \
-		CXX=$(tc-getCXX) \
-		CFLAGS="${CFLAGS}" \
-		LDFLAGS="${LDFLAGS}"
-}
-
-src_install() {
-	dobin ${PN}
-}
diff --git a/sci-chemistry/mtz2sca/Manifest b/sci-chemistry/mtz2sca/Manifest
deleted file mode 100644
index 3dcdf1281..000000000
--- a/sci-chemistry/mtz2sca/Manifest
+++ /dev/null
@@ -1 +0,0 @@
-DIST mtz2sca_v0.3.tar.gz 17190 BLAKE2B ee21bbac0bce5d7d87ec06b270f53b46434e5b8d634ecc815f4ff787ef41d82860606780ba537e8c72d90b80f4f0ae6f96d082fee59019d8eee2fb6a25f73a10 SHA512 b74eb3dd03276e0ffa78a92820362306a9f0974bafd178cda93a4c960fb67cedf5b6410e51bdf71d230a86b6d8b9eb35d239eb6c2a5c4596cf049150337d42b2
diff --git a/sci-chemistry/mtz2sca/files/0.3-gentoo.patch b/sci-chemistry/mtz2sca/files/0.3-gentoo.patch
deleted file mode 100644
index bbab8d2f6..000000000
--- a/sci-chemistry/mtz2sca/files/0.3-gentoo.patch
+++ /dev/null
@@ -1,26 +0,0 @@
---- Makefile	2007-11-19 09:20:45.000000000 +0100
-+++ Makefile.new	2009-07-16 22:42:22.000000000 +0200
-@@ -1,11 +1,11 @@
- CC      = gcc
- CXX     = g++
- CFLAGS  = -g
--COPT    = -O2
-+COPT    = 
- DEFS    = 
- CCP4    = /usr/local/crystallography/libs/gpp4-1.0.4
--LDFLAGS = -static -L${CCP4}/lib -lgpp4
--INCL    = -I${CCP4}/include/gpp4
-+LIBS = -lccp4c
-+INCL    = -I/usr/include/cpp4
- TARGET  = mtz2sca
- OBJS    = label.o \
- 	  mtzin.o \
-@@ -17,7 +17,7 @@
- 	  mtz2sca.o
- 	  
- all:	$(OBJS) defines.h
--	$(CXX) $(CFLAGS) $(DEFS) $(INCL) $(OBJS)  -o $(TARGET) $(LDFLAGS)
-+	$(CXX) $(CFLAGS) $(LDFLAGS) -o $(TARGET) $(DEFS) $(INCL) $(OBJS) $(LIBS)
- 
- %.o:	%.cpp defines.h
- 	$(CXX) -c $(INCL) $(DEFS) $(CFLAGS) $(COPT) $<
diff --git a/sci-chemistry/mtz2sca/metadata.xml b/sci-chemistry/mtz2sca/metadata.xml
deleted file mode 100644
index da36ecbfc..000000000
--- a/sci-chemistry/mtz2sca/metadata.xml
+++ /dev/null
@@ -1,8 +0,0 @@
-<?xml version="1.0" encoding="UTF-8"?>
-<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
-<pkgmetadata>
-	<maintainer type="project">
-		<email>sci-chemistry@gentoo.org</email>
-		<name>Gentoo Chemistry Project</name>
-	</maintainer>
-</pkgmetadata>
diff --git a/sci-chemistry/mtz2sca/mtz2sca-0.3.ebuild b/sci-chemistry/mtz2sca/mtz2sca-0.3.ebuild
deleted file mode 100644
index 4ecbc0b82..000000000
--- a/sci-chemistry/mtz2sca/mtz2sca-0.3.ebuild
+++ /dev/null
@@ -1,35 +0,0 @@
-# Copyright 1999-2015 Gentoo Foundation
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=5
-
-inherit eutils toolchain-funcs
-
-DESCRIPTION="Converts CCP4 mtz-files containing anomalous data to Scalepack format"
-HOMEPAGE="http://shelx.uni-ac.gwdg.de/~tg/research/programs/conv/mtz2x/mtz2sca/"
-SRC_URI="http://shelx.uni-ac.gwdg.de/~tg/research/programs/conv/mtz2x/${PN}/binaries/${PV}/${PN}_v${PV}.tar.gz"
-
-LICENSE="GPL-3"
-SLOT="0"
-KEYWORDS="~amd64 ~x86"
-IUSE=""
-
-RDEPEND="sci-libs/libccp4"
-DEPEND="${RDEPEND}"
-
-S="${WORKDIR}"/
-
-src_prepare() {
-	epatch "${FILESDIR}"/${PV}-gentoo.patch
-}
-
-src_compile() {
-	emake \
-		CXX=$(tc-getCXX) \
-		CFLAGS="${CFLAGS}" \
-		LDFLAGS="${LDFLAGS}"
-}
-
-src_install() {
-	dobin ${PN}
-}
diff --git a/sci-chemistry/nMOLDYN/Manifest b/sci-chemistry/nMOLDYN/Manifest
deleted file mode 100644
index 64434849a..000000000
--- a/sci-chemistry/nMOLDYN/Manifest
+++ /dev/null
@@ -1 +0,0 @@
-DIST nMOLDYN-3.0.10.zip 34692698 BLAKE2B 9f364ff6a2909469754384b927efd8cf40e660558db7bf45da4a53879defd3a208194e4c1499c0f31a3358318d89ad81d83b25b52b493a585c5fd52d043933f2 SHA512 49c6bd04d89143e73dddeda4d3ad0061747e018ad63dfa42e17c2388b6107c7b88f59d7d0d2e59a5c1faf4fe3a188e94d41f9f5ae171194db1ff56648742982a
diff --git a/sci-chemistry/nMOLDYN/metadata.xml b/sci-chemistry/nMOLDYN/metadata.xml
deleted file mode 100644
index 7daa2ce7e..000000000
--- a/sci-chemistry/nMOLDYN/metadata.xml
+++ /dev/null
@@ -1,12 +0,0 @@
-<?xml version="1.0" encoding="UTF-8"?>
-<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
-<pkgmetadata>
-	<maintainer type="person">
-		<email>alexxy@gentoo.org</email>
-		<name>Alexey Shvetsov</name>
-	</maintainer>
-	<maintainer type="project">
-		<email>sci-chemistry@gentoo.org</email>
-		<name>Gentoo Chemistry Project</name>
-	</maintainer>
-</pkgmetadata>
diff --git a/sci-chemistry/nMOLDYN/nMOLDYN-3.0.10.ebuild b/sci-chemistry/nMOLDYN/nMOLDYN-3.0.10.ebuild
deleted file mode 100644
index eb69809da..000000000
--- a/sci-chemistry/nMOLDYN/nMOLDYN-3.0.10.ebuild
+++ /dev/null
@@ -1,23 +0,0 @@
-# Copyright 1999-2014 Gentoo Foundation
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=5
-
-PYTHON_COMPAT=( python2_7 )
-
-inherit distutils-r1
-
-DESCRIPTION="nMOLDYN is an interactive analysis program for Molecular Dynamics simulations"
-HOMEPAGE="http://dirac.cnrs-orleans.fr/plone/software/nmoldyn/"
-SRC_URI="https://forge.epn-campus.eu/attachments/download/1161/${P}.zip"
-
-LICENSE="CeCILL-2"
-SLOT="0"
-KEYWORDS="~amd64 ~x86"
-IUSE=""
-
-DEPEND="
-	dev-python/numpy
-	sci-libs/mmtk
-"
-RDEPEND="${DEPEND}"
diff --git a/sci-chemistry/nmrpipe/Manifest b/sci-chemistry/nmrpipe/Manifest
index 07a18544f..c54650082 100644
--- a/sci-chemistry/nmrpipe/Manifest
+++ b/sci-chemistry/nmrpipe/Manifest
@@ -1,6 +1,6 @@
-DIST NMRPipeX-8.7.2015.320.15.26.tZ 86276925 BLAKE2B b0e663e987a927dd0760cffa5f2e3f11dfd70cefb002cfb1d58b38f5ce4e4009643f7255c4445139a6155ea8cbf241b91159e11a065744abda849d2ea3da3005 SHA512 06823ca19580e7b9f035cd4e428353b5de099f2374115a78b17a37fd6500866f5c71ab6b0ca258acf1033fafdfda15b6d7f08736091e6d14361d501eed09a0f3
-DIST binval-8.7.2015.320.15.26.com 3872 BLAKE2B b9d580e6570fbd2bfa1555ef4873f3ae7378bb8a034441beb5aad03d6d917a048039b1611f823e21cba7e63ca5d6ee71407699b17236c72e4af21625b3a0be21 SHA512 2b3b4a8b839a83d0bd1e1b8439f315c323370a9ae0ccde48e229636f372f9383a5c1281c80ae9b81ee75af82fe0056ec84bdad3095b526b8714e53933e3f5228
-DIST dyn-8.7.2015.320.15.26.tZ 143850933 BLAKE2B 703fb181161d8ad2ccc8968e7fd1c1b372522b9cece3ce574c9fb64d7c3b597c576c34ece3ff31b49c5e5e13cd9f902c94f2e517d004e33a1e68b24f83c47187 SHA512 315392cce53021f2417ac15ca508f9036f7aeb7ebacc647e91888f7bed3350af86586bf17c5d15f7b4a31c7247c52b170c608d83e70c519d84d693067f5dc51e
-DIST install-8.7.2015.320.15.26.com 46104 BLAKE2B 7498513fab9d109b3fd1a8d7fd35779d3532e852c5e2807c69e8a86b8826b064ebffbbefc8e04ae4649bcb326c6b1f62edea902e93d85a1a8e17f69b3a4c8c5d SHA512 2c771eefed667202987accb839d816732de456b52faa4ed0107dbc083eb9124b1153c0768e03d4a03e0ce76fdb1c8c5e52ecfccb036354fabef98227d152da85
-DIST plugin.smile-8.7.2015.320.15.26.tZ 5784757 BLAKE2B 723fb7d78112294fc62814b15103125f135fbd45fc42c9829878b27ac2e9313c919df81ce6ff1822b1195eda20a1f9ea96c82edfdb78ec1c208b16d8c6b12e7e SHA512 1a13abfd977050cc51398e976c484e0fb6d53d44c0015860df318962855cc07e819b99ee2988ac314e7cd84c281dde54fd0eec0583c17a77e4626f79aa85c883
-DIST talos-8.7.2015.320.15.26.tZ 192502073 BLAKE2B 56618c2117980a65c79ad64f346a9d8096c473915ba2cb1c348c1790a737356827a26f59ed26aa349f1e3be5bdaffd83e05786a27fe15cc1783e29db6132fa7a SHA512 c77ebc40f52cfb897edc6704288194480559d751caa7b377c9dfa1912830657413b355fa53a2c370882de3f14d669268596c0e0b6287b0f8a76e3523befcff8f
+DIST NMRPipeX-8.7.20230206.tZ 100114853 BLAKE2B 6e0dda8ef3946ea2397f2a394529a2c20b09f4f6dc7f56205b17c35d0a0d09519f92899f0628070cf5f24aec41d71b54fc606f7d6a01f0ccb79f69fe59234b56 SHA512 0ec09385f0181af58a5ad1ba5335e32e1544d73b1322b2764b738474cbb96128158b6739684e0e008411c27bed831d58fd44953494c790bf20796cf82750792e
+DIST binval-8.7.20230206.com 4004 BLAKE2B cf8d84c533431b6eeaa031285071abdd241a5774c4731a650084e312c2e3094c2a26e54432e8e9abb42280f2968dee276918659ba9e036587e799618d5dfb829 SHA512 ef47c209848a479e0c6f7f9a472279e6260cb56311e9571da22b474e520515abc64e75cc5dd7817bb629497e0a83c53a6f847904e08004e0b2d09ba035f688a9
+DIST dyn-8.7.20230206.tZ 301148865 BLAKE2B 11cdebd68efa2ed758309f27ba8fd57b6e659d9cdf98d3708c85f65b181eca42dc6fae832db13e9684e4f710d8f0ec7d60d7cc4d5dc698f730dcce317df0d56a SHA512 e5dc12af048f8f87c13c60c020df5ae47afaaa869852134563124bcc2f344176f1da452ce92169ed3cf2c7c4e505d6498bd60fb5ba1b3de489a9791e25f0354c
+DIST install-8.7.20230206.com 50938 BLAKE2B ad8039df53d5069ed5b74be3d085fb0b11fda0a3b585d7992ed3634f383bb8b21c31c808befb9e917882392a0333da898a97d423c61cad49ac351f12fd8c4df4 SHA512 0b1aea3ab316dd29108cce60a4d1aa84835ab088389d6e46d8ee3c7bffb75d38506bac35f5e0c202dc9bf040e2e8418697126a3aa8dc6f256e3c75614b52a30c
+DIST plugin.smile-8.7.20230206.tZ 73190777 BLAKE2B 94471d441a82a35feb9ce7c7fca52e343ea5ad4d8688dce09e23c9f6a76288de3a080cb587e4b44800d0c1401aebc0586753a83b4b6370030221519b2f34ba13 SHA512 511c39bbf3d9bd608cfb53a8720f26a1e201d3065e0109f8a11ee513ff0f160f3866099f88d359ec301cdfde05ef84b43a694846494bd4231bf4b401dd33e6b3
+DIST talos-8.7.20230206.tZ 209640635 BLAKE2B bb5fc9a925dbc5e553711a63177c69e8c01d4cdfacf4ec04960fe21d4996aeee35287686d89452dfc51f94712c1c42e9ab316073072f92f9576418ec282f9988 SHA512 3225f40dd4437e18d3dc8d3c1874df10b7257ee6f556cef8d2e77e90d64308799499aa70020b6c2b7152121c1124fac744e553b770097b544a9b888505250711
diff --git a/sci-chemistry/nmrpipe/files/nmrpipe-8.7.2015.320.15.26-lib.patch b/sci-chemistry/nmrpipe/files/nmrpipe-8.7.2015.320.15.26-lib.patch
deleted file mode 100644
index 91abd611d..000000000
--- a/sci-chemistry/nmrpipe/files/nmrpipe-8.7.2015.320.15.26-lib.patch
+++ /dev/null
@@ -1,36 +0,0 @@
---- nmrbin.linux9/nmrDraw	2009-10-07 23:33:21.000000000 +0200
-+++ nmrbin.linux9/nmrDraw.new	2009-10-24 16:29:03.000000000 +0200
-@@ -2,6 +2,17 @@
- 
- setenv EXTRASMENU $NMRTXT/dot.text_extras_menu
- 
-+setenv NMRBIN ${NMRBASE}/bin/
-+setenv NMRLIB ${NMRBIN}/lib
-+setenv AUXLIB ${NMRBIN}/openwin/lib
-+
-+if (!($?LD_LIBRARY_PATH)) then
-+   setenv LD_LIBRARY_PATH ${NMRLIB}:${AUXLIB}
-+else
-+   setenv LD_LIBRARY_PATH ${NMRLIB}:${LD_LIBRARY_PATH}:${AUXLIB}
-+endif
-+
-+
- if ($DISPLAY == "") then
-    echo Warning: DISPLAY environment variable is not set.
-    exit 1
---- nmrbin.linux9/xNotify	2009-10-07 23:33:21.000000000 +0200
-+++ nmrbin.linux9/xNotify.new	2009-10-24 16:29:42.000000000 +0200
-@@ -1,2 +1,13 @@
- #!/bin/csh -f
-+
-+setenv NMRBIN ${NMRBASE}/bin
-+setenv NMRLIB ${NMRBIN}/lib
-+setenv AUXLIB ${NMRBIN}/openwin/lib
-+
-+if (!($?LD_LIBRARY_PATH)) then
-+   setenv LD_LIBRARY_PATH ${NMRLIB}:${AUXLIB}
-+else
-+   setenv LD_LIBRARY_PATH ${NMRLIB}:${LD_LIBRARY_PATH}:${AUXLIB}
-+endif
-+
- xnotify.exe -Wfsdb $*
diff --git a/sci-chemistry/nmrpipe/nmrpipe-8.7.2015.320.15.26.ebuild b/sci-chemistry/nmrpipe/nmrpipe-8.7.2015.320.15.26.ebuild
deleted file mode 100644
index d0bc331c2..000000000
--- a/sci-chemistry/nmrpipe/nmrpipe-8.7.2015.320.15.26.ebuild
+++ /dev/null
@@ -1,190 +0,0 @@
-# Copyright 1999-2017 Gentoo Foundation
-# Distributed under the terms of the GNU General Public License v2
-
-# Versioning is output of nmrPipe -help
-
-EAPI=6
-
-inherit eutils virtualx
-
-DESCRIPTION="Spectral visualisation, analysis and Fourier processing"
-HOMEPAGE="http://spin.niddk.nih.gov/bax/software/NMRPipe/"
-#SRC_URI="
-#	NMRPipeX.tZ
-#	talos.tZ
-#	dyn.tZ
-#	binval.com
-#	install.com"
-SRC_URI="
-	http://spin.niddk.nih.gov/NMRPipe/install/download/install.com -> install-${PV}.com
-	http://spin.niddk.nih.gov/NMRPipe/install/download/binval.com -> binval-${PV}.com
-	http://spin.niddk.nih.gov/NMRPipe/install/download/NMRPipeX.tZ -> NMRPipeX-${PV}.tZ
-	http://spin.niddk.nih.gov/NMRPipe/install/download/plugin.smile.tZ -> plugin.smile-${PV}.tZ
-	http://spin.niddk.nih.gov/NMRPipe/install/download/talos.tZ -> talos-${PV}.tZ
-	http://spin.niddk.nih.gov/NMRPipe/install/download/dyn.tZ -> dyn-${PV}.tZ
-	"
-
-SLOT="0"
-LICENSE="nmrpipe"
-# Right now, precompiled executables are only available for Linux on the
-# x86 architecture. The maintainer chose to keep the sources closed, but
-# says he will gladly provide precompiled executables for other platforms
-# if there are such requests.
-KEYWORDS=""
-IUSE=""
-
-RESTRICT="strip"
-
-DEPEND="app-shells/tcsh"
-RDEPEND="${DEPEND}
-	app-editors/nedit
-	dev-lang/tk
-	dev-tcltk/blt
-	media-fonts/font-sun-misc
-	!sci-chemistry/sparta+
-	!sci-chemistry/talos+
-	sys-libs/ncurses:5/5
-	x11-apps/xset
-	|| ( x11-libs/xview x11-libs/xview-bin )
-	!prefix? ( >=x11-libs/libX11-1.6.2[abi_x86_32(-)] )
-	prefix? ( dev-util/patchelf )"
-
-S="${WORKDIR}/NMR"
-
-NMRBASE="/opt/${PN}"
-ENMRBASE="${EPREFIX}/${NMRBASE}"
-
-QA_PREBUILT="opt/.*"
-
-src_unpack() {
-	# The installation script will unpack the package. We just provide symlinks
-	# to the archive files, ...
-	for i in NMRPipeX-${PV}.tZ plugin.smile-${PV}.tZ talos-${PV}.tZ dyn-${PV}.tZ; do
-		ln -sf "${DISTDIR}"/${i} ${i/-${PV}/} || die
-	done
-	mkdir "${S}" && cd "${S}" || die
-	# ... copy the installation scripts ...
-	cp -L "${DISTDIR}"/install-${PV}.com install.com || die
-	cp -L "${DISTDIR}"/binval-${PV}.com binval.com || die
-	# ... and make the installation scripts executable.
-	chmod +x *.com || die
-	VIRTUALX_COMMAND="csh"
-	virtualmake \
-		./install.com \
-		+type $(usex x86 linux9 linux212_64) \
-		+src "${WORKDIR}" \
-		+dest "${S}" \
-		+nopost +nocshrc
-}
-
-src_prepare() {
-	local bin i
-	epatch "${FILESDIR}"/${P}-lib.patch
-
-	mv nmrbin.$(usex x86 linux9 linux212_64)/nmr{W,w}ish || die
-
-	ebegin "Cleaning installation"
-
-	# Remove some of the bundled applications and libraries; they are provided by Gentoo instead.
-	rm -rf nmrbin.linux*/{lib/*.timestamp,*timestamp,xv,gnuplot*,rasmol*,nc,nedit} \
-		nmrbin.{linux,mac} nmruser format \
-		$(usex x86 nmrbin.linux212_64 nmrbin.linux9) \
-		|| die "Failed to remove unnecessary libraries."
-	# As long as xview is not fixed for amd64 we do this
-	rm nmrbin.linux*/lib/{libxview.so*,libolgx.so*} || die
-	# Remove the initialisation script generated during the installation.
-	# It contains incorrect hardcoded paths; only the "nmrInit.com" script
-	# should be used.
-	rm -f com/nmrInit.linux*.com || die "Failed to remove broken init script."
-	# Remove installation log files.
-	rm -f README_NMRPIPE_USERS *.log install.com binval.com || die "Failed to remove installation log."
-	# Remove unused binaries
-	rm -f {talos*,spartaplus,promega}/bin/*{linux,mac,sgi6x,winxp} pdb/misc/addSeg || die
-
-	# Some scripts are on the wrong place
-	cp -f nmrtxt/*.com com/
-	rm -f {acme,com}/{nmrproc,fid,install}.com || die
-	eend
-
-	ebegin "Fixing paths in scripts"
-
-	# Set the correct path to NMRPipe in the auxiliary scripts.
-	for i in $(find com/ dynamo/surface/misc/ nmrtxt/ talos/misc talosplus/com -type f); do
-		sed -e "s%/u/delaglio%${ENMRBASE}%" -i ${i} || die \
-			"Failed patching scripts."
-	done
-	sed -i "s:${WORKDIR}:${ENMRBASE}:g" com/font.com || die
-
-	sed \
-		-e "s:!/bin:!${EPREFIX}/bin:g" \
-		-e "s:!/usr/bin:!${EPREFIX}/usr/bin:g" \
-		-e "s:!/usr/local/bin:!${EPREFIX}/usr/bin:g" \
-		-e "s: /bin: ${EPREFIX}/bin:g" \
-		-e "s: /usr/bin: ${EPREFIX}/usr/bin:g" \
-		-e "s: /usr/local/bin: ${EPREFIX}/usr/bin:g" \
-		-i $(find "${S}" \( -name "*.tcl" -o -name "*.com" -o -name "*.ksh" \)) \
-			{com/,nmrtxt/*.com,nmrtxt/nt/*.com,dynamo/tcl/,talos*/com/,dynamo/tcl/}* \
-			nmrbin.linux*/{nmrDraw,xNotify} || die
-	eend
-
-	if use prefix; then
-		sed \
-			-e "s: sh : \"${EPREFIX}/bin/sh\" :g" \
-			-e "s: csh : \"${EPREFIX}/bin/csh\" :g" \
-			-e "s: bash : \"${EPREFIX}/bin/bash\" :g" \
-			-e "s:appTerm -e:appTerm -e \"${EPREFIX}/bin/csh\":g" \
-			-i com/* || die
-
-		ebegin "Setting RPATH in binaries"
-		for bin in $(find nmrbin.linux*/ -type f -maxdepth 1); do
-			patchelf --set-rpath "${EPREFIX}/usr/lib/" ${bin}
-		done
-		eend $?
-	fi
-}
-
-src_install() {
-	cat >> "${T}"/nmrWish <<- EOF
-	#!${EPREFIX}/bin/csh -f
-	setenv NMRBIN \${NMRBASE}/bin/
-	setenv NMRLIB \${NMRBIN}/lib
-	setenv AUXLIB \${NMRBIN}/openwin/lib
-	setenv TCLPATH \${NMRBASE}/com
-	setenv TCL_LIBRARY \${NMRBASE}/nmrtcl/tcl8.4
-	setenv TK_LIBRARY \${NMRBASE}/nmrtcl/tk8.4
-	setenv BLT_LIBRARY \${NMRBASE}/nmrtcl/blt2.4
-	setenv NMRPIPE_TCL_LIB \${NMRBASE}/nmrtcl/tcl8.4
-	setenv NMRPIPE_TK_LIB \${NMRBASE}/nmrtcl/tk8.4
-	setenv NMRPIPE_BLT_LIB \${NMRBASE}/nmrtcl/blt2.4
-
-	if (!(\$?LD_LIBRARY_PATH)) then
-		setenv LD_LIBRARY_PATH \${NMRLIB}:\${AUXLIB}
-	else
-		setenv LD_LIBRARY_PATH \${NMRLIB}:\${LD_LIBRARY_PATH}:\${AUXLIB}
-	endif
-
-	nmrwish \$*
-	EOF
-
-	sed \
-		-e "s:/opt/nmrpipe:${EPREFIX}/opt/nmrpipe:g" \
-		-e "s:@BINTYPE@:$(usex x86 linux9 linux212_64):g" \
-		"${FILESDIR}"/env-${PN} \
-		> "${T}"/env-${PN} || die
-	newenvd "${T}"/env-${PN} 40${PN}
-
-	insinto ${NMRBASE}
-	doins -r *
-
-	dosym nmrbin.linux* ${NMRBASE}/bin
-
-	ebegin "Fixing permissions"
-	chmod 775 "${ED}"/${NMRBASE}/{talos*/bin/,sparta*/bin/,nmrbin.linux*/,com/,dynamo/tcl/,nmrtxt/*.com,talos*/com/,promega/bin/}* || die
-	eend
-
-	exeinto ${NMRBASE}/nmrbin.$(usex x86 linux9 linux212_64)
-	doexe "${T}"/nmrWish
-
-	insinto ${NMRBASE}/nmrtxt
-	doins "${FILESDIR}"/extract.M
-}
diff --git a/sci-chemistry/nmrpipe/nmrpipe-8.7.20230206.ebuild b/sci-chemistry/nmrpipe/nmrpipe-8.7.20230206.ebuild
new file mode 100644
index 000000000..650c35305
--- /dev/null
+++ b/sci-chemistry/nmrpipe/nmrpipe-8.7.20230206.ebuild
@@ -0,0 +1,187 @@
+# Copyright 1999-2021 Gentoo Authors
+# Distributed under the terms of the GNU General Public License v2
+
+# Versioning is output of nmrPipe -help
+
+EAPI=8
+
+inherit virtualx
+
+DESCRIPTION="Spectral visualisation, analysis and Fourier processing"
+HOMEPAGE="https://www.ibbr.umd.edu/nmrpipe"
+#SRC_URI="
+#	NMRPipeX.tZ
+#	talos.tZ
+#	dyn.tZ
+#	binval.com
+#	install.com"
+SRC_URI="
+	https://www.ibbr.umd.edu/nmrpipe/install.com -> install-${PV}.com
+	https://www.ibbr.umd.edu/nmrpipe/binval.com -> binval-${PV}.com
+	https://www.ibbr.umd.edu/nmrpipe/NMRPipeX.tZ -> NMRPipeX-${PV}.tZ
+	https://www.ibbr.umd.edu/nmrpipe/plugin.smile.tZ -> plugin.smile-${PV}.tZ
+	https://www.ibbr.umd.edu/nmrpipe/talos.tZ -> talos-${PV}.tZ
+	https://www.ibbr.umd.edu/nmrpipe/dyn.tZ -> dyn-${PV}.tZ
+	"
+
+SLOT="0"
+LICENSE="nmrpipe"
+# Right now, precompiled executables are only available for Linux on the
+# x86 architecture. The maintainer chose to keep the sources closed, but
+# says he will gladly provide precompiled executables for other platforms
+# if there are such requests.
+KEYWORDS="~amd64 ~x86"
+
+RESTRICT="strip bindist mirror !test? ( test )"
+
+DEPEND="app-shells/tcsh"
+RDEPEND="${DEPEND}
+	app-editors/nedit
+	dev-lang/tk
+	dev-tcltk/blt
+	media-fonts/font-sun-misc
+	sys-libs/ncurses-compat:5/5
+	x11-apps/xset
+	x11-libs/xview-bin
+	!prefix? ( >=x11-libs/libX11-1.6.2 )
+	prefix? ( dev-util/patchelf )"
+
+S="${WORKDIR}/NMR"
+
+NMRBASE="/opt/${PN}"
+ENMRBASE="${EPREFIX}/${NMRBASE}"
+
+QA_PREBUILT="opt/.*"
+
+src_unpack() {
+	# The installation script will unpack the package. We just provide symlinks
+	# to the archive files, ...
+	for i in NMRPipeX-${PV}.tZ plugin.smile-${PV}.tZ talos-${PV}.tZ dyn-${PV}.tZ; do
+		ln -sf "${DISTDIR}"/${i} ${i/-${PV}/} || die
+	done
+	mkdir "${S}" && cd "${S}" || die
+	# ... copy the installation scripts ...
+	cp -L "${DISTDIR}"/install-${PV}.com install.com || die
+	cp -L "${DISTDIR}"/binval-${PV}.com binval.com || die
+	# ... and make the installation scripts executable.
+	chmod +x *.com || die
+	VIRTUALX_COMMAND="csh"
+	virtx \
+		./install.com \
+		+type $(usex x86 linux9 linux212_64) \
+		+src "${WORKDIR}" \
+		+dest "${S}" \
+		+nopost +nocshrc
+}
+
+src_prepare() {
+	default
+	local bin i
+
+	mv nmrbin.$(usex x86 linux9 linux212_64)/nmr{W,w}ish || die
+
+	ebegin "Cleaning installation"
+
+	# Remove some of the bundled applications and libraries; they are provided by Gentoo instead.
+	rm -rf nmrbin.linux*/{lib/*.timestamp,*timestamp,xv,gnuplot*,rasmol*,nc,nedit} \
+		nmrbin.{linux,mac} nmruser format \
+		$(usex x86 nmrbin.linux212_64 nmrbin.linux9) \
+		|| die "Failed to remove unnecessary libraries."
+	# As long as xview is not fixed for amd64 we do this
+	rm nmrbin.linux*/lib/{libxview.so*,libolgx.so*} || die
+	# Remove the initialisation script generated during the installation.
+	# It contains incorrect hardcoded paths; only the "nmrInit.com" script
+	# should be used.
+	rm -f com/nmrInit.linux*.com || die "Failed to remove broken init script."
+	# Remove installation log files.
+	rm -f README_NMRPIPE_USERS *.log install.com binval.com || die "Failed to remove installation log."
+	# Remove unused binaries
+	rm -f {talos*,spartaplus,promega}/bin/*{linux,mac,sgi6x,winxp} pdb/misc/addSeg || die
+
+	# Some scripts are on the wrong place
+	cp -f nmrtxt/*.com com/
+	rm -f {acme,com}/{nmrproc,fid,install}.com || die
+	eend
+
+	ebegin "Fixing paths in scripts"
+
+	# Set the correct path to NMRPipe in the auxiliary scripts.
+	for i in $(find com/ dynamo/surface/misc/ nmrtxt/ talos/misc talosplus/com -type f); do
+		sed -e "s%/u/delaglio%${ENMRBASE}%" -i ${i} || die \
+			"Failed patching scripts."
+	done
+	sed -i "s:${WORKDIR}:${ENMRBASE}:g" com/font.com || die
+
+	sed \
+		-e "s:!/bin:!${EPREFIX}/bin:g" \
+		-e "s:!/usr/bin:!${EPREFIX}/usr/bin:g" \
+		-e "s:!/usr/local/bin:!${EPREFIX}/usr/bin:g" \
+		-e "s: /bin: ${EPREFIX}/bin:g" \
+		-e "s: /usr/bin: ${EPREFIX}/usr/bin:g" \
+		-e "s: /usr/local/bin: ${EPREFIX}/usr/bin:g" \
+		-i $(find "${S}" \( -name "*.tcl" -o -name "*.com" -o -name "*.ksh" \)) \
+			{com/,nmrtxt/*.com,nmrtxt/nt/*.com,dynamo/tcl/,talos*/com/,dynamo/tcl/}* \
+			nmrbin.linux*/{nmrDraw,xNotify} || die
+	eend
+
+	if use prefix; then
+		sed \
+			-e "s: sh : \"${EPREFIX}/bin/sh\" :g" \
+			-e "s: csh : \"${EPREFIX}/bin/csh\" :g" \
+			-e "s: bash : \"${EPREFIX}/bin/bash\" :g" \
+			-e "s:appTerm -e:appTerm -e \"${EPREFIX}/bin/csh\":g" \
+			-i com/* || die
+
+		ebegin "Setting RPATH in binaries"
+		for bin in $(find nmrbin.linux*/ -type f -maxdepth 1); do
+			patchelf --set-rpath "${EPREFIX}/usr/lib/" ${bin}
+		done
+		eend $?
+	fi
+}
+
+src_install() {
+	cat >> "${T}"/nmrWish <<- EOF
+	#!${EPREFIX}/bin/csh -f
+	setenv NMRBIN \${NMRBASE}/bin/
+	setenv NMRLIB \${NMRBIN}/lib
+	setenv AUXLIB \${NMRBIN}/openwin/lib
+	setenv TCLPATH \${NMRBASE}/com
+	setenv TCL_LIBRARY \${NMRBASE}/nmrtcl/tcl8.4
+	setenv TK_LIBRARY \${NMRBASE}/nmrtcl/tk8.4
+	setenv BLT_LIBRARY \${NMRBASE}/nmrtcl/blt2.4
+	setenv NMRPIPE_TCL_LIB \${NMRBASE}/nmrtcl/tcl8.4
+	setenv NMRPIPE_TK_LIB \${NMRBASE}/nmrtcl/tk8.4
+	setenv NMRPIPE_BLT_LIB \${NMRBASE}/nmrtcl/blt2.4
+
+	if (!(\$?LD_LIBRARY_PATH)) then
+		setenv LD_LIBRARY_PATH \${NMRLIB}:\${AUXLIB}
+	else
+		setenv LD_LIBRARY_PATH \${NMRLIB}:\${LD_LIBRARY_PATH}:\${AUXLIB}
+	endif
+
+	nmrwish \$*
+	EOF
+
+	sed \
+		-e "s:/opt/nmrpipe:${EPREFIX}/opt/nmrpipe:g" \
+		-e "s:@BINTYPE@:$(usex x86 linux9 linux212_64):g" \
+		"${FILESDIR}"/env-${PN} \
+		> "${T}"/env-${PN} || die
+	newenvd "${T}"/env-${PN} 40${PN}
+
+	insinto ${NMRBASE}
+	doins -r *
+
+	dosym nmrbin.linux* ${NMRBASE}/bin
+
+	ebegin "Fixing permissions"
+	chmod 775 "${ED}"/${NMRBASE}/{talos*/bin/,sparta*/bin/,nmrbin.linux*/,com/,dynamo/tcl/,nmrtxt/*.com,talos*/com/,promega/bin/}* || die
+	eend
+
+	exeinto ${NMRBASE}/nmrbin.$(usex x86 linux9 linux212_64)
+	doexe "${T}"/nmrWish
+
+	insinto ${NMRBASE}/nmrtxt
+	doins "${FILESDIR}"/extract.M
+}
diff --git a/sci-chemistry/nmrview/Manifest b/sci-chemistry/nmrview/Manifest
deleted file mode 100644
index c5cae1ddf..000000000
--- a/sci-chemistry/nmrview/Manifest
+++ /dev/null
@@ -1,2 +0,0 @@
-DIST nmrview5.2.2.lib.tar.gz 4097039 SHA256 96965ab68566b4d4b3873d53e0cf88f0bb5757d9d30dcabbbcb7e062008aac4e SHA512 6d5675a329371a63f16a0119cb71fcc8377a4a827c3d9e5eb3fc1dcef671ad28adc95ac19b99ffcc8431af5057715beda90c7d2853b65fe6c5aa40a272db6b16 WHIRLPOOL 8759f05384187c4146e7c7591fac72729c3ec808bed451c5fd53400e557b073250856e65ddb04fdf65f960af0d0a461afd9a8afcb542c28be9e78dc12a6e5cd2
-DIST nmrview5_2_2_01_linux.gz 963243 SHA256 ac60d882c6c1c9179f612e37e4257dbab819b5b4fbc215189441124815525b55 SHA512 99745586cde0927cb0942d3c5c2f4b9ef9d52f0c650325971526b9fa4d14bdd5fad89561805526f62e667d6ad9bc18e0929eb0a5d75a17e040bd3142d88c37cf WHIRLPOOL 1851ab48029443e294a4cb2b961c4b9bde1ef19e15e70208a163b374da3964e1573184856d9010c4181a7649d471333d71370db6326cba5429c1cee4e1c8f330
diff --git a/sci-chemistry/nmrview/files/README.Gentoo b/sci-chemistry/nmrview/files/README.Gentoo
deleted file mode 100644
index fbb0fdf2f..000000000
--- a/sci-chemistry/nmrview/files/README.Gentoo
+++ /dev/null
@@ -1,17 +0,0 @@
-Using NMRView on Gentoo
-
-NMRView may be launched via the "nmrview "wrapper script installed in
-"/usr/bin". The script will pass on all positional parameters to the NMRView
-binary, so you may specify a start up script or a database to open on the
-command line.
-
-If you want a convenient way to set up multiple configurations, you can use
-shell aliases to redefine the "nmrview" command or to add new commands starting
-nmrview with different startup scripts, databases, etc. The following example
-alias declarations (for bash) could be put in "~/.bashrc" to redefine the
-"nmrview" command to launch NMRView with a default startup file, and to add a 
-new command to launch the program with an alternative startup file and
-application name.
-
-alias nmrview="nmrview -- -s ${HOME}/.nmrview/startup"
-alias nmrview-dyn="nmrview -name nmrview-dyn -- -s ${HOME}/.nmrview/startup-dyn"
diff --git a/sci-chemistry/nmrview/files/nmrview.sh b/sci-chemistry/nmrview/files/nmrview.sh
deleted file mode 100644
index d879865e8..000000000
--- a/sci-chemistry/nmrview/files/nmrview.sh
+++ /dev/null
@@ -1,6 +0,0 @@
-#!/bin/bash
-
-export NMRVIEW5HOME="/opt/nmrview"
-export TK_LIBRARY="/opt/nmrview/tk8.4"
-export TCL_LIBRARY="/opt/nmrview/tcl8.4"
-/opt/nmrview/nmrview5_2_2_01_linux
diff --git a/sci-chemistry/nmrview/files/nmrview.sh-r1 b/sci-chemistry/nmrview/files/nmrview.sh-r1
deleted file mode 100644
index 9e122d0c5..000000000
--- a/sci-chemistry/nmrview/files/nmrview.sh-r1
+++ /dev/null
@@ -1,6 +0,0 @@
-#!/bin/bash
-
-export NMRVIEW5HOME="/opt/nmrview"
-export TK_LIBRARY="/opt/nmrview/tk8.4"
-export TCL_LIBRARY="/opt/nmrview/tcl8.4"
-/opt/nmrview/nmrview5_2_2_01_linux $@
diff --git a/sci-chemistry/nmrview/metadata.xml b/sci-chemistry/nmrview/metadata.xml
deleted file mode 100644
index 79d42af98..000000000
--- a/sci-chemistry/nmrview/metadata.xml
+++ /dev/null
@@ -1,12 +0,0 @@
-<?xml version="1.0" encoding="UTF-8"?>
-<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
-<pkgmetadata>
-	<maintainer type="person">
-		<email>jlec@gentoo.org</email>
-		<name>Justin Lecher</name>
-	</maintainer>
-	<maintainer type="project">
-		<email>sci-chemistry@gentoo.org</email>
-		<name>Gentoo Chemistry Project</name>
-	</maintainer>
-</pkgmetadata>
diff --git a/sci-chemistry/nmrview/nmrview-5.2.2-r3.ebuild b/sci-chemistry/nmrview/nmrview-5.2.2-r3.ebuild
deleted file mode 100644
index 394dc5096..000000000
--- a/sci-chemistry/nmrview/nmrview-5.2.2-r3.ebuild
+++ /dev/null
@@ -1,59 +0,0 @@
-# Copyright 1999-2014 Gentoo Foundation
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=5
-
-DESCRIPTION="Visualisation and analysis of processed NMR data"
-HOMEPAGE="http://www.onemoonscientific.com/nmrview/"
-SRC_URI="
-	${PN}${PV}.lib.tar.gz
-	${PN}${PV//./_}_01_linux.gz"
-
-SLOT="0"
-LICENSE="all-rights-reserved"
-IUSE=""
-KEYWORDS="-* ~amd64 ~x86 ~amd64-linux ~x86-linux"
-
-RDEPEND="x11-libs/libX11"
-DEPEND=""
-
-RESTRICT="fetch"
-
-S="${WORKDIR}"
-
-INSTDIR="/opt/nmrview"
-
-QA_PREBUILT="/opt/nmrview/nmrview5_2_2_01_linux"
-
-pkg_nofetch() {
-	einfo "Please visit:"
-	einfo "\t${HOMEPAGE}"
-	echo
-	einfo "Complete the registration process, then download the following files:"
-	einfo "\t${A}"
-	echo
-	einfo "Place the downloaded files in your distfiles directory:"
-	einfo "\t${DISTDIR}"
-	echo
-}
-
-src_install() {
-	insinto ${INSTDIR}
-
-	sed \
-		-e "s:/opt:${EPREFIX}/opt:g" \
-		"${FILESDIR}"/${PN}.sh-r1 \
-		> "${T}"/${PN} || die
-
-	dobin "${T}"/${PN}
-	exeinto ${INSTDIR}
-	doexe ${PN}${PV//./_}_01_linux
-
-	DIRS="help html images nvtcl nvtclC nvtclExt reslib star tcl8.4 tk8.4 tools"
-	doins -r ${DIRS}
-
-	dodoc "${FILESDIR}"/README.Gentoo
-	doins README
-	dosym ${INSTDIR}/html /usr/share/doc/${PF}/html
-	dosym ${INSTDIR}/README /usr/share/doc/${PF}/README
-}
diff --git a/sci-chemistry/nwchem/Manifest b/sci-chemistry/nwchem/Manifest
deleted file mode 100644
index d1057d43d..000000000
--- a/sci-chemistry/nwchem/Manifest
+++ /dev/null
@@ -1,31 +0,0 @@
-DIST Bcast_ccsd.patch.gz 591 BLAKE2B 7ecd6cadb17e42316b01ebca1bc03f3182ccce2455685333d792e9e63eaa8a4d2ebe3eaced3009428d7dd90ee90dae97bf63ecf7b86551332a4d79e3ade2f0e8 SHA512 04e08e5fee5e2b3c3d89553ad36998e180e79a59f692b1cb6848df561319c92747a307596164e86fb5b244f61df432b2b5c3170e26bc25bccdf426ba268a39d3
-DIST Config_libs66.patch.gz 682 BLAKE2B e49dc7e14265b754aa9947dfcf3438778b0cdd8d11ef81e2ec059b242f9806d5b2a5462434b058b0f6f53c26d846f3e10305bee436863e94d5d1d309fece0e45 SHA512 50924c169e3086a419840e7593dc3126297854fac14f8e5ca9c3c47d9478bbd66d79c1e5f9f114cbe6f2a81d0197cbbf1b4085f59ac399fe076e7b96066a1946
-DIST Cosmo_dftprint.patch.gz 424 BLAKE2B b54dc16462d06a1f70a0696e3f2276dcee3c6b6763070c49a8b8824a681c66197c824e388d3c7357187295b38a4f2f80c3fe14a96eb18fe99a5794dc41283159 SHA512 f0930c0130bd779f7704ce8b59c1af01062ffede00102b880d1ade534fdd4867e194f5d4a9a9834f557b5708504ddceec5f3320c4ebfb5af47989261dd523920
-DIST Cosmo_meminit.patch.gz 1659 BLAKE2B 2490c41baa64ea2406f165ae5ab1f878ac47c1d80bc595175aef2d437fb8652bb025a6581ef009402665dde4eff210112a49c16a2cab05a98999205a16255d89 SHA512 51a7fba5a8bc3d70254bdb3d8f3ed2c538b680c3074813906cb3d068c42e7972151f9ca24ffbefc44a8b8f8478cd085feea080c6c8dae9358d62d1823b398ccd
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-DIST Driver_smalleig.patch.gz 255 BLAKE2B 1697ae4e690773f0c8cf78ee904cf4121f33cae8bf1a75309bdbe648868af42a4d1fd8e9234c0259684ec186812f100054c41e50b2593fe5cb915683ee9d4bf1 SHA512 ae9b80e3c962404f5e41b6fd151c7b0b5758a34795be06590b5105c1ac959ee0a01c5aed9f1c6bb01765a8ecc9e5f6e24a0b80f6d80bd0612521d6dcfce4b87d
-DIST Elpa_syncs.patch.gz 554 BLAKE2B afc5d784b89a46fce7ff5fe88608dc8089355574c580591b8620c432ef27a688f1c58d37d0b6557b8194b3b7834ea6f2bc68b424f2d2fd683ba35e75ce2f356d SHA512 c6b6a11dbd40ec4ccd8e230cfd33f2667122c05572deb693ee5c516f0a7dfdefcca0bae8aef518b9cd88ce0a1aec413d3518cf29d14c0f91afdd3024ef9fd506
-DIST Ga_argv.patch.gz 244 BLAKE2B e0d66eb41baf31770dd1a06017e993b1b01901186f094512f873c7b1dcbb9f75b3f3e611202e92a909756ca81cd92f6a853c689445d0db73d5fb6688a98ff644 SHA512 63acab29c96fe2063c452d97a86bedfa9abf1b62bcb99303b13c24d40301af5f5f7427e38c8dd25e0c8225665c0412c36aa99890d5dc902e81bc65ea8b0e79e3
-DIST Ga_defs.patch.gz 321 BLAKE2B 4df879035c1724a25df8e6aba44ad01281fd1a1863cca0bde360394b7c197d4075a5a9bd008b44795d9094e6f082e64346238853f6c6cc7d42b824ccd9fd16b9 SHA512 fb71dd6544659f8ee8d6a26efc33e335da2522759dbc380ab044ec1e827315ae1e93ad57c0cee502bb7d74584e4ca2b9d97bffcf65e3554ddc82dda42518cd44
-DIST Hbar.patch.gz 458 BLAKE2B ab178c392d671c6e335f9dbdb3f4a511e43115cdcd920259d668b9147f7273648d3da45b7cccb35fabb6c973b2af10a81461cbe8291b5314c0c005fdba7e6a13 SHA512 595d5250dd3d462e9d2e0b385a3b41ac828da0792e19606b0365f27b47c839e81ff16cdae590f91f48fa0ac52a4dfcee1c4929bd9054651ee27f9e7c3bf54dbc
-DIST Hnd_giaxyz_noinline.patch.gz 368 BLAKE2B eb4468b68936b49377ddd437b117f94c24ea31e57a9785bbbb76b5a21a9683746a8e41d9e6801df21d2b25fc17b7d07cf59fdf4af2441f9c189f2d014003e188 SHA512 a798412821e35fb3be28ff2df59ce578506635532b08f0f247bae39c85f1c0c912e5205f201f94407d9e3360e66bfb98119596bacc693165fc2b6924800c283c
-DIST Hnd_rys.patch.gz 1585 BLAKE2B 025c5e5f671286737e66381e7c778434b2913c30133b5ba66579eab6e8bcbe072d69372f14875b757ac5bc158f20d7461d28ff143dbfc0faf515ac32ad105aed SHA512 5e95ec72e1b1e17b324d43f3cc68003b5724295e3cad03a9ab8c58636d43ad62ab1cc42e90a5f386854bfeb02b8327ee0f6632c5bd532320e3f34080628b8d84
-DIST Ifort15_fpp_offload.patch.gz 1326 BLAKE2B 6e78f864fd8893559a66782277d04dcf1d88d25850f484946b1f1c8d9ca99c1e700fe58dd4ffb21e799fb6dd9675ad20f685fe32431f6e26e417aa24b3dc99f0 SHA512 fd5559b334fd14006ef984157e22c7fb5297cad7bb29d5696dfe6eb458ba6822b3c2972b8e83e87375091dac4dc18863dd4a817e8b1a64f720de6af99d34aa19
-DIST Makefile_gcc4x.patch.gz 1493 BLAKE2B 0fa596d5bedfcabe133ce2764ebf0ece6ae556eda96e19d11a4b6db58ffaf515133408440e39d3fffbeccff26de97b5d8d7996720b32d1c8c236ff3a1041d39c SHA512 35d46f78da48519ccf21b8853bfc32b958419a600ef7897135f52bc8f7dcfe733883f6600cfd88e75a8c68c3fe9fb0f6302493889df7fbc84f1dd7be29929136
-DIST Nwchem-6.3.revision2-src.2013-10-17.tar.gz 112262489 BLAKE2B ed5ee2c3be8743911f51026a90c34ba0ceb51c283e4666ac032fc506f9363d84d97d41418be857acba40ee1f380f97eda16bcada35899a890d73e1f491b3543f SHA512 28b812b62bba464e6a9c76ccae17145b42ab92c460cc4372bfb6e5d48db0b618d06e778bd2f4787ffcb2d95e60e869af60739181b2f334430592764b41e5f988
-DIST Nwchem-6.5.revision26243-src.2014-09-10.tar.gz 131069464 BLAKE2B 4c5e56841a5734fef847778b9685f5db8a5c12d8fc73b48d8ae4dcdbe7a7526de03d0fe96ebbf5357fc2944e7660acd153f4e66e0e5e4fe08e61847204ae9dc0 SHA512 d4e22819bc40b3bda915dd64c68434f162ad1abccf854a480feb083858a6c8c6b9ef3347e1c5c247149347ecbb2c6dc8d4e70127b90e3b18c08d2cbf16c90843
-DIST Nwchem-6.6.revision27746-src.2015-10-20.tar.bz2 98351363 BLAKE2B b09173f4afa06ecdd264a7aeeb07c5584293fe616c460d72c31b38971a312a539f55e364e7893591fd2f52e3c7476e3e99905cc145d2ed4a85e0ef95438217e0 SHA512 4159cd8bcde1a703ecf221df2e0778dab4cd2239260b648d44ad7d245b8ff0b0042ec2b542892ac2b5d6a2ef86aab40f72a2db2b82d1a88a77d9872b0a42be1d
-DIST Parallelmpi.patch.gz 216 BLAKE2B ada3436a92c63265b243f242f63bf68bece29ff37b9cba9bc1bda0d67673f1b626b17244459df7656323d4b6b7c5c8acd369e3c8f12c318656fe086893da8987 SHA512 21d9020f77814056d3690dca71783e635a4eb951785cf12addc1ff4082b582c82399eb3c3f4f01892d5249fc30a8de1a9a18c1bf37841957bfc924d579f8f7ea
-DIST Print1e.patch.gz 463 BLAKE2B ae71f6980e6384bfbc075ae600a30a2a8d92c75ef024876a04efa08d7399501e4988e1bb6525014378e072bc2144afa0b2f3d7998befef34d9d824d7104de08a SHA512 c53105fb01bb307f7483e55adcd920a4c538cb8634af2c3fa0a13ae1899060603d67fc19392c53ae7499bef48434d667ce690ce66a50dd084bc0583fbe1d95d9
-DIST Raman_displ.patch.gz 3024 BLAKE2B fbff471bc6e068259981f026ee84db4f770a55b66c61420c9c9311be096faf386168d4aa44a299ce39085e5bb409b46e87b38d5a1f1979e39e376d6b7a861ec2 SHA512 8804e2ca36a6e9724ed37bc8a3c71687ce8c560e9afeba89e6c3a51ef7818d0b5481aeb43d918dab9da9dbfb1318a86a6321980be33d2d08758f08abd1ef5e15
-DIST Sym_abelian.patch.gz 281 BLAKE2B c5b6620d1ffe36f46e0716d138abd261b38d98ec506593430f00242fde454c2fc6386a4bb470ac370b64cdb2c0933afa2cd30dfc75a4f752fd8025adfefd9e21 SHA512 4a0728a2730ab6c7f5bfbc2ffa1f18ee83f12e287dc4a10568f10ebfadd5a6b9be281860553e5c144ae24600bb7e2549c5c8b55b5b14064e6720b14b2ab75c56
-DIST Tcenxtask.patch.gz 1556 BLAKE2B 2f4229e0885cb065b43c7e272846e626aff6ac600e99e0f6fdfdb7b16295a83f81fff441bad5901302a6d7dbe867a4206fa7eb2a58ee23b2e089266e18a2b2bf SHA512 9e11a2566c20b07a458cbd0ebe58e006b3ef04831625f3b88e38d20570945ff5138c18f148491bf890f8431699af3c180d948fe6677acf82d557c44e9a7384b5
-DIST Tddft_grad.patch.gz 1301 BLAKE2B 3afa0ea8355739e86e28c2b2feaaa60627baf61547db93442980655e460640a294c6561d03a42baa6ce694b6ae1a56e20d59558e807f9c436bc1ddf38228b2e7 SHA512 5b047f9bbd42cf5b02e651a43b65a4be95208139a75fe959267a9445fd84c8a47667d7dde24a7c02aa380a9d0d40b7dd74a4ad1051657f8bf582aa1345d45632
-DIST Tddft_mxvec20.patch.gz 55611 BLAKE2B 607dc8f3ae8b7c085b09f0d80ff55f9c456e1cae91f6368f82222246535067a041741300701678d376a2a1235a82e782e1ab652471ef919a31403e4a21962d39 SHA512 c86299e11db3924d78c553be178ba14ccff3d2375a22b08d369908e3616ee2d890c4b4a87891a0ba7f629cd43e07e42caffa9eb1b5f06a48b3c907c91a9f9cae
-DIST Texas_iorb.patch.gz 378 BLAKE2B e47880d8f805d44e0a14ebc27e61184da7c37baa6883b817d763a2d86a8e2c080126c7d3b5be8d833c28c0283d2a7093ec92a18d7e94a7232a74526d95f45dcd SHA512 9dc89172999606245e899a884aac073ebd40a102ba6e4164b0e548ad6cc3b37d5744b70896309c2e53871694aeb63b231b90b12e32c019ec84547b2b12e9c2f2
-DIST Tools_lib64.patch.gz 286 BLAKE2B 5ce342c2b350efe82ae8298b880a5efcd95e3cd3b273ab1a98414957513b1b1642e027f9075eee0bff600ec69690438d51031a636fd02a5193bef123cdd040bd SHA512 ded09149db5074306d590dc3dfa8e8286570207bdef228831e69a4cb4189886859f10b3ebeffe99f2c8820778a864ade85f09cef624a3eddeb42b9dfa4aee260
-DIST Util_md_sockets.patch.gz 324 BLAKE2B 5a890dd5b8d6095b7811888407ba99763f4f200a1ef3af3eeb588bd0d4995d6be6444eff3476a44fada9ed1f3f12a02c23982648f581f521c289cafca801ba9e SHA512 743ae8d7cdbe6612a26a10ce845003abab08c1704956940bccf249d00c1d07cf169cfb3cf648c209d5c1dc564abfeddeb8d216259f463c0d564f617c099f5e82
-DIST Xccvs98.patch.gz 669 BLAKE2B f4021444cc6aaf2aea18c29e510a67f5657d2156709df0bb2c31617ed03611fb0e87e5753dcbe15797e6941f87209cad83ec4c0415e06b64cb989a91d68eea38 SHA512 e14c85ee22bf696d9e8e9f090c9c8b30b23659da28dafd020eeb18be8ab44ec66a6d4550295505b43e3428f0771e47b8c61c3ad60a0b3778b3b4e87280065d60
-DIST Xlmpoles_ifort15.patch.gz 256 BLAKE2B f30f763037cd96afb0d65ba02d4946a1bf61ff85104e6a08919279730bca630aef2e40f2c2bd47bc98a594ca72f38f443b77fb783f2a621a83e4df240acaa275 SHA512 f770263a22d5f680c92d52a521ddbd748633dcdf125fe75f353d70d4557fe4c8f0c25ad07e05d8452124f78523552bb87446bff10532cfccc5bc2ce941aac855
-DIST Zgesvd.patch.gz 714 BLAKE2B 31fdc2e5bf49d36af3e8abbaca2cfd7d5ee6195ea9d86a362a8fe289ad743982e4fa875c7d5cb2197850b5731fc42e3aaca0b10d85a72daf136252d8db40f243 SHA512 4d057169c23fe7d109f92d1c63412c0d640f4a275c10467bce609488e54c70977af83af5afbfc4971d083ac0128652153c7af4728bb98cb3aa2b63a28c9f2cff
diff --git a/sci-chemistry/nwchem/files/nwchem-6.1.1-adjust-dir-length.patch b/sci-chemistry/nwchem/files/nwchem-6.1.1-adjust-dir-length.patch
deleted file mode 100644
index 859c76469..000000000
--- a/sci-chemistry/nwchem/files/nwchem-6.1.1-adjust-dir-length.patch
+++ /dev/null
@@ -1,22 +0,0 @@
---- src/nwpw/libraryps/GNUmakefile	2012-01-26 08:24:05.189490945 +0100
-+++ src/nwpw/libraryps/GNUmakefile	2012-01-26 08:24:16.499490923 +0100
-@@ -10,7 +10,7 @@
- 
-     USES_BLAS = 
- 
--   LONGNWTOP = $(shell if [ `echo $(SRCDIR) |wc -m` -gt 64 ]; then echo "Y"; fi  )
-+   LONGNWTOP = $(shell if [ `echo $(SRCDIR) |wc -m` -gt 80 ]; then echo "Y"; fi  )
- ifeq ($(LONGNWTOP),Y)
- errorlongpwd:
- 	@echo " "
---- src/basis/GNUmakefile	2012-01-26 08:25:03.999490829 +0100
-+++ src/basis/GNUmakefile	2012-01-26 08:25:15.549490805 +0100
-@@ -34,7 +34,7 @@
- ########################################################
- 
-    LIB_TARGETS = testbasis testbasis.o libcheck
--   LONGNWTOP = $(shell if [ `echo $(SRCDIR) |wc -m` -gt 64 ]; then echo "Y"; fi  )
-+   LONGNWTOP = $(shell if [ `echo $(SRCDIR) |wc -m` -gt 80 ]; then echo "Y"; fi  )
- ifeq ($(LONGNWTOP),Y)
- errorlongpwd:
- 	@echo " "
diff --git a/sci-chemistry/nwchem/files/nwchem-6.1.1-makefile.patch b/sci-chemistry/nwchem/files/nwchem-6.1.1-makefile.patch
deleted file mode 100644
index a74d887af..000000000
--- a/sci-chemistry/nwchem/files/nwchem-6.1.1-makefile.patch
+++ /dev/null
@@ -1,14 +0,0 @@
---- src/tools/global/GNUmakefile	2011-12-03 14:34:01.000000000 +0100
-+++ src/tools/global/GNUmakefile	2011-12-03 14:37:40.000000000 +0100
-@@ -68,7 +68,10 @@
- $(LIBRARY): 
- 	(echo TARGET is $(TARGET); cd ./src; $(MAKE) || exit 1;) 
- 
--$(TESTS) %.x:	$(LIBRARY)
-+%.x: $(LIBRARY)
-+	(cd ./testing; $(MAKE) $@ || exit 1;)
-+
-+$(TESTS): $(LIBRARY)
- 	(cd ./testing; $(MAKE) $@  || exit 1;)
- 
- all: $(TESTS)
diff --git a/sci-chemistry/nwchem/files/nwchem-6.1.1-nwchemrc.patch b/sci-chemistry/nwchem/files/nwchem-6.1.1-nwchemrc.patch
deleted file mode 100644
index 4e1e0af1e..000000000
--- a/sci-chemistry/nwchem/files/nwchem-6.1.1-nwchemrc.patch
+++ /dev/null
@@ -1,13 +0,0 @@
---- nwchemrc	2011-12-04 11:29:37.000000000 +0100
-+++ nwchemrc	2011-12-04 11:29:26.000000000 +0100
-@@ -0,0 +1,10 @@
-+nwchem_basis_library /usr/share/NWChem/basis/libraries/
-+nwchem_nwpw_library /usr/share/NWChem/nwpw/libraryps/
-+ffield amber
-+amber_1 /usr/share/NWChem/data/amber_s/
-+amber_2 /usr/share/NWChem/data/amber_q/
-+amber_3 /usr/share/NWChem/data/amber_x/
-+amber_4 /usr/share/NWChem/data/amber_u/
-+spce    /usr/share/NWChem/data/solvents/spce.rst
-+charmm_s /usr/share/NWChem/data/charmm_s/
-+charmm_x /usr/share/NWChem/data/charmm_x/
diff --git a/sci-chemistry/nwchem/files/nwchem-6.1.1-python_makefile.patch b/sci-chemistry/nwchem/files/nwchem-6.1.1-python_makefile.patch
deleted file mode 100644
index 16973b648..000000000
--- a/sci-chemistry/nwchem/files/nwchem-6.1.1-python_makefile.patch
+++ /dev/null
@@ -1,12 +0,0 @@
---- src/config/makefile.h	2011-12-04 12:00:52.000000000 +0100
-+++ src/config/makefile.h	2011-12-04 12:01:56.000000000 +0100
-@@ -2133,7 +2133,7 @@
- endif
- ifdef USE_PYTHON64
--  CORE_LIBS += $(PYTHONHOME)/lib64/python$(PYTHONVERSION)/config/libpython$(PYTHONVERSION).$(PYTHONLIBTYPE)
-+  CORE_LIBS += $(PYTHONHOME)/lib64/libpython$(PYTHONVERSION).$(PYTHONLIBTYPE)
- else
--  CORE_LIBS += $(PYTHONHOME)/lib/python$(PYTHONVERSION)/config/libpython$(PYTHONVERSION).$(PYTHONLIBTYPE)
-+  CORE_LIBS += $(PYTHONHOME)/lib/libpython$(PYTHONVERSION).$(PYTHONLIBTYPE)
- endif
- endif
diff --git a/sci-chemistry/nwchem/files/nwchem-6.3-r1-html_doc.patch b/sci-chemistry/nwchem/files/nwchem-6.3-r1-html_doc.patch
deleted file mode 100644
index de7377bd2..000000000
--- a/sci-chemistry/nwchem/files/nwchem-6.3-r1-html_doc.patch
+++ /dev/null
@@ -1,13 +0,0 @@
-diff -Naurp old/doc/update_www new/doc/update_www
---- doc/update_www	2013-05-18 00:40:51.000000000 +0000
-+++ doc/update_www	2013-05-22 12:15:27.543414281 +0000
-@@ -16,7 +16,8 @@ set document = $argv[1]
- echo Updating WWW pages for $document.tex
- #...............   public 
- #foreach WWWDIR (/msrc/www/pub/docs/nwchem/doc)
--foreach WWWDIR (/msrc/emslweb/docs/nwchem/doc)
-+#foreach WWWDIR (/msrc/emslweb/docs/nwchem/doc)
-+foreach WWWDIR ("${NWCHEM_TOP}"/web)
- #
- # Now copy the revised source into the EMSL public WWW tree
-   echo "update_www: Public pages .. "
diff --git a/sci-chemistry/nwchem/files/nwchem-6.5-icosahedron_zcoord.patch b/sci-chemistry/nwchem/files/nwchem-6.5-icosahedron_zcoord.patch
deleted file mode 100644
index acd60d3b3..000000000
--- a/sci-chemistry/nwchem/files/nwchem-6.5-icosahedron_zcoord.patch
+++ /dev/null
@@ -1,12 +0,0 @@
-diff -Naurp nwchem.orig/src/geom/geom_hnd.F nwchem/src/geom/geom_hnd.F
---- nwchem.orig/src/geom/geom_hnd.F	2014-09-10 18:11:03.000000000 +0000
-+++ nwchem/src/geom/geom_hnd.F	2015-01-28 16:14:38.249027101 +0000
-@@ -1644,7 +1644,7 @@ c
-          nlnba=3*mxlnba
-          if (.not. zdone) goto 55555 ! attempt to recover
- c
--         if (nzvar .gt. 10*(max(6,3*nat-6))) then
-+         if (nzvar .gt. 20*(max(6,3*nat-6))) then
- c
- c     Made a z-matrix but it is asburdly big.  Nothing yet to fix this
- c
diff --git a/sci-chemistry/nwchem/files/nwchem-6.5-python_makefile.patch b/sci-chemistry/nwchem/files/nwchem-6.5-python_makefile.patch
deleted file mode 100644
index c37310c79..000000000
--- a/sci-chemistry/nwchem/files/nwchem-6.5-python_makefile.patch
+++ /dev/null
@@ -1,15 +0,0 @@
---- src/config/makefile.h	2014-11-03 14:00:59.808794970 +0100
-+++ src/config/makefile.h	2014-11-03 14:29:13.353470102 +0100
-@@ -2521,10 +2521,10 @@
- endif
- ifdef USE_PYTHON64
--	CORE_LIBS += $(PYTHONHOME)/lib64/python$(PYTHONVERSION)/$(PYTHONCONFIGDIR)/libpython$(PYTHONVERSION).$(PYTHONLIBTYPE)
-+	CORE_LIBS += $(PYTHONHOME)/lib64/libpython$(PYTHONVERSION).$(PYTHONLIBTYPE)
- else
-   ifeq ($(GOTMINGW32),1)
-   CORE_LIBS += $(PYTHONHOME)/libs/libpython$(PYTHONVERSION).$(PYTHONLIBTYPE)
-   else
--  CORE_LIBS += $(PYTHONHOME)/lib/python$(PYTHONVERSION)/$(PYTHONCONFIGDIR)/libpython$(PYTHONVERSION).$(PYTHONLIBTYPE)
-+  CORE_LIBS += $(PYTHONHOME)/lib/libpython$(PYTHONVERSION).$(PYTHONLIBTYPE)
-   endif
- endif
diff --git a/sci-chemistry/nwchem/files/nwchem-6.6-unique_tags.patch b/sci-chemistry/nwchem/files/nwchem-6.6-unique_tags.patch
deleted file mode 100644
index e129406e1..000000000
--- a/sci-chemistry/nwchem/files/nwchem-6.6-unique_tags.patch
+++ /dev/null
@@ -1,12 +0,0 @@
-diff -Naurp nwchem-6.6.orig/src/util/nwc_const.fh nwchem-6.6/src/util/nwc_const.fh
---- nwchem-6.6.orig/src/util/nwc_const.fh	2015-10-01 17:33:14.000000000 +0000
-+++ nwchem-6.6/src/util/nwc_const.fh	2015-11-26 10:53:46.386110924 +0000
-@@ -62,7 +62,7 @@
- * Maximum number of unique tags
- *
-       integer nw_max_unq_tags
--      parameter (nw_max_unq_tags = 40)
-+      parameter (nw_max_unq_tags = nw_max_atom)
- *------------------------------------------------------------------------------
- * Maximum number of general contractions in a shell
- *
diff --git a/sci-chemistry/nwchem/metadata.xml b/sci-chemistry/nwchem/metadata.xml
deleted file mode 100644
index 61993bb4b..000000000
--- a/sci-chemistry/nwchem/metadata.xml
+++ /dev/null
@@ -1,34 +0,0 @@
-<?xml version="1.0" encoding="UTF-8"?>
-<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
-<pkgmetadata>
-	<maintainer type="person">
-		<email>alexxy@gentoo.org</email>
-		<name>Alexey Shvetsov</name>
-	</maintainer>
-	<maintainer type="project">
-		<email>sci-chemistry@gentoo.org</email>
-		<name>Gentoo Chemistry Project</name>
-	</maintainer>
-	<use>
-		<flag name="blas">
-Use external BLAS library instead of the internal routines
-</flag>
-		<flag name="cuda">
-Enable CUDA GPU support for the Tensor Contraction Engine generated
-methods (CI, MBPT, CC)
-</flag>
-		<flag name="int64">
-Use 64 bits integers
-</flag>
-		<flag name="lapack">
-Use external LAPACK library instead of the internal routines
-</flag>
-		<flag name="mrcc">
-Compile the routines for Multi Reference Coupled Clusters theory
-</flag>
-		<flag name="nwchem-tests">Install qa tests data</flag>
-		<flag name="scalapack">
-Use external SCALAPACK library
-</flag>
-	</use>
-</pkgmetadata>
diff --git a/sci-chemistry/nwchem/nwchem-6.3_p2-r1.ebuild b/sci-chemistry/nwchem/nwchem-6.3_p2-r1.ebuild
deleted file mode 100644
index 980b6f392..000000000
--- a/sci-chemistry/nwchem/nwchem-6.3_p2-r1.ebuild
+++ /dev/null
@@ -1,206 +0,0 @@
-# Copyright 1999-2014 Gentoo Foundation
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=5
-
-PYTHON_COMPAT=( python2_7 )
-
-inherit eutils flag-o-matic fortran-2 multilib python-single-r1 toolchain-funcs
-
-DATE="2013-10-17"
-
-DESCRIPTION="Delivering High-Performance Computational Chemistry to Science"
-HOMEPAGE="http://www.nwchem-sw.org/index.php/Main_Page"
-SRC_URI="http://www.nwchem-sw.org/images/Nwchem-${PV%_p*}.revision${PV#*_p}-src.${DATE}.tar.gz"
-
-LICENSE="ECL-2.0"
-SLOT="0"
-KEYWORDS="~amd64 ~x86"
-IUSE="blas mpi doc examples nwchem-tests openmp mrcc python"
-
-REQUIRED_USE="python? ( ${PYTHON_REQUIRED_USE} )"
-
-RDEPEND="
-	sys-fs/sysfsutils
-	python? ( ${PYTHON_DEPS} )"
-DEPEND="${RDEPEND}
-	app-shells/tcsh
-	mpi? ( virtual/mpi[fortran] )
-	doc? (
-		dev-texlive/texlive-latex
-		dev-tex/latex2html )"
-
-LONG_S="${WORKDIR}/${PN}-${PV%_p*}.revision${PV#*_p}-src.${DATE}"
-S="${WORKDIR}/${PN}"
-
-pkg_setup() {
-	# fortran-2.eclass does not handle mpi wrappers
-	if use mpi; then
-		export FC="mpif90"
-		export F77="mpif77"
-		export CC="mpicc"
-		export CXX="mpic++"
-	else
-		tc-export FC F77 CC CXX
-	fi
-
-	use openmp && FORTRAN_NEED_OPENMP=1
-
-	fortran-2_pkg_setup
-
-	if use openmp; then
-		# based on _fortran-has-openmp() of fortran-2.eclass
-		local openmp=""
-		local fcode=ebuild-openmp-flags.f
-		local _fc=$(tc-getFC)
-
-		pushd "${T}"
-		cat <<- EOF > "${fcode}"
-		1     call omp_get_num_threads
-		2     end
-		EOF
-
-		for openmp in -fopenmp -xopenmp -openmp -mp -omp -qsmp=omp; do
-			"${_fc}" "${openmp}" "${fcode}" -o "${fcode}.x" && break
-		done
-
-		rm -f "${fcode}.*"
-		popd
-
-		append-flags "${openmp}"
-	fi
-
-	use python && python-single-r1_pkg_setup
-}
-
-src_unpack() {
-	unpack ${A}
-	mv "${LONG_S}" "${S}"
-}
-
-src_prepare() {
-	epatch \
-		"${FILESDIR}"/nwchem-6.1.1-makefile.patch \
-		"${FILESDIR}"/nwchem-6.1.1-nwchemrc.patch \
-		"${FILESDIR}"/nwchem-6.1.1-adjust-dir-length.patch
-	use python && epatch "${FILESDIR}"/nwchem-6.1.1-python_makefile.patch
-	use doc && epatch "${FILESDIR}"/nwchem-6.3-r1-html_doc.patch
-
-	sed \
-		-e "s:DBASIS_LIBRARY=\"'\$(SRCDIR)'\":DBASIS_LIBRARY=\"'${EPREFIX}/usr/share/NWChem'\":g" \
-		-i src/basis/MakeFile src/basis/GNUmakefile || die
-	sed \
-		-e "s:DNWPW_LIBRARY=\"'\$(SRCDIR)'\":DNWPW_LIBRARY=\"'${EPREFIX}/usr/share/NWChem'\":g" \
-		-i src/nwpw/libraryps/GNUmakefile || die
-	sed \
-		-e "s:-DCOMPILATION_DIR=\"'\$(TOPDIR)'\":-DCOMPILATION_DIR=\"''\":g" \
-		-i src/GNUmakefile src/MakeFile || die
-
-	if [[ $(tc-getFC) == *-*-*-*-gfortran ]]; then
-		sed \
-			-e "s:ifneq (\$(FC),gfortran):ifneq (\$(FC),$(tc-getFC)):g" \
-			-e "s:ifeq (\$(FC),gfortran):ifeq (\$(FC),$(tc-getFC)):g" \
-			-i src/config/makefile.h || die
-	fi
-}
-
-src_compile() {
-	export USE_SUBGROUPS=yes
-	if use mpi ; then
-		export MSG_COMMS=MPI
-		export USE_MPI=y
-		export USE_MPIF=y
-		export MPI_LOC="${EPREFIX}"/usr
-		export MPI_INCLUDE=$MPI_LOC/include
-		export MPI_LIB=$MPI_LOC/$(get_libdir)
-		export LIBMPI="$(mpif90 -showme:link)"
-	else
-		unset USE_MPI
-		unset USE_MPIF
-		export MSG_COMMS=TCGMSG
-		export ARMCI_NETWORK=SOCKETS
-	fi
-	if [ "$ARCH" = "amd64" ]; then
-		export NWCHEM_TARGET=LINUX64
-	elif [ "$ARCH" = "ia64" ]; then
-		export NWCHEM_TARGET=LINUX64
-	elif [ "$ARCH" = "x86" ]; then
-		export NWCHEM_TARGET=LINUX
-	elif [ "$ARCH" = "ppc" ]; then
-		export NWCHEM_TARGET=LINUX
-	else
-		die "Unknown architecture"
-	fi
-	if use python ; then
-		if [ "$ARCH" = "amd64" ] || [ "$ARCH" = "ia64" ]; then
-			export USE_PYTHON64=yes
-		fi
-		export PYTHONHOME=/usr
-		export PYTHONVERSION=$(eselect python show --python2 |awk -Fpython '{ print $2 }')
-		export PYTHONPATH="./:${S}/contrib/python/"
-		export NWCHEM_MODULES="all python"
-	else
-		export NWCHEM_MODULES="all"
-	fi
-	use mrcc && export MRCC_THEORY="TRUE"
-	if use blas; then
-		export HAS_BLAS=yes
-		export BLASOPT="$(pkg-config --libs blas)"
-	else
-		unset HAS_BLAS
-		unset BLASOPT
-	fi
-	export LARGE_FILES="TRUE"
-
-	cd src
-	emake \
-		DIAG=PAR \
-		FC=$(tc-getFC) \
-		CC=$(tc-getCC) \
-		CXX=$(tc-getCXX) \
-		NWCHEM_TOP="${S}" \
-		NWCHEM_EXECUTABLE="${S}/bin/${NWCHEM_TARGET}/nwchem"
-
-	if use doc; then
-		cd "${S}"/doc
-		export VARTEXFONTS="${T}/fonts"
-		emake \
-			DIAG=PAR \
-			NWCHEM_TOP="${S}" \
-			pdf html
-	fi
-}
-
-src_install() {
-	dobin bin/${NWCHEM_TARGET}/nwchem
-
-	insinto /usr/share/NWChem/basis/
-	doins -r src/basis/libraries src/data
-	insinto /usr/share/NWChem/nwpw
-	doins -r src/nwpw/libraryps
-
-	insinto /etc
-	doins nwchemrc
-
-	use examples && \
-		insinto /usr/share/NWChem/ && \
-		doins -r examples
-
-	use nwchem-tests && \
-		insinto /usr/share/NWChem && \
-		doins -r QA/tests
-
-	use doc && \
-		insinto /usr/share/doc/"${P}" && \
-		doins -r doc/nwahtml && \
-		doins -r web
-
-}
-
-pkg_postinst() {
-	echo
-	elog "The user will need to link \$HOME/.nwchemrc to /etc/nwchemrc"
-	elog "or copy it in order to tell NWChem the right position of the"
-	elog "basis library and other necessary data."
-	echo
-}
diff --git a/sci-chemistry/nwchem/nwchem-6.5_p26243-r7.ebuild b/sci-chemistry/nwchem/nwchem-6.5_p26243-r7.ebuild
deleted file mode 100644
index f11a699df..000000000
--- a/sci-chemistry/nwchem/nwchem-6.5_p26243-r7.ebuild
+++ /dev/null
@@ -1,292 +0,0 @@
-# Copyright 1999-2015 Gentoo Foundation
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=5
-
-PYTHON_COMPAT=( python2_7 )
-
-inherit eutils flag-o-matic fortran-2 multilib python-single-r1 toolchain-funcs
-
-DATE="2014-09-10"
-
-DESCRIPTION="Delivering High-Performance Computational Chemistry to Science"
-HOMEPAGE="http://www.nwchem-sw.org/index.php/Main_Page"
-SRC_URI="http://www.nwchem-sw.org/images/Nwchem-${PV%_p*}.revision${PV#*_p}-src.${DATE}.tar.gz
-	http://www.nwchem-sw.org/images/Util_md_sockets.patch.gz
-	http://www.nwchem-sw.org/images/Hbar.patch.gz
-	http://www.nwchem-sw.org/images/Tcenxtask.patch.gz
-	http://www.nwchem-sw.org/images/Hnd_giaxyz_noinline.patch.gz
-	http://www.nwchem-sw.org/images/Parallelmpi.patch.gz
-	http://www.nwchem-sw.org/images/Makefile_gcc4x.patch.gz
-	http://www.nwchem-sw.org/images/Bcast_ccsd.patch.gz
-	http://www.nwchem-sw.org/images/Elpa_syncs.patch.gz
-	http://www.nwchem-sw.org/images/Xlmpoles_ifort15.patch.gz
-	http://www.nwchem-sw.org/images/Ifort15_fpp_offload.patch.gz
-	http://www.nwchem-sw.org/images/Texas_iorb.patch.gz
-	http://www.nwchem-sw.org/images/Dmapp_inc.patch.gz
-	http://www.nwchem-sw.org/images/Print1e.patch.gz
-	http://www.nwchem-sw.org/images/Hnd_rys.patch.gz
-	http://www.nwchem-sw.org/images/Tddft_grad.patch.gz"
-
-LICENSE="ECL-2.0"
-SLOT="0"
-KEYWORDS="~amd64 ~x86"
-IUSE="blas cuda doc examples infiniband int64 lapack mrcc nwchem-tests openmp python scalapack"
-
-REQUIRED_USE="python? ( ${PYTHON_REQUIRED_USE} )
-	scalapack? ( !int64 )
-	lapack? ( blas )
-	scalapack? ( blas )"
-
-RDEPEND="
-	sys-fs/sysfsutils
-	blas? ( virtual/blas )
-	lapack? ( virtual/lapack )
-	scalapack? ( virtual/scalapack )
-	cuda? ( dev-util/nvidia-cuda-sdk )
-	int64? (
-		blas? ( virtual/blas[int64] )
-		lapack? ( virtual/lapack[int64] )
-	)
-	python? ( ${PYTHON_DEPS} )"
-DEPEND="${RDEPEND}
-	virtual/pkgconfig
-	app-shells/tcsh
-	virtual/mpi[fortran]
-	infiniband? ( || (
-		sys-cluster/openmpi[fortran,openmpi_fabrics_ofed]
-		sys-cluster/mvapich2[fortran]
-	) )
-	doc? (
-		dev-texlive/texlive-latex
-		dev-tex/latex2html )"
-
-LONG_S="${WORKDIR}/Nwchem-${PV%_p*}.revision${PV#*_p}-src.${DATE}"
-S="${WORKDIR}/${PN}"
-
-pkg_setup() {
-	# fortran-2.eclass does not handle mpi wrappers
-	export FC="mpif90"
-	export F77="mpif77"
-	export CC="mpicc"
-	export CXX="mpic++"
-
-	use openmp && FORTRAN_NEED_OPENMP=1
-
-	fortran-2_pkg_setup
-
-	if use openmp; then
-		# based on _fortran-has-openmp() of fortran-2.eclass
-		local openmp=""
-		local fcode=ebuild-openmp-flags.f
-		local _fc=$(tc-getFC)
-
-		pushd "${T}"
-		cat <<- EOF > "${fcode}"
-		1     call omp_get_num_threads
-		2     end
-		EOF
-
-		for openmp in -fopenmp -xopenmp -openmp -mp -omp -qsmp=omp; do
-			"${_fc}" "${openmp}" "${fcode}" -o "${fcode}.x" && break
-		done
-
-		rm -f "${fcode}.*"
-		popd
-
-#		append-flags "${openmp}"
-#		append-ldflags "${openmp}
-		export FC="${FC} ${openmp}"
-		export F77="${F77} ${openmp}"
-		export CC="${CC} ${openmp}"
-		export CXX="${CXX} ${openmp}"
-	fi
-
-	use python && python-single-r1_pkg_setup
-}
-
-src_unpack() {
-	unpack ${A}
-	mv "${LONG_S}" "${S}"
-}
-
-src_prepare() {
-	pushd "${S}"/src
-		for p in Util_md_sockets Hbar Tcenxtask Parallelmpi Makefile_gcc4x Bcast_ccsd Elpa_syncs Xlmpoles_ifort15 Ifort15_fpp_offload Texas_iorb Dmapp_inc Print1e Hnd_rys Tddft_grad
-			do epatch "${WORKDIR}"/"${p}.patch"
-		done
-		cd NWints/hondo
-		epatch "${WORKDIR}"/Hnd_giaxyz_noinline.patch
-	popd
-	epatch "${FILESDIR}"/nwchem-6.1.1-nwchemrc.patch
-	epatch "${FILESDIR}"/nwchem-6.5-icosahedron_zcoord.patch
-	use python && epatch "${FILESDIR}"/nwchem-6.5-python_makefile.patch
-	use doc && epatch "${FILESDIR}"/nwchem-6.3-r1-html_doc.patch
-
-	sed \
-		-e "s:DBASIS_LIBRARY=\"'\$(SRCDIR)'\":DBASIS_LIBRARY=\"'${EPREFIX}/usr/share/NWChem'\":g" \
-		-i src/basis/MakeFile src/basis/GNUmakefile || die
-	sed \
-		-e "s:DNWPW_LIBRARY=\"'\$(SRCDIR)'\":DNWPW_LIBRARY=\"'${EPREFIX}/usr/share/NWChem'\":g" \
-		-i src/nwpw/libraryps/GNUmakefile || die
-	sed \
-		-e "s:-DCOMPILATION_DIR=\"'\$(TOPDIR)'\":-DCOMPILATION_DIR=\"''\":g" \
-		-i src/GNUmakefile src/MakeFile || die
-
-	if [[ $(tc-getFC) == *-*-*-*-gfortran ]]; then
-		sed \
-			-e "s:ifneq (\$(FC),gfortran):ifneq (\$(FC),$(tc-getFC)):g" \
-			-e "s:ifeq (\$(FC),gfortran):ifeq (\$(FC),$(tc-getFC)):g" \
-			-i src/config/makefile.h || die
-	fi
-}
-
-src_compile() {
-	export NWCHEM_LONG_PATHS=Y
-	use openmp && export USE_OPENMP=1
-	export USE_MPI=y
-	export USE_MPIF=y
-	export USE_MPIF4=y
-	export MPI_LOC="${EPREFIX}"/usr
-	export MPI_INCLUDE=$MPI_LOC/include
-	export MPI_LIB=$MPI_LOC/$(get_libdir)
-	export LIBMPI="$(mpif90 -showme:link)"
-	if use infiniband; then
-		export ARMCI_NETWORK=OPENIB
-		export MSG_COMMS=MPI
-	else
-		unset ARMCI_NETWORK
-	fi
-	if [ "$ARCH" = "amd64" ]; then
-		export NWCHEM_TARGET=LINUX64
-	elif [ "$ARCH" = "ia64" ]; then
-		export NWCHEM_TARGET=LINUX64
-	elif [ "$ARCH" = "x86" ]; then
-		export NWCHEM_TARGET=LINUX
-	elif [ "$ARCH" = "ppc" ]; then
-		export NWCHEM_TARGET=LINUX
-	else
-		die "Unknown architecture"
-	fi
-	if use python ; then
-		if [ "$ARCH" = "amd64" ] || [ "$ARCH" = "ia64" ]; then
-			export USE_PYTHON64=yes
-		fi
-		export PYTHONHOME=/usr
-		export PYTHONVERSION=$(eselect python show --python2 |awk -Fpython '{ print $2 }')
-		export PYTHONPATH="./:${S}/contrib/python/"
-		export NWCHEM_MODULES="all python"
-	else
-		export NWCHEM_MODULES="all"
-	fi
-	use mrcc && export MRCC_METHODS="TRUE" # Multi Reference Coupled Clusters
-	export CCSDTQ="TRUE"                   # Coupled Clusters Singlets + Dublets + Triplets + Quadruplets
-	export CCSDTLR="TRUE"                  # CCSDT (and CCSDTQ?) Linear Response
-	export EACCSD="TRUE"                   # Electron Affinities at the CCSD level
-	export IPCCSD="TRUE"                   # Ionisation Potentials at the CCSD level
-	unset BLASOPT
-	local blaspkg="blas"
-	local lapackpkg="lapack"
-	if use int64; then
-		blaspkg="blas-int64"
-		lapackpkg="lapack-int64"
-	fi
-	use blas && export BLASOPT="$($(tc-getPKG_CONFIG) --libs ${blaspkg})"
-	use lapack && export BLASOPT+=" $($(tc-getPKG_CONFIG) --libs ${lapackpkg})"
-	use scalapack && export BLASOPT+=" $($(tc-getPKG_CONFIG) --libs scalapack)"
-	if use cuda; then
-		export TCE_CUDA=Y
-		export CUDA_PATH=/opt/cuda
-		export CUDA=${CUDA_PATH}/bin/nvcc
-		export CUDA_FLAGS="-arch=compute_20 -code=sm_20,compute_20"
-		export CUDA_INCLUDE="-I${CUDA_PATH}/include"
-		export CUDA_LIBS="-L${CUDA_PATH}/$(get_libdir) -lcublas -lcufft -lcudart -lcuda -lstdc++"
-	fi
-	export LARGE_FILES="TRUE"
-
-	cd src
-	if use blas && [ "$NWCHEM_TARGET" = "LINUX64" ]; then
-		if use int64; then
-			export BLAS_SIZE=8
-			export LAPACK_SIZE=8
-			export SCALAPACK_SIZE=8
-		else
-			emake \
-				DIAG=PAR \
-				FC="$(tc-getFC)" \
-				CC="$(tc-getCC)" \
-				CXX="$(tc-getCXX)" \
-				NWCHEM_TOP="${S}" \
-				clean
-			emake \
-				DIAG=PAR \
-				FC="$(tc-getFC)" \
-				CC="$(tc-getCC)" \
-				CXX="$(tc-getCXX)" \
-				NWCHEM_TOP="${S}" \
-				64_to_32
-			export BLAS_SIZE=4
-			export LAPACK_SIZE=4
-			export SCALAPACK_SIZE=4
-			export USE_64TO32=y
-		fi
-	fi
-	emake \
-		DIAG=PAR \
-		FC="$(tc-getFC)" \
-		CC="$(tc-getCC)" \
-		CXX="$(tc-getCXX)" \
-		NWCHEM_TOP="${S}" \
-		NWCHEM_EXECUTABLE="${S}/bin/${NWCHEM_TARGET}/nwchem" \
-		nwchem_config
-	emake \
-		DIAG=PAR \
-		FC="$(tc-getFC)" \
-		CC="$(tc-getCC)" \
-		CXX="$(tc-getCXX)" \
-		NWCHEM_TOP="${S}" \
-		NWCHEM_EXECUTABLE="${S}/bin/${NWCHEM_TARGET}/nwchem"
-
-	if use doc; then
-		cd "${S}"/doc
-		export VARTEXFONTS="${T}/fonts"
-		emake \
-			DIAG=PAR \
-			NWCHEM_TOP="${S}" \
-			pdf html
-	fi
-}
-
-src_install() {
-	dobin bin/${NWCHEM_TARGET}/nwchem
-
-	insinto /usr/share/NWChem/basis/
-	doins -r src/basis/libraries src/data
-	insinto /usr/share/NWChem/nwpw
-	doins -r src/nwpw/libraryps
-
-	insinto /etc
-	doins nwchemrc
-
-	use examples && \
-		insinto /usr/share/NWChem/ && \
-		doins -r examples
-
-	use nwchem-tests && \
-		insinto /usr/share/NWChem && \
-		doins -r QA/tests
-
-	use doc && \
-		insinto /usr/share/doc/"${P}" && \
-		doins -r doc/nwahtml && \
-		doins -r web
-
-}
-
-pkg_postinst() {
-	echo
-	elog "The user will need to link \$HOME/.nwchemrc to /etc/nwchemrc"
-	elog "or copy it in order to tell NWChem the right position of the"
-	elog "basis library and other necessary data."
-	echo
-}
diff --git a/sci-chemistry/nwchem/nwchem-6.6_p27746-r2.ebuild b/sci-chemistry/nwchem/nwchem-6.6_p27746-r2.ebuild
deleted file mode 100644
index fc2f110e9..000000000
--- a/sci-chemistry/nwchem/nwchem-6.6_p27746-r2.ebuild
+++ /dev/null
@@ -1,278 +0,0 @@
-# Copyright 1999-2017 Gentoo Foundation
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=5
-
-PYTHON_COMPAT=( python2_7 )
-
-inherit eutils flag-o-matic fortran-2 multilib python-single-r1 toolchain-funcs
-
-DATE="2015-10-20"
-
-DESCRIPTION="Delivering High-Performance Computational Chemistry to Science"
-HOMEPAGE="http://www.nwchem-sw.org/index.php/Main_Page"
-PATCH_REPO="http://www.nwchem-sw.org/images"
-PATCH_LIST="Tddft_mxvec20 Tools_lib64 Config_libs66 Cosmo_meminit Sym_abelian
-Xccvs98 Dplot_tolrho Driver_smalleig Ga_argv Raman_displ Ga_defs Zgesvd Cosmo_dftprint"
-SRC_URI="http://www.nwchem-sw.org/images/Nwchem-${PV%_p*}.revision${PV#*_p}-src.${DATE}.tar.bz2
-	$(for p in ${PATCH_LIST[@]}; do echo ${PATCH_REPO}/${p}.patch.gz; done)"
-
-LICENSE="ECL-2.0"
-SLOT="0"
-KEYWORDS="~amd64 ~x86"
-IUSE="blas cuda doc examples infiniband int64 lapack mrcc nwchem-tests openmp python scalapack"
-
-REQUIRED_USE="python? ( ${PYTHON_REQUIRED_USE} )
-	scalapack? ( !int64 )
-	lapack? ( blas )
-	scalapack? ( blas )"
-
-RDEPEND="
-	sys-fs/sysfsutils
-	blas? ( virtual/blas )
-	lapack? ( virtual/lapack )
-	scalapack? ( virtual/scalapack )
-	cuda? ( dev-util/nvidia-cuda-sdk )
-	int64? (
-		blas? ( virtual/blas[int64] )
-		lapack? ( virtual/lapack[int64] )
-	)
-	python? ( ${PYTHON_DEPS} )"
-DEPEND="${RDEPEND}
-	virtual/pkgconfig
-	app-shells/tcsh
-	virtual/mpi[fortran]
-	infiniband? ( || (
-		sys-cluster/openmpi[fortran,openmpi_fabrics_ofed]
-		sys-cluster/mvapich2[fortran]
-	) )
-	doc? (
-		dev-texlive/texlive-latex
-		dev-tex/latex2html )"
-
-LONG_S="${WORKDIR}/Nwchem-${PV%_p*}.revision${PV#*_p}-src.${DATE}"
-S="${WORKDIR}/${PN}-${PV%_p*}"
-
-pkg_setup() {
-	# fortran-2.eclass does not handle mpi wrappers
-	export FC="mpif90"
-	export F77="mpif77"
-	export CC="mpicc"
-	export CXX="mpic++"
-
-	use openmp && FORTRAN_NEED_OPENMP=1
-
-	fortran-2_pkg_setup
-
-	if use openmp; then
-		# based on _fortran-has-openmp() of fortran-2.eclass
-		local openmp=""
-		local fcode=ebuild-openmp-flags.f
-		local _fc=$(tc-getFC)
-
-		pushd "${T}"
-		cat <<- EOF > "${fcode}"
-		1     call omp_get_num_threads
-		2     end
-		EOF
-
-		for openmp in -fopenmp -xopenmp -openmp -mp -omp -qsmp=omp; do
-			"${_fc}" "${openmp}" "${fcode}" -o "${fcode}.x" && break
-		done
-
-		rm -f "${fcode}.*"
-		popd
-
-		export FC="${FC} ${openmp}"
-		export F77="${F77} ${openmp}"
-		export CC="${CC} ${openmp}"
-		export CXX="${CXX} ${openmp}"
-	fi
-
-	use python && python-single-r1_pkg_setup
-}
-
-src_unpack() {
-	unpack ${A}
-	mv "${LONG_S}" "${S}"
-}
-
-src_prepare() {
-	for p in ${PATCH_LIST[@]}
-		do epatch "${WORKDIR}"/"${p}.patch"
-	done
-	epatch "${FILESDIR}"/nwchem-6.1.1-nwchemrc.patch
-	epatch "${FILESDIR}"/nwchem-6.5-icosahedron_zcoord.patch
-	epatch "${FILESDIR}"/nwchem-6.6-unique_tags.patch
-	use python && epatch "${FILESDIR}"/nwchem-6.5-python_makefile.patch
-	use doc && epatch "${FILESDIR}"/nwchem-6.3-r1-html_doc.patch
-
-	sed \
-		-e "s:DBASIS_LIBRARY=\"'\$(SRCDIR)'\":DBASIS_LIBRARY=\"'${EPREFIX}/usr/share/NWChem'\":g" \
-		-i src/basis/MakeFile src/basis/GNUmakefile || die
-	sed \
-		-e "s:DNWPW_LIBRARY=\"'\$(SRCDIR)'\":DNWPW_LIBRARY=\"'${EPREFIX}/usr/share/NWChem'\":g" \
-		-i src/nwpw/libraryps/GNUmakefile || die
-	sed \
-		-e "s:-DCOMPILATION_DIR=\"'\$(TOPDIR)'\":-DCOMPILATION_DIR=\"''\":g" \
-		-i src/GNUmakefile src/MakeFile || die
-
-	if [[ $(tc-getFC) == *-*-*-*-gfortran ]]; then
-		sed \
-			-e "s:ifneq (\$(FC),gfortran):ifneq (\$(FC),$(tc-getFC)):g" \
-			-e "s:ifeq (\$(FC),gfortran):ifeq (\$(FC),$(tc-getFC)):g" \
-			-i src/config/makefile.h || die
-	fi
-}
-
-src_compile() {
-	export NWCHEM_LONG_PATHS=Y
-	use openmp && export USE_OPENMP=1
-	export USE_MPI=y
-	export USE_MPIF=y
-	export USE_MPIF4=y
-	export MPI_LOC="${EPREFIX}"/usr
-	export MPI_INCLUDE=$MPI_LOC/include
-	export MPI_LIB=$MPI_LOC/$(get_libdir)
-	export LIBMPI="$(mpif90 -showme:link)"
-	if use infiniband; then
-		export ARMCI_NETWORK=OPENIB
-		export MSG_COMMS=MPI
-		export IB_INCLUDE="-I${MPI_INCLUDE}"
-		export IB_LIB="-L${MPI_LIB}"
-	else
-		unset ARMCI_NETWORK
-	fi
-	if [ "$ARCH" = "amd64" ]; then
-		export NWCHEM_TARGET=LINUX64
-	elif [ "$ARCH" = "ia64" ]; then
-		export NWCHEM_TARGET=LINUX64
-	elif [ "$ARCH" = "x86" ]; then
-		export NWCHEM_TARGET=LINUX
-	elif [ "$ARCH" = "ppc" ]; then
-		export NWCHEM_TARGET=LINUX
-	else
-		die "Unknown architecture"
-	fi
-	if use python ; then
-		if [ "$ARCH" = "amd64" ] || [ "$ARCH" = "ia64" ]; then
-			export USE_PYTHON64=yes
-		fi
-		export PYTHONHOME=/usr
-		export PYTHONVERSION=$(eselect python show --python2 |awk -Fpython '{ print $2 }')
-		export PYTHONPATH="./:${S}/contrib/python/"
-		export NWCHEM_MODULES="all python"
-	else
-		export NWCHEM_MODULES="all"
-	fi
-	use mrcc && export MRCC_METHODS="TRUE" # Multi Reference Coupled Clusters
-	export CCSDTQ="TRUE"                   # Coupled Clusters Singlets + Dublets + Triplets + Quadruplets
-	export CCSDTLR="TRUE"                  # CCSDT (and CCSDTQ?) Linear Response
-	export EACCSD="TRUE"                   # Electron Affinities at the CCSD level
-	export IPCCSD="TRUE"                   # Ionisation Potentials at the CCSD level
-	unset BLASOPT
-	local blaspkg="blas"
-	local lapackpkg="lapack"
-	if use int64; then
-		blaspkg="blas-int64"
-		lapackpkg="lapack-int64"
-	fi
-	use blas && export BLASOPT="$($(tc-getPKG_CONFIG) --libs ${blaspkg})"
-	use lapack && export BLASOPT+=" $($(tc-getPKG_CONFIG) --libs ${lapackpkg})"
-	use scalapack && export BLASOPT+=" $($(tc-getPKG_CONFIG) --libs scalapack)"
-	if use cuda; then
-		export TCE_CUDA=Y
-		export CUDA_PATH=/opt/cuda
-		export CUDA=${CUDA_PATH}/bin/nvcc
-		export CUDA_FLAGS="-arch=compute_20 -code=sm_20,compute_20"
-		export CUDA_INCLUDE="-I${CUDA_PATH}/include"
-		export CUDA_LIBS="-L${CUDA_PATH}/$(get_libdir) -lcublas -lcufft -lcudart -lcuda -lstdc++"
-	fi
-	export LARGE_FILES="TRUE"
-
-	cd src
-	if use blas && [ "$NWCHEM_TARGET" = "LINUX64" ]; then
-		if use int64; then
-			export BLAS_SIZE=8
-			export LAPACK_SIZE=8
-			export SCALAPACK_SIZE=8
-		else
-			emake \
-				DIAG=PAR \
-				FC="$(tc-getFC)" \
-				CC="$(tc-getCC)" \
-				CXX="$(tc-getCXX)" \
-				NWCHEM_TOP="${S}" \
-				clean
-			emake \
-				DIAG=PAR \
-				FC="$(tc-getFC)" \
-				CC="$(tc-getCC)" \
-				CXX="$(tc-getCXX)" \
-				NWCHEM_TOP="${S}" \
-				64_to_32
-			export BLAS_SIZE=4
-			export LAPACK_SIZE=4
-			export SCALAPACK_SIZE=4
-			export USE_64TO32=y
-		fi
-	fi
-	emake \
-		DIAG=PAR \
-		FC="$(tc-getFC)" \
-		CC="$(tc-getCC)" \
-		CXX="$(tc-getCXX)" \
-		NWCHEM_TOP="${S}" \
-		NWCHEM_EXECUTABLE="${S}/bin/${NWCHEM_TARGET}/nwchem" \
-		nwchem_config
-	emake \
-		DIAG=PAR \
-		FC="$(tc-getFC)" \
-		CC="$(tc-getCC)" \
-		CXX="$(tc-getCXX)" \
-		NWCHEM_TOP="${S}" \
-		NWCHEM_EXECUTABLE="${S}/bin/${NWCHEM_TARGET}/nwchem"
-
-	if use doc; then
-		cd "${S}"/doc
-		export VARTEXFONTS="${T}/fonts"
-		emake \
-			DIAG=PAR \
-			NWCHEM_TOP="${S}" \
-			pdf html
-	fi
-}
-
-src_install() {
-	dobin bin/${NWCHEM_TARGET}/nwchem
-
-	insinto /usr/share/NWChem/basis/
-	doins -r src/basis/libraries src/data
-	insinto /usr/share/NWChem/nwpw
-	doins -r src/nwpw/libraryps
-
-	insinto /etc
-	doins nwchemrc
-
-	use examples && \
-		insinto /usr/share/NWChem/ && \
-		doins -r examples
-
-	use nwchem-tests && \
-		insinto /usr/share/NWChem && \
-		doins -r QA/tests
-
-	use doc && \
-		insinto /usr/share/doc/"${P}" && \
-		doins -r doc/nwahtml && \
-		doins -r web
-
-}
-
-pkg_postinst() {
-	echo
-	elog "The user will need to link \$HOME/.nwchemrc to /etc/nwchemrc"
-	elog "or copy it in order to tell NWChem the right position of the"
-	elog "basis library and other necessary data."
-	echo
-}
diff --git a/sci-chemistry/openbabel-java/metadata.xml b/sci-chemistry/openbabel-java/metadata.xml
deleted file mode 100644
index 2a1736c4d..000000000
--- a/sci-chemistry/openbabel-java/metadata.xml
+++ /dev/null
@@ -1,18 +0,0 @@
-<?xml version="1.0" encoding="UTF-8"?>
-<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
-<pkgmetadata>
-	<maintainer type="project">
-		<email>sci-chemistry@gentoo.org</email>
-		<name>Gentoo Chemistry Project</name>
-	</maintainer>
-	<longdescription>
-Open Babel is a chemical toolbox designed to speak the many languages of
-chemical data. It's an open, collaborative project allowing anyone to
-search, convert, analyze, or store data from molecular modeling, chemistry,
-solid-state materials, biochemistry, or related areas. This package enables
-to access Open Babel library from Java (Scala, etc.) programs.
-</longdescription>
-	<upstream>
-		<remote-id type="sourceforge">openbabel</remote-id>
-	</upstream>
-</pkgmetadata>
diff --git a/sci-chemistry/openbabel-java/openbabel-java-9999.ebuild b/sci-chemistry/openbabel-java/openbabel-java-9999.ebuild
deleted file mode 100644
index ebc26d321..000000000
--- a/sci-chemistry/openbabel-java/openbabel-java-9999.ebuild
+++ /dev/null
@@ -1,65 +0,0 @@
-# Copyright 1999-2016 Gentoo Foundation
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=5
-
-inherit cmake-utils eutils java-pkg-2 git-r3
-
-DESCRIPTION="Java bindings for OpenBabel"
-HOMEPAGE="http://openbabel.sourceforge.net/"
-SRC_URI=""
-EGIT_REPO_URI="https://github.com/openbabel/openbabel.git"
-
-LICENSE="GPL-2"
-SLOT="0"
-KEYWORDS=""
-IUSE=""
-
-COMMON_DEP="~sci-chemistry/openbabel-${PV}"
-
-DEPEND="${COMMON_DEP}
-	>=dev-lang/swig-1.3.29
-	>=virtual/jdk-1.7"
-RDEPEND="${COMMON_DEP}
-	>=virtual/jre-1.7"
-
-CMAKE_IN_SOURCE_BUILD=1
-
-src_configure() {
-	local mycmakeargs=(
-		-DCMAKE_INSTALL_RPATH=
-		-DBINDINGS_ONLY=ON
-		-DOPTIMIZE_NATIVE=OFF
-		-DBABEL_SYSTEM_LIBRARY="${EPREFIX}"/usr/$(get_libdir)/libopenbabel.so
-		-DOB_MODULE_PATH="${EPREFIX}"/usr/$(get_libdir)/openbabel/"${PV}"
-		-DLIB_INSTALL_DIR="${S}"/$(get_libdir)
-		-DJAVA_BINDINGS=ON
-		-DJAVA_INCLUDE_PATH="${EPREFIX}"/etc/java-config-2/current-system-vm/include
-		-DJAVA_INCLUDE_PATH2="${EPREFIX}"/etc/java-config-2/current-system-vm/include/linux
-		-DJAVA_AWT_INCLUDE_PATH="${EPREFIX}"/etc/java-config-2/current-system-vm/include
-		-DJAVA_AWT_LIBRARY="${EPREFIX}"/etc/java-config-2/current-system-vm/jre/lib/"${ABI}"/libjawt.so
-		-DJAVA_JVM_LIBRARY="${EPREFIX}"/etc/java-config-2/current-system-vm/jre/lib/"${ABI}"/server/libjvm.so
-		-DRUN_SWIG=ON
-	)
-
-	cmake-utils_src_configure
-}
-
-src_compile() {
-	cmake-utils_src_make bindings_java
-}
-
-src_test() {
-	cd scripts/java || die
-	einfo "Running test: ${S}/scripts/java/OBTest.java"
-	CLASSPATH="openbabel.jar" LD_LIBRARY_PATH="${S}/$(get_libdir)" javac OBTest.java || die
-	CLASSPATH=".:openbabel.jar" LD_LIBRARY_PATH="${S}/$(get_libdir)" java OBTest || die
-}
-
-src_install() {
-	# Let cmake take care of RPATH setting and the like
-	cmake -DCOMPONENT=bindings_java -P cmake_install.cmake
-
-	java-pkg_dojar "${S}/$(get_libdir)/openbabel.jar"
-	java-pkg_doso "${S}/$(get_libdir)/libopenbabel_java.so"
-}
diff --git a/sci-chemistry/openbabel-perl/metadata.xml b/sci-chemistry/openbabel-perl/metadata.xml
deleted file mode 100644
index 3dc4c5711..000000000
--- a/sci-chemistry/openbabel-perl/metadata.xml
+++ /dev/null
@@ -1,18 +0,0 @@
-<?xml version="1.0" encoding="UTF-8"?>
-<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
-<pkgmetadata>
-	<maintainer type="project">
-		<email>sci-chemistry@gentoo.org</email>
-		<name>Gentoo Chemistry Project</name>
-	</maintainer>
-	<longdescription>
-Open Babel is a chemical toolbox designed to speak the many languages of
-chemical data. It's an open, collaborative project allowing anyone to
-search, convert, analyze, or store data from molecular modeling, chemistry,
-solid-state materials, biochemistry, or related areas.
-This package enables to access Open Babel library from Perl programs.
-</longdescription>
-	<upstream>
-		<remote-id type="sourceforge">openbabel</remote-id>
-	</upstream>
-</pkgmetadata>
diff --git a/sci-chemistry/openbabel-perl/openbabel-perl-9999.ebuild b/sci-chemistry/openbabel-perl/openbabel-perl-9999.ebuild
deleted file mode 100644
index b9eaa3570..000000000
--- a/sci-chemistry/openbabel-perl/openbabel-perl-9999.ebuild
+++ /dev/null
@@ -1,62 +0,0 @@
-# Copyright 1999-2016 Gentoo Foundation
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=5
-
-inherit cmake-utils eutils git-r3 perl-module
-
-DESCRIPTION="Perl bindings for OpenBabel"
-HOMEPAGE="http://openbabel.sourceforge.net/"
-EGIT_REPO_URI="https://github.com/openbabel/openbabel.git"
-
-LICENSE="GPL-2"
-SLOT="0"
-KEYWORDS=""
-IUSE=""
-
-RDEPEND="
-	dev-lang/perl
-	~sci-chemistry/openbabel-${PV}"
-DEPEND="${RDEPEND}
-	>=dev-util/cmake-2.4.8
-	>=dev-lang/swig-2"
-
-src_unpack() {
-	git-r3_src_unpack
-}
-
-src_configure() {
-	perl_set_version
-	local mycmakeargs=(
-		-DOPTIMIZE_NATIVE=OFF
-		-DCMAKE_INSTALL_RPATH=
-		-DBINDINGS_ONLY=ON
-		-DBABEL_SYSTEM_LIBRARY="${EPREFIX}"/usr/$(get_libdir)/libopenbabel.so
-		-DOB_MODULE_PATH="${EPREFIX}"/usr/$(get_libdir)/openbabel/${PV}
-		-DLIB_INSTALL_DIR="${ED}/${VENDOR_ARCH}"
-		-DPERL_BINDINGS=ON
-		-DRUN_SWIG=ON
-	)
-
-	cmake-utils_src_configure
-}
-
-src_compile() {
-	cmake-utils_src_compile bindings_perl
-}
-
-src_test() {
-	mkdir "${BUILD_DIR}/$(get_libdir)/Chemistry"
-	cp \
-		"${CMAKE_USE_DIR}/scripts/perl/OpenBabel.pm" \
-		"${BUILD_DIR}/$(get_libdir)/Chemistry/"
-	for i in "${CMAKE_USE_DIR}"/scripts/perl/t/*; do
-		einfo "Running test: ${i}"
-		perl -I"${BUILD_DIR}/$(get_libdir)" "${i}" || die
-	done
-}
-
-src_install() {
-	cd "${BUILD_DIR}" || die
-	cmake -DCOMPONENT=bindings_perl -P cmake_install.cmake
-}
diff --git a/sci-chemistry/openbabel-python/metadata.xml b/sci-chemistry/openbabel-python/metadata.xml
deleted file mode 100644
index 1acf891c7..000000000
--- a/sci-chemistry/openbabel-python/metadata.xml
+++ /dev/null
@@ -1,18 +0,0 @@
-<?xml version="1.0" encoding="UTF-8"?>
-<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
-<pkgmetadata>
-	<maintainer type="project">
-		<email>sci-chemistry@gentoo.org</email>
-		<name>Gentoo Chemistry Project</name>
-	</maintainer>
-	<longdescription>
-Open Babel is a chemical toolbox designed to speak the many languages of
-chemical data. It's an open, collaborative project allowing anyone to
-search, convert, analyze, or store data from molecular modeling, chemistry,
-solid-state materials, biochemistry, or related areas. This package enables
-to access Open Babel library from Python programs.
-</longdescription>
-	<upstream>
-		<remote-id type="sourceforge">openbabel</remote-id>
-	</upstream>
-</pkgmetadata>
diff --git a/sci-chemistry/openbabel-python/openbabel-python-9999.ebuild b/sci-chemistry/openbabel-python/openbabel-python-9999.ebuild
deleted file mode 100644
index 7d4ab0f8e..000000000
--- a/sci-chemistry/openbabel-python/openbabel-python-9999.ebuild
+++ /dev/null
@@ -1,83 +0,0 @@
-# Copyright 1999-2016 Gentoo Foundation
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=5
-
-PYTHON_COMPAT=( python2_7 python3_{3,4} )
-
-inherit cmake-utils eutils git-r3 multilib python-r1
-
-DESCRIPTION="Python bindings for OpenBabel (including Pybel)"
-HOMEPAGE="http://openbabel.sourceforge.net/"
-SRC_URI=""
-EGIT_REPO_URI="https://github.com/openbabel/openbabel.git"
-
-LICENSE="GPL-2"
-SLOT="0"
-KEYWORDS=""
-IUSE=""
-
-REQUIRED_USE="${PYTHON_REQUIRED_USE}"
-
-RDEPEND="${PYTHON_DEPS}
-	~sci-chemistry/openbabel-${PV}
-	sys-libs/zlib"
-DEPEND="${RDEPEND}
-	>=dev-lang/swig-2"
-
-src_prepare() {
-	cmake-utils_src_prepare
-	sed \
-		-e "s:\"\.\.\":\"${EPREFIX}/usr\":g" \
-		-i test/testbabel.py || die
-	swig -python -c++ -small -O -templatereduce -naturalvar \
-		-I"${EPREFIX}/usr/include/openbabel-2.0" \
-		-o scripts/python/openbabel-python.cpp \
-		-DHAVE_EIGEN \
-		-outdir scripts/python \
-		scripts/openbabel-python.i \
-		|| die "Regeneration of openbabel-python.cpp failed"
-}
-
-src_configure() {
-	my_impl_src_configure() {
-		local mycmakeargs=(
-			-DCMAKE_INSTALL_RPATH=
-			-DOPTIMIZE_NATIVE=OFF
-			-DBINDINGS_ONLY=ON
-			-DBABEL_SYSTEM_LIBRARY="${EPREFIX}/usr/$(get_libdir)/libopenbabel.so"
-			-DOB_MODULE_PATH="${EPREFIX}/usr/$(get_libdir)/openbabel/${PV}"
-			-DPYTHON_BINDINGS=ON
-			-DPYTHON_EXECUTABLE=${PYTHON}
-			-DCMAKE_INSTALL_PREFIX="${D}/usr"
-			-DPYTHON_INCLUDE_DIR="$(python_get_includedir)"
-			-DPYTHON_INCLUDE_PATH="$(python_get_includedir)"
-			-DPYTHON_LIBRARY="$(python_get_library_path)"
-			-DENABLE_TESTS=ON
-		)
-
-		cmake-utils_src_configure
-	}
-
-	python_foreach_impl my_impl_src_configure
-}
-
-src_compile() {
-	python_foreach_impl cmake-utils_src_make bindings_python
-}
-
-src_test() {
-	python_foreach_impl cmake-utils_src_test -R py
-}
-
-src_install() {
-	my_impl_src_install() {
-		cd "${BUILD_DIR}" || die
-
-		cmake -DCOMPONENT=bindings_python -P cmake_install.cmake
-
-		python_optimize
-	}
-
-	python_foreach_impl my_impl_src_install
-}
diff --git a/sci-chemistry/openbabel-ruby/metadata.xml b/sci-chemistry/openbabel-ruby/metadata.xml
deleted file mode 100644
index cc3c28852..000000000
--- a/sci-chemistry/openbabel-ruby/metadata.xml
+++ /dev/null
@@ -1,18 +0,0 @@
-<?xml version="1.0" encoding="UTF-8"?>
-<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
-<pkgmetadata>
-	<maintainer type="project">
-		<email>sci-chemistry@gentoo.org</email>
-		<name>Gentoo Chemistry Project</name>
-	</maintainer>
-	<longdescription>
-Open Babel is a chemical toolbox designed to speak the many languages of
-chemical data. It's an open, collaborative project allowing anyone to
-search, convert, analyze, or store data from molecular modeling, chemistry,
-solid-state materials, biochemistry, or related areas. This package enables
-to access Open Babel library from Ruby programs.
-</longdescription>
-	<upstream>
-		<remote-id type="sourceforge">openbabel</remote-id>
-	</upstream>
-</pkgmetadata>
diff --git a/sci-chemistry/openbabel-ruby/openbabel-ruby-9999.ebuild b/sci-chemistry/openbabel-ruby/openbabel-ruby-9999.ebuild
deleted file mode 100644
index fb014277b..000000000
--- a/sci-chemistry/openbabel-ruby/openbabel-ruby-9999.ebuild
+++ /dev/null
@@ -1,81 +0,0 @@
-# Copyright 1999-2016 Gentoo Foundation
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=5
-
-USE_RUBY="ruby20 ruby21"
-
-inherit cmake-utils eutils ruby-ng git-r3
-
-DESCRIPTION="Ruby bindings for OpenBabel"
-HOMEPAGE="http://openbabel.sourceforge.net/"
-SRC_URI=""
-EGIT_REPO_URI="https://github.com/openbabel/openbabel.git"
-
-LICENSE="GPL-2"
-SLOT="0"
-KEYWORDS=""
-IUSE=""
-
-DEPEND="${DEPEND}
-	~sci-chemistry/openbabel-${PV}
-	>=dev-lang/swig-1.3.29"
-RDEPEND="${RDEPEND}
-	~sci-chemistry/openbabel-${PV}"
-
-CMAKE_IN_SOURCE_BUILD=1
-
-EGIT_CHECKOUT_DIR="${WORKDIR}/all"
-
-src_unpack() {
-	all_ruby_unpack() {
-		git-r3_src_unpack
-	}
-
-	ruby-ng_src_unpack
-}
-
-all_ruby_prepare() {
-	swig -ruby -c++ -small -O -templatereduce -naturalvar -autorename \
-		-I"${EPREFIX}/usr/include/openbabel-2.0" \
-		-o scripts/ruby/openbabel-ruby.cpp \
-		-outdir scripts/ruby \
-		scripts/openbabel-ruby.i \
-		|| die "Generation of openbabel-ruby.cpp failed"
-	sed 's/void Init_OpenBabel/void Init_openbabel/' -i scripts/ruby/openbabel-ruby.cpp || die
-}
-
-each_ruby_configure() {
-	CMAKE_USE_DIR="${WORKDIR}/${environment}"
-	local mycmakeargs=(
-		-DCMAKE_INSTALL_RPATH=
-		-DBINDINGS_ONLY=ON
-		-DOPTIMIZE_NATIVE=OFF
-		-DBABEL_SYSTEM_LIBRARY="${EPREFIX}"/usr/$(get_libdir)/libopenbabel.so
-		-DOB_MODULE_PATH="${EPREFIX}"/usr/$(get_libdir)/openbabel/"${PV}"
-		-DLIB_INSTALL_DIR="${ED}"/$(ruby_rbconfig_value sitearchdir)
-		-DRUBY_BINDINGS=ON
-		-DRUBY_EXECUTABLE="${RUBY}"
-		-DRUBY_INCLUDE_DIR=$(ruby_get_hdrdir) -I$(ruby_get_hdrdir)/$(ruby_rbconfig_value sitearch)
-		-DRUBY_LIBRARY=$(ruby_get_libruby)
-	)
-
-	cmake-utils_src_configure
-}
-
-each_ruby_compile() {
-	CMAKE_USE_DIR="${WORKDIR}/${environment}"
-	cmake-utils_src_make bindings_ruby
-}
-
-each_ruby_test() {
-	for i in scripts/ruby/examples/*; do
-		einfo "Running test: ${WORKDIR}/${environment}/${i}"
-		${RUBY} -I"${WORKDIR}/${environment}/$(get_libdir)" "${i}" || die
-	done
-}
-
-each_ruby_install() {
-	CMAKE_USE_DIR="${WORKDIR}/${environment}"
-	cmake -DCOMPONENT=bindings_ruby -P cmake_install.cmake
-}
diff --git a/sci-chemistry/openbabel/metadata.xml b/sci-chemistry/openbabel/metadata.xml
deleted file mode 100644
index 1b001391d..000000000
--- a/sci-chemistry/openbabel/metadata.xml
+++ /dev/null
@@ -1,26 +0,0 @@
-<?xml version="1.0" encoding="UTF-8"?>
-<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
-<pkgmetadata>
-	<maintainer type="project">
-		<email>sci-chemistry@gentoo.org</email>
-		<name>Gentoo Chemistry Project</name>
-	</maintainer>
-	<longdescription>
-Open Babel is a chemical toolbox designed to speak the many languages of
-chemical data. It's an open, collaborative project allowing anyone to
-search, convert, analyze, or store data from molecular modeling, chemistry,
-solid-state materials, biochemistry, or related areas.
-</longdescription>
-	<use>
-		<flag name="doc">Install API dicumentation.</flag>
-		<flag name="openmp">Enable parallelization using OpenMP.</flag>
-		<flag name="java">Install Java bindings.</flag>
-		<flag name="perl">Install Perl bindings.</flag>
-		<flag name="python">Install Python bindings and PyBel.</flag>
-		<flag name="ruby">Install Ruby bindings.</flag>
-		<flag name="wxwidgets">Build Open Babel GUI.</flag>
-	</use>
-	<upstream>
-		<remote-id type="sourceforge">openbabel</remote-id>
-	</upstream>
-</pkgmetadata>
diff --git a/sci-chemistry/openbabel/openbabel-9999.ebuild b/sci-chemistry/openbabel/openbabel-9999.ebuild
deleted file mode 100644
index 84b2e6f38..000000000
--- a/sci-chemistry/openbabel/openbabel-9999.ebuild
+++ /dev/null
@@ -1,91 +0,0 @@
-# Copyright 1999-2016 Gentoo Foundation
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=5
-
-WX_GTK_VER="2.8"
-
-inherit cmake-utils eutils git-r3 wxwidgets
-
-DESCRIPTION="Interconverts file formats used in molecular modeling"
-HOMEPAGE="http://openbabel.sourceforge.net/"
-SRC_URI=""
-EGIT_REPO_URI="https://github.com/openbabel/openbabel.git"
-
-LICENSE="GPL-2"
-SLOT="0"
-KEYWORDS=""
-IUSE="doc java openmp perl python ruby test wxwidgets"
-
-RDEPEND="
-	dev-cpp/eigen:3
-	dev-libs/libxml2:2
-	!sci-chemistry/babel
-	sci-libs/inchi
-	sys-libs/zlib
-	wxwidgets? ( x11-libs/wxGTK:${WX_GTK_VER}[X] )"
-DEPEND="${RDEPEND}
-	>=dev-util/cmake-2.4.8
-	doc? ( app-doc/doxygen )"
-PDEPEND="
-	java? ( sci-chemistry/openbabel-java )
-	perl? ( sci-chemistry/openbabel-perl )
-	python? ( sci-chemistry/openbabel-python )
-	ruby? ( sci-chemistry/openbabel-ruby )"
-
-DOCS="AUTHORS NEWS README.md THANKS doc/*.inc doc/README* doc/*.mol2"
-
-pkg_setup() {
-	if use openmp; then
-		if [[ $(tc-getCC) == *gcc ]] && ! tc-has-openmp; then
-			ewarn "OpenMP is not available in your current selected gcc"
-			die "need openmp capable gcc"
-		fi
-		FORTRAN_NEED_OPENMP=1
-	fi
-}
-
-src_configure() {
-	local mycmakeargs=""
-	mycmakeargs="${mycmakeargs}
-		-DOPENBABEL_USE_SYSTEM_INCHI=ON
-		-DOPTIMIZE_NATIVE=OFF
-		$(cmake-utils_use_enable openmp OPENMP)
-		$(cmake-utils_use wxwidgets BUILD_GUI)"
-
-	cmake-utils_src_configure
-}
-
-src_test() {
-	local mycmakeargs=""
-	mycmakeargs="${mycmakeargs}
-		-DOPENBABEL_USE_SYSTEM_INCHI=ON
-		-DOPTIMIZE_NATIVE=OFF
-		-DPYTHON_EXECUTABLE=false
-		$(cmake-utils_use wxwidgets BUILD_GUI)
-		$(cmake-utils_use_enable openmp OPENMP)
-		$(cmake-utils_use_enable test TESTS)"
-
-	cmake-utils_src_configure
-	cmake-utils_src_compile
-	cmake-utils_src_test -E py
-}
-
-src_install() {
-	docinto html
-	dodoc doc/{*.html,*.png}
-	if use doc; then
-		docinto html/API
-		dodoc doc/API/html/*
-	fi
-
-	cmake-utils_src_install
-
-	# Ensure that modules are allways in openbabel/${PV}
-	pushd "${ED}/usr/$(get_libdir)/openbabel" > /dev/null || die
-	ver=$(ls -d * | grep -E '([0-9]+[.]){2}[0-9]+')
-	if [ "${ver}" != "${PV}" ] ; then
-		ln -s ${ver} ${PV} || die
-	fi
-	popd > /dev/null || die
-}
diff --git a/sci-chemistry/pales-bin/pales-bin-0_pre140717.ebuild b/sci-chemistry/pales-bin/pales-bin-0_pre140717.ebuild
index e7df0f5ed..a712364fb 100644
--- a/sci-chemistry/pales-bin/pales-bin-0_pre140717.ebuild
+++ b/sci-chemistry/pales-bin/pales-bin-0_pre140717.ebuild
@@ -1,7 +1,7 @@
-# Copyright 1999-2014 Gentoo Foundation
+# Copyright 1999-2021 Gentoo Authors
 # Distributed under the terms of the GNU General Public License v2
 
-EAPI=5
+EAPI=7
 
 DESCRIPTION="Prediction of alignment from structure"
 HOMEPAGE="http://www3.mpibpc.mpg.de/groups/zweckstetter/_links/software_pales.htm"
@@ -10,7 +10,6 @@ SRC_URI="http://www3.mpibpc.mpg.de/groups/zweckstetter/_software_files/_pales/pa
 SLOT="0"
 LICENSE="all-rights-reserved"
 KEYWORDS="~amd64 ~x86 ~amd64-linux ~x86-linux"
-IUSE=""
 
 QA_PREBUILT="opt/bin/.*"
 
diff --git a/sci-chemistry/panav/panav-0.20130730.ebuild b/sci-chemistry/panav/panav-0.20130730.ebuild
index ad98f0187..cd315c348 100644
--- a/sci-chemistry/panav/panav-0.20130730.ebuild
+++ b/sci-chemistry/panav/panav-0.20130730.ebuild
@@ -1,33 +1,32 @@
-# Copyright 1999-2015 Gentoo Foundation
+# Copyright 1999-2021 Gentoo Authors
 # Distributed under the terms of the GNU General Public License v2
 
-EAPI=5
+EAPI=7
 
 inherit java-pkg-2
 
 MY_PN="PANAV"
 
 DESCRIPTION="Probabilistic approach for validating protein NMR chemical shift assignments"
-HOMEPAGE="http://link.springer.com/article/10.1007%2Fs10858-010-9407-y/fulltext.html"
-SRC_URI="http://www.wishartlab.com/download/${MY_PN}.zip -> ${P}.zip"
+HOMEPAGE="https://link.springer.com/article/10.1007%2Fs10858-010-9407-y/fulltext.html"
+SRC_URI="https://www.wishartlab.com/download/${MY_PN}.zip -> ${P}.zip"
 
 SLOT="0"
 LICENSE="all-rights-reserved"
-KEYWORDS=""
-IUSE=""
+KEYWORDS="~amd64"
 
-RDEPEND="
-	dev-java/cos
-	>=virtual/jre-1.6:*"
+RDEPEND=">=virtual/jre-1.7:*"
 DEPEND="${RDEPEND}"
+BDEPEND="app-arch/unzip"
 
 S="${WORKDIR}"/${MY_PN}
 
-src_compile() { :; }
+src_compile() {
+	return
+}
 
 src_install() {
 	java-pkg_newjar ${MY_PN}.jar ${PN}.jar
 	java-pkg_dolauncher
-	java-pkg_regjar "${EPREFIX}"/usr/share/cos/lib/cos.jar
 	dodoc README
 }
diff --git a/sci-chemistry/pesto/metadata.xml b/sci-chemistry/pesto/metadata.xml
deleted file mode 100644
index 58a4e2600..000000000
--- a/sci-chemistry/pesto/metadata.xml
+++ /dev/null
@@ -1,11 +0,0 @@
-<?xml version="1.0" encoding="UTF-8"?>
-<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
-<pkgmetadata>
-	<maintainer type="project">
-		<email>sci-chemistry@gentoo.org</email>
-		<name>Gentoo Chemistry Project</name>
-	</maintainer>
-	<upstream>
-		<remote-id type="sourceforge">pesto</remote-id>
-	</upstream>
-</pkgmetadata>
diff --git a/sci-chemistry/pesto/pesto-9999.ebuild b/sci-chemistry/pesto/pesto-9999.ebuild
deleted file mode 100644
index 7ff4e721d..000000000
--- a/sci-chemistry/pesto/pesto-9999.ebuild
+++ /dev/null
@@ -1,37 +0,0 @@
-# Copyright 1999-2014 Gentoo Foundation
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=5
-
-PYTHON_COMPAT=( python2_7 )
-
-inherit distutils-r1 flag-o-matic fortran-2 mercurial toolchain-funcs
-
-IUSE=""
-SRC_URI=""
-EHG_REPO_URI="http://hg.code.sf.net/p/pesto/code-1"
-
-DESCRIPTION="Potential Energy Surface Tools"
-HOMEPAGE="http://sourceforge.net/projects/pesto/"
-
-LICENSE="BSD"
-SLOT="0"
-KEYWORDS=""
-
-RDEPEND="virtual/blas
-	virtual/lapack
-	dev-python/numpy[${PYTHON_USEDEP},lapack]
-	sci-libs/k3match[${PYTHON_USEDEP}]
-	sci-libs/scipy[${PYTHON_USEDEP}]"
-
-DEPEND="${RDEPEND}"
-
-DOCS=( README.txt )
-EXAMPLES=( examples )
-DISTUTILS_IN_SOURCE_BUILD=1
-
-src_configure() {
-	append-fflags "-shared -fPIC"
-	append-ldflags "-shared"
-	distutils-r1_src_configure
-}
diff --git a/sci-chemistry/polygon/Manifest b/sci-chemistry/polygon/Manifest
deleted file mode 100644
index 8d4dee088..000000000
--- a/sci-chemistry/polygon/Manifest
+++ /dev/null
@@ -1,2 +0,0 @@
-DIST pdb_2009-04-29_ord.zip 4371434 BLAKE2B 9df6b03ae04a030e5e66d268a279a746533e6954e3bc487548800d145b1ecbc3b33301483ab922011920d79e7ba982cb00ad988624e96ead9cfdefbe18f8b847 SHA512 3d1621c96f7e65197a5a7b7e655648ec957717bc38622b64f900142bac98d9b6450c8c9d128055dc9d673ae031c0a7b379a7d28ae97b22a070337b9563169287
-DIST polygon0612.tcl 124276 BLAKE2B f0cde1a81f6e57546643042196ec8940354af245fc9a857146f6631e3daa7a8263fa6fea44d6f25cf7ae83a387a829bf36c6959c46a0c6905c58ec42a339cd34 SHA512 20d5e2011d28fe38c39f92be3d2221186f43048f173eb8b3971238836b5a09ae55cb44c0aad9e9efb3206e3c8a6e0017b749ce3911455e63dd8fcdba5c7c9dfe
diff --git a/sci-chemistry/polygon/files/0612-db.patch b/sci-chemistry/polygon/files/0612-db.patch
deleted file mode 100644
index a12225f29..000000000
--- a/sci-chemistry/polygon/files/0612-db.patch
+++ /dev/null
@@ -1,11 +0,0 @@
---- polygon0612.tcl	2009-10-15 16:11:36.000000000 +0200
-+++ polygon0612.tcl.new	2009-10-23 17:59:32.723500534 +0200
-@@ -22,7 +22,7 @@
- #
- #database name
- #
--set currentFile1 pdb_2009-04-29_ord.txt
-+set currentFile1 /usr/share/polygon/pdb_2009-04-29_ord.txt
- 
- # numcol - number of columns in the database
-   set numcol 63
diff --git a/sci-chemistry/polygon/metadata.xml b/sci-chemistry/polygon/metadata.xml
deleted file mode 100644
index da36ecbfc..000000000
--- a/sci-chemistry/polygon/metadata.xml
+++ /dev/null
@@ -1,8 +0,0 @@
-<?xml version="1.0" encoding="UTF-8"?>
-<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
-<pkgmetadata>
-	<maintainer type="project">
-		<email>sci-chemistry@gentoo.org</email>
-		<name>Gentoo Chemistry Project</name>
-	</maintainer>
-</pkgmetadata>
diff --git a/sci-chemistry/polygon/polygon-0612.ebuild b/sci-chemistry/polygon/polygon-0612.ebuild
deleted file mode 100644
index e1d86c3d6..000000000
--- a/sci-chemistry/polygon/polygon-0612.ebuild
+++ /dev/null
@@ -1,42 +0,0 @@
-# Copyright 1999-2014 Gentoo Foundation
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=5
-
-inherit eutils
-
-DB="pdb_2009-04-29_ord"
-MY_P="${PN}${PV}"
-
-DESCRIPTION="shows qualitatively if some models parameters are over- or under-refined"
-HOMEPAGE="http://www-ibmc.u-strasbg.fr/arn/Site_UPR9002/Polygon/Polygon.html"
-SRC_URI="
-	http://www-ibmc.u-strasbg.fr/arn/Site_UPR9002/Polygon/${MY_P}.tcl
-	http://www-ibmc.u-strasbg.fr/arn/Site_UPR9002/Polygon/${DB}.zip
-"
-
-SLOT="0"
-LICENSE="all-rights-reserved"
-KEYWORDS="~amd64 ~x86"
-IUSE=""
-
-RDEPEND="dev-lang/tcl"
-DEPEND="app-arch/unzip"
-
-S="${WORKDIR}"
-
-src_unpack() {
-	unpack ${DB}.zip
-	cp "${DISTDIR}"/${MY_P}.tcl "${S}" || die
-}
-
-src_prepare() {
-	epatch "${FILESDIR}"/${PV}-db.patch
-}
-
-src_install() {
-	edos2unix ${MY_P}.tcl
-	newbin ${MY_P}.tcl ${PN}
-	insinto /usr/share/${PN}
-	doins ${DB}.txt
-}
diff --git a/sci-chemistry/pymol-plugins-ezviz/Manifest b/sci-chemistry/pymol-plugins-ezviz/Manifest
deleted file mode 100644
index 34dd08076..000000000
--- a/sci-chemistry/pymol-plugins-ezviz/Manifest
+++ /dev/null
@@ -1 +0,0 @@
-DIST pymol-plugins-ezviz-1.0.2005.zip 137431 BLAKE2B d9ea03e9daf5caa11f359a8a008d745652c0eeb7c942b9c3d73e1385e3394f459ec144e301a5afd6be309af078a8288b38d8fc3f4876e55ff4631266a5e8d736 SHA512 d0281e16dac76e519c725945bdaa5da233f8975411b9d39258a03206c39349014a05e52b6f8cd08b0c667e9d6a177eba2545861ee853ba43810f9ed0d4beb7a1
diff --git a/sci-chemistry/pymol-plugins-ezviz/files/gentoo.patch b/sci-chemistry/pymol-plugins-ezviz/files/gentoo.patch
deleted file mode 100644
index ba28af325..000000000
--- a/sci-chemistry/pymol-plugins-ezviz/files/gentoo.patch
+++ /dev/null
@@ -1,85 +0,0 @@
-diff --git a/ez-viz.py b/ez-viz.py
-index 1d8e847..8d50e6b 100755
---- a/ez-viz.py
-+++ b/ez-viz.py
-@@ -363,27 +363,27 @@ class PGUI:
-     global splash
-     
-     # Images used in Presets tab
--    defaultImage = PhotoImage( file="modules\pmg_tk\startup\default.gif")
--    chains = PhotoImage(file="modules\pmg_tk\startup\chains.GIF")
--    heteroImg = PhotoImage(file="modules\pmg_tk\startup\heteroAtom.GIF")
--    ballStickImg = PhotoImage(file="C:\Program Files\DeLano Scientific\PyMOL\modules\pmg_tk\startup\showBallStick.GIF")
--    surfaceImg = PhotoImage(file="modules\pmg_tk\startup\surface.GIF")
--    polarityImg = PhotoImage(file="modules\pmg_tk\startup\polarity.GIF")
--    puttyImg = PhotoImage(file="modules\pmg_tk\startup\putty.GIF")
--    aromaticsImg = PhotoImage(file="modules\pmg_tk\startup\showAromatics.GIF")
--    dnaImg = PhotoImage(file="modules\pmg_tk\startup\dna.GIF")
-+    defaultImage = PhotoImage( file="GENTOOPYMOL/pmg_tk/startup/ez-viz/default.gif")
-+    chains = PhotoImage(file="GENTOOPYMOL/pmg_tk/startup/ez-viz/chains.gif")
-+    heteroImg = PhotoImage(file="GENTOOPYMOL/pmg_tk/startup/ez-viz/heteroAtom.gif")
-+    ballStickImg = PhotoImage(file="GENTOOPYMOL/pmg_tk/startup/ez-viz/showBallStick.gif")
-+    surfaceImg = PhotoImage(file="GENTOOPYMOL/pmg_tk/startup/ez-viz/surface.gif")
-+    polarityImg = PhotoImage(file="GENTOOPYMOL/pmg_tk/startup/ez-viz/polarity.gif")
-+    puttyImg = PhotoImage(file="GENTOOPYMOL/pmg_tk/startup/ez-viz/putty.gif")
-+    aromaticsImg = PhotoImage(file="GENTOOPYMOL/pmg_tk/startup/ez-viz/showAromatics.gif")
-+    dnaImg = PhotoImage(file="GENTOOPYMOL/pmg_tk/startup/ez-viz/dna.gif")
-     
-     # Movie tab images
--    ligand = PhotoImage(file="modules\pmg_tk\startup\zoom.GIF")
--    build = PhotoImage(file="modules\pmg_tk\startup\prot.GIF")
--    chainsMovieImg = PhotoImage(file="modules\pmg_tk\startup\chainsMovie.GIF")
--    rotateImg = PhotoImage(file="modules\pmg_tk\startup\Rotate.GIF")
--    playButton = PhotoImage(file="modules\pmg_tk\startup\play.GIF")
--    stopButton = PhotoImage(file="modules\pmg_tk\startup\stop.GIF")
--    rewindButton = PhotoImage(file="modules\pmg_tk\startup\Rewind.GIF")
-+    ligand = PhotoImage(file="GENTOOPYMOL/pmg_tk/startup/ez-viz/zoom.gif")
-+    build = PhotoImage(file="GENTOOPYMOL/pmg_tk/startup/ez-viz/prot.gif")
-+    chainsMovieImg = PhotoImage(file="GENTOOPYMOL/pmg_tk/startup/ez-viz/chainsMovie.gif")
-+    rotateImg = PhotoImage(file="GENTOOPYMOL/pmg_tk/startup/ez-viz/Rotate.gif")
-+    playButton = PhotoImage(file="GENTOOPYMOL/pmg_tk/startup/ez-viz/play.gif")
-+    stopButton = PhotoImage(file="GENTOOPYMOL/pmg_tk/startup/ez-viz/stop.gif")
-+    rewindButton = PhotoImage(file="GENTOOPYMOL/pmg_tk/startup/ez-viz/Rewind.gif")
-     
-     # Welcome tab image
--    splash = PhotoImage(file="modules\pmg_tk\startup\splash.GIF")
-+    splash = PhotoImage(file="GENTOOPYMOL/pmg_tk/startup/ez-viz/splash.gif")
-     #--------------------------------------#
-     #					   #
-     #         PRESETS METHODS              #
-@@ -1035,7 +1035,7 @@ class PGUI:
- 	if tkMessageBox.askyesno('Ray Trace Image', "Do you want to ray trace you image before saving it? Depending on your image "+
- 					"this make take a few minutes if you select yes."):
- 		cmd.ray()    	
--    	file = tkFileDialog.asksaveasfilename(defaultextension=".png", initialdir="C:/Program Files/DeLano Scientific/PyMOL/")
-+    	file = tkFileDialog.asksaveasfilename(defaultextension=".png", initialdir="./")
-     	if len(file)>0:
-     		cmd.save(file)
-     	
-@@ -1045,7 +1045,7 @@ class PGUI:
-     	import tkFileDialog
-     	import tkMessageBox 
-     	
--    	file = tkFileDialog.asksaveasfilename(defaultextension=".pse", initialdir='C:/Program Files/Delano Scientific/PyMOL/')
-+    	file = tkFileDialog.asksaveasfilename(defaultextension=".pse", initialdir='./')
-     	print file
-         if len(file)>0:
-     		cmd.save(file)      
-@@ -1574,7 +1574,7 @@ class PGUI:
-     #------Open Help File---------#
-     def help(self):
-     	import webbrowser
--    	webbrowser.open('modules\pmg_tk\startup\Help\EZ-VizWebMain.html')
-+    	webbrowser.open('GENTOOPYMOL/pmg_tk/startup/ez-vizHelp\EZ-VizWebMain.html')
-     			
-     #---------------------------------------------------------------#
-     #								    #
-@@ -2188,7 +2188,7 @@ class PGUI:
-         import tkFileDialog
-     
-         if result == 'Open':
--            file=tkFileDialog.askopenfilename(initialdir='C:/Documents and Settings/Administrator/My Documents/')
-+            file=tkFileDialog.askopenfilename(initialdir='./')
-             if file:
-             	cmd.load(file)
-             	self.pdbCode = file
diff --git a/sci-chemistry/pymol-plugins-ezviz/metadata.xml b/sci-chemistry/pymol-plugins-ezviz/metadata.xml
deleted file mode 100644
index a534b14c2..000000000
--- a/sci-chemistry/pymol-plugins-ezviz/metadata.xml
+++ /dev/null
@@ -1,22 +0,0 @@
-<?xml version="1.0" encoding="UTF-8"?>
-<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
-<pkgmetadata>
-	<maintainer type="person">
-		<email>jlec@gentoo.org</email>
-	</maintainer>
-	<maintainer type="project">
-		<email>sci-chemistry@gentoo.org</email>
-		<name>Gentoo Chemistry Project</name>
-	</maintainer>
-	<longdescription>
-EZ-Viz was developed as an assistance tool for the difficult to 
-understand user interface of PyMOL. The standard interface is 
-very complex takes a long time to learn, especially for students 
-unfamiliar with the chemistry and busy researchers with little 
-time to learn the commands necessary to use the PyMOL software 
-to its full extent. EZ-Viz allows for users to navigate through 
-PyMOL using a series of clickable buttons and tabs to complete 
-all functions of the PyMol software without ever having to type 
-a single command.
-</longdescription>
-</pkgmetadata>
diff --git a/sci-chemistry/pymol-plugins-ezviz/pymol-plugins-ezviz-1.0.2005-r1.ebuild b/sci-chemistry/pymol-plugins-ezviz/pymol-plugins-ezviz-1.0.2005-r1.ebuild
deleted file mode 100644
index b51fcfe4e..000000000
--- a/sci-chemistry/pymol-plugins-ezviz/pymol-plugins-ezviz-1.0.2005-r1.ebuild
+++ /dev/null
@@ -1,55 +0,0 @@
-# Copyright 1999-2014 Gentoo Foundation
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=5
-
-PYTHON_COMPAT=( python2_7 )
-
-inherit eutils python-r1
-
-DESCRIPTION="Assistance tool for the difficult to understand user interface of PyMOL"
-HOMEPAGE="http://www.rit.edu/cos/ezviz/index.html"
-SRC_URI="http://www.rit.edu/cos/ezviz/EZ_Viz.zip -> ${P}.zip"
-
-SLOT="0"
-LICENSE="all-rights-reserved"
-KEYWORDS="~amd64 ~x86"
-IUSE="doc"
-
-REQUIRED_USE="${PYTHON_REQUIRED_USE}"
-
-RDEPEND="
-	${PYTHON_DEPS}
-	sci-chemistry/pymol[${PYTHON_USEDEP}]"
-DEPEND="app-arch/unzip"
-
-S="${WORKDIR}/EZ_Viz Folder"
-
-src_prepare() {
-	edos2unix ez-viz.py
-	epatch "${FILESDIR}"/gentoo.patch
-	for gif in *.GIF; do
-		mv ${gif} ${gif/.GIF/.gif} || die
-	done
-	python_copy_sources
-	preperation() {
-		cd "${BUILD_DIR}" || die
-		sed \
-			-e "s:GENTOOPYMOL:${EPREFIX}/$(python_get_sitedir):g" \
-			-i ez-viz.py || die
-	}
-	python_foreach_impl preperation
-}
-
-src_install() {
-	installation() {
-		cd "${BUILD_DIR}" || die
-		python_moduleinto pmg_tk/startup/
-		python_domodule *.py
-		python_moduleinto pmg_tk/startup/ez-viz/
-		python_domodule *.gif
-	}
-	python_foreach_impl installation
-	python_foreach_impl python_optimize
-	dodoc readme.txt
-}
diff --git a/sci-chemistry/pymol-plugins-psico/metadata.xml b/sci-chemistry/pymol-plugins-psico/metadata.xml
deleted file mode 100644
index 9d384241e..000000000
--- a/sci-chemistry/pymol-plugins-psico/metadata.xml
+++ /dev/null
@@ -1,14 +0,0 @@
-<?xml version="1.0" encoding="UTF-8"?>
-<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
-<pkgmetadata>
-	<maintainer type="person">
-		<email>jlec@gentoo.org</email>
-	</maintainer>
-	<maintainer type="project">
-		<email>sci-chemistry@gentoo.org</email>
-		<name>Gentoo Chemistry Project</name>
-	</maintainer>
-	<upstream>
-		<remote-id type="github">speleo3/pymol-psico</remote-id>
-	</upstream>
-</pkgmetadata>
diff --git a/sci-chemistry/pymol-plugins-psico/pymol-plugins-psico-9999.ebuild b/sci-chemistry/pymol-plugins-psico/pymol-plugins-psico-9999.ebuild
deleted file mode 100644
index 9cbfd0ace..000000000
--- a/sci-chemistry/pymol-plugins-psico/pymol-plugins-psico-9999.ebuild
+++ /dev/null
@@ -1,37 +0,0 @@
-# Copyright 1999-2015 Gentoo Foundation
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=5
-
-PYTHON_COMPAT=( python2_7 )
-
-inherit distutils-r1 git-r3
-
-DESCRIPTION="Pymol ScrIpt COllection"
-HOMEPAGE="https://github.com/speleo3/pymol-psico/"
-SRC_URI=""
-EGIT_REPO_URI="git://github.com/speleo3/pymol-psico.git"
-
-SLOT="0"
-KEYWORDS=""
-LICENSE="BSD-2"
-IUSE="minimal"
-
-RDEPEND="
-	dev-python/numpy[${PYTHON_USEDEP}]
-	sci-biology/biopython[${PYTHON_USEDEP}]
-	!minimal? (
-		media-libs/qhull
-		media-video/mplayer
-		sci-biology/stride
-		sci-chemistry/dssp
-		sci-chemistry/mm-align
-		sci-chemistry/pdbmat
-		sci-chemistry/theseus
-		sci-chemistry/tm-align
-		sci-mathematics/diagrtb
-	)"
-
-pkg_post_inst() {
-	optfeature sci-libs/mmtk "Normal modes via mmtk"
-}
diff --git a/sci-chemistry/pymol/Manifest b/sci-chemistry/pymol/Manifest
deleted file mode 100644
index a20983695..000000000
--- a/sci-chemistry/pymol/Manifest
+++ /dev/null
@@ -1 +0,0 @@
-DIST pymol-1.7.0.0.png.xz 5392 BLAKE2B b61a625231c050f3244c5f1b6bd662531f67a45de82a5f4408b09de84a5548f79e3cdbd49d833970b88fe4caef46f341227f8366ffcfcfec2a17c948ed90e7ab SHA512 24bb1584b28688f5d5824e938f8500ca9887838adf490b4284c52f8c0da4c5ec4a56051ee80f48e4f34541ab53f9a4e00c849c382f1fd37c232fbea12d700105
diff --git a/sci-chemistry/pymol/metadata.xml b/sci-chemistry/pymol/metadata.xml
deleted file mode 100644
index d36c262f4..000000000
--- a/sci-chemistry/pymol/metadata.xml
+++ /dev/null
@@ -1,14 +0,0 @@
-<?xml version="1.0" encoding="UTF-8"?>
-<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
-<pkgmetadata>
-	<maintainer type="person">
-		<email>jlec@gentoo.org</email>
-	</maintainer>
-	<maintainer type="project">
-		<email>sci-chemistry@gentoo.org</email>
-		<name>Gentoo Chemistry Project</name>
-	</maintainer>
-	<use>
-		<flag name="web">Install Pymodule needed for web app support</flag>
-	</use>
-</pkgmetadata>
diff --git a/sci-chemistry/pymol/pymol-9999.ebuild b/sci-chemistry/pymol/pymol-9999.ebuild
deleted file mode 100644
index 5a8e51c63..000000000
--- a/sci-chemistry/pymol/pymol-9999.ebuild
+++ /dev/null
@@ -1,113 +0,0 @@
-# Copyright 1999-2015 Gentoo Foundation
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=5
-
-PYTHON_COMPAT=( python2_7 )
-PYTHON_REQ_USE="tk"
-
-inherit distutils-r1 eutils fdo-mime flag-o-matic subversion versionator
-
-DESCRIPTION="A Python-extensible molecular graphics system"
-HOMEPAGE="http://www.pymol.org/"
-SRC_URI="http://dev.gentoo.org/~jlec/distfiles/${PN}-1.7.0.0.png.xz"
-ESVN_REPO_URI="svn://svn.code.sf.net/p/pymol/code/trunk/pymol"
-
-LICENSE="PSF-2.2"
-SLOT="0"
-KEYWORDS=""
-IUSE="web"
-
-DEPEND="
-	dev-python/numpy[${PYTHON_USEDEP}]
-	dev-python/pyopengl[${PYTHON_USEDEP}]
-	media-libs/freeglut
-	media-libs/freetype:2
-	media-libs/glew:0=
-	media-libs/libpng:0=
-	media-video/mpeg-tools
-	sys-libs/zlib
-	virtual/python-pmw[${PYTHON_USEDEP}]
-	!sci-chemistry/pymol-apbs-plugin[${PYTHON_USEDEP}]
-	web? ( !dev-python/webpy[${PYTHON_USEDEP}] )"
-RDEPEND="${DEPEND}"
-
-src_unpack() {
-	unpack ${A}
-	subversion_src_unpack
-}
-
-python_prepare_all() {
-	sed \
-		-e "s:\"/usr:\"${EPREFIX}/usr:g" \
-		-e "/ext_comp_args.*+=/s:\[.*\]$:\[\]:g" \
-		-e "/import/s:argparse:argparseX:g" \
-		-i setup.py || die
-
-	sed \
-		-e "s:/opt/local:${EPREFIX}/usr:g" \
-		-e '/ext_comp_args/s:\[.*\]:[]:g' \
-		-i setup.py || die
-
-	append-cxxflags -std=c++0x
-
-	distutils-r1_python_prepare_all
-}
-
-src_prepare() {
-	subversion_src_prepare
-	distutils-r1_src_prepare
-}
-
-python_install() {
-	distutils-r1_python_install --pymol-path="${EPREFIX}/usr/share/pymol"
-
-	sed \
-		-e '1d' \
-		-e "/APBS_BINARY_LOCATION/s:None:\"${EPREFIX}/usr/bin/apbs\":g" \
-		-e "/APBS_PSIZE_LOCATION/s:None:\"$(python_get_sitedir)/pdb2pqr/src/\":g" \
-		-e "/APBS_PDB2PQR_LOCATION/s:None:\"$(python_get_sitedir)/pdb2pqr/\":g" \
-		-i "${D}/$(python_get_sitedir)"/pmg_tk/startup/apbs_tools.py || die
-}
-
-python_install_all() {
-	distutils-r1_python_install_all
-
-	sed \
-		-e '1i#!/usr/bin/env python' \
-		"${D}/$(python_get_sitedir)"/pymol/__init__.py > "${T}"/${PN} || die
-
-	python_foreach_impl python_doscript "${T}"/${PN}
-
-	# These environment variables should not go in the wrapper script, or else
-	# it will be impossible to use the PyMOL libraries from Python.
-	cat >> "${T}"/20pymol <<- EOF
-		PYMOL_PATH="${EPREFIX}/usr/share/pymol"
-		PYMOL_DATA="${EPREFIX}/usr/share/pymol/data"
-		PYMOL_SCRIPTS="${EPREFIX}/usr/share/pymol/scripts"
-	EOF
-
-	doenvd "${T}"/20pymol
-
-	newicon "${WORKDIR}"/${PN}-1.7.0.0.png ${PN}.png
-	make_desktop_entry ${PN} PyMol ${PN} \
-		"Graphics;Education;Science;Chemistry;" \
-		"MimeType=chemical/x-pdb;chemical/x-mdl-molfile;chemical/x-mol2;chemical/seq-aa-fasta;chemical/seq-na-fasta;chemical/x-xyz;chemical/x-mdl-sdf;"
-
-	if ! use web; then
-		rm -rf "${D}/$(python_get_sitedir)/web" || die
-	fi
-
-	rm -f "${ED}"/usr/share/${PN}/LICENSE || die
-}
-
-pkg_postinst() {
-	fdo-mime_desktop_database_update
-	fdo-mime_mime_database_update
-	optfeature "Electrostatic calculations" sci-chemistry/apbs sci-chemistry/pdb2pqr
-}
-
-pkg_postrm() {
-	fdo-mime_desktop_database_update
-	fdo-mime_mime_database_update
-}
diff --git a/sci-chemistry/pyquante/Manifest b/sci-chemistry/pyquante/Manifest
deleted file mode 100644
index bb2f3bb8b..000000000
--- a/sci-chemistry/pyquante/Manifest
+++ /dev/null
@@ -1,2 +0,0 @@
-DIST PyQuante-1.6.3.tar.gz 329029 BLAKE2B ddad13666d2489d9e666fc42e3ec939f6d7b19177b24c152fb778e34e2b2b0e26f2a4dfaf0a7561195115ad0ce88c1e3ddcd060f4d0a599333bc6b073df60305 SHA512 7442fd1a25bf10db81f86d6811a3e57c38a3c5a6ac26764663e25028b45a1a3ae5da896a5219e467265d7128829386e2295fccf470018c45dc70b8a20d592fbf
-DIST PyQuante-1.6.4.tar.gz 883872 BLAKE2B bacd0c29e092167826ae31eae44369d95eaea32a03bfe09176ca89890a7a77bd665a3f9781343fca1292088df97365d4b10d41d05cd61fa28f35a16d1f7f4dee SHA512 57a4f236c9682d03d855d9dece0666daa7fdd66994b07906564bace62965c9ecb3bc4a6bb067b928f9f35cff651ed7e1da881e4b21e058922921c47005192189
diff --git a/sci-chemistry/pyquante/metadata.xml b/sci-chemistry/pyquante/metadata.xml
deleted file mode 100644
index 9f3ad9572..000000000
--- a/sci-chemistry/pyquante/metadata.xml
+++ /dev/null
@@ -1,11 +0,0 @@
-<?xml version="1.0" encoding="UTF-8"?>
-<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
-<pkgmetadata>
-	<maintainer type="project">
-		<email>sci-chemistry@gentoo.org</email>
-		<name>Gentoo Chemistry Project</name>
-	</maintainer>
-	<upstream>
-		<remote-id type="sourceforge">pyquante</remote-id>
-	</upstream>
-</pkgmetadata>
diff --git a/sci-chemistry/pyquante/pyquante-1.6.3-r1.ebuild b/sci-chemistry/pyquante/pyquante-1.6.3-r1.ebuild
deleted file mode 100644
index bf9928ef7..000000000
--- a/sci-chemistry/pyquante/pyquante-1.6.3-r1.ebuild
+++ /dev/null
@@ -1,22 +0,0 @@
-# Copyright 1999-2014 Gentoo Foundation
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=5
-
-PYTHON_COMPAT=( python2_7 )
-
-inherit distutils-r1
-
-MY_PN="PyQuante"
-MY_P="${MY_PN}-${PV}"
-
-DESCRIPTION="Quantum chemistry package written in Python"
-HOMEPAGE="http://pyquante.sourceforge.net/"
-SRC_URI="mirror://sourceforge/${PN}/${MY_P}.tar.gz"
-
-SLOT="0"
-LICENSE="GPL-2"
-KEYWORDS="~amd64 ~x86"
-IUSE=""
-
-S="${WORKDIR}/${MY_P}"
diff --git a/sci-chemistry/pyquante/pyquante-1.6.4.ebuild b/sci-chemistry/pyquante/pyquante-1.6.4.ebuild
deleted file mode 100644
index bf9928ef7..000000000
--- a/sci-chemistry/pyquante/pyquante-1.6.4.ebuild
+++ /dev/null
@@ -1,22 +0,0 @@
-# Copyright 1999-2014 Gentoo Foundation
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=5
-
-PYTHON_COMPAT=( python2_7 )
-
-inherit distutils-r1
-
-MY_PN="PyQuante"
-MY_P="${MY_PN}-${PV}"
-
-DESCRIPTION="Quantum chemistry package written in Python"
-HOMEPAGE="http://pyquante.sourceforge.net/"
-SRC_URI="mirror://sourceforge/${PN}/${MY_P}.tar.gz"
-
-SLOT="0"
-LICENSE="GPL-2"
-KEYWORDS="~amd64 ~x86"
-IUSE=""
-
-S="${WORKDIR}/${MY_P}"
diff --git a/sci-chemistry/relion/Manifest b/sci-chemistry/relion/Manifest
new file mode 100644
index 000000000..75b932e28
--- /dev/null
+++ b/sci-chemistry/relion/Manifest
@@ -0,0 +1,2 @@
+DIST class_ranker_0.1.3_torch_1.0.1.pt.tar.gz 2190018 BLAKE2B 157d380693cb97f2f94aea5ee8b1c9b64c50cead45c65d8d95584b12a4901622df025e4bdfccfc9c87286a3d442ffc26ed2a89953b9361f59d7ae2852fcc3a6b SHA512 0e9d4046a9ba211c07abcc44d0b51c7d69805eb946ed96abdd1663760906188050d476268214b4e7a84f529f51226c39f40c3b418373437fae2f4bb24990f338
+DIST relion-4.0.0.tar.gz 3342593 BLAKE2B d2293531cdf3c5779a8f6beb5bc753931388f1c577faa89a927c6ccd72436db0d9a84fbe08b836601b466bc23e9df6500f9e87da1630adecd2b0cf0e245d63e6 SHA512 1e873868bc54a13a7cca74c4a623f5f2aeeec7bd2df04f74d0421127a9c9a3b40a56ebc5b04a9f4138cca1208417b05a30c38ae78106d53b92deeadbeeaf4209
diff --git a/sci-chemistry/relion/files/relion-4.0.0-build.patch b/sci-chemistry/relion/files/relion-4.0.0-build.patch
new file mode 100644
index 000000000..d7cb7bf2e
--- /dev/null
+++ b/sci-chemistry/relion/files/relion-4.0.0-build.patch
@@ -0,0 +1,39 @@
+From 138b9c71b41a3c8782c991053a28bfe074bffdd9 Mon Sep 17 00:00:00 2001
+From: Takanori Nakane <nakane.t@gmail.com>
+Date: Fri, 28 Oct 2022 19:51:29 +0900
+Subject: [PATCH] Repaired the build failure reported in #826 (by
+ @prehensilecode and @acaprez)
+
+---
+ src/apps/CMakeLists.txt | 16 ++++++++--------
+ 1 file changed, 8 insertions(+), 8 deletions(-)
+
+diff --git a/src/apps/CMakeLists.txt b/src/apps/CMakeLists.txt
+index 9870b735..30985aa7 100644
+--- a/src/apps/CMakeLists.txt
++++ b/src/apps/CMakeLists.txt
+@@ -273,16 +273,16 @@ if (CUDA_FOUND)
+ 
+ 
+ 
+-	file(GLOB REL_JAZ_CUDA_SRC "${CMAKE_SOURCE_DIR}/src/jaz/cuda/*.cu" "${CMAKE_SOURCE_DIR}/src/jaz/cuda/kernels/*.cu" )
++	file(GLOB REL_JAZ_CUDA_SRC "${CMAKE_SOURCE_DIR}/src/jaz/cuda/*.cu")
+ 	cuda_add_library(relion_jaz_gpu_util ${REL_JAZ_CUDA_SRC})
+ 
+-	#list(APPEND EXTRA_LIBS "${CUDA_CUFFT_LIBRARIES}")
+-	#if(BUILD_SHARED_LIBS)
+-	#	install (TARGETS relion_jaz_gpu_util LIBRARY DESTINATION lib)
+-	#else()
+-	#	target_link_libraries(relion_jaz_gpu_util relion_lib)
+-	#	target_link_libraries(relion_jaz_gpu_util ${CUDA_CUFFT_LIBRARIES})
+-	#endif()
++	list(APPEND EXTRA_LIBS "${CUDA_CUFFT_LIBRARIES}")
++	if(BUILD_SHARED_LIBS)
++		install (TARGETS relion_jaz_gpu_util LIBRARY DESTINATION lib)
++	else()
++		target_link_libraries(relion_jaz_gpu_util relion_lib)
++		target_link_libraries(relion_jaz_gpu_util ${CUDA_CUFFT_LIBRARIES})
++	endif()
+ 
+ 	target_link_libraries(relion_lib relion_jaz_gpu_util ${CUDA_CUFFT_LIBRARIES})
+ 	target_link_libraries(relion_lib relion_jaz_gpu_util ${CUDA_CUFFT_LIBRARIES} ${CUDA_curand_LIBRARY})
diff --git a/sci-chemistry/relion/metadata.xml b/sci-chemistry/relion/metadata.xml
new file mode 100644
index 000000000..101a056b9
--- /dev/null
+++ b/sci-chemistry/relion/metadata.xml
@@ -0,0 +1,19 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
+<pkgmetadata>
+	<maintainer type="project">
+		<email>sci-chemistry@gentoo.org</email>
+		<name>Gentoo Chemistry Project</name>
+	</maintainer>
+	<maintainer type="person">
+		<email>alexxy@gentoo.org</email>
+		<name>Alexey Shvetsov</name>
+	</maintainer>
+	<use>
+		<flag name="gui">Enable relion gui</flag>
+		<flag name="cuda">Enable CUDA support</flag>
+	</use>
+	<upstream>
+		<remote-id type="github">3dem/relion</remote-id>
+	</upstream>
+</pkgmetadata>
diff --git a/sci-chemistry/relion/relion-4.0.0.ebuild b/sci-chemistry/relion/relion-4.0.0.ebuild
new file mode 100644
index 000000000..c6d7d90db
--- /dev/null
+++ b/sci-chemistry/relion/relion-4.0.0.ebuild
@@ -0,0 +1,71 @@
+# Copyright 2019-2021 Gentoo Authors
+# Distributed under the terms of the GNU General Public License v2
+
+EAPI=8
+
+inherit cmake
+
+DESCRIPTION="Image-processing software for cryo-electron microscopy"
+HOMEPAGE="https://www3.mrc-lmb.cam.ac.uk/relion/index.php/Main_Page"
+
+if [[ ${PV} = *9999* ]]; then
+	EGIT_REPO_URI="https://github.com/3dem/relion.git"
+	[[ ${PV} = 9999 ]] && EGIT_BRANCH="master" || EGIT_BRANCH="ver${PV:0:4}"
+	inherit git-r3
+	SRC_URI="ftp://ftp.mrc-lmb.cam.ac.uk/pub/dari/class_ranker_0.1.3_torch_1.0.1.pt.tar.gz"
+else
+	SRC_URI="
+	https://github.com/3dem/relion/archive/${PV}.tar.gz -> ${P}.tar.gz
+	ftp://ftp.mrc-lmb.cam.ac.uk/pub/dari/class_ranker_0.1.3_torch_1.0.1.pt.tar.gz
+	"
+	KEYWORDS="~amd64"
+fi
+
+LICENSE="GPL-2"
+SLOT="0"
+IUSE="+gui cuda"
+
+DEPEND="
+	gui? ( x11-libs/fltk )
+	cuda? ( dev-util/nvidia-cuda-toolkit )
+	dev-cpp/tbb
+	sci-libs/fftw:3.0
+	media-libs/tiff
+	virtual/mpi
+"
+RDEPEND="
+	${DEPEND}
+	sci-chemistry/ctffind
+"
+BDEPEND="${DEPEND}"
+
+PATCHES=( "${FILESDIR}/${PN}-4.0.0-build.patch" )
+
+src_unpack() {
+	git-r3_src_unpack
+	default
+}
+
+src_prepare() {
+	cmake_src_prepare
+	mkdir -p "${S}/external/torch_models/"
+	cp "${DISTDIR}/class_ranker_0.1.3_torch_1.0.1.pt.tar.gz" "${S}/external/torch_models/"
+	mkdir -p "${S}/external/torch_models/class_ranker/"
+	cp "${WORKDIR}/class_ranker_0.1.3_torch_1.0.1.pt" "${S}/external/torch_models/class_ranker/"
+	sed -e "s:{CMAKE_INSTALL_PREFIX}/lib:{CMAKE_INSTALL_PREFIX}/$(get_libdir):g" -i CMakeLists.txt || die
+	sed -e "s:LIBRARY DESTINATION lib:LIBRARY DESTINATION $(get_libdir):g" -i src/apps/CMakeLists.txt || die
+}
+
+src_configure() {
+	CMAKE_BUILD_TYPE=Release
+	mycmakeargs=(
+		-DBUILD_SHARED_LIBS=ON
+		-DALTCPU=$(usex !cuda)
+		-DFORCE_OWN_FFTW=OFF
+		-DFORCE_OWN_FLTK=OFF
+		-DFORCE_OWN_TBB=OFF
+		-DCUDA=$(usex cuda)
+		-DGUI=$(usex gui)
+	)
+	cmake_src_configure
+}
diff --git a/sci-chemistry/relion/relion-9999.ebuild b/sci-chemistry/relion/relion-9999.ebuild
new file mode 100644
index 000000000..12e09d2fe
--- /dev/null
+++ b/sci-chemistry/relion/relion-9999.ebuild
@@ -0,0 +1,69 @@
+# Copyright 2019-2021 Gentoo Authors
+# Distributed under the terms of the GNU General Public License v2
+
+EAPI=8
+
+inherit cmake
+
+DESCRIPTION="Image-processing software for cryo-electron microscopy"
+HOMEPAGE="https://www3.mrc-lmb.cam.ac.uk/relion/index.php/Main_Page"
+
+if [[ ${PV} = *9999* ]]; then
+	EGIT_REPO_URI="https://github.com/3dem/relion.git"
+	[[ ${PV} = 9999 ]] && EGIT_BRANCH="master" || EGIT_BRANCH="ver${PV:0:4}"
+	inherit git-r3
+	SRC_URI="ftp://ftp.mrc-lmb.cam.ac.uk/pub/dari/class_ranker_0.1.3_torch_1.0.1.pt.tar.gz"
+else
+	SRC_URI="
+	https://github.com/3dem/relion/archive/${PV}.tar.gz -> ${P}.tar.gz
+	ftp://ftp.mrc-lmb.cam.ac.uk/pub/dari/class_ranker_0.1.3_torch_1.0.1.pt.tar.gz
+	"
+	KEYWORDS="~amd64"
+fi
+
+LICENSE="GPL-2"
+SLOT="0"
+IUSE="+gui cuda"
+
+DEPEND="
+	gui? ( x11-libs/fltk )
+	cuda? ( dev-util/nvidia-cuda-toolkit )
+	dev-cpp/tbb
+	sci-libs/fftw:3.0
+	media-libs/tiff
+	virtual/mpi
+"
+RDEPEND="
+	${DEPEND}
+	sci-chemistry/ctffind
+"
+BDEPEND="${DEPEND}"
+
+src_unpack() {
+	git-r3_src_unpack
+	default
+}
+
+src_prepare() {
+	cmake_src_prepare
+	mkdir -p "${S}/external/torch_models/"
+	cp "${DISTDIR}/class_ranker_0.1.3_torch_1.0.1.pt.tar.gz" "${S}/external/torch_models/"
+	mkdir -p "${S}/external/torch_models/class_ranker/"
+	cp "${WORKDIR}/class_ranker_0.1.3_torch_1.0.1.pt" "${S}/external/torch_models/class_ranker/"
+	sed -e "s:{CMAKE_INSTALL_PREFIX}/lib:{CMAKE_INSTALL_PREFIX}/$(get_libdir):g" -i CMakeLists.txt || die
+	sed -e "s:LIBRARY DESTINATION lib:LIBRARY DESTINATION $(get_libdir):g" -i src/apps/CMakeLists.txt || die
+}
+
+src_configure() {
+	CMAKE_BUILD_TYPE=Release
+	mycmakeargs=(
+		-DBUILD_SHARED_LIBS=ON
+		-DALTCPU=$(usex !cuda)
+		-DFORCE_OWN_FFTW=OFF
+		-DFORCE_OWN_FLTK=OFF
+		-DFORCE_OWN_TBB=OFF
+		-DCUDA=$(usex cuda)
+		-DGUI=$(usex gui)
+	)
+	cmake_src_configure
+}
diff --git a/sci-chemistry/rosetta-tools/Manifest b/sci-chemistry/rosetta-tools/Manifest
deleted file mode 100644
index 912e8c895..000000000
--- a/sci-chemistry/rosetta-tools/Manifest
+++ /dev/null
@@ -1 +0,0 @@
-DIST BioTools-3.0.tgz 41121 SHA256 363689571fd131ba0e9b4fdbe239868c3a78b7104270f5b2d0285b0f96af4f9c
diff --git a/sci-chemistry/rosetta-tools/metadata.xml b/sci-chemistry/rosetta-tools/metadata.xml
deleted file mode 100644
index a5629e344..000000000
--- a/sci-chemistry/rosetta-tools/metadata.xml
+++ /dev/null
@@ -1,11 +0,0 @@
-<?xml version="1.0" encoding="UTF-8"?>
-<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
-<pkgmetadata>
-	<maintainer type="project">
-		<email>sci-chemistry@gentoo.org</email>
-		<name>Gentoo Chemistry Project</name>
-	</maintainer>
-	<upstream>
-		<remote-id type="sourceforge">dylans-biotools</remote-id>
-	</upstream>
-</pkgmetadata>
diff --git a/sci-chemistry/rosetta-tools/rosetta-tools-3.0.ebuild b/sci-chemistry/rosetta-tools/rosetta-tools-3.0.ebuild
deleted file mode 100644
index b28d0ace9..000000000
--- a/sci-chemistry/rosetta-tools/rosetta-tools-3.0.ebuild
+++ /dev/null
@@ -1,30 +0,0 @@
-# Copyright 1999-2014 Gentoo Foundation
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=5
-
-MY_PN="BioTools"
-MY_P="${MY_PN}-${PV}"
-
-DESCRIPTION="Additional scripts for rosetta"
-HOMEPAGE="http://www.rosettacommons.org/ http://dylans-biotools.sourceforge.net/"
-SRC_URI="${MY_P}.tgz"
-
-LICENSE="BSD"
-SLOT="0"
-KEYWORDS="~amd64 ~x86"
-IUSE=""
-
-DEPEND=""
-RDEPEND="dev-lang/perl"
-
-RESTRICT="fetch"
-
-S="${WORKDIR}/${MY_PN}"
-
-src_install() {
-	local x
-	for x in $(ls *.pl); do
-		newbin ${x} ${x%.pl}
-	done
-}
diff --git a/sci-chemistry/rosetta/Manifest b/sci-chemistry/rosetta/Manifest
deleted file mode 100644
index cf6a0a086..000000000
--- a/sci-chemistry/rosetta/Manifest
+++ /dev/null
@@ -1,2 +0,0 @@
-DIST patch_rosetta3.4_to_CSROSETTA3_ver1.3.txt 1187168 SHA256 071b11f6934ed308fa1f4594ee5500353d72b951c5d795fcbf4792d96e3f53c3 SHA512 7f59e0c41ad3f0a044d23bd3a4e877910aaec8a70478e1ffdf8474d77b0f4a7a5b39ca217180f888d69d1fbd5879dba80ff23b9dba4bc2fb7017a00a344916bf WHIRLPOOL 4bf39a527476e670f7459b4a03394ac800d204e45ddd7eca6d52cb36f04217b5e0ba3374a5166a55c6142939c82bd3b42055b40a320274c73bcead6e0ec120f0
-DIST rosetta3.4_source.tgz 89734375 SHA256 5ad2d06f7e4e08ef7e87c91bfe7c6d5687601f609892203c75b1abe465954e19 SHA512 d887e3660a8baecc91609463e5d64a86a48c76c72394b211cc388bf6eb49d5696a531eb1cfe19342c3bf9d399b49f1b0fb0a9682a0e166ab6594acc050a5f31e WHIRLPOOL f28706d46335da74934a4339c24c71b084fc8b2a2a2177f16a959ee2b9ea23710598b41c136ba4e18699ae7ddacb327f02a58620782554777651d50281e97fd2
diff --git a/sci-chemistry/rosetta/files/rosetta-3.4-boinc.patch b/sci-chemistry/rosetta/files/rosetta-3.4-boinc.patch
deleted file mode 100644
index 1f6da965c..000000000
--- a/sci-chemistry/rosetta/files/rosetta-3.4-boinc.patch
+++ /dev/null
@@ -1,53 +0,0 @@
---- src/protocols/boinc/boinc_shmem.hh	2009-02-03 22:47:07.000000000 +0100
-+++ src/protocols/boinc/boinc_shmem.hh.new	2009-04-09 14:59:15.000000000 +0200
-@@ -18,7 +18,7 @@
- #include <core/types.hh>
- 
- #ifdef BOINC
--#include "boinc_api.h"
-+#include "boinc/boinc_api.h"
- #endif
- 
- namespace protocols {
---- src/protocols/boinc/boinc.hh	2009-02-03 22:47:07.000000000 +0100
-+++ src/protocols/boinc/boinc.hh.new	2009-04-09 15:00:57.000000000 +0200
-@@ -20,11 +20,11 @@
- #include <boinc_win.h>
- #include <str_util.h>
- #endif
--#include <boinc_api.h>
--#include <diagnostics.h>
--#include <error_numbers.h>
-+#include <boinc/boinc_api.h>
-+#include <boinc/diagnostics.h>
-+#include <boinc/error_numbers.h>
- #ifdef BOINC_GRAPHICS
--#include <graphics2.h>
--#include <util.h>
--#include <shmem.h>
-+#include <boinc/graphics2.h>
-+#include <boinc/util.h>
-+#include <boinc/shmem.h>
- 
---- src/utility/exit.cc	2009-02-03 22:47:28.000000000 +0100
-+++ src/utility/exit.cc.new	2009-04-09 16:23:18.000000000 +0200
-@@ -23,7 +23,7 @@
- // Boinc headers
- #ifdef BOINC
- #include <utility/io/izstream.hh>
--#include <boinc_api.h>
-+#include <boinc/boinc_api.h>
- #include <string>
- #endif
- 
---- src/utility/boinc/boinc_util.cc	2009-02-03 22:47:30.000000000 +0100
-+++ src/utility/boinc/boinc_util.cc.new	2009-04-09 16:25:16.000000000 +0200
-@@ -20,7 +20,7 @@
- //#ifdef _WIN32
- //#include <boinc_win.h>
- //#endif
--#include <boinc_api.h>
-+#include <boinc/boinc_api.h>
- 
- // C++ headers
- #include <iostream>
diff --git a/sci-chemistry/rosetta/files/rosetta-3.4-boost.patch b/sci-chemistry/rosetta/files/rosetta-3.4-boost.patch
deleted file mode 100644
index 7c1e1ffc2..000000000
--- a/sci-chemistry/rosetta/files/rosetta-3.4-boost.patch
+++ /dev/null
@@ -1,16 +0,0 @@
- tools/build/basic.settings | 2 +-
- 1 file changed, 1 insertion(+), 1 deletion(-)
-
-diff --git a/tools/build/basic.settings b/tools/build/basic.settings
-index ecf3237..356cd61 100644
---- a/tools/build/basic.settings
-+++ b/tools/build/basic.settings
-@@ -610,7 +610,7 @@ settings = {
-     "gcc, boost_thread" : {
-         "appends" : {
-             "defines" : [ "MULTI_THREADED" ],
--            "libraries"     : [ "pthread", "boost_thread" ],
-+            "libraries"     : [ "pthread", "boost_thread", "boost_system" ],
- 	    "library_path"  : [ "/usr/local/lib", "/opt/boost/lib" ],
-             "flags"         : {
-                 "compile"   : [ "pthread" ],
diff --git a/sci-chemistry/rosetta/files/rosetta-3.4-boost157.patch b/sci-chemistry/rosetta/files/rosetta-3.4-boost157.patch
deleted file mode 100644
index c2d7594b6..000000000
--- a/sci-chemistry/rosetta/files/rosetta-3.4-boost157.patch
+++ /dev/null
@@ -1,16 +0,0 @@
- src/protocols/moves/StructureRestrictor.cc | 2 +-
- 1 file changed, 1 insertion(+), 1 deletion(-)
-
-diff --git a/src/protocols/moves/StructureRestrictor.cc b/src/protocols/moves/StructureRestrictor.cc
-index 1e1f1d4..da69796 100644
---- a/src/protocols/moves/StructureRestrictor.cc
-+++ b/src/protocols/moves/StructureRestrictor.cc
-@@ -40,7 +40,7 @@
- 
- using namespace std;
- using namespace boost;
--using namespace core;
-+using namespace boost::core;
-   using namespace pose;
-   using namespace protocols::jd2;
- 
diff --git a/sci-chemistry/rosetta/files/rosetta-3.4-fix-scons-warnings.patch b/sci-chemistry/rosetta/files/rosetta-3.4-fix-scons-warnings.patch
deleted file mode 100644
index 321d0a784..000000000
--- a/sci-chemistry/rosetta/files/rosetta-3.4-fix-scons-warnings.patch
+++ /dev/null
@@ -1,82 +0,0 @@
---- src/SConscript.src	2009-02-03 22:44:31.000000000 +0100
-+++ src/SConscript.src.new	2009-04-07 16:25:30.000000000 +0200
-@@ -85,7 +85,7 @@
- 
- # Transform the modified settings into SCons Environment variables.
- # Gives priority to project settings over global settings.
--env = build.environment.Copy()
-+env = build.environment.Clone()
- env.Prepend(**actual.symbols())
- 
- 
---- tools/build/setup.py	2009-02-03 22:44:32.000000000 +0100
-+++ tools/build/setup.py.new	2009-04-07 16:43:42.000000000 +0200
-@@ -42,21 +42,21 @@
-     # Read in the options from the .settings files (1st pass)
-     # This has to be done in two passes, because some legal values
-     # (version numbers) are dependent on the other values
--    options.AddOptions(
-+    options.AddVariables(
-         # Options for the build.  Modifiable on the command-line.
--        EnumOption("cxx", "Select the C++ compiler to build with",
-+        EnumVariable("cxx", "Select the C++ compiler to build with",
-                    defaults.cxx, supported.cxx),
--        EnumOption("os", "Select the operating system to build for",
-+        EnumVariable("os", "Select the operating system to build for",
-                    defaults.os, supported.os),
--        EnumOption("arch", "Select the processor architecture to build for",
-+        EnumVariable("arch", "Select the processor architecture to build for",
-                    defaults.arch, supported.arch),
--        EnumOption("mode", "Select the optimization mode",
-+        EnumVariable("mode", "Select the optimization mode",
-                    defaults.mode, supported.mode),
--        ListOption("cat", "Select the build category",
-+        ListVariable("cat", "Select the build category",
-                    defaults.cat, supported.cat),
--        ListOption("extras", "Select any extras",
-+        ListVariable("extras", "Select any extras",
-                    defaults.extras, supported.extras),
--        ListOption("log", "Log debugging output",
-+        ListVariable("log", "Log debugging output",
-                    defaults.log, supported.log),
-     )
- 
---- tools/build/setup.py	2009-04-07 16:44:26.000000000 +0200
-+++ tools/build/setup.py.new	2009-04-07 16:46:45.000000000 +0200
-@@ -37,7 +37,7 @@
- 
-     # Incorporate options in site and user options
-     option_files = [ "%s.options" % (name) for name in ("site", "user") ]
--    options = Options(option_files)
-+    options = Variables(option_files)
- 
-     # Read in the options from the .settings files (1st pass)
-     # This has to be done in two passes, because some legal values
-@@ -68,12 +68,12 @@
-     cxx  = env["cxx"]
-     os   = env["os"]
-     arch = env["arch"]
--    options.AddOptions(
--        EnumOption("cxx_ver", "Select the C++ compiler version",
-+    options.AddVariables(
-+        EnumVariable("cxx_ver", "Select the C++ compiler version",
-                    defaults.cxx_ver, supported.cxx[cxx]),
--        EnumOption("os_ver", "Select the operating system version",
-+        EnumVariable("os_ver", "Select the operating system version",
-                    defaults.os_ver, supported.os[os]),
--        EnumOption("arch_size", "Select the architecture bit-size",
-+        EnumVariable("arch_size", "Select the architecture bit-size",
-                    defaults.arch_size, supported.arch[arch]),
-         )
- 
---- src/SConscript.apps	2009-02-03 22:44:31.000000000 +0100
-+++ src/SConscript.apps.new	2009-04-07 16:48:06.000000000 +0200
-@@ -92,7 +92,7 @@
- 
- # Transform the modified settings into SCons Environment variables.
- # Gives priority to project settings over global settings.
--env = build.environment.Copy()
-+env = build.environment.Clone()
- env.Prepend(**actual.symbols())
- if "static" not in build.options.extras:
-   env["RPATH"] = build.toplevel + "/build/src/" + build.platform
diff --git a/sci-chemistry/rosetta/files/rosetta-3.4-fix-valgrind.patch b/sci-chemistry/rosetta/files/rosetta-3.4-fix-valgrind.patch
deleted file mode 100644
index bc98773c1..000000000
--- a/sci-chemistry/rosetta/files/rosetta-3.4-fix-valgrind.patch
+++ /dev/null
@@ -1,11 +0,0 @@
---- tools/build/options.settings	2009-02-03 22:44:32.000000000 +0100
-+++ tools/build/options.settings.new	2009-04-07 18:12:00.000000000 +0200
-@@ -76,7 +76,7 @@
-         # Build so that valgrind can follow the memory use.
-         # Valgrind normally works fine with most executables but not
-         # with static builds, which we are doing.
--        "valgrind",
-+        "shared",
- 
-         # Build using static linking.
-         "static",
diff --git a/sci-chemistry/rosetta/files/rosetta-3.4-gcc4.7.patch b/sci-chemistry/rosetta/files/rosetta-3.4-gcc4.7.patch
deleted file mode 100644
index d0893c183..000000000
--- a/sci-chemistry/rosetta/files/rosetta-3.4-gcc4.7.patch
+++ /dev/null
@@ -1,32 +0,0 @@
- tools/build/options.settings | 2 +-
- 1 file changed, 1 insertion(+), 1 deletion(-)
-
-diff --git a/tools/build/options.settings b/tools/build/options.settings
-index 30fb65e..f79ef5b 100644
---- a/tools/build/options.settings
-+++ b/tools/build/options.settings
-@@ -9,7 +9,7 @@
- options = {
- 
-     "cxx" : {
--        "gcc"     : [ "3.3", "3.4", "4.0", "4.1", "4.2", "4.3","4.4","4.5", "4.6", "*" ],
-+        "gcc"     : [ "3.3", "3.4", "4.0", "4.1", "4.2", "4.3","4.4","4.5", "4.6", "4.7", "*" ],
-         "icc"     : [ "8.0", "8.1", "9.0", "9.1", "10.0", "10.1", "11.1", "*" ], #PBHACK
-         "msvc"    : [ "7.0", "7.1", "8.0", "8.1", "*" ],
-         "xlc"     : [ "7.0", "8.0", "9.0", "XL", "*" ],
- src/protocols/jd2/SingleFileBuffer.cc | 2 ++
- 1 file changed, 2 insertions(+)
-
-diff --git a/src/protocols/jd2/SingleFileBuffer.cc b/src/protocols/jd2/SingleFileBuffer.cc
-index aa78d91..61ca823 100644
---- a/src/protocols/jd2/SingleFileBuffer.cc
-+++ b/src/protocols/jd2/SingleFileBuffer.cc
-@@ -28,6 +28,8 @@
- #include <ctime>      // for clock()
- #endif
- 
-+#include <unistd.h>
-+
- namespace protocols {
- namespace jd2 {
- using namespace core;
diff --git a/sci-chemistry/rosetta/files/rosetta-3.4-gcc4.78.patch b/sci-chemistry/rosetta/files/rosetta-3.4-gcc4.78.patch
deleted file mode 100644
index 882534bfd..000000000
--- a/sci-chemistry/rosetta/files/rosetta-3.4-gcc4.78.patch
+++ /dev/null
@@ -1,32 +0,0 @@
- tools/build/options.settings | 2 +-
- 1 file changed, 1 insertion(+), 1 deletion(-)
-
-diff --git a/tools/build/options.settings b/tools/build/options.settings
-index 30fb65e..f79ef5b 100644
---- a/tools/build/options.settings
-+++ b/tools/build/options.settings
-@@ -9,7 +9,7 @@
- options = {
- 
-     "cxx" : {
--        "gcc"     : [ "3.3", "3.4", "4.0", "4.1", "4.2", "4.3","4.4","4.5", "4.6", "*" ],
-+        "gcc"     : [ "3.3", "3.4", "4.0", "4.1", "4.2", "4.3","4.4","4.5", "4.6", "4.7", "4.8", "*" ],
-         "icc"     : [ "8.0", "8.1", "9.0", "9.1", "10.0", "10.1", "11.1", "*" ], #PBHACK
-         "msvc"    : [ "7.0", "7.1", "8.0", "8.1", "*" ],
-         "xlc"     : [ "7.0", "8.0", "9.0", "XL", "*" ],
- src/protocols/jd2/SingleFileBuffer.cc | 2 ++
- 1 file changed, 2 insertions(+)
-
-diff --git a/src/protocols/jd2/SingleFileBuffer.cc b/src/protocols/jd2/SingleFileBuffer.cc
-index aa78d91..61ca823 100644
---- a/src/protocols/jd2/SingleFileBuffer.cc
-+++ b/src/protocols/jd2/SingleFileBuffer.cc
-@@ -28,6 +28,8 @@
- #include <ctime>      // for clock()
- #endif
- 
-+#include <unistd.h>
-+
- namespace protocols {
- namespace jd2 {
- using namespace core;
diff --git a/sci-chemistry/rosetta/files/rosetta-3.4-gcc4.789.patch b/sci-chemistry/rosetta/files/rosetta-3.4-gcc4.789.patch
deleted file mode 100644
index e11532ac4..000000000
--- a/sci-chemistry/rosetta/files/rosetta-3.4-gcc4.789.patch
+++ /dev/null
@@ -1,32 +0,0 @@
- tools/build/options.settings | 2 +-
- 1 file changed, 1 insertion(+), 1 deletion(-)
-
-diff --git a/tools/build/options.settings b/tools/build/options.settings
-index 30fb65e..f79ef5b 100644
---- a/tools/build/options.settings
-+++ b/tools/build/options.settings
-@@ -9,7 +9,7 @@
- options = {
- 
-     "cxx" : {
--        "gcc"     : [ "3.3", "3.4", "4.0", "4.1", "4.2", "4.3","4.4","4.5", "4.6", "*" ],
-+        "gcc"     : [ "3.3", "3.4", "4.0", "4.1", "4.2", "4.3","4.4","4.5", "4.6", "4.7", "4.8", "4.9", "*" ],
-         "icc"     : [ "8.0", "8.1", "9.0", "9.1", "10.0", "10.1", "11.1", "*" ], #PBHACK
-         "msvc"    : [ "7.0", "7.1", "8.0", "8.1", "*" ],
-         "xlc"     : [ "7.0", "8.0", "9.0", "XL", "*" ],
- src/protocols/jd2/SingleFileBuffer.cc | 2 ++
- 1 file changed, 2 insertions(+)
-
-diff --git a/src/protocols/jd2/SingleFileBuffer.cc b/src/protocols/jd2/SingleFileBuffer.cc
-index aa78d91..61ca823 100644
---- a/src/protocols/jd2/SingleFileBuffer.cc
-+++ b/src/protocols/jd2/SingleFileBuffer.cc
-@@ -28,6 +28,8 @@
- #include <ctime>      // for clock()
- #endif
- 
-+#include <unistd.h>
-+
- namespace protocols {
- namespace jd2 {
- using namespace core;
diff --git a/sci-chemistry/rosetta/files/rosetta-3.4-lange-fix.patch b/sci-chemistry/rosetta/files/rosetta-3.4-lange-fix.patch
deleted file mode 100644
index 17e85f882..000000000
--- a/sci-chemistry/rosetta/files/rosetta-3.4-lange-fix.patch
+++ /dev/null
@@ -1,22 +0,0 @@
- tools/build/setup.py | 8 +++++++-
- 1 file changed, 7 insertions(+), 1 deletion(-)
-
-diff --git a/tools/build/setup.py b/tools/build/setup.py
-index 4e57ff6..d8a2a08 100644
---- a/tools/build/setup.py
-+++ b/tools/build/setup.py
-@@ -354,7 +354,13 @@ what SCons will use to build the system.
-             symbols = setting.appends.symbols()
-             if symbols.has_key("ENV"):
-                 for key, value in symbols["ENV"].items():
--                    env["ENV"][key] += value
-+                    if key == "PATH":
-+                        env["ENV"][key] = value
-+                    else:
-+                        try:
-+                            env["ENV"][key] += value
-+                        except:
-+                            print key, value
-                 del symbols["ENV"]
-             env.Append(**symbols)
-         if setting.prepends:
diff --git a/sci-chemistry/rosetta/files/rosetta-3.4-platform.patch b/sci-chemistry/rosetta/files/rosetta-3.4-platform.patch
deleted file mode 100644
index 82f0ba63f..000000000
--- a/sci-chemistry/rosetta/files/rosetta-3.4-platform.patch
+++ /dev/null
@@ -1,11 +0,0 @@
---- ./tools/build/setup_platforms.py	2009-02-03 22:44:32.000000000 +0100
-+++ ./tools/build/setup_platforms.py.new	2009-04-07 16:16:44.000000000 +0200
-@@ -274,7 +274,7 @@
-     """
-     # Note that these are very different values, and need processing
-     if globals().has_key("platform"):
--        return platform.processor() or _uname()[4]
-+        return platform.machine() or _uname()[4]
-     else:
-         return _uname()[4]
- 
diff --git a/sci-chemistry/rosetta/files/rosetta-3.4-unbundle.patch b/sci-chemistry/rosetta/files/rosetta-3.4-unbundle.patch
deleted file mode 100644
index ba810b162..000000000
--- a/sci-chemistry/rosetta/files/rosetta-3.4-unbundle.patch
+++ /dev/null
@@ -1,47 +0,0 @@
- src/core/pack/dunbrack/RotamericSingleResidueDunbrackLibrary.tmpl.hh   | 3 +--
- .../pack/dunbrack/SemiRotamericSingleResidueDunbrackLibrary.tmpl.hh    | 3 +--
- src/utility/io/zipstream.hpp                                           | 3 +--
- 3 files changed, 3 insertions(+), 6 deletions(-)
-
-diff --git a/src/core/pack/dunbrack/RotamericSingleResidueDunbrackLibrary.tmpl.hh b/src/core/pack/dunbrack/RotamericSingleResidueDunbrackLibrary.tmpl.hh
-index 0aa44a6..299e0c5 100644
---- a/src/core/pack/dunbrack/RotamericSingleResidueDunbrackLibrary.tmpl.hh
-+++ b/src/core/pack/dunbrack/RotamericSingleResidueDunbrackLibrary.tmpl.hh
-@@ -402,8 +402,7 @@
- #include <boost/function.hpp>
- #include <boost/pool/detail/mutex.hpp>
- #include <boost/pool/poolfwd.hpp>
--#include <zlib/zlib.h>
--#include <zlib/zutil.h>
-+#include <zlib.h>
- 
- namespace core {
- namespace pack {
-diff --git a/src/core/pack/dunbrack/SemiRotamericSingleResidueDunbrackLibrary.tmpl.hh b/src/core/pack/dunbrack/SemiRotamericSingleResidueDunbrackLibrary.tmpl.hh
-index 2396126..700e78d 100644
---- a/src/core/pack/dunbrack/SemiRotamericSingleResidueDunbrackLibrary.tmpl.hh
-+++ b/src/core/pack/dunbrack/SemiRotamericSingleResidueDunbrackLibrary.tmpl.hh
-@@ -405,8 +405,7 @@
- #include <boost/function.hpp>
- #include <boost/pool/detail/mutex.hpp>
- #include <boost/pool/poolfwd.hpp>
--#include <zlib/zlib.h>
--#include <zlib/zutil.h>
-+#include <zlib.h>
- 
- namespace core {
- namespace pack {
-diff --git a/src/utility/io/zipstream.hpp b/src/utility/io/zipstream.hpp
-index adaf88c..c7d36d0 100644
---- a/src/utility/io/zipstream.hpp
-+++ b/src/utility/io/zipstream.hpp
-@@ -43,8 +43,7 @@
- 
- 
- // Zlib headers
--#include <zlib/zlib.h>
--#include <zlib/zutil.h>
-+#include <zlib.h>
- 
- 
- 
diff --git a/sci-chemistry/rosetta/files/rosetta-3.4-user-settings.patch b/sci-chemistry/rosetta/files/rosetta-3.4-user-settings.patch
deleted file mode 100644
index d7297cfc0..000000000
--- a/sci-chemistry/rosetta/files/rosetta-3.4-user-settings.patch
+++ /dev/null
@@ -1,29 +0,0 @@
- tools/build/user.settings | 8 +++++++-
- 1 file changed, 7 insertions(+), 1 deletion(-)
-
-diff --git a/tools/build/user.settings b/tools/build/user.settings
-index 27a001f..9696e3e 100644
---- a/tools/build/user.settings
-+++ b/tools/build/user.settings
-@@ -22,7 +22,7 @@
- # and select between them from the options.  For now there is only the
- # single "user" settings.
- 
--#import os
-+import os
- settings = {
-     "user" : {
-         "prepends" : {
-@@ -38,6 +38,12 @@ settings = {
-             #"program_path"  : os.environ["PATH"].split(":"),
-         },
-         "overrides" : {
-+            "flags" : {
-+                  "compile" : [ GENTOO_CXXFLAGS ],
-+                  "link"    : [ GENTOO_LDFLAGS ],
-+            },
-+            "cc"     : os.environ["CC"],
-+            "cxx"     : os.environ["CXX"],
-         },
-         "removes" : {
-         },
diff --git a/sci-chemistry/rosetta/files/rosetta-3.4-zlib.patch b/sci-chemistry/rosetta/files/rosetta-3.4-zlib.patch
deleted file mode 100644
index 18060add4..000000000
--- a/sci-chemistry/rosetta/files/rosetta-3.4-zlib.patch
+++ /dev/null
@@ -1,12 +0,0 @@
---- src/utility/io/zipstream.hpp	2009-02-03 22:47:27.000000000 +0100
-+++ src/utility/io/zipstream.hpp.new	2009-04-07 19:57:09.000000000 +0200
-@@ -36,8 +36,7 @@
- 
- 
- // Zlib headers
--#include <zlib/zlib.h>
--#include <zlib/zutil.h>
-+#include <zlib.h>
- 
- // C++ headers
- #include <algorithm>
diff --git a/sci-chemistry/rosetta/metadata.xml b/sci-chemistry/rosetta/metadata.xml
deleted file mode 100644
index dcf5c02f4..000000000
--- a/sci-chemistry/rosetta/metadata.xml
+++ /dev/null
@@ -1,17 +0,0 @@
-<?xml version="1.0" encoding="UTF-8"?>
-<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
-<pkgmetadata>
-	<maintainer type="project">
-		<email>sci-chemistry@gentoo.org</email>
-		<name>Gentoo Chemistry Project</name>
-	</maintainer>
-	<use>
-		<flag name="boinc">compile rosetta as a rosetta@home client</flag>
-		<flag name="boost">compile rosetta with boost supported code</flag>
-		<flag name="float">Build with floats rather than doubles</flag>
-		<flag name="lange">Apply patches from www.csrosetta.org</flag>
-	</use>
-	<upstream>
-		<bugs-to>mailto:general-support@mail.rosettacommons.org</bugs-to>
-	</upstream>
-</pkgmetadata>
diff --git a/sci-chemistry/rosetta/rosetta-3.4.ebuild b/sci-chemistry/rosetta/rosetta-3.4.ebuild
deleted file mode 100644
index bf40276a7..000000000
--- a/sci-chemistry/rosetta/rosetta-3.4.ebuild
+++ /dev/null
@@ -1,171 +0,0 @@
-# Copyright 1999-2015 Gentoo Foundation
-# Distributed under the terms of the GNU General Public License v2
-
-# boinc support is BROKEN !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!
-
-EAPI=5
-
-inherit eutils multilib prefix scons-utils toolchain-funcs versionator
-
-#MY_P="${PN}$(get_major_version)_source"
-MY_P="${PN}${PV}_source"
-
-DESCRIPTION="Prediction of protein structures and protein-protein interactions"
-HOMEPAGE="http://www.rosettacommons.org/"
-SRC_URI="${MY_P}.tgz patch_rosetta3.4_to_CSROSETTA3_ver1.3.txt"
-
-LICENSE="|| ( rosetta-academic rosetta-commercial )"
-SLOT="0"
-KEYWORDS="~amd64 ~x86 ~amd64-linux ~x86-linux"
-IUSE="boinc +boost custom-cflags debug doc float +lange mpi +openmp X"
-
-REQUIRED_USE="?? ( mpi boinc )"
-
-RESTRICT="fetch"
-
-RDEPEND="
-	dev-db/cppdb
-	mpi? ( virtual/mpi )
-	boinc? ( sci-misc/boinc[X?] )
-	boost? ( dev-libs/boost )
-	sci-libs/rosetta-db"
-DEPEND="${RDEPEND}
-	dev-util/scons
-	doc? ( app-doc/doxygen )
-	X? ( media-libs/freeglut )"
-
-MYCONF=""
-
-S="${WORKDIR}/${PN}_source"
-
-pkg_nofetch() {
-	einfo "Go to ${HOMEPAGE} and get ${A}"
-	einfo "which must be placed in ${DISTDIR}"
-}
-
-src_prepare() {
-	local myCXXFLAGS
-	local myLDFLAGS
-
-	use custom-cflags || \
-		export CXXFLAGS="-O3 -ffast-math -funroll-loops -finline-functions -finline-limit=20000 -pipe"
-
-	export LD_LIBRARY_PATH=""
-	use lange && \
-		epatch \
-			"${DISTDIR}"/patch_${PN}${PV}_to_CSROSETTA3_ver1.3.txt \
-			"${FILESDIR}"/${P}-lange-fix.patch
-
-	epatch \
-		"${FILESDIR}"/${P}-platform.patch \
-		"${FILESDIR}"/${P}-user-settings.patch \
-		"${FILESDIR}"/${P}-fix-valgrind.patch \
-		"${FILESDIR}"/${P}-boinc.patch \
-		"${FILESDIR}"/${P}-boost.patch \
-		"${FILESDIR}"/${P}-boost157.patch \
-		"${FILESDIR}"/${P}-gcc4.789.patch
-
-	eprefixify tools/build/*
-
-	rm bin/* external/{dbio,scons-local,lib} -rfv || die
-
-	find external/boost_1_46_1 -name "*.hpp" -delete || die
-
-	for i in ${CXXFLAGS}; do
-		myCXXFLAGS="${myCXXFLAGS} \"${i/-/}\","
-	done
-
-	for i in ${LDFLAGS}; do
-		myLDFLAGS="${myLDFLAGS} \"${i/-/}\","
-	done
-
-	sed \
-		-e "s:GENTOO_CXXFLAGS:${myCXXFLAGS}:g" \
-		-e "s:GENTOO_LDFLAGS:${myCXXFLAGS} ${myLDFLAGS}:g" \
-		-e "s:GENTOO_LIBDIR:$(get_libdir):g" \
-		-e "/program_path/s:#::g" \
-		-i tools/build/user.settings || die
-
-	tc-export CC CXX
-
-	if use mpi; then
-		sed \
-			-e 's:mpiCC:mpicxx:g' \
-			-i tools/build/basic.settings || die
-		sed \
-			-e "/cxx/d" \
-			-i tools/build/user.settings || die
-	fi
-}
-
-src_configure() {
-	local myextras=""
-	local mymode=""
-	local mycxx=""
-
-	use boinc && EXTRAS="boinc"
-	use boost && EXTRAS=$(my_list_append "${EXTRAS}" "boost")
-	use boost && EXTRAS=$(my_list_append "${EXTRAS}" "boost_thread")
-	use float && EXTRAS=$(my_list_append "${EXTRAS}" "rosetta_float")
-	use openmp && EXTRAS=$(my_list_append "${EXTRAS}" "omp")
-	use X && EXTRAS=$(my_list_append "${EXTRAS}" "graphics")
-	use mpi && EXTRAS=$(my_list_append "${EXTRAS}" "mpi")
-
-	COMPILER=$(expr match "$(tc-getCC)" '.*\([a-z]cc\)')
-	mycxx="cxx=${COMPILER}"
-
-	test -n "${EXTRAS}" && myextras="extras=${EXTRAS}"
-
-	if use debug; then
-		mymode="debug"
-	else
-		mymode="release"
-	fi
-
-	MYCONF="mode=${mymode} ${myextras} ${mycxx}"
-}
-
-src_compile() {
-	einfo "running 'scons bin cat=src ${MYCONF}' ..."
-	escons bin cat=src ${MYCONF}
-
-	if use doc; then
-		einfo "running 'scons ${MYCONF} cat=doc' ..."
-		scons ${MYCONF} cat=doc || die "scons failed to build documentation"
-	fi
-}
-
-src_install() {
-	dolib.so build/src/release/linux/*/*/*/*/*/${EXTRAS//,/-}/*.so*
-
-	use doc && dohtml build/doc/rosetta++/docs/*
-
-	cd bin || die
-	for BIN in *; do
-		newbin ${BIN} ${BIN%%.*} || die "could not install rosetta program files"
-	done
-
-	if [[ -e "${ED}"/usr/bin/cluster ]]; then
-		mv "${ED}"/usr/bin/cluster{,-${PN}} || die
-	fi
-
-	if [[ -e "${ED}"/usr/bin/benchmark ]]; then
-		mv "${ED}"/usr/bin/benchmark{,-${PN}} || die
-	fi
-}
-
-my_filter_option() {
-	local value="$1"
-	local exp="$2"
-	local result=`echo ${value} | sed -e s/${exp}//g`
-	echo "${result}"
-	return 0;
-}
-
-my_list_append() {
-	local old_value="$1"
-	local new_value="$2"
-	test -n "${old_value}" && old_value="${old_value},"
-	echo "${old_value}${new_value}"
-	return 0;
-}
diff --git a/sci-chemistry/shiftx/Manifest b/sci-chemistry/shiftx/Manifest
deleted file mode 100644
index 48f1b893a..000000000
--- a/sci-chemistry/shiftx/Manifest
+++ /dev/null
@@ -1 +0,0 @@
-DIST shiftx-1.1.tar.gz 504915 BLAKE2B 11dfcb29c91160265fbab20fbed7f1a41619df8bbfee1858cda09f38d4404c60915fb8a1e5b5a7313b46893d343d325570730457aa4bf35ec9815aac7f267a6f SHA512 2396ef31a9ce0c059b0c5cb0be60d7ab0489775e03439dcf3c62b8559a13b0e8ad37c8ef02e6422dd6b93acfe579c1abc86f520473836240d48840c7f38aed1f
diff --git a/sci-chemistry/shiftx/files/1.1-Makefile.patch b/sci-chemistry/shiftx/files/1.1-Makefile.patch
deleted file mode 100644
index f208d087f..000000000
--- a/sci-chemistry/shiftx/files/1.1-Makefile.patch
+++ /dev/null
@@ -1,27 +0,0 @@
- Makefile | 6 +++---
- 1 file changed, 3 insertions(+), 3 deletions(-)
-
-diff --git a/Makefile b/Makefile
-index 5401c07..ffd8157 100644
---- a/Makefile
-+++ b/Makefile
-@@ -6,8 +6,8 @@
- # E-Mail:   anip@redpoll.pharmacy.ualberta.ca
- #
- #CC=gcc -Xcpluscomm -cckr
--CC=/usr/bin/gcc
--CFLAGS=-O
-+#CC=/usr/bin/gcc
-+#CFLAGS=-O
- SYSLIB=
- INCLUDES=-I/usr/include
- LIBS=$(SYSLIB) -lm 
-@@ -25,7 +25,7 @@ OBJS=Main.o Nn.o Ssbond.o Residue.o Hetatm.o Vector.o Torison.o Cs.o Phipsi.o \
- all: shiftx
- 
- shiftx:	$(OBJS)
--	$(CC) $(OBJS) $(CFLAGS) $(LIBS) -o $@
-+	$(CC) $(CFLAGS) $(LDFLAGS) $(OBJS) $(LIBS) -o $@
- 
- Main.o:		Main.c main.h states.h nn.h ssbond.h residue.h hetatm.h cs.h \
-                 phipsi.h torison.h hydrogens.h rings.h es.h proline.h hbond.h \
diff --git a/sci-chemistry/shiftx/files/1.1-bfr-overflow.patch b/sci-chemistry/shiftx/files/1.1-bfr-overflow.patch
deleted file mode 100644
index 68507a364..000000000
--- a/sci-chemistry/shiftx/files/1.1-bfr-overflow.patch
+++ /dev/null
@@ -1,16 +0,0 @@
- Display.c | 2 +-
- 1 file changed, 1 insertion(+), 1 deletion(-)
-
-diff --git a/Display.c b/Display.c
-index 671d3ee..9a03c48 100644
---- a/Display.c
-+++ b/Display.c
-@@ -85,7 +85,7 @@ DISPLAY_DATA   *CreateDisplayData( int len, int prop, int nuc )
- void  display_selected_nucleus( DISPLAY_DATA *d )

- {

-   int   i, j;

--  char  nucleus[5];

-+  char  nucleus[8];

- 

-   /* Print Header Information */

- 

diff --git a/sci-chemistry/shiftx/metadata.xml b/sci-chemistry/shiftx/metadata.xml
deleted file mode 100644
index da36ecbfc..000000000
--- a/sci-chemistry/shiftx/metadata.xml
+++ /dev/null
@@ -1,8 +0,0 @@
-<?xml version="1.0" encoding="UTF-8"?>
-<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
-<pkgmetadata>
-	<maintainer type="project">
-		<email>sci-chemistry@gentoo.org</email>
-		<name>Gentoo Chemistry Project</name>
-	</maintainer>
-</pkgmetadata>
diff --git a/sci-chemistry/shiftx/shiftx-1.1.ebuild b/sci-chemistry/shiftx/shiftx-1.1.ebuild
deleted file mode 100644
index c25718308..000000000
--- a/sci-chemistry/shiftx/shiftx-1.1.ebuild
+++ /dev/null
@@ -1,37 +0,0 @@
-# Copyright 1999-2014 Gentoo Foundation
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=5
-
-inherit eutils toolchain-funcs
-
-DESCRIPTION="Prediction of 1H, 13C and 15N chemical shifts for proteins"
-HOMEPAGE="http://shiftx.wishartlab.com/"
-SRC_URI="http://shiftx.wishartlab.com/download/${PN}.tar.gz -> ${P}.tar.gz"
-
-LICENSE="all-rights-reserved"
-SLOT="0"
-KEYWORDS="~amd64 ~x86"
-IUSE=""
-
-DEPEND=""
-RDEPEND="sci-chemistry/shiftx2"
-
-S="${WORKDIR}"/${PN}
-
-DOCS="README FEATURES *.pdb *.out"
-
-src_prepare() {
-	epatch \
-		"${FILESDIR}"/${PV}-Makefile.patch \
-		"${FILESDIR}"/${PV}-bfr-overflow.patch
-}
-
-src_compile() {
-	emake CC="$(tc-getCC)"
-}
-
-src_install() {
-	dobin ${PN}
-	dodoc ${DOCS}
-}
diff --git a/sci-chemistry/shiftx2/Manifest b/sci-chemistry/shiftx2/Manifest
deleted file mode 100644
index 45150380b..000000000
--- a/sci-chemistry/shiftx2/Manifest
+++ /dev/null
@@ -1 +0,0 @@
-DIST shiftx2-v107-linux-20120106.tgz 114164215 BLAKE2B 33615b7e739acb2711b1946c0db84becf68ebd4e77dc773c5c3c672174d5e1932c4f88bfec1e38a24957bb0d7838ee4fa9c24e95462d620f06b38b895b934a93 SHA512 b1fa6ce19e988a938e6645fdbd14f7903b4db13754a476c67da0bf74909675e07b7cec4df63be30d7190ea645e8822eef551e6dd26625172e585da279f1f7396
diff --git a/sci-chemistry/shiftx2/files/shiftx2-1.07_p20120106-format-security.patch b/sci-chemistry/shiftx2/files/shiftx2-1.07_p20120106-format-security.patch
deleted file mode 100644
index fc4a61eb5..000000000
--- a/sci-chemistry/shiftx2/files/shiftx2-1.07_p20120106-format-security.patch
+++ /dev/null
@@ -1,16 +0,0 @@
- modules/resmf/libc/misc.lib.c | 2 +-
- 1 file changed, 1 insertion(+), 1 deletion(-)
-
-diff --git a/modules/resmf/libc/misc.lib.c b/modules/resmf/libc/misc.lib.c
-index 0ef12a4..1e22424 100755
---- a/modules/resmf/libc/misc.lib.c
-+++ b/modules/resmf/libc/misc.lib.c
-@@ -71,7 +71,7 @@ void show_msg(msg)
- char	*msg;
- {
- 
--	fprintf(stdout, msg);
-+	fprintf(stdout, "%s", msg);
- 
- }	/* show_msg */
- 
diff --git a/sci-chemistry/shiftx2/files/shiftx2-1.07_p20120106-internal-name.patch b/sci-chemistry/shiftx2/files/shiftx2-1.07_p20120106-internal-name.patch
deleted file mode 100644
index 4fa5447db..000000000
--- a/sci-chemistry/shiftx2/files/shiftx2-1.07_p20120106-internal-name.patch
+++ /dev/null
@@ -1,25 +0,0 @@
- modules/resmf/hydropho_cal.c | 4 ++--
- 1 file changed, 2 insertions(+), 2 deletions(-)
-
-diff --git a/modules/resmf/hydropho_cal.c b/modules/resmf/hydropho_cal.c
-index 1fde394..a889d08 100755
---- a/modules/resmf/hydropho_cal.c
-+++ b/modules/resmf/hydropho_cal.c
-@@ -184,7 +184,7 @@ float hydroscore(Hydroscale *scale, char residue){
- }
- 
- /* function for copying string */
--char * strndup (const char *s, size_t n)
-+char * new_strndup (const char *s, size_t n)
- {
-   char *result;
-   size_t len = strlen (s);
-@@ -206,7 +206,7 @@ char* substring(const char* str, size_t begin, size_t len)
- {
-   if (str == 0 || strlen(str) == 0 || strlen(str) < begin || strlen(str) < (begin+len))
-     return 0;
--  return (char *) strndup(str + begin, len);
-+  return (char *) new_strndup(str + begin, len);
- }
- 
- /* calculate the average value from begin to end in the given array */
diff --git a/sci-chemistry/shiftx2/files/shiftx2-1.07_p20120106-java.patch b/sci-chemistry/shiftx2/files/shiftx2-1.07_p20120106-java.patch
deleted file mode 100644
index ea64cea2d..000000000
--- a/sci-chemistry/shiftx2/files/shiftx2-1.07_p20120106-java.patch
+++ /dev/null
@@ -1,227 +0,0 @@
-diff --git a/shiftx2-v107-linux/src/LimitedCShift.java b/shiftx2-v107-linux/src/LimitedCShift.java
-index cd27fbf..9e72208 100755
---- a/shiftx2-v107-linux/src/LimitedCShift.java
-+++ b/shiftx2-v107-linux/src/LimitedCShift.java
-@@ -13,8 +13,8 @@ public class LimitedCShift {
- 	public void loadLimitedCShift () {		
-                 // System.out.println("SHIFTX2_DIR: "+ShiftXp.SHIFTX2_DIR);
- 
--		String filename = ShiftXp.SHIFTX2_DIR + "/lib/limitedcshift.dat";
--		String objFilename = ShiftXp.SHIFTX2_DIR + "/lib/limitedcshift.osf";
-+		String filename = ShiftXp.GENTOO_SHARE_PATH + "/limitedcshift.dat";
-+		String objFilename = ShiftXp.GENTOO_SHARE_PATH + "/limitedcshift.osf";
- 		
- 		File f = new File(objFilename);
- 		if (f.exists()) {
-@@ -44,7 +44,7 @@ public class LimitedCShift {
- 				br.close();
- 				
- 				// save object into object file format for speed up
--				saveObjectFile(objFilename, limshift);
-+				//saveObjectFile(objFilename, limshift);
- 
- 			} catch(IOException ex){
- 				ex.printStackTrace();
-diff --git a/shiftx2-v107-linux/src/ModuleExecutor.java b/shiftx2-v107-linux/src/ModuleExecutor.java
-index 36cfeb1..704451f 100755
---- a/shiftx2-v107-linux/src/ModuleExecutor.java
-+++ b/shiftx2-v107-linux/src/ModuleExecutor.java
-@@ -22,12 +22,12 @@ public class ModuleExecutor {
- 	// private static final String WORKING_DIR = "./wkdir/";
- 	private static String WORKING_DIR = "";
- 
--	private static final String RESMF_EXE = "/modules/resmf/resmf";
--	private static final String EFFECTS_EXE = "/modules/effects/caleffect"; 
--	private static final String ANGLES_EXE = "/modules/angles/get_angles";	
--	private static final String ANGLES_REDUCE_DIR = "/modules/angles";
-+	private static final String RESMF_EXE = "resmf";
-+	private static final String EFFECTS_EXE = "caleffect"; 
-+	private static final String ANGLES_EXE = "get_angles";	
-+	private static final String ANGLES_REDUCE_DIR = "angles";
- 
--    private static String SHIFTXP_DIR = ShiftXp.SHIFTX2_DIR;
-+//    private static String SHIFTXP_DIR = ShiftXp.SHIFTX2_DIR;
- 
- 	private static final String REDUCE_FLAG = "1"; // 1 or 0
- 
-@@ -80,8 +80,8 @@ public class ModuleExecutor {
- 		if(DEBUG) System.out.println("> Processing [Major Features] with " + pdbfile);
-         // Update: add pdbdir both input pdbfile and output result, pdbId (2011.03.17)
- 		// cmd = RESMF_EXE + " -f " + pdbdir +"/"+ pdbfile + " -o " + WORKING_DIR + pdbId + ".resmf";
--		cmd = SHIFTXP_DIR + RESMF_EXE + " -f " + pdbdir + pdbfile + " -o " + WORKING_DIR + pdbId + ".resmf" 
--                      + " -d " + SHIFTXP_DIR + "/modules/resmf/lib";
-+		cmd = RESMF_EXE + " -f " + pdbdir + pdbfile + " -o " + WORKING_DIR + pdbId + ".resmf" 
-+                      + " -d " + ShiftXp.GENTOO_SHARE_PATH + "/vader";
- 
- 		if(DEBUG){ System.out.println("\t"+cmd); }
- 		execCode = execute_command(cmd); 
-@@ -93,7 +93,7 @@ public class ModuleExecutor {
- 		
- 		/* call effects for calculating ring current calculator */
- 		if(DEBUG) System.out.println("> processing [Effects] with " + pdbfile);
--		cmd = SHIFTXP_DIR + EFFECTS_EXE + " 1 " + pdbdir + pdbfile + " " + WORKING_DIR + pdbfile + ".dummy";
-+		cmd = EFFECTS_EXE + " 1 " + pdbdir + pdbfile + " " + WORKING_DIR + pdbfile + ".dummy";
- 
- 		if(DEBUG){ System.out.println("\t"+cmd); }
- 		execCode = execute_command(cmd); 
-@@ -106,7 +106,7 @@ public class ModuleExecutor {
- 		/* call angle calculator : output must be redirected to file using PrintStream */
- 		if(DEBUG) System.out.println("> Processing [Angle] with " + pdbfile);
- 		// cmd = ANGLES_EXE + " " + ANGLES_REDUCE_DIR + " " + pdbfile ;
--		cmd = SHIFTXP_DIR + ANGLES_EXE + " " + SHIFTXP_DIR + ANGLES_REDUCE_DIR + " " + pdbdir + pdbfile + " "+ REDUCE_FLAG;
-+		cmd = ANGLES_EXE + " " + ShiftXp.GENTOO_SHARE_PATH + " " + pdbdir + pdbfile + " "+ REDUCE_FLAG;
- 		String outpath = WORKING_DIR + pdbId + ".angles";
- 
- 		if(DEBUG){ System.out.println("\t"+cmd); }
-diff --git a/shiftx2-v107-linux/src/PredictionModels.java b/shiftx2-v107-linux/src/PredictionModels.java
-index a77d1cb..fb84666 100755
---- a/shiftx2-v107-linux/src/PredictionModels.java
-+++ b/shiftx2-v107-linux/src/PredictionModels.java
-@@ -13,9 +13,7 @@ public class PredictionModels {
-     private final static String MODEL_FILE_SIDECHAIN_ONLY = "predmodels_sidechain.sobj";
- 
-     private final static String OBJECT_MODEL_DIRECTORY = "/lib";
--    private final static String MODEL_DIRECTORY = "/lib/predmodels";
--
--    private static String SHIFTXP_DIR = ShiftXp.SHIFTX2_DIR;
-+    private final static String MODEL_DIRECTORY = "predmodels";
- 
-     HashMap<String, Classifier> hsmap_predmodel = new HashMap<String, Classifier>();
- 
-@@ -36,7 +34,7 @@ public class PredictionModels {
-        // System.out.println("SHIFTXP_DIR:" + SHIFTXP_DIR+"\n\n");
-        // System.out.println("SHIFTX2_DIR:" + ShiftXp.SHIFTX2_DIR+"\n\n");
- 
--        String headerfilename = ShiftXp.SHIFTX2_DIR + "/lib/data-header.arff"; 
-+        String headerfilename = ShiftXp.GENTOO_SHARE_PATH + "/data-header.arff"; 
- 
-         try {
-             // assigned instance header from data-header.arff
-@@ -150,7 +148,7 @@ public class PredictionModels {
-             // if option is not sidechain only, put backbone models into modeling file 
-             if ( ! this.prediction_type.equals("SIDECHAIN") ) {
-                 for(int i=0; i < BACKBONE_MODEL_LENGTH; i++)  {
--                    ois = new ObjectInputStream( new BufferedInputStream( new FileInputStream( ShiftXp.SHIFTX2_DIR + MODEL_DIRECTORY + "/" + modelFileArray[i]) ));
-+                    ois = new ObjectInputStream( new BufferedInputStream( new FileInputStream( ShiftXp.GENTOO_SHARE_PATH + "/" + MODEL_DIRECTORY + "/" + modelFileArray[i]) ));
-                     classifier = (Classifier) ois.readObject();
-                     hsmap_predmodel.put(atomNameArray[i],classifier);
-                     ois.close();
-@@ -160,7 +158,7 @@ public class PredictionModels {
-             // if option is not backbone only, put/append sidechain models into modeling file
-             if ( ! this.prediction_type.equals("BACKBONE") ) {
-                 for(int i=BACKBONE_MODEL_LENGTH; i < (BACKBONE_MODEL_LENGTH + SIDECHAIN_MODEL_LENGTH); i++)  {
--                    ois = new ObjectInputStream( new BufferedInputStream( new FileInputStream( ShiftXp.SHIFTX2_DIR + MODEL_DIRECTORY + "/" + modelFileArray[i]) ));
-+                    ois = new ObjectInputStream( new BufferedInputStream( new FileInputStream( ShiftXp.GENTOO_SHARE_PATH + "/" + MODEL_DIRECTORY + "/" + modelFileArray[i]) ));
-                     classifier = (Classifier) ois.readObject();
-                     hsmap_predmodel.put(atomNameArray[i], classifier);
-                     ois.close();
-@@ -185,11 +183,11 @@ public class PredictionModels {
-         */
- 
-         if ( this.prediction_type.equals("ALL") == true) {
--            model_file = ShiftXp.SHIFTX2_DIR + OBJECT_MODEL_DIRECTORY + "/" + MODEL_FILE_ALLATOMS;
-+            model_file = ShiftXp.GENTOO_SHARE_PATH + "/" + MODEL_FILE_ALLATOMS;
-         } else if ( this.prediction_type.equals("BACKBONE") == true) {
--            model_file = ShiftXp.SHIFTX2_DIR + OBJECT_MODEL_DIRECTORY + "/" + MODEL_FILE_BACKBONE_ONLY;
-+            model_file = ShiftXp.GENTOO_SHARE_PATH + "/" + MODEL_FILE_BACKBONE_ONLY;
-         } else if ( this.prediction_type.equals("SIDECHAIN") == true) {
--            model_file = ShiftXp.SHIFTX2_DIR + OBJECT_MODEL_DIRECTORY + "/" + MODEL_FILE_SIDECHAIN_ONLY;
-+            model_file = ShiftXp.GENTOO_SHARE_PATH + "/" + MODEL_FILE_SIDECHAIN_ONLY;
-         } 
- 
-         File f = new File( model_file );
-@@ -198,7 +196,7 @@ public class PredictionModels {
-             readHashObjectPredModelFile( model_file );
-         } else {
-             setHashMap(); 
--            saveHashObjectPredModelFile( model_file ); 
-+//            saveHashObjectPredModelFile( model_file ); 
-         }
-     }
- 
-diff --git a/shiftx2-v107-linux/src/RandomCoil.java b/shiftx2-v107-linux/src/RandomCoil.java
-index 25a8999..7442938 100755
---- a/shiftx2-v107-linux/src/RandomCoil.java
-+++ b/shiftx2-v107-linux/src/RandomCoil.java
-@@ -33,11 +33,9 @@ public class RandomCoil {
- 	public void loadRandomCoil() {		
- 
-         // change path as absolute path
--        String SHIFTXP_DIR = ShiftXp.SHIFTX2_DIR;
--
--		String filename = SHIFTXP_DIR + "/lib/RandomCoil.csv";
--		String objFilename = SHIFTXP_DIR + "/lib/RandomCoil.osf";
--		String objAtomListname = SHIFTXP_DIR + "/lib/RCoilAtomlist.osf";
-+		String filename = ShiftXp.GENTOO_SHARE_PATH + "/RandomCoil.csv";
-+		String objFilename = ShiftXp.GENTOO_SHARE_PATH + "/RandomCoil.osf";
-+		String objAtomListname = ShiftXp.GENTOO_SHARE_PATH + "/RCoilAtomlist.osf";
- 		
- 		
- 		File f = new File(objFilename);
-@@ -85,8 +83,8 @@ public class RandomCoil {
- 				br.close();
- 				
- 				// save object into object file format for speed up
--				saveObjectFile(objFilename, rcoil);				
--				saveObjectFile(objAtomListname, restypeAtomStringList);
-+//				saveObjectFile(objFilename, rcoil);				
-+//				saveObjectFile(objAtomListname, restypeAtomStringList);
- 
- 			} catch(IOException ex){
- 				ex.printStackTrace();
-diff --git a/shiftx2-v107-linux/src/ShiftXp.java b/shiftx2-v107-linux/src/ShiftXp.java
-index 505a3f6..920f420 100755
---- a/shiftx2-v107-linux/src/ShiftXp.java
-+++ b/shiftx2-v107-linux/src/ShiftXp.java
-@@ -27,7 +27,7 @@ public class ShiftXp {
-     static final boolean DEBUG = false; 
-     static boolean RCOIL_PRINTOUT = false;
-     static String SHIFTX2_DIR = ".";  // to support running on other directory
--
-+    public static final String GENTOO_SHARE_PATH = "PUT_GENTOO_SHARE_PATH_HERE";
-     // Loading only one time, that's why these are here 
-     static RandomCoil rcoil = new RandomCoil();
-     static LimitedCShift chkcshift = new LimitedCShift();
-@@ -41,7 +41,7 @@ public class ShiftXp {
-         buf.append("Detail information: http://www.shiftx2.ca or http://redpoll.pharmacy.ualberta.ca\n");
-         buf.append("--------------------------------------------------------------------------------\n\n");
- 
--        buf.append("SYNOPSIS\n\t java -Xmx1500m -cp <SHIFTX+ dir>/bin:<SHIFTX+ dir>/lib/weka.jar ShiftXp [options]\n");
-+        buf.append("SYNOPSIS\n\t jshiftx2 [options]\n");
- 
-         buf.append("OPTIONS:\n");
-         buf.append("\t -i [<directory/> infile.pdb | ALLPDB]\n");
-@@ -54,10 +54,10 @@ public class ShiftXp {
-         buf.append("\t -temp <number>        Temperature, default=298\n");
-         buf.append("\t -d [TRUE | FALSE]  Deuterated pdb, default=FALSE \n"); 
-         buf.append("\t -r [TRUE | FALSE]  Print randon coild shift (only for CSV format), default=FALSE \n"); 
--        buf.append("\t -dir <SHIFTX+ directory>  The installed directory of SHIFTX+/SHIFTX2\n\n");
-+//        buf.append("\t -dir <SHIFTX+ directory>  The installed directory of SHIFTX+/SHIFTX2\n\n");
- 
-         buf.append("EXAMPLE:\n");
--        buf.append("\t java -Xmx1500m -cp ~/shiftx2/bin:~/shiftx2/lib/weka.jar ShiftXp -i 1ubq.pdb\n\n");
-+        buf.append("\t jshiftx2 -i 1ubq.pdb\n\n");
-         buf.append("\n");
- 
-         System.out.println( buf );
-@@ -138,20 +138,6 @@ public class ShiftXp {
-            }     
-         }
- 
--        // check execute directory 
--        // 2011.08.31 changed shiftx2_main.py --> shiftx2.py
--        if ( !( new File( SHIFTX2_DIR + "/shiftx2.py").exists() 
--             &&  new File(SHIFTX2_DIR + "/lib/weka.jar").exists() )  )  {
--
--           System.err.println("\n********************************************************************************");
--           System.err.println("[Error]\t Required: When the SHIFTX2 execute on other directory,\n"
--                             +"\t it should be set as a parameter. Use '-dir' option.");
--           System.err.println("> Current directory: "+System.getProperty("user.dir"));
--           System.err.println("********************************************************************************\n");
--
--           usage();
--        }
--
-         if ( inPDBFile == null || inPDBFile.length() < 1)  {
-            System.err.println("\n********************************************************************************");
-            System.err.println("[Error] Required: There is no input PDB filename.");
diff --git a/sci-chemistry/shiftx2/files/shiftx2-1.07_p20120106-system.patch b/sci-chemistry/shiftx2/files/shiftx2-1.07_p20120106-system.patch
deleted file mode 100644
index 7625f7442..000000000
--- a/sci-chemistry/shiftx2/files/shiftx2-1.07_p20120106-system.patch
+++ /dev/null
@@ -1,231 +0,0 @@
- natsorted.py         |  1 -
- script/combine_cs.py |  2 +-
- shiftx2.py           | 39 +++++++++++++++++++--------------------
- shiftx2_util.py      |  3 +--
- shifty3/shifty3.py   |  2 +-
- 5 files changed, 22 insertions(+), 25 deletions(-)
-
-diff --git a/natsorted.py b/natsorted.py
-index 415b393..6fc909e 100755
---- a/natsorted.py
-+++ b/natsorted.py
-@@ -1,4 +1,3 @@
--#!/usr/bin/env python
- ############################################################
- # functions for performing natural sort
- ############################################################
-diff --git a/script/combine_cs.py b/script/combine_cs.py
-index 4d1dd4f..5182958 100755
---- a/script/combine_cs.py
-+++ b/script/combine_cs.py
-@@ -9,7 +9,7 @@
- # last updated: Jan 06st, 2012 (by Beomsoo Han)
- #################################################################################
- import sys, re, os
--from natsorted import *
-+from shiftx2.natsorted import *
- from math import exp  ## add for new combine rule
- # from numpy import *
- tablerows = {} # a hash table for all rows in the table, mapping from residue number to table entry object
-diff --git a/shiftx2.py b/shiftx2.py
-index 0a171c8..72ecbfe 100755
---- a/shiftx2.py
-+++ b/shiftx2.py
-@@ -14,7 +14,7 @@
- #######################################################################
- import os, sys, getopt, re, fnmatch
- from optparse import OptionParser
--from shiftx2_util import *
-+from shiftx2.shiftx2util import *
- 
- DEUTERATED = None
- NOSHIFTY = None
-@@ -26,7 +26,7 @@ CHAINID = None
- EXPLICIT = None
- SHIFTTYPE = None
- 
--SHIFTX2ROOT = ""
-+SHIFTX2ROOT = "@GENTOO_PORTAGE_EPREFIX@/opt/shiftx2"
- 
- # temporary file name
- 
-@@ -136,8 +136,7 @@ def batch_mode(pattern_str):
-         print "## Running SHIFTX+ modules ..."  ## Add by B HAN
- 
-         ## switch os.path.abspath("") with SHIFTX2ROOT (set from sys.path[0]) by B HAN
--        cmd_prefix = "java -cp " + SHIFTX2ROOT + "/bin:" + SHIFTX2ROOT + \
--            "/lib/weka.jar ShiftXp -b " + "'" +  BATCH + "'" + " -atoms " + options.atoms + \
-+        cmd_prefix = "jshiftx2" + " -b " + "'" +  BATCH + "'" + " -atoms " + options.atoms + \
-             " -ph " + str(options.ph) + " -temp " + str(options.temp) 
-         if DEUTERATED:
-             cmd_prefix = cmd_prefix + " -d TRUE"
-@@ -154,14 +153,14 @@ def batch_mode(pattern_str):
-         for infile in pdb_list:
-             # run SHIFTX
-             ## cmd_prefix = "modules/shiftx/shiftx 1 " + os.path.abspath("") + "/" + \
--            cmd_prefix = SHIFTX2ROOT + "/modules/shiftx/shiftx 1 " + infile + " " + infile + ".sx"
-+            cmd_prefix = "shiftx 1 " + infile + " " + infile + ".sx"
-             os.system(cmd_prefix)
-             if VERBOSE:
-                 print cmd_prefix
-             # convert from table format to CSV
-             ## cmd_prefix = "python script/shiftx2shiftxp.py " + os.path.abspath("") + "/" + \
-             ##    infile + ".sx " + os.path.abspath("") + "/" + infile + ".sxp"
--            cmd_prefix = "python "+ SHIFTX2ROOT +"/script/shiftx2shiftxp.py " + \
-+            cmd_prefix = "shiftx2shiftxp.py " + \
-                 infile + ".sx " +  infile + ".sxp"
-             ## switched by B HAN
-             ## infile + ".sx " + os.path.abspath("") + "/" + infile.split('.')[0] + ".sxp"
-@@ -180,7 +179,7 @@ def batch_mode(pattern_str):
-             ## os.chdir(os.path.abspath("shifty3"))
-             sys.path.append(SHIFTX2ROOT+"/shifty3")
-             os.chdir(SHIFTX2ROOT+"/shifty3")
--            shifty_cmd = "python shifty3.py -i " + \
-+            shifty_cmd = "shifty3 -i " + \
-                 infile + " -o " + infile + ".shifty -c 40 "
-             if DEUTERATED:
-                 shifty_cmd = shifty_cmd + " -d"
-@@ -207,7 +206,7 @@ def batch_mode(pattern_str):
-             errmsg = "Error: SHIFTX+ cannot make a prediction file."
-             return errmsg
- 
--        combine_cmd = "python " + SHIFTX2ROOT +"/script/combine_cs.py " + sx_outfile + " " + infile + ".shifty " 
-+        combine_cmd = "combine_cs.py " + sx_outfile + " " + infile + ".shifty " 
-         if not options.outfile:
-             combine_cmd = combine_cmd + infile + ".cs" 
-         else:
-@@ -248,7 +247,7 @@ def model_batch(pattern_str):
-     # run shiftx1 or shiftx+
-     if not SHIFTX1:
-         # run SHIFTX+ 
--        cmd_prefix = "java -cp " + SHIFTX2ROOT + "/bin:" + SHIFTX2ROOT + "/lib/weka.jar ShiftXp -b " + \
-+        cmd_prefix = "jshiftx2 -b " + \
-             "'" +  pattern_str + "'" + " -atoms " + options.atoms + \
-             " -ph " + str(options.ph) + " -temp " + str(options.temp) 
-         if DEUTERATED:
-@@ -263,14 +262,14 @@ def model_batch(pattern_str):
-     else:
-         for infile in pdb_list:
-             # run SHIFTX
--            cmd_prefix = SHIFTX2ROOT + "/modules/shiftx/shiftx 1 " + infile + \
-+            cmd_prefix = "shiftx 1 " + infile + \
-                 " " + infile + ".sx"
-             os.system(cmd_prefix)
-             if VERBOSE:
-                 print cmd_prefix
- 
-             # convert from table format to CSV
--            cmd_prefix = "python "+ SHIFTX2ROOT +"/script/shiftx2shiftxp.py " + \
-+            cmd_prefix = "shiftx2shiftxp.py " + \
-                 infile + ".sx " + infile + ".sxp"
- 
-             os.system(cmd_prefix)
-@@ -328,7 +327,7 @@ def nmr_mode(infile, obs_cs):
-     if not NOSHIFTY:
-         sys.path.append( SHIFTX2ROOT + "/shifty3")
-         os.chdir(SHIFTX2ROOT + "/shifty3")
--        shifty_cmd = "python shifty3.py -i " + infile + \
-+        shifty_cmd = "shifty3 -i " + infile + \
-             " -o " + infile + ".shifty -c 40 "
-         if DEUTERATED:
-             shifty_cmd = shifty_cmd + " -d"
-@@ -350,7 +349,7 @@ def nmr_mode(infile, obs_cs):
-         return errmsg
- 
-     # combine result
--    combine_cmd = "python "+ SHIFTX2ROOT + "/script/combine_cs.py " + infile_prefix + ".sxp " + infile + ".shifty " 
-+    combine_cmd = "combine_cs.py " + infile_prefix + ".sxp " + infile + ".shifty " 
-     if not options.outfile:
-         combine_cmd = combine_cmd + infile + ".cs" 
-         ## add by B HAN; if it does not exist, error message will occur
-@@ -367,7 +366,7 @@ def nmr_mode(infile, obs_cs):
-     # should be accomplished in a function
-     if obs_cs!= None:
-         # calculate correlation
--        cmd = "python " + SHIFTX2ROOT +"/script/model_corr.py " + obs_cs + " " + infile_prefix + ".modelcorr " + ' '.join(model_outfiles)
-+        cmd = "model_corr.py " + obs_cs + " " + infile_prefix + ".modelcorr " + ' '.join(model_outfiles)
-         os.system(cmd)
-                
-         # plot correlation graphs, plot line graph but no barplots
-@@ -456,7 +455,7 @@ def single_mode(infile, outfile):
-     
-     if not SHIFTX1:
-         # run SHIFTX+ 
--        cmd_prefix = "java -cp " + SHIFTX2ROOT + "/bin:" + SHIFTX2ROOT + "/lib/weka.jar ShiftXp -i " + inputfile \
-+        cmd_prefix = "jshiftx2 -i " + inputfile \
-                    + " -atoms " + options.atoms + " -ph " + str(options.ph) + " -temp " + str(options.temp) 
-         if DEUTERATED:
-             cmd_prefix = cmd_prefix + " -d TRUE"
-@@ -476,12 +475,12 @@ def single_mode(infile, outfile):
-             sys.exit(-1)
-     else:
-         # run SHIFTX
--        cmd_prefix = SHIFTX2ROOT + "/modules/shiftx/shiftx 1 " + inputfile + " " + sx1_outfile
-+        cmd_prefix = "shiftx 1 " + inputfile + " " + sx1_outfile
-         os.system(cmd_prefix)
-         if VERBOSE:
-             print cmd_prefix
-         # convert from table format to CSV
--        cmd_prefix = "python " + SHIFTX2ROOT + "/script/shiftx2shiftxp.py " + sx1_outfile + "  " + sxp_outfile
-+        cmd_prefix = "shiftx2shiftxp.py " + sx1_outfile + "  " + sxp_outfile
-         os.system(cmd_prefix)
-         if VERBOSE:
-             print cmd_prefix
-@@ -490,7 +489,7 @@ def single_mode(infile, outfile):
-     if not NOSHIFTY:
-         sys.path.append(SHIFTX2ROOT + "/shifty3")
-         os.chdir(SHIFTX2ROOT +"/shifty3")
--        shifty_cmd = "python shifty3.py -i " + inputfile + " -o " + sy_outfile + " -c 40 "
-+        shifty_cmd = "shifty3 -i " + inputfile + " -o " + sy_outfile + " -c 40 "
-         if DEUTERATED:
-             shifty_cmd = shifty_cmd + " -d"
-         if VERBOSE:
-@@ -513,7 +512,7 @@ def single_mode(infile, outfile):
-         return errmsg
-     
-     # combine result
--    combine_cmd = "python script/combine_cs.py " + sxp_outfile + " " + sy_outfile + " "
-+    combine_cmd = "combine_cs.py " + sxp_outfile + " " + sy_outfile + " "
-     combine_cmd = combine_cmd + outfile # specify output file name
- 
-     combine_cmd = add_atom_format_option(combine_cmd)
-@@ -543,7 +542,7 @@ def cleanup_tempfiles(files):
- if __name__ == '__main__':
-     print "## SHIFTX2 Ver 1.07 (Released 4 Jan. 2012) ##"
-     
--    SHIFTX2ROOT = sys.path[0]
-+    #SHIFTX2ROOT = sys.path[0]
- 
-     #if len(sys.argv)<3:
-     #    print "Usage: python shiftx2_main.py [input.pdb] [-atoms: all]"
-diff --git a/shiftx2_util.py b/shiftx2_util.py
-index d357a8e..6ce5e6c 100755
---- a/shiftx2_util.py
-+++ b/shiftx2_util.py
-@@ -1,4 +1,3 @@
--#!/usr/bin/env python
- ####################################################################
- # shiftx2_util.py: utility functions supporting shiftx2_main.py
- # 
-@@ -6,7 +5,7 @@
- # date: April 13th, 2011
- ####################################################################
- import sys, os
--from natsorted import *
-+from shiftx2.natsorted import *
- 
- # FUNCTIONS FOR SPLITING PDB FILE WITH MULTIPLE NMR MODELS
- 
-diff --git a/shifty3/shifty3.py b/shifty3/shifty3.py
-index 796af32..9360b87 100755
---- a/shifty3/shifty3.py
-+++ b/shifty3/shifty3.py
-@@ -12,7 +12,7 @@ import sys, os, re, datetime, time
- ###############################################################
- # path for xalign and blast executibles and blast databases
- XALIGN_EXE = "xalign_x" # executable for xalign
--BLASTP_EXE = "./blast/bin/blastall -p blastp" # executable for blast
-+BLASTP_EXE = "blastall -p blastp" # executable for blast
- 
- BLASTDB = "blastdb" # folder containing the blast database
- SHIFTDB = "refdb" # folder containing the BMRB shift database
diff --git a/sci-chemistry/shiftx2/metadata.xml b/sci-chemistry/shiftx2/metadata.xml
deleted file mode 100644
index e35d2bc02..000000000
--- a/sci-chemistry/shiftx2/metadata.xml
+++ /dev/null
@@ -1,42 +0,0 @@
-<?xml version="1.0" encoding="UTF-8"?>
-<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
-<pkgmetadata>
-	<maintainer type="project">
-		<email>sci-chemistry@gentoo.org</email>
-		<name>Gentoo Chemistry Project</name>
-	</maintainer>
-	<longdescription>
-SHIFTX2 predicts both the backbone and side chain 1H, 13C and 15N chemical
-shifts for proteins using their structural (PDB) coordinates as input.
-SHIFTX2 combines ensemble machine learning methods with sequence
-alignment-based methods to calculate protein chemical shifts for
-backbone
-and side chain atoms. SHIFTX2 has been trained on a carefully selected
-set of
-197 proteins and tested on a separate set of 61 proteins. Both the
-training
-and testing sets consisted of high resolution X-ray structures (less
-2.1A)
-with carefully verified chemical shifts assignments. SHIFTX2 is able to
-attain
-correlation coefficients between experimentally observed and predicted
-backbone chemical shifts of 0.9800 (15N), 0.9959 (13CA), 0.9992 (13CB),
-0.9676 (13CO), 0.9714 (1HN), 0.9744 (1HA) and RMS errors of 1.1169, 0.4412,
-0.5163, 0.5330, 0.1711, and 0.1231 ppm, respectively. Comparisons to
-other
-chemical shift predictors using the same testing data set indicates that
-SHIFTX2 is substantially more accurate (up to 26% better by
-correlation
-coefficient with an RMS error that is up to 3.3X smaller) than any other
-program.
-
-Please cite the following: Beomsoo Han, Yifeng Liu, Simon Ginzinger, and
-David Wishart. (2011) SHIFTX2: significantly improved protein chemical
-shift
-prediction. Journal of Biomolecular NMR, Volume 50, Number 1, 43-57.
-doi: 10.1007/s10858-011-9478-4.
-</longdescription>
-	<use>
-		<flag name="debug">Enables debug output in the shiftx2 java part</flag>
-	</use>
-</pkgmetadata>
diff --git a/sci-chemistry/shiftx2/shiftx2-1.07_p20120106.ebuild b/sci-chemistry/shiftx2/shiftx2-1.07_p20120106.ebuild
deleted file mode 100644
index 2b7a478af..000000000
--- a/sci-chemistry/shiftx2/shiftx2-1.07_p20120106.ebuild
+++ /dev/null
@@ -1,130 +0,0 @@
-# Copyright 1999-2015 Gentoo Foundation
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=5
-
-PYTHON_COMPAT=( python2_7 )
-
-inherit java-pkg-2 java-pkg-simple prefix python-r1 versionator
-
-MY_PV="$(delete_all_version_separators $(get_version_component_range 1-2))"
-MY_PATCH="20120106"
-MY_P="${PN}-v${MY_PV}-linux"
-
-DESCRIPTION="Predicts of backbone and side chain 1H, 13C and 15N CS for proteins"
-HOMEPAGE="http://shiftx2.wishartlab.com/"
-SRC_URI="http://shiftx2.wishartlab.com/download/${MY_P}-${MY_PATCH}.tgz"
-
-SLOT="0"
-LICENSE="all-rights-reserved"
-KEYWORDS="~amd64 ~x86 ~amd64-linux ~x86-linux"
-IUSE="debug"
-
-REQUIRED_USE="${PYTHON_REQUIRED_USE}"
-
-CDEPEND="dev-util/weka ${PYTHON_DEPS}"
-
-RDEPEND="${CDEPEND}
-	${PYTHON_DEPS}
-	dev-lang/R
-	sci-biology/ncbi-tools
-	sci-chemistry/reduce
-	>=virtual/jre-1.5"
-DEPEND="${CDEPEND}
-	>=virtual/jdk-1.5"
-
-S="${WORKDIR}"/${MY_P}
-
-QA_PREBUILT="/opt/.*"
-
-src_prepare() {
-	epatch \
-		"${FILESDIR}"/${P}-java.patch \
-		"${FILESDIR}"/${P}-system.patch \
-		"${FILESDIR}"/${P}-internal-name.patch \
-		"${FILESDIR}"/${P}-format-security.patch
-
-	rm "${S}"/src/FeatureRanges.java || die
-
-	shared=$(echo "${EPREFIX}/usr/share/${PN}" | sed -e 's/\//\\\//g')
-	sed -i -e "s/PUT_GENTOO_SHARE_PATH_HERE/${shared}/g" "${S}/src/ShiftXp.java" || die
-
-	if use debug; then
-		sed -i -e 's/DEBUG = false/DEBUG = true/g' "${S}/src/ShiftXp.java" || die
-	fi
-
-	# hack alert!
-	sed \
-		-e '/-o/s:$(GCC):$(GCC) $(LDFLAGS):g' \
-		-e '/-o/s:$(CC):$(CC) $(LDFLAGS):g' \
-		-i modules/*/Makefile || die
-
-	sed -e '/-o/s:$: -lm:g' -i "${S}/modules/resmf/Makefile" || die
-
-	eprefixify ${PN}.py
-}
-
-src_compile() {
-	mkdir "${S}"/build || die
-	ejavac -classpath "$(java-pkg_getjars weka)" -nowarn \
-		-d "${S}"/build $(find src/ -name "*.java")
-	jar cf "${PN}.jar" -C "${S}"/build . || die
-
-	einfo "Building module angles"
-	cd "${S}"/modules/angles || die
-	emake clean
-	emake CFLAGS="${CFLAGS}" GCC=$(tc-getCC) LINK="${LDFLAGS}" get_angles phipsi
-
-	einfo "Building module resmf"
-	cd "${S}"/modules/resmf || die
-	emake clean
-	emake CFLAGS="${CFLAGS}" GCC=$(tc-getCC) LINK="${LDFLAGS}" resmf
-
-	einfo "Building module effects"
-	cd "${S}"/modules/effects || die
-	emake clean
-	emake CFLAGS="${CFLAGS}" CC=$(tc-getCC) LINK="${LDFLAGS}" all
-}
-
-src_install() {
-	java-pkg_dojar "${PN}.jar"
-	java-pkg_dolauncher j${PN} --main "ShiftXp" --pkg_args "-dir ${EPREFIX}/usr/bin"
-
-	insinto /usr/share/${PN}
-	doins "${S}"/lib/{limitedcshift.dat,RandomCoil.csv,data-header.arff}
-	doins -r "${S}"/lib/predmodels
-
-	insinto /usr/share/${PN}/vader
-	doins -r "${S}"/modules/resmf/lib/*
-
-	local instdir="/opt/${PN}"
-	dodoc README 1UBQ.pdb
-	python_foreach_impl python_newscript ${PN}.py ${PN}
-	mv shiftx2_util.py shiftx2util.py || die
-	python_moduleinto ${PN}
-	touch __init__.py
-	python_foreach_impl python_domodule natsorted.py shiftx2util.py __init__.py
-
-	# other modules
-	dobin \
-		"${S}"/modules/angles/{get_angles,phipsi} \
-		"${S}"/modules/resmf/resmf \
-		"${S}"/modules/effects/caleffect
-
-	# script
-	python_foreach_impl python_doscript "${S}"/script/*py
-	exeinto ${instdir}/script
-	doexe "${S}"/script/*.r
-
-	# shifty3
-	python_foreach_impl python_newscript "${S}"/shifty3/*py shifty3
-	exeinto ${instdir}/shifty3
-	doexe "${S}"/shifty3/xalign_x
-	dosym ../${PN}/shifty3/xalign_x /opt/bin/xalign_x
-
-	insinto ${instdir}/shifty3
-	doins -r "${S}"/shifty3/{blastdb,refdb,xalign.parms,wt.rbo}
-
-	python_foreach_impl python_doscript "${S}"/shifty3/utils/*py
-	dobin "${S}"/shifty3/utils/create_blastdb.sh
-}
diff --git a/sci-chemistry/smmp/Manifest b/sci-chemistry/smmp/Manifest
deleted file mode 100644
index 1b54b5bcf..000000000
--- a/sci-chemistry/smmp/Manifest
+++ /dev/null
@@ -1 +0,0 @@
-DIST SMMP-3.0.5.tar.bz2 233378 SHA256 70d6b719d2c2ef1d34fd9897ad1c89a37c4d7531d80c904eee39dc8855aca31c SHA512 7a6701f267fc09ee966ec34854ca12443725dc01e3bdf6283eaac7fc82764030abbc10bd0c6eefef2652bb64a70d5a09dc338448ce9d0c31021219358d40920d WHIRLPOOL 1c2b390b85ad5a9cc4f00df6838f92b8dd29403648ca1a07bf8d71b409cc396fb3671201f271a65f4fecc70a99d25ed0be95c9f26ab15d6ce431c220c9e1d991
diff --git a/sci-chemistry/smmp/files/3.0.5-flags.patch b/sci-chemistry/smmp/files/3.0.5-flags.patch
deleted file mode 100644
index 6e37fdba8..000000000
--- a/sci-chemistry/smmp/files/3.0.5-flags.patch
+++ /dev/null
@@ -1,81 +0,0 @@
-diff --git a/Makefile b/Makefile
-index adf6cda..5104567 100644
---- a/Makefile
-+++ b/Makefile
-@@ -3,15 +3,15 @@
- #.SILENT:
- 
- %_p.o : %_p.f
--	$(MPIF90) $(F_FLAGS) $<
-+	$(FC) $(CFLAGS) -c $<
- 	
- .SUFFIXES:	.o .f
- .f.o:
--	$(F90) $(F_FLAGS) $<
-+	$(FC) $(CFLAGS) -c $<
- 
- .SUFFIXES:	.o .f90
- .f90.o:
--	$(F90) $(F_FLAGS) $<
-+	$(FC) $(CFLAGS) -c $<
- 
- # ==================================== Variables for compiling and linking
- # L_FLAGS=-g
-@@ -87,11 +87,11 @@ anneal canon  outpdb  minim  regul contacts interhbond hbond
- # ============================================== Linking
- 
- $(PROG):	$(OBJ) $(SOBJ) main.o
--	$(F90) -o $(PROG) $(L_FLAGS) main.o $(OBJ) $(SOBJ)
-+	$(FC) $(LDFLAGS) $(CFLAGS) -o $(PROG) main.o $(OBJ) $(SOBJ)
- 
- # Build parallel version of SMMP.
- parallel: $(OBJ) $(POBJ) main_p.o 
--	$(MPIF90) -o $(PROG) $(L_FLAGS) main_p.o $(OBJ) $(POBJ)
-+	$(FC) $(LDFLAGS) $(CFLAGS) -o $(PROG) main_p.o $(OBJ) $(POBJ)
- 
- # Cross compile for BlueGene/P 
- bgl: BGL_L_FLAGS = -L$(BGLSYS)/lib -lmpich.rts -lfmpich.rts -lmsglayer.rts -lrts.rts -ldevices.rts -qextname=flush
-diff --git a/EXAMPLES/Makefile b/EXAMPLES/Makefile
-index e30d086..1ccf590 100644
---- a/EXAMPLES/Makefile
-+++ b/EXAMPLES/Makefile
-@@ -2,15 +2,15 @@
- 
- #.SILENT:
- %_p.o : %_p.f
--	$(MPIF90) $(F_FLAGS) $<
-+	$(FC) $(CFLAGS) -c $<
- 
- .SUFFIXES:	.o .f
- .f.o:
--	$(F90) $(F_FLAGS) $<
-+	$(FC) $(CFLAGS) -c $<
- 
- .SUFFIXES:	.o .f90
- .f90.o:
--	$(F90) $(F_FLAGS) $<
-+	$(FC) $(CFLAGS) -c $<
- 
- # ==================================== Variables for compiling and linking
- # L_FLAGS=-O0 -g
-@@ -59,16 +59,16 @@ MCOBJ = ../canon.o ../metropolis.o ../rgyr.o
- all: minimization annealing multicanonical regularization parallel_tempering_s # rootmeansquaredev
- 
- minimization:	$(BASEOBJ) $(ENOBJ) minimization.o 
--	$(F90) -o minimization $(L_FLAGS) $(BASEOBJ) $(ENOBJ) minimization.o
-+	$(F90) $(LDFLAGS) -o minimization $(BASEOBJ) $(ENOBJ) minimization.o
- 
- annealing:	$(BASEOBJ) $(MCOBJS) $(ENOBJ) annealing.o
--	$(F90) -o annealing $(L_FLAGS) $(BASEOBJ) $(MCOBJ) $(ENOBJ) ../anneal.o ../zimmer.o annealing.o
-+	$(F90) $(LDFLAGS) -o annealing $(BASEOBJ) $(MCOBJ) $(ENOBJ) ../anneal.o ../zimmer.o annealing.o
- 
- multicanonical:	$(BASEOBJ) $(MCOBJS) $(ENOBJ) multicanonical.o ../mulcan_par_mod.o 
--	$(F90) -o multicanonical $(L_FLAGS) $(BASEOBJ) $(MCOBJ) $(ENOBJ) multicanonical.o ../mulcan_par_mod.o
-+	$(F90) $(LDFLAGS) -o multicanonical $(BASEOBJ) $(MCOBJ) $(ENOBJ) multicanonical.o ../mulcan_par_mod.o
- 
- regularization:	$(BASEOBJ) $(ENOBJ) regularization.o 
--	$(F90) -o regularization $(L_FLAGS) $(BASEOBJ) $(ENOBJ) regularization.o
-+	$(F90) $(LDFLAGS) -o regularization $(BASEOBJ) $(ENOBJ) regularization.o
- 
- # rootmeansquaredev:	$(BASEOBJ) $(ENOBJ) rootmeansquaredev.o
- #	$(F90) -o rootmeansquaredev $(L_FLAGS) $(BASEOBJ) $(ENOBJ) rootmeansquaredev.o
diff --git a/sci-chemistry/smmp/metadata.xml b/sci-chemistry/smmp/metadata.xml
deleted file mode 100644
index da36ecbfc..000000000
--- a/sci-chemistry/smmp/metadata.xml
+++ /dev/null
@@ -1,8 +0,0 @@
-<?xml version="1.0" encoding="UTF-8"?>
-<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
-<pkgmetadata>
-	<maintainer type="project">
-		<email>sci-chemistry@gentoo.org</email>
-		<name>Gentoo Chemistry Project</name>
-	</maintainer>
-</pkgmetadata>
diff --git a/sci-chemistry/smmp/smmp-3.0.5.ebuild b/sci-chemistry/smmp/smmp-3.0.5.ebuild
deleted file mode 100644
index a98764754..000000000
--- a/sci-chemistry/smmp/smmp-3.0.5.ebuild
+++ /dev/null
@@ -1,59 +0,0 @@
-# Copyright 1999-2014 Gentoo Foundation
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=5
-
-PYTHON_COMPAT=( python2_7 )
-
-inherit eutils fortran-2 python-r1 toolchain-funcs
-
-MY_PN="SMMP"
-MY_P="${MY_PN}-${PV}"
-
-DESCRIPTION="Simple Molecular Mechanics for Proteins"
-HOMEPAGE="http://smmp.berlios.de/"
-SRC_URI="mirror://berlios/${PN}/${MY_P}.tar.bz2"
-
-SLOT="0"
-LICENSE="GPL-2"
-KEYWORDS="~amd64 ~x86"
-IUSE="doc mpi test"
-
-REQUIRED_USE="${PYTHON_REQUIRED_USE}"
-
-RDEPEND="
-	${PYTHON_DEPS}
-	mpi? ( virtual/mpi )"
-DEPEND="${RDEPEND}
-	doc? ( app-doc/doxygen )"
-
-S="${WORKDIR}/${MY_P}"
-
-src_prepare() {
-	epatch "${FILESDIR}"/${PV}-flags.patch
-}
-
-src_compile() {
-	if use mpi; then
-		FC="mpif90"
-		target="parallel"
-	else
-		target="${PN}"
-	fi
-
-	emake ${target}
-}
-
-src_test() {
-	emake examples
-	cd EXAMPLES || die
-	bash smmp.cmd || die
-}
-
-src_install() {
-	dobin ${PN}
-	python_moduleinto ${PN}
-	python_foreach_impl python_domodule *.py
-	python_foreach_impl python_optimize
-	dodoc README
-}
diff --git a/sci-chemistry/ssp/ssp-09.11.ebuild b/sci-chemistry/ssp/ssp-09.11.ebuild
index baa761bc3..9b57c3350 100644
--- a/sci-chemistry/ssp/ssp-09.11.ebuild
+++ b/sci-chemistry/ssp/ssp-09.11.ebuild
@@ -1,7 +1,7 @@
-# Copyright 1999-2014 Gentoo Foundation
+# Copyright 1999-2021 Gentoo Authors
 # Distributed under the terms of the GNU General Public License v2
 
-EAPI=5
+EAPI=7
 
 DESCRIPTION="Secondary structure propensities"
 HOMEPAGE="http://abragam.med.utoronto.ca/software.html"
@@ -10,14 +10,14 @@ SRC_URI="http://pound.med.utoronto.ca/${PN}-Nov09.tar.gz"
 SLOT="0"
 LICENSE="all-rights-reserved"
 KEYWORDS="~amd64 ~x86 ~amd64-linux ~x86-linux"
-IUSE=""
 
 RDEPEND="dev-lang/perl"
-DEPEND=""
+DEPEND="${RDEPEND}"
 
-S="${WORKDIR}"/${PN}
+S="${WORKDIR}/${PN}"
 
 src_prepare() {
+	default
 	sed \
 		-e "s:\(REF\/\):${EPREFIX}/usr/share/${PN}/\1:g" \
 		-i ${PN} || die
diff --git a/sci-chemistry/talosn/Manifest b/sci-chemistry/talosn/Manifest
deleted file mode 100644
index 5f72416f1..000000000
--- a/sci-chemistry/talosn/Manifest
+++ /dev/null
@@ -1,2 +0,0 @@
-DIST talosn-4.01.2013.148.15.55.tgz 136721210 BLAKE2B 3ad589487ab4a8e53260ae47e00a3c20713f8447440e01f396d5a5cb330a1ca5b22050167f3f581a8e15e3d4c53f7e9b65c4b0ed171354715aea67be51b377f5 SHA512 3e6d38bff46f537dff7f6cc1b7dc9ea077e10aa3be5aaf167cc0fd4adc301f535a21012e3bc435a1db442843e9c7c4e1a7b0ad84d912afcfbb6b9f937743b053
-DIST talosn-4.12.2015.147.15.40.tgz 137958678 BLAKE2B 26aaa30afe21b35f2f2ea19010d4e8a517f7505eaae4340d15b1766beed8db9cc30b22e9be2448932ab52cdb9c4594409963a3a1cbdad78b5d1c661f50140337 SHA512 31804b7a03a7c16ea33845cd0c3e67744bba1910b3da4d89e59cd3e8038aec724877b70e597bc6dd749d5923818a470d2ff2748aba290a396f39677815297643
diff --git a/sci-chemistry/talosn/metadata.xml b/sci-chemistry/talosn/metadata.xml
deleted file mode 100644
index da36ecbfc..000000000
--- a/sci-chemistry/talosn/metadata.xml
+++ /dev/null
@@ -1,8 +0,0 @@
-<?xml version="1.0" encoding="UTF-8"?>
-<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
-<pkgmetadata>
-	<maintainer type="project">
-		<email>sci-chemistry@gentoo.org</email>
-		<name>Gentoo Chemistry Project</name>
-	</maintainer>
-</pkgmetadata>
diff --git a/sci-chemistry/talosn/talosn-4.01.2013.148.15.55-r3.ebuild b/sci-chemistry/talosn/talosn-4.01.2013.148.15.55-r3.ebuild
deleted file mode 100644
index d308ded66..000000000
--- a/sci-chemistry/talosn/talosn-4.01.2013.148.15.55-r3.ebuild
+++ /dev/null
@@ -1,67 +0,0 @@
-# Copyright 1999-2015 Gentoo Foundation
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=5
-
-inherit java-pkg-opt-2
-
-DESCRIPTION="Prediction of Protein bb and sc Torsion Angles from NMR Chemical Shifts"
-HOMEPAGE="http://spin.niddk.nih.gov/bax/software/TALOS-N/"
-SRC_URI="http://spin.niddk.nih.gov/bax/software/TALOS-N/talosn.tZ -> ${P}.tgz"
-
-SLOT="0"
-LICENSE="all-rights-reserved"
-KEYWORDS="~amd64 ~x86 ~amd64-linux ~x86-linux"
-IUSE="examples"
-
-DEPEND=">=virtual/jre-1.5:*"
-RDEPEND="${DEPEND}
-	app-shells/tcsh
-	sci-biology/ncbi-tools"
-
-S="${WORKDIR}"
-
-QA_PREBUILT="/opt/.*"
-
-src_prepare() {
-	local s64
-	use amd64 || s64="_x64"
-	rm -f bin/TALOSN.{linux,mac,static.*,winxp,linux9${s64}} || die
-
-	sed \
-		-e '/setenv TALOSN_DIR/d' \
-		-e "/set BLAST/s:=.*:= \"${EPREFIX}/usr/bin/blastpgp\":g" \
-		-e '/set NR_DBNAME/s:=.*:= ${BLASTDB}:g' \
-		-i talosn_ss || die
-}
-
-src_install() {
-	local TALOSN="/opt/${PN}"
-	exeinto ${TALOSN}/bin
-	doexe bin/*
-
-	exeinto ${TALOSN}/com
-	doexe com/*
-
-	exeinto /opt/bin
-	doexe talosn{,_ss}
-
-	insinto ${TALOSN}
-	doins -r tab
-
-	java-pkg_jarinto ${TALOSN}
-	java-pkg_dojar rama.jar
-
-	java-pkg_dolauncher jrama --jar rama.jar -into /opt/
-
-	if use examples; then
-		insinto /usr/share/${PN}
-		doins -r demo
-	fi
-
-	cat >> "${T}"/40talosn <<- EOF
-	TALOSN_DIR="${EPREFIX}/${TALOSN}"
-	#BLASTDB=
-	EOF
-	doenvd "${T}"/40talosn
-}
diff --git a/sci-chemistry/talosn/talosn-4.12.2015.147.15.40.ebuild b/sci-chemistry/talosn/talosn-4.12.2015.147.15.40.ebuild
deleted file mode 100644
index d308ded66..000000000
--- a/sci-chemistry/talosn/talosn-4.12.2015.147.15.40.ebuild
+++ /dev/null
@@ -1,67 +0,0 @@
-# Copyright 1999-2015 Gentoo Foundation
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=5
-
-inherit java-pkg-opt-2
-
-DESCRIPTION="Prediction of Protein bb and sc Torsion Angles from NMR Chemical Shifts"
-HOMEPAGE="http://spin.niddk.nih.gov/bax/software/TALOS-N/"
-SRC_URI="http://spin.niddk.nih.gov/bax/software/TALOS-N/talosn.tZ -> ${P}.tgz"
-
-SLOT="0"
-LICENSE="all-rights-reserved"
-KEYWORDS="~amd64 ~x86 ~amd64-linux ~x86-linux"
-IUSE="examples"
-
-DEPEND=">=virtual/jre-1.5:*"
-RDEPEND="${DEPEND}
-	app-shells/tcsh
-	sci-biology/ncbi-tools"
-
-S="${WORKDIR}"
-
-QA_PREBUILT="/opt/.*"
-
-src_prepare() {
-	local s64
-	use amd64 || s64="_x64"
-	rm -f bin/TALOSN.{linux,mac,static.*,winxp,linux9${s64}} || die
-
-	sed \
-		-e '/setenv TALOSN_DIR/d' \
-		-e "/set BLAST/s:=.*:= \"${EPREFIX}/usr/bin/blastpgp\":g" \
-		-e '/set NR_DBNAME/s:=.*:= ${BLASTDB}:g' \
-		-i talosn_ss || die
-}
-
-src_install() {
-	local TALOSN="/opt/${PN}"
-	exeinto ${TALOSN}/bin
-	doexe bin/*
-
-	exeinto ${TALOSN}/com
-	doexe com/*
-
-	exeinto /opt/bin
-	doexe talosn{,_ss}
-
-	insinto ${TALOSN}
-	doins -r tab
-
-	java-pkg_jarinto ${TALOSN}
-	java-pkg_dojar rama.jar
-
-	java-pkg_dolauncher jrama --jar rama.jar -into /opt/
-
-	if use examples; then
-		insinto /usr/share/${PN}
-		doins -r demo
-	fi
-
-	cat >> "${T}"/40talosn <<- EOF
-	TALOSN_DIR="${EPREFIX}/${TALOSN}"
-	#BLASTDB=
-	EOF
-	doenvd "${T}"/40talosn
-}
diff --git a/sci-chemistry/trajng/Manifest b/sci-chemistry/trajng/Manifest
deleted file mode 100644
index 513f1086c..000000000
--- a/sci-chemistry/trajng/Manifest
+++ /dev/null
@@ -1 +0,0 @@
-DIST trajng-0.6.1.tar.gz 391388 SHA256 32f3fab1c11d5d0957b7d04a85421240dd6ec7bc1d8278a52363d784a6becb4b SHA512 def39733e45763aa919c58ab56206c067996ac557b6a9bdcd81a2c7080c505aabba42ee1aa0ab9cb4086fcf01ad6dfc46aa5645534e366d38f085e5e7216e489 WHIRLPOOL 062f87bad7e9e3f24cf6ce0f38794f004dd441abb6eeae35b43c80a87d29ebb55d764a20fe43f0ee0828e53a885bbc908538b68fe7c05c3486404b3520106e48
diff --git a/sci-chemistry/trajng/metadata.xml b/sci-chemistry/trajng/metadata.xml
deleted file mode 100644
index 7daa2ce7e..000000000
--- a/sci-chemistry/trajng/metadata.xml
+++ /dev/null
@@ -1,12 +0,0 @@
-<?xml version="1.0" encoding="UTF-8"?>
-<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
-<pkgmetadata>
-	<maintainer type="person">
-		<email>alexxy@gentoo.org</email>
-		<name>Alexey Shvetsov</name>
-	</maintainer>
-	<maintainer type="project">
-		<email>sci-chemistry@gentoo.org</email>
-		<name>Gentoo Chemistry Project</name>
-	</maintainer>
-</pkgmetadata>
diff --git a/sci-chemistry/trajng/trajng-0.6.1.ebuild b/sci-chemistry/trajng/trajng-0.6.1.ebuild
deleted file mode 100644
index d7011169e..000000000
--- a/sci-chemistry/trajng/trajng-0.6.1.ebuild
+++ /dev/null
@@ -1,27 +0,0 @@
-# Copyright 1999-2014 Gentoo Foundation
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=5
-
-DESCRIPTION="TrajNG - Trajectory compression library"
-HOMEPAGE="http://www.uppmax.uu.se/Members/daniels/trajng-trajectory-compression-library"
-SRC_URI="http://www.uppmax.uu.se/Members/daniels/trajng-trajectory-compression-library/${P}.tar.gz"
-
-LICENSE="LGPL-2"
-SLOT="0"
-KEYWORDS="~amd64 ~amd64-linux ~x86-linux"
-IUSE="fortran mpi"
-
-DEPEND="
-	sci-libs/xdrfile
-	fortran? ( virtual/fortran )
-	mpi? ( virtual/mpi )
-"
-RDEPEND="${DEPEND}"
-
-src_configure() {
-	econf \
-		--with-xdrlib="${EPREFIX}/usr" \
-		$(use_enable fortran) \
-		$(use_enable mpi)
-}
diff --git a/sci-chemistry/unio/Manifest b/sci-chemistry/unio/Manifest
deleted file mode 100644
index 736a1b1df..000000000
--- a/sci-chemistry/unio/Manifest
+++ /dev/null
@@ -1 +0,0 @@
-DIST UNIO10-Distribution19Dec2013.tar.gz 57868953 BLAKE2B 549091997290b933b13ea3bc87b852f618b7d38e38fe407460bc1776aa1b045f058559f6a6f65e62a44f8379cf551c62a7ac4847418186675e639a6fc94ebf37 SHA512 92b2c747997cd012429768f677ab8c603ce678ebddf362c38c91c325e4ba01ca0ee7e763efa10a42cbbd1d7c13929d9af7adba128691780e3e0fc121c95d1d84
diff --git a/sci-chemistry/unio/metadata.xml b/sci-chemistry/unio/metadata.xml
deleted file mode 100644
index da36ecbfc..000000000
--- a/sci-chemistry/unio/metadata.xml
+++ /dev/null
@@ -1,8 +0,0 @@
-<?xml version="1.0" encoding="UTF-8"?>
-<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
-<pkgmetadata>
-	<maintainer type="project">
-		<email>sci-chemistry@gentoo.org</email>
-		<name>Gentoo Chemistry Project</name>
-	</maintainer>
-</pkgmetadata>
diff --git a/sci-chemistry/unio/unio-2.0.3-r1.ebuild b/sci-chemistry/unio/unio-2.0.3-r1.ebuild
deleted file mode 100644
index bbafdb824..000000000
--- a/sci-chemistry/unio/unio-2.0.3-r1.ebuild
+++ /dev/null
@@ -1,68 +0,0 @@
-# Copyright 1999-2015 Gentoo Foundation
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=5
-
-MY_P="UNIO10-Distribution19Dec2013"
-
-DESCRIPTION="Automated NMR Data Analysis"
-HOMEPAGE="http://perso.ens-lyon.fr/torsten.herrmann/Herrmann/Software.html"
-#SRC_URI="http://perso.ens-lyon.fr/torsten.herrmann/Academic//Academic_Download_files/${MY_P}.tar.gz"
-SRC_URI="${MY_P}.tar.gz"
-
-SLOT="0"
-KEYWORDS=""
-LICENSE="unio"
-IUSE=""
-
-RDEPEND="
-	app-shells/ksh
-	!prefix? (
-		>=x11-libs/libX11-1.6.2[abi_x86_32(-)]
-		>=x11-libs/libXext-1.3.2[abi_x86_32(-)]
-	)"
-DEPEND=""
-
-S="${WORKDIR}/UNIO_10"
-RESTRICT="fetch"
-
-QA_PREBUILT="opt/unio/*"
-
-pkg_nofetch() {
-	einfo "Please visit ${HOMEPAGE}"
-	einfo "and fetch ${A}"
-	einfo "into ${DISTDIR}"
-}
-
-src_install() {
-	mv Unio\'10 Unio10 || die
-	mv Unio10/Linux/{Unio\'10,Unio10} || die
-	rm -rf \
-		Unio10/MacOSX \
-		UnioAlgorithms/.DS_Store \
-		UnioAlgorithms/unio-2.0.2/src/unio/unioexe.Darwin* \
-		UnioAlgorithms/unio-2.0.2/src/echo/libEcho.a \
-		UnioAlgorithms/unio-2.0.2/License.pdf || die
-
-	insinto /opt/${PN}
-	doins -r Unio10 UnioAlgorithms UnioDocumentations
-	fperms 755 \
-		/opt/${PN}/Unio10/Linux/Unio10 \
-		/opt/${PN}/Unio10/Linux/Externals/revzip.so
-	chmod 755 \
-		"${ED}"/opt/${PN}/UnioAlgorithms/${PN}-2.0.2/bin/* \
-		"${ED}"/opt/${PN}/UnioAlgorithms/${PN}-2.0.2/src/${PN}/* || die
-
-	cat >> "${T}/${PN}" <<- EOF
-	#!${EPREFIX}/bin/bash
-	cd "${EPREFIX}/opt/${PN}"
-	exec Unio10/Linux/Unio10 \$@
-	EOF
-
-	dobin "${T}/${PN}"
-
-	local i
-	for i in ExecuteMatch ExecuteAtnosCandid ExecuteAtnosAscan; do
-		dosym ../${PN}/UnioAlgorithms/${PN}-2.0.2/bin/${i} /opt/bin/${i}
-	done
-}
diff --git a/sci-chemistry/usf-tools/Manifest b/sci-chemistry/usf-tools/Manifest
deleted file mode 100644
index 4e9816897..000000000
--- a/sci-chemistry/usf-tools/Manifest
+++ /dev/null
@@ -1,2 +0,0 @@
-DIST usf-tools-9999.tar.gz 108530172 BLAKE2B 5927d7630a9c80a6ff18188e8edf6b0aaca3b357c7420c08cad7a7521adbc246473039c35c983bf3bf48f892a601a305e46ecb2b6af1431e64b89016af39546f SHA512 2ec2d13080aa5f893cc6f980b3f014c107f6f8f822b36cdd57f6e6f046994d36c8d1eea629f6846d8ea608603d003fd74e543fc41410e50baf1433c56b179464
-DIST usf-tools-autotools-001.tar.xz 4916 BLAKE2B 7cb645333fae6d9f9d1c2a078a38548134c74af536a6da01afad614c3b4bf0d85df06e0a8b7efcc874bd11568c7daab58ec471361c28c2e858cd656e16112fa0 SHA512 04599fd4011e8b612d7f96e23917f363689f7e8619649ad9669a8f62ef25056b2c1c26bc8728b6acf97c9165f2106c35d4be7495342c27fc2accdd5626c24048
diff --git a/sci-chemistry/usf-tools/files/usf-tools-9999-longline.patch b/sci-chemistry/usf-tools/files/usf-tools-9999-longline.patch
deleted file mode 100644
index 028c0f45b..000000000
--- a/sci-chemistry/usf-tools/files/usf-tools-9999-longline.patch
+++ /dev/null
@@ -1,57 +0,0 @@
- gklib/pckrho.f |   24 ++++++++++++++++++------
- 1 files changed, 18 insertions(+), 6 deletions(-)
-
-diff --git a/gklib/pckrho.f b/gklib/pckrho.f
-index 31eefad..2dd5104 100644
---- a/gklib/pckrho.f
-+++ b/gklib/pckrho.f
-@@ -21,23 +21,33 @@ c        print *,'IX,IY,IZ    - ',ix, iy, iz
- c        print *,'JX,JY,LEVEL - ',jx,jy,level
- c        print *,'UVW         - ',uvw
- c
--	if (uvw(1) .eq. 1 .and. uvw(2) .eq. 2 .and. uvw(3) .eq. 3) then
-+        if (  uvw(1) .eq. 1
-+     :  .and. uvw(2) .eq. 2
-+     :  .and. uvw(3) .eq. 3) then
- 	  do 100 i=1,iy
- 	  do 100 j=1,ix
- 100	    sav(j,i,level) = rho(j,i)
--	else if (uvw(1) .eq. 1 .and. uvw(2) .eq. 3 .and. uvw(3) .eq. 2) then
-+        else if (uvw(1) .eq. 1
-+     :  .and.    uvw(2) .eq. 3
-+     :  .and.    uvw(3) .eq. 2) then
- 	  do 110 i=1,iz
- 	  do 110 j=1,ix
- 110	    sav(j,level,i) = rho(j,i)
--	else if (uvw(1) .eq. 2 .and. uvw(2) .eq. 1 .and. uvw(3) .eq. 3) then
-+        else if (uvw(1) .eq. 2
-+     :  .and.    uvw(2) .eq. 1
-+     :  .and.    uvw(3) .eq. 3) then
- 	  do 120 j=1,iy
- 	  do 120 i=1,ix
- 120	    sav(i,j,level) = rho(j,i)
--	else if (uvw(1) .eq. 2 .and. uvw(2) .eq. 3 .and. uvw(3) .eq. 1) then
-+        else if (uvw(1) .eq. 2
-+     :  .and.    uvw(2) .eq. 3
-+     :  .and.    uvw(3) .eq. 1) then
- 	  do 130 i=1,iz
- 	  do 130 j=1,iy
- 130	    sav(level,j,i) = rho(j,i)
--	else if (uvw(1) .eq. 3 .and. uvw(2) .eq. 1 .and. uvw(3) .eq. 2) then
-+        else if (uvw(1) .eq. 3
-+     :  .and.    uvw(2) .eq. 1
-+     :  .and.    uvw(3) .eq. 2) then
- 	  do 140 i=1,ix
- cxyz
- c          call ivalut (' I(x) now :',1,i)
-@@ -47,7 +57,9 @@ c            call ivalut (' J(z) now :',1,j)
- c            call rvalut (' RHO(j,i) :',1,rho(j,i))
- c            call rvalut (' SAV(I,LEVEL,J) :',1,sav(i,level,j))
- 140	    sav(i,level,j) = rho(j,i)
--	else if (uvw(1) .eq. 3 .and. uvw(2) .eq. 2 .and. uvw(3) .eq. 1) then
-+        else if (uvw(1) .eq. 3
-+     :  .and.    uvw(2) .eq. 2
-+     :  .and.    uvw(3) .eq. 1) then
- 	  do 150 i=1,iy
- 	  do 150 j=1,iz
- 150	    sav(level,i,j) = rho(j,i)
diff --git a/sci-chemistry/usf-tools/metadata.xml b/sci-chemistry/usf-tools/metadata.xml
deleted file mode 100644
index da36ecbfc..000000000
--- a/sci-chemistry/usf-tools/metadata.xml
+++ /dev/null
@@ -1,8 +0,0 @@
-<?xml version="1.0" encoding="UTF-8"?>
-<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
-<pkgmetadata>
-	<maintainer type="project">
-		<email>sci-chemistry@gentoo.org</email>
-		<name>Gentoo Chemistry Project</name>
-	</maintainer>
-</pkgmetadata>
diff --git a/sci-chemistry/usf-tools/usf-tools-9999.ebuild b/sci-chemistry/usf-tools/usf-tools-9999.ebuild
deleted file mode 100644
index b6561aad4..000000000
--- a/sci-chemistry/usf-tools/usf-tools-9999.ebuild
+++ /dev/null
@@ -1,33 +0,0 @@
-# Copyright 1999-2015 Gentoo Foundation
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=5
-
-AUTOTOOLS_AUTORECONF=y
-
-inherit autotools-utils flag-o-matic  fortran-2
-
-_AP=001
-
-DESCRIPTION="The USF program suite"
-HOMEPAGE="http://xray.bmc.uu.se/usf/"
-SRC_URI="
-	http://xray.bmc.uu.se/markh/usf/usf_distribution_kit.tar.gz -> ${P}.tar.gz
-	http://dev.gentoo.org/~jlec/distfiles/${PN}-autotools-${_AP}.tar.xz"
-
-SLOT="0"
-LICENSE="all-rights-reserved"
-KEYWORDS=""
-IUSE="static-libs"
-
-RDEPEND="
-	sci-libs/libccp4
-	sci-libs/mmdb:0"
-DEPEND="${RDEPEND}"
-
-S="${WORKDIR}"/usf_export
-
-src_prepare() {
-	append-fflags -ffixed-line-length-132 -DLINUX -cpp
-	autotools-utils_src_prepare
-}
diff --git a/sci-chemistry/wxmacmolplt/Manifest b/sci-chemistry/wxmacmolplt/Manifest
deleted file mode 100644
index 2e9c5e4b9..000000000
--- a/sci-chemistry/wxmacmolplt/Manifest
+++ /dev/null
@@ -1 +0,0 @@
-DIST wxmacmolplt-7.6.2.tar.gz 2360572 BLAKE2B 4fccd580a7dc65cc25defa9d809b23fbfd248106ba0c7816ceafb41b30ba566633a09bb2976a5397524ace74be8ea2055c9b3a236246abcb6e03cc7be3663e1b SHA512 6b7c36f3833b7fda984c9c05a361185912a9bb447409c74cdd60835df9c68ab8ce1a47596ff365f4dc6f70566b64ab185dc57367975d16bec1ec27159515b711
diff --git a/sci-chemistry/wxmacmolplt/metadata.xml b/sci-chemistry/wxmacmolplt/metadata.xml
deleted file mode 100644
index fdedec61f..000000000
--- a/sci-chemistry/wxmacmolplt/metadata.xml
+++ /dev/null
@@ -1,23 +0,0 @@
-<?xml version="1.0" encoding="UTF-8"?>
-<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
-<pkgmetadata>
-	<maintainer type="project">
-		<email>sci-chemistry@gentoo.org</email>
-		<name>Gentoo Chemistry Project</name>
-	</maintainer>
-	<longdescription>
-wxMacMolPlt is a program for plotting 3D molecular structures and normal
-modes (vibrations), various orbitals and electron density maps. It reads a
-variety of file formats including any GAMESS input, log or IRC file
-directly to create animations. It has a simple GAMESS input (.inp) builder
-and a primitive molecule builder.
-</longdescription>
-	<use>
-		<flag name="flash">
-Add support for flash movie generation using <pkg>media-libs/ming</pkg>
-</flag>
-	</use>
-	<upstream>
-		<remote-id type="github">brettbode/wxmacmolplt</remote-id>
-	</upstream>
-</pkgmetadata>
diff --git a/sci-chemistry/wxmacmolplt/wxmacmolplt-7.6.2.ebuild b/sci-chemistry/wxmacmolplt/wxmacmolplt-7.6.2.ebuild
deleted file mode 100644
index b806425b5..000000000
--- a/sci-chemistry/wxmacmolplt/wxmacmolplt-7.6.2.ebuild
+++ /dev/null
@@ -1,46 +0,0 @@
-# Copyright 1999-2017 Gentoo Foundation
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=6
-
-WX_GTK_VER=3.0
-
-inherit autotools eutils wxwidgets
-
-DESCRIPTION="Chemical 3D graphics program with GAMESS input builder"
-HOMEPAGE="http://brettbode.github.io/wxmacmolplt/"
-SRC_URI="https://github.com/brettbode/${PN}/archive/v${PV}.tar.gz -> ${P}.tar.gz"
-
-LICENSE="GPL-2"
-KEYWORDS="~amd64 ~x86"
-SLOT="0"
-IUSE="flash"
-
-RDEPEND="
-	media-libs/glew:0=
-	media-libs/mesa
-	x11-libs/wxGTK:${WX_GTK_VER}[X,opengl]
-	flash? ( media-libs/ming )"
-DEPEND="${RDEPEND}
-	virtual/pkgconfig"
-
-src_prepare() {
-	default
-
-	sed \
-		-e "/^dist_doc_DATA/d" \
-		-i Makefile.am || die "Failed to disable installation of LICENSE file"
-	eautoreconf
-}
-
-src_configure() {
-	econf \
-		--with-glew \
-		$(use_with flash ming)
-}
-
-src_install() {
-	default
-	doicon resources/${PN}.png
-	make_desktop_entry ${PN} wxMacMolPlt ${PN} "Science;DataVisualization;"
-}
diff --git a/sci-chemistry/xplor-nih/Manifest b/sci-chemistry/xplor-nih/Manifest
deleted file mode 100644
index 8239f141a..000000000
--- a/sci-chemistry/xplor-nih/Manifest
+++ /dev/null
@@ -1,2 +0,0 @@
-DIST xplor-nih-2.38-Linux_x86_64.tar.gz 289483789 BLAKE2B e3cd0ac5a13ff9926d27697c44ebd8db459601891ec0392bb18f07aa59ff2e92604c710589c3bf452864474cbe627b5a63927aeafa3b141c80124dcfd03733aa SHA512 0da2df4dec086691ce75d0a2cc81e403c6ff06a360646fc53d71001dc3b976d43aa555b5e53e3f62f7ac0a6d5200c070c6f9f8fe3dafd611cd81739f6d12f530
-DIST xplor-nih-2.38-db.tar.gz 55856892 BLAKE2B c2882ee623634f9e446d61179565cb1c76d6c50ce680e9d797a01e287836f2d30cd0ac395e4f10e9c790714e6adba424a8aac9c169d7bd6736c06eabc63ba6be SHA512 d05001f0468126a8e65b4d234aeddefb87b41c743bcc04e27766224b16f8cd9f3cb85a7ae85f39787eaa0c9b792790b16fd3f7e1f108e81666dcf85034d76f33
diff --git a/sci-chemistry/xplor-nih/metadata.xml b/sci-chemistry/xplor-nih/metadata.xml
deleted file mode 100644
index b7595a302..000000000
--- a/sci-chemistry/xplor-nih/metadata.xml
+++ /dev/null
@@ -1,8 +0,0 @@
-<?xml version="1.0" encoding="UTF-8"?>
-<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
-<pkgmetadata>
-	<maintainer type="person">
-		<email>jlec@gentoo.org</email>
-		<name>Justin Lecher</name>
-	</maintainer>
-</pkgmetadata>
diff --git a/sci-chemistry/xplor-nih/xplor-nih-2.38.ebuild b/sci-chemistry/xplor-nih/xplor-nih-2.38.ebuild
deleted file mode 100644
index 57a727778..000000000
--- a/sci-chemistry/xplor-nih/xplor-nih-2.38.ebuild
+++ /dev/null
@@ -1,53 +0,0 @@
-# Copyright 1999-2017 Gentoo Foundation
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=6
-
-PYTHON_COMPAT=( python2_7 )
-
-inherit python-single-r1
-
-DESCRIPTION="Structure determination program which builds on the X-PLOR program"
-HOMEPAGE="http://nmr.cit.nih.gov/xplor-nih/"
-SRC_URI="
-	${P}-Linux_x86_64.tar.gz
-	${P}-db.tar.gz
-	"
-
-SLOT="0"
-LICENSE="XPLOR-NIH"
-KEYWORDS="~amd64 ~x86 ~amd64-linux ~x86-linux"
-IUSE=""
-
-REQUIRED_USE="${PYTHON_REQUIRED_USE}"
-
-RDEPEND="${PYTHON_DEPS}
-	dev-lang/tcl:8.5
-	dev-lang/tk:8.5
-	dev-libs/libedit
-	sys-libs/ncurses:5/5
-"
-DEPEND="${RDEPEND}"
-
-RESTRICT="fetch"
-
-QA_PREBUILT="opt/.*"
-
-pkg_nofetch() {
-	elog "Please visit ${HOMEPAGE} and download ${A}"
-	elog "into ${DISTDIR}"
-}
-
-src_configure() { :; }
-
-src_install() {
-	dodoc Changes INSTALL README.beowulf README.dist References parallel.txt
-
-	dodir /opt/${P} /opt/bin
-	mv * "${ED}"/opt/${P}/ || die
-
-	cd "${ED}"/opt/${P} || die
-	bash ./configure -symlinks "${ED}"/opt/bin || die
-
-	python_optimize /opt/${P}
-}
diff --git a/sci-electronics/minipro/Manifest b/sci-electronics/minipro/Manifest
new file mode 100644
index 000000000..d37c88485
--- /dev/null
+++ b/sci-electronics/minipro/Manifest
@@ -0,0 +1 @@
+DIST minipro-0.5.tar.gz 388754 BLAKE2B c22110c269405e7b8ff81fd7c649c2b652bc39da84d92cf9a151da71a1c6d4a202baa6ae13a1fb789a04c8e57f3cc9a60403bcef82896320d95e2507c5960f01 SHA512 e2341213bc43ef53b106211d07a488a142083fe4b6dd6ced0f02595164ce2e0e47f6bdc0a6f6c63f19b9b9438c8f5ad173485953d8a29cb39f89272f8e70dc7c
diff --git a/sci-electronics/minipro/files/minipro-0.5-makefile.patch b/sci-electronics/minipro/files/minipro-0.5-makefile.patch
new file mode 100644
index 000000000..221643895
--- /dev/null
+++ b/sci-electronics/minipro/files/minipro-0.5-makefile.patch
@@ -0,0 +1,12 @@
+can't seem to override PREFIX at build time, so patch it
+--- minipro-0.5/Makefile	2020-11-04 21:35:31.000000000 -0800
++++ minipro-0.5/Makefile	2022-07-22 11:42:54.866390621 -0700
+@@ -9,7 +9,7 @@
+ 
+ # Normally minipro is installed to /usr/local.  If you want to put it
+ # somewhere else, define that location here.
+-PREFIX ?= /usr/local
++PREFIX ?= /usr
+ MANDIR ?= $(PREFIX)/share/man
+ 
+ # Some older releases of MacOS need some extra library flags.
diff --git a/sci-electronics/minipro/metadata.xml b/sci-electronics/minipro/metadata.xml
index 430c9ea1b..438079e92 100644
--- a/sci-electronics/minipro/metadata.xml
+++ b/sci-electronics/minipro/metadata.xml
@@ -5,6 +5,13 @@
 		<email>sci-electronics@gentoo.org</email>
 		<name>Gentoo Electronics Project</name>
 	</maintainer>
+	<maintainer type="person">
+		<email>scott@alfter.us</email>
+		<name>Scott Alfter</name>
+	</maintainer>
+	<longdescription lang="en">
+		an open-source program for controlling the MiniPRO TL866xx series of chip programmers
+	</longdescription>
 	<upstream>
 		<remote-id type="github">vdudouyt/minipro</remote-id>
 	</upstream>
diff --git a/sci-electronics/minipro/minipro-0.5.ebuild b/sci-electronics/minipro/minipro-0.5.ebuild
new file mode 100644
index 000000000..60854d55c
--- /dev/null
+++ b/sci-electronics/minipro/minipro-0.5.ebuild
@@ -0,0 +1,27 @@
+# Copyright 1999-2022 Gentoo Authors
+# Distributed under the terms of the GNU General Public License v2
+
+EAPI=8
+
+inherit udev
+
+DESCRIPTION="A free and open TL866XX programmer"
+HOMEPAGE="https://gitlab.com/DavidGriffith/minipro"
+SRC_URI="https://gitlab.com/DavidGriffith/minipro/-/archive/${PV}/${P}.tar.gz"
+
+LICENSE="GPL-3"
+SLOT="0"
+KEYWORDS="~amd64"
+
+RDEPEND="virtual/libusb:1"
+DEPEND="${RDEPEND}"
+
+PATCHES=( "${FILESDIR}/${P}-makefile.patch" )
+
+pkg_postinst() {
+	udev_reload
+}
+
+pkg_postrm() {
+	udev_reload
+}
diff --git a/sci-electronics/minipro/minipro-9999.ebuild b/sci-electronics/minipro/minipro-9999.ebuild
deleted file mode 100644
index 4d0d0924b..000000000
--- a/sci-electronics/minipro/minipro-9999.ebuild
+++ /dev/null
@@ -1,26 +0,0 @@
-# Copyright 1999-2016 Gentoo Foundation
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=6
-
-inherit bash-completion-r1 git-r3 udev
-
-DESCRIPTION="A free and open TL866XX programmer"
-HOMEPAGE="https://github.com/vdudouyt/minipro"
-EGIT_REPO_URI="https://github.com/vdudouyt/minipro.git"
-
-LICENSE="GPL-3"
-SLOT="0"
-KEYWORDS=""
-IUSE=""
-
-RDEPEND="virtual/libusb:1"
-DEPEND="${RDEPEND}"
-
-src_install() {
-	dobin ${PN}{,-query-db,hex}
-	udev_dorules udev/rules.d/80-${PN}.rules
-	doman man/${PN}.1
-	dobashcomp bash_completion.d/${PN}
-	bashcomp_alias ${PN} ${PN}-query-db
-}
diff --git a/sci-electronics/mpremote/Manifest b/sci-electronics/mpremote/Manifest
new file mode 100644
index 000000000..1e55b52d3
--- /dev/null
+++ b/sci-electronics/mpremote/Manifest
@@ -0,0 +1,2 @@
+DIST mpremote-0.4.0.tar.gz 27266 BLAKE2B b31b6184d0f4fc5c525ea7d5d8d2722404e9ce82ce143ea9a14b8bdef28af3260514dd25ec756a0ac2507d5b206fa9d07ce67bd2228b1568d9495c9082bdace8 SHA512 580f0286d8973a93105a04c681428f798e0d72b4b75debbc43f8e49ea7a81da849987aeab795baff66c9cf40607fde27fb54b7b32ab311ae5e9fb3b8f8f976fc
+DIST mpremote-1.22.0.tar.gz 24042 BLAKE2B 8bd6df4b9a46c10a93d42974a569adb42577d2783cb78b5b76ac6a6750f8219611ca49106ed91cb7f69910e3dfb28bb07a4522dbd721af0baac94d3e793c0576 SHA512 a3135e3be347370c967b7dc936f112e1ed5898288fa2dda4c485d216ebf432cb9706e539299d6769c1982ac02e456e9594ed2a7a86cbac2a1c7d08f2ff8a980b
diff --git a/sci-electronics/mpremote/files/mpremote-1.22.0-requirements_txt.patch b/sci-electronics/mpremote/files/mpremote-1.22.0-requirements_txt.patch
new file mode 100644
index 000000000..4d06c25aa
--- /dev/null
+++ b/sci-electronics/mpremote/files/mpremote-1.22.0-requirements_txt.patch
@@ -0,0 +1,12 @@
+--- a/pyproject.toml	2020-02-01 19:00:00.000000000 -0500
++++ b/pyproject.toml	2024-01-22 03:59:19.414593373 -0500
+@@ -33,9 +33,6 @@
+ [project.scripts]
+ mpremote = "mpremote.main:main"
+
+-[tool.hatch.metadata.hooks.requirements_txt]
+-files = ["requirements.txt"]
+-
+ # This will be PEP-440 normalised into either:
+ # mpremote-X.Y.Z (on vX.Y.Z release tag)
+ # mpremote-X.Y.Zrc0 (on vX.Y.Z-preview tag, i.e. first commit in the cycle)
diff --git a/sci-electronics/mpremote/metadata.xml b/sci-electronics/mpremote/metadata.xml
new file mode 100644
index 000000000..820065154
--- /dev/null
+++ b/sci-electronics/mpremote/metadata.xml
@@ -0,0 +1,20 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
+<pkgmetadata>
+	<maintainer type="project">
+		<email>sci-electronics@gentoo.org</email>
+		<name>Gentoo Electronics Project</name>
+	</maintainer>
+	<maintainer type="person">
+		<email>gentoo@chymera.eu</email>
+		<name>Horea Christian</name>
+	</maintainer>
+	<longdescription lang="en">
+		This CLI tool provides an integrated set of utilities to remotely interact with
+		and automate a MicroPython device over a serial connection.
+	</longdescription>
+	<upstream>
+		<remote-id type="github">micropython/micropython</remote-id>
+		<remote-id type="pypi">mpremote</remote-id>
+	</upstream>
+</pkgmetadata>
diff --git a/sci-electronics/mpremote/mpremote-0.4.0.ebuild b/sci-electronics/mpremote/mpremote-0.4.0.ebuild
new file mode 100644
index 000000000..80056b01e
--- /dev/null
+++ b/sci-electronics/mpremote/mpremote-0.4.0.ebuild
@@ -0,0 +1,28 @@
+# Copyright 1999-2023 Gentoo Authors
+# Distributed under the terms of the GNU General Public License v2
+
+EAPI=8
+
+PYTHON_COMPAT=( python3_{10..11} )
+# Next release will move to hatchling:
+# https://github.com/micropython/micropython/pull/10645
+#DISTUTILS_USE_PEP517=hatchling
+DISTUTILS_USE_PEP517=setuptools
+
+inherit distutils-r1 pypi
+
+DESCRIPTION="MicroPython remote control"
+HOMEPAGE="https://github.com/micropython/micropython/tree/master/tools/mpremote"
+
+LICENSE="MIT"
+SLOT="0"
+KEYWORDS="~amd64 ~x86"
+
+RDEPEND="
+	dev-python/pyserial[${PYTHON_USEDEP}]
+	dev-python/importlib-metadata[${PYTHON_USEDEP}]
+"
+
+# The package might not have a test suite:
+# https://github.com/orgs/micropython/discussions/11308
+#distutils_enable_tests pytest
diff --git a/sci-electronics/mpremote/mpremote-1.22.0.ebuild b/sci-electronics/mpremote/mpremote-1.22.0.ebuild
new file mode 100644
index 000000000..741478265
--- /dev/null
+++ b/sci-electronics/mpremote/mpremote-1.22.0.ebuild
@@ -0,0 +1,29 @@
+# Copyright 1999-2023 Gentoo Authors
+# Distributed under the terms of the GNU General Public License v2
+
+EAPI=8
+
+PYTHON_COMPAT=( python3_{10..12} )
+DISTUTILS_USE_PEP517=hatchling
+
+inherit distutils-r1 pypi
+
+DESCRIPTION="MicroPython remote control"
+HOMEPAGE="https://github.com/micropython/micropython/tree/master/tools/mpremote"
+
+LICENSE="MIT"
+SLOT="0"
+KEYWORDS="~amd64 ~x86"
+
+RDEPEND="
+	dev-python/pyserial[${PYTHON_USEDEP}]
+	dev-python/importlib-metadata[${PYTHON_USEDEP}]
+"
+
+PATCHES=(
+	"${FILESDIR}/${P}-requirements_txt.patch"
+)
+
+# The package might not have a test suite:
+# https://github.com/orgs/micropython/discussions/11308
+#distutils_enable_tests pytest
diff --git a/sci-electronics/player/Manifest b/sci-electronics/player/Manifest
deleted file mode 100644
index 6f16ebe09..000000000
--- a/sci-electronics/player/Manifest
+++ /dev/null
@@ -1 +0,0 @@
-DIST player-2.0.4.tar.bz2 1707996 BLAKE2B 14edfb5309d437d86e5c731687e50ab580349dea7b056f8f5b7a168bc13e67aaba58fd76f35daf2190638b715af5679adc0215933c86b76bd881e509bca60801 SHA512 b420a4e389e8d02c988acff66d352af36edf38e8479dd065c0bec3a5a52964030801d5518c2a03c18a75b9cefe71617da09dc8f12a4eb485c820e1785c8c6262
diff --git a/sci-electronics/player/metadata.xml b/sci-electronics/player/metadata.xml
deleted file mode 100644
index ddd7312d4..000000000
--- a/sci-electronics/player/metadata.xml
+++ /dev/null
@@ -1,17 +0,0 @@
-<?xml version="1.0" encoding="UTF-8"?>
-<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
-<pkgmetadata>
-	<maintainer type="project">
-		<email>sci-electronics@gentoo.org</email>
-		<name>Gentoo Electronics Project</name>
-	</maintainer>
-	<use>
-		<flag name="sphinx2">Automatically generated description for sphinx2</flag>
-		<flag name="boost">Automatically generated description for boost</flag>
-		<flag name="openssl">Automatically generated description for openssl</flag>
-		<flag name="festival">Automatically generated description for festival</flag>
-	</use>
-	<upstream>
-		<remote-id type="sourceforge">playerstage</remote-id>
-	</upstream>
-</pkgmetadata>
diff --git a/sci-electronics/player/player-2.0.4.ebuild b/sci-electronics/player/player-2.0.4.ebuild
deleted file mode 100644
index a0058a12d..000000000
--- a/sci-electronics/player/player-2.0.4.ebuild
+++ /dev/null
@@ -1,126 +0,0 @@
-# Copyright 1999-2015 Gentoo Foundation
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=5
-
-PYTHON_COMPAT=( python2_7 )
-
-inherit eutils java-pkg-opt-2 python-single-r1
-
-DESCRIPTION="A network server for robot control"
-HOMEPAGE="http://playerstage.sourceforge.net/index.php?src=player"
-SRC_URI="mirror://sourceforge/playerstage/${P}.tar.bz2"
-
-LICENSE="GPL-2"
-SLOT="0"
-KEYWORDS="~amd64 ~x86"
-
-#DRIVERS NOT INCLUDED
-#	nd            - unknown
-#	passthrough   - unknown
-#   artoolkitplus - needs arToolKitPlus (not in portage)
-#	garcia        - needs Garcia (not in portage)
-#	imageseq      - needs openCV (not in portage)
-#	shapetracker  - needs openCV (not in portage)
-#	simpleshape   - needs openCV (not in portage)
-#	upcbarcode    - needs openCV (not in portage)
-#	isense        - needs iSense (not in portage)
-#	nomad         - needs Creative Nomad (maybe in portage)
-#	yarpimage     - needs YarpCam (not in portage)
-#	rcore_xbridge - needs libparticle (not in portage)
-
-IUSE="ieee1394 imagemagick sphinx2 test v4l wifi
-	boost gnome gtk openssl festival
-	opengl glut gsl java python doc"
-
-REQUIRED_USE="python? ( ${PYTHON_REQUIRED_USE} )"
-
-RDEPEND="
-	virtual/jpeg:0
-	boost? ( dev-libs/boost:= )
-	festival? ( app-accessibility/festival )
-	gtk? ( x11-libs/gtk+:2 )
-	glut? ( media-libs/freeglut )
-	gnome? ( >=gnome-base/libgnomecanvas-2.0 )
-	gsl? ( sci-libs/gsl )
-	ieee1394? ( sys-libs/libraw1394 media-libs/libdc1394 )
-	imagemagick? ( media-gfx/imagemagick )
-	java? ( virtual/jdk:* )
-	opengl? ( virtual/opengl )
-	openssl? ( dev-libs/openssl:0= )
-	python? ( ${PYTHON_DEPS} )
-	sphinx2? ( app-accessibility/sphinx2 )"
-DEPEND="${RDEPEND}
-	doc? ( app-doc/doxygen )
-	java? ( dev-lang/swig:0 )
-	python? ( dev-lang/swig:0 )"
-
-pkg_setup () {
-	use python && python-single-r1_pkg_setup
-	use java && java-pkg-opt-2_pkg_setup
-}
-
-src_prepare() {
-	use java && java-pkg-opt-2_src_prepare
-}
-
-src_configure() {
-	local drivers driver nodep_drivers
-
-	nodep_drivers="acoustics acts amcl amtecpowercube
-		aodv bumpersafe canonvcc4 clodbuster cmucam2
-		cmvision dummy er1 fakelocalize flockofbirds
-		garminnmea iwspy khepera laserbar laserbarcode
-		lasercspace laserposeinterpolator laserrescan
-		lasersafe laservisualbarcode laservisualbw
-		lifomcom linuxjoystick logfile mapcspace
-		microstrain mixer obot p2os erratic wbr914
-		ptu46 reb relay kartowriter rflex segwayrmp
-		service_adv_mdns sicklms200 sicknav200 sickpls
-		sicks3000 highspeedsick sonyevid30 urglaser	vfh
-		vmapfile waveaudio roomba wavefront insideM300
-		skyetekM1 mica2 cameracompress"
-
-	for driver in ${NODEP_DRIVERS}; do
-		drivers="${drivers} $(use_enable ${driver})"
-	done
-	drivers="${drivers}
-		$(use_enable sphinx2)
-		$(use_enable gtk mapfile)
-		$(use_enable gtk mapscale)
-		$(use_enable wifi linuxwifi)
-		$(use_enable festival)
-		$(use_enable v4l camerauvc)
-		$(use_enable v4l camerav4l)
-		$(use_enable v4l sphere)
-		$(use_enable ieee1394 camera1394)"
-
-	econf \
-		$(use_enable java jplayer) \
-		$(use_enable openssl md5) \
-		$(use_enable python libplayerc-py) \
-		$(use_enable gtk rtkgui) \
-		$(use_enable test tests) \
-		--with-playercc \
-		${drivers}
-}
-
-src_compile() {
-	# Parallel make will fail
-	emake -j1
-
-	if use doc; then
-		cd doc || die
-		emake doc
-	fi
-}
-
-src_install() {
-	default
-
-	if use doc; then
-		cd doc || die
-		emake DESTDIR="${D}" doc-install
-	fi
-
-}
diff --git a/sci-electronics/stage/Manifest b/sci-electronics/stage/Manifest
deleted file mode 100644
index 5e2dd2614..000000000
--- a/sci-electronics/stage/Manifest
+++ /dev/null
@@ -1 +0,0 @@
-DIST stage-2.0.3.tar.bz2 451664 BLAKE2B 3ffb33a6cca96ed25abdde6d88c6ceaa11d1d79ec4c477fb40060357e7aff4ccc1cb287b6aef57662d05adc5cbf1559b93075da827b96345834ef92bee94f4b8 SHA512 1126b923dce49a8ea278fba39e3af87cf79273102e7349ec5418e421853f39dbc0512e71246b503bc34d96d424512f327a501ff5c1a22ba80c585ccf07f63de3
diff --git a/sci-electronics/stage/files/stage-2.0.3-docdst-fix.patch b/sci-electronics/stage/files/stage-2.0.3-docdst-fix.patch
deleted file mode 100644
index 889a03d22..000000000
--- a/sci-electronics/stage/files/stage-2.0.3-docdst-fix.patch
+++ /dev/null
@@ -1,12 +0,0 @@
-diff -ur stage-2.0.3/docsrc/Makefile.am stage-2.0.3-fix/docsrc/Makefile.am
---- stage-2.0.3/docsrc/Makefile.am	2006-06-09 02:39:47.000000000 +0200
-+++ stage-2.0.3-fix/docsrc/Makefile.am	2007-07-14 15:06:31.414020298 +0200
-@@ -9,7 +9,7 @@
- 
- #header.html
- 
--DOCDIR = $(prefix)/share/doc
-+DOCDIR = $(DESTDIR)$(prefix)/share/doc
- 
- # build docs manually with 'make doc'
- doc:
diff --git a/sci-electronics/stage/metadata.xml b/sci-electronics/stage/metadata.xml
deleted file mode 100644
index c131c2eda..000000000
--- a/sci-electronics/stage/metadata.xml
+++ /dev/null
@@ -1,11 +0,0 @@
-<?xml version="1.0" encoding="UTF-8"?>
-<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
-<pkgmetadata>
-	<maintainer type="project">
-		<email>sci-electronics@gentoo.org</email>
-		<name>Gentoo Electronics Project</name>
-	</maintainer>
-	<upstream>
-		<remote-id type="sourceforge">playerstage</remote-id>
-	</upstream>
-</pkgmetadata>
diff --git a/sci-electronics/stage/stage-2.0.3.ebuild b/sci-electronics/stage/stage-2.0.3.ebuild
deleted file mode 100644
index fe93f8fcb..000000000
--- a/sci-electronics/stage/stage-2.0.3.ebuild
+++ /dev/null
@@ -1,60 +0,0 @@
-# Copyright 1999-2015 Gentoo Foundation
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=5
-
-inherit autotools eutils
-
-DESCRIPTION="2D multiple-robot simulator"
-HOMEPAGE="http://playerstage.sourceforge.net/index.php?src=stage"
-SRC_URI="mirror://sourceforge/playerstage/stage-${PV}.tar.bz2"
-
-LICENSE="GPL-2"
-SLOT="0"
-KEYWORDS="~amd64 ~x86"
-
-IUSE="doc"
-
-RDEPEND="
-	x11-libs/gtk+:2
-	>=sci-electronics/player-2.0.2
-	x11-apps/rgb"
-DEPEND="${RDEPEND}
-	doc? ( app-doc/doxygen )"
-
-src_prepare() {
-	epatch "${FILESDIR}"/${P}-docdst-fix.patch
-	sed -i \
-		-e 's;/usr/X11R6/lib/X11/rgb.txt;/usr/share/X11/rgb.txt;' \
-		configure.ac || die "sed failed"
-	eautoreconf
-}
-
-src_configure() {
-	#Disable gnome-canvas since its experimental
-	econf --disable-gnomecanvas
-}
-
-src_compile() {
-	default
-
-	if use doc; then
-		pushd docsrc
-		doxygen -u stage.dox || die "doxygen failed"
-		touch header.html || die
-		emake "doc"
-		popd
-	fi
-}
-
-src_install() {
-	default
-
-	if use doc; then
-		pushd docsrc
-		emake DESTDIR="${D}" "doc-install"
-		popd
-	fi
-
-	dodoc AUTHORS ChangeLog NEWS README
-}
diff --git a/sci-electronics/tnt/Manifest b/sci-electronics/tnt/Manifest
deleted file mode 100644
index 24c7319a9..000000000
--- a/sci-electronics/tnt/Manifest
+++ /dev/null
@@ -1 +0,0 @@
-DIST tnt-1.2.2.tar.gz 2020099 BLAKE2B 311bf62634c7585ccf8d0267ffa2f1b91593e63dd267e767a54d94b98d1adc4b38bb617a1bdb6a2f23758b5ac48708e3a7b11f7aac153825cbb0b4aef1aad19d SHA512 7e0c1f1b39d52529a19f85c5a5a9e4f55575afa4214607a4616e60afff552a7b29c63240d409b2dd230479b3c16162d37bbd34faaf4d726cfe17e59775a89467
diff --git a/sci-electronics/tnt/files/tnt-1.2.2-autotools.patch b/sci-electronics/tnt/files/tnt-1.2.2-autotools.patch
deleted file mode 100644
index 36fe517b9..000000000
--- a/sci-electronics/tnt/files/tnt-1.2.2-autotools.patch
+++ /dev/null
@@ -1,277 +0,0 @@
- bem/Makefile.am                         |  5 +++--
- calcCAP/Makefile.am                     |  3 ++-
- calcRL/Makefile.am                      |  3 ++-
- csdl/Makefile.am                        |  5 +++--
- gui/Makefile.am                         | 12 +++---------
- sppdgTcllib/Makefile.am                 |  3 ++-
- sppdgTcllib/addressDialog/Makefile.am   |  3 ++-
- sppdgTcllib/addressDialog/configure.ac  |  2 +-
- sppdgTcllib/configure.ac                |  2 +-
- sppdgTcllib/console/Makefile.am         |  7 +++----
- sppdgTcllib/console/configure.ac        |  4 ++--
- sppdgTcllib/getFilePreview/Makefile.am  |  3 ++-
- sppdgTcllib/getFilePreview/configure.ac |  2 +-
- sppdgTcllib/sgraph/Makefile.am          |  3 ++-
- sppdgTcllib/sgraph/configure.ac         |  2 +-
- units/Makefile.am                       |  3 ++-
- 16 files changed, 32 insertions(+), 30 deletions(-)
-
-diff --git a/bem/Makefile.am b/bem/Makefile.am
-index c2af1cd..9b784ca 100755
---- a/bem/Makefile.am
-+++ b/bem/Makefile.am
-@@ -31,9 +31,10 @@ AUTOMAKE_OPTIONS = foreign subdir-objects
- #---------------------------------------------------------------
- # tcl/tk scripts that may need to be installed.
- #---------------------------------------------------------------
--pkglib_SCRIPTS = \
-+scriptsdir=${pkgdatadir}/scripts
-+scripts_DATA = \
-         lib/bem.tcl \
--	lib/bem_gpge.itcl \
-+        lib/bem_gpge.itcl \
-         lib/bem_graphs.itcl \
-         lib/bem_iterate.tcl \
-         lib/bem_parameters.tcl \
-diff --git a/calcCAP/Makefile.am b/calcCAP/Makefile.am
-index 703cb0f..ce34995 100755
---- a/calcCAP/Makefile.am
-+++ b/calcCAP/Makefile.am
-@@ -30,7 +30,8 @@ AUTOMAKE_OPTIONS = foreign subdir-objects
- #---------------------------------------------------------------
- # tcl/tk scripts that may need to be installed.
- #---------------------------------------------------------------
--pkglib_SCRIPTS = \
-+scriptsdir=${pkgdatadir}/scripts
-+scripts_DATA = \
- 	lib/calcCAP_exe.tcl  \
- 	lib/calcCAP.tcl \
- 	lib/epl.bit \
-diff --git a/calcRL/Makefile.am b/calcRL/Makefile.am
-index 34dbb8d..9c2986c 100755
---- a/calcRL/Makefile.am
-+++ b/calcRL/Makefile.am
-@@ -31,7 +31,8 @@ AUTOMAKE_OPTIONS = foreign subdir-objects
- #---------------------------------------------------------------
- # tcl/tk scripts that may need to be installed.
- #---------------------------------------------------------------
--pkglib_SCRIPTS = \
-+scriptsdir=${pkgdatadir}/scripts
-+scripts_SCRIPTS = \
- 	lib/calcRL.tcl \
- 	lib/calcRL_exe.tcl \
- 	lib/pkgIndex.tcl
-diff --git a/csdl/Makefile.am b/csdl/Makefile.am
-index c49af20..2b74c89 100755
---- a/csdl/Makefile.am
-+++ b/csdl/Makefile.am
-@@ -31,7 +31,8 @@ AUTOMAKE_OPTIONS = foreign subdir-objects
- #---------------------------------------------------------------
- # tcl/tk scripts that may need to be installed.
- #---------------------------------------------------------------
--pkglib_SCRIPTS = \
-+scriptsdir=${pkgdatadir}/scripts
-+scripts_DATA = \
- 	csdl.tcl \
- 	csdl_hlcsdl.itcl \
- 	csdl_llcsdl.itcl \
-@@ -44,4 +45,4 @@ pkglib_SCRIPTS = \
- #---------------------------------------------------------------
- pkglibdir = $(libdir)/$(PACKAGE)$(PACKAGE_VERSION)
- 
--
-+ 
-diff --git a/gui/Makefile.am b/gui/Makefile.am
-index 44a4308..df8c284 100755
---- a/gui/Makefile.am
-+++ b/gui/Makefile.am
-@@ -30,7 +30,8 @@ AUTOMAKE_OPTIONS = foreign
- #---------------------------------------------------------------
- # tcl/tk scripts to be installed.
- #---------------------------------------------------------------
--pkglib_SCRIPTS = \
-+scriptsdir=${pkgdatadir}/scripts
-+scripts_DATA = \
- 	canvas_functions.tcl \
- 	gui.tcl \
- 	gui_build.tcl \
-@@ -41,14 +42,7 @@ pkglib_SCRIPTS = \
- 	gui_xmission.tcl \
- 	pkgIndex.tcl \
- 	splash.tcl \
--	style.tcl
--
--
--
--#---------------------------------------------------------------
--#  Data files to be installed
--#---------------------------------------------------------------
--pkglib_DATA = \
-+	style.tcl \
- 	MayoSPPDGlogo.gif \
- 	conductivity.list \
- 	loss_tangent.list \
-diff --git a/sppdgTcllib/Makefile.am b/sppdgTcllib/Makefile.am
-index 589874b..e16b83e 100755
---- a/sppdgTcllib/Makefile.am
-+++ b/sppdgTcllib/Makefile.am
-@@ -33,7 +33,8 @@ AUTOMAKE_OPTIONS = foreign subdir-objects
- #---------------------------------------------------------------
- #  Only one script that needs to be installed.
- #---------------------------------------------------------------
--pkglib_SCRIPTS = \
-+scriptsdir=${pkgdatadir}/scripts
-+scripts_DATA = \
- 	pkgIndex.tcl
- 
- #---------------------------------------------------------------
-diff --git a/sppdgTcllib/addressDialog/Makefile.am b/sppdgTcllib/addressDialog/Makefile.am
-index 32fc525..47ef097 100755
---- a/sppdgTcllib/addressDialog/Makefile.am
-+++ b/sppdgTcllib/addressDialog/Makefile.am
-@@ -14,7 +14,8 @@ AUTOMAKE_OPTIONS = foreign subdir-objects
- #---------------------------------------------------------------
- # tcl/tk scripts that may need to be installed.
- #---------------------------------------------------------------
--pkglib_SCRIPTS = \
-+scriptsdir=${pkgdatadir}/scripts
-+scripts_DATA = \
- 	addressDialog.tcl \
- 	pkgIndex.tcl
- 
-diff --git a/sppdgTcllib/addressDialog/configure.ac b/sppdgTcllib/addressDialog/configure.ac
-index 488ed2c..288faf3 100755
---- a/sppdgTcllib/addressDialog/configure.ac
-+++ b/sppdgTcllib/addressDialog/configure.ac
-@@ -21,7 +21,7 @@ AC_INIT(ADDRESSDIALOG, 1.0, schrauf@mayo.edu)
- #  we're going to use automake later.
- #----------------------------------------------------------------
- AC_CONFIG_SRCDIR
--AM_INIT_AUTOMAKE(addressDialog, 1.0)
-+AM_INIT_AUTOMAKE
- 
- 
- #----------------------------------------------------------------
-diff --git a/sppdgTcllib/configure.ac b/sppdgTcllib/configure.ac
-index e4e8d54..6e010e1 100755
---- a/sppdgTcllib/configure.ac
-+++ b/sppdgTcllib/configure.ac
-@@ -28,7 +28,7 @@ AC_INIT(sppdgTcllib, 1.0, techentin.robert@mayo.edu)
- #  we're going to use automake later.
- #----------------------------------------------------------------
- AC_CONFIG_SRCDIR
--AM_INIT_AUTOMAKE(sppdgTcllib, 1.0)
-+AM_INIT_AUTOMAKE
- 
- 
- #---------------------------------------------------------------
-diff --git a/sppdgTcllib/console/Makefile.am b/sppdgTcllib/console/Makefile.am
-index 92d5a2f..9bbe657 100755
---- a/sppdgTcllib/console/Makefile.am
-+++ b/sppdgTcllib/console/Makefile.am
-@@ -33,13 +33,12 @@ AUTOMAKE_OPTIONS = foreign
- #---------------------------------------------------------------
- # tcl/tk scripts that may need to be installed.
- #---------------------------------------------------------------
--pkglib_SCRIPTS = \
-+scriptsdir=${pkgdatadir}/scripts
-+scripts_DATA = \
- 	console.tcl \
- 	console_demo.tcl \
- 	tkcon.tcl \
--	pkgIndex.tcl
--
--pkglib_DATA = \
-+	pkgIndex.tcl \
- 	README
- 
- #---------------------------------------------------------------
-diff --git a/sppdgTcllib/console/configure.ac b/sppdgTcllib/console/configure.ac
-index 1ce7a3c..bf4d12c 100755
---- a/sppdgTcllib/console/configure.ac
-+++ b/sppdgTcllib/console/configure.ac
-@@ -22,14 +22,14 @@
- #  Declare the package name and version.
- #  All the bouquets and brickbats go to Bob. :-)
- #----------------------------------------------------------------
--AC_INIT(console, 1.1, techentin.robert@mayo.edu)
-+AC_INIT([console], [1.1], techentin.robert@mayo.edu)
- 
- #----------------------------------------------------------------
- #  Give autoconf a point of reference, and tell it that
- #  we're going to use automake later.
- #----------------------------------------------------------------
- AC_CONFIG_SRCDIR
--AM_INIT_AUTOMAKE(console, 1.1)
-+AM_INIT_AUTOMAKE
- 
- 
- #----------------------------------------------------------------
-diff --git a/sppdgTcllib/getFilePreview/Makefile.am b/sppdgTcllib/getFilePreview/Makefile.am
-index 94394c3..c0c6394 100755
---- a/sppdgTcllib/getFilePreview/Makefile.am
-+++ b/sppdgTcllib/getFilePreview/Makefile.am
-@@ -32,7 +32,8 @@ AUTOMAKE_OPTIONS = foreign
- #---------------------------------------------------------------
- # tcl/tk scripts that may need to be installed.
- #---------------------------------------------------------------
--pkglib_SCRIPTS = \
-+scriptsdir=${pkgdatadir}/scripts
-+scripts_DATA = \
- 	getFilePreview.tcl \
- 	pkgIndex.tcl
- 
-diff --git a/sppdgTcllib/getFilePreview/configure.ac b/sppdgTcllib/getFilePreview/configure.ac
-index ccf33a3..50b1838 100755
---- a/sppdgTcllib/getFilePreview/configure.ac
-+++ b/sppdgTcllib/getFilePreview/configure.ac
-@@ -28,7 +28,7 @@ AC_INIT(getFilePreview, 1.0, techentin.robert@mayo.edu)
- #  we're going to use automake later.
- #----------------------------------------------------------------
- AC_CONFIG_SRCDIR
--AM_INIT_AUTOMAKE(getFilePreview, 1.0)
-+AM_INIT_AUTOMAKE
- 
- 
- #----------------------------------------------------------------
-diff --git a/sppdgTcllib/sgraph/Makefile.am b/sppdgTcllib/sgraph/Makefile.am
-index b02a876..b1da3e1 100755
---- a/sppdgTcllib/sgraph/Makefile.am
-+++ b/sppdgTcllib/sgraph/Makefile.am
-@@ -32,7 +32,8 @@ AUTOMAKE_OPTIONS = foreign subdir-objects
- #---------------------------------------------------------------
- # tcl/tk scripts that may need to be installed.
- #---------------------------------------------------------------
--pkglib_SCRIPTS = \
-+scriptsdir=${pkgdatadir}/scripts
-+scripts_DATA = \
- 	sgraph.tcl \
- 	pkgIndex.tcl
- 
-diff --git a/sppdgTcllib/sgraph/configure.ac b/sppdgTcllib/sgraph/configure.ac
-index 8eb7ef7..e28b7dd 100755
---- a/sppdgTcllib/sgraph/configure.ac
-+++ b/sppdgTcllib/sgraph/configure.ac
-@@ -29,7 +29,7 @@ AC_INIT(SGRAPH, 1.0, zahn.sharon@mayo.edu)
- #  we're going to use automake later.
- #----------------------------------------------------------------
- AC_CONFIG_SRCDIR
--AM_INIT_AUTOMAKE(sgraph, 1.0)
-+AM_INIT_AUTOMAKE
- 
- 
- #----------------------------------------------------------------
-diff --git a/units/Makefile.am b/units/Makefile.am
-index c47ec3c..ea941a9 100755
---- a/units/Makefile.am
-+++ b/units/Makefile.am
-@@ -31,7 +31,8 @@ AUTOMAKE_OPTIONS = foreign subdir-objects
- #---------------------------------------------------------------
- # tcl/tk scripts that may need to be installed.
- #---------------------------------------------------------------
--pkglib_SCRIPTS = \
-+scriptsdir=${pkgdatadir}/scripts
-+scripts_DATA = \
- 	units.tcl \
- 	pkgIndex.tcl \
- 	units.html
diff --git a/sci-electronics/tnt/files/tnt-1.2.2-bem-nmmtl.patch b/sci-electronics/tnt/files/tnt-1.2.2-bem-nmmtl.patch
deleted file mode 100644
index c990c462a..000000000
--- a/sci-electronics/tnt/files/tnt-1.2.2-bem-nmmtl.patch
+++ /dev/null
@@ -1,11 +0,0 @@
---- bem/src/nmmtl.cpp.org	2011-02-19 16:12:58.000000000 -0800
-+++ bem/src/nmmtl.cpp	2011-02-19 16:15:36.000000000 -0800
-@@ -352,7 +352,7 @@
-     sprintf (filespec, "%s.result", filename); 
-     if( (output_file1 = fopen(filespec,"w")) == NULL )
-     {
--      printf ("*** Could not open %s for output ***\n");
-+      printf ("*** Could not open %s for output ***\n", filespec); 
-       return 0;  /* Fatal error; could not open output file */
-     }
-     
diff --git a/sci-electronics/tnt/files/tnt-1.2.2-calc.patch b/sci-electronics/tnt/files/tnt-1.2.2-calc.patch
deleted file mode 100644
index 59e11c4f2..000000000
--- a/sci-electronics/tnt/files/tnt-1.2.2-calc.patch
+++ /dev/null
@@ -1,503 +0,0 @@
-# Adapt this old source to the new C++ standards
-# These patches fix a c++ scope issue, gcc was for some reason
-# not able to discover friend function of class Complex.
-# This has been solved by making this functions a member instead of a friend.
-# George Reitsma <g.p.reitsma@gmail.com>
-
-diff -ruN tnt-1.2.2-0-vanilla/calcCAP/src/calcCAP.cpp tnt-1.2.2/calcCAP/src/calcCAP.cpp
---- tnt-1.2.2-0-vanilla/calcCAP/src/calcCAP.cpp	2004-07-22 21:29:12.000000000 +0200
-+++ tnt-1.2.2/calcCAP/src/calcCAP.cpp	2011-02-24 19:29:44.000000000 +0100
-@@ -14,6 +14,8 @@
- #endif
- #include <time.h>
- #include <stdio.h>
-+#include <string.h>
-+using namespace std;
- 
- /********************** Global variables *******************/
- 
-@@ -287,7 +289,7 @@
-       
-       for ( i1 = 0; i1 < Nc; i1 ++ ) {
- 	
--	sumc[i1] = cmplx( 0.0, 0.0 );
-+	sumc[i1] = Complex( 0.0, 0.0 );
- 
- 	
- 	for ( j1 = 0; j1 < Nw; j1 ++ ) {
-diff -ruN tnt-1.2.2-0-vanilla/calcCAP/src/cmplxmat.cpp tnt-1.2.2/calcCAP/src/cmplxmat.cpp
---- tnt-1.2.2-0-vanilla/calcCAP/src/cmplxmat.cpp	2004-07-22 21:29:12.000000000 +0200
-+++ tnt-1.2.2/calcCAP/src/cmplxmat.cpp	2011-02-24 19:29:44.000000000 +0100
-@@ -378,7 +378,7 @@
-   Matrix result(d_i,d_j);
-   for(int i = 0; i < d_i; i++)
-     for(int j = 0; j < d_j; j++)
--      result(i,j)=::real(elem(i,j));
-+      result(i,j)=elem(i,j).real(); // result(i,j)=::real(elem(i,j));
-   return (result);
- }
- 
-@@ -387,7 +387,7 @@
-   Matrix result(d_i,d_j);
-   for(int i = 0; i < d_i; i++)
-     for(int j = 0; j < d_j; j++)
--      result(i,j)=::imag(elem(i,j));
-+      result(i,j)=elem(i,j).imag(); // result(i,j)=::imag(elem(i,j));
-   return (result);
- }
- 
-@@ -396,7 +396,7 @@
-   Matrix result(d_i,d_j);
-   for(int i = 0; i < d_i; i++)
-     for(int j = 0; j < d_j; j++)
--      result(i,j)=::cabs(elem(i,j));
-+      result(i,j)=elem(i,j).cabs(); // result(i,j)=::cabs(elem(i,j));
-   return (result);
- }
- 
-@@ -405,7 +405,7 @@
-   CmplxMatrix result(d_i,d_j);
-   for(int i = 0; i < d_i; i++)
-     for(int j = 0; j < d_j; j++)
--      result(i,j)=::conjg(elem(i,j));
-+      result(i,j)=elem(i,j).conjg(); // result(i,j)=::conjg(elem(i,j));
-   return (result);
- }
-      
-diff -ruN tnt-1.2.2-0-vanilla/calcCAP/src/cmplxvec.cpp tnt-1.2.2/calcCAP/src/cmplxvec.cpp
---- tnt-1.2.2-0-vanilla/calcCAP/src/cmplxvec.cpp	2004-07-22 21:29:12.000000000 +0200
-+++ tnt-1.2.2/calcCAP/src/cmplxvec.cpp	2011-02-24 19:29:44.000000000 +0100
-@@ -287,7 +287,7 @@
-  
-  int n = d;
-  CmplxVector tmp(n);
-- for(int i = 0; i < n; i++)  tmp[i] = ::conjg(v[i]);
-+ for(int i = 0; i < n; i++)  tmp[i] = v[i].conjg(); // tmp[i] = ::conjg(v[i]);
-  return (tmp);
- }
- 
-@@ -295,7 +295,7 @@
-  
-  Vector tmp(d);
-  int n = d;
-- while(n--) tmp[n] = ::real(v[n]);
-+ while(n--) tmp[n] = v[n].real(); // tmp[n] = ::real(v[n]);
-  return (tmp);
- }
- 
-@@ -303,7 +303,7 @@
-  
-  Vector tmp(d);
-  int n = d;
-- while(n--) tmp[n] = ::imag(v[n]);
-+ while(n--) tmp[n] = v[n].imag(); // tmp[n] = ::imag(v[n]);
-  return (tmp);
- }
- 
-@@ -311,7 +311,7 @@
- 
-   Vector result(d);
-   for(int i = 0; i < d; i++)
--      result[i]=::cabs(v[i]);
-+    result[i]=v[i].cabs(); // result[i]=::cabs(v[i]);
-   return (result);
- }
- 
-diff -ruN tnt-1.2.2-0-vanilla/calcCAP/src/complex.cpp tnt-1.2.2/calcCAP/src/complex.cpp
---- tnt-1.2.2-0-vanilla/calcCAP/src/complex.cpp	2002-10-10 15:46:00.000000000 +0200
-+++ tnt-1.2.2/calcCAP/src/complex.cpp	2011-02-24 19:29:44.000000000 +0100
-@@ -203,6 +203,54 @@
-   return(result);
- }
- 
-+double Complex::real(void) {
-+ 
-+  return(re);
-+}
-+
-+double Complex::imag(void) {
-+ 
-+  return(im);
-+}
-+
-+double Complex::arg(void) {
-+
-+  return((im == 0.0)&&(re == 0.0) ? 0 : atan2(im, re));
-+}
-+
-+double Complex::cabs(void) {
-+ 
-+  double x, y, ans, temp;
-+  x = fabs(re);
-+  y = fabs(im);
-+  if (x == 0.0)
-+     ans = y;
-+  else if (y == 0.0)    
-+     ans = x;
-+  else if (x > y) {
-+     temp = y/x;
-+     ans = x*sqrt(1.0+temp*temp);
-+  } else {
-+     temp = x/y;
-+     ans = y*sqrt(1.0+temp*temp);
-+  }
-+  return ans;  
-+}
-+
-+double Complex::cabsm(void) {
-+ 
-+  return(sqrt(re*re + im*im));
-+}
-+
-+Complex Complex::conjg(void) {
-+ 
-+  Complex com;
-+  com.re =  re;
-+  com.im = -im;
-+  return(com);
-+}
-+
-+
- /********************* friends *****************************/
- 
- Complex operator*(const double& r, const Complex& c) { 
-diff -ruN tnt-1.2.2-0-vanilla/calcCAP/src/complex.h tnt-1.2.2/calcCAP/src/complex.h
---- tnt-1.2.2-0-vanilla/calcCAP/src/complex.h	2002-10-10 15:46:00.000000000 +0200
-+++ tnt-1.2.2/calcCAP/src/complex.h	2011-02-24 19:29:44.000000000 +0100
-@@ -1,10 +1,13 @@
- #ifndef _complex__h_
- #define _complex__h_
- 
--#include <iostream.h>
-+#include <iostream>
-+using namespace std;
- 
- class Complex
- {
-+ public:
-+
-    friend Complex operator*(const double&, const Complex&);
-    friend Complex operator+(const double&, const Complex&);
-    friend Complex operator-(const double&, const Complex&);
-@@ -16,6 +19,14 @@
-    friend double     cabs(const Complex&);
-    friend double     cabsm(const Complex&);
-    friend Complex   conjg(const Complex&);
-+
-+   double     real(void);
-+   double     imag(void);
-+   double     arg(void);
-+   double     cabs(void);
-+   double     cabsm(void);
-+   Complex   conjg(void);
-+
-    friend Complex   cmplx(const double,const double);  
-    friend Complex   polar(const double&, const double&);
-    friend Complex   cos(const Complex&);
-@@ -37,7 +48,6 @@
-    friend ostream& operator<<(ostream&, Complex&);
-    friend istream& operator>>(istream&, Complex&);
- 
-- public:
-    Complex(){}                       // constructors
-    Complex(double r, double i = 0.0);
-    Complex(const Complex&);
-diff -ruN tnt-1.2.2-0-vanilla/calcCAP/src/data.cpp tnt-1.2.2/calcCAP/src/data.cpp
---- tnt-1.2.2-0-vanilla/calcCAP/src/data.cpp	2002-10-10 15:46:01.000000000 +0200
-+++ tnt-1.2.2/calcCAP/src/data.cpp	2011-02-24 19:29:44.000000000 +0100
-@@ -260,7 +260,7 @@
-       }
-     }
-     
--    Ic = cmplx( 0.0, 1.0 );
-+    Ic = Complex( 0.0, 1.0 );
-     
-     Nc4 = 11*Nh+1;
-     step_w = 1.0/power( 2.0, J );
-diff -ruN tnt-1.2.2-0-vanilla/calcRL/src/calcRL.cpp tnt-1.2.2/calcRL/src/calcRL.cpp
---- tnt-1.2.2-0-vanilla/calcRL/src/calcRL.cpp	2004-07-22 21:29:37.000000000 +0200
-+++ tnt-1.2.2/calcRL/src/calcRL.cpp	2011-02-24 19:29:53.000000000 +0100
-@@ -43,7 +43,8 @@
- #endif
- #include <time.h>
- #include <stdio.h>
--
-+#include <string.h>
-+using namespace std;
- /********************** Global variables *******************/
- 
-    int     Nc, Die, Rec, Cir, Tri, Ell, Pol, Gnd, Tra;
-@@ -564,7 +565,7 @@
- 	tmp4 = Circum[i] / double(Nw);
- 	tmpsum1 = 0.0;
- 	tmpsum2 = 0.0;
--	sum2[i] = cmplx( 0.0, 0.0 );
-+	sum2[i] = Complex( 0.0, 0.0 );
- 	
- 	for (j = 0; j < Nw; j ++) {
- 	  
-diff -ruN tnt-1.2.2-0-vanilla/calcRL/src/cmplxmat.cpp tnt-1.2.2/calcRL/src/cmplxmat.cpp
---- tnt-1.2.2-0-vanilla/calcRL/src/cmplxmat.cpp	2004-07-22 21:29:37.000000000 +0200
-+++ tnt-1.2.2/calcRL/src/cmplxmat.cpp	2011-02-24 19:29:53.000000000 +0100
-@@ -386,7 +386,7 @@
-   Matrix result(d_i,d_j);
-   for(int i = 0; i < d_i; i++)
-     for(int j = 0; j < d_j; j++)
--      result(i,j)=::real(elem(i,j));
-+      result(i,j)=elem(i,j).real(); // result(i,j)=::real(elem(i,j));
-   return (result);
- }
- 
-@@ -395,7 +395,7 @@
-   Matrix result(d_i,d_j);
-   for(int i = 0; i < d_i; i++)
-     for(int j = 0; j < d_j; j++)
--      result(i,j)=::imag(elem(i,j));
-+      result(i,j)=elem(i,j).imag(); // result(i,j)=::imag(elem(i,j));
-   return (result);
- }
- 
-@@ -404,7 +404,7 @@
-   Matrix result(d_i,d_j);
-   for(int i = 0; i < d_i; i++)
-     for(int j = 0; j < d_j; j++)
--      result(i,j)=::cabs(elem(i,j));
-+      result(i,j)=elem(i,j).cabs(); // result(i,j)=::cabj(elem(i,j));
-   return (result);
- }
- 
-@@ -413,7 +413,7 @@
-   CmplxMatrix result(d_i,d_j);
-   for(int i = 0; i < d_i; i++)
-     for(int j = 0; j < d_j; j++)
--      result(i,j)=::conjg(elem(i,j));
-+      result(i,j)=elem(i,j).conjg(); // result(i,j)=::conjg(elem(i,j));
-   return (result);
- }
-      
-diff -ruN tnt-1.2.2-0-vanilla/calcRL/src/cmplxvec.cpp tnt-1.2.2/calcRL/src/cmplxvec.cpp
---- tnt-1.2.2-0-vanilla/calcRL/src/cmplxvec.cpp	2004-07-22 21:29:37.000000000 +0200
-+++ tnt-1.2.2/calcRL/src/cmplxvec.cpp	2011-02-24 19:29:53.000000000 +0100
-@@ -289,7 +289,7 @@
-  
-  int n = d;
-  CmplxVector tmp(n);
-- for(int i = 0; i < n; i++)  tmp[i] = ::conjg(v[i]);
-+ for(int i = 0; i < n; i++)  tmp[i] = v[i].conjg(); // tmp[i] = ::conjg(v[i]);
-  return (tmp);
- }
- 
-@@ -297,7 +297,7 @@
-  
-  Vector tmp(d);
-  int n = d;
-- while(n--) tmp[n] = ::real(v[n]);
-+ while(n--) tmp[n] = v[n].real(); // tmp[n] = ::real(v[n]);
-  return (tmp);
- }
- 
-@@ -305,7 +305,7 @@
-  
-  Vector tmp(d);
-  int n = d;
-- while(n--) tmp[n] = ::imag(v[n]);
-+ while(n--) tmp[n] = v[n].imag(); // tmp[n] = ::imag(v[n])
-  return (tmp);
- }
- 
-@@ -313,7 +313,7 @@
- 
-   Vector result(d);
-   for(int i = 0; i < d; i++)
--      result[i]=::cabs(v[i]);
-+    result[i]=v[i].cabs(); // result[i]=::cabs(v[i]);
-   return (result);
- }
- 
-diff -ruN tnt-1.2.2-0-vanilla/calcRL/src/complex.cpp tnt-1.2.2/calcRL/src/complex.cpp
---- tnt-1.2.2-0-vanilla/calcRL/src/complex.cpp	2002-10-09 22:23:38.000000000 +0200
-+++ tnt-1.2.2/calcRL/src/complex.cpp	2011-02-24 19:29:53.000000000 +0100
-@@ -17,6 +17,53 @@
- 
- /*********************** members *********************************/
- 
-+double Complex::real(void) {
-+ 
-+  return(re);
-+}
-+
-+double Complex::imag(void) {
-+ 
-+  return(im);
-+}
-+
-+double Complex::arg(void) {
-+
-+  return((im == 0.0)&&(re == 0.0) ? 0 : atan2(im, re));
-+}
-+
-+double Complex::cabs(void) {
-+ 
-+  double x, y, ans, temp;
-+  x = fabs(re);
-+  y = fabs(im);
-+  if (x == 0.0)
-+     ans = y;
-+  else if (y == 0.0)    
-+     ans = x;
-+  else if (x > y) {
-+     temp = y/x;
-+     ans = x*sqrt(1.0+temp*temp);
-+  } else {
-+     temp = x/y;
-+     ans = y*sqrt(1.0+temp*temp);
-+  }
-+  return ans;  
-+}
-+
-+double Complex::cabsm(void) {
-+ 
-+  return(sqrt(re*re + im*im));
-+}
-+
-+Complex Complex::conjg(void) {
-+ 
-+  Complex com;
-+  com.re =  re;
-+  com.im = -im;
-+  return(com);
-+}
-+
- /********************* friends *****************************/
- 
- Complex operator*(const double& r, const Complex& c) { 
-diff -ruN tnt-1.2.2-0-vanilla/calcRL/src/complex.h tnt-1.2.2/calcRL/src/complex.h
---- tnt-1.2.2-0-vanilla/calcRL/src/complex.h	2002-10-09 22:23:39.000000000 +0200
-+++ tnt-1.2.2/calcRL/src/complex.h	2011-02-24 19:29:53.000000000 +0100
-@@ -3,10 +3,12 @@
- 
- #include <stdlib.h>
- #include <math.h>
--#include <iostream.h>
-+#include <iostream>
-+using namespace std;
- 
- class Complex
- {
-+ public:
-    friend Complex operator*(const double&, const Complex&);
-    friend Complex operator+(const double&, const Complex&);
-    friend Complex operator-(const double&, const Complex&);
-@@ -14,6 +16,14 @@
- 
-    friend double     real(const Complex&);
-    friend double     imag(const Complex&);
-+   double     real(void);
-+   double     imag(void);
-+   double     arg(void);
-+   double     cabs(void);
-+   double     cabsm(void);
-+   Complex   conjg(void);
-+   
-+
-    friend double     arg(const Complex&);
-    friend double     cabs(const Complex&);
-    friend double     cabsm(const Complex&);
-@@ -39,7 +49,7 @@
-    friend ostream& operator<<(ostream&, Complex&);
-    friend istream& operator>>(istream&, Complex&);
- 
-- public:
-+
-    Complex(){}                       // constructors
-    Complex(double r, double i = 0.0);
-    Complex(const Complex&);
-diff -ruN tnt-1.2.2-0-vanilla/calcRL/src/data.cpp tnt-1.2.2/calcRL/src/data.cpp
---- tnt-1.2.2-0-vanilla/calcRL/src/data.cpp	2004-07-22 21:29:37.000000000 +0200
-+++ tnt-1.2.2/calcRL/src/data.cpp	2011-02-24 19:29:53.000000000 +0100
-@@ -251,7 +251,7 @@
-       }
-     }
-     
--    Ic = cmplx( 0.0, 1.0 );
-+    Ic = Complex( 0.0, 1.0 );
-     
-     Nc4 = 11*Nh+1;
-     step_w = 1.0/power( 2.0, J );
-diff -ruN tnt-1.2.2-0-vanilla/calcRL/src/hankel.cpp tnt-1.2.2/calcRL/src/hankel.cpp
---- tnt-1.2.2-0-vanilla/calcRL/src/hankel.cpp	2002-10-09 22:23:40.000000000 +0200
-+++ tnt-1.2.2/calcRL/src/hankel.cpp	2011-02-24 19:29:53.000000000 +0100
-@@ -19,7 +19,7 @@
- 
-    hank01( vj0, vy0, x, 1 );
- 
--   return( cmplx( vj0, -vy0 ) );
-+   return( Complex( vj0, -vy0 ) );
- }
- 
- /***** Function Hank21 - to calculate H^(2)_1(x), x - double  ****/
-@@ -30,7 +30,7 @@
- 
-    hank11( vj1, vy1, x, 1 );
- 
--   return( cmplx( vj1, -vy1 ) );
-+   return( Complex( vj1, -vy1 ) );
- }
- 
- /***** Function Hank10 - to calculate H^(1)_0(x), x - double  ****/
-@@ -41,7 +41,7 @@
- 
-    hank01( vj0, vy0, x, 1 );
- 
--   return( cmplx( vj0, vy0 ) );
-+   return( Complex( vj0, vy0 ) );
- }
- 
- /***** Function Hank11 - to calculate H^(1)_1(x), x - double  ****/
-@@ -52,7 +52,7 @@
- 
-    hank11( vj1, vy1, x, 1 );
- 
--   return( cmplx( vj1, vy1 ) );
-+   return( Complex( vj1, vy1 ) );
- }
- 
- int hank01( double& vj0, double& vy0, double xd, int n ) {
-diff -ruN tnt-1.2.2-0-vanilla/calcRL/src/kelvin.cpp tnt-1.2.2/calcRL/src/kelvin.cpp
---- tnt-1.2.2-0-vanilla/calcRL/src/kelvin.cpp	2002-10-09 22:23:42.000000000 +0200
-+++ tnt-1.2.2/calcRL/src/kelvin.cpp	2011-02-24 19:29:53.000000000 +0100
-@@ -332,20 +332,20 @@
-   return(keip);
- }
- 
--static Complex  seta_p1 = cmplx(0.0,-0.3926991);
--static Complex  seta_p2 = cmplx(0.0110486,0.0);
--static Complex  seta_p3 = cmplx(0.0,-0.0009765);
--static Complex  seta_p4 = cmplx(-0.0000906,-0.0000901);
--static Complex  seta_p5 = cmplx(-0.0000252,0.0);
--static Complex  seta_p6 = cmplx(-0.0000034,0.0000051);
--static Complex  seta_p7 = cmplx(0.0000006,.0000019);
--static Complex  dphi_p1 = cmplx(0.7071068,0.7071068);
--static Complex  dphi_p2 = cmplx(-0.0625001,-0.0000001);
--static Complex  dphi_p3 = cmplx(-0.0013813,0.0013811);
--static Complex  dphi_p4 = cmplx(0.0000005,0.0002452);
--static Complex  dphi_p5 = cmplx(0.0000346,0.0000338);
--static Complex  dphi_p6 = cmplx(0.0000117,-0.0000024);
--static Complex  dphi_p7 = cmplx(0.0000016,-0.0000032);
-+static Complex  seta_p1 = Complex(0.0,-0.3926991);
-+static Complex  seta_p2 = Complex(0.0110486,0.0);
-+static Complex  seta_p3 = Complex(0.0,-0.0009765);
-+static Complex  seta_p4 = Complex(-0.0000906,-0.0000901);
-+static Complex  seta_p5 = Complex(-0.0000252,0.0);
-+static Complex  seta_p6 = Complex(-0.0000034,0.0000051);
-+static Complex  seta_p7 = Complex(0.0000006,.0000019);
-+static Complex  dphi_p1 = Complex(0.7071068,0.7071068);
-+static Complex  dphi_p2 = Complex(-0.0625001,-0.0000001);
-+static Complex  dphi_p3 = Complex(-0.0013813,0.0013811);
-+static Complex  dphi_p4 = Complex(0.0000005,0.0002452);
-+static Complex  dphi_p5 = Complex(0.0000346,0.0000338);
-+static Complex  dphi_p6 = Complex(0.0000117,-0.0000024);
-+static Complex  dphi_p7 = Complex(0.0000016,-0.0000032);
- 
- 
- 
diff --git a/sci-electronics/tnt/files/tnt-1.2.2-docs.patch b/sci-electronics/tnt/files/tnt-1.2.2-docs.patch
deleted file mode 100644
index 77fe50445..000000000
--- a/sci-electronics/tnt/files/tnt-1.2.2-docs.patch
+++ /dev/null
@@ -1,66 +0,0 @@
-diff -ruN tnt-1.2.2-5-tkcon/Makefile.am tnt-1.2.2/Makefile.am
---- tnt-1.2.2-5-tkcon/Makefile.am	2004-07-22 16:23:32.000000000 +0200
-+++ tnt-1.2.2/Makefile.am	2011-02-24 23:43:41.000000000 +0100
-@@ -51,14 +51,16 @@
- #  a prefix.  If not, then I suppose README will go into
- #  /usr.
- #---------------------------------------------------------------
--appdocsdir = $(prefix)
--appdocs_DATA = \
--	AUTHORS$(TXTEXT) \
--	COPYING$(TXTEXT) \
--	ChangeLog$(TXTEXT) \
--	NEWS$(TXTEXT) \
--	README$(TXTEXT) \
--	THANKS$(TXTEXT)
-+#
-+# Portage takes care for this
-+#appdocsdir = $(prefix)
-+#appdocs_DATA = \
-+#	AUTHORS$(TXTEXT) \
-+#	COPYING$(TXTEXT) \
-+#	ChangeLog$(TXTEXT) \
-+#	NEWS$(TXTEXT) \
-+#	README$(TXTEXT) \
-+#	THANKS$(TXTEXT)
- 
- #---------------------------------------------------------------
- #  Convert application documents to text files on Windows.
-diff -ruN tnt-1.2.2-5-tkcon/doc/Makefile.am tnt-1.2.2/doc/Makefile.am
---- tnt-1.2.2-5-tkcon/doc/Makefile.am	2004-07-21 17:45:26.000000000 +0200
-+++ tnt-1.2.2/doc/Makefile.am	2011-02-24 23:43:45.000000000 +0100
-@@ -43,7 +43,7 @@
- #
- #---------------------------------------------------------------
- 
--docdir = $(prefix)/doc
-+#docdir = $(prefix)/doc
- doc_DATA = \
- 	user-guide.pdf 
- 
-@@ -73,15 +73,17 @@
- 	pdflatex $*
- 	latex2html -split 4 -show_section_numbers -local_icons $<
- 
-+# Removed, because portage takes care of it.
-+#
- #  Custom installation rule
--install-data-local:
--	for f in $(doc_DATA); do \
--	  $(mkinstalldirs) $(docdir); \
--	  $(INSTALL_DATA) $$f $(docdir)/$$f; \
--	  d=`basename $$f .pdf`; \
--	  $(mkinstalldirs) $(docdir)/$$d; \
--	  $(INSTALL_DATA) $$d/* $(docdir)/$$d; \
--	done
-+#install-data-local:
-+#	for f in $(doc_DATA); do \
-+#	  $(mkinstalldirs) $(docdir); \
-+#	  $(INSTALL_DATA) $$f $(docdir)/$$f; \
-+#	  d=`basename $$f .pdf`; \
-+#	  $(mkinstalldirs) $(docdir)/$$d; \
-+#	  $(INSTALL_DATA) $$d/* $(docdir)/$$d; \
-+#	done
- 
- #---------------------------------------------------------------
- #  clean
diff --git a/sci-electronics/tnt/files/tnt-1.2.2-f77.patch b/sci-electronics/tnt/files/tnt-1.2.2-f77.patch
deleted file mode 100644
index b1f3fa150..000000000
--- a/sci-electronics/tnt/files/tnt-1.2.2-f77.patch
+++ /dev/null
@@ -1,14 +0,0 @@
-diff -ruN tnt-1.2.2-3-namespace/bem/configure.ac tnt-1.2.2-4-g77/bem/configure.ac
---- tnt-1.2.2-3-namespace/bem/configure.ac	2004-04-22 22:07:12.000000000 +0200
-+++ tnt-1.2.2-4-g77/bem/configure.ac	2011-02-24 23:55:35.000000000 +0100
-@@ -74,9 +74,7 @@
- ;;
- *linux*)
- 	#  For Linux, all flavors...
--	#  Use the GNU compilers for C++ and FORTRAN.
--	CXX="g++"
--	F77="g77"
-+	#  Use the GNU compilers for C++ and FORTRAN and rely on portage
- 	AM_CXXFLAGS="-DFORTRAN_UNDERBARS"
- ;;
- esac
diff --git a/sci-electronics/tnt/files/tnt-1.2.2-gui.patch b/sci-electronics/tnt/files/tnt-1.2.2-gui.patch
deleted file mode 100644
index e2a9b4ca4..000000000
--- a/sci-electronics/tnt/files/tnt-1.2.2-gui.patch
+++ /dev/null
@@ -1,24 +0,0 @@
-diff -ruN tnt-1.2.2-6-docs/gui/gui_help.tcl tnt-1.2.2/gui/gui_help.tcl
---- tnt-1.2.2-6-docs/gui/gui_help.tcl	2004-07-26 15:37:52.000000000 +0200
-+++ tnt-1.2.2/gui/gui_help.tcl	2011-02-24 23:45:27.000000000 +0100
-@@ -26,7 +26,7 @@
-     switch -exact $helpTopic {
- 
- 	userguide {
--	    display_online_help user-guide/index.html
-+	    display_online_help /usr/share/doc/package_name/html/index.html
- 	}
- 
-     }
-diff -ruN tnt-1.2.2-6-docs/gui/splash.tcl tnt-1.2.2/gui/splash.tcl
---- tnt-1.2.2-6-docs/gui/splash.tcl	2004-07-22 15:16:21.000000000 +0200
-+++ tnt-1.2.2/gui/splash.tcl	2011-02-24 23:45:23.000000000 +0100
-@@ -81,7 +81,7 @@
-     } else {
- 	set filename COPYING
-     }
--    set licenseFile [file join $::scriptDir .. $filename]
-+    set licenseFile [file join /usr share doc package_name html $filename]
-     if { [file exists $licenseFile] } {
- 	::gui::guiPopupFile $licenseFile
-     } else {
diff --git a/sci-electronics/tnt/files/tnt-1.2.2-namespaces.patch b/sci-electronics/tnt/files/tnt-1.2.2-namespaces.patch
deleted file mode 100644
index 74bf0ee49..000000000
--- a/sci-electronics/tnt/files/tnt-1.2.2-namespaces.patch
+++ /dev/null
@@ -1,230 +0,0 @@
-diff -ruN tnt-1.2.2-2-bem/bem/src/magicad.h tnt-1.2.2/bem/src/magicad.h
---- tnt-1.2.2-2-bem/bem/src/magicad.h	2002-10-23 00:29:27.000000000 +0200
-+++ tnt-1.2.2/bem/src/magicad.h	2011-02-24 19:36:32.000000000 +0100
-@@ -100,7 +100,8 @@
- #include <stdlib.h>
- #include <string.h>
- #ifdef __cplusplus
--#include <iostream.h>
-+#include <iostream>
-+using namespace std;
- #endif
- #include <limits.h>
- #if !defined(PATH_MAX) || defined(__hpux)
-diff -ruN tnt-1.2.2-2-bem/calcCAP/src/bicgstab.cpp tnt-1.2.2/calcCAP/src/bicgstab.cpp
---- tnt-1.2.2-2-bem/calcCAP/src/bicgstab.cpp	2004-07-22 21:29:12.000000000 +0200
-+++ tnt-1.2.2/calcCAP/src/bicgstab.cpp	2011-02-24 19:36:32.000000000 +0100
-@@ -9,7 +9,8 @@
- 
- 
- //#include "stdafx.h"
--#include <iostream.h>
-+#include <iostream>
-+using namespace std;
- #include <math.h>
- 
- #include "vector.h"
-diff -ruN tnt-1.2.2-2-bem/calcCAP/src/diffrm.cpp tnt-1.2.2/calcCAP/src/diffrm.cpp
---- tnt-1.2.2-2-bem/calcCAP/src/diffrm.cpp	2002-10-10 15:46:02.000000000 +0200
-+++ tnt-1.2.2/calcCAP/src/diffrm.cpp	2011-02-24 19:36:41.000000000 +0100
-@@ -8,8 +8,10 @@
- 
- //#include "stdafx.h"
- #include <math.h>
--#include <iostream.h>
--#include <iomanip.h>
-+#include <iostream>
-+using namespace std;
-+#include <iomanip>
-+using namespace std;
- #include <stdlib.h>
- 
- #include "complex.h"
-diff -ruN tnt-1.2.2-2-bem/calcCAP/src/ivectorl.h tnt-1.2.2/calcCAP/src/ivectorl.h
---- tnt-1.2.2-2-bem/calcCAP/src/ivectorl.h	2002-10-10 15:46:04.000000000 +0200
-+++ tnt-1.2.2/calcCAP/src/ivectorl.h	2011-02-24 19:36:32.000000000 +0100
-@@ -1,6 +1,7 @@
- #ifndef _IVectorl__h_
- #define _IVectorl__h_
--#include <iostream.h>
-+#include <iostream>
-+using namespace std;
- 
- class IVectorl
- {
-diff -ruN tnt-1.2.2-2-bem/calcCAP/src/prony.cpp tnt-1.2.2/calcCAP/src/prony.cpp
---- tnt-1.2.2-2-bem/calcCAP/src/prony.cpp	2002-10-10 15:46:06.000000000 +0200
-+++ tnt-1.2.2/calcCAP/src/prony.cpp	2011-02-24 19:36:41.000000000 +0100
-@@ -1,6 +1,7 @@
- #include "stdafx.h"
- #include <math.h>
--#include <iomanip.h>
-+#include <iomanip>
-+using namespace std;
- #include <stdlib.h>
- #include "complex.h"
- #include "vector.h"
-diff -ruN tnt-1.2.2-2-bem/calcCAP/src/sparse.cpp tnt-1.2.2/calcCAP/src/sparse.cpp
---- tnt-1.2.2-2-bem/calcCAP/src/sparse.cpp	2004-07-22 21:29:12.000000000 +0200
-+++ tnt-1.2.2/calcCAP/src/sparse.cpp	2011-02-24 19:36:41.000000000 +0100
-@@ -2,9 +2,11 @@
- 
- //#include "stdafx.h"
- #include <math.h>
--#include <iostream.h>
-+#include <iostream>
-+using namespace std;
- #include <stdlib.h>
--#include <iomanip.h>
-+#include <iomanip>
-+using namespace std;
- 
- #include "complex.h" 
- #include "vector.h" 
-diff -ruN tnt-1.2.2-2-bem/calcCAP/src/stdafx.h tnt-1.2.2/calcCAP/src/stdafx.h
---- tnt-1.2.2-2-bem/calcCAP/src/stdafx.h	2002-10-10 15:46:08.000000000 +0200
-+++ tnt-1.2.2/calcCAP/src/stdafx.h	2011-02-24 19:36:50.000000000 +0100
-@@ -2,11 +2,15 @@
- #define _stdafx__h_
- 
- #include <math.h>
--#include <iostream.h>
--#include <iomanip.h>
--#include <fstream.h>
-+#include <iostream>
-+using namespace std;
-+#include <iomanip>
-+using namespace std;
-+#include <fstream>
-+using namespace std;
- #include <stdlib.h>
--#include <iomanip.h>
-+#include <iomanip>
-+using namespace std;
- 
- #include "complex.h"
- #include "vector.h"
-diff -ruN tnt-1.2.2-2-bem/calcCAP/src/systsolv.cpp tnt-1.2.2/calcCAP/src/systsolv.cpp
---- tnt-1.2.2-2-bem/calcCAP/src/systsolv.cpp	2002-10-10 15:46:08.000000000 +0200
-+++ tnt-1.2.2/calcCAP/src/systsolv.cpp	2011-02-24 19:36:32.000000000 +0100
-@@ -3,7 +3,8 @@
- 
- //#include "stdafx.h"
- 
--#include <iostream.h>
-+#include <iostream>
-+using namespace std;
- #include <math.h>
- #include <stdlib.h>
- #include "complex.h"
-diff -ruN tnt-1.2.2-2-bem/calcCAP/src/vector.h tnt-1.2.2/calcCAP/src/vector.h
---- tnt-1.2.2-2-bem/calcCAP/src/vector.h	2002-10-10 15:46:09.000000000 +0200
-+++ tnt-1.2.2/calcCAP/src/vector.h	2011-02-24 19:36:41.000000000 +0100
-@@ -1,8 +1,10 @@
- #ifndef _Vector__h_
- #define _Vector__h_
- 
--#include <iostream.h>
--#include <iomanip.h>
-+#include <iostream>
-+using namespace std;
-+#include <iomanip>
-+using namespace std;
- 
- class Vector
- {
-diff -ruN tnt-1.2.2-2-bem/calcRL/src/bicgstab.cpp tnt-1.2.2/calcRL/src/bicgstab.cpp
---- tnt-1.2.2-2-bem/calcRL/src/bicgstab.cpp	2004-07-22 21:29:37.000000000 +0200
-+++ tnt-1.2.2/calcRL/src/bicgstab.cpp	2011-02-24 19:36:32.000000000 +0100
-@@ -9,7 +9,8 @@
- 
- 
- //#include "stdafx.h"
--#include <iostream.h>
-+#include <iostream>
-+using namespace std;
- #include <math.h>
- 
- #include "vector.h"
-diff -ruN tnt-1.2.2-2-bem/calcRL/src/ivectorl.h tnt-1.2.2/calcRL/src/ivectorl.h
---- tnt-1.2.2-2-bem/calcRL/src/ivectorl.h	2002-10-09 22:23:41.000000000 +0200
-+++ tnt-1.2.2/calcRL/src/ivectorl.h	2011-02-24 19:36:32.000000000 +0100
-@@ -2,7 +2,8 @@
- #define _IVectorl__h_
- #include <stdlib.h>
- #include <math.h>
--#include <iostream.h>
-+#include <iostream>
-+using namespace std;
- 
- class IVectorl
- {
-diff -ruN tnt-1.2.2-2-bem/calcRL/src/sparse.cpp tnt-1.2.2/calcRL/src/sparse.cpp
---- tnt-1.2.2-2-bem/calcRL/src/sparse.cpp	2002-10-09 22:23:45.000000000 +0200
-+++ tnt-1.2.2/calcRL/src/sparse.cpp	2011-02-24 19:36:41.000000000 +0100
-@@ -1,9 +1,11 @@
- /******* functions, needed for sparse matrices  *******/
- 
- #include <math.h>
--#include <iostream.h>
-+#include <iostream>
-+using namespace std;
- #include <stdlib.h>
--#include <iomanip.h>
-+#include <iomanip>
-+using namespace std;
- 
- #include "complex.h" 
- #include "vector.h" 
-diff -ruN tnt-1.2.2-2-bem/calcRL/src/stdafx.h tnt-1.2.2/calcRL/src/stdafx.h
---- tnt-1.2.2-2-bem/calcRL/src/stdafx.h	2002-10-09 22:23:56.000000000 +0200
-+++ tnt-1.2.2/calcRL/src/stdafx.h	2011-02-24 19:36:50.000000000 +0100
-@@ -2,11 +2,15 @@
- #define _stdafx__h_
- 
- #include <math.h>
--#include <iostream.h>
--#include <iomanip.h>
--#include <fstream.h>
-+#include <iostream>
-+using namespace std;
-+#include <iomanip>
-+using namespace std;
-+#include <fstream>
-+using namespace std;
- #include <stdlib.h>
--#include <iomanip.h>
-+#include <iomanip>
-+using namespace std;
- 
- #include "complex.h"
- #include "vector.h"
-diff -ruN tnt-1.2.2-2-bem/calcRL/src/systsolv.cpp tnt-1.2.2/calcRL/src/systsolv.cpp
---- tnt-1.2.2-2-bem/calcRL/src/systsolv.cpp	2002-10-09 22:23:57.000000000 +0200
-+++ tnt-1.2.2/calcRL/src/systsolv.cpp	2011-02-24 19:36:32.000000000 +0100
-@@ -2,7 +2,8 @@
-      /*****Source - "NUMERICAL RECIPES IN C", www.nr.com*****/
- 
- //#include "stdafx.h"
--#include <iostream.h>
-+#include <iostream>
-+using namespace std;
- #include <math.h>
- #include <stdlib.h>
- #include "complex.h"
-diff -ruN tnt-1.2.2-2-bem/calcRL/src/vector.h tnt-1.2.2/calcRL/src/vector.h
---- tnt-1.2.2-2-bem/calcRL/src/vector.h	2002-10-09 22:23:59.000000000 +0200
-+++ tnt-1.2.2/calcRL/src/vector.h	2011-02-24 19:36:41.000000000 +0100
-@@ -3,8 +3,10 @@
- 
- #include <stdlib.h>
- #include <math.h>
--#include <iostream.h>
--#include <iomanip.h>
-+#include <iostream>
-+using namespace std;
-+#include <iomanip>
-+using namespace std;
- 
- class Vector
- {
diff --git a/sci-electronics/tnt/files/tnt-1.2.2-tkcon.patch b/sci-electronics/tnt/files/tnt-1.2.2-tkcon.patch
deleted file mode 100644
index 4c603c739..000000000
--- a/sci-electronics/tnt/files/tnt-1.2.2-tkcon.patch
+++ /dev/null
@@ -1,16 +0,0 @@
---- sppdgTcllib/console/tkcon.tcl.org	2011-02-19 01:46:57.000000000 -0800
-+++ sppdgTcllib/console/tkcon.tcl	2011-02-19 01:47:36.000000000 -0800
-@@ -43,9 +43,10 @@
- 
- if {$tcl_version < 8.0} {
-     return -code error "tkcon requires at least Tcl/Tk8"
--} else {
--    package require -exact Tk $tcl_version
--}
-+} 
-+#else {
-+#    package require -exact Tk $tcl_version
-+#}
- 
- catch {package require bogus-package-name}
- foreach pkg [info loaded {}] {
diff --git a/sci-electronics/tnt/metadata.xml b/sci-electronics/tnt/metadata.xml
deleted file mode 100644
index 28b4e4efa..000000000
--- a/sci-electronics/tnt/metadata.xml
+++ /dev/null
@@ -1,11 +0,0 @@
-<?xml version="1.0" encoding="UTF-8"?>
-<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
-<pkgmetadata>
-	<maintainer type="project">
-		<email>sci-electronics@gentoo.org</email>
-		<name>Gentoo Electronics Project</name>
-	</maintainer>
-	<upstream>
-		<remote-id type="sourceforge">mmtl</remote-id>
-	</upstream>
-</pkgmetadata>
diff --git a/sci-electronics/tnt/tnt-1.2.2.ebuild b/sci-electronics/tnt/tnt-1.2.2.ebuild
deleted file mode 100644
index bfe7e4891..000000000
--- a/sci-electronics/tnt/tnt-1.2.2.ebuild
+++ /dev/null
@@ -1,62 +0,0 @@
-# Copyright 1999-2015 Gentoo Foundation
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=5
-
-AUTOTOOLS_AUTORECONF=true
-
-inherit autotools-utils fortran-2 toolchain-funcs
-
-DESCRIPTION="MoM 2.5 D stripline simulator"
-HOMEPAGE="http://mmtl.sourceforge.net/"
-SRC_URI="mirror://sourceforge/mmtl/${P}.tar.gz"
-
-SLOT="0"
-LICENSE="BSD GPL-2"
-KEYWORDS="~amd64 ~x86"
-IUSE="doc"
-
-RDEPEND="
-	dev-lang/tcl:0=
-	dev-tcltk/tcllib
-	dev-tcltk/itcl
-	dev-tcltk/bwidget"
-DEPEND="${RDEPEND}
-	dev-texlive/texlive-latex
-	dev-tex/latex2html
-	media-gfx/imagemagick"
-
-PATCHES=( "${FILESDIR}/${P}"-{calc,bem-nmmtl,namespaces,f77,tkcon,docs,gui,autotools}.patch )
-
-src_prepare() {
-	#adjust new document location in gui
-	sed -i "s/package_name/${PF}/" gui/splash.tcl || die
-	sed -i "s/package_name/${PF}/" gui/gui_help.tcl || die
-
-	autotools-utils_src_prepare
-}
-
-AUTOTOOLS_IN_SOURCE_BUILD=1
-
-src_install () {
-	# tcl cannot handle the archives created by dodoc
-	if use doc; then
-		DOCS=( doc/*.pdf doc/*.png )
-		HTML_DOCS=( doc/user-guide/* )
-	fi
-
-	autotools-utils_src_install
-
-	# Install icon
-	convert gui/logo.gif gui/tnt.png
-	docinto "examples"
-	dodoc examples/*
-	doicon gui/tnt.png
-	make_desktop_entry ${PN} "tnt" ${PN}
-}
-
-pkg_postinst() {
-	elog "Warning: the sources are not under development anymore."
-	elog "We made it compile, but users should check if the results make sense."
-	elog "Examples are in the /usr/share/doc/tnt-1.2.2 folder."
-}
diff --git a/sci-geosciences/pydap/Manifest b/sci-geosciences/pydap/Manifest
deleted file mode 100644
index 8def36006..000000000
--- a/sci-geosciences/pydap/Manifest
+++ /dev/null
@@ -1,2 +0,0 @@
-DIST Pydap-3.1.1.tar.gz 3090985 BLAKE2B e6eb8bd3eb4d910997bd5337ba28efccc9b260f78829abc6be3088b36a86c86e05cb174a08fed6fb250737d855c097e80256179b652403ffe58a3d213fe1659d SHA512 1b29359aa8fb2ac256f464220429c4e425a8722b05ddf4f1ca036b63c3eb1489b2b020c39b94a20503eb103ec1b2663f8438278f71382b451421ea0fe2ac489e
-DIST Pydap-3.1.tar.gz 3098212 BLAKE2B 1c929e98581f19bc10a95d64cc921086483c8d2273832f76faa210dd85ab42a53bea324e249850cbf51a69bcc2dad39ba1e2d0e8b4f28c80c48003c8ecea8243 SHA512 3cae2cd21c73813c640c6fdf9d1ba10d704a60a1b9c93124631dc0727f575a9ee334923693a44dbd16c950203ec7dd9e9124abd48ae33113d191db4256e8fcfb
diff --git a/sci-geosciences/pydap/metadata.xml b/sci-geosciences/pydap/metadata.xml
deleted file mode 100644
index 21edfa452..000000000
--- a/sci-geosciences/pydap/metadata.xml
+++ /dev/null
@@ -1,18 +0,0 @@
-<?xml version="1.0" encoding="UTF-8"?>
-<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
-<pkgmetadata>
-	<maintainer type="person">
-		<email>tim@cerazone.net</email>
-		<name>Tim Cera</name>
-	</maintainer>
-	<maintainer type="project">
-		<email>sci-geosciences@gentoo.org</email>
-		<name>Gentoo Geosciences Project</name>
-	</maintainer>
-	<longdescription lang="en">
-Pydap is a pure Python library implementing the Data Access Protocol.
-</longdescription>
-	<upstream>
-		<remote-id type="pypi">Pydap</remote-id>
-	</upstream>
-</pkgmetadata>
diff --git a/sci-geosciences/pydap/pydap-3.1.1.ebuild b/sci-geosciences/pydap/pydap-3.1.1.ebuild
deleted file mode 100644
index 72c6bd14e..000000000
--- a/sci-geosciences/pydap/pydap-3.1.1.ebuild
+++ /dev/null
@@ -1,37 +0,0 @@
-# Copyright 1999-2014 Gentoo Foundation
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=5
-
-PYTHON_COMPAT=( python2_7 )
-
-inherit distutils-r1
-
-MY_PN=${PN/pydap/Pydap}
-MY_P=${P/pydap/Pydap}
-MY_P=${MY_P/_rc/.rc.}
-
-DESCRIPTION="Data Access Protocol client and server"
-HOMEPAGE="http://pydap.org"
-SRC_URI="mirror://pypi/${MY_PN:0:1}/${MY_PN}/${MY_P}.tar.gz"
-
-LICENSE="pydap"
-SLOT="0"
-KEYWORDS="~amd64"
-IUSE=""
-
-DEPEND=">=dev-python/setuptools-0.6_rc3[${PYTHON_USEDEP}]"
-RDEPEND="
-	dev-python/wsgiintercept[${PYTHON_USEDEP}]
-	>=dev-python/numpy-1.2.1[${PYTHON_USEDEP}]
-	>=dev-python/httplib2-0.4.0[${PYTHON_USEDEP}]
-	>=dev-python/genshi-0.5.1[${PYTHON_USEDEP}]
-	>=dev-python/paste-1.7.2[${PYTHON_USEDEP}]
-	>=dev-python/pastescript-1.7.2[${PYTHON_USEDEP}]
-	>=dev-python/pastedeploy-1.3.3[${PYTHON_USEDEP}]"
-
-S="$WORKDIR"/${MY_P}
-
-python_test() {
-	esetup.py test
-}
diff --git a/sci-geosciences/pydap/pydap-3.1.ebuild b/sci-geosciences/pydap/pydap-3.1.ebuild
deleted file mode 100644
index 72c6bd14e..000000000
--- a/sci-geosciences/pydap/pydap-3.1.ebuild
+++ /dev/null
@@ -1,37 +0,0 @@
-# Copyright 1999-2014 Gentoo Foundation
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=5
-
-PYTHON_COMPAT=( python2_7 )
-
-inherit distutils-r1
-
-MY_PN=${PN/pydap/Pydap}
-MY_P=${P/pydap/Pydap}
-MY_P=${MY_P/_rc/.rc.}
-
-DESCRIPTION="Data Access Protocol client and server"
-HOMEPAGE="http://pydap.org"
-SRC_URI="mirror://pypi/${MY_PN:0:1}/${MY_PN}/${MY_P}.tar.gz"
-
-LICENSE="pydap"
-SLOT="0"
-KEYWORDS="~amd64"
-IUSE=""
-
-DEPEND=">=dev-python/setuptools-0.6_rc3[${PYTHON_USEDEP}]"
-RDEPEND="
-	dev-python/wsgiintercept[${PYTHON_USEDEP}]
-	>=dev-python/numpy-1.2.1[${PYTHON_USEDEP}]
-	>=dev-python/httplib2-0.4.0[${PYTHON_USEDEP}]
-	>=dev-python/genshi-0.5.1[${PYTHON_USEDEP}]
-	>=dev-python/paste-1.7.2[${PYTHON_USEDEP}]
-	>=dev-python/pastescript-1.7.2[${PYTHON_USEDEP}]
-	>=dev-python/pastedeploy-1.3.3[${PYTHON_USEDEP}]"
-
-S="$WORKDIR"/${MY_P}
-
-python_test() {
-	esetup.py test
-}
diff --git a/sci-geosciences/pydap_handlers_csv/Manifest b/sci-geosciences/pydap_handlers_csv/Manifest
deleted file mode 100644
index a16f6ffaa..000000000
--- a/sci-geosciences/pydap_handlers_csv/Manifest
+++ /dev/null
@@ -1 +0,0 @@
-DIST pydap.handlers.csv-0.1.1.tar.gz 34248 BLAKE2B 36e1879f68c8bb9226e3388fad6408306950253c7c3f1c3c0d2eda27531a7a989ba5ff9e7b9b0255227607e9539c1ca19e51a041fbf06fc575662f52f653441a SHA512 c9dade5beb809ff1d6ec0591368dbc7e9dbd2cb1c13f6b3beeddf30742b40430f152ed7e999cc2f287c9f45a3642885005ab686867c3b2394d183856f092bb93
diff --git a/sci-geosciences/pydap_handlers_csv/metadata.xml b/sci-geosciences/pydap_handlers_csv/metadata.xml
deleted file mode 100644
index 065b999bf..000000000
--- a/sci-geosciences/pydap_handlers_csv/metadata.xml
+++ /dev/null
@@ -1,19 +0,0 @@
-<?xml version="1.0" encoding="UTF-8"?>
-<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
-<pkgmetadata>
-	<maintainer type="person">
-		<email>tim@cerazone.net</email>
-		<name>Tim Cera</name>
-	</maintainer>
-	<maintainer type="project">
-		<email>sci-geosciences@gentoo.org</email>
-		<name>Gentoo Geosciences Project</name>
-	</maintainer>
-	<longdescription lang="en">
-Pydap is a pure Python library implementing the Data Access Protocol.
-pydap_handlers_csv allows Pydap server to serve CSV formatted files.
-</longdescription>
-	<upstream>
-		<remote-id type="pypi">pydap.handlers.csv</remote-id>
-	</upstream>
-</pkgmetadata>
diff --git a/sci-geosciences/pydap_handlers_csv/pydap_handlers_csv-0.1.1.ebuild b/sci-geosciences/pydap_handlers_csv/pydap_handlers_csv-0.1.1.ebuild
deleted file mode 100644
index e65b18396..000000000
--- a/sci-geosciences/pydap_handlers_csv/pydap_handlers_csv-0.1.1.ebuild
+++ /dev/null
@@ -1,25 +0,0 @@
-# Copyright 1999-2014 Gentoo Foundation
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=5
-
-PYTHON_COMPAT=( python2_7 )
-
-inherit distutils-r1
-
-MY_PN=${PN//_/.}
-MY_P=${P//_/.}
-
-DESCRIPTION="Comma Separated Values (CSV) handler for Pydap server"
-HOMEPAGE="http://pydap.org/handlers.html#csv"
-SRC_URI="mirror://pypi/${MY_PN:0:1}/${MY_PN}/${MY_P}.tar.gz"
-
-LICENSE="pydap"
-SLOT="0"
-KEYWORDS="~amd64"
-IUSE=""
-
-DEPEND=">=dev-python/setuptools-0.6_rc3[${PYTHON_USEDEP}]"
-RDEPEND=">=sci-geosciences/pydap-3.0_rc10[${PYTHON_USEDEP}]"
-
-S="$WORKDIR/$MY_P"
diff --git a/sci-geosciences/pydap_handlers_hdf5/Manifest b/sci-geosciences/pydap_handlers_hdf5/Manifest
deleted file mode 100644
index 04fd0149c..000000000
--- a/sci-geosciences/pydap_handlers_hdf5/Manifest
+++ /dev/null
@@ -1 +0,0 @@
-DIST pydap.handlers.hdf5-0.1.7.tar.gz 36420 BLAKE2B 85a29145a4ad769a36f51c8c43f828e366edc7e2a0acacd2c127b92c4acf3417be13bcbeaf823bde94f5a9030c963f9aff0e2afb2c86dc27cbed63a57e89411d SHA512 5ab368808db71b90e3640234bdc022d90b0b27ec74ece0af11b03a71fa4c5d547b5b61b625e414a9c3c758d3d6c3161a2a34ec24c4e1c8ce29eca0f67df513f7
diff --git a/sci-geosciences/pydap_handlers_hdf5/metadata.xml b/sci-geosciences/pydap_handlers_hdf5/metadata.xml
deleted file mode 100644
index 62c4ab0ec..000000000
--- a/sci-geosciences/pydap_handlers_hdf5/metadata.xml
+++ /dev/null
@@ -1,19 +0,0 @@
-<?xml version="1.0" encoding="UTF-8"?>
-<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
-<pkgmetadata>
-	<maintainer type="person">
-		<email>tim@cerazone.net</email>
-		<name>Tim Cera</name>
-	</maintainer>
-	<maintainer type="project">
-		<email>sci-geosciences@gentoo.org</email>
-		<name>Gentoo Geosciences Project</name>
-	</maintainer>
-	<longdescription lang="en">
-Pydap is a pure Python library implementing the Data Access Protocol.
-pydap_handlers_hdf5 allows Pydap server to serve hdf5 formatted files.
-</longdescription>
-	<upstream>
-		<remote-id type="pypi">pydap.handlers.hdf5</remote-id>
-	</upstream>
-</pkgmetadata>
diff --git a/sci-geosciences/pydap_handlers_hdf5/pydap_handlers_hdf5-0.1.7.ebuild b/sci-geosciences/pydap_handlers_hdf5/pydap_handlers_hdf5-0.1.7.ebuild
deleted file mode 100644
index 8d30d1a69..000000000
--- a/sci-geosciences/pydap_handlers_hdf5/pydap_handlers_hdf5-0.1.7.ebuild
+++ /dev/null
@@ -1,36 +0,0 @@
-# Copyright 1999-2014 Gentoo Foundation
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=5
-
-PYTHON_COMPAT=( python2_7 )
-
-inherit distutils-r1
-
-MY_PN=${PN//_/.}
-MY_P=${P//_/.}
-
-DESCRIPTION="HDF5 file handler for Pydap Data Access Protocol server"
-HOMEPAGE="http://pydap.org/"
-SRC_URI="mirror://pypi/${MY_PN:0:1}/${MY_PN}/${MY_P}.tar.gz"
-
-LICENSE="pydap"
-SLOT="0"
-KEYWORDS="~amd64"
-IUSE=""
-
-DEPEND="
-	>=dev-python/setuptools-0.6_rc3[${PYTHON_USEDEP}]
-	>=dev-python/paver-1.0.4[${PYTHON_USEDEP}]"
-RDEPEND="
-	>=sci-geosciences/pydap-3.0[${PYTHON_USEDEP}]
-	>=dev-python/pupynere-1.0.8[${PYTHON_USEDEP}]
-	>=dev-python/arrayterator-1.0.1[${PYTHON_USEDEP}]
-	>=dev-python/h5py-2.0[${PYTHON_USEDEP}]"
-
-S="${WORKDIR}/${MY_P}"
-
-python_prepare_all() {
-	paver generate_setup || die
-	distutils-r1_python_prepare_all
-}
diff --git a/sci-geosciences/pydap_handlers_nca/Manifest b/sci-geosciences/pydap_handlers_nca/Manifest
deleted file mode 100644
index 355cc77ac..000000000
--- a/sci-geosciences/pydap_handlers_nca/Manifest
+++ /dev/null
@@ -1 +0,0 @@
-DIST pydap.handlers.nca-0.1.3.tar.gz 35588 BLAKE2B 327b4755e417394944d34802c902258ad1e7c91909f29f7dd263a7caf45798c7b539ed66433e25336d63e8feac47701f2fefe59accb8f397fc868283ae7851cc SHA512 70b074dd912a66b91fdd7d3e1624d4d11868b3fe9fca90046b212b545494aa4c598bfea4436603654e7c01f12174b7eb7b977cdc33981299efebf87d118e04f8
diff --git a/sci-geosciences/pydap_handlers_nca/metadata.xml b/sci-geosciences/pydap_handlers_nca/metadata.xml
deleted file mode 100644
index 472b4eb86..000000000
--- a/sci-geosciences/pydap_handlers_nca/metadata.xml
+++ /dev/null
@@ -1,19 +0,0 @@
-<?xml version="1.0" encoding="UTF-8"?>
-<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
-<pkgmetadata>
-	<maintainer type="person">
-		<email>tim@cerazone.net</email>
-		<name>Tim Cera</name>
-	</maintainer>
-	<maintainer type="project">
-		<email>sci-geosciences@gentoo.org</email>
-		<name>Gentoo Geosciences Project</name>
-	</maintainer>
-	<longdescription lang="en">
-Pydap is a pure Python library implementing the Data Access Protocol.
-pydap_handlers_nca allows Pydap server to serve aggregated NetCDF formatted files.
-</longdescription>
-	<upstream>
-		<remote-id type="pypi">pydap.handlers.nca</remote-id>
-	</upstream>
-</pkgmetadata>
diff --git a/sci-geosciences/pydap_handlers_nca/pydap_handlers_nca-0.1.3.ebuild b/sci-geosciences/pydap_handlers_nca/pydap_handlers_nca-0.1.3.ebuild
deleted file mode 100644
index c4c8386fe..000000000
--- a/sci-geosciences/pydap_handlers_nca/pydap_handlers_nca-0.1.3.ebuild
+++ /dev/null
@@ -1,28 +0,0 @@
-# Copyright 1999-2014 Gentoo Foundation
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=5
-
-PYTHON_COMPAT=( python2_7 )
-
-inherit distutils-r1
-
-MY_PN=${PN//_/.}
-MY_P=${P//_/.}
-
-DESCRIPTION="Aggregated NetCDF handler for Pydap Data Access Protocol server"
-HOMEPAGE="http://pydap.org/"
-SRC_URI="mirror://pypi/${MY_PN:0:1}/${MY_PN}/${MY_P}.tar.gz"
-
-LICENSE="pydap"
-SLOT="0"
-KEYWORDS="~amd64"
-IUSE=""
-
-DEPEND=">=dev-python/setuptools-0.6_rc3[${PYTHON_USEDEP}]"
-RDEPEND="
-	>=sci-geosciences/pydap-3.0_rc8[${PYTHON_USEDEP}]
-	>=dev-python/pupynere-1.0.8[${PYTHON_USEDEP}]
-	>=dev-python/configobj-4.6.0[${PYTHON_USEDEP}]"
-
-S="${WORKDIR}/${MY_P}"
diff --git a/sci-geosciences/pydap_handlers_netcdf/Manifest b/sci-geosciences/pydap_handlers_netcdf/Manifest
deleted file mode 100644
index 030d0ac85..000000000
--- a/sci-geosciences/pydap_handlers_netcdf/Manifest
+++ /dev/null
@@ -1 +0,0 @@
-DIST pydap.handlers.netcdf-0.6.4.tar.gz 33459 BLAKE2B 8f648aadc85f5f50eebf32c6a61288eead9ee7018fd72b87784698e92276660cc520ddd6dfae6608a16c1ac9f5e7eb2c74467fbc5e4c30742edbcc30d68f82cc SHA512 59924b3402cf2c6d4a9a754b50413094e93ac0f64f018a0d1949e9388d38b72ad185dfcd1f495d710f0dd059591601b54c5a37e2363b3d6bd5a6dcf582cc70ee
diff --git a/sci-geosciences/pydap_handlers_netcdf/metadata.xml b/sci-geosciences/pydap_handlers_netcdf/metadata.xml
deleted file mode 100644
index 542600cfe..000000000
--- a/sci-geosciences/pydap_handlers_netcdf/metadata.xml
+++ /dev/null
@@ -1,19 +0,0 @@
-<?xml version="1.0" encoding="UTF-8"?>
-<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
-<pkgmetadata>
-	<maintainer type="person">
-		<email>tim@cerazone.net</email>
-		<name>Tim Cera</name>
-	</maintainer>
-	<maintainer type="project">
-		<email>sci-geosciences@gentoo.org</email>
-		<name>Gentoo Geosciences Project</name>
-	</maintainer>
-	<longdescription lang="en">
-Pydap is a pure Python library implementing the Data Access Protocol.
-pydap_handlers_netcdf allows Pydap server to serve NetCDF formatted files.
-</longdescription>
-	<upstream>
-		<remote-id type="pypi">pydap.handlers.netcdf</remote-id>
-	</upstream>
-</pkgmetadata>
diff --git a/sci-geosciences/pydap_handlers_netcdf/pydap_handlers_netcdf-0.6.4.ebuild b/sci-geosciences/pydap_handlers_netcdf/pydap_handlers_netcdf-0.6.4.ebuild
deleted file mode 100644
index 3eb8f5426..000000000
--- a/sci-geosciences/pydap_handlers_netcdf/pydap_handlers_netcdf-0.6.4.ebuild
+++ /dev/null
@@ -1,35 +0,0 @@
-# Copyright 1999-2014 Gentoo Foundation
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=5
-
-PYTHON_COMPAT=( python2_7 )
-
-inherit distutils-r1
-
-MY_PN=${PN//_/.}
-MY_P=${P//_/.}
-
-DESCRIPTION="NetCDF handler for Pydap Data Access Protocol server"
-HOMEPAGE="http://pydap.org/"
-SRC_URI="mirror://pypi/${MY_PN:0:1}/${MY_PN}/${MY_P}.tar.gz"
-
-LICENSE="pydap"
-SLOT="0"
-KEYWORDS="~amd64"
-IUSE=""
-
-DEPEND="
-	>=dev-python/setuptools-0.6_rc3[${PYTHON_USEDEP}]
-	>=dev-python/paver-1.0.4[${PYTHON_USEDEP}]"
-RDEPEND="
-	>=sci-geosciences/pydap-3.0_rc8[${PYTHON_USEDEP}]
-	>=dev-python/pupynere-1.0.8[${PYTHON_USEDEP}]
-	>=dev-python/arrayterator-1.0.1[${PYTHON_USEDEP}]"
-
-S="${WORKDIR}/${MY_P}"
-
-python_prepare_all() {
-	paver generate_setup || die
-	distutils-r1_python_prepare_all
-}
diff --git a/sci-geosciences/pydap_handlers_proxy/Manifest b/sci-geosciences/pydap_handlers_proxy/Manifest
deleted file mode 100644
index de1758eeb..000000000
--- a/sci-geosciences/pydap_handlers_proxy/Manifest
+++ /dev/null
@@ -1 +0,0 @@
-DIST pydap.handlers.proxy-0.1.1.tar.gz 31416 BLAKE2B 67645d52308109440c615783a2d1ab8e5460e6796220d37bceb4642fab14968f07a4d94062073f8a02377125ce6f53846767b3ac856263f76145f6aed137bede SHA512 c1fa783c856c6bf3706d3608d28a3543b92ddcb58ac205507e9506f52d81df87c4413e31cf79eda7f47edaa3be184e7760aad0722d9163eb654bce7291cf28ed
diff --git a/sci-geosciences/pydap_handlers_proxy/metadata.xml b/sci-geosciences/pydap_handlers_proxy/metadata.xml
deleted file mode 100644
index 0f68ac6d7..000000000
--- a/sci-geosciences/pydap_handlers_proxy/metadata.xml
+++ /dev/null
@@ -1,19 +0,0 @@
-<?xml version="1.0" encoding="UTF-8"?>
-<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
-<pkgmetadata>
-	<maintainer type="person">
-		<email>tim@cerazone.net</email>
-		<name>Tim Cera</name>
-	</maintainer>
-	<maintainer type="project">
-		<email>sci-geosciences@gentoo.org</email>
-		<name>Gentoo Geosciences Project</name>
-	</maintainer>
-	<longdescription lang="en">
-Pydap is a pure Python library implementing the Data Access Protocol.
-pydap_handlers_proxy allows Pydap server to serve data from other web sites.
-</longdescription>
-	<upstream>
-		<remote-id type="pypi">pydap.handlers.proxy</remote-id>
-	</upstream>
-</pkgmetadata>
diff --git a/sci-geosciences/pydap_handlers_proxy/pydap_handlers_proxy-0.1.1.ebuild b/sci-geosciences/pydap_handlers_proxy/pydap_handlers_proxy-0.1.1.ebuild
deleted file mode 100644
index fc6fc85aa..000000000
--- a/sci-geosciences/pydap_handlers_proxy/pydap_handlers_proxy-0.1.1.ebuild
+++ /dev/null
@@ -1,28 +0,0 @@
-# Copyright 1999-2014 Gentoo Foundation
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=5
-
-PYTHON_COMPAT=( python2_7 )
-
-inherit distutils-r1
-
-MY_PN=${PN//_/.}
-MY_P=${P//_/.}
-
-DESCRIPTION="Proxy handler for Pydap server that can serve data from other web sites"
-HOMEPAGE="http://pydap.org/handlers.html#cdms"
-SRC_URI="mirror://pypi/${MY_PN:0:1}/${MY_PN}/${MY_P}.tar.gz"
-
-LICENSE="pydap"
-SLOT="0"
-KEYWORDS="~amd64"
-IUSE=""
-
-DEPEND=">=dev-python/setuptools-0.6_rc3[${PYTHON_USEDEP}]"
-RDEPEND="
-	>=sci-geosciences/pydap-3.0_rc8[${PYTHON_USEDEP}]
-	>=dev-python/paste-1.7.2[${PYTHON_USEDEP}]
-	>=dev-python/configobj-4.6.0[${PYTHON_USEDEP}]"
-
-S="$WORKDIR/$MY_P"
diff --git a/sci-geosciences/pydap_handlers_sqlite/Manifest b/sci-geosciences/pydap_handlers_sqlite/Manifest
deleted file mode 100644
index abdcc734e..000000000
--- a/sci-geosciences/pydap_handlers_sqlite/Manifest
+++ /dev/null
@@ -1 +0,0 @@
-DIST pydap.handlers.sqlite-0.1.0.tar.gz 35434 BLAKE2B b5aa04b4d8aa849ada0083a51085dd743e9742d4553fdd77210cc1182e97417d5a202c14b290087e458febc795fa01801ca534a4cbb76e3e63c0c202a11ad7b7 SHA512 92a6da176ba6af7062c68f4b3c38f14215bec7b210ea2698c36744214c3c27e9cc9c7824cc8b8fc199846e1aaa6fd5cdcd6628fa88575f5cab6d4877080f0819
diff --git a/sci-geosciences/pydap_handlers_sqlite/metadata.xml b/sci-geosciences/pydap_handlers_sqlite/metadata.xml
deleted file mode 100644
index a533b0703..000000000
--- a/sci-geosciences/pydap_handlers_sqlite/metadata.xml
+++ /dev/null
@@ -1,19 +0,0 @@
-<?xml version="1.0" encoding="UTF-8"?>
-<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
-<pkgmetadata>
-	<maintainer type="person">
-		<email>tim@cerazone.net</email>
-		<name>Tim Cera</name>
-	</maintainer>
-	<maintainer type="project">
-		<email>sci-geosciences@gentoo.org</email>
-		<name>Gentoo Geosciences Project</name>
-	</maintainer>
-	<longdescription lang="en">
-Pydap is a pure Python library implementing the Data Access Protocol.
-pydap_handlers_sqlite allows Pydap server to serve data from SQLite files.
-</longdescription>
-	<upstream>
-		<remote-id type="pypi">pydap.handlers.sqlite</remote-id>
-	</upstream>
-</pkgmetadata>
diff --git a/sci-geosciences/pydap_handlers_sqlite/pydap_handlers_sqlite-0.1.0.ebuild b/sci-geosciences/pydap_handlers_sqlite/pydap_handlers_sqlite-0.1.0.ebuild
deleted file mode 100644
index e066751bf..000000000
--- a/sci-geosciences/pydap_handlers_sqlite/pydap_handlers_sqlite-0.1.0.ebuild
+++ /dev/null
@@ -1,28 +0,0 @@
-# Copyright 1999-2014 Gentoo Foundation
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=5
-
-PYTHON_COMPAT=( python2_7 )
-
-inherit distutils-r1
-
-MY_PN=${PN//_/.}
-MY_P=${P//_/.}
-
-DESCRIPTION="Handler for Pydap server that allows serving data from SQLite files"
-HOMEPAGE="http://pydap.org/handlers.html#sqlite"
-SRC_URI="mirror://pypi/${MY_PN:0:1}/${MY_PN}/${MY_P}.tar.gz"
-
-LICENSE="pydap"
-SLOT="0"
-KEYWORDS="~amd64"
-IUSE=""
-
-DEPEND=">=dev-python/setuptools-0.6_rc3[${PYTHON_USEDEP}]"
-RDEPEND="
-	>=sci-geosciences/pydap-3.0[${PYTHON_USEDEP}]
-	>=dev-python/simplejson-2.1.6[${PYTHON_USEDEP}]
-	>=dev-python/numpy-1.5.1[${PYTHON_USEDEP}]"
-
-S="$WORKDIR/$MY_P"
diff --git a/sci-geosciences/pydap_responses_kml/Manifest b/sci-geosciences/pydap_responses_kml/Manifest
deleted file mode 100644
index 42e72aacd..000000000
--- a/sci-geosciences/pydap_responses_kml/Manifest
+++ /dev/null
@@ -1 +0,0 @@
-DIST pydap.responses.kml-0.4.6.tar.gz 37168 BLAKE2B 8d207620d93c6439937b1fb0559a12604dc8c35c9257a32424ec8ffffa4b46406e69dfdbd9e0fd58592f63ebc0b2ba8c5df06d968b2c91d8b1c4c0b92258f3f7 SHA512 0c45f114bf6d8adb1dd2ed37ebe7e9fbe311bb3aebea9c20c8a122bce763d2b34b6dfccf8fdabb89815d152bab817f3db5fe24270bc069872db102aba27aca78
diff --git a/sci-geosciences/pydap_responses_kml/metadata.xml b/sci-geosciences/pydap_responses_kml/metadata.xml
deleted file mode 100644
index e9acccf5f..000000000
--- a/sci-geosciences/pydap_responses_kml/metadata.xml
+++ /dev/null
@@ -1,20 +0,0 @@
-<?xml version="1.0" encoding="UTF-8"?>
-<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
-<pkgmetadata>
-	<maintainer type="person">
-		<email>tim@cerazone.net</email>
-		<name>Tim Cera</name>
-	</maintainer>
-	<maintainer type="project">
-		<email>sci-geosciences@gentoo.org</email>
-		<name>Gentoo Geosciences Project</name>
-	</maintainer>
-	<longdescription lang="en">
-Pydap is a pure Python library implementing the Data Access Protocol.
-pydap_responses_kml allows Pydap server to use Google Earth to visualize
-data.
-</longdescription>
-	<upstream>
-		<remote-id type="pypi">pydap.responses.kml</remote-id>
-	</upstream>
-</pkgmetadata>
diff --git a/sci-geosciences/pydap_responses_kml/pydap_responses_kml-0.4.6.ebuild b/sci-geosciences/pydap_responses_kml/pydap_responses_kml-0.4.6.ebuild
deleted file mode 100644
index 925c7fda9..000000000
--- a/sci-geosciences/pydap_responses_kml/pydap_responses_kml-0.4.6.ebuild
+++ /dev/null
@@ -1,25 +0,0 @@
-# Copyright 1999-2014 Gentoo Foundation
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=5
-
-PYTHON_COMPAT=( python2_7 )
-
-inherit distutils-r1
-
-MY_PN=${PN//_/.}
-MY_P=${P//_/.}
-
-DESCRIPTION="KML responses for Pydap Data Access Protocol server"
-HOMEPAGE="http://pydap.org"
-SRC_URI="mirror://pypi/${MY_PN:0:1}/${MY_PN}/${MY_P}.tar.gz"
-
-LICENSE="pydap"
-SLOT="0"
-KEYWORDS="~amd64"
-IUSE=""
-
-DEPEND=">=dev-python/setuptools-0.6_rc3[${PYTHON_USEDEP}]"
-RDEPEND=">=sci-geosciences/pydap-3.0_rc10[${PYTHON_USEDEP}]"
-
-S="$WORKDIR/$MY_P"
diff --git a/sci-geosciences/pydap_responses_matlab/Manifest b/sci-geosciences/pydap_responses_matlab/Manifest
deleted file mode 100644
index 1df38c633..000000000
--- a/sci-geosciences/pydap_responses_matlab/Manifest
+++ /dev/null
@@ -1 +0,0 @@
-DIST pydap.responses.matlab-0.2.1.tar.gz 36142 BLAKE2B b129bea35aa345e4539ccbdbf50dccf24b3ccb05b3aa945ccb678699060eba41aba5d934885a17e4c517e410e35e576c262a7b9d2adf566a827b6ad4b2823ea6 SHA512 f318418d9a04f4377a9a671db746ff918c2e72227ae1ed8ba6162ef181d9b1123d25829b9a903ce987c1a2a38eb9641709ccdd0c4b6f538a99ab69100d414ba3
diff --git a/sci-geosciences/pydap_responses_matlab/metadata.xml b/sci-geosciences/pydap_responses_matlab/metadata.xml
deleted file mode 100644
index 5370903f5..000000000
--- a/sci-geosciences/pydap_responses_matlab/metadata.xml
+++ /dev/null
@@ -1,19 +0,0 @@
-<?xml version="1.0" encoding="UTF-8"?>
-<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
-<pkgmetadata>
-	<maintainer type="person">
-		<email>tim@cerazone.net</email>
-		<name>Tim Cera</name>
-	</maintainer>
-	<maintainer type="project">
-		<email>sci-geosciences@gentoo.org</email>
-		<name>Gentoo Geosciences Project</name>
-	</maintainer>
-	<longdescription lang="en">
-Pydap is a pure Python library implementing the Data Access Protocol.
-pydap_responses_matlab allows Pydap server to deliver data to Matlab.
-</longdescription>
-	<upstream>
-		<remote-id type="pypi">pydap.responses.matlab</remote-id>
-	</upstream>
-</pkgmetadata>
diff --git a/sci-geosciences/pydap_responses_matlab/pydap_responses_matlab-0.2.1.ebuild b/sci-geosciences/pydap_responses_matlab/pydap_responses_matlab-0.2.1.ebuild
deleted file mode 100644
index a2590cce5..000000000
--- a/sci-geosciences/pydap_responses_matlab/pydap_responses_matlab-0.2.1.ebuild
+++ /dev/null
@@ -1,34 +0,0 @@
-# Copyright 1999-2014 Gentoo Foundation
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=5
-
-PYTHON_COMPAT=( python2_7 )
-
-inherit distutils-r1
-
-MY_PN=${PN//_/.}
-MY_P=${MY_PN}-${PV}
-
-DESCRIPTION="MatLab response for Pydap Data Access Protocol server"
-HOMEPAGE="http://pydap.org"
-SRC_URI="mirror://pypi/${MY_PN:0:1}/${MY_PN}/${MY_P}.tar.gz"
-
-LICENSE="pydap"
-SLOT="0"
-KEYWORDS="~amd64"
-IUSE=""
-
-DEPEND="
-	>=dev-python/setuptools-0.6_rc3[${PYTHON_USEDEP}]
-	>=dev-python/paver-1.0.4[${PYTHON_USEDEP}]"
-RDEPEND="
-	>=sci-geosciences/pydap-3.0_rc10[${PYTHON_USEDEP}]
-	>=sci-libs/scipy-0.7.2-r1[${PYTHON_USEDEP}]"
-
-S="$WORKDIR/$MY_P"
-
-python_prepare_all() {
-	paver generate_setup || die
-	distutils-r1_python_prepare_all
-}
diff --git a/sci-geosciences/pydap_responses_netcdf/Manifest b/sci-geosciences/pydap_responses_netcdf/Manifest
deleted file mode 100644
index c4a7b30f7..000000000
--- a/sci-geosciences/pydap_responses_netcdf/Manifest
+++ /dev/null
@@ -1 +0,0 @@
-DIST pydap.responses.netcdf-0.1.4.1.tar.gz 36280 BLAKE2B 9050ebf03f05ce47cb2e6ac6a0188e948b8f62ff4ca7bc178e6ae31f721ba186055e9e88fc3a22e9cf99305270584d738223ebe1dd1c091b61b14b6c523a938a SHA512 c55389440470434bfbfec092863cc5aa26b1f1630c54da536c75719b219eb8666f8ab2f77711a0f8400534bf0dcf7c6b0515de6752bf22348f5aaf6b8adcb0d2
diff --git a/sci-geosciences/pydap_responses_netcdf/metadata.xml b/sci-geosciences/pydap_responses_netcdf/metadata.xml
deleted file mode 100644
index da0f64af0..000000000
--- a/sci-geosciences/pydap_responses_netcdf/metadata.xml
+++ /dev/null
@@ -1,19 +0,0 @@
-<?xml version="1.0" encoding="UTF-8"?>
-<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
-<pkgmetadata>
-	<maintainer type="person">
-		<email>tim@cerazone.net</email>
-		<name>Tim Cera</name>
-	</maintainer>
-	<maintainer type="project">
-		<email>sci-geosciences@gentoo.org</email>
-		<name>Gentoo Geosciences Project</name>
-	</maintainer>
-	<longdescription lang="en">
-Pydap is a pure Python library implementing the Data Access Protocol.
-pydap_responses_netcdf allows Pydap server to serve NetCDF formatted files.
-</longdescription>
-	<upstream>
-		<remote-id type="pypi">pydap.responses.netcdf</remote-id>
-	</upstream>
-</pkgmetadata>
diff --git a/sci-geosciences/pydap_responses_netcdf/pydap_responses_netcdf-0.1.4.1.ebuild b/sci-geosciences/pydap_responses_netcdf/pydap_responses_netcdf-0.1.4.1.ebuild
deleted file mode 100644
index 181d9652c..000000000
--- a/sci-geosciences/pydap_responses_netcdf/pydap_responses_netcdf-0.1.4.1.ebuild
+++ /dev/null
@@ -1,34 +0,0 @@
-# Copyright 1999-2014 Gentoo Foundation
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=5
-
-PYTHON_COMPAT=( python2_7 )
-
-inherit distutils-r1
-
-MY_PN=${PN//_/.}
-MY_P=${P//_/.}
-
-DESCRIPTION="NetCDF responses for Pydap Data Access Protocol server"
-HOMEPAGE="http://pydap.org"
-SRC_URI="mirror://pypi/${MY_PN:0:1}/${MY_PN}/${MY_P}.tar.gz"
-
-LICENSE="pydap"
-SLOT="0"
-KEYWORDS="~amd64"
-IUSE=""
-
-DEPEND="
-	>=dev-python/setuptools-0.6_rc3[${PYTHON_USEDEP}]
-	>=dev-python/paver-1.0.4[${PYTHON_USEDEP}]"
-RDEPEND="
-	>=sci-geosciences/pydap-3.0_rc10[${PYTHON_USEDEP}]
-	>=dev-python/pupynere-1.0.13[${PYTHON_USEDEP}]"
-
-S="$WORKDIR/$MY_P"
-
-python_prepare_all() {
-	paver generate_setup || die
-	distutils-r1_python_prepare_all
-}
diff --git a/sci-geosciences/pydap_responses_wms/Manifest b/sci-geosciences/pydap_responses_wms/Manifest
deleted file mode 100644
index e772fa362..000000000
--- a/sci-geosciences/pydap_responses_wms/Manifest
+++ /dev/null
@@ -1 +0,0 @@
-DIST pydap.responses.wms-0.5.4.tar.gz 55821 BLAKE2B 73b06c062dea93c4772eb259c88d033e74a023a661ecf7bfcc9a39cd0bf0f0eb887ed1f66f8817ec8ee0f58129fbc9acf2ba10ba2a0aacf7ec3bead65ae2395d SHA512 0f7375d7e3511e818b11ccbffbf844de0e4336224a766a9a1c9615fe2df0248a01e3017e7f5021d1a5ba55ac9a1fc49e4848e72bb637dfbd59ed4045bba661d3
diff --git a/sci-geosciences/pydap_responses_wms/metadata.xml b/sci-geosciences/pydap_responses_wms/metadata.xml
deleted file mode 100644
index ac0d9ed30..000000000
--- a/sci-geosciences/pydap_responses_wms/metadata.xml
+++ /dev/null
@@ -1,20 +0,0 @@
-<?xml version="1.0" encoding="UTF-8"?>
-<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
-<pkgmetadata>
-	<maintainer type="person">
-		<email>tim@cerazone.net</email>
-		<name>Tim Cera</name>
-	</maintainer>
-	<maintainer type="project">
-		<email>sci-geosciences@gentoo.org</email>
-		<name>Gentoo Geosciences Project</name>
-	</maintainer>
-	<longdescription lang="en">
-Pydap is a pure Python library implementing the Data Access Protocol.
-pydap_responses_wms allows Pydap server to deliver maps via Web Mapping
-Service protocol.
-</longdescription>
-	<upstream>
-		<remote-id type="pypi">pydap.responses.wms</remote-id>
-	</upstream>
-</pkgmetadata>
diff --git a/sci-geosciences/pydap_responses_wms/pydap_responses_wms-0.5.4.ebuild b/sci-geosciences/pydap_responses_wms/pydap_responses_wms-0.5.4.ebuild
deleted file mode 100644
index 3d693d5bd..000000000
--- a/sci-geosciences/pydap_responses_wms/pydap_responses_wms-0.5.4.ebuild
+++ /dev/null
@@ -1,28 +0,0 @@
-# Copyright 1999-2014 Gentoo Foundation
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=5
-
-PYTHON_COMPAT=( python2_7 )
-
-inherit distutils-r1
-
-MY_PN=${PN//_/.}
-MY_P=${P//_/.}
-
-DESCRIPTION="WMS responses for Pydap Data Access Protocol server"
-HOMEPAGE="http://pydap.org"
-SRC_URI="mirror://pypi/${MY_PN:0:1}/${MY_PN}/${MY_P}.tar.gz"
-
-LICENSE="pydap"
-SLOT="0"
-KEYWORDS="~amd64"
-IUSE=""
-
-DEPEND=">=dev-python/setuptools-0.6_rc3[${PYTHON_USEDEP}]"
-RDEPEND="
-	>=sci-geosciences/pydap-3.0_rc10[${PYTHON_USEDEP}]
-	>=dev-python/paste-1.7.2[${PYTHON_USEDEP}]
-	dev-python/matplotlib[${PYTHON_USEDEP}]"
-
-S="$WORKDIR/$MY_P"
diff --git a/sci-geosciences/pydap_responses_xls/Manifest b/sci-geosciences/pydap_responses_xls/Manifest
deleted file mode 100644
index 7b9f66f5c..000000000
--- a/sci-geosciences/pydap_responses_xls/Manifest
+++ /dev/null
@@ -1 +0,0 @@
-DIST pydap.responses.xls-0.1.2.tar.gz 32075 BLAKE2B 9c26e2b3009f21ab8e2c47edeee733cb0cd98fb2098c575a5784bef781c537a6f2df87537eca3a5a6681611021af84710fa4e1ce5ae97eb77e58ffbfeee5a2a3 SHA512 c1134318fa587f53ff063038e32305cc563e886b82fe68f577cf3dc01436f942ed4b9db56f92b356a6a52bf36ba5d6abb4362099aa2b7549357b3db56af145c3
diff --git a/sci-geosciences/pydap_responses_xls/metadata.xml b/sci-geosciences/pydap_responses_xls/metadata.xml
deleted file mode 100644
index 9a1f3e724..000000000
--- a/sci-geosciences/pydap_responses_xls/metadata.xml
+++ /dev/null
@@ -1,20 +0,0 @@
-<?xml version="1.0" encoding="UTF-8"?>
-<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
-<pkgmetadata>
-	<maintainer type="person">
-		<email>tim@cerazone.net</email>
-		<name>Tim Cera</name>
-	</maintainer>
-	<maintainer type="project">
-		<email>sci-geosciences@gentoo.org</email>
-		<name>Gentoo Geosciences Project</name>
-	</maintainer>
-	<longdescription lang="en">
-Pydap is a pure Python library implementing the Data Access Protocol.
-pydap_responses_xls allows Pydap server to deliver an Excel file of the
-data.
-</longdescription>
-	<upstream>
-		<remote-id type="pypi">pydap.responses.xls</remote-id>
-	</upstream>
-</pkgmetadata>
diff --git a/sci-geosciences/pydap_responses_xls/pydap_responses_xls-0.1.2.ebuild b/sci-geosciences/pydap_responses_xls/pydap_responses_xls-0.1.2.ebuild
deleted file mode 100644
index a01b5e018..000000000
--- a/sci-geosciences/pydap_responses_xls/pydap_responses_xls-0.1.2.ebuild
+++ /dev/null
@@ -1,27 +0,0 @@
-# Copyright 1999-2014 Gentoo Foundation
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=5
-
-PYTHON_COMPAT=( python2_7 )
-
-inherit distutils-r1
-
-MY_PN=${PN//_/.}
-MY_P=${MY_PN}-${PV}
-
-DESCRIPTION="Excel responses for Pydap Data Access Protocol server"
-HOMEPAGE="http://pydap.org"
-SRC_URI="mirror://pypi/${MY_PN:0:1}/${MY_PN}/${MY_P}.tar.gz"
-
-LICENSE="pydap"
-SLOT="0"
-KEYWORDS="~amd64"
-IUSE=""
-
-DEPEND=">=dev-python/setuptools-0.6_rc3[${PYTHON_USEDEP}]"
-RDEPEND="
-	>=sci-geosciences/pydap-3.0_rc10[${PYTHON_USEDEP}]
-	>=dev-python/xlwt-0.7.2[${PYTHON_USEDEP}]"
-
-S="$WORKDIR/$MY_P"
diff --git a/sci-libs/Cgraph/Cgraph-2.04.ebuild b/sci-libs/Cgraph/Cgraph-2.04.ebuild
deleted file mode 100644
index 85ab332a7..000000000
--- a/sci-libs/Cgraph/Cgraph-2.04.ebuild
+++ /dev/null
@@ -1,40 +0,0 @@
-# Copyright 1999-2015 Gentoo Foundation
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=5
-
-inherit eutils flag-o-matic multilib
-
-DESCRIPTION="C functions that generate PostScript for publication quality scientific plots"
-HOMEPAGE="http://neurovision.berkeley.edu/software/A_Cgraph.html"
-SRC_URI="http://neurovision.berkeley.edu/software/${PN}${PV}.tar.gz"
-
-LICENSE="GPL-2"
-SLOT="0"
-KEYWORDS="~amd64 ~x86"
-IUSE=""
-
-RDEPEND="!media-gfx/graphviz"
-DEPEND=""
-
-S="${WORKDIR}"/${PN}/source
-
-src_prepare() {
-	epatch \
-		"${FILESDIR}"/Makefile.patch \
-		"${FILESDIR}"/fix-src.patch
-}
-
-src_compile() {
-	use amd64 && append-flags -fPIC && append-ldflags -fPIC
-	emake CC=$(tc-getCC) CCFLAGS="${CFLAGS}"
-}
-
-src_install() {
-	emake DESTDIR="${D}" LIB_DIR=/usr/$(get_libdir) install
-	dolib.so libcgraph.so.0.0.0
-	dosym libcgraph.so.0.0.0 /usr/$(get_libdir)/libcgraph.so.0
-	dosym libcgraph.so.0.0.0 /usr/$(get_libdir)/libcgraph.so
-
-	dodoc ../docs/*
-}
diff --git a/sci-libs/Cgraph/Manifest b/sci-libs/Cgraph/Manifest
deleted file mode 100644
index 96e44f882..000000000
--- a/sci-libs/Cgraph/Manifest
+++ /dev/null
@@ -1 +0,0 @@
-DIST Cgraph2.04.tar.gz 198572 BLAKE2B be3b6791d13867f5e1f9a0f0c8c3674649e6aac59faaa29c25e22d969599453efa8d2c30b42275af16945fd0e542d220e903137352a37d69bc14f1fd1d842414 SHA512 a24383cc2ed19907bbd08e56260f934975340443d842eb060099d8b2d2dd96d1f5a813a464cf390357e62972e04c973ec7d3d36a1bc4e82b4e84399dd9b03f54
diff --git a/sci-libs/Cgraph/files/Makefile.patch b/sci-libs/Cgraph/files/Makefile.patch
deleted file mode 100644
index 038c16853..000000000
--- a/sci-libs/Cgraph/files/Makefile.patch
+++ /dev/null
@@ -1,169 +0,0 @@
---- source/Makefile	2009-03-01 12:19:16.000000000 +0100
-+++ source/Makefile.new	2009-03-01 14:45:35.000000000 +0100
-@@ -3,17 +3,18 @@
- #CC=gcc
- CC=cc
- 
--INCLUDE_DIR=/usr/local/include
-+INCLUDE_DIR=/usr/include
- LIB_DIR=/usr/local/lib
- 
- #LIB_FILE=libcgraph.sl
- LIB_FILE=libcgraph.a
-+LIB_FILE_SO=libcgraph.so
- 
- 
- # NEXTSTEP/OPENSTEP multiple architecture compile flags
- #ARCHS=
- #ARCHS=-arch i386 -arch m68k -arch sparc -arch hppa
--ARCHS=-arch i386 -arch m68k
-+#ARCHS=-arch i386 -arch m68k
- 
- 
- #CCFLAGS =  -c -O -fpic -I/usr/include/X11R5
-@@ -33,15 +34,18 @@
- install:
- #	mkdir -p $(LIB_DIR)
- #	mkdir -p $(INCLUDE_DIR)
--	cp $(LIB_FILE) $(LIB_DIR)
--	ranlib -s $(LIB_DIR)/$(LIB_FILE)
--	cp cgraph.h $(INCLUDE_DIR)
-+	mkdir -p $(DESTDIR)/$(LIB_DIR)/
-+	mkdir -p $(DESTDIR)/$(INCLUDE_DIR)/cgraph/
-+	cp $(LIB_FILE) $(DESTDIR)/$(LIB_DIR)/
-+	ranlib $(DESTDIR)/$(LIB_DIR)/$(LIB_FILE)
-+	cp cgraph.h $(DESTDIR)/$(INCLUDE_DIR)/cgraph/
- 
- # For NeXT
- $(LIB_FILE):  $(OBJS) Makefile
- 	rm -f $(LIB_FILE)
- 	ar r $(LIB_FILE) $(OBJS)
--	ranlib -s $(LIB_FILE)
-+	ranlib $(LIB_FILE)
-+	$(CC) -shared $(CCFLAGS) $(LDFLAGS) -Wl,-soname,$(LIB_FILE_SO).0 -o $(LIB_FILE_SO).0.0.0 $(OBJS) -lc -lm
- 
- # For Unix
- #$(LIB_FILE):  $(OBJS) Makefile
-@@ -49,92 +52,92 @@
- 
- 
- cg_newfuncs.o:  cglobals.h cgaxes.h cgfont.h
--	$(CC) $(CCFLAGS) $(ARCHS) cg_newfuncs.c
-+	$(CC) $(CCFLAGS) $(ARCHS) -c cg_newfuncs.c
- 
- cgprint.o:  cgprint.c cglobals.h
--	$(CC) $(CCFLAGS) $(ARCHS) cgprint.c
-+	$(CC) $(CCFLAGS) $(ARCHS) -c cgprint.c
- 	
- cgsave.o:  cgsave.c cglobals.h
--	$(CC) $(CCFLAGS) $(ARCHS) cgsave.c
-+	$(CC) $(CCFLAGS) $(ARCHS) -c cgsave.c
- 
- gaxlabel.o:  gaxlabel.c cglobals.h cgaxes.h  
--	$(CC) $(CCFLAGS) $(ARCHS) gaxlabel.c
-+	$(CC) $(CCFLAGS) $(ARCHS) -c gaxlabel.c
- 	
- gbott.o:  gbott.c    cglobals.h
--	$(CC) $(CCFLAGS) $(ARCHS) gbott.c
-+	$(CC) $(CCFLAGS) $(ARCHS) -c gbott.c
- 	
- bginit.o:  bginit.c cglobals.h cgaxes.h cgfont.h version.h cgraph.h
--	$(CC) $(CCFLAGS) $(ARCHS) bginit.c
-+	$(CC) $(CCFLAGS) $(ARCHS) -c bginit.c
- 	
- bgstart.o:  bgstart.c cglobals.h cgaxes.h cgfont.h version.h
--	$(CC) $(CCFLAGS) $(ARCHS) bgstart.c	
-+	$(CC) $(CCFLAGS) $(ARCHS) -c bgstart.c	
- 	
- gmark.o:   gmark.c cglobals.h  
--	$(CC) $(CCFLAGS) $(ARCHS) gmark.c
-+	$(CC) $(CCFLAGS) $(ARCHS) -c gmark.c
- 	
- glcmp.o:   glcmp.c cglobals.h 
--	$(CC) $(CCFLAGS) $(ARCHS) glcmp.c
-+	$(CC) $(CCFLAGS) $(ARCHS) -c glcmp.c
- 	
- gxaxs.o:   gxaxs.c cglobals.h cgaxes.h cgfont.h  
--	$(CC) $(CCFLAGS) $(ARCHS) gxaxs.c
-+	$(CC) $(CCFLAGS) $(ARCHS) -c gxaxs.c
- 	
- gxlog.o:   gxlog.c cglobals.h cgaxes.h cgfont.h  
--	$(CC) $(CCFLAGS) $(ARCHS) gxlog.c
-+	$(CC) $(CCFLAGS) $(ARCHS) -c gxlog.c
- 	
- gyaxs.o:   gyaxs.c cgaxes.h cgfont.h   cglobals.h
--	$(CC) $(CCFLAGS) $(ARCHS) gyaxs.c
-+	$(CC) $(CCFLAGS) $(ARCHS) -c gyaxs.c
- 	
- gylog.o:   gylog.c cglobals.h cgaxes.h  cgfont.h  
--	$(CC) $(CCFLAGS) $(ARCHS) gylog.c
-+	$(CC) $(CCFLAGS) $(ARCHS) -c gylog.c
- 	
- gtext.o:  gtext.c cglobals.h  
--	$(CC) $(CCFLAGS) $(ARCHS) gtext.c
-+	$(CC) $(CCFLAGS) $(ARCHS) -c gtext.c
- 	
- gtrnc.o:  gtrnc.c  cglobals.h
--	$(CC) $(CCFLAGS) $(ARCHS) gtrnc.c
-+	$(CC) $(CCFLAGS) $(ARCHS) -c gtrnc.c
- 	
- gmesh.o:  gmesh.c cglobals.h cgaxes.h  
--	$(CC) $(CCFLAGS) $(ARCHS) gmesh.c
-+	$(CC) $(CCFLAGS) $(ARCHS) -c gmesh.c
- 	
- gstyl.o:  gstyl.c cgaxes.h cglobals.h
--	$(CC) $(CCFLAGS) $(ARCHS) gstyl.c
-+	$(CC) $(CCFLAGS) $(ARCHS) -c gstyl.c
- 	
- gwdth.o:  gwdth.c  cglobals.h
--	$(CC) $(CCFLAGS) $(ARCHS) gwdth.c
-+	$(CC) $(CCFLAGS) $(ARCHS) -c gwdth.c
- 	
- gfont.o:  gfont.c cglobals.h cgfont.h PS_font_names.h
--	$(CC) $(CCFLAGS) $(ARCHS) gfont.c
-+	$(CC) $(CCFLAGS) $(ARCHS) -c gfont.c
- 	
- grmle.o:  grmle.c cglobals.h  
--	$(CC) $(CCFLAGS) $(ARCHS) grmle.c
-+	$(CC) $(CCFLAGS) $(ARCHS) -c grmle.c
- 	
- gmlin.o:  gmlin.c cglobals.h  
--	$(CC) $(CCFLAGS) $(ARCHS) gmlin.c
-+	$(CC) $(CCFLAGS) $(ARCHS) -c gmlin.c
- 	
- gcord.o:  gcord.c cglobals.h
--	$(CC) $(CCFLAGS) $(ARCHS) gcord.c
-+	$(CC) $(CCFLAGS) $(ARCHS) -c gcord.c
- 	
- gorig.o:  gorig.c cglobals.h
--	$(CC) $(CCFLAGS) $(ARCHS) gorig.c 
-+	$(CC) $(CCFLAGS) $(ARCHS) -c gorig.c 
- 	
- 	
- bgdash.o:  bgdash.c cglobals.h
--	$(CC) $(CCFLAGS) $(ARCHS) bgdash.c
-+	$(CC) $(CCFLAGS) $(ARCHS) -c bgdash.c
- 	
- gprim.o:  gprim.c cglobals.h  
--	$(CC) $(CCFLAGS) $(ARCHS) gprim.c
-+	$(CC) $(CCFLAGS) $(ARCHS) -c gprim.c
- 	
- grset.o:  grset.c cglobals.h
--	$(CC) $(CCFLAGS) $(ARCHS) grset.c
-+	$(CC) $(CCFLAGS) $(ARCHS) -c grset.c
- 	
- ggraycolor.o:  ggraycolor.c cglobals.h
--	$(CC) $(CCFLAGS) $(ARCHS) ggraycolor.c
-+	$(CC) $(CCFLAGS) $(ARCHS) -c ggraycolor.c
- 	
- gstrk.o:  gstrk.c cglobals.h
--	$(CC) $(CCFLAGS) $(ARCHS) gstrk.c
-+	$(CC) $(CCFLAGS) $(ARCHS) -c gstrk.c
- 	
- bgshow.o:  bgshow.c cglobals.h
--	$(CC) $(CCFLAGS) $(ARCHS) bgshow.c
-+	$(CC) $(CCFLAGS) $(ARCHS) -c bgshow.c
- 
- clean:
- 	rm -f *.o *.a *.sl
-
diff --git a/sci-libs/Cgraph/files/fix-src.patch b/sci-libs/Cgraph/files/fix-src.patch
deleted file mode 100644
index a19f23845..000000000
--- a/sci-libs/Cgraph/files/fix-src.patch
+++ /dev/null
@@ -1,42 +0,0 @@
-diff -uarN source/cgaxes.h source.new/cgaxes.h
---- source/cgaxes.h	1996-09-02 21:20:34.000000000 +0200
-+++ source.new/cgaxes.h	2009-03-01 18:53:22.000000000 +0100
-@@ -10,7 +10,7 @@
-     float cgxticks,cgyticks;	/* tick spacing for linear graphs	*/
-     double cgldecy,cgldecx; 	/* the upper end of the lowest decade of */
- 				/*   a log graph */
--    double cgudecy,cgudecx; 	/* the lower end of the highest decade 
-+    double cgudecy,cgudecx; 	/* the lower end of the highest decade */
- 				/*  of a log graph */
-     int cgxtix,cgytix;	   	/* used for logarithmic tick marks	*/
-     int cgprecision=	4;  	/* max # digits on screen graphs	*/
-diff -uarN source/gfont.c source.new/gfont.c
---- source/gfont.c	1998-08-31 19:27:43.000000000 +0200
-+++ source.new/gfont.c	2009-03-01 18:46:27.000000000 +0100
-@@ -5,7 +5,7 @@
- /*	   9-09-87  starting					  */
- /******************************************************************/
- 
--/*	Modified on 5/13/92 to work on NeXt's
-+/*	Modified on 5/13/92 to work on NeXt's */
- 
- 
- #include <string.h>								  
-diff -uarN source/grset.c source.new/grset.c
---- source/grset.c	1996-09-02 21:20:30.000000000 +0200
-+++ source.new/grset.c	2009-03-01 18:46:07.000000000 +0100
-@@ -14,10 +14,10 @@
- 
- int cg_reset(void)
- {
--    lw_aorigin(-cgxorig,-cgyorig); /* Go to the bottom left corner of the page */
--    lw_linewidth(1.0);
--    lw_gray(0.0);
--    lw_dash(0,0.);
-+    cg_aorigin(-cgxorig,-cgyorig); /* Go to the bottom left corner of the page */
-+    cg_linewidth(1.0);
-+    cg_gray(0.0);
-+    cg_dash(0,0.);
-     return(0);
- }
- 
diff --git a/sci-libs/Cgraph/metadata.xml b/sci-libs/Cgraph/metadata.xml
deleted file mode 100644
index ae9640ffb..000000000
--- a/sci-libs/Cgraph/metadata.xml
+++ /dev/null
@@ -1,8 +0,0 @@
-<?xml version="1.0" encoding="UTF-8"?>
-<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
-<pkgmetadata>
-	<maintainer type="project">
-		<email>sci@gentoo.org</email>
-		<name>Gentoo Science Project</name>
-	</maintainer>
-</pkgmetadata>
diff --git a/sci-libs/HDF5Plugin-Zstandard/HDF5Plugin-Zstandard-0_pre20201121-r1.ebuild b/sci-libs/HDF5Plugin-Zstandard/HDF5Plugin-Zstandard-0_pre20201121-r1.ebuild
new file mode 100644
index 000000000..d1257f0ee
--- /dev/null
+++ b/sci-libs/HDF5Plugin-Zstandard/HDF5Plugin-Zstandard-0_pre20201121-r1.ebuild
@@ -0,0 +1,27 @@
+# Copyright 2020-2022 Gentoo Authors
+# Distributed under the terms of the GNU General Public License v2
+
+EAPI=7
+
+inherit cmake
+
+DESCRIPTION="ZSTD plugin for hdf5"
+HOMEPAGE="https://github.com/aparamon/HDF5Plugin-Zstandard"
+COMMIT="d5afdb5f04116d5c2d1a869dc9c7c0c72832b143"
+SRC_URI="https://github.com/aparamon/HDF5Plugin-Zstandard/archive/${COMMIT}.tar.gz -> ${P}.tar.gz"
+
+LICENSE="Apache-2.0"
+SLOT="0"
+KEYWORDS="~amd64 ~x86"
+
+DEPEND="app-arch/zstd >=sci-libs/hdf5-1.12.2-r5"
+RDEPEND="${DEPEND}"
+
+S=${WORKDIR}/${PN}-${COMMIT}
+
+src_configure() {
+	local mycmakeargs=(
+		-DPLUGIN_INSTALL_PATH="${EPREFIX}/usr/$(get_libdir)/hdf5/plugin"
+	)
+	cmake_src_configure
+}
diff --git a/sci-libs/HDF5Plugin-Zstandard/Manifest b/sci-libs/HDF5Plugin-Zstandard/Manifest
new file mode 100644
index 000000000..80a0da53a
--- /dev/null
+++ b/sci-libs/HDF5Plugin-Zstandard/Manifest
@@ -0,0 +1 @@
+DIST HDF5Plugin-Zstandard-0_pre20201121.tar.gz 6405 BLAKE2B 6d1f169375297872751ee95f0ab6c9b3afaddb222a65c685786bd40ded357c9950d1ae895063c17935ff9fd9f819ba1eb58192daf7bac7d4a1be5e2caa28b322 SHA512 642afc2cc7e9439f5f0c34e1616b1f9d4c883c954ae1027933c98ac99564854513c5d4e4ce589594f3b739ad441d2880a218ee3518318949ed9f18ecff3dc4a7
diff --git a/sci-libs/HDF5Plugin-Zstandard/metadata.xml b/sci-libs/HDF5Plugin-Zstandard/metadata.xml
new file mode 100644
index 000000000..a171606a6
--- /dev/null
+++ b/sci-libs/HDF5Plugin-Zstandard/metadata.xml
@@ -0,0 +1,11 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
+<pkgmetadata>
+	<maintainer type="person">
+		<email>xgreenlandforwyy@gmail.com</email>
+		<name>Yiyang Wu</name>
+	</maintainer>
+	<upstream>
+		<remote-id type="github">aparamon/HDF5Plugin-Zstandard</remote-id>
+	</upstream>
+</pkgmetadata>
diff --git a/sci-libs/amber99sb_phipsi/Manifest b/sci-libs/amber99sb_phipsi/Manifest
index a2d956c1e..32dc12511 100644
--- a/sci-libs/amber99sb_phipsi/Manifest
+++ b/sci-libs/amber99sb_phipsi/Manifest
@@ -1 +1 @@
-DIST amber99sb_phipsi-0_pre130901.tar 52736 SHA256 213a9e9b5adfe0418b925541e3b83012953a0bca2397c43e07f0749956e92305 SHA512 1c7a4bc5364eccc8a112b9244aaf83159417d09f5989de5ea56c3d237129ebc1b190d8ef72a9f48eb815cd4ac1906bb51454712b5517eba641ec53fbe047717e WHIRLPOOL 048051596b00bc385efb8278b2b3d82fc54112d4a42468a75411a467881204e7b29155d556d8cf28dd39c10c7d5fe1f1ff9f2e19ffb03fe1afba9d16290429c5
+DIST amber99sb_phipsi-0_pre130901.tar 52736 BLAKE2B 9ff2d5a7b15be15f7cb25685609c44533c8649ea90c83e52bb8b7c3657d6f0daffa833e6241aee07eb16cd399810a2504e15a99389ab1ede5fb905d9736cdbb0 SHA512 1c7a4bc5364eccc8a112b9244aaf83159417d09f5989de5ea56c3d237129ebc1b190d8ef72a9f48eb815cd4ac1906bb51454712b5517eba641ec53fbe047717e
diff --git a/sci-libs/amber99sb_phipsi/amber99sb_phipsi-0_pre130901.ebuild b/sci-libs/amber99sb_phipsi/amber99sb_phipsi-0_pre130901.ebuild
index ff0f15f1c..e52bda099 100644
--- a/sci-libs/amber99sb_phipsi/amber99sb_phipsi-0_pre130901.ebuild
+++ b/sci-libs/amber99sb_phipsi/amber99sb_phipsi-0_pre130901.ebuild
@@ -1,16 +1,15 @@
-# Copyright 1999-2014 Gentoo Foundation
+# Copyright 1999-2021 Gentoo Authors
 # Distributed under the terms of the GNU General Public License v2
 
-EAPI=5
+EAPI=7
 
 DESCRIPTION="AMBER99SB PHI PSI table (Lindorff-Larsen et al., Proteins 78, 1950-58, 2010)"
-HOMEPAGE="https://research.chemistry.ohio-state.edu/bruschweiler/protein-force-field/"
-SRC_URI="http://research.chemistry.ohio-state.edu/bruschweiler/files/2013/09/cmap.itp_.tar -> ${P}.tar"
+HOMEPAGE="https://research.cbc.osu.edu/bruschweiler.1/protein-force-field/"
+SRC_URI="https://research.cbc.osu.edu/bruschweiler.1/wp-content/uploads/2013/09/cmap.itp_.tar -> ${P}.tar"
 
 SLOT="0"
 LICENSE="all-rights-reserved"
 KEYWORDS="~amd64 ~x86 ~amd64-linux ~x86-linux"
-IUSE=""
 
 S="${WORKDIR}"
 
diff --git a/sci-libs/amber99sbnmr-ildn/amber99sbnmr-ildn-0_pre130901.ebuild b/sci-libs/amber99sbnmr-ildn/amber99sbnmr-ildn-0_pre130901.ebuild
index b21ba6f11..c0bd20470 100644
--- a/sci-libs/amber99sbnmr-ildn/amber99sbnmr-ildn-0_pre130901.ebuild
+++ b/sci-libs/amber99sbnmr-ildn/amber99sbnmr-ildn-0_pre130901.ebuild
@@ -1,11 +1,11 @@
-# Copyright 1999-2015 Gentoo Foundation
+# Copyright 1999-2021 Gentoo Authors
 # Distributed under the terms of the GNU General Public License v2
 
-EAPI=5
+EAPI=7
 
 DESCRIPTION="AMBER99SBnmr1-ILDN FF (Lindorff-Larsen et al., Proteins 78, 1950-58, 2010)"
-HOMEPAGE="https://research.chemistry.ohio-state.edu/bruschweiler/protein-force-field/"
-SRC_URI="http://research.chemistry.ohio-state.edu/bruschweiler/files/2013/09/nmr1-ildn.tar -> ${P}.tar"
+HOMEPAGE="https://research.cbc.osu.edu/bruschweiler.1/protein-force-field/"
+SRC_URI="https://research.cbc.osu.edu/bruschweiler.1/wp-content/uploads/2013/09/nmr1-ildn.tar -> ${P}.tar"
 
 SLOT="0"
 LICENSE="all-rights-reserved"
diff --git a/sci-libs/amber99sbnmr/Manifest b/sci-libs/amber99sbnmr/Manifest
index 474ceadb4..fa06db441 100644
--- a/sci-libs/amber99sbnmr/Manifest
+++ b/sci-libs/amber99sbnmr/Manifest
@@ -1 +1 @@
-DIST amber99sbnmr-0_pre130901.tar 256000 SHA256 9e50fe1aec6b233d507b7048023e4191fc1dd2c83d190fa7585bb7c2e65ef56f SHA512 70b3750e5a5c297131e56b001a2667809f38c31b0f74afd27dc7373386091ea91ba0a98890c405f35a1103af86fa22f34d8b288755608659522bc2b5b4ace93e WHIRLPOOL cdf7398ac5ee52319ca9fdbadb91574ca5b2681902ba113819edc62b520d20122d311f5c2c769a30c9390fdf71cefef295d32e953d173b5da6911e343afa0390
+DIST amber99sbnmr-0_pre130901.tar 256000 BLAKE2B 9b868d8b7e8c574840f8dd3ba3c9b09788ce656a9469d98599687858cb02690782f8eb1875a2159496ed863d5fd53956fad1e4053ba4e7ff608686743b9d7e97 SHA512 70b3750e5a5c297131e56b001a2667809f38c31b0f74afd27dc7373386091ea91ba0a98890c405f35a1103af86fa22f34d8b288755608659522bc2b5b4ace93e
diff --git a/sci-libs/amber99sbnmr/amber99sbnmr-0_pre130901.ebuild b/sci-libs/amber99sbnmr/amber99sbnmr-0_pre130901.ebuild
index b6af2f90f..e2c83399f 100644
--- a/sci-libs/amber99sbnmr/amber99sbnmr-0_pre130901.ebuild
+++ b/sci-libs/amber99sbnmr/amber99sbnmr-0_pre130901.ebuild
@@ -1,16 +1,15 @@
-# Copyright 1999-2014 Gentoo Foundation
+# Copyright 1999-2021 Gentoo Authors
 # Distributed under the terms of the GNU General Public License v2
 
-EAPI=5
+EAPI=7
 
 DESCRIPTION="AMBER99SBnmr1 force field (Lindorff-Larsen et al., Proteins 78, 1950-58, 2010)"
-HOMEPAGE="https://research.chemistry.ohio-state.edu/bruschweiler/protein-force-field/"
-SRC_URI="http://research.chemistry.ohio-state.edu/bruschweiler/files/2013/09/nmr1.tar -> ${P}.tar"
+HOMEPAGE="https://research.cbc.osu.edu/bruschweiler.1/protein-force-field/"
+SRC_URI="https://research.cbc.osu.edu/bruschweiler.1/wp-content/uploads/2013/09/nmr1.tar -> ${P}.tar"
 
 SLOT="0"
 LICENSE="all-rights-reserved"
 KEYWORDS="~amd64 ~x86 ~amd64-linux ~x86-linux"
-IUSE=""
 
 S="${WORKDIR}"
 
@@ -18,7 +17,5 @@ RESTRICT="strip binchecks"
 
 src_install() {
 	insinto /usr/share/gromacs/top/
-	dodoc */*.doc
-	rm */*.doc || die
 	doins -r *
 }
diff --git a/sci-libs/amdlibm/Manifest b/sci-libs/amdlibm/Manifest
deleted file mode 100644
index aaaf90902..000000000
--- a/sci-libs/amdlibm/Manifest
+++ /dev/null
@@ -1 +0,0 @@
-DIST amdlibm-3.1-lin64.tar.gz 1478277 SHA256 c94ba6c25d5786aed59bd77f8f9cbc79e028da9a30705cfd8e18e90c3e11a36c SHA512 4ed16c953ea0a4b4f672c34333d17841cf939c75a12106161b3bd619d4fcdff17ea9043b665e9318a605fd02c607dc0ecbf4cde78de26d9193022c8ca556ddbc WHIRLPOOL f815af701753ac9b1cadb256573ed4748237cdf8816464665085f7857ca2b33d8165f82c088a31995926d51a11bfb4c1121356b917cf394111542b85eb6d4997
diff --git a/sci-libs/amdlibm/amdlibm-3.1.ebuild b/sci-libs/amdlibm/amdlibm-3.1.ebuild
deleted file mode 100644
index 1253d1006..000000000
--- a/sci-libs/amdlibm/amdlibm-3.1.ebuild
+++ /dev/null
@@ -1,72 +0,0 @@
-# Copyright 1999-2015 Gentoo Foundation
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=5
-
-inherit multilib
-
-MYP=${PN}-${PV}-lin64
-
-DESCRIPTION="Optimized libm replacement from AMD for x86_64 architectures"
-HOMEPAGE="http://developer.amd.com/tools/cpu-development/libm/"
-SRC_URI="${MYP}.tar.gz"
-LICENSE="AMD"
-SLOT="0"
-KEYWORDS="-* ~amd64 ~amd64-linux"
-IUSE="examples static-libs"
-RESTRICT="fetch strip"
-
-S="${WORKDIR}/${MYP}"
-
-QA_PREBUILT="opt/${PN}/$(get_libdir)/lib${PN}.so"
-QA_TEXTRELS="${QA_PREBUILT}"
-
-pkg_nofetch() {
-	einfo "The package's license prohibits redistribution."
-	einfo "Please download ${A} from"
-	einfo "   ${HOMEPAGE}"
-	einfo "and place it into ${DISTDIR}."
-}
-
-src_prepare() {
-	cat <<- EOF > "${T}"/99${PN}
-		LDPATH="${EROOT%/}/opt/${PN}/$(get_libdir)"
-	EOF
-
-	cat <<- EOF > "${T}"/${PN}.pc
-		prefix=${EROOT%/}/opt/${PN}
-		exec_prefix=\${prefix}
-		libdir=\${prefix}/$(get_libdir)
-		includedir=\${prefix}/include
-		Name: ${PN}
-		Description: ${DESCRIPTION}
-		Version: ${PV}
-		Libs: -L\${libdir} -l${PN}
-		Cflags: -I\${includedir}
-	EOF
-}
-
-src_test() {
-	cd examples || die
-	sh build_and_run.sh || die
-}
-
-src_install() {
-	dodoc ReleaseNotes.txt
-
-	into /opt/${PN}
-	dolib.so lib/dynamic/lib${PN}.so
-	use static-libs && dolib.a lib/static/lib${PN}.a
-
-	insinto /opt/${PN}
-	doins -r include
-
-	if use examples; then
-		insinto /usr/share/doc/${PF}
-		doins -r examples
-	fi
-
-	insinto /usr/$(get_libdir)/pkgconfig
-	doins "${T}"/${PN}.pc
-	doenvd "${T}"/99${PN}
-}
diff --git a/sci-libs/amdlibm/metadata.xml b/sci-libs/amdlibm/metadata.xml
deleted file mode 100644
index 51af055a9..000000000
--- a/sci-libs/amdlibm/metadata.xml
+++ /dev/null
@@ -1,13 +0,0 @@
-<?xml version="1.0" encoding="UTF-8"?>
-<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
-<pkgmetadata>
-	<maintainer type="project">
-		<email>sci@gentoo.org</email>
-		<name>Gentoo Science Project</name>
-	</maintainer>
-	<longdescription lang="en">
-AMD LibM is a software library containing a collection of basic math
-functions optimized for x86-64 processor based machines. It provides
-many routines from the list of standard C99 math functions.
-</longdescription>
-</pkgmetadata>
diff --git a/sci-libs/aocl-libm/Manifest b/sci-libs/aocl-libm/Manifest
new file mode 100644
index 000000000..3f320d8be
--- /dev/null
+++ b/sci-libs/aocl-libm/Manifest
@@ -0,0 +1,2 @@
+DIST aocl-libm-linux-aocc-3.1.0.tar.gz 1234123 BLAKE2B d63c5e5a5e5445de59ed5726ae5cc285fa7e9416255b861f337c7f649d460d6f95d4deb2b635166a5ed99f216eefb47054b11f3949c54a2fb06c4fc7bc9098d7 SHA512 0806b50b2f20bfe05a3d3eff16be09c4597f07f1dad15861cb289f1f0850cc9ed53601d4cf41174f6ad1f67963a94f7a6fee66394f787d302bf1a9c7b17e45cc
+DIST aocl-libm-linux-gcc-3.1.0.tar.gz 1281295 BLAKE2B 953fbc381182afb7e3b26a93643f4ab18c9fb7b331d686bde75b63f512668a5045fa74209031849a4b3701fd51000c386c96ad7a3d4567913b68b04b9115351a SHA512 3df4700498713c510ff2cc04ad37db12b3b3c174caf6118bfd364f95899a10eeefca566d898c13fb3732f5b7390792f1c786c64dbf928ed9021b11546d5c04c9
diff --git a/sci-libs/aocl-libm/aocl-libm-3.1.0.ebuild b/sci-libs/aocl-libm/aocl-libm-3.1.0.ebuild
new file mode 100644
index 000000000..890414de2
--- /dev/null
+++ b/sci-libs/aocl-libm/aocl-libm-3.1.0.ebuild
@@ -0,0 +1,71 @@
+# Copyright 1999-2022 Gentoo Authors
+# Distributed under the terms of the GNU General Public License v2
+
+EAPI=8
+
+inherit toolchain-funcs
+
+DESCRIPTION="Optimized libm replacement from AMD for x86_64 architectures"
+HOMEPAGE="https://developer.amd.com/amd-aocl/amd-math-library-libm/"
+SRC_URI="
+	aocc? ( aocl-libm-linux-aocc-${PV}.tar.gz )
+	!aocc? ( aocl-libm-linux-gcc-${PV}.tar.gz )
+"
+S="${WORKDIR}/amd-libm"
+
+LICENSE="AMD"
+SLOT="0"
+KEYWORDS="-* ~amd64 ~amd64-linux"
+IUSE="aocc examples static-libs test"
+RESTRICT="fetch strip !test? ( test )"
+
+QA_PREBUILT="*"
+QA_TEXTRELS="*"
+
+pkg_nofetch() {
+	einfo "The package's license prohibits redistribution."
+	einfo "Please download the package from"
+	einfo "\t ${HOMEPAGE}"
+	einfo "and place it into your DISTDIR folder"
+}
+
+src_prepare() {
+	default
+
+	sed -e "s/^CC =.*$/CC = $(tc-getCC)/" -i examples/Makefile || die
+
+	cat <<- EOF > "${T}"/amdlibm.pc || die
+		prefix=${EPREFIX}/usr
+		exec_prefix=\${prefix}
+		libdir=\${prefix}/$(get_libdir)
+		includedir=\${prefix}/include
+
+		Name: ${PN}
+		Description: ${DESCRIPTION}
+		Version: ${PV}
+		Libs: -L\${libdir} -lamdlibm
+		Cflags: -I\${includedir}
+	EOF
+}
+
+src_test() {
+	cd examples || die
+	AOCL_ROOT=".." emake test_libm
+	LD_LIBRARY_PATH=../lib ./test_libm || die
+}
+
+src_install() {
+	dodoc ReleaseNotes.txt
+
+	doheader include/*
+
+	dolib.so lib/*.so
+	use static-libs && dolib.a  lib/*.a
+
+	if use examples; then
+		dodoc -r examples
+	fi
+
+	insinto /usr/$(get_libdir)/pkgconfig
+	doins "${T}"/amdlibm.pc
+}
diff --git a/sci-libs/aocl-libm/metadata.xml b/sci-libs/aocl-libm/metadata.xml
new file mode 100644
index 000000000..8c9afa236
--- /dev/null
+++ b/sci-libs/aocl-libm/metadata.xml
@@ -0,0 +1,16 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
+<pkgmetadata>
+	<maintainer type="project">
+		<email>sci@gentoo.org</email>
+		<name>Gentoo Science Project</name>
+	</maintainer>
+	<longdescription lang="en">
+		AMD LibM is a software library containing a collection of basic math
+		functions optimized for x86-64 processor based machines. It provides
+		many routines from the list of standard C99 math functions.
+	</longdescription>
+	<use>
+		<flag name="aocc">install the library built using AOCC, else use the GCC version</flag>
+	</use>
+</pkgmetadata>
diff --git a/sci-libs/aocl-sparse/Manifest b/sci-libs/aocl-sparse/Manifest
new file mode 100644
index 000000000..2ec0d6554
--- /dev/null
+++ b/sci-libs/aocl-sparse/Manifest
@@ -0,0 +1 @@
+DIST aocl-sparse-2.2.tar.gz 29556 BLAKE2B 9dbd0d7e721fcd07350f9558f141df7070b8b6af2cb11deb7bf6af9f6909fa970e1a96d52594abbf023ece677862cbd4b205135d65c23a9aff9f6654dbb57f29 SHA512 6163caee937f0865c0dc0b89ed4df70cfa744365201a1ca9fe17bafb158f6e7a4d100bff96ed52d2ba1471cbb75395fb1cb46549591eb0cec70d00e64ca84ea5
diff --git a/sci-libs/aocl-sparse/aocl-sparse-2.2.ebuild b/sci-libs/aocl-sparse/aocl-sparse-2.2.ebuild
new file mode 100644
index 000000000..ad755cf03
--- /dev/null
+++ b/sci-libs/aocl-sparse/aocl-sparse-2.2.ebuild
@@ -0,0 +1,51 @@
+# Copyright 1999-2020 Gentoo Authors
+# Distributed under the terms of the GNU General Public License v2
+
+EAPI=7
+
+CMAKE_BUILD_TYPE=Release
+CMAKE_MAKEFILE_GENERATOR=emake
+inherit cmake
+
+DESCRIPTION="AMD library for optimized sparse BLAS operations"
+HOMEPAGE="https://developer.amd.com/amd-aocl/"
+
+if [[ ${PV} == 9999 ]]; then
+	inherit git-r3
+	EGIT_REPO_URI="https://github.com/amd/aocl-sparse"
+else
+	SRC_URI="https://github.com/amd/aocl-sparse/archive/${PV}.tar.gz -> ${P}.tar.gz"
+	KEYWORDS="~amd64"
+fi
+
+LICENSE="BSD"
+SLOT="0"
+
+BDEPEND="dev-vcs/git"
+
+src_prepare() {
+	sed -e 's/-march=native//' \
+	    -e '/^[[:space:]]*set[[:space:]]*([[:space:]]*CMAKE_INSTALL_LIBDIR[[:space:]].*)/I{s/^/#_cmake_modify_IGNORE /g}' \
+	    -i CMakeLists.txt || die
+	sed -e 's:${CMAKE_INSTALL_PREFIX}/lib:${CMAKE_INSTALL_PREFIX}/${CMAKE_INSTALL_LIBDIR}:' \
+	    -i library/CMakeLists.txt || die
+	sed -e 's:$AOCLSPARSE_ROOT/lib/:$AOCLSPARSE_ROOT/library:' \
+	    -e 's:-O3::' \
+	    -i tests/test.sh || die
+	cmake_src_prepare
+}
+
+src_compile() {
+	cmake_src_compile
+
+	cd tests
+	emake -f - <<EOF
+test_aocl_sparse:
+	\$(CXX) -DNDEBUG -o test_aocl_sparse sample_csrmv.cpp -I../library/include -I${BUILD_DIR}/include -L${BUILD_DIR}/library -laoclsparse
+EOF
+}
+
+src_test() {
+	cd tests
+	LD_LIBRARY_PATH=${BUILD_DIR}/library ./test_aocl_sparse || die
+}
diff --git a/sci-libs/aocl-sparse/aocl-sparse-9999.ebuild b/sci-libs/aocl-sparse/aocl-sparse-9999.ebuild
new file mode 100644
index 000000000..ad755cf03
--- /dev/null
+++ b/sci-libs/aocl-sparse/aocl-sparse-9999.ebuild
@@ -0,0 +1,51 @@
+# Copyright 1999-2020 Gentoo Authors
+# Distributed under the terms of the GNU General Public License v2
+
+EAPI=7
+
+CMAKE_BUILD_TYPE=Release
+CMAKE_MAKEFILE_GENERATOR=emake
+inherit cmake
+
+DESCRIPTION="AMD library for optimized sparse BLAS operations"
+HOMEPAGE="https://developer.amd.com/amd-aocl/"
+
+if [[ ${PV} == 9999 ]]; then
+	inherit git-r3
+	EGIT_REPO_URI="https://github.com/amd/aocl-sparse"
+else
+	SRC_URI="https://github.com/amd/aocl-sparse/archive/${PV}.tar.gz -> ${P}.tar.gz"
+	KEYWORDS="~amd64"
+fi
+
+LICENSE="BSD"
+SLOT="0"
+
+BDEPEND="dev-vcs/git"
+
+src_prepare() {
+	sed -e 's/-march=native//' \
+	    -e '/^[[:space:]]*set[[:space:]]*([[:space:]]*CMAKE_INSTALL_LIBDIR[[:space:]].*)/I{s/^/#_cmake_modify_IGNORE /g}' \
+	    -i CMakeLists.txt || die
+	sed -e 's:${CMAKE_INSTALL_PREFIX}/lib:${CMAKE_INSTALL_PREFIX}/${CMAKE_INSTALL_LIBDIR}:' \
+	    -i library/CMakeLists.txt || die
+	sed -e 's:$AOCLSPARSE_ROOT/lib/:$AOCLSPARSE_ROOT/library:' \
+	    -e 's:-O3::' \
+	    -i tests/test.sh || die
+	cmake_src_prepare
+}
+
+src_compile() {
+	cmake_src_compile
+
+	cd tests
+	emake -f - <<EOF
+test_aocl_sparse:
+	\$(CXX) -DNDEBUG -o test_aocl_sparse sample_csrmv.cpp -I../library/include -I${BUILD_DIR}/include -L${BUILD_DIR}/library -laoclsparse
+EOF
+}
+
+src_test() {
+	cd tests
+	LD_LIBRARY_PATH=${BUILD_DIR}/library ./test_aocl_sparse || die
+}
diff --git a/sci-libs/aocl-sparse/metadata.xml b/sci-libs/aocl-sparse/metadata.xml
new file mode 100644
index 000000000..188515bd2
--- /dev/null
+++ b/sci-libs/aocl-sparse/metadata.xml
@@ -0,0 +1,15 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
+<pkgmetadata>
+	<maintainer type="person">
+		<email>gentoo@aisha.cc</email>
+		<name>Aisha Tammy</name>
+	</maintainer>
+	<maintainer type="project">
+		<email>sci@gentoo.org</email>
+		<name>Gentoo Science Project</name>
+	</maintainer>
+	<upstream>
+		<remote-id type="github">amd/aocl-sparse</remote-id>
+	</upstream>
+</pkgmetadata>
diff --git a/sci-libs/armadillo/Manifest b/sci-libs/armadillo/Manifest
deleted file mode 100644
index 874b79ad8..000000000
--- a/sci-libs/armadillo/Manifest
+++ /dev/null
@@ -1 +0,0 @@
-DIST armadillo-6.700.5.tar.gz 5470242 SHA256 d5817a8ff07da3bd8753b1e037ef39e7a6c81d88bb7119a2a8e6c3dc93b48db1 SHA512 1472056a809cc9f79c4e235c871253c689aa359c05efb158c98c8816b9ce7e4997e17bdaf6965711b3d1cc408d2ca74e1d438dcc5aa08cd322b352935f75887d WHIRLPOOL 803f7f02a726dc6ace0b980aac1503509d0d741e4794f1a8578e5c8d9665038007ae8841e1c59f8d63002ea91cd86139e22b6d64d3f2317929adf239bba8808b
diff --git a/sci-libs/armadillo/armadillo-6.700.5.ebuild b/sci-libs/armadillo/armadillo-6.700.5.ebuild
deleted file mode 100644
index eb62a2209..000000000
--- a/sci-libs/armadillo/armadillo-6.700.5.ebuild
+++ /dev/null
@@ -1,121 +0,0 @@
-# Copyright 1999-2016 Gentoo Foundation
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=6
-
-CMAKE_IN_SOURCE_BUILD=1
-
-inherit cmake-utils toolchain-funcs
-
-DESCRIPTION="Streamlined C++ linear algebra library"
-HOMEPAGE="http://arma.sourceforge.net/"
-SRC_URI="mirror://sourceforge/arma/${P}.tar.gz"
-
-LICENSE="MPL-2.0"
-SLOT="0/6"
-KEYWORDS="~amd64 ~x86 ~amd64-linux ~x86-linux"
-IUSE="arpack atlas blas debug doc examples hdf5 lapack mkl superlu tbb test"
-REQUIRED_USE="test? ( lapack )"
-
-RDEPEND="
-	dev-libs/boost
-	arpack? ( sci-libs/arpack )
-	atlas? ( sci-libs/atlas[lapack] )
-	blas? ( virtual/blas )
-	lapack? ( virtual/lapack )
-	superlu? ( sci-libs/superlu )
-"
-DEPEND="${RDEPEND}
-	arpack? ( virtual/pkgconfig )
-	atlas? ( virtual/pkgconfig )
-	blas? ( virtual/pkgconfig )
-	hdf5? ( sci-libs/hdf5 )
-	lapack? ( virtual/pkgconfig )
-	mkl? ( sci-libs/mkl )
-	tbb? ( dev-cpp/tbb )"
-PDEPEND="${RDEPEND}
-	hdf5? ( sci-libs/hdf5 )
-	mkl? ( sci-libs/mkl )
-	tbb? ( dev-cpp/tbb )"
-
-src_prepare() {
-	# avoid the automagic cmake macros
-	sed -i -e '/ARMA_Find/d' CMakeLists.txt || die
-	cmake-utils_src_prepare
-}
-
-src_configure() {
-	local mycmakeargs=(
-		-DINSTALL_LIB_DIR="${EPREFIX}/usr/$(get_libdir)"
-		-DARMA_EXTRA_DEBUG="$(usex debug)"
-		-DARMA_USE_MKL_ALLOC="$(usex mkl)"
-		-DARMA_USE_TBB_ALLOC="$(usex tbb)"
-	)
-	if use arpack; then
-		mycmakeargs+=(
-			-DARPACK_FOUND=ON
-			-DARPACK_LIBRARY="$($(tc-getPKG_CONFIG) --libs arpack)"
-		)
-	fi
-	if use atlas; then
-		local c=atlas-cblas l=atlas-clapack
-		$(tc-getPKG_CONFIG) --exists ${c}-threads && c+=-threads
-		$(tc-getPKG_CONFIG) --exists ${l}-threads && l+=-threads
-		mycmakeargs+=(
-			-DCBLAS_FOUND=ON
-			-DCBLAS_INCLUDE_DIR="$($(tc-getPKG_CONFIG) --cflags-only-I ${c} | sed 's/-I//')"
-			-DCBLAS_LIBRARIES="$($(tc-getPKG_CONFIG) --libs ${c})"
-			-DCLAPACK_FOUND=ON
-			-DCLAPACK_INCLUDE_DIR="$($(tc-getPKG_CONFIG) --cflags-only-I ${l} | sed 's/-I//')"
-			-DCLAPACK_LIBRARIES="$($(tc-getPKG_CONFIG) --libs ${l})"
-		)
-	fi
-	if use blas; then
-		mycmakeargs+=(
-			-DBLAS_FOUND=ON
-			-DBLAS_LIBRARIES="$($(tc-getPKG_CONFIG) --libs blas)"
-		)
-	fi
-	if use hdf5; then
-		mycmakeargs+=(
-			-DHDF5_FOUND=ON
-			-DHDF5_LIBRARIES="-lhdf5"
-		)
-	fi
-	if use lapack; then
-		mycmakeargs+=(
-			-DLAPACK_FOUND=ON
-			-DLAPACK_LIBRARIES="$($(tc-getPKG_CONFIG) --libs lapack)"
-		)
-	fi
-	if use superlu; then
-		mycmakeargs+=(
-			-DSuperLU_FOUND=ON
-			-DSuperLU_LIBRARIES="$($(tc-getPKG_CONFIG) --libs superlu)"
-			-DSuperLU_INCLUDE_DIR="$($(tc-getPKG_CONFIG) --cflags-only-I superlu | awk '{print $1}' | sed 's/-I//')"
-		)
-	fi
-
-	cmake-utils_src_configure
-}
-
-src_test() {
-	pushd examples > /dev/null
-	emake \
-		CXX="$(tc-getCXX)" \
-		CXXFLAGS="-I../include ${CXXFLAGS} -DARMA_USE_BLAS -DARMA_USE_LAPACK" \
-		LIB_FLAGS="-L.. $($(tc-getPKG_CONFIG) --libs blas lapack)"
-	LD_LIBRARY_PATH="..:${LD_LIBRARY_PATH}" ./example1 || die
-	emake clean
-	popd > /dev/null
-}
-
-src_install() {
-	cmake-utils_src_install
-	dodoc README.txt
-	use doc && dodoc *pdf *html
-	if use examples; then
-		insinto /usr/share/examples/${PF}
-		doins -r examples/*
-	fi
-}
diff --git a/sci-libs/armadillo/metadata.xml b/sci-libs/armadillo/metadata.xml
deleted file mode 100644
index af1c24703..000000000
--- a/sci-libs/armadillo/metadata.xml
+++ /dev/null
@@ -1,43 +0,0 @@
-<?xml version="1.0" encoding="UTF-8"?>
-<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
-<pkgmetadata>
-	<maintainer type="project">
-		<email>sci@gentoo.org</email>
-		<name>Gentoo Science Project</name>
-	</maintainer>
-	<longdescription lang="en">
-Armadillo is a C++ linear algebra library (matrix maths) aiming
-towards a good balance between speed and ease of use. Integer,
-floating point and complex numbers are supported, as well as a
-subset of trigonometric and statistics functions. Various matrix
-decompositions are provided through optional integration with LAPACK
-and ATLAS libraries. 
-A delayed evaluation approach is employed (during compile time) to
-combine several operations into one and reduce (or eliminate) the
-need for temporaries. This is accomplished through recursive
-templates and template meta-programming.
-</longdescription>
-	<use>
-		<flag name="atlas">
-Link with <pkg>sci-libs/atlas</pkg> libraries for cblas and
-clapack
-</flag>
-		<flag name="arpack">
-Link with <pkg>sci-libs/arpack</pkg> libraries for eigen decomposition
-</flag>
-		<flag name="mkl">
-Use matrix allocation from the Intel MKL <pkg>sci-libs/mkl</pkg>
-</flag>
-		<flag name="tbb">
-Use matrix allocation from the Threads Building Blocks
-<pkg>dev-cpp/tbb</pkg>
-</flag>
-		<flag name="superlu">
-Use SuperLU for sparse linear equation solving
-<pkg>sci-libs/superlu</pkg>
-</flag>
-	</use>
-	<upstream>
-		<remote-id type="sourceforge">arma</remote-id>
-	</upstream>
-</pkgmetadata>
diff --git a/sci-libs/arrayfire/Manifest b/sci-libs/arrayfire/Manifest
index 609ed0ca4..584d98ad5 100644
--- a/sci-libs/arrayfire/Manifest
+++ b/sci-libs/arrayfire/Manifest
@@ -1,5 +1,3 @@
-DIST arrayfire-3.1.3.tar.bz2 23740458 BLAKE2B 8f9440cd26610e0f1dd3dab448962b669d13d47f0d245f5d8316c27159bdaf9fa208c4477eb57de7bc90b90e10f504e603f47d4e3179003dc4b2acd2892d3a21 SHA512 500fd7652494fed5891f0c8bc31ca3ab87cc0c8587f13793621bb5f8c348c3dddccfc1805b99360251c87998765e0c3221e55c49fa4ac2eb3a1c06c1aeb680ee
-DIST arrayfire-3.2.2.tar.bz2 30359885 BLAKE2B fe5b95ac4c06cbef2f7f5ab1007ffde0a1bbeae8f5bf765877cffb862584b676a4214d0dd363d190a452b0645e29ab490bbb7f79eaa470e3885260a9aaac57aa SHA512 ff897eb24d85d83bf844a7507181f2091ac7d902260b9f4b4b2d4aea898c3e818a4694eb57dfff67aaeeabc6180b5e6e1e295eab5ccdab639e280fa62b5e0945
-DIST arrayfire-3.3.2.tar.bz2 34100522 BLAKE2B b3392d2b59d31e1061c900ab1bc44d1471d4d44eda2f7505f4655c683a1478a33f948864aea2cf41af352c9f8e5c3f4e19db82bcd678d0ef5f644bc676f56056 SHA512 0f7101af887d52eea537c8cbe41e26676f3acb26d2af903e2e6152433ecceb5349633b5f6e8a677854839fbc5ff5a64e88d31d85e80c4c55cab9836ccba579fb
-DIST arrayfire-3.4.2.tar.bz2 33288191 BLAKE2B c21e7e8763c842a88cdbaa64393a608b1f44716fb6507989239fe6c427d9ddfe61be8f8e642aa6b23ca7d59baa45661fca152c54ab404b53eb98cc42cd109c3d SHA512 c8b139ca314224c33ff45a1b304dc5fc5ed2a5eca726606b316f4b355680c842fac434f19e6cd3820065845d94359a62e684e20521136f1944015760aa004368
-DIST gtest-1.7.0.zip 1164254 BLAKE2B ba8cf5dc336e3a6889b58922b62497cdac94d9f77bc5cbac3d72e4a88f33cbe572b6f61b5323acb7ea6dfc67f92c0ba231bedc5251c276831ea7a9e77ab6d570 SHA512 8859369f2dd32cbc2ac01aba029aa3ff20a321f40658b9643aff442d34c33468221866b801b28c66a28af47dbcd362d26941fc98db92b6efb7e41ea5b7be1a07
+DIST arrayfire-3.7.2.tar.bz2 53973398 BLAKE2B 33323516c4b708affb0d5457a55e4defae363b913b30d1c74a7b7d8956c9e85397a030c4c9e1b6e2605dd1703763b261beca9a5cfb69ff8a183cc95e51670748 SHA512 733f5931cca9397dd45945fde05d887207d11891fcc5ff0d2b5f30ac6bd4881240c595bd24d1d7b8f89c74e249b3fe16a15c2640586940bf101cd0fbaec998a6
+DIST arrayfire-3.7.3.tar.bz2 53956721 BLAKE2B b5c28ea71d0f88befd7bc747eec20d90b006e50ca2a614ce6237eb3d842fc1ddffb87f72a50a2b921c52cad1fa79668f4463bf7b7c6f73f65400e5557ef5db12 SHA512 e94545b9e02c95ceff863ff73717250a8a7dd818d9c598f3e18f9aedb808977ee5062a6a1da212bd8c22996d2324153b2d1dfc9ecb4114a07b4927383881e230
+DIST arrayfire-3.8.0.tar.bz2 53964142 BLAKE2B c5325066f72e794f6bf8883306eb2848a299107f8aaeb2694933159f72fe43ee733347cf5fd0999905ab2ef89f3eca99e2e3725f686d90429d7f8f374446e425 SHA512 f36bee89a0f1a0a48ca2cae3a7b2527d63830e3070cb31174ff7f5c42f065aad6981d5142a8b7af7215a3c7dbf67ae13d1ea3543cd94eb70cff509c8cb95c739
diff --git a/sci-libs/arrayfire/arrayfire-3.1.3-r1.ebuild b/sci-libs/arrayfire/arrayfire-3.1.3-r1.ebuild
deleted file mode 100644
index 9dff4b2c7..000000000
--- a/sci-libs/arrayfire/arrayfire-3.1.3-r1.ebuild
+++ /dev/null
@@ -1,109 +0,0 @@
-# Copyright 1999-2017 Gentoo Foundation
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=6
-
-inherit cmake-utils multilib
-
-GTEST_PV="1.7.0"
-
-DESCRIPTION="A general purpose GPU library"
-HOMEPAGE="http://www.arrayfire.com/"
-SRC_URI="
-	http://arrayfire.com/arrayfire_source/${PN}-full-${PV}.tar.bz2 -> ${P}.tar.bz2
-	test? ( https://github.com/google/googletest/archive/release-${GTEST_PV}.zip -> gtest-${GTEST_PV}.zip )"
-
-LICENSE="
-	BSD
-	nonfree? ( OpenSIFT )"
-SLOT="0"
-IUSE="+examples +cpu cuda nonfree opencl test graphics"
-KEYWORDS="~amd64"
-
-RDEPEND="
-	>=sys-devel/gcc-4.7:*
-	media-libs/freeimage
-	cuda? (
-		>=dev-util/nvidia-cuda-toolkit-7.5.18-r1
-		dev-libs/boost
-	)
-	cpu? (
-		virtual/blas
-		virtual/cblas
-		virtual/lapacke
-		sci-libs/fftw:3.0
-	)
-	opencl? (
-		virtual/blas
-		virtual/cblas
-		virtual/lapacke
-		>=sci-libs/clblas-2.4
-		>=sci-libs/clfft-2.6.1
-		dev-libs/boost
-		|| ( dev-libs/boost-compute >=dev-libs/boost-1.61.0 )
-	)
-	graphics? (
-		media-libs/glew:=
-		>=media-libs/glfw-3.1.1
-		~sci-visualization/forge-3.1.2
-	)"
-DEPEND="${RDEPEND}"
-
-S="${WORKDIR}/${PN}-full-${PV}"
-BUILD_DIR="${S}/build"
-CMAKE_BUILD_TYPE=Release
-
-# We need write acccess /dev/nvidiactl, /dev/nvidia0 and /dev/nvidia-uvm and the portage
-# user is (usually) not in the video group
-RESTRICT="userpriv"
-
-pkg_pretend() {
-	if [[ ${MERGE_TYPE} != binary ]]; then
-		if [[ $(gcc-major-version) -lt 4 ]] || ( [[ $(gcc-major-version) -eq 4 && $(gcc-minor-version) -lt 7 ]] ) ; then
-			die "Compilation with gcc older than 4.7 is not supported."
-		fi
-	fi
-}
-
-src_unpack() {
-	default
-
-	if ! use nonfree; then
-		find "${WORKDIR}" -name "*_nonfree*" -delete || die
-	fi
-
-	if use test; then
-		mkdir -p "${BUILD_DIR}"/third_party/src/ || die
-		mv "${WORKDIR}"/gtest-"${GTEST_PV}" "${BUILD_DIR}"/third_party/src/googletest || die
-	fi
-}
-
-src_configure() {
-	if use cuda; then
-		addwrite /dev/nvidiactl
-		addwrite /dev/nvidia0
-		addwrite /dev/nvidia-uvm
-	fi
-
-	local mycmakeargs=(
-		-DBUILD_CPU="$(usex cpu)"
-		-DBUILD_CUDA="$(usex cuda)"
-		-DBUILD_OPENCL="$(usex opencl)"
-		-DBUILD_EXAMPLES="$(usex examples)"
-		-DBUILD_TEST="$(usex test)"
-		-DBUILD_GRAPHICS="$(usex graphics)"
-		-DBUILD_NONFREE="$(usex nonfree)"
-		-DUSE_SYSTEM_BOOST_COMPUTE=ON
-		-DUSE_SYSTEM_CLBLAS=ON
-		-DUSE_SYSTEM_CLFFT=ON
-		-DUSE_SYSTEM_FORGE=ON
-		-DAF_INSTALL_CMAKE_DIR=/usr/$(get_libdir)/cmake/ArrayFire
-	)
-	cmake-utils_src_configure
-}
-
-src_install() {
-	cmake-utils_src_install
-
-	dobin "${BUILD_DIR}/bin2cpp"
-}
diff --git a/sci-libs/arrayfire/arrayfire-3.2.2.ebuild b/sci-libs/arrayfire/arrayfire-3.2.2.ebuild
deleted file mode 100644
index 614f29593..000000000
--- a/sci-libs/arrayfire/arrayfire-3.2.2.ebuild
+++ /dev/null
@@ -1,110 +0,0 @@
-# Copyright 1999-2017 Gentoo Foundation
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=6
-
-inherit cmake-utils multilib
-
-GTEST_PV="1.7.0"
-
-DESCRIPTION="A general purpose GPU library"
-HOMEPAGE="http://www.arrayfire.com/"
-SRC_URI="
-	http://arrayfire.com/arrayfire_source/${PN}-full-${PV}.tar.bz2 -> ${P}.tar.bz2
-	test? ( https://github.com/google/googletest/archive/release-${GTEST_PV}.zip -> gtest-${GTEST_PV}.zip )"
-
-LICENSE="
-	BSD
-	nonfree? ( OpenSIFT )"
-SLOT="0"
-IUSE="+examples +cpu cuda nonfree opencl test unified graphics"
-KEYWORDS="~amd64"
-
-RDEPEND="
-	>=sys-devel/gcc-4.7:*
-	media-libs/freeimage
-	cuda? (
-		>=dev-util/nvidia-cuda-toolkit-7.5.18-r1
-		dev-libs/boost
-	)
-	cpu? (
-		virtual/blas
-		virtual/cblas
-		virtual/lapacke
-		sci-libs/fftw:3.0
-	)
-	opencl? (
-		virtual/blas
-		virtual/cblas
-		virtual/lapacke
-		>=sci-libs/clblas-2.4
-		>=sci-libs/clfft-2.6.1
-		dev-libs/boost
-		|| ( dev-libs/boost-compute >=dev-libs/boost-1.61.0 )
-	)
-	graphics? (
-		media-libs/glew:=
-		>=media-libs/glfw-3.1.1
-		~sci-visualization/forge-3.2.2
-	)"
-DEPEND="${RDEPEND}"
-
-S="${WORKDIR}/${PN}-full-${PV}"
-BUILD_DIR="${S}/build"
-CMAKE_BUILD_TYPE=Release
-
-# We need write acccess /dev/nvidiactl, /dev/nvidia0 and /dev/nvidia-uvm and the portage
-# user is (usually) not in the video group
-RESTRICT="userpriv"
-
-pkg_pretend() {
-	if [[ ${MERGE_TYPE} != binary ]]; then
-		if [[ $(gcc-major-version) -lt 4 ]] || ( [[ $(gcc-major-version) -eq 4 && $(gcc-minor-version) -lt 7 ]] ) ; then
-			die "Compilation with gcc older than 4.7 is not supported."
-		fi
-	fi
-}
-
-src_unpack() {
-	default
-
-	if ! use nonfree; then
-		find "${WORKDIR}" -name "*_nonfree*" -delete || die
-	fi
-
-	if use test; then
-		mkdir -p "${BUILD_DIR}"/third_party/src/ || die
-		mv "${WORKDIR}"/gtest-"${GTEST_PV}" "${BUILD_DIR}"/third_party/src/googletest || die
-	fi
-}
-
-src_configure() {
-	if use cuda; then
-		addwrite /dev/nvidiactl
-		addwrite /dev/nvidia0
-		addwrite /dev/nvidia-uvm
-	fi
-
-	local mycmakeargs=(
-		-DBUILD_CPU="$(usex cpu)"
-		-DBUILD_CUDA="$(usex cuda)"
-		-DBUILD_OPENCL="$(usex opencl)"
-		-DBUILD_EXAMPLES="$(usex examples)"
-		-DBUILD_TEST="$(usex test)"
-		-DBUILD_GRAPHICS="$(usex graphics)"
-		-DBUILD_NONFREE="$(usex nonfree)"
-		-DBUILD_UNIFIED="$(usex unified)"
-		-DUSE_SYSTEM_BOOST_COMPUTE=ON
-		-DUSE_SYSTEM_CLBLAS=ON
-		-DUSE_SYSTEM_CLFFT=ON
-		-DUSE_SYSTEM_FORGE=ON
-		-DAF_INSTALL_CMAKE_DIR=/usr/$(get_libdir)/cmake/ArrayFire
-	)
-	cmake-utils_src_configure
-}
-
-src_install() {
-	cmake-utils_src_install
-
-	dobin "${BUILD_DIR}/bin2cpp"
-}
diff --git a/sci-libs/arrayfire/arrayfire-3.3.2.ebuild b/sci-libs/arrayfire/arrayfire-3.3.2.ebuild
deleted file mode 100644
index 900c7218f..000000000
--- a/sci-libs/arrayfire/arrayfire-3.3.2.ebuild
+++ /dev/null
@@ -1,112 +0,0 @@
-# Copyright 1999-2017 Gentoo Foundation
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=6
-
-inherit cmake-utils multilib
-
-GTEST_PV="1.7.0"
-
-DESCRIPTION="A general purpose GPU library"
-HOMEPAGE="http://www.arrayfire.com/"
-SRC_URI="
-	http://arrayfire.com/arrayfire_source/${PN}-full-${PV}.tar.bz2 -> ${P}.tar.bz2
-	test? ( https://github.com/google/googletest/archive/release-${GTEST_PV}.zip -> gtest-${GTEST_PV}.zip )"
-
-LICENSE="
-	BSD
-	nonfree? ( OpenSIFT )"
-SLOT="0"
-IUSE="+examples +cpu cuda nonfree opencl test unified graphics"
-KEYWORDS="~amd64"
-
-RDEPEND="
-	>=sys-devel/gcc-4.7:*
-	media-libs/freeimage
-	cuda? (
-		>=dev-util/nvidia-cuda-toolkit-7.5.18-r1
-		dev-libs/boost
-	)
-	cpu? (
-		virtual/blas
-		virtual/cblas
-		virtual/lapacke
-		sci-libs/fftw:3.0
-	)
-	opencl? (
-		virtual/blas
-		virtual/cblas
-		virtual/lapacke
-		>=sci-libs/clblas-2.4
-		>=sci-libs/clfft-2.6.1
-		dev-libs/boost
-		|| ( dev-libs/boost-compute >=dev-libs/boost-1.61.0 )
-	)
-	graphics? (
-		media-libs/glew:=
-		>=media-libs/glfw-3.1.1
-		~sci-visualization/forge-3.2.2
-	)"
-DEPEND="${RDEPEND}"
-
-S="${WORKDIR}/${PN}-full-${PV}"
-BUILD_DIR="${S}/build"
-CMAKE_BUILD_TYPE=Release
-
-PATCHES=("${FILESDIR}/${P}-FindLAPACKE.patch")
-
-# We need write acccess /dev/nvidiactl, /dev/nvidia0 and /dev/nvidia-uvm and the portage
-# user is (usually) not in the video group
-RESTRICT="userpriv"
-
-pkg_pretend() {
-	if [[ ${MERGE_TYPE} != binary ]]; then
-		if [[ $(gcc-major-version) -lt 4 ]] || ( [[ $(gcc-major-version) -eq 4 && $(gcc-minor-version) -lt 7 ]] ) ; then
-			die "Compilation with gcc older than 4.7 is not supported."
-		fi
-	fi
-}
-
-src_unpack() {
-	default
-
-	if ! use nonfree; then
-		find "${WORKDIR}" -name "*_nonfree*" -delete || die
-	fi
-
-	if use test; then
-		mkdir -p "${BUILD_DIR}"/third_party/src/ || die
-		mv "${WORKDIR}"/gtest-"${GTEST_PV}" "${BUILD_DIR}"/third_party/src/googletest || die
-	fi
-}
-
-src_configure() {
-	if use cuda; then
-		addwrite /dev/nvidiactl
-		addwrite /dev/nvidia0
-		addwrite /dev/nvidia-uvm
-	fi
-
-	local mycmakeargs=(
-		-DBUILD_CPU="$(usex cpu)"
-		-DBUILD_CUDA="$(usex cuda)"
-		-DBUILD_OPENCL="$(usex opencl)"
-		-DBUILD_EXAMPLES="$(usex examples)"
-		-DBUILD_TEST="$(usex test)"
-		-DBUILD_GRAPHICS="$(usex graphics)"
-		-DBUILD_NONFREE="$(usex nonfree)"
-		-DBUILD_UNIFIED="$(usex unified)"
-		-DUSE_SYSTEM_BOOST_COMPUTE=ON
-		-DUSE_SYSTEM_CLBLAS=ON
-		-DUSE_SYSTEM_CLFFT=ON
-		-DUSE_SYSTEM_FORGE=ON
-		-DAF_INSTALL_CMAKE_DIR=/usr/$(get_libdir)/cmake/ArrayFire
-	)
-	cmake-utils_src_configure
-}
-
-src_install() {
-	cmake-utils_src_install
-
-	dobin "${BUILD_DIR}/bin2cpp"
-}
diff --git a/sci-libs/arrayfire/arrayfire-3.4.2-r1.ebuild b/sci-libs/arrayfire/arrayfire-3.4.2-r1.ebuild
deleted file mode 100644
index 0a9ff57d4..000000000
--- a/sci-libs/arrayfire/arrayfire-3.4.2-r1.ebuild
+++ /dev/null
@@ -1,114 +0,0 @@
-# Copyright 1999-2017 Gentoo Foundation
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=6
-
-inherit cmake-utils multilib
-
-GTEST_PV="1.7.0"
-
-DESCRIPTION="A general purpose GPU library"
-HOMEPAGE="http://www.arrayfire.com/"
-SRC_URI="
-	http://arrayfire.com/arrayfire_source/${PN}-full-${PV}.tar.bz2 -> ${P}.tar.bz2
-	test? ( https://github.com/google/googletest/archive/release-${GTEST_PV}.zip -> gtest-${GTEST_PV}.zip )"
-
-LICENSE="
-	BSD
-	nonfree? ( OpenSIFT )"
-SLOT="0"
-IUSE="+examples +cpu cuda nonfree opencl test unified graphics"
-KEYWORDS="~amd64"
-
-RDEPEND="
-	>=sys-devel/gcc-4.7:*
-	media-libs/freeimage
-	cuda? (
-		>=dev-util/nvidia-cuda-toolkit-8.0.44
-		dev-libs/boost
-	)
-	cpu? (
-		virtual/blas
-		virtual/cblas
-		virtual/lapacke
-		sci-libs/fftw:3.0
-	)
-	opencl? (
-		virtual/blas
-		virtual/cblas
-		virtual/lapacke
-		>=sci-libs/clblas-2.4
-		>=sci-libs/clfft-2.6.1
-		>=dev-libs/boost-1.61.0
-		dev-libs/opencl-clhpp
-	)
-	graphics? (
-		media-libs/glbinding
-		>=media-libs/glfw-3.1.1
-		~sci-visualization/forge-0.9.2
-	)"
-DEPEND="${RDEPEND}"
-
-S="${WORKDIR}/${PN}-full-${PV}"
-BUILD_DIR="${S}/build"
-CMAKE_BUILD_TYPE=Release
-
-PATCHES=("${FILESDIR}/${P}-Build-fix-for-CUDA-Compile-PTX-generated-names.patch")
-
-# We need write acccess /dev/nvidiactl, /dev/nvidia0 and /dev/nvidia-uvm and the portage
-# user is (usually) not in the video group
-RESTRICT="userpriv"
-
-pkg_pretend() {
-	if [[ ${MERGE_TYPE} != binary ]]; then
-		if [[ $(gcc-major-version) -lt 4 ]] || ( [[ $(gcc-major-version) -eq 4 && $(gcc-minor-version) -lt 7 ]] ) ; then
-			die "Compilation with gcc older than 4.7 is not supported."
-		fi
-	fi
-}
-
-src_unpack() {
-	default
-
-	if ! use nonfree; then
-		find "${WORKDIR}" -name "*_nonfree*" -delete || die
-	fi
-
-	if use test; then
-		mkdir -p "${BUILD_DIR}"/third_party/src/ || die
-		mv "${WORKDIR}"/gtest-"${GTEST_PV}" "${BUILD_DIR}"/third_party/src/googletest || die
-	fi
-}
-
-src_configure() {
-	if use cuda; then
-		addwrite /dev/nvidiactl
-		addwrite /dev/nvidia0
-		addwrite /dev/nvidia-uvm
-	fi
-
-	local mycmakeargs=(
-		-DBUILD_CPU="$(usex cpu)"
-		-DBUILD_CUDA="$(usex cuda)"
-		-DBUILD_OPENCL="$(usex opencl)"
-		-DBUILD_EXAMPLES="$(usex examples)"
-		-DBUILD_TEST="$(usex test)"
-		-DBUILD_GRAPHICS="$(usex graphics)"
-		-DBUILD_NONFREE="$(usex nonfree)"
-		-DBUILD_UNIFIED="$(usex unified)"
-		-DUSE_SYSTEM_BOOST_COMPUTE=ON
-		-DUSE_SYSTEM_CL2HPP=ON
-		-DUSE_SYSTEM_CLBLAS=ON
-		-DUSE_SYSTEM_CLFFT=ON
-		-DUSE_SYSTEM_FORGE=ON
-		-DUSE_SYSTEM_GLBINDING=ON
-		-DAF_INSTALL_CMAKE_DIR=/usr/$(get_libdir)/cmake/ArrayFire
-	)
-	cmake-utils_src_configure
-}
-
-src_install() {
-	cmake-utils_src_install
-
-	dobin "${BUILD_DIR}/bin2cpp"
-}
diff --git a/sci-libs/arrayfire/arrayfire-3.7.2.ebuild b/sci-libs/arrayfire/arrayfire-3.7.2.ebuild
new file mode 100644
index 000000000..5d2f3c7a4
--- /dev/null
+++ b/sci-libs/arrayfire/arrayfire-3.7.2.ebuild
@@ -0,0 +1,96 @@
+# Copyright 1999-2021 Gentoo Authors
+# Distributed under the terms of the GNU General Public License v2
+
+EAPI=7
+
+inherit cmake
+
+DESCRIPTION="general purpose GPU library"
+HOMEPAGE="https://arrayfire.com/"
+SRC_URI="https://github.com/arrayfire/arrayfire/releases/download/v${PV}/${PN}-full-${PV}.tar.bz2 -> ${P}.tar.bz2"
+S="${WORKDIR}"/${PN}-full-${PV}
+BUILD_DIR="${S}/build"
+
+KEYWORDS="~amd64"
+
+LICENSE="BSD nonfree? ( OpenSIFT )"
+SLOT="0"
+IUSE="examples +cache cuda doc mkl nonfree opencl test +trace"
+RESTRICT="bindist mirror !test? ( test )"
+
+RDEPEND="
+	media-libs/freeimage
+	media-libs/glbinding
+	>=media-libs/glfw-3.1
+	~sci-visualization/forge-1.0.5
+	virtual/blas
+	virtual/cblas
+	virtual/lapacke
+	sci-libs/fftw:3.0
+	cuda? (
+		dev-libs/cudnn
+		>=dev-util/nvidia-cuda-toolkit-9.0.0
+		>=dev-libs/boost-1.70.0
+	)
+	mkl? (
+	     sci-libs/mkl
+	)
+	opencl? (
+		>=dev-libs/boost-1.70.0
+		>=sci-libs/clblas-2.4
+		>=sci-libs/clfft-2.6.1
+		virtual/opencl
+	)
+"
+DEPEND="${RDEPEND}"
+BDEPEND="
+	doc? ( app-text/doxygen )
+	virtual/pkgconfig
+"
+
+src_unpack() {
+	default
+
+	if ! use nonfree; then
+		find "${WORKDIR}" -name "*_nonfree*" -delete || die
+	fi
+}
+
+src_configure() {
+	if use cuda; then
+		addwrite /dev/nvidiactl
+		addwrite /dev/nvidia0
+		addwrite /dev/nvidia-uvm
+	fi
+
+	# forge headers are needed, so submodule
+	# has to stay, hence a ~ on forge dependency
+	local mycmakeargs=(
+		-DAF_BUILD_CPU=ON
+		-DAF_BUILD_CUDA="$(usex cuda)"
+		-DAF_BUILD_OPENCL="$(usex opencl)"
+		-DAF_BUILD_UNIFIED=ON
+		-DAF_BUILD_DOCS="$(usex doc)"
+		-DAF_BUILD_EXAMPLES="$(usex examples)"
+		-DAF_WITH_CUDNN="$(usex cuda)"
+		-DAF_BUILD_FORGE=OFF
+		-DAF_WITH_NONFREE="$(usex nonfree)"
+		-DAF_WITH_LOGGING=ON
+		-DAF_WITH_STACKTRACE="$(usex trace)"
+		-DAF_CACHE_KERNELS_TO_DISK="$(usex cache)"
+		-DAF_WITH_STATIC_MKL="$(usex mkl)"
+		-DAF_INSTALL_STANDALONE=OFF
+		-DAF_WITH_STATIC_FREEIMAGE=OFF
+		-DAF_INSTALL_CMAKE_DIR=/usr/$(get_libdir)/cmake/ArrayFire
+	)
+	cmake_src_configure
+}
+
+src_install() {
+	cmake_src_install
+
+	dodoc -r "${ED}"/usr/LICENSES
+	rm -r "${ED}"/usr/LICENSES || die
+
+	dobin "${BUILD_DIR}"/bin2cpp
+}
diff --git a/sci-libs/arrayfire/arrayfire-3.7.3.ebuild b/sci-libs/arrayfire/arrayfire-3.7.3.ebuild
new file mode 100644
index 000000000..5d2f3c7a4
--- /dev/null
+++ b/sci-libs/arrayfire/arrayfire-3.7.3.ebuild
@@ -0,0 +1,96 @@
+# Copyright 1999-2021 Gentoo Authors
+# Distributed under the terms of the GNU General Public License v2
+
+EAPI=7
+
+inherit cmake
+
+DESCRIPTION="general purpose GPU library"
+HOMEPAGE="https://arrayfire.com/"
+SRC_URI="https://github.com/arrayfire/arrayfire/releases/download/v${PV}/${PN}-full-${PV}.tar.bz2 -> ${P}.tar.bz2"
+S="${WORKDIR}"/${PN}-full-${PV}
+BUILD_DIR="${S}/build"
+
+KEYWORDS="~amd64"
+
+LICENSE="BSD nonfree? ( OpenSIFT )"
+SLOT="0"
+IUSE="examples +cache cuda doc mkl nonfree opencl test +trace"
+RESTRICT="bindist mirror !test? ( test )"
+
+RDEPEND="
+	media-libs/freeimage
+	media-libs/glbinding
+	>=media-libs/glfw-3.1
+	~sci-visualization/forge-1.0.5
+	virtual/blas
+	virtual/cblas
+	virtual/lapacke
+	sci-libs/fftw:3.0
+	cuda? (
+		dev-libs/cudnn
+		>=dev-util/nvidia-cuda-toolkit-9.0.0
+		>=dev-libs/boost-1.70.0
+	)
+	mkl? (
+	     sci-libs/mkl
+	)
+	opencl? (
+		>=dev-libs/boost-1.70.0
+		>=sci-libs/clblas-2.4
+		>=sci-libs/clfft-2.6.1
+		virtual/opencl
+	)
+"
+DEPEND="${RDEPEND}"
+BDEPEND="
+	doc? ( app-text/doxygen )
+	virtual/pkgconfig
+"
+
+src_unpack() {
+	default
+
+	if ! use nonfree; then
+		find "${WORKDIR}" -name "*_nonfree*" -delete || die
+	fi
+}
+
+src_configure() {
+	if use cuda; then
+		addwrite /dev/nvidiactl
+		addwrite /dev/nvidia0
+		addwrite /dev/nvidia-uvm
+	fi
+
+	# forge headers are needed, so submodule
+	# has to stay, hence a ~ on forge dependency
+	local mycmakeargs=(
+		-DAF_BUILD_CPU=ON
+		-DAF_BUILD_CUDA="$(usex cuda)"
+		-DAF_BUILD_OPENCL="$(usex opencl)"
+		-DAF_BUILD_UNIFIED=ON
+		-DAF_BUILD_DOCS="$(usex doc)"
+		-DAF_BUILD_EXAMPLES="$(usex examples)"
+		-DAF_WITH_CUDNN="$(usex cuda)"
+		-DAF_BUILD_FORGE=OFF
+		-DAF_WITH_NONFREE="$(usex nonfree)"
+		-DAF_WITH_LOGGING=ON
+		-DAF_WITH_STACKTRACE="$(usex trace)"
+		-DAF_CACHE_KERNELS_TO_DISK="$(usex cache)"
+		-DAF_WITH_STATIC_MKL="$(usex mkl)"
+		-DAF_INSTALL_STANDALONE=OFF
+		-DAF_WITH_STATIC_FREEIMAGE=OFF
+		-DAF_INSTALL_CMAKE_DIR=/usr/$(get_libdir)/cmake/ArrayFire
+	)
+	cmake_src_configure
+}
+
+src_install() {
+	cmake_src_install
+
+	dodoc -r "${ED}"/usr/LICENSES
+	rm -r "${ED}"/usr/LICENSES || die
+
+	dobin "${BUILD_DIR}"/bin2cpp
+}
diff --git a/sci-libs/arrayfire/arrayfire-3.8.0.ebuild b/sci-libs/arrayfire/arrayfire-3.8.0.ebuild
new file mode 100644
index 000000000..5d2f3c7a4
--- /dev/null
+++ b/sci-libs/arrayfire/arrayfire-3.8.0.ebuild
@@ -0,0 +1,96 @@
+# Copyright 1999-2021 Gentoo Authors
+# Distributed under the terms of the GNU General Public License v2
+
+EAPI=7
+
+inherit cmake
+
+DESCRIPTION="general purpose GPU library"
+HOMEPAGE="https://arrayfire.com/"
+SRC_URI="https://github.com/arrayfire/arrayfire/releases/download/v${PV}/${PN}-full-${PV}.tar.bz2 -> ${P}.tar.bz2"
+S="${WORKDIR}"/${PN}-full-${PV}
+BUILD_DIR="${S}/build"
+
+KEYWORDS="~amd64"
+
+LICENSE="BSD nonfree? ( OpenSIFT )"
+SLOT="0"
+IUSE="examples +cache cuda doc mkl nonfree opencl test +trace"
+RESTRICT="bindist mirror !test? ( test )"
+
+RDEPEND="
+	media-libs/freeimage
+	media-libs/glbinding
+	>=media-libs/glfw-3.1
+	~sci-visualization/forge-1.0.5
+	virtual/blas
+	virtual/cblas
+	virtual/lapacke
+	sci-libs/fftw:3.0
+	cuda? (
+		dev-libs/cudnn
+		>=dev-util/nvidia-cuda-toolkit-9.0.0
+		>=dev-libs/boost-1.70.0
+	)
+	mkl? (
+	     sci-libs/mkl
+	)
+	opencl? (
+		>=dev-libs/boost-1.70.0
+		>=sci-libs/clblas-2.4
+		>=sci-libs/clfft-2.6.1
+		virtual/opencl
+	)
+"
+DEPEND="${RDEPEND}"
+BDEPEND="
+	doc? ( app-text/doxygen )
+	virtual/pkgconfig
+"
+
+src_unpack() {
+	default
+
+	if ! use nonfree; then
+		find "${WORKDIR}" -name "*_nonfree*" -delete || die
+	fi
+}
+
+src_configure() {
+	if use cuda; then
+		addwrite /dev/nvidiactl
+		addwrite /dev/nvidia0
+		addwrite /dev/nvidia-uvm
+	fi
+
+	# forge headers are needed, so submodule
+	# has to stay, hence a ~ on forge dependency
+	local mycmakeargs=(
+		-DAF_BUILD_CPU=ON
+		-DAF_BUILD_CUDA="$(usex cuda)"
+		-DAF_BUILD_OPENCL="$(usex opencl)"
+		-DAF_BUILD_UNIFIED=ON
+		-DAF_BUILD_DOCS="$(usex doc)"
+		-DAF_BUILD_EXAMPLES="$(usex examples)"
+		-DAF_WITH_CUDNN="$(usex cuda)"
+		-DAF_BUILD_FORGE=OFF
+		-DAF_WITH_NONFREE="$(usex nonfree)"
+		-DAF_WITH_LOGGING=ON
+		-DAF_WITH_STACKTRACE="$(usex trace)"
+		-DAF_CACHE_KERNELS_TO_DISK="$(usex cache)"
+		-DAF_WITH_STATIC_MKL="$(usex mkl)"
+		-DAF_INSTALL_STANDALONE=OFF
+		-DAF_WITH_STATIC_FREEIMAGE=OFF
+		-DAF_INSTALL_CMAKE_DIR=/usr/$(get_libdir)/cmake/ArrayFire
+	)
+	cmake_src_configure
+}
+
+src_install() {
+	cmake_src_install
+
+	dodoc -r "${ED}"/usr/LICENSES
+	rm -r "${ED}"/usr/LICENSES || die
+
+	dobin "${BUILD_DIR}"/bin2cpp
+}
diff --git a/sci-libs/arrayfire/arrayfire-9999.ebuild b/sci-libs/arrayfire/arrayfire-9999.ebuild
deleted file mode 100644
index 356bccb0c..000000000
--- a/sci-libs/arrayfire/arrayfire-9999.ebuild
+++ /dev/null
@@ -1,110 +0,0 @@
-# Copyright 1999-2017 Gentoo Foundation
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=6
-
-inherit cmake-utils git-r3 multilib
-
-GTEST_PV="1.7.0"
-
-DESCRIPTION="A general purpose GPU library"
-HOMEPAGE="http://www.arrayfire.com/"
-SRC_URI="test? ( https://github.com/google/googletest/archive/release-${GTEST_PV}.zip -> gtest-${GTEST_PV}.zip )"
-EGIT_REPO_URI="https://github.com/${PN}/${PN}.git git://github.com/${PN}/${PN}.git"
-
-LICENSE="
-	BSD
-	nonfree? ( OpenSIFT )"
-SLOT="0"
-IUSE="+examples +cpu cuda nonfree opencl test unified graphics"
-KEYWORDS=""
-
-RDEPEND="
-	>=sys-devel/gcc-4.7:*
-	media-libs/freeimage
-	cuda? (
-		>=dev-util/nvidia-cuda-toolkit-7.5.18-r1
-		dev-libs/boost
-	)
-	cpu? (
-		virtual/blas
-		virtual/cblas
-		virtual/lapacke
-		sci-libs/fftw:3.0
-	)
-	opencl? (
-		virtual/blas
-		virtual/cblas
-		virtual/lapacke
-		>=sci-libs/clblas-2.4
-		>=sci-libs/clfft-2.6.1
-		dev-libs/boost
-		|| ( dev-libs/boost-compute >=dev-libs/boost-1.61.0 )
-	)
-	graphics? (
-		media-libs/glew:=
-		>=media-libs/glfw-3.1.1
-		~sci-visualization/forge-3.2.2
-	)"
-DEPEND="${RDEPEND}"
-
-BUILD_DIR="${S}/build"
-CMAKE_BUILD_TYPE=Release
-
-# We need write acccess /dev/nvidiactl, /dev/nvidia0 and /dev/nvidia-uvm and the portage
-# user is (usually) not in the video group
-RESTRICT="userpriv"
-
-pkg_pretend() {
-	if [[ ${MERGE_TYPE} != binary ]]; then
-		if [[ $(gcc-major-version) -lt 4 ]] || ( [[ $(gcc-major-version) -eq 4 && $(gcc-minor-version) -lt 7 ]] ) ; then
-			die "Compilation with gcc older than 4.7 is not supported."
-		fi
-	fi
-}
-
-src_unpack() {
-	git-r3_src_unpack
-
-	if ! use nonfree; then
-		find "${WORKDIR}" -name "*_nonfree*" -delete || die
-	fi
-
-	if use test; then
-		mkdir -p "${BUILD_DIR}"/third_party/src/ || die
-		cd "${BUILD_DIR}"/third_party/src/ || die
-		unpack ${A}
-		mv "${BUILD_DIR}"/third_party/src/gtest-"${GTEST_PV}" "${BUILD_DIR}"/third_party/src/googletest || die
-	fi
-}
-
-src_configure() {
-	if use cuda; then
-		addwrite /dev/nvidiactl
-		addwrite /dev/nvidia0
-		addwrite /dev/nvidia-uvm
-	fi
-
-	local mycmakeargs=(
-		-DBUILD_CPU="$(usex cpu)"
-		-DBUILD_CUDA="$(usex cuda)"
-		-DBUILD_OPENCL="$(usex opencl)"
-		-DBUILD_EXAMPLES="$(usex examples)"
-		-DBUILD_TEST="$(usex test)"
-		-DBUILD_GRAPHICS="$(usex graphics)"
-		-DBUILD_NONFREE="$(usex nonfree)"
-		-DBUILD_UNIFIED="$(usex unified)"
-		-DUSE_SYSTEM_BOOST_COMPUTE=ON
-		-DUSE_SYSTEM_CLBLAS=ON
-		-DUSE_SYSTEM_CLFFT=ON
-		-DUSE_SYSTEM_FORGE=ON
-		-DAF_INSTALL_CMAKE_DIR=/usr/$(get_libdir)/cmake/ArrayFire
-	)
-	cmake-utils_src_configure
-}
-
-src_install() {
-	cmake-utils_src_install
-
-	dobin "${BUILD_DIR}/bin2cpp"
-}
diff --git a/sci-libs/arrayfire/files/arrayfire-3.3.2-FindLAPACKE.patch b/sci-libs/arrayfire/files/arrayfire-3.3.2-FindLAPACKE.patch
deleted file mode 100644
index ab9b2f5e9..000000000
--- a/sci-libs/arrayfire/files/arrayfire-3.3.2-FindLAPACKE.patch
+++ /dev/null
@@ -1,28 +0,0 @@
-https://github.com/arrayfire/arrayfire/issues/1419
-
-
-From 2691d99693d6185d4f322a7776b1ced0e76877d2 Mon Sep 17 00:00:00 2001
-From: Shehzan Mohammed <shehzan@arrayfire.com>
-Date: Wed, 18 May 2016 10:18:34 -0400
-Subject: [PATCH] BUGFIX Correctly handle lapacke found by package config
-
----
- CMakeModules/FindLAPACKE.cmake | 2 +-
- 1 file changed, 1 insertion(+), 1 deletion(-)
-
-diff --git a/CMakeModules/FindLAPACKE.cmake b/CMakeModules/FindLAPACKE.cmake
-index 5ecf7be..2ebd8dd 100644
---- a/CMakeModules/FindLAPACKE.cmake
-+++ b/CMakeModules/FindLAPACKE.cmake
-@@ -143,7 +143,7 @@ ELSE(PC_LAPACKE_FOUND)
-     ENDIF(LAPACKE_ROOT_DIR)
- ENDIF(PC_LAPACKE_FOUND)
- 
--IF(LAPACKE_LIB AND LAPACK_LIB)
-+IF(PC_LAPACKE_FOUND OR (LAPACKE_LIB AND LAPACK_LIB))
-     SET(LAPACK_LIBRARIES ${LAPACKE_LIB} ${LAPACK_LIB})
- ENDIF()
- IF(LAPACKE_INCLUDES)
--- 
-2.7.3
-
diff --git a/sci-libs/arrayfire/files/arrayfire-3.4.2-Build-fix-for-CUDA-Compile-PTX-generated-names.patch b/sci-libs/arrayfire/files/arrayfire-3.4.2-Build-fix-for-CUDA-Compile-PTX-generated-names.patch
deleted file mode 100644
index 3cc51b1b3..000000000
--- a/sci-libs/arrayfire/files/arrayfire-3.4.2-Build-fix-for-CUDA-Compile-PTX-generated-names.patch
+++ /dev/null
@@ -1,34 +0,0 @@
-From 13c484e10537b52bcd012e6850520659769cece6 Mon Sep 17 00:00:00 2001
-From: Shehzan Mohammed <shehzan@arrayfire.com>
-Date: Thu, 22 Dec 2016 18:10:54 -0500
-Subject: [PATCH] Build fix for CUDA Compile PTX generated names by CMake 3.7
-
----
- src/backend/cuda/CMakeLists.txt | 10 +++++++++-
- 1 file changed, 9 insertions(+), 1 deletion(-)
-
-diff --git a/src/backend/cuda/CMakeLists.txt b/src/backend/cuda/CMakeLists.txt
-index 9cfa8a5..2f2045d 100644
---- a/src/backend/cuda/CMakeLists.txt
-+++ b/src/backend/cuda/CMakeLists.txt
-@@ -315,8 +315,16 @@ foreach(ptx_src_file ${ptx_sources})
- 
-       get_filename_component(_name "${ptx_src_file}" NAME_WE)
- 
-+      # CUDA_COMPILE_PTX from CMake 3.7 has new features that require this change
-+      # TODO Fix this with a more complete solution
-+      IF(CMAKE_VERSION VERSION_LESS 3.7) # Before 3.7
-+        SET(NAME_APPEND "")
-+      ELSE(CMAKE_VERSION VERSION_LESS 3.7)  # 3.7 and newer
-+        SET(NAME_APPEND "_1")
-+      ENDIF(CMAKE_VERSION VERSION_LESS 3.7)
-+
-       set(_gen_file_name
--        "${PROJECT_BINARY_DIR}/src/backend/cuda/cuda_compile_ptx_generated_${_name}.cu.ptx")
-+        "${PROJECT_BINARY_DIR}/src/backend/cuda/cuda_compile_ptx${NAME_APPEND}_generated_${_name}.cu.ptx")
-       set(_out_file_name
-         "${PROJECT_BINARY_DIR}/src/backend/cuda/${_name}.ptx")
- 
--- 
-2.10.2
-
diff --git a/sci-libs/arrayfire/metadata.xml b/sci-libs/arrayfire/metadata.xml
index 9048a1aeb..a45aaf1e4 100644
--- a/sci-libs/arrayfire/metadata.xml
+++ b/sci-libs/arrayfire/metadata.xml
@@ -2,39 +2,27 @@
 <!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
 <pkgmetadata>
 	<maintainer type="person">
-		<email>marbre@linux.sungazer.de</email>
-		<name>Marius Brehler</name>
+		<email>gentoo@aisha.cc</email>
+		<name>Aisha Tammy</name>
 	</maintainer>
 	<maintainer type="project">
 		<email>sci@gentoo.org</email>
 		<name>Gentoo Science Project</name>
 	</maintainer>
 	<longdescription>
-ArrayFire is a high performance software library for parallel
-computing with an easy-to-use API. Its array based function set
-makes parallel programming simple. ArrayFire's multiple backends
-(CUDA, OpenCL and native CPU) make it platform independent and
-highly portable.
-</longdescription>
+		ArrayFire is a high performance software library for parallel
+		computing with an easy-to-use API. Its array based function set
+		makes parallel programming simple. ArrayFire's multiple backends
+		(CUDA, OpenCL and native CPU) make it platform independent and
+		highly portable.
+	</longdescription>
 	<use>
-		<flag name="cpu">
-Build CPU backend.
-</flag>
-		<flag name="cuda">
-Build CUDA backend.
-</flag>
-		<flag name="opencl">
-Build OpenCL backend.
-</flag>
-		<flag name="nonfree">
-Build ArrayFire nonfree algorithms.
-</flag>
-		<flag name="graphics">
-Build with Forge graphics.
-</flag>
-		<flag name="unified">
-Build Backend-Independent API.
-</flag>
+		<flag name="cache">cache kernals to disk.</flag>
+		<flag name="cuda">Build CUDA backend.</flag>
+		<flag name="mkl">Build against static MKL.</flag>
+		<flag name="nonfree">build.</flag>
+		<flag name="opencl">build OpenCL backend.</flag>
+		<flag name="trace">enable additional traces during logging.</flag>
 	</use>
 	<upstream>
 		<remote-id type="github">google/googletest</remote-id>
diff --git a/sci-libs/asl/Manifest b/sci-libs/asl/Manifest
index 8cbb846f4..7da601468 100644
--- a/sci-libs/asl/Manifest
+++ b/sci-libs/asl/Manifest
@@ -1,2 +1 @@
-DIST asl-0.1.6.tar.gz 586423 BLAKE2B 16b272e32a3baa3311fe0cb6ec0ade8a8193fe082242733e470cbc2815413eb0f90081b1b7655e286b3868a8a80deb10744f36f760cbe1f95395dbb54cae7e92 SHA512 15b980a4e44eadcc751f5a8fff564ff28fdbdb45582f9632c6a9d4010439c4b19a00507f8f4ae97ac0b687aad00591cbd96520dd4690975e9daefef46ce6b33e
 DIST asl-0.1.7.tar.gz 588208 BLAKE2B a29259f2d7cc4851170840397e4aabfcac877f0c503ad94b5707e6b7cd7de7acd15b74b5f7f5852e65758d3edd5d59b39d3d7e3603f0fcccc64db9ff30dfe989 SHA512 337754adefa8619bbc2ab0e06fc811dd1cc550252b165241a265f87224aa84c5ee69fb3bf60324093df5b21aa87712e2210d4bcdd8593f0740183574528a30bd
diff --git a/sci-libs/asl/asl-0.1.6.ebuild b/sci-libs/asl/asl-0.1.6.ebuild
deleted file mode 100644
index 397f4b260..000000000
--- a/sci-libs/asl/asl-0.1.6.ebuild
+++ /dev/null
@@ -1,47 +0,0 @@
-# Copyright 1999-2016 Gentoo Foundation
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=5
-
-MY_PN=ASL
-
-if [[ ${PV} == "9999" ]] ; then
-	inherit git-r3
-	EGIT_REPO_URI="git://github.com/AvtechScientific/${MY_PN}.git"
-else
-	SRC_URI="https://github.com/AvtechScientific/${MY_PN}/archive/v${PV}.tar.gz -> ${P}.tar.gz"
-	KEYWORDS="~amd64 ~x86"
-	S="${WORKDIR}/${MY_PN}-${PV}"
-fi
-
-CMAKE_MIN_VERSION=3.0.2
-CMAKE_MAKEFILE_GENERATOR="${CMAKE_MAKEFILE_GENERATOR:-ninja}"
-
-inherit cmake-utils
-
-DESCRIPTION="Advanced Simulation Library - multiphysics simulation software package"
-HOMEPAGE="http://asl.org.il/"
-LICENSE="AGPL-3"
-SLOT="0"
-IUSE="doc examples matlab"
-
-RDEPEND="
-	>=dev-libs/boost-1.55:=
-	>=sci-libs/vtk-6.1
-	>=virtual/opencl-0-r2
-"
-DEPEND="${RDEPEND}
-	doc? ( app-doc/doxygen[dot] )
-	matlab? ( >=sci-libs/matio-1.5.2 )
-"
-
-src_configure() {
-	local mycmakeargs=(
-		-DCMAKE_INSTALL_DOCDIR=/usr/share/doc/${PF}
-		-DCMAKE_SKIP_RPATH=yes
-		$(cmake-utils_use_with doc API_DOC)
-		$(cmake-utils_use_with examples)
-		$(cmake-utils_use_with matlab)
-	)
-	cmake-utils_src_configure
-}
diff --git a/sci-libs/asl/asl-0.1.7.ebuild b/sci-libs/asl/asl-0.1.7.ebuild
index 062763511..cbfbde5c6 100644
--- a/sci-libs/asl/asl-0.1.7.ebuild
+++ b/sci-libs/asl/asl-0.1.7.ebuild
@@ -1,13 +1,12 @@
-# Copyright 1999-2016 Gentoo Foundation
+# Copyright 1999-2021 Gentoo Authors
 # Distributed under the terms of the GNU General Public License v2
 
-EAPI=6
+EAPI=7
 
 MY_PN=ASL
-CMAKE_MIN_VERSION=3.0.2
 CMAKE_MAKEFILE_GENERATOR="${CMAKE_MAKEFILE_GENERATOR:-ninja}"
 
-inherit cmake-utils
+inherit cmake
 
 DESCRIPTION="Hardware accelerated multiphysics simulation platform"
 HOMEPAGE="http://asl.org.il/"
@@ -15,21 +14,28 @@ SRC_URI="https://github.com/AvtechScientific/${MY_PN}/archive/v${PV}.tar.gz -> $
 
 LICENSE="AGPL-3"
 SLOT="0"
-IUSE="doc examples matlab"
 KEYWORDS="~amd64 ~x86"
 
+IUSE="doc examples matlab"
+
 RDEPEND="
 	>=dev-libs/boost-1.53:=
 	>=sci-libs/vtk-6.1
 	>=virtual/opencl-0-r2
 "
 DEPEND="${RDEPEND}
-	doc? ( app-doc/doxygen[dot] )
 	matlab? ( >=sci-libs/matio-1.5.2 )
 "
+BDEPEND="doc? ( app-text/doxygen[dot] )"
 
 S="${WORKDIR}/${MY_PN}-${PV}"
 
+src_prepare() {
+	cmake_src_prepare
+	# allow use of vtk 8.2
+	sed -i -e 's/find_package(VTK 7.0/find_package(VTK 8.2/g' CMakeLists.txt || die
+}
+
 src_configure() {
 	local mycmakeargs=(
 		-DCMAKE_INSTALL_DOCDIR=/usr/share/doc/${PF}
@@ -38,5 +44,5 @@ src_configure() {
 		-DWITH_EXAMPLES="$(usex examples)"
 		-DWITH_MATIO="$(usex matlab)"
 	)
-	cmake-utils_src_configure
+	cmake_src_configure
 }
diff --git a/sci-libs/asl/asl-9999.ebuild b/sci-libs/asl/asl-9999.ebuild
index 7f540d17a..905c8813a 100644
--- a/sci-libs/asl/asl-9999.ebuild
+++ b/sci-libs/asl/asl-9999.ebuild
@@ -1,23 +1,20 @@
-# Copyright 1999-2016 Gentoo Foundation
+# Copyright 1999-2021 Gentoo Authors
 # Distributed under the terms of the GNU General Public License v2
 
-EAPI=6
+EAPI=7
 
 MY_PN=ASL
-CMAKE_MIN_VERSION=3.0.2
 CMAKE_MAKEFILE_GENERATOR="${CMAKE_MAKEFILE_GENERATOR:-ninja}"
 
-inherit cmake-utils git-r3
+inherit cmake git-r3
 
 DESCRIPTION="Hardware accelerated multiphysics simulation platform"
 HOMEPAGE="http://asl.org.il/"
-SRC_URI=""
 EGIT_REPO_URI="git://github.com/AvtechScientific/${MY_PN}.git"
 
 LICENSE="AGPL-3"
 SLOT="0"
 IUSE="doc examples matlab"
-KEYWORDS=""
 
 RDEPEND="
 	>=dev-libs/boost-1.53:=
@@ -25,9 +22,15 @@ RDEPEND="
 	>=virtual/opencl-0-r2
 "
 DEPEND="${RDEPEND}
-	doc? ( app-doc/doxygen[dot] )
 	matlab? ( >=sci-libs/matio-1.5.2 )
 "
+BDEPEND="doc? ( app-text/doxygen[dot] )"
+
+src_prepare() {
+	cmake_src_prepare
+	# allow use of vtk 8.2
+	sed -i -e 's/find_package(VTK 7.0/find_package(VTK 8.2/g' CMakeLists.txt || die
+}
 
 src_configure() {
 	local mycmakeargs=(
@@ -37,5 +40,5 @@ src_configure() {
 		-DWITH_EXAMPLES="$(usex examples)"
 		-DWITH_MATIO="$(usex matlab)"
 	)
-	cmake-utils_src_configure
+	cmake_src_configure
 }
diff --git a/sci-libs/atlas/Manifest b/sci-libs/atlas/Manifest
deleted file mode 100644
index 3c284b351..000000000
--- a/sci-libs/atlas/Manifest
+++ /dev/null
@@ -1,8 +0,0 @@
-DIST atlas3.10.1.tar.bz2 4900179 BLAKE2B cf84660064b2a6888de5fd2691c559cfed4ebfaff9fa1a8b7f17009a03e193e78dcc616152978fd518510bfe02f9ece4ed4436efd0d627c1bc3d24d25086618a SHA512 027c8eea79bc584a4586e198fd9cc0ef7fffda3983082c11c2cf618837a24ba25cb26a831f55c35ac9a425e1b4bd1f379c62d99ef0c4e060bc4b1de59f3cf5fc
-DIST atlas3.10.2.tar.bz2 4904923 BLAKE2B e2fb0d307907549644cb678c32c4befce7ce6809c348a11fa6084e17d696da8681b3388dd63d8bdee6040999d9ab38a75f1788b42640121a536eb5f13e6f8939 SHA512 9fe04cfa1f89449db047d1a4659a656964d13117c783cbbe43344eb32555736f037d9cd30c5ae1514c08ad5b8949a3982d7fe102d707ddb62288e76b2607fbb1
-DIST atlas3.10.3.tar.bz2 5156852 BLAKE2B cd3880a6d0c43b5840d4da26ac996cc9fe7615fc996229193ef1f936daa2c54c5465643def19f59dd5c481c447176e2ba3cf85d38c0b5008c2dc1bc18be0e65b SHA512 bf17306f09f2aa973cb776e2c9eacfb2409ad4d95d19802e1c4e0597d0a099fccdb5eaafe273c2682a41e41a3c6fabc8bbba4ce03180cffea40ede5df1d1f56e
-DIST atlas3.11.38.tar.bz2 5399435 BLAKE2B ad8928ad58b8399b167bd26ba914efe5e4c99d49c78d69647fb1aea0c609159539da0f995c213b55a6f9f3628f729c91bf7db824992cc6727258edbdd1204be7 SHA512 4ca54b741228523d344bae86ef3ac8c7d54cbb610624d1db1403c59aa5cbcb4b2af509ea435204bf8f65d823349314013d8cc1494243723ce9fa89e9fc2802ce
-DIST atlas3.11.39.tar.bz2 5821852 BLAKE2B c1a511c9728af8ae7b4731493f8af6ab653cceb0f107e44f79fa6a676b8e47ef076739711dc40a496157aca2c4116db00663382745082a116b2a8493cb824d46 SHA512 bdb64e2a0a7ce4142182a5e6cdb52d44f6e99963392b5daa4b0ea1659c8b6fff93b61119ce83386c4e81b1cd63009df334aa95971a7b0a5c6eb27537a05855e9
-DIST lapack-3.5.0.tgz 6313139 BLAKE2B c23a35f107cfc5c887491fd148c1c76851a4580c98ad86aff9c391ac3d393c31ba67427ed445fe821c7666418e9fcf19523a3a668f8009337508994cf1a68c04 SHA512 b948a0a0db032bda455ec4f519d4e89e4c29e29cecb5b6258ca61f68faaeeac9fdf4ece5c39ffcd0154c5505facbc392c7d09c8348b1d60bdd2685153ab2543f
-DIST lapack-3.6.0.tgz 6792324 BLAKE2B 438f3376b63b38ef0fe70f6becac847816f3a11c01f5ab237dc0d941792ceb54dbd2f8dc22d56286f5dab3499289ed94e67521ea951a98973c9640abc294ad6c SHA512 bc50441d415ef8896dd7626d77c6104184b996e758704366288089f03d4c99d068e33153b0d13305310886017e5d2e716130f812a95cfcad36ef37fe20417ab8
-DIST lapack-3.7.0.tgz 7359812 BLAKE2B 20aa42e22d8c920d1360afe41ceec7b36f6cd5fbe43ca9d7848ef7cc45a64a0314cb1321941c1a7c03654f41e28ec805445882ded0ca0ea07674e70b66cba6b5 SHA512 e4f4c7d0ba8a096eeb813160c6dbcdd535647df6b2ad5beac9181908158956b31d1a9554ec9b9836fd44fe7404c1f377b297cbb20d744f20d70e357fd246c91b
diff --git a/sci-libs/atlas/atlas-3.10.1-r2.ebuild b/sci-libs/atlas/atlas-3.10.1-r2.ebuild
deleted file mode 100644
index 7a4a1d6e4..000000000
--- a/sci-libs/atlas/atlas-3.10.1-r2.ebuild
+++ /dev/null
@@ -1,270 +0,0 @@
-# Copyright 1999-2015 Gentoo Foundation
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=5
-
-FORTRAN_NEEDED=fortran
-
-inherit alternatives-2 eutils fortran-2 multilib toolchain-funcs versionator
-
-LAPACKP=lapack-3.5.0.tgz
-
-DESCRIPTION="Automatically Tuned Linear Algebra Software"
-HOMEPAGE="http://math-atlas.sourceforge.net/"
-SRC_URI="mirror://sourceforge/math-atlas/${PN}${PV}.tar.bz2
-	fortran? ( lapack? ( http://www.netlib.org/lapack/${LAPACKP} ) )"
-
-LICENSE="BSD"
-SLOT="0"
-KEYWORDS="~amd64 ~x86 ~amd64-linux ~x86-linux"
-IUSE="doc fortran generic lapack static-libs threads"
-
-RDEPEND=""
-DEPEND="${RDEPEND}"
-
-S="${WORKDIR}/ATLAS"
-
-pkg_setup() {
-	local _cpufreq
-	for _cpufreq in /sys/devices/system/cpu/cpu*/cpufreq/scaling_governor; do
-		if [ -f ${_cpufreq} ]; then
-			if ! grep -q performance ${_cpufreq}; then
-				echo 2> /dev/null performance > ${_cpufreq} || \
-					die "${PN} needs all cpu set to performance"
-			fi
-		fi
-	done
-	use fortran && fortran-2_pkg_setup
-}
-
-src_prepare() {
-	epatch "${FILESDIR}"/${PN}-3.10.0-x32-support.patch
-}
-
-src_configure() {
-	# hack needed to trick the flaky gcc detection
-	local mycc="$(type -P $(tc-getCC))"
-	[[ ${mycc} == *gcc* ]] && mycc=gcc
-	atlas_configure() {
-		local myconf=(
-			--prefix="${ED}/usr"
-			--libdir="${ED}/usr/$(get_libdir)"
-			--incdir="${ED}/usr/include"
-			--cc="$(tc-getCC)"
-			"-D c -DWALL"
-			"-C acg '${mycc}'"
-			"-F acg '${CFLAGS}'"
-			"-Ss pmake '\$(MAKE) ${MAKEOPTS}'"
-		)
-
-		# OpenMP shown to decreased performance over POSIX threads
-		# (at least in 3.9.x, see atlas-dev mailing list)
-		if use threads; then
-			if use generic; then # 2 threads is most generic
-				myconf+=( "-t 2" "-Si omp 0" )
-			else
-				myconf+=( "-t -1" "-Si omp 0" )
-			fi
-		else
-			myconf+=( "-t  0" "-Si omp 0" )
-		fi
-
-		if use amd64 || use ppc64 || use sparc; then
-			if [ ${ABI} = amd64 ] || [ ${ABI} = ppc64 ] || [ ${ABI} = sparc64 ] ; then
-				myconf+=( "-b 64" )
-			elif [ ${ABI} = x86 ] || [ ${ABI} = ppc ] || [ ${ABI} = sparc32 ] ; then
-				myconf+=( "-b 32" )
-			elif [ ${ABI} = x32 ] ; then
-				myconf+=( "-b 48" )
-			else
-				myconf+=( "-b 64" )
-			fi
-		elif use ppc || use x86; then
-			myconf+=( "-b 32" )
-		elif use ia64; then
-			myconf+=( "-b 64" )
-		fi
-		if use fortran; then
-			myconf+=(
-				"-C if '$(type -P $(tc-getFC))'"
-				"-F if '${FFLAGS}'"
-			)
-			if use lapack; then
-				myconf+=(
-					"-Si latune 1"
-					"--with-netlib-lapack-tarfile=${DISTDIR}/${LAPACKP}"
-				)
-			else
-				myconf+=( "-Si latune 0" )
-			fi
-		else
-			myconf+=( "-Si latune 0" "--nof77" )
-		fi
-		# generic stuff found by make make xprint_enums in atlas build dir
-		# basically assuming sse2+sse1 and 2 threads max
-		use generic && use x86   && myconf+=( "-V 384 -A 13")
-		use generic && use amd64 && myconf+=( "-V 384 -A 24")
-
-		local confdir="${S}_${1}"; shift
-		myconf+=( $@ )
-		mkdir "${confdir}" && cd "${confdir}"
-		# for debugging
-		echo ${myconf[@]} > myconf.out
-		"${S}"/configure ${myconf[@]} || die "configure in ${confdir} failed"
-	}
-
-	atlas_configure shared "-Fa alg -fPIC" ${EXTRA_ECONF}
-	use static-libs && atlas_configure static ${EXTRA_ECONF}
-}
-
-src_compile() {
-	atlas_compile() {
-		pushd "${S}_${1}" > /dev/null
-		# atlas does its own parallel builds
-		emake -j1 build
-		cd lib
-		emake libclapack.a
-		[[ -e libptcblas.a ]] && emake libptclapack.a
-		popd > /dev/null
-	}
-
-	atlas_compile shared
-	use static-libs && atlas_compile static
-}
-
-src_test() {
-	cd "${S}_shared"
-	emake -j1 check time
-}
-
-# transform a static archive into a shared library and install them
-# atlas_install_libs <mylib.a> [extra link flags]
-atlas_install_libs() {
-	local libname=$(basename ${1%.*})
-	einfo "Installing ${libname}"
-	local soname=${libname}.so.$(get_major_version)
-	shift
-	pushd "${S}_shared"/lib > /dev/null
-	${LINK:-$(tc-getCC)} ${LDFLAGS} -shared -Wl,-soname=${soname} \
-		-Wl,--whole-archive ${libname}.a -Wl,--no-whole-archive \
-		"$@" -o ${soname} || die "Creating ${soname} failed"
-	dolib.so ${soname}
-	ln -s ${soname} ${soname%.*}
-	dosym ${soname} /usr/$(get_libdir)/${soname%.*}
-	popd > /dev/null
-	use static-libs && dolib.a "${S}_static"/lib/${libname}.a
-}
-
-# create and install a pkgconfig file
-# atlas_install_pc <libname> <pkg name> [extra link flags]
-atlas_install_pc() {
-	local libname=${1} ; shift
-	local pcname=${1} ; shift
-	cat <<-EOF > ${pcname}.pc
-		prefix=${EPREFIX}/usr
-		libdir=\${prefix}/$(get_libdir)
-		includedir=\${prefix}/include
-		Name: ${pcname}
-		Description: ${PN} ${pcname}
-		Version: ${PV}
-		URL: ${HOMEPAGE}
-		Libs: -L\${libdir} -l${libname} $@
-		Libs.private: -L\${libdir} -latlas -lm ${PTLIBS}
-		Cflags: -I\${includedir}/${PN}
-		${PCREQ}
-	EOF
-	insinto /usr/$(get_libdir)/pkgconfig
-	doins ${pcname}.pc
-}
-
-src_install() {
-	cd "${S}_shared/lib"
-	# rename to avoid collision with other packages
-	local l
-	for l in {,c}{blas,lapack}; do
-		if [[ -e lib${l}.a ]]; then
-			mv lib{,atl}${l}.a
-			use static-libs && mv "${S}"_static/lib/lib{,atl}${l}.a
-		fi
-	done
-
-	[[ -e libptcblas.a ]] && PTLIBS="-lpthread"
-
-	# atlas
-	atlas_install_libs libatlas.a -lm ${PTLIBS}
-
-	# cblas
-	atlas_install_libs libatlcblas.a -lm -L. -latlas
-	atlas_install_pc atlcblas atlas-cblas
-	alternatives_for cblas atlas 0 \
-		/usr/$(get_libdir)/pkgconfig/cblas.pc atlas-cblas.pc \
-		/usr/include/cblas.h atlas/cblas.h
-
-	# cblas threaded
-	if [[ -e libptcblas.a ]]; then
-		atlas_install_libs libptcblas.a -lm -L. -latlas ${PTLIBS}
-		atlas_install_pc ptcblas atlas-cblas-threads
-		alternatives_for cblas atlas-threads 0 \
-			/usr/$(get_libdir)/pkgconfig/cblas.pc atlas-cblas-threads.pc \
-			/usr/include/cblas.h atlas/cblas.h
-	fi
-
-	if use lapack; then
-		PCREQ="Requires: cblas"
-		# clapack
-		atlas_install_libs libatlclapack.a -lm -L. -latlas -latlcblas
-		atlas_install_pc atlclapack atlas-clapack
-
-		# clapack threaded
-		if [[ -e libptclapack.a ]]; then
-			atlas_install_libs libptclapack.a -lm -L. -latlas -lptcblas ${PTLIBS}
-			atlas_install_pc ptclapack atlas-clapack-threads
-		fi
-	fi
-
-	if use fortran; then
-		LINK=$(tc-getF77) PCREQ=
-
-		# blas
-		atlas_install_libs libf77blas.a -lm -L. -latlas
-		atlas_install_pc f77blas atlas-blas
-		alternatives_for blas atlas 0 \
-			/usr/$(get_libdir)/pkgconfig/blas.pc atlas-blas.pc
-
-		# blas threaded
-		if [[ -e libptf77blas.a ]]; then
-			atlas_install_libs libptf77blas.a -lm -L. -latlas ${PTLIBS}
-			atlas_install_pc ptf77blas atlas-blas-threads
-			alternatives_for blas atlas-threads 0 \
-				/usr/$(get_libdir)/pkgconfig/blas.pc atlas-blas-threads.pc
-		fi
-
-		if use lapack; then
-			PCREQ="Requires: blas cblas"
-			# lapack
-			atlas_install_libs libatllapack.a \
-				-lm -L. -latlas -latlcblas -lf77blas
-			atlas_install_pc atllapack atlas-lapack
-			alternatives_for lapack atlas 0 \
-				/usr/$(get_libdir)/pkgconfig/lapack.pc atlas-lapack.pc
-			# lapack threaded
-			if [[ -e libptlapack.a ]]; then
-				atlas_install_libs libptlapack.a \
-					-lm -L. -latlas -lptcblas -lptf77blas ${PTLIBS}
-				atlas_install_pc ptlapack atlas-lapack-threads
-				alternatives_for lapack atlas-threads 0 \
-					/usr/$(get_libdir)/pkgconfig/lapack.pc atlas-lapack-threads.pc
-			fi
-		fi
-	fi
-
-	cd "${S}"
-	insinto /usr/include/${PN}
-	doins include/*.h
-
-	cd "${S}/doc"
-	dodoc INDEX.txt AtlasCredits.txt ChangeLog
-	use doc && dodoc atlas*pdf cblas.pdf cblasqref.pdf
-	use doc && use fortran && dodoc f77blas*pdf
-	use doc && use fortran && use lapack && dodoc *lapack*pdf
-}
diff --git a/sci-libs/atlas/atlas-3.10.2.ebuild b/sci-libs/atlas/atlas-3.10.2.ebuild
deleted file mode 100644
index 5e480dd3e..000000000
--- a/sci-libs/atlas/atlas-3.10.2.ebuild
+++ /dev/null
@@ -1,272 +0,0 @@
-# Copyright 1999-2015 Gentoo Foundation
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=5
-
-FORTRAN_NEEDED=fortran
-
-inherit alternatives-2 eutils fortran-2 multilib toolchain-funcs versionator
-
-LAPACKP=lapack-3.6.0.tgz
-
-DESCRIPTION="Automatically Tuned Linear Algebra Software"
-HOMEPAGE="http://math-atlas.sourceforge.net/"
-SRC_URI="mirror://sourceforge/math-atlas/${PN}${PV}.tar.bz2
-	fortran? ( lapack? ( http://www.netlib.org/lapack/${LAPACKP} ) )"
-
-LICENSE="BSD"
-SLOT="0"
-KEYWORDS="~amd64 ~x86 ~amd64-linux ~x86-linux"
-IUSE="doc fortran generic lapack static-libs threads"
-
-RDEPEND=""
-DEPEND="${RDEPEND}"
-
-S="${WORKDIR}/ATLAS"
-
-pkg_setup() {
-	local _cpufreq
-	for _cpufreq in /sys/devices/system/cpu/cpu*/cpufreq/scaling_governor; do
-		if [ -f ${_cpufreq} ]; then
-			if ! grep -q performance ${_cpufreq}; then
-				echo 2> /dev/null performance > ${_cpufreq} || \
-					die "${PN} needs all cpu set to performance"
-			fi
-		fi
-	done
-	use fortran && fortran-2_pkg_setup
-}
-
-src_prepare() {
-	epatch \
-		"${FILESDIR}"/${PN}-3.10.0-x32-support.patch \
-		"${FILESDIR}"/${P1}format-security.patch
-}
-
-src_configure() {
-	# hack needed to trick the flaky gcc detection
-	local mycc="$(type -P $(tc-getCC))"
-	[[ ${mycc} == *gcc* ]] && mycc=gcc
-	atlas_configure() {
-		local myconf=(
-			--prefix="${ED}/usr"
-			--libdir="${ED}/usr/$(get_libdir)"
-			--incdir="${ED}/usr/include"
-			--cc="$(tc-getCC)"
-			"-D c -DWALL"
-			"-C acg '${mycc}'"
-			"-F acg '${CFLAGS}'"
-			"-Ss pmake '\$(MAKE) ${MAKEOPTS}'"
-		)
-
-		# OpenMP shown to decreased performance over POSIX threads
-		# (at least in 3.9.x, see atlas-dev mailing list)
-		if use threads; then
-			if use generic; then # 2 threads is most generic
-				myconf+=( "-t 2" "-Si omp 0" )
-			else
-				myconf+=( "-t -1" "-Si omp 0" )
-			fi
-		else
-			myconf+=( "-t  0" "-Si omp 0" )
-		fi
-
-		if use amd64 || use ppc64 || use sparc; then
-			if [ ${ABI} = amd64 ] || [ ${ABI} = ppc64 ] || [ ${ABI} = sparc64 ] ; then
-				myconf+=( "-b 64" )
-			elif [ ${ABI} = x86 ] || [ ${ABI} = ppc ] || [ ${ABI} = sparc32 ] ; then
-				myconf+=( "-b 32" )
-			elif [ ${ABI} = x32 ] ; then
-				myconf+=( "-b 48" )
-			else
-				myconf+=( "-b 64" )
-			fi
-		elif use ppc || use x86; then
-			myconf+=( "-b 32" )
-		elif use ia64; then
-			myconf+=( "-b 64" )
-		fi
-		if use fortran; then
-			myconf+=(
-				"-C if '$(type -P $(tc-getFC))'"
-				"-F if '${FFLAGS}'"
-			)
-			if use lapack; then
-				myconf+=(
-					"-Si latune 1"
-					"--with-netlib-lapack-tarfile=${DISTDIR}/${LAPACKP}"
-				)
-			else
-				myconf+=( "-Si latune 0" )
-			fi
-		else
-			myconf+=( "-Si latune 0" "--nof77" )
-		fi
-		# generic stuff found by make make xprint_enums in atlas build dir
-		# basically assuming sse2+sse1 and 2 threads max
-		use generic && use x86   && myconf+=( "-V 384 -A 13")
-		use generic && use amd64 && myconf+=( "-V 384 -A 24")
-
-		local confdir="${S}_${1}"; shift
-		myconf+=( $@ )
-		mkdir "${confdir}" && cd "${confdir}"
-		# for debugging
-		echo ${myconf[@]} > myconf.out
-		"${S}"/configure ${myconf[@]} || die "configure in ${confdir} failed"
-	}
-
-	atlas_configure shared "-Fa alg -fPIC" ${EXTRA_ECONF}
-	use static-libs && atlas_configure static ${EXTRA_ECONF}
-}
-
-src_compile() {
-	atlas_compile() {
-		pushd "${S}_${1}" > /dev/null
-		# atlas does its own parallel builds
-		emake -j1 build
-		cd lib
-		emake libclapack.a
-		[[ -e libptcblas.a ]] && emake libptclapack.a
-		popd > /dev/null
-	}
-
-	atlas_compile shared
-	use static-libs && atlas_compile static
-}
-
-src_test() {
-	cd "${S}_shared"
-	emake -j1 check time
-}
-
-# transform a static archive into a shared library and install them
-# atlas_install_libs <mylib.a> [extra link flags]
-atlas_install_libs() {
-	local libname=$(basename ${1%.*})
-	einfo "Installing ${libname}"
-	local soname=${libname}.so.$(get_major_version)
-	shift
-	pushd "${S}_shared"/lib > /dev/null
-	${LINK:-$(tc-getCC)} ${LDFLAGS} -shared -Wl,-soname=${soname} \
-		-Wl,--whole-archive ${libname}.a -Wl,--no-whole-archive \
-		"$@" -o ${soname} || die "Creating ${soname} failed"
-	dolib.so ${soname}
-	ln -s ${soname} ${soname%.*}
-	dosym ${soname} /usr/$(get_libdir)/${soname%.*}
-	popd > /dev/null
-	use static-libs && dolib.a "${S}_static"/lib/${libname}.a
-}
-
-# create and install a pkgconfig file
-# atlas_install_pc <libname> <pkg name> [extra link flags]
-atlas_install_pc() {
-	local libname=${1} ; shift
-	local pcname=${1} ; shift
-	cat <<-EOF > ${pcname}.pc
-		prefix=${EPREFIX}/usr
-		libdir=\${prefix}/$(get_libdir)
-		includedir=\${prefix}/include
-		Name: ${pcname}
-		Description: ${PN} ${pcname}
-		Version: ${PV}
-		URL: ${HOMEPAGE}
-		Libs: -L\${libdir} -l${libname} $@
-		Libs.private: -L\${libdir} -latlas -lm ${PTLIBS}
-		Cflags: -I\${includedir}/${PN}
-		${PCREQ}
-	EOF
-	insinto /usr/$(get_libdir)/pkgconfig
-	doins ${pcname}.pc
-}
-
-src_install() {
-	cd "${S}_shared/lib"
-	# rename to avoid collision with other packages
-	local l
-	for l in {,c}{blas,lapack}; do
-		if [[ -e lib${l}.a ]]; then
-			mv lib{,atl}${l}.a
-			use static-libs && mv "${S}"_static/lib/lib{,atl}${l}.a
-		fi
-	done
-
-	[[ -e libptcblas.a ]] && PTLIBS="-lpthread"
-
-	# atlas
-	atlas_install_libs libatlas.a -lm ${PTLIBS}
-
-	# cblas
-	atlas_install_libs libatlcblas.a -lm -L. -latlas
-	atlas_install_pc atlcblas atlas-cblas
-	alternatives_for cblas atlas 0 \
-		/usr/$(get_libdir)/pkgconfig/cblas.pc atlas-cblas.pc \
-		/usr/include/cblas.h atlas/cblas.h
-
-	# cblas threaded
-	if [[ -e libptcblas.a ]]; then
-		atlas_install_libs libptcblas.a -lm -L. -latlas ${PTLIBS}
-		atlas_install_pc ptcblas atlas-cblas-threads
-		alternatives_for cblas atlas-threads 0 \
-			/usr/$(get_libdir)/pkgconfig/cblas.pc atlas-cblas-threads.pc \
-			/usr/include/cblas.h atlas/cblas.h
-	fi
-
-	if use lapack; then
-		PCREQ="Requires: cblas"
-		# clapack
-		atlas_install_libs libatlclapack.a -lm -L. -latlas -latlcblas
-		atlas_install_pc atlclapack atlas-clapack
-
-		# clapack threaded
-		if [[ -e libptclapack.a ]]; then
-			atlas_install_libs libptclapack.a -lm -L. -latlas -lptcblas ${PTLIBS}
-			atlas_install_pc ptclapack atlas-clapack-threads
-		fi
-	fi
-
-	if use fortran; then
-		LINK=$(tc-getF77) PCREQ=
-
-		# blas
-		atlas_install_libs libf77blas.a -lm -L. -latlas
-		atlas_install_pc f77blas atlas-blas
-		alternatives_for blas atlas 0 \
-			/usr/$(get_libdir)/pkgconfig/blas.pc atlas-blas.pc
-
-		# blas threaded
-		if [[ -e libptf77blas.a ]]; then
-			atlas_install_libs libptf77blas.a -lm -L. -latlas ${PTLIBS}
-			atlas_install_pc ptf77blas atlas-blas-threads
-			alternatives_for blas atlas-threads 0 \
-				/usr/$(get_libdir)/pkgconfig/blas.pc atlas-blas-threads.pc
-		fi
-
-		if use lapack; then
-			PCREQ="Requires: blas cblas"
-			# lapack
-			atlas_install_libs libatllapack.a \
-				-lm -L. -latlas -latlcblas -lf77blas
-			atlas_install_pc atllapack atlas-lapack
-			alternatives_for lapack atlas 0 \
-				/usr/$(get_libdir)/pkgconfig/lapack.pc atlas-lapack.pc
-			# lapack threaded
-			if [[ -e libptlapack.a ]]; then
-				atlas_install_libs libptlapack.a \
-					-lm -L. -latlas -lptcblas -lptf77blas ${PTLIBS}
-				atlas_install_pc ptlapack atlas-lapack-threads
-				alternatives_for lapack atlas-threads 0 \
-					/usr/$(get_libdir)/pkgconfig/lapack.pc atlas-lapack-threads.pc
-			fi
-		fi
-	fi
-
-	cd "${S}"
-	insinto /usr/include/${PN}
-	doins include/*.h
-
-	cd "${S}/doc"
-	dodoc INDEX.txt AtlasCredits.txt ChangeLog
-	use doc && dodoc atlas*pdf cblas.pdf cblasqref.pdf
-	use doc && use fortran && dodoc f77blas*pdf
-	use doc && use fortran && use lapack && dodoc *lapack*pdf
-}
diff --git a/sci-libs/atlas/atlas-3.10.3.ebuild b/sci-libs/atlas/atlas-3.10.3.ebuild
deleted file mode 100644
index 131790147..000000000
--- a/sci-libs/atlas/atlas-3.10.3.ebuild
+++ /dev/null
@@ -1,279 +0,0 @@
-# Copyright 1999-2017 Gentoo Foundation
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=5
-
-FORTRAN_NEEDED=fortran
-
-inherit alternatives-2 eutils fortran-2 multilib toolchain-funcs versionator
-
-LAPACKP=lapack-3.6.0.tgz
-
-DESCRIPTION="Automatically Tuned Linear Algebra Software"
-HOMEPAGE="http://math-atlas.sourceforge.net/"
-SRC_URI="mirror://sourceforge/math-atlas/${PN}${PV}.tar.bz2
-	fortran? ( lapack? ( http://www.netlib.org/lapack/${LAPACKP} ) )"
-
-LICENSE="BSD"
-SLOT="0"
-KEYWORDS="~amd64 ~x86 ~amd64-linux ~x86-linux"
-IUSE="+deprecated doc +fortran generic +lapack static-libs threads"
-
-REQUIRED_USE="
-	deprecated? ( lapack )
-	lapack? ( fortran )"
-
-S="${WORKDIR}/ATLAS"
-
-pkg_setup() {
-	local _cpufreq
-	for _cpufreq in /sys/devices/system/cpu/cpu*/cpufreq/scaling_governor; do
-		if [ -f ${_cpufreq} ]; then
-			if ! grep -q performance ${_cpufreq}; then
-				echo 2> /dev/null performance > ${_cpufreq} || \
-					die "${PN} needs all cpu set to performance"
-			fi
-		fi
-	done
-	use fortran && fortran-2_pkg_setup
-}
-
-src_prepare() {
-	epatch \
-		"${FILESDIR}"/${PN}-3.10.0-x32-support.patch \
-		"${FILESDIR}"/${P1}format-security.patch
-}
-
-src_configure() {
-	# hack needed to trick the flaky gcc detection
-	local mycc="$(type -P $(tc-getCC))"
-	[[ ${mycc} == *gcc* ]] && mycc=gcc
-	atlas_configure() {
-		local myconf=(
-			--prefix="${ED}/usr"
-			--libdir="${ED}/usr/$(get_libdir)"
-			--incdir="${ED}/usr/include"
-			--cc="$(tc-getCC)"
-			"-D c -DWALL"
-			"-C acg '${mycc}'"
-			"-F acg '${CFLAGS}'"
-			"-Ss pmake '\$(MAKE) ${MAKEOPTS}'"
-		)
-
-		# OpenMP shown to decreased performance over POSIX threads
-		# (at least in 3.9.x, see atlas-dev mailing list)
-		if use threads; then
-			if use generic; then # 2 threads is most generic
-				myconf+=( "-t 2" "-Si omp 0" )
-			else
-				myconf+=( "-t -1" "-Si omp 0" )
-			fi
-		else
-			myconf+=( "-t  0" "-Si omp 0" )
-		fi
-
-		if use amd64 || use ppc64 || use sparc; then
-			if [ ${ABI} = amd64 ] || [ ${ABI} = ppc64 ] || [ ${ABI} = sparc64 ] ; then
-				myconf+=( "-b 64" )
-			elif [ ${ABI} = x86 ] || [ ${ABI} = ppc ] || [ ${ABI} = sparc32 ] ; then
-				myconf+=( "-b 32" )
-			elif [ ${ABI} = x32 ] ; then
-				myconf+=( "-b 48" )
-			else
-				myconf+=( "-b 64" )
-			fi
-		elif use ppc || use x86; then
-			myconf+=( "-b 32" )
-		elif use ia64; then
-			myconf+=( "-b 64" )
-		fi
-		if use fortran; then
-			myconf+=(
-				"-C if '$(type -P $(tc-getFC))'"
-				"-F if '${FFLAGS}'"
-			)
-			if use lapack; then
-				myconf+=(
-					"-Si latune 1"
-					"--with-netlib-lapack-tarfile=${DISTDIR}/${LAPACKP}"
-				)
-			else
-				myconf+=( "-Si latune 0" )
-			fi
-		else
-			myconf+=( "-Si latune 0" "--nof77" )
-		fi
-		# generic stuff found by make make xprint_enums in atlas build dir
-		# basically assuming sse2+sse1 and 2 threads max
-		use generic && use x86   && myconf+=( "-V 384 -A 13")
-		use generic && use amd64 && myconf+=( "-V 384 -A 24")
-
-		local confdir="${S}_${1}"; shift
-		myconf+=( $@ )
-		mkdir "${confdir}" && cd "${confdir}" || die
-		# for debugging
-		echo ${myconf[@]} > myconf.out
-		"${S}"/configure ${myconf[@]} || die "configure in ${confdir} failed"
-
-		if use deprecated; then
-			echo "BUILD_DEPRECATED=1" >> src/lapack/reference/make.inc.example || die
-		fi
-	}
-
-	atlas_configure shared "-Fa alg -fPIC" ${EXTRA_ECONF}
-	use static-libs && atlas_configure static ${EXTRA_ECONF}
-}
-
-src_compile() {
-	atlas_compile() {
-		pushd "${S}_${1}" > /dev/null || die
-		# atlas does its own parallel builds
-		emake -j1 build
-		cd lib || die
-		emake libclapack.a
-		[[ -e libptcblas.a ]] && emake libptclapack.a
-		popd > /dev/null || die
-	}
-
-	atlas_compile shared
-	use static-libs && atlas_compile static
-}
-
-src_test() {
-	cd "${S}_shared" || die
-	emake -j1 check time
-}
-
-# transform a static archive into a shared library and install them
-# atlas_install_libs <mylib.a> [extra link flags]
-atlas_install_libs() {
-	local libname=$(basename ${1%.*})
-	einfo "Installing ${libname}"
-	local soname=${libname}.so.$(get_major_version)
-	shift
-	pushd "${S}_shared"/lib > /dev/null
-	${LINK:-$(tc-getCC)} ${LDFLAGS} -shared -Wl,-soname=${soname} \
-		-Wl,--whole-archive ${libname}.a -Wl,--no-whole-archive \
-		"$@" -o ${soname} || die "Creating ${soname} failed"
-	dolib.so ${soname}
-	ln -s ${soname} ${soname%.*}
-	dosym ${soname} /usr/$(get_libdir)/${soname%.*}
-	popd > /dev/null || die
-	use static-libs && dolib.a "${S}_static"/lib/${libname}.a
-}
-
-# create and install a pkgconfig file
-# atlas_install_pc <libname> <pkg name> [extra link flags]
-atlas_install_pc() {
-	local libname=${1} ; shift
-	local pcname=${1} ; shift
-	cat <<-EOF > ${pcname}.pc
-		prefix=${EPREFIX}/usr
-		libdir=\${prefix}/$(get_libdir)
-		includedir=\${prefix}/include
-		Name: ${pcname}
-		Description: ${PN} ${pcname}
-		Version: ${PV}
-		URL: ${HOMEPAGE}
-		Libs: -L\${libdir} -l${libname} $@
-		Libs.private: -L\${libdir} -latlas -lm ${PTLIBS}
-		Cflags: -I\${includedir}/${PN}
-		${PCREQ}
-	EOF
-	insinto /usr/$(get_libdir)/pkgconfig
-	doins ${pcname}.pc
-}
-
-src_install() {
-	cd "${S}_shared/lib" || die
-	# rename to avoid collision with other packages
-	local l
-	for l in {,c}{blas,lapack}; do
-		if [[ -e lib${l}.a ]]; then
-			mv lib{,atl}${l}.a || die
-			if use static-libs; then
-				mv "${S}"_static/lib/lib{,atl}${l}.a || die
-			fi
-		fi
-	done
-
-	[[ -e libptcblas.a ]] && PTLIBS="-lpthread"
-
-	# atlas
-	atlas_install_libs libatlas.a -lm ${PTLIBS}
-
-	# cblas
-	atlas_install_libs libatlcblas.a -lm -L. -latlas
-	atlas_install_pc atlcblas atlas-cblas
-	alternatives_for cblas atlas 0 \
-		/usr/$(get_libdir)/pkgconfig/cblas.pc atlas-cblas.pc \
-		/usr/include/cblas.h atlas/cblas.h
-
-	# cblas threaded
-	if [[ -e libptcblas.a ]]; then
-		atlas_install_libs libptcblas.a -lm -L. -latlas ${PTLIBS}
-		atlas_install_pc ptcblas atlas-cblas-threads
-		alternatives_for cblas atlas-threads 0 \
-			/usr/$(get_libdir)/pkgconfig/cblas.pc atlas-cblas-threads.pc \
-			/usr/include/cblas.h atlas/cblas.h
-	fi
-
-	if use lapack; then
-		PCREQ="Requires: cblas"
-		# clapack
-		atlas_install_libs libatlclapack.a -lm -L. -latlas -latlcblas
-		atlas_install_pc atlclapack atlas-clapack
-
-		# clapack threaded
-		if [[ -e libptclapack.a ]]; then
-			atlas_install_libs libptclapack.a -lm -L. -latlas -lptcblas ${PTLIBS}
-			atlas_install_pc ptclapack atlas-clapack-threads
-		fi
-	fi
-
-	if use fortran; then
-		LINK=$(tc-getF77) PCREQ=
-
-		# blas
-		atlas_install_libs libf77blas.a -lm -L. -latlas
-		atlas_install_pc f77blas atlas-blas
-		alternatives_for blas atlas 0 \
-			/usr/$(get_libdir)/pkgconfig/blas.pc atlas-blas.pc
-
-		# blas threaded
-		if [[ -e libptf77blas.a ]]; then
-			atlas_install_libs libptf77blas.a -lm -L. -latlas ${PTLIBS}
-			atlas_install_pc ptf77blas atlas-blas-threads
-			alternatives_for blas atlas-threads 0 \
-				/usr/$(get_libdir)/pkgconfig/blas.pc atlas-blas-threads.pc
-		fi
-
-		if use lapack; then
-			PCREQ="Requires: blas cblas"
-			# lapack
-			atlas_install_libs libatllapack.a \
-				-lm -L. -latlas -latlcblas -lf77blas
-			atlas_install_pc atllapack atlas-lapack
-			alternatives_for lapack atlas 0 \
-				/usr/$(get_libdir)/pkgconfig/lapack.pc atlas-lapack.pc
-			# lapack threaded
-			if [[ -e libptlapack.a ]]; then
-				atlas_install_libs libptlapack.a \
-					-lm -L. -latlas -lptcblas -lptf77blas ${PTLIBS}
-				atlas_install_pc ptlapack atlas-lapack-threads
-				alternatives_for lapack atlas-threads 0 \
-					/usr/$(get_libdir)/pkgconfig/lapack.pc atlas-lapack-threads.pc
-			fi
-		fi
-	fi
-
-	cd "${S}" || die
-	insinto /usr/include/${PN}
-	doins include/*.h
-
-	cd "${S}/doc" || die
-	dodoc INDEX.txt AtlasCredits.txt ChangeLog
-	use doc && dodoc atlas*pdf cblas.pdf cblasqref.pdf
-	use doc && use fortran && dodoc f77blas*pdf
-	use doc && use fortran && use lapack && dodoc *lapack*pdf
-}
diff --git a/sci-libs/atlas/atlas-3.11.38-r1.ebuild b/sci-libs/atlas/atlas-3.11.38-r1.ebuild
deleted file mode 100644
index 5db98d96b..000000000
--- a/sci-libs/atlas/atlas-3.11.38-r1.ebuild
+++ /dev/null
@@ -1,281 +0,0 @@
-# Copyright 1999-2017 Gentoo Foundation
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=5
-
-FORTRAN_NEEDED=fortran
-
-inherit alternatives-2 eutils fortran-2 linux-info multilib numeric toolchain-funcs versionator
-
-LAPACKP=lapack-3.6.0.tgz
-
-DESCRIPTION="Automatically Tuned Linear Algebra Software"
-HOMEPAGE="http://math-atlas.sourceforge.net/"
-SRC_URI="mirror://sourceforge/math-atlas/${PN}${PV}.tar.bz2
-	fortran? ( lapack? ( http://www.netlib.org/lapack/${LAPACKP} ) )"
-
-LICENSE="BSD"
-SLOT="0"
-KEYWORDS="~amd64 ~x86 ~amd64-linux ~x86-linux"
-IUSE="+deprecated doc +fortran generic ifko +lapack static-libs threads"
-
-REQUIRED_USE="
-	deprecated? ( lapack )
-	lapack? ( fortran )"
-
-S="${WORKDIR}/ATLAS"
-
-pkg_setup() {
-	local _cpufreq
-	for _cpufreq in /sys/devices/system/cpu/cpu*/cpufreq/scaling_governor; do
-		if [ -f ${_cpufreq} ]; then
-			if ! grep -q performance ${_cpufreq}; then
-				echo 2> /dev/null performance > ${_cpufreq} || \
-					die "${PN} needs all cpu set to performance"
-			fi
-		fi
-	done
-	[[ -e /sys/devices/system/cpu/intel_pstate ]] \
-		&& die "Intel P-State driver detected. Please reboot with 'intel_pstate=disable' in your cmdline"
-	use fortran && fortran-2_pkg_setup
-	CONFIG_CHECK="
-		!~X86_P4_CLOCKMOD
-		!~X86_INTEL_PSTATE
-	"
-	ERROR_KERNEL_X86_P4_CLOCKMOD="P4 Clockmod frequency scaling influences tuning and needs to be disabled at compile time."
-	ERROR_KERNEL_X86_INTEL_PSTATE="Intel Pstate frequency scaling influences tuning and needs to be disabled at compile time."
-	linux-info_pkg_setup
-}
-
-src_configure() {
-	# hack needed to trick the flaky gcc detection
-	local mycc="$(type -P $(tc-getCC))"
-	[[ ${mycc} == *gcc* ]] && mycc=gcc
-	atlas_configure() {
-		local myconf=(
-			--prefix="${ED}/usr"
-			--libdir="${ED}/usr/$(get_libdir)"
-			--incdir="${ED}/usr/include"
-			--cc="$(tc-getCC)"
-			"-D c -DWALL"
-			"-C acg '${mycc}'"
-			"-F acg '${CFLAGS}'"
-			"-Ss pmake '\$(MAKE) ${MAKEOPTS}'"
-		)
-
-		# OpenMP shown to decreased performance over POSIX threads
-		# (at least in 3.9.x, see atlas-dev mailing list)
-		if use threads; then
-			if use generic; then # 2 threads is most generic
-				myconf+=( "-t 2" "-Si omp 0" )
-			else
-				myconf+=( "-t -1" "-Si omp 0" )
-			fi
-		else
-			myconf+=( "-t  0" "-Si omp 0" )
-		fi
-
-		if use amd64 || use ppc64 || use sparc; then
-			if [ ${ABI} = amd64 ] || [ ${ABI} = ppc64 ] || [ ${ABI} = sparc64 ] ; then
-				myconf+=( "-b 64" )
-			elif [ ${ABI} = x86 ] || [ ${ABI} = ppc ] || [ ${ABI} = sparc32 ] ; then
-				myconf+=( "-b 32" )
-			elif [ ${ABI} = x32 ] ; then
-				myconf+=( "-b 48" )
-			else
-				myconf+=( "-b 64" )
-			fi
-		elif use ppc || use x86; then
-			myconf+=( "-b 32" )
-		elif use ia64; then
-			myconf+=( "-b 64" )
-		fi
-		if use fortran; then
-			myconf+=(
-				"-C if '$(type -P $(tc-getFC))'"
-				"-F if '${FFLAGS}'"
-			)
-			if use lapack; then
-				myconf+=(
-					"-Si latune 1"
-					"--with-netlib-lapack-tarfile=${DISTDIR}/${LAPACKP}"
-				)
-			else
-				myconf+=( "-Si latune 0" )
-			fi
-		else
-			myconf+=( "-Si latune 0" "--nof77" )
-		fi
-		# generic stuff found by make make xprint_enums in atlas build dir
-		# basically assuming sse2+sse1 and 2 threads max
-		use generic && use x86   && myconf+=( "-V 384 -A 13")
-		use generic && use amd64 && myconf+=( "-V 384 -A 24")
-
-		local confdir="${S}_${1}"; shift
-		myconf+=( $(usex ifko "--use-ifko" "") )
-		myconf+=( $@ )
-		mkdir "${confdir}" && cd "${confdir}" || die
-		# for debugging
-		echo ${myconf[@]} > myconf.out
-		"${S}"/configure ${myconf[@]} || die "configure in ${confdir} failed"
-
-		if use deprecated; then
-			echo "BUILD_DEPRECATED=1" >> src/lapack/reference/make.inc.example || die
-		fi
-	}
-
-	atlas_configure shared "-Fa alg -fPIC" ${EXTRA_ECONF}
-	use static-libs && atlas_configure static ${EXTRA_ECONF}
-}
-
-src_compile() {
-	atlas_compile() {
-		pushd "${S}_${1}" > /dev/null || die
-		# atlas does its own parallel builds
-		emake -j1 build
-		cd lib || die
-		emake libclapack.a
-		[[ -e libptcblas.a ]] && emake libptclapack.a
-		popd > /dev/null || die
-	}
-
-	atlas_compile shared
-	use static-libs && atlas_compile static
-}
-
-src_test() {
-	cd "${S}_shared" || die
-	emake -j1 check time
-}
-
-# transform a static archive into a shared library and install them
-# atlas_install_libs <mylib.a> [extra link flags]
-atlas_install_libs() {
-	local libname=$(basename ${1%.*})
-	einfo "Installing ${libname}"
-	local soname=${libname}.so.$(get_major_version)
-	local _cmd
-	shift
-	pushd "${S}_shared"/lib > /dev/null
-	_cmd="${LINK:-$(tc-getCC)}"
-	_cmd+=" ${LDFLAGS} -shared -Wl,--no-undefined -Wl,-soname=${soname}"
-	_cmd+=" -Wl,--whole-archive ${libname}.a -Wl,--no-whole-archive"
-	_cmd+=" $@ -o ${soname}"
-	einfo "${_cmd}"
-	${_cmd} || die "Creating ${soname} failed"
-	dolib.so ${soname}
-	dosym ${soname} /usr/$(get_libdir)/${soname%.*}
-	popd > /dev/null || die
-	use static-libs && dolib.a "${S}_static"/lib/${libname}.a
-}
-
-# create and install a pkgconfig file
-# atlas_install_pc <libname> <pkg name> [extra link flags]
-atlas_install_pc() {
-	local libname=${1} ; shift
-	local pcname=${1} ; shift
-	local extra=()
-	[[ ${PCREQ} ]] && extra+=( --requires "${PCREQ}" )
-	create_pkgconfig \
-		--name "${pcname}" \
-		--description "${PN} ${pcname}" \
-		--libs "-L\${libdir} -l${libname} $@" \
-		--libs-private "-L\${libdir} -latlas -lm ${PTLIBS}" \
-		--cflags "-I\${includedir}/${PN}" \
-		"${extra[@]}" \
-		${pcname}
-}
-
-src_install() {
-	cd "${S}_shared/lib" || die
-	# rename to avoid collision with other packages
-	local l
-	for l in {,c}{blas,lapack}; do
-		if [[ -e lib${l}.a ]]; then
-			mv lib{,atl}${l}.a || die
-			if use static-libs; then
-				mv "${S}"_static/lib/lib{,atl}${l}.a || die
-			fi
-		fi
-	done
-
-	[[ -e libptcblas.a ]] && PTLIBS="-lpthread"
-
-	# atlas
-	atlas_install_libs libatlas.a -lm ${PTLIBS}
-
-	# cblas
-	atlas_install_libs libatlcblas.a -L. -latlas -lm
-	atlas_install_pc atlcblas atlas-cblas
-	alternatives_for cblas atlas 0 \
-		/usr/$(get_libdir)/pkgconfig/cblas.pc atlas-cblas.pc \
-		/usr/include/cblas.h atlas/cblas.h
-
-	# cblas threaded
-	if [[ -e libptcblas.a ]]; then
-		atlas_install_libs libptcblas.a -L. -latlas -lm ${PTLIBS}
-		atlas_install_pc ptcblas atlas-cblas-threads
-		alternatives_for cblas atlas-threads 0 \
-			/usr/$(get_libdir)/pkgconfig/cblas.pc atlas-cblas-threads.pc \
-			/usr/include/cblas.h atlas/cblas.h
-	fi
-
-	if use lapack; then
-		PCREQ="cblas"
-		# clapack
-		atlas_install_libs libatlclapack.a -L. -latlcblas -latlas -lm
-		atlas_install_pc atlclapack atlas-clapack
-
-		# clapack threaded
-		if [[ -e libptclapack.a ]]; then
-			atlas_install_libs libptclapack.a -L. -lptcblas -latlas -lm ${PTLIBS}
-			atlas_install_pc ptclapack atlas-clapack-threads
-		fi
-	fi
-
-	if use fortran; then
-		LINK=$(tc-getF77) PCREQ=
-
-		# blas
-		atlas_install_libs libf77blas.a -L. -latlas -lm
-		atlas_install_pc f77blas atlas-blas
-		alternatives_for blas atlas 0 \
-			/usr/$(get_libdir)/pkgconfig/blas.pc atlas-blas.pc
-
-		# blas threaded
-		if [[ -e libptf77blas.a ]]; then
-			atlas_install_libs libptf77blas.a -L. -latlas -lm ${PTLIBS}
-			atlas_install_pc ptf77blas atlas-blas-threads
-			alternatives_for blas atlas-threads 0 \
-				/usr/$(get_libdir)/pkgconfig/blas.pc atlas-blas-threads.pc
-		fi
-
-		if use lapack; then
-			PCREQ="blas cblas"
-			# lapack
-			atlas_install_libs libatllapack.a \
-				-L. -latlcblas -lf77blas -latlas -lm
-			atlas_install_pc atllapack atlas-lapack
-			alternatives_for lapack atlas 0 \
-				/usr/$(get_libdir)/pkgconfig/lapack.pc atlas-lapack.pc
-			# lapack threaded
-			if [[ -e libptlapack.a ]]; then
-				atlas_install_libs libptlapack.a \
-					-L. -lptcblas -lptf77blas -latlas -lm ${PTLIBS}
-				atlas_install_pc ptlapack atlas-lapack-threads
-				alternatives_for lapack atlas-threads 0 \
-					/usr/$(get_libdir)/pkgconfig/lapack.pc atlas-lapack-threads.pc
-			fi
-		fi
-	fi
-
-	cd "${S}" || die
-	insinto /usr/include/${PN}
-	doins include/*.h
-
-	cd "${S}/doc" || die
-	dodoc INDEX.txt AtlasCredits.txt ChangeLog
-	use doc && dodoc atlas*pdf cblas.pdf cblasqref.pdf
-	use doc && use fortran && dodoc f77blas*pdf
-	use doc && use fortran && use lapack && dodoc *lapack*pdf
-}
diff --git a/sci-libs/atlas/atlas-3.11.39.ebuild b/sci-libs/atlas/atlas-3.11.39.ebuild
deleted file mode 100644
index f4b65140c..000000000
--- a/sci-libs/atlas/atlas-3.11.39.ebuild
+++ /dev/null
@@ -1,285 +0,0 @@
-# Copyright 1999-2017 Gentoo Foundation
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=6
-
-FORTRAN_NEEDED=fortran
-
-inherit alternatives-2 eutils fortran-2 linux-info multilib numeric toolchain-funcs versionator
-
-LAPACKP=lapack-3.7.0.tgz
-
-DESCRIPTION="Automatically Tuned Linear Algebra Software"
-HOMEPAGE="http://math-atlas.sourceforge.net/"
-SRC_URI="mirror://sourceforge/math-atlas/${PN}${PV}.tar.bz2
-	fortran? ( lapack? ( http://www.netlib.org/lapack/${LAPACKP} ) )"
-
-LICENSE="BSD"
-SLOT="0"
-KEYWORDS="~amd64 ~x86 ~amd64-linux ~x86-linux"
-IUSE="+deprecated doc +fortran generic ifko +lapack static-libs threads"
-
-REQUIRED_USE="
-	deprecated? ( lapack )
-	lapack? ( fortran )"
-
-S="${WORKDIR}/ATLAS"
-
-PATCHES=(
-	"${FILESDIR}"/${P}-dolastcomp.patch
-)
-
-pkg_setup() {
-	local _cpufreq
-	for _cpufreq in /sys/devices/system/cpu/cpu*/cpufreq/scaling_governor; do
-		if [ -f ${_cpufreq} ]; then
-			if ! grep -q performance ${_cpufreq}; then
-				echo 2> /dev/null performance > ${_cpufreq} || \
-					die "${PN} needs all cpu set to performance"
-			fi
-		fi
-	done
-	[[ -e /sys/devices/system/cpu/intel_pstate ]] \
-		&& die "Intel P-State driver detected. Please reboot with 'intel_pstate=disable' in your cmdline"
-	use fortran && fortran-2_pkg_setup
-	CONFIG_CHECK="
-		!~X86_P4_CLOCKMOD
-		!~X86_INTEL_PSTATE
-	"
-	ERROR_KERNEL_X86_P4_CLOCKMOD="P4 Clockmod frequency scaling influences tuning and needs to be disabled at compile time."
-	ERROR_KERNEL_X86_INTEL_PSTATE="Intel Pstate frequency scaling influences tuning and needs to be disabled at compile time."
-	linux-info_pkg_setup
-}
-
-src_configure() {
-	# hack needed to trick the flaky gcc detection
-	local mycc="$(type -P $(tc-getCC))"
-	[[ ${mycc} == *gcc* ]] && mycc=gcc
-	atlas_configure() {
-		local myconf=(
-			--prefix="${ED}/usr"
-			--libdir="${ED}/usr/$(get_libdir)"
-			--incdir="${ED}/usr/include"
-			--cc="$(tc-getCC)"
-			"-D c -DWALL"
-			"-C acg '${mycc}'"
-			"-F acg '${CFLAGS}'"
-			"-Ss pmake '\$(MAKE) ${MAKEOPTS}'"
-		)
-
-		# OpenMP shown to decreased performance over POSIX threads
-		# (at least in 3.9.x, see atlas-dev mailing list)
-		if use threads; then
-			if use generic; then # 2 threads is most generic
-				myconf+=( "-t 2" "-Si omp 0" )
-			else
-				myconf+=( "-t -1" "-Si omp 0" )
-			fi
-		else
-			myconf+=( "-t  0" "-Si omp 0" )
-		fi
-
-		if use amd64 || use ppc64 || use sparc; then
-			if [ ${ABI} = amd64 ] || [ ${ABI} = ppc64 ] || [ ${ABI} = sparc64 ] ; then
-				myconf+=( "-b 64" )
-			elif [ ${ABI} = x86 ] || [ ${ABI} = ppc ] || [ ${ABI} = sparc32 ] ; then
-				myconf+=( "-b 32" )
-			elif [ ${ABI} = x32 ] ; then
-				myconf+=( "-b 48" )
-			else
-				myconf+=( "-b 64" )
-			fi
-		elif use ppc || use x86; then
-			myconf+=( "-b 32" )
-		elif use ia64; then
-			myconf+=( "-b 64" )
-		fi
-		if use fortran; then
-			myconf+=(
-				"-C if '$(type -P $(tc-getFC))'"
-				"-F if '${FFLAGS}'"
-			)
-			if use lapack; then
-				myconf+=(
-					"-Si latune 1"
-					"--with-netlib-lapack-tarfile=${DISTDIR}/${LAPACKP}"
-				)
-			else
-				myconf+=( "-Si latune 0" )
-			fi
-		else
-			myconf+=( "-Si latune 0" "--nof77" )
-		fi
-		# generic stuff found by make make xprint_enums in atlas build dir
-		# basically assuming sse2+sse1 and 2 threads max
-		use generic && use x86   && myconf+=( "-V 384 -A 13")
-		use generic && use amd64 && myconf+=( "-V 384 -A 24")
-
-		local confdir="${S}_${1}"; shift
-		myconf+=( $(usex ifko "--use-ifko" "") )
-		myconf+=( $@ )
-		mkdir "${confdir}" && cd "${confdir}" || die
-		# for debugging
-		echo ${myconf[@]} > myconf.out
-		"${S}"/configure ${myconf[@]} || die "configure in ${confdir} failed"
-
-		if use deprecated; then
-			echo "BUILD_DEPRECATED=1" >> src/lapack/reference/make.inc.example || die
-		fi
-	}
-
-	atlas_configure shared "-Fa alg -fPIC" ${EXTRA_ECONF}
-	use static-libs && atlas_configure static ${EXTRA_ECONF}
-}
-
-src_compile() {
-	atlas_compile() {
-		pushd "${S}_${1}" > /dev/null || die
-		# atlas does its own parallel builds
-		emake -j1 build
-		cd lib || die
-		emake libclapack.a
-		[[ -e libptcblas.a ]] && emake libptclapack.a
-		popd > /dev/null || die
-	}
-
-	atlas_compile shared
-	use static-libs && atlas_compile static
-}
-
-src_test() {
-	cd "${S}_shared" || die
-	emake -j1 check time
-}
-
-# transform a static archive into a shared library and install them
-# atlas_install_libs <mylib.a> [extra link flags]
-atlas_install_libs() {
-	local libname=$(basename ${1%.*})
-	einfo "Installing ${libname}"
-	local soname=${libname}.so.$(get_major_version)
-	local _cmd
-	shift
-	pushd "${S}_shared"/lib > /dev/null
-	_cmd="${LINK:-$(tc-getCC)}"
-	_cmd+=" ${LDFLAGS} -shared -Wl,--no-undefined -Wl,-soname=${soname}"
-	_cmd+=" -Wl,--whole-archive ${libname}.a -Wl,--no-whole-archive"
-	_cmd+=" $@ -o ${soname}"
-	einfo "${_cmd}"
-	${_cmd} || die "Creating ${soname} failed"
-	dolib.so ${soname}
-	dosym ${soname} /usr/$(get_libdir)/${soname%.*}
-	popd > /dev/null || die
-	use static-libs && dolib.a "${S}_static"/lib/${libname}.a
-}
-
-# create and install a pkgconfig file
-# atlas_install_pc <libname> <pkg name> [extra link flags]
-atlas_install_pc() {
-	local libname=${1} ; shift
-	local pcname=${1} ; shift
-	local extra=()
-	[[ ${PCREQ} ]] && extra+=( --requires "${PCREQ}" )
-	create_pkgconfig \
-		--name "${pcname}" \
-		--description "${PN} ${pcname}" \
-		--libs "-L\${libdir} -l${libname} $@" \
-		--libs-private "-L\${libdir} -latlas -lm ${PTLIBS}" \
-		--cflags "-I\${includedir}/${PN}" \
-		"${extra[@]}" \
-		${pcname}
-}
-
-src_install() {
-	cd "${S}_shared/lib" || die
-	# rename to avoid collision with other packages
-	local l
-	for l in {,c}{blas,lapack}; do
-		if [[ -e lib${l}.a ]]; then
-			mv lib{,atl}${l}.a || die
-			if use static-libs; then
-				mv "${S}"_static/lib/lib{,atl}${l}.a || die
-			fi
-		fi
-	done
-
-	[[ -e libptcblas.a ]] && PTLIBS="-lpthread"
-
-	# atlas
-	atlas_install_libs libatlas.a -lm ${PTLIBS}
-
-	# cblas
-	atlas_install_libs libatlcblas.a -L. -latlas -lm
-	atlas_install_pc atlcblas atlas-cblas
-	alternatives_for cblas atlas 0 \
-		/usr/$(get_libdir)/pkgconfig/cblas.pc atlas-cblas.pc \
-		/usr/include/cblas.h atlas/cblas.h
-
-	# cblas threaded
-	if [[ -e libptcblas.a ]]; then
-		atlas_install_libs libptcblas.a -L. -latlas -lm ${PTLIBS}
-		atlas_install_pc ptcblas atlas-cblas-threads
-		alternatives_for cblas atlas-threads 0 \
-			/usr/$(get_libdir)/pkgconfig/cblas.pc atlas-cblas-threads.pc \
-			/usr/include/cblas.h atlas/cblas.h
-	fi
-
-	if use lapack; then
-		PCREQ="cblas"
-		# clapack
-		atlas_install_libs libatlclapack.a -L. -latlcblas -latlas -lm
-		atlas_install_pc atlclapack atlas-clapack
-
-		# clapack threaded
-		if [[ -e libptclapack.a ]]; then
-			atlas_install_libs libptclapack.a -L. -lptcblas -latlas -lm ${PTLIBS}
-			atlas_install_pc ptclapack atlas-clapack-threads
-		fi
-	fi
-
-	if use fortran; then
-		LINK=$(tc-getF77) PCREQ=
-
-		# blas
-		atlas_install_libs libf77blas.a -L. -latlas -lm
-		atlas_install_pc f77blas atlas-blas
-		alternatives_for blas atlas 0 \
-			/usr/$(get_libdir)/pkgconfig/blas.pc atlas-blas.pc
-
-		# blas threaded
-		if [[ -e libptf77blas.a ]]; then
-			atlas_install_libs libptf77blas.a -L. -latlas -lm ${PTLIBS}
-			atlas_install_pc ptf77blas atlas-blas-threads
-			alternatives_for blas atlas-threads 0 \
-				/usr/$(get_libdir)/pkgconfig/blas.pc atlas-blas-threads.pc
-		fi
-
-		if use lapack; then
-			PCREQ="blas cblas"
-			# lapack
-			atlas_install_libs libatllapack.a \
-				-L. -latlcblas -lf77blas -latlas -lm
-			atlas_install_pc atllapack atlas-lapack
-			alternatives_for lapack atlas 0 \
-				/usr/$(get_libdir)/pkgconfig/lapack.pc atlas-lapack.pc
-			# lapack threaded
-			if [[ -e libptlapack.a ]]; then
-				atlas_install_libs libptlapack.a \
-					-L. -lptcblas -lptf77blas -latlas -lm ${PTLIBS}
-				atlas_install_pc ptlapack atlas-lapack-threads
-				alternatives_for lapack atlas-threads 0 \
-					/usr/$(get_libdir)/pkgconfig/lapack.pc atlas-lapack-threads.pc
-			fi
-		fi
-	fi
-
-	cd "${S}" || die
-	insinto /usr/include/${PN}
-	doins include/*.h
-
-	cd "${S}/doc" || die
-	dodoc INDEX.txt AtlasCredits.txt ChangeLog
-	use doc && dodoc atlas*pdf cblas.pdf cblasqref.pdf
-	use doc && use fortran && dodoc f77blas*pdf
-	use doc && use fortran && use lapack && dodoc *lapack*pdf
-}
diff --git a/sci-libs/atlas/files/atlas-3.10.0-x32-support.patch b/sci-libs/atlas/files/atlas-3.10.0-x32-support.patch
deleted file mode 100644
index 82e698069..000000000
--- a/sci-libs/atlas/files/atlas-3.10.0-x32-support.patch
+++ /dev/null
@@ -1,93 +0,0 @@
---- ATLAS/CONFIG/src/SpewMakeInc.c.orig	2012-05-24 00:56:27.000000000 +0200
-+++ ATLAS/CONFIG/src/SpewMakeInc.c	2012-06-06 15:17:40.000000000 +0200
-@@ -370,7 +370,7 @@
-    }
-    *f2cdefs = fdefs;
-    *ecdefs = cdefs;
--   if (*ptrbits != 32 && *ptrbits != 64)
-+   if (*ptrbits != 32 && *ptrbits != 64 && *ptrbits != 48)
-       *ptrbits = 0;
- }
- char *GetPtrbitsFlag(enum OSTYPE OS, enum MACHTYPE arch, int ptrbits,
-@@ -418,6 +418,8 @@
-          sp = "-m64";
-        else if (ptrbits == 32)
-          sp = "-m32";
-+       else if (ptrbits == 48 && MachIsX86(arch))
-+         sp = "-mx32";
-    }
-    return(sp);
- }
---- ATLAS/CONFIG/src/gnuccw.c.orig	2012-06-06 15:30:05.000000000 +0200
-+++ ATLAS/CONFIG/src/gnuccw.c	2012-06-06 15:33:29.000000000 +0200
-@@ -363,7 +363,7 @@
-  *          -m64/32 args get passed to comp, asm & linker
-  */
-             else if (at->len == 4 &&
--                     (!strcmp(at->arg, "-m64") || !strcmp(at->arg, "-m32")))
-+                     (!strcmp(at->arg, "-m64") || !strcmp(at->arg, "-m32") || !strcmp(at->arg, "-mx32")))
-             {
-                if (at->arg[2] == '6')
-                   *BITS = 64;
---- ATLAS/CONFIG/src/gcc3p.c.orig	2012-06-06 15:29:38.000000000 +0200
-+++ ATLAS/CONFIG/src/gcc3p.c	2012-06-06 15:31:17.000000000 +0200
-@@ -352,7 +352,7 @@
-  *          -m64/32 args get passed to comp, asm & linker
-  */
-             else if (at->len == 4 &&
--                     (!strcmp(at->arg, "-m64") || !strcmp(at->arg, "-m32")))
-+                     (!strcmp(at->arg, "-m64") || !strcmp(at->arg, "-m32") || !strcmp(at->arg, "-mx32")))
-             {
-                if (at->arg[2] == '6')
-                {
---- ATLAS/CONFIG/src/gnuf90w.c.orig	2012-06-06 15:29:28.000000000 +0200
-+++ ATLAS/CONFIG/src/gnuf90w.c	2012-06-06 15:30:36.000000000 +0200
-@@ -363,7 +363,7 @@
-  *          -m64/32 args get passed to comp, asm & linker
-  */
-             else if (at->len == 4 &&
--                     (!strcmp(at->arg, "-m64") || !strcmp(at->arg, "-m32")))
-+                     (!strcmp(at->arg, "-m64") || !strcmp(at->arg, "-m32") || !strcmp(at->arg, "-mx32")))
-             {
-                if (at->arg[2] == '6')
-                   *BITS = 64;
---- ATLAS/CONFIG/src/probe_comp.c.orig	2012-06-06 15:29:51.000000000 +0200
-+++ ATLAS/CONFIG/src/probe_comp.c	2012-06-06 15:32:50.000000000 +0200
-@@ -614,6 +614,8 @@
-          sp = "-m64";
-        else if (ptrbits == 32)
-          sp = "-m32";
-+       else if (ptrbits == 48)
-+         sp = "-mx32";
-    }
-    return(sp);
- }
-@@ -1691,7 +1693,7 @@
-          }
-       }
-    }
--   if (*ptrbits != 32 && *ptrbits != 64)
-+   if (*ptrbits != 32 && *ptrbits != 64 && *ptrbits != 48)
-       *ptrbits = 0;
- }
- 
---- ATLAS/CONFIG/src/config.c.orig	2012-06-06 15:59:53.000000000 +0200
-+++ ATLAS/CONFIG/src/config.c	2012-06-06 16:00:07.000000000 +0200
-@@ -183,7 +183,7 @@
-    i = sprintf(ln, "make IRun_comp args=\"-v %d -o atlconf.txt -O %d -A %d -Si nof77 %d -V %d %s %s",
-                verb, OS, arch, nof77, vecext, targarg, flags);
-    free(flags);
--   if (ptrbits == 64 || ptrbits == 32)
-+   if (ptrbits == 64 || ptrbits == 32 || ptrbits == 48)
-    {
-       sprintf(stmp, "-b %d", ptrbits);
-       ln = NewAppendedString(ln, stmp);
-@@ -1272,7 +1272,7 @@
-    }
-    *f2cdefs = fdefs;
-    *ecdefs = cdefs;
--   if (*ptrbits != 32 && *ptrbits != 64)
-+   if (*ptrbits != 32 && *ptrbits != 64 && *ptrbits != 48)
-       *ptrbits = 0;
- }
- 
diff --git a/sci-libs/atlas/files/atlas-3.11.39-dolastcomp.patch b/sci-libs/atlas/files/atlas-3.11.39-dolastcomp.patch
deleted file mode 100644
index 3cd554cf4..000000000
--- a/sci-libs/atlas/files/atlas-3.11.39-dolastcomp.patch
+++ /dev/null
@@ -1,13 +0,0 @@
-diff --git a/src/threads/blas/level3/ATL_tammm_G.c b/src/threads/blas/level3/ATL_tammm_G.c
-index a43a08b..77c78f4 100644
---- a/src/threads/blas/level3/ATL_tammm_G.c
-+++ b/src/threads/blas/level3/ATL_tammm_G.c
-@@ -479,7 +479,7 @@ static void DoCompNoCopy(ATL_tamm_gOOO_t *pd, ATL_UINT rank, TYPE *wC)
- #ifndef TCPLX
-    #undef rC
- #endif
--void DoLastComp(ATL_tamm_gOOO_t *pd, ATL_UINT rank, TYPE *wC)
-+static void DoLastComp(ATL_tamm_gOOO_t *pd, ATL_UINT rank, TYPE *wC)
- {
-    ipinfo_t *ip=pd->ip;
-    TYPE *wA=pd->wA, *wB=pd->wB, *C=pd->C;
diff --git a/sci-libs/atlas/files/format-security.patch b/sci-libs/atlas/files/format-security.patch
deleted file mode 100644
index f3f45d774..000000000
--- a/sci-libs/atlas/files/format-security.patch
+++ /dev/null
@@ -1,198 +0,0 @@
- bin/atlas_install.c | 46 +++++++++++++++++++++++-----------------------
- 1 file changed, 23 insertions(+), 23 deletions(-)
-
-diff --git a/bin/atlas_install.c b/bin/atlas_install.c
-index 2753cbf..21b716d 100644
---- a/bin/atlas_install.c
-+++ b/bin/atlas_install.c
-@@ -483,9 +483,9 @@ void PrintStartStop(FILE *fp0, FILE *fp1, int nspc, int START, int sec,
-          fprintf(fp1, "\n\n");
-    }
-    if (fp0)
--      fprintf(fp0, ln);
-+      fprintf(fp0, "%s", ln);
-    if (fp1)
--      fprintf(fp1, ln);
-+      fprintf(fp1, "%s", ln);
- }
- 
- int LnIsCont(char *ln)
-@@ -776,11 +776,11 @@ void GoToTown(int ARCHDEF, int L1DEF, int TuneLA)
-          if (DefInstall)
-          {
-             sprintf(ln, "%s IRunMMDef pre=%c %s %s\n", fmake, pre, redir, ln2);
--            fprintf(stdout, ln);
-+            fprintf(stdout, "%s", ln);
-             ATL_Cassert(system(ln)==0, "BUILDING BLOCK MATMUL TUNE", ln2);
-          }
-          sprintf(ln, "%s %s pre=%c %s %s\n", fmake, fnam, pre, redir, ln2);
--         fprintf(stdout, ln);
-+         fprintf(stdout, "%s", ln);
-          ATL_Cassert(system(ln)==0, "BUILDING BLOCK MATMUL TUNE", ln2);
-          PrintBanner(ln2, 0, 2, ip+1, 1);
-       }
-@@ -836,7 +836,7 @@ void GoToTown(int ARCHDEF, int L1DEF, int TuneLA)
-       if (!FileExists(fnam))
-       {
-          sprintf(ln, "%s %s pre=%c %s %s", fmake, fnam, pre, redir, ln2);
--         fprintf(stdout, ln);
-+         fprintf(stdout, "%s", ln);
-          ATL_Cassert(system(ln)==0, "BUILDING BLOCK MATMUL TUNE", ln2);
-       }
-       fp = fopen(fnam, "r");
-@@ -854,7 +854,7 @@ void GoToTown(int ARCHDEF, int L1DEF, int TuneLA)
-             {
-                sprintf(ln, "%s %s pre=%c nb=%d %s %s",
-                        fmake, fnam, pre, ncnb, redir, ln2);
--               fprintf(stdout, ln);
-+               fprintf(stdout, "%s", ln);
-                ATL_Cassert(system(ln)==0, "BUILDING BLOCK MATMUL TUNE", ln2);
-             }
-             GetInstLogFile(fnam, pre, &muladd, &pf, &lat, &nb, &mu, &nu, &ku,
-@@ -881,7 +881,7 @@ void GoToTown(int ARCHDEF, int L1DEF, int TuneLA)
-       }
- 
-       sprintf(ln, "%s MMinstall pre=%c %s %s\n", fmake, pre, redir, ln2);
--      fprintf(stdout, ln);
-+      fprintf(stdout, "%s", ln);
-       ATL_Cassert(system(ln)==0, "BUILDING BLOCK MATMUL TUNE", ln2);
- 
-       fprintf(fpsum, "\n");
-@@ -896,7 +896,7 @@ void GoToTown(int ARCHDEF, int L1DEF, int TuneLA)
-          PrintBanner(ln2, 1, 2, ip+1, 2);
-          sprintf(ln, "%s INSTALL_LOG/atlas_cacheedge.h pre=%c %s %s\n",
-                  fmake, pre, redir, ln2);
--         fprintf(stdout, ln);
-+         fprintf(stdout, "%s", ln);
-          ATL_Cassert(system(ln)==0, "CACHEEDGE DETECTION", ln2);
-          PrintBanner(ln2, 0, 2, ip+1, 2);
-       }
-@@ -922,7 +922,7 @@ void GoToTown(int ARCHDEF, int L1DEF, int TuneLA)
-          {
-             sprintf(ln, "%s %s pre=%c %s %s\n",
-                     fmake, ln3, pre, redir, ln2);
--            fprintf(stdout, ln);
-+            fprintf(stdout, "%s", ln);
-             ATL_Cassert(system(ln)==0, "CACHEEDGE DETECTION", ln2);
-          }
-          fp = fopen(ln3, "r");
-@@ -955,7 +955,7 @@ void GoToTown(int ARCHDEF, int L1DEF, int TuneLA)
-               "\n\n   STAGE 2-%d-3: COPY/NO-COPY CROSSOVER DETECTION\n", ip+1);
- 
-          sprintf(ln, "%s %s pre=%c %s %s\n", fmake, fnam, pre, redir, ln2);
--         fprintf(stdout, ln);
-+         fprintf(stdout, "%s", ln);
-          ATL_Cassert(system(ln)==0, "COPY/NO-COPY CROSSOVER DETECTION", ln2);
-          PrintBanner(ln2, 0, 2, ip+1, 3);
-          fprintf(stdout, "      done.\n");
-@@ -970,17 +970,17 @@ void GoToTown(int ARCHDEF, int L1DEF, int TuneLA)
-       {
-          sprintf(ln, "%s INSTALL_LOG/atlas_%ctrsmXover.h pre=%c %s %s\n",
-                  fmake, pre, pre, redir, ln2);
--         fprintf(stdout, ln);
-+         fprintf(stdout, "%s", ln);
-          ATL_Cassert(system(ln)==0, "L3BLAS TUNING", ln2);
-       }
-       else
-       {
-          sprintf(ln, "%s Il3lib pre=%c %s %s\n", fmake, pre, redir, ln2);
--         fprintf(stdout, ln);
-+         fprintf(stdout, "%s", ln);
-          ATL_Cassert(system(ln)==0, "L3BLAS TUNING", ln2);
-       }
-       sprintf(ln, "%s %ccblaslib %s %s\n", fmake, pre, redir, ln2); /* cblas */
--      fprintf(stdout, ln);
-+      fprintf(stdout, "%s", ln);
-       ATL_Cassert(system(ln)==0, "L3BLAS TUNING", ln2);
-       PrintBanner(ln2, 0, 2, ip+1, 5);
-       PrintStartStop(stdout, fpsum, 3, 0, 2, ip+1, 4, "L3BLAS TUNE");
-@@ -993,7 +993,7 @@ void GoToTown(int ARCHDEF, int L1DEF, int TuneLA)
-          sprintf(ln2, "INSTALL_LOG/%cMVNTUNE.LOG", pre);
-          PrintBanner(ln2, 1, 2, ip+1, 7);
-          sprintf(ln, "%s %s pre=%c %s %s\n", fmake, fnam, pre, redir, ln2);
--         fprintf(stdout, ln);
-+         fprintf(stdout, "%s", ln);
-          ATL_Cassert(system(ln)==0, "MVNTUNE", ln2);
-          ATL_Cassert(FileIsThere(fnam), "MVNTUNE", ln2);
-          PrintBanner(ln2, 0, 2, ip+1, 7);
-@@ -1026,7 +1026,7 @@ void GoToTown(int ARCHDEF, int L1DEF, int TuneLA)
-          sprintf(ln2, "INSTALL_LOG/%cMVTTUNE.LOG", pre);
-          PrintBanner(ln2, 1, 2, ip+1, 7);
-          sprintf(ln, "%s %s pre=%c %s %s\n", fmake, fnam, pre, redir, ln2);
--         fprintf(stdout, ln);
-+         fprintf(stdout, "%s", ln);
-          ATL_Cassert(system(ln)==0, "MVTTUNE", ln2);
-          ATL_Cassert(FileIsThere(fnam), "MVTTUNE", ln2);
-          PrintBanner(ln2, 0, 2, ip+1, 7);
-@@ -1061,7 +1061,7 @@ void GoToTown(int ARCHDEF, int L1DEF, int TuneLA)
-          sprintf(ln2, "INSTALL_LOG/%cR1TUNE.LOG", pre);
-          PrintBanner(ln2, 1, 2, ip+1, 7);
-          sprintf(ln, "%s %s pre=%c %s %s\n", fmake, fnam, pre, redir, ln2);
--         fprintf(stdout, ln);
-+         fprintf(stdout, "%s", ln);
-          ATL_Cassert(system(ln)==0, "R1TUNE", ln2);
-          ATL_Cassert(FileIsThere(fnam), "R1TUNE", ln2);
-          PrintBanner(ln2, 0, 2, ip+1, 7);
-@@ -1099,7 +1099,7 @@ void GoToTown(int ARCHDEF, int L1DEF, int TuneLA)
-    sprintf(ln2, "INSTALL_LOG/LIBBUILD.LOG");
-    PrintBanner(ln2, 1, 3, 1, 1);
-    sprintf(ln, "%s IBuildLibs %s %s\n", fmake, redir, ln2);
--   fprintf(stdout, ln);
-+   fprintf(stdout, "%s", ln);
-    ATL_Cassert(system(ln)==0, "LIBRARY BUILD", ln2);
-    ATL_Cassert(FileIsThere(fnam), "LIBRARY BUILD", ln2);
-    PrintBanner(ln2, 0, 3, 1, 1);
-@@ -1110,7 +1110,7 @@ void GoToTown(int ARCHDEF, int L1DEF, int TuneLA)
-    PrintBanner(ln2, 1, 4, 1, 1);
-    PrintStartStop(stdout, fpsum, 3, 1, 4, 1, 1, "TRSM TUNE");
-    sprintf(ln, "%s IPostTune %s %s\n", fmake, redir, ln2);
--   fprintf(stdout, ln);
-+   fprintf(stdout, "%s", ln);
-    ATL_Cassert(system(ln)==0, "POST-BUILD TUNE", ln2);
-    PrintStartStop(stdout, fpsum, 3, 0, 4, 1, 0, NULL);
-    ATL_Cassert(FileIsThere(fnam), "POST-BUILD TUNE", ln2);
-@@ -1121,7 +1121,7 @@ void GoToTown(int ARCHDEF, int L1DEF, int TuneLA)
-    sprintf(ln2, "INSTALL_LOG/PTTUNE.LOG");
-    PrintBanner(ln2, 1, 4, 2, 0);
-    sprintf(ln, "%s IPTtune %s %s\n", fmake, redir, ln2);
--   fprintf(stdout, ln);
-+   fprintf(stdout, "%s", ln);
-    ATL_Cassert(system(ln)==0, "THREADING TUNE", ln2);
-    PrintStartStop(stdout, fpsum, 3, 0, 4, 2, 0, "THREADING TUNE");
- 
-@@ -1129,7 +1129,7 @@ void GoToTown(int ARCHDEF, int L1DEF, int TuneLA)
-    sprintf(ln2, "INSTALL_LOG/LIBPTBUILD.LOG");
-    PrintBanner(ln2, 1, 4, 2, 1);
-    sprintf(ln, "%s IBuildPtlibs %s %s\n", fmake, redir, ln2);
--   fprintf(stdout, ln);
-+   fprintf(stdout, "%s", ln);
-    ATL_Cassert(system(ln)==0, "PTLIBRARY BUILD", ln2);
-    PrintBanner(ln2, 0, 4, 2, 1);
-    PrintStartStop(stdout, fpsum, 3, 0, 4, 2, 1, "THREADING BUILD");
-@@ -1144,7 +1144,7 @@ void GoToTown(int ARCHDEF, int L1DEF, int TuneLA)
-          PrintStartStop(stdout, fpsum, 6, 1, 4, 3, ip+1, ln2);
-          sprintf(ln2, "INSTALL_LOG/%cLATUNE.LOG", pre);
-          PrintBanner(ln2, 1, 4, 3, ip+1);
--         fprintf(stdout, ln);
-+         fprintf(stdout, "%s", ln);
-          sprintf(ln, "%s ILATune pre=%c %s %s\n", fmake, pre, redir, ln2);
-          ATL_Cassert(system(ln)==0, "LAPACK TUNE", ln2);
-          PrintStartStop(stdout, fpsum, 6, 0, 4, 3, ip+1, NULL);
-@@ -1162,7 +1162,7 @@ void GoToTown(int ARCHDEF, int L1DEF, int TuneLA)
-    #else
-       sprintf(ln, "%s IBuildLibs %s %s\n", fmake, redir, ln2);
-    #endif
--   fprintf(stdout, ln);
-+   fprintf(stdout, "%s", ln);
-    ATL_Cassert(system(ln)==0, "STATIC LIBRARY UPDATE", ln2);
-    PrintBanner(ln2, 0, 5, 1, 1);
-    PrintStartStop(stdout, fpsum, 3, 0, 5, 1, 0, "FINAL STATIC LIBRARY UPDATE");
-@@ -1172,7 +1172,7 @@ void GoToTown(int ARCHDEF, int L1DEF, int TuneLA)
-    sprintf(ln2, "INSTALL_LOG/LIBDYBUILD.LOG");
-    PrintBanner(ln2, 1, 5, 2, 1);
-    sprintf(ln, "%s IBuildDyLibs %s %s\n", fmake, redir, ln2);
--   fprintf(stdout, ln);
-+   fprintf(stdout, "%s", ln);
-    ATL_Cassert(system(ln)==0, "DYLIBRARY BUILD", ln2);
-    PrintBanner(ln2, 0, 5, 2, 1);
-    PrintStartStop(stdout, fpsum, 3, 0, 5, 2, 0, NULL);
diff --git a/sci-libs/atlas/metadata.xml b/sci-libs/atlas/metadata.xml
deleted file mode 100644
index 616e09a4c..000000000
--- a/sci-libs/atlas/metadata.xml
+++ /dev/null
@@ -1,24 +0,0 @@
-<?xml version="1.0" encoding="UTF-8"?>
-<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
-<pkgmetadata>
-	<maintainer type="project">
-		<email>sci@gentoo.org</email>
-		<name>Gentoo Science Project</name>
-	</maintainer>
-	<longdescription lang="en">
-ATLAS is an approach for the automatic generation and optimization of
-numerical software. Currently ATLAS supplies optimized versions for the
-complete set of linear algebra kernels known as the Basic Linear Algebra
-Subroutines (BLAS) for both c and F77 interfaces. It can also build
-a subset of the linear algebra routine LAPACK library or the full
-LAPACK using the reference LAPACK from Netlib.
-</longdescription>
-	<use>
-		<flag name="deprecated">Build deprecated routines</flag>
-		<flag name="generic">Build atlas assuming a fairly generic architecture (sse2 for x86, core2 for amd64)</flag>
-		<flag name="ifko">Use iFKO to improve ATLAS performance (ATTENTION!!! Increases builtime enormously)</flag>
-	</use>
-	<upstream>
-		<remote-id type="sourceforge">math-atlas</remote-id>
-	</upstream>
-</pkgmetadata>
diff --git a/sci-libs/bids-validator/Manifest b/sci-libs/bids-validator/Manifest
new file mode 100644
index 000000000..d51971ebd
--- /dev/null
+++ b/sci-libs/bids-validator/Manifest
@@ -0,0 +1 @@
+DIST bids-validator-1.4.4.tar.gz 2751351 BLAKE2B a7f5f797ab7e1e10061dd64210b4ab258c30e0eab235caba2da20eab709223566765bfd1216f73efd39e42d6f13ce6452d8de8dace06344cd50da26c5ff4abac SHA512 79148eb6184a16b2924f021cb636e6ffa7aa8ce617cb863068d9c3890a8a091aa4158ef7badf208e6a98d1a0b8fcfbadadaa90ab50769ab6083475173951e0bd
diff --git a/sci-libs/bids-validator/bids-validator-1.4.4.ebuild b/sci-libs/bids-validator/bids-validator-1.4.4.ebuild
new file mode 100644
index 000000000..a4f7f0340
--- /dev/null
+++ b/sci-libs/bids-validator/bids-validator-1.4.4.ebuild
@@ -0,0 +1,22 @@
+# Copyright 1999-2023 Gentoo Authors
+# Distributed under the terms of the GNU General Public License v2
+
+EAPI=8
+
+PYTHON_COMPAT=( python3_{10..11} )
+
+inherit distutils-r1
+
+DESCRIPTION="Validator for the Brain Imaging Data Structure"
+HOMEPAGE="https://github.com/bids-standard/bids-validator"
+SRC_URI="https://github.com/bids-standard/bids-validator/archive/v${PV}.tar.gz -> ${P}.tar.gz"
+
+LICENSE="MIT"
+SLOT="0"
+KEYWORDS="~amd64"
+IUSE=""
+
+DEPEND=""
+RDEPEND=""
+
+S="${WORKDIR}/${P}/${PN}"
diff --git a/sci-libs/bids-validator/metadata.xml b/sci-libs/bids-validator/metadata.xml
new file mode 100644
index 000000000..403bc69f1
--- /dev/null
+++ b/sci-libs/bids-validator/metadata.xml
@@ -0,0 +1,20 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
+<pkgmetadata>
+	<maintainer type="person">
+		<email>gentoo@chymera.eu</email>
+		<name>Horea Christian</name>
+	</maintainer>
+	<maintainer type="project">
+		<email>sci@gentoo.org</email>
+		<name>Gentoo Science Project</name>
+	</maintainer>
+	<longdescription lang="en">
+		A limited library of helper functions written in Python, the main
+		function of which is to determine whether a file path is compliant
+		with the BIDS specification.
+	</longdescription>
+	<upstream>
+		<remote-id type="github">bids-standard/bids-validator</remote-id>
+	</upstream>
+</pkgmetadata>
diff --git a/sci-libs/bigdft-abi/Manifest b/sci-libs/bigdft-abi/Manifest
deleted file mode 100644
index 49efc5411..000000000
--- a/sci-libs/bigdft-abi/Manifest
+++ /dev/null
@@ -1,2 +0,0 @@
-DIST bigdft-abi-1.0.4-0005.patch 190680 BLAKE2B c79821e3f7b94a9d78794ea864dab143ef5532db97bd8abf3b164eab450c4a292fb40c95a6d53156af978dad2aa940bab6342e77e23818dd554b1dff7d41689f SHA512 b0f7b34d621b2b40c8427a98320b28d0a2975742dea8ca1095db86ac712e6d8f4c3f8223f07fa0c2b73b5d6711fc0ee16e4fef312e1254b11ba0a7a047bd8a91
-DIST bigdft-abi-1.0.4.tar.gz 8982260 BLAKE2B 013008aa1aea2fc3954f8618075a6e3fe8c5cc395e6b4789e3ddfa24fae9a7e6e2fa7c8e30182deb1a5e61c0fc50046b4f53471dbbde5dfb63f3f03e6982f20e SHA512 556001d1ffd08be70b97f07a8a150d5d033a4611957180a7a25b41963754e0e3d2bb2a4e9d5b6beb8ff6fb1eb6f4ae9b51633cfe3d7f5a8ed20a85be21031c35
diff --git a/sci-libs/bigdft-abi/bigdft-abi-1.0.4-r3.ebuild b/sci-libs/bigdft-abi/bigdft-abi-1.0.4-r3.ebuild
deleted file mode 100644
index 73471b0dc..000000000
--- a/sci-libs/bigdft-abi/bigdft-abi-1.0.4-r3.ebuild
+++ /dev/null
@@ -1,181 +0,0 @@
-# Copyright 1999-2014 Gentoo Foundation
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=5
-
-PYTHON_COMPAT=( python2_7 )
-
-inherit autotools-utils eutils flag-o-matic fortran-2 python-any-r1 toolchain-funcs
-
-DESCRIPTION="A DFT electronic structure code using a wavelet basis set"
-HOMEPAGE="http://www.abinit.org/downloads/plug-in-sources"
-SRC_URI="
-	http://forge.abinit.org/fallbacks/${P}.tar.gz
-	https://raw.githubusercontent.com/gentoo-science/sci/master/patches/bigdft-abi-1.0.4-0005.patch
-	"
-
-LICENSE="GPL-3"
-SLOT="0"
-KEYWORDS="~amd64 ~x86 ~amd64-linux"
-IUSE="cuda doc etsf_io glib mpi netcdf openmp opencl scalapack test"
-
-RDEPEND="
-	>=sci-libs/libxc-1.2.0-r1[fortran]
-	virtual/blas
-	virtual/fortran
-	virtual/lapack
-	dev-libs/libyaml
-	mpi? ( virtual/mpi )
-	cuda? ( dev-util/nvidia-cuda-sdk )
-	opencl? ( virtual/opencl )
-	glib? ( >=dev-libs/glib-2.22 )
-	etsf_io? ( >=sci-libs/etsf_io-1.0.3-r2 )
-	netcdf? (
-		|| (
-			sci-libs/netcdf[fortran]
-			sci-libs/netcdf-fortran
-			)
-		)
-	scalapack? ( virtual/scalapack )"
-DEPEND="${RDEPEND}
-	virtual/pkgconfig
-	>=sys-devel/autoconf-2.59
-	doc? ( virtual/latex-base )
-	${PYTHON_DEPS}
-	dev-python/pyyaml[libyaml]
-	dev-util/gdbus-codegen
-	app-arch/tar
-	app-arch/gzip"
-
-DOCS=( README INSTALL ChangeLog AUTHORS NEWS )
-
-FORTRAN_STANDARD=90
-
-pkg_setup() {
-	# fortran-2.eclass does not handle mpi wrappers
-	if use mpi; then
-		export FC="mpif90"
-		export F77="mpif77"
-		export CC="mpicc"
-	else
-		tc-export FC F77 CC
-	fi
-
-	# This should be correct.
-	#   It is gcc-centric because toolchain-funcs.eclass is gcc-centric.
-	#   Should a bug be filed against toolchain-funcs.eclass?
-	# if use openmp; then
-		#         tc-has-openmp || \
-		#                 die "Please select an openmp capable compiler like gcc[openmp]"
-		# fi
-	#
-	# Luckily Abinit is a fortran package.
-	#   fortran-2.eclass has its own test for OpenMP support,
-	#   more general than toolchain-funcs.eclass
-	#   The test itself proceeds inside fortran-2_pkg_setup
-	if use openmp; then FORTRAN_NEED_OPENMP=1; fi
-
-	fortran-2_pkg_setup
-
-	if use openmp; then
-		# based on _fortran-has-openmp() of fortran-2.eclass
-		local openmp=""
-		local fcode=ebuild-openmp-flags.f
-		local _fc=$(tc-getFC)
-
-		pushd "${T}"
-		cat <<- EOF > "${fcode}"
-		1     call omp_get_num_threads
-		2     end
-		EOF
-
-		for openmp in -fopenmp -xopenmp -openmp -mp -omp -qsmp=omp; do
-			"${_fc}" "${openmp}" "${fcode}" -o "${fcode}.x" && break
-		done
-
-		rm -f "${fcode}.*"
-		popd
-
-		append-flags "${openmp}"
-	fi
-
-	python-any-r1_pkg_setup
-}
-
-src_prepare() {
-	epatch \
-		"${FILESDIR}"/${P}-0002.patch \
-		"${FILESDIR}"/${P}-0003.patch \
-		"${FILESDIR}"/${P}-0004.patch \
-		"${DISTDIR}"/${P}-0005.patch \
-		"${FILESDIR}"/${P}-0006.patch \
-		"${FILESDIR}"/${P}-0007.patch \
-		"${FILESDIR}"/${P}-CUDA_gethostname.patch
-
-	eautoreconf
-}
-
-src_configure() {
-	local modules="${EPREFIX}/usr/include"
-	local netcdff_libs="-lnetcdff"
-	filter-flags '-m*' '-O*' "-pipe"
-	local nvcflags="${CFLAGS}"
-	_filter-var nvcflags '-m*' '-O*' "-pipe" "-W*"
-	use cuda && filter-ldflags '-m*' '-O*' "-pipe" "-W*"
-	local mylapack="lapack"
-	use scalapack && mylapack="scalapack"
-	local myeconfargs=(
-		$(use_enable mpi)
-		--enable-optimised-convolution
-		--enable-pseudo
-		--enable-libbigdft
-		--enable-binaries
-		--disable-minima-hopping
-		--disable-internal-libyaml
-		--enable-internal-libabinit
-		--with-moduledir="${modules}"
-		--with-ext-linalg="$($(tc-getPKG_CONFIG) --libs-only-l "${mylapack}")"
-		--with-ext-linalg-path="$($(tc-getPKG_CONFIG) --libs-only-L "${mylapack}")"
-		--with-libxc="yes"
-		--disable-internal-libxc
-		$(use_enable cuda cuda-gpu)
-		$(use_with cuda cuda-path /opt/cuda)
-		$(use_with cuda nvcc-flags "${nvcflags}")
-		$(use_enable opencl)
-		$(use_with etsf_io etsf-io)
-		"$(use etsf_io && echo "--with-netcdf-libs=$($(tc-getPKG_CONFIG) --libs netcdf) ${netcdff_libs}")"
-		$(use_with glib gobject)
-		$(use_with scalapack)
-		$(use_with scalapack scalapack-path "${EPREFIX}/usr/$(get_libdir)")
-		$(use_with scalapack blacs)
-		$(use_with scalapack blacs-path "${EPREFIX}/usr/$(get_libdir)")
-		PKG_CONFIG="$(tc-getPKG_CONFIG)"
-		FCFLAGS="${FCFLAGS}"
-		LD="$(tc-getLD)"
-		CPP="$(tc-getCPP)"
-		)
-	autotools-utils_src_configure
-}
-
-src_compile() {
-	#autotools-utils_src_compile() expanded
-	_check_build_dir
-	pushd "${AUTOTOOLS_BUILD_DIR}" > /dev/null
-	emake -j1
-	sed -i -e's%\$(top_builddir)/[^ ]*/lib\([^ /$-]*\)\.a%-l\1%g' bigdft.pc || die
-	popd > /dev/null
-
-	#autotools-utils_src_compile
-	if use doc; then
-		VARTEXFONTS="${T}/fonts"
-		autotools-utils_src_compile doc
-	fi
-}
-
-src_test() {
-	ewarn "The tests broken upstream. NOT testing"
-}
-
-src_install() {
-	autotools-utils_src_install
-}
diff --git a/sci-libs/bigdft-abi/files/bigdft-abi-1.0.4-0002.patch b/sci-libs/bigdft-abi/files/bigdft-abi-1.0.4-0002.patch
deleted file mode 100644
index e533022c7..000000000
--- a/sci-libs/bigdft-abi/files/bigdft-abi-1.0.4-0002.patch
+++ /dev/null
@@ -1,37 +0,0 @@
-*** bigdft-abi-1.0.4/src/wfn_opt/applyh.f90	Tue May 28 15:42:28 2013
---- bigdft-patch/src/wfn_opt/applyh.f90	Thu Jun  6 11:29:13 2013
-***************
-*** 1104,1110 ****
-          istart_c=1

-          if(at%npspcode(iatype)==7) then

-            call atom_projector_paw(ikpt,iat,idir,istart_c,iproj,nlpspd%nprojel,&

-!                lr,hx,hy,hz,rxyz(1,iat),at,orbs,nlpspd%plr(iat),proj,nwarnings,proj_G(iatype))

-          else

-            call atom_projector(ikpt,iat,idir,istart_c,iproj,nlpspd%nprojel,&

-                 lr,hx,hy,hz,rxyz(1,iat),at,orbs,nlpspd%plr(iat),proj,nwarnings)

---- 1104,1110 ----
-          istart_c=1

-          if(at%npspcode(iatype)==7) then

-            call atom_projector_paw(ikpt,iat,idir,istart_c,iproj,nlpspd%nprojel,&

-!                lr,hx,hy,hz,paw%rpaw(iatype),rxyz(1,iat),at,orbs,nlpspd%plr(iat),proj,nwarnings,proj_G(iatype))

-          else

-            call atom_projector(ikpt,iat,idir,istart_c,iproj,nlpspd%nprojel,&

-                 lr,hx,hy,hz,rxyz(1,iat),at,orbs,nlpspd%plr(iat),proj,nwarnings)

-***************
-*** 1116,1122 ****
-             istart_c=1

-             if(at%npspcode(iatype)==7) then

-             !    PAW case:

-!               call apply_atproj_iorb_paw(iat,iorb,nlpspd%nprojel,&

-                     at,orbs,wfd,nlpspd%plr(iat),proj,&

-                     psi(ispsi),hpsi(ispsi),eproj_sum,proj_G(iatype),paw)

-             else

---- 1116,1123 ----
-             istart_c=1

-             if(at%npspcode(iatype)==7) then

-             !    PAW case:

-!               call apply_atproj_iorb_paw(iat,iorb,ispsi,istart_c,&

-!                    nlpspd%nprojel,&

-                     at,orbs,wfd,nlpspd%plr(iat),proj,&

-                     psi(ispsi),hpsi(ispsi),eproj_sum,proj_G(iatype),paw)

-             else

diff --git a/sci-libs/bigdft-abi/files/bigdft-abi-1.0.4-0003.patch b/sci-libs/bigdft-abi/files/bigdft-abi-1.0.4-0003.patch
deleted file mode 100644
index 5b406a9a7..000000000
--- a/sci-libs/bigdft-abi/files/bigdft-abi-1.0.4-0003.patch
+++ /dev/null
@@ -1,49 +0,0 @@
-*** bigdft-abi-1.0.4/src/init/gautowav.f90	Mon Jul  9 16:43:33 2012
---- bigdft-patch/src/init/gautowav.f90	Mon Jun 10 11:16:37 2013
-***************
-*** 675,680 ****
---- 675,681 ----
-    integer :: i_stat,i_all,ishell,iexpo,icoeff,iat,isat,ng,l,m,i,nterm,ig
-    integer :: nterms_max,nterms,iterm,n_gau,ml1,mu1,ml2,mu2,ml3,mu3 !n(c) iscoeff
-    real(gp) :: rx,ry,rz,gau_a
-+   real(gp) :: gau_cut !only for PAW
-    integer, dimension(nterm_max) :: lx,ly,lz
-    real(gp), dimension(nterm_max) :: fac_arr
-    real(wp), allocatable, dimension(:,:,:) :: work
-***************
-*** 746,762 ****
-                      gau_a=G%xp(1,iexpo+ig-1)
-                      n_gau=lx(i)
-                      !print *,'x',gau_a,nterm,ncplx,kx,ky,kz,ml1,mu1,lr%d%n1
-!                     call gauss_to_daub_k(hx,kx*hx,ncplx,1,ncplx,fac_arr(i),rx,gau_a,n_gau,&
-                           lr%ns1,lr%d%n1,ml1,mu1,&
-                           wx(1,0,1,iterm),work,nw,perx) 
-                      n_gau=ly(i)
-                      !print *,'y',ml2,mu2,lr%d%n2
-!                     call gauss_to_daub_k(hy,ky*hy,ncplx,1,ncplx,wfn_gau(icoeff),ry,gau_a,n_gau,&
-                           lr%ns2,lr%d%n2,ml2,mu2,&
-                           wy(1,0,1,iterm),work,nw,pery) 
-                      n_gau=lz(i) 
-                      !print *,'z',ml3,mu3,lr%d%n3
-!                     call gauss_to_daub_k(hz,kz*hz,ncplx,1,ncplx,G%psiat(:,iexpo+ig-1),rz,gau_a,n_gau,&
-                           lr%ns3,lr%d%n3,ml3,mu3,&
-                           wz(1,0,1,iterm),work,nw,perz)
-                      iterm=iterm+1
---- 747,763 ----
-                      gau_a=G%xp(1,iexpo+ig-1)
-                      n_gau=lx(i)
-                      !print *,'x',gau_a,nterm,ncplx,kx,ky,kz,ml1,mu1,lr%d%n1
-!                     call gauss_to_daub_k(hx,kx*hx,ncplx,1,ncplx,fac_arr(i),rx,gau_a,gau_cut,n_gau,&
-                           lr%ns1,lr%d%n1,ml1,mu1,&
-                           wx(1,0,1,iterm),work,nw,perx) 
-                      n_gau=ly(i)
-                      !print *,'y',ml2,mu2,lr%d%n2
-!                     call gauss_to_daub_k(hy,ky*hy,ncplx,1,ncplx,wfn_gau(icoeff),ry,gau_a,gau_cut,n_gau,&
-                           lr%ns2,lr%d%n2,ml2,mu2,&
-                           wy(1,0,1,iterm),work,nw,pery) 
-                      n_gau=lz(i) 
-                      !print *,'z',ml3,mu3,lr%d%n3
-!                     call gauss_to_daub_k(hz,kz*hz,ncplx,1,ncplx,G%psiat(:,iexpo+ig-1),rz,gau_a,gau_cut,n_gau,&
-                           lr%ns3,lr%d%n3,ml3,mu3,&
-                           wz(1,0,1,iterm),work,nw,perz)
-                      iterm=iterm+1
diff --git a/sci-libs/bigdft-abi/files/bigdft-abi-1.0.4-0004.patch b/sci-libs/bigdft-abi/files/bigdft-abi-1.0.4-0004.patch
deleted file mode 100644
index e9af11a58..000000000
--- a/sci-libs/bigdft-abi/files/bigdft-abi-1.0.4-0004.patch
+++ /dev/null
@@ -1,20 +0,0 @@
-*** bigdft-abi-1.0.4/src/hpsiortho.f90	Wed Jan 30 10:10:56 2013
---- bigdft-patch/src/hpsiortho.f90	Tue Jun 11 09:49:22 2013
-***************
-*** 720,726 ****
-                 if(at%npspcode(1)==7) then
-                   call atom_projector_paw(ikpt,iat,0,istart_c,iproj,&
-                        nlpspd%nprojel,&
-!                       Lzd%Glr,Lzd%hgrids(1),Lzd%hgrids(2),Lzd%hgrids(3),rxyz(1,iat),at,orbs,&
-                        nlpspd%plr(iat),proj,nwarnings,proj_G(iatype))
-                 else
-                   call atom_projector(ikpt,iat,0,istart_c,iproj,&
---- 720,727 ----
-                 if(at%npspcode(1)==7) then
-                   call atom_projector_paw(ikpt,iat,0,istart_c,iproj,&
-                        nlpspd%nprojel,&
-!                       Lzd%Glr,Lzd%hgrids(1),Lzd%hgrids(2),Lzd%hgrids(3),&
-!                       paw%rpaw(iatype),rxyz(1,iat),at,orbs,&
-                        nlpspd%plr(iat),proj,nwarnings,proj_G(iatype))
-                 else
-                   call atom_projector(ikpt,iat,0,istart_c,iproj,&
diff --git a/sci-libs/bigdft-abi/files/bigdft-abi-1.0.4-0006.patch b/sci-libs/bigdft-abi/files/bigdft-abi-1.0.4-0006.patch
deleted file mode 100644
index 56a67fc66..000000000
--- a/sci-libs/bigdft-abi/files/bigdft-abi-1.0.4-0006.patch
+++ /dev/null
@@ -1,43 +0,0 @@
-diff -urN bigdft-abi-1.0.4.old/configure bigdft-abi-1.0.4.new/configure
---- bigdft-abi-1.0.4.old/configure	2012-10-05 15:10:27.000000000 +0200
-+++ bigdft-abi-1.0.4.new/configure	2013-06-11 16:51:00.000000000 +0200
-@@ -9185,15 +9185,15 @@
-   withlibabinit=no
- fi
- 
--    as_ac_File=`$as_echo "ac_cv_file_$ac_libabinit_dir/include/ab6_moldyn.$ax_fc_mod_ext" | $as_tr_sh`
--{ $as_echo "$as_me:${as_lineno-$LINENO}: checking for $ac_libabinit_dir/include/ab6_moldyn.$ax_fc_mod_ext" >&5
--$as_echo_n "checking for $ac_libabinit_dir/include/ab6_moldyn.$ax_fc_mod_ext... " >&6; }
-+    as_ac_File=`$as_echo "ac_cv_file_$ac_libabinit_dir/include/ab7_moldyn.$ax_fc_mod_ext" | $as_tr_sh`
-+{ $as_echo "$as_me:${as_lineno-$LINENO}: checking for $ac_libabinit_dir/include/ab7_moldyn.$ax_fc_mod_ext" >&5
-+$as_echo_n "checking for $ac_libabinit_dir/include/ab7_moldyn.$ax_fc_mod_ext... " >&6; }
- if eval \${$as_ac_File+:} false; then :
-   $as_echo_n "(cached) " >&6
- else
-   test "$cross_compiling" = yes &&
-   as_fn_error $? "cannot check for file existence when cross compiling" "$LINENO" 5
--if test -r "$ac_libabinit_dir/include/ab6_moldyn.$ax_fc_mod_ext"; then
-+if test -r "$ac_libabinit_dir/include/ab7_moldyn.$ax_fc_mod_ext"; then
-   eval "$as_ac_File=yes"
- else
-   eval "$as_ac_File=no"
-@@ -9208,15 +9208,15 @@
-   moldyn="no"
- fi
- 
--    as_ac_File=`$as_echo "ac_cv_file_$ac_libabinit_dir/include/ab6_symmetry.$ax_fc_mod_ext" | $as_tr_sh`
--{ $as_echo "$as_me:${as_lineno-$LINENO}: checking for $ac_libabinit_dir/include/ab6_symmetry.$ax_fc_mod_ext" >&5
--$as_echo_n "checking for $ac_libabinit_dir/include/ab6_symmetry.$ax_fc_mod_ext... " >&6; }
-+    as_ac_File=`$as_echo "ac_cv_file_$ac_libabinit_dir/include/ab7_symmetry.$ax_fc_mod_ext" | $as_tr_sh`
-+{ $as_echo "$as_me:${as_lineno-$LINENO}: checking for $ac_libabinit_dir/include/ab7_symmetry.$ax_fc_mod_ext" >&5
-+$as_echo_n "checking for $ac_libabinit_dir/include/ab7_symmetry.$ax_fc_mod_ext... " >&6; }
- if eval \${$as_ac_File+:} false; then :
-   $as_echo_n "(cached) " >&6
- else
-   test "$cross_compiling" = yes &&
-   as_fn_error $? "cannot check for file existence when cross compiling" "$LINENO" 5
--if test -r "$ac_libabinit_dir/include/ab6_symmetry.$ax_fc_mod_ext"; then
-+if test -r "$ac_libabinit_dir/include/ab7_symmetry.$ax_fc_mod_ext"; then
-   eval "$as_ac_File=yes"
- else
-   eval "$as_ac_File=no"
diff --git a/sci-libs/bigdft-abi/files/bigdft-abi-1.0.4-0007.patch b/sci-libs/bigdft-abi/files/bigdft-abi-1.0.4-0007.patch
deleted file mode 100644
index 8f871d8fd..000000000
--- a/sci-libs/bigdft-abi/files/bigdft-abi-1.0.4-0007.patch
+++ /dev/null
@@ -1,344 +0,0 @@
-diff -crB bigdft-abi-1.0.4/src/init/projectors.f90 bigdft-patch/src/init/projectors.f90
-*** bigdft-abi-1.0.4/src/init/projectors.f90	Thu Nov 29 11:09:02 2012
---- bigdft-patch/src/init/projectors.f90	Thu Jun  6 11:31:46 2013
-***************
-*** 383,394 ****
-  END SUBROUTINE fill_projectors
-  
-  subroutine atom_projector_paw(ikpt,iat,idir,istart_c,iproj,nprojel,&
-!      lr,hx,hy,hz,rxyz,at,orbs,plr,proj,nwarnings,proj_G)
-    use module_base
-    use module_types
-    implicit none
-    integer, intent(in) :: iat,idir,ikpt,nprojel
-!   real(gp), intent(in) :: hx,hy,hz
-    type(atoms_data), intent(in) :: at
-    type(orbitals_data), intent(in) :: orbs
-    type(locreg_descriptors), intent(in) :: plr
---- 383,394 ----
-  END SUBROUTINE fill_projectors
-  
-  subroutine atom_projector_paw(ikpt,iat,idir,istart_c,iproj,nprojel,&
-!      lr,hx,hy,hz,rpaw,rxyz,at,orbs,plr,proj,nwarnings,proj_G)
-    use module_base
-    use module_types
-    implicit none
-    integer, intent(in) :: iat,idir,ikpt,nprojel
-!   real(gp), intent(in) :: hx,hy,hz,rpaw
-    type(atoms_data), intent(in) :: at
-    type(orbitals_data), intent(in) :: orbs
-    type(locreg_descriptors), intent(in) :: plr
-***************
-*** 460,466 ****
-          !     plr%wfd%keyvglob,plr%wfd%keyglob,proj_tmp(1),nwarnings)
-          !END DEBUG
-          call projector_paw(at%geocode,at%atomnames(ityp),iat,idir,l,i,&
-!              proj_G%psiat(:,jj),proj_G%xp(:,jj),rxyz(1),lr,&
-               hx,hy,hz,kx,ky,kz,proj_G%ncplx,ncplx_k,&
-               mbvctr_c,mbvctr_f,mbseg_c,mbseg_f,&
-               plr%wfd%keyvglob,plr%wfd%keyglob,proj_tmp(1),nwarnings)
---- 460,466 ----
-          !     plr%wfd%keyvglob,plr%wfd%keyglob,proj_tmp(1),nwarnings)
-          !END DEBUG
-          call projector_paw(at%geocode,at%atomnames(ityp),iat,idir,l,i,&
-!              proj_G%psiat(:,jj),proj_G%xp(:,jj),rpaw,rxyz(1),lr,&
-               hx,hy,hz,kx,ky,kz,proj_G%ncplx,ncplx_k,&
-               mbvctr_c,mbvctr_f,mbseg_c,mbseg_f,&
-               plr%wfd%keyvglob,plr%wfd%keyglob,proj_tmp(1),nwarnings)
-***************
-*** 646,651 ****
---- 646,652 ----
-    integer :: istart_c,nterm,idir2
-    real(gp) :: fpi,factor,rx,ry,rz
-    real(dp) :: scpr
-+   real(gp) :: gau_cut !dummy here just for PAW
-    integer, dimension(3) :: nterm_arr
-    integer, dimension(nterm_max) :: lx,ly,lz
-    integer, dimension(3,nterm_max,3) :: lxyz_arr
-***************
-*** 709,715 ****
-       
-       call crtproj(geocode,nterm,lr,hx,hy,hz,kx,ky,kz,&
-            ncplx_g,ncplx,&
-!           gau_a,factors,rx,ry,rz,lx,ly,lz,&
-            mbvctr_c,mbvctr_f,mseg_c,mseg_f,keyv_p,keyg_p,proj(istart_c))
-  
-       ! testing
---- 710,716 ----
-       
-       call crtproj(geocode,nterm,lr,hx,hy,hz,kx,ky,kz,&
-            ncplx_g,ncplx,&
-!           gau_a,gau_cut,factors,rx,ry,rz,lx,ly,lz,&
-            mbvctr_c,mbvctr_f,mseg_c,mseg_f,keyv_p,keyg_p,proj(istart_c))
-  
-       ! testing
-***************
-*** 1055,1061 ****
-  end subroutine projector_paw_isf
-  
-  subroutine projector_paw(geocode,atomname,iat,idir,l,i,&
-!      factor,gau_a,rxyz,lr,&
-       hx,hy,hz,kx,ky,kz,ncplx_g,ncplx_k,&
-       mbvctr_c,mbvctr_f,mseg_c,mseg_f,keyv_p,keyg_p,proj,nwarnings)
-    use module_base
---- 1056,1062 ----
-  end subroutine projector_paw_isf
-  
-  subroutine projector_paw(geocode,atomname,iat,idir,l,i,&
-!      factor,gau_a,gau_cut,rxyz,lr,&
-       hx,hy,hz,kx,ky,kz,ncplx_g,ncplx_k,&
-       mbvctr_c,mbvctr_f,mseg_c,mseg_f,keyv_p,keyg_p,proj,nwarnings)
-    use module_base
-***************
-*** 1066,1072 ****
-    integer, intent(in) :: iat,idir,l,i,mbvctr_c,mbvctr_f,mseg_c,mseg_f
-    integer, intent(in) :: ncplx_k,ncplx_g
-    type(locreg_descriptors),intent(in) :: lr
-!   real(gp), intent(in) :: hx,hy,hz,kx,ky,kz
-    !integer, dimension(2,3), intent(in) :: nboxp_c,nboxp_f
-    integer, dimension(mseg_c+mseg_f), intent(in) :: keyv_p
-    integer, dimension(2,mseg_c+mseg_f), intent(in) :: keyg_p
---- 1067,1073 ----
-    integer, intent(in) :: iat,idir,l,i,mbvctr_c,mbvctr_f,mseg_c,mseg_f
-    integer, intent(in) :: ncplx_k,ncplx_g
-    type(locreg_descriptors),intent(in) :: lr
-!   real(gp), intent(in) :: hx,hy,hz,kx,ky,kz,gau_cut
-    !integer, dimension(2,3), intent(in) :: nboxp_c,nboxp_f
-    integer, dimension(mseg_c+mseg_f), intent(in) :: keyv_p
-    integer, dimension(2,mseg_c+mseg_f), intent(in) :: keyg_p
-***************
-*** 1131,1137 ****
-  
-       call crtproj(geocode,nterm,lr,hx,hy,hz,kx,ky,kz,&
-            ncplx_g,ncplx_k,&
-!           gau_a,factors(1:ncplx_g,1:nterm),&
-            rx,ry,rz,lx(1:nterm),ly(1:nterm),lz(1:nterm),&
-            mbvctr_c,mbvctr_f,mseg_c,mseg_f,keyv_p,keyg_p,&
-            proj(istart_c))
---- 1132,1138 ----
-  
-       call crtproj(geocode,nterm,lr,hx,hy,hz,kx,ky,kz,&
-            ncplx_g,ncplx_k,&
-!           gau_a,gau_cut,factors(1:ncplx_g,1:nterm),&
-            rx,ry,rz,lx(1:nterm),ly(1:nterm),lz(1:nterm),&
-            mbvctr_c,mbvctr_f,mseg_c,mseg_f,keyv_p,keyg_p,&
-            proj(istart_c))
-***************
-*** 1248,1254 ****
-  !!   in the arrays proj_c, proj_f
-  subroutine crtproj(geocode,nterm,lr, & 
-       hx,hy,hz,kx,ky,kz,ncplx_g,ncplx_k,&
-!      gau_a,fac_arr,rx,ry,rz,lx,ly,lz, & 
-       mvctr_c,mvctr_f,mseg_c,mseg_f,keyv_p,keyg_p,proj)
-    use module_base
-    use module_types
---- 1249,1255 ----
-  !!   in the arrays proj_c, proj_f
-  subroutine crtproj(geocode,nterm,lr, & 
-       hx,hy,hz,kx,ky,kz,ncplx_g,ncplx_k,&
-!      gau_a,gau_cut,fac_arr,rx,ry,rz,lx,ly,lz, & 
-       mvctr_c,mvctr_f,mseg_c,mseg_f,keyv_p,keyg_p,proj)
-    use module_base
-    use module_types
-***************
-*** 1256,1262 ****
-    character(len=1), intent(in) :: geocode
-    integer, intent(in) :: nterm,mvctr_c,mvctr_f,mseg_c,mseg_f
-    integer, intent(in) :: ncplx_g,ncplx_k
-!   real(gp), intent(in) :: hx,hy,hz,rx,ry,rz,kx,ky,kz
-    integer, dimension(nterm), intent(in) :: lx,ly,lz
-    real(gp), dimension(ncplx_g,nterm), intent(in) :: fac_arr
-    real(gp), dimension(ncplx_g),intent(in):: gau_a
---- 1257,1263 ----
-    character(len=1), intent(in) :: geocode
-    integer, intent(in) :: nterm,mvctr_c,mvctr_f,mseg_c,mseg_f
-    integer, intent(in) :: ncplx_g,ncplx_k
-!   real(gp), intent(in) :: hx,hy,hz,rx,ry,rz,kx,ky,kz,gau_cut
-    integer, dimension(nterm), intent(in) :: lx,ly,lz
-    real(gp), dimension(ncplx_g,nterm), intent(in) :: fac_arr
-    real(gp), dimension(ncplx_g),intent(in):: gau_a
-***************
-*** 1313,1327 ****
-  
-       factor(:)=fac_arr(:,iterm)
-       n_gau=lx(iterm) 
-!      call gauss_to_daub_k(hx,kx*hx,ncplx_w,ncplx_g,ncplx_k,factor,rx,gau_a,n_gau,ns1,n1,ml1,mu1,&
-            wprojx(1,0,1,iterm),work,nw,perx) 
-       
-       n_gau=ly(iterm) 
-!      call gauss_to_daub_k(hy,ky*hy,ncplx_w,ncplx_g,ncplx_k,1.d0,ry,gau_a,n_gau,ns2,n2,ml2,mu2,&
-            wprojy(1,0,1,iterm),work,nw,pery) 
-  
-       n_gau=lz(iterm) 
-!      call gauss_to_daub_k(hz,kz*hz,ncplx_w,ncplx_g,ncplx_k,1.d0,rz,gau_a,n_gau,ns3,n3,ml3,mu3,&
-            wprojz(1,0,1,iterm),work,nw,perz)
-    end do
-    !the filling of the projector should be different if ncplx_k==1 or 2
---- 1314,1328 ----
-  
-       factor(:)=fac_arr(:,iterm)
-       n_gau=lx(iterm) 
-!      call gauss_to_daub_k(hx,kx*hx,ncplx_w,ncplx_g,ncplx_k,factor,rx,gau_a,gau_cut,n_gau,ns1,n1,ml1,mu1,&
-            wprojx(1,0,1,iterm),work,nw,perx) 
-       
-       n_gau=ly(iterm) 
-!      call gauss_to_daub_k(hy,ky*hy,ncplx_w,ncplx_g,ncplx_k,1.d0,ry,gau_a,gau_cut,n_gau,ns2,n2,ml2,mu2,&
-            wprojy(1,0,1,iterm),work,nw,pery) 
-  
-       n_gau=lz(iterm) 
-!      call gauss_to_daub_k(hz,kz*hz,ncplx_w,ncplx_g,ncplx_k,1.d0,rz,gau_a,gau_cut,n_gau,ns3,n3,ml3,mu3,&
-            wprojz(1,0,1,iterm),work,nw,perz)
-    end do
-    !the filling of the projector should be different if ncplx_k==1 or 2
-diff -crB bigdft-abi-1.0.4/src/modules/types.f90 bigdft-patch/src/modules/types.f90
-*** bigdft-abi-1.0.4/src/modules/types.f90	Thu Jan  3 10:18:08 2013
---- bigdft-patch/src/modules/types.f90	Thu Jun  6 11:27:48 2013
-***************
-*** 1119,1124 ****
---- 1119,1125 ----
-      type(cprj_objects),dimension(:,:),allocatable :: cprj
-      real(wp),dimension(:),pointer :: spsi
-      real(wp),dimension(:,:),pointer :: sij
-+     real(dp),dimension(:),pointer :: rpaw
-    end type paw_objects
-  
-  contains
-***************
-*** 2090,2095 ****
---- 2091,2097 ----
-    nullify(paw%indlmn) 
-    nullify(paw%spsi) 
-    nullify(paw%sij) 
-+   nullify(paw%rpaw)
-  
-    if(present(rholoc)) then
-     nullify(rholoc%msz)
-diff -crB bigdft-abi-1.0.4/src/wavelib/gauss_to_daub.f90 bigdft-patch/src/wavelib/gauss_to_daub.f90
-*** bigdft-abi-1.0.4/src/wavelib/gauss_to_daub.f90	Mon Jul  9 16:43:33 2012
---- bigdft-patch/src/wavelib/gauss_to_daub.f90	Thu Jun  6 13:01:01 2013
-***************
-*** 448,454 ****
-  !!  In this version, we dephase the projector to wrt the center of the gaussian
-  !!  this should not have an impact on the results since the operator is unchanged
-  subroutine gauss_to_daub_k(hgrid,kval,ncplx_w,ncplx_g,ncplx_k,&
-!      factor,gau_cen,gau_a,n_gau,&!no err, errsuc
-       nstart,nmax,n_left,n_right,c,& 
-       ww,nwork,periodic)      !added work arrays ww with dimension nwork
-    use module_base
---- 448,454 ----
-  !!  In this version, we dephase the projector to wrt the center of the gaussian
-  !!  this should not have an impact on the results since the operator is unchanged
-  subroutine gauss_to_daub_k(hgrid,kval,ncplx_w,ncplx_g,ncplx_k,&
-!      factor,gau_cen,gau_a,gau_cut,n_gau,&!no err, errsuc
-       nstart,nmax,n_left,n_right,c,& 
-       ww,nwork,periodic)      !added work arrays ww with dimension nwork
-    use module_base
-***************
-*** 458,464 ****
-    integer, intent(in) :: ncplx_w !size of the ww matrix
-    integer, intent(in) :: ncplx_g !1 or 2 for simple or complex gaussians, respectively.
-    integer, intent(in) :: ncplx_k !use 2 for k-points.
-!   real(gp), intent(in) :: hgrid,gau_cen,kval
-    real(gp),dimension(ncplx_g),intent(in)::factor,gau_a
-    real(wp), dimension(0:nwork,2,ncplx_w), intent(inout) :: ww 
-    integer, intent(out) :: n_left,n_right
---- 458,464 ----
-    integer, intent(in) :: ncplx_w !size of the ww matrix
-    integer, intent(in) :: ncplx_g !1 or 2 for simple or complex gaussians, respectively.
-    integer, intent(in) :: ncplx_k !use 2 for k-points.
-!   real(gp), intent(in) :: hgrid,gau_cen,kval,gau_cut
-    real(gp),dimension(ncplx_g),intent(in)::factor,gau_a
-    real(wp), dimension(0:nwork,2,ncplx_w), intent(inout) :: ww 
-    integer, intent(out) :: n_left,n_right
-***************
-*** 467,473 ****
-    character(len=*), parameter :: subname='gauss_to_daub_k'
-    integer :: i_all,i_stat
-    integer :: rightx,leftx,right_t,i0,i,k,length,j,icplx
-!   real(gp) :: a1,a2,z0,h,x,r,coeff,r2,rk
-    real(gp) :: fac(ncplx_g)
-    real(wp) :: func,cval,sval,cval2,sval2
-    real(wp), dimension(:,:,:), allocatable :: cc
---- 467,473 ----
-    character(len=*), parameter :: subname='gauss_to_daub_k'
-    integer :: i_all,i_stat
-    integer :: rightx,leftx,right_t,i0,i,k,length,j,icplx
-!   real(gp) :: a1,a2,z0,h,x,r,coeff,r2,rk,gcut
-    real(gp) :: fac(ncplx_g)
-    real(wp) :: func,cval,sval,cval2,sval2
-    real(wp), dimension(:,:,:), allocatable :: cc
-***************
-*** 487,492 ****
---- 487,493 ----
-    end if
-    i0=nint(gau_cen/hgrid) ! the array is centered at i0
-    z0=gau_cen/hgrid-real(i0,gp)
-+   gcut=gau_cut/hgrid
-    h=.125_gp*.5_gp
-  
-    !calculate the array sizes;
-***************
-*** 655,681 ****
-              do i=leftx,rightx
-                 x=real(i-i0*16,gp)*h
-                 r=x-z0
-!                r2=r*r
-!                cval=real(cos(a2*r2),wp)
-!                sval=real(sin(a2*r2),wp)
-!                r2=0.5_gp*r2/(a1**2)
-!                func=real(dexp(-real(r2,kind=8)),wp)
-!                ww(i-leftx,1,1)=func*cval
-!                ww(i-leftx,1,2)=func*sval
-              enddo
-           else
-              do i=leftx,rightx
-                 x=real(i-i0*16,gp)*h
-                 r=x-z0
-!                r2=r*r
-!                cval=real(cos(a2*r2),wp)
-!                sval=real(sin(a2*r2),wp)
-!                coeff=r**n_gau
-!                r2=0.5_gp*r2/(a1**2)
-!                func=real(dexp(-real(r2,kind=8)),wp)
-!                func=real(coeff,wp)*func
-!                ww(i-leftx,1,1)=func*cval
-!                ww(i-leftx,1,2)=func*sval
-              enddo
-           end if
-  
---- 656,690 ----
-              do i=leftx,rightx
-                 x=real(i-i0*16,gp)*h
-                 r=x-z0
-!                if(abs(r)-gcut < 1e-8) then
-!                  r2=r*r
-!                  cval=real(cos(a2*r2),wp)
-!                  sval=real(sin(a2*r2),wp)
-!                  r2=0.5_gp*r2/(a1**2)
-!                  func=real(dexp(-real(r2,kind=8)),wp)
-!                  ww(i-leftx,1,1)=func*cval
-!                  ww(i-leftx,1,2)=func*sval
-!                else
-!                  ww(i-leftx,1,:)=0.0_wp
-!                end if
-              enddo
-           else
-              do i=leftx,rightx
-                 x=real(i-i0*16,gp)*h
-                 r=x-z0
-!                if( abs(r)-gcut < 1e-8 ) then
-!                  r2=r*r
-!                  cval=real(cos(a2*r2),wp)
-!                  sval=real(sin(a2*r2),wp)
-!                  coeff=r**n_gau
-!                  r2=0.5_gp*r2/(a1**2)
-!                  func=real(dexp(-real(r2,kind=8)),wp)
-!                  func=real(coeff,wp)*func
-!                  ww(i-leftx,1,1)=func*cval
-!                  ww(i-leftx,1,2)=func*sval
-!                else
-!                  ww(i-leftx,1,:)=0.0_wp
-!                end if
-              enddo
-           end if
-  
diff --git a/sci-libs/bigdft-abi/files/bigdft-abi-1.0.4-CUDA_gethostname.patch b/sci-libs/bigdft-abi/files/bigdft-abi-1.0.4-CUDA_gethostname.patch
deleted file mode 100644
index 04c45b4d7..000000000
--- a/sci-libs/bigdft-abi/files/bigdft-abi-1.0.4-CUDA_gethostname.patch
+++ /dev/null
@@ -1,22 +0,0 @@
-diff -Naurp bigdft-abi-1.0.4-orig/S_GPU/src/class_utils.h bigdft-abi-1.0.4/S_GPU/src/class_utils.h
---- bigdft-abi-1.0.4-orig/S_GPU/src/class_utils.h	2012-07-09 14:43:33.000000000 +0000
-+++ bigdft-abi-1.0.4/S_GPU/src/class_utils.h	2013-06-27 09:52:17.000000000 +0000
-@@ -32,6 +32,7 @@
- #include <config.h>
- #endif
- 
-+#include <unistd.h>
- #include <sstream>
- 
- class deleter
-diff -Naurp bigdft-abi-1.0.4-orig/src/CUDA/check_cuda.h bigdft-abi-1.0.4/src/CUDA/check_cuda.h
---- bigdft-abi-1.0.4-orig/src/CUDA/check_cuda.h	2012-07-09 14:43:33.000000000 +0000
-+++ bigdft-abi-1.0.4/src/CUDA/check_cuda.h	2013-06-27 09:51:50.000000000 +0000
-@@ -1,6 +1,7 @@
- #ifndef __checkcuda__
- #define __checkcuda__
- 
-+#include <unistd.h>
- #include <string>
- #include <sstream>
- 
diff --git a/sci-libs/bigdft-abi/metadata.xml b/sci-libs/bigdft-abi/metadata.xml
deleted file mode 100644
index b5efea318..000000000
--- a/sci-libs/bigdft-abi/metadata.xml
+++ /dev/null
@@ -1,29 +0,0 @@
-<?xml version="1.0" encoding="UTF-8"?>
-<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
-<pkgmetadata>
-	<maintainer type="project">
-		<email>sci-physics@gentoo.org</email>
-		<name>Gentoo Physics Project</name>
-	</maintainer>
-	<longdescription lang="en">
-BigDFT is a package whose main program allows one to find the total energy, 
-charge density and electronic structure of systems made of electrons and nuclei 
-(molecules and periodic solids) within Density Functional Theory (DFT), using 
-pseudopotentials and a wavelets basis. BigDFT-ABI is its fork by ABINIT developers
-to serve as a library for sci-physics/abinit.
-</longdescription>
-	<use>
-		<flag name="cuda">Enable support for nVidia CUDA</flag>
-		<flag name="etsf_io">
-Enable support for reading and writing the European Theoretical
-Spectroscopy facility (ETSF) file format
-</flag>
-		<flag name="glib">
-Compile with GLib Object System support
-</flag>
-		<flag name="opencl">Enable support for OpenCL GPU acceleration</flag>
-		<flag name="scalapack">
-Use ScaLAPACK, a subset of LAPACK routines redesigned for heterogenous computing
-</flag>
-	</use>
-</pkgmetadata>
diff --git a/sci-libs/blas-reference/Manifest b/sci-libs/blas-reference/Manifest
deleted file mode 100644
index b2a69b1f8..000000000
--- a/sci-libs/blas-reference/Manifest
+++ /dev/null
@@ -1,2 +0,0 @@
-DIST lapack-3.7.0.tgz 7359812 BLAKE2B 20aa42e22d8c920d1360afe41ceec7b36f6cd5fbe43ca9d7848ef7cc45a64a0314cb1321941c1a7c03654f41e28ec805445882ded0ca0ea07674e70b66cba6b5 SHA512 e4f4c7d0ba8a096eeb813160c6dbcdd535647df6b2ad5beac9181908158956b31d1a9554ec9b9836fd44fe7404c1f377b297cbb20d744f20d70e357fd246c91b
-DIST lapack-3.8.0.tar.gz 7426094 BLAKE2B 27cd75eea498250382b2df6f5d7dc95fdee8d37b1a0faba5296ca0145ec40a1165a4ecc727aa1647086be6783b50cf475f79cea0f30f541da789051db99b2f37 SHA512 17786cb7306fccdc9b4a242de7f64fc261ebe6a10b6ec55f519deb4cb673cb137e8742aa5698fd2dc52f1cd56d3bd116af3f593a01dcf6770c4dcc86c50b2a7f
diff --git a/sci-libs/blas-reference/blas-reference-20161223-r100.ebuild b/sci-libs/blas-reference/blas-reference-20161223-r100.ebuild
deleted file mode 100644
index 596d49844..000000000
--- a/sci-libs/blas-reference/blas-reference-20161223-r100.ebuild
+++ /dev/null
@@ -1,110 +0,0 @@
-# Copyright 1999-2017 Gentoo Foundation
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=6
-
-PYTHON_COMPAT=( python2_7 )
-
-NUMERIC_MODULE_NAME="refblas"
-
-inherit alternatives-2 cmake-utils eutils fortran-2 numeric-int64-multibuild python-any-r1 toolchain-funcs
-
-LPN=lapack
-LPV=3.7.0
-
-DESCRIPTION="Reference implementation of BLAS"
-HOMEPAGE="http://www.netlib.org/lapack/"
-SRC_URI="http://www.netlib.org/${LPN}/${LPN}-${LPV}.tgz"
-
-LICENSE="BSD"
-SLOT="0/${LPV}"
-KEYWORDS="~amd64 ~x86 ~amd64-linux ~x86-linux"
-IUSE="static-libs test"
-
-REQUIRED_USE="test? ( ${PYTHON_REQUIRED_USE} )"
-
-RDEPEND=""
-DEPEND="${RDEPEND}
-	test? ( ${PYTHON_DEPS} )
-	virtual/pkgconfig"
-
-S="${WORKDIR}/${LPN}-${LPV}"
-PATCHES=( "${FILESDIR}/lapack-reference-${LPV}-fix-build-system.patch" )
-
-src_prepare() {
-	default
-
-	# rename library to avoid collision with other blas implementations
-	# ${LIBNAME} and ${PROFNAME} are not defined here, they are in single
-	# quotes in the following seds.  They are later set by defining cmake
-	# variables with -DPROFNAME etc in src_configure
-	sed -i \
-		-e 's:\([^xc]\)blas:\1${LIBNAME}:g' \
-		-e '/PROPERTIES/s:blas:${LIBNAME}:g' \
-		CMakeLists.txt \
-		BLAS/SRC/CMakeLists.txt || die
-	sed -i \
-		-e '/Name: /s:blas:@PROFNAME@:' \
-		-e 's:-lblas:-l@LIBNAME@:g' \
-		 BLAS/blas.pc.in || die
-	sed -i \
-		-e 's:blas):${LIBNAME}):' \
-		BLAS/TESTING/CMakeLists.txt || die
-	sed -i \
-		-e 's:BINARY_DIR}/blas:BINARY_DIR}/${PROFNAME}:' \
-		BLAS/CMakeLists.txt || die
-}
-
-src_configure() {
-	blas_configure() {
-		local FCFLAGS="${FCFLAGS}"
-		append-fflags $($(tc-getPKG_CONFIG) --cflags ${blas_profname})
-		append-fflags $(get_abi_CFLAGS)
-		append-fflags $(numeric-int64_get_fortran_int64_abi_fflags)
-
-		local profname=$(numeric-int64_get_module_name)
-		local libname="${profname//-/_}"
-
-		local mycmakeargs=(
-			-Wno-dev
-			-DPROFNAME="${profname}"
-			-DLIBNAME="${libname}"
-			-DUSE_OPTIMIZED_BLAS=OFF
-			-DCMAKE_Fortran_FLAGS="${FCFLAGS}"
-			-DLAPACK_PKGCONFIG_FFLAGS="$(numeric-int64_get_fortran_int64_abi_fflags)"
-			-DBUILD_TESTING="$(usex test)"
-		)
-		if $(numeric-int64_is_static_build); then
-			mycmakeargs+=(
-				-DBUILD_SHARED_LIBS=OFF
-				-DBUILD_STATIC_LIBS=ON
-			)
-		else
-			mycmakeargs+=(
-				-DBUILD_SHARED_LIBS=ON
-				-DBUILD_STATIC_LIBS=OFF
-			)
-		fi
-		cmake-utils_src_configure
-	}
-	numeric-int64-multibuild_foreach_all_abi_variants blas_configure
-}
-
-src_compile() {
-	local each target_dirs=( BLAS )
-	use test && target_dirs+=( TESTING )
-	for each in ${target_dirs[@]}; do
-		numeric-int64-multibuild_foreach_all_abi_variants \
-			cmake-utils_src_compile -C ${each}
-	done
-
-}
-
-src_test() {
-	numeric-int64-multibuild_foreach_all_abi_variants cmake-utils_src_test
-}
-
-src_install() {
-	numeric-int64-multibuild_foreach_all_abi_variants cmake-utils_src_install -C BLAS
-	numeric-int64-multibuild_install_alternative blas reference
-}
diff --git a/sci-libs/blas-reference/blas-reference-20171112-r100.ebuild b/sci-libs/blas-reference/blas-reference-20171112-r100.ebuild
deleted file mode 100644
index 72bcfd5f3..000000000
--- a/sci-libs/blas-reference/blas-reference-20171112-r100.ebuild
+++ /dev/null
@@ -1,109 +0,0 @@
-# Copyright 1999-2018 Gentoo Foundation
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=6
-
-PYTHON_COMPAT=( python2_7 )
-
-NUMERIC_MODULE_NAME="refblas"
-
-inherit alternatives-2 cmake-utils eutils fortran-2 numeric-int64-multibuild python-any-r1 toolchain-funcs
-
-LPN=lapack
-LPV=3.8.0
-
-DESCRIPTION="Reference implementation of BLAS"
-HOMEPAGE="http://www.netlib.org/lapack/"
-SRC_URI="http://www.netlib.org/${LPN}/${LPN}-${LPV}.tar.gz"
-
-LICENSE="BSD"
-SLOT="0/${LPV}"
-KEYWORDS="~amd64 ~x86 ~amd64-linux ~x86-linux"
-IUSE="static-libs test"
-
-REQUIRED_USE="test? ( ${PYTHON_REQUIRED_USE} )"
-
-RDEPEND=""
-DEPEND="${RDEPEND}
-	test? ( ${PYTHON_DEPS} )
-	virtual/pkgconfig"
-
-S="${WORKDIR}/${LPN}-${LPV}"
-
-src_prepare() {
-	cmake-utils_src_prepare
-
-	# rename library to avoid collision with other blas implementations
-	# ${LIBNAME} and ${PROFNAME} are not defined here, they are in single
-	# quotes in the following seds.  They are later set by defining cmake
-	# variables with -DPROFNAME etc in src_configure
-	sed -i \
-		-e 's:\([^xc]\)blas:\1${LIBNAME}:g' \
-		-e '/PROPERTIES/s:blas:${LIBNAME}:g' \
-		CMakeLists.txt \
-		BLAS/SRC/CMakeLists.txt || die
-	sed -i \
-		-e '/Name: /s:blas:@PROFNAME@:' \
-		-e 's:-lblas:-l@LIBNAME@:g' \
-		 BLAS/blas.pc.in || die
-	sed -i \
-		-e 's:blas):${LIBNAME}):' \
-		BLAS/TESTING/CMakeLists.txt || die
-	sed -i \
-		-e 's:BINARY_DIR}/blas:BINARY_DIR}/${PROFNAME}:' \
-		BLAS/CMakeLists.txt || die
-}
-
-src_configure() {
-	blas_configure() {
-		local FCFLAGS="${FCFLAGS}"
-		append-fflags $($(tc-getPKG_CONFIG) --cflags ${blas_profname})
-		append-fflags $(get_abi_CFLAGS)
-		append-fflags $(numeric-int64_get_fortran_int64_abi_fflags)
-
-		local profname=$(numeric-int64_get_module_name)
-		local libname="${profname//-/_}"
-
-		local mycmakeargs=(
-			-Wno-dev
-			-DPROFNAME="${profname}"
-			-DLIBNAME="${libname}"
-			-DUSE_OPTIMIZED_BLAS=OFF
-			-DCMAKE_Fortran_FLAGS="${FCFLAGS}"
-			-DLAPACK_PKGCONFIG_FFLAGS="$(numeric-int64_get_fortran_int64_abi_fflags)"
-			-DBUILD_TESTING="$(usex test)"
-		)
-		if $(numeric-int64_is_static_build); then
-			mycmakeargs+=(
-				-DBUILD_SHARED_LIBS=OFF
-				-DBUILD_STATIC_LIBS=ON
-			)
-		else
-			mycmakeargs+=(
-				-DBUILD_SHARED_LIBS=ON
-				-DBUILD_STATIC_LIBS=OFF
-			)
-		fi
-		cmake-utils_src_configure
-	}
-	numeric-int64-multibuild_foreach_all_abi_variants blas_configure
-}
-
-src_compile() {
-	local each target_dirs=( BLAS )
-	use test && target_dirs+=( TESTING )
-	for each in ${target_dirs[@]}; do
-		numeric-int64-multibuild_foreach_all_abi_variants \
-			cmake-utils_src_compile -C ${each}
-	done
-
-}
-
-src_test() {
-	numeric-int64-multibuild_foreach_all_abi_variants cmake-utils_src_test
-}
-
-src_install() {
-	numeric-int64-multibuild_foreach_all_abi_variants cmake-utils_src_install -C BLAS
-	numeric-int64-multibuild_install_alternative blas reference
-}
diff --git a/sci-libs/blas-reference/blas-reference-99999999.ebuild b/sci-libs/blas-reference/blas-reference-99999999.ebuild
deleted file mode 100644
index 71b81ca97..000000000
--- a/sci-libs/blas-reference/blas-reference-99999999.ebuild
+++ /dev/null
@@ -1,108 +0,0 @@
-# Copyright 1999-2018 Gentoo Foundation
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=6
-
-PYTHON_COMPAT=( python2_7 )
-
-NUMERIC_MODULE_NAME="refblas"
-
-inherit alternatives-2 cmake-utils fortran-2 numeric-int64-multibuild python-any-r1 toolchain-funcs subversion
-
-LPN=lapack
-LPV=3.8.0
-
-DESCRIPTION="Reference implementation of BLAS"
-HOMEPAGE="http://www.netlib.org/lapack/"
-ESVN_REPO_URI="https://icl.cs.utk.edu/svn/lapack-dev/${LPN}/trunk"
-
-LICENSE="BSD"
-SLOT="0/${LPV}"
-KEYWORDS=""
-IUSE="static-libs test"
-
-REQUIRED_USE="test? ( ${PYTHON_REQUIRED_USE} )"
-
-RDEPEND=""
-DEPEND="${RDEPEND}
-	test? ( ${PYTHON_DEPS} )
-	virtual/pkgconfig"
-
-S="${WORKDIR}/${LPN}-${LPV}"
-
-src_prepare() {
-	cmake-utils_src_prepare
-	# rename library to avoid collision with other blas implementations
-	# ${LIBNAME} and ${PROFNAME} are not defined here, they are in single
-	# quotes in the following seds.  They are later set by defining cmake
-	# variables with -DPROFNAME etc in src_configure
-	sed -i \
-		-e 's:\([^xc]\)blas:\1${LIBNAME}:g' \
-		-e '/PROPERTIES/s:blas:${LIBNAME}:g' \
-		CMakeLists.txt \
-		BLAS/SRC/CMakeLists.txt || die
-	sed -i \
-		-e '/Name: /s:blas:${PROFNAME}:' \
-		-e 's:-lblas:-l${LIBNAME}:g' \
-		 BLAS/blas.pc.in || die
-	sed -i \
-		-e 's:blas):${LIBNAME}):' \
-		BLAS/TESTING/CMakeLists.txt || die
-	sed -i \
-		-e 's:BINARY_DIR}/blas:BINARY_DIR}/${PROFNAME}:' \
-		BLAS/CMakeLists.txt || die
-}
-
-src_configure() {
-	blas_configure() {
-		local FCFLAGS="${FCFLAGS}"
-		append-fflags $($(tc-getPKG_CONFIG) --cflags ${blas_profname})
-		append-fflags $(get_abi_CFLAGS)
-		append-fflags $(numeric-int64_get_fortran_int64_abi_fflags)
-
-		local profname=$(numeric-int64_get_module_name)
-		local libname="${profname//-/_}"
-
-		local mycmakeargs=(
-			-Wno-dev
-			-DPROFNAME="${profname}"
-			-DLIBNAME="${libname}"
-			-DUSE_OPTIMIZED_BLAS=OFF
-			-DCMAKE_Fortran_FLAGS="${FCFLAGS}"
-			-DLAPACK_PKGCONFIG_FFLAGS="$(numeric-int64_get_fortran_int64_abi_fflags)"
-			$(cmake-utils_use_build test TESTING)
-		)
-		if $(numeric-int64_is_static_build); then
-			mycmakeargs+=(
-				-DBUILD_SHARED_LIBS=OFF
-				-DBUILD_STATIC_LIBS=ON
-			)
-		else
-			mycmakeargs+=(
-				-DBUILD_SHARED_LIBS=ON
-				-DBUILD_STATIC_LIBS=OFF
-			)
-		fi
-		cmake-utils_src_configure
-	}
-	numeric-int64-multibuild_foreach_all_abi_variants blas_configure
-}
-
-src_compile() {
-	local each target_dirs=( BLAS )
-	use test && target_dirs+=( TESTING )
-	for each in ${target_dirs[@]}; do
-		numeric-int64-multibuild_foreach_all_abi_variants \
-			cmake-utils_src_compile -C ${each}
-	done
-
-}
-
-src_test() {
-	numeric-int64-multibuild_foreach_all_abi_variants cmake-utils_src_test
-}
-
-src_install() {
-	numeric-int64-multibuild_foreach_all_abi_variants cmake-utils_src_install -C BLAS
-	numeric-int64-multibuild_install_alternative blas reference
-}
diff --git a/sci-libs/blas-reference/files/lapack-fix-build-system.patch b/sci-libs/blas-reference/files/lapack-fix-build-system.patch
deleted file mode 100644
index 8661709d3..000000000
--- a/sci-libs/blas-reference/files/lapack-fix-build-system.patch
+++ /dev/null
@@ -1,92 +0,0 @@
---- lapack-3.6.0/BLAS/blas.pc.in
-+++ lapack-3.6.0/BLAS/blas.pc.in
-@@ -1,5 +1,7 @@
--prefix=@prefix@
--libdir=@libdir@
-+prefix=@CMAKE_INSTALL_PREFIX@
-+exec_prefix=${prefix}
-+libdir=${exec_prefix}/@CMAKE_INSTALL_LIBDIR@
-+includedir=${prefix}/include
- 
- Name: blas
- Description: Basic Linear Algebra Subprograms F77 reference implementations
---- lapack-3.6.0/BLAS/CMakeLists.txt
-+++ lapack-3.6.0/BLAS/CMakeLists.txt
-@@ -2,7 +2,7 @@
- if(BUILD_TESTING)
- add_subdirectory(TESTING)
- endif(BUILD_TESTING)
--configure_file(${CMAKE_CURRENT_SOURCE_DIR}/blas.pc.in ${CMAKE_CURRENT_BINARY_DIR}/blas.pc)
-+configure_file(${CMAKE_CURRENT_SOURCE_DIR}/blas.pc.in ${CMAKE_CURRENT_BINARY_DIR}/blas.pc @ONLY)
- install(FILES
-   ${CMAKE_CURRENT_BINARY_DIR}/blas.pc
-   DESTINATION ${PKG_CONFIG_DIR}
---- lapack-3.6.0/CBLAS/cblas.pc.in
-+++ lapack-3.6.0/CBLAS/cblas.pc.in
-@@ -1,5 +1,7 @@
--prefix=@prefix@
--libdir=@libdir@
-+prefix=@CMAKE_INSTALL_PREFIX@
-+exec_prefix=${prefix}
-+libdir=${exec_prefix}/@CMAKE_INSTALL_LIBDIR@
-+includedir=${prefix}/include
- 
- Name: lapacke
- Description: C Standard Interface to BLAS Linear Algebra PACKage
---- lapack-3.6.0/CBLAS/CMakeLists.txt
-+++ lapack-3.6.0/CBLAS/CMakeLists.txt
-@@ -71,7 +71,7 @@
-   ${LAPACK_BINARY_DIR}/cblas-config.cmake @ONLY)
- 
- 
--configure_file(${CMAKE_CURRENT_SOURCE_DIR}/cblas.pc.in ${CMAKE_CURRENT_BINARY_DIR}/cblas.pc)
-+configure_file(${CMAKE_CURRENT_SOURCE_DIR}/cblas.pc.in ${CMAKE_CURRENT_BINARY_DIR}/cblas.pc @ONLY)
-   install(FILES
-   ${CMAKE_CURRENT_BINARY_DIR}/cblas.pc
-   DESTINATION ${PKG_CONFIG_DIR}
---- lapack-3.6.0/CMakeLists.txt
-+++ lapack-3.6.0/CMakeLists.txt
-@@ -333,7 +333,7 @@
-   ${LAPACK_BINARY_DIR}/lapack-config.cmake @ONLY)
- 
- 
--configure_file(${CMAKE_CURRENT_SOURCE_DIR}/lapack.pc.in ${CMAKE_CURRENT_BINARY_DIR}/lapack.pc)
-+configure_file(${CMAKE_CURRENT_SOURCE_DIR}/lapack.pc.in ${CMAKE_CURRENT_BINARY_DIR}/lapack.pc @ONLY)
-   install(FILES
-   ${CMAKE_CURRENT_BINARY_DIR}/lapack.pc
-   DESTINATION ${PKG_CONFIG_DIR}
---- lapack-3.6.0/LAPACKE/CMakeLists.txt
-+++ lapack-3.6.0/LAPACKE/CMakeLists.txt
-@@ -65,7 +65,7 @@
- endif(BUILD_TESTING)
- 
- 
--configure_file(${CMAKE_CURRENT_SOURCE_DIR}/lapacke.pc.in ${CMAKE_CURRENT_BINARY_DIR}/lapacke.pc)
-+configure_file(${CMAKE_CURRENT_SOURCE_DIR}/lapacke.pc.in ${CMAKE_CURRENT_BINARY_DIR}/lapacke.pc @ONLY)
-  install(FILES
-   ${CMAKE_CURRENT_BINARY_DIR}/lapacke.pc
-   DESTINATION ${PKG_CONFIG_DIR}
---- lapack-3.6.0/LAPACKE/lapacke.pc.in
-+++ lapack-3.6.0/LAPACKE/lapacke.pc.in
-@@ -1,5 +1,7 @@
--prefix=@prefix@
--libdir=@libdir@
-+prefix=@CMAKE_INSTALL_PREFIX@
-+exec_prefix=${prefix}
-+libdir=${exec_prefix}/@CMAKE_INSTALL_LIBDIR@
-+includedir=${prefix}/include
- 
- Name: lapacke
- Description: C Standard Interface to LAPACK Linear Algebra PACKage
---- lapack-3.6.0/lapack.pc.in
-+++ lapack-3.6.0/lapack.pc.in
-@@ -1,5 +1,7 @@
--prefix=@prefix@
--libdir=@libdir@
-+prefix=@CMAKE_INSTALL_PREFIX@
-+exec_prefix=${prefix}
-+libdir=${exec_prefix}/@CMAKE_INSTALL_LIBDIR@
-+includedir=${prefix}/include
- 
- Name: lapack
- Description: FORTRAN reference implementation of LAPACK Linear Algebra PACKage
diff --git a/sci-libs/blas-reference/files/lapack-reference-3.7.0-fix-build-system.patch b/sci-libs/blas-reference/files/lapack-reference-3.7.0-fix-build-system.patch
deleted file mode 100644
index 70f7cb0ee..000000000
--- a/sci-libs/blas-reference/files/lapack-reference-3.7.0-fix-build-system.patch
+++ /dev/null
@@ -1,56 +0,0 @@
-diff --git a/BLAS/blas.pc.in b/BLAS/blas.pc.in
-index 7fd6f1e..e52f3ad 100644
---- a/BLAS/blas.pc.in
-+++ b/BLAS/blas.pc.in
-@@ -1,5 +1,7 @@
--prefix=@prefix@
--libdir=@libdir@
-+prefix=@CMAKE_INSTALL_PREFIX@
-+exec_prefix=${prefix}
-+libdir=${exec_prefix}/@CMAKE_INSTALL_LIBDIR@
-+includedir=${prefix}/include
- 
- Name: BLAS
- Description: FORTRAN reference implementation of BLAS Basic Linear Algebra Subprograms
-diff --git a/CBLAS/cblas.pc.in b/CBLAS/cblas.pc.in
-index 4a938fe..311aed9 100644
---- a/CBLAS/cblas.pc.in
-+++ b/CBLAS/cblas.pc.in
-@@ -1,5 +1,7 @@
--prefix=@prefix@
--libdir=@libdir@
-+prefix=@CMAKE_INSTALL_PREFIX@
-+exec_prefix=${prefix}
-+libdir=${exec_prefix}/@CMAKE_INSTALL_LIBDIR@
-+includedir=${prefix}/include
- 
- Name: CBLAS
- Description: C Standard Interface to BLAS Basic Linear Algebra Subprograms
-diff --git a/LAPACKE/lapacke.pc.in b/LAPACKE/lapacke.pc.in
-index 028f8da..dc092b1 100644
---- a/LAPACKE/lapacke.pc.in
-+++ b/LAPACKE/lapacke.pc.in
-@@ -1,5 +1,7 @@
--prefix=@prefix@
--libdir=@libdir@
-+prefix=@CMAKE_INSTALL_PREFIX@
-+exec_prefix=${prefix}
-+libdir=${exec_prefix}/@CMAKE_INSTALL_LIBDIR@
-+includedir=${prefix}/include
- 
- Name: LAPACKE
- Description: C Standard Interface to LAPACK Linear Algebra PACKage
-diff --git a/lapack.pc.in b/lapack.pc.in
-index 878efc2..2cca4c2 100644
---- a/lapack.pc.in
-+++ b/lapack.pc.in
-@@ -1,5 +1,7 @@
--prefix=@prefix@
--libdir=@libdir@
-+prefix=@CMAKE_INSTALL_PREFIX@
-+exec_prefix=${prefix}
-+libdir=${exec_prefix}/@CMAKE_INSTALL_LIBDIR@
-+includedir=${prefix}/include
- 
- Name: LAPACK
- Description: FORTRAN reference implementation of LAPACK Linear Algebra PACKage
diff --git a/sci-libs/blas-reference/metadata.xml b/sci-libs/blas-reference/metadata.xml
deleted file mode 100644
index 17dbcb54a..000000000
--- a/sci-libs/blas-reference/metadata.xml
+++ /dev/null
@@ -1,20 +0,0 @@
-<?xml version="1.0" encoding="UTF-8"?>
-<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
-<pkgmetadata>
-	<maintainer type="project">
-		<email>sci@gentoo.org</email>
-		<name>Gentoo Science Project</name>
-	</maintainer>
-	<longdescription lang="en">
-The BLAS (Basic Linear Algebra Subprograms) are high quality "building
-block" routines for performing basic vector and matrix operations. Level 1
-BLAS do vector-vector operations, Level 2 BLAS do matrix-vector operations,
-and Level 3 BLAS do matrix-matrix operations. Because the BLAS are
-efficient, portable, and widely available, they're commonly used in the
-development of high quality linear algebra software, LAPACK for
-example. This packages implements the reference FORTRAN 77 library.
-</longdescription>
-	<use>
-		<flag name="int64">Build the 64 bits integer library</flag>
-	</use>
-</pkgmetadata>
diff --git a/sci-libs/blastdb/blastdb-9999.ebuild b/sci-libs/blastdb/blastdb-9999.ebuild
deleted file mode 100644
index 4165929f4..000000000
--- a/sci-libs/blastdb/blastdb-9999.ebuild
+++ /dev/null
@@ -1,26 +0,0 @@
-# Copyright 1999-2014 Gentoo Foundation
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=5
-
-DESCRIPTION="The BLAST NR database"
-HOMEPAGE="http://blast.ncbi.nlm.nih.gov/Blast.cgi?CMD=Web&PAGE_TYPE=BlastDocs&DOC_TYPE=ProgSelectionGuide"
-SRC_URI=""
-
-SLOT="0"
-LICENSE="all-rights-reserved"
-KEYWORDS=""
-IUSE=""
-
-RDEPEND=""
-DEPEND="sci-biology/ncbi-tools++"
-
-RESTRICT="binchecks strip"
-
-src_unpack() {
-	if [[ -n ${ESLEEP} ]]; then
-		elog "Will sleep for ${ESLEEP}"
-		sleep ${ESLEEP}
-	fi
-	update_blastdb.pl --verbose --verbose --decompress nr || die
-}
diff --git a/sci-libs/blastdb/metadata.xml b/sci-libs/blastdb/metadata.xml
deleted file mode 100644
index ae9640ffb..000000000
--- a/sci-libs/blastdb/metadata.xml
+++ /dev/null
@@ -1,8 +0,0 @@
-<?xml version="1.0" encoding="UTF-8"?>
-<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
-<pkgmetadata>
-	<maintainer type="project">
-		<email>sci@gentoo.org</email>
-		<name>Gentoo Science Project</name>
-	</maintainer>
-</pkgmetadata>
diff --git a/sci-libs/bloom/bloom-9999.ebuild b/sci-libs/bloom/bloom-9999.ebuild
deleted file mode 100644
index 6176c6c70..000000000
--- a/sci-libs/bloom/bloom-9999.ebuild
+++ /dev/null
@@ -1,27 +0,0 @@
-# Copyright 1999-2016 Gentoo Foundation
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=5
-
-[ "$PV" == "9999" ] && inherit git-r3
-
-DESCRIPTION="C++ Bloom Filter Library"
-HOMEPAGE="https://github.com/arashpartow/bloom"
-if [ "$PV" == "9999" ]; then
-	EGIT_REPO_URI="https://github.com/ArashPartow/bloom.git"
-else
-	SRC_URI=""
-fi
-
-LICENSE="MPL-1.1"
-SLOT="0"
-KEYWORDS=""
-IUSE=""
-
-DEPEND=""
-RDEPEND="${DEPEND}"
-
-src_prepare(){
-	sed -e "s#-c++#$(tc-getCXX)#;s#-O3#${CXXFLAGS}#" -i Makefile || die
-	sed -e "s#-pedantic-errors -ansi -Wall -Wextra -Werror -Wno-long-long##" -i Makefile || die
-}
diff --git a/sci-libs/bloom/metadata.xml b/sci-libs/bloom/metadata.xml
deleted file mode 100644
index c6496f530..000000000
--- a/sci-libs/bloom/metadata.xml
+++ /dev/null
@@ -1,15 +0,0 @@
-<?xml version="1.0" encoding="UTF-8"?>
-<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
-<pkgmetadata>
-	<maintainer type="person">
-		<email>mmokrejs@fold.natur.cuni.cz</email>
-		<name>Martin Mokrejs</name>
-	</maintainer>
-	<maintainer type="project">
-		<email>sci-biology@gentoo.org</email>
-		<name>Gentoo Biology Project</name>
-	</maintainer>
-	<upstream>
-		<remote-id type="github">arashpartow/bloom</remote-id>
-	</upstream>
-</pkgmetadata>
diff --git a/sci-libs/calculix-ccx/Manifest b/sci-libs/calculix-ccx/Manifest
deleted file mode 100644
index b74e7e9f3..000000000
--- a/sci-libs/calculix-ccx/Manifest
+++ /dev/null
@@ -1,3 +0,0 @@
-DIST ccx_2.10.ps.tar.bz2 2421249 SHA256 e7f5278b8a6efd92ca97b022afb1964792e9256b42ef9b26eb966d496a60db43 SHA512 9578d358255331045dfb3d5eccb6281f3cbaf7fdb4d0cef5cd0c19d622cba857216c7d5cba95146a1396b940a0131508509c830200c82e8c7e5ea558907aac43 WHIRLPOOL 4d1510f3ae5d327b5826753badef2671c959b2b43477f5c151ca528b0a88f66a21ab243ef6aebdcd973a723d6aa3dc7c2e75a637ab3a0cf30b58d183e15fed0c
-DIST ccx_2.10.src.tar.bz2 1005712 BLAKE2B 3450423fd6d57f188d9f9dff9c7c99ef4606ae66e7b39e694c11f3b3cf0c638d37c1e40e07a97e9b86bb199322ba9bee6ac06658bf28975cea456f0ef278e4d3 SHA512 bdd852a7fa5e327ed248058370bfaa5f029e4d98c9ee7d0e0a12f2bca480e5fc402a228e23c45f94149b2de427ebff32805f9c2a4ddbb223ff6333c26076743b
-DIST ccx_2.10.test.tar.bz2 9083192 SHA256 a5e00abc7f9b2a5a5f1a4f7b414617dc65cd0be9b2a66c93e20b5a25c1392a75 SHA512 9dac892b5d3d2070cc266ceeceec2aba205a81db6bb3b688a803f7768d0223c10c545cbd617628ed3ca39b13d154834eab3529a43f360991ad41d6a7771446f2 WHIRLPOOL 757fcadbb6356d9a904973ff0e6fb5644d2ec0c36ac15a0f058d310eb43c2cb91f0c34d7bfd62e0da2d8c44a4cf6ea963975e5a247a173cf80afdad78ba326b7
diff --git a/sci-libs/calculix-ccx/calculix-ccx-2.10.ebuild b/sci-libs/calculix-ccx/calculix-ccx-2.10.ebuild
deleted file mode 100644
index 9b7efa9f3..000000000
--- a/sci-libs/calculix-ccx/calculix-ccx-2.10.ebuild
+++ /dev/null
@@ -1,74 +0,0 @@
-# Copyright 1999-2017 Gentoo Foundation
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=6
-
-inherit eutils toolchain-funcs flag-o-matic fortran-2
-
-MY_P=ccx_${PV/_/}
-
-DESCRIPTION="A Free Software Three-Dimensional Structural Finite Element Program"
-HOMEPAGE="http://www.calculix.de/"
-SRC_URI="
-	http://www.dhondt.de/${MY_P}.src.tar.bz2
-	doc? ( http://www.dhondt.de/${MY_P}.ps.tar.bz2 )
-	examples? ( http://www.dhondt.de/${MY_P}.test.tar.bz2 )"
-
-LICENSE="GPL-2"
-SLOT="0"
-KEYWORDS="~amd64 ~x86"
-IUSE="arpack doc examples openmp threads"
-
-RDEPEND="
-	arpack? ( >=sci-libs/arpack-3.1.3 )
-	>=sci-libs/spooles-2.2[threads=]
-	virtual/lapack
-	virtual/blas"
-DEPEND="${RDEPEND}
-	virtual/pkgconfig
-	doc? ( app-text/ghostscript-gpl )"
-
-S=${WORKDIR}/CalculiX/${MY_P}/src
-
-PATCHES=(
-	"${FILESDIR}/01_${MY_P}_Makefile_custom_cc_flags_spooles_arpack.patch"
-)
-
-src_configure() {
-	# Technically we currently only need this when arpack is not used.
-	# Keeping things this way in case we change pkgconfig for arpack
-	export LAPACK=$($(tc-getPKG_CONFIG) --libs lapack)
-
-	append-cflags "-I/usr/include/spooles -DSPOOLES"
-	if use threads; then
-		append-cflags "-DUSE_MT"
-	fi
-
-	if use openmp; then
-		append-fflags "-fopenmp"
-		append-cflags "-fopenmp"
-	fi
-
-	if use arpack; then
-		export ARPACKLIB=$($(tc-getPKG_CONFIG) --libs arpack)
-		append-cflags "-DARPACK"
-	fi
-	export CC="$(tc-getCC)"
-	export FC="$(tc-getFC)"
-}
-
-src_install () {
-	dobin ${MY_P}
-	dosym ${MY_P} /usr/bin/ccx
-
-	if use doc; then
-		cd "${S}/../doc" || die
-		ps2pdf ${MY_P}.ps ${MY_P}.pdf || die "ps2pdf failed"
-		dodoc ${MY_P}.pdf
-	fi
-
-	if use examples; then
-		insinto /usr/share/doc/${PF}/examples
-		doins -r "${S}"/../test/*
-	fi
-}
diff --git a/sci-libs/calculix-ccx/files/01_ccx_2.10_Makefile_custom_cc_flags_spooles_arpack.patch b/sci-libs/calculix-ccx/files/01_ccx_2.10_Makefile_custom_cc_flags_spooles_arpack.patch
deleted file mode 100644
index 83caf80f9..000000000
--- a/sci-libs/calculix-ccx/files/01_ccx_2.10_Makefile_custom_cc_flags_spooles_arpack.patch
+++ /dev/null
@@ -1,35 +0,0 @@
-Fix Makefile to make it use custom CFLAGS and system libraries.
-
-diff -uwrN ccx_2.10.ORIG/src/Makefile ccx_2.10/src/Makefile
---- src/Makefile	2016-03-07 04:57:09.462878788 +0100
-+++ ccx_2.10/src/Makefile	2016-03-07 06:05:44.150786978 +0100
-@@ -1,9 +1,6 @@
- 
--CFLAGS = -Wall -O3 -fopenmp -I ../../../SPOOLES.2.2 -DARCH="Linux" -DSPOOLES -DARPACK -DMATRIXSTORAGE
--FFLAGS = -Wall -O3 -fopenmp
--
--CC=cc
--FC=gfortran
-+CFLAGS := -Wall -DARCH="Linux" -DMATRIXSTORAGE $(CFLAGS)
-+FFLAGS := -Wall $(FFLAGS)
- 
- .c.o :
- 	$(CC) $(CFLAGS) -c $<
-@@ -18,15 +15,10 @@
- OCCXC = $(SCCXC:.c=.o)
- OCCXMAIN = $(SCCXMAIN:.c=.o)
- 
--DIR=../../../SPOOLES.2.2
--
--LIBS = \
--       $(DIR)/spooles.a \
--	../../../ARPACK/libarpack_INTEL.a \
--       -lpthread -lm -lc
-+LIBS = $(ARPACKLIB) $(LAPACK) -lm -lc -lspooles -lpthread
- 
- ccx_2.10: $(OCCXMAIN) ccx_2.10.a  $(LIBS)
--	./date.pl; $(CC) $(CFLAGS) -c ccx_2.10.c; $(FC) -fopenmp -Wall -O3 -o $@ $(OCCXMAIN) ccx_2.10.a $(LIBS)
-+	./date.pl; $(CC) $(CFLAGS) -c ccx_2.10.c; $(FC) $(FFLAGS) -o $@ $(OCCXMAIN) ccx_2.10.a $(LIBS)
- 
- ccx_2.10.a: $(OCCXF) $(OCCXC)
- 	ar vr $@ $?
diff --git a/sci-libs/calculix-ccx/metadata.xml b/sci-libs/calculix-ccx/metadata.xml
deleted file mode 100644
index a62eacf73..000000000
--- a/sci-libs/calculix-ccx/metadata.xml
+++ /dev/null
@@ -1,11 +0,0 @@
-<?xml version="1.0" encoding="UTF-8"?>
-<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
-<pkgmetadata>
-	<maintainer type="project">
-		<email>sci@gentoo.org</email>
-		<name>Gentoo Science Project</name>
-	</maintainer>
-	<use>
-		<flag name="arpack"> Add sparse eigen value support via sci-libs/arpack </flag>
-	</use>
-</pkgmetadata>
diff --git a/sci-libs/calculix-cgx/Manifest b/sci-libs/calculix-cgx/Manifest
deleted file mode 100644
index b5d231084..000000000
--- a/sci-libs/calculix-cgx/Manifest
+++ /dev/null
@@ -1,2 +0,0 @@
-DIST cgx_2.10.all.tar.bz2 1701663 SHA256 b2ea974003374c28b8e24f76f8a6c142db470a8c2a53013e3735efe78e98e84d SHA512 ac4dce3ffee63aa7be7ee441b7ae31a3839e6322175b70449e3c72bff3ed0bf3ade66170dd47f00d6ef488729f987f622a7db9cde3e69ad7cf38b9b096c931fd WHIRLPOOL a5186a8667e6272c669ed1f5214028235ca2179eb59f08abaa09ded64875aaeae6ab2541da6fbd6494b16b489ca2f1e68185e726fc3bc5be6bf03ed1df9d1b40
-DIST cgx_2.10.pdf 1178710 SHA256 b9bc56222496283948e151e3b1e07e4295cefba20ff9a567221bfbdb2c68b654 SHA512 cedf7556e85f631aa475d25325587aea2ecad650c325762080524dd056ba1e247d677c9ae2bcb2736b9c0a402a9060dbdebff834d8c10e3d127ecc3af9106385 WHIRLPOOL a10b68ec7772a0f98aa620b70c17b6293bf6a44647ee0a293b0629f5db6488a232b2c32cb632d77550b756293e307c4dfcd52fc3f3ccb8f73ec8ef9c6c4a4aef
diff --git a/sci-libs/calculix-cgx/calculix-cgx-2.10.ebuild b/sci-libs/calculix-cgx/calculix-cgx-2.10.ebuild
deleted file mode 100644
index e7535f52f..000000000
--- a/sci-libs/calculix-cgx/calculix-cgx-2.10.ebuild
+++ /dev/null
@@ -1,58 +0,0 @@
-# Copyright 1999-2014 Gentoo Foundation
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=6
-
-inherit eutils
-
-MY_P=cgx_${PV}
-
-DESCRIPTION="A Free Software Three-Dimensional Structural Finite Element Program"
-HOMEPAGE="http://www.calculix.de/"
-SRC_URI="http://www.dhondt.de/${MY_P}.all.tar.bz2
-	doc? ( http://www.dhondt.de/${MY_P}.pdf )"
-
-LICENSE="GPL-2"
-SLOT="0"
-KEYWORDS="~amd64 ~x86"
-# nptl removed since I cannot work around it
-IUSE="doc examples"
-
-RDEPEND="media-libs/mesa[nptl]
-	>=media-libs/freeglut-1.0
-	virtual/opengl
-	x11-libs/libX11
-	x11-libs/libXmu
-	x11-libs/libXi
-	x11-libs/libXext
-	x11-libs/libXt
-	x11-libs/libSM
-	x11-libs/libICE"
-DEPEND="${RDEPEND}
-	doc? ( app-text/ghostscript-gpl )"
-
-S=${WORKDIR}/CalculiX/${MY_P}/src/
-
-PATCHES=(
-	"${FILESDIR}"/01_${MY_P}_Makefile_custom_cxx_flags.patch
-	"${FILESDIR}"/02_${MY_P}_menu_fix-freeglut_2.8.1.patch
-)
-
-src_configure () {
-	# Does not compile without -lpthread
-	export PTHREAD="-lpthread"
-	export LFLAGS="-L/usr/$(get_libdir) ${LFLAGS}"
-}
-
-src_install () {
-	dobin cgx
-
-	if use doc; then
-		dodoc "${DISTDIR}/${MY_P}.pdf"
-	fi
-
-	if use examples; then
-		insinto /usr/share/doc/${PF}/examples
-		doins -r "${S}"/../examples/*
-	fi
-}
diff --git a/sci-libs/calculix-cgx/files/01_cgx_2.10_Makefile_custom_cxx_flags.patch b/sci-libs/calculix-cgx/files/01_cgx_2.10_Makefile_custom_cxx_flags.patch
deleted file mode 100644
index d6e22f9c9..000000000
--- a/sci-libs/calculix-cgx/files/01_cgx_2.10_Makefile_custom_cxx_flags.patch
+++ /dev/null
@@ -1,73 +0,0 @@
-diff -uwrN cgx_2.10.ORIG/src/Makefile cgx_2.10/src/Makefile
---- src/Makefile	2016-01-13 12:41:40.398930000 +0100
-+++ cgx_2.10/src/Makefile	2016-03-08 11:02:59.591853482 +0100
-@@ -1,15 +1,15 @@
--CFLAGS = -O3 -Wall \
-+CFLAGS += -Wall \
-   -I./ \
-   -I/usr/include \
-   -I/usr/include/GL \
-   -I../../libSNL/src \
-   -I../../glut-3.5/src \
--  -I/usr/X11/include 
-+  -I/usr/include/X11
- 
--LFLAGS = \
--  -L/usr/lib64 -lGL -lGLU \
--  -L/usr/X11R6/lib64 -lX11 -lXi -lXmu -lXext -lXt -lSM -lICE \
--  -lm -lpthread -lrt
-+LFLAGS += \
-+  -lGL -lGLU -lglut\
-+  -lX11 -lXi -lXmu -lXext -lXt -lSM -lICE \
-+  -lm $(PTHREAD) -lrt
- 
- 
- # on 32bit systems change lib64 to lib
-@@ -22,41 +22,6 @@
-  userFunction.c
- 
- SUTIL = \
-- ../../glut-3.5/src/layerutil.c \
-- ../../glut-3.5/src/glut_dials.c \
-- ../../glut-3.5/src/glut_ext.c \
-- ../../glut-3.5/src/glut_mesa.c \
-- ../../glut-3.5/src/glut_menu.c \
-- ../../glut-3.5/src/glut_modifier.c \
-- ../../glut-3.5/src/glut_space.c \
-- ../../glut-3.5/src/glut_shapes.c \
-- ../../glut-3.5/src/glut_tablet.c \
-- ../../glut-3.5/src/glut_warp.c \
-- ../../glut-3.5/src/glut_8x13.c \
-- ../../glut-3.5/src/glut_9x15.c \
-- ../../glut-3.5/src/glut_hel10.c \
-- ../../glut-3.5/src/glut_hel18.c \
-- ../../glut-3.5/src/glut_hel12.c \
-- ../../glut-3.5/src/glut_tr10.c \
-- ../../glut-3.5/src/glut_tr24.c \
-- ../../glut-3.5/src/glut_bitmap.c \
-- ../../glut-3.5/src/glut_cursor.c \
-- ../../glut-3.5/src/glut_event.c \
-- ../../glut-3.5/src/glut_get.c \
-- ../../glut-3.5/src/glut_overlay.c \
-- ../../glut-3.5/src/glut_input.c \
-- ../../glut-3.5/src/glut_stroke.c \
-- ../../glut-3.5/src/glut_teapot.c \
-- ../../glut-3.5/src/glut_winmisc.c \
-- ../../glut-3.5/src/glut_fullscrn.c \
-- ../../glut-3.5/src/glut_cindex.c \
-- ../../glut-3.5/src/glut_roman.c \
-- ../../glut-3.5/src/glut_mroman.c \
-- ../../glut-3.5/src/glut_swidth.c \
-- ../../glut-3.5/src/glut_bwidth.c \
-- ../../glut-3.5/src/glut_win.c \
-- ../../glut-3.5/src/glut_init.c \
-- ../../glut-3.5/src/glut_util.c \
-  uselibSNL.cpp \
-  generateTet.cpp \
-  ../../libSNL/src/*.cpp
-@@ -66,7 +31,7 @@
- OUTIL = $(SUTIL:.c=.o)
- 
- cgx: $(OLIB) $(OUTIL) $(OULIB)
--	g++  $(OULIB)  $(OLIB) $(OUTIL)  $(CFLAGS) $(LFLAGS) -o  $@
-+	$(CXX) $(OULIB) $(OLIB) $(OUTIL) $(CFLAGS) $(LFLAGS) -o $@
diff --git a/sci-libs/calculix-cgx/files/02_cgx_2.10_menu_fix-freeglut_2.8.1.patch b/sci-libs/calculix-cgx/files/02_cgx_2.10_menu_fix-freeglut_2.8.1.patch
deleted file mode 100644
index ff440b44e..000000000
--- a/sci-libs/calculix-cgx/files/02_cgx_2.10_menu_fix-freeglut_2.8.1.patch
+++ /dev/null
@@ -1,72 +0,0 @@
-diff -uwrN cgx_2.10.ORIG/src/cgx.c cgx_2.10/src/cgx.c
---- src/cgx.c   2016-03-04 20:40:43.429549000 +0100
-+++ cgx_2.10/src/cgx.c   2016-03-08 10:53:56.816865592 +0100
-@@ -242,6 +242,9 @@
- int   subsubmenu_animTune=-1, subsubmenu_animSteps=-1;
- int   subsubmenu_animPeriod=-1;
- 
-+char recompileFlag=0; /* 0 if nothing to recompile */
-+int recompileMenu=0; /* If recompile needed, set to lc */
-+
- GLfloat lmodel_twoside[] = { GL_TRUE };
- GLfloat lmodel_oneside[] = { GL_FALSE };
- double dx ,dy;                                      /* Mauskoordinaten im bereich +-1*/
-@@ -400,7 +403,11 @@
- #endif
- }
- 
--
-+void queueRecompileEntitiesInMenu(int lc) 
-+{
-+  recompileFlag = 1;
-+  recompileMenu = lc;
-+}
- 
- /* the node pointer must not be changed inside the function. Since that is the case the *node is changed to *node_dummy
-    and the global *node is used which is always correct so far */
-@@ -3201,7 +3208,7 @@
-       seqLC[2]=anz->l-1;
-   }/* no sequence until a new entity is selected and all data are prepared */
- 
--  recompileEntitiesInMenu(pre_lc);
-+  queueRecompileEntitiesInMenu(pre_lc);
- }
- 
- 
-@@ -3229,7 +3236,15 @@
-   glutSetWindow( activWindow);
- }
- 
--
-+void processMenuStatus(int status, int x, int y) 
-+{
-+  if (status == GLUT_MENU_NOT_IN_USE) {
-+    if (recompileFlag) {
-+      recompileEntitiesInMenu(recompileMenu);
-+      recompileFlag = 0;
-+    }
-+  }
-+}
- 
- void recompileEntitiesInMenu(int lc)
- {
-@@ -5918,6 +5933,7 @@
-   glutSpecialFunc ( specialKeyboard );
-   glutEntryFunc ( entryfunktion );
-   glutPassiveMotionFunc ( Mouse );
-+  glutMenuStatusFunc( processMenuStatus );
-   glDisable(GL_DITHER);
-   glLightModelfv(GL_LIGHT_MODEL_TWO_SIDE, lmodel_oneside);
-   glCullFace ( GL_BACK );
-diff -uwrN cgx_2.10.ORIG/src/extUtil.h cgx_2.10/src/extUtil.h
---- src/extUtil.h   2016-02-13 02:21:44.342442000 +0100
-+++ cgx_2.10/src/extUtil.h   2016-03-08 10:55:36.194863375 +0100
-@@ -34,7 +34,7 @@
- }
-   #endif
- #else
--  #include <GL/glut_cgx.h>
-+  #include <GL/glut.h>
- #endif
- 
- #define     PI          3.14159265358979323846264338327950288
\ No newline at end of file
diff --git a/sci-libs/calculix-cgx/metadata.xml b/sci-libs/calculix-cgx/metadata.xml
deleted file mode 100644
index ae9640ffb..000000000
--- a/sci-libs/calculix-cgx/metadata.xml
+++ /dev/null
@@ -1,8 +0,0 @@
-<?xml version="1.0" encoding="UTF-8"?>
-<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
-<pkgmetadata>
-	<maintainer type="project">
-		<email>sci@gentoo.org</email>
-		<name>Gentoo Science Project</name>
-	</maintainer>
-</pkgmetadata>
diff --git a/sci-libs/cblas-reference/Manifest b/sci-libs/cblas-reference/Manifest
deleted file mode 100644
index c1cefc8c3..000000000
--- a/sci-libs/cblas-reference/Manifest
+++ /dev/null
@@ -1,3 +0,0 @@
-DIST cblas-reference-20110218.tgz 197468 BLAKE2B 8c9aefae422e7beac3ef433f121a152a7669345d0438b76d9bf8278f2a9b22ca29e01f5dbcb816b3f2759979a07d4883834037ba46a3b1d90f734989a5b57f4e SHA512 1c64e6814529cd716890504d213e8cd90150348b9105e8da030718383241a5660d145a14f26e20d27b2aea72c87a9d46b754c6e48935e168d62842c04ba56401
-DIST lapack-3.6.0.tgz 6792324 BLAKE2B 438f3376b63b38ef0fe70f6becac847816f3a11c01f5ab237dc0d941792ceb54dbd2f8dc22d56286f5dab3499289ed94e67521ea951a98973c9640abc294ad6c SHA512 bc50441d415ef8896dd7626d77c6104184b996e758704366288089f03d4c99d068e33153b0d13305310886017e5d2e716130f812a95cfcad36ef37fe20417ab8
-DIST lapack-3.7.0.tgz 7359812 BLAKE2B 20aa42e22d8c920d1360afe41ceec7b36f6cd5fbe43ca9d7848ef7cc45a64a0314cb1321941c1a7c03654f41e28ec805445882ded0ca0ea07674e70b66cba6b5 SHA512 e4f4c7d0ba8a096eeb813160c6dbcdd535647df6b2ad5beac9181908158956b31d1a9554ec9b9836fd44fe7404c1f377b297cbb20d744f20d70e357fd246c91b
diff --git a/sci-libs/cblas-reference/cblas-reference-20110218-r100.ebuild b/sci-libs/cblas-reference/cblas-reference-20110218-r100.ebuild
deleted file mode 100644
index 0d44ec5f2..000000000
--- a/sci-libs/cblas-reference/cblas-reference-20110218-r100.ebuild
+++ /dev/null
@@ -1,144 +0,0 @@
-# Copyright 1999-2016 Gentoo Foundation
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=5
-
-NUMERIC_MODULE_NAME="refcblas"
-
-inherit alternatives-2 flag-o-matic fortran-2 multilib numeric numeric-int64-multibuild toolchain-funcs versionator
-
-MYPN="${PN/-reference/}"
-
-DESCRIPTION="C wrapper interface to the F77 reference BLAS implementation"
-HOMEPAGE="http://www.netlib.org/blas/"
-SRC_URI="http://www.netlib.org/blas/blast-forum/${MYPN}.tgz -> ${P}.tgz"
-
-SLOT="0"
-LICENSE="public-domain"
-KEYWORDS="~amd64 ~x86 ~amd64-linux ~x86-linux"
-IUSE="static-libs"
-
-RDEPEND="virtual/blas"
-DEPEND="${RDEPEND}
-	virtual/pkgconfig"
-
-S="${WORKDIR}/CBLAS"
-
-MULTILIB_WRAPPED_HEADERS=(
-	/usr/include/cblas/cblas.h
-)
-
-static_to_shared() {
-	local libstatic=$1
-	shift || die
-	local libname=$(basename ${libstatic%.a})
-	local soname=${libname}$(get_libname $(get_version_component_range 1-2))
-	local libdir=$(dirname ${libstatic})
-
-	einfo "Making ${soname} from ${libstatic}"
-	if [[ ${CHOST} == *-darwin* ]] ; then
-		${LINK:-$(tc-getCC)} ${LDFLAGS}  \
-			-dynamiclib -install_name "${EPREFIX}"/usr/$(get_libdir)/${soname} \
-			-Wl,-all_load -Wl,${libstatic} \
-			"$@" -o ${libdir}/${soname} || die "${soname} failed"
-	else
-		${LINK:-$(tc-getCC)} ${LDFLAGS}  \
-			-shared -Wl,-soname=${soname} \
-			-Wl,--whole-archive ${libstatic} -Wl,--no-whole-archive \
-			"$@" -o ${libdir}/${soname} || die "${soname} failed"
-		if [[ $(get_version_component_count) -gt 1 ]]; then
-			ln -s ${soname} ${libdir}/${libname}$(get_libname $(get_major_version)) || die
-		fi
-	fi
-	ln -s ${soname} ${libdir}/${libname}$(get_libname) || die
-}
-
-src_prepare() {
-	numeric-int64_ensure_blas_int_support
-	find . -name Makefile -exec sed -i \
-		-e 's:make:$(MAKE):g' '{}' \; || die
-	numeric-int64-multibuild_copy_sources
-}
-
-src_configure() {
-	cblas_configure() {
-		local profname=$(numeric-int64_get_module_name)
-		local libname="${profname//-/_}"
-		append-cflags -DADD_
-		cat > Makefile.in <<-EOF
-			BLLIB=$($(tc-getPKG_CONFIG) --libs $(numeric-int64_get_blas_alternative))
-			FC=$(tc-getFC) $(get_abi_CFLAGS) $(numeric-int64_get_fortran_int64_abi_fflags)
-			CC=$(tc-getCC)
-			CBLIB=../lib/lib${libname}.a
-			LOADER=\$(FC)
-			ARCH=$(tc-getAR)
-			ARCHFLAGS=cr
-			RANLIB=$(tc-getRANLIB)
-		EOF
-	}
-	numeric-int64-multibuild_foreach_all_abi_variants run_in_build_dir cblas_configure
-}
-
-src_compile() {
-	cblas_src_compile() {
-		local profname=$(numeric-int64_get_module_name)
-		local libname="${profname//-/_}"
-		emake \
-			FFLAGS="${FFLAGS} -fPIC" \
-			CFLAGS="${CFLAGS} -fPIC" \
-			alllib
-		static_to_shared lib/lib${libname}.a $($(tc-getPKG_CONFIG) --libs $(numeric-int64_get_blas_alternative))
-		if use static-libs; then
-			emake clean
-			emake alllib
-		fi
-	}
-	numeric-int64-multibuild_foreach_all_abi_variants run_in_build_dir cblas_src_compile
-}
-
-src_test() {
-	cblas_src_test () {
-		local profname=$(numeric-int64_get_module_name)
-		local libname="${profname//-/_}"
-		cd testing || die
-		emake && emake run
-	}
-	numeric-int64-multibuild_foreach_all_abi_variants run_in_build_dir cblas_src_test
-}
-
-src_install() {
-	cblas_src_install() {
-		local profname=$(numeric-int64_get_module_name)
-		local libname="${profname//-/_}"
-		# On linux dynamic libraries are of the form .so.${someversion}
-		# On  OS X dynamic libraries are of the form ${someversion}.dylib
-		if numeric-int64_is_static_build; then
-			dolib.a lib/lib${libname}.a
-		else
-			dolib.so lib/lib${libname}*$(get_libname)*
-			insinto /usr/include/cblas
-			doins include/cblas.h
-			create_pkgconfig \
-				--name "${profname}" \
-				--libs "-L\${libdir} -l${libname}" \
-				--libs-private "-lm" \
-				--cflags "-I\${includedir}/cblas $(numeric-int64_get_fortran_int64_abi_fflags)" \
-				--requires $(numeric-int64_get_blas_alternative) \
-				${profname}
-		fi
-
-		if [[ ${#MULTIBUILD_VARIANTS[@]} -gt 1 ]]; then
-			multilib_prepare_wrappers
-			multilib_check_headers
-		fi
-	}
-	numeric-int64-multibuild_foreach_all_abi_variants run_in_build_dir cblas_src_install
-
-	numeric-int64-multibuild_install_alternative cblas reference /usr/include/cblas.h cblas/cblas.h
-
-	multilib_install_wrappers
-
-	dodoc README
-	docinto examples
-	dodoc examples/*.c
-}
diff --git a/sci-libs/cblas-reference/cblas-reference-20151113-r100.ebuild b/sci-libs/cblas-reference/cblas-reference-20151113-r100.ebuild
deleted file mode 100644
index 97b7d012f..000000000
--- a/sci-libs/cblas-reference/cblas-reference-20151113-r100.ebuild
+++ /dev/null
@@ -1,126 +0,0 @@
-# Copyright 1999-2016 Gentoo Foundation
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=5
-
-PYTHON_COMPAT=( python2_7 )
-
-NUMERIC_MODULE_NAME="refcblas"
-
-inherit alternatives-2 cmake-utils eutils fortran-2 numeric-int64-multibuild python-any-r1 toolchain-funcs
-
-LPN=lapack
-LPV=3.6.0
-
-DESCRIPTION="C wrapper interface to the F77 reference BLAS implementation"
-HOMEPAGE="http://www.netlib.org/cblas/"
-SRC_URI="http://www.netlib.org/${LPN}/${LPN}-${LPV}.tgz"
-
-LICENSE="BSD"
-SLOT="0/${LPV}"
-KEYWORDS="~amd64 ~x86 ~amd64-linux ~x86-linux"
-IUSE="static-libs test"
-
-REQUIRED_USE="test? ( ${PYTHON_REQUIRED_USE} )"
-
-RDEPEND="virtual/blas"
-DEPEND="${RDEPEND}
-	test? ( ${PYTHON_DEPS} )
-	virtual/pkgconfig"
-
-S="${WORKDIR}/${LPN}-${LPV}"
-PATCHES=( "${FILESDIR}/lapack-fix-build-system.patch" )
-
-MULTILIB_WRAPPED_HEADERS=(
-	/usr/include/cblas/cblas.h
-)
-src_prepare() {
-	# the lapack(e)/(c)blas build system is somewhat broken
-	# with respect to its pkg-config files.
-	epatch "${PATCHES[@]}"
-
-	# rename library to avoid collision with other blas implementations
-	# ${LIBNAME} and ${PROFNAME} are not defined here, they are in single
-	# quotes in the following seds.  They are later set by defining cmake
-	# variables with -DPROFNAME etc in src_configure
-	sed -i \
-		-e 's:\([^xc]\)blas:\1${LIBNAME}:g' \
-		-e '/ALL_TARGETS/s:cblas):${LIBNAME}):' \
-		-e '/_librar/s:cblas:${LIBNAME}:' \
-		CMakeLists.txt \
-		CBLAS/src/CMakeLists.txt || die
-	sed -i \
-		-e 's:/CMAKE/:/cmake/:g' \
-		CBLAS/CMakeLists.txt || die
-	sed -i \
-		-e '/Name: /s:cblas:@PROFNAME@:' \
-		-e 's:-lcblas:-l@LIBNAME@:g' \
-		 CBLAS/cblas.pc.in || die
-	sed -i \
-		-e 's:cblas):${LIBNAME}):' \
-		CBLAS/testing/CMakeLists.txt || die
-	sed -i \
-		-e 's:BINARY_DIR}/cblas:BINARY_DIR}/${PROFNAME}:' \
-		-e '/CBLAS_INCLUDE/s:include ):include/${PROFNAME} ):g' \
-		CBLAS/CMakeLists.txt || die
-}
-
-src_configure() {
-	cblas_configure() {
-		local FCFLAGS="${FCFLAGS}"
-		append-fflags $($(tc-getPKG_CONFIG) --cflags ${blas_profname})
-		append-fflags $(get_abi_CFLAGS)
-		append-fflags $(numeric-int64_get_fortran_int64_abi_fflags)
-
-		local blas_profname=$(numeric-int64_get_blas_alternative)
-		local profname=$(numeric-int64_get_module_name)
-		local libname="${profname//-/_}"
-
-		local mycmakeargs=(
-			-Wno-dev
-			-DCBLAS=ON
-			-DPROFNAME="${profname}"
-			-DLIBNAME="${libname}"
-			-DUSE_OPTIMIZED_BLAS=ON
-			-DBLAS_LIBRARIES="$($(tc-getPKG_CONFIG) --libs ${blas_profname})"
-			-DCMAKE_C_FLAGS="$($(tc-getPKG_CONFIG) --cflags ${blas_profname}) ${CFLAGS}"
-			-DCMAKE_CXX_FLAGS="$($(tc-getPKG_CONFIG) --cflags ${blas_profname}) ${CXXFLAGS}"
-			-DCMAKE_Fortran_FLAGS="$($(tc-getPKG_CONFIG) --cflags ${blas_profname}) $(get_abi_CFLAGS) $(numeric-int64_get_fortran_int64_abi_fflags) ${FCFLAGS}"
-			-DLAPACK_PKGCONFIG_FFLAGS="$(numeric-int64_get_fortran_int64_abi_fflags)"
-			$(cmake-utils_use_build test TESTING)
-		)
-		if $(numeric-int64_is_static_build); then
-			mycmakeargs+=(
-				-DBUILD_SHARED_LIBS=OFF
-				-DBUILD_STATIC_LIBS=ON
-			)
-		else
-			mycmakeargs+=(
-				-DBUILD_SHARED_LIBS=ON
-				-DBUILD_STATIC_LIBS=OFF
-			)
-		fi
-		cmake-utils_src_configure
-	}
-	numeric-int64-multibuild_foreach_all_abi_variants cblas_configure
-}
-
-src_compile() {
-	local each target_dirs=( CBLAS )
-	use test && target_dirs+=( testing )
-	for each in ${target_dirs[@]}; do
-		numeric-int64-multibuild_foreach_all_abi_variants \
-			cmake-utils_src_compile -C ${each}
-	done
-
-}
-
-src_test() {
-	numeric-int64-multibuild_foreach_all_abi_variants cmake-utils_src_test
-}
-
-src_install() {
-	numeric-int64-multibuild_foreach_all_abi_variants cmake-utils_src_install -C CBLAS
-	numeric-int64-multibuild_install_alternative cblas reference /usr/include/cblas.h refcblas/cblas.h
-	multilib_install_wrappers
-}
diff --git a/sci-libs/cblas-reference/cblas-reference-20161223-r101.ebuild b/sci-libs/cblas-reference/cblas-reference-20161223-r101.ebuild
deleted file mode 100644
index 152e56324..000000000
--- a/sci-libs/cblas-reference/cblas-reference-20161223-r101.ebuild
+++ /dev/null
@@ -1,124 +0,0 @@
-# Copyright 1999-2018 Gentoo Authors
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=6
-
-PYTHON_COMPAT=( python2_7 )
-
-NUMERIC_MODULE_NAME="refcblas"
-
-inherit alternatives-2 cmake-utils eutils fortran-2 numeric-int64-multibuild python-any-r1 toolchain-funcs
-
-LPN=lapack
-LPV=3.7.0
-
-DESCRIPTION="C wrapper interface to the F77 reference BLAS implementation"
-HOMEPAGE="http://www.netlib.org/cblas/"
-SRC_URI="http://www.netlib.org/${LPN}/${LPN}-${LPV}.tgz"
-
-LICENSE="BSD"
-SLOT="0/${LPV}"
-KEYWORDS="~amd64 ~x86 ~amd64-linux ~x86-linux"
-IUSE="static-libs test"
-
-REQUIRED_USE="test? ( ${PYTHON_REQUIRED_USE} )"
-
-RDEPEND="virtual/blas"
-DEPEND="${RDEPEND}
-	test? ( ${PYTHON_DEPS} )
-	virtual/pkgconfig"
-
-S="${WORKDIR}/${LPN}-${LPV}"
-PATCHES=( "${FILESDIR}/lapack-reference-${LPV}-fix-build-system.patch" )
-
-MULTILIB_WRAPPED_HEADERS=(
-	/usr/include/cblas/cblas.h
-)
-
-src_prepare() {
-	cmake-utils_src_prepare
-
-	# rename library to avoid collision with other blas implementations
-	# ${LIBNAME} and ${PROFNAME} are not defined here, they are in single
-	# quotes in the following seds.  They are later set by defining cmake
-	# variables with -DPROFNAME etc in src_configure
-	sed -i \
-		-e 's:\([^xc]\)blas:\1${LIBNAME}:g' \
-		-e '/ALL_TARGETS/s:cblas):${LIBNAME}):' \
-		-e '/_librar/s:cblas:${LIBNAME}:' \
-		CMakeLists.txt \
-		CBLAS/src/CMakeLists.txt || die
-	sed -i \
-		-e 's:/CMAKE/:/cmake/:g' \
-		CBLAS/CMakeLists.txt || die
-	sed -i \
-		-e '/Name: /s:cblas:@PROFNAME@:' \
-		-e 's:-lcblas:-l@LIBNAME@:g' \
-		 CBLAS/cblas.pc.in || die
-	sed -i \
-		-e 's:cblas):${LIBNAME}):' \
-		CBLAS/testing/CMakeLists.txt || die
-	sed -i \
-		-e 's:BINARY_DIR}/cblas:BINARY_DIR}/${PROFNAME}:' \
-		-e '/install/s:include):include/${PROFNAME}):g' \
-		CBLAS/CMakeLists.txt || die
-}
-
-src_configure() {
-	cblas_configure() {
-		local FCFLAGS="${FCFLAGS}"
-		append-fflags $($(tc-getPKG_CONFIG) --cflags ${blas_profname})
-		append-fflags $(get_abi_CFLAGS)
-		append-fflags $(numeric-int64_get_fortran_int64_abi_fflags)
-
-		local blas_profname=$(numeric-int64_get_blas_alternative)
-		local profname=$(numeric-int64_get_module_name)
-		local libname="${profname//-/_}"
-
-		local mycmakeargs=(
-			-Wno-dev
-			-DCBLAS=ON
-			-DPROFNAME="${profname}"
-			-DLIBNAME="${libname}"
-			-DUSE_OPTIMIZED_BLAS=ON
-			-DCMAKE_C_FLAGS="$($(tc-getPKG_CONFIG) --cflags ${blas_profname}) ${CFLAGS}"
-			-DCMAKE_CXX_FLAGS="$($(tc-getPKG_CONFIG) --cflags ${blas_profname}) ${CXXFLAGS}"
-			-DCMAKE_Fortran_FLAGS="$($(tc-getPKG_CONFIG) --cflags ${blas_profname}) $(get_abi_CFLAGS) $(numeric-int64_get_fortran_int64_abi_fflags) ${FCFLAGS}"
-			-DLAPACK_PKGCONFIG_FFLAGS="$(numeric-int64_get_fortran_int64_abi_fflags)"
-			-DBUILD_TESTING=$(usex test)
-		)
-		if $(numeric-int64_is_static_build); then
-			mycmakeargs+=(
-				-DBUILD_SHARED_LIBS=OFF
-				-DBUILD_STATIC_LIBS=ON
-			)
-		else
-			mycmakeargs+=(
-				-DBUILD_SHARED_LIBS=ON
-				-DBUILD_STATIC_LIBS=OFF
-			)
-		fi
-		cmake-utils_src_configure
-	}
-	numeric-int64-multibuild_foreach_all_abi_variants cblas_configure
-}
-
-src_compile() {
-	local each target_dirs=( CBLAS )
-	use test && target_dirs+=( testing )
-	for each in ${target_dirs[@]}; do
-		numeric-int64-multibuild_foreach_all_abi_variants \
-			cmake-utils_src_compile -C ${each}
-	done
-
-}
-
-src_test() {
-	numeric-int64-multibuild_foreach_all_abi_variants cmake-utils_src_test
-}
-
-src_install() {
-	numeric-int64-multibuild_foreach_all_abi_variants cmake-utils_src_install -C CBLAS
-	numeric-int64-multibuild_install_alternative cblas reference /usr/include/cblas.h refcblas/cblas.h
-	multilib_install_wrappers
-}
diff --git a/sci-libs/cblas-reference/files/lapack-fix-build-system.patch b/sci-libs/cblas-reference/files/lapack-fix-build-system.patch
deleted file mode 100644
index a187dac21..000000000
--- a/sci-libs/cblas-reference/files/lapack-fix-build-system.patch
+++ /dev/null
@@ -1,124 +0,0 @@
- BLAS/CMakeLists.txt    | 2 +-
- BLAS/blas.pc.in        | 6 ++++--
- CBLAS/CMakeLists.txt   | 2 +-
- CBLAS/cblas.pc.in      | 9 ++++++---
- CMakeLists.txt         | 2 +-
- LAPACKE/CMakeLists.txt | 2 +-
- LAPACKE/lapacke.pc.in  | 6 ++++--
- lapack.pc.in           | 6 ++++--
- 8 files changed, 22 insertions(+), 13 deletions(-)
-
-diff --git a/BLAS/CMakeLists.txt b/BLAS/CMakeLists.txt
-index 45e68e9..56c8354 100644
---- a/BLAS/CMakeLists.txt
-+++ b/BLAS/CMakeLists.txt
-@@ -2,7 +2,7 @@ add_subdirectory(SRC)
- if(BUILD_TESTING)
- add_subdirectory(TESTING)
- endif(BUILD_TESTING)
--configure_file(${CMAKE_CURRENT_SOURCE_DIR}/blas.pc.in ${CMAKE_CURRENT_BINARY_DIR}/blas.pc)
-+configure_file(${CMAKE_CURRENT_SOURCE_DIR}/blas.pc.in ${CMAKE_CURRENT_BINARY_DIR}/blas.pc @ONLY)
- install(FILES
-   ${CMAKE_CURRENT_BINARY_DIR}/blas.pc
-   DESTINATION ${PKG_CONFIG_DIR}
-diff --git a/BLAS/blas.pc.in b/BLAS/blas.pc.in
-index 845a25c..7a53ea5 100644
---- a/BLAS/blas.pc.in
-+++ b/BLAS/blas.pc.in
-@@ -1,5 +1,7 @@
--prefix=@prefix@
--libdir=@libdir@
-+prefix=@CMAKE_INSTALL_PREFIX@
-+exec_prefix=${prefix}
-+libdir=${exec_prefix}/@CMAKE_INSTALL_LIBDIR@
-+includedir=${prefix}/include
- 
- Name: blas
- Description: Basic Linear Algebra Subprograms F77 reference implementations
-diff --git a/CBLAS/CMakeLists.txt b/CBLAS/CMakeLists.txt
-index 98b481f..8f98b04 100644
---- a/CBLAS/CMakeLists.txt
-+++ b/CBLAS/CMakeLists.txt
-@@ -71,7 +71,7 @@ configure_file(${CMAKE_CURRENT_SOURCE_DIR}/CMAKE/cblas-config-build.cmake.in
-   ${LAPACK_BINARY_DIR}/cblas-config.cmake @ONLY)
- 
- 
--configure_file(${CMAKE_CURRENT_SOURCE_DIR}/cblas.pc.in ${CMAKE_CURRENT_BINARY_DIR}/cblas.pc)
-+configure_file(${CMAKE_CURRENT_SOURCE_DIR}/cblas.pc.in ${CMAKE_CURRENT_BINARY_DIR}/cblas.pc @ONLY)
-   install(FILES
-   ${CMAKE_CURRENT_BINARY_DIR}/cblas.pc
-   DESTINATION ${PKG_CONFIG_DIR}
-diff --git a/CBLAS/cblas.pc.in b/CBLAS/cblas.pc.in
-index ee20206..14a141e 100644
---- a/CBLAS/cblas.pc.in
-+++ b/CBLAS/cblas.pc.in
-@@ -1,9 +1,12 @@
--prefix=@prefix@
--libdir=@libdir@
-+prefix=@CMAKE_INSTALL_PREFIX@
-+exec_prefix=${prefix}
-+libdir=${exec_prefix}/@CMAKE_INSTALL_LIBDIR@
-+includedir=${prefix}/include/@PROFNAME@
- 
--Name: lapacke
-+Name: cblas-reference
- Description: C Standard Interface to BLAS Linear Algebra PACKage
- Version: @LAPACK_VERSION@
- URL: http://www.netlib.org/lapack/
- Libs: -L${libdir} -lcblas
-+Cflags: -I${includedir}
- Requires: blas
-diff --git a/CMakeLists.txt b/CMakeLists.txt
-index ab29bd2..31b878a 100644
---- a/CMakeLists.txt
-+++ b/CMakeLists.txt
-@@ -333,7 +333,7 @@ configure_file(${LAPACK_SOURCE_DIR}/CMAKE/lapack-config-build.cmake.in
-   ${LAPACK_BINARY_DIR}/lapack-config.cmake @ONLY)
- 
- 
--configure_file(${CMAKE_CURRENT_SOURCE_DIR}/lapack.pc.in ${CMAKE_CURRENT_BINARY_DIR}/lapack.pc)
-+configure_file(${CMAKE_CURRENT_SOURCE_DIR}/lapack.pc.in ${CMAKE_CURRENT_BINARY_DIR}/lapack.pc @ONLY)
-   install(FILES
-   ${CMAKE_CURRENT_BINARY_DIR}/lapack.pc
-   DESTINATION ${PKG_CONFIG_DIR}
-diff --git a/LAPACKE/CMakeLists.txt b/LAPACKE/CMakeLists.txt
-index 008f24c..d8c4cb0 100644
---- a/LAPACKE/CMakeLists.txt
-+++ b/LAPACKE/CMakeLists.txt
-@@ -65,7 +65,7 @@ if(BUILD_TESTING)
- endif(BUILD_TESTING)
- 
- 
--configure_file(${CMAKE_CURRENT_SOURCE_DIR}/lapacke.pc.in ${CMAKE_CURRENT_BINARY_DIR}/lapacke.pc)
-+configure_file(${CMAKE_CURRENT_SOURCE_DIR}/lapacke.pc.in ${CMAKE_CURRENT_BINARY_DIR}/lapacke.pc @ONLY)
-  install(FILES
-   ${CMAKE_CURRENT_BINARY_DIR}/lapacke.pc
-   DESTINATION ${PKG_CONFIG_DIR}
-diff --git a/LAPACKE/lapacke.pc.in b/LAPACKE/lapacke.pc.in
-index 75e6871..ce5201b 100644
---- a/LAPACKE/lapacke.pc.in
-+++ b/LAPACKE/lapacke.pc.in
-@@ -1,5 +1,7 @@
--prefix=@prefix@
--libdir=@libdir@
-+prefix=@CMAKE_INSTALL_PREFIX@
-+exec_prefix=${prefix}
-+libdir=${exec_prefix}/@CMAKE_INSTALL_LIBDIR@
-+includedir=${prefix}/include
- 
- Name: lapacke
- Description: C Standard Interface to LAPACK Linear Algebra PACKage
-diff --git a/lapack.pc.in b/lapack.pc.in
-index d34c870..0d0750f 100644
---- a/lapack.pc.in
-+++ b/lapack.pc.in
-@@ -1,5 +1,7 @@
--prefix=@prefix@
--libdir=@libdir@
-+prefix=@CMAKE_INSTALL_PREFIX@
-+exec_prefix=${prefix}
-+libdir=${exec_prefix}/@CMAKE_INSTALL_LIBDIR@
-+includedir=${prefix}/include
- 
- Name: lapack
- Description: FORTRAN reference implementation of LAPACK Linear Algebra PACKage
diff --git a/sci-libs/cblas-reference/files/lapack-reference-3.7.0-fix-build-system.patch b/sci-libs/cblas-reference/files/lapack-reference-3.7.0-fix-build-system.patch
deleted file mode 100644
index 40f3aaa02..000000000
--- a/sci-libs/cblas-reference/files/lapack-reference-3.7.0-fix-build-system.patch
+++ /dev/null
@@ -1,61 +0,0 @@
-diff --git a/BLAS/blas.pc.in b/BLAS/blas.pc.in
-index 7fd6f1e..e52f3ad 100644
---- a/BLAS/blas.pc.in
-+++ b/BLAS/blas.pc.in
-@@ -1,5 +1,7 @@
--prefix=@prefix@
--libdir=@libdir@
-+prefix=@CMAKE_INSTALL_PREFIX@
-+exec_prefix=${prefix}
-+libdir=${exec_prefix}/@CMAKE_INSTALL_LIBDIR@
-+includedir=${prefix}/include
- 
- Name: BLAS
- Description: FORTRAN reference implementation of BLAS Basic Linear Algebra Subprograms
-diff --git a/CBLAS/cblas.pc.in b/CBLAS/cblas.pc.in
-index 4a938fe..269a254 100644
---- a/CBLAS/cblas.pc.in
-+++ b/CBLAS/cblas.pc.in
-@@ -1,9 +1,12 @@
--prefix=@prefix@
--libdir=@libdir@
-+prefix=@CMAKE_INSTALL_PREFIX@
-+exec_prefix=${prefix}
-+libdir=${exec_prefix}/@CMAKE_INSTALL_LIBDIR@
-+includedir=${prefix}/include/@PROFNAME@
- 
- Name: CBLAS
- Description: C Standard Interface to BLAS Basic Linear Algebra Subprograms
- Version: @LAPACK_VERSION@
- URL: http://www.netlib.org/blas/#_cblas
-+Cflags: -I${includedir}
- Libs: -L${libdir} -lcblas
- Requires: blas
-diff --git a/LAPACKE/lapacke.pc.in b/LAPACKE/lapacke.pc.in
-index 028f8da..dc092b1 100644
---- a/LAPACKE/lapacke.pc.in
-+++ b/LAPACKE/lapacke.pc.in
-@@ -1,5 +1,7 @@
--prefix=@prefix@
--libdir=@libdir@
-+prefix=@CMAKE_INSTALL_PREFIX@
-+exec_prefix=${prefix}
-+libdir=${exec_prefix}/@CMAKE_INSTALL_LIBDIR@
-+includedir=${prefix}/include
- 
- Name: LAPACKE
- Description: C Standard Interface to LAPACK Linear Algebra PACKage
-diff --git a/lapack.pc.in b/lapack.pc.in
-index 878efc2..2cca4c2 100644
---- a/lapack.pc.in
-+++ b/lapack.pc.in
-@@ -1,5 +1,7 @@
--prefix=@prefix@
--libdir=@libdir@
-+prefix=@CMAKE_INSTALL_PREFIX@
-+exec_prefix=${prefix}
-+libdir=${exec_prefix}/@CMAKE_INSTALL_LIBDIR@
-+includedir=${prefix}/include
- 
- Name: LAPACK
- Description: FORTRAN reference implementation of LAPACK Linear Algebra PACKage
diff --git a/sci-libs/cblas-reference/metadata.xml b/sci-libs/cblas-reference/metadata.xml
deleted file mode 100644
index eb9d2972b..000000000
--- a/sci-libs/cblas-reference/metadata.xml
+++ /dev/null
@@ -1,21 +0,0 @@
-<?xml version="1.0" encoding="UTF-8"?>
-<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
-<pkgmetadata>
-	<maintainer type="project">
-		<email>sci@gentoo.org</email>
-		<name>Gentoo Science Project</name>
-	</maintainer>
-	<longdescription lang="en">
-The BLAS (Basic Linear Algebra Subprograms) are high quality "building
-block" routines for performing basic vector and matrix operations. Level 1
-BLAS do vector-vector operations, Level 2 BLAS do matrix-vector operations,
-and Level 3 BLAS do matrix-matrix operations. Because the BLAS are
-efficient, portable, and widely available, they're commonly used in the
-development of high quality linear algebra software, LAPACK for
-example. This packages implements the reference C library as a wrapper
-to the FORTRAN 77 BLAS library.
-</longdescription>
-	<use>
-		<flag name="int64">Build the 64 bits integer library</flag>
-	</use>
-</pkgmetadata>
diff --git a/sci-libs/ccif/Manifest b/sci-libs/ccif/Manifest
index 5d9dddd6f..9f2e8cd36 100644
--- a/sci-libs/ccif/Manifest
+++ b/sci-libs/ccif/Manifest
@@ -1 +1 @@
-DIST ccif-0.3.20111209.tar.gz 745587 SHA256 fb68592c82320f5c962eac31865e5dc1bc22d8442628d0468c988f4e6b34eea6 SHA512 7338d2356a5b40d2e5d949a3223318a17f59416cb3a2a1ad953bd2fb239c48168f769638d5658f1e1999a0a415b19e65a9773ac7ba448263f7e488b688dbecfb WHIRLPOOL feee2e3a4d4a72622de7c5536eff35f6e375e859a6c57a26ca0d5d8e55a1c0ded80fe08b880d89e462ebfc2b4b969a8d21065f0b6f2af53e3173203809107b21
+DIST ccif-0.4.20120917.tar.bz2 742256 BLAKE2B 8e5ff458c94adbfc13e20661c1c6d2948867aa0b72eea0a7d043135e7d81cb923561318366e79df5e6d30e1d69ecea43cd5dc9139cad47647d987e7bb82e72a0 SHA512 1209cd16039a9b05b796c0e06454d9e9753da586d40883fa2b60883bc757b1868c3b58654cf930be9337e1002a366c32d4970d8acba4eae14b65f86946162e0e
diff --git a/sci-libs/ccif/ccif-0.3.20111209.ebuild b/sci-libs/ccif/ccif-0.3.20111209.ebuild
deleted file mode 100644
index a9263b99d..000000000
--- a/sci-libs/ccif/ccif-0.3.20111209.ebuild
+++ /dev/null
@@ -1,18 +0,0 @@
-# Copyright 1999-2015 Gentoo Foundation
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=5
-
-inherit autotools-utils fortran-2
-
-DESCRIPTION="CCP4 ccif lib"
-HOMEPAGE="http://www.ccp4.ac.uk/"
-SRC_URI="ftp://ftp.ccp4.ac.uk/opensource/${P}.tar.gz"
-
-SLOT="0"
-KEYWORDS="~amd64 ~x86 ~amd64-linux ~x86-linux"
-LICENSE="LGPL-3"
-IUSE="static-libs"
-
-RDEPEND="virtual/fortran"
-DEPEND="${RDEPEND}"
diff --git a/sci-libs/ccif/ccif-0.4.20120917.ebuild b/sci-libs/ccif/ccif-0.4.20120917.ebuild
new file mode 100644
index 000000000..d1a97a90a
--- /dev/null
+++ b/sci-libs/ccif/ccif-0.4.20120917.ebuild
@@ -0,0 +1,17 @@
+# Copyright 1999-2021 Gentoo Authors
+# Distributed under the terms of the GNU General Public License v2
+
+EAPI=7
+
+inherit fortran-2
+
+DESCRIPTION="CCP4 ccif lib"
+HOMEPAGE="https://www.ccp4.ac.uk/"
+SRC_URI="ftp://ftp.ccp4.ac.uk/opensource/${P}.tar.bz2"
+
+SLOT="0"
+KEYWORDS="~amd64 ~x86 ~amd64-linux ~x86-linux"
+LICENSE="LGPL-3"
+
+RDEPEND="virtual/fortran"
+DEPEND="${RDEPEND}"
diff --git a/sci-libs/cgnstools/Manifest b/sci-libs/cgnstools/Manifest
deleted file mode 100644
index 291273ebf..000000000
--- a/sci-libs/cgnstools/Manifest
+++ /dev/null
@@ -1 +0,0 @@
-DIST cgnstools-2-5-4.tar.gz 1339468 BLAKE2B 90664f29773e816c5891a3792680247eb943e810d06f104c6b7590336b5a824037e6cbeee8aa345452b6953573261a2f45e572ce86268777ab66fc84ad3a5bbc SHA512 84720ec61dc686315f53c5d76f5721a177df567ee43020cb4e45a87b501d70283d7df28584ad2656605677677e477e14c4a78482f45fff018aac877d1e099eca
diff --git a/sci-libs/cgnstools/cgnstools-2.5.4-r1.ebuild b/sci-libs/cgnstools/cgnstools-2.5.4-r1.ebuild
deleted file mode 100644
index 250cb60ed..000000000
--- a/sci-libs/cgnstools/cgnstools-2.5.4-r1.ebuild
+++ /dev/null
@@ -1,63 +0,0 @@
-# Copyright 1999-2015 Gentoo Foundation
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=5
-
-inherit eutils multilib versionator
-
-MY_P="${PN}-$(replace_all_version_separators '-')"
-
-DESCRIPTION="The CFD General Notation System (CGNS) tools"
-HOMEPAGE="http://www.cgns.org/"
-SRC_URI="mirror://sourceforge/cgns/${MY_P}.tar.gz"
-
-LICENSE="ZLIB"
-SLOT="0"
-KEYWORDS="~amd64 ~x86"
-IUSE="hdf5 tcl tk X"
-
-DEPEND="
-	hdf5? ( sci-libs/cgnslib[hdf5] )
-	!hdf5? ( sci-libs/cgnslib[-hdf5] )
-	tcl? ( dev-lang/tcl:0= )
-	tk? ( dev-lang/tk:0= )"
-
-RDEPEND="${DEPEND}"
-
-S=${WORKDIR}/${PN}
-
-PATCHES=(
-	"${FILESDIR}"/${P}.patch
-	"${FILESDIR}"/${P}_cgns_to_vtk2D.patch
-	"${FILESDIR}"/${P}_gcc4.4.patch
-	"${FILESDIR}"/${P}_tcltk.patch
-)
-
-src_prepare() {
-	epatch "${PATCHES[@]}"
-}
-
-src_configure() {
-	local myconf
-	myconf="${myconf} --enable-gcc --enable-64bit --with-cgns=/usr/include --bindir=${D}/usr/bin --datadir=${D}/usr/share/${PN}"
-	use hdf5 && myconf="${myconf} --with-adfh=/usr/include/adfh"
-
-	if use tcl ; then
-		TCLVER="$(echo 'puts [info tclversion]' | $(type -P tclsh))"
-		myconf="${myconf} $(use_with tcl tcl /usr/$(get_libdir)/tcl${TCLVER})"
-		sed -i -e "s|TKLIBS = |TKLIBS = -ltcl${TCLVER} |" make.defs.in || die
-	fi
-
-	if use tk ; then
-		# no, there's no tkversion, and type -P wish requires running X
-		TKVER="$(echo 'puts [info tclversion]' | $(type -P tclsh))"
-		myconf="${myconf} $(use_with tk tk /usr/$(get_libdir)/tk${TKVER})"
-		sed -i -e "s|TKLIBS = |TKLIBS = -ltk${TKVER} |" make.defs.in || die
-	fi
-
-	econf \
-		$(use_with X x) \
-		${myconf}
-
-	sed -i -e "s|${D}||" cgconfig || die
-}
diff --git a/sci-libs/cgnstools/files/cgnstools-2.5.4.patch b/sci-libs/cgnstools/files/cgnstools-2.5.4.patch
deleted file mode 100644
index 2ca665966..000000000
--- a/sci-libs/cgnstools/files/cgnstools-2.5.4.patch
+++ /dev/null
@@ -1,121 +0,0 @@
---- cgnstools-2.5.2.orig/configure
-+++ cgnstools-2.5.2/configure
-@@ -1568,9 +1568,9 @@
-   fi
-   cgnslib=`grep "^LIBCGNS *=" $CGNSDIR/make.$SYSTEM | sed "s/^LIBCGNS *= *//"`
-   if test -z `echo $cgnslib | grep "/"`; then
--    CGNSLIB=\$\(CGNSDIR\)/lib/\$\(LIBCGNS\)
-+    CGNSLIB=/usr/lib/libcgns.so
-   else
--    CGNSLIB=\$\(CGNSDIR\)/\$\(LIBCGNS\)
-+    CGNSLIB=/usr/lib/libcgns.so
-   fi
-   HDF5LIBS="\$(HDF5LIB) \$(SZIPLIB) \$(ZLIBLIB)"
- else
-@@ -1583,7 +1583,7 @@
-       `ls -dr ../* 2>/dev/null` \
-       `ls -dr ../../* 2>/dev/null` \
-       `ls -dr ../../../* 2>/dev/null` ; do
--      if test -f "$d/src/ADF.h" && test -f "$d/src/ADFH.h"; then
-+      if test -f "$d/ADF.h" && test -f "$d/src/ADFH.h"; then
-         adfhdir=`(cd $d; pwd)`
-         echo "$ac_t""$adfhdir" 1>&6
-         break
-@@ -1591,12 +1591,12 @@
-     done
-   else
-     echo "$ac_t""$adfhdir" 1>&6
--    if test ! -f "$adfhdir/src/ADF.h" || test ! -f "$adfhdir/src/ADFH.h"; then
-+    if test ! -f "$adfhdir/ADF.h" || test ! -f "$adfhdir/ADFH.h"; then
-       { echo "configure: error: $adfhdir directory does not contain src/ADF.h and src/ADFH.h" 1>&2; exit 1; }
-     fi
-   fi
--  ADFDIR=$adfhdir/src
--  CGNSLIB=$adfhdir/\$\(SYSTEM\)/libcgns.\$\(A\)
-+  ADFDIR=$adfhdir
-+  CGNSLIB=/usr/lib/libcgns.so
-   if test -f "$adfhdir/make.$SYSTEM"; then
-     hdf5lib=`grep "^HDF5LIB *=" $adfhdir/make.$SYSTEM | sed "s/^HDF5LIB *= *//"`
-     sziplib=`grep "^SZIPLIB *=" $adfhdir/make.$SYSTEM | sed "s/^SZIPLIB *= *//"`
-@@ -1997,7 +1997,7 @@
-       `ls -dr ../tk8* 2>/dev/null` \
-       `ls -dr ../../tk8* 2>/dev/null` \
-       `ls -dr ../../../tk8* 2>/dev/null` ; do
--      if test -f "$d/unix/tkConfig.sh"; then
-+      if test -f "$d/../tkConfig.sh"; then
-         tkdir=`(cd $d; pwd)`
-         break
-       fi
-@@ -2034,13 +2034,13 @@
-     { echo "configure: error: Tcl directory $tcldir not found" 1>&2; exit 1; }
-   fi
-   tcldir=`(cd $tcldir; pwd)`
--  if test ! -f "$tcldir/unix/tclConfig.sh"; then
-+  if test ! -f "$tcldir/../tclConfig.sh"; then
-     { echo "configure: error: tclConfig.sh not found in $tcldir/unix" 1>&2; exit 1; }
-   fi
-   if test -z "$tkdir"; then
-     dir=`dirname $tcldir`
-     for d in `ls -dr $dir/tk* 2>/dev/null` ; do
--      if test -f "$d/unix/tkConfig.sh"; then
-+      if test -f "$d/../tkConfig.sh"; then
-         tkdir=$d
-         break
-       fi
-@@ -2056,14 +2056,14 @@
-     { echo "configure: error: Tk directory $tkdir not found" 1>&2; exit 1; }
-   fi
-   tkdir=`(cd $tkdir; pwd)`
--  TKCONFIG="$tkdir/unix/tkConfig.sh"
-+  TKCONFIG="$tkdir/../tkConfig.sh"
-   if test ! -f "$TKCONFIG"; then
-     { echo "configure: error: tkConfig.sh not found in $tkdir/unix" 1>&2; exit 1; }
-   fi
-   if test -z "$tcldir"; then
-     dir=`dirname $tkdir`
-     for d in `ls -dr $dir/tcl* 2>/dev/null` ; do
--      if test -f "$d/unix/tclConfig.sh"; then
-+      if test -f "$d/../tclConfig.sh"; then
-         tcldir=$d
-         break
-       fi
-@@ -2073,8 +2073,8 @@
-     fi
-   fi
-   . $TKCONFIG
--  tcllib=`ls -d $tcldir/unix/libtcl8* 2>/dev/null`
--  tklib=`ls -d $tkdir/unix/libtk8* 2>/dev/null`
-+  tcllib=`ls -d $tcldir/libtcl8* 2>/dev/null`
-+  tklib=`ls -d $tkdir/libtk8* 2>/dev/null`
-   X11LIBS=""
-   TKINCS="-I$tcldir/generic -I$tkdir/generic"
-   if test "$ac_cv_cygwin" = "yes"; then
---- cgnstools-2.5.2.orig/make.defs.in
-+++ cgnstools-2.5.2/make.defs.in
-@@ -3,7 +3,7 @@
- SYSTEM = @SYSTEM@
- CGNSDIR = @CGNSDIR@
- 
--include $(CGNSDIR)/make.$(SYSTEM)
-+# include $(CGNSDIR)/make.$(SYSTEM)
- 
- ADFINC = @ADFDIR@
- 
-@@ -40,7 +40,7 @@
- # strip command for executables - set to true if not used
- #------------------------------------------------------------------------
- 
--STRIP = @STRIP@
-+STRIP = true
- 
- #------------------------------------------------------------------------
- # library archiver and ranlib
-@@ -78,7 +78,7 @@
- 
- BIN_INSTALL_DIR = @BIN_INSTALL_DIR@
- EXE_INSTALL_DIR = @EXE_INSTALL_DIR@
--WSH_INSTALL_DIR = $(EXE_INSTALL_DIR)/cgnswish
-+WSH_INSTALL_DIR = $(EXE_INSTALL_DIR)
- LIB_INSTALL_DIR = @LIB_INSTALL_DIR@
- 
- #-----------------------------------------------------------------------
diff --git a/sci-libs/cgnstools/files/cgnstools-2.5.4_cgns_to_vtk2D.patch b/sci-libs/cgnstools/files/cgnstools-2.5.4_cgns_to_vtk2D.patch
deleted file mode 100644
index aa9972dd1..000000000
--- a/sci-libs/cgnstools/files/cgnstools-2.5.4_cgns_to_vtk2D.patch
+++ /dev/null
@@ -1,49 +0,0 @@
---- cgnstools-2.5.4.orig/utilities/cgns_to_vtk.c	2007-09-05 18:24:50.000000000 +0200
-+++ cgnstools-2.5.4/utilities/cgns_to_vtk.c	2009-10-30 19:44:58.000000000 +0100
-@@ -197,7 +197,7 @@
- 
- static int get_nodes (int nz, ZoneType_t zonetype, int *sizes)
- {
--    int i, j, n, ncoords;
-+    int i, j, n, ncoords, ii, jj;
-     int rind[6], rng[2][3];
-     DataType_t datatype;
-     float *xyz;
-@@ -248,6 +248,14 @@
-     strcpy (coordtype, "   ");
-     xyz = (float *) malloc (nnodes * sizeof(float));
-     nodes = (Node *) malloc (nnodes * sizeof(Node));
-+
-+    // make sure the array is initialized with 0.0 (important for 2D meshes)
-+    for(jj= 0; jj < nnodes; jj++){
-+        for(ii= 0; ii < 3; ii++){
-+                nodes[jj][ii] = 0.0;
-+                }
-+        }
-+
-     if (xyz == NULL || nodes == NULL)
-         FATAL ("malloc failed for nodes");
- 
-@@ -980,7 +988,7 @@
-         FATAL (NULL);
-     printf ("  using base %d - %s\n", cgnsbase, name);
-     fflush (stdout);
--    if (PhyDim != 3 /*|| (CellDim != 1 && CellDim != 3)*/)
-+    if (PhyDim != 3 && CellDim != 2)
-         FATAL ("cell and/or physical dimension invalid");
- 
-     if (cg_nzones (cgnsfn, cgnsbase, &nzones))
-@@ -1043,8 +1051,12 @@
-         fprintf (fp, "%s\n", ascii ? "ASCII" : "BINARY");
-         if (zonetype == Structured) {
-             fprintf (fp, "DATASET STRUCTURED_GRID\n");
-+            int dim3 = sizes[2];
-+            if ( CellDim == 2 ) {
-+                dim3 = 1;
-+            }
-             fprintf (fp, "DIMENSIONS %d %d %d\n",
--                sizes[0], sizes[1], sizes[2]);
-+                sizes[0], sizes[1], dim3);
-         }
-         else
-             fprintf (fp, "DATASET UNSTRUCTURED_GRID\n");
diff --git a/sci-libs/cgnstools/files/cgnstools-2.5.4_gcc4.4.patch b/sci-libs/cgnstools/files/cgnstools-2.5.4_gcc4.4.patch
deleted file mode 100644
index 1df1a9aea..000000000
--- a/sci-libs/cgnstools/files/cgnstools-2.5.4_gcc4.4.patch
+++ /dev/null
@@ -1,84 +0,0 @@
---- cgnstools-2.5.4.orig/utilities/tecplot_to_cgns.c
-+++ cgnstools-2.5.4/utilities/tecplot_to_cgns.c
-@@ -60,11 +60,11 @@
-     }
- }
- 
--/*---------- getline ------------------------------------------------
-+/*---------- getlineCGNS ------------------------------------------------
-  * get next non-blank line
-  *-------------------------------------------------------------------*/
- 
--static char *getline (FILE *fp)
-+static char *getlineCGNS (FILE *fp)
- {
-     char *p;
- 
-@@ -285,7 +285,7 @@
-         cgnsImportBase (basename);
- 
-     nz = 0;
--    p = getline (fp);
-+    p = getlineCGNS (fp);
- 
-     while (p != NULL) {
- 
-@@ -295,14 +295,14 @@
-             for (p += 9; *p && isspace(*p); p++)
-                 ;
-             if (*p++ != '=') {
--                p = getline (fp);
-+                p = getlineCGNS (fp);
-                 continue;
-             }
-             nvar = 0;
-             xloc = yloc = zloc = -1;
-             while (1) {
-                 if ((s = getvar (&p)) == NULL) {
--                    p = getline (fp);
-+                    p = getlineCGNS (fp);
-                     if (p == NULL || (s = getvar (&p)) == NULL) break;
-                 }
-                 if (0 == strcasecmp ("x", s))
-@@ -337,7 +337,7 @@
-                         cgnsImportFatal ("end of file while reading zone");
-                     ungetc (n, fp);
-                     if (!isalpha (n)) break;
--                    p = getline (fp);
-+                    p = getlineCGNS (fp);
-                     continue;
-                 }
-                 switch (n) {
-@@ -389,7 +389,7 @@
-             if (nn == -1) {
-                 if (ni < 2 || nj < 2 || nk < 2) {
-                     printf("missing I, J and K - skipping zone\n");
--                    p = getline(fp);
-+                    p = getlineCGNS(fp);
-                     continue;
-                 }
-                 nn = ni * nj * nk;
-@@ -400,12 +400,12 @@
-                 if (nn < 3 || ne < 1 || et < 0) {
-                     printf("%d nodes, %d %s elements - skipping zone\n",
-                         nn, ne, elemname);
--                    p = getline(fp);
-+                    p = getlineCGNS(fp);
-                     continue;
-                 }
-                 if (et < 2) {
-                     printf ("%s elements - skipping zone\n", elemname);
--                    p = getline (fp);
-+                    p = getlineCGNS (fp);
-                     continue;
-                 }
-             }
-@@ -478,7 +478,7 @@
-             cgnsImportWrite ();
-         }
- 
--        p = getline (fp);
-+        p = getlineCGNS (fp);
-     }
- 
-     fclose (fp);
diff --git a/sci-libs/cgnstools/files/cgnstools-2.5.4_tcltk.patch b/sci-libs/cgnstools/files/cgnstools-2.5.4_tcltk.patch
deleted file mode 100644
index d9036d0bf..000000000
--- a/sci-libs/cgnstools/files/cgnstools-2.5.4_tcltk.patch
+++ /dev/null
@@ -1,114 +0,0 @@
-From c9606ed1914d88c40e9b076b645bc5f7a8046c86 Mon Sep 17 00:00:00 2001
-From: James Cloos <cloos@jhcloos.com>
-Date: Wed, 16 Jan 2013 20:40:23 -0500
-Subject: [PATCH] Update for current tcl/tk, based on cgns svn trunk.
-
-Signed-off-by: James Cloos <cloos@jhcloos.com>
----
- tkogl/nurbs.c    |  4 +++-
- tkogl/printstr.c |  4 +++-
- tkogl/quadric.c  |  4 +++-
- tkogl/tess.c     |  4 +++-
- tkogl/tkogl.c    | 12 +++++++++---
- 5 files changed, 21 insertions(+), 7 deletions(-)
-
-diff --git a/tkogl/nurbs.c b/tkogl/nurbs.c
-index 6d89be7..34086a3 100644
---- a/tkogl/nurbs.c
-+++ b/tkogl/nurbs.c
-@@ -278,7 +278,9 @@ done:
-    DestroyFloatArray (cPoint);
- 
-    if (result == TCL_OK) {
--      sprintf (interp->result, "%d", dlist);
-+      char tmp[128];
-+      sprintf (tmp, "%d", dlist);
-+      Tcl_SetResult(interp, tmp, TCL_VOLATILE);
-    }
- 
-    return result;
-diff --git a/tkogl/printstr.c b/tkogl/printstr.c
-index 8807525..e3d04f6 100644
---- a/tkogl/printstr.c
-+++ b/tkogl/printstr.c
-@@ -131,7 +131,9 @@ int LoadBitmapFont(Tcl_Interp *interp, int argc, char* argv [])
- 	return TCL_ERROR;
-     }
- 
--    sprintf (interp->result, "%d", fontOffset);
-+    char tmp[128];
-+    sprintf (tmp, "%d", fontOffset);
-+    Tcl_SetResult(interp, tmp, TCL_VOLATILE);
-     return TCL_OK;
- }
- 
-diff --git a/tkogl/quadric.c b/tkogl/quadric.c
-index ea8e7b3..859e440 100644
---- a/tkogl/quadric.c
-+++ b/tkogl/quadric.c
-@@ -147,7 +147,9 @@ done:
-    if (dlist != 0) glEndList(); else return result;
- 
-    if (result == TCL_OK) {
--      sprintf (interp->result, "%d", dlist);
-+      char tmp[128];
-+      sprintf (tmp, "%d", dlist);
-+      Tcl_SetResult(interp, tmp, TCL_VOLATILE);
-    }
-    else {
-       glDeleteLists (dlist, 1);
-diff --git a/tkogl/tess.c b/tkogl/tess.c
-index fa9cf37..c054820 100644
---- a/tkogl/tess.c
-+++ b/tkogl/tess.c
-@@ -122,7 +122,9 @@ Tesselate (Tcl_Interp *interp, int argc, char* argv [])
-    }
-    
-    if (dlist != 0) {
--      sprintf (interp->result, "%d", dlist);
-+      char tmp[128];
-+      sprintf (tmp, "%d", dlist);
-+      Tcl_SetResult(interp, tmp, TCL_VOLATILE);
-    }
-    return TCL_OK;
- }
-diff --git a/tkogl/tkogl.c b/tkogl/tkogl.c
-index 1e7323d..6c91dd1 100644
---- a/tkogl/tkogl.c
-+++ b/tkogl/tkogl.c
-@@ -641,7 +641,7 @@ OGLwinCmd(clientData, interp, argc, argv)
-     ARRANGE_REDRAW(glxwinPtr);
-     GetAbsXY (glxwinPtr);
-     
--    interp->result = Tk_PathName(glxwinPtr->tkwin);
-+    Tcl_SetResult(interp, Tk_PathName(glxwinPtr->tkwin), TCL_VOLATILE);
-     return TCL_OK;
- }
- 
-@@ -998,7 +998,11 @@ OGLwinWidgetCmd(clientData, interp, argc, argv)
- 	        argv += narg;
-         }
-         glEndList();
--        if (result == TCL_OK) sprintf (interp->result, "%d", newlist);
-+        if (result == TCL_OK) {
-+	  char tmp[128];
-+	  sprintf (tmp, "%d", newlist);
-+	  Tcl_SetResult(interp, tmp, TCL_VOLATILE);
-+	}
-    }
-    else if ((c == 'e') && (strncmp(argv[1], "eval", length) == 0)) {
-       /* sends the gl commands directly */
-@@ -1090,7 +1094,9 @@ OGLwinWidgetCmd(clientData, interp, argc, argv)
- 				viewport, &x, &y, &z);	 
-       }
-       if (retval) {
--    	 sprintf (interp->result, "%f %f %f", x, y, z);
-+    	 char tmp[128];
-+	 sprintf (tmp, "%f %f %f", x, y, z);
-+	 Tcl_SetResult(interp, tmp, TCL_VOLATILE);
-       }
-    } 
-    else if ((c == 'r') && (strncmp(argv[1], "redraw", length) == 0)) {
--- 
-1.8.1
-
diff --git a/sci-libs/cgnstools/metadata.xml b/sci-libs/cgnstools/metadata.xml
deleted file mode 100644
index 32379f114..000000000
--- a/sci-libs/cgnstools/metadata.xml
+++ /dev/null
@@ -1,11 +0,0 @@
-<?xml version="1.0" encoding="UTF-8"?>
-<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
-<pkgmetadata>
-	<maintainer type="project">
-		<email>sci@gentoo.org</email>
-		<name>Gentoo Science Project</name>
-	</maintainer>
-	<upstream>
-		<remote-id type="sourceforge">cgns</remote-id>
-	</upstream>
-</pkgmetadata>
diff --git a/sci-libs/ciftilib/Manifest b/sci-libs/ciftilib/Manifest
index 7eecc1b4d..ddc2bbc19 100644
--- a/sci-libs/ciftilib/Manifest
+++ b/sci-libs/ciftilib/Manifest
@@ -1 +1 @@
-DIST ciftilib-1.5.3.tar.gz 1727910 BLAKE2B 21433e6bfdfa51b741bf90d1dfa18fc812fb3e2017a5d2b77c73d01d4ed59389f47b50423cf67d98cf92f6c662c2803c7af2978278f509ae933e70ca85fcf40b SHA512 bb264b532edd50a47ddf48f5e7a48843a70632c2a3d8770c3b2ce4937c5559111047e553d7d48a06bc32acafd2fe251ae61859f80b17e63df7a02a2e4e669fc0
+DIST ciftilib-1.6.0.tar.gz 1728524 BLAKE2B 37144e477709fbab4afa63fb3947216de5a4b21bc36057f119625eea0beaa79ccb0ddc1ce77f4b28f2bee8eb8a5b6e0360df0ccbcc8d80d3033dd64ec7961f12 SHA512 414cb598800abb3dc9c52d9fcc1db1ec4ee019497e5dc950f7cfc3110ea2d83f7da3a5f16bc337058be74afbabe1bba8b1376dc984bb8ec27ba48f80ee89f85a
diff --git a/sci-libs/ciftilib/ciftilib-1.5.3-r1.ebuild b/sci-libs/ciftilib/ciftilib-1.5.3-r1.ebuild
deleted file mode 100644
index ad4894dd1..000000000
--- a/sci-libs/ciftilib/ciftilib-1.5.3-r1.ebuild
+++ /dev/null
@@ -1,61 +0,0 @@
-# Copyright 1999-2018 Gentoo Authors
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI="6"
-
-inherit cmake-utils
-
-DESCRIPTION="C++ Library for reading and writing CIFTI-2 and CIFTI-1 files"
-HOMEPAGE="https://github.com/Washington-University/CiftiLib"
-SRC_URI="https://github.com/Washington-University/CiftiLib/archive/v${PV}.tar.gz -> ${P}.tar.gz"
-
-LICENSE="BSD-2"
-SLOT="0"
-KEYWORDS="~amd64 ~x86"
-IUSE="qt5"
-
-DEPEND="
-	dev-libs/boost
-	qt5? ( dev-qt/qtcore:5 )
-	!qt5? ( dev-cpp/libxmlpp:2.6 )
-	sys-libs/zlib
-	"
-RDEPEND="${DEPEND}"
-
-PATCHES=(
-	"${FILESDIR}"/${PN}-1.5.3-openmp_in_pc.patch
-	)
-
-S="${WORKDIR}/CiftiLib-${PV}"
-
-#TODO: Enable doc building and installation
-
-src_prepare(){
-	# Make sure that CiftiLib headers and code can
-	# coexist with nifti_io headers.
-	# This takes care of the guard in the nifti1.h header
-	# found in both code base.
-	sed \
-		-e "s:NIFTI_:CIFTI_NIFTI__:g" \
-		-i `grep -rl NIFTI_ *`
-	sed \
-		-e "s:DT_:CIFTI_DT_:g" \
-		-i `grep -rl DT_ *`
-
-	cmake-utils_src_prepare
-}
-
-src_configure() {
-	local mycmakeargs=(-DBUILD_SHARED_LIBS=ON)
-	use qt5 || mycmakeargs+=(-DIGNORE_QT=TRUE)
-
-	cmake-utils_src_configure
-}
-
-src_test(){
-	#The testsuite is not designed to run in parallel
-	local myctestargs=(
-			-j1
-	)
-	cmake-utils_src_test
-}
diff --git a/sci-libs/ciftilib/ciftilib-1.6.0.ebuild b/sci-libs/ciftilib/ciftilib-1.6.0.ebuild
new file mode 100644
index 000000000..fffd4f9c1
--- /dev/null
+++ b/sci-libs/ciftilib/ciftilib-1.6.0.ebuild
@@ -0,0 +1,63 @@
+# Copyright 1999-2021 Gentoo Authors
+# Distributed under the terms of the GNU General Public License v2
+
+EAPI=7
+
+inherit cmake
+
+DESCRIPTION="C++ Library for reading and writing CIFTI-2 and CIFTI-1 files"
+HOMEPAGE="https://github.com/Washington-University/CiftiLib"
+SRC_URI="https://github.com/Washington-University/CiftiLib/archive/v${PV}.tar.gz -> ${P}.tar.gz"
+
+LICENSE="BSD-2"
+SLOT="0"
+KEYWORDS="~amd64 ~x86"
+IUSE="qt5"
+
+DEPEND="
+	dev-libs/boost
+	qt5? ( dev-qt/qtcore:5 )
+	!qt5? ( dev-cpp/libxmlpp:2.6 )
+	sys-libs/zlib
+	"
+RDEPEND="${DEPEND}"
+
+S="${WORKDIR}/CiftiLib-${PV}"
+
+# fix submitted upstream
+# https://github.com/Washington-University/CiftiLib/pull/23
+PATCHES=(
+	"${FILESDIR}/${P}-version.patch"
+)
+
+#TODO: Enable doc building and installation
+
+src_prepare(){
+	# Make sure that CiftiLib headers and code can
+	# coexist with nifti_io headers.
+	# This takes care of the guard in the nifti1.h header
+	# found in both code base.
+	sed \
+		-e "s:NIFTI_:CIFTI_NIFTI__:g" \
+		-i `grep -rl NIFTI_ *`
+	sed \
+		-e "s:DT_:CIFTI_DT_:g" \
+		-i `grep -rl DT_ *`
+
+	cmake_src_prepare
+}
+
+src_configure() {
+	local mycmakeargs=(-DBUILD_SHARED_LIBS=ON)
+	use qt5 || mycmakeargs+=(-DIGNORE_QT=TRUE)
+
+	cmake_src_configure
+}
+
+src_test(){
+	#The testsuite is not designed to run in parallel
+	local myctestargs=(
+			-j1
+	)
+	cmake_src_test
+}
diff --git a/sci-libs/ciftilib/files/ciftilib-1.5.3-openmp_in_pc.patch b/sci-libs/ciftilib/files/ciftilib-1.5.3-openmp_in_pc.patch
deleted file mode 100644
index 6fd35159a..000000000
--- a/sci-libs/ciftilib/files/ciftilib-1.5.3-openmp_in_pc.patch
+++ /dev/null
@@ -1,12 +0,0 @@
-diff --git a/CiftiLib.pc.in b/CiftiLib.pc.in
-index 13cd78c..8db6c46 100644
---- a/CiftiLib.pc.in
-+++ b/CiftiLib.pc.in
-@@ -5,6 +5,6 @@ Name: CiftiLib
- Description: C++ Library for reading and writing CIFTI-2 and CIFTI-1 files
- Version: @CIFTILIB_VERSION@
- URL: https://github.com/Washington-University/CiftiLib
--Cflags: -I${includedir}/CiftiLib @CIFTILIB_PKGCONFIG_DEFINE@
-+Cflags: -I${includedir}/CiftiLib @CIFTILIB_PKGCONFIG_DEFINE@ @OpenMP_CXX_FLAGS@
- Libs: -L${libdir} -lCifti
- @CIFTILIB_PKGCONFIG_REQUIRES_LINE@
diff --git a/sci-libs/ciftilib/files/ciftilib-1.6.0-version.patch b/sci-libs/ciftilib/files/ciftilib-1.6.0-version.patch
new file mode 100644
index 000000000..e64a55f2f
--- /dev/null
+++ b/sci-libs/ciftilib/files/ciftilib-1.6.0-version.patch
@@ -0,0 +1,27 @@
+--- a/CMakeLists.txt
++++ b/CMakeLists.txt
+@@ -83,18 +83,18 @@ ENDIF (NOT QT_FOUND)
+ INCLUDE_DIRECTORIES(${Boost_INCLUDE_DIRS})
+ SET(LIBS ${LIBS} ${Boost_LIBRARIES})
+ #boost quirks
+-IF (Boost_VERSION LESS 104400)
++IF (Boost_VERSION VERSION_LESS 1.44.00)
+     #absolute() was added in 1.44.0, with filesystem v3
+     ADD_DEFINITIONS(-DCIFTILIB_BOOST_NO_FSV3)
+-ENDIF (Boost_VERSION LESS 104400)
+-IF (Boost_VERSION LESS 104800)
++ENDIF (Boost_VERSION VERSION_LESS 1.44.00)
++IF (Boost_VERSION VERSION_LESS 1.48.00)
+     #canonical() was added in 1.48.0
+     ADD_DEFINITIONS(-DCIFTILIB_BOOST_NO_CANONICAL)
+-ENDIF (Boost_VERSION LESS 104800)
+-IF (Boost_VERSION LESS 105600)
++ENDIF (Boost_VERSION VERSION_LESS 1.48.00)
++IF (Boost_VERSION VERSION_LESS 1.56.00)
+     #try_lexical_cast was added in 1.56.0
+     ADD_DEFINITIONS(-DCIFTILIB_BOOST_NO_TRY_LEXICAL)
+-ENDIF (Boost_VERSION LESS 105600)
++ENDIF (Boost_VERSION VERSION_LESS 1.56.00)
+
+ #zlib, useful for volume reading
+ FIND_PACKAGE(ZLIB)
diff --git a/sci-libs/ciftilib/metadata.xml b/sci-libs/ciftilib/metadata.xml
index 41b3ce0fc..99e2180fa 100644
--- a/sci-libs/ciftilib/metadata.xml
+++ b/sci-libs/ciftilib/metadata.xml
@@ -3,7 +3,7 @@
 <pkgmetadata>
 	<maintainer type="project">
 		<name>Horea Christian</name>
-		<email>horea.christian@gmail.com</email>
+		<email>gentoo@chymera.eu</email>
 	</maintainer>
 	<maintainer type="person">
 		<email>slis@gentoo.org</email>
diff --git a/sci-libs/clblas/Manifest b/sci-libs/clblas/Manifest
deleted file mode 100644
index 7eefa4b8f..000000000
--- a/sci-libs/clblas/Manifest
+++ /dev/null
@@ -1,2 +0,0 @@
-DIST clblas-2.10.tar.gz 1154117 BLAKE2B 67035b03ab3a8fa07f32cb8d1d40af39fd885ceb21d9754f8a49a62adcfacbeeec703dfdae922ec0fc915a2dcadff2fc2f07a6c5ced74db3da6cd85c6c63f4d5 SHA512 5ed43104aae565292e0df4cc9e014cf483ccc0ff89257ebb5817f6508bfc9593585ed658da639f2167fbfb5d92ef116be4d5de3694f56e1a1e228bd42b1c05c6
-DIST clblas-2.8.tar.gz 1144713 BLAKE2B e6afbfe902ff0309f0d420c7f9d257f97364dce8563d2a107b1a1ba864759e0d62ef1523df3dc1efb14c8ccc6f50eca6dbf388ac6f16d5a0afb41a96026e1532 SHA512 866b02b995f6c717e954cea0d05dcbbde13906e0f9fbdcf81373a1317a4b61bb6565afb45271f943f99e5742155e9a1d2b5224e469f757a7c02d6adb5b43055a
diff --git a/sci-libs/clblas/clblas-2.10.ebuild b/sci-libs/clblas/clblas-2.10.ebuild
deleted file mode 100644
index 01d8a1825..000000000
--- a/sci-libs/clblas/clblas-2.10.ebuild
+++ /dev/null
@@ -1,69 +0,0 @@
-# Copyright 1999-2017 Gentoo Foundation
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=6
-
-PYTHON_COMPAT=( python2_7 )
-
-inherit cmake-utils python-single-r1
-
-MY_PN="clBLAS"
-
-DESCRIPTION="A software library containing BLAS routines for OpenCL"
-HOMEPAGE="https://github.com/clMathLibraries/clBLAS"
-SRC_URI="https://github.com/clMathLibraries/${MY_PN}/archive/v${PV}.tar.gz -> ${P}.tar.gz"
-
-LICENSE="Apache-2.0"
-SLOT="0"
-KEYWORDS="~amd64"
-IUSE="+client examples +ktest performance test"
-
-REQUIRED_USE="performance? ( ${PYTHON_REQUIRED_USE} )"
-
-RDEPEND="
-	dev-libs/boost
-	virtual/opencl
-	|| ( >=dev-util/amdapp-2.9 dev-util/intel-ocl-sdk )
-	performance? ( ${PYTHON_DEPS} )
-	"
-DEPEND="${RDEPEND}"
-#	test? (
-#		>=dev-cpp/gtest-1.6.0
-#	)"
-
-# The tests only get compiled to an executable named Test, which is not recogniozed by cmake.
-# Therefore src_test() won't execute any test.
-RESTRICT="test"
-
-S="${WORKDIR}/${MY_PN}-${PV}/src"
-
-pkg_pretend() {
-	if [[ ${MERGE_TYPE} != binary ]]; then
-		if [[ $(gcc-major-version) -lt 4 ]] || ( [[ $(gcc-major-version) -eq 4 && $(gcc-minor-version) -lt 6 ]] ) ; then
-			die "Compilation with gcc older than 4.6 is not supported."
-		fi
-	fi
-
-	if [ ! -d "${EPREFIX}/usr/include/CL" ]; then
-		eerror "As a temporary workaround for Bug #521734, a symlink pointing to"
-		eerror "OpenCL headers >= 1.2 is needed. A symlink pointing to the CL-1.2"
-		eerror "headers, normally provided by the eselect-opencl package, can be"
-		eerror "manually created with"
-		eerror ""
-		eerror "  ln -s ${EPREFIX}/usr/lib64/OpenCL/global/include/CL-1.2/ ${EPREFIX}/usr/include/CL"
-		eerror ""
-		die "${EPREFIX}/usr/include/CL not found"
-	fi
-}
-
-src_configure() {
-	local mycmakeargs=(
-		-DBUILD_CLIENT="$(usex client)"
-		-DBUILD_SAMPLE="$(usex examples)"
-		-DBUILD_KTEST="$(usex ktest)"
-		-DBUILD_PERFORMANCE="$(usex performance)"
-		-DBUILD_TEST="$(usex test)"
-		-DOPENCL_ROOT="/usr/local/include"
-	)
-	cmake-utils_src_configure
-}
diff --git a/sci-libs/clblas/clblas-2.8.ebuild b/sci-libs/clblas/clblas-2.8.ebuild
deleted file mode 100644
index 01d8a1825..000000000
--- a/sci-libs/clblas/clblas-2.8.ebuild
+++ /dev/null
@@ -1,69 +0,0 @@
-# Copyright 1999-2017 Gentoo Foundation
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=6
-
-PYTHON_COMPAT=( python2_7 )
-
-inherit cmake-utils python-single-r1
-
-MY_PN="clBLAS"
-
-DESCRIPTION="A software library containing BLAS routines for OpenCL"
-HOMEPAGE="https://github.com/clMathLibraries/clBLAS"
-SRC_URI="https://github.com/clMathLibraries/${MY_PN}/archive/v${PV}.tar.gz -> ${P}.tar.gz"
-
-LICENSE="Apache-2.0"
-SLOT="0"
-KEYWORDS="~amd64"
-IUSE="+client examples +ktest performance test"
-
-REQUIRED_USE="performance? ( ${PYTHON_REQUIRED_USE} )"
-
-RDEPEND="
-	dev-libs/boost
-	virtual/opencl
-	|| ( >=dev-util/amdapp-2.9 dev-util/intel-ocl-sdk )
-	performance? ( ${PYTHON_DEPS} )
-	"
-DEPEND="${RDEPEND}"
-#	test? (
-#		>=dev-cpp/gtest-1.6.0
-#	)"
-
-# The tests only get compiled to an executable named Test, which is not recogniozed by cmake.
-# Therefore src_test() won't execute any test.
-RESTRICT="test"
-
-S="${WORKDIR}/${MY_PN}-${PV}/src"
-
-pkg_pretend() {
-	if [[ ${MERGE_TYPE} != binary ]]; then
-		if [[ $(gcc-major-version) -lt 4 ]] || ( [[ $(gcc-major-version) -eq 4 && $(gcc-minor-version) -lt 6 ]] ) ; then
-			die "Compilation with gcc older than 4.6 is not supported."
-		fi
-	fi
-
-	if [ ! -d "${EPREFIX}/usr/include/CL" ]; then
-		eerror "As a temporary workaround for Bug #521734, a symlink pointing to"
-		eerror "OpenCL headers >= 1.2 is needed. A symlink pointing to the CL-1.2"
-		eerror "headers, normally provided by the eselect-opencl package, can be"
-		eerror "manually created with"
-		eerror ""
-		eerror "  ln -s ${EPREFIX}/usr/lib64/OpenCL/global/include/CL-1.2/ ${EPREFIX}/usr/include/CL"
-		eerror ""
-		die "${EPREFIX}/usr/include/CL not found"
-	fi
-}
-
-src_configure() {
-	local mycmakeargs=(
-		-DBUILD_CLIENT="$(usex client)"
-		-DBUILD_SAMPLE="$(usex examples)"
-		-DBUILD_KTEST="$(usex ktest)"
-		-DBUILD_PERFORMANCE="$(usex performance)"
-		-DBUILD_TEST="$(usex test)"
-		-DOPENCL_ROOT="/usr/local/include"
-	)
-	cmake-utils_src_configure
-}
diff --git a/sci-libs/clblas/clblas-9999.ebuild b/sci-libs/clblas/clblas-9999.ebuild
deleted file mode 100644
index 5371921f7..000000000
--- a/sci-libs/clblas/clblas-9999.ebuild
+++ /dev/null
@@ -1,69 +0,0 @@
-# Copyright 1999-2017 Gentoo Foundation
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=6
-
-PYTHON_COMPAT=( python2_7 )
-
-inherit cmake-utils git-r3 python-single-r1
-
-MY_PN="clBLAS"
-
-DESCRIPTION="A software library containing BLAS routines for OpenCL"
-HOMEPAGE="https://github.com/clMathLibraries/clBLAS"
-EGIT_REPO_URI="https://github.com/clMathLibraries/${MY_PN}.git"
-
-LICENSE="Apache-2.0"
-SLOT="0"
-KEYWORDS=""
-IUSE="+client examples +ktest performance test"
-
-REQUIRED_USE="performance? ( ${PYTHON_REQUIRED_USE} )"
-
-RDEPEND="
-	dev-libs/boost
-	virtual/opencl
-	|| ( >=dev-util/amdapp-2.9 dev-util/intel-ocl-sdk )
-	performance? ( ${PYTHON_DEPS} )
-	"
-DEPEND="${RDEPEND}"
-#	test? (
-#		>=dev-cpp/gtest-1.6.0
-#	)"
-
-# The tests only get compiled to an executable named Test, which is not recogniozed by cmake.
-# Therefore src_test() won't execute any test.
-RESTRICT="test"
-
-S="${WORKDIR}/${P}/src"
-
-pkg_pretend() {
-	if [[ ${MERGE_TYPE} != binary ]]; then
-		if [[ $(gcc-major-version) -lt 4 ]] || ( [[ $(gcc-major-version) -eq 4 && $(gcc-minor-version) -lt 6 ]] ) ; then
-			die "Compilation with gcc older than 4.6 is not supported."
-		fi
-	fi
-
-	if [ ! -d "${EPREFIX}/usr/include/CL" ]; then
-		eerror "As a temporary workaround for Bug #521734, a symlink pointing to"
-		eerror "OpenCL headers >= 1.2 is needed. A symlink pointing to the CL-1.2"
-		eerror "headers, normally provided by the eselect-opencl package, can be"
-		eerror "manually created with"
-		eerror ""
-		eerror "  ln -s ${EPREFIX}/usr/lib64/OpenCL/global/include/CL-1.2/ ${EPREFIX}/usr/include/CL"
-		eerror ""
-		die "${EPREFIX}/usr/include/CL not found"
-	fi
-}
-
-src_configure() {
-	local mycmakeargs=(
-		-DBUILD_CLIENT="$(usex client)"
-		-DBUILD_SAMPLE="$(usex examples)"
-		-DBUILD_KTEST="$(usex ktest)"
-		-DBUILD_PERFORMANCE="$(usex performance)"
-		-DBUILD_TEST="$(usex test)"
-		-DOPENCL_ROOT="/usr/local/include"
-	)
-	cmake-utils_src_configure
-}
diff --git a/sci-libs/clblas/metadata.xml b/sci-libs/clblas/metadata.xml
deleted file mode 100644
index 3aec2f51f..000000000
--- a/sci-libs/clblas/metadata.xml
+++ /dev/null
@@ -1,29 +0,0 @@
-<?xml version="1.0" encoding="UTF-8"?>
-<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
-<pkgmetadata>
-	<maintainer type="project">
-		<email>sci@gentoo.org</email>
-		<name>Gentoo Science Project</name>
-	</maintainer>
-	<longdescription>
-clBLAS is the code for the OpenCL BLAS portion of clMath. The
-complete set of BLAS level 1, 2 and 3 routines is implemented. See
-Netlib BLAS for the list of supported routines. In addition to GPU
-devices, the library also supports running on CPU devices to
-facilitate debugging and multicore programming.
-</longdescription>
-	<use>
-		<flag name="client">
-Build a command line clBLAS client program.
-</flag>
-		<flag name="ktest">
-A command line tool for testing single clBLAS kernel.
-</flag>
-		<flag name="performance">
-Copy performance scripts that can measure and graph performance.
-</flag>
-	</use>
-	<upstream>
-		<remote-id type="github">clMathLibraries/clBLAS</remote-id>
-	</upstream>
-</pkgmetadata>
diff --git a/sci-libs/clfft/Manifest b/sci-libs/clfft/Manifest
index 10f5aec57..1bba03d7f 100644
--- a/sci-libs/clfft/Manifest
+++ b/sci-libs/clfft/Manifest
@@ -1,3 +1 @@
-DIST clfft-2.12.0.tar.gz 1008780 BLAKE2B 0c5e311c041d8ab85853aca3a31c62db071e604c469e067efcb77d78caaf7a5f159141f2c8fd311b65cbeb6261b825fca996f8e1b1c830586e4781719b05dbad SHA512 8ee21847f2877989a1b6a62f62807e2cfd6d6845ed36702de775eb9dbccfed898e9969cce7bb93827745b5d65a5d91aaf07c565c92e65b6fefe3028efa9c23c9
-DIST clfft-2.12.1.tar.gz 1009856 BLAKE2B 6058eb61b9b50025c7da01b5ad1e24bf6d2306e010e72bc76af6216c6bc050fe169f48e865a83932230117398306a5b220c21539ae919d8e5c6f372973ea4960 SHA512 7eb5f1df45766d7ba80cf266264450e1dd733652a13e3fdb97109b7426515e04a96d887f11295f11fc9fe3fa43157652b65ec59a8c4a74a1dd384c47801b513f
 DIST clfft-2.12.2.tar.gz 1010182 BLAKE2B 01e2b2a459ce39d87f5a6db89b8c7cad213a6c6918dc0fc2c0c7d99c61f635ce08ef51261c0c4e9d9000508d5a27b5d2ee7a665171d8f4f9e32a085be5f15b48 SHA512 19e9a4e06f76ae7c7808d1188677d5553c43598886a75328b7801ab2ca68e35206839a58fe2f958a44a6f7c83284dc9461cd0e21c37d1042bf82e24aad066be8
diff --git a/sci-libs/clfft/clfft-2.12.0.ebuild b/sci-libs/clfft/clfft-2.12.0.ebuild
deleted file mode 100644
index c008c602c..000000000
--- a/sci-libs/clfft/clfft-2.12.0.ebuild
+++ /dev/null
@@ -1,52 +0,0 @@
-# Copyright 1999-2016 Gentoo Foundation
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=6
-
-inherit cmake-utils
-
-MY_PN="clFFT"
-
-DESCRIPTION="Library containing FFT functions written in OpenCL"
-HOMEPAGE="https://github.com/clMathLibraries/clFFT"
-SRC_URI="https://github.com/clMathLibraries/${MY_PN}/archive/v${PV}.tar.gz -> ${P}.tar.gz"
-
-LICENSE="Apache-2.0"
-SLOT="0"
-KEYWORDS="~amd64"
-IUSE="callback_client +client examples test"
-
-RDEPEND="
-	>=sys-devel/gcc-4.6:*
-	virtual/opencl
-	dev-libs/boost"
-DEPEND="${RDEPEND}"
-#	test? (
-#		dev-cpp/gtest
-#		sci-libs/fftw:3.0
-#	)"
-
-# The tests only get compiled to an executable named Test, which is not recogniozed by cmake.
-# Therefore src_test() won't execute any test.
-RESTRICT="test"
-
-S="${WORKDIR}/${MY_PN}-${PV}/src"
-
-pkg_pretend() {
-	if [[ ${MERGE_TYPE} != binary ]]; then
-		if [[ $(gcc-major-version) -lt 4 ]] || ( [[ $(gcc-major-version) -eq 4 && $(gcc-minor-version) -lt 6 ]] ) ; then
-			die "Compilation with gcc older than 4.6 is not supported."
-		fi
-	fi
-}
-
-src_configure() {
-	local mycmakeargs=(
-		-DBUILD_CALLBACK_CLIENT="$(usex callback_client)"
-		-DBUILD_CLIENT="$(usex client)"
-		-DBUILD_SAMPLE="$(usex examples)"
-		-DBUILD_TEST="$(usex test)"
-		-DBoost_USE_STATIC_LIBS=OFF
-	)
-	cmake-utils_src_configure
-}
diff --git a/sci-libs/clfft/clfft-2.12.1.ebuild b/sci-libs/clfft/clfft-2.12.1.ebuild
deleted file mode 100644
index c008c602c..000000000
--- a/sci-libs/clfft/clfft-2.12.1.ebuild
+++ /dev/null
@@ -1,52 +0,0 @@
-# Copyright 1999-2016 Gentoo Foundation
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=6
-
-inherit cmake-utils
-
-MY_PN="clFFT"
-
-DESCRIPTION="Library containing FFT functions written in OpenCL"
-HOMEPAGE="https://github.com/clMathLibraries/clFFT"
-SRC_URI="https://github.com/clMathLibraries/${MY_PN}/archive/v${PV}.tar.gz -> ${P}.tar.gz"
-
-LICENSE="Apache-2.0"
-SLOT="0"
-KEYWORDS="~amd64"
-IUSE="callback_client +client examples test"
-
-RDEPEND="
-	>=sys-devel/gcc-4.6:*
-	virtual/opencl
-	dev-libs/boost"
-DEPEND="${RDEPEND}"
-#	test? (
-#		dev-cpp/gtest
-#		sci-libs/fftw:3.0
-#	)"
-
-# The tests only get compiled to an executable named Test, which is not recogniozed by cmake.
-# Therefore src_test() won't execute any test.
-RESTRICT="test"
-
-S="${WORKDIR}/${MY_PN}-${PV}/src"
-
-pkg_pretend() {
-	if [[ ${MERGE_TYPE} != binary ]]; then
-		if [[ $(gcc-major-version) -lt 4 ]] || ( [[ $(gcc-major-version) -eq 4 && $(gcc-minor-version) -lt 6 ]] ) ; then
-			die "Compilation with gcc older than 4.6 is not supported."
-		fi
-	fi
-}
-
-src_configure() {
-	local mycmakeargs=(
-		-DBUILD_CALLBACK_CLIENT="$(usex callback_client)"
-		-DBUILD_CLIENT="$(usex client)"
-		-DBUILD_SAMPLE="$(usex examples)"
-		-DBUILD_TEST="$(usex test)"
-		-DBoost_USE_STATIC_LIBS=OFF
-	)
-	cmake-utils_src_configure
-}
diff --git a/sci-libs/clfft/clfft-2.12.2-r1.ebuild b/sci-libs/clfft/clfft-2.12.2-r1.ebuild
new file mode 100644
index 000000000..8be3d24d0
--- /dev/null
+++ b/sci-libs/clfft/clfft-2.12.2-r1.ebuild
@@ -0,0 +1,52 @@
+# Copyright 1999-2022 Gentoo Authors
+# Distributed under the terms of the GNU General Public License v2
+
+EAPI=8
+
+MY_PN="clFFT"
+
+DOCS_BUILDER="doxygen"
+DOCS_DIR="../docs"
+DOCS_CONFIG_NAME="${MY_PN}.doxy"
+
+inherit cmake docs
+
+DESCRIPTION="Library containing FFT functions written in OpenCL"
+HOMEPAGE="https://github.com/clMathLibraries/clFFT"
+SRC_URI="https://github.com/clMathLibraries/${MY_PN}/archive/v${PV}.tar.gz -> ${P}.tar.gz"
+
+LICENSE="Apache-2.0"
+SLOT="0"
+KEYWORDS="~amd64"
+IUSE="callback-client +client test"
+
+RDEPEND="
+	virtual/opencl
+	dev-libs/boost
+"
+DEPEND="${RDEPEND}"
+BDEPEND="test? (
+	dev-cpp/gtest
+	sci-libs/fftw:3.0
+)"
+
+# The tests only get compiled to an executable named Test, which is not recogniozed by cmake.
+# Therefore src_test() won't execute any test.
+RESTRICT="test"
+
+S="${WORKDIR}/${MY_PN}-${PV}/src"
+
+src_configure() {
+	local mycmakeargs=(
+		-DBUILD_CALLBACK_CLIENT="$(usex callback-client)"
+		-DBUILD_CLIENT="$(usex client)"
+		-DBUILD_TEST="$(usex test)"
+		-DBoost_USE_STATIC_LIBS=OFF
+	)
+	cmake_src_configure
+}
+
+src_compile() {
+	docs_compile
+	cmake_src_compile
+}
diff --git a/sci-libs/clfft/clfft-2.12.2.ebuild b/sci-libs/clfft/clfft-2.12.2.ebuild
deleted file mode 100644
index c008c602c..000000000
--- a/sci-libs/clfft/clfft-2.12.2.ebuild
+++ /dev/null
@@ -1,52 +0,0 @@
-# Copyright 1999-2016 Gentoo Foundation
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=6
-
-inherit cmake-utils
-
-MY_PN="clFFT"
-
-DESCRIPTION="Library containing FFT functions written in OpenCL"
-HOMEPAGE="https://github.com/clMathLibraries/clFFT"
-SRC_URI="https://github.com/clMathLibraries/${MY_PN}/archive/v${PV}.tar.gz -> ${P}.tar.gz"
-
-LICENSE="Apache-2.0"
-SLOT="0"
-KEYWORDS="~amd64"
-IUSE="callback_client +client examples test"
-
-RDEPEND="
-	>=sys-devel/gcc-4.6:*
-	virtual/opencl
-	dev-libs/boost"
-DEPEND="${RDEPEND}"
-#	test? (
-#		dev-cpp/gtest
-#		sci-libs/fftw:3.0
-#	)"
-
-# The tests only get compiled to an executable named Test, which is not recogniozed by cmake.
-# Therefore src_test() won't execute any test.
-RESTRICT="test"
-
-S="${WORKDIR}/${MY_PN}-${PV}/src"
-
-pkg_pretend() {
-	if [[ ${MERGE_TYPE} != binary ]]; then
-		if [[ $(gcc-major-version) -lt 4 ]] || ( [[ $(gcc-major-version) -eq 4 && $(gcc-minor-version) -lt 6 ]] ) ; then
-			die "Compilation with gcc older than 4.6 is not supported."
-		fi
-	fi
-}
-
-src_configure() {
-	local mycmakeargs=(
-		-DBUILD_CALLBACK_CLIENT="$(usex callback_client)"
-		-DBUILD_CLIENT="$(usex client)"
-		-DBUILD_SAMPLE="$(usex examples)"
-		-DBUILD_TEST="$(usex test)"
-		-DBoost_USE_STATIC_LIBS=OFF
-	)
-	cmake-utils_src_configure
-}
diff --git a/sci-libs/clfft/clfft-9999.ebuild b/sci-libs/clfft/clfft-9999.ebuild
index 55f39f28d..10e6ed148 100644
--- a/sci-libs/clfft/clfft-9999.ebuild
+++ b/sci-libs/clfft/clfft-9999.ebuild
@@ -1,34 +1,36 @@
-# Copyright 1999-2016 Gentoo Foundation
+# Copyright 1999-2022 Gentoo Authors
 # Distributed under the terms of the GNU General Public License v2
 
-EAPI=6
-
-inherit cmake-utils git-r3
+EAPI=8
 
 MY_PN="clFFT"
 
+DOCS_BUILDER="doxygen"
+DOCS_DIR="../docs"
+DOCS_CONFIG_NAME="${MY_PN}.doxy"
+
+inherit cmake docs git-r3
+
 DESCRIPTION="Library containing FFT functions written in OpenCL"
 HOMEPAGE="https://github.com/clMathLibraries/clFFT"
 EGIT_REPO_URI="
 	https://github.com/clMathLibraries/${MY_PN}.git
 	git://github.com/clMathLibraries/${MY_PN}.git
-	"
+"
 EGIT_BRANCH="develop"
 
 LICENSE="Apache-2.0"
 SLOT="0"
-KEYWORDS=""
-IUSE="callback_client +client examples test"
+IUSE="callback-client +client test"
 
 RDEPEND="
-	>=sys-devel/gcc-4.6:*
 	virtual/opencl
 	dev-libs/boost"
 DEPEND="${RDEPEND}"
-#	test? (
-#		dev-cpp/gtest
-#		sci-libs/fftw:3.0
-#	)"
+BDEPEND="test? (
+	dev-cpp/gtest
+	sci-libs/fftw:3.0
+)"
 
 # The tests only get compiled to an executable named Test, which is not recogniozed by cmake.
 # Therefore src_test() won't execute any test.
@@ -36,21 +38,17 @@ RESTRICT="test"
 
 S="${WORKDIR}/${P}/src"
 
-pkg_pretend() {
-	if [[ ${MERGE_TYPE} != binary ]]; then
-		if [[ $(gcc-major-version) -lt 4 ]] || ( [[ $(gcc-major-version) -eq 4 && $(gcc-minor-version) -lt 6 ]] ) ; then
-			die "Compilation with gcc older than 4.6 is not supported."
-		fi
-	fi
-}
-
 src_configure() {
 	local mycmakeargs=(
-		-DBUILD_CALLBACK_CLIENT="$(usex callback_client)"
+		-DBUILD_CALLBACK_CLIENT="$(usex callback-client)"
 		-DBUILD_CLIENT="$(usex client)"
-		-DBUILD_SAMPLE="$(usex examples)"
 		-DBUILD_TEST="$(usex test)"
 		-DBoost_USE_STATIC_LIBS=OFF
 	)
-	cmake-utils_src_configure
+	cmake_src_configure
+}
+
+src_compile() {
+	docs_compile
+	cmake_src_compile
 }
diff --git a/sci-libs/clfft/metadata.xml b/sci-libs/clfft/metadata.xml
index e353d590c..911f5977b 100644
--- a/sci-libs/clfft/metadata.xml
+++ b/sci-libs/clfft/metadata.xml
@@ -18,7 +18,7 @@ clFFT is part of the clMath sofware library, which is the
 successor of APPML.
 </longdescription>
 	<use>
-		<flag name="callback_client">
+		<flag name="callback-client">
 Build a command line clFFT client program that tests callback functionality.
 </flag>
 		<flag name="client">
diff --git a/sci-libs/clrng/Manifest b/sci-libs/clrng/Manifest
new file mode 100644
index 000000000..307d3c660
--- /dev/null
+++ b/sci-libs/clrng/Manifest
@@ -0,0 +1 @@
+DIST clrng-1.0.0_beta_p20160304.tar.gz 128376 BLAKE2B cd1e8446390b1d541930780cc2b880b2da514d5c935bc108809c9538a12720dbc9d5c06637d1d2a775f39a300f099e1836bd575e8723d964c4e57d198864742a SHA512 28bda5d2a156e7394917f8c40bd1e8e7b52cf680abc0ef50c2650b1d546c0a1d0bd47ceeccce3cd7c79c90a15494c3d27829e153613a7d8e18267ce7262eeb6e
diff --git a/sci-libs/clrng/clrng-1.0.0_beta_p20160304.ebuild b/sci-libs/clrng/clrng-1.0.0_beta_p20160304.ebuild
new file mode 100644
index 000000000..049493e93
--- /dev/null
+++ b/sci-libs/clrng/clrng-1.0.0_beta_p20160304.ebuild
@@ -0,0 +1,57 @@
+# Copyright 1999-2021 Gentoo Authors
+# Distributed under the terms of the GNU General Public License v2
+
+EAPI=7
+
+DOCS_BUILDER="doxygen"
+DOCS_DIR="../docs"
+DOCS_CONFIG_NAME="clRNG.doxy"
+
+inherit cmake docs
+
+MY_PN="clRNG"
+
+DESCRIPTION="A library for uniform random number generation in OpenCL"
+HOMEPAGE="https://github.com/clMathLibraries/clRNG"
+
+if [ ${PV} == "9999" ] ; then
+	inherit git-r3
+	EGIT_REPO_URI="https://github.com/clMathLibraries/${MY_PN}.git"
+	S="${WORKDIR}/${P}/src"
+else
+	COMMIT="4a16519ddf52ee0a5f0b7e6288b0803b9019c13b"
+	SRC_URI="https://github.com/clMathLibraries/${MY_PN}/archive/${COMMIT}.tar.gz -> ${P}.tar.gz"
+	KEYWORDS="~amd64"
+	S="${WORKDIR}/${MY_PN}-${COMMIT}/src"
+fi
+
+LICENSE="BSD-2 BSD"
+SLOT="0"
+
+IUSE="+client test"
+
+RDEPEND="
+	virtual/opencl
+	dev-util/intel-ocl-sdk
+	dev-libs/boost
+"
+DEPEND="${RDEPEND}"
+
+# The tests only get compiled to an executable named Test, which is not recogniozed by cmake.
+# Therefore src_test() won't execute any test.
+RESTRICT="test"
+
+PATCHES=( "${FILESDIR}/clrng-allow-newer-gcc.patch" )
+
+src_configure() {
+	local mycmakeargs=(
+		$(use_with client CLIENT)
+		$(use_with test TEST)
+	)
+	cmake_src_configure
+}
+
+src_compile() {
+	default
+	docs_compile
+}
diff --git a/sci-libs/clrng/clrng-9999.ebuild b/sci-libs/clrng/clrng-9999.ebuild
index d49f9c8f7..de250bee8 100644
--- a/sci-libs/clrng/clrng-9999.ebuild
+++ b/sci-libs/clrng/clrng-9999.ebuild
@@ -1,9 +1,13 @@
-# Copyright 1999-2015 Gentoo Foundation
+# Copyright 1999-2021 Gentoo Authors
 # Distributed under the terms of the GNU General Public License v2
 
-EAPI=5
+EAPI=7
 
-inherit cmake-utils
+DOCS_BUILDER="doxygen"
+DOCS_DIR="../docs"
+DOCS_CONFIG_NAME="clRNG.doxy"
+
+inherit cmake docs
 
 MY_PN="clRNG"
 
@@ -12,7 +16,7 @@ HOMEPAGE="https://github.com/clMathLibraries/clRNG"
 
 if [ ${PV} == "9999" ] ; then
 	inherit git-r3
-	EGIT_REPO_URI="https://github.com/clMathLibraries/${MY_PN}.git git://github.com/clMathLibraries/${MY_PN}.git"
+	EGIT_REPO_URI="https://github.com/clMathLibraries/${MY_PN}.git"
 	S="${WORKDIR}/${P}/src"
 else
 	SRC_URI="https://github.com/clMathLibraries/${MY_PN}/archive/v${PV}.tar.gz -> ${P}.tar.gz"
@@ -22,32 +26,31 @@ fi
 
 LICENSE="BSD-2 BSD"
 SLOT="0"
+
 IUSE="+client test"
 
 RDEPEND="
-	>=sys-devel/gcc-4.8:*
 	virtual/opencl
-	|| ( >=dev-util/amdapp-2.9 dev-util/intel-ocl-sdk )
+	dev-util/intel-ocl-sdk
 	dev-libs/boost
-	"
+"
 DEPEND="${RDEPEND}"
 
 # The tests only get compiled to an executable named Test, which is not recogniozed by cmake.
 # Therefore src_test() won't execute any test.
 RESTRICT="test"
 
-pkg_pretend() {
-	if [[ ${MERGE_TYPE} != binary ]]; then
-		if [[ $(gcc-major-version) -lt 4 ]] || ( [[ $(gcc-major-version) -eq 4 && $(gcc-minor-version) -lt 8 ]] ) ; then
-			die "Compilation with gcc older than 4.8 is not supported."
-		fi
-	fi
-}
+PATCHES=( "${FILESDIR}/clrng-allow-newer-gcc.patch" )
 
 src_configure() {
 	local mycmakeargs=(
-		$(cmake-utils_use_build client CLIENT)
-		$(cmake-utils_use_build test TEST)
+		$(use_with client CLIENT)
+		$(use_with test TEST)
 	)
-	cmake-utils_src_configure
+	cmake_src_configure
+}
+
+src_compile() {
+	default
+	docs_compile
 }
diff --git a/sci-libs/clrng/files/clrng-allow-newer-gcc.patch b/sci-libs/clrng/files/clrng-allow-newer-gcc.patch
new file mode 100644
index 000000000..4419e5f69
--- /dev/null
+++ b/sci-libs/clrng/files/clrng-allow-newer-gcc.patch
@@ -0,0 +1,159 @@
+diff --git a//include/clRNG/private/Random123/features/compilerfeatures.h b//include/clRNG/private/Random123/features/compilerfeatures.h
+index a2a56bf..48d2ed2 100644
+--- a//include/clRNG/private/Random123/features/compilerfeatures.h
++++ b//include/clRNG/private/Random123/features/compilerfeatures.h
+@@ -253,7 +253,7 @@ added to each of the *features.h files, AND to examples/ut_features.cpp.
+ #endif
+ 
+ #ifndef R123_STATIC_ASSERT
+-#if R123_USE_CXX11_STATIC_ASSERT
++#ifdef R123_USE_CXX11_STATIC_ASSERT
+ #define R123_STATIC_ASSERT(expr, msg) static_assert(expr, msg)
+ #else
+     /* if msg always_looked_like_this, we could paste it into the name.  Worth it? */
+@@ -262,7 +262,7 @@ added to each of the *features.h files, AND to examples/ut_features.cpp.
+ #endif
+ 
+ #ifndef R123_CONSTEXPR
+-#if R123_USE_CXX11_CONSTEXPR
++#ifdef R123_USE_CXX11_CONSTEXPR
+ #define R123_CONSTEXPR constexpr
+ #else
+ #define R123_CONSTEXPR
+diff --git a//include/clRNG/private/Random123/features/sse.h b//include/clRNG/private/Random123/features/sse.h
+index 88efd65..d95cf67 100644
+--- a//include/clRNG/private/Random123/features/sse.h
++++ b//include/clRNG/private/Random123/features/sse.h
+@@ -32,36 +32,33 @@ OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
+ #ifndef _Random123_sse_dot_h__
+ #define _Random123_sse_dot_h__
+ 
+-#if R123_USE_SSE
++#ifdef R123_USE_SSE
+ 
+-#if R123_USE_X86INTRIN_H
++#ifdef R123_USE_X86INTRIN_H
+ #include <x86intrin.h>
+-#endif
+-#if R123_USE_IA32INTRIN_H
++#elif defined R123_USE_IA32INTRIN_H
+ #include <ia32intrin.h>
+ #endif
+-#if R123_USE_XMMINTRIN_H
++#ifdef R123_USE_XMMINTRIN_H
+ #include <xmmintrin.h>
+ #endif
+-#if R123_USE_EMMINTRIN_H
++#ifdef R123_USE_EMMINTRIN_H
+ #include <emmintrin.h>
+ #endif
+-#if R123_USE_SMMINTRIN_H
++#ifdef R123_USE_SMMINTRIN_H
+ #include <smmintrin.h>
+ #endif
+-#if R123_USE_WMMINTRIN_H
++#ifdef R123_USE_WMMINTRIN_H
+ #include <wmmintrin.h>
+ #endif
+-#if R123_USE_INTRIN_H
+-#include <intrin.h>
+-#endif
++
+ #ifdef __cplusplus
+ #include <iostream>
+ #include <limits>
+ #include <stdexcept>
+ #endif
+ 
+-#if R123_USE_ASM_GNU
++#ifdef R123_USE_ASM_GNU
+ 
+ /* bit25 of CX tells us whether AES is enabled. */
+ R123_STATIC_INLINE int haveAESNI(){
+@@ -147,7 +144,7 @@ R123_STATIC_INLINE __m128 _mm_castsi128_ps(__m128i si){
+ 
+ struct r123m128i{
+     __m128i m;
+-#if R123_USE_CXX11_UNRESTRICTED_UNIONS
++#ifdef R123_USE_CXX11_UNRESTRICTED_UNIONS
+     // C++98 forbids a union member from having *any* constructors.
+     // C++11 relaxes this, and allows union members to have constructors
+     // as long as there is a "trivial" default construtor.  So in C++11
+@@ -158,7 +155,7 @@ struct r123m128i{
+ #endif
+     r123m128i& operator=(const __m128i& rhs){ m=rhs; return *this;}
+     r123m128i& operator=(R123_ULONG_LONG n){ m = _mm_set_epi64x(0, n); return *this;}
+-#if R123_USE_CXX11_EXPLICIT_CONVERSIONS
++#ifdef R123_USE_CXX11_EXPLICIT_CONVERSIONS
+     // With C++0x we can attach explicit to the bool conversion operator
+     // to disambiguate undesired promotions.  For g++, this works
+     // only in 4.5 and above.
+@@ -171,7 +168,7 @@ struct r123m128i{
+     operator __m128i() const {return m;}
+ 
+ private:
+-#if R123_USE_SSE4_1
++#ifdef R123_USE_SSE4_1
+     bool _bool() const{ return !_mm_testz_si128(m,m); }
+ #else
+     bool _bool() const{ return 0xf != _mm_movemask_ps(_mm_castsi128_ps(_mm_cmpeq_epi32(m, _mm_setzero_si128()))); }
+@@ -183,7 +180,7 @@ R123_STATIC_INLINE r123m128i& operator++(r123m128i& v){
+     __m128i zeroone = _mm_set_epi64x(R123_64BIT(0), R123_64BIT(1));
+     c = _mm_add_epi64(c, zeroone);
+     //return c;
+-#if R123_USE_SSE4_1
++#ifdef R123_USE_SSE4_1
+     __m128i zerofff = _mm_set_epi64x(0, ~(R123_64BIT(0)));
+     if( R123_BUILTIN_EXPECT(_mm_testz_si128(c,zerofff), 0) ){
+         __m128i onezero = _mm_set_epi64x(R123_64BIT(1), R123_64BIT(0));
+diff --git a//include/clRNG/private/Random123/philox.h b//include/clRNG/private/Random123/philox.h
+index 9c87384..96ebcc6 100644
+--- a//include/clRNG/private/Random123/philox.h
++++ b//include/clRNG/private/Random123/philox.h
+@@ -171,7 +171,7 @@ R123_STATIC_INLINE Word mulhilo##W(Word a, Word b, Word *hip){               \
+ // which *might* compile into better code than
+ // _mulhilo_dword_tpl 
+ */
+-#if R123_USE_MULHILO32_ASM
++#ifdef R123_USE_MULHILO32_ASM
+ #ifdef __powerpc__
+ _mulhilo_asm_tpl(32, uint32_t, "mulhwu")
+ #else
+@@ -181,8 +181,8 @@ _mulhilo_asm_tpl(32, uint32_t, "mull")
+ _mulhilo_dword_tpl(32, uint32_t, uint64_t)
+ #endif
+ 
+-#if R123_USE_PHILOX_64BIT
+-#if R123_USE_MULHILO64_ASM
++#ifdef R123_USE_PHILOX_64BIT
++#ifdef R123_USE_MULHILO64_ASM
+ #ifdef __powerpc64__
+ _mulhilo_asm_tpl(64, uint64_t, "mulhdu")
+ #else
+@@ -337,7 +337,7 @@ _philox4xWround_tpl(32, uint32_t)            /* philo4x32round */
+ /** \endcond */
+ _philoxNxW_tpl(2, 1, 32, uint32_t)    /* philox2x32bijection */
+ _philoxNxW_tpl(4, 2, 32, uint32_t)    /* philox4x32bijection */
+-#if R123_USE_PHILOX_64BIT
++#ifdef R123_USE_PHILOX_64BIT
+ /** \cond HIDDEN_FROM_DOXYGEN */
+ _philox2xWbumpkey_tpl(64)
+ _philox4xWbumpkey_tpl(64)
+@@ -350,7 +350,7 @@ _philoxNxW_tpl(4, 2, 64, uint64_t)    /* philox4x64bijection */
+ 
+ #define philox2x32(c,k) philox2x32_R(philox2x32_rounds, c, k)
+ #define philox4x32(c,k) philox4x32_R(philox4x32_rounds, c, k)
+-#if R123_USE_PHILOX_64BIT
++#ifdef R123_USE_PHILOX_64BIT
+ #define philox2x64(c,k) philox2x64_R(philox2x64_rounds, c, k)
+ #define philox4x64(c,k) philox4x64_R(philox4x64_rounds, c, k)
+ #endif /* R123_USE_PHILOX_64BIT */
+@@ -379,7 +379,7 @@ typedef Philox##N##x##W##_R<philox##N##x##W##_rounds> Philox##N##x##W; \
+ 
+ _PhiloxNxW_base_tpl(r123array2x32, r123array1x32, 2, 32) // Philox2x32_R<R>
+ _PhiloxNxW_base_tpl(r123array4x32, r123array2x32, 4, 32) // Philox4x32_R<R>
+-#if R123_USE_PHILOX_64BIT
++#ifdef R123_USE_PHILOX_64BIT
+ _PhiloxNxW_base_tpl(r123array2x64, r123array1x64, 2, 64) // Philox2x64_R<R>
+ _PhiloxNxW_base_tpl(r123array4x64, r123array2x64, 4, 64) // Philox4x64_R<R>
+ #endif
diff --git a/sci-libs/cs-rosetta-db/Manifest b/sci-libs/cs-rosetta-db/Manifest
index 6107c9f81..53e1b29b0 100644
--- a/sci-libs/cs-rosetta-db/Manifest
+++ b/sci-libs/cs-rosetta-db/Manifest
@@ -1,7 +1,7 @@
-DIST cs-rosetta-db-1.01.2009.1109.11-ANGLESS.hyb.tar.gz 33906372 BLAKE2B fc8017998db79c511ef3e9c05b68bde0b5c0d4df724e7f9488da168515c8aab2f7db24b488fde3500d113e9a429edd6a09812cbd1ddf04244c7848332f0c9813 SHA512 b74d164bd28ebf39655de57c6f6bf1c62c7a3163282197dbab2190fbbe0af35f52b0f9f981b3c507a8da30e188238cd27db9d33d27e1d6b02c1b8c92e2bccfce
-DIST cs-rosetta-db-1.01.2009.1109.11-ANGLESS.tar.Z 21354277 BLAKE2B e3fda59bfeacc389c73c48744da052f8b79b47c3a4b16a370ebb4109238b6f2b7f4a9bbf6b615208ba881221012f4688593223d21632995553cb31431de37cdf SHA512 95f3229bada553b31a594d9502049c8ee0d09e14ec1203d1a1ccd276d729f0bd40c2cc87677356ee4d15531836dec021bc3399816733e4739c0ac4032984d83c
-DIST cs-rosetta-db-1.01.2009.1109.11-CS.hyb.tar.gz 159942908 BLAKE2B aba0c70e62a5fe0a2865dd8e491ef070242dff20f57c8f8466116481260810b9e4fd96a8ef49c080686ee6653cdcea020d5d7376063e9758a48c420ad1c05b2e SHA512 b3d9f7daa60e9ebb8a85a79090da24e6e7f95932b217eafb368b0fbfb5b6dc08e43ae29564e3c7744929f99fce5faa600f1aee37a8f4e92132bf6e90e21d4d11
-DIST cs-rosetta-db-1.01.2009.1109.11-CS.tar.Z 88180729 BLAKE2B 72f1d413e82cf35f3f4f6446737dfc06c01c1654869e4ed9d87048219b20375394194ae310f2e008e5fe4ba2f9e4ed02b0d2a6c2adb15f6670bc8a4c5cbdced9 SHA512 f05e6d0834aab99d12841f5cfb91fe13cbeada5eaa645372f13600e5b9cd0f463f53f4a23a71e017e3ddb9d6086061eeae2a1cfe707bc53ba37332a1d48e0d87
-DIST cs-rosetta-db-1.01.2009.1109.11-PDBH.hyb.tar.gz 229319028 BLAKE2B 7315d8cd1d9c54c253dafadb852643938c0d0b7488f178946592c2ca07a8abdd52a29870647244895be832e99eb7333c46c80ab0cb430a6f6bc232a9bd331727 SHA512 03a80404dc703fd9886b57ee1ca47e6a3477d296be99d111e590fdc9589330bc60a9363f4f3fd85e76e653a7e52a607236645fbb8ef89a7814e26ef8d74d1117
-DIST cs-rosetta-db-1.01.2009.1109.11-PDBH.tar.Z 160897298 BLAKE2B 87cdf26e87ce86402f83f5536d857ff8abcb4c6abd9dfffcf34a17f7ab932c7ebd9539f4d7abd620fd787c095ecc3e4729990297d3bdacf2d47771b07489fa77 SHA512 a4a509f361a5fd7e29ede7fea094133beff8e9dee63823c478e5edd37eeee3ddf5077b34fb6ec3f0f53cb9fcefdbaf2b1fe95cbd9d36ab1895a9860279eab762
-DIST cs-rosetta-db-1.01.2009.1109.11-vall.dat.apr24.gz 141860182 BLAKE2B 0a7e19832f27ce3d82077b423c3ffe71c1ecb6382c1685d5d9aab98f755b3cc9df51c3a6bd5fd5360a7b55cba1860bcabbf91c51de591d40e5478b825e28dd32 SHA512 a633ede28b548710d03b5c8da83d82259046bdad079b7265276649ed95765b4608479186b9c5b3025b7faaa1aa8bcdb3afc1e413e3e7f201b0c669bb6058c12a
+DIST cs-rosetta-db-2.01.2019.06-ANGLESS.hyb.tar.gz 33906372 BLAKE2B fc8017998db79c511ef3e9c05b68bde0b5c0d4df724e7f9488da168515c8aab2f7db24b488fde3500d113e9a429edd6a09812cbd1ddf04244c7848332f0c9813 SHA512 b74d164bd28ebf39655de57c6f6bf1c62c7a3163282197dbab2190fbbe0af35f52b0f9f981b3c507a8da30e188238cd27db9d33d27e1d6b02c1b8c92e2bccfce
+DIST cs-rosetta-db-2.01.2019.06-ANGLESS.tar.Z 21354277 BLAKE2B e3fda59bfeacc389c73c48744da052f8b79b47c3a4b16a370ebb4109238b6f2b7f4a9bbf6b615208ba881221012f4688593223d21632995553cb31431de37cdf SHA512 95f3229bada553b31a594d9502049c8ee0d09e14ec1203d1a1ccd276d729f0bd40c2cc87677356ee4d15531836dec021bc3399816733e4739c0ac4032984d83c
+DIST cs-rosetta-db-2.01.2019.06-CS.hyb.tar.gz 159942908 BLAKE2B aba0c70e62a5fe0a2865dd8e491ef070242dff20f57c8f8466116481260810b9e4fd96a8ef49c080686ee6653cdcea020d5d7376063e9758a48c420ad1c05b2e SHA512 b3d9f7daa60e9ebb8a85a79090da24e6e7f95932b217eafb368b0fbfb5b6dc08e43ae29564e3c7744929f99fce5faa600f1aee37a8f4e92132bf6e90e21d4d11
+DIST cs-rosetta-db-2.01.2019.06-CS.tar.Z 88180729 BLAKE2B 72f1d413e82cf35f3f4f6446737dfc06c01c1654869e4ed9d87048219b20375394194ae310f2e008e5fe4ba2f9e4ed02b0d2a6c2adb15f6670bc8a4c5cbdced9 SHA512 f05e6d0834aab99d12841f5cfb91fe13cbeada5eaa645372f13600e5b9cd0f463f53f4a23a71e017e3ddb9d6086061eeae2a1cfe707bc53ba37332a1d48e0d87
+DIST cs-rosetta-db-2.01.2019.06-PDBH.hyb.tar.gz 229319028 BLAKE2B 7315d8cd1d9c54c253dafadb852643938c0d0b7488f178946592c2ca07a8abdd52a29870647244895be832e99eb7333c46c80ab0cb430a6f6bc232a9bd331727 SHA512 03a80404dc703fd9886b57ee1ca47e6a3477d296be99d111e590fdc9589330bc60a9363f4f3fd85e76e653a7e52a607236645fbb8ef89a7814e26ef8d74d1117
+DIST cs-rosetta-db-2.01.2019.06-PDBH.tar.Z 160897298 BLAKE2B 87cdf26e87ce86402f83f5536d857ff8abcb4c6abd9dfffcf34a17f7ab932c7ebd9539f4d7abd620fd787c095ecc3e4729990297d3bdacf2d47771b07489fa77 SHA512 a4a509f361a5fd7e29ede7fea094133beff8e9dee63823c478e5edd37eeee3ddf5077b34fb6ec3f0f53cb9fcefdbaf2b1fe95cbd9d36ab1895a9860279eab762
+DIST cs-rosetta-db-2.01.2019.06-vall.dat.apr24.gz 141860182 BLAKE2B 0a7e19832f27ce3d82077b423c3ffe71c1ecb6382c1685d5d9aab98f755b3cc9df51c3a6bd5fd5360a7b55cba1860bcabbf91c51de591d40e5478b825e28dd32 SHA512 a633ede28b548710d03b5c8da83d82259046bdad079b7265276649ed95765b4608479186b9c5b3025b7faaa1aa8bcdb3afc1e413e3e7f201b0c669bb6058c12a
diff --git a/sci-libs/cs-rosetta-db/cs-rosetta-db-1.01.2009.1109.11.ebuild b/sci-libs/cs-rosetta-db/cs-rosetta-db-1.01.2009.1109.11.ebuild
deleted file mode 100644
index 16b1149ab..000000000
--- a/sci-libs/cs-rosetta-db/cs-rosetta-db-1.01.2009.1109.11.ebuild
+++ /dev/null
@@ -1,60 +0,0 @@
-# Copyright 1999-2014 Gentoo Foundation
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=5
-
-inherit flag-o-matic toolchain-funcs
-
-MY_PN="${PN%-db}"
-
-DESCRIPTION="System for chemical shifts based protein structure prediction using ROSETTA"
-HOMEPAGE="http://spin.niddk.nih.gov/bax/software/CSROSETTA/"
-SRC_URI="
-	http://spin.niddk.nih.gov/bax/software/CSROSETTA/PDBH.tar.Z -> ${P}-PDBH.tar.Z
-	http://spin.niddk.nih.gov/bax/software/CSROSETTA/hybrid/PDBH.hyb.tar.gz ->  ${P}-PDBH.hyb.tar.gz
-	http://spin.niddk.nih.gov/bax/software/CSROSETTA/CS.tar.Z -> ${P}-CS.tar.Z
-	http://spin.niddk.nih.gov/bax/software/CSROSETTA/hybrid/CS.hyb.tar.gz -> ${P}-CS.hyb.tar.gz
-	http://spin.niddk.nih.gov/bax/software/CSROSETTA/ANGLESS.tar.Z -> ${P}-ANGLESS.tar.Z
-	http://spin.niddk.nih.gov/bax/software/CSROSETTA/hybrid/ANGLESS.hyb.tar.gz -> ${P}-ANGLESS.hyb.tar.gz
-	http://spin.niddk.nih.gov/bax/software/CSROSETTA/hybrid/vall.dat.apr24.gz -> ${P}-vall.dat.apr24.gz"
-
-SLOT="0"
-LICENSE="all-rights-reserved"
-KEYWORDS="~amd64 ~x86 ~amd64-linux ~x86-linux"
-IUSE=""
-
-RESTRICT="binchecks mirror strip"
-
-S="${WORKDIR}"
-
-src_unpack() {
-	local i
-	unpack ${P}-{PDBH,CS,ANGLESS}.hyb.tar.gz
-
-	for i in *; do
-		mv -v ${i}{,.hyb} || die
-	done
-
-	unpack ${P}-vall.dat.apr24.gz
-	mv ${P}-vall.dat.apr24 vall.dat.apr24 || die
-
-	unpack ${P}-{PDBH,CS,ANGLESS}.tar.Z
-}
-
-src_prepare() {
-	cat >> "${T}"/39${PN} <<- EOF
-	CS_DIR="${EPREFIX}/opt/${MY_PN}/CS"
-	CSHYB_DIR="${EPREFIX}/opt/${MY_PN}/CS"
-	PDBH_DIR="${EPREFIX}/opt/${MY_PN}/PDBH"
-	PDBHYB_DIR="${EPREFIX}/opt/${MY_PN}/PDBH"
-	PDBH_TAB="${EPREFIX}/opt/${MY_PN}/PDBH/resolution.tab"
-	ANGLESS_DIR="${EPREFIX}/opt/${MY_PN}/ANGLESS"
-	ANGLESSHYB_DIR="${EPREFIX}/opt/${MY_PN}/ANGLESS"
-	EOF
-}
-
-src_install() {
-	insinto /opt/${MY_PN}/
-	doins -r *
-	doenvd "${T}"/39${PN}
-}
diff --git a/sci-libs/cs-rosetta-db/cs-rosetta-db-2.01.2019.06.ebuild b/sci-libs/cs-rosetta-db/cs-rosetta-db-2.01.2019.06.ebuild
new file mode 100644
index 000000000..ba866df11
--- /dev/null
+++ b/sci-libs/cs-rosetta-db/cs-rosetta-db-2.01.2019.06.ebuild
@@ -0,0 +1,58 @@
+# Copyright 1999-2021 Gentoo Authors
+# Distributed under the terms of the GNU General Public License v2
+
+EAPI=7
+
+MY_PN="${PN%-db}"
+
+DESCRIPTION="System for chemical shifts based protein structure prediction using ROSETTA"
+HOMEPAGE="https://spin.niddk.nih.gov/bax/software/CSROSETTA/"
+SRC_URI="
+	https://spin.niddk.nih.gov/bax/software/CSROSETTA/PDBH.tar.Z -> ${P}-PDBH.tar.Z
+	https://spin.niddk.nih.gov/bax/software/CSROSETTA/hybrid/PDBH.hyb.tar.gz ->  ${P}-PDBH.hyb.tar.gz
+	https://spin.niddk.nih.gov/bax/software/CSROSETTA/CS.tar.Z -> ${P}-CS.tar.Z
+	https://spin.niddk.nih.gov/bax/software/CSROSETTA/hybrid/CS.hyb.tar.gz -> ${P}-CS.hyb.tar.gz
+	https://spin.niddk.nih.gov/bax/software/CSROSETTA/ANGLESS.tar.Z -> ${P}-ANGLESS.tar.Z
+	https://spin.niddk.nih.gov/bax/software/CSROSETTA/hybrid/ANGLESS.hyb.tar.gz -> ${P}-ANGLESS.hyb.tar.gz
+	https://spin.niddk.nih.gov/bax/software/CSROSETTA/hybrid/vall.dat.apr24.gz -> ${P}-vall.dat.apr24.gz"
+
+SLOT="0"
+LICENSE="all-rights-reserved"
+KEYWORDS="~amd64 ~x86 ~amd64-linux ~x86-linux"
+
+RESTRICT="binchecks mirror strip"
+
+S="${WORKDIR}"
+
+src_unpack() {
+	local i
+	unpack ${P}-{PDBH,CS,ANGLESS}.hyb.tar.gz
+
+	for i in *; do
+		mv -v ${i}{,.hyb} || die
+	done
+
+	unpack ${P}-vall.dat.apr24.gz
+	mv ${P}-vall.dat.apr24 vall.dat.apr24 || die
+
+	unpack ${P}-{PDBH,CS,ANGLESS}.tar.Z
+}
+
+src_prepare() {
+	default
+	cat >> "${T}"/39${PN} <<- EOF
+	CS_DIR="${EPREFIX}/opt/${MY_PN}/CS"
+	CSHYB_DIR="${EPREFIX}/opt/${MY_PN}/CS"
+	PDBH_DIR="${EPREFIX}/opt/${MY_PN}/PDBH"
+	PDBHYB_DIR="${EPREFIX}/opt/${MY_PN}/PDBH"
+	PDBH_TAB="${EPREFIX}/opt/${MY_PN}/PDBH/resolution.tab"
+	ANGLESS_DIR="${EPREFIX}/opt/${MY_PN}/ANGLESS"
+	ANGLESSHYB_DIR="${EPREFIX}/opt/${MY_PN}/ANGLESS"
+	EOF
+}
+
+src_install() {
+	insinto /opt/${MY_PN}/
+	doins -r *
+	doenvd "${T}"/39${PN}
+}
diff --git a/sci-libs/daal4py/Manifest b/sci-libs/daal4py/Manifest
new file mode 100644
index 000000000..0d9bbdab2
--- /dev/null
+++ b/sci-libs/daal4py/Manifest
@@ -0,0 +1 @@
+DIST daal4py-2023.0.2.tar.gz 13864043 BLAKE2B dfc082a8b008553e0d20cf7a24417fecd510dd8e6b3286a57a633b1e3b79cecc87fc1189df6f4a3440d7ccb74077c54a9f6eaf58bfbb19181cb4b437b3e06ae6 SHA512 dd8c983365d4f32d2640caab17319970c86bfed5ad6852d15dce35ba66a3584c51b94fa5ef0d8073b917332ea18a8c9af95ef8da125edb47190f27e9b8cab424
diff --git a/sci-libs/daal4py/daal4py-2023.0.2.ebuild b/sci-libs/daal4py/daal4py-2023.0.2.ebuild
new file mode 100644
index 000000000..f23e1c738
--- /dev/null
+++ b/sci-libs/daal4py/daal4py-2023.0.2.ebuild
@@ -0,0 +1,64 @@
+# Copyright 2022 Gentoo Authors
+# Distributed under the terms of the GNU General Public License v2
+
+EAPI=8
+
+PYTHON_COMPAT=( python3_{10..11} )
+DISTUTILS_USE_PEP517=setuptools
+inherit distutils-r1
+
+DESCRIPTION="Python API to the oneAPI Data Analytics Library"
+HOMEPAGE="https://github.com/intel/scikit-learn-intelex"
+SRC_URI="https://github.com/intel/scikit-learn-intelex/archive/${PV}.tar.gz -> ${P}.tar.gz"
+S="${WORKDIR}/scikit-learn-intelex-${PV}"
+
+LICENSE="Apache-2.0"
+SLOT="0"
+KEYWORDS="~amd64"
+
+BDEPEND="
+	dev-python/cython[${PYTHON_USEDEP}]
+	dev-python/pybind11[${PYTHON_USEDEP}]
+	dev-build/cmake
+	sys-devel/DPC++
+	test? (
+		sci-libs/scikit-learn[${PYTHON_USEDEP}]
+		sci-libs/scikit-learn-intelx[${PYTHON_USEDEP}]
+		dev-python/pandas[${PYTHON_USEDEP}]
+	)
+"
+
+DEPEND="
+	dev-python/jinja[${PYTHON_USEDEP}]
+	dev-python/numpy[${PYTHON_USEDEP}]
+	dev-python/dpctl[${PYTHON_USEDEP}]
+	sci-libs/oneDAL
+	virtual/mpi
+"
+RDEPEND="${DEPEND}"
+
+distutils_enable_tests pytest
+
+PATCHES=(
+	"${FILESDIR}/${PN}-2023.0.2-dont-use-entire-include.patch"
+)
+
+python_prepare_all() {
+	# DPC++ compiler required for full functionality
+	export CC="${ESYSROOT}/usr/lib/llvm/intel/bin/clang"
+	export CXX="${ESYSROOT}/usr/lib/llvm/intel/bin/clang++"
+	export DPCPPROOT="${ESYSROOT}/usr/lib/llvm/intel"
+	export CPLUS_INCLUDE_PATH="${ESYSROOT}/usr/lib/llvm/intel/include:${ESYSROOT}/usr/lib/llvm/intel/include/sycl:${ESYSROOT}/usr/lib/llvm/intel/include/sycl/CL/sycl"
+	export MPIROOT="${ESYSROOT}/usr"
+	export DALROOT="${ESYSROOT}/usr"
+	# Parallel build is broken
+	export MAKEOPTS="-j1"
+
+	distutils-r1_python_prepare_all
+}
+
+python_test() {
+	export PYTHONPATH="${BUILD_DIR}/install/usr/lib/${EPYTHON}/site-packages"
+	# We don't use epytest because it overwrites our PYTHONPATH
+	pytest -vv || die
+}
diff --git a/sci-libs/daal4py/files/daal4py-2023.0.2-dont-use-entire-include.patch b/sci-libs/daal4py/files/daal4py-2023.0.2-dont-use-entire-include.patch
new file mode 100644
index 000000000..d26414105
--- /dev/null
+++ b/sci-libs/daal4py/files/daal4py-2023.0.2-dont-use-entire-include.patch
@@ -0,0 +1,104 @@
+diff --git a/generator/gen_daal4py.py b/generator/gen_daal4py.py
+index 203c870..7fdac1e 100755
+--- a/generator/gen_daal4py.py
++++ b/generator/gen_daal4py.py
+@@ -34,7 +34,7 @@ from .wrappers import (required, ignore, defaults, has_dist, ifaces,
+                        enum_maps, enum_params, wrap_algo, result_to_compute)
+ from .wrapper_gen import wrapper_gen
+ from .format import mk_var
+-from shutil import copytree, rmtree
++from shutil import copytree, copyfile, rmtree
+ from subprocess import call
+ 
+ try:
+@@ -1045,7 +1045,13 @@ def gen_daal4py(daalroot, outdir, version, warn_all=False,
+     head_path = jp("build", "include")
+     algo_path = jp(head_path, "algorithms")
+     rmtree(head_path, ignore_errors=True)
+-    copytree(orig_path, head_path)
++    copytree(jp(orig_path, 'services'), jp(head_path, 'services'))
++    copytree(jp(orig_path, 'oneapi', 'dal'), jp(head_path, 'oneapi', 'dal'))
++    copytree(jp(orig_path, 'data_management'), jp(head_path, 'data_management'))
++    copytree(jp(orig_path, 'algorithms'), jp(head_path, 'algorithms'))
++    copyfile(jp(orig_path, 'daal.h'), jp(head_path, 'daal.h'))
++    copyfile(jp(orig_path, 'daal_sycl.h'), jp(head_path, 'daal_sycl.h'))
++    copyfile(jp(orig_path, 'oneapi', 'dal.hpp'), jp(head_path, 'oneapi', 'dal.hpp'))
+     for (dirpath, dirnames, filenames) in os.walk(algo_path):
+         for filename in filenames:
+             call([shutil.which("clang-format"), "-i", jp(dirpath, filename)])
+diff --git a/scripts/build_backend.py b/scripts/build_backend.py
+index dd314e4..ec1ec2c 100755
+--- a/scripts/build_backend.py
++++ b/scripts/build_backend.py
+@@ -118,20 +118,12 @@ def custom_build_cmake_clib(iface, cxx=None, onedal_major_binary_version=1):
+     python_library_dir = win_python_path_lib if IS_WIN else get_config_var('LIBDIR')

+     numpy_include = np.get_include()

+ 

+-    if iface == 'dpc':

+-        if IS_WIN:

+-            cxx = 'icx'

+-        else:

+-            cxx = 'icpx'

+-    elif cxx is None:

+-        raise RuntimeError('CXX compiler shall be specified')

+-

+     cmake_args = [

+         "cmake",

+         cmake_generator,

+         "-S" + builder_directory,

+         "-B" + abs_build_temp_path,

+-        "-DCMAKE_CXX_COMPILER=" + cxx,

++        "-DCMAKE_CXX_COMPILER=" + os.environ.get('CXX'),

+         "-DCMAKE_INSTALL_PREFIX=" + install_directory,

+         "-DCMAKE_PREFIX_PATH=" + install_directory,

+         "-DIFACE=" + iface,

+@@ -140,7 +132,7 @@ def custom_build_cmake_clib(iface, cxx=None, onedal_major_binary_version=1):
+         "-DNUMPY_INCLUDE_DIRS=" + numpy_include,

+         "-DPYTHON_LIBRARY_DIR=" + python_library_dir,

+         "-DoneDAL_INCLUDE_DIRS=" + jp(os.environ['DALROOT'], 'include'),

+-        "-DoneDAL_LIBRARY_DIR=" + jp(os.environ['DALROOT'], 'lib', 'intel64'),

++        "-DoneDAL_LIBRARY_DIR=" + jp(os.environ['DALROOT'], 'lib', 'lib64'),

+         "-Dpybind11_DIR=" + pybind11.get_cmake_dir(),

+     ]

+ 

+diff --git a/setup.py b/setup.py
+index 8f56b48..36260ea 100644
+--- a/setup.py
++++ b/setup.py
+@@ -48,13 +48,13 @@ if dal_root is None:
+ 
+ if 'linux' in sys.platform:
+     IS_LIN = True
+-    lib_dir = jp(dal_root, 'lib', 'intel64')
++    lib_dir = jp(dal_root, 'lib', 'lib64')
+ elif sys.platform == 'darwin':
+     IS_MAC = True
+     lib_dir = jp(dal_root, 'lib')
+ elif sys.platform in ['win32', 'cygwin']:
+     IS_WIN = True
+-    lib_dir = jp(dal_root, 'lib', 'intel64')
++    lib_dir = jp(dal_root, 'lib', 'lib64')
+ else:
+     assert False, sys.platform + ' not supported'
+ 
+@@ -178,7 +178,8 @@ def get_build_options():
+         'icc', 'icpc', 'icl', 'dpcpp', 'icx', 'icpx']
+     eca = ['-DPY_ARRAY_UNIQUE_SYMBOL=daal4py_array_API',
+            '-DD4P_VERSION="' + d4p_version + '"', '-DNPY_ALLOW_THREADS=1']
+-    ela = []
++    ela = os.environ.get('LDFLAGS').split(" ")
++    eca += os.environ.get('CFLAGS').split(" ")
+ 
+     if using_intel and IS_WIN:
+         include_dir_plat.append(
+@@ -311,8 +312,8 @@ def build_oneapi_backend():
+     ela = ['-fsycl'] + ['-fsycl-device-code-split=per_kernel'] + ela
+ 
+     return build_backend.build_cpp(
+-        cc=cc,
+-        cxx=cxx,
++        cc=os.environ.get('CC'),
++        cxx=os.environ.get('CXX'),
+         sources=['src/oneapi/oneapi_backend.cpp'],
+         targetname='oneapi_backend',
+         targetprefix='' if IS_WIN else 'lib',
diff --git a/sci-libs/daal4py/metadata.xml b/sci-libs/daal4py/metadata.xml
new file mode 100644
index 000000000..247707c87
--- /dev/null
+++ b/sci-libs/daal4py/metadata.xml
@@ -0,0 +1,11 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
+<pkgmetadata>
+	<maintainer type="project">
+		<email>sci@gentoo.org</email>
+		<name>Gentoo Science Project</name>
+	</maintainer>
+	<upstream>
+		<remote-id type="github">intel/scikit-learn-intelex</remote-id>
+	</upstream>
+</pkgmetadata>
diff --git a/sci-libs/dcmtk/Manifest b/sci-libs/dcmtk/Manifest
deleted file mode 100644
index 55d0fef4d..000000000
--- a/sci-libs/dcmtk/Manifest
+++ /dev/null
@@ -1,2 +0,0 @@
-DIST 07_doxygen.patch 88142 BLAKE2B 779f233396b16193892077113506f1d0f24758c918455ac6077737aab8049f6ddd5cacb5eff70cb7a96bae2790c750e7f1fca2d9741e71451e3ce0feefa5d6bb SHA512 61ed0891c998dc24cb44457a2625eba6842b991d261d503dfe5191d71296b338130586e68d70e3915b103bf5cb58b1164b7594921b3703664bd436a1248dccea
-DIST dcmtk-3.6.0.tar.gz 4673121 BLAKE2B 5694669bf4e612fbc39c5785a1498097972d47ecd5c66e437603dd2259258783b36ac86ea2dd57cc74b3af1701c933965e53c433dd09e1acd94dbb768b81b365 SHA512 2a9d866bafcaea72d889d24b51ff2341ee39c717aacf9ae5825c8588cd5cb01c3e341b6173abce751f6cb32c45be8888e81ccb08967cae2cca7fdcb2b61be53c
diff --git a/sci-libs/dcmtk/dcmtk-3.6.0.ebuild b/sci-libs/dcmtk/dcmtk-3.6.0.ebuild
deleted file mode 100644
index dbcd65680..000000000
--- a/sci-libs/dcmtk/dcmtk-3.6.0.ebuild
+++ /dev/null
@@ -1,74 +0,0 @@
-# Copyright 1999-2015 Gentoo Foundation
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=5
-
-inherit cmake-utils
-
-DESCRIPTION="OFFIS DICOM image files library and tools"
-HOMEPAGE="http://dicom.offis.de/dcmtk.php.en"
-SRC_URI="
-	http://dicom.offis.de/download/dcmtk/release/${P}.tar.gz
-	https://raw.githubusercontent.com/gentoo-science/sci/master/patches/07_doxygen.patch
-	"
-
-LICENSE="BSD"
-KEYWORDS="~amd64 ~x86 ~amd64-linux ~x86-linux"
-SLOT="0"
-IUSE="doc png ssl tcpd +threads tiff xml zlib"
-
-RDEPEND="
-	virtual/jpeg:0=
-	png? ( media-libs/libpng:0= )
-	ssl? ( dev-libs/openssl:= )
-	tcpd? ( sys-apps/tcp-wrappers )
-	tiff? ( media-libs/tiff:0= )
-	xml? ( dev-libs/libxml2:2= )
-	zlib? ( sys-libs/zlib:0= )"
-DEPEND="${RDEPEND}
-	doc? ( app-doc/doxygen[dot] )"
-
-PATCHES=(
-	"${FILESDIR}"/${PN}-asneeded.patch
-	"${FILESDIR}"/02_dcmtk_3.6.0-1.patch
-	"${DISTDIR}"/07_doxygen.patch
-	"${FILESDIR}"/prefs.patch
-	"${FILESDIR}"/dcmtk_version_number.patch
-	"${FILESDIR}"/regression_stacksequenceisodd.patch
-	"${FILESDIR}"/bug674361.patch
-	"${FILESDIR}"/use_correct_number_of_TS.patch
-	"${FILESDIR}"/fixnull.patch
-	"${FILESDIR}"/nothrow.patch
-	"${FILESDIR}"/noleak.patch
-	"${FILESDIR}"/doubledes.patch
-)
-
-src_prepare() {
-	sed -i \
-		-e "s:/usr/local/bin:$(type -P perl):g" \
-		dcmwlm/perl/*.pl || die
-	sed -i \
-		-e "s:share/doc/dcmtk:share/doc/${PF}:" \
-		-e "s:/lib\":/$(get_libdir)\":" \
-		-e "s:COPYRIGHT::" \
-		CMakeLists.txt || die
-	cmake-utils_src_prepare
-}
-
-src_configure() {
-	local mycmakeargs=(
-		-DBUILD_SHARED_LIBS=ON
-		$(cmake-utils_use doc DCMTK_WITH_DOXYGEN)
-		$(cmake-utils_use png DCMTK_WITH_PNG)
-		$(cmake-utils_use ssl DCMTK_WITH_OPENSSL)
-		$(cmake-utils_use threads DCMTK_WITH_THREADS)
-		$(cmake-utils_use tiff DCMTK_WITH_TIFF)
-		$(cmake-utils_use xml DCMTK_WITH_XML)
-		$(cmake-utils_use zlib DCMTK_WITH_ZLIB)
-	)
-	cmake-utils_src_configure
-}
-
-src_compile() {
-	cmake-utils_src_compile all $(usex doc "html" "")
-}
diff --git a/sci-libs/dcmtk/files/02_dcmtk_3.6.0-1.patch b/sci-libs/dcmtk/files/02_dcmtk_3.6.0-1.patch
deleted file mode 100644
index 11aaaec37..000000000
--- a/sci-libs/dcmtk/files/02_dcmtk_3.6.0-1.patch
+++ /dev/null
@@ -1,89 +0,0 @@
-Author: Jürgen Salk <jsa@debian.org>
-Description: The original maintainer Jürgen Salk applied
- a set of patches to the original code.  This file contains
- changes to C++ code
-
-Index: dcmtk-3.6.0/dcmqrdb/etc/dcmqrscp.cfg
-===================================================================
---- dcmtk-3.6.0.orig/dcmqrdb/etc/dcmqrscp.cfg	2010-09-09 19:20:25.000000000 +0200
-+++ dcmtk-3.6.0/dcmqrdb/etc/dcmqrscp.cfg	2011-01-28 09:49:02.000000000 +0100
-@@ -10,6 +10,9 @@
- NetworkTCPPort  = 104
- MaxPDUSize      = 16384
- MaxAssociations = 16
-+UserName        = "dcmtk"
-+GroupName       = "dcmtk"
-+
- #
- # UserName      = <not used>
- # GroupName     = <not used>
-@@ -28,12 +31,13 @@
- # NOTE: in the current implementation you cannot substitute an IP address
- # for a hostname.
- #
--acme1           = (ACME1, acmehost1, 5678)
--acme2           = (ACME2, acmehost2, 5678)
--acmeCTcompany   = acme1, acme2
--united1         = (UNITED1, unitedhost1, 104)
--united2         = (UNITED2, unitedhost2, 104)
--unitedMRcompany = united1, united2
-+# Example:
-+#acme1           = (ACME1, acmehost1, 5678)
-+#acme2           = (ACME2, acmehost2, 5678)
-+#acmeCTcompany   = acme1, acme2
-+#united1         = (UNITED1, unitedhost1, 104)
-+#united2         = (UNITED2, unitedhost2, 104)
-+#unitedMRcompany = united1, united2
- #
- HostTable END
- 
-@@ -51,8 +55,9 @@
- #       VendorName = SymbolicName
- # The symbolic name should be defined in the HostTable.
- #
--"Acme CT Company"   = acmeCTcompany
--"United MR Company" = unitedMRcompany
-+# Example:
-+#"Acme CT Company"   = acmeCTcompany
-+#"United MR Company" = unitedMRcompany
- #
- VendorTable END
- 
-@@ -70,8 +75,13 @@
- #               Entry in HostTable                      |
- #               ANY
- #
--COMMON       /home/dicom/db/COMMON       R  (200, 1024mb) ANY
--ACME_STORE   /home/dicom/db/ACME_STORE   RW (9, 1024mb)   acmeCTcompany
--UNITED_STORE /home/dicom/db/UNITED_STORE RW (9, 1024mb)   unitedMRcompany
-+# Example:
-+#
-+#ACME_STORE   /var/lib/dcmtk/db/ACME_STORE   RW (9, 1024mb)   acmeCTcompany
-+#UNITED_STORE /var/lib/dcmtk/db/UNITED_STORE RW (9, 1024mb)   unitedMRcompany
-+#
-+# Uncomment and adjust the following lines for a common r/rw storage area:
-+#READWRITE     /var/lib/dcmtk/db/READWRITE    RW (10, 1024mb)  ANY
-+#READ          /var/lib/dcmtk/db/READ         R  (200, 1024mb) ANY
- #
- AETable END
-Index: dcmtk-3.6.0/dcmqrdb/docs/dcmqrcnf.txt
-===================================================================
---- dcmtk-3.6.0.orig/dcmqrdb/docs/dcmqrcnf.txt	2010-09-09 19:20:12.000000000 +0200
-+++ dcmtk-3.6.0/dcmqrdb/docs/dcmqrcnf.txt	2011-01-28 09:46:02.000000000 +0100
-@@ -44,8 +44,8 @@
- NetworkTCPPort  = 104
- MaxPDUSize      = 8192
- MaxAssociations = 20
--UserName        = (do not change user)
--GroupName       = (do not change group)
-+UserName        = "dcmtk"
-+GroupName       = "dcmtk"
- 
- NOTE: You must have root privileges to bind port 104 for DICOM association 
- requests on Unix/Linux/Posix platforms as this is a privileged port number 
-Index: dcmtk-3.6.0/dcmwlm/wlistdb/OFFIS/lockfile
-===================================================================
---- /dev/null	1970-01-01 00:00:00.000000000 +0000
-+++ dcmtk-3.6.0/dcmwlm/wlistdb/OFFIS/lockfile	2011-01-28 09:46:02.000000000 +0100
-@@ -0,0 +1 @@
-+
diff --git a/sci-libs/dcmtk/files/bug674361.patch b/sci-libs/dcmtk/files/bug674361.patch
deleted file mode 100644
index f335deed6..000000000
--- a/sci-libs/dcmtk/files/bug674361.patch
+++ /dev/null
@@ -1,1015 +0,0 @@
-From dbadc0d8f3760f65504406c8b2cb8633f868a258 Mon Sep 17 00:00:00 2001
-From: Joerg Riesmeier <dicom@offis.de>
-Date: Thu, 17 Nov 2011 16:13:14 +0000
-Subject: [PATCH] Minor fixes to keep XCode 4.2 on Mac OS X Lion (clang compiler) quiet.
-
----
- CHANGES.361                                |   24 ++++++++++++++++++++++++
- dcmimage/include/dcmtk/dcmimage/diargpxt.h |   25 ++++++++++++++-----------
- dcmimage/include/dcmtk/dcmimage/dicmypxt.h |   11 +++++++----
- dcmimage/include/dcmtk/dcmimage/dicocpt.h  |   11 +++++++----
- dcmimage/include/dcmtk/dcmimage/dicoflt.h  |   17 ++++++++++-------
- dcmimage/include/dcmtk/dcmimage/dicorot.h  |   17 ++++++++++-------
- dcmimage/include/dcmtk/dcmimage/dicosct.h  |   13 ++++++++-----
- dcmimage/include/dcmtk/dcmimage/dihsvpxt.h |   11 +++++++----
- dcmimage/include/dcmtk/dcmimage/dipalpxt.h |   11 +++++++----
- dcmimage/include/dcmtk/dcmimage/dirgbpxt.h |   15 +++++++++------
- dcmimage/include/dcmtk/dcmimage/diybrpxt.h |   15 +++++++++------
- dcmimage/include/dcmtk/dcmimage/diyf2pxt.h |   11 +++++++----
- dcmimage/include/dcmtk/dcmimage/diyp2pxt.h |   11 +++++++----
- dcmimgle/include/dcmtk/dcmimgle/diflipt.h  |   11 +++++++----
- dcmimgle/include/dcmtk/dcmimgle/dimoflt.h  |   15 +++++++++------
- dcmimgle/include/dcmtk/dcmimgle/dimoipxt.h |   13 ++++++++-----
- dcmimgle/include/dcmtk/dcmimgle/dimorot.h  |   15 +++++++++------
- dcmimgle/include/dcmtk/dcmimgle/dimosct.h  |   11 +++++++----
- dcmimgle/include/dcmtk/dcmimgle/dirotat.h  |   11 +++++++----
- dcmimgle/include/dcmtk/dcmimgle/discalet.h |   19 +++++++++++--------
- ofstd/include/dcmtk/ofstd/ofoset.h         |   13 ++++++++-----
- ofstd/libsrc/ofchrenc.cc                   |   13 +++++++++++--
- 22 files changed, 203 insertions(+), 110 deletions(-)
-
-Index: dcmtk-3.6.0/dcmimage/include/dcmtk/dcmimage/diargpxt.h
-===================================================================
---- dcmtk-3.6.0.orig/dcmimage/include/dcmtk/dcmimage/diargpxt.h	2010-10-14 13:16:29.000000000 +0000
-+++ dcmtk-3.6.0/dcmimage/include/dcmtk/dcmimage/diargpxt.h	2012-05-25 09:16:23.791876809 +0000
-@@ -1,6 +1,6 @@
- /*
-  *
-- *  Copyright (C) 1996-2010, OFFIS e.V.
-+ *  Copyright (C) 1996-2011, OFFIS e.V.
-  *  All rights reserved.  See COPYRIGHT file for details.
-  *
-  *  This software and supporting documentation were developed by
-@@ -18,8 +18,8 @@
-  *  Purpose: DicomARGBPixelTemplate (Header) - UNTESTED !!!
-  *
-  *  Last Update:      $Author: joergr $
-- *  Update Date:      $Date: 2010-10-14 13:16:29 $
-- *  CVS/RCS Revision: $Revision: 1.21 $
-+ *  Update Date:      $Date: 2011-11-17 16:13:14 $
-+ *  CVS/RCS Revision: $Revision: 1.22 $
-  *  Status:           $State: Exp $
-  *
-  *  CVS/RCS Log at end of file
-@@ -91,7 +91,7 @@
-                  const unsigned long planeSize,
-                  const int bits)
-     {                                             // not very much optimized, but no one really uses ARGB !!
--        if (Init(pixel))
-+        if (this->Init(pixel))
-         {
-             register T2 value;
-             const T1 offset = OFstatic_cast(T1, DicomImageClass::maxval(bits - 1));
-@@ -103,9 +103,9 @@
- /*
-                 register const T1 *a = pixel;                                   // points to alpha plane
-                 const T1 *rgb[3];
--                rgb[0] = a + this->InputCount;                                        // points to red plane
--                rgb[1] = rgb[0] + this->InputCount;                                   // points to green plane
--                rgb[2] = rgb[1] + this->InputCount;                                   // points to blue plane
-+                rgb[0] = a + this->InputCount;                                  // points to red plane
-+                rgb[1] = rgb[0] + this->InputCount;                             // points to green plane
-+                rgb[2] = rgb[1] + this->InputCount;                             // points to blue plane
-                 for (i = 0; i < count; ++i)
-                 {
-                     value = OFstatic_cast(T2, *(a++));                          // get alpha value
-@@ -141,10 +141,10 @@
-                     /* convert a single frame */
-                     for (l = planeSize; (l != 0) && (i < count); --l, ++i)
-                     {
--                        value = OFstatic_cast(T2, *(a++));                          // get alpha value
-+                        value = OFstatic_cast(T2, *(a++));                      // get alpha value
-                         if (value > 0)
-                         {
--                            for (int j = 0; j < 3; ++j)                             // set palette color
-+                            for (int j = 0; j < 3; ++j)                         // set palette color
-                             {
-                                 if (value <= palette[j]->getFirstEntry(value))
-                                     this->Data[j][i] = OFstatic_cast(T3, palette[j]->getFirstValue());
-@@ -152,12 +152,12 @@
-                                     this->Data[j][i] = OFstatic_cast(T3, palette[j]->getLastValue());
-                                 else
-                                     this->Data[j][i] = OFstatic_cast(T3, palette[j]->getValue(value));
--                                ++rgb[j];                                           // skip RGB values
-+                                ++rgb[j];                                       // skip RGB values
-                             }
-                         }
-                         else
-                         {
--                            for (int j = 0; j < 3; ++j)                             // copy RGB values
-+                            for (int j = 0; j < 3; ++j)                         // copy RGB values
-                                 this->Data[j][i] = OFstatic_cast(T3, removeSign(*(rgb[j]++), offset));
-                         }
-                     }
-@@ -204,6 +204,9 @@
-  *
-  * CVS/RCS Log:
-  * $Log: diargpxt.h,v $
-+ * Revision 1.22  2011-11-17 16:13:14  joergr
-+ * Minor fixes to keep XCode 4.2 on Mac OS X Lion (clang compiler) quiet.
-+ *
-  * Revision 1.21  2010-10-14 13:16:29  joergr
-  * Updated copyright header. Added reference to COPYRIGHT file.
-  *
-Index: dcmtk-3.6.0/dcmimage/include/dcmtk/dcmimage/dicmypxt.h
-===================================================================
---- dcmtk-3.6.0.orig/dcmimage/include/dcmtk/dcmimage/dicmypxt.h	2010-10-14 13:16:29.000000000 +0000
-+++ dcmtk-3.6.0/dcmimage/include/dcmtk/dcmimage/dicmypxt.h	2012-05-25 09:16:23.791876809 +0000
-@@ -1,6 +1,6 @@
- /*
-  *
-- *  Copyright (C) 1996-2010, OFFIS e.V.
-+ *  Copyright (C) 1996-2011, OFFIS e.V.
-  *  All rights reserved.  See COPYRIGHT file for details.
-  *
-  *  This software and supporting documentation were developed by
-@@ -18,8 +18,8 @@
-  *  Purpose: DicomCMYKPixelTemplate (Header)
-  *
-  *  Last Update:      $Author: joergr $
-- *  Update Date:      $Date: 2010-10-14 13:16:29 $
-- *  CVS/RCS Revision: $Revision: 1.20 $
-+ *  Update Date:      $Date: 2011-11-17 16:13:14 $
-+ *  CVS/RCS Revision: $Revision: 1.21 $
-  *  Status:           $State: Exp $
-  *
-  *  CVS/RCS Log at end of file
-@@ -87,7 +87,7 @@
-                  const unsigned long planeSize,
-                  const int bits)
-     {
--        if (Init(pixel))
-+        if (this->Init(pixel))
-         {
-             // use the number of input pixels derived from the length of the 'PixelData'
-             // attribute), but not more than the size of the intermediate buffer
-@@ -157,6 +157,9 @@
-  *
-  * CVS/RCS Log:
-  * $Log: dicmypxt.h,v $
-+ * Revision 1.21  2011-11-17 16:13:14  joergr
-+ * Minor fixes to keep XCode 4.2 on Mac OS X Lion (clang compiler) quiet.
-+ *
-  * Revision 1.20  2010-10-14 13:16:29  joergr
-  * Updated copyright header. Added reference to COPYRIGHT file.
-  *
-Index: dcmtk-3.6.0/dcmimage/include/dcmtk/dcmimage/dicocpt.h
-===================================================================
---- dcmtk-3.6.0.orig/dcmimage/include/dcmtk/dcmimage/dicocpt.h	2010-10-14 13:16:29.000000000 +0000
-+++ dcmtk-3.6.0/dcmimage/include/dcmtk/dcmimage/dicocpt.h	2012-05-25 09:16:23.791876809 +0000
-@@ -1,6 +1,6 @@
- /*
-  *
-- *  Copyright (C) 1998-2010, OFFIS e.V.
-+ *  Copyright (C) 1998-2011, OFFIS e.V.
-  *  All rights reserved.  See COPYRIGHT file for details.
-  *
-  *  This software and supporting documentation were developed by
-@@ -18,8 +18,8 @@
-  *  Purpose: DicomColorCopyTemplate (Header)
-  *
-  *  Last Update:      $Author: joergr $
-- *  Update Date:      $Date: 2010-10-14 13:16:29 $
-- *  CVS/RCS Revision: $Revision: 1.12 $
-+ *  Update Date:      $Date: 2011-11-17 16:13:14 $
-+ *  CVS/RCS Revision: $Revision: 1.13 $
-  *  Status:           $State: Exp $
-  *
-  *  CVS/RCS Log at end of file
-@@ -86,7 +86,7 @@
-     inline void copy(const T *pixel[3],
-                      const unsigned long offset)
-     {
--        if (Init(pixel))
-+        if (this->Init(pixel))
-         {
-             for (int j = 0; j < 3; j++)
-                 OFBitmanipTemplate<T>::copyMem(pixel[j] + offset, this->Data[j], this->getCount());
-@@ -102,6 +102,9 @@
-  *
-  * CVS/RCS Log:
-  * $Log: dicocpt.h,v $
-+ * Revision 1.13  2011-11-17 16:13:14  joergr
-+ * Minor fixes to keep XCode 4.2 on Mac OS X Lion (clang compiler) quiet.
-+ *
-  * Revision 1.12  2010-10-14 13:16:29  joergr
-  * Updated copyright header. Added reference to COPYRIGHT file.
-  *
-Index: dcmtk-3.6.0/dcmimage/include/dcmtk/dcmimage/dicoflt.h
-===================================================================
---- dcmtk-3.6.0.orig/dcmimage/include/dcmtk/dcmimage/dicoflt.h	2010-10-14 13:16:29.000000000 +0000
-+++ dcmtk-3.6.0/dcmimage/include/dcmtk/dcmimage/dicoflt.h	2012-05-25 09:16:23.795876809 +0000
-@@ -1,6 +1,6 @@
- /*
-  *
-- *  Copyright (C) 1998-2010, OFFIS e.V.
-+ *  Copyright (C) 1998-2011, OFFIS e.V.
-  *  All rights reserved.  See COPYRIGHT file for details.
-  *
-  *  This software and supporting documentation were developed by
-@@ -18,8 +18,8 @@
-  *  Purpose: DicomColorFlipTemplate (Header)
-  *
-  *  Last Update:      $Author: joergr $
-- *  Update Date:      $Date: 2010-10-14 13:16:29 $
-- *  CVS/RCS Revision: $Revision: 1.15 $
-+ *  Update Date:      $Date: 2011-11-17 16:13:14 $
-+ *  CVS/RCS Revision: $Revision: 1.16 $
-  *  Status:           $State: Exp $
-  *
-  *  CVS/RCS Log at end of file
-@@ -98,14 +98,14 @@
-                      const int horz,
-                      const int vert)
-     {
--        if (Init(pixel))
-+        if (this->Init(pixel))
-         {
-             if (horz && vert)
--                flipHorzVert(pixel, this->Data);
-+                this->flipHorzVert(pixel, this->Data);
-             else if (horz)
--                flipHorz(pixel, this->Data);
-+                this->flipHorz(pixel, this->Data);
-             else if (vert)
--                flipVert(pixel, this->Data);
-+                this->flipVert(pixel, this->Data);
-         }
-     }
- };
-@@ -118,6 +118,9 @@
-  *
-  * CVS/RCS Log:
-  * $Log: dicoflt.h,v $
-+ * Revision 1.16  2011-11-17 16:13:14  joergr
-+ * Minor fixes to keep XCode 4.2 on Mac OS X Lion (clang compiler) quiet.
-+ *
-  * Revision 1.15  2010-10-14 13:16:29  joergr
-  * Updated copyright header. Added reference to COPYRIGHT file.
-  *
-Index: dcmtk-3.6.0/dcmimage/include/dcmtk/dcmimage/dicorot.h
-===================================================================
---- dcmtk-3.6.0.orig/dcmimage/include/dcmtk/dcmimage/dicorot.h	2010-10-14 13:16:29.000000000 +0000
-+++ dcmtk-3.6.0/dcmimage/include/dcmtk/dcmimage/dicorot.h	2012-05-25 09:16:23.795876809 +0000
-@@ -1,6 +1,6 @@
- /*
-  *
-- *  Copyright (C) 1998-2010, OFFIS e.V.
-+ *  Copyright (C) 1998-2011, OFFIS e.V.
-  *  All rights reserved.  See COPYRIGHT file for details.
-  *
-  *  This software and supporting documentation were developed by
-@@ -18,8 +18,8 @@
-  *  Purpose: DicomColorRotateTemplate (Header)
-  *
-  *  Last Update:      $Author: joergr $
-- *  Update Date:      $Date: 2010-10-14 13:16:29 $
-- *  CVS/RCS Revision: $Revision: 1.15 $
-+ *  Update Date:      $Date: 2011-11-17 16:13:14 $
-+ *  CVS/RCS Revision: $Revision: 1.16 $
-  *  Status:           $State: Exp $
-  *
-  *  CVS/RCS Log at end of file
-@@ -98,14 +98,14 @@
-     inline void rotate(const T *pixel[3],
-                        const int degree)
-     {
--        if (Init(pixel))
-+        if (this->Init(pixel))
-         {
-             if (degree == 90)
--                rotateRight(pixel, this->Data);
-+                this->rotateRight(pixel, this->Data);
-             else if (degree == 180)
--                rotateTopDown(pixel, this->Data);
-+                this->rotateTopDown(pixel, this->Data);
-             else  if (degree == 270)
--                rotateLeft(pixel, this->Data);
-+                this->rotateLeft(pixel, this->Data);
-         }
-     }
- };
-@@ -118,6 +118,9 @@
-  *
-  * CVS/RCS Log:
-  * $Log: dicorot.h,v $
-+ * Revision 1.16  2011-11-17 16:13:14  joergr
-+ * Minor fixes to keep XCode 4.2 on Mac OS X Lion (clang compiler) quiet.
-+ *
-  * Revision 1.15  2010-10-14 13:16:29  joergr
-  * Updated copyright header. Added reference to COPYRIGHT file.
-  *
-Index: dcmtk-3.6.0/dcmimage/include/dcmtk/dcmimage/dicosct.h
-===================================================================
---- dcmtk-3.6.0.orig/dcmimage/include/dcmtk/dcmimage/dicosct.h	2010-10-14 13:16:29.000000000 +0000
-+++ dcmtk-3.6.0/dcmimage/include/dcmtk/dcmimage/dicosct.h	2012-05-25 09:16:23.795876809 +0000
-@@ -1,6 +1,6 @@
- /*
-  *
-- *  Copyright (C) 1996-2010, OFFIS e.V.
-+ *  Copyright (C) 1996-2011, OFFIS e.V.
-  *  All rights reserved.  See COPYRIGHT file for details.
-  *
-  *  This software and supporting documentation were developed by
-@@ -18,8 +18,8 @@
-  *  Purpose: DicomColorScaleTemplate (Header)
-  *
-  *  Last Update:      $Author: joergr $
-- *  Update Date:      $Date: 2010-10-14 13:16:29 $
-- *  CVS/RCS Revision: $Revision: 1.21 $
-+ *  Update Date:      $Date: 2011-11-17 16:13:14 $
-+ *  CVS/RCS Revision: $Revision: 1.22 $
-  *  Status:           $State: Exp $
-  *
-  *  CVS/RCS Log at end of file
-@@ -107,8 +107,8 @@
-     inline void scale(const T *pixel[3],
-                       const int interpolate)
-     {
--        if (Init(pixel))
--            scaleData(pixel, this->Data, interpolate);
-+        if (this->Init(pixel))
-+            this->scaleData(pixel, this->Data, interpolate);
-     }
- };
- 
-@@ -120,6 +120,9 @@
-  *
-  * CVS/RCS Log:
-  * $Log: dicosct.h,v $
-+ * Revision 1.22  2011-11-17 16:13:14  joergr
-+ * Minor fixes to keep XCode 4.2 on Mac OS X Lion (clang compiler) quiet.
-+ *
-  * Revision 1.21  2010-10-14 13:16:29  joergr
-  * Updated copyright header. Added reference to COPYRIGHT file.
-  *
-Index: dcmtk-3.6.0/dcmimage/include/dcmtk/dcmimage/dihsvpxt.h
-===================================================================
---- dcmtk-3.6.0.orig/dcmimage/include/dcmtk/dcmimage/dihsvpxt.h	2010-10-14 13:16:29.000000000 +0000
-+++ dcmtk-3.6.0/dcmimage/include/dcmtk/dcmimage/dihsvpxt.h	2012-05-25 09:16:23.795876809 +0000
-@@ -1,6 +1,6 @@
- /*
-  *
-- *  Copyright (C) 1996-2010, OFFIS e.V.
-+ *  Copyright (C) 1996-2011, OFFIS e.V.
-  *  All rights reserved.  See COPYRIGHT file for details.
-  *
-  *  This software and supporting documentation were developed by
-@@ -18,8 +18,8 @@
-  *  Purpose: DicomHSVPixelTemplate (Header)
-  *
-  *  Last Update:      $Author: joergr $
-- *  Update Date:      $Date: 2010-10-14 13:16:29 $
-- *  CVS/RCS Revision: $Revision: 1.25 $
-+ *  Update Date:      $Date: 2011-11-17 16:13:14 $
-+ *  CVS/RCS Revision: $Revision: 1.26 $
-  *  Status:           $State: Exp $
-  *
-  *  CVS/RCS Log at end of file
-@@ -87,7 +87,7 @@
-                  const unsigned long planeSize,
-                  const int bits)
-     {
--        if (Init(pixel))
-+        if (this->Init(pixel))
-         {
-             register T2 *r = this->Data[0];
-             register T2 *g = this->Data[1];
-@@ -221,6 +221,9 @@
-  *
-  * CVS/RCS Log:
-  * $Log: dihsvpxt.h,v $
-+ * Revision 1.26  2011-11-17 16:13:14  joergr
-+ * Minor fixes to keep XCode 4.2 on Mac OS X Lion (clang compiler) quiet.
-+ *
-  * Revision 1.25  2010-10-14 13:16:29  joergr
-  * Updated copyright header. Added reference to COPYRIGHT file.
-  *
-Index: dcmtk-3.6.0/dcmimage/include/dcmtk/dcmimage/dipalpxt.h
-===================================================================
---- dcmtk-3.6.0.orig/dcmimage/include/dcmtk/dcmimage/dipalpxt.h	2010-10-14 13:16:29.000000000 +0000
-+++ dcmtk-3.6.0/dcmimage/include/dcmtk/dcmimage/dipalpxt.h	2012-05-25 09:16:23.795876809 +0000
-@@ -1,6 +1,6 @@
- /*
-  *
-- *  Copyright (C) 1996-2010, OFFIS e.V.
-+ *  Copyright (C) 1996-2011, OFFIS e.V.
-  *  All rights reserved.  See COPYRIGHT file for details.
-  *
-  *  This software and supporting documentation were developed by
-@@ -18,8 +18,8 @@
-  *  Purpose: DicomPalettePixelTemplate (Header)
-  *
-  *  Last Update:      $Author: joergr $
-- *  Update Date:      $Date: 2010-10-14 13:16:29 $
-- *  CVS/RCS Revision: $Revision: 1.24 $
-+ *  Update Date:      $Date: 2011-11-17 16:13:14 $
-+ *  CVS/RCS Revision: $Revision: 1.25 $
-  *  Status:           $State: Exp $
-  *
-  *  CVS/RCS Log at end of file
-@@ -92,7 +92,7 @@
-     void convert(const T1 *pixel,
-                  DiLookupTable *palette[3])
-     {                                                                // can be optimized if necessary !
--        if (Init(pixel))
-+        if (this->Init(pixel))
-         {
-             register const T1 *p = pixel;
-             register T2 value = 0;
-@@ -126,6 +126,9 @@
-  *
-  * CVS/RCS Log:
-  * $Log: dipalpxt.h,v $
-+ * Revision 1.25  2011-11-17 16:13:14  joergr
-+ * Minor fixes to keep XCode 4.2 on Mac OS X Lion (clang compiler) quiet.
-+ *
-  * Revision 1.24  2010-10-14 13:16:29  joergr
-  * Updated copyright header. Added reference to COPYRIGHT file.
-  *
-Index: dcmtk-3.6.0/dcmimage/include/dcmtk/dcmimage/dirgbpxt.h
-===================================================================
---- dcmtk-3.6.0.orig/dcmimage/include/dcmtk/dcmimage/dirgbpxt.h	2010-10-14 13:16:30.000000000 +0000
-+++ dcmtk-3.6.0/dcmimage/include/dcmtk/dcmimage/dirgbpxt.h	2012-05-25 09:16:23.795876809 +0000
-@@ -1,6 +1,6 @@
- /*
-  *
-- *  Copyright (C) 1996-2010, OFFIS e.V.
-+ *  Copyright (C) 1996-2011, OFFIS e.V.
-  *  All rights reserved.  See COPYRIGHT file for details.
-  *
-  *  This software and supporting documentation were developed by
-@@ -18,8 +18,8 @@
-  *  Purpose: DicomRGBPixelTemplate (Header)
-  *
-  *  Last Update:      $Author: joergr $
-- *  Update Date:      $Date: 2010-10-14 13:16:30 $
-- *  CVS/RCS Revision: $Revision: 1.18 $
-+ *  Update Date:      $Date: 2011-11-17 16:13:14 $
-+ *  CVS/RCS Revision: $Revision: 1.19 $
-  *  Status:           $State: Exp $
-  *
-  *  CVS/RCS Log at end of file
-@@ -87,7 +87,7 @@
-                  const unsigned long planeSize,
-                  const int bits)
-     {
--        if (Init(pixel))
-+        if (this->Init(pixel))
-         {
-             // use the number of input pixels derived from the length of the 'PixelData'
-             // attribute), but not more than the size of the intermediate buffer
-@@ -129,9 +129,9 @@
-             {
-                 register int j;
-                 register unsigned long i;
--                for (i = 0; i < count; ++i)                         /* for all pixel ... */
-+                for (i = 0; i < count; ++i)                             /* for all pixel ... */
-                     for (j = 0; j < 3; ++j)
--                        this->Data[j][i] = removeSign(*(p++), offset);    /* ... copy planes */
-+                        this->Data[j][i] = removeSign(*(p++), offset);  /* ... copy planes */
-             }
-         }
-     }
-@@ -145,6 +145,9 @@
-  *
-  * CVS/RCS Log:
-  * $Log: dirgbpxt.h,v $
-+ * Revision 1.19  2011-11-17 16:13:14  joergr
-+ * Minor fixes to keep XCode 4.2 on Mac OS X Lion (clang compiler) quiet.
-+ *
-  * Revision 1.18  2010-10-14 13:16:30  joergr
-  * Updated copyright header. Added reference to COPYRIGHT file.
-  *
-Index: dcmtk-3.6.0/dcmimage/include/dcmtk/dcmimage/diybrpxt.h
-===================================================================
---- dcmtk-3.6.0.orig/dcmimage/include/dcmtk/dcmimage/diybrpxt.h	2010-10-14 13:16:30.000000000 +0000
-+++ dcmtk-3.6.0/dcmimage/include/dcmtk/dcmimage/diybrpxt.h	2012-05-25 09:16:23.795876809 +0000
-@@ -1,6 +1,6 @@
- /*
-  *
-- *  Copyright (C) 1998-2010, OFFIS e.V.
-+ *  Copyright (C) 1998-2011, OFFIS e.V.
-  *  All rights reserved.  See COPYRIGHT file for details.
-  *
-  *  This software and supporting documentation were developed by
-@@ -18,8 +18,8 @@
-  *  Purpose: DicomYBRPixelTemplate (Header)
-  *
-  *  Last Update:      $Author: joergr $
-- *  Update Date:      $Date: 2010-10-14 13:16:30 $
-- *  CVS/RCS Revision: $Revision: 1.19 $
-+ *  Update Date:      $Date: 2011-11-17 16:13:14 $
-+ *  CVS/RCS Revision: $Revision: 1.20 $
-  *  Status:           $State: Exp $
-  *
-  *  CVS/RCS Log at end of file
-@@ -91,7 +91,7 @@
-                  const int bits,
-                  const OFBool rgb)
-     {
--        if (Init(pixel))
-+        if (this->Init(pixel))
-         {
-             const T1 offset = OFstatic_cast(T1, DicomImageClass::maxval(bits - 1));
-             // use the number of input pixels derived from the length of the 'PixelData'
-@@ -266,9 +266,9 @@
-                 {
-                     register int j;
-                     register unsigned long i;
--                    for (i = 0; i < count; ++i)                         /* for all pixel ... */
-+                    for (i = 0; i < count; ++i)                             /* for all pixel ... */
-                         for (j = 0; j < 3; ++j)
--                            this->Data[j][i] = removeSign(*(p++), offset);    /* ... copy planes */
-+                            this->Data[j][i] = removeSign(*(p++), offset);  /* ... copy planes */
-                 }
-             }
-         }
-@@ -295,6 +295,9 @@
-  *
-  * CVS/RCS Log:
-  * $Log: diybrpxt.h,v $
-+ * Revision 1.20  2011-11-17 16:13:14  joergr
-+ * Minor fixes to keep XCode 4.2 on Mac OS X Lion (clang compiler) quiet.
-+ *
-  * Revision 1.19  2010-10-14 13:16:30  joergr
-  * Updated copyright header. Added reference to COPYRIGHT file.
-  *
-Index: dcmtk-3.6.0/dcmimage/include/dcmtk/dcmimage/diyf2pxt.h
-===================================================================
---- dcmtk-3.6.0.orig/dcmimage/include/dcmtk/dcmimage/diyf2pxt.h	2010-10-14 13:16:30.000000000 +0000
-+++ dcmtk-3.6.0/dcmimage/include/dcmtk/dcmimage/diyf2pxt.h	2012-05-25 09:16:23.795876809 +0000
-@@ -1,6 +1,6 @@
- /*
-  *
-- *  Copyright (C) 1998-2010, OFFIS e.V.
-+ *  Copyright (C) 1998-2011, OFFIS e.V.
-  *  All rights reserved.  See COPYRIGHT file for details.
-  *
-  *  This software and supporting documentation were developed by
-@@ -18,8 +18,8 @@
-  *  Purpose: DicomYBR422PixelTemplate (Header)
-  *
-  *  Last Update:      $Author: joergr $
-- *  Update Date:      $Date: 2010-10-14 13:16:30 $
-- *  CVS/RCS Revision: $Revision: 1.25 $
-+ *  Update Date:      $Date: 2011-11-17 16:13:14 $
-+ *  CVS/RCS Revision: $Revision: 1.26 $
-  *  Status:           $State: Exp $
-  *
-  *  CVS/RCS Log at end of file
-@@ -95,7 +95,7 @@
-                  const int bits,
-                  const OFBool rgb)
-     {
--        if (Init(pixel))
-+        if (this->Init(pixel))
-         {
-             const T1 offset = OFstatic_cast(T1, DicomImageClass::maxval(bits - 1));
-             register unsigned long i;
-@@ -167,6 +167,9 @@
-  *
-  * CVS/RCS Log:
-  * $Log: diyf2pxt.h,v $
-+ * Revision 1.26  2011-11-17 16:13:14  joergr
-+ * Minor fixes to keep XCode 4.2 on Mac OS X Lion (clang compiler) quiet.
-+ *
-  * Revision 1.25  2010-10-14 13:16:30  joergr
-  * Updated copyright header. Added reference to COPYRIGHT file.
-  *
-Index: dcmtk-3.6.0/dcmimage/include/dcmtk/dcmimage/diyp2pxt.h
-===================================================================
---- dcmtk-3.6.0.orig/dcmimage/include/dcmtk/dcmimage/diyp2pxt.h	2010-10-14 13:16:30.000000000 +0000
-+++ dcmtk-3.6.0/dcmimage/include/dcmtk/dcmimage/diyp2pxt.h	2012-05-25 09:16:23.795876809 +0000
-@@ -1,6 +1,6 @@
- /*
-  *
-- *  Copyright (C) 1998-2010, OFFIS e.V.
-+ *  Copyright (C) 1998-2011, OFFIS e.V.
-  *  All rights reserved.  See COPYRIGHT file for details.
-  *
-  *  This software and supporting documentation were developed by
-@@ -18,8 +18,8 @@
-  *  Purpose: DicomYBRPart422PixelTemplate (Header)
-  *
-  *  Last Update:      $Author: joergr $
-- *  Update Date:      $Date: 2010-10-14 13:16:30 $
-- *  CVS/RCS Revision: $Revision: 1.23 $
-+ *  Update Date:      $Date: 2011-11-17 16:13:14 $
-+ *  CVS/RCS Revision: $Revision: 1.24 $
-  *  Status:           $State: Exp $
-  *
-  *  CVS/RCS Log at end of file
-@@ -91,7 +91,7 @@
-     void convert(const T1 *pixel,
-                  const int bits)
-     {
--        if (Init(pixel))
-+        if (this->Init(pixel))
-         {
-             register T2 *r = this->Data[0];
-             register T2 *g = this->Data[1];
-@@ -147,6 +147,9 @@
-  *
-  * CVS/RCS Log:
-  * $Log: diyp2pxt.h,v $
-+ * Revision 1.24  2011-11-17 16:13:14  joergr
-+ * Minor fixes to keep XCode 4.2 on Mac OS X Lion (clang compiler) quiet.
-+ *
-  * Revision 1.23  2010-10-14 13:16:30  joergr
-  * Updated copyright header. Added reference to COPYRIGHT file.
-  *
-Index: dcmtk-3.6.0/dcmimgle/include/dcmtk/dcmimgle/diflipt.h
-===================================================================
---- dcmtk-3.6.0.orig/dcmimgle/include/dcmtk/dcmimgle/diflipt.h	2010-10-14 13:16:26.000000000 +0000
-+++ dcmtk-3.6.0/dcmimgle/include/dcmtk/dcmimgle/diflipt.h	2012-05-25 09:16:23.795876809 +0000
-@@ -1,6 +1,6 @@
- /*
-  *
-- *  Copyright (C) 1996-2010, OFFIS e.V.
-+ *  Copyright (C) 1996-2011, OFFIS e.V.
-  *  All rights reserved.  See COPYRIGHT file for details.
-  *
-  *  This software and supporting documentation were developed by
-@@ -18,8 +18,8 @@
-  *  Purpose: DicomFlipTemplate (Header)
-  *
-  *  Last Update:      $Author: joergr $
-- *  Update Date:      $Date: 2010-10-14 13:16:26 $
-- *  CVS/RCS Revision: $Revision: 1.23 $
-+ *  Update Date:      $Date: 2011-11-17 16:13:16 $
-+ *  CVS/RCS Revision: $Revision: 1.24 $
-  *  Status:           $State: Exp $
-  *
-  *  CVS/RCS Log at end of file
-@@ -129,7 +129,7 @@
-             else if (vert)
-                 flipVert(src, dest);
-             else
--                copyPixel(src, dest);
-+                this->copyPixel(src, dest);
-         }
-     }
- 
-@@ -345,6 +345,9 @@
-  *
-  * CVS/RCS Log:
-  * $Log: diflipt.h,v $
-+ * Revision 1.24  2011-11-17 16:13:16  joergr
-+ * Minor fixes to keep XCode 4.2 on Mac OS X Lion (clang compiler) quiet.
-+ *
-  * Revision 1.23  2010-10-14 13:16:26  joergr
-  * Updated copyright header. Added reference to COPYRIGHT file.
-  *
-Index: dcmtk-3.6.0/dcmimgle/include/dcmtk/dcmimgle/dimoflt.h
-===================================================================
---- dcmtk-3.6.0.orig/dcmimgle/include/dcmtk/dcmimgle/dimoflt.h	2010-10-14 13:16:26.000000000 +0000
-+++ dcmtk-3.6.0/dcmimgle/include/dcmtk/dcmimgle/dimoflt.h	2012-05-25 09:16:23.795876809 +0000
-@@ -1,6 +1,6 @@
- /*
-  *
-- *  Copyright (C) 1996-2010, OFFIS e.V.
-+ *  Copyright (C) 1996-2011, OFFIS e.V.
-  *  All rights reserved.  See COPYRIGHT file for details.
-  *
-  *  This software and supporting documentation were developed by
-@@ -18,8 +18,8 @@
-  *  Purpose: DicomMonochromeFlipTemplate (Header)
-  *
-  *  Last Update:      $Author: joergr $
-- *  Update Date:      $Date: 2010-10-14 13:16:26 $
-- *  CVS/RCS Revision: $Revision: 1.15 $
-+ *  Update Date:      $Date: 2011-11-17 16:13:16 $
-+ *  CVS/RCS Revision: $Revision: 1.16 $
-  *  Status:           $State: Exp $
-  *
-  *  CVS/RCS Log at end of file
-@@ -106,11 +106,11 @@
-             if (this->Data != NULL)
-             {
-                 if (horz && vert)
--                    flipHorzVert(&pixel, &this->Data);
-+                    this->flipHorzVert(&pixel, &this->Data);
-                 else if (horz)
--                    flipHorz(&pixel, &this->Data);
-+                    this->flipHorz(&pixel, &this->Data);
-                 else if (vert)
--                    flipVert(&pixel, &this->Data);
-+                    this->flipVert(&pixel, &this->Data);
-             }
-         }
-     }
-@@ -124,6 +124,9 @@
-  *
-  * CVS/RCS Log:
-  * $Log: dimoflt.h,v $
-+ * Revision 1.16  2011-11-17 16:13:16  joergr
-+ * Minor fixes to keep XCode 4.2 on Mac OS X Lion (clang compiler) quiet.
-+ *
-  * Revision 1.15  2010-10-14 13:16:26  joergr
-  * Updated copyright header. Added reference to COPYRIGHT file.
-  *
-Index: dcmtk-3.6.0/dcmimgle/include/dcmtk/dcmimgle/dimoipxt.h
-===================================================================
---- dcmtk-3.6.0.orig/dcmimgle/include/dcmtk/dcmimgle/dimoipxt.h	2010-10-14 13:16:26.000000000 +0000
-+++ dcmtk-3.6.0/dcmimgle/include/dcmtk/dcmimgle/dimoipxt.h	2012-05-25 09:16:23.799876809 +0000
-@@ -1,6 +1,6 @@
- /*
-  *
-- *  Copyright (C) 1996-2010, OFFIS e.V.
-+ *  Copyright (C) 1996-2011, OFFIS e.V.
-  *  All rights reserved.  See COPYRIGHT file for details.
-  *
-  *  This software and supporting documentation were developed by
-@@ -18,8 +18,8 @@
-  *  Purpose: DicomMonochromeInputPixelTemplate (Header)
-  *
-  *  Last Update:      $Author: joergr $
-- *  Update Date:      $Date: 2010-10-14 13:16:26 $
-- *  CVS/RCS Revision: $Revision: 1.40 $
-+ *  Update Date:      $Date: 2011-11-17 16:13:16 $
-+ *  CVS/RCS Revision: $Revision: 1.41 $
-  *  Status:           $State: Exp $
-  *
-  *  CVS/RCS Log at end of file
-@@ -76,10 +76,10 @@
-             else if ((this->Modality != NULL) && this->Modality->hasRescaling())
-             {
-                 rescale(pixel, this->Modality->getRescaleSlope(), this->Modality->getRescaleIntercept());
--                determineMinMax(OFstatic_cast(T3, this->Modality->getMinValue()), OFstatic_cast(T3, this->Modality->getMaxValue()));
-+                this->determineMinMax(OFstatic_cast(T3, this->Modality->getMinValue()), OFstatic_cast(T3, this->Modality->getMaxValue()));
-             } else {
-                 rescale(pixel);                     // "copy" or reference pixel data
--                determineMinMax(OFstatic_cast(T3, this->Modality->getMinValue()), OFstatic_cast(T3, this->Modality->getMaxValue()));
-+                this->determineMinMax(OFstatic_cast(T3, this->Modality->getMinValue()), OFstatic_cast(T3, this->Modality->getMaxValue()));
-             }
-         }
-     }
-@@ -280,6 +280,9 @@
-  *
-  * CVS/RCS Log:
-  * $Log: dimoipxt.h,v $
-+ * Revision 1.41  2011-11-17 16:13:16  joergr
-+ * Minor fixes to keep XCode 4.2 on Mac OS X Lion (clang compiler) quiet.
-+ *
-  * Revision 1.40  2010-10-14 13:16:26  joergr
-  * Updated copyright header. Added reference to COPYRIGHT file.
-  *
-Index: dcmtk-3.6.0/dcmimgle/include/dcmtk/dcmimgle/dimorot.h
-===================================================================
---- dcmtk-3.6.0.orig/dcmimgle/include/dcmtk/dcmimgle/dimorot.h	2010-10-14 13:16:26.000000000 +0000
-+++ dcmtk-3.6.0/dcmimgle/include/dcmtk/dcmimgle/dimorot.h	2012-05-25 09:16:23.799876809 +0000
-@@ -1,6 +1,6 @@
- /*
-  *
-- *  Copyright (C) 1996-2010, OFFIS e.V.
-+ *  Copyright (C) 1996-2011, OFFIS e.V.
-  *  All rights reserved.  See COPYRIGHT file for details.
-  *
-  *  This software and supporting documentation were developed by
-@@ -18,8 +18,8 @@
-  *  Purpose: DicomMonochromeRotateTemplate (Header)
-  *
-  *  Last Update:      $Author: joergr $
-- *  Update Date:      $Date: 2010-10-14 13:16:26 $
-- *  CVS/RCS Revision: $Revision: 1.16 $
-+ *  Update Date:      $Date: 2011-11-17 16:13:16 $
-+ *  CVS/RCS Revision: $Revision: 1.17 $
-  *  Status:           $State: Exp $
-  *
-  *  CVS/RCS Log at end of file
-@@ -105,11 +105,11 @@
-             if (this->Data != NULL)
-             {
-                 if (degree == 90)
--                    rotateRight(&pixel, &(this->Data));
-+                    this->rotateRight(&pixel, &(this->Data));
-                 else if (degree == 180)
--                    rotateTopDown(&pixel, &(this->Data));
-+                    this->rotateTopDown(&pixel, &(this->Data));
-                 else if (degree == 270)
--                    rotateLeft(&pixel, &(this->Data));
-+                    this->rotateLeft(&pixel, &(this->Data));
-             }
-         }
-     }
-@@ -123,6 +123,9 @@
-  *
-  * CVS/RCS Log:
-  * $Log: dimorot.h,v $
-+ * Revision 1.17  2011-11-17 16:13:16  joergr
-+ * Minor fixes to keep XCode 4.2 on Mac OS X Lion (clang compiler) quiet.
-+ *
-  * Revision 1.16  2010-10-14 13:16:26  joergr
-  * Updated copyright header. Added reference to COPYRIGHT file.
-  *
-Index: dcmtk-3.6.0/dcmimgle/include/dcmtk/dcmimgle/dimosct.h
-===================================================================
---- dcmtk-3.6.0.orig/dcmimgle/include/dcmtk/dcmimgle/dimosct.h	2010-10-14 13:16:26.000000000 +0000
-+++ dcmtk-3.6.0/dcmimgle/include/dcmtk/dcmimgle/dimosct.h	2012-05-25 09:16:23.799876809 +0000
-@@ -1,6 +1,6 @@
- /*
-  *
-- *  Copyright (C) 1996-2010, OFFIS e.V.
-+ *  Copyright (C) 1996-2011, OFFIS e.V.
-  *  All rights reserved.  See COPYRIGHT file for details.
-  *
-  *  This software and supporting documentation were developed by
-@@ -18,8 +18,8 @@
-  *  Purpose: DicomMonochromeScaleTemplate (Header)
-  *
-  *  Last Update:      $Author: joergr $
-- *  Update Date:      $Date: 2010-10-14 13:16:26 $
-- *  CVS/RCS Revision: $Revision: 1.20 $
-+ *  Update Date:      $Date: 2011-11-17 16:13:16 $
-+ *  CVS/RCS Revision: $Revision: 1.21 $
-  *  Status:           $State: Exp $
-  *
-  *  CVS/RCS Log at end of file
-@@ -124,7 +124,7 @@
-             {
-                 const T value = OFstatic_cast(T, OFstatic_cast(double, DicomImageClass::maxval(bits)) *
-                     OFstatic_cast(double, pvalue) / OFstatic_cast(double, DicomImageClass::maxval(WIDTH_OF_PVALUES)));
--                scaleData(&pixel, &this->Data, interpolate, value);
-+                this->scaleData(&pixel, &this->Data, interpolate, value);
-              }
-         }
-     }
-@@ -138,6 +138,9 @@
-  *
-  * CVS/RCS Log:
-  * $Log: dimosct.h,v $
-+ * Revision 1.21  2011-11-17 16:13:16  joergr
-+ * Minor fixes to keep XCode 4.2 on Mac OS X Lion (clang compiler) quiet.
-+ *
-  * Revision 1.20  2010-10-14 13:16:26  joergr
-  * Updated copyright header. Added reference to COPYRIGHT file.
-  *
-Index: dcmtk-3.6.0/dcmimgle/include/dcmtk/dcmimgle/dirotat.h
-===================================================================
---- dcmtk-3.6.0.orig/dcmimgle/include/dcmtk/dcmimgle/dirotat.h	2010-10-14 13:16:27.000000000 +0000
-+++ dcmtk-3.6.0/dcmimgle/include/dcmtk/dcmimgle/dirotat.h	2012-05-25 09:16:23.799876809 +0000
-@@ -1,6 +1,6 @@
- /*
-  *
-- *  Copyright (C) 1996-2010, OFFIS e.V.
-+ *  Copyright (C) 1996-2011, OFFIS e.V.
-  *  All rights reserved.  See COPYRIGHT file for details.
-  *
-  *  This software and supporting documentation were developed by
-@@ -18,8 +18,8 @@
-  *  Purpose: DicomRotateTemplate (Header)
-  *
-  *  Last Update:      $Author: joergr $
-- *  Update Date:      $Date: 2010-10-14 13:16:27 $
-- *  CVS/RCS Revision: $Revision: 1.21 $
-+ *  Update Date:      $Date: 2011-11-17 16:13:16 $
-+ *  CVS/RCS Revision: $Revision: 1.22 $
-  *  Status:           $State: Exp $
-  *
-  *  CVS/RCS Log at end of file
-@@ -132,7 +132,7 @@
-         else if (degree == 270)
-             rotateLeft(src, dest);
-         else
--            copyPixel(src, dest);
-+            this->copyPixel(src, dest);
-     }
- 
- 
-@@ -358,6 +358,9 @@
-  *
-  * CVS/RCS Log:
-  * $Log: dirotat.h,v $
-+ * Revision 1.22  2011-11-17 16:13:16  joergr
-+ * Minor fixes to keep XCode 4.2 on Mac OS X Lion (clang compiler) quiet.
-+ *
-  * Revision 1.21  2010-10-14 13:16:27  joergr
-  * Updated copyright header. Added reference to COPYRIGHT file.
-  *
-Index: dcmtk-3.6.0/dcmimgle/include/dcmtk/dcmimgle/discalet.h
-===================================================================
---- dcmtk-3.6.0.orig/dcmimgle/include/dcmtk/dcmimgle/discalet.h	2010-10-14 13:16:27.000000000 +0000
-+++ dcmtk-3.6.0/dcmimgle/include/dcmtk/dcmimgle/discalet.h	2012-05-25 09:16:23.799876809 +0000
-@@ -1,6 +1,6 @@
- /*
-  *
-- *  Copyright (C) 1996-2010, OFFIS e.V.
-+ *  Copyright (C) 1996-2011, OFFIS e.V.
-  *  All rights reserved.  See COPYRIGHT file for details.
-  *
-  *  This software and supporting documentation were developed by
-@@ -18,8 +18,8 @@
-  *  Purpose: DicomScaleTemplates (Header)
-  *
-  *  Last Update:      $Author: joergr $
-- *  Update Date:      $Date: 2010-10-14 13:16:27 $
-- *  CVS/RCS Revision: $Revision: 1.35 $
-+ *  Update Date:      $Date: 2011-11-17 16:13:16 $
-+ *  CVS/RCS Revision: $Revision: 1.36 $
-  *  Status:           $State: Exp $
-  *
-  *  CVS/RCS Log at end of file
-@@ -206,12 +206,12 @@
-                 (Left >= OFstatic_cast(signed long, Columns)) || (Top >= OFstatic_cast(signed long, Rows)))
-             {                                                                         // no image to be displayed
-                 DCMIMGLE_DEBUG("clipping area is fully outside the image boundaries");
--                fillPixel(dest, value);                                               // ... fill bitmap
-+                this->fillPixel(dest, value);                                         // ... fill bitmap
-             }
-             else if ((this->Src_X == this->Dest_X) && (this->Src_Y == this->Dest_Y))  // no scaling
-             {
-                 if ((Left == 0) && (Top == 0) && (Columns == this->Src_X) && (Rows == this->Src_Y))
--                    copyPixel(src, dest);                                             // copying
-+                    this->copyPixel(src, dest);                                       // copying
-                 else if ((Left >= 0) && (OFstatic_cast(Uint16, Left + this->Src_X) <= Columns) &&
-                          (Top >= 0) && (OFstatic_cast(Uint16, Top + this->Src_Y) <= Rows))
-                     clipPixel(src, dest);                                             // clipping
-@@ -567,7 +567,7 @@
-         if ((xtemp == NULL) || (xvalue == NULL))
-         {
-             DCMIMGLE_ERROR("can't allocate temporary buffers for interpolation scaling");
--            clearPixel(dest);
-+            this->clearPixel(dest);
-         } else {
-             for (int j = 0; j < this->Planes; ++j)
-             {
-@@ -905,7 +905,7 @@
-         if (pTemp == NULL)
-         {
-             DCMIMGLE_ERROR("can't allocate temporary buffer for interpolation scaling");
--            clearPixel(dest);
-+            this->clearPixel(dest);
-         } else {
- 
-             /*
-@@ -1029,7 +1029,7 @@
-         if (pTemp == NULL)
-         {
-             DCMIMGLE_ERROR("can't allocate temporary buffer for interpolation scaling");
--            clearPixel(dest);
-+            this->clearPixel(dest);
-         } else {
- 
-             /*
-@@ -1190,6 +1190,9 @@
-  *
-  * CVS/RCS Log:
-  * $Log: discalet.h,v $
-+ * Revision 1.36  2011-11-17 16:13:16  joergr
-+ * Minor fixes to keep XCode 4.2 on Mac OS X Lion (clang compiler) quiet.
-+ *
-  * Revision 1.35  2010-10-14 13:16:27  joergr
-  * Updated copyright header. Added reference to COPYRIGHT file.
-  *
-Index: dcmtk-3.6.0/ofstd/include/dcmtk/ofstd/ofoset.h
-===================================================================
---- dcmtk-3.6.0.orig/ofstd/include/dcmtk/ofstd/ofoset.h	2010-10-14 13:15:50.000000000 +0000
-+++ dcmtk-3.6.0/ofstd/include/dcmtk/ofstd/ofoset.h	2012-05-25 09:16:23.799876809 +0000
-@@ -1,6 +1,6 @@
- /*
-  *
-- *  Copyright (C) 2002-2010, OFFIS e.V.
-+ *  Copyright (C) 2002-2011, OFFIS e.V.
-  *  All rights reserved.  See COPYRIGHT file for details.
-  *
-  *  This software and supporting documentation were developed by
-@@ -19,8 +19,8 @@
-  *           of an arbitrary type.
-  *
-  *  Last Update:      $Author: joergr $
-- *  Update Date:      $Date: 2010-10-14 13:15:50 $
-- *  CVS/RCS Revision: $Revision: 1.11 $
-+ *  Update Date:      $Date: 2011-11-17 16:13:18 $
-+ *  CVS/RCS Revision: $Revision: 1.12 $
-  *  Status:           $State: Exp $
-  *
-  *  CVS/RCS Log at end of file
-@@ -146,7 +146,7 @@
-       {
-         // if size equals num, we need more space
-         if( this->size == this->num )
--          Resize( this->size * 2 );
-+          this->Resize( this->size * 2 );
- 
-         // copy item
-         T *newItem = new T( item );
-@@ -189,7 +189,7 @@
-         {
-           // if size equals num, we need more space
-           if( this->size == this->num )
--            Resize( this->size * 2 );
-+            this->Resize( this->size * 2 );
- 
-           // copy item
-           T *newItem = new T( item );
-@@ -508,6 +508,9 @@
- /*
- ** CVS/RCS Log:
- ** $Log: ofoset.h,v $
-+** Revision 1.12  2011-11-17 16:13:18  joergr
-+** Minor fixes to keep XCode 4.2 on Mac OS X Lion (clang compiler) quiet.
-+**
- ** Revision 1.11  2010-10-14 13:15:50  joergr
- ** Updated copyright header. Added reference to COPYRIGHT file.
- **
diff --git a/sci-libs/dcmtk/files/dcmtk-asneeded.patch b/sci-libs/dcmtk/files/dcmtk-asneeded.patch
deleted file mode 100644
index e3434e644..000000000
--- a/sci-libs/dcmtk/files/dcmtk-asneeded.patch
+++ /dev/null
@@ -1,70 +0,0 @@
---- dcmimgle/libsrc/CMakeLists.txt
-+++ dcmimgle/libsrc/CMakeLists.txt
-@@ -1,5 +1,5 @@
- # create library from source files
- ADD_LIBRARY(dcmimgle dcmimage dibaslut diciefn dicielut didislut didispfn didocu digsdfn digsdlut diimage diinpx diluptab dimo1img dimo2img dimoimg dimoimg3 dimoimg4 dimoimg5 dimomod dimoopx dimopx diovdat diovlay diovlimg diovpln diutils)
--
-+TARGET_LINK_LIBRARIES(dcmimgle dcmdata)
- # declare installation files
- INSTALL_TARGETS(${INSTALL_LIBDIR} dcmimgle)
---- dcmpstat/libsrc/CMakeLists.txt
-+++ dcmpstat/libsrc/CMakeLists.txt
-@@ -1,5 +1,5 @@
- # create library from source files
- ADD_LIBRARY(dcmpstat dcmpstat dviface dvpsab dvpsabl dvpsal dvpsall dvpscf dvpscu dvpscul dvpsda dvpsdal dvpsfs dvpsga dvpsgal dvpsgl dvpsgll dvpsgr dvpsgrl dvpshlp dvpsib dvpsibl dvpsmsg dvpsov dvpsovl dvpspl dvpspl2 dvpspll dvpspr dvpsprt dvpsri dvpsril dvpsrs dvpsrsl dvpssp dvpsspl dvpssv dvpssvl dvpstat dvpstx dvpstxl dvpsvl dvpsvll dvpsvw dvpsvwl dvsighdl)
--
-+TARGET_LINK_LIBRARIES(dcmpstat dcmdsig dcmtls)
- # declare installation files
- INSTALL_TARGETS(${INSTALL_LIBDIR} dcmpstat)
---- dcmsign/libsrc/CMakeLists.txt
-+++ dcmsign/libsrc/CMakeLists.txt
-@@ -1,5 +1,5 @@
- # create library from source files
- ADD_LIBRARY(dcmdsig dcsignat siautopr sibrsapr sicert sicertvf sicreapr sidsa simaccon simd5 sinullpr siprivat siripemd sirsa sisha1 sisprof sitypes)
--
-+TARGET_LINK_LIBRARIES(dcmdsig ${OPENSSL_LIBS})
- # declare installation files
- INSTALL_TARGETS(${INSTALL_LIBDIR} dcmdsig)
---- dcmimage/libsrc/CMakeLists.txt
-+++ dcmimage/libsrc/CMakeLists.txt
-@@ -1,5 +1,5 @@
- # create library from source files
- ADD_LIBRARY(dcmimage diargimg dicmyimg dicoimg dicoopx dicopx dihsvimg dilogger dipalimg dipipng dipitiff diqtctab diqtfs diqthash diqthitl diqtpbox diquant diregist dirgbimg diybrimg diyf2img diyp2img)
--
-+TARGET_LINK_LIBRARIES(dcmimage ${LIBTIFF_LIBS} ${LIBPNG_LIBS})
- # declare installation files
- INSTALL_TARGETS(${INSTALL_LIBDIR} dcmimage)
---- dcmdata/libsrc/CMakeLists.txt
-+++ dcmdata/libsrc/CMakeLists.txt
-@@ -1,5 +1,5 @@
- # create library from source files
- ADD_LIBRARY(dcmdata cmdlnarg dcbytstr dcchrstr dccodec dcdatset dcddirif dcdicdir dcdicent dcdict dcdictzz dcdirrec dcelem dcerror dcfilefo dchashdi dcistrma dcistrmb dcistrmf dcistrmz dcitem dclist dcmetinf dcobject dcostrma dcostrmb dcostrmf dcostrmz dcpcache dcpixel dcpixseq dcpxitem dcrleccd dcrlecce dcrlecp dcrledrg dcrleerg dcrlerp dcsequen dcstack dcswap dctag dctagkey dctypes dcuid dcwcache dcvm dcvr dcvrae dcvras dcvrat dcvrcs dcvrda dcvrds dcvrdt dcvrfd dcvrfl dcvris dcvrlo dcvrlt dcvrobow dcvrof dcvrpn dcvrpobw dcvrsh dcvrsl dcvrss dcvrst dcvrtm dcvrui dcvrul dcvrulup dcvrus dcvrut dcxfer dcpath vrscan vrscanl)
--
-+TARGET_LINK_LIBRARIES(dcmdata ${ZLIB_LIBS})
- # declare installation files
- INSTALL_TARGETS(${INSTALL_LIBDIR} dcmdata)
---- dcmsr/libsrc/CMakeLists.txt
-+++ dcmsr/libsrc/CMakeLists.txt
-@@ -1,5 +1,5 @@
- # create library from source files
- ADD_LIBRARY(dcmsr dsrcitem dsrcodtn dsrcodvl dsrcomtn dsrcomvl dsrcontn dsrcsidl dsrdattn dsrdoc dsrdoctn dsrdoctr dsrdtitn dsrimgfr dsrimgtn dsrimgvl dsrnumtn dsrnumvl dsrpnmtn dsrreftn dsrscogr dsrsc3gr dsrscotn dsrsc3tn dsrscovl dsrsc3vl dsrsoprf dsrstrvl dsrtcodt dsrtcosp dsrtcotn dsrtcoto dsrtcovl dsrtextn dsrtimtn dsrtncsr dsrtree dsrtypes dsruidtn dsrwavch dsrwavtn dsrwavvl dsrxmlc dsrxmld dsriodcc dsrbascc dsrenhcc dsrcomcc dsrkeycc dsrmamcc dsrchecc dsrcolcc dsrprocc dsrxrdcc dsrspecc dsrmaccc)
--
-+TARGET_LINK_LIBRARIES(dcmsr ${LIBXML_LIBS})
- # declare installation files
- INSTALL_TARGETS(${INSTALL_LIBDIR} dcmsr)
---- oflog/libsrc/CMakeLists.txt	2014-04-09 15:20:21.160489941 -0700
-+++ oflog/libsrc/CMakeLists.txt	2014-04-09 15:19:31.161173872 -0700
-@@ -9,4 +9,5 @@
- ADD_LIBRARY(oflog oflog apndimpl appender config consap factory fileap filter globinit hierarchy hierlock layout logger logimpl logevent loglevel loglog lloguser ndc ntelogap nullap objreg patlay pointer property rootlog sleep socketap sockbuff socket strhelp syncprims syslogap threads timehelp ${OFLOG_PLATFORM_LIBRARIES})
- 
- # declare installation files
-+TARGET_LINK_LIBRARIES(oflog ${THREAD_LIBS})
- INSTALL_TARGETS(${INSTALL_LIBDIR} oflog)
---- ofstd/libsrc/CMakeLists.txt	2014-04-09 15:21:06.841778722 -0700
-+++ ofstd/libsrc/CMakeLists.txt	2014-04-09 15:21:14.478827209 -0700
-@@ -2,4 +2,5 @@
- ADD_LIBRARY(ofstd ofcmdln ofconapp ofcond ofconfig ofconsol ofcrc32 ofdate ofdatime offname oflist ofstd ofstring ofthread oftime)
- 
- # declare installation files
-+TARGET_LINK_LIBRARIES(ofstd ${THREAD_LIBS})
- INSTALL_TARGETS(${INSTALL_LIBDIR} ofstd)
diff --git a/sci-libs/dcmtk/files/dcmtk_version_number.patch b/sci-libs/dcmtk/files/dcmtk_version_number.patch
deleted file mode 100644
index 130a3bfb8..000000000
--- a/sci-libs/dcmtk/files/dcmtk_version_number.patch
+++ /dev/null
@@ -1,131 +0,0 @@
-From: Joerg Riesmeier <dicom@offis.de>
-Date: Tue, 1 Feb 2011 17:01:14 +0000 (+0000)
-Subject: Made sure that OFFIS_DCMTK_VERSION_NUMBER is really a number and not a
-X-Git-Url: http://git.dcmtk.org/web?p=dcmtk.git;a=commitdiff_plain;h=12c35ca
-
-Made sure that OFFIS_DCMTK_VERSION_NUMBER is really a number and not a
-string.
----
-
-Index: dcmtk-3.6.0/CMake/osconfig.h.in
-===================================================================
---- dcmtk-3.6.0.orig/CMake/osconfig.h.in	2010-11-24 14:53:32.000000000 +0100
-+++ dcmtk-3.6.0/CMake/osconfig.h.in	2011-06-17 14:34:56.000000000 +0200
-@@ -677,7 +677,7 @@
- #define PACKAGE_VERSION_SUFFIX "@DCMTK_PACKAGE_VERSION_SUFFIX@"
- 
- /* Define to the version number of this package. */
--#define PACKAGE_VERSION_NUMBER "@DCMTK_PACKAGE_VERSION_NUMBER@"
-+#define PACKAGE_VERSION_NUMBER @DCMTK_PACKAGE_VERSION_NUMBER@
- 
- /* Define path separator */
- #define PATH_SEPARATOR '@PATH_SEPARATOR@'
-Index: dcmtk-3.6.0/CMakeLists.txt
-===================================================================
---- dcmtk-3.6.0.orig/CMakeLists.txt	2011-01-06 11:48:43.000000000 +0100
-+++ dcmtk-3.6.0/CMakeLists.txt	2011-06-17 14:34:56.000000000 +0200
-@@ -21,7 +21,7 @@
- SET(DCMTK_PACKAGE_DATE "2011-01-06")
- #SET(DCMTK_PACKAGE_TARNAME "dcmtk-3.6.0")
- SET(DCMTK_PACKAGE_VERSION "3.6.0")
--SET(DCMTK_PACKAGE_VERSION_NUMBER "360")
-+SET(DCMTK_PACKAGE_VERSION_NUMBER 360)
- SET(DCMTK_PACKAGE_VERSION_SUFFIX "")
- #SET(DCMTK_PACKAGE_STRING "dcmtk 3.6.0")
- #SET(DCMTK_PACKAGE_BUGREPORT "dicom-bugs@offis.de")
-Index: dcmtk-3.6.0/config/configure
-===================================================================
---- dcmtk-3.6.0.orig/config/configure	2011-01-06 11:48:47.000000000 +0100
-+++ dcmtk-3.6.0/config/configure	2011-06-17 14:34:56.000000000 +0200
-@@ -1774,13 +1774,13 @@
- 
- 
- 
--PACKAGE_VERSION_NUMBER="360"
-+PACKAGE_VERSION_NUMBER=360
- PACKAGE_VERSION_SUFFIX=""
- PACKAGE_DATE="2011-01-06"
- 
- 
- cat >>confdefs.h <<_ACEOF
--#define PACKAGE_VERSION_NUMBER "${PACKAGE_VERSION_NUMBER}"
-+#define PACKAGE_VERSION_NUMBER ${PACKAGE_VERSION_NUMBER}
- _ACEOF
- 
- 
-Index: dcmtk-3.6.0/config/configure.in
-===================================================================
---- dcmtk-3.6.0.orig/config/configure.in	2011-01-06 11:48:47.000000000 +0100
-+++ dcmtk-3.6.0/config/configure.in	2011-06-17 14:34:56.000000000 +0200
-@@ -8,11 +8,11 @@
- dnl Additional Package Information
- dnl -------------------------------------------------------
- 
--PACKAGE_VERSION_NUMBER="360"
-+PACKAGE_VERSION_NUMBER=360
- PACKAGE_VERSION_SUFFIX=""
- PACKAGE_DATE="2011-01-06"
- 
--AC_DEFINE_UNQUOTED(PACKAGE_VERSION_NUMBER,"${PACKAGE_VERSION_NUMBER}",[Define to the version number of this package.])
-+AC_DEFINE_UNQUOTED(PACKAGE_VERSION_NUMBER,${PACKAGE_VERSION_NUMBER},[Define to the version number of this package.])
- AC_DEFINE_UNQUOTED(PACKAGE_VERSION_SUFFIX,"${PACKAGE_VERSION_SUFFIX}",[Define to the version suffix of this package.])
- AC_DEFINE_UNQUOTED(PACKAGE_DATE,"${PACKAGE_DATE}",[Define to the release date of this package.])
- 
-Index: dcmtk-3.6.0/dcmdata/include/dcmtk/dcmdata/dcuid.h
-===================================================================
---- dcmtk-3.6.0.orig/dcmdata/include/dcmtk/dcmdata/dcuid.h	2010-11-05 11:26:10.000000000 +0100
-+++ dcmtk-3.6.0/dcmdata/include/dcmtk/dcmdata/dcuid.h	2011-06-17 14:34:56.000000000 +0200
-@@ -1,6 +1,6 @@
- /*
-  *
-- *  Copyright (C) 1994-2010, OFFIS e.V.
-+ *  Copyright (C) 1994-2011, OFFIS e.V.
-  *  All rights reserved.  See COPYRIGHT file for details.
-  *
-  *  This software and supporting documentation were developed by
-@@ -20,8 +20,8 @@
-  *  routines for finding and creating UIDs.
-  *
-  *  Last Update:      $Author: joergr $
-- *  Update Date:      $Date: 2010-11-05 10:26:10 $
-- *  CVS/RCS Revision: $Revision: 1.89 $
-+ *  Update Date:      $Date: 2011-02-01 17:01:33 $
-+ *  CVS/RCS Revision: $Revision: 1.90 $
-  *  Status:           $State: Exp $
-  *
-  *  CVS/RCS Log at end of file
-@@ -165,16 +165,21 @@
- #error Required compiler definition PACKAGE_VERSION_NUMBER undefined
- #endif
- 
-+// helper macros for version number conversion
-+
-+#define PACKAGE_VERSION_NUMBER_TO_STRING_( x ) #x
-+#define PACKAGE_VERSION_NUMBER_TO_STRING( x ) PACKAGE_VERSION_NUMBER_TO_STRING_( x )
-+
- /* NOTE: Implementation version name VR=SH may not be longer than 16 chars
-  *       The second name is used to identify files written without dcmdata
-  *       (i.e. using the --bit-preserving switch in various tools)
-  */
- 
- /// implementation version name for this version of the toolkit
--#define OFFIS_DTK_IMPLEMENTATION_VERSION_NAME   "OFFIS_DCMTK_" PACKAGE_VERSION_NUMBER
-+#define OFFIS_DTK_IMPLEMENTATION_VERSION_NAME   "OFFIS_DCMTK_" PACKAGE_VERSION_NUMBER_TO_STRING(PACKAGE_VERSION_NUMBER)
- 
- /// implementation version name for this version of the toolkit, used for files received in "bit preserving" mode
--#define OFFIS_DTK_IMPLEMENTATION_VERSION_NAME2  "OFFIS_DCMBP_" PACKAGE_VERSION_NUMBER
-+#define OFFIS_DTK_IMPLEMENTATION_VERSION_NAME2  "OFFIS_DCMBP_" PACKAGE_VERSION_NUMBER_TO_STRING(PACKAGE_VERSION_NUMBER)
- 
- /// release date of current toolkit release
- #ifdef DCMTK_BUILD_DATE
-@@ -704,6 +709,10 @@
- /*
- ** CVS/RCS Log:
- ** $Log: dcuid.h,v $
-+** Revision 1.90  2011-02-01 17:01:33  joergr
-+** Made sure that OFFIS_DCMTK_VERSION_NUMBER is really a number and not a
-+** string.
-+**
- ** Revision 1.89  2010-11-05 10:26:10  joergr
- ** Added new SOP Class UIDs from Supplement 131 and 134 (Implant Templates).
- **
diff --git a/sci-libs/dcmtk/files/doubledes.patch b/sci-libs/dcmtk/files/doubledes.patch
deleted file mode 100644
index 76ff257a1..000000000
--- a/sci-libs/dcmtk/files/doubledes.patch
+++ /dev/null
@@ -1,31 +0,0 @@
-From d229d6fe6650427ca7319e5c86032291a5bfe39d Mon Sep 17 00:00:00 2001
-From: Michael Onken <dicom@offis.de>
-Date: Fri, 26 Jul 2013 22:51:07 +0200
-Subject: [PATCH] Fixed possible doubled destruction of association.
-
----
- CHANGES.361          |    5 +++++
- dcmnet/libsrc/scp.cc |    3 +--
- 2 files changed, 6 insertions(+), 2 deletions(-)
-
-Index: dcmtk-3.6.0/dcmnet/libsrc/scp.cc
-===================================================================
---- dcmtk-3.6.0.orig/dcmnet/libsrc/scp.cc	2010-10-20 10:09:34.000000000 +0200
-+++ dcmtk-3.6.0/dcmnet/libsrc/scp.cc	2013-09-02 11:00:10.455689161 +0200
-@@ -650,7 +650,6 @@
-   {
-     notifyReleaseRequest();
-     ASC_acknowledgeRelease(m_assoc);
--    ASC_dropSCPAssociation(m_assoc);
-   }
-   else if( cond == DUL_PEERABORTEDASSOCIATION )
-   {
-@@ -1416,7 +1415,7 @@
-   if (m_assoc)
-   {
-     notifyAssociationTermination();
--    ASC_dropAssociation( m_assoc );
-+    ASC_dropSCPAssociation( m_assoc );
-     ASC_destroyAssociation( &m_assoc );
-   }
- }
diff --git a/sci-libs/dcmtk/files/fixnull.patch b/sci-libs/dcmtk/files/fixnull.patch
deleted file mode 100644
index 6b6391c5d..000000000
--- a/sci-libs/dcmtk/files/fixnull.patch
+++ /dev/null
@@ -1,36 +0,0 @@
-From 9fc7bd358d1791a14afdd14c81ce9266b7e12b8a Mon Sep 17 00:00:00 2001
-From: Michael Onken <dicom@offis.de>
-Date: Mon, 27 May 2013 14:52:57 +0200
-Subject: [PATCH] Make sure memcpy does not copy to NULL destination. Thanks to Francesco Gigante
- for the report.
-
----
- CHANGES.361              |    6 ++++++
- dcmdata/libsrc/dcelem.cc |    7 ++++---
- 2 files changed, 10 insertions(+), 3 deletions(-)
-
-Index: dcmtk-3.6.0/dcmdata/libsrc/dcelem.cc
-===================================================================
---- dcmtk-3.6.0.orig/dcmdata/libsrc/dcelem.cc	2010-11-05 10:34:14.000000000 +0100
-+++ dcmtk-3.6.0/dcmdata/libsrc/dcelem.cc	2013-05-28 14:11:47.534895101 +0200
-@@ -112,7 +112,8 @@
-         if (pad && fValue)
-             fValue[getLengthField()] = 0;
- 
--        memcpy(fValue, elem.fValue, size_t(getLengthField() + pad));
-+        if (fValue)
-+            memcpy(fValue, elem.fValue, size_t(getLengthField() + pad));
-     }
- 
-     if (elem.fLoadValue)
-@@ -179,8 +180,8 @@
- 
-         if (pad && fValue)
-             fValue[getLengthField()] = 0;
--
--        memcpy(fValue, obj.fValue, size_t(getLengthField()+pad));
-+        if (fValue)
-+            memcpy(fValue, obj.fValue, size_t(getLengthField()+pad));
-     }
- 
-     if (obj.fLoadValue)
diff --git a/sci-libs/dcmtk/files/noleak.patch b/sci-libs/dcmtk/files/noleak.patch
deleted file mode 100644
index ce4a0f759..000000000
--- a/sci-libs/dcmtk/files/noleak.patch
+++ /dev/null
@@ -1,36 +0,0 @@
-From 904d810a9d62ab0e1e0aac857371b936f0b70289 Mon Sep 17 00:00:00 2001
-From: Joerg Riesmeier <dicom@jriesmeier.com>
-Date: Fri, 5 Apr 2013 12:32:52 +0200
-Subject: [PATCH] Fixed two possible memory leaks.
-
-These leaks were found by static code analysis, e.g. using cppcheck.
----
- CHANGES.361            |    4 ++++
- dcmnet/libsrc/assoc.cc |   14 +++++++++++---
- 2 files changed, 15 insertions(+), 3 deletions(-)
-
-Index: dcmtk-3.6.0/dcmnet/libsrc/assoc.cc
-===================================================================
---- dcmtk-3.6.0.orig/dcmnet/libsrc/assoc.cc	2010-12-01 09:26:35.000000000 +0100
-+++ dcmtk-3.6.0/dcmnet/libsrc/assoc.cc	2013-05-28 14:47:09.770871207 +0200
-@@ -1740,10 +1740,18 @@
-     if (cond.bad()) return cond;
- 
-     cond = ASC_setTransportLayerType(params, useSecureLayer);
--    if (cond.bad()) return cond;
-+    if (cond.bad())
-+    {
-+        ASC_destroyAssociationParameters(&params);
-+        return cond;
-+    }
- 
-     *assoc = (T_ASC_Association *) malloc(sizeof(**assoc));
--    if (*assoc == NULL) return EC_MemoryExhausted;
-+    if (*assoc == NULL)
-+    {
-+        ASC_destroyAssociationParameters(&params);
-+        return EC_MemoryExhausted;
-+    }
-     bzero((char*)*assoc, sizeof(**assoc));
- 
-     (*assoc)->params = params;
diff --git a/sci-libs/dcmtk/files/nothrow.patch b/sci-libs/dcmtk/files/nothrow.patch
deleted file mode 100644
index 09e8ad2b0..000000000
--- a/sci-libs/dcmtk/files/nothrow.patch
+++ /dev/null
@@ -1,76 +0,0 @@
-From 873af0c229b92e5ceba62e5a3f78180a18b395d4 Mon Sep 17 00:00:00 2001
-From: Joerg Riesmeier <dicom@jriesmeier.com>
-Date: Fri, 5 Apr 2013 11:40:36 +0200
-Subject: [PATCH] Use non-throwing new and delete operator.
-
-Use a non-throwing new and delete operator for large memory buffers
-(e.g. pixel data) in order to avoid exceptions.
----
- CHANGES.361                               |    7 +++++++
- dcmimgle/include/dcmtk/dcmimgle/diinpxt.h |   26 +++++++++++++++++++++++---
- 2 files changed, 30 insertions(+), 3 deletions(-)
-
-Index: dcmtk-3.6.0/dcmimgle/include/dcmtk/dcmimgle/diinpxt.h
-===================================================================
---- dcmtk-3.6.0.orig/dcmimgle/include/dcmtk/dcmimgle/diinpxt.h	2010-10-14 15:16:26.000000000 +0200
-+++ dcmtk-3.6.0/dcmimgle/include/dcmtk/dcmimgle/diinpxt.h	2013-05-28 14:47:03.782871278 +0200
-@@ -172,7 +172,12 @@
-      */
-     virtual ~DiInputPixelTemplate()
-     {
-+#if defined(HAVE_STD__NOTHROW) && defined(HAVE_NOTHROW_DELETE)
-+        /* use a non-throwing delete (if available) */
-+        operator delete[] (Data, std::nothrow);
-+#else
-         delete[] Data;
-+#endif
-     }
- 
-     /** determine minimum and maximum pixel value
-@@ -382,7 +387,12 @@
- #endif
-             /* allocate temporary buffer, even number of bytes required for getUncompressedFrame() */
-             const Uint32 extraByte = ((sizeof(T1) == 1) && (count_T1 & 1)) ? 1 : 0;
-+#ifdef HAVE_STD__NOTHROW
-+            /* use a non-throwing new here (if available) because the allocated buffer can be huge */
-+            pixel = new (std::nothrow) T1[count_T1 + extraByte];
-+#else
-             pixel = new T1[count_T1 + extraByte];
-+#endif
-             if (pixel != NULL)
-             {
-                 if (uncompressed)
-@@ -444,7 +454,12 @@
- //          # old code: Count = ((lengthBytes * 8) + bitsAllocated - 1) / bitsAllocated;
-             Count = 8 * length_B1 + (8 * length_B2 + bitsAllocated - 1) / bitsAllocated;
-             register unsigned long i;
-+#ifdef HAVE_STD__NOTHROW
-+            /* use a non-throwing new here (if available) because the allocated buffer can be huge */
-+            Data = new (std::nothrow) T2[Count];
-+#else
-             Data = new T2[Count];
-+#endif
-             if (Data != NULL)
-             {
-                 DCMIMGLE_TRACE("Input length: " << lengthBytes << " bytes, Pixel count: " << Count
-@@ -609,13 +624,18 @@
-                 }
-             }
-         } else {
--            // in case of error, reset pixel count variable
-+            /* in case of error, reset pixel count variable */
-             Count = 0;
-         }
-         if (deletePixel)
-         {
--            // delete temporary buffer
-+            /* delete temporary buffer */
-+#if defined(HAVE_STD__NOTHROW) && defined(HAVE_NOTHROW_DELETE)
-+            /* use a non-throwing delete (if available) */
-+            operator delete[] (pixel, std::nothrow);
-+#else
-             delete[] pixel;
-+#endif
-         }
-     }
- 
diff --git a/sci-libs/dcmtk/files/prefs.patch b/sci-libs/dcmtk/files/prefs.patch
deleted file mode 100644
index de9fc9df7..000000000
--- a/sci-libs/dcmtk/files/prefs.patch
+++ /dev/null
@@ -1,26 +0,0 @@
-Author: Jürgen Salk <jsa@debian.org>
-Description: The original maintainer Jürgen Salk applied
- a set of patches to the original code.  The part which fixes
- the path to the perl executable is collected in this patch set.
-
-Index: dcmtk-3.6.0/dcmwlm/perl/prefs.ph
-===================================================================
---- dcmtk-3.6.0.orig/dcmwlm/perl/prefs.ph	2011-01-28 10:10:01.000000000 +0100
-+++ dcmtk-3.6.0/dcmwlm/perl/prefs.ph	2011-01-28 10:10:03.000000000 +0100
-@@ -45,13 +45,13 @@
- # --------------------- WWW Server Configuration ---------------------
- 
- # RELATIVE path to the WWW script directory, as seen by httpd
--$prefs{'cgi_path'}  = '/cgi-bin/worklist';
-+$prefs{'cgi_path'}  = '/cgi-bin/dcmtk_wlm';
- 
- # RELATIVE path to the WWW html directory, as seen by httpd
--$prefs{'html_path'}  = '/worklist';
-+$prefs{'html_path'}  = '/dcmtk_wlm';
- 
- # ABSOLUTE path to the data directory
--$prefs{'data_path'} = '/home/www/wl-data';
-+$prefs{'data_path'} = '/var/lib/dcmtk/wl-data';
- 
- # ------------------ Constants - Please do not change! ------------------
- 
diff --git a/sci-libs/dcmtk/files/regression_stacksequenceisodd.patch b/sci-libs/dcmtk/files/regression_stacksequenceisodd.patch
deleted file mode 100644
index f95cb2ef3..000000000
--- a/sci-libs/dcmtk/files/regression_stacksequenceisodd.patch
+++ /dev/null
@@ -1,98 +0,0 @@
-From: Joerg Riesmeier <dicom@offis.de>
-Date: Tue, 1 Mar 2011 10:04:16 +0000 (+0000)
-Subject: Fixed some private tags copied from Philips MR Achieva conformance statement.
-X-Git-Url: http://git.dcmtk.org/web?p=dcmtk.git;a=commitdiff_plain;h=0d3d794e71a3b9035c154a266834f93383083819;hp=0025bc0f762e96afec42dfff505386b3d591f6f7
-
-Fixed some private tags copied from Philips MR Achieva conformance statement.
-Also added a couple of new private tags from the same conformance statement.
----
-
-Index: dcmtk-3.6.0/dcmdata/data/private.dic
-===================================================================
---- dcmtk-3.6.0.orig/dcmdata/data/private.dic	2010-11-22 11:39:26.000000000 +0100
-+++ dcmtk-3.6.0/dcmdata/data/private.dic	2011-06-17 14:40:20.000000000 +0200
-@@ -35,6 +35,7 @@
- #   - Philips Digital Diagnost 1.3 conformance statement
- #   - Philips Integris H, catheterization laboratory, RIS-interface
- #   - Philips Intera Achieva Conformance Statement
-+#   - Philips MR Achieva Conformance Statement
- #   - Siemens Somatom syngo VA40B conformance statement
- #   - Siemens AXIOM Artis VB30 conformance statement
- #   - SonoWand Invite 2.1.1 conformance statement
-@@ -1159,7 +1160,7 @@
- (2001,"Philips Imaging DD 001",35)	SS	StackSliceNumber	1
- (2001,"Philips Imaging DD 001",36)	CS	StackType	1
- (2001,"Philips Imaging DD 001",3f)	CS	ZoomMode	1
--(2001,"Philips Imaging DD 001",5f)	SQ	StackSequence	1-n
-+(2001,"Philips Imaging DD 001",5f)	SQ	StackSequence	1
- (2001,"Philips Imaging DD 001",60)	SL	NumberOfStacks	1
- (2001,"Philips Imaging DD 001",61)	CS	SeriesTransmitted	1
- (2001,"Philips Imaging DD 001",62)	CS	SeriesCommitted	1
-@@ -1204,7 +1205,7 @@
- (2001,"PHILIPS IMAGING DD 001",35)	SS	StackSliceNumber	1
- (2001,"PHILIPS IMAGING DD 001",36)	CS	StackType	1
- (2001,"PHILIPS IMAGING DD 001",3f)	CS	ZoomMode	1
--(2001,"PHILIPS IMAGING DD 001",5f)	SQ	StackSequence	1-n
-+(2001,"PHILIPS IMAGING DD 001",5f)	SQ	StackSequence	1
- (2001,"PHILIPS IMAGING DD 001",60)	SL	NumberOfStacks	1
- (2001,"PHILIPS IMAGING DD 001",61)	CS	SeriesTransmitted	1
- (2001,"PHILIPS IMAGING DD 001",62)	CS	SeriesCommitted	1
-@@ -1221,12 +1222,6 @@
- (2005,"Philips MR Imaging DD 001",1f)	SH	MPRProtocol	1
- (2005,"Philips MR Imaging DD 001",20)	SL	NumberOfChemicalShifts	1
- (2005,"Philips MR Imaging DD 001",2d)	SS	NumberOfStackSlices	1
--(2005,"Philips MR Imaging DD 001",32)	FL	StackRadialAngle	1
--(2005,"Philips MR Imaging DD 001",33)	CS	StackRadialAxis	1
--(2005,"Philips MR Imaging DD 001",35)	SS	StackSliceNumber	1
--(2005,"Philips MR Imaging DD 001",36)	CS	StackType	1
--(2005,"Philips MR Imaging DD 001",a1)	CS	SyncraScanType	1
--(2005,"Philips MR Imaging DD 001",5f)	SQ	StackSequence	1
- (2005,"Philips MR Imaging DD 001",83)	SQ	Unknown	1
- 
- (2005,"Philips MR Imaging DD 005",02)	SQ	Unknown	1
-@@ -1240,12 +1235,6 @@
- (2005,"PHILIPS MR IMAGING DD 001",1f)	SH	MPRProtocol	1
- (2005,"PHILIPS MR IMAGING DD 001",20)	SL	NumberOfChemicalShifts	1
- (2005,"PHILIPS MR IMAGING DD 001",2d)	SS	NumberOfStackSlices	1
--(2005,"PHILIPS MR IMAGING DD 001",32)	FL	StackRadialAngle	1
--(2005,"PHILIPS MR IMAGING DD 001",33)	CS	StackRadialAxis	1
--(2005,"PHILIPS MR IMAGING DD 001",35)	SS	StackSliceNumber	1
--(2005,"PHILIPS MR IMAGING DD 001",36)	CS	StackType	1
--(2005,"PHILIPS MR IMAGING DD 001",a1)	CS	SyncraScanType	1
--(2005,"PHILIPS MR IMAGING DD 001",5f)	SQ	StackSequence	1
- (2005,"PHILIPS MR IMAGING DD 001",83)	SQ	Unknown	1
- 
- (0019,"PHILIPS MR R5.5/PART",1000)	DS	FieldOfView	1
-Index: dcmtk-3.6.0/dcmdata/libsrc/dcdictzz.cc
-===================================================================
---- dcmtk-3.6.0.orig/dcmdata/libsrc/dcdictzz.cc	2010-11-22 11:48:17.000000000 +0100
-+++ dcmtk-3.6.0/dcmdata/libsrc/dcdictzz.cc	2011-06-17 14:41:07.000000000 +0200
-@@ -20753,11 +20817,11 @@
-       DcmDictRange_Unspecified, DcmDictRange_Unspecified,
-       "PHILIPS IMAGING DD 001" }
-   , { 0x2001, 0x005f, 0x2001, 0x005f,
--      EVR_SQ, "StackSequence", 1, -1, "DICOM",
-+      EVR_SQ, "StackSequence", 1, 1, "DICOM",
-       DcmDictRange_Unspecified, DcmDictRange_Unspecified,
-       "Philips Imaging DD 001" }
-   , { 0x2001, 0x005f, 0x2001, 0x005f,
--      EVR_SQ, "StackSequence", 1, -1, "DICOM",
-+      EVR_SQ, "StackSequence", 1, 1, "DICOM",
-       DcmDictRange_Unspecified, DcmDictRange_Unspecified,
-       "PHILIPS IMAGING DD 001" }
-   , { 0x2001, 0x0060, 0x2001, 0x0060,
-@@ -20884,14 +20996,6 @@
-       EVR_CS, "StackType", 1, 1, "DICOM",
-       DcmDictRange_Unspecified, DcmDictRange_Unspecified,
-       "PHILIPS MR IMAGING DD 001" }
--  , { 0x2005, 0x005f, 0x2005, 0x005f,
--      EVR_SQ, "StackSequence", 1, 1, "DICOM",
--      DcmDictRange_Unspecified, DcmDictRange_Unspecified,
--      "Philips MR Imaging DD 001" }
--  , { 0x2005, 0x005f, 0x2005, 0x005f,
--      EVR_SQ, "StackSequence", 1, 1, "DICOM",
--      DcmDictRange_Unspecified, DcmDictRange_Unspecified,
--      "PHILIPS MR IMAGING DD 001" }
-   , { 0x2005, 0x0083, 0x2005, 0x0083,
-       EVR_SQ, "Unknown", 1, 1, "DICOM",
-       DcmDictRange_Unspecified, DcmDictRange_Unspecified,
diff --git a/sci-libs/dcmtk/files/use_correct_number_of_TS.patch b/sci-libs/dcmtk/files/use_correct_number_of_TS.patch
deleted file mode 100644
index efb686ea2..000000000
--- a/sci-libs/dcmtk/files/use_correct_number_of_TS.patch
+++ /dev/null
@@ -1,19 +0,0 @@
-Description: Fixed crash if less than four transfer syntaxes are enabled.
- This fixes debian bug #703716.
- Affects: dcmqrdb/libsrc/dcmqrsrv.cc
-Author: Uli Schlachter <Uli.Schlachter@Informatik.Uni-Oldenburg.DE>
-Bug-Debian: http://bugs.debian.org/703716
-
-Index: dcmtk-3.6.0/dcmqrdb/libsrc/dcmqrsrv.cc
-===================================================================
---- dcmtk-3.6.0.orig/dcmqrdb/libsrc/dcmqrsrv.cc	2010-10-14 15:14:36.000000000 +0200
-+++ dcmtk-3.6.0/dcmqrdb/libsrc/dcmqrsrv.cc	2013-05-15 09:39:13.327725435 +0200
-@@ -786,7 +786,7 @@
-       cond = ASC_acceptContextsWithPreferredTransferSyntaxes(
-         assoc->params,
-         dcmAllStorageSOPClassUIDs, numberOfAllDcmStorageSOPClassUIDs,
--        (const char**)transferSyntaxes, DIM_OF(transferSyntaxes));
-+        (const char**)transferSyntaxes, numTransferSyntaxes);
-       if (cond.bad()) {
-         DCMQRDB_ERROR("Cannot accept presentation contexts: " << DimseCondition::dump(temp_str, cond));
-       }
diff --git a/sci-libs/dcmtk/metadata.xml b/sci-libs/dcmtk/metadata.xml
deleted file mode 100644
index 0d60702ee..000000000
--- a/sci-libs/dcmtk/metadata.xml
+++ /dev/null
@@ -1,22 +0,0 @@
-<?xml version="1.0" encoding="UTF-8"?>
-<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
-<pkgmetadata>
-	<maintainer type="project">
-		<email>sci@gentoo.org</email>
-		<name>Gentoo Science Project</name>
-	</maintainer>
-	<longdescription lang="en">
-DCMTK is a collection of libraries and applications implementing large
-parts the DICOM standard. It includes software for examining,
-constructing and converting DICOM image files, handling offline media,
-sending and receiving images over a network connection, as well as
-demonstrative image storage and worklist servers.
-</longdescription>
-	<longdescription lang="fr">
-DCMTK est un ensemble de bibliothèques et d'application implémentant
-une grande partie du standard DICOM. Cela comprend des logiciels de
-visualisation et de conversion des fichier image, de manipulation de
-médias locaux, de réception et d'envoi d'images à travers un réseau
-ainsi qu'un serveur d'images et de worklist de demonstration.
-</longdescription>
-</pkgmetadata>
diff --git a/sci-libs/dealii/Manifest b/sci-libs/dealii/Manifest
deleted file mode 100644
index 7a4bdddc4..000000000
--- a/sci-libs/dealii/Manifest
+++ /dev/null
@@ -1,4 +0,0 @@
-DIST dealii-8.5.0-offline_documentation.tar.gz 158982121 SHA256 e003e2d863992855b977fbb6c4a050ee9e32b5cf95fd5dbaa04e51e64967aa85 SHA512 ccf5de81ab23f698d9d8331286524328fa8934ef36c251b9c5c999c9532114b550e4ab7899a02925a6b41fc7b4f9554c3796a62c0f4397e1cbe6abbf898fdab8 WHIRLPOOL 6044e9aa48731ce0e9ea3eef3c06d9f8b2a10dd0ab6a89c092e9995503e65aa9835e7a051019b0f77f1878433355dbe36c8a4009d7dda8b178edd50d7cb2aa66
-DIST dealii-8.5.0.tar.gz 14919546 BLAKE2B 686ff5d66ce20d2da8a37e44bdca04a249881da8ab09b1fbd1e6fb0496b53e14b05ce576dcf3539b30443cec680e89c5bae3f3442417c66af726709de39ccfa3 SHA512 58a8cb18aa166a46e25c03335d0b65515452080858593fe35b93623e45cd340fbc7bce1059388c055736c2f5c154c4b68df1620cf8ad9ff6b07644541b60accc
-DIST dealii-9.0.1-offline_documentation.tar.gz 171325206 BLAKE2B 8e912b4b44a9fe6a11677cbf48898cd8f2673669e58aacfed639b0dceb375f9e5d63fee13a399532d014ea5186af598c10dcb8f9a7ed4578c67ff8d18b38856a SHA512 d300c317003db4b4a201dfe89166fb9e019c57e68799d9b475d8856571e86c38dadda163030102220aed4c267e1cf020928456e82e8f6819a92cd756f4c90aad
-DIST dealii-9.0.1.tar.gz 17637370 BLAKE2B 2b7010e3c76f7e14da63d13f77ce35edb107f2aed24616c883858be72e2f1bb5f2dbb800f168d22fa8f68e8fd80c354a618d62bd6f1597646d571663e50987b1 SHA512 cb01083ac3870728c8ffe5e2a542219e24f4611009ede819b6ff8c0d6fc92de2de052f39d5e5cbc3a36159763db9b3f5b4652f300d105108b046b327c447ee26
diff --git a/sci-libs/dealii/dealii-8.5.0.ebuild b/sci-libs/dealii/dealii-8.5.0.ebuild
deleted file mode 100644
index 50b6e6d7e..000000000
--- a/sci-libs/dealii/dealii-8.5.0.ebuild
+++ /dev/null
@@ -1,128 +0,0 @@
-# Copyright 1999-2017 Gentoo Foundation
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=6
-
-inherit cmake-utils eutils multilib
-
-# deal.II uses its own FindLAPACK.cmake file that calls into the system
-# FindLAPACK.cmake module and does additional internal setup. Do not remove
-# any of these modules:
-CMAKE_REMOVE_MODULES_LIST=""
-
-DESCRIPTION="Solving partial differential equations with the finite element method"
-HOMEPAGE="http://www.dealii.org/"
-
-if [[ ${PV} = *9999* ]]; then
-	inherit git-r3
-	EGIT_REPO_URI="git://github.com/dealii/dealii.git"
-	SRC_URI=""
-	KEYWORDS=""
-else
-	MY_PV="${PV//0_rc/rc}"
-	MY_P="${PN}-${MY_PV}"
-	SRC_URI="https://github.com/dealii/dealii/archive/v${MY_PV}.tar.gz -> ${P}.tar.gz
-		doc? (
-			https://github.com/${PN}/${PN}/releases/download/v${MY_PV}/${MY_P}-offline_documentation.tar.gz
-			-> ${P}-offline_documentation.tar.gz
-			)"
-	KEYWORDS="~amd64 ~x86 ~amd64-linux ~x86-linux"
-	S="${WORKDIR}/${PN}-${MY_PV}"
-fi
-
-LICENSE="LGPL-2.1+"
-SLOT="0"
-IUSE="
-	arpack cpu_flags_x86_avx cpu_flags_x86_sse2 c++11 +debug doc +examples
-	+gsl hdf5 +lapack metis mpi muparser opencascade netcdf p4est petsc
-	slepc +sparse static-libs +tbb trilinos
-"
-
-# TODO: add slepc use flag once slepc is packaged for gentoo-science
-REQUIRED_USE="
-	p4est? ( mpi )
-	slepc? ( petsc )
-	trilinos? ( mpi )"
-
-RDEPEND="dev-libs/boost
-	app-arch/bzip2
-	sys-libs/zlib
-	arpack? ( sci-libs/arpack[mpi=] )
-	gsl? ( sci-libs/gsl )
-	hdf5? ( sci-libs/hdf5[mpi=] )
-	lapack? ( virtual/lapack )
-	metis? ( >=sci-libs/parmetis-4 )
-	mpi? ( virtual/mpi )
-	muparser? ( dev-cpp/muParser )
-	netcdf? ( sci-libs/netcdf-cxx:0 )
-	opencascade? ( sci-libs/opencascade:* )
-	p4est? ( sci-libs/p4est[mpi] )
-	petsc? ( sci-mathematics/petsc[mpi=] )
-	slepc? ( sci-mathematics/slepc[mpi=] )
-	sparse? ( sci-libs/umfpack )
-	tbb? ( dev-cpp/tbb )
-	trilinos? ( sci-libs/trilinos )"
-
-DEPEND="${RDEPEND}
-	virtual/pkgconfig
-	doc? ( app-doc/doxygen[dot] dev-lang/perl )"
-
-src_configure() {
-	# deal.II needs a custom build type:
-	local CMAKE_BUILD_TYPE=$(usex debug DebugRelease Release)
-
-	local mycmakeargs=(
-		-DCMAKE_INSTALL_RPATH_USE_LINK_PATH=OFF
-		-DDEAL_II_ALLOW_AUTODETECTION=OFF
-		-DDEAL_II_ALLOW_BUNDLED=OFF
-		-DDEAL_II_ALLOW_PLATFORM_INTROSPECTION=OFF
-		-DDEAL_II_COMPILE_EXAMPLES=OFF
-		-DDEAL_II_DOCHTML_RELDIR="share/doc/${P}/html"
-		-DDEAL_II_DOCREADME_RELDIR="share/doc/${P}"
-		-DDEAL_II_EXAMPLES_RELDIR="share/doc/${P}/examples"
-		-DDEAL_II_LIBRARY_RELDIR="$(get_libdir)"
-		-DDEAL_II_SHARE_RELDIR="share/${PN}"
-		-DDEAL_II_WITH_BZIP2=ON
-		-DDEAL_II_WITH_ZLIB=ON
-		-DDEAL_II_WITH_ARPACK="$(usex arpack)"
-		-DDEAL_II_WITH_CXX11="$(usex c++11)"
-		-DDEAL_II_HAVE_AVX="$(usex cpu_flags_x86_avx)"
-		-DDEAL_II_HAVE_SSE2="$(usex cpu_flags_x86_sse2)"
-		-DDEAL_II_COMPONENT_DOCUMENTATION="$(usex doc)"
-		-DDEAL_II_COMPONENT_EXAMPLES="$(usex examples)"
-		-DDEAL_II_WITH_GSL="$(usex gsl)"
-		-DDEAL_II_WITH_HDF5="$(usex hdf5)"
-		-DDEAL_II_WITH_LAPACK="$(usex lapack)"
-		-DDEAL_II_WITH_METIS="$(usex metis)"
-		-DDEAL_II_WITH_MPI="$(usex mpi)"
-		-DDEAL_II_WITH_MUPARSER="$(usex muparser)"
-		-DDEAL_II_WITH_NETCDF="$(usex netcdf)"
-		-DOPENCASCADE_DIR="${CASROOT}"
-		-DDEAL_II_WITH_OPENCASCADE="$(usex opencascade)"
-		-DDEAL_II_WITH_P4EST="$(usex p4est)"
-		-DDEAL_II_WITH_PETSC="$(usex petsc)"
-		-DDEAL_II_WITH_SLEPC="$(usex slepc)"
-		-DDEAL_II_WITH_UMFPACK="$(usex sparse)"
-		-DBUILD_SHARED_LIBS="$(usex !static-libs)"
-		-DDEAL_II_PREFER_STATIC_LIBS="$(usex static-libs)"
-		-DDEAL_II_WITH_THREADS="$(usex tbb)"
-		-DDEAL_II_WITH_TRILINOS="$(usex trilinos)"
-	)
-	cmake-utils_src_configure
-}
-
-src_install() {
-	if use doc && [[ ${PV} != *9999* ]]; then
-		# copy missing images to the build directory:
-		cp -r "${WORKDIR}"/doc/doxygen/deal.II/images \
-			"${BUILD_DIR}"/doc/doxygen/deal.II || die
-		# replace links:
-		sed -i \
-			's#"http://www.dealii.org/images/steps/developer/\(step-.*\)"#"images/\1"#g' \
-			"${BUILD_DIR}"/doc/doxygen/deal.II/step_*.html || die "sed failed"
-	fi
-	cmake-utils_src_install
-
-	# decompress the installed example sources:
-	use examples && docompress -x /usr/share/doc/${PF}/examples
-}
diff --git a/sci-libs/dealii/dealii-9.0.1.ebuild b/sci-libs/dealii/dealii-9.0.1.ebuild
deleted file mode 100644
index e95ceab6e..000000000
--- a/sci-libs/dealii/dealii-9.0.1.ebuild
+++ /dev/null
@@ -1,143 +0,0 @@
-# Copyright 1999-2018 Gentoo Authors
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=6
-
-inherit cmake-utils eutils multilib
-
-# deal.II uses its own FindLAPACK.cmake file that calls into the system
-# FindLAPACK.cmake module and does additional internal setup. Do not remove
-# any of these modules:
-CMAKE_REMOVE_MODULES_LIST=""
-
-DESCRIPTION="Solving partial differential equations with the finite element method"
-HOMEPAGE="http://www.dealii.org/"
-
-if [[ ${PV} = *9999* ]]; then
-	inherit git-r3
-	EGIT_REPO_URI="https://github.com/dealii/dealii.git"
-	SRC_URI=""
-	KEYWORDS=""
-else
-	MY_PV="${PV//0_rc/rc}"
-	MY_P="${PN}-${MY_PV}"
-	SRC_URI="https://github.com/${PN}/${PN}/releases/download/v${MY_PV}/${MY_P}.tar.gz
-		doc? (
-			https://github.com/${PN}/${PN}/releases/download/v${MY_PV}/${MY_P}-offline_documentation.tar.gz
-			-> ${P}-offline_documentation.tar.gz
-			)"
-	KEYWORDS="~amd64 ~x86 ~amd64-linux ~x86-linux"
-	S="${WORKDIR}/${PN}-${MY_PV}"
-fi
-
-LICENSE="LGPL-2.1+"
-SLOT="0"
-IUSE="
-	adolc assimp arpack cpu_flags_x86_avx cpu_flags_x86_sse2 cuda +debug
-	doc +examples gmsh +gsl hdf5 +lapack metis mpi muparser nanoflann
-	opencascade netcdf p4est petsc scalapack slepc +sparse static-libs
-	sundials +tbb trilinos
-"
-
-# TODO: add slepc use flag once slepc is packaged for gentoo-science
-REQUIRED_USE="
-	p4est? ( mpi )
-	slepc? ( petsc )
-	trilinos? ( mpi )"
-
-RDEPEND="dev-libs/boost
-	app-arch/bzip2
-	sys-libs/zlib
-	adolc? ( sci-libs/adolc )
-	arpack? ( sci-libs/arpack[mpi=] )
-	assimp? ( media-libs/assimp )
-	cuda? ( dev-util/nvidia-cuda-sdk )
-	gmsh? ( sci-libs/gmsh )
-	gsl? ( sci-libs/gsl )
-	hdf5? ( sci-libs/hdf5[mpi=] )
-	lapack? ( virtual/lapack )
-	metis? ( >=sci-libs/parmetis-4 )
-	mpi? ( virtual/mpi )
-	muparser? ( dev-cpp/muParser )
-	nanoflann? ( sci-libs/nanoflann )
-	netcdf? ( sci-libs/netcdf-cxx:0 )
-	opencascade? ( sci-libs/opencascade:* )
-	p4est? ( sci-libs/p4est[mpi] )
-	petsc? ( sci-mathematics/petsc[mpi=] )
-	scalapack? ( sci-libs/scalapack )
-	slepc? ( sci-mathematics/slepc[mpi=] )
-	sparse? ( sci-libs/umfpack )
-	sundials? ( sci-libs/sundials )
-	tbb? ( dev-cpp/tbb )
-	trilinos? ( sci-libs/trilinos )"
-
-DEPEND="${RDEPEND}
-	virtual/pkgconfig
-	doc? ( app-doc/doxygen[dot] dev-lang/perl )"
-
-src_configure() {
-	# deal.II needs a custom build type:
-	local CMAKE_BUILD_TYPE=$(usex debug DebugRelease Release)
-
-	local mycmakeargs=(
-		-DDEAL_II_PACKAGE_VERSION=9999
-		-DCMAKE_INSTALL_RPATH_USE_LINK_PATH=OFF
-		-DDEAL_II_ALLOW_AUTODETECTION=OFF
-		-DDEAL_II_ALLOW_BUNDLED=OFF
-		-DDEAL_II_ALLOW_PLATFORM_INTROSPECTION=OFF
-		-DDEAL_II_COMPILE_EXAMPLES=OFF
-		-DDEAL_II_DOCHTML_RELDIR="share/doc/${P}/html"
-		-DDEAL_II_DOCREADME_RELDIR="share/doc/${P}"
-		-DDEAL_II_COMPILE_EXAMPLES=OFF
-		-DDEAL_II_EXAMPLES_RELDIR="share/doc/${P}/examples"
-		-DDEAL_II_LIBRARY_RELDIR="$(get_libdir)"
-		-DDEAL_II_SHARE_RELDIR="share/${PN}"
-		-DDEAL_II_WITH_ZLIB=ON
-		-DDEAL_II_WITH_ADOLC="$(usex adolc)"
-		-DDEAL_II_WITH_ASSIMP="$(usex assimp)"
-		-DDEAL_II_WITH_ARPACK="$(usex arpack)"
-		-DDEAL_II_HAVE_AVX="$(usex cpu_flags_x86_avx)"
-		-DDEAL_II_WITH_CUDA="$(usex cuda)"
-		-DDEAL_II_HAVE_SSE2="$(usex cpu_flags_x86_sse2)"
-		-DDEAL_II_COMPONENT_DOCUMENTATION="$(usex doc)"
-		-DDEAL_II_COMPONENT_EXAMPLES="$(usex examples)"
-		-DDEAL_II_WITH_GMSH="$(usex gmsh)"
-		-DDEAL_II_WITH_GSL="$(usex gsl)"
-		-DDEAL_II_WITH_HDF5="$(usex hdf5)"
-		-DDEAL_II_WITH_LAPACK="$(usex lapack)"
-		-DDEAL_II_WITH_METIS="$(usex metis)"
-		-DDEAL_II_WITH_MPI="$(usex mpi)"
-		-DDEAL_II_WITH_MUPARSER="$(usex muparser)"
-		-DDEAL_II_WITH_NANOFLANN="$(usex nanoflann)"
-		-DDEAL_II_WITH_NETCDF="$(usex netcdf)"
-		-DOPENCASCADE_DIR="${CASROOT}"
-		-DDEAL_II_WITH_OPENCASCADE="$(usex opencascade)"
-		-DDEAL_II_WITH_P4EST="$(usex p4est)"
-		-DDEAL_II_WITH_PETSC="$(usex petsc)"
-		-DDEAL_II_WITH_SCALAPACK="$(usex scalapack)"
-		-DDEAL_II_WITH_SLEPC="$(usex slepc)"
-		-DDEAL_II_WITH_SUNDIALS="$(usex sundials)"
-		-DDEAL_II_WITH_UMFPACK="$(usex sparse)"
-		-DBUILD_SHARED_LIBS="$(usex !static-libs)"
-		-DDEAL_II_PREFER_STATIC_LIBS="$(usex static-libs)"
-		-DDEAL_II_WITH_THREADS="$(usex tbb)"
-		-DDEAL_II_WITH_TRILINOS="$(usex trilinos)"
-	)
-	cmake-utils_src_configure
-}
-
-src_install() {
-	if use doc && [[ ${PV} != *9999* ]]; then
-		# copy missing images to the build directory:
-		cp -r "${WORKDIR}"/doc/doxygen/deal.II/images \
-			"${BUILD_DIR}"/doc/doxygen/deal.II || die
-		# replace links:
-		sed -i \
-			's#"http://www.dealii.org/images/steps/developer/\(step-.*\)"#"images/\1"#g' \
-			"${BUILD_DIR}"/doc/doxygen/deal.II/step_*.html || die "sed failed"
-	fi
-	cmake-utils_src_install
-
-	# decompress the installed example sources:
-	use examples && docompress -x /usr/share/doc/${PF}/examples
-}
diff --git a/sci-libs/dealii/dealii-9999.ebuild b/sci-libs/dealii/dealii-9999.ebuild
deleted file mode 100644
index 06c63c906..000000000
--- a/sci-libs/dealii/dealii-9999.ebuild
+++ /dev/null
@@ -1,143 +0,0 @@
-# Copyright 1999-2018 Gentoo Foundation
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=6
-
-inherit cmake-utils eutils multilib
-
-# deal.II uses its own FindLAPACK.cmake file that calls into the system
-# FindLAPACK.cmake module and does additional internal setup. Do not remove
-# any of these modules:
-CMAKE_REMOVE_MODULES_LIST=""
-
-DESCRIPTION="Solving partial differential equations with the finite element method"
-HOMEPAGE="http://www.dealii.org/"
-
-if [[ ${PV} = *9999* ]]; then
-	inherit git-r3
-	EGIT_REPO_URI="https://github.com/dealii/dealii.git"
-	SRC_URI=""
-	KEYWORDS=""
-else
-	MY_PV="${PV//0_rc/rc}"
-	MY_P="${PN}-${MY_PV}"
-	SRC_URI="https://github.com/dealii/dealii/archive/v${MY_PV}.tar.gz -> ${P}.tar.gz
-		doc? (
-			https://github.com/${PN}/${PN}/releases/download/v${MY_PV}/${MY_P}-offline_documentation.tar.gz
-			-> ${P}-offline_documentation.tar.gz
-			)"
-	KEYWORDS="~amd64 ~x86 ~amd64-linux ~x86-linux"
-	S="${WORKDIR}/${PN}-${MY_PV}"
-fi
-
-LICENSE="LGPL-2.1+"
-SLOT="0"
-IUSE="
-	adolc assimp arpack cpu_flags_x86_avx cpu_flags_x86_sse2 cuda +debug
-	doc +examples gmsh +gsl hdf5 +lapack metis mpi muparser nanoflann
-	opencascade netcdf p4est petsc scalapack slepc +sparse static-libs
-	sundials +tbb trilinos
-"
-
-# TODO: add slepc use flag once slepc is packaged for gentoo-science
-REQUIRED_USE="
-	p4est? ( mpi )
-	slepc? ( petsc )
-	trilinos? ( mpi )"
-
-RDEPEND="dev-libs/boost
-	app-arch/bzip2
-	sys-libs/zlib
-	adolc? ( sci-libs/adolc )
-	arpack? ( sci-libs/arpack[mpi=] )
-	assimp? ( media-libs/assimp )
-	cuda? ( dev-util/nvidia-cuda-sdk )
-	gmsh? ( sci-libs/gmsh )
-	gsl? ( sci-libs/gsl )
-	hdf5? ( sci-libs/hdf5[mpi=] )
-	lapack? ( virtual/lapack )
-	metis? ( >=sci-libs/parmetis-4 )
-	mpi? ( virtual/mpi )
-	muparser? ( dev-cpp/muParser )
-	nanoflann? ( sci-libs/nanoflann )
-	netcdf? ( sci-libs/netcdf-cxx:0 )
-	opencascade? ( sci-libs/opencascade:* )
-	p4est? ( sci-libs/p4est[mpi] )
-	petsc? ( sci-mathematics/petsc[mpi=] )
-	scalapack? ( sci-libs/scalapack )
-	slepc? ( sci-mathematics/slepc[mpi=] )
-	sparse? ( sci-libs/umfpack )
-	sundials? ( sci-libs/sundials )
-	tbb? ( dev-cpp/tbb )
-	trilinos? ( sci-libs/trilinos )"
-
-DEPEND="${RDEPEND}
-	virtual/pkgconfig
-	doc? ( app-doc/doxygen[dot] dev-lang/perl )"
-
-src_configure() {
-	# deal.II needs a custom build type:
-	local CMAKE_BUILD_TYPE=$(usex debug DebugRelease Release)
-
-	local mycmakeargs=(
-		-DDEAL_II_PACKAGE_VERSION=9999
-		-DCMAKE_INSTALL_RPATH_USE_LINK_PATH=OFF
-		-DDEAL_II_ALLOW_AUTODETECTION=OFF
-		-DDEAL_II_ALLOW_BUNDLED=OFF
-		-DDEAL_II_ALLOW_PLATFORM_INTROSPECTION=OFF
-		-DDEAL_II_COMPILE_EXAMPLES=OFF
-		-DDEAL_II_DOCHTML_RELDIR="share/doc/${P}/html"
-		-DDEAL_II_DOCREADME_RELDIR="share/doc/${P}"
-		-DDEAL_II_COMPILE_EXAMPLES=OFF
-		-DDEAL_II_EXAMPLES_RELDIR="share/doc/${P}/examples"
-		-DDEAL_II_LIBRARY_RELDIR="$(get_libdir)"
-		-DDEAL_II_SHARE_RELDIR="share/${PN}"
-		-DDEAL_II_WITH_ZLIB=ON
-		-DDEAL_II_WITH_ADOLC="$(usex adolc)"
-		-DDEAL_II_WITH_ASSIMP="$(usex assimp)"
-		-DDEAL_II_WITH_ARPACK="$(usex arpack)"
-		-DDEAL_II_HAVE_AVX="$(usex cpu_flags_x86_avx)"
-		-DDEAL_II_WITH_CUDA="$(usex cuda)"
-		-DDEAL_II_HAVE_SSE2="$(usex cpu_flags_x86_sse2)"
-		-DDEAL_II_COMPONENT_DOCUMENTATION="$(usex doc)"
-		-DDEAL_II_COMPONENT_EXAMPLES="$(usex examples)"
-		-DDEAL_II_WITH_GMSH="$(usex gmsh)"
-		-DDEAL_II_WITH_GSL="$(usex gsl)"
-		-DDEAL_II_WITH_HDF5="$(usex hdf5)"
-		-DDEAL_II_WITH_LAPACK="$(usex lapack)"
-		-DDEAL_II_WITH_METIS="$(usex metis)"
-		-DDEAL_II_WITH_MPI="$(usex mpi)"
-		-DDEAL_II_WITH_MUPARSER="$(usex muparser)"
-		-DDEAL_II_WITH_NANOFLANN="$(usex nanoflann)"
-		-DDEAL_II_WITH_NETCDF="$(usex netcdf)"
-		-DOPENCASCADE_DIR="${CASROOT}"
-		-DDEAL_II_WITH_OPENCASCADE="$(usex opencascade)"
-		-DDEAL_II_WITH_P4EST="$(usex p4est)"
-		-DDEAL_II_WITH_PETSC="$(usex petsc)"
-		-DDEAL_II_WITH_SCALAPACK="$(usex scalapack)"
-		-DDEAL_II_WITH_SLEPC="$(usex slepc)"
-		-DDEAL_II_WITH_SUNDIALS="$(usex sundials)"
-		-DDEAL_II_WITH_UMFPACK="$(usex sparse)"
-		-DBUILD_SHARED_LIBS="$(usex !static-libs)"
-		-DDEAL_II_PREFER_STATIC_LIBS="$(usex static-libs)"
-		-DDEAL_II_WITH_THREADS="$(usex tbb)"
-		-DDEAL_II_WITH_TRILINOS="$(usex trilinos)"
-	)
-	cmake-utils_src_configure
-}
-
-src_install() {
-	if use doc && [[ ${PV} != *9999* ]]; then
-		# copy missing images to the build directory:
-		cp -r "${WORKDIR}"/doc/doxygen/deal.II/images \
-			"${BUILD_DIR}"/doc/doxygen/deal.II || die
-		# replace links:
-		sed -i \
-			's#"http://www.dealii.org/images/steps/developer/\(step-.*\)"#"images/\1"#g' \
-			"${BUILD_DIR}"/doc/doxygen/deal.II/step_*.html || die "sed failed"
-	fi
-	cmake-utils_src_install
-
-	# decompress the installed example sources:
-	use examples && docompress -x /usr/share/doc/${PF}/examples
-}
diff --git a/sci-libs/dealii/metadata.xml b/sci-libs/dealii/metadata.xml
deleted file mode 100644
index 3b17832a7..000000000
--- a/sci-libs/dealii/metadata.xml
+++ /dev/null
@@ -1,45 +0,0 @@
-<?xml version="1.0" encoding="UTF-8"?>
-<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
-<pkgmetadata>
-	<maintainer type="person">
-		<email>tamiko@gentoo.org</email>
-		<name>Matthias Maier</name>
-	</maintainer>
-	<maintainer type="project">
-		<email>sci@gentoo.org</email>
-		<name>Gentoo Science Project</name>
-	</maintainer>
-	<longdescription lang="en">
-deal.II is a C++ program library targeted at the computational solution
-of partial differential equations using adaptive finite elements. It uses
-state-of-the-art programming techniques to offer you a modern interface
-to the complex data structures and algorithms required.
-</longdescription>
-	<use>
-		<flag name="adolc">Adds support for ADOL-C (<pkg>sci-libs/adolc</pkg>)</flag>
-		<flag name="arpack">Adds support for ARPACK (<pkg>sci-libs/arpack</pkg>)</flag>
-		<flag name="debug">
-Build an additional debug library with extra debug codepaths, like asserts
-and extra output. If you want to get meaningful backtraces see
-&lt;http://www.gentoo.org/proj/en/qa/backtraces.xml&gt;</flag>
-		<flag name="c++11">Compile the library with -std=c++11</flag>
-		<flag name="gmsh">Add support for gmsh (<pkg>sci-libs/gmsh</pkg>)</flag>
-		<flag name="metis">Add support for metis (<pkg>sci-libs/metis</pkg>)</flag>
-		<flag name="muparser">Add support for muparser (<pkg>dev-cpp/muParser</pkg>)</flag>
-		<flag name="nanoflann">Adds support for nanoflann (<pkg>sci-libs/nanoflann</pkg>)</flag>
-		<flag name="opencascade">Add support for opencascade (<pkg>sci-libs/opencascade</pkg>)</flag>
-		<flag name="p4est">Add support for p4est (<pkg>sci-mathematics/p4est</pkg>)</flag>
-		<flag name="petsc">Add support for petsc (<pkg>sci-mathematics/petsc</pkg>)</flag>
-		<flag name="scalapack">Add support for ScaLAPACK (<pkg>sci-libs/scalapack</pkg>)</flag>
-		<flag name="slepc">Add support for slepc (<pkg>sci-mathematics/slepc</pkg>)</flag>
-		<flag name="sparse">Add support for suitesparse (<pkg>sci-libs/suitesparse</pkg>)</flag>
-		<flag name="tbb">Add threading support with the help of the tbb library (<pkg>dev-cpp/tbb</pkg>)</flag>
-		<flag name="trilinos">Add support for trilinos (<pkg>sci-libs/trilinos</pkg>)</flag>
-		<flag name="assimp">Add support for assimp (<pkg>media-libs/assimp</pkg>)</flag>
-		<flag name="cuda">Add support for cuda assimp (<pkg>dev-util/nvidia-cuda-sdk</pkg>)</flag>
-		<flag name="sundials">Add support for sundials assimp (<pkg>sci-libs/sundials</pkg>)</flag>
-	</use>
-	<upstream>
-		<remote-id type="github">dealii/dealii</remote-id>
-	</upstream>
-</pkgmetadata>
diff --git a/sci-libs/elmer-eio/Manifest b/sci-libs/elmer-eio/Manifest
deleted file mode 100644
index 2fe59554f..000000000
--- a/sci-libs/elmer-eio/Manifest
+++ /dev/null
@@ -1 +0,0 @@
-DIST elmer-eio-6.0_p4651.tar.gz 147064 SHA256 80748e1386f03ef4b3a4c68271b1c724563a8960ffffcc36ba23e70e8519426e SHA512 52ce490810787e5100524858d41f3ad3d17ebfe5b747ea042acd8b8106028bb3aa7dd87ef80d3ce4ae2ffbf9439ad86c5f1a5f2e2c3cfb1cca5800c0fa166924 WHIRLPOOL 28837ee89756d81db5be96909f9682b1c627f31955179b668097c4d9c3efd55936a8e4c7334eda76051664dbb7043b246ad5d77a6b8950bb20f11a88ae53aa89
diff --git a/sci-libs/elmer-eio/elmer-eio-6.0_p4651.ebuild b/sci-libs/elmer-eio/elmer-eio-6.0_p4651.ebuild
deleted file mode 100644
index 3e3e95c1a..000000000
--- a/sci-libs/elmer-eio/elmer-eio-6.0_p4651.ebuild
+++ /dev/null
@@ -1,32 +0,0 @@
-# Copyright 1999-2014 Gentoo Foundation
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=5
-
-AUTOTOOLS_AUTORECONF=true
-
-inherit autotools-utils
-
-ELMER_ROOT="elmerfem"
-MY_PN=${PN/elmer-/}
-
-DESCRIPTION="Finite element programs, libraries, and visualization tools - elmer I/O library"
-HOMEPAGE="http://www.csc.fi/english/pages/elmer"
-SRC_URI="http://elmerfem.svn.sourceforge.net/viewvc/${ELMER_ROOT}/release/${PV%_p*}/${MY_PN}/?view=tar&pathrev=4651 -> ${P}.tar.gz"
-
-LICENSE="GPL-2"
-SLOT="0"
-KEYWORDS="~amd64 ~x86"
-IUSE="debug static-libs"
-
-S="${WORKDIR}/eio"
-
-PATCHES=( "${FILESDIR}"/${P}-shared.patch )
-
-src_configure() {
-	local myeconfargs=(
-		--enable-shared
-		$(use_with debug)
-	)
-	autotools-utils_src_configure
-}
diff --git a/sci-libs/elmer-eio/elmer-eio-9999.ebuild b/sci-libs/elmer-eio/elmer-eio-9999.ebuild
deleted file mode 100644
index ef0e1e8c8..000000000
--- a/sci-libs/elmer-eio/elmer-eio-9999.ebuild
+++ /dev/null
@@ -1,39 +0,0 @@
-# Copyright 1999-2014 Gentoo Foundation
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=5
-
-AUTOTOOLS_AUTORECONF=true
-
-inherit autotools-utils subversion
-
-ELMER_ROOT="elmerfem"
-MY_PN=${PN/elmer-/}
-
-DESCRIPTION="Finite element programs, libraries, and visualization tools - elmer I/O library"
-HOMEPAGE="http://www.csc.fi/english/pages/elmer"
-SRC_URI=""
-ESVN_REPO_URI="https://elmerfem.svn.sourceforge.net/svnroot/elmerfem/trunk/${MY_PN}"
-ESVN_PROJECT="${MY_PN}"
-
-LICENSE="GPL-2"
-SLOT="0"
-KEYWORDS=""
-IUSE="debug static-libs"
-
-S="${WORKDIR}/eio"
-
-PATCHES=( "${FILESDIR}"/${PN}-6.0_p4651-shared.patch )
-
-src_prepare() {
-	subversion_src_prepare
-	autotools-utils_src_prepare
-}
-
-src_configure() {
-	local myeconfargs=(
-		--enable-shared
-		$(use_with debug)
-	)
-	autotools-utils_src_configure
-}
diff --git a/sci-libs/elmer-eio/files/elmer-eio-6.0_p4651-shared.patch b/sci-libs/elmer-eio/files/elmer-eio-6.0_p4651-shared.patch
deleted file mode 100644
index f5a701ce3..000000000
--- a/sci-libs/elmer-eio/files/elmer-eio-6.0_p4651-shared.patch
+++ /dev/null
@@ -1,37 +0,0 @@
- configure.in    | 2 +-
- src/Makefile.am | 6 +++---
- 2 files changed, 4 insertions(+), 4 deletions(-)
-
-diff --git a/configure.in b/configure.in
-index ac5ce92..cd8fc53 100755
---- a/configure.in
-+++ b/configure.in
-@@ -1,5 +1,5 @@
- AC_INIT(src/eio_api_f.cpp)
--
-+LT_INIT
- dnl the fortran stuff needs to be pretty new to work on SunOS
- dnl AC_PREREQ(2.59c)
- 
-diff --git a/src/Makefile.am b/src/Makefile.am
-index 1836aba..4d73a4b 100755
---- a/src/Makefile.am
-+++ b/src/Makefile.am
-@@ -15,8 +15,8 @@ COMMON_SRCS =  \
- 	EIOPartWriter.cpp \
- 	EIOSolverAgent.cpp 
- 
--libeioc_a_SOURCES = $(COMMON_SRCS) eio_api_c.cpp
--libeiof_a_SOURCES = $(COMMON_SRCS) eio_api_f.cpp
-+libeioc_la_SOURCES = $(COMMON_SRCS) eio_api_c.cpp
-+libeiof_la_SOURCES = $(COMMON_SRCS) eio_api_f.cpp
- 
- # if USE_SHARED_LIBS
- # noinst_LIBRARIES = libeioc.a libeiof.a
-@@ -28,5 +28,5 @@ libeiof_a_SOURCES = $(COMMON_SRCS) eio_api_f.cpp
- # libeiof.$(SHLEXT): libeiof.a
- # 	$(SH_LD2) $(SH_LDFLAGS) $(B64FLAGS) $(LDFLAGS) -o $@ libeiof.a
- # else
--lib_LIBRARIES = libeioc.a libeiof.a
-+lib_LTLIBRARIES = libeioc.la libeiof.la
- # endif
diff --git a/sci-libs/elmer-eio/metadata.xml b/sci-libs/elmer-eio/metadata.xml
deleted file mode 100644
index 070aa2029..000000000
--- a/sci-libs/elmer-eio/metadata.xml
+++ /dev/null
@@ -1,11 +0,0 @@
-<?xml version="1.0" encoding="UTF-8"?>
-<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
-<pkgmetadata>
-	<maintainer type="project">
-		<email>sci@gentoo.org</email>
-		<name>Gentoo Science Project</name>
-	</maintainer>
-	<upstream>
-		<remote-id type="sourceforge">svn</remote-id>
-	</upstream>
-</pkgmetadata>
diff --git a/sci-libs/elmer-hutiter/Manifest b/sci-libs/elmer-hutiter/Manifest
deleted file mode 100644
index 964e2323a..000000000
--- a/sci-libs/elmer-hutiter/Manifest
+++ /dev/null
@@ -1 +0,0 @@
-DIST elmer-hutiter-6.0_p4651.tar.gz 446301 SHA256 1467a2efd66824f3691d242958ce8ee845a96968a1a8d4bd09bef904f6784cd1 SHA512 e2ec85a8f97a9d6935bc1903b013816169902902eaf6b8fc2fc3a1dd2fa7e310e0547a4ed0a7ec5758cf3934e002ea56b84a379a67cf743356e9376d535aa9dc WHIRLPOOL 1ad638a081c80d80b30e37485ee3570272b5fa5a085d60ea45f21496ccb829a9858d9757473b9454e88945792cb39f8c33a624a9f2da761032013c2527309d93
diff --git a/sci-libs/elmer-hutiter/elmer-hutiter-6.0_p4651.ebuild b/sci-libs/elmer-hutiter/elmer-hutiter-6.0_p4651.ebuild
deleted file mode 100644
index 9cf9a3c00..000000000
--- a/sci-libs/elmer-hutiter/elmer-hutiter-6.0_p4651.ebuild
+++ /dev/null
@@ -1,37 +0,0 @@
-# Copyright 1999-2014 Gentoo Foundation
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=5
-
-AUTOTOOLS_AUTORECONF=true
-
-inherit autotools-utils toolchain-funcs
-
-ELMER_ROOT="elmerfem"
-MY_PN=${PN/elmer-/}
-
-DESCRIPTION="Finite element programs, libraries, and visualization tools - hutiter library"
-HOMEPAGE="http://www.csc.fi/english/pages/elmer"
-SRC_URI="http://elmerfem.svn.sourceforge.net/viewvc/${ELMER_ROOT}/release/${PV%_p*}/${MY_PN}/?view=tar&pathrev=4651 -> ${P}.tar.gz"
-
-LICENSE="GPL-2"
-SLOT="0"
-KEYWORDS="~amd64 ~x86"
-IUSE="debug static-libs"
-
-RDEPEND="virtual/blas"
-DEPEND="${RDEPEND}
-	virtual/pkgconfig"
-
-S="${WORKDIR}"/hutiter
-
-PATCHES=( "${FILESDIR}"/${P}-shared.patch )
-
-src_configure() {
-	local myeconfargs=(
-		--enable-shared
-		$(use_with debug) \
-		--with-blas="$($(tc-getPKG_CONFIG) --libs blas)"
-	)
-	autotools-utils_src_configure
-}
diff --git a/sci-libs/elmer-hutiter/elmer-hutiter-9999.ebuild b/sci-libs/elmer-hutiter/elmer-hutiter-9999.ebuild
deleted file mode 100644
index 7e053befa..000000000
--- a/sci-libs/elmer-hutiter/elmer-hutiter-9999.ebuild
+++ /dev/null
@@ -1,44 +0,0 @@
-# Copyright 1999-2014 Gentoo Foundation
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=5
-
-AUTOTOOLS_AUTORECONF=true
-
-inherit autotools-utils toolchain-funcs subversion
-
-ELMER_ROOT="elmerfem"
-MY_PN=${PN/elmer-/}
-
-DESCRIPTION="Finite element programs, libraries, and visualization tools - hutiter library"
-HOMEPAGE="http://www.csc.fi/english/pages/elmer"
-SRC_URI=""
-ESVN_REPO_URI="https://elmerfem.svn.sourceforge.net/svnroot/elmerfem/trunk/${MY_PN}"
-ESVN_PROJECT="${MY_PN}"
-
-LICENSE="GPL-2"
-SLOT="0"
-KEYWORDS=""
-IUSE="debug static-libs"
-
-RDEPEND="virtual/blas"
-DEPEND="${RDEPEND}
-	virtual/pkgconfig"
-
-S="${WORKDIR}"/hutiter
-
-PATCHES=( "${FILESDIR}"/${PN}-6.0_p4651-shared.patch )
-
-src_prepare() {
-	subversion_src_prepare
-	autotools-utils_src_prepare
-}
-
-src_configure() {
-	local myeconfargs=(
-		--enable-shared
-		$(use_with debug) \
-		--with-blas="$($(tc-getPKG_CONFIG) --libs blas)"
-	)
-	autotools-utils_src_configure
-}
diff --git a/sci-libs/elmer-hutiter/files/elmer-hutiter-6.0_p4651-shared.patch b/sci-libs/elmer-hutiter/files/elmer-hutiter-6.0_p4651-shared.patch
deleted file mode 100644
index cc7e0cd11..000000000
--- a/sci-libs/elmer-hutiter/files/elmer-hutiter-6.0_p4651-shared.patch
+++ /dev/null
@@ -1,33 +0,0 @@
- src/Makefile.am | 5 +++--
- 1 file changed, 3 insertions(+), 2 deletions(-)
-
-diff --git a/src/Makefile.am b/src/Makefile.am
-index bdfb73f..8800d1a 100755
---- a/src/Makefile.am
-+++ b/src/Makefile.am
-@@ -49,8 +49,9 @@ COMMON_SRCS =  \
- 
- 
- 
--lib_LIBRARIES = libhuti.a
--libhuti_a_SOURCES = $(COMMON_SRCS)
-+lib_LTLIBRARIES = libhuti.la
-+libhuti_la_SOURCES = $(COMMON_SRCS)
-+libhuti_la_LIBADD = 
- 
- #################################################################################
- # If sources are missing generate them with the preprocessor.
- configure.in | 2 +-
- 1 file changed, 1 insertion(+), 1 deletion(-)
-
-diff --git a/configure.in b/configure.in
-index 5b25b28..7356ca4 100755
---- a/configure.in
-+++ b/configure.in
-@@ -1,5 +1,5 @@
- AC_INIT(src/huti_cg.src)
--
-+LT_INIT
- dnl AC_PREREQ(2.59c)
- 
- AC_CANONICAL_HOST
diff --git a/sci-libs/elmer-hutiter/metadata.xml b/sci-libs/elmer-hutiter/metadata.xml
deleted file mode 100644
index 070aa2029..000000000
--- a/sci-libs/elmer-hutiter/metadata.xml
+++ /dev/null
@@ -1,11 +0,0 @@
-<?xml version="1.0" encoding="UTF-8"?>
-<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
-<pkgmetadata>
-	<maintainer type="project">
-		<email>sci@gentoo.org</email>
-		<name>Gentoo Science Project</name>
-	</maintainer>
-	<upstream>
-		<remote-id type="sourceforge">svn</remote-id>
-	</upstream>
-</pkgmetadata>
diff --git a/sci-libs/ensmallen/Manifest b/sci-libs/ensmallen/Manifest
new file mode 100644
index 000000000..d74da89b9
--- /dev/null
+++ b/sci-libs/ensmallen/Manifest
@@ -0,0 +1,5 @@
+DIST ensmallen-2.14.2.tar.gz 1262697 BLAKE2B c3ecd10271a476cdb03de0a74dd1e7d250273481b540d9cadb44ff7292cdb1f4abbefaf7c1a90bd33c68928f766db8afafd45f253735a36de9def6ab222597bb SHA512 9f29d70f66748d6131b44fc2a580e9fc07131a3aeecaa9f6113fd635eaff8b52db90e487a389393a1976dcccb8c1f5850ea50e03308af90b58ba1c12fde2bd21
+DIST ensmallen-2.15.0.tar.gz 1266409 BLAKE2B 379ea897d3b29440e89d65cb60c65dca3c34a530dd8a4cee321349d177455b020d4aa19ee1e701b46a325a8f56028c236ab80b0383bee84018952034106f7161 SHA512 7e8ea0d64788287e58ee14e922c81c18e1804a23dba3d144fe6e66de8a81dfd3755c9f36a1e8a480aa6e15f0f7b1ff886e0aeecde0be35993db0ba69ca7e12e0
+DIST ensmallen-2.15.1.tar.gz 1266496 BLAKE2B 7ff803207c59be03fa47e7fddafb49176d307fbea89f5688bd591898fb36d7d8ee018dec933b59a06063dc6c2a7117d3ec0d330cd37d475e4f387528f2d86f6a SHA512 4f0cda1ad0d02e823042fb6af03635677e3d5cac28f7f13fab20fc7f4b3d7fbe1b182777c573187a403eff5e5fd7e1e577e290a4b624a9c2a71cbfd347e14afa
+DIST ensmallen-2.16.0.tar.gz 1264948 BLAKE2B a58de7e7d8aa88988b08d76c2a5746daf9074ccc39bc8df9d21b61d745741d6521922b578e01b60e0d1657f84f377f411172a01d50bbcd30cca7142da0baeb7b SHA512 39afc19936710d5595218292f5d6a055b4f644ca157f9fc2329fb18b71318b9f613dc26169921e1fda3dd949d06847dee4f09f13c1902a92e38826e122c1adc5
+DIST ensmallen-2.16.2.tar.gz 1294240 BLAKE2B b388f2c99f289dd20f6d94b5b185d872abc553637c6081ea3a80a3c82ce9ac8b1327496bf3eae6dc5cbf5f4ae12a9fd1e8ccf9c296007f9af9cbfc7560cd0301 SHA512 290932f8e423be7c57d8ba38783a29798df52a7505ded7683f969fa30391398edcca584daca1b1c42977f06180a802d4c3640a9ec24cd787a3914723e4eb6f8d
diff --git a/sci-libs/ensmallen/ensmallen-2.14.2.ebuild b/sci-libs/ensmallen/ensmallen-2.14.2.ebuild
new file mode 100644
index 000000000..bb93e8246
--- /dev/null
+++ b/sci-libs/ensmallen/ensmallen-2.14.2.ebuild
@@ -0,0 +1,28 @@
+# Copyright 1999-2020 Gentoo Authors
+# Distributed under the terms of the GNU General Public License v2
+
+EAPI=7
+
+inherit cmake
+
+DESCRIPTION="header only C++ library for numerical optimization"
+HOMEPAGE="https://ensmallen.org"
+SRC_URI="https://github.com/mlpack/ensmallen/archive/${PV}.tar.gz -> ${P}.tar.gz"
+
+KEYWORDS="~amd64"
+
+LICENSE="BSD"
+SLOT="0"
+IUSE="openmp test"
+RESTRICT="!test? ( test )"
+
+RDEPEND="sci-libs/armadillo[lapack]"
+DEPEND="${RDEPEND}"
+
+src_configure() {
+	local mycmakeargs=(
+		-DUSE_OPENMP=$(usex openmp)
+		-DBUILD_TESTS=$(usex test)
+	)
+	cmake_src_configure
+}
diff --git a/sci-libs/ensmallen/ensmallen-2.15.0.ebuild b/sci-libs/ensmallen/ensmallen-2.15.0.ebuild
new file mode 100644
index 000000000..bb93e8246
--- /dev/null
+++ b/sci-libs/ensmallen/ensmallen-2.15.0.ebuild
@@ -0,0 +1,28 @@
+# Copyright 1999-2020 Gentoo Authors
+# Distributed under the terms of the GNU General Public License v2
+
+EAPI=7
+
+inherit cmake
+
+DESCRIPTION="header only C++ library for numerical optimization"
+HOMEPAGE="https://ensmallen.org"
+SRC_URI="https://github.com/mlpack/ensmallen/archive/${PV}.tar.gz -> ${P}.tar.gz"
+
+KEYWORDS="~amd64"
+
+LICENSE="BSD"
+SLOT="0"
+IUSE="openmp test"
+RESTRICT="!test? ( test )"
+
+RDEPEND="sci-libs/armadillo[lapack]"
+DEPEND="${RDEPEND}"
+
+src_configure() {
+	local mycmakeargs=(
+		-DUSE_OPENMP=$(usex openmp)
+		-DBUILD_TESTS=$(usex test)
+	)
+	cmake_src_configure
+}
diff --git a/sci-libs/ensmallen/ensmallen-2.15.1.ebuild b/sci-libs/ensmallen/ensmallen-2.15.1.ebuild
new file mode 100644
index 000000000..bb93e8246
--- /dev/null
+++ b/sci-libs/ensmallen/ensmallen-2.15.1.ebuild
@@ -0,0 +1,28 @@
+# Copyright 1999-2020 Gentoo Authors
+# Distributed under the terms of the GNU General Public License v2
+
+EAPI=7
+
+inherit cmake
+
+DESCRIPTION="header only C++ library for numerical optimization"
+HOMEPAGE="https://ensmallen.org"
+SRC_URI="https://github.com/mlpack/ensmallen/archive/${PV}.tar.gz -> ${P}.tar.gz"
+
+KEYWORDS="~amd64"
+
+LICENSE="BSD"
+SLOT="0"
+IUSE="openmp test"
+RESTRICT="!test? ( test )"
+
+RDEPEND="sci-libs/armadillo[lapack]"
+DEPEND="${RDEPEND}"
+
+src_configure() {
+	local mycmakeargs=(
+		-DUSE_OPENMP=$(usex openmp)
+		-DBUILD_TESTS=$(usex test)
+	)
+	cmake_src_configure
+}
diff --git a/sci-libs/ensmallen/ensmallen-2.16.0.ebuild b/sci-libs/ensmallen/ensmallen-2.16.0.ebuild
new file mode 100644
index 000000000..bd1c0530b
--- /dev/null
+++ b/sci-libs/ensmallen/ensmallen-2.16.0.ebuild
@@ -0,0 +1,28 @@
+# Copyright 1999-2021 Gentoo Authors
+# Distributed under the terms of the GNU General Public License v2
+
+EAPI=7
+
+inherit cmake
+
+DESCRIPTION="header only C++ library for numerical optimization"
+HOMEPAGE="https://ensmallen.org"
+SRC_URI="https://github.com/mlpack/ensmallen/archive/${PV}.tar.gz -> ${P}.tar.gz"
+
+KEYWORDS="~amd64"
+
+LICENSE="BSD"
+SLOT="0"
+IUSE="openmp test"
+RESTRICT="!test? ( test )"
+
+RDEPEND="sci-libs/armadillo[lapack]"
+DEPEND="${RDEPEND}"
+
+src_configure() {
+	local mycmakeargs=(
+		-DUSE_OPENMP=$(usex openmp)
+		-DBUILD_TESTS=$(usex test)
+	)
+	cmake_src_configure
+}
diff --git a/sci-libs/ensmallen/ensmallen-2.16.2.ebuild b/sci-libs/ensmallen/ensmallen-2.16.2.ebuild
new file mode 100644
index 000000000..bd1c0530b
--- /dev/null
+++ b/sci-libs/ensmallen/ensmallen-2.16.2.ebuild
@@ -0,0 +1,28 @@
+# Copyright 1999-2021 Gentoo Authors
+# Distributed under the terms of the GNU General Public License v2
+
+EAPI=7
+
+inherit cmake
+
+DESCRIPTION="header only C++ library for numerical optimization"
+HOMEPAGE="https://ensmallen.org"
+SRC_URI="https://github.com/mlpack/ensmallen/archive/${PV}.tar.gz -> ${P}.tar.gz"
+
+KEYWORDS="~amd64"
+
+LICENSE="BSD"
+SLOT="0"
+IUSE="openmp test"
+RESTRICT="!test? ( test )"
+
+RDEPEND="sci-libs/armadillo[lapack]"
+DEPEND="${RDEPEND}"
+
+src_configure() {
+	local mycmakeargs=(
+		-DUSE_OPENMP=$(usex openmp)
+		-DBUILD_TESTS=$(usex test)
+	)
+	cmake_src_configure
+}
diff --git a/sci-libs/ensmallen/metadata.xml b/sci-libs/ensmallen/metadata.xml
new file mode 100644
index 000000000..043f7babc
--- /dev/null
+++ b/sci-libs/ensmallen/metadata.xml
@@ -0,0 +1,15 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
+<pkgmetadata>
+	<maintainer type="person">
+		<email>gentoo@aisha.cc</email>
+		<name>Aisha Tammy</name>
+	</maintainer>
+	<maintainer type="project">
+		<email>sci@gentoo.org</email>
+		<name>Gentoo Science Project</name>
+	</maintainer>
+	<upstream>
+		<remote-id type="github">mlpack/ensmallen</remote-id>
+	</upstream>
+</pkgmetadata>
diff --git a/sci-libs/etsf_io/Manifest b/sci-libs/etsf_io/Manifest
index 5d8533840..04d02c7aa 100644
--- a/sci-libs/etsf_io/Manifest
+++ b/sci-libs/etsf_io/Manifest
@@ -1,2 +1 @@
-DIST etsf_io-1.0.3.tar 453734 SHA256 a02ead44b9634bdb6e47e50d76f35d56c10df468743e6fe5259c0dc478f7b32e SHA512 2a60533a588587da5629687942044ed58b72a554c484d3c22263314cbeb21aa819d5097e6637b599de06474d4d92cc84ea94fa365123e677311be3bf7b8e7bf5 WHIRLPOOL 714cfa983b5f3411a04df88ad54513f71b482368cba93b790d5d93388a9aea346cd83de80311ed0fe5fdc51fac4af8be4428764119a0cf9f17df24e91f2ae74a
 DIST etsf_io-1.0.4.tar.gz 475617 BLAKE2B ad29d713b7e1ebaf6440b71f2786fc00a60cfbbd795d289c0c8a5a89f34301c48845fa0570f5ac7d752158acdbd1e281626ae4f9dc01132fb6cd95bc8e8297fb SHA512 a251384da49832c4d673af450167095ada783f5483ecb94e79efe0c5b538bdfd6aa55f7bb6e49735dc85b4b894b1255746e72d89426073b2ffbe12512adb7803
diff --git a/sci-libs/etsf_io/etsf_io-1.0.3-r2.ebuild b/sci-libs/etsf_io/etsf_io-1.0.3-r2.ebuild
deleted file mode 100644
index 091b2b54c..000000000
--- a/sci-libs/etsf_io/etsf_io-1.0.3-r2.ebuild
+++ /dev/null
@@ -1,35 +0,0 @@
-# Copyright 1999-2014 Gentoo Foundation
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=5
-
-inherit fortran-2 multilib
-
-DESCRIPTION="A library of F90 routines to read/write the ETSF file format"
-HOMEPAGE="http://www.etsf.eu/resources/software/libraries_and_tools/"
-SRC_URI="http://www.etsf.eu/sites/default/files/${P}.tar.gz -> ${P}.tar"
-
-LICENSE="LGPL-2"
-SLOT="0"
-IUSE="examples"
-KEYWORDS="~amd64 ~x86"
-
-RDEPEND="
-	|| (
-		sci-libs/netcdf[fortran]
-		sci-libs/netcdf-fortran
-	)
-	virtual/fortran"
-DEPEND="${RDEPEND}"
-
-FORTRAN_STANDARD="90"
-
-src_configure() {
-	# fortran 90 uses FCFLAGS
-	export FCFLAGS="${FFLAGS:--O2}"
-	econf \
-		$(use_enable examples build-tutorials) \
-		--prefix="${EPREFIX}/usr" \
-		--with-netcdf-ldflags="-L${EPREFIX}/usr/$(get_libdir) -lnetcdff" \
-		--with-moduledir="${EPREFIX}/usr/include"
-}
diff --git a/sci-libs/etsf_io/etsf_io-1.0.4-r1.ebuild b/sci-libs/etsf_io/etsf_io-1.0.4-r1.ebuild
deleted file mode 100644
index a7a0e6589..000000000
--- a/sci-libs/etsf_io/etsf_io-1.0.4-r1.ebuild
+++ /dev/null
@@ -1,35 +0,0 @@
-# Copyright 1999-2015 Gentoo Foundation
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=5
-
-inherit fortran-2 multilib
-
-DESCRIPTION="A library of F90 routines to read/write the ETSF file format"
-HOMEPAGE="http://www.etsf.eu/resources/software/libraries_and_tools/"
-SRC_URI="http://www.etsf.eu/system/files/${P}.tar.gz"
-
-LICENSE="LGPL-2"
-SLOT="0"
-IUSE="examples pic"
-KEYWORDS="~amd64 ~x86"
-
-RDEPEND="
-	|| (
-		sci-libs/netcdf[fortran]
-		sci-libs/netcdf-fortran
-	)
-	virtual/fortran"
-DEPEND="${RDEPEND}"
-
-FORTRAN_STANDARD="90"
-
-src_configure() {
-	# fortran 90 uses FCFLAGS
-	export FCFLAGS="${FFLAGS:--O2}"
-	use pic && export FCFLAGS="-fPIC ${FCFLAGS}"
-	econf \
-		$(use_enable examples build-tutorials) \
-		--prefix="${EPREFIX}/usr" \
-		--with-moduledir="${EPREFIX}/usr/include"
-}
diff --git a/sci-libs/etsf_io/etsf_io-1.0.4-r2.ebuild b/sci-libs/etsf_io/etsf_io-1.0.4-r2.ebuild
new file mode 100644
index 000000000..3961e4951
--- /dev/null
+++ b/sci-libs/etsf_io/etsf_io-1.0.4-r2.ebuild
@@ -0,0 +1,34 @@
+# Copyright 1999-2021 Gentoo Authors
+# Distributed under the terms of the GNU General Public License v2
+
+EAPI=7
+
+inherit fortran-2
+
+DESCRIPTION="A library of F90 routines to read/write the ETSF file format"
+HOMEPAGE="https://github.com/ElectronicStructureLibrary/libetsf_io"
+SRC_URI="https://launchpad.net/etsf-io/$(ver_cut 1-2)/${PV}/+download/${P}.tar.gz"
+
+LICENSE="LGPL-2"
+SLOT="0"
+KEYWORDS="~amd64 ~x86"
+
+IUSE="examples pic"
+RESTRICT="test"
+
+RDEPEND="
+	sci-libs/netcdf-fortran
+	virtual/fortran"
+DEPEND="${RDEPEND}"
+
+FORTRAN_STANDARD="90"
+
+src_configure() {
+	# fortran 90 uses FCFLAGS
+	export FCFLAGS="${FFLAGS:--O2}"
+	use pic && export FCFLAGS="-fPIC ${FCFLAGS}"
+	econf \
+		$(use_enable examples build-tutorials) \
+		--prefix="${EPREFIX}/usr" \
+		--with-moduledir="${EPREFIX}/usr/include"
+}
diff --git a/sci-libs/etsf_io/metadata.xml b/sci-libs/etsf_io/metadata.xml
index 5c8a3611e..d8e7a0e60 100644
--- a/sci-libs/etsf_io/metadata.xml
+++ b/sci-libs/etsf_io/metadata.xml
@@ -7,4 +7,8 @@
 	<use>
 		<flag name="pic">Compile Position Independent Code</flag>
 	</use>
+	<upstream>
+		<remote-id type="github">ElectronicStructureLibrary/libetsf_io</remote-id>
+		<remote-id type="launchpad">etsf-io</remote-id>
+	</upstream>
 </pkgmetadata>
diff --git a/sci-libs/factory/Manifest b/sci-libs/factory/Manifest
deleted file mode 100644
index 36d74fbf3..000000000
--- a/sci-libs/factory/Manifest
+++ /dev/null
@@ -1 +0,0 @@
-DIST factory-3-1-1.tar.gz 540431 BLAKE2B 7b06f0847d1547fe801c51737e6a3ee85479c8044ab3947295ea3d3894f86f44f0a64ecb30ea82db98af12f7f4e838a4b45b448eddc1db6deb9c9f96a7ef409a SHA512 e57a558e80f2f1bfa472ff65b52ad2872419e588e48d343708d07b15daa9c57a7d0264fceb9b67cf0ef754fd98c70e859d1bc98c2f0b06610fc7f33d43f59e94
diff --git a/sci-libs/factory/factory-3.1.1-r2.ebuild b/sci-libs/factory/factory-3.1.1-r2.ebuild
deleted file mode 100644
index bba1ea824..000000000
--- a/sci-libs/factory/factory-3.1.1-r2.ebuild
+++ /dev/null
@@ -1,46 +0,0 @@
-# Copyright 1999-2015 Gentoo Foundation
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=5
-
-inherit autotools-utils versionator
-
-MY_PV=$(replace_all_version_separators '-')
-
-DESCRIPTION="C++ library for representing multivariate polynomials"
-HOMEPAGE="http://www.mathematik.uni-kl.de/pub/Math/Singular/Factory"
-SRC_URI="ftp://www.mathematik.uni-kl.de/pub/Math/Singular/Factory/${PN}-${MY_PV}.tar.gz"
-
-LICENSE="GPL-2"
-SLOT="0"
-KEYWORDS="~amd64 ~x86"
-IUSE="singular static-libs"
-
-DEPEND="
-	dev-libs/gmp:0=
-	>=dev-libs/ntl-5.4.1"
-RDEPEND="${DEPEND}"
-
-S="${WORKDIR}/${PN}"
-
-AUTOTOOLS_IN_SOURCE_BUILD="1"
-DOCS=( README NEWS )
-PATCHES=( "${FILESDIR}"/${P}-gentoo.diff )
-
-pkg_setup() {
-	tc-export CC CPP CXX
-}
-
-src_configure() {
-	myeconfargs=( $(use_with singular Singular) )
-
-	autotools-utils_src_configure
-}
-
-src_install() {
-	autotools-utils_src_install
-
-	# Passing --disable-static to configure won't disable the build of static libs,
-	# as libtool isn't used. Therefore the static libs are deleted after installed to ${D}.
-	use !static-libs || find "${ED}" -type f -name "*.a" -delete || die
-}
diff --git a/sci-libs/factory/files/factory-3.1.1-gentoo.diff b/sci-libs/factory/files/factory-3.1.1-gentoo.diff
deleted file mode 100644
index 0283eea2d..000000000
--- a/sci-libs/factory/files/factory-3.1.1-gentoo.diff
+++ /dev/null
@@ -1,165 +0,0 @@
---- GNUmakefile.in
-+++ GNUmakefile.in
-@@ -43,7 +43,10 @@
- # - the name of the game.
- #
- libfactory =	@libfactory@
--
-+libfactory_so 		= $(libfactory:.a=.so)
-+libfactory_sover	= $(libfactory_so).@factory_version@
-+libcfmem_so			= libcfmem.so
-+libcfmem_sover		= libcfmem.so.$(version)
- #
- # - programs.
- #
-@@ -51,7 +54,7 @@
- CXX =		@CXX@
- # seems configure sometimes finds non-BSD install, so we better
- # hardcode path to our install-sh
--INSTALL =	$(srcdir)/bin/install-sh -c
-+INSTALL =	@INSTALL@
- INSTALL_DATA =	@INSTALL_DATA@
- INSTALL_PROGRAM=@INSTALL_PROGRAM@
- RANLIB =	@RANLIB@
-@@ -200,8 +203,8 @@
- # factory object files and dependencies
- factoryobj1 :=  $(factorysrc:%.cc=%.o)
- factoryobj :=   $(factoryobj1:%.y=%.o)
--factorygobj :=  $(factorysrc:%.cc=%.og)
--factorypobj :=  $(factorysrc:%.cc=%.op)
-+factoryobj1 :=  $(factorysrc:%.cc=%.o_pic)
-+factoryobj_pic := $(factoryobj1:%.y=%.o_pic)
- factorydep :=	$(factorysrc:%.cc=%.d)
- factorydep :=	$(factorydep:%.y=%.d)
- 
-@@ -295,6 +298,8 @@
- # memory manager object files and dependencies
- memmanobj :=	$(memmansrc:.cc=.o)
- memmanobj :=	$(memmanobj:.c=.o)
-+memmanobj_pic :=	$(memmansrc:.cc=.o_pic)
-+memmanobj_pic :=	$(memmanobj_pic:.c=.o_pic)
- memmandep :=	$(memmansrc:.cc=.d)
- memmandep :=	$(memmandep:.c=.d)
- 
-@@ -426,16 +431,14 @@
- #
- 
- # how to create library objets
--%.o: %.cc config.h
-+%.o: %.cc config.h factoryconf.h
- 	$(CXX) -c $< $(LIBCXXFLAGS) -o $@
--%.o: %.c config.h
-+%.o: %.c config.h factoryconf.h
- 	$(CC) -c $< $(LIBCFLAGS) -o $@
--# the debug version:
--%.og: %.cc config.h
--	$(CXX) -g -c $< $(LIBCGGFLAGS) -o $@
--# the profiling version:
--%.op: %.cc config.h
--	$(CXX) -O -pg -c $< $(LIBCGGFLAGS) -o $@
-+%.o_pic: %.cc config.h factoryconf.h
-+	$(CXX) -c $< $(LIBCXXFLAGS) -fPIC -o $@
-+%.o_pic: %.c config.h factoryconf.h
-+	$(CC) -c $< $(LIBCFLAGS) -fPIC -o $@
- 
- # how to create dependency files.  To avoid broken dependency files
- # (which in turn break this GNUmakefile) we first generate them in
-@@ -463,9 +466,9 @@
- #
- all:		$(alltargets)
- 
--cf:		factoryconf.h factory.h $(libfactory) libsingcf_g.a
-+cf:		factoryconf.h factory.h $(libfactory) $(libfactory_sover)
- 
--mem:		libcfmem.a
-+mem:		libcfmem.a $(libcfmem_sover)
- 
- #
- # - explicit targets.
-@@ -474,18 +477,16 @@
- 		$(AR) $(ARFLAGS) $@ $^
- 		$(RANLIB) $@
- 
--libsingcf_g.a:	$(factorygobj)
--		$(AR) $(ARFLAGS) $@ $^
--		$(RANLIB) $@
--
--libsingcf_p.a:	$(factorypobj)
--		$(AR) $(ARFLAGS) $@ $^
--		$(RANLIB) $@
-+$(libfactory_sover): $(factoryobj_pic)
-+		$(CXX) -shared -Wl,-soname,$(libfactory_so).3 $(LDFLAGS) -o $@ $^ $(LIBS)
- 
- libcfmem.a:	$(memmanobj)
- 		$(AR) $(ARFLAGS) $@ $^
- 		$(RANLIB) $@
- 
-+$(libcfmem_sover): $(memmanobj_pic)
-+		$(CXX) -shared -Wl,-soname,$(libcfmem_so).3 $(LDFLAGS) -o $@ $^ $(LIBS)
-+
- ftmpl_inst.o:	ftmpl_inst.cc factoryconf.h factory.h \
- 		$(addprefix templates/,$(templatesrc)) \
- 		$(addprefix templates/,$(templateincl))
-@@ -605,45 +606,41 @@
- #
- install:	$(installtargets)
- 
--install_all:	install libsingcf_p.a
--		-$(INSTALL_DATA) libsingcf_p.a $(libdir)/libsingcf_p.a
--
- install-nolns: install
- 
- installcf:	cf
--		$(MKINSTALLDIRS) $(libdir)
--		$(MKINSTALLDIRS) $(includedir)
--		$(MKINSTALLDIRS) $(templatedir)
--		$(INSTALL_DATA) $(libfactory) $(libdir)/$(libfactory)
--		-$(INSTALL_DATA) libsingcf_g.a $(libdir)/libsingcf_g.a
--		$(INSTALL_DATA) factory.h $(includedir)/factory.h
--		$(INSTALL_DATA) cf_gmp.h $(includedir)/cf_gmp.h
--		$(INSTALL_DATA) factoryconf.h $(includedir)/factoryconf.h
--		$(INSTALL_DATA) $(srcdir)/ftmpl_inst.cc $(templatedir)/ftmpl_inst.cc
-+		$(INSTALL_DATA) -D $(libfactory) $(DESTDIR)$(libdir)/$(libfactory)
-+		$(INSTALL_PROGRAM) -D $(libfactory_sover) $(DESTDIR)$(libdir)/$(libfactory_sover)
-+		$(LN_S) $(libfactory_sover) $(DESTDIR)$(libdir)/$(libfactory_so).3
-+		$(LN_S) $(libfactory_sover) $(DESTDIR)$(libdir)/$(libfactory_so)
-+		$(INSTALL_DATA) -D factory.h $(DESTDIR)$(includedir)/factory.h
-+		$(INSTALL_DATA) cf_gmp.h $(DESTDIR)$(includedir)/cf_gmp.h
-+		$(INSTALL_DATA) factoryconf.h $(DESTDIR)$(includedir)/factoryconf.h
-+		$(INSTALL_DATA) -D $(srcdir)/ftmpl_inst.cc $(DESTDIR)$(templatedir)/ftmpl_inst.cc
- 		for file in $(templatesrc) $(templateincl); do \
--		  $(INSTALL_DATA) $(srcdir)/templates/$$file $(templatedir)/$$file; \
-+		  $(INSTALL_DATA) $(srcdir)/templates/$$file $(DESTDIR)$(templatedir)/$$file; \
- 		done
- # we run `ranlib' another time for SUN machines
--		$(RANLIB) $(libdir)/$(libfactory)
-+		$(RANLIB) $(DESTDIR)$(libdir)/$(libfactory)
- 
- installmem:	mem
--		$(MKINSTALLDIRS) $(libdir)
--		$(INSTALL_DATA) libcfmem.a $(libdir)/libcfmem.a
-+		$(INSTALL_DATA) -D libcfmem.a $(DESTDIR)$(libdir)/libcfmem.a
-+		$(INSTALL_PROGRAM) $(libcfmem_sover) $(DESTDIR)$(libdir)/$(libcfmem_sover)
-+		$(LN_S) $(libcfmem_sover) $(DESTDIR)$(libdir)/$(libcfmem_so).3
-+		$(LN_S) $(libcfmem_sover) $(DESTDIR)$(libdir)/$(libcfmem_so)
- # once again: another run for SUN
--		$(RANLIB) $(libdir)/libcfmem.a
-+		$(RANLIB) $(DESTDIR)$(libdir)/libcfmem.a
- 
- # to a pity, this cannot be done automatically ...
- installgftables:
- 		@echo "Copying GF(q) tables ..."
- 		@if test -d gftables; then \
--		  $(MKINSTALLDIRS) $(gftabledir); \
- 		  for file in gftables/gftable.*.*; do \
--		    $(INSTALL_DATA) $$file $(gftabledir); \
-+		    $(INSTALL_DATA) -D $$file $(DESTDIR)$(gftabledir); \
- 		  done \
- 		elif test -d "$(srcdir)"/gftables; then \
--		  $(MKINSTALLDIRS) $(gftabledir); \
- 		  for file in "$(srcdir)"/gftables/gftable.*.*; do \
--		    $(INSTALL_DATA) $$file $(gftabledir); \
-+		    $(INSTALL_DATA) -D $$file $(DESTDIR)$(gftabledir); \
- 		  done \
- 		else \
- 		  echo "Run 'make gftables' before installing them"; \
diff --git a/sci-libs/factory/metadata.xml b/sci-libs/factory/metadata.xml
deleted file mode 100644
index 5d8333c29..000000000
--- a/sci-libs/factory/metadata.xml
+++ /dev/null
@@ -1,18 +0,0 @@
-<?xml version="1.0" encoding="UTF-8"?>
-<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
-<pkgmetadata>
-	<maintainer type="person">
-		<email>tom111@gmx.de</email>
-		<name>Thomas Kahle</name>
-	</maintainer>
-	<maintainer type="project">
-		<email>sci@gentoo.org</email>
-		<name>Gentoo Science Project</name>
-	</maintainer>
-	<longdescription lang="en">
-factory is a template library to handle recursive polynomial data
-</longdescription>
-	<use>
-		<flag name="singular">Enable support for <pkg>sci-mathematics/singular</pkg></flag>
-	</use>
-</pkgmetadata>
diff --git a/sci-libs/fast5/Manifest b/sci-libs/fast5/Manifest
deleted file mode 100644
index cc50f8f31..000000000
--- a/sci-libs/fast5/Manifest
+++ /dev/null
@@ -1 +0,0 @@
-DIST fast5-0.6.4.tar.gz 93660 BLAKE2B 8f7fd749fa90d6b5d4a530401b1f07a7ff05914fdd7b957e6555ac6e513cfa38529c3ea2973eea04228b9ff6332bfa0688fc65d6a032936fe05852c0a181efa6 SHA512 e3489cdc55f13bf12ae31759eaebea17128506999c3ea3dbd7e40418180dd5cb6e1d27f26f769f9edcf7a39390b6a84bd2832495f17fa3367065168760a0deaf
diff --git a/sci-libs/fast5/fast5-0.6.4.ebuild b/sci-libs/fast5/fast5-0.6.4.ebuild
deleted file mode 100644
index 181c2e593..000000000
--- a/sci-libs/fast5/fast5-0.6.4.ebuild
+++ /dev/null
@@ -1,42 +0,0 @@
-# Copyright 1999-2018 Gentoo Foundation
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=6
-
-PYTHON_COMPAT=( python{2_7,3_4} )
-
-inherit distutils-r1 multilib
-
-DESCRIPTION="C++ header-only library for reading Oxford Nanopore Fast5 files"
-HOMEPAGE="https://github.com/mateidavid/fast5"
-SRC_URI="https://github.com/mateidavid/fast5/archive/v${PV}.tar.gz -> ${P}.tar.gz"
-
-LICENSE="MIT"
-SLOT="0"
-KEYWORDS="" # the install step is broken (python modules integration, upstream binary code)
-IUSE=""
-
-DEPEND="
-	dev-python/cython[${PYTHON_USEDEP}]
-	sci-libs/hdf5"
-# TODO: more deps
-# https://github.com/mateidavid/tclap.git
-# https://github.com/mateidavid/hpptools.git
-RDEPEND="${DEPEND}"
-
-src_compile(){
-	emake -C python develop-user HDF5_DIR="${EPREFIX}"/usr HDF5_LIB_DIR="${EPREFIX}"/usr/$(get_libdir)
-}
-
-src_install(){
-	dobin src/hufftk
-	insinto /usr/include
-	doins src/*.hpp
-	dobin python/bin/* # bindled binaries
-	dolib python/fast5.so # bundled library
-}
-
-python_install_all() {
-	cd python || die
-	distutils-r1_src_install_all
-}
diff --git a/sci-libs/fast5/fast5-9999.ebuild b/sci-libs/fast5/fast5-9999.ebuild
deleted file mode 100644
index 6574116c5..000000000
--- a/sci-libs/fast5/fast5-9999.ebuild
+++ /dev/null
@@ -1,28 +0,0 @@
-# Copyright 1999-2018 Gentoo Foundation
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=6
-
-PYTHON_COMPAT=( python{2_7,3_4} )
-
-inherit distutils-r1 multilib git-r3
-
-DESCRIPTION="C++ header-only library for reading Oxford Nanopore Fast5 files"
-HOMEPAGE="https://github.com/mateidavid/fast5"
-EGIT_REPO_URI="https://github.com/mateidavid/fast5.git"
-
-LICENSE="MIT"
-SLOT="0"
-KEYWORDS=""
-IUSE=""
-
-DEPEND="
-	dev-python/cython[${PYTHON_USEDEP}]
-	sci-libs/hdf5"
-RDEPEND="${DEPEND}"
-
-src_compile(){
-	emake -C python develop-user HDF5_DIR="${EPREFIX}"/usr HDF5_LIB_DIR="${EPREFIX}"/usr/$(get_libdir)
-}
-
-# BUG: python stuff and binaries get installed into "${IMAGEDIR}"/homedir/.local/
diff --git a/sci-libs/fast5/metadata.xml b/sci-libs/fast5/metadata.xml
deleted file mode 100644
index 138cb7705..000000000
--- a/sci-libs/fast5/metadata.xml
+++ /dev/null
@@ -1,12 +0,0 @@
-<?xml version="1.0" encoding="UTF-8"?>
-<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
-<pkgmetadata>
-	<maintainer type="person">
-		<email>mmokrejs@fold.natur.cuni.cz</email>
-		<name>Martin Mokrejs</name>
-	</maintainer>
-	<maintainer type="project">
-		<email>sci-biology@gentoo.org</email>
-		<name>Gentoo Biology Project</name>
-	</maintainer>
-</pkgmetadata>
diff --git a/sci-libs/fdlibm/Manifest b/sci-libs/fdlibm/Manifest
index 10f436f11..56e946d61 100644
--- a/sci-libs/fdlibm/Manifest
+++ b/sci-libs/fdlibm/Manifest
@@ -1 +1 @@
-DIST fdlibm-5.3.tar.bz2 61723 BLAKE2B f7614b8fcf26d5237515a9a762473c228214338c72ee29a8ba270cc025d648a1a5105e5ad4c86906fbb2a857d7830646d3adbf5473e675c52766067767ed4202 SHA512 f7db65681c6bfb8d7bbf61f505ec2ddfbbb9dbdd3badbf1100dd70427c20c8916a5981ae2e1d59ab290ac0f2eeb992e14f89d5685e55b045377bbcdf0f09da03
+DIST fdlibm-5.3.1.tar.gz 76046 BLAKE2B 13d7a47d4845f572ffc0abc5abbfd19be2f14e08fe7aa284eec1ad527fb92708413bc0fd4bc328b38ead0a79bd8e7b8c3e933a537aed81b2e174a4cb8f7e523d SHA512 13cdcec6d7a8d22b3233586809aade41e354a254eac53742ac192f62aa75219faaa6c9a6973de48049b072e966f5fe353181e9579e254913417752d86f8cfc6c
diff --git a/sci-libs/fdlibm/fdlibm-5.3.1.ebuild b/sci-libs/fdlibm/fdlibm-5.3.1.ebuild
new file mode 100644
index 000000000..d03ecb7fc
--- /dev/null
+++ b/sci-libs/fdlibm/fdlibm-5.3.1.ebuild
@@ -0,0 +1,28 @@
+# Copyright 1999-2021 Gentoo Authors
+# Distributed under the terms of the GNU General Public License v2
+
+EAPI=7
+
+inherit cmake
+
+DESCRIPTION="C math library supporting IEEE 754 floating-point arithmetic"
+HOMEPAGE="https://www.netlib.org/fdlibm"
+SRC_URI="https://github.com/batlogic/fdlibm/archive/v${PV}.tar.gz -> ${P}.tar.gz"
+
+LICENSE="freedist"
+SLOT="0"
+KEYWORDS="~amd64 ~x86 ~amd64-linux ~x86-linux"
+
+PATCHES=(
+	"${FILESDIR}/${PN}-no-Werror.patch"
+)
+
+src_prepare() {
+	mv CMakelists.txt CMakeLists.txt || die
+	cmake_src_prepare
+}
+
+src_install() {
+	cmake_src_install
+	mv "${ED}/usr/lib" "${ED}/usr/$(get_libdir)" || die
+}
diff --git a/sci-libs/fdlibm/fdlibm-5.3.ebuild b/sci-libs/fdlibm/fdlibm-5.3.ebuild
deleted file mode 100644
index 4876249fc..000000000
--- a/sci-libs/fdlibm/fdlibm-5.3.ebuild
+++ /dev/null
@@ -1,57 +0,0 @@
-# Copyright 1999-2015 Gentoo Foundation
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=5
-
-inherit toolchain-funcs flag-o-matic versionator multilib
-
-DESCRIPTION="C math library supporting IEEE 754 floating-point arithmetic"
-HOMEPAGE="http://www.netlib.org/fdlibm"
-SRC_URI="http://dev.gentoo.org/~bicatali/distfiles/${P}.tar.bz2"
-
-LICENSE="freedist"
-SLOT="0"
-KEYWORDS="~amd64 ~x86 ~amd64-linux ~x86-linux"
-IUSE="static-libs"
-
-static_to_shared() {
-	local libstatic=${1}; shift
-	local libname=$(basename ${libstatic%.a})
-	local soname=${libname}$(get_libname $(get_version_component_range 1-2))
-	local libdir=$(dirname ${libstatic})
-
-	einfo "Making ${soname} from ${libstatic}"
-	if [[ ${CHOST} == *-darwin* ]] ; then
-		${LINK:-$(tc-getCC)} ${LDFLAGS}  \
-			-dynamiclib -install_name "${EPREFIX}"/usr/lib/"${soname}" \
-			-Wl,-all_load -Wl,${libstatic} \
-			"$@" -o ${libdir}/${soname} || die "${soname} failed"
-	else
-		${LINK:-$(tc-getCC)} ${LDFLAGS}  \
-			-shared -Wl,-soname=${soname} \
-			-Wl,--whole-archive ${libstatic} -Wl,--no-whole-archive \
-			"$@" -o ${libdir}/${soname} || die "${soname} failed"
-		[[ $(get_version_component_count) -gt 1 ]] && \
-			ln -s ${soname} ${libdir}/${libname}$(get_libname $(get_major_version)) || die
-		ln -s ${soname} ${libdir}/${libname}$(get_libname) || die
-	fi
-}
-
-src_compile() {
-	append-cflags -D_IEEE_LIBM
-	emake CFLAGS="${CFLAGS} -fPIC" CC=$(tc-getCC)
-	mv libm.a lib${PN}.a || die
-	static_to_shared lib${PN}.a
-	if use static-libs; then
-		rm -f *.o || die
-		emake CFLAGS="${CFLAGS}" CC=$(tc-getCC)
-		mv libm.a lib${PN}.a || die
-	fi
-}
-
-src_install() {
-	dolib.so lib${PN}$(get_libname)*
-	use static-libs && dolib.a lib${PN}.a
-	doheader fdlibm.h
-	dodoc readme
-}
diff --git a/sci-libs/fdlibm/files/fdlibm-no-Werror.patch b/sci-libs/fdlibm/files/fdlibm-no-Werror.patch
new file mode 100644
index 000000000..30c935ce7
--- /dev/null
+++ b/sci-libs/fdlibm/files/fdlibm-no-Werror.patch
@@ -0,0 +1,25 @@
+diff --git a/CMakeLists.txt b/CMakeLists.txt
+index 74bd751..e9d6912 100644
+--- a/CMakeLists.txt
++++ b/CMakeLists.txt
+@@ -1,20 +1,6 @@
+ cmake_minimum_required(VERSION 3.10)
+ project (fdlibm)
+ 
+-#need to change optimization level to O1 in visual studio
+-#so intrinsics aren't included
+-if(MSVC)
+-    add_compile_options("/W4" "$<$<CONFIG:RELEASE>:/O1>")
+-else()
+-    add_compile_options("-Wall" "-Wextra" "-Werror" "$<$<CONFIG:RELEASE>:-O3>")
+-    if("${CMAKE_CXX_COMPILER_ID}" STREQUAL "Clang")
+-        add_compile_options("-stdlib=libc++")
+-    else()
+-        # nothing special for gcc at the moment
+-    endif()
+-endif()
+-
+-
+ #
+ #extlib - javascript
+ #
diff --git a/sci-libs/fgsl/Manifest b/sci-libs/fgsl/Manifest
index 3f939f5ef..f9433e48e 100644
--- a/sci-libs/fgsl/Manifest
+++ b/sci-libs/fgsl/Manifest
@@ -1 +1 @@
-DIST fgsl-0.9.4.tar.gz 999825 BLAKE2B cc30d69d5a52af02f0aad6a5ea11d5b38e42072a8c7ecc5259bca80ccd2711d225800ce2d085d174c7b7e78688536c96b21b1d6e17987b1009ab482d27b57afb SHA512 45186a17d2b7e46968a29e99cbb1c7bb4cb22c14b322337e0166ee2e05e6bd63f709d6da566c30e7b350231dff268e65908e542288bdec7ca88ff1cb505eae3e
+DIST fgsl-1.3.0.tar.gz 1756037 BLAKE2B 62cd7df4dd1a73bb24bedb2fe450f4ff147eccfdaa1832778e82083adf0ccf64c1241deb4d44b9d34d19dfd0739c0648ce974a7d0dae03d279fcd0256ff9b43b SHA512 2b13d873a260d6d94d6b0adabf8cd095dc30c458e3cdd86e5f7797aa03959034ef4a9f721221623a0903948ebd0f4e811bf6c1fbe4f82b8319a9517489bb9ad4
diff --git a/sci-libs/fgsl/fgsl-0.9.4.ebuild b/sci-libs/fgsl/fgsl-0.9.4.ebuild
deleted file mode 100644
index dc4dc2adf..000000000
--- a/sci-libs/fgsl/fgsl-0.9.4.ebuild
+++ /dev/null
@@ -1,60 +0,0 @@
-# Copyright 1999-2015 Gentoo Foundation
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=5
-
-inherit eutils fortran-2 multilib toolchain-funcs
-
-DESCRIPTION="A Fortran interface to the GNU Scientific Library"
-HOMEPAGE="http://www.lrz.de/services/software/mathematik/gsl/fortran/"
-SRC_URI="http://www.lrz.de/services/software/mathematik/gsl/fortran/${P}.tar.gz"
-
-LICENSE="GPL-2"
-SLOT="0"
-KEYWORDS="~amd64 ~amd64-linux"
-IUSE="static-libs"
-
-RDEPEND=">=sci-libs/gsl-1.14"
-DEPEND="${RDEPEND}
-	virtual/pkgconfig"
-#TODO: make docs
-
-FORTRAN_STANDARD=90
-
-src_prepare() {
-	epatch "${FILESDIR}"/${PN}-0.9.3-sharedlibs.patch
-	if use amd64; then
-		ln -s interface/integer_ilp64.finc integer.finc || die
-	elif use x86; then
-		ln -s interface/integer_ilp32.finc integer.finc || die
-	else
-		die "Don't know who you are"
-	fi
-
-	cat <<- EOF > "${S}/make.inc"
-		F90 = $(tc-getFC)
-		CC = $(tc-getCC)
-		GSL_LIB = $($(tc-getPKG_CONFIG) --libs gsl)
-		GSL_INC = $($(tc-getPKG_CONFIG) --cflags gsl)
-		PREFIX = /usr
-		ARFLAGS = -csrv
-		FPP = -cpp
-		LIB = $(get_libdir)
-	EOF
-
-	use static-libs && echo "STATIC_LIBS = yes" >> "${S}/make.inc"
-}
-
-src_configure() {
-:
-}
-
-src_install() {
-	dodoc NEWS README
-	ln -s lib${PN}.so.0.0.0 lib${PN}.so.0 || die
-	ln -s lib${PN}.so.0.0.0 lib${PN}.so || die
-	dolib.so lib${PN}.so*
-	doheader ${PN}.mod
-	use static-libs && \
-		newlib.a lib${PN}_$(tc-getFC).a lib${PN}.a
-}
diff --git a/sci-libs/fgsl/fgsl-1.3.0.ebuild b/sci-libs/fgsl/fgsl-1.3.0.ebuild
new file mode 100644
index 000000000..01c415ad2
--- /dev/null
+++ b/sci-libs/fgsl/fgsl-1.3.0.ebuild
@@ -0,0 +1,37 @@
+# Copyright 1999-2021 Gentoo Authors
+# Distributed under the terms of the GNU General Public License v2
+
+EAPI=7
+
+DOCS_BUILDER="doxygen"
+DOCS_DEPEND="media-gfx/graphviz"
+
+inherit docs fortran-2
+
+DESCRIPTION="A Fortran interface to the GNU Scientific Library"
+HOMEPAGE="https://doku.lrz.de/display/PUBLIC/FGSL+-+A+Fortran+interface+to+the+GNU+Scientific+Library/"
+SRC_URI="https://doku.lrz.de/download/attachments/43321199/${P}.tar.gz"
+
+LICENSE="GPL-2+"
+SLOT="0"
+KEYWORDS="~amd64 ~amd64-linux"
+IUSE="static-libs"
+
+RDEPEND=">=sci-libs/gsl-2.4"
+DEPEND="${RDEPEND}"
+BDEPEDN="virtual/pkgconfig"
+
+FORTRAN_STANDARD=90
+
+DOCS=( NEWS README )
+
+src_compile() {
+	# With -j higher than 1 we get file not found errors
+	emake -j1
+	docs_compile
+}
+
+src_install() {
+	default
+	mv "${ED}/usr/share/doc/fgsl" "${ED}/usr/share/doc/${PF}" || die
+}
diff --git a/sci-libs/fgsl/files/fgsl-0.9.3-sharedlibs.patch b/sci-libs/fgsl/files/fgsl-0.9.3-sharedlibs.patch
deleted file mode 100644
index 401d75098..000000000
--- a/sci-libs/fgsl/files/fgsl-0.9.3-sharedlibs.patch
+++ /dev/null
@@ -1,27 +0,0 @@
---- Makefile.orig	2010-05-01 23:35:17.000000000 +0200
-+++ Makefile	2010-08-17 10:15:38.117694977 +0200
-@@ -14,7 +14,23 @@
- 	@cd tests; $(MAKE) clean; $(MAKE) -j 8 run
- 
- 
--lib : libfgsl_$(F90).a 
-+ifeq ($(STATIC_LIBS),)
-+lib : libfgsl.so.0.0.0
-+else
-+lib : libfgsl_$(F90).a libfgsl.so.0.0.0
-+endif
-+
-+libfgsl.so.0.0.0: fgsl.lo fgsl_utils.lo
-+	$(F90) -shared $(LDFLAGS) -Wl,-soname,libfgsl.so.0 -o $@ $^ $(GSL_LIB)
-+
-+fgsl.lo : fgsl.f90 api/*.finc interface/*.finc
-+	$(F90) -fPIC $(FFLAGS) $(DEBUG) -c  fgsl.f90 -o $@
-+
-+%.lo: %.f90
-+	$(F90) -fPIC $(FFLAGS) $(DEBUG) -c -o $@ $^
-+
-+%.lo: %.c
-+	$(CC) -fPIC -c $(GSL_INC) $(CFLAGS) $(CDEBUG) -o $@ $^
- 
- libfgsl_$(F90).a : fgsl.o fgsl_utils.o
- 	ar $(ARFLAGS) libfgsl_$(F90).a $^
diff --git a/sci-libs/fgsl/metadata.xml b/sci-libs/fgsl/metadata.xml
index 51d30f204..4aad8620d 100644
--- a/sci-libs/fgsl/metadata.xml
+++ b/sci-libs/fgsl/metadata.xml
@@ -9,5 +9,4 @@
 		<email>sci@gentoo.org</email>
 		<name>Gentoo Science Project</name>
 	</maintainer>
-	<longdescription>FGSL: A Fortran interface to the GNU Scientific Library</longdescription>
 </pkgmetadata>
diff --git a/sci-libs/fox/Manifest b/sci-libs/fox/Manifest
index f7d246555..24834d5f8 100644
--- a/sci-libs/fox/Manifest
+++ b/sci-libs/fox/Manifest
@@ -1,5 +1,5 @@
 DIST FoX-4.1.2-dom.tar.gz 225371 BLAKE2B 7c04239ed22b8a4efa6e8c1ce1ede46c2bee4a114ce7f05c05b9af18533b60932fbc8f1eb14d04f16fe4268ab81aa588d8af4a4bee1ac4ca92e06647761034c2 SHA512 de846d40ad442d2fff33dda17793f7334a87065d760920f17605926d4f91624cb134515b6c77392aa77a17532275e256301bdefa157eecbb0c13887bcaa7fe4c
-DIST FoX-4.1.2-full.tar.gz 1025375 SHA256 99f660a3d3cf9b9eb50e36d67dac3b80cfac92473462c3d6f3b340ba8d7c9b24 SHA512 bfd994768f4b8067cf2859949d51723c851521c444ba6a342901ae5e6ae86ed2832d59eac5f29048e1c2e5b27af6d1be4e7f026062832d650d894a865f1827c1 WHIRLPOOL 4f665380ae0e3c69efa5b9448d32d866efda6fa6e853bf1016088c45f704cafaa389cf0342041d0e07461ea32622fe967f3626668e153b316f2b162e08f0195d
+DIST FoX-4.1.2-full.tar.gz 1025375 BLAKE2B bd0b27396d4871add2324ed8b0b40b39fee9f6770f49b05f1987c0091de5a78b5fd40bc0a31206da6edce6475fd3b1b9039fc5e006fec40b84b5b445ac325e03 SHA512 bfd994768f4b8067cf2859949d51723c851521c444ba6a342901ae5e6ae86ed2832d59eac5f29048e1c2e5b27af6d1be4e7f026062832d650d894a865f1827c1
 DIST FoX-4.1.2-sax.tar.gz 164451 BLAKE2B 68ea97172c504694aab2f5d16dd9a1968350d4e0071ba3dc1570764ee1b2943d8fc799ac926ec27b3b1b721848a08a4ce5020325ba68381cd4190867848dc8a8 SHA512 7391ed23c70b52cd4155da0fbef60fda8a628e682b93b9340478d0a7bef0e9bd0016610fb45141b54063c001a5031baeb8ec66239e5b763cdc226fb5680f3de2
 DIST FoX-4.1.2-wcml.tar.gz 163504 BLAKE2B 968ad348268315f521dee7d8e3621d6bff1bdc2539010e70b9560bf00f52c25ee4a26d2559d0be187f53bc66814783f21744388d3d0d5237697903b884f919f0 SHA512 32a1bea6e52926958ec7ca24256dd824bf97f84ae1ce691d01d607b4f7fc4e1c811ead36a9f1260aa4696aeba964d9b3db1673a011b5a8f1d1b9c96590be8ffb
 DIST FoX-4.1.2-wkml.tar.gz 207539 BLAKE2B 7f59bc87249d827efa804cfc6f84e11bb63d7d61805e9ac020b57d61982e10b27f1e35b5478a2788245c95989738f1e7c92cf2310c1eb2b3082aedcfd4db7151 SHA512 1f3e0f2750e8a500e4c8c1d6f03f8a52615cea1448c69d35750ea8bd06bdcb02ac136a34ba1af07a363dfe018cf6bf28e54f7ce19e6d06cc554391219525f1f3
diff --git a/sci-libs/fox/files/4.1.2-r2-install-customizations.patch b/sci-libs/fox/files/4.1.2-r2-install-customizations.patch
index 15bb837f0..901a14042 100644
--- a/sci-libs/fox/files/4.1.2-r2-install-customizations.patch
+++ b/sci-libs/fox/files/4.1.2-r2-install-customizations.patch
@@ -1,6 +1,6 @@
-diff -Naur tmp-old/Makefile tmp-new/Makefile
---- Makefile	2009-03-07 22:44:12.000000000 +0000
-+++ Makefile	2009-03-07 22:42:59.000000000 +0000
+diff -Naur a/Makefile b/Makefile
+--- a/Makefile	2009-03-07 22:44:12.000000000 +0000
++++ b/Makefile	2009-03-07 22:42:59.000000000 +0000
 @@ -9,9 +9,9 @@
  	mkdir -p objs/lib objs/finclude
  #
@@ -14,8 +14,8 @@ diff -Naur tmp-old/Makefile tmp-new/Makefile
  #
  examples_build:
 diff -Naur tmp-old/arch.make.in tmp-new/arch.make.in
---- arch.make.in	2009-03-07 22:44:19.000000000 +0000
-+++ arch.make.in	2009-03-07 22:43:07.000000000 +0000
+--- a/arch.make.in	2009-03-07 22:44:19.000000000 +0000
++++ b/arch.make.in	2009-03-07 22:43:07.000000000 +0000
 @@ -5,7 +5,7 @@
  
  VPATH=@VPATH@
diff --git a/sci-libs/fox/fox-4.1.2-r2.ebuild b/sci-libs/fox/fox-4.1.2-r2.ebuild
index 64518b4ce..a8900c153 100644
--- a/sci-libs/fox/fox-4.1.2-r2.ebuild
+++ b/sci-libs/fox/fox-4.1.2-r2.ebuild
@@ -1,37 +1,38 @@
-# Copyright 1999-2014 Gentoo Foundation
+# Copyright 1999-2021 Gentoo Authors
 # Distributed under the terms of the GNU General Public License v2
 
-EAPI=5
+EAPI=7
 
-inherit eutils
+inherit fortran-2
 
 MY_PN="FoX"
 MY_P="${MY_PN}-${PV}"
 
 DESCRIPTION="A library designed to allow the easy use of XML from Fortran"
-HOMEPAGE="http://www1.gly.bris.ac.uk/~walker/FoX/"
+HOMEPAGE="https://homepages.see.leeds.ac.uk/~earawa/FoX//"
 
 LICENSE="BSD ZLIB"
 SLOT="0"
 KEYWORDS="~amd64 ~x86 ~amd64-linux"
 IUSE="debug doc +dom +fast +sax +wcml +wkml +wxml"
 
-SRC_URI=" doc? ( http://www1.gly.bris.ac.uk/~walker/FoX/source/${MY_P}-full.tar.gz )
+SRC_URI="
+	doc? ( http://www1.gly.bris.ac.uk/~walker/FoX/source/${MY_P}-full.tar.gz )
 	!doc? ( http://www1.gly.bris.ac.uk/~walker/FoX/source/${MY_P}.tar.gz
 		dom? ( http://www1.gly.bris.ac.uk/~walker/FoX/source/${MY_P}-dom.tar.gz )
 		sax? ( http://www1.gly.bris.ac.uk/~walker/FoX/source/${MY_P}-sax.tar.gz )
 		wcml? ( http://www1.gly.bris.ac.uk/~walker/FoX/source/${MY_P}-wcml.tar.gz )
 		wkml? ( http://www1.gly.bris.ac.uk/~walker/FoX/source/${MY_P}-wkml.tar.gz )
-		wxml? ( http://www1.gly.bris.ac.uk/~walker/FoX/source/${MY_P}-wxml.tar.gz ) )"
+		wxml? ( http://www1.gly.bris.ac.uk/~walker/FoX/source/${MY_P}-wxml.tar.gz ) )
+"
 
 S="${WORKDIR}/${MY_P}"
 
 FORTRAN_STANDARD=90
 
-src_prepare() {
-	epatch "${FILESDIR}"/4.1.2-r2-install-customizations.patch
-}
-
+PATCHES=(
+	"${FILESDIR}"/4.1.2-r2-install-customizations.patch
+)
 src_configure() {
 		econf --prefix="${EPREFIX}/usr" \
 		$(use_enable debug) \
@@ -63,6 +64,6 @@ src_install() {
 	dodoc README.FoX.txt
 	if use doc; then
 		dodoc Changelog
-		dohtml -r DoX/
+		dodoc -r DoX/
 	fi
 }
diff --git a/sci-libs/framewave/Manifest b/sci-libs/framewave/Manifest
deleted file mode 100644
index 3b7f27aff..000000000
--- a/sci-libs/framewave/Manifest
+++ /dev/null
@@ -1 +0,0 @@
-DIST FRAMEWAVE_1.3.1_SRC.tar.gz 5405064 BLAKE2B 6db75eb0a2f606d4f96e67a44e4e967dd8b75449a600dd687650470af0dbc0ac6462a3e994531276d660f17b443e4d063da4366148a0d2037a56f729dfa3075a SHA512 3690fe59d0d19b613341751866c92a1288e548f4432ef5a4cc980b6337ba7ff870524ad680080e8156a636ee34a1df1e4b4ffaba35885c332b2254062a6b7e33
diff --git a/sci-libs/framewave/framewave-1.3.1.ebuild b/sci-libs/framewave/framewave-1.3.1.ebuild
deleted file mode 100644
index dd1056a95..000000000
--- a/sci-libs/framewave/framewave-1.3.1.ebuild
+++ /dev/null
@@ -1,47 +0,0 @@
-# Copyright 1999-2015 Gentoo Foundation
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=5
-
-inherit scons-utils
-
-MY_P="FRAMEWAVE_${PV}_SRC"
-
-DESCRIPTION="A collection of popular image and signal processing routines"
-HOMEPAGE="http://framewave.sourceforge.net/"
-SRC_URI="mirror://sourceforge/${PN}/${MY_P}.tar.gz"
-
-LICENSE="Apache-2.0"
-SLOT="0"
-KEYWORDS="~amd64 ~x86"
-IUSE=""
-
-RDEPEND=""
-DEPEND="dev-util/scons"
-
-S="${WORKDIR}/${MY_P}"
-
-src_prepare() {
-	sed -e "s#\(-install_name /usr\)/local/lib/\${BITNESS}#\1#" \
-		-i BuildTools/buildscripts/fwflags_gcc.py || die "sed failed"
-}
-
-src_compile() {
-	cd Framewave || die
-
-	local bits="32"
-	use amd64 && bits="64"
-
-	escons \
-		CCFLAGS="${CFLAGS}" bitness="${bits}" variant="release" \
-		libtype="shared" ${MAKEOPTS}|| die "make failed"
-}
-
-src_install() {
-	local bits="32"
-	use amd64 && bits="64"
-
-	dolib.so Framewave/build/bin/release_shared_${bits}/*.so*
-
-	doheader Framewave/build/include/*
-}
diff --git a/sci-libs/framewave/metadata.xml b/sci-libs/framewave/metadata.xml
deleted file mode 100644
index e22f8986c..000000000
--- a/sci-libs/framewave/metadata.xml
+++ /dev/null
@@ -1,16 +0,0 @@
-<?xml version="1.0" encoding="UTF-8"?>
-<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
-<pkgmetadata>
-	<maintainer type="project">
-		<email>sci@gentoo.org</email>
-		<name>Gentoo Science Project</name>
-	</maintainer>
-	<longdescription>Derived from the AMD Performance Library, Framewave is a
-free and open-source collection of popular image and signal processing
-routines designed to accelerate application development, debugging,
-multi-threading and optimization on x86-class processor platforms.
-</longdescription>
-	<upstream>
-		<remote-id type="sourceforge">framewave</remote-id>
-	</upstream>
-</pkgmetadata>
diff --git a/sci-libs/gdcm/Manifest b/sci-libs/gdcm/Manifest
new file mode 100644
index 000000000..64b9caefd
--- /dev/null
+++ b/sci-libs/gdcm/Manifest
@@ -0,0 +1,2 @@
+DIST gdcm-3.0.14.tar.bz2 2992355 BLAKE2B a97209a8bb6896095bfc59ac974b667386c8711f20118252567cf983f15165d259da7858ccfd6bfdfbb25194d7687c98512953b480913acec4bf6d176af7a005 SHA512 9c7d70723d288bf116a8b594c02dd965a4e80476e1c79a7c3cbd09584a229c83ad67f082c9b286305e3bb64150c8267ced06b5fb963adbeeb36e383f76612220
+DIST gdcmData.tar.gz 121157465 BLAKE2B 19b13efc2094d3e373f0f658f1120b1c83ea6da1be73fb392b815433725b4a6db2debb9ab7d9f2caa665637f152f70694cdf226c934850dfda344107050a14a6 SHA512 ddc67a7a0b41b2d6e1e03defb6fb8a06ceeb2e9dd9bb47dfa4f7283d79df7c1e52577b799c00e930719ae6cdda46bded9497a67b8241359f238f5366085ec9ee
diff --git a/sci-libs/gdcm/files/gdcm-3.0.14-include-math-h.patch b/sci-libs/gdcm/files/gdcm-3.0.14-include-math-h.patch
new file mode 100644
index 000000000..ba99c3547
--- /dev/null
+++ b/sci-libs/gdcm/files/gdcm-3.0.14-include-math-h.patch
@@ -0,0 +1,15 @@
+https://cgit.freebsd.org/ports/plain/devel/gdcm/files/patch-Utilities_VTK_vtkImageMapToWindowLevelColors2.cxx?id=8f5541298099b722e34632ca9ed388bda91064e7
+
+- workaround for https://sourceforge.net/p/gdcm/bugs/536/
+
+--- a/Utilities/VTK/vtkImageMapToWindowLevelColors2.cxx	2022-06-26 20:39:45 UTC
++++ b/Utilities/VTK/vtkImageMapToWindowLevelColors2.cxx
+@@ -37,6 +37,8 @@
+ #include "vtkScalarsToColors.h"
+ #include "vtkPointData.h"
+ 
++#include <math.h>
++
+ //vtkCxxRevisionMacro(vtkImageMapToWindowLevelColors2, "$Revision: 1.3 $")
+ vtkStandardNewMacro(vtkImageMapToWindowLevelColors2)
+ 
diff --git a/sci-libs/gdcm/files/gdcm_support_vtk9.patch b/sci-libs/gdcm/files/gdcm_support_vtk9.patch
new file mode 100644
index 000000000..3818a82b5
--- /dev/null
+++ b/sci-libs/gdcm/files/gdcm_support_vtk9.patch
@@ -0,0 +1,70 @@
+--- a/Utilities/VTK/CMakeLists.txt
++++ b/Utilities/VTK/CMakeLists.txt
+@@ -26,6 +26,11 @@
+   )
+ endif()
+ 
++if( ${VTK_MAJOR_VERSION} GREATER_EQUAL 9 )
++  set(VTK_INCLUDE_DIRS "${VTK_PREFIX_PATH}/include/vtk-${VTK_MAJOR_VERSION}.${VTK_MINOR_VERSION}")
++  include_directories(AFTER ${VTK_INCLUDE_DIRS})
++endif()
++
+ include(CheckCXXSourceCompiles)
+ set(CMAKE_REQUIRED_INCLUDES ${VTK_INCLUDE_DIRS})
+ CHECK_CXX_SOURCE_COMPILES(
+@@ -94,6 +99,10 @@
+   endforeach()
+ endif()
+ 
++if( ${VTK_MAJOR_VERSION} GREATER_EQUAL 9 )
++  string(REGEX REPLACE "vtk([^;]+)" "VTK::\\1" vtkgdcm_LIBS "${vtkgdcm_LIBS}")
++endif()
++
+ # Use wrapping hints for this project.
+ #set(VTK_WRAP_HINTS "${PROJECT_SOURCE_DIR}/hints")
+ 
+--- a/Utilities/VTK/Applications/CMakeLists.txt
++++ b/Utilities/VTK/Applications/CMakeLists.txt
+@@ -25,6 +25,11 @@
+     )
+ endif()
+ 
++set(vtk_ioxml vtkIOXML)
++if( ${VTK_MAJOR_VERSION} GREATER_EQUAL 9 )
++  set(vtk_ioxml VTK::IOXML)
++endif()
++
+ foreach(app ${GDCM_VTK_APPS})
+   add_executable(${app} ${app}.cxx)
+   if(GDCM_EXECUTABLE_PROPERTIES)
+@@ -42,7 +47,7 @@
+     endif()
+   else()
+     # >= 6.0
+-    target_link_libraries(${app} ${VTK_LIBRARIES} vtkIOXML)
++    target_link_libraries(${app} ${VTK_LIBRARIES} ${vtk_ioxml})
+   endif()
+   if(WIN32 AND NOT CYGWIN)
+     target_link_libraries(${app} gdcmgetopt)
+--- a/Utilities/VTK/vtkGDCMPolyDataWriter.cxx
++++ b/Utilities/VTK/vtkGDCMPolyDataWriter.cxx
+@@ -496,6 +496,9 @@
+   sqi = new SequenceOfItems;
+ 
+   vtkIdType npts = 0;
++#if VTK_MAJOR_VERSION >= 9
++  const
++#endif
+   vtkIdType *indx = 0;
+   double v[3];
+   unsigned int cellnum = 0;
+@@ -759,6 +762,9 @@
+     vtkPoints *pts;
+     vtkCellArray *polys;
+     vtkIdType npts = 0;
++#if VTK_MAJOR_VERSION >= 9
++  const
++#endif
+     vtkIdType *indx = 0;
+     pts = theData->GetPoints();
+     polys = theData->GetPolys();
diff --git a/sci-libs/gdcm/gdcm-3.0.14.ebuild b/sci-libs/gdcm/gdcm-3.0.14.ebuild
new file mode 100644
index 000000000..467fa623c
--- /dev/null
+++ b/sci-libs/gdcm/gdcm-3.0.14.ebuild
@@ -0,0 +1,121 @@
+# Copyright 2022 Gentoo Authors
+# Distributed under the terms of the GNU General Public License v2
+
+EAPI=8
+
+PYTHON_COMPAT=( python3_10 )
+
+inherit cmake python-single-r1
+
+DESCRIPTION="Cross-platform DICOM implementation"
+HOMEPAGE="http://gdcm.sourceforge.net/"
+SRC_URI="https://downloads.sourceforge.net/gdcm/${P}.tar.bz2
+	test? ( https://downloads.sourceforge.net/gdcm/gdcmData.tar.gz )" # 3.0.14: .bz2 is broken, should be checked in next release
+
+LICENSE="BSD"
+SLOT="0"
+KEYWORDS="~amd64 ~x86"
+IUSE="doc python test vtk"
+RESTRICT="!test? ( test )"
+
+DEPEND="
+	app-text/poppler:0=[cxx]
+	dev-libs/expat:0=
+	dev-libs/json-c:0=
+	dev-libs/libxml2:2=
+	dev-libs/openssl:0=
+	>=media-libs/charls-2.0.0:0=
+	>=media-libs/openjpeg-2.0.0:2=
+	sys-apps/util-linux:0=
+	sys-libs/zlib:0=
+	python? ( ${PYTHON_DEPS} )
+	vtk? (
+		sci-libs/vtk[rendering]
+		python? (
+			sci-libs/vtk[python,${PYTHON_SINGLE_USEDEP}]
+		)
+	)
+"
+RDEPEND="${DEPEND}"
+BDEPEND="
+	dev-libs/libxslt
+	app-text/docbook-xsl-ns-stylesheets
+	doc? ( app-text/doxygen[dot] )
+	python? (
+		${PYTHON_DEPS}
+		>=dev-lang/swig-3.0.7
+	)"
+
+REQUIRED_USE="python? ( ${PYTHON_REQUIRED_USE} )"
+
+PATCHES=(
+	"${FILESDIR}/gdcm_support_vtk9.patch"
+	"${FILESDIR}/gdcm-3.0.14-include-math-h.patch"
+)
+
+pkg_setup() {
+	use python && python-single-r1_pkg_setup
+}
+
+src_prepare() {
+	# drop unbundled libs
+	local -a DROPS=( gdcmcharls gdcmexpat gdcmopenjpeg gdcmuuid gdcmzlib getopt pvrg KWStyle Release )
+	local x
+	for x in "${DROPS[@]}"; do
+		ebegin "Dropping bundled ${x#gdcm}"
+		rm -r "Utilities/${x}" || die
+		sed -i "s,^[ \t]*APPEND_COPYRIGHT(\\\${CMAKE_CURRENT_SOURCE_DIR}/${x}/,#&," "Utilities/CMakeLists.txt" || die
+		eend $?
+	done
+	find Utilities -mindepth 1 -maxdepth 1 '!' -name doxygen '!' -name VTK -type d \
+		-exec ewarn "Using bundled" {} ';' || die
+
+	# fix charls include case
+	sed -i 's:CharLS/charls\.h:charls/charls.h:' CMake/FindCharLS.cmake Utilities/gdcm_charls.h || die
+	sed -i 's:NAMES CharLS:NAMES charls:' CMake/FindCharLS.cmake || die
+
+	# Use prefixed socket++ (to avoid potential conflicts)
+	sed -i '/target_link_libraries(/s/socketxx/gdcm&/' \
+		Source/MessageExchangeDefinition/CMakeLists.txt \
+		Applications/Cxx/CMakeLists.txt \
+		|| die
+
+	cmake_src_prepare
+}
+
+src_configure() {
+	local mycmakeargs=(
+		-DCMAKE_SKIP_RPATH=ON
+		-DGDCM_BUILD_SHARED_LIBS=ON
+		-DGDCM_DATA_ROOT="${WORKDIR}/gdcmData"
+		-DGDCM_INSTALL_LIB_DIR="$(get_libdir)"
+		-DGDCM_INSTALL_DOC_DIR="share/doc/${P}"
+		-DGDCM_INSTALL_PYTHONMODULE_DIR="lib/${EPYTHON}/site-packages"
+		-DGDCM_USE_SYSTEM_ZLIB=ON
+		-DGDCM_USE_SYSTEM_OPENSSL=ON
+		-DGDCM_USE_SYSTEM_UUID=ON
+		-DGDCM_USE_SYSTEM_EXPAT=ON
+		-DGDCM_USE_SYSTEM_JSON=ON
+		-DGDCM_USE_SYSTEM_PAPYRUS3=OFF
+		-DGDCM_USE_SYSTEM_SOCKETXX=OFF
+		-DSOCKETXX_NAMESPACE=GDCMSOCKETXX
+		-DGDCM_USE_SYSTEM_LJPEG=OFF
+		-DGDCM_USE_SYSTEM_OPENJPEG=ON
+		-DGDCM_USE_SYSTEM_CHARLS=ON
+		-DGDCM_USE_SYSTEM_POPPLER=ON
+		-DGDCM_USE_SYSTEM_LIBXML2=ON
+		-DGDCM_BUILD_TESTING=$(usex test)
+		-DGDCM_WRAP_PYTHON=$(usex python)
+		$(usex python "-DGDCM_DEFAULT_PYTHON_VERSION=${EPYTHON#python}" "")
+		-DGDCM_WRAP_PERL=OFF
+		-DGDCM_WRAP_PHP=OFF
+		-DGDCM_WRAP_JAVA=OFF
+		-DGDCM_WRAP_CSHARP=OFF
+		-DGDCM_DOCUMENTATION=$(usex doc)
+		$(usex doc "-DGDCM_PDF_DOCUMENTATION=OFF" "")
+		-DGDCM_BUILD_EXAMPLES=OFF
+		-DGDCM_BUILD_APPLICATIONS=ON
+		-DGDCM_USE_VTK=$(usex vtk)
+	)
+	cmake_src_configure
+}
diff --git a/sci-libs/gdcm/metadata.xml b/sci-libs/gdcm/metadata.xml
new file mode 100644
index 000000000..1845bf1bd
--- /dev/null
+++ b/sci-libs/gdcm/metadata.xml
@@ -0,0 +1,14 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<!DOCTYPE pkgmetadata SYSTEM "https://www.gentoo.org/dtd/metadata.dtd">
+<pkgmetadata>
+	<maintainer type="person">
+		<email>fx.carton91@gmail.com</email>
+		<name>François-Xavier Carton</name>
+	</maintainer>
+	<use>
+		<flag name="vtk">Build <pkg>sci-libs/vtk</pkg> bridge</flag>
+	</use>
+	<upstream>
+		<remote-id type="sourceforge">gdcm</remote-id>
+	</upstream>
+</pkgmetadata>
diff --git a/sci-libs/geom/Manifest b/sci-libs/geom/Manifest
deleted file mode 100644
index 4ba17bc04..000000000
--- a/sci-libs/geom/Manifest
+++ /dev/null
@@ -1 +0,0 @@
-DIST geom-5.1.2.7.tar.gz 612914 BLAKE2B df4818b3fbd95914a6f78dd679bf725985a6e987c01b338abcd5e9f07b4aa7a3ff15e3bd82c6c01530adce6f0dba99174ec8d654e778145703240510bf527cca SHA512 06454a4a92959fa08f2e81d8e5fcfdb957a49cdf51bd5e7efd6895ab2d1aedbd99dfb30ddc4b278b10d125f9d2d66260eff584e670716c96e2d0ec10b169fb08
diff --git a/sci-libs/geom/geom-5.1.2.7.ebuild b/sci-libs/geom/geom-5.1.2.7.ebuild
deleted file mode 100644
index a739b1e34..000000000
--- a/sci-libs/geom/geom-5.1.2.7.ebuild
+++ /dev/null
@@ -1,39 +0,0 @@
-# Copyright 1999-2015 Gentoo Foundation
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=5
-
-inherit autotools eutils
-
-DESCRIPTION="A complete OpenCascade - OCAF based CAD framework"
-HOMEPAGE="http://sourceforge.net/projects/salomegeometry/"
-SRC_URI="mirror://sourceforge/salomegeometry/${P}.tar.gz"
-
-LICENSE="LGPL-2"
-SLOT="0"
-KEYWORDS="~amd64 ~x86"
-IUSE="doc"
-
-RDEPEND="sci-libs/opencascade:*"
-DEPEND="${RDEPEND}
-	doc? ( app-doc/doxygen )"
-
-S=${WORKDIR}/adm/lin/
-
-src_prepare() {
-	eautoreconf
-	ln -fs {../../src,../../inc,../../resources} . || die 'linking failed'
-}
-
-src_compile() {
-	default
-	if use doc ; then
-		cd ../../doc/src || die
-		doxygen || die 'doxygen failed'
-	fi
-}
-
-src_install() {
-	default
-	use doc && dohtml -r ../../doc/html/*
-}
diff --git a/sci-libs/geom/metadata.xml b/sci-libs/geom/metadata.xml
deleted file mode 100644
index 930d607dc..000000000
--- a/sci-libs/geom/metadata.xml
+++ /dev/null
@@ -1,13 +0,0 @@
-<?xml version="1.0" encoding="UTF-8"?>
-<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
-<pkgmetadata>
-	<maintainer type="project">
-		<email>sci@gentoo.org</email>
-		<name>Gentoo Science Project</name>
-	</maintainer>
-	<use>
-</use>
-	<upstream>
-		<remote-id type="sourceforge">salomegeometry</remote-id>
-	</upstream>
-</pkgmetadata>
diff --git a/sci-libs/ghmm/files/ghmm-9999-clapack.patch b/sci-libs/ghmm/files/ghmm-9999-clapack.patch
deleted file mode 100644
index d36cb2ab5..000000000
--- a/sci-libs/ghmm/files/ghmm-9999-clapack.patch
+++ /dev/null
@@ -1,11 +0,0 @@
---- ghmm/matrixop.c
-+++ ghmm/matrixop.c
-@@ -45,7 +45,7 @@
- #endif
- 
- #ifdef DO_WITH_ATLAS
--#include <clapack.h>
-+#include <clapack/clapack.h>
- #endif
- 
- /*============================================================================*/
diff --git a/sci-libs/ghmm/files/ghmm-9999-link.patch b/sci-libs/ghmm/files/ghmm-9999-link.patch
deleted file mode 100644
index 9b4e919ec..000000000
--- a/sci-libs/ghmm/files/ghmm-9999-link.patch
+++ /dev/null
@@ -1,24 +0,0 @@
-Index: tools/Makefile.am
-===================================================================
---- tools/Makefile.am	(revision 2332)
-+++ tools/Makefile.am	(working copy)
-@@ -23,5 +23,5 @@
- smix_hmm_SOURCES = smix_hmm.c
- smo2xml_SOURCES = smo2xml.c
- 
--LDADD = $(top_builddir)/ghmm/.libs/libghmm.a
-+LDADD = $(top_builddir)/ghmm/libghmm.la
- bin_SCRIPTS = ghmm-config
-Index: tests/Makefile.am
-===================================================================
---- tests/Makefile.am	(revision 2332)
-+++ tests/Makefile.am	(working copy)
-@@ -34,7 +34,7 @@
- 		  read_fa \
-                   mcmc
- 
--LDADD = $(top_builddir)/ghmm/.libs/libghmm.a
-+LDADD = $(top_builddir)/ghmm/libghmm.la
- 
- TESTS_ENVIRONMENT = GHMM_SILENT_TESTS
- TESTS =           root_finder_test \
diff --git a/sci-libs/ghmm/files/ghmm-9999-obsolete.patch b/sci-libs/ghmm/files/ghmm-9999-obsolete.patch
deleted file mode 100644
index 2e6be54d0..000000000
--- a/sci-libs/ghmm/files/ghmm-9999-obsolete.patch
+++ /dev/null
@@ -1,13 +0,0 @@
-Index: configure.in
-===================================================================
---- configure.in	(revision 2332)
-+++ configure.in	(working copy)
-@@ -293,7 +293,7 @@
- CFLAGS="$CFLAGS $LIBXML2_CFLAGS"
- 
- dnl final configuration
--SUBDIRS="ghmm tools tests"
-+SUBDIRS="ghmm"
- 
- dnl python wrapper can be switched on or off
- AC_ARG_WITH(python,
diff --git a/sci-libs/ghmm/files/ghmm-9999-out-of-source.patch b/sci-libs/ghmm/files/ghmm-9999-out-of-source.patch
deleted file mode 100644
index 6197d9ba1..000000000
--- a/sci-libs/ghmm/files/ghmm-9999-out-of-source.patch
+++ /dev/null
@@ -1,40 +0,0 @@
-Index: tools/Makefile.am
-===================================================================
---- tools/Makefile.am	(revision 2332)
-+++ tools/Makefile.am	(working copy)
-@@ -12,7 +12,7 @@
- MAINTAINERCLEANFILES = Makefile.in
- 
- BUILT_SOURCES = 
--INCLUDES = -I$(top_srcdir)
-+INCLUDES = -I$(top_srcdir) -I$(top_builddir)/ghmm
- 
- bin_PROGRAMS = probdist cluster scluster smix_hmm $(OBSOLETE_TOOLS)
- EXTRA_PROGRAMS = smo2xml
-Index: tests/Makefile.am
-===================================================================
---- tests/Makefile.am	(revision 2332)
-+++ tests/Makefile.am	(working copy)
-@@ -15,7 +15,7 @@
- MAINTAINERCLEANFILES = Makefile.in
- # stuff from dejagnu
- 
--INCLUDES=-I$(top_srcdir)
-+INCLUDES=-I$(top_srcdir) -I$(top_builddir)/ghmm
- 
- #these tests will not be installed
- # in progress: test_sdfoba nullmodel ciscreen test_sdmodel 
-Index: ghmmwrapper/Makefile.am
-===================================================================
---- ghmmwrapper/Makefile.am	(revision 2332)
-+++ ghmmwrapper/Makefile.am	(working copy)
-@@ -47,7 +47,9 @@
-                  testdata/model_label.xml \
-                  testdata/tiny.txt.sqd
- 
-+INCLUDES=-I$(top_builddir)
- 
-+
- EXTRA_DIST = ${SWIG_INTERFACE_FILES} ${EXTENSION_C_FILES} ${PYTHON_FILES} ${PYTHON_GATO_FILES} ${TESTDATA_FILES}
- 
- all: setup.py ghmm.py ${SWIG_INTERFACE_FILES}
diff --git a/sci-libs/ghmm/files/ghmm-9999-respect.patch b/sci-libs/ghmm/files/ghmm-9999-respect.patch
deleted file mode 100644
index cc70a0780..000000000
--- a/sci-libs/ghmm/files/ghmm-9999-respect.patch
+++ /dev/null
@@ -1,10 +0,0 @@
---- ghmmwrapper/setup.py
-+++ ghmmwrapper/setup.py
-@@ -48,7 +48,6 @@
-                                include_dirs = ['..'],
-                                library_dirs = ['../ghmm/.libs'],
-                                libraries = ['ghmm', 'm', 'pthread', 'xml2', 'z'],
--                               extra_compile_args = ["-O2", "-pipe", "-Wall"], # -g might help debugging
-                                depends = ['wrapper_alphabet.i', 'wrapper_bayes.i', 'wrapper_cmodel.i', 'wrapper_cseq.i',
-                                           'wrapper_dmodel.i', 'wrapper_dpmodel.i', 'wrapper_dpseq.i',
-                                           'wrapper_dseq.i', 'wrapper_xmlfile.i']
diff --git a/sci-libs/ghmm/ghmm-9999.ebuild b/sci-libs/ghmm/ghmm-9999.ebuild
deleted file mode 100644
index 012fc6499..000000000
--- a/sci-libs/ghmm/ghmm-9999.ebuild
+++ /dev/null
@@ -1,67 +0,0 @@
-# Copyright 1999-2015 Gentoo Foundation
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=5
-
-AUTOTOOLS_AUTORECONF=true
-
-PYTHON_COMPAT=( python2_7 )
-
-inherit autotools-utils distutils-r1 subversion
-
-DESCRIPTION="General Hidden Markov Model library"
-HOMEPAGE="http://ghmm.sourceforge.net/"
-SRC_URI=""
-ESVN_REPO_URI="https://ghmm.svn.sourceforge.net/svnroot/ghmm/trunk/ghmm"
-
-LICENSE="LGPL-2.1"
-SLOT="0"
-KEYWORDS=""
-IUSE="gsl lapack +python static-libs"
-
-RDEPEND="
-	dev-libs/libxml2
-	gsl? ( sci-libs/gsl )
-	lapack? (
-		sci-libs/clapack
-		virtual/lapack
-		)"
-DEPEND="${RDEPEND}"
-
-S="${WORKDIR}/${PN}"
-
-ESVN_BOOTSTRAP="autotools-utils_src_prepare"
-
-PATCHES=(
-	"${FILESDIR}"/${P}-clapack.patch
-	"${FILESDIR}"/${P}-out-of-source.patch
-	"${FILESDIR}"/${P}-link.patch
-	"${FILESDIR}"/${P}-respect.patch
-	"${FILESDIR}"/${P}-obsolete.patch
-)
-
-src_prepare() {
-	use python && AUTOTOOLS_IN_SOURCE_BUILD=1
-	autotools-utils_src_prepare
-	use python && cd "${S}"/ghmmwrapper && distutils-r1_python_prepare
-}
-
-src_configure() {
-	local myeconfargs=(
-		--without-python
-		--disable-obsolete
-		$(use_enable gsl)
-		$(use_enable lapack atlas)
-	)
-	autotools-utils_src_configure
-}
-
-src_compile() {
-	autotools-utils_src_compile
-	use python && cd "${S}"/ghmmwrapper && distutils-r1_src_compile
-}
-
-src_install() {
-	autotools-utils_src_install
-	use python && cd "${S}"/ghmmwrapper && distutils-r1_src_install
-}
diff --git a/sci-libs/ghmm/metadata.xml b/sci-libs/ghmm/metadata.xml
deleted file mode 100644
index 5fc8aa771..000000000
--- a/sci-libs/ghmm/metadata.xml
+++ /dev/null
@@ -1,11 +0,0 @@
-<?xml version="1.0" encoding="UTF-8"?>
-<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
-<pkgmetadata>
-	<maintainer type="project">
-		<email>sci@gentoo.org</email>
-		<name>Gentoo Science Project</name>
-	</maintainer>
-	<upstream>
-		<remote-id type="sourceforge">ghmm</remote-id>
-	</upstream>
-</pkgmetadata>
diff --git a/sci-libs/givaro/Manifest b/sci-libs/givaro/Manifest
deleted file mode 100644
index 7a839b1ef..000000000
--- a/sci-libs/givaro/Manifest
+++ /dev/null
@@ -1,3 +0,0 @@
-DIST givaro-3.2.13.tar.gz 601026 SHA256 cef5972a79038c7fdbbcc80c90917ed0b339614723e9cd12436b55358ef34eb0 SHA512 ba792f00003940aedadbea388ff652bc7df3472a9451a950c0818d5424e2656d479ee32a4cf40c2e91f3437c13882a0067040585f9744f309b77067360a267d7 WHIRLPOOL 6840ee4a39f3b2b1f464dd864128825cbfc6adc6b71bf62a81bb8fccc55ec21cfafee971e59be1e5026d22749f813547f73a412190fb5b68e8bd44533f9a1375
-DIST givaro-3.3.0.tar.gz 643288 SHA256 90677ee9af4a33f827dfce48359c2c419302dfb46227fb8cc16de23f18ac757e SHA512 0121917855989b31ce888280229e022fafcdb4f1da4411328d79accac3ce1f057805d4efa23798e3c888b3ddcdcbde8d6e841d415c6509ed4a299287482f5032 WHIRLPOOL ced6bc6ce47e767087feb993922f53e1e160bfa328f9ea12a5b715937bf6aa06ee876abf891f9055da434566642aabb5cd2317dcf302651ec239f65e2f170d53
-DIST givaro-3.8.0.tar.gz 823507 BLAKE2B a67a7d4ca065d892389bb88d0e51871c1838f3bb9f222293a96f0c4dec796ff353b9a0850724c67c6936ccd23d569bac166ee33ecc275cd4746672da975e96ba SHA512 067a89093501bb4a9627b2141653b4f0636dd2e9323503e6b9c9e6d25e50240d30a6fc9971415ef5c0f227449493a585e4408ebbc4da6f5ee7363faee78f88fb
diff --git a/sci-libs/givaro/givaro-3.2.13.ebuild b/sci-libs/givaro/givaro-3.2.13.ebuild
deleted file mode 100644
index d1dee7b59..000000000
--- a/sci-libs/givaro/givaro-3.2.13.ebuild
+++ /dev/null
@@ -1,26 +0,0 @@
-# Copyright 1999-2015 Gentoo Foundation
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=5
-
-DESCRIPTION="C++ library for arithmetic and algebraic computations"
-HOMEPAGE="http://ljk.imag.fr/CASYS/LOGICIELS/givaro/"
-SRC_URI="http://ljk.imag.fr/CASYS/LOGICIELS/givaro/Downloads/${P}.tar.gz"
-
-LICENSE="GPL-2"
-SLOT="0"
-KEYWORDS="~amd64 ~x86"
-IUSE=""
-
-RDEPEND=">=dev-libs/gmp-4.1-r1:0="
-DEPEND="${RDEPEND}"
-
-src_configure(){
-	econf "--enable-shared"
-}
-
-pkg_postinst() {
-	elog "The givaro ebuild is still under development."
-	elog "Help us improve the ebuild in:"
-	elog "http://bugs.gentoo.org/show_bug.cgi?id=227803"
-}
diff --git a/sci-libs/givaro/givaro-3.3.0.ebuild b/sci-libs/givaro/givaro-3.3.0.ebuild
deleted file mode 100644
index b7eaf2412..000000000
--- a/sci-libs/givaro/givaro-3.3.0.ebuild
+++ /dev/null
@@ -1,26 +0,0 @@
-# Copyright 1999-2015 Gentoo Foundation
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=5
-
-DESCRIPTION="C++ library for arithmetic and algebraic computations"
-HOMEPAGE="http://ljk.imag.fr/CASYS/LOGICIELS/givaro/"
-SRC_URI="http://ljk.imag.fr/CASYS/LOGICIELS/givaro/Downloads/${P}.tar.gz"
-
-LICENSE="GPL-3"
-SLOT="0"
-KEYWORDS="~amd64 ~x86"
-IUSE=""
-
-RDEPEND=">=dev-libs/gmp-4.1-r1:0="
-DEPEND="${RDEPEND}"
-
-src_configure(){
-	econf "--enable-shared"
-}
-
-pkg_postinst() {
-	elog "The givaro ebuild is still under development."
-	elog "Help us improve the ebuild in:"
-	elog "http://bugs.gentoo.org/show_bug.cgi?id=227803"
-}
diff --git a/sci-libs/givaro/givaro-3.8.0.ebuild b/sci-libs/givaro/givaro-3.8.0.ebuild
deleted file mode 100644
index 42dabbab8..000000000
--- a/sci-libs/givaro/givaro-3.8.0.ebuild
+++ /dev/null
@@ -1,20 +0,0 @@
-# Copyright 1999-2015 Gentoo Foundation
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=5
-
-DESCRIPTION="C++ library for arithmetic and algebraic computations"
-HOMEPAGE="http://ljk.imag.fr/CASYS/LOGICIELS/givaro/"
-SRC_URI="https://forge.imag.fr/frs/download.php/592/${P}.tar.gz"
-
-LICENSE="CeCILL-B"
-SLOT="0"
-KEYWORDS="~amd64 ~x86"
-IUSE=""
-
-RDEPEND=">=dev-libs/gmp-4.1-r1:0="
-DEPEND="${RDEPEND}"
-
-src_configure(){
-	econf "--enable-shared"
-}
diff --git a/sci-libs/givaro/metadata.xml b/sci-libs/givaro/metadata.xml
deleted file mode 100644
index 90d08b5bf..000000000
--- a/sci-libs/givaro/metadata.xml
+++ /dev/null
@@ -1,9 +0,0 @@
-<?xml version="1.0" encoding="UTF-8"?>
-<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
-<pkgmetadata>
-	<maintainer type="project">
-		<email>sci@gentoo.org</email>
-		<name>Gentoo Science Project</name>
-	</maintainer>
-	<longdescription>Givaro is a C++ library for arithmetic and algebraic computations. Its main features are implementations of the basic arithmetic of many mathematical entities: Primes fields, Extensions Fields, Finite Fields, Finite Rings, Polynomials, Algebraic numbers, Arbitrary precision integers and rationals (C++ wrappers over gmp) It also provides data-structures and templated classes for the manipulation of basic algebraic objects, such as vectors, matrices (dense, sparse, structured), univariate polynomials (and therefore recursive multivariate).</longdescription>
-</pkgmetadata>
diff --git a/sci-libs/gmsh/Manifest b/sci-libs/gmsh/Manifest
deleted file mode 100644
index c64941ce4..000000000
--- a/sci-libs/gmsh/Manifest
+++ /dev/null
@@ -1,3 +0,0 @@
-DIST gmsh-2.16.0-source.tgz 10867812 BLAKE2B a769fb19e4201b245c5c525e1581253cf93489a7720180ebb05d4656d274b9f8aa5a3258090966119249f9240de82d942be82ae5cb4b5418f35be9d9ca2b88bd SHA512 00b26232dbd8e95826f608f11a9e93eca750db2c70334e3c0c957856dddeeaf68ccba3e727e00f916762eeba54e58558c8795934ebeef3c99844c22cc7dfacf7
-DIST gmsh-3.0.6-source.tgz 12663776 BLAKE2B 041ab0ba8af5e4b96dd27bbbb146b4f9582dc425c07a35665df0392ae545f185852bc2f5cddb53fed4754904762585e14da1ed2067cafecf9eaa550b6b69424f SHA512 6221c1e68bcfed41b6ad13bfadf79a5d5a2b2d8e577d94c984364b480c330f9e2d9fa20f7374ac58cd124f57530c51d8977061f4179879a03d0b31b27869485a
-DIST gmsh-4.0.2-source.tgz 12764404 BLAKE2B b7b9d24c44d59efc5ea5d9ce525488c60f7de764bc3d6d192aca6a09583cd1bd426df72b5a36553867c796c3a90733a27d76cc5a8bb6f6d4a13400872f9a8faa SHA512 95557000a8007b3a006b341af438fa9511eb9460371ba1a4d53ff7cc70c81695a5aa26e8edde84efdfe2beb874ba8f5465e3016ef89f9b53d7c5ab47d7e6501b
diff --git a/sci-libs/gmsh/gmsh-2.16.0.ebuild b/sci-libs/gmsh/gmsh-2.16.0.ebuild
deleted file mode 100644
index ed7fc8be3..000000000
--- a/sci-libs/gmsh/gmsh-2.16.0.ebuild
+++ /dev/null
@@ -1,93 +0,0 @@
-# Copyright 1999-2017 Gentoo Foundation
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=6
-
-PYTHON_COMPAT=( python2_7 )
-
-inherit cmake-utils flag-o-matic fortran-2 toolchain-funcs
-
-DESCRIPTION="A three-dimensional finite element mesh generator"
-HOMEPAGE="http://www.geuz.org/gmsh/"
-SRC_URI="http://www.geuz.org/gmsh/src/${P}-source.tgz"
-
-## gmsh comes with its own copies of (at least) metis, netgen and tetgen, therefore inform the user of their special licenses
-LICENSE="GPL-3 free-noncomm"
-SLOT="0"
-KEYWORDS="~amd64 ~x86"
-## cgns is not compiling ATM, maybe fix cgns lib first
-IUSE="blas cgns chaco doc examples jpeg lua med metis mpi netgen opencascade petsc png python taucs tetgen X zlib"
-
-RDEPEND="
-	virtual/fortran
-	X? ( x11-libs/fltk:1 )
-	blas? ( virtual/blas virtual/lapack sci-libs/fftw:3.0 )
-	cgns? ( sci-libs/cgnslib )
-	jpeg? ( virtual/jpeg:0 )
-	lua? ( dev-lang/lua:0 )
-	med? ( sci-libs/med )
-	opencascade? ( sci-libs/opencascade:* )
-	png? ( media-libs/libpng:0 )
-	petsc? ( sci-mathematics/petsc )
-	zlib? ( sys-libs/zlib )
-	mpi? ( virtual/mpi[cxx] )
-	taucs? ( sci-libs/taucs )"
-
-REQUIRED_USE="
-	taucs? ( || ( metis ) )
-	"
-
-DEPEND="${RDEPEND}
-	virtual/pkgconfig
-	doc? ( virtual/latex-base )
-	python? ( dev-lang/swig:0 )
-	"
-
-S=${WORKDIR}/${P}-source
-
-pkg_setup() {
-	fortran-2_pkg_setup
-}
-
-src_configure() {
-	local mycmakeargs=( )
-
-	use blas && \
-		mycmakeargs+=(-DCMAKE_Fortran_COMPILER=$(tc-getF77))
-
-	mycmakeargs+=(
-		-DENABLE_BLAS_LAPACK="$(usex blas)"
-		-DENABLE_CGNS="$(usex cgns)"
-		-DENABLE_CHACO="$(usex chaco)"
-		-DENABLE_FLTK="$(usex X)"
-		-DENABLE_GRAPHICS="$(usex X)"
-		-DENABLE_MED="$(usex med)"
-		-DENABLE_METIS="$(usex metis)"
-		-DENABLE_NETGEN="$(usex netgen)"
-		-DENABLE_TAUCS="$(usex taucs)"
-		-DENABLE_TETGEN="$(usex tetgen)"
-		-DENABLE_OCC="$(usex opencascade)"
-		-DENABLE_PETSC="$(usex petsc)"
-		-DENABLE_WRAP_PYTHON="$(usex python)")
-
-	cmake-utils_src_configure mycmakeargs
-}
-
-src_compile() {
-	cmake-utils_src_compile
-	if use doc ; then
-		cd "${BUILD_DIR}" || die
-		emake pdf
-		cd "${S}" || die
-		dodoc doc/texinfo/gmsh.pdf
-	fi
-}
-
-src_install() {
-	cmake-utils_src_install
-
-	if use examples ; then
-		insinto /usr/share/doc/${PF}
-		doins -r demos tutorial
-	fi
-}
diff --git a/sci-libs/gmsh/gmsh-3.0.6.ebuild b/sci-libs/gmsh/gmsh-3.0.6.ebuild
deleted file mode 100644
index 8975cd76e..000000000
--- a/sci-libs/gmsh/gmsh-3.0.6.ebuild
+++ /dev/null
@@ -1,93 +0,0 @@
-# Copyright 1999-2018 Gentoo Foundation
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=6
-
-PYTHON_COMPAT=( python2_7 )
-
-inherit cmake-utils flag-o-matic fortran-2 toolchain-funcs
-
-DESCRIPTION="A three-dimensional finite element mesh generator"
-HOMEPAGE="http://www.geuz.org/gmsh/"
-SRC_URI="http://www.geuz.org/gmsh/src/${P}-source.tgz"
-
-## gmsh comes with its own copies of (at least) metis, netgen and tetgen, therefore inform the user of their special licenses
-LICENSE="GPL-3 free-noncomm"
-SLOT="0"
-KEYWORDS="~amd64 ~x86"
-## cgns is not compiling ATM, maybe fix cgns lib first
-IUSE="blas cgns chaco doc examples jpeg lua med metis mpi netgen opencascade petsc png python taucs tetgen X zlib"
-
-RDEPEND="
-	virtual/fortran
-	X? ( x11-libs/fltk:1 )
-	blas? ( virtual/blas virtual/lapack sci-libs/fftw:3.0 )
-	cgns? ( sci-libs/cgnslib )
-	jpeg? ( virtual/jpeg:0 )
-	lua? ( dev-lang/lua:0 )
-	med? ( sci-libs/med )
-	opencascade? ( sci-libs/opencascade:* )
-	png? ( media-libs/libpng:0 )
-	petsc? ( sci-mathematics/petsc )
-	zlib? ( sys-libs/zlib )
-	mpi? ( virtual/mpi[cxx] )
-	taucs? ( sci-libs/taucs )"
-
-REQUIRED_USE="
-	taucs? ( || ( metis ) )
-	"
-
-DEPEND="${RDEPEND}
-	virtual/pkgconfig
-	doc? ( virtual/latex-base )
-	python? ( dev-lang/swig:0 )
-	"
-
-S=${WORKDIR}/${P}-source
-
-pkg_setup() {
-	fortran-2_pkg_setup
-}
-
-src_configure() {
-	local mycmakeargs=( )
-
-	use blas && \
-		mycmakeargs+=(-DCMAKE_Fortran_COMPILER=$(tc-getF77))
-
-	mycmakeargs+=(
-		-DENABLE_BLAS_LAPACK="$(usex blas)"
-		-DENABLE_CGNS="$(usex cgns)"
-		-DENABLE_CHACO="$(usex chaco)"
-		-DENABLE_FLTK="$(usex X)"
-		-DENABLE_GRAPHICS="$(usex X)"
-		-DENABLE_MED="$(usex med)"
-		-DENABLE_METIS="$(usex metis)"
-		-DENABLE_NETGEN="$(usex netgen)"
-		-DENABLE_TAUCS="$(usex taucs)"
-		-DENABLE_TETGEN="$(usex tetgen)"
-		-DENABLE_OCC="$(usex opencascade)"
-		-DENABLE_PETSC="$(usex petsc)"
-		-DENABLE_WRAP_PYTHON="$(usex python)")
-
-	cmake-utils_src_configure mycmakeargs
-}
-
-src_compile() {
-	cmake-utils_src_compile
-	if use doc ; then
-		cd "${BUILD_DIR}" || die
-		emake pdf
-		cd "${S}" || die
-		dodoc doc/texinfo/gmsh.pdf
-	fi
-}
-
-src_install() {
-	cmake-utils_src_install
-
-	if use examples ; then
-		insinto /usr/share/doc/${PF}
-		doins -r demos tutorial
-	fi
-}
diff --git a/sci-libs/gmsh/gmsh-4.0.2.ebuild b/sci-libs/gmsh/gmsh-4.0.2.ebuild
deleted file mode 100644
index 7f4690090..000000000
--- a/sci-libs/gmsh/gmsh-4.0.2.ebuild
+++ /dev/null
@@ -1,93 +0,0 @@
-# Copyright 1999-2018 Gentoo Authors
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=6
-
-PYTHON_COMPAT=( python2_7 )
-
-inherit cmake-utils flag-o-matic fortran-2 toolchain-funcs
-
-DESCRIPTION="A three-dimensional finite element mesh generator"
-HOMEPAGE="http://www.geuz.org/gmsh/"
-SRC_URI="http://www.geuz.org/gmsh/src/${P}-source.tgz"
-
-## gmsh comes with its own copies of (at least) metis, netgen and tetgen, therefore inform the user of their special licenses
-LICENSE="GPL-3 free-noncomm"
-SLOT="0"
-KEYWORDS="~amd64 ~x86"
-## cgns is not compiling ATM, maybe fix cgns lib first
-IUSE="blas cgns chaco doc examples jpeg lua med metis mpi netgen opencascade petsc png python taucs tetgen X zlib"
-
-RDEPEND="
-	virtual/fortran
-	X? ( x11-libs/fltk:1 )
-	blas? ( virtual/blas virtual/lapack sci-libs/fftw:3.0 )
-	cgns? ( sci-libs/cgnslib )
-	jpeg? ( virtual/jpeg:0 )
-	lua? ( dev-lang/lua:0 )
-	med? ( sci-libs/med )
-	opencascade? ( sci-libs/opencascade:* )
-	png? ( media-libs/libpng:0 )
-	petsc? ( sci-mathematics/petsc )
-	zlib? ( sys-libs/zlib )
-	mpi? ( virtual/mpi[cxx] )
-	taucs? ( sci-libs/taucs )"
-
-REQUIRED_USE="
-	taucs? ( || ( metis ) )
-	"
-
-DEPEND="${RDEPEND}
-	virtual/pkgconfig
-	doc? ( virtual/latex-base )
-	python? ( dev-lang/swig:0 )
-	"
-
-S=${WORKDIR}/${P}-source
-
-pkg_setup() {
-	fortran-2_pkg_setup
-}
-
-src_configure() {
-	local mycmakeargs=( )
-
-	use blas && \
-		mycmakeargs+=(-DCMAKE_Fortran_COMPILER=$(tc-getF77))
-
-	mycmakeargs+=(
-		-DENABLE_BLAS_LAPACK="$(usex blas)"
-		-DENABLE_CGNS="$(usex cgns)"
-		-DENABLE_CHACO="$(usex chaco)"
-		-DENABLE_FLTK="$(usex X)"
-		-DENABLE_GRAPHICS="$(usex X)"
-		-DENABLE_MED="$(usex med)"
-		-DENABLE_METIS="$(usex metis)"
-		-DENABLE_NETGEN="$(usex netgen)"
-		-DENABLE_TAUCS="$(usex taucs)"
-		-DENABLE_TETGEN="$(usex tetgen)"
-		-DENABLE_OCC="$(usex opencascade)"
-		-DENABLE_PETSC="$(usex petsc)"
-		-DENABLE_WRAP_PYTHON="$(usex python)")
-
-	cmake-utils_src_configure mycmakeargs
-}
-
-src_compile() {
-	cmake-utils_src_compile
-	if use doc ; then
-		cd "${BUILD_DIR}" || die
-		emake pdf
-		cd "${S}" || die
-		dodoc doc/texinfo/gmsh.pdf
-	fi
-}
-
-src_install() {
-	cmake-utils_src_install
-
-	if use examples ; then
-		insinto /usr/share/doc/${PF}
-		doins -r demos tutorial
-	fi
-}
diff --git a/sci-libs/gmsh/metadata.xml b/sci-libs/gmsh/metadata.xml
deleted file mode 100644
index 8c538ca2a..000000000
--- a/sci-libs/gmsh/metadata.xml
+++ /dev/null
@@ -1,19 +0,0 @@
-<?xml version="1.0" encoding="UTF-8"?>
-<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
-<pkgmetadata>
-	<maintainer type="project">
-		<email>sci@gentoo.org</email>
-		<name>Gentoo Science Project</name>
-	</maintainer>
-	<use>
-		<flag name="chaco"> Enables chaco partitioner support</flag>
-		<flag name="cgns"> Enables cgns output support</flag>
-		<flag name="metis"> Enables metis support</flag>
-		<flag name="med"> Enables med support</flag>
-		<flag name="netgen"> Enable 3D Frontal triangulation using netgen lib</flag>
-		<flag name="petsc"> Enable sci-mathematics/petsc support</flag>
-		<flag name="opencascade"> Enable OpenCASCADE support</flag>
-		<flag name="taucs"> Enable sci-libs/taucs support</flag>
-		<flag name="tetgen"> Enable 3D delauny triangulation using tetgen lib</flag>
-	</use>
-</pkgmetadata>
diff --git a/sci-libs/gotoblas2/Manifest b/sci-libs/gotoblas2/Manifest
deleted file mode 100644
index f89426897..000000000
--- a/sci-libs/gotoblas2/Manifest
+++ /dev/null
@@ -1 +0,0 @@
-DIST GotoBLAS2-1.13_bsd.tar.gz 3165294 BLAKE2B 1fdaa8f8db8660de42010f3c8c1b6573f0607f68569b53835dec92e666cf517ac1aa3372becef21bae383abb6a5d76e0b6cf328244f724884bb900fd7a3dfdb1 SHA512 086e1fd8c37448c1406814af2ad55bfc19dd65dcd5bff69eae91ba3b1bf14f9225e73e20b23602b259ae1e22c84d954688ef1eefee34668fe77421f5f05c0ba0
diff --git a/sci-libs/gotoblas2/files/gotoblas2-1.13-aliasing.patch b/sci-libs/gotoblas2/files/gotoblas2-1.13-aliasing.patch
deleted file mode 100644
index 874de7080..000000000
--- a/sci-libs/gotoblas2/files/gotoblas2-1.13-aliasing.patch
+++ /dev/null
@@ -1,11 +0,0 @@
---- driver/others/init.c.orig	2011-05-31 23:23:24.000000000 +0100
-+++ driver/others/init.c	2011-05-31 23:23:49.000000000 +0100
-@@ -215,7 +215,7 @@
-   for (node = 0; node < MAX_NODES; node ++) common -> node_info[node] = 0;
- 
-   while ((dir = readdir(dp)) != NULL) {
--    if (*(unsigned int *) dir -> d_name == 0x065646f6eU) {
-+    if (*(char *) dir -> d_name == 0x065646f6eU) {
- 
-       node = atoi(&dir -> d_name[4]);
- 
diff --git a/sci-libs/gotoblas2/files/gotoblas2-1.13-dynamic.patch b/sci-libs/gotoblas2/files/gotoblas2-1.13-dynamic.patch
deleted file mode 100644
index 71021e435..000000000
--- a/sci-libs/gotoblas2/files/gotoblas2-1.13-dynamic.patch
+++ /dev/null
@@ -1,17 +0,0 @@
-Authors:  Elias Pipping <pipping@exherbo.org>
-Upstream: no
-Synopsis: Fix compilation under KATMAI and PRESCOTT architecture.
---- old/driver/others/dynamic.c 2010-01-20 17:28:45.000000000 +0100
-+++ new/driver/others/dynamic.c 2010-05-28 16:04:10.190975461 +0200
-@@ -181,9 +181,9 @@
-   gotoblas = get_coretype();
-   
- #ifdef ARCH_X86
--  if (gotoblas == NULL) gotoblas = gotoblas_KATMAI;
-+  if (gotoblas == NULL) gotoblas = &gotoblas_KATMAI;
- #else
--  if (gotoblas == NULL) gotoblas = gotoblas_PRESCOTT;
-+  if (gotoblas == NULL) gotoblas = &gotoblas_PRESCOTT;
- #endif
-   
-   if (gotoblas && gotoblas -> init) {
diff --git a/sci-libs/gotoblas2/files/gotoblas2-1.13-fcheck.patch b/sci-libs/gotoblas2/files/gotoblas2-1.13-fcheck.patch
deleted file mode 100644
index 809a1edc1..000000000
--- a/sci-libs/gotoblas2/files/gotoblas2-1.13-fcheck.patch
+++ /dev/null
@@ -1,10 +0,0 @@
---- f_check.orig	2011-05-31 23:12:41.508268623 +0100
-+++ f_check	2011-05-31 23:12:50.208268398 +0100
-@@ -274,6 +274,7 @@
- 	    && ($flags !~ /kernel32/)
- 	    && ($flags !~ /advapi32/)
- 	    && ($flags !~ /shell32/)
-+	    && ($flags !~ /^\-l$/)
- 	    ) {
- 	    $linker_l .= $flags . " ";
- 	}
diff --git a/sci-libs/gotoblas2/files/gotoblas2-1.13-sharedlibs.patch b/sci-libs/gotoblas2/files/gotoblas2-1.13-sharedlibs.patch
deleted file mode 100644
index 862a00c24..000000000
--- a/sci-libs/gotoblas2/files/gotoblas2-1.13-sharedlibs.patch
+++ /dev/null
@@ -1,54 +0,0 @@
---- exports/Makefile.orig	2010-02-06 05:01:00.000000000 +1300
-+++ exports/Makefile	2012-03-16 11:43:30.028487068 +1300
-@@ -84,7 +84,7 @@
- 	perl ./gensymbol win2khpl $(ARCH) dummy $(EXPRECISION) $(NO_CBLAS) > $(@F)
- 
- $(LIBDYNNAME) : ../$(LIBNAME) osx.def
--	$(PREFIX)gcc $(CFLAGS) -all_load -dynamiclib -o $(LIBDYNNAME) $< -Wl,-exported_symbols_list,osx.def  $(FEXTRALIB)
-+	$(PREFIX)gcc $(CFLAGS) -all_load -dynamiclib -o ../$(LIBDYNNAME) $< -Wl,-exported_symbols_list,osx.def  $(FEXTRALIB)
- 
- symbol.$(SUFFIX) : symbol.S
- 	$(CC) $(CFLAGS) -c -o $(@F) $^
-@@ -97,10 +97,10 @@
- so : ../$(LIBSONAME)
- 
- ../$(LIBSONAME) : ../$(LIBNAME) linux.def linktest.c
--	$(CC) $(CFLAGS) -shared -o ../$(LIBSONAME) \
--	-Wl,--whole-archive ../$(LIBNAME) -Wl,--no-whole-archive \
--	-Wl,--retain-symbols-file=linux.def $(EXTRALIB)
--	$(CC) $(CFLAGS) -w -o linktest linktest.c ../$(LIBSONAME) $(FEXTRALIB) && echo OK.
-+	$(CC) $(LDFLAGS) -shared  \
-+	-Wl,--whole-archive ../$(LIBNAME) -Wl,--no-whole-archive -Wl,--soname=$(LIBSONAME) \
-+	-Wl,--retain-symbols-file=linux.def $(EXTRALIB) -o ../$(LIBSONAME)
-+	$(CC) $(CFLAGS) -w linktest.c ../$(LIBSONAME) $(FEXTRALIB) -o linktest && echo OK.
- 	rm -f linktest
- 
- endif
-@@ -110,10 +110,10 @@
- so : ../$(LIBSONAME)
- 
- ../$(LIBSONAME) : ../$(LIBNAME) linux.def linktest.c
--	$(CC) $(CFLAGS)  -shared -o ../$(LIBSONAME) \
--	-Wl,--whole-archive ../$(LIBNAME) -Wl,--no-whole-archive \
--	-Wl,--retain-symbols-file=linux.def $(EXTRALIB)
--	$(CC) $(CFLAGS) -w -o linktest linktest.c ../$(LIBSONAME) $(FEXTRALIB) && echo OK.
-+	$(CC) $(LDFLAGS)  -shared \
-+	-Wl,--whole-archive ../$(LIBNAME) -Wl,--no-whole-archive -Wl,--soname=$(LIBSONAME) \
-+	-Wl,--retain-symbols-file=linux.def $(EXTRALIB) -o ../$(LIBSONAME)
-+	$(CC) $(CFLAGS) -w linktest.c ../$(LIBSONAME) $(FEXTRALIB) -o linktest && echo OK.
- 	rm -f linktest
- 
- endif
-@@ -129,9 +129,9 @@
- ifeq ($(OSNAME), SunOS)
- 
- so : ../$(LIBSONAME)
--	$(CC) $(CFLAGS)  -shared -o ../$(LIBSONAME) \
--	-Wl,--whole-archive ../$(LIBNAME) -Wl,--no-whole-archive $(EXTRALIB)
--	$(CC) $(CFLAGS) -w -o linktest linktest.c ../$(LIBSONAME) $(FEXTRALIB) && echo OK.
-+	$(CC) $(LDFLAGS) -shared -Wl,--soname=$(LIBSONAME) \
-+	-Wl,--whole-archive ../$(LIBNAME) -Wl,--no-whole-archive $(EXTRALIB) -o ../$(LIBSONAME) 
-+	$(CC) $(CFLAGS) -w  linktest.c ../$(LIBSONAME) $(FEXTRALIB) -o linktest && echo OK.
- 	rm -f linktest
- 
- endif
diff --git a/sci-libs/gotoblas2/gotoblas2-1.13-r1.ebuild b/sci-libs/gotoblas2/gotoblas2-1.13-r1.ebuild
deleted file mode 100644
index 9e3ab9d3f..000000000
--- a/sci-libs/gotoblas2/gotoblas2-1.13-r1.ebuild
+++ /dev/null
@@ -1,130 +0,0 @@
-# Copyright 1999-2015 Gentoo Foundation
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=5
-
-NUMERIC_MODULE_NAME=goto2
-
-inherit eutils numeric-int64-multibuild fortran-2 multilib toolchain-funcs
-
-MYPN="GotoBLAS2"
-MYP="${MYPN}-${PV}_bsd"
-
-DESCRIPTION="Fast implementations of the Basic Linear Algebra Subroutines"
-HOMEPAGE="http://www.tacc.utexas.edu/tacc-projects/gotoblas2/"
-# change to gentoo mirror when in
-SRC_URI="http://dev.gentoo.org/~bicatali/${MYP}.tar.gz"
-
-LICENSE="BSD"
-SLOT="0"
-KEYWORDS="~amd64 ~x86"
-IUSE="+incblas +openmp static-libs threads"
-
-REQUIRED_USE="|| ( openmp threads )"
-
-S="${WORKDIR}/${MYPN}"
-
-src_prepare() {
-	epatch "${FILESDIR}"/${P}-{dynamic,sharedlibs,fcheck,aliasing}.patch
-	# respect LDFLAGS
-	sed -i -e '/^LDFLAGS\s*=/d' Makefile.* || die
-	sed -i \
-		-e "/^COMMON_OPT/s/-O2/${CFLAGS}/" \
-		Makefile.rule || die
-	# fix executable stacks
-	local i
-	for i in $(find . -name \*.S); do
-		cat >> ${i} <<-EOF
-			#if defined(__ELF__)
-			.section .note.GNU-stack,"",%progbits
-			#endif
-		EOF
-	done
-	numeric-int64-multibuild_copy_sources
-}
-
-src_configure() {
-	myconfigure() {
-		sed \
-			-e "s:^#\s*\(NO_LAPACK\)\s*=.*:\1=1:" \
-			-e "s:^#\s*\(CC\)\s*=.*:\1=$(tc-getCC):" \
-			-e "s:^#\s*\(FC\)\s*=.*:\1=$(tc-getFC):" \
-			-e "s:^#\s*\(USE_THREAD\)\s*=.*:\1=$(usex threads 1 0):" \
-			-e "s:^#\s*\(USE_OPENMP\)\s*=.*:\1=$(usex openmp 1 ""):" \
-			-e "s:^#\s*\(DYNAMIC_ARCH\)\s*=.*:\1=1:" \
-			-e "s:^#\s*\(INTERFACE64\)\s*=.*:\1=$(numeric-int64_is_int64_build && echo 1 || echo ""):" \
-			-e "s:^#\s*\(NO_CBLAS\)\s*=.*:\1=$(usex incblas 1 ""):" \
-			-i Makefile.rule || die
-		if numeric-int64_is_int64_build; then
-			sed \
-				-e 's:libgoto2:libgoto2_int64:g' \
-				-i Makefile* || die
-		fi
-	}
-	numeric-int64-multibuild_foreach_all_abi_variants run_in_build_dir myconfigure
-}
-
-src_compile() {
-	mycompile() {
-		if numeric-int64_is_static_build; then
-			use static-libs && emake clean && emake libs NEED_PIC=
-		else
-			mkdir solibs || die
-			emake libs shared && mv *$(get_libname) solibs/ || die
-		fi
-	}
-	numeric-int64-multibuild_foreach_all_abi_variants run_in_build_dir mycompile
-}
-
-src_test() {
-	numeric-int64-multibuild_foreach_all_abi_variants run_in_build_dir emake tests
-}
-
-src_install() {
-	myinstall() {
-		local profname=$(numeric-int64_get_module_name)
-		local libname=libgoto2
-		local libs="-L\${libdir} -lm"
-		if numeric-int64_is_int64_build; then
-			libs+=" -lgoto2_int64"
-		else
-			libs+=" -lgoto2"
-		fi
-		use threads && libs+=" -pthread"
-
-		numeric-int64_is_static_build && libname=libgoto2_int64
-
-		if numeric-int64_is_static_build; then
-			dolib.a lib*.a
-		else
-			dolib.so solibs/lib*$(get_libname)
-
-			create_pkgconfig \
-				--name "${MYPN}" \
-				--libs "${libs}" \
-				--cflags "-I\${includedir}/${PN}" \
-				${profname}
-		fi
-
-		if use incblas; then
-			insinto /usr/include/${PN}
-			doins cblas.h
-		fi
-	}
-	numeric-int64-multibuild_foreach_all_abi_variants run_in_build_dir myinstall
-
-	numeric-int64-multibuild_install_alternative blas ${NUMERIC_MODULE_NAME}
-	numeric-int64-multibuild_install_alternative cblas ${NUMERIC_MODULE_NAME} /usr/include/cblas.h ${PN}/cblas.h
-
-	dodoc 01Readme.txt 03FAQ.txt 05LargePage 06WeirdPerformance
-
-	if [[ ${CHOST} == *-darwin* ]] ; then
-		cd "${ED}"/usr/$(get_libdir) || die
-		local d
-		for d in *.dylib ; do
-			ebegin "correcting install_name of ${d}"
-			install_name_tool -id "${EPREFIX}/usr/$(get_libdir)/${d}" "${d}" || die
-			eend $?
-		done
-	fi
-}
diff --git a/sci-libs/gotoblas2/metadata.xml b/sci-libs/gotoblas2/metadata.xml
deleted file mode 100644
index ea48649a1..000000000
--- a/sci-libs/gotoblas2/metadata.xml
+++ /dev/null
@@ -1,21 +0,0 @@
-<?xml version="1.0" encoding="UTF-8"?>
-<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
-<pkgmetadata>
-	<maintainer type="project">
-		<email>sci@gentoo.org</email>
-		<name>Gentoo Science Project</name>
-	</maintainer>
-	<longdescription lang="en">
-The GotoBLAS codes are one of the fastest implementations
-of the Basic Linear Algebra Subroutines(BLAS).
-To achieve performance it starts by observing that for current
-generation architectures, much of the overhead comes from Translation
-Look-aside Buffer (TLB) table misses. While the importance of caches
-is also taken into consideration, it is the minimization of such TLB
-misses that drives the approach.
-</longdescription>
-	<use>
-		<flag name="int64">Build the 64 bits integer library</flag>
-		<flag name="incblas">Build the CBLAS interface</flag>
-	</use>
-</pkgmetadata>
diff --git a/sci-libs/gsl/Manifest b/sci-libs/gsl/Manifest
deleted file mode 100644
index 7b6e10425..000000000
--- a/sci-libs/gsl/Manifest
+++ /dev/null
@@ -1,5 +0,0 @@
-DIST gsl-1.16.tar.gz 3534080 BLAKE2B 1c55a41e5ed57b57f671074240d23416aa8f23e3cc2bb832e455d4f44d307e6be6adfa3671dbbf2aa14604ea49f96ff636de7909f3532cdc811f6bd99b0aa59d SHA512 94e998953f30d701e1cd0a5e05d572c5cca7b6f40f0533aa85394ba4218946826408093ffe3049a0ab13d6ba87034fcec1a7d52a67d0b8860dc02b5fd4feb8eb
-DIST gsl-2.1.tar.gz 3827265 BLAKE2B 2b359dc9f74ed69aa033508923cff4541894c26a6d2e5c606ee5cf4e4e95c58d270351998537c8c4f4bc8130ee5870b6f64133ede9079f20d8309d83637164f5 SHA512 d63660fdfae9c9ec9f4fd1894b0af705297cefb6169973ef10faacd0b8a3d52f537508e9c07f4f9f4253138cc48e5570bb10ef303538226d7febd92e8fd184b0
-DIST gsl-2.3.tar.gz 4510731 BLAKE2B 5bc58346340a04f039405d4b256598b14f33e9b4e265c4fb159e691f5ea3372a0f9b7526b6ea6e259d5968ef8e7ce5b4d4e2465a78fb0b42f85a383fdc32d4bf SHA512 ada622079f4ac667d95f74b38aa368726fc1b18fd34555bcefe90920d3da93a9289ebff966be43325af806107001bc8973daf9f8418e6c97b866be2296b566ff
-DIST gsl-2.4.tar.gz 5916715 BLAKE2B f22c07b2d5759a383e05b8bfdba70071672cc27f12ff2a8c755451fe7e10c8e2d80e3fcc601508c5e9942e4cfd05e51c43ba96666326b760e4390eb0c2552886 SHA512 12442b023dd959e8b22a9c486646b5cedec7fdba0daf2604cda365cf96d10d99aefdec2b42e59c536cc071da1525373454e5ed6f4b15293b305ca9b1dc6db130
-DIST gsl-2.5.tar.gz 7303881 BLAKE2B 7c6d10c21071a1af1f03123f83244476d2e90fcd27d05a115b03a74fe631eb7d8081f5260e534ae58ab0997c1111f980a5e4cb50d110ca626fe810c44be70180 SHA512 5b4c5c023f9029ce220f4e09aa4d0234fed94d42ac224d58fda095fe0532d54237a7c33278f8b5d0ba051f6004486edb38d0adb4fcb49337a8c1d8a18cf4a24a
diff --git a/sci-libs/gsl/files/gsl-1.16-cblas-external.patch b/sci-libs/gsl/files/gsl-1.16-cblas-external.patch
deleted file mode 100644
index c29ef5294..000000000
--- a/sci-libs/gsl/files/gsl-1.16-cblas-external.patch
+++ /dev/null
@@ -1,294 +0,0 @@
-diff -Nur gsl-1.16.orig/ax_cblas.m4 gsl-1.16/ax_cblas.m4
---- gsl-1.16.orig/ax_cblas.m4	1969-12-31 16:00:00.000000000 -0800
-+++ gsl-1.16/ax_cblas.m4	2013-08-19 15:48:54.376300825 -0700
-@@ -0,0 +1,69 @@
-+AC_DEFUN([AX_CBLAS],[
-+
-+  ext_cblas=no
-+  ext_cblas_libs="-lcblas"
-+  ext_cblas_cflags=""
-+
-+  AC_ARG_WITH(cblas-external,
-+	[AS_HELP_STRING([--with-cblas-external], 
-+			[Use external CBLAS library (default is no)])],
-+	[with_ext_cblas=$withval],
-+	[with_ext_cblas=no])
-+
-+  case $with_ext_cblas in
-+	no) ext_cblas=no ;;
-+	yes) ext_cblas=yes ;;
-+	-* | */* | *.a | *.so | *.so.* | *.o) 
-+	   ext_cblas=yes
-+	   ext_cblas_libs="$with_cblas" ;;
-+	*) ext_cblas=yes
-+	   ext_cblas_libs="-l$with_cblas" ;;
-+  esac
-+
-+  AC_ARG_WITH(cblas-external-libs,
-+	[AS_HELP_STRING([--with-cblas-external-libs=<libs>],
-+			[External cblas libraries to link with (default is "$ext_cblas_libs")])],
-+	[ext_cblas_libs=$withval],
-+	[])
-+
-+  AC_ARG_WITH(cblas-external-cflags,
-+	[AS_HELP_STRING([--with-cblas-external-cflags=<flags>],
-+			[Pre-processing flags to compile with external cblas ("-I<dir>")])],
-+	[ext_cblas_cflags=$withval],
-+	[])
-+
-+  if test x$ext_cblas != xno; then
-+	if test "x$CBLAS_LIBS" = x; then
-+	   CBLAS_LIBS="$ext_cblas_libs"
-+     	fi
-+     	if test "x$CBLAS_CFLAGS" = x; then
-+       	   CBLAS_CFLAGS="$ext_cblas_cflags"
-+   	fi
-+
-+   	CFLAGS_sav="$CFLAGS"
-+   	CFLAGS="$CFLAGS $CBLAS_CFLAGS"
-+   	AC_CHECK_HEADER(cblas.h, ,
-+		[AC_MSG_ERROR([
-+	   	*** Header file cblas.h not found.
-+	   	*** If you installed cblas header in a non standard place,
-+	   	*** specify its install prefix using the following option
-+	   	***  --with-cblas-external-cflags="-I<include_dir>"])
-+	 	])
-+   	CFLAGS="$CFLAGS_sav"
-+
-+   	LIBS_sav="$LIBS"
-+   	LIBS="$LIBS $CBLAS_LIBS -lm"
-+   	AC_MSG_CHECKING([for cblas_sgemm in $CBLAS_LIBS])
-+   	AC_TRY_LINK_FUNC(cblas_sgemm, [ext_cblas=yes],
-+    		[AC_MSG_ERROR([
-+	    	*** Linking with cblas with $LIBS failed.
-+       	    	*** If you installed cblas library in a non standard place,
-+   	    	*** specify its install prefix using the following option
-+	    	***  --with-cblas-external-libs="-L<lib_dir> -l<lib>"])
-+	 	])
-+   	AC_MSG_RESULT($ext_cblas)
-+   	LIBS="$LIBS_sav"
-+	AC_SUBST([CBLAS_CFLAGS])
-+	AC_SUBST([CBLAS_LIBS])
-+ fi
-+])
-diff -Nur gsl-1.16.orig/bspline/Makefile.am gsl-1.16/bspline/Makefile.am
---- gsl-1.16.orig/bspline/Makefile.am	2013-07-17 13:04:26.000000000 -0700
-+++ gsl-1.16/bspline/Makefile.am	2013-08-19 15:25:27.728497742 -0700
-@@ -12,6 +12,6 @@
- 
- TESTS = $(check_PROGRAMS)
- 
--test_LDADD = libgslbspline.la ../linalg/libgsllinalg.la ../permutation/libgslpermutation.la ../blas/libgslblas.la ../matrix/libgslmatrix.la ../vector/libgslvector.la ../block/libgslblock.la ../complex/libgslcomplex.la ../cblas/libgslcblas.la ../ieee-utils/libgslieeeutils.la  ../err/libgslerr.la ../test/libgsltest.la ../sys/libgslsys.la ../utils/libutils.la ../statistics/libgslstatistics.la
-+test_LDADD = libgslbspline.la ../linalg/libgsllinalg.la ../permutation/libgslpermutation.la ../blas/libgslblas.la ../matrix/libgslmatrix.la ../vector/libgslvector.la ../block/libgslblock.la ../complex/libgslcomplex.la @CBLAS_LINK_LIBS@ ../ieee-utils/libgslieeeutils.la  ../err/libgslerr.la ../test/libgsltest.la ../sys/libgslsys.la ../utils/libutils.la ../statistics/libgslstatistics.la
- 
- test_SOURCES = test.c
-diff -Nur gsl-1.16.orig/configure.ac gsl-1.16/configure.ac
---- gsl-1.16.orig/configure.ac	2013-07-19 08:14:45.000000000 -0700
-+++ gsl-1.16/configure.ac	2013-08-19 15:28:24.172640793 -0700
-@@ -191,6 +191,16 @@
-   AC_CHECK_LIB(m, cos)
- fi
- 
-+sinclude(ax_cblas.m4)
-+AX_CBLAS
-+if test "x$CBLAS_LIBS" != "x"; then
-+   CBLAS_LINK_LIBS="$CBLAS_LIBS"
-+else
-+   CBLAS_LINK_LIBS="\$(top_builddir)/cblas/libgslcblas.la"
-+   CBLAS_LIBS="-lgslcblas"
-+fi
-+AC_SUBST(CBLAS_LINK_LIBS)
-+
- dnl Remember to put a definition in acconfig.h for each of these
- AC_CHECK_DECLS(feenableexcept,,,[#define _GNU_SOURCE 1
- #include <fenv.h>]) 
-diff -Nur gsl-1.16.orig/eigen/Makefile.am gsl-1.16/eigen/Makefile.am
---- gsl-1.16.orig/eigen/Makefile.am	2013-07-17 13:04:26.000000000 -0700
-+++ gsl-1.16/eigen/Makefile.am	2013-08-19 15:25:27.728497742 -0700
-@@ -11,7 +11,7 @@
- 
- TESTS = $(check_PROGRAMS)
- 
--test_LDADD = libgsleigen.la  ../test/libgsltest.la ../linalg/libgsllinalg.la ../permutation/libgslpermutation.la ../blas/libgslblas.la ../cblas/libgslcblas.la ../matrix/libgslmatrix.la ../vector/libgslvector.la ../block/libgslblock.la  ../complex/libgslcomplex.la ../ieee-utils/libgslieeeutils.la ../sys/libgslsys.la ../err/libgslerr.la ../utils/libutils.la ../rng/libgslrng.la ../sort/libgslsort.la
-+test_LDADD = libgsleigen.la  ../test/libgsltest.la ../linalg/libgsllinalg.la ../permutation/libgslpermutation.la ../blas/libgslblas.la @CBLAS_LINK_LIBS@ ../matrix/libgslmatrix.la ../vector/libgslvector.la ../block/libgslblock.la  ../complex/libgslcomplex.la ../ieee-utils/libgslieeeutils.la ../sys/libgslsys.la ../err/libgslerr.la ../utils/libutils.la ../rng/libgslrng.la ../sort/libgslsort.la
- 
- test_SOURCES = test.c
- 
-diff -Nur gsl-1.16.orig/gsl-config.in gsl-1.16/gsl-config.in
---- gsl-1.16.orig/gsl-config.in	2013-07-17 13:04:26.000000000 -0700
-+++ gsl-1.16/gsl-config.in	2013-08-19 15:25:27.728497742 -0700
-@@ -58,11 +58,11 @@
- 	;;
- 
-     --cflags)
--       	echo @GSL_CFLAGS@ 
-+       	echo @GSL_CFLAGS@ @CBLAS_CFLAGS@ 
-        	;;
- 
-     --libs)
--        : ${GSL_CBLAS_LIB=-lgslcblas}
-+        : ${GSL_CBLAS_LIB=@CBLAS_LIBS@}
- 	echo @GSL_LIBS@ $GSL_CBLAS_LIB @GSL_LIBM@
-        	;;
- 
-diff -Nur gsl-1.16.orig/gsl.pc.in gsl-1.16/gsl.pc.in
---- gsl-1.16.orig/gsl.pc.in	2013-07-17 13:04:26.000000000 -0700
-+++ gsl-1.16/gsl.pc.in	2013-08-19 15:25:27.728497742 -0700
-@@ -2,7 +2,7 @@
- exec_prefix=@exec_prefix@
- libdir=@libdir@
- includedir=@includedir@
--GSL_CBLAS_LIB=-lgslcblas
-+GSL_CBLAS_LIB=@CBLAS_LIBS@
- 
- Name: GSL
- Description: GNU Scientific Library
-diff -Nur gsl-1.16.orig/interpolation/Makefile.am gsl-1.16/interpolation/Makefile.am
---- gsl-1.16.orig/interpolation/Makefile.am	2013-07-17 13:04:26.000000000 -0700
-+++ gsl-1.16/interpolation/Makefile.am	2013-08-19 15:25:27.729497736 -0700
-@@ -10,7 +10,7 @@
- 
- TESTS = $(check_PROGRAMS)
- 
--test_LDADD = libgslinterpolation.la ../poly/libgslpoly.la ../linalg/libgsllinalg.la ../permutation/libgslpermutation.la ../blas/libgslblas.la ../matrix/libgslmatrix.la ../vector/libgslvector.la ../block/libgslblock.la ../complex/libgslcomplex.la ../cblas/libgslcblas.la ../ieee-utils/libgslieeeutils.la  ../err/libgslerr.la ../test/libgsltest.la ../sys/libgslsys.la ../utils/libutils.la
-+test_LDADD = libgslinterpolation.la ../poly/libgslpoly.la ../linalg/libgsllinalg.la ../permutation/libgslpermutation.la ../blas/libgslblas.la ../matrix/libgslmatrix.la ../vector/libgslvector.la ../block/libgslblock.la ../complex/libgslcomplex.la @CBLAS_LINK_LIBS@ ../ieee-utils/libgslieeeutils.la  ../err/libgslerr.la ../test/libgsltest.la ../sys/libgslsys.la ../utils/libutils.la
- 
- test_SOURCES = test.c
- 
-diff -Nur gsl-1.16.orig/linalg/Makefile.am gsl-1.16/linalg/Makefile.am
---- gsl-1.16.orig/linalg/Makefile.am	2013-07-17 13:04:26.000000000 -0700
-+++ gsl-1.16/linalg/Makefile.am	2013-08-19 15:25:27.729497736 -0700
-@@ -12,7 +12,7 @@
- 
- check_PROGRAMS = test
- 
--test_LDADD = libgsllinalg.la ../blas/libgslblas.la ../cblas/libgslcblas.la ../permutation/libgslpermutation.la ../matrix/libgslmatrix.la ../vector/libgslvector.la ../block/libgslblock.la ../complex/libgslcomplex.la ../ieee-utils/libgslieeeutils.la ../err/libgslerr.la ../test/libgsltest.la ../sys/libgslsys.la ../utils/libutils.la
-+test_LDADD = libgsllinalg.la ../blas/libgslblas.la @CBLAS_LINK_LIBS@ ../permutation/libgslpermutation.la ../matrix/libgslmatrix.la ../vector/libgslvector.la ../block/libgslblock.la ../complex/libgslcomplex.la ../ieee-utils/libgslieeeutils.la ../err/libgslerr.la ../test/libgsltest.la ../sys/libgslsys.la ../utils/libutils.la
- 
- test_SOURCES = test.c
- 
-diff -Nur gsl-1.16.orig/Makefile.am gsl-1.16/Makefile.am
---- gsl-1.16.orig/Makefile.am	2013-07-17 13:04:26.000000000 -0700
-+++ gsl-1.16/Makefile.am	2013-08-19 15:25:27.729497736 -0700
-@@ -19,13 +19,12 @@
- 
- lib_LTLIBRARIES = libgsl.la
- libgsl_la_SOURCES = version.c
--libgsl_la_LIBADD = $(SUBLIBS)
-+libgsl_la_LIBADD = $(SUBLIBS) @CBLAS_LINK_LIBS@
- libgsl_la_LDFLAGS = -version-info $(GSL_LT_VERSION)
- noinst_HEADERS = templates_on.h templates_off.h build.h
- 
- MINGW32_HOST = @MINGW32_HOST@
- if MINGW32_HOST
--libgsl_la_LIBADD += cblas/libgslcblas.la
- libgsl_la_LDFLAGS += -no-undefined
- endif
- 
-@@ -35,10 +34,10 @@
- bin_PROGRAMS = gsl-randist gsl-histogram
- 
- gsl_randist_SOURCES = gsl-randist.c
--gsl_randist_LDADD = libgsl.la cblas/libgslcblas.la
-+gsl_randist_LDADD = libgsl.la
- 
- gsl_histogram_SOURCES = gsl-histogram.c
--gsl_histogram_LDADD = libgsl.la cblas/libgslcblas.la
-+gsl_histogram_LDADD = libgsl.la
- 
- check_SCRIPTS = test_gsl_histogram.sh pkgconfig.test
- TESTS = test_gsl_histogram.sh pkgconfig.test
-@@ -57,6 +56,8 @@
- 	-e 's|@GSL_CFLAGS[@]|$(GSL_CFLAGS)|g' \
- 	-e 's|@GSL_LIBM[@]|$(GSL_LIBM)|g' \
- 	-e 's|@GSL_LIBS[@]|$(GSL_LIBS)|g' \
-+	-e 's|@CBLAS_CFLAGS[@]|$(CBLAS_CFLAGS)|g' \
-+	-e 's|@CBLAS_LIBS[@]|$(CBLAS_LIBS)|g' \
- 	-e 's|@LIBS[@]|$(LIBS)|g' \
- 	-e 's|@VERSION[@]|$(VERSION)|g'
- 
---- gsl-1.16.orig/multifit/Makefile.am	2013-07-18 06:04:26.000000000 +1000
-+++ gsl-1.16/multifit/Makefile.am	2013-11-22 16:57:26.170330257 +1100
-@@ -13,8 +13,8 @@
- TESTS = $(check_PROGRAMS)
- 
- test_SOURCES = test.c
--test_LDADD = libgslmultifit.la ../linalg/libgsllinalg.la ../permutation/libgslpermutation.la ../blas/libgslblas.la ../cblas/libgslcblas.la ../matrix/libgslmatrix.la ../sort/libgslsort.la ../statistics/libgslstatistics.la ../vector/libgslvector.la ../block/libgslblock.la  ../complex/libgslcomplex.la ../ieee-utils/libgslieeeutils.la ../err/libgslerr.la ../test/libgsltest.la ../utils/libutils.la ../sys/libgslsys.la
-+test_LDADD = libgslmultifit.la ../linalg/libgsllinalg.la ../permutation/libgslpermutation.la ../blas/libgslblas.la @CBLAS_LINK_LIBS@ ../matrix/libgslmatrix.la ../sort/libgslsort.la ../statistics/libgslstatistics.la ../vector/libgslvector.la ../block/libgslblock.la  ../complex/libgslcomplex.la ../ieee-utils/libgslieeeutils.la ../err/libgslerr.la ../test/libgsltest.la ../utils/libutils.la ../sys/libgslsys.la
- 
- #demo_SOURCES = demo.c
--#demo_LDADD = libgslmultifit.la ../linalg/libgsllinalg.la ../permutation/libgslpermutation.la ../blas/libgslblas.la ../cblas/libgslcblas.la ../matrix/libgslmatrix.la ../vector/libgslvector.la ../block/libgslblock.la ../randist/libgslrandist.la ../rng/libgslrng.la ../complex/libgslcomplex.la ../ieee-utils/libgslieeeutils.la ../err/libgslerr.la ../test/libgsltest.la ../utils/libutils.la ../sys/libgslsys.la
-+#demo_LDADD = libgslmultifit.la ../linalg/libgsllinalg.la ../permutation/libgslpermutation.la ../blas/libgslblas.la @CBLAS_LINK_LIBS@ ../matrix/libgslmatrix.la ../vector/libgslvector.la ../block/libgslblock.la ../randist/libgslrandist.la ../rng/libgslrng.la ../complex/libgslcomplex.la ../ieee-utils/libgslieeeutils.la ../err/libgslerr.la ../test/libgsltest.la ../utils/libutils.la ../sys/libgslsys.la
- 
-diff -Nur gsl-1.16.orig/multimin/Makefile.am gsl-1.16/multimin/Makefile.am
---- gsl-1.16.orig/multimin/Makefile.am	2013-07-17 13:04:26.000000000 -0700
-+++ gsl-1.16/multimin/Makefile.am	2013-08-19 15:25:27.729497736 -0700
-@@ -13,8 +13,8 @@
- TESTS = $(check_PROGRAMS) 
- 
- test_SOURCES = test.c test_funcs.c test_funcs.h
--test_LDADD = libgslmultimin.la ../min/libgslmin.la ../poly/libgslpoly.la ../blas/libgslblas.la ../cblas/libgslcblas.la ../linalg/libgsllinalg.la ../permutation/libgslpermutation.la ../matrix/libgslmatrix.la ../vector/libgslvector.la ../block/libgslblock.la ../complex/libgslcomplex.la ../ieee-utils/libgslieeeutils.la ../err/libgslerr.la ../test/libgsltest.la ../sys/libgslsys.la ../utils/libutils.la
-+test_LDADD = libgslmultimin.la ../min/libgslmin.la ../poly/libgslpoly.la ../blas/libgslblas.la @CBLAS_LINK_LIBS@ ../linalg/libgsllinalg.la ../permutation/libgslpermutation.la ../matrix/libgslmatrix.la ../vector/libgslvector.la ../block/libgslblock.la ../complex/libgslcomplex.la ../ieee-utils/libgslieeeutils.la ../err/libgslerr.la ../test/libgsltest.la ../sys/libgslsys.la ../utils/libutils.la
- 
- #demo_SOURCES = demo.c 
--#demo_LDADD = libgslmultimin.la ../min/libgslmin.la ../blas/libgslblas.la ../cblas/libgslcblas.la ../linalg/libgsllinalg.la ../matrix/libgslmatrix.la ../vector/libgslvector.la ../block/libgslblock.la ../complex/libgslcomplex.la ../ieee-utils/libgslieeeutils.la ../err/libgslerr.la ../test/libgsltest.la ../sys/libgslsys.la ../utils/libutils.la
-+#demo_LDADD = libgslmultimin.la ../min/libgslmin.la ../blas/libgslblas.la @CBLAS_LINK_LIBS@ ../linalg/libgsllinalg.la ../matrix/libgslmatrix.la ../vector/libgslvector.la ../block/libgslblock.la ../complex/libgslcomplex.la ../ieee-utils/libgslieeeutils.la ../err/libgslerr.la ../test/libgsltest.la ../sys/libgslsys.la ../utils/libutils.la
- 
-diff -Nur gsl-1.16.orig/multiroots/Makefile.am gsl-1.16/multiroots/Makefile.am
---- gsl-1.16.orig/multiroots/Makefile.am	2013-07-17 13:04:26.000000000 -0700
-+++ gsl-1.16/multiroots/Makefile.am	2013-08-19 15:25:27.729497736 -0700
-@@ -15,5 +15,5 @@
- TESTS = $(check_PROGRAMS)
- 
- test_SOURCES = test.c test_funcs.c test_funcs.h
--test_LDADD = libgslmultiroots.la ../linalg/libgsllinalg.la ../blas/libgslblas.la ../cblas/libgslcblas.la ../permutation/libgslpermutation.la ../matrix/libgslmatrix.la ../vector/libgslvector.la ../block/libgslblock.la ../complex/libgslcomplex.la ../ieee-utils/libgslieeeutils.la  ../err/libgslerr.la ../test/libgsltest.la ../sys/libgslsys.la ../utils/libutils.la
-+test_LDADD = libgslmultiroots.la ../linalg/libgsllinalg.la ../blas/libgslblas.la @CBLAS_LINK_LIBS@ ../permutation/libgslpermutation.la ../matrix/libgslmatrix.la ../vector/libgslvector.la ../block/libgslblock.la ../complex/libgslcomplex.la ../ieee-utils/libgslieeeutils.la  ../err/libgslerr.la ../test/libgsltest.la ../sys/libgslsys.la ../utils/libutils.la
- 
-diff -Nur gsl-1.16.orig/ode-initval/Makefile.am gsl-1.16/ode-initval/Makefile.am
---- gsl-1.16.orig/ode-initval/Makefile.am	2013-07-17 13:04:26.000000000 -0700
-+++ gsl-1.16/ode-initval/Makefile.am	2013-08-19 15:25:27.729497736 -0700
-@@ -12,7 +12,7 @@
- 
- TESTS = $(check_PROGRAMS)
- 
--test_LDADD = libgslodeiv.la ../linalg/libgsllinalg.la ../blas/libgslblas.la ../cblas/libgslcblas.la ../matrix/libgslmatrix.la ../permutation/libgslpermutation.la ../vector/libgslvector.la ../block/libgslblock.la ../complex/libgslcomplex.la ../ieee-utils/libgslieeeutils.la  ../err/libgslerr.la ../test/libgsltest.la ../sys/libgslsys.la ../utils/libutils.la 
-+test_LDADD = libgslodeiv.la ../linalg/libgsllinalg.la ../blas/libgslblas.la @CBLAS_LINK_LIBS@ ../matrix/libgslmatrix.la ../permutation/libgslpermutation.la ../vector/libgslvector.la ../block/libgslblock.la ../complex/libgslcomplex.la ../ieee-utils/libgslieeeutils.la  ../err/libgslerr.la ../test/libgsltest.la ../sys/libgslsys.la ../utils/libutils.la 
- 
- test_SOURCES = test.c
- 
-diff -Nur gsl-1.16.orig/poly/Makefile.am gsl-1.16/poly/Makefile.am
---- gsl-1.16.orig/poly/Makefile.am	2013-07-17 13:04:26.000000000 -0700
-+++ gsl-1.16/poly/Makefile.am	2013-08-19 15:25:27.729497736 -0700
-@@ -10,7 +10,7 @@
- 
- TESTS = $(check_PROGRAMS)
- 
--check_PROGRAMS = test
-+#check_PROGRAMS = test
- 
- test_SOURCES = test.c
- test_LDADD = libgslpoly.la ../ieee-utils/libgslieeeutils.la ../err/libgslerr.la ../test/libgsltest.la ../sys/libgslsys.la ../utils/libutils.la ../sort/libgslsort.la
-diff -Nur gsl-1.16.orig/specfunc/Makefile.am gsl-1.16/specfunc/Makefile.am
---- gsl-1.16.orig/specfunc/Makefile.am	2013-07-17 13:04:26.000000000 -0700
-+++ gsl-1.16/specfunc/Makefile.am	2013-08-19 15:25:27.729497736 -0700
-@@ -12,7 +12,7 @@
- 
- check_PROGRAMS = test
- 
--test_LDADD = libgslspecfunc.la ../eigen/libgsleigen.la ../linalg/libgsllinalg.la  ../sort/libgslsort.la ../matrix/libgslmatrix.la ../vector/libgslvector.la ../blas/libgslblas.la ../cblas/libgslcblas.la ../block/libgslblock.la ../complex/libgslcomplex.la ../ieee-utils/libgslieeeutils.la  ../err/libgslerr.la ../test/libgsltest.la ../sys/libgslsys.la ../utils/libutils.la
-+test_LDADD = libgslspecfunc.la ../eigen/libgsleigen.la ../linalg/libgsllinalg.la  ../sort/libgslsort.la ../matrix/libgslmatrix.la ../vector/libgslvector.la ../blas/libgslblas.la @CBLAS_LINK_LIBS@ ../block/libgslblock.la ../complex/libgslcomplex.la ../ieee-utils/libgslieeeutils.la  ../err/libgslerr.la ../test/libgsltest.la ../sys/libgslsys.la ../utils/libutils.la
- 
- test_SOURCES = test_sf.c test_sf.h test_airy.c test_bessel.c test_coulomb.c test_dilog.c test_gamma.c test_hyperg.c test_legendre.c test_mathieu.c
-   
-diff -Nur gsl-1.16.orig/wavelet/Makefile.am gsl-1.16/wavelet/Makefile.am
---- gsl-1.16.orig/wavelet/Makefile.am	2013-07-17 13:04:26.000000000 -0700
-+++ gsl-1.16/wavelet/Makefile.am	2013-08-19 15:25:27.729497736 -0700
-@@ -10,7 +10,7 @@
- 
- TESTS = $(check_PROGRAMS)
- 
--test_LDADD = libgslwavelet.la ../blas/libgslblas.la ../cblas/libgslcblas.la ../matrix/libgslmatrix.la ../vector/libgslvector.la ../block/libgslblock.la ../ieee-utils/libgslieeeutils.la  ../err/libgslerr.la ../test/libgsltest.la ../sys/libgslsys.la ../utils/libutils.la
-+test_LDADD = libgslwavelet.la ../blas/libgslblas.la @CBLAS_LINK_LIBS@ ../matrix/libgslmatrix.la ../vector/libgslvector.la ../block/libgslblock.la ../ieee-utils/libgslieeeutils.la  ../err/libgslerr.la ../test/libgsltest.la ../sys/libgslsys.la ../utils/libutils.la
- 
- test_SOURCES = test.c
- 
diff --git a/sci-libs/gsl/files/gsl-2.1-cblas-external.patch b/sci-libs/gsl/files/gsl-2.1-cblas-external.patch
deleted file mode 100644
index 54cc8802c..000000000
--- a/sci-libs/gsl/files/gsl-2.1-cblas-external.patch
+++ /dev/null
@@ -1,326 +0,0 @@
- Makefile.am               |  8 +++---
- ax_cblas.m4               | 69 +++++++++++++++++++++++++++++++++++++++++++++++
- bspline/Makefile.am       |  2 +-
- configure.ac              | 10 +++++++
- eigen/Makefile.am         |  2 +-
- gsl-config.in             |  4 +--
- gsl.pc.in                 |  2 +-
- interpolation/Makefile.am |  2 +-
- linalg/Makefile.am        |  2 +-
- multifit/Makefile.am      |  4 +--
- multimin/Makefile.am      |  4 +--
- multiroots/Makefile.am    |  2 +-
- ode-initval/Makefile.am   |  2 +-
- poly/Makefile.am          |  2 +-
- specfunc/Makefile.am      |  2 +-
- wavelet/Makefile.am       |  2 +-
- 16 files changed, 100 insertions(+), 19 deletions(-)
-
-diff --git a/Makefile.am b/Makefile.am
-index 278dcd9..a75418c 100644
---- a/Makefile.am
-+++ b/Makefile.am
-@@ -19,7 +19,7 @@ EXTRA_DIST = autogen.sh gsl-config.in gsl.pc.in configure.ac THANKS BUGS gsl.spe
- 
- lib_LTLIBRARIES = libgsl.la
- libgsl_la_SOURCES = version.c
--libgsl_la_LIBADD = $(GSL_LIBADD) $(SUBLIBS)
-+libgsl_la_LIBADD = $(GSL_LIBADD) $(SUBLIBS) @CBLAS_LINK_LIBS@
- libgsl_la_LDFLAGS = $(GSL_LDFLAGS) -version-info $(GSL_LT_VERSION)
- noinst_HEADERS = templates_on.h templates_off.h build.h
- 
-@@ -29,10 +29,10 @@ m4data_DATA = gsl.m4
- bin_PROGRAMS = gsl-randist gsl-histogram
- 
- gsl_randist_SOURCES = gsl-randist.c
--gsl_randist_LDADD = libgsl.la cblas/libgslcblas.la
-+gsl_randist_LDADD = libgsl.la
- 
- gsl_histogram_SOURCES = gsl-histogram.c
--gsl_histogram_LDADD = libgsl.la cblas/libgslcblas.la
-+gsl_histogram_LDADD = libgsl.la
- 
- check_SCRIPTS = test_gsl_histogram.sh pkgconfig.test
- TESTS = test_gsl_histogram.sh pkgconfig.test
-@@ -51,6 +51,8 @@ edit = $(SED) \
- 	-e 's|@GSL_CFLAGS[@]|$(GSL_CFLAGS)|g' \
- 	-e 's|@GSL_LIBM[@]|$(GSL_LIBM)|g' \
- 	-e 's|@GSL_LIBS[@]|$(GSL_LIBS)|g' \
-+	-e 's|@CBLAS_CFLAGS[@]|$(CBLAS_CFLAGS)|g' \
-+	-e 's|@CBLAS_LIBS[@]|$(CBLAS_LIBS)|g' \
- 	-e 's|@LIBS[@]|$(LIBS)|g' \
- 	-e 's|@VERSION[@]|$(VERSION)|g'
- 
-diff --git a/ax_cblas.m4 b/ax_cblas.m4
-new file mode 100644
-index 0000000..6ef143a
---- /dev/null
-+++ b/ax_cblas.m4
-@@ -0,0 +1,69 @@
-+AC_DEFUN([AX_CBLAS],[
-+
-+  ext_cblas=no
-+  ext_cblas_libs="-lcblas"
-+  ext_cblas_cflags=""
-+
-+  AC_ARG_WITH(cblas-external,
-+	[AS_HELP_STRING([--with-cblas-external], 
-+			[Use external CBLAS library (default is no)])],
-+	[with_ext_cblas=$withval],
-+	[with_ext_cblas=no])
-+
-+  case $with_ext_cblas in
-+	no) ext_cblas=no ;;
-+	yes) ext_cblas=yes ;;
-+	-* | */* | *.a | *.so | *.so.* | *.o) 
-+	   ext_cblas=yes
-+	   ext_cblas_libs="$with_cblas" ;;
-+	*) ext_cblas=yes
-+	   ext_cblas_libs="-l$with_cblas" ;;
-+  esac
-+
-+  AC_ARG_WITH(cblas-external-libs,
-+	[AS_HELP_STRING([--with-cblas-external-libs=<libs>],
-+			[External cblas libraries to link with (default is "$ext_cblas_libs")])],
-+	[ext_cblas_libs=$withval],
-+	[])
-+
-+  AC_ARG_WITH(cblas-external-cflags,
-+	[AS_HELP_STRING([--with-cblas-external-cflags=<flags>],
-+			[Pre-processing flags to compile with external cblas ("-I<dir>")])],
-+	[ext_cblas_cflags=$withval],
-+	[])
-+
-+  if test x$ext_cblas != xno; then
-+	if test "x$CBLAS_LIBS" = x; then
-+	   CBLAS_LIBS="$ext_cblas_libs"
-+     	fi
-+     	if test "x$CBLAS_CFLAGS" = x; then
-+       	   CBLAS_CFLAGS="$ext_cblas_cflags"
-+   	fi
-+
-+   	CFLAGS_sav="$CFLAGS"
-+   	CFLAGS="$CFLAGS $CBLAS_CFLAGS"
-+   	AC_CHECK_HEADER(cblas.h, ,
-+		[AC_MSG_ERROR([
-+	   	*** Header file cblas.h not found.
-+	   	*** If you installed cblas header in a non standard place,
-+	   	*** specify its install prefix using the following option
-+	   	***  --with-cblas-external-cflags="-I<include_dir>"])
-+	 	])
-+   	CFLAGS="$CFLAGS_sav"
-+
-+   	LIBS_sav="$LIBS"
-+   	LIBS="$LIBS $CBLAS_LIBS -lm"
-+   	AC_MSG_CHECKING([for cblas_sgemm in $CBLAS_LIBS])
-+   	AC_TRY_LINK_FUNC(cblas_sgemm, [ext_cblas=yes],
-+    		[AC_MSG_ERROR([
-+	    	*** Linking with cblas with $LIBS failed.
-+       	    	*** If you installed cblas library in a non standard place,
-+   	    	*** specify its install prefix using the following option
-+	    	***  --with-cblas-external-libs="-L<lib_dir> -l<lib>"])
-+	 	])
-+   	AC_MSG_RESULT($ext_cblas)
-+   	LIBS="$LIBS_sav"
-+	AC_SUBST([CBLAS_CFLAGS])
-+	AC_SUBST([CBLAS_LIBS])
-+ fi
-+])
-diff --git a/bspline/Makefile.am b/bspline/Makefile.am
-index 3f4f950..d413036 100644
---- a/bspline/Makefile.am
-+++ b/bspline/Makefile.am
-@@ -12,6 +12,6 @@ check_PROGRAMS = test
- 
- TESTS = $(check_PROGRAMS)
- 
--test_LDADD = libgslbspline.la ../linalg/libgsllinalg.la ../permutation/libgslpermutation.la ../blas/libgslblas.la ../matrix/libgslmatrix.la ../vector/libgslvector.la ../block/libgslblock.la ../complex/libgslcomplex.la ../cblas/libgslcblas.la ../ieee-utils/libgslieeeutils.la  ../err/libgslerr.la ../test/libgsltest.la ../sys/libgslsys.la ../utils/libutils.la ../statistics/libgslstatistics.la
-+test_LDADD = libgslbspline.la ../linalg/libgsllinalg.la ../permutation/libgslpermutation.la ../blas/libgslblas.la ../matrix/libgslmatrix.la ../vector/libgslvector.la ../block/libgslblock.la ../complex/libgslcomplex.la @CBLAS_LINK_LIBS@ ../ieee-utils/libgslieeeutils.la  ../err/libgslerr.la ../test/libgsltest.la ../sys/libgslsys.la ../utils/libutils.la ../statistics/libgslstatistics.la
- 
- test_SOURCES = test.c
-diff --git a/configure.ac b/configure.ac
-index d6b673f..c642454 100644
---- a/configure.ac
-+++ b/configure.ac
-@@ -205,6 +205,16 @@ if test "x$LIBS" = "x" ; then
-   AC_CHECK_LIB(m, cos)
- fi
- 
-+sinclude(ax_cblas.m4)
-+AX_CBLAS
-+if test "x$CBLAS_LIBS" != "x"; then
-+   CBLAS_LINK_LIBS="$CBLAS_LIBS"
-+else
-+   CBLAS_LINK_LIBS="\$(top_builddir)/cblas/libgslcblas.la"
-+   CBLAS_LIBS="-lgslcblas"
-+fi
-+AC_SUBST(CBLAS_LINK_LIBS)
-+
- dnl Remember to put a definition in acconfig.h for each of these
- AC_CHECK_DECLS(feenableexcept,,,[#define _GNU_SOURCE 1
- #include <fenv.h>]) 
-diff --git a/eigen/Makefile.am b/eigen/Makefile.am
-index c28bfde..14197a4 100644
---- a/eigen/Makefile.am
-+++ b/eigen/Makefile.am
-@@ -11,7 +11,7 @@ noinst_HEADERS =  qrstep.c
- 
- TESTS = $(check_PROGRAMS)
- 
--test_LDADD = libgsleigen.la  ../test/libgsltest.la ../linalg/libgsllinalg.la ../permutation/libgslpermutation.la ../blas/libgslblas.la ../cblas/libgslcblas.la ../matrix/libgslmatrix.la ../vector/libgslvector.la ../block/libgslblock.la  ../complex/libgslcomplex.la ../ieee-utils/libgslieeeutils.la ../sys/libgslsys.la ../err/libgslerr.la ../utils/libutils.la ../rng/libgslrng.la ../sort/libgslsort.la
-+test_LDADD = libgsleigen.la  ../test/libgsltest.la ../linalg/libgsllinalg.la ../permutation/libgslpermutation.la ../blas/libgslblas.la @CBLAS_LINK_LIBS@ ../matrix/libgslmatrix.la ../vector/libgslvector.la ../block/libgslblock.la  ../complex/libgslcomplex.la ../ieee-utils/libgslieeeutils.la ../sys/libgslsys.la ../err/libgslerr.la ../utils/libutils.la ../rng/libgslrng.la ../sort/libgslsort.la
- 
- test_SOURCES = test.c
- 
-diff --git a/gsl-config.in b/gsl-config.in
-old mode 100755
-new mode 100644
-index 3f3fa61..c9c4262
---- a/gsl-config.in
-+++ b/gsl-config.in
-@@ -58,11 +58,11 @@ while test $# -gt 0; do
- 	;;
- 
-     --cflags)
--       	echo @GSL_CFLAGS@ 
-+       	echo @GSL_CFLAGS@ @CBLAS_CFLAGS@ 
-        	;;
- 
-     --libs)
--        : ${GSL_CBLAS_LIB=-lgslcblas}
-+        : ${GSL_CBLAS_LIB=@CBLAS_LIBS@}
- 	echo @GSL_LIBS@ $GSL_CBLAS_LIB @GSL_LIBM@
-        	;;
- 
-diff --git a/gsl.pc.in b/gsl.pc.in
-index 5e9ef21..5a7a0f3 100644
---- a/gsl.pc.in
-+++ b/gsl.pc.in
-@@ -2,7 +2,7 @@ prefix=@prefix@
- exec_prefix=@exec_prefix@
- libdir=@libdir@
- includedir=@includedir@
--GSL_CBLAS_LIB=-lgslcblas
-+GSL_CBLAS_LIB=@CBLAS_LIBS@
- 
- Name: GSL
- Description: GNU Scientific Library
-diff --git a/interpolation/Makefile.am b/interpolation/Makefile.am
-index 1d80755..e45bd51 100644
---- a/interpolation/Makefile.am
-+++ b/interpolation/Makefile.am
-@@ -12,7 +12,7 @@ AM_CPPFLAGS = -I$(top_srcdir)
- 
- TESTS = $(check_PROGRAMS)
- 
--test_LDADD = libgslinterpolation.la ../poly/libgslpoly.la ../linalg/libgsllinalg.la ../permutation/libgslpermutation.la ../blas/libgslblas.la ../matrix/libgslmatrix.la ../vector/libgslvector.la ../block/libgslblock.la ../complex/libgslcomplex.la ../cblas/libgslcblas.la ../ieee-utils/libgslieeeutils.la  ../err/libgslerr.la ../test/libgsltest.la ../sys/libgslsys.la ../utils/libutils.la
-+test_LDADD = libgslinterpolation.la ../poly/libgslpoly.la ../linalg/libgsllinalg.la ../permutation/libgslpermutation.la ../blas/libgslblas.la ../matrix/libgslmatrix.la ../vector/libgslvector.la ../block/libgslblock.la ../complex/libgslcomplex.la @CBLAS_LINK_LIBS@ ../ieee-utils/libgslieeeutils.la  ../err/libgslerr.la ../test/libgsltest.la ../sys/libgslsys.la ../utils/libutils.la
- 
- test_SOURCES = test.c
- 
-diff --git a/linalg/Makefile.am b/linalg/Makefile.am
-index 8fb6e7c..90d22e0 100644
---- a/linalg/Makefile.am
-+++ b/linalg/Makefile.am
-@@ -12,7 +12,7 @@ TESTS = $(check_PROGRAMS)
- 
- check_PROGRAMS = test
- 
--test_LDADD = libgsllinalg.la ../blas/libgslblas.la ../cblas/libgslcblas.la ../permutation/libgslpermutation.la ../matrix/libgslmatrix.la ../vector/libgslvector.la ../block/libgslblock.la ../complex/libgslcomplex.la ../ieee-utils/libgslieeeutils.la ../err/libgslerr.la ../test/libgsltest.la ../sys/libgslsys.la ../utils/libutils.la
-+test_LDADD = libgsllinalg.la ../blas/libgslblas.la @CBLAS_LINK_LIBS@ ../permutation/libgslpermutation.la ../matrix/libgslmatrix.la ../vector/libgslvector.la ../block/libgslblock.la ../complex/libgslcomplex.la ../ieee-utils/libgslieeeutils.la ../err/libgslerr.la ../test/libgsltest.la ../sys/libgslsys.la ../utils/libutils.la
- 
- test_SOURCES = test.c
- 
-diff --git a/multifit/Makefile.am b/multifit/Makefile.am
-index 891964b..b33f71e 100644
---- a/multifit/Makefile.am
-+++ b/multifit/Makefile.am
-@@ -67,8 +67,8 @@ check_PROGRAMS = test #demo
- TESTS = $(check_PROGRAMS)
- 
- test_SOURCES = test.c
--test_LDADD = libgslmultifit.la ../linalg/libgsllinalg.la ../permutation/libgslpermutation.la ../blas/libgslblas.la ../cblas/libgslcblas.la ../matrix/libgslmatrix.la ../sort/libgslsort.la ../statistics/libgslstatistics.la ../vector/libgslvector.la ../block/libgslblock.la  ../complex/libgslcomplex.la ../ieee-utils/libgslieeeutils.la ../err/libgslerr.la ../test/libgsltest.la ../utils/libutils.la ../sys/libgslsys.la ../rng/libgslrng.la ../specfunc/libgslspecfunc.la
-+test_LDADD = libgslmultifit.la ../linalg/libgsllinalg.la ../permutation/libgslpermutation.la ../blas/libgslblas.la @CBLAS_LINK_LIBS@ ../matrix/libgslmatrix.la ../sort/libgslsort.la ../statistics/libgslstatistics.la ../vector/libgslvector.la ../block/libgslblock.la  ../complex/libgslcomplex.la ../ieee-utils/libgslieeeutils.la ../err/libgslerr.la ../test/libgsltest.la ../utils/libutils.la ../sys/libgslsys.la ../rng/libgslrng.la ../specfunc/libgslspecfunc.la
- 
- #demo_SOURCES = demo.c
--#demo_LDADD = libgslmultifit.la ../linalg/libgsllinalg.la ../permutation/libgslpermutation.la ../blas/libgslblas.la ../cblas/libgslcblas.la ../matrix/libgslmatrix.la ../vector/libgslvector.la ../block/libgslblock.la ../randist/libgslrandist.la ../rng/libgslrng.la ../complex/libgslcomplex.la ../ieee-utils/libgslieeeutils.la ../err/libgslerr.la ../test/libgsltest.la ../utils/libutils.la ../sys/libgslsys.la
-+#demo_LDADD = libgslmultifit.la ../linalg/libgsllinalg.la ../permutation/libgslpermutation.la ../blas/libgslblas.la @CBLAS_LINK_LIBS@ ../matrix/libgslmatrix.la ../vector/libgslvector.la ../block/libgslblock.la ../randist/libgslrandist.la ../rng/libgslrng.la ../complex/libgslcomplex.la ../ieee-utils/libgslieeeutils.la ../err/libgslerr.la ../test/libgsltest.la ../utils/libutils.la ../sys/libgslsys.la
- 
-diff --git a/multimin/Makefile.am b/multimin/Makefile.am
-index 7071359..65a488a 100644
---- a/multimin/Makefile.am
-+++ b/multimin/Makefile.am
-@@ -13,8 +13,8 @@ check_PROGRAMS = test #demo
- TESTS = $(check_PROGRAMS) 
- 
- test_SOURCES = test.c test_funcs.c test_funcs.h
--test_LDADD = libgslmultimin.la ../min/libgslmin.la ../poly/libgslpoly.la ../blas/libgslblas.la ../cblas/libgslcblas.la ../linalg/libgsllinalg.la ../permutation/libgslpermutation.la ../matrix/libgslmatrix.la ../vector/libgslvector.la ../block/libgslblock.la ../complex/libgslcomplex.la ../ieee-utils/libgslieeeutils.la ../err/libgslerr.la ../test/libgsltest.la ../sys/libgslsys.la ../utils/libutils.la
-+test_LDADD = libgslmultimin.la ../min/libgslmin.la ../poly/libgslpoly.la ../blas/libgslblas.la @CBLAS_LINK_LIBS@ ../linalg/libgsllinalg.la ../permutation/libgslpermutation.la ../matrix/libgslmatrix.la ../vector/libgslvector.la ../block/libgslblock.la ../complex/libgslcomplex.la ../ieee-utils/libgslieeeutils.la ../err/libgslerr.la ../test/libgsltest.la ../sys/libgslsys.la ../utils/libutils.la
- 
- #demo_SOURCES = demo.c 
--#demo_LDADD = libgslmultimin.la ../min/libgslmin.la ../blas/libgslblas.la ../cblas/libgslcblas.la ../linalg/libgsllinalg.la ../matrix/libgslmatrix.la ../vector/libgslvector.la ../block/libgslblock.la ../complex/libgslcomplex.la ../ieee-utils/libgslieeeutils.la ../err/libgslerr.la ../test/libgsltest.la ../sys/libgslsys.la ../utils/libutils.la
-+#demo_LDADD = libgslmultimin.la ../min/libgslmin.la ../blas/libgslblas.la @CBLAS_LINK_LIBS@ ../linalg/libgsllinalg.la ../matrix/libgslmatrix.la ../vector/libgslvector.la ../block/libgslblock.la ../complex/libgslcomplex.la ../ieee-utils/libgslieeeutils.la ../err/libgslerr.la ../test/libgsltest.la ../sys/libgslsys.la ../utils/libutils.la
- 
-diff --git a/multiroots/Makefile.am b/multiroots/Makefile.am
-index a351c3f..6178448 100644
---- a/multiroots/Makefile.am
-+++ b/multiroots/Makefile.am
-@@ -15,5 +15,5 @@ check_PROGRAMS = test
- TESTS = $(check_PROGRAMS)
- 
- test_SOURCES = test.c test_funcs.c test_funcs.h
--test_LDADD = libgslmultiroots.la ../linalg/libgsllinalg.la ../blas/libgslblas.la ../cblas/libgslcblas.la ../permutation/libgslpermutation.la ../matrix/libgslmatrix.la ../vector/libgslvector.la ../block/libgslblock.la ../complex/libgslcomplex.la ../ieee-utils/libgslieeeutils.la  ../err/libgslerr.la ../test/libgsltest.la ../sys/libgslsys.la ../utils/libutils.la
-+test_LDADD = libgslmultiroots.la ../linalg/libgsllinalg.la ../blas/libgslblas.la @CBLAS_LINK_LIBS@ ../permutation/libgslpermutation.la ../matrix/libgslmatrix.la ../vector/libgslvector.la ../block/libgslblock.la ../complex/libgslcomplex.la ../ieee-utils/libgslieeeutils.la  ../err/libgslerr.la ../test/libgsltest.la ../sys/libgslsys.la ../utils/libutils.la
- 
-diff --git a/ode-initval/Makefile.am b/ode-initval/Makefile.am
-index 9c774b5..346c381 100644
---- a/ode-initval/Makefile.am
-+++ b/ode-initval/Makefile.am
-@@ -12,7 +12,7 @@ check_PROGRAMS = test
- 
- TESTS = $(check_PROGRAMS)
- 
--test_LDADD = libgslodeiv.la ../linalg/libgsllinalg.la ../blas/libgslblas.la ../cblas/libgslcblas.la ../matrix/libgslmatrix.la ../permutation/libgslpermutation.la ../vector/libgslvector.la ../block/libgslblock.la ../complex/libgslcomplex.la ../ieee-utils/libgslieeeutils.la  ../err/libgslerr.la ../test/libgsltest.la ../sys/libgslsys.la ../utils/libutils.la 
-+test_LDADD = libgslodeiv.la ../linalg/libgsllinalg.la ../blas/libgslblas.la @CBLAS_LINK_LIBS@ ../matrix/libgslmatrix.la ../permutation/libgslpermutation.la ../vector/libgslvector.la ../block/libgslblock.la ../complex/libgslcomplex.la ../ieee-utils/libgslieeeutils.la  ../err/libgslerr.la ../test/libgsltest.la ../sys/libgslsys.la ../utils/libutils.la 
- 
- test_SOURCES = test.c
- 
-diff --git a/poly/Makefile.am b/poly/Makefile.am
-index f1dae5d..e0f8e83 100644
---- a/poly/Makefile.am
-+++ b/poly/Makefile.am
-@@ -10,7 +10,7 @@ noinst_HEADERS = balance.c companion.c qr.c
- 
- TESTS = $(check_PROGRAMS)
- 
--check_PROGRAMS = test
-+#check_PROGRAMS = test
- 
- test_SOURCES = test.c
- test_LDADD = libgslpoly.la ../ieee-utils/libgslieeeutils.la ../err/libgslerr.la ../test/libgsltest.la ../sys/libgslsys.la ../utils/libutils.la ../sort/libgslsort.la
-diff --git a/specfunc/Makefile.am b/specfunc/Makefile.am
-index 0a7e672..d1361d0 100644
---- a/specfunc/Makefile.am
-+++ b/specfunc/Makefile.am
-@@ -12,7 +12,7 @@ TESTS = $(check_PROGRAMS)
- 
- check_PROGRAMS = test
- 
--test_LDADD = libgslspecfunc.la ../eigen/libgsleigen.la ../linalg/libgsllinalg.la  ../sort/libgslsort.la ../matrix/libgslmatrix.la ../vector/libgslvector.la ../blas/libgslblas.la ../cblas/libgslcblas.la ../block/libgslblock.la ../complex/libgslcomplex.la ../ieee-utils/libgslieeeutils.la  ../err/libgslerr.la ../test/libgsltest.la ../sys/libgslsys.la ../utils/libutils.la
-+test_LDADD = libgslspecfunc.la ../eigen/libgsleigen.la ../linalg/libgsllinalg.la  ../sort/libgslsort.la ../matrix/libgslmatrix.la ../vector/libgslvector.la ../blas/libgslblas.la @CBLAS_LINK_LIBS@ ../block/libgslblock.la ../complex/libgslcomplex.la ../ieee-utils/libgslieeeutils.la  ../err/libgslerr.la ../test/libgsltest.la ../sys/libgslsys.la ../utils/libutils.la
- 
- test_SOURCES = test_sf.c test_sf.h test_airy.c test_bessel.c test_coulomb.c test_dilog.c test_gamma.c test_hyperg.c test_legendre.c test_mathieu.c
-   
-diff --git a/wavelet/Makefile.am b/wavelet/Makefile.am
-index 9da20d8..8cdbd77 100644
---- a/wavelet/Makefile.am
-+++ b/wavelet/Makefile.am
-@@ -10,7 +10,7 @@ check_PROGRAMS = test
- 
- TESTS = $(check_PROGRAMS)
- 
--test_LDADD = libgslwavelet.la ../blas/libgslblas.la ../cblas/libgslcblas.la ../matrix/libgslmatrix.la ../vector/libgslvector.la ../block/libgslblock.la ../ieee-utils/libgslieeeutils.la  ../err/libgslerr.la ../test/libgsltest.la ../sys/libgslsys.la ../utils/libutils.la
-+test_LDADD = libgslwavelet.la ../blas/libgslblas.la @CBLAS_LINK_LIBS@ ../matrix/libgslmatrix.la ../vector/libgslvector.la ../block/libgslblock.la ../ieee-utils/libgslieeeutils.la  ../err/libgslerr.la ../test/libgsltest.la ../sys/libgslsys.la ../utils/libutils.la
- 
- test_SOURCES = test.c
- 
diff --git a/sci-libs/gsl/files/gsl-2.3-cblas-external.patch b/sci-libs/gsl/files/gsl-2.3-cblas-external.patch
deleted file mode 100644
index 38b25aacc..000000000
--- a/sci-libs/gsl/files/gsl-2.3-cblas-external.patch
+++ /dev/null
@@ -1,101 +0,0 @@
-diff --git a/Makefile.am b/Makefile.am
-index c522001..4513bc8 100644
---- a/Makefile.am
-+++ b/Makefile.am
-@@ -19,7 +19,7 @@ EXTRA_DIST = autogen.sh gsl-config.in gsl.pc.in configure.ac THANKS BUGS gsl.spe
- 
- lib_LTLIBRARIES = libgsl.la
- libgsl_la_SOURCES = version.c
--libgsl_la_LIBADD = $(GSL_LIBADD) $(SUBLIBS)
-+libgsl_la_LIBADD = $(GSL_LIBADD) $(SUBLIBS) @CBLAS_LINK_LIBS@
- libgsl_la_LDFLAGS = $(GSL_LDFLAGS) -version-info $(GSL_LT_VERSION)
- noinst_HEADERS = templates_on.h templates_off.h build.h
- 
-@@ -29,10 +29,10 @@ m4data_DATA = gsl.m4
- bin_PROGRAMS = gsl-randist gsl-histogram
- 
- gsl_randist_SOURCES = gsl-randist.c
--gsl_randist_LDADD = libgsl.la cblas/libgslcblas.la
-+gsl_randist_LDADD = libgsl.la
- 
- gsl_histogram_SOURCES = gsl-histogram.c
--gsl_histogram_LDADD = libgsl.la cblas/libgslcblas.la
-+gsl_histogram_LDADD = libgsl.la
- 
- check_SCRIPTS = test_gsl_histogram.sh pkgconfig.test
- TESTS = test_gsl_histogram.sh pkgconfig.test
-@@ -51,6 +51,8 @@ edit = $(SED) \
- 	-e 's|@GSL_CFLAGS[@]|$(GSL_CFLAGS)|g' \
- 	-e 's|@GSL_LIBM[@]|$(GSL_LIBM)|g' \
- 	-e 's|@GSL_LIBS[@]|$(GSL_LIBS)|g' \
-+	-e 's|@CBLAS_CFLAGS[@]|$(CBLAS_CFLAGS)|g' \
-+	-e 's|@CBLAS_LIBS[@]|$(CBLAS_LIBS)|g' \
- 	-e 's|@LIBS[@]|$(LIBS)|g' \
- 	-e 's|@VERSION[@]|$(VERSION)|g'
- 
-diff --git a/configure.ac b/configure.ac
-index a26fc1e..564d426 100644
---- a/configure.ac
-+++ b/configure.ac
-@@ -208,6 +208,16 @@ if test "x$LIBS" = "x" ; then
-   AC_CHECK_LIB(m, cos)
- fi
- 
-+sinclude(ax_cblas.m4)
-+AX_CBLAS
-+if test "x$CBLAS_LIBS" != "x"; then
-+   CBLAS_LINK_LIBS="$CBLAS_LIBS"
-+else
-+   CBLAS_LINK_LIBS="\$(top_builddir)/cblas/libgslcblas.la"
-+   CBLAS_LIBS="-lgslcblas"
-+fi
-+AC_SUBST(CBLAS_LINK_LIBS)
-+
- dnl Remember to put a definition in acconfig.h for each of these
- AC_CHECK_DECLS(feenableexcept,,,[#define _GNU_SOURCE 1
- #include <fenv.h>]) 
-diff --git a/doc/examples/Makefile.am b/doc/examples/Makefile.am
-index f0dcc02..b2f0c0e 100644
---- a/doc/examples/Makefile.am
-+++ b/doc/examples/Makefile.am
-@@ -8,5 +8,5 @@ examples_txt = blas.txt block.txt bspline.txt cblas.txt cdf.txt cheb.txt combina
- 
- dist_noinst_DATA = $(examples_src) $(examples_txt)
- 
--LDADD = ../../libgsl.la ../../cblas/libgslcblas.la
-+LDADD = ../../libgsl.la @CBLAS_LINK_LIBS@
- AM_DEFAULT_SOURCE_EXT = .c
-diff --git a/gsl-config.in b/gsl-config.in
-old mode 100755
-new mode 100644
-index 3f3fa61..c9c4262
---- a/gsl-config.in
-+++ b/gsl-config.in
-@@ -58,11 +58,11 @@ while test $# -gt 0; do
- 	;;
- 
-     --cflags)
--       	echo @GSL_CFLAGS@ 
-+       	echo @GSL_CFLAGS@ @CBLAS_CFLAGS@ 
-        	;;
- 
-     --libs)
--        : ${GSL_CBLAS_LIB=-lgslcblas}
-+        : ${GSL_CBLAS_LIB=@CBLAS_LIBS@}
- 	echo @GSL_LIBS@ $GSL_CBLAS_LIB @GSL_LIBM@
-        	;;
- 
-diff --git a/gsl.pc.in b/gsl.pc.in
-index 5e9ef21..5a7a0f3 100644
---- a/gsl.pc.in
-+++ b/gsl.pc.in
-@@ -2,7 +2,7 @@ prefix=@prefix@
- exec_prefix=@exec_prefix@
- libdir=@libdir@
- includedir=@includedir@
--GSL_CBLAS_LIB=-lgslcblas
-+GSL_CBLAS_LIB=@CBLAS_LIBS@
- 
- Name: GSL
- Description: GNU Scientific Library
- 
diff --git a/sci-libs/gsl/gsl-1.16-r2.ebuild b/sci-libs/gsl/gsl-1.16-r2.ebuild
deleted file mode 100644
index a28f92b5c..000000000
--- a/sci-libs/gsl/gsl-1.16-r2.ebuild
+++ /dev/null
@@ -1,64 +0,0 @@
-# Copyright 1999-2017 Gentoo Foundation
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=5
-
-AUTOTOOLS_AUTORECONF=1
-MULTILIB_COMPAT=( abi_x86_{32,64} )
-
-inherit alternatives-2 autotools-multilib eutils toolchain-funcs
-
-DESCRIPTION="GNU Scientific Library"
-HOMEPAGE="https://www.gnu.org/software/gsl/"
-SRC_URI="mirror://gnu/${PN}/${P}.tar.gz"
-
-LICENSE="GPL-3"
-SLOT="0"
-KEYWORDS="~amd64 ~x86 ~amd64-linux ~x86-linux"
-IUSE="cblas-external static-libs"
-
-RDEPEND="cblas-external? ( >=virtual/cblas-2.0-r3[${MULTILIB_USEDEP}] )"
-DEPEND="${RDEPEND}
-	>=virtual/pkgconfig-0-r1[${MULTILIB_USEDEP}]"
-
-PATCHES=( "${FILESDIR}"/${P}-cblas-external.patch )
-
-src_configure() {
-	if use cblas-external; then
-		export CBLAS_LIBS="$($(tc-getPKG_CONFIG) --libs cblas)"
-		export CBLAS_CFLAGS="$($(tc-getPKG_CONFIG) --cflags cblas)"
-	fi
-	local myeconfargs=(
-		$(use_with cblas-external)
-	)
-	autotools-multilib_src_configure
-}
-
-multilib_src_install() {
-	autotools-utils_src_install
-	local libname=gslcblas
-
-	cat <<-EOF > ${libname}.pc
-		prefix=${EPREFIX}/usr
-		libdir=\${prefix}/$(get_libdir)
-		includedir=\${prefix}/include
-		Name: ${libname}
-		Description: ${DESCRIPTION} CBLAS implementation
-		Version: ${PV}
-		URL: ${HOMEPAGE}
-		Libs: -L\${libdir} -l${libname}
-		Libs.private: -lm
-		Cflags: -I\${includedir}
-	EOF
-	insinto /usr/$(get_libdir)/pkgconfig
-	doins ${libname}.pc
-
-	GSL_ALTERNATIVES+=( /usr/$(get_libdir)/pkgconfig/cblas.pc ${libname}.pc )
-}
-
-multilib_src_install_all() {
-	# Don't add gsl as a cblas alternative if using cblas-external
-	use cblas-external || alternatives_for cblas gsl 0 \
-		${GSL_ALTERNATIVES[@]} \
-		/usr/include/cblas.h gsl/gsl_cblas.h
-}
diff --git a/sci-libs/gsl/gsl-2.1.ebuild b/sci-libs/gsl/gsl-2.1.ebuild
deleted file mode 100644
index 299a889fc..000000000
--- a/sci-libs/gsl/gsl-2.1.ebuild
+++ /dev/null
@@ -1,72 +0,0 @@
-# Copyright 1999-2017 Gentoo Foundation
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=6
-
-inherit alternatives-2 autotools multilib-build numeric toolchain-funcs
-
-DESCRIPTION="GNU Scientific Library"
-HOMEPAGE="https://www.gnu.org/software/gsl/"
-SRC_URI="mirror://gnu/${PN}/${P}.tar.gz"
-
-LICENSE="GPL-3"
-SLOT="0/19"
-KEYWORDS="~amd64 ~x86 ~amd64-linux ~x86-linux"
-IUSE="cblas-external static-libs"
-
-RDEPEND="cblas-external? ( >=virtual/cblas-2.0-r3[${MULTILIB_USEDEP}] )"
-DEPEND="${RDEPEND}
-	>=virtual/pkgconfig-0-r1[${MULTILIB_USEDEP}]"
-
-PATCHES=( "${FILESDIR}"/${P}-cblas-external.patch )
-
-src_prepare() {
-	default
-	eautoreconf
-	multilib_copy_sources
-}
-
-src_configure() {
-	gsl_configure() {
-		if use cblas-external; then
-			export CBLAS_LIBS="$($(tc-getPKG_CONFIG) --libs cblas)"
-			export CBLAS_CFLAGS="$($(tc-getPKG_CONFIG) --cflags cblas)"
-		fi
-		econf $(use_with cblas-external)
-	}
-	multilib_foreach_abi run_in_build_dir gsl_configure
-}
-
-src_compile() {
-	multilib_foreach_abi run_in_build_dir default
-}
-
-src_test() {
-	multilib_foreach_abi run_in_build_dir default
-}
-
-src_install() {
-	gsl_install() {
-		local libname=gslcblas
-
-		create_pkgconfig \
-				--name  "${libname}" \
-				--description "${PN} CBLAS implementation" \
-				--libs "-l${libname}" \
-				--libs-private "-lm" \
-				--cflags "-I\${includedir}/${PN}" \
-				--version "${PV}" \
-				--url "${HOMEPAGE}" \
-				"${libname}"
-
-		GSL_ALTERNATIVES+=( /usr/$(get_libdir)/pkgconfig/cblas.pc ${libname}.pc )
-
-		default
-	}
-	multilib_foreach_abi run_in_build_dir gsl_install
-
-	# Don't add gsl as a cblas alternative if using cblas-external
-	use cblas-external || alternatives_for cblas gsl 0 \
-		${GSL_ALTERNATIVES[@]} \
-		/usr/include/cblas.h gsl/gsl_cblas.h
-}
diff --git a/sci-libs/gsl/gsl-2.3.ebuild b/sci-libs/gsl/gsl-2.3.ebuild
deleted file mode 100644
index 296d8e964..000000000
--- a/sci-libs/gsl/gsl-2.3.ebuild
+++ /dev/null
@@ -1,74 +0,0 @@
-# Copyright 1999-2017 Gentoo Foundation
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=6
-
-inherit alternatives-2 autotools multilib-build numeric toolchain-funcs
-
-DESCRIPTION="GNU Scientific Library"
-HOMEPAGE="https://www.gnu.org/software/gsl/"
-SRC_URI="mirror://gnu/${PN}/${P}.tar.gz"
-
-LICENSE="GPL-3"
-SLOT="0/19"
-KEYWORDS="~amd64 ~x86 ~amd64-linux ~x86-linux"
-IUSE="cblas-external static-libs"
-
-RDEPEND="cblas-external? ( >=virtual/cblas-2.0-r3[${MULTILIB_USEDEP}] )"
-DEPEND="${RDEPEND}
-	>=virtual/pkgconfig-0-r1[${MULTILIB_USEDEP}]"
-
-PATCHES=(
-	"${FILESDIR}"/${PN}-2.3-cblas-external.patch
-	)
-
-src_prepare() {
-	default
-	eautoreconf
-	multilib_copy_sources
-}
-
-src_configure() {
-	gsl_configure() {
-		if use cblas-external; then
-			export CBLAS_LIBS="$($(tc-getPKG_CONFIG) --libs cblas)"
-			export CBLAS_CFLAGS="$($(tc-getPKG_CONFIG) --cflags cblas)"
-		fi
-		econf $(use_with cblas-external)
-	}
-	multilib_foreach_abi run_in_build_dir gsl_configure
-}
-
-src_compile() {
-	multilib_foreach_abi run_in_build_dir default
-}
-
-src_test() {
-	multilib_foreach_abi run_in_build_dir default
-}
-
-src_install() {
-	gsl_install() {
-		local libname=gslcblas
-
-		create_pkgconfig \
-				--name  "${libname}" \
-				--description "${PN} CBLAS implementation" \
-				--libs "-l${libname}" \
-				--libs-private "-lm" \
-				--cflags "-I\${includedir}/${PN}" \
-				--version "${PV}" \
-				--url "${HOMEPAGE}" \
-				"${libname}"
-
-		GSL_ALTERNATIVES+=( /usr/$(get_libdir)/pkgconfig/cblas.pc ${libname}.pc )
-
-		default
-	}
-	multilib_foreach_abi run_in_build_dir gsl_install
-
-	# Don't add gsl as a cblas alternative if using cblas-external
-	use cblas-external || alternatives_for cblas gsl 0 \
-		${GSL_ALTERNATIVES[@]} \
-		/usr/include/cblas.h gsl/gsl_cblas.h
-}
diff --git a/sci-libs/gsl/gsl-2.4.ebuild b/sci-libs/gsl/gsl-2.4.ebuild
deleted file mode 100644
index f8cb47e0f..000000000
--- a/sci-libs/gsl/gsl-2.4.ebuild
+++ /dev/null
@@ -1,78 +0,0 @@
-# Copyright 1999-2017 Gentoo Foundation
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=6
-
-inherit alternatives-2 autotools flag-o-matic multilib-build numeric toolchain-funcs
-
-DESCRIPTION="GNU Scientific Library"
-HOMEPAGE="https://www.gnu.org/software/gsl/"
-SRC_URI="mirror://gnu/${PN}/${P}.tar.gz"
-
-LICENSE="GPL-3"
-SLOT="0/23"
-KEYWORDS="~amd64 ~x86 ~amd64-linux ~x86-linux"
-IUSE="cblas-external static-libs"
-
-RDEPEND="cblas-external? ( >=virtual/cblas-2.0-r3[${MULTILIB_USEDEP}] )"
-DEPEND="${RDEPEND}
-	>=virtual/pkgconfig-0-r1[${MULTILIB_USEDEP}]"
-
-PATCHES=(
-	"${FILESDIR}"/${PN}-2.3-cblas-external.patch
-	)
-
-src_prepare() {
-	default
-	eautoreconf
-	multilib_copy_sources
-}
-
-src_configure() {
-	gsl_configure() {
-		if use cblas-external; then
-			export CBLAS_LIBS="$($(tc-getPKG_CONFIG) --libs cblas)"
-			export CBLAS_CFLAGS="$($(tc-getPKG_CONFIG) --cflags cblas)"
-		fi
-		econf $(use_with cblas-external)
-	}
-	# fma flags, which can be enabled by -march=native, cause some tests to fail.
-	# https://github.com/gentoo/sci/pull/815
-	append-cflags $(test-flags-CC -mno-fma -mno-fma4)
-
-	multilib_foreach_abi run_in_build_dir gsl_configure
-}
-
-src_compile() {
-	multilib_foreach_abi run_in_build_dir default
-}
-
-src_test() {
-	multilib_foreach_abi run_in_build_dir default
-}
-
-src_install() {
-	gsl_install() {
-		local libname=gslcblas
-
-		create_pkgconfig \
-				--name  "${libname}" \
-				--description "${PN} CBLAS implementation" \
-				--libs "-l${libname}" \
-				--libs-private "-lm" \
-				--cflags "-I\${includedir}/${PN}" \
-				--version "${PV}" \
-				--url "${HOMEPAGE}" \
-				"${libname}"
-
-		GSL_ALTERNATIVES+=( /usr/$(get_libdir)/pkgconfig/cblas.pc ${libname}.pc )
-
-		default
-	}
-	multilib_foreach_abi run_in_build_dir gsl_install
-
-	# Don't add gsl as a cblas alternative if using cblas-external
-	use cblas-external || alternatives_for cblas gsl 0 \
-		${GSL_ALTERNATIVES[@]} \
-		/usr/include/cblas.h gsl/gsl_cblas.h
-}
diff --git a/sci-libs/gsl/gsl-2.5.ebuild b/sci-libs/gsl/gsl-2.5.ebuild
deleted file mode 100644
index 3dda7b878..000000000
--- a/sci-libs/gsl/gsl-2.5.ebuild
+++ /dev/null
@@ -1,78 +0,0 @@
-# Copyright 1999-2018 Gentoo Authors
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=7
-
-inherit alternatives-2 autotools flag-o-matic multilib-build numeric toolchain-funcs
-
-DESCRIPTION="GNU Scientific Library"
-HOMEPAGE="https://www.gnu.org/software/gsl/"
-SRC_URI="mirror://gnu/${PN}/${P}.tar.gz"
-
-LICENSE="GPL-3"
-SLOT="0/23"
-KEYWORDS="~amd64 ~x86 ~amd64-linux ~x86-linux"
-IUSE="cblas-external static-libs"
-
-RDEPEND="cblas-external? ( >=virtual/cblas-2.0-r3[${MULTILIB_USEDEP}] )"
-DEPEND="${RDEPEND}
-	>=virtual/pkgconfig-0-r1[${MULTILIB_USEDEP}]"
-
-PATCHES=(
-	"${FILESDIR}"/${PN}-2.3-cblas-external.patch
-	)
-
-src_prepare() {
-	default
-	eautoreconf
-	multilib_copy_sources
-}
-
-src_configure() {
-	gsl_configure() {
-		if use cblas-external; then
-			export CBLAS_LIBS="$($(tc-getPKG_CONFIG) --libs cblas)"
-			export CBLAS_CFLAGS="$($(tc-getPKG_CONFIG) --cflags cblas)"
-		fi
-		econf $(use_with cblas-external)
-	}
-	# fma flags, which can be enabled by -march=native, cause some tests to fail.
-	# https://github.com/gentoo/sci/pull/815
-	append-cflags $(test-flags-CC -mno-fma -mno-fma4)
-
-	multilib_foreach_abi run_in_build_dir gsl_configure
-}
-
-src_compile() {
-	multilib_foreach_abi run_in_build_dir default
-}
-
-src_test() {
-	multilib_foreach_abi run_in_build_dir default
-}
-
-src_install() {
-	gsl_install() {
-		local libname=gslcblas
-
-		create_pkgconfig \
-				--name  "${libname}" \
-				--description "${PN} CBLAS implementation" \
-				--libs "-l${libname}" \
-				--libs-private "-lm" \
-				--cflags "-I\${includedir}/${PN}" \
-				--version "${PV}" \
-				--url "${HOMEPAGE}" \
-				"${libname}"
-
-		GSL_ALTERNATIVES+=( /usr/$(get_libdir)/pkgconfig/cblas.pc ${libname}.pc )
-
-		default
-	}
-	multilib_foreach_abi run_in_build_dir gsl_install
-
-	# Don't add gsl as a cblas alternative if using cblas-external
-	use cblas-external || alternatives_for cblas gsl 0 \
-		${GSL_ALTERNATIVES[@]} \
-		/usr/include/cblas.h gsl/gsl_cblas.h
-}
diff --git a/sci-libs/gsl/metadata.xml b/sci-libs/gsl/metadata.xml
deleted file mode 100644
index 06112a27a..000000000
--- a/sci-libs/gsl/metadata.xml
+++ /dev/null
@@ -1,25 +0,0 @@
-<?xml version="1.0" encoding="UTF-8"?>
-<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
-<pkgmetadata>
-	<maintainer type="project">
-		<email>sci@gentoo.org</email>
-		<name>Gentoo Science Project</name>
-	</maintainer>
-	<longdescription lang="en">
-The GNU Scientific Library (GSL) is a collection of routines for
-numerical analysis. The routines are written from scratch by the GSL
-team in C, and present a modern API for C programmers, while allowing
-wrappers to be written for very high level languages.
-
-GSL includes data types and routines for complex numbers, vectors,
-matrices, basic linear algebra subroutines (BLAS), eigensystems,
-simulated annealing, minimization, root finding, pseudo-random
-numbers, least-squares fitting, fast Fourier transforms (FFT),
-differential equations, quadrature, Monte Carlo integration, special
-functions, physical constants, and much more. 
-</longdescription>
-	<use>
-		<flag name="cblas-external">Link gsl with external cblas provided by
-(<pkg>virtual/cblas</pkg>) instead of shipped internal version</flag>
-	</use>
-</pkgmetadata>
diff --git a/sci-libs/gvar/Manifest b/sci-libs/gvar/Manifest
new file mode 100644
index 000000000..16bdf1de2
--- /dev/null
+++ b/sci-libs/gvar/Manifest
@@ -0,0 +1 @@
+DIST gvar-13.0.2.tar.gz 1001282 BLAKE2B 5c4032406e3d514351bac6f21b5353c8db4e2081efd26b758cce126cce4a3df350ac8086e89895c73ffc27367773a43354138e8598490cbe8f7bacdde216f0bd SHA512 541cb5cc44909cf44e9f808a08a959aa5e3e91c49356fb8865879a9dbb5fe6f3c4b46d88bc4f9346d9b83163c938dfd697e73b7b9a00815ed6dc383630795cb4
diff --git a/sci-libs/gvar/gvar-13.0.2.ebuild b/sci-libs/gvar/gvar-13.0.2.ebuild
new file mode 100644
index 000000000..b9d9121e4
--- /dev/null
+++ b/sci-libs/gvar/gvar-13.0.2.ebuild
@@ -0,0 +1,22 @@
+EAPI=8
+
+DISTUTILS_EXT=1
+PYTHON_COMPAT=( python3_{10..12} )
+DISTUTILS_USE_PEP517=setuptools
+inherit distutils-r1 pypi
+
+DESCRIPTION="Gaussian random variables."
+HOMEPAGE="https://github.com/gplepage/gvar"
+
+LICENSE="GPL-3"
+SLOT="0"
+KEYWORDS="~amd64 ~arm64"
+
+RDEPEND="
+	>=dev-python/cython-0.17[${PYTHON_USEDEP}]
+	>=dev-python/numpy-1.16[${PYTHON_USEDEP}]
+	dev-python/scipy[${PYTHON_USEDEP}]
+"
+BDEPEND="${RDEPEND}"
+
+distutils_enable_tests unittest
diff --git a/sci-libs/gvar/metadata.xml b/sci-libs/gvar/metadata.xml
new file mode 100644
index 000000000..31346f0dd
--- /dev/null
+++ b/sci-libs/gvar/metadata.xml
@@ -0,0 +1,19 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
+<pkgmetadata>
+	<maintainer type="project">
+		<email>sci@gentoo.org</email>
+		<name>Gentoo Science Project</name>
+	</maintainer>
+	<maintainer type="person">
+		<email>alexander@neuwirth-informatik.de</email>
+		<name>Alexander Puck Neuwirth</name>
+	</maintainer>
+	<longdescription lang="en">
+	This package facilitates the creation and manipulation of arbitrarily complicated (correlated) multi-dimensional Gaussian random variables. The random variables are represented by a new data type (gvar.GVar) that can be used in arithmetic expressions and pure Python functions. Such expressions/functions create new Gaussian random variables while automatically tracking statistical correlations between the new and old variables. This data type is useful for simple error propagation, but also is heavily used by the Bayesian least-squares fitting module lsqfit.py to define priors and specify fit results, while accounting for correlations between all variables.
+	</longdescription>
+	<upstream>
+		<remote-id type="pypi">gvar</remote-id>
+		<remote-id type="github">gplepage/gvar</remote-id>
+	</upstream>
+</pkgmetadata>
diff --git a/sci-libs/handyg/Manifest b/sci-libs/handyg/Manifest
new file mode 100644
index 000000000..3487702bd
--- /dev/null
+++ b/sci-libs/handyg/Manifest
@@ -0,0 +1 @@
+DIST handyg-v0.1.5.tar.gz 107946 BLAKE2B 338b0027f51fd8b329c1af4e6a0e76dda7b9a3d29a12cffcf60948c5800ee8e280ff97726359df483b60dc3d76a26c40bf21804113d318d83539828e54c4a1ff SHA512 f6f068e05c80c6dccf1c4c8a284da752d04d4fd3f15a78eee933227c6a93906fe794ef3ada359831a4098c00b0a7684af91e2f9cca2a06dd8d0381c1c20c59be
diff --git a/sci-libs/handyg/files/handyg-0.1.5-so.patch b/sci-libs/handyg/files/handyg-0.1.5-so.patch
new file mode 100644
index 000000000..48815780e
--- /dev/null
+++ b/sci-libs/handyg/files/handyg-0.1.5-so.patch
@@ -0,0 +1,23 @@
+--- a/configure	2022-09-19 22:54:12.742507414 +0200
++++ b/configure	2022-09-19 23:00:13.452378883 +0200
+@@ -839,7 +839,7 @@
+ objects = \$(addprefix build/,\$(files))
+ 
+ 
+-all: libhandyg.a handyg.mod ${CONF_MPREP:+handyG} geval test
++all: libhandyg.a libhandyg.so handyg.mod ${CONF_MPREP:+handyG} geval test
+ 
+ EOF
+ 
+@@ -868,6 +868,11 @@
+ 		@echo "AR \$@"
+ 		@\$(AR) \$@ \$^
+ 
++libhandyg.so:\$(objects)
++		@echo "\$(FC) \$@"
++		\$(FC) \$(LFLAGS) -Wl,-soname,libhandyg.so -shared -o \$@ \$^
++
++
+ handyg.mod: build/handyg.mod
+ 		cp \$< \$@
+ 
diff --git a/sci-libs/handyg/handyg-0.1.5.ebuild b/sci-libs/handyg/handyg-0.1.5.ebuild
new file mode 100644
index 000000000..97a18c08e
--- /dev/null
+++ b/sci-libs/handyg/handyg-0.1.5.ebuild
@@ -0,0 +1,44 @@
+# Copyright 2022 Gentoo Authors
+# Distributed under the terms of the GNU General Public License v2
+
+EAPI=8
+
+inherit toolchain-funcs
+MY_P=${PN}-v${PV}
+
+DESCRIPTION="Rapid numerical evaluation of generalised polylogarithms"
+HOMEPAGE="https://gitlab.com/mule-tools/handyg"
+SRC_URI="https://gitlab.com/mule-tools/${PN}/-/archive/v${PV}/${MY_P}.tar.gz"
+S="${WORKDIR}/${MY_P}"
+
+LICENSE="GPL-3+"
+SLOT="0"
+KEYWORDS="~amd64"
+
+DEPEND=""
+RDEPEND="${DEPEND}"
+BDEPEND="
+	virtual/fortran
+"
+
+PATCHES=(
+	"${FILESDIR}/${P}-so.patch"
+)
+
+src_configure() {
+	tc-export CC CXX FC AR
+	FFLAGS="${FFLAGS} -fPIC" LD="${FC}" ./configure --prefix="${EPREFIX}/usr" LDFLAGS="${LDFLAGS}"
+}
+
+src_compile() {
+	# single thread force needed since fortan mods depend on each other
+	export MAKEOPTS=-j1
+	emake all
+}
+
+src_install() {
+	dolib.a libhandyg.a
+	dolib.so libhandyg.so
+	doheader handyg.mod
+	dobin geval
+}
diff --git a/sci-libs/handyg/metadata.xml b/sci-libs/handyg/metadata.xml
new file mode 100644
index 000000000..bdee6992b
--- /dev/null
+++ b/sci-libs/handyg/metadata.xml
@@ -0,0 +1,12 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
+<pkgmetadata>
+	<maintainer type="person">
+		<email>alexander@neuwirth-informatik.de</email>
+		<name>Alexander Puck Neuwirth</name>
+	</maintainer>
+	<maintainer type="project">
+		<email>sci-physics@gentoo.org</email>
+		<name>Gentoo Physics Project</name>
+	</maintainer>
+</pkgmetadata>
diff --git a/sci-libs/htslib-plugins/Manifest b/sci-libs/htslib-plugins/Manifest
index 487223b67..e387f4c5e 100644
--- a/sci-libs/htslib-plugins/Manifest
+++ b/sci-libs/htslib-plugins/Manifest
@@ -1 +1 @@
-DIST htslib-plugins-201609.tar.gz 9191 BLAKE2B 37abd0a84cd3f456f9f7593ecfa45f59b8f612fc4f169bc3b6535730194deab1d1e24bb5a0c5b169e5752cfeb0d887748b7abb1e167ffd1351d9af2d37568c1a SHA512 952d909e57d1710e8a607f2f97f71b46e6606cb4b6d47e4b79984ddd7a3c4bd7fdc2c86338c07af08661085e0fc49fc73d59c8d74ca5a994022c60408ae9feff
+DIST htslib-plugins-201712.tar.gz 9323 BLAKE2B c4dd98ec7c554abfed5808de046169449f050f7a7f3030d196f76244593ac7ef4393eff9bb123c55cc6ad60ea33c246090ef24126049e716eb73a4df099b79d2 SHA512 93eff2fde19e0f0e0b33e4a61439a3e5b8da03c932be8ae64ba9af9ea64b2d9995ffbcf58b61e0848cd30ec01d935dd4429650f88701d076a0ff905d1e08f436
diff --git a/sci-libs/htslib-plugins/htslib-plugins-201609.ebuild b/sci-libs/htslib-plugins/htslib-plugins-201609.ebuild
deleted file mode 100644
index 8c5bffe6b..000000000
--- a/sci-libs/htslib-plugins/htslib-plugins-201609.ebuild
+++ /dev/null
@@ -1,16 +0,0 @@
-# Copyright 1999-2017 Gentoo Foundation
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=6
-
-DESCRIPTION="iRODs plugins for >=htslib-1.4"
-HOMEPAGE="https://github.com/samtools/htslib-plugins"
-SRC_URI="https://github.com/samtools/htslib-plugins/archive/201609.tar.gz -> ${P}.tar.gz"
-
-LICENSE="MIT"
-SLOT="0"
-KEYWORDS=""
-IUSE=""
-
-DEPEND=">=sci-libs/iRODS-3"
-RDEPEND="${DEPEND}"
diff --git a/sci-libs/htslib-plugins/htslib-plugins-201712.ebuild b/sci-libs/htslib-plugins/htslib-plugins-201712.ebuild
new file mode 100644
index 000000000..2965f59bc
--- /dev/null
+++ b/sci-libs/htslib-plugins/htslib-plugins-201712.ebuild
@@ -0,0 +1,15 @@
+# Copyright 1999-2021 Gentoo Authors
+# Distributed under the terms of the GNU General Public License v2
+
+EAPI=7
+
+DESCRIPTION="iRODs plugins for >=htslib-1.4"
+HOMEPAGE="https://github.com/samtools/htslib-plugins"
+SRC_URI="https://github.com/samtools/htslib-plugins/archive/${PV}.tar.gz -> ${P}.tar.gz"
+
+LICENSE="MIT"
+SLOT="0"
+KEYWORDS=""
+
+DEPEND=">=sci-libs/iRODS-3"
+RDEPEND="${DEPEND}"
diff --git a/sci-libs/iRODS/Manifest b/sci-libs/iRODS/Manifest
index 766891753..8466e3408 100644
--- a/sci-libs/iRODS/Manifest
+++ b/sci-libs/iRODS/Manifest
@@ -1 +1,2 @@
-DIST iRODS-4.2.0.tar.gz 1683048 BLAKE2B 4cbe2875bbdad00d55a50d15bc5bc58421cfe7eeb73ce11d80611313ade29fb86423b472977646c246c771757a99d7ed586e30d423d08c678a081c499667210c SHA512 122b473fb815a5a4f61f2e0d5634234f68021c8fbfe52a7758287328364caeafab02adf1b482e5ae455357ff6848f2b470adac36acb5ed4687c412f4806e56e3
+DIST iRODS-4.2.11.tar.gz 2183164 BLAKE2B 8c87938e7c8aa731282bf64ec8e017fe0f9ee70c46f07b4c136973bf0ca50954898d93c045440c79eecab84d8adbda6905f1e8eae434c8094ca50ce9f2c1b5dc SHA512 6f938ecc5b872326a4b59b82f119f1c5526c438e7b5c44248b5bba735445e4bc8b287f3bc0eb53b684b17a247aff31cb48b0211a10fc92870d29bdef978715e5
+DIST iRODS-4.2.11_schema_messaging.tar.gz 454 BLAKE2B 09f1f48e22f05545233017db85b84472d0a84b3926b706af6d81cbaaf5d919f508856572daa6e5c61a5a4830527fb982df2df2eb11540a0c7841513eee206ee2 SHA512 d77b0e9d9f80b1513eacc9a86f14ffb02ff5172df41527c41cd49fea26831f11f2c87dc2ea21ae7ad5fb6e0399f8a72248d9accea65101a08158710c5012184a
diff --git a/sci-libs/iRODS/iRODS-4.2.0.ebuild b/sci-libs/iRODS/iRODS-4.2.0.ebuild
deleted file mode 100644
index f2b5d1067..000000000
--- a/sci-libs/iRODS/iRODS-4.2.0.ebuild
+++ /dev/null
@@ -1,21 +0,0 @@
-# Copyright 1999-2017 Gentoo Foundation
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=6
-
-inherit cmake-utils
-
-DESCRIPTION="Integrated Rule Oriented Data System, a data management software"
-HOMEPAGE="https://irods.org"
-SRC_URI="https://github.com/irods/irods/archive/4.2.0.tar.gz -> ${P}.tar.gz"
-
-LICENSE="BSD-with-attribution"
-SLOT="0"
-KEYWORDS=""
-IUSE=""
-
-CDEPEND="sys-devel/clang"
-DEPEND=""
-RDEPEND="${DEPEND}"
-
-S="${WORKDIR}"/irods-"${PV}"
diff --git a/sci-libs/iRODS/iRODS-4.2.11.ebuild b/sci-libs/iRODS/iRODS-4.2.11.ebuild
new file mode 100644
index 000000000..849a7c509
--- /dev/null
+++ b/sci-libs/iRODS/iRODS-4.2.11.ebuild
@@ -0,0 +1,76 @@
+# Copyright 1999-2022 Gentoo Authors
+# Distributed under the terms of the GNU General Public License v2
+
+EAPI=7
+
+inherit cmake llvm
+
+MESSAGING_COMMIT="24c73702c88e94c3b159dac97fe7a0640dfc209d"
+
+DESCRIPTION="Integrated Rule Oriented Data System, a data management software"
+HOMEPAGE="https://irods.org"
+SRC_URI="
+	https://github.com/irods/irods/archive/${PV}.tar.gz -> ${P}.tar.gz
+	https://github.com/irods/irods_schema_messaging/archive/${MESSAGING_COMMIT}.tar.gz -> ${P}_schema_messaging.tar.gz
+"
+S="${WORKDIR}/irods-${PV}"
+
+LICENSE="BSD"
+SLOT="0"
+# need the c++ version of avro
+KEYWORDS=""
+
+DEPEND="
+	app-arch/libarchive
+	dev-cpp/catch:0
+	dev-libs/avro-c
+	dev-libs/boost:=
+	dev-libs/jansson
+	dev-libs/json-c
+	dev-libs/libfmt
+	dev-libs/openssl
+	dev-libs/spdlog
+	sys-libs/libcxx
+	sys-libs/pam
+	net-libs/cppzmq
+	net-libs/zeromq
+"
+RDEPEND="${DEPEND}"
+BDEPEND="
+	sys-devel/clang
+"
+
+src_unpack() {
+	default
+	mv "${WORKDIR}/irods_schema_messaging-${MESSAGING_COMMIT}/v1" "${S}/irods_schema_messaging/" || die
+}
+
+src_prepare() {
+	cmake_src_prepare
+	# use the correct lib dir
+	find . -name "CMakeLists.txt" -exec sed -i \
+		-e '/${IRODS_EXTERNALS_FULLPATH_.*}/s/\/lib\//\/lib64\//g' \
+		{} + || die
+}
+
+src_configure() {
+	local mycmakeargs=(
+		-DIRODS_EXTERNALS_FULLPATH_CLANG="$(get_llvm_prefix)"
+		-DIRODS_EXTERNALS_FULLPATH_CLANG_RUNTIME="$(get_llvm_prefix)"
+		-DIRODS_EXTERNALS_FULLPATH_ARCHIVE="${EPREFIX}/usr"
+		-DIRODS_EXTERNALS_FULLPATH_AVRO="${EPREFIX}/usr"
+		-DIRODS_EXTERNALS_FULLPATH_BOOST="${EPREFIX}/usr"
+		-DIRODS_EXTERNALS_FULLPATH_CATCH2="${EPREFIX}/usr"
+		-DIRODS_EXTERNALS_FULLPATH_FMT="${EPREFIX}/usr"
+		-DIRODS_EXTERNALS_FULLPATH_ZMQ="${EPREFIX}/usr"
+		-DIRODS_EXTERNALS_FULLPATH_JANSSON="${EPREFIX}/usr"
+		-DIRODS_EXTERNALS_FULLPATH_SPDLOG="${EPREFIX}/usr"
+		-DIRODS_EXTERNALS_FULLPATH_CPPZMQ="${EPREFIX}/usr"
+		-DIRODS_EXTERNALS_FULLPATH_JSON="${EPREFIX}/usr"
+		-DIRODS_EXTERNALS_FULLPATH_NANODBC="${EPREFIX}/usr"
+		# pretend we are Arch, otherwise fatal error
+		-DIRODS_LINUX_DISTRIBUTION_NAME="arch"
+		-DIRODS_LINUX_DISTRIBUTION_VERSION_MAJOR="1"
+	)
+	cmake_src_configure
+}
diff --git a/sci-libs/iml/Manifest b/sci-libs/iml/Manifest
deleted file mode 100644
index 23be05009..000000000
--- a/sci-libs/iml/Manifest
+++ /dev/null
@@ -1,2 +0,0 @@
-DIST iml-1.0.4.tar.bz2 407347 BLAKE2B 074ed0cc6b5ec5dde406640508180bab353e5a790ce46959e79c5134c890e0e407086f2ea0b06019c5a30bd79811f1122714bbc9a5f13ba0c42b8a912dbcea1e SHA512 21cb4f124b7e06526238aff053eb9249eece9342122ec00e7ab2aec68b1c6298a30bee3dd183e322ad4cce636faa679d11422d7cc72b524d8a9b5936017fd209
-DIST iml-1.0.5.tar.bz2 391757 BLAKE2B 5895b353269ce19e17e2522f78eb705c89a47ed3c6cce54d1b7ab3003f59d0a13050b30ce9cedbf38392c737c169740b6c2433f1a74856b0f9d4e6e007ebf804 SHA512 b5a85982636035cc50acba7dcff5478c6271be3669313f01915b2761302d4c77617c0dd7932daf74433098670d3ffdb2ef19eb24450b40709750a0b7c8f797f1
diff --git a/sci-libs/iml/files/iml-1.0.4-use-any-cblas-implementation.patch b/sci-libs/iml/files/iml-1.0.4-use-any-cblas-implementation.patch
deleted file mode 100644
index 3d88a3906..000000000
--- a/sci-libs/iml/files/iml-1.0.4-use-any-cblas-implementation.patch
+++ /dev/null
@@ -1,22 +0,0 @@
-Patch to detect ATLAS or cblas. Ported from 1.0.3 to 1.0.4.
-
-Patch by Marius Brehler.
---- configure.ac
-+++ configure.ac
-@@ -76,15 +76,7 @@ location with the options --with-gmp-inc
- respectively when running configure.
- )])
- 
--IML_CHECK_CBLAS(,,[AC_MSG_WARN(
--CBLAS not found!
--Please make sure that --with-cblas=<linker flags> and optional --with-cblas-include=<path> and --with-cblas-lib=<path> are correctly set.
--Trying legacy ATLAS configuration.)
--IML_CHECK_ATLAS(,,[AC_MSG_ERROR(
--ATLAS not found! 
--ATLAS version 3.0 or greater is required for this library to compile. Please make sure ATLAS is installed and specify the header and libraries location with the options --with-atlas-include=<path> and --with-atlas-lib=<path> respectively when running configure.)
--])
--])
-+PKG_CHECK_MODULES([ATLAS], [cblas])
- 
- AC_SUBST(LIBIML_LDFLAGS)
- AC_SUBST(LDFLAGS)
diff --git a/sci-libs/iml/iml-1.0.4.ebuild b/sci-libs/iml/iml-1.0.4.ebuild
deleted file mode 100644
index 9c3e94a24..000000000
--- a/sci-libs/iml/iml-1.0.4.ebuild
+++ /dev/null
@@ -1,34 +0,0 @@
-# Copyright 1999-2015 Gentoo Foundation
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=5
-
-inherit autotools-utils
-
-DESCRIPTION="Integer Matrix Library"
-HOMEPAGE="http://www.cs.uwaterloo.ca/~astorjoh/iml.html"
-SRC_URI="http://www.cs.uwaterloo.ca/~astorjoh/${P}.tar.bz2"
-
-LICENSE="GPL-2"
-SLOT="0"
-KEYWORDS="~amd64 ~x86 ~amd64-linux ~x86-linux"
-IUSE="static-libs"
-
-RESTRICT="mirror"
-
-DEPEND="virtual/cblas"
-RDEPEND="${DEPEND}"
-
-AUTOTOOLS_AUTORECONF=yes
-AT_M4DIR="config"
-DOCS=( AUTHORS ChangeLog README )
-PATCHES=(
-	"${FILESDIR}"/${P}-use-any-cblas-implementation.patch
-)
-
-src_configure() {
-	myeconfargs=(
-		--with-default="${EPREFIX}"/usr
-	)
-	autotools-utils_src_configure
-}
diff --git a/sci-libs/iml/iml-1.0.5.ebuild b/sci-libs/iml/iml-1.0.5.ebuild
deleted file mode 100644
index 67b4d0153..000000000
--- a/sci-libs/iml/iml-1.0.5.ebuild
+++ /dev/null
@@ -1,36 +0,0 @@
-# Copyright 1999-2015 Gentoo Foundation
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=5
-
-AUTOTOOLS_AUTORECONF=yes
-
-inherit autotools-utils
-
-DESCRIPTION="Integer Matrix Library"
-HOMEPAGE="http://www.cs.uwaterloo.ca/~astorjoh/iml.html"
-SRC_URI="http://www.cs.uwaterloo.ca/~astorjoh/${P}.tar.bz2"
-
-LICENSE="GPL-2"
-SLOT="0"
-KEYWORDS="~amd64 ~x86 ~amd64-linux ~x86-linux"
-IUSE="static-libs"
-
-RESTRICT="mirror"
-
-DEPEND="virtual/cblas"
-RDEPEND="${DEPEND}"
-
-AT_M4DIR="config"
-DOCS=( AUTHORS ChangeLog README )
-
-PATCHES=(
-	"${FILESDIR}"/${PN}-1.0.4-use-any-cblas-implementation.patch
-)
-
-src_configure() {
-	myeconfargs=(
-		--with-default="${EPREFIX}"/usr
-	)
-	autotools-utils_src_configure
-}
diff --git a/sci-libs/iml/metadata.xml b/sci-libs/iml/metadata.xml
deleted file mode 100644
index 673326db1..000000000
--- a/sci-libs/iml/metadata.xml
+++ /dev/null
@@ -1,9 +0,0 @@
-<?xml version="1.0" encoding="UTF-8"?>
-<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
-<pkgmetadata>
-	<maintainer type="project">
-		<email>sci@gentoo.org</email>
-		<name>Gentoo Science Project</name>
-	</maintainer>
-	<longdescription>a free library of C source code which implements algorithms for computing exact solutions to dense systems of linear equations over the integers</longdescription>
-</pkgmetadata>
diff --git a/sci-libs/io_lib/Manifest b/sci-libs/io_lib/Manifest
deleted file mode 100644
index bf2a90999..000000000
--- a/sci-libs/io_lib/Manifest
+++ /dev/null
@@ -1,2 +0,0 @@
-DIST io_lib-1.14.11.tar.gz 3391926 BLAKE2B 42ac0408101d39c00d6480f4511bc4b9173a564da31901976cde41ccc81d4da3ed3abb012170365a28ee20605417237d97b4667159182d67f5521a9a894eedac SHA512 b20c9b407b4708909d9172ba835f4ae40f94dfc8967f3db82f658053dcd689986d44a9b69645ca43e9e07c3c93e0a0c1ff3eaacf55a756f76d46d19b050e5879
-DIST io_lib-1.14.9.tar.gz 1708486 BLAKE2B 47cf8cba2540d889590cb06b8be75c190579214ffbef2e6ba9dda6e99475699fef3da7f7c7732f83128dc959e24c3fd902c1aaa3f7e5b9ac2a092c89865b4dd1 SHA512 425fde2e5beed1737406dca7d62883053183c099160556bbf5c058de8808ea59739b15758e99116d40bb38020791a28822e5ba4dd30de7ec19975379bbbaf054
diff --git a/sci-libs/io_lib/io_lib-1.14.11.ebuild b/sci-libs/io_lib/io_lib-1.14.11.ebuild
deleted file mode 100644
index 0d8fcc5ca..000000000
--- a/sci-libs/io_lib/io_lib-1.14.11.ebuild
+++ /dev/null
@@ -1,71 +0,0 @@
-# Copyright 2019 Gentoo Authors
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=5
-
-inherit autotools-utils eutils versionator
-MY_PV=$(replace_all_version_separators '-')
-
-DESCRIPTION="General purpose trace and experiment file reading/writing interface"
-HOMEPAGE="https://github.com/jkbonfield/io_lib
-	http://staden.sourceforge.net/"
-SRC_URI="https://github.com/jkbonfield/io_lib/archive/${PN}-${MY_PV}.tar.gz -> ${P}.tar.gz"
-
-LICENSE="BSD"
-SLOT="0"
-KEYWORDS="~amd64 ~x86 ~amd64-linux ~x86-linux"
-IUSE="+bzip2 curl +libdeflate lzma static-libs"
-
-S="${WORKDIR}"/"${PN}-${PN}-${MY_PV}"
-
-# >>> Working in BUILD_DIR: "/scratch/var/tmp/portage/sci-libs/io_lib-1.14.11/work/io_lib-1.14.11_build"
-# /scratch/var/tmp/portage/sci-libs/io_lib-1.14.11/temp/environment: line 530: pushd: /scratch/var/tmp/portage/sci-libs/io_lib-1.14.11/work/io_lib-1.14.11_build: No such file or directory
-#  * ERROR: sci-libs/io_lib-1.14.11::science failed (install phase):
-#  *   (no error message)
-#  * 
-#  * Call stack:
-#  *     ebuild.sh, line  124:  Called src_install
-#  *   environment, line 2506:  Called autotools-utils_src_install
-#  *   environment, line  530:  Called die
-#  * The specific snippet of code:
-#  *       pushd "${BUILD_DIR}" > /dev/null || die;
-# 
-BUILD_DIR="${S}"
-
-# Prototype changes in io_lib-1.9.0 create incompatibilities with BioPerl. (Only
-# versions 1.8.11 and 1.8.12 will work with the BioPerl Staden extensions.)
-#DEPEND="!sci-biology/bioperl"
-DEPEND="
-	libdeflate? ( app-arch/libdeflate )
-	lzma? ( app-arch/xz-utils:= app-arch/lzma )
-	bzip2? ( app-arch/bzip2 )
-	curl? ( net-misc/curl )
-	sys-libs/zlib"
-RDEPEND="${DEPEND}"
-
-src_prepare(){
-	# https://github.com/jkbonfield/io_lib/issues/12
-	eautoreconf
-	default
-}
-
-src_configure(){
-	# https://github.com/jkbonfield/io_lib/issues/11
-	# https://github.com/jkbonfield/io_lib/issues/13
-	local myconf=()
-	! use static-libs && myconf+=( "--enable-static=no" )
-	econf ${myconf[@]} $(use_with libdeflate)
-}
-
-src_compile(){
-	# BUG: "have to" provide my own src_compile() because ${P}_build dir is missing now
-	# alternatively BUILD_DIR="${S}" would probably help here too
-	emake
-}
-
-src_install() {
-	# cd "${S}" || die # this does not help to get around the ${P}_build missing
-	# what helped was to set BUILD_DIR="${S}" above
-	autotools-utils_src_install
-	dodoc docs/{Hash_File_Format,ZTR_format}
-}
diff --git a/sci-libs/io_lib/io_lib-1.14.9.ebuild b/sci-libs/io_lib/io_lib-1.14.9.ebuild
deleted file mode 100644
index f5b992183..000000000
--- a/sci-libs/io_lib/io_lib-1.14.9.ebuild
+++ /dev/null
@@ -1,28 +0,0 @@
-# Copyright 1999-2017 Gentoo Foundation
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=5
-
-inherit autotools-utils
-
-DESCRIPTION="General purpose trace and experiment file reading/writing interface"
-HOMEPAGE="http://staden.sourceforge.net/"
-SRC_URI="mirror://sourceforge/staden/${P}.tar.gz"
-
-LICENSE="BSD"
-SLOT="0"
-KEYWORDS="~amd64 ~x86 ~amd64-linux ~x86-linux"
-IUSE="static-libs"
-
-# Prototype changes in io_lib-1.9.0 create incompatibilities with BioPerl. (Only
-# versions 1.8.11 and 1.8.12 will work with the BioPerl Staden extensions.)
-#DEPEND="!sci-biology/bioperl"
-DEPEND="
-	net-misc/curl
-	sys-libs/zlib"
-RDEPEND="${DEPEND}"
-
-src_install() {
-	autotools-utils_src_install
-	dodoc docs/{Hash_File_Format,ZTR_format}
-}
diff --git a/sci-libs/io_lib/metadata.xml b/sci-libs/io_lib/metadata.xml
deleted file mode 100644
index 9d56a9c0f..000000000
--- a/sci-libs/io_lib/metadata.xml
+++ /dev/null
@@ -1,20 +0,0 @@
-<?xml version="1.0" encoding="UTF-8"?>
-<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
-<pkgmetadata>
-	<maintainer type="project">
-		<email>sci@gentoo.org</email>
-		<name>Gentoo Science Project</name>
-	</maintainer>
-	<longdescription>
-io_lib is a library of file reading and writing code to provide a
-general purpose trace file (and Experiment File) reading interface. The
-programmer simply calls the (eg) read_reading to create a "Read" C structure
-with the data loaded into memory.
-	</longdescription>
-	<use>
-		<flag name="libdeflate">Use libdeflate for faster decompression than zlib</flag>
-	</use>
-	<upstream>
-		<remote-id type="sourceforge">staden</remote-id>
-	</upstream>
-</pkgmetadata>
diff --git a/sci-libs/ipp/Manifest b/sci-libs/ipp/Manifest
deleted file mode 100644
index ac43ecaf8..000000000
--- a/sci-libs/ipp/Manifest
+++ /dev/null
@@ -1 +0,0 @@
-DIST parallel_studio_xe_2018_update2_professional_edition.tgz 3877755304 BLAKE2B c8852df23abf080f482002a37af7781b3fbae3ecec448914ea5a237fa2b925073d1a3dc2dd94ba64002ff0f6c7e9b18b25fa7ada811a83b10344eb9b92cb37ff SHA512 a9b644b0305d83a9d0daa14d146cb3ce79949db55a410afe48d62259414e6256d9ef533a04bb50807103511db2016c4abcbbf769146854a25638f402a6d0f2be
diff --git a/sci-libs/ipp/ipp-18.0.2.199.ebuild b/sci-libs/ipp/ipp-18.0.2.199.ebuild
deleted file mode 100644
index 0d5975c4d..000000000
--- a/sci-libs/ipp/ipp-18.0.2.199.ebuild
+++ /dev/null
@@ -1,43 +0,0 @@
-# Copyright 1999-2018 Gentoo Foundation
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=6
-
-INTEL_DIST_SKU=3235
-INTEL_DIST_PV=2018_update2_professional_edition
-
-inherit intel-sdp-r1
-
-DESCRIPTION="Intel Integrated Performance Primitive library"
-HOMEPAGE="http://software.intel.com/en-us/articles/intel-ipp/"
-
-IUSE="doc"
-KEYWORDS="-* ~amd64 ~x86 ~amd64-linux ~x86-linux"
-
-DEPEND=""
-RDEPEND="~dev-libs/intel-common-${PV}[compiler]"
-
-CHECKREQS_DISK_BUILD=6500M
-
-INTEL_DIST_DAT_RPMS=(
-	"ipp-common-2018.2-199-2018.2-199.noarch.rpm"
-	"ipp-common-ps-2018.2-199-2018.2-199.noarch.rpm")
-INTEL_DIST_AMD64_RPMS=(
-	"ipp-mt-2018.2-199-2018.2-199.x86_64.rpm"
-	"ipp-mt-devel-2018.2-199-2018.2-199.x86_64.rpm"
-	"ipp-st-2018.2-199-2018.2-199.x86_64.rpm"
-	"ipp-st-devel-2018.2-199-2018.2-199.x86_64.rpm"
-	"ipp-st-devel-ps-2018.2-199-2018.2-199.x86_64.rpm")
-INTEL_DIST_X86_RPMS=(
-	"ipp-mt-32bit-2018.2-199-2018.2-199.x86_64.rpm"
-	"ipp-mt-devel-32bit-2018.2-199-2018.2-199.x86_64.rpm"
-	"ipp-st-32bit-2018.2-199-2018.2-199.x86_64.rpm"
-	"ipp-st-devel-32bit-2018.2-199-2018.2-199.x86_64.rpm"
-	"ipp-st-devel-ps-32bit-2018.2-199-2018.2-199.x86_64.rpm")
-
-pkg_setup() {
-	if use doc; then
-		INTEL_DIST_DAT_RPMS+=(
-			"ipp-doc-2018-2018.2-199.noarch.rpm")
-	fi
-}
diff --git a/sci-libs/ipp/metadata.xml b/sci-libs/ipp/metadata.xml
deleted file mode 100644
index 7bd17909e..000000000
--- a/sci-libs/ipp/metadata.xml
+++ /dev/null
@@ -1,13 +0,0 @@
-<?xml version="1.0" encoding="UTF-8"?>
-<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
-<pkgmetadata>
-	<maintainer type="project">
-		<email>sci@gentoo.org</email>
-		<name>Gentoo Science Project</name>
-	</maintainer>
-	<longdescription lang="en">
-Intel(R) Integrated Performance Primitives (Intel(R) IPP) is a
-library of multi-core-ready, optimized software functions for
-multimedia data processing, and communications applications.
-</longdescription>
-</pkgmetadata>
diff --git a/sci-libs/itk/Manifest b/sci-libs/itk/Manifest
index cae86acd2..87328da27 100644
--- a/sci-libs/itk/Manifest
+++ b/sci-libs/itk/Manifest
@@ -1,5 +1,12 @@
-DIST DoxygenInsightToolkit-4.4.0.tar.gz 779393284 SHA256 a2e9a74dad840f6af7e3f3a518f43d75cad511d6b6b4b09d61f5b1b1b72d25c3 SHA512 9bdd6cedcdf5c30afb7f73130074983a56c397db776b927aae78b15a80d1158cca4563f92795d804ade34f4860b350cbbd157ed6924d53cb2ddfccf478e403c6 WHIRLPOOL 114f6ebb4052a8845559a9fa7f2883aa7bba90ff07dd7cd64d4e305e5ffdb35969b8b18b31b631e99d293fe06d95389359b23697544797a7703d9a973bd23246
-DIST DoxygenInsightToolkit-4.5.0.tar.gz 871324021 SHA256 bcc66662aa836cbb287a184870ba0aaf1b94e47d16d8e5d8bd2d30d77172781e SHA512 0bdf870c1600d847a635eefb8109dc12030387124de70c5c2b03f6a61bab796ce39c56792fcaa5779f741fce9c4d9bc621dcd70b389a805301e14c01422202a1 WHIRLPOOL 6315d22958bbfd7435d9948f1da6f3c1695abf441fc80b6c3545ad48cff42c4c0e871c091251c40cc7a2db422123304d4feaf08527c67236b34ced11c569487d
-DIST InsightToolkit-4.12.0.tar.xz 12246508 BLAKE2B c14cf0b4b1fab8a6f27f1e863ff79228473dd1d9c7fe76bca3791d8c3fad39a4f448ee81cee9ca52a974df166db7b22cd6896353482bf8c587c272266501ea5a SHA512 b0ed1a9e02d238783edf68706ae9bdd23d2cf3e90274caa0f09faafab2d55729663a45f4ef4f5884f07a2160c5dcfb179ec445718b83e235007a0002a7e19e96
-DIST InsightToolkit-4.4.2.tar.gz 231905134 BLAKE2B 910c08916b3c22f0245aed39378c8f73191d57294032c9fafae1dbe168644312921512e9520c96ba7ed409c20631f9d6a9d71241162cbb868cba4638614b7a04 SHA512 c65beca4dd60aa769871bb3089cbb421729a2dcbd8bd3ec42c378ed60828e4327f1faf062f77bcca34306315a1daee6bc29d858dab9aea1c08f4843405fd21e3
-DIST InsightToolkit-4.5.1.tar.xz 212785824 BLAKE2B 1586da2a7d4ff2c65d70459b7f6ddd9dcd04facb2c50fee6b11b6ab78eb2b4bf26b1f4bcbf7c622d7dce098348b9e510bf6f3974a047a7ad9ba3ee58abf44e11 SHA512 a613d37236e3fad68bf83c023141cef72ebfd901ebe371157f474446e0b98fc291f8c5b82b7cb60f01868b78621b919d3602b3768272173e2fe3be96f0813dbb
+DIST ITKAdaptiveDenoising-5.2.1.tar.gz 757851 BLAKE2B 3d94e1db6d2524adf7491e6e24308618b7b69e54184cbfe29a7084b55b8a337228a308233e0f0ab2cef04df9c8f42010a758e0071efdfd4905c28ca6399bfdfd SHA512 7e9c5a6681cd9777b33f11d1a1a5f6d8b1b6f7d2ec2d4d829398c78045b53b247bddea99e4a5450ba8d6666a31b5216ef6e07a2c874c5723af072e0d3c8cf9f4
+DIST ITKAdaptiveDenoising-5.3.0.tar.gz 757851 BLAKE2B 3d94e1db6d2524adf7491e6e24308618b7b69e54184cbfe29a7084b55b8a337228a308233e0f0ab2cef04df9c8f42010a758e0071efdfd4905c28ca6399bfdfd SHA512 7e9c5a6681cd9777b33f11d1a1a5f6d8b1b6f7d2ec2d4d829398c78045b53b247bddea99e4a5450ba8d6666a31b5216ef6e07a2c874c5723af072e0d3c8cf9f4
+DIST ITKGenericLabelInterpolator-1.2.0.tar.gz 137697 BLAKE2B f7bb877654e852f56f8eb1086f988ec3b71106b6528d5cf03734a3c3eb4ce5ac875b52081e0a1339ac237e1616b0516b8cc8efb4429ec0e5ef64ac5461a40836 SHA512 bc1fcd3c13cb182420bb4a5d2c9c789553f8b7b581fd7d0b7d687331e22c90d30efdd338bfbc22dfb8c97d3ab7209f761425c4d12755655d86d81ffb231d881c
+DIST ITKGenericLabelInterpolator-5.2.1.tar.gz 140427 BLAKE2B b19703872926516d9d07acd4078d343e02f00a162d2cb8b6787d6210223be375a059e767cf9c32dd234e77ff51d1af5e08d9a9844c34e23a531938c7d3ded4a9 SHA512 69e53b281cd3f7c136ad9e7ded2c362e0d9e22dc2bd595f42abcefe2cf9ec4fa0f44192efc3d328290be4adaee1ebd74be3035b18147081cc8b8479a333cdea6
+DIST InsightData-5.2.1.tar.gz 293448802 BLAKE2B fd2bb012c0d96243d3543993a87e73c43be0626b0478959e36633f22c7e8d48a46d0f4d18fa3a8d952d4a705ca20594d92c07044000b8e1bc65390ce981af3e7 SHA512 93eae6bdf62ce29ea6dfb1dddedffe4046400a86074dd4d47e3ddcd7ff9ab10031363275cb7f9741add7c02343f1f3e6a41b0ec6533531f4a3a42607c51aa704
+DIST InsightData-5.3.0.tar.gz 366826437 BLAKE2B ae3cbb3f7a51d6b86717a073c0eb55c528baeff240f44413c25ce11319a7e0ef9ff073d1cb94d2d15d104687fe5b8e95d0d4286832dbb02993da8fe706fecb28 SHA512 3caf7d1d64543312d668ef1a6b8c879161a37deee5c980fbfeb14e299a296a2825ae48463bff915f50c98ec0ccdbef3e1aff7c4f52604a93c6028951f90a4757
+DIST InsightToolkit-5.2.1.tar.gz 20702482 BLAKE2B 06dc73a80b4999baff3fc75e225c8720d00927fd268bd0398bb0eea44679777b777836f307f02a2df3641a300e17c9c2ee9f77d2a87539bf8a6ed49ce341bf23 SHA512 6786e39cdf3d0c3a31abd1e23481e30f6dc9dac189ffe372dde3db688f2f57686a8beb321778327e1ff683ed844d41f1dee937b0ba542b2365e2195dfca398c7
+DIST InsightToolkit-5.3.0.tar.gz 21577835 BLAKE2B 7538b673cbe17ab23d6b70e2cb2486e6711df6a79d6806c641a10a8b624c4723ca5f562b97be814551c79c42dea772ac64ed7bc8fdf2d28f5a95cb6462e50638 SHA512 29359839c0fb13acd430410e6adadbecb4d9d8cb4871a0aba0ac67b539c235354a591655dd654f43daa5f035a33721671d665eee8a4a129a9d0d3419e2356e97
+DIST itk-5.2.1-testingdata.tar.gz 2411475710 BLAKE2B edb8ba9bea8bf890749aa46ab3fb29f7d3e25e0f8bb7da7d7cca8c6524f75778b823232536602ade763c025b8e0fe134a555e6fcf652b8d42cc08f08cbd0c29b SHA512 89b160dc5f7781e148aad065f539b80b9accb9ec384e424398287e62b42a88cff610afcf41622a6d3e4e12c1938e7403b3dae65fa13bfb40c29a6b2f90a02398
+DIST itk-5.3.0-testingdata.tar.gz 2569680868 BLAKE2B a358bdb3a9f6de883e9fe41129af88d7a476acc4839fd17075d484a441db40d7f1f2f247d07701817464de5c997b18066628921652630a5f110e238d3f2419ec SHA512 5fa0834c25d128c915b5bdaefb13574952e680fe52a5c99ced614737e52f57abce59510be764766ce43769ae5731c35c7d646cdf3e21f495aee14fbb7d1835b4
+DIST itk-test-a5e11ea71164ff78c65fcf259db01ea5db981a9d868e60045ff2bffca92984df1174bf984a1076e450f0d5d69b4f0191ed1a61465c220e2c91a893b5df150c0a 214819 BLAKE2B cd65212e72cb80eff54ee3f22d05b55036470684c582334fe94826a2d4ed49c840c50a214996f64f2bcd710e5973c2d46201ef31732fe847a43504379df62e25 SHA512 a5e11ea71164ff78c65fcf259db01ea5db981a9d868e60045ff2bffca92984df1174bf984a1076e450f0d5d69b4f0191ed1a61465c220e2c91a893b5df150c0a
+DIST itk-test-bcdbb347f3704262d1f00be7179d6a0a6e68aed56c0653e8072ee5a94985c713bd229c935b1226a658af84fb7f1fffc2458c98364fc35303a2303b12f9f7ce2f 215417 BLAKE2B 318a6c55ba259a5af1e3e19cf859267caa0a612b05abfd9a83d9943902fd7edc25ec002707ed4ec85f7aebd4c5a82411942b5cfe2dc713c905a5bb5d1aa5ef23 SHA512 bcdbb347f3704262d1f00be7179d6a0a6e68aed56c0653e8072ee5a94985c713bd229c935b1226a658af84fb7f1fffc2458c98364fc35303a2303b12f9f7ce2f
diff --git a/sci-libs/itk/files/0001-BUG-Wrap-TransformFileReader-TransformFileWriter.patch b/sci-libs/itk/files/0001-BUG-Wrap-TransformFileReader-TransformFileWriter.patch
deleted file mode 100644
index 094ee3229..000000000
--- a/sci-libs/itk/files/0001-BUG-Wrap-TransformFileReader-TransformFileWriter.patch
+++ /dev/null
@@ -1,50 +0,0 @@
-From d069b7b94287dae15fcaf707775f5dd2bbebcc38 Mon Sep 17 00:00:00 2001
-From: Matt McCormick <matt.mccormick@kitware.com>
-Date: Wed, 5 Feb 2014 15:52:34 -0500
-Subject: [PATCH 1/3] BUG: Wrap TransformFileReader, TransformFileWriter.
-
-Missing CMakeLists.txt in the wrapping directory.  Need to explicitly include
-the headers after "Template" was appended to the class name.
-
-Suggested-by: Sami Koho <sami.koho@gmail.com>
-
-Change-Id: I6f994bb18f37d5adf1d0f0311fa73506c41239a7
----
- Modules/IO/TransformBase/wrapping/CMakeLists.txt              | 3 +++
- Modules/IO/TransformBase/wrapping/itkTransformFileReader.wrap | 2 ++
- Modules/IO/TransformBase/wrapping/itkTransformFileWriter.wrap | 2 ++
- 3 files changed, 7 insertions(+)
- create mode 100644 Modules/IO/TransformBase/wrapping/CMakeLists.txt
-
-diff --git a/Modules/IO/TransformBase/wrapping/CMakeLists.txt b/Modules/IO/TransformBase/wrapping/CMakeLists.txt
-new file mode 100644
-index 0000000..6072567
---- /dev/null
-+++ b/Modules/IO/TransformBase/wrapping/CMakeLists.txt
-@@ -0,0 +1,3 @@
-+itk_wrap_module(ITKIOTransformBase)
-+itk_auto_load_submodules()
-+itk_end_wrap_module()
-diff --git a/Modules/IO/TransformBase/wrapping/itkTransformFileReader.wrap b/Modules/IO/TransformBase/wrapping/itkTransformFileReader.wrap
-index 9b52fbc..662df9e 100644
---- a/Modules/IO/TransformBase/wrapping/itkTransformFileReader.wrap
-+++ b/Modules/IO/TransformBase/wrapping/itkTransformFileReader.wrap
-@@ -1,3 +1,5 @@
-+set(WRAPPER_AUTO_INCLUDE_HEADERS OFF)
-+itk_wrap_include("itkTransformFileReader.h")
- itk_wrap_class("itk::TransformFileReaderTemplate" POINTER)
-   foreach(t ${WRAP_ITK_REAL})
-     itk_wrap_template("${ITKM_${t}}" "${ITKT_${t}}")
-diff --git a/Modules/IO/TransformBase/wrapping/itkTransformFileWriter.wrap b/Modules/IO/TransformBase/wrapping/itkTransformFileWriter.wrap
-index 4f1ac4a..356aaf3 100644
---- a/Modules/IO/TransformBase/wrapping/itkTransformFileWriter.wrap
-+++ b/Modules/IO/TransformBase/wrapping/itkTransformFileWriter.wrap
-@@ -1,3 +1,5 @@
-+set(WRAPPER_AUTO_INCLUDE_HEADERS OFF)
-+itk_wrap_include("itkTransformFileWriter.h")
- itk_wrap_class("itk::TransformFileWriterTemplate" POINTER)
-   foreach(t ${WRAP_ITK_REAL})
-     itk_wrap_template("${ITKM_${t}}" "${ITKT_${t}}")
--- 
-1.8.5.3
-
diff --git a/sci-libs/itk/files/0002-COMP-Fixed-itkQuasiNewtonOptimizerv4-wrapping-warnin.patch b/sci-libs/itk/files/0002-COMP-Fixed-itkQuasiNewtonOptimizerv4-wrapping-warnin.patch
deleted file mode 100644
index 4c74d5451..000000000
--- a/sci-libs/itk/files/0002-COMP-Fixed-itkQuasiNewtonOptimizerv4-wrapping-warnin.patch
+++ /dev/null
@@ -1,28 +0,0 @@
-From 66d2955fbe5528d9df216c639277d1d2686447e5 Mon Sep 17 00:00:00 2001
-From: Michka Popoff <michkapopoff@gmail.com>
-Date: Fri, 7 Feb 2014 19:24:49 +0100
-Subject: [PATCH 2/3] COMP: Fixed itkQuasiNewtonOptimizerv4 wrapping warnings
-
-The warning :
-/scratch/dashboards/Linux-x86_64-gcc4.4-WrapITK/ITK-build/Wrapping/Modules/ITKOptimizersv4/itkQuasiNewtonOptimizerv4.xml: warning(5): Unknown type type: itk::QuasiNewtonOptimizerv4 [typedef]
-/scratch/dashboards/Linux-x86_64-gcc4.4-WrapITK/ITK-build/Wrapping/Modules/ITKOptimizersv4/itkQuasiNewtonOptimizerv4.xml: warning(4): ITK type not wrapped, or currently not known: itk::QuasiNewtonOptimizerv4Template< double >
----
- .../Numerics/Optimizersv4/wrapping/itkQuasiNewtonOptimizerv4.wrap | 8 +++++++-
- 1 file changed, 7 insertions(+), 1 deletion(-)
-
-diff --git a/Modules/Numerics/Optimizersv4/wrapping/itkQuasiNewtonOptimizerv4.wrap b/Modules/Numerics/Optimizersv4/wrapping/itkQuasiNewtonOptimizerv4.wrap
-index 4a43dd4..7eed11c 100644
---- a/Modules/Numerics/Optimizersv4/wrapping/itkQuasiNewtonOptimizerv4.wrap
-+++ b/Modules/Numerics/Optimizersv4/wrapping/itkQuasiNewtonOptimizerv4.wrap
-@@ -1 +1,7 @@
--itk_wrap_simple_class("itk::QuasiNewtonOptimizerv4" POINTER)
-+set(WRAPPER_AUTO_INCLUDE_HEADERS OFF)
-+itk_wrap_include("itkQuasiNewtonOptimizerv4.h")
-+itk_wrap_class("itk::QuasiNewtonOptimizerv4Template" POINTER)
-+  foreach(t ${WRAP_ITK_REAL})
-+    itk_wrap_template("${ITKM_${t}}" "${ITKT_${t}}")
-+  endforeach(t)
-+itk_end_wrap_class()
--- 
-1.8.5.3
-
diff --git a/sci-libs/itk/files/0003-COMP-Fixed-itkGradientDescentOptimizerv4-wrapping-wa.patch b/sci-libs/itk/files/0003-COMP-Fixed-itkGradientDescentOptimizerv4-wrapping-wa.patch
deleted file mode 100644
index d77345edf..000000000
--- a/sci-libs/itk/files/0003-COMP-Fixed-itkGradientDescentOptimizerv4-wrapping-wa.patch
+++ /dev/null
@@ -1,73 +0,0 @@
-From fced46ce8769b4edc7971ea0928045390b5c3f84 Mon Sep 17 00:00:00 2001
-From: Michka Popoff <michkapopoff@gmail.com>
-Date: Mon, 10 Feb 2014 09:41:42 +0100
-Subject: [PATCH 3/3] COMP: Fixed itkGradientDescentOptimizerv4 wrapping
- warnings
-
-I splitted the 3 wrapping calls in 3 separate files and fixed the wrapping.
-
-The warnings :
-/home/kevin/kitware/ITK_Build/Wrapping/Modules/ITKOptimizersv4/itkGradientDescentOptimizerv4.xml: warning(5): Unknown type type: itk::GradientDescentOptimizerBasev4 [typedef]
-/home/kevin/kitware/ITK_Build/Wrapping/Modules/ITKOptimizersv4/itkGradientDescentOptimizerv4.xml: warning(5): Unknown type type: itk::GradientDescentOptimizerv4 [typedef]
-/home/kevin/kitware/ITK_Build/Wrapping/Modules/ITKOptimizersv4/itkGradientDescentOptimizerv4.xml: warning(5): Unknown type type: itk::ObjectToObjectOptimizerBase [typedef]
-/home/kevin/kitware/ITK_Build/Wrapping/Modules/ITKOptimizersv4/itkGradientDescentOptimizerv4.xml: warning(4): ITK type not wrapped, or currently not known: itk::GradientDescentOptimizerBasev4Template< double >
-/home/kevin/kitware/ITK_Build/Wrapping/Modules/ITKOptimizersv4/itkGradientDescentOptimizerv4.xml: warning(4): ITK type not wrapped, or currently not known: itk::GradientDescentOptimizerv4Template< double >
-/home/kevin/kitware/ITK_Build/Wrapping/Modules/ITKOptimizersv4/itkGradientDescentOptimizerv4.xml: warning(4): ITK type not wrapped, or currently not known: itk::ObjectToObjectOptimizerBaseTemplate< double >
-
-Should also hopefully fix the new error on the dashboard I introduced by fixing the itkQuasiNewtonOptimizerv4 warnings (http://review.source.kitware.com/#/c/14317/)
-/home/kevin/kitware/ITK_Build/Wrapping/Typedefs/itkQuasiNewtonOptimizerv4.i:87: Warning 401: Nothing known about base class 'itk::GradientDescentOptimizerv4Template< float >'. Ignored.
-/home/kevin/kitware/ITK_Build/Wrapping/Typedefs/itkQuasiNewtonOptimizerv4.i:87: Warning 401: Maybe you forgot to instantiate 'itk::GradientDescentOptimizerv4Template< float >' using %template.
-
-Change-Id: I15b6af11690ed6efeaced68f73af5212ab5dc364
----
- .../wrapping/itkGradientDescentOptimizerBasev4.wrap            |  7 +++++++
- .../Optimizersv4/wrapping/itkGradientDescentOptimizerv4.wrap   | 10 +++++++---
- .../Optimizersv4/wrapping/itkObjectToObjectOptimizerBase.wrap  |  7 +++++++
- 3 files changed, 21 insertions(+), 3 deletions(-)
- create mode 100644 Modules/Numerics/Optimizersv4/wrapping/itkGradientDescentOptimizerBasev4.wrap
- create mode 100644 Modules/Numerics/Optimizersv4/wrapping/itkObjectToObjectOptimizerBase.wrap
-
-diff --git a/Modules/Numerics/Optimizersv4/wrapping/itkGradientDescentOptimizerBasev4.wrap b/Modules/Numerics/Optimizersv4/wrapping/itkGradientDescentOptimizerBasev4.wrap
-new file mode 100644
-index 0000000..74f5a6c
---- /dev/null
-+++ b/Modules/Numerics/Optimizersv4/wrapping/itkGradientDescentOptimizerBasev4.wrap
-@@ -0,0 +1,7 @@
-+set(WRAPPER_AUTO_INCLUDE_HEADERS OFF)
-+itk_wrap_include("itkGradientDescentOptimizerBasev4.h")
-+itk_wrap_class("itk::GradientDescentOptimizerBasev4Template" POINTER)
-+  foreach(t ${WRAP_ITK_REAL})
-+    itk_wrap_template("${ITKM_${t}}" "${ITKT_${t}}")
-+  endforeach(t)
-+itk_end_wrap_class()
-diff --git a/Modules/Numerics/Optimizersv4/wrapping/itkGradientDescentOptimizerv4.wrap b/Modules/Numerics/Optimizersv4/wrapping/itkGradientDescentOptimizerv4.wrap
-index d53a176..3236448 100644
---- a/Modules/Numerics/Optimizersv4/wrapping/itkGradientDescentOptimizerv4.wrap
-+++ b/Modules/Numerics/Optimizersv4/wrapping/itkGradientDescentOptimizerv4.wrap
-@@ -1,3 +1,7 @@
--itk_wrap_simple_class("itk::ObjectToObjectOptimizerBase" POINTER)
--itk_wrap_simple_class("itk::GradientDescentOptimizerBasev4" POINTER)
--itk_wrap_simple_class("itk::GradientDescentOptimizerv4" POINTER)
-+set(WRAPPER_AUTO_INCLUDE_HEADERS OFF)
-+itk_wrap_include("itkGradientDescentOptimizerv4.h")
-+itk_wrap_class("itk::GradientDescentOptimizerv4Template" POINTER)
-+  foreach(t ${WRAP_ITK_REAL})
-+    itk_wrap_template("${ITKM_${t}}" "${ITKT_${t}}")
-+  endforeach(t)
-+itk_end_wrap_class()
-diff --git a/Modules/Numerics/Optimizersv4/wrapping/itkObjectToObjectOptimizerBase.wrap b/Modules/Numerics/Optimizersv4/wrapping/itkObjectToObjectOptimizerBase.wrap
-new file mode 100644
-index 0000000..61b2c44
---- /dev/null
-+++ b/Modules/Numerics/Optimizersv4/wrapping/itkObjectToObjectOptimizerBase.wrap
-@@ -0,0 +1,7 @@
-+set(WRAPPER_AUTO_INCLUDE_HEADERS OFF)
-+itk_wrap_include("itkObjectToObjectOptimizerBase.h")
-+itk_wrap_class("itk::ObjectToObjectOptimizerBaseTemplate" POINTER)
-+  foreach(t ${WRAP_ITK_REAL})
-+    itk_wrap_template("${ITKM_${t}}" "${ITKT_${t}}")
-+  endforeach(t)
-+itk_end_wrap_class()
--- 
-1.8.5.3
-
diff --git a/sci-libs/itk/files/0004-COMP-Warp-OptimizerParameterScalesEstimatorTemplate.patch b/sci-libs/itk/files/0004-COMP-Warp-OptimizerParameterScalesEstimatorTemplate.patch
deleted file mode 100644
index 83b395626..000000000
--- a/sci-libs/itk/files/0004-COMP-Warp-OptimizerParameterScalesEstimatorTemplate.patch
+++ /dev/null
@@ -1,30 +0,0 @@
-Author: Matt McCormick <matt.mccormick@kitware.com>
-Date:   Thu Feb 6 10:26:49 2014 -0500
-
-    COMP: Wrap OptimizerParameterScalesEstimatorTemplate.
-    
-    The class name changed and it became templated.  Fixes:
-    
-      /playpen/blowekamp/MacOSX-WrapITK/ITK-build/Wrapping/Modules/ITKOptimizersv4/itkOptimizerParameterScalesEstimator.xml:
-      warning(5): Unknown type type: itk::OptimizerParameterScalesEstimator
-      [typedef]
-      /playpen/blowekamp/MacOSX-WrapITK/ITK-build/Wrapping/Modules/ITKOptimizersv4/itkOptimizerParameterScalesEstimator.xml:
-      warning(4): ITK type not wrapped, or currently not known:
-      itk::OptimizerParameterScalesEstimatorTemplate< double >
-    
-    Change-Id: Ic6b4d6fba10d5d6c7b58de8d842bad6511e1ae7b
-
-diff --git a/Modules/Numerics/Optimizersv4/wrapping/itkOptimizerParameterScalesEstimator.wrap b/Modules/Numerics/Optimizersv4/wrapping/itkOptim
-index efd6a8c..a647ee4 100644
---- a/Modules/Numerics/Optimizersv4/wrapping/itkOptimizerParameterScalesEstimator.wrap
-+++ b/Modules/Numerics/Optimizersv4/wrapping/itkOptimizerParameterScalesEstimator.wrap
-@@ -1 +1,7 @@
--itk_wrap_simple_class("itk::OptimizerParameterScalesEstimator" POINTER)
-+set(WRAPPER_AUTO_INCLUDE_HEADERS OFF)
-+itk_wrap_include("itkOptimizerParameterScalesEstimator.h")
-+itk_wrap_class("itk::OptimizerParameterScalesEstimatorTemplate" POINTER)
-+  foreach(t ${WRAP_ITK_REAL})
-+    itk_wrap_template("${ITKM_${t}}" "${ITKT_${t}}")
-+  endforeach(t)
-+itk_end_wrap_class()
-
diff --git a/sci-libs/itk/files/0005-make-gdcm-helper-library-static.patch b/sci-libs/itk/files/0005-make-gdcm-helper-library-static.patch
deleted file mode 100644
index d760ac7ba..000000000
--- a/sci-libs/itk/files/0005-make-gdcm-helper-library-static.patch
+++ /dev/null
@@ -1,11 +0,0 @@
-diff --git a/Modules/ThirdParty/GDCM/src/CMakeLists.txt b/Modules/ThirdParty/GDCM/src/CMakeLists.txt
-index e98077c..70f4286 100644
---- a/Modules/ThirdParty/GDCM/src/CMakeLists.txt
-+++ b/Modules/ThirdParty/GDCM/src/CMakeLists.txt
-@@ -1,5 +1,5 @@
- if(ITK_USE_SYSTEM_GDCM)
--  add_library(ITKGDCM ITK-GDCM.cxx)
-+  add_library(ITKGDCM STATIC ITK-GDCM.cxx)
-   target_link_libraries(ITKGDCM gdcmDICT gdcmMSFF)
-   itk_module_target(ITKGDCM)
-   return()
diff --git a/sci-libs/itk/files/itk-5.2.1-fix-castxml-clang-attr-malloc.patch b/sci-libs/itk/files/itk-5.2.1-fix-castxml-clang-attr-malloc.patch
new file mode 100644
index 000000000..05c9d5635
--- /dev/null
+++ b/sci-libs/itk/files/itk-5.2.1-fix-castxml-clang-attr-malloc.patch
@@ -0,0 +1,25 @@
+From: François-Xavier Carton <fx.carton91@gmail.com>
+Date: Thu, 9 Jun 2022 14:56:22 +0200
+Subject: [PATCH] fix attr malloc error with recent glibc/gcc
+
+Recent GCC has support for __attribute__((__malloc__)) with arguments, but clang
+does not. castxml uses clang internally. And recent glibc/gcc uses the attribute
+with arguments. Mix all this, and you get:
+
+error: '__malloc__' attribute takes no arguments
+
+when compiling itk with python wrapping.
+
+To fix this, we add a define to castxml flags to remove the extra arguments.
+
+--- a/Wrapping/Generators/CastXML/CMakeLists.txt	2022-06-09 14:53:15.582352715 +0200
++++ b/Wrapping/Generators/CastXML/CMakeLists.txt	2022-06-09 14:54:38.182351433 +0200
+@@ -237,7 +237,7 @@
+       set(_castxml_cc ${_castxml_cc} "-D_HAS_TR1=0")
+     endif()
+   else()
+-    set(_castxml_cc --castxml-cc-gnu ( "${CMAKE_CXX_COMPILER}" ${_castxml_cc_flags} ))
++    set(_castxml_cc --castxml-cc-gnu ( "${CMAKE_CXX_COMPILER}" ${_castxml_cc_flags} -D__malloc__\(a,b\)=__malloc__ ))
+   endif()
+   set(_target)
+   if(CMAKE_CROSSCOMPILING)
diff --git a/sci-libs/itk/files/itk-5.2.1-system-openjpeg.patch b/sci-libs/itk/files/itk-5.2.1-system-openjpeg.patch
new file mode 100644
index 000000000..ad717f677
--- /dev/null
+++ b/sci-libs/itk/files/itk-5.2.1-system-openjpeg.patch
@@ -0,0 +1,558 @@
+--- a/Modules/ThirdParty/OpenJPEG/CMakeLists.txt
++++ b/Modules/ThirdParty/OpenJPEG/CMakeLists.txt
+@@ -1,16 +1,32 @@
+ project(ITKOpenJPEG)
+ set(ITKOpenJPEG_THIRD_PARTY 1)
+ 
+-set(ITKOpenJPEG_INCLUDE_DIRS
+-  ${ITKOpenJPEG_BINARY_DIR}/src/openjpeg
+-  ${ITKOpenJPEG_SOURCE_DIR}/src/openjpeg
+-  )
+-set(ITKOpenJPEG_LIBRARIES itkopenjpeg)
++option(ITK_USE_SYSTEM_OPENJPEG "Use system-installed openjpeg" ${ITK_USE_SYSTEM_LIBRARIES})
++mark_as_advanced(ITK_USE_SYSTEM_OPENJPEG)
++
++if(ITK_USE_SYSTEM_OPENJPEG)
++  find_package(OpenJPEG REQUIRED)
++  set(ITKOpenJPEG_INCLUDE_DIRS
++    ${ITKOpenJPEG_BINARY_DIR}/src
++    )
++  set(ITKOpenJPEG_SYSTEM_INCLUDE_DIRS
++    ${OPENJPEG_INCLUDE_DIRS}
++    )
++  set(ITKOpenJPEG_LIBRARIES "${OPENJPEG_LIBRARIES}")
++  set(ITKOpenJPEG_NO_SRC 1)
++else()
++  set(ITKOpenJPEG_INCLUDE_DIRS
++    ${ITKOpenJPEG_BINARY_DIR}/src/openjpeg
++    ${ITKOpenJPEG_SOURCE_DIR}/src/openjpeg
++    )
++  set(ITKOpenJPEG_LIBRARIES itkopenjpeg)
++endif()
++
++configure_file(src/itk_openjpeg.h.in src/itk_openjpeg.h)
+ set(ITK_LIBRARY_PROPERTIES WINDOWS_EXPORT_ALL_SYMBOLS FALSE)
+-
+ itk_module_impl()
+ 
+-install(FILES ${ITKOpenJPEG_SOURCE_DIR}/src/itk_openjpeg.h
++install(FILES ${ITKOpenJPEG_BINARY_DIR}/src/itk_openjpeg.h
+   DESTINATION ${ITKOpenJPEG_INSTALL_INCLUDE_DIR}
+   COMPONENT Development
+   )
+diff --git a/Modules/ThirdParty/OpenJPEG/src/itk_openjpeg.h b/Modules/ThirdParty/OpenJPEG/src/itk_openjpeg.h.in
+rename from Modules/ThirdParty/OpenJPEG/src/itk_openjpeg.h
+rename to Modules/ThirdParty/OpenJPEG/src/itk_openjpeg.h.in
+--- a/Modules/ThirdParty/OpenJPEG/src/itk_openjpeg.h
++++ b/Modules/ThirdParty/OpenJPEG/src/itk_openjpeg.h.in
+@@ -25,6 +25,12 @@
+ #ifndef itk_openjpeg_h
+ #define itk_openjpeg_h
+ 
+-#include <itkopenjpeg/openjpeg.h>
++/* Use the openjpeg library configured for ITK.  */
++#cmakedefine ITK_USE_SYSTEM_OPENJPEG
++#ifdef ITK_USE_SYSTEM_OPENJPEG
++# include <openjpeg.h>
++#else
++# include <itkopenjpeg/openjpeg.h>
++#endif
+ 
+ #endif
+--- a/Modules/IO/JPEG2000/src/itkJPEG2000ImageIO.cxx
++++ b/Modules/IO/JPEG2000/src/itkJPEG2000ImageIO.cxx
+@@ -27,8 +27,6 @@
+ extern "C"
+ {
+ #include "openjpeg.h"
+-#include "j2k.h"
+-#include "jp2.h"
+ }
+ 
+ 
+@@ -139,11 +137,11 @@
+ {
+   itkDebugMacro(<< "ReadImageInformation()");
+ 
+-  FILE * l_file = fopen(this->m_FileName.c_str(), "rb");
+-
+-  /* decompression parameters */
++  /* set decoding parameters to default values */
++  opj_set_default_decoder_parameters(&(this->m_Internal->m_DecompressionParameters));
+ 
+-  if (!l_file)
++  opj_stream_t * cio = opj_stream_create_default_file_stream(this->m_FileName.c_str(), true);
++  if (!cio)
+   {
+     itkExceptionMacro("JPEG2000ImageIO failed to open file for reading: " << this->GetFileName() << std::endl
+                                                                           << "Reason: "
+@@ -151,10 +149,5 @@
+   }
+ 
+-  /* set decoding parameters to default values */
+-  opj_set_default_decoder_parameters(&(this->m_Internal->m_DecompressionParameters));
+-
+-  opj_stream_t * cio = opj_stream_create_default_file_stream(l_file, true);
+-
+   this->m_Internal->m_Dinfo = nullptr; /* handle to a decompressor */
+ 
+   opj_image_t * l_image = nullptr;
+@@ -188,9 +181,8 @@
+ 
+       /* get a decoder handle */
+-      this->m_Internal->m_Dinfo = opj_create_decompress(CODEC_J2K);
++      this->m_Internal->m_Dinfo = opj_create_decompress(OPJ_CODEC_J2K);
+       if (!this->m_Internal->m_Dinfo)
+       {
+         opj_stream_destroy(cio);
+-        fclose(l_file);
+         itkExceptionMacro("JPEG2000ImageIO failed to read file: "
+                           << this->GetFileName() << std::endl
+@@ -202,10 +194,9 @@
+     {
+       /* JPEG 2000 compressed image data */
+       /* get a decoder handle */
+-      this->m_Internal->m_Dinfo = opj_create_decompress(CODEC_JP2);
++      this->m_Internal->m_Dinfo = opj_create_decompress(OPJ_CODEC_JP2);
+       if (!this->m_Internal->m_Dinfo)
+       {
+         opj_stream_destroy(cio);
+-        fclose(l_file);
+         itkExceptionMacro("JPEG2000ImageIO failed to read file: "
+                           << this->GetFileName() << std::endl
+@@ -217,10 +208,9 @@
+     {
+       /* JPEG 2000, JPIP */
+       /* get a decoder handle */
+-      this->m_Internal->m_Dinfo = opj_create_decompress(CODEC_JPT);
++      this->m_Internal->m_Dinfo = opj_create_decompress(OPJ_CODEC_JPT);
+       if (!this->m_Internal->m_Dinfo)
+       {
+         opj_stream_destroy(cio);
+-        fclose(l_file);
+         itkExceptionMacro("JPEG2000ImageIO failed to read file: "
+                           << this->GetFileName() << std::endl
+@@ -230,7 +220,6 @@
+     }
+     default:
+       opj_stream_destroy(cio);
+-      fclose(l_file);
+       itkExceptionMacro("JPEG2000ImageIO failed to read file: "
+                         << this->GetFileName() << std::endl
+                         << "Reason: "
+@@ -248,26 +237,8 @@
+   }
+ 
+-  // Image parameters - first tile
+-  OPJ_INT32 l_tile_x0;
+-  OPJ_INT32 l_tile_y0;
+-
+-  // Image parameters - tile width, height and number of tiles
+-  OPJ_UINT32 l_tile_width;
+-  OPJ_UINT32 l_tile_height;
+-  OPJ_UINT32 l_nb_tiles_x;
+-  OPJ_UINT32 l_nb_tiles_y;
+-
+   itkDebugMacro(<< "Trying to read header now...");
+ 
+-  bResult = opj_read_header(this->m_Internal->m_Dinfo,
+-                            &l_image,
+-                            &l_tile_x0,
+-                            &l_tile_y0,
+-                            &l_tile_width,
+-                            &l_tile_height,
+-                            &l_nb_tiles_x,
+-                            &l_nb_tiles_y,
+-                            cio);
++  bResult = opj_read_header(cio, this->m_Internal->m_Dinfo, &l_image);
+ 
+   if (!bResult)
+   {
+@@ -284,13 +255,21 @@
+   }
+ 
+-  this->m_Internal->m_TileStartX = l_tile_x0;
+-  this->m_Internal->m_TileStartY = l_tile_y0;
++  opj_codestream_info_v2_t* cp = opj_get_cstr_info(this->m_Internal->m_Dinfo);
++  if (!cp)
++  {
++    opj_stream_destroy(cio);
++    opj_image_destroy(l_image);
++    itkExceptionMacro("JPEG2000ImageIO failed to read file: " << this->GetFileName() << std::endl
++                                                              << "Reason: Error while reading image header");
++  }
++  this->m_Internal->m_TileStartX = cp->tx0;
++  this->m_Internal->m_TileStartY = cp->ty0;
+ 
+-  this->m_Internal->m_TileWidth = l_tile_width;
+-  this->m_Internal->m_TileHeight = l_tile_height;
++  this->m_Internal->m_TileWidth = cp->tdx;
++  this->m_Internal->m_TileHeight = cp->tdy;
+ 
+-  this->m_Internal->m_NumberOfTilesInX = l_nb_tiles_x;
+-  this->m_Internal->m_NumberOfTilesInY = l_nb_tiles_y;
++  this->m_Internal->m_NumberOfTilesInX = cp->tw;
++  this->m_Internal->m_NumberOfTilesInY = cp->th;
+ 
+ 
+   itkDebugMacro(<< "Number of Components = " << l_image->numcomps);
+@@ -307,6 +286,7 @@
+   else
+   {
+     opj_stream_destroy(cio);
++    opj_image_destroy(l_image);
+     itkExceptionMacro("JPEG2000ImageIO failed to read file: " << this->GetFileName() << std::endl
+                                                               << "Reason: "
+                                                               << "Unknown precision in file: "
+@@ -320,6 +300,6 @@
+       break;
+     case 3:
+-      if (l_image->color_space != CLRSPC_SRGB)
++      if (l_image->color_space != OPJ_CLRSPC_SRGB)
+       {
+         itkWarningMacro(<< "file does not specify color space, assuming sRGB");
+       }
+@@ -349,7 +329,6 @@
+ 
+   /* close the byte stream */
+   opj_stream_destroy(cio);
+-  fclose(l_file);
+ 
+   if (this->m_Internal->m_Dinfo)
+   {
+@@ -368,16 +347,7 @@
+ {
+   itkDebugMacro(<< "JPEG2000ImageIO::Read() Begin");
+ 
+-  FILE * l_file = fopen(this->m_FileName.c_str(), "rb");
+-
+-  if (!l_file)
+-  {
+-    itkExceptionMacro("JPEG2000ImageIO failed to open file for reading: " << this->GetFileName() << std::endl
+-                                                                          << "Reason: "
+-                                                                          << itksys::SystemTools::GetLastSystemError());
+-  }
+-
+-  opj_stream_t * l_stream = opj_stream_create_default_file_stream(l_file, true);
++  opj_stream_t * l_stream = opj_stream_create_default_file_stream(this->m_FileName.c_str(), true);
+   if (!l_stream)
+   {
+     itkExceptionMacro("JPEG2000ImageIO failed to read file: "
+@@ -397,9 +367,10 @@
+     {
+       /* JPEG-2000 codestream */
+       /* get a decoder handle */
+-      this->m_Internal->m_Dinfo = opj_create_decompress(CODEC_J2K);
++      this->m_Internal->m_Dinfo = opj_create_decompress(OPJ_CODEC_J2K);
+       if (!this->m_Internal->m_Dinfo)
+       {
++        opj_stream_destroy(l_stream);
+         itkExceptionMacro("JPEG2000ImageIO failed to read file: "
+                           << this->GetFileName() << std::endl
+                           << "Reason: opj_create_decompress(CODEC_J2K) returns nullptr");
+@@ -410,9 +381,10 @@
+     {
+       /* JPEG 2000 compressed image data */
+       /* get a decoder handle */
+-      this->m_Internal->m_Dinfo = opj_create_decompress(CODEC_JP2);
++      this->m_Internal->m_Dinfo = opj_create_decompress(OPJ_CODEC_JP2);
+       if (!this->m_Internal->m_Dinfo)
+       {
++        opj_stream_destroy(l_stream);
+         itkExceptionMacro("JPEG2000ImageIO failed to read file: "
+                           << this->GetFileName() << std::endl
+                           << "Reason: opj_create_decompress(CODEC_JP2) returns nullptr");
+@@ -423,9 +395,10 @@
+     {
+       /* JPEG 2000, JPIP */
+       /* get a decoder handle */
+-      this->m_Internal->m_Dinfo = opj_create_decompress(CODEC_JPT);
++      this->m_Internal->m_Dinfo = opj_create_decompress(OPJ_CODEC_JPT);
+       if (!this->m_Internal->m_Dinfo)
+       {
++        opj_stream_destroy(l_stream);
+         itkExceptionMacro("JPEG2000ImageIO failed to read file: "
+                           << this->GetFileName() << std::endl
+                           << "Reason: opj_create_decompress(CODEC_JPT) returns nullptr");
+@@ -433,7 +406,7 @@
+       break;
+     }
+     default:
+-      fclose(l_file);
++      opj_stream_destroy(l_stream);
+       itkExceptionMacro("JPEG2000ImageIO failed to read file: "
+                         << this->GetFileName() << std::endl
+                         << "Reason: "
+@@ -445,32 +418,17 @@
+   if (!opj_setup_decoder(this->m_Internal->m_Dinfo, &(this->m_Internal->m_DecompressionParameters)))
+   {
++    opj_stream_destroy(l_stream);
+     itkExceptionMacro("JPEG2000ImageIO failed to read file: " << this->GetFileName() << std::endl
+                                                               << "Reason: opj_setup_decoder returns false");
+   }
+ 
+-  OPJ_INT32 l_tile_x0, l_tile_y0;
+-
+-  OPJ_UINT32 l_tile_width;
+-  OPJ_UINT32 l_tile_height;
+-  OPJ_UINT32 l_nb_tiles_x;
+-  OPJ_UINT32 l_nb_tiles_y;
+-
+-  bool bResult = opj_read_header(this->m_Internal->m_Dinfo,
+-                                 &l_image,
+-                                 &l_tile_x0,
+-                                 &l_tile_y0,
+-                                 &l_tile_width,
+-                                 &l_tile_height,
+-                                 &l_nb_tiles_x,
+-                                 &l_nb_tiles_y,
+-                                 l_stream);
++  bool bResult = opj_read_header(l_stream, this->m_Internal->m_Dinfo, &l_image);
+ 
+   if (!bResult)
+   {
+     opj_destroy_codec(this->m_Internal->m_Dinfo);
+     this->m_Internal->m_Dinfo = nullptr;
+     opj_stream_destroy(l_stream);
+-    fclose(l_file);
+     itkExceptionMacro("JPEG2000ImageIO failed to read file: " << this->GetFileName() << std::endl
+                                                               << "Reason: opj_read_header returns false");
+   }
+@@ -499,7 +457,7 @@
+   itkDebugMacro(<< "p_end_x = " << p_end_x);
+   itkDebugMacro(<< "p_end_y = " << p_end_y);
+ 
+-  bResult = opj_set_decode_area(this->m_Internal->m_Dinfo, p_start_x, p_start_y, p_end_x, p_end_y);
++  bResult = opj_set_decode_area(this->m_Internal->m_Dinfo, l_image, p_start_x, p_start_y, p_end_x, p_end_y);
+ 
+   itkDebugMacro(<< "opj_set_decode_area() after");
+ 
+@@ -509,6 +467,5 @@
+     this->m_Internal->m_Dinfo = nullptr;
+     opj_stream_destroy(l_stream);
+-    fclose(l_file);
+     itkExceptionMacro("JPEG2000ImageIO failed to read file: " << this->GetFileName() << std::endl
+                                                               << "Reason: opj_set_decode_area returns false");
+   }
+@@ -525,13 +482,14 @@
+ 
+   OPJ_UINT32 l_max_data_size = 1000;
+ 
+-  bool l_go_on = true;
++  OPJ_BOOL l_go_on = true;
+ 
+   auto * l_data = (OPJ_BYTE *)malloc(1000);
+ 
+   while (l_go_on)
+   {
+     bool tileHeaderRead = opj_read_tile_header(this->m_Internal->m_Dinfo,
++                                               l_stream,
+                                                &l_tile_index,
+                                                &l_data_size,
+                                                &l_current_tile_x0,
+@@ -540,13 +498,11 @@
+                                                &l_current_tile_y1,
+                                                &l_nb_comps,
+-                                               &l_go_on,
+-                                               l_stream);
++                                               &l_go_on);
+ 
+     if (!tileHeaderRead)
+     {
+       free(l_data);
+       opj_stream_destroy(l_stream);
+-      fclose(l_file);
+       opj_destroy_codec(this->m_Internal->m_Dinfo);
+       opj_image_destroy(l_image);
+       itkExceptionMacro("JPEG2000ImageIO failed to read file: " << this->GetFileName() << std::endl
+@@ -571,7 +527,6 @@
+         if (!l_data)
+         {
+           opj_stream_destroy(l_stream);
+-          fclose(l_file);
+           opj_destroy_codec(this->m_Internal->m_Dinfo);
+           opj_image_destroy(l_image);
+           itkExceptionMacro("JPEG2000ImageIO failed to read file: " << this->GetFileName() << std::endl
+@@ -590,7 +545,6 @@
+       {
+         free(l_data);
+         opj_stream_destroy(l_stream);
+-        fclose(l_file);
+         opj_destroy_codec(this->m_Internal->m_Dinfo);
+         opj_image_destroy(l_image);
+         itkExceptionMacro("JPEG2000ImageIO failed to read file: " << this->GetFileName() << std::endl
+@@ -654,7 +608,6 @@
+   {
+     free(l_data);
+     opj_stream_destroy(l_stream);
+-    fclose(l_file);
+     opj_destroy_codec(this->m_Internal->m_Dinfo);
+     opj_image_destroy(l_image);
+     itkExceptionMacro("JPEG2000ImageIO failed to read file: " << this->GetFileName() << std::endl
+@@ -667,13 +620,11 @@
+     this->m_Internal->m_Dinfo = nullptr;
+     opj_stream_destroy(l_stream);
+-    fclose(l_file);
+     itkExceptionMacro("JPEG2000ImageIO failed to read file: " << this->GetFileName() << std::endl
+                                                               << "Reason: error whle reading image");
+   }
+ 
+   /* close the byte stream */
+   opj_stream_destroy(l_stream);
+-  fclose(l_file);
+ 
+   if (this->m_Internal->m_Dinfo)
+   {
+@@ -775,6 +726,6 @@
+   }
+ 
+-  for (int i = 0; i < parameters.numpocs; i++)
++  for (OPJ_UINT32 i = 0; i < parameters.numpocs; i++)
+   {
+     if (parameters.POC[i].prg == -1)
+     {
+@@ -840,13 +791,13 @@
+ 
+   parameters.numresolution = numberOfResolutions;
+ 
+-  OPJ_COLOR_SPACE      color_space = CLRSPC_GRAY;
++  OPJ_COLOR_SPACE      color_space = OPJ_CLRSPC_GRAY;
+   opj_image_cmptparm_t cmptparms[3];
+ 
+   if (this->GetNumberOfComponents() == 3)
+   {
+ 
+-    color_space = (this->GetPixelType() == IOPixelEnum::RGB) ? CLRSPC_SRGB : CLRSPC_UNSPECIFIED;
++    color_space = (this->GetPixelType() == IOPixelEnum::RGB) ? OPJ_CLRSPC_SRGB : OPJ_CLRSPC_UNSPECIFIED;
+ 
+     /* initialize image components */
+     memset(&cmptparms[0], 0, 3 * sizeof(opj_image_cmptparm_t));
+@@ -864,7 +815,7 @@
+ 
+   if (this->GetNumberOfComponents() == 1)
+   {
+-    color_space = CLRSPC_GRAY;
++    color_space = OPJ_CLRSPC_GRAY;
+ 
+     /* initialize image components */
+     memset(&cmptparms[0], 0, sizeof(opj_image_cmptparm_t));
+@@ -941,8 +892,9 @@
+   if (extension == ".j2k")
+   {
+-    cinfo = opj_create_compress(CODEC_J2K);
++    cinfo = opj_create_compress(OPJ_CODEC_J2K);
+     if (!cinfo)
+     {
++      opj_image_destroy(l_image);
+       itkExceptionMacro("JPEG2000ImageIO failed to write file: "
+                         << this->GetFileName() << std::endl
+                         << "Reason: opj_create_compress(CODEC_J2K) returns nullptr");
+@@ -950,9 +902,10 @@
+   }
+   else if (extension == ".jp2")
+   {
+-    cinfo = opj_create_compress(CODEC_JP2);
++    cinfo = opj_create_compress(OPJ_CODEC_JP2);
+     if (!cinfo)
+     {
++      opj_image_destroy(l_image);
+       itkExceptionMacro("JPEG2000ImageIO failed to write file: "
+                         << this->GetFileName() << std::endl
+                         << "Reason: opj_create_compress(CODEC_JP2) returns nullptr");
+@@ -960,9 +913,10 @@
+   }
+   else if (extension == ".jpt")
+   {
+-    cinfo = opj_create_compress(CODEC_JPT);
++    cinfo = opj_create_compress(OPJ_CODEC_JPT);
+     if (!cinfo)
+     {
++      opj_image_destroy(l_image);
+       itkExceptionMacro("JPEG2000ImageIO failed to write file: "
+                         << this->GetFileName() << std::endl
+                         << "Reason: opj_create_compress(CODEC_JPT) returns nullptr");
+@@ -970,6 +924,7 @@
+   }
+   else
+   {
++    opj_image_destroy(l_image);
+     itkExceptionMacro("JPEG2000ImageIO failed to write file: " << this->GetFileName() << std::endl
+                                                                << "Reason: unknown encode format: " << extension);
+   }
+@@ -985,23 +940,19 @@
+ 
+   if (!opj_setup_encoder(cinfo, &parameters, l_image))
+   {
++    opj_destroy_codec(cinfo);
++    opj_image_destroy(l_image);
+     itkExceptionMacro("JPEG2000ImageIO failed to write file: " << this->GetFileName() << std::endl
+                                                                << "Reason: opj_setup_encoder returns false");
+   }
+ 
+-  FILE * l_file = fopen(parameters.outfile, "wb");
+-  if (!l_file)
+-  {
+-    itkExceptionMacro("JPEG2000ImageIO failed to open file for writing: " << this->GetFileName() << std::endl
+-                                                                          << "Reason: "
+-                                                                          << itksys::SystemTools::GetLastSystemError());
+-  }
+-
+   /* open a byte stream for writing */
+   /* allocate memory for all tiles */
+-  opj_stream_t * cio = opj_stream_create_default_file_stream(l_file, false);
++  opj_stream_t * cio = opj_stream_create_default_file_stream(parameters.outfile, false);
+   if (!cio)
+   {
++    opj_destroy_codec(cinfo);
++    opj_image_destroy(l_image);
+     itkExceptionMacro("JPEG2000ImageIO failed to write file: "
+                       << this->GetFileName() << std::endl
+                       << "Reason: "
+@@ -1017,7 +968,8 @@
+   if (!bSuccess)
+   {
+     opj_stream_destroy(cio);
+-    fclose(l_file);
++    opj_destroy_codec(cinfo);
++    opj_image_destroy(l_image);
+     itkExceptionMacro("JPEG2000ImageIO failed to write file: " << this->GetFileName() << std::endl
+                                                                << "Reason: opj_start_compress returns false");
+   }
+@@ -1026,7 +978,8 @@
+   if (!bSuccess)
+   {
+     opj_stream_destroy(cio);
+-    fclose(l_file);
++    opj_destroy_codec(cinfo);
++    opj_image_destroy(l_image);
+     itkExceptionMacro("JPEG2000ImageIO failed to write file: " << this->GetFileName() << std::endl
+                                                                << "Reason: opj_encode returns false");
+   }
+@@ -1035,14 +988,14 @@
+   if (!bSuccess)
+   {
+     opj_stream_destroy(cio);
+-    fclose(l_file);
++    opj_destroy_codec(cinfo);
++    opj_image_destroy(l_image);
+     itkExceptionMacro("JPEG2000ImageIO failed to write file: " << this->GetFileName() << std::endl
+                                                                << "Reason: opj_end_compress returns false");
+   }
+ 
+   /* close and free the byte stream */
+   opj_stream_destroy(cio);
+-  fclose(l_file);
+ 
+   /* free remaining compression structures */
+   opj_destroy_codec(cinfo);
+--- a/Modules/Nonunit/Review/src/CMakeLists.txt
++++ b/Modules/Nonunit/Review/src/CMakeLists.txt
+@@ -5,7 +5,7 @@
+ 
+ add_library(ITKReview ${ITKReview_SRC})
+ itk_module_link_dependencies()
+-target_link_libraries(ITKReview LINK_PUBLIC ${ITKTestKernel_LIBRARIES} ${ITKIOLSM_LIBRARIES} itkopenjpeg)
++target_link_libraries(ITKReview LINK_PUBLIC ${ITKTestKernel_LIBRARIES} ${ITKIOLSM_LIBRARIES} ${ITKOpenJPEG_LIBRARIES})
+ itk_module_target(ITKReview)
+ 
+ 
diff --git a/sci-libs/itk/files/itk-5.2.1-system-tiff-has-64.patch b/sci-libs/itk/files/itk-5.2.1-system-tiff-has-64.patch
new file mode 100644
index 000000000..25c44db2c
--- /dev/null
+++ b/sci-libs/itk/files/itk-5.2.1-system-tiff-has-64.patch
@@ -0,0 +1,18 @@
+From: François-Xavier Carton <fx.carton91@gmail.com>
+Date: Wed, 8 Jun 2022 19:36:48 +0200
+Subject: [PATCH] system libtiff has INT64
+
+Enabling this, otherwise using system libtiff leads to errors. In particular
+tests fail because there is some IFD8 data but the itkTIFFDataSize function
+returns 0 instead of 8, resulting in invalid mem access.
+
+--- a/Modules/ThirdParty/TIFF/src/itk_tiff.h.in.orig	2022-06-08 19:34:04.412431969 +0200
++++ b/Modules/ThirdParty/TIFF/src/itk_tiff.h.in	2022-06-08 19:34:26.240431631 +0200
+@@ -34,6 +34,7 @@
+ #cmakedefine ITK_TIFF_HAS_TIFFFieldReadCount
+ #cmakedefine ITK_TIFF_HAS_TIFFField
+ #ifdef ITK_USE_SYSTEM_TIFF
++# define TIFF_INT64_T int64_t
+ # include <tiffio.h>
+ #else
+ # include "itktiff/tiffio.h"
diff --git a/sci-libs/itk/files/itk-5.2.1-upstream-fixes.patch b/sci-libs/itk/files/itk-5.2.1-upstream-fixes.patch
new file mode 100644
index 000000000..2af8c4998
--- /dev/null
+++ b/sci-libs/itk/files/itk-5.2.1-upstream-fixes.patch
@@ -0,0 +1,309 @@
+https://github.com/InsightSoftwareConsortium/ITK/commit/2a7f5ed199926999b67f61a97c2c9a2595a11558.patch
+https://github.com/InsightSoftwareConsortium/ITK/commit/0c31aa688e82a34e5430873bc6176740fd09ad75.patch
+https://github.com/InsightSoftwareConsortium/ITK/commit/28325d921a9b8793e6aaefd612f53989f951d19c.patch
+https://github.com/InsightSoftwareConsortium/ITK/commit/aafd1f9631d0fad60e1b6f53e049e95a50c48bd1.patch
+
+From 2a7f5ed199926999b67f61a97c2c9a2595a11558 Mon Sep 17 00:00:00 2001
+From: Niels Dekker <N.Dekker@lumc.nl>
+Date: Thu, 24 Jun 2021 18:00:01 +0200
+Subject: [PATCH] COMP: Add missing `#include <iostream>` to Deprecated module
+ test
+
+Fixed a Visual C++ 2019 error, saying:
+
+> Deprecated\test\itkSimpleFastMutexLockTest.cxx(48,12): error C2039: 'cout': is not a member of 'std'
+---
+ .../Deprecated/test/itkSimpleFastMutexLockTest.cxx              | 2 ++
+ 1 file changed, 2 insertions(+)
+
+diff --git a/Modules/Compatibility/Deprecated/test/itkSimpleFastMutexLockTest.cxx b/Modules/Compatibility/Deprecated/test/itkSimpleFastMutexLockTest.cxx
+index 11ad0c52700..60aa1c065b4 100644
+--- a/Modules/Compatibility/Deprecated/test/itkSimpleFastMutexLockTest.cxx
++++ b/Modules/Compatibility/Deprecated/test/itkSimpleFastMutexLockTest.cxx
+@@ -19,6 +19,8 @@
+ 
+ #include "itkSimpleFastMutexLock.h"
+ 
++#include <iostream> // For cout.
++
+ 
+ int
+ itkSimpleFastMutexLockTest(int, char *[])
+From 0c31aa688e82a34e5430873bc6176740fd09ad75 Mon Sep 17 00:00:00 2001
+From: Pablo Hernandez-Cerdan <pablo.hernandez.cerdan@outlook.com>
+Date: Tue, 20 Apr 2021 17:21:21 +0200
+Subject: [PATCH] COMP: CastXML, ITKVtkGlue, include only when property exists
+
+Some targets (VTK libraries) didn't have the property INTERFACE_INCLUDE_DIRECTORIES
+
+```bash
+CMake Error in Modules/Bridge/VtkGlue/wrapping/CMakeLists.txt:
+  Found relative path while evaluating include directories of
+  "ITKVtkGluePython":
+
+    "_vtk_lib_include_dirs-NOTFOUND"
+```
+
+Triggered when compiling Slicer with `Slicer_BUILD_ITKPython:BOOL=ON`
+aka `ITK_WRAP_PYTHON:BOOL=ON`.
+
+Full error log with extra printing:
+
+```bash
+
+CMake Warning at Modules/Bridge/VtkGlue/wrapping/CMakeLists.txt:3 (message):
+  ITKVtkGlue_VTK_LIBRARIES:
+  VTK::IOImage;VTK::ImagingSources;VTK::WrappingPythonCore;VTK::CommonCore;VTK::CommonDataModel;VTK::kwiml;VTK::CommonExecutionModel;VTK::RenderingOpenGL2;VTK::RenderingFreeType;VTK::InteractionStyle;VTK::InteractionWidgets
+
+CMake Warning at Modules/Bridge/VtkGlue/wrapping/CMakeLists.txt:6 (message):
+  _vtk_lib_include_dirs: _vtk_lib_include_dirs-NOTFOUND
+
+CMake Warning at Modules/Bridge/VtkGlue/wrapping/CMakeLists.txt:6 (message):
+  _vtk_lib_include_dirs: _vtk_lib_include_dirs-NOTFOUND
+
+CMake Warning at Modules/Bridge/VtkGlue/wrapping/CMakeLists.txt:6 (message):
+  _vtk_lib_include_dirs:
+  build/VTK-build/Wrapping/PythonCore;build/VTK/Wrapping/PythonCore
+
+CMake Warning at Modules/Bridge/VtkGlue/wrapping/CMakeLists.txt:6 (message):
+  _vtk_lib_include_dirs: _vtk_lib_include_dirs-NOTFOUND
+
+CMake Warning at Modules/Bridge/VtkGlue/wrapping/CMakeLists.txt:6 (message):
+  _vtk_lib_include_dirs: _vtk_lib_include_dirs-NOTFOUND
+
+CMake Warning at Modules/Bridge/VtkGlue/wrapping/CMakeLists.txt:6 (message):
+  _vtk_lib_include_dirs:
+  build/VTK-build/Utilities/KWIML;build/VTK/Utilities/KWIML
+
+CMake Warning at Modules/Bridge/VtkGlue/wrapping/CMakeLists.txt:6 (message):
+  _vtk_lib_include_dirs: _vtk_lib_include_dirs-NOTFOUND
+
+CMake Warning at Modules/Bridge/VtkGlue/wrapping/CMakeLists.txt:6 (message):
+  _vtk_lib_include_dirs: _vtk_lib_include_dirs-NOTFOUND
+
+CMake Warning at Modules/Bridge/VtkGlue/wrapping/CMakeLists.txt:6 (message):
+  _vtk_lib_include_dirs: _vtk_lib_include_dirs-NOTFOUND
+
+CMake Warning at Modules/Bridge/VtkGlue/wrapping/CMakeLists.txt:6 (message):
+  _vtk_lib_include_dirs: _vtk_lib_include_dirs-NOTFOUND
+
+CMake Warning at Modules/Bridge/VtkGlue/wrapping/CMakeLists.txt:6 (message):
+  _vtk_lib_include_dirs: _vtk_lib_include_dirs-NOTFOUND
+
+-- ITKVtkGlue: Creating module.
+-- ITKVtkGlue: Creating itkImageToVTKImageFilter submodule.
+-- ITKVtkGlue: Creating itkVTKImageToImageFilter submodule.
+-- ITKVtkGlue: Creating itkViewImage submodule.
+-- MGHIO: Creating module.
+-- MGHIO: Creating itkMGHImageIO submodule.
+-- MorphologicalContourInterpolation: Creating module.
+-- MorphologicalContourInterpolation: Creating itkMorphologicalContourInterpolator submodule.
+-- ITKPyUtils: Creating module.
+-- ITKPyUtils: Creating itkPyCommand submodule.
+-- ITKPyUtils: Creating itkPyImageFilter submodule.
+-- Configuring done
+CMake Error: The following variables are used in this project, but they are set to NOTFOUND.
+Please set them or make sure they are set and tested correctly in the CMake files:
+_vtk_lib_include_dirs
+   used as include directory in directory build/ITK/Modules/Bridge/VtkGlue/wrapping
+   used as include directory in directory build/ITK/Modules/Bridge/VtkGlue/wrapping
+   used as include directory in directory build/ITK/Modules/Bridge/VtkGlue/wrapping
+   used as include directory in directory build/ITK/Modules/Bridge/VtkGlue/wrapping
+   used as include directory in directory build/ITK/Modules/Bridge/VtkGlue/wrapping
+   used as include directory in directory build/ITK/Modules/Bridge/VtkGlue/wrapping
+   used as include directory in directory build/ITK/Modules/Bridge/VtkGlue/wrapping
+   used as include directory in directory build/ITK/Modules/Bridge/VtkGlue/wrapping
+   used as include directory in directory build/ITK/Modules/Bridge/VtkGlue/wrapping
+   used as include directory in directory build/ITK/Modules/Bridge/VtkGlue/wrapping
+   used as include directory in directory build/ITK/Modules/Bridge/VtkGlue/wrapping
+   used as include directory in directory build/ITK/Modules/Bridge/VtkGlue/wrapping
+   used as include directory in directory build/ITK/Modules/Bridge/VtkGlue/wrapping
+   used as include directory in directory build/ITK/Modules/Bridge/VtkGlue/wrapping
+   used as include directory in directory build/ITK/Modules/Bridge/VtkGlue/wrapping
+   used as include directory in directory build/ITK/Modules/Bridge/VtkGlue/wrapping
+   used as include directory in directory build/ITK/Modules/Bridge/VtkGlue/wrapping
+   used as include directory in directory build/ITK/Modules/Bridge/VtkGlue/wrapping
+   used as include directory in directory build/ITK/Modules/Bridge/VtkGlue/wrapping
+   used as include directory in directory build/ITK/Modules/Bridge/VtkGlue/wrapping
+   used as include directory in directory build/ITK/Modules/Bridge/VtkGlue/wrapping
+   used as include directory in directory build/ITK/Modules/Bridge/VtkGlue/wrapping
+   used as include directory in directory build/ITK/Modules/Bridge/VtkGlue/wrapping
+   used as include directory in directory build/ITK/Modules/Bridge/VtkGlue/wrapping
+   used as include directory in directory build/ITK/Modules/Bridge/VtkGlue/wrapping
+   used as include directory in directory build/ITK/Modules/Bridge/VtkGlue/wrapping
+   used as include directory in directory build/ITK/Modules/Bridge/VtkGlue/wrapping
+   used as include directory in directory build/ITK/Modules/Bridge/VtkGlue/wrapping
+   used as include directory in directory build/ITK/Modules/Bridge/VtkGlue/wrapping
+   used as include directory in directory build/ITK/Modules/Bridge/VtkGlue/wrapping
+   used as include directory in directory build/ITK/Modules/Bridge/VtkGlue/wrapping
+   used as include directory in directory build/ITK/Modules/Bridge/VtkGlue/wrapping
+   used as include directory in directory build/ITK/Modules/Bridge/VtkGlue/wrapping
+   used as include directory in directory build/ITK/Modules/Bridge/VtkGlue/wrapping
+   used as include directory in directory build/ITK/Modules/Bridge/VtkGlue/wrapping
+   used as include directory in directory build/ITK/Modules/Bridge/VtkGlue/wrapping
+   used as include directory in directory build/ITK/Modules/Bridge/VtkGlue/wrapping
+   used as include directory in directory build/ITK/Modules/Bridge/VtkGlue/wrapping
+   used as include directory in directory build/ITK/Modules/Bridge/VtkGlue/wrapping
+   used as include directory in directory build/ITK/Modules/Bridge/VtkGlue/wrapping
+   used as include directory in directory build/ITK/Modules/Bridge/VtkGlue/wrapping
+   used as include directory in directory build/ITK/Modules/Bridge/VtkGlue/wrapping
+   used as include directory in directory build/ITK/Modules/Bridge/VtkGlue/wrapping
+   used as include directory in directory build/ITK/Modules/Bridge/VtkGlue/wrapping
+   used as include directory in directory build/ITK/Modules/Bridge/VtkGlue/wrapping
+   used as include directory in directory build/ITK/Modules/Bridge/VtkGlue/wrapping
+   used as include directory in directory build/ITK/Modules/Bridge/VtkGlue/wrapping
+   used as include directory in directory build/ITK/Modules/Bridge/VtkGlue/wrapping
+   used as include directory in directory build/ITK/Modules/Bridge/VtkGlue/wrapping
+   used as include directory in directory build/ITK/Modules/Bridge/VtkGlue/wrapping
+   used as include directory in directory build/ITK/Modules/Bridge/VtkGlue/wrapping
+   used as include directory in directory build/ITK/Modules/Bridge/VtkGlue/wrapping
+   used as include directory in directory build/ITK/Modules/Bridge/VtkGlue/wrapping
+   used as include directory in directory build/ITK/Modules/Bridge/VtkGlue/wrapping
+   used as include directory in directory build/ITK/Modules/Bridge/VtkGlue/wrapping
+   used as include directory in directory build/ITK/Modules/Bridge/VtkGlue/wrapping
+   used as include directory in directory build/ITK/Modules/Bridge/VtkGlue/wrapping
+   used as include directory in directory build/ITK/Modules/Bridge/VtkGlue/wrapping
+   used as include directory in directory build/ITK/Modules/Bridge/VtkGlue/wrapping
+   used as include directory in directory build/ITK/Modules/Bridge/VtkGlue/wrapping
+   used as include directory in directory build/ITK/Modules/Bridge/VtkGlue/wrapping
+   used as include directory in directory build/ITK/Modules/Bridge/VtkGlue/wrapping
+   used as include directory in directory build/ITK/Modules/Bridge/VtkGlue/wrapping
+   used as include directory in directory build/ITK/Modules/Bridge/VtkGlue/wrapping
+   used as include directory in directory build/ITK/Modules/Bridge/VtkGlue/wrapping
+   used as include directory in directory build/ITK/Modules/Bridge/VtkGlue/wrapping
+   used as include directory in directory build/ITK/Modules/Bridge/VtkGlue/wrapping
+   used as include directory in directory build/ITK/Modules/Bridge/VtkGlue/wrapping
+   used as include directory in directory build/ITK/Modules/Bridge/VtkGlue/wrapping
+   used as include directory in directory build/ITK/Modules/Bridge/VtkGlue/wrapping
+   used as include directory in directory build/ITK/Modules/Bridge/VtkGlue/wrapping
+   used as include directory in directory build/ITK/Modules/Bridge/VtkGlue/wrapping
+   used as include directory in directory build/ITK/Modules/Bridge/VtkGlue/wrapping
+   used as include directory in directory build/ITK/Modules/Bridge/VtkGlue/wrapping
+   used as include directory in directory build/ITK/Modules/Bridge/VtkGlue/wrapping
+   used as include directory in directory build/ITK/Modules/Bridge/VtkGlue/wrapping
+   used as include directory in directory build/ITK/Modules/Bridge/VtkGlue/wrapping
+   used as include directory in directory build/ITK/Modules/Bridge/VtkGlue/wrapping
+   used as include directory in directory build/ITK/Modules/Bridge/VtkGlue/wrapping
+   used as include directory in directory build/ITK/Modules/Bridge/VtkGlue/wrapping
+   used as include directory in directory build/ITK/Modules/Bridge/VtkGlue/wrapping
+   used as include directory in directory build/ITK/Modules/Bridge/VtkGlue/wrapping
+   used as include directory in directory build/ITK/Modules/Bridge/VtkGlue/wrapping
+   used as include directory in directory build/ITK/Modules/Bridge/VtkGlue/wrapping
+   used as include directory in directory build/ITK/Modules/Bridge/VtkGlue/wrapping
+   used as include directory in directory build/ITK/Modules/Bridge/VtkGlue/wrapping
+   used as include directory in directory build/ITK/Modules/Bridge/VtkGlue/wrapping
+   used as include directory in directory build/ITK/Modules/Bridge/VtkGlue/wrapping
+   used as include directory in directory build/ITK/Modules/Bridge/VtkGlue/wrapping
+   used as include directory in directory build/ITK/Modules/Bridge/VtkGlue/wrapping
+   used as include directory in directory build/ITK/Modules/Bridge/VtkGlue/wrapping
+   used as include directory in directory build/ITK/Modules/Bridge/VtkGlue/wrapping
+   used as include directory in directory build/ITK/Modules/Bridge/VtkGlue/wrapping
+   used as include directory in directory build/ITK/Modules/Bridge/VtkGlue/wrapping
+   used as include directory in directory build/ITK/Modules/Bridge/VtkGlue/wrapping
+   used as include directory in directory build/ITK/Modules/Bridge/VtkGlue/wrapping
+   used as include directory in directory build/ITK/Modules/Bridge/VtkGlue/wrapping
+   used as include directory in directory build/ITK/Modules/Bridge/VtkGlue/wrapping
+   used as include directory in directory build/ITK/Modules/Bridge/VtkGlue/wrapping
+
+CMake Error in Modules/Bridge/VtkGlue/wrapping/CMakeLists.txt:
+  Found relative path while evaluating include directories of
+  "ITKVtkGluePython":
+
+    "_vtk_lib_include_dirs-NOTFOUND"
+
+```
+---
+ Modules/Bridge/VtkGlue/wrapping/CMakeLists.txt | 4 +++-
+ 1 file changed, 3 insertions(+), 1 deletion(-)
+
+diff --git a/Modules/Bridge/VtkGlue/wrapping/CMakeLists.txt b/Modules/Bridge/VtkGlue/wrapping/CMakeLists.txt
+index 3f3322957e1..2fd6a5af8f6 100644
+--- a/Modules/Bridge/VtkGlue/wrapping/CMakeLists.txt
++++ b/Modules/Bridge/VtkGlue/wrapping/CMakeLists.txt
+@@ -2,7 +2,9 @@
+ if(NOT VTK_RENDERING_BACKEND STREQUAL "None")
+   foreach(_vtk_lib IN LISTS ITKVtkGlue_VTK_LIBRARIES)
+     get_target_property(_vtk_lib_include_dirs ${_vtk_lib} INTERFACE_INCLUDE_DIRECTORIES)
+-    include_directories(${_vtk_lib_include_dirs})
++    if(_vtk_lib_include_dirs)
++      include_directories(${_vtk_lib_include_dirs})
++    endif()
+   endforeach()
+ endif()
+ 
+From 28325d921a9b8793e6aaefd612f53989f951d19c Mon Sep 17 00:00:00 2001
+From: Butui Hu <hot123tea123@gmail.com>
+Date: Mon, 1 Aug 2022 14:26:39 +0800
+Subject: [PATCH] COMP: use sysconfig.get_path as PEP 632 deprecate distutils
+ module
+
+---
+ Wrapping/Generators/Python/CMakeLists.txt | 2 +-
+ 1 file changed, 1 insertion(+), 1 deletion(-)
+
+diff --git a/Wrapping/Generators/Python/CMakeLists.txt b/Wrapping/Generators/Python/CMakeLists.txt
+index fca3d999b87..3b7a1d37334 100644
+--- a/Wrapping/Generators/Python/CMakeLists.txt
++++ b/Wrapping/Generators/Python/CMakeLists.txt
+@@ -36,7 +36,7 @@ file(MAKE_DIRECTORY ${WRAPPER_MASTER_INDEX_OUTPUT_DIR}/python)
+ ###############################################################################
+ # Configure Python wrapping installation
+ if(Python3_EXECUTABLE AND NOT PY_SITE_PACKAGES_PATH)
+-  set(python_check "try:\n    import distutils.sysconfig\n    print(distutils.sysconfig.get_python_lib(plat_specific=1, prefix=''))\nexcept:\n    pass")
++  set(python_check "try:\n    import sysconfig\n    print(sysconfig.get_path('platlib'))\nexcept:\n    pass")
+   file(WRITE ${CMAKE_CURRENT_BINARY_DIR}/detect_site_package_path.py ${python_check})
+   execute_process(COMMAND "${Python3_EXECUTABLE}" "${CMAKE_CURRENT_BINARY_DIR}/detect_site_package_path.py"
+     OUTPUT_VARIABLE py_spp
+From aafd1f9631d0fad60e1b6f53e049e95a50c48bd1 Mon Sep 17 00:00:00 2001
+From: Hans Johnson <hans-johnson@uiowa.edu>
+Date: Wed, 15 Dec 2021 08:10:58 -0600
+Subject: [PATCH] COMP: Remove inclusion of .hxx files as headers
+
+The ability to include either .h or .hxx files as
+header files required recursively reading the
+.h files twice.  The added complexity is
+unnecessary, costly, and can confuse static
+analysis tools that monitor header guardes (due
+to reaching the maximum depth of recursion
+limits for nested #ifdefs in checking).
+
+Co-authored-by: Simon Rit <simon.rit@creatis.insa-lyon.fr>
+---
+ CMake/ITKModuleHeaderTest.cmake          | 3 +--
+ Utilities/Maintenance/BuildHeaderTest.py | 4 ----
+ 2 files changed, 1 insertion(+), 6 deletions(-)
+
+diff --git a/CMake/ITKModuleHeaderTest.cmake b/CMake/ITKModuleHeaderTest.cmake
+index eb809d7e93d..82ad192a6f8 100644
+--- a/CMake/ITKModuleHeaderTest.cmake
++++ b/CMake/ITKModuleHeaderTest.cmake
+@@ -36,8 +36,7 @@ macro( itk_module_headertest _name )
+     # effected.
+     set( _include ${${_name}_SOURCE_DIR}/include )
+     file( GLOB _h_files ${_include}/*.h )
+-    file( GLOB _hxx_files ${_include}/*.hxx )
+-    set( _header_files ${_h_files} ${_hxx_files} )
++    set( _header_files ${_h_files} )
+     list( LENGTH _h_files _num_headers )
+     set( _outputs ${${_name}_BINARY_DIR}/test/${_name}HeaderTest1.cxx )
+     set( _test_num 1 )
+diff --git a/Utilities/Maintenance/BuildHeaderTest.py b/Utilities/Maintenance/BuildHeaderTest.py
+index 26a4b6ccb3f..f8ed9f7901e 100755
+--- a/Utilities/Maintenance/BuildHeaderTest.py
++++ b/Utilities/Maintenance/BuildHeaderTest.py
+@@ -130,15 +130,11 @@ def main():
+         else:
+             max_idx = added_header_idx + maximum_number_of_headers
+         for i in range(added_header_idx, max_idx):
+-            # Use the .hxx if possible.
+-            hxx_file = h_files[i][:-1] + "hxx"
+             # Files that include VTK headers need to link to VTK.
+             if h_files[i] in BANNED_HEADERS or h_files[i].lower().find("vtk") != -1:
+                 to_include = (
+                     '// #include "' + h_files[i] + '" // Banned in BuildHeaderTest.py\n'
+                 )
+-            elif os.path.exists(os.path.join(module_source_path, "include", hxx_file)):
+-                to_include = '#include "' + hxx_file + '"\n'
+             else:
+                 to_include = '#include "' + h_files[i] + '"\n'
+ 
diff --git a/sci-libs/itk/files/itk-5.3.0-system-openjpeg.patch b/sci-libs/itk/files/itk-5.3.0-system-openjpeg.patch
new file mode 100644
index 000000000..27f139553
--- /dev/null
+++ b/sci-libs/itk/files/itk-5.3.0-system-openjpeg.patch
@@ -0,0 +1,550 @@
+--- a/Modules/ThirdParty/OpenJPEG/CMakeLists.txt
++++ b/Modules/ThirdParty/OpenJPEG/CMakeLists.txt
+@@ -1,16 +1,32 @@
+ project(ITKOpenJPEG)
+ set(ITKOpenJPEG_THIRD_PARTY 1)
+ 
+-set(ITKOpenJPEG_INCLUDE_DIRS
+-  ${ITKOpenJPEG_BINARY_DIR}/src/openjpeg
+-  ${ITKOpenJPEG_SOURCE_DIR}/src/openjpeg
+-  )
+-set(ITKOpenJPEG_LIBRARIES itkopenjpeg)
++option(ITK_USE_SYSTEM_OPENJPEG "Use system-installed openjpeg" ${ITK_USE_SYSTEM_LIBRARIES})
++mark_as_advanced(ITK_USE_SYSTEM_OPENJPEG)
++
++if(ITK_USE_SYSTEM_OPENJPEG)
++  find_package(OpenJPEG REQUIRED)
++  set(ITKOpenJPEG_INCLUDE_DIRS
++    ${ITKOpenJPEG_BINARY_DIR}/src
++    )
++  set(ITKOpenJPEG_SYSTEM_INCLUDE_DIRS
++    ${OPENJPEG_INCLUDE_DIRS}
++    )
++  set(ITKOpenJPEG_LIBRARIES "${OPENJPEG_LIBRARIES}")
++  set(ITKOpenJPEG_NO_SRC 1)
++else()
++  set(ITKOpenJPEG_INCLUDE_DIRS
++    ${ITKOpenJPEG_BINARY_DIR}/src/openjpeg
++    ${ITKOpenJPEG_SOURCE_DIR}/src/openjpeg
++    )
++  set(ITKOpenJPEG_LIBRARIES itkopenjpeg)
++endif()
++
++configure_file(src/itk_openjpeg.h.in src/itk_openjpeg.h)
+ set(ITK_LIBRARY_PROPERTIES WINDOWS_EXPORT_ALL_SYMBOLS FALSE)
+-
+ itk_module_impl()
+ 
+-install(FILES ${ITKOpenJPEG_SOURCE_DIR}/src/itk_openjpeg.h
++install(FILES ${ITKOpenJPEG_BINARY_DIR}/src/itk_openjpeg.h
+   DESTINATION ${ITKOpenJPEG_INSTALL_INCLUDE_DIR}
+   COMPONENT Development
+   )
+diff --git a/Modules/ThirdParty/OpenJPEG/src/itk_openjpeg.h b/Modules/ThirdParty/OpenJPEG/src/itk_openjpeg.h.in
+rename from Modules/ThirdParty/OpenJPEG/src/itk_openjpeg.h
+rename to Modules/ThirdParty/OpenJPEG/src/itk_openjpeg.h.in
+--- a/Modules/ThirdParty/OpenJPEG/src/itk_openjpeg.h
++++ b/Modules/ThirdParty/OpenJPEG/src/itk_openjpeg.h.in
+@@ -25,6 +25,12 @@
+ #ifndef itk_openjpeg_h
+ #define itk_openjpeg_h
+ 
+-#include <itkopenjpeg/openjpeg.h>
++/* Use the openjpeg library configured for ITK.  */
++#cmakedefine ITK_USE_SYSTEM_OPENJPEG
++#ifdef ITK_USE_SYSTEM_OPENJPEG
++# include <openjpeg.h>
++#else
++# include <itkopenjpeg/openjpeg.h>
++#endif
+ 
+ #endif
+--- a/Modules/IO/JPEG2000/src/itkJPEG2000ImageIO.cxx
++++ b/Modules/IO/JPEG2000/src/itkJPEG2000ImageIO.cxx
+@@ -27,8 +27,6 @@
+ extern "C"
+ {
+ #include "openjpeg.h"
+-#include "j2k.h"
+-#include "jp2.h"
+ }
+ 
+ 
+@@ -139,11 +137,11 @@
+ {
+   itkDebugMacro(<< "ReadImageInformation()");
+ 
+-  FILE * l_file = fopen(this->m_FileName.c_str(), "rb");
+-
+-  /* decompression parameters */
++  /* set decoding parameters to default values */
++  opj_set_default_decoder_parameters(&(this->m_Internal->m_DecompressionParameters));
+ 
+-  if (!l_file)
++  opj_stream_t * cio = opj_stream_create_default_file_stream(this->m_FileName.c_str(), true);
++  if (!cio)
+   {
+     itkExceptionMacro("JPEG2000ImageIO failed to open file for reading: " << this->GetFileName() << std::endl
+                                                                           << "Reason: "
+@@ -151,10 +149,5 @@
+   }
+ 
+-  /* set decoding parameters to default values */
+-  opj_set_default_decoder_parameters(&(this->m_Internal->m_DecompressionParameters));
+-
+-  opj_stream_t * cio = opj_stream_create_default_file_stream(l_file, true);
+-
+   this->m_Internal->m_Dinfo = nullptr; /* handle to a decompressor */
+ 
+   opj_image_t * l_image = nullptr;
+@@ -188,9 +181,8 @@
+ 
+       /* get a decoder handle */
+-      this->m_Internal->m_Dinfo = opj_create_decompress(CODEC_J2K);
++      this->m_Internal->m_Dinfo = opj_create_decompress(OPJ_CODEC_J2K);
+       if (!this->m_Internal->m_Dinfo)
+       {
+         opj_stream_destroy(cio);
+-        fclose(l_file);
+         itkExceptionMacro("JPEG2000ImageIO failed to read file: "
+                           << this->GetFileName() << std::endl
+@@ -202,10 +194,9 @@
+     {
+       /* JPEG 2000 compressed image data */
+       /* get a decoder handle */
+-      this->m_Internal->m_Dinfo = opj_create_decompress(CODEC_JP2);
++      this->m_Internal->m_Dinfo = opj_create_decompress(OPJ_CODEC_JP2);
+       if (!this->m_Internal->m_Dinfo)
+       {
+         opj_stream_destroy(cio);
+-        fclose(l_file);
+         itkExceptionMacro("JPEG2000ImageIO failed to read file: "
+                           << this->GetFileName() << std::endl
+@@ -217,10 +208,9 @@
+     {
+       /* JPEG 2000, JPIP */
+       /* get a decoder handle */
+-      this->m_Internal->m_Dinfo = opj_create_decompress(CODEC_JPT);
++      this->m_Internal->m_Dinfo = opj_create_decompress(OPJ_CODEC_JPT);
+       if (!this->m_Internal->m_Dinfo)
+       {
+         opj_stream_destroy(cio);
+-        fclose(l_file);
+         itkExceptionMacro("JPEG2000ImageIO failed to read file: "
+                           << this->GetFileName() << std::endl
+@@ -230,7 +220,6 @@
+     }
+     default:
+       opj_stream_destroy(cio);
+-      fclose(l_file);
+       itkExceptionMacro("JPEG2000ImageIO failed to read file: "
+                         << this->GetFileName() << std::endl
+                         << "Reason: "
+@@ -248,26 +237,8 @@
+   }
+ 
+-  // Image parameters - first tile
+-  OPJ_INT32 l_tile_x0;
+-  OPJ_INT32 l_tile_y0;
+-
+-  // Image parameters - tile width, height and number of tiles
+-  OPJ_UINT32 l_tile_width;
+-  OPJ_UINT32 l_tile_height;
+-  OPJ_UINT32 l_nb_tiles_x;
+-  OPJ_UINT32 l_nb_tiles_y;
+-
+   itkDebugMacro(<< "Trying to read header now...");
+ 
+-  bResult = opj_read_header(this->m_Internal->m_Dinfo,
+-                            &l_image,
+-                            &l_tile_x0,
+-                            &l_tile_y0,
+-                            &l_tile_width,
+-                            &l_tile_height,
+-                            &l_nb_tiles_x,
+-                            &l_nb_tiles_y,
+-                            cio);
++  bResult = opj_read_header(cio, this->m_Internal->m_Dinfo, &l_image);
+ 
+   if (!bResult)
+   {
+@@ -284,13 +255,21 @@
+   }
+ 
+-  this->m_Internal->m_TileStartX = l_tile_x0;
+-  this->m_Internal->m_TileStartY = l_tile_y0;
++  opj_codestream_info_v2_t* cp = opj_get_cstr_info(this->m_Internal->m_Dinfo);
++  if (!cp)
++  {
++    opj_stream_destroy(cio);
++    opj_image_destroy(l_image);
++    itkExceptionMacro("JPEG2000ImageIO failed to read file: " << this->GetFileName() << std::endl
++                                                              << "Reason: Error while reading image header");
++  }
++  this->m_Internal->m_TileStartX = cp->tx0;
++  this->m_Internal->m_TileStartY = cp->ty0;
+ 
+-  this->m_Internal->m_TileWidth = l_tile_width;
+-  this->m_Internal->m_TileHeight = l_tile_height;
++  this->m_Internal->m_TileWidth = cp->tdx;
++  this->m_Internal->m_TileHeight = cp->tdy;
+ 
+-  this->m_Internal->m_NumberOfTilesInX = l_nb_tiles_x;
+-  this->m_Internal->m_NumberOfTilesInY = l_nb_tiles_y;
++  this->m_Internal->m_NumberOfTilesInX = cp->tw;
++  this->m_Internal->m_NumberOfTilesInY = cp->th;
+ 
+ 
+   itkDebugMacro(<< "Number of Components = " << l_image->numcomps);
+@@ -307,6 +286,7 @@
+   else
+   {
+     opj_stream_destroy(cio);
++    opj_image_destroy(l_image);
+     itkExceptionMacro("JPEG2000ImageIO failed to read file: " << this->GetFileName() << std::endl
+                                                               << "Reason: "
+                                                               << "Unknown precision in file: "
+@@ -320,6 +300,6 @@
+       break;
+     case 3:
+-      if (l_image->color_space != CLRSPC_SRGB)
++      if (l_image->color_space != OPJ_CLRSPC_SRGB)
+       {
+         itkWarningMacro(<< "file does not specify color space, assuming sRGB");
+       }
+@@ -349,7 +329,6 @@
+ 
+   /* close the byte stream */
+   opj_stream_destroy(cio);
+-  fclose(l_file);
+ 
+   if (this->m_Internal->m_Dinfo)
+   {
+@@ -368,16 +347,7 @@
+ {
+   itkDebugMacro(<< "JPEG2000ImageIO::Read() Begin");
+ 
+-  FILE * l_file = fopen(this->m_FileName.c_str(), "rb");
+-
+-  if (!l_file)
+-  {
+-    itkExceptionMacro("JPEG2000ImageIO failed to open file for reading: " << this->GetFileName() << std::endl
+-                                                                          << "Reason: "
+-                                                                          << itksys::SystemTools::GetLastSystemError());
+-  }
+-
+-  opj_stream_t * l_stream = opj_stream_create_default_file_stream(l_file, true);
++  opj_stream_t * l_stream = opj_stream_create_default_file_stream(this->m_FileName.c_str(), true);
+   if (!l_stream)
+   {
+     itkExceptionMacro("JPEG2000ImageIO failed to read file: "
+@@ -397,9 +367,10 @@
+     {
+       /* JPEG-2000 codestream */
+       /* get a decoder handle */
+-      this->m_Internal->m_Dinfo = opj_create_decompress(CODEC_J2K);
++      this->m_Internal->m_Dinfo = opj_create_decompress(OPJ_CODEC_J2K);
+       if (!this->m_Internal->m_Dinfo)
+       {
++        opj_stream_destroy(l_stream);
+         itkExceptionMacro("JPEG2000ImageIO failed to read file: "
+                           << this->GetFileName() << std::endl
+                           << "Reason: opj_create_decompress(CODEC_J2K) returns nullptr");
+@@ -410,9 +381,10 @@
+     {
+       /* JPEG 2000 compressed image data */
+       /* get a decoder handle */
+-      this->m_Internal->m_Dinfo = opj_create_decompress(CODEC_JP2);
++      this->m_Internal->m_Dinfo = opj_create_decompress(OPJ_CODEC_JP2);
+       if (!this->m_Internal->m_Dinfo)
+       {
++        opj_stream_destroy(l_stream);
+         itkExceptionMacro("JPEG2000ImageIO failed to read file: "
+                           << this->GetFileName() << std::endl
+                           << "Reason: opj_create_decompress(CODEC_JP2) returns nullptr");
+@@ -423,9 +395,10 @@
+     {
+       /* JPEG 2000, JPIP */
+       /* get a decoder handle */
+-      this->m_Internal->m_Dinfo = opj_create_decompress(CODEC_JPT);
++      this->m_Internal->m_Dinfo = opj_create_decompress(OPJ_CODEC_JPT);
+       if (!this->m_Internal->m_Dinfo)
+       {
++        opj_stream_destroy(l_stream);
+         itkExceptionMacro("JPEG2000ImageIO failed to read file: "
+                           << this->GetFileName() << std::endl
+                           << "Reason: opj_create_decompress(CODEC_JPT) returns nullptr");
+@@ -433,7 +406,7 @@
+       break;
+     }
+     default:
+-      fclose(l_file);
++      opj_stream_destroy(l_stream);
+       itkExceptionMacro("JPEG2000ImageIO failed to read file: "
+                         << this->GetFileName() << std::endl
+                         << "Reason: "
+@@ -445,32 +418,17 @@
+   if (!opj_setup_decoder(this->m_Internal->m_Dinfo, &(this->m_Internal->m_DecompressionParameters)))
+   {
++    opj_stream_destroy(l_stream);
+     itkExceptionMacro("JPEG2000ImageIO failed to read file: " << this->GetFileName() << std::endl
+                                                               << "Reason: opj_setup_decoder returns false");
+   }
+ 
+-  OPJ_INT32 l_tile_x0, l_tile_y0;
+-
+-  OPJ_UINT32 l_tile_width;
+-  OPJ_UINT32 l_tile_height;
+-  OPJ_UINT32 l_nb_tiles_x;
+-  OPJ_UINT32 l_nb_tiles_y;
+-
+-  bool bResult = opj_read_header(this->m_Internal->m_Dinfo,
+-                                 &l_image,
+-                                 &l_tile_x0,
+-                                 &l_tile_y0,
+-                                 &l_tile_width,
+-                                 &l_tile_height,
+-                                 &l_nb_tiles_x,
+-                                 &l_nb_tiles_y,
+-                                 l_stream);
++  bool bResult = opj_read_header(l_stream, this->m_Internal->m_Dinfo, &l_image);
+ 
+   if (!bResult)
+   {
+     opj_destroy_codec(this->m_Internal->m_Dinfo);
+     this->m_Internal->m_Dinfo = nullptr;
+     opj_stream_destroy(l_stream);
+-    fclose(l_file);
+     itkExceptionMacro("JPEG2000ImageIO failed to read file: " << this->GetFileName() << std::endl
+                                                               << "Reason: opj_read_header returns false");
+   }
+@@ -499,7 +457,7 @@
+   itkDebugMacro(<< "p_end_x = " << p_end_x);
+   itkDebugMacro(<< "p_end_y = " << p_end_y);
+ 
+-  bResult = opj_set_decode_area(this->m_Internal->m_Dinfo, p_start_x, p_start_y, p_end_x, p_end_y);
++  bResult = opj_set_decode_area(this->m_Internal->m_Dinfo, l_image, p_start_x, p_start_y, p_end_x, p_end_y);
+ 
+   itkDebugMacro(<< "opj_set_decode_area() after");
+ 
+@@ -509,6 +467,5 @@
+     this->m_Internal->m_Dinfo = nullptr;
+     opj_stream_destroy(l_stream);
+-    fclose(l_file);
+     itkExceptionMacro("JPEG2000ImageIO failed to read file: " << this->GetFileName() << std::endl
+                                                               << "Reason: opj_set_decode_area returns false");
+   }
+@@ -525,13 +482,14 @@
+ 
+   OPJ_UINT32 l_max_data_size = 1000;
+ 
+-  bool l_go_on = true;
++  OPJ_BOOL l_go_on = true;
+ 
+   auto * l_data = (OPJ_BYTE *)malloc(1000);
+ 
+   while (l_go_on)
+   {
+     bool tileHeaderRead = opj_read_tile_header(this->m_Internal->m_Dinfo,
++                                               l_stream,
+                                                &l_tile_index,
+                                                &l_data_size,
+                                                &l_current_tile_x0,
+@@ -540,13 +498,11 @@
+                                                &l_current_tile_y1,
+                                                &l_nb_comps,
+-                                               &l_go_on,
+-                                               l_stream);
++                                               &l_go_on);
+ 
+     if (!tileHeaderRead)
+     {
+       free(l_data);
+       opj_stream_destroy(l_stream);
+-      fclose(l_file);
+       opj_destroy_codec(this->m_Internal->m_Dinfo);
+       opj_image_destroy(l_image);
+       itkExceptionMacro("JPEG2000ImageIO failed to read file: " << this->GetFileName() << std::endl
+@@ -571,7 +527,6 @@
+         if (!l_data)
+         {
+           opj_stream_destroy(l_stream);
+-          fclose(l_file);
+           opj_destroy_codec(this->m_Internal->m_Dinfo);
+           opj_image_destroy(l_image);
+           itkExceptionMacro("JPEG2000ImageIO failed to read file: " << this->GetFileName() << std::endl
+@@ -590,7 +545,6 @@
+       {
+         free(l_data);
+         opj_stream_destroy(l_stream);
+-        fclose(l_file);
+         opj_destroy_codec(this->m_Internal->m_Dinfo);
+         opj_image_destroy(l_image);
+         itkExceptionMacro("JPEG2000ImageIO failed to read file: " << this->GetFileName() << std::endl
+@@ -654,7 +608,6 @@
+   {
+     free(l_data);
+     opj_stream_destroy(l_stream);
+-    fclose(l_file);
+     opj_destroy_codec(this->m_Internal->m_Dinfo);
+     opj_image_destroy(l_image);
+     itkExceptionMacro("JPEG2000ImageIO failed to read file: " << this->GetFileName() << std::endl
+@@ -667,13 +620,11 @@
+     this->m_Internal->m_Dinfo = nullptr;
+     opj_stream_destroy(l_stream);
+-    fclose(l_file);
+     itkExceptionMacro("JPEG2000ImageIO failed to read file: " << this->GetFileName() << std::endl
+                                                               << "Reason: error whle reading image");
+   }
+ 
+   /* close the byte stream */
+   opj_stream_destroy(l_stream);
+-  fclose(l_file);
+ 
+   if (this->m_Internal->m_Dinfo)
+   {
+@@ -840,13 +791,13 @@
+ 
+   parameters.numresolution = numberOfResolutions;
+ 
+-  OPJ_COLOR_SPACE      color_space = CLRSPC_GRAY;
++  OPJ_COLOR_SPACE      color_space = OPJ_CLRSPC_GRAY;
+   opj_image_cmptparm_t cmptparms[3];
+ 
+   if (this->GetNumberOfComponents() == 3)
+   {
+ 
+-    color_space = (this->GetPixelType() == IOPixelEnum::RGB) ? CLRSPC_SRGB : CLRSPC_UNSPECIFIED;
++    color_space = (this->GetPixelType() == IOPixelEnum::RGB) ? OPJ_CLRSPC_SRGB : OPJ_CLRSPC_UNSPECIFIED;
+ 
+     /* initialize image components */
+     memset(&cmptparms[0], 0, 3 * sizeof(opj_image_cmptparm_t));
+@@ -864,7 +815,7 @@
+ 
+   if (this->GetNumberOfComponents() == 1)
+   {
+-    color_space = CLRSPC_GRAY;
++    color_space = OPJ_CLRSPC_GRAY;
+ 
+     /* initialize image components */
+     memset(&cmptparms[0], 0, sizeof(opj_image_cmptparm_t));
+@@ -941,8 +892,9 @@
+   if (extension == ".j2k")
+   {
+-    cinfo = opj_create_compress(CODEC_J2K);
++    cinfo = opj_create_compress(OPJ_CODEC_J2K);
+     if (!cinfo)
+     {
++      opj_image_destroy(l_image);
+       itkExceptionMacro("JPEG2000ImageIO failed to write file: "
+                         << this->GetFileName() << std::endl
+                         << "Reason: opj_create_compress(CODEC_J2K) returns nullptr");
+@@ -950,9 +902,10 @@
+   }
+   else if (extension == ".jp2")
+   {
+-    cinfo = opj_create_compress(CODEC_JP2);
++    cinfo = opj_create_compress(OPJ_CODEC_JP2);
+     if (!cinfo)
+     {
++      opj_image_destroy(l_image);
+       itkExceptionMacro("JPEG2000ImageIO failed to write file: "
+                         << this->GetFileName() << std::endl
+                         << "Reason: opj_create_compress(CODEC_JP2) returns nullptr");
+@@ -960,9 +913,10 @@
+   }
+   else if (extension == ".jpt")
+   {
+-    cinfo = opj_create_compress(CODEC_JPT);
++    cinfo = opj_create_compress(OPJ_CODEC_JPT);
+     if (!cinfo)
+     {
++      opj_image_destroy(l_image);
+       itkExceptionMacro("JPEG2000ImageIO failed to write file: "
+                         << this->GetFileName() << std::endl
+                         << "Reason: opj_create_compress(CODEC_JPT) returns nullptr");
+@@ -970,6 +924,7 @@
+   }
+   else
+   {
++    opj_image_destroy(l_image);
+     itkExceptionMacro("JPEG2000ImageIO failed to write file: " << this->GetFileName() << std::endl
+                                                                << "Reason: unknown encode format: " << extension);
+   }
+@@ -985,23 +940,19 @@
+ 
+   if (!opj_setup_encoder(cinfo, &parameters, l_image))
+   {
++    opj_destroy_codec(cinfo);
++    opj_image_destroy(l_image);
+     itkExceptionMacro("JPEG2000ImageIO failed to write file: " << this->GetFileName() << std::endl
+                                                                << "Reason: opj_setup_encoder returns false");
+   }
+ 
+-  FILE * l_file = fopen(parameters.outfile, "wb");
+-  if (!l_file)
+-  {
+-    itkExceptionMacro("JPEG2000ImageIO failed to open file for writing: " << this->GetFileName() << std::endl
+-                                                                          << "Reason: "
+-                                                                          << itksys::SystemTools::GetLastSystemError());
+-  }
+-
+   /* open a byte stream for writing */
+   /* allocate memory for all tiles */
+-  opj_stream_t * cio = opj_stream_create_default_file_stream(l_file, false);
++  opj_stream_t * cio = opj_stream_create_default_file_stream(parameters.outfile, false);
+   if (!cio)
+   {
++    opj_destroy_codec(cinfo);
++    opj_image_destroy(l_image);
+     itkExceptionMacro("JPEG2000ImageIO failed to write file: "
+                       << this->GetFileName() << std::endl
+                       << "Reason: "
+@@ -1017,7 +968,8 @@
+   if (!bSuccess)
+   {
+     opj_stream_destroy(cio);
+-    fclose(l_file);
++    opj_destroy_codec(cinfo);
++    opj_image_destroy(l_image);
+     itkExceptionMacro("JPEG2000ImageIO failed to write file: " << this->GetFileName() << std::endl
+                                                                << "Reason: opj_start_compress returns false");
+   }
+@@ -1026,7 +978,8 @@
+   if (!bSuccess)
+   {
+     opj_stream_destroy(cio);
+-    fclose(l_file);
++    opj_destroy_codec(cinfo);
++    opj_image_destroy(l_image);
+     itkExceptionMacro("JPEG2000ImageIO failed to write file: " << this->GetFileName() << std::endl
+                                                                << "Reason: opj_encode returns false");
+   }
+@@ -1035,14 +988,14 @@
+   if (!bSuccess)
+   {
+     opj_stream_destroy(cio);
+-    fclose(l_file);
++    opj_destroy_codec(cinfo);
++    opj_image_destroy(l_image);
+     itkExceptionMacro("JPEG2000ImageIO failed to write file: " << this->GetFileName() << std::endl
+                                                                << "Reason: opj_end_compress returns false");
+   }
+ 
+   /* close and free the byte stream */
+   opj_stream_destroy(cio);
+-  fclose(l_file);
+ 
+   /* free remaining compression structures */
+   opj_destroy_codec(cinfo);
+--- a/Modules/Nonunit/Review/src/CMakeLists.txt
++++ b/Modules/Nonunit/Review/src/CMakeLists.txt
+@@ -5,7 +5,7 @@
+ 
+ add_library(ITKReview ${ITKReview_SRC})
+ itk_module_link_dependencies()
+-target_link_libraries(ITKReview LINK_PUBLIC ${ITKTestKernel_LIBRARIES} ${ITKIOLSM_LIBRARIES} itkopenjpeg)
++target_link_libraries(ITKReview LINK_PUBLIC ${ITKTestKernel_LIBRARIES} ${ITKIOLSM_LIBRARIES} ${ITKOpenJPEG_LIBRARIES})
+ itk_module_target(ITKReview)
+ 
+ 
diff --git a/sci-libs/itk/files/itk-5.3.0-uint8.patch b/sci-libs/itk/files/itk-5.3.0-uint8.patch
new file mode 100644
index 000000000..724314574
--- /dev/null
+++ b/sci-libs/itk/files/itk-5.3.0-uint8.patch
@@ -0,0 +1,10 @@
+--- a/Modules/Filtering/MathematicalMorphology/include/itkMathematicalMorphologyEnums.h
++++ b/Modules/Filtering/MathematicalMorphology/include/itkMathematicalMorphologyEnums.h
+@@ -20,6 +20,7 @@
+ 
+ #include <iostream>
+ #include "ITKMathematicalMorphologyExport.h"
++#include <cstdint>
+ 
+ 
+ namespace itk
diff --git a/sci-libs/itk/files/nrrdio-linking.patch b/sci-libs/itk/files/nrrdio-linking.patch
deleted file mode 100644
index a549650d2..000000000
--- a/sci-libs/itk/files/nrrdio-linking.patch
+++ /dev/null
@@ -1,15 +0,0 @@
-Description: Link libITKNrrdIO with -lm (needed for sqrt)
-Author: Steve Robbins <smr@debian.org>
-Forwarded: no
-
---- insighttoolkit4-4.5.0.orig/Modules/ThirdParty/NrrdIO/src/NrrdIO/CMakeLists.txt
-+++ insighttoolkit4-4.5.0/Modules/ThirdParty/NrrdIO/src/NrrdIO/CMakeLists.txt
-@@ -64,7 +64,7 @@
- ADD_DEFINITIONS(-DTEEM_ZLIB=1)
- 
- ADD_LIBRARY(ITKNrrdIO ${nrrdio_SRCS} )
--TARGET_LINK_LIBRARIES(ITKNrrdIO ${ITKZLIB_LIBRARIES})
-+TARGET_LINK_LIBRARIES(ITKNrrdIO ${ITKZLIB_LIBRARIES} -lm)
- 
- IF(ITK_LIBRARY_PROPERTIES)
-   SET_TARGET_PROPERTIES(ITKNrrdIO PROPERTIES ${ITK_LIBRARY_PROPERTIES})
diff --git a/sci-libs/itk/itk-4.12.0.ebuild b/sci-libs/itk/itk-4.12.0.ebuild
deleted file mode 100644
index a9633748b..000000000
--- a/sci-libs/itk/itk-4.12.0.ebuild
+++ /dev/null
@@ -1,136 +0,0 @@
-# Copyright 1999-2017 Gentoo Foundation
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=6
-
-PYTHON_COMPAT=( python2_7 )
-
-inherit eutils toolchain-funcs cmake-utils python-single-r1
-
-MYPN=InsightToolkit
-MYP=${MYPN}-${PV}
-DOC_PV=4.5.0
-
-DESCRIPTION="NLM Insight Segmentation and Registration Toolkit"
-HOMEPAGE="http://www.itk.org"
-SRC_URI="mirror://sourceforge/${PN}/${MYP}.tar.xz
-	doc? ( mirror://sourceforge/${PN}/Doxygen${MYPN}-${DOC_PV}.tar.gz )"
-RESTRICT="primaryuri"
-
-LICENSE="Apache-2.0"
-SLOT="0"
-KEYWORDS="~amd64 ~x86 ~amd64-linux ~x86-linux"
-IUSE="debug doc examples +fftw itkv3compat python review cpu_flags_x86_sse2 test vtkglue"
-
-RDEPEND="
-	dev-libs/double-conversion:0=
-	media-libs/libpng:0=
-	media-libs/tiff:0=
-	sci-libs/dcmtk:0=
-	sci-libs/hdf5:0=[cxx]
-	sys-libs/zlib:0=
-	virtual/jpeg:0=
-	fftw? ( sci-libs/fftw:3.0= )
-	vtkglue? ( sci-libs/vtk:0=[python?] )
-"
-DEPEND="${RDEPEND}
-	python? (
-		${PYTHON_DEPS}
-		>=dev-lang/swig-2.0:0
-		>=dev-cpp/gccxml-0.9.0_pre20120309
-	)
-	doc? ( app-doc/doxygen )
-"
-
-REQUIRED_USE="python? ( ${PYTHON_REQUIRED_USE} )"
-
-S="${WORKDIR}/${MYP}"
-
-PATCHES=(
-	"${FILESDIR}/nrrdio-linking.patch"
-)
-
-get_memory() {
-	free --giga | grep Mem | cut -d ' ' -f 15 || die 'unable to get memory size'
-}
-
-src_configure() {
-	sed -i \
-		-e '/find_package/d' \
-		Modules/ThirdParty/DoubleConversion/CMakeLists.txt || die
-
-	local mycmakeargs=(
-		-DBUILD_SHARED_LIBS=ON
-		-DITK_USE_SYSTEM_DCMTK=ON
-		-DITK_USE_SYSTEM_DOUBLECONVERSION=ON
-		-DITK_USE_SYSTEM_HDF5=ON
-		-DITK_USE_SYSTEM_JPEG=ON
-		-DITK_USE_SYSTEM_PNG=ON
-		-DITK_USE_SYSTEM_SWIG=ON
-		-DITK_USE_SYSTEM_TIFF=ON
-		-DITK_USE_SYSTEM_ZLIB=ON
-		-DITK_BUILD_DEFAULT_MODULES=ON
-		-DITK_COMPUTER_MEMORY_SIZE="$(get_memory)"
-		-DITK_WRAP_JAVA=OFF
-		-DITK_WRAP_TCL=OFF
-		-DBUILD_TESTING=$(usex test)
-		-DBUILD_EXAMPLES=$(usex examples)
-		-DITK_USE_REVIEW=$(usex review)
-		-DITKV3_COMPATIBILITY=$(usex itkv3compat)
-		-DVNL_CONFIG_ENABLE_SSE2=$(usex cpu_flags_x86_sse2)
-	)
-	if use fftw; then
-		mycmakeargs+=(
-			-DUSE_FFTWD=ON
-			-DUSE_FFTWF=ON
-			-DUSE_SYSTEM_FFTW=ON
-			-DITK_USE_SYSTEM_FFTW=ON
-			-DITK_WRAPPING=ON
-			-DITK_WRAP_double=ON
-			-DITK_WRAP_vector_double=ON
-			-DITK_WRAP_covariant_vector_double=ON
-			-DITK_WRAP_complex_double=ON
-		)
-	fi
-	if use vtkglue; then
-		mycmakeargs+=(
-			-DModule_ITKVtkGlue=ON
-		)
-	fi
-	mycmakeargs+=(
-		-DITK_WRAP_PYTHON=$(usex python ON OFF)
-	)
-
-	cmake-utils_src_configure
-}
-
-src_install() {
-	cmake-utils_src_install
-
-	if use examples; then
-		insinto /usr/share/doc/${PF}/examples
-		docompress -x /usr/share/doc/${PF}/examples
-		doins -r "${S}"/Examples/*
-	fi
-
-	echo "ITK_DATA_ROOT=${EROOT%/}/usr/share/${PN}/data" > ${T}/40${PN}
-	local ldpath="${EROOT%/}/usr/$(get_libdir)/InsightToolkit"
-	if use python; then
-		echo "PYTHONPATH=${EROOT%/}/usr/$(get_libdir)/InsightToolkit/WrapITK/Python" >> "${T}"/40${PN}
-		ldpath="${ldpath}:${EROOT%/}/usr/$(get_libdir)/InsightToolkit/WrapITK/lib"
-	fi
-	echo "LDPATH=${ldpath}" >> "${T}"/40${PN}
-	doenvd "${T}"/40${PN}
-
-	if use doc; then
-		insinto /usr/share/doc/${PF}/api-docs
-		cd "${WORKDIR}"/html
-		rm  *.md5 || die "Failed to remove superfluous hashes"
-		einfo "Installing API docs. This may take some time."
-		insinto /usr/share/doc/${PF}/api-docs
-		doins -r *
-	fi
-
-	mv "${D}/usr/lib" "${D}/usr/$(get_libdir)" || \
-		die 'unable to fix libdir'
-}
diff --git a/sci-libs/itk/itk-4.4.2-r1.ebuild b/sci-libs/itk/itk-4.4.2-r1.ebuild
deleted file mode 100644
index 93a03a5f8..000000000
--- a/sci-libs/itk/itk-4.4.2-r1.ebuild
+++ /dev/null
@@ -1,135 +0,0 @@
-# Copyright 1999-2015 Gentoo Foundation
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=5
-
-PYTHON_COMPAT=( python2_7 )
-
-inherit eutils toolchain-funcs cmake-utils python-single-r1
-
-MYPN=InsightToolkit
-MYP=${MYPN}-${PV}
-
-DESCRIPTION="NLM Insight Segmentation and Registration Toolkit"
-HOMEPAGE="http://www.itk.org"
-SRC_URI="
-	mirror://sourceforge/${PN}/${MYP}.tar.gz
-	doc? ( mirror://sourceforge/${PN}/Doxygen${MYPN}-4.4.0.tar.gz )"
-RESTRICT="primaryuri"
-
-LICENSE="Apache-2.0"
-SLOT="0"
-KEYWORDS="~amd64 ~x86 ~amd64-linux ~x86-linux"
-IUSE="debug doc examples fftw itkv3compat python review cpu_flags_x86_sse2 test vtkglue"
-
-RDEPEND="
-	sci-libs/hdf5[cxx]
-	virtual/jpeg:0=
-	media-libs/libpng:0=
-	media-libs/tiff:0=
-	sys-libs/zlib
-	fftw? ( sci-libs/fftw:3.0 )
-	vtkglue? ( sci-libs/vtk )
-"
-DEPEND="${RDEPEND}
-	python? (
-		${PYTHON_DEPS}
-		>=dev-lang/swig-2.0:0
-		>=dev-cpp/gccxml-0.9.0_pre20120309
-	)
-	doc? ( app-doc/doxygen )
-"
-
-S="${WORKDIR}/${MYP}"
-
-pkg_pretend() {
-	if [[ -z ${ITK_COMPUTER_MEMORY_SIZE} ]]; then
-		elog "To tune ITK to make the best use ouf working memory you can set"
-		elog "    ITK_COMPUTER_MEMORY_SIZE=XX"
-		elog "in make.conf, default is 1 (unit is GB)"
-	fi
-	if use python && [[ -z ${ITK_WRAP_DIMS} ]]; then
-		elog "For Python language bindings, you can define the dimensions"
-		elog "you want to create bindings for by setting"
-		elog "    ITK_WRAP_DIMS=X;Y;Z..."
-		elog "in make.conf, default is 2;3 for 2D and 3D data"
-	fi
-}
-
-src_configure() {
-	local mycmakeargs=(
-		-DWRAP_ITK_JAVA=OFF
-		-DWRAP_ITK_TCL=OFF
-		-DITK_USE_SYSTEM_HDF5=ON
-		-DITK_USE_SYSTEM_JPEG=ON
-		-DITK_USE_SYSTEM_PNG=ON
-		-DITK_USE_SYSTEM_TIFF=ON
-		-DITK_USE_SYSTEM_ZLIB=ON
-		-DITK_USE_SYSTEM_GCCXML=ON
-		-DITK_USE_SYSTEM_SWIG=ON
-		-DITK_BUILD_ALL_MODULES=ON
-		-DBUILD_SHARED_LIBS=ON
-		-DBUILD_EXAMPLES=OFF
-		-DITK_COMPUTER_MEMORY_SIZE="${ITK_COMPUTER_MEMORY_SIZE:-1}"
-		$(cmake-utils_use_build test TESTING)
-		$(cmake-utils_use review ITK_USE_REVIEW)
-		$(cmake-utils_use itkv3compat ITKV3_COMPATIBILITY)
-		$(cmake-utils_use cpu_flags_x86_sse2 VNL_CONFIG_ENABLE_SSE2)
-	)
-	if use fftw; then
-		mycmakeargs+=(
-			-DUSE_FFTWD=ON
-			-DUSE_FFTWF=ON
-			-DUSE_SYSTEM_FFTW=ON
-			-DITK_WRAP_double=ON
-			-DITK_WRAP_vector_double=ON
-			-DITK_WRAP_covariant_vector_double=ON
-			-DITK_WRAP_complex_double=ON
-		)
-	fi
-	if use vtkglue; then
-		mycmakeargs+=(
-			-DModule_ITKVtkGlue=ON
-		)
-	fi
-	if use python; then
-		mycmakeargs+=(
-			-DITK_WRAP_PYTHON=ON
-			-DITK_WRAP_DIMS="${ITK_WRAP_DIMS:-2;3}"
-		)
-	else
-		mycmakeargs+=(
-			-DITK_WRAP_PYTHON=OFF
-		)
-	fi
-	cmake-utils_src_configure
-}
-
-src_install() {
-	cmake-utils_src_install
-
-	if use examples; then
-		insinto /usr/share/doc/${PF}/examples
-		docompress -x /usr/share/doc/${PF}/examples
-		doins -r "${S}"/Examples/*
-	fi
-
-	echo "ITK_DATA_ROOT=${EROOT}/usr/share/${PN}/data" > ${T}/40${PN}
-	local ldpath="${EROOT}/usr/$(get_libdir)/InsightToolkit"
-	if use python; then
-		echo "PYTHONPATH=${EROOT}/usr/$(get_libdir)/InsightToolkit/WrapITK/Python" >> ${T}/40${PN}
-		ldpath="${ldpath}:${EROOT}/usr/$(get_libdir)/InsightToolkit/WrapITK/lib"
-	fi
-	echo "LDPATH=${ldpath}" >> ${T}/40${PN}
-
-	if use doc; then
-		insinto "/usr/share/doc/${PF}/api-docs"
-		cd "${WORKDIR}"/html
-		rm -f *.md5 || die "Failed to remove superfluous hashes"
-		einfo "Installing API docs. This may take some time."
-		insinto "/usr/share/doc/${PF}/api-docs"
-		doins -r ./*
-	fi
-
-	doenvd "${T}"/40${PN}
-}
diff --git a/sci-libs/itk/itk-4.4.2.ebuild b/sci-libs/itk/itk-4.4.2.ebuild
deleted file mode 100644
index 2d3b9f961..000000000
--- a/sci-libs/itk/itk-4.4.2.ebuild
+++ /dev/null
@@ -1,115 +0,0 @@
-# Copyright 1999-2015 Gentoo Foundation
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=5
-
-PYTHON_COMPAT=( python2_7 )
-
-inherit eutils toolchain-funcs cmake-utils python-single-r1
-
-MYP=InsightToolkit-${PV}
-
-DESCRIPTION="NLM Insight Segmentation and Registration Toolkit"
-HOMEPAGE="http://www.itk.org"
-SRC_URI="mirror://sourceforge/${PN}/${MYP}.tar.gz"
-
-LICENSE="Apache-2.0"
-SLOT="0"
-KEYWORDS="~amd64 ~x86 ~amd64-linux ~x86-linux"
-IUSE="debug examples fftw itkv3compat python review cpu_flags_x86_sse2 test"
-
-RDEPEND="
-	sci-libs/hdf5[cxx]
-	virtual/jpeg:0=
-	media-libs/libpng:0=
-	media-libs/tiff:0=
-	sys-libs/zlib
-	fftw? ( sci-libs/fftw:3.0 )
-"
-DEPEND="${RDEPEND}
-	python? (
-		${PYTHON_DEPS}
-		>=dev-lang/swig-2.0:0
-		>=dev-cpp/gccxml-0.9.0_pre20120309
-	)
-"
-
-S="${WORKDIR}/${MYP}"
-
-pkg_pretend() {
-	if [[ -z ${ITK_COMPUTER_MEMORY_SIZE} ]]; then
-		elog "To tune ITK to make the best use ouf working memory you can set"
-		elog "    ITK_COMPUTER_MEMORY_SIZE=XX"
-		elog "in make.conf, default is 1 (unit is GB)"
-	fi
-	if use python && [[ -z ${ITK_WRAP_DIMS} ]]; then
-		elog "For Python language bindings, you can define the dimensions"
-		elog "you want to create bindings for by setting"
-		elog "    ITK_WRAP_DIMS=X;Y;Z..."
-		elog "in make.conf, default is 2;3 for 2D and 3D data"
-	fi
-}
-
-src_configure() {
-	local mycmakeargs=(
-		-DWRAP_ITK_JAVA=OFF
-		-DWRAP_ITK_TCL=OFF
-		-DITK_USE_SYSTEM_HDF5=ON
-		-DITK_USE_SYSTEM_JPEG=ON
-		-DITK_USE_SYSTEM_PNG=ON
-		-DITK_USE_SYSTEM_TIFF=ON
-		-DITK_USE_SYSTEM_ZLIB=ON
-		-DITK_USE_SYSTEM_GCCXML=ON
-		-DITK_USE_SYSTEM_SWIG=ON
-		-DITK_BUILD_ALL_MODULES=ON
-		-DBUILD_SHARED_LIBS=ON
-		-DBUILD_EXAMPLES=OFF
-		-DITK_COMPUTER_MEMORY_SIZE="${ITK_COMPUTER_MEMORY_SIZE:-1}"
-		$(cmake-utils_use_build test TESTING)
-		$(cmake-utils_use review ITK_USE_REVIEW)
-		$(cmake-utils_use itkv3compat ITKV3_COMPATIBILITY)
-		$(cmake-utils_use cpu_flags_x86_sse2 VNL_CONFIG_ENABLE_SSE2)
-	)
-	if use fftw; then
-		mycmakeargs+=(
-			-DUSE_FFTWD=ON
-			-DUSE_FFTWF=ON
-			-DUSE_SYSTEM_FFTW=ON
-			-DITK_WRAP_double=ON
-			-DITK_WRAP_vector_double=ON
-			-DITK_WRAP_covariant_vector_double=ON
-			-DITK_WRAP_complex_double=ON
-		)
-	fi
-	if use python; then
-		mycmakeargs+=(
-			-DITK_WRAP_PYTHON=ON
-			-DITK_WRAP_DIMS="${ITK_WRAP_DIMS:-2;3}"
-		)
-	else
-		mycmakeargs+=(
-			-DITK_WRAP_PYTHON=OFF
-		)
-	fi
-	cmake-utils_src_configure
-}
-
-src_install() {
-	cmake-utils_src_install
-
-	if use examples; then
-		insinto /usr/share/doc/${PF}/examples
-		docompress -x /usr/share/doc/${PF}/examples
-		doins -r "${S}"/Examples/*
-	fi
-
-	echo "ITK_DATA_ROOT=${EROOT}/usr/share/${PN}/data" > ${T}/40${PN}
-	local ldpath="${EROOT}/usr/$(get_libdir)/InsightToolkit"
-	if use python; then
-		echo "PYTHONPATH=${EROOT}/usr/$(get_libdir)/InsightToolkit/WrapITK/Python" >> ${T}/40${PN}
-		ldpath="${ldpath}:${EROOT}/usr/$(get_libdir)/InsightToolkit/WrapITK/lib"
-	fi
-	echo "LDPATH=${ldpath}" >> ${T}/40${PN}
-
-	doenvd "${T}"/40${PN}
-}
diff --git a/sci-libs/itk/itk-4.5.1.ebuild b/sci-libs/itk/itk-4.5.1.ebuild
deleted file mode 100644
index 199c03659..000000000
--- a/sci-libs/itk/itk-4.5.1.ebuild
+++ /dev/null
@@ -1,155 +0,0 @@
-# Copyright 1999-2015 Gentoo Foundation
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=5
-
-PYTHON_COMPAT=( python2_7 )
-
-inherit eutils toolchain-funcs cmake-utils python-single-r1
-
-MYPN=InsightToolkit
-MYP=${MYPN}-${PV}
-DOC_PV=4.5.0
-
-DESCRIPTION="NLM Insight Segmentation and Registration Toolkit"
-HOMEPAGE="http://www.itk.org"
-SRC_URI="mirror://sourceforge/${PN}/${MYP}.tar.xz
-	doc? ( mirror://sourceforge/${PN}/Doxygen${MYPN}-${DOC_PV}.tar.gz )"
-RESTRICT="primaryuri"
-
-LICENSE="Apache-2.0"
-SLOT="0"
-KEYWORDS="~amd64 ~x86 ~amd64-linux ~x86-linux"
-IUSE="debug doc examples fftw itkv3compat python review cpu_flags_x86_sse2 test vtkglue"
-
-RDEPEND="
-	dev-libs/double-conversion:0=
-	media-libs/libpng:0=
-	media-libs/tiff:0=
-	sci-libs/dcmtk:0=
-	sci-libs/hdf5:0=[cxx]
-	sys-libs/zlib:0=
-	virtual/jpeg:0=
-	fftw? ( sci-libs/fftw:3.0= )
-	vtkglue? ( sci-libs/vtk:0=[python?] )
-"
-DEPEND="${RDEPEND}
-	python? (
-		${PYTHON_DEPS}
-		>=dev-lang/swig-2.0:0
-		>=dev-cpp/gccxml-0.9.0_pre20120309
-	)
-	doc? ( app-doc/doxygen )
-"
-
-REQUIRED_USE="python? ( ${PYTHON_REQUIRED_USE} )"
-
-S="${WORKDIR}/${MYP}"
-
-PATCHES=(
-	"${FILESDIR}"/0001-BUG-Wrap-TransformFileReader-TransformFileWriter.patch
-	"${FILESDIR}"/0002-COMP-Fixed-itkQuasiNewtonOptimizerv4-wrapping-warnin.patch
-	"${FILESDIR}"/0003-COMP-Fixed-itkGradientDescentOptimizerv4-wrapping-wa.patch
-	"${FILESDIR}"/0004-COMP-Warp-OptimizerParameterScalesEstimatorTemplate.patch
-	"${FILESDIR}"/0005-make-gdcm-helper-library-static.patch
-	"${FILESDIR}"/nrrdio-linking.patch
-)
-
-pkg_pretend() {
-	if [[ -z ${ITK_COMPUTER_MEMORY_SIZE} ]]; then
-		elog "To tune ITK to make the best use of working memory you can set"
-		elog "    ITK_COMPUTER_MEMORY_SIZE=XX"
-		elog "in make.conf, default is 1 (unit is GB)"
-	fi
-	if use python && [[ -z ${ITK_WRAP_DIMS} ]]; then
-		elog "For Python language bindings, you can define the dimensions"
-		elog "you want to create bindings for by setting"
-		elog "    ITK_WRAP_DIMS=X;Y;Z..."
-		elog "in make.conf, default is 2;3 for 2D and 3D data"
-	fi
-}
-
-src_configure() {
-	sed -i \
-		-e '/find_package/d' \
-		Modules/ThirdParty/DoubleConversion/CMakeLists.txt || die
-
-	local mycmakeargs=(
-		-DBUILD_SHARED_LIBS=ON
-		-DITK_USE_SYSTEM_DCMTK=ON
-		-DITK_USE_SYSTEM_DOUBLECONVERSION=ON
-		-DITK_USE_SYSTEM_GCCXML=ON
-		-DITK_USE_SYSTEM_HDF5=ON
-		-DITK_USE_SYSTEM_JPEG=ON
-		-DITK_USE_SYSTEM_PNG=ON
-		-DITK_USE_SYSTEM_SWIG=ON
-		-DITK_USE_SYSTEM_TIFF=ON
-		-DITK_USE_SYSTEM_ZLIB=ON
-		-DITK_BUILD_DEFAULT_MODULES=ON
-		-DITK_COMPUTER_MEMORY_SIZE="${ITK_COMPUTER_MEMORY_SIZE:-1}"
-		-DWRAP_ITK_JAVA=OFF
-		-DWRAP_ITK_TCL=OFF
-		-Ddouble-conversion_INCLUDE_DIRS="${EPREFIX}/usr/include/double-conversion"
-		-Ddouble-conversion_LIBRARIES="-ldouble-conversion"
-		$(cmake-utils_use_build test TESTING)
-		$(cmake-utils_use_build examples EXAMPLES)
-		$(cmake-utils_use review ITK_USE_REVIEW)
-		$(cmake-utils_use itkv3compat ITKV3_COMPATIBILITY)
-		$(cmake-utils_use cpu_flags_x86_sse2 VNL_CONFIG_ENABLE_SSE2)
-	)
-	if use fftw; then
-		mycmakeargs+=(
-			-DUSE_FFTWD=ON
-			-DUSE_FFTWF=ON
-			-DUSE_SYSTEM_FFTW=ON
-			-DITK_WRAP_double=ON
-			-DITK_WRAP_vector_double=ON
-			-DITK_WRAP_covariant_vector_double=ON
-			-DITK_WRAP_complex_double=ON
-		)
-	fi
-	if use vtkglue; then
-		mycmakeargs+=(
-			-DModule_ITKVtkGlue=ON
-		)
-	fi
-	if use python; then
-		mycmakeargs+=(
-			-DITK_WRAP_PYTHON=ON
-			-DITK_WRAP_DIMS="${ITK_WRAP_DIMS:-2;3}"
-		)
-	else
-		mycmakeargs+=(
-			-DITK_WRAP_PYTHON=OFF
-		)
-	fi
-	cmake-utils_src_configure
-}
-
-src_install() {
-	cmake-utils_src_install
-
-	if use examples; then
-		insinto /usr/share/doc/${PF}/examples
-		docompress -x /usr/share/doc/${PF}/examples
-		doins -r "${S}"/Examples/*
-	fi
-
-	echo "ITK_DATA_ROOT=${EROOT%/}/usr/share/${PN}/data" > ${T}/40${PN}
-	local ldpath="${EROOT%/}/usr/$(get_libdir)/InsightToolkit"
-	if use python; then
-		echo "PYTHONPATH=${EROOT%/}/usr/$(get_libdir)/InsightToolkit/WrapITK/Python" >> "${T}"/40${PN}
-		ldpath="${ldpath}:${EROOT%/}/usr/$(get_libdir)/InsightToolkit/WrapITK/lib"
-	fi
-	echo "LDPATH=${ldpath}" >> "${T}"/40${PN}
-	doenvd "${T}"/40${PN}
-
-	if use doc; then
-		insinto /usr/share/doc/${PF}/api-docs
-		cd "${WORKDIR}"/html
-		rm  *.md5 || die "Failed to remove superfluous hashes"
-		einfo "Installing API docs. This may take some time."
-		insinto /usr/share/doc/${PF}/api-docs
-		doins -r *
-	fi
-}
diff --git a/sci-libs/itk/itk-5.2.1-r2.ebuild b/sci-libs/itk/itk-5.2.1-r2.ebuild
new file mode 100644
index 000000000..0b1f25860
--- /dev/null
+++ b/sci-libs/itk/itk-5.2.1-r2.ebuild
@@ -0,0 +1,250 @@
+# Copyright 1999-2022 Gentoo Authors
+# Distributed under the terms of the GNU General Public License v2
+
+EAPI=8
+
+PYTHON_COMPAT=( python3_{10..11} )
+VIRTUALX_REQUIRED="manual"
+
+inherit cmake python-single-r1 virtualx
+
+MY_PN="InsightToolkit"
+MY_P="${MY_PN}-${PV}"
+GLI_HASH="89da9305f5750d3990ca9fd35ecc5ce0b39c71a6"
+IAD_HASH="24825c8d246e941334f47968553f0ae388851f0c"
+TEST_HASH="7ab9d41ad5b42ccbe8adcaf0b24416d439a264d0"
+declare -a GLI_TEST_HASHES=(
+	"a5e11ea71164ff78c65fcf259db01ea5db981a9d868e60045ff2bffca92984df1174bf984a1076e450f0d5d69b4f0191ed1a61465c220e2c91a893b5df150c0a"
+	"bcdbb347f3704262d1f00be7179d6a0a6e68aed56c0653e8072ee5a94985c713bd229c935b1226a658af84fb7f1fffc2458c98364fc35303a2303b12f9f7ce2f"
+)
+
+GLI_TEST_SRC=""
+for i in "${GLI_TEST_HASHES[@]}"; do
+	GLI_TEST_SRC+="https://data.kitware.com/api/v1/file/hashsum/sha512/${i}/download -> ${PN}-test-${i} "
+done
+
+DESCRIPTION="NLM Insight Segmentation and Registration Toolkit"
+HOMEPAGE="https://itk.org"
+SRC_URI="
+	https://github.com/InsightSoftwareConsortium/ITK/releases/download/v${PV}/${MY_P}.tar.gz
+	https://github.com/InsightSoftwareConsortium/ITKGenericLabelInterpolator/archive/${GLI_HASH}.tar.gz -> ITKGenericLabelInterpolator-${PV}.tar.gz
+	https://github.com/ntustison/ITKAdaptiveDenoising/archive/${IAD_HASH}.tar.gz -> ITKAdaptiveDenoising-${PV}.tar.gz
+	test? (
+		https://github.com/InsightSoftwareConsortium/ITK/releases/download/v${PV}/InsightData-${PV}.tar.gz
+		https://github.com/InsightSoftwareConsortium/ITKTestingData/archive/${TEST_HASH}.tar.gz -> ${P}-testingdata.tar.gz
+		${GLI_TEST_SRC}
+		)
+	"
+
+LICENSE="Apache-2.0"
+SLOT="0"
+KEYWORDS="~amd64 ~x86"
+IUSE="debug doc examples fftw itkv4-compat python review test vtkglue"
+REQUIRED_USE="python? ( ${PYTHON_REQUIRED_USE} )"
+
+RESTRICT="!test? ( test )"
+
+RDEPEND="
+	dev-cpp/eigen:3
+	dev-libs/double-conversion:0=
+	dev-libs/expat:0=
+	media-libs/openjpeg:2
+	media-libs/libpng:0=
+	media-libs/tiff:0=[jpeg]
+	sci-libs/dcmtk:0=
+	sci-libs/hdf5:0=[cxx]
+	sci-libs/gdcm:0=
+	sys-libs/zlib:0=
+	media-libs/libjpeg-turbo:0=
+	fftw? ( sci-libs/fftw:3.0= )
+	vtkglue? (
+		sci-libs/vtk:0=[rendering]
+		python? (
+			sci-libs/vtk:0=[python,${PYTHON_SINGLE_USEDEP}]
+		)
+	)
+	python? ( ${PYTHON_DEPS} )
+"
+DEPEND="${RDEPEND}
+	sys-apps/coreutils
+	python? (
+		>=dev-lang/swig-2.0:0
+		dev-libs/castxml
+	)
+	doc? ( app-text/doxygen )
+"
+BDEPEND="
+	test? (
+		vtkglue? ( ${VIRTUALX_DEPEND} )
+		python? (
+			$(python_gen_cond_dep 'dev-python/numpy[${PYTHON_USEDEP}]')
+		)
+	)
+"
+
+S="${WORKDIR}/${MY_P}"
+
+PATCHES=(
+	"${FILESDIR}/${P}-upstream-fixes.patch"
+	"${FILESDIR}/${P}-system-tiff-has-64.patch"
+	"${FILESDIR}/${P}-fix-castxml-clang-attr-malloc.patch"
+	"${FILESDIR}/${P}-system-openjpeg.patch"
+)
+
+pkg_pretend() {
+	if [[ -z ${ITK_COMPUTER_MEMORY_SIZE} ]]; then
+		elog "To tune ITK to make the best use of working memory you can set"
+		elog "    ITK_COMPUTER_MEMORY_SIZE=XX"
+		elog "in make.conf, default is 1 (unit is GB)"
+	fi
+	if use python && [[ -z ${ITK_WRAP_DIMS} ]]; then
+		elog "For Python language bindings, you can define the dimensions"
+		elog "you want to create bindings for by setting"
+		elog "    ITK_WRAP_DIMS=X;Y;Z..."
+		elog "in make.conf, default is 2;3 for 2D and 3D data"
+	fi
+}
+
+src_prepare() {
+	# drop bundled libs
+	local -a DROPS=(
+		DoubleConversion/src/double-conversion
+		Eigen3/src/itkeigen
+		Expat/src/expat
+		GDCM/src/gdcm
+		JPEG/src/itkjpeg
+		HDF5/src/itkhdf5
+		OpenJPEG/src/openjpeg
+		PNG/src/itkpng
+		TIFF/src/itktiff
+		ZLIB/src/itkzlib
+	)
+	local x
+	for x in "${DROPS[@]}"; do
+		ebegin "Dropping bundled ${x%%/*}"
+		rm -r "Modules/ThirdParty/${x}" || die
+		eend $?
+	done
+	{
+		find Modules/ThirdParty -mindepth 2 -maxdepth 2 -type d -name src -printf '%P\n'
+		printf '%s\n' "${DROPS[@]}" | sed 's,/[^/]*$,,'
+	} | sort | uniq -u | xargs -n 1 ewarn "Using bundled" || die
+
+	# Remote modules
+	ln -sr "../ITKGenericLabelInterpolator-${GLI_HASH}" Modules/External/ITKGenericLabelInterpolator || die
+	ln -sr "../ITKAdaptiveDenoising-${IAD_HASH}" Modules/External/ITKAdaptiveDenoising || die
+
+	cmake_src_prepare
+
+	if use test; then
+		cp -rf "../ITKTestingData-${TEST_HASH}/"* ".ExternalData/" || die
+		mv "../ITKTestingData-${TEST_HASH}" "${BUILD_DIR}/.ExternalData" || die
+		for i in "${GLI_TEST_HASHES[@]}"; do
+			cp "${DISTDIR}/${PN}-test-${i}" ".ExternalData/SHA512/${i}" || die
+			cp "${DISTDIR}/${PN}-test-${i}" "${BUILD_DIR}/.ExternalData/SHA512/${i}" || die
+		done
+	fi
+}
+
+src_configure() {
+	local mycmakeargs=(
+		-DITK_BUILD_DOCUMENTATION="$(usex doc ON OFF)"
+		-DITK_INSTALL_DOC_DIR="share/doc/${P}"
+		-DBUILD_EXAMPLES="$(usex examples ON OFF)"
+		-DBUILD_SHARED_LIBS=ON
+		-DBUILD_TESTING="$(usex test ON OFF)"
+		-Ddouble-conversion_INCLUDE_DIRS="${EPREFIX}/usr/include/double-conversion"
+		-DExternalData_OBJECT_STORES="${WORKDIR}/InsightToolkit-${PV}/.ExternalData"
+		-DGDCM_USE_SYSTEM_OPENJPEG=ON
+		-DITK_FORBID_DOWNLOADS:BOOL=ON
+		-DITK_INSTALL_LIBRARY_DIR=$(get_libdir)
+		-DITK_USE_REVIEW="$(usex review ON OFF)"
+		-DITK_USE_SYSTEM_DCMTK=ON
+		-DITK_USE_SYSTEM_DOUBLECONVERSION=ON
+		-DITK_USE_SYSTEM_CASTXML=ON
+		-DITK_USE_SYSTEM_EIGEN=ON
+		-DITK_USE_SYSTEM_EXPAT=ON
+		-DITK_USE_SYSTEM_GDCM=ON
+		-DITK_USE_SYSTEM_HDF5=ON
+		-DITK_USE_SYSTEM_JPEG=ON
+		-DITK_USE_SYSTEM_OPENJPEG=ON
+		-DITK_USE_SYSTEM_PNG=ON
+		-DITK_USE_SYSTEM_SWIG=ON
+		-DITK_USE_SYSTEM_TIFF=ON
+		-DITK_USE_SYSTEM_ZLIB=ON
+		-DITK_USE_KWSTYLE=OFF
+		-DITK_BUILD_DEFAULT_MODULES=ON
+		-DITK_COMPUTER_MEMORY_SIZE="${ITK_COMPUTER_MEMORY_SIZE:-1}"
+		-DModule_AdaptiveDenoising:BOOL=ON
+		-DModule_GenericLabelInterpolator:BOOL=ON
+		-DModule_ITKReview:BOOL=ON
+		-DWRAP_ITK_JAVA=OFF
+		-DWRAP_ITK_TCL=OFF
+		-DITKV4_COMPATIBILITY:BOOL=$(usex itkv4-compat)
+	)
+	if use fftw; then
+		mycmakeargs+=(
+			-DUSE_FFTWD=ON
+			-DUSE_FFTWF=ON
+			-DUSE_SYSTEM_FFTW=ON
+			-DITK_WRAP_double=ON
+			-DITK_WRAP_vector_double=ON
+			-DITK_WRAP_covariant_vector_double=ON
+			-DITK_WRAP_complex_double=ON
+		)
+	fi
+	if use vtkglue; then
+		mycmakeargs+=(
+			-DModule_ITKVtkGlue=ON
+		)
+	fi
+	if use python; then
+		mycmakeargs+=(
+			-DITK_WRAP_PYTHON=ON
+			-DPython3_EXECUTABLE="${PYTHON}"
+			-DITK_WRAP_DIMS="${ITK_WRAP_DIMS:-2;3}"
+		)
+	else
+		mycmakeargs+=(
+			-DITK_WRAP_PYTHON=OFF
+		)
+	fi
+	cmake_src_configure
+}
+
+src_install() {
+	cmake_src_install
+
+	if use examples; then
+		docinto examples
+		docompress -x /usr/share/doc/${PF}/examples
+		dodoc -r "${S}"/Examples/*
+	fi
+
+	echo "ITK_DATA_ROOT=${EPREFIX}/usr/share/${PN}/data" > ${T}/40${PN} || die
+	local ldpath="${EPREFIX}/usr/$(get_libdir)/InsightToolkit"
+	if use python; then
+		echo "PYTHONPATH=${EPREFIX}/usr/$(get_libdir)/InsightToolkit/WrapITK/Python" >> "${T}"/40${PN} || die
+		ldpath="${ldpath}:${EPREFIX}/usr/$(get_libdir)/InsightToolkit/WrapITK/lib"
+	fi
+	echo "LDPATH=${ldpath}" >> "${T}"/40${PN} || die
+	doenvd "${T}"/40${PN}
+
+	if use doc; then
+		cd "${WORKDIR}"/html || die
+		rm  *.md5 || die "Failed to remove superfluous hashes"
+		einfo "Installing API docs. This may take some time."
+		docinto api-docs
+		dodoc -r *
+	fi
+
+	use python && python_optimize
+}
+
+src_test() {
+	if use vtkglue; then
+		virtx cmake_src_test
+	else
+		cmake_src_test
+	fi
+}
diff --git a/sci-libs/itk/itk-5.3.0-r1.ebuild b/sci-libs/itk/itk-5.3.0-r1.ebuild
new file mode 100644
index 000000000..b2c3af801
--- /dev/null
+++ b/sci-libs/itk/itk-5.3.0-r1.ebuild
@@ -0,0 +1,269 @@
+# Copyright 1999-2023 Gentoo Authors
+# Distributed under the terms of the GNU General Public License v2
+
+EAPI=8
+
+PYTHON_COMPAT=( python3_{10..11} )
+VIRTUALX_REQUIRED="manual"
+
+inherit cmake python-single-r1 virtualx
+
+MY_PN="InsightToolkit"
+MY_P="${MY_PN}-${PV}"
+GLI_V="1.2.0"
+IAD_HASH="24825c8d246e941334f47968553f0ae388851f0c"
+TEST_HASH="bb6d3b9a932333901465c75417fe8859124f5fed"
+declare -a GLI_TEST_HASHES=(
+	"a5e11ea71164ff78c65fcf259db01ea5db981a9d868e60045ff2bffca92984df1174bf984a1076e450f0d5d69b4f0191ed1a61465c220e2c91a893b5df150c0a"
+	"bcdbb347f3704262d1f00be7179d6a0a6e68aed56c0653e8072ee5a94985c713bd229c935b1226a658af84fb7f1fffc2458c98364fc35303a2303b12f9f7ce2f"
+)
+
+GLI_TEST_SRC=""
+for i in "${GLI_TEST_HASHES[@]}"; do
+	GLI_TEST_SRC+="https://data.kitware.com/api/v1/file/hashsum/sha512/${i}/download -> ${PN}-test-${i} "
+done
+
+DESCRIPTION="NLM Insight Segmentation and Registration Toolkit"
+HOMEPAGE="https://itk.org"
+SRC_URI="
+	https://github.com/InsightSoftwareConsortium/ITK/releases/download/v${PV}/${MY_P}.tar.gz
+	https://github.com/InsightSoftwareConsortium/ITKGenericLabelInterpolator/archive/refs/tags/v${GLI_V}.tar.gz -> ITKGenericLabelInterpolator-${GLI_V}.tar.gz
+	https://github.com/ntustison/ITKAdaptiveDenoising/archive/${IAD_HASH}.tar.gz -> ITKAdaptiveDenoising-${PV}.tar.gz
+	test? (
+		https://github.com/InsightSoftwareConsortium/ITK/releases/download/v${PV}/InsightData-${PV}.tar.gz
+		https://github.com/InsightSoftwareConsortium/ITKTestingData/archive/${TEST_HASH}.tar.gz -> ${P}-testingdata.tar.gz
+		${GLI_TEST_SRC}
+		)
+	"
+
+LICENSE="Apache-2.0"
+SLOT="0"
+KEYWORDS="~amd64 ~x86"
+IUSE="debug doc examples fftw itkv4-compat python review test vtkglue"
+REQUIRED_USE="python? ( ${PYTHON_REQUIRED_USE} )"
+
+RESTRICT="!test? ( test )"
+
+RDEPEND="
+	dev-cpp/eigen:3
+	dev-libs/double-conversion:0=
+	dev-libs/expat:0=
+	dev-libs/icu:0=
+	media-libs/libjpeg-turbo:0=
+	media-libs/libpng:0=
+	media-libs/openjpeg:2
+	media-libs/tiff:0=[jpeg]
+	sci-libs/dcmtk:0=
+	sci-libs/gdcm:0=
+	sci-libs/hdf5:0=[cxx]
+	sys-libs/zlib-ng
+	fftw? ( sci-libs/fftw:3.0=[threads] )
+	vtkglue? (
+		sci-libs/vtk:0=[rendering]
+		python? (
+			sci-libs/vtk:0=[python,${PYTHON_SINGLE_USEDEP}]
+		)
+	)
+	python? ( ${PYTHON_DEPS} )
+"
+# Might also need:
+# dev-libs/kwsys::guru
+# kwiml
+# minc
+# metaio
+# niftilib
+# sci-lib/vxl::science
+DEPEND="${RDEPEND}
+	sys-apps/coreutils
+	python? (
+		>=dev-lang/swig-2.0:0
+		dev-libs/castxml
+	)
+	doc? ( app-text/doxygen )
+"
+BDEPEND="
+	test? (
+		vtkglue? ( ${VIRTUALX_DEPEND} )
+		python? (
+			$(python_gen_cond_dep 'dev-python/numpy[${PYTHON_USEDEP}]')
+		)
+	)
+"
+
+S="${WORKDIR}/${MY_P}"
+
+# uint patch applied by upstream for next release.
+PATCHES=(
+	"${FILESDIR}/${PN}-5.2.1-system-tiff-has-64.patch"
+	"${FILESDIR}/${PN}-5.3.0-system-openjpeg.patch"
+	"${FILESDIR}/${PN}-5.3.0-uint8.patch"
+)
+
+pkg_pretend() {
+	if [[ -z ${ITK_COMPUTER_MEMORY_SIZE} ]]; then
+		elog "To tune ITK to make the best use of working memory you can set"
+		elog "    ITK_COMPUTER_MEMORY_SIZE=XX"
+		elog "in make.conf, default is 1 (unit is GB)"
+	fi
+	if use python && [[ -z ${ITK_WRAP_DIMS} ]]; then
+		elog "For Python language bindings, you can define the dimensions"
+		elog "you want to create bindings for by setting"
+		elog "    ITK_WRAP_DIMS=X;Y;Z..."
+		elog "in make.conf, default is 2;3 for 2D and 3D data"
+	fi
+}
+
+src_prepare() {
+	# drop bundled libs
+	local -a DROPS=(
+		DoubleConversion/src/double-conversion
+		Eigen3/src/itkeigen
+		Expat/src/expat
+		GDCM/src/gdcm
+		JPEG/src/itkjpeg
+		HDF5/src/itkhdf5
+		OpenJPEG/src/openjpeg
+		PNG/src/itkpng
+		TIFF/src/itktiff
+		ZLIB/src/itkzlib-ng
+	)
+	local x
+	for x in "${DROPS[@]}"; do
+		ebegin "Dropping bundled ${x%%/*}"
+		rm -r "Modules/ThirdParty/${x}" || die
+		eend $?
+	done
+	{
+		find Modules/ThirdParty -mindepth 2 -maxdepth 2 -type d -name src -printf '%P\n'
+		printf '%s\n' "${DROPS[@]}" | sed 's,/[^/]*$,,'
+	} | sort | uniq -u | xargs -n 1 ewarn "Using bundled" || die
+
+	# Remote modules
+	ln -sr "../ITKGenericLabelInterpolator-${GLI_V}" Modules/External/ITKGenericLabelInterpolator || die
+	ln -sr "../ITKAdaptiveDenoising-${IAD_HASH}" Modules/External/ITKAdaptiveDenoising || die
+
+	cmake_src_prepare
+
+	if use test; then
+		cp -rf "../ITKTestingData-${TEST_HASH}/"* ".ExternalData/" || die
+		mv "../ITKTestingData-${TEST_HASH}" "${BUILD_DIR}/.ExternalData" || die
+		for i in "${GLI_TEST_HASHES[@]}"; do
+			cp "${DISTDIR}/${PN}-test-${i}" ".ExternalData/SHA512/${i}" || die
+			cp "${DISTDIR}/${PN}-test-${i}" "${BUILD_DIR}/.ExternalData/SHA512/${i}" || die
+		done
+	fi
+}
+
+src_configure() {
+	local mycmakeargs=(
+		-DITK_BUILD_DOCUMENTATION="$(usex doc ON OFF)"
+		-DITK_INSTALL_DOC_DIR="share/doc/${P}"
+		-DBUILD_EXAMPLES="$(usex examples ON OFF)"
+		-DBUILD_SHARED_LIBS=ON
+		-DBUILD_TESTING="$(usex test ON OFF)"
+		-Ddouble-conversion_INCLUDE_DIRS="${EPREFIX}/usr/include/double-conversion"
+		-DExternalData_OBJECT_STORES="${WORKDIR}/InsightToolkit-${PV}/.ExternalData"
+		-DGDCM_USE_SYSTEM_OPENJPEG=ON
+		-DITK_FORBID_DOWNLOADS:BOOL=ON
+		-DITK_INSTALL_LIBRARY_DIR=$(get_libdir)
+		-DITK_USE_REVIEW="$(usex review ON OFF)"
+		-DITK_USE_SYSTEM_ICU=ON
+		-DITK_USE_SYSTEM_DCMTK=ON
+		-DITK_USE_SYSTEM_DOUBLECONVERSION=ON
+		-DITK_USE_SYSTEM_CASTXML=ON
+		-DITK_USE_SYSTEM_EIGEN=ON
+		-DITK_USE_SYSTEM_EXPAT=ON
+		-DITK_USE_SYSTEM_GDCM=ON
+		-DITK_USE_SYSTEM_HDF5=ON
+		-DITK_USE_SYSTEM_JPEG=ON
+		-DITK_USE_SYSTEM_OPENJPEG=ON
+		-DITK_USE_SYSTEM_PNG=ON
+		-DITK_USE_SYSTEM_SWIG=ON
+		-DITK_USE_SYSTEM_TIFF=ON
+		-DITK_USE_SYSTEM_ZLIB=ON
+		-DITK_USE_KWSTYLE=OFF
+		-DITK_BUILD_DEFAULT_MODULES=ON
+		-DITK_COMPUTER_MEMORY_SIZE="${ITK_COMPUTER_MEMORY_SIZE:-1}"
+		-DModule_AdaptiveDenoising:BOOL=ON
+		-DModule_GenericLabelInterpolator:BOOL=ON
+		-DModule_ITKReview:BOOL=ON
+		-DWRAP_ITK_JAVA=OFF
+		-DWRAP_ITK_TCL=OFF
+		-DITKV4_COMPATIBILITY:BOOL=$(usex itkv4-compat)
+	)
+	if use fftw; then
+		mycmakeargs+=(
+			-DITK_USE_FFTWD:BOOL=ON
+			-DITK_USE_FFTWF:BOOL=ON
+			-DITK_USE_SYSTEM_FFTW:BOOL=ON
+			-DITK_WRAP_double=ON
+			-DITK_WRAP_vector_double=ON
+			-DITK_WRAP_covariant_vector_double=ON
+			-DITK_WRAP_complex_double=ON
+		)
+	else
+		mycmakeargs+=(
+			-DITK_USE_FFTWD:BOOL=OFF
+			-DITK_USE_FFTWF:BOOL=OFF
+			-DITK_USE_SYSTEM_FFTW:BOOL=OFF
+			-DITK_WRAP_double=OFF
+			-DITK_WRAP_vector_double=OFF
+			-DITK_WRAP_covariant_vector_double=OFF
+			-DITK_WRAP_complex_double=OFF
+		)
+	fi
+	if use vtkglue; then
+		mycmakeargs+=(
+			-DModule_ITKVtkGlue=ON
+		)
+	fi
+	if use python; then
+		mycmakeargs+=(
+			-DITK_WRAP_PYTHON=ON
+			-DPython3_EXECUTABLE="${PYTHON}"
+			-DITK_WRAP_DIMS="${ITK_WRAP_DIMS:-2;3}"
+		)
+	else
+		mycmakeargs+=(
+			-DITK_WRAP_PYTHON=OFF
+		)
+	fi
+	cmake_src_configure
+}
+
+src_install() {
+	cmake_src_install
+
+	if use examples; then
+		docinto examples
+		docompress -x /usr/share/doc/${PF}/examples
+		dodoc -r "${S}"/Examples/*
+	fi
+
+	echo "ITK_DATA_ROOT=${EPREFIX}/usr/share/${PN}/data" > ${T}/40${PN} || die
+	local ldpath="${EPREFIX}/usr/$(get_libdir)/InsightToolkit"
+	if use python; then
+		echo "PYTHONPATH=${EPREFIX}/usr/$(get_libdir)/InsightToolkit/WrapITK/Python" >> "${T}"/40${PN} || die
+		ldpath="${ldpath}:${EPREFIX}/usr/$(get_libdir)/InsightToolkit/WrapITK/lib"
+	fi
+	echo "LDPATH=${ldpath}" >> "${T}"/40${PN} || die
+	doenvd "${T}"/40${PN}
+
+	if use doc; then
+		cd "${WORKDIR}"/html || die
+		rm  *.md5 || die "Failed to remove superfluous hashes"
+		einfo "Installing API docs. This may take some time."
+		docinto api-docs
+		dodoc -r *
+	fi
+
+	use python && python_optimize
+}
+
+src_test() {
+	if use vtkglue; then
+		virtx cmake_src_test
+	else
+		cmake_src_test
+	fi
+}
diff --git a/sci-libs/itk/metadata.xml b/sci-libs/itk/metadata.xml
index 8485fb7e1..5da2678ec 100644
--- a/sci-libs/itk/metadata.xml
+++ b/sci-libs/itk/metadata.xml
@@ -9,16 +9,17 @@
 		<name>Gentoo Biology Project</name>
 	</maintainer>
 	<longdescription lang="en">
-Insight Segmentation and Registration Toolkit (ITK) is a library
-that provides developers with an extensive suite of tools for image
-analysis.
-</longdescription>
-	<use>
-		<flag name="itkv3compat">Enable compatibility with ITK version 3</flag>
+		Insight Segmentation and Registration Toolkit (ITK) is a library
+		that provides developers with an extensive suite of tools for image
+		analysis.
+	</longdescription>
+		<use>
+		<flag name="itkv4-compat">Compatibility for applications using ITKv4 API</flag>
 		<flag name="review">Enable compilation of methods under review</flag>
 		<flag name="vtkglue">PLEASE FIX MY DESCRIPTION</flag>
 	</use>
 	<upstream>
+		<remote-id type="github">InsightSoftwareConsortium/ITK</remote-id>
 		<remote-id type="sourceforge">itk</remote-id>
 	</upstream>
 </pkgmetadata>
diff --git a/sci-libs/jhdf5/Manifest b/sci-libs/jhdf5/Manifest
deleted file mode 100644
index 3bc4752e4..000000000
--- a/sci-libs/jhdf5/Manifest
+++ /dev/null
@@ -1 +0,0 @@
-DIST sis-jhdf5-14.12.1-r33502.zip 30916751 BLAKE2B 9605b88a856fcfc66f0315d35a1635999099b3c4a4182c7ae4eb33ae540602f6e69ec4e99e0962c37c7164bf38787ab2b1e5485ad3b7cdee00e4974b424dbf5c SHA512 bc6104a829f50639cf913b3497c6ca815aff70782de0c509d9091087d7bcbd01649d5955e2df91d23ed4e058cdf90f7acfa40f1170059ca4039ba376ca11f800
diff --git a/sci-libs/jhdf5/jhdf5-14.12.1.ebuild b/sci-libs/jhdf5/jhdf5-14.12.1.ebuild
deleted file mode 100644
index 587bc370e..000000000
--- a/sci-libs/jhdf5/jhdf5-14.12.1.ebuild
+++ /dev/null
@@ -1,25 +0,0 @@
-# Copyright 1999-2015 Gentoo Foundation
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=5
-
-inherit java-pkg-2 java-ant-2
-
-DESCRIPTION="Java binding for HDF5 compatible with HDF5 1.6/1.8"
-HOMEPAGE="https://wiki-bsse.ethz.ch/display/JHDF5
-	https://wiki-bsse.ethz.ch/pages/viewpage.action?pageId=26609113"
-SRC_URI="https://wiki-bsse.ethz.ch/download/attachments/26609237/sis-jhdf5-14.12.1-r33502.zip"
-# first SIS release: https://wiki-bsse.ethz.ch/download/attachments/26609237/sis-jhdf5-14.12.0-r33145.zip
-# last CISD release: https://wiki-bsse.ethz.ch/download/attachments/26609237/cisd-jhdf5-13.06.2-r29633.zip
-
-LICENSE="Apache-2.0"
-SLOT="0"
-KEYWORDS=""
-IUSE=""
-
-# versions <=12.02 required >=java-1.5
-DEPEND=">=virtual/jdk-1.6:*"
-RDEPEND="${DEPEND}
-	>=virtual/jre-1.6:*"
-
-S="${WORKDIR}"/sis-jhdf5
diff --git a/sci-libs/jhdf5/metadata.xml b/sci-libs/jhdf5/metadata.xml
deleted file mode 100644
index 138cb7705..000000000
--- a/sci-libs/jhdf5/metadata.xml
+++ /dev/null
@@ -1,12 +0,0 @@
-<?xml version="1.0" encoding="UTF-8"?>
-<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
-<pkgmetadata>
-	<maintainer type="person">
-		<email>mmokrejs@fold.natur.cuni.cz</email>
-		<name>Martin Mokrejs</name>
-	</maintainer>
-	<maintainer type="project">
-		<email>sci-biology@gentoo.org</email>
-		<name>Gentoo Biology Project</name>
-	</maintainer>
-</pkgmetadata>
diff --git a/sci-libs/k3match/Manifest b/sci-libs/k3match/Manifest
deleted file mode 100644
index 55e1cd3c7..000000000
--- a/sci-libs/k3match/Manifest
+++ /dev/null
@@ -1 +0,0 @@
-DIST k3match-1.1.tar.gz 20192 SHA256 f8c2668cee7db91e51719d63ef7598606540b7ccdb0f01b42deaf593b2241963 SHA512 c377079af8f6b1a0a9b02dbcafa26db8fdfaefe9240346d6414a1251d25630ce860d9de78afbfd12e106c24c08ccd5689ff93cbbbeb3e091a1db3c7b39c99552 WHIRLPOOL f44166d3827e2db72ed8f01041101fcb82c12f29d0f964e761985d8f7fc139bca6f3b36e3a3613a1eb2b198def25e41b4e15da4da58f5108e09c6366409254fb
diff --git a/sci-libs/k3match/k3match-1.1.ebuild b/sci-libs/k3match/k3match-1.1.ebuild
deleted file mode 100644
index 22a049103..000000000
--- a/sci-libs/k3match/k3match-1.1.ebuild
+++ /dev/null
@@ -1,21 +0,0 @@
-# Copyright 1999-2014 Gentoo Foundation
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=5
-
-PYTHON_COMPAT=( python2_7 )
-PYTHON_REQ_USE="threads"
-
-inherit distutils-r1
-
-DESCRIPTION="Fast matching of large sets of points in 3D space, in O(N log N) time"
-HOMEPAGE="http://pschella.github.com/k3match/"
-SRC_URI="http://www.astro.ru.nl/~pschella/files/software/${PN}/${P}.tar.gz"
-
-LICENSE="GPL-3"
-SLOT="0"
-KEYWORDS="~amd64 ~x86"
-IUSE=" "
-
-DEPEND=">=dev-python/numpy-1.4.0[${PYTHON_USEDEP}]"
-RDEPEND="${DEPEND}"
diff --git a/sci-libs/k3match/metadata.xml b/sci-libs/k3match/metadata.xml
deleted file mode 100644
index 27bcacd8e..000000000
--- a/sci-libs/k3match/metadata.xml
+++ /dev/null
@@ -1,12 +0,0 @@
-<?xml version="1.0" encoding="UTF-8"?>
-<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
-<pkgmetadata>
-	<maintainer type="person">
-		<email>AstroFloyd@gmail.com</email>
-		<name>AstroFloyd</name>
-	</maintainer>
-	<maintainer type="project">
-		<email>sci@gentoo.org</email>
-		<name>Gentoo Science Project</name>
-	</maintainer>
-</pkgmetadata>
diff --git a/sci-libs/labbookdb/Manifest b/sci-libs/labbookdb/Manifest
index dedc4343b..d8aab8660 100644
--- a/sci-libs/labbookdb/Manifest
+++ b/sci-libs/labbookdb/Manifest
@@ -1 +1 @@
-DIST 0.0.2.tar.gz 39013 BLAKE2B 53f6aebdbfe1308fc774b17c70e02d5fbb245c1fb8d73dd6c5a11a15b2e0c9e6e0275a55b81acc4a20da2e963af163607ee2390d7a0c54d6da477c6b70b4ff2b SHA512 62797e11a70f2fd0a3fd8be18cd0d8a56ebca81b21edd047b393cd13b7b35d6459ea5ce125da012b0af3461ebf8d176fadbd6ebeb87a8c16dcacaa4cc765feeb
+DIST labbookdb-0.1.tar.gz 40352 BLAKE2B 3aba5dd99865ed1e2361542ec7a0cd6d693ec332461701119bc063bc664efde6ea56f665ecf8a8a00935ffc8bf6772c4bfe25d902d57e464b9df507bd9c3f711 SHA512 86b9ecf9cc5fe08c32c7dbeacab856f7ad689dd159c033f6136b3a71ed8f1e9a3abe9f3a86c9ed1fda9866f70ff86dbc36e23da4515a4cd0187978c24c0194ab
diff --git a/sci-libs/labbookdb/labbookdb-0.0.2.ebuild b/sci-libs/labbookdb/labbookdb-0.0.2.ebuild
deleted file mode 100644
index a2df37ad0..000000000
--- a/sci-libs/labbookdb/labbookdb-0.0.2.ebuild
+++ /dev/null
@@ -1,28 +0,0 @@
-# Copyright 1999-2018 Gentoo Authors
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=7
-
-PYTHON_COMPAT=( python{2_7,3_4,3_5,3_6} )
-
-inherit distutils-r1
-
-DESCRIPTION="Lab Book Database Framework"
-HOMEPAGE="https://github.com/TheChymera/LabbookDB"
-SRC_URI="https://github.com/TheChymera/LabbookDB/archive/${PV}.tar.gz"
-
-LICENSE="GPL-3"
-SLOT="0"
-IUSE=""
-KEYWORDS="~amd64 ~x86"
-
-DEPEND=""
-RDEPEND="
-	dev-python/argh[${PYTHON_USEDEP}]
-	dev-python/numpy[${PYTHON_USEDEP}]
-	dev-python/pandas[${PYTHON_USEDEP}]
-	dev-python/simplejson[${PYTHON_USEDEP}]
-	dev-python/sqlalchemy[${PYTHON_USEDEP}]
-	"
-
-S="${WORKDIR}/LabbookDB-${PV}"
diff --git a/sci-libs/labbookdb/labbookdb-0.1.ebuild b/sci-libs/labbookdb/labbookdb-0.1.ebuild
new file mode 100644
index 000000000..57c90a390
--- /dev/null
+++ b/sci-libs/labbookdb/labbookdb-0.1.ebuild
@@ -0,0 +1,28 @@
+# Copyright 1999-2023 Gentoo Authors
+# Distributed under the terms of the GNU General Public License v2
+
+EAPI=8
+
+PYTHON_COMPAT=( python3_{10..11} )
+
+inherit distutils-r1
+
+DESCRIPTION="Lab Book Database Framework"
+HOMEPAGE="https://github.com/TheChymera/LabbookDB"
+SRC_URI="https://github.com/TheChymera/LabbookDB/archive/${PV}.tar.gz -> ${P}.tar.gz"
+
+LICENSE="GPL-3"
+SLOT="0"
+IUSE=""
+KEYWORDS="~amd64 ~x86"
+
+DEPEND=""
+RDEPEND="
+	dev-python/argh[${PYTHON_USEDEP}]
+	dev-python/numpy[${PYTHON_USEDEP}]
+	dev-python/pandas[${PYTHON_USEDEP}]
+	dev-python/simplejson[${PYTHON_USEDEP}]
+	dev-python/sqlalchemy[${PYTHON_USEDEP}]
+	"
+
+S="${WORKDIR}/LabbookDB-${PV}"
diff --git a/sci-libs/labbookdb/labbookdb-9999.ebuild b/sci-libs/labbookdb/labbookdb-9999.ebuild
deleted file mode 100644
index 2755a0a4a..000000000
--- a/sci-libs/labbookdb/labbookdb-9999.ebuild
+++ /dev/null
@@ -1,27 +0,0 @@
-# Copyright 1999-2018 Gentoo Authors
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=7
-
-PYTHON_COMPAT=( python{2_7,3_4,3_5,3_6} )
-
-inherit distutils-r1 git-r3
-
-DESCRIPTION="Lab Book Database Framework"
-HOMEPAGE="https://github.com/TheChymera/LabbookDB"
-SRC_URI=""
-EGIT_REPO_URI="https://github.com/TheChymera/LabbookDB"
-
-LICENSE="GPL-3"
-SLOT="0"
-IUSE=""
-KEYWORDS="~amd64 ~x86"
-
-DEPEND=""
-RDEPEND="
-	dev-python/argh[${PYTHON_USEDEP}]
-	dev-python/numpy[${PYTHON_USEDEP}]
-	dev-python/pandas[${PYTHON_USEDEP}]
-	dev-python/simplejson[${PYTHON_USEDEP}]
-	dev-python/sqlalchemy[${PYTHON_USEDEP}]
-	"
diff --git a/sci-libs/labbookdb/metadata.xml b/sci-libs/labbookdb/metadata.xml
index 113831aa4..4dcb13a52 100644
--- a/sci-libs/labbookdb/metadata.xml
+++ b/sci-libs/labbookdb/metadata.xml
@@ -2,7 +2,7 @@
 <!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
 <pkgmetadata>
 	<maintainer type="person">
-		<email>horea.christ@gmail.com</email>
+		<email>gentoo@chymera.eu</email>
 		<name>Horea Christian</name>
 	</maintainer>
 	<longdescription lang="en">
diff --git a/sci-libs/lapack-reference/Manifest b/sci-libs/lapack-reference/Manifest
deleted file mode 100644
index b2a69b1f8..000000000
--- a/sci-libs/lapack-reference/Manifest
+++ /dev/null
@@ -1,2 +0,0 @@
-DIST lapack-3.7.0.tgz 7359812 BLAKE2B 20aa42e22d8c920d1360afe41ceec7b36f6cd5fbe43ca9d7848ef7cc45a64a0314cb1321941c1a7c03654f41e28ec805445882ded0ca0ea07674e70b66cba6b5 SHA512 e4f4c7d0ba8a096eeb813160c6dbcdd535647df6b2ad5beac9181908158956b31d1a9554ec9b9836fd44fe7404c1f377b297cbb20d744f20d70e357fd246c91b
-DIST lapack-3.8.0.tar.gz 7426094 BLAKE2B 27cd75eea498250382b2df6f5d7dc95fdee8d37b1a0faba5296ca0145ec40a1165a4ecc727aa1647086be6783b50cf475f79cea0f30f541da789051db99b2f37 SHA512 17786cb7306fccdc9b4a242de7f64fc261ebe6a10b6ec55f519deb4cb673cb137e8742aa5698fd2dc52f1cd56d3bd116af3f593a01dcf6770c4dcc86c50b2a7f
diff --git a/sci-libs/lapack-reference/files/3.3.1-blas-libs.patch b/sci-libs/lapack-reference/files/3.3.1-blas-libs.patch
deleted file mode 100644
index 95a640d86..000000000
--- a/sci-libs/lapack-reference/files/3.3.1-blas-libs.patch
+++ /dev/null
@@ -1,35 +0,0 @@
-Index: CMakeLists.txt
-===================================================================
---- CMakeLists.txt	(revision 975)
-+++ CMakeLists.txt	(working copy)
-@@ -68,24 +68,24 @@
- option(USE_OPTIMIZED_BLAS "Whether or not to use an optimized BLAS library instead of included netlib BLAS" OFF)
- 
- # Check the usage of the user provided BLAS libraries
--if(BLAS_LIBRAIRIES)
-+if(BLAS_LIBRARIES)
-   include(CheckFortranFunctionExists)
--  set(CMAKE_REQUIRED_LIBRARIES ${BLAS_LIBRAIRIES})
-+  set(CMAKE_REQUIRED_LIBRARIES ${BLAS_LIBRARIES})
-   CHECK_FORTRAN_FUNCTION_EXISTS("dgemm" BLAS_FOUND)
-   unset( CMAKE_REQUIRED_LIBRARIES )
-   if(BLAS_FOUND)
--    message(STATUS "--> BLAS supplied by user is WORKING, will use ${BLAS_LIBRAIRIES}.")
-+    message(STATUS "--> BLAS supplied by user is WORKING, will use ${BLAS_LIBRARIES}.")
-   else(BLAS_FOUND)
--    message(ERROR "--> BLAS supplied by user is not WORKING, CANNOT USE ${BLAS_LIBRAIRIES}.")
-+    message(ERROR "--> BLAS supplied by user is not WORKING, CANNOT USE ${BLAS_LIBRARIES}.")
-     message(ERROR "-->     Will use REFERENCE BLAS (by default)")
--    message(ERROR "-->     Or Correct your BLAS_LIBRAIRIES entry ")
-+    message(ERROR "-->     Or Correct your BLAS_LIBRARIES entry ")
-     message(ERROR "-->     Or Consider checking USE_OPTIMIZED_BLAS")
-   endif(BLAS_FOUND)
- 
- # User did not provide a BLAS Library but specified to search for one
- elseif( USE_OPTIMIZED_BLAS )
-   find_package( BLAS )
--endif (BLAS_LIBRAIRIES)
-+endif (BLAS_LIBRARIES)
- 
- # Neither user specified or optimized BLAS libraries can be used
- if(NOT BLAS_FOUND)
diff --git a/sci-libs/lapack-reference/files/3.3.1-xblas-libs.patch b/sci-libs/lapack-reference/files/3.3.1-xblas-libs.patch
deleted file mode 100644
index 382529e12..000000000
--- a/sci-libs/lapack-reference/files/3.3.1-xblas-libs.patch
+++ /dev/null
@@ -1,44 +0,0 @@
-Index: SRC/CMakeLists.txt
-===================================================================
---- SRC/CMakeLists.txt	(revision 975)
-+++ SRC/CMakeLists.txt	(working copy)
-@@ -373,7 +373,7 @@
-    zla_lin_berr.f zlarscl2.f zlascl2.f zla_wwaddw.f)
- 
- 
--if( USEXBLAS)
-+if( USE_XBLAS)
-   set(ALLXOBJ ${SXLASRC} ${DXLASRC} ${CXLASRC} ${ZXLASRC} ${ALLXAUX})
- endif()
- 
-@@ -392,5 +392,5 @@
-   set(ALLOBJ  ${ZLASRC} ${ALLAUX} ${DZLAUX} ${ZCLASRC})
- endif()
- add_library(lapack ${ALLOBJ} ${ALLXOBJ})
--target_link_libraries(lapack ${BLAS_LIBRARIES})
-+target_link_libraries(lapack ${BLAS_LIBRARIES} ${XBLAS_LIBRARY})
- lapack_install_library(lapack)
-Index: CMakeLists.txt
-===================================================================
---- CMakeLists.txt	(revision 975)
-+++ CMakeLists.txt	(working copy)
-@@ -67,6 +67,7 @@
- 
- option(USE_OPTIMIZED_BLAS "Whether or not to use an optimized BLAS library instead of included netlib BLAS" OFF)
- 
-+
- # Check the usage of the user provided BLAS libraries
- if(BLAS_LIBRAIRIES)
-   include(CheckFortranFunctionExists)
-@@ -103,6 +104,11 @@
-     "${CMAKE_SHARED_LINKER_FLAGS} ${BLAS_LINKER_FLAGS}" 
-     CACHE STRING "Linker flags for shared libs" FORCE)
- endif( NOT BLAS_FOUND )
-+
-+option(USE_XBLAS "Build extended precision (needs XBLAS)" OFF)
-+if (USE_XBLAS)
-+  find_library(XBLAS_LIBRARY NAMES xblas)
-+endif(USE_XBLAS)
-    
- add_subdirectory(SRC)
- if(BUILD_TESTING)
diff --git a/sci-libs/lapack-reference/files/lapack-3.4.1-cmake.patch b/sci-libs/lapack-reference/files/lapack-3.4.1-cmake.patch
deleted file mode 100644
index 78dece8ed..000000000
--- a/sci-libs/lapack-reference/files/lapack-3.4.1-cmake.patch
+++ /dev/null
@@ -1,208 +0,0 @@
-Index: CMakeLists.txt
-===================================================================
---- CMakeLists.txt	(revision 1294)
-+++ CMakeLists.txt	(working copy)
-@@ -94,10 +94,6 @@
- # Precision to build
- # By default all precisions are generated
- 
--option(BUILD_SINGLE "Build LAPACK Single Precision" ON)
--option(BUILD_DOUBLE "Build LAPACK Double Precision" ON)
--option(BUILD_COMPLEX "Build LAPACK Complex Precision" ON)
--option(BUILD_COMPLEX16 "Build LAPACK Double Complex Precision" ON)
- 
- # --------------------------------------------------
- # Subdirectories that need to be processed
-@@ -147,7 +143,49 @@
-   find_library(XBLAS_LIBRARY NAMES xblas)
- endif(USE_XBLAS)
-    
--add_subdirectory(SRC)
-+option(USE_OPTIMIZED_LAPACK "Whether or not to use an optimized LAPACK library instead of included netlib LAPACK" OFF)
-+
-+# Check the usage of the user provided LAPACK libraries
-+if(LAPACK_LIBRARIES)
-+  include(CheckFortranFunctionExists)
-+  set(CMAKE_REQUIRED_LIBRARIES ${LAPACK_LIBRARIES})
-+  CHECK_FORTRAN_FUNCTION_EXISTS("dpotrf" LAPACK_FOUND)
-+  unset( CMAKE_REQUIRED_LIBRARIES )
-+  if(LAPACK_FOUND)
-+    message(STATUS "--> LAPACK supplied by user is WORKING, will use ${LAPACK_LIBRARIES}.")
-+  else(LAPACK_FOUND)
-+    message(ERROR "--> LAPACK supplied by user is not WORKING, CANNOT USE $LAPACK_LIBRARIES}.")
-+    message(ERROR "-->     Will use REFERENCE LAPACK (by default)")
-+    message(ERROR "-->     Or Correct your LAPACK_LIBRARIES entry ")
-+    message(ERROR "-->     Or Consider checking USE_OPTIMIZED_LAPACK")
-+  endif(LAPACK_FOUND)
-+  
-+  # User did not provide a LAPACK Library but specified to search for one
-+elseif( USE_OPTIMIZED_LAPACK )
-+  find_package( LAPACK )
-+endif (LAPACK_LIBRARIES)
-+
-+# Neither user specified or optimized LAPACK libraries can be used
-+if(NOT LAPACK_FOUND)
-+  message(STATUS "Using supplied NETLIB LAPACK implementation")
-+  set( LAPACK_LIBRARIES lapack )
-+  option(BUILD_SINGLE "Build LAPACK Single Precision" ON)
-+  option(BUILD_DOUBLE "Build LAPACK Double Precision" ON)
-+  option(BUILD_COMPLEX "Build LAPACK Complex Precision" ON)
-+  option(BUILD_COMPLEX16 "Build LAPACK Double Complex Precision" ON)
-+  add_subdirectory(SRC)
-+else()
-+  set( CMAKE_EXE_LINKER_FLAGS 
-+    "${CMAKE_EXE_LINKER_FLAGS} ${LAPACK_LINKER_FLAGS}" 
-+    CACHE STRING "Linker flags for executables" FORCE)
-+  set( CMAKE_MODULE_LINKER_FLAGS 
-+    "${CMAKE_MODULE_LINKER_FLAGS} ${LAPACK_LINKER_FLAGS}" 
-+    CACHE STRING "Linker flags for modules" FORCE)
-+  set( CMAKE_SHARED_LINKER_FLAGS 
-+    "${CMAKE_SHARED_LINKER_FLAGS} ${LAPACK_LINKER_FLAGS}" 
-+    CACHE STRING "Linker flags for shared libs" FORCE)
-+endif( NOT LAPACK_FOUND )
-+
- if(BUILD_TESTING)
-   add_subdirectory(TESTING)
- endif(BUILD_TESTING)
-@@ -155,6 +193,10 @@
- # --------------------------------------------------
- # LAPACKE
- option(LAPACKE "Build LAPACKE" OFF)
-+if(LAPACKE)
-+  add_subdirectory(lapacke)
-+endif(LAPACKE)
-+
- # LAPACKE has also the interface to some routines from tmglib,
- # if LAPACKE_WITH_TMG is selected, we need to add those routines to LAPACKE
- option(LAPACKE_WITH_TMG "Build LAPACKE with tmglib routines" OFF)
-@@ -162,9 +204,6 @@
-   option(LAPACKE "Build LAPACKE" ON)
- endif(LAPACKE_WITH_TMG)
- 
--if(LAPACKE)
--  add_subdirectory(lapacke)
--endif(LAPACKE)
- 
- # --------------------------------------------------
- # CPACK Packaging 
-@@ -202,20 +241,24 @@
- OPTION(BUILD_STATIC_LIBS "Build static libraries" ON )
- #OPTION(BUILD_SHARED_LIBS "Build shared libraries" ON )
- 
--if( NOT BLAS_FOUND )
--  if(LAPACKE)
--     export(TARGETS blas lapack tmglib lapacke FILE lapack-targets.cmake)
--  else (LAPACKE)
--     export(TARGETS blas lapack tmglib FILE lapack-targets.cmake)
--  endif(LAPACKE)
--else( NOT BLAS_FOUND )
--  if(LAPACKE)
--     export(TARGETS lapack tmglib lapacke FILE lapack-targets.cmake)
--  else (LAPACKE)
--     export(TARGETS lapack tmglib FILE lapack-targets.cmake)
--  endif(LAPACKE)
--endif( NOT BLAS_FOUND )
-+if(NOT BLAS_FOUND)
-+  set(ALL_TARGETS ${ALL_TARGETS} blas)
-+endif(NOT BLAS_FOUND)
- 
-+if(NOT LAPACK_FOUND)
-+  set(ALL_TARGETS ${ALL_TARGETS} lapack)
-+endif(NOT LAPACK_FOUND)
-+
-+if(BUILD_TESTING OR LAPACKE_WITH_TMG)
-+  set(ALL_TARGETS ${ALL_TARGETS} tmglib)
-+endif(BUILD_TESTING OR LAPACKE_WITH_TMG)
-+
-+if(LAPACKE)
-+  set(ALL_TARGETS ${ALL_TARGETS} lapacke)
-+endif(LAPACKE)
-+
-+export(TARGETS ${ALL_TARGETS} FILE lapack-targets.cmake)
-+
- configure_file(${LAPACK_SOURCE_DIR}/CMAKE/lapack-config-version.cmake.in
-   ${LAPACK_BINARY_DIR}/lapack-config-version.cmake @ONLY)
- configure_file(${LAPACK_SOURCE_DIR}/CMAKE/lapack-config-build.cmake.in
-Index: lapacke/example/CMakeLists.txt
-===================================================================
---- lapacke/example/CMakeLists.txt	(revision 1294)
-+++ lapacke/example/CMakeLists.txt	(working copy)
-@@ -1,8 +1,8 @@
- add_executable(xexample_DGESV_rowmajor example_DGESV_rowmajor.c)
- add_executable(xexample_ZGESV_rowmajor example_ZGESV_rowmajor.c)
- 
--target_link_libraries(xexample_DGESV_rowmajor lapacke lapack ${BLAS_LIBRARIES})
--target_link_libraries(xexample_ZGESV_rowmajor lapacke lapack ${BLAS_LIBRARIES})
-+target_link_libraries(xexample_DGESV_rowmajor lapacke ${LAPACK_LIBRARIES} ${BLAS_LIBRARIES})
-+target_link_libraries(xexample_ZGESV_rowmajor lapacke ${LAPACK_LIBRARIES} ${BLAS_LIBRARIES})
- 
- add_test(example_DGESV_rowmajor ${CMAKE_RUNTIME_OUTPUT_DIRECTORY}/xexample_DGESV_rowmajor)
- add_test(example_ZGESV_rowmajor ${CMAKE_RUNTIME_OUTPUT_DIRECTORY}/xexample_ZGESV_rowmajor)
-Index: lapacke/CMakeLists.txt
-===================================================================
---- lapacke/CMakeLists.txt	(revision 1294)
-+++ lapacke/CMakeLists.txt	(working copy)
-@@ -45,14 +45,14 @@
- 
- if (USE_XBLAS)
-    add_library(lapacke ${SRC_OBJ} ${SRCX_OBJ} ${UTILS_OBJ})
--   target_link_libraries(lapacke lapack ${BLAS_LIBRARIES}  ${XBLAS_LIBRARY})
-+   target_link_libraries(lapacke ${LAPACK_LIBRARIES} ${BLAS_LIBRARIES} ${XBLAS_LIBRARY})
- else (USE_XBLAS)
-   if (LAPACKE_WITH_TMG)
-    add_library(lapacke ${SRC_OBJ} ${MATGEN_OBJ} ${UTILS_OBJ})
--   target_link_libraries(lapacke tmglib lapack ${BLAS_LIBRARIES} )
-+   target_link_libraries(lapacke tmglib ${LAPACK_LIBRARIES} ${BLAS_LIBRARIES})
-   else (LAPACKE_WITH_TMG)
-    add_library(lapacke ${SRC_OBJ} ${UTILS_OBJ})
--   target_link_libraries(lapacke lapack ${BLAS_LIBRARIES} )
-+   target_link_libraries(lapacke ${LAPACK_LIBRARIES} ${BLAS_LIBRARIES})
-   endif(LAPACKE_WITH_TMG)
- endif(USE_XBLAS)
- 
-Index: TESTING/LIN/CMakeLists.txt
-===================================================================
---- TESTING/LIN/CMakeLists.txt	(revision 1294)
-+++ TESTING/LIN/CMakeLists.txt	(working copy)
-@@ -193,7 +193,7 @@
- 
- macro(add_lin_executable name )
-   add_executable(${name} ${ARGN})
--  target_link_libraries(${name} tmglib lapack)
-+  target_link_libraries(${name} tmglib ${LAPACK_LIBRARIES})
- endmacro(add_lin_executable)
- 
- IF(BUILD_SINGLE)
-Index: TESTING/EIG/CMakeLists.txt
-===================================================================
---- TESTING/EIG/CMakeLists.txt	(revision 1294)
-+++ TESTING/EIG/CMakeLists.txt	(working copy)
-@@ -119,7 +119,7 @@
- 
- macro(add_eig_executable name )
-   add_executable(${name} ${ARGN})
--  target_link_libraries(${name} tmglib lapack )
-+  target_link_libraries(${name} tmglib ${LAPACK_LIBRARIES})
- endmacro(add_eig_executable)
- 
- if (BUILD_SINGLE)
-Index: TESTING/MATGEN/CMakeLists.txt
-===================================================================
---- TESTING/MATGEN/CMakeLists.txt	(revision 1294)
-+++ TESTING/MATGEN/CMakeLists.txt	(working copy)
-@@ -64,12 +64,12 @@
-   set(ALLOBJ ${ALLOBJ} ${ZMATGEN} ${DZATGEN})
- endif()
- 
--list(REMOVE_DUPLICATES ALLOBJ)
--
- if (NOT ALLOBJ)
- set(ALLOBJ ${SMATGEN} ${CMATGEN} ${SCATGEN} ${DMATGEN} ${ZMATGEN}
-   ${DZATGEN})
-+else()
-+  list(REMOVE_DUPLICATES ALLOBJ)
- endif()
- add_library(tmglib ${ALLOBJ} )
--target_link_libraries(tmglib lapack)
-+target_link_libraries(tmglib ${LAPACK_LIBRARIES})
- lapack_install_library(tmglib)
diff --git a/sci-libs/lapack-reference/files/lapack-3.6.1-fix-build-system.patch b/sci-libs/lapack-reference/files/lapack-3.6.1-fix-build-system.patch
deleted file mode 100644
index b16cb3e19..000000000
--- a/sci-libs/lapack-reference/files/lapack-3.6.1-fix-build-system.patch
+++ /dev/null
@@ -1,88 +0,0 @@
---- lapack-3.6.1/BLAS/blas.pc.in
-+++ lapack-3.6.1/BLAS/blas.pc.in
-@@ -1,5 +1,7 @@
- prefix=@CMAKE_INSTALL_PREFIX@
-+exec_prefix=${prefix}
- libdir=@CMAKE_INSTALL_PREFIX@/@CMAKE_INSTALL_LIBDIR@
-+includedir=${prefix}/include
- 
- Name: blas
- Description: Basic Linear Algebra Subprograms F77 reference implementations
---- lapack-3.6.1/BLAS/CMakeLists.txt
-+++ lapack-3.6.1/BLAS/CMakeLists.txt
-@@ -2,7 +2,7 @@
- if(BUILD_TESTING)
- add_subdirectory(TESTING)
- endif(BUILD_TESTING)
--configure_file(${CMAKE_CURRENT_SOURCE_DIR}/blas.pc.in ${CMAKE_CURRENT_BINARY_DIR}/blas.pc)
-+configure_file(${CMAKE_CURRENT_SOURCE_DIR}/blas.pc.in ${CMAKE_CURRENT_BINARY_DIR}/blas.pc @ONLY)
- install(FILES
-   ${CMAKE_CURRENT_BINARY_DIR}/blas.pc
-   DESTINATION ${PKG_CONFIG_DIR}
---- lapack-3.6.1/CBLAS/cblas.pc.in
-+++ lapack-3.6.1/CBLAS/cblas.pc.in
-@@ -1,5 +1,7 @@
--prefix=@prefix@
--libdir=@libdir@
-+prefix=@CMAKE_INSTALL_PREFIX@
-+exec_prefix=${prefix}
-+libdir=${exec_prefix}/@CMAKE_INSTALL_LIBDIR@
-+includedir=${prefix}/include
- 
- Name: lapacke
- Description: C Standard Interface to BLAS Linear Algebra PACKage
---- lapack-3.6.1/CBLAS/CMakeLists.txt
-+++ lapack-3.6.1/CBLAS/CMakeLists.txt
-@@ -71,7 +71,7 @@
-   ${LAPACK_BINARY_DIR}/cblas-config.cmake @ONLY)
- 
- 
--configure_file(${CMAKE_CURRENT_SOURCE_DIR}/cblas.pc.in ${CMAKE_CURRENT_BINARY_DIR}/cblas.pc)
-+configure_file(${CMAKE_CURRENT_SOURCE_DIR}/cblas.pc.in ${CMAKE_CURRENT_BINARY_DIR}/cblas.pc @ONLY)
-   install(FILES
-   ${CMAKE_CURRENT_BINARY_DIR}/cblas.pc
-   DESTINATION ${PKG_CONFIG_DIR}
---- lapack-3.6.1/CMakeLists.txt
-+++ lapack-3.6.1/CMakeLists.txt
-@@ -333,7 +333,7 @@
-   ${LAPACK_BINARY_DIR}/lapack-config.cmake @ONLY)
- 
- 
--configure_file(${CMAKE_CURRENT_SOURCE_DIR}/lapack.pc.in ${CMAKE_CURRENT_BINARY_DIR}/lapack.pc)
-+configure_file(${CMAKE_CURRENT_SOURCE_DIR}/lapack.pc.in ${CMAKE_CURRENT_BINARY_DIR}/lapack.pc @ONLY)
-   install(FILES
-   ${CMAKE_CURRENT_BINARY_DIR}/lapack.pc
-   DESTINATION ${PKG_CONFIG_DIR}
---- lapack-3.6.1/LAPACKE/CMakeLists.txt
-+++ lapack-3.6.1/LAPACKE/CMakeLists.txt
-@@ -65,7 +65,7 @@
- endif(BUILD_TESTING)
- 
- 
--configure_file(${CMAKE_CURRENT_SOURCE_DIR}/lapacke.pc.in ${CMAKE_CURRENT_BINARY_DIR}/lapacke.pc)
-+configure_file(${CMAKE_CURRENT_SOURCE_DIR}/lapacke.pc.in ${CMAKE_CURRENT_BINARY_DIR}/lapacke.pc @ONLY)
-  install(FILES
-   ${CMAKE_CURRENT_BINARY_DIR}/lapacke.pc
-   DESTINATION ${PKG_CONFIG_DIR}
---- lapack-3.6.1/LAPACKE/lapacke.pc.in
-+++ lapack-3.6.1/LAPACKE/lapacke.pc.in
-@@ -1,5 +1,7 @@
--prefix=@prefix@
--libdir=@libdir@
-+prefix=@CMAKE_INSTALL_PREFIX@
-+exec_prefix=${prefix}
-+libdir=${exec_prefix}/@CMAKE_INSTALL_LIBDIR@
-+includedir=${prefix}/include
- 
- Name: lapacke
- Description: C Standard Interface to LAPACK Linear Algebra PACKage
---- lapack-3.6.1/lapack.pc.in
-+++ lapack-3.6.1/lapack.pc.in
-@@ -1,5 +1,7 @@
- prefix=@CMAKE_INSTALL_PREFIX@
-+exec_prefix=${prefix}
- libdir=@CMAKE_INSTALL_PREFIX@/@CMAKE_INSTALL_LIBDIR@
-+includedir=${prefix}/include
- 
- Name: lapack
- Description: FORTRAN reference implementation of LAPACK Linear Algebra PACKage
diff --git a/sci-libs/lapack-reference/files/lapack-fix-build-system.patch b/sci-libs/lapack-reference/files/lapack-fix-build-system.patch
deleted file mode 100644
index 8661709d3..000000000
--- a/sci-libs/lapack-reference/files/lapack-fix-build-system.patch
+++ /dev/null
@@ -1,92 +0,0 @@
---- lapack-3.6.0/BLAS/blas.pc.in
-+++ lapack-3.6.0/BLAS/blas.pc.in
-@@ -1,5 +1,7 @@
--prefix=@prefix@
--libdir=@libdir@
-+prefix=@CMAKE_INSTALL_PREFIX@
-+exec_prefix=${prefix}
-+libdir=${exec_prefix}/@CMAKE_INSTALL_LIBDIR@
-+includedir=${prefix}/include
- 
- Name: blas
- Description: Basic Linear Algebra Subprograms F77 reference implementations
---- lapack-3.6.0/BLAS/CMakeLists.txt
-+++ lapack-3.6.0/BLAS/CMakeLists.txt
-@@ -2,7 +2,7 @@
- if(BUILD_TESTING)
- add_subdirectory(TESTING)
- endif(BUILD_TESTING)
--configure_file(${CMAKE_CURRENT_SOURCE_DIR}/blas.pc.in ${CMAKE_CURRENT_BINARY_DIR}/blas.pc)
-+configure_file(${CMAKE_CURRENT_SOURCE_DIR}/blas.pc.in ${CMAKE_CURRENT_BINARY_DIR}/blas.pc @ONLY)
- install(FILES
-   ${CMAKE_CURRENT_BINARY_DIR}/blas.pc
-   DESTINATION ${PKG_CONFIG_DIR}
---- lapack-3.6.0/CBLAS/cblas.pc.in
-+++ lapack-3.6.0/CBLAS/cblas.pc.in
-@@ -1,5 +1,7 @@
--prefix=@prefix@
--libdir=@libdir@
-+prefix=@CMAKE_INSTALL_PREFIX@
-+exec_prefix=${prefix}
-+libdir=${exec_prefix}/@CMAKE_INSTALL_LIBDIR@
-+includedir=${prefix}/include
- 
- Name: lapacke
- Description: C Standard Interface to BLAS Linear Algebra PACKage
---- lapack-3.6.0/CBLAS/CMakeLists.txt
-+++ lapack-3.6.0/CBLAS/CMakeLists.txt
-@@ -71,7 +71,7 @@
-   ${LAPACK_BINARY_DIR}/cblas-config.cmake @ONLY)
- 
- 
--configure_file(${CMAKE_CURRENT_SOURCE_DIR}/cblas.pc.in ${CMAKE_CURRENT_BINARY_DIR}/cblas.pc)
-+configure_file(${CMAKE_CURRENT_SOURCE_DIR}/cblas.pc.in ${CMAKE_CURRENT_BINARY_DIR}/cblas.pc @ONLY)
-   install(FILES
-   ${CMAKE_CURRENT_BINARY_DIR}/cblas.pc
-   DESTINATION ${PKG_CONFIG_DIR}
---- lapack-3.6.0/CMakeLists.txt
-+++ lapack-3.6.0/CMakeLists.txt
-@@ -333,7 +333,7 @@
-   ${LAPACK_BINARY_DIR}/lapack-config.cmake @ONLY)
- 
- 
--configure_file(${CMAKE_CURRENT_SOURCE_DIR}/lapack.pc.in ${CMAKE_CURRENT_BINARY_DIR}/lapack.pc)
-+configure_file(${CMAKE_CURRENT_SOURCE_DIR}/lapack.pc.in ${CMAKE_CURRENT_BINARY_DIR}/lapack.pc @ONLY)
-   install(FILES
-   ${CMAKE_CURRENT_BINARY_DIR}/lapack.pc
-   DESTINATION ${PKG_CONFIG_DIR}
---- lapack-3.6.0/LAPACKE/CMakeLists.txt
-+++ lapack-3.6.0/LAPACKE/CMakeLists.txt
-@@ -65,7 +65,7 @@
- endif(BUILD_TESTING)
- 
- 
--configure_file(${CMAKE_CURRENT_SOURCE_DIR}/lapacke.pc.in ${CMAKE_CURRENT_BINARY_DIR}/lapacke.pc)
-+configure_file(${CMAKE_CURRENT_SOURCE_DIR}/lapacke.pc.in ${CMAKE_CURRENT_BINARY_DIR}/lapacke.pc @ONLY)
-  install(FILES
-   ${CMAKE_CURRENT_BINARY_DIR}/lapacke.pc
-   DESTINATION ${PKG_CONFIG_DIR}
---- lapack-3.6.0/LAPACKE/lapacke.pc.in
-+++ lapack-3.6.0/LAPACKE/lapacke.pc.in
-@@ -1,5 +1,7 @@
--prefix=@prefix@
--libdir=@libdir@
-+prefix=@CMAKE_INSTALL_PREFIX@
-+exec_prefix=${prefix}
-+libdir=${exec_prefix}/@CMAKE_INSTALL_LIBDIR@
-+includedir=${prefix}/include
- 
- Name: lapacke
- Description: C Standard Interface to LAPACK Linear Algebra PACKage
---- lapack-3.6.0/lapack.pc.in
-+++ lapack-3.6.0/lapack.pc.in
-@@ -1,5 +1,7 @@
--prefix=@prefix@
--libdir=@libdir@
-+prefix=@CMAKE_INSTALL_PREFIX@
-+exec_prefix=${prefix}
-+libdir=${exec_prefix}/@CMAKE_INSTALL_LIBDIR@
-+includedir=${prefix}/include
- 
- Name: lapack
- Description: FORTRAN reference implementation of LAPACK Linear Algebra PACKage
diff --git a/sci-libs/lapack-reference/files/lapack-reference-3.7.0-fix-build-system.patch b/sci-libs/lapack-reference/files/lapack-reference-3.7.0-fix-build-system.patch
deleted file mode 100644
index 70f7cb0ee..000000000
--- a/sci-libs/lapack-reference/files/lapack-reference-3.7.0-fix-build-system.patch
+++ /dev/null
@@ -1,56 +0,0 @@
-diff --git a/BLAS/blas.pc.in b/BLAS/blas.pc.in
-index 7fd6f1e..e52f3ad 100644
---- a/BLAS/blas.pc.in
-+++ b/BLAS/blas.pc.in
-@@ -1,5 +1,7 @@
--prefix=@prefix@
--libdir=@libdir@
-+prefix=@CMAKE_INSTALL_PREFIX@
-+exec_prefix=${prefix}
-+libdir=${exec_prefix}/@CMAKE_INSTALL_LIBDIR@
-+includedir=${prefix}/include
- 
- Name: BLAS
- Description: FORTRAN reference implementation of BLAS Basic Linear Algebra Subprograms
-diff --git a/CBLAS/cblas.pc.in b/CBLAS/cblas.pc.in
-index 4a938fe..311aed9 100644
---- a/CBLAS/cblas.pc.in
-+++ b/CBLAS/cblas.pc.in
-@@ -1,5 +1,7 @@
--prefix=@prefix@
--libdir=@libdir@
-+prefix=@CMAKE_INSTALL_PREFIX@
-+exec_prefix=${prefix}
-+libdir=${exec_prefix}/@CMAKE_INSTALL_LIBDIR@
-+includedir=${prefix}/include
- 
- Name: CBLAS
- Description: C Standard Interface to BLAS Basic Linear Algebra Subprograms
-diff --git a/LAPACKE/lapacke.pc.in b/LAPACKE/lapacke.pc.in
-index 028f8da..dc092b1 100644
---- a/LAPACKE/lapacke.pc.in
-+++ b/LAPACKE/lapacke.pc.in
-@@ -1,5 +1,7 @@
--prefix=@prefix@
--libdir=@libdir@
-+prefix=@CMAKE_INSTALL_PREFIX@
-+exec_prefix=${prefix}
-+libdir=${exec_prefix}/@CMAKE_INSTALL_LIBDIR@
-+includedir=${prefix}/include
- 
- Name: LAPACKE
- Description: C Standard Interface to LAPACK Linear Algebra PACKage
-diff --git a/lapack.pc.in b/lapack.pc.in
-index 878efc2..2cca4c2 100644
---- a/lapack.pc.in
-+++ b/lapack.pc.in
-@@ -1,5 +1,7 @@
--prefix=@prefix@
--libdir=@libdir@
-+prefix=@CMAKE_INSTALL_PREFIX@
-+exec_prefix=${prefix}
-+libdir=${exec_prefix}/@CMAKE_INSTALL_LIBDIR@
-+includedir=${prefix}/include
- 
- Name: LAPACK
- Description: FORTRAN reference implementation of LAPACK Linear Algebra PACKage
diff --git a/sci-libs/lapack-reference/lapack-reference-3.7.0-r100.ebuild b/sci-libs/lapack-reference/lapack-reference-3.7.0-r100.ebuild
deleted file mode 100644
index d9378271a..000000000
--- a/sci-libs/lapack-reference/lapack-reference-3.7.0-r100.ebuild
+++ /dev/null
@@ -1,121 +0,0 @@
-# Copyright 1999-2017 Gentoo Foundation
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=6
-
-PYTHON_COMPAT=( python2_7 )
-
-NUMERIC_MODULE_NAME="reflapack"
-
-inherit alternatives-2 cmake-utils eutils fortran-2 numeric-int64-multibuild python-any-r1
-
-MY_PN=lapack
-MYP=${MY_PN}-${PV}
-
-DESCRIPTION="Reference implementation of LAPACK"
-HOMEPAGE="http://www.netlib.org/lapack/"
-SRC_URI="http://www.netlib.org/lapack/${MYP}.tgz"
-
-LICENSE="BSD"
-SLOT="0/${PV}"
-KEYWORDS="~amd64 ~x86 ~amd64-linux ~x86-linux"
-IUSE="+deprecated static-libs test xblas"
-
-REQUIRED_USE="test? ( ${PYTHON_REQUIRED_USE} )"
-
-RDEPEND="
-	>=virtual/blas-2.1-r3[int64?,${MULTILIB_USEDEP}]
-	xblas? ( sci-libs/xblas[fortran,int64?] )"
-DEPEND="${RDEPEND}
-	virtual/pkgconfig
-	test? ( ${PYTHON_DEPS} )"
-
-S="${WORKDIR}/${MYP}"
-PATCHES=( "${FILESDIR}/lapack-reference-${PV}-fix-build-system.patch" )
-
-src_prepare() {
-	numeric-int64_ensure_blas_int_support
-
-	default
-
-	# rename library to avoid collision with other lapack implementations
-	# ${PROFNAME}, ${LIBNAME} and ${BLAS_REQUIRES} are not defined here, they
-	# are in single quotes in the following seds.  They are set later by
-	# defining a cmake variables with -DPROFNAME etc in src_configure.
-	sed \
-		-e 's:BINARY_DIR}/lapack.pc:BINARY_DIR}/${PROFNAME}.pc:' \
-		-e '/ALL_TARGETS/s:lapack):${LIBNAME}):' \
-		-e '/LAPACK_LIBRARIES/s:lapack:${LIBNAME}:g' \
-		-i CMakeLists.txt || die
-	sed -i \
-		-e 's:(lapack:(${LIBNAME}:g' \
-		-e '/PROPERTIES/s:lapack:${LIBNAME}:g' \
-		SRC/CMakeLists.txt || die
-	sed -i \
-		-e '/Name: /s:lapack:@PROFNAME@:' \
-		-e 's:-llapack:-l@LIBNAME@:g' \
-		-e '/Requires: /s:blas:@BLAS_REQUIRES@\nFflags\: ${LAPACK_PKGCONFIG_FFLAGS}:' \
-		lapack.pc.in || die
-	# some string does not get passed properly
-	sed -i \
-		-e '/lapack_testing.py/d' \
-		CTestCustom.cmake.in || die
-	# separate ebuild to tmglib
-	sed -i \
-		-e '/lapack_install_library(tmglib)/d' \
-		TESTING/MATGEN/CMakeLists.txt || die
-}
-
-src_configure() {
-	lapack_configure() {
-		local profname=$(numeric-int64_get_module_name)
-		local libname="${profname//-/_}"
-		local blas_profname=$(numeric-int64_get_blas_alternative)
-		local xblas_profname=$(numeric-int64_get_xblas_alternative)
-		local xblas_libname="${xblas_profname//-/_}"
-		local blas_requires="${blas_profname}"
-		use xblas && \
-			blas_requires+=" ${xblas_profname}"
-		local mycmakeargs=(
-			-DPROFNAME="${profname}"
-			-DBLAS_REQUIRES="${blas_requires}"
-			-DLIBNAME="${libname}"
-			-DUSE_OPTIMIZED_BLAS=ON
-			-DBUILD_TESTING="$(usex test)"
-			-DUSE_XBLAS="$(usex xblas)"
-			-DBUILD_DEPRECATED="$(usex deprecated)"
-			-DCMAKE_C_FLAGS="$($(tc-getPKG_CONFIG) --cflags ${blas_profname}) ${CFLAGS}"
-			-DCMAKE_CXX_FLAGS="$($(tc-getPKG_CONFIG) --cflags ${blas_profname}) ${CXXFLAGS}"
-			-DCMAKE_Fortran_FLAGS="$($(tc-getPKG_CONFIG) --cflags ${blas_profname}) $(get_abi_CFLAGS) $(numeric-int64_get_fortran_int64_abi_fflags) ${FCFLAGS}"
-			-DLAPACK_PKGCONFIG_FFLAGS="$(numeric-int64_get_fortran_int64_abi_fflags)"
-		)
-		use xblas && \
-			mycmakeargs+=( -DXBLAS_LIBRARY:FILEPATH="${EROOT}usr/$(get_libdir)/lib${xblas_libname}.so" )
-		if $(numeric-int64_is_static_build); then
-			mycmakeargs+=(
-				-DBUILD_SHARED_LIBS=OFF
-				-DBUILD_STATIC_LIBS=ON
-			)
-		else
-			mycmakeargs+=(
-				-DBUILD_SHARED_LIBS=ON
-				-DBUILD_STATIC_LIBS=OFF
-			)
-		fi
-		cmake-utils_src_configure
-	}
-	numeric-int64-multibuild_foreach_all_abi_variants lapack_configure
-}
-
-src_compile() {
-	numeric-int64-multibuild_foreach_all_abi_variants cmake-utils_src_compile
-}
-
-src_test() {
-	numeric-int64-multibuild_foreach_all_abi_variants cmake-utils_src_test
-}
-
-src_install() {
-	numeric-int64-multibuild_foreach_all_abi_variants cmake-utils_src_install
-	numeric-int64-multibuild_install_alternative lapack reference
-}
diff --git a/sci-libs/lapack-reference/lapack-reference-3.8.0-r100.ebuild b/sci-libs/lapack-reference/lapack-reference-3.8.0-r100.ebuild
deleted file mode 100644
index 32b0cd5db..000000000
--- a/sci-libs/lapack-reference/lapack-reference-3.8.0-r100.ebuild
+++ /dev/null
@@ -1,120 +0,0 @@
-# Copyright 1999-2018 Gentoo Foundation
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=6
-
-PYTHON_COMPAT=( python2_7 )
-
-NUMERIC_MODULE_NAME="reflapack"
-
-inherit alternatives-2 cmake-utils eutils fortran-2 numeric-int64-multibuild python-any-r1
-
-MY_PN=lapack
-MYP=${MY_PN}-${PV}
-
-DESCRIPTION="Reference implementation of LAPACK"
-HOMEPAGE="http://www.netlib.org/lapack/"
-SRC_URI="http://www.netlib.org/lapack/${MYP}.tar.gz"
-
-LICENSE="BSD"
-SLOT="0/${PV}"
-KEYWORDS="~amd64 ~x86 ~amd64-linux ~x86-linux"
-IUSE="+deprecated static-libs test xblas"
-
-REQUIRED_USE="test? ( ${PYTHON_REQUIRED_USE} )"
-
-RDEPEND="
-	>=virtual/blas-2.1-r3[int64?,${MULTILIB_USEDEP}]
-	xblas? ( sci-libs/xblas[fortran,int64?] )"
-DEPEND="${RDEPEND}
-	virtual/pkgconfig
-	test? ( ${PYTHON_DEPS} )"
-
-S="${WORKDIR}/${MYP}"
-
-src_prepare() {
-	numeric-int64_ensure_blas_int_support
-
-	cmake-utils_src_prepare
-
-	# rename library to avoid collision with other lapack implementations
-	# ${PROFNAME}, ${LIBNAME} and ${BLAS_REQUIRES} are not defined here, they
-	# are in single quotes in the following seds.  They are set later by
-	# defining a cmake variables with -DPROFNAME etc in src_configure.
-	sed \
-		-e 's:BINARY_DIR}/lapack.pc:BINARY_DIR}/${PROFNAME}.pc:' \
-		-e '/ALL_TARGETS/s:lapack):${LIBNAME}):' \
-		-e '/LAPACK_LIBRARIES/s:lapack:${LIBNAME}:g' \
-		-i CMakeLists.txt || die
-	sed -i \
-		-e 's:(lapack:(${LIBNAME}:g' \
-		-e '/PROPERTIES/s:lapack:${LIBNAME}:g' \
-		SRC/CMakeLists.txt || die
-	sed -i \
-		-e '/Name: /s:lapack:@PROFNAME@:' \
-		-e 's:-llapack:-l@LIBNAME@:g' \
-		-e '/Requires: /s:blas:@BLAS_REQUIRES@\nFflags\: ${LAPACK_PKGCONFIG_FFLAGS}:' \
-		lapack.pc.in || die
-	# some string does not get passed properly
-	sed -i \
-		-e '/lapack_testing.py/d' \
-		CTestCustom.cmake.in || die
-	# separate ebuild to tmglib
-	sed -i \
-		-e '/lapack_install_library(tmglib)/d' \
-		TESTING/MATGEN/CMakeLists.txt || die
-}
-
-src_configure() {
-	lapack_configure() {
-		local profname=$(numeric-int64_get_module_name)
-		local libname="${profname//-/_}"
-		local blas_profname=$(numeric-int64_get_blas_alternative)
-		local xblas_profname=$(numeric-int64_get_xblas_alternative)
-		local xblas_libname="${xblas_profname//-/_}"
-		local blas_requires="${blas_profname}"
-		use xblas && \
-			blas_requires+=" ${xblas_profname}"
-		local mycmakeargs=(
-			-DPROFNAME="${profname}"
-			-DBLAS_REQUIRES="${blas_requires}"
-			-DLIBNAME="${libname}"
-			-DUSE_OPTIMIZED_BLAS=ON
-			-DBUILD_TESTING="$(usex test)"
-			-DUSE_XBLAS="$(usex xblas)"
-			-DBUILD_DEPRECATED="$(usex deprecated)"
-			-DCMAKE_C_FLAGS="$($(tc-getPKG_CONFIG) --cflags ${blas_profname}) ${CFLAGS}"
-			-DCMAKE_CXX_FLAGS="$($(tc-getPKG_CONFIG) --cflags ${blas_profname}) ${CXXFLAGS}"
-			-DCMAKE_Fortran_FLAGS="$($(tc-getPKG_CONFIG) --cflags ${blas_profname}) $(get_abi_CFLAGS) $(numeric-int64_get_fortran_int64_abi_fflags) ${FCFLAGS}"
-			-DLAPACK_PKGCONFIG_FFLAGS="$(numeric-int64_get_fortran_int64_abi_fflags)"
-		)
-		use xblas && \
-			mycmakeargs+=( -DXBLAS_LIBRARY:FILEPATH="${EROOT}usr/$(get_libdir)/lib${xblas_libname}.so" )
-		if $(numeric-int64_is_static_build); then
-			mycmakeargs+=(
-				-DBUILD_SHARED_LIBS=OFF
-				-DBUILD_STATIC_LIBS=ON
-			)
-		else
-			mycmakeargs+=(
-				-DBUILD_SHARED_LIBS=ON
-				-DBUILD_STATIC_LIBS=OFF
-			)
-		fi
-		cmake-utils_src_configure
-	}
-	numeric-int64-multibuild_foreach_all_abi_variants lapack_configure
-}
-
-src_compile() {
-	numeric-int64-multibuild_foreach_all_abi_variants cmake-utils_src_compile
-}
-
-src_test() {
-	numeric-int64-multibuild_foreach_all_abi_variants cmake-utils_src_test
-}
-
-src_install() {
-	numeric-int64-multibuild_foreach_all_abi_variants cmake-utils_src_install
-	numeric-int64-multibuild_install_alternative lapack reference
-}
diff --git a/sci-libs/lapack-reference/lapack-reference-9999.ebuild b/sci-libs/lapack-reference/lapack-reference-9999.ebuild
deleted file mode 100644
index a22d2d722..000000000
--- a/sci-libs/lapack-reference/lapack-reference-9999.ebuild
+++ /dev/null
@@ -1,124 +0,0 @@
-# Copyright 1999-2018 Gentoo Foundation
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=6
-
-PYTHON_COMPAT=( python2_7 )
-
-NUMERIC_MODULE_NAME="reflapack"
-
-inherit alternatives-2 cmake-utils fortran-2 git-r3 numeric-int64-multibuild python-any-r1
-
-# The master ESVN_REPO_URI is difficult to access, the git mirror is easier
-# ESVN_REPO_URI="https://icl.cs.utk.edu/svn/lapack-dev/lapack/trunk"
-# MY_PN=lapack
-# inherit subversion
-
-MY_PN=lapack-reference
-MYP=${MY_PN}-${PV}
-
-DESCRIPTION="Reference implementation of LAPACK"
-HOMEPAGE="http://www.netlib.org/lapack/"
-EGIT_REPO_URI="https://github.com/nschloe/lapack.git"
-
-LICENSE="BSD"
-SLOT="0/${PV}"
-KEYWORDS=""
-IUSE="static-libs test xblas"
-
-REQUIRED_USE="test? ( ${PYTHON_REQUIRED_USE} )"
-
-RDEPEND="
-	>=virtual/blas-2.1-r3[int64?,${MULTILIB_USEDEP}]
-	xblas? ( sci-libs/xblas[fortran,int64?] )"
-DEPEND="${RDEPEND}
-	virtual/pkgconfig
-	test? ( ${PYTHON_DEPS} )"
-
-S="${WORKDIR}/${MYP}"
-
-src_prepare() {
-	numeric-int64_ensure_blas_int_support
-
-	cmake-utils_src_prepare
-
-	# rename library to avoid collision with other lapack implementations
-	# ${PROFNAME}, ${LIBNAME} and ${BLAS_REQUIRES} are not defined here, they
-	# are in single quotes in the following seds.  They are set later by
-	# defining a cmake variables with -DPROFNAME etc in src_configure.
-	sed -i \
-		-e 's:BINARY_DIR}/lapack.pc:BINARY_DIR}/${PROFNAME}.pc:' \
-		-e '/ALL_TARGETS/s:lapack):${LIBNAME}):' \
-		-e '/LAPACK_LIBRARIES/s:lapack:${LIBNAME}:g' \
-		CMakeLists.txt || die
-	sed -i \
-		-e 's:(lapack:(${LIBNAME}:g' \
-		SRC/CMakeLists.txt || die
-	sed -i \
-		-e '/Name: /s:lapack:${PROFNAME}:' \
-		-e 's:-llapack:-l${LIBNAME}:g' \
-		-e '/Requires: /s:blas:${BLAS_REQUIRES}\nFflags=${LAPACK_PKGCONFIG_FFLAGS}:' \
-		lapack.pc.in || die
-	# some string does not get passed properly
-	sed -i \
-		-e '/lapack_testing.py/d' \
-		CTestCustom.cmake.in || die
-	# separate ebuild to tmglib
-	sed -i \
-		-e '/lapack_install_library(tmglib)/d' \
-		TESTING/MATGEN/CMakeLists.txt || die
-}
-
-src_configure() {
-	lapack_configure() {
-		local profname=$(numeric-int64_get_module_name)
-		local libname="${profname//-/_}"
-		local blas_profname=$(numeric-int64_get_blas_alternative)
-		local xblas_profname=$(numeric-int64_get_xblas_alternative)
-		local xblas_libname="${xblas_profname//-/_}"
-		local blas_requires="${blas_profname}"
-		use xblas && \
-			blas_requires+=" ${xblas_profname}"
-		local mycmakeargs=(
-			-DPROFNAME="${profname}"
-			-DBLAS_REQUIRES="${blas_requires}"
-			-DLIBNAME="${libname}"
-			-DUSE_OPTIMIZED_BLAS=ON
-			-DBLAS_LIBRARIES="$($(tc-getPKG_CONFIG) --libs ${blas_profname})"
-			$(cmake-utils_use_build test TESTING)
-			$(cmake-utils_use_use xblas XBLAS)
-			-DCMAKE_C_FLAGS="$($(tc-getPKG_CONFIG) --cflags ${blas_profname}) ${CFLAGS}"
-			-DCMAKE_CXX_FLAGS="$($(tc-getPKG_CONFIG) --cflags ${blas_profname}) ${CXXFLAGS}"
-			-DCMAKE_Fortran_FLAGS="$($(tc-getPKG_CONFIG) --cflags ${blas_profname}) $(get_abi_CFLAGS) $(numeric-int64_get_fortran_int64_abi_fflags) ${FCFLAGS}"
-			-DLAPACK_PKGCONFIG_FFLAGS="$(numeric-int64_get_fortran_int64_abi_fflags)"
-		)
-		use xblas && \
-			mycmakeargs+=( -DXBLAS_LIBRARY:FILEPATH="${EROOT}usr/$(get_libdir)/lib${xblas_libname}.so" )
-		if $(numeric-int64_is_static_build); then
-			mycmakeargs+=(
-				-DBUILD_SHARED_LIBS=OFF
-				-DBUILD_STATIC_LIBS=ON
-			)
-		else
-			mycmakeargs+=(
-				-DBUILD_SHARED_LIBS=ON
-				-DBUILD_STATIC_LIBS=OFF
-			)
-		fi
-		cmake-utils_src_configure
-	}
-	numeric-int64-multibuild_foreach_all_abi_variants lapack_configure
-}
-
-src_compile() {
-	numeric-int64-multibuild_foreach_all_abi_variants cmake-utils_src_compile
-}
-
-src_test() {
-	numeric-int64-multibuild_foreach_all_abi_variants cmake-utils_src_test
-}
-
-src_install() {
-	numeric-int64-multibuild_foreach_all_abi_variants cmake-utils_src_install
-	numeric-int64-multibuild_install_alternative lapack reference
-}
diff --git a/sci-libs/lapack-reference/metadata.xml b/sci-libs/lapack-reference/metadata.xml
deleted file mode 100644
index 2fd11ecf7..000000000
--- a/sci-libs/lapack-reference/metadata.xml
+++ /dev/null
@@ -1,25 +0,0 @@
-<?xml version="1.0" encoding="UTF-8"?>
-<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
-<pkgmetadata>
-	<maintainer type="project">
-		<email>sci@gentoo.org</email>
-		<name>Gentoo Science Project</name>
-	</maintainer>
-	<longdescription lang="en">
-The Linear Algebra PACKage (LAPACK) is a comprehensive library that
-does linear algebra operations including matrix inversions, least
-squared solutions to linear sets of equations, eigenvector analysis,
-singular value decomposition, etc. It is a very comprehensive and
-reputable package that has found extensive use in the scientific community.
-This package installs the reference FORTRAN 77 implementation from
-Netlib for LAPACK and optionnally the one for the Basic Linear
-Algebra Subprogram (BLAS).
-</longdescription>
-	<use>
-		<flag name="deprecated">Build deprecated routines</flag>
-		<flag name="int64">Build the 64 bits integer library</flag>
-		<flag name="xblas">
-Build LAPACK with extra precision (needs <pkg>sci-libs/xblas</pkg>)
-</flag>
-	</use>
-</pkgmetadata>
diff --git a/sci-libs/lapacke-reference/Manifest b/sci-libs/lapacke-reference/Manifest
deleted file mode 100644
index 1bfd4e51c..000000000
--- a/sci-libs/lapacke-reference/Manifest
+++ /dev/null
@@ -1,2 +0,0 @@
-DIST lapack-3.5.0.tgz 6313139 BLAKE2B c23a35f107cfc5c887491fd148c1c76851a4580c98ad86aff9c391ac3d393c31ba67427ed445fe821c7666418e9fcf19523a3a668f8009337508994cf1a68c04 SHA512 b948a0a0db032bda455ec4f519d4e89e4c29e29cecb5b6258ca61f68faaeeac9fdf4ece5c39ffcd0154c5505facbc392c7d09c8348b1d60bdd2685153ab2543f
-DIST lapack-3.6.0.tgz 6792324 BLAKE2B 438f3376b63b38ef0fe70f6becac847816f3a11c01f5ab237dc0d941792ceb54dbd2f8dc22d56286f5dab3499289ed94e67521ea951a98973c9640abc294ad6c SHA512 bc50441d415ef8896dd7626d77c6104184b996e758704366288089f03d4c99d068e33153b0d13305310886017e5d2e716130f812a95cfcad36ef37fe20417ab8
diff --git a/sci-libs/lapacke-reference/files/lapack-fix-build-system.patch b/sci-libs/lapacke-reference/files/lapack-fix-build-system.patch
deleted file mode 100644
index 8661709d3..000000000
--- a/sci-libs/lapacke-reference/files/lapack-fix-build-system.patch
+++ /dev/null
@@ -1,92 +0,0 @@
---- lapack-3.6.0/BLAS/blas.pc.in
-+++ lapack-3.6.0/BLAS/blas.pc.in
-@@ -1,5 +1,7 @@
--prefix=@prefix@
--libdir=@libdir@
-+prefix=@CMAKE_INSTALL_PREFIX@
-+exec_prefix=${prefix}
-+libdir=${exec_prefix}/@CMAKE_INSTALL_LIBDIR@
-+includedir=${prefix}/include
- 
- Name: blas
- Description: Basic Linear Algebra Subprograms F77 reference implementations
---- lapack-3.6.0/BLAS/CMakeLists.txt
-+++ lapack-3.6.0/BLAS/CMakeLists.txt
-@@ -2,7 +2,7 @@
- if(BUILD_TESTING)
- add_subdirectory(TESTING)
- endif(BUILD_TESTING)
--configure_file(${CMAKE_CURRENT_SOURCE_DIR}/blas.pc.in ${CMAKE_CURRENT_BINARY_DIR}/blas.pc)
-+configure_file(${CMAKE_CURRENT_SOURCE_DIR}/blas.pc.in ${CMAKE_CURRENT_BINARY_DIR}/blas.pc @ONLY)
- install(FILES
-   ${CMAKE_CURRENT_BINARY_DIR}/blas.pc
-   DESTINATION ${PKG_CONFIG_DIR}
---- lapack-3.6.0/CBLAS/cblas.pc.in
-+++ lapack-3.6.0/CBLAS/cblas.pc.in
-@@ -1,5 +1,7 @@
--prefix=@prefix@
--libdir=@libdir@
-+prefix=@CMAKE_INSTALL_PREFIX@
-+exec_prefix=${prefix}
-+libdir=${exec_prefix}/@CMAKE_INSTALL_LIBDIR@
-+includedir=${prefix}/include
- 
- Name: lapacke
- Description: C Standard Interface to BLAS Linear Algebra PACKage
---- lapack-3.6.0/CBLAS/CMakeLists.txt
-+++ lapack-3.6.0/CBLAS/CMakeLists.txt
-@@ -71,7 +71,7 @@
-   ${LAPACK_BINARY_DIR}/cblas-config.cmake @ONLY)
- 
- 
--configure_file(${CMAKE_CURRENT_SOURCE_DIR}/cblas.pc.in ${CMAKE_CURRENT_BINARY_DIR}/cblas.pc)
-+configure_file(${CMAKE_CURRENT_SOURCE_DIR}/cblas.pc.in ${CMAKE_CURRENT_BINARY_DIR}/cblas.pc @ONLY)
-   install(FILES
-   ${CMAKE_CURRENT_BINARY_DIR}/cblas.pc
-   DESTINATION ${PKG_CONFIG_DIR}
---- lapack-3.6.0/CMakeLists.txt
-+++ lapack-3.6.0/CMakeLists.txt
-@@ -333,7 +333,7 @@
-   ${LAPACK_BINARY_DIR}/lapack-config.cmake @ONLY)
- 
- 
--configure_file(${CMAKE_CURRENT_SOURCE_DIR}/lapack.pc.in ${CMAKE_CURRENT_BINARY_DIR}/lapack.pc)
-+configure_file(${CMAKE_CURRENT_SOURCE_DIR}/lapack.pc.in ${CMAKE_CURRENT_BINARY_DIR}/lapack.pc @ONLY)
-   install(FILES
-   ${CMAKE_CURRENT_BINARY_DIR}/lapack.pc
-   DESTINATION ${PKG_CONFIG_DIR}
---- lapack-3.6.0/LAPACKE/CMakeLists.txt
-+++ lapack-3.6.0/LAPACKE/CMakeLists.txt
-@@ -65,7 +65,7 @@
- endif(BUILD_TESTING)
- 
- 
--configure_file(${CMAKE_CURRENT_SOURCE_DIR}/lapacke.pc.in ${CMAKE_CURRENT_BINARY_DIR}/lapacke.pc)
-+configure_file(${CMAKE_CURRENT_SOURCE_DIR}/lapacke.pc.in ${CMAKE_CURRENT_BINARY_DIR}/lapacke.pc @ONLY)
-  install(FILES
-   ${CMAKE_CURRENT_BINARY_DIR}/lapacke.pc
-   DESTINATION ${PKG_CONFIG_DIR}
---- lapack-3.6.0/LAPACKE/lapacke.pc.in
-+++ lapack-3.6.0/LAPACKE/lapacke.pc.in
-@@ -1,5 +1,7 @@
--prefix=@prefix@
--libdir=@libdir@
-+prefix=@CMAKE_INSTALL_PREFIX@
-+exec_prefix=${prefix}
-+libdir=${exec_prefix}/@CMAKE_INSTALL_LIBDIR@
-+includedir=${prefix}/include
- 
- Name: lapacke
- Description: C Standard Interface to LAPACK Linear Algebra PACKage
---- lapack-3.6.0/lapack.pc.in
-+++ lapack-3.6.0/lapack.pc.in
-@@ -1,5 +1,7 @@
--prefix=@prefix@
--libdir=@libdir@
-+prefix=@CMAKE_INSTALL_PREFIX@
-+exec_prefix=${prefix}
-+libdir=${exec_prefix}/@CMAKE_INSTALL_LIBDIR@
-+includedir=${prefix}/include
- 
- Name: lapack
- Description: FORTRAN reference implementation of LAPACK Linear Algebra PACKage
diff --git a/sci-libs/lapacke-reference/lapacke-reference-3.5.0.ebuild b/sci-libs/lapacke-reference/lapacke-reference-3.5.0.ebuild
deleted file mode 100644
index e71514161..000000000
--- a/sci-libs/lapacke-reference/lapacke-reference-3.5.0.ebuild
+++ /dev/null
@@ -1,95 +0,0 @@
-# Copyright 1999-2015 Gentoo Foundation
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=5
-
-FORTRAN_NEEDED=test
-
-inherit alternatives-2 cmake-utils eutils fortran-2 toolchain-funcs
-
-MYP=lapack-${PV}
-
-DESCRIPTION="C Interface to LAPACK"
-HOMEPAGE="http://www.netlib.org/lapack/"
-SRC_URI="http://www.netlib.org/lapack/${MYP}.tgz"
-
-LICENSE="BSD"
-SLOT="0"
-KEYWORDS="~amd64 ~x86 ~amd64-linux ~x86-linux"
-IUSE="static-libs test tmg xblas"
-
-RDEPEND="
-	virtual/blas
-	virtual/lapack
-	tmg? ( sci-libs/tmglib )
-	xblas? ( sci-libs/xblas )"
-DEPEND="${RDEPEND}
-	virtual/pkgconfig"
-
-S="${WORKDIR}/${MYP}"
-
-src_prepare() {
-	# rename libraries to avoid collision with other lapacke
-	sed -i \
-		-e 's:BINARY_DIR}/lapacke.pc:BINARY_DIR}/reflapacke.pc:' \
-		-e '/export/s:lapacke:reflapacke:g' \
-		-e '/ALL_TARGETS/s:lapacke):reflapacke):' \
-		-e '/LAPACK_LIBRARIES/s:lapacke:reflapacke:g' \
-		CMakeLists.txt || die
-	sed -i \
-		-e '/librar/s:(lapacke:(reflapacke:g' \
-		lapacke/CMakeLists.txt || die
-	sed -i \
-		-e '/librar/s:lapacke:reflapacke:g' \
-		lapacke/example/CMakeLists.txt || die
-	local tmgpc; use tmg && tmgpc=" -ltmglib"
-	sed -i \
-		-e "s:-llapacke:-lreflapacke${tmgpc}:g" \
-		lapacke/lapacke.pc.in || die
-	use static-libs && mkdir "${WORKDIR}/${PN}_static"
-}
-
-src_configure() {
-	lapack_configure() {
-		local mycmakeargs=(
-			-DUSE_OPTIMIZED_BLAS=ON
-			-DUSE_OPTIMIZED_LAPACK=ON
-			-DLAPACKE=ON
-			-DBLAS_LIBRARIES="$($(tc-getPKG_CONFIG) --libs blas)"
-			-DLAPACK_LIBRARIES="$($(tc-getPKG_CONFIG) --libs lapack)"
-			$(cmake-utils_use tmg LAPACKE_WITH_TMG)
-			$(cmake-utils_use_build test TESTING)
-			$(cmake-utils_use_use xblas XBLAS)
-			$@
-		)
-		cmake-utils_src_configure
-	}
-
-	lapack_configure -DBUILD_SHARED_LIBS=ON -DBUILD_STATIC_LIBS=OFF
-	use static-libs && \
-		BUILD_DIR="${WORKDIR}/${PN}_static" lapack_configure \
-		-DBUILD_SHARED_LIBS=OFF -DBUILD_STATIC_LIBS=ON
-}
-
-src_compile() {
-	use test && cmake-utils_src_compile -C TESTING/MATGEN
-	cmake-utils_src_compile -C lapacke
-	use static-libs \
-		&& BUILD_DIR="${WORKDIR}/${PN}_static" cmake-utils_src_compile -C lapacke
-}
-
-src_test() {
-	pushd "${BUILD_DIR}/lapacke" > /dev/null || die
-	local ctestargs
-	[[ -n ${TEST_VERBOSE} ]] && ctestargs="--extra-verbose --output-on-failure"
-	ctest ${ctestargs} || die
-	popd > /dev/null || die
-}
-
-src_install() {
-	cmake-utils_src_install -C lapacke
-	use static-libs \
-		&& BUILD_DIR="${WORKDIR}/${PN}_static" cmake-utils_src_install -C lapacke
-	alternatives_for lapacke reference 0 \
-		/usr/$(get_libdir)/pkgconfig/lapacke.pc reflapacke.pc
-}
diff --git a/sci-libs/lapacke-reference/lapacke-reference-3.6.0-r2.ebuild b/sci-libs/lapacke-reference/lapacke-reference-3.6.0-r2.ebuild
deleted file mode 100644
index 65177ade1..000000000
--- a/sci-libs/lapacke-reference/lapacke-reference-3.6.0-r2.ebuild
+++ /dev/null
@@ -1,102 +0,0 @@
-# Copyright 1999-2016 Gentoo Foundation
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=5
-
-FORTRAN_NEEDED=test
-
-inherit alternatives-2 cmake-utils eutils fortran-2 toolchain-funcs
-
-MYP=lapack-${PV}
-
-DESCRIPTION="C Interface to LAPACK"
-HOMEPAGE="http://www.netlib.org/lapack/"
-SRC_URI="http://www.netlib.org/lapack/${MYP}.tgz"
-
-LICENSE="BSD"
-SLOT="0"
-KEYWORDS="~amd64 ~x86 ~amd64-linux ~x86-linux"
-IUSE="+deprecated static-libs test tmg xblas"
-
-RDEPEND="
-	virtual/blas
-	virtual/lapack
-	tmg? ( sci-libs/tmglib )
-	xblas? ( sci-libs/xblas )"
-DEPEND="${RDEPEND}
-	virtual/pkgconfig"
-
-S="${WORKDIR}/${MYP}"
-PATCHES=( "${FILESDIR}/lapack-fix-build-system.patch" )
-
-src_prepare() {
-	# the lapack(e)/(c)blas build system is somewhat broken
-	# with respect to its pkg-config files.
-	epatch "${PATCHES[@]}"
-
-	# rename libraries to avoid collision with other lapacke
-	sed -i \
-		-e 's:BINARY_DIR}/lapacke.pc:BINARY_DIR}/reflapacke.pc:' \
-		-e '/export/s:lapacke:reflapacke:g' \
-		-e '/ALL_TARGETS/s:lapacke):reflapacke):' \
-		-e '/LAPACK_LIBRARIES/s:lapacke:reflapacke:g' \
-		LAPACKE/CMakeLists.txt \
-		CMakeLists.txt || die
-	sed -i \
-		-e '/librar/s:(lapacke:(reflapacke:g' \
-		LAPACKE/CMakeLists.txt || die
-	sed -i \
-		-e '/librar/s:lapacke:reflapacke:g' \
-		LAPACKE/example/CMakeLists.txt || die
-	local tmgpc; use tmg && tmgpc=" -ltmglib"
-	sed -i \
-		-e "s:-llapacke:-lreflapacke${tmgpc}:g" \
-		LAPACKE/lapacke.pc.in || die
-	use static-libs && mkdir "${WORKDIR}/${PN}_static"
-}
-
-src_configure() {
-	lapack_configure() {
-		local mycmakeargs=(
-			-DUSE_OPTIMIZED_BLAS=ON
-			-DUSE_OPTIMIZED_LAPACK=ON
-			-DLAPACKE=ON
-			-DBLAS_LIBRARIES="$($(tc-getPKG_CONFIG) --libs blas)"
-			-DLAPACK_LIBRARIES="$($(tc-getPKG_CONFIG) --libs lapack)"
-			$(cmake-utils_use tmg LAPACKE_WITH_TMG)
-			$(cmake-utils_use_build test TESTING)
-			$(cmake-utils_use_use xblas XBLAS)
-			$(cmake-utils_use_build deprecated DEPRECATED)
-			$@
-		)
-		cmake-utils_src_configure
-	}
-
-	lapack_configure -DBUILD_SHARED_LIBS=ON -DBUILD_STATIC_LIBS=OFF
-	use static-libs && \
-		BUILD_DIR="${WORKDIR}/${PN}_static" lapack_configure \
-		-DBUILD_SHARED_LIBS=OFF -DBUILD_STATIC_LIBS=ON
-}
-
-src_compile() {
-	use test && cmake-utils_src_compile -C TESTING/MATGEN
-	cmake-utils_src_compile -C LAPACKE
-	use static-libs \
-		&& BUILD_DIR="${WORKDIR}/${PN}_static" cmake-utils_src_compile -C LAPACKE
-}
-
-src_test() {
-	pushd "${BUILD_DIR}/LAPACKE" > /dev/null || die
-	local ctestargs
-	[[ -n ${TEST_VERBOSE} ]] && ctestargs="--extra-verbose --output-on-failure"
-	ctest ${ctestargs} || die
-	popd > /dev/null || die
-}
-
-src_install() {
-	cmake-utils_src_install -C LAPACKE
-	use static-libs \
-		&& BUILD_DIR="${WORKDIR}/${PN}_static" cmake-utils_src_install -C LAPACKE
-	alternatives_for lapacke reference 0 \
-		/usr/$(get_libdir)/pkgconfig/lapacke.pc reflapacke.pc
-}
diff --git a/sci-libs/lapacke-reference/lapacke-reference-9999.ebuild b/sci-libs/lapacke-reference/lapacke-reference-9999.ebuild
deleted file mode 100644
index 87462c46a..000000000
--- a/sci-libs/lapacke-reference/lapacke-reference-9999.ebuild
+++ /dev/null
@@ -1,95 +0,0 @@
-# Copyright 1999-2018 Gentoo Foundation
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=6
-
-FORTRAN_NEEDED=test
-
-inherit alternatives-2 cmake-utils eutils fortran-2 subversion toolchain-funcs
-
-MYP=lapack-${PV}
-
-DESCRIPTION="C Interface to LAPACK"
-HOMEPAGE="http://www.netlib.org/lapack/"
-ESVN_REPO_URI="https://icl.cs.utk.edu/svn/lapack-dev/lapack/trunk"
-
-LICENSE="BSD"
-SLOT="0"
-KEYWORDS=""
-IUSE="static-libs test tmg xblas"
-
-RDEPEND="
-	virtual/blas
-	virtual/lapack
-	tmg? ( sci-libs/tmglib )
-	xblas? ( sci-libs/xblas )"
-DEPEND="${RDEPEND}
-	virtual/pkgconfig"
-
-S="${WORKDIR}/${MYP}"
-
-src_prepare() {
-	# rename libraries to avoid collision with other lapacke
-	sed -i \
-		-e 's:BINARY_DIR}/lapacke.pc:BINARY_DIR}/reflapacke.pc:' \
-		-e '/export/s:lapacke:reflapacke:g' \
-		-e '/ALL_TARGETS/s:lapacke):reflapacke):' \
-		-e '/LAPACK_LIBRARIES/s:lapacke:reflapacke:g' \
-		CMakeLists.txt || die
-	sed -i \
-		-e '/librar/s:(lapacke:(reflapacke:g' \
-		LAPACKE/CMakeLists.txt || die
-	sed -i \
-		-e '/librar/s:lapacke:reflapacke:g' \
-		LAPACKE/example/CMakeLists.txt || die
-	local tmgpc; use tmg && tmgpc=" -ltmglib"
-	sed -i \
-		-e "s:-llapacke:-lreflapacke${tmgpc}:g" \
-		LAPACKE/lapacke.pc.in || die
-	use static-libs && mkdir "${WORKDIR}/${PN}_static"
-}
-
-src_configure() {
-	lapack_configure() {
-		local mycmakeargs=(
-			-DUSE_OPTIMIZED_BLAS=ON
-			-DUSE_OPTIMIZED_LAPACK=ON
-			-DLAPACKE=ON
-			-DBLAS_LIBRARIES="$($(tc-getPKG_CONFIG) --libs blas)"
-			-DLAPACK_LIBRARIES="$($(tc-getPKG_CONFIG) --libs lapack)"
-			-DLAPACKE_WITH_TMG=$(usex tmg)
-			-DBUILD_TESTING=$(usex test)
-			-DUSE_XBLAS=$(usex xblas)
-			$@
-		)
-		cmake-utils_src_configure
-	}
-
-	lapack_configure -DBUILD_SHARED_LIBS=ON -DBUILD_STATIC_LIBS=OFF
-	use static-libs && \
-		BUILD_DIR="${WORKDIR}/${PN}_static" lapack_configure \
-		-DBUILD_SHARED_LIBS=OFF -DBUILD_STATIC_LIBS=ON
-}
-
-src_compile() {
-	use test && cmake-utils_src_compile -C TESTING/MATGEN
-	cmake-utils_src_compile -C LAPACKE
-	use static-libs \
-		&& BUILD_DIR="${WORKDIR}/${PN}_static" cmake-utils_src_compile -C LAPACKE
-}
-
-src_test() {
-	pushd "${BUILD_DIR}/lapacke" > /dev/null || die
-	local ctestargs
-	[[ -n ${TEST_VERBOSE} ]] && ctestargs="--extra-verbose --output-on-failure"
-	ctest ${ctestargs} || die
-	popd > /dev/null || die
-}
-
-src_install() {
-	cmake-utils_src_install -C LAPACKE
-	use static-libs \
-		&& BUILD_DIR="${WORKDIR}/${PN}_static" cmake-utils_src_install -C LAPACKE
-	alternatives_for lapacke reference 0 \
-		/usr/$(get_libdir)/pkgconfig/lapacke.pc reflapacke.pc
-}
diff --git a/sci-libs/lapacke-reference/metadata.xml b/sci-libs/lapacke-reference/metadata.xml
deleted file mode 100644
index 26d2a3499..000000000
--- a/sci-libs/lapacke-reference/metadata.xml
+++ /dev/null
@@ -1,19 +0,0 @@
-<?xml version="1.0" encoding="UTF-8"?>
-<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
-<pkgmetadata>
-	<maintainer type="project">
-		<email>sci@gentoo.org</email>
-		<name>Gentoo Science Project</name>
-	</maintainer>
-	<longdescription lang="en">
-This implementation provides a native C interface to LAPACK routines
-available at www.netlib.org/lapack to facilitate usage of LAPACK
-functionality for C programmers. 
-</longdescription>
-	<use>
-		<flag name="deprecated">Build deprecated routines</flag>
-		<flag name="tmg">Build LAPACKE with a Test Matrix Generator library</flag>
-		<flag name="xblas">Build LAPACKE with extra precision (needs
-<pkg>sci-libs/xblas</pkg>)</flag>
-	</use>
-</pkgmetadata>
diff --git a/sci-libs/lapackpp/Manifest b/sci-libs/lapackpp/Manifest
deleted file mode 100644
index effbb5ac0..000000000
--- a/sci-libs/lapackpp/Manifest
+++ /dev/null
@@ -1 +0,0 @@
-DIST lapackpp-2.5.4.tar.gz 635178 BLAKE2B e5a0ef9075c9cae81604cece514a0d0af037984a82860d619d915695a1b532bbeaf5e4003d79b46cf7b60f47455a3967c9bdb33a28a1cc0897e4f09f79fb9a26 SHA512 3c6c411a9fbb04880224c995dcdf69b4050f03691d087e6ddc0d93ffe149661511f570b8bc8c0837afdc03d5e14d39b5902890df3fe39c5eb67f7cddbbb10b6b
diff --git a/sci-libs/lapackpp/lapackpp-2.5.4.ebuild b/sci-libs/lapackpp/lapackpp-2.5.4.ebuild
deleted file mode 100644
index 0b04b4ba1..000000000
--- a/sci-libs/lapackpp/lapackpp-2.5.4.ebuild
+++ /dev/null
@@ -1,46 +0,0 @@
-# Copyright 1999-2015 Gentoo Foundation
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=5
-
-inherit toolchain-funcs
-
-DESCRIPTION="C++ wrapper for LAPACK libraries"
-HOMEPAGE="http://lapackpp.sourceforge.net"
-SRC_URI="mirror://sourceforge/${PN}/${P}.tar.gz"
-
-LICENSE="LGPL-2.1"
-
-SLOT="0"
-KEYWORDS="~amd64 ~x86 ~amd64-linux ~x86-linux"
-IUSE="doc static-libs"
-
-RDEPEND="
-	virtual/blas
-	virtual/lapack"
-DEPEND="${RDEPEND}
-	virtual/pkgconfig
-	doc? ( app-doc/doxygen[latex] )"
-
-src_prepare() {
-	# Parallel build issues
-	sed -i 's/\bmake\b/$(MAKE)/' Makefile.in || die
-}
-
-src_configure() {
-	econf \
-		$(use_enable static-libs static) \
-		--disable-atlas \
-		--with-blas="$($(tc-getPKG_CONFIG) --libs blas)" \
-		--with-lapack="$($(tc-getPKG_CONFIG) --libs lapack)"
-}
-
-src_compile() {
-	default
-	use doc && emake srcdoc
-}
-
-src_install() {
-	default
-	use doc && dohtml -r api-doc/html/*
-}
diff --git a/sci-libs/lapackpp/metadata.xml b/sci-libs/lapackpp/metadata.xml
deleted file mode 100644
index 762285c1d..000000000
--- a/sci-libs/lapackpp/metadata.xml
+++ /dev/null
@@ -1,23 +0,0 @@
-<?xml version="1.0" encoding="UTF-8"?>
-<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
-<pkgmetadata>
-	<maintainer type="project">
-		<email>sci@gentoo.org</email>
-		<name>Gentoo Science Project</name>
-	</maintainer>
-	<longdescription lang="en">
-LAPACK++ (Linear Algebra PACKage in C++) is a software library for
-numerical linear algebra that solves systems of linear equations and
-eigenvalue problems on high performance computer architectures.
-Computational support is provided for supports various matrix classes
-for vectors, non-symmetric matrices, SPD matrices, symmetric matrices,
-banded, triangular, and tridiagonal matrices; however, it does not
-include all of the capabilities of original f77 LAPACK. Emphasis is
-given to routines for solving linear systems consisting of non-symmetric
-matrices, symmetric positive definite systems, and solving linear
-least-square systems.
-</longdescription>
-	<upstream>
-		<remote-id type="sourceforge">lapackpp</remote-id>
-	</upstream>
-</pkgmetadata>
diff --git a/sci-libs/lib2bit/files/lib2bit-0.2.1_respect_DESTDIR.patch b/sci-libs/lib2bit/files/lib2bit-0.2.1_respect_DESTDIR.patch
deleted file mode 100644
index 0f64b325f..000000000
--- a/sci-libs/lib2bit/files/lib2bit-0.2.1_respect_DESTDIR.patch
+++ /dev/null
@@ -1,11 +0,0 @@
---- lib2bit-0.2.1/Makefile.ori	2017-03-31 22:09:48.387098439 +0200
-+++ lib2bit-0.2.1/Makefile	2017-03-31 22:10:29.889020564 +0200
-@@ -8,7 +8,7 @@
- LDLIBS =
- INCLUDES = 
- 
--prefix = /usr/local
-+prefix = $(DESTDIR)/usr/local
- includedir = $(prefix)/include
- libdir = $(exec_prefix)/lib
- 
diff --git a/sci-libs/lib2bit/files/lib2bit-0.2.1_respect_LDFLAGS.patch b/sci-libs/lib2bit/files/lib2bit-0.2.1_respect_LDFLAGS.patch
new file mode 100644
index 000000000..92a5b5d43
--- /dev/null
+++ b/sci-libs/lib2bit/files/lib2bit-0.2.1_respect_LDFLAGS.patch
@@ -0,0 +1,11 @@
+--- lib2bit-0.2.1/Makefile.ori	2020-03-19 11:41:21.896527937 +0000
++++ lib2bit-0.2.1/Makefile	2020-03-19 11:41:00.339977405 +0000
+@@ -4,7 +4,7 @@
+ CFLAGS ?= -g -Wall -O3
+ LIBS =
+ EXTRA_CFLAGS_PIC = -fpic
+-LDFLAGS =
++LDFLAGS ?=
+ LDLIBS =
+ INCLUDES = 
+ 
diff --git a/sci-libs/lib2bit/files/lib2bit-0.2.1_test_support_python3.patch b/sci-libs/lib2bit/files/lib2bit-0.2.1_test_support_python3.patch
new file mode 100644
index 000000000..2cee88ada
--- /dev/null
+++ b/sci-libs/lib2bit/files/lib2bit-0.2.1_test_support_python3.patch
@@ -0,0 +1,11 @@
+--- lib2bit-0.2.1/test/test.py.ori	2020-03-19 11:28:53.301344896 +0000
++++ lib2bit-0.2.1/test/test.py	2020-03-19 11:28:11.968283978 +0000
+@@ -14,7 +14,7 @@
+     p2 = Popen(["md5sum"], stdin=p1.stdout, stdout=PIPE)
+ except:
+     p2 = Popen(["md5"], stdin=p1.stdout, stdout=PIPE)
+-md5sum = p2.communicate()[0].strip().split()[0]
++md5sum = p2.communicate()[0].strip().split()[0].decode('utf-8')
+ assert(md5sum == "0274c32c7f3dd75e8991f6107dca6a5f")
+ 
+ print("Passed!")
diff --git a/sci-libs/lib2bit/lib2bit-0.2.1.ebuild b/sci-libs/lib2bit/lib2bit-0.2.1.ebuild
index c547dcca9..5f012de35 100644
--- a/sci-libs/lib2bit/lib2bit-0.2.1.ebuild
+++ b/sci-libs/lib2bit/lib2bit-0.2.1.ebuild
@@ -1,31 +1,27 @@
-# Copyright 1999-2017 Gentoo Foundation
+# Copyright 1999-2021 Gentoo Authors
 # Distributed under the terms of the GNU General Public License v2
 
-EAPI=6
-
-inherit eutils
+EAPI=7
 
 DESCRIPTION="C library for accessing 2bit files"
 HOMEPAGE="https://github.com/dpryan79/lib2bit"
-SRC_URI="https://github.com/dpryan79/lib2bit/archive/0.2.1.tar.gz -> ${P}.tar.gz"
+SRC_URI="https://github.com/dpryan79/lib2bit/archive/${PV}.tar.gz -> ${P}.tar.gz"
 
 LICENSE="MIT"
 SLOT="0"
 KEYWORDS="~amd64 ~x86"
 IUSE="static"
 
-DEPEND=""
-RDEPEND="${DEPEND}"
-
-src_prepare(){
-	default
-	epatch "${FILESDIR}"/${P}_respect_DESTDIR.patch
-	sed -e 's#/usr/local#/usr#' -i Makefile || die
-}
+PATCHES=(
+	"${FILESDIR}"/${P}_respect_LDFLAGS.patch
+	"${FILESDIR}"/${P}_test_support_python3.patch
+)
 
 src_install(){
-	emake DESTDIR="${ED}" install
-	if not use static; then
-		rm "${ED}"/usr/lib/lib2bit.a || die
+	dodoc README.md
+	dolib.so lib2bit.so
+	doheader 2bit.h
+	if use static; then
+		dolib.a lib2bit.a
 	fi
 }
diff --git a/sci-libs/libStatGen/Manifest b/sci-libs/libStatGen/Manifest
index 8f3385c86..e3f88de93 100644
--- a/sci-libs/libStatGen/Manifest
+++ b/sci-libs/libStatGen/Manifest
@@ -1,2 +1 @@
-DIST libStatGen-1.0.13.tar.gz 558682 BLAKE2B 8e9308c698110e2e3a735e14171954c2bf1e7ac7f05d6c86072389aa697246d69033a0844f4bfccce1dc74623e847c551e388e19b00469274d5ef945e080811c SHA512 bcce3dd2f343e5941857d5bca0f2960d69b3e1083da6312e018a96bb92fb8dbc91ac511e062b024720c45508aa805d3f4f6511f60201438176a898ab789e746f
-DIST libStatGen-1.0.14.tar.gz 558924 BLAKE2B 0216caaf114574c35fd4458795e21a53f25e9f24905320d5cc161b226575bd8a6d80b1ced765ea9f03205bdd0d0740a3dd398185440775a07ee9cbf0690428a6 SHA512 c7a1d4d56803b7ca741961a77dc8419277f01e8c683c8f5d494f3af242a2b5075462179b14601a41842a1624017c812a754f912a622dc1af3f5e4b1dc4722508
+DIST libStatGen-1.0.15.tar.gz 560782 BLAKE2B e605adc37291aa3b6563698bbad0990239d71dd2ac6c4e1f70232f58a75ae2cc328f7e27c799c41caf6214c25d125083fdb6f4b77663a5a6e34d94ec199a9864 SHA512 6408ab47b9781df7fdf65302d47e90acc6fd58985680a0c5ef794d8dd2bba343cacb39b32774d60f931d98b99cd156cf7059c9af87cde5b672739bac5bda0569
diff --git a/sci-libs/libStatGen/libStatGen-1.0.13.ebuild b/sci-libs/libStatGen/libStatGen-1.0.13.ebuild
deleted file mode 100644
index fa9f58f5c..000000000
--- a/sci-libs/libStatGen/libStatGen-1.0.13.ebuild
+++ /dev/null
@@ -1,21 +0,0 @@
-# Copyright 1999-2017 Gentoo Foundation
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=6
-
-DESCRIPTION="Set of classes for creating statistical genetic programs"
-HOMEPAGE="https://github.com/statgen/libStatGen"
-SRC_URI="https://github.com/statgen/libStatGen/archive/v${PV}.tar.gz -> ${P}.tar.gz"
-
-LICENSE="GPL-3+"
-SLOT="0"
-KEYWORDS="~amd64 ~x86"
-IUSE=""
-
-DEPEND="dev-libs/openssl:0="
-RDEPEND="${DEPEND}"
-
-src_install(){
-	default
-	dolib libStatGen.* # package only makes a static library
-}
diff --git a/sci-libs/libStatGen/libStatGen-1.0.14.ebuild b/sci-libs/libStatGen/libStatGen-1.0.14.ebuild
deleted file mode 100644
index fa9f58f5c..000000000
--- a/sci-libs/libStatGen/libStatGen-1.0.14.ebuild
+++ /dev/null
@@ -1,21 +0,0 @@
-# Copyright 1999-2017 Gentoo Foundation
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=6
-
-DESCRIPTION="Set of classes for creating statistical genetic programs"
-HOMEPAGE="https://github.com/statgen/libStatGen"
-SRC_URI="https://github.com/statgen/libStatGen/archive/v${PV}.tar.gz -> ${P}.tar.gz"
-
-LICENSE="GPL-3+"
-SLOT="0"
-KEYWORDS="~amd64 ~x86"
-IUSE=""
-
-DEPEND="dev-libs/openssl:0="
-RDEPEND="${DEPEND}"
-
-src_install(){
-	default
-	dolib libStatGen.* # package only makes a static library
-}
diff --git a/sci-libs/libStatGen/libStatGen-1.0.15.ebuild b/sci-libs/libStatGen/libStatGen-1.0.15.ebuild
new file mode 100644
index 000000000..fba3dde57
--- /dev/null
+++ b/sci-libs/libStatGen/libStatGen-1.0.15.ebuild
@@ -0,0 +1,30 @@
+# Copyright 1999-2021 Gentoo Authors
+# Distributed under the terms of the GNU General Public License v2
+
+EAPI=7
+
+DOCS_BUILDER="doxygen"
+DOCS_DEPEND="media-gfx/graphviz"
+
+inherit docs
+
+DESCRIPTION="Set of classes for creating statistical genetic programs"
+HOMEPAGE="https://github.com/statgen/libStatGen"
+SRC_URI="https://github.com/statgen/libStatGen/archive/v${PV}.tar.gz -> ${P}.tar.gz"
+
+LICENSE="GPL-3+"
+SLOT="0"
+KEYWORDS="~amd64 ~x86"
+
+DEPEND="dev-libs/openssl:0="
+RDEPEND="${DEPEND}"
+
+src_compile() {
+	default
+	docs_compile
+}
+
+src_install(){
+	default
+	dolib.a libStatGen.a # package only makes a static library
+}
diff --git a/sci-libs/libcgnsoo/Manifest b/sci-libs/libcgnsoo/Manifest
deleted file mode 100644
index 3c22fce61..000000000
--- a/sci-libs/libcgnsoo/Manifest
+++ /dev/null
@@ -1 +0,0 @@
-DIST libcgnsoo-3.0_1728.orig.tar.gz 363425 BLAKE2B 904125c4a3ff86a9617567109f909e994e32b1a6f8b07b44c3bc811866210a39008f0245c9ea350453ad81dae96b31fdb56da723d109aaa8ab4e44c57c9bdea5 SHA512 4759d2921cfc0e997222f1f970ce02f618ff9f0ba9ac53ebe573e355cafaf3a1b112894fb03efff25e4f951d4c1522a971ddd1c7f83e610073216061d64c2cef
diff --git a/sci-libs/libcgnsoo/libcgnsoo-1728.ebuild b/sci-libs/libcgnsoo/libcgnsoo-1728.ebuild
deleted file mode 100644
index 34556d99b..000000000
--- a/sci-libs/libcgnsoo/libcgnsoo-1728.ebuild
+++ /dev/null
@@ -1,26 +0,0 @@
-# Copyright 1999-2015 Gentoo Foundation
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=5
-
-MY_PV="3.0"
-MY_PN=${PN}-${MY_PV}
-
-DESCRIPTION="Object-oriented interface to the CGNS Mid-level library"
-HOMEPAGE="http://openfoam-extend.sourceforge.net"
-SRC_URI="http://ppa.launchpad.net/cae-team/ppa/ubuntu/pool/main/libc/${MY_PN}/${MY_PN}_${PV}.orig.tar.gz"
-
-LICENSE="GPL-2"
-SLOT="0"
-KEYWORDS="~amd64 ~x86"
-IUSE=""
-
-DEPEND="sci-libs/cgnslib"
-RDEPEND="${DEPEND}"
-
-S=${WORKDIR}/${MY_PN}-${PV}
-
-src_configure() {
-	chmod +x configure
-	econf --with-CGNSLIBHOME="/usr"
-}
diff --git a/sci-libs/libcgnsoo/metadata.xml b/sci-libs/libcgnsoo/metadata.xml
deleted file mode 100644
index b501da7f8..000000000
--- a/sci-libs/libcgnsoo/metadata.xml
+++ /dev/null
@@ -1,11 +0,0 @@
-<?xml version="1.0" encoding="UTF-8"?>
-<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
-<pkgmetadata>
-	<maintainer type="project">
-		<email>sci@gentoo.org</email>
-		<name>Gentoo Science Project</name>
-	</maintainer>
-	<upstream>
-		<remote-id type="sourceforge">openfoam-extend</remote-id>
-	</upstream>
-</pkgmetadata>
diff --git a/sci-libs/libfac/Manifest b/sci-libs/libfac/Manifest
deleted file mode 100644
index 1e3cf3ce4..000000000
--- a/sci-libs/libfac/Manifest
+++ /dev/null
@@ -1 +0,0 @@
-DIST libfac-3-1-1.tar.gz 90104 BLAKE2B ad5f2ab11f2aaaa7ca3f9ab2f117db7795485564e0bbb1f1c09d8861e0cedfc05c07a60b064e24d951e9cf59ea913bae19c6eb86d30cc5f807b00d65292eb0b5 SHA512 d920bd40c9fb3938d2c08ff0d750bd26df0c7627af388f2ee0592947e4bc78c9841b9bae95775af53642daeee7b8d42761af4bf564e7f899f2ac03ba7ac83a67
diff --git a/sci-libs/libfac/libfac-3.1.1.ebuild b/sci-libs/libfac/libfac-3.1.1.ebuild
deleted file mode 100644
index e8f8749fa..000000000
--- a/sci-libs/libfac/libfac-3.1.1.ebuild
+++ /dev/null
@@ -1,26 +0,0 @@
-# Copyright 1999-2015 Gentoo Foundation
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=5
-
-inherit eutils versionator
-
-MY_PV=$(replace_all_version_separators '-')
-
-DESCRIPTION="libfac is an extension of Singular-factory to finite fields"
-HOMEPAGE="ftp://www.mathematik.uni-kl.de/pub/Math/Singular/Libfac/"
-SRC_URI="ftp://www.mathematik.uni-kl.de/pub/Math/Singular/Libfac/${PN}-${MY_PV}.tar.gz"
-
-LICENSE="GPL-2"
-SLOT="0"
-KEYWORDS="~amd64 ~x86"
-IUSE="singular"
-
-DEPEND=">=sci-libs/factory-${PV}[singular=]"
-RDEPEND="${DEPEND}"
-
-S="${WORKDIR}/${PN}"
-
-src_configure() {
-	econf $(use_with singular Singular)
-}
diff --git a/sci-libs/libfac/metadata.xml b/sci-libs/libfac/metadata.xml
deleted file mode 100644
index 40ae88f5b..000000000
--- a/sci-libs/libfac/metadata.xml
+++ /dev/null
@@ -1,18 +0,0 @@
-<?xml version="1.0" encoding="UTF-8"?>
-<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
-<pkgmetadata>
-	<maintainer type="person">
-		<email>tom111@gmx.de</email>
-		<name>Thomas Kahle</name>
-	</maintainer>
-	<maintainer type="project">
-		<email>sci@gentoo.org</email>
-		<name>Gentoo Science Project</name>
-	</maintainer>
-	<longdescription lang="en">
-libfac is an extension of Singular-factory to finite fields
-</longdescription>
-	<use>
-		<flag name="singular">Automatically generated description for singular</flag>
-	</use>
-</pkgmetadata>
diff --git a/sci-libs/libflame-amd/Manifest b/sci-libs/libflame-amd/Manifest
new file mode 100644
index 000000000..422282045
--- /dev/null
+++ b/sci-libs/libflame-amd/Manifest
@@ -0,0 +1 @@
+DIST libflame-amd-3.1.tar.gz 26635219 BLAKE2B 43f5db65bb53a818259e62e01d373ba8db2052c11b5839d28805e37e2b9033e16410efc4b6ce3379f3d92067511b834ef16dbca22987945608167a90e4f31871 SHA512 b6a05dbadd169e05645bc4ae456f00b6c84f2c3eeaf1e1bd74d273e540ca1f99915bd221427bce0e4f73fed050daf2db8902891451d5b2b9273af48c8e2f4479
diff --git a/sci-libs/libflame-amd/libflame-amd-3.1.ebuild b/sci-libs/libflame-amd/libflame-amd-3.1.ebuild
new file mode 100644
index 000000000..cdadccb5c
--- /dev/null
+++ b/sci-libs/libflame-amd/libflame-amd-3.1.ebuild
@@ -0,0 +1,46 @@
+# Copyright 1999-2022 Gentoo Authors
+# Distributed under the terms of the GNU General Public License v2
+
+EAPI=8
+
+inherit fortran-2
+FORTRAN_NEED_OPENMP=1
+
+DESCRIPTION="AMD optimized high-performance object-based library for DLA computations"
+HOMEPAGE="https://developer.amd.com/amd-aocl/"
+SRC_URI="https://github.com/amd/libflame/archive/${PV}.tar.gz -> ${P}.tar.gz"
+S="${WORKDIR}/libflame-${PV}"
+
+KEYWORDS="~amd64"
+LICENSE="BSD"
+SLOT="0"
+
+CPU_FLAGS=( sse3 )
+IUSE_CPU_FLAGS_X86="${CPU_FLAGS[@]/#/cpu_flags_x86_}"
+IUSE="scc supermatrix ${IUSE_CPU_FLAGS_X86[@]}"
+
+DEPEND="virtual/cblas"
+RDEPEND="${DEPEND}"
+BDEPEND="dev-vcs/git"
+
+src_configure() {
+	local myconf=(
+		--disable-optimizations
+		--enable-multithreading=openmp
+		--enable-verbose-make-output
+		--enable-lapack2flame
+		--enable-cblas-interfaces
+		--enable-max-arg-list-hack
+		--enable-dynamic-build
+		--enable-vector-intrinsics=$(usex cpu_flags_x86_sse3 sse none)
+		$(use_enable scc)
+		$(use_enable supermatrix)
+	)
+	econf "${myconf[@]}"
+}
+
+src_install() {
+	# -j1 because otherwise cannot create file that already exists
+	DESTDIR="${ED}" emake -j1 install
+	einstalldocs
+}
diff --git a/sci-libs/libflame-amd/metadata.xml b/sci-libs/libflame-amd/metadata.xml
new file mode 100644
index 000000000..36ca842dd
--- /dev/null
+++ b/sci-libs/libflame-amd/metadata.xml
@@ -0,0 +1,19 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
+<pkgmetadata>
+	<maintainer type="person">
+		<email>gentoo@aisha.cc</email>
+		<name>Aisha Tammy</name>
+	</maintainer>
+	<maintainer type="project">
+		<email>sci@gentoo.org</email>
+		<name>Gentoo Science Project</name>
+	</maintainer>
+	<upstream>
+		<remote-id type="github">amd/libflame</remote-id>
+	</upstream>
+	<use>
+		<flag name="scc">Enable code that takes advantage of the SCC multicore architecture, recommended to use supermatrix if scc is enabled.</flag>
+		<flag name="supermatrix">Enable Ernie Chan's dependency-aware task scheduling and parallel execution system.</flag>
+	</use>
+</pkgmetadata>
diff --git a/sci-libs/libmatheval/Manifest b/sci-libs/libmatheval/Manifest
index 12875885d..abfd278d3 100644
--- a/sci-libs/libmatheval/Manifest
+++ b/sci-libs/libmatheval/Manifest
@@ -1 +1 @@
-DIST libmatheval-1.1.10.tar.gz 551835 BLAKE2B e7b4293d0f356021872c02cd2179f7e41bda622acc1aa67d25831cff53378b614f39b8a4d58d29a74ddcf749a3bc15f436fe99637c04b08724e074c648be598e SHA512 6e71431deed56ac2b1be560ecff590fc90e0bfe5a98e1ef7a58a3dd6be314fd52abb04e54b0de0055843c28ad63505c282a0f27f01f211c901654adbc4dfedb6
+DIST libmatheval-1.1.11.tar.gz 551770 BLAKE2B 65c5198a4ffc922b2a57e98720b26cd13319d32438f6960ec5fcd42e6911aadbc7444c7595c6d02e0dc9ec57d32dc4fc525964f727d5d7c90aca2c363e55a189 SHA512 854c35dce7c9a956ea1d7406ed6799375f039dc7305fea20af92d5b1c97b242d23716d0e83d2ff2daa89e3ca06669934a86684faf714a8458a569c5cde09953c
diff --git a/sci-libs/libmatheval/files/libmatheval-1.1.11_update_configure.ac.patch b/sci-libs/libmatheval/files/libmatheval-1.1.11_update_configure.ac.patch
new file mode 100644
index 000000000..0dd3a3abe
--- /dev/null
+++ b/sci-libs/libmatheval/files/libmatheval-1.1.11_update_configure.ac.patch
@@ -0,0 +1,40 @@
+Update configure.ac build script
+Remove references to guile which is only used for tests and breaks the package due to needing masked guile-1*
+sed command in ebuild removes references to these tests
+Taken from git repo which has updated the package: https://gitlab.com/Grimler/libmatheval/-/blob/master/configure.ac
+
+--- a/configure.ac
++++ b/configure.ac
+@@ -21,10 +21,8 @@ dnl Process this file with autoconf to produce a configure script.
+ AC_PREREQ(2.53)
+ AC_INIT([libmatheval],[1.1.11],[asamardzic@gnu.org])
+ AC_CONFIG_AUX_DIR([config])
+-AC_CONFIG_MACRO_DIR([m4])
+-AC_SUBST([ac_aux_dir])
+-AM_INIT_AUTOMAKE([libmatheval], [1.1.11])
+-AC_CONFIG_SRCDIR([configure.in])
++AC_CONFIG_MACRO_DIRS([m4])
++AM_INIT_AUTOMAKE
+ AM_CONFIG_HEADER([config.h])
+ 
+ dnl Initialize the test suite.
+@@ -44,7 +42,6 @@ AC_PROG_LIBTOOL
+ AC_PROG_MAKE_SET
+ AC_PROG_YACC
+ AM_MISSING_PROG([AUTOM4TE], [autom4te])
+-GUILE_FLAGS
+ 
+ dnl Checks for libraries.
+ 
+@@ -59,11 +56,5 @@ AC_TYPE_SIZE_T
+ dnl Checks for library functions.
+ AC_CHECK_FUNCS([bzero memset], [break])
+ 
+-dnl Additional Guile feature checks.
+-AC_CHECK_TYPE([scm_t_bits], [AC_DEFINE([HAVE_SCM_T_BITS], [1], [Define to 1 if you have the `scm_t_bits' type.])], [], [#include <libguile.h>])
+-AC_CHECK_LIB([guile], [scm_c_define_gsubr], [AC_DEFINE([HAVE_SCM_C_DEFINE_GSUBR], [1], [Define to 1 if you have the `scm_c_define_gsubr' function.])], [], [$GUILE_LDFLAGS])
+-AC_CHECK_LIB([guile], [scm_make_gsubr], [AC_DEFINE([HAVE_SCM_MAKE_GSUBR], [1], [Define to 1 if you have the `scm_make_gsubr' function.])], [], [$GUILE_LDFLAGS])
+-AC_CHECK_LIB([guile], [scm_num2dbl], [AC_DEFINE([HAVE_SCM_NUM2DBL], [1], [Define to 1 if you have the `scm_num2dbl' function.])], [], [$GUILE_LDFLAGS])
+-
+ AC_CONFIG_FILES([Makefile doc/Makefile lib/Makefile])
+ AC_OUTPUT(libmatheval.pc)
diff --git a/sci-libs/libmatheval/libmatheval-1.1.10.ebuild b/sci-libs/libmatheval/libmatheval-1.1.10.ebuild
deleted file mode 100644
index 9b0144249..000000000
--- a/sci-libs/libmatheval/libmatheval-1.1.10.ebuild
+++ /dev/null
@@ -1,16 +0,0 @@
-# Copyright 1999-2014 Gentoo Foundation
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=5
-
-inherit autotools-utils
-
-DESCRIPTION="library to parse and evaluate symbolic expressions"
-
-HOMEPAGE="http://www.gnu.org/software/libmatheval/"
-SRC_URI="mirror://gnu/${PN}/${PF}.tar.gz"
-
-LICENSE="GPL-2"
-SLOT="0"
-KEYWORDS="~amd64 ~x86"
-IUSE="static-libs"
diff --git a/sci-libs/libmatheval/libmatheval-1.1.11-r1.ebuild b/sci-libs/libmatheval/libmatheval-1.1.11-r1.ebuild
new file mode 100644
index 000000000..9fad1cafa
--- /dev/null
+++ b/sci-libs/libmatheval/libmatheval-1.1.11-r1.ebuild
@@ -0,0 +1,32 @@
+# Copyright 1999-2021 Gentoo Authors
+# Distributed under the terms of the GNU General Public License v2
+
+EAPI=8
+
+inherit autotools
+
+DESCRIPTION="library to parse and evaluate symbolic expressions"
+HOMEPAGE="https://www.gnu.org/software/libmatheval/"
+SRC_URI="mirror://gnu/${PN}/${P}.tar.gz"
+
+LICENSE="GPL-3+"
+SLOT="0"
+KEYWORDS="~amd64 ~x86"
+IUSE="static-libs"
+
+PATCHES=( "${FILESDIR}"/"${P}"_update_configure.ac.patch  )
+
+src_prepare() {
+	# rename configure.in -> configure.ac for Q/A
+	mv configure.in configure.ac || die
+	# patch configure.ac
+	default
+	# remove test subdirectory depends on masked guile-1*
+	# Bug: https://bugs.gentoo.org/755353
+	sed -e 's/SUBDIRS = doc lib tests/SUBDIRS = doc lib/' -i Makefile.am || die
+	eautoreconf
+}
+
+src_configure() {
+	econf $(use_enable static-libs static)
+}
diff --git a/sci-libs/libmatheval/libmatheval-1.1.11.ebuild b/sci-libs/libmatheval/libmatheval-1.1.11.ebuild
new file mode 100644
index 000000000..f5f072943
--- /dev/null
+++ b/sci-libs/libmatheval/libmatheval-1.1.11.ebuild
@@ -0,0 +1,12 @@
+# Copyright 1999-2021 Gentoo Authors
+# Distributed under the terms of the GNU General Public License v2
+
+EAPI=7
+
+DESCRIPTION="library to parse and evaluate symbolic expressions"
+HOMEPAGE="https://www.gnu.org/software/libmatheval/"
+SRC_URI="mirror://gnu/${PN}/${PF}.tar.gz"
+
+LICENSE="GPL-2"
+SLOT="0"
+KEYWORDS="~amd64 ~x86"
diff --git a/sci-libs/libmaus/Manifest b/sci-libs/libmaus/Manifest
deleted file mode 100644
index a23ba42e4..000000000
--- a/sci-libs/libmaus/Manifest
+++ /dev/null
@@ -1 +0,0 @@
-DIST 0.0.185-release-20141201090944.tar.gz 2492768 BLAKE2B 367659630a0c2ee72b501d75cd9f600ea8a1dfb387068c1d8ec6dc5655094776adfdaa098615226ce632940c188f9cd4979ba022200167355dd08a447d8ee477 SHA512 574a690a271f975c31604d88daed68bce86d130fc63e9bc69e711457ec05fa74e4caf901e98df7a6a85776cd0dae16c347b79ba8aa9b556bb217819cc94d9d8e
diff --git a/sci-libs/libmaus/libmaus-0.0.185.ebuild b/sci-libs/libmaus/libmaus-0.0.185.ebuild
deleted file mode 100644
index cac8548c2..000000000
--- a/sci-libs/libmaus/libmaus-0.0.185.ebuild
+++ /dev/null
@@ -1,17 +0,0 @@
-# Copyright 1999-2017 Gentoo Foundation
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=6
-
-FULLVER=${PV}-release-20141201090944
-
-DESCRIPTION="Library for biobambam"
-HOMEPAGE="https://github.com/gt1/libmaus"
-SRC_URI="https://github.com/gt1/libmaus/archive/${FULLVER}.tar.gz"
-
-LICENSE="GPL-3"
-SLOT="0"
-KEYWORDS="~x86"
-IUSE=""
-
-S="${WORKDIR}"/${PN}-${FULLVER}
diff --git a/sci-libs/libmaus/metadata.xml b/sci-libs/libmaus/metadata.xml
deleted file mode 100644
index 80f68639f..000000000
--- a/sci-libs/libmaus/metadata.xml
+++ /dev/null
@@ -1,20 +0,0 @@
-<?xml version="1.0" encoding="UTF-8"?>
-<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
-<pkgmetadata>
-	<maintainer type="project">
-		<email>sci-biology@gentoo.org</email>
-		<name>Gentoo Biology Project</name>
-	</maintainer>
-	<longdescription lang="en">
-libmaus is a collection of data structures and algorithms. It contains
-
-I/O classes (single byte and UTF-8)
-bitio classes (input, output and various forms of bit level manipulation)
-text indexing classes (suffix and LCP array, fulltext and minute (FM), ...)
-BAM sequence alignment files input/output (simple and collating)
-and many lower level support classes.
-</longdescription>
-	<upstream>
-		<remote-id type="github">gt1/libmaus</remote-id>
-	</upstream>
-</pkgmetadata>
diff --git a/sci-libs/libmaus2/Manifest b/sci-libs/libmaus2/Manifest
index 3b40b8924..0ba3165c0 100644
--- a/sci-libs/libmaus2/Manifest
+++ b/sci-libs/libmaus2/Manifest
@@ -1 +1 @@
-DIST libmaus2-2.0.587.tar.gz 3692835 BLAKE2B 624c19d065f4f383888baacf228c53c76f2ff63b425e251b82687a6932c89b069974771f0c15d5bb6d2054ecaa323f0d8c8562572d566044089315c12dd8a2e6 SHA512 f0df4832f8bf7104550ea348653664049d116dfec19132cff71046269e87a4b396f9325abe1a9bea549dd2880931bf68427704df60b88016ff74ab9ffed9ec3e
+DIST libmaus2-2.0.689.tar.gz 3479996 BLAKE2B 30aa0b43ba247e7724d1d8120a13a040f168d5eef1cd74d00a0ff5daa29f05d8991afddbfab8ab2dee0c0040f6c90331f12180a5ee26ab08b92581d63311a55b SHA512 8aedc71b29e8852b46f0eda4bcedbf746c1fbc7685fd96db91f7a66c77521c8af4f98a47ccf0f00672795b8573033bd2cd612cd4c188ed4354024ef717869b79
diff --git a/sci-libs/libmaus2/libmaus2-2.0.587.ebuild b/sci-libs/libmaus2/libmaus2-2.0.587.ebuild
deleted file mode 100644
index 1c61df056..000000000
--- a/sci-libs/libmaus2/libmaus2-2.0.587.ebuild
+++ /dev/null
@@ -1,41 +0,0 @@
-# Copyright 2019 Gentoo Authors
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=7
-
-inherit autotools
-
-DESCRIPTION="Library for biobambam2"
-HOMEPAGE="https://github.com/gt1/libmaus"
-SRC_URI="https://gitlab.com/german.tischler/libmaus2/-/archive/master/${P}.tar.gz"
-
-LICENSE="BSD-2 GPL-2 GPL-3 MIT ZLIB" # BUG: incomplete list of licenses, see AUTHORS
-SLOT="0"
-KEYWORDS="~amd64 ~x86"
-IUSE="cpu_flags_x86_ssse3 cpu_flags_x86_sse4_1 cpu_flags_x86_sse4_2"
-
-DEPEND="
-	!sci-libs/libmaus
-	>=sci-libs/io_lib-1.14.11
-	app-arch/snappy
-	sci-libs/fftw
-	sci-libs/hdf5
-	net-libs/gnutls
-	dev-libs/nettle"
-# --with-daligner
-# --with-irods
-S="${WORKDIR}"/libmaus2-master-27828cd78121d5e4b19c263c5527e462360f5901
-
-src_configure(){
-	local CONFIG_OPTS
-	use cpu_flags_x86_ssse3 && CONFIG_OPTS+=( --enable-ssse3 )
-	( use cpu_flags_x86_sse4_1 || use cpu_flags_x86_sse4_2 ) && CONFIG_OPTS+=( --enable-sse4 )
-	econf --with-snappy --with-io_lib $CONFIG_OPTS \
-		--with-lzma --with-gnutls --with-nettle --with-hdf5 --with-gmp --with-fftw
-}
-
-pkg_postinst(){
-	einfo "The io_lib, snappy dependencies are not strictly needed"
-	einfo "but were forced for optimal libmaus2 performance."
-	einfo "igzip is only used if gzip level is set to 11."
-}
diff --git a/sci-libs/libmaus2/libmaus2-2.0.689.ebuild b/sci-libs/libmaus2/libmaus2-2.0.689.ebuild
new file mode 100644
index 000000000..4b50c2030
--- /dev/null
+++ b/sci-libs/libmaus2/libmaus2-2.0.689.ebuild
@@ -0,0 +1,40 @@
+# Copyright 2019-2021 Gentoo Authors
+# Distributed under the terms of the GNU General Public License v2
+
+EAPI=7
+
+release_data="20191120141844"
+DESCRIPTION="Library for biobambam2"
+HOMEPAGE="https://github.com/gt1/libmaus"
+SRC_URI="https://gitlab.com/german.tischler/${PN}/-/archive/${PV}-release-${release_data}/${P}-release-${release_data}.tar.gz -> ${P}.tar.gz"
+
+LICENSE="BSD-2 GPL-2 GPL-3 MIT ZLIB" # BUG: incomplete list of licenses, see AUTHORS
+SLOT="0"
+KEYWORDS="~amd64 ~x86"
+IUSE="cpu_flags_x86_ssse3 cpu_flags_x86_sse4_1 cpu_flags_x86_sse4_2"
+
+DEPEND="
+	app-arch/snappy
+	sci-libs/fftw
+	sci-libs/hdf5
+	net-libs/gnutls
+	dev-libs/nettle"
+# --with-daligner
+# --with-irods
+S="${WORKDIR}/${P}-release-${release_data}"
+
+src_configure(){
+	local CONFIG_OPTS
+	use cpu_flags_x86_ssse3 && CONFIG_OPTS+=( --enable-ssse3 )
+	( use cpu_flags_x86_sse4_1 || use cpu_flags_x86_sse4_2 ) && CONFIG_OPTS+=( --enable-sse4 )
+	econf --with-snappy $CONFIG_OPTS \
+		--with-lzma --with-gnutls --with-nettle --with-hdf5 --with-gmp --with-fftw
+	# --with-io_lib
+	# will require >=sci-libs/io_lib-1.14.11 which is not yet available in ::gentoo
+}
+
+pkg_postinst(){
+	einfo "The snappy dependency is not strictly needed"
+	einfo "but were forced for optimal libmaus2 performance."
+	einfo "igzip is only used if gzip level is set to 11."
+}
diff --git a/sci-libs/libmaus2/libmaus2-9999.ebuild b/sci-libs/libmaus2/libmaus2-9999.ebuild
index c371d5432..d2cbd9439 100644
--- a/sci-libs/libmaus2/libmaus2-9999.ebuild
+++ b/sci-libs/libmaus2/libmaus2-9999.ebuild
@@ -1,4 +1,4 @@
-# Copyright 2019 Gentoo Authors
+# Copyright 2019-2020 Gentoo Authors
 # Distributed under the terms of the GNU General Public License v2
 
 EAPI=7
@@ -15,8 +15,6 @@ KEYWORDS=""
 IUSE="cpu_flags_x86_ssse3 cpu_flags_x86_sse4_1 cpu_flags_x86_sse4_2"
 
 DEPEND="
-	!sci-libs/libmaus
-	>=sci-libs/io_lib-1.14.11
 	app-arch/snappy
 	sci-libs/fftw
 	sci-libs/hdf5
@@ -34,12 +32,14 @@ src_configure(){
 	local CONFIG_OPTS
 	use cpu_flags_x86_ssse3 && CONFIG_OPTS+=( --enable-ssse3 )
 	( use cpu_flags_x86_sse4_1 || use cpu_flags_x86_sse4_2 ) && CONFIG_OPTS+=( --enable-sse4 )
-	econf --with-snappy --with-io_lib $CONFIG_OPTS \
+	econf --with-snappy $CONFIG_OPTS \
 		--with-lzma --with-gnutls --with-nettle --with-hdf5 --with-gmp --with-fftw
+	# --with-io_lib
+	# will require >=sci-libs/io_lib-1.14.11 which is not yet available in ::gentoo
 }
 
 pkg_postinst(){
-	einfo "The io_lib, snappy dependencies are not strictly needed"
+	einfo "The snappy dependency is not strictly needed"
 	einfo "but were forced for optimal libmaus2 performance."
 	einfo "igzip is only used if gzip level is set to 11."
 }
diff --git a/sci-libs/libmaus2/metadata.xml b/sci-libs/libmaus2/metadata.xml
index 80f68639f..4b4685854 100644
--- a/sci-libs/libmaus2/metadata.xml
+++ b/sci-libs/libmaus2/metadata.xml
@@ -15,6 +15,6 @@ BAM sequence alignment files input/output (simple and collating)
 and many lower level support classes.
 </longdescription>
 	<upstream>
-		<remote-id type="github">gt1/libmaus</remote-id>
+		<remote-id type="gitlab">german.tischler/libmaus2</remote-id>
 	</upstream>
 </pkgmetadata>
diff --git a/sci-libs/libmed/Manifest b/sci-libs/libmed/Manifest
deleted file mode 100644
index 161dc1e35..000000000
--- a/sci-libs/libmed/Manifest
+++ /dev/null
@@ -1 +0,0 @@
-DIST med-3.1.0.tar.gz 57313780 BLAKE2B 44de0c8752391f9f689886b8483c7516fb8ea4de4a61351956e2f1e065a5540803f048f9f3378c0c4478ec17b44cc70559fff29d79a0125d4475612b972387ef SHA512 c46933e12182144632e788cae1e1f00599c8ef03e2ff94310f8227bc3d7912e1cd7c2b449c83517dfcbb07634f432092f48c0a91486eca498013e764ac935983
diff --git a/sci-libs/libmed/files/libmed-3.1.0-cmake-fortran.patch b/sci-libs/libmed/files/libmed-3.1.0-cmake-fortran.patch
deleted file mode 100644
index 490c14aee..000000000
--- a/sci-libs/libmed/files/libmed-3.1.0-cmake-fortran.patch
+++ /dev/null
@@ -1,20 +0,0 @@
-Make cmake properly disable fortran upon user requirments
-
---- ./CMakeLists.txt.orig	2016-07-01 15:28:57.139304608 +0300
-+++ ./CMakeLists.txt	2016-07-01 15:34:22.295899455 +0300
-@@ -8,10 +8,13 @@
- 
- INCLUDE(CheckLanguage)
- CHECK_LANGUAGE(Fortran)
--IF(CMAKE_Fortran_COMPILER)
-+OPTION (MEDFILE_BUILD_FORTRAN "Build fortran library" ON)
-+IF(MEDFILE_BUILD_FORTRAN)
-   ENABLE_LANGUAGE(Fortran)
-+  IF(NOT CMAKE_Fortran_COMPILER)
-+      MESSAGE(FATAL_EROOR "Fortran support was requested but not found")
-+  ENDIF()
- ELSE()
--  MESSAGE(STATUS "No Fortran support")
- ENDIF()
- 
- ## Version number 
diff --git a/sci-libs/libmed/files/libmed-3.1.0-fix-swig-build.patch b/sci-libs/libmed/files/libmed-3.1.0-fix-swig-build.patch
deleted file mode 100644
index cd6b230c6..000000000
--- a/sci-libs/libmed/files/libmed-3.1.0-fix-swig-build.patch
+++ /dev/null
@@ -1,19 +0,0 @@
-Fix wierd typedefs macroses in the header witch made swing to fail
-
-diff --git a/include/H5public_extract.h.in b/include/H5public_extract.h.in
-index ba07342..28318f4 100644
---- a/include/H5public_extract.h.in
-+++ b/include/H5public_extract.h.in
-@@ -28,9 +28,9 @@ extern "C" {
- @HDF5_TYPEDEF_HID_T@
- @HDF5_TYPEDEF_HSIZE_T@
- 
--#typedef int herr_t;
--#typedef int hid_t;
--#typedef unsigned long long   hsize_t;
-+typedef int herr_t;
-+typedef int hid_t;
-+typedef unsigned long long   hsize_t;
- 
- #ifdef __cplusplus
- }
diff --git a/sci-libs/libmed/libmed-3.1.0.ebuild b/sci-libs/libmed/libmed-3.1.0.ebuild
deleted file mode 100644
index 504add91f..000000000
--- a/sci-libs/libmed/libmed-3.1.0.ebuild
+++ /dev/null
@@ -1,63 +0,0 @@
-# Copyright 1999-2016 Gentoo Foundation
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=6
-
-FORTRAN_NEEDED=fortran
-# NOTE:The build for multiple python versions should be possible but complecated for the build system
-PYTHON_COMPAT=( python2_7 python3_{3,4,5} )
-
-inherit eutils toolchain-funcs fortran-2 python-single-r1 cmake-utils
-
-MY_P="med-${PV}"
-
-DESCRIPTION="A library to store and exchange meshed data or computation results"
-HOMEPAGE="http://www.salome-platform.org/"
-SRC_URI="http://files.salome-platform.org/Salome/other/${MY_P}.tar.gz"
-
-LICENSE="GPL-3 LGPL-3"
-SLOT="0"
-KEYWORDS="~amd64 ~x86"
-IUSE="doc fortran python static-libs test"
-
-REQUIRED_USE="python? ( ${PYTHON_REQUIRED_USE} )"
-RDEPEND="
-	sci-libs/hdf5[fortran=]
-	sys-cluster/openmpi[fortran=]
-	python? ( ${PYTHON_DEPS} )
-"
-DEPEND="${RDEPEND}
-	python? ( >=dev-lang/swig-2.0.9:0 )
-"
-
-S=${WORKDIR}/${MY_P}_SRC
-
-PATCHES=(
-	"${FILESDIR}/${P}-cmake-fortran.patch"
-	"${FILESDIR}/${P}-fix-swig-build.patch"
-)
-
-DOCS=( AUTHORS ChangeLog INSTALL README )
-
-pkg_setup() {
-	use python && python-single-r1_pkg_setup
-	use fortran && fortran-2_pkg_setup
-}
-
-src_configure() {
-	local mycmakeargs=(
-		-DMEDFILE_BUILD_FORTRAN="$(usex fortran)"
-		-DMEDFILE_BUILD_STATIC_LIBS="$(usex static-libs)"
-		-DMEDFILE_INSTALL_DOC="$(usex doc)"
-		-DMEDFILE_BUILD_PYTHON="$(usex python)"
-		-DMEDFILE_BUILD_TESTS="$(usex test)"
-	)
-
-	cmake-utils_src_configure
-}
-
-src_install() {
-	cmake-utils_src_install
-	# Prevent test executables being installed
-	use test && rm -rf "${D}/usr/bin/"{testc,testf}
-}
diff --git a/sci-libs/libmed/metadata.xml b/sci-libs/libmed/metadata.xml
deleted file mode 100644
index ae9640ffb..000000000
--- a/sci-libs/libmed/metadata.xml
+++ /dev/null
@@ -1,8 +0,0 @@
-<?xml version="1.0" encoding="UTF-8"?>
-<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
-<pkgmetadata>
-	<maintainer type="project">
-		<email>sci@gentoo.org</email>
-		<name>Gentoo Science Project</name>
-	</maintainer>
-</pkgmetadata>
diff --git a/sci-libs/libspatialindex/Manifest b/sci-libs/libspatialindex/Manifest
deleted file mode 100644
index 5ecea354f..000000000
--- a/sci-libs/libspatialindex/Manifest
+++ /dev/null
@@ -1 +0,0 @@
-DIST spatialindex-src-1.8.5.tar.bz2 407871 BLAKE2B 936d0fc4950b4c685088c84019aa22e720371c623bd1883725dc497380e90072333c25f979e13fbc91b7d164b87cb21a285c037bdbe0b8df84eb3876590e8dd1 SHA512 d3e47982cc2809d04490fae27796b31cdb59675790010d8b45e1a98b5a23048a4a44e321a2470dd36c01aba6f6e7620cafc4988a02b55e4f59d1b7fa9b588b06
diff --git a/sci-libs/libspatialindex/files/libspatialindex-1.8.1-QA.patch b/sci-libs/libspatialindex/files/libspatialindex-1.8.1-QA.patch
deleted file mode 100644
index 446452dc9..000000000
--- a/sci-libs/libspatialindex/files/libspatialindex-1.8.1-QA.patch
+++ /dev/null
@@ -1,15 +0,0 @@
---- spatialindex-src-1.8.0/configure.ac
-+++ spatialindex-src-1.8.0/configure.ac
-@@ -49,10 +49,10 @@
- AC_ARG_ENABLE(debug, [  --enable-debug=[no/yes] turn on debugging [default=$debug_default]],, enable_debug=$debug_default)
- 
- if test "x$enable_debug" = "xyes"; then
--	CXXFLAGS="$CXXFLAGS -g -DDEBUG"
-+	CXXFLAGS="$CXXFLAGS -DDEBUG"
- 	AC_MSG_RESULT(checking wether debug information is enabled... yes)
- else
--	CXXFLAGS="$CXXFLAGS -O2 -DNDEBUG"
-+	CXXFLAGS="$CXXFLAGS -DNDEBUG"
- 	AC_MSG_RESULT(checking wether debug information is enabled... no)
- fi
- 
diff --git a/sci-libs/libspatialindex/libspatialindex-1.8.5.ebuild b/sci-libs/libspatialindex/libspatialindex-1.8.5.ebuild
deleted file mode 100644
index fcaab8bc9..000000000
--- a/sci-libs/libspatialindex/libspatialindex-1.8.5.ebuild
+++ /dev/null
@@ -1,31 +0,0 @@
-# Copyright 1999-2015 Gentoo Foundation
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=5
-
-AUTOTOOLS_AUTORECONF=yes
-
-inherit autotools-utils
-
-MY_PN="spatialindex-src"
-MY_P="${MY_PN}-${PV}"
-
-DESCRIPTION="General framework for developing spatial indices"
-HOMEPAGE="http://libspatialindex.github.com/"
-SRC_URI="http://download.osgeo.org/libspatialindex/${MY_P}.tar.bz2"
-
-SLOT="0/4"
-LICENSE="MIT"
-KEYWORDS="~amd64 ~x86"
-IUSE="debug static-libs"
-
-S=${WORKDIR}/${MY_P}
-
-PATCHES=( "${FILESDIR}"/${PN}-1.8.1-QA.patch )
-
-AUTOTOOLS_IN_SOURCE_BUILD=1
-
-src_configure() {
-	local myeconfargs=( $(use_enable debug) )
-	autotools-utils_src_configure
-}
diff --git a/sci-libs/libspatialindex/metadata.xml b/sci-libs/libspatialindex/metadata.xml
deleted file mode 100644
index c874fefce..000000000
--- a/sci-libs/libspatialindex/metadata.xml
+++ /dev/null
@@ -1,12 +0,0 @@
-<?xml version="1.0" encoding="UTF-8"?>
-<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
-<pkgmetadata>
-	<maintainer type="person">
-		<email>hasufell@posteo.de</email>
-		<name>Julian Ospald</name>
-	</maintainer>
-	<maintainer type="project">
-		<email>sci-geosciences@gentoo.org</email>
-		<name>Gentoo Geosciences Project</name>
-	</maintainer>
-</pkgmetadata>
diff --git a/sci-libs/libsufr/Manifest b/sci-libs/libsufr/Manifest
index afcb17fac..2ba7a16c9 100644
--- a/sci-libs/libsufr/Manifest
+++ b/sci-libs/libsufr/Manifest
@@ -1,3 +1 @@
-DIST libsufr-0.5.4.tar.gz 59469 BLAKE2B e20d51eef5e41719d46e68b401264609cb22455ab59fe336370ee066589c5b15c75d6d06dd02588ccafd46b664845abfbc4db1210e9b1b2d887df07b52e5cce2 SHA512 3711af7db10398e8dcb92982d4fedcc866fa5257f8a3b108ad1a5caef174fa4c0c9ed0b4e3e3b620d0e0d5f4cdaa56691c9657e57980c27a7aef00e45fcdd773
-DIST libsufr-0.6.3.tar.gz 65861 BLAKE2B 97e132252acbb39d54b8c73b1bc80933d957309c2f39be4b20a5ecb4570b7db8b6a473434698462d67fac07174c1984027b42a72d380fc95a3fc603b0f53734b SHA512 e7ba094a5891d7f08dd9bfe4670d45378973bbabae289465c54436886fa1e2e66da8106a3abad86b33f494970bf2afe3727ef6f56f7177f7c5ca536ff3e55ecf
-DIST libsufr-0.6.4.tar.gz 66073 BLAKE2B 5d66e14d0fadf6239141af9863647f33205c850715b01a4ceb14f275c141560aad62a4a84b4818e1a43a50e11c3761627a5a4838282d731c9acdb7a4419651f2 SHA512 cf3f610d418664265e854a8a2def0fce11918748231eec025a43c72a172481a8d1336b30c204ef43ea1e0cf44353f2e0083992d6417a94ccd9445dd184b24fc7
+DIST libsufr-0.7.7.tar.gz 207409 BLAKE2B ba366ee8ce19c6b4fed0d45cf8bde39bc9589f46e4e428cc0346966f76e8a185edec6947fb14a5ff63414b3c08b8df56c2367b4f47fe53ed96ae0d26e1d67951 SHA512 c24cb69361f8db31396e554a48eb864b7cc2c8ac437b2c0d3113e02adf9a53017973e2ff49cc9a7a6debeaaea5d9f20c8aa8d505b23e1974f19b3560fded9ca4
diff --git a/sci-libs/libsufr/libsufr-0.5.4.ebuild b/sci-libs/libsufr/libsufr-0.5.4.ebuild
deleted file mode 100644
index 0131c6629..000000000
--- a/sci-libs/libsufr/libsufr-0.5.4.ebuild
+++ /dev/null
@@ -1,27 +0,0 @@
-# Copyright 1999-2014 Gentoo Foundation
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=5
-
-inherit cmake-utils fortran-2
-
-DESCRIPTION="LIBrary of Some Useful Fortran Routines"
-HOMEPAGE="http://libsufr.sourceforge.net/"
-SRC_URI="mirror://sourceforge/${PN}/${P}.tar.gz"
-
-LICENSE="GPL-3"
-SLOT="0"
-KEYWORDS="~amd64 ~x86"
-IUSE="static-libs"
-
-DEPEND="virtual/fortran"
-RDEPEND="${DEPEND}"
-
-src_configure() {
-	mycmakeargs=(
-		$(cmake-utils_use static-libs CREATE_STATICLIB)
-	)
-	cmake-utils_src_configure
-}
-
-DOCS="CHANGELOG README VERSION"
diff --git a/sci-libs/libsufr/libsufr-0.6.3.ebuild b/sci-libs/libsufr/libsufr-0.6.3.ebuild
deleted file mode 100644
index 2502a7f4b..000000000
--- a/sci-libs/libsufr/libsufr-0.6.3.ebuild
+++ /dev/null
@@ -1,27 +0,0 @@
-# Copyright 1999-2015 Gentoo Foundation
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=5
-
-inherit cmake-utils fortran-2
-
-DESCRIPTION="LIBrary of Some Useful Fortran Routines"
-HOMEPAGE="http://libsufr.sourceforge.net/"
-SRC_URI="mirror://sourceforge/${PN}/${P}.tar.gz"
-
-LICENSE="GPL-3"
-SLOT="0"
-KEYWORDS="~amd64 ~x86"
-IUSE="static-libs"
-
-DEPEND="virtual/fortran"
-RDEPEND="${DEPEND}"
-
-src_configure() {
-	mycmakeargs=(
-		$(cmake-utils_use static-libs CREATE_STATICLIB)
-	)
-	cmake-utils_src_configure
-}
-
-DOCS="CHANGELOG README VERSION"
diff --git a/sci-libs/libsufr/libsufr-0.6.4.ebuild b/sci-libs/libsufr/libsufr-0.6.4.ebuild
deleted file mode 100644
index 2502a7f4b..000000000
--- a/sci-libs/libsufr/libsufr-0.6.4.ebuild
+++ /dev/null
@@ -1,27 +0,0 @@
-# Copyright 1999-2015 Gentoo Foundation
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=5
-
-inherit cmake-utils fortran-2
-
-DESCRIPTION="LIBrary of Some Useful Fortran Routines"
-HOMEPAGE="http://libsufr.sourceforge.net/"
-SRC_URI="mirror://sourceforge/${PN}/${P}.tar.gz"
-
-LICENSE="GPL-3"
-SLOT="0"
-KEYWORDS="~amd64 ~x86"
-IUSE="static-libs"
-
-DEPEND="virtual/fortran"
-RDEPEND="${DEPEND}"
-
-src_configure() {
-	mycmakeargs=(
-		$(cmake-utils_use static-libs CREATE_STATICLIB)
-	)
-	cmake-utils_src_configure
-}
-
-DOCS="CHANGELOG README VERSION"
diff --git a/sci-libs/libsufr/libsufr-0.7.7.ebuild b/sci-libs/libsufr/libsufr-0.7.7.ebuild
new file mode 100644
index 000000000..cd49de6b5
--- /dev/null
+++ b/sci-libs/libsufr/libsufr-0.7.7.ebuild
@@ -0,0 +1,36 @@
+# Copyright 1999-2022 Gentoo Authors
+# Distributed under the terms of the GNU General Public License v2
+
+EAPI=8
+
+CMAKE_BUILD_TYPE=Release
+CMAKE_MAKEFILE_GENERATOR="emake"
+inherit cmake fortran-2
+
+DESCRIPTION="LIBrary of Some Useful Fortran Routines"
+HOMEPAGE="http://libsufr.sourceforge.net/"
+SRC_URI="https://downloads.sourceforge.net/${PN}/${P}.tar.gz"
+
+LICENSE="GPL-3"
+SLOT="0"
+KEYWORDS="~amd64 ~x86"
+IUSE="static-libs"
+
+DEPEND="virtual/fortran"
+RDEPEND="${DEPEND}"
+
+DOCS=( "CHANGELOG" "README" "VERSION" )
+
+src_unpack() {
+	default
+	gunzip -r "${S}"/man || die
+}
+
+src_configure() {
+	local mycmakeargs=(
+		-DCMAKE_VERBOSE_MAKEFILE=ON
+		-DCREATE_SHAREDLIB=ON
+		-DCREATE_STATICLIB=$(usex static-libs)
+	)
+	cmake_src_configure
+}
diff --git a/sci-libs/libsufr/metadata.xml b/sci-libs/libsufr/metadata.xml
index 784cc759a..eff9aab5c 100644
--- a/sci-libs/libsufr/metadata.xml
+++ b/sci-libs/libsufr/metadata.xml
@@ -2,12 +2,8 @@
 <!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
 <pkgmetadata>
 	<maintainer type="person">
-		<email>AstroFloyd@gmail.com</email>
-		<name>AstroFloyd</name>
-	</maintainer>
-	<maintainer type="person">
-		<email>xarthisius@gentoo.org</email>
-		<name>Kacper Kowalik</name>
+		<email>git@vandersluys.nl</email>
+		<name>MarcvdSluys</name>
 	</maintainer>
 	<maintainer type="project">
 		<email>sci@gentoo.org</email>
diff --git a/sci-libs/lwpr/lwpr-1.2.5.ebuild b/sci-libs/lwpr/lwpr-1.2.5.ebuild
index 9ae5de227..2f040a86e 100644
--- a/sci-libs/lwpr/lwpr-1.2.5.ebuild
+++ b/sci-libs/lwpr/lwpr-1.2.5.ebuild
@@ -1,47 +1,44 @@
-# Copyright 1999-2014 Gentoo Foundation
+# Copyright 1999-2021 Gentoo Authors
 # Distributed under the terms of the GNU General Public License v2
 
-EAPI=5
+EAPI=7
 
-AUTOTOOLS_IN_SOURCE_BUILD=1
-inherit autotools-utils
+DOCS_BUILDER="doxygen"
+
+inherit docs
 
 DESCRIPTION="The Locally Weighted Projection Regression Library"
-HOMEPAGE="http://www.ipab.inf.ed.ac.uk/slmc/software/lwpr/"
-SRC_URI="mirror://sourceforge/${PN}/${P}.tar.gz"
+HOMEPAGE="https://web.inf.ed.ac.uk/slmc"
+SRC_URI="https://downloads.sourceforge.net/${PN}/${P}.tar.gz"
 
 LICENSE="LGPL-2.1"
 SLOT="0"
 KEYWORDS="~amd64 ~x86 ~amd64-linux ~x86-linux"
-IUSE="doc examples octave static-libs"
+IUSE="examples octave static-libs"
 
-RDEPEND="
-	octave? ( >=sci-mathematics/octave-3 )"
-DEPEND="${RDEPEND}
-	doc? ( app-doc/doxygen )"
+RDEPEND="octave? ( >=sci-mathematics/octave-3 )"
+DEPEND="${RDEPEND}"
 
 src_configure() {
-	local myeconfargs=(
-		--enable-threads=3
-		$(use_with octave octave "$(octave-config -p PREFIX)")
-	)
-	autotools-utils_src_configure
+	econf \
+		--enable-threads=3 \
+		$(use_with octave octave)
 }
 
 src_compile() {
-	autotools-utils_src_compile
-	if use doc; then
-		doxygen Doxyfile || die "doxygen failed"
-	fi
+	default
+	docs_compile
 }
 
 src_install() {
-	autotools-utils_src_install \
-		 mexflags="-DMATLAB -I../include -L./.libs -llwproctave"
-	use doc && dodoc doc/lwpr_doc.pdf && dohtml html/*
+	default
+	if use doc; then
+	dodoc doc/lwpr_doc.pdf
+	dodoc html/*
+	fi
 	if use examples ; then
-		insinto /usr/share/doc/${PF}/examples
-		doins example_c/cross.c example_cpp/cross.cc
+		docinto /usr/share/doc/${PF}/examples
+		dodoc example_c/cross.c example_cpp/cross.cc
 	fi
 	if use octave; then
 		insinto /usr/share/octave/packages/${P}
diff --git a/sci-libs/matc/Manifest b/sci-libs/matc/Manifest
deleted file mode 100644
index 1daa9eefc..000000000
--- a/sci-libs/matc/Manifest
+++ /dev/null
@@ -1,3 +0,0 @@
-DIST MATCManual.pdf 103341 SHA256 a49945c6965cdb28dfaa98f36d46813a56c7f792c4b5634d02e6afc0ae361e9c SHA512 0f9efea84ed2f6848c431b0a9647c8d300b3bcf06a83c4f6bc7cd3640ec5fc003516b442f90b022a246b3cac54f2cdac1118283e929d2c9547f5469f2b9912cb WHIRLPOOL 27eedcf4b62cedacaaa8821d87e2d2ee8a0623cf7e48f99c3310e292d0ee5a3f412546e8cbfcce34a274cf318be2b86c96af6053ff2add24c7c8569a75f670fd
-DIST matc-6.0_p4651.tar.gz 203543 SHA256 b174036ebafa2d0bff51db283831e4f9a165e6fa9798224dc3658dc2dc5e99b1 SHA512 ada3e4a1d02a0125ee5ccb7a791975d3f728d89ff21fac6461060e4458b086edb34adef058f3aa84f924f28b7d652a539d63f61d9bfce208d0b8540b812ef7be WHIRLPOOL b47b025bff1fbb88ccbabb0c42a8656c905f09ce4345c12cd83e8effb6b9c12f5cfece69741c2655fc3c60dd4e652a9867c14989d9043ae23b338815f800927a
-DIST matc-8.0.tar.gz 45051199 BLAKE2B 221e68c46c7340e2a5bf829ade317bdf5a5908941dea9f123a7d15dbf3472d73a59007ba6522d12a0fd40d506c737ac16daf3886050d7a6bce6829e4a3a336a3 SHA512 bc34c6dbbdb2c24f2110d377e02c4515cb4886de36b30bc3caf79c9b954e5b7ba81cabedaa35fad1802287c396ab88ef074505efc904411061f7c98c9bea3497
diff --git a/sci-libs/matc/files/matc-6.0_p4651-shared.patch b/sci-libs/matc/files/matc-6.0_p4651-shared.patch
deleted file mode 100644
index a2287dabb..000000000
--- a/sci-libs/matc/files/matc-6.0_p4651-shared.patch
+++ /dev/null
@@ -1,32 +0,0 @@
- configure.in    | 2 +-
- src/Makefile.am | 6 +++---
- 2 files changed, 4 insertions(+), 4 deletions(-)
-
-diff --git a/configure.in b/configure.in
-index 3e5cd27..1d8b065 100755
---- a/configure.in
-+++ b/configure.in
-@@ -4,7 +4,7 @@ dnl TODO: get fortran name mangling sceme and use it in the fortran api (spfortr
- dnl using the convenience macros provided by automake
- 
- AC_INIT(src/eig.c)
--
-+LT_INIT
- AC_CANONICAL_HOST
- AC_CANONICAL_TARGET
- 
-diff --git a/src/Makefile.am b/src/Makefile.am
-index 2e39c11..e10a91d 100755
---- a/src/Makefile.am
-+++ b/src/Makefile.am
-@@ -45,7 +45,7 @@ matc_SOURCES = main.c
- 
- endif
- 
--matc_LDADD = libmatc.a
-+matc_LDADD = libmatc.la
- 
--lib_LIBRARIES = libmatc.a
--libmatc_a_SOURCES = $(COMMON_SRCS)
-+lib_LTLIBRARIES = libmatc.la
-+libmatc_la_SOURCES = $(COMMON_SRCS)
diff --git a/sci-libs/matc/matc-6.0_p4651.ebuild b/sci-libs/matc/matc-6.0_p4651.ebuild
deleted file mode 100644
index c0234a2ef..000000000
--- a/sci-libs/matc/matc-6.0_p4651.ebuild
+++ /dev/null
@@ -1,43 +0,0 @@
-# Copyright 1999-2015 Gentoo Foundation
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=5
-
-AUTOTOOLS_AUTORECONF=true
-
-inherit autotools-utils
-
-ELMER_ROOT="elmerfem"
-MY_PN=${PN/elmer-/}
-
-DESCRIPTION="Finite element programs, libraries, and visualization tools - math C library"
-HOMEPAGE="http://www.csc.fi/english/pages/elmer"
-SRC_URI="
-	http://elmerfem.svn.sourceforge.net/viewvc/${ELMER_ROOT}/release/${PV%_p*}/${MY_PN}/?view=tar&pathrev=4651 -> ${P}.tar.gz
-	doc? ( http://www.nic.funet.fi/pub/sci/physics/elmer/doc/MATCManual.pdf )"
-
-LICENSE="GPL-2"
-SLOT="0"
-KEYWORDS="~amd64 ~x86"
-IUSE="doc debug static-libs"
-
-RDEPEND="
-	sys-libs/ncurses:0=
-	sys-libs/readline:0="
-DEPEND="${RDEPEND}"
-
-S="${WORKDIR}"/${PN}
-
-PATCHES=( "${FILESDIR}"/${P}-shared.patch )
-
-src_configure() {
-	local myeconfargs=(
-		$(use_with debug)
-	)
-	autotools-utils_src_configure
-}
-
-src_install() {
-	use doc && DOCS=( "${DISTDIR}"/MATCManual.pdf )
-	autotools-utils_src_install
-}
diff --git a/sci-libs/matc/matc-8.0.ebuild b/sci-libs/matc/matc-8.0.ebuild
deleted file mode 100644
index 8b7686f8d..000000000
--- a/sci-libs/matc/matc-8.0.ebuild
+++ /dev/null
@@ -1,40 +0,0 @@
-# Copyright 1999-2015 Gentoo Foundation
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=5
-
-AUTOTOOLS_AUTORECONF=true
-
-inherit autotools-utils
-
-DESCRIPTION="Finite element programs, libraries, and visualization tools - math C library"
-HOMEPAGE="http://www.csc.fi/english/pages/elmer"
-SRC_URI="
-	https://github.com/ElmerCSC/elmerfem/archive/release-${PV}.tar.gz -> ${P}.tar.gz
-	doc? ( http://www.nic.funet.fi/pub/sci/physics/elmer/doc/MATCManual.pdf )"
-
-LICENSE="GPL-2 LGPL-2.1"
-SLOT="0"
-KEYWORDS="~amd64 ~x86"
-IUSE="doc debug static-libs"
-
-RDEPEND="
-	sys-libs/ncurses:0=
-	sys-libs/readline:0="
-DEPEND="${RDEPEND}"
-
-S="${WORKDIR}/elmerfem-release-${PV}/${PN}"
-
-#PATCHES=( "${FILESDIR}"/${P}-shared.patch )
-
-src_configure() {
-	local myeconfargs=(
-		$(use_with debug)
-	)
-	autotools-utils_src_configure
-}
-
-src_install() {
-	use doc && DOCS=( "${DISTDIR}"/MATCManual.pdf )
-	autotools-utils_src_install
-}
diff --git a/sci-libs/matc/matc-9999.ebuild b/sci-libs/matc/matc-9999.ebuild
deleted file mode 100644
index 7c520a9ff..000000000
--- a/sci-libs/matc/matc-9999.ebuild
+++ /dev/null
@@ -1,42 +0,0 @@
-# Copyright 1999-2015 Gentoo Foundation
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=5
-
-AUTOTOOLS_AUTORECONF=true
-
-inherit autotools-utils git-r3
-
-ELMER_ROOT="elmerfem"
-MY_PN=${PN/elmer-/}
-
-DESCRIPTION="Finite element programs, libraries, and visualization tools - math C library"
-HOMEPAGE="http://www.csc.fi/english/pages/elmer"
-SRC_URI="doc? ( http://www.nic.funet.fi/pub/sci/physics/elmer/doc/MATCManual.pdf )"
-EGIT_REPO_URI="https://github.com/ElmerCSC/elmerfem.git git://github.com/ElmerCSC/elmerfem.git"
-
-LICENSE="GPL-2 LGPL-2.1"
-SLOT="0"
-KEYWORDS=""
-IUSE="doc debug static-libs"
-
-RDEPEND="
-	sys-libs/ncurses:0=
-	sys-libs/readline:0="
-DEPEND="${RDEPEND}"
-
-S="${WORKDIR}/${P}/${PN}"
-
-#PATCHES=( "${FILESDIR}"/${PN}-6.0_p4651-shared.patch )
-
-src_configure() {
-	local myeconfargs=(
-		$(use_with debug)
-	)
-	autotools-utils_src_configure
-}
-
-src_install() {
-	use doc && DOCS=( "${DISTDIR}"/MATCManual.pdf )
-	autotools-utils_src_install
-}
diff --git a/sci-libs/matc/metadata.xml b/sci-libs/matc/metadata.xml
deleted file mode 100644
index 70c9ebc20..000000000
--- a/sci-libs/matc/metadata.xml
+++ /dev/null
@@ -1,12 +0,0 @@
-<?xml version="1.0" encoding="UTF-8"?>
-<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
-<pkgmetadata>
-	<maintainer type="project">
-		<email>sci@gentoo.org</email>
-		<name>Gentoo Science Project</name>
-	</maintainer>
-	<upstream>
-		<remote-id type="github">ElmerCSC/elmerfem</remote-id>
-		<remote-id type="sourceforge">svn</remote-id>
-	</upstream>
-</pkgmetadata>
diff --git a/sci-libs/med/Manifest b/sci-libs/med/Manifest
deleted file mode 100644
index ba004499a..000000000
--- a/sci-libs/med/Manifest
+++ /dev/null
@@ -1 +0,0 @@
-DIST med-fichier_2.3.6.orig.tar.gz 2286615 SHA256 bccf533b4b9ea9ff2a2ad937466aa5304bd44f7bdc3d58aff74f9d6ce17e64ef SHA512 d49d5a3d625918668c21521624fbfcbef431b07efdbf80e3916b4a4787e46c66637cb12350160f8d4f9a691131b200d7c96767c8572824f1bdd9cc0437e48028 WHIRLPOOL 81472f705a9c9c7a1cf89e3fb2462ca6087b6cc771bf976427797ee0799f52df05138c334841328b1510cea2084fd7a83c001e4bc3e8de92178ab750d71fe0a1
diff --git a/sci-libs/med/files/med-2.3.5-gcc-4.3.patch b/sci-libs/med/files/med-2.3.5-gcc-4.3.patch
deleted file mode 100644
index 106e5febc..000000000
--- a/sci-libs/med/files/med-2.3.5-gcc-4.3.patch
+++ /dev/null
@@ -1,22 +0,0 @@
-diff -aur med-2.3.5.old/tools/medimport/include/MAJ_21_22.h med-2.3.5/tools/medimport/include/MAJ_21_22.h
---- med-2.3.5.old/tools/medimport/include/MAJ_21_22.h	2009-09-13 17:05:38.000000000 +0200
-+++ med-2.3.5/tools/medimport/include/MAJ_21_22.h	2009-09-13 17:18:20.000000000 +0200
-@@ -22,6 +22,7 @@
- #ifdef __cplusplus
- 
- #include "MEDerreur.hxx"
-+#include <cstring>
- 
- #endif
- 
-diff -aur med-2.3.5.old/tools/medimport/include/MAJ_231_232.h med-2.3.5/tools/medimport/include/MAJ_231_232.h
---- med-2.3.5.old/tools/medimport/include/MAJ_231_232.h	2009-09-13 17:05:38.000000000 +0200
-+++ med-2.3.5/tools/medimport/include/MAJ_231_232.h	2009-09-13 17:23:10.000000000 +0200
-@@ -22,6 +22,7 @@
- 
- #ifdef __cplusplus
- # include "MEDerreur.hxx"
-+#include <cstring>
- #endif
- 
- extern void MAJ_231_232_champs(med_idt fid);
diff --git a/sci-libs/med/med-2.3.6.ebuild b/sci-libs/med/med-2.3.6.ebuild
deleted file mode 100644
index 127b1f35a..000000000
--- a/sci-libs/med/med-2.3.6.ebuild
+++ /dev/null
@@ -1,63 +0,0 @@
-# Copyright 1999-2014 Gentoo Foundation
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=5
-
-inherit eutils flag-o-matic
-
-DESCRIPTION="Modeling and Exchange of Data library"
-HOMEPAGE="http://www.code-aster.org/outils/med/"
-SRC_URI="http://dev.gentoo.org/~jauhien/distfiles/med-fichier_${PV}.orig.tar.gz"
-
-LICENSE="LGPL-2.1"
-SLOT="0"
-KEYWORDS="~amd64 ~x86"
-IUSE="doc examples"
-
-DEPEND=">=sci-libs/hdf5-1.6.4"
-RDEPEND=${DEPEND}
-
-S=${WORKDIR}/med-${PV}_SRC
-
-src_prepare() {
-	has_version ">=sci-libs/hdf5-1.8.3" &&	append-cppflags -DH5_USE_16_API
-}
-
-src_configure() {
-	local myconf
-
-	myconf="--docdir=/usr/share/doc/${PF}"
-	## has been desabled, in order to compile salome-med
-	#use amd64 && myconf="${myconf} --with-med_int=long"
-	econf ${myconf}
-}
-
-src_install() {
-	default
-
-	rm -R "${ED}"/usr/share/doc/* "${ED}"/usr/bin/testc "${ED}"/usr/bin/testf
-
-	use doc && \
-		dohtml -r doc/index.html doc/med.css doc/html doc/jpg \
-			doc/png doc/gif doc/tests
-
-	if use examples; then
-		dodir /usr/share/doc/${PF}/examples/c/.libs
-		exeinto /usr/share/doc/${PF}/examples/c
-		for i in `ls tests/c/*.o` ;
-		do
-			doexe tests/c/`basename ${i} .o` "doexe failed"
-		done
-		exeinto /usr/share/doc/${PF}/examples/c/.libs
-		doexe  tests/c/.libs/* "doexe failed"
-
-		dodir /usr/share/doc/${PF}/examples/f/.libs
-		exeinto /usr/share/doc/${PF}/examples/f
-		for i in `ls tests/f/*.o` ;
-		do
-			doexe tests/f/`basename ${i} .o` "doexe failed"
-		done
-		exeinto /usr/share/doc/${PF}/examples/f/.libs
-		doexe tests/f/.libs/* "doexe failed"
-	fi
-}
diff --git a/sci-libs/med/metadata.xml b/sci-libs/med/metadata.xml
deleted file mode 100644
index ae9640ffb..000000000
--- a/sci-libs/med/metadata.xml
+++ /dev/null
@@ -1,8 +0,0 @@
-<?xml version="1.0" encoding="UTF-8"?>
-<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
-<pkgmetadata>
-	<maintainer type="project">
-		<email>sci@gentoo.org</email>
-		<name>Gentoo Science Project</name>
-	</maintainer>
-</pkgmetadata>
diff --git a/sci-libs/mesquite/mesquite-2.3.0.ebuild b/sci-libs/mesquite/mesquite-2.3.0.ebuild
index 3ef96a174..ca8b04be9 100644
--- a/sci-libs/mesquite/mesquite-2.3.0.ebuild
+++ b/sci-libs/mesquite/mesquite-2.3.0.ebuild
@@ -1,18 +1,15 @@
-# Copyright 1999-2015 Gentoo Foundation
+# Copyright 1999-2021 Gentoo Authors
 # Distributed under the terms of the GNU General Public License v2
 
-EAPI=5
-
-inherit eutils
+EAPI=7
 
 DESCRIPTION="Mesh Quality Improvement Toolkit"
-HOMEPAGE="http://www.cs.sandia.gov/optimization/knupp/Mesquite.html"
+HOMEPAGE="https://trilinos.github.io/mesquite.html"
 SRC_URI="https://software.sandia.gov/${PN}/${P}.tar.gz"
 
 LICENSE="LGPL-2"
 SLOT="0"
 KEYWORDS="~amd64 ~x86"
-IUSE=""
 
 src_configure() {
 	econf \
diff --git a/sci-libs/mkl/Manifest b/sci-libs/mkl/Manifest
deleted file mode 100644
index ac43ecaf8..000000000
--- a/sci-libs/mkl/Manifest
+++ /dev/null
@@ -1 +0,0 @@
-DIST parallel_studio_xe_2018_update2_professional_edition.tgz 3877755304 BLAKE2B c8852df23abf080f482002a37af7781b3fbae3ecec448914ea5a237fa2b925073d1a3dc2dd94ba64002ff0f6c7e9b18b25fa7ada811a83b10344eb9b92cb37ff SHA512 a9b644b0305d83a9d0daa14d146cb3ce79949db55a410afe48d62259414e6256d9ef533a04bb50807103511db2016c4abcbbf769146854a25638f402a6d0f2be
diff --git a/sci-libs/mkl/metadata.xml b/sci-libs/mkl/metadata.xml
deleted file mode 100644
index 5d7029a9d..000000000
--- a/sci-libs/mkl/metadata.xml
+++ /dev/null
@@ -1,19 +0,0 @@
-<?xml version="1.0" encoding="UTF-8"?>
-<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
-<pkgmetadata>
-	<maintainer type="project">
-		<email>sci@gentoo.org</email>
-		<name>Gentoo Science Project</name>
-	</maintainer>
-	<longdescription lang="en">
-The Intel(R) Math Kernel Library is a mathematical library mostly
-optimized for Intel processors (also works on AMDs). It contains BLAS
-and LAPACK implementations, Fast Fourier Transforms, a vector math
-library, and random number generators. It also has multiprocessor
-capacities. The package is installed as binary and has a restrictive
-license. Please see license terms and home page for proper use.
-</longdescription>
-	<use>
-		<flag name="int64">Build the 64 bits integer library</flag>
-	</use>
-</pkgmetadata>
diff --git a/sci-libs/mkl/mkl-18.0.2.199.ebuild b/sci-libs/mkl/mkl-18.0.2.199.ebuild
deleted file mode 100644
index ad98b798f..000000000
--- a/sci-libs/mkl/mkl-18.0.2.199.ebuild
+++ /dev/null
@@ -1,108 +0,0 @@
-# Copyright 1999-2018 Gentoo Foundation
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=6
-
-INTEL_DIST_SKU=3235
-INTEL_DIST_PV=2018_update2_professional_edition
-
-inherit alternatives-2 intel-sdp-r1 numeric-int64-multibuild
-
-DESCRIPTION="Intel Math Kernel Library: linear algebra, fft, math functions"
-HOMEPAGE="http://software.intel.com/en-us/articles/intel-mkl/"
-
-IUSE="doc int64"
-KEYWORDS="-* ~amd64 ~x86 ~amd64-linux ~x86-linux"
-
-DEPEND=""
-RDEPEND="~dev-libs/intel-common-${PV}[compiler]"
-
-CHECKREQS_DISK_BUILD=3500M
-
-INTEL_DIST_DAT_RPMS=(
-	"mkl-cluster-c-2018.2-199-2018.2-199.noarch.rpm"
-	"mkl-cluster-common-2018.2-199-2018.2-199.noarch.rpm"
-	"mkl-cluster-f-2018.2-199-2018.2-199.noarch.rpm"
-	"mkl-common-2018.2-199-2018.2-199.noarch.rpm"
-	"mkl-common-c-2018.2-199-2018.2-199.noarch.rpm"
-	"mkl-common-c-ps-2018.2-199-2018.2-199.noarch.rpm"
-	"mkl-common-f-2018.2-199-2018.2-199.noarch.rpm"
-	"mkl-common-ps-2018.2-199-2018.2-199.noarch.rpm"
-	"mkl-f95-common-2018.2-199-2018.2-199.noarch.rpm")
-INTEL_DIST_AMD64_RPMS=(
-	"mkl-cluster-2018.2-199-2018.2-199.x86_64.rpm"
-	"mkl-cluster-rt-2018.2-199-2018.2-199.x86_64.rpm"
-	"mkl-core-2018.2-199-2018.2-199.x86_64.rpm"
-	"mkl-core-c-2018.2-199-2018.2-199.x86_64.rpm"
-	"mkl-core-f-2018.2-199-2018.2-199.x86_64.rpm"
-	"mkl-core-ps-2018.2-199-2018.2-199.x86_64.rpm"
-	"mkl-core-rt-2018.2-199-2018.2-199.x86_64.rpm"
-	"mkl-f95-2018.2-199-2018.2-199.x86_64.rpm"
-	"mkl-gnu-2018.2-199-2018.2-199.x86_64.rpm"
-	"mkl-gnu-c-2018.2-199-2018.2-199.x86_64.rpm"
-	"mkl-gnu-f-2018.2-199-2018.2-199.x86_64.rpm"
-	"mkl-gnu-f-rt-2018.2-199-2018.2-199.x86_64.rpm"
-	"mkl-gnu-rt-2018.2-199-2018.2-199.x86_64.rpm"
-	"mkl-pgi-2018.2-199-2018.2-199.x86_64.rpm"
-	"mkl-pgi-c-2018.2-199-2018.2-199.x86_64.rpm"
-	"mkl-pgi-f-2018.2-199-2018.2-199.x86_64.rpm"
-	"mkl-pgi-rt-2018.2-199-2018.2-199.x86_64.rpm"
-	"mkl-tbb-2018.2-199-2018.2-199.x86_64.rpm"
-	"mkl-tbb-rt-2018.2-199-2018.2-199.x86_64.rpm")
-INTEL_DIST_X86_RPMS=(
-	"mkl-core-32bit-2018.2-199-2018.2-199.x86_64.rpm"
-	"mkl-core-c-32bit-2018.2-199-2018.2-199.x86_64.rpm"
-	"mkl-core-f-32bit-2018.2-199-2018.2-199.x86_64.rpm"
-	"mkl-core-ps-32bit-2018.2-199-2018.2-199.x86_64.rpm"
-	"mkl-core-rt-32bit-2018.2-199-2018.2-199.x86_64.rpm"
-	"mkl-f95-32bit-2018.2-199-2018.2-199.x86_64.rpm"
-	"mkl-gnu-32bit-2018.2-199-2018.2-199.x86_64.rpm"
-	"mkl-gnu-c-32bit-2018.2-199-2018.2-199.x86_64.rpm"
-	"mkl-gnu-f-32bit-2018.2-199-2018.2-199.x86_64.rpm"
-	"mkl-gnu-f-rt-32bit-2018.2-199-2018.2-199.x86_64.rpm"
-	"mkl-gnu-rt-32bit-2018.2-199-2018.2-199.x86_64.rpm"
-	"mkl-tbb-32bit-2018.2-199-2018.2-199.x86_64.rpm"
-	"mkl-tbb-rt-32bit-2018.2-199-2018.2-199.x86_64.rpm")
-
-pkg_setup() {
-	if use doc; then
-		INTEL_DIST_DAT_RPMS+=(
-			"mkl-doc-2018-2018.2-199.noarch.rpm"
-			"mkl-doc-ps-2018-2018.2-199.noarch.rpm")
-	fi
-}
-
-_mkl_add_alternative_provider() {
-	local prov=$1; shift
-	local alt
-	for alt in $*; do
-		NUMERIC_MODULE_NAME=${prov} \
-			numeric-int64-multibuild_install_alternative ${alt} ${prov}
-	done
-}
-
-src_install() {
-	intel-sdp-r1_src_install
-
-	sed -i -e "s#<INSTALLDIR>#$(isdp_get-sdp-edir)/linux#" \
-		"${ED}"/opt/intel/compilers_and_libraries_2018.2.199/linux/mkl/bin/pkgconfig/* \
-		|| die "sed failed"
-
-	mkdir -p "${ED}"/usr/$(get_libdir)/pkgconfig/ || die "mkdir failed"
-	cp "${ED}"/opt/intel/compilers_and_libraries_2018.2.199/linux/mkl/bin/pkgconfig/* \
-		"${ED}"/usr/$(get_libdir)/pkgconfig/ || die "cp failed"
-
-	if use int64; then
-		_mkl_add_alternative_provider mkl-dynamic-ilp64-seq blas lapack cblas lapacke scalapack
-		_mkl_add_alternative_provider mkl-dynamic-ilp64-iomp blas lapack cblas lapacke scalapack
-	else
-		_mkl_add_alternative_provider mkl-dynamic-lp64-seq blas lapack cblas lapacke scalapack
-		_mkl_add_alternative_provider mkl-dynamic-lp64-iomp blas lapack cblas lapacke scalapack
-	fi
-
-	local ldpath="LDPATH="
-	use abi_x86_64 && ldpath+=":$(isdp_get-sdp-edir)/linux/mkl/lib/$(isdp_convert2intel-arch abi_x86_64)"
-	use abi_x86_32 && ldpath+=":$(isdp_get-sdp-edir)/linux/mkl/lib/$(isdp_convert2intel-arch abi_x86_32)"
-	echo "${ldpath}" > "${T}"/35mkl || die
-	doenvd "${T}"/35mkl
-}
diff --git a/sci-libs/mlpack/Manifest b/sci-libs/mlpack/Manifest
deleted file mode 100644
index d596691cd..000000000
--- a/sci-libs/mlpack/Manifest
+++ /dev/null
@@ -1 +0,0 @@
-DIST mlpack-1.0.8.tar.gz 1141590 BLAKE2B 77410f64b5f300c98e9af9082d1b511323542ae61d4c7cd40f5a5350b199e3ad3f0e1880a46d50c682b99c4d0c6338709610190ab0975b12c0719fa6490d0d42 SHA512 ab06affb6fe60370d5c741962092926cb09b909a288c9f0bd7b392307f5f994d270bcee166ceba8fab4ee7e6389ce6738620ecd4ebd4af089107d0b0ac4147bb
diff --git a/sci-libs/mlpack/files/mlpack-1.0.4-libdir.patch b/sci-libs/mlpack/files/mlpack-1.0.4-libdir.patch
deleted file mode 100644
index c22c8110a..000000000
--- a/sci-libs/mlpack/files/mlpack-1.0.4-libdir.patch
+++ /dev/null
@@ -1,13 +0,0 @@
---- mlpack-1.0.4/src/mlpack/CMakeLists.txt.old	2013-02-08 16:45:45.218117489 -0500
-+++ mlpack-1.0.4/src/mlpack/CMakeLists.txt	2013-02-08 16:45:59.938263211 -0500
-@@ -62,8 +62,8 @@
- # be entered...
- install(TARGETS mlpack
-   RUNTIME DESTINATION bin
--  LIBRARY DESTINATION lib
--  ARCHIVE DESTINATION lib)
-+  LIBRARY DESTINATION ${CMAKE_INSTALL_LIBDIR}
-+  ARCHIVE DESTINATION ${CMAKE_INSTALL_LIBDIR})
- 
- # For 'make test'.
- add_custom_target(test
diff --git a/sci-libs/mlpack/files/mlpack-1.0.8-uint32_t.patch b/sci-libs/mlpack/files/mlpack-1.0.8-uint32_t.patch
deleted file mode 100644
index f2dbc4176..000000000
--- a/sci-libs/mlpack/files/mlpack-1.0.8-uint32_t.patch
+++ /dev/null
@@ -1,16 +0,0 @@
---- src/mlpack/core/math/random.hpp	2014-02-15 20:47:24.897408021 +0200
-+++ src/mlpack/core/math/random.hpp	2014-02-15 20:49:36.190907865 +0200
-@@ -26,10 +26,13 @@
- #include <float.h>
- 
- #include <boost/random.hpp>
-+#include <boost/cstdint.hpp>
- 
- namespace mlpack {
- namespace math /** Miscellaneous math routines. */ {
- 
-+using boost::uint32_t;
-+
- // Annoying Boost versioning issues.
- #include <boost/version.hpp>
- 
diff --git a/sci-libs/mlpack/metadata.xml b/sci-libs/mlpack/metadata.xml
deleted file mode 100644
index 1ce896b0f..000000000
--- a/sci-libs/mlpack/metadata.xml
+++ /dev/null
@@ -1,16 +0,0 @@
-<?xml version="1.0" encoding="UTF-8"?>
-<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
-<pkgmetadata>
-	<maintainer type="project">
-		<email>sci@gentoo.org</email>
-		<name>Gentoo Science Project</name>
-	</maintainer>
-	<longdescription lang="en">
-mlpack is a C++ machine learning library with emphasis on
-scalability, speed, and ease-of-use. Its aim is to make machine
-learning possible for novice users by means of a simple, consistent
-API, while simultaneously exploiting C++ language features to
-provide maximum performance and maximum flexibility for expert
-users.
-</longdescription>
-</pkgmetadata>
diff --git a/sci-libs/mlpack/mlpack-1.0.8.ebuild b/sci-libs/mlpack/mlpack-1.0.8.ebuild
deleted file mode 100644
index 9ef9e87ce..000000000
--- a/sci-libs/mlpack/mlpack-1.0.8.ebuild
+++ /dev/null
@@ -1,56 +0,0 @@
-# Copyright 1999-2014 Gentoo Foundation
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=5
-
-inherit cmake-utils eutils toolchain-funcs
-
-DESCRIPTION="Scalable c++ machine learning library"
-HOMEPAGE="http://www.mlpack.org/"
-SRC_URI="http://www.mlpack.org/files/${P}.tar.gz"
-
-LICENSE="LGPL-3"
-SLOT="0"
-KEYWORDS="~amd64 ~x86 ~amd64-linux ~x86-linux"
-IUSE="debug doc"
-
-RDEPEND="
-	dev-libs/boost
-	dev-libs/libxml2
-	>=sci-libs/armadillo-3.6.0[lapack]"
-
-DEPEND="${DEPEND}
-	app-text/txt2man
-	virtual/pkgconfig
-	doc? ( app-doc/doxygen )"
-
-DOCS=( HISTORY.txt )
-
-src_prepare() {
-	epatch \
-		"${FILESDIR}/${PN}-1.0.4-libdir.patch" \
-		"${FILESDIR}/${PN}-1.0.8-uint32_t.patch"
-	sed -i \
-		-e "s:share/doc/mlpack:share/doc/${PF}:" \
-		-e 's/-O3//g' \
-		CMakeLists.txt || die
-	sed -i \
-		-e "s|\(set(ARMADILLO_LIBRARIES\)|\1 $($(tc-getPKG_CONFIG) --libs blas lapack)|" \
-		CMake/FindArmadillo.cmake || die
-}
-
-src_configure() {
-	local mycmakeargs=(
-		$(cmake-utils_use debug DEBUG)
-		$(cmake-utils_use debug PROFILE)
-	)
-	cmake-utils_src_configure
-}
-
-src_compile() {
-	cmake-utils_src_compile all $(use doc && echo doc)
-}
-
-src_test() {
-	emake -C "${BUILD_DIR}" test
-}
diff --git a/sci-libs/modglue/Manifest b/sci-libs/modglue/Manifest
deleted file mode 100644
index 1f7db367c..000000000
--- a/sci-libs/modglue/Manifest
+++ /dev/null
@@ -1 +0,0 @@
-DIST modglue-1.19.tar.gz 94435 SHA256 f228e6666e328a44472a3b8755aba317d38330af322023ce404146d504544f73 SHA512 cdf069dd28674076f9f7275112b4bd96b58c1bfd238ec9570a29a13bca1d8fcdad8c1b8d1fd78aca3ece95890a54d4a8d13db2a3299f4ec6f6475d13145599bf WHIRLPOOL 7b3ae11d18737b859a32a65787e1c445a9e63eaa66cd1a93f06828ec875891f50fcdb069bf7e1173e61e3f04ccbf9e55f071a26ffbe0936030df3a6c24ee2ef5
diff --git a/sci-libs/modglue/files/modglue-1.19-Makefiles.patch b/sci-libs/modglue/files/modglue-1.19-Makefiles.patch
deleted file mode 100644
index a1dae99f0..000000000
--- a/sci-libs/modglue/files/modglue-1.19-Makefiles.patch
+++ /dev/null
@@ -1,113 +0,0 @@
---- Makefile.in.orig	2013-02-24 11:18:44.000000000 +1300
-+++ Makefile.in	2013-09-20 10:05:25.316018672 +1200
-@@ -3,12 +3,15 @@
- 
- .PHONY: all install library static examples uninstall clean distclean
- 
-+prefix = @prefix@
-+exec_prefix = @exec_prefix@
-+
- all: library 
- #examples
- 
- library:
- 	echo @libdir@
--	( cd src && $(MAKE) );
-+	( cd src $(MAKE) library tools );
- 
- static:
- 	( cd src && $(MAKE) static );
-@@ -18,8 +21,8 @@
- 
- install:
- 	( cd src && $(MAKE) install );
--	@INSTALL@ -d -m 755 ${DESTDIR}@prefix@/@libdir@/pkgconfig
--	@INSTALL@ -m 644 modglue.pc ${DESTDIR}@prefix@/@libdir@/pkgconfig/
-+	@INSTALL@ -d -m 755 ${DESTDIR}@libdir@/pkgconfig
-+	@INSTALL@ -m 644 modglue.pc ${DESTDIR}@libdir@/pkgconfig/
- 	@INSTALL@ -d -m 755 ${DESTDIR}@prefix@/share/man/man1
- 	@INSTALL@ man/man1/prompt.1 ${DESTDIR}@prefix@/share/man/man1
- 	@INSTALL@ man/man1/ptywrap.1 ${DESTDIR}@prefix@/share/man/man1
---- src/Makefile.in.orig	2013-02-24 11:18:44.000000000 +1300
-+++ src/Makefile.in	2013-09-20 10:07:56.956164930 +1200
-@@ -1,6 +1,8 @@
- 
- 
- MACTEST= @MAC_OS_X@
-+prefix = @prefix@
-+exec_prefix = @exec_prefix@
- 
- ifeq ($(strip $(MACTEST)),)
- LIBTOOL = libtool
-@@ -21,11 +23,11 @@
- LTRELEASE = `echo ${RELEASE} | sed -e "s/\./:/g"`
- 
- CPHASE = ${LIBTOOL} --tag=CXX --mode=compile @CXX@ -c @CFLAGS@
--LPHASE = ${LIBTOOL} --tag=CXX --mode=link @CXX@ -version-info ${LTRELEASE} -rpath @prefix@@libdir@ @LIBS@
-+LPHASE = ${LIBTOOL} --tag=CXX --mode=link @CXX@ -version-info ${LTRELEASE} -rpath @libdir@ @LIBS@
- #LPHASE = ${LIBTOOL} --tag=CXX --mode=link @CXX@ -version-info ${LTRELEASE} @LIBS@
- MPHASE = ${LIBTOOL} --tag=CXX --mode=link @CXX@
- IPHASE = ${LIBTOOL} --mode=install @INSTALL@
--FPHASE = ${LIBTOOL} --mode=finish @prefix@/@libdir@
-+FPHASE = ${LIBTOOL} --mode=finish ${DESTDIR}@libdir@
- 
- TIMESTAMP = -D"DATETIME=\"`date | sed -e 's/  / /'`\"" -DHOSTNAME=\"`hostname`\"
- 
-@@ -56,21 +58,21 @@
- 
- #------- Tests ----------------------------------------
- 
--test_child_process: test_child_process.o
-+test_child_process: library test_child_process.o
- 	${MPHASE} -o test_child_process $< libmodglue.la
- 
--test_ext_process: test_ext_process.o
-+test_ext_process: library test_ext_process.o
- 	${MPHASE} -o test_ext_process $< libmodglue.la
- 
--test_pipe: test_pipe.o
-+test_pipe: library test_pipe.o
- 	${MPHASE} -o test_pipe $< libmodglue.la
- 
--test_writes: test_writes.o
-+test_writes: library test_writes.o
- 	${MPHASE} -o test_writes $< libmodglue.la
- 
- #------- Tools ----------------------------------------
- 
--prompt: prompt.o
-+prompt: library prompt.o
- 	${MPHASE} -o prompt prompt.o `pkg-config sigc++-2.0 --libs` libmodglue.la 
- #	chrpath -d .libs/prompt
- 
-@@ -85,10 +87,10 @@
- endif
- 
- 
--ptywrap: ptywrap.o
-+ptywrap: library ptywrap.o
- 	${MPHASE} -o ptywrap ptywrap.o @LINK_UTIL@
- 
--ptywrap_static: ptywrap.o
-+ptywrap_static: library ptywrap.o
- 	${CPHASE} ${TIMESTAMP} -o ptywrap.o \
-           -I@top_srcdir@/include -DSTATICBUILD ptywrap.cc
- ifeq ($(strip $(MACTEST)),)
-@@ -109,13 +111,13 @@
- 	DEVDESTDIR=${DESTDIR}
- endif
- 	@INSTALL@ -m 755 -d ${DESTDIR}@prefix@
--	@INSTALL@ -m 755 -d ${DESTDIR}@prefix@/@libdir@
--	@INSTALL@ -m 755 -d ${DEVDESTDIR}@prefix@/@libdir@
-+	@INSTALL@ -m 755 -d ${DESTDIR}@libdir@
-+	@INSTALL@ -m 755 -d ${DEVDESTDIR}@libdir@
- 	@INSTALL@ -m 755 -d ${DESTDIR}@prefix@/bin
- 	@INSTALL@ -m 755 -d ${DEVDESTDIR}@prefix@/include/modglue
--	${IPHASE} libmodglue.la ${DESTDIR}@prefix@/@libdir@
-+	${IPHASE} libmodglue.la ${DESTDIR}@libdir@
- ifneq ($(DESTDIR),$(DEVDESTDIR))
--	mv ${DESTDIR}@prefix@/@libdir@/libmodglue*.so ${DEVDESTDIR}@prefix@/@libdir@
-+	mv ${DESTDIR}@libdir@/libmodglue*.so ${DEVDESTDIR}@libdir@
- endif
- #	${IPHASE} libmid.la ${DESTDIR}@prefix@/lib
- 	${FPHASE}
diff --git a/sci-libs/modglue/metadata.xml b/sci-libs/modglue/metadata.xml
deleted file mode 100644
index bb455de54..000000000
--- a/sci-libs/modglue/metadata.xml
+++ /dev/null
@@ -1,19 +0,0 @@
-<?xml version="1.0" encoding="UTF-8"?>
-<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
-<pkgmetadata>
-	<maintainer type="project">
-		<email>sci@gentoo.org</email>
-		<name>Gentoo Science Project</name>
-	</maintainer>
-	<longdescription>
-The libModglue library is a C++ library with classes for forking external
-processes and asynchronous reading from streams. It takes away the burden of all
-subtleties involving the Unix fork call. The asynchronous read facility enables
-one to read on multiple input streams at the same time, without loosing any of
-the standard C++ stream facilities. There are also several small additional
-programs bundled with modglue, such as a program to add readline capability
-to any command line program. Moreover, the modglue library extends the idea of
-standard Unix pipes by providing a general framework for the creation of new
-processes with more than just the standard stdin/stdout/stderr pipes.
-</longdescription>
-</pkgmetadata>
diff --git a/sci-libs/modglue/modglue-1.19.ebuild b/sci-libs/modglue/modglue-1.19.ebuild
deleted file mode 100644
index 9005c3f2b..000000000
--- a/sci-libs/modglue/modglue-1.19.ebuild
+++ /dev/null
@@ -1,39 +0,0 @@
-# Copyright 1999-2014 Gentoo Foundation
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=5
-
-inherit autotools-utils eutils
-
-DESCRIPTION="C++ library for handling of multiple co-processes"
-HOMEPAGE="http://cadabra.phi-sci.com"
-SRC_URI="http://cadabra.phi-sci.com/${P}.tar.gz"
-
-RESTRICT="mirror"
-
-LICENSE="GPL-2"
-SLOT="0"
-KEYWORDS="~amd64 ~x86"
-IUSE="doc"
-
-RDEPEND="dev-libs/libsigc++:2"
-DEPEND="${RDEPEND}
-	virtual/pkgconfig"
-
-AUTOTOOLS_IN_SOURCE_BUILD=1
-
-PATCHES=(
-	# consolidated (src/)Makefile.in patch
-	"${FILESDIR}"/${PN}-1.19-Makefiles.patch
-	)
-
-src_install() {
-	use doc && HTML_DOCS=( "${S}"/doc/. )
-	autotools-utils_src_install DEVDESTDIR="${D}"
-}
-
-pkg_postinst() {
-	elog "This version of the modglue ebuild is still under development."
-	elog "Help us improve the ebuild in:"
-	elog "http://bugs.gentoo.org/show_bug.cgi?id=194393"
-}
diff --git a/sci-libs/mpfun90/Manifest b/sci-libs/mpfun90/Manifest
new file mode 100644
index 000000000..56d64f14c
--- /dev/null
+++ b/sci-libs/mpfun90/Manifest
@@ -0,0 +1 @@
+DIST 2023-02-26.tar.gz 66883 BLAKE2B 3b93099977b614e0d9a16df76f7f3c1eda9b76905664db3f0dc0ad0bd00b503105649aeb4c960d7293e7d536e3a902dbe8cb62f89be3bce655e9bae963097f35 SHA512 7280ecba6cb95f15cea91ea95f5cf21b69f76a490a3c92bef40cf8a1dfadd651cb93480bddddd684d0f18144db65cdb1590964df11d37a9f35eaeeb94f369d63
diff --git a/sci-libs/mpfun90/metadata.xml b/sci-libs/mpfun90/metadata.xml
new file mode 100644
index 000000000..e3eb0d9c1
--- /dev/null
+++ b/sci-libs/mpfun90/metadata.xml
@@ -0,0 +1,18 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
+<pkgmetadata>
+	<maintainer type="person">
+		<email>alexander@neuwirth-informatik.de</email>
+		<name>Alexander Puck Neuwirth</name>
+	</maintainer>
+	<maintainer type="project">
+		<email>sci-physics@gentoo.org</email>
+		<name>Gentoo Physics Project</name>
+	</maintainer>
+	<longdescription lang="en">
+	This package permits one to perform floating-point computations (real and complex) to arbitrarily high numeric precision
+	</longdescription>
+	<upstream>
+		<remote-id type="github">APN-Pucky/mpfun90</remote-id>
+	</upstream>
+</pkgmetadata>
diff --git a/sci-libs/mpfun90/mpfun90-2023.02.26.ebuild b/sci-libs/mpfun90/mpfun90-2023.02.26.ebuild
new file mode 100644
index 000000000..4f885fa2c
--- /dev/null
+++ b/sci-libs/mpfun90/mpfun90-2023.02.26.ebuild
@@ -0,0 +1,29 @@
+# Copyright 2023 Gentoo Authors
+# Distributed under the terms of the GNU General Public License v2
+
+EAPI=8
+
+inherit toolchain-funcs fortran-2
+
+DESCRIPTION="High-Precision Software"
+HOMEPAGE="
+	https://www.davidhbailey.com/dhbsoftware/
+	https://github.com/APN-Pucky/mpfun90
+"
+MY_PV=$(ver_rs 1- '-')
+SRC_URI="https://github.com/APN-Pucky/mpfun90/archive/refs/tags/${MY_PV}.tar.gz"
+S="${WORKDIR}/mpfun90-${MY_PV}"
+
+LICENSE="BSD"
+SLOT="0"
+KEYWORDS="~amd64"
+
+src_compile() {
+	emake -j1 dynamic
+}
+
+src_install() {
+	doheader *.mod
+	dolib.so libmpfun90.so
+	dolib.a libmpfun90.a
+}
diff --git a/sci-libs/mpiblacs/Manifest b/sci-libs/mpiblacs/Manifest
deleted file mode 100644
index b7a90a4ad..000000000
--- a/sci-libs/mpiblacs/Manifest
+++ /dev/null
@@ -1,3 +0,0 @@
-DIST blacstester.tgz 81937 BLAKE2B 05cb0e7cc0206f654f488cbbdedbbfce1581e4b33bda4b1450900e53da6c44ec97337e634296eb05f1d43c497093b3c4ef3fbf263116258780afe481c6eed6e3 SHA512 ebd1f86b74bffda112bfe4c641e078b67ae08fb10123ea60b18ac681d8750b92ab08838e82c70b60a44999b9516fe7c77c293b42e1b1cd8faba8ef84ddccb003
-DIST mpiblacs-patch03.tgz 30505 BLAKE2B d6976fedda02b7330f009a063aee058bdbd8b0dbd896cf0ac17d230e64d8fa7af9d0648d26617c5338633eff6b294e380b2f0cf240109313775cd2694c4deffb SHA512 ed1513461ee5578548b6d30cc906b156ea08da52b6365851e03aa9578aaa466aabee3b505ed3028e09eeb63288eff7be6bc3ed523e2ff8d824ec8a827a092279
-DIST mpiblacs.tgz 152823 BLAKE2B a1afc77ffd164d1213b2f08ce6713530caa62e1baa91588cab8c9a0fa25c3b43307a5a02dd92bc1286c00e40da4a1b95d00ddd0d6897eff547c632ff4ce9435f SHA512 00f28b77727740a115a337cb86411556a7653c072c380ee9d1428ce62a101183ac3f60bd016a590bdb320e6b97680a1c8cd16f2e688ba4f53f7ced058950f325
diff --git a/sci-libs/mpiblacs/metadata.xml b/sci-libs/mpiblacs/metadata.xml
deleted file mode 100644
index e90a78797..000000000
--- a/sci-libs/mpiblacs/metadata.xml
+++ /dev/null
@@ -1,15 +0,0 @@
-<?xml version="1.0" encoding="UTF-8"?>
-<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
-<pkgmetadata>
-	<maintainer type="project">
-		<email>sci@gentoo.org</email>
-		<name>Gentoo Science Project</name>
-	</maintainer>
-	<longdescription lang="en">
-The BLACS (Basic Linear Algebra Communication Subprograms)
-project is an ongoing investigation whose purpose is to create
-a linear algebra oriented message passing interface
-that may be implemented efficiently and uniformly across
-a large range of distributed memory platforms.
-</longdescription>
-</pkgmetadata>
diff --git a/sci-libs/mpiblacs/mpiblacs-1.1-r1.ebuild b/sci-libs/mpiblacs/mpiblacs-1.1-r1.ebuild
deleted file mode 100644
index 0c0ba0801..000000000
--- a/sci-libs/mpiblacs/mpiblacs-1.1-r1.ebuild
+++ /dev/null
@@ -1,127 +0,0 @@
-# Copyright 1999-2015 Gentoo Foundation
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=5
-inherit eutils toolchain-funcs versionator alternatives-2 multilib
-
-DESCRIPTION="Basic Linear Algebra Communication Subprograms with MPI"
-HOMEPAGE="http://www.netlib.org/blacs/"
-SRC_URI="${HOMEPAGE}/${PN}.tgz
-	${HOMEPAGE}/${PN}-patch03.tgz
-	test? ( ${HOMEPAGE}/blacstester.tgz )"
-
-LICENSE="BSD"
-SLOT="0"
-KEYWORDS="~amd64 ~x86 ~amd64-linux ~x86-linux"
-IUSE="static-libs test"
-
-RDEPEND="virtual/mpi[fortran]
-	virtual/blas
-	!>sci-libs/scalapack-2"
-DEPEND="${RDEPEND}
-	virtual/pkgconfig"
-
-S="${WORKDIR}/BLACS"
-
-static_to_shared() {
-	local libstatic=${1}; shift
-	local libname=$(basename ${libstatic%.a})
-	local soname=${libname}$(get_libname $(get_version_component_range 1-2))
-	local libdir=$(dirname ${libstatic})
-
-	einfo "Making ${soname} from ${libstatic}"
-	if [[ ${CHOST} == *-darwin* ]] ; then
-		${LINK:-$(tc-getCC)} ${LDFLAGS}  \
-			-dynamiclib -install_name "${EPREFIX}"/usr/lib/"${soname}" \
-			-Wl,-all_load -Wl,${libstatic} \
-			"$@" -o ${libdir}/${soname} || die "${soname} failed"
-	else
-		${LINK:-$(tc-getCC)} ${LDFLAGS}  \
-			-shared -Wl,-soname=${soname} \
-			-Wl,--whole-archive ${libstatic} -Wl,--no-whole-archive \
-			"$@" -o ${libdir}/${soname} || die "${soname} failed"
-		[[ $(get_version_component_count) -gt 1 ]] && \
-			ln -s ${soname} ${libdir}/${libname}$(get_libname $(get_major_version)) || die
-		ln -s ${soname} ${libdir}/${libname}$(get_libname) || die
-	fi
-}
-
-src_prepare() {
-	find . -name Makefile -exec sed -i -e 's:make:$(MAKE):g' '{}' \; || die
-
-	sed -e "s:\(SHELL\s*=\).*:\1$(type -P sh):" \
-		-e "s:\(BTOPdir\s*=\).*:\1${S}:" \
-		-e "s:\(BLACSFINIT\s*=\).*:\1\$(BLACSdir)/lib${PN}F77init.a:" \
-		-e "s:\(BLACSCINIT\s*=\).*:\1\$(BLACSdir)/lib${PN}Cinit.a:" \
-		-e "s:\(BLACSLIB\s*=\).*:\1\$(BLACSdir)/lib${PN}.a:" \
-		-e "s:\(MPIINCdir\s*=\).*:\1${EPREFIX}/usr/include:" \
-		-e "s:\(MPILIB\s*=\).*:\1:" \
-		-e '/SYSINC.*=/d' \
-		-e 's:\(INTFACE\s*=\).*:\1-DAdd_:' \
-		-e 's:\(TRANSCOMM\s*=\).*:\1-DUseMpi2:' \
-		-e "s:\(F77\s*=\).*:\1mpif77:" \
-		-e "s:\(F77NO_OPTFLAGS\s*=\).*:\1-O0:" \
-		-e "s:\(F77FLAGS\s*=\).*:\1${FFLAGS}:" \
-		-e "s:\(F77LOADFLAGS\s*=\).*:\1${LDFLAGS}:" \
-		-e "s:\(CC\s*=\).*:\1mpicc:" \
-		-e "s:\(CCFLAGS\s*=\).*:\1${CFLAGS}:" \
-		-e "s:\(CCLOADFLAGS\s*=\).*:\1${LDFLAGS}:" \
-		-e "s:\(ARCH\s*=\).*:\1$(tc-getAR):" \
-		-e "s:\(RANLIB\s*=\).*:\1$(tc-getRANLIB):" \
-		BMAKES/Bmake.MPI-LINUX > Bmake.inc || die
-}
-
-src_compile() {
-	emake \
-		F77NO_OPTFLAGS="-O0 -fPIC" \
-		F77FLAGS="${FFLAGS} -fPIC" \
-		CCFLAGS="${CFLAGS} -fPIC" \
-		mpi
-	LINK=mpif77 static_to_shared LIB/lib${PN}.a
-	LINK=mpicc static_to_shared LIB/lib${PN}Cinit.a -LLIB -l${PN}
-	LINK=mpif77 static_to_shared LIB/lib${PN}F77init.a -LLIB -l${PN}
-	if use static-libs; then
-		emake clean -C SRC/MPI && rm -f LIB/*.a
-		emake mpi
-	fi
-}
-
-src_test() {
-	emake tester
-	cd TESTING/EXE
-	local x
-	# do not die because we are expecting an abort
-	for x in ./x*; do
-		mpirun -np 4 $x 2>&1 | tee $x.log
-		grep -q "\*\*\*" $x.log && die "$x failed"
-	done
-}
-
-src_install() {
-	pushd LIB
-	dolib.so lib*$(get_libname)*
-	use static-libs && dolib.a lib*.a
-	cat <<-EOF > ${PN}.pc
-		prefix=${EPREFIX}/usr
-		libdir=\${prefix}/$(get_libdir)
-		includedir=\${prefix}/include
-		Name: ${PN}
-		Description: ${DESCRIPTION}
-		Version: ${PV}
-		URL: ${HOMEPAGE}
-		Libs: -L\${libdir} -l${PN} -l${PN}Cinit -l${PN}F77init
-		Private: -lm
-		Cflags: -I\${includedir}/${PN}
-		Requires: blas
-	EOF
-	insinto /usr/$(get_libdir)/pkgconfig
-	doins ${PN}.pc
-	alternatives_for blacs ${PN} 0 \
-		/usr/$(get_libdir)/pkgconfig/blacs.pc ${PN}.pc
-	popd > /dev/null
-
-	pushd SRC/MPI > /dev/null
-	insinto /usr/include/blacs
-	doins Bconfig.h Bdef.h
-	popd > /dev/null
-}
diff --git a/sci-libs/msms/Manifest b/sci-libs/msms/Manifest
deleted file mode 100644
index 366b14ae4..000000000
--- a/sci-libs/msms/Manifest
+++ /dev/null
@@ -1 +0,0 @@
-DIST mgltools_source_1.5.6.tar.gz 40275811 BLAKE2B 98a2d71f33fc92233f1082637b54d63a180b6cf1fa8cc052cb497380ba1ea4c8bb1af023d492acfcbf11e23c33f4af7d297eada113838cb6f0133a55684546f3 SHA512 4ed956197f08b7c3779f0bb39393b40cdaff3461071b48815200c6ad0dce2de87375cda96fe20d3ace4ab81ba6b8cdb50b58d82f5e5b54fe2c7751201ff2f63e
diff --git a/sci-libs/msms/files/build-with-linux-3.0.patch b/sci-libs/msms/files/build-with-linux-3.0.patch
deleted file mode 100644
index 849f80a9e..000000000
--- a/sci-libs/msms/files/build-with-linux-3.0.patch
+++ /dev/null
@@ -1,11 +0,0 @@
---- mslib-1.5.4.orig/setup.py	2011-07-30 07:46:02.628300605 -0500
-+++ mslib-1.5.4/setup.py	2011-07-30 07:46:30.628188677 -0500
-@@ -18,7 +18,7 @@
- platform =  sys.platform
- 
- # amd64
--if (platform == "linux2"):
-+if platform in ["linux2", "linux3"]:
-     lUname = os.uname()
-     if lUname[-1] == 'x86_64':
-         platform = lUname[-1] + lUname[0] + lUname[2][0]
diff --git a/sci-libs/msms/metadata.xml b/sci-libs/msms/metadata.xml
deleted file mode 100644
index da36ecbfc..000000000
--- a/sci-libs/msms/metadata.xml
+++ /dev/null
@@ -1,8 +0,0 @@
-<?xml version="1.0" encoding="UTF-8"?>
-<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
-<pkgmetadata>
-	<maintainer type="project">
-		<email>sci-chemistry@gentoo.org</email>
-		<name>Gentoo Chemistry Project</name>
-	</maintainer>
-</pkgmetadata>
diff --git a/sci-libs/msms/msms-1.5.6.ebuild b/sci-libs/msms/msms-1.5.6.ebuild
deleted file mode 100644
index 738e1c92a..000000000
--- a/sci-libs/msms/msms-1.5.6.ebuild
+++ /dev/null
@@ -1,43 +0,0 @@
-# Copyright 1999-2014 Gentoo Foundation
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=5
-
-PYTHON_COMPAT=( python2_7 )
-
-inherit distutils-r1
-
-MY_PN="mslib"
-MY_P="${MY_PN}-${PV/_rc2/}"
-
-DESCRIPTION="MSMS library python extension module"
-HOMEPAGE="http://mgltools.scripps.edu/downloads#msms"
-SRC_URI="http://mgltools.scripps.edu/downloads/tars/releases/REL${PV}/mgltools_source_${PV}.tar.gz"
-
-LICENSE="MGLTOOLS"
-SLOT="0"
-KEYWORDS="~amd64 ~x86"
-IUSE=""
-
-RDEPEND=""
-DEPEND="${RDEPEND}
-	dev-lang/swig"
-
-S="${WORKDIR}"/${MY_P}
-
-PATCHES=( "${FILESDIR}"/build-with-linux-3.0.patch )
-
-src_unpack() {
-	tar xzpf "${DISTDIR}"/${A} mgltools_source_${PV/_/}/MGLPACKS/${MY_P}.tar.gz
-	tar xzpf mgltools_source_${PV/_/}/MGLPACKS/${MY_P}.tar.gz
-}
-
-python_prepare_all() {
-	distutils-r1_python_prepare_all
-	pushd "${S}"/lib >/dev/null
-	# Set up symlinks for 3.x kernels
-	for x in *inux2; do
-		ln -s ${x} ${x%2}3
-	done
-	popd >/dev/null
-}
diff --git a/sci-libs/nexus/Manifest b/sci-libs/nexus/Manifest
index ae681fa5b..f13f71021 100644
--- a/sci-libs/nexus/Manifest
+++ b/sci-libs/nexus/Manifest
@@ -1 +1 @@
-DIST nexus-4.4.1.tar.gz 4820168 BLAKE2B e0d06a9371eaf44682ddee25fc22d3bb1f4c37c53441d6edafbaf552b5e62b0a34c60aa004783f39edb408e6f5f018fbe7175ab43a21fe17d138cb1c7021c3d1 SHA512 f561e5dcb48d6bb5d8acbfecae0e447fe7ca5c82ef85d03d3a9874a2f31e47769ac4229579a31321e2462160f39f6a1f1af28e7d05d5ff9985b1c4281cf053d1
+DIST nexus-4.4.3_p20200126.tar.gz 4984113 BLAKE2B 34e1332a9e674f6bd60950185d031f2ca996c2fbd097a0bd66e7c9a0bdbaa3393aba44cf1142b46eef61aef31dcd9c3e0324ab55d1d75df2f1c9217e5f88f183 SHA512 8bfc4aaa82b1115956d7f77715693bf0d6a59e0fd662d326aba907ffc5694505099ee7b11eaef2969234cf7afe356c1696b9b10172fa2046bfe31c94807f8989
diff --git a/sci-libs/nexus/metadata.xml b/sci-libs/nexus/metadata.xml
index ef8f9fd1a..f4859bfa6 100644
--- a/sci-libs/nexus/metadata.xml
+++ b/sci-libs/nexus/metadata.xml
@@ -2,26 +2,23 @@
 <!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
 <pkgmetadata>
 	<maintainer type="person">
-		<email>c.kerr@embl-hamburg.de</email>
-		<name>Chris Kerr</name>
-		<description>I occasionally submit patches to NeXus</description>
+		<email>gentoo@aisha.cc</email>
+		<name>Aisha Tammy</name>
 	</maintainer>
 	<maintainer type="project">
 		<email>sci@gentoo.org</email>
 		<name>Gentoo Science Project</name>
 	</maintainer>
-	<longdescription>Libraries and tools for the NeXus data format, developed
-collaboratively by scientists from major scientific facilities to facilitate
-analysis and visualisation of neutron, x-ray and muon data.
-NeXus is based on HDF5.</longdescription>
+	<longdescription>
+		Libraries and tools for the NeXus data format, developed
+		collaboratively by scientists from major scientific facilities to facilitate
+		analysis and visualisation of neutron, x-ray and muon data.
+		NeXus is based on HDF5.</longdescription>
 	<use>
 		<flag name="xml">Allow using the verbose XML representation of NeXus data</flag>
 		<flag name="hdf4">Support the old HDF4 representation</flag>
 		<flag name="hdf5">Support the standard representation (HDF5)</flag>
-		<flag name="doc">Generate library documentation with <pkg>app-doc/doxygen</pkg></flag>
-		<flag name="fortran">Build the Fortran bindings</flag>
 		<flag name="java">Build the Java bindings</flag>
-		<flag name="utils">Build optional utility applications</flag>
 	</use>
 	<upstream>
 		<remote-id type="github">nexusformat/code</remote-id>
diff --git a/sci-libs/nexus/nexus-4.4.1.ebuild b/sci-libs/nexus/nexus-4.4.1.ebuild
deleted file mode 100644
index 253a81115..000000000
--- a/sci-libs/nexus/nexus-4.4.1.ebuild
+++ /dev/null
@@ -1,56 +0,0 @@
-# Copyright 1999-2016 Gentoo Foundation
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=5
-
-FORTRAN_NEEDED=fortran
-FORTRAN_STANDARD="77 90"
-inherit cmake-utils fortran-2 java-pkg-opt-2
-
-DESCRIPTION="Data format for neutron and x-ray scattering data"
-HOMEPAGE="http://nexusformat.org/"
-SRC_URI="https://github.com/nexusformat/code/archive/v${PV}.tar.gz -> ${P}.tar.gz"
-
-LICENSE="LGPL-2.1"
-SLOT="0"
-KEYWORDS="~amd64"
-IUSE="doc cxx fortran -hdf4 +hdf5 java utils xml"
-
-REQUIRED_USE=" || ( hdf4 hdf5 xml ) "
-
-RDEPEND="
-	xml? ( dev-libs/mxml )
-	hdf4? ( sci-libs/hdf )
-	hdf5? ( sci-libs/hdf5[zlib] )
-	utils? ( sys-libs/readline:0 sys-libs/libtermcap-compat dev-libs/libxml2 )
-"
-
-DEPEND="${RDEPEND}
-	doc? ( app-doc/doxygen dev-tex/xcolor )
-"
-
-S="${WORKDIR}/code-${PV}"
-
-pkg_setup() {
-	# Handling of dependencies between Fortran module files doesn't play well with parallel make
-	use fortran && export MAKEOPTS="${MAKEOPTS} -j1 "
-	use fortran && fortran-2_pkg_setup
-	java-pkg-opt-2_pkg_setup
-}
-
-src_configure() {
-	# Linking between Fortran libraries gives a relocation error, using workaround suggested at:
-	# http://www.gentoo.org/proj/en/base/amd64/howtos/?part=1&chap=3
-	use fortran && append-fflags -fPIC
-
-	cmake-utils_src_configure \
-		$(cmake-utils_use_enable hdf4) \
-		$(cmake-utils_use_enable hdf5) \
-		$(cmake-utils_use_enable xml MXML) \
-		$(cmake-utils_use_enable cxx) \
-		$(cmake-utils_use_enable fortran FORTRAN90) \
-		$(cmake-utils_use_enable fortran FORTRAN77) \
-		$(cmake-utils_use_enable java) \
-		$(cmake-utils_use_enable utils APPS) \
-		$(cmake-utils_use_enable utils CONTRIB)
-}
diff --git a/sci-libs/nexus/nexus-4.4.3_p20200126.ebuild b/sci-libs/nexus/nexus-4.4.3_p20200126.ebuild
new file mode 100644
index 000000000..58d8264cf
--- /dev/null
+++ b/sci-libs/nexus/nexus-4.4.3_p20200126.ebuild
@@ -0,0 +1,58 @@
+# Copyright 1999-2020 Gentoo Authors
+# Distributed under the terms of the GNU General Public License v2
+
+EAPI=7
+
+inherit cmake java-pkg-opt-2
+
+DESCRIPTION="Data format for neutron and x-ray scattering data"
+HOMEPAGE="http://nexusformat.org/"
+COMMIT=5b803b3a0014bd9759b3d846da3cd3c1cfafd7d5
+SRC_URI="https://github.com/nexusformat/code/archive/${COMMIT}.tar.gz -> ${P}.tar.gz"
+
+S="${WORKDIR}"/code-${COMMIT}
+
+LICENSE="LGPL-2.1"
+SLOT="0"
+KEYWORDS="~amd64"
+IUSE="cxx hdf4 +hdf5 java xml"
+
+REQUIRED_USE=" || ( hdf4 hdf5 xml ) "
+
+RDEPEND="
+	dev-libs/libxml2
+	sys-libs/readline
+	sys-libs/libtermcap-compat
+	xml? ( dev-libs/mxml )
+	hdf4? ( sci-libs/hdf )
+	hdf5? ( sci-libs/hdf5[zlib] )
+"
+DEPEND="${RDEPEND}"
+BDEPEND="
+	app-text/doxygen[dot]
+"
+
+pkg_setup() {
+	java-pkg-opt-2_pkg_setup
+}
+
+src_prepare() {
+	java-pkg-opt-2_src_prepare
+	cmake_src_prepare
+}
+
+src_configure() {
+	# no fortran, doesn't compile
+	local mycmakeargs=(
+		-DENABLE_APPS=ON
+		-DENABLE_CONTRIB=ON
+		-DENABLE_HDF4=$(usex hdf4)
+		-DENABLE_HDF5=$(usex hdf5)
+		-DENABLE_MXML=$(usex xml)
+		-DENABLE_CXX=$(usex cxx)
+		-DENABLE_FORTRAN90=NO
+		-DENABLE_FORTRAN77=NO
+		-DENABLE_JAVA=$(usex java)
+	)
+	cmake_src_configure
+}
diff --git a/sci-libs/ni-visa/Manifest b/sci-libs/ni-visa/Manifest
deleted file mode 100644
index 1fde772c2..000000000
--- a/sci-libs/ni-visa/Manifest
+++ /dev/null
@@ -1 +0,0 @@
-DIST NI-VISA-0.0.1.iso 1 SHA256 01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b
diff --git a/sci-libs/ni-visa/files/70nivisa b/sci-libs/ni-visa/files/70nivisa
deleted file mode 100644
index 6220209fd..000000000
--- a/sci-libs/ni-visa/files/70nivisa
+++ /dev/null
@@ -1 +0,0 @@
-SEARCH_DIRS_MASK="/usr/local/lib/LabVIEW-8.0 /usr/local/lib/LabVIEW-8.2"
diff --git a/sci-libs/ni-visa/metadata.xml b/sci-libs/ni-visa/metadata.xml
deleted file mode 100644
index 90bb64f30..000000000
--- a/sci-libs/ni-visa/metadata.xml
+++ /dev/null
@@ -1,7 +0,0 @@
-<?xml version="1.0" encoding="UTF-8"?>
-<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
-<pkgmetadata>
-	<maintainer type="person">
-		<email>mail@akhuettel.de</email>
-	</maintainer>
-</pkgmetadata>
diff --git a/sci-libs/ni-visa/ni-visa-0.0.1.ebuild b/sci-libs/ni-visa/ni-visa-0.0.1.ebuild
deleted file mode 100644
index bbf9ba363..000000000
--- a/sci-libs/ni-visa/ni-visa-0.0.1.ebuild
+++ /dev/null
@@ -1,30 +0,0 @@
-# Copyright 1999-2014 Gentoo Foundation
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=5
-
-DESCRIPTION="Placeholder for an NI-VISA library ebuild"
-HOMEPAGE="http://www.ni.com/"
-SRC_URI="NI-VISA-0.0.1.iso"
-
-LICENSE="ni-visa"
-KEYWORDS="-* ~amd64 ~x86"
-IUSE=""
-SLOT="0"
-
-RESTRICT="fetch"
-
-src_install() {
-	insinto /etc/revdep-rebuild
-	doins "${FILESDIR}/70nivisa"
-}
-
-pkg_nofetch() {
-	elog Please download the NI-VISA library for linux from
-	elog    http://joule.ni.com/nidu/cds/view/p/id/2044/lang/en
-	elog and install it.
-	elog Afterwards run the command "echo > /usr/portage/distfiles/NI-VISA-0.0.1.iso"
-	echo
-	elog Yes I know this is an ugly hack but the NI installer is even uglier...
-	elog See for more information http://decibel.ni.com/content/message/16917
-}
diff --git a/sci-libs/nibabel/Manifest b/sci-libs/nibabel/Manifest
index f360a8bfc..d50b1b3b7 100644
--- a/sci-libs/nibabel/Manifest
+++ b/sci-libs/nibabel/Manifest
@@ -1,4 +1,2 @@
-DIST nibabel-2.0.1.tar.gz 3390853 BLAKE2B 862e3482f73f335207d74c1384a4c608aef0879752c722af2b5cfaba728d862168aa8ce601e840ef196dd1c5536f4ad0cb1a5613caf2ae3eedd910fed7749775 SHA512 ed7bc0d8e8b4f31ed16215fe768b5c1ed27cd6459248b8600b92455e770fc83fc81361eb9533a15ff334352e72bc0400a924df40853c2fad23940f9d3c230b14
-DIST nibabel-2.1.0.tar.gz 3609462 BLAKE2B 26246f59ac6f5982884eb3316e96f6d484db763135c6dde4ed77b29576a9062aff4f7b2326e84851f5d6b3f0bb7381c7016df66a3672b5b742c8e86309bfc22f SHA512 772e216b68d4d26601d99daaa3a08b53a8d21cbbe5c5eef9e5829d10d9667850f5528f5ec02d1f98e3e98158f639c39aa806c41b28889062430c7f1f6a052f0d
-DIST nibabel-2.3.0.tar.gz 4174114 BLAKE2B 9f0561f4a82fb23302406704d5147ea248601e86ecf4a5423172ccd7cf76ef5b8a8169d29e1cb6c6c7409bb9b1a55447139447bc1813f60c3dc48dc57659bcdf SHA512 9d6cb394152b4e5d49ed750958077998185d78bd01386f267733276a68455024af83b98f9b1f1ca1528655bd4becaec8ded1a02141a8e7464b528ffcec607f4a
-DIST nibabel-2.3.1.tar.gz 4182633 BLAKE2B 75d7f53da93945bd67cf5e0fb5583cd7fd62311c0a1107735277be14c6e3f9012d055ad8ae94bf6dcc34169495a5f4b08827b40d15d7c34cdfb5ed7f16c5115b SHA512 c76d50fbefa24bcbd1a9e8365963c54b8f4ac4e842fa3d45b40184fd687d123cc1c8a1013ca0370e07f9ed9185dd0cec5036ac7c4665789c121ea8fe49157f6b
+DIST nibabel-5.0.0.tar.gz 4480342 BLAKE2B ef5c8fcd27fda60ae85fb657b360453a3b6ae58ea2b8e4eb55bfeb4bdecf6aa94cf1594d0b90a3187f6f3bad32fa9c721bba0827ec0966f799e5b59720778956 SHA512 5f27c03518c47856ecb33b878e9969ea33c7ebb717e6f4f9d89d9fdf415459e47675353051cdb824efea4e6a819759e0bf61cf49caa7212411c63423a77ed0d4
+DIST nibabel-5.1.0.tar.gz 4522882 BLAKE2B 62ffd86e14f66ab57bcfa127e9d0da0b46a04224739b61493080848305295f25136b51bc6fae69c0ec653b4185a28a1b5c323573588abc02f6ebb7372808b8fe SHA512 a07b4c2742ac3af8c0a87a0fa0562ed55c1377fb2067a7813fa2482cab4fc407f013b13b541dd863fa9620c644058296040487aeaba0b26818ff783b2dc2474e
diff --git a/sci-libs/nibabel/metadata.xml b/sci-libs/nibabel/metadata.xml
index 59e566e2d..4944bcbba 100644
--- a/sci-libs/nibabel/metadata.xml
+++ b/sci-libs/nibabel/metadata.xml
@@ -2,7 +2,7 @@
 <!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
 <pkgmetadata>
 	<maintainer type="person">
-		<email>horea.christ@gmail.com</email>
+		<email>gentoo@chymera.eu</email>
 		<name>Horea Christian</name>
 	</maintainer>
 	<maintainer type="project">
@@ -10,12 +10,12 @@
 		<name>Gentoo Science Project</name>
 	</maintainer>
 	<longdescription lang="en">
-The package provides read and write access to some common medical and
-neuroimaging file formats, including: ANALYZE (plain, SPM99, SPM2), GIFTI,
-NIfTI1, MINC, MGH and ECAT as well as PAR/REC. It can read and write Freesurfer
-geometry, and read Freesurfer morphometry and annotation files. There is some
-very limited support for DICOM. NiBabel is the successor of PyNIfTI.
-</longdescription>
+		The package provides read and write access to some common medical and
+		neuroimaging file formats, including: ANALYZE (plain, SPM99, SPM2), GIFTI,
+		NIfTI1, MINC, MGH and ECAT as well as PAR/REC. It can read and write Freesurfer
+		geometry, and read Freesurfer morphometry and annotation files. There is some
+		very limited support for DICOM. NiBabel is the successor of PyNIfTI.
+	</longdescription>
 	<use>
 		<flag name="dicom">Adds limited read support for the DICOM imaging format.</flag>
 	</use>
diff --git a/sci-libs/nibabel/nibabel-2.0.1.ebuild b/sci-libs/nibabel/nibabel-2.0.1.ebuild
deleted file mode 100644
index 71dc0fff3..000000000
--- a/sci-libs/nibabel/nibabel-2.0.1.ebuild
+++ /dev/null
@@ -1,44 +0,0 @@
-# Copyright 1999-2016 Gentoo Foundation
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=6
-
-PYTHON_COMPAT=( python{2_7,3_4,3_5} )
-
-inherit distutils-r1
-
-DESCRIPTION="Access a cacophony of neuro-imaging file formats"
-HOMEPAGE="http://nipy.org/nibabel/"
-SRC_URI="https://github.com/nipy/nibabel/archive/${PV}.tar.gz -> ${P}.tar.gz"
-
-KEYWORDS="~amd64 ~x86"
-
-LICENSE="MIT"
-SLOT="0"
-IUSE="dicom doc test"
-
-RDEPEND="
-	dev-python/numpy[${PYTHON_USEDEP}]
-	sci-libs/scipy[${PYTHON_USEDEP}]
-	dev-python/mock[${PYTHON_USEDEP}]
-	dicom? (
-		sci-libs/pydicom[${PYTHON_USEDEP}]
-		dev-python/pillow[${PYTHON_USEDEP}]
-		)
-	"
-
-DEPEND="
-	dev-python/setuptools[${PYTHON_USEDEP}]
-	test? (
-		${RDEPEND}
-		dev-python/nose[${PYTHON_USEDEP}]
-		)
-	doc? ( dev-python/sphinx[${PYTHON_USEDEP}] )
-	"
-
-python_test() {
-	distutils-r1_install_for_testing
-	cd "${BUILD_DIR}" || die
-	echo "backend: Agg" > matplotlibrc
-	MPLCONFIGDIR=. nosetests || die
-}
diff --git a/sci-libs/nibabel/nibabel-2.1.0.ebuild b/sci-libs/nibabel/nibabel-2.1.0.ebuild
deleted file mode 100644
index d25151e1a..000000000
--- a/sci-libs/nibabel/nibabel-2.1.0.ebuild
+++ /dev/null
@@ -1,44 +0,0 @@
-# Copyright 1999-2018 Gentoo Foundation
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=7
-
-PYTHON_COMPAT=( python{2_7,3_4,3_5,3_6} )
-
-inherit distutils-r1
-
-DESCRIPTION="Access a cacophony of neuro-imaging file formats"
-HOMEPAGE="http://nipy.org/nibabel/"
-SRC_URI="https://github.com/nipy/nibabel/archive/${PV}.tar.gz -> ${P}.tar.gz"
-
-KEYWORDS="~amd64 ~x86"
-
-LICENSE="MIT"
-SLOT="0"
-IUSE="dicom doc test"
-
-RDEPEND="
-	dev-python/numpy[${PYTHON_USEDEP}]
-	sci-libs/scipy[${PYTHON_USEDEP}]
-	dev-python/mock[${PYTHON_USEDEP}]
-	dicom? (
-		sci-libs/pydicom[${PYTHON_USEDEP}]
-		dev-python/pillow[${PYTHON_USEDEP}]
-		)
-	"
-
-DEPEND="
-	dev-python/setuptools[${PYTHON_USEDEP}]
-	test? (
-		${RDEPEND}
-		dev-python/nose[${PYTHON_USEDEP}]
-		)
-	doc? ( dev-python/sphinx[${PYTHON_USEDEP}] )
-	"
-
-python_test() {
-	distutils-r1_install_for_testing
-	cd "${BUILD_DIR}" || die
-	echo "backend: Agg" > matplotlibrc
-	MPLCONFIGDIR=. nosetests || die
-}
diff --git a/sci-libs/nibabel/nibabel-2.3.0.ebuild b/sci-libs/nibabel/nibabel-2.3.0.ebuild
deleted file mode 100644
index d25151e1a..000000000
--- a/sci-libs/nibabel/nibabel-2.3.0.ebuild
+++ /dev/null
@@ -1,44 +0,0 @@
-# Copyright 1999-2018 Gentoo Foundation
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=7
-
-PYTHON_COMPAT=( python{2_7,3_4,3_5,3_6} )
-
-inherit distutils-r1
-
-DESCRIPTION="Access a cacophony of neuro-imaging file formats"
-HOMEPAGE="http://nipy.org/nibabel/"
-SRC_URI="https://github.com/nipy/nibabel/archive/${PV}.tar.gz -> ${P}.tar.gz"
-
-KEYWORDS="~amd64 ~x86"
-
-LICENSE="MIT"
-SLOT="0"
-IUSE="dicom doc test"
-
-RDEPEND="
-	dev-python/numpy[${PYTHON_USEDEP}]
-	sci-libs/scipy[${PYTHON_USEDEP}]
-	dev-python/mock[${PYTHON_USEDEP}]
-	dicom? (
-		sci-libs/pydicom[${PYTHON_USEDEP}]
-		dev-python/pillow[${PYTHON_USEDEP}]
-		)
-	"
-
-DEPEND="
-	dev-python/setuptools[${PYTHON_USEDEP}]
-	test? (
-		${RDEPEND}
-		dev-python/nose[${PYTHON_USEDEP}]
-		)
-	doc? ( dev-python/sphinx[${PYTHON_USEDEP}] )
-	"
-
-python_test() {
-	distutils-r1_install_for_testing
-	cd "${BUILD_DIR}" || die
-	echo "backend: Agg" > matplotlibrc
-	MPLCONFIGDIR=. nosetests || die
-}
diff --git a/sci-libs/nibabel/nibabel-2.3.1.ebuild b/sci-libs/nibabel/nibabel-2.3.1.ebuild
deleted file mode 100644
index 4018c7f41..000000000
--- a/sci-libs/nibabel/nibabel-2.3.1.ebuild
+++ /dev/null
@@ -1,43 +0,0 @@
-# Copyright 1999-2018 Gentoo Authors
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=7
-
-PYTHON_COMPAT=( python{2_7,3_4,3_5,3_6} )
-
-inherit distutils-r1
-
-DESCRIPTION="Access a cacophony of neuro-imaging file formats"
-HOMEPAGE="http://nipy.org/nibabel/"
-SRC_URI="https://github.com/nipy/nibabel/archive/${PV}.tar.gz -> ${P}.tar.gz"
-
-KEYWORDS="~amd64 ~x86"
-
-LICENSE="MIT"
-SLOT="0"
-IUSE="dicom doc test"
-
-RDEPEND="
-	dev-python/numpy[${PYTHON_USEDEP}]
-	sci-libs/scipy[${PYTHON_USEDEP}]
-	dev-python/mock[${PYTHON_USEDEP}]
-	dicom? (
-		sci-libs/pydicom[${PYTHON_USEDEP}]
-		dev-python/pillow[${PYTHON_USEDEP}]
-		)
-	"
-
-DEPEND="
-	dev-python/setuptools[${PYTHON_USEDEP}]
-	test? (
-		${RDEPEND}
-		dev-python/nose[${PYTHON_USEDEP}]
-		)
-	doc? ( dev-python/sphinx[${PYTHON_USEDEP}] )
-	"
-
-python_test() {
-	cd "${BUILD_DIR}" || die
-	echo "backend: Agg" > matplotlibrc
-	MPLCONFIGDIR=. nosetests || die
-}
diff --git a/sci-libs/nibabel/nibabel-5.0.0.ebuild b/sci-libs/nibabel/nibabel-5.0.0.ebuild
new file mode 100644
index 000000000..0fec805b1
--- /dev/null
+++ b/sci-libs/nibabel/nibabel-5.0.0.ebuild
@@ -0,0 +1,35 @@
+# Copyright 1999-2023 Gentoo Authors
+# Distributed under the terms of the GNU General Public License v2
+
+EAPI=8
+
+PYTHON_COMPAT=( python3_{10..11} )
+DISTUTILS_USE_PEP517=hatchling
+
+inherit distutils-r1
+
+DESCRIPTION="Access a cacophony of neuro-imaging file formats"
+HOMEPAGE="https://nipy.org/nibabel/"
+SRC_URI="https://github.com/nipy/nibabel/archive/${PV}.tar.gz -> ${P}.tar.gz"
+
+LICENSE="MIT"
+SLOT="0"
+KEYWORDS="~amd64 ~x86"
+IUSE="dicom"
+
+RDEPEND="
+	dev-python/numpy[${PYTHON_USEDEP}]
+	dev-python/packaging[${PYTHON_USEDEP}]
+	dev-python/scipy[${PYTHON_USEDEP}]
+	dicom? (
+		dev-python/pillow[${PYTHON_USEDEP}]
+		sci-libs/pydicom
+	)
+"
+
+BDEPEND="test? (
+	dev-python/pytest-httpserver[${PYTHON_USEDEP}]
+)"
+
+distutils_enable_sphinx doc/source dev-python/texext dev-python/numpydoc dev-python/matplotlib
+distutils_enable_tests pytest
diff --git a/sci-libs/nibabel/nibabel-5.1.0.ebuild b/sci-libs/nibabel/nibabel-5.1.0.ebuild
new file mode 100644
index 000000000..0fec805b1
--- /dev/null
+++ b/sci-libs/nibabel/nibabel-5.1.0.ebuild
@@ -0,0 +1,35 @@
+# Copyright 1999-2023 Gentoo Authors
+# Distributed under the terms of the GNU General Public License v2
+
+EAPI=8
+
+PYTHON_COMPAT=( python3_{10..11} )
+DISTUTILS_USE_PEP517=hatchling
+
+inherit distutils-r1
+
+DESCRIPTION="Access a cacophony of neuro-imaging file formats"
+HOMEPAGE="https://nipy.org/nibabel/"
+SRC_URI="https://github.com/nipy/nibabel/archive/${PV}.tar.gz -> ${P}.tar.gz"
+
+LICENSE="MIT"
+SLOT="0"
+KEYWORDS="~amd64 ~x86"
+IUSE="dicom"
+
+RDEPEND="
+	dev-python/numpy[${PYTHON_USEDEP}]
+	dev-python/packaging[${PYTHON_USEDEP}]
+	dev-python/scipy[${PYTHON_USEDEP}]
+	dicom? (
+		dev-python/pillow[${PYTHON_USEDEP}]
+		sci-libs/pydicom
+	)
+"
+
+BDEPEND="test? (
+	dev-python/pytest-httpserver[${PYTHON_USEDEP}]
+)"
+
+distutils_enable_sphinx doc/source dev-python/texext dev-python/numpydoc dev-python/matplotlib
+distutils_enable_tests pytest
diff --git a/sci-libs/nibabel/nibabel-9999.ebuild b/sci-libs/nibabel/nibabel-9999.ebuild
deleted file mode 100644
index ab88031a7..000000000
--- a/sci-libs/nibabel/nibabel-9999.ebuild
+++ /dev/null
@@ -1,44 +0,0 @@
-# Copyright 1999-2018 Gentoo Authors
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=7
-
-PYTHON_COMPAT=( python{2_7,3_4,3_5,3_6} )
-
-inherit distutils-r1 git-r3
-
-DESCRIPTION="Access a cacophony of neuro-imaging file formats"
-HOMEPAGE="http://nipy.org/nibabel/"
-SRC_URI=""
-EGIT_REPO_URI="https://github.com/nipy/nibabel.git"
-
-LICENSE="MIT"
-SLOT="0"
-IUSE="dicom doc test"
-KEYWORDS=""
-
-RDEPEND="
-	dev-python/numpy[${PYTHON_USEDEP}]
-	sci-libs/scipy[${PYTHON_USEDEP}]
-	dev-python/mock[${PYTHON_USEDEP}]
-	dicom? (
-		sci-libs/pydicom[${PYTHON_USEDEP}]
-		dev-python/pillow[${PYTHON_USEDEP}]
-		)
-	"
-
-DEPEND="
-	dev-python/setuptools[${PYTHON_USEDEP}]
-	test? (
-		${RDEPEND}
-		dev-python/nose[${PYTHON_USEDEP}]
-		)
-	doc? ( dev-python/sphinx[${PYTHON_USEDEP}] )
-	"
-
-python_test() {
-	distutils-r1_install_for_testing
-	cd "${BUILD_DIR}" || die
-	echo "backend: Agg" > matplotlibrc
-	MPLCONFIGDIR=. nosetests || die
-}
diff --git a/sci-libs/nipy-data/Manifest b/sci-libs/nipy-data/Manifest
deleted file mode 100644
index 7ba8a436b..000000000
--- a/sci-libs/nipy-data/Manifest
+++ /dev/null
@@ -1 +0,0 @@
-DIST nipy-data-0.2.tar.gz 81515168 BLAKE2B ac240639b91dbbdea8bee3892b1e9679d8a738982cae2fb4210436181ff097c9e5459728b6226ee3e3836e5478519383629f5951479648daec6dc2d1d0dd86eb SHA512 6f9a6593973d55fa9f43a6d9fca68bfcaa52228bb0186fe62a21adf4cddd5874c80312c7087fc2004d2df6e4f1c9d74ed07174c784882f8fa144d036fe401ea4
diff --git a/sci-libs/nipy-data/metadata.xml b/sci-libs/nipy-data/metadata.xml
deleted file mode 100644
index 920dec48f..000000000
--- a/sci-libs/nipy-data/metadata.xml
+++ /dev/null
@@ -1,15 +0,0 @@
-<?xml version="1.0" encoding="UTF-8"?>
-<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
-<pkgmetadata>
-	<maintainer type="person">
-		<email>horea.christ@gmail.com</email>
-		<name>Horea Christian</name>
-	</maintainer>
-	<maintainer type="project">
-		<email>sci@gentoo.org</email>
-		<name>Gentoo Science Project</name>
-	</maintainer>
-	<longdescription lang="en">
-Nipy-data is a package containing data files needed for many nipy demo tutorials.
-</longdescription>
-</pkgmetadata>
diff --git a/sci-libs/nipy-data/nipy-data-0.2.ebuild b/sci-libs/nipy-data/nipy-data-0.2.ebuild
deleted file mode 100644
index 7fb12a06f..000000000
--- a/sci-libs/nipy-data/nipy-data-0.2.ebuild
+++ /dev/null
@@ -1,20 +0,0 @@
-# Copyright 1999-2015 Gentoo Foundation
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=6
-
-PYTHON_COMPAT=( python2_7 )
-
-inherit distutils-r1
-
-DESCRIPTION="Demo Data for Python Neuroimaging"
-HOMEPAGE="http://nipy.org/"
-SRC_URI="http://nipy.org/data-packages/${P}.tar.gz"
-
-LICENSE="BSD"
-SLOT="0"
-KEYWORDS="~amd64 ~x86 ~amd64-linux ~x86-linux"
-IUSE=""
-
-RDEPEND=""
-DEPEND=""
diff --git a/sci-libs/nipy-templates/Manifest b/sci-libs/nipy-templates/Manifest
deleted file mode 100644
index 1f50b881b..000000000
--- a/sci-libs/nipy-templates/Manifest
+++ /dev/null
@@ -1 +0,0 @@
-DIST nipy-templates-0.2.tar.gz 4270844 BLAKE2B cafeb4dd1ddf52b3ce12695ab9e927cfc05a5bd9c480000cd3e8a14907d07d73f201849b2517b10038cc3736123547f03923ed2ca866ed6b45172da4e6c168d5 SHA512 3e68e4ce77988f7ddccb85b1ee024cc0717f80316f311ae281dd07f728265d62afb7bc60a7d2e60f88853586627595f601d0248ee5ee64036936c001aeae1e4d
diff --git a/sci-libs/nipy-templates/metadata.xml b/sci-libs/nipy-templates/metadata.xml
deleted file mode 100644
index 1b34497a7..000000000
--- a/sci-libs/nipy-templates/metadata.xml
+++ /dev/null
@@ -1,15 +0,0 @@
-<?xml version="1.0" encoding="UTF-8"?>
-<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
-<pkgmetadata>
-	<maintainer type="person">
-		<email>horea.christ@gmail.com</email>
-		<name>Horea Christian</name>
-	</maintainer>
-	<maintainer type="project">
-		<email>sci@gentoo.org</email>
-		<name>Gentoo Science Project</name>
-	</maintainer>
-	<longdescription lang="en">
-Nipy-templates is a package containing template files needed by some nipy functions.
-</longdescription>
-</pkgmetadata>
diff --git a/sci-libs/nipy-templates/nipy-templates-0.2.ebuild b/sci-libs/nipy-templates/nipy-templates-0.2.ebuild
deleted file mode 100644
index 0cde31df8..000000000
--- a/sci-libs/nipy-templates/nipy-templates-0.2.ebuild
+++ /dev/null
@@ -1,20 +0,0 @@
-# Copyright 1999-2015 Gentoo Foundation
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=6
-
-PYTHON_COMPAT=( python2_7 )
-
-inherit distutils-r1
-
-DESCRIPTION="Normalization templates for Python Neuroimaging"
-HOMEPAGE="http://nipy.org/"
-SRC_URI="http://nipy.org/data-packages/${P}.tar.gz"
-
-LICENSE="BSD"
-SLOT="0"
-KEYWORDS="~amd64 ~x86 ~amd64-linux ~x86-linux"
-IUSE=""
-
-RDEPEND=""
-DEPEND=""
diff --git a/sci-libs/nipy/Manifest b/sci-libs/nipy/Manifest
index 567545563..9444a9dd3 100644
--- a/sci-libs/nipy/Manifest
+++ b/sci-libs/nipy/Manifest
@@ -1,3 +1 @@
-DIST nipy-0.4.0.tar.gz 2282476 BLAKE2B 1048195fa42d762a236306157db5312c2a0f952a98e223066b82e421c4ea9ea1f9ff04818468b27cf669b20af6588c3d71e2701db5d1ab04734133edba915f41 SHA512 b565b421490a015986e6ab55c22e14acffb4c782b18a248b4e0e2e84d332ed83dd92217ea56067a09405613a733474acd67c8bcc06d478394abf03904861fb94
-DIST nipy-0.4.1.tar.gz 2386728 BLAKE2B 33582761d2ab9e0a970f41cc5626074f13b6a4935abc893116b16e814a6953edbad43f6e67264c986fb205e858ade2d6b01fb9231d4fad44672b605f1a1bf682 SHA512 385621e45e8301bbb71765bb7e8e1eca31644c5bd713672c673e8074ab666a28001152a66da992c7fe51f149097c526458956df4323e8c65ca5e1fdf6468090a
-DIST nipy-0.4.2.tar.gz 2403688 BLAKE2B 883377356787652450bb5a8090be48708144c9d11473232248d48e8bc36eb292cdd672ae30b337de6fb8c5e593a772489908c9575c2f97a8dbd82a8e4d6ad0df SHA512 730654e422c9fd15c0abf7ce0e0cb5e9569788527a35e9cc6deb71e2384b0ed2dbbf82f9eafe9cd739647bb1dc3a3d43606d0244fae5accd0896f1fc5bb3a8cc
+DIST nipy-0.6.0.gh.tar.gz 1650342 BLAKE2B 5f375e23fb2d895cfb4320b8ec92cefcf902f3768b6b8dc2ba26b4db30168eb4a29d38be1241e2ae5ae9d87013beb64427c8aca1ac2adaa92d083c700dc0453a SHA512 a59485ccd677c443b9d1e2358c3b3d523ddfa9f390c180661e9afaf3b69943e1b1670c44410954e1bba11c88b9ca20e9e586392804b5c99e9f58b5b68df4641f
diff --git a/sci-libs/nipy/metadata.xml b/sci-libs/nipy/metadata.xml
index 275ece9ff..30440d9a2 100644
--- a/sci-libs/nipy/metadata.xml
+++ b/sci-libs/nipy/metadata.xml
@@ -2,17 +2,15 @@
 <!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
 <pkgmetadata>
 	<maintainer type="person">
-		<email>horea.christ@gmail.com</email>
+		<email>gentoo@chymera.eu</email>
 		<name>Horea Christian</name>
 	</maintainer>
 	<maintainer type="project">
 		<email>sci@gentoo.org</email>
 		<name>Gentoo Science Project</name>
 	</maintainer>
-	<longdescription lang="en">
-NIPY is a python project for analysis of structural and functional neuroimaging data.
-</longdescription>
 	<upstream>
 		<remote-id type="pypi">nipy</remote-id>
+		<remote-id type="github">nipy/nipy</remote-id>
 	</upstream>
 </pkgmetadata>
diff --git a/sci-libs/nipy/nipy-0.4.0.ebuild b/sci-libs/nipy/nipy-0.4.0.ebuild
deleted file mode 100644
index ab2562f34..000000000
--- a/sci-libs/nipy/nipy-0.4.0.ebuild
+++ /dev/null
@@ -1,36 +0,0 @@
-# Copyright 1999-2018 Gentoo Foundation
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=7
-
-PYTHON_COMPAT=( python{2_7,3_4,3_5,3_6} )
-
-inherit distutils-r1 eutils multilib flag-o-matic
-
-DESCRIPTION="Neuroimaging tools for Python"
-HOMEPAGE="http://nipy.org/"
-SRC_URI="mirror://pypi/${P:0:1}/${PN}/${P}.tar.gz"
-
-LICENSE="BSD"
-SLOT="0"
-KEYWORDS="~amd64 ~x86 ~amd64-linux ~x86-linux"
-IUSE=""
-
-RDEPEND="
-	dev-python/prov[${PYTHON_USEDEP}]
-	sci-libs/scipy[${PYTHON_USEDEP}]
-	dev-python/sympy[${PYTHON_USEDEP}]
-	>=sci-libs/nibabel-1.2[${PYTHON_USEDEP}]
-	dev-python/numpy[${PYTHON_USEDEP}]"
-DEPEND="${RDEPEND}
-	dev-python/setuptools[${PYTHON_USEDEP}]"
-
-python_prepare_all() {
-	distutils-r1_python_prepare_all
-	# bug #397605
-	[[ ${CHOST} == *-darwin* ]] \
-		&& append-ldflags -bundle "-undefined dynamic_lookup" \
-		|| append-ldflags -shared
-
-	# nipy uses the horrible numpy.distutils automagic
-}
diff --git a/sci-libs/nipy/nipy-0.4.1.ebuild b/sci-libs/nipy/nipy-0.4.1.ebuild
deleted file mode 100644
index 74ad89b9b..000000000
--- a/sci-libs/nipy/nipy-0.4.1.ebuild
+++ /dev/null
@@ -1,40 +0,0 @@
-# Copyright 1999-2018 Gentoo Foundation
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=7
-
-PYTHON_COMPAT=( python{2_7,3_4,3_5,3_6} )
-
-inherit distutils-r1 eutils multilib flag-o-matic
-
-DESCRIPTION="Neuroimaging tools for Python"
-HOMEPAGE="http://nipy.org/"
-SRC_URI="https://github.com/${PN}/${PN}/archive/${PV}.tar.gz -> ${P}.tar.gz"
-
-LICENSE="BSD"
-SLOT="0"
-KEYWORDS="~amd64 ~x86 ~amd64-linux ~x86-linux"
-IUSE=""
-
-RDEPEND="
-	dev-python/prov[${PYTHON_USEDEP}]
-	sci-libs/scipy[${PYTHON_USEDEP}]
-	dev-python/sympy[${PYTHON_USEDEP}]
-	>=sci-libs/nibabel-1.2[${PYTHON_USEDEP}]
-	dev-python/numpy[${PYTHON_USEDEP}]
-	"
-
-DEPEND="
-	${RDEPEND}
-	dev-python/setuptools[${PYTHON_USEDEP}]
-	"
-
-python_prepare_all() {
-	distutils-r1_python_prepare_all
-	# bug #397605
-	[[ ${CHOST} == *-darwin* ]] \
-		&& append-ldflags -bundle "-undefined dynamic_lookup" \
-		|| append-ldflags -shared
-
-	# nipy uses the horrible numpy.distutils automagic
-}
diff --git a/sci-libs/nipy/nipy-0.4.2.ebuild b/sci-libs/nipy/nipy-0.4.2.ebuild
deleted file mode 100644
index 6da963822..000000000
--- a/sci-libs/nipy/nipy-0.4.2.ebuild
+++ /dev/null
@@ -1,53 +0,0 @@
-# Copyright 1999-2018 Gentoo Foundation
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=7
-
-PYTHON_COMPAT=( python{2_7,3_4,3_5,3_6} )
-
-inherit distutils-r1 eutils multilib flag-o-matic
-
-DESCRIPTION="Neuroimaging tools for Python"
-HOMEPAGE="http://nipy.org/"
-SRC_URI="https://github.com/${PN}/${PN}/archive/${PV}.tar.gz -> ${P}.tar.gz"
-
-LICENSE="BSD"
-SLOT="0"
-KEYWORDS="~amd64 ~x86 ~amd64-linux ~x86-linux"
-IUSE=""
-
-RDEPEND="
-	dev-python/prov[${PYTHON_USEDEP}]
-	sci-libs/scipy[${PYTHON_USEDEP}]
-	dev-python/sympy[${PYTHON_USEDEP}]
-	>=sci-libs/nibabel-1.2[${PYTHON_USEDEP}]
-	dev-python/numpy[${PYTHON_USEDEP}]
-	"
-
-DEPEND="
-	${RDEPEND}
-	dev-python/setuptools[${PYTHON_USEDEP}]
-	"
-
-python_prepare_all() {
-	distutils-r1_python_prepare_all
-	# bug #397605
-	[[ ${CHOST} == *-darwin* ]] \
-		&& append-ldflags -bundle "-undefined dynamic_lookup" \
-		|| append-ldflags -shared
-
-	# nipy uses the horrible numpy.distutils automagic
-}
-
-python_test() {
-	distutils-r1_install_for_testing
-	cp nipy/testing/*.nii.gz "${BUILD_DIR}/lib/nipy/testing/"
-	cp nipy/modalities/fmri/tests/*.{mat,npz,txt} "${BUILD_DIR}/lib/nipy/modalities/fmri/tests/"
-	cp nipy/algorithms/statistics/models/tests/test_data.bin "${BUILD_DIR}/lib/nipy/algorithms/statistics/models/tests"
-	cp nipy/labs/spatial_models/tests/some_blobs.nii "${BUILD_DIR}/lib/nipy/labs/spatial_models/tests/some_blobs.nii"
-	mkdir "${BUILD_DIR}/lib/nipy/algorithms/diagnostics/tests/data/"
-	cp nipy/algorithms/diagnostics/tests/data/tsdiff_results.mat "${BUILD_DIR}/lib/nipy/algorithms/diagnostics/tests/data/"
-	cd "${BUILD_DIR}" || die
-	echo "backend : agg" > matplotlibrc
-	nosetests || die
-}
diff --git a/sci-libs/nipy/nipy-0.6.0.ebuild b/sci-libs/nipy/nipy-0.6.0.ebuild
new file mode 100644
index 000000000..8f8ea83e8
--- /dev/null
+++ b/sci-libs/nipy/nipy-0.6.0.ebuild
@@ -0,0 +1,37 @@
+# Copyright 1999-2023 Gentoo Authors
+# Distributed under the terms of the GNU General Public License v2
+
+EAPI=8
+
+DISTUTILS_USE_PEP517=meson-python
+PYTHON_COMPAT=( python3_{10..11} )
+DISTUTILS_EXT=1
+
+inherit distutils-r1
+
+DESCRIPTION="Neuroimaging tools for Python"
+HOMEPAGE="https://nipy.org/"
+SRC_URI="https://github.com/nipy/nipy/archive/refs/tags/${PV}.tar.gz -> ${P}.gh.tar.gz"
+
+LICENSE="BSD"
+SLOT="0"
+KEYWORDS="~amd64 ~x86"
+IUSE=""
+# Test data unavailable:
+# https://github.com/nipy/nipy/issues/561#event-11866547632
+RESTRICT="test"
+
+RDEPEND="
+	dev-python/scipy[${PYTHON_USEDEP}]
+	dev-python/sympy[${PYTHON_USEDEP}]
+	sci-libs/nibabel[${PYTHON_USEDEP}]
+	dev-python/numpy[${PYTHON_USEDEP}]
+	"
+DEPEND=""
+
+distutils_enable_tests pytest
+
+python_test() {
+	rm -rf nipy || die
+	epytest
+}
diff --git a/sci-libs/nipy/nipy-9999.ebuild b/sci-libs/nipy/nipy-9999.ebuild
deleted file mode 100644
index 658e8d984..000000000
--- a/sci-libs/nipy/nipy-9999.ebuild
+++ /dev/null
@@ -1,37 +0,0 @@
-# Copyright 1999-2018 Gentoo Foundation
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=7
-
-PYTHON_COMPAT=( python{2_7,3_4,3_5,3_6} )
-
-inherit distutils-r1 multilib git-r3 flag-o-matic
-
-DESCRIPTION="Neuroimaging tools for Python"
-HOMEPAGE="http://nipy.org/"
-SRC_URI=""
-EGIT_REPO_URI="https://github.com/nipy/nipy"
-
-LICENSE="BSD"
-SLOT="0"
-IUSE=""
-KEYWORDS=""
-
-DEPEND="
-	dev-python/prov[${PYTHON_USEDEP}]
-	dev-python/setuptools[${PYTHON_USEDEP}]
-	dev-python/numpy[${PYTHON_USEDEP}]"
-RDEPEND="${DEPEND}
-	sci-libs/scipy[${PYTHON_USEDEP}]
-	dev-python/sympy[${PYTHON_USEDEP}]
-	>=sci-libs/nibabel-1.2[${PYTHON_USEDEP}]"
-
-python_prepare_all() {
-	distutils-r1_python_prepare_all
-	# bug #397605
-	[[ ${CHOST} == *-darwin* ]] \
-		&& append-ldflags -bundle "-undefined dynamic_lookup" \
-		|| append-ldflags -shared
-
-	# nipy uses the horrible numpy.distutils automagic
-}
diff --git a/sci-libs/nipype/Manifest b/sci-libs/nipype/Manifest
index c2f36c177..6c9059e1c 100644
--- a/sci-libs/nipype/Manifest
+++ b/sci-libs/nipype/Manifest
@@ -1,5 +1,2 @@
-DIST nipype-0.12.0.tar.gz 3088339 BLAKE2B 640ef5192c5502aa0eb12354547ac701de150fcd44a65a48d393263612ae69760186daed9400ad92823a52e303980eca0df3a481e93287160ded2f332c4f37a9 SHA512 cb882fb8d20ae8a12b1f333cb5812a1de608158cee0e75b367d97980c6b55e27e8217dbfbd57f5df7da980dd8ac86692c393553ac66ea0e77f7b9a232b6be728
-DIST nipype-0.12.1.tar.gz 3092631 BLAKE2B 2081274ba8e5aaa993f29ffc46421e0910759861513f5445a3960298446e7f69d3d482fe5c4569dd2313a0c933b80ff2f66e2b2121325389fa13f3942bc96df0 SHA512 feab0f71c1274a19f6861d73e7c94cd2d35858404c8ef1bf62a35da030ad5fc96ad86370043f018e919c90574b70d56051c3894709c139cecae5117cb2681527
-DIST nipype-0.14.0_pre20170830.tar.gz 3290267 BLAKE2B ef5ca5000e4d0d6d0079dd39e9f798aae5bff9de4ac58c8418bd46e2425ac3ec0d8cc9038a6cff9987b9b7c3e702f29c16d00e4896c2218afac03376fa0978a5 SHA512 0280312e6c80b10ee5463991baeff12cef5ff46c05ea294cdb889594b74cf92bdd5d5d93a9c8facbf888d11d60cdd549df82f262356ae1c59b6eb1bfff813b5e
-DIST nipype-1.1.0.tar.gz 3352721 BLAKE2B a30b8100b79bc16d9113a8ff48812e8a2a0081790400a2d1491ac528afe4aabef9d5d923ecaf1d93a827c0b3c186635095dbc836b6cfb4a8ec5283d32cb1596b SHA512 24066c7f3cf1c6dee366790800545eb1e7975c22986c819926c3b5e18bf0c4b97aab6f58bdbbba66f71495ba43677d8e59d6c02ec200cc609674b8945b2c65e1
-DIST nipype-1.1.1.tar.gz 3353518 BLAKE2B 509b6c2b18aab8c8ddfad3ca4ac87401caf0608ee566edecaa20a4329a3bfd9d67dae730ac45342600b4026b66c5043d753d09e5230269d3fc4b946d049ad11e SHA512 dba749ff3b53dfe19992a27f9ad9aedcd360b51b3bf7233bf4b83387ae7181425b27ef43d23747553e9f8eb368b6769d6bec62650e1303ec353dde4de84f1769
+DIST nipype-1.8.4.tar.gz 2914433 BLAKE2B c25b82c22641f6df2b57c8a07fd318034bb4fe4eaa1037baebc1ffc03d3e1add347d9f0c94139144fc17043a5c97926c88b40755f19794cc71366d76ba339698 SHA512 8949226accd7c158b6a3ec92389a11760a9b306098ccb8ef50844efbddb4e6a9108bb6a32ec7b0402c4ea56881a3548b052fe7f5e757d2771aea5b2eebc9377b
+DIST nipype-1.8.6.tar.gz 2921102 BLAKE2B 79a2131b8265f1b0a3a8d2fa6ff56cbbc2d393c79099178cf036d82357a971a72f024b132d7b4d7d4af85165f562192b6cc5cfc9e797105bdc009734e8a89033 SHA512 23140beb02f4c3807d9d0291bde41ce8c1b06e48dc94001b007f193caaa89428387d1528fa20ae328d2c4a781024c9acf07f7be9ce507ecb2f1daf338c092eec
diff --git a/sci-libs/nipype/files/98nipype b/sci-libs/nipype/files/98nipype
new file mode 100644
index 000000000..c848f7c2a
--- /dev/null
+++ b/sci-libs/nipype/files/98nipype
@@ -0,0 +1 @@
+export NIPYPE_NO_ET=1
diff --git a/sci-libs/nipype/files/nipype-1.5.0-collections.patch b/sci-libs/nipype/files/nipype-1.5.0-collections.patch
new file mode 100644
index 000000000..e784ba48b
--- /dev/null
+++ b/sci-libs/nipype/files/nipype-1.5.0-collections.patch
@@ -0,0 +1,28 @@
+--- a/nipype/interfaces/base/traits_extension.py	2020-06-03 11:08:30.000000000 -0400
++++ b/nipype/interfaces/base/traits_extension.py 	2022-07-11 14:09:31.847784312 -0400
+@@ -19,7 +19,10 @@
+ (usually by Robert Kern).
+
+ """
+-from collections import Sequence
++try:
++    from collections import Sequence
++except ImportError:
++    from collections.abc import Sequence
+
+ # perform all external trait imports here
+ from traits import __version__ as traits_version
+--- a/nipype/utils/misc.py	2020-06-03 11:08:30.000000000 -0400
++++ b/nipype/utils/misc.py	2020-06-03 14:08:57.951408897 -0400
+@@ -6,7 +6,10 @@
+ import os
+ import sys
+ import re
+-from collections import Iterator
++try:
++    from collections import Iterator
++except ImportError:
++    from collections.abc import Iterator
+ from warnings import warn
+
+ from distutils.version import LooseVersion
diff --git a/sci-libs/nipype/files/nipype-1.5.0-version_check.patch b/sci-libs/nipype/files/nipype-1.5.0-version_check.patch
new file mode 100644
index 000000000..043523b24
--- /dev/null
+++ b/sci-libs/nipype/files/nipype-1.5.0-version_check.patch
@@ -0,0 +1,45 @@
+From b4d57d7ca4359b0990636bbc6091c49706c6ff39 Mon Sep 17 00:00:00 2001
+From: Horea Christian <gentoo@chymera.eu>
+Date: Fri, 7 Aug 2020 01:12:38 -0400
+Subject: [PATCH] ENH: no more auto-failing on misparsed versions
+
+---
+ nipype/interfaces/base/core.py | 18 ++++++++++++++++++
+ 1 file changed, 18 insertions(+)
+
+diff --git a/nipype/interfaces/base/core.py b/nipype/interfaces/base/core.py
+index 82da393a84..1e626fe1b5 100644
+--- a/nipype/interfaces/base/core.py
++++ b/nipype/interfaces/base/core.py
+@@ -276,6 +276,15 @@ def _check_version_requirements(self, trait_object, raise_exception=True):
+             version = LooseVersion(str(self.version))
+             for name in names:
+                 min_ver = LooseVersion(str(trait_object.traits()[name].min_ver))
++                try:
++                    min_ver > version
++                except TypeError:
++                    iflogger.warning(
++                        'Nipype is having issues parsing the package version '
++                        f'for Trait {name} ({self.__class__.__name__})'
++                        f'You may want to check whether {version} is larger than {min_ver}'
++                        )
++                    continue
+                 if min_ver > version:
+                     unavailable_traits.append(name)
+                     if not isdefined(getattr(trait_object, name)):
+@@ -293,6 +302,15 @@ def _check_version_requirements(self, trait_object, raise_exception=True):
+             version = LooseVersion(str(self.version))
+             for name in names:
+                 max_ver = LooseVersion(str(trait_object.traits()[name].max_ver))
++                try:
++                    max_ver > version
++                except TypeError:
++                    iflogger.warning(
++                        'Nipype is having issues parsing the package version '
++                        f'for Trait {name} ({self.__class__.__name__})'
++                        f'You may want to check whether {version} is smaller than {max_ver}'
++                        )
++                    continue
+                 if max_ver < version:
+                     unavailable_traits.append(name)
+                     if not isdefined(getattr(trait_object, name)):
diff --git a/sci-libs/nipype/files/nipype-1.8.4-dependency_compatibility.patch b/sci-libs/nipype/files/nipype-1.8.4-dependency_compatibility.patch
new file mode 100644
index 000000000..9811139e7
--- /dev/null
+++ b/sci-libs/nipype/files/nipype-1.8.4-dependency_compatibility.patch
@@ -0,0 +1,575 @@
+From a31870d0f9dc0e774f1cf9d18351586f78ecb252 Mon Sep 17 00:00:00 2001
+From: Chris Markiewicz <effigies@gmail.com>
+Date: Sat, 28 Jan 2023 08:11:54 -0500
+Subject: [PATCH 1/9] FIX: Set dtypes for integer test images
+
+NiBabel 4 began warning that int64 images would error, and NiBabel 5
+began erroring if not passed an explicit dtype or header.
+
+We don't need int64 images, just set some sensible dtypes.
+---
+ nipype/algorithms/tests/test_ErrorMap.py | 2 +-
+ nipype/algorithms/tests/test_TSNR.py     | 3 ++-
+ nipype/algorithms/tests/test_metrics.py  | 2 +-
+ 3 files changed, 4 insertions(+), 3 deletions(-)
+
+diff --git a/nipype/algorithms/tests/test_ErrorMap.py b/nipype/algorithms/tests/test_ErrorMap.py
+index 98f05d8e17..adac507bad 100644
+--- a/nipype/algorithms/tests/test_ErrorMap.py
++++ b/nipype/algorithms/tests/test_ErrorMap.py
+@@ -17,7 +17,7 @@ def test_errormap(tmpdir):
+     volume1 = np.array([[[2.0, 8.0], [1.0, 2.0]], [[1.0, 9.0], [0.0, 3.0]]])
+     # Alan Turing's birthday
+     volume2 = np.array([[[0.0, 7.0], [2.0, 3.0]], [[1.0, 9.0], [1.0, 2.0]]])
+-    mask = np.array([[[1, 0], [0, 1]], [[1, 0], [0, 1]]])
++    mask = np.array([[[1, 0], [0, 1]], [[1, 0], [0, 1]]], dtype=np.uint8)
+ 
+     img1 = nb.Nifti1Image(volume1, np.eye(4))
+     img2 = nb.Nifti1Image(volume2, np.eye(4))
+diff --git a/nipype/algorithms/tests/test_TSNR.py b/nipype/algorithms/tests/test_TSNR.py
+index 26c1019b63..320bec8ab2 100644
+--- a/nipype/algorithms/tests/test_TSNR.py
++++ b/nipype/algorithms/tests/test_TSNR.py
+@@ -131,5 +131,6 @@ def assert_unchanged(self, expected_ranges):
+         [
+             [[[2, 4, 3, 9, 1], [3, 6, 4, 7, 4]], [[8, 3, 4, 6, 2], [4, 0, 4, 4, 2]]],
+             [[[9, 7, 5, 5, 7], [7, 8, 4, 8, 4]], [[0, 4, 7, 1, 7], [6, 8, 8, 8, 7]]],
+-        ]
++        ],
++        dtype=np.int16,
+     )
+diff --git a/nipype/algorithms/tests/test_metrics.py b/nipype/algorithms/tests/test_metrics.py
+index ad7502992e..3652fc2ce5 100644
+--- a/nipype/algorithms/tests/test_metrics.py
++++ b/nipype/algorithms/tests/test_metrics.py
+@@ -45,7 +45,7 @@ def test_fuzzy_overlap(tmpdir):
+ 
+     # Just considering the mask, the central pixel
+     # that raised the index now is left aside.
+-    data = np.zeros((3, 3, 3), dtype=int)
++    data = np.zeros((3, 3, 3), dtype=np.uint8)
+     data[0, 0, 0] = 1
+     data[2, 2, 2] = 1
+     nb.Nifti1Image(data, np.eye(4)).to_filename("mask.nii.gz")
+
+From 443492e82f3b197ad739cb244912ced652853a8d Mon Sep 17 00:00:00 2001
+From: Chris Markiewicz <effigies@gmail.com>
+Date: Sat, 28 Jan 2023 08:43:07 -0500
+Subject: [PATCH 2/9] FIX: Coerce depidx to lil_matrix
+
+---
+ nipype/pipeline/plugins/base.py | 18 +++++++++++++-----
+ 1 file changed, 13 insertions(+), 5 deletions(-)
+
+diff --git a/nipype/pipeline/plugins/base.py b/nipype/pipeline/plugins/base.py
+index a927b24686..3d600dda55 100644
+--- a/nipype/pipeline/plugins/base.py
++++ b/nipype/pipeline/plugins/base.py
+@@ -21,6 +21,18 @@
+ logger = logging.getLogger("nipype.workflow")
+ 
+ 
++def _graph_to_lil_matrix(graph, nodelist):
++    """Provide a sparse linked list matrix across various NetworkX versions"""
++    import scipy.sparse as ssp
++
++    try:
++        from networkx import to_scipy_sparse_array
++    except ImportError:  # NetworkX < 2.7
++        from networkx import to_scipy_sparse_matrix as to_scipy_sparse_array
++
++    return ssp.lil_matrix(to_scipy_sparse_array(graph, nodelist=nodelist, format="lil"))
++
++
+ class PluginBase(object):
+     """Base class for plugins."""
+ 
+@@ -431,12 +443,8 @@ def _task_finished_cb(self, jobid, cached=False):
+ 
+     def _generate_dependency_list(self, graph):
+         """Generates a dependency list for a list of graphs."""
+-        import networkx as nx
+-
+         self.procs, _ = topological_sort(graph)
+-        self.depidx = nx.to_scipy_sparse_matrix(
+-            graph, nodelist=self.procs, format="lil"
+-        )
++        self.depidx = _graph_to_lil_matrix(graph, nodelist=self.procs)
+         self.refidx = self.depidx.astype(int)
+         self.proc_done = np.zeros(len(self.procs), dtype=bool)
+         self.proc_pending = np.zeros(len(self.procs), dtype=bool)
+
+From 34ef6c2ff89f327fcf2951b792ef38b6d56f8c4e Mon Sep 17 00:00:00 2001
+From: Chris Markiewicz <effigies@gmail.com>
+Date: Sat, 28 Jan 2023 11:57:54 -0500
+Subject: [PATCH 3/9] FIX: Accept "str" in dipy type (includes "string")
+
+---
+ nipype/interfaces/dipy/base.py | 6 +++---
+ 1 file changed, 3 insertions(+), 3 deletions(-)
+
+diff --git a/nipype/interfaces/dipy/base.py b/nipype/interfaces/dipy/base.py
+index d8a1c0fbf5..161ed33227 100644
+--- a/nipype/interfaces/dipy/base.py
++++ b/nipype/interfaces/dipy/base.py
+@@ -110,7 +110,7 @@ def convert_to_traits_type(dipy_type, is_file=False):
+     """Convert DIPY type to Traits type."""
+     dipy_type = dipy_type.lower()
+     is_mandatory = bool("optional" not in dipy_type)
+-    if "variable" in dipy_type and "string" in dipy_type:
++    if "variable" in dipy_type and "str" in dipy_type:
+         return traits.ListStr, is_mandatory
+     elif "variable" in dipy_type and "int" in dipy_type:
+         return traits.ListInt, is_mandatory
+@@ -120,9 +120,9 @@ def convert_to_traits_type(dipy_type, is_file=False):
+         return traits.ListBool, is_mandatory
+     elif "variable" in dipy_type and "complex" in dipy_type:
+         return traits.ListComplex, is_mandatory
+-    elif "string" in dipy_type and not is_file:
++    elif "str" in dipy_type and not is_file:
+         return traits.Str, is_mandatory
+-    elif "string" in dipy_type and is_file:
++    elif "str" in dipy_type and is_file:
+         return File, is_mandatory
+     elif "int" in dipy_type:
+         return traits.Int, is_mandatory
+
+From 83c8cf86d6bbb0dc04aa58dbe5119fd864342d9c Mon Sep 17 00:00:00 2001
+From: Chris Markiewicz <effigies@gmail.com>
+Date: Sat, 28 Jan 2023 11:55:34 -0500
+Subject: [PATCH 4/9] MNT: Update requirements from info.py
+
+---
+ requirements.txt | 6 +++---
+ 1 file changed, 3 insertions(+), 3 deletions(-)
+
+diff --git a/requirements.txt b/requirements.txt
+index afec34ebfd..331e2c5def 100644
+--- a/requirements.txt
++++ b/requirements.txt
+@@ -2,8 +2,7 @@
+ click>=6.6.0
+ networkx>=2.0
+ nibabel>=2.1.0
+-numpy>=1.13 ; python_version < "3.7"
+-numpy>=1.15.3 ; python_version >= "3.7"
++numpy>=1.17
+ packaging
+ prov>=1.5.2
+ pydot>=1.2.3
+@@ -11,6 +10,7 @@ python-dateutil>=2.2
+ rdflib>=5.0.0
+ scipy>=0.14
+ simplejson>=3.8.0
+-traits>=4.6,!=5.0
++traits>=4.6,<6.4,!=5.0
+ filelock>=3.0.0
+ etelemetry>=0.2.0
++looseversion
+
+From 24c55a6f48aa658320ff35283b6f91ec38b13a40 Mon Sep 17 00:00:00 2001
+From: Horea Christian <chr@chymera.eu>
+Date: Thu, 26 Jan 2023 02:28:33 -0500
+Subject: [PATCH 5/9] Writing pickles directly as networkx no longer ships
+ write_gpickle
+
+---
+ nipype/interfaces/cmtk/cmtk.py           | 12 ++++++++----
+ nipype/interfaces/cmtk/nbs.py            |  7 +++++--
+ nipype/interfaces/cmtk/nx.py             | 12 ++++++++----
+ nipype/interfaces/cmtk/tests/test_nbs.py |  4 +++-
+ 4 files changed, 24 insertions(+), 11 deletions(-)
+
+diff --git a/nipype/interfaces/cmtk/cmtk.py b/nipype/interfaces/cmtk/cmtk.py
+index 8775a8517e..8df7a1c5ad 100644
+--- a/nipype/interfaces/cmtk/cmtk.py
++++ b/nipype/interfaces/cmtk/cmtk.py
+@@ -226,7 +226,8 @@ def cmat(
+     # Add node information from specified parcellation scheme
+     path, name, ext = split_filename(resolution_network_file)
+     if ext == ".pck":
+-        gp = nx.read_gpickle(resolution_network_file)
++        with open(resolution_network_file, 'rb') as f:
++            gp = pickle.load(f)
+     elif ext == ".graphml":
+         gp = nx.read_graphml(resolution_network_file)
+     else:
+@@ -379,7 +380,8 @@ def cmat(
+                 fibdev.add_edge(u, v, weight=di["fiber_length_std"])
+ 
+     iflogger.info("Writing network as %s", matrix_name)
+-    nx.write_gpickle(G, op.abspath(matrix_name))
++    with open(op.abspath(matrix_name), 'wb') as f:
++        pickle.dump(G, f, pickle.HIGHEST_PROTOCOL)
+ 
+     numfib_mlab = nx.to_numpy_matrix(numfib, dtype=int)
+     numfib_dict = {"number_of_fibers": numfib_mlab}
+@@ -394,7 +396,8 @@ def cmat(
+         path, name, ext = split_filename(matrix_name)
+         intersection_matrix_name = op.abspath(name + "_intersections") + ext
+         iflogger.info("Writing intersection network as %s", intersection_matrix_name)
+-        nx.write_gpickle(I, intersection_matrix_name)
++        with open(intersection_matrix_name, 'wb') as f:
++            pickle.dump(I, f, pickle.HIGHEST_PROTOCOL)
+ 
+     path, name, ext = split_filename(matrix_mat_name)
+     if not ext == ".mat":
+@@ -1070,7 +1073,8 @@ def create_nodes(roi_file, resolution_network_file, out_filename):
+             )
+         )
+         G.nodes[int(u)]["dn_position"] = tuple([xyz[0], xyz[2], -xyz[1]])
+-    nx.write_gpickle(G, out_filename)
++    with open(out_filename, 'wb') as f:
++        pickle.dump(G, f, pickle.HIGHEST_PROTOCOL)
+     return out_filename
+ 
+ 
+diff --git a/nipype/interfaces/cmtk/nbs.py b/nipype/interfaces/cmtk/nbs.py
+index 4e1db9ffb7..57d63897c7 100644
+--- a/nipype/interfaces/cmtk/nbs.py
++++ b/nipype/interfaces/cmtk/nbs.py
+@@ -6,6 +6,7 @@
+ 
+ import numpy as np
+ import networkx as nx
++import pickle
+ 
+ from ... import logging
+ from ..base import (
+@@ -172,12 +173,14 @@ def _run_interface(self, runtime):
+ 
+         path = op.abspath("NBS_Result_" + details)
+         iflogger.info(path)
+-        nx.write_gpickle(nbsgraph, path)
++        with open(path, 'wb') as f:
++            pickle.dump(nbsgraph, f, pickle.HIGHEST_PROTOCOL)
+         iflogger.info("Saving output NBS edge network as %s", path)
+ 
+         pval_path = op.abspath("NBS_P_vals_" + details)
+         iflogger.info(pval_path)
+-        nx.write_gpickle(nbs_pval_graph, pval_path)
++        with open(pval_path, 'wb') as f:
++            pickle.dump(nbs_pval_graph, f, pickle.HIGHEST_PROTOCOL)
+         iflogger.info("Saving output p-value network as %s", pval_path)
+         return runtime
+ 
+diff --git a/nipype/interfaces/cmtk/nx.py b/nipype/interfaces/cmtk/nx.py
+index aaf4bece39..a662eb65c6 100644
+--- a/nipype/interfaces/cmtk/nx.py
++++ b/nipype/interfaces/cmtk/nx.py
+@@ -200,7 +200,8 @@ def average_networks(in_files, ntwk_res_file, group_id):
+ 
+     # Writes the networks and returns the name
+     network_name = group_id + "_average.pck"
+-    nx.write_gpickle(avg_ntwk, op.abspath(network_name))
++    with open(op.abspath(network_name), 'wb') as f:
++        pickle.dump(avg_ntwk, f, pickle.HIGHEST_PROTOCOL)
+     iflogger.info("Saving average network as %s", op.abspath(network_name))
+     avg_ntwk = fix_keys_for_gexf(avg_ntwk)
+     network_name = group_id + "_average.gexf"
+@@ -483,7 +484,8 @@ def _run_interface(self, runtime):
+         for key in list(node_measures.keys()):
+             newntwk = add_node_data(node_measures[key], ntwk)
+             out_file = op.abspath(self._gen_outfilename(key, "pck"))
+-            nx.write_gpickle(newntwk, out_file)
++            with open(out_file, 'wb') as f:
++                pickle.dump(newntwk, f, pickle.HIGHEST_PROTOCOL)
+             nodentwks.append(out_file)
+         if isdefined(self.inputs.out_node_metrics_matlab):
+             node_out_file = op.abspath(self.inputs.out_node_metrics_matlab)
+@@ -497,7 +499,8 @@ def _run_interface(self, runtime):
+         for key in list(edge_measures.keys()):
+             newntwk = add_edge_data(edge_measures[key], ntwk)
+             out_file = op.abspath(self._gen_outfilename(key, "pck"))
+-            nx.write_gpickle(newntwk, out_file)
++            with open(out_file, 'wb') as f:
++                pickle.dump(newntwk, f, pickle.HIGHEST_PROTOCOL)
+             edgentwks.append(out_file)
+         if isdefined(self.inputs.out_edge_metrics_matlab):
+             edge_out_file = op.abspath(self.inputs.out_edge_metrics_matlab)
+@@ -521,7 +524,8 @@ def _run_interface(self, runtime):
+                 out_file = op.abspath(
+                     self._gen_outfilename(self.inputs.out_k_crust, "pck")
+                 )
+-            nx.write_gpickle(ntwk_measures[key], out_file)
++            with open(out_file, 'wb') as f:
++                pickle.dump(ntwk_measures[key], f, pickle.HIGHEST_PROTOCOL)
+             kntwks.append(out_file)
+         gpickled.extend(kntwks)
+ 
+diff --git a/nipype/interfaces/cmtk/tests/test_nbs.py b/nipype/interfaces/cmtk/tests/test_nbs.py
+index 46da939f1a..7a60b407a4 100644
+--- a/nipype/interfaces/cmtk/tests/test_nbs.py
++++ b/nipype/interfaces/cmtk/tests/test_nbs.py
+@@ -2,6 +2,7 @@
+ from ....utils.misc import package_check
+ import numpy as np
+ import networkx as nx
++import pickle
+ import pytest
+ 
+ have_cv = True
+@@ -20,7 +21,8 @@ def creating_graphs(tmpdir):
+         G = nx.from_numpy_matrix(graph)
+         out_file = tmpdir.strpath + graphnames[idx] + ".pck"
+         # Save as pck file
+-        nx.write_gpickle(G, out_file)
++        with open(out_file, 'wb') as f:
++            pickle.dump(G, f, pickle.HIGHEST_PROTOCOL)
+         graphlist.append(out_file)
+     return graphlist
+ 
+
+From b9a8e2000be9ce30a94aca85453d5cf4e32e10ec Mon Sep 17 00:00:00 2001
+From: Horea Christian <chr@chymera.eu>
+Date: Thu, 26 Jan 2023 02:03:39 -0500
+Subject: [PATCH 6/9] updating networkx from_numpy_{matrix,array}
+
+---
+ nipype/interfaces/cmtk/cmtk.py           | 2 +-
+ nipype/interfaces/cmtk/nbs.py            | 4 ++--
+ nipype/interfaces/cmtk/tests/test_nbs.py | 2 +-
+ 3 files changed, 4 insertions(+), 4 deletions(-)
+
+diff --git a/nipype/interfaces/cmtk/cmtk.py b/nipype/interfaces/cmtk/cmtk.py
+index 8df7a1c5ad..fc730b1166 100644
+--- a/nipype/interfaces/cmtk/cmtk.py
++++ b/nipype/interfaces/cmtk/cmtk.py
+@@ -264,7 +264,7 @@ def cmat(
+         )
+         intersection_matrix = np.matrix(intersection_matrix)
+         I = G.copy()
+-        H = nx.from_numpy_matrix(np.matrix(intersection_matrix))
++        H = nx.from_numpy_array(np.matrix(intersection_matrix))
+         H = nx.relabel_nodes(H, lambda x: x + 1)  # relabel nodes so they start at 1
+         I.add_weighted_edges_from(
+             ((u, v, d["weight"]) for u, v, d in H.edges(data=True))
+diff --git a/nipype/interfaces/cmtk/nbs.py b/nipype/interfaces/cmtk/nbs.py
+index 57d63897c7..b0a8b5df33 100644
+--- a/nipype/interfaces/cmtk/nbs.py
++++ b/nipype/interfaces/cmtk/nbs.py
+@@ -150,8 +150,8 @@ def _run_interface(self, runtime):
+             pADJ[x, y] = PVAL[idx]
+ 
+         # Create networkx graphs from the adjacency matrix
+-        nbsgraph = nx.from_numpy_matrix(ADJ)
+-        nbs_pval_graph = nx.from_numpy_matrix(pADJ)
++        nbsgraph = nx.from_numpy_array(ADJ)
++        nbs_pval_graph = nx.from_numpy_array(pADJ)
+ 
+         # Relabel nodes because they should not start at zero for our convention
+         nbsgraph = nx.relabel_nodes(nbsgraph, lambda x: x + 1)
+diff --git a/nipype/interfaces/cmtk/tests/test_nbs.py b/nipype/interfaces/cmtk/tests/test_nbs.py
+index 7a60b407a4..6323546c1e 100644
+--- a/nipype/interfaces/cmtk/tests/test_nbs.py
++++ b/nipype/interfaces/cmtk/tests/test_nbs.py
+@@ -18,7 +18,7 @@ def creating_graphs(tmpdir):
+     graphnames = ["name" + str(i) for i in range(6)]
+     for idx, name in enumerate(graphnames):
+         graph = np.random.rand(10, 10)
+-        G = nx.from_numpy_matrix(graph)
++        G = nx.from_numpy_array(graph)
+         out_file = tmpdir.strpath + graphnames[idx] + ".pck"
+         # Save as pck file
+         with open(out_file, 'wb') as f:
+
+From 7aa7c5968cf28afed9aca658bca28470afbfeb9f Mon Sep 17 00:00:00 2001
+From: Chris Markiewicz <effigies@gmail.com>
+Date: Sat, 28 Jan 2023 12:45:17 -0500
+Subject: [PATCH 7/9] FIX: Purge nx.to_numpy_matrix
+
+---
+ nipype/interfaces/cmtk/cmtk.py | 8 ++++----
+ nipype/interfaces/cmtk/nbs.py  | 2 +-
+ 2 files changed, 5 insertions(+), 5 deletions(-)
+
+diff --git a/nipype/interfaces/cmtk/cmtk.py b/nipype/interfaces/cmtk/cmtk.py
+index fc730b1166..00c134fc37 100644
+--- a/nipype/interfaces/cmtk/cmtk.py
++++ b/nipype/interfaces/cmtk/cmtk.py
+@@ -383,13 +383,13 @@ def cmat(
+     with open(op.abspath(matrix_name), 'wb') as f:
+         pickle.dump(G, f, pickle.HIGHEST_PROTOCOL)
+ 
+-    numfib_mlab = nx.to_numpy_matrix(numfib, dtype=int)
++    numfib_mlab = nx.to_numpy_array(numfib, dtype=int)
+     numfib_dict = {"number_of_fibers": numfib_mlab}
+-    fibmean_mlab = nx.to_numpy_matrix(fibmean, dtype=np.float64)
++    fibmean_mlab = nx.to_numpy_array(fibmean, dtype=np.float64)
+     fibmean_dict = {"mean_fiber_length": fibmean_mlab}
+-    fibmedian_mlab = nx.to_numpy_matrix(fibmedian, dtype=np.float64)
++    fibmedian_mlab = nx.to_numpy_array(fibmedian, dtype=np.float64)
+     fibmedian_dict = {"median_fiber_length": fibmedian_mlab}
+-    fibdev_mlab = nx.to_numpy_matrix(fibdev, dtype=np.float64)
++    fibdev_mlab = nx.to_numpy_array(fibdev, dtype=np.float64)
+     fibdev_dict = {"fiber_length_std": fibdev_mlab}
+ 
+     if intersections:
+diff --git a/nipype/interfaces/cmtk/nbs.py b/nipype/interfaces/cmtk/nbs.py
+index b0a8b5df33..2560ed8e3c 100644
+--- a/nipype/interfaces/cmtk/nbs.py
++++ b/nipype/interfaces/cmtk/nbs.py
+@@ -40,7 +40,7 @@ def ntwks_to_matrices(in_files, edge_key):
+                 raise KeyError(
+                     "the graph edges do not have {} attribute".format(edge_key)
+                 )
+-        matrix[:, :, idx] = nx.to_numpy_matrix(graph)  # Retrieve the matrix
++        matrix[:, :, idx] = nx.to_numpy_array(graph)  # Retrieve the matrix
+     return matrix
+ 
+ 
+
+From f20035c303a88fba3e207ac60388397665bb97be Mon Sep 17 00:00:00 2001
+From: Chris Markiewicz <effigies@gmail.com>
+Date: Sat, 28 Jan 2023 12:45:38 -0500
+Subject: [PATCH 8/9] FIX: Purge nx.read_gpickle
+
+---
+ nipype/interfaces/cmtk/convert.py |  9 ++++++++-
+ nipype/interfaces/cmtk/nbs.py     | 11 ++++++++---
+ nipype/interfaces/cmtk/nx.py      | 11 ++++++++---
+ 3 files changed, 24 insertions(+), 7 deletions(-)
+
+diff --git a/nipype/interfaces/cmtk/convert.py b/nipype/interfaces/cmtk/convert.py
+index 321a40fbba..a45daddcd6 100644
+--- a/nipype/interfaces/cmtk/convert.py
++++ b/nipype/interfaces/cmtk/convert.py
+@@ -18,6 +18,13 @@
+ from .base import CFFBaseInterface, have_cfflib
+ 
+ 
++def _read_pickle(fname):
++    import pickle
++
++    with open(fname, 'rb') as f:
++        return pickle.load(f)
++
++
+ class CFFConverterInputSpec(BaseInterfaceInputSpec):
+     graphml_networks = InputMultiPath(
+         File(exists=True), desc="list of graphML networks"
+@@ -135,7 +142,7 @@ def _run_interface(self, runtime):
+             unpickled = []
+             for ntwk in self.inputs.gpickled_networks:
+                 _, ntwk_name, _ = split_filename(ntwk)
+-                unpickled = nx.read_gpickle(ntwk)
++                unpickled = _read_pickle(ntwk)
+                 cnet = cf.CNetwork(name=ntwk_name)
+                 cnet.set_with_nxgraph(unpickled)
+                 a.add_connectome_network(cnet)
+diff --git a/nipype/interfaces/cmtk/nbs.py b/nipype/interfaces/cmtk/nbs.py
+index 2560ed8e3c..a2bd42abee 100644
+--- a/nipype/interfaces/cmtk/nbs.py
++++ b/nipype/interfaces/cmtk/nbs.py
+@@ -24,13 +24,18 @@
+ iflogger = logging.getLogger("nipype.interface")
+ 
+ 
++def _read_pickle(fname):
++    with open(fname, 'rb') as f:
++        return pickle.load(f)
++
++
+ def ntwks_to_matrices(in_files, edge_key):
+-    first = nx.read_gpickle(in_files[0])
++    first = _read_pickle(in_files[0])
+     files = len(in_files)
+     nodes = len(first.nodes())
+     matrix = np.zeros((nodes, nodes, files))
+     for idx, name in enumerate(in_files):
+-        graph = nx.read_gpickle(name)
++        graph = _read_pickle(name)
+         for u, v, d in graph.edges(data=True):
+             try:
+                 graph[u][v]["weight"] = d[
+@@ -162,7 +167,7 @@ def _run_interface(self, runtime):
+         else:
+             node_ntwk_name = self.inputs.in_group1[0]
+ 
+-        node_network = nx.read_gpickle(node_ntwk_name)
++        node_network = _read_pickle(node_ntwk_name)
+         iflogger.info(
+             "Populating node dictionaries with attributes from %s", node_ntwk_name
+         )
+diff --git a/nipype/interfaces/cmtk/nx.py b/nipype/interfaces/cmtk/nx.py
+index a662eb65c6..991ca89dcf 100644
+--- a/nipype/interfaces/cmtk/nx.py
++++ b/nipype/interfaces/cmtk/nx.py
+@@ -24,11 +24,16 @@
+ iflogger = logging.getLogger("nipype.interface")
+ 
+ 
++def _read_pickle(fname):
++    with open(fname, 'rb') as f:
++        return pickle.load(f)
++
++
+ def read_unknown_ntwk(ntwk):
+     if not isinstance(ntwk, nx.classes.graph.Graph):
+         _, _, ext = split_filename(ntwk)
+         if ext == ".pck":
+-            ntwk = nx.read_gpickle(ntwk)
++            ntwk = _read_pickle(ntwk)
+         elif ext == ".graphml":
+             ntwk = nx.read_graphml(ntwk)
+     return ntwk
+@@ -121,7 +126,7 @@ def average_networks(in_files, ntwk_res_file, group_id):
+         counting_ntwk = ntwk.copy()
+         # Sums all the relevant variables
+         for index, subject in enumerate(in_files):
+-            tmp = nx.read_gpickle(subject)
++            tmp = _read_pickle(subject)
+             iflogger.info("File %s has %i edges", subject, tmp.number_of_edges())
+             edges = list(tmp.edges())
+             for edge in edges:
+@@ -461,7 +466,7 @@ def _run_interface(self, runtime):
+         edgentwks = list()
+         kntwks = list()
+         matlab = list()
+-        ntwk = nx.read_gpickle(self.inputs.in_file)
++        ntwk = _read_pickle(self.inputs.in_file)
+ 
+         # Each block computes, writes, and saves a measure
+         # The names are then added to the output .pck file list
+
+From f6bf0af19c044709de5be79a4488dcfd4d08f305 Mon Sep 17 00:00:00 2001
+From: Chris Markiewicz <effigies@gmail.com>
+Date: Sat, 28 Jan 2023 13:23:33 -0500
+Subject: [PATCH 9/9] FIX: Add dtypes to nilearn interface/tests
+
+---
+ nipype/interfaces/nilearn.py            | 2 +-
+ nipype/interfaces/tests/test_nilearn.py | 5 +++--
+ 2 files changed, 4 insertions(+), 3 deletions(-)
+
+diff --git a/nipype/interfaces/nilearn.py b/nipype/interfaces/nilearn.py
+index 053902e2bd..95494e7f5f 100644
+--- a/nipype/interfaces/nilearn.py
++++ b/nipype/interfaces/nilearn.py
+@@ -155,7 +155,7 @@ def _process_inputs(self):
+         if self.inputs.include_global:
+             global_label_data = label_data.dataobj.sum(axis=3)  # sum across all regions
+             global_label_data = (
+-                np.rint(global_label_data).astype(int).clip(0, 1)
++                np.rint(global_label_data).clip(0, 1).astype('u1')
+             )  # binarize
+             global_label_data = self._4d(global_label_data, label_data.affine)
+             global_masker = nl.NiftiLabelsMasker(
+diff --git a/nipype/interfaces/tests/test_nilearn.py b/nipype/interfaces/tests/test_nilearn.py
+index 2066c00768..4f94bbb87b 100644
+--- a/nipype/interfaces/tests/test_nilearn.py
++++ b/nipype/interfaces/tests/test_nilearn.py
+@@ -184,10 +184,11 @@ def assert_expected_output(self, labels, wanted):
+                 [[2, -2, -1, -2, -5], [3, 0, 3, -5, -2]],
+                 [[-4, -2, -2, 1, -2], [3, 1, 4, -3, -2]],
+             ],
+-        ]
++        ],
++        np.int16,
+     )
+ 
+-    fake_label_data = np.array([[[1, 0], [3, 1]], [[2, 0], [1, 3]]])
++    fake_label_data = np.array([[[1, 0], [3, 1]], [[2, 0], [1, 3]]], np.uint8)
+ 
+     fake_equiv_4d_label_data = np.array(
+         [
diff --git a/sci-libs/nipype/files/nipype-1.8.4-no_etelemetry.patch b/sci-libs/nipype/files/nipype-1.8.4-no_etelemetry.patch
new file mode 100644
index 000000000..b5c223422
--- /dev/null
+++ b/sci-libs/nipype/files/nipype-1.8.4-no_etelemetry.patch
@@ -0,0 +1,50 @@
+diff --git a/nipype/__init__.py b/nipype/__init__.py
+index 06084e823..2e42dcbce 100644
+--- a/nipype/__init__.py
++++ b/nipype/__init__.py
+@@ -73,23 +73,6 @@ from .interfaces import (
+ )
+ 
+ 
+-def check_latest_version(raise_exception=False):
+-    """
+-    Check for the latest version of the library.
+-
+-    Parameters
+-    ----------
+-    raise_exception: bool
+-        Raise a RuntimeError if a bad version is being used
+-    """
+-    import etelemetry
+-
+-    logger = logging.getLogger("nipype.utils")
+-    return etelemetry.check_available_version(
+-        "nipy/nipype", __version__, logger, raise_exception
+-    )
+-
+-
+ # Run telemetry on import for interactive sessions, such as IPython, Jupyter notebooks, Python REPL
+ if config.getboolean("execution", "check_version"):
+     import __main__
+@@ -98,4 +81,4 @@ if config.getboolean("execution", "check_version"):
+         from .interfaces.base import BaseInterface
+ 
+         if BaseInterface._etelemetry_version_data is None:
+-            BaseInterface._etelemetry_version_data = check_latest_version() or "n/a"
++            BaseInterface._etelemetry_version_data = "n/a"
+diff --git a/nipype/interfaces/base/core.py b/nipype/interfaces/base/core.py
+index c8099be63..f7770dbfc 100644
+--- a/nipype/interfaces/base/core.py
++++ b/nipype/interfaces/base/core.py
+@@ -183,10 +183,9 @@ class BaseInterface(Interface):
+             config.getboolean("execution", "check_version")
+             and "NIPYPE_NO_ET" not in os.environ
+         ):
+-            from ... import check_latest_version
+ 
+             if BaseInterface._etelemetry_version_data is None:
+-                BaseInterface._etelemetry_version_data = check_latest_version() or "n/a"
++                BaseInterface._etelemetry_version_data = "n/a"
+ 
+         if not self.input_spec:
+             raise Exception("No input_spec in class: %s" % self.__class__.__name__)
diff --git a/sci-libs/nipype/metadata.xml b/sci-libs/nipype/metadata.xml
index fddca4ca4..3c226af5f 100644
--- a/sci-libs/nipype/metadata.xml
+++ b/sci-libs/nipype/metadata.xml
@@ -2,7 +2,7 @@
 <!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
 <pkgmetadata>
 	<maintainer type="person">
-		<email>horea.christ@gmail.com</email>
+		<email>gentoo@chymera.eu</email>
 		<name>Horea Christian</name>
 	</maintainer>
 	<maintainer type="project">
diff --git a/sci-libs/nipype/nipype-0.12.0.ebuild b/sci-libs/nipype/nipype-0.12.0.ebuild
deleted file mode 100644
index 3b1397b0f..000000000
--- a/sci-libs/nipype/nipype-0.12.0.ebuild
+++ /dev/null
@@ -1,38 +0,0 @@
-# Copyright 1999-2016 Gentoo Foundation
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=6
-
-PYTHON_COMPAT=( python{2_7,3_4,3_5} )
-PYTHON_REQ_USE="threads(+),sqlite"
-
-inherit distutils-r1
-
-DESCRIPTION="Neuroimaging in Python: Pipelines and Interfaces"
-HOMEPAGE="http://nipy.sourceforge.net/nipype/"
-SRC_URI="https://github.com/nipy/nipype/archive/${PV}.tar.gz -> ${P}.tar.gz"
-
-LICENSE="BSD"
-SLOT="0"
-KEYWORDS="~amd64"
-IUSE="test"
-
-DEPEND="
-	dev-python/future[${PYTHON_USEDEP}]
-	dev-python/numpy[${PYTHON_USEDEP}]
-	dev-python/setuptools[${PYTHON_USEDEP}]
-	sci-libs/nibabel[${PYTHON_USEDEP}]
-	test? ( dev-python/mock[${PYTHON_USEDEP}] )
-	"
-RDEPEND="
-	dev-python/networkx[${PYTHON_USEDEP}]
-	dev-python/pydotplus[${PYTHON_USEDEP}]
-	dev-python/pygraphviz[${PYTHON_USEDEP}]
-	dev-python/traits[${PYTHON_USEDEP}]
-	sci-libs/scipy[${PYTHON_USEDEP}]
-	dev-python/simplejson[${PYTHON_USEDEP}]
-	"
-
-python_test() {
-	nosetests -v || die
-}
diff --git a/sci-libs/nipype/nipype-0.12.1.ebuild b/sci-libs/nipype/nipype-0.12.1.ebuild
deleted file mode 100644
index 3b1397b0f..000000000
--- a/sci-libs/nipype/nipype-0.12.1.ebuild
+++ /dev/null
@@ -1,38 +0,0 @@
-# Copyright 1999-2016 Gentoo Foundation
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=6
-
-PYTHON_COMPAT=( python{2_7,3_4,3_5} )
-PYTHON_REQ_USE="threads(+),sqlite"
-
-inherit distutils-r1
-
-DESCRIPTION="Neuroimaging in Python: Pipelines and Interfaces"
-HOMEPAGE="http://nipy.sourceforge.net/nipype/"
-SRC_URI="https://github.com/nipy/nipype/archive/${PV}.tar.gz -> ${P}.tar.gz"
-
-LICENSE="BSD"
-SLOT="0"
-KEYWORDS="~amd64"
-IUSE="test"
-
-DEPEND="
-	dev-python/future[${PYTHON_USEDEP}]
-	dev-python/numpy[${PYTHON_USEDEP}]
-	dev-python/setuptools[${PYTHON_USEDEP}]
-	sci-libs/nibabel[${PYTHON_USEDEP}]
-	test? ( dev-python/mock[${PYTHON_USEDEP}] )
-	"
-RDEPEND="
-	dev-python/networkx[${PYTHON_USEDEP}]
-	dev-python/pydotplus[${PYTHON_USEDEP}]
-	dev-python/pygraphviz[${PYTHON_USEDEP}]
-	dev-python/traits[${PYTHON_USEDEP}]
-	sci-libs/scipy[${PYTHON_USEDEP}]
-	dev-python/simplejson[${PYTHON_USEDEP}]
-	"
-
-python_test() {
-	nosetests -v || die
-}
diff --git a/sci-libs/nipype/nipype-0.14.0_pre20170830.ebuild b/sci-libs/nipype/nipype-0.14.0_pre20170830.ebuild
deleted file mode 100644
index ce6a52d9b..000000000
--- a/sci-libs/nipype/nipype-0.14.0_pre20170830.ebuild
+++ /dev/null
@@ -1,62 +0,0 @@
-# Copyright 1999-2018 Gentoo Foundation
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=7
-
-PYTHON_COMPAT=( python{2_7,3_4,3_5,3_6} )
-PYTHON_REQ_USE="threads(+),sqlite"
-
-inherit distutils-r1
-
-COMMIT="7055313c91de52bf65518284b42df446466fe581"
-
-DESCRIPTION="Neuroimaging in Python: Pipelines and Interfaces"
-HOMEPAGE="http://nipy.sourceforge.net/nipype/"
-SRC_URI="https://github.com/nipy/nipype/archive/${COMMIT}.tar.gz -> ${P}.tar.gz"
-
-LICENSE="BSD"
-SLOT="0"
-KEYWORDS="~amd64 ~x86"
-IUSE="test"
-
-DEPEND="
-	dev-python/future[${PYTHON_USEDEP}]
-	~dev-python/prov-1.5.0[${PYTHON_USEDEP}]
-	dev-python/numpy[${PYTHON_USEDEP}]
-	dev-python/setuptools[${PYTHON_USEDEP}]
-	>=sci-libs/nibabel-2.0.1[${PYTHON_USEDEP}]
-	test? (
-		dev-python/mock[${PYTHON_USEDEP}]
-		dev-python/pytest[${PYTHON_USEDEP}]
-	)
-	$(python_gen_cond_dep 'dev-python/configparser[${PYTHON_USEDEP}]' python2_7)
-	"
-RDEPEND="
-	>=dev-python/click-6.6[${PYTHON_USEDEP}]
-	dev-python/funcsigs[${PYTHON_USEDEP}]
-	dev-python/networkx[${PYTHON_USEDEP}]
-	dev-python/packaging[${PYTHON_USEDEP}]
-	dev-python/pydotplus[${PYTHON_USEDEP}]
-	dev-python/pygraphviz[${PYTHON_USEDEP}]
-	dev-python/pytest[${PYTHON_USEDEP}]
-	dev-python/python-dateutil[${PYTHON_USEDEP}]
-	>=dev-python/traits-4.6.0[${PYTHON_USEDEP}]
-	sci-libs/scipy[${PYTHON_USEDEP}]
-	dev-python/simplejson[${PYTHON_USEDEP}]
-	"
-
-S="${WORKDIR}/${PN}-${COMMIT}"
-
-python_prepare_all() {
-	distutils-r1_python_prepare_all
-	EXISTING_REQUIRE="setup_requires=\['future', 'configparser'\]"
-	CORRECTED_REQUIRE="setup_requires=\['future'\]"
-	sed \
-		-e "s/${EXISTING_REQUIRE}/${CORRECTED_REQUIRE}/g" \
-		-i setup.py \
-		|| die "sed setup.py"
-}
-
-python_test() {
-	nosetests -v || die
-}
diff --git a/sci-libs/nipype/nipype-1.1.0.ebuild b/sci-libs/nipype/nipype-1.1.0.ebuild
deleted file mode 100644
index 84e7e852b..000000000
--- a/sci-libs/nipype/nipype-1.1.0.ebuild
+++ /dev/null
@@ -1,54 +0,0 @@
-# Copyright 1999-2018 Gentoo Foundation
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=7
-
-PYTHON_COMPAT=( python{2_7,3_4,3_5,3_6} )
-PYTHON_REQ_USE="threads(+),sqlite"
-
-inherit distutils-r1
-
-DESCRIPTION="Neuroimaging in Python: Pipelines and Interfaces"
-HOMEPAGE="http://nipy.sourceforge.net/nipype/"
-SRC_URI="https://github.com/nipy/nipype/archive/${PV}.tar.gz -> ${P}.tar.gz"
-
-LICENSE="BSD"
-SLOT="0"
-KEYWORDS="~amd64 ~x86"
-IUSE="test"
-
-DEPEND="
-	dev-python/future[${PYTHON_USEDEP}]
-	dev-python/numpy[${PYTHON_USEDEP}]
-	~dev-python/prov-1.5.0[${PYTHON_USEDEP}]
-	dev-python/setuptools[${PYTHON_USEDEP}]
-	sci-libs/nibabel[${PYTHON_USEDEP}]
-	test? (
-		dev-python/mock[${PYTHON_USEDEP}]
-		dev-python/pytest[${PYTHON_USEDEP}]
-		dev-python/pytest-xdist[${PYTHON_USEDEP}]
-		${RDEPEND}
-		)
-	$(python_gen_cond_dep 'dev-python/configparser[${PYTHON_USEDEP}]' python2_7)
-	"
-RDEPEND="
-	>=dev-python/click-6.6[${PYTHON_USEDEP}]
-	dev-python/networkx[${PYTHON_USEDEP}]
-	dev-python/packaging[${PYTHON_USEDEP}]
-	dev-python/pydotplus[${PYTHON_USEDEP}]
-	dev-python/pygraphviz[${PYTHON_USEDEP}]
-	dev-python/python-dateutil[${PYTHON_USEDEP}]
-	dev-python/simplejson[${PYTHON_USEDEP}]
-	dev-python/traits[${PYTHON_USEDEP}]
-	sci-libs/scipy[${PYTHON_USEDEP}]
-	virtual/python-funcsigs[${PYTHON_USEDEP}]
-	"
-
-python_test() {
-	py.test -v --cov nipype\
-		--cov-config .coveragerc\
-		--cov-report xml:cov.xml\
-		-c nipype/pytest.ini\
-		--doctest-modules nipype\
-		|| die
-}
diff --git a/sci-libs/nipype/nipype-1.1.1.ebuild b/sci-libs/nipype/nipype-1.1.1.ebuild
deleted file mode 100644
index 70a0c37aa..000000000
--- a/sci-libs/nipype/nipype-1.1.1.ebuild
+++ /dev/null
@@ -1,57 +0,0 @@
-# Copyright 1999-2019 Gentoo Authors
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=7
-
-PYTHON_COMPAT=( python{2_7,3_4,3_5,3_6} )
-PYTHON_REQ_USE="threads(+),sqlite"
-
-inherit distutils-r1
-
-DESCRIPTION="Neuroimaging in Python: Pipelines and Interfaces"
-HOMEPAGE="http://nipy.sourceforge.net/nipype/"
-SRC_URI="https://github.com/nipy/nipype/archive/${PV}.tar.gz -> ${P}.tar.gz"
-
-LICENSE="BSD"
-SLOT="0"
-KEYWORDS="~amd64 ~x86"
-IUSE="test"
-
-DEPEND="
-	dev-python/future[${PYTHON_USEDEP}]
-	dev-python/numpy[${PYTHON_USEDEP}]
-	~dev-python/prov-1.5.0[${PYTHON_USEDEP}]
-	dev-python/setuptools[${PYTHON_USEDEP}]
-	sci-libs/nibabel[${PYTHON_USEDEP}]
-	test? (
-		dev-python/mock[${PYTHON_USEDEP}]
-		dev-python/pytest[${PYTHON_USEDEP}]
-		dev-python/pytest-xdist[${PYTHON_USEDEP}]
-		${RDEPEND}
-		)
-	$(python_gen_cond_dep '
-		dev-python/futures[${PYTHON_USEDEP}]
-		dev-python/configparser[${PYTHON_USEDEP}]' python2_7)
-	"
-RDEPEND="
-	>=dev-python/click-6.6[${PYTHON_USEDEP}]
-	dev-python/networkx[${PYTHON_USEDEP}]
-	dev-python/packaging[${PYTHON_USEDEP}]
-	dev-python/pydot[${PYTHON_USEDEP}]
-	dev-python/pydotplus[${PYTHON_USEDEP}]
-	dev-python/pygraphviz[${PYTHON_USEDEP}]
-	dev-python/python-dateutil[${PYTHON_USEDEP}]
-	dev-python/simplejson[${PYTHON_USEDEP}]
-	dev-python/traits[${PYTHON_USEDEP}]
-	sci-libs/scipy[${PYTHON_USEDEP}]
-	virtual/python-funcsigs[${PYTHON_USEDEP}]
-	"
-
-python_test() {
-	py.test -v --cov nipype\
-		--cov-config .coveragerc\
-		--cov-report xml:cov.xml\
-		-c nipype/pytest.ini\
-		--doctest-modules nipype\
-		|| die
-}
diff --git a/sci-libs/nipype/nipype-1.8.4-r1.ebuild b/sci-libs/nipype/nipype-1.8.4-r1.ebuild
new file mode 100644
index 000000000..7c2e801ff
--- /dev/null
+++ b/sci-libs/nipype/nipype-1.8.4-r1.ebuild
@@ -0,0 +1,94 @@
+# Copyright 1999-2023 Gentoo Authors
+# Distributed under the terms of the GNU General Public License v2
+
+EAPI=8
+
+DISTUTILS_USE_PEP517=setuptools
+PYTHON_COMPAT=( python3_{10..11} )
+PYTHON_REQ_USE="threads(+),sqlite"
+
+inherit distutils-r1
+
+DESCRIPTION="Neuroimaging in Python: Pipelines and Interfaces"
+HOMEPAGE="https://nipype.readthedocs.io/"
+SRC_URI="https://github.com/nipy/nipype/archive/${PV}.tar.gz -> ${P}.tar.gz"
+
+LICENSE="BSD"
+SLOT="0"
+KEYWORDS="~amd64"
+IUSE="test"
+RESTRICT="!test? ( test )"
+
+DEPEND="
+	dev-python/numpy[${PYTHON_USEDEP}]
+	dev-python/prov[${PYTHON_USEDEP}]
+	sci-libs/nibabel[${PYTHON_USEDEP}]
+	test? (
+		dev-python/mock[${PYTHON_USEDEP}]
+		dev-python/pytest[${PYTHON_USEDEP}]
+		${RDEPEND}
+		)
+"
+
+RDEPEND="
+	dev-python/click[${PYTHON_USEDEP}]
+	dev-python/filelock[${PYTHON_USEDEP}]
+	dev-python/looseversion[${PYTHON_USEDEP}]
+	dev-python/networkx[${PYTHON_USEDEP}]
+	dev-python/packaging[${PYTHON_USEDEP}]
+	dev-python/pydot[${PYTHON_USEDEP}]
+	dev-python/python-dateutil[${PYTHON_USEDEP}]
+	dev-python/rdflib[${PYTHON_USEDEP}]
+	dev-python/scipy[${PYTHON_USEDEP}]
+	dev-python/simplejson[${PYTHON_USEDEP}]
+	<dev-python/traits-6.4.0[${PYTHON_USEDEP}]
+"
+
+PATCHES=(
+	"${FILESDIR}/${PN}-1.8.4-dependency_compatibility.patch"
+)
+
+src_prepare() {
+	# Remove etelemetry
+	sed -i '/"etelemetry/d' nipype/info.py requirements.txt || die
+
+	# Mark failing tests
+	sed -i \
+		-e "/def test_no_et(tmp_path):/i@pytest.mark.skip('Known to fail by upstream: https://github.com/nipy/nipype/issues/3196#issuecomment-606003186')" \
+		nipype/tests/test_nipype.py || die
+	sed -i \
+		-e "/def test_fslversion():/i@pytest.mark.skip('Known to fail by upstream: https://github.com/nipy/nipype/issues/3196#issuecomment-605997462')" \
+		nipype/interfaces/fsl/tests/test_base.py || die
+	default
+}
+
+python_install_all() {
+	distutils-r1_python_install_all
+	doenvd "${FILESDIR}/98nipype"
+}
+
+# Reported upstream:
+# https://github.com/nipy/nipype/issues/3540
+EPYTEST_DESELECT=(
+	nipype/interfaces/tests/test_io.py::test_s3datagrabber_communication
+)
+
+python_test() {
+	# Setting environment variable to disable etelemetry version check:
+	# https://github.com/nipy/nipype/issues/3196#issuecomment-605980044
+	NIPYPE_NO_ET=1 epytest
+	# Upstream test configuration fails
+		#-c nipype/pytest.ini\
+		#--doctest-modules nipype\
+		#--cov nipype\
+		#--cov-config .coveragerc\
+		#--cov-report xml:cov.xml\
+}
+
+pkg_postinst() {
+	echo
+	einfo "Please run the following commands if you"
+	einfo "intend to use nipype from an existing shell:"
+	einfo "source /etc/profile"
+	echo
+}
diff --git a/sci-libs/nipype/nipype-1.8.4-r2.ebuild b/sci-libs/nipype/nipype-1.8.4-r2.ebuild
new file mode 100644
index 000000000..4c3da70b3
--- /dev/null
+++ b/sci-libs/nipype/nipype-1.8.4-r2.ebuild
@@ -0,0 +1,96 @@
+# Copyright 1999-2023 Gentoo Authors
+# Distributed under the terms of the GNU General Public License v2
+
+EAPI=8
+
+DISTUTILS_USE_PEP517=setuptools
+PYTHON_COMPAT=( python3_{10..11} )
+PYTHON_REQ_USE="threads(+),sqlite"
+
+inherit distutils-r1
+
+DESCRIPTION="Neuroimaging in Python: Pipelines and Interfaces"
+HOMEPAGE="https://nipype.readthedocs.io/"
+SRC_URI="https://github.com/nipy/nipype/archive/${PV}.tar.gz -> ${P}.tar.gz"
+
+LICENSE="BSD"
+SLOT="0"
+KEYWORDS="~amd64 ~x86"
+IUSE="test"
+RESTRICT="!test? ( test )"
+
+DEPEND="
+	dev-python/numpy[${PYTHON_USEDEP}]
+	dev-python/prov[${PYTHON_USEDEP}]
+	sci-libs/nibabel[${PYTHON_USEDEP}]
+	test? (
+		dev-python/mock[${PYTHON_USEDEP}]
+		dev-python/pytest[${PYTHON_USEDEP}]
+		${RDEPEND}
+		)
+"
+
+RDEPEND="
+	dev-python/click[${PYTHON_USEDEP}]
+	dev-python/filelock[${PYTHON_USEDEP}]
+	dev-python/looseversion[${PYTHON_USEDEP}]
+	dev-python/networkx[${PYTHON_USEDEP}]
+	dev-python/packaging[${PYTHON_USEDEP}]
+	dev-python/pydot[${PYTHON_USEDEP}]
+	dev-python/python-dateutil[${PYTHON_USEDEP}]
+	dev-python/rdflib[${PYTHON_USEDEP}]
+	dev-python/scipy[${PYTHON_USEDEP}]
+	dev-python/simplejson[${PYTHON_USEDEP}]
+	<dev-python/traits-6.4.0[${PYTHON_USEDEP}]
+"
+
+PATCHES=(
+	"${FILESDIR}/${PN}-1.8.4-dependency_compatibility.patch"
+	"${FILESDIR}/${PN}-1.8.4-no_etelemetry.patch"
+)
+
+src_prepare() {
+	# Remove etelemetry
+	# Doing this separately since the file is affected by another patch.
+	sed -i '/"etelemetry/d' nipype/info.py requirements.txt || die
+
+	# Mark failing tests
+	sed -i \
+		-e "/def test_no_et(tmp_path):/i@pytest.mark.skip('Known to fail by upstream: https://github.com/nipy/nipype/issues/3196#issuecomment-606003186')" \
+		nipype/tests/test_nipype.py || die
+	sed -i \
+		-e "/def test_fslversion():/i@pytest.mark.skip('Known to fail by upstream: https://github.com/nipy/nipype/issues/3196#issuecomment-605997462')" \
+		nipype/interfaces/fsl/tests/test_base.py || die
+	default
+}
+
+python_install_all() {
+	distutils-r1_python_install_all
+	doenvd "${FILESDIR}/98nipype"
+}
+
+# Reported upstream:
+# https://github.com/nipy/nipype/issues/3540
+EPYTEST_DESELECT=(
+	nipype/interfaces/tests/test_io.py::test_s3datagrabber_communication
+)
+
+python_test() {
+	# Setting environment variable to disable etelemetry version check:
+	# https://github.com/nipy/nipype/issues/3196#issuecomment-605980044
+	NIPYPE_NO_ET=1 epytest
+	# Upstream test configuration fails
+		#-c nipype/pytest.ini\
+		#--doctest-modules nipype\
+		#--cov nipype\
+		#--cov-config .coveragerc\
+		#--cov-report xml:cov.xml\
+}
+
+pkg_postinst() {
+	echo
+	einfo "Please run the following commands if you"
+	einfo "intend to use nipype from an existing shell:"
+	einfo "source /etc/profile"
+	echo
+}
diff --git a/sci-libs/nipype/nipype-1.8.6.ebuild b/sci-libs/nipype/nipype-1.8.6.ebuild
new file mode 100644
index 000000000..88bc23395
--- /dev/null
+++ b/sci-libs/nipype/nipype-1.8.6.ebuild
@@ -0,0 +1,97 @@
+# Copyright 1999-2023 Gentoo Authors
+# Distributed under the terms of the GNU General Public License v2
+
+EAPI=8
+
+DISTUTILS_USE_PEP517=setuptools
+PYTHON_COMPAT=( python3_{10..11} )
+PYTHON_REQ_USE="threads(+),sqlite"
+
+inherit distutils-r1
+
+DESCRIPTION="Neuroimaging in Python: Pipelines and Interfaces"
+HOMEPAGE="https://nipype.readthedocs.io/"
+SRC_URI="https://github.com/nipy/nipype/archive/${PV}.tar.gz -> ${P}.tar.gz"
+
+LICENSE="BSD"
+SLOT="0"
+KEYWORDS="~amd64 ~x86"
+IUSE="test"
+# Tests fail with numpy import error:
+# https://github.com/nipy/nipype/issues/3626
+RESTRICT="test"
+
+DEPEND="
+	dev-python/numpy[${PYTHON_USEDEP}]
+	dev-python/prov[${PYTHON_USEDEP}]
+	sci-libs/nibabel[${PYTHON_USEDEP}]
+	test? (
+		dev-python/mock[${PYTHON_USEDEP}]
+		dev-python/pytest[${PYTHON_USEDEP}]
+		${RDEPEND}
+		)
+"
+
+RDEPEND="
+	dev-python/click[${PYTHON_USEDEP}]
+	dev-python/filelock[${PYTHON_USEDEP}]
+	dev-python/looseversion[${PYTHON_USEDEP}]
+	dev-python/networkx[${PYTHON_USEDEP}]
+	dev-python/packaging[${PYTHON_USEDEP}]
+	dev-python/pydot[${PYTHON_USEDEP}]
+	dev-python/python-dateutil[${PYTHON_USEDEP}]
+	dev-python/rdflib[${PYTHON_USEDEP}]
+	dev-python/scipy[${PYTHON_USEDEP}]
+	dev-python/simplejson[${PYTHON_USEDEP}]
+	<dev-python/traits-6.4.0[${PYTHON_USEDEP}]
+"
+
+PATCHES=(
+	"${FILESDIR}/${PN}-1.8.4-no_etelemetry.patch"
+)
+
+src_prepare() {
+	# Remove etelemetry
+	# Doing this separately since the file is affected by another patch.
+	sed -i '/"etelemetry/d' nipype/info.py requirements.txt || die
+
+	# Mark failing tests
+	sed -i \
+		-e "/def test_no_et(tmp_path):/i@pytest.mark.skip('Known to fail by upstream: https://github.com/nipy/nipype/issues/3196#issuecomment-606003186')" \
+		nipype/tests/test_nipype.py || die
+	sed -i \
+		-e "/def test_fslversion():/i@pytest.mark.skip('Known to fail by upstream: https://github.com/nipy/nipype/issues/3196#issuecomment-605997462')" \
+		nipype/interfaces/fsl/tests/test_base.py || die
+	default
+}
+
+python_install_all() {
+	distutils-r1_python_install_all
+	doenvd "${FILESDIR}/98nipype"
+}
+
+# Reported upstream:
+# https://github.com/nipy/nipype/issues/3540
+EPYTEST_DESELECT=(
+	nipype/interfaces/tests/test_io.py::test_s3datagrabber_communication
+)
+
+python_test() {
+	# Setting environment variable to disable etelemetry version check:
+	# https://github.com/nipy/nipype/issues/3196#issuecomment-605980044
+	NIPYPE_NO_ET=1 epytest
+	# Upstream test configuration fails
+		#-c nipype/pytest.ini\
+		#--doctest-modules nipype\
+		#--cov nipype\
+		#--cov-config .coveragerc\
+		#--cov-report xml:cov.xml\
+}
+
+pkg_postinst() {
+	echo
+	einfo "Please run the following commands if you"
+	einfo "intend to use nipype from an existing shell:"
+	einfo "source /etc/profile"
+	echo
+}
diff --git a/sci-libs/nipype/nipype-9999.ebuild b/sci-libs/nipype/nipype-9999.ebuild
deleted file mode 100644
index df9829dbd..000000000
--- a/sci-libs/nipype/nipype-9999.ebuild
+++ /dev/null
@@ -1,58 +0,0 @@
-# Copyright 1999-2019 Gentoo Authors
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=7
-
-PYTHON_COMPAT=( python{2_7,3_4,3_5,3_6} )
-PYTHON_REQ_USE="threads(+),sqlite"
-
-inherit distutils-r1 git-r3
-
-DESCRIPTION="Neuroimaging in Python: Pipelines and Interfaces"
-HOMEPAGE="http://nipy.sourceforge.net/nipype/"
-SRC_URI=""
-EGIT_REPO_URI="https://github.com/nipy/nipype"
-
-LICENSE="Apache-2.0"
-SLOT="0"
-KEYWORDS=""
-IUSE="test"
-
-DEPEND="
-	dev-python/future[${PYTHON_USEDEP}]
-	dev-python/numpy[${PYTHON_USEDEP}]
-	~dev-python/prov-1.5.0[${PYTHON_USEDEP}]
-	dev-python/setuptools[${PYTHON_USEDEP}]
-	sci-libs/nibabel[${PYTHON_USEDEP}]
-	test? (
-		dev-python/mock[${PYTHON_USEDEP}]
-		dev-python/pytest[${PYTHON_USEDEP}]
-		dev-python/pytest-xdist[${PYTHON_USEDEP}]
-		${RDEPEND}
-		)
-	$(python_gen_cond_dep '
-		dev-python/futures[${PYTHON_USEDEP}]
-		dev-python/configparser[${PYTHON_USEDEP}]' python2_7)
-	"
-RDEPEND="
-	>=dev-python/click-6.6[${PYTHON_USEDEP}]
-	dev-python/networkx[${PYTHON_USEDEP}]
-	dev-python/packaging[${PYTHON_USEDEP}]
-	dev-python/pydot[${PYTHON_USEDEP}]
-	dev-python/pydotplus[${PYTHON_USEDEP}]
-	dev-python/pygraphviz[${PYTHON_USEDEP}]
-	dev-python/python-dateutil[${PYTHON_USEDEP}]
-	dev-python/simplejson[${PYTHON_USEDEP}]
-	dev-python/traits[${PYTHON_USEDEP}]
-	sci-libs/scipy[${PYTHON_USEDEP}]
-	virtual/python-funcsigs[${PYTHON_USEDEP}]
-	"
-
-python_test() {
-	py.test -v --cov nipype\
-		--cov-config .coveragerc\
-		--cov-report xml:cov.xml\
-		-c nipype/pytest.ini\
-		--doctest-modules nipype\
-		|| die
-}
diff --git a/sci-libs/o2scl/Manifest b/sci-libs/o2scl/Manifest
deleted file mode 100644
index fc05a1690..000000000
--- a/sci-libs/o2scl/Manifest
+++ /dev/null
@@ -1 +0,0 @@
-DIST o2scl-0.915.tar.gz 19066580 BLAKE2B 2c401c4c1dd5161f3f6925eabbfcf37d1978af4dbc298dc9e943181a98d653793c1dce4c17eaf22d711b801f499d43025b8b26e17c4a3db8563ed985b4686319 SHA512 7603def9ad961bb3d3051a9c55e96e5e91e75d396b8770519bb2e4560ba0fb3b4c06f4f0913bbfabce829128878dc80b0ae0616c612f3f1617846ed05a9e7d7d
diff --git a/sci-libs/o2scl/metadata.xml b/sci-libs/o2scl/metadata.xml
deleted file mode 100644
index 20d390281..000000000
--- a/sci-libs/o2scl/metadata.xml
+++ /dev/null
@@ -1,18 +0,0 @@
-<?xml version="1.0" encoding="UTF-8"?>
-<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
-<pkgmetadata>
-	<maintainer type="project">
-		<email>sci@gentoo.org</email>
-		<name>Gentoo Science Project</name>
-	</maintainer>
-	<longdescription lang="en">
-O2scl is a C++ class library for object-oriented numerical
-programming. It includes classes based on numerical routines from
-GSL and CERNLIB and two sub-libraries: thermodynamics of ideal and
-nearly-ideal particles with quantum statistics and e quations of
-state for finite density relevant for neutron stars.
-</longdescription>
-	<upstream>
-		<remote-id type="sourceforge">o2scl</remote-id>
-	</upstream>
-</pkgmetadata>
diff --git a/sci-libs/o2scl/o2scl-0.915.ebuild b/sci-libs/o2scl/o2scl-0.915.ebuild
deleted file mode 100644
index e7290d78d..000000000
--- a/sci-libs/o2scl/o2scl-0.915.ebuild
+++ /dev/null
@@ -1,46 +0,0 @@
-# Copyright 1999-2014 Gentoo Foundation
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=5
-
-AUTOTOOLS_IN_SOURCE_BUILD=1
-inherit autotools-utils flag-o-matic
-
-DESCRIPTION="Object-oriented Scientific Computing Library"
-HOMEPAGE="http://o2scl.sourceforge.net/"
-SRC_URI="mirror://sourceforge/${PN}/${P}.tar.gz"
-
-LICENSE="GPL-3"
-SLOT="0"
-KEYWORDS="~amd64 ~x86 ~amd64-linux ~x86-linux"
-IUSE="debug doc examples hdf5 static-libs"
-
-RDEPEND="
-	dev-libs/boost:0=
-	sci-libs/gsl:0=
-	hdf5? ( sci-libs/hdf5:0= )"
-DEPEND="${RDEPEND}"
-
-src_configure() {
-	use debug || append-cppflags -DO2SCL_NO_RANGE_CHECK
-	local myeconfargs=(
-		$(use_enable hdf5 hdf)
-		$(use_enable hdf5 partlib)
-		$(use_enable hdf5 eoslib)
-	)
-	autotools-utils_src_configure
-}
-
-src_test() {
-	autotools-utils_src_test o2scl-test
-}
-
-src_install() {
-	autotools-utils_src_install
-	rm -r "${ED}"/usr/doc || die
-	use doc && dohtml -r doc/o2scl/html/*
-	if use examples; then
-		insinto /usr/share/doc/${PF}
-		doins -r examples
-	fi
-}
diff --git a/sci-libs/oasa/Manifest b/sci-libs/oasa/Manifest
deleted file mode 100644
index 0ea538000..000000000
--- a/sci-libs/oasa/Manifest
+++ /dev/null
@@ -1 +0,0 @@
-DIST oasa-0.13.1.tar.gz 165293 BLAKE2B c692c94224fbed1268c9f374a1234a098699944429ff0312b297eb594c66e15daf1b7bc5d766937c0fb82878c04fddbba88012ca1749adc686c321b28f09fd4c SHA512 9aa8f682b8f9d8eacee05df41bb072cc583f12a69ff0ea88e8311b6e074b42e00b4f4909056adba827de5c4cd1af0da9d2faeaa974f0b9720e2847f39af47c0c
diff --git a/sci-libs/oasa/metadata.xml b/sci-libs/oasa/metadata.xml
deleted file mode 100644
index e66cf80b9..000000000
--- a/sci-libs/oasa/metadata.xml
+++ /dev/null
@@ -1,14 +0,0 @@
-<?xml version="1.0" encoding="UTF-8"?>
-<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
-<pkgmetadata>
-	<maintainer type="project">
-		<email>sci-chemistry@gentoo.org</email>
-		<name>Gentoo Chemistry Project</name>
-	</maintainer>
-	<longdescription>
-OASA is a python library for manipulation of chemical formats that forms the base of BKChem. It is in separate package, because there are other programs using it (e.g. Pybel in <pkg>sci-chemistry/openbabel-python</pkg>).
-</longdescription>
-	<use>
-		<flag name="cairo">Add support for Cairo graphics library using <pkg>dev-python/pycairo</pkg></flag>
-	</use>
-</pkgmetadata>
diff --git a/sci-libs/oasa/oasa-0.13.1.ebuild b/sci-libs/oasa/oasa-0.13.1.ebuild
deleted file mode 100644
index af02300ad..000000000
--- a/sci-libs/oasa/oasa-0.13.1.ebuild
+++ /dev/null
@@ -1,20 +0,0 @@
-# Copyright 1999-2014 Gentoo Foundation
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=5
-
-PYTHON_COMPAT=( python2_7 )
-
-inherit distutils-r1
-
-DESCRIPTION="Python library for manipulation of chemical structures"
-HOMEPAGE="http://bkchem.zirael.org/oasa_en.html"
-SRC_URI="http://bkchem.zirael.org/download/${P}.tar.gz"
-
-LICENSE="GPL-2"
-SLOT="0"
-KEYWORDS="~amd64 ~x86"
-IUSE="cairo"
-
-DEPEND=""
-RDEPEND="cairo? ( >=dev-python/pycairo-1.2[${PYTHON_USEDEP}] )"
diff --git a/sci-libs/omalloc/Manifest b/sci-libs/omalloc/Manifest
deleted file mode 100644
index 1e1200355..000000000
--- a/sci-libs/omalloc/Manifest
+++ /dev/null
@@ -1 +0,0 @@
-DIST Singular-3-1-1-2.tar.gz 19397418 BLAKE2B 24f853864bcaac5e5af48970a47fe77ab50383e739d0b35d7a4477d4e771c3069027e257e5303e601528b74c906d4f017ba37202c79dc4b78a68a2c2a5dd0924 SHA512 340ad7580a35f47ffcb314970b3fb800d4bf3b6d08761c0403dd80c7e944b790e06f84f28ede8f09871cdaf2e3770847264f5d5190ebbbe91dd9b0d1820772cd
diff --git a/sci-libs/omalloc/files/omalloc-0.9.6-gentoo.diff b/sci-libs/omalloc/files/omalloc-0.9.6-gentoo.diff
deleted file mode 100644
index 6491bf47e..000000000
--- a/sci-libs/omalloc/files/omalloc-0.9.6-gentoo.diff
+++ /dev/null
@@ -1,133 +0,0 @@
---- Makefile.in
-+++ Makefile.in
-@@ -8,7 +8,8 @@
- 
- SHELL		= /bin/sh
- VERSION 	= @VERSION@
--
-+LIBOMALLOC_SO	= libomalloc.so
-+LIBOMALLOC_SOVER= libomalloc.so.$(VERSION)
- ##
- ## various paths
- ##
-@@ -83,9 +84,11 @@
- omAllocSystem.h        omFindExec.h           omStats.h		\
- omBin.h                omDefaultConfig.h      omStructs.h	\
- omBinPage.h            omInline.h             omGetBackTrace.h  \
--omReturn.h	       omRet2Info.h	      omAllocFunc.h		
-+omReturn.h	       omRet2Info.h	      omAllocFunc.h	\
-+omTables.h
- 
- OBJS := $(CSOURCES:.c=.o)  $(GSOURCES:.c=.o)
-+OBJS_SHARED := $(CSOURCES:.c=.o_pic)  $(GSOURCES:.c=.o_pic)
- OBJS_NDEBUG := $(CSOURCES:.c=.o_ndebug) $(GSOURCES:.c=.o_ndebug)
- 
- SOURCES=${CSOURCES} omGetPageSize.h omMallocSystem.h gmalloc.c dlmalloc.h dlmalloc.c \
-@@ -103,6 +106,9 @@
- %.o: %.c omConfig.h omlimits.h omTables.h omalloc.h omTables.inc
- 	${CC} ${CFLAGS} ${CPPFLAGS} ${DEFS} -c $<
- 
-+%.o_pic: %.c omConfig.h omlimits.h mylimits.h omTables.h omalloc.h omTables.inc
-+	${CC} ${CFLAGS} ${CPPFLAGS} ${DEFS} -fPIC -c $< -o $@
-+
- %.o_ndebug: %.c omConfig.h omlimits.h mylimits.h omTables.h omalloc.h omTables.inc
- 	${CC} ${CFLAGS} ${CPPFLAGS} ${DEFS} -DOM_NDEBUG -c $< -o $@
- 
-@@ -113,9 +119,12 @@
- %.aso: %.aso.o
- 	./$< > $@
- 
--all:	libomalloc.a libomalloc_ndebug.a omalloc.h omalloc.o omalloc_debug.o
-+all: lib omalloc.h omalloc.o omalloc_debug.o
-+
-+lib: libomalloc.a $(LIBOMALLOC_SOVER)
- 
--lib: libomalloc.a
-+$(LIBOMALLOC_SOVER): $(OBJS_SHARED) Makefile omConfig.h omlimits.h mylimits.h
-+	$(CC) -shared -Wl,-soname,$(LIBOMALLOC_SO).0 $(LDFLAGS) -o $@ $(OBJS_SHARED)
- 
- libomalloc.a: $(OBJS) Makefile omConfig.h omlimits.h mylimits.h
- 	rm -f $@
-@@ -130,10 +139,10 @@
- omalloc.h: $(HEADERS)
- 	./makeheader om_Alloc.h $@
- 
--omalloc.o: omalloc.c
-+omalloc.o: omalloc.c omalloc.h
- 	${CC} ${CFLAGS} ${CPPFLAGS} ${DEFS} -DOM_NDEBUG -c $< -o $@
- 
--omalloc_debug.o: omalloc_debug.c
-+omalloc_debug.o: omalloc_debug.c omalloc.h
- 	${CC} ${CFLAGS} ${CPPFLAGS} ${DEFS} -c $< -o $@
- 
- omTables.inc: omTables
-@@ -190,37 +199,32 @@
- install-nolns: install
- 
- install-libsingular:
--	$(MKINSTALLDIRS) $(includedir)/singular
--	$(INSTALL) omalloc.h $(includedir)/singular
-+	$(INSTALL) -D omalloc.h $(DESTDIR)$(includedir)/singular
- 
- install: all
--	$(MKINSTALLDIRS) $(libdir)
--	$(MKINSTALLDIRS) $(includedir)
--	$(INSTALL_DATA) libomalloc.a $(libdir)
--	$(RANLIB) $(libdir)/libomalloc.a
--	$(INSTALL_DATA) libomalloc_ndebug.a $(libdir)
--	$(RANLIB) $(libdir)/libomalloc_ndebug.a
--	$(INSTALL_DATA) omalloc.o $(libdir)
--	$(INSTALL_DATA) omalloc_debug.o $(libdir)
--	$(INSTALL_DATA) omalloc.h $(includedir)
--	$(INSTALL_DATA) omalloc.c $(includedir)
--	$(INSTALL_DATA) omlimits.h $(includedir)
--	$(INSTALL_DATA) mylimits.h $(includedir)
-+	$(INSTALL_DATA) -D $(LIBOMALLOC_SOVER) $(DESTDIR)$(libdir)/$(LIBOMALLOC_SOVER)
-+	$(LN_S) $(LIBOMALLOC_SOVER) $(DESTDIR)$(libdir)/$(LIBOMALLOC_SO)
-+	$(LN_S) $(LIBOMALLOC_SOVER) $(DESTDIR)$(libdir)/$(LIBOMALLOC_SO).0
-+	$(INSTALL_DATA) -D libomalloc.a $(DESTDIR)$(libdir)/libomalloc.a
-+	$(RANLIB) $(DESTDIR)$(libdir)/libomalloc.a
-+	$(INSTALL_DATA) omalloc.o $(DESTDIR)$(libdir)/omalloc.o
-+	$(INSTALL_DATA) -D omalloc.h $(DESTDIR)$(includedir)/omalloc.h
-+	$(INSTALL_DATA) omalloc.c $(DESTDIR)$(includedir)/omalloc.c
-+	$(INSTALL_DATA) omlimits.h $(DESTDIR)$(includedir)/omlimits.h
-+	$(INSTALL_DATA) mylimits.h $(DESTDIR)$(includedir)/mylimits.h
- 
- install_all: install libomalloc_p.a
--	$(INSTALL_DATA) libomalloc_p.a $(libdir)
--	$(RANLIB) $(libdir)/libomalloc_p.a
-+	$(INSTALL_DATA) -D libomalloc_p.a $(DESTDIR)$(libdir)/libomalloc_p.a
-+	$(RANLIB) $(DESTDIR)$(libdir)/libomalloc_p.a
- 
--install_min: libomalloc_ndebug.a omalloc.o
--	$(MKINSTALLDIRS) $(libdir)
--	$(MKINSTALLDIRS) $(includedir)
--	$(INSTALL_DATA) libomalloc_ndebug.a $(libdir)
--	$(RANLIB) $(libdir)/libomalloc_ndebug.a
--	$(INSTALL_DATA) omalloc.o $(libdir)
--	$(INSTALL_DATA) omalloc.h $(includedir)
--	$(INSTALL_DATA) omalloc.c $(includedir)
--	$(INSTALL_DATA) omlimits.h $(includedir)
--	$(INSTALL_DATA) mylimits.h $(includedir)
-+install_min: omalloc.o
-+	$(INSTALL_DATA) -D libomalloc.a $(DESTDIR)$(libdir)/libomalloc.a
-+	$(RANLIB) $(DESTDIR)$(libdir)/libomalloc.a
-+	$(INSTALL_DATA) omalloc.o $(DESTDIR)$(libdir)/omalloc.o
-+	$(INSTALL_DATA) -D omalloc.h $(DESTDIR)$(includedir)/omalloc.h
-+	$(INSTALL_DATA) omalloc.c $(DESTDIR)$(includedir)/omalloc.c
-+	$(INSTALL_DATA) omlimits.h $(DESTDIR)$(includedir)/omlimits.h
-+	$(INSTALL_DATA) mylimits.h $(DESTDIR)$(includedir)/mylimits.h
- 
- uninstall:
- 	rm -f $(includedir)/omalloc.h $(includedir)/omalloc.c
-@@ -266,9 +270,8 @@
- ## check
- ##
- 
--check: omtTest omtTest_ndebug
-+check: omtTest
- 	./omtTest
--	./omtTest_ndebug
- 
- ##
- ## Below here is stuff for developpers
diff --git a/sci-libs/omalloc/files/parallel-build.patch b/sci-libs/omalloc/files/parallel-build.patch
deleted file mode 100644
index 45aeb641d..000000000
--- a/sci-libs/omalloc/files/parallel-build.patch
+++ /dev/null
@@ -1,25 +0,0 @@
---- Makefile.in.org	2010-07-05 12:00:56.000000000 +0200
-+++ Makefile.in	2010-07-05 12:05:02.000000000 +0200
-@@ -83,7 +83,8 @@
- omAllocSystem.h        omFindExec.h           omStats.h		\
- omBin.h                omDefaultConfig.h      omStructs.h	\
- omBinPage.h            omInline.h             omGetBackTrace.h  \
--omReturn.h	       omRet2Info.h	      omAllocFunc.h		
-+omReturn.h	       omRet2Info.h	      omAllocFunc.h     \
-+omTables.h
- 
- OBJS := $(CSOURCES:.c=.o)  $(GSOURCES:.c=.o)
- OBJS_NDEBUG := $(CSOURCES:.c=.o_ndebug) $(GSOURCES:.c=.o_ndebug)
-@@ -130,10 +131,10 @@
- omalloc.h: $(HEADERS)
- 	./makeheader om_Alloc.h $@
- 
--omalloc.o: omalloc.c
-+omalloc.o: omalloc.c omalloc.h
- 	${CC} ${CFLAGS} ${CPPFLAGS} ${DEFS} -DOM_NDEBUG -c $< -o $@
- 
--omalloc_debug.o: omalloc_debug.c
-+omalloc_debug.o: omalloc_debug.c omalloc.h
- 	${CC} ${CFLAGS} ${CPPFLAGS} ${DEFS} -c $< -o $@
- 
- omTables.inc: omTables
diff --git a/sci-libs/omalloc/metadata.xml b/sci-libs/omalloc/metadata.xml
deleted file mode 100644
index aa6213746..000000000
--- a/sci-libs/omalloc/metadata.xml
+++ /dev/null
@@ -1,15 +0,0 @@
-<?xml version="1.0" encoding="UTF-8"?>
-<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
-<pkgmetadata>
-	<maintainer type="person">
-		<email>tom111@gmx.de</email>
-		<name>Thomas Kahle</name>
-	</maintainer>
-	<maintainer type="project">
-		<email>sci@gentoo.org</email>
-		<name>Gentoo Science Project</name>
-	</maintainer>
-	<longdescription lang="en">
-omalloc is the memory management of Singular
-</longdescription>
-</pkgmetadata>
diff --git a/sci-libs/omalloc/omalloc-0.9.6.ebuild b/sci-libs/omalloc/omalloc-0.9.6.ebuild
deleted file mode 100644
index bfb71ea88..000000000
--- a/sci-libs/omalloc/omalloc-0.9.6.ebuild
+++ /dev/null
@@ -1,39 +0,0 @@
-# Copyright 1999-2015 Gentoo Foundation
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=5
-
-inherit eutils toolchain-funcs versionator
-
-Sing_PV=$(replace_all_version_separators -)
-Sing_DIR=$(get_version_component_range 1-3 ${MY_PV})
-MY_PV_SHARE=${MY_PV}
-
-DESCRIPTION="omalloc is the memory management of the Singular algebra system"
-HOMEPAGE="http://www.singular.uni-kl.de/"
-SRC_COM="http://www.mathematik.uni-kl.de/ftp/pub/Math/Singular/SOURCES/3-1-1"
-SRC_URI="${SRC_COM}/Singular-3-1-1-2.tar.gz"
-
-LICENSE="GPL-2"
-SLOT="0"
-KEYWORDS="~amd64 ~x86"
-IUSE=""
-
-S=${WORKDIR}/Singular-3-1-1/omalloc
-
-pkg_setup() {
-	tc-export CC CXX
-}
-
-src_prepare (){
-	epatch "${FILESDIR}"/${P}-gentoo.diff
-}
-
-src_configure() {
-	econf \
-		$(use_with debug)
-}
-
-src_test () {
-	emake check
-}
diff --git a/sci-libs/oneDAL/Manifest b/sci-libs/oneDAL/Manifest
new file mode 100644
index 000000000..4ea34591f
--- /dev/null
+++ b/sci-libs/oneDAL/Manifest
@@ -0,0 +1,4 @@
+DIST mklfpk_lnx_20221214.tgz 88817211 BLAKE2B 3416ce8fe8c768c0d8598536d23f68aafe9e47590d854ce19e8ac79108aa5f10a2fd2fdbf7c96aec9f083ef8ad3ae7a1515e5f5b0e565f0c1686cc5fc0eeb02d SHA512 c0a0beb56c3f41deff9b587d116e7cd366ff31b393a78d4ad608ef620d5b503bc80b720eb61b9355c8d5547a3a566f223d5deb3421c97498fbff90997d8d7e62
+DIST mklgpufpk_lnx_20221214.tgz 15283052 BLAKE2B 54137083613cef5114cd95cade61e58456a0858bd46ecc9fe2294ba06d5bd405bbb1259b16f9003ba466a91cfa0b3801dc8485338fd11d612f09811741ff25a2 SHA512 2cf035133269ac24fa7d39aecaa673d21a65b772d86179a04fec20e4d6e1ad20122ae8ce262f2814ad768272258c512e6fedf0ab978ed687ba54949bb7b6b3b5
+DIST oneDAL-2023.0.1.tar.gz 61208026 BLAKE2B 2a9509fe59808ee1211b39b2ae0da34b37ba73e747316fdb407112611bbba1b808d451f5aef0afc9552178839adaae71bbe80c2fdeea39a23048674f87b159c1 SHA512 58e9aacc5c09bae67d5bdc6477b7e5d6f0c696513e532d778ae427314e35f629c6c3b8d94f382638ab736786f4ae965dcbdf2e25ab018efc863ee21000116894
+DIST oneDAL-2023.2.1.tar.gz 50938584 BLAKE2B c14bbdc7a1d4faf5266f47a0849a1a9403824c6824ca392f5bafc5fe7c9e6abd6448647cb73d1ffd9cec8b347bba2ca3d58d86306af185896a0a5880132e593a SHA512 d412bd8f353a017929b31411ff2788fada04ceee9cb4f6d98828e5bb10a50a28dc4d73f89da0a0db21baf1cb4accebfb647198331748f95a6af9299c4977d5b7
diff --git a/sci-libs/oneDAL/files/oneDAL-2021.7.1_p20221207-fix-compile.patch b/sci-libs/oneDAL/files/oneDAL-2021.7.1_p20221207-fix-compile.patch
new file mode 100644
index 000000000..553e742ab
--- /dev/null
+++ b/sci-libs/oneDAL/files/oneDAL-2021.7.1_p20221207-fix-compile.patch
@@ -0,0 +1,164 @@
+diff --git a/dev/bazel/deps/onedal.bzl b/dev/bazel/deps/onedal.bzl
+index f0f7662..6b9d11f 100644
+--- a/dev/bazel/deps/onedal.bzl
++++ b/dev/bazel/deps/onedal.bzl
+@@ -21,18 +21,12 @@ onedal_repo = repos.prebuilt_libs_repo_rule(
+         "include",
+     ],
+     libs = [
+-        # Static
+-        "lib/intel64/libonedal_core.a",
+-        "lib/intel64/libonedal_thread.a",
+-        "lib/intel64/libonedal.a",
+-        "lib/intel64/libonedal_dpc.a",
+-        "lib/intel64/libonedal_sycl.a",
+-
+         # Dynamic
+         "lib/intel64/libonedal_core.so",
+         "lib/intel64/libonedal_thread.so",
+         "lib/intel64/libonedal.so",
+         "lib/intel64/libonedal_dpc.so",
++        "lib/intel64/libonedal_sycl.so",
+     ],
+     build_template = "@onedal//dev/bazel/deps:onedal.tpl.BUILD",
+ )
+diff --git a/dev/bazel/deps/onedal.tpl.BUILD b/dev/bazel/deps/onedal.tpl.BUILD
+index 60be678..0f7990e 100644
+--- a/dev/bazel/deps/onedal.tpl.BUILD
++++ b/dev/bazel/deps/onedal.tpl.BUILD
+@@ -9,62 +9,17 @@ cc_library(
+     includes = [ "include" ],
+ )
+ 
+-cc_library(
+-    name = "core_static",
+-    srcs = [
+-        "lib/intel64/libonedal_core.a",
+-    ],
+-    deps = [
+-        ":headers",
+-        # TODO: Currently vml_ipp lib depends on TBB, but it shouldn't
+-        #       Remove TBB from deps once problem with vml_ipp is resolved
+-        "@tbb//:tbb_binary",
+-    ],
+-)
+-
+-cc_library(
+-    name = "thread_static",
+-    srcs = [
+-        "lib/intel64/libonedal_thread.a",
+-    ],
+-    deps = [
+-        ":headers",
+-        "@tbb//:tbb_binary",
+-        "@tbb//:tbbmalloc_binary",
+-    ],
+-)
+ 
+ cc_library(
+     name = "onedal_sycl",
+     srcs = [
+-        "lib/intel64/libonedal_sycl.a",
+-    ],
+-    deps = [
+-        ":headers",
+-    ],
+-)
+-
+-cc_library(
+-    name = "onedal_static",
+-    srcs = [
+-        "lib/intel64/libonedal.a",
++        "lib/intel64/libonedal_sycl.so",
+     ],
+     deps = [
+         ":headers",
+     ],
+ )
+ 
+-cc_library(
+-    name = "onedal_static_dpc",
+-    srcs = [
+-        "lib/intel64/libonedal_dpc.a",
+-    ],
+-    deps = [
+-        ":headers",
+-        ":onedal_sycl",
+-    ],
+-)
+-
+ cc_library(
+     name = "core_dynamic",
+     srcs = [
+diff --git a/dev/make/cmplr.dpcpp.mk b/dev/make/cmplr.dpcpp.mk
+index 2ac2ed9..bd0e182 100644
+--- a/dev/make/cmplr.dpcpp.mk
++++ b/dev/make/cmplr.dpcpp.mk
+@@ -28,13 +28,13 @@ CORE.SERV.COMPILER.dpcpp = generic
+ -Zl.dpcpp =
+ -DEBC.dpcpp = -g
+ 
+-COMPILER.lnx.dpcpp = icpx -fsycl $(if $(IA_is_ia32),-m32,-m64) -stdlib=libstdc++ -fgnu-runtime -fwrapv \
+-                     -Werror -Wreturn-type -fsycl-device-code-split=per_kernel
+-COMPILER.win.dpcpp = icx -fsycl $(if $(MSVC_RT_is_release),-MD, -MDd /debug:none) -nologo -WX \
++COMPILER.lnx.dpcpp = $(CXX) $(CXXFLAGS) -fsycl $(if $(IA_is_ia32),-m32,-m64) -stdlib=libstdc++ -fgnu-runtime -fwrapv \
++                     -Wreturn-type -fsycl-device-code-split=per_kernel
++COMPILER.win.dpcpp = $(CC) $(CFLAGS) -fsycl $(if $(MSVC_RT_is_release),-MD, -MDd /debug:none) -nologo -WX \
+                      -Wno-deprecated-declarations -fsycl-device-code-split=per_kernel
+ 
+-link.dynamic.lnx.dpcpp = icpx -fsycl $(if $(IA_is_ia32),-m32,-m64) -fsycl-device-code-split=per_kernel
+-link.dynamic.win.dpcpp = icx -fsycl $(if $(IA_is_ia32),-m32,-m64) -fsycl-device-code-split=per_kernel
++link.dynamic.lnx.dpcpp = $(CXX) $(LDFLAGS) -fsycl $(if $(IA_is_ia32),-m32,-m64) -fsycl-device-code-split=per_kernel
++link.dynamic.win.dpcpp = $(CC) $(LDFLAGS) -fsycl $(if $(IA_is_ia32),-m32,-m64) -fsycl-device-code-split=per_kernel
+ 
+ pedantic.opts.lnx.dpcpp = -pedantic \
+                           -Wall \
+diff --git a/dev/make/cmplr.icx.mk b/dev/make/cmplr.icx.mk
+index 28ce293..7c478b0 100644
+--- a/dev/make/cmplr.icx.mk
++++ b/dev/make/cmplr.icx.mk
+@@ -24,14 +24,14 @@ CMPLRDIRSUFF.icx = _icx
+ 
+ CORE.SERV.COMPILER.icx = generic
+ 
+--Zl.icx =  -no-intel-lib=libirc
++-Zl.icx =
+ -DEBC.icx = -g
+ 
+-COMPILER.lnx.icx = icpx $(if $(IA_is_ia32),-m32,-m64) \
+-                     -Werror -Wreturn-type
++COMPILER.lnx.icx = $(CXX) $(CXXFLAGS) $(if $(IA_is_ia32),-m32,-m64) \
++                     -Wreturn-type
+ 
+ 
+-link.dynamic.lnx.icx = icpx $(if $(IA_is_ia32),-m32,-m64)
++link.dynamic.lnx.icx = $(CXX) $(LDFLAGS) $(if $(IA_is_ia32),-m32,-m64)
+ 
+ pedantic.opts.icx = -pedantic \
+                       -Wall \
+diff --git a/makefile b/makefile
+index 9c51bad..20aaff5 100644
+--- a/makefile
++++ b/makefile
+@@ -219,7 +219,7 @@ TBBDIR.2 := $(if $(TBBDIR.2),$(TBBDIR.2),$(error Can`t find TBB neither in $(DIR
+ 
+ TBBDIR.include := $(if $(TBBDIR),$(TBBDIR)/include/tbb $(TBBDIR)/include)
+ 
+-TBBDIR.libia.prefix := $(TBBDIR.2)/lib
++TBBDIR.libia.prefix := $(TBBDIR.2)/lib64
+ 
+ TBBDIR.libia.win.vc1  := $(if $(OS_is_win),$(if $(wildcard $(call frompf1,$(TBBDIR.libia.prefix))/$(_IA)/vc_mt),$(TBBDIR.libia.prefix)/$(_IA)/vc_mt,$(if $(wildcard $(call frompf1,$(TBBDIR.libia.prefix))/$(_IA)/vc14),$(TBBDIR.libia.prefix)/$(_IA)/vc14)))
+ TBBDIR.libia.win.vc2  := $(if $(OS_is_win),$(if $(TBBDIR.libia.win.vc1),,$(firstword $(filter $(call topf,$$TBBROOT)%,$(subst ;,$(space),$(call topf,$$LIB))))))
+@@ -227,10 +227,10 @@ TBBDIR.libia.win.vc22 := $(if $(OS_is_win),$(if $(TBBDIR.libia.win.vc2),$(wildca
+ 
+ TBBDIR.libia.win:= $(if $(OS_is_win),$(if $(TBBDIR.libia.win.vc22),$(TBBDIR.libia.win.vc2),$(if $(TBBDIR.libia.win.vc1),$(TBBDIR.libia.win.vc1),$(error Can`t find TBB libs nether in $(call frompf,$(TBBDIR.libia.prefix))/$(_IA)/vc_mt not in $(firstword $(filter $(TBBROOT)%,$(subst ;,$(space),$(LIB)))).))))
+ 
+-TBBDIR.libia.lnx.gcc1 := $(if $(OS_is_lnx),$(if $(wildcard $(TBBDIR.libia.prefix)/$(_IA)/gcc4.8/*),$(TBBDIR.libia.prefix)/$(_IA)/gcc4.8))
++TBBDIR.libia.lnx.gcc1 := $(if $(OS_is_lnx),$(if $(wildcard $(TBBDIR.libia.prefix)/*),$(TBBDIR.libia.prefix)))
+ TBBDIR.libia.lnx.gcc2  := $(if $(OS_is_lnx),$(if $(TBBDIR.libia.lnx.gcc1),,$(firstword $(filter $(TBBROOT)%,$(subst :,$(space),$(LD_LIBRARY_PATH))))))
+ TBBDIR.libia.lnx.gcc22 := $(if $(OS_is_lnx),$(if $(TBBDIR.libia.lnx.gcc2),$(wildcard $(TBBDIR.libia.lnx.gcc2)/libtbb.so)))
+-TBBDIR.libia.lnx := $(if $(OS_is_lnx),$(if $(TBBDIR.libia.lnx.gcc22),$(TBBDIR.libia.lnx.gcc2),$(if $(TBBDIR.libia.lnx.gcc1),$(TBBDIR.libia.lnx.gcc1),$(error Can`t find TBB runtimes nether in $(TBBDIR.libia.prefix)/$(_IA)/gcc4.8 not in $(firstword $(filter $(TBBROOT)%,$(subst :,$(space),$(LD_LIBRARY_PATH)))).))))
++TBBDIR.libia.lnx := $(if $(OS_is_lnx),$(if $(TBBDIR.libia.lnx.gcc22),$(TBBDIR.libia.lnx.gcc2),$(if $(TBBDIR.libia.lnx.gcc1),$(TBBDIR.libia.lnx.gcc1),$(error Can`t find TBB runtimes nether in $(TBBDIR.libia.prefix) not in $(firstword $(filter $(TBBROOT)%,$(subst :,$(space),$(LD_LIBRARY_PATH)))).))))
+ 
+ TBBDIR.libia.mac.clang1  := $(if $(OS_is_mac),$(if $(wildcard $(TBBDIR.libia.prefix)/*),$(TBBDIR.libia.prefix)))
+ TBBDIR.libia.mac.clang2  := $(if $(OS_is_mac),$(if $(TBBDIR.libia.mac.clang1),,$(firstword $(filter $(TBBROOT)%,$(subst :,$(space),$(LIBRARY_PATH))))))
diff --git a/sci-libs/oneDAL/files/oneDAL-2023.2.1-fix-compile.patch b/sci-libs/oneDAL/files/oneDAL-2023.2.1-fix-compile.patch
new file mode 100644
index 000000000..50731570d
--- /dev/null
+++ b/sci-libs/oneDAL/files/oneDAL-2023.2.1-fix-compile.patch
@@ -0,0 +1,162 @@
+diff --git a/dev/bazel/deps/onedal.bzl b/dev/bazel/deps/onedal.bzl
+index f0f7662c0..6b9d11ff2 100644
+--- a/dev/bazel/deps/onedal.bzl
++++ b/dev/bazel/deps/onedal.bzl
+@@ -21,18 +21,12 @@ onedal_repo = repos.prebuilt_libs_repo_rule(
+         "include",
+     ],
+     libs = [
+-        # Static
+-        "lib/intel64/libonedal_core.a",
+-        "lib/intel64/libonedal_thread.a",
+-        "lib/intel64/libonedal.a",
+-        "lib/intel64/libonedal_dpc.a",
+-        "lib/intel64/libonedal_sycl.a",
+-
+         # Dynamic
+         "lib/intel64/libonedal_core.so",
+         "lib/intel64/libonedal_thread.so",
+         "lib/intel64/libonedal.so",
+         "lib/intel64/libonedal_dpc.so",
++        "lib/intel64/libonedal_sycl.so",
+     ],
+     build_template = "@onedal//dev/bazel/deps:onedal.tpl.BUILD",
+ )
+diff --git a/dev/bazel/deps/onedal.tpl.BUILD b/dev/bazel/deps/onedal.tpl.BUILD
+index 60be67856..0f7990ef5 100644
+--- a/dev/bazel/deps/onedal.tpl.BUILD
++++ b/dev/bazel/deps/onedal.tpl.BUILD
+@@ -9,62 +9,17 @@ cc_library(
+     includes = [ "include" ],
+ )
+ 
+-cc_library(
+-    name = "core_static",
+-    srcs = [
+-        "lib/intel64/libonedal_core.a",
+-    ],
+-    deps = [
+-        ":headers",
+-        # TODO: Currently vml_ipp lib depends on TBB, but it shouldn't
+-        #       Remove TBB from deps once problem with vml_ipp is resolved
+-        "@tbb//:tbb_binary",
+-    ],
+-)
+-
+-cc_library(
+-    name = "thread_static",
+-    srcs = [
+-        "lib/intel64/libonedal_thread.a",
+-    ],
+-    deps = [
+-        ":headers",
+-        "@tbb//:tbb_binary",
+-        "@tbb//:tbbmalloc_binary",
+-    ],
+-)
+ 
+ cc_library(
+     name = "onedal_sycl",
+     srcs = [
+-        "lib/intel64/libonedal_sycl.a",
+-    ],
+-    deps = [
+-        ":headers",
+-    ],
+-)
+-
+-cc_library(
+-    name = "onedal_static",
+-    srcs = [
+-        "lib/intel64/libonedal.a",
++        "lib/intel64/libonedal_sycl.so",
+     ],
+     deps = [
+         ":headers",
+     ],
+ )
+ 
+-cc_library(
+-    name = "onedal_static_dpc",
+-    srcs = [
+-        "lib/intel64/libonedal_dpc.a",
+-    ],
+-    deps = [
+-        ":headers",
+-        ":onedal_sycl",
+-    ],
+-)
+-
+ cc_library(
+     name = "core_dynamic",
+     srcs = [
+diff --git a/dev/make/cmplr.dpcpp.mk b/dev/make/cmplr.dpcpp.mk
+index 2a78043b7..b431e1255 100644
+--- a/dev/make/cmplr.dpcpp.mk
++++ b/dev/make/cmplr.dpcpp.mk
+@@ -28,13 +28,13 @@ CORE.SERV.COMPILER.dpcpp = generic
+ -Zl.dpcpp =
+ -DEBC.dpcpp = -g
+ 
+-COMPILER.lnx.dpcpp = icpx -fsycl -m64 -stdlib=libstdc++ -fgnu-runtime -fwrapv \
++COMPILER.lnx.dpcpp = $(CXX) $(CXXFLAGS) -fsycl -m64 -stdlib=libstdc++ -fgnu-runtime -fwrapv \
+                      -Werror -Wreturn-type -fsycl-device-code-split=per_kernel
+-COMPILER.win.dpcpp = icx -fsycl $(if $(MSVC_RT_is_release),-MD, -MDd /debug:none) -nologo -WX \
++COMPILER.win.dpcpp = $(CC) $(CFLAGS) -fsycl $(if $(MSVC_RT_is_release),-MD, -MDd /debug:none) -nologo -WX \
+                      -Wno-deprecated-declarations -fsycl-device-code-split=per_kernel
+ 
+-link.dynamic.lnx.dpcpp = icpx -fsycl -m64 -fsycl-device-code-split=per_kernel
+-link.dynamic.win.dpcpp = icx -fsycl -m64 -fsycl-device-code-split=per_kernel
++link.dynamic.lnx.dpcpp = $(CXX) $(LDFLAGS) -fsycl -m64 -fsycl-device-code-split=per_kernel
++link.dynamic.win.dpcpp = $(CC) $(LDFLAGS) -fsycl -m64 -fsycl-device-code-split=per_kernel
+ 
+ pedantic.opts.lnx.dpcpp = -pedantic \
+                           -Wall \
+diff --git a/dev/make/cmplr.icx.mk b/dev/make/cmplr.icx.mk
+index cbcde1a7e..61ef3583c 100644
+--- a/dev/make/cmplr.icx.mk
++++ b/dev/make/cmplr.icx.mk
+@@ -24,14 +24,14 @@ CMPLRDIRSUFF.icx = _icx
+ 
+ CORE.SERV.COMPILER.icx = generic
+ 
+--Zl.icx =  -no-intel-lib=libirc
++-Zl.icx =
+ -DEBC.icx = -g
+ 
+-COMPILER.lnx.icx = icpx -m64 \
++COMPILER.lnx.icx = $(CXX) $(CXXFLAGS) -m64 \
+                      -Werror -Wreturn-type
+ 
+ 
+-link.dynamic.lnx.icx = icpx -m64
++link.dynamic.lnx.icx = $(CXX) $(LDFLAGS) -m64
+ 
+ pedantic.opts.icx = -pedantic \
+                       -Wall \
+diff --git a/makefile b/makefile
+index 525e52728..db864e9cb 100644
+--- a/makefile
++++ b/makefile
+@@ -215,7 +215,7 @@ TBBDIR.2 := $(if $(TBBDIR.2),$(TBBDIR.2),$(error Can`t find TBB neither in $(DIR
+ 
+ TBBDIR.include := $(if $(TBBDIR),$(TBBDIR)/include/tbb $(TBBDIR)/include)
+ 
+-TBBDIR.libia.prefix := $(TBBDIR.2)/lib
++TBBDIR.libia.prefix := $(TBBDIR.2)/lib64
+ 
+ TBBDIR.libia.win.vc1  := $(if $(OS_is_win),$(if $(wildcard $(call frompf1,$(TBBDIR.libia.prefix))/$(_IA)/vc_mt),$(TBBDIR.libia.prefix)/$(_IA)/vc_mt,$(if $(wildcard $(call frompf1,$(TBBDIR.libia.prefix))/$(_IA)/vc14),$(TBBDIR.libia.prefix)/$(_IA)/vc14)))
+ TBBDIR.libia.win.vc2  := $(if $(OS_is_win),$(if $(TBBDIR.libia.win.vc1),,$(firstword $(filter $(call topf,$$TBBROOT)%,$(subst ;,$(space),$(call topf,$$LIB))))))
+@@ -223,10 +223,10 @@ TBBDIR.libia.win.vc22 := $(if $(OS_is_win),$(if $(TBBDIR.libia.win.vc2),$(wildca
+ 
+ TBBDIR.libia.win:= $(if $(OS_is_win),$(if $(TBBDIR.libia.win.vc22),$(TBBDIR.libia.win.vc2),$(if $(TBBDIR.libia.win.vc1),$(TBBDIR.libia.win.vc1),$(error Can`t find TBB libs nether in $(call frompf,$(TBBDIR.libia.prefix))/$(_IA)/vc_mt not in $(firstword $(filter $(TBBROOT)%,$(subst ;,$(space),$(LIB)))).))))
+ 
+-TBBDIR.libia.lnx.gcc1 := $(if $(OS_is_lnx),$(if $(wildcard $(TBBDIR.libia.prefix)/$(_IA)/gcc4.8/*),$(TBBDIR.libia.prefix)/$(_IA)/gcc4.8))
++TBBDIR.libia.lnx.gcc1 := $(if $(OS_is_lnx),$(if $(wildcard $(TBBDIR.libia.prefix)/*),$(TBBDIR.libia.prefix)))
+ TBBDIR.libia.lnx.gcc2  := $(if $(OS_is_lnx),$(if $(TBBDIR.libia.lnx.gcc1),,$(firstword $(filter $(TBBROOT)%,$(subst :,$(space),$(LD_LIBRARY_PATH))))))
+ TBBDIR.libia.lnx.gcc22 := $(if $(OS_is_lnx),$(if $(TBBDIR.libia.lnx.gcc2),$(wildcard $(TBBDIR.libia.lnx.gcc2)/libtbb.so)))
+-TBBDIR.libia.lnx := $(if $(OS_is_lnx),$(if $(TBBDIR.libia.lnx.gcc22),$(TBBDIR.libia.lnx.gcc2),$(if $(TBBDIR.libia.lnx.gcc1),$(TBBDIR.libia.lnx.gcc1),$(error Can`t find TBB runtimes nether in $(TBBDIR.libia.prefix)/$(_IA)/gcc4.8 not in $(firstword $(filter $(TBBROOT)%,$(subst :,$(space),$(LD_LIBRARY_PATH)))).))))
++TBBDIR.libia.lnx := $(if $(OS_is_lnx),$(if $(TBBDIR.libia.lnx.gcc22),$(TBBDIR.libia.lnx.gcc2),$(if $(TBBDIR.libia.lnx.gcc1),$(TBBDIR.libia.lnx.gcc1),$(error Can`t find TBB runtimes nether in $(TBBDIR.libia.prefix) not in $(firstword $(filter $(TBBROOT)%,$(subst :,$(space),$(LD_LIBRARY_PATH)))).))))
+ 
+ TBBDIR.libia.mac.clang1  := $(if $(OS_is_mac),$(if $(wildcard $(TBBDIR.libia.prefix)/*),$(TBBDIR.libia.prefix)))
+ TBBDIR.libia.mac.clang2  := $(if $(OS_is_mac),$(if $(TBBDIR.libia.mac.clang1),,$(firstword $(filter $(TBBROOT)%,$(subst :,$(space),$(LIBRARY_PATH))))))
diff --git a/sci-libs/oneDAL/metadata.xml b/sci-libs/oneDAL/metadata.xml
new file mode 100644
index 000000000..2793ac235
--- /dev/null
+++ b/sci-libs/oneDAL/metadata.xml
@@ -0,0 +1,11 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
+<pkgmetadata>
+	<maintainer type="project">
+		<email>sci@gentoo.org</email>
+		<name>Gentoo Science Project</name>
+	</maintainer>
+	<upstream>
+		<remote-id type="github">oneapi-src/oneDAL</remote-id>
+	</upstream>
+</pkgmetadata>
diff --git a/sci-libs/oneDAL/oneDAL-2023.0.1.ebuild b/sci-libs/oneDAL/oneDAL-2023.0.1.ebuild
new file mode 100644
index 000000000..589a74960
--- /dev/null
+++ b/sci-libs/oneDAL/oneDAL-2023.0.1.ebuild
@@ -0,0 +1,85 @@
+# Copyright 2022 Gentoo Authors
+# Distributed under the terms of the GNU General Public License v2
+
+EAPI=8
+
+PYTHON_COMPAT=( python3_{10..11} )
+inherit python-any-r1 java-pkg-2
+
+MKLFPK_VER="20221214"
+MKLGPUFPK_VER="20221214"
+
+DESCRIPTION="oneAPI Data Analytics Library"
+HOMEPAGE="https://github.com/oneapi-src/oneDAL"
+# Secondary urls extracted from dev/download_micromkl.sh
+SRC_URI="
+	https://github.com/oneapi-src/oneDAL/archive/${PV}.tar.gz -> ${P}.tar.gz
+	https://github.com/oneapi-src/oneDAL/releases/download/Dependencies/mklgpufpk_lnx_${MKLGPUFPK_VER}.tgz
+	https://github.com/oneapi-src/oneDAL/releases/download/Dependencies/mklfpk_lnx_${MKLFPK_VER}.tgz
+"
+
+LICENSE="Apache-2.0"
+SLOT="0"
+KEYWORDS="~amd64"
+
+BDEPEND="sys-devel/DPC++"
+
+RDEPEND="
+	dev-cpp/tbb:=
+	dev-libs/opencl-icd-loader
+	virtual/jdk:17
+"
+DEPEND="
+	${DEPEND}
+	${PYTHON_DEPS}
+"
+
+PATCHES=(
+	"${FILESDIR}/${PN}-2021.7.1_p20221207-fix-compile.patch"
+)
+
+pkg_setup() {
+	python-any-r1_pkg_setup
+	java-pkg-2_pkg_setup
+}
+
+src_unpack() {
+	unpack "${P}.tar.gz"
+	mkdir -p "${S}/__deps/mklfpk/" "${S}/__deps/mklgpufpk/lnx" || die
+	cd "${S}/__deps/mklfpk/" || die
+	unpack "mklfpk_lnx_${MKLFPK_VER}.tgz"
+	cd "${S}/__deps/mklgpufpk/lnx" || die
+	unpack "mklgpufpk_lnx_${MKLGPUFPK_VER}.tgz"
+}
+
+src_prepare() {
+	# DPC++ compiler required for full functionality
+	export CC="${ESYSROOT}/usr/lib/llvm/intel/bin/clang"
+	export CXX="${ESYSROOT}/usr/lib/llvm/intel/bin/clang++"
+	export TBBROOT="${ESYSROOT}/usr"
+	export CPLUS_INCLUDE_PATH="./cpp/daal/include:${ESYSROOT}/usr/lib/llvm/intel/include"
+	export JAVA_HOME="${ESYSROOT}/usr/lib64/openjdk-17/"
+	export PATH="${JAVA_HOME}/bin:${PATH}"
+	export CPATH="${JAVA_HOME}/include:${JAVA_HOME}/include/linux:${CPATH}"
+
+	default
+}
+
+src_compile() {
+	emake PLAT=lnx32e COMPILER=icx daal oneapi
+}
+
+src_install() {
+	einstalldocs
+	cd __release_lnx_icx/daal/latest || die
+	docinto examples
+	dodoc -r examples/*
+	docinto samples
+	dodoc -r samples/*
+	doheader -r include/*
+	dolib.so lib/intel64/*.so*
+	dolib.a lib/intel64/*.a*
+	insinto /usr/share/pkgconfig
+	doins -r lib/pkgconfig/*
+	java-pkg_dojar lib/*.jar
+}
diff --git a/sci-libs/oneDAL/oneDAL-2023.2.1.ebuild b/sci-libs/oneDAL/oneDAL-2023.2.1.ebuild
new file mode 100644
index 000000000..9007f7a51
--- /dev/null
+++ b/sci-libs/oneDAL/oneDAL-2023.2.1.ebuild
@@ -0,0 +1,85 @@
+# Copyright 2022 Gentoo Authors
+# Distributed under the terms of the GNU General Public License v2
+
+EAPI=8
+
+PYTHON_COMPAT=( python3_{10..11} )
+inherit python-any-r1 java-pkg-2
+
+MKLFPK_VER="20221214"
+MKLGPUFPK_VER="20221214"
+
+DESCRIPTION="oneAPI Data Analytics Library"
+HOMEPAGE="https://github.com/oneapi-src/oneDAL"
+# Secondary urls extracted from dev/download_micromkl.sh
+SRC_URI="
+	https://github.com/oneapi-src/oneDAL/archive/${PV}.tar.gz -> ${P}.tar.gz
+	https://github.com/oneapi-src/oneDAL/releases/download/Dependencies/mklgpufpk_lnx_${MKLGPUFPK_VER}.tgz
+	https://github.com/oneapi-src/oneDAL/releases/download/Dependencies/mklfpk_lnx_${MKLFPK_VER}.tgz
+"
+
+LICENSE="Apache-2.0"
+SLOT="0"
+KEYWORDS="~amd64"
+
+BDEPEND="sys-devel/DPC++"
+
+RDEPEND="
+	dev-cpp/tbb:=
+	dev-libs/opencl-icd-loader
+	virtual/jdk:17
+"
+DEPEND="
+	${DEPEND}
+	${PYTHON_DEPS}
+"
+
+PATCHES=(
+	"${FILESDIR}/${PN}-2023.2.1-fix-compile.patch"
+)
+
+pkg_setup() {
+	python-any-r1_pkg_setup
+	java-pkg-2_pkg_setup
+}
+
+src_unpack() {
+	unpack "${P}.tar.gz"
+	mkdir -p "${S}/__deps/mklfpk/" "${S}/__deps/mklgpufpk/lnx" || die
+	cd "${S}/__deps/mklfpk/" || die
+	unpack "mklfpk_lnx_${MKLFPK_VER}.tgz"
+	cd "${S}/__deps/mklgpufpk/lnx" || die
+	unpack "mklgpufpk_lnx_${MKLGPUFPK_VER}.tgz"
+}
+
+src_prepare() {
+	# DPC++ compiler required for full functionality
+	export CC="${ESYSROOT}/usr/lib/llvm/intel/bin/clang"
+	export CXX="${ESYSROOT}/usr/lib/llvm/intel/bin/clang++"
+	export TBBROOT="${ESYSROOT}/usr"
+	export CPLUS_INCLUDE_PATH="./cpp/daal/include:${ESYSROOT}/usr/lib/llvm/intel/include"
+	export JAVA_HOME="${ESYSROOT}/usr/lib64/openjdk-17/"
+	export PATH="${JAVA_HOME}/bin:${PATH}"
+	export CPATH="${JAVA_HOME}/include:${JAVA_HOME}/include/linux:${CPATH}"
+
+	default
+}
+
+src_compile() {
+	emake PLAT=lnx32e COMPILER=icx daal oneapi
+}
+
+src_install() {
+	einstalldocs
+	cd __release_lnx_icx/daal/latest || die
+	docinto examples
+	dodoc -r examples/*
+	docinto samples
+	dodoc -r samples/*
+	doheader -r include/*
+	dolib.so lib/intel64/*.so*
+	dolib.a lib/intel64/*.a*
+	insinto /usr/share/pkgconfig
+	doins -r lib/pkgconfig/*
+	java-pkg_dojar lib/*.jar
+}
diff --git a/sci-libs/oneMKL/Manifest b/sci-libs/oneMKL/Manifest
new file mode 100644
index 000000000..9999712a5
--- /dev/null
+++ b/sci-libs/oneMKL/Manifest
@@ -0,0 +1,2 @@
+DIST oneMKL-0.2_p20221201.tar.gz 958514 BLAKE2B 14fe7ca0095440f90ae74f9480be1693677c405071d123b10044d3ce09c7e2f8cb42f262ecfe617ba7d68efdf506ccd6aa31c52e376ff3bd1789f4923597b2b5 SHA512 e474f3d37aa58978aba417073f466507c91e428477c7a4b6f52206584e4ba6c307df7157b5b6e6e9b82e8bd1d9b6537eebef569fe8170cf053f6d1d87d2c1176
+DIST oneMKL-0.2_p20230221.tar.gz 983270 BLAKE2B 73f399301989938c78620dfd833cc895050e253d5880d4b7b6a416438179ac3299278f7dfef8198ba81aa55c33e95bb37d62c523345aa5d876177ca482cbaab7 SHA512 b502b0511613927e74e0d40186c0d91864f12bd23880eb029876a30b89cf1d495f0af9bfefe0278ee102b6d0bb7f698b50a3280ad53b33a9ebce32ec5ce84e85
diff --git a/sci-libs/oneMKL/files/oneMKL-0.2_p20221201-find-lapacke.patch b/sci-libs/oneMKL/files/oneMKL-0.2_p20221201-find-lapacke.patch
new file mode 100644
index 000000000..2c2fc1367
--- /dev/null
+++ b/sci-libs/oneMKL/files/oneMKL-0.2_p20221201-find-lapacke.patch
@@ -0,0 +1,22 @@
+diff --git a/cmake/FindLAPACKE.cmake b/cmake/FindLAPACKE.cmake
+index 42a5b7d..080108a 100644
+--- a/cmake/FindLAPACKE.cmake
++++ b/cmake/FindLAPACKE.cmake
+@@ -19,13 +19,13 @@
+ 
+ include_guard()
+ 
+-find_library(LAPACKE64_file NAMES lapacke64.dll.lib lapacke64.lib lapacke64 HINTS ${REF_LAPACK_ROOT} PATH_SUFFIXES lib lib64)
++find_library(LAPACKE64_file NAMES lapacke64.dll.lib lapacke64.lib lapacke HINTS ${REF_LAPACK_ROOT} PATH_SUFFIXES lib lib64)
+ find_package_handle_standard_args(LAPACKE REQUIRED_VARS LAPACKE64_file)
+-find_library(LAPACK64_file NAMES lapack64.dll.lib lapack64.lib lapack64 HINTS ${REF_LAPACK_ROOT} PATH_SUFFIXES lib lib64)
++find_library(LAPACK64_file NAMES lapack64.dll.lib lapack64.lib lapack HINTS ${REF_LAPACK_ROOT} PATH_SUFFIXES lib lib64)
+ find_package_handle_standard_args(LAPACKE REQUIRED_VARS LAPACK64_file)
+-find_library(CBLAS64_file NAMES cblas64.dll.lib cblas64.lib cblas64 HINTS ${REF_LAPACK_ROOT} PATH_SUFFIXES lib lib64)
++find_library(CBLAS64_file NAMES cblas64.dll.lib cblas64.lib cblas HINTS ${REF_LAPACK_ROOT} PATH_SUFFIXES lib lib64)
+ find_package_handle_standard_args(LAPACKE REQUIRED_VARS CBLAS64_file)
+-find_library(BLAS64_file NAMES blas64.dll.lib blas64.lib blas64 HINTS ${REF_LAPACK_ROOT} PATH_SUFFIXES lib lib64)
++find_library(BLAS64_file NAMES blas64.dll.lib blas64.lib blas HINTS ${REF_LAPACK_ROOT} PATH_SUFFIXES lib lib64)
+ find_package_handle_standard_args(LAPACKE REQUIRED_VARS BLAS64_file)
+ 
+ get_filename_component(LAPACKE64_LIB_DIR ${LAPACKE64_file} DIRECTORY)
diff --git a/sci-libs/oneMKL/metadata.xml b/sci-libs/oneMKL/metadata.xml
new file mode 100644
index 000000000..77e2dd702
--- /dev/null
+++ b/sci-libs/oneMKL/metadata.xml
@@ -0,0 +1,11 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
+<pkgmetadata>
+	<maintainer type="project">
+		<email>sci@gentoo.org</email>
+		<name>Gentoo Science Project</name>
+	</maintainer>
+	<upstream>
+		<remote-id type="github">oneapi-src/oneMKL</remote-id>
+	</upstream>
+</pkgmetadata>
diff --git a/sci-libs/oneMKL/oneMKL-0.2_p20221201.ebuild b/sci-libs/oneMKL/oneMKL-0.2_p20221201.ebuild
new file mode 100644
index 000000000..35d773397
--- /dev/null
+++ b/sci-libs/oneMKL/oneMKL-0.2_p20221201.ebuild
@@ -0,0 +1,59 @@
+# Copyright 2022 Gentoo Authors
+# Distributed under the terms of the GNU General Public License v2
+
+EAPI=8
+
+inherit cmake
+
+COMMIT="f4866ab2648cd7cff4a047b91be5f94ff7b73ba1"
+
+DESCRIPTION="oneAPI Math Kernel Library Interfaces "
+HOMEPAGE="https://github.com/oneapi-src/oneMKL"
+SRC_URI="https://github.com/oneapi-src/oneMKL/archive/${COMMIT}.tar.gz -> ${P}.tar.gz"
+S="${WORKDIR}/${PN}-${COMMIT}"
+
+LICENSE="Apache-2.0"
+SLOT="0"
+KEYWORDS="~amd64"
+
+IUSE="test"
+# Tests don't compile properly
+# RESTRICT="!test? ( test )"
+RESTRICT="test"
+
+BDEPEND="sys-devel/DPC++"
+
+DEPEND="
+	dev-cpp/tbb:=
+	sci-libs/lapack[lapacke]
+	sci-libs/mkl
+"
+RDEPEND="${DEPEND}"
+
+PATCHES=(
+	"${FILESDIR}/${P}-find-lapacke.patch"
+)
+
+src_prepare() {
+	# DPC++ compiler required for full functionality
+	export CC="${ESYSROOT}/usr/lib/llvm/intel/bin/clang"
+	export CXX="${ESYSROOT}/usr/lib/llvm/intel/bin/clang++"
+
+	cmake_src_prepare
+}
+
+src_configure() {
+	local mycmakeargs=(
+		-DCMAKE_CXX_COMPILER="${ESYSROOT}/usr/lib/llvm/intel/bin/clang++"
+		-DCMAKE_C_COMPILER="${ESYSROOT}/usr/lib/llvm/intel/bin/clang"
+		-DMKL_ROOT="${ESYSROOT}/opt/intel/oneapi/mkl/latest"
+		-DBUILD_FUNCTIONAL_TESTS="$(usex test)"
+	)
+	cmake_src_configure
+}
+
+src_install() {
+	cmake_src_install
+	# Move into the correct libdid
+	mv "${ED}/usr/lib" "${ED}/usr/$(get_libdir)" || die
+}
diff --git a/sci-libs/oneMKL/oneMKL-0.2_p20230221.ebuild b/sci-libs/oneMKL/oneMKL-0.2_p20230221.ebuild
new file mode 100644
index 000000000..896ed4566
--- /dev/null
+++ b/sci-libs/oneMKL/oneMKL-0.2_p20230221.ebuild
@@ -0,0 +1,59 @@
+# Copyright 2022 Gentoo Authors
+# Distributed under the terms of the GNU General Public License v2
+
+EAPI=8
+
+inherit cmake
+
+COMMIT="793c771c60f5105c12eaf59e1534eeb21d1cfe4a"
+
+DESCRIPTION="oneAPI Math Kernel Library Interfaces "
+HOMEPAGE="https://github.com/oneapi-src/oneMKL"
+SRC_URI="https://github.com/oneapi-src/oneMKL/archive/${COMMIT}.tar.gz -> ${P}.tar.gz"
+S="${WORKDIR}/${PN}-${COMMIT}"
+
+LICENSE="Apache-2.0"
+SLOT="0"
+KEYWORDS="~amd64"
+
+IUSE="test"
+# Tests don't compile properly
+# RESTRICT="!test? ( test )"
+RESTRICT="test"
+
+BDEPEND="sys-devel/DPC++"
+
+DEPEND="
+	dev-cpp/tbb:=
+	sci-libs/lapack[lapacke]
+	sci-libs/mkl
+"
+RDEPEND="${DEPEND}"
+
+PATCHES=(
+	"${FILESDIR}/${PN}-0.2_p20221201-find-lapacke.patch"
+)
+
+src_prepare() {
+	# DPC++ compiler required for full functionality
+	export CC="${ESYSROOT}/usr/lib/llvm/intel/bin/clang"
+	export CXX="${ESYSROOT}/usr/lib/llvm/intel/bin/clang++"
+
+	cmake_src_prepare
+}
+
+src_configure() {
+	local mycmakeargs=(
+		-DCMAKE_CXX_COMPILER="${ESYSROOT}/usr/lib/llvm/intel/bin/clang++"
+		-DCMAKE_C_COMPILER="${ESYSROOT}/usr/lib/llvm/intel/bin/clang"
+		-DMKL_ROOT="${ESYSROOT}/opt/intel/oneapi/mkl/latest"
+		-DBUILD_FUNCTIONAL_TESTS="$(usex test)"
+	)
+	cmake_src_configure
+}
+
+src_install() {
+	cmake_src_install
+	# Move into the correct libdir
+	mv "${ED}/usr/lib" "${ED}/usr/$(get_libdir)" || die
+}
diff --git a/sci-libs/openblas/Manifest b/sci-libs/openblas/Manifest
deleted file mode 100644
index e9aa9fc50..000000000
--- a/sci-libs/openblas/Manifest
+++ /dev/null
@@ -1,6 +0,0 @@
-DIST openblas-0.2.11-gentoo.patch 246353 BLAKE2B 2e7220052cdb5a8e2fbffe29c5ad0595f065e93938b2da383671545c8bdfb7d295cfd0ef04f2caaeac6700e1771a7174010607dcb78c726f778590de59407808 SHA512 4d8fcec9e44f873c31214d48492a171dd00dc18524a7ab51e51fa27c038b62bfd07be281b5af899943e10fb45c6d0b5b704ba3fa93c6bec74aca0a3a6c0f48ab
-DIST openblas-0.2.14.tar.gz 9862952 BLAKE2B 62ca22fe9e073c16bc501463899dbd3d9f7d9367d06f3c8c81711574f711ecef086ec8a2e7f0b80537bca1e5fd191b1d0761192ef6d532f0bb6752e29857e5b2 SHA512 5028c0cae1eea168593d951c053d2c3692ea4bf34257b2d6cd533d43dd98d1e4ab982f56c57232e53dcc358a2f8e1e51e15a746235ff6eb64d427a97b1449b60
-DIST openblas-0.2.15.tar.gz 9968430 BLAKE2B af67dd17edb981965f82aed2989451d6d22a420102e734ec254748f5e3b638adffb1d0c3e313737bd5951ce4464ce4be67d080841179231a2ea9b0e8e0998f1b SHA512 7c95de975b4dc4a1277289be4f44e8af01eea93886fd1f278c28ffa7d543310ec7b81c897928f7c6a0905bc6f9aa6f63cb18e2843cf5b47806379a4e499577b7
-DIST openblas-0.2.19-clang-3.9.patch 22096 BLAKE2B a571eb5fc3510cfc5ef6fcd471ae770ab2aeb5e2896bf9fe24c6ae7f60b81d538ab3cf42e0ba9c54c99a7eab13c87761402e3df76b3a3a8ccea154fc40bcb8b3 SHA512 dd216c50f36c978bdf397211e875564b4da221ff51962402651570aa2bc909f3ac9500cdbaee644c368a990ae70f20bcac810c87f79facba53c349f2966aad91
-DIST openblas-0.2.19.tar.gz 10838468 BLAKE2B a168f1ba341cfb1291c951ceaccced77b67ba395b74b8cbccb88dccdc8115f6335ebfcd37ae0e8028e76d37397603eeb597227f225e8cc7436a92770e6cb1d30 SHA512 7ca5e1fdcba2efc0d827874242a7e7da51710e97ca07f4f97cfb9a7f6154553b2b8898a4e999e717b809aa67e08cb7c81dca7550a90f3abeb71a3336d3f7f99f
-DIST openblas-0.2.20.tar.gz 11637494 BLAKE2B 6622116e77c90fa98afde358deff520bac191193a3e636169db609b7c6e3440c42b42f1caf3e18cb396628f913a3763d682254561fc1ff7780af59725679df4d SHA512 eac09f01408dd326d872d8b54705c8ff7891348fb31a163a65ceceb1659756fecbaa56c62211584ba4d59805c7e014cb9a88347fa525acd0b16fe19c21f997fb
diff --git a/sci-libs/openblas/files/openblas-0.2.11-cpuid_x86.patch b/sci-libs/openblas/files/openblas-0.2.11-cpuid_x86.patch
deleted file mode 100644
index c6f299132..000000000
--- a/sci-libs/openblas/files/openblas-0.2.11-cpuid_x86.patch
+++ /dev/null
@@ -1,27 +0,0 @@
---- openblas-9999-orig/cpuid_x86.c	2014-02-23 15:25:22.199394761 +1100
-+++ openblas-9999/cpuid_x86.c	2014-02-23 16:41:02.727372869 +1100
-@@ -57,9 +57,23 @@
- void cpuid(int op, int *eax, int *ebx, int *ecx, int *edx);
- #else
- static inline void cpuid(int op, int *eax, int *ebx, int *ecx, int *edx){
-+#if __x86_64
-   __asm__ __volatile__
-     ("cpuid": "=a" (*eax), "=b" (*ebx), "=c" (*ecx), "=d" (*edx) : "a" (op) : "cc");
--
-+#else
-+  __asm volatile(
-+    "push %%ebx\n\t"
-+    "cpuid\n\t"
-+    "mov %%ebx, (%4)\n\t"
-+    "pop %%ebx"
-+    :"=a" (*eax),
-+    "=c" (*ecx),
-+    "=d" (*edx)
-+    :"a" (op),
-+    "cc"
-+    "S" (ebx)
-+    :"memory");
-+#endif
- }
- #endif
- 
diff --git a/sci-libs/openblas/files/openblas-0.2.19-MAKE.patch b/sci-libs/openblas/files/openblas-0.2.19-MAKE.patch
deleted file mode 100644
index c77dd0f93..000000000
--- a/sci-libs/openblas/files/openblas-0.2.19-MAKE.patch
+++ /dev/null
@@ -1,29 +0,0 @@
-diff --git a/Makefile b/Makefile
-index 2ae0047..2071e10 100644
---- a/Makefile
-+++ b/Makefile
-@@ -278,13 +278,13 @@ lapack-timing : large.tgz timing.tgz
- ifndef NOFORTRAN
- 	(cd $(NETLIB_LAPACK_DIR); $(TAR) zxf ../timing.tgz TIMING)
- 	(cd $(NETLIB_LAPACK_DIR)/TIMING; $(TAR) zxf ../../large.tgz )
--	make -C $(NETLIB_LAPACK_DIR)/TIMING
-+	$(MAKE) -C $(NETLIB_LAPACK_DIR)/TIMING
- endif
- 
- 
- lapack-test :
- 	(cd $(NETLIB_LAPACK_DIR)/TESTING && rm -f x* *.out)
--	make -j 1 -C $(NETLIB_LAPACK_DIR)/TESTING xeigtstc  xeigtstd  xeigtsts  xeigtstz  xlintstc  xlintstd  xlintstds  xlintstrfd  xlintstrfz  xlintsts  xlintstz  xlintstzc xlintstrfs xlintstrfc
-+	$(MAKE) -j 1 -C $(NETLIB_LAPACK_DIR)/TESTING xeigtstc  xeigtstd  xeigtsts  xeigtstz  xlintstc  xlintstd  xlintstds  xlintstrfd  xlintstrfz  xlintsts  xlintstz  xlintstzc xlintstrfs xlintstrfc
- ifneq ($(CROSS), 1)
- 	( cd $(NETLIB_LAPACK_DIR)/INSTALL; ./testlsame; ./testslamch; ./testdlamch; \
-         ./testsecond; ./testdsecnd; ./testieee; ./testversion )
-@@ -299,7 +299,7 @@ lapack-runtest:
- 
- blas-test:
- 	(cd $(NETLIB_LAPACK_DIR)/BLAS && rm -f x* *.out)
--	make -j 1 -C $(NETLIB_LAPACK_DIR) blas_testing
-+	$(MAKE) -j 1 -C $(NETLIB_LAPACK_DIR) blas_testing
- 	(cd $(NETLIB_LAPACK_DIR)/BLAS && cat *.out)
- 
- 
diff --git a/sci-libs/openblas/files/openblas-0.2.19-utest_ldflags.patch b/sci-libs/openblas/files/openblas-0.2.19-utest_ldflags.patch
deleted file mode 100644
index 2ffd5babe..000000000
--- a/sci-libs/openblas/files/openblas-0.2.19-utest_ldflags.patch
+++ /dev/null
@@ -1,13 +0,0 @@
-diff --git a/utest/Makefile b/utest/Makefile
-index 3ccc0a0..ce809e3 100644
---- a/utest/Makefile
-+++ b/utest/Makefile
-@@ -18,7 +18,7 @@ endif
- all : run_test
- 
- $(UTESTBIN): $(OBJS)
--	$(CC) $(CFLAGS) -o $@ $^ ../$(LIBNAME) $(EXTRALIB) $(FEXTRALIB)
-+	$(CC) $(CFLAGS) $(LDFLAGS) -o $@ $^ ../$(LIBNAME) $(EXTRALIB) $(FEXTRALIB)
- 
- run_test: $(UTESTBIN)
- ifndef CROSS
diff --git a/sci-libs/openblas/files/openblas-0.2.20-non-glibc.patch b/sci-libs/openblas/files/openblas-0.2.20-non-glibc.patch
deleted file mode 100644
index afde85585..000000000
--- a/sci-libs/openblas/files/openblas-0.2.20-non-glibc.patch
+++ /dev/null
@@ -1,144 +0,0 @@
-From 480e697681763cf31f015eb1ebad49a495f562c5 Mon Sep 17 00:00:00 2001
-From: Martin Kroeker <martin@ruby.chemie.uni-freiburg.de>
-Date: Mon, 24 Jul 2017 16:17:50 +0200
-Subject: [PATCH] Revert "Honor cgroup/cpuset limits when enumerating cpus"
- (#1246)
-
----
- driver/others/init.c   | 49 +++++--------------------------------------------
- driver/others/memory.c | 37 -------------------------------------
- 2 files changed, 5 insertions(+), 81 deletions(-)
-
-diff --git a/driver/others/init.c b/driver/others/init.c
-index 4c75d72e4..3e6176967 100644
---- a/driver/others/init.c
-+++ b/driver/others/init.c
-@@ -778,11 +778,11 @@ static int initialized = 0;
- void gotoblas_affinity_init(void) {
- 
-   int cpu, num_avail;
--#ifndef USE_OPENMP	
-+#ifndef USE_OPENMP
-   cpu_set_t cpu_mask;
- #endif
-   int i;
--	
-+
-   if (initialized) return;
- 
-   initialized = 1;
-@@ -826,54 +826,15 @@ void gotoblas_affinity_init(void) {
-   common -> shmid = pshmid;
- 
-   if (common -> magic != SH_MAGIC) {
--    cpu_set_t *cpusetp;
--    int nums;
--    int ret;
--
- #ifdef DEBUG
-     fprintf(stderr, "Shared Memory Initialization.\n");
- #endif
- 
-     //returns the number of processors which are currently online
--
--    nums = sysconf(_SC_NPROCESSORS_CONF);
--     
--#if !defined(__GLIBC_PREREQ) || !__GLIBC_PREREQ(2, 3)
--    common->num_procs = nums;
--#elif __GLIBC_PREREQ(2, 7)
--    cpusetp = CPU_ALLOC(nums);
--    if (cpusetp == NULL) {
--        common->num_procs = nums;
--    } else {
--        size_t size;
--        size = CPU_ALLOC_SIZE(nums);
--        ret = sched_getaffinity(0,size,cpusetp);
--        if (ret!=0) 
--            common->num_procs = nums;
--        else
--            common->num_procs = CPU_COUNT_S(size,cpusetp);
--    }
--    CPU_FREE(cpusetp);
--#else
--    ret = sched_getaffinity(0,sizeof(cpu_set_t), cpusetp);
--    if (ret!=0) {
--        common->num_procs = nums;
--    } else {
--#if !__GLIBC_PREREQ(2, 6)  
--    int i;
--    int n = 0;
--    for (i=0;i<nums;i++)
--        if (CPU_ISSET(i,cpusetp)) n++;
--    common->num_procs = n;
--    }
--#else
--    common->num_procs = CPU_COUNT(sizeof(cpu_set_t),cpusetp);
--#endif
--
--#endif 
-+    common -> num_procs = sysconf(_SC_NPROCESSORS_CONF);;
- 
-     if(common -> num_procs > MAX_CPUS) {
--      fprintf(stderr, "\nOpenBLAS Warning : The number of CPU/Cores(%d) is beyond the limit(%d). Terminated.\n", common->num_procs, MAX_CPUS);
-+      fprintf(stderr, "\nOpenBLAS Warining : The number of CPU/Cores(%d) is beyond the limit(%d). Terminated.\n", common->num_procs, MAX_CPUS);
-       exit(1);
-     }
- 
-@@ -886,7 +847,7 @@ void gotoblas_affinity_init(void) {
-     if (common -> num_nodes > 1) numa_mapping();
- 
-     common -> final_num_procs = 0;
--    for(i = 0; i < common -> avail_count; i++) common -> final_num_procs += rcount(common -> avail[i]) + 1;   //Make the max cpu number.
-+    for(i = 0; i < common -> avail_count; i++) common -> final_num_procs += rcount(common -> avail[i]) + 1;   //Make the max cpu number. 
- 
-     for (cpu = 0; cpu < common -> final_num_procs; cpu ++) common -> cpu_use[cpu] =  0;
- 
-diff --git a/driver/others/memory.c b/driver/others/memory.c
-index 38d063715..916950315 100644
---- a/driver/others/memory.c
-+++ b/driver/others/memory.c
-@@ -175,44 +175,7 @@ int get_num_procs(void);
- #else
- int get_num_procs(void) {
-   static int nums = 0;
--cpu_set_t *cpusetp;
--size_t size;
--int ret;
--int i,n;
--
-   if (!nums) nums = sysconf(_SC_NPROCESSORS_CONF);
--#if !defined(OS_LINUX)
--     return nums;
--#endif
--     
--#if !defined(__GLIBC_PREREQ)
--   return nums;
--#endif   
--#if !__GLIBC_PREREQ(2, 3)
--   return nums;
--#endif   
--
--#if !__GLIBC_PREREQ(2, 7)
--  ret = sched_getaffinity(0,sizeof(cpu_set_t), cpusetp);
--  if (ret!=0) return nums;
--  n=0;
--#if !__GLIBC_PREREQ(2, 6)  
--  for (i=0;i<nums;i++)
--     if (CPU_ISSET(i,cpusetp)) n++;
--  nums=n;   
--#else
--  nums = CPU_COUNT(sizeof(cpu_set_t),cpusetp);
--#endif
--  return nums;
--#endif
--
--  cpusetp = CPU_ALLOC(nums);
--  if (cpusetp == NULL) return nums;
--  size = CPU_ALLOC_SIZE(nums);
--  ret = sched_getaffinity(0,size,cpusetp);
--  if (ret!=0) return nums;
--  nums = CPU_COUNT_S(size,cpusetp);
--  CPU_FREE(cpusetp);
-   return nums;
- }
- #endif
diff --git a/sci-libs/openblas/metadata.xml b/sci-libs/openblas/metadata.xml
deleted file mode 100644
index 55f42abc3..000000000
--- a/sci-libs/openblas/metadata.xml
+++ /dev/null
@@ -1,19 +0,0 @@
-<?xml version="1.0" encoding="UTF-8"?>
-<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
-<pkgmetadata>
-	<maintainer type="project">
-		<email>sci@gentoo.org</email>
-		<name>Gentoo Science Project</name>
-	</maintainer>
-	<longdescription lang="en">
-OpenBLAS is an optimized BLAS library based on GotoBLAS2 1.13 BSD
-version. See <pkg>sci-libs/gotoblas2</pkg> for more on GotoBLAS2.
-</longdescription>
-	<use>
-		<flag name="int64">Build the 64 bits integer library</flag>
-		<flag name="dynamic">Build dynamic architecture detection at run time (for multi targets)</flag>
-	</use>
-	<upstream>
-		<remote-id type="github">xianyi/OpenBLAS</remote-id>
-	</upstream>
-</pkgmetadata>
diff --git a/sci-libs/openblas/openblas-0.2.14-r1.ebuild b/sci-libs/openblas/openblas-0.2.14-r1.ebuild
deleted file mode 100644
index ba7aa8298..000000000
--- a/sci-libs/openblas/openblas-0.2.14-r1.ebuild
+++ /dev/null
@@ -1,187 +0,0 @@
-# Copyright 1999-2017 Gentoo Foundation
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=6
-
-NUMERIC_MODULE_NAME="openblas"
-
-inherit alternatives-2 eutils multilib numeric numeric-int64-multibuild
-
-DESCRIPTION="Optimized BLAS library based on GotoBLAS2"
-HOMEPAGE="http://xianyi.github.com/OpenBLAS/"
-SRC_URI="
-	https://github.com/xianyi/OpenBLAS/tarball/v${PV} -> ${P}.tar.gz
-	https://dev.gentoo.org/~gienah/distfiles/${PN}-0.2.11-gentoo.patch"
-
-LICENSE="BSD"
-SLOT="0"
-KEYWORDS="~amd64 ~x86 ~amd64-linux ~x86-linux"
-IUSE="dynamic openmp static-libs threads"
-
-RDEPEND=""
-DEPEND="${RDEPEND}
-	virtual/pkgconfig"
-
-MULTILIB_WRAPPED_HEADERS=(
-	/usr/include/openblas/openblas_config.h
-)
-
-PATCHES=(
-	"${DISTDIR}"/${PN}-0.2.11-gentoo.patch
-)
-
-get_openblas_flags() {
-	local openblas_flags=()
-	use dynamic && \
-		openblas_flags+=( DYNAMIC_ARCH=1 TARGET=GENERIC NUM_THREADS=64 NO_AFFINITY=1 )
-	$(numeric-int64_is_int64_build) && \
-		openblas_flags+=( INTERFACE64=1 )
-	# choose posix threads over openmp when the two are set
-	# yet to see the need of having the two profiles simultaneously
-	if use threads; then
-		openblas_flags+=( USE_THREAD=1 USE_OPENMP=0 )
-	elif use openmp; then
-		openblas_flags+=( USE_OPENMP=1 )
-	fi
-	local profname=$(numeric-int64_get_module_name)
-	local libname="${profname//-/_}"
-	local underscoresuffix="${libname#${PN}}"
-	if [[ "${underscoresuffix}" != "_" ]]; then
-		local libnamesuffix="${underscoresuffix#_}"
-		openblas_flags+=( LIBNAMESUFFIX=${libnamesuffix} )
-	fi
-
-	[[ "${ABI}" == "x86" ]] && openblas_flags+=( BINARY=32 )
-
-	echo "${openblas_flags[@]}"
-}
-
-get_openblas_abi_cflags() {
-	local openblas_abi_cflags=()
-	if [[ "${ABI}" == "x86" ]]; then
-		openblas_abi_cflags=( -DOPENBLAS_ARCH_X86=1 -DOPENBLAS___32BIT__=1 )
-	else
-		openblas_abi_cflags=( -DOPENBLAS_ARCH_X86_64=1 -DOPENBLAS___64BIT__=1 )
-	fi
-	$(numeric-int64_is_int64_build) && \
-		openblas_abi_cflags+=( -DOPENBLAS_USE64BITINT )
-	echo "${openblas_abi_cflags[@]}"
-}
-
-src_unpack() {
-	default
-	find "${WORKDIR}" -maxdepth 1 -type d -name \*OpenBLAS\* && \
-		mv "${WORKDIR}"/*OpenBLAS* "${S}" || die
-}
-
-src_prepare() {
-	default
-
-	# lapack and lapacke are not modified from upstream lapack
-	sed \
-		-e "s:^#\s*\(NO_LAPACK\)\s*=.*:\1=1:" \
-		-e "s:^#\s*\(NO_LAPACKE\)\s*=.*:\1=1:" \
-		-i Makefile.rule || die
-	numeric-int64-multibuild_copy_sources
-}
-
-src_configure() {
-	blas_configure() {
-		local openblas_abi_cflags="$(get_openblas_abi_cflags)"
-		local internal_openblas_abi_cflags="${openblas_abi_cflags//OPENBLAS_}"
-		sed \
-			-e "s:^#\s*\(CC\)\s*=.*:\1=$(tc-getCC) $(get_abi_CFLAGS):" \
-			-e "s:^#\s*\(FC\)\s*=.*:\1=$(tc-getFC) $(get_abi_CFLAGS):" \
-			-e "s:^#\s*\(COMMON_OPT\)\s*=.*:\1=${CFLAGS} ${internal_openblas_abi_cflags}:" \
-			-i Makefile.rule || die
-	}
-	numeric-int64-multibuild_foreach_all_abi_variants run_in_build_dir blas_configure
-}
-
-src_compile() {
-	# openblas already does multi-jobs
-	MAKEOPTS+=" -j1"
-	my_src_compile () {
-		local openblas_flags=$(get_openblas_flags)
-		# cflags already defined twice
-		unset CFLAGS || die
-		emake clean && emake libs shared ${openblas_flags}
-		mkdir -p libs && mv libopenblas* libs/ || die
-		# avoid pic when compiling static libraries, so re-compiling
-		if use static-libs; then
-			emake clean
-			emake libs ${openblas_flags} NO_SHARED=1 NEED_PIC=
-			mv libopenblas* libs/ || die
-		fi
-
-		mv libs/libopenblas* . || die
-	}
-	numeric-int64-multibuild_foreach_all_abi_variants run_in_build_dir my_src_compile
-}
-
-src_test() {
-	my_src_test () {
-		local openblas_flags=$(get_openblas_flags)
-		emake tests ${openblas_flags}
-	}
-	numeric-int64-multibuild_foreach_all_abi_variants run_in_build_dir my_src_test
-}
-
-src_install() {
-	my_src_install() {
-		local openblas_flags=$(get_openblas_flags)
-		local profname=$(numeric-int64_get_module_name)
-		local pcfile
-		# The file /usr/include/openblas/openblas_config.h is generated during the install.
-		# The sed on config_last.h removes the #define's OPENBLAS_USE64BITINT
-		# OPENBLASS__32BIT__ OPENBLASS__64BIT__ OPENBLAS__ARCH_X86 OPENBLAS__ARCH_X86_64
-		# from /usr/include/openblas/openblas_config.h.  We then specify it in Cflags in
-		# the /usr/lib64/pkg-config/openblas-int64-{threads,openmp}.pc file.
-		sed -e '/#define USE64BITINT/d' \
-			-e '/#define ARCH_X86/d' \
-			-e '/#define __\(32\|64\)BIT__/d' \
-			-i config_last.h \
-			|| die "Could not ensure there is no definition of USE64BITINT in config_last.h"
-		emake install \
-			DESTDIR="${D}" PREFIX="${EPREFIX}" ${openblas_flags} \
-			OPENBLAS_INCLUDE_DIR='$(PREFIX)'/usr/include/${PN} \
-			OPENBLAS_LIBRARY_DIR='$(PREFIX)'/usr/$(get_libdir)
-		if ! use static-libs; then
-			rm "${ED}"usr/$(get_libdir)/lib*.a || die
-		fi
-
-		local openblas_abi_cflags=$(get_openblas_abi_cflags)
-		local openblas_abi_fflags=$(numeric-int64_get_fortran_int64_abi_fflags)
-		local libname="${profname//-/_}"
-
-		create_pkgconfig \
-			--name "${profname}" \
-			--libs "-L\${libdir} -l${libname}" \
-			--libs-private "-lm" \
-			--cflags "-I\${includedir}/${PN} ${openblas_abi_cflags}" \
-			${profname}
-
-		if [[ ${CHOST} == *-darwin* ]] ; then
-			cd "${ED}"/usr/$(get_libdir) || die
-			local d
-			for d in *.dylib; do
-				ebegin "Correcting install_name of ${d}"
-				install_name_tool -id "${EPREFIX}/usr/$(get_libdir)/${d}" "${d}" || die
-				eend $?
-			done
-		fi
-		if [[ ${#MULTIBUILD_VARIANTS[@]} -gt 1 ]]; then
-			multilib_prepare_wrappers
-			multilib_check_headers
-		fi
-	}
-	numeric-int64-multibuild_foreach_all_abi_variants run_in_build_dir my_src_install
-
-	printf "/usr/include/cblas.h ${PN}/cblas.h" > "${T}"/alternative-cblas-generic.sh || die
-	numeric-int64-multibuild_install_alternative blas ${NUMERIC_MODULE_NAME}
-	numeric-int64-multibuild_install_alternative cblas ${NUMERIC_MODULE_NAME}
-
-	multilib_install_wrappers
-
-	dodoc GotoBLAS_{01Readme,03FAQ,04FAQ,05LargePage,06WeirdPerformance}.txt *md Changelog.txt
-}
diff --git a/sci-libs/openblas/openblas-0.2.15-r1.ebuild b/sci-libs/openblas/openblas-0.2.15-r1.ebuild
deleted file mode 100644
index e4f0c89ed..000000000
--- a/sci-libs/openblas/openblas-0.2.15-r1.ebuild
+++ /dev/null
@@ -1,188 +0,0 @@
-# Copyright 1999-2017 Gentoo Foundation
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=6
-
-NUMERIC_MODULE_NAME="openblas"
-
-inherit alternatives-2 eutils multilib numeric numeric-int64-multibuild
-
-DESCRIPTION="Optimized BLAS library based on GotoBLAS2"
-HOMEPAGE="http://xianyi.github.com/OpenBLAS/"
-SRC_URI="
-	https://github.com/xianyi/OpenBLAS/tarball/v${PV} -> ${P}.tar.gz
-	https://dev.gentoo.org/~gienah/distfiles/${PN}-0.2.11-gentoo.patch"
-
-LICENSE="BSD"
-SLOT="0"
-KEYWORDS="~amd64 ~x86 ~amd64-linux ~x86-linux"
-IUSE="dynamic openmp static-libs threads"
-
-RDEPEND=""
-DEPEND="${RDEPEND}
-	virtual/pkgconfig"
-
-MULTILIB_WRAPPED_HEADERS=(
-	/usr/include/openblas/openblas_config.h
-)
-
-PATCHES=(
-	"${DISTDIR}"/${PN}-0.2.11-gentoo.patch
-)
-
-get_openblas_flags() {
-	local openblas_flags=()
-	use dynamic && \
-		openblas_flags+=( DYNAMIC_ARCH=1 TARGET=GENERIC NUM_THREADS=64 NO_AFFINITY=1 )
-	$(numeric-int64_is_int64_build) && \
-		openblas_flags+=( INTERFACE64=1 )
-	# choose posix threads over openmp when the two are set
-	# yet to see the need of having the two profiles simultaneously
-	if use threads; then
-		openblas_flags+=( USE_THREAD=1 USE_OPENMP=0 )
-	elif use openmp; then
-		openblas_flags+=( USE_OPENMP=1 )
-	fi
-	local profname=$(numeric-int64_get_module_name)
-	local libname="${profname//-/_}"
-	local underscoresuffix="${libname#${PN}}"
-	if [[ "${underscoresuffix}" != "_" ]]; then
-		local libnamesuffix="${underscoresuffix#_}"
-		openblas_flags+=( LIBNAMESUFFIX=${libnamesuffix} )
-	fi
-
-	[[ "${ABI}" == "x86" ]] && openblas_flags+=( BINARY=32 )
-
-	echo "${openblas_flags[@]}"
-}
-
-get_openblas_abi_cflags() {
-	local openblas_abi_cflags=()
-	if [[ "${ABI}" == "x86" ]]; then
-		openblas_abi_cflags=( -DOPENBLAS_ARCH_X86=1 -DOPENBLAS___32BIT__=1 )
-	else
-		openblas_abi_cflags=( -DOPENBLAS_ARCH_X86_64=1 -DOPENBLAS___64BIT__=1 )
-	fi
-	$(numeric-int64_is_int64_build) && \
-		openblas_abi_cflags+=( -DOPENBLAS_USE64BITINT )
-	use openmp && openblas_abi_cflags+=( -fopenmp )
-	echo "${openblas_abi_cflags[@]}"
-}
-
-src_unpack() {
-	default
-	find "${WORKDIR}" -maxdepth 1 -type d -name \*OpenBLAS\* && \
-		mv "${WORKDIR}"/*OpenBLAS* "${S}" || die
-}
-
-src_prepare() {
-	default
-
-	# lapack and lapacke are not modified from upstream lapack
-	sed \
-		-e "s:^#\s*\(NO_LAPACK\)\s*=.*:\1=1:" \
-		-e "s:^#\s*\(NO_LAPACKE\)\s*=.*:\1=1:" \
-		-i Makefile.rule || die
-	numeric-int64-multibuild_copy_sources
-}
-
-src_configure() {
-	blas_configure() {
-		local openblas_abi_cflags="$(get_openblas_abi_cflags)"
-		local internal_openblas_abi_cflags="${openblas_abi_cflags//OPENBLAS_}"
-		sed \
-			-e "s:^#\s*\(CC\)\s*=.*:\1=$(tc-getCC) $(get_abi_CFLAGS):" \
-			-e "s:^#\s*\(FC\)\s*=.*:\1=$(tc-getFC) $(get_abi_CFLAGS):" \
-			-e "s:^#\s*\(COMMON_OPT\)\s*=.*:\1=${CFLAGS} ${internal_openblas_abi_cflags}:" \
-			-i Makefile.rule || die
-	}
-	numeric-int64-multibuild_foreach_all_abi_variants run_in_build_dir blas_configure
-}
-
-src_compile() {
-	# openblas already does multi-jobs
-	MAKEOPTS+=" -j1"
-	my_src_compile () {
-		local openblas_flags=$(get_openblas_flags)
-		# cflags already defined twice
-		unset CFLAGS || die
-		emake clean && emake libs shared ${openblas_flags}
-		mkdir -p libs && mv libopenblas* libs/ || die
-		# avoid pic when compiling static libraries, so re-compiling
-		if use static-libs; then
-			emake clean
-			emake libs ${openblas_flags} NO_SHARED=1 NEED_PIC=
-			mv libopenblas* libs/ || die
-		fi
-
-		mv libs/libopenblas* . || die
-	}
-	numeric-int64-multibuild_foreach_all_abi_variants run_in_build_dir my_src_compile
-}
-
-src_test() {
-	my_src_test () {
-		local openblas_flags=$(get_openblas_flags)
-		emake tests ${openblas_flags}
-	}
-	numeric-int64-multibuild_foreach_all_abi_variants run_in_build_dir my_src_test
-}
-
-src_install() {
-	my_src_install() {
-		local openblas_flags=$(get_openblas_flags)
-		local profname=$(numeric-int64_get_module_name)
-		local pcfile
-		# The file /usr/include/openblas/openblas_config.h is generated during the install.
-		# The sed on config_last.h removes the #define's OPENBLAS_USE64BITINT
-		# OPENBLASS__32BIT__ OPENBLASS__64BIT__ OPENBLAS__ARCH_X86 OPENBLAS__ARCH_X86_64
-		# from /usr/include/openblas/openblas_config.h.  We then specify it in Cflags in
-		# the /usr/lib64/pkg-config/openblas-int64-{threads,openmp}.pc file.
-		sed -e '/#define USE64BITINT/d' \
-			-e '/#define ARCH_X86/d' \
-			-e '/#define __\(32\|64\)BIT__/d' \
-			-i config_last.h \
-			|| die "Could not ensure there is no definition of USE64BITINT in config_last.h"
-		emake install \
-			DESTDIR="${D}" PREFIX="${EPREFIX}" ${openblas_flags} \
-			OPENBLAS_INCLUDE_DIR='$(PREFIX)'/usr/include/${PN} \
-			OPENBLAS_LIBRARY_DIR='$(PREFIX)'/usr/$(get_libdir)
-		if ! use static-libs; then
-			rm "${ED}"usr/$(get_libdir)/lib*.a || die
-		fi
-
-		local openblas_abi_cflags=$(get_openblas_abi_cflags)
-		local openblas_abi_fflags=$(numeric-int64_get_fortran_int64_abi_fflags)
-		local libname="${profname//-/_}"
-
-		create_pkgconfig \
-			--name "${profname}" \
-			--libs "-L\${libdir} -l${libname}" \
-			--libs-private "-lm" \
-			--cflags "-I\${includedir}/${PN} ${openblas_abi_cflags}" \
-			${profname}
-
-		if [[ ${CHOST} == *-darwin* ]] ; then
-			cd "${ED}"/usr/$(get_libdir) || die
-			local d
-			for d in *.dylib; do
-				ebegin "Correcting install_name of ${d}"
-				install_name_tool -id "${EPREFIX}/usr/$(get_libdir)/${d}" "${d}" || die
-				eend $?
-			done
-		fi
-		if [[ ${#MULTIBUILD_VARIANTS[@]} -gt 1 ]]; then
-			multilib_prepare_wrappers
-			multilib_check_headers
-		fi
-	}
-	numeric-int64-multibuild_foreach_all_abi_variants run_in_build_dir my_src_install
-
-	printf "/usr/include/cblas.h ${PN}/cblas.h" > "${T}"/alternative-cblas-generic.sh || die
-	numeric-int64-multibuild_install_alternative blas ${NUMERIC_MODULE_NAME}
-	numeric-int64-multibuild_install_alternative cblas ${NUMERIC_MODULE_NAME}
-
-	multilib_install_wrappers
-
-	dodoc GotoBLAS_{01Readme,03FAQ,04FAQ,05LargePage,06WeirdPerformance}.txt *md Changelog.txt
-}
diff --git a/sci-libs/openblas/openblas-0.2.19-r1.ebuild b/sci-libs/openblas/openblas-0.2.19-r1.ebuild
deleted file mode 100644
index 38378cecd..000000000
--- a/sci-libs/openblas/openblas-0.2.19-r1.ebuild
+++ /dev/null
@@ -1,193 +0,0 @@
-# Copyright 1999-2017 Gentoo Foundation
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=6
-
-NUMERIC_MODULE_NAME="openblas"
-
-inherit alternatives-2 eutils multilib numeric numeric-int64-multibuild
-
-DESCRIPTION="Optimized BLAS library based on GotoBLAS2"
-HOMEPAGE="http://xianyi.github.com/OpenBLAS/"
-SRC_URI="https://github.com/xianyi/OpenBLAS/tarball/v${PV} -> ${P}.tar.gz
-	https://sagetrac.lipn.univ-paris13.fr/sage/${PN}-0.2.19-clang-3.9.patch"
-
-LICENSE="BSD"
-SLOT="0"
-KEYWORDS="~amd64 ~x86 ~amd64-linux ~x86-linux ~x64-macos ~x86-macos"
-IUSE="dynamic openmp static-libs threads"
-
-RDEPEND=""
-DEPEND="${RDEPEND}
-	virtual/pkgconfig"
-
-MULTILIB_WRAPPED_HEADERS=(
-	/usr/include/openblas/openblas_config.h
-)
-
-PATCHES=(
-	"${DISTDIR}"/${PN}-0.2.19-clang-3.9.patch
-	"${FILESDIR}"/${PN}-0.2.19-MAKE.patch
-	"${FILESDIR}"/${PN}-0.2.19-utest_ldflags.patch
-	)
-
-get_openblas_flags() {
-	local openblas_flags=()
-	use dynamic && \
-		openblas_flags+=( DYNAMIC_ARCH=1 TARGET=GENERIC NUM_THREADS=64 NO_AFFINITY=1 )
-	$(numeric-int64_is_int64_build) && \
-		openblas_flags+=( INTERFACE64=1 )
-	# choose posix threads over openmp when the two are set
-	# yet to see the need of having the two profiles simultaneously
-	if use threads; then
-		openblas_flags+=( USE_THREAD=1 USE_OPENMP=0 )
-	elif use openmp; then
-		openblas_flags+=( USE_OPENMP=1 )
-	fi
-	local profname=$(numeric-int64_get_module_name)
-	local libname="${profname//-/_}"
-	local underscoresuffix="${libname#${PN}}"
-	if [[ "${underscoresuffix}" != "_" ]]; then
-		local libnamesuffix="${underscoresuffix#_}"
-		openblas_flags+=( LIBNAMESUFFIX=${libnamesuffix} )
-	fi
-
-	[[ "${ABI}" == "x86" ]] && openblas_flags+=( BINARY=32 )
-
-	echo "${openblas_flags[@]}"
-}
-
-get_openblas_abi_cflags() {
-	local openblas_abi_cflags=()
-	if [[ "${ABI}" == "x86" ]]; then
-		openblas_abi_cflags=( -DARCH_X86=1 -DOPENBLAS___32BIT__=1 )
-	elif [[ "${ABI}" == "amd64" ]]; then
-		openblas_abi_cflags=( -DARCH_X86_64=1 -DOPENBLAS___64BIT__=1 )
-	elif [[ "${ABI}" == "ppc64" ]]; then
-		openblas_abi_cflags=( -DARCH_POWER=1 -DOPENBLAS___64BIT__=1 )
-	else
-		die "unsupported abi: ${ABI}"
-	fi
-	$(numeric-int64_is_int64_build) && \
-		openblas_abi_cflags+=( -DOPENBLAS_USE64BITINT )
-	use openmp && openblas_abi_cflags+=( -fopenmp )
-	echo "${openblas_abi_cflags[@]}"
-}
-
-src_unpack() {
-	default
-	find "${WORKDIR}" -maxdepth 1 -type d -name \*OpenBLAS\* && \
-		mv "${WORKDIR}"/*OpenBLAS* "${S}" || die
-}
-
-src_prepare() {
-	default
-
-	# lapack and lapacke are not modified from upstream lapack
-	sed \
-		-e "s:^#\s*\(NO_LAPACK\)\s*=.*:\1=1:" \
-		-e "s:^#\s*\(NO_LAPACKE\)\s*=.*:\1=1:" \
-		-i Makefile.rule || die
-	numeric-int64-multibuild_copy_sources
-}
-
-src_configure() {
-	blas_configure() {
-		local openblas_abi_cflags="$(get_openblas_abi_cflags)"
-		local internal_openblas_abi_cflags="${openblas_abi_cflags//OPENBLAS_}"
-		sed \
-			-e "s:^#\s*\(CC\)\s*=.*:\1=$(tc-getCC) $(get_abi_CFLAGS):" \
-			-e "s:^#\s*\(FC\)\s*=.*:\1=$(tc-getFC) $(get_abi_CFLAGS):" \
-			-e "s:^#\s*\(COMMON_OPT\)\s*=.*:\1=${CFLAGS} ${internal_openblas_abi_cflags}:" \
-			-i Makefile.rule || die
-	}
-	numeric-int64-multibuild_foreach_all_abi_variants run_in_build_dir blas_configure
-}
-
-src_compile() {
-	# openblas already does multi-jobs
-	MAKEOPTS+=" -j1"
-	my_src_compile () {
-		local openblas_flags=$(get_openblas_flags)
-		# cflags already defined twice
-		unset CFLAGS || die
-		emake clean && emake libs shared ${openblas_flags}
-		mkdir -p libs && mv libopenblas* libs/ || die
-		# avoid pic when compiling static libraries, so re-compiling
-		if use static-libs; then
-			emake clean
-			emake libs ${openblas_flags} NO_SHARED=1 NEED_PIC=
-			mv libopenblas* libs/ || die
-		fi
-
-		mv libs/libopenblas* . || die
-	}
-	numeric-int64-multibuild_foreach_all_abi_variants run_in_build_dir my_src_compile
-}
-
-src_test() {
-	my_src_test () {
-		local openblas_flags=$(get_openblas_flags)
-		emake tests ${openblas_flags}
-	}
-	numeric-int64-multibuild_foreach_all_abi_variants run_in_build_dir my_src_test
-}
-
-src_install() {
-	my_src_install() {
-		local openblas_flags=$(get_openblas_flags)
-		local profname=$(numeric-int64_get_module_name)
-		local pcfile
-		# The file /usr/include/openblas/openblas_config.h is generated during the install.
-		# The sed on config_last.h removes the #define's OPENBLAS_USE64BITINT
-		# OPENBLASS__32BIT__ OPENBLASS__64BIT__ OPENBLAS__ARCH_X86 OPENBLAS__ARCH_X86_64
-		# from /usr/include/openblas/openblas_config.h.  We then specify it in Cflags in
-		# the /usr/lib64/pkg-config/openblas-int64-{threads,openmp}.pc file.
-		sed -e '/#define USE64BITINT/d' \
-			-e '/#define ARCH_X86/d' \
-			-e '/#define __\(32\|64\)BIT__/d' \
-			-i config_last.h \
-			|| die "Could not ensure there is no definition of USE64BITINT in config_last.h"
-		emake install \
-			DESTDIR="${D}" PREFIX="${EPREFIX}" ${openblas_flags} \
-			OPENBLAS_INCLUDE_DIR='$(PREFIX)'/usr/include/${PN} \
-			OPENBLAS_LIBRARY_DIR='$(PREFIX)'/usr/$(get_libdir)
-		if ! use static-libs; then
-			rm "${ED}"usr/$(get_libdir)/lib*.a || die
-		fi
-
-		local openblas_abi_cflags=$(get_openblas_abi_cflags)
-		local openblas_abi_fflags=$(numeric-int64_get_fortran_int64_abi_fflags)
-		local libname="${profname//-/_}"
-
-		create_pkgconfig \
-			--name "${profname}" \
-			--libs "-l${libname}" \
-			--libs-private "-lm" \
-			--cflags "-I\${includedir}/${PN} ${openblas_abi_cflags}" \
-			${profname}
-
-		if [[ ${CHOST} == *-darwin* ]] ; then
-			cd "${ED}"/usr/$(get_libdir) || die
-			local d
-			for d in *.dylib; do
-				ebegin "Correcting install_name of ${d}"
-				install_name_tool -id "${EPREFIX}/usr/$(get_libdir)/${d}" "${d}" || die
-				eend $?
-			done
-		fi
-		if [[ ${#MULTIBUILD_VARIANTS[@]} -gt 1 ]]; then
-			multilib_prepare_wrappers
-			multilib_check_headers
-		fi
-	}
-	numeric-int64-multibuild_foreach_all_abi_variants run_in_build_dir my_src_install
-
-	printf "/usr/include/cblas.h ${PN}/cblas.h" > "${T}"/alternative-cblas-generic.sh || die
-	numeric-int64-multibuild_install_alternative blas ${NUMERIC_MODULE_NAME}
-	numeric-int64-multibuild_install_alternative cblas ${NUMERIC_MODULE_NAME}
-
-	multilib_install_wrappers
-
-	dodoc GotoBLAS_{01Readme,03FAQ,04FAQ,05LargePage,06WeirdPerformance}.txt *md Changelog.txt
-}
diff --git a/sci-libs/openblas/openblas-0.2.20.ebuild b/sci-libs/openblas/openblas-0.2.20.ebuild
deleted file mode 100644
index 838c334d6..000000000
--- a/sci-libs/openblas/openblas-0.2.20.ebuild
+++ /dev/null
@@ -1,192 +0,0 @@
-# Copyright 1999-2017 Gentoo Foundation
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=6
-
-NUMERIC_MODULE_NAME="openblas"
-
-inherit alternatives-2 eutils multilib numeric numeric-int64-multibuild
-
-DESCRIPTION="Optimized BLAS library based on GotoBLAS2"
-HOMEPAGE="http://xianyi.github.com/OpenBLAS/"
-SRC_URI="https://github.com/xianyi/OpenBLAS/tarball/v${PV} -> ${P}.tar.gz"
-
-LICENSE="BSD"
-SLOT="0"
-KEYWORDS="~amd64 ~x86 ~amd64-linux ~x86-linux ~x64-macos ~x86-macos"
-IUSE="dynamic openmp static-libs threads"
-
-RDEPEND=""
-DEPEND="${RDEPEND}
-	virtual/pkgconfig"
-
-MULTILIB_WRAPPED_HEADERS=(
-	/usr/include/openblas/openblas_config.h
-)
-
-PATCHES=(
-	"${FILESDIR}"/${PN}-0.2.20-non-glibc.patch
-	)
-
-get_openblas_flags() {
-	local openblas_flags=()
-	use dynamic && \
-		openblas_flags+=( DYNAMIC_ARCH=1 TARGET=GENERIC NUM_THREADS=64 NO_AFFINITY=1 )
-	$(numeric-int64_is_int64_build) && \
-		openblas_flags+=( INTERFACE64=1 )
-	# choose posix threads over openmp when the two are set
-	# yet to see the need of having the two profiles simultaneously
-	if use threads; then
-		openblas_flags+=( USE_THREAD=1 USE_OPENMP=0 )
-	elif use openmp; then
-		openblas_flags+=( USE_OPENMP=1 )
-	else
-		openblas_flags+=( USE_THREAD=0 ) # single-threaded
-	fi
-	local profname=$(numeric-int64_get_module_name)
-	local libname="${profname//-/_}"
-	local underscoresuffix="${libname#${PN}}"
-	if [[ "${underscoresuffix}" != "_" ]]; then
-		local libnamesuffix="${underscoresuffix#_}"
-		openblas_flags+=( LIBNAMESUFFIX=${libnamesuffix} )
-	fi
-
-	[[ "${ABI}" == "x86" ]] && openblas_flags+=( BINARY=32 )
-
-	echo "${openblas_flags[@]}"
-}
-
-get_openblas_abi_cflags() {
-	local openblas_abi_cflags=()
-	if [[ "${ABI}" == "x86" ]]; then
-		openblas_abi_cflags=( -DARCH_X86=1 -DOPENBLAS___32BIT__=1 )
-	elif [[ "${ABI}" == "amd64" ]]; then
-		openblas_abi_cflags=( -DARCH_X86_64=1 -DOPENBLAS___64BIT__=1 )
-	elif [[ "${ABI}" == "ppc64" ]]; then
-		openblas_abi_cflags=( -DARCH_POWER=1 -DOPENBLAS___64BIT__=1 )
-	else
-		die "unsupported abi: ${ABI}"
-	fi
-	$(numeric-int64_is_int64_build) && \
-		openblas_abi_cflags+=( -DOPENBLAS_USE64BITINT )
-	use openmp && openblas_abi_cflags+=( -fopenmp )
-	echo "${openblas_abi_cflags[@]}"
-}
-
-src_unpack() {
-	default
-	find "${WORKDIR}" -maxdepth 1 -type d -name \*OpenBLAS\* && \
-		mv "${WORKDIR}"/*OpenBLAS* "${S}" || die
-}
-
-src_prepare() {
-	default
-
-	# lapack and lapacke are not modified from upstream lapack
-	sed \
-		-e "s:^#\s*\(NO_LAPACK\)\s*=.*:\1=1:" \
-		-e "s:^#\s*\(NO_LAPACKE\)\s*=.*:\1=1:" \
-		-i Makefile.rule || die
-	numeric-int64-multibuild_copy_sources
-}
-
-src_configure() {
-	blas_configure() {
-		local openblas_abi_cflags="$(get_openblas_abi_cflags)"
-		local internal_openblas_abi_cflags="${openblas_abi_cflags//OPENBLAS_}"
-		sed \
-			-e "s:^#\s*\(CC\)\s*=.*:\1=$(tc-getCC) $(get_abi_CFLAGS):" \
-			-e "s:^#\s*\(FC\)\s*=.*:\1=$(tc-getFC) $(get_abi_CFLAGS):" \
-			-e "s:^#\s*\(COMMON_OPT\)\s*=.*:\1=${CFLAGS} ${internal_openblas_abi_cflags}:" \
-			-i Makefile.rule || die
-	}
-	numeric-int64-multibuild_foreach_all_abi_variants run_in_build_dir blas_configure
-}
-
-src_compile() {
-	# openblas already does multi-jobs
-	MAKEOPTS+=" -j1"
-	my_src_compile () {
-		local openblas_flags=$(get_openblas_flags)
-		# cflags already defined twice
-		unset CFLAGS || die
-		emake clean && emake libs shared ${openblas_flags}
-		mkdir -p libs && mv libopenblas* libs/ || die
-		# avoid pic when compiling static libraries, so re-compiling
-		if use static-libs; then
-			emake clean
-			emake libs ${openblas_flags} NO_SHARED=1 NEED_PIC=
-			mv libopenblas* libs/ || die
-		fi
-
-		mv libs/libopenblas* . || die
-	}
-	numeric-int64-multibuild_foreach_all_abi_variants run_in_build_dir my_src_compile
-}
-
-src_test() {
-	my_src_test () {
-		local openblas_flags=$(get_openblas_flags)
-		emake tests ${openblas_flags}
-	}
-	numeric-int64-multibuild_foreach_all_abi_variants run_in_build_dir my_src_test
-}
-
-src_install() {
-	my_src_install() {
-		local openblas_flags=$(get_openblas_flags)
-		local profname=$(numeric-int64_get_module_name)
-		local pcfile
-		# The file /usr/include/openblas/openblas_config.h is generated during the install.
-		# The sed on config_last.h removes the #define's OPENBLAS_USE64BITINT
-		# OPENBLASS__32BIT__ OPENBLASS__64BIT__ OPENBLAS__ARCH_X86 OPENBLAS__ARCH_X86_64
-		# from /usr/include/openblas/openblas_config.h.  We then specify it in Cflags in
-		# the /usr/lib64/pkg-config/openblas-int64-{threads,openmp}.pc file.
-		sed -e '/#define USE64BITINT/d' \
-			-e '/#define ARCH_X86/d' \
-			-e '/#define __\(32\|64\)BIT__/d' \
-			-i config_last.h \
-			|| die "Could not ensure there is no definition of USE64BITINT in config_last.h"
-		emake install \
-			DESTDIR="${D}" PREFIX="${EPREFIX}" ${openblas_flags} \
-			OPENBLAS_INCLUDE_DIR='$(PREFIX)'/usr/include/${PN} \
-			OPENBLAS_LIBRARY_DIR='$(PREFIX)'/usr/$(get_libdir)
-		if ! use static-libs; then
-			rm "${ED}"usr/$(get_libdir)/lib*.a || die
-		fi
-
-		local openblas_abi_cflags=$(get_openblas_abi_cflags)
-		local openblas_abi_fflags=$(numeric-int64_get_fortran_int64_abi_fflags)
-		local libname="${profname//-/_}"
-
-		create_pkgconfig \
-			--name "${profname}" \
-			--libs "-l${libname}" \
-			--libs-private "-lm" \
-			--cflags "-I\${includedir}/${PN} ${openblas_abi_cflags}" \
-			${profname}
-
-		if [[ ${CHOST} == *-darwin* ]] ; then
-			cd "${ED}"/usr/$(get_libdir) || die
-			local d
-			for d in *.dylib; do
-				ebegin "Correcting install_name of ${d}"
-				install_name_tool -id "${EPREFIX}/usr/$(get_libdir)/${d}" "${d}" || die
-				eend $?
-			done
-		fi
-		if [[ ${#MULTIBUILD_VARIANTS[@]} -gt 1 ]]; then
-			multilib_prepare_wrappers
-			multilib_check_headers
-		fi
-	}
-	numeric-int64-multibuild_foreach_all_abi_variants run_in_build_dir my_src_install
-
-	printf "/usr/include/cblas.h ${PN}/cblas.h" > "${T}"/alternative-cblas-generic.sh || die
-	numeric-int64-multibuild_install_alternative blas ${NUMERIC_MODULE_NAME}
-	numeric-int64-multibuild_install_alternative cblas ${NUMERIC_MODULE_NAME}
-
-	multilib_install_wrappers
-
-	dodoc GotoBLAS_{01Readme,03FAQ,04FAQ,05LargePage,06WeirdPerformance}.txt *md Changelog.txt
-}
diff --git a/sci-libs/openblas/openblas-9999.ebuild b/sci-libs/openblas/openblas-9999.ebuild
deleted file mode 100644
index e4ed2800f..000000000
--- a/sci-libs/openblas/openblas-9999.ebuild
+++ /dev/null
@@ -1,181 +0,0 @@
-# Copyright 1999-2017 Gentoo Foundation
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=6
-
-NUMERIC_MODULE_NAME="openblas"
-
-inherit alternatives-2 eutils git-r3 multilib numeric numeric-int64-multibuild
-
-DESCRIPTION="Optimized BLAS library based on GotoBLAS2"
-HOMEPAGE="http://xianyi.github.com/OpenBLAS/"
-SRC_URI="https://dev.gentoo.org/~gienah/distfiles/${PN}-0.2.11-gentoo.patch"
-EGIT_REPO_URI="https://github.com/xianyi/OpenBLAS.git"
-EGIT_BRANCH="develop"
-
-LICENSE="BSD"
-SLOT="0"
-KEYWORDS=""
-IUSE="dynamic openmp static-libs threads"
-
-RDEPEND=""
-DEPEND="${RDEPEND}
-	virtual/pkgconfig"
-
-MULTILIB_WRAPPED_HEADERS=(
-	/usr/include/openblas/openblas_config.h
-)
-
-PATCHES=(
-	"${DISTDIR}"/${PN}-0.2.11-gentoo.patch
-)
-
-get_openblas_flags() {
-	local openblas_flags=()
-	use dynamic && \
-		openblas_flags+=( DYNAMIC_ARCH=1 TARGET=GENERIC NUM_THREADS=64 NO_AFFINITY=1 )
-	$(numeric-int64_is_int64_build) && \
-		openblas_flags+=( INTERFACE64=1 )
-	# choose posix threads over openmp when the two are set
-	# yet to see the need of having the two profiles simultaneously
-	if use threads; then
-		openblas_flags+=( USE_THREAD=1 USE_OPENMP=0 )
-	elif use openmp; then
-		openblas_flags+=( USE_OPENMP=1 )
-	fi
-	local profname=$(numeric-int64_get_module_name)
-	local libname="${profname//-/_}"
-	local underscoresuffix="${libname#${PN}}"
-	if [[ "${underscoresuffix}" != "_" ]]; then
-		local libnamesuffix="${underscoresuffix#_}"
-		openblas_flags+=( LIBNAMESUFFIX=${libnamesuffix} )
-	fi
-
-	[[ "${ABI}" == "x86" ]] && openblas_flags+=( BINARY=32 )
-
-	echo "${openblas_flags[@]}"
-}
-
-get_openblas_abi_cflags() {
-	local openblas_abi_cflags=()
-	if [[ "${ABI}" == "x86" ]]; then
-		openblas_abi_cflags=( -DOPENBLAS_ARCH_X86=1 -DOPENBLAS___32BIT__=1 )
-	else
-		openblas_abi_cflags=( -DOPENBLAS_ARCH_X86_64=1 -DOPENBLAS___64BIT__=1 )
-	fi
-	$(numeric-int64_is_int64_build) && \
-		openblas_abi_cflags+=( -DOPENBLAS_USE64BITINT )
-	echo "${openblas_abi_cflags[@]}"
-}
-
-src_prepare() {
-	default
-
-	# lapack and lapacke are not modified from upstream lapack
-	sed \
-		-e "s:^#\s*\(NO_LAPACK\)\s*=.*:\1=1:" \
-		-e "s:^#\s*\(NO_LAPACKE\)\s*=.*:\1=1:" \
-		-i Makefile.rule || die
-	numeric-int64-multibuild_copy_sources
-}
-
-src_configure() {
-	blas_configure() {
-		local openblas_abi_cflags="$(get_openblas_abi_cflags)"
-		local internal_openblas_abi_cflags="${openblas_abi_cflags//OPENBLAS_}"
-		sed \
-			-e "s:^#\s*\(CC\)\s*=.*:\1=$(tc-getCC) $(get_abi_CFLAGS):" \
-			-e "s:^#\s*\(FC\)\s*=.*:\1=$(tc-getFC) $(get_abi_CFLAGS):" \
-			-e "s:^#\s*\(COMMON_OPT\)\s*=.*:\1=${CFLAGS} ${internal_openblas_abi_cflags}:" \
-			-i Makefile.rule || die
-	}
-	numeric-int64-multibuild_foreach_all_abi_variants run_in_build_dir blas_configure
-}
-
-src_compile() {
-	# openblas already does multi-jobs
-	MAKEOPTS+=" -j1"
-	my_src_compile () {
-		local openblas_flags=$(get_openblas_flags)
-		# cflags already defined twice
-		unset CFLAGS || die
-		emake clean && emake libs shared ${openblas_flags}
-		mkdir -p libs && mv libopenblas* libs/ || die
-		# avoid pic when compiling static libraries, so re-compiling
-		if use static-libs; then
-			emake clean
-			emake libs ${openblas_flags} NO_SHARED=1 NEED_PIC=
-			mv libopenblas* libs/ || die
-		fi
-
-		mv libs/libopenblas* . || die
-	}
-	numeric-int64-multibuild_foreach_all_abi_variants run_in_build_dir my_src_compile
-}
-
-src_test() {
-	my_src_test () {
-		local openblas_flags=$(get_openblas_flags)
-		emake tests ${openblas_flags}
-	}
-	numeric-int64-multibuild_foreach_all_abi_variants run_in_build_dir my_src_test
-}
-
-src_install() {
-	my_src_install() {
-		local openblas_flags=$(get_openblas_flags)
-		local profname=$(numeric-int64_get_module_name)
-		local pcfile
-		# The file /usr/include/openblas/openblas_config.h is generated during the install.
-		# The sed on config_last.h removes the #define's OPENBLAS_USE64BITINT
-		# OPENBLASS__32BIT__ OPENBLASS__64BIT__ OPENBLAS__ARCH_X86 OPENBLAS__ARCH_X86_64
-		# from /usr/include/openblas/openblas_config.h.  We then specify it in Cflags in
-		# the /usr/lib64/pkg-config/openblas-int64-{threads,openmp}.pc file.
-		sed -e '/#define USE64BITINT/d' \
-			-e '/#define ARCH_X86/d' \
-			-e '/#define __\(32\|64\)BIT__/d' \
-			-i config_last.h \
-			|| die "Could not ensure there is no definition of USE64BITINT in config_last.h"
-		emake install \
-			PREFIX="${ED}"usr ${openblas_flags} \
-			OPENBLAS_INCLUDE_DIR="${ED}"usr/include/${PN} \
-			OPENBLAS_LIBRARY_DIR="${ED}"usr/$(get_libdir)
-		if ! use static-libs; then
-			rm "${ED}"usr/$(get_libdir)/lib*.a || die
-		fi
-
-		local openblas_abi_cflags=$(get_openblas_abi_cflags)
-		local openblas_abi_fflags=$(numeric-int64_get_fortran_int64_abi_fflags)
-		local libname="${profname//-/_}"
-
-		create_pkgconfig \
-			--name "${profname}" \
-			--libs "-L\${libdir} -l${libname}" \
-			--libs-private "-lm" \
-			--cflags "-I\${includedir}/${PN} ${openblas_abi_cflags}" \
-			${profname}
-
-		if [[ ${CHOST} == *-darwin* ]] ; then
-			cd "${ED}"/usr/$(get_libdir) || die
-			local d
-			for d in *.dylib; do
-				ebegin "Correcting install_name of ${d}"
-				install_name_tool -id "${EPREFIX}/usr/$(get_libdir)/${d}" "${d}" || die
-				eend $?
-			done
-		fi
-		if [[ ${#MULTIBUILD_VARIANTS[@]} -gt 1 ]]; then
-			multilib_prepare_wrappers
-			multilib_check_headers
-		fi
-	}
-	numeric-int64-multibuild_foreach_all_abi_variants run_in_build_dir my_src_install
-
-	printf "/usr/include/cblas.h ${PN}/cblas.h" > "${T}"/alternative-cblas-generic.sh
-	numeric-int64-multibuild_install_alternative blas ${NUMERIC_MODULE_NAME}
-	numeric-int64-multibuild_install_alternative cblas ${NUMERIC_MODULE_NAME}
-
-	multilib_install_wrappers
-
-	dodoc GotoBLAS_{01Readme,03FAQ,04FAQ,05LargePage,06WeirdPerformance}.txt *md Changelog.txt
-}
diff --git a/sci-libs/openlibm/files/openlibm-respect-toolchain.patch b/sci-libs/openlibm/files/openlibm-respect-toolchain.patch
deleted file mode 100644
index 365aa17ec..000000000
--- a/sci-libs/openlibm/files/openlibm-respect-toolchain.patch
+++ /dev/null
@@ -1,42 +0,0 @@
---- Make.inc.orig	2013-07-16 15:50:21.227405299 -0700
-+++ Make.inc	2013-07-16 15:52:17.539087715 -0700
-@@ -2,26 +2,18 @@
- 
- OS := $(shell uname)
- 
--FC = gfortran
--FFLAGS += -O3
-+FC := gfortran
- 
--USEGCC = 1
--USECLANG = 0
- 
--ifeq ($(OS), Darwin)
--USEGCC = 0
--USECLANG = 1
--endif
--
--AR = ar
-+AR := ar
- 
--ifeq ($(USECLANG),1)
-+ifneq (,$(findstring clang,$(CC)))
- USEGCC = 0
- CC = clang
- CFLAGS_add += -fno-builtin
- endif
- 
--ifeq ($(USEGCC),1)
-+ifneq (,$(findstring gcc,$(CC)))
- CC = gcc
- CFLAGS_add += -fno-gnu89-inline
- endif
-@@ -31,7 +23,7 @@
- $(error "the mingw32 compiler you are using fails the openblas testsuite. please see the Julia README.windows.md document for a replacement")
- endif
- 
--CFLAGS_add += -std=c99 -Wall -O3 -I$(OPENLIBM_HOME) -I$(OPENLIBM_HOME)/include -I$(OPENLIBM_HOME)/ld80 -I$(OPENLIBM_HOME)/$(ARCH) -I$(OPENLIBM_HOME)/src -DASSEMBLER -D__BSD_VISIBLE -Wno-implicit-function-declaration
-+CFLAGS_add += -std=c99 -Wall -I$(OPENLIBM_HOME) -I$(OPENLIBM_HOME)/include -I$(OPENLIBM_HOME)/ld80 -I$(OPENLIBM_HOME)/$(ARCH) -I$(OPENLIBM_HOME)/src -DASSEMBLER -D__BSD_VISIBLE -Wno-implicit-function-declaration
- 
- default: all
- 
diff --git a/sci-libs/openlibm/metadata.xml b/sci-libs/openlibm/metadata.xml
deleted file mode 100644
index eee1adbcf..000000000
--- a/sci-libs/openlibm/metadata.xml
+++ /dev/null
@@ -1,16 +0,0 @@
-<?xml version="1.0" encoding="UTF-8"?>
-<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
-<pkgmetadata>
-	<maintainer type="project">
-		<email>sci@gentoo.org</email>
-		<name>Gentoo Science Project</name>
-	</maintainer>
-	<longdescription lang="en">
-OpenLibm is an effort to have a high quality, portable, standalone C
-mathematical library (libm). It can be used standalone in applications
-and programming language implementations.
-The project was born out of a need to have a good libm for the Julia
-programming langage that worked consistently across compilers and
-operating systems, and in 32-bit and 64-bit environments.
-</longdescription>
-</pkgmetadata>
diff --git a/sci-libs/openlibm/openlibm-9999.ebuild b/sci-libs/openlibm/openlibm-9999.ebuild
deleted file mode 100644
index de78d6715..000000000
--- a/sci-libs/openlibm/openlibm-9999.ebuild
+++ /dev/null
@@ -1,38 +0,0 @@
-# Copyright 1999-2014 Gentoo Foundation
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=5
-
-inherit git-r3 eutils fortran-2
-
-DESCRIPTION="High quality system independent, open source libm"
-HOMEPAGE="http://julialang.org/"
-SRC_URI=""
-EGIT_REPO_URI="git://github.com/JuliaLang/openlibm.git"
-
-LICENSE="public-domain MIT ISC BSD-2 LGPL-2.1+"
-SLOT="0"
-KEYWORDS=""
-
-IUSE="static-libs"
-
-src_prepare() {
-	epatch \
-		"${FILESDIR}"/${PN}-respect-toolchain.patch
-}
-
-src_compile() {
-	emake libopenlibm.so
-	use static-libs && emake libopenlibm.a
-}
-
-src_test() {
-	default
-}
-
-src_install() {
-	dolib.so libopenlibm.so*
-	use static-libs && dolib.a libopenlibm.a
-	doheader include/{cdefs,types}-compat.h src/openlibm.h
-	dodoc README.md
-}
diff --git a/sci-libs/optpp/optpp-2.4.ebuild b/sci-libs/optpp/optpp-2.4.ebuild
index c384880ef..054be4c11 100644
--- a/sci-libs/optpp/optpp-2.4.ebuild
+++ b/sci-libs/optpp/optpp-2.4.ebuild
@@ -1,13 +1,13 @@
-# Copyright 1999-2014 Gentoo Foundation
+# Copyright 1999-2021 Gentoo Authors
 # Distributed under the terms of the GNU General Public License v2
 
-EAPI=5
+EAPI=7
 
-inherit autotools-utils toolchain-funcs
+inherit toolchain-funcs
 
 DESCRIPTION="C++ library for non-linear optimization"
 HOMEPAGE="https://software.sandia.gov/opt++/"
-SRC_URI="${HOMEPAGE}/downloads/${P}.tar.gz"
+SRC_URI="https://software.sandia.gov/opt++/downloads/${P}.tar.gz"
 
 LICENSE="LGPL-2"
 KEYWORDS="~amd64 ~x86 ~amd64-linux ~x86-linux"
@@ -16,19 +16,21 @@ IUSE="doc mpi static-libs"
 
 RDEPEND="
 	virtual/blas
-	mpi? ( virtual/mpi )"
-DEPEND="${RDEPEND}
-	virtual/pkgconfig"
+	virtual/lapack
+	mpi? ( virtual/mpi )
+"
+DEPEND="${RDEPEND}"
+BDEPEND="virtual/pkgconfig"
 
 src_configure() {
-	local myeconfargs=(
-		--with-blas="$($(tc-getPKG_CONFIG) --libs blas)"
+	econf \
+		--with-blas="$($(tc-getPKG_CONFIG) --libs blas)" \
 		$(use_enable mpi)
-	)
-	autotools-utils_src_configure
 }
 
 src_install() {
-	autotools-utils_src_install
-	use doc && dohtml -r docs/*
+	default
+	# avoid file collision with sci-libs/lapack
+	rm "${ED}/usr/include/cblas.h"
+	use doc && dodoc -r docs/*
 }
diff --git a/sci-libs/pagmo/metadata.xml b/sci-libs/pagmo/metadata.xml
deleted file mode 100644
index cc59fd48c..000000000
--- a/sci-libs/pagmo/metadata.xml
+++ /dev/null
@@ -1,16 +0,0 @@
-<?xml version="1.0" encoding="UTF-8"?>
-<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
-<pkgmetadata>
-	<maintainer type="project">
-		<email>sci-astronomy@gentoo.org</email>
-		<name>Gentoo Astronomy Project</name>
-	</maintainer>
-	<use>
-		<flag name="nlopt">Use nlopt, a non-linear optimization library</flag>
-		<flag name="ipopt">Use ipopt, a interior-point optimizer</flag>
-		<flag name="eigen">Use eigen, a c++ linear algebra library, for algorithms like CAMES</flag>
-	</use>
-	<upstream>
-		<remote-id type="github">esa/pagmo2</remote-id>
-	</upstream>
-</pkgmetadata>
diff --git a/sci-libs/pagmo/pagmo-9999.ebuild b/sci-libs/pagmo/pagmo-9999.ebuild
deleted file mode 100644
index 84665a0ae..000000000
--- a/sci-libs/pagmo/pagmo-9999.ebuild
+++ /dev/null
@@ -1,47 +0,0 @@
-# Copyright 1999-2017 Gentoo Foundation
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=6
-
-PYTHON_COMPAT=( python2_7 )
-
-inherit cmake-utils git-r3 python-single-r1
-
-DESCRIPTION="Parallelization engine for optimization problems"
-HOMEPAGE="https://github.com/esa/pagmo"
-SRC_URI=""
-EGIT_REPO_URI="https://github.com/esa/${PN}2.git git://github.com/esa/${PN}2.git"
-
-LICENSE="GPL-3"
-SLOT="2"
-KEYWORDS=""
-IUSE="eigen nlopt ipopt python test"
-
-REQUIRED_USE="python? ( ${PYTHON_REQUIRED_USE} )"
-
-RDEPEND="
-	dev-libs/boost
-	eigen? ( dev-cpp/eigen:3 )
-	python? (
-		${PYTHON_DEPS}
-		dev-libs/boost[${PYTHON_USEDEP}]
-		)
-	nlopt? ( sci-libs/nlopt )
-	ipopt? ( sci-libs/ipopt )
-"
-DEPEND="${RDEPEND}"
-
-pkg_setup() {
-	use python && python-single-r1_pkg_setup
-}
-
-src_configure() {
-	mycmakeargs=(
-		-DPAGMO_BUILD_PYGMO=$(usex python)
-		-DPAGMO_WITH_EIGEN3=$(usex eigen)
-		-DPAGMO_WITH_NLOPT=$(usex nlopt)
-		-DPAGMO_WITH_IPOPT=$(usex ipopt)
-		-DPAGMO_BUILD_TESTS=$(usex test)
-	)
-	cmake-utils_src_configure
-}
diff --git a/sci-libs/pfft/Manifest b/sci-libs/pfft/Manifest
index 293098cb1..79b8e81db 100644
--- a/sci-libs/pfft/Manifest
+++ b/sci-libs/pfft/Manifest
@@ -1 +1 @@
-DIST pfft-1.0.7-alpha.tar.gz 598527 BLAKE2B eb6836fb2c023061ced2b822420964716919ccbab990322a935e0c3eeeecb888008cd1c16eae16778bbafe50a7ae38c55b7af13adcc3ca7712114b6cde054abb SHA512 77cce8927ce2674b83f9b642661b8a44e9b856fb5f6118ad1ab71d6b6b10b22196f48c269fc45896a249c10ff1ddc621850998b1289eedde46b1261949503aae
+DIST pfft-1.0.8-alpha.tar.gz 1077484 BLAKE2B 65468a50cf62ce1bc691d120c0952def7f521b773e99b29e9d78062434b2cefe819adc423d578deea47db11d98225f7fc9330a71e4c3b4601e912810ad85542c SHA512 eaab5d66f66997fba0404f6c24aa7acd023266acfa7fde0131242ab7e11e1d9cd2f5615aabc5b7c6a8cf2ef178a02684770155501afe75f1c331f1c352cb09de
diff --git a/sci-libs/pfft/pfft-1.0.7_alpha.ebuild b/sci-libs/pfft/pfft-1.0.7_alpha.ebuild
deleted file mode 100644
index 612564e0b..000000000
--- a/sci-libs/pfft/pfft-1.0.7_alpha.ebuild
+++ /dev/null
@@ -1,53 +0,0 @@
-# Copyright 1999-2017 Gentoo Foundation
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=5
-
-inherit autotools-utils fortran-2 multibuild
-
-DESCRIPTION="Parallel 3d FFT"
-HOMEPAGE="https://www-user.tu-chemnitz.de/~potts/workgroup/pippig/software.php.en"
-
-if [[ $PV = *9999 ]] ; then
-	inherit git-r3
-	EGIT_REPO_URI="https://github.com/mpip/pfft.git"
-	KEYWORDS=""
-	AUTOTOOLS_AUTORECONF=1
-else
-	SRC_URI="https://www-user.tu-chemnitz.de/~potts/workgroup/pippig/software/${P//_/-}.tar.gz"
-	KEYWORDS="~amd64 ~x86"
-	S="${WORKDIR}/${P//_/-}"
-fi
-
-LICENSE="GPL-3"
-SLOT="0"
-IUSE="static-libs"
-
-RDEPEND="
-	sci-libs/fftw:3.0[mpi,fortran]
-	virtual/mpi
-	"
-
-DEPEND="
-	${RDEPEND}
-	"
-
-src_configure() {
-	MULTIBUILD_VARIANTS=( single double long-double )
-	my_src_configure() {
-		local myeconfargs=(
-			$([[ ${MULTIBUILD_VARIANT} != double ]] && echo "--enable-${MULTIBUILD_VARIANT}")
-		)
-		autotools-utils_src_configure
-	}
-
-	multibuild_parallel_foreach_variant my_src_configure
-}
-
-src_compile() {
-	multibuild_foreach_variant autotools-utils_src_compile
-}
-
-src_install() {
-	multibuild_parallel_foreach_variant autotools-utils_src_install
-}
diff --git a/sci-libs/pfft/pfft-1.0.8_alpha.ebuild b/sci-libs/pfft/pfft-1.0.8_alpha.ebuild
new file mode 100644
index 000000000..af9a0f88e
--- /dev/null
+++ b/sci-libs/pfft/pfft-1.0.8_alpha.ebuild
@@ -0,0 +1,47 @@
+# Copyright 1999-2021 Gentoo Authors
+# Distributed under the terms of the GNU General Public License v2
+
+EAPI=7
+
+inherit fortran-2 multibuild
+
+DESCRIPTION="Parallel 3d FFT"
+HOMEPAGE="https://www-user.tu-chemnitz.de/~potts/workgroup/pippig/software.php.en"
+
+if [[ $PV = *9999 ]] ; then
+	inherit git-r3
+	EGIT_REPO_URI="https://github.com/mpip/pfft.git"
+	AUTOTOOLS_AUTORECONF=1
+else
+	SRC_URI="https://www-user.tu-chemnitz.de/~potts/workgroup/pippig/software/${P//_/-}.tar.gz"
+	KEYWORDS="~amd64 ~x86"
+	S="${WORKDIR}/${P//_/-}"
+fi
+
+LICENSE="GPL-3"
+SLOT="0"
+IUSE="static-libs"
+
+RDEPEND="
+	sci-libs/fftw:3.0[mpi,fortran]
+	virtual/mpi
+"
+
+DEPEND="${RDEPEND}"
+
+src_configure() {
+	MULTIBUILD_VARIANTS=( single double long-double )
+	my_src_configure() {
+		econf $([[ ${MULTIBUILD_VARIANT} != double ]] && echo "--enable-${MULTIBUILD_VARIANT}")
+	}
+
+	multibuild_foreach_variant my_src_configure
+}
+
+src_compile() {
+	multibuild_foreach_variant emake
+}
+
+src_install() {
+	multibuild_foreach_variant emake install DESTDIR="${D}"
+}
diff --git a/sci-libs/pfft/pfft-9999.ebuild b/sci-libs/pfft/pfft-9999.ebuild
index 1ad55311a..af9a0f88e 100644
--- a/sci-libs/pfft/pfft-9999.ebuild
+++ b/sci-libs/pfft/pfft-9999.ebuild
@@ -1,9 +1,9 @@
-# Copyright 1999-2014 Gentoo Foundation
+# Copyright 1999-2021 Gentoo Authors
 # Distributed under the terms of the GNU General Public License v2
 
-EAPI=5
+EAPI=7
 
-inherit autotools-utils fortran-2 multibuild
+inherit fortran-2 multibuild
 
 DESCRIPTION="Parallel 3d FFT"
 HOMEPAGE="https://www-user.tu-chemnitz.de/~potts/workgroup/pippig/software.php.en"
@@ -11,11 +11,10 @@ HOMEPAGE="https://www-user.tu-chemnitz.de/~potts/workgroup/pippig/software.php.e
 if [[ $PV = *9999 ]] ; then
 	inherit git-r3
 	EGIT_REPO_URI="https://github.com/mpip/pfft.git"
-	KEYWORDS=""
 	AUTOTOOLS_AUTORECONF=1
 else
 	SRC_URI="https://www-user.tu-chemnitz.de/~potts/workgroup/pippig/software/${P//_/-}.tar.gz"
-	KEYWORDS="~x86 ~amd64"
+	KEYWORDS="~amd64 ~x86"
 	S="${WORKDIR}/${P//_/-}"
 fi
 
@@ -26,28 +25,23 @@ IUSE="static-libs"
 RDEPEND="
 	sci-libs/fftw:3.0[mpi,fortran]
 	virtual/mpi
-	"
+"
 
-DEPEND="
-	${RDEPEND}
-	"
+DEPEND="${RDEPEND}"
 
 src_configure() {
 	MULTIBUILD_VARIANTS=( single double long-double )
 	my_src_configure() {
-		local myeconfargs=(
-			$([[ ${MULTIBUILD_VARIANT} != double ]] && echo "--enable-${MULTIBUILD_VARIANT}")
-		)
-		autotools-utils_src_configure
+		econf $([[ ${MULTIBUILD_VARIANT} != double ]] && echo "--enable-${MULTIBUILD_VARIANT}")
 	}
 
-	multibuild_parallel_foreach_variant my_src_configure
+	multibuild_foreach_variant my_src_configure
 }
 
 src_compile() {
-	multibuild_foreach_variant autotools-utils_src_compile
+	multibuild_foreach_variant emake
 }
 
 src_install() {
-	multibuild_parallel_foreach_variant autotools-utils_src_install
+	multibuild_foreach_variant emake install DESTDIR="${D}"
 }
diff --git a/sci-libs/pg2plplot/Manifest b/sci-libs/pg2plplot/Manifest
index 159e6df26..7a4b1af78 100644
--- a/sci-libs/pg2plplot/Manifest
+++ b/sci-libs/pg2plplot/Manifest
@@ -1,2 +1 @@
-DIST pg2plplot-0.2.0.tar.gz 34232 BLAKE2B a497e0a6deb50d6d2dd73bcb24324719d84adb2987367b7574d4783aa7676447086cbd2f3fda5b7a3ed96a08afa9cc555baca478918ba9e403558c9648e8f185 SHA512 04d79f5c730965450d2cebd3a28d9d7908ccda9dcb6d6c0ae6fd91dae4149f2b837006eb35cd7f9e4fdb7245a971eb575a40abb8a445904614815af164e3cc8d
-DIST pg2plplot-0.3.1.tar.gz 35176 BLAKE2B 8c83c590ca504f3e5a3ac76ac279f99eee3351282e079efc129c263d86ccb2b3132bc9fdfe8e2776c9cc37eabf0b2620567f6e94e5455edb32798670ceeda9e8 SHA512 adb35806682bf62870353adbe954af1d384f8343eb2d7092d5c87328001bbcefe0fcf1963215190783932a6f2489c10947913946f0b53de8ab2e3ebc12f00d02
+DIST pg2plplot-5.13.1.tar.gz 39935 BLAKE2B c233e68548652145dd845640ec54de6d7f64dc89b52b2f6794b1eb2ee3d02af6333c192c3754d69cd2655474b7fd14f03e7e8e827493e91eae03c4f6374bee2d SHA512 d594630b1154b56009ed9b8f97b2d4e9d401ce06387954eda05e04de230586965b3868fd7a257a8628e53ac1624092850bfa4ccf0e8238daecfc40c3bc6af03c
diff --git a/sci-libs/pg2plplot/pg2plplot-0.2.0.ebuild b/sci-libs/pg2plplot/pg2plplot-0.2.0.ebuild
deleted file mode 100644
index 7810ecee6..000000000
--- a/sci-libs/pg2plplot/pg2plplot-0.2.0.ebuild
+++ /dev/null
@@ -1,32 +0,0 @@
-# Copyright 1999-2015 Gentoo Foundation
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=5
-
-inherit cmake-utils fortran-2
-
-DESCRIPTION="Assist the transition from PGPlot to PLplot in Fortran programs"
-HOMEPAGE="http://pg2plplot.sourceforge.net"
-SRC_URI="mirror://sourceforge/${PN}/${P}.tar.gz"
-
-LICENSE="GPL-3"
-SLOT="0"
-KEYWORDS="~amd64 ~x86"
-IUSE="X png postscript static-libs"
-
-DEPEND="sci-libs/plplot[fortran]"
-
-# If USE="png" or "postscript", ensure PLplot has USE="cairo":
-RDEPEND="${DEPEND}
-	 sci-libs/plplot[fortran,X?]
-	 png? ( sci-libs/plplot[cairo] )
-	 postscript? ( sci-libs/plplot[cairo] )"
-
-src_configure() {
-	local mycmakeargs=(
-		$(cmake-utils_use static-libs CREATE_STATICLIB)
-	)
-	cmake-utils_src_configure
-}
-
-DOCS="CHANGELOG README VERSION"
diff --git a/sci-libs/pg2plplot/pg2plplot-0.3.1.ebuild b/sci-libs/pg2plplot/pg2plplot-0.3.1.ebuild
deleted file mode 100644
index 139ac426e..000000000
--- a/sci-libs/pg2plplot/pg2plplot-0.3.1.ebuild
+++ /dev/null
@@ -1,39 +0,0 @@
-# Copyright 1999-2015 Gentoo Foundation
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=5
-
-FORTRAN_STANDARD=90
-
-inherit cmake-utils fortran-2
-
-DESCRIPTION="Assist the transition from PGPlot to PLplot in Fortran programs"
-HOMEPAGE="http://pg2plplot.sourceforge.net"
-SRC_URI="mirror://sourceforge/${PN}/${P}.tar.gz"
-
-LICENSE="GPL-3"
-SLOT="0"
-KEYWORDS="~amd64 ~x86 ~amd64-linux ~x86-linux"
-IUSE="X png postscript static-libs"
-
-DEPEND="sci-libs/plplot[fortran]"
-
-# If USE="png" or "postscript", ensure PLplot has USE="cairo":
-RDEPEND="${DEPEND}
-	sci-libs/plplot[fortran,X?]
-	png? ( sci-libs/plplot[cairo] )
-	postscript? ( sci-libs/plplot[cairo] )"
-
-DOCS=( CHANGELOG README VERSION )
-
-src_prepare() {
-	sed -i -e "s:/usr:${EPREFIX}/usr:g" CMake/CMakeLocations.cmake || die
-	cmake-utils_src_prepare
-}
-
-src_configure() {
-	local mycmakeargs=(
-		$(cmake-utils_use static-libs CREATE_STATICLIB)
-	)
-	cmake-utils_src_configure
-}
diff --git a/sci-libs/pg2plplot/pg2plplot-5.13.1.ebuild b/sci-libs/pg2plplot/pg2plplot-5.13.1.ebuild
new file mode 100644
index 000000000..123404533
--- /dev/null
+++ b/sci-libs/pg2plplot/pg2plplot-5.13.1.ebuild
@@ -0,0 +1,36 @@
+# Copyright 1999-2022 Gentoo Authors
+# Distributed under the terms of the GNU General Public License v2
+
+EAPI=8
+
+CMAKE_BUILD_TYPE=Release
+CMAKE_MAKEFILE_GENERATOR="emake"
+inherit cmake fortran-2
+
+DESCRIPTION="Assist the transition from PGPlot to PLplot in Fortran programs"
+HOMEPAGE="http://pg2plplot.sourceforge.net"
+SRC_URI="https://downloads.sourceforge.net/${PN}/${P}.tar.gz"
+
+LICENSE="GPL-3"
+SLOT="0"
+KEYWORDS="~amd64 ~x86"
+IUSE="X png postscript static-libs"
+
+DEPEND="
+	virtual/fortran
+	sci-libs/plplot[fortran]
+"
+
+# If USE="png" or "postscript", ensure PLplot has USE="cairo":
+RDEPEND="${DEPEND}
+	sci-libs/plplot[fortran,X?]
+	png? ( sci-libs/plplot[cairo] )
+	postscript? ( sci-libs/plplot[cairo] )
+"
+
+src_configure() {
+	local mycmakeargs=(
+		-DCREATE_STATICLIB="$(usex static-libs)"
+	)
+	cmake_src_configure
+}
diff --git a/sci-libs/plasma/Manifest b/sci-libs/plasma/Manifest
deleted file mode 100644
index de70a9590..000000000
--- a/sci-libs/plasma/Manifest
+++ /dev/null
@@ -1,2 +0,0 @@
-DIST plasma_2.5.2.tar.gz 5354770 BLAKE2B 95530ade853e78a6db8372e6aa844b6a1472af40317611cc4e9a93fb0c0bc6f7088f8644e3d91e5991367a1321a0ceef544eb5dbb3a7bacd74a90bc36cba2bb9 SHA512 0ee93bd25fee721a76a28118ef21edcda84830516226ec97806cf52602c4f6df600f14db06d569413ccc83d4ae7f6d9d3ad0853132d0824b3e3efa41b53a8a3f
-DIST plasma_2.6.0.tar.gz 6264802 BLAKE2B 95ac398f3d1fcff38aa7c4dfd7317c43cdf3b6145ca859b43ff0e9c97ba56b07ca3439506d8839c86f9d1c3b1d64971d88b359329815addb22d58241a6861f6f SHA512 887ca2a121e67e9e8279a8da002a3a1e44d10e26e8bdbe7a9f30e6d10cee7ff6b78d95f39412a347c6a89f9fc2ff7fea02f71fdacca3c4fb9353d39381f35f2b
diff --git a/sci-libs/plasma/metadata.xml b/sci-libs/plasma/metadata.xml
deleted file mode 100644
index b21b3df93..000000000
--- a/sci-libs/plasma/metadata.xml
+++ /dev/null
@@ -1,15 +0,0 @@
-<?xml version="1.0" encoding="UTF-8"?>
-<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
-<pkgmetadata>
-	<maintainer type="project">
-		<email>sci@gentoo.org</email>
-		<name>Gentoo Science Project</name>
-	</maintainer>
-	<longdescription lang="en">
-The Parallel Linear Algebra for Scalable Multi-core Architectures
-(PLASMA) project aims to address the critical and highly disruptive
-situation that is facing the Linear Algebra and High Performance
-Computing community due to the introduction of multi-core
-architectures.
-</longdescription>
-</pkgmetadata>
diff --git a/sci-libs/plasma/plasma-2.5.2.ebuild b/sci-libs/plasma/plasma-2.5.2.ebuild
deleted file mode 100644
index 1a33d3630..000000000
--- a/sci-libs/plasma/plasma-2.5.2.ebuild
+++ /dev/null
@@ -1,140 +0,0 @@
-# Copyright 1999-2014 Gentoo Foundation
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=5
-inherit eutils fortran-2 toolchain-funcs versionator multilib flag-o-matic
-
-MYP=${PN}_${PV}
-
-DESCRIPTION="Parallel Linear Algebra for Scalable Multi-core Architecture"
-HOMEPAGE="http://icl.cs.utk.edu/plasma/"
-SRC_URI="http://icl.cs.utk.edu/projectsfiles/plasma/pubs/${MYP}.tar.gz"
-
-LICENSE="BSD"
-SLOT="0"
-KEYWORDS="~amd64 ~x86 ~amd64-linux ~x86-linux"
-IUSE="doc examples fortran static-libs test"
-
-RDEPEND="
-	sys-apps/hwloc
-	virtual/blas
-	virtual/cblas
-	virtual/lapack
-	virtual/lapacke"
-DEPEND="${RDEPEND}
-	virtual/pkgconfig
-	test? ( sci-libs/lapacke-reference[tmg] )"
-
-S="${WORKDIR}/${MYP}"
-
-# TODO: virtual/{blas,cblas,lapack} serial and threaded. plasma works properly
-# with serial blas/lapack (see README). not doable dynamically with atlas
-
-static_to_shared() {
-	local libstatic=${1}; shift
-	local libname=$(basename ${libstatic%.a})
-	local soname=${libname}$(get_libname $(get_version_component_range 1-2))
-	local libdir=$(dirname ${libstatic})
-
-	einfo "Making ${soname} from ${libstatic}"
-	if [[ ${CHOST} == *-darwin* ]] ; then
-		${LINK:-$(tc-getCC)} ${LDFLAGS}  \
-			-dynamiclib -install_name "${EPREFIX}"/usr/lib/"${soname}" \
-			-Wl,-all_load -Wl,${libstatic} \
-			"$@" -o ${libdir}/${soname} || die "${soname} failed"
-	else
-		${LINK:-$(tc-getCC)} ${LDFLAGS}  \
-			-shared -Wl,-soname=${soname} \
-			-Wl,--whole-archive ${libstatic} -Wl,--no-whole-archive \
-			"$@" -o ${libdir}/${soname} || die "${soname} failed"
-		[[ $(get_version_component_count) -gt 1 ]] && \
-			ln -s ${soname} ${libdir}/${libname}$(get_libname $(get_major_version))
-		ln -s ${soname} ${libdir}/${libname}$(get_libname)
-	fi
-}
-
-src_prepare() {
-	# rename plasma to avoid collision (https://github.com/gentoo-science/sci/issues/34)
-	# lib name conflict with kde plasma, rename
-	PLASMA_LIBNAME=plasmca
-	sed -i \
-		-e "s/-lplasma/-l${PLASMA_LIBNAME}/g" \
-		-e "s/libplasma.a/lib${PLASMA_LIBNAME}.a/" \
-		Makefile.internal || die
-
-	# distributed pc file not so useful, so redo it
-	cat <<-EOF > ${PN}.pc
-		prefix=${EPREFIX}/usr
-		libdir=\${prefix}/$(get_libdir)
-		includedir=\${prefix}/include/${PN}
-		Name: ${PN}
-		Description: ${DESCRIPTION}
-		Version: ${PV}
-		URL: ${HOMEPAGE}
-		Libs: -L\${libdir} -l${PLASMA_LIBNAME} -lcoreblas -lquark
-		Libs.private: -lm
-		Cflags: -I\${includedir}
-		Requires: blas cblas lapack lapacke hwloc
-	EOF
-}
-
-src_configure() {
-	cat <<-EOF > make.inc
-		ARCH = $(tc-getAR)
-		ARCHFLAGS = cr
-		RANLIB = $(tc-getRANLIB)
-		CC = $(tc-getCC)
-		FC = $(tc-getFC)
-		CFLAGS = ${CFLAGS} -DADD_ -fPIC $(has_version ">=virtual/lapacke-3.5" && echo "-DDOXYGEN_SHOULD_SKIP_THIS=1")
-		FFLAGS = ${FFLAGS} -fPIC
-		LOADER = $(tc-getFC)
-		LIBBLAS = $($(tc-getPKG_CONFIG) --libs blas)
-		LIBCBLAS = $($(tc-getPKG_CONFIG) --libs cblas)
-		LIBLAPACK = $($(tc-getPKG_CONFIG) --libs lapack) -ltmglib
-		LIBCLAPACK = $($(tc-getPKG_CONFIG) --libs lapacke)
-		$(use fortran && echo "PLASMA_F90 = 1")
-	EOF
-}
-
-src_compile() {
-	emake lib
-	#mv lib/libplasma.a lib/lib${PLASMA_LIBNAME}.a || die
-	static_to_shared quark/libquark.a $($(tc-getPKG_CONFIG --libs hwloc)) -pthread
-	static_to_shared lib/libcoreblas.a quark/libquark.so $($(tc-getPKG_CONFIG --libs cblas lapacke))
-	static_to_shared lib/lib${PLASMA_LIBNAME}.a quark/libquark.so lib/libcoreblas.so
-	if use static-libs; then
-		emake cleanall
-		sed 's/-fPIC//g' make.inc
-		emake lib
-	fi
-}
-
-src_test() {
-	emake test
-	cd testing
-	LD_LIBRARY_PATH="../lib:../quark:${LD_LIBRARY_PATH}" ./plasma_testing.py || die
-}
-
-src_install() {
-	dolib.so lib/lib*$(get_libname)* quark/libquark$(get_libname)*
-	use static-libs && dolib.a lib/lib*.a quark/libquark.a
-	insinto /usr/include/${PN}
-	doins quark/quark{,_unpack_args}.h quark/icl_{hash,list}.h include/*.h
-	use fortran && doins include/*.mod
-	insinto /usr/$(get_libdir)/pkgconfig
-	doins ${PN}.pc
-	dodoc README ToDo ReleaseNotes
-	use doc && dodoc docs/pdf/*.pdf && dohtml docs/doxygen/out/html/*
-	if use examples; then
-		emake -C examples cleanall
-		insinto /usr/share/doc/${PF}
-		doins -r examples
-	fi
-}
-
-pkg_postinst() {
-	elog "The plasma linear algebra library file has been renamed ${PLASMA_LIBNAME}"
-	elog "to avoid collision with KDE plasma."
-	elog "Compile and link your programs using the following command:"
-	elog "     pkg-config --cflags --libs plasma"
-}
diff --git a/sci-libs/plasma/plasma-2.6.0.ebuild b/sci-libs/plasma/plasma-2.6.0.ebuild
deleted file mode 100644
index 851a4d00e..000000000
--- a/sci-libs/plasma/plasma-2.6.0.ebuild
+++ /dev/null
@@ -1,141 +0,0 @@
-# Copyright 1999-2014 Gentoo Foundation
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=5
-inherit eutils fortran-2 toolchain-funcs versionator multilib flag-o-matic
-
-MYP=${PN}_${PV}
-SOVER=$(get_version_component_range 1)
-
-DESCRIPTION="Parallel Linear Algebra for Scalable Multi-core Architecture"
-HOMEPAGE="http://icl.cs.utk.edu/plasma/"
-SRC_URI="http://icl.cs.utk.edu/projectsfiles/plasma/pubs/${MYP}.tar.gz"
-
-LICENSE="BSD"
-SLOT="0/${SOVER}"
-KEYWORDS="~amd64 ~x86 ~amd64-linux ~x86-linux"
-IUSE="doc examples fortran static-libs test"
-
-RDEPEND="
-	sys-apps/hwloc
-	virtual/blas
-	virtual/cblas
-	virtual/lapack
-	virtual/lapacke"
-DEPEND="${RDEPEND}
-	virtual/pkgconfig
-	test? ( sci-libs/lapacke-reference[tmg] )"
-
-S="${WORKDIR}/${MYP}"
-
-# TODO: virtual/{blas,cblas,lapack} serial and threaded. plasma works properly
-# with serial blas/lapack (see README). not doable dynamically with atlas
-
-static_to_shared() {
-	local libstatic=${1}; shift
-	local libname=$(basename ${libstatic%.a})
-	local soname=${libname}$(get_libname ${SOVER})
-	local libdir=$(dirname ${libstatic})
-
-	einfo "Making ${soname} from ${libstatic}"
-	if [[ ${CHOST} == *-darwin* ]] ; then
-		${LINK:-$(tc-getCC)} ${LDFLAGS}  \
-			-dynamiclib -install_name "${EPREFIX}"/usr/lib/"${soname}" \
-			-Wl,-all_load -Wl,${libstatic} \
-			"$@" -o ${libdir}/${soname} || die "${soname} failed"
-	else
-		${LINK:-$(tc-getCC)} ${LDFLAGS}  \
-			-shared -Wl,-soname=${soname} \
-			-Wl,--whole-archive ${libstatic} -Wl,--no-whole-archive \
-			"$@" -o ${libdir}/${soname} || die "${soname} failed"
-		[[ $(get_version_component_count) -gt 1 ]] && \
-			ln -s ${soname} ${libdir}/${libname}$(get_libname $(get_major_version))
-		ln -s ${soname} ${libdir}/${libname}$(get_libname)
-	fi
-}
-
-src_prepare() {
-	# rename plasma to avoid collision (https://github.com/gentoo-science/sci/issues/34)
-	# lib name conflict with kde plasma, rename
-	PLASMA_LIBNAME=plasmca
-	sed -i \
-		-e "s/-lplasma/-l${PLASMA_LIBNAME}/g" \
-		-e "s/libplasma.a/lib${PLASMA_LIBNAME}.a/" \
-		Makefile.internal || die
-
-	# distributed pc file not so useful, so redo it
-	cat <<-EOF > ${PN}.pc
-		prefix=${EPREFIX}/usr
-		libdir=\${prefix}/$(get_libdir)
-		includedir=\${prefix}/include/${PN}
-		Name: ${PN}
-		Description: ${DESCRIPTION}
-		Version: ${PV}
-		URL: ${HOMEPAGE}
-		Libs: -L\${libdir} -l${PLASMA_LIBNAME} -lcoreblas -lquark
-		Libs.private: -lm
-		Cflags: -I\${includedir}
-		Requires: blas cblas lapack lapacke hwloc
-	EOF
-}
-
-src_configure() {
-	cat <<-EOF > make.inc
-		ARCH = $(tc-getAR)
-		ARCHFLAGS = cr
-		RANLIB = $(tc-getRANLIB)
-		CC = $(tc-getCC)
-		FC = $(tc-getFC)
-		CFLAGS = ${CFLAGS} -DADD_ -fPIC $(has_version ">=virtual/lapacke-3.5" && echo "-DDOXYGEN_SHOULD_SKIP_THIS=1")
-		FFLAGS = ${FFLAGS} -fPIC
-		LOADER = $(tc-getFC)
-		LIBBLAS = $($(tc-getPKG_CONFIG) --libs blas)
-		LIBCBLAS = $($(tc-getPKG_CONFIG) --libs cblas)
-		LIBLAPACK = $($(tc-getPKG_CONFIG) --libs lapack) -ltmglib
-		LIBCLAPACK = $($(tc-getPKG_CONFIG) --libs lapacke)
-		$(use fortran && echo "PLASMA_F90 = 1")
-	EOF
-}
-
-src_compile() {
-	emake lib
-	#mv lib/libplasma.a lib/lib${PLASMA_LIBNAME}.a || die
-	static_to_shared quark/libquark.a $($(tc-getPKG_CONFIG --libs hwloc)) -pthread
-	static_to_shared lib/libcoreblas.a quark/libquark.so $($(tc-getPKG_CONFIG --libs cblas lapacke))
-	static_to_shared lib/lib${PLASMA_LIBNAME}.a quark/libquark.so lib/libcoreblas.so
-	if use static-libs; then
-		emake cleanall
-		sed 's/-fPIC//g' make.inc
-		emake lib
-	fi
-}
-
-src_test() {
-	emake test
-	cd testing
-	LD_LIBRARY_PATH="../lib:../quark:${LD_LIBRARY_PATH}" ./plasma_testing.py || die
-}
-
-src_install() {
-	dolib.so lib/lib*$(get_libname)* quark/libquark$(get_libname)*
-	use static-libs && dolib.a lib/lib*.a quark/libquark.a
-	insinto /usr/include/${PN}
-	doins quark/quark{,_unpack_args}.h quark/icl_{hash,list}.h include/*.h
-	use fortran && doins include/*.mod
-	insinto /usr/$(get_libdir)/pkgconfig
-	doins ${PN}.pc
-	dodoc README ToDo ReleaseNotes
-	use doc && dodoc docs/pdf/*.pdf && dohtml docs/doxygen/out/html/*
-	if use examples; then
-		emake -C examples cleanall
-		insinto /usr/share/doc/${PF}
-		doins -r examples
-	fi
-}
-
-pkg_postinst() {
-	elog "The plasma linear algebra library file has been renamed ${PLASMA_LIBNAME}"
-	elog "to avoid collision with KDE plasma."
-	elog "Compile and link your programs using the following command:"
-	elog "     pkg-config --cflags --libs plasma"
-}
diff --git a/sci-libs/pmx/metadata.xml b/sci-libs/pmx/metadata.xml
deleted file mode 100644
index 81b693168..000000000
--- a/sci-libs/pmx/metadata.xml
+++ /dev/null
@@ -1,19 +0,0 @@
-<?xml version="1.0" encoding="UTF-8"?>
-<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
-<pkgmetadata>
-	<maintainer type="project">
-		<email>sci-chemistry@gentoo.org</email>
-		<name>Gentoo Chemistry Project</name>
-	</maintainer>
-	<longdescription>
-pmx (formerly pymacs) has started as a small bunch of classes to read
-structure files such as pdb or gro and trajectory data in gromacs xtc
-format. Over the years it has been extended towards a versatile (bio-)
-molecular structure manipulation package with some additional
-functionalities, e.g. gromacs file parsers and scripts for setup and
-analysis of free energy calculations.
-</longdescription>
-	<upstream>
-		<remote-id type="github">dseeliger/pmx</remote-id>
-	</upstream>
-</pkgmetadata>
diff --git a/sci-libs/pmx/pmx-9999.ebuild b/sci-libs/pmx/pmx-9999.ebuild
deleted file mode 100644
index dc1708491..000000000
--- a/sci-libs/pmx/pmx-9999.ebuild
+++ /dev/null
@@ -1,23 +0,0 @@
-# Copyright 1999-2019 Gentoo Authors
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=7
-
-PYTHON_COMPAT=( python2_7 )
-
-inherit eutils distutils-r1 git-r3
-
-DESCRIPTION="Python library to read PDB, GRO or Gromacs XTC files"
-HOMEPAGE="https://github.com/deGrootLab/pmx"
-EGIT_REPO_URI="https://github.com/deGrootLab/${PN}.git"
-
-LICENSE="LGPL-3"
-SLOT="0"
-IUSE=""
-
-DEPEND="
-	sci-chemistry/gromacs
-	sci-libs/scipy[${PYTHON_USEDEP}]
-	dev-python/numpy[${PYTHON_USEDEP}]
-	"
-RDEPEND="${DEPEND}"
diff --git a/sci-libs/pybids/Manifest b/sci-libs/pybids/Manifest
index e3e63b7cf..fc1863ad9 100644
--- a/sci-libs/pybids/Manifest
+++ b/sci-libs/pybids/Manifest
@@ -1 +1,3 @@
-DIST pybids-0.5.0.tar.gz 2814050 BLAKE2B b4bd548989d09e6f49d94c9262fb225a25a37bd5797fe33d2296943808a8dbebeaf17b81e4ea0513c620bcf4c4b4cbae394123fabe7244363205c73328f00e8b SHA512 7d39198fa321535a2f1761348069c18e7ba113174b8d034dd20e5ea3ac11013840da89b5b7bbe6d9b0458c46a5bc07200a97c5efa1a6ff716c524390bd0a3a65
+DIST pybids-0.10.2.tar.gz 3013772 BLAKE2B 70255fbca7a7d5a51efa454ee20d30a9527703d6028a965b51da883aa10f8b63d180f72fd127e12b27249c3f388825a9bb2ba4604680c57f3a512ec7093c01c4 SHA512 c90b7e471d73b070e86452ca5d03639d0263e74c3c79386b52ed2c5fc49576f985bc923f2327882ee56bc4691631105c831ebe40f78aade5b9943be83909ba16
+DIST pybids-0.12.4.tar.gz 3031862 BLAKE2B de9d1ba0a0eb400da1de44189f4920a8d1f003dba1c47b18e339d593c68b5a80c340a9acc5267dbfbf730a59aad004035568a1f8b0de30dbab9c211b11790fbd SHA512 1f2f3a784a1e3f0e74919c6ada2ae0365ab89315d724f0a6b6b38a0416c1e6f7e938966b2dda80f090ef2bbf84ce0bcf0bb214a652743432b1d193d9569eb7b1
+DIST pybids-0.6.5.tar.gz 2915557 BLAKE2B d7765b872917bbffcd2706488d7c789976be5bbb1eb5d112cb0b7bcedb483236643f8bf7c177f4a64a44a4d50787a4df1d39fbec8e826bfffd2e2e6f891b3ef3 SHA512 9eef42f00440dddf0147d91f90e07db81f9f95a650f0e47c04304771173ca8691cdb366bd0df1d752c0444f102a4aa010c2343ba75df96528cceb9a98f9d8a0e
diff --git a/sci-libs/pybids/metadata.xml b/sci-libs/pybids/metadata.xml
index 143b3ea21..30567f542 100644
--- a/sci-libs/pybids/metadata.xml
+++ b/sci-libs/pybids/metadata.xml
@@ -2,7 +2,7 @@
 <!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
 <pkgmetadata>
 	<maintainer type="person">
-		<email>horea.christ@gmail.com</email>
+		<email>gentoo@chymera.eu</email>
 		<name>Horea Christian</name>
 	</maintainer>
 	<maintainer type="project">
diff --git a/sci-libs/pybids/pybids-0.10.2.ebuild b/sci-libs/pybids/pybids-0.10.2.ebuild
new file mode 100644
index 000000000..5f2776855
--- /dev/null
+++ b/sci-libs/pybids/pybids-0.10.2.ebuild
@@ -0,0 +1,32 @@
+# Copyright 1999-2023 Gentoo Authors
+# Distributed under the terms of the GNU General Public License v2
+
+EAPI=8
+
+PYTHON_COMPAT=( python3_{10..11} )
+
+inherit distutils-r1
+
+DESCRIPTION="Python package to access BIDS datasets"
+HOMEPAGE="https://github.com/INCF/pybids"
+SRC_URI="https://github.com/INCF/pybids/archive/${PV}.tar.gz -> ${P}.tar.gz"
+
+LICENSE="MIT"
+SLOT="0"
+KEYWORDS="~amd64"
+IUSE="test"
+RESTRICT="!test? ( test )"
+
+DEPEND=""
+RDEPEND="
+	dev-python/num2words[${PYTHON_USEDEP}]
+	dev-python/numpy[${PYTHON_USEDEP}]
+	dev-python/pandas[${PYTHON_USEDEP}]
+	dev-python/patsy[${PYTHON_USEDEP}]
+	dev-python/sqlalchemy[${PYTHON_USEDEP}]
+	sci-libs/bids-validator[${PYTHON_USEDEP}]
+	sci-libs/nibabel[${PYTHON_USEDEP}]
+	dev-python/scipy[${PYTHON_USEDEP}]
+	"
+
+distutils_enable_tests pytest
diff --git a/sci-libs/pybids/pybids-0.12.4.ebuild b/sci-libs/pybids/pybids-0.12.4.ebuild
new file mode 100644
index 000000000..7860d69c9
--- /dev/null
+++ b/sci-libs/pybids/pybids-0.12.4.ebuild
@@ -0,0 +1,33 @@
+# Copyright 1999-2023 Gentoo Authors
+# Distributed under the terms of the GNU General Public License v2
+
+EAPI=8
+
+PYTHON_COMPAT=( python3_{10..11} )
+DISTUTILS_USE_SETUPTOOLS=rdepend
+
+inherit distutils-r1
+
+DESCRIPTION="Python package to access BIDS datasets"
+HOMEPAGE="https://github.com/INCF/pybids"
+SRC_URI="https://github.com/INCF/pybids/archive/${PV}.tar.gz -> ${P}.tar.gz"
+
+LICENSE="MIT"
+SLOT="0"
+KEYWORDS="~amd64"
+
+BDEPEND="test? (	dev-python/mock[${PYTHON_USEDEP}] )"
+
+RDEPEND="
+	dev-python/click[${PYTHON_USEDEP}]
+	dev-python/num2words[${PYTHON_USEDEP}]
+	dev-python/numpy[${PYTHON_USEDEP}]
+	dev-python/pandas[${PYTHON_USEDEP}]
+	dev-python/patsy[${PYTHON_USEDEP}]
+	dev-python/sqlalchemy[${PYTHON_USEDEP}]
+	sci-libs/bids-validator[${PYTHON_USEDEP}]
+	sci-libs/nibabel[${PYTHON_USEDEP}]
+	dev-python/scipy[${PYTHON_USEDEP}]
+"
+
+distutils_enable_tests pytest
diff --git a/sci-libs/pybids/pybids-0.5.0.ebuild b/sci-libs/pybids/pybids-0.5.0.ebuild
deleted file mode 100644
index 65c268624..000000000
--- a/sci-libs/pybids/pybids-0.5.0.ebuild
+++ /dev/null
@@ -1,34 +0,0 @@
-# Copyright 1999-2018 Gentoo Foundation
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=7
-
-PYTHON_COMPAT=( python{2_7,3_4,3_5,3_6} )
-
-inherit distutils-r1
-
-DESCRIPTION="Python package to access BIDS datasets"
-HOMEPAGE="https://github.com/INCF/pybids"
-SRC_URI="https://github.com/INCF/pybids/archive/${PV}.tar.gz -> ${P}.tar.gz"
-
-LICENSE="MIT"
-SLOT="0"
-KEYWORDS="~amd64"
-IUSE=""
-
-DEPEND="
-	dev-python/setuptools[${PYTHON_USEDEP}]
-	"
-RDEPEND="
-	dev-python/grabbit[${PYTHON_USEDEP}]
-	dev-python/num2words[${PYTHON_USEDEP}]
-	dev-python/numpy[${PYTHON_USEDEP}]
-	dev-python/pandas[${PYTHON_USEDEP}]
-	dev-python/patsy[${PYTHON_USEDEP}]
-	dev-python/six[${PYTHON_USEDEP}]
-	sci-libs/nibabel[${PYTHON_USEDEP}]
-	sci-libs/scipy[${PYTHON_USEDEP}]
-	"
-
-# Tests are broken: https://github.com/INCF/pybids/issues/138
-RESTRICT="test"
diff --git a/sci-libs/pybids/pybids-0.6.5.ebuild b/sci-libs/pybids/pybids-0.6.5.ebuild
new file mode 100644
index 000000000..6103c3191
--- /dev/null
+++ b/sci-libs/pybids/pybids-0.6.5.ebuild
@@ -0,0 +1,42 @@
+# Copyright 1999-2023 Gentoo Authors
+# Distributed under the terms of the GNU General Public License v2
+
+EAPI=8
+
+PYTHON_COMPAT=( python3_{10..11} )
+
+inherit distutils-r1
+
+DESCRIPTION="Python package to access BIDS datasets"
+HOMEPAGE="https://github.com/INCF/pybids"
+SRC_URI="https://github.com/INCF/pybids/archive/${PV}.tar.gz -> ${P}.tar.gz"
+
+LICENSE="MIT"
+SLOT="0"
+KEYWORDS="~amd64"
+IUSE=""
+
+DEPEND="
+	dev-python/setuptools[${PYTHON_USEDEP}]
+	"
+RDEPEND="
+	dev-python/grabbit[${PYTHON_USEDEP}]
+	dev-python/num2words[${PYTHON_USEDEP}]
+	dev-python/numpy[${PYTHON_USEDEP}]
+	dev-python/pandas[${PYTHON_USEDEP}]
+	dev-python/patsy[${PYTHON_USEDEP}]
+	dev-python/six[${PYTHON_USEDEP}]
+	sci-libs/nibabel[${PYTHON_USEDEP}]
+	dev-python/scipy[${PYTHON_USEDEP}]
+	"
+
+RESTRICT="test"
+# Fails because fixtures are called directly
+# https://github.com/bids-standard/pybids/issues/289#issuecomment-476853673
+
+python_test() {
+	rm bids/tests/test_config.py || die
+	distutils_install_for_testing
+	pytest -vv || die
+	die
+}
diff --git a/sci-libs/pybids/pybids-9999.ebuild b/sci-libs/pybids/pybids-9999.ebuild
deleted file mode 100644
index 397820db4..000000000
--- a/sci-libs/pybids/pybids-9999.ebuild
+++ /dev/null
@@ -1,37 +0,0 @@
-# Copyright 1999-2018 Gentoo Foundation
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=6
-
-PYTHON_COMPAT=( python{2_7,3_4,3_5} )
-
-inherit distutils-r1 git-r3
-
-DESCRIPTION="Python package to access BIDS datasets"
-HOMEPAGE="https://github.com/INCF/pybids"
-SRC_URI=""
-EGIT_REPO_URI="https://github.com/INCF/pybids"
-
-LICENSE="MIT"
-SLOT="0"
-KEYWORDS=""
-IUSE="test"
-
-DEPEND="
-	dev-python/setuptools[${PYTHON_USEDEP}]
-	test? ( dev-python/pytest[${PYTHON_USEDEP}] )
-	"
-RDEPEND="
-	dev-python/grabbit[${PYTHON_USEDEP}]
-	dev-python/num2words[${PYTHON_USEDEP}]
-	dev-python/numpy[${PYTHON_USEDEP}]
-	dev-python/pandas[${PYTHON_USEDEP}]
-	dev-python/patsy[${PYTHON_USEDEP}]
-	dev-python/six[${PYTHON_USEDEP}]
-	sci-libs/nibabel[${PYTHON_USEDEP}]
-	sci-libs/scipy[${PYTHON_USEDEP}]
-	"
-
-python_test() {
-	py.test -v || die
-}
diff --git a/sci-libs/pydicom/Manifest b/sci-libs/pydicom/Manifest
index 18fbb7f9d..b5e5f2a75 100644
--- a/sci-libs/pydicom/Manifest
+++ b/sci-libs/pydicom/Manifest
@@ -1,2 +1,2 @@
-DIST pydicom-0.9.9.tar.gz 422348 BLAKE2B 68ffa180ab926ebce2bd30f8fa6ff2442dfacf0fb2832f179010afda7092e7b4a4cbac2738aff5c7188b04c433b08bc19d64c1c9ebe07ae5dac5cd120e77e92f SHA512 3c2f3af6cc1f4a4a53894f236f55c33658bb448ad71571521fabe5d8b2a0e48b9cfaec491aa6f524cf7bbe294d9a784c5290d31a312ebd26701bacaac8253da7
-DIST pydicom-1.1.0.tar.gz 6724086 BLAKE2B efdcdd722bc877b9b9cf137ecd2a3fa6fb2b7da022bdab49f03dbcdb5a3e3dc8bc24b6b0d8eb9ab946934ec182c13ec1df671461c357476f543afb6f435f604c SHA512 ffca9eb4333d29accea1d6e5a5b4c3c0bd0f8c12fdf00c5c84d83769db621e8f348c9200dff1dc1cd6016cbf5d76b00f08c3b112ba653433a84ce31ad1ab33d5
+DIST pydicom-2.2.2.tar.gz 2149674 BLAKE2B d109975c6ac0081a02c534bb014040ca767968d276fb841a0000ab4f7b4884ab604276b7092f8cc699d24d0429426cf5be3225ae56b8b8ebdad89cf541ab065a SHA512 5f1829d445c462884debb75328f59471dea4da51701835a3a97a1c22c1c0b75730e0688558cb76ef3f7a4b29f350028190a515d73f88968a7fda09ed414ec145
+DIST pydicom-2.3.1.tar.gz 2164956 BLAKE2B ffdf14c582a7a783ae963008de9d8d9dd54c6d6889f10ebb767ff87abf00ab36406ea3dbab50304bcf1902af745b871b9dc1702d8824fb9ed163d1d909e88ac5 SHA512 bf2856b8afa13f6477a37abdc7d723337f532746705832b0eb01cfcf468f318ec4b74af5aade3b8629d050947a87e87fb39aca965ff98d0a348170a900d7dd57
diff --git a/sci-libs/pydicom/pydicom-0.9.9.ebuild b/sci-libs/pydicom/pydicom-0.9.9.ebuild
deleted file mode 100644
index df6e11172..000000000
--- a/sci-libs/pydicom/pydicom-0.9.9.ebuild
+++ /dev/null
@@ -1,17 +0,0 @@
-# Copyright 1999-2018 Gentoo Foundation
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=7
-
-PYTHON_COMPAT=( python{2_7,3_4,3_5,3_6} )
-
-inherit distutils-r1
-
-DESCRIPTION="A pure python package for parsing DICOM files"
-HOMEPAGE="http://www.pydicom.org/"
-SRC_URI="mirror://pypi/${PN:0:1}/${PN}/${P}.tar.gz"
-
-LICENSE="MIT"
-SLOT="0"
-KEYWORDS="~amd64 ~x86"
-IUSE=""
diff --git a/sci-libs/pydicom/pydicom-1.1.0.ebuild b/sci-libs/pydicom/pydicom-1.1.0.ebuild
deleted file mode 100644
index 0c2e1b15e..000000000
--- a/sci-libs/pydicom/pydicom-1.1.0.ebuild
+++ /dev/null
@@ -1,27 +0,0 @@
-# Copyright 1999-2018 Gentoo Foundation
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=7
-
-PYTHON_COMPAT=( python{2_7,3_4,3_5,3_6} )
-
-inherit distutils-r1
-
-DESCRIPTION="A pure python package for parsing DICOM files"
-HOMEPAGE="http://www.pydicom.org/"
-SRC_URI="mirror://pypi/${PN:0:1}/${PN}/${P}.tar.gz"
-
-LICENSE="MIT"
-SLOT="0"
-KEYWORDS="~amd64 ~x86"
-IUSE="test"
-
-# Upstream bug: https://github.com/pydicom/pydicom/issues/663
-RESTRICT="test"
-
-DEPEND="test? ( dev-python/pytest[${PYTHON_USEDEP}] )"
-
-python_test() {
-	distutils-r1_install_for_testing
-	py.test --cov=pydicom -r sx --pyargs pydicom --verbose || die
-}
diff --git a/sci-libs/pydicom/pydicom-2.2.2.ebuild b/sci-libs/pydicom/pydicom-2.2.2.ebuild
new file mode 100644
index 000000000..69cbed0c7
--- /dev/null
+++ b/sci-libs/pydicom/pydicom-2.2.2.ebuild
@@ -0,0 +1,28 @@
+# Copyright 1999-2023 Gentoo Authors
+# Distributed under the terms of the GNU General Public License v2
+
+EAPI=8
+
+DISTUTILS_USE_PEP517=setuptools
+PYTHON_COMPAT=( python3_{10..12} )
+
+inherit distutils-r1 pypi
+
+DESCRIPTION="A pure python package for parsing DICOM files"
+HOMEPAGE="https://pydicom.github.io/pydicom/dev/"
+
+LICENSE="MIT"
+SLOT="0"
+KEYWORDS="~amd64 ~x86"
+IUSE="test"
+
+# Reported upstream:
+# https://github.com/pydicom/pydicom/issues/1800
+RESTRICT="test"
+
+DEPEND="test? ( dev-python/pytest[${PYTHON_USEDEP}] )"
+
+python_test() {
+	distutils-r1_install_for_testing
+	py.test -r sx --pyargs pydicom --verbose || die
+}
diff --git a/sci-libs/pydicom/pydicom-2.3.1.ebuild b/sci-libs/pydicom/pydicom-2.3.1.ebuild
new file mode 100644
index 000000000..69cbed0c7
--- /dev/null
+++ b/sci-libs/pydicom/pydicom-2.3.1.ebuild
@@ -0,0 +1,28 @@
+# Copyright 1999-2023 Gentoo Authors
+# Distributed under the terms of the GNU General Public License v2
+
+EAPI=8
+
+DISTUTILS_USE_PEP517=setuptools
+PYTHON_COMPAT=( python3_{10..12} )
+
+inherit distutils-r1 pypi
+
+DESCRIPTION="A pure python package for parsing DICOM files"
+HOMEPAGE="https://pydicom.github.io/pydicom/dev/"
+
+LICENSE="MIT"
+SLOT="0"
+KEYWORDS="~amd64 ~x86"
+IUSE="test"
+
+# Reported upstream:
+# https://github.com/pydicom/pydicom/issues/1800
+RESTRICT="test"
+
+DEPEND="test? ( dev-python/pytest[${PYTHON_USEDEP}] )"
+
+python_test() {
+	distutils-r1_install_for_testing
+	py.test -r sx --pyargs pydicom --verbose || die
+}
diff --git a/sci-libs/pydicom/pydicom-9999.ebuild b/sci-libs/pydicom/pydicom-9999.ebuild
deleted file mode 100644
index 10a12a436..000000000
--- a/sci-libs/pydicom/pydicom-9999.ebuild
+++ /dev/null
@@ -1,20 +0,0 @@
-# Copyright 1999-2018 Gentoo Foundation
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=7
-
-PYTHON_COMPAT=( python{2_7,3_4,3_5,3_6} )
-
-inherit distutils-r1 git-r3
-
-DESCRIPTION="A pure python package for parsing DICOM files"
-HOMEPAGE="http://www.pydicom.org/"
-SRC_URI=""
-EGIT_REPO_URI="https://github.com/darcymason/pydicom"
-
-LICENSE="MIT"
-SLOT="0"
-KEYWORDS=""
-IUSE=""
-
-S="${S}/source"
diff --git a/sci-libs/rdkit/Manifest b/sci-libs/rdkit/Manifest
index 986f3e392..50005a850 100644
--- a/sci-libs/rdkit/Manifest
+++ b/sci-libs/rdkit/Manifest
@@ -1 +1 @@
-DIST rdkit-2015.03.1.tar.gz 24859988 BLAKE2B 84e80f370a605fb6edf178720a429f3d3d60f3ea9d535d69550b3035a7a757eacc221c3e0b9c9756367ab117c7c0f6cab3c248929684c7ccbf356d635e49c0f0 SHA512 dd76bfa260e126b2e2ec59ee049ef9f4dfdb2b51c784b750148c39f26447f77f1cfe58ae0694b8286627d622447678935590724b835bab09cdb54dca4a15f386
+DIST rdkit-2021.09.4.tar.gz 78474802 BLAKE2B 8c78c787a0e414b5e035998d9575322edca955acecb6d2df173610398f91cffd0b9053e7fc2c9284a2117afd720f313b7a63ed7e9ab67c708f25a5735b838f59 SHA512 c761fd5c3340ec38141165996b8666c3dcd4ed46ab91ca0d5a43ae3daedfc423ae36ec5882f085e1bd0c4c13dfe1f09497d05ec95e4847048c0acff8bcd0b1db
diff --git a/sci-libs/rdkit/files/rdkit-2021.09.4-find-rapidjson.patch b/sci-libs/rdkit/files/rdkit-2021.09.4-find-rapidjson.patch
new file mode 100644
index 000000000..94a209e0f
--- /dev/null
+++ b/sci-libs/rdkit/files/rdkit-2021.09.4-find-rapidjson.patch
@@ -0,0 +1,22 @@
+diff --git a/Code/GraphMol/MolInterchange/CMakeLists.txt b/Code/GraphMol/MolInterchange/CMakeLists.txt
+index 8027444..6a8c715 100644
+--- a/Code/GraphMol/MolInterchange/CMakeLists.txt
++++ b/Code/GraphMol/MolInterchange/CMakeLists.txt
+@@ -1,16 +1,5 @@
+ 
+-if(NOT EXISTS "${CMAKE_SOURCE_DIR}/External/rapidjson-1.1.0")
+-    downloadAndCheckMD5("https://github.com/Tencent/rapidjson/archive/v1.1.0.tar.gz"
+-          "${CMAKE_SOURCE_DIR}/External/rapidjson-1.1.0.tar.gz"
+-          "badd12c511e081fec6c89c43a7027bce")
+-    execute_process(COMMAND ${CMAKE_COMMAND} -E tar zxf
+-      ${CMAKE_SOURCE_DIR}/External/rapidjson-1.1.0.tar.gz
+-      WORKING_DIRECTORY ${CMAKE_SOURCE_DIR}/External)
+-else()
+-  message("-- Found RapidJSON source in ${CMAKE_SOURCE_DIR}/External")
+-endif()
+-
+-include_directories(${CMAKE_SOURCE_DIR}/External/rapidjson-1.1.0/include)
++include_directories(/usr/include/rapidjson)
+ 
+ 
+ rdkit_library(MolInterchange
diff --git a/sci-libs/rdkit/rdkit-2015.03.1.ebuild b/sci-libs/rdkit/rdkit-2015.03.1.ebuild
deleted file mode 100644
index 818630481..000000000
--- a/sci-libs/rdkit/rdkit-2015.03.1.ebuild
+++ /dev/null
@@ -1,40 +0,0 @@
-# Copyright 1999-2015 Gentoo Foundation
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=5
-
-PYTHON_COMPAT=( python{2_7,3_4} )
-
-inherit cmake-utils python-r1
-
-DESCRIPTION="Cheminformatics and machine-learning software written in C++ and Python"
-HOMEPAGE="http://www.rdkit.org/"
-SRC_URI="https://github.com/rdkit/rdkit/archive/Release_${PV//./_}.tar.gz -> ${P}.tar.gz"
-
-LICENSE="BSD"
-SLOT="0"
-KEYWORDS="~amd64 ~x86 ~amd64-linux ~x86-linux"
-IUSE="+python -static-libs"
-REQUIRED_USE="python? ( ${PYTHON_REQUIRED_USE} )"
-
-RDEPEND="dev-libs/boost
-	python? (
-		dev-libs/boost[python,${PYTHON_USEDEP}]
-		dev-python/numpy[${PYTHON_USEDEP}]
-	)
-	>=dev-db/sqlite-3"
-DEPEND="${RDEPEND}"
-
-S="${WORKDIR}"/rdkit-Release_${PV//./_}
-
-src_configure() {
-	local mycmakeargs=(
-		-DCMAKE_INSTALL_PREFIX:PATH="${EPREFIX}"/usr
-		-DRDK_INSTALL_INTREE=0
-		-DRDK_BUILD_CPP_TESTS=OFF
-		$(cmake-utils_use static-libs RDK_INSTALL_STATIC_LIBS)
-		$(cmake-utils_use python RDK_BUILD_PYTHON_WRAPPERS)
-	)
-
-	cmake-utils_src_configure
-}
diff --git a/sci-libs/rdkit/rdkit-2021.09.4.ebuild b/sci-libs/rdkit/rdkit-2021.09.4.ebuild
new file mode 100644
index 000000000..a1621ea79
--- /dev/null
+++ b/sci-libs/rdkit/rdkit-2021.09.4.ebuild
@@ -0,0 +1,58 @@
+# Copyright 1999-2022 Gentoo Authors
+# Distributed under the terms of the GNU General Public License v2
+
+EAPI=8
+
+PYTHON_COMPAT=( python3_10 )
+
+inherit cmake python-single-r1
+
+DESCRIPTION="Cheminformatics and machine-learning software written in C++ and Python"
+HOMEPAGE="http://www.rdkit.org/"
+SRC_URI="https://github.com/rdkit/rdkit/archive/Release_${PV//./_}.tar.gz -> ${P}.tar.gz"
+S="${WORKDIR}/rdkit-Release_${PV//./_}"
+
+LICENSE="BSD"
+SLOT="0"
+KEYWORDS="~amd64"
+IUSE="+python static-libs test"
+REQUIRED_USE="python? ( ${PYTHON_REQUIRED_USE} )"
+RESTRICT="!test? ( test )"
+
+RDEPEND="dev-libs/boost
+	python? (
+		$(python_gen_cond_dep '
+		dev-libs/boost:=[numpy,python,${PYTHON_USEDEP}]
+		dev-python/numpy[${PYTHON_USEDEP}]
+		')
+		${PYTHON_DEPS}
+	)
+	dev-cpp/catch:0
+	dev-libs/rapidjson
+	>=dev-db/sqlite-3"
+DEPEND="${RDEPEND}"
+
+PATCHES=(
+	"${FILESDIR}/${PN}-2021.09.4-find-rapidjson.patch"
+)
+
+src_configure() {
+	local mycmakeargs=(
+		-DCATCH_DIR="${EPREFIX}/usr/include/catch2"
+		-DCMAKE_INSTALL_PREFIX:PATH="${EPREFIX}/usr"
+		-DRDK_INSTALL_INTREE=0
+		-DRDK_BUILD_CPP_TESTS="$(usex test)"
+		-DRDK_INSTALL_STATIC_LIBS="$(usex static-libs)"
+		-DRDK_BUILD_PYTHON_WRAPPERS="$(usex python)"
+		# Disable things that trigger fetching and are not packaged
+		-DRDK_INSTALL_COMIC_FONTS=OFF
+		-DRDK_BUILD_COORDGEN_SUPPORT=OFF
+		-DRDK_BUILD_MAEPARSER_SUPPORT=OFF
+		-DRDK_USE_URF=OFF
+	)
+	cmake_src_configure
+}
+
+src_test() {
+	RDBASE="${WORKDIR}/${PN}-Release_2021_09_4_build" cmake_src_test
+}
diff --git a/sci-libs/rdkit/rdkit-9999.ebuild b/sci-libs/rdkit/rdkit-9999.ebuild
deleted file mode 100644
index 1c4a4e45a..000000000
--- a/sci-libs/rdkit/rdkit-9999.ebuild
+++ /dev/null
@@ -1,39 +0,0 @@
-# Copyright 1999-2015 Gentoo Foundation
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=5
-
-PYTHON_COMPAT=( python{2_7,3_4} )
-
-inherit cmake-utils python-r1 git-r3
-
-DESCRIPTION="Cheminformatics and machine-learning software written in C++ and Python"
-HOMEPAGE="http://www.rdkit.org/"
-SRC_URI=""
-EGIT_REPO_URI="https://github.com/rdkit/rdkit.git"
-
-LICENSE="BSD"
-SLOT="0"
-KEYWORDS="~amd64 ~x86 ~amd64-linux ~x86-linux"
-IUSE="+python -static-libs"
-REQUIRED_USE="python? ( ${PYTHON_REQUIRED_USE} )"
-
-RDEPEND="dev-libs/boost
-	python? (
-		dev-libs/boost[python,${PYTHON_USEDEP}]
-		dev-python/numpy[${PYTHON_USEDEP}]
-	)
-	>=dev-db/sqlite-3"
-DEPEND="${RDEPEND}"
-
-src_configure() {
-	local mycmakeargs=(
-		-DCMAKE_INSTALL_PREFIX:PATH="${EPREFIX}"/usr
-		-DRDK_INSTALL_INTREE=0
-		-DRDK_BUILD_CPP_TESTS=OFF
-		$(cmake-utils_use static-libs RDK_INSTALL_STATIC_LIBS)
-		$(cmake-utils_use python RDK_BUILD_PYTHON_WRAPPERS)
-	)
-
-	cmake-utils_src_configure
-}
diff --git a/sci-libs/scalapack/Manifest b/sci-libs/scalapack/Manifest
deleted file mode 100644
index 5a13f9544..000000000
--- a/sci-libs/scalapack/Manifest
+++ /dev/null
@@ -1 +0,0 @@
-DIST scalapack-2.0.2.tgz 4779534 BLAKE2B c2aabd87bc8f7c0d9af31bd8ad8c933703dcbba399658d15c1e5256da2350c1a0feac2ca4a205f697b1c48083df89cbcd64ba432da036081c0f33d5d2acddc9b SHA512 92c71d3de0900955511c527ab3ca57ff69d6d9edc390e69f93ac3769d32ce83a714326bcb6218c8c74b8874be2fdc8aad5e42c912a12581e8d4ce8829ea39248
diff --git a/sci-libs/scalapack/metadata.xml b/sci-libs/scalapack/metadata.xml
deleted file mode 100644
index 9515f4005..000000000
--- a/sci-libs/scalapack/metadata.xml
+++ /dev/null
@@ -1,15 +0,0 @@
-<?xml version="1.0" encoding="UTF-8"?>
-<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
-<pkgmetadata>
-	<maintainer type="project">
-		<email>sci@gentoo.org</email>
-		<name>Gentoo Science Project</name>
-	</maintainer>
-	<longdescription lang="en">
-The ScaLAPACK (or Scalable LAPACK) library includes a subset of LAPACK routines
-redesigned for distributed memory MIMD parallel computers. It is currently
-written in a Single-Program-Multiple-Data style using explicit message
-passing for interprocessor communication. It assumes matrices are laid out
-in a two-dimensional block cyclic decomposition.
-</longdescription>
-</pkgmetadata>
diff --git a/sci-libs/scalapack/scalapack-2.0.2-r1.ebuild b/sci-libs/scalapack/scalapack-2.0.2-r1.ebuild
deleted file mode 100644
index 55d6aed37..000000000
--- a/sci-libs/scalapack/scalapack-2.0.2-r1.ebuild
+++ /dev/null
@@ -1,71 +0,0 @@
-# Copyright 1999-2014 Gentoo Foundation
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=5
-
-inherit alternatives-2 cmake-utils eutils fortran-2
-
-DESCRIPTION="Subset of LAPACK routines redesigned for heterogenous computing"
-HOMEPAGE="http://www.netlib.org/scalapack/"
-SRC_URI="${HOMEPAGE}/${P}.tgz"
-
-LICENSE="BSD"
-SLOT="0"
-KEYWORDS="~amd64 ~x86 ~amd64-linux ~x86-linux"
-IUSE="static-libs test"
-
-RDEPEND="
-	virtual/lapack
-	virtual/mpi
-	!sci-libs/mpiblacs"
-DEPEND="${RDEPEND}
-	virtual/pkgconfig"
-
-src_prepare() {
-	# gentoo fix to avoid collision with other scalapack
-	sed -i \
-		-e 's:BINARY_DIR}/scalapack.pc:BINARY_DIR}/refscalapack.pc:g' \
-		CMakeLists.txt || die
-	use static-libs && mkdir "${WORKDIR}/${PN}_static"
-	# mpi does not have a pc file
-	sed -i -e 's/mpi//' scalapack.pc.in || die
-}
-
-src_configure() {
-	scalapack_configure() {
-		local mycmakeargs=(
-			-DUSE_OPTIMIZED_LAPACK_BLAS=ON
-			-DBLAS_LIBRARIES="$($(tc-getPKG_CONFIG) --libs blas)"
-			-DLAPACK_LIBRARIES="$($(tc-getPKG_CONFIG) --libs lapack)"
-			$(cmake-utils_use_build test TESTING)
-			$@
-		)
-		cmake-utils_src_configure
-	}
-
-	scalapack_configure -DBUILD_SHARED_LIBS=ON -DBUILD_STATIC_LIBS=OFF
-	use static-libs && \
-		BUILD_DIR="${WORKDIR}/${PN}_static" scalapack_configure \
-		-DBUILD_SHARED_LIBS=OFF -DBUILD_STATIC_LIBS=ON
-}
-
-src_compile() {
-	cmake-utils_src_compile
-	use static-libs && \
-		BUILD_DIR="${WORKDIR}/${PN}_static" cmake-utils_src_compile
-}
-
-src_install() {
-	cmake-utils_src_install
-	use static-libs && \
-		BUILD_DIR="${WORKDIR}/${PN}_static" cmake-utils_src_install
-
-	insinto /usr/include/blacs
-	doins BLACS/SRC/*.h
-
-	insinto /usr/include/scalapack
-	doins PBLAS/SRC/*.h
-
-	alternatives_for scalapack reference 0 \
-		/usr/$(get_libdir)/pkgconfig/scalapack.pc refscalapack.pc
-}
diff --git a/sci-libs/scikit-learn-intelx/Manifest b/sci-libs/scikit-learn-intelx/Manifest
new file mode 100644
index 000000000..d14b31510
--- /dev/null
+++ b/sci-libs/scikit-learn-intelx/Manifest
@@ -0,0 +1 @@
+DIST scikit-learn-intelx-2023.0.2.tar.gz 13864043 BLAKE2B dfc082a8b008553e0d20cf7a24417fecd510dd8e6b3286a57a633b1e3b79cecc87fc1189df6f4a3440d7ccb74077c54a9f6eaf58bfbb19181cb4b437b3e06ae6 SHA512 dd8c983365d4f32d2640caab17319970c86bfed5ad6852d15dce35ba66a3584c51b94fa5ef0d8073b917332ea18a8c9af95ef8da125edb47190f27e9b8cab424
diff --git a/sci-libs/scikit-learn-intelx/metadata.xml b/sci-libs/scikit-learn-intelx/metadata.xml
new file mode 100644
index 000000000..247707c87
--- /dev/null
+++ b/sci-libs/scikit-learn-intelx/metadata.xml
@@ -0,0 +1,11 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
+<pkgmetadata>
+	<maintainer type="project">
+		<email>sci@gentoo.org</email>
+		<name>Gentoo Science Project</name>
+	</maintainer>
+	<upstream>
+		<remote-id type="github">intel/scikit-learn-intelex</remote-id>
+	</upstream>
+</pkgmetadata>
diff --git a/sci-libs/scikit-learn-intelx/scikit-learn-intelx-2023.0.2.ebuild b/sci-libs/scikit-learn-intelx/scikit-learn-intelx-2023.0.2.ebuild
new file mode 100644
index 000000000..29288cbcf
--- /dev/null
+++ b/sci-libs/scikit-learn-intelx/scikit-learn-intelx-2023.0.2.ebuild
@@ -0,0 +1,49 @@
+# Copyright 2022 Gentoo Authors
+# Distributed under the terms of the GNU General Public License v2
+
+EAPI=8
+
+PYTHON_COMPAT=( python3_{10..11} )
+DISTUTILS_USE_PEP517=setuptools
+inherit distutils-r1
+
+DESCRIPTION="Seamless way to speed up your Scikit-learn application"
+HOMEPAGE="https://github.com/intel/scikit-learn-intelex"
+SRC_URI="https://github.com/intel/scikit-learn-intelex/archive/refs/tags/${PV}.tar.gz -> ${P}.tar.gz"
+S="${WORKDIR}/scikit-learn-intelex-${PV}"
+
+LICENSE="Apache-2.0"
+SLOT="0"
+KEYWORDS="~amd64"
+
+DEPEND="
+	dev-python/numpy[${PYTHON_USEDEP}]
+	sci-libs/daal4py[${PYTHON_USEDEP}]
+	sci-libs/scikit-learn[${PYTHON_USEDEP}]
+"
+RDEPEND="${DEPEND}"
+
+distutils_enable_tests pytest
+
+python_prepare_all() {
+	# DPC++ compiler required for full functionality
+	export CC="${ESYSROOT}/usr/lib/llvm/intel/bin/clang"
+	export CXX="${ESYSROOT}/usr/lib/llvm/intel/bin/clang++"
+	export DPCPPROOT="${ESYSROOT}/usr/lib/llvm/intel"
+	export CPLUS_INCLUDE_PATH="${ESYSROOT}/usr/lib/llvm/intel/include:${ESYSROOT}/usr/lib/llvm/intel/include/sycl"
+	export MPIROOT="${ESYSROOT}/usr"
+	export DALROOT="${ESYSROOT}/usr"
+
+	# remove the daal4py setup files, and rename skleanex setup files
+	rm setup.py setup.cfg || die
+	mv setup_sklearnex.cfg setup.cfg || die
+	mv setup_sklearnex.py setup.py || die
+
+	distutils-r1_python_prepare_all
+}
+
+python_test() {
+	export PYTHONPATH="${BUILD_DIR}/install/usr/lib/${EPYTHON}/site-packages"
+	# We don't use epytest because it overwrites our PYTHONPATH
+	pytest -vv || die
+}
diff --git a/sci-libs/shtools/Manifest b/sci-libs/shtools/Manifest
deleted file mode 100644
index 4949ead8e..000000000
--- a/sci-libs/shtools/Manifest
+++ /dev/null
@@ -1 +0,0 @@
-DIST shtools-4.0.tar.gz 17372252 BLAKE2B 7c3ab722ae9c86ced3442ee936bccc9fc30aea73fea65a749d9658ec7e4f828e3da68c88ed447d45f1c6718ba6fbe3fc69d62d4bcfe733673b0e6aa5c6b63ac7 SHA512 13dae982d0b8b45a9193b9ffdf8433624b862fec5c071f4eed7f4883a498c36a039d7b037024eab6cef5d54a0459464e4dcc1771785e575e27c2a94131de90a3
diff --git a/sci-libs/shtools/metadata.xml b/sci-libs/shtools/metadata.xml
deleted file mode 100644
index 2fc842248..000000000
--- a/sci-libs/shtools/metadata.xml
+++ /dev/null
@@ -1,21 +0,0 @@
-<?xml version="1.0" encoding="UTF-8"?>
-<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
-<pkgmetadata>
-	<maintainer type="person">
-		<email>heroxbd@gentoo.org</email>
-		<name>Benda Xu</name>
-	</maintainer>
-	<maintainer type="project">
-		<email>sci@gentoo.org</email>
-		<name>Gentoo Science Project</name>
-	</maintainer>
-	<longdescription>
-SHTOOLS is an archive of Fortran 95 and Python software that can
-be used to perform spherical harmonic transforms and
-reconstructions, rotations of data expressed in spherical
-harmonics, and multitaper spectral analyses on the sphere.
-</longdescription>
-	<upstream>
-		<remote-id type="github">SHTOOLS/SHTOOLS</remote-id>
-	</upstream>
-</pkgmetadata>
diff --git a/sci-libs/shtools/shtools-4.0.ebuild b/sci-libs/shtools/shtools-4.0.ebuild
deleted file mode 100644
index 82c690943..000000000
--- a/sci-libs/shtools/shtools-4.0.ebuild
+++ /dev/null
@@ -1,77 +0,0 @@
-# Copyright 1999-2017 Gentoo Foundation
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=6
-
-if [[ ${PV} == 9999 ]]; then
-	_ECLASS="git-r3"
-	EGIT_REPO_URI="https://github.com/heroxbd/${PN^^}.git"
-	S="${WORKDIR}"/${P}
-else
-	SRC_URI="https://github.com/${PN^^}/${PN^^}/archive/v${PV/_/-}.tar.gz -> ${P}.tar.gz"
-	KEYWORDS="~amd64"
-	S="${WORKDIR}"/${PN^^}-${PV/_/-}
-fi
-
-PYTHON_COMPAT=( python{2_7,3_{4,5}} )
-
-inherit fortran-2 flag-o-matic python-single-r1 toolchain-funcs ${_ECLASS}
-
-DESCRIPTION="Spherical harmonic transforms and reconstructions, rotations"
-HOMEPAGE="http://shtools.ipgp.fr"
-
-LICENSE="BSD-4"
-SLOT="0"
-KEYWORDS="~amd64"
-IUSE="static-libs"
-
-RDEPEND="
-	dev-python/numpy[${PYTHON_USEDEP}]
-	dev-python/matplotlib[${PYTHON_USEDEP}]
-	sci-libs/fftw:3.0=
-	virtual/lapack
-	virtual/blas
-	${PYTHON_DEPS}"
-
-DEPEND="${RDEPEND}
-	virtual/pkgconfig
-"
-
-src_prepare() {
-	append-ldflags -shared # needed by f2py
-	# needed by f2py in fortran 77 mode
-	append-fflags -fPIC
-	[[ $(tc-getFC) =~ gfortran ]] && append-fflags -fno-second-underscore
-	export _pyver=$(python_is_python3 && echo 3 || echo 2)
-	export OPTS=(
-		LAPACK=$($(tc-getPKG_CONFIG) lapack --libs-only-l)
-		BLAS=$($(tc-getPKG_CONFIG) blas --libs-only-l)
-		FFTW=$($(tc-getPKG_CONFIG) fftw3 --libs-only-l)
-		F95=$(tc-getFC)
-		F95FLAGS="${FCFLAGS}"
-		AR=$(tc-getAR)
-		RLIB=$(tc-getRANLIB)
-		PYTHON_VERSION=${_pyver}
-	)
-
-	sed \
-		-e '/mv/s:.so:*.so:g' \
-		-e "/SYSDOCPATH/s:${PN}:${PF}:g" \
-		-e "/www/s:/$:/html/:g" \
-		-i Makefile || die
-
-	default
-}
-
-src_compile() {
-	emake fortran "${OPTS[@]}"
-	emake python${_pyver} "${OPTS[@]}"
-}
-
-src_install() {
-	emake PREFIX="${EPREFIX}/usr" DESTDIR="${D}" "${OPTS[@]}" install-fortran
-	emake PREFIX="${EPREFIX}/usr" DESTDIR="${D}" "${OPTS[@]}" install-python${_pyver}
-	if ! use static-libs; then
-		rm -rf "${ED}"/usr/$(get_libdir)/*.a || die
-	fi
-}
diff --git a/sci-libs/simpleitk/Manifest b/sci-libs/simpleitk/Manifest
new file mode 100644
index 000000000..b571c4ad6
--- /dev/null
+++ b/sci-libs/simpleitk/Manifest
@@ -0,0 +1,2 @@
+DIST SimpleITK-1.2.4.tar.gz 1894019 BLAKE2B dce92a95fc330a852ccf7bab0023ecac9d1cc765cfe90e6cad867f4b32d6923a76dd1f50b0952afc7d829288640e5cfb6eb669c7ace1f17e35bd15b4052234f8 SHA512 49395b284fa03cc75dbd68f7f63008ea5d03a0771f0144f2d6d62ae034d66c93a14e262b48b12b6f0e6beb3d42d6f60022f502da02d2e87c6e47bd5d38637025
+DIST SimpleITKData-1.2.4.tar.gz 112145576 BLAKE2B fb38283c75a5a4bbd8f1007ba326febdcef94db7f0e7fd5f7217fef637947825243d6bfcc0193233d4f9696037b1588d312f7c333aadfda1e6f08539f0f22cdf SHA512 1dd73d5bfeba0a7d72088dc2c966db764f5d7deb173bea17a9f6c5a9fae849ddc781b9fbf9b25ab898742268de4ca0dc5a64f72e985e3c72d4d95c7e5e79e92f
diff --git a/sci-libs/simpleitk/files/simpleitk-1.2.4-int-cast.patch b/sci-libs/simpleitk/files/simpleitk-1.2.4-int-cast.patch
new file mode 100644
index 000000000..9477194c4
--- /dev/null
+++ b/sci-libs/simpleitk/files/simpleitk-1.2.4-int-cast.patch
@@ -0,0 +1,64 @@
+From 73caeaa545859cffd68f9aebe1e8b66de5ab812d Mon Sep 17 00:00:00 2001
+From: Bradley Lowekamp <blowekamp@mail.nih.gov>
+Date: Fri, 14 Feb 2020 09:35:29 -0500
+Subject: [PATCH] Explicitly cast int to ITK strongly typed enums
+
+---
+ Code/IO/src/sitkImageReaderBase.cxx | 12 ++++++------
+ 1 file changed, 6 insertions(+), 6 deletions(-)
+
+diff --git a/Code/IO/src/sitkImageReaderBase.cxx b/Code/IO/src/sitkImageReaderBase.cxx
+index b8c93a2ac..a5e6d9cd9 100644
+--- a/Code/IO/src/sitkImageReaderBase.cxx
++++ b/Code/IO/src/sitkImageReaderBase.cxx
+@@ -214,7 +214,7 @@ ::GetPixelIDFromImageIO( const ImageIOBase *iobase,
+   if (numberOfComponents == 1 &&
+       ( pixelType == itk::ImageIOBase::SCALAR || pixelType == itk::ImageIOBase::COMPLEX ) )
+     {
+-    outPixelType = this->ExecuteInternalReadScalar( componentType );
++    outPixelType = this->ExecuteInternalReadScalar( static_cast<int>(componentType) );
+     return;
+     }
+   // we try to load anything else into a VectorImage
+@@ -226,12 +226,12 @@ ::GetPixelIDFromImageIO( const ImageIOBase *iobase,
+             pixelType == itk::ImageIOBase::POINT ||
+             pixelType == itk::ImageIOBase::OFFSET )
+     {
+-    outPixelType = this->ExecuteInternalReadVector( componentType );
++    outPixelType = this->ExecuteInternalReadVector( static_cast<int>(componentType) );
+     return;
+     }
+   else if ( pixelType == itk::ImageIOBase::COMPLEX )
+     {
+-    outPixelType = this->ExecuteInternalReadComplex( componentType );
++    outPixelType = this->ExecuteInternalReadComplex( static_cast<int>(componentType) );
+     return;
+     }
+   else
+@@ -268,7 +268,7 @@ ::ExecuteInternalReadScalar( int componentType )
+ {
+   const unsigned int UnusedDimension = 2;
+ 
+-  switch(componentType)
++  switch(static_cast<ImageIOBase::IOComponentType>(componentType))
+     {
+     case itk::ImageIOBase::CHAR:
+       return ImageTypeToPixelIDValue< itk::Image<int8_t, UnusedDimension> >::Result;
+@@ -326,7 +326,7 @@ ::ExecuteInternalReadComplex( int componentType )
+ {
+   const unsigned int UnusedDimension = 2;
+ 
+-  switch(componentType)
++  switch(static_cast<ImageIOBase::IOComponentType>(componentType))
+     {
+     case itk::ImageIOBase::FLOAT:
+       return ImageTypeToPixelIDValue< itk::Image<std::complex<float>, UnusedDimension> >::Result;
+@@ -346,7 +346,7 @@ ::ExecuteInternalReadVector( int componentType )
+ {
+   const unsigned int UnusedDimension = 2;
+ 
+-  switch(componentType)
++  switch(static_cast<ImageIOBase::IOComponentType>(componentType))
+     {
+     case itk::ImageIOBase::CHAR:
+       return ImageTypeToPixelIDValue< itk::VectorImage<int8_t, UnusedDimension> >::Result;
diff --git a/sci-libs/simpleitk/files/simpleitk-1.2.4-module.patch b/sci-libs/simpleitk/files/simpleitk-1.2.4-module.patch
new file mode 100644
index 000000000..9b40d5e02
--- /dev/null
+++ b/sci-libs/simpleitk/files/simpleitk-1.2.4-module.patch
@@ -0,0 +1,22 @@
+From 9a9f67416683d69c1c8d2362ba6e50c4848803b2 Mon Sep 17 00:00:00 2001
+From: Bradley Lowekamp <blowekamp@mail.nih.gov>
+Date: Wed, 20 Nov 2019 15:30:50 -0500
+Subject: [PATCH] Update SLICImageFilter's module
+
+---
+ Code/BasicFilters/json/SLICImageFilter.json | 2 +-
+ 1 file changed, 1 insertion(+), 1 deletion(-)
+
+diff --git a/Code/BasicFilters/json/SLICImageFilter.json b/Code/BasicFilters/json/SLICImageFilter.json
+index 2ffba2f4c..0e9ced7d7 100644
+--- a/Code/BasicFilters/json/SLICImageFilter.json
++++ b/Code/BasicFilters/json/SLICImageFilter.json
+@@ -156,7 +156,7 @@
+       ]
+     }
+   ],
+-  "itk_module" : "SimpleITKFilters",
++  "itk_module" : "ITKSuperPixel",
+   "detaileddescription" : "The Simple Linear Iterative Clustering (SLIC) algorithm groups pixels into a set of labeled regions or super-pixels. Super-pixels follow natural image boundaries, are compact, and are nearly uniform regions which can be used as a larger primitive for more efficient computation. The SLIC algorithm can be viewed as a spatially constrained iterative k-means method.\n\nThe original algorithm was designed to cluster on the joint domain of the images index space and it's CIELAB color space. This implementation works with images of arbitrary dimension as well as scalar, single channel, images and most multi-component image types including ITK's arbitrary length VectorImage .\n\nThe distance between a pixel and a cluster is the sum of squares of the difference between their joint range and domains ( index and value ). The computation is done in index space with scales provided by the SpatialProximityWeight parameters.\n\nThe output is a label image with each label representing a superpixel cluster. Every pixel in the output is labeled, and the starting label id is zero.\n\nThis code was contributed in the Insight Journal paper: \"Scalable Simple Linear Iterative Clustering (SSLIC) Using a\nGeneric and Parallel Approach\" by Lowekamp B. C., Chen D. T., Yaniv Z.",
+   "briefdescription" : "Simple Linear Iterative Clustering (SLIC) super-pixel segmentation."
+ }
diff --git a/sci-libs/simpleitk/metadata.xml b/sci-libs/simpleitk/metadata.xml
new file mode 100644
index 000000000..1d31afb55
--- /dev/null
+++ b/sci-libs/simpleitk/metadata.xml
@@ -0,0 +1,19 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
+<pkgmetadata>
+	<maintainer type="project">
+		<email>chr@chymera.eu</email>
+		<name>Horea Christian</name>
+	</maintainer>
+	<longdescription lang="en">
+		SimpleITK is an image analysis toolkit with a large number of components
+		supporting general filtering operations, image segmentation and registration.
+		It is built on top of the Insight Segmentation and Registration Toolkit ITK
+		with the intent of providing a simplified interface to ITK. SimpleITK itself
+		is written in C++ but is available for a large number of programming
+		languages.
+	</longdescription>
+	<upstream>
+		<remote-id type="github">SimpleITK/SimpleITK</remote-id>
+	</upstream>
+</pkgmetadata>
diff --git a/sci-libs/simpleitk/simpleitk-1.2.4.ebuild b/sci-libs/simpleitk/simpleitk-1.2.4.ebuild
new file mode 100644
index 000000000..26e0c688d
--- /dev/null
+++ b/sci-libs/simpleitk/simpleitk-1.2.4.ebuild
@@ -0,0 +1,65 @@
+# Copyright 1999-2022 Gentoo Authors
+# Distributed under the terms of the GNU General Public License v2
+
+EAPI=8
+
+PYTHON_COMPAT=( python3_10 )
+LUA_COMPAT=( lua5-{1..3} )
+
+inherit lua-single cmake python-single-r1
+
+MY_PN="SimpleITK"
+
+DESCRIPTION="Layer on top of ITK for rapid prototyping, education and interpreted languages."
+HOMEPAGE="https://simpleitk.org/"
+SRC_URI="
+	https://github.com/SimpleITK/SimpleITK/releases/download/v${PV}/SimpleITK-${PV}.tar.gz
+	https://github.com/SimpleITK/SimpleITK/releases/download/v${PV}/SimpleITKData-${PV}.tar.gz
+"
+
+LICENSE="Apache-2.0"
+SLOT="0"
+KEYWORDS="~amd64 ~x86"
+
+IUSE="python"
+REQUIRED_USE="${PYTHON_REQUIRED_USE}"
+
+BDEPEND="dev-lang/swig"
+RDEPEND="
+	${LUA_DEPS}
+	dev-cpp/gtest
+	sci-libs/itk
+	dev-python/virtualenv
+	python? ( ${PYTHON_DEPS} )
+"
+DEPEND="${RDEPEND}"
+
+PATCHES=(
+	"${FILESDIR}/${P}-module.patch"
+	"${FILESDIR}/${P}-int-cast.patch"
+)
+
+S="${WORKDIR}/${MY_PN}-${PV}"
+
+src_prepare() {
+	cmake_src_prepare
+	cp -rf "../${MY_PN}-${PV}/.ExternalData" "${BUILD_DIR}/" || die
+}
+
+src_configure() {
+	local mycmakeargs=(
+		-DUSE_SYSTEM_GTEST=ON
+		-DUSE_SYSTEM_ITK=ON
+		-DUSE_SYSTEM_LUA=ON
+		-DUSE_SYSTEM_SWIG=ON
+		-DUSE_SYSTEM_VIRTUALENV=ON
+		-DBUILD_TESTING:BOOL=OFF
+		-DSimpleITK_FORBID_DOWNLOADS=ON
+		-DSimpleITK_PYTHON_USE_VIRTUALENV:BOOL=OFF
+		-DSimpleITK_EXPLICIT_INSTANTIATION=OFF
+		-DModule_SimpleITKFilters:BOOL=ON
+		-DExternalData_OBJECT_STORES:STRING="${BUILD_DIR}/.ExternalData"
+		-DSimpleITK_INSTALL_LIBRARY_DIR=$(get_libdir)
+	)
+	cmake_src_configure
+}
diff --git a/sci-libs/spams-python/Manifest b/sci-libs/spams-python/Manifest
deleted file mode 100644
index a86d9e583..000000000
--- a/sci-libs/spams-python/Manifest
+++ /dev/null
@@ -1 +0,0 @@
-DIST spams-python-2.6.tar.gz 1721573 BLAKE2B b172ecb06b1bd008e9c9a7cd6b8ba41468dc5797c3f7cf7f025c49c19b78911ca346578ee7e87e6b3dfcfc97eea8e5625a4162844bc183a83f1460dbae45c3a5 SHA512 e9ddd53eacaf95aca2d1dc3e84403bf30705ec5b87969480a710ec529c7a503de7526b66bf7060e958ae090d0d25ffa82593e7bc0c902516a5c04be11f853941
diff --git a/sci-libs/spams-python/metadata.xml b/sci-libs/spams-python/metadata.xml
deleted file mode 100644
index d1fbb3db3..000000000
--- a/sci-libs/spams-python/metadata.xml
+++ /dev/null
@@ -1,24 +0,0 @@
-<?xml version="1.0" encoding="UTF-8"?>
-<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
-<pkgmetadata>
-	<maintainer type="person">
-		<email>horea.christ@gmail.com</email>
-		<name>Horea Christian</name>
-	</maintainer>
-	<maintainer type="project">
-		<email>sci@gentoo.org</email>
-		<name>Gentoo Science Project</name>
-	</maintainer>
-	<longdescription lang="en">
-		SPAMS (SPArse Modeling Software) is an optimization toolbox for solving
-		various sparse estimation problems, such as: Dictionary learning and
-		matrix factorization (NMF, sparse PCA, ...); solving sparse decomposition
-		problems with LARS, coordinate descent, OMP, SOMP, proximal methods; and 
-		Solving structured sparse decomposition problems (l1/l2, l1/linf, sparse
-		group lasso, tree-structured regularization, structured sparsity with
-		overlapping groups,...). 
-	</longdescription>
-	<upstream>
-		<remote-id type="github">samuelstjean/spams-python</remote-id>
-	</upstream>
-</pkgmetadata>
diff --git a/sci-libs/spams-python/spams-python-2.6.ebuild b/sci-libs/spams-python/spams-python-2.6.ebuild
deleted file mode 100644
index 59a809762..000000000
--- a/sci-libs/spams-python/spams-python-2.6.ebuild
+++ /dev/null
@@ -1,59 +0,0 @@
-# Copyright 1999-2018 Gentoo Foundation
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=7
-
-PYTHON_COMPAT=( python{2_7,3_4,3_5,3_6} )
-
-inherit distutils-r1 toolchain-funcs
-
-DESCRIPTION="Optimization toolbox for solving various sparse estimation problems"
-HOMEPAGE="http://spams-devel.gforge.inria.fr/index.html"
-SRC_URI="https://github.com/samuelstjean/${PN}/archive/v${PV}.tar.gz -> ${P}.tar.gz"
-
-LICENSE="GPL-3"
-SLOT="0"
-IUSE=""
-KEYWORDS="~amd64"
-
-DEPEND="
-	dev-python/numpy[${PYTHON_USEDEP}]
-	virtual/blas
-	virtual/lapack
-	"
-RDEPEND="${DEPEND}
-	sci-libs/scipy[${PYTHON_USEDEP}]
-	"
-
-pc_libdir() {
-	$(tc-getPKG_CONFIG) --libs-only-L $@ | \
-		sed -e 's/^-L//' -e 's/[ ]*-L/:/g' -e 's/[ ]*$//' -e 's|^,||'
-}
-
-pc_libs() {
-	$(tc-getPKG_CONFIG) --libs-only-l $@ | \
-		sed -e 's/[ ]-l*\(pthread\|m\)\([ ]\|$\)//g' \
-		-e 's/^-l//' -e 's/[ ]*-l/,/g' -e 's/[ ]*$//' \
-		| tr ',' '\n' | sort -u | tr '\n' ',' | sed -e 's|,$||'
-}
-pkg_pretend() {
-	[[ ${MERGE_TYPE} != binary ]] && tc-check-openmp
-}
-
-pkg_setup() {
-	[[ ${MERGE_TYPE} != binary ]] && tc-check-openmp
-}
-
-python_prepare_all() {
-	local libdir="${EPREFIX}"/usr/$(get_libdir)
-	MY_LAPACK=$(pc_libs lapack)
-	MY_BLAS=$(pc_libs blas)
-	MY_LIBDIRS="$(pc_libdir blas lapack)'${libdir}'"
-	sed -i -e "s/'blas', 'lapack'/'${MY_BLAS}', '${MY_LAPACK}'/g" setup.py || die
-	sed -i -e "s|libdirs = \[\]|libdirs = [${MY_LIBDIRS}]|g" setup.py || die
-	distutils-r1_python_prepare_all
-}
-
-python_test() {
-	${EPYTHON} test_spams.py
-}
diff --git a/sci-libs/spglib/Manifest b/sci-libs/spglib/Manifest
deleted file mode 100644
index 51719ffea..000000000
--- a/sci-libs/spglib/Manifest
+++ /dev/null
@@ -1,2 +0,0 @@
-DIST spglib-1.6.0.tar.gz 915285 BLAKE2B 44b7f5446dd82f9e949e2f0c207cb7685da09dbef83490594e8bfb46193c720ce5089815f1bba93c8e380f274655e0b06837b1e0485ec61d5adb8cbfed727449 SHA512 c480f2de4d2ead5f89b896e5edba3f5aa838d7319dd8c25979c9e3c11c9c9912f1632436d7215dffcb7fa604cae16a68e7474a16e0f7154f7b28fd48caa208df
-DIST spglib-1.9.0.tar.gz 974496 BLAKE2B 017363930350922c1d56c66dee0462becc1444f07d51a09fc4f4cce64e1c39566d7414bb90cef1b1abecf76657752c1c115c5d9071d19f153ec762593ccd4fa8 SHA512 8a678d720bf95ff4c57045663b495558335f9d844e43e7c641435ea48104ba9ed1f0a32aa10b49c50e9bf26bcbe6ac288bf89a0e3091f3d5d6a2cbb28342ddc6
diff --git a/sci-libs/spglib/files/spglib-1.9.0-openmp.patch b/sci-libs/spglib/files/spglib-1.9.0-openmp.patch
deleted file mode 100644
index 2600d1b27..000000000
--- a/sci-libs/spglib/files/spglib-1.9.0-openmp.patch
+++ /dev/null
@@ -1,22 +0,0 @@
---- spglib-1.9.0/configure.ac
-+++ spglib-1.9.0/configure.ac
-@@ -17,6 +17,9 @@
- # Checks for libraries.
- AC_CHECK_FUNCS([sqrt])
- 
-+# Checks for OpenMP.
-+AC_OPENMP
-+
- # Checks for header files.
- AC_HEADER_STDC
- AC_CHECK_HEADERS([stdlib.h string.h math.h])
---- spglib-1.9.0/src/Makefile.am
-+++ spglib-1.9.0/src/Makefile.am
-@@ -60,4 +60,6 @@
- version.h
- 
- # libsymspg_la_LDFLAGS = -version-info 0:1:0
--libsymspg_la_LIBADD = -lm
-+libsymspg_la_LIBADD = -lm @OPENMP_CFLAGS@
-+
-+AM_CFLAGS = @OPENMP_CFLAGS@
diff --git a/sci-libs/spglib/files/spglib-openmp.patch b/sci-libs/spglib/files/spglib-openmp.patch
deleted file mode 100644
index 616c008fe..000000000
--- a/sci-libs/spglib/files/spglib-openmp.patch
+++ /dev/null
@@ -1,22 +0,0 @@
-diff -Naur spglib-1.6.0/configure.ac spglib-1.6.0-new/configure.ac
---- spglib-1.6.0/configure.ac	2014-01-07 01:44:11.000000000 -0700
-+++ spglib-1.6.0-new/configure.ac	2014-03-11 12:33:21.000000000 -0600
-@@ -14,7 +14,8 @@
- AM_PROG_CC_C_O
- AM_PROG_LIBTOOL
- 
--# Checks for libraries.
-+# Checks for OpenMP.
-+AC_OPENMP
- 
- # Checks for header files.
- AC_HEADER_STDC
-diff -Naur spglib-1.6.0/src/Makefile.am spglib-1.6.0-new/src/Makefile.am
---- spglib-1.6.0/src/Makefile.am	2014-01-06 19:54:45.000000000 -0700
-+++ spglib-1.6.0-new/src/Makefile.am	2014-03-11 12:37:21.000000000 -0600
-@@ -57,3 +57,5 @@
- 
- # libsymspg_la_LDFLAGS = -version-info 0:1:0
- libsymspg_la_LIBADD = -lm
-+
-+AM_CFLAGS = ${OPENMP_CFLAGS}
diff --git a/sci-libs/spglib/metadata.xml b/sci-libs/spglib/metadata.xml
deleted file mode 100644
index aa3560014..000000000
--- a/sci-libs/spglib/metadata.xml
+++ /dev/null
@@ -1,18 +0,0 @@
-<?xml version="1.0" encoding="UTF-8"?>
-<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
-<pkgmetadata>
-	<maintainer type="person">
-		<email>nicolasbock@gentoo.org</email>
-		<name>Nicolas Bock</name>
-	</maintainer>
-	<maintainer type="project">
-		<email>sci@gentoo.org</email>
-		<name>Gentoo Science Project</name>
-	</maintainer>
-	<longdescription lang="en">
-Spglib is a C library for finding and handling crystal symmetries.
-</longdescription>
-	<upstream>
-		<remote-id type="sourceforge">downloads</remote-id>
-	</upstream>
-</pkgmetadata>
diff --git a/sci-libs/spglib/spglib-1.6.0.ebuild b/sci-libs/spglib/spglib-1.6.0.ebuild
deleted file mode 100644
index d851189cd..000000000
--- a/sci-libs/spglib/spglib-1.6.0.ebuild
+++ /dev/null
@@ -1,33 +0,0 @@
-# Copyright 1999-2014 Gentoo Foundation
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=5
-
-AUTOTOOLS_AUTORECONF=1
-
-inherit autotools-utils versionator
-
-MY_PV=$(get_version_component_range 1-2 ${PV})
-
-DESCRIPTION="Spglib is a C library for finding and handling crystal symmetries"
-HOMEPAGE="http://spglib.sourceforge.net/"
-SRC_URI="http://downloads.sourceforge.net/project/${PN}/${PN}/${PN}-${MY_PV}/${P}.tar.gz"
-
-LICENSE="BSD"
-SLOT="0"
-KEYWORDS="~amd64"
-IUSE="openmp"
-
-DEPEND=""
-RDEPEND="${DEPEND}"
-
-PATCHES=( "${FILESDIR}/${PN}-openmp.patch" )
-
-src_configure() {
-	local myconf=$(use_enable openmp)
-	econf ${myconf}
-}
-
-src_compile() {
-	default
-}
diff --git a/sci-libs/spglib/spglib-1.9.0.ebuild b/sci-libs/spglib/spglib-1.9.0.ebuild
deleted file mode 100644
index 48051aa82..000000000
--- a/sci-libs/spglib/spglib-1.9.0.ebuild
+++ /dev/null
@@ -1,36 +0,0 @@
-# Copyright 1999-2016 Gentoo Foundation
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=6
-
-inherit autotools eutils versionator
-
-MY_PV=$(get_version_component_range 1-2 ${PV})
-
-DESCRIPTION="Spglib is a C library for finding and handling crystal symmetries"
-HOMEPAGE="http://spglib.sourceforge.net/"
-SRC_URI="http://downloads.sourceforge.net/project/${PN}/${PN}/${PN}-${MY_PV}/${P}.tar.gz"
-
-LICENSE="BSD"
-SLOT="0"
-KEYWORDS="~amd64"
-IUSE="openmp"
-
-PATCHES=(
-	"${FILESDIR}/${P}-openmp.patch"
-)
-
-src_prepare() {
-	default
-	eautoreconf
-}
-
-src_configure() {
-	econf --disable-static \
-		$(use_enable openmp)
-}
-
-src_install() {
-	default
-	prune_libtool_files --all
-}
diff --git a/sci-libs/spyking-circus/Manifest b/sci-libs/spyking-circus/Manifest
new file mode 100644
index 000000000..d74a84da5
--- /dev/null
+++ b/sci-libs/spyking-circus/Manifest
@@ -0,0 +1 @@
+DIST spyking-circus-1.1.0.tar.gz 4822364 BLAKE2B e862cc40618db0dab45d0d8d2461a0e72b6ba442af7701ccb2af8c96afe4116715b5a8758670ac37b462fdfc5e5b2815a7ffb4d485c3d5bfec667fb6137a3b41 SHA512 87aa7f6c6efd1a419fd9394cc2e5467d4d8da96afdca46761df10215a1f5fd198e78a39cf75f4b0c5310b21ada9db831d2a14878c6ad0de37c86c63bd9ce4807
diff --git a/sci-libs/spyking-circus/metadata.xml b/sci-libs/spyking-circus/metadata.xml
new file mode 100644
index 000000000..89a208f6f
--- /dev/null
+++ b/sci-libs/spyking-circus/metadata.xml
@@ -0,0 +1,22 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
+<pkgmetadata>
+	<maintainer type="person">
+		<email>gentoo@chymera.eu</email>
+		<name>Horea Christian</name>
+	</maintainer>
+	<maintainer type="person">
+		<email>malfatti@disroot.org</email>
+		<name>T Malfatti</name>
+	</maintainer>
+	<longdescription lang="en">
+		SpyKING CIRCUS is a Python code to allow fast spike sorting on multi
+		channel recordings. A publication on the algorithm can be found at
+		https://elifesciences.org/articles/34518 . The software has been tested
+		on datasets coming from in vitro retina with 252 electrodes MEA, from in
+		vivo hippocampus with tetrodes, and in vivo and in vitro cortex data.
+	</longdescription>
+	<upstream>
+		<remote-id type="github">spyking-circus/spyking-circus</remote-id>
+	</upstream>
+</pkgmetadata>
diff --git a/sci-libs/spyking-circus/spyking-circus-1.1.0.ebuild b/sci-libs/spyking-circus/spyking-circus-1.1.0.ebuild
new file mode 100644
index 000000000..9b9233020
--- /dev/null
+++ b/sci-libs/spyking-circus/spyking-circus-1.1.0.ebuild
@@ -0,0 +1,37 @@
+# Copyright 1999-2022 Gentoo Authors
+# Distributed under the terms of the GNU General Public License v2
+
+EAPI=8
+
+PYTHON_COMPAT=( python3_10 )
+
+inherit distutils-r1
+
+DESCRIPTION="Fast spike sorting by template matching"
+HOMEPAGE="https://github.com/spyking-circus/spyking-circus/"
+SRC_URI="https://github.com/spyking-circus/spyking-circus/archive/${PV}.tar.gz -> ${P}.tar.gz"
+
+LICENSE="CeCILL-2"
+SLOT="0"
+KEYWORDS="~amd64"
+
+# Wants to run mpirun (and fails)
+RESTRICT="test"
+
+RDEPEND="
+	>=dev-python/blosc-1.8[${PYTHON_USEDEP}]
+	>=dev-python/colorama-0.4.1[${PYTHON_USEDEP}]
+	>=dev-python/cython-0.29.14[${PYTHON_USEDEP}]
+	>=dev-python/h5py-2.9.0[${PYTHON_USEDEP}]
+	>=dev-python/matplotlib-2.2.4[${PYTHON_USEDEP}]
+	>=dev-python/mpi4py-3.0.0[${PYTHON_USEDEP}]
+	>=dev-python/numpy-1.17.4[${PYTHON_USEDEP}]
+	>=dev-python/psutil-5.6.7[${PYTHON_USEDEP}]
+	dev-python/statsmodels[${PYTHON_USEDEP}]
+	>=dev-python/tqdm-4.40.0[${PYTHON_USEDEP}]
+	>=dev-python/scipy-1.3.1[${PYTHON_USEDEP}]
+"
+DEPEND="${RDEPEND}"
+
+distutils_enable_sphinx docs_sphinx --no-autodoc
+distutils_enable_tests --install pytest
diff --git a/sci-libs/starparse/Manifest b/sci-libs/starparse/Manifest
new file mode 100644
index 000000000..1f47416e5
--- /dev/null
+++ b/sci-libs/starparse/Manifest
@@ -0,0 +1 @@
+DIST starparse-0.9.tar.gz 339051 BLAKE2B 72fd956c5b5dc4d323df5b8dc5df90e90ff71595ab3017cd88db6ec68b19ff2ed1d36b6d6de5d12e691ef2401304fdc079b00a4da2604af0712bb2040ffde3d2 SHA512 7544e9bbda0f22ab038fc6b008f12f6c44dcbc9916f212adb4c0abde5ed3afc886074bff1db174a99e197bc90c281f4829b995cbc8053678ae033c7a7be8e218
diff --git a/sci-libs/starparse/files/starparse-9999-guile1.8.patch b/sci-libs/starparse/files/starparse-9999-guile1.8.patch
deleted file mode 100644
index 1d6e176b0..000000000
--- a/sci-libs/starparse/files/starparse-9999-guile1.8.patch
+++ /dev/null
@@ -1,60 +0,0 @@
---- src/guile-binding.c
-+++ src/guile-binding.c
-@@ -61,10 +61,10 @@
-   char* filter_string = NULL;
-   char* fname = "-";
- 
--  if (SCM_NFALSEP(filter_string_scm))
-+  if (scm_is_true(filter_string_scm))
-     filter_string = scm_to_locale_string(filter_string_scm);
- 
--  if (SCM_NFALSEP(fname_scm))
-+  if (scm_is_true(fname_scm))
-     fname = scm_to_locale_string(fname_scm);
-   
-   ship_item_cb = ship_item_scm;
---- src/Makefile.am
-+++ src/Makefile.am
-@@ -6,13 +6,10 @@
- libstarparse_la_SOURCES =\
- 	parser.y lexer.l starparse.h
- 
--libstarparse_la_CFLAGS =
--libstarparse_la_LDFLAGS = 
--
- if ENABLE_GUILE
- libstarparse_la_SOURCES += guile-binding.c guile-compat.h
--libstarparse_la_CFLAGS += @GUILE_CFLAGS@
--libstarparse_la_LDFLAGS += @GUILE_LDFLAGS@ -lpthread
-+libstarparse_la_CFLAGS = @GUILE_CFLAGS@
-+libstarparse_la_LIBADD = @GUILE_LIBS@ -lpthread
- endif
- 
- 
---- configure.ac
-+++ configure.ac
-@@ -10,18 +10,13 @@
- 
- AM_INIT_AUTOMAKE
- 
--AC_ARG_ENABLE(guile,
-+AC_ARG_ENABLE([guile],
- 	      AS_HELP_STRING([--enable-guile],
--                             [build bindings for guile scheme interpreter]),
--              USE_GUILE=$enable_guile,
--              USE_GUILE=yes)  # default value
--
--if test "x$USE_GUILE" = "xyes";
--then
--  GUILE_FLAGS
--fi
--
--AM_CONDITIONAL(ENABLE_GUILE, test "x$USE_GUILE" = "xyes")
-+                             [build bindings for guile scheme interpreter]))
-+AS_IF([test "x$enable_guile" = "xyes"], [
-+  PKG_CHECK_MODULES([GUILE], [guile-1.8])
-+])
-+AM_CONDITIONAL(ENABLE_GUILE, test "x$enable_guile" = "xyes")
- 
- AC_CONFIG_FILES([Makefile
-                  starparse-env
diff --git a/sci-libs/starparse/starparse-0.9.ebuild b/sci-libs/starparse/starparse-0.9.ebuild
new file mode 100644
index 000000000..a18173e1b
--- /dev/null
+++ b/sci-libs/starparse/starparse-0.9.ebuild
@@ -0,0 +1,25 @@
+# Copyright 1999-2021 Gentoo Authors
+# Distributed under the terms of the GNU General Public License v2
+
+EAPI=7
+
+DESCRIPTION="Library for parsing NMR star files (peak-list format) and CIF files"
+HOMEPAGE="http://burrow-owl.sourceforge.net/"
+SRC_URI="https://downloads.sourceforge.net/project/burrow-owl/starparse/${PV}/${P}.tar.gz"
+
+LICENSE="GPL-2"
+SLOT="0"
+KEYWORDS="~amd64"
+
+IUSE="guile test"
+RESTRICT="!test? ( test )"
+
+REQUIRED_USE="test? ( guile )"
+
+RDEPEND="guile? ( dev-scheme/guile:12 )"
+DEPEND="${RDEPEND}"
+BDEPEND="virtual/pkgconfig"
+
+src_configure() {
+	econf $(use_enable guile)
+}
diff --git a/sci-libs/starparse/starparse-9999.ebuild b/sci-libs/starparse/starparse-9999.ebuild
deleted file mode 100644
index 4024c09f8..000000000
--- a/sci-libs/starparse/starparse-9999.ebuild
+++ /dev/null
@@ -1,30 +0,0 @@
-# Copyright 1999-2014 Gentoo Foundation
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=5
-
-AUTOTOOLS_AUTORECONF=yes
-
-inherit autotools-utils git-r3
-
-DESCRIPTION="Library for parsing NMR star files (peak-list format) and CIF files"
-HOMEPAGE="http://burrow-owl.sourceforge.net/"
-EGIT_REPO_URI="git://burrow-owl.git.sourceforge.net/gitroot/burrow-owl/starparse"
-
-LICENSE="GPL-2"
-SLOT="0"
-KEYWORDS=""
-IUSE="guile static-libs test"
-
-REQUIRED_USE="test? ( guile )"
-
-RDEPEND="guile? ( dev-scheme/guile:12 )"
-DEPEND="${RDEPEND}
-	virtual/pkgconfig"
-
-PATCHES=( "${FILESDIR}"/${P}-guile1.8.patch )
-
-src_configure() {
-	local myeconfargs=( $(use_enable guile) )
-	autotools-utils_src_configure
-}
diff --git a/sci-libs/superlu_dist/Manifest b/sci-libs/superlu_dist/Manifest
deleted file mode 100644
index 47bed7c23..000000000
--- a/sci-libs/superlu_dist/Manifest
+++ /dev/null
@@ -1 +0,0 @@
-DIST superlu_dist_3.3.tar.gz 2146029 BLAKE2B d16942c6e879c1137c1783394bc2dd91db5d20bb26ccf35f03da58a3b44c71b4e93acca09438e4d4cb56c312de1418e412a158d9417f8c5c27c3c30dddfca66d SHA512 673f5a51a39531d5e59a274dfe3cef95a619fdd3fbe003e306376d12f78e3893813c3718befc1360f905344bb5a68cc9c14d5e3790cbfad7b6d4261cf2c8c170
diff --git a/sci-libs/superlu_dist/files/superlu_dist-3.3-duplicate-symbols.patch b/sci-libs/superlu_dist/files/superlu_dist-3.3-duplicate-symbols.patch
deleted file mode 100644
index b27647d81..000000000
--- a/sci-libs/superlu_dist/files/superlu_dist-3.3-duplicate-symbols.patch
+++ /dev/null
@@ -1,70 +0,0 @@
-diff -Nur SRC.orig/dcomplex.c SRC/dcomplex.c
---- SRC.orig/dcomplex.c	2013-07-15 13:31:52.013335511 -0700
-+++ SRC/dcomplex.c	2013-07-15 13:41:52.346722312 -0700
-@@ -11,6 +11,7 @@
- 
- #include <math.h>
- #include <stdio.h>
-+#include <stdlib.h>
- #include "dcomplex.h"
- 
- 
-diff -Nur SRC.orig/dreadtriple.c SRC/dreadtriple.c
---- SRC.orig/dreadtriple.c	2013-07-15 13:31:52.015335487 -0700
-+++ SRC/dreadtriple.c	2013-07-15 13:32:57.202697327 -0700
-@@ -150,21 +150,4 @@
- }
- 
- 
--void dreadrhs(int m, double *b)
--{
--    FILE *fp, *fopen();
--    int i, j;
--
--    if ( !(fp = fopen("b.dat", "r")) ) {
--        fprintf(stderr, "dreadrhs: file does not exist\n");
--	exit(-1);
--    }
--    for (i = 0; i < m; ++i)
--      fscanf(fp, "%lf\n", &b[i]);
--      /*fscanf(fp, "%d%lf\n", &j, &b[i]);*/
--    /*        readpair_(j, &b[i]);*/
--
--    fclose(fp);
--}
--
- 
-diff -Nur SRC.orig/xerbla.c SRC/xerbla.c
---- SRC.orig/xerbla.c	2013-07-15 13:31:52.016335478 -0700
-+++ SRC/xerbla.c	2013-07-15 13:51:47.522154563 -0700
-@@ -8,6 +8,7 @@
-        September 30, 1994   
- </pre> 
- */
-+#include <stdio.h>
- #include "Cnames.h"
- 
- /* Subroutine */ 
-diff -Nur SRC.orig/zreadtriple.c SRC/zreadtriple.c
---- SRC.orig/zreadtriple.c	2013-07-15 13:31:52.014335499 -0700
-+++ SRC/zreadtriple.c	2013-07-15 13:33:27.409864866 -0700
-@@ -149,19 +149,5 @@
- }
- 
- 
--void zreadrhs(int m, doublecomplex *b)
--{
--    FILE *fp, *fopen();
--    int i, j;
--
--    if ( !(fp = fopen("b.dat", "r")) ) {
--        fprintf(stderr, "zreadrhs: file does not exist\n");
--	exit(-1);
--    }
--    for (i = 0; i < m; ++i)
--      fscanf(fp, "%lf%lf\n", &(b[i].r), &(b[i].i));
--
--    fclose(fp);
--}
- 
- 
diff --git a/sci-libs/superlu_dist/metadata.xml b/sci-libs/superlu_dist/metadata.xml
deleted file mode 100644
index 0bd32bba5..000000000
--- a/sci-libs/superlu_dist/metadata.xml
+++ /dev/null
@@ -1,26 +0,0 @@
-<?xml version="1.0" encoding="UTF-8"?>
-<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
-<pkgmetadata>
-	<maintainer type="project">
-		<email>sci@gentoo.org</email>
-		<name>Gentoo Science Project</name>
-	</maintainer>
-	<longdescription lang="en">
-SuperLU is a general purpose library for the direct solution of
-large, sparse, nonsymmetric systems of linear equations on high
-performance machines. The library is written in C and is callable
-from either C or Fortran. The library routines will perform an LU
-decomposition with partial pivoting and triangular system solves
-through forward and back substitution. The LU factorization routines
-can handle non-square matrices but the triangular solves are
-performed only for square matrices. The matrix columns may be
-preordered (before factorization) either through library or user
-supplied routines. This preordering for sparsity is completely
-separate from the factorization. Working precision iterative
-refinement subroutines are provided for improved backward
-stability. Routines are also provided to equilibrate the system,
-estimate the condition number, calculate the relative backward
-error, and estimate error bounds for the refined solutions.
-This is the distributed version (MPI based).
-</longdescription>
-</pkgmetadata>
diff --git a/sci-libs/superlu_dist/superlu_dist-3.3.ebuild b/sci-libs/superlu_dist/superlu_dist-3.3.ebuild
deleted file mode 100644
index 4af8d9b3b..000000000
--- a/sci-libs/superlu_dist/superlu_dist-3.3.ebuild
+++ /dev/null
@@ -1,81 +0,0 @@
-# Copyright 1999-2014 Gentoo Foundation
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=5
-
-inherit eutils toolchain-funcs
-
-MYPN=SuperLU_DIST
-
-DESCRIPTION="MPI distributed sparse LU factorization library"
-HOMEPAGE="http://crd.lbl.gov/~xiaoye/SuperLU/"
-SRC_URI="${HOMEPAGE}/${PN}_${PV}.tar.gz"
-
-LICENSE="BSD"
-SLOT="0"
-KEYWORDS="~amd64 ~x86 ~amd64-linux ~x86-linux"
-IUSE="doc examples static-libs"
-
-RDEPEND="
-	sci-libs/parmetis
-	virtual/mpi"
-DEPEND="${RDEPEND}
-	virtual/pkgconfig"
-
-S="${WORKDIR}/${MYPN}_${PV}"
-
-src_prepare() {
-	epatch "${FILESDIR}"/${P}-duplicate-symbols.patch
-}
-
-src_configure() {
-	sed -i \
-		-e 's/^\(PLAT\s*=\).*/\1/' \
-		-e "s:^\(CC\s*=\).*:\1 mpicc:" \
-		-e "/CFLAGS/s:-fast -Mipa=fast,safe:${CFLAGS} \$(PIC):" \
-		-e "s:^\(PREDEFS\s*=\).*:\1 ${CPPFLAGS} -DUSE_VENDOR_BLAS \$(CTHREADS)$:" \
-		-e "s:^\(NOOPTS\s*=.*\):\1 \$(PIC):" \
-		-e "s:^\(FORTRAN\s*=\).*:\1 mpif77:" \
-		-e "s:^\(F90FLAGS\s*=\).*:\1 ${FFLAGS} \$(PIC):" \
-		-e "s:^\(ARCH\s*=\).*:\1 $(tc-getAR):" \
-		-e "s:^\(RANLIB\s*=\).*:\1 $(tc-getRANLIB):" \
-		-e "s:^\(LOADER\s*=\).*:\1 mpicc:" \
-		-e "s:^\(LOADOPTS\s*=\).*:\1 ${LDFLAGS} \$(LDTHREADS):" \
-		-e '/^FLIBS/d' \
-		-e "s:^\(METISLIB\s*=\).*:\1 -lmetis:" \
-		-e "s:^\(PARMETISLIB\s*=\).*:\1 -lparmetis:" \
-		-e "s:^\(BLASLIB\s*=\).*:\1 $($(tc-getPKG_CONFIG) --libs blas):" \
-		-e "s:^\(DSUPERLULIB\s*=\).*:\1 ../lib/libsuperlu_dist.a:" \
-		make.inc || die
-	SONAME=libsuperlu_dist.so.0
-	sed -i \
-		-e 's|../make.inc|make.inc|' \
-		-e "s|../SRC|${EPREFIX}/usr/include/${PN}|" \
-		-e '/:.*$(DSUPERLULIB)/s|../lib/$(DSUPERLULIB)||g' \
-		-e 's|../lib/$(DSUPERLULIB)|-lsuperlu_dist|g' \
-		EXAMPLE/Makefile || die
-}
-
-src_compile() {
-	emake superlulib \
-		PIC="-fPIC" ARCH="echo" ARCHFLAGS="" RANLIB="echo"
-	$(tc-getCC) ${LDFLAGS} ${LDTHREADS} -shared -Wl,-soname=${SONAME} SRC/*.o \
-		$($(tc-getPKG_CONFIG) --libs blas) -lm -o lib/${SONAME} || die
-	ln -s ${SONAME} lib/libsuperlu_dist.so || die
-
-	use static-libs && rm -f SRC/*.o &&	emake superlulib \
-		PIC="" ARCH="$(tc-getAR)" ARCHFLAGS="cr" RANLIB="$(tc-getRANLIB)"
-}
-
-src_install() {
-	dolib.so lib/*so*
-	use static-libs && dolib.a lib/*.a
-	insinto /usr/include/${PN}
-	doins SRC/*h
-	dodoc README
-	use doc && dodoc DOC/ug.pdf
-	if use examples; then
-		insinto /usr/share/doc/${PF}/examples
-		doins -r EXAMPLE/* make.inc
-	fi
-}
diff --git a/sci-libs/symengine/Manifest b/sci-libs/symengine/Manifest
deleted file mode 100644
index aba2a0499..000000000
--- a/sci-libs/symengine/Manifest
+++ /dev/null
@@ -1 +0,0 @@
-DIST symengine-0.1.0.tar.gz 373272 SHA256 daba3ba0ae91983a772f66bf755b1953c354fe6dc353588b23705d9a79b011fc SHA512 6b1bd6f7a1d04f3af993d38449431e270b257f8cc78a4f14c762b973f37e988c6da13a48d82fd8de55ce271627272760ef73f89efc8a8a2c229d637e22a89df1 WHIRLPOOL e838d93c3eb71ed1aef51e0eb9c5423431136bc7be2886ac1bc8c3d31831e05a319cafeaf36c9fdea8b913eefbe3dfb6a377468e56c74e5e62cb882844377d24
diff --git a/sci-libs/symengine/metadata.xml b/sci-libs/symengine/metadata.xml
deleted file mode 100644
index 5f5840260..000000000
--- a/sci-libs/symengine/metadata.xml
+++ /dev/null
@@ -1,18 +0,0 @@
-<?xml version="1.0" encoding="UTF-8"?>
-<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
-<pkgmetadata>
-	<maintainer type="person">
-		<email>mschu.dev@gmail.com</email>
-		<name>Michael Schubert</name>
-	</maintainer>
-	<maintainer type="project">
-		<email>sci-mathematics@gentoo.org</email>
-		<name>Gentoo Mathematics Project</name>
-	</maintainer>
-	<upstream>
-		<remote-id type="github">sympy/symengine</remote-id>
-	</upstream>
-	<use>
-		<flag name="boost">Add support for boost (<pkg>dev-libs/boost</pkg>)</flag>
-	</use>
-</pkgmetadata>
diff --git a/sci-libs/symengine/symengine-0.1.0.ebuild b/sci-libs/symengine/symengine-0.1.0.ebuild
deleted file mode 100644
index 658f6700a..000000000
--- a/sci-libs/symengine/symengine-0.1.0.ebuild
+++ /dev/null
@@ -1,59 +0,0 @@
-# Copyright 1999-2015 Gentoo Foundation
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=5
-
-PYTHON_COMPAT=( python2_7 )
-
-inherit cmake-utils python-single-r1
-
-DESCRIPTION="Fast symbolic manipulation library, written in C++"
-HOMEPAGE="https://github.com/sympy/symengine"
-SRC_URI="https://github.com/sympy/${PN}/archive/v${PV}.tar.gz -> ${P}.tar.gz"
-
-LICENSE="MIT"
-SLOT="0"
-KEYWORDS="~amd64 ~x86 ~amd64-linux ~x86-linux"
-IUSE="boost openmp python threads"
-REQUIRED_USE="
-	python? ( ${PYTHON_REQUIRED_USE} )
-	?? ( openmp threads )"
-
-RDEPEND="
-	dev-libs/jemalloc
-	boost? ( dev-libs/boost )
-	python? ( dev-python/numpy[${PYTHON_USEDEP}] )"
-DEPEND="${RDEPEND}
-	python? (
-		dev-python/cython[${PYTHON_USEDEP}]
-		dev-python/setuptools[${PYTHON_USEDEP}] )"
-
-CMAKE_BUILD_TYPE=Release
-
-pkg_pretend() {
-	if use openmp && [[ ${MERGE_TYPE} != binary ]]; then
-		if [[ $(tc-getCC) == *gcc ]] && ! tc-has-openmp; then
-			ewarn "OpenMP is not available in your current selected gcc"
-			die "need openmp capable gcc"
-		fi
-	fi
-}
-
-src_configure() {
-	local mycmakeargs=(
-		-DCMAKE_INSTALL_PREFIX:PATH="${EPREFIX}"/usr
-		$(cmake-utils_use_with boost)
-		$(cmake-utils_use_with openmp)
-		$(cmake-utils_use_with python)
-	)
-
-	if use threads; then
-		mycmakeargs+=(
-			-DWITH_TCMALLOC:BOOL=ON
-			-DWITH_PTHREAD:BOOL=ON
-			-DWITH_SYMENGINE_THREAD_SAFE:BOOL=ON
-		)
-	fi
-
-	cmake-utils_src_configure
-}
diff --git a/sci-libs/symengine/symengine-9999.ebuild b/sci-libs/symengine/symengine-9999.ebuild
deleted file mode 100644
index 3448694d2..000000000
--- a/sci-libs/symengine/symengine-9999.ebuild
+++ /dev/null
@@ -1,51 +0,0 @@
-# Copyright 1999-2015 Gentoo Foundation
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=5
-
-inherit git-r3 cmake-utils
-
-DESCRIPTION="Fast symbolic manipulation library, written in C++"
-HOMEPAGE="https://github.com/sympy/symengine"
-SRC_URI=""
-EGIT_REPO_URI="https://github.com/sympy/symengine.git"
-
-LICENSE="MIT"
-SLOT="0"
-KEYWORDS="~amd64 ~x86 ~amd64-linux ~x86-linux"
-IUSE="boost openmp threads"
-REQUIRED_USE="?? ( openmp threads )"
-
-RDEPEND="
-	dev-libs/jemalloc
-	boost? ( dev-libs/boost )"
-DEPEND="${RDEPEND}"
-
-CMAKE_BUILD_TYPE=Release
-
-pkg_pretend() {
-	if use openmp && [[ ${MERGE_TYPE} != binary ]]; then
-		if [[ $(tc-getCC) == *gcc ]] && ! tc-has-openmp; then
-			ewarn "OpenMP is not available in your current selected gcc"
-			die "need openmp capable gcc"
-		fi
-	fi
-}
-
-src_configure() {
-	local mycmakeargs=(
-		-DCMAKE_INSTALL_PREFIX:PATH="${EPREFIX}"/usr
-		$(cmake-utils_use_with boost)
-		$(cmake-utils_use_with openmp)
-	)
-
-	if use threads; then
-		mycmakeargs+=(
-			-DWITH_TCMALLOC:BOOL=ON
-			-DWITH_PTHREAD:BOOL=ON
-			-DWITH_SYMENGINE_THREAD_SAFE:BOOL=ON
-		)
-	fi
-
-	cmake-utils_src_configure
-}
diff --git a/sci-libs/symmetrica/Manifest b/sci-libs/symmetrica/Manifest
deleted file mode 100644
index cfcdc961d..000000000
--- a/sci-libs/symmetrica/Manifest
+++ /dev/null
@@ -1 +0,0 @@
-DIST symmetrica-2.0.tar.gz 720154 BLAKE2B b9c5ae175128e9f79527c6033f5d7d2cef005e11b830b772f45be4f48eaf53af78dc1a7fd83c67b6afac650ea6e581977b10dff9fd2ed09ad565a5eb012ba51e SHA512 48be02bc17311003741c5d87df53e8168635d45cbe2e0890b465e41e27a934f882e876d03f8b0910305daefb05c298386c3641bb59302397ede34f45f8e41e36
diff --git a/sci-libs/symmetrica/files/makefile b/sci-libs/symmetrica/files/makefile
deleted file mode 100644
index c3be8aa7c..000000000
--- a/sci-libs/symmetrica/files/makefile
+++ /dev/null
@@ -1,53 +0,0 @@
-OBJS=bar.o bi.o boe.o bruch.o classical.o de.o di.o ff.o galois.o ga.o gra.o hash.o hiccup.o \

-	io.o ko.o list.o lo.o ma.o mee.o mem.o mes.o mhe.o mhh.o mhm.o mhp.o mhs.o mmm.o mms.o \

-	mod_dg_sbd.o mo.o mpp.o mps.o mse.o msh.o msm.o mss.o muir.o na.o nb.o nc.o nu.o part.o pee.o \

-	peh.o pem.o perm.o pes.o phe.o phh.o phm.o phs.o plet.o pme.o pmh.o poly.o ppe.o pph.o ppm.o \

-	ppp.o pps.o pr.o pse.o psh.o psm.o pss.o rest.o rh.o sab.o sb.o sc.o sr.o ta.o teh.o tem.o \

-	tep.o tes.o the.o thm.o thp.o ths.o tme.o tmh.o tmp.o tms.o tpe.o tph.o tpm.o tps.o tse.o \

-	tsh.o tsm.o tsp.o vc.o zo.o zykelind.o zyk.o

-SHOBJS=bar.lo bi.lo boe.lo bruch.lo classical.lo de.lo di.lo ff.lo galois.lo ga.lo gra.lo hash.lo hiccup.lo \

-	io.lo ko.lo list.lo lo.lo ma.lo mee.lo mem.lo mes.lo mhe.lo mhh.lo mhm.lo mhp.lo mhs.lo mmm.lo mms.lo \

-	mod_dg_sbd.lo mo.lo mpp.lo mps.lo mse.lo msh.lo msm.lo mss.lo muir.lo na.lo nb.lo nc.lo nu.lo part.lo pee.lo \

-	peh.lo pem.lo perm.lo pes.lo phe.lo phh.lo phm.lo phs.lo plet.lo pme.lo pmh.lo poly.lo ppe.lo pph.lo ppm.lo \

-	ppp.lo pps.lo pr.lo pse.lo psh.lo psm.lo pss.lo rest.lo rh.lo sab.lo sb.lo sc.lo sr.lo ta.lo teh.lo tem.lo \

-	tep.lo tes.lo the.lo thm.lo thp.lo ths.lo tme.lo tmh.lo tmp.lo tms.lo tpe.lo tph.lo tpm.lo tps.lo tse.lo \

-	tsh.lo tsm.lo tsp.lo vc.lo zo.lo zykelind.lo zyk.lo

-LIBS=-lm

-CC?=gcc

-CFLAGS?=-O1

-FPICFLAG?=-fPIC

-VERSION=2.0

-DIRNAME=symmetrica-$(VERSION)

-TARGETS=libsymmetrica.a libsymmetrica.so

-PREFIX?=/usr

-

-all: $(TARGETS)

-

- .c.o:

-	$(CC) -c $(CFLAGS) -DFAST -DALLTRUE $<

-

-.SUFFIXES: .lo

- .c.lo:

-	$(CC) -c $(CFLAGS) $(FPICFLAG) -DFAST -DALLTRUE -o $@ $<

-

-

-test: test.c $(OBJS)

-	$(CC) -DALLTRUE -DFAST test.c $(OBJS) $(LIBS) -o test

-

-libsymmetrica.a: $(OBJS)

-	ar crs $@ $(OBJS)

-	ranlib $@

-

-libsymmetrica.so: $(SHOBJS)

-	$(CC) $(CFLAGS) $(FPICFLAG) -shared -Wl,-soname,lib$(DIRNAME).so $(LIBS) -o lib$(DIRNAME).so $(SHOBJS)

-	ln -s lib$(DIRNAME).so $@

-

-install: all

-	mkdir -p $(DESTDIR)$(PREFIX)/lib

-	install -p lib$(DIRNAME).so libsymmetrica.a $(DESTDIR)$(PREFIX)/lib

-	ln -s lib$(DIRNAME).so $(DESTDIR)$(PREFIX)/lib/libsymmetrica.so

-	mkdir -p $(DESTDIR)$(PREFIX)/include/symmetrica

-	install -p def.h macro.h $(DESTDIR)$(PREFIX)/include/symmetrica/

-

-clean:

-	rm -f $(OBJS) $(SHOBJS) $(TARGETS) test

diff --git a/sci-libs/symmetrica/files/symmetrica-2.0-banner.patch b/sci-libs/symmetrica/files/symmetrica-2.0-banner.patch
deleted file mode 100644
index ec4aa2000..000000000
--- a/sci-libs/symmetrica/files/symmetrica-2.0-banner.patch
+++ /dev/null
@@ -1,11 +0,0 @@
---- src/de.c
-+++ b/de.c
-@@ -24,7 +24,7 @@
- OP cons_negeins;/* global INTEGER variable -1 */
- OP cons_null;   /* global INTEGER variable 0 */
- FILE *texout;   /* global variable for texoutput */
--INT no_banner = FALSE; /* AK 281293 */
-+INT no_banner = TRUE; /* AK 281293 */
- INT no_mem_check=TRUE; /* AK 100893 */
- INT english_tableau=FALSE; /* AK 290995 */
- 
diff --git a/sci-libs/symmetrica/files/symmetrica-2.0-freeing_errors.patch b/sci-libs/symmetrica/files/symmetrica-2.0-freeing_errors.patch
deleted file mode 100644
index 935cc6ab5..000000000
--- a/sci-libs/symmetrica/files/symmetrica-2.0-freeing_errors.patch
+++ /dev/null
@@ -1,39 +0,0 @@
-Patch imported from sage-on-gentoo.
---- src/bruch.c
-+++ b/bruch.c
-@@ -975,14 +975,16 @@
-     ggterg = ggt_i(S_B_UI(bruch),S_B_OI(bruch));
- 
-     if (ggterg == S_B_UI(bruch)) {
-+        INT tmp = S_B_OI(bruch);
-         freeself_bruch(bruch);
--        M_I_I(S_B_OI(bruch) / ggterg,bruch);
-+        M_I_I(tmp / ggterg,bruch);
-         goto ende;
-         }
- 
-     if (-ggterg == S_B_UI(bruch)) {
-+        INT tmp = S_B_OI(bruch);
-         freeself_bruch(bruch);
--        M_I_I(- S_B_OI(bruch) / ggterg,bruch);
-+        M_I_I(- tmp / ggterg,bruch);
-         goto ende;
-         }
- 
-@@ -1032,12 +1034,14 @@
- 
-     if (S_O_K(S_B_U(bruch)) == INTEGER)
-         if (S_B_UI(bruch) == 1) { 
-+            INT tmp = S_B_OI(bruch);
-             freeself_bruch(bruch);
--            M_I_I(S_B_OI(bruch),bruch); 
-+            M_I_I(tmp,bruch); 
-             goto ende; }
-         else if (S_B_UI(bruch) == -1) { 
-+            INT tmp = S_B_OI(bruch);
-             freeself_bruch(bruch);
--            M_I_I( - S_B_OI(bruch),bruch); 
-+            M_I_I( - tmp,bruch); 
-             goto ende; }
-     if (NEGP(S_B_O(bruch)) && NEGP(S_B_U(bruch)))
-         {
diff --git a/sci-libs/symmetrica/files/symmetrica-2.0-function_names.patch b/sci-libs/symmetrica/files/symmetrica-2.0-function_names.patch
deleted file mode 100644
index 66a156cc1..000000000
--- a/sci-libs/symmetrica/files/symmetrica-2.0-function_names.patch
+++ /dev/null
@@ -1,329 +0,0 @@
-Patch imported from sage-on-gentoo.
---- a/bar.c
-+++ b/bar.c
-@@ -237,7 +237,7 @@
-     g = callocobject();
-     e = S_V_I(a,0L);
-     f = S_V_I(a,1L);
--    erg += sum(f,g);
-+    erg += sym_sum(f,g);
-     j=0L;
-     for (i=0L;i<S_V_LI(e);i++)
-         j += S_V_II(e,i)*(i+1L);
-@@ -427,7 +427,7 @@
-     for (i=0L;i<S_V_LI(b);i++)
-         erg += kranztypus_to_matrix(S_V_I(c,i),S_V_I(b,i));
-     erg += freeall(c);
--    erg += sort(b); /* AK 130592 */
-+    erg += sym_sort(b); /* AK 130592 */
-     ENDR("makevectorof_class_bar");
- }
- 
-@@ -615,7 +615,7 @@
-     c = callocobject();
-     d = callocobject();
-     erg += lehmercode_bar(a,c);
--    erg += sum(S_V_I(c,1L),b);
-+    erg += sym_sum(S_V_I(c,1L),b);
-     for(i=0L;i<S_P_LI(a);i++)
-         {
-         if (S_V_II(S_V_I(c,0L),i) == 1L)
---- a/def.h
-+++ b/def.h
-@@ -3105,7 +3105,7 @@
- extern INT so_character ();
- extern INT so_dimension ();
- extern OBJECTKIND s_o_k();
--extern INT sort();
-+extern INT sym_sort();
- extern INT sort_rows_tableaux_apply();
- extern INT sort_vector();
- extern OBJECTSELF s_o_s();
-@@ -3271,7 +3271,7 @@
- extern INT sub_part_part();
- extern INT substitute_one_matrix ();
- extern INT substitute_one_monopoly ();
--extern INT sum();
-+extern INT sym_sum();
- extern INT sum_integervector();
- extern INT sum_matrix();
- extern INT sum_vector();
---- a/di.c
-+++ b/di.c
-@@ -1355,7 +1355,7 @@
- 				m_il_nv(0L,weight_watcher);
- 				m_il_nv(0L,perm_vec);
- 				copy(S_V_I(FP,0L),fix);
--				sort(fix);
-+				sym_sort(fix);
- 
- 				get_perm(hweight,p,b,S_I_I(n),S_I_I(m),0L,
- 						 perm_vec,weight_watcher,fix);
-@@ -1502,7 +1502,7 @@
- 	if(ind == m)
- 	{
- 		mult_perm_fix(p,fix,hfix);
--		sort(hfix);
-+		sym_sort(hfix);
- 		if(!hfix_in_ww(hfix,ww))
- 		{
- 			inc(ww);
---- a/ga.c
-+++ b/ga.c
-@@ -632,7 +632,7 @@
-     else if (what == 0L)
-         erg += vertikal_sum(S_V_L(a),c);
-     erg += copy(a,d);
--    erg += sort(d);
-+    erg += sym_sort(d);
-     erg += m_il_p(S_V_II(d,S_V_LI(d)-1L),e); /* identitaet */
-     for (i=0L,k=0L,j=S_V_LI(d);i<S_P_LI(e);i++)
-         if (i+1L == S_V_II(d,k) )
-@@ -722,7 +722,7 @@
- 
-     j=0L;
-     erg += append(h,g,h2); 
--    erg += sort(h2);
-+    erg += sym_sort(h2);
-     for (i=0L;i<S_V_LI(g);i++)
-         {
-         erg += m_i_i(S_V_II(g,i),S_P_I(a,j));
---- a/galois.c
-+++ b/galois.c
-@@ -758,7 +758,7 @@
- 		}
-         }
-     FREEALL2(v,nv);
--    sort(res);
-+    sym_sort(res);
-     }
-     S3R(k,phg_c,phg_d,"all_points_phg_store",res);
-     ENDR("all_points");
---- a/macro.h
-+++ b/macro.h
-@@ -1,6 +1,8 @@
- /* file: macro.h symmetrica source code */
- #ifndef MACRO_H
- 
-+#include "string.h"
-+
- #ifdef SYMMAGMA
- #define SYM_MALLOC(a) mem_malloc(a)
- #else
- #define C_O_K(a,b) ((a)->ob_kind = (OBJECTKIND)(b))
---- a/nc.c
-+++ b/nc.c
-@@ -204,7 +204,7 @@
-     erg += mult(S_NC_C(a),S_NC_C(b),d);
-     erg += m_gl_co(S_NC_GL(a),e);
-     erg += mult_apply(e,d);
--    erg += sum(d,e);
-+    erg += sym_sum(d,e);
-     erg += m_gl_go(S_NC_GL(a),d);
-     erg += div(e,d,c);
-     erg += freeall(e);
-@@ -617,7 +617,7 @@
-         erg += mult_nc_kranz(c,a,e);
-         erg += mult(S_V_I(e,1L),f,c);
-         erg += div(c,g,c);
--        erg += sum(c,S_V_I(S_NC_C(b),S_I_I(d)));
-+        erg += sym_sum(c,S_V_I(S_NC_C(b),S_I_I(d)));
-     }
-     erg += freeall(c); 
-     erg += freeall(d); 
-@@ -712,7 +712,7 @@
-     for(j = 0L; j<S_V_LI(c);j++) {
-         kranztypus_to_matrix(S_V_I(c,j),S_V_I(a,j)); 
-     }
--    sort(a);
-+    sym_sort(a);
-     freeall(f); freeall(h); freeall(c);
-     return OK;
- }
-@@ -739,7 +739,7 @@
-         kranztypus_to_matrix(S_V_I(c,j),S_V_I(h,j)); 
-         }
-     
--    sort(h); 
-+    sym_sort(h); 
-     m_l_v(S_V_L(h),a);
-     for(j = 0L; j<S_V_LI(c);j++) {
-         typusorder(S_V_I(h,j), zb, za, S_V_I(a,j), f);
-@@ -789,7 +789,7 @@
-         erg += kranztypus_to_matrix(S_V_I(c,j),S_V_I(h,j)); 
-     }
-     
--    erg += sort(h);
-+    erg += sym_sort(h);
-     erg += typusorder(S_V_I(h,S_I_I(i)), zb, za, a, f);
-     erg += freeall(f); 
-     erg += freeall(c); 
---- a/nu.c
-+++ b/nu.c
-@@ -531,13 +531,13 @@
-     ENDR("add");
- }
- 
--INT sort(a) OP a;
-+INT sym_sort(a) OP a;
- /* sortiert das object in aufsteigender reihenfolge AK 270787 */
- /* AK 160986 */ /* AK 280689 V1.0 */ /* AK 050390 V1.1 */
- /* AK 070891 V1.3 */
- {
-     INT erg = OK;
--    EOP("sort(1)",a);
-+    EOP("sym_sort(1)",a);
- 
-     switch(S_O_K(a))
-     {
-@@ -547,9 +547,9 @@
-         erg += sort_vector(a);break;
- #endif /* VECTORTRUE */
-     default:
--        erg += WTO("sort",a); break;
-+        erg += WTO("sym_sort",a); break;
-     };
--    ENDR("sort");
-+    ENDR("sym_sort");
- }
- 
- INT length(a,d) OP a,d;
-@@ -641,7 +641,7 @@
-     ENDR("content");
- }
- 
--INT sum(a,res) OP a,res;
-+INT sym_sum(a,res) OP a,res;
- /* AK 280689 V1.0 */ /* AK 050390 V1.1 */ /* AK 120391 V1.2 */
- /* AK 140891 V1.3 */
- /* AK 170298 V2.0 */
-@@ -649,7 +649,7 @@
-     INT erg = OK;
-     COP("sum(1)",a);
-     COP("sum(2)",res);
--    CE2(a,res,sum);
-+    CE2(a,res,sym_sum);
- 
-     switch(S_O_K(a))
-     {
-@@ -680,7 +680,7 @@
-         erg += WTO("sum",a); break;
-     };
- 
--    ENDR("sum");
-+    ENDR("sym_sum");
- }
- 
- 
---- a/part.c
-+++ b/part.c
-@@ -347,7 +347,7 @@
-     if (a == b) { /* a := a+a */
-         if (S_PA_K(a) == VECTOR) {
-             erg += append_apply_vector(S_PA_S(a),S_PA_S(b));
--            erg += sort(S_PA_S(a));
-+            erg += sym_sort(S_PA_S(a));
-             goto endr_ende;
-         }
-         else if (S_PA_K(a) == EXPONENT) {
-@@ -406,7 +406,7 @@
-             k=S_PA_LI(b)-1;
- /*
-             erg += append_apply_vector(S_PA_S(a),S_PA_S(b));
--            erg += sort(S_PA_S(a));
-+            erg += sym_sort(S_PA_S(a));
- */
-             inc_vector_co(S_PA_S(a),S_PA_LI(b));
-             for (j=S_PA_LI(a)-1;j>=0;j--)
---- a/perm.c
-+++ b/perm.c
-@@ -833,9 +833,9 @@
-     /* s = Anzahl der spalten */
-         
-     s = S_V_LI(S_V_I(a,0L));
--    sum(S_V_I(a,0L),summe);/* composition ist vector */
-+    sym_sum(S_V_I(a,0L),summe);/* composition ist vector */
-     z = S_I_I(summe);
--    FREEALL(summe); 
-+    FREEALL(summe);
-     m_ilih_nm(s,z,b); 
-     C_O_K(b,KRANZTYPUS);
-     for (i=0L;i<s;i++)
-@@ -1114,7 +1114,7 @@
-         erg += kranztypus_to_matrix(S_V_I(c,i),S_V_I(h,i)); 
-     }
-     
--    erg += sort(h);
-+    erg += sym_sort(h);
- 
-     erg += chartafel(b,ct);
- 
-@@ -1926,7 +1926,7 @@
-     OP c;
-     c = CALLOCOBJECT();
-     erg += lehmercode_permutation(a,c); /*result is a vector */
--    erg += sum(c,b); 
-+    erg += sym_sum(c,b); 
-     FREEALL(c);
-     }
-     ENDR("numberof_inversionen");
-@@ -2364,7 +2364,7 @@
-     COP("rz_lehmercode(2)",b);
- 
-     zw = callocobject();
--    erg += sum(lc,zw); 
-+    erg += sym_sum(lc,zw); 
-     if (NULLP(zw)) 
-         {
-         erg += m_il_integervector((INT)0,b);
---- a/rest.c
-+++ b/rest.c
-@@ -3998,7 +3998,7 @@
-                 oj = j;
-                 }
-         }
--    erg += sum(c,b);
-+    erg += sym_sum(c,b);
- eee:
-     erg += freeall(c);
-     ENDR("charge_word");
---- a/ta.c
-+++ b/ta.c
-@@ -1596,7 +1596,7 @@
-     {
-     OP d,e;
-     e = CALLOCOBJECT();
--    erg += sum(content,e); /* AK 271098 */
-+    erg += sym_sum(content,e); /* AK 271098 */
-     d = CALLOCOBJECT();
-     erg += weight(shape,d);
-     if (NEQ(d,e))
-@@ -1821,7 +1821,7 @@
-     CE3(matrix, column_index, row_index,matrix_twoword);
-     c = callocobject();
-     erg += zeilen_summe(matrix,c);
--    erg += sum(c,c);
-+    erg += sym_sum(c,c);
-     erg += m_l_v(c,column_index);
-     erg += m_l_v(c,row_index);
-     for(i=0,l=0;i<S_M_HI(matrix);i++)
---- a/zyk.c
-+++ b/zyk.c
-@@ -804,7 +804,7 @@
-     zykeltypvec = CALLOCOBJECT();
-     ak_order = CALLOCOBJECT();
- 
--    sum(numztvec,ak_order); /* AK 060295 */
-+    sym_sum(numztvec,ak_order); /* AK 060295 */
- 
- 
- 
-@@ -1176,7 +1176,7 @@
-     erg += m_i_i(0,c);
-     while (z!=NULL)
-         {
--        erg += sum(S_PO_S(z),e);
-+        erg += sym_sum(S_PO_S(z),e);
-         erg += hoch(b,e,e);
-         erg += mult_apply(S_PO_K(z),e);
-         erg += add_apply(e,c);
diff --git a/sci-libs/symmetrica/files/symmetrica-2.0-integersize.patch b/sci-libs/symmetrica/files/symmetrica-2.0-integersize.patch
deleted file mode 100644
index 32e5751df..000000000
--- a/sci-libs/symmetrica/files/symmetrica-2.0-integersize.patch
+++ /dev/null
@@ -1,37 +0,0 @@
-Patch imported from sage-on-gentoo.
---- src/def.h
-+++ c/def.h
-@@ -2,14 +2,9 @@
- /* INT should always be 4 byte */
- #ifndef DEF_H
- 
--
--#ifdef __alpha
--typedef  int INT;
--typedef unsigned  int  UINT;
--#else /* __alpha */
--typedef long INT;
--typedef unsigned long UINT;
--#endif /* __alpha */
-+#include <stdint.h>
-+typedef int32_t INT;
-+typedef uint32_t UINT;
- 
- #include <stdio.h>
- #include <memory.h>
-@@ -65,10 +60,13 @@
- 
- 
- /* definitionen fuer object.c */
--typedef INT OBJECTKIND;   /* 4 byte */
-+/* NOTE: partition code assumes that there is no unused space in the
-+ * object struct when an INT is stored. This requires both OBJECTKIND
-+ * and OBJECTSELF to have a size equal to a machine word. */
-+typedef intptr_t OBJECTKIND;
- 
- typedef union {
--	INT ob_INT;
-+	intptr_t ob_INT;
- 	INT * ob_INTpointer;
- 	char *ob_charpointer;
- 	struct bruch *ob_bruch;
diff --git a/sci-libs/symmetrica/metadata.xml b/sci-libs/symmetrica/metadata.xml
deleted file mode 100644
index 147f97496..000000000
--- a/sci-libs/symmetrica/metadata.xml
+++ /dev/null
@@ -1,9 +0,0 @@
-<?xml version="1.0" encoding="UTF-8"?>
-<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
-<pkgmetadata>
-	<maintainer type="project">
-		<email>sci@gentoo.org</email>
-		<name>Gentoo Science Project</name>
-	</maintainer>
-	<longdescription>A collection of routines handling a variety of mathematical subjects: ordinary representation theory of the symmetric group and related groups, ordinary representation theory of the classical groups, modular representation theory of the symmetric group, projective representation theory of the symmetric group, combinatorics of tableaux, symmetric functions and polynomials, commutative and non commutative Schubert polynomials, operations of finite groups, ordinary representation theory of Hecke algebras of type A_n</longdescription>
-</pkgmetadata>
diff --git a/sci-libs/symmetrica/symmetrica-2.0-r1.ebuild b/sci-libs/symmetrica/symmetrica-2.0-r1.ebuild
deleted file mode 100644
index a2ad9fa0b..000000000
--- a/sci-libs/symmetrica/symmetrica-2.0-r1.ebuild
+++ /dev/null
@@ -1,39 +0,0 @@
-# Copyright 1999-2015 Gentoo Foundation
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=5
-
-inherit eutils
-
-DESCRIPTION="A collection of routine to handle a variety of topics"
-HOMEPAGE="http://www.neu.uni-bayreuth.de/de/Uni_Bayreuth/Fakultaeten/1_Mathematik_Physik_und_Informatik/Fachgruppe_Informatik/prof_diskrete_algorithmen/en/research/SYMMETRICA/index.html"
-MY_P=SYM${PV//./_}
-SRC_URI="http://www.neu.uni-bayreuth.de/de/Uni_Bayreuth/Fakultaeten/1_Mathematik_Physik_und_Informatik/Fachgruppe_Informatik/prof_diskrete_algorithmen/en/research/SYMMETRICA/${MY_P}_tar.gz -> ${P}.tar.gz"
-
-LICENSE="MIT"
-SLOT="0"
-KEYWORDS="~amd64 ~x86"
-IUSE="doc"
-
-S="${WORKDIR}"
-
-PATCHES=(
-	"${FILESDIR}/${P}-banner.patch"
-	"${FILESDIR}/${P}-freeing_errors.patch"
-	"${FILESDIR}/${P}-function_names.patch"
-	"${FILESDIR}/${P}-integersize.patch"
-)
-
-src_prepare() {
-	epatch ${PATCHES[@]}
-	# symmetrica by itself is just a bunch of files and a few headers
-	# plus documentation that you can use as you wish in your programs.
-	# For sage and ease of use we make it into a library with the following
-	# makefile (developped by F. Bissey and T. Abbott (sage on debian).
-	cp "${FILESDIR}/makefile" "${S}/makefile" || die
-}
-
-src_install() {
-	default
-	use doc && dodoc *.doc
-}
diff --git a/sci-libs/symmetrica/symmetrica-2.0.ebuild b/sci-libs/symmetrica/symmetrica-2.0.ebuild
deleted file mode 100644
index 799043b0b..000000000
--- a/sci-libs/symmetrica/symmetrica-2.0.ebuild
+++ /dev/null
@@ -1,29 +0,0 @@
-# Copyright 1999-2015 Gentoo Foundation
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=5
-
-DESCRIPTION="A collection of routine to handle a variety of topics"
-HOMEPAGE="http://www.neu.uni-bayreuth.de/de/Uni_Bayreuth/Fakultaeten/1_Mathematik_Physik_und_Informatik/Fachgruppe_Informatik/prof_diskrete_algorithmen/en/research/SYMMETRICA/index.html"
-MY_P=SYM${PV//./_}
-SRC_URI="http://www.neu.uni-bayreuth.de/de/Uni_Bayreuth/Fakultaeten/1_Mathematik_Physik_und_Informatik/Fachgruppe_Informatik/prof_diskrete_algorithmen/en/research/SYMMETRICA/${MY_P}_tar.gz -> ${P}.tar.gz"
-
-LICENSE="MIT"
-SLOT="0"
-KEYWORDS="~amd64 ~x86"
-IUSE="doc"
-
-S="${WORKDIR}"
-
-src_prepare() {
-#	symmetrica by itself is just a bunch of files and a few headers
-#	plus documentation that you can use as you wish in your programs.
-#	For sage and ease of use we make it into a library with the following
-#	makefile (developped by F. Bissey and T. Abbott (sage on debian).
-	cp "${FILESDIR}/makefile" "${S}/makefile" || die
-}
-
-src_install() {
-	default
-	use doc && dodoc *.doc
-}
diff --git a/sci-libs/tensorflow/Manifest b/sci-libs/tensorflow/Manifest
deleted file mode 100644
index c11e6952f..000000000
--- a/sci-libs/tensorflow/Manifest
+++ /dev/null
@@ -1,5 +0,0 @@
-DIST tensorflow-1.0.1.tar.gz 10919903 BLAKE2B 1ce4de131436b2b7fec909251a8b4c03d872920cbe788eb9914c5670803fc0baf8462d1d6498c9ee3ef4e941bd0286bebda44745ac49d8044627a93fac28c746 SHA512 49f22cd6baca8770401aacd870b30b33f4eaa576c9f2d3caae0a00225d40041352d5300cb3dc5ec90ec9f0e8865eb542a7d3d6a0f39ceb6d0f2606cc4725f0a7
-DIST tensorflow-1.5.0.tar.gz 19155285 BLAKE2B 32000e583b85f195fc62acafc22254d8806b26a59f06b024c2be98c0a3b5770cbfc60f73957a3f11cdbf7488b8891978f73a22b6d642fdd763ecd95f18e38d65 SHA512 63240d72b9946db29279800b1081adc4cc08b6cd7dc35155a529cc335bfc1dd16fb525fb6047f6cc0dcec547a54e7e100698a176ee93f5633965cfab2a8ad9eb
-DIST tensorflow-1.7.0.tar.gz 21202162 BLAKE2B 28ce2e002aa6c44681aa4f55af6172b05a3b4f797b5093db23ab67adf06170df9d1a9c64705613e17e6c1ff0f95fe9a1115464c697585ab83fef7baee5ea0985 SHA512 68fffad324be7f6e3726ea539670572729bd72c7dc935edfdb31771f821f1a8fe90c3d7c293969f660a25e5fd76249cc9b74c5f8511c7bd3e2189d3328044f29
-DIST tensorflow-1.8.0-bazel-cache-repos.tar.xz 92733476 BLAKE2B c2ec4fd574031d88bc216f2a64f3867afe27f78a9336fe93f9b64f0156af16c026e2ef56e065b30644f7e2b4f086bcf4dfc0b409ac2e69f1c5811dbe8edc310b SHA512 983123e686cd904dd6e1300819708287bd2dc5077c33e68ad70bb233727e2d9f5c181a9967d1ae8e63b99bb6fe280648f09379fb821dd036d728ffed78a9121b
-DIST tensorflow-1.8.0.tar.gz 22649439 BLAKE2B 7384c2cf742fb5a8b4e266e95080ae2513c1b112ab97f74839fa8e81bd91bd24645be8afb02e4447ad5fba9f47c4d146f59aa12085937cd3a364ec34c99590f3 SHA512 7280e65d26fb3f15d95f7217ee3bc08d1424cd144cf25bf638fa114fa835b2505dfaf457c55700067d24f485b77120973d094ec568e6d1b1054857402f9c352d
diff --git a/sci-libs/tensorflow/metadata.xml b/sci-libs/tensorflow/metadata.xml
deleted file mode 100644
index b94b432fa..000000000
--- a/sci-libs/tensorflow/metadata.xml
+++ /dev/null
@@ -1,15 +0,0 @@
-<?xml version="1.0" encoding="UTF-8"?>
-<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
-<pkgmetadata>
-	<maintainer type="person">
-		<email>mmokrejs@fold.natur.cuni.cz</email>
-		<name>Martin Mokrejs</name>
-	</maintainer>
-	<maintainer type="project">
-		<email>sci-biology@gentoo.org</email>
-		<name>Gentoo Biology Project</name>
-	</maintainer>
-	<use>
-		<flag name="cuda">Enable CUDA support</flag>
-	</use>
-</pkgmetadata>
diff --git a/sci-libs/tensorflow/tensorflow-1.0.1.ebuild b/sci-libs/tensorflow/tensorflow-1.0.1.ebuild
deleted file mode 100644
index b2e2e596a..000000000
--- a/sci-libs/tensorflow/tensorflow-1.0.1.ebuild
+++ /dev/null
@@ -1,28 +0,0 @@
-# Copyright 1999-2018 Gentoo Foundation
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=6
-
-PYTHON_COMPAT=( python2_7 python3_{3,4,5,6} )
-
-inherit distutils-r1 eutils
-
-DESCRIPTION="Library for numerical computation using data flow graphs"
-HOMEPAGE="https://www.tensorflow.org
-	https://github.com/tensorflow/tensorflow"
-SRC_URI="https://github.com/${PN}/${PN}/archive/v${PV}.tar.gz -> ${P}.tar.gz"
-
-LICENSE="Apache-2.0"
-SLOT="0"
-KEYWORDS=""
-IUSE="cuda mpi"
-
-DEPEND="dev-util/bazel
-	dev-python/wheel
-	dev-python/numpy
-	dev-libs/protobuf-c
-	cuda? ( x11-drivers/nvidia-drivers dev-util/nvidia-cuda-toolkit )
-	mpi? ( virtual/mpi )"
-RDEPEND="${DEPEND}"
-
-# TODO: seems it also support some MPI implementation
diff --git a/sci-libs/tensorflow/tensorflow-1.5.0.ebuild b/sci-libs/tensorflow/tensorflow-1.5.0.ebuild
deleted file mode 100644
index 0dae0c1d0..000000000
--- a/sci-libs/tensorflow/tensorflow-1.5.0.ebuild
+++ /dev/null
@@ -1,43 +0,0 @@
-# Copyright 1999-2018 Gentoo Foundation
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=6
-
-PYTHON_COMPAT=( python2_7 python3_{3,4,5,6} )
-
-inherit distutils-r1 eutils
-
-DESCRIPTION="Library for numerical computation using data flow graphs"
-HOMEPAGE="https://www.tensorflow.org
-	https://github.com/tensorflow/tensorflow"
-SRC_URI="https://github.com/${PN}/${PN}/archive/v${PV}.tar.gz -> ${P}.tar.gz"
-
-LICENSE="Apache-2.0"
-SLOT="0"
-KEYWORDS=""
-IUSE="cuda mpi"
-
-# TensorFlow 1.7 may be the last time we support Cuda versions below 8.0.
-# Starting with TensorFlow 1.8 release, 8.0 will be the minimum supported
-# version.
-# TensorFlow 1.7 may be the last time we support cuDNN versions below 6.0.
-# Starting with TensorFlow 1.8 release, 6.0 will be the minimum supported
-# version.
-DEPEND="dev-util/bazel
-	dev-python/wheel
-	dev-python/numpy
-	dev-libs/protobuf-c
-	cuda? ( >=dev-util/nvidia-cuda-toolkit-7.0[profiler] >=dev-libs/cudnn-3 )
-	mpi? ( virtual/mpi )"
-RDEPEND="${DEPEND}"
-
-# TODO: seems it also supports some MPI implementation
-
-src_configure(){
-	# there is no setup.py but there is configure
-	# https://www.tensorflow.org/install/install_sources
-	# https://www.tensorflow.org/install/install_linux#InstallingNativePip
-	#
-	# usage: configure.py [-h] [--workspace WORKSPACE]
-	./configure || die
-}
diff --git a/sci-libs/tensorflow/tensorflow-1.7.0.ebuild b/sci-libs/tensorflow/tensorflow-1.7.0.ebuild
deleted file mode 100644
index 758872b99..000000000
--- a/sci-libs/tensorflow/tensorflow-1.7.0.ebuild
+++ /dev/null
@@ -1,111 +0,0 @@
-# Copyright 1999-2018 Gentoo Foundation
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=6
-
-PYTHON_COMPAT=( python2_7 python3_{3,4,5,6} )
-
-inherit python-r1 distutils-r1 eutils
-
-DESCRIPTION="Library for numerical computation using data flow graphs"
-HOMEPAGE="https://www.tensorflow.org
-	https://github.com/tensorflow/tensorflow"
-SRC_URI="https://github.com/${PN}/${PN}/archive/v${PV}.tar.gz -> ${P}.tar.gz"
-
-LICENSE="Apache-2.0"
-SLOT="0"
-KEYWORDS=""
-IUSE="cuda mpi"
-
-# TensorFlow 1.7 may be the last time we support Cuda versions below 8.0.
-# Starting with TensorFlow 1.8 release, 8.0 will be the minimum supported
-# version.
-# TensorFlow 1.7 may be the last time we support cuDNN versions below 6.0.
-# Starting with TensorFlow 1.8 release, 6.0 will be the minimum supported
-# version.
-DEPEND="
-	dev-util/bazel
-	dev-python/wheel
-	dev-python/numpy
-	dev-libs/protobuf-c
-	dev-python/absl-py
-	cuda? ( >=dev-util/nvidia-cuda-toolkit-7.0[profiler] >=dev-libs/cudnn-3 )
-	mpi? ( virtual/mpi )"
-	#opencl? ( virtual/opencl )"
-RDEPEND="${DEPEND}"
-
-# TODO: seems it also supports some MPI implementations
-src_configure(){
-	# there is no setup.py but there is configure
-	# https://www.tensorflow.org/install/install_sources
-	# https://www.tensorflow.org/install/install_linux#InstallingNativePip
-	#
-	# usage: configure.py [-h] [--workspace WORKSPACE]
-	python_configure() {
-		export PYTHON_BIN_PATH=${PYTHON}
-		export PYTHON_LIB_PATH=${PYTHON_SITEDIR}
-		export TF_NEED_JEMALLOC=1
-		export TF_NEED_GCP=0
-		export TF_NEED_HDFS=0
-		export TF_NEED_S3=0
-		export TF_NEED_KAFKA=0
-		export TF_ENABLE_XLA=0
-		export TF_NEED_GDR=0
-		export TF_NEED_VERBS=0
-		export TF_NEED_OPENCL=0
-		if use cuda; then
-			export TF_NEED_CUDA=1
-		else
-			export TF_NEED_CUDA=0
-		fi
-		if use mpi; then
-			export TF_NEED_MPI=1
-		else
-			export TF_NEED_MPI=0
-		fi
-		export TF_NEED_OPENCL_SYCL=0
-		export CC_OPT_FLAGS=${CFLAGS}
-		export JAVA_HOME=$(java-config -O)
-		# TODO: protect by a USE flag test --config=mkl
-		./configure || die
-	}
-	python_foreach_impl python_configure
-}
-
-src_compile() {
-	python_compile() {
-		# huh, by default tensorflow links static libs? See BUILD file
-		# set framework_shared_object=true somehow
-		if use cuda; then
-			local opt="--config=cuda"
-		else
-			local opt=""
-		fi
-		bazel build --config=opt ${opt} /tensorflow/tools/pip_package:build_pip_package || die
-		bazel-bin/tensorflow/tools/pip_package/build_pip_package tensorflow_pkg || die
-		unzip -o -d tensorflow_pkg tensorflow_pkg/${P}-cp35-cp35m-linux_x86_64.whl || die
-		python_domodule tensorflow_pkg/${P}.data/purelib/tensorflow
-		bazel test || die
-		bazel shutdown || die
-	}
-	python_foreach_impl python_compile
-}
-
-src_test() {
-	python_foreach_impl python_test
-}
-
-src_install() {
-	python_install() {
-		# steal site-package path determination from sci-mathematics/z3
-		local PYTHON_SITEDIR
-		python_export PYTHON_SITEDIR
-		cp -av tensorflow_pkg/"${P}".data/purelib/tensorflow/ "$PYTHON_SITEDIR" || die
-		cp -av tensorflow_pkg/"${P}".dist-info "$PYTHON_SITEDIR" || die
-		# mkdir -p "${D}/usr/$(get_libdir)/python3.6/site-packages" || die
-		# cp -av tensorflow_pkg/"${P}".data/purelib/tensorflow/ "${ED}/usr/$(get_libdir)/python3.6/site-packages/" || die
-		# cp -av tensorflow_pkg/"${P}".dist-info "${ED}/usr/$(get_libdir)/python3.6/site-packages/" || die
-	}
-	python_foreach_impl python_install
-	einstalldocs
-}
diff --git a/sci-libs/tensorflow/tensorflow-1.8.0.ebuild b/sci-libs/tensorflow/tensorflow-1.8.0.ebuild
deleted file mode 100644
index 557095bc7..000000000
--- a/sci-libs/tensorflow/tensorflow-1.8.0.ebuild
+++ /dev/null
@@ -1,200 +0,0 @@
-# Copyright 1999-2018 Gentoo Foundation
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=6
-
-PYTHON_COMPAT=( python2_7 python3_{3,4,5,6} )
-
-inherit python-r1 distutils-r1 eutils versionator
-
-DESCRIPTION="Library for numerical computation using data flow graphs"
-HOMEPAGE="https://www.tensorflow.org
-	https://github.com/tensorflow/tensorflow"
-SRC_URI="https://github.com/${PN}/${PN}/archive/v${PV}.tar.gz -> ${P}.tar.gz
-	https://dev.gentoo.org/~gienah/snapshots/${P}-bazel-cache-repos.tar.xz"
-
-LICENSE="Apache-2.0"
-SLOT="0"
-KEYWORDS="~amd64"
-IUSE="cuda cxx mpi"
-
-# To create the cache repo tar file, temporarilly remove the
-# ${P}-bazel-cache-repos.tar.xz from SRC_URI and src_upack.  Then build
-# it so that bazel will download the files:
-# FEATURES="noclean -network-sandbox" emerge -av sci-libs/tensorflow
-# cd /var/tmp/portage/sci-libs/${P}
-# tar --owner=portage --group=portage -cJvf \
-# /usr/portage/distfiles/${P}-bazel-cache-repos.tar.xz \
-# homedir/.cache/bazel/_bazel_portage/cache/repos/v1
-
-# TensorFlow 1.7 may be the last time we support Cuda versions below 8.0.
-# Starting with TensorFlow 1.8 release, 8.0 will be the minimum supported
-# version.
-# TensorFlow 1.7 may be the last time we support cuDNN versions below 6.0.
-# Starting with TensorFlow 1.8 release, 6.0 will be the minimum supported
-# version.
-# Possibly missing deps:
-# 	dev-python/gast
-DEPEND="
-	cxx? ( dev-libs/protobuf )
-	dev-python/absl-py[${PYTHON_USEDEP}]
-	dev-python/astor[${PYTHON_USEDEP}]
-	dev-python/numpy[${PYTHON_USEDEP}]
-	dev-python/protobuf-python[${PYTHON_USEDEP}]
-	dev-python/six[${PYTHON_USEDEP}]
-	dev-python/termcolor[${PYTHON_USEDEP}]
-	dev-python/wheel[${PYTHON_USEDEP}]
-	dev-libs/jemalloc
-	dev-libs/protobuf-c
-	dev-util/bazel
-	media-libs/giflib
-	virtual/jpeg:0
-	cuda? ( >=dev-util/nvidia-cuda-toolkit-8.0[profiler] >=dev-libs/cudnn-6 )
-	mpi? ( virtual/mpi )"
-	#opencl? ( virtual/opencl )"
-RDEPEND="${DEPEND}"
-
-src_unpack() {
-	unpack ${P}.tar.gz
-	pushd .. || die
-	unpack distdir/${P}-bazel-cache-repos.tar.xz
-	popd || die
-}
-
-# TODO: seems it also supports some MPI implementations
-src_configure(){
-	# there is no setup.py but there is configure
-	# https://www.tensorflow.org/install/install_sources
-	# https://www.tensorflow.org/install/install_linux#InstallingNativePip
-	#
-	# usage: configure.py [-h] [--workspace WORKSPACE]
-	python_configure() {
-		export PYTHON_BIN_PATH=${PYTHON}
-		export PYTHON_LIB_PATH=${PYTHON_SITEDIR}
-		export TF_NEED_JEMALLOC=1
-		export TF_NEED_GCP=0
-		export TF_NEED_HDFS=0
-		export TF_NEED_S3=0
-		export TF_NEED_KAFKA=0
-		export TF_ENABLE_XLA=0
-		export TF_NEED_GDR=0
-		export TF_NEED_VERBS=0
-		export TF_NEED_OPENCL=0
-		if use cuda; then
-			export TF_NEED_CUDA=1
-		else
-			export TF_NEED_CUDA=0
-		fi
-		if use mpi; then
-			export TF_NEED_MPI=1
-		else
-			export TF_NEED_MPI=0
-		fi
-		export TF_NEED_OPENCL_SYCL=0
-		export CC_OPT_FLAGS=${CFLAGS}
-		export JAVA_HOME=$(java-config -O)
-		# TODO: protect by a USE flag test --config=mkl
-		./configure || die
-	}
-	python_foreach_impl python_configure
-}
-
-bazel-get-flags() {
-	local fs=""
-	for i in ${CXXFLAGS}; do
-		[[ -n "${fs}" ]] && fs+=" "
-		fs+="--cxxopt=${i}"
-	done
-	for i in ${CPPFLAGS}; do
-		[[ -n "${fs}" ]] && fs+=" "
-		fs+="--copt=${i}"
-		fs+="--cxxopt=${i}"
-	done
-	for i in ${LDFLAGS}; do
-		[[ -n "${fs}" ]] && fs+=" "
-		fs+="--linkopt=${i}"
-	done
-	echo "${fs}"
-}
-
-src_compile() {
-	# F: fopen_wr
-	# S: deny
-	# P: /proc/self/setgroups
-	# A: /proc/self/setgroups
-	# R: /proc/7712/setgroups
-	# C: unable to read /proc/1/cmdline
-	addpredict /proc
-
-	local opt=$(usex cuda "--config=cuda" "")
-	einfo ">>> Compiling ${PN} C"$(usex cxx " and C++" "")
-	einfo "	bazel build \\"
-	einfo "	  --config=opt ${opt} \\"
-	einfo "	  $(bazel-get-flags) \\"
-	einfo "	  //tensorflow:libtensorflow.so \\"
-	einfo "   //tensorflow:libtensorflow_framework.so \\"
-	einfo "	  "$(usex cxx "//tensorflow:libtensorflow_cc.so" "")
-	bazel build \
-		  --config=opt ${opt} \
-		  $(bazel-get-flags) \
-		  //tensorflow:libtensorflow.so \
-		  //tensorflow:libtensorflow_framework.so \
-		  $(usex cxx "//tensorflow:libtensorflow_cc.so" "") || die
-
-	python_compile() {
-		einfo ">>> Compiling ${PN} ${MULTIBUILD_VARIANT}"
-		einfo "	bazel build \\"
-		einfo "	  --config=opt ${opt} \\"
-		einfo "	  $(bazel-get-flags) \\"
-		einfo "   //tensorflow/tools/pip_package:build_pip_package"
-		bazel build \
-			  --config=opt ${opt} \
-			  $(bazel-get-flags) \
-			  //tensorflow/tools/pip_package:build_pip_package || die
-		bazel-bin/tensorflow/tools/pip_package/build_pip_package tensorflow_pkg || die
-		unzip -o -d ${PN}_pkg_${MULTIBUILD_VARIANT} ${PN}_pkg/${P}-*.whl || die
-		rm -f ${PN}_pkg_${MULTIBUILD_VARIANT}/lib${PN}_framework.so || die
-	}
-	python_foreach_impl python_compile
-	bazel shutdown || die
-}
-
-src_test() {
-	python_foreach_impl python_test
-}
-
-src_install() {
-	local SO1=$(get_major_version)
-	local SOVER=$(version_format_string '$1.$2')
-	local tl="${PN} ${PN}_framework"
-	dodir /usr/include/${PN}/${PN}/c
-	insinto /usr/include/${PN}/${PN}/c
-	doins ${PN}/c/c_api.h
-	if use cxx; then
-		for i in $(find ${PN}/cc ${PN}/core third_party/eigen3 -type f \
-						\( -name \*.h -o \
-						-wholename third_party/eigen3/Eigen/\* \) -print); do
-			dodir $(dirname /usr/include/${PN}/${i})
-			insinto $(dirname /usr/include/${PN}/${i})
-			doins ${i}
-		done
-		tl+=" ${PN}_cc"
-	fi
-	for i in ${tl}; do
-		dolib.so bazel-bin/${PN}/lib${i}.so
-		dosym "lib${i}.so" \
-			  "/usr/$(get_libdir)/lib${i}.so.${SO1}" \
-			|| die "Could not create /usr/$(get_libdir)/lib${i}.so.${SO1} symlink"
-		dosym "lib${i}.so" \
-			  "/usr/$(get_libdir)/lib${i}.so.${SOVER}" \
-			|| die "Could not create /usr/$(get_libdir)/lib${i}.so.${SOVER} symlink"
-	done
-	python_install() {
-		python_domodule ${PN}_pkg_${MULTIBUILD_VARIANT}/${P}.data/purelib/${PN}
-		dosym "../../../lib${PN}_framework.so" \
-			  "$(python_get_sitedir)/${PN}/lib${PN}_framework.so" \
-			|| die "Could not create $(python_get_sitedir)/lib${PN}_framework.so symlink for python module"
-	}
-	python_foreach_impl python_install
-	einstalldocs
-}
diff --git a/sci-libs/tmglib/Manifest b/sci-libs/tmglib/Manifest
deleted file mode 100644
index 1bfd4e51c..000000000
--- a/sci-libs/tmglib/Manifest
+++ /dev/null
@@ -1,2 +0,0 @@
-DIST lapack-3.5.0.tgz 6313139 BLAKE2B c23a35f107cfc5c887491fd148c1c76851a4580c98ad86aff9c391ac3d393c31ba67427ed445fe821c7666418e9fcf19523a3a668f8009337508994cf1a68c04 SHA512 b948a0a0db032bda455ec4f519d4e89e4c29e29cecb5b6258ca61f68faaeeac9fdf4ece5c39ffcd0154c5505facbc392c7d09c8348b1d60bdd2685153ab2543f
-DIST lapack-3.6.0.tgz 6792324 BLAKE2B 438f3376b63b38ef0fe70f6becac847816f3a11c01f5ab237dc0d941792ceb54dbd2f8dc22d56286f5dab3499289ed94e67521ea951a98973c9640abc294ad6c SHA512 bc50441d415ef8896dd7626d77c6104184b996e758704366288089f03d4c99d068e33153b0d13305310886017e5d2e716130f812a95cfcad36ef37fe20417ab8
diff --git a/sci-libs/tmglib/metadata.xml b/sci-libs/tmglib/metadata.xml
deleted file mode 100644
index cbd1ba7ba..000000000
--- a/sci-libs/tmglib/metadata.xml
+++ /dev/null
@@ -1,12 +0,0 @@
-<?xml version="1.0" encoding="UTF-8"?>
-<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
-<pkgmetadata>
-	<maintainer type="project">
-		<email>sci@gentoo.org</email>
-		<name>Gentoo Science Project</name>
-	</maintainer>
-	<longdescription lang="en">
-This is a library to generate matrices to test LAPACK
-implementations.
-</longdescription>
-</pkgmetadata>
diff --git a/sci-libs/tmglib/tmglib-3.5.0.ebuild b/sci-libs/tmglib/tmglib-3.5.0.ebuild
deleted file mode 100644
index b6be5eb1f..000000000
--- a/sci-libs/tmglib/tmglib-3.5.0.ebuild
+++ /dev/null
@@ -1,65 +0,0 @@
-# Copyright 1999-2015 Gentoo Foundation
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=5
-
-PYTHON_COMPAT=( python2_7 )
-
-inherit cmake-utils fortran-2 python-any-r1
-
-MYP=lapack-${PV}
-
-DESCRIPTION="Test Matrix Generator library for LAPACK"
-HOMEPAGE="http://www.netlib.org/lapack/"
-SRC_URI="http://www.netlib.org/lapack/${MYP}.tgz"
-
-LICENSE="BSD"
-SLOT="0"
-KEYWORDS="~amd64 ~x86 ~amd64-linux ~x86-linux"
-IUSE="static-libs test"
-
-REQUIRED_USE="test? ( ${PYTHON_REQUIRED_USE} )"
-
-RDEPEND="
-	virtual/blas
-	virtual/lapack"
-DEPEND="${RDEPEND}
-	test? ( ${PYTHON_DEPS} )
-	virtual/pkgconfig"
-
-S="${WORKDIR}/${MYP}"
-
-src_prepare() {
-	use static-libs && mkdir "${WORKDIR}/${PN}_static"
-}
-
-src_configure() {
-	tmg_configure() {
-		local mycmakeargs=(
-			-DUSE_OPTIMIZED_BLAS=ON
-			-DUSE_OPTIMIZED_LAPACK=ON
-			-DBLAS_LIBRARIES="$($(tc-getPKG_CONFIG) --libs blas)"
-			-DLAPACK_LIBRARIES="$($(tc-getPKG_CONFIG) --libs lapack)"
-			-DTESTING=ON
-			$@
-		)
-		cmake-utils_src_configure
-	}
-
-	tmg_configure -DBUILD_SHARED_LIBS=ON -DBUILD_STATIC_LIBS=OFF
-	use static-libs && \
-		BUILD_DIR="${WORKDIR}/${PN}_static" tmg_configure \
-		-DBUILD_SHARED_LIBS=OFF -DBUILD_STATIC_LIBS=ON
-}
-
-src_compile() {
-	cmake-utils_src_compile -C TESTING/MATGEN
-	use static-libs && BUILD_DIR="${WORKDIR}/${PN}_static" \
-		cmake-utils_src_compile -C TESTING/MATGEN
-}
-
-src_install() {
-	cmake-utils_src_install -C TESTING/MATGEN
-	use static-libs && BUILD_DIR="${WORKDIR}/${PN}_static" \
-			cmake-utils_src_install -C TESTING/MATGEN
-}
diff --git a/sci-libs/tmglib/tmglib-3.6.0.ebuild b/sci-libs/tmglib/tmglib-3.6.0.ebuild
deleted file mode 100644
index cac26b9df..000000000
--- a/sci-libs/tmglib/tmglib-3.6.0.ebuild
+++ /dev/null
@@ -1,65 +0,0 @@
-# Copyright 1999-2015 Gentoo Foundation
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=5
-
-PYTHON_COMPAT=( python2_7 )
-
-inherit cmake-utils fortran-2 python-any-r1
-
-MYP=lapack-${PV}
-
-DESCRIPTION="Test Matrix Generator library for LAPACK"
-HOMEPAGE="http://www.netlib.org/lapack/"
-SRC_URI="http://www.netlib.org/lapack/${MYP}.tgz"
-
-LICENSE="BSD"
-SLOT="0"
-KEYWORDS="~amd64 ~x86 ~amd64-linux ~x86-linux"
-IUSE="static-libs test"
-
-REQUIRED_USE="test? ( ${PYTHON_REQUIRED_USE} )"
-
-RDEPEND="
-	virtual/blas
-	virtual/lapack"
-DEPEND="${RDEPEND}
-	test? ( ${PYTHON_DEPS} )
-	virtual/pkgconfig"
-
-S="${WORKDIR}/${MYP}"
-
-src_prepare() {
-	use static-libs && mkdir "${WORKDIR}/${PN}_static"
-}
-
-src_configure() {
-	tmg_configure() {
-		local mycmakeargs=(
-			-DUSE_OPTIMIZED_BLAS=ON
-			-DUSE_OPTIMIZED_LAPACK=ON
-			-DBLAS_LIBRARIES="$($(tc-getPKG_CONFIG) --libs blas)"
-			-DLAPACK_LIBRARIES="$($(tc-getPKG_CONFIG) --libs lapack)"
-			-DTESTING=ON
-			$@
-		)
-		cmake-utils_src_configure
-	}
-
-	tmg_configure -DBUILD_SHARED_LIBS=ON -DBUILD_STATIC_LIBS=OFF
-	use static-libs && \
-		BUILD_DIR="${WORKDIR}/${PN}_static" tmg_configure \
-		-DBUILD_SHARED_LIBS=OFF -DBUILD_STATIC_LIBS=ON
-}
-
-src_compile() {
-	cmake-utils_src_compile -C TESTING/MATGEN
-	use static-libs && BUILD_DIR="${WORKDIR}/${PN}_static" \
-		cmake-utils_src_compile -C TESTING/MATGEN
-}
-
-src_install() {
-	cmake-utils_src_install -C TESTING/MATGEN
-	use static-libs \
-		&& BUILD_DIR="${WORKDIR}/${PN}_static" cmake-utils_src_install -C TESTING/MATGEN
-}
diff --git a/sci-libs/torchvision/Manifest b/sci-libs/torchvision/Manifest
new file mode 100644
index 000000000..7cf5fa956
--- /dev/null
+++ b/sci-libs/torchvision/Manifest
@@ -0,0 +1,2 @@
+DIST torchvision-0.14.1.tar.gz 9265179 BLAKE2B 0708635b00ac7c2cf4e54799f1190f01f3240f53233695819f691313b8a369b8922520e2f3cf96184bab671877b5826b84e0936d9ca5b58004d6e2a098c6cbbf SHA512 08fb1e35da1c3f1d0446ef879d9b6a7ae839a5137c3b5b46ef8111c2ae890299e2b555d1bd3b3d61f96b8778b831d8f895487cf8a4e36e371fcd4b8acda67d1f
+DIST torchvision-0.17.1.tar.gz 13091686 BLAKE2B db25faab565412f2892ca4cf8d13c459b8045aaab83009a686a93272f0b3e3e8c0da930f1d7b0682e0adc7a600195b035ca19f71fd15a26f77b349206e3ed324 SHA512 c9ef5704a337a43c1ab3a5865b2a20d09d07a9b5eeda66c7aa1e1931772bad9acee822bb400cf627960a84ace01188cd32e95f0e709eb392bf9028d36cfc50be
diff --git a/sci-libs/torchvision/files/torchvision-0.17.1-ffmpeg-6.patch b/sci-libs/torchvision/files/torchvision-0.17.1-ffmpeg-6.patch
new file mode 100644
index 000000000..7a3637f3a
--- /dev/null
+++ b/sci-libs/torchvision/files/torchvision-0.17.1-ffmpeg-6.patch
@@ -0,0 +1,36 @@
+From 86620bd84b872b76db0acafec167949dca03a29e Mon Sep 17 00:00:00 2001
+From: =?UTF-8?q?Zolt=C3=A1n=20B=C3=B6sz=C3=B6rm=C3=A9nyi?=
+ <zboszor@gmail.com>
+Date: Tue, 7 Nov 2023 10:43:11 +0100
+Subject: [PATCH] Fix build with ffmpeg 6.0
+MIME-Version: 1.0
+Content-Type: text/plain; charset=UTF-8
+Content-Transfer-Encoding: 8bit
+
+Signed-off-by: Zoltán Böszörményi <zboszor@gmail.com>
+---
+ torchvision/csrc/io/decoder/stream.cpp | 11 ++---------
+ 1 file changed, 2 insertions(+), 9 deletions(-)
+
+diff --git a/torchvision/csrc/io/decoder/stream.cpp b/torchvision/csrc/io/decoder/stream.cpp
+index 0d625ef211c..8c914050587 100644
+--- a/torchvision/csrc/io/decoder/stream.cpp
++++ b/torchvision/csrc/io/decoder/stream.cpp
+@@ -63,15 +63,8 @@ int Stream::openCodec(std::vector<DecoderMetadata>* metadata, int num_threads) {
+     codecCtx_->thread_count = num_threads;
+   } else {
+     // otherwise set sensible defaults
+-    // with the special case for the different MPEG4 codecs
+-    // that don't have threading context functions
+-    if (codecCtx_->codec->capabilities & AV_CODEC_CAP_INTRA_ONLY) {
+-      codecCtx_->thread_type = FF_THREAD_FRAME;
+-      codecCtx_->thread_count = 2;
+-    } else {
+-      codecCtx_->thread_count = 8;
+-      codecCtx_->thread_type = FF_THREAD_SLICE;
+-    }
++    codecCtx_->thread_count = 8;
++    codecCtx_->thread_type = FF_THREAD_SLICE;
+   }
+ 
+   int ret;
diff --git a/sci-libs/torchvision/metadata.xml b/sci-libs/torchvision/metadata.xml
new file mode 100644
index 000000000..9c4ddaefd
--- /dev/null
+++ b/sci-libs/torchvision/metadata.xml
@@ -0,0 +1,11 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
+<pkgmetadata>
+	<maintainer type="person">
+		<email>jpizarrocallejas@gmail.com</email>
+		<name>Jorge Pizarro Callejas</name>
+	</maintainer>
+	<upstream>
+		<remote-id type="github">pytorch/vision</remote-id>
+	</upstream>
+</pkgmetadata>
diff --git a/sci-libs/torchvision/torchvision-0.14.1.ebuild b/sci-libs/torchvision/torchvision-0.14.1.ebuild
new file mode 100644
index 000000000..7f40fe556
--- /dev/null
+++ b/sci-libs/torchvision/torchvision-0.14.1.ebuild
@@ -0,0 +1,40 @@
+# Copyright 2020-2021 Gentoo Authors
+# Distributed under the terms of the GNU General Public License v2
+
+EAPI=8
+
+PYTHON_COMPAT=( python3_10 )
+DISTUTILS_SINGLE_IMPL=1
+DISTUTILS_USE_PEP517=setuptools
+inherit distutils-r1
+
+DESCRIPTION="Datasets, transforms and models to specific to computer vision"
+HOMEPAGE="https://github.com/pytorch/vision"
+SRC_URI="https://github.com/pytorch/vision/archive/v${PV}.tar.gz -> ${P}.tar.gz"
+S="${WORKDIR}/vision-${PV}"
+
+LICENSE="BSD"
+SLOT="0"
+KEYWORDS="~amd64"
+
+RDEPEND="
+	$(python_gen_cond_dep '
+		dev-python/numpy[${PYTHON_USEDEP}]
+		dev-python/typing-extensions[${PYTHON_USEDEP}]
+		dev-python/pillow[${PYTHON_USEDEP}]
+		dev-python/requests[${PYTHON_USEDEP}]
+		dev-python/scipy[${PYTHON_USEDEP}]
+	')
+	sci-libs/pytorch[${PYTHON_SINGLE_USEDEP}]
+	media-video/ffmpeg
+	dev-qt/qtcore:5
+"
+DEPEND="${RDEPEND}"
+BDEPEND="
+	test? (
+		$(python_gen_cond_dep '
+		dev-python/mock[${PYTHON_USEDEP}]
+		')
+	)"
+
+distutils_enable_tests pytest
diff --git a/sci-libs/torchvision/torchvision-0.17.1.ebuild b/sci-libs/torchvision/torchvision-0.17.1.ebuild
new file mode 100644
index 000000000..e0c72684c
--- /dev/null
+++ b/sci-libs/torchvision/torchvision-0.17.1.ebuild
@@ -0,0 +1,45 @@
+# Copyright 2020-2024 Gentoo Authors
+# Distributed under the terms of the GNU General Public License v2
+
+EAPI=8
+
+PYTHON_COMPAT=( python3_{10..12} )
+DISTUTILS_SINGLE_IMPL=1
+DISTUTILS_USE_PEP517=setuptools
+DISTUTILS_EXT=1
+inherit distutils-r1 multiprocessing
+
+DESCRIPTION="Datasets, transforms and models to specific to computer vision"
+HOMEPAGE="https://github.com/pytorch/vision"
+SRC_URI="https://github.com/pytorch/vision/archive/v${PV}.tar.gz -> ${P}.tar.gz"
+S="${WORKDIR}/vision-${PV}"
+
+LICENSE="BSD"
+SLOT="0"
+KEYWORDS="~amd64"
+RESTRICT="test"
+
+RDEPEND="
+	$(python_gen_cond_dep '
+		dev-python/numpy[${PYTHON_USEDEP}]
+		dev-python/typing-extensions[${PYTHON_USEDEP}]
+		dev-python/pillow[${PYTHON_USEDEP}]
+		dev-python/requests[${PYTHON_USEDEP}]
+		dev-python/scipy[${PYTHON_USEDEP}]
+	')
+	sci-libs/pytorch[${PYTHON_SINGLE_USEDEP}]
+	media-video/ffmpeg:=
+"
+DEPEND="${RDEPEND}"
+
+PATCHES=( "${FILESDIR}/${PN}-0.17.1-ffmpeg-6.patch" )
+
+src_compile()
+{
+	export MAX_JOBS="$(makeopts_jobs)" # Let ninja respect MAKEOPTS
+
+	# Ensure some ext_module sources are compiled before linking
+	export MAKEOPTS="-j1"
+
+	distutils-r1_src_compile
+}
diff --git a/sci-libs/trilinos/Manifest b/sci-libs/trilinos/Manifest
deleted file mode 100644
index 38b8b8262..000000000
--- a/sci-libs/trilinos/Manifest
+++ /dev/null
@@ -1 +0,0 @@
-DIST trilinos-12.12.1-Source.tar.gz 99892109 BLAKE2B e9abdbbe664500a4c32776c687c6ffe9726c59d4f41fac7b86440b851e15533ba4cd8b6248743386e83e9a4b370cbcb0b7b9dbf9f136588f25608d56116cb70a SHA512 ebe1198f85a1ea84e53f6b420cff809bb3c1887b67281d95838479162c89ec60ce728ed5d87554d5b59d6b3615b2f72fa4d14c54104b29dc228c1e8a9924a7bf
diff --git a/sci-libs/trilinos/files/trilinos-11.14.1-fix-install-paths.patch b/sci-libs/trilinos/files/trilinos-11.14.1-fix-install-paths.patch
deleted file mode 100644
index 32f25f326..000000000
--- a/sci-libs/trilinos/files/trilinos-11.14.1-fix-install-paths.patch
+++ /dev/null
@@ -1,61 +0,0 @@
-diff --git a/cmake/tribits/package_arch/TribitsWriteClientExportFiles.cmake b/cmake/tribits/package_arch/TribitsWriteClientExportFiles.cmake
-index e1c633f..864488f 100644
---- a/cmake/tribits/core/package_arch/TribitsWriteClientExportFiles.cmake
-+++ b/cmake/tribits/core/package_arch/TribitsWriteClientExportFiles.cmake
-@@ -494,8 +494,8 @@ INCLUDE(\"${PROJECT_BINARY_DIR}/${PACKAGE_NAME}Targets.cmake\")"
-   FOREACH(PATH ${PATH_LIST})
-     SET(RELATIVE_PATH "${RELATIVE_PATH}/..")
-   ENDFOREACH()
--  SET(FULL_LIBRARY_DIRS_SET "\${CMAKE_CURRENT_LIST_DIR}/${RELATIVE_PATH}/${${PROJECT_NAME}_INSTALL_LIB_DIR}")
--  SET(FULL_INCLUDE_DIRS_SET "\${CMAKE_CURRENT_LIST_DIR}/${RELATIVE_PATH}/${${PROJECT_NAME}_INSTALL_INCLUDE_DIR}")
-+  SET(FULL_LIBRARY_DIRS_SET "${${PROJECT_NAME}_INSTALL_LIB_DIR}")
-+  SET(FULL_INCLUDE_DIRS_SET "${${PROJECT_NAME}_INSTALL_INCLUDE_DIR}")
- 
-   # Custom code in configuration file.
-   SET(PACKAGE_CONFIG_CODE "")
-@@ -574,14 +574,14 @@ FUNCTION(TRIBITS_WRITE_PROJECT_CLIENT_EXPORT_FILES_INSTALL_TARGETS PACKAGE_NAME)
-   IF (${PROJECT_NAME}_ENABLE_INSTALL_CMAKE_CONFIG_FILES)
-     INSTALL(
-       FILES ${CMAKE_CURRENT_BINARY_DIR}/CMakeFiles/${PACKAGE_NAME}Config_install.cmake
--      DESTINATION "${${PROJECT_NAME}_INSTALL_LIB_DIR}/cmake/${PACKAGE_NAME}"
-+      DESTINATION "${${PROJECT_NAME}_INSTALL_CONFIG_DIR}/${PACKAGE_NAME}"
-       RENAME ${PACKAGE_NAME}Config.cmake
-       )
- 
-     IF(${PACKAGE_NAME}_HAS_NATIVE_LIBRARIES)
-       INSTALL(
-         EXPORT ${PACKAGE_NAME}
--        DESTINATION "${${PROJECT_NAME}_INSTALL_LIB_DIR}/cmake/${PACKAGE_NAME}"
-+        DESTINATION "${${PROJECT_NAME}_INSTALL_CONFIG_DIR}/${PACKAGE_NAME}"
-         FILE ${PACKAGE_NAME}Targets.cmake
-         )
-     ENDIF()
-@@ -819,8 +819,8 @@ include(\"${${TRIBITS_PACKAGE}_BINARY_DIR}/${TRIBITS_PACKAGE}Config.cmake\")")
-   FOREACH(PATH ${PATH_LIST})
-     SET(RELATIVE_PATH "${RELATIVE_PATH}/..")
-   ENDFOREACH()
--  SET(${PROJECT_NAME}_CONFIG_INCLUDE_DIRS "\${CMAKE_CURRENT_LIST_DIR}/${RELATIVE_PATH}/${${PROJECT_NAME}_INSTALL_INCLUDE_DIR}")
--  SET(${PROJECT_NAME}_CONFIG_LIBRARY_DIRS "\${CMAKE_CURRENT_LIST_DIR}/${RELATIVE_PATH}/${${PROJECT_NAME}_INSTALL_LIB_DIR}")
-+  SET(${PROJECT_NAME}_CONFIG_INCLUDE_DIRS "${${PROJECT_NAME}_INSTALL_INCLUDE_DIR}")
-+  SET(${PROJECT_NAME}_CONFIG_LIBRARY_DIRS "${${PROJECT_NAME}_INSTALL_LIB_DIR}")
- 
-   # Write the specification of the rpath if necessary. This is only needed if we're building shared libraries.
-   IF(BUILD_SHARED_LIBS)
-@@ -845,7 +845,7 @@ include(\"\${CMAKE_CURRENT_LIST_DIR}/../${TRIBITS_PACKAGE}/${TRIBITS_PACKAGE}Con
- 
-     INSTALL(
-       FILES ${CMAKE_CURRENT_BINARY_DIR}/${PROJECT_NAME}Config_install.cmake
--      DESTINATION "${${PROJECT_NAME}_INSTALL_LIB_DIR}/cmake/${PROJECT_NAME}"
-+      DESTINATION "${${PROJECT_NAME}_INSTALL_CONFIG_DIR}/${PROJECT_NAME}"
-       RENAME ${PROJECT_NAME}Config.cmake
-       )
-   ENDIF()
-@@ -890,7 +890,7 @@ include(\"\${CMAKE_CURRENT_LIST_DIR}/../${TRIBITS_PACKAGE}/${TRIBITS_PACKAGE}Con
-     )
-   INSTALL(
-     FILES ${CMAKE_CURRENT_BINARY_DIR}/${PROJECT_NAME}ConfigVersion.cmake
--    DESTINATION "${${PROJECT_NAME}_INSTALL_LIB_DIR}/cmake/${PROJECT_NAME}"
-+    DESTINATION "${${PROJECT_NAME}_INSTALL_CONFIG_DIR}/${PROJECT_NAME}"
-     )
- 
- ENDFUNCTION()
diff --git a/sci-libs/trilinos/files/trilinos-12.12.1-fix_install_paths_for_destdir.patch b/sci-libs/trilinos/files/trilinos-12.12.1-fix_install_paths_for_destdir.patch
deleted file mode 100644
index d4e04a438..000000000
--- a/sci-libs/trilinos/files/trilinos-12.12.1-fix_install_paths_for_destdir.patch
+++ /dev/null
@@ -1,1069 +0,0 @@
-diff --git a/commonTools/gtest/CMakeLists.txt b/commonTools/gtest/CMakeLists.txt
-index 4b96030..34aef5f 100644
---- a/commonTools/gtest/CMakeLists.txt
-+++ b/commonTools/gtest/CMakeLists.txt
-@@ -36,7 +36,7 @@ TRIBITS_ADD_LIBRARY(
-   )
- 
- #install gtest header into the correct subdir.
--INSTALL(FILES ${HEADERS} DESTINATION ${CMAKE_INSTALL_PREFIX}/${Trilinos_INSTALL_INCLUDE_DIR}/gtest/)
-+INSTALL(FILES ${HEADERS} DESTINATION ${Trilinos_INSTALL_INCLUDE_DIR}/gtest/)
- 
- 
- 
-diff --git a/packages/rol/adapters/arrayfire/src/CMakeLists.txt b/packages/rol/adapters/arrayfire/src/CMakeLists.txt
-index 2c6b4b0..6184d3d 100644
---- a/packages/rol/adapters/arrayfire/src/CMakeLists.txt
-+++ b/packages/rol/adapters/arrayfire/src/CMakeLists.txt
-@@ -36,4 +36,4 @@ IF (ROL_ENABLE_ArrayFireCPU)
-  )
- ENDIF()
- 
--INSTALL(FILES ${HEADERS} DESTINATION ${CMAKE_INSTALL_PREFIX}/${${PROJECT_NAME}_INSTALL_INCLUDE_DIR})
-+INSTALL(FILES ${HEADERS} DESTINATION ${${PROJECT_NAME}_INSTALL_INCLUDE_DIR})
-diff --git a/packages/rol/adapters/belos/src/CMakeLists.txt b/packages/rol/adapters/belos/src/CMakeLists.txt
-index 109f28e..3749b75 100644
---- a/packages/rol/adapters/belos/src/CMakeLists.txt
-+++ b/packages/rol/adapters/belos/src/CMakeLists.txt
-@@ -39,4 +39,4 @@ IF (ROL_ENABLE_Belos)
-   )
- ENDIF()
- 
--INSTALL(FILES ${HEADERS} DESTINATION ${CMAKE_INSTALL_PREFIX}/${${PROJECT_NAME}_INSTALL_INCLUDE_DIR})
-+INSTALL(FILES ${HEADERS} DESTINATION ${${PROJECT_NAME}_INSTALL_INCLUDE_DIR})
-diff --git a/packages/rol/adapters/epetra/src/CMakeLists.txt b/packages/rol/adapters/epetra/src/CMakeLists.txt
-index f2b329b..d96b18d 100644
---- a/packages/rol/adapters/epetra/src/CMakeLists.txt
-+++ b/packages/rol/adapters/epetra/src/CMakeLists.txt
-@@ -42,4 +42,4 @@ IF (ROL_ENABLE_Epetra)
-   )
- ENDIF()
- 
--INSTALL(FILES ${HEADERS} DESTINATION ${CMAKE_INSTALL_PREFIX}/${${PROJECT_NAME}_INSTALL_INCLUDE_DIR})
-+INSTALL(FILES ${HEADERS} DESTINATION ${${PROJECT_NAME}_INSTALL_INCLUDE_DIR})
-diff --git a/packages/rol/adapters/minitensor/src/CMakeLists.txt b/packages/rol/adapters/minitensor/src/CMakeLists.txt
-index 0da2642..d91a4a7 100644
---- a/packages/rol/adapters/minitensor/src/CMakeLists.txt
-+++ b/packages/rol/adapters/minitensor/src/CMakeLists.txt
-@@ -67,4 +67,4 @@ IF (ROL_ENABLE_Boost AND ROL_ENABLE_MiniTensor)
-   )
- ENDIF()
- 
--INSTALL(FILES ${HEADERS} DESTINATION ${CMAKE_INSTALL_PREFIX}/${${PROJECT_NAME}_INSTALL_INCLUDE_DIR})
-+INSTALL(FILES ${HEADERS} DESTINATION ${${PROJECT_NAME}_INSTALL_INCLUDE_DIR})
-diff --git a/packages/rol/adapters/sacado/src/CMakeLists.txt b/packages/rol/adapters/sacado/src/CMakeLists.txt
-index 1ac1a19..a808d63 100644
---- a/packages/rol/adapters/sacado/src/CMakeLists.txt
-+++ b/packages/rol/adapters/sacado/src/CMakeLists.txt
-@@ -37,4 +37,4 @@ IF (ROL_ENABLE_Sacado)
-   )
- ENDIF()
- 
--INSTALL(FILES ${HEADERS} DESTINATION ${CMAKE_INSTALL_PREFIX}/${${PROJECT_NAME}_INSTALL_INCLUDE_DIR})
-+INSTALL(FILES ${HEADERS} DESTINATION ${${PROJECT_NAME}_INSTALL_INCLUDE_DIR})
-diff --git a/packages/rol/adapters/teuchos/src/CMakeLists.txt b/packages/rol/adapters/teuchos/src/CMakeLists.txt
-index 802760c..34aae17 100644
---- a/packages/rol/adapters/teuchos/src/CMakeLists.txt
-+++ b/packages/rol/adapters/teuchos/src/CMakeLists.txt
-@@ -42,4 +42,4 @@ INCLUDE_DIRECTORIES(${CMAKE_CURRENT_SOURCE_DIR}/function)
- )
- 
- 
--INSTALL(FILES ${HEADERS} DESTINATION ${CMAKE_INSTALL_PREFIX}/${${PROJECT_NAME}_INSTALL_INCLUDE_DIR})
-+INSTALL(FILES ${HEADERS} DESTINATION ${${PROJECT_NAME}_INSTALL_INCLUDE_DIR})
-diff --git a/packages/rol/adapters/thyra/src/CMakeLists.txt b/packages/rol/adapters/thyra/src/CMakeLists.txt
-index 725cad8..357e799 100644
---- a/packages/rol/adapters/thyra/src/CMakeLists.txt
-+++ b/packages/rol/adapters/thyra/src/CMakeLists.txt
-@@ -49,4 +49,4 @@ IF (ROL_ENABLE_Thyra)
-   )
- ENDIF()
- 
--INSTALL(FILES ${HEADERS} DESTINATION ${CMAKE_INSTALL_PREFIX}/${${PROJECT_NAME}_INSTALL_INCLUDE_DIR})
-+INSTALL(FILES ${HEADERS} DESTINATION ${${PROJECT_NAME}_INSTALL_INCLUDE_DIR})
-diff --git a/packages/rol/adapters/tpetra/src/CMakeLists.txt b/packages/rol/adapters/tpetra/src/CMakeLists.txt
-index 1367681..65d0cb3 100644
---- a/packages/rol/adapters/tpetra/src/CMakeLists.txt
-+++ b/packages/rol/adapters/tpetra/src/CMakeLists.txt
-@@ -46,4 +46,4 @@ IF (ROL_ENABLE_Tpetra)
-   )
- ENDIF()
- 
--INSTALL(FILES ${HEADERS} DESTINATION ${CMAKE_INSTALL_PREFIX}/${${PROJECT_NAME}_INSTALL_INCLUDE_DIR})
-+INSTALL(FILES ${HEADERS} DESTINATION ${${PROJECT_NAME}_INSTALL_INCLUDE_DIR})
-diff --git a/packages/rol/adapters/trikota/src/CMakeLists.txt b/packages/rol/adapters/trikota/src/CMakeLists.txt
-index 37d3c0e..bca4b82 100644
---- a/packages/rol/adapters/trikota/src/CMakeLists.txt
-+++ b/packages/rol/adapters/trikota/src/CMakeLists.txt
-@@ -45,4 +45,4 @@ IF (ROL_ENABLE_TriKota)
-   )
- ENDIF()
- 
--INSTALL(FILES ${HEADERS} DESTINATION ${CMAKE_INSTALL_PREFIX}/${${PROJECT_NAME}_INSTALL_INCLUDE_DIR})
-+INSTALL(FILES ${HEADERS} DESTINATION ${${PROJECT_NAME}_INSTALL_INCLUDE_DIR})
-diff --git a/packages/seacas/libraries/exoIIv2for32/CMakeLists.txt b/packages/seacas/libraries/exoIIv2for32/CMakeLists.txt
-index d967154..987e207 100644
---- a/packages/seacas/libraries/exoIIv2for32/CMakeLists.txt
-+++ b/packages/seacas/libraries/exoIIv2for32/CMakeLists.txt
-@@ -25,7 +25,7 @@ if (${CMAKE_PROJECT_NAME} STREQUAL "SEACASProj")
-       ${CMAKE_CURRENT_SOURCE_DIR}/src/exo_jack_32.c
-     )
-     set_target_properties(exoIIv2for32_static PROPERTIES OUTPUT_NAME exoIIv2for32)
--    INSTALL(TARGETS exoIIv2for32_static DESTINATION ${CMAKE_INSTALL_PREFIX}/lib)
-+    INSTALL(TARGETS exoIIv2for32_static DESTINATION lib)
-   endif()
- endif()
- 
-diff --git a/packages/seacas/libraries/exodus/CMakeLists.txt b/packages/seacas/libraries/exodus/CMakeLists.txt
-index b0fcc59..69aca93 100644
---- a/packages/seacas/libraries/exodus/CMakeLists.txt
-+++ b/packages/seacas/libraries/exodus/CMakeLists.txt
-@@ -47,7 +47,7 @@ if (${CMAKE_PROJECT_NAME} STREQUAL "SEACASProj")
-               ${SOURCES} ${DEP_SOURCES}
-       )
-       set_target_properties(exodus_static PROPERTIES OUTPUT_NAME exodus)
--      INSTALL(TARGETS exodus_static DESTINATION ${CMAKE_INSTALL_PREFIX}/lib)
-+      INSTALL(TARGETS exodus_static DESTINATION lib)
-    endif(BUILD_SHARED_LIBS)
- 
-    # For backwards compatability, the C exodus library was called libexoIIv2c.a
-diff --git a/packages/seacas/libraries/exodus_for/CMakeLists.txt b/packages/seacas/libraries/exodus_for/CMakeLists.txt
-index 3b9d270..5660c72 100644
---- a/packages/seacas/libraries/exodus_for/CMakeLists.txt
-+++ b/packages/seacas/libraries/exodus_for/CMakeLists.txt
-@@ -29,7 +29,7 @@ if (${CMAKE_PROJECT_NAME} STREQUAL "SEACASProj")
-       ${SOURCES}
-     )
-     set_target_properties(exodus_for_static PROPERTIES OUTPUT_NAME exodus_for)
--    INSTALL(TARGETS exodus_for_static DESTINATION ${CMAKE_INSTALL_PREFIX}/lib)
-+    INSTALL(TARGETS exodus_for_static DESTINATION lib)
-   endif()
- 
-   # For backwards compatability, the Fortran exodus library was called libexoIIv2for.a
-diff --git a/packages/trios/libraries/support/CMakeLists.txt b/packages/trios/libraries/support/CMakeLists.txt
-index 3b8c4fd..175f736 100644
---- a/packages/trios/libraries/support/CMakeLists.txt
-+++ b/packages/trios/libraries/support/CMakeLists.txt
-@@ -168,6 +168,6 @@ TRIBITS_ADD_LIBRARY(
- 
- ########### install targets ###############
- 
--# INSTALL(FILES ${MODULES} DESTINATION ${CMAKE_INSTALL_PREFIX}/include)
-+# INSTALL(FILES ${MODULES} DESTINATION include)
- 
- TRIBITS_SUBPACKAGE_POSTPROCESS()
-diff --git a/packages/zoltan/src/CMakeLists.txt b/packages/zoltan/src/CMakeLists.txt
-index 84f1e82..10a8a89 100644
---- a/packages/zoltan/src/CMakeLists.txt
-+++ b/packages/zoltan/src/CMakeLists.txt
-@@ -681,5 +681,5 @@ TRIBITS_ADD_LIBRARY(
-   IMPORTEDLIBS ${IMPORTEDLIBS}
-   )
- 
--INSTALL(FILES ${MODULES} DESTINATION ${CMAKE_INSTALL_PREFIX}/include)
-+INSTALL(FILES ${MODULES} DESTINATION include)
- 
-diff --git a/packages/zoltan/src/fdriver/CMakeLists.txt b/packages/zoltan/src/fdriver/CMakeLists.txt
-index 32913f3..8dd9cba 100644
---- a/packages/zoltan/src/fdriver/CMakeLists.txt
-+++ b/packages/zoltan/src/fdriver/CMakeLists.txt
-@@ -33,6 +33,6 @@ IF(${PROJECT_NAME}_ENABLE_Fortran AND BUILD_ZOLTAN_F90_INTERFACE)
- 
- #  What is a good location for executables zdrive and zCPPdrive?
- #  When should they be moved there?  During install?  Or build?
--#INSTALL(FILES ${CMAKE_CURRENT_BINARY_DIR}/zfdrive.exe DESTINATION ${CMAKE_INSTALL_PREFIX}/bin)
-+#INSTALL(FILES ${CMAKE_CURRENT_BINARY_DIR}/zfdrive.exe DESTINATION bin)
- 
- ENDIF()
-diff --git a/packages/ForTrilinos/docs/CMakeLists.txt b/packages/ForTrilinos/docs/CMakeLists.txt
-index 0ea4b83..a4b2aae 100644
---- a/packages/ForTrilinos/docs/CMakeLists.txt
-+++ b/packages/ForTrilinos/docs/CMakeLists.txt
-@@ -9,5 +9,5 @@ ADD_CUSTOM_TARGET(docs ALL
- )
- 
- INSTALL(DIRECTORY "${CMAKE_CURRENT_BINARY_DIR}/html"
--    DESTINATION "${CMAKE_INSTALL_PREFIX}/docs"
-+    DESTINATION " docs"
- )
-diff --git a/packages/kokkos-kernels/src/CMakeLists.txt b/packages/kokkos-kernels/src/CMakeLists.txt
-index 8db1b51..78deb76 100644
---- a/packages/kokkos-kernels/src/CMakeLists.txt
-+++ b/packages/kokkos-kernels/src/CMakeLists.txt
-@@ -4,7 +4,7 @@ TRIBITS_CONFIGURE_FILE(${PACKAGE_NAME}_config.h)
- INCLUDE_DIRECTORIES(${CMAKE_CURRENT_BINARY_DIR})
- INCLUDE_DIRECTORIES(${CMAKE_CURRENT_SOURCE_DIR})
- 
--SET(TRILINOS_INCDIR ${CMAKE_INSTALL_PREFIX}/${${PROJECT_NAME}_INSTALL_INCLUDE_DIR})
-+SET(TRILINOS_INCDIR ${${PROJECT_NAME}_INSTALL_INCLUDE_DIR})
- 
- #-----------------------------------------------------------------------------
- 
-diff --git a/packages/kokkos/cmake/kokkos.cmake b/packages/kokkos/cmake/kokkos.cmake
-index 235b7ea..52477cb 100644
---- a/packages/kokkos/cmake/kokkos.cmake
-+++ b/packages/kokkos/cmake/kokkos.cmake
-@@ -985,14 +985,6 @@ ENDIF()
- SET(INSTALL_CMAKE_DIR ${DEF_INSTALL_CMAKE_DIR} CACHE PATH
-     "Installation directory for CMake files")
- 
--# Make relative paths absolute (needed later on)
--FOREACH(p LIB BIN INCLUDE CMAKE)
--  SET(var INSTALL_${p}_DIR)
--  IF(NOT IS_ABSOLUTE "${${var}}")
--    SET(${var} "${CMAKE_INSTALL_PREFIX}/${${var}}")
--  ENDIF()
--ENDFOREACH()
--
- # set up include-directories
- SET (Kokkos_INCLUDE_DIRS
-     ${Kokkos_SOURCE_DIR}/core/src
-@@ -1022,9 +1014,9 @@ IF(KOKKOS_SEPARATE_LIBS)
- 
-   # Install the kokkoscore library
-   INSTALL (TARGETS kokkoscore
--           ARCHIVE DESTINATION ${CMAKE_INSTALL_PREFIX}/lib
--           LIBRARY DESTINATION ${CMAKE_INSTALL_PREFIX}/lib
--           RUNTIME DESTINATION ${CMAKE_INSTALL_PREFIX}/bin
-+    ARCHIVE DESTINATION ${${PROJECT_NAME}_INSTALL_LIB_DIR}
-+    LIBRARY DESTINATION ${${PROJECT_NAME}_INSTALL_LIB_DIR}
-+    RUNTIME DESTINATION bin
-   )
- 
-   # Install the kokkoscore headers
-@@ -1059,9 +1051,10 @@ IF(KOKKOS_SEPARATE_LIBS)
- 
-   # Install the kokkocontainers library
-   INSTALL (TARGETS kokkoscontainers
--           ARCHIVE DESTINATION ${CMAKE_INSTALL_PREFIX}/lib
--           LIBRARY DESTINATION ${CMAKE_INSTALL_PREFIX}/lib
--           RUNTIME DESTINATION ${CMAKE_INSTALL_PREFIX}/bin)
-+    ARCHIVE DESTINATION ${${PROJECT_NAME}_INSTALL_LIB_DIR}
-+    LIBRARY DESTINATION ${${PROJECT_NAME}_INSTALL_LIB_DIR}
-+    RUNTIME DESTINATION bin
-+    )
- 
-   # Install the kokkoscontainers headers
-   INSTALL (DIRECTORY
-@@ -1088,9 +1081,10 @@ IF(KOKKOS_SEPARATE_LIBS)
- 
-   # Install the kokkoalgorithms library
-   INSTALL (TARGETS kokkosalgorithms
--           ARCHIVE DESTINATION ${CMAKE_INSTALL_PREFIX}/lib
--           LIBRARY DESTINATION ${CMAKE_INSTALL_PREFIX}/lib
--           RUNTIME DESTINATION ${CMAKE_INSTALL_PREFIX}/bin)
-+    ARCHIVE DESTINATION ${${PROJECT_NAME}_INSTALL_LIB_DIR}
-+    LIBRARY DESTINATION ${${PROJECT_NAME}_INSTALL_LIB_DIR}
-+    RUNTIME DESTINATION bin
-+    )
- 
-   # Install the kokkosalgorithms headers
-   INSTALL (DIRECTORY
-@@ -1128,9 +1122,10 @@ ELSE()
-   # Install the kokkos library
-   INSTALL (TARGETS kokkos
-            EXPORT KokkosTargets
--           ARCHIVE DESTINATION ${CMAKE_INSTALL_PREFIX}/lib
--           LIBRARY DESTINATION ${CMAKE_INSTALL_PREFIX}/lib
--           RUNTIME DESTINATION ${CMAKE_INSTALL_PREFIX}/bin)
-+    ARCHIVE DESTINATION ${${PROJECT_NAME}_INSTALL_LIB_DIR}
-+    LIBRARY DESTINATION ${${PROJECT_NAME}_INSTALL_LIB_DIR}
-+    RUNTIME DESTINATION bin
-+    )
- 
- 
-   # Install the kokkos headers
-diff --git a/packages/kokkos/containers/src/CMakeLists.txt b/packages/kokkos/containers/src/CMakeLists.txt
-index da5a791..65a7c76 100644
---- a/packages/kokkos/containers/src/CMakeLists.txt
-+++ b/packages/kokkos/containers/src/CMakeLists.txt
-@@ -15,7 +15,7 @@ FILE(GLOB HEADERS *.hpp)
- FILE(GLOB HEADERS_IMPL impl/*.hpp)

- FILE(GLOB SOURCES impl/*.cpp)

- 

--SET(TRILINOS_INCDIR ${CMAKE_INSTALL_PREFIX}/${${PROJECT_NAME}_INSTALL_INCLUDE_DIR})

-+SET(TRILINOS_INCDIR ${${PROJECT_NAME}_INSTALL_INCLUDE_DIR})

- 

- INSTALL(FILES ${HEADERS_IMPL} DESTINATION ${TRILINOS_INCDIR}/impl/)

- 

-diff --git a/packages/kokkos/core/src/CMakeLists.txt b/packages/kokkos/core/src/CMakeLists.txt
-index 492470d..3c8eeea 100644
---- a/packages/kokkos/core/src/CMakeLists.txt
-+++ b/packages/kokkos/core/src/CMakeLists.txt
-@@ -40,7 +40,7 @@ INCLUDE_DIRECTORIES(${CMAKE_CURRENT_SOURCE_DIR})
- 

- #-----------------------------------------------------------------------------

- 

--SET(TRILINOS_INCDIR ${CMAKE_INSTALL_PREFIX}/${${PROJECT_NAME}_INSTALL_INCLUDE_DIR})

-+SET(TRILINOS_INCDIR ${${PROJECT_NAME}_INSTALL_INCLUDE_DIR})

- 

- #-----------------------------------------------------------------------------

- 

-diff --git a/packages/kokkos/core/src/impl/CMakeLists.txt b/packages/kokkos/core/src/impl/CMakeLists.txt
-index c543194..1021f42 100644
---- a/packages/kokkos/core/src/impl/CMakeLists.txt
-+++ b/packages/kokkos/core/src/impl/CMakeLists.txt
-@@ -12,7 +12,7 @@ TRIBITS_ADD_LIBRARY(
-     DEPLIBS 

-     )

- 

--SET(TRILINOS_INCDIR ${CMAKE_INSTALL_PREFIX}/${${PROJECT_NAME}_INSTALL_INCLUDE_DIR})

-+SET(TRILINOS_INCDIR ${${PROJECT_NAME}_INSTALL_INCLUDE_DIR})

- 

- INSTALL(FILES ${HEADERS} DESTINATION ${TRILINOS_INCDIR}/impl/)

- 

-diff --git a/packages/seacas/libraries/exodus/CMakeLists.txt b/packages/seacas/libraries/exodus/CMakeLists.txt
-index 69aca93..9d80c9c 100644
---- a/packages/seacas/libraries/exodus/CMakeLists.txt
-+++ b/packages/seacas/libraries/exodus/CMakeLists.txt
-@@ -52,7 +52,7 @@ if (${CMAKE_PROJECT_NAME} STREQUAL "SEACASProj")
- 
-    # For backwards compatability, the C exodus library was called libexoIIv2c.a
-    # Create a symbolic link from libexodus.a to libexoIIv2c.a -- do only for static lib
--   InstallSymLink(libexodus.a ${CMAKE_INSTALL_PREFIX}/lib/libexoIIv2c.a)
-+   InstallSymLink(libexodus.a  lib/libexoIIv2c.a)
- endif()
- 
- TRIBITS_ADD_TEST_DIRECTORIES(test)
-diff --git a/packages/seacas/libraries/exodus_for/CMakeLists.txt b/packages/seacas/libraries/exodus_for/CMakeLists.txt
-index 5660c72..f9c0511 100644
---- a/packages/seacas/libraries/exodus_for/CMakeLists.txt
-+++ b/packages/seacas/libraries/exodus_for/CMakeLists.txt
-@@ -34,7 +34,7 @@ if (${CMAKE_PROJECT_NAME} STREQUAL "SEACASProj")
- 
-   # For backwards compatability, the Fortran exodus library was called libexoIIv2for.a
-   # Create a symbolic link from libexodus_for.a to libexoIIv2for.a -- do only for static lib
--  InstallSymLink(libexodus_for.a ${CMAKE_INSTALL_PREFIX}/lib/libexoIIv2for.a)
-+  InstallSymLink(libexodus_for.a  lib/libexoIIv2for.a)
- endif()
- 
- TRIBITS_ADD_TEST_DIRECTORIES(test)
-diff --git a/packages/seacas/libraries/ioss/src/visualization/ParaViewCatalystIossAdapter/CMakeLists.txt b/packages/seacas/libraries/ioss/src/visualization/ParaViewCatalystIossAdapter/CMakeLists.txt
-index f4704d3..0b4d7c6 100644
---- a/packages/seacas/libraries/ioss/src/visualization/ParaViewCatalystIossAdapter/CMakeLists.txt
-+++ b/packages/seacas/libraries/ioss/src/visualization/ParaViewCatalystIossAdapter/CMakeLists.txt
-@@ -23,11 +23,11 @@ endif()
- 
- SET(CMAKE_SKIP_BUILD_RPATH FALSE)
- SET(CMAKE_BUILD_WITH_INSTALL_RPATH FALSE)
--SET(CMAKE_INSTALL_RPATH "${CMAKE_INSTALL_PREFIX}/lib" ${PARAVIEW_PYTHON_LIBRARY_RPATH_DIRECTORY})
-+SET(CMAKE_INSTALL_RPATH " lib" ${PARAVIEW_PYTHON_LIBRARY_RPATH_DIRECTORY})
- SET(CMAKE_INSTALL_RPATH_USE_LINK_PATH TRUE)
--LIST(FIND CMAKE_PLATFORM_IMPLICIT_LINK_DIRECTORIES "${CMAKE_INSTALL_PREFIX}/lib" isSystemDir)
-+LIST(FIND CMAKE_PLATFORM_IMPLICIT_LINK_DIRECTORIES " lib" isSystemDir)
- IF("${isSystemDir}" STREQUAL "-1")
--   SET(CMAKE_INSTALL_RPATH "${CMAKE_INSTALL_PREFIX}/lib")
-+   SET(CMAKE_INSTALL_RPATH " lib")
- ENDIF("${isSystemDir}" STREQUAL "-1")
- 
- include_directories("include")
-diff --git a/packages/shylu/basker/src/CMakeLists.txt b/packages/shylu/basker/src/CMakeLists.txt
-index b52c4a3..671ca7b 100644
---- a/packages/shylu/basker/src/CMakeLists.txt
-+++ b/packages/shylu/basker/src/CMakeLists.txt
-@@ -6,7 +6,7 @@ INCLUDE_DIRECTORIES(${CMAKE_CURRENT_SOURCE_DIR})
- 

- #-----------------------------------------------------------------------------

- 

--SET(TRILINOS_INCDIR ${CMAKE_INSTALL_PREFIX}/${${PROJECT_NAME}_INSTALL_INCLUDE_DIR})

-+SET(TRILINOS_INCDIR ${${PROJECT_NAME}_INSTALL_INCLUDE_DIR})

- 

- #-----------------------------------------------------------------------------

- 

-diff --git a/packages/shylu/bddc/src/CMakeLists.txt b/packages/shylu/bddc/src/CMakeLists.txt
-index bcb8f2e..bfece1a 100644
---- a/packages/shylu/bddc/src/CMakeLists.txt
-+++ b/packages/shylu/bddc/src/CMakeLists.txt
-@@ -6,7 +6,7 @@ INCLUDE_DIRECTORIES(${CMAKE_CURRENT_SOURCE_DIR})
- 
- #-----------------------------------------------------------------------------
- 
--SET(TRILINOS_INCDIR ${CMAKE_INSTALL_PREFIX}/${${PROJECT_NAME}_INSTALL_INCLUDE_DIR})
-+SET(TRILINOS_INCDIR ${${PROJECT_NAME}_INSTALL_INCLUDE_DIR})
- 
- #-----------------------------------------------------------------------------
- 
-diff --git a/packages/shylu/fastilu/src/CMakeLists.txt b/packages/shylu/fastilu/src/CMakeLists.txt
-index 9ad8846..e226b30 100644
---- a/packages/shylu/fastilu/src/CMakeLists.txt
-+++ b/packages/shylu/fastilu/src/CMakeLists.txt
-@@ -6,7 +6,7 @@ INCLUDE_DIRECTORIES(${CMAKE_CURRENT_SOURCE_DIR})
- 
- #-----------------------------------------------------------------------------
- 
--SET(TRILINOS_INCDIR ${CMAKE_INSTALL_PREFIX}/${${PROJECT_NAME}_INSTALL_INCLUDE_DIR})
-+SET(TRILINOS_INCDIR ${${PROJECT_NAME}_INSTALL_INCLUDE_DIR})
- 
- #-----------------------------------------------------------------------------
- 
-diff --git a/packages/shylu/hts/src/CMakeLists.txt b/packages/shylu/hts/src/CMakeLists.txt
-index d8ec572..c7807f8 100644
---- a/packages/shylu/hts/src/CMakeLists.txt
-+++ b/packages/shylu/hts/src/CMakeLists.txt
-@@ -18,7 +18,7 @@ TRIBITS_CONFIGURE_FILE(${PACKAGE_NAME}_config.h)
- INCLUDE_DIRECTORIES(${CMAKE_CURRENT_BINARY_DIR})
- INCLUDE_DIRECTORIES(${CMAKE_CURRENT_SOURCE_DIR})
- 
--SET(TRILINOS_INCDIR ${CMAKE_INSTALL_PREFIX}/${${PROJECT_NAME}_INSTALL_INCLUDE_DIR})
-+SET(TRILINOS_INCDIR ${${PROJECT_NAME}_INSTALL_INCLUDE_DIR})
- 
- SET(SOURCES shylu_hts.cpp)
- SET(HEADERS_PUBLIC shylu_hts.hpp shylu_hts_decl.hpp shylu_hts_impl.hpp shylu_hts_impl_def.hpp)
-diff --git a/packages/shylu/tacho/core/src/CMakeLists.txt b/packages/shylu/tacho/core/src/CMakeLists.txt
-index 1e44b1e..b24e994 100644
---- a/packages/shylu/tacho/core/src/CMakeLists.txt
-+++ b/packages/shylu/tacho/core/src/CMakeLists.txt
-@@ -6,7 +6,7 @@ INCLUDE_DIRECTORIES(${CMAKE_CURRENT_SOURCE_DIR})
- 

- #-----------------------------------------------------------------------------

- 

--SET(TRILINOS_INCDIR ${CMAKE_INSTALL_PREFIX}/${${PROJECT_NAME}_INSTALL_INCLUDE_DIR})

-+SET(TRILINOS_INCDIR ${${PROJECT_NAME}_INSTALL_INCLUDE_DIR})

- 

- #-----------------------------------------------------------------------------

- 

-diff --git a/packages/shylu/tacho/deprecated/src/CMakeLists.txt b/packages/shylu/tacho/deprecated/src/CMakeLists.txt
-index 54ce6d8..7697514 100644
---- a/packages/shylu/tacho/deprecated/src/CMakeLists.txt
-+++ b/packages/shylu/tacho/deprecated/src/CMakeLists.txt
-@@ -6,7 +6,7 @@ INCLUDE_DIRECTORIES(${CMAKE_CURRENT_SOURCE_DIR})
- 

- #-----------------------------------------------------------------------------

- 

--SET(TRILINOS_INCDIR ${CMAKE_INSTALL_PREFIX}/${${PROJECT_NAME}_INSTALL_INCLUDE_DIR})

-+SET(TRILINOS_INCDIR ${${PROJECT_NAME}_INSTALL_INCLUDE_DIR})

- 

- #-----------------------------------------------------------------------------

- 

-diff --git a/packages/shylu/tacho/refactor/src/CMakeLists.txt b/packages/shylu/tacho/refactor/src/CMakeLists.txt
-index e3dd6d1..83abb98 100644
---- a/packages/shylu/tacho/refactor/src/CMakeLists.txt
-+++ b/packages/shylu/tacho/refactor/src/CMakeLists.txt
-@@ -6,7 +6,7 @@ INCLUDE_DIRECTORIES(${CMAKE_CURRENT_SOURCE_DIR})
- 

- #-----------------------------------------------------------------------------

- 

--SET(TRILINOS_INCDIR ${CMAKE_INSTALL_PREFIX}/${${PROJECT_NAME}_INSTALL_INCLUDE_DIR})

-+SET(TRILINOS_INCDIR ${${PROJECT_NAME}_INSTALL_INCLUDE_DIR})

- 

- #-----------------------------------------------------------------------------

- 

-diff --git a/packages/stk/stk_classic/stk_adapt/stk_adapt/CMakeLists.txt b/packages/stk/stk_classic/stk_adapt/stk_adapt/CMakeLists.txt
-index 695b21d..4a24142 100644
---- a/packages/stk/stk_classic/stk_adapt/stk_adapt/CMakeLists.txt
-+++ b/packages/stk/stk_classic/stk_adapt/stk_adapt/CMakeLists.txt
-@@ -46,7 +46,7 @@ TRIBITS_ADD_LIBRARY(
- )
- 
- INSTALL(FILES ${HEADERS} DESTINATION
--${CMAKE_INSTALL_PREFIX}/${${PROJECT_NAME}_INSTALL_INCLUDE_DIR}/stk_adapt/)
-+ ${${PROJECT_NAME}_INSTALL_INCLUDE_DIR}/stk_adapt/)
- 
- ADD_SUBDIRECTORY(main)
- 
-diff --git a/packages/stk/stk_classic/stk_adapt/stk_adapt/sierra_element/CMakeLists.txt b/packages/stk/stk_classic/stk_adapt/stk_adapt/sierra_element/CMakeLists.txt
-index db930be..50fbe8b 100644
---- a/packages/stk/stk_classic/stk_adapt/stk_adapt/sierra_element/CMakeLists.txt
-+++ b/packages/stk/stk_classic/stk_adapt/stk_adapt/sierra_element/CMakeLists.txt
-@@ -34,5 +34,5 @@ ENDIF()
- 
- 
- INSTALL(FILES ${HEADERS} DESTINATION
--    ${CMAKE_INSTALL_PREFIX}/${${PROJECT_NAME}_INSTALL_INCLUDE_DIR}/stk_adapt/sierra_element/)
-+     ${${PROJECT_NAME}_INSTALL_INCLUDE_DIR}/stk_adapt/sierra_element/)
- 
-diff --git a/packages/stk/stk_classic/stk_algsup/stk_algsup/CMakeLists.txt b/packages/stk/stk_classic/stk_algsup/stk_algsup/CMakeLists.txt
-index e4b4503..16411f9 100644
---- a/packages/stk/stk_classic/stk_algsup/stk_algsup/CMakeLists.txt
-+++ b/packages/stk/stk_classic/stk_algsup/stk_algsup/CMakeLists.txt
-@@ -21,5 +21,5 @@ TRIBITS_ADD_LIBRARY(
-   )
- 
- INSTALL(FILES ${HEADERS} DESTINATION
--    ${CMAKE_INSTALL_PREFIX}/${${PROJECT_NAME}_INSTALL_INCLUDE_DIR}/stk_algsup/)
-+     ${${PROJECT_NAME}_INSTALL_INCLUDE_DIR}/stk_algsup/)
- 
-diff --git a/packages/stk/stk_classic/stk_expreval/stk_expreval/CMakeLists.txt b/packages/stk/stk_classic/stk_expreval/stk_expreval/CMakeLists.txt
-index ef47a26..c83420b 100644
---- a/packages/stk/stk_classic/stk_expreval/stk_expreval/CMakeLists.txt
-+++ b/packages/stk/stk_classic/stk_expreval/stk_expreval/CMakeLists.txt
-@@ -46,4 +46,4 @@ TRIBITS_ADD_LIBRARY(
-   )
- 
- INSTALL(FILES ${HEADERS} DESTINATION
--    ${CMAKE_INSTALL_PREFIX}/${${PROJECT_NAME}_INSTALL_INCLUDE_DIR}/stk_expreval)
-+     ${${PROJECT_NAME}_INSTALL_INCLUDE_DIR}/stk_expreval)
-diff --git a/packages/stk/stk_classic/stk_io/stk_io/CMakeLists.txt b/packages/stk/stk_classic/stk_io/stk_io/CMakeLists.txt
-index cf6032d..2d04b5b 100644
---- a/packages/stk/stk_classic/stk_io/stk_io/CMakeLists.txt
-+++ b/packages/stk/stk_classic/stk_io/stk_io/CMakeLists.txt
-@@ -49,7 +49,7 @@ TRIBITS_ADD_LIBRARY(
-   )
- 
- INSTALL(FILES ${HEADERS} DESTINATION
--${CMAKE_INSTALL_PREFIX}/${${PROJECT_NAME}_INSTALL_INCLUDE_DIR}/stk_io/)
-+ ${${PROJECT_NAME}_INSTALL_INCLUDE_DIR}/stk_io/)
- 
- # AGS: I moved this to the bottom so that the link order was correct
- # with  -lstk_io_uti before -lstk_io.  I think the DEPLIBS added in
-diff --git a/packages/stk/stk_classic/stk_io/stk_io/util/CMakeLists.txt b/packages/stk/stk_classic/stk_io/stk_io/util/CMakeLists.txt
-index e5befd0..da4fac6 100644
---- a/packages/stk/stk_classic/stk_io/stk_io/util/CMakeLists.txt
-+++ b/packages/stk/stk_classic/stk_io/stk_io/util/CMakeLists.txt
-@@ -45,4 +45,4 @@ TRIBITS_ADD_LIBRARY(
-   )
- 
- INSTALL(FILES ${HEADERS} DESTINATION
--    ${CMAKE_INSTALL_PREFIX}/${${PROJECT_NAME}_INSTALL_INCLUDE_DIR}/stk_io/util/)
-+     ${${PROJECT_NAME}_INSTALL_INCLUDE_DIR}/stk_io/util/)
-diff --git a/packages/stk/stk_classic/stk_mesh/stk_mesh/base/CMakeLists.txt b/packages/stk/stk_classic/stk_mesh/stk_mesh/base/CMakeLists.txt
-index fc50a5b..cc2cf5b 100644
---- a/packages/stk/stk_classic/stk_mesh/stk_mesh/base/CMakeLists.txt
-+++ b/packages/stk/stk_classic/stk_mesh/stk_mesh/base/CMakeLists.txt
-@@ -54,7 +54,7 @@ TRIBITS_ADD_LIBRARY(
-   )
- 
- INSTALL(FILES ${HEADERS} DESTINATION
--    ${CMAKE_INSTALL_PREFIX}/${${PROJECT_NAME}_INSTALL_INCLUDE_DIR}/stk_mesh/base/)
-+     ${${PROJECT_NAME}_INSTALL_INCLUDE_DIR}/stk_mesh/base/)
- 
- INSTALL(FILES ${HEADERS_IMPL} DESTINATION
--    ${CMAKE_INSTALL_PREFIX}/${${PROJECT_NAME}_INSTALL_INCLUDE_DIR}/stk_mesh/baseImpl/)
-+     ${${PROJECT_NAME}_INSTALL_INCLUDE_DIR}/stk_mesh/baseImpl/)
-diff --git a/packages/stk/stk_classic/stk_mesh/stk_mesh/fem/CMakeLists.txt b/packages/stk/stk_classic/stk_mesh/stk_mesh/fem/CMakeLists.txt
-index 54ef03e..c1d67db 100644
---- a/packages/stk/stk_classic/stk_mesh/stk_mesh/fem/CMakeLists.txt
-+++ b/packages/stk/stk_classic/stk_mesh/stk_mesh/fem/CMakeLists.txt
-@@ -48,5 +48,5 @@ TRIBITS_ADD_LIBRARY(
-   )
- 
- INSTALL(FILES ${HEADERS} DESTINATION
--    ${CMAKE_INSTALL_PREFIX}/${${PROJECT_NAME}_INSTALL_INCLUDE_DIR}/stk_mesh/fem/)
-+     ${${PROJECT_NAME}_INSTALL_INCLUDE_DIR}/stk_mesh/fem/)
- 
-diff --git a/packages/stk/stk_classic/stk_mesh/stk_mesh/fixtures/CMakeLists.txt b/packages/stk/stk_classic/stk_mesh/stk_mesh/fixtures/CMakeLists.txt
-index 18e8e08..f0e2a4d 100644
---- a/packages/stk/stk_classic/stk_mesh/stk_mesh/fixtures/CMakeLists.txt
-+++ b/packages/stk/stk_classic/stk_mesh/stk_mesh/fixtures/CMakeLists.txt
-@@ -54,4 +54,4 @@ TRIBITS_ADD_LIBRARY(
-   )
- 
- INSTALL(FILES ${HEADERS} DESTINATION
--    ${CMAKE_INSTALL_PREFIX}/${${PROJECT_NAME}_INSTALL_INCLUDE_DIR}/stk_mesh/fixtures/)
-+     ${${PROJECT_NAME}_INSTALL_INCLUDE_DIR}/stk_mesh/fixtures/)
-diff --git a/packages/stk/stk_classic/stk_percept/stk_percept/CMakeLists.txt b/packages/stk/stk_classic/stk_percept/stk_percept/CMakeLists.txt
-index 854268d..4357edc 100644
---- a/packages/stk/stk_classic/stk_percept/stk_percept/CMakeLists.txt
-+++ b/packages/stk/stk_classic/stk_percept/stk_percept/CMakeLists.txt
-@@ -68,5 +68,5 @@ TRIBITS_ADD_LIBRARY(
- )
- 
- INSTALL(FILES ${HEADERS} DESTINATION
--${CMAKE_INSTALL_PREFIX}/${${PROJECT_NAME}_INSTALL_INCLUDE_DIR}/stk_percept/)
-+ ${${PROJECT_NAME}_INSTALL_INCLUDE_DIR}/stk_percept/)
- 
-diff --git a/packages/stk/stk_classic/stk_percept/stk_percept/fixtures/CMakeLists.txt b/packages/stk/stk_classic/stk_percept/stk_percept/fixtures/CMakeLists.txt
-index 10868c3..3fa5425 100644
---- a/packages/stk/stk_classic/stk_percept/stk_percept/fixtures/CMakeLists.txt
-+++ b/packages/stk/stk_classic/stk_percept/stk_percept/fixtures/CMakeLists.txt
-@@ -35,5 +35,5 @@ ENDIF()
- 
- 
- INSTALL(FILES ${HEADERS} DESTINATION
--    ${CMAKE_INSTALL_PREFIX}/${${PROJECT_NAME}_INSTALL_INCLUDE_DIR}/stk_percept/fixtures/)
-+     ${${PROJECT_NAME}_INSTALL_INCLUDE_DIR}/stk_percept/fixtures/)
- 
-diff --git a/packages/stk/stk_classic/stk_percept/stk_percept/function/CMakeLists.txt b/packages/stk/stk_classic/stk_percept/stk_percept/function/CMakeLists.txt
-index a60a1a8..40e0d03 100644
---- a/packages/stk/stk_classic/stk_percept/stk_percept/function/CMakeLists.txt
-+++ b/packages/stk/stk_classic/stk_percept/stk_percept/function/CMakeLists.txt
-@@ -37,5 +37,5 @@ ENDIF()
- 
- 
- INSTALL(FILES ${HEADERS} DESTINATION
--    ${CMAKE_INSTALL_PREFIX}/${${PROJECT_NAME}_INSTALL_INCLUDE_DIR}/stk_percept/function/)
-+     ${${PROJECT_NAME}_INSTALL_INCLUDE_DIR}/stk_percept/function/)
- 
-diff --git a/packages/stk/stk_classic/stk_percept/stk_percept/function/internal/CMakeLists.txt b/packages/stk/stk_classic/stk_percept/stk_percept/function/internal/CMakeLists.txt
-index ebea648..698207f 100644
---- a/packages/stk/stk_classic/stk_percept/stk_percept/function/internal/CMakeLists.txt
-+++ b/packages/stk/stk_classic/stk_percept/stk_percept/function/internal/CMakeLists.txt
-@@ -36,5 +36,5 @@ ENDIF()
- 
- 
- INSTALL(FILES ${HEADERS} DESTINATION
--    ${CMAKE_INSTALL_PREFIX}/${${PROJECT_NAME}_INSTALL_INCLUDE_DIR}/stk_percept/function/internal/)
-+     ${${PROJECT_NAME}_INSTALL_INCLUDE_DIR}/stk_percept/function/internal/)
- 
-diff --git a/packages/stk/stk_classic/stk_percept/stk_percept/math/CMakeLists.txt b/packages/stk/stk_classic/stk_percept/stk_percept/math/CMakeLists.txt
-index 2b256f1..417eebb 100644
---- a/packages/stk/stk_classic/stk_percept/stk_percept/math/CMakeLists.txt
-+++ b/packages/stk/stk_classic/stk_percept/stk_percept/math/CMakeLists.txt
-@@ -35,5 +35,5 @@ ENDIF()
- 
- 
- INSTALL(FILES ${HEADERS} DESTINATION
--    ${CMAKE_INSTALL_PREFIX}/${${PROJECT_NAME}_INSTALL_INCLUDE_DIR}/stk_percept/math/)
-+     ${${PROJECT_NAME}_INSTALL_INCLUDE_DIR}/stk_percept/math/)
- 
-diff --git a/packages/stk/stk_classic/stk_percept/stk_percept/mesh/gen/CMakeLists.txt b/packages/stk/stk_classic/stk_percept/stk_percept/mesh/gen/CMakeLists.txt
-index 2acb307..5680bb1 100644
---- a/packages/stk/stk_classic/stk_percept/stk_percept/mesh/gen/CMakeLists.txt
-+++ b/packages/stk/stk_classic/stk_percept/stk_percept/mesh/gen/CMakeLists.txt
-@@ -35,5 +35,5 @@ ENDIF()
- 
- 
- INSTALL(FILES ${HEADERS} DESTINATION
--    ${CMAKE_INSTALL_PREFIX}/${${PROJECT_NAME}_INSTALL_INCLUDE_DIR}/stk_percept/mesh/gen/)
-+     ${${PROJECT_NAME}_INSTALL_INCLUDE_DIR}/stk_percept/mesh/gen/)
- 
-diff --git a/packages/stk/stk_classic/stk_percept/stk_percept/norm/CMakeLists.txt b/packages/stk/stk_classic/stk_percept/stk_percept/norm/CMakeLists.txt
-index e9c2a8c..9509d0a 100644
---- a/packages/stk/stk_classic/stk_percept/stk_percept/norm/CMakeLists.txt
-+++ b/packages/stk/stk_classic/stk_percept/stk_percept/norm/CMakeLists.txt
-@@ -35,5 +35,5 @@ ENDIF()
- 
- 
- INSTALL(FILES ${HEADERS} DESTINATION
--    ${CMAKE_INSTALL_PREFIX}/${${PROJECT_NAME}_INSTALL_INCLUDE_DIR}/stk_percept/norm/)
-+     ${${PROJECT_NAME}_INSTALL_INCLUDE_DIR}/stk_percept/norm/)
- 
-diff --git a/packages/stk/stk_classic/stk_percept/stk_percept/util/CMakeLists.txt b/packages/stk/stk_classic/stk_percept/stk_percept/util/CMakeLists.txt
-index 63ae85d..cb496d0 100644
---- a/packages/stk/stk_classic/stk_percept/stk_percept/util/CMakeLists.txt
-+++ b/packages/stk/stk_classic/stk_percept/stk_percept/util/CMakeLists.txt
-@@ -35,5 +35,5 @@ ENDIF()
- 
- 
- INSTALL(FILES ${HEADERS} DESTINATION
--    ${CMAKE_INSTALL_PREFIX}/${${PROJECT_NAME}_INSTALL_INCLUDE_DIR}/stk_percept/util/)
-+     ${${PROJECT_NAME}_INSTALL_INCLUDE_DIR}/stk_percept/util/)
- 
-diff --git a/packages/stk/stk_classic/stk_rebalance/stk_rebalance/CMakeLists.txt b/packages/stk/stk_classic/stk_rebalance/stk_rebalance/CMakeLists.txt
-index 9a6f4cc..1248233 100644
---- a/packages/stk/stk_classic/stk_rebalance/stk_rebalance/CMakeLists.txt
-+++ b/packages/stk/stk_classic/stk_rebalance/stk_rebalance/CMakeLists.txt
-@@ -46,4 +46,4 @@ TRIBITS_ADD_LIBRARY(
-   )
- 
- INSTALL(FILES ${HEADERS} DESTINATION
--    ${CMAKE_INSTALL_PREFIX}/${${PROJECT_NAME}_INSTALL_INCLUDE_DIR}/stk_rebalance/)
-+     ${${PROJECT_NAME}_INSTALL_INCLUDE_DIR}/stk_rebalance/)
-diff --git a/packages/stk/stk_classic/stk_rebalance/stk_rebalance_utils/CMakeLists.txt b/packages/stk/stk_classic/stk_rebalance/stk_rebalance_utils/CMakeLists.txt
-index e13d37c..e817940 100644
---- a/packages/stk/stk_classic/stk_rebalance/stk_rebalance_utils/CMakeLists.txt
-+++ b/packages/stk/stk_classic/stk_rebalance/stk_rebalance_utils/CMakeLists.txt
-@@ -18,4 +18,4 @@ TRIBITS_ADD_LIBRARY(
-   )
- 
- INSTALL(FILES ${HEADERS} DESTINATION
--  ${CMAKE_INSTALL_PREFIX}/${${PROJECT_NAME}_INSTALL_INCLUDE_DIR}/stk_rebalance_utils)
-+   ${${PROJECT_NAME}_INSTALL_INCLUDE_DIR}/stk_rebalance_utils)
-diff --git a/packages/stk/stk_classic/stk_search/stk_search/CMakeLists.txt b/packages/stk/stk_classic/stk_search/stk_search/CMakeLists.txt
-index 62e9b60..2c27272 100644
---- a/packages/stk/stk_classic/stk_search/stk_search/CMakeLists.txt
-+++ b/packages/stk/stk_classic/stk_search/stk_search/CMakeLists.txt
-@@ -62,4 +62,4 @@ TRIBITS_ADD_LIBRARY(
-   )
- 
- INSTALL(FILES ${HEADERS} DESTINATION
--    ${CMAKE_INSTALL_PREFIX}/${${PROJECT_NAME}_INSTALL_INCLUDE_DIR}/stk_search)
-+     ${${PROJECT_NAME}_INSTALL_INCLUDE_DIR}/stk_search)
-diff --git a/packages/stk/stk_classic/stk_search/stk_search/diag/CMakeLists.txt b/packages/stk/stk_classic/stk_search/stk_search/diag/CMakeLists.txt
-index 63d60b9..a4309d1 100644
---- a/packages/stk/stk_classic/stk_search/stk_search/diag/CMakeLists.txt
-+++ b/packages/stk/stk_classic/stk_search/stk_search/diag/CMakeLists.txt
-@@ -34,5 +34,5 @@ ENDIF()
- 
- 
- INSTALL(FILES ${HEADERS} DESTINATION
--    ${CMAKE_INSTALL_PREFIX}/${${PROJECT_NAME}_INSTALL_INCLUDE_DIR}/stk_search/diag/)
-+     ${${PROJECT_NAME}_INSTALL_INCLUDE_DIR}/stk_search/diag/)
- 
-diff --git a/packages/stk/stk_classic/stk_search_util/stk_search_util/stk_mesh/CMakeLists.txt b/packages/stk/stk_classic/stk_search_util/stk_search_util/stk_mesh/CMakeLists.txt
-index 925daf5..2d42fef 100644
---- a/packages/stk/stk_classic/stk_search_util/stk_search_util/stk_mesh/CMakeLists.txt
-+++ b/packages/stk/stk_classic/stk_search_util/stk_search_util/stk_mesh/CMakeLists.txt
-@@ -54,4 +54,4 @@ TRIBITS_ADD_LIBRARY(
-   )
- 
- #INSTALL(FILES ${HEADERS} DESTINATION
--#    ${CMAKE_INSTALL_PREFIX}/${${PROJECT_NAME}_INSTALL_INCLUDE_DIR}/stk_search)
-+#     ${${PROJECT_NAME}_INSTALL_INCLUDE_DIR}/stk_search)
-diff --git a/packages/stk/stk_classic/stk_util/stk_util/CMakeLists.txt b/packages/stk/stk_classic/stk_util/stk_util/CMakeLists.txt
-index 4a91d34..956f411 100644
---- a/packages/stk/stk_classic/stk_util/stk_util/CMakeLists.txt
-+++ b/packages/stk/stk_classic/stk_util/stk_util/CMakeLists.txt
-@@ -16,6 +16,6 @@ ENDIF()
- TRIBITS_CONFIGURE_FILE(${PACKAGE_NAME}_config.h)
- 
- INSTALL(FILES stk_config.h DESTINATION
--    ${CMAKE_INSTALL_PREFIX}/${${PROJECT_NAME}_INSTALL_INCLUDE_DIR}/stk_util/)
-+     ${${PROJECT_NAME}_INSTALL_INCLUDE_DIR}/stk_util/)
- INSTALL(FILES ${CMAKE_CURRENT_BINARY_DIR}/STKClassic_config.h DESTINATION
--    ${CMAKE_INSTALL_PREFIX}/${${PROJECT_NAME}_INSTALL_INCLUDE_DIR})
-+     ${${PROJECT_NAME}_INSTALL_INCLUDE_DIR})
-diff --git a/packages/stk/stk_classic/stk_util/stk_util/diag/CMakeLists.txt b/packages/stk/stk_classic/stk_util/stk_util/diag/CMakeLists.txt
-index 2c0dea4..ea16b39 100644
---- a/packages/stk/stk_classic/stk_util/stk_util/diag/CMakeLists.txt
-+++ b/packages/stk/stk_classic/stk_util/stk_util/diag/CMakeLists.txt
-@@ -82,5 +82,5 @@ TRIBITS_ADD_LIBRARY(
- 
- 
- INSTALL(FILES ${HEADERS} DESTINATION
--    ${CMAKE_INSTALL_PREFIX}/${${PROJECT_NAME}_INSTALL_INCLUDE_DIR}/stk_util/diag/)
-+     ${${PROJECT_NAME}_INSTALL_INCLUDE_DIR}/stk_util/diag/)
- 
-diff --git a/packages/stk/stk_classic/stk_util/stk_util/environment/CMakeLists.txt b/packages/stk/stk_classic/stk_util/stk_util/environment/CMakeLists.txt
-index 93fc5a9..5965b25 100644
---- a/packages/stk/stk_classic/stk_util/stk_util/environment/CMakeLists.txt
-+++ b/packages/stk/stk_classic/stk_util/stk_util/environment/CMakeLists.txt
-@@ -80,4 +80,4 @@ TRIBITS_ADD_LIBRARY(
-   )
- 
- INSTALL(FILES ${HEADERS} DESTINATION
--        ${CMAKE_INSTALL_PREFIX}/${${PROJECT_NAME}_INSTALL_INCLUDE_DIR}/stk_util/environment/)
-+         ${${PROJECT_NAME}_INSTALL_INCLUDE_DIR}/stk_util/environment/)
-diff --git a/packages/stk/stk_classic/stk_util/stk_util/parallel/CMakeLists.txt b/packages/stk/stk_classic/stk_util/stk_util/parallel/CMakeLists.txt
-index 1640ef5..d979eed 100644
---- a/packages/stk/stk_classic/stk_util/stk_util/parallel/CMakeLists.txt
-+++ b/packages/stk/stk_classic/stk_util/stk_util/parallel/CMakeLists.txt
-@@ -61,4 +61,4 @@ TRIBITS_ADD_LIBRARY(
-   )
- 
- INSTALL(FILES ${HEADERS} DESTINATION
--    ${CMAKE_INSTALL_PREFIX}/${${PROJECT_NAME}_INSTALL_INCLUDE_DIR}/stk_util/parallel/)
-+     ${${PROJECT_NAME}_INSTALL_INCLUDE_DIR}/stk_util/parallel/)
-diff --git a/packages/stk/stk_classic/stk_util/stk_util/unit_test_support/CMakeLists.txt b/packages/stk/stk_classic/stk_util/stk_util/unit_test_support/CMakeLists.txt
-index 769bd69..76cb55e 100644
---- a/packages/stk/stk_classic/stk_util/stk_util/unit_test_support/CMakeLists.txt
-+++ b/packages/stk/stk_classic/stk_util/stk_util/unit_test_support/CMakeLists.txt
-@@ -50,4 +50,4 @@ TRIBITS_ADD_LIBRARY(
-   )
- 
- INSTALL(FILES ${HEADERS} DESTINATION
--    ${CMAKE_INSTALL_PREFIX}/${${PROJECT_NAME}_INSTALL_INCLUDE_DIR}/stk_util/unit_test_support/)
-+     ${${PROJECT_NAME}_INSTALL_INCLUDE_DIR}/stk_util/unit_test_support/)
-diff --git a/packages/stk/stk_classic/stk_util/stk_util/use_cases/CMakeLists.txt b/packages/stk/stk_classic/stk_util/stk_util/use_cases/CMakeLists.txt
-index 4585b22..9177777 100644
---- a/packages/stk/stk_classic/stk_util/stk_util/use_cases/CMakeLists.txt
-+++ b/packages/stk/stk_classic/stk_util/stk_util/use_cases/CMakeLists.txt
-@@ -49,4 +49,4 @@ TRIBITS_ADD_LIBRARY(
-   )
- 
- #INSTALL(FILES ${HEADERS} DESTINATION
--#    ${CMAKE_INSTALL_PREFIX}/${${PROJECT_NAME}_INSTALL_INCLUDE_DIR}/stk_util/use_cases/)
-+#     ${${PROJECT_NAME}_INSTALL_INCLUDE_DIR}/stk_util/use_cases/)
-diff --git a/packages/stk/stk_classic/stk_util/stk_util/util/CMakeLists.txt b/packages/stk/stk_classic/stk_util/stk_util/util/CMakeLists.txt
-index b49c92e..76fab68 100644
---- a/packages/stk/stk_classic/stk_util/stk_util/util/CMakeLists.txt
-+++ b/packages/stk/stk_classic/stk_util/stk_util/util/CMakeLists.txt
-@@ -46,4 +46,4 @@ TRIBITS_ADD_LIBRARY(
-   )
- 
- INSTALL(FILES ${HEADERS} DESTINATION
--    ${CMAKE_INSTALL_PREFIX}/${${PROJECT_NAME}_INSTALL_INCLUDE_DIR}/stk_util/util/)
-+     ${${PROJECT_NAME}_INSTALL_INCLUDE_DIR}/stk_util/util/)
-diff --git a/packages/stk/stk_expreval/stk_expreval/CMakeLists.txt b/packages/stk/stk_expreval/stk_expreval/CMakeLists.txt
-index 66e4eb8..806f453 100644
---- a/packages/stk/stk_expreval/stk_expreval/CMakeLists.txt
-+++ b/packages/stk/stk_expreval/stk_expreval/CMakeLists.txt
-@@ -77,4 +77,4 @@ TRIBITS_ADD_LIBRARY(
-   )
- 
- INSTALL(FILES ${HEADERS} DESTINATION
--    ${CMAKE_INSTALL_PREFIX}/${${PROJECT_NAME}_INSTALL_INCLUDE_DIR}/stk_expreval)
-+     ${${PROJECT_NAME}_INSTALL_INCLUDE_DIR}/stk_expreval)
-diff --git a/packages/stk/stk_io/stk_io/CMakeLists.txt b/packages/stk/stk_io/stk_io/CMakeLists.txt
-index eac6ed0..d587e6c 100644
---- a/packages/stk/stk_io/stk_io/CMakeLists.txt
-+++ b/packages/stk/stk_io/stk_io/CMakeLists.txt
-@@ -78,7 +78,7 @@ TRIBITS_ADD_LIBRARY(
-   )
- 
- INSTALL(FILES ${HEADERS} DESTINATION
--${CMAKE_INSTALL_PREFIX}/${${PROJECT_NAME}_INSTALL_INCLUDE_DIR}/stk_io/)
-+ ${${PROJECT_NAME}_INSTALL_INCLUDE_DIR}/stk_io/)
- 
- # AGS: I moved this to the bottom so that the link order was correct
- # with  -lstk_io_uti before -lstk_io.  I think the DEPLIBS added in
-diff --git a/packages/stk/stk_io/stk_io/util/CMakeLists.txt b/packages/stk/stk_io/stk_io/util/CMakeLists.txt
-index 687821f..0fa165e 100644
---- a/packages/stk/stk_io/stk_io/util/CMakeLists.txt
-+++ b/packages/stk/stk_io/stk_io/util/CMakeLists.txt
-@@ -76,4 +76,4 @@ TRIBITS_ADD_LIBRARY(
-   )
- 
- INSTALL(FILES ${HEADERS} DESTINATION
--    ${CMAKE_INSTALL_PREFIX}/${${PROJECT_NAME}_INSTALL_INCLUDE_DIR}/stk_io/util/)
-+     ${${PROJECT_NAME}_INSTALL_INCLUDE_DIR}/stk_io/util/)
-diff --git a/packages/stk/stk_mesh/stk_mesh/base/CMakeLists.txt b/packages/stk/stk_mesh/stk_mesh/base/CMakeLists.txt
-index 67bab20..868f7dd 100644
---- a/packages/stk/stk_mesh/stk_mesh/base/CMakeLists.txt
-+++ b/packages/stk/stk_mesh/stk_mesh/base/CMakeLists.txt
-@@ -84,14 +84,14 @@ TRIBITS_ADD_LIBRARY(
- TRIBITS_CONFIGURE_FILE(${PACKAGE_NAME}_config.h)
- 
- INSTALL(FILES ${HEADERS} DESTINATION
--    ${CMAKE_INSTALL_PREFIX}/${${PROJECT_NAME}_INSTALL_INCLUDE_DIR}/stk_mesh/base/)
-+     ${${PROJECT_NAME}_INSTALL_INCLUDE_DIR}/stk_mesh/base/)
- 
- INSTALL(FILES ${HEADERS_IMPL} DESTINATION
--    ${CMAKE_INSTALL_PREFIX}/${${PROJECT_NAME}_INSTALL_INCLUDE_DIR}/stk_mesh/baseImpl/)
-+     ${${PROJECT_NAME}_INSTALL_INCLUDE_DIR}/stk_mesh/baseImpl/)
- 
- INSTALL(FILES ${HEADERS_ELEMGRAPH} DESTINATION
--    ${CMAKE_INSTALL_PREFIX}/${${PROJECT_NAME}_INSTALL_INCLUDE_DIR}/stk_mesh/baseImpl/elementGraph)
-+     ${${PROJECT_NAME}_INSTALL_INCLUDE_DIR}/stk_mesh/baseImpl/elementGraph)
- 
- INSTALL(FILES ${CMAKE_CURRENT_BINARY_DIR}/${PACKAGE_NAME}_config.h DESTINATION
--        ${CMAKE_INSTALL_PREFIX}/${${PROJECT_NAME}_INSTALL_INCLUDE_DIR})
-+         ${${PROJECT_NAME}_INSTALL_INCLUDE_DIR})
- 
-diff --git a/packages/stk/stk_search/stk_search/CMakeLists.txt b/packages/stk/stk_search/stk_search/CMakeLists.txt
-index ae6cc04..2db70c5 100644
---- a/packages/stk/stk_search/stk_search/CMakeLists.txt
-+++ b/packages/stk/stk_search/stk_search/CMakeLists.txt
-@@ -69,4 +69,4 @@ TRIBITS_ADD_LIBRARY(
-   )
- 
- INSTALL(FILES ${HEADERS} DESTINATION
--    ${CMAKE_INSTALL_PREFIX}/${${PROJECT_NAME}_INSTALL_INCLUDE_DIR}/stk_search)
-+     ${${PROJECT_NAME}_INSTALL_INCLUDE_DIR}/stk_search)
-diff --git a/packages/stk/stk_search_util/stk_search_util/CMakeLists.txt b/packages/stk/stk_search_util/stk_search_util/CMakeLists.txt
-index ca6e439..6f3e687 100644
---- a/packages/stk/stk_search_util/stk_search_util/CMakeLists.txt
-+++ b/packages/stk/stk_search_util/stk_search_util/CMakeLists.txt
-@@ -68,5 +68,5 @@ TRIBITS_ADD_LIBRARY(
-   )
- 
- INSTALL(FILES ${HEADERS} DESTINATION
--    ${CMAKE_INSTALL_PREFIX}/${${PROJECT_NAME}_INSTALL_INCLUDE_DIR}/stk_search_util)
-+     ${${PROJECT_NAME}_INSTALL_INCLUDE_DIR}/stk_search_util)
-     
-diff --git a/packages/stk/stk_simd/stk_math/CMakeLists.txt b/packages/stk/stk_simd/stk_math/CMakeLists.txt
-index 2c5028c..73dd3cf 100644
---- a/packages/stk/stk_simd/stk_math/CMakeLists.txt
-+++ b/packages/stk/stk_simd/stk_math/CMakeLists.txt
-@@ -64,5 +64,5 @@ FILE(GLOB HEADERS *.hpp)
- #
- 
- INSTALL(FILES ${HEADERS} DESTINATION
--${CMAKE_INSTALL_PREFIX}/${${PROJECT_NAME}_INSTALL_INCLUDE_DIR}/stk_math)
-+ ${${PROJECT_NAME}_INSTALL_INCLUDE_DIR}/stk_math)
- 
-diff --git a/packages/stk/stk_simd/stk_simd/CMakeLists.txt b/packages/stk/stk_simd/stk_simd/CMakeLists.txt
-index 68dee72..5eea375 100644
---- a/packages/stk/stk_simd/stk_simd/CMakeLists.txt
-+++ b/packages/stk/stk_simd/stk_simd/CMakeLists.txt
-@@ -69,5 +69,5 @@ FILE(GLOB HEADERS *.hpp)
- #
- 
- INSTALL(FILES ${HEADERS} DESTINATION
--${CMAKE_INSTALL_PREFIX}/${${PROJECT_NAME}_INSTALL_INCLUDE_DIR}/stk_simd/)
-+ ${${PROJECT_NAME}_INSTALL_INCLUDE_DIR}/stk_simd/)
- 
-diff --git a/packages/stk/stk_simd/stk_simd/avx/CMakeLists.txt b/packages/stk/stk_simd/stk_simd/avx/CMakeLists.txt
-index 1cf5b6a..78cccf2 100644
---- a/packages/stk/stk_simd/stk_simd/avx/CMakeLists.txt
-+++ b/packages/stk/stk_simd/stk_simd/avx/CMakeLists.txt
-@@ -64,5 +64,5 @@ FILE(GLOB HEADERS *.hpp)
- #
- 
- INSTALL(FILES ${HEADERS} DESTINATION
--${CMAKE_INSTALL_PREFIX}/${${PROJECT_NAME}_INSTALL_INCLUDE_DIR}/stk_simd/avx)
-+ ${${PROJECT_NAME}_INSTALL_INCLUDE_DIR}/stk_simd/avx)
- 
-diff --git a/packages/stk/stk_simd/stk_simd/avx512/CMakeLists.txt b/packages/stk/stk_simd/stk_simd/avx512/CMakeLists.txt
-index adc5405..7caf056 100644
---- a/packages/stk/stk_simd/stk_simd/avx512/CMakeLists.txt
-+++ b/packages/stk/stk_simd/stk_simd/avx512/CMakeLists.txt
-@@ -64,5 +64,5 @@ FILE(GLOB HEADERS *.hpp)
- #
- 
- INSTALL(FILES ${HEADERS} DESTINATION
--${CMAKE_INSTALL_PREFIX}/${${PROJECT_NAME}_INSTALL_INCLUDE_DIR}/stk_simd/avx512)
-+ ${${PROJECT_NAME}_INSTALL_INCLUDE_DIR}/stk_simd/avx512)
- 
-diff --git a/packages/stk/stk_simd/stk_simd/no_simd/CMakeLists.txt b/packages/stk/stk_simd/stk_simd/no_simd/CMakeLists.txt
-index 7baf709..c200f4f 100644
---- a/packages/stk/stk_simd/stk_simd/no_simd/CMakeLists.txt
-+++ b/packages/stk/stk_simd/stk_simd/no_simd/CMakeLists.txt
-@@ -64,5 +64,5 @@ FILE(GLOB HEADERS *.hpp)
- #
- 
- INSTALL(FILES ${HEADERS} DESTINATION
--${CMAKE_INSTALL_PREFIX}/${${PROJECT_NAME}_INSTALL_INCLUDE_DIR}/stk_simd/no_simd)
-+ ${${PROJECT_NAME}_INSTALL_INCLUDE_DIR}/stk_simd/no_simd)
- 
-diff --git a/packages/stk/stk_simd/stk_simd/sse/CMakeLists.txt b/packages/stk/stk_simd/stk_simd/sse/CMakeLists.txt
-index 970cbc6..9c45e37 100644
---- a/packages/stk/stk_simd/stk_simd/sse/CMakeLists.txt
-+++ b/packages/stk/stk_simd/stk_simd/sse/CMakeLists.txt
-@@ -64,5 +64,5 @@ FILE(GLOB HEADERS *.hpp)
- #
- 
- INSTALL(FILES ${HEADERS} DESTINATION
--${CMAKE_INSTALL_PREFIX}/${${PROJECT_NAME}_INSTALL_INCLUDE_DIR}/stk_simd/sse)
-+ ${${PROJECT_NAME}_INSTALL_INCLUDE_DIR}/stk_simd/sse)
- 
-diff --git a/packages/stk/stk_simd/stk_simd_view/CMakeLists.txt b/packages/stk/stk_simd/stk_simd_view/CMakeLists.txt
-index b1b5c34..0b73634 100644
---- a/packages/stk/stk_simd/stk_simd_view/CMakeLists.txt
-+++ b/packages/stk/stk_simd/stk_simd_view/CMakeLists.txt
-@@ -64,5 +64,5 @@ FILE(GLOB HEADERS *.hpp)
- #
- 
- INSTALL(FILES ${HEADERS} DESTINATION
--${CMAKE_INSTALL_PREFIX}/${${PROJECT_NAME}_INSTALL_INCLUDE_DIR}/stk_simd_view)
-+ ${${PROJECT_NAME}_INSTALL_INCLUDE_DIR}/stk_simd_view)
- 
-diff --git a/packages/stk/stk_topology/stk_topology/CMakeLists.txt b/packages/stk/stk_topology/stk_topology/CMakeLists.txt
-index 6898eea..ec418db 100644
---- a/packages/stk/stk_topology/stk_topology/CMakeLists.txt
-+++ b/packages/stk/stk_topology/stk_topology/CMakeLists.txt
-@@ -71,7 +71,7 @@ TRIBITS_ADD_LIBRARY(
-   )
- 
- INSTALL(FILES ${HEADERS} DESTINATION
--    ${CMAKE_INSTALL_PREFIX}/${${PROJECT_NAME}_INSTALL_INCLUDE_DIR}/stk_topology/)
-+     ${${PROJECT_NAME}_INSTALL_INCLUDE_DIR}/stk_topology/)
- 
- INSTALL(FILES ${DETAIL_HEADERS} DESTINATION
--    ${CMAKE_INSTALL_PREFIX}/${${PROJECT_NAME}_INSTALL_INCLUDE_DIR}/stk_topology/topology_detail)
-+     ${${PROJECT_NAME}_INSTALL_INCLUDE_DIR}/stk_topology/topology_detail)
-diff --git a/packages/stk/stk_transfer/stk_transfer/CMakeLists.txt b/packages/stk/stk_transfer/stk_transfer/CMakeLists.txt
-index e9d96ef..ed20e03 100644
---- a/packages/stk/stk_transfer/stk_transfer/CMakeLists.txt
-+++ b/packages/stk/stk_transfer/stk_transfer/CMakeLists.txt
-@@ -5,7 +5,7 @@
- FILE(GLOB HEADERS *.hpp)
- 
- INSTALL(FILES ${HEADERS} DESTINATION
--${CMAKE_INSTALL_PREFIX}/${${PROJECT_NAME}_INSTALL_INCLUDE_DIR}/stk_transfer/)
-+ ${${PROJECT_NAME}_INSTALL_INCLUDE_DIR}/stk_transfer/)
- 
- FILE(GLOB HEADERS_IMPL ${CMAKE_CURRENT_SOURCE_DIR}/copy_by_id/*.hpp)
- FILE(GLOB SOURCES_IMPL  ${CMAKE_CURRENT_SOURCE_DIR}/copy_by_id/*.cpp)
-diff --git a/packages/stk/stk_unit_test_utils/CMakeLists.txt b/packages/stk/stk_unit_test_utils/CMakeLists.txt
-index 91d6527..42be71d 100644
---- a/packages/stk/stk_unit_test_utils/CMakeLists.txt
-+++ b/packages/stk/stk_unit_test_utils/CMakeLists.txt
-@@ -12,7 +12,7 @@ FILE(GLOB SOURCES *.cpp)
- LIST(REMOVE_ITEM SOURCES "${CMAKE_CURRENT_SOURCE_DIR}/unittestMeshUtils.cpp")
- 
- INSTALL(FILES ${HEADERS} DESTINATION
--    ${CMAKE_INSTALL_PREFIX}/${${PROJECT_NAME}_INSTALL_INCLUDE_DIR}/stk_unit_test_utils/)
-+     ${${PROJECT_NAME}_INSTALL_INCLUDE_DIR}/stk_unit_test_utils/)
-     
- TRIBITS_ADD_LIBRARY(
-   stk_unit_test_utils
-diff --git a/packages/stk/stk_unit_test_utils/comparison/CMakeLists.txt b/packages/stk/stk_unit_test_utils/comparison/CMakeLists.txt
-index 175fe19..196ea02 100644
---- a/packages/stk/stk_unit_test_utils/comparison/CMakeLists.txt
-+++ b/packages/stk/stk_unit_test_utils/comparison/CMakeLists.txt
-@@ -64,5 +64,5 @@ FILE(GLOB HEADERS *.hpp)
- #
- 
- INSTALL(FILES ${HEADERS} DESTINATION
--${CMAKE_INSTALL_PREFIX}/${${PROJECT_NAME}_INSTALL_INCLUDE_DIR}/stk_unit_test_utils/comparison)
-+ ${${PROJECT_NAME}_INSTALL_INCLUDE_DIR}/stk_unit_test_utils/comparison)
- 
-diff --git a/packages/stk/stk_unit_tests/stk_mesh_fixtures/CMakeLists.txt b/packages/stk/stk_unit_tests/stk_mesh_fixtures/CMakeLists.txt
-index 650aa7d..88372c8 100644
---- a/packages/stk/stk_unit_tests/stk_mesh_fixtures/CMakeLists.txt
-+++ b/packages/stk/stk_unit_tests/stk_mesh_fixtures/CMakeLists.txt
-@@ -71,4 +71,4 @@ TRIBITS_ADD_LIBRARY(
-   )
- 
- INSTALL(FILES ${HEADERS} DESTINATION
--    ${CMAKE_INSTALL_PREFIX}/${${PROJECT_NAME}_INSTALL_INCLUDE_DIR}/stk_unit_tests/stk_mesh_fixtures)
-+     ${${PROJECT_NAME}_INSTALL_INCLUDE_DIR}/stk_unit_tests/stk_mesh_fixtures)
-diff --git a/packages/stk/stk_util/stk_util/CMakeLists.txt b/packages/stk/stk_util/stk_util/CMakeLists.txt
-index 2107505..5027d4e 100644
---- a/packages/stk/stk_util/stk_util/CMakeLists.txt
-+++ b/packages/stk/stk_util/stk_util/CMakeLists.txt
-@@ -18,6 +18,6 @@ TRIBITS_CONFIGURE_FILE(STK_Trilinos_config.h)
- INCLUDE_DIRECTORIES(${CMAKE_CURRENT_BINARY_DIR})
- 
- INSTALL(FILES stk_config.h stk_kokkos_macros.h DESTINATION
--    ${CMAKE_INSTALL_PREFIX}/${${PROJECT_NAME}_INSTALL_INCLUDE_DIR}/stk_util/)
-+     ${${PROJECT_NAME}_INSTALL_INCLUDE_DIR}/stk_util/)
- INSTALL(FILES ${CMAKE_CURRENT_BINARY_DIR}/STK_Trilinos_config.h DESTINATION
--    ${CMAKE_INSTALL_PREFIX}/${${PROJECT_NAME}_INSTALL_INCLUDE_DIR}/stk_util/)
-+     ${${PROJECT_NAME}_INSTALL_INCLUDE_DIR}/stk_util/)
-diff --git a/packages/stk/stk_util/stk_util/diag/CMakeLists.txt b/packages/stk/stk_util/stk_util/diag/CMakeLists.txt
-index 3a86247..289aeee 100644
---- a/packages/stk/stk_util/stk_util/diag/CMakeLists.txt
-+++ b/packages/stk/stk_util/stk_util/diag/CMakeLists.txt
-@@ -75,5 +75,5 @@ TRIBITS_ADD_LIBRARY(
- 
- 
- INSTALL(FILES ${HEADERS} DESTINATION
--    ${CMAKE_INSTALL_PREFIX}/${${PROJECT_NAME}_INSTALL_INCLUDE_DIR}/stk_util/diag/)
-+     ${${PROJECT_NAME}_INSTALL_INCLUDE_DIR}/stk_util/diag/)
- 
-diff --git a/packages/stk/stk_util/stk_util/environment/CMakeLists.txt b/packages/stk/stk_util/stk_util/environment/CMakeLists.txt
-index 50c9e86..bae352b 100644
---- a/packages/stk/stk_util/stk_util/environment/CMakeLists.txt
-+++ b/packages/stk/stk_util/stk_util/environment/CMakeLists.txt
-@@ -73,4 +73,4 @@ TRIBITS_ADD_LIBRARY(
-   )
- 
- INSTALL(FILES ${HEADERS} DESTINATION
--        ${CMAKE_INSTALL_PREFIX}/${${PROJECT_NAME}_INSTALL_INCLUDE_DIR}/stk_util/environment/)
-+         ${${PROJECT_NAME}_INSTALL_INCLUDE_DIR}/stk_util/environment/)
-diff --git a/packages/stk/stk_util/stk_util/parallel/CMakeLists.txt b/packages/stk/stk_util/stk_util/parallel/CMakeLists.txt
-index b6b4635..536172d 100644
---- a/packages/stk/stk_util/stk_util/parallel/CMakeLists.txt
-+++ b/packages/stk/stk_util/stk_util/parallel/CMakeLists.txt
-@@ -90,4 +90,4 @@ TRIBITS_ADD_LIBRARY(
-   )
- 
- INSTALL(FILES ${HEADERS} DESTINATION
--    ${CMAKE_INSTALL_PREFIX}/${${PROJECT_NAME}_INSTALL_INCLUDE_DIR}/stk_util/parallel/)
-+     ${${PROJECT_NAME}_INSTALL_INCLUDE_DIR}/stk_util/parallel/)
-diff --git a/packages/stk/stk_util/stk_util/registry/CMakeLists.txt b/packages/stk/stk_util/stk_util/registry/CMakeLists.txt
-index 0708dfc..4449b56 100644
---- a/packages/stk/stk_util/stk_util/registry/CMakeLists.txt
-+++ b/packages/stk/stk_util/stk_util/registry/CMakeLists.txt
-@@ -70,5 +70,5 @@ TRIBITS_ADD_LIBRARY(
- 
- 
- INSTALL(FILES ${HEADERS} DESTINATION
--    ${CMAKE_INSTALL_PREFIX}/${${PROJECT_NAME}_INSTALL_INCLUDE_DIR}/stk_util/registry/)
-+     ${${PROJECT_NAME}_INSTALL_INCLUDE_DIR}/stk_util/registry/)
- 
-diff --git a/packages/stk/stk_util/stk_util/unit_test_support/CMakeLists.txt b/packages/stk/stk_util/stk_util/unit_test_support/CMakeLists.txt
-index 6b92b6b..07ac185 100644
---- a/packages/stk/stk_util/stk_util/unit_test_support/CMakeLists.txt
-+++ b/packages/stk/stk_util/stk_util/unit_test_support/CMakeLists.txt
-@@ -78,4 +78,4 @@ TRIBITS_ADD_LIBRARY(
-   )
- 
- INSTALL(FILES ${HEADERS} DESTINATION
--    ${CMAKE_INSTALL_PREFIX}/${${PROJECT_NAME}_INSTALL_INCLUDE_DIR}/stk_util/unit_test_support/)
-+     ${${PROJECT_NAME}_INSTALL_INCLUDE_DIR}/stk_util/unit_test_support/)
-diff --git a/packages/stk/stk_util/stk_util/util/CMakeLists.txt b/packages/stk/stk_util/stk_util/util/CMakeLists.txt
-index b90c66b..3a83bb3 100644
---- a/packages/stk/stk_util/stk_util/util/CMakeLists.txt
-+++ b/packages/stk/stk_util/stk_util/util/CMakeLists.txt
-@@ -75,4 +75,4 @@ TRIBITS_ADD_LIBRARY(
-   )
- 
- INSTALL(FILES ${HEADERS} DESTINATION
--    ${CMAKE_INSTALL_PREFIX}/${${PROJECT_NAME}_INSTALL_INCLUDE_DIR}/stk_util/util/)
-+     ${${PROJECT_NAME}_INSTALL_INCLUDE_DIR}/stk_util/util/)
-diff --git a/packages/teuchos/kokkoscompat/src/CMakeLists.txt b/packages/teuchos/kokkoscompat/src/CMakeLists.txt
-index 030a7c6..c0d49dc 100644
---- a/packages/teuchos/kokkoscompat/src/CMakeLists.txt
-+++ b/packages/teuchos/kokkoscompat/src/CMakeLists.txt
-@@ -27,7 +27,7 @@ TRIBITS_ADD_LIBRARY(
- # FIXME (mfh 19 Dec 2014) We should rely on TriBITS to handle
- # installation.
- 
--SET(TRILINOS_INCDIR ${CMAKE_INSTALL_PREFIX}/${${PROJECT_NAME}_INSTALL_INCLUDE_DIR})
-+SET(TRILINOS_INCDIR ${${PROJECT_NAME}_INSTALL_INCLUDE_DIR})
- 
- INSTALL(FILES ${HEADERS} DESTINATION ${TRILINOS_INCDIR}/)
- 
diff --git a/sci-libs/trilinos/files/trilinos-12.12.1-fix_sundance_compilation.patch b/sci-libs/trilinos/files/trilinos-12.12.1-fix_sundance_compilation.patch
deleted file mode 100644
index 377485bfe..000000000
--- a/sci-libs/trilinos/files/trilinos-12.12.1-fix_sundance_compilation.patch
+++ /dev/null
@@ -1,33 +0,0 @@
-diff --git a/packages/Sundance/Playa/src/NOX_Playa_Vector.cpp b/packages/Sundance/Playa/src/NOX_Playa_Vector.cpp
-index 637936e..3dbf1a9 100644
---- a/packages/Sundance/Playa/src/NOX_Playa_Vector.cpp
-+++ b/packages/Sundance/Playa/src/NOX_Playa_Vector.cpp
-@@ -191,6 +191,14 @@ NOX::Abstract::Vector& NOX::NOXPlaya::Vector::init(double value)
-   return *this;
- }
- 
-+NOX::Abstract::Vector& NOX::NOXPlaya::Vector::random(bool useSeed, int seed)
-+{
-+  if (useSeed)
-+    Playa::Rand::setLocalSeed(x.comm(), seed);
-+  x.randomize();
-+  return *this;
-+}
-+
- 
- NOX::Abstract::Vector& NOX::NOXPlaya::Vector::abs(
- 					     const NOX::Abstract::Vector& base)
-diff --git a/packages/Sundance/Playa/src/NOX_Playa_Vector.hpp b/packages/Sundance/Playa/src/NOX_Playa_Vector.hpp
-index bdf70e2..3143059 100644
---- a/packages/Sundance/Playa/src/NOX_Playa_Vector.hpp
-+++ b/packages/Sundance/Playa/src/NOX_Playa_Vector.hpp
-@@ -116,6 +116,9 @@ public:
-   /** Initialize all elements to a constant */
-   NOX::Abstract::Vector& init(double value);
- 
-+  /** Initialize all elements of this vector with a random value */
-+  NOX::Abstract::Vector& random(bool useSeed = false, int seed = 1);
-+
-   /** Assignment operator */
-   NOX::Abstract::Vector& operator=(const NOX::NOXPlaya::Vector& y);
-   /** Assignment operator */
diff --git a/sci-libs/trilinos/files/trilinos-12.12.1-superlu-5.patch b/sci-libs/trilinos/files/trilinos-12.12.1-superlu-5.patch
deleted file mode 100644
index 24e8dbabd..000000000
--- a/sci-libs/trilinos/files/trilinos-12.12.1-superlu-5.patch
+++ /dev/null
@@ -1,161 +0,0 @@
-From 83bec239ac6a63ed895a52567eab18925dd6a8cb Mon Sep 17 00:00:00 2001
-From: =?UTF-8?q?Nico=20Schl=C3=B6mer?= <nico.schloemer@gmail.com>
-Date: Wed, 1 Jun 2016 19:38:01 +0200
-Subject: [PATCH] compatibility with SuperLU 5
-
-Thanks to Eric Bavier <bavier@cray.com>.
----
- cmake/TPLs/FindTPLSuperLU.cmake          | 42 +++++++++++++++++++++++-
- packages/amesos/cmake/Amesos_config.h.in |  3 ++
- packages/amesos/src/Amesos_Superlu.cpp   | 15 ++++++---
- packages/ifpack/cmake/Ifpack_config.h.in |  3 ++
- packages/ifpack/src/Ifpack_SILU.cpp      |  6 +++-
- packages/ifpack/src/Ifpack_SILU.h        |  2 ++
- 6 files changed, 65 insertions(+), 6 deletions(-)
-
-diff --git a/cmake/TPLs/FindTPLSuperLU.cmake b/cmake/TPLs/FindTPLSuperLU.cmake
-index fae2db230b0..f2321ba93dc 100644
---- a/cmake/TPLs/FindTPLSuperLU.cmake
-+++ b/cmake/TPLs/FindTPLSuperLU.cmake
-@@ -56,5 +56,45 @@
- 
- TRIBITS_TPL_FIND_INCLUDE_DIRS_AND_LIBRARIES( SuperLU
-   REQUIRED_HEADERS supermatrix.h slu_ddefs.h
--  REQUIRED_LIBS_NAMES "superlu superlu_3.0 superlu_4.0 superlu_4.1 superlu_4.2 superlu_4.3"
-+  REQUIRED_LIBS_NAMES "superlu superlu_3.0 superlu_4.0 superlu_4.1 superlu_4.2 superlu_4.3 superlu_5.0"
-   )
-+
-+include(CheckCSourceCompiles)
-+include(MultilineSet)
-+
-+# API change in SuperLU 5.0 requires a 'GlobalLU_t' parameter for
-+# *gssvx, *gsisx, *gstrf, and *gsitrf routines.  Check whether these
-+# parameters are needed.
-+
-+FUNCTION(CHECK_SUPERLU_GLOBALLU_T_ARG  VARNAME)
-+  SET(SOURCE
-+  "
-+#include <slu_ddefs.h>
-+
-+int main()
-+{
-+  GlobalLU_t lu;
-+  superlu_options_t opt;
-+  SuperMatrix M;
-+  int *i;
-+  double *d;
-+  void *v;
-+  char *c;
-+  SuperLUStat_t stat;
-+  mem_usage_t mem;
-+
-+  dgsisx(&opt,&M,i,i,i,c,d,d,&M,&M,v,*i,&M,&M,d,d,&lu,&mem,&stat,i);
-+  return 0;
-+}
-+"
-+  )
-+
-+  SET(CMAKE_REQUIRED_INCLUDES ${TPL_SuperLU_INCLUDE_DIRS})
-+  SET(CMAKE_REQUIRED_LIBRARIES ${TPL_SuperLU_LIBRARIES} ${TPL_METIS_LIBRARIES} ${TPL_BLAS_LIBRARIES})
-+  SET(CMAKE_REQUIRED_FLAGS ${CMAKE_EXE_LINKER_FLAGS})
-+  CHECK_C_SOURCE_COMPILES("${SOURCE}" ${VARNAME})
-+ENDFUNCTION()
-+
-+IF (TPL_ENABLE_SuperLU)
-+  CHECK_SUPERLU_GLOBALLU_T_ARG(HAVE_SUPERLU_GLOBALLU_T_ARG)
-+ENDIF(TPL_ENABLE_SuperLU)
-diff --git a/packages/amesos/cmake/Amesos_config.h.in b/packages/amesos/cmake/Amesos_config.h.in
-index bc4967e3433..6150ed80d2f 100644
---- a/packages/amesos/cmake/Amesos_config.h.in
-+++ b/packages/amesos/cmake/Amesos_config.h.in
-@@ -93,3 +93,6 @@
- 
- /* Define to 1 if SuperLU_DIST's LUstructInit is declared with 2 arguments. */
- #cmakedefine HAVE_SUPERLUDIST_LUSTRUCTINIT_2ARG
-+
-+/* Define to 1 if SuperLU's *gssvx and *gsisx routines need a GlobalLU_t argument. */
-+#cmakedefine HAVE_SUPERLU_GLOBALLU_T_ARG
-diff --git a/packages/amesos/src/Amesos_Superlu.cpp b/packages/amesos/src/Amesos_Superlu.cpp
-index 3651b65f4da..7adf0dff62d 100644
---- a/packages/amesos/src/Amesos_Superlu.cpp
-+++ b/packages/amesos/src/Amesos_Superlu.cpp
-@@ -55,6 +55,7 @@ class SLUData {
- #endif
-   SLU::superlu_options_t SLU_options;
-   SLU::mem_usage_t mem_usage;
-+  SLU::GlobalLU_t lu;	     // Use for gssvx and gsisx in SuperLU 5.0
-   SLU::fact_t refactor_option ;         //  SamePattern or SamePattern_SameRowPerm
- 
-   SLUData() {
-@@ -480,8 +481,11 @@ int Amesos_Superlu::NumericFactorization()
-             &perm_c_[0], &perm_r_[0], &etree_[0], &equed_, &R_[0],
-             &C_[0], &(data_->L), &(data_->U), NULL, 0,
-             &(data_->B), &(data_->X), &rpg, &rcond, &ferr_[0],
--            &berr_[0], &(data_->mem_usage), &SLU_stat,
--            &Ierr[0] );
-+            &berr_[0],
-+#ifdef HAVE_SUPERLU_GLOBALLU_T_ARG
-+            &(data_->lu),
-+#endif
-+            &(data_->mem_usage), &SLU_stat, &Ierr[0] );
-     SLU::StatFree( &SLU_stat ) ;
-   }
- 
-@@ -611,8 +615,11 @@ int Amesos_Superlu::Solve()
-             &perm_c_[0], &perm_r_[0], &etree_[0], &equed_, &R_[0],
-             &C_[0], &(data_->L), &(data_->U), NULL, 0,
-             &(data_->B), &(data_->X), &rpg, &rcond, &ferr_[0],
--            &berr_[0], &(data_->mem_usage), &SLU_stat,
--            &Ierr);
-+            &berr_[0],
-+#ifdef HAVE_SUPERLU_GLOBALLU_T_ARG
-+            &(data_->lu),
-+#endif
-+            &(data_->mem_usage), &SLU_stat, &Ierr);
-     //    assert( equed_ == 'N' ) ;
-     StatFree( &SLU_stat ) ;
-   }
-diff --git a/packages/ifpack/cmake/Ifpack_config.h.in b/packages/ifpack/cmake/Ifpack_config.h.in
-index 81fba21a99f..91f11101f87 100644
---- a/packages/ifpack/cmake/Ifpack_config.h.in
-+++ b/packages/ifpack/cmake/Ifpack_config.h.in
-@@ -53,6 +53,9 @@
- /* Define if Ifpack_DynamicFactory is enabled */
- #cmakedefine HAVE_IFPACK_DYNAMIC_FACTORY
- 
-+/* Define to 1 if SuperLU's dgsitrf routine needs a GlobalLU_t argument. */
-+#cmakedefine HAVE_SUPERLU_GLOBALLU_T_ARG
-+
- /* Add macros for declaring functions deprecated */
- @IFPACK_DEPRECATED_DECLARATIONS@
- 
-diff --git a/packages/ifpack/src/Ifpack_SILU.cpp b/packages/ifpack/src/Ifpack_SILU.cpp
-index e69f32b1277..32b58e1a60b 100644
---- a/packages/ifpack/src/Ifpack_SILU.cpp
-+++ b/packages/ifpack/src/Ifpack_SILU.cpp
-@@ -297,7 +297,11 @@ int Ifpack_SILU::Compute()
-   int panel_size = sp_ienv(1);
-   int relax      = sp_ienv(2);
-   int info=0;
--  dgsitrf(&options_,&SAc_,relax,panel_size,etree_,NULL,0,perm_c_,perm_r_,&SL_,&SU_,&stat_,&info);
-+  dgsitrf(&options_,&SAc_,relax,panel_size,etree_,NULL,0,perm_c_,perm_r_,&SL_,&SU_,
-+#ifdef HAVE_SUPERLU_GLOBALLU_T_ARG
-+          &lu_,
-+#endif
-+          &stat_,&info);
-   if(info<0) IFPACK_CHK_ERR(info);
- 
-   IsComputed_ = true;
-diff --git a/packages/ifpack/src/Ifpack_SILU.h b/packages/ifpack/src/Ifpack_SILU.h
-index a1c7b1a86f0..0a7a7d8dc63 100644
---- a/packages/ifpack/src/Ifpack_SILU.h
-+++ b/packages/ifpack/src/Ifpack_SILU.h
-@@ -428,6 +428,8 @@ class Ifpack_SILU: public Ifpack_Preconditioner {
-   mutable double ApplyInverseTime_;
-   //! Used for timing issues
-   mutable Epetra_Time Time_;
-+  //! SuperLU global LU data
-+  mutable GlobalLU_t lu_;
-   //! SuperLU stats
-   mutable SuperLUStat_t stat_;
-   //! SuperLU options
diff --git a/sci-libs/trilinos/metadata.xml b/sci-libs/trilinos/metadata.xml
deleted file mode 100644
index 30049396c..000000000
--- a/sci-libs/trilinos/metadata.xml
+++ /dev/null
@@ -1,51 +0,0 @@
-<?xml version="1.0" encoding="UTF-8"?>
-<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
-<pkgmetadata>
-	<maintainer type="person">
-		<email>tamiko@gentoo.org</email>
-		<name>Matthias Maier</name>
-	</maintainer>
-	<maintainer type="person">
-		<email>andyspiros@gmail.com</email>
-	</maintainer>
-	<maintainer type="project">
-		<email>sci@gentoo.org</email>
-		<name>Gentoo Science Project</name>
-	</maintainer>
-	<longdescription lang="en">
-The Trilinos Project is an effort to develop algorithms and enabling
-technologies within an object-oriented software framework for the solution
-of large-scale, complex multi-physics engineering and scientific problems.
-</longdescription>
-	<use>
-		<flag name="adolc">Add support for adolc (<pkg>sci-libs/adolc</pkg>)</flag>
-		<flag name="arprec">Add support for arprec (<pkg>sci-libs/arprec</pkg>)</flag>
-		<flag name="boost">Add support for boost (<pkg>dev-libs/boost</pkg>)</flag>
-		<flag name="clp">Add support for clp (<pkg>sci-libs/coinor-clp</pkg>)</flag>
-		<flag name="cppunit">Add support for (...)</flag>
-		<flag name="cuda">Add support for cuda (<pkg>dev-util/nvidia-cuda-toolkit</pkg>)</flag>
-		<flag name="eigen">Add support for eigen (<pkg>dev-cpp/eigen</pkg>)</flag>
-		<flag name="glpk">Add support for (...)</flag>
-		<flag name="gtest">Add support for gtest (<pkg>dev-cpp/gtest</pkg>)</flag>
-		<flag name="hwloc">Add support for hwloc (<pkg>sys-apps/hwloc</pkg>)</flag>
-		<flag name="hdf5">Add support for hdf5 (<pkg>sci-libs/hdf5</pkg>)</flag>
-		<flag name="hypre">Add support for hypre (<pkg>sci-libs/hypre</pkg>)</flag>
-		<flag name="matio">Add support for matio (<pkg>sci-libs/matio</pkg>)</flag>
-		<flag name="metis">
-Add support for metis (<pkg>sci-libs/metis</pkg> or <pkg>sci-libs/parmetis</pkg>)
-</flag>
-		<flag name="mkl">Add support for mkl (<pkg>sci-libs/mkl</pkg>)</flag>
-		<flag name="mumps">Add support for mumps (<pkg>sci-libs/mumps</pkg>)</flag>
-		<flag name="netcdf">Add support for netcdf (<pkg>sci-libs/netcdf</pkg>)</flag>
-		<flag name="petsc">Add support for petsc (<pkg>sci-mathematics/petsc</pkg>)</flag>
-		<flag name="qd">Add support for qd (<pkg>sci-libs/qd</pkg>)</flag>
-		<flag name="scalapack">Add support for scalapack (<pkg>virtual/scalapack</pkg>)</flag>
-		<flag name="scotch">Add support for scotch (<pkg>sci-libs/scotch</pkg>)</flag>
-		<flag name="sparse">Add support for sparse matrix solvers (<pkg>sci-libs/umfpack</pkg>)</flag>
-		<flag name="superlu">Add support for superlu (<pkg>sci-libs/superlu</pkg>)</flag>
-		<flag name="taucs">Add support for taucs (<pkg>sci-libs/taucs</pkg>)</flag>
-		<flag name="tbb">Add support for threading building blocks library (<pkg>dev-cpp/tbb</pkg>)</flag>
-		<flag name="tvmet">Add support for tvmet (<pkg>dev-libs/tvmet</pkg>)</flag>
-		<flag name="yaml">Add support for yaml (<pkg>dev-cpp/yaml</pkg>)</flag>
-	</use>
-</pkgmetadata>
diff --git a/sci-libs/trilinos/trilinos-12.12.1-r1.ebuild b/sci-libs/trilinos/trilinos-12.12.1-r1.ebuild
deleted file mode 100644
index 432977e10..000000000
--- a/sci-libs/trilinos/trilinos-12.12.1-r1.ebuild
+++ /dev/null
@@ -1,206 +0,0 @@
-# Copyright 1999-2018 Gentoo Foundation
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=6
-
-inherit cmake-utils toolchain-funcs multilib toolchain-funcs
-
-DESCRIPTION="Scientific library collection for large scale problems"
-HOMEPAGE="http://trilinos.sandia.gov/"
-SRC_URI="http://trilinos.org/oldsite/download/files/${P}-Source.tar.gz"
-
-KEYWORDS="~amd64 ~x86 ~amd64-linux ~x86-linux"
-
-LICENSE="BSD LGPL-2.1"
-SLOT="0"
-
-IUSE="
-	adolc arprec boost clp cppunit cuda eigen glpk gtest hdf5 hwloc hypre
-	matio metis mkl mumps netcdf petsc qd scalapack scotch sparse
-	superlu taucs tbb test threads tvmet yaml zlib X
-"
-
-# TODO: fix export cmake function for tests
-RESTRICT="test"
-
-RDEPEND="
-	sys-libs/binutils-libs
-	virtual/blas
-	virtual/lapack
-	virtual/mpi
-	adolc? ( sci-libs/adolc )
-	arprec? ( sci-libs/arprec )
-	boost? ( dev-libs/boost )
-	clp? ( sci-libs/coinor-clp )
-	cuda? ( >=dev-util/nvidia-cuda-toolkit-3.2 )
-	eigen? ( dev-cpp/eigen:3 )
-	gtest? ( dev-cpp/gtest )
-	hdf5? ( sci-libs/hdf5[mpi] )
-	hypre? ( sci-libs/hypre )
-	hwloc? ( sys-apps/hwloc )
-	matio? ( sci-libs/matio )
-	mkl? ( sci-libs/mkl )
-	metis? ( || ( sci-libs/parmetis sci-libs/metis ) )
-	mumps? ( sci-libs/mumps )
-	netcdf? ( sci-libs/netcdf )
-	petsc? ( sci-mathematics/petsc )
-	qd? ( sci-libs/qd )
-	scalapack? ( virtual/scalapack )
-	scotch? ( sci-libs/scotch )
-	sparse? ( sci-libs/cxsparse sci-libs/umfpack )
-	superlu? ( sci-libs/superlu )
-	taucs? ( sci-libs/taucs )
-	tbb? ( dev-cpp/tbb )
-	tvmet? ( dev-libs/tvmet )
-	yaml? ( dev-cpp/yaml-cpp )
-	zlib? ( sys-libs/zlib )
-	X? ( x11-libs/libX11 )"
-DEPEND="${RDEPEND}
-	virtual/pkgconfig"
-
-S="${WORKDIR}/${P}-Source"
-
-PATCHES=(
-	"${FILESDIR}"/${PN}-11.14.1-fix-install-paths.patch \
-	"${FILESDIR}"/${P}-fix_install_paths_for_destdir.patch
-	"${FILESDIR}"/${P}-fix_sundance_compilation.patch
-	"${FILESDIR}"/${P}-superlu-5.patch
-)
-
-trilinos_conf() {
-	local dirs libs d
-	for d in $($(tc-getPKG_CONFIG) --libs-only-L $1); do
-		dirs="${dirs};${d:2}"
-	done
-	[[ -n ${dirs} ]] && mycmakeargs+=( "-D${2}_LIBRARY_DIRS=${dirs:1}" )
-	for d in $($(tc-getPKG_CONFIG) --libs-only-l $1); do
-		libs="${libs};${d:2}"
-	done
-	[[ -n ${libs} ]] && mycmakeargs+=( "-D${2}_LIBRARY_NAMES=${libs:1}" )
-	dirs=""
-	for d in $($(tc-getPKG_CONFIG) --cflags-only-I $1); do
-		dirs="${dirs};${d:2}"
-	done
-	[[ -n ${dirs} ]] && mycmakeargs+=( "-D${2}_INCLUDE_DIRS=${dirs:1}" )
-}
-
-src_configure() {
-	local mycmakeargs=(
-		-DBUILD_SHARED_LIBS=ON
-		-DCMAKE_INSTALL_PREFIX="${EPREFIX}"
-		-DTrilinos_INSTALL_CONFIG_DIR="${EPREFIX}/usr/$(get_libdir)/cmake"
-		-DTrilinos_INSTALL_INCLUDE_DIR="${EPREFIX}/usr/include/trilinos"
-		-DTrilinos_INSTALL_LIB_DIR="${EPREFIX}/usr/$(get_libdir)/trilinos"
-		-DTrilinos_ENABLE_ALL_PACKAGES=ON
-		-DTrilinos_ENABLE_CTrilinos=OFF
-		-DTrilinos_ENABLE_PyTrilinos=OFF
-		-DTrilinos_ENABLE_SEACASExodiff="$(usex netcdf)"
-		-DTrilinos_ENABLE_SEACASExodus="$(usex netcdf)"
-		-DTrilinos_ENABLE_TESTS="$(usex test)"
-		-DZoltan2_ENABLE_Experimental=ON
-		-DTPL_ENABLE_BinUtils=ON
-		-DTPL_ENABLE_BLAS=ON
-		-DTPL_ENABLE_LAPACK=ON
-		-DTPL_ENABLE_MPI=ON
-		-DTPL_ENABLE_ADOLC="$(usex adolc)"
-		-DTPL_ENABLE_AMD="$(usex sparse)"
-		-DTPL_ENABLE_ARPREC="$(usex arprec)"
-		-DTPL_ENABLE_BLACS="$(usex scalapack)"
-		-DTPL_ENABLE_BoostLib="$(usex boost)"
-		-DTPL_ENABLE_Boost="$(usex boost)"
-		-DTPL_ENABLE_Clp="$(usex clp)"
-		-DTPL_ENABLE_Cppunit="$(usex cppunit)"
-		-DTPL_ENABLE_CSparse="$(usex sparse)"
-		-DTPL_ENABLE_CUDA="$(usex cuda)"
-		-DTPL_ENABLE_CUSPARSE="$(usex cuda)"
-		-DTPL_ENABLE_Eigen="$(usex eigen)"
-		-DTPL_ENABLE_GLPK="$(usex glpk)"
-		-DTPL_ENABLE_gtest="$(usex gtest)"
-		-DTPL_ENABLE_HDF5="$(usex hdf5)"
-		-DTPL_ENABLE_HWLOC="$(usex hwloc)"
-		-DTPL_ENABLE_HYPRE="$(usex hypre)"
-		-DTPL_ENABLE_Matio="$(usex matio)"
-		-DTPL_ENABLE_METIS="$(usex metis)"
-		-DTPL_ENABLE_MKL="$(usex mkl)"
-		-DTPL_ENABLE_MUMPS="$(usex mumps)"
-		-DTPL_ENABLE_Netcdf="$(usex netcdf)"
-		-DTPL_ENABLE_PARDISO_MKL="$(usex mkl)"
-		-DTPL_ENABLE_PETSC="$(usex petsc)"
-		-DTPL_ENABLE_Pthread="$(usex threads)"
-		-DTPL_ENABLE_QD="$(usex qd)"
-		-DTPL_ENABLE_SCALAPACK="$(usex scalapack)"
-		-DTPL_ENABLE_Scotch="$(usex scotch)"
-		-DTPL_ENABLE_SuperLU="$(usex superlu)"
-		-DTPL_ENABLE_TAUCS="$(usex taucs)"
-		-DTPL_ENABLE_TBB="$(usex tbb)"
-		-DTPL_ENABLE_Thrust="$(usex cuda)"
-		-DTPL_ENABLE_TVMET="$(usex tvmet)"
-		-DTPL_ENABLE_UMFPACK="$(usex sparse)"
-		-DTPL_ENABLE_X11="$(usex X)"
-		-DTPL_ENABLE_yaml-cpp="$(usex yaml)"
-		-DTPL_ENABLE_Zlib="$(usex zlib)"
-	)
-
-	use eigen && \
-		mycmakeargs+=(
-		-DEigen_INCLUDE_DIRS="${EPREFIX}/usr/include/eigen3"
-	)
-	use hypre && \
-		mycmakeargs+=(
-		-DHYPRE_INCLUDE_DIRS="${EPREFIX}/usr/include/hypre"
-	)
-	use scotch && \
-		mycmakeargs+=(
-		-DScotch_INCLUDE_DIRS="${EPREFIX}/usr/include/scotch"
-	)
-
-	# cxsparse is a rewrite of csparse + extras
-	use sparse && \
-		mycmakeargs+=(
-		-DCSparse_LIBRARY_NAMES="cxsparse"
-	)
-
-	# mandatory blas and lapack
-	trilinos_conf blas BLAS
-	trilinos_conf lapack LAPACK
-	use superlu && trilinos_conf superlu SuperLU
-	use metis && trilinos_conf metis METIS
-
-	# blacs library is included in scalapack these days
-	if use scalapack; then
-		trilinos_conf scalapack SCALAPACK
-		mycmakeargs+=(
-			-DBLACS_LIBRARY_NAMES="scalapack"
-			-DBLACS_INCLUDE_DIRS="${EPREFIX}/usr/include/blacs"
-		)
-	fi
-
-	#
-	# Make sure we use the compiler wrappers in order to build trilinos.
-	#
-	export CC=mpicc CXX=mpicxx && tc-export CC CXX
-
-	#
-	# cmake-utils eclass patches the base directory CMakeLists.txt
-	# which does not work for complex Trilinos CMake modules
-	#
-	CMAKE_BUILD_TYPE=RELEASE cmake-utils_src_configure
-}
-
-src_install() {
-	cmake-utils_src_install
-
-	# Clean up the mess:
-	rm -r "${ED}"/TrilinosRepoVersion.txt "${ED}"/lib || die "rm failed"
-	mv "${ED}"/bin "${ED}/usr/$(get_libdir)"/trilinos || die "mv failed"
-
-	#
-	# register $(get_libdir)/trilinos in LDPATH so that the dynamic linker
-	# has a chance to pick up the libraries...
-	#
-	cat >> "${T}"/99trilinos <<- EOF
-	LDPATH="${EPREFIX}/usr/$(get_libdir)/trilinos"
-	PATH="${EPREFIX}/usr/$(get_libdir)/trilinos/bin"
-	EOF
-	doenvd "${T}"/99trilinos
-}
diff --git a/sci-libs/vegas/Manifest b/sci-libs/vegas/Manifest
new file mode 100644
index 000000000..c636ac4c2
--- /dev/null
+++ b/sci-libs/vegas/Manifest
@@ -0,0 +1 @@
+DIST vegas-6.0.1.tar.gz 1535565 BLAKE2B 3cd30387e9369ce7efe62e1f5838f87c73bb93e1690c131602a8e0b77a6671e9d9cadb6b909e1f9ba548cd4a32cb09bd6d1d50bfaf536b7c3fbd269c4595ed04 SHA512 ead47a9f194846d704e229d62163233a7b063dab504e665d620f59be5c9abe2b31facf14cad612b102d4bf64d60d9f6f53c0b4bca0ba78d1e62cbd9bda77e0b1
diff --git a/sci-libs/vegas/metadata.xml b/sci-libs/vegas/metadata.xml
new file mode 100644
index 000000000..8ae183900
--- /dev/null
+++ b/sci-libs/vegas/metadata.xml
@@ -0,0 +1,19 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
+<pkgmetadata>
+	<maintainer type="project">
+		<email>sci@gentoo.org</email>
+		<name>Gentoo Science Project</name>
+	</maintainer>
+	<maintainer type="person">
+		<email>alexander@neuwirth-informatik.de</email>
+		<name>Alexander Puck Neuwirth</name>
+	</maintainer>
+	<longdescription lang="en">
+	The vegas package is for evaluating multidimensional integrals using an improved version of the adaptive Monte Carlo vegas algorithm (G. P. Lepage, J. Comput. Phys. 27(1978) 192). 
+	</longdescription>
+	<upstream>
+		<remote-id type="pypi">vegas</remote-id>
+		<remote-id type="github">gplepage/vegas</remote-id>
+	</upstream>
+</pkgmetadata>
diff --git a/sci-libs/vegas/vegas-6.0.1.ebuild b/sci-libs/vegas/vegas-6.0.1.ebuild
new file mode 100644
index 000000000..7654563e4
--- /dev/null
+++ b/sci-libs/vegas/vegas-6.0.1.ebuild
@@ -0,0 +1,24 @@
+EAPI=8
+
+DISTUTILS_EXT=1
+PYTHON_COMPAT=( python3_{10..12} )
+DISTUTILS_USE_PEP517=setuptools
+inherit distutils-r1 pypi
+
+DESCRIPTION="Adaptive multidimensional Monte Carlo integration."
+HOMEPAGE="https://github.com/gplepage/vegas"
+
+LICENSE="GPL-3"
+SLOT="0"
+KEYWORDS="~amd64 ~arm64"
+
+RDEPEND="
+	>=dev-python/numpy-1.16[${PYTHON_USEDEP}]
+	>=sci-libs/gvar-13.0.2[${PYTHON_USEDEP}]
+"
+DEPEND="${RDEPEND}"
+BDEPEND="
+	>=dev-python/cython-0.17[${PYTHON_USEDEP}]
+"
+
+distutils_enable_tests unittest
diff --git a/sci-libs/vxl/Manifest b/sci-libs/vxl/Manifest
new file mode 100644
index 000000000..59438eca7
--- /dev/null
+++ b/sci-libs/vxl/Manifest
@@ -0,0 +1 @@
+DIST vxl-2.0.2.tar.gz 44159163 BLAKE2B 338535c08a7f2728f4c8bce1e84a4c60a23907ba2907dcf137ebdff271e9b6cf9bf1543732b9a95eda967127b571512f5eced0262e99c04febd60e79cf78272b SHA512 113a94cd4e904d39d6ee9a854523de09f607570b97acef8e83ce95f71439549abe9f15b0bc367a0c193b2da2b68acea6b4263660bcf979fc0f87c10193253fb3
diff --git a/sci-libs/vxl/metadata.xml b/sci-libs/vxl/metadata.xml
index 22feba67c..f7d43af09 100644
--- a/sci-libs/vxl/metadata.xml
+++ b/sci-libs/vxl/metadata.xml
@@ -13,5 +13,6 @@ written in ANSI/ISO C++ and is designed to be portable over many platforms.
 </longdescription>
 	<upstream>
 		<remote-id type="sourceforge">vxl</remote-id>
+		<remote-id type="github">vxl/vxl</remote-id>
 	</upstream>
 </pkgmetadata>
diff --git a/sci-libs/vxl/vxl-2.0.2.ebuild b/sci-libs/vxl/vxl-2.0.2.ebuild
new file mode 100644
index 000000000..4db9621f4
--- /dev/null
+++ b/sci-libs/vxl/vxl-2.0.2.ebuild
@@ -0,0 +1,23 @@
+# Copyright 1999-2021 Gentoo Authors
+# Distributed under the terms of the GNU General Public License v2
+
+EAPI=7
+
+inherit cmake
+
+DESCRIPTION="C++ computer vision research libraries"
+HOMEPAGE="https://vxl.github.io/"
+SRC_URI="https://github.com/vxl/vxl/archive/v${PV}.tar.gz -> ${P}.tar.gz"
+
+LICENSE="BSD"
+SLOT="0"
+KEYWORDS="~amd64"
+
+DEPEND="sci-libs/libgeotiff"
+RDEPEND="${DEPEND}"
+
+src_install() {
+	cmake_src_install
+	# install lib files to correct dir
+	mv "${ED}/usr/lib" "${ED}/usr/$(get_libdir)"
+}
diff --git a/sci-libs/vxl/vxl-9999.ebuild b/sci-libs/vxl/vxl-9999.ebuild
deleted file mode 100644
index ab92e482e..000000000
--- a/sci-libs/vxl/vxl-9999.ebuild
+++ /dev/null
@@ -1,16 +0,0 @@
-# Copyright 1999-2015 Gentoo Foundation
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=5
-
-inherit cmake-utils git-r3
-
-DESCRIPTION="C++ computer vision research libraries"
-HOMEPAGE="http://vxl.sourceforge.net"
-SRC_URI=""
-EGIT_REPO_URI="http://git.code.sf.net/p/vxl/git"
-
-LICENSE="BSD"
-SLOT="0"
-IUSE=""
-KEYWORDS=""
diff --git a/sci-libs/wannier90/Manifest b/sci-libs/wannier90/Manifest
index a64e8f61b..eb7675dee 100644
--- a/sci-libs/wannier90/Manifest
+++ b/sci-libs/wannier90/Manifest
@@ -1,3 +1 @@
-DIST wannier90-1.2.tar.gz 5643731 BLAKE2B bbee32a853659fc3a7533d71d553ee7dc02786dcdde2b7d983d262d4b5825cbd78eb7fb9dcbfa78802bd8b4c1bd808832e7f05d4e0b02adea0be969369a3bbd3 SHA512 323d078d0cdeeb361389600c39501410ca0da2879e8ba7d3262b49a76167e5385c09484eed47607d83feb68c9f16cfb6cdcebe89f7846157e0c71a8598238853
-DIST wannier90-2.0.1.1.tar.gz 48721795 BLAKE2B 3f4307e6d8be2ff4c5595d776aab1c8ad80cac9cc730559f7ae7bb23dbd5320f27202252b4a7a4ec8dd8b11e1ece6a30ef4e99b7ea08a73257fcc45e43c2a50e SHA512 1522ee93314f265debe6d565d47007c591e2ee3d192fbe4ef05851aea49bce67398e16f5f59c384ddc3e2fc8660ce46d4bd48065789f09595a4c6166025622b7
-DIST wannier90-2.0.1.tar.gz 48327121 BLAKE2B ba077be65b7990c492b36bf0d385726f3f23ed3ac5442db3d1038788385fa5832d63da1c322aa7fd8fa9a4ee2ed1c55cda95d3bba97b1ba786488c7df1f544fe SHA512 dd7deb43272a9f0697ae59e272816a74ae15f7adb95f4c5d7ea40d98f8293b678da97494df471077a096f207d7a194a27ed09d6f456a8db20fe91e4f596602c4
+DIST wannier90-3.1.0.tar.gz 101211573 BLAKE2B 521caf8ee69b2381e518c276f0a8c6701a5bc57d8061a4106de740420cb4f9a5d7d509a01d700016d258ea0056e14a9aa30651f339c466528054909d0162ef48 SHA512 e31ea204210e9a3f719b5589e83410118eb9cd7dc331a4619df6d0a2a6d8ffb606e631dccd589dfe5334ae960c572a7289b77592d3a3d60fd464236f71ef1a18
diff --git a/sci-libs/wannier90/files/wannier90-1.1-0001.patch b/sci-libs/wannier90/files/wannier90-1.1-0001.patch
deleted file mode 100644
index e68c5f4fe..000000000
--- a/sci-libs/wannier90/files/wannier90-1.1-0001.patch
+++ /dev/null
@@ -1,16 +0,0 @@
-diff -urN wannier90-1.1.old/src/wannier_lib.F90 wannier90-1.1.new/src/wannier_lib.F90
---- wannier90-1.1.old/src/wannier_lib.F90	2007-12-20 10:58:37.000000000 +0100
-+++ wannier90-1.1.new/src/wannier_lib.F90	2008-04-28 17:27:19.000000000 +0200
-@@ -166,6 +166,12 @@
-      exclude_bands_loc(1:num_exclude_bands) = exclude_bands(1:num_exclude_bands)
-   end if
- 
-+  if (postproc_setup) then
-+   call kmesh_write()
-+   write(stdout,'(1x,a25,f11.3,a)') 'Time to write kmesh      ',io_time(),' (sec)'
-+   write(stdout,'(/a)') ' '//trim(seedname)//'.nnkp written.'
-+  endif
-+
- 
-   call kmesh_dealloc()
-   call param_dealloc()
diff --git a/sci-libs/wannier90/files/wannier90-1.1-0002.patch b/sci-libs/wannier90/files/wannier90-1.1-0002.patch
deleted file mode 100644
index 391a34ca2..000000000
--- a/sci-libs/wannier90/files/wannier90-1.1-0002.patch
+++ /dev/null
@@ -1,105 +0,0 @@
-diff -urN wannier90-1.1.old/src/disentangle.F90 wannier90-1.1.new/src/disentangle.F90
---- wannier90-1.1.old/src/disentangle.F90	2009-03-07 15:44:11.000000000 +0100
-+++ wannier90-1.1.new/src/disentangle.F90	2009-03-07 15:48:05.000000000 +0100
-@@ -1784,9 +1784,9 @@
-       ! [BIG ITERATION LOOP (iter)]
- 
-       if (.not.dis_converged) then
--         write(stdout,'(/5x,a)') '<<< Warning: Maximum number of disentanglement &
--              &iterations reached >>>'
--         write(stdout,'(10x,a)')  '<<< Disentanglement convergence criteria not satisfied >>>'
-+         write(stdout,'(/5x,a)') &
-+          '<<< Warning: Maximum number of disentanglement iterations reached >>>'
-+         write(stdout,'(10x,a)') '<<< Disentanglement convergence criteria not satisfied >>>'
-       endif
- 
-       if (icompflag.eq.1) then
-@@ -2551,8 +2551,8 @@
-       ! [BIG ITERATION LOOP (iter)]
- 
-       if (.not.dis_converged) then
--         write(stdout,'(/5x,a)') '<<< Warning: Maximum number of disentanglement &
--              &iterations reached >>>'
-+         write(stdout,'(/5x,a)') &
-+           '<<< Warning: Maximum number of disentanglement iterations reached >>>'
-          write(stdout,'(10x,a)')  '<<< Disentanglement convergence criteria not satisfied >>>'
-       endif
- 
-diff -urN wannier90-1.1.old/src/overlap.F90 wannier90-1.1.new/src/overlap.F90
---- wannier90-1.1.old/src/overlap.F90	2009-03-07 15:44:11.000000000 +0100
-+++ wannier90-1.1.new/src/overlap.F90	2009-03-07 15:48:36.000000000 +0100
-@@ -141,8 +141,8 @@
-                    nn_found=.true.
-                    nn=inn
-                 else
--                   call io_error('Error reading '//trim(seedname)//'.mmn.&
--                        & More than one matching nearest neighbour found')
-+                   call io_error('Error reading '//trim(seedname)// &
-+                        '.mmn. More than one matching nearest neighbour found')
-                 endif
-              endif
-           end do
-diff -urN wannier90-1.1.old/src/parameters.F90 wannier90-1.1.new/src/parameters.F90
---- wannier90-1.1.old/src/parameters.F90	2009-03-07 15:44:11.000000000 +0100
-+++ wannier90-1.1.new/src/parameters.F90	2009-03-07 15:50:46.000000000 +0100
-@@ -1054,8 +1054,9 @@
-        write(stdout,'(1x,a)') '+----------------------------------------------------------------------------+'
-        do nsp=1,num_species
-           do nat=1,atoms_species_num(nsp)
--             write(stdout,'(1x,a1,1x,a2,1x,i3,3F10.5,3x,a1,1x,3F10.5,4x,a1)') '|',atoms_symbol(nsp),nat,atoms_pos_frac(:,nat,nsp),&
--                  '|',atoms_pos_cart(:,nat,nsp)*lenconfac,'|'
-+             write(stdout,'(1x,a1,1x,a2,1x,i3,3F10.5,3x,a1,1x,3F10.5,4x,a1)') &
-+&                 '|',atoms_symbol(nsp),nat,atoms_pos_frac(:,nat,nsp),&
-+&                 '|',atoms_pos_cart(:,nat,nsp)*lenconfac,'|'
-           end do
-        end do
-        write(stdout,'(1x,a)') '*----------------------------------------------------------------------------*'
-@@ -1073,8 +1074,8 @@
-        write(stdout,'(1x,a)') '|     Frac. Coord.   l mr  r        z-axis               x-axis          Z/a |'
-        write(stdout,'(1x,a)') '+----------------------------------------------------------------------------+'
-        do nsp=1,num_proj
--          write(stdout,'(1x,a1,3(1x,f5.2),1x,i2,1x,i2,1x,i2,3(1x,f6.3),3(1x,f6.3),&
--               & 2x,f4.1,1x,a1)')  '|',proj_site(1,nsp),proj_site(2,nsp),&
-+          write(stdout,'(1x,a1,3(1x,f5.2),1x,i2,1x,i2,1x,i2,3(1x,f6.3),3(1x,f6.3),2x,f4.1,1x,a1)')&
-+&              '|',proj_site(1,nsp),proj_site(2,nsp),&
-                proj_site(3,nsp),proj_l(nsp), proj_m(nsp),proj_radial(nsp),&
-                proj_z(1,nsp),proj_z(2,nsp),proj_z(3,nsp),proj_x(1,nsp),&
-                proj_x(2,nsp),proj_x(3,nsp),proj_zona(nsp),'|'
-@@ -2738,8 +2739,8 @@
-            dummy=utility_strip(in_data(line))
-            dummy=adjustl(dummy)
-            pos1=index(dummy,':')
--           if(pos1==0) call io_error('param_read_projection: malformed projection &
--                &definition: '//trim(dummy))
-+           if(pos1==0) &
-+              call io_error('param_read_projection: malformed projection definition: '//trim(dummy))
-            sites=0
-            ctemp=dummy(:pos1-1)
-            ! Read the atomic site
-@@ -2980,11 +2981,11 @@
-               endif
-            end if
-            if(sites==-1) then
--              if(counter+sum(ang_states) > num_proj) call io_error('param_get_projection: &
--                   &too many projections defined')
-+              if(counter+sum(ang_states) > num_proj) &
-+                 call io_error('param_get_projection: too many projections defined')
-            else
--              if(counter+sites*sum(ang_states) > num_proj) call io_error('param_get_projection:&
--                   & too many projections defined')
-+              if(counter+sites*sum(ang_states) > num_proj) &
-+                 call io_error('param_get_projection: too many projections defined')
-            end if
-            !
-            if(sites==-1) then
-@@ -3025,8 +3026,8 @@
- 
-         ! check there are enough projections and add random projections if required
-         if (.not. lpartrandom) then
--              if (counter.ne.num_proj) call io_error('param_get_projections:&
--                   & Fewer projections defined than the number of Wannier functions requested')
-+              if (counter.ne.num_proj) call io_error(&
-+               'param_get_projections: Fewer projections defined than the number of Wannier functions requested')
-         else
-            call random_seed()
-            do loop=counter+1,num_proj
diff --git a/sci-libs/wannier90/files/wannier90-2.0.1.1-runtest.patch b/sci-libs/wannier90/files/wannier90-2.0.1.1-runtest.patch
deleted file mode 100644
index c9656ac31..000000000
--- a/sci-libs/wannier90/files/wannier90-2.0.1.1-runtest.patch
+++ /dev/null
@@ -1,12 +0,0 @@
-diff -Naurp wannier90-2.0.1.1.orig/tests/run_test.pl wannier90-2.0.1.1/tests/run_test.pl
---- wannier90-2.0.1.1.orig/tests/run_test.pl	2016-02-08 11:51:52.000000000 +0000
-+++ wannier90-2.0.1.1/tests/run_test.pl	2017-01-05 12:10:29.584850729 +0000
-@@ -2,7 +2,7 @@
- #
- use Cwd;
- my $cwd = cwd();
--$wanex="../wannier90.x" ;
-+$wanex="../src/wannier90.x" ;
- $wanex=$cwd."/".$wanex ;
- print " Running test set of inputs\n";
- @tests_found = <./test*>;
diff --git a/sci-libs/wannier90/metadata.xml b/sci-libs/wannier90/metadata.xml
index 07476ed95..273952673 100644
--- a/sci-libs/wannier90/metadata.xml
+++ b/sci-libs/wannier90/metadata.xml
@@ -10,13 +10,14 @@
 		<name>Honza Machá�ek</name>
 	</maintainer>
 	<longdescription lang="en">
-Wannier90 is an electronic-structure software computing maximally-localized Wannier functions (MLWF).
-It works on top of other electronic-structure software, such as Abinit, FLEUR, and PwSCF.
-The project and associated repository on Launchpad only deal with patches over the official release,
-as well as its packaging into the Debian and Ubuntu distributions.
-</longdescription>
+		Wannier90 is an electronic-structure software computing maximally-localized Wannier functions (MLWF).
+		It works on top of other electronic-structure software, such as Abinit, FLEUR, and PwSCF.
+		The project and associated repository on Launchpad only deal with patches over the official release,
+		as well as its packaging into the Debian and Ubuntu distributions.
+	</longdescription>
 	<upstream>
 		<doc>http://www.wannier.org/</doc>
 		<remote-id type="launchpad">wannier90</remote-id>
+		<remote-id type="github">wannier-developers/wannier90</remote-id>
 	</upstream>
 </pkgmetadata>
diff --git a/sci-libs/wannier90/wannier90-1.2-r3.ebuild b/sci-libs/wannier90/wannier90-1.2-r3.ebuild
deleted file mode 100644
index 952c9baaf..000000000
--- a/sci-libs/wannier90/wannier90-1.2-r3.ebuild
+++ /dev/null
@@ -1,70 +0,0 @@
-# Copyright 1999-2015 Gentoo Foundation
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=5
-
-inherit eutils fortran-2 multilib toolchain-funcs
-
-DESCRIPTION="Calculates maximally localized Wannier functions (MLWFs)"
-HOMEPAGE="http://www.wannier.org/"
-SRC_URI="http://wannier.org/code/${P}.tar.gz"
-
-LICENSE="GPL-2"
-SLOT="0"
-KEYWORDS="~amd64 ~x86 ~amd64-linux"
-IUSE="doc examples perl static-libs test"
-
-RDEPEND="
-	virtual/blas
-	virtual/lapack
-	perl? ( dev-lang/perl )"
-DEPEND="${RDEPEND}
-	virtual/pkgconfig
-	doc? ( virtual/latex-base
-		dev-texlive/texlive-latexextra
-	)"
-
-src_prepare() {
-	# Patch taken from sci-physics/abinit-5.7.3 bundled version
-	epatch \
-		"${FILESDIR}"/${PN}-1.1-0001.patch \
-		"${FILESDIR}"/${PN}-1.1-0002.patch
-}
-
-src_configure() {
-	cat <<- EOF >> "${S}"/make.sys
-		F90 = $(tc-getFC)
-		FCOPTS = ${FCFLAGS:- ${FFLAGS:- -O2}}
-		LDOPTS = ${LDFLAGS}
-		LIBS = $($(tc-getPKG_CONFIG) --libs blas lapack)
-	EOF
-}
-
-src_compile() {
-	emake -j1 wannier
-	emake -j1 lib
-	if use doc; then
-		VARTEXFONTS="${T}/fonts"
-		emake -j1 doc
-	fi
-}
-
-src_test() {
-	einfo "Compare the 'Standard' and 'Current' outputs of this test."
-	cd tests
-	emake test
-	cat wantest.log
-}
-
-src_install() {
-	dobin wannier90.x
-	use perl && dobin utility/kmesh.pl
-	use static-libs && dolib.a libwannier.a
-	doheader src/*.mod
-	if use examples; then
-		insinto /usr/share/${PN}
-		doins -r examples
-	fi
-	use doc && dodoc doc/*.pdf
-	dodoc README README.install CHANGE.log
-}
diff --git a/sci-libs/wannier90/wannier90-2.0.1.1.ebuild b/sci-libs/wannier90/wannier90-2.0.1.1.ebuild
deleted file mode 100644
index cd58f4bcd..000000000
--- a/sci-libs/wannier90/wannier90-2.0.1.1.ebuild
+++ /dev/null
@@ -1,96 +0,0 @@
-# Copyright 1999-2017 Gentoo Foundation
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=5
-
-inherit autotools-utils eutils fortran-2 multilib toolchain-funcs
-
-DESCRIPTION="Calculates maximally localized Wannier functions (MLWFs)"
-HOMEPAGE="http://www.wannier.org/"
-#SRC_URI="http://wannier.org/code/${P}.tar.gz"
-SRC_URI="https://launchpad.net/${PN}/2.0/${PV}/+download/${P}.tar.gz"
-
-LICENSE="GPL-2"
-SLOT="0"
-KEYWORDS="~amd64 ~x86 ~amd64-linux"
-IUSE="doc mpi perl test"
-
-RDEPEND="
-	virtual/blas
-	virtual/lapack
-	perl? ( dev-lang/perl )"
-DEPEND="${RDEPEND}
-	virtual/pkgconfig
-	doc? ( virtual/latex-base
-		dev-texlive/texlive-latexextra
-		dev-tex/revtex
-	)"
-
-pkg_setup() {
-	# fortran-2.eclass does not handle mpi wrappers
-	if use mpi; then
-		export FC="mpif90"
-		export F77="mpif77"
-		export CC="mpicc"
-		export CXX="mpic++"
-		export MPIFC="mpif90"
-		export MPICC="mpicc"
-	else
-		tc-export FC F77 CC CXX
-	fi
-
-	# Preprocesor macross can make some lines really long
-	append-fflags -ffree-line-length-none
-
-	fortran-2_pkg_setup
-}
-
-src_prepare() {
-	epatch "${FILESDIR}"/"$P"-runtest.patch
-}
-
-src_configure() {
-	export LINALG_INCLUDES="$($(tc-getPKG_CONFIG) --cflags blas lapack)"
-	export LINALG_LIBS="$($(tc-getPKG_CONFIG) --libs blas lapack)"
-	autotools-utils_src_configure
-}
-
-src_compile() {
-	autotools-utils_src_compile
-	pushd "${BUILD_DIR}"/utility > /dev/null || die
-	emake || die "emake in utility failed"
-	popd > /dev/null || die
-	if use doc; then
-		VARTEXFONTS="${T}/fonts"
-		pushd "${BUILD_DIR}"/doc/user_guide > /dev/null || die
-		emake || die 'emake in doc/user_guide failed'
-		cd "${BUILD_DIR}"/doc/tutorial
-		emake || die 'emake in doc/tutorial failed'
-		cd "${BUILD_DIR}"/utility/w90vdw/doc
-		emake || die 'emake in utility/w90vdw/doc failed'
-		cd "${BUILD_DIR}"/utility/w90pov/doc
-		emake || die 'emake in utility/w90pov/doc failed'
-		popd > /dev/null || die
-	fi
-}
-
-src_test() {
-	einfo "Compare the 'Standard' and 'Current' outputs of this test."
-#	cd tests
-#	emake test
-	autotools-utils_src_compile check
-	cat "${BUILD_DIR}"/tests/wantest.log
-}
-
-src_install() {
-	autotools-utils_src_install
-	dobin "${BUILD_DIR}"/utility/w90pov/src/w90pov.x
-	dobin "${BUILD_DIR}"/utility/PL_assessment/w90_pl_assess.x
-	use perl && dobin "$S"/utility/w90_kmesh.pl
-	if use doc; then
-		dodoc "${BUILD_DIR}"/doc/tutorial/tutorial.pdf
-		dodoc "${BUILD_DIR}"/doc/user_guide/user_guide.pdf
-		dodoc "${BUILD_DIR}"/utility/w90vdw/doc/w90vdw.pdf
-		dodoc "${BUILD_DIR}"/utility/w90pov/doc/w90pov.pdf
-	fi
-}
diff --git a/sci-libs/wannier90/wannier90-2.0.1.ebuild b/sci-libs/wannier90/wannier90-2.0.1.ebuild
deleted file mode 100644
index 3eafd6a88..000000000
--- a/sci-libs/wannier90/wannier90-2.0.1.ebuild
+++ /dev/null
@@ -1,64 +0,0 @@
-# Copyright 1999-2015 Gentoo Foundation
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=5
-
-inherit eutils fortran-2 multilib toolchain-funcs
-
-DESCRIPTION="Calculates maximally localized Wannier functions (MLWFs)"
-HOMEPAGE="http://www.wannier.org/"
-SRC_URI="http://wannier.org/code/${P}.tar.gz"
-
-LICENSE="GPL-2"
-SLOT="0"
-KEYWORDS="~amd64 ~x86 ~amd64-linux"
-IUSE="doc examples perl static-libs test"
-
-RDEPEND="
-	virtual/blas
-	virtual/lapack
-	perl? ( dev-lang/perl )"
-DEPEND="${RDEPEND}
-	virtual/pkgconfig
-	doc? ( virtual/latex-base
-		dev-texlive/texlive-latexextra
-		dev-tex/revtex
-	)"
-
-src_configure() {
-	cat <<- EOF >> "${S}"/make.sys
-		F90 = $(tc-getFC)
-		FCOPTS = ${FCFLAGS:- ${FFLAGS:- -O2}}
-		LDOPTS = ${LDFLAGS}
-		LIBS = $($(tc-getPKG_CONFIG) --libs blas lapack)
-	EOF
-}
-
-src_compile() {
-	emake -j1 wannier
-	emake -j1 lib
-	if use doc; then
-		VARTEXFONTS="${T}/fonts"
-		emake -j1 doc
-	fi
-}
-
-src_test() {
-	einfo "Compare the 'Standard' and 'Current' outputs of this test."
-	cd tests
-	emake test
-	cat wantest.log
-}
-
-src_install() {
-	dobin wannier90.x
-	use perl && dobin utility/kmesh.pl
-	use static-libs && dolib.a libwannier.a
-	doheader src/obj/*.mod
-	if use examples; then
-		insinto /usr/share/${PN}
-		doins -r examples
-	fi
-	use doc && dodoc doc/*.pdf
-	dodoc README README.install CHANGE.log
-}
diff --git a/sci-libs/wannier90/wannier90-3.1.0.ebuild b/sci-libs/wannier90/wannier90-3.1.0.ebuild
new file mode 100644
index 000000000..ca53b3863
--- /dev/null
+++ b/sci-libs/wannier90/wannier90-3.1.0.ebuild
@@ -0,0 +1,56 @@
+# Copyright 1999-2021 Gentoo Authors
+# Distributed under the terms of the GNU General Public License v2
+
+EAPI=7
+
+inherit fortran-2 toolchain-funcs
+
+DESCRIPTION="Calculates maximally localized Wannier functions (MLWFs)"
+HOMEPAGE="http://www.wannier.org/"
+SRC_URI="https://github.com/wannier-developers/wannier90/archive/v${PV}.tar.gz -> ${P}.tar.gz"
+
+LICENSE="GPL-2"
+SLOT="0"
+KEYWORDS="~amd64 ~x86 ~amd64-linux"
+
+IUSE="examples perl static-libs"
+
+RDEPEND="
+	virtual/blas
+	virtual/lapack
+	virtual/mpi
+	perl? ( dev-lang/perl )
+"
+DEPEND="${RDEPEND}"
+BDEPEND="virtual/pkgconfig"
+
+src_prepare() {
+	default
+	cp config/make.inc.gfort make.inc || die
+}
+
+src_configure() {
+	cat <<- EOF >> "${S}"/make.sys
+		F90 = $(tc-getFC)
+		FCOPTS = ${FCFLAGS:- ${FFLAGS:- -O2}}
+		LDOPTS = ${LDFLAGS}
+		LIBS = $($(tc-getPKG_CONFIG) --libs blas lapack)
+	EOF
+}
+
+src_test() {
+	einfo "Compare the 'Standard' and 'Current' outputs of this test."
+	cd test-suite || die
+	./run_tests --default || die
+}
+
+src_install() {
+	dobin wannier90.x
+	use perl && dobin utility/kmesh.pl
+	use static-libs && dolib.a libwannier.a
+	doheader src/obj/*.mod
+	if use examples; then
+		insinto /usr/share/${PN}
+		doins -r examples
+	fi
+}
diff --git a/sci-libs/xblas/Manifest b/sci-libs/xblas/Manifest
deleted file mode 100644
index 4919da836..000000000
--- a/sci-libs/xblas/Manifest
+++ /dev/null
@@ -1 +0,0 @@
-DIST xblas-1.0.248.tar.gz 2087424 BLAKE2B 47f446f95f033260baec4053f4d761eda54e753bd39477cdf0636f3b68f1a3748f6c48aa32eaa693a486a8bb92b259b2742e42a2663fa1b3a75de1d3ff93daac SHA512 4a3c3a6aea0e12a5620ba1c4d328ca9f20764da4871b2bac48c21366c25afed31daa3a3ef291973159b890b2bbf033bdc14503634637b50ff4514f425b4356ad
diff --git a/sci-libs/xblas/metadata.xml b/sci-libs/xblas/metadata.xml
deleted file mode 100644
index 11b4b52f7..000000000
--- a/sci-libs/xblas/metadata.xml
+++ /dev/null
@@ -1,17 +0,0 @@
-<?xml version="1.0" encoding="UTF-8"?>
-<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
-<pkgmetadata>
-	<maintainer type="project">
-		<email>sci@gentoo.org</email>
-		<name>Gentoo Science Project</name>
-	</maintainer>
-	<longdescription lang="en">
-The XBLAS library of routines is part of a reference implementation for 
-the Dense and Banded Basic Linear Algebra Subroutines, along with their 
-Extended and Mixed Precision versions, as documented in Chapters 2 and 4 
-of the new BLAS Standard.
-</longdescription>
-	<use>
-		<flag name="int64">Build the 64 bits integer library</flag>
-	</use>
-</pkgmetadata>
diff --git a/sci-libs/xblas/xblas-1.0.248-r1.ebuild b/sci-libs/xblas/xblas-1.0.248-r1.ebuild
deleted file mode 100644
index a04d2a926..000000000
--- a/sci-libs/xblas/xblas-1.0.248-r1.ebuild
+++ /dev/null
@@ -1,109 +0,0 @@
-# Copyright 1999-2014 Gentoo Foundation
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=5
-
-NUMERIC_MODULE_NAME="xblas"
-FORTRAN_NEEDED=fortran
-
-inherit flag-o-matic fortran-2 numeric-int64-multibuild toolchain-funcs versionator
-
-DESCRIPTION="Extra Precise Basic Linear Algebra Subroutines"
-HOMEPAGE="http://www.netlib.org/xblas"
-SRC_URI="${HOMEPAGE}/${P}.tar.gz"
-
-LICENSE="BSD"
-SLOT="0"
-KEYWORDS="~amd64 ~x86 ~amd64-linux ~x86-linux"
-IUSE="doc fortran static-libs"
-
-RDEPEND=""
-DEPEND="${RDEPEND}
-	sys-devel/m4"
-
-static_to_shared() {
-	local libstatic=${1}; shift
-	local libname=$(basename ${libstatic%.a})
-	local soname=${libname}$(get_libname $(get_version_component_range 1-2))
-	local libdir=$(dirname ${libstatic})
-
-	einfo "Making ${soname} from ${libstatic}"
-	if [[ ${CHOST} == *-darwin* ]] ; then
-		${LINK:-$(tc-getCC)} ${LDFLAGS}  \
-			-dynamiclib -install_name "${EPREFIX}"/usr/lib/"${soname}" \
-			-Wl,-all_load -Wl,${libstatic} \
-			"$@" -o ${libdir}/${soname} || die "${soname} failed"
-	else
-		${LINK:-$(tc-getCC)} ${LDFLAGS}  \
-			-shared -Wl,-soname=${soname} \
-			-Wl,--whole-archive ${libstatic} -Wl,--no-whole-archive \
-			"$@" -o ${libdir}/${soname} || die "${soname} failed"
-		[[ $(get_version_component_count) -gt 1 ]] && \
-			ln -s ${soname} ${libdir}/${libname}$(get_libname $(get_major_version)) || die
-		ln -s ${soname} ${libdir}/${libname}$(get_libname) || die
-	fi
-}
-
-pkg_setup() {
-	use fortran && fortran-2_pkg_setup
-}
-
-src_prepare() {
-	numeric-int64-multibuild_copy_sources
-}
-
-src_configure() {
-	xblas_configure() {
-		export FCFLAGS="${FCFLAGS} $(get_abi_CFLAGS) $(numeric-int64_get_fortran_int64_abi_fflags)"
-		econf $(use_enable fortran)
-	}
-	numeric-int64-multibuild_foreach_all_abi_variants run_in_build_dir xblas_configure
-}
-
-src_compile() {
-	xblas_src_compile() {
-		local profname=$(numeric-int64_get_module_name)
-		local libname="${profname//-/_}"
-		# default target builds and runs tests - split
-		# build first static libs because of fPIC afterwards
-		# and we link tests with shared ones
-		if use static-libs; then
-			emake makefiles
-			emake lib XBLASLIB=lib${libname}_nonpic.a
-			emake clean
-		fi
-		sed -i \
-			-e 's:\(CFLAGS.*\).*:\1 -fPIC:' \
-			make.inc || die
-		emake makefiles
-		emake lib XBLASLIB=lib${libname}.a
-		static_to_shared lib${libname}.a
-	}
-	numeric-int64-multibuild_foreach_all_abi_variants run_in_build_dir xblas_src_compile
-}
-
-src_test() {
-	numeric-int64-multibuild_foreach_all_abi_variants run_in_build_dir emake tests
-}
-
-src_install() {
-	xblas_src_install() {
-		local profname=$(numeric-int64_get_module_name)
-		local libname="${profname//-/_}"
-		if numeric-int64_is_static_build; then
-			use static-libs && newlib.a lib${libname}_nonpic.a lib${libname}.a
-		else
-			dolib.so lib${libname}$(get_libname)*
-
-			create_pkgconfig \
-				--name  ${profname} \
-				--libs "-L\${libdir} -l${libname}" \
-				--cflags "-I\${includedir} $(numeric-int64_get_fortran_int64_abi_fflags)" \
-				${profname}
-		fi
-	}
-	numeric-int64-multibuild_foreach_all_abi_variants run_in_build_dir xblas_src_install
-
-	dodoc README README.devel
-	use doc && dodoc doc/report.ps
-}
diff --git a/sci-libs/xraylib/Manifest b/sci-libs/xraylib/Manifest
deleted file mode 100644
index 991d8eede..000000000
--- a/sci-libs/xraylib/Manifest
+++ /dev/null
@@ -1,2 +0,0 @@
-DIST xraylib-2.16.0.tar.gz 39669898 BLAKE2B 1a81e9d0fa954833c4388e84af784fe0913ca183ee12e5ed4d645d0965cad6b8dcd9eae95d772ce40a9d276191ed1bf73ac31807735e8f3669bd40705d9255c3 SHA512 0232bea0f934cb13fd30a9964aa52fc8eeae82fc40c263f7196041d58b272c99e177254268b43f091361b51c0046bedb9dfce88684a01c9da0ad33878b2b753c
-DIST xraylib-3.1.0.tar.gz 32882324 BLAKE2B f7ac4214971a147b2ef08434401cf37ab756afa9081c0575291ac42c16ff86ec6a7704df81d43f5afe205c2187c8706456477891711a23f8e9f9653b2de6de73 SHA512 0b090e6096d047a32552477a4cfe46203b69f8d858bae2b053f877cf713219432b8a0779dfc6eaa48c82568407ba56bbf565c8491d6416001f9c8fb80b714f01
diff --git a/sci-libs/xraylib/metadata.xml b/sci-libs/xraylib/metadata.xml
deleted file mode 100644
index e924a8916..000000000
--- a/sci-libs/xraylib/metadata.xml
+++ /dev/null
@@ -1,44 +0,0 @@
-<?xml version="1.0" encoding="UTF-8"?>
-<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
-<pkgmetadata>
-	<maintainer type="person">
-		<email>cjk34@cam.ac.uk</email>
-	</maintainer>
-	<maintainer type="project">
-		<email>sci@gentoo.org</email>
-		<name>Gentoo Science Project</name>
-	</maintainer>
-	<longdescription lang="en">
-Quantitative estimate of elemental composition by spectroscopic and imaging
-techniques using X-ray fluorescence requires the availability of accurate data
-of X-ray interaction with matter. Although a wide number of computer codes
-and data sets are reported in literature, none of them is presented in the
-form of freely available library functions which can be easily included in
-software applications for X-ray fluorescence. This work presents a compilation
-of data sets from different published works and an xraylib interface in the
-form of callable functions. Although the target applications are on X-ray
-fluorescence, cross sections of interactions like photoionization, coherent
-scattering and Compton scattering, as well as form factors and anomalous
-scattering functions, are also available.
-
-xraylib provides access to some of the most respected databases of physical
-data in the field of x-rays. The core of xraylib is a library, written in ANSI
-C, containing over 40 functions to be used to retrieve data from these
-databases. This C library can be directly linked with any program written in
-C, C++ or Objective-C. Furthermore, the xraylib package contains bindings to
-several popular programming languages: Fortran 2003, Perl, Python, Java, IDL,
-Lua and .NET, as well as a command-line utility which can be used as a
-pocket-calculator. Although not officially supported, xraylib has been
-reported to be useable from within Matlab and LabView.
-
-Reference: T. Schoonjans, A. Brunetti, B. Golosio, M. Sanchez del Rio, 
-V. A. Solé, C. Ferrero and L. Vincze, "The xraylib library for X-ray--matter 
-interactions. Recent developments", Spectrochimica Acta B 66 (2011) 776-784 
-( doi: http://dx.doi.org/10.1016/j.sab.2011.09.011 )
-</longdescription>
-	<use>
-</use>
-	<upstream>
-		<remote-id type="github">tschoonj/xraylib</remote-id>
-	</upstream>
-</pkgmetadata>
diff --git a/sci-libs/xraylib/xraylib-2.16.0.ebuild b/sci-libs/xraylib/xraylib-2.16.0.ebuild
deleted file mode 100644
index 97905e356..000000000
--- a/sci-libs/xraylib/xraylib-2.16.0.ebuild
+++ /dev/null
@@ -1,83 +0,0 @@
-# Copyright 1999-2015 Gentoo Foundation
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=5
-
-AUTOTOOLS_AUTORECONF=true
-FORTRAN_NEEDED=fortran
-FORTRAN_STANDARD=2003
-PYTHON_COMPAT=( python2_7 ) # python 3 supported by github master
-
-inherit eutils autotools-utils python-single-r1 java-pkg-opt-2 fortran-2
-
-DESCRIPTION="X-ray matter interaction cross sections for X-ray fluorescence library"
-HOMEPAGE="https://github.com/tschoonj/xraylib"
-SRC_URI="https://github.com/tschoonj/xraylib/archive/${P}.tar.gz"
-
-LICENSE="BSD"
-SLOT="0"
-KEYWORDS="~amd64"
-IUSE="examples fortran java lua perl python"
-
-REQUIRED_USE="python? ( ${PYTHON_REQUIRED_USE} )"
-
-RDEPEND="
-	java? ( >=virtual/jre-1.4:* )
-	lua? ( dev-lang/lua:0 )
-	perl? ( dev-lang/perl )
-	python? ( ${PYTHON_DEPS} )"
-
-DEPEND="${RDEPEND}
-	java? ( >=virtual/jdk-1.4:* )"
-
-S="${WORKDIR}/${PN}-${P}"
-
-DOCS=(AUTHORS BUGS Changelog README TODO)
-
-pkg_setup() {
-	fortran-2_pkg_setup
-	java-pkg-opt-2_pkg_setup
-	use python && python-single-r1_pkg_setup
-}
-
-src_prepare() {
-	java-pkg-opt-2_src_prepare
-	autotools-utils_src_prepare
-}
-
-src_configure() {
-	local myeconfargs=(
-		--disable-idl
-		$(use_enable fortran fortran2003)
-		$(use_enable java)
-		$(use_enable lua)
-		$(use_enable perl)
-		$(use_enable python)
-		$(use_enable python python-integration)
-	)
-	autotools-utils_src_configure
-}
-
-src_compile() {
-	# see https://github.com/tschoonj/xraylib/issues/11
-	if use fortran || use java; then
-		MAKEOPTS+=" -j1"
-	fi
-	autotools-utils_src_compile
-}
-
-src_install() {
-	autotools-utils_src_install
-
-	if use examples; then
-		insinto /usr/share/doc/${PF}/examples
-		doins example/*.c example/*.cpp
-		use java && doins example/*.java
-		use lua && doins example/*.lua
-		use perl && doins example/*.pl
-		use python && doins example/*.py
-		docompress -x /usr/share/doc/${PF}/examples # Don't compress examples
-	fi
-
-	use java && java-pkg_regso /usr/share/xraylib/java/libxraylib.so
-}
diff --git a/sci-libs/xraylib/xraylib-3.1.0.ebuild b/sci-libs/xraylib/xraylib-3.1.0.ebuild
deleted file mode 100644
index 97905e356..000000000
--- a/sci-libs/xraylib/xraylib-3.1.0.ebuild
+++ /dev/null
@@ -1,83 +0,0 @@
-# Copyright 1999-2015 Gentoo Foundation
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=5
-
-AUTOTOOLS_AUTORECONF=true
-FORTRAN_NEEDED=fortran
-FORTRAN_STANDARD=2003
-PYTHON_COMPAT=( python2_7 ) # python 3 supported by github master
-
-inherit eutils autotools-utils python-single-r1 java-pkg-opt-2 fortran-2
-
-DESCRIPTION="X-ray matter interaction cross sections for X-ray fluorescence library"
-HOMEPAGE="https://github.com/tschoonj/xraylib"
-SRC_URI="https://github.com/tschoonj/xraylib/archive/${P}.tar.gz"
-
-LICENSE="BSD"
-SLOT="0"
-KEYWORDS="~amd64"
-IUSE="examples fortran java lua perl python"
-
-REQUIRED_USE="python? ( ${PYTHON_REQUIRED_USE} )"
-
-RDEPEND="
-	java? ( >=virtual/jre-1.4:* )
-	lua? ( dev-lang/lua:0 )
-	perl? ( dev-lang/perl )
-	python? ( ${PYTHON_DEPS} )"
-
-DEPEND="${RDEPEND}
-	java? ( >=virtual/jdk-1.4:* )"
-
-S="${WORKDIR}/${PN}-${P}"
-
-DOCS=(AUTHORS BUGS Changelog README TODO)
-
-pkg_setup() {
-	fortran-2_pkg_setup
-	java-pkg-opt-2_pkg_setup
-	use python && python-single-r1_pkg_setup
-}
-
-src_prepare() {
-	java-pkg-opt-2_src_prepare
-	autotools-utils_src_prepare
-}
-
-src_configure() {
-	local myeconfargs=(
-		--disable-idl
-		$(use_enable fortran fortran2003)
-		$(use_enable java)
-		$(use_enable lua)
-		$(use_enable perl)
-		$(use_enable python)
-		$(use_enable python python-integration)
-	)
-	autotools-utils_src_configure
-}
-
-src_compile() {
-	# see https://github.com/tschoonj/xraylib/issues/11
-	if use fortran || use java; then
-		MAKEOPTS+=" -j1"
-	fi
-	autotools-utils_src_compile
-}
-
-src_install() {
-	autotools-utils_src_install
-
-	if use examples; then
-		insinto /usr/share/doc/${PF}/examples
-		doins example/*.c example/*.cpp
-		use java && doins example/*.java
-		use lua && doins example/*.lua
-		use perl && doins example/*.pl
-		use python && doins example/*.py
-		docompress -x /usr/share/doc/${PF}/examples # Don't compress examples
-	fi
-
-	use java && java-pkg_regso /usr/share/xraylib/java/libxraylib.so
-}
diff --git a/sci-libs/zarja/Manifest b/sci-libs/zarja/Manifest
index 530a3371e..edb1a2e29 100644
--- a/sci-libs/zarja/Manifest
+++ b/sci-libs/zarja/Manifest
@@ -1 +1 @@
-DIST zarja-1.1.1.tar.gz 1368076 BLAKE2B 262d57285d4587df4bb64f2b690c015ce61f62e3bbe43756ef64f60f0a6d702573dc6e4eef1bd4fff137eb14446e3664296235d7d97866c9e38421bb4b2e73d2 SHA512 4618a4a558656b34025749e2f8b2dad8ee897dfb1eebfa4ac157b75f66d499d15d2d3a8a5e207aaa6aa9498c8d69e5a470875f1201be6056e7739f3b25dab06d
+DIST zarja-2.2.0.tar.gz 872503 BLAKE2B 26b0ef8ea36bda2af0173cc9a33e334219d9e87c4eafae4beaa31d235beb19da7594b7e504fa362fc1c37967f388b5c3523f8eba38ab5cb2b697d7220bf79754 SHA512 914ac12669e3597a354c48813014141a6070e5cbfea28a682ef85c8a5740069db025832944726ca3a65cff8e23939b1672177e9c68e1f3c579e5fb9e4bb8ec20
diff --git a/sci-libs/zarja/zarja-1.1.1.ebuild b/sci-libs/zarja/zarja-1.1.1.ebuild
deleted file mode 100644
index d5ce3856c..000000000
--- a/sci-libs/zarja/zarja-1.1.1.ebuild
+++ /dev/null
@@ -1,40 +0,0 @@
-# Copyright 1999-2014 Gentoo Foundation
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=5
-
-DESCRIPTION="Scientific multi-agent simulation library"
-HOMEPAGE="http://sourceforge.net/projects/zarja/"
-SRC_URI="mirror://sourceforge/${PN}/${P}.tar.gz"
-
-LICENSE="GPL-2"
-SLOT="0"
-KEYWORDS="~amd64 ~x86"
-IUSE="doc"
-
-RDEPEND="
-	sci-libs/gsl
-	virtual/lapack
-	sci-libs/fftw:3.0
-	dev-libs/boost
-	dev-cpp/tclap"
-DEPEND="${RDEPEND}
-	virtual/pkgconfig
-	doc? ( app-doc/doxygen )"
-
-src_configure() {
-	econf --includedir=/usr/include/zarja
-}
-
-src_compile() {
-	default
-	if use doc; then
-		doxygen Doxyfile || die "doc generation failed"
-	fi
-}
-
-src_install() {
-	DOCS=( FAQ )
-	use doc && HTML_DOCS=( html/. )
-	default
-}
diff --git a/sci-libs/zarja/zarja-2.2.0.ebuild b/sci-libs/zarja/zarja-2.2.0.ebuild
new file mode 100644
index 000000000..405786ce7
--- /dev/null
+++ b/sci-libs/zarja/zarja-2.2.0.ebuild
@@ -0,0 +1,27 @@
+# Copyright 1999-2021 Gentoo Authors
+# Distributed under the terms of the GNU General Public License v2
+
+EAPI=7
+
+DESCRIPTION="Scientific multi-agent simulation library"
+HOMEPAGE="https://sourceforge.net/projects/zarja/"
+# latest version is binary only?
+SRC_URI="https://downloads.sourceforge.net/project/${PN}/${PN}/${PN}_${PV}.tar.gz -> ${P}.tar.gz"
+
+LICENSE="GPL-2"
+SLOT="0"
+KEYWORDS="~amd64 ~x86"
+
+RDEPEND="
+	sci-libs/gsl
+	virtual/lapack
+	sci-libs/fftw:3.0
+	dev-libs/boost
+	dev-cpp/tclap"
+DEPEND="${RDEPEND}"
+
+S="${WORKDIR}/${PN}_${PV}"
+
+src_install() {
+	cp -a "${S}"/* "${ED}" || die
+}
diff --git a/sci-mathematics/Macaulay2/Macaulay2-9999.ebuild b/sci-mathematics/Macaulay2/Macaulay2-9999.ebuild
deleted file mode 100644
index 46e370ce0..000000000
--- a/sci-mathematics/Macaulay2/Macaulay2-9999.ebuild
+++ /dev/null
@@ -1,176 +0,0 @@
-# Copyright 1999-2014 Gentoo Foundation
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=5
-
-PYTHON_COMPAT=( python2_7 )
-
-inherit autotools elisp-common eutils flag-o-matic git-r3 python-single-r1 toolchain-funcs
-
-FACTORY="factory-4.0.0+m4"
-FACTORY_GFTABLES="factory.4.0.1-gftables"
-
-DESCRIPTION="Research tool for commutative algebra and algebraic geometry"
-HOMEPAGE="http://www.math.uiuc.edu/Macaulay2/"
-BASE_URI="http://www.math.uiuc.edu/Macaulay2/Downloads/OtherSourceCode/trunk"
-SRC_URI="
-	${BASE_URI}/${FACTORY}.tar.gz
-	${BASE_URI}/${FACTORY_GFTABLES}.tar.gz
-	${BASE_URI}/gtest-1.7.0.tar.gz"
-EGIT_REPO_URI="git://github.com/Macaulay2/M2.git"
-
-SLOT="0"
-LICENSE="GPL-2"
-KEYWORDS=""
-IUSE="debug emacs +optimization"
-
-REQUIRED_USE="${PYTHON_REQUIRED_USE}"
-
-DEPEND="${PYTHON_DEPS}
-	sys-process/time
-	virtual/pkgconfig
-	app-arch/unzip
-	app-text/dos2unix"
-# Unzip and dos2unix just for normaliz
-
-RDEPEND="${PYTHON_DEPS}
-	sys-libs/gdbm
-	dev-libs/ntl
-	sci-mathematics/pari[gmp]
-	>=sys-libs/readline-6.1
-	dev-libs/libxml2:2
-	sci-mathematics/flint[gc]
-	sci-mathematics/frobby
-	sci-mathematics/4ti2
-	sci-mathematics/nauty
-	>=sci-mathematics/normaliz-2.8
-	sci-mathematics/gfan
-	sci-libs/mpir[cxx]
-	dev-libs/mpfr
-	sci-libs/cdd+
-	sci-libs/cddlib
-	sci-libs/lrslib[gmp]
-	virtual/blas
-	virtual/lapack
-	dev-util/ctags
-	sys-libs/ncurses
-	>=dev-libs/boehm-gc-7.2_alpha6[threads]
-	dev-libs/libatomic_ops
-	emacs? ( virtual/emacs )"
-
-SITEFILE=70Macaulay2-gentoo.el
-
-S="${WORKDIR}/${PN}-${PV}/"
-
-RESTRICT="mirror"
-
-src_unpack (){
-	# unpack "Normaliz2.8.zip"
-	git-r3_src_unpack
-	# Undo one level of directory until git allows to checkout
-	# subdirectories
-	mv "${S}"/M2/* "${S}" || die
-	# Need to get rid of this now because install wants this location later
-	rm -r "${S}/M2" || die
-}
-
-pkg_setup () {
-	tc-export CC CPP CXX PKG_CONFIG
-	append-cppflags "-I/usr/include/frobby"
-	# gtest needs python:2
-	python-single-r1_pkg_setup
-}
-
-src_prepare() {
-	# Put updated Normaliz.m2 in place
-	# cp "${WORKDIR}/Normaliz2.8/Macaulay2/Normaliz.m2" \
-	# 	"${S}/Macaulay2/packages" || die
-	# dos2unix "${S}/Macaulay2/packages/Normaliz.m2" || die
-
-	# Patching .m2 files to look for external programs in
-	# /usr/bin
-	epatch "${FILESDIR}"/${PV}-paths-of-external-programs.patch
-
-	# Shortcircuit lapack tests
-	epatch "${FILESDIR}"/${PV}-lapack.patch
-
-	# Factory is a statically linked library which (in this flavor) are not used by any
-	# other program. We build it internally and don't install it.
-	cp "${DISTDIR}/${FACTORY}.tar.gz" "${S}/BUILD/tarfiles/" \
-		|| die "copy failed"
-	cp "${DISTDIR}/${FACTORY_GFTABLES}.tar.gz" "${S}/BUILD/tarfiles/" \
-		|| die "copy failed"
-	# Macaulay2 developers want that gtest is built internally because
-	# the documentation says it may fail if build with options not the
-	# same as the tested program.
-	cp "${DISTDIR}/gtest-1.7.0.tar.gz" "${S}/BUILD/tarfiles/" \
-		|| die "copy failed"
-
-	eautoreconf
-}
-
-src_configure (){
-	# Recommended in bug #268064 Possibly unecessary
-	# but should not hurt anybody.
-	if ! use emacs; then
-		tags="ctags"
-	fi
-
-	# configure instead of econf to enable install with --prefix
-	./configure LIBS="$($(tc-getPKG_CONFIG) --libs lapack)" \
-		--prefix="${D}/usr" \
-		--disable-encap \
-		--disable-strip \
-		--with-issue=Gentoo \
-		$(use_enable optimization optimize) \
-		$(use_enable debug) \
-		--enable-build-libraries="factory" \
-		--with-unbuilt-programs="4ti2 gfan normaliz nauty cddplus lrslib" \
-		|| die "failed to configure Macaulay"
-}
-
-src_compile() {
-	# Parallel build not supported yet
-	# emake -j1
-	# For trunk builds we may wish to ignore example errors
-	emake IgnoreExampleErrors=true -j1
-
-	if use emacs; then
-		cd "${S}/Macaulay2/emacs" || die
-		elisp-compile *.el
-	fi
-}
-
-src_test() {
-	# No parallel tests yet & Need to increase the time
-	# limit for long running tests in Schubert2 to pass
-	emake TLIMIT=550 -j1 check
-}
-
-src_install () {
-	# Parallel install not supported yet
-	# NumericalAlgebraicGeometry fails (during install too?)
-	emake IgnoreExampleErrors=true -j1 install
-
-	# Remove emacs files and install them in the
-	# correct place if use emacs
-	rm -rf "${ED}"/usr/share/emacs/site-lisp || die
-	if use emacs; then
-		cd "${S}/Macaulay2/emacs" || die
-		elisp-install ${PN} *.elc *.el
-		elisp-site-file-install "${FILESDIR}/${SITEFILE}"
-	fi
-}
-
-pkg_postinst() {
-	if use emacs; then
-		elisp-site-regen
-		elog "If you want to set a hot key for Macaulay2 in Emacs add a line similar to"
-		elog "(global-set-key [ f12 ] 'M2)"
-		elog "in order to set it to F12 (or choose a different one)."
-	fi
-}
-
-pkg_postrm() {
-	use emacs && elisp-site-regen
-}
diff --git a/sci-mathematics/Macaulay2/Manifest b/sci-mathematics/Macaulay2/Manifest
deleted file mode 100644
index 53f184fa9..000000000
--- a/sci-mathematics/Macaulay2/Manifest
+++ /dev/null
@@ -1,3 +0,0 @@
-DIST factory-4.0.0+m4.tar.gz 4711126 SHA256 9b2498cc7fc6765f1c586e8061ebe236cdce4b32a44721a235ad2644ec3124fb SHA512 1dacb9aae52e655bccbbc960397b02351050791594dd9c39771f0da7f8c6e8130a8827c2a675c3fbaaa214606e123ac9776e1c73d143649353cefc50cadeea3e WHIRLPOOL 47c4d6261fc6cc9c172035d8774f0cde9fa669fa164fc4a0f47e84ba789d69d14f5a16d042451564412fdedddec71335714ad751508495c22cea25b69f10b925
-DIST factory.4.0.1-gftables.tar.gz 2974152 SHA256 9cd158ceb1c2b1c47bdca2c0b004bba92cb0e0aaa0ea6a43ca784ebdce10eebd SHA512 060c58fe6e4565dd5e7649bfa070f14dec3c383a55ebab52a9f02b58a6405e2183e0c7e08964cddb87b81e872c0d8a52d7bd4575d07269547be544cf6a725a76 WHIRLPOOL a721a6824681118578c7289cea77a3f47e5c7654f30dc454eaac76b19cc89e416ae54b8d21a69f897d7087d4b67990634fc960f81df2ea53f428868d608dc9c2
-DIST gtest-1.7.0.tar.gz 1001582 SHA256 c0f860eee47c86e0aeb462fd0bdfd70e3975297e0b8b178e0e03a95e1f6c9bc4 SHA512 a9f5c047b39efb2d11b55ee9913662ca402ac6837b3ad2d278ecfbd1caf32ed4546f169e3e92503d57bf3b62ccf89cd062da1c7ea3638aae98e868d2766363c3 WHIRLPOOL 36edbdf8be7c3793a89918a3c43d74e75a6281a37c394f7d2f20506130a76aab04a3beddba01bf7f0e9b6901c7e834ca014c31c913c0ea846d3f6be9c93599d2
diff --git a/sci-mathematics/Macaulay2/files/70Macaulay2-gentoo.el b/sci-mathematics/Macaulay2/files/70Macaulay2-gentoo.el
deleted file mode 100644
index ac86e2132..000000000
--- a/sci-mathematics/Macaulay2/files/70Macaulay2-gentoo.el
+++ /dev/null
@@ -1,11 +0,0 @@
-;; sci-mathematics/Macaulay2 init file
-
-(add-to-list 'load-path "/usr/share/emacs/site-lisp/Macaulay2")
-
-(defvar M2-exe "/usr/bin/M2" "*The default Macaulay2 executable name.")
-(autoload 'M2 "M2.el" "Run Macaulay 2 in a buffer." t)
-(autoload 'Macaulay2 "M2" "Run Macaulay 2 in a buffer, non-interactive." t)
-(autoload 'M2-mode "M2" "Macaulay 2 editing mode" t)
-(autoload 'm2-mode "M2" "Macaulay 2 editing mode, name in lower case" t)
-(autoload 'm2-comint-mode "M2" "Macaulay 2 command interpreter mode, name in lower case" t)
-(setq auto-mode-alist (append auto-mode-alist '(("\\.m2$" . M2-mode))))
\ No newline at end of file
diff --git a/sci-mathematics/Macaulay2/files/9999-lapack.patch b/sci-mathematics/Macaulay2/files/9999-lapack.patch
deleted file mode 100644
index e9a434eeb..000000000
--- a/sci-mathematics/Macaulay2/files/9999-lapack.patch
+++ /dev/null
@@ -1,50 +0,0 @@
---- configure.ac	2012-10-24 09:29:55.240498786 -0700
-+++ configure.ac.2	2012-10-30 15:07:27.172846300 -0700
-@@ -1285,46 +1285,7 @@
- done
- test $BUILD_factory = yes && BUILTLIBS="$SINGULARLIBS $BUILTLIBS"
- 
--# we need to do the fortran library testing last, in case AC_SEARCH_LIBS adds
--# one of them to $LIBS, making it impossible to check for the presence of C or
--# C++ libraries.  (I'm not sure why putting -llapack on the gcc command line
--# needlessly causes the library to be linked against.)
--FORTRANUSED=no
--if test "$LAPACK" = yes
--then AC_MSG_CHECKING([whether the vecLib framework is available])
--     SAVELIBS=$LIBS LIBS="-framework vecLib $LIBS"
--     AC_LANG(C)
--     AC_LINK_IFELSE(
--	 [AC_LANG_PROGRAM(,[sgemv_();dgetrf_();])],
--	 [
--	     AC_MSG_RESULT(yes)
--	     ],
--	 [
--	     AC_MSG_RESULT(no)
--	     LIBS=$SAVELIBS
--	     FORTRANUSED=yes
--	     if test $BUILD_lapack = no
--	     then AC_LANG(Fortran)
--	     	  if test "$FC" = ""
--		  then AC_MSG_ERROR(no fortran compiler found)
--		  else AC_MSG_NOTICE(using fortran compiler $FC)
--		  fi
--		  AC_SEARCH_LIBS(sgemv,blas f77blas,,BUILD_lapack=yes)
--		  AC_SEARCH_LIBS(dgetrf,lapack,,BUILD_lapack=yes)
--	     fi
--	 ])
--fi
--test $BUILD_lapack = yes && BUILTLIBS="-llapack -lblas $BUILTLIBS"
--
--if test $BUILD_lapack = yes
--then # test whether the fortran compiler can handle lapack, which, starting with
--     # version 3.2, requires fortran 90, not fortran 77
--    AC_LANG(Fortran)
--    AC_MSG_CHECKING([whether the fortran compiler is modern enough for lapack])
--    AC_COMPILE_IFELSE([instrinsic maxloc],
--	AC_MSG_ERROR(the fortran compiler ($FC) does not support the Fortran 90 language required for compiling lapack),
--	AC_MSG_RESULT(yes))
--fi
-+BUILTLIBS="$(${PKG_CONFIG} --libs lapack) $BUILTLIBS"
- 
- if test $BUILD_memtailor = yes
- then BUILTLIBS="-lmemtailor $BUILTLIBS"
diff --git a/sci-mathematics/Macaulay2/files/9999-paths-of-external-programs.patch b/sci-mathematics/Macaulay2/files/9999-paths-of-external-programs.patch
deleted file mode 100644
index 4c090deec..000000000
--- a/sci-mathematics/Macaulay2/files/9999-paths-of-external-programs.patch
+++ /dev/null
@@ -1,73 +0,0 @@
-diff -U 3 -dHrN M2source/Macaulay2/packages/FourTiTwo.m2 M2source.patch/Macaulay2/packages/FourTiTwo.m2
---- M2source/Macaulay2/packages/FourTiTwo.m2	2011-09-22 14:36:51.000000000 +0100
-+++ M2source.patch/Macaulay2/packages/FourTiTwo.m2	2011-09-24 21:24:12.000000000 +0100
-@@ -47,7 +47,7 @@
- 
- path'4ti2 = (options FourTiTwo).Configuration#"path"
- -- NOTE: the absolute path should be put into the .init file for 4ti2 inside the .Macaulay2 directory.
--if path'4ti2 == "" then path'4ti2 = prefixDirectory | currentLayout#"programs"
-+if path'4ti2 == "" then path'4ti2 = "/usr/bin/"
- 
- getFilename = () -> (
-      filename := temporaryFileName();
-diff -U 3 -dHrN M2source/Macaulay2/packages/gfanInterface.m2 M2source.patch/Macaulay2/packages/gfanInterface.m2
---- M2source/Macaulay2/packages/gfanInterface.m2	2011-05-14 12:00:59.000000000 +0100
-+++ M2source.patch/Macaulay2/packages/gfanInterface.m2	2011-09-24 21:24:12.000000000 +0100
-@@ -25,7 +25,7 @@
-      }
- 
- gfan'path = gfanInterface#Options#Configuration#"path"
--if gfan'path == "" then gfan'path = prefixDirectory | currentLayout#"programs"
-+if gfan'path == "" then gfan'path = "/usr/bin/"
- if instance(gfan'path, String) then gfan'path = {gfan'path}
- if not instance(gfan'path,List) then error "expected configuration option gfan'path to be a list of strings or a string"
- gfan'path = join(
-diff -U 3 -dHrN M2source/Macaulay2/packages/NautyGraphs.m2 M2source.patch/Macaulay2/packages/NautyGraphs.m2
---- M2source/Macaulay2/packages/NautyGraphs.m2	2011-08-26 11:05:30.000000000 +0100
-+++ M2source.patch/Macaulay2/packages/NautyGraphs.m2	2011-09-24 21:25:53.000000000 +0100
-@@ -32,7 +32,7 @@
- -- Check the ~/.Macaulay2/init-NautyGraphs.m2 file for the absolute path.
- -- If it's not there, then use the M2-Programs directory.
- nauty'path = (options NautyGraphs).Configuration#"path";
--if nauty'path == "" then nauty'path = prefixDirectory | currentLayout#"programs";
-+if nauty'path == "" then nauty'path = "/usr/bin/";
- 
- -------------------
- -- Exports
-diff -U 3 -dHrN M2source/Macaulay2/packages/Nauty.m2 M2source.patch/Macaulay2/packages/Nauty.m2
---- M2source/Macaulay2/packages/Nauty.m2	2011-08-26 11:05:30.000000000 +0100
-+++ M2source.patch/Macaulay2/packages/Nauty.m2	2011-09-24 21:24:12.000000000 +0100
-@@ -48,7 +48,8 @@
- -- Check the ~/.Macaulay2/init-Nauty.m2 file for the absolute path.
- -- If it's not there, then use the M2-Programs directory.
- nauty'path = (options Nauty).Configuration#"path";
--if nauty'path == "" then nauty'path = prefixDirectory | currentLayout#"programs";
-+if nauty'path == "" then nauty'path = "/usr/bin/";
-+
- 
- -------------------
- -- Exports
-diff -U 3 -dHrN M2source/Macaulay2/packages/Normaliz.m2 M2source.patch/Macaulay2/packages/Normaliz.m2
---- M2source/Macaulay2/packages/Normaliz.m2	2011-05-25 16:47:50.000000000 +0100
-+++ M2source.patch/Macaulay2/packages/Normaliz.m2	2011-09-24 21:24:12.000000000 +0100
-@@ -166,7 +166,7 @@
-         nmzExec="normaliz";
-     );
- --    return nmzExec;
--    return prefixDirectory | currentLayout#"programs" | nmzExec;
-+    return "/usr/bin/" | nmzExec;
- );
- 
- 
-diff -U 3 -dHrN M2source/Macaulay2/packages/StatePolytope.m2 M2source.patch/Macaulay2/packages/StatePolytope.m2
---- M2source/Macaulay2/packages/StatePolytope.m2	2010-09-10 16:47:20.000000000 +0100
-+++ M2source.patch/Macaulay2/packages/StatePolytope.m2	2011-09-24 21:24:12.000000000 +0100
-@@ -31,7 +31,7 @@
- 
- 
- gfanCommand = (options StatePolytope)#Configuration#"gfan command"
--if gfanCommand === "gfan" then gfanCommand = prefixDirectory | currentLayout#"programs" | gfanCommand
-+if gfanCommand === "gfan" then gfanCommand = "/usr/bin/" | gfanCommand
- gfanCommand = "!" | gfanCommand
- 
- --The next two functions print out the ring and the ideal in the format required by gfan
diff --git a/sci-mathematics/Macaulay2/files/paths-of-dependencies.patch b/sci-mathematics/Macaulay2/files/paths-of-dependencies.patch
deleted file mode 100644
index f8117a5fa..000000000
--- a/sci-mathematics/Macaulay2/files/paths-of-dependencies.patch
+++ /dev/null
@@ -1,48 +0,0 @@
-diff -rupN 1.3.1/Macaulay2/packages/FourTiTwo.m2 1.3.1-pathspatched/Macaulay2/packages/FourTiTwo.m2
---- 1.3.1/Macaulay2/packages/FourTiTwo.m2	2009-11-12 18:40:50.000000000 +0100
-+++ 1.3.1-pathspatched/Macaulay2/packages/FourTiTwo.m2	2009-11-16 11:41:01.000000000 +0100
-@@ -47,7 +47,7 @@ export {
- 
- path'4ti2 = (options FourTiTwo).Configuration#"path"
- -- NOTE: the absolute path should be put into the .init file for 4ti2 inside the .Macaulay2 directory.
--if path'4ti2 == "" then path'4ti2 = prefixDirectory | currentLayout#"programs"
-+if path'4ti2 == "" then path'4ti2 = "/usr/bin/"
- 
- getFilename = () -> (
-      filename := temporaryFileName();
-diff -rupN 1.3.1/Macaulay2/packages/gfanInterface.m2 1.3.1-pathspatched/Macaulay2/packages/gfanInterface.m2
---- 1.3.1/Macaulay2/packages/gfanInterface.m2	2009-11-12 18:40:50.000000000 +0100
-+++ 1.3.1-pathspatched/Macaulay2/packages/gfanInterface.m2	2009-11-16 11:41:17.000000000 +0100
-@@ -26,7 +26,7 @@ export {
-      }
- 
- gfan'path = gfanInterface#Options#Configuration#"path"
--if gfan'path == "" then gfan'path = prefixDirectory | currentLayout#"programs"
-+if gfan'path == "" then gfan'path = "/usr/bin/"
- 
- fig2dev'path = gfanInterface#Options#Configuration#"fig2devpath"
- 
-diff -rupN 1.3.1/Macaulay2/packages/Normaliz.m2 1.3.1-pathspatched/Macaulay2/packages/Normaliz.m2
---- 1.3.1/Macaulay2/packages/Normaliz.m2	2009-11-12 18:40:50.000000000 +0100
-+++ 1.3.1-pathspatched/Macaulay2/packages/Normaliz.m2	2009-11-16 11:42:01.000000000 +0100
-@@ -30,7 +30,7 @@ export{setNmzExecPath, getNmzExecPath,
- 
- 
- -- initialising some values
--nmzExecPath=prefixDirectory|currentLayout#"programs";
-+nmzExecPath="/usr/bin/";
- nmzDataPath="";
- nmzFilename="";
- nmzUserCalled=true;  -- wether the user calls a method
-diff -rupN 1.3.1/Macaulay2/packages/StatePolytope.m2 1.3.1-pathspatched/Macaulay2/packages/StatePolytope.m2
---- 1.3.1/Macaulay2/packages/StatePolytope.m2	2009-11-12 18:40:50.000000000 +0100
-+++ 1.3.1-pathspatched/Macaulay2/packages/StatePolytope.m2	2009-11-16 11:41:13.000000000 +0100
-@@ -31,7 +31,7 @@ export { 
- 
- 
- gfanCommand = (options StatePolytope)#Configuration#"gfan command"
--if gfanCommand === "gfan" then gfanCommand = prefixDirectory | currentLayout#"programs" | gfanCommand
-+if gfanCommand === "gfan" then gfanCommand = "/usr/bin/" | gfanCommand
- gfanCommand = "!" | gfanCommand
- 
- --The next two functions print out the ring and the ideal in the format required by gfan
diff --git a/sci-mathematics/Macaulay2/metadata.xml b/sci-mathematics/Macaulay2/metadata.xml
deleted file mode 100644
index 05e3f791a..000000000
--- a/sci-mathematics/Macaulay2/metadata.xml
+++ /dev/null
@@ -1,19 +0,0 @@
-<?xml version="1.0" encoding="UTF-8"?>
-<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
-<pkgmetadata>
-	<maintainer type="person">
-		<email>tom111@gmx.de</email>
-		<name>Thomas Kahle</name>
-	</maintainer>
-	<maintainer type="project">
-		<email>sci-mathematics@gentoo.org</email>
-		<name>Gentoo Mathematics Project</name>
-	</maintainer>
-	<use>
-		<flag name="optimization">Disable to build with -O0 for debugging.</flag>
-	</use>
-	<longdescription lang="en">
-Macaulay2 is a research tool for algraic geometry and commutative
-algebra. 
-</longdescription>
-</pkgmetadata>
diff --git a/sci-mathematics/Oid/Manifest b/sci-mathematics/Oid/Manifest
index 109bdc2b8..dbc9c4bab 100644
--- a/sci-mathematics/Oid/Manifest
+++ b/sci-mathematics/Oid/Manifest
@@ -1,2 +1,2 @@
-DIST Oid4-0.tar.gz 244760 BLAKE2B 6acf06087bffac9bca6ed14bdd2319201e14d126b3299049ee713ebe87c00dfdc783559df06f2e8c1e56af469cdce296a42cb1927bae0b878a4c8187b67b7b9d SHA512 82d4039c3d8d499f7ad4e2df3626782c6c92629f141c12dd78b3b9d9175cfd3aeb0a4ed3a211e3aa7a6b0fec3b0b9112deb6c28c866013e1cf62cb165e786ef5
+DIST Oid-4.0.tar.gz 244760 BLAKE2B 6acf06087bffac9bca6ed14bdd2319201e14d126b3299049ee713ebe87c00dfdc783559df06f2e8c1e56af469cdce296a42cb1927bae0b878a4c8187b67b7b9d SHA512 82d4039c3d8d499f7ad4e2df3626782c6c92629f141c12dd78b3b9d9175cfd3aeb0a4ed3a211e3aa7a6b0fec3b0b9112deb6c28c866013e1cf62cb165e786ef5
 DIST OidUserManual4-0.pdf 191264 BLAKE2B bddb1aa328195adb02d9ce25670a2c5c6feea5104168d7a4f65e2d69c0c106ac193dc63bc661c1efebc4feedbaf1db10cdf1fc41eb4d16dd26d2698e3f0e0776 SHA512 bccefaf64a9765bb3bf3927091f2d467e773c12b4694dcf7fd42d761545ad324a3bc4398ae5d3fdffef466e3731fcbc322016af9148cd81705df52d4da756043
diff --git a/sci-mathematics/Oid/Oid-4.0.ebuild b/sci-mathematics/Oid/Oid-4.0.ebuild
index bbc267637..ce967fd46 100644
--- a/sci-mathematics/Oid/Oid-4.0.ebuild
+++ b/sci-mathematics/Oid/Oid-4.0.ebuild
@@ -1,35 +1,38 @@
-# Copyright 1999-2015 Gentoo Foundation
+# Copyright 1999-2021 Gentoo Authors
 # Distributed under the terms of the GNU General Public License v2
 
-EAPI=5
+EAPI=7
 
-inherit eutils java-pkg-2 versionator
+inherit java-pkg-2
 
-MY_PV=$(replace_version_separator 1 '-')
+MY_PV="${PV//./-}"
 MY_P="${PN}${MY_PV}"
 
 DESCRIPTION="An interactive, extensible software system for experimenting with matroids"
-HOMEPAGE="http://sites.google.com/site/wwwmatroids/"
+HOMEPAGE="https://sites.google.com/site/wwwmatroids/"
 SRC_URI="
-	http://sites.google.com/site/wwwmatroids/${MY_P}.tar.gz
-	doc? ( http://sites.google.com/site/wwwmatroids/${PN}UserManual${MY_PV}.pdf )"
+	https://sites.google.com/site/wwwmatroids/${MY_P}.tar.gz -> ${P}.tar.gz
+	https://sites.google.com/site/wwwmatroids/${PN}UserManual${MY_PV}.pdf
+"
 
 KEYWORDS="~amd64 ~x86"
 SLOT="0"
 LICENSE="GPL-2"
-IUSE="doc"
 
 DEPEND=">=virtual/jdk-1.4:*"
 RDEPEND=">=virtual/jre-1.4:*"
 
 # The source uses 'enum' as an identifier, therefore:
 JAVA_PKG_WANT_SOURCE="1.4"
+S="${WORKDIR}"
 
 src_prepare () {
 	mkdir classes || die
 
-# change path names
+	# change path names
 	sed -i -e 's:NAME = ":NAME = "/usr/share/Oid/:' MatroidToolkit.java || die
+
+	default
 }
 
 src_compile () {
@@ -42,8 +45,7 @@ src_install () {
 
 	java-pkg_dojar Oid.jar
 	java-pkg_dolauncher
-
-	use doc && dodoc "${DISTDIR}"/OidUserManual4-0.pdf
+	dodoc "${DISTDIR}"/OidUserManual4-0.pdf
 
 	insinto /usr/share/Oid
 	doins matroid*.txt
diff --git a/sci-mathematics/Oid/metadata.xml b/sci-mathematics/Oid/metadata.xml
index a457ecd20..7206a3f8f 100644
--- a/sci-mathematics/Oid/metadata.xml
+++ b/sci-mathematics/Oid/metadata.xml
@@ -9,7 +9,4 @@
 		<email>sci-mathematics@gentoo.org</email>
 		<name>Gentoo Mathematics Project</name>
 	</maintainer>
-	<longdescription lang="en">
-Oid is a tool to experiment with matroids
-</longdescription>
 </pkgmetadata>
diff --git a/sci-mathematics/acl2/Manifest b/sci-mathematics/acl2/Manifest
deleted file mode 100644
index 1444f00a9..000000000
--- a/sci-mathematics/acl2/Manifest
+++ /dev/null
@@ -1 +0,0 @@
-DIST acl2-7.1.tar.gz 63345284 SHA256 1a8503095a4e1deb6a6b0f3bc51823ba65cad38466def8d6845f193d73338f9d SHA512 5875b88615930fc841cd1d7ed30ada7c04b241a391eeee22184b4e3630e57cc6304a51e445e33ca1284576c2b4110c269f9eb59c47bd2eb47659134450151e27 WHIRLPOOL 632012e3d8998c67f70cd19b8fa7c7ff8000dbdba2d87dfdd56d5b4b39ebb390503d243e051c308c8a5aea0097bb48fa4e5c510b24478886a4a8bfca2c8d0645
diff --git a/sci-mathematics/acl2/acl2-7.1.ebuild b/sci-mathematics/acl2/acl2-7.1.ebuild
deleted file mode 100644
index 774c5a6d3..000000000
--- a/sci-mathematics/acl2/acl2-7.1.ebuild
+++ /dev/null
@@ -1,50 +0,0 @@
-# Copyright 1999-2015 Gentoo Foundation
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=5
-
-inherit eutils
-
-DESCRIPTION="Industrial strength theorem prover"
-HOMEPAGE="http://www.cs.utexas.edu/users/moore/acl2/"
-MY_PN=${PN}-devel
-SRC_URI="https://github.com/${MY_PN}/${MY_PN}/archive/${PV}.tar.gz -> ${P}.tar.gz"
-
-SLOT="0"
-LICENSE="BSD"
-KEYWORDS="~amd64 ~x86"
-IUSE="books"
-
-DEPEND="
-	dev-lisp/sbcl:=
-	books? ( dev-lang/perl )"
-RDEPEND="${DEPEND}"
-S="${WORKDIR}/${MY_PN}-${PV}"
-
-src_compile() {
-	emake LISP="sbcl --noinform --noprint \
-		--no-sysinit --no-userinit --disable-debugger"
-
-	if use books; then
-		echo
-		einfo "Building certificates ..."
-		einfo "(this may take hours to finish)"
-		emake certify-books
-	fi
-}
-
-src_install() {
-	SAVED_NAME=saved_acl2
-	sed -e "s:${S}:/usr/share/acl2:g" -i ${SAVED_NAME} || die
-	if use books; then
-		sed -e "/5/a export ACL2_SYSTEM_BOOKS=/usr/share/acl2/books/" \
-			-i ${SAVED_NAME} || die
-	fi
-	dobin ${SAVED_NAME}
-
-	insinto /usr/share/acl2
-	doins TAGS ${SAVED_NAME}.core
-	if use books; then
-		doins -r books
-	fi
-}
diff --git a/sci-mathematics/acl2/metadata.xml b/sci-mathematics/acl2/metadata.xml
deleted file mode 100644
index b77817aa3..000000000
--- a/sci-mathematics/acl2/metadata.xml
+++ /dev/null
@@ -1,27 +0,0 @@
-<?xml version="1.0" encoding="UTF-8"?>
-<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
-<pkgmetadata>
-	<maintainer type="person">
-		<email>dongxuli2011@gmail.com</email>
-		<name>Dongxu Li</name>
-		<description>Industrial strength theorem prover</description>
-	</maintainer>
-	<maintainer type="project">
-		<email>sci-mathematics@gentoo.org</email>
-		<name>Gentoo Mathematics Project</name>
-	</maintainer>
-	<longdescription>
-ACL2 is both a programming language in which you can model computer systems and
-a tool to help you prove properties of those models. ACL2 is part of the
-Boyer-Moore family of provers, for which its authors have received the 2005 ACM
-Software System Award.
-</longdescription>
-	<use>
-		<flag name="books">
-build community books, the canonical collection of open-source libraries
-</flag>
-	</use>
-	<upstream>
-		<remote-id type="github">acl2-devel/acl2-devel</remote-id>
-	</upstream>
-</pkgmetadata>
diff --git a/sci-mathematics/alt-ergo/Manifest b/sci-mathematics/alt-ergo/Manifest
deleted file mode 100644
index ad6a8ca8d..000000000
--- a/sci-mathematics/alt-ergo/Manifest
+++ /dev/null
@@ -1 +0,0 @@
-DIST alt-ergo-0.95.2.tar.gz 233778 SHA256 5a6cd4349c144653be19a1ba4c254bbf626bdfd97c54d1c13ba63e396006eeac SHA512 e4bb73719d67e44bac058ea53082879534c93d47fd931ec927e7f1e59330a60915ae73c662153207e6229ae914a5c0b8b16c04763f1ae3e251668a336a11d382 WHIRLPOOL aa5f8f0bf46eb93d4e8e4be4e6a30facd7b97d35fd110e4081a61826edb1def7dc5724db08c05f714c3bc1a70add9aaa961e9757492aa47f9c97ad48069f5ae9
diff --git a/sci-mathematics/alt-ergo/alt-ergo-0.95.2.ebuild b/sci-mathematics/alt-ergo/alt-ergo-0.95.2.ebuild
deleted file mode 100644
index 3532fdc0c..000000000
--- a/sci-mathematics/alt-ergo/alt-ergo-0.95.2.ebuild
+++ /dev/null
@@ -1,42 +0,0 @@
-# Copyright 1999-2016 Gentoo Foundation
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=5
-
-inherit eutils
-
-DESCRIPTION="Alt-Ergo is an automatic theorem prover"
-HOMEPAGE="http://alt-ergo.ocamlpro.com"
-SRC_URI="http://dev.gentoo.org/~jauhien/distfiles/${P}.tar.gz"
-
-LICENSE="CeCILL-C"
-SLOT="0"
-KEYWORDS="~amd64"
-IUSE="+ocamlopt gtk"
-
-DEPEND="
-	>=dev-lang/ocaml-3.12.1[ocamlopt?]
-	>=dev-ml/ocamlgraph-1.8.2[gtk?,ocamlopt?]
-	dev-ml/zarith
-	gtk? (
-		>=x11-libs/gtksourceview-2.8:2.0
-		>=dev-ml/lablgtk-2.14[sourceview,ocamlopt?]
-	)"
-RDEPEND="${DEPEND}"
-
-src_prepare(){
-	sed \
-		-e 's: /usr/share/: $(DESTDIR)/usr/share/:g' \
-		-e 's:cp -f altgr-ergo.opt:mkdir -p $(DESTDIR)/usr/share/gtksourceview-2.0/language-specs/\n\tcp -f altgr-ergo.opt:g' \
-		-i "${S}"/Makefile.in || die
-}
-src_compile(){
-	default
-	use gtk && emake gui
-}
-
-src_install(){
-	default
-	use gtk && emake install-gui DESTDIR="${D}"
-	dodoc README.md CHANGES
-}
diff --git a/sci-mathematics/alt-ergo/metadata.xml b/sci-mathematics/alt-ergo/metadata.xml
deleted file mode 100644
index a28eb2ec7..000000000
--- a/sci-mathematics/alt-ergo/metadata.xml
+++ /dev/null
@@ -1,15 +0,0 @@
-<?xml version="1.0" encoding="UTF-8"?>
-<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
-<pkgmetadata>
-	<maintainer type="project">
-		<email>sci-mathematics@gentoo.org</email>
-		<name>Gentoo Mathematics Project</name>
-	</maintainer>
-	<longdescription>
-Alt-Ergo is an open source automatic theorem prover dedicated to program verification.
-It is an SMT solver based on CC(X): a congruence closure algorithm parameterized by an
-equational theory X. Alt-Ergo is based on a home-made SAT-solver and implements an
-instantiation mechanism for quantified formulas. Its architecture is summarized by the
-the following picture.
-</longdescription>
-</pkgmetadata>
diff --git a/sci-mathematics/apron/Manifest b/sci-mathematics/apron/Manifest
deleted file mode 100644
index 280448adb..000000000
--- a/sci-mathematics/apron/Manifest
+++ /dev/null
@@ -1 +0,0 @@
-DIST apron-0.9.10.tgz 1694989 BLAKE2B 434366f9ead2bc233ff24d0ac65c76d35ccf66b11b97e8a1fcad561629d0c9bb6a817dae800dc41f323f5b484790adfb2e6dd8db333ade5ff6b18f484b276357 SHA512 9b84bf6b5d34ee34558e8224ecd09d48ff2013b7a301a8749512aaea8b8c99da394bb0550055b9bc37692187ca8956bf25e74535c1d41ac1907e161163bc6e8a
diff --git a/sci-mathematics/apron/apron-0.9.10-r1.ebuild b/sci-mathematics/apron/apron-0.9.10-r1.ebuild
deleted file mode 100644
index c2fd73233..000000000
--- a/sci-mathematics/apron/apron-0.9.10-r1.ebuild
+++ /dev/null
@@ -1,71 +0,0 @@
-# Copyright 1999-2015 Gentoo Foundation
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=5
-
-inherit eutils toolchain-funcs
-
-DESCRIPTION="Static analysis of the numerical variables by Abstract Interpretation"
-HOMEPAGE="http://apron.cri.ensmp.fr/library/"
-SRC_URI="http://apron.cri.ensmp.fr/library/${P}.tgz"
-
-LICENSE="LGPL-2 GPL-2"
-SLOT="0"
-KEYWORDS="~amd64 ~x86"
-IUSE="doc ocaml"
-
-RDEPEND="
-	ocaml? (
-		>=dev-lang/ocaml-3.09
-		dev-ml/camlidl
-		dev-ml/mlgmpidl
-	)
-		dev-libs/gmp:0=
-		dev-libs/mpfr:0="
-DEPEND="${RDEPEND}
-	doc? (
-		app-text/texlive
-		app-text/ghostscript-gpl
-	)"
-
-src_prepare() {
-	mv Makefile.config.model Makefile.config || die
-
-	#fix compile process
-	sed -i Makefile.config \
-		-e "s/FLAGS = \\\/FLAGS += \\\/g" \
-		-e "s/-O3 -DNDEBUG/-DNDEBUG/g" \
-		-e "s/APRON_PREFIX =.*/APRON_PREFIX = \$(DESTDIR)\/usr/g" \
-		-e "s/MLGMPIDL_PREFIX =.*/MLGMPIDL_PREFIX = \$(DESTDIR)\/usr/g" \
-		|| die
-
-	#fix doc building process
-	sed -i Makefile -e "s/; make html/; make/g"
-	sed -i apronxx/Makefile \
-		-e "s:cd doc/latex && make:cd doc/latex; rubber refman.tex; dvipdf refman.dvi:g"
-	sed -i apronxx/doc/Doxyfile \
-		-e "s/OUTPUT_DIRECTORY       = \/.*/OUTPUT_DIRECTORY       = .\//g" \
-		-e "s/STRIP_FROM_PATH        = \/.*/STRIP_FROM_PATH        = .\//g"
-
-	if [[ "$(gcc-major-version)" == "4" ]]; then
-		sed -i -e "s/# HAS_LONG_DOUBLE = 1/HAS_LONG_DOUBLE = 1/g" Makefile.config
-	fi
-	if use !ocaml; then
-		sed -i -e "s/HAS_OCAML = 1/#HAS_OCAML = 0/g" Makefile.config
-	fi
-}
-
-src_compile() {
-	emake -j1
-}
-
-src_install(){
-	default
-
-	if use doc; then
-		dodoc apron/apron.pdf
-		if use ocaml; then
-			dodoc mlapronidl/mlapronidl.pdf
-		fi
-	fi
-}
diff --git a/sci-mathematics/apron/metadata.xml b/sci-mathematics/apron/metadata.xml
deleted file mode 100644
index d31da6be0..000000000
--- a/sci-mathematics/apron/metadata.xml
+++ /dev/null
@@ -1,18 +0,0 @@
-<?xml version="1.0" encoding="UTF-8"?>
-<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
-<pkgmetadata>
-	<maintainer type="project">
-		<email>sci-mathematics@gentoo.org</email>
-		<name>Gentoo Mathematics Project</name>
-	</maintainer>
-	<longdescription>
-The APRON library is dedicated to the static analysis of the numerical
-variables of a program by Abstract Interpretation. The aim of such an
-analysis is to infer invariants about these variables. The APRON library
-is intended to be a common interface to various underlying
-libraries/abstract domains and to provide additional services that can
-be implemented independently from the underlying library/abstract
-domain, as shown by the poster on the right (presented at the SAS 2007
-conference.
-</longdescription>
-</pkgmetadata>
diff --git a/sci-mathematics/aribas/Manifest b/sci-mathematics/aribas/Manifest
deleted file mode 100644
index 3425d4c91..000000000
--- a/sci-mathematics/aribas/Manifest
+++ /dev/null
@@ -1 +0,0 @@
-DIST aribas-1.63.tar.gz 291939 BLAKE2B 6bd58fce7b64a8808b566446930f62647afcddcea7e72a6c6d62b57d669a270c37a1392300853d228a2b39cde14b1d9825fc769085ea4e72f031f873af3c9573 SHA512 740d03c96c9b12ba4ce62edc63952419bd07fed26f9de6f36fdeda1cac52e01ddd9c8d817b746a2ab3668549f6457ecfced2184fceb8a4307f204a185a765059
diff --git a/sci-mathematics/aribas/aribas-1.63.ebuild b/sci-mathematics/aribas/aribas-1.63.ebuild
deleted file mode 100644
index 0759b3158..000000000
--- a/sci-mathematics/aribas/aribas-1.63.ebuild
+++ /dev/null
@@ -1,76 +0,0 @@
-# Copyright 1999-2015 Gentoo Foundation
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=5
-
-inherit elisp-common versionator
-
-DESCRIPTION="Interpreter for big integer and multi-precision floating point arithmetic"
-HOMEPAGE="http://www.mathematik.uni-muenchen.de/~forster/sw/${PN}.html"
-SRC_URI="ftp://ftp.mathematik.uni-muenchen.de/pub/forster/${PN}/UNIX_LINUX/${P}.tar.gz"
-
-LICENSE="GPL-2"
-SLOT="0"
-KEYWORDS="~x86"
-IUSE="doc emacs examples"
-
-RDEPEND="emacs? ( virtual/emacs )"
-DEPEND="${RDEPEND}"
-
-SITEFILE=64${PN}-gentoo.el
-CH_PV=$(delete_all_version_separators)
-
-src_prepare() {
-	# Linux x86 assembly piece
-	if use x86; then
-		mv LINUX/arito386.S . || die
-		mv LINUX/Makefile.linux Makefile || die
-	fi
-
-	# removing strip
-	sed -e '/^	strip \$(PROGRAM)$/d' -i Makefile || die "sed failed"
-}
-
-src_compile() {
-	cd src || die
-	if use x86; then
-		emake CFLAGS="-DLiNUX -DPROTO ${CFLAGS}"
-	else
-		emake CC=gcc CFLAGS="-DUNiX -DPROTO ${CFLAGS}"
-	fi
-
-	if use emacs; then
-		cd EL || doe
-		elisp-compile *.el
-	fi
-}
-
-src_install() {
-	dobin src/${PN}
-	doman doc/*.1
-	dodoc CHANGES${CH_PV}.txt
-
-	if use doc; then
-		dodoc doc/${PN}.doc doc/${PN}.tut
-	fi
-
-	if use examples; then
-		insinto /usr/share/${P}
-		doins -r examples
-	fi
-
-	if use emacs; then
-		cd src/EL || die
-		elisp-install ${PN} *.el *.elc
-		elisp-site-file-install "${FILESDIR}"/${SITEFILE}
-		newdoc EL/README README.emacs
-	fi
-}
-
-pkg_postinst() {
-	use emacs && elisp-site-regen
-}
-
-pkg_postrm() {
-	use emacs && elisp-site-regen
-}
diff --git a/sci-mathematics/aribas/files/64aribas-gentoo.el b/sci-mathematics/aribas/files/64aribas-gentoo.el
deleted file mode 100644
index 3598e39ca..000000000
--- a/sci-mathematics/aribas/files/64aribas-gentoo.el
+++ /dev/null
@@ -1,3 +0,0 @@
-;; aribas mode
-(add-to-list 'load-path "@SITELISP@")
-(autoload 'run-aribas "aribas" "Run ARIBAS." t)
diff --git a/sci-mathematics/aribas/metadata.xml b/sci-mathematics/aribas/metadata.xml
deleted file mode 100644
index 146901339..000000000
--- a/sci-mathematics/aribas/metadata.xml
+++ /dev/null
@@ -1,13 +0,0 @@
-<?xml version="1.0" encoding="UTF-8"?>
-<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
-<pkgmetadata>
-	<maintainer type="person">
-		<email>grozin@gentoo.org</email>
-		<name>Andrey Grozin</name>
-	</maintainer>
-	<maintainer type="project">
-		<email>sci-mathematics@gentoo.org</email>
-		<name>Gentoo Mathematics Project</name>
-	</maintainer>
-	<longdescription>Interpreter for big integer and multi-precision floating point arithmetic</longdescription>
-</pkgmetadata>
diff --git a/sci-mathematics/axiom/Manifest b/sci-mathematics/axiom/Manifest
deleted file mode 100644
index 5f29166eb..000000000
--- a/sci-mathematics/axiom/Manifest
+++ /dev/null
@@ -1 +0,0 @@
-DIST axiom-aug2014-src.tgz 166822164 BLAKE2B 44d7c89278405a8e5dfa1e0cee9f32a095c62cb95708a6d8edead54eb7d0c1481d7c52bf2c1d6d91cf5bbe62feb66e5bf0ebb94425120df553957bcaf1eaf697 SHA512 88a27967a6e0b4d5ab1beffeb8a3d0968c432f71258e8d21d77191e8ad79e77ba3c316850af976a52b28d4d05f1001fba39a966c6f008a89bf493569fb183be0
diff --git a/sci-mathematics/axiom/axiom-201408.ebuild b/sci-mathematics/axiom/axiom-201408.ebuild
deleted file mode 100644
index 99483d63b..000000000
--- a/sci-mathematics/axiom/axiom-201408.ebuild
+++ /dev/null
@@ -1,67 +0,0 @@
-# Copyright 1999-2015 Gentoo Foundation
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=5
-
-inherit eutils flag-o-matic multilib
-
-DESCRIPTION="Axiom is a general purpose Computer Algebra system"
-HOMEPAGE="http://axiom.axiom-developer.org/"
-SRC_URI="http://axiom.axiom-developer.org/axiom-website/downloads/axiom-aug2014-src.tgz"
-
-LICENSE="BSD-2"
-SLOT="0"
-KEYWORDS=""
-IUSE=""
-
-# NOTE: Do not strip since this seems to remove some crucial
-# runtime paths as well, thereby, breaking axiom
-RESTRICT="strip"
-
-# Seems to need a working version of pstricks package these days Bummer: <gmp-5 is needed for the
-# interal gcl, otherwise axiom will try to build an internal copy of gmp-4 which fails.
-RDEPEND="
-	dev-libs/gmp:0=
-	x11-libs/libXaw"
-DEPEND="${RDEPEND}
-	app-text/dvipdfm
-	dev-texlive/texlive-pstricks
-	sys-apps/debianutils
-	sys-process/procps
-	virtual/latex-base"
-
-S="${WORKDIR}"/${PN}
-
-src_prepare() {
-	append-flags -fno-strict-aliasing
-}
-
-src_compile() {
-	sed -e "s:X11R6/lib:$(get_libdir):g" -i Makefile.pamphlet \
-		|| die "Failed to fix libXpm lib paths"
-
-	# This will fix the internal gmp. This package will stay unkeyworded until this is resolved
-	# upstream.
-	unset ABI
-
-	# Let the fun begin...
-	AXIOM="${S}"/mnt/linux emake -j1
-}
-
-src_install() {
-	emake DESTDIR="${ED}"/opt/axiom COMMAND="${ED}"/opt/axiom/mnt/linux/bin/axiom install
-
-	mv "${ED}"/opt/axiom/mnt/linux/* "${ED}"/opt/axiom \
-		|| die "Failed to mv axiom into its final destination path."
-	rm -fr "${ED}"/opt/axiom/mnt \
-		|| die "Failed to remove old directory."
-
-	dosym ../../axiom/bin/axiom /usr/bin/axiom
-
-	sed \
-		-e "2d;3i AXIOM=/opt/axiom" \
-		-i "${D}"/opt/axiom/bin/axiom \
-		|| die "Failed to patch axiom runscript!"
-
-	dodoc changelog readme faq
-}
diff --git a/sci-mathematics/axiom/metadata.xml b/sci-mathematics/axiom/metadata.xml
deleted file mode 100644
index 514f7304d..000000000
--- a/sci-mathematics/axiom/metadata.xml
+++ /dev/null
@@ -1,8 +0,0 @@
-<?xml version="1.0" encoding="UTF-8"?>
-<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
-<pkgmetadata>
-	<maintainer type="project">
-		<email>sci-mathematics@gentoo.org</email>
-		<name>Gentoo Mathematics Project</name>
-	</maintainer>
-</pkgmetadata>
diff --git a/sci-mathematics/burrtools/Manifest b/sci-mathematics/burrtools/Manifest
deleted file mode 100644
index ca9d6fa8c..000000000
--- a/sci-mathematics/burrtools/Manifest
+++ /dev/null
@@ -1,2 +0,0 @@
-DIST burrtools-0.5.2-A4.pdf 1268505 BLAKE2B ca62f01883959e28d3e98523b4f122c819f2134e39d1d5f0db4a868b969cc3f81cb1937949bf8d15b705dcfdd0cd9ba9d98e5ca1786e6e37adff1dae56d80bd1 SHA512 560bfb05a2fe84eb4502a9f9503edd2e8af2a0c67f5e05819d3ae8df6e599d8f39c917577d49ff4103b1c330ca8a61eba430c206a1b895be06b154386dadfccd
-DIST burrtools-0.5.2.tar.gz 1920561 BLAKE2B d796ffa916df237e7bbe12fc8a421f20ab15d8e40401d9cb8c7eb8b0e737d19a0986ba4b7fdff9c77b599e5369c5ce79f17ba07213d49f1806558812ade244c3 SHA512 7b73b619c6d042fd7e879ef675e8abd6977c9df276b410cb466e555810a83906e51d7b085679096e828929b62851be5ca304292f1e500b963053d81d968860e8
diff --git a/sci-mathematics/burrtools/burrtools-0.5.2-r1.ebuild b/sci-mathematics/burrtools/burrtools-0.5.2-r1.ebuild
deleted file mode 100644
index 3f5280649..000000000
--- a/sci-mathematics/burrtools/burrtools-0.5.2-r1.ebuild
+++ /dev/null
@@ -1,42 +0,0 @@
-# Copyright 1999-2015 Gentoo Foundation
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=5
-
-DESCRIPTION="Program to solve assembly and interlocking puzzles"
-HOMEPAGE="http://burrtools.sourceforge.net/"
-SRC_URI="
-	mirror://sourceforge/${PN}/${P}.tar.gz
-	doc? ( mirror://sourceforge/${PN}/${P}-A4.pdf )"
-
-SLOT="0"
-LICENSE="GPL-2"
-KEYWORDS="~x86"
-IUSE="doc examples"
-
-DEPEND="
-	x11-libs/fltk:1
-	media-libs/libpng:0="
-RDEPEND="${DEPEND}
-	app-text/htmldoc"
-
-src_compile() {
-	default
-	cd doc || die
-	cp ../doc_src/*.png . || die
-	echo "User Guide for BurrTools ${PV}" > doc/userGuide.t2t
-	cat ../doc_src/userGuide.t2t >> userGuide.t2t
-	mkdir html || die
-	../doc_src/txt2tags.py -t html -o - userGuide.t2t > userGuide.html
-	htmldoc --format htmlsep --toclevels 2 --outdir html userGuide.html || die
-	cd .. || die
-}
-
-src_install() {
-	default
-	use doc && dodoc "${DISTDIR}"/${P}-A4.pdf
-	if use examples; then
-		insinto /usr/share/${PN}
-		doins -r examples
-	fi
-}
diff --git a/sci-mathematics/burrtools/metadata.xml b/sci-mathematics/burrtools/metadata.xml
deleted file mode 100644
index a7fbeb904..000000000
--- a/sci-mathematics/burrtools/metadata.xml
+++ /dev/null
@@ -1,17 +0,0 @@
-<?xml version="1.0" encoding="UTF-8"?>
-<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
-<pkgmetadata>
-	<maintainer type="project">
-		<email>sci-mathematics@gentoo.org</email>
-		<name>Gentoo Mathematics Project</name>
-	</maintainer>
-	<longdescription lang="en">
-This (set of) program(s) will help you solve a certain kind of puzzle.
-Namely puzzles that are made out of square or dice shaped units, spheres or
-prisms with an equilateral triangle as base and where the pieces are also
-aligned along those grids in the solutions.
-</longdescription>
-	<upstream>
-		<remote-id type="sourceforge">burrtools</remote-id>
-	</upstream>
-</pkgmetadata>
diff --git a/sci-mathematics/cadabra/Manifest b/sci-mathematics/cadabra/Manifest
deleted file mode 100644
index 045c33e9d..000000000
--- a/sci-mathematics/cadabra/Manifest
+++ /dev/null
@@ -1 +0,0 @@
-DIST cadabra-1.39.tar.gz 1377279 SHA256 a1fda2f9c43b3b56c3cfcd0e6fce2a692b3f4fb2941fd7e2a0033c39fe013507 SHA512 e4c81bfbd1102449114d135d596526340451ce284c5ce796ffd3367c4040d434266564760628b367f40fe61bc59d7e6f067f8150601a7fa4f88101da60fbab06 WHIRLPOOL 4b36c377a42ad4d22d56712b9f9ae4a1c58265e86eb2a728e1926ea74e07f984b42475cee6eb1ff2d47f994c3904e99bb80d2c61b6fb5b4098af4b0719f3c5b7
diff --git a/sci-mathematics/cadabra/cadabra-1.39.ebuild b/sci-mathematics/cadabra/cadabra-1.39.ebuild
deleted file mode 100644
index 095ab87dd..000000000
--- a/sci-mathematics/cadabra/cadabra-1.39.ebuild
+++ /dev/null
@@ -1,88 +0,0 @@
-# Copyright 1999-2015 Gentoo Foundation
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=5
-
-inherit eutils texlive-common
-
-DESCRIPTION="Field-theory motivated computer algebra system"
-HOMEPAGE="http://cadabra.phi-sci.com"
-SRC_URI="http://cadabra.phi-sci.com/${P}.tar.gz"
-
-LICENSE="GPL-2"
-SLOT="0"
-KEYWORDS="~amd64 ~x86"
-IUSE="doc examples X test"
-
-CDEPEND="
-	sci-libs/modglue
-	sci-mathematics/lie
-	dev-libs/gmp[cxx]
-	dev-libs/libpcre
-	X? (
-		x11-libs/gtk+:2
-		dev-cpp/gtkmm:2.4
-		dev-cpp/pangomm:1.4
-		app-text/dvipng )"
-DEPEND="${CDEPEND}
-	doc? (
-		app-doc/doxygen
-		dev-texlive/texlive-latexextra
-		app-text/texlive-core
-		)
-	test? ( sys-process/time )"
-RDEPEND="${CDEPEND}
-	virtual/latex-base
-	dev-texlive/texlive-latexrecommended"
-
-src_prepare(){
-	# fixing the flag mess
-	epatch "${FILESDIR}/${P}-FLAGS.patch"
-}
-
-src_configure(){
-	econf $(use_enable X gui) \
-		--disable-runtime-dependency-check
-}
-
-src_compile() {
-	default
-
-	if use doc; then
-		cd "${S}/doc" || die
-		default
-		cd doxygen/latex || die
-		emake pdf
-	fi
-}
-
-src_install() {
-	# cadabra strip binaries unless you are on OS X.
-	# So faking it to avoid outright stripping.
-	emake DESTDIR="${D}" DEVDESTDIR="${D}" MACTEST=1 install
-
-	dodoc AUTHORS ChangeLog INSTALL
-
-	if use doc;	then
-		cd "${S}/doc/doxygen" || die
-		dohtml html/*
-		dodoc latex/*.pdf
-	fi
-
-	if use examples; then
-		dodoc -r "${S}/examples/"
-	fi
-
-	rm -rf "${D}/usr/share/TeXmacs" || die
-}
-
-pkg_postinst() {
-	etexmf-update
-	elog "This version of the cadabra ebuild is still under development."
-	elog "Help us improve the ebuild in:"
-	elog "http://bugs.gentoo.org/show_bug.cgi?id= 194393"
-}
-
-pkg_postrm() {
-	etexmf-update
-}
diff --git a/sci-mathematics/cadabra/files/cadabra-1.33-FLAGS.patch b/sci-mathematics/cadabra/files/cadabra-1.33-FLAGS.patch
deleted file mode 100644
index 2d78e9327..000000000
--- a/sci-mathematics/cadabra/files/cadabra-1.33-FLAGS.patch
+++ /dev/null
@@ -1,171 +0,0 @@
---- Makefile.in.orig	2013-09-05 21:45:20.026339263 +1200
-+++ Makefile.in	2013-09-05 21:48:20.859739672 +1200
-@@ -24,7 +24,7 @@
- 	( cd src && $(MAKE) static );
- 
- profile:
--	( export CFLAGS=-pg && export LDFLAGS=-pg && cd src && $(MAKE) );
-+	( export CFLAGS="$(CFLAGS) -pg" && CXXFLAGS="$(CXXFLAGS) -pg" && cd src && $(MAKE) );
- 
- doc:
- 	( cd doc && $(MAKE) );
---- src/Makefile.in.orig	2013-09-05 21:45:35.546373837 +1200
-+++ src/Makefile.in	2013-09-05 21:53:51.146459582 +1200
-@@ -22,12 +22,13 @@
- 
- SRCS      = `find . -name "*.cc"`
- MCFLAGS   = @CFLAGS@ -I. -I@top_srcdir@/src `pkg-config modglue --cflags`
-+MCXXFLAGS = @CXXFLAGS@ -I. -I@top_srcdir@/src `pkg-config modglue --cflags`
- TIMESTAMP = -D"RELEASE=\"${RELEASE}\"" -D"DATETIME=\"`date | sed -e 's/  / /'`\"" -DHOSTNAME=\"`hostname`\"
- 
- 
- 
- %.o: %.cc
--	@CXX@ ${MCFLAGS} ${TIMESTAMP} -c -o $@ $<
-+	@CXX@ ${MCXXFLAGS} ${TIMESTAMP} -c -o $@ $<
- 
- modules/xperm.o: modules/xperm.c
- 	@CC@ @NESTED@ ${MCFLAGS} ${TIMESTAMP} -c -o $@ $<
-@@ -42,10 +43,10 @@
- 
- ifeq ($(strip $(MACTEST)),)
- cadabra: $(OBJS) $(MOBJS)
--	@CXX@ -o cadabra ${LDFLAGS} -Wl,--as-needed $+ `pkg-config modglue --libs` -lgmpxx -lpcrecpp -lgmp
-+	@CXX@ -o cadabra ${MCXXFLAGS} ${LDFLAGS} -Wl,--as-needed $+ `pkg-config modglue --libs` -lgmpxx -lpcrecpp -lgmp
- else
- cadabra: $(OBJS) $(MOBJS)
--	@CXX@ -o cadabra ${LDFLAGS} -Wl,-dead_strip_dylibs $+ `pkg-config modglue --libs` -lgmpxx -lpcrecpp -lgmp
-+	@CXX@ -o cadabra ${MCXXFLAGS} ${LDFLAGS} -Wl,-dead_strip_dylibs $+ `pkg-config modglue --libs` -lgmpxx -lpcrecpp -lgmp
- endif
- 
- #`pkg-config glib-2.0 --libs` 
-@@ -53,15 +54,15 @@
- 
- cadabra_static: $(OBJS) $(MOBJS)
- 	rm -f main.o
--	@CXX@ -Wall -g ${MCFLAGS} ${TIMESTAMP} -DSTATICBUILD -c -o main.o main.cc
-+	@CXX@ -Wall -g ${MCXXFLAGS} ${TIMESTAMP} -DSTATICBUILD -c -o main.o main.cc
- ifeq ($(strip $(MACTEST)),)
--	@CXX@ -o cadabra -static $+ ${LDFLAGS} `pkg-config modglue --libs` -lmodglue \
-+	@CXX@ -o cadabra -static ${MCXXFLAGS} $+ ${LDFLAGS} `pkg-config modglue --libs` -lmodglue \
-                              -lgmpxx -lgmp -lpcrecpp -lpcre \
-                              `pkg-config sigc++-2.0 --libs` -lsigc-2.0 -lutil
- 
- else
- 	export MACOSX_DEPLOYMENT_TARGET=10.3
--	@CXX@ -o cadabra $+ ${LDFLAGS} `pkg-config modglue --libs` \
-+	@CXX@ -o cadabra ${MCXXFLAGS} $+ ${LDFLAGS} `pkg-config modglue --libs` \
-           -lgmp -lgmpxx -lpcre++ -lpcre -lexpect
- endif
- 
-@@ -77,32 +78,32 @@
- # 	@CXX@ -c -o defaults.o defaults.cc
- 
- test_tree: test_tree.o 
--	@CXX@ -o test_tree test_tree.o
-+	@CXX@ ${MCXXFLAGS} -o test_tree test_tree.o
- 
- test_lie: test_lie.o modules/lie.o
- ifeq ($(strip $(MACTEST)),)
--	@CXX@ -o test_lie test_lie.o modules/lie.o `pkg-config --libs modglue`
-+	@CXX@ ${MCXXFLAGS} -o test_lie test_lie.o modules/lie.o `pkg-config --libs modglue`
- else
--	@CXX@ -o test_lie test_lie.o modules/lie.o `pkg-config --libs modglue`
-+	@CXX@ ${MCXXFLAGS} -o test_lie test_lie.o modules/lie.o `pkg-config --libs modglue`
- endif
- 
- tree_regression_tests: tree_regression_tests.o 
--	@CXX@ -o tree_regression_tests tree_regression_tests.o
-+	@CXX@ ${MCXXFLAGS} -o tree_regression_tests tree_regression_tests.o
- 
- test_xperm: test_xperm.o modules/xperm.o
--	@CXX@ -o test_xperm test_xperm.o modules/xperm.o
-+	@CXX@ ${MCXXFLAGS} -o test_xperm test_xperm.o modules/xperm.o
- 
- tree_example: tree_example.o tree.hh
--	@CXX@ -o tree_example tree_example.o
-+	@CXX@ ${MCXXFLAGS} -o tree_example tree_example.o
- 
- test_combinatorics: test_combinatorics.o combinatorics.o
--	@CXX@ -o test_combinatorics test_combinatorics.o combinatorics.o
-+	@CXX@ ${MCXXFLAGS} -o test_combinatorics test_combinatorics.o combinatorics.o
- 
- test_young: test_young.o youngtab.o combinatorics.o
--	@CXX@ -o test_young test_young.o youngtab.o combinatorics.o ${LDFLAGS} -lgmpxx -lgmp
-+	@CXX@ ${MCXXFLAGS} -o test_young test_young.o youngtab.o combinatorics.o ${LDFLAGS} -lgmpxx -lgmp
- 
- test_preprocessor: test_preprocessor.o preprocessor.o
--	@CXX@ -o test_preprocessor test_preprocessor.o preprocessor.o ${LDFLAGS} -lgmpxx -lgmp
-+	@CXX@ ${MCXXFLAGS} -o test_preprocessor test_preprocessor.o preprocessor.o ${LDFLAGS} -lgmpxx -lgmp
- 
- mpi_pass_tree: mpi_pass_tree.o
- 	@CXX@ -o mpi_pass_tree mpi_pass_tree.o -L/usr/lib/mpich/lib -lmpich++ -lpmpich -lmpich
-@@ -133,13 +134,13 @@
- # Then the actual compilation.
- 
- lex.yy.o: lex.yy.c parser2.tab.h
--	@CXX@ -c -o lex.yy.o lex.yy.c
-+	@CXX@ ${MCXXFLAGS} -c -o lex.yy.o lex.yy.c
- 
- parser2.tab.o: parser2.tab.c
--	@CXX@ -c -o parser2.tab.o parser2.tab.c
-+	@CXX@ ${MCXXFLAGS} -c -o parser2.tab.o parser2.tab.c
- 
- parser2: parser2.tab.o lex.yy.o storage.o props.o 
--	@CXX@ -o parser2 $+ -ll -ly -lgmpxx -lgmp -lpcrecpp
-+	@CXX@ ${MCXXFLAGS} -o parser2 $+ -ll -ly -lgmpxx -lgmp -lpcrecpp
- 
- 
- 
-@@ -170,7 +171,7 @@
- .depend:
- 	rm -f .depend
- 	for i in ${SRCS}; \
--		do    @CXX@ ${MCFLAGS} -E -MM -MT `echo $$i | sed -e 's/\.\///' -e 's/\.cc/\.o/'` ${CFLAGS} $$i >> .depend; \
-+		do    @CXX@ ${MCXXFLAGS} -E -MM -MT `echo $$i | sed -e 's/\.\///' -e 's/\.cc/\.o/'` ${CXXFLAGS} $$i >> .depend; \
- 		done
- 
- include .depend
---- gui/Makefile.in.orig	2013-09-05 21:45:50.989408184 +1200
-+++ gui/Makefile.in	2013-09-05 21:57:17.495902104 +1200
-@@ -8,26 +8,26 @@
- static: xcadabra_static
- 
- OBJS   = help.o widgets.o window.o main.o ../src/stopwatch.o
--CFLAGS = -O2 -I. -I@top_srcdir@/include `pkg-config modglue --cflags` `pkg-config --cflags gtkmm-2.4` \
-+MCXXFLAGS = -O2 $(CXXFLAGS) -I. -I@top_srcdir@/include `pkg-config modglue --cflags` `pkg-config --cflags gtkmm-2.4` \
-          `pkg-config --cflags pango`
- SRCS   = `find . -name "*.cc"`
- TIMESTAMP = -D"RELEASE=\"${RELEASE}\"" -D"DATETIME=\"`date | sed -e 's/  / /'`\"" -DHOSTNAME=\"`hostname`\"
- 
- %.o: %.cc
--	@CXX@ -Wall @CFLAGS@ -D"DESTDIR=\"@prefix@\"" ${TIMESTAMP} ${CFLAGS} -c -o $@ $<
-+	@CXX@ -Wall $(MCXXFLAGS) -D"DESTDIR=\"@prefix@\"" ${TIMESTAMP} -c -o $@ $<
- 
- main.o: $(OBJS) Makefile
- 
- xcadabra: $(OBJS)
--	@CXX@ -o xcadabra $+ `pkg-config modglue --libs` `pkg-config --libs gtkmm-2.4` -lpcrecpp
-+	@CXX@ $(MCXXFLAGS) -o xcadabra $+ $(LDFLAGS) `pkg-config modglue --libs` `pkg-config --libs gtkmm-2.4` -lpcrecpp
- 
- xcadabra_static: $(OBJS)
--	@CXX@ -o xcadabra -static $+  -L@prefix@/lib `pkg-config modglue --libs` \
-+	@CXX@ $(MCXXFLAGS) -o xcadabra -static $+  $(LDFLAGS) -L@prefix@/lib `pkg-config modglue --libs` \
-                     `pkg-config --libs gtkmm-2.4` `pkg-config libxml++-2.6` \
-                     -lpthread -lexpat
- 
- test_texit: texit.o test_texit.o
--	@CXX@ -o test_texit `pkg-config modglue --libs` `pkg-config --libs gtkmm-2.4` $+ 
-+	@CXX@ $(MCXXFLAGS) -o test_texit `pkg-config modglue --libs` `pkg-config --libs gtkmm-2.4` $+ 
- 
- install:
- ifeq ($(strip $(MACTEST)),)
-@@ -50,7 +50,7 @@
- .depend:
- 	rm -f .depend
- 	for i in ${SRCS}; \
--		do    g++ -E -MM -MT `echo $$i | sed -e 's/\.\///' -e 's/\.cc/\.o/'` ${CFLAGS} $$i >> .depend; \
-+		do    g++ -E -MM -MT `echo $$i | sed -e 's/\.\///' -e 's/\.cc/\.o/'` ${MCXXFLAGS} $$i >> .depend; \
- 		done
- 
- include .depend
diff --git a/sci-mathematics/cadabra/files/cadabra-1.39-FLAGS.patch b/sci-mathematics/cadabra/files/cadabra-1.39-FLAGS.patch
deleted file mode 100644
index 2f18edb2a..000000000
--- a/sci-mathematics/cadabra/files/cadabra-1.39-FLAGS.patch
+++ /dev/null
@@ -1,171 +0,0 @@
---- Makefile.in
-+++ Makefile.in
-@@ -24,7 +24,7 @@
- 	( cd src && $(MAKE) static );
- 
- profile:
--	( export CFLAGS=-pg && export LDFLAGS=-pg && cd src && $(MAKE) );
-+	( export CFLAGS="$(CFLAGS) -pg" && CXXFLAGS="$(CXXFLAGS) -pg" && cd src && $(MAKE) );
- 
- doc:
- 	( cd doc && $(MAKE) );
---- gui/Makefile.in
-+++ gui/Makefile.in
-@@ -8,26 +8,26 @@
- static: xcadabra_static
- 
- OBJS   = help.o widgets.o window.o main.o ../src/stopwatch.o
--CFLAGS = -O2 -I. -I@top_srcdir@/include `pkg-config modglue --cflags` `pkg-config --cflags gtkmm-2.4` \
-+MCXXFLAGS = -O2 $(CXXFLAGS) -I. -I@top_srcdir@/include `pkg-config modglue --cflags` `pkg-config --cflags gtkmm-2.4` \
-          `pkg-config --cflags pango`
- SRCS   = `find . -name "*.cc"`
- TIMESTAMP = -D"RELEASE=\"${RELEASE}\"" -D"DATETIME=\"`date | sed -e 's/  / /'`\"" -DHOSTNAME=\"`hostname`\"
- 
- %.o: %.cc
--	@CXX@ -Wall @CFLAGS@ -D"DESTDIR=\"@prefix@\"" ${TIMESTAMP} ${CFLAGS} -c -o $@ $<
-+	@CXX@ -Wall $(MCXXFLAGS) -D"DESTDIR=\"@prefix@\"" ${TIMESTAMP} -c -o $@ $<
- 
- main.o: $(OBJS) Makefile
- 
- xcadabra: $(OBJS)
--	@CXX@ -o xcadabra $+ `pkg-config modglue --libs` `pkg-config --libs gtkmm-2.4` -lpcrecpp
-+	@CXX@ $(MCXXFLAGS) -o xcadabra $+ $(LDFLAGS) `pkg-config modglue --libs` `pkg-config --libs gtkmm-2.4` -lpcrecpp
- 
- xcadabra_static: $(OBJS)
--	@CXX@ -o xcadabra -static $+  -L@prefix@/lib `pkg-config modglue --libs` \
-+	@CXX@ $(MCXXFLAGS) -o xcadabra -static $+  $(LDFLAGS) -L@prefix@/lib `pkg-config modglue --libs` \
-                     `pkg-config --libs gtkmm-2.4` `pkg-config libxml++-2.6` \
-                     -lpthread -lexpat
- 
- test_texit: texit.o test_texit.o
--	@CXX@ -o test_texit `pkg-config modglue --libs` `pkg-config --libs gtkmm-2.4` $+ 
-+	@CXX@ $(MCXXFLAGS) -o test_texit `pkg-config modglue --libs` `pkg-config --libs gtkmm-2.4` $+ 
- 
- install:
- ifeq ($(strip $(MACTEST)),)
-@@ -50,7 +50,7 @@
- .depend:
- 	rm -f .depend
- 	for i in ${SRCS}; \
--		do    g++ -E -MM -MT `echo $$i | sed -e 's/\.\///' -e 's/\.cc/\.o/'` ${CFLAGS} $$i >> .depend; \
-+		do    g++ -E -MM -MT `echo $$i | sed -e 's/\.\///' -e 's/\.cc/\.o/'` ${MCXXFLAGS} $$i >> .depend; \
- 		done
- 
- include .depend
-diff -u -r cadabra-1.39.orig/src/Makefile.in cadabra-1.39/src/Makefile.in
---- src/Makefile.in
-+++ src/Makefile.in
-@@ -22,12 +22,13 @@
- 
- SRCS      = `find . -name "*.cc"`
- MCFLAGS   = @CFLAGS@ -I. -I@top_srcdir@/src `pkg-config modglue --cflags`
-+MCXXFLAGS = @CXXFLAGS@ -I. -I@top_srcdir@/src `pkg-config modglue --cflags`
- TIMESTAMP = -D"RELEASE=\"${RELEASE}\"" -D"DATETIME=\"`date | sed -e 's/  / /'`\"" -DHOSTNAME=\"`hostname`\"
- 
- 
- 
- %.o: %.cc
--	@CXX@ ${MCFLAGS} ${TIMESTAMP} -c -o $@ $<
-+	@CXX@ ${MCXXFLAGS} ${TIMESTAMP} -c -o $@ $<
- 
- # modules/xperm.o: modules/xperm.c
- # 	@CC@ @NESTED@ ${MCFLAGS} ${TIMESTAMP} -c -o $@ $<
-@@ -42,10 +43,10 @@
- 
- ifeq ($(strip $(MACTEST)),)
- cadabra: $(OBJS) $(MOBJS)
--	@CXX@ -o cadabra ${LDFLAGS} -Wl,--as-needed $+ `pkg-config modglue --libs` -lgmpxx -lpcrecpp -lgmp
-+	@CXX@ -o cadabra ${MCXXFLAGS} ${LDFLAGS} -Wl,--as-needed $+ `pkg-config modglue --libs` -lgmpxx -lpcrecpp -lgmp
- else
- cadabra: $(OBJS) $(MOBJS)
--	@CXX@ -o cadabra ${LDFLAGS} -Wl,-dead_strip_dylibs $+ `pkg-config modglue --libs` -lgmpxx -lpcrecpp -lgmp
-+	@CXX@ -o cadabra ${MCXXFLAGS} ${LDFLAGS} -Wl,-dead_strip_dylibs $+ `pkg-config modglue --libs` -lgmpxx -lpcrecpp -lgmp
- endif
- 
- #`pkg-config glib-2.0 --libs` 
-@@ -53,15 +54,15 @@
- 
- cadabra_static: $(OBJS) $(MOBJS)
- 	rm -f main.o
--	@CXX@ -Wall -g ${MCFLAGS} ${TIMESTAMP} -DSTATICBUILD -c -o main.o main.cc
-+	@CXX@ -Wall -g ${MCXXFLAGS} ${TIMESTAMP} -DSTATICBUILD -c -o main.o main.cc
- ifeq ($(strip $(MACTEST)),)
--	@CXX@ -o cadabra -static $+ ${LDFLAGS} `pkg-config modglue --libs` -lmodglue \
-+	@CXX@ -o cadabra -static ${MCXXFLAGS} $+ ${LDFLAGS} `pkg-config modglue --libs` -lmodglue \
-                              -lgmpxx -lgmp -lpcrecpp -lpcre \
-                              `pkg-config sigc++-2.0 --libs` -lsigc-2.0 -lutil
- 
- else
- 	export MACOSX_DEPLOYMENT_TARGET=10.3
--	@CXX@ -o cadabra $+ ${LDFLAGS} `pkg-config modglue --libs` \
-+	@CXX@ -o cadabra ${MCXXFLAGS} $+ ${LDFLAGS} `pkg-config modglue --libs` \
-           -lgmp -lgmpxx -lpcre++ -lpcre -lexpect
- endif
- 
-@@ -77,32 +78,32 @@
- # 	@CXX@ -c -o defaults.o defaults.cc
- 
- test_tree: test_tree.o 
--	@CXX@ -o test_tree test_tree.o
-+	@CXX@ ${MCXXFLAGS} -o test_tree test_tree.o
- 
- test_lie: test_lie.o modules/lie.o
- ifeq ($(strip $(MACTEST)),)
--	@CXX@ -o test_lie test_lie.o modules/lie.o `pkg-config --libs modglue`
-+	@CXX@ ${MCXXFLAGS} -o test_lie test_lie.o modules/lie.o `pkg-config --libs modglue`
- else
--	@CXX@ -o test_lie test_lie.o modules/lie.o `pkg-config --libs modglue`
-+	@CXX@ ${MCXXFLAGS} -o test_lie test_lie.o modules/lie.o `pkg-config --libs modglue`
- endif
- 
- tree_regression_tests: tree_regression_tests.o 
--	@CXX@ -o tree_regression_tests tree_regression_tests.o
-+	@CXX@ ${MCXXFLAGS} -o tree_regression_tests tree_regression_tests.o
- 
- #test_xperm: test_xperm.o modules/xperm_new.o
- #	@CXX@ -o test_xperm test_xperm.o modules/xperm_new.o
- 
- tree_example: tree_example.o tree.hh
--	@CXX@ -o tree_example tree_example.o
-+	@CXX@ ${MCXXFLAGS} -o tree_example tree_example.o
- 
- test_combinatorics: test_combinatorics.o combinatorics.o
--	@CXX@ -o test_combinatorics test_combinatorics.o combinatorics.o
-+	@CXX@ ${MCXXFLAGS} -o test_combinatorics test_combinatorics.o combinatorics.o
- 
- test_young: test_young.o youngtab.o combinatorics.o
--	@CXX@ -o test_young test_young.o youngtab.o combinatorics.o ${LDFLAGS} -lgmpxx -lgmp
-+	@CXX@ ${MCXXFLAGS} -o test_young test_young.o youngtab.o combinatorics.o ${LDFLAGS} -lgmpxx -lgmp
- 
- test_preprocessor: test_preprocessor.o preprocessor.o
--	@CXX@ -o test_preprocessor test_preprocessor.o preprocessor.o ${LDFLAGS} -lgmpxx -lgmp
-+	@CXX@ ${MCXXFLAGS} -o test_preprocessor test_preprocessor.o preprocessor.o ${LDFLAGS} -lgmpxx -lgmp
- 
- mpi_pass_tree: mpi_pass_tree.o
- 	@CXX@ -o mpi_pass_tree mpi_pass_tree.o -L/usr/lib/mpich/lib -lmpich++ -lpmpich -lmpich
-@@ -133,13 +134,13 @@
- # Then the actual compilation.
- 
- lex.yy.o: lex.yy.c parser2.tab.h
--	@CXX@ -c -o lex.yy.o lex.yy.c
-+	@CXX@ ${MCXXFLAGS} -c -o lex.yy.o lex.yy.c
- 
- parser2.tab.o: parser2.tab.c
--	@CXX@ -c -o parser2.tab.o parser2.tab.c
-+	@CXX@ ${MCXXFLAGS} -c -o parser2.tab.o parser2.tab.c
- 
- parser2: parser2.tab.o lex.yy.o storage.o props.o 
--	@CXX@ -o parser2 $+ -ll -ly -lgmpxx -lgmp -lpcrecpp
-+	@CXX@ ${MCXXFLAGS} -o parser2 $+ -ll -ly -lgmpxx -lgmp -lpcrecpp
- 
- 
- 
-@@ -170,7 +171,7 @@
- .depend:
- 	rm -f .depend
- 	for i in ${SRCS}; \
--		do    @CXX@ ${MCFLAGS} -E -MM -MT `echo $$i | sed -e 's/\.\///' -e 's/\.cc/\.o/'` ${CFLAGS} $$i >> .depend; \
-+		do    @CXX@ ${MCXXFLAGS} -E -MM -MT `echo $$i | sed -e 's/\.\///' -e 's/\.cc/\.o/'` ${CXXFLAGS} $$i >> .depend; \
- 		done
- 
- include .depend
diff --git a/sci-mathematics/cadabra/metadata.xml b/sci-mathematics/cadabra/metadata.xml
deleted file mode 100644
index 0cc2fca48..000000000
--- a/sci-mathematics/cadabra/metadata.xml
+++ /dev/null
@@ -1,9 +0,0 @@
-<?xml version="1.0" encoding="UTF-8"?>
-<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
-<pkgmetadata>
-	<maintainer type="project">
-		<email>sci-mathematics@gentoo.org</email>
-		<name>Gentoo Mathematics Project</name>
-	</maintainer>
-	<longdescription>Cadabra is a computer algebra system (CAS) designed specifically for the solution of problems encountered in field theory. It has extensive functionality for tensor computer algebra, tensor polynomial simplification including multi-term symmetries, fermions and anti-commuting variables, Clifford algebras and Fierz transformations, implicit coordinate dependence, multiple index types and many more.</longdescription>
-</pkgmetadata>
diff --git a/sci-mathematics/cipi/cipi-1.0-r1.ebuild b/sci-mathematics/cipi/cipi-1.0-r1.ebuild
new file mode 100644
index 000000000..6cd189e33
--- /dev/null
+++ b/sci-mathematics/cipi/cipi-1.0-r1.ebuild
@@ -0,0 +1,51 @@
+# Copyright 1999-2021 Gentoo Authors
+# Distributed under the terms of the GNU General Public License v2
+
+EAPI=8
+
+inherit cmake flag-o-matic
+
+DESCRIPTION="Computing information projections iteratively"
+HOMEPAGE="https://github.com/tom111/cipi"
+SRC_URI="https://github.com/tom111/cipi/archive/${PV}.tar.gz -> ${P}.tar.gz"
+
+LICENSE="GPL-3"
+SLOT="0"
+KEYWORDS="~amd64 ~x86"
+
+IUSE="doc"
+
+DEPEND="
+	dev-libs/boost:=
+	doc? ( virtual/latex-base )"
+RDEPEND="${DEPEND}"
+
+DOCS="AUTHORS README"
+
+CMAKE_IN_SOURCE_BUILD="yes"
+
+PATCHES=(
+	"${FILESDIR}/${P}-boost.patch"
+)
+
+src_prepare() {
+	cmake_src_prepare
+	append-ldflags -Wl,--copy-dt-needed-entries
+}
+
+src_configure() {
+	mycmakeargs=(
+		-DENABLE_DOC=$(usex doc ON OFF)
+	)
+
+	cmake_src_configure
+}
+
+pkg_postinst() {
+	elog
+	elog "The sample PARAM file has been installed to /usr/share/${PN}-${PV}"
+	elog
+	if use doc; then
+		elog "A pdf manual has been installed to /usr/share/${PN}-${PV}"
+	fi
+}
diff --git a/sci-mathematics/cipi/cipi-1.0.ebuild b/sci-mathematics/cipi/cipi-1.0.ebuild
index 03c1afef3..33d744c7c 100644
--- a/sci-mathematics/cipi/cipi-1.0.ebuild
+++ b/sci-mathematics/cipi/cipi-1.0.ebuild
@@ -1,17 +1,18 @@
-# Copyright 1999-2014 Gentoo Foundation
+# Copyright 1999-2021 Gentoo Authors
 # Distributed under the terms of the GNU General Public License v2
 
-EAPI=5
+EAPI=7
 
-inherit cmake-utils
+inherit cmake flag-o-matic
 
 DESCRIPTION="Computing information projections iteratively"
-HOMEPAGE="http://github.com/tom111/cipi"
-SRC_URI="https://github.com/tom111/cipi/archive/1.0.tar.gz -> ${P}.tar.gz"
+HOMEPAGE="https://github.com/tom111/cipi"
+SRC_URI="https://github.com/tom111/cipi/archive/${PV}.tar.gz -> ${P}.tar.gz"
 
 LICENSE="GPL-3"
 SLOT="0"
 KEYWORDS="~amd64 ~x86"
+
 IUSE="doc"
 
 DEPEND="
@@ -23,12 +24,17 @@ DOCS="AUTHORS README"
 
 CMAKE_IN_SOURCE_BUILD="yes"
 
+src_prepare() {
+	cmake_src_prepare
+	append-ldflags -Wl,--copy-dt-needed-entries
+}
+
 src_configure() {
 	mycmakeargs=(
-		$(cmake-utils_use_enable doc)
+		$(use_enable doc)
 	)
 
-	cmake-utils_src_configure
+	cmake_src_configure
 }
 
 pkg_postinst() {
diff --git a/sci-mathematics/cipi/files/cipi-1.0-boost.patch b/sci-mathematics/cipi/files/cipi-1.0-boost.patch
new file mode 100644
index 000000000..66aa9fd3f
--- /dev/null
+++ b/sci-mathematics/cipi/files/cipi-1.0-boost.patch
@@ -0,0 +1,11 @@
+--- a/src/CMakeLists.txt	2024-02-16 21:36:58.808186061 +0100
++++ b/src/CMakeLists.txt	2024-02-16 21:36:55.288131610 +0100
+@@ -8,7 +8,7 @@
+   Message("Boost found" ${Boost_LIBRARY_DIR})
+   INCLUDE_DIRECTORIES(${Boost_INCLUDE_DIR})
+   #MESSAGE("Boost was found" ${Boost_INCLUDE_DIR})
+-  TARGET_LINK_LIBRARIES (cipi boost_thread-mt)
++  TARGET_LINK_LIBRARIES (cipi boost_thread)
+ ENDIF (Boost_FOUND)
+ 
+ INSTALL(PROGRAMS cipi DESTINATION bin)
diff --git a/sci-mathematics/dolfin/Manifest b/sci-mathematics/dolfin/Manifest
deleted file mode 100644
index 67b7f0be8..000000000
--- a/sci-mathematics/dolfin/Manifest
+++ /dev/null
@@ -1,3 +0,0 @@
-DIST dolfin-0.9.9.tar.gz 10229504 BLAKE2B dc59633d82b8e1b98a1b270c0e24332bd2f80e5bbf017b54268c951fd843172101813dc66c5c6eb5c5276adf4c4e5820d9a547fe02d8d7ac0b6794f050e23545 SHA512 1b9e3dfe7dca47a535328c9dab29128262075ac28b7ec18878704d244a27ec417c7d9c00b518dbaa782c2daccaa3affe4b8f9f60df19e1e9b4ca2c70fc2a2483
-DIST dolfin-2016.2.0.tar.gz 9702541 BLAKE2B 0e6b73419bbaf5b24e63d5b5347e9e8ee280b86868f02aadae06ee638053554b55277fecfe124982b99debc0402744cddb5aa81283d8413c5d5cde9c39cd12bc SHA512 1886513b433845c1026c37a7ac574d8bb7d08e896e5e54a0cca7f2ba3dde02b5c3551c005a408de151a915ca890ba8e65ebfd53abaef980132cc636c47f8f5fa
-DIST dolfin-2017.1.0.tar.gz 13264977 BLAKE2B 1fa0c0921196749e19582201cbf7ed19c38b59436fad01afc766dc2dc77387385d2765e844b62741481292652b4154035f811f454bda4e85e93bcd0b7fd1bab4 SHA512 60b6c2128b5249eb94551e23b3c1e2eb014af7336ddea629c8d496be0d3782bcdc03b494b6a12ba3fc948e8dcca8bffce412da1a7c7038464e5a747ec5430f94
diff --git a/sci-mathematics/dolfin/dolfin-0.9.9.ebuild b/sci-mathematics/dolfin/dolfin-0.9.9.ebuild
deleted file mode 100644
index 4677e51b2..000000000
--- a/sci-mathematics/dolfin/dolfin-0.9.9.ebuild
+++ /dev/null
@@ -1,56 +0,0 @@
-# Copyright 1999-2015 Gentoo Foundation
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=5
-
-PYTHON_COMPAT=( python2_7 )
-
-inherit cmake-utils eutils python-single-r1
-
-DESCRIPTION="C++/Python interface of FEniCS"
-HOMEPAGE="https://launchpad.net/dolfin/"
-SRC_URI="https://launchpad.net/${PN}/0.x/${PV}/+download/${P}.tar.gz"
-
-LICENSE="LGPL-2.1"
-SLOT="0"
-KEYWORDS="~amd64"
-IUSE="cgal cholmod gmp mpi parmetis python scotch umfpack zlib"
-# scotch and parmetis require mpi; wait for EAPI 4
-
-REQUIRED_USE="python? ( ${PYTHON_REQUIRED_USE} )"
-
-DEPEND="
-	dev-libs/boost
-	dev-libs/libxml2:2
-	sci-libs/armadillo
-	sci-mathematics/ufc
-	python? (
-		${PYTHON_DEPS}
-		dev-python/ufl[${PYTHON_USEDEP}]
-		dev-python/ffc[${PYTHON_USEDEP}]
-		dev-python/fiat[${PYTHON_USEDEP}]
-		dev-python/instant[${PYTHON_USEDEP}]
-		dev-python/viper[${PYTHON_USEDEP}]
-		)"
-RDEPEND="${DEPEND}"
-
-pkg_setup() {
-	use python && python-single-r1_pkg_setup
-}
-
-src_prepare() {
-	epatch "${FILESDIR}"/"${P}"-find-armadillo.patch
-}
-
-pkg_setup() {
-	mycmakeargs="${mycmakeargs}
-		$(cmake-utils_use cgal DOLFIN_ENABLE_CGAL)
-		$(cmake-utils_use cholmod DOLFIN_ENABLE_CHOLMOD)
-		$(cmake-utils_use gmp DOLFIN_ENABLE_GMP)
-		$(cmake-utils_use mpi DOLFIN_ENABLE_MPI)
-		$(cmake-utils_use parmetis DOLFIN_ENABLE_PARMETIS)
-		$(cmake-utils_use python DOLFIN_ENABLE_PYTHON)
-		$(cmake-utils_use scotch DOLFIN_ENABLE_SCOTCH)
-		$(cmake-utils_use umfpack DOLFIN_ENABLE_UMFPACK)
-		$(cmake-utils_use zlib DOLFIN_ENABLE_ZLIB)"
-}
diff --git a/sci-mathematics/dolfin/dolfin-2016.2.0-r2.ebuild b/sci-mathematics/dolfin/dolfin-2016.2.0-r2.ebuild
deleted file mode 100644
index 4d5d8f716..000000000
--- a/sci-mathematics/dolfin/dolfin-2016.2.0-r2.ebuild
+++ /dev/null
@@ -1,80 +0,0 @@
-# Copyright 1999-2017 Gentoo Foundation
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=6
-
-PYTHON_COMPAT=( python2_7 )
-
-inherit cmake-utils eutils python-single-r1
-
-DESCRIPTION="C++/Python interface of FEniCS"
-HOMEPAGE="https://bitbucket.org/fenics-project/dolfin"
-SRC_URI="https://bitbucket.org/fenics-project/${PN}/downloads/${P}.tar.gz"
-
-LICENSE="LGPL-2.1"
-SLOT="0"
-KEYWORDS="~amd64"
-IUSE="hdf5 mpi parmetis petsc scotch trilinos umfpack zlib vtk"
-
-REQUIRED_USE="${PYTHON_REQUIRED_USE}
-	trilinos? ( mpi )"
-
-# Yes, swig is an RDEPEND
-DEPEND="
-	${PYTHON_DEPS}
-	dev-cpp/eigen:3
-	dev-lang/swig:0=
-	dev-libs/boost:=
-	dev-libs/libxml2:2
-	~dev-python/dijitso-${PV}[${PYTHON_USEDEP}]
-	~dev-python/ffc-${PV}[${PYTHON_USEDEP}]
-	~dev-python/fiat-${PV}[${PYTHON_USEDEP}]
-	~dev-python/instant-${PV}[${PYTHON_USEDEP}]
-	dev-python/sympy
-	~dev-python/ufl-${PV}[${PYTHON_USEDEP}]
-	virtual/blas
-	virtual/lapack
-	hdf5? ( sci-libs/hdf5[mpi=] )
-	mpi? ( virtual/mpi )
-	parmetis? ( sci-libs/parmetis[mpi(+)] )
-	petsc? ( sci-mathematics/petsc[mpi=] )
-	sci-libs/armadillo
-	scotch? ( sci-libs/scotch )
-	trilinos? ( sci-libs/trilinos )
-	umfpack? (
-		sci-libs/amd
-		sci-libs/cholmod
-		sci-libs/umfpack
-	)
-	vtk? ( sci-libs/vtk )
-	zlib? ( sys-libs/zlib )"
-RDEPEND="${DEPEND}"
-
-PATCHES=(
-	"${FILESDIR}"/${P}-trilinos-superlu.patch
-)
-
-pkg_setup() {
-	python-single-r1_pkg_setup
-}
-
-src_configure() {
-	# *sigh*
-	addpredict /proc/mtrr
-	addpredict /sys/devices/system/cpu/
-
-	mycmakeargs=(
-		-DDOLFIN_ENABLE_CHOLMOD="$(usex umfpack)"
-		-DDOLFIN_ENABLE_HDF5="$(usex hdf5)"
-		-DDOLFIN_ENABLE_MPI="$(usex mpi)"
-		-DDOLFIN_ENABLE_PARMETIS="$(usex parmetis)"
-		-DDOLFIN_ENABLE_PETSC="$(usex petsc)"
-		-DDOLFIN_ENABLE_PYTHON="yes"
-		-DDOLFIN_ENABLE_SCOTCH="$(usex scotch)"
-		-DDOLFIN_ENABLE_TRILINOS="$(usex trilinos)"
-		-DDOLFIN_ENABLE_UMFPACK="$(usex umfpack)"
-		-DDOLFIN_ENABLE_VTK="$(usex vtk)"
-		-DDOLFIN_ENABLE_ZLIB="$(usex zlib)"
-	)
-	cmake-utils_src_configure
-}
diff --git a/sci-mathematics/dolfin/dolfin-2017.1.0.ebuild b/sci-mathematics/dolfin/dolfin-2017.1.0.ebuild
deleted file mode 100644
index 64e736315..000000000
--- a/sci-mathematics/dolfin/dolfin-2017.1.0.ebuild
+++ /dev/null
@@ -1,80 +0,0 @@
-# Copyright 1999-2017 Gentoo Foundation
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=6
-
-PYTHON_COMPAT=( python3_4 python3_5 python3_6 )
-
-inherit cmake-utils eutils python-single-r1
-
-DESCRIPTION="C++/Python interface of FEniCS"
-HOMEPAGE="https://bitbucket.org/fenics-project/dolfin"
-SRC_URI="https://bitbucket.org/fenics-project/${PN}/downloads/${P}.tar.gz"
-
-LICENSE="LGPL-2.1"
-SLOT="0"
-KEYWORDS="~amd64"
-IUSE="hdf5 mpi parmetis petsc scotch trilinos umfpack zlib vtk"
-
-REQUIRED_USE="${PYTHON_REQUIRED_USE}
-	trilinos? ( mpi )"
-
-# Yes, swig is an RDEPEND
-DEPEND="
-	${PYTHON_DEPS}
-	dev-cpp/eigen:3
-	dev-lang/swig:0=
-	dev-libs/boost:=
-	dev-libs/libxml2:2
-	~dev-python/dijitso-${PV}[${PYTHON_USEDEP}]
-	~dev-python/ffc-${PV}[${PYTHON_USEDEP}]
-	~dev-python/fiat-${PV}[${PYTHON_USEDEP}]
-	~dev-python/instant-${PV}[${PYTHON_USEDEP}]
-	dev-python/sympy
-	~dev-python/ufl-${PV}[${PYTHON_USEDEP}]
-	virtual/blas
-	virtual/lapack
-	hdf5? ( sci-libs/hdf5[mpi=] )
-	mpi? ( virtual/mpi )
-	parmetis? ( sci-libs/parmetis[mpi(+)] )
-	petsc? ( sci-mathematics/petsc[mpi=] )
-	sci-libs/armadillo
-	scotch? ( sci-libs/scotch )
-	trilinos? ( sci-libs/trilinos )
-	umfpack? (
-		sci-libs/amd
-		sci-libs/cholmod
-		sci-libs/umfpack
-	)
-	vtk? ( sci-libs/vtk )
-	zlib? ( sys-libs/zlib )"
-RDEPEND="${DEPEND}"
-
-PATCHES=(
-	"${FILESDIR}"/${PN}-2016.2.0-trilinos-superlu.patch
-)
-
-pkg_setup() {
-	python-single-r1_pkg_setup
-}
-
-src_configure() {
-	# *sigh*
-	addpredict /proc/mtrr
-	addpredict /sys/devices/system/cpu/
-
-	mycmakeargs=(
-		-DDOLFIN_ENABLE_CHOLMOD="$(usex umfpack)"
-		-DDOLFIN_ENABLE_HDF5="$(usex hdf5)"
-		-DDOLFIN_ENABLE_MPI="$(usex mpi)"
-		-DDOLFIN_ENABLE_PARMETIS="$(usex parmetis)"
-		-DDOLFIN_ENABLE_PETSC="$(usex petsc)"
-		-DDOLFIN_ENABLE_PYTHON="yes"
-		-DDOLFIN_ENABLE_SCOTCH="$(usex scotch)"
-		-DDOLFIN_ENABLE_TRILINOS="$(usex trilinos)"
-		-DDOLFIN_ENABLE_UMFPACK="$(usex umfpack)"
-		-DDOLFIN_ENABLE_VTK="$(usex vtk)"
-		-DDOLFIN_ENABLE_ZLIB="$(usex zlib)"
-	)
-	cmake-utils_src_configure
-}
diff --git a/sci-mathematics/dolfin/files/dolfin-0.9.9-find-armadillo.patch b/sci-mathematics/dolfin/files/dolfin-0.9.9-find-armadillo.patch
deleted file mode 100644
index 677a78aab..000000000
--- a/sci-mathematics/dolfin/files/dolfin-0.9.9-find-armadillo.patch
+++ /dev/null
@@ -1,25 +0,0 @@
-diff -Naur a/cmake/modules/FindArmadillo.cmake b/cmake/modules/FindArmadillo.cmake
---- a/cmake/modules/FindArmadillo.cmake	2010-09-02 02:49:57.000000000 +0200
-+++ b/cmake/modules/FindArmadillo.cmake	2010-12-15 14:21:34.810300165 +0100
-@@ -95,8 +95,8 @@
- #include <armadillo>
- int main()
- {
-- arma::mat A = arma::rand(4, 4);
-- arma::vec b = arma::rand(4);
-+ arma::mat A = arma::randu(4, 4);
-+ arma::vec b = arma::randu(4);
-  arma::vec x = arma::solve(A, b);
-  return 0;
- }
-@@ -112,8 +112,8 @@
- #include <armadillo>
- int main()
- {
-- arma::mat A = arma::rand(4, 4);
-- arma::vec b = arma::rand(4);
-+ arma::mat A = arma::randu(4, 4);
-+ arma::vec b = arma::randu(4);
-  arma::vec x = arma::solve(A, b);
-  return 0;
- }
diff --git a/sci-mathematics/dolfin/files/dolfin-2016.2.0-trilinos-superlu.patch b/sci-mathematics/dolfin/files/dolfin-2016.2.0-trilinos-superlu.patch
deleted file mode 100644
index 7282766fe..000000000
--- a/sci-mathematics/dolfin/files/dolfin-2016.2.0-trilinos-superlu.patch
+++ /dev/null
@@ -1,21 +0,0 @@
-diff --git a/dolfin/CMakeLists.txt b/dolfin/CMakeLists.txt
-index 26bc21a..0caf7ca 100644
---- a/dolfin/CMakeLists.txt
-+++ b/dolfin/CMakeLists.txt
-@@ -2,6 +2,7 @@ set(DOLFIN_H dolfin.h)
- install(FILES ${DOLFIN_H} DESTINATION ${DOLFIN_INCLUDE_DIR}
-   COMPONENT Development)
- 
-+
- # Configure and install dolfin/common/version.h file
- string(REPLACE "+" "" DOLFIN_VERSION_MICRO_STRIPPED ${DOLFIN_VERSION_MICRO})
- configure_file(${DOLFIN_SOURCE_DIR}/dolfin/common/version.h.in
-@@ -12,6 +13,8 @@ install(FILES ${CMAKE_BINARY_DIR}/dolfin/common/version.h
-   )
- include_directories(${CMAKE_BINARY_DIR})
- 
-+include_directories(/usr/include/superlu)
-+
- #------------------------------------------------------------------------------
- # DOLFIN source directories
- 
diff --git a/sci-mathematics/dolfin/metadata.xml b/sci-mathematics/dolfin/metadata.xml
deleted file mode 100644
index 26a0480f0..000000000
--- a/sci-mathematics/dolfin/metadata.xml
+++ /dev/null
@@ -1,26 +0,0 @@
-<?xml version="1.0" encoding="UTF-8"?>
-<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
-<pkgmetadata>
-	<maintainer type="project">
-		<email>sci-mathematics@gentoo.org</email>
-		<name>Gentoo Mathematics Project</name>
-	</maintainer>
-	<longdescription lang="en">
-DOLFIN is the C++/Python interface of FEniCS, providing a consistent PSE (Problem Solving Environment) for ordinary and partial differential equations.
-</longdescription>
-	<use>
-		<flag name="cgal">Adds support for geometric algorithms with <pkg>sci-mathematics/cgal</pkg></flag>
-		<flag name="cholmod">Adds support for sparse Cholesky factorization with <pkg>sci-libs/cholmod</pkg></flag>
-		<flag name="hdf5">Adds support for <pkg>sci-libs/hdf5</pkg></flag>
-		<flag name="parmetis">Adds support for parallel graph partitioning with <pkg>sci-libs/parmetis</pkg></flag>
-		<flag name="petsc">Adds support for numerical linear algebra toolkit <pkg>sci-mathematics/petsc</pkg></flag>
-		<flag name="scotch">Adds support for graph partitioning with <pkg>sci-libs/scotch</pkg></flag>
-		<flag name="trilinos">Adds support for numerical linear algebra toolkit  <pkg>sci-libs/trilinos</pkg></flag>
-		<flag name="umfpack">Adds support for sparse solving with <pkg>sci-libs/umfpack</pkg></flag>
-		<flag name="vtk">Adds support for the visualization toolkit <pkg>sci-libs/vtk</pkg></flag>
-	</use>
-	<upstream>
-		<remote-id type="bitbucket">fenics-project/dolfin</remote-id>
-		<remote-id type="launchpad">dolfin</remote-id>
-	</upstream>
-</pkgmetadata>
diff --git a/sci-mathematics/dsfmt/Manifest b/sci-mathematics/dsfmt/Manifest
deleted file mode 100644
index cd9c966ec..000000000
--- a/sci-mathematics/dsfmt/Manifest
+++ /dev/null
@@ -1 +0,0 @@
-DIST dSFMT-src-2.2.tar.gz 291253 BLAKE2B 0b9762094450fb8d21a8786531df0a91a9750bddec9882e4d68607def42caaf5cf37a6f9ec41f84794e971bb60e708568f6b152610bafa72d757cb43d4512abb SHA512 e59d54166dc2df9f6e6abd68658c3624082feabe445215256fead47a8944c41578d11c2b4ba57eac174587a45e445b2aabd867db24fd9e951842513cf914f60b
diff --git a/sci-mathematics/dsfmt/dsfmt-2.2.ebuild b/sci-mathematics/dsfmt/dsfmt-2.2.ebuild
deleted file mode 100644
index 173384bac..000000000
--- a/sci-mathematics/dsfmt/dsfmt-2.2.ebuild
+++ /dev/null
@@ -1,26 +0,0 @@
-# Copyright 1999-2014 Gentoo Foundation
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=5
-
-MYP=dSFMT-src-${PV}
-
-DESCRIPTION="Double precision SIMD-oriented Fast Mersenne Twister library"
-HOMEPAGE="http://www.math.sci.hiroshima-u.ac.jp/~m-mat/MT/SFMT"
-SRC_URI="${HOMEPAGE}/${MYP}.tar.gz"
-
-LICENSE="BSD"
-SLOT="0"
-KEYWORDS="~amd64 ~x86 ~amd64-linux ~x86-linux"
-IUSE=""
-
-S="${WORKDIR}/${MYP}"
-
-src_test() {
-	emake std-check
-}
-
-src_install() {
-	doheader dSFMT.c d*.h
-	dodoc README*txt CHANGE*
-}
diff --git a/sci-mathematics/dsfmt/metadata.xml b/sci-mathematics/dsfmt/metadata.xml
deleted file mode 100644
index d2482ce5f..000000000
--- a/sci-mathematics/dsfmt/metadata.xml
+++ /dev/null
@@ -1,17 +0,0 @@
-<?xml version="1.0" encoding="UTF-8"?>
-<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
-<pkgmetadata>
-	<maintainer type="project">
-		<email>sci-mathematics@gentoo.org</email>
-		<name>Gentoo Mathematics Project</name>
-	</maintainer>
-	<longdescription lang="en">
-The purpose of Double precision SIMD-oriented Fast Mersenne Twister (dSFMT)
-is to speed up the generation by avoiding the expensive conversion
-of integer to double (floating point). dSFMT directly generates
-double precision floating point pseudorandom numbers which have the
-IEEE Standard for Binary Floating-Point Arithmetic (ANSI/IEEE Std
-754-1985) format. dSFMT is only available on the CPUs which use IEEE
-754 format double precision floating point numbers.
-</longdescription>
-</pkgmetadata>
diff --git a/sci-mathematics/flocq/Manifest b/sci-mathematics/flocq/Manifest
deleted file mode 100644
index 25a417be1..000000000
--- a/sci-mathematics/flocq/Manifest
+++ /dev/null
@@ -1 +0,0 @@
-DIST flocq-2.3.0.tar.gz 155465 BLAKE2B 8cf3c10799643b24b17b50c118bf344d95fba1ecb6faa0d12e559f15f449eb1c6b75f2b1707e6e770abbffeb26d73e094941828a785224f426c4cf6e6fc13a2d SHA512 964b87f3df3ab76549dace5d8c16c7e7890dc70b64f54db3555023dcd6b32648b19030ad25ecb5b6e99bca5139f289a2ecfd3a1fe8bc1e1dfe7429f3d4f1ebc3
diff --git a/sci-mathematics/flocq/flocq-2.3.0.ebuild b/sci-mathematics/flocq/flocq-2.3.0.ebuild
deleted file mode 100644
index d875e9186..000000000
--- a/sci-mathematics/flocq/flocq-2.3.0.ebuild
+++ /dev/null
@@ -1,35 +0,0 @@
-# Copyright 1999-2014 Gentoo Foundation
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=5
-
-DESCRIPTION="A floating-point formalization for the Coq system"
-HOMEPAGE="http://flocq.gforge.inria.fr/"
-SRC_URI="https://gforge.inria.fr/frs/download.php/33502/${P}.tar.gz"
-
-LICENSE="LGPL-3"
-SLOT="0"
-KEYWORDS="~amd64 ~x86"
-IUSE=""
-
-DEPEND="sci-mathematics/coq"
-RDEPEND="${DEPEND}"
-
-src_prepare() {
-	sed -i Remakefile.in \
-		-e "s:mkdir -p @libdir@:mkdir -p \${DESTDIR}@libdir@:g" \
-		-e "s:cp \$f @libdir@:cp \$f \${DESTDIR}@libdir@:g"
-}
-
-src_configure() {
-	econf --libdir="`coqc -where`/user-contrib/Flocq"
-}
-
-src_compile() {
-	./remake || die "emake failed"
-}
-
-src_install() {
-	DESTDIR="${D}" ./remake install || die
-	dodoc NEWS README AUTHORS ChangeLog
-}
diff --git a/sci-mathematics/flocq/metadata.xml b/sci-mathematics/flocq/metadata.xml
deleted file mode 100644
index de5ba354b..000000000
--- a/sci-mathematics/flocq/metadata.xml
+++ /dev/null
@@ -1,14 +0,0 @@
-<?xml version="1.0" encoding="UTF-8"?>
-<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
-<pkgmetadata>
-	<maintainer type="project">
-		<email>sci-mathematics@gentoo.org</email>
-		<name>Gentoo Mathematics Project</name>
-	</maintainer>
-	<longdescription>
-Flocq (Floats for Coq) is a floating-point formalization for the Coq
-system. It provides a comprehensive library of theorems on a multi-radix
-multi-precision arithmetic. It also supports efficient numerical
-computations inside Coq.
-</longdescription>
-</pkgmetadata>
diff --git a/sci-mathematics/frama-c/Manifest b/sci-mathematics/frama-c/Manifest
index 8380c7673..9681962f9 100644
--- a/sci-mathematics/frama-c/Manifest
+++ b/sci-mathematics/frama-c/Manifest
@@ -1 +1 @@
-DIST frama-c-Neon-20140301.tar.gz 3122492 BLAKE2B ba11361ac48e2416dd3fe05ceb2dd57a83a03b42c38d8670b16e6e9f9e1df12c7332820813d1986e9560a82f7535acad1b9946cb3c8fc593de2b3017d55e9609 SHA512 9cfe4c986004b4b991dbd2d7dc31777100bf85910c488d575c670d40d53b3e309667dfee75f22d121a6351f23753ed31decffbee08929ea129daf56f0c9a01e8
+DIST frama-c-22.0-Titanium.tar.gz 6008520 BLAKE2B 957f1fd383913718598c8d14bd0ff4b6251cc5350633888ca061fa0e44fae17273b379dcc1b70fe8a187975364aee1f255e0df232a4ee349ff29f9cb922a7b60 SHA512 7366127da4726ffec0022adc06fd867b6ea37fc23b6a5ddccbe7562fcaa635abc6894397d0101fcb0afc339c565299c6d637006305c8331aa62a8ce734740a0f
diff --git a/sci-mathematics/frama-c/files/ocamlgraph185_compat.patch b/sci-mathematics/frama-c/files/ocamlgraph185_compat.patch
deleted file mode 100644
index 798d17fd3..000000000
--- a/sci-mathematics/frama-c/files/ocamlgraph185_compat.patch
+++ /dev/null
@@ -1,254 +0,0 @@
-From: Mehdi Dogguy <mehdi@debian.org>
-Date: Sun, 27 Apr 2014 13:46:16 +0200
-Subject: Port to OCamlgraph 1.8.5
-
----
- src/impact/reason_graph.ml          |    2 +-
- src/kernel/stmts_graph.ml           |   10 +++++-----
- src/logic/property_status.ml        |    8 ++++----
- src/misc/service_graph.ml           |    4 ++--
- src/pdg_types/pdgTypes.ml           |    6 +++---
- src/postdominators/print.ml         |    2 +-
- src/semantic_callgraph/register.ml  |    4 ++--
- src/slicing/printSlice.ml           |   10 +++++-----
- src/syntactic_callgraph/register.ml |    4 ++--
- src/wp/cil2cfg.ml                   |   12 ++++++------
- 10 files changed, 31 insertions(+), 31 deletions(-)
-
-diff --git a/src/impact/reason_graph.ml b/src/impact/reason_graph.ml
-index eabacb0..ce19b4a 100644
---- a/src/impact/reason_graph.ml
-+++ b/src/impact/reason_graph.ml
-@@ -139,7 +139,7 @@ module Printer (X: AdditionalInfo) = struct
- 
-   let graph_attributes _ = [`Label "Impact graph"]
- 
--  let default_vertex_attributes _g = [`Style [`Filled]; `Shape `Box]
-+  let default_vertex_attributes _g = [`Style `Filled; `Shape `Box]
-   let default_edge_attributes _g = []
- 
-   let vertex_attributes v =
-diff --git a/src/kernel/stmts_graph.ml b/src/kernel/stmts_graph.ml
-index a8fe121..16059c3 100644
---- a/src/kernel/stmts_graph.ml
-+++ b/src/kernel/stmts_graph.ml
-@@ -157,12 +157,12 @@ module TP = struct
- 
-   let vertex_attributes s =
-     match s.skind with
--    | Loop _ -> [`Color 0xFF0000; `Style [`Filled]]
--    | If _ -> [`Color 0x00FF00; `Style [`Filled]; `Shape `Diamond]
--    | Return _ -> [`Color 0x0000FF; `Style [`Filled]]
-+    | Loop _ -> [`Color 0xFF0000; `Style `Filled]
-+    | If _ -> [`Color 0x00FF00; `Style `Filled; `Shape `Diamond]
-+    | Return _ -> [`Color 0x0000FF; `Style `Filled]
-     | Block _ -> [`Shape `Box; `Fontsize 8]
--    | Goto _ -> [`Shape `Diamond; `Color 0x00FFFF ; `Style [`Filled]]
--    | Instr (Skip _) -> [`Color 0x00FFFF ; `Style [`Filled]]
-+    | Goto _ -> [`Shape `Diamond; `Color 0x00FFFF ; `Style `Filled]
-+    | Instr (Skip _) -> [`Color 0x00FFFF ; `Style `Filled]
-     | _ -> []
-   let default_vertex_attributes _ = []
- 
-diff --git a/src/logic/property_status.ml b/src/logic/property_status.ml
-index f7c278d..47485f6 100644
---- a/src/logic/property_status.ml
-+++ b/src/logic/property_status.ml
-@@ -1481,12 +1481,12 @@ module Consolidation_graph = struct
-                 let s = get_status p in
- 		let color = status_color p s in
-                 let style = match s with
--                  | Never_tried -> [`Style [`Bold]; `Width 0.8 ]
--                  | _ -> [`Style [`Filled]]
-+                  | Never_tried -> [`Style `Bold; `Width 0.8 ]
-+                  | _ -> [`Style `Filled]
-                 in
- 		style @ [ label v; `Color color; `Shape `Box ]
-               | Emitter _ as v -> 
--		[ label v; `Shape `Diamond; `Color 0xb0c4de; `Style [`Filled] ]
-+		[ label v; `Shape `Diamond; `Color 0xb0c4de; `Style `Filled ]
-               | Tuning_parameter _ as v ->
- 		[ label v; (*`Style `Dotted;*) `Color 0xb0c4de;  ]
- 	      (*| Correctness_parameter _ (*as v*) -> assert false (*[ label v; `Color 0xb0c4de ]*)*)
-@@ -1495,7 +1495,7 @@ module Consolidation_graph = struct
- 	      | None -> []
- 	      | Some s ->
- 		let c = emitted_status_color s in
--		[ `Color c; `Fontcolor c; `Style [`Bold] ]
-+		[ `Color c; `Fontcolor c; `Style `Bold ]
- 
-         let default_vertex_attributes _ = []
-         let default_edge_attributes _ = []
-diff --git a/src/misc/service_graph.ml b/src/misc/service_graph.ml
-index 4f866c5..d158028 100644
---- a/src/misc/service_graph.ml
-+++ b/src/misc/service_graph.ml
-@@ -289,7 +289,7 @@ Src root:%s in %s (is_root:%b) Dst:%s in %s (is_root:%b) [2d case]"
-         color e
-       else
-         match CallG.E.label e with
--        | Inter_services -> [ `Style [`Invis] ]
-+        | Inter_services -> [ `Style `Invis ]
-         | Inter_functions | Both -> color e
- 
-     let default_edge_attributes _ = []
-@@ -303,7 +303,7 @@ Src root:%s in %s (is_root:%b) Dst:%s in %s (is_root:%b) [2d case]"
-           sg_attributes =
-             [ `Label ("S " ^ cs);
-               `Color (Extlib.number_to_color id);
--              `Style [`Bold] ] }
-+              `Style `Bold ] }
- 
-   end
- 
-diff --git a/src/pdg_types/pdgTypes.ml b/src/pdg_types/pdgTypes.ml
-index 05754e4..74cdebf 100644
---- a/src/pdg_types/pdgTypes.ml
-+++ b/src/pdg_types/pdgTypes.ml
-@@ -626,7 +626,7 @@ module Pdg = struct
- 
-     let graph_attributes _ = [`Rankdir `TopToBottom ]
- 
--    let default_vertex_attributes _ = [`Style [`Filled]]
-+    let default_vertex_attributes _ = [`Style `Filled]
-     let vertex_name v = string_of_int (Node.id v)
- 
-     let vertex_attributes v =
-@@ -711,13 +711,13 @@ module Pdg = struct
-         if Dpd.is_ctrl d then (`Arrowtail `Odot)::attrib else attrib
-       in
-       let attrib =
--        if Dpd.is_addr d then (`Style [`Dotted])::attrib else attrib
-+        if Dpd.is_addr d then (`Style `Dotted)::attrib else attrib
-       in
-         attrib
- 
-     let get_subgraph v =
-       let mk_subgraph name attrib =
--        let attrib = (`Style [`Filled]) :: attrib in
-+        let attrib = (`Style `Filled) :: attrib in
-         Some { Graph.Graphviz.DotAttributes.sg_name= name;
-                sg_parent = None;
-                sg_attributes = attrib }
-diff --git a/src/postdominators/print.ml b/src/postdominators/print.ml
-index f2e3a25..15f4ff2 100644
---- a/src/postdominators/print.ml
-+++ b/src/postdominators/print.ml
-@@ -63,7 +63,7 @@ module Printer = struct
- 
-   let graph_attributes (title, _) = [`Label title]
- 
--  let default_vertex_attributes _g = [`Style [`Filled]]
-+  let default_vertex_attributes _g = [`Style `Filled]
-   let default_edge_attributes _g = []
- 
-   let vertex_attributes (s, has_postdom) =
-diff --git a/src/semantic_callgraph/register.ml b/src/semantic_callgraph/register.ml
-index 1c79dcc..071f061 100644
---- a/src/semantic_callgraph/register.ml
-+++ b/src/semantic_callgraph/register.ml
-@@ -102,8 +102,8 @@ module Service =
-          let name = Kernel_function.get_name
-          let attributes v =
-            [ `Style
--               [if Kernel_function.is_definition v then `Bold
--                else `Dotted] ]
-+               (if Kernel_function.is_definition v then `Bold
-+                else `Dotted) ]
-          let entry_point () =
-            try Some (fst (Globals.entry_point ()))
-            with Globals.No_such_entry_point _ -> None
-diff --git a/src/slicing/printSlice.ml b/src/slicing/printSlice.ml
-index c5363f9..211e0bb 100644
---- a/src/slicing/printSlice.ml
-+++ b/src/slicing/printSlice.ml
-@@ -227,7 +227,7 @@ module PrintProject = struct
- 
-   let graph_attributes (name, _) = [`Label name]
- 
--  let default_vertex_attributes _ = [`Style [`Filled]]
-+  let default_vertex_attributes _ = [`Style `Filled]
- 
-   let vertex_name v = match v with
-     | Src fi -> SlicingMacros.fi_name fi
-@@ -280,16 +280,16 @@ module PrintProject = struct
- 
-   let edge_attributes (e, call) =
-     let attrib = match e with
--    | (Src _, Src _) -> [`Style [`Invis]]
--    | (OptSliceCallers _, _) -> [`Style [`Invis]]
--    | (_, OptSliceCallers _) -> [`Style [`Invis]]
-+    | (Src _, Src _) -> [`Style `Invis]
-+    | (OptSliceCallers _, _) -> [`Style `Invis]
-+    | (_, OptSliceCallers _) -> [`Style `Invis]
-     | _ -> []
-     in match call with None -> attrib
-       | Some call -> (`Label (string_of_int call.sid)):: attrib
- 
-   let get_subgraph v =
-     let mk_subgraph name attrib =
--      let attrib = (*(`Label name) ::*) (`Style [`Filled]) :: attrib in
-+      let attrib = (*(`Label name) ::*) (`Style `Filled) :: attrib in
-           Some { Graph.Graphviz.DotAttributes.sg_name= name;
-                  sg_parent = None;
-                  sg_attributes = attrib }
-diff --git a/src/syntactic_callgraph/register.ml b/src/syntactic_callgraph/register.ml
-index d4669c4..d41980e 100644
---- a/src/syntactic_callgraph/register.ml
-+++ b/src/syntactic_callgraph/register.ml
-@@ -37,8 +37,8 @@ module Service =
-          let name v = nodeName v.cnInfo
-          let attributes v =
-            [ match v.cnInfo with
--             | NIVar (_,b) when not !b -> `Style [`Dotted]
--             | _ -> `Style [`Bold] ]
-+             | NIVar (_,b) when not !b -> `Style `Dotted
-+             | _ -> `Style `Bold ]
-          let equal v1 v2 = id v1 = id v2
- 	 let compare v1 v2 = 
- 	   let i1 = id v1 in
-diff --git a/src/wp/cil2cfg.ml b/src/wp/cil2cfg.ml
-index 6d8cf09..ba5f410 100644
---- a/src/wp/cil2cfg.ml
-+++ b/src/wp/cil2cfg.ml
-@@ -1278,9 +1278,9 @@ module Printer (PE : sig val edge_txt : edge -> string end) = struct
-       | Vstart | Vend | Vexit -> [`Color 0x0000FF; `Shape `Doublecircle]
-       | VfctIn | VfctOut -> [`Color 0x0000FF; `Shape `Box]
-       | VblkIn _ | VblkOut _ -> [`Shape `Box]
--      | Vloop _ | Vloop2 _ -> [`Color 0xFF0000; `Style [`Filled]]
-+      | Vloop _ | Vloop2 _ -> [`Color 0xFF0000; `Style `Filled]
-       | Vtest _ | Vswitch _ ->
--        [`Color 0x00FF00; `Style [`Filled]; `Shape `Diamond]
-+        [`Color 0x00FF00; `Style `Filled; `Shape `Diamond]
-       | Vcall _ | Vstmt _ -> []
-     in (`Label (String.escaped label))::attr
- 
-@@ -1290,15 +1290,15 @@ module Printer (PE : sig val edge_txt : edge -> string end) = struct
-     let attr = [] in
-     let attr = (`Label (String.escaped (PE.edge_txt e)))::attr in
-     let attr =
--      if is_back_edge e then (`Constraint false)::(`Style [`Bold])::attr
-+      if is_back_edge e then (`Constraint false)::(`Style `Bold)::attr
-       else attr
-     in
-     let attr = match (edge_type e) with
-       | Ethen | EbackThen -> (`Color 0x00FF00)::attr
-       | Eelse | EbackElse -> (`Color 0xFF0000)::attr
--      | Ecase [] -> (`Color 0x0000FF)::(`Style [`Dashed])::attr
-+      | Ecase [] -> (`Color 0x0000FF)::(`Style `Dashed)::attr
-       | Ecase _ -> (`Color 0x0000FF)::attr
--      | Enext -> (`Style [`Dotted])::attr
-+      | Enext -> (`Style `Dotted)::attr
-       | Eback -> attr (* see is_back_edge above *)
-       | Enone -> attr
-     in
-@@ -1308,7 +1308,7 @@ module Printer (PE : sig val edge_txt : edge -> string end) = struct
- 
-   let get_subgraph v =
-      let mk_subgraph name attrib =
--      let attrib = (`Style [`Filled]) :: attrib in
-+      let attrib = (`Style `Filled) :: attrib in
-           Some { Graph.Graphviz.DotAttributes.sg_name= name;
-                  sg_parent = None;
-                  sg_attributes = attrib }
--- 
diff --git a/sci-mathematics/frama-c/frama-c-20140301.ebuild b/sci-mathematics/frama-c/frama-c-20140301.ebuild
deleted file mode 100644
index 0d7376d21..000000000
--- a/sci-mathematics/frama-c/frama-c-20140301.ebuild
+++ /dev/null
@@ -1,69 +0,0 @@
-# Copyright 1999-2016 Gentoo Foundation
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=5
-
-inherit autotools eutils
-
-DESCRIPTION="Framework for analysis of source codes written in C"
-HOMEPAGE="http://frama-c.com"
-NAME="Neon"
-SRC_URI="http://frama-c.com/download/${PN/-c/-c-$NAME}-${PV/_/-}.tar.gz"
-
-LICENSE="LGPL-2"
-SLOT="0"
-KEYWORDS="~amd64"
-IUSE="doc gtk +ocamlopt"
-RESTRICT="strip"
-
-DEPEND="
-	>=dev-lang/ocaml-3.12.1[ocamlopt?]
-	>=dev-ml/ocamlgraph-1.8.5[gtk?,ocamlopt?]
-	dev-ml/zarith
-	sci-mathematics/coq
-	sci-mathematics/ltl2ba
-	sci-mathematics/alt-ergo
-	gtk? (
-		>=x11-libs/gtksourceview-2.8:2.0
-		>=gnome-base/libgnomecanvas-2.26
-		>=dev-ml/lablgtk-2.14[sourceview,gnomecanvas,ocamlopt?]
-	)"
-RDEPEND="${DEPEND}"
-
-S="${WORKDIR}/${PN/-c/-c-$NAME}-${PV/_/-}"
-
-src_prepare(){
-	touch config_file || die
-	rm -f ocamlgraph.tar.gz || die
-	epatch "${FILESDIR}/ocamlgraph185_compat.patch"
-	eautoreconf
-}
-
-src_configure(){
-	if use gtk; then
-		myconf="--enable-gui"
-	else
-		myconf="--disable-gui"
-	fi
-	econf ${myconf}
-}
-
-src_compile(){
-	# dependencies can not be processed in parallel,
-	# this is the intended behavior.
-	emake -j1 depend
-	emake all top DESTDIR="/"
-
-	if use doc; then
-		emake -j1 doc doc-tgz
-		tar -xzf frama-c-api.tar.gz -C doc/
-	fi
-}
-
-src_install(){
-	default
-
-	if use doc; then
-		dohtml -A svg -r doc/frama-c-api/*
-	fi
-}
diff --git a/sci-mathematics/frama-c/frama-c-22.0.ebuild b/sci-mathematics/frama-c/frama-c-22.0.ebuild
new file mode 100644
index 000000000..aaf815f4f
--- /dev/null
+++ b/sci-mathematics/frama-c/frama-c-22.0.ebuild
@@ -0,0 +1,61 @@
+# Copyright 1999-2021 Gentoo Authors
+# Distributed under the terms of the GNU General Public License v2
+
+EAPI=7
+
+inherit autotools
+
+NAME="Titanium"
+
+DESCRIPTION="Framework for analysis of source codes written in C"
+HOMEPAGE="https://frama-c.com"
+SRC_URI="https://frama-c.com/download/${P}-${NAME}.tar.gz"
+
+LICENSE="LGPL-2"
+SLOT="0"
+KEYWORDS="~amd64"
+
+IUSE="doc gtk +ocamlopt"
+RESTRICT="strip"
+
+DEPEND="
+	>=dev-lang/ocaml-3.12.1[ocamlopt?]
+	>=dev-ml/ocamlgraph-1.8.5[ocamlopt?]
+	dev-ml/zarith
+	dev-ml/yojson
+	sci-mathematics/coq
+	sci-mathematics/ltl2ba
+	sci-mathematics/alt-ergo
+	gtk? (
+		>=x11-libs/gtksourceview-2.8:2.0
+		>=gnome-base/libgnomecanvas-2.26
+		>=dev-ml/lablgtk-2.14[sourceview,gnomecanvas(-),ocamlopt?]
+	)"
+RDEPEND="${DEPEND}"
+
+S="${WORKDIR}/${P}-${NAME}"
+
+src_prepare(){
+	touch config_file || die
+	rm -f ocamlgraph.tar.gz || die
+	default
+	eautoreconf
+}
+
+src_configure(){
+	econf "$(use_enable gtk gui )"
+}
+
+src_compile(){
+	# dependencies can not be processed in parallel,
+	# this is the intended behavior.
+	emake depend
+	emake all top DESTDIR="/"
+
+	use doc && emake doc
+}
+
+src_install(){
+	default
+	use doc && dodoc -r doc/doxygen/html/*
+}
diff --git a/sci-mathematics/freefem++/Manifest b/sci-mathematics/freefem++/Manifest
index 1ab28a71b..cde77c554 100644
--- a/sci-mathematics/freefem++/Manifest
+++ b/sci-mathematics/freefem++/Manifest
@@ -1 +1 @@
-DIST freefem++-3.8.tar.gz 21848854 BLAKE2B 6d4c725d553be936a899a341ae74ee6672ee94fcf799a27f984eca839cef2d88be56172e24dc3de9216b68c5f1c791bcf98b5fbea5ac034c72481625e64340c3 SHA512 357dbbe1d5598da43ce2d6071bc939daac4c2b2f700879e8f9b47e68a15c95be030b69da48d49a097b02814d6596250cc5c2e50417bef23c2db2da6222909519
+DIST freefem++-4.10.tar.gz 12607380 BLAKE2B 2adcbcb48555c218bdec087b52b955fef7d2b8c0b17045be64d8acf9cde0910dd9c1a1856c046582e3d3e3024848db284cf8262f2e7c9a2e46024768f0dbad7a SHA512 768e8657884e92cd32f08ea82b3f384ed1522d1a693c6de95281fe1bf49e61d084d7d4d5c6c31f70a05ed95ba7cc0af75979242225466d06c2173176e862995e
diff --git a/sci-mathematics/freefem++/files/freefem++-acoptim.patch b/sci-mathematics/freefem++/files/freefem++-acoptim.patch
deleted file mode 100644
index 087b077cb..000000000
--- a/sci-mathematics/freefem++/files/freefem++-acoptim.patch
+++ /dev/null
@@ -1,17 +0,0 @@
---- freefem++-2.20-1/acoptim.m4	2006-01-27 16:51:16.000000000 +0100
-+++ freefem++-2.20-1.new/acoptim.m4	2007-11-14 18:50:37.000000000 +0100
-@@ -16,14 +16,6 @@
- AC_ARG_ENABLE(debug,[  --enable-debug	Turn on debug versions of FreeFem++])
- AC_ARG_ENABLE(optim,[  --enable-optim	Turn on compiler optimization])
- 
--# Autoconf always chooses -O2. -O2 in gcc makes some functions
--# disappear. This is not ideal for debugging. And when we optimize, we
--# do not use -O2 anyway.
--
--CFLAGS="`echo $CFLAGS | sed 's/-O2//g'`"
--FFLAGS="`echo $FFLAGS | sed 's/-O2//g'`"
--CXXFLAGS="`echo $CXXFLAGS | sed 's/-O2//g'`"
--
- if test "$enable_debug" = yes;
- then
- 	AC_MSG_RESULT(yes)
\ No newline at end of file
diff --git a/sci-mathematics/freefem++/files/freefem++-no-doc-autobuild.patch b/sci-mathematics/freefem++/files/freefem++-no-doc-autobuild.patch
deleted file mode 100644
index add003aea..000000000
--- a/sci-mathematics/freefem++/files/freefem++-no-doc-autobuild.patch
+++ /dev/null
@@ -1,30 +0,0 @@
-diff -urN freefem++-3.4.old/DOC/Makefile.am freefem++-3.4.new/DOC/Makefile.am
---- freefem++-3.4.old/DOC/Makefile.am	2009-07-15 17:19:57.000000000 +0200
-+++ freefem++-3.4.new/DOC/Makefile.am	2009-07-15 17:20:22.000000000 +0200
-@@ -1,4 +1,4 @@
--dist_pkgdata_DATA=$(DOCPDF)
-+all:
- documentation: $(DOCPDF) 
- docps:  $(DOCPS) $(DOCPSGZ) 
- docpdf: $(DOCPDF) 
-@@ -117,4 +117,4 @@
- 
- 
- # do not delete the copy figure to long to created 
--.PRECIOUS: $(CPFIGS_PDF) $(CPFIGS_EPS)
-\ No newline at end of file
-+.PRECIOUS: $(CPFIGS_PDF) $(CPFIGS_EPS)
-diff -urN freefem++-3.4.old/Makefile.am freefem++-3.4.new/Makefile.am
---- freefem++-3.4.old/Makefile.am	2009-07-15 17:19:57.000000000 +0200
-+++ freefem++-3.4.new/Makefile.am	2009-07-15 17:55:42.000000000 +0200
-@@ -147,10 +147,6 @@
- 
- # Native MacOS packaging
- # ----------------------
--install-exec-local:: 
--	$(mkinstalldirs) -m 755 $(DESTDIR)$(pkgdatadir)/$(VERSION)
--	tar cvf - $(FF_EXAMPLES_FILES)| (cd $(DESTDIR)$(pkgdatadir)/$(VERSION); tar xvf -)
--
- ListFiles-natives: .FORCE 
- #	echo COPYRIGHT HISTORY HISTORY_BEFORE_2005 README BUGS TODO INSTALL INSTALL-MacOSX INNOVATION >$@	
- #	echo mode-mi-edp.zip >> $@
diff --git a/sci-mathematics/freefem++/files/freefem++-path.patch b/sci-mathematics/freefem++/files/freefem++-path.patch
deleted file mode 100644
index bc30a238d..000000000
--- a/sci-mathematics/freefem++/files/freefem++-path.patch
+++ /dev/null
@@ -1,105 +0,0 @@
-diff -up freefem++-3.8/configure.ac.r freefem++-3.8/configure.ac
---- freefem++-3.8/configure.ac.r	2010-02-04 14:48:19.000000000 +0100
-+++ freefem++-3.8/configure.ac	2010-02-25 22:53:52.000000000 +0100
-@@ -353,7 +355,7 @@ AC_DEFINE_UNQUOTED(VersionFreeFempp,$ff_
- # date is only useful for config-version.h
- 
- test "$prefix" = NONE && prefix="$ac_default_prefix"
--ff_prefix_dir="${prefix}/lib/ff++/$VERSION"   
-+ff_prefix_dir="${libdir}/freefem++"
- AC_MSG_CHECKING(prefix dir freefem++  )
- AC_MSG_RESULT($ff_prefix_dir)	 
- 
-@@ -1250,7 +1252,7 @@ then
- 		AC_CHECK_LIB(umfpack,umf_i_malloc,
- 			ff_umfpack_libs=" -lumfpack $ff_umfpack_libs"
- 			ff_umfpack_ok=yes,,$ff_umfpack_libs)
--		if test "$ff_umfpack_ok" != yes -o "$ff_umfpack_header" != yes ; then
-+		if test "$ff_umfpack_ok" = yes -a "$ff_umfpack_header" != yes ; then
- 			AC_MSG_WARN([		Sorry we find UMFPACK lib but not the include umfpack.h file])
- 		fi
- 	fi	
-diff -up freefem++-3.8/examples++-3d/Makefile.am.r freefem++-3.8/examples++-3d/Makefile.am
---- freefem++-3.8/examples++-3d/Makefile.am.r	2009-11-10 20:28:06.000000000 +0100
-+++ freefem++-3.8/examples++-3d/Makefile.am	2010-02-25 22:41:45.000000000 +0100
-@@ -31,8 +31,8 @@ freefem++.pref:
- 	echo loadpath += \"./\" >>freefem++.pref
- 
- install-exec-local:: 
--	$(mkinstalldirs) -m 755 $(DESTDIR)$(ff_prefix_dir)/idp
--	$(INSTALL)  -m 555  $(LIST_IDP)  $(DESTDIR)$(ff_prefix_dir)/idp
-+	$(mkinstalldirs) -m 755 $(DESTDIR)$(datadir)/freefem++/idp
-+	$(INSTALL)  -m 555  $(LIST_IDP)  $(DESTDIR)$(datadir)/freefem++/idp
- 
- 
- 
-diff -up freefem++-3.8/examples++-load/load.link.in.r freefem++-3.8/examples++-load/load.link.in
---- freefem++-3.8/examples++-load/load.link.in.r	2009-12-04 15:53:45.000000000 +0100
-+++ freefem++-3.8/examples++-load/load.link.in	2010-02-25 22:41:45.000000000 +0100
-@@ -26,8 +26,8 @@ if [ -z "$INCFF" ] ; then
- 	INCFF="-Iinclude"
-     elif [ -f "FFAPPLI_INC/ff++.hpp" ] ; then 
- 	INCFF="-IFFAPPLI_INC" 
--    elif [ -f '@ff_prefix_dir@/include/ff++.hpp' ] ; then 
--	INCFF='-I@ff_prefix_dir@/include' 
-+    elif [ -f '@includedir@/freefem++/ff++.hpp' ] ; then
-+	INCFF='-I@includedir@/freefem++'
-     else
- 	ff=`which freefem++.exe`;
- 	ffinc=`dirname "$ff"`/examples++-load/include
-diff -up freefem++-3.8/examples++-load/Makefile.am.r freefem++-3.8/examples++-load/Makefile.am
---- freefem++-3.8/examples++-load/Makefile.am.r	2010-01-28 20:38:21.000000000 +0100
-+++ freefem++-3.8/examples++-load/Makefile.am	2010-02-25 23:13:32.000000000 +0100
-@@ -95,7 +95,7 @@ all.edp: 
- regtests.edp: regtests.m4 ../regtests.m4
- 	m4 -DASSERT regtests.m4 > regtests.edp
- 
--$(LIST_COMPILE):ff-c++ include Makefile 
-+$(LIST_COMPILE) $(LIST_COMPILE_PKG):ff-c++ include Makefile 
- 
- clean-local:
- 	-rm *.o  load.link WHERE_LIBRARY-download ff-get-dep ff-c++ ff-pkg-download \
-@@ -121,19 +121,19 @@ WHERE_LIBRARY-download:ff-pkg-download 
- freefem++.pref:
- 	echo loadpath = \"./\" >freefem++.pref
- install-exec-local:: load_compile
--	$(mkinstalldirs) -m 755 $(DESTDIR)$(ff_prefix_dir)/lib
--	$(mkinstalldirs) -m 755 $(DESTDIR)$(ff_prefix_dir)/include
--	$(mkinstalldirs) -m 755 $(DESTDIR)$(ff_prefix_dir)/etc
--	$(INSTALL_DATA)  include/* $(DESTDIR)$(ff_prefix_dir)/include
--	$(INSTALL)  -m 555 $(LIST_COMPILE) $(DESTDIR)$(ff_prefix_dir)/lib
--	echo loadpath += \"./\"  >$(DESTDIR)$(ff_prefix_dir)/etc/freefem++.pref
--	echo loadpath += \"$(ff_prefix_dir)/lib\"  >>$(DESTDIR)$(ff_prefix_dir)/etc/freefem++.pref
--	echo includepath += \"$(ff_prefix_dir)/idp\"  >>$(DESTDIR)$(ff_prefix_dir)/etc/freefem++.pref
-+	$(mkinstalldirs) -m 755 $(DESTDIR)$(libdir)/freefem++
-+	$(mkinstalldirs) -m 755 $(DESTDIR)$(includedir)/freefem++
-+	$(mkinstalldirs) -m 755 $(DESTDIR)$(sysconfdir)
-+	$(INSTALL_DATA)  include/* $(DESTDIR)$(includedir)/freefem++
-+	$(INSTALL)  -m 555 $(LIST_COMPILE) $(DESTDIR)$(libdir)/freefem++
-+	echo loadpath += \"./\"  >$(DESTDIR)$(sysconfdir)/freefem++.pref
-+	echo loadpath += \"$(libdir)/freefem++\"  >>$(DESTDIR)$(sysconfdir)/freefem++.pref
-+	echo includepath += \"$(datadir)/freefem++/idp\"  >>$(DESTDIR)$(sysconfdir)/freefem++.pref
- 	$(INSTALL_SCRIPT) ff-c++  $(DESTDIR)${bindir}
- 	$(INSTALL_SCRIPT) ff-pkg-download  $(DESTDIR)${bindir}
- 	$(INSTALL_SCRIPT) ff-get-dep  $(DESTDIR)${bindir}
- 	-for i in $(LIST_COMPILE_PKG); do \
--	 if [ -f $$i ] ; then 	$(INSTALL)  -m 555 $$i $(DESTDIR)$(ff_prefix_dir)/lib; fi; done
-+	 if [ -f $$i ] ; then 	$(INSTALL)  -m 555 $$i $(DESTDIR)$(libdir)/freefem++; fi; done
- 
- 
- 
-diff -up freefem++-3.8/src/lglib/Makefile.am.r freefem++-3.8/src/lglib/Makefile.am
---- freefem++-3.8/src/lglib/Makefile.am.r	2010-01-10 22:47:14.000000000 +0100
-+++ freefem++-3.8/src/lglib/Makefile.am	2010-02-25 22:41:45.000000000 +0100
-@@ -9,9 +9,9 @@ INCLUDES=-I../fflib -I../bamglib -I../Gr
- BUILT_SOURCES=lg.tab.hpp lg.tab.cpp
- 
- lg.tab.hpp  lg.tab.cpp: lg.ypp
--	-rm lg.tab.hpp  lg.tab.cpp lg.tab.cpp.h
-+	-rm -f lg.tab.hpp  lg.tab.cpp lg.tab.cpp.h
- 	bison -dtv -p lg  $< -o lg.tab.cpp
--	-mv lg.tab.cpp.h  lg.tab.hpp # pour un  pb entre des versions de bison 
-+	-mv -f lg.tab.cpp.h  lg.tab.hpp # pour un  pb entre des versions de bison 
- libfreefem++.dylib: lg.tab.o ../fflib/libff.a
- 	g++ -bundle lg.tab.o  ../fflib/libff.a $(UMFPACKLIB) $(ARPACKLIB) $(BLASLIB) $(LIBS) -o libfreefem++.dylib
- EXTRA_DIST=lg.ypp
diff --git a/sci-mathematics/freefem++/freefem++-3.8.ebuild b/sci-mathematics/freefem++/freefem++-3.8.ebuild
deleted file mode 100644
index 545301816..000000000
--- a/sci-mathematics/freefem++/freefem++-3.8.ebuild
+++ /dev/null
@@ -1,127 +0,0 @@
-# Copyright 1999-2015 Gentoo Foundation
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=5
-
-inherit autotools eutils flag-o-matic mpi versionator toolchain-funcs
-
-MY_PV=$(replace_version_separator 2 '-')
-
-DESCRIPTION="Solve PDEs using FEM on 2d and 3d domains"
-HOMEPAGE="http://www.freefem.org/ff++/"
-SRC_URI="http://www.freefem.org/ff++/ftp/old-v3/${PN}-${MY_PV}.tar.gz"
-
-LICENSE="LGPL-2.1"
-SLOT="0"
-KEYWORDS="~amd64"
-IUSE="doc examples mpi opengl X"
-
-RDEPEND="
-	sci-libs/fftw:3.0
-	virtual/cblas
-	virtual/lapack
-	sci-libs/umfpack
-	sci-libs/arpack
-	mpi? ( $(mpi_pkg_deplist) )
-	opengl? (
-		media-libs/freeglut
-		virtual/opengl
-		)
-	X? (
-		media-fonts/font-misc-misc
-		x11-libs/libX11
-		x11-libs/libXext
-		x11-libs/libXpm
-		x11-libs/libXxf86vm
-		)"
-
-DEPEND="${RDEPEND}
-	virtual/pkgconfig
-	doc? (
-		dev-texlive/texlive-latexrecommended
-		dev-texlive/texlive-latexextra
-		virtual/latex-base
-		media-gfx/imagemagick
-		)"
-
-S="${WORKDIR}/${PN}-${MY_PV}"
-
-src_prepare() {
-	# acoptim.m4 forced -O2 removal
-	epatch "${FILESDIR}"/${PN}-acoptim.patch
-	# do not try to do a forced "manual" installation of
-	# examples and documentation
-	epatch "${FILESDIR}"/${PN}-no-doc-autobuild.patch
-	# Honor FHS
-	epatch "${FILESDIR}"/${PN}-path.patch
-
-	eautoreconf
-}
-
-src_configure() {
-	local myconf
-
-	if use mpi; then
-		myconf="${myconf} --with-mpi=$(mpi_pkg_cxx)"
-	else
-		myconf="--without-mpi"
-	fi
-
-	econf \
-		--disable-download \
-		--disable-optim \
-		--enable-generic \
-		--with-blas="$($(tc-getPKG_CONFIG) --libs blas)" \
-		--with-lapack="$($(tc-getPKG_CONFIG) --libs lapack)" \
-		$(use_enable opengl) \
-		$(use_with X x) \
-		${myconf}
-}
-
-src_compile() {
-	default
-
-	if use doc; then
-		emake documentation
-	fi
-}
-
-src_test() {
-	if use mpi; then
-		# This may depend on the used MPI implementation. It is needed
-		# with mpich2, but should not be needed with lam-mpi or mpich
-		# (if the system is configured correctly).
-		ewarn "Please check that your MPI root ring is on before running"
-		ewarn "the test phase. Failing to start it before that phase may"
-		ewarn "result in a failing emerge."
-		epause
-	fi
-	emake -j1 check
-}
-
-src_install() {
-	default
-
-	insinto /usr/share/doc/${PF}
-	if use doc; then
-		doins DOC/freefem++doc.pdf
-	fi
-
-	if use examples; then
-		einfo "Installing examples..."
-
-		# Remove compiled examples:
-		emake clean
-
-		einfo "Some of the installed examples assumes that the user has write"
-		einfo "permissions in the working directory and other will look for"
-		einfo "data files in the working directory. For this reason in order to"
-		einfo "run the examples it's better to temporary copy them somewhere"
-		einfo "in the user folder. For example to run the tutorial examples"
-		einfo "it's better to copy the entire examples++-tutorial folder into"
-		einfo "the user directory."
-
-		rm -f examples*/Makefile* || die
-		doins -r examples*
-	fi
-}
diff --git a/sci-mathematics/freefem++/freefem++-4.10.ebuild b/sci-mathematics/freefem++/freefem++-4.10.ebuild
new file mode 100644
index 000000000..5791c4bf6
--- /dev/null
+++ b/sci-mathematics/freefem++/freefem++-4.10.ebuild
@@ -0,0 +1,99 @@
+# Copyright 1999-2022 Gentoo Authors
+# Distributed under the terms of the GNU General Public License v2
+
+EAPI=8
+
+inherit autotools toolchain-funcs
+
+DESCRIPTION="Solve PDEs using FEM on 2d and 3d domains"
+HOMEPAGE="https://freefem.org/"
+SRC_URI="https://github.com/FreeFem/FreeFem-sources/archive/v${PV}.tar.gz -> ${P}.tar.gz"
+S="${WORKDIR}/FreeFem-sources-${PV}"
+
+LICENSE="LGPL-2.1"
+SLOT="0"
+KEYWORDS="~amd64"
+IUSE="examples mpi opengl X"
+
+RDEPEND="
+	sci-libs/fftw:3.0
+	virtual/cblas
+	virtual/lapack
+	sci-libs/umfpack
+	sci-libs/arpack
+	sci-libs/hdf5[cxx]
+	mpi? ( virtual/mpi )
+	opengl? (
+		media-libs/freeglut
+		virtual/opengl
+		)
+	X? (
+		media-fonts/font-misc-misc
+		x11-libs/libX11
+		x11-libs/libXext
+		x11-libs/libXpm
+		x11-libs/libXxf86vm
+		)"
+
+DEPEND="${RDEPEND}"
+BDEPEND="virtual/pkgconfig"
+
+src_prepare() {
+	default
+
+	eautoreconf
+}
+
+src_configure() {
+	local myconf
+
+	if use mpi; then
+		myconf="${myconf} --with-mpi=/usr/bin/mpi"
+	else
+		myconf="--without-mpi"
+	fi
+
+	econf \
+		--disable-download \
+		--disable-optim \
+		--enable-generic \
+		--with-blas="$($(tc-getPKG_CONFIG) --libs blas)" \
+		--with-lapack="$($(tc-getPKG_CONFIG) --libs lapack)" \
+		$(use_enable opengl) \
+		${myconf}
+}
+
+src_test() {
+	if use mpi; then
+		# This may depend on the used MPI implementation. It is needed
+		# with mpich2, but should not be needed with lam-mpi or mpich
+		# (if the system is configured correctly).
+		ewarn "Please check that your MPI root ring is on before running"
+		ewarn "the test phase. Failing to start it before that phase may"
+		ewarn "result in a failing emerge."
+		epause
+	fi
+	emake -j1 check
+}
+
+src_install() {
+	default
+
+	if use examples; then
+		einfo "Installing examples..."
+
+		# Remove compiled examples:
+		emake clean
+
+		einfo "Some of the installed examples assumes that the user has write"
+		einfo "permissions in the working directory and other will look for"
+		einfo "data files in the working directory. For this reason in order to"
+		einfo "run the examples it's better to temporary copy them somewhere"
+		einfo "in the user folder. For example to run the tutorial examples"
+		einfo "it's better to copy the entire examples++-tutorial folder into"
+		einfo "the user directory."
+
+		rm -f examples*/Makefile* || die
+		doins -r examples*
+	fi
+}
diff --git a/sci-mathematics/freefem++/metadata.xml b/sci-mathematics/freefem++/metadata.xml
index a605d78d7..5cee338ce 100644
--- a/sci-mathematics/freefem++/metadata.xml
+++ b/sci-mathematics/freefem++/metadata.xml
@@ -10,4 +10,7 @@ FreeFem++ is an implementation of a language dedicated to the finite
 element method. It enables you to solve Partial Differential Equations
 (PDE) easily.
 </longdescription>
+	<upstream>
+		<remote-id type="github">FreeFem/FreeFem-sources</remote-id>
+	</upstream>
 </pkgmetadata>
diff --git a/sci-mathematics/gap/Manifest b/sci-mathematics/gap/Manifest
deleted file mode 100644
index 9ee58f2a4..000000000
--- a/sci-mathematics/gap/Manifest
+++ /dev/null
@@ -1,2 +0,0 @@
-DIST gap4r4p12.tar.bz2 47715810 BLAKE2B a1b3dfa34b62cf62de34cc8513d12d692ccd8345c35afcc3c4175ed629bec7a737c41958d9c85ee6fe6105ac169e5e56b60b23cb396569049521292075082608 SHA512 2b97e8678a34ba4e90b47d90cefe426dbb68f9c0fbb984b6552a069481bfe370fdc0e0646b58d18ee414055980e25391d92bc3cab8de962a38ae9e66c7314034
-DIST xtom1r1p4.tar.bz2 4817504 BLAKE2B cc0bfb0afd5eaa78595a163a391c07c360df2dd3c4eb3d2d856dab623f3e53888bbc54b623093c08d1c9e9e09c760bb7c1b93dcc02c98ea4198bdb202a781741 SHA512 d24b2aa6d42e8080e235620a3ecc39dcf4b02d3a2713f1eada33adabcb4c3af3d9cbf9aace0f6e15f085692c2248b820091acce0199c66777458805fa44fcec1
diff --git a/sci-mathematics/gap/files/64gap-gentoo.el b/sci-mathematics/gap/files/64gap-gentoo.el
deleted file mode 100644
index 24756c0b1..000000000
--- a/sci-mathematics/gap/files/64gap-gentoo.el
+++ /dev/null
@@ -1,10 +0,0 @@
-;; gap mode
-(autoload 'gap-mode "gap-mode" "Gap editing mode" t)
-(setq auto-mode-alist (append (list '("\\.g$" . gap-mode)
-                                    '("\\.gap$" . gap-mode))
-                              auto-mode-alist))
-(autoload 'gap "gap-process" "Run GAP in emacs buffer" t)
-
-(setq gap-executable "/usr/bin/gap")
-(setq gap-start-options ())
-;; end gap mode
diff --git a/sci-mathematics/gap/gap-4.4.12.ebuild b/sci-mathematics/gap/gap-4.4.12.ebuild
deleted file mode 100644
index 5cd6089e6..000000000
--- a/sci-mathematics/gap/gap-4.4.12.ebuild
+++ /dev/null
@@ -1,79 +0,0 @@
-# Copyright 1999-2015 Gentoo Foundation
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=5
-
-inherit elisp-common versionator
-
-XTOM_VERSION=1r1p4
-
-PV1=$(get_version_component_range 1-2 )
-PV2=$(get_version_component_range 3 )
-PV1=$(replace_version_separator 1 'r' ${PV1} )
-PV2=${PV1}p${PV2}
-
-DESCRIPTION="System for computational discrete algebra"
-HOMEPAGE="http://www.gap-system.org/"
-SRC_URI="
-	ftp://ftp.gap-system.org/pub/gap/gap44/tar.bz2/${PN}${PV2}.tar.bz2
-	xtom? ( ftp://ftp.gap-system.org/pub/gap/gap44/tar.bz2/xtom${XTOM_VERSION}.tar.bz2 )"
-
-SLOT="0"
-IUSE="emacs vim-syntax xtom"
-LICENSE="GPL-2"
-KEYWORDS="~amd64 ~x86"
-
-RDEPEND="
-	emacs? ( virtual/emacs )
-	vim-syntax? ( || ( app-editors/vim app-editors/gvim ) )"
-DEPEND="${RDEPEND}"
-
-S="${WORKDIR}"/${PN}${PV1}
-
-src_compile() {
-	emake CFLAGS="${CFLAGS}" LDFLAGS="${LDFLAGS}" compile
-}
-
-src_test() {
-	emake teststandard
-}
-
-src_install() {
-	dodoc README description*
-	insinto /usr/share/${PN}
-	doins -r doc grp lib pkg prim small trans tst sysinfo.gap
-	source sysinfo.gap
-	exeinto /usr/libexec/${PN}
-	doexe bin/${GAParch}/gap
-	sed -e "s|@gapdir@|/usr/share/${PN}|" \
-		-e "s|@target@-@CC@|/usr/libexec/${PN}|" \
-		-e "s|@EXEEXT@||" \
-		-e 's|$GAP_DIR/bin/||' \
-		gap.shi > gap || doe
-	dobin gap
-
-	if use emacs ; then
-		elisp-site-file-install etc/emacs/gap-mode.el
-		elisp-site-file-install etc/emacs/gap-process.el
-		elisp-site-file-install "${FILESDIR}"/64gap-gentoo.el
-		dodoc etc/emacs/gap-mode.doc
-	fi
-
-	if use vim-syntax ; then
-		insinto /usr/share/vim/vimfiles/syntax
-		doins etc/gap.vim
-		insinto /usr/share/vim/vimfiles/indent
-		newins etc/gap_indent.vim gap.vim
-		insinto /usr/share/vim/vimfiles/plugin
-		newins etc/debug.vim debug_gap.vim
-		dodoc etc/README.vim-utils etc/debugvim.txt
-	fi
-}
-
-pkg_postinst() {
-	use emacs && elisp-site-regen
-}
-
-pkg_postrm() {
-	use emacs && elisp-site-regen
-}
diff --git a/sci-mathematics/gap/metadata.xml b/sci-mathematics/gap/metadata.xml
deleted file mode 100644
index 2d5c1a14d..000000000
--- a/sci-mathematics/gap/metadata.xml
+++ /dev/null
@@ -1,25 +0,0 @@
-<?xml version="1.0" encoding="UTF-8"?>
-<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
-<pkgmetadata>
-	<maintainer type="person">
-		<email>A.G.Grozin@inp.nsk.su</email>
-		<name>Andrey Grozin</name>
-	</maintainer>
-	<maintainer type="project">
-		<email>sci-mathematics@gentoo.org</email>
-		<name>Gentoo Mathematics Project</name>
-	</maintainer>
-	<longdescription lang="en">
-Groups, Algorithms, Programming is a system for computational
-discrete algebra, with particular emphasis on Computational Group
-Theory. GAP provides a  programming language, a library of thousands
-of functions implementing algebraic algorithms written in the GAP
-language as well as large data libraries of algebraic objects. GAP
-is used in research and teaching for studying groups and their
-representations, rings, vector spaces, algebras, combinatorial
-structures, and more.
-</longdescription>
-	<use>
-		<flag name="xtom">Automatically generated description for xtom</flag>
-	</use>
-</pkgmetadata>
diff --git a/sci-mathematics/gappa/Manifest b/sci-mathematics/gappa/Manifest
deleted file mode 100644
index 416caf81e..000000000
--- a/sci-mathematics/gappa/Manifest
+++ /dev/null
@@ -1 +0,0 @@
-DIST gappa-1.1.1.tar.gz 399606 BLAKE2B 761439b96885434f42f57c253313b4cf8130bff6cc313a62480984d31bc3688c690da6ec688dcb97cb9f2d62533bccaa646d4df67222d8237cf06bdc314ba321 SHA512 95b01733554585729d73078522720f0c318f6e86eec02b869717e591bd1477a663c8f71d6c9362f8d5ec83d0a856be5771a27add426d8ac0eca429c4ded01a0e
diff --git a/sci-mathematics/gappa/gappa-1.1.1.ebuild b/sci-mathematics/gappa/gappa-1.1.1.ebuild
deleted file mode 100644
index 29de6ffa5..000000000
--- a/sci-mathematics/gappa/gappa-1.1.1.ebuild
+++ /dev/null
@@ -1,39 +0,0 @@
-# Copyright 1999-2015 Gentoo Foundation
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=5
-
-DESCRIPTION="Verifying and proving properties on floating-point or fixed-point arithmetic"
-HOMEPAGE="http://gappa.gforge.inria.fr/"
-SRC_URI="http://gforge.inria.fr/frs/download.php/33486/${P}.tar.gz"
-
-LICENSE="|| ( CeCILL-2.0 GPL-2 )"
-SLOT="0"
-KEYWORDS="~amd64 ~x86"
-IUSE="doc"
-
-RDEPEND="
-	dev-libs/gmp:0=
-	dev-libs/mpfr:0=
-	dev-libs/boost"
-DEPEND="${RDEPEND}
-	doc? ( app-doc/doxygen )"
-
-src_prepare() {
-	sed -i Remakefile.in \
-		-e "s:mkdir -p @bindir@:mkdir -p \${DESTDIR}@bindir@:g" \
-		-e "s:cp src/gappa @bindir@:cp src/gappa \${DESTDIR}@bindir@:g"
-}
-
-src_compile() {
-	./remake -d ${MAKEOPTS} || die "emake failed"
-	if use doc; then
-		./remake doc/html/index.html
-	fi
-}
-
-src_install() {
-	DESTDIR="${D}" ./remake install
-	dodoc NEWS README AUTHORS ChangeLog
-	use doc && dohtml -A png -r doc/html/*
-}
diff --git a/sci-mathematics/gappa/metadata.xml b/sci-mathematics/gappa/metadata.xml
deleted file mode 100644
index 448d16798..000000000
--- a/sci-mathematics/gappa/metadata.xml
+++ /dev/null
@@ -1,15 +0,0 @@
-<?xml version="1.0" encoding="UTF-8"?>
-<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
-<pkgmetadata>
-	<maintainer type="project">
-		<email>sci-mathematics@gentoo.org</email>
-		<name>Gentoo Mathematics Project</name>
-	</maintainer>
-	<longdescription>
-Gappa is a tool intended to help verifying and formally proving
-properties on numerical programs dealing with floating-point or
-fixed-point arithmetic. It has been used to write robust floating-point
-filters for CGAL and it is used to certify elementary functions in
-CRlibm.
-</longdescription>
-</pkgmetadata>
diff --git a/sci-mathematics/gappalib-coq/Manifest b/sci-mathematics/gappalib-coq/Manifest
deleted file mode 100644
index d3808c01f..000000000
--- a/sci-mathematics/gappalib-coq/Manifest
+++ /dev/null
@@ -1 +0,0 @@
-DIST gappalib-coq-1.0.0.tar.gz 118901 BLAKE2B a72ae81f8003bd0e4fd58e57cd10612d5cea4657d4d1c59a17ef04075aed5de0ee836c632e904024553f912a8c52b221ed79d62377686fea5fe1c3b4982b98f5 SHA512 1aed7eafc24d82fbb3431e267ae0882560b34864f443fa95b450f465fe571cae558bc0ddf31db96477092518dd20a9870a9f8360ad8a0b3967d6f912c2bd0b67
diff --git a/sci-mathematics/gappalib-coq/gappalib-coq-1.0.0.ebuild b/sci-mathematics/gappalib-coq/gappalib-coq-1.0.0.ebuild
deleted file mode 100644
index 6aef54089..000000000
--- a/sci-mathematics/gappalib-coq/gappalib-coq-1.0.0.ebuild
+++ /dev/null
@@ -1,33 +0,0 @@
-# Copyright 1999-2014 Gentoo Foundation
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=5
-
-DESCRIPTION="Allows the certificates Gappa generates to be imported by the Coq"
-HOMEPAGE="http://gappa.gforge.inria.fr/"
-SRC_URI="http://gforge.inria.fr/frs/download.php/32743/${P}.tar.gz"
-
-LICENSE="LGPL-2"
-SLOT="0"
-KEYWORDS="~amd64 ~x86"
-IUSE=""
-
-DEPEND="sci-mathematics/gappa
-		sci-mathematics/coq
-		sci-mathematics/flocq"
-RDEPEND="${DEPEND}"
-
-src_prepare() {
-	sed -i Remakefile.in \
-		-e "s:mkdir -p @libdir@:mkdir -p \${DESTDIR}@libdir@:g" \
-		-e "s:cp \$(OBJS) \$(MLTARGETS) @libdir@:cp \$(OBJS) \$(MLTARGETS) \${DESTDIR}@libdir@:g"
-}
-
-src_compile() {
-	./remake || die "emake failed"
-}
-
-src_install() {
-	DESTDIR="${D}" ./remake install || die "emake install failed"
-	dodoc NEWS README AUTHORS ChangeLog
-}
diff --git a/sci-mathematics/gappalib-coq/metadata.xml b/sci-mathematics/gappalib-coq/metadata.xml
deleted file mode 100644
index 182ed0520..000000000
--- a/sci-mathematics/gappalib-coq/metadata.xml
+++ /dev/null
@@ -1,13 +0,0 @@
-<?xml version="1.0" encoding="UTF-8"?>
-<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
-<pkgmetadata>
-	<maintainer type="project">
-		<email>sci-mathematics@gentoo.org</email>
-		<name>Gentoo Mathematics Project</name>
-	</maintainer>
-	<longdescription>
-While Gappa is intended to be used directly, it can also act as a
-backend prover for the Why software verification plateform or as an
-automatic tactic for the Coq proof assistant.
-</longdescription>
-</pkgmetadata>
diff --git a/sci-mathematics/giac/Manifest b/sci-mathematics/giac/Manifest
deleted file mode 100644
index e523daca1..000000000
--- a/sci-mathematics/giac/Manifest
+++ /dev/null
@@ -1 +0,0 @@
-DIST giac-1.1.0.tar.bz2 43295079 SHA256 8d4f96a577d526caa201d8311f462828b92eead2938b00e563b208b4e255a340 SHA512 2b34c7913a6a24aa770094bc839c01f7f3d16689ed9673d56b72ce39d07004e20218e039c85fb15e9f39f5f9e6993e6cfff62e755997f1107cddf7e601658434 WHIRLPOOL ca761a1f2bd6ad88655a079a29f54344d101542ba7a0c09fe7d8e0077e36ab06235341210a7b2a0ef98d09d416756be2725b9cc7be676957eaa199a67d67e375
diff --git a/sci-mathematics/giac/giac-1.1.0.ebuild b/sci-mathematics/giac/giac-1.1.0.ebuild
deleted file mode 100644
index 520a56151..000000000
--- a/sci-mathematics/giac/giac-1.1.0.ebuild
+++ /dev/null
@@ -1,74 +0,0 @@
-# Copyright 1999-2016 Gentoo Foundation
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=5
-
-DESCRIPTION="A free C++ CAS (Computer Algebra System) library and its interfaces"
-HOMEPAGE="http://www-fourier.ujf-grenoble.fr/~parisse/giac.html"
-SRC_URI="http://www-fourier.ujf-grenoble.fr/~parisse/${PN}/${P}.tar.bz2"
-LICENSE="GPL-2"
-
-SLOT="0"
-KEYWORDS="~amd64 ~x86"
-IUSE="doc examples fltk"
-
-AUTOTOOLS_IN_SOURCE_BUILD=true
-inherit autotools-utils flag-o-matic pax-utils
-
-RDEPEND=">=dev-libs/gmp-3
-		>=sys-libs/readline-4.2
-		fltk? ( >=x11-libs/fltk-1.1.9 )
-		dev-libs/mpfr
-		sci-libs/gsl
-		>=sci-mathematics/pari-2.3
-		>=dev-libs/ntl-5.2"
-
-src_prepare(){
-	sed -e "s:\$(prefix)/share:\$(DESTDIR)\$(prefix)/share:g" \
-		-e "s:config.h \$(includedir)/giac:config.h \$(DESTDIR)\$(includedir)/giac:g" \
-		-e "s:\$(DESTDIR)\$(DESTDIR):\$(DESTDIR):g"	\
-		-e "s:\$(DESTDIR)/\$(DESTDIR):\$(DESTDIR):g" \
-		-i `find -name Makefile\*` || die
-	if use !fltk; then
-		sed -e "s: gl2ps\.[chlo]*::g" -i src/Makefile.* || die
-	fi
-}
-
-src_configure(){
-	if use fltk
-	then
-		append-cppflags -I$(fltk-config --includedir)
-		append-lfs-flags
-		append-libs $(fltk-config --ldflags | sed -e 's/\(-L\S*\)\s.*/\1/') || die
-	fi
-	local myeconfargs=(
-		$(use_enable fltk gui)
-	)
-	autotools-utils_src_configure
-}
-
-src_install() {
-	emake install DESTDIR="${D}"
-	dobin src/aide
-	rm "${D}"/usr/bin/*cas_help || die
-	dodoc AUTHORS ChangeLog INSTALL NEWS README TROUBLES
-	if use !fltk; then
-		rm "${D}"/usr/bin/x* || die
-	elif host-is-pax; then
-		pax-mark -m "${D}"/usr/bin/x*
-	fi
-	if use !doc; then
-		rm -R "${D}"/usr/share/doc "${D}"/usr/share/giac/doc/ || die
-	else
-		for LANG in el en es fr pt; do
-			if echo ${LINGUAS} | grep -v "$LANG" &> /dev/null; then
-				rm -R "${D}"/usr/share/giac/doc/"$LANG"
-			else
-				ln "${D}"/usr/share/giac/doc/aide_cas "${D}"/usr/share/giac/doc/"$LANG"/aide_cas || die
-			fi
-		done
-	fi
-	if use !examples; then
-		rm -R "${D}"/usr/share/giac/examples || die
-	fi
-}
diff --git a/sci-mathematics/giac/metadata.xml b/sci-mathematics/giac/metadata.xml
deleted file mode 100644
index 60502e1d7..000000000
--- a/sci-mathematics/giac/metadata.xml
+++ /dev/null
@@ -1,15 +0,0 @@
-<?xml version="1.0" encoding="UTF-8"?>
-<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
-<pkgmetadata>
-	<maintainer type="project">
-		<email>sci-mathematics@gentoo.org</email>
-		<name>Gentoo Mathematics Project</name>
-	</maintainer>
-	<longdescription>
-Giac is a free computer algebra system that can be used to perform
-computer algebra, function graphs, interactive geometry (2-d and 3-d),
-spreadsheet and statistics, programmation. It may be used as a replacement
-for high end graphic calculators for example on netbooks (for about
-the same price as a calculator but with much more performances).
-</longdescription>
-</pkgmetadata>
diff --git a/sci-mathematics/htk/Manifest b/sci-mathematics/htk/Manifest
deleted file mode 100644
index c9f41b030..000000000
--- a/sci-mathematics/htk/Manifest
+++ /dev/null
@@ -1,2 +0,0 @@
-DIST HDecode-3.4.1.tar.gz 101930 SHA256 9517b25a91200e3e84ebed0d615f73715196dbfaf32ef854c2e964442175bee5
-DIST HTK-3.4.1.tar.gz 2101024 SHA256 42297b036ce3a47adeab26aaa42f51ac4b370ead7f53bab75fd27a52d38ae5ac
diff --git a/sci-mathematics/htk/files/include_make_destdir.patch b/sci-mathematics/htk/files/include_make_destdir.patch
deleted file mode 100644
index 55ea2c773..000000000
--- a/sci-mathematics/htk/files/include_make_destdir.patch
+++ /dev/null
@@ -1,73 +0,0 @@
-diff -Naur htk.old//HLMTools/Makefile.in htk//HLMTools/Makefile.in
---- htk.old//HLMTools/Makefile.in	2009-03-11 07:07:18.000000000 -0300
-+++ htk//HLMTools/Makefile.in	2011-09-02 18:46:15.452348315 -0300
-@@ -71,9 +71,9 @@
- 	-rm -f *.o $(PROGS) Makefile *.exe
- 
- install: mkinstalldir $(PROGS)
--	for program in $(PROGS) ; do $(INSTALL) -m 755 $${program}@BINARY_EXTENSION@ $(bindir) ; done
-+	for program in $(PROGS) ; do $(INSTALL) -m 755 $${program}@BINARY_EXTENSION@ $(DESTDIR)$(bindir) ; done
- 
- mkinstalldir:
--        if [ ! -d $(bindir) -a X_@TRADHTK@ = X_yes ] ; then mkdir -p $(bindir) ; fi
-+	if [ ! -d $(DESTDIR)$(bindir) -a X_@TRADHTK@ = X_yes ] ; then mkdir -p $(DESTDIR)$(bindir) ; fi
- 
- .PHONY: all strip clean cleanup distclean install mkinstalldir
-diff -Naur htk.old//HTKLVRec/Makefile.in htk//HTKLVRec/Makefile.in
---- htk.old//HTKLVRec/Makefile.in	2009-03-11 06:56:05.000000000 -0300
-+++ htk//HTKLVRec/Makefile.in	2011-09-02 18:44:40.072737063 -0300
-@@ -112,11 +112,11 @@
- 	-rm -f *.o HDecode HDecode.mod Makefile
- 
- install: mkinstalldir
--	$(INSTALL) -m 755 HDecode $(bindir)
--	$(INSTALL) -m 755 HDecode.mod $(bindir)
-+	$(INSTALL) -m 755 HDecode $(DESTDIR)$(bindir)
-+	$(INSTALL) -m 755 HDecode.mod $(DESTDIR)$(bindir)
- 
- mkinstalldir:
--	-mkdir -p $(bindir)
-+	-mkdir -p $(DESTDIR)$(bindir)
- 
- .PHONY: std mod all strip clean cleanup distclean install mkinstalldir
- 
-diff -Naur htk.old//HTKTools/Makefile.in htk//HTKTools/Makefile.in
---- htk.old//HTKTools/Makefile.in	2009-03-11 09:50:53.000000000 -0300
-+++ htk//HTKTools/Makefile.in	2011-09-02 18:45:41.423059972 -0300
-@@ -73,10 +73,10 @@
- 	-rm -f *.o $(PROGS) *.exe Makefile
- 
- install: mkinstalldir $(PROGS)
--	for program in $(PROGS) ; do $(INSTALL) -m 755 $${program} $(bindir) ; done
-+	for program in $(PROGS) ; do $(INSTALL) -m 755 $${program} $(DESTDIR)$(bindir) ; done
- 
- mkinstalldir:
--	if [ ! -d $(bindir) ] ; then mkdir $(bindir) ; fi
-+	if [ ! -d $(DESTDIR)$(bindir) ] ; then mkdir -p $(DESTDIR)$(bindir) ; fi
- 
- 
- .PHONY: all strip clean cleanup distclean install mkinstalldir
-diff -Naur htk.old//Makefile.in htk//Makefile.in
---- htk.old//Makefile.in	2009-03-11 07:08:06.000000000 -0300
-+++ htk//Makefile.in	2011-09-02 18:44:40.073737098 -0300
-@@ -119,16 +119,16 @@
- 
- # installation
- install-htktools: htktools
--	(cd $(HTKTOOLS) && $(MAKE) install) \
-+	(cd $(HTKTOOLS) && $(MAKE) DESTDIR=$(DESTDIR) install) \
- 	|| case "$(MFLAGS)" in *k*) fail=yes;; *) exit 1;; esac;
- install-hlmtools: hlmtools
--	(cd $(HLMTOOLS) && $(MAKE) install) \
-+	(cd $(HLMTOOLS) && $(MAKE) DESTDIR=$(DESTDIR) install) \
- 	|| case "$(MFLAGS)" in *k*) fail=yes;; *) exit 1;; esac;
- install-hdecode:
--	(cd $(LVREC) && $(MAKE) install) \
-+	(cd $(LVREC) && $(MAKE) DESTDIR=$(DESTDIR) install) \
- 	|| case "$(MFLAGS)" in *k*) fail=yes;; *) exit 1;; esac;
- install-book: book
--	(cd $(HTKBOOK) && $(MAKE) install) \
-+	(cd $(HTKBOOK) && $(MAKE) DESTDIR=$(DESTDIR) install) \
- 	|| case "$(MFLAGS)" in *k*) fail=yes;; *) exit 1;; esac;
- 
- clean:
diff --git a/sci-mathematics/htk/htk-3.4.1.ebuild b/sci-mathematics/htk/htk-3.4.1.ebuild
deleted file mode 100644
index 08da48a4b..000000000
--- a/sci-mathematics/htk/htk-3.4.1.ebuild
+++ /dev/null
@@ -1,55 +0,0 @@
-# Copyright 1999-2015 Gentoo Foundation
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=5
-
-inherit eutils
-
-DESCRIPTION="Toolkit for building and manipulating hidden Markov models"
-HOMEPAGE="http://htk.eng.cam.ac.uk/"
-SRC_URI="
-	http://htk.eng.cam.ac.uk/ftp/software/HTK-3.4.1.tar.gz -> HTK-3.4.1.tar.gz
-	hdecode? (
-		http://htk.eng.cam.ac.uk/ftp/software/hdecode/HDecode-3.4.1.tar.gz -> HDecode-3.4.1.tar.gz
-	)"
-HDECODE_HOME="http://htk.eng.cam.ac.uk/extensions/index.shtml"
-
-LICENSE="HTKCambridge hdecode? ( HDecodeCambridge )"
-SLOT="0"
-KEYWORDS="~amd64"
-IUSE="-hlmtools -hslab -htkbook -hdecode"
-
-RESTRICT="fetch"
-
-S="${WORKDIR}/${PN}"
-
-pkg_nofetch() {
-	elog "Please download"
-	elog "  - HTK-3.4.1.tar.gz"
-	elog "from ${HOMEPAGE}"
-	if use hdecode; then
-		elog "  - HDecode-3.4.1.tar.gz"
-		elog "from ${HDECODE_HOME}"
-	fi
-	elog "and place them in ${DISTDIR}"
-}
-
-src_prepare() {
-	epatch "${FILESDIR}/include_make_destdir.patch"
-}
-
-src_configure() {
-	econf \
-		$(use_enable hlmtools) \
-		$(use_enable hslab) \
-		$(use_enable htkbook) \
-		$(use_enable hdecode)
-}
-
-src_compile() {
-	if use hlmtools || use hdecode; then
-		emake -j1
-	else
-		default
-	fi
-}
diff --git a/sci-mathematics/htk/metadata.xml b/sci-mathematics/htk/metadata.xml
deleted file mode 100644
index c948fe4f4..000000000
--- a/sci-mathematics/htk/metadata.xml
+++ /dev/null
@@ -1,19 +0,0 @@
-<?xml version="1.0" encoding="UTF-8"?>
-<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
-<pkgmetadata>
-	<maintainer type="person">
-		<email>pedosb@gmail.com</email>
-		<name>Pedro Batista</name>
-	</maintainer>
-	<maintainer type="project">
-		<email>sci-mathematics@gentoo.org</email>
-		<name>Gentoo Mathematics Project</name>
-	</maintainer>
-	<longdescription>The Hidden Markov Model Toolkit (HTK) is a portable toolkit for building and manipulating hidden Markov models</longdescription>
-	<use>
-		<flag name="hlmtools">Install the tools for manipulation of language models</flag>
-		<flag name="hdecode">Install HDecode, a large vocabulary word recogniser</flag>
-		<flag name="htkbook">Build the HTK documentation (HTK Book)</flag>
-		<flag name="hslab">Install HSLab a label editor for speech label manipulation</flag>
-	</use>
-</pkgmetadata>
diff --git a/sci-mathematics/kash-bin/Manifest b/sci-mathematics/kash-bin/Manifest
deleted file mode 100644
index 79cf5b878..000000000
--- a/sci-mathematics/kash-bin/Manifest
+++ /dev/null
@@ -1,2 +0,0 @@
-DIST KASH3-Linux-i686-2008-07-31.tar.bz2 17334852 BLAKE2B c2167825c7c3db866c4d7bfce4f6d7facc86203d094af9cadc54a0546408c307bf5b2b2b588303a2da4e6a318de4af4881935c12323abb0fa752f473532159d5 SHA512 7366692e8bca6dca0e706d9ecbd2466115fd0c5bf6d9614a26aedd309f50ec98fed5c6a34688f8733d6f9ec5bc917ed149b642ec5e1706bab8bc66a4b091557e
-DIST KASH3-lib-archindep-2008-07-31.tar.bz2 3367591 BLAKE2B 55f7062ed117ade7e031a2aac52277d5fb312bd0b62a134d3a606aefb70c43f22213ca7e58baa203696af9c8145cacf15a3b2846203a9e2defed306ebdf38858 SHA512 f7a3318bf57b4dbd41f88e2405252828a3e4cc00f52b7e9363c5657e8213a2b158b4f8127eb30734c14b2b87c94daf932ca8dc6b832bd4f1b9ba9b3c4f5ee93b
diff --git a/sci-mathematics/kash-bin/kash-bin-3.ebuild b/sci-mathematics/kash-bin/kash-bin-3.ebuild
deleted file mode 100644
index 29ddbe0df..000000000
--- a/sci-mathematics/kash-bin/kash-bin-3.ebuild
+++ /dev/null
@@ -1,46 +0,0 @@
-# Copyright 1999-2015 Gentoo Foundation
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=5
-
-# inherit eutils
-
-DESCRIPTION="software package for algebraic number theory"
-HOMEPAGE="http://page.math.tu-berlin.de/~kant/kash.html"
-SRC_URI="
-	ftp://ftp.math.tu-berlin.de/pub/algebra/Kant/Kash_3/KASH3-Linux-i686-2008-07-31.tar.bz2
-	ftp://ftp.math.tu-berlin.de/pub/algebra/Kant/Kash_3/KASH3-lib-archindep-2008-07-31.tar.bz2"
-
-LICENSE="kash"
-SLOT="0"
-KEYWORDS="~amd64 ~x86 ~amd64-linux ~x86-linux"
-IUSE=""
-
-MY_P="kash3"
-S="${WORKDIR}/${MY_P}"
-
-# This is a binary package:
-QA_PREBUILT="opt/${MY_P}/kash3"
-
-src_unpack() {
-	default
-	mkdir "${S}" && cd "${S}" || die
-	mv KASH3-Linux*/* "${S}" || die
-	mv KASH3-lib*/lib/* "${S}/lib/" || die
-}
-
-# Binary package
-# src_configure() { : }
-#
-# src_compile() { : }
-#
-src_install() {
-	cat > kash3.sh <<- EOF
-	#!"${EPREFIX}/bin/sh"
-	/opt/${MY_P}/kash3 -l "${EROOT}opt/${MY_P}/lib"
-	EOF
-	chmod 755 kash3.sh
-	dodir /opt/${MY_P}
-	cp -R "${S}/" "${ED}"opt/ || die
-	dosym ../${MY_P}/kash3.sh /opt/bin/kash3
-}
diff --git a/sci-mathematics/kash-bin/metadata.xml b/sci-mathematics/kash-bin/metadata.xml
deleted file mode 100644
index fc53f2207..000000000
--- a/sci-mathematics/kash-bin/metadata.xml
+++ /dev/null
@@ -1,19 +0,0 @@
-<?xml version="1.0" encoding="UTF-8"?>
-<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
-<pkgmetadata>
-	<maintainer type="person">
-		<email>tomka@gentoo.org</email>
-	</maintainer>
-	<maintainer type="project">
-		<email>sci-mathematics@gentoo.org</email>
-		<name>Gentoo Mathematics Project</name>
-	</maintainer>
-	<longdescription>
-KANT is a computer algebra system for sophisticated computations in algebraic
-number fields that has been developed under the project leadership of
-Prof. Dr. M. E. Pohst at Technische Universität Berlin.
-
-The KANT functions are accessible through a user-friendly shell named KASH
-(KAnt SHell) that is freely available.
-</longdescription>
-</pkgmetadata>
diff --git a/sci-mathematics/lattE-macchiato/Manifest b/sci-mathematics/lattE-macchiato/Manifest
deleted file mode 100644
index 6bb5a9ff4..000000000
--- a/sci-mathematics/lattE-macchiato/Manifest
+++ /dev/null
@@ -1 +0,0 @@
-DIST latte-for-tea-too-1.2-mk-0.9.3.tar.gz 12782533 BLAKE2B 4d52a4add865077ff137c222a686792ac7c594e09711854d5befe96e305cb7b45f6b8ad26f18076c63322915699bfe07243bd3ab2b15faead5fb022a421cd751 SHA512 40bf1f4d830afcd092d38a329049096138d2ac840843493842a4d4636f51d8d8252eafe11609ed8f19a592baf1d7f4112a7c82d4c465ac3b89b326e268db5981
diff --git a/sci-mathematics/lattE-macchiato/files/buildpackages.patch b/sci-mathematics/lattE-macchiato/files/buildpackages.patch
deleted file mode 100644
index f35a0fe75..000000000
--- a/sci-mathematics/lattE-macchiato/files/buildpackages.patch
+++ /dev/null
@@ -1,224 +0,0 @@
---- ../latte-for-tea-too-1.2-mk-0.9.3/Makefile.am	2008-12-17 22:56:12.000000000 +0100
-+++ Makefile.am	2010-02-05 23:43:42.000000000 +0100
-@@ -6,29 +6,7 @@
- 
- ## Distribution variables.
- 
--PACKAGES=gmp cddplus cddlib ntl latte
--if ENABLE_LIDIA
--PACKAGES+=lidia
--endif
--if ENABLE_4TI2
--PACKAGES+=glpk 4ti2
--endif
--
--GMP_VERSION=4.2.4
--GMP_TARGZ=$(top_srcdir)/gmp-$(GMP_VERSION).tar.gz
--GMP_DIR=gmp-$(GMP_VERSION)
--
--CDDPLUS_VERSION=077a
--CDDPLUS_TARGZ=$(top_srcdir)/cdd+-$(CDDPLUS_VERSION).tar.gz
--CDDPLUS_DIR=cdd+-$(CDDPLUS_VERSION)
--
--CDDLIB_VERSION=094f
--CDDLIB_TARGZ=$(top_srcdir)/cddlib-$(CDDLIB_VERSION).tar.gz
--CDDLIB_DIR=cddlib-$(CDDLIB_VERSION)
--
--NTL_VERSION=5.4.2
--NTL_TARGZ=$(top_srcdir)/ntl-$(NTL_VERSION).tar.gz
--NTL_DIR=ntl-$(NTL_VERSION)
-+PACKAGES=latte lidia
- 
- LIDIA_VERSION=2.2.1-pre1+svn-1069+lattepatches-0.1
- LIDIA_TARGZ=$(top_srcdir)/lidia-base-$(LIDIA_VERSION).tar.gz $(top_srcdir)/lidia-FF-$(LIDIA_VERSION).tar.gz $(top_srcdir)/lidia-LA-$(LIDIA_VERSION).tar.gz
-@@ -39,16 +17,6 @@
- LATTE_TARGZ=$(top_srcdir)/latte-$(LATTE_VERSION).tar.gz
- LATTE_DIR=latte-$(LATTE_VERSION)
- 
--# GLPK is a prerequisite of 4ti2
--GLPK_VERSION=4.13
--GLPK_TARGZ=$(top_srcdir)/glpk-$(GLPK_VERSION).tar.gz
--GLPK_DIR=glpk-$(GLPK_VERSION)
--
--FORTYTWO_VERSION=1.3.2
--FORTYTWO_TARGZ=$(top_srcdir)/4ti2-$(FORTYTWO_VERSION).tar.gz
--FORTYTWO_DIR=4ti2-$(FORTYTWO_VERSION)
--
--
- INSTALL_DIR=$(CURDIR)/dest
- 
- ## Exported variables. 
-@@ -87,140 +55,27 @@
- EXTRA_DIST+=$(GMP_TARGZ) $(CDDPLUS_TARGZ) $(CDDLIB_TARGZ) $(NTL_TARGZ)  \
- 	$(LIDIA_TARGZ) $(LATTE_TARGZ) $(GLPK_TARGZ) $(FORTYTWO_TARGZ)
- 
--# GMP.  
--#
--# We do not give our CFLAGS and CXXFLAGS to GMP; it is easy to
--# miscompile GMP if we force it to use our values of these variables.
--
--build_gmp: $(GMP_DIR)/.built_gmp
--configure_gmp: $(GMP_DIR)/config.status
--#EXTRA_DIST += gmp-4.2.1-patch
--$(GMP_DIR)/.unpacked_gmp: $(GMP_TARGZ)
--	gunzip < $(GMP_TARGZ) | $(TAR) xf - 					\
--	&& touch $@
--# (cd $(GMP_DIR) && patch -t -p1 ) < $(top_srcdir)/gmp-4.2.1-patch	
--$(GMP_DIR)/config.status: $(GMP_DIR)/.unpacked_gmp
--	( cd $(GMP_DIR) && unset CFLAGS CXXFLAGS; ./configure --prefix="$(INSTALL_DIR)" --enable-cxx --disable-shared  $(GMP_CONFIGURE_OPTIONS) )
--$(GMP_DIR)/.built_gmp: $(GMP_DIR)/config.status
--	( cd $(GMP_DIR) && $(MAKE) && $(MAKE) install ) && touch $@
--clean_gmp: 
--	-( rm -f $(GMP_DIR)/.built_gmp && cd $(GMP_DIR) && $(MAKE) clean )
--distclean_gmp: 
--	-( rm -f $(GMP_DIR)/.built_gmp && cd $(GMP_DIR) && $(MAKE) distclean )
--
--# NTL.
--
--NTL_CONFIG_FILE=$(NTL_DIR)/src/makefile
--build_ntl: .built_ntl
--configure_ntl: $(NTL_CONFIG_FILE)
--.unpacked_ntl: $(NTL_TARGZ)
--	gunzip < $(NTL_TARGZ) | $(TAR) xf - 					\
--	&& touch $@ 
--
--## cd $(NTL_DIR) && patch -t -p1 ) < $(top_srcdir)/ntl-5.4-patch	\
--## EXTRA_DIST += ntl-5.4-patch
--$(NTL_CONFIG_FILE): .unpacked_ntl $(GMP_DIR)/.built_gmp
--	( cd $(NTL_DIR)/src && ./configure CC="$(CC)" CXX="$(CXX)" CFLAGS="$(CFLAGS)" CXXFLAGS="$(CXXFLAGS)" PREFIX="$(INSTALL_DIR)" GMP_PREFIX="$(INSTALL_DIR)" NTL_GMP_LIP=on ) 
--.built_ntl: $(NTL_CONFIG_FILE) $(GMP_DIR)/.built_gmp
--	( cd $(NTL_DIR)/src && $(MAKE) setup1 && $(MAKE) setup2 && $(MAKE) setup3 && $(MAKE) setup4 && $(MAKE) ntl.a && $(MAKE) install ) && touch $@
--clean_ntl: 
--	-( rm -f .built_ntl && cd $(NTL_DIR)/src && $(MAKE) clean )
--distclean_ntl: 
--	-( rm -f .built_ntl && cd $(NTL_DIR)/src && $(MAKE) clean; rm -f $(NTL_CONFIG_FILE) )
--
- # LiDIA.
- 
- build_lidia: $(LIDIA_DIR)/.built_lidia
--configure_lidia: $(LIDIA_DIR)/config.status $(GMP_DIR)/.built_gmp
-+configure_lidia: $(LIDIA_DIR)/config.status 
- #EXTRA_DIST += lidia-2.2.0.patch lidia-2.2.0-2.patch
- $(LIDIA_DIR)/.unpacked_lidia: $(LIDIA_TARGZ)
- 	for a in $(LIDIA_TARGZ); do					\
- 	  gunzip < $$a | $(TAR) xf - || exit 1;				\
- 	done 								\
- 	&& touch $@
--$(LIDIA_DIR)/config.status: $(LIDIA_DIR)/.unpacked_lidia $(GMP_DIR)/.built_gmp
--	( cd $(LIDIA_DIR) && ./configure --with-arithmetic=gmp --disable-nf --disable-ec --disable-eco --disable-gec --with-extra-includes="$(INSTALL_DIR)"/include --with-extra-libs="$(INSTALL_DIR)"/lib --prefix="$(INSTALL_DIR)"  --disable-shared) 
-+$(LIDIA_DIR)/config.status: $(LIDIA_DIR)/.unpacked_lidia 
-+	( cd $(LIDIA_DIR) && ./configure --with-arithmetic=gmp --disable-nf --disable-ec --disable-eco --disable-gec --with-extra-includes="$(INSTALL_DIR)"/include --with-extra-libs="$(INSTALL_DIR)"/lib --prefix="/usr"  --disable-shared) 
- # LiDIA 2.2.0 installs its headers into lidia/ but expects them in LiDIA!?!
- # So we make a symbolic link, just in case.
--$(LIDIA_DIR)/.built_lidia: $(LIDIA_DIR)/config.status $(GMP_DIR)/.built_gmp
--	( cd $(LIDIA_DIR) && $(MAKE) && $(MAKE) install ) && ( cd "$(INSTALL_DIR)"/include && if [ ! -r LiDIA ] ; then ln -s lidia LiDIA; fi  || true ) && touch $@
-+$(LIDIA_DIR)/.built_lidia: $(LIDIA_DIR)/config.status 
-+	( cd $(LIDIA_DIR) && $(MAKE) ) && ( cd "$(INSTALL_DIR)"/include && if [ ! -r LiDIA ] ; then ln -s lidia LiDIA; fi  || true ) && touch $@
- clean_lidia: 
- 	-( rm -f $(LIDIA_DIR)/.built_lidia && cd $(LIDIA_DIR) && $(MAKE) clean )
- distclean_lidia: 
- 	-( rm -f $(LIDIA_DIR)/.built_lidia && cd $(LIDIA_DIR) && $(MAKE) distclean )
- 
--# cddlib.
--#
--# cddlib 094b has a hard-coded location of GMP in /usr/local in its Makefile.am(!)
--# We work around this by passing LDFLAGS to both configure and make.
--build_cddlib: .built_cddlib
--configure_cddlib: $(CDDLIB_DIR)/config.status $(GMP_DIR)/.built_gmp
--.unpacked_cddlib: $(CDDLIB_TARGZ)
--	for a in $(CDDLIB_TARGZ); do \
--	  gunzip < $$a | $(TAR) xf - || exit 1; \
--	done && touch $@
--$(CDDLIB_DIR)/config.status: .unpacked_cddlib $(GMP_DIR)/.built_gmp
--	( cd $(CDDLIB_DIR) && ./configure CXX="$(CXX)" CFLAGS="$(CFLAGS) -I$(INSTALL_DIR)/include" CXXFLAGS="$(CXXFLAGS) -I$(INSTALL_DIR)/include" LDFLAGS="$(LDFLAGS) -L$(INSTALL_DIR)/lib" --prefix="$(INSTALL_DIR)"  --disable-shared) 
--.built_cddlib: $(CDDLIB_DIR)/config.status $(GMP_DIR)/.built_gmp
--	( cd $(CDDLIB_DIR) && $(MAKE) LDFLAGS="$(LDFLAGS) -L$(INSTALL_DIR)/lib" && $(MAKE) install ) && touch $@
--clean_cddlib: 
--	-( rm -f .built_cddlib && cd $(CDDLIB_DIR) && $(MAKE) clean )
--distclean_cddlib: 
--	-( rm -f .built_cddlib && cd $(CDDLIB_DIR) && $(MAKE) distclean )
--
--# cdd+.
--
--CDDPLUS_VARIABLES=CC="$(CXX)" LIBDIR="$(INSTALL_DIR)"/lib GMPLIBDIR="$(INSTALL_DIR)"/lib INCLUDEDIR="$(INSTALL_DIR)"/include GMPINCLUDEDIR="$(INSTALL_DIR)"/include OPTFLAGS="$(CXXFLAGS)"
--build_cddplus: $(CDDPLUS_DIR)/.built_cddplus
--configure_cddplus: .unpacked_cddplus $(GMP_DIR)/.built_gmp
--EXTRA_DIST += cdd+-077a.patch
--.unpacked_cddplus: $(CDDPLUS_TARGZ)
--	for a in $(CDDPLUS_TARGZ); do						\
--	  gunzip < $$a | $(TAR) xf - || exit 1;					\
--	done									\
--	&& (cd $(CDDPLUS_DIR) && $(PATCH) -p0) < $(top_srcdir)/cdd+-077a.patch	\
--	&& touch $@
--$(CDDPLUS_DIR)/.built_cddplus: .unpacked_cddplus $(GMP_DIR)/.built_gmp
--	( cd $(CDDPLUS_DIR) && $(MAKE) $(CDDPLUS_VARIABLES) cddr+ cddf+ && $(mkinstalldirs) "$(INSTALL_DIR)"/bin && $(INSTALL) cddr+ cddf+ "$(INSTALL_DIR)"/bin ) && touch $@
--clean_cddplus: 
--	-( rm -f $(CDDPLUS_DIR)/.built_cddplus && cd $(CDDPLUS_DIR) && $(MAKE) clean )
--distclean_cddplus: 
--	-( rm -f $(CDDPLUS_DIR)/.built_cddplus && cd $(CDDPLUS_DIR) && $(MAKE) clean )
--
--# GLPK.
--build_glpk: $(GLPK_DIR)/.built_glpk
--configure_glpk: $(GLPK_DIR)/config.status $(GMP_DIR)/.built_gmp
--$(GLPK_DIR)/.unpacked_glpk: $(GLPK_TARGZ)
--	gunzip < $(GLPK_TARGZ) | $(TAR) xf - 					\
--	&& touch $@
--$(GLPK_DIR)/config.status: $(GLPK_DIR)/.unpacked_glpk $(GMP_DIR)/.built_gmp
--	( cd $(GLPK_DIR) && CC="$(CC)" CXX="$(CXX)" CPPFLAGS="$(CPPFLAGS) -I$(INSTALL_DIR)/include" CFLAGS="$(CFLAGS) -I$(INSTALL_DIR)/include" CXXFLAGS="$(CXXFLAGS) -I$(INSTALL_DIR)/include" LDFLAGS="$(LDFLAGS) -L$(INSTALL_DIR)/lib" ./configure --prefix="$(INSTALL_DIR)" --disable-shared $(GLPK_CONFIGURE_OPTIONS) )
--$(GLPK_DIR)/.built_glpk: $(GLPK_DIR)/config.status
--	( cd $(GLPK_DIR) && $(MAKE) && $(MAKE) install ) && touch $@
--clean_glpk: 
--	-( rm -f $(GLPK_DIR)/.built_glpk && cd $(GLPK_DIR) && $(MAKE) clean )
--distclean_glpk: 
--	-( rm -f $(GLPK_DIR)/.built_glpk && cd $(GLPK_DIR) && $(MAKE) distclean )
--
--# 4ti2.
--build_4ti2: $(FORTYTWO_DIR)/.built_4ti2
--configure_4ti2: $(FORTYTWO_DIR)/config.status $(GLPK_DIR)/.built_glpk $(GMP_DIR)/.built_gmp
--$(FORTYTWO_DIR)/.unpacked_4ti2: $(FORTYTWO_TARGZ)
--	gunzip < $(FORTYTWO_TARGZ) | $(TAR) xf - 					\
--	&& touch $@
--$(FORTYTWO_DIR)/config.status: $(FORTYTWO_DIR)/.unpacked_4ti2 $(GLPK_DIR)/.built_glpk $(GMP_DIR)/.built_gmp
--	( cd $(FORTYTWO_DIR) && CC="$(CC)" CXX="$(CXX)" CPPFLAGS="$(CPPFLAGS) -I$(INSTALL_DIR)/include" CFLAGS="$(CFLAGS) -I$(INSTALL_DIR)/include" CXXFLAGS="$(CXXFLAGS) -I$(INSTALL_DIR)/include" LDFLAGS="$(LDFLAGS) -L$(INSTALL_DIR)/lib" ./configure --prefix="$(INSTALL_DIR)" --with-gmp="$(INSTALL_DIR)" --with-glpk="$(INSTALL_DIR)" --disable-shared $(FORTYTWO_CONFIGURE_OPTIONS) )
--## We currently have header file clashes between zsolve and groebner on Mac OS,
--## due to semi-case-insensitivity.  Work around for now, by only installing 
--## the header files of groebner -- we only need those... 
--## (This is already fixed for the upcoming 4ti2 releases.)
--$(FORTYTWO_DIR)/.built_4ti2: $(FORTYTWO_DIR)/config.status
--	( cd $(FORTYTWO_DIR) && $(MAKE) && $(MAKE) install-exec && (cd src/groebner && $(MAKE) install )) && touch $@
--clean_4ti2: 
--	-( rm -f $(FORTYTWO_DIR)/.built_4ti2 && cd $(FORTYTWO_DIR) && $(MAKE) clean )
--distclean_4ti2: 
--	-( rm -f $(FORTYTWO_DIR)/.built_4ti2 && cd $(FORTYTWO_DIR) && $(MAKE) distclean )
--
- # LattE.
- 
- if ENABLE_LIDIA
-@@ -236,19 +91,18 @@
- endif
- 
- build_latte: .built_latte
--configure_latte: $(LATTE_DIR)/config.status $(GMP_DIR)/.built_gmp .built_cddlib $(CDDPLUS_DIR)/.built_cddplus  .built_ntl
-+configure_latte: $(LATTE_DIR)/config.status 
- .unpacked_latte: $(LATTE_TARGZ)
- 	for a in $(LATTE_TARGZ); do \
--	  gunzip < $$a | $(TAR) xf - || exit 1; \
-+	  (gunzip < $$a | $(TAR) xf - || exit 1;) && (sed "s/-lwrapgmp-gcc4//g" -i $(LATTE_DIR)/configure || exit 1;) \
- 	done && touch $@
--$(LATTE_DIR)/config.status: .unpacked_latte $(GMP_DIR)/.built_gmp .built_cddlib $(CDDPLUS_DIR)/.built_cddplus $(BUILT_LIDIA) .built_ntl $(BUILT_4TI2)
--	( cd $(LATTE_DIR) && ./configure --with-default="$(INSTALL_DIR)" --prefix="$(INSTALL_DIR)" ) 
--.built_latte: $(LATTE_DIR)/config.status $(GMP_DIR)/.built_gmp .built_cddlib $(CDDPLUS_DIR)/.built_cddplus $(BUILT_LIDIA) .built_ntl $(BUILT_4TI2)
--	( cd $(LATTE_DIR) && $(MAKE) && $(MAKE) install ) && touch $@
-+$(LATTE_DIR)/config.status: .unpacked_latte $(BUILT_LIDIA)
-+	( cd $(LATTE_DIR) && ./configure --prefix="/usr" --with-topcom="/" ) 
-+.built_latte: $(LATTE_DIR)/config.status $(BUILT_LIDIA) 
-+	( cd $(LATTE_DIR) && $(MAKE) ) && touch $@
- clean_latte: 
- 	-( rm -f .built_latte && cd $(LATTE_DIR) && $(MAKE) clean )
- distclean_latte: 
- 	-( rm -f .built_latte && cd $(LATTE_DIR) && $(MAKE) distclean )
- 
--## Maintainer targets
--
-+## Maintainer targets
-\ No newline at end of file
diff --git a/sci-mathematics/lattE-macchiato/lattE-macchiato-0.9.3.ebuild b/sci-mathematics/lattE-macchiato/lattE-macchiato-0.9.3.ebuild
deleted file mode 100644
index 2b0505090..000000000
--- a/sci-mathematics/lattE-macchiato/lattE-macchiato-0.9.3.ebuild
+++ /dev/null
@@ -1,47 +0,0 @@
-# Copyright 1999-2015 Gentoo Foundation
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=5
-
-inherit autotools eutils flag-o-matic
-
-DESCRIPTION="lattE-macchiato consists of tools for lattice point enumeration"
-HOMEPAGE="http://www.math.ucdavis.edu/~mkoeppe/latte/"
-SRC_URI="http://www.math.ucdavis.edu/~mkoeppe/latte/download/latte-for-tea-too-1.2-mk-0.9.3.tar.gz"
-#	mirror://gentoo/${P}-src.tar.bz2
-
-SLOT="0"
-LICENSE="GPL-2"
-KEYWORDS="~amd64 ~x86"
-IUSE=""
-
-DEPEND="
-	dev-libs/gmp:0=[cxx]
-	>=dev-libs/ntl-5.4.2
-	sci-mathematics/4ti2
-	>=sci-libs/cdd+-077a
-	>=sci-mathematics/glpk-4.13
-	>=sci-libs/cddlib-094f"
-RDEPEND="${DEPEND}"
-
-S="${WORKDIR}/latte-for-tea-too-1.2-mk-0.9.3"
-
-# For now LattE builds an internal version of Lidia.
-# This will not be split off for now because it is heavily patched
-# and based on a version that was not even released.
-
-src_prepare() {
-	epatch "${FILESDIR}/buildpackages.patch"
-
-	eautoreconf
-}
-
-src_install() {
-	# install
-	cd "${S}"/lidia-2.2.1-pre1+svn-1069+lattepatches-0.1/
-	default
-	cd "${S}"/latte-1.2-mk-0.9.3/ || die
-	default
-	# ... and get rid of minimize which is provided by 4ti2:
-	rm "${ED}"/usr/bin/minimize || die "Removing minimize failed"
-}
diff --git a/sci-mathematics/lattE-macchiato/metadata.xml b/sci-mathematics/lattE-macchiato/metadata.xml
deleted file mode 100644
index f043b5060..000000000
--- a/sci-mathematics/lattE-macchiato/metadata.xml
+++ /dev/null
@@ -1,16 +0,0 @@
-<?xml version="1.0" encoding="UTF-8"?>
-<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
-<pkgmetadata>
-	<maintainer type="person">
-		<email>tom111@gmx.de</email>
-		<name>Thomas Kahle</name>
-	</maintainer>
-	<maintainer type="project">
-		<email>sci-mathematics@gentoo.org</email>
-		<name>Gentoo Mathematics Project</name>
-	</maintainer>
-	<longdescription lang="en">
-Macaulay2 is a research tool for algraic geometry and commutative
-algebra. 
-</longdescription>
-</pkgmetadata>
diff --git a/sci-mathematics/libsfmt/libsfmt-1.3.0.ebuild b/sci-mathematics/libsfmt/libsfmt-1.3.0.ebuild
index e90437e41..c933eb0ac 100644
--- a/sci-mathematics/libsfmt/libsfmt-1.3.0.ebuild
+++ b/sci-mathematics/libsfmt/libsfmt-1.3.0.ebuild
@@ -1,7 +1,7 @@
-# Copyright 1999-2015 Gentoo Foundation
+# Copyright 1999-2021 Gentoo Authors
 # Distributed under the terms of the GNU General Public License v2
 
-EAPI=5
+EAPI=7
 
 DESCRIPTION="SIMD-oriented Fast Mersenne Twister"
 HOMEPAGE="http://www.math.sci.hiroshima-u.ac.jp/~m-mat/MT/SFMT/index.html"
@@ -10,6 +10,7 @@ SRC_URI="http://www.math.sci.hiroshima-u.ac.jp/~m-mat/MT/SFMT/VERSIONS/ARCHIVES/
 LICENSE="BSD"
 SLOT="0"
 KEYWORDS="~amd64 ~x86"
+
 IUSE="cpu_flags_x86_sse2"
 
 src_configure() {
diff --git a/sci-mathematics/lie/files/lie-2.2.2-debian.patch b/sci-mathematics/lie/files/lie-2.2.2-debian.patch
new file mode 100644
index 000000000..4710cf60b
--- /dev/null
+++ b/sci-mathematics/lie/files/lie-2.2.2-debian.patch
@@ -0,0 +1,170 @@
+diff --git a/Makefile b/Makefile
+index c049e89..48b5c87 100644
+--- a/Makefile
++++ b/Makefile
+@@ -1,11 +1,11 @@
+ srcdir     :=$(shell pwd)
+ 
+-CFLAGS= -O
++CFLAGS?= -O
+ fixed-flags = -I$(srcdir) -I$(srcdir)/box
+ all-C-flags:= -ansi $(fixed-flags) $(CFLAGS)
+ non-ansi-flags :=  $(fixed-flags) $(CFLAGS)
+ 
+-CC = gcc # some compiler for ANSI/ISO C
++CC ?= gcc # some compiler for ANSI/ISO C
+ 
+ # These settings should also be used in subdirectories:
+ export CC all-C-flags fixed-flags CFLAGS
+@@ -24,20 +24,34 @@ GAP_objects=$(common_objects) gapprint.o gapgetl.o
+ 
+ # Global organisation (phony targets)
+ 
+-.PHONY: install all script finish no_readline
++.PHONY: preinstall all finish no_readline
+ .PHONY:	math_functions binding_functions
+ 
+ # The first target makes everything to get an operational LiE program
+-install: all script INFO.a
++preinstall: all INFO.a
++
++install:
++	install -d $(DESTDIR)/usr/bin
++	install -d $(DESTDIR)/usr/share/lie
++	install Lie.exe $(DESTDIR)/usr/bin/Lie.exe
++	install lie $(DESTDIR)/usr/bin/lie
++	install -m 644 *.ind $(DESTDIR)/usr/share/lie
++	install -m 644 INFO.a $(DESTDIR)/usr/share/lie
++	install -m 644 INFO.* $(DESTDIR)/usr/share/lie
++#	install -d $(DESTDIR)/usr/share/doc/lie
++#	install manual/manual.dvi $(DESTDIR)/usr/share/doc/lie
++	install -d $(DESTDIR)/usr/share/man/man1
++	install debian/lie.1 $(DESTDIR)/usr/share/man/man1
++#	gzip -f9 $(DESTDIR)/usr/share/man/man1/lie.1
++#	install debian/lie.1 $(DESTDIR)/usr/share/man/man1/Lie.exe.1
++#	gzip -f9 $(DESTDIR)/usr/share/man/man1/Lie.exe.1
+ 
+ # To 'make all', we first descend into the subdirectories, and afterwards
+ # return to finish here.
+ 
+-all:
+-	$(MAKE) math_functions binding_functions
+-	$(MAKE) finish
++all: math_functions binding_functions finish
+ 
+-finish: Lie.exe LEARN.ind INFO.ind # do not call 'make finish' directly
++finish: lie Lie.exe LEARN.ind INFO.ind # do not call 'make finish' directly
+ 
+ math_functions:
+ 	$(MAKE) -C box all
+@@ -82,13 +96,13 @@ gapgetl.o: getl.c
+ # been set to the most recent one of object files in the respective
+ # subdirectories, whence taking that dummy file as dependency suffices.
+ 
+-date.o: date.c $(objects) box/.last_compiled static/.last_compiled
++date.o: date.c $(objects) math_functions binding_functions
+ 	$(CC) -ansi -c date.c
+-gapdate.o: date.c $(GAP_objects) box/.last_compiled static/.last_compiled
++gapdate.o: date.c $(GAP_objects) math_functions binding_functions
+ 	$(CC) -ansi -c -o gapdate.o date.c
+ 
+-Lie.exe: date.o
+-	$(CC) -o Lie.exe $(objects) date.o static/*.o box/*.o -lreadline
++Lie.exe: math_functions binding_functions date.o
++	$(CC) -o Lie.exe $(LDFLAGS) $(objects) date.o static/*.o box/*.o -lreadline -lncurses
+ 	chmod g+w Lie.exe
+ Liegap.exe: gapdate.o
+ 	$(CC) -o Liegap.exe $(GAP_objects) gapdate.o static/*.o box/*.o
+@@ -101,8 +115,8 @@ noreadline: math_functions binding_functions $(common_objects) print.o
+ 	chmod g+w Lie.exe
+ 	$(MAKE) LEARN.ind INFO.ind script INFO.a
+ 
+-script:
+-	./make_lie
++lie:
++	./make_lie $(DESTDIR)
+ 
+ INFO.ind:	INFO.0 INFO.1 INFO.2 INFO.3 INFO.4 infoind
+ 	./infoind
+@@ -115,7 +129,7 @@ infoind: util/infoind.c
+ learnind: util/learnind.c
+ 	$(MAKE) -C util ../learnind
+ 
+-INFO.a: progs/maxsub progs/maxsub0 progs/eqrank
++INFO.a: Lie.exe progs/maxsub progs/maxsub0 progs/eqrank
+ 	rm -f INFO.a
+ 	./Lie.exe < progs/maxsub
+ 
+@@ -123,5 +137,8 @@ INFO.a: progs/maxsub progs/maxsub0 progs/eqrank
+ clean:
+ 	$(MAKE) -C box clean
+ 	$(MAKE) -C static clean
+-	rm -f *~ *.o parser.[ch] INFO.a LEARN.ind
+-	rm -f Lie.exe Liegap.exe infoind learnind util/*.o
++	rm -f *~ *.o parser.[ch] INFO.a LEARN.ind INFO.ind
++	rm -f lie Lie.exe Liegap.exe infoind learnind util/*.o
++	rm -f debian/lie/usr/bin/Lie.exe
++	rm -f debian/lie/usr/bin/lie
++	rm -f debian/lie/usr/share/lie/*
+diff --git a/debian/lie.1 b/debian/lie.1
+new file mode 100644
+index 0000000..10bf50d
+--- /dev/null
++++ b/debian/lie.1
+@@ -0,0 +1,27 @@
++.TH LIE 1 "December 12, 2006" "" ""
++
++.SH NAME
++LiE -  A computer algebra package for Lie group computations
++.SH SYNOPSIS
++.BR "lie"
++.SH DESCRIPTION
++.B LiE
++LiE is a computer algebra system that is specialised in computations
++involving (reductive) Lie groups and their representations.
++
++Full documentation about the program and the underlying mathematics
++can be found in /usr/share/doc/lie/manual.dvi.
++
++Run-time help can be obtained by typing '?' for a list of help entries
++or '?help' for help information.
++
++See the web page at
++.BR "http://young.sp2mi.univ-poitiers.fr/~marc/LiE/"
++for the CWEBx source code.
++.SH AUTHORS
++LiE was written by Arjeh M. Cohen <amc@win.tue.nl>, Marc van Leeuwen
++<maavl@mathlabo.univ-poitiers.fr> and Bert Lisser.
++.PP
++This manual page was written by Kasper Peeters
++<kasper.peeters@aei.mpg.de>, for the Debian project (but may be used
++by others).
+diff --git a/lie b/lie
+new file mode 100644
+index 0000000..5a7a906
+--- /dev/null
++++ b/lie
+@@ -0,0 +1,4 @@
++#!/bin/sh
++PTH=`which ${0} | sed -e 's/bin\/lie//'`
++
++exec ${PTH}/bin/Lie.exe initfile ${PTH}/share/lie
+diff --git a/lie_script b/lie_script
+index 76f3701..62972c0 100644
+--- a/lie_script
++++ b/lie_script
+@@ -1,2 +1,3 @@
+-LD=actual directory gets substituted here
+-exec $LD/Lie.exe initfile $LD
++#!/bin/sh
++#LD=actual directory gets substituted here
++exec /usr/bin/Lie.exe initfile /usr/share/lie
+diff --git a/make_lie b/make_lie
+index 5f059d7..1b5320b 100755
+--- a/make_lie
++++ b/make_lie
+@@ -1,3 +1,3 @@
+ #!/bin/sh
+-sed -e "s!LD=.*!LD=`/bin/pwd`!"  <lie_script >lie
++sed -e "s!LD=.*!LD=$1!"  <lie_script >lie
+ chmod a+x lie
diff --git a/sci-mathematics/lie/files/lie-2.2.2-make.patch b/sci-mathematics/lie/files/lie-2.2.2-make.patch
deleted file mode 100644
index cf6bd4537..000000000
--- a/sci-mathematics/lie/files/lie-2.2.2-make.patch
+++ /dev/null
@@ -1,131 +0,0 @@
-diff -u -r -P --new-file --exclude=CVS lie-2.2.2/debian/lie.1 lie-2.2.2-1/debian/lie.1
---- lie-2.2.2/debian/lie.1	1970-01-01 01:00:00.000000000 +0100
-+++ lie-2.2.2-1/debian/lie.1	2007-02-13 14:32:47.000000000 +0000
-@@ -0,0 +1,27 @@
-+.TH LIE 1 "December 12, 2006" "" ""
-+
-+.SH NAME
-+LiE -  A computer algebra package for Lie group computations
-+.SH SYNOPSIS
-+.BR "lie"
-+.SH DESCRIPTION
-+.B LiE
-+LiE is a computer algebra system that is specialised in computations
-+involving (reductive) Lie groups and their representations.
-+
-+Full documentation about the program and the underlying mathematics
-+can be found in /usr/share/doc/lie/manual.dvi.
-+
-+Run-time help can be obtained by typing '?' for a list of help entries
-+or '?help' for help information.
-+
-+See the web page at
-+.BR "http://young.sp2mi.univ-poitiers.fr/~marc/LiE/"
-+for the CWEBx source code.
-+.SH AUTHORS
-+LiE was written by Arjeh M. Cohen <amc@win.tue.nl>, Marc van Leeuwen
-+<maavl@mathlabo.univ-poitiers.fr> and Bert Lisser.
-+.PP
-+This manual page was written by Kasper Peeters
-+<kasper.peeters@aei.mpg.de>, for the Debian project (but may be used
-+by others).
-diff -u -r -P --new-file --exclude=CVS lie-2.2.2/lie lie-2.2.2-1/lie
---- lie-2.2.2/lie	1970-01-01 01:00:00.000000000 +0100
-+++ lie-2.2.2-1/lie	2007-02-20 21:47:37.000000000 +0000
-@@ -0,0 +1,4 @@
-+#!/bin/sh
-+PTH=`which ${0} | sed -e 's/bin\/lie//'`
-+
-+exec ${PTH}/bin/Lie.exe initfile ${PTH}/share/lie
-diff -u -r -P --new-file --exclude=CVS lie-2.2.2/lie_script lie-2.2.2-1/lie_script
---- lie-2.2.2/lie_script	1996-09-16 16:14:38.000000000 +0100
-+++ lie-2.2.2-1/lie_script	2006-12-17 13:42:23.000000000 +0000
-@@ -1,2 +1,3 @@
--LD=actual directory gets substituted here
--exec $LD/Lie.exe initfile $LD
-+#!/bin/sh
-+#LD=actual directory gets substituted here
-+exec /usr/bin/Lie.exe initfile /usr/share/lie
-diff -u -r -P --new-file --exclude=CVS lie-2.2.2/Makefile lie-2.2.2-1/Makefile
---- lie-2.2.2/Makefile	2000-04-07 08:46:28.000000000 +0100
-+++ lie-2.2.2-1/Makefile	2007-02-20 20:41:22.000000000 +0000
-@@ -24,20 +24,36 @@
- 
- # Global organisation (phony targets)
- 
--.PHONY: install all script finish no_readline
-+.PHONY: preinstall all finish no_readline
- .PHONY:	math_functions binding_functions
- 
- # The first target makes everything to get an operational LiE program
--install: all script INFO.a
-+preinstall: all INFO.a
-+
-+install:
-+	install -d $(DESTDIR)/usr/bin
-+	install -d $(DESTDIR)/usr/share/lie
-+	install Lie.exe $(DESTDIR)/usr/bin/Lie.exe
-+	install lie $(DESTDIR)/usr/bin/lie
-+	install -m 644 *.ind $(DESTDIR)/usr/share/lie
-+	install -m 644 INFO.a $(DESTDIR)/usr/share/lie
-+	install -m 644 INFO.* $(DESTDIR)/usr/share/lie
-+#	install -d $(DESTDIR)/usr/share/doc/lie
-+#	install manual/manual.dvi $(DESTDIR)/usr/share/doc/lie
-+	install -d $(DESTDIR)/usr/share/man/man1
-+	install debian/lie.1 $(DESTDIR)/usr/share/man/man1
-+	gzip -f9 $(DESTDIR)/usr/share/man/man1/lie.1
-+#	install debian/lie.1 $(DESTDIR)/usr/share/man/man1/Lie.exe.1
-+#	gzip -f9 $(DESTDIR)/usr/share/man/man1/Lie.exe.1
- 
- # To 'make all', we first descend into the subdirectories, and afterwards
- # return to finish here.
- 
- all:
--	$(MAKE) math_functions binding_functions
-+	$(MAKE) math_functions binding_functions 
- 	$(MAKE) finish
- 
--finish: Lie.exe LEARN.ind INFO.ind # do not call 'make finish' directly
-+finish: lie Lie.exe LEARN.ind INFO.ind # do not call 'make finish' directly
- 
- math_functions:
- 	$(MAKE) -C box all
-@@ -88,7 +104,7 @@
- 	$(CC) -ansi -c -o gapdate.o date.c
- 
- Lie.exe: date.o
--	$(CC) -o Lie.exe $(objects) date.o static/*.o box/*.o -lreadline
-+	$(CC) -o Lie.exe $(LDFLAGS) $(objects) date.o static/*.o box/*.o -lreadline -lncurses
- 	chmod g+w Lie.exe
- Liegap.exe: gapdate.o
- 	$(CC) -o Liegap.exe $(GAP_objects) gapdate.o static/*.o box/*.o
-@@ -101,8 +117,8 @@
- 	chmod g+w Lie.exe
- 	$(MAKE) LEARN.ind INFO.ind script INFO.a
- 
--script:
--	./make_lie
-+lie:
-+	./make_lie $(DESTDIR)
- 
- INFO.ind:	INFO.0 INFO.1 INFO.2 INFO.3 INFO.4 infoind
- 	./infoind
-@@ -123,5 +139,8 @@
- clean:
- 	$(MAKE) -C box clean
- 	$(MAKE) -C static clean
--	rm -f *~ *.o parser.[ch] INFO.a LEARN.ind
--	rm -f Lie.exe Liegap.exe infoind learnind util/*.o
-+	rm -f *~ *.o parser.[ch] INFO.a LEARN.ind INFO.ind
-+	rm -f lie Lie.exe Liegap.exe infoind learnind util/*.o
-+	rm -f debian/lie/usr/bin/Lie.exe
-+	rm -f debian/lie/usr/bin/lie
-+	rm -f debian/lie/usr/share/lie/*
-diff -u -r -P --new-file --exclude=CVS lie-2.2.2/make_lie lie-2.2.2-1/make_lie
---- lie-2.2.2/make_lie	1996-09-16 16:19:07.000000000 +0100
-+++ lie-2.2.2-1/make_lie	2006-12-17 13:42:23.000000000 +0000
-@@ -1,3 +1,3 @@
- #!/bin/sh
--sed -e "s!LD=.*!LD=`/bin/pwd`!"  <lie_script >lie
-+sed -e "s!LD=.*!LD=$1!"  <lie_script >lie
- chmod a+x lie
diff --git a/sci-mathematics/lie/files/parrallelmake-lie-2.2.2.patch b/sci-mathematics/lie/files/parrallelmake-lie-2.2.2.patch
deleted file mode 100644
index 5bd54b403..000000000
--- a/sci-mathematics/lie/files/parrallelmake-lie-2.2.2.patch
+++ /dev/null
@@ -1,52 +0,0 @@
---- Makefile.orig	2010-08-16 23:59:45.463692224 +1200
-+++ Makefile	2010-08-17 00:00:45.069692939 +1200
-@@ -1,11 +1,11 @@
- srcdir     :=$(shell pwd)
- 
--CFLAGS= -O
-+CFLAGS?= -O
- fixed-flags = -I$(srcdir) -I$(srcdir)/box
- all-C-flags:= -ansi $(fixed-flags) $(CFLAGS)
- non-ansi-flags :=  $(fixed-flags) $(CFLAGS)
- 
--CC = gcc # some compiler for ANSI/ISO C
-+CC ?= gcc # some compiler for ANSI/ISO C
- 
- # These settings should also be used in subdirectories:
- export CC all-C-flags fixed-flags CFLAGS
-@@ -49,9 +49,7 @@
- # To 'make all', we first descend into the subdirectories, and afterwards
- # return to finish here.
- 
--all:
--	$(MAKE) math_functions binding_functions 
--	$(MAKE) finish
-+all: math_functions binding_functions finish
- 
- finish: lie Lie.exe LEARN.ind INFO.ind # do not call 'make finish' directly
- 
-@@ -98,12 +96,12 @@
- # been set to the most recent one of object files in the respective
- # subdirectories, whence taking that dummy file as dependency suffices.
- 
--date.o: date.c $(objects) box/.last_compiled static/.last_compiled
-+date.o: date.c $(objects) math_functions binding_functions
- 	$(CC) -ansi -c date.c
--gapdate.o: date.c $(GAP_objects) box/.last_compiled static/.last_compiled
-+gapdate.o: date.c $(GAP_objects) math_functions binding_functions
- 	$(CC) -ansi -c -o gapdate.o date.c
- 
--Lie.exe: date.o
-+Lie.exe: math_functions binding_functions date.o
- 	$(CC) -o Lie.exe $(LDFLAGS) $(objects) date.o static/*.o box/*.o -lreadline -lncurses
- 	chmod g+w Lie.exe
- Liegap.exe: gapdate.o
-@@ -131,7 +129,7 @@
- learnind: util/learnind.c
- 	$(MAKE) -C util ../learnind
- 
--INFO.a: progs/maxsub progs/maxsub0 progs/eqrank
-+INFO.a: Lie.exe progs/maxsub progs/maxsub0 progs/eqrank
- 	rm -f INFO.a
- 	./Lie.exe < progs/maxsub
- 
diff --git a/sci-mathematics/lie/lie-2.2.2.ebuild b/sci-mathematics/lie/lie-2.2.2.ebuild
index 1e386d356..173e0715e 100644
--- a/sci-mathematics/lie/lie-2.2.2.ebuild
+++ b/sci-mathematics/lie/lie-2.2.2.ebuild
@@ -1,15 +1,14 @@
-# Copyright 1999-2015 Gentoo Foundation
+# Copyright 1999-2021 Gentoo Authors
 # Distributed under the terms of the GNU General Public License v2
 
-EAPI=5
+EAPI=7
 
-inherit eutils toolchain-funcs
+inherit toolchain-funcs
 
 DESCRIPTION="A Computer algebra package for Lie group computations"
-HOMEPAGE="http://www-math.univ-poitiers.fr/~maavl/LiE/"
+HOMEPAGE="http://www-math.univ-poitiers.fr/~maavl/LiE/" # no https, invalid certificate
 SRC_URI="http://wwwmathlabo.univ-poitiers.fr/~maavl/LiE/conLiE.tar.gz -> ${P}.tar.gz"
-#### Remove the following line when moving this ebuild to the main tree!
-RESTRICT="mirror"
+S="${WORKDIR}/LiE"
 
 LICENSE="LGPL-2.1"
 ##### See http://packages.debian.org/changelogs/pool/main/l/lie/lie_2.2.2+dfsg-1/lie.copyright
@@ -17,20 +16,16 @@ SLOT="0"
 KEYWORDS="~amd64 ~x86"
 IUSE="doc"
 
-DEPEND="
+RDEPEND="
+	sys-libs/readline:=
+	sys-libs/ncurses:=
+"
+DEPEND="${RDEPEND}"
+BDEPEND="
 	sys-devel/bison
-	sys-libs/readline:0=
-	sys-libs/ncurses:0="
-RDEPEND="sys-libs/readline:=
-	sys-libs/ncurses"
-
-S="${WORKDIR}/LiE"
+"
 
-src_prepare() {
-	epatch \
-		"${FILESDIR}"/${P}-make.patch \
-		"${FILESDIR}"/parrallelmake-${P}.patch
-}
+PATCHES=( "${FILESDIR}"/${P}-debian.patch )
 
 src_compile() {
 	emake CC=$(tc-getCC)
@@ -38,11 +33,5 @@ src_compile() {
 
 src_install() {
 	default
-	use doc && dodoc "${S}"/manual/*
-}
-
-pkg_postinst() {
-	elog "This version of the LiE ebuild is still under development."
-	elog "Help us improve the ebuild in:"
-	elog "http://bugs.gentoo.org/show_bug.cgi?id=194393"
+	use doc && dodoc "${S}"/manual/
 }
diff --git a/sci-mathematics/lie/metadata.xml b/sci-mathematics/lie/metadata.xml
index 5041a04a0..f3e755ec1 100644
--- a/sci-mathematics/lie/metadata.xml
+++ b/sci-mathematics/lie/metadata.xml
@@ -5,5 +5,12 @@
 		<email>sci-mathematics@gentoo.org</email>
 		<name>Gentoo Mathematics Project</name>
 	</maintainer>
-	<longdescription>LiE is the name of a software package that enables mathematicians and physicists to perform computations of a Lie group theoretic nature. It focuses on the representation theory of complex semisimple (reductive) Lie groups and algebras, and on the structure of their Weyl groups and root systems.</longdescription>
+	<longdescription>
+		LiE is the name of a software package that enables
+		mathematicians and physicists to perform computations
+		of a Lie group theoretic nature. It focuses on the
+		representation theory of complex semisimple (reductive)
+		Lie groups and algebras, and on the structure of their
+		Weyl groups and root systems.
+	</longdescription>
 </pkgmetadata>
diff --git a/sci-mathematics/ltl2ba/Manifest b/sci-mathematics/ltl2ba/Manifest
index 4d6528d6b..659c1c6e6 100644
--- a/sci-mathematics/ltl2ba/Manifest
+++ b/sci-mathematics/ltl2ba/Manifest
@@ -1 +1,3 @@
 DIST ltl2ba-1.1.tar.gz 29629 BLAKE2B 06ba7f7b5e3c6b72d2f0ea3b991346c803669e24d66dc38e311109ee08ed6dcc72bfd9f2ebe0f8864b0f80f010a4438029f4f5dbbf0087469ca2d07cdfce6b3f SHA512 8d010e2bb59fa5d682a56a50133865da938fd3bfcde6386184880eec6989bc1b694d6af9146b4b708cefdcdbcf98248f87074b8c973ea8cab65d658b394ccf69
+DIST ltl2ba-1.2.tar.gz 33026 BLAKE2B f19359e33d4eeb4dde75425ed03d940c08f46dd265b1b9c6773807e7dca67fd44f694f685d4153ca786118e336fab736104a865c5d0e9883390fca694f72b492 SHA512 148ffb1b4dbe134b69c6e946a4a9f1a95a809bf36ef3533117eedeceb721dd4c8a3238bbda2de5782a79b7aee70e33adf6ff193917441092a1ccb4e56a53a655
+DIST ltl2ba-1.3.tar.gz 38265 BLAKE2B bd74d9b9e22589ac00fbaa15f745dd6371894f68b50f85507694648274d9391ad3a90cdf1ee6c342abbceb04d0e2eb5d71473d43969b469a933517cfcd1e16c1 SHA512 1bcef13d98879c083dc907939c652e694802ed91c33a5d90bbeb6fc22d6265a0b153932c5fb3f8557aad30582322c16d0be822bf4208f40faf9384b367a84aa6
diff --git a/sci-mathematics/ltl2ba/ltl2ba-1.1.ebuild b/sci-mathematics/ltl2ba/ltl2ba-1.1.ebuild
index 29609c146..6172bb985 100644
--- a/sci-mathematics/ltl2ba/ltl2ba-1.1.ebuild
+++ b/sci-mathematics/ltl2ba/ltl2ba-1.1.ebuild
@@ -1,29 +1,31 @@
 # Copyright 1999-2015 Gentoo Foundation
 # Distributed under the terms of the GNU General Public License v2
 
-EAPI=5
+EAPI=7
+
+inherit flag-o-matic
 
 DESCRIPTION="Fast LTL to Buechi Automata Translation"
-HOMEPAGE="http://www.lsv.ens-cachan.fr/~gastin/${PN}/"
+HOMEPAGE="http://www.lsv.ens-cachan.fr/~gastin/ltl2ba"
 SRC_URI="http://www.lsv.ens-cachan.fr/~gastin/${PN}/${P}.tar.gz"
 
 LICENSE="GPL-2"
 SLOT="0"
 KEYWORDS="~amd64 ~x86"
-IUSE=""
-
-RDEPEND=""
-DEPEND=""
 
-src_compile() {
+src_prepare() {
+	default
 	sed -i Makefile \
 		-e "s/CC=gcc/#CC=gcc/g" \
-		-e "s/CFLAGS= -O3 -ansi -DNXT/CFLAGS+= -ansi -DNXT/g"
+		-e "s/CFLAGS= -O3 -ansi -DNXT/CFLAGS+= -ansi -DNXT/g" || die
+}
 
+src_configure() {
+	append-cflags -fcommon
 	default
 }
 
 src_install() {
-	dobin ltl2ba || die "dobin failed"
+	dobin ltl2ba
 	dodoc README
 }
diff --git a/sci-mathematics/ltl2ba/ltl2ba-1.2.ebuild b/sci-mathematics/ltl2ba/ltl2ba-1.2.ebuild
new file mode 100644
index 000000000..0678dcf8e
--- /dev/null
+++ b/sci-mathematics/ltl2ba/ltl2ba-1.2.ebuild
@@ -0,0 +1,31 @@
+# Copyright 1999-2015 Gentoo Foundation
+# Distributed under the terms of the GNU General Public License v2
+
+EAPI=8
+
+inherit flag-o-matic
+
+DESCRIPTION="Fast LTL to Buechi Automata Translation"
+HOMEPAGE="http://www.lsv.ens-cachan.fr/~gastin/ltl2ba"
+SRC_URI="http://www.lsv.ens-cachan.fr/~gastin/${PN}/${P}.tar.gz"
+
+LICENSE="GPL-2"
+SLOT="0"
+KEYWORDS="~amd64 ~x86"
+
+src_prepare() {
+	default
+	sed -i Makefile \
+		-e "s/CC=gcc/#CC=gcc/g" \
+		-e "s/CFLAGS= -O3 -ansi -DNXT/CFLAGS+= -ansi -DNXT/g" || die
+}
+
+src_configure() {
+	append-cflags -fcommon
+	default
+}
+
+src_install() {
+	dobin ltl2ba
+	dodoc README
+}
diff --git a/sci-mathematics/ltl2ba/ltl2ba-1.3.ebuild b/sci-mathematics/ltl2ba/ltl2ba-1.3.ebuild
new file mode 100644
index 000000000..0678dcf8e
--- /dev/null
+++ b/sci-mathematics/ltl2ba/ltl2ba-1.3.ebuild
@@ -0,0 +1,31 @@
+# Copyright 1999-2015 Gentoo Foundation
+# Distributed under the terms of the GNU General Public License v2
+
+EAPI=8
+
+inherit flag-o-matic
+
+DESCRIPTION="Fast LTL to Buechi Automata Translation"
+HOMEPAGE="http://www.lsv.ens-cachan.fr/~gastin/ltl2ba"
+SRC_URI="http://www.lsv.ens-cachan.fr/~gastin/${PN}/${P}.tar.gz"
+
+LICENSE="GPL-2"
+SLOT="0"
+KEYWORDS="~amd64 ~x86"
+
+src_prepare() {
+	default
+	sed -i Makefile \
+		-e "s/CC=gcc/#CC=gcc/g" \
+		-e "s/CFLAGS= -O3 -ansi -DNXT/CFLAGS+= -ansi -DNXT/g" || die
+}
+
+src_configure() {
+	append-cflags -fcommon
+	default
+}
+
+src_install() {
+	dobin ltl2ba
+	dodoc README
+}
diff --git a/sci-mathematics/mdp/Manifest b/sci-mathematics/mdp/Manifest
deleted file mode 100644
index a1eb88b49..000000000
--- a/sci-mathematics/mdp/Manifest
+++ /dev/null
@@ -1,2 +0,0 @@
-DIST MDP-3.3.tar.gz 471439 BLAKE2B f16d2075d325ebcfdb9c2628f6568f626f1b9ffe11874b62b878fef07bf557bab14e1912ea196c3b0a73b0eb73518c0d5fa854a593f5f1dddfdb663ffd36d027 SHA512 fdbecd38e86aae970c6091c3ff7cd8e576556bf449051e5d998852e294041587907acc0701d3415059da7aaac73c04803138a04c9990bcc2a168a8f6f83d91cf
-DIST MDP-3.5.tar.gz 335420 BLAKE2B ea1a5d941af33220c4d03b4a70d70410b8d7d0ad4f541a1cb07914d745912a766013b551476ad4db39155a4ea998baa98d21f9db312e48434bbd7b622f10677c SHA512 5c4f6264ce566b65d4580bb38be711e93d764b7cf1c507df3e0f9efef23c93646a2ba8aab7de5c3f7c07bee16f9f4ebe1739a780c6dc966da48007d733747c58
diff --git a/sci-mathematics/mdp/mdp-3.3.ebuild b/sci-mathematics/mdp/mdp-3.3.ebuild
deleted file mode 100644
index 509639188..000000000
--- a/sci-mathematics/mdp/mdp-3.3.ebuild
+++ /dev/null
@@ -1,35 +0,0 @@
-# Copyright 1999-2014 Gentoo Foundation
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=6
-
-PYTHON_COMPAT=( python3_{4,5} )
-
-inherit distutils-r1
-
-MY_P="${P/mdp/MDP}"
-MY_P="${MY_P/_rc/RC}"
-
-DESCRIPTION="Data processing framework in python"
-HOMEPAGE="http://mdp-toolkit.sourceforge.net/index.html"
-SRC_URI="mirror://sourceforge/mdp-toolkit/${MY_P}.tar.gz"
-
-LICENSE="GPL-2"
-SLOT="0"
-KEYWORDS="~amd64 ~x86"
-IUSE=""
-
-DEPEND=""
-RDEPEND="
-	|| (
-		>=dev-python/numpy-1.1[${PYTHON_USEDEP}]
-		>=sci-libs/scipy-0.5.2[${PYTHON_USEDEP}]
-)"
-
-S="${WORKDIR}/${MY_P}"
-
-python_test() {
-	distutils_install_for_testing
-	cd "${BUILD_DIR}" || die
-	"${PYTHON}" -c "import mdp;mdp.test()" || die
-}
diff --git a/sci-mathematics/mdp/mdp-3.5.ebuild b/sci-mathematics/mdp/mdp-3.5.ebuild
deleted file mode 100644
index 6136fc36d..000000000
--- a/sci-mathematics/mdp/mdp-3.5.ebuild
+++ /dev/null
@@ -1,34 +0,0 @@
-# Copyright 1999-2016 Gentoo Foundation
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=6
-
-PYTHON_COMPAT=( python{2_7,3_4,3_5} )
-
-inherit distutils-r1
-
-MY_P="${P/mdp/MDP}"
-MY_P="${MY_P/_rc/RC}"
-
-DESCRIPTION="Data processing framework in python"
-HOMEPAGE="http://mdp-toolkit.sourceforge.net/index.html"
-SRC_URI="mirror://sourceforge/mdp-toolkit/${MY_P}.tar.gz"
-
-LICENSE="GPL-2"
-SLOT="0"
-KEYWORDS="~amd64 ~x86"
-IUSE=""
-
-DEPEND=""
-RDEPEND="|| (
-	>=dev-python/numpy-1.1[${PYTHON_USEDEP}]
-	>=sci-libs/scipy-0.5.2[${PYTHON_USEDEP}]
-	)"
-
-S="${WORKDIR}/${MY_P}"
-
-python_test() {
-	distutils_install_for_testing
-	cd "${BUILD_DIR}" || die
-	"${PYTHON}" -c "import mdp;mdp.test()" || die
-}
diff --git a/sci-mathematics/mdp/mdp-9999.ebuild b/sci-mathematics/mdp/mdp-9999.ebuild
deleted file mode 100644
index 9be3d648a..000000000
--- a/sci-mathematics/mdp/mdp-9999.ebuild
+++ /dev/null
@@ -1,33 +0,0 @@
-# Copyright 1999-2014 Gentoo Foundation
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=5
-
-PYTHON_COMPAT=( python{2_7,3_3} )
-
-inherit distutils-r1 git-r3
-
-MY_P="${P/mdp/MDP}"
-MY_P="${MY_P/_rc/RC}"
-
-DESCRIPTION="Modular data processing framework for python"
-HOMEPAGE="http://mdp-toolkit.sourceforge.net/index.html"
-SRC_URI=""
-EGIT_REPO_URI="git://github.com/mdp-toolkit/mdp-toolkit.git"
-
-LICENSE="GPL-2"
-SLOT="0"
-KEYWORDS=""
-IUSE=""
-
-DEPEND=""
-RDEPEND="|| (
-			>=dev-python/numpy-1.1[${PYTHON_USEDEP}]
-			>=sci-libs/scipy-0.5.2[${PYTHON_USEDEP}]
-			)"
-
-python_test() {
-	distutils_install_for_testing
-	cd "${BUILD_DIR}" || die
-	"${PYTHON}" -c "import mdp;mdp.test()" || die
-}
diff --git a/sci-mathematics/mdp/metadata.xml b/sci-mathematics/mdp/metadata.xml
deleted file mode 100644
index 4a8c55d36..000000000
--- a/sci-mathematics/mdp/metadata.xml
+++ /dev/null
@@ -1,23 +0,0 @@
-<?xml version="1.0" encoding="UTF-8"?>
-<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
-<pkgmetadata>
-	<maintainer type="person">
-		<email>tim@cerazone.net</email>
-		<name>Tim Cera</name>
-	</maintainer>
-	<maintainer type="project">
-		<email>sci-mathematics@gentoo.org</email>
-		<name>Gentoo Mathematics Project</name>
-	</maintainer>
-	<longdescription lang="en">
-Modular toolkit for Data Processing (MDP) is a Python data processing
-framework. Implemented algorithms include: Principal Component Analysis
-(PCA), Independent Component Analysis (ICA), Slow Feature Analysis (SFA),
-Independent Slow Feature Analysis (ISFA), Growing Neural Gas (GNG), Factor
-Analysis, Fisher Discriminant Analysis (FDA), Gaussian Classifiers, and
-Restricted Boltzmann Machines.
-</longdescription>
-	<upstream>
-		<remote-id type="sourceforge">mdp-toolkit</remote-id>
-	</upstream>
-</pkgmetadata>
diff --git a/sci-mathematics/netgen/Manifest b/sci-mathematics/netgen/Manifest
deleted file mode 100644
index a53b896bc..000000000
--- a/sci-mathematics/netgen/Manifest
+++ /dev/null
@@ -1,3 +0,0 @@
-DIST netgen-4.9.13.tar.gz 1829916 BLAKE2B f863c0dd4a1df1d0bf14bedc8d5afade7cfcf1209d71f402509bd24989813485051c192456bfb7f102e66991a8d89c7eac72520f9fa6090eea853a597250b445 SHA512 6cfe6ea799f37a35dc74112f5c370fd369277a55965769649c00632eba308061901fd7563fe7eb4b427b0702d39f4f004854da9f02f2e6f11ccd3a72e6b6afa3
-DIST netgen-5.0.0.tar.gz 1835004 BLAKE2B 145d1285ea2989b4b829576ef830bcacf90ada9c2aae47b6e7c1d2a6575696e0dc91d51f47443b69d4e7258d67c1c035e6d730dc77e8c37b4d9669bd804a84d3 SHA512 27f46feaa1cf9d269c4898c093cca404fdc5e5fbfc8c9684d0d2f2ec2f2f9af85dd8b3d3372044f63fca08e1a079fd042fbcdc7b9ca881c38a3cfe67586b34b4
-DIST netgen-5.3.1.tar.gz 1857185 BLAKE2B 943c0d94f9f74d9d83674bde416ad63d2b0b1eb1029d901504d95285530998e03a92b6e71b4d844aab541c3e6a533613f0e90e4343c38f20f28321118b8e73c5 SHA512 6f5b5b8ab47fc3bf57281b26f26b13675aa719146c90a928eda3d704163e20a0a3baf27d520978ec6c4828ee6323eaef65deb851988eefef5d768a9ecad69fc8
diff --git a/sci-mathematics/netgen/files/netgen-5.x-compile-against-occ-6.5.x.patch b/sci-mathematics/netgen/files/netgen-5.x-compile-against-occ-6.5.x.patch
deleted file mode 100644
index ce581cee3..000000000
--- a/sci-mathematics/netgen/files/netgen-5.x-compile-against-occ-6.5.x.patch
+++ /dev/null
@@ -1,28 +0,0 @@
---- libsrc/occ/Partition_Spliter.cxx.old	2012-11-14 16:14:39.440625195 +0100
-+++ libsrc/occ/Partition_Spliter.cxx	2012-11-14 16:15:20.035646075 +0100
-@@ -1169,8 +1169,8 @@
-           for (; j<=nbj && ok; ++j) {
-             if (Extrema.IsMin(j)) {
- 	      hasMin = Standard_True;
--	      ok = Extrema.Value(j) <= tol;  // V6.3
--	      // ok = Extrema.SquareDistance(j) <= tol;  // V6.5
-+	      // ok = Extrema.Value(j) <= tol;  // V6.3
-+	      ok = Extrema.SquareDistance(j) <= tol;  // V6.5
- 	    }
-           }
-         }
---- libsrc/occ/Partition_Inter3d.cxx.old	2012-11-14 16:13:11.149581085 +0100
-+++ libsrc/occ/Partition_Inter3d.cxx	2012-11-14 16:14:20.017615214 +0100
-@@ -243,9 +243,9 @@
-       Standard_Integer i, nbExt = anExtPS.NbExt();
-       Extrema_POnSurf aPOnSurf;
-       for (i = 1; i <= nbExt; ++i )
--	if (anExtPS.Value( i ) <= TolE)               // V6.3
--	  // if (anExtPS.SquareDistance( i ) <= TolE)   // V6.5
--	  {
-+	//	if (anExtPS.Value( i ) <= TolE)               // V6.3
-+	if (anExtPS.SquareDistance( i ) <= TolE)   // V6.5
-+	{
-           aPOnSurf = anExtPS.Point( i );
-           break;
-         }
diff --git a/sci-mathematics/netgen/files/netgen-5.x-fedora-fixes.patch b/sci-mathematics/netgen/files/netgen-5.x-fedora-fixes.patch
deleted file mode 100644
index 5cb399edb..000000000
--- a/sci-mathematics/netgen/files/netgen-5.x-fedora-fixes.patch
+++ /dev/null
@@ -1,223 +0,0 @@
-diff -uwrN netgen-5.3.1/libsrc/meshing/meshtype.cpp netgen/libsrc/meshing/meshtype.cpp
---- netgen-5.3.1/libsrc/meshing/meshtype.cpp	2016-02-20 21:55:59.226450843 +0100
-+++ netgen/libsrc/meshing/meshtype.cpp	2016-02-20 23:54:12.293646166 +0100
-@@ -1,4 +1,5 @@
- #include <mystdlib.h>
-+#include <float.h> // to get DBL_MIN defined
- 
- #include "meshing.hpp"  
- 
-@@ -666,7 +667,8 @@
- 
-         double det = trans.Det();
- 
--        if (det <= 0)
-+        // if (det <= 0)
-+        if (det <= DBL_MIN) // avoid FPE
-           err += 1e12;
-         else
-           err += frob * frob / det;
-@@ -722,7 +724,8 @@
- 
-             double det = trans(0,0)*trans(1,1)-trans(1,0)*trans(0,1);
- 
--            if (det <= 0)
-+            // if (det <= 0)
-+            if (det <= DBL_MIN)  // avoid FPE
-               {
-                 dd = 0;
-                 return 1e12;
-@@ -806,7 +809,8 @@
-           = dtrans(0,0) * trans(1,1) - trans(0,1) * dtrans(1,0)
-           + trans(0,0) * dtrans(1,1) - dtrans(0,1) * trans(1,0);
- 
--        if (det <= 0)
-+        // if (det <= 0)
-+        if (det <= DBL_MIN) // avoid FPE
-           err += 1e12;
-         else
-           {
-@@ -856,7 +860,8 @@
-         frob /= 2;
- 
-         double det = trans.Det();
--        if (det <= 0)
-+        //if (det <= 0)
-+        if (det <= DBL_MIN) // avoid FPE
-           err += 1e12;
-         else
-           err += frob * frob / det;
-@@ -1864,7 +1869,8 @@
-       case PYRAMID:
-         {
-           double noz = 1-p(2);
--          if (noz == 0.0) noz = 1e-10;
-+          //if (noz == 0.0) noz = 1e-10;
-+          if (noz <= DBL_MIN) noz = 1e-10; // avoid FPE
- 
-           double xi  = p(0) / noz;
-           double eta = p(1) / noz;
-@@ -2513,10 +2519,10 @@
- 
-   MeshingParameters :: MeshingParameters ()
-   {
--    optimize3d = "cmdmustm";
-+    optimize3d = (char*)"cmdmustm"; // optimize3d = "cmdmustm";
-     //optimize3d = "cmdmstm";
-     optsteps3d = 3;
--    optimize2d = "smsmsmSmSmSm";
-+    optimize2d = (char*)"smsmsmSmSmSm"; // optimize2d = "smsmsmSmSmSm";
-     optsteps2d = 3;
-     opterrpow = 2;
-     blockfill = 1;
-diff -uwrN netgen-5.3.1/libsrc/meshing/meshtype.hpp netgen/libsrc/meshing/meshtype.hpp
---- netgen-5.3.1/libsrc/meshing/meshtype.hpp	2016-02-20 21:55:59.226450843 +0100
-+++ netgen/libsrc/meshing/meshtype.hpp	2016-02-20 23:54:12.295646166 +0100
-@@ -15,6 +15,7 @@
-     Classes for NETGEN
-   */
- 
-+class Mesh; // added due to compilation errors on some platforms
- 
- 
-   enum ELEMENT_TYPE { 
-diff -uwrN netgen-5.3.1/libsrc/meshing/smoothing2.cpp netgen/libsrc/meshing/smoothing2.cpp
---- netgen-5.3.1/libsrc/meshing/smoothing2.cpp	2016-02-20 21:55:59.228450843 +0100
-+++ netgen/libsrc/meshing/smoothing2.cpp	2016-02-20 23:54:12.298646166 +0100
-@@ -361,7 +361,8 @@
-     vgrad = 0;
-     double badness = 0;
- 
--    ld.meshthis -> GetNormalVector (ld.surfi, ld.sp1, ld.gi1, n);
-+    //normal already computed: ld.meshthis -> GetNormalVector (ld.surfi, ld.sp1, ld.gi1, n);
-+    n = ld.normal;
-     pp1 = ld.sp1 + x(0) * ld.t1 + x(1) * ld.t2;
- 
-     //  meshthis -> ProjectPoint (surfi, pp1);
-@@ -577,7 +578,8 @@
-     vgrad = 0;
-     badness = 0;
- 
--    ld.meshthis -> GetNormalVector (ld.surfi, ld.sp1, ld.gi1, n);
-+    //normal already computed: ld.meshthis -> GetNormalVector (ld.surfi, ld.sp1, ld.gi1, n);
-+    n = ld.normal;
- 
-     pp1 = ld.sp1 + x(0) * ld.t1 + x(1) * ld.t2;
- 
-@@ -649,7 +651,8 @@
-     vgrad = 0;
-     badness = 0;
- 
--    ld.meshthis -> GetNormalVector (ld.surfi, ld.sp1, ld.gi1, n);
-+    //normal already computed: ld.meshthis -> GetNormalVector (ld.surfi, ld.sp1, ld.gi1, n);
-+    n = ld.normal;
- 
-     // pp1 = sp1;
-     //    pp1.Add2 (x.Get(1), t1, x.Get(2), t2);
-diff -uwrN netgen-5.3.1/libsrc/occ/occconstruction.cpp netgen/libsrc/occ/occconstruction.cpp
---- netgen-5.3.1/libsrc/occ/occconstruction.cpp	2016-02-20 21:53:44.420447131 +0100
-+++ netgen/libsrc/occ/occconstruction.cpp	2016-02-20 23:54:12.299646166 +0100
-@@ -28,7 +28,7 @@
- #include <BRepAlgoAPI_Common.hxx>
- #include <BRepAlgoAPI_Fuse.hxx>
- #include <BRepAlgoAPI_Section.hxx>
--#include <BRepOffsetAPI_Sewing.hxx>
-+//#include <BRepOffsetAPI_Sewing.hxx>
- //#include <BRepAlgo_Sewing.hxx>
- #include <BRepOffsetAPI_MakeOffsetShape.hxx>
- #include <ShapeFix_Shape.hxx>
-diff -uwrN netgen-5.3.1/libsrc/occ/occmeshsurf.cpp netgen/libsrc/occ/occmeshsurf.cpp
---- netgen-5.3.1/libsrc/occ/occmeshsurf.cpp	2016-02-20 21:53:44.421447131 +0100
-+++ netgen/libsrc/occ/occmeshsurf.cpp	2016-02-20 23:54:12.310646166 +0100
-@@ -6,6 +6,7 @@
- #include <meshing.hpp>
- #include <GeomLProp_SLProps.hxx>
- #include <ShapeAnalysis_Surface.hxx>
-+#include <GeomAPI_ProjectPointOnCurve.hxx> // -- moved here from occgeom.hpp
- 
- 
- namespace netgen
-@@ -689,7 +691,7 @@
-       }
-   
-     newp = hnewp;
--  }
-+  }//; -- to compile with -Wall -pedantic
- 
- 
-   void OCCRefinementSurfaces ::  
- 
- 
-diff -uwrN netgen-5.3.1/libsrc/occ/Partition_Inter3d.cxx netgen/libsrc/occ/Partition_Inter3d.cxx
---- netgen-5.3.1/libsrc/occ/Partition_Inter3d.cxx	2016-02-20 21:53:44.418447131 +0100
-+++ netgen/libsrc/occ/Partition_Inter3d.cxx	2016-02-20 23:54:12.311646166 +0100
-@@ -243,8 +243,10 @@
-       Standard_Integer i, nbExt = anExtPS.NbExt();
-       Extrema_POnSurf aPOnSurf;
-       for (i = 1; i <= nbExt; ++i )
-+       // porting to OCCT6.5.1
- 	  // if (anExtPS.Value( i ) <= TolE)               // V6.3
--	  if (anExtPS.SquareDistance( i ) <= TolE)   // V6.5
-+       // if (anExtPS.SquareDistance( i ) <= TolE)   // V6.5
-+       if (anExtPS.SquareDistance( i ) <= TolE * TolE)
- 	  {
-           aPOnSurf = anExtPS.Point( i );
-           break;
-diff -uwrN netgen-5.3.1/libsrc/occ/Partition_Spliter.cxx netgen/libsrc/occ/Partition_Spliter.cxx
---- netgen-5.3.1/libsrc/occ/Partition_Spliter.cxx	2016-02-20 21:53:44.420447131 +0100
-+++ netgen/libsrc/occ/Partition_Spliter.cxx	2016-02-20 23:54:12.313646166 +0100
-@@ -1169,8 +1169,10 @@
-           for (; j<=nbj && ok; ++j) {
-             if (Extrema.IsMin(j)) {
- 	      hasMin = Standard_True;
-+	      // porting to OCCT6.5.1
- 	      // ok = Extrema.Value(j) <= tol;  // V6.3
--	      ok = Extrema.SquareDistance(j) <= tol;  // V6.5
-+	      // ok = Extrema.SquareDistance(j) <= tol;  // V6.5
-+	      ok = Extrema.SquareDistance(j) <= tol * tol;
- 	    }
-           }
-         }
-diff -uwrN netgen-5.3.1/libsrc/occ/utilities.h netgen/libsrc/occ/utilities.h
---- netgen-5.3.1/libsrc/occ/utilities.h	2016-02-20 21:53:44.421447131 +0100
-+++ netgen/libsrc/occ/utilities.h	2016-02-20 23:54:12.314646166 +0100
-@@ -33,6 +33,7 @@
- 
- #include <string>
- #include <iostream>
-+#include <iomanip>
- #include <cstdlib>
- // #include "SALOME_Log.hxx"
- 
-diff -uwrN netgen-5.3.1/libsrc/stlgeom/stlgeommesh.cpp netgen/libsrc/stlgeom/stlgeommesh.cpp
---- netgen-5.3.1/libsrc/stlgeom/stlgeommesh.cpp	2016-02-20 21:55:59.234450844 +0100
-+++ netgen/libsrc/stlgeom/stlgeommesh.cpp	2016-02-20 23:54:12.315646166 +0100
-@@ -1435,7 +1435,8 @@
- 	  /*
- 	  if (!optstring || strlen(optstring) == 0)
- 	    {
--	      mparam.optimize2d = "smcm";
-+	      //mparam.optimize2d = (char*)"smcm";
-+              mparam.optimize2d = (char*)"smcm";
- 	    }
- 	  else
- 	    {
-@@ -1453,7 +1454,7 @@
- 	      mesh -> LoadLocalMeshSize (mparam.meshsizefilename);	      
- 	      mesh -> CalcLocalHFromSurfaceCurvature (mparam.grading, 
- 						      stlparam.resthsurfmeshcurvfac);
--	      mparam.optimize2d = "cmsmSm";
-+	      mparam.optimize2d = "(char*)cmsmSm";
- 	      STLSurfaceOptimization (*stlgeometry, *mesh, mparam);
- #ifdef STAT_STREAM
- 	      (*statout) << GetTime() << " & ";
-@@ -1560,7 +1561,8 @@
- 	  /*
- 	  if (!optstring || strlen(optstring) == 0)
- 	    {
--	      mparam.optimize3d = "cmdmstm";
-+              //mparam.optimize3d = "cmdmstm";
-+	      mparam.optimize3d = (char*)"cmdmstm";
- 	    }
- 	  else
- 	    {
diff --git a/sci-mathematics/netgen/files/netgen-5.x-includes-fixes.patch b/sci-mathematics/netgen/files/netgen-5.x-includes-fixes.patch
deleted file mode 100644
index 650b575c9..000000000
--- a/sci-mathematics/netgen/files/netgen-5.x-includes-fixes.patch
+++ /dev/null
@@ -1,29 +0,0 @@
-diff -uwrN -x.git netgen-5.3.1/libsrc/include/meshing.hpp netgen/libsrc/include/meshing.hpp
---- netgen-5.3.1/libsrc/include/meshing.hpp	2016-02-21 20:12:55.885186643 +0100
-+++ netgen/libsrc/include/meshing.hpp	2016-02-21 20:09:26.275180871 +0100
-@@ -1 +1 @@
--#include <../meshing/meshing.hpp>
-+#include "../meshing/meshing.hpp"
-diff -uwrN -x.git netgen-5.3.1/libsrc/include/myadt.hpp netgen/libsrc/include/myadt.hpp
---- netgen-5.3.1/libsrc/include/myadt.hpp	2016-02-21 20:12:55.886186643 +0100
-+++ netgen/libsrc/include/myadt.hpp	2016-02-21 20:09:26.275180871 +0100
-@@ -1 +1 @@
--#include <../general/myadt.hpp>
-+#include "../general/myadt.hpp"
-diff -uwrN -x.git netgen-5.3.1/libsrc/include/stlgeom.hpp netgen/libsrc/include/stlgeom.hpp
---- netgen-5.3.1/libsrc/include/stlgeom.hpp	2016-02-21 20:12:55.886186643 +0100
-+++ netgen/libsrc/include/stlgeom.hpp	2016-02-21 20:09:26.275180871 +0100
-@@ -1 +1 @@
--#include <../stlgeom/stlgeom.hpp>
-+#include "../stlgeom/stlgeom.hpp"
-diff -uwrN -x.git netgen-5.3.1/libsrc/meshing/parallelmesh.cpp netgen/libsrc/meshing/parallelmesh.cpp
---- netgen-5.3.1/libsrc/meshing/parallelmesh.cpp	2016-02-21 20:12:55.888186643 +0100
-+++ netgen/libsrc/meshing/parallelmesh.cpp	2016-02-21 20:09:26.276180871 +0100
-@@ -1,6 +1,6 @@
- #ifdef PARALLEL
- 
--#include <meshing.hpp>
-+#include "meshing.hpp"
- #include "paralleltop.hpp"
- 
- // #define METIS4
diff --git a/sci-mathematics/netgen/files/netgen-5.x-makefiles-fixes.patch b/sci-mathematics/netgen/files/netgen-5.x-makefiles-fixes.patch
deleted file mode 100644
index b6c8fd4c1..000000000
--- a/sci-mathematics/netgen/files/netgen-5.x-makefiles-fixes.patch
+++ /dev/null
@@ -1,412 +0,0 @@
-diff -uwrN -x.git netgen-5.3.1/configure.ac netgen/configure.ac
---- netgen-5.3.1/configure.ac	2016-02-21 21:40:41.852331652 +0100
-+++ netgen/configure.ac	2016-02-21 21:39:31.355329711 +0100
-@@ -14,7 +14,6 @@
- AC_DISABLE_STATIC
- 
- AC_LANG([C++])
--AM_PROG_AR
- AC_PROG_CXX
- 
- AC_OPENMP
-@@ -36,15 +35,15 @@
-         [AC_HELP_STRING([--with-occ=dir],[use OpenCascade installed in directory dir])],
-         [occdir=$withval] 
- 	[occon=true],
--	[occdir=/opt/OpenCASCADE]
-+	[occdir=$CASROOT]
-         )
- 
- 
- 
- if test a$occon = atrue ; then
- 
--	AC_SUBST([OCCFLAGS], ["-DOCCGEOMETRY -I$occdir/inc -I/usr/include/opencascade"])
--	AC_SUBST([OCCLIBS], ["-L$occdir/lib -lTKernel -lTKGeomBase -lTKMath -lTKG2d -lTKG3d -lTKXSBase -lTKOffset -lTKFillet -lTKShHealing -lTKMesh -lTKMeshVS -lTKTopAlgo -lTKGeomAlgo -lTKBool -lTKPrim -lTKBO -lTKIGES -lTKBRep -lTKSTEPBase -lTKSTEP -lTKSTL -lTKSTEPAttr -lTKSTEP209 -lTKXDESTEP -lTKXDEIGES -lTKXCAF -lTKLCAF -lFWOSPlugin"])
-+	AC_SUBST([OCCFLAGS], ["-DOCCGEOMETRY -I$occdir/inc"])
-+	AC_SUBST([OCCLIBS], ["-lTKernel -lTKGeomBase -lTKMath -lTKG2d -lTKG3d -lTKXSBase -lTKOffset -lTKFillet -lTKShHealing -lTKMesh -lTKMeshVS -lTKTopAlgo -lTKGeomAlgo -lTKBool -lTKPrim -lTKBO -lTKIGES -lTKBRep -lTKSTEPBase -lTKSTEP -lTKSTL -lTKSTEPAttr -lTKSTEP209 -lTKXDESTEP -lTKXDEIGES -lTKXCAF -lTKLCAF -lFWOSPlugin"])
- 
- #  -lTKDCAF
- 
-@@ -90,18 +89,18 @@
-         [AC_HELP_STRING([--disable-gui],[don't build netgen with GUI])],
-         [if test "$enableval" = yes; then ngguion=true; else ngguion=false; fi])
- 
--metisdir=/usr/local
-+metisdir=/usr
- AC_ARG_WITH([metis], 
-         [AC_HELP_STRING([--with-metis=dir],[path to metis 5.x])],
-         [metisdir=$withval],
--        [metisdir=/usr/local]
-+        [metisdir=/usr]
- 	)
- 
- AC_ARG_ENABLE([parallel],
-         [AC_HELP_STRING([--enable-parallel],[enable mpi parallelization])],
--	[AC_SUBST([MPI_INCLUDES], "-I$metisdir/include -DMETIS")]
-+	[AC_SUBST([MPI_INCLUDES], "-DMETIS")]
-         [CXXFLAGS="$CXXFLAGS -DPARALLEL"]
--	[AC_SUBST([MPI_LIBS], "-L$metisdir/lib -lmetis")]
-+	[AC_SUBST([MPI_LIBS], "-lmetis")]
-         )       
- #          -DVTRACE
- #          -lvt-hyb
-diff -uwrN -x.git netgen-5.3.1/libsrc/csg/Makefile.am netgen/libsrc/csg/Makefile.am
---- netgen-5.3.1/libsrc/csg/Makefile.am	2016-02-21 21:40:41.852331652 +0100
-+++ netgen/libsrc/csg/Makefile.am	2016-02-21 21:39:31.355329711 +0100
-@@ -8,24 +8,24 @@
- AM_CPPFLAGS = -I$(top_srcdir)/libsrc/include  $(TCL_INCLUDES)
- METASOURCES = AUTO
- 
--lib_LTLIBRARIES = libcsg.la
-+lib_LTLIBRARIES = libngcsg.la
- 
- 
--libcsg_la_SOURCES = algprim.cpp brick.cpp   \
-+libngcsg_la_SOURCES = algprim.cpp brick.cpp   \
- bspline2d.cpp csgeom.cpp csgparser.cpp curve2d.cpp edgeflw.cpp	       \
- explicitcurve2d.cpp extrusion.cpp gencyl.cpp genmesh.cpp identify.cpp  \
- manifold.cpp meshsurf.cpp polyhedra.cpp revolution.cpp singularref.cpp \
- solid.cpp specpoin.cpp spline3d.cpp surface.cpp triapprox.cpp
- 
--libcsg_la_LIBADD =  $(top_builddir)/libsrc/meshing/libmesh.la
-+libngcsg_la_LIBADD =  $(top_builddir)/libsrc/meshing/libngmesh.la
- 
- 
- 
- if NGGUI
--lib_LTLIBRARIES += libcsgvis.la 
-+lib_LTLIBRARIES += libngcsgvis.la
- 
--libcsgvis_la_SOURCES = vscsg.cpp csgpkg.cpp
--libcsgvis_la_LIBADD = libcsg.la
-+libngcsgvis_la_SOURCES = vscsg.cpp csgpkg.cpp
-+libngcsgvis_la_LIBADD = libngcsg.la
- endif
- 
- #   $(top_builddir)/libsrc/geom2d/libgeom2d.la 
-diff -uwrN -x.git netgen-5.3.1/libsrc/general/Makefile.am netgen/libsrc/general/Makefile.am
---- netgen-5.3.1/libsrc/general/Makefile.am	2016-02-21 21:40:41.852331652 +0100
-+++ netgen/libsrc/general/Makefile.am	2016-02-21 21:39:31.356329711 +0100
-@@ -4,8 +4,8 @@
- 
- AM_CPPFLAGS =  $(MPI_INCLUDES) -I$(top_srcdir)/libsrc/include
- METASOURCES = AUTO
--noinst_LTLIBRARIES = libgen.la
--libgen_la_SOURCES = array.cpp bitarray.cpp dynamicmem.cpp flags.cpp \
-+noinst_LTLIBRARIES = libnggen.la
-+libnggen_la_SOURCES = array.cpp bitarray.cpp dynamicmem.cpp flags.cpp \
- 	hashtabl.cpp mystring.cpp ngexception.cpp optmem.cpp parthreads.cpp \
- 	profiler.cpp seti.cpp sort.cpp spbita2d.cpp symbolta.cpp table.cpp \
- 	mpi_interface.cpp gzstream.cpp
-diff -uwrN -x.git netgen-5.3.1/libsrc/geom2d/Makefile.am netgen/libsrc/geom2d/Makefile.am
---- netgen-5.3.1/libsrc/geom2d/Makefile.am	2016-02-21 21:40:41.852331652 +0100
-+++ netgen/libsrc/geom2d/Makefile.am	2016-02-21 21:39:31.356329711 +0100
-@@ -4,18 +4,18 @@
- 
- METASOURCES = AUTO
- 
--lib_LTLIBRARIES = libgeom2d.la 
-+lib_LTLIBRARIES = libnggeom2d.la 
- 
- if NGGUI
--lib_LTLIBRARIES += libgeom2dvis.la 
-+lib_LTLIBRARIES += libnggeom2dvis.la 
- endif
- 
- 
- 
--libgeom2d_la_SOURCES = genmesh2d.cpp geom2dmesh.cpp geometry2d.cpp
--libgeom2d_la_LIBADD = 	$(top_builddir)/libsrc/meshing/libmesh.la
-+libnggeom2d_la_SOURCES = genmesh2d.cpp geom2dmesh.cpp geometry2d.cpp
-+libnggeom2d_la_LIBADD = $(top_builddir)/libsrc/meshing/libngmesh.la $(MPI_LIBS)
- 
--libgeom2dvis_la_SOURCES = geom2dpkg.cpp vsgeom2d.cpp
--libgeom2dvis_la_LIBADD = libgeom2d.la
-+libnggeom2dvis_la_SOURCES = geom2dpkg.cpp vsgeom2d.cpp
-+libnggeom2dvis_la_LIBADD = libnggeom2d.la -lGL $(MPI_LIBS)
- 
- 
-diff -uwrN -x.git netgen-5.3.1/libsrc/gprim/Makefile.am netgen/libsrc/gprim/Makefile.am
---- netgen-5.3.1/libsrc/gprim/Makefile.am	2016-02-21 21:40:41.853331652 +0100
-+++ netgen/libsrc/gprim/Makefile.am	2016-02-21 21:39:31.357329711 +0100
-@@ -2,6 +2,6 @@
- 
- AM_CPPFLAGS = -I$(top_srcdir)/libsrc/include
- METASOURCES = AUTO
--noinst_LTLIBRARIES = libgprim.la
--libgprim_la_SOURCES = adtree.cpp geom2d.cpp geom3d.cpp geomfuncs.cpp \
-+noinst_LTLIBRARIES = libnggprim.la
-+libnggprim_la_SOURCES = adtree.cpp geom2d.cpp geom3d.cpp geomfuncs.cpp \
- 	geomtest3d.cpp transform3d.cpp spline.cpp splinegeometry.cpp
-diff -uwrN -x.git netgen-5.3.1/libsrc/interface/Makefile.am netgen/libsrc/interface/Makefile.am
---- netgen-5.3.1/libsrc/interface/Makefile.am	2016-02-21 21:40:41.853331652 +0100
-+++ netgen/libsrc/interface/Makefile.am	2016-02-21 21:39:31.357329711 +0100
-@@ -2,14 +2,14 @@
- 
- AM_CPPFLAGS = -I$(top_srcdir)/libsrc/include -I$(top_srcdir)/libsrc/interface  $(MPI_INCLUDES) $(TCL_INCLUDES) -DOPENGL
- METASOURCES = AUTO
--lib_LTLIBRARIES = libinterface.la
--libinterface_la_SOURCES = nginterface.cpp nginterface_v2.cpp \
-+lib_LTLIBRARIES = libnginterface.la
-+libnginterface_la_SOURCES = nginterface.cpp nginterface_v2.cpp \
- 	read_fnf_mesh.cpp readtetmesh.cpp readuser.cpp writeabaqus.cpp writediffpack.cpp \
- 	writedolfin.cpp writeelmer.cpp writefeap.cpp writefluent.cpp writegmsh.cpp writejcm.cpp \
- 	writepermas.cpp writetecplot.cpp writetet.cpp writetochnog.cpp writeuser.cpp \
- 	wuchemnitz.cpp writegmsh2.cpp writeOpenFOAM15x.cpp 
- 
- 
--libinterface_la_LIBADD = $(top_builddir)/libsrc/meshing/libmesh.la
-+libnginterface_la_LIBADD = $(top_builddir)/libsrc/meshing/libngmesh.la
- 
- # libinterface_la_LDFLAGS = -rdynamic
-diff -uwrN -x.git netgen-5.3.1/libsrc/linalg/Makefile.am netgen/libsrc/linalg/Makefile.am
---- netgen-5.3.1/libsrc/linalg/Makefile.am	2016-02-21 21:40:41.853331652 +0100
-+++ netgen/libsrc/linalg/Makefile.am	2016-02-21 21:39:31.357329711 +0100
-@@ -1,8 +1,8 @@
- noinst_HEADERS = densemat.hpp linalg.hpp polynomial.hpp vector.hpp opti.hpp
- AM_CPPFLAGS = -I$(top_srcdir)/libsrc/include
- METASOURCES = AUTO
--noinst_LTLIBRARIES = libla.la
--libla_la_SOURCES = densemat.cpp polynomial.cpp bfgs.cpp linopt.cpp linsearch.cpp
-+noinst_LTLIBRARIES = libngla.la
-+libngla_la_SOURCES = densemat.cpp polynomial.cpp bfgs.cpp linopt.cpp linsearch.cpp
- 
- #  vector.cpp
- 
-diff -uwrN -x.git netgen-5.3.1/libsrc/meshing/Makefile.am netgen/libsrc/meshing/Makefile.am
---- netgen-5.3.1/libsrc/meshing/Makefile.am	2016-02-21 21:40:41.853331652 +0100
-+++ netgen/libsrc/meshing/Makefile.am	2016-02-21 21:39:31.358329711 +0100
-@@ -15,9 +15,9 @@
- 
- METASOURCES = AUTO
- 
--lib_LTLIBRARIES = libmesh.la
-+lib_LTLIBRARIES = libngmesh.la
- 
--libmesh_la_SOURCES = adfront2.cpp adfront3.cpp bisect.cpp boundarylayer.cpp \
-+libngmesh_la_SOURCES = adfront2.cpp adfront3.cpp bisect.cpp boundarylayer.cpp \
- 	clusters.cpp curvedelems.cpp delaunay.cpp delaunay2d.cpp	    \
- 	geomsearch.cpp global.cpp hprefinement.cpp improve2.cpp		    \
- 	improve2gen.cpp improve3.cpp localh.cpp meshclass.cpp		    \
-@@ -30,8 +30,8 @@
- 	topology.cpp triarls.cpp validate.cpp zrefine.cpp bcfunctions.cpp   \
- 	parallelmesh.cpp  paralleltop.cpp  paralleltop.hpp basegeom.cpp 
- 
--libmesh_la_LIBADD =  $(top_builddir)/libsrc/linalg/libla.la \
--	$(top_builddir)/libsrc/gprim/libgprim.la \
--	$(top_builddir)/libsrc/general/libgen.la \
--	-lz
-+libngmesh_la_LIBADD =  $(top_builddir)/libsrc/linalg/libngla.la \
-+	$(top_builddir)/libsrc/gprim/libnggprim.la \
-+	$(top_builddir)/libsrc/general/libnggen.la \
-+	$(MPI_LIBS) -lz
- 
-diff -uwrN -x.git netgen-5.3.1/libsrc/occ/Makefile.am netgen/libsrc/occ/Makefile.am
---- netgen-5.3.1/libsrc/occ/Makefile.am	2016-02-21 21:40:41.853331652 +0100
-+++ netgen/libsrc/occ/Makefile.am	2016-02-21 21:39:31.358329711 +0100
-@@ -14,20 +14,20 @@
- 
- METASOURCES = AUTO
- 
--lib_LTLIBRARIES = libocc.la
-+lib_LTLIBRARIES = libngocc.la
- 
- if NGGUI
--lib_LTLIBRARIES += liboccvis.la 
-+lib_LTLIBRARIES += libngoccvis.la 
- endif
- 
- 
--libocc_la_SOURCES = Partition_Inter2d.cxx Partition_Inter3d.cxx \
-+libngocc_la_SOURCES = Partition_Inter2d.cxx Partition_Inter3d.cxx \
- 	Partition_Loop.cxx Partition_Loop2d.cxx Partition_Loop3d.cxx Partition_Spliter.cxx \
- 	occconstruction.cpp occgenmesh.cpp occgeom.cpp occmeshsurf.cpp
- 
--libocc_la_LIBADD = $(OCCLIBS)
-+libngocc_la_LIBADD = $(OCCLIBS)
- 
--liboccvis_la_SOURCES = occpkg.cpp vsocc.cpp
--liboccvis_la_LIBADD = libocc.la
-+libngoccvis_la_SOURCES = occpkg.cpp vsocc.cpp
-+libngoccvis_la_LIBADD = libngocc.la $(TCL_LIB_SPEC)
- 
- 
-diff -uwrN -x.git netgen-5.3.1/libsrc/stlgeom/Makefile.am netgen/libsrc/stlgeom/Makefile.am
---- netgen-5.3.1/libsrc/stlgeom/Makefile.am	2016-02-21 21:40:41.854331653 +0100
-+++ netgen/libsrc/stlgeom/Makefile.am	2016-02-21 21:39:31.359329711 +0100
-@@ -4,18 +4,18 @@
- AM_CPPFLAGS = -I$(top_srcdir)/libsrc/include $(TCL_INCLUDES)
- METASOURCES = AUTO
- 
--lib_LTLIBRARIES = libstl.la 
-+lib_LTLIBRARIES = libngstl.la 
- 
- if NGGUI
--lib_LTLIBRARIES += libstlvis.la 
-+lib_LTLIBRARIES += libngstlvis.la 
- endif
- 
--libstl_la_SOURCES = meshstlsurface.cpp stlgeom.cpp stlgeomchart.cpp \
-+libngstl_la_SOURCES = meshstlsurface.cpp stlgeom.cpp stlgeomchart.cpp \
- 	stlgeommesh.cpp stlline.cpp stltool.cpp stltopology.cpp
- 
- 
--libstlvis_la_SOURCES = stlpkg.cpp vsstl.cpp
--libstlvis_la_LIBADD = libstl.la
--libstl_la_LIBADD =  $(top_builddir)/libsrc/meshing/libmesh.la
-+libngstlvis_la_SOURCES = stlpkg.cpp vsstl.cpp
-+libngstlvis_la_LIBADD = libngstl.la  -lGL $(MPI_LIBS) $(TCL_LIB_SPEC)
-+libngstl_la_LIBADD = $(top_builddir)/libsrc/meshing/libngmesh.la $(MPI_LIBS)
- # libstlvis_la_LIBADD = libstl.la $(top_builddir)/libsrc/linalg/libla.la 
- 
-diff -uwrN -x.git netgen-5.3.1/libsrc/visualization/Makefile.am netgen/libsrc/visualization/Makefile.am
---- netgen-5.3.1/libsrc/visualization/Makefile.am	2016-02-21 21:40:41.854331653 +0100
-+++ netgen/libsrc/visualization/Makefile.am	2016-02-21 21:39:31.359329711 +0100
-@@ -7,11 +7,11 @@
- METASOURCES = AUTO
- 
- if NGGUI
--noinst_LTLIBRARIES = libvisual.la
-+noinst_LTLIBRARIES = libngvisual.la
- endif
- 
- 
--libvisual_la_SOURCES = meshdoc.cpp mvdraw.cpp \
-+libngvisual_la_SOURCES = meshdoc.cpp mvdraw.cpp \
- 	vsfieldlines.cpp vsmesh.cpp vssolution.cpp importsolution.cpp
- 
--
-+libngvisual_la_LIBADD = -lGL
-diff -uwrN -x.git netgen-5.3.1/libsrc/visualization/Makefile.in netgen/libsrc/visualization/Makefile.in
---- netgen-5.3.1/libsrc/visualization/Makefile.in	2016-02-21 21:40:41.855331653 +0100
-+++ netgen/libsrc/visualization/Makefile.in	2016-02-21 21:39:31.360329711 +0100
-@@ -275,7 +275,7 @@
- visual.hpp vssolution.hpp
- 
- include_HEADERS = soldata.hpp
--AM_CPPFLAGS = $(MPI_INCLUDES) -I$(top_srcdir)/libsrc/include  -DOPENGL -D$(TOGL_WINDOWINGSYSTEM) $(OCCFLAGS) $(TCL_INCLUDES)
-+AM_CPPFLAGS = $(MPI_INCLUDES) -I$(top_srcdir)/libsrc/include  -DOPENGL $(OCCFLAGS) $(TCL_INCLUDES)
- METASOURCES = AUTO
- @NGGUI_TRUE@noinst_LTLIBRARIES = libvisual.la
- libvisual_la_SOURCES = meshdoc.cpp mvdraw.cpp \
-diff -uwrN -x.git netgen-5.3.1/ng/Makefile.am netgen/ng/Makefile.am
---- netgen-5.3.1/ng/Makefile.am	2016-02-21 21:40:41.855331653 +0100
-+++ netgen/ng/Makefile.am	2016-02-21 21:39:31.360329711 +0100
-@@ -1,6 +1,6 @@
- include_HEADERS = 
- 
--AM_CPPFLAGS = -I$(top_srcdir)/libsrc/include -I$(top_srcdir)/libsrc/interface -DOPENGL  -D$(TOGL_WINDOWINGSYSTEM)  $(TCL_INCLUDES) $(MPI_INCLUDES) $(FFMPEG_INCLUDES) $(JPEGLIB_INCLUDES) 
-+AM_CPPFLAGS = -I$(top_srcdir)/libsrc/include -I$(top_srcdir)/libsrc/interface -DOPENGL $(TCL_INCLUDES) $(MPI_INCLUDES) $(FFMPEG_INCLUDES) $(JPEGLIB_INCLUDES) 
- 
- 
- if NGGUI
-@@ -17,21 +17,18 @@
- endif
- # -lpardiso500-GNU472-X86-64 -lgfortran
- 
--netgen_LDADD = $(top_builddir)/libsrc/visualization/libvisual.la \
--	$(top_builddir)/libsrc/csg/libcsgvis.la \
--	$(top_builddir)/libsrc/csg/libcsg.la \
--	$(top_builddir)/libsrc/interface/libinterface.la \
--	$(top_builddir)/libsrc/meshing/libmesh.la \
--	-L$(TK_BIN_DIR)/Togl1.7 $(TOGLLIBDIR) -lTogl $(LIBGLU) $(TK_LIB_SPEC) $(TCL_LIB_SPEC) $(MPI_LIBS) $(FFMPEG_LIBS) $(JPEGLIB_LIBS) $(PKG_LIBS) $(MKL_LIBS) 
--
--
--#
--#	$(top_builddir)/libsrc/occ/liboccvis.la 
--#	$(top_builddir)/libsrc/occ/libocc.la 
--#	$(top_builddir)/libsrc/stlgeom/libstlvis.la 
--#	$(top_builddir)/libsrc/stlgeom/libstl.la 
--#	$(top_builddir)/libsrc/geom2d/libgeom2d.la 
--#	$(top_builddir)/libsrc/geom2d/libgeom2dvis.la 
-+netgen_LDADD = $(top_builddir)/libsrc/visualization/libngvisual.la \
-+	$(top_builddir)/libsrc/csg/libngcsgvis.la \
-+	$(top_builddir)/libsrc/csg/libngcsg.la \
-+	$(top_builddir)/libsrc/interface/libnginterface.la \
-+	$(top_builddir)/libsrc/meshing/libngmesh.la \
-+	$(top_builddir)/libsrc/occ/libngoccvis.la \
-+	$(top_builddir)/libsrc/occ/libngocc.la \
-+	$(top_builddir)/libsrc/stlgeom/libngstlvis.la \
-+	$(top_builddir)/libsrc/stlgeom/libngstl.la \
-+	$(top_builddir)/libsrc/geom2d/libnggeom2d.la \
-+	$(top_builddir)/libsrc/geom2d/libnggeom2dvis.la \
-+	-L$(TK_BIN_DIR)/Togl1.7 $(TOGLLIBDIR) -lTogl1.7 -ldl -lX11 $(LIBGLU) $(TK_LIB_SPEC) $(TCL_LIB_SPEC) $(MPI_LIBS) $(FFMPEG_LIBS) $(JPEGLIB_LIBS) $(PKG_LIBS) $(MKL_LIBS)
- 
- 
- # add for static linkage of ngsolve:
-diff -uwrN -x.git netgen-5.3.1/ng/Makefile.in netgen/ng/Makefile.in
---- netgen-5.3.1/ng/Makefile.in	2016-02-21 21:40:41.856331653 +0100
-+++ netgen/ng/Makefile.in	2016-02-21 21:39:31.361329711 +0100
-@@ -302,7 +302,7 @@
- include_HEADERS = 
- AM_CPPFLAGS = -I$(top_srcdir)/libsrc/include \
- 	-I$(top_srcdir)/libsrc/interface -DOPENGL \
--	-D$(TOGL_WINDOWINGSYSTEM) $(TCL_INCLUDES) $(MPI_INCLUDES) \
-+	$(TCL_INCLUDES) $(MPI_INCLUDES) \
- 	$(FFMPEG_INCLUDES) $(JPEGLIB_INCLUDES) $(am__append_1)
- netgen_SOURCES = demoview.cpp ngappinit.cpp onetcl.cpp parallelfunc.cpp ngpkg.cpp demoview.hpp parallelfunc.hpp togl_1_7.h
- @NGMKL_TRUE@MKL_LIBS = -L$(MKLROOT)/lib/intel64  -lmkl_intel_lp64 -lmkl_gnu_thread -lmkl_core -lmkl_def
-diff -uwrN -x.git netgen-5.3.1/nglib/Makefile.am netgen/nglib/Makefile.am
---- netgen-5.3.1/nglib/Makefile.am	2016-02-21 21:40:41.856331653 +0100
-+++ netgen/nglib/Makefile.am	2016-02-21 21:39:31.362329711 +0100
-@@ -8,15 +8,15 @@
- libnglib_la_SOURCES = nglib.cpp 
- 
- libnglib_la_LIBADD = \
--	$(top_builddir)/libsrc/interface/libinterface.la \
--	$(top_builddir)/libsrc/geom2d/libgeom2d.la \
--	$(top_builddir)/libsrc/csg/libcsg.la \
--	$(top_builddir)/libsrc/stlgeom/libstl.la \
--	$(top_builddir)/libsrc/occ/libocc.la \
--	$(top_builddir)/libsrc/meshing/libmesh.la \
-+	$(top_builddir)/libsrc/interface/libnginterface.la \
-+	$(top_builddir)/libsrc/geom2d/libnggeom2d.la \
-+	$(top_builddir)/libsrc/csg/libngcsg.la \
-+	$(top_builddir)/libsrc/stlgeom/libngstl.la \
-+	$(top_builddir)/libsrc/occ/libngocc.la \
-+	$(top_builddir)/libsrc/meshing/libngmesh.la \
- 	$(OCCLIBS) $(MPI_LIBS)
- 
--libnglib_la_LDFLAGS = -avoid-version
-+libnglib_la_LDFLAGS = -release $(PACKAGE_VERSION)
- #  -rdynamic
- 
- 
-@@ -25,24 +25,24 @@
- 
- ng_vol_SOURCES = ng_vol.cpp
- ng_vol_LDADD = libnglib.la \
--	$(top_builddir)/libsrc/interface/libinterface.la \
--	$(top_builddir)/libsrc/geom2d/libgeom2d.la \
--	$(top_builddir)/libsrc/csg/libcsg.la \
--	$(top_builddir)/libsrc/stlgeom/libstl.la \
--	$(top_builddir)/libsrc/occ/libocc.la \
--	$(top_builddir)/libsrc/meshing/libmesh.la \
-+	$(top_builddir)/libsrc/interface/libnginterface.la \
-+	$(top_builddir)/libsrc/geom2d/libnggeom2d.la \
-+	$(top_builddir)/libsrc/csg/libngcsg.la \
-+	$(top_builddir)/libsrc/stlgeom/libngstl.la \
-+	$(top_builddir)/libsrc/occ/libngocc.la \
-+	$(top_builddir)/libsrc/meshing/libngmesh.la \
- 	$(OCCLIBS) $(MPI_LIBS)
- 
- 
- 
- ng_stl_SOURCES = ng_stl.cpp
- ng_stl_LDADD = libnglib.la \
--	$(top_builddir)/libsrc/interface/libinterface.la \
--	$(top_builddir)/libsrc/geom2d/libgeom2d.la \
--	$(top_builddir)/libsrc/csg/libcsg.la \
--	$(top_builddir)/libsrc/stlgeom/libstl.la \
--	$(top_builddir)/libsrc/occ/libocc.la \
--	$(top_builddir)/libsrc/meshing/libmesh.la \
-+	$(top_builddir)/libsrc/interface/libnginterface.la \
-+	$(top_builddir)/libsrc/geom2d/libnggeom2d.la \
-+	$(top_builddir)/libsrc/csg/libngcsg.la \
-+	$(top_builddir)/libsrc/stlgeom/libngstl.la \
-+	$(top_builddir)/libsrc/occ/libngocc.la \
-+	$(top_builddir)/libsrc/meshing/libngmesh.la \
- 	$(OCCLIBS) $(MPI_LIBS)
- 
- # ng_occ_SOURCES = ng_occ.cpp
diff --git a/sci-mathematics/netgen/files/netgen-5.x-metis-fixes.patch b/sci-mathematics/netgen/files/netgen-5.x-metis-fixes.patch
deleted file mode 100644
index cf59613e4..000000000
--- a/sci-mathematics/netgen/files/netgen-5.x-metis-fixes.patch
+++ /dev/null
@@ -1,102 +0,0 @@
---- netgen-5.3.1.ORIG/libsrc/meshing/parallelmesh.cpp	2014-08-29 11:54:05.000000000 +0200
-+++ netgen/libsrc/meshing/parallelmesh.cpp	2016-02-20 23:07:00.350568182 +0100
-@@ -14,7 +14,7 @@
- 
- #if METIS_VER_MAJOR >= 5
- #define METIS5
--    typedef idx_t idxtype;   
-+    typedef metis::idx_t idxtype;
- #else
- #define METIS4
-     typedef idxtype idx_t;  
-@@ -794,10 +794,10 @@
-     eptr.Append (eind.Size());
-     Array<idx_t> epart(ne), npart(nn);
- 
--    int nparts = ntasks-1;
--    int edgecut;
-+    metis::idx_t nparts = ntasks-1;
-+    metis::idx_t edgecut;
- 
--    int ncommon = 3;
-+    metis::idx_t ncommon = 3;
-     METIS_PartMeshDual (&ne, &nn, &eptr[0], &eind[0], NULL, NULL, &ncommon, &nparts,
- 			NULL, NULL,
- 			&edgecut, &epart[0], &npart[0]);
-@@ -1029,11 +1029,11 @@
-     eptr.Append (eind.Size());
-     Array<idx_t> epart(ne), npart(nn);
- 
--    int nparts = ntasks-1;
--    int edgecut;
-+    metis::idx_t nparts = ntasks-1;
-+    metis::idx_t edgecut;
- 
- 
--    int ncommon = 3;
-+    metis::idx_t ncommon = 3;
-     METIS_PartMeshDual (&ne, &nn, &eptr[0], &eind[0], &nwgt[0], NULL, &ncommon, &nparts,
- 			NULL, NULL,
- 			&edgecut, &epart[0], &npart[0]);
-@@ -1266,7 +1266,7 @@
- 
-     for ( int vert = 0; vert < nn; vert++ )
-       {
--	FlatArray<int> array ( cnt[vert], &adjacency[ xadj[vert] ] );
-+	FlatArray<metis::idx_t> array ( cnt[vert], &adjacency[ xadj[vert] ] );
- 	BubbleSort(array);
-       }
- 
-@@ -1318,7 +1318,7 @@
-     idxtype  *xadj, * adjacency, *v_weights = NULL, *e_weights = NULL;
- 
-     int weightflag = 0;
--    // int numflag = 0;
-+    int numflag = 0;
-     int nparts = ntasks - 1;
- 
-     int options[5];
-@@ -1377,7 +1377,7 @@
- 
-     for ( int el = 0; el < ne; el++ )
-       {
--	FlatArray<int> array ( cnt[el], &adjacency[ xadj[el] ] );
-+	FlatArray<metis::idx_t> array ( cnt[el], &adjacency[ xadj[el] ] );
- 	BubbleSort(array);
-       }
- 
-@@ -1428,8 +1428,8 @@
-   void Mesh :: PartDualHybridMesh2D ( ) 
-   {
- #ifdef METIS
--    int ne = GetNSE();
--    int nv = GetNV();
-+    metis::idx_t ne = GetNSE();
-+    metis::idx_t nv = GetNV();
- 
-     Array<idxtype> xadj(ne+1);
-     Array<idxtype> adjacency(ne*4);
-@@ -1484,18 +1484,18 @@
- 
-     idxtype *v_weights = NULL, *e_weights = NULL;
- 
--    int weightflag = 0;
--    // int numflag = 0;
--    int nparts = ntasks - 1;
-+    metis::idx_t weightflag = 0;
-+    metis::idx_t numflag = 0;
-+    metis::idx_t nparts = ntasks - 1;
- 
--    int edgecut;
-+    metis::idx_t edgecut;
-     Array<idxtype> part(ne);
- 
-     for ( int el = 0; el < ne; el++ )
-       BubbleSort (adjacency.Range (xadj[el], xadj[el+1]));
- 
- #ifdef METIS4	
--    int options[5];
-+    metis::idx_t options[5];
-     options[0] = 0;
-     METIS_PartGraphKway ( &ne, &xadj[0], &adjacency[0], v_weights, e_weights, &weightflag, 
- 			  &numflag, &nparts, options, &edgecut, &part[0] );
diff --git a/sci-mathematics/netgen/files/netgen-5.x-missing-define.patch b/sci-mathematics/netgen/files/netgen-5.x-missing-define.patch
deleted file mode 100644
index d9d8f99ef..000000000
--- a/sci-mathematics/netgen/files/netgen-5.x-missing-define.patch
+++ /dev/null
@@ -1,38 +0,0 @@
---- a/libsrc/occ/Partition_Loop2d.cxx	2012-11-14 21:16:22.876287910 +0100
-+++ b/libsrc/occ/Partition_Loop2d.cxx	2012-11-14 21:22:30.909650554 +0100
-@@ -13,6 +13,7 @@
- 
- //using namespace std;
- #include <climits>
-+#include <cmath>
- #include "Partition_Loop2d.ixx"
- 
- #include "utilities.h"
-@@ -210,7 +211,7 @@
-     Cc->D1(uc, PC, CTg1);
-     if (!isForward) CTg1.Reverse();
- 
--    Standard_Real anglemin = 3 * PI, tolAng = 1.e-8;
-+    Standard_Real anglemin = 3 * M_PI, tolAng = 1.e-8;
- 
-     // select an edge whose first derivative is most left of CTg1
-     // ie an angle between Tg1 and CTg1 is least
-@@ -234,7 +235,7 @@
-       // -PI < angle < PI
-       Standard_Real angle = Tg1.Angle(CTg1);
- 
--      if (PI - Abs(angle) <= tolAng)
-+      if (M_PI - Abs(angle) <= tolAng)
-       {
-         // an angle is too close to PI; assure that an angle sign really
-         // reflects an edge position: +PI - an edge is worst,
---- a/configure.ac	2012-11-15 14:55:45.048938870 +0100
-+++ b/configure.ac	2012-11-15 14:55:12.545923777 +0100
-@@ -14,6 +14,7 @@
- AC_DISABLE_STATIC
- 
- AC_LANG([C++])
-+AM_PROG_AR
- AC_PROG_CXX
- AC_PROG_LIBTOOL
- LT_INIT
diff --git a/sci-mathematics/netgen/files/netgen-5.x-occ-stl-api-change.patch b/sci-mathematics/netgen/files/netgen-5.x-occ-stl-api-change.patch
deleted file mode 100644
index 0452d6b73..000000000
--- a/sci-mathematics/netgen/files/netgen-5.x-occ-stl-api-change.patch
+++ /dev/null
@@ -1,94 +0,0 @@
---- a/libsrc/occ/occgeom.cpp	2014-08-29 11:54:03.000000000 +0200
-+++ b/libsrc/occ/occgeom.cpp	2016-02-12 21:14:49.258982206 +0100
-@@ -149,7 +149,7 @@
- 

-          for (exp0.Init (shape, TopAbs_FACE); exp0.More(); exp0.Next())

-          {

--            // Variable to hold the colour (if there exists one) of 

-+            // Variable to hold the colour (if there exists one) of

-             // the current face being processed

-             Quantity_Color face_colour;

- 

-@@ -190,7 +190,7 @@
-                rebuild->Replace(face, newface, Standard_False);

-             }

- 

--            // Set the original colour of the face to the newly created 

-+            // Set the original colour of the face to the newly created

-             // face (after the healing process)

-             face = TopoDS::Face (exp0.Current());

-             face_colours->SetColor(face,face_colour,XCAFDoc_ColorSurf);

-@@ -815,11 +815,11 @@
-       face_maxh.SetSize (fmap.Extent());

-       face_maxh = mparam.maxh;

- 

--      // Philippose - 15/01/2010      

--      face_maxh_modified.DeleteAll();      

--      face_maxh_modified.SetSize(fmap.Extent());      

-+      // Philippose - 15/01/2010

-+      face_maxh_modified.DeleteAll();

-+      face_maxh_modified.SetSize(fmap.Extent());

-       face_maxh_modified = 0;

--      

-+

- 

-       // Philippose - 17/01/2009

-       face_sel_status.DeleteAll();

-@@ -845,7 +845,7 @@
-       cout << "Trying to sew faces ..." << flush;

- 

-       BRepOffsetAPI_Sewing sewedObj(1);

-- 

-+

-       for (int i = 1; i <= fmap.Extent(); i++)

-       {

-          TopoDS_Face face = TopoDS::Face (fmap(i));

-@@ -1038,9 +1038,6 @@
-    {

-       cout << "writing stl..."; cout.flush();

-       StlAPI_Writer writer;

--      writer.RelativeMode() = Standard_False;

--

--      writer.SetDeflection(0.02);

-       writer.Write(shape,filename);

- 

-       cout << "done" << endl;

-@@ -1109,7 +1106,7 @@
-       }

- 

- 

--      // For the IGES Reader, all the shapes can be exported as one compund shape 

-+      // For the IGES Reader, all the shapes can be exported as one compund shape

-       // using the "OneShape" member

-       occgeo->shape = reader.OneShape();

-       occgeo->face_colours = iges_colour_contents;

-@@ -1187,7 +1184,7 @@
-       }

- 

- 

--      // For the STEP File Reader in OCC, the 1st Shape contains the entire 

-+      // For the STEP File Reader in OCC, the 1st Shape contains the entire

-       // compound geometry as one shape

-       occgeo->shape = step_shape_contents->GetShape(step_shapes.Value(1));

-       occgeo->face_colours = step_colour_contents;

-@@ -1218,7 +1215,7 @@
-       }

- 

-       // Philippose - 23/02/2009

--      // Fixed a bug in the OpenCascade XDE Colour handling when 

-+      // Fixed a bug in the OpenCascade XDE Colour handling when

-       // opening BREP Files, since BREP Files have no colour data.

-       // Hence, the face_colours Handle needs to be created as a NULL handle.

-       occgeo->face_colours = Handle_XCAFDoc_ColorTool();

-@@ -1236,9 +1233,9 @@
-   void OCCGeometry :: Save (string sfilename) const

-   {

-     const char * filename = sfilename.c_str();

--    if (strlen(filename) < 4) 

-+    if (strlen(filename) < 4)

-       throw NgException ("illegal filename");

--    

-+

-     if (strcmp (&filename[strlen(filename)-3], "igs") == 0)

-       {

- 	IGESControl_Writer writer("millimeters", 1);

diff --git a/sci-mathematics/netgen/files/netgen-5.x-parallelmetis4-fix.patch b/sci-mathematics/netgen/files/netgen-5.x-parallelmetis4-fix.patch
deleted file mode 100644
index 0170fb8c3..000000000
--- a/sci-mathematics/netgen/files/netgen-5.x-parallelmetis4-fix.patch
+++ /dev/null
@@ -1,36 +0,0 @@
-diff -uwrN -x.git netgen-5.3.1/libsrc/meshing/parallelmesh.cpp netgen/libsrc/meshing/parallelmesh.cpp
---- netgen-5.3.1/libsrc/meshing/parallelmesh.cpp	2016-02-22 00:22:28.885598956 +0100
-+++ netgen/libsrc/meshing/parallelmesh.cpp	2016-02-22 00:46:17.030638283 +0100
-@@ -962,10 +962,15 @@
-   }
-   
- 
--#ifdef METIS5
-+#ifdef METIS
-   void Mesh :: ParallelMetis (Array<int> & volume_weights , Array<int> & surface_weights, Array<int> & segment_weights)  
-   {
-+
-+  	#ifdef METIS5
-     PrintMessage (3, "call metis 5 with weights ...");
-+    #else
-+    PrintMessage (3, "call metis 4 with weights ...");
-+    #endif
-     
-     // cout << "segment_weights " << segment_weights << endl;
-     // cout << "surface_weights " << surface_weights << endl;
-@@ -1034,9 +1039,15 @@
- 
- 
-     metis::idx_t ncommon = 3;
-+    #ifdef METIS5
-     METIS_PartMeshDual (&ne, &nn, &eptr[0], &eind[0], &nwgt[0], NULL, &ncommon, &nparts,
- 			NULL, NULL,
- 			&edgecut, &epart[0], &npart[0]);
-+    #else
-+    int numflag = 0;
-+    METIS_PartMeshDual (&ne, &nn, &eptr[0], &eind[0], &numflag, &nparts,
-+    	&edgecut, &epart[0], &npart[0]);
-+    #endif
-     /*
-     METIS_PartMeshNodal (&ne, &nn, &eptr[0], &eind[0], NULL, NULL, &nparts,
- 			 NULL, NULL,
diff --git a/sci-mathematics/netgen/files/netgen.desktop b/sci-mathematics/netgen/files/netgen.desktop
deleted file mode 100644
index 714ba53c4..000000000
--- a/sci-mathematics/netgen/files/netgen.desktop
+++ /dev/null
@@ -1,8 +0,0 @@
-[Desktop Entry]
-Name=Netgen
-Comment=3D modeling, Mesh generation.
-Exec=/usr/bin/netgen
-Icon=netgen
-Terminal=false
-Type=Application
-Categories=Graphics;
diff --git a/sci-mathematics/netgen/files/netgen.png b/sci-mathematics/netgen/files/netgen.png
deleted file mode 100644
index cb2fd8466..000000000
--- a/sci-mathematics/netgen/files/netgen.png
+++ /dev/null
diff --git a/sci-mathematics/netgen/metadata.xml b/sci-mathematics/netgen/metadata.xml
deleted file mode 100644
index a2cd926a4..000000000
--- a/sci-mathematics/netgen/metadata.xml
+++ /dev/null
@@ -1,14 +0,0 @@
-<?xml version="1.0" encoding="UTF-8"?>
-<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
-<pkgmetadata>
-	<maintainer type="project">
-		<email>sci-mathematics@gentoo.org</email>
-		<name>Gentoo Mathematics Project</name>
-	</maintainer>
-	<use>
-		<flag name="opencascade"> Enable OpenCASCADE support</flag>
-	</use>
-	<upstream>
-		<remote-id type="sourceforge">netgen-mesher</remote-id>
-	</upstream>
-</pkgmetadata>
diff --git a/sci-mathematics/netgen/netgen-4.9.13.ebuild b/sci-mathematics/netgen/netgen-4.9.13.ebuild
deleted file mode 100644
index ef4f19b3e..000000000
--- a/sci-mathematics/netgen/netgen-4.9.13.ebuild
+++ /dev/null
@@ -1,77 +0,0 @@
-# Copyright 1999-2015 Gentoo Foundation
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=5
-
-inherit eutils flag-o-matic multilib versionator
-
-DESCRIPTION="Automatic 3d tetrahedral mesh generator"
-HOMEPAGE="http://www.hpfem.jku.at/netgen/"
-SRC_URI="mirror://sourceforge/netgen-mesher/${P}.tar.gz"
-
-SLOT="0"
-LICENSE="LGPL-2.1"
-KEYWORDS="~amd64 ~x86"
-IUSE="-ffmpeg jpeg -mpi opencascade"
-
-DEPEND="
-	dev-tcltk/tix
-	dev-tcltk/togl:1.7
-	virtual/opengl
-	x11-libs/libXmu
-	opencascade? ( sci-libs/opencascade:* )
-	ffmpeg? ( media-video/ffmpeg )
-	jpeg? ( virtual/jpeg:0= )
-	mpi? ( virtual/mpi ) "
-RDEPEND="${DEPEND}"
-# Note, MPI has not be tested.
-
-src_configure() {
-	# This is not the most clever way to deal with these flags
-	# but --disable-xxx does not seem to work correcly, so...
-	local myconf="--with-togl=/usr/$(get_libdir)/Togl1.7"
-
-	if use opencascade; then
-		myconf="${myconf} --enable-occ --with-occ=$CASROOT"
-		append-ldflags -L$CASROOT/lin/$(get_libdir)
-	fi
-
-	use mpi && myconf="${myconf} --enable-parallel"
-	use ffmpeg && myconf="${myconf} --enable-ffmpeg"
-	use jpeg && myconf="${myconf} --enable-jpeglib"
-
-	append-flags -I/usr/include/togl-1.7
-
-	econf \
-		${myconf}
-
-	# This would be the more elegant way:
-# 	econf \
-# 		$(use_enable opencascade occ) \
-# 		$(use_with opencascade "occ=$CASROOT") \
-# 		$(use_enable mpi parallel) \
-# 		$(use_enable ffmpeg) \
-# 		$(use_enable jpeg jpeglib)
-}
-
-src_install() {
-	local NETGENDIR="/usr/share/netgen"
-
-	echo -e "NETGENDIR=${NETGENDIR} \nLDPATH=/usr/$(get_libdir)/Togl1.7" > ./99netgen
-	doenvd 99netgen
-
-	default
-	mv "${D}"/usr/bin/{*.tcl,*.ocf} "${D}${NETGENDIR}"
-
-	# Install icon and .desktop for menu entry
-	doicon "${FILESDIR}"/${PN}.png
-	domenu "${FILESDIR}"/${PN}.desktop
-}
-
-pkg_postinst() {
-	elog "Please make sure to update your environment variables:"
-	elog "env-update && source /etc/profile"
-	elog "Netgen ebuild is still under development."
-	elog "Help us improve the ebuild in:"
-	elog "http://bugs.gentoo.org/show_bug.cgi?id=155424"
-}
diff --git a/sci-mathematics/netgen/netgen-5.0.0.ebuild b/sci-mathematics/netgen/netgen-5.0.0.ebuild
deleted file mode 100644
index 2e5d37fde..000000000
--- a/sci-mathematics/netgen/netgen-5.0.0.ebuild
+++ /dev/null
@@ -1,88 +0,0 @@
-# Copyright 1999-2015 Gentoo Foundation
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=5
-
-inherit autotools eutils flag-o-matic multilib versionator
-
-MY_PN=${PN}-mesher
-MY_PV=$(get_version_component_range 1-2)
-DESCRIPTION="NETGEN is an automatic 3d tetrahedral mesh generator"
-HOMEPAGE="http://www.hpfem.jku.at/netgen/"
-SRC_URI="mirror://sourceforge/project/${MY_PN}/${MY_PN}/${MY_PV}/${P}.tar.gz"
-
-SLOT="0"
-LICENSE="LGPL-2.1"
-KEYWORDS="~amd64 ~x86"
-IUSE="-ffmpeg jpeg -mpi opencascade"
-
-DEPEND="
-	dev-tcltk/tix
-	dev-tcltk/togl:1.7
-	virtual/opengl
-	x11-libs/libXmu
-	opencascade? ( sci-libs/opencascade:* )
-	ffmpeg? ( media-video/ffmpeg )
-	jpeg? ( virtual/jpeg:0= )
-	mpi? ( virtual/mpi ( || ( sci-libs/parmetis sci-libs/metis ) ) ) "
-RDEPEND="${DEPEND}"
-# Note, MPI has not be tested.
-
-src_prepare() {
-	# Adapted from http://sourceforge.net/projects/netgen-mesher/forums/forum/905307/topic/5422824
-	epatch "${FILESDIR}/${PN}-5.x-compile-against-occ-6.5.x.patch"
-	epatch "${FILESDIR}/${PN}-5.x-missing-define.patch"
-	eautoreconf
-}
-
-src_configure() {
-	# This is not the most clever way to deal with these flags
-	# but --disable-xxx does not seem to work correcly, so...
-	sed -i -e 's:-lTogl:-lTogl1.7:' ng/Makefile.am || die
-	local myconf="--with-togl=/usr/$(get_libdir)/Togl1.7"
-
-	if use opencascade; then
-		myconf="${myconf} --enable-occ --with-occ=$CASROOT"
-		append-ldflags -L$CASROOT/lin/$(get_libdir)
-	fi
-	if use mpi; then
-		myconf="${myconf} --enable-parallel"
-		append-cppflags -I/usr/include/metis
-	fi
-	use ffmpeg && myconf="${myconf} --enable-ffmpeg"
-	use jpeg && myconf="${myconf} --enable-jpeglib"
-	append-cppflags -I/usr/include/togl-1.7
-
-	econf \
-		${myconf}
-
-	# This would be the more elegant way:
-# 	econf \
-# 		$(use_enable opencascade occ) \
-# 		$(use_with opencascade "occ=$CASROOT") \
-# 		$(use_enable mpi parallel) \
-# 		$(use_enable ffmpeg) \
-# 		$(use_enable jpeg jpeglib)
-}
-
-src_install() {
-	local NETGENDIR="/usr/share/netgen"
-
-	echo -e "NETGENDIR=${NETGENDIR} \nLDPATH=/usr/$(get_libdir)/Togl1.7" > ./99netgen
-	doenvd 99netgen
-
-	default
-	mv "${D}"/usr/bin/{*.tcl,*.ocf} "${D}${NETGENDIR}" || die
-
-	# Install icon and .desktop for menu entry
-	doicon "${FILESDIR}"/${PN}.png
-	domenu "${FILESDIR}"/${PN}.desktop
-}
-
-pkg_postinst() {
-	elog "Please make sure to update your environment variables:"
-	elog "env-update && source /etc/profile"
-	elog "Netgen ebuild is still under development."
-	elog "Help us improve the ebuild in:"
-	elog "http://bugs.gentoo.org/show_bug.cgi?id=155424"
-}
diff --git a/sci-mathematics/netgen/netgen-5.3.1.ebuild b/sci-mathematics/netgen/netgen-5.3.1.ebuild
deleted file mode 100644
index 4dd089d1a..000000000
--- a/sci-mathematics/netgen/netgen-5.3.1.ebuild
+++ /dev/null
@@ -1,119 +0,0 @@
-# Copyright 1999-2016 Gentoo Foundation
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=6
-
-inherit autotools eutils flag-o-matic multilib versionator
-
-MY_PN=${PN}-mesher
-MY_PV=$(get_version_component_range 1-2)
-DESCRIPTION="Automatic 3d tetrahedral mesh generator"
-HOMEPAGE="http://www.hpfem.jku.at/netgen/"
-SRC_URI="mirror://sourceforge/project/${MY_PN}/${MY_PN}/${MY_PV}/${P}.tar.gz"
-
-SLOT="0"
-LICENSE="LGPL-2.1"
-KEYWORDS="~amd64 ~x86"
-IUSE="-ffmpeg jpeg -mpi opencascade openmp"
-
-DEPEND="
-	dev-lang/tcl:0
-	dev-lang/tk:0
-	dev-tcltk/tix
-	dev-tcltk/togl:1.7
-	virtual/opengl
-	x11-libs/libX11
-	x11-libs/libXmu
-	opencascade? ( sci-libs/opencascade:* )
-	ffmpeg? ( media-video/ffmpeg )
-	jpeg? ( virtual/jpeg:0= )
-	mpi? ( virtual/mpi || ( sci-libs/parmetis <sci-libs/metis-5.0 ) opencascade? ( sci-libs/hdf5[mpi] ) ) "
-RDEPEND="${DEPEND}"
-# Note, MPI has not be tested.
-
-PATCHES=(
-	# Adapted from http://sourceforge.net/projects/netgen-mesher/forums/forum/905307/topic/5422824
-	"${FILESDIR}"/${PN}-5.x-missing-define.patch
-	# Adapted from http://pkgs.fedoraproject.org/cgit/rpms/netgen-mesher.git/tree/netgen-5.3.0_metis.patch
-	"${FILESDIR}"/${PN}-5.x-metis-fixes.patch
-	"${FILESDIR}"/${PN}-5.x-occ-stl-api-change.patch
-	# Adapted from http://pkgs.fedoraproject.org/cgit/rpms/netgen-mesher.git/tree/netgen-5.3.1_build.patch
-	"${FILESDIR}"/${PN}-5.x-makefiles-fixes.patch
-	# Adapted from http://pkgs.fedoraproject.org/cgit/rpms/netgen-mesher.git/tree/netgen-5.3.0_fixes.patch
-	"${FILESDIR}"/${PN}-5.x-fedora-fixes.patch
-	"${FILESDIR}"/${PN}-5.x-includes-fixes.patch
-	"${FILESDIR}"/${PN}-5.x-parallelmetis4-fix.patch
-)
-
-src_prepare() {
-	default
-	if use mpi; then
-		export CC=mpicc
-		export CXX=mpic++
-		export FC=mpif90
-		export F90=mpif90
-		export F77=mpif77
-	fi
-	eautoreconf
-}
-
-src_configure() {
-	# This is not the most clever way to deal with these flags
-	# but --disable-xxx does not seem to work correcly, so...
-	local myconf=( --with-togl=/usr/$(get_libdir)/Togl1.7 )
-
-	myconf+=( $(use_enable openmp) )
-
-	if use opencascade; then
-		myconf+=( --enable-occ --with-occ=$CASROOT )
-		append-ldflags -L$CASROOT/$(get_libdir)
-	fi
-	if use mpi; then
-		ewarn "*************************************************************************"
-		ewarn ""
-		ewarn "MPI has not been tested, you should probably deactivate the mpi use flag"
-		ewarn ""
-		ewarn "*************************************************************************"
-		myconf+=( --enable-parallel )
-		append-cppflags -I/usr/include/metis
-		append-ldflags -L/usr/$(get_libdir)/openmpi/
-	fi
-	use ffmpeg && myconf+=( --enable-ffmpeg )
-	use jpeg && myconf+=( --enable-jpeglib )
-	append-cppflags -I/usr/include/togl-1.7
-
-	econf \
-		${myconf[@]}
-
-	# This would be the more elegant way:
-# 	econf \
-# 		$(use_enable opencascade occ) \
-# 		$(use_with opencascade "occ=$CASROOT") \
-# 		$(use_enable mpi parallel) \
-# 		$(use_enable ffmpeg) \
-# 		$(use_enable jpeg jpeglib)
-}
-
-src_install() {
-	local NETGENDIR="/usr/share/netgen"
-
-	echo -e "NETGENDIR=${NETGENDIR} \nLDPATH=/usr/$(get_libdir)/Togl1.7" > ./99netgen
-	doenvd 99netgen
-
-	default
-	mv "${D}"/usr/bin/{*.tcl,*.ocf} "${D}${NETGENDIR}" || die
-
-	# Install icon and .desktop for menu entry
-	doicon "${FILESDIR}"/${PN}.png
-	domenu "${FILESDIR}"/${PN}.desktop
-
-	prune_libtool_files
-}
-
-pkg_postinst() {
-	elog "Please make sure to update your environment variables:"
-	elog "env-update && source /etc/profile"
-	elog "Netgen ebuild is still under development."
-	elog "Help us improve the ebuild in:"
-	elog "http://bugs.gentoo.org/show_bug.cgi?id=155424"
-}
diff --git a/sci-mathematics/open-axiom/Manifest b/sci-mathematics/open-axiom/Manifest
deleted file mode 100644
index a0dc72105..000000000
--- a/sci-mathematics/open-axiom/Manifest
+++ /dev/null
@@ -1 +0,0 @@
-DIST open-axiom-1.4.2.tar.bz2 9862899 BLAKE2B 998961529a9cd632bca0c82b0575ec5f24260e896ef4b74d54160242a7b033680b990a3cf8fa3e4182c27d9bbe998f697bb9c1b47050c2101ab30c62f56e3fe1 SHA512 7db25874c9427e0fe5903f3d9e8ef8d265f132bf839e184efa290795f65b8f1752e8ffd0602142c2260404d79e30793b1cd37a2a25db4a4258d7b7682b8acc1a
diff --git a/sci-mathematics/open-axiom/metadata.xml b/sci-mathematics/open-axiom/metadata.xml
deleted file mode 100644
index c9b1f5cd4..000000000
--- a/sci-mathematics/open-axiom/metadata.xml
+++ /dev/null
@@ -1,17 +0,0 @@
-<?xml version="1.0" encoding="UTF-8"?>
-<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
-<pkgmetadata>
-	<maintainer type="project">
-		<email>sci-mathematics@gentoo.org</email>
-		<name>Gentoo Mathematics Project</name>
-	</maintainer>
-	<longdescription lang="en">
-OpenAxiom is an open source platform for symbolic, algebraic, and
-numerical computations. It offers an interactive environment, an expressive
-programming language, a compiler, a large set of mathematical libraries of
-interest to researchers and practitioners of computational sciences.
-</longdescription>
-	<upstream>
-		<remote-id type="sourceforge">open-axiom</remote-id>
-	</upstream>
-</pkgmetadata>
diff --git a/sci-mathematics/open-axiom/open-axiom-1.4.2.ebuild b/sci-mathematics/open-axiom/open-axiom-1.4.2.ebuild
deleted file mode 100644
index 402e19eb2..000000000
--- a/sci-mathematics/open-axiom/open-axiom-1.4.2.ebuild
+++ /dev/null
@@ -1,36 +0,0 @@
-# Copyright 1999-2018 Gentoo Foundation
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=6
-
-DESCRIPTION="Symbolic and algebraic computations system"
-HOMEPAGE="http://www.open-axiom.org/"
-SRC_URI="mirror://sourceforge/project/${PN}/${PV}/${P}.tar.bz2"
-
-LICENSE="BSD"
-SLOT="0"
-KEYWORDS=""
-
-IUSE="X"
-
-RDEPEND="X? ( x11-libs/libXpm )"
-DEPEND="${RDEPEND}
-	app-text/noweb
-	>=dev-lisp/sbcl-1.0.22"
-
-DOCS="MAINTAINERS TODO STYLES"
-
-src_configure() {
-	# There is an option to compile with other lisps. However:
-	# - gcl is getting obsolete and unmaintained and is hard masked
-	# - could not make it work with ecls
-	econf \
-		--with-lisp=sbcl \
-		$(use_with X x)
-}
-
-src_compile() {
-	# unfortunately could not track down the broken parallel build
-	# -j5 ok but -j30 sbcl stalled
-	emake -j1
-}
diff --git a/sci-mathematics/petsc/Manifest b/sci-mathematics/petsc/Manifest
deleted file mode 100644
index d4dff3c12..000000000
--- a/sci-mathematics/petsc/Manifest
+++ /dev/null
@@ -1,4 +0,0 @@
-DIST petsc-3.10.0.tar.gz 30850631 BLAKE2B 597f2d428f98b785b13b4819dfffe249401ba630873b75f2f65672126affc0f68b387f67dfd53e8a666e6b7fdeee50de1cf35c4934bcf3afc8053382b4874b0f SHA512 67c657dcbb84d8ede391846d0d79f4f312b770c691438b9909a26cfae119629599079c7f6b60a7ff3766be8335c2cede67ea6368949337fd1c5f12cb4f575aa2
-DIST petsc-3.10.4.tar.gz 31115815 BLAKE2B 772943d19acbeb95798d48244a2a2591391a0ac2cf912042b1841e9e62e84f1747b83fde4eabf36df3db88d50ea5164e9cdca1bec7775a4d40936a8b5d03da6e SHA512 f62915bda21b0fef4d4fa5ff6cf1d9607739caad466c97fd4694584ad7e5281442728777b3e63e0c8a37108134f929aff8e1f550993a93910ade25f6dd983466
-DIST petsc-3.8.4.tar.gz 27946435 BLAKE2B c4d71439695855bce0b6bd46ad434142adc9fd7a0d0b899fa5f02b9fefd65926470db02dfe250376416000031b54c230d338d3085472bad3d61a61b9f30f0713 SHA512 c186e143619c12d2175d01046c26221c462091706af0b68515ba1d2c93f97738ec375df7aa0551c5a14c240e80ca744f9d796778f4937a8c8021d64abe1f3b2c
-DIST petsc-3.9.4.tar.gz 29400362 BLAKE2B 702dc05c65805e485713289b66561aaf3fc17131f03c58639f7d676cc026b4143f89ff23c58b196ff0817f1207f379e087992475b4ef5d0eac5a049c4c21448f SHA512 daca9d3ecb9f599988c954ce079f8d6b940f48cef5fcdc56b497e67b1226fc7eb70424eb4696ac90f7b9e75967653967702ce8c7f8b0f906328386697121aa9e
diff --git a/sci-mathematics/petsc/files/petsc-3.7.0-disable-rpath.patch b/sci-mathematics/petsc/files/petsc-3.7.0-disable-rpath.patch
deleted file mode 100644
index 8d0d99330..000000000
--- a/sci-mathematics/petsc/files/petsc-3.7.0-disable-rpath.patch
+++ /dev/null
@@ -1,18 +0,0 @@
-diff --git a/config/BuildSystem/config/setCompilers.py b/config/BuildSystem/config/setCompilers.py
-index 219a35b..ad2ed8c 100644
---- a/config/BuildSystem/config/setCompilers.py
-+++ b/config/BuildSystem/config/setCompilers.py
-@@ -1385,12 +1385,7 @@ class Configure(config.base.Configure):
-     for language in languages:
-       flag = '-L'
-       self.pushLanguage(language)
--      # test '-R' before '-rpath' as sun compilers [c,fortran] don't give proper errors with wrong options.
--      if not Configure.isDarwin(self.log):
--        testFlags = ['-Wl,-rpath,', '-R','-rpath ' , '-Wl,-R,']
--      else:
--        testFlags = ['-Wl,-rpath,']
--      # test '-R' before '-Wl,-rpath' for SUN compilers [as cc on linux accepts -Wl,-rpath, but  f90 & CC do not.
-+      testFlags = []
-       if self.isSun(self.framework.getCompiler(), self.log):
-         testFlags.insert(0,'-R')
-       for testFlag in testFlags:
diff --git a/sci-mathematics/petsc/files/petsc-3.8.3-fix_sandbox_violation.patch b/sci-mathematics/petsc/files/petsc-3.8.3-fix_sandbox_violation.patch
deleted file mode 100644
index 4f51aee81..000000000
--- a/sci-mathematics/petsc/files/petsc-3.8.3-fix_sandbox_violation.patch
+++ /dev/null
@@ -1,17 +0,0 @@
-diff --git a/config/PETSc/options/installDir.py b/config/PETSc/options/installDir.py
-index 975dc8a..c216941 100644
---- a/config/PETSc/options/installDir.py
-+++ b/config/PETSc/options/installDir.py
-@@ -39,12 +39,6 @@ class Configure(config.base.Configure):
-     if self.framework.argDB['prefix']:
-       self.dir = os.path.abspath(os.path.expanduser(self.framework.argDB['prefix']))
-       self.addMakeMacro('PREFIXDIR',self.dir)
--      try:
--        os.makedirs(os.path.join(self.dir,'PETScTestDirectory'))
--        os.rmdir(os.path.join(self.dir,'PETScTestDirectory'))
--      except:
--        self.installSudoMessage = 'You do not have write permissions to the --prefix directory '+self.dir+'\nYou will be prompted for the sudo password for any external package installs'
--        self.installSudo = 'sudo '
-     else:
-       self.dir = os.path.abspath(os.path.join(self.petscdir.dir, self.arch.arch))
-     self.confDir = os.path.abspath(os.path.join(self.petscdir.dir, self.arch.arch))
diff --git a/sci-mathematics/petsc/files/petsc-3.9.0-fix_sandbox_violation.patch b/sci-mathematics/petsc/files/petsc-3.9.0-fix_sandbox_violation.patch
deleted file mode 100644
index 97f8dfed4..000000000
--- a/sci-mathematics/petsc/files/petsc-3.9.0-fix_sandbox_violation.patch
+++ /dev/null
@@ -1,17 +0,0 @@
-diff --git a/config/PETSc/options/installDir.py b/config/PETSc/options/installDir.py
-index 92f190d..047c85b 100644
---- a/config/PETSc/options/installDir.py
-+++ b/config/PETSc/options/installDir.py
-@@ -41,12 +41,6 @@ class Configure(config.base.Configure):
-       self.dir = os.path.abspath(os.path.expanduser(self.framework.argDB['prefix']))
-       self.petscDir = self.dir
-       self.petscArch = ''
--      try:
--        os.makedirs(os.path.join(self.dir,'PETScTestDirectory'))
--        os.rmdir(os.path.join(self.dir,'PETScTestDirectory'))
--      except:
--        self.installSudoMessage = 'You do not have write permissions to the --prefix directory '+self.dir+'\nYou will be prompted for the sudo password for any external package installs'
--        self.installSudo = 'sudo '
-     else:
-       self.dir = os.path.abspath(os.path.join(self.petscdir.dir, self.arch.arch))
-       self.petscDir = self.petscdir.dir
diff --git a/sci-mathematics/petsc/metadata.xml b/sci-mathematics/petsc/metadata.xml
deleted file mode 100644
index 8c9c01d83..000000000
--- a/sci-mathematics/petsc/metadata.xml
+++ /dev/null
@@ -1,23 +0,0 @@
-<?xml version="1.0" encoding="UTF-8"?>
-<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
-<pkgmetadata>
-	<maintainer type="person">
-		<email>tamiko@gentoo.org</email>
-		<name>Matthias Maier</name>
-	</maintainer>
-	<maintainer type="project">
-		<email>sci-mathematics@gentoo.org</email>
-		<name>Gentoo Mathematics Project</name>
-	</maintainer>
-	<use>
-		<flag name="afterimage">Use Afterstep image library (media-libs/libafterimage)</flag>
-		<flag name="boost">Use boost (dev-libs/boost)</flag>
-		<flag name="hypre">Use HYPRE (sci-mathematics/hypre) and for preconditioning</flag>
-		<flag name="complex-scalars">Make scalars complex</flag>
-		<flag name="metis">Add support for metis (<pkg>sci-libs/parmetis</pkg>)</flag>
-		<flag name="sparse">Use suitesparse (sci-libs/suitesparse) including cholmod (sci-libs/cholmod) for sparse factorization</flag>
-		<flag name="superlu">Use superlu (sci-libs/superlu) for preconditioning</flag>
-		<flag name="mumps">Add support for mumps (<pkg>sci-libs/mumps</pkg>)</flag>
-		<flag name="scotch">Add support for scotch (<pkg>sci-libs/scotch</pkg>)</flag>
-	</use>
-</pkgmetadata>
diff --git a/sci-mathematics/petsc/petsc-3.10.0.ebuild b/sci-mathematics/petsc/petsc-3.10.0.ebuild
deleted file mode 100644
index b67536ef6..000000000
--- a/sci-mathematics/petsc/petsc-3.10.0.ebuild
+++ /dev/null
@@ -1,196 +0,0 @@
-# Copyright 1999-2018 Gentoo Foundation
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=6
-
-PYTHON_COMPAT=( python2_7 )
-
-inherit eutils flag-o-matic fortran-2 python-any-r1 toolchain-funcs versionator
-
-MY_P="${PN}-$(replace_version_separator _ -)"
-
-DESCRIPTION="Portable, Extensible Toolkit for Scientific Computation"
-HOMEPAGE="http://www.mcs.anl.gov/petsc/"
-SRC_URI="http://ftp.mcs.anl.gov/pub/petsc/release-snapshots/${MY_P}.tar.gz"
-
-LICENSE="BSD-2"
-SLOT="0"
-KEYWORDS="~amd64 ~x86"
-IUSE="afterimage boost complex-scalars cxx debug doc fftw
-	fortran hdf5 hypre mpi metis mumps scotch sparse superlu threads X"
-
-# hypre and superlu curretly exclude each other due to missing linking to hypre
-# if both are enabled
-REQUIRED_USE="
-	afterimage? ( X )
-	complex-scalars? ( !hypre !superlu )
-	hdf5? ( mpi )
-	hypre? ( cxx mpi !superlu )
-	mumps? ( mpi scotch )
-	scotch? ( mpi )
-	superlu? ( !hypre )
-"
-
-RDEPEND="
-	virtual/blas
-	virtual/lapack
-	afterimage? ( media-libs/libafterimage )
-	boost? ( dev-libs/boost )
-	fftw? ( sci-libs/fftw:3.0[mpi?] )
-	hdf5? ( sci-libs/hdf5[mpi?] )
-	hypre? ( >=sci-libs/hypre-2.8.0b[mpi?] )
-	metis? ( >=sci-libs/parmetis-4 )
-	mpi? ( virtual/mpi[cxx?,fortran?] )
-	mumps? ( sci-libs/mumps[mpi?] sci-libs/scalapack )
-	scotch? ( sci-libs/scotch[mpi?] )
-	sparse? ( sci-libs/suitesparse >=sci-libs/cholmod-1.7.0 )
-	superlu? ( >=sci-libs/superlu-5 )
-	X? ( x11-libs/libX11 )
-"
-
-DEPEND="${RDEPEND}
-	${PYTHON_DEPS}
-	virtual/pkgconfig
-	dev-util/cmake
-"
-
-S="${WORKDIR}/${MY_P}"
-
-PATCHES=(
-	"${FILESDIR}"/${PN}-3.7.0-disable-rpath.patch \
-	"${FILESDIR}"/${PN}-3.9.0-fix_sandbox_violation.patch
-)
-
-src_prepare() {
-	default
-
-	sed -i -e 's%/usr/bin/env python%/usr/bin/env python2%' configure || die
-}
-
-# petsc uses --with-blah=1 and --with-blah=0 to en/disable options
-petsc_enable() {
-	use "$1" && echo "--with-${2:-$1}=1" || echo "--with-${2:-$1}=0"
-}
-# add external library:
-# petsc_with use_flag libname libdir
-# petsc_with use_flag libname include linking_libs
-petsc_with() {
-	local myuse p=${2:-${1}}
-	if use ${1}; then
-		myuse="--with-${p}=1"
-		if [[ $# -ge 4 ]]; then
-			myuse="${myuse} --with-${p}-include=${EPREFIX}${3}"
-			shift 3
-			myuse="${myuse} --with-${p}-lib=$@"
-		else
-			myuse="${myuse} --with-${p}-dir=${EPREFIX}${3:-/usr}"
-		fi
-	else
-		myuse="--with-${p}=0"
-	fi
-	echo ${myuse}
-}
-
-# select between configure options depending on use flag
-petsc_select() {
-	use "$1" && echo "--with-$2=$3" || echo "--with-$2=$4"
-}
-
-src_configure() {
-	# bug 548498
-	# PETSc runs mpi processes during configure that result in a sandbox
-	# violation by trying to open /proc/mtrr rw. This is not easy to
-	# mitigate because it happens in libpciaccess.so called by libhwloc.so,
-	# which is used by libmpi.so.
-	addpredict /proc/mtrr
-	# if mpi is built with knem support it needs /dev/knem too
-	addpredict /dev/knem
-
-	# configureMPITypes with openmpi-2* insists on accessing the scaling
-	# governor rw.
-	addpredict /sys/devices/system/cpu/
-
-	local mylang
-	local myopt
-
-	use cxx && mylang="cxx" || mylang="c"
-	use debug && myopt="debug" || myopt="opt"
-
-	# environmental variables expected by petsc during build
-
-	export PETSC_DIR="${S}"
-	export PETSC_ARCH="linux-gnu-${mylang}-${myopt}"
-
-	if use debug; then
-		strip-flags
-		filter-flags -O*
-	fi
-
-	# C Support on CXX builds is enabled if possible i.e. when not using
-	# complex scalars (no complex type for both available at the same time)
-
-	econf \
-		scrollOutput=1 \
-		FFLAGS="${FFLAGS} -fPIC" \
-		CFLAGS="${CFLAGS} -fPIC" \
-		CXXFLAGS="${CXXFLAGS} -fPIC" \
-		LDFLAGS="${LDFLAGS}" \
-		--prefix="${EPREFIX}/usr/$(get_libdir)/petsc" \
-		--with-shared-libraries \
-		--with-single-library \
-		--with-clanguage=${mylang} \
-		$(use cxx && ! use complex-scalars && echo "with-c-support=1") \
-		--with-petsc-arch=${PETSC_ARCH} \
-		--with-precision=double \
-		--with-gnu-compilers \
-		--with-blas-lapack-lib="$($(tc-getPKG_CONFIG) --libs lapack)" \
-		$(petsc_enable debug debugging) \
-		$(petsc_enable mpi) \
-		$(petsc_select mpi cc mpicc $(tc-getCC)) \
-		$(petsc_select mpi cxx mpicxx $(tc-getCXX)) \
-		$(petsc_enable fortran) \
-		$(use fortran && echo "$(petsc_select mpi fc mpif77 $(tc-getF77))") \
-		$(petsc_enable mpi mpi-compilers) \
-		$(petsc_select complex-scalars scalar-type complex real) \
-		--with-windows-graphics=0 \
-		--with-matlab=0 \
-		--with-cmake=cmake \
-		$(petsc_enable threads pthread) \
-		$(petsc_with afterimage afterimage \
-			/usr/include/libAfterImage -lAfterImage) \
-		$(petsc_with hdf5) \
-		$(petsc_with hypre hypre \
-			/usr/include/hypre -lHYPRE) \
-		$(petsc_with sparse suitesparse) \
-		$(petsc_with superlu superlu \
-			/usr/include/superlu -lsuperlu) \
-		$(petsc_with X x) \
-		$(petsc_with X x11) \
-		$(petsc_with scotch ptscotch \
-			/usr/include/scotch \
-		[-lptesmumps,-lptscotch,-lptscotcherr,-lscotch,-lscotcherr]) \
-		$(petsc_with mumps scalapack \
-			/usr/include/scalapack -lscalapack) \
-		$(petsc_with mumps mumps \
-			/usr/include \
-			[-lcmumps,-ldmumps,-lsmumps,-lzmumps,-lmumps_common,-lpord]) \
-		--with-imagemagick=0 \
-		--with-python=0 \
-		$(petsc_with boost) \
-		$(petsc_with fftw)
-}
-
-src_install() {
-	emake DESTDIR="${ED}" install
-
-	# add PETSC_DIR to environmental variables
-	cat >> 99petsc <<- EOF
-		PETSC_DIR=${EPREFIX}/usr/$(get_libdir)/petsc
-	EOF
-	doenvd 99petsc
-
-	if use doc ; then
-		dodoc docs/developers.pdf docs/manual.pdf
-		dohtml -r docs/*.html docs/changes docs/manualpages
-	fi
-}
diff --git a/sci-mathematics/petsc/petsc-3.10.4.ebuild b/sci-mathematics/petsc/petsc-3.10.4.ebuild
deleted file mode 100644
index bc9a4b110..000000000
--- a/sci-mathematics/petsc/petsc-3.10.4.ebuild
+++ /dev/null
@@ -1,196 +0,0 @@
-# Copyright 1999-2019 Gentoo Authors
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=6
-
-PYTHON_COMPAT=( python2_7 )
-
-inherit eutils flag-o-matic fortran-2 python-any-r1 toolchain-funcs versionator
-
-MY_P="${PN}-$(replace_version_separator _ -)"
-
-DESCRIPTION="Portable, Extensible Toolkit for Scientific Computation"
-HOMEPAGE="http://www.mcs.anl.gov/petsc/"
-SRC_URI="http://ftp.mcs.anl.gov/pub/petsc/release-snapshots/${MY_P}.tar.gz"
-
-LICENSE="BSD-2"
-SLOT="0"
-KEYWORDS="~amd64 ~x86"
-IUSE="afterimage boost complex-scalars cxx debug doc fftw
-	fortran hdf5 hypre mpi metis mumps scotch sparse superlu threads X"
-
-# hypre and superlu curretly exclude each other due to missing linking to hypre
-# if both are enabled
-REQUIRED_USE="
-	afterimage? ( X )
-	complex-scalars? ( !hypre !superlu )
-	hdf5? ( mpi )
-	hypre? ( cxx mpi !superlu )
-	mumps? ( mpi scotch )
-	scotch? ( mpi )
-	superlu? ( !hypre )
-"
-
-RDEPEND="
-	virtual/blas
-	virtual/lapack
-	afterimage? ( media-libs/libafterimage )
-	boost? ( dev-libs/boost )
-	fftw? ( sci-libs/fftw:3.0[mpi?] )
-	hdf5? ( sci-libs/hdf5[mpi?] )
-	hypre? ( >=sci-libs/hypre-2.8.0b[mpi?] )
-	metis? ( >=sci-libs/parmetis-4 )
-	mpi? ( virtual/mpi[cxx?,fortran?] )
-	mumps? ( sci-libs/mumps[mpi?] sci-libs/scalapack )
-	scotch? ( sci-libs/scotch[mpi?] )
-	sparse? ( sci-libs/suitesparse >=sci-libs/cholmod-1.7.0 )
-	superlu? ( >=sci-libs/superlu-5 )
-	X? ( x11-libs/libX11 )
-"
-
-DEPEND="${RDEPEND}
-	${PYTHON_DEPS}
-	virtual/pkgconfig
-	dev-util/cmake
-"
-
-S="${WORKDIR}/${MY_P}"
-
-PATCHES=(
-	"${FILESDIR}"/${PN}-3.7.0-disable-rpath.patch \
-	"${FILESDIR}"/${PN}-3.9.0-fix_sandbox_violation.patch
-)
-
-src_prepare() {
-	default
-
-	sed -i -e 's%/usr/bin/env python%/usr/bin/env python2%' configure || die
-}
-
-# petsc uses --with-blah=1 and --with-blah=0 to en/disable options
-petsc_enable() {
-	use "$1" && echo "--with-${2:-$1}=1" || echo "--with-${2:-$1}=0"
-}
-# add external library:
-# petsc_with use_flag libname libdir
-# petsc_with use_flag libname include linking_libs
-petsc_with() {
-	local myuse p=${2:-${1}}
-	if use ${1}; then
-		myuse="--with-${p}=1"
-		if [[ $# -ge 4 ]]; then
-			myuse="${myuse} --with-${p}-include=${EPREFIX}${3}"
-			shift 3
-			myuse="${myuse} --with-${p}-lib=$@"
-		else
-			myuse="${myuse}"
-		fi
-	else
-		myuse="--with-${p}=0"
-	fi
-	echo ${myuse}
-}
-
-# select between configure options depending on use flag
-petsc_select() {
-	use "$1" && echo "--with-$2=$3" || echo "--with-$2=$4"
-}
-
-src_configure() {
-	# bug 548498
-	# PETSc runs mpi processes during configure that result in a sandbox
-	# violation by trying to open /proc/mtrr rw. This is not easy to
-	# mitigate because it happens in libpciaccess.so called by libhwloc.so,
-	# which is used by libmpi.so.
-	addpredict /proc/mtrr
-	# if mpi is built with knem support it needs /dev/knem too
-	addpredict /dev/knem
-
-	# configureMPITypes with openmpi-2* insists on accessing the scaling
-	# governor rw.
-	addpredict /sys/devices/system/cpu/
-
-	local mylang
-	local myopt
-
-	use cxx && mylang="cxx" || mylang="c"
-	use debug && myopt="debug" || myopt="opt"
-
-	# environmental variables expected by petsc during build
-
-	export PETSC_DIR="${S}"
-	export PETSC_ARCH="linux-gnu-${mylang}-${myopt}"
-
-	if use debug; then
-		strip-flags
-		filter-flags -O*
-	fi
-
-	# C Support on CXX builds is enabled if possible i.e. when not using
-	# complex scalars (no complex type for both available at the same time)
-
-	econf \
-		scrollOutput=1 \
-		FFLAGS="${FFLAGS} -fPIC" \
-		CFLAGS="${CFLAGS} -fPIC" \
-		CXXFLAGS="${CXXFLAGS} -fPIC" \
-		LDFLAGS="${LDFLAGS}" \
-		--prefix="${EPREFIX}/usr/$(get_libdir)/petsc" \
-		--with-shared-libraries \
-		--with-single-library \
-		--with-clanguage=${mylang} \
-		$(use cxx && ! use complex-scalars && echo "with-c-support=1") \
-		--with-petsc-arch=${PETSC_ARCH} \
-		--with-precision=double \
-		--with-gnu-compilers \
-		--with-blas-lapack-lib="$($(tc-getPKG_CONFIG) --libs lapack)" \
-		$(petsc_enable debug debugging) \
-		$(petsc_enable mpi) \
-		$(petsc_select mpi cc mpicc $(tc-getCC)) \
-		$(petsc_select mpi cxx mpicxx $(tc-getCXX)) \
-		$(petsc_enable fortran) \
-		$(use fortran && echo "$(petsc_select mpi fc mpif77 $(tc-getF77))") \
-		$(petsc_enable mpi mpi-compilers) \
-		$(petsc_select complex-scalars scalar-type complex real) \
-		--with-windows-graphics=0 \
-		--with-matlab=0 \
-		--with-cmake=true \
-		$(petsc_enable threads pthread) \
-		$(petsc_with afterimage afterimage \
-			/usr/include/libAfterImage -lAfterImage) \
-		$(petsc_with hdf5) \
-		$(petsc_with hypre hypre \
-			/usr/include/hypre -lHYPRE) \
-		$(petsc_with sparse suitesparse) \
-		$(petsc_with superlu superlu \
-			/usr/include/superlu -lsuperlu) \
-		$(petsc_with X x) \
-		$(petsc_with X x11) \
-		$(petsc_with scotch ptscotch \
-			/usr/include/scotch \
-		[-lptesmumps,-lptscotch,-lptscotcherr,-lscotch,-lscotcherr]) \
-		$(petsc_with mumps scalapack \
-			/usr/include/scalapack -lscalapack) \
-		$(petsc_with mumps mumps \
-			/usr/include \
-			[-lcmumps,-ldmumps,-lsmumps,-lzmumps,-lmumps_common,-lpord]) \
-		--with-imagemagick=0 \
-		--with-python=0 \
-		$(petsc_with boost) \
-		$(petsc_with fftw)
-}
-
-src_install() {
-	emake DESTDIR="${ED}" install
-
-	# add PETSC_DIR to environmental variables
-	cat >> 99petsc <<- EOF
-		PETSC_DIR=${EPREFIX}/usr/$(get_libdir)/petsc
-	EOF
-	doenvd 99petsc
-
-	if use doc ; then
-		dodoc docs/developers.pdf docs/manual.pdf
-		dohtml -r docs/*.html docs/changes docs/manualpages
-	fi
-}
diff --git a/sci-mathematics/petsc/petsc-3.8.4.ebuild b/sci-mathematics/petsc/petsc-3.8.4.ebuild
deleted file mode 100644
index c47619aaf..000000000
--- a/sci-mathematics/petsc/petsc-3.8.4.ebuild
+++ /dev/null
@@ -1,205 +0,0 @@
-# Copyright 1999-2018 Gentoo Foundation
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=6
-
-PYTHON_COMPAT=( python2_7 )
-
-inherit eutils flag-o-matic fortran-2 python-any-r1 toolchain-funcs versionator
-
-MY_P="${PN}-$(replace_version_separator _ -)"
-
-DESCRIPTION="Portable, Extensible Toolkit for Scientific Computation"
-HOMEPAGE="http://www.mcs.anl.gov/petsc/"
-SRC_URI="http://ftp.mcs.anl.gov/pub/petsc/release-snapshots/${MY_P}.tar.gz"
-
-LICENSE="BSD-2"
-SLOT="0"
-KEYWORDS="~amd64 ~x86"
-IUSE="afterimage boost complex-scalars cxx debug doc fftw
-	fortran hdf5 hypre mpi metis mumps scotch sparse superlu threads X"
-
-# hypre and superlu curretly exclude each other due to missing linking to hypre
-# if both are enabled
-REQUIRED_USE="
-	afterimage? ( X )
-	complex-scalars? ( !hypre !superlu )
-	hdf5? ( mpi )
-	hypre? ( cxx mpi !superlu )
-	mumps? ( mpi scotch )
-	scotch? ( mpi )
-	superlu? ( !hypre )
-"
-
-RDEPEND="
-	virtual/blas
-	virtual/lapack
-	afterimage? ( media-libs/libafterimage )
-	boost? ( dev-libs/boost )
-	fftw? ( sci-libs/fftw:3.0[mpi?] )
-	hdf5? ( sci-libs/hdf5[mpi?] )
-	hypre? ( >=sci-libs/hypre-2.8.0b[mpi?] )
-	metis? ( >=sci-libs/parmetis-4 )
-	mpi? ( virtual/mpi[cxx?,fortran?] )
-	mumps? ( sci-libs/mumps[mpi?] sci-libs/scalapack )
-	scotch? ( sci-libs/scotch[mpi?] )
-	sparse? ( sci-libs/suitesparse >=sci-libs/cholmod-1.7.0 )
-	superlu? ( >=sci-libs/superlu-5 )
-	X? ( x11-libs/libX11 )
-"
-
-DEPEND="${RDEPEND}
-	${PYTHON_DEPS}
-	virtual/pkgconfig
-	dev-util/cmake
-"
-
-#
-# PETSc does not want its Makefiles to be invoked with anything higher than
-# -j1. The underlying build system does automatically invoke a parallel
-# build. This might not be what you want, but *hey* not your choice.
-#
-# V=1 enables verbose output with full compiler and linker invocation
-#
-MAKEOPTS="${MAKEOPTS} -j1 V=1"
-
-S="${WORKDIR}/${MY_P}"
-
-PATCHES=(
-	"${FILESDIR}"/${PN}-3.7.0-disable-rpath.patch \
-	"${FILESDIR}"/${PN}-3.8.3-fix_sandbox_violation.patch
-)
-
-src_prepare() {
-	default
-
-	sed -i -e 's%/usr/bin/env python%/usr/bin/env python2%' configure || die
-}
-
-# petsc uses --with-blah=1 and --with-blah=0 to en/disable options
-petsc_enable() {
-	use "$1" && echo "--with-${2:-$1}=1" || echo "--with-${2:-$1}=0"
-}
-# add external library:
-# petsc_with use_flag libname libdir
-# petsc_with use_flag libname include linking_libs
-petsc_with() {
-	local myuse p=${2:-${1}}
-	if use ${1}; then
-		myuse="--with-${p}=1"
-		if [[ $# -ge 4 ]]; then
-			myuse="${myuse} --with-${p}-include=${EPREFIX}${3}"
-			shift 3
-			myuse="${myuse} --with-${p}-lib=$@"
-		else
-			myuse="${myuse} --with-${p}-dir=${EPREFIX}${3:-/usr}"
-		fi
-	else
-		myuse="--with-${p}=0"
-	fi
-	echo ${myuse}
-}
-
-# select between configure options depending on use flag
-petsc_select() {
-	use "$1" && echo "--with-$2=$3" || echo "--with-$2=$4"
-}
-
-src_configure() {
-	# bug 548498
-	# PETSc runs mpi processes during configure that result in a sandbox
-	# violation by trying to open /proc/mtrr rw. This is not easy to
-	# mitigate because it happens in libpciaccess.so called by libhwloc.so,
-	# which is used by libmpi.so.
-	addpredict /proc/mtrr
-	# if mpi is built with knem support it needs /dev/knem too
-	addpredict /dev/knem
-
-	# configureMPITypes with openmpi-2* insists on accessing the scaling
-	# governor rw.
-	addpredict /sys/devices/system/cpu/
-
-	local mylang
-	local myopt
-
-	use cxx && mylang="cxx" || mylang="c"
-	use debug && myopt="debug" || myopt="opt"
-
-	# environmental variables expected by petsc during build
-
-	export PETSC_DIR="${S}"
-	export PETSC_ARCH="linux-gnu-${mylang}-${myopt}"
-
-	if use debug; then
-		strip-flags
-		filter-flags -O*
-	fi
-
-	# C Support on CXX builds is enabled if possible i.e. when not using
-	# complex scalars (no complex type for both available at the same time)
-
-	econf \
-		scrollOutput=1 \
-		FFLAGS="${FFLAGS} -fPIC" \
-		CFLAGS="${CFLAGS} -fPIC" \
-		CXXFLAGS="${CXXFLAGS} -fPIC" \
-		LDFLAGS="${LDFLAGS}" \
-		--prefix="${EPREFIX}/usr/$(get_libdir)/petsc" \
-		--with-shared-libraries \
-		--with-single-library \
-		--with-clanguage=${mylang} \
-		$(use cxx && ! use complex-scalars && echo "with-c-support=1") \
-		--with-petsc-arch=${PETSC_ARCH} \
-		--with-precision=double \
-		--with-gnu-compilers \
-		--with-blas-lapack-lib="$($(tc-getPKG_CONFIG) --libs lapack)" \
-		$(petsc_enable debug debugging) \
-		$(petsc_enable mpi) \
-		$(petsc_select mpi cc mpicc $(tc-getCC)) \
-		$(petsc_select mpi cxx mpicxx $(tc-getCXX)) \
-		$(petsc_enable fortran) \
-		$(use fortran && echo "$(petsc_select mpi fc mpif77 $(tc-getF77))") \
-		$(petsc_enable mpi mpi-compilers) \
-		$(petsc_select complex-scalars scalar-type complex real) \
-		--with-windows-graphics=0 \
-		--with-matlab=0 \
-		--with-cmake=cmake \
-		$(petsc_enable threads pthread) \
-		$(petsc_with afterimage afterimage \
-			/usr/include/libAfterImage -lAfterImage) \
-		$(petsc_with hdf5) \
-		$(petsc_with hypre hypre \
-			/usr/include/hypre -lHYPRE) \
-		$(petsc_with sparse suitesparse) \
-		$(petsc_with superlu superlu \
-			/usr/include/superlu -lsuperlu) \
-		$(petsc_with X x) \
-		$(petsc_with X x11) \
-		$(petsc_with scotch ptscotch \
-			/usr/include/scotch \
-		[-lptesmumps,-lptscotch,-lptscotcherr,-lscotch,-lscotcherr]) \
-		$(petsc_with mumps scalapack \
-			/usr/include/scalapack -lscalapack) \
-		$(petsc_with mumps mumps \
-			/usr/include \
-			[-lcmumps,-ldmumps,-lsmumps,-lzmumps,-lmumps_common,-lpord]) \
-		--with-imagemagick=0 \
-		--with-python=0 \
-		$(petsc_with boost) \
-		$(petsc_with fftw)
-}
-
-src_install() {
-	emake DESTDIR="${D}/usr/$(get_libdir)/petsc" install
-
-	# add PETSC_DIR to environmental variables
-	cat >> 99petsc <<- EOF
-		PETSC_DIR=${EPREFIX}/usr/$(get_libdir)/petsc
-	EOF
-	doenvd 99petsc
-
-	if use doc ; then
-		dodoc docs/developers.pdf docs/manual.pdf
-		dohtml -r docs/*.html docs/changes docs/manualpages
-	fi
-}
diff --git a/sci-mathematics/petsc/petsc-3.9.4.ebuild b/sci-mathematics/petsc/petsc-3.9.4.ebuild
deleted file mode 100644
index b67536ef6..000000000
--- a/sci-mathematics/petsc/petsc-3.9.4.ebuild
+++ /dev/null
@@ -1,196 +0,0 @@
-# Copyright 1999-2018 Gentoo Foundation
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=6
-
-PYTHON_COMPAT=( python2_7 )
-
-inherit eutils flag-o-matic fortran-2 python-any-r1 toolchain-funcs versionator
-
-MY_P="${PN}-$(replace_version_separator _ -)"
-
-DESCRIPTION="Portable, Extensible Toolkit for Scientific Computation"
-HOMEPAGE="http://www.mcs.anl.gov/petsc/"
-SRC_URI="http://ftp.mcs.anl.gov/pub/petsc/release-snapshots/${MY_P}.tar.gz"
-
-LICENSE="BSD-2"
-SLOT="0"
-KEYWORDS="~amd64 ~x86"
-IUSE="afterimage boost complex-scalars cxx debug doc fftw
-	fortran hdf5 hypre mpi metis mumps scotch sparse superlu threads X"
-
-# hypre and superlu curretly exclude each other due to missing linking to hypre
-# if both are enabled
-REQUIRED_USE="
-	afterimage? ( X )
-	complex-scalars? ( !hypre !superlu )
-	hdf5? ( mpi )
-	hypre? ( cxx mpi !superlu )
-	mumps? ( mpi scotch )
-	scotch? ( mpi )
-	superlu? ( !hypre )
-"
-
-RDEPEND="
-	virtual/blas
-	virtual/lapack
-	afterimage? ( media-libs/libafterimage )
-	boost? ( dev-libs/boost )
-	fftw? ( sci-libs/fftw:3.0[mpi?] )
-	hdf5? ( sci-libs/hdf5[mpi?] )
-	hypre? ( >=sci-libs/hypre-2.8.0b[mpi?] )
-	metis? ( >=sci-libs/parmetis-4 )
-	mpi? ( virtual/mpi[cxx?,fortran?] )
-	mumps? ( sci-libs/mumps[mpi?] sci-libs/scalapack )
-	scotch? ( sci-libs/scotch[mpi?] )
-	sparse? ( sci-libs/suitesparse >=sci-libs/cholmod-1.7.0 )
-	superlu? ( >=sci-libs/superlu-5 )
-	X? ( x11-libs/libX11 )
-"
-
-DEPEND="${RDEPEND}
-	${PYTHON_DEPS}
-	virtual/pkgconfig
-	dev-util/cmake
-"
-
-S="${WORKDIR}/${MY_P}"
-
-PATCHES=(
-	"${FILESDIR}"/${PN}-3.7.0-disable-rpath.patch \
-	"${FILESDIR}"/${PN}-3.9.0-fix_sandbox_violation.patch
-)
-
-src_prepare() {
-	default
-
-	sed -i -e 's%/usr/bin/env python%/usr/bin/env python2%' configure || die
-}
-
-# petsc uses --with-blah=1 and --with-blah=0 to en/disable options
-petsc_enable() {
-	use "$1" && echo "--with-${2:-$1}=1" || echo "--with-${2:-$1}=0"
-}
-# add external library:
-# petsc_with use_flag libname libdir
-# petsc_with use_flag libname include linking_libs
-petsc_with() {
-	local myuse p=${2:-${1}}
-	if use ${1}; then
-		myuse="--with-${p}=1"
-		if [[ $# -ge 4 ]]; then
-			myuse="${myuse} --with-${p}-include=${EPREFIX}${3}"
-			shift 3
-			myuse="${myuse} --with-${p}-lib=$@"
-		else
-			myuse="${myuse} --with-${p}-dir=${EPREFIX}${3:-/usr}"
-		fi
-	else
-		myuse="--with-${p}=0"
-	fi
-	echo ${myuse}
-}
-
-# select between configure options depending on use flag
-petsc_select() {
-	use "$1" && echo "--with-$2=$3" || echo "--with-$2=$4"
-}
-
-src_configure() {
-	# bug 548498
-	# PETSc runs mpi processes during configure that result in a sandbox
-	# violation by trying to open /proc/mtrr rw. This is not easy to
-	# mitigate because it happens in libpciaccess.so called by libhwloc.so,
-	# which is used by libmpi.so.
-	addpredict /proc/mtrr
-	# if mpi is built with knem support it needs /dev/knem too
-	addpredict /dev/knem
-
-	# configureMPITypes with openmpi-2* insists on accessing the scaling
-	# governor rw.
-	addpredict /sys/devices/system/cpu/
-
-	local mylang
-	local myopt
-
-	use cxx && mylang="cxx" || mylang="c"
-	use debug && myopt="debug" || myopt="opt"
-
-	# environmental variables expected by petsc during build
-
-	export PETSC_DIR="${S}"
-	export PETSC_ARCH="linux-gnu-${mylang}-${myopt}"
-
-	if use debug; then
-		strip-flags
-		filter-flags -O*
-	fi
-
-	# C Support on CXX builds is enabled if possible i.e. when not using
-	# complex scalars (no complex type for both available at the same time)
-
-	econf \
-		scrollOutput=1 \
-		FFLAGS="${FFLAGS} -fPIC" \
-		CFLAGS="${CFLAGS} -fPIC" \
-		CXXFLAGS="${CXXFLAGS} -fPIC" \
-		LDFLAGS="${LDFLAGS}" \
-		--prefix="${EPREFIX}/usr/$(get_libdir)/petsc" \
-		--with-shared-libraries \
-		--with-single-library \
-		--with-clanguage=${mylang} \
-		$(use cxx && ! use complex-scalars && echo "with-c-support=1") \
-		--with-petsc-arch=${PETSC_ARCH} \
-		--with-precision=double \
-		--with-gnu-compilers \
-		--with-blas-lapack-lib="$($(tc-getPKG_CONFIG) --libs lapack)" \
-		$(petsc_enable debug debugging) \
-		$(petsc_enable mpi) \
-		$(petsc_select mpi cc mpicc $(tc-getCC)) \
-		$(petsc_select mpi cxx mpicxx $(tc-getCXX)) \
-		$(petsc_enable fortran) \
-		$(use fortran && echo "$(petsc_select mpi fc mpif77 $(tc-getF77))") \
-		$(petsc_enable mpi mpi-compilers) \
-		$(petsc_select complex-scalars scalar-type complex real) \
-		--with-windows-graphics=0 \
-		--with-matlab=0 \
-		--with-cmake=cmake \
-		$(petsc_enable threads pthread) \
-		$(petsc_with afterimage afterimage \
-			/usr/include/libAfterImage -lAfterImage) \
-		$(petsc_with hdf5) \
-		$(petsc_with hypre hypre \
-			/usr/include/hypre -lHYPRE) \
-		$(petsc_with sparse suitesparse) \
-		$(petsc_with superlu superlu \
-			/usr/include/superlu -lsuperlu) \
-		$(petsc_with X x) \
-		$(petsc_with X x11) \
-		$(petsc_with scotch ptscotch \
-			/usr/include/scotch \
-		[-lptesmumps,-lptscotch,-lptscotcherr,-lscotch,-lscotcherr]) \
-		$(petsc_with mumps scalapack \
-			/usr/include/scalapack -lscalapack) \
-		$(petsc_with mumps mumps \
-			/usr/include \
-			[-lcmumps,-ldmumps,-lsmumps,-lzmumps,-lmumps_common,-lpord]) \
-		--with-imagemagick=0 \
-		--with-python=0 \
-		$(petsc_with boost) \
-		$(petsc_with fftw)
-}
-
-src_install() {
-	emake DESTDIR="${ED}" install
-
-	# add PETSC_DIR to environmental variables
-	cat >> 99petsc <<- EOF
-		PETSC_DIR=${EPREFIX}/usr/$(get_libdir)/petsc
-	EOF
-	doenvd 99petsc
-
-	if use doc ; then
-		dodoc docs/developers.pdf docs/manual.pdf
-		dohtml -r docs/*.html docs/changes docs/manualpages
-	fi
-}
diff --git a/sci-mathematics/pff/Manifest b/sci-mathematics/pff/Manifest
deleted file mode 100644
index eabef8165..000000000
--- a/sci-mathematics/pff/Manifest
+++ /dev/null
@@ -1 +0,0 @@
-DIST Float8.4.tgz 352313 SHA256 3436b4521ac8bb24850920f404994579174f5b20d1178d48dbd686ec109ef27c SHA512 4e53aad0a59d6875f071584a34b91029a51e8d797e2f5c1a51c772973b241ebda093463532653dbc54245bd03b2414d648648670c6658547c908403cbe6d1275 WHIRLPOOL 2bfe679b50a5ccb6aec88403a85766b774a416c56d94dd640d00577a35d2d3a06b7d91795285ba0e57c17f6bdcc19d71ffa2a7ab5f796b4e2e2366c195f557b5
diff --git a/sci-mathematics/pff/metadata.xml b/sci-mathematics/pff/metadata.xml
deleted file mode 100644
index 0c97b245d..000000000
--- a/sci-mathematics/pff/metadata.xml
+++ /dev/null
@@ -1,14 +0,0 @@
-<?xml version="1.0" encoding="UTF-8"?>
-<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
-<pkgmetadata>
-	<maintainer type="project">
-		<email>sci-mathematics@gentoo.org</email>
-		<name>Gentoo Mathematics Project</name>
-	</maintainer>
-	<longdescription>
-PFF (Preuves Formelles sur les Flottants = Formal Proofs about Floats)
-is a repository of a Coq library about floating-point arithmetic. It
-contains both definitions and proofs of basic facts, old and new
-properties and algorithms.
-</longdescription>
-</pkgmetadata>
diff --git a/sci-mathematics/pff/pff-8.4.ebuild b/sci-mathematics/pff/pff-8.4.ebuild
deleted file mode 100644
index 951b49edc..000000000
--- a/sci-mathematics/pff/pff-8.4.ebuild
+++ /dev/null
@@ -1,32 +0,0 @@
-# Copyright 1999-2014 Gentoo Foundation
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=5
-
-DESCRIPTION="Library for reasoning about floating point numbers in coq"
-HOMEPAGE="http://lipforge.ens-lyon.fr/www/pff/"
-SRC_URI="http://lipforge.ens-lyon.fr/frs/download.php/165/Float${PV}.tgz"
-
-LICENSE="LGPL-2"
-SLOT="0"
-KEYWORDS="~amd64 ~x86"
-IUSE=""
-
-DEPEND="sci-mathematics/coq"
-RDEPEND="${DEPEND}"
-
-S="${WORKDIR}/Float${PV}"
-
-src_prepare() {
-	sed -i Makefile \
-		-e "s|\`\$(COQC) -where\`/user-contrib|\$(DSTROOT)/\`\$(COQC) -where\`/user-contrib|g" \
-		-e "s|VOFILESINC=\$(filter \$(wildcard \./\*),\$(VOFILES))|VOFILESINC:=\$(filter-out ,\$(VOFILES))|g"
-}
-
-src_compile(){
-	default
-}
-
-src_install(){
-	emake install DSTROOT="${D}"
-}
diff --git a/sci-mathematics/pulp/Manifest b/sci-mathematics/pulp/Manifest
index e47e45371..abe10a827 100644
--- a/sci-mathematics/pulp/Manifest
+++ b/sci-mathematics/pulp/Manifest
@@ -1 +1 @@
-DIST PuLP-1.5.6.zip 9105984 BLAKE2B 0a6b41abca5dfe12db9b09f37f6deb3093ebd0b25244960eab83acdb7d1bf7d10c0983845f254e103be650d1f5f3a6657a4ffcc7bb4501043d865e37e9101f38 SHA512 9feed42d7943d1d9ef8484a99184bd695303a1b0f00b7dfaa65f67fe07b1fa24a67d83a0de1bd664e59cda614c9810ab28b84e2606fb3701e4d336d2a2d93c6f
+DIST pulp-2.7.0.gh.tar.gz 28000854 BLAKE2B d2ec0f2e795ffc93051189e236ddefc92c1e0fbfc825f8bd32b6f8569c1e0ec290acaa418e93768587238ff25c3ae9a4d27457c7e5eb0635fc919ebb80b3de3b SHA512 be89eaeaac81cb79f6533b8764283f1f4ba85570f7626db6fa3e760124a26dcc1ee3ff3b293c67de2ed48083fe611ae0ca93db83da801456a34fe7cff816ba61
diff --git a/sci-mathematics/pulp/metadata.xml b/sci-mathematics/pulp/metadata.xml
index ce584d233..c86c3b501 100644
--- a/sci-mathematics/pulp/metadata.xml
+++ b/sci-mathematics/pulp/metadata.xml
@@ -7,5 +7,6 @@
 	</maintainer>
 	<upstream>
 		<remote-id type="pypi">PuLP</remote-id>
+		<remote-id type="github">coin-or/pulp</remote-id>
 	</upstream>
 </pkgmetadata>
diff --git a/sci-mathematics/pulp/pulp-1.5.6-r1.ebuild b/sci-mathematics/pulp/pulp-1.5.6-r1.ebuild
deleted file mode 100644
index 88878fdcc..000000000
--- a/sci-mathematics/pulp/pulp-1.5.6-r1.ebuild
+++ /dev/null
@@ -1,39 +0,0 @@
-# Copyright 1999-2016 Gentoo Foundation
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=5
-
-PYTHON_COMPAT=( python{2_7,3_4} pypy )
-
-inherit distutils-r1
-
-MY_PN="PuLP"
-MY_P="${MY_PN}-${PV}"
-
-DESCRIPTION="Create MPS/LP files, call solvers, and present results"
-HOMEPAGE="http://pulp-or.googlecode.com/"
-SRC_URI="mirror://pypi/P/PuLP/${MY_P}.zip"
-
-LICENSE="BSD-2"
-KEYWORDS="~amd64"
-SLOT="0"
-IUSE="examples"
-
-DEPEND="dev-python/setuptools"
-RDEPEND="
-	dev-python/setuptools
-	dev-python/pyparsing
-	sci-libs/coinor-cbc
-	>=sci-mathematics/glpk-4.35"
-
-S="${WORKDIR}/${MY_P}"
-
-python_prepare_all() {
-	rm -rf ./src/pulp/solverdir/cbc* || die
-	distutils-r1_python_prepare_all
-}
-
-python_install_all() {
-	use examples && EXAMPLES=( examples/. )
-	distutils-r1_python_install_all
-}
diff --git a/sci-mathematics/pulp/pulp-2.7.0.ebuild b/sci-mathematics/pulp/pulp-2.7.0.ebuild
new file mode 100644
index 000000000..641a91622
--- /dev/null
+++ b/sci-mathematics/pulp/pulp-2.7.0.ebuild
@@ -0,0 +1,21 @@
+# Copyright 1999-2021 Gentoo Authors
+# Distributed under the terms of the GNU General Public License v2
+
+EAPI=8
+
+PYTHON_COMPAT=( python3_{10..11} )
+DISTUTILS_USE_PEP517=setuptools
+
+inherit distutils-r1
+
+DESCRIPTION="Create MPS/LP files, call solvers, and present results"
+HOMEPAGE="https://coin-or.github.io/pulp/"
+SRC_URI="https://github.com/coin-or/${PN}/archive/${PV}.tar.gz -> ${P}.gh.tar.gz"
+
+LICENSE="BSD-2"
+KEYWORDS="~amd64 ~x86"
+SLOT="0"
+
+distutils_enable_tests setup.py
+# ToDo: package theme
+#distutils_enable_sphinx doc/source dev-python/sphinx_glpi_theme
diff --git a/sci-mathematics/ripser/Manifest b/sci-mathematics/ripser/Manifest
new file mode 100644
index 000000000..5b2d33259
--- /dev/null
+++ b/sci-mathematics/ripser/Manifest
@@ -0,0 +1 @@
+DIST ripser-1.1.tar.gz 3253697 BLAKE2B 8c1fccfabfd1db22e386b14707d1e078281921f6c353ce406bb35d37a8453a0e93e7423d8a52ee61d15a62d65708f070614a4ba4d3e13bc45f5d8aeb22d78997 SHA512 22bbce287abbf3cf5594e6dd1d5b754ea4707d21a9711ed9646a6c06715861ff0c79bb6090be5031c8e093ac586d9c3110e6aba84c5fabeefb165d4bc729705c
diff --git a/sci-mathematics/ripser/files/ripser-Makefile.patch b/sci-mathematics/ripser/files/ripser-Makefile.patch
new file mode 100644
index 000000000..e8135fd27
--- /dev/null
+++ b/sci-mathematics/ripser/files/ripser-Makefile.patch
@@ -0,0 +1,51 @@
+diff --git a/Makefile b/Makefile
+index ab410bd..cb0a1c1 100644
+--- a/Makefile
++++ b/Makefile
+@@ -1,15 +1,35 @@
+-build: ripser
++TARGET	=	ripser
+
++DESTDIR	?=
+
+-all: ripser ripser-coeff ripser-debug
++prefix	?= /usr/local
++exec_prefix	?= $(prefix)
++bindir	?= $(exec_prefix)/bin
+
++CFLAGS	+= -std=c++11 -Wall -Wextra -Wpedantic -Wstrict-overflow
++
++ifeq ($(INDICATE_PROGRESS),1)
++	CFLAGS += -D INDICATE_PROGRESS
++endif
++
++ifeq ($(USE_GOOGLE_HASHMAP),1)
++	CFLAGS += -D USE_GOOGLE_HASHMAP
++endif
++
++ifeq ($(NDEBUG),1)
++	CFLAGS += -D NDEBUG
++endif
++
++build: all
++
++all: ripser ripser-coeff
+
+ ripser: ripser.cpp
+-	c++ -std=c++11 -Wall ripser.cpp -o ripser -Ofast -D NDEBUG
++	$(CXX) $(CFLAGS) $(CXXFLAGS) ripser.cpp -o ripser
+
+ ripser-coeff: ripser.cpp
+-	c++ -std=c++11 -Wall ripser.cpp -o ripser-coeff -Ofast -D NDEBUG -D USE_COEFFICIENTS
+-
+-ripser-debug: ripser.cpp
+-	c++ -std=c++11 -Wall ripser.cpp -o ripser-debug -g
++	$(CXX) $(CFLAGS) $(CXXFLAGS) -D USE_COEFFICIENTS ripser.cpp -o ripser-coeff
+
++install: all
++	install -d ${DESTDIR}${bindir}
++	install -m 755 ripser ripser-coeff ${DESTDIR}$(bindir)
+
+ clean:
+-	rm -f ripser ripser-coeff ripser-debug
++	rm -f ripser ripser-coeff
diff --git a/sci-mathematics/ripser/metadata.xml b/sci-mathematics/ripser/metadata.xml
new file mode 100644
index 000000000..05f38b851
--- /dev/null
+++ b/sci-mathematics/ripser/metadata.xml
@@ -0,0 +1,19 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
+<pkgmetadata>
+	<maintainer type="person">
+		<email>gentoo@aisha.cc</email>
+		<name>Aisha Tammy</name>
+	</maintainer>
+	<maintainer type="project">
+		<email>sci@gentoo.org</email>
+		<name>Gentoo Science Project</name>
+	</maintainer>
+	<use>
+		<flag name="progress">print progress of calculations in console</flag>
+		<flag name="sparsehash">use google sparsehash for storage</flag>
+	</use>
+	<upstream>
+		<remote-id type="github">Ripser/ripser</remote-id>
+	</upstream>
+</pkgmetadata>
diff --git a/sci-mathematics/ripser/ripser-1.1.ebuild b/sci-mathematics/ripser/ripser-1.1.ebuild
new file mode 100644
index 000000000..809faa019
--- /dev/null
+++ b/sci-mathematics/ripser/ripser-1.1.ebuild
@@ -0,0 +1,33 @@
+# Copyright 2019-2021 Gentoo Authors
+# Distributed under the terms of the GNU General Public License v2
+
+EAPI=7
+
+DESCRIPTION="efficient computation of Vietoris-Rips persistence barcodes"
+HOMEPAGE="https://github.com/Ripser/ripser"
+SRC_URI="https://github.com/Ripser/ripser/archive/v${PV}.tar.gz -> ${P}.tar.gz"
+
+KEYWORDS="~amd64"
+
+LICENSE="MIT"
+SLOT="0"
+IUSE="debug progress sparsehash"
+
+BDEPEND="
+	sparsehash? ( dev-cpp/sparsehash )
+"
+
+PATCHES=(
+	"${FILESDIR}/ripser-Makefile.patch"
+)
+
+src_compile() {
+	emake USE_GOOGLE_HASHMAP=$(usex sparsehash 1 0) \
+		  INDICATE_PROGRESS=$(usex progress 1 0) \
+		  NDEBUG=$(usex debug 0 1)\
+		  all
+}
+
+src_install() {
+	emake prefix="/usr" DESTDIR="${D}" install
+}
diff --git a/sci-mathematics/scilab-bin/Manifest b/sci-mathematics/scilab-bin/Manifest
new file mode 100644
index 000000000..6029dc30e
--- /dev/null
+++ b/sci-mathematics/scilab-bin/Manifest
@@ -0,0 +1,2 @@
+DIST scilab-2023.1.0.bin.x86_64-linux-gnu.tar.xz 182801620 BLAKE2B 19847145a8d70550afa77591854aa651ee5fe23f9998eee21c11acdd4112397fb5e2e82c6bc7edbc2f808048f70905dc0df37db00c43b5794bf304e9a0807ca4 SHA512 af0f71d270513f283ac732e2004094854a117ce4550c5ab579eda5c5ec52bde76a8fa5dd7649db84d68d43124524342f2fdc5f1ba269a60a3930c578ef3391f8
+DIST scilab-6.1.1.bin.linux-x86_64.tar.gz 215840619 BLAKE2B dcfb88f2488cf26371c5beee1e905a33e4c6fc343bb490bb43a73334960f0c13df7d372841949a46d7dc5b6c0a404e6648828104717274518a8ff905a0ae15ad SHA512 ed386e01869cfac3d12881ddb4ae0258bb02e1d4a919a82405dbedce77406c04269883b6e1456dbad52551217307a7baebbb355a699168b77810263f5e357895
diff --git a/sci-mathematics/scilab-bin/metadata.xml b/sci-mathematics/scilab-bin/metadata.xml
new file mode 100644
index 000000000..dc2f8c0b5
--- /dev/null
+++ b/sci-mathematics/scilab-bin/metadata.xml
@@ -0,0 +1,15 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
+<pkgmetadata>
+	<maintainer type="project">
+		<email>sci-mathematics@gentoo.org</email>
+		<name>Gentoo Mathematics Project</name>
+	</maintainer>
+	<longdescription lang="en">
+		Scilab is a matrix-based scientific software package. Scilab contains
+		hundreds of built-in mathematical functions, rich data structures
+		(including polynomials, rationals,linear systems, lists, etc...) and
+		comes with a number of specific toolboxes for control, signal
+		processing, ...
+	</longdescription>
+</pkgmetadata>
diff --git a/sci-mathematics/scilab-bin/scilab-bin-2023.1.0.ebuild b/sci-mathematics/scilab-bin/scilab-bin-2023.1.0.ebuild
new file mode 100644
index 000000000..83d189b8a
--- /dev/null
+++ b/sci-mathematics/scilab-bin/scilab-bin-2023.1.0.ebuild
@@ -0,0 +1,78 @@
+# Copyright 1999-2022 Gentoo Authors
+# Distributed under the terms of the GNU General Public License v2
+
+EAPI=8
+
+inherit xdg
+
+MY_PN="${PN//-bin}"
+MY_P="${MY_PN}-${PV}"
+
+DESCRIPTION="Scientific software package for numerical computations"
+HOMEPAGE="https://www.scilab.org/"
+SRC_URI="https://www.scilab.org/download/${PV}/${MY_P}.bin.x86_64-linux-gnu.tar.xz"
+S="${WORKDIR}/${P//-bin}"
+
+LICENSE="GPL-2 Apache-2.0 sun-bcla-jhall jing MPL-1.0 MIT"
+SLOT="0"
+KEYWORDS="-* ~amd64"
+
+# Bundled dependencies not packaged in ::gentoo
+# sci-libs/hdf5[cxx]:0/9
+# libgluegen.so (in ::sci)
+# libjogl_desktop.so (in ::sci)
+# libOpenXLSX.so (in ::sci)
+#
+# Bundled dependencies in ::gentoo
+# 	dev-lang/tcl
+# 	dev-libs/openssl:0/1.1
+# 	dev-libs/newt
+# 	dev-libs/libpcre
+# 	net-misc/curl
+# 	sci-libs/amd
+# 	sci-libs/arpack
+# 	sci-libs/camd
+# 	sci-libs/ccolamd
+# 	sci-libs/cholmod
+# 	sci-libs/colamd
+# 	sci-libs/fftw:3.0/3
+# 	sci-libs/lapack
+# 	sci-libs/matio
+# 	sci-libs/openblas
+# 	sci-libs/umfpack
+
+RDEPEND="
+	sys-libs/ncurses-compat
+	virtual/jre:1.8
+"
+
+QA_PREBUILT=( "opt/${MY_PN}/*" )
+
+src_prepare() {
+	default
+	local SCILAB_HOME="/opt/${MY_PN}"
+	# fix the .pc file to reflect the dirs where we are installing stuff
+	sed -i -e "/^prefix=/c prefix=${SCILAB_HOME}" lib/pkgconfig/scilab.pc || die
+
+	# move appdata to metainfo
+	mv share/appdata share/metainfo || die
+}
+
+src_install() {
+	local SCILAB_HOME="/opt/${MY_PN}"
+	dodir "${SCILAB_HOME}"
+
+	# make convenience symlinks in PATH
+	for file in bin/*; do
+		dosym "../${MY_PN}/${file}" "/opt/${file}"
+	done
+
+	# copy all the things
+	cp -r "${S}/"*  "${ED}/${SCILAB_HOME}" || die
+
+	# move out dekstop, icons etc
+	dodir /usr/share
+	mv "${ED}/${SCILAB_HOME}/share/"{metainfo,applications,icons,locale,mime} "${ED}/usr/share/" || die
+	dodir /usr/lib64/pkgconfig
+	mv "${ED}/${SCILAB_HOME}/lib/pkgconfig/scilab.pc" "${ED}/usr/lib64/pkgconfig/" || die
+}
diff --git a/sci-mathematics/scilab-bin/scilab-bin-6.1.1.ebuild b/sci-mathematics/scilab-bin/scilab-bin-6.1.1.ebuild
new file mode 100644
index 000000000..07b7da8ee
--- /dev/null
+++ b/sci-mathematics/scilab-bin/scilab-bin-6.1.1.ebuild
@@ -0,0 +1,78 @@
+# Copyright 1999-2022 Gentoo Authors
+# Distributed under the terms of the GNU General Public License v2
+
+EAPI=8
+
+inherit xdg
+
+MY_PN="${PN//-bin}"
+MY_P="${MY_PN}-${PV}"
+
+DESCRIPTION="Scientific software package for numerical computations"
+HOMEPAGE="https://www.scilab.org/"
+SRC_URI="https://www.scilab.org/download/${PV}/${MY_P}.bin.linux-x86_64.tar.gz"
+S="${WORKDIR}/${P//-bin}"
+
+LICENSE="GPL-2 Apache-2.0 sun-bcla-jhall jing MPL-1.0 MIT"
+SLOT="0"
+KEYWORDS="-* ~amd64"
+
+# Bundled dependencies not packaged in ::gentoo
+# sci-libs/hdf5[cxx]:0/9
+# libgluegen.so (in ::sci)
+# libjogl_desktop.so (in ::sci)
+# libOpenXLSX.so (in ::sci)
+#
+# Bundled dependencies in ::gentoo
+# 	dev-lang/tcl
+# 	dev-libs/openssl:0/1.1
+# 	dev-libs/newt
+# 	dev-libs/libpcre
+# 	net-misc/curl
+# 	sci-libs/amd
+# 	sci-libs/arpack
+# 	sci-libs/camd
+# 	sci-libs/ccolamd
+# 	sci-libs/cholmod
+# 	sci-libs/colamd
+# 	sci-libs/fftw:3.0/3
+# 	sci-libs/lapack
+# 	sci-libs/matio
+# 	sci-libs/openblas
+# 	sci-libs/umfpack
+
+RDEPEND="
+	sys-libs/ncurses-compat
+	virtual/jre:1.8
+"
+
+QA_PREBUILT=( "opt/${MY_PN}/*" )
+
+src_prepare() {
+	default
+	local SCILAB_HOME="/opt/${MY_PN}"
+	# fix the .pc file to reflect the dirs where we are installing stuff
+	sed -i -e "/^prefix=/c prefix=${SCILAB_HOME}" lib/pkgconfig/scilab.pc || die
+
+	# move appdata to metainfo
+	mv share/appdata share/metainfo || die
+}
+
+src_install() {
+	local SCILAB_HOME="/opt/${MY_PN}"
+	dodir "${SCILAB_HOME}"
+
+	# make convenience symlinks in PATH
+	for file in bin/*; do
+		dosym "../${MY_PN}/${file}" "/opt/${file}"
+	done
+
+	# copy all the things
+	cp -r "${S}/"*  "${ED}/${SCILAB_HOME}" || die
+
+	# move out dekstop, icons etc
+	dodir /usr/share
+	mv "${ED}/${SCILAB_HOME}/share/"{metainfo,applications,icons,locale,mime} "${ED}/usr/share/" || die
+	dodir /usr/lib64/pkgconfig
+	mv "${ED}/${SCILAB_HOME}/lib/pkgconfig/scilab.pc" "${ED}/usr/lib64/pkgconfig/" || die
+}
diff --git a/sci-mathematics/scilab/Manifest b/sci-mathematics/scilab/Manifest
deleted file mode 100644
index 0253bcef2..000000000
--- a/sci-mathematics/scilab/Manifest
+++ /dev/null
@@ -1 +0,0 @@
-DIST scilab-5.5.2-src.tar.gz 69626327 BLAKE2B 6180bb91d878e646838a085894dcf6da7127b60788a234f1900dc19b6a981af789c10e78f08ed1357fbec82b32d0fe0ba4b8ffe3350ac4a9f5ee0843bbb3b177 SHA512 7f00ac837e36b5524a9c9a3106bdaefebb71559eb2932b2a16e4fac53fa1f9e66b87eabf98b3006ede25f8ab1d16d6ef1c7561ed29b67ddb42c98610fa72fe79
diff --git a/sci-mathematics/scilab/files/scilab-5.5.2-accessviolation.patch b/sci-mathematics/scilab/files/scilab-5.5.2-accessviolation.patch
deleted file mode 100644
index a7e5c6d5f..000000000
--- a/sci-mathematics/scilab/files/scilab-5.5.2-accessviolation.patch
+++ /dev/null
@@ -1,21 +0,0 @@
-diff -urN scilab-5.5.0-orig/bin/scilab scilab-5.5.0/bin/scilab
---- a/bin/scilab	2014-07-12 15:24:17.105686656 -0400
-+++ b/bin/scilab	2014-07-12 15:25:29.307725409 -0400
-@@ -647,17 +647,6 @@
- GTK_MODULES=$(echo $GTK_MODULES | sed s/gnomebreakpad//g)
- export GTK_MODULES
- 
--# libEGL may be partially supported by the closed-source NVIDIA driver.
--# Until they release an EGL driver, we force the egl_glx driver.
--# http://bugzilla.scilab.org/show_bug.cgi?id=12940
--if test -x /usr/bin/glxinfo; then
--    NVIDIA_GLX_VENDOR=$(/usr/bin/glxinfo |grep "NVIDIA Corporation")
--    if test ! -z "$NVIDIA_GLX_VENDOR"; then
--        EGL_DRIVER=egl_glx
--        export EGL_DRIVER
--    fi
--fi
--
- if test $SCIVERBOSE -ne 0; then
-     echo "SCI : $SCI"
-     echo "SCIBIN : $SCIBIN"
diff --git a/sci-mathematics/scilab/files/scilab-5.5.2-batik-1.8.patch b/sci-mathematics/scilab/files/scilab-5.5.2-batik-1.8.patch
deleted file mode 100644
index 007d530ad..000000000
--- a/sci-mathematics/scilab/files/scilab-5.5.2-batik-1.8.patch
+++ /dev/null
@@ -1,99 +0,0 @@
-From: Bryan Gardiner <bog@khumba.net>
-Project-Bug-URL: https://bugzilla.scilab.org/show_bug.cgi?id=13813
-Gentoo-Bug-URL: https://github.com/gentoo-science/sci/pull/456
-
-Updates Scilab to build against (and require) Batik >=1.8, fixing an API change
-with SAXSVGDocumentFactory being moved.  This is not tested beyond "yes Scilab
-still links to Batik to export SVGs," as I'm not sure of a good test case, and
-it's awaiting upstream review.
-
---- a/configure
-+++ b/configure
-@@ -16600,8 +16600,8 @@ $as_echo "$as_me: WARNING: Could not find or use the Java package/jar batik used
-                 fi
- 
- 
--    { $as_echo "$as_me:${as_lineno-$LINENO}: checking minimal version (1.7) of batik" >&5
--$as_echo_n "checking minimal version (1.7) of batik... " >&6; }
-+    { $as_echo "$as_me:${as_lineno-$LINENO}: checking minimal version (1.8) of batik" >&5
-+$as_echo_n "checking minimal version (1.8) of batik... " >&6; }
-    saved_ac_java_classpath=$ac_java_classpath
-    export ac_java_classpath="$BATIK:$ac_java_classpath"
-    if test "x" == "x"; then
-@@ -16614,7 +16614,7 @@ import org.apache.batik.Version;
- 
- public class conftest {
-     public static void main(String[] argv) {
--        String minVersion="1.7";
-+        String minVersion="1.8";
- 
-                             System.out.println(Version.getVersion());
-                                   if (compare(minVersion, Version.getVersion()) > 0) {
-@@ -16663,7 +16663,7 @@ EOF
-                    STDOUT=`cat conftest.java.output`
-                 fi
-                 echo "configure: CLASSPATH was $CLASSPATH" >&5
--                  as_fn_error $? "Wrong version of batik. Expected at least 1.7. Found $STDOUT" "$LINENO" 5
-+                  as_fn_error $? "Wrong version of batik. Expected at least 1.8. Found $STDOUT" "$LINENO" 5
-                             fi
-         fi
-         if test -f conftest.java.output; then
-@@ -16673,7 +16673,7 @@ EOF
-         echo "configure: failed program was:" >&5
-         cat conftest.java >&5
-         echo "configure: CLASSPATH was $CLASSPATH" >&5
--          as_fn_error $? "Wrong version of batik. Expected at least 1.7. Found $STDOUT" "$LINENO" 5
-+          as_fn_error $? "Wrong version of batik. Expected at least 1.8. Found $STDOUT" "$LINENO" 5
-             fi
- 
-    else
-@@ -16686,7 +16686,7 @@ import org.apache.batik.Version;
- 
- public class conftest {
-     public static void main(String[] argv) {
--        String minVersion="1.7";
-+        String minVersion="1.8";
- 
-                             System.out.println(Version.getVersion());
-                                   if (compare(minVersion, Version.getVersion()) != 0) {
-@@ -16735,7 +16735,7 @@ EOF
-                    STDOUT=`cat conftest.java.output`
-                 fi
-                 echo "configure: CLASSPATH was $CLASSPATH" >&5
--                  as_fn_error $? "Wrong version of batik. Expected exact version 1.7. Found $STDOUT" "$LINENO" 5
-+                  as_fn_error $? "Wrong version of batik. Expected exact version 1.8. Found $STDOUT" "$LINENO" 5
-                             fi
-         fi
-         if test -f conftest.java.output; then
-@@ -16745,7 +16745,7 @@ EOF
-         echo "configure: failed program was:" >&5
-         cat conftest.java >&5
-         echo "configure: CLASSPATH was $CLASSPATH" >&5
--          as_fn_error $? "Wrong version of batik. Expected exact version 1.7. Found $STDOUT" "$LINENO" 5
-+          as_fn_error $? "Wrong version of batik. Expected exact version 1.8. Found $STDOUT" "$LINENO" 5
-             fi
- 
-     fi
---- a/configure.ac
-+++ b/configure.ac
-@@ -1038,7 +1038,7 @@ interface for JOGL2 - or libGL (OpenGL library) are installed and if the version
-                    BATIK=$PACKAGE_JAR_FILE
-                 fi
-                 AC_SUBST(BATIK)
--                AC_JAVA_CHECK_VERSION_PACKAGE([batik],[import org.apache.batik.Version;],$BATIK,[1.7],[Version.getVersion()])
-+                AC_JAVA_CHECK_VERSION_PACKAGE([batik],[import org.apache.batik.Version;],$BATIK,[1.8],[Version.getVersion()])
- 
-                 # Commons I/O library
-                 AC_JAVA_CHECK_PACKAGE([commons-io],[org.apache.commons.io.output.CountingOutputStream],[Commons I/O library])
---- a/modules/graph/src/java/org/scilab/modules/graph/utils/ScilabGraphUtils.java
-+++ b/modules/graph/src/java/org/scilab/modules/graph/utils/ScilabGraphUtils.java
-@@ -28,7 +28,7 @@ import org.apache.batik.bridge.DocumentLoader;
- import org.apache.batik.bridge.GVTBuilder;
- import org.apache.batik.bridge.UserAgent;
- import org.apache.batik.bridge.UserAgentAdapter;
--import org.apache.batik.dom.svg.SAXSVGDocumentFactory;
-+import org.apache.batik.anim.dom.SAXSVGDocumentFactory;
- import org.apache.batik.gvt.GraphicsNode;
- import org.apache.batik.util.XMLResourceDescriptor;
- import org.scilab.forge.jlatexmath.ParseException;
-
diff --git a/sci-mathematics/scilab/files/scilab-5.5.2-fix-random-runtime-failure.patch b/sci-mathematics/scilab/files/scilab-5.5.2-fix-random-runtime-failure.patch
deleted file mode 100644
index da7b6e485..000000000
--- a/sci-mathematics/scilab/files/scilab-5.5.2-fix-random-runtime-failure.patch
+++ /dev/null
@@ -1,12 +0,0 @@
-diff -urN scilab-orig/modules/api_scilab/src/cpp/api_double.cpp scilab/modules/api_scilab/src/cpp/api_double.cpp
---- a/modules/api_scilab/src/cpp/api_double.cpp	2012-08-06 23:26:31.342617365 -0400
-+++ b/modules/api_scilab/src/cpp/api_double.cpp	2012-08-06 23:27:34.838621420 -0400
-@@ -497,7 +497,7 @@
- /*--------------------------------------------------------------------------*/
- int createScalarDouble(void* _pvCtx, int _iVar, double _dblReal)
- {
--    return createCommonScalarDouble(_pvCtx, _iVar, 0, _dblReal, NULL);
-+    return createCommonScalarDouble(_pvCtx, _iVar, 0, _dblReal, 0);
- }
- /*--------------------------------------------------------------------------*/
- int createScalarComplexDouble(void* _pvCtx, int _iVar, double _dblReal, double _dblImg)
diff --git a/sci-mathematics/scilab/files/scilab-5.5.2-followlinks.patch b/sci-mathematics/scilab/files/scilab-5.5.2-followlinks.patch
deleted file mode 100644
index a3f60bee7..000000000
--- a/sci-mathematics/scilab/files/scilab-5.5.2-followlinks.patch
+++ /dev/null
@@ -1,11 +0,0 @@
---- a/m4/java.m4	2014-02-11 23:43:03.030430258 -0500
-+++ b/m4/java.m4	2014-02-11 23:43:54.008428766 -0500
-@@ -839,7 +839,7 @@
-       for jar in "$jardir/$1.jar" "$jardir/lib$1.jar" "$jardir/lib$1-java.jar" "$jardir/$1*.jar"; do
- 
- # TODO check the behaviour when spaces
--        jars_resolved=`ls $jar 2>/dev/null`
-+        jars_resolved=$(realpath $(ls $jar 2>/dev/null) 2>/dev/null)
-         for jar_resolved in $jars_resolved; do # If several jars matches
-           if test -e "$jar_resolved"; then
-             export ac_java_classpath="$jar_resolved:$ac_java_classpath"
diff --git a/sci-mathematics/scilab/files/scilab-5.5.2-fop-2.0.patch b/sci-mathematics/scilab/files/scilab-5.5.2-fop-2.0.patch
deleted file mode 100644
index 18bdaac1d..000000000
--- a/sci-mathematics/scilab/files/scilab-5.5.2-fop-2.0.patch
+++ /dev/null
@@ -1,38 +0,0 @@
-From: Bryan Gardiner <bog@khumba.net>
-Project-Bug-URL: https://bugzilla.scilab.org/show_bug.cgi?id=14009
-Gentoo-Bug-URL: https://github.com/gentoo-science/sci/pull/456
-
-Updates Scilab to build against FOP >=2.0.  This is not tested, as I'm not sure
-of a test case, and it's awaiting upstream review.
-
---- a/modules/helptools/src/java/org/scilab/modules/helptools/FopConverter.java
-+++ b/modules/helptools/src/java/org/scilab/modules/helptools/FopConverter.java
-@@ -43,10 +43,10 @@ public class FopConverter extends ContainerConverter {
-         String fileName = outputDirectory + "/" + baseName + "." + format.name().toLowerCase();
- 
-         try {
--            FopFactory fopFactory = FopFactory.newInstance();
-+            FopFactory fopFactory =
-+                FopFactory.newInstance(new File(System.getenv("SCI") + "/modules/helptools/etc/fopconf.xml"));
-             fopFactory.addElementMapping(new JLaTeXMathElementMapping());
-             fopFactory.getXMLHandlerRegistry().addXMLHandler(new JLaTeXMathXMLHandler());
--            fopFactory.setUserConfig(new File(System.getenv("SCI") + "/modules/helptools/etc/fopconf.xml"));
- 
-             // Step 3: Construct fop with desired output format
-             OutputStream out = new BufferedOutputStream(new FileOutputStream(fileName));
---- a/modules/scinotes/src/java/org/scilab/modules/scinotes/utils/CodeExporter.java
-+++ b/modules/scinotes/src/java/org/scilab/modules/scinotes/utils/CodeExporter.java
-@@ -114,11 +114,11 @@ public class CodeExporter extends FOCodeConverter {
-      * @param format the page format
-      */
-     public void convert(String code, int[] lineNumberArray, String fileName, String type, String title, PageFormat format) {
--        FopFactory fopFactory = FopFactory.newInstance();
-         OutputStream out = null;
- 
-         try {
--            fopFactory.setUserConfig(new File(ScilabConstants.SCI + "/modules/helptools/etc/fopconf.xml"));
-+            FopFactory fopFactory =
-+                FopFactory.newInstance(new File(ScilabConstants.SCI + "/modules/helptools/etc/fopconf.xml"));
-             FOUserAgent userAgent = fopFactory.newFOUserAgent();
-             userAgent.setProducer(CREATOR);
-             userAgent.setTitle(title);
diff --git a/sci-mathematics/scilab/files/scilab-5.5.2-freehep.patch b/sci-mathematics/scilab/files/scilab-5.5.2-freehep.patch
deleted file mode 100644
index 46825cb29..000000000
--- a/sci-mathematics/scilab/files/scilab-5.5.2-freehep.patch
+++ /dev/null
@@ -1,12 +0,0 @@
-diff -uNr scilab-5.5.2-orig/configure.ac scilab-5.5.2/configure.ac
---- a/configure.ac	2016-06-05 12:30:06.582735449 -0400
-+++ b/configure.ac	2016-06-05 12:31:29.706708157 -0400
-@@ -1024,7 +1024,7 @@
-                     AC_SUBST(FREEHEP_IO)
- 
-                     # Freehep Util
--                    AC_JAVA_CHECK_PACKAGE([freehep-util],[org.freehep.util.StringUtilities],[Freehep Util])
-+                    AC_JAVA_CHECK_PACKAGE([freehep-graphicsbase],[org.freehep.graphicsbase.util.UserProperties],[Freehep Util])
-                     FREEHEP_UTIL=$PACKAGE_JAR_FILE
-                     AC_SUBST(FREEHEP_UTIL)
-                 fi
diff --git a/sci-mathematics/scilab/files/scilab-5.5.2-gluegen.patch b/sci-mathematics/scilab/files/scilab-5.5.2-gluegen.patch
deleted file mode 100644
index d75c31e9a..000000000
--- a/sci-mathematics/scilab/files/scilab-5.5.2-gluegen.patch
+++ /dev/null
@@ -1,11 +0,0 @@
---- a/modules/gui/src/java/org/scilab/modules/gui/SwingView.java	2014-03-24 22:38:00.928934500 -0400
-+++ b/modules/gui/src/java/org/scilab/modules/gui/SwingView.java	2014-03-24 22:37:33.947567043 -0400
-@@ -157,7 +157,7 @@
- 
-     static {
-         try {
--            System.loadLibrary("gluegen2-rt");
-+            System.loadLibrary("gluegen-rt");
-         } catch (Exception e) {
-             System.err.println(e);
-         }
diff --git a/sci-mathematics/scilab/files/scilab-5.5.2-java-heap.patch b/sci-mathematics/scilab/files/scilab-5.5.2-java-heap.patch
deleted file mode 100644
index ca17e52a6..000000000
--- a/sci-mathematics/scilab/files/scilab-5.5.2-java-heap.patch
+++ /dev/null
@@ -1,11 +0,0 @@
---- a/etc/jvm_options.xml	2014-02-12 00:05:34.323390688 -0500
-+++ b/etc/jvm_options.xml	2014-02-12 00:05:53.977390112 -0500
-@@ -22,7 +22,7 @@
-     <!-- ENABLE Just In Time java compiler -->
-     <option value="-Djava.compiler=JIT"/>
-     <!-- Set Java Heap space to 256mb -->
--    <option value="-Xmx256m"/>
-+    <option value="-Xmx512m"/>
-     <!-- Avoid jvm to handle sigint (& other signals)  -->
-     <option value="-Xrs"/>
-     
diff --git a/sci-mathematics/scilab/files/scilab-5.5.2-missinglib.patch b/sci-mathematics/scilab/files/scilab-5.5.2-missinglib.patch
deleted file mode 100644
index 25b281820..000000000
--- a/sci-mathematics/scilab/files/scilab-5.5.2-missinglib.patch
+++ /dev/null
@@ -1,11 +0,0 @@
-diff -urN scilab-5.5.1-orig/Makefile.am scilab-5.5.1/Makefile.am
---- a/Makefile.am	2014-10-09 18:22:21.994610695 -0400
-+++ b/Makefile.am	2014-10-09 18:24:28.208333575 -0400
-@@ -74,6 +74,7 @@
- if NEED_JAVA
- scilab_bin_LDADD += \
- 			$(top_builddir)/modules/console/libsciconsole.la \
-+			$(top_builddir)/modules/console/libsciconsole-minimal.la \
- 			$(top_builddir)/modules/jvm/libscijvm.la \
- 			$(top_builddir)/modules/commons/libscicommons.la
- else
diff --git a/sci-mathematics/scilab/files/scilab-5.5.2-nogui.patch b/sci-mathematics/scilab/files/scilab-5.5.2-nogui.patch
deleted file mode 100644
index f83fa31d0..000000000
--- a/sci-mathematics/scilab/files/scilab-5.5.2-nogui.patch
+++ /dev/null
@@ -1,13 +0,0 @@
---- a/Makefile.in	2014-01-09 22:29:06.534469383 -0500
-+++ b/Makefile.in	2014-01-09 22:29:40.368471544 -0500
-@@ -2247,8 +2247,8 @@
- @BUILD_HELP_TRUE@	done; \
- @BUILD_HELP_TRUE@	fi
- # Also install scirenderer.jar
--@EXTERNAL_SCIRENDERER_FALSE@	$(mkinstalldirs) $(DESTDIR)$(pkgdatadir)/$(PATHTOSCIRENDERER)
--@EXTERNAL_SCIRENDERER_FALSE@	$(INSTALL_DATA) $(top_builddir)/$(PATHTOSCIRENDERER)/$(SCIRENDERERJAR) $(DESTDIR)$(pkgdatadir)/$(PATHTOSCIRENDERER)/
-+@EXTERNAL_SCIRENDERER_FALSE@@NEED_JAVA_TRUE@	$(mkinstalldirs) $(DESTDIR)$(pkgdatadir)/$(PATHTOSCIRENDERER)
-+@EXTERNAL_SCIRENDERER_FALSE@@NEED_JAVA_TRUE@	$(INSTALL_DATA) $(top_builddir)/$(PATHTOSCIRENDERER)/$(SCIRENDERERJAR) $(DESTDIR)$(pkgdatadir)/$(PATHTOSCIRENDERER)/
- 
- .PHONY: macros localization doc
- 
diff --git a/sci-mathematics/scilab/files/scilab-5.5.2-xmlgraphics-common-2.0.patch b/sci-mathematics/scilab/files/scilab-5.5.2-xmlgraphics-common-2.0.patch
deleted file mode 100644
index 4d90f30c7..000000000
--- a/sci-mathematics/scilab/files/scilab-5.5.2-xmlgraphics-common-2.0.patch
+++ /dev/null
@@ -1,91 +0,0 @@
-From: Bryan Gardiner <bog@khumba.net>
-Project-Bug-URL: https://bugzilla.scilab.org/show_bug.cgi?id=13724
-Gentoo-Bug-URL: https://github.com/gentoo-science/sci/pull/456
-
-Updates Scilab 5.5.2 to build against xmlgraphics-common >=2.0.  This is not
-tested, as I'm not sure of a test case, and a similar patch (where the
-super.processShape calls are passed cached=true) is already awaiting upstream
-review.
-
---- a/modules/graphic_export/src/java/org/scilab/modules/graphic_export/Export.java
-+++ b/modules/graphic_export/src/java/org/scilab/modules/graphic_export/Export.java
-@@ -857,7 +857,7 @@ public class Export {
-                     }
- 
-                     @Override
--                    public int processShape(Shape s) throws IOException {
-+                    public int processShape(Shape s, boolean cached) throws IOException {
-                         if (s instanceof Ellipse2D.Double) {
-                             Ellipse2D.Double ell = (Ellipse2D.Double) s;
-                             if (ell.height == ell.width) {
-@@ -880,10 +880,10 @@ public class Export {
-                                     buffer.append("[").append(gen.formatDouble(coords[0])).append(" ").append(gen.formatDouble(coords[1]));
-                                     it.next();
-                                 } else {
--                                    return super.processShape(s);
-+                                    return super.processShape(s, cached);
-                                 }
-                             } else {
--                                return super.processShape(s);
-+                                return super.processShape(s, cached);
-                             }
- 
-                             for (; !it.isDone(); it.next()) {
-@@ -891,7 +891,7 @@ public class Export {
-                                 if (type == PathIterator.SEG_LINETO) {
-                                     buffer.append(" ").append(gen.formatDouble(coords[0])).append(" ").append(gen.formatDouble(coords[1]));
-                                 } else {
--                                    return super.processShape(s);
-+                                    return super.processShape(s, cached);
-                                 }
-                             }
-                             buffer.append("] DP");
-@@ -899,7 +899,7 @@ public class Export {
-                             return PathIterator.WIND_NON_ZERO;
-                         }
- 
--                        return super.processShape(s);
-+                        return super.processShape(s, cached);
-                     }
-                 };
-                 g2d.setGraphicContext(new GraphicContext());
-@@ -1029,7 +1029,7 @@ public class Export {
-                     }
- 
-                     @Override
--                    public int processShape(Shape s) throws IOException {
-+                    public int processShape(Shape s, boolean cached) throws IOException {
-                         if (s instanceof Ellipse2D.Double) {
-                             Ellipse2D.Double ell = (Ellipse2D.Double) s;
-                             if (ell.height == ell.width) {
-@@ -1052,10 +1052,10 @@ public class Export {
-                                     buffer.append("[").append(gen.formatDouble(coords[0])).append(" ").append(gen.formatDouble(coords[1]));
-                                     it.next();
-                                 } else {
--                                    return super.processShape(s);
-+                                    return super.processShape(s, cached);
-                                 }
-                             } else {
--                                return super.processShape(s);
-+                                return super.processShape(s, cached);
-                             }
- 
-                             for (; !it.isDone(); it.next()) {
-@@ -1063,7 +1063,7 @@ public class Export {
-                                 if (type == PathIterator.SEG_LINETO) {
-                                     buffer.append(" ").append(gen.formatDouble(coords[0])).append(" ").append(gen.formatDouble(coords[1]));
-                                 } else {
--                                    return super.processShape(s);
-+                                    return super.processShape(s, cached);
-                                 }
-                             }
-                             buffer.append("] DP");
-@@ -1071,7 +1071,7 @@ public class Export {
-                             return PathIterator.WIND_NON_ZERO;
-                         }
- 
--                        return super.processShape(s);
-+                        return super.processShape(s, cached);
-                     }
- 
-                 };
diff --git a/sci-mathematics/scilab/files/scilab.bash_completion b/sci-mathematics/scilab/files/scilab.bash_completion
deleted file mode 100644
index c289e8632..000000000
--- a/sci-mathematics/scilab/files/scilab.bash_completion
+++ /dev/null
@@ -1,54 +0,0 @@
-# Scilab completion
-# Scilab ( http://www.scilab.org/ ) - This file is part of Scilab
-# Copyright (C) DIGITEO - 2010 - Sylvestre Ledru
-# This file must be used under the terms of the CeCILL.
-# This source file is licensed as described in the file COPYING, which
-# you should have received as part of this distribution.  The terms
-# are also available at    
-# http://www.cecill.info/licences/Licence_CeCILL_V2-en.txt
-
-_scilab()
-{
-    local cur prev options
-    COMPREPLY=()
-    cur=${COMP_WORDS[COMP_CWORD]}
-    prev=${COMP_WORDS[COMP_CWORD-1]}
-
-    # List all options. Note that 
-    options='-ns -nb -nw -nwni -nogui -debug -debug-kdbg -d -display -profiling -profiling-visu -l -mem -version -e -f -nouserstartup -args -mem -h --help'
-
-    # Loop on the arguments to manage conflicting options
-    for (( i=0; i < ${#COMP_WORDS[@]}-1; i++ )); do
-	#exclude some mutually exclusive options
-	[[ ${COMP_WORDS[i]} == '-nwni' ]] && options=${options/-nw}
-        [[ ${COMP_WORDS[i]} == '-nw' ]] && options=${options/-nwni}
-        [[ ${COMP_WORDS[i]} == '-e' ]] && options=${options/-f}
-    done
-    
-    case "$1" in
-    	 *scilab-cli*)
-		# Option -nw is not available
-            	options=${options/-nw}
-	;;
-    esac
-
-    case $prev in
-        -f)
-		_filedir '@(sci|sce|SCI|SCE|tst|TST)'
-		return 0
-            ;;
-        -e|-l|-d|-display|-mem)
-		cur=${cur#[\"\']}
-		eqext='='
-            ;;
-	
-        *)
-            COMPREPLY=( $( compgen -W "$options" | grep "^$cur" ) )
-            ;;
-    esac
-
-    return 0
-}
-complete -F _scilab $filenames scilab scilab-cli scilab-adv-cli
-
-
diff --git a/sci-mathematics/scilab/files/scilab.xml b/sci-mathematics/scilab/files/scilab.xml
deleted file mode 100644
index 8594e7bdc..000000000
--- a/sci-mathematics/scilab/files/scilab.xml
+++ /dev/null
@@ -1,13 +0,0 @@
-<?xml version="1.0" encoding="UTF-8"?>
-<mime-info xmlns="http://www.freedesktop.org/standards/shared-mime-info">
-  <mime-type type="text/x-sci">
-    <comment>Scilab Function</comment>
-        <sub-class-of type="text/plain"/>
-	<glob pattern="*.sci"/> 
-  </mime-type>
-  <mime-type type="text/x-sce">
-    <comment>Scilab Script</comment>
-        <sub-class-of type="text/plain"/>
-	<glob pattern="*.sce"/> 
-  </mime-type>
-</mime-info>
diff --git a/sci-mathematics/scilab/metadata.xml b/sci-mathematics/scilab/metadata.xml
deleted file mode 100644
index ef72c6a0f..000000000
--- a/sci-mathematics/scilab/metadata.xml
+++ /dev/null
@@ -1,24 +0,0 @@
-<?xml version="1.0" encoding="UTF-8"?>
-<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
-<pkgmetadata>
-	<maintainer type="project">
-		<email>sci-mathematics@gentoo.org</email>
-		<name>Gentoo Mathematics Project</name>
-	</maintainer>
-	<longdescription lang="en">
-Scilab is a matrix-based scientific software package. Scilab contains
-hundreds of built-in mathematical functions, rich data structures
-(including polynomials, rationals,linear systems, lists, etc...) and
-comes with a number of specific toolboxes for control, signal
-processing, ...
-</longdescription>
-	<use>
-		<flag name="gui">Build the Java base graphical interface</flag>
-		<flag name="umfpack">Adds support for sparse solving
-with <pkg>sci-libs/umfpack</pkg></flag>
-		<flag name="matio">Enable support for MATLAB file through <pkg>sci-libs/matio</pkg></flag>
-		<flag name="xcos">Enable building hybrid dynamic systems modeler and
-simulator Xcos</flag>
-		<flag name="emf">Add suport for exporting to emf files</flag>
-	</use>
-</pkgmetadata>
diff --git a/sci-mathematics/scilab/scilab-5.5.2-r1.ebuild b/sci-mathematics/scilab/scilab-5.5.2-r1.ebuild
deleted file mode 100644
index c655c1324..000000000
--- a/sci-mathematics/scilab/scilab-5.5.2-r1.ebuild
+++ /dev/null
@@ -1,290 +0,0 @@
-# Copyright 1999-2018 Gentoo Foundation
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=6
-
-JAVA_PKG_OPT_USE="gui"
-VIRTUALX_REQUIRED="manual"
-
-inherit autotools bash-completion-r1 check-reqs eutils flag-o-matic \
-	fortran-2 java-pkg-opt-2 pax-utils toolchain-funcs virtualx xdg-utils
-
-DESCRIPTION="Scientific software package for numerical computations"
-HOMEPAGE="http://www.scilab.org/"
-SRC_URI="http://www.scilab.org/download/${PV}/${P}-src.tar.gz"
-
-LICENSE="CeCILL-2.1"
-SLOT="0"
-KEYWORDS=""
-IUSE="bash-completion debug doc emf fftw +gui +matio mpi nls openmp
-	static-libs test tk +umfpack +xcos"
-REQUIRED_USE="xcos? ( gui ) doc? ( gui )"
-
-RESTRICT="test"
-
-IUSE_L10N="fr zh zh ru ca de es pt ja it uk pl cs"
-L10N_DOC="fr pt ja ru"
-
-map_lang() {
-	local lang=${1/_/-}
-	case $1 in
-		# Retain the following, which have a specific subtag
-		de_*|en_*|pt_*|zh_*) ;;
-		# Consider all other xx_XX as duplicates of the generic xx tag
-		*_*) lang=${1%%_*} ;;
-	esac
-	echo ${lang}
-}
-
-prev_l=
-for l in ${IUSE_L10N}; do
-	l=$(map_lang ${l})
-	[[ ${l} != "${prev_l}" ]] && IUSE+=" l10n_${l}"
-	prev_l=${l}
-done
-unset l prev_l
-
-CDEPEND="
-	dev-libs/libpcre
-	dev-libs/libxml2:2
-	sci-libs/hdf5[mpi=]
-	>=sci-libs/arpack-3
-	sys-devel/gettext
-	sys-libs/ncurses:0=
-	sys-libs/readline:0=
-	virtual/lapack
-	emf? (
-		dev-java/freehep-graphicsio:0
-		dev-java/freehep-graphicsio-emf:0
-		dev-java/freehep-graphics2d:0
-		dev-java/freehep-io:0
-		dev-java/freehep-graphicsbase:0
-	)
-	fftw? ( sci-libs/fftw:3.0 )
-	gui? (
-		dev-java/avalon-framework:4.2
-		>=dev-java/batik-1.8-r2:1.8
-		dev-java/commons-io:1
-		dev-java/commons-logging:0
-		>=dev-java/flexdock-1.2.4:0
-		>=dev-java/fop-2.0:0
-		=dev-java/gluegen-2.2.4:2.2
-		dev-java/javahelp:0
-		dev-java/jeuclid-core:0
-		dev-java/jgoodies-looks:2.6
-		>=dev-java/jlatexmath-1.0.3:1
-		>=dev-java/jlatexmath-fop-1.0.3:1
-		=dev-java/jogl-2.2.4:2.2
-		>=dev-java/jrosetta-1.0.4:0
-		dev-java/skinlf:0
-		dev-java/xmlgraphics-commons:2
-		virtual/opengl
-		xcos? ( dev-java/jgraphx:2.5 )
-		)
-	matio? ( >=sci-libs/matio-1.5 )
-	tk? ( dev-lang/tk:0= )
-	umfpack? ( sci-libs/umfpack )"
-
-RDEPEND="${CDEPEND}
-	gui? ( >=virtual/jre-1.5 )"
-
-DEPEND="${CDEPEND}
-	virtual/pkgconfig
-	debug? ( dev-util/lcov )
-	gui? (
-		>=virtual/jdk-1.6
-		doc? ( app-text/docbook-xsl-stylesheets
-			   dev-java/xml-commons-external:1.4
-			   dev-java/saxon:9 )
-		xcos? ( dev-lang/ocaml )
-		)
-	test? (
-		dev-java/junit:4
-		gui? ( ${VIRTUALX_DEPEND} ) )"
-
-DOCS=( "ACKNOWLEDGEMENTS" "README_Unix" "Readme_Visual.txt" )
-
-PATCHES=(
-	"${FILESDIR}/${P}-followlinks.patch"
-	"${FILESDIR}/${P}-gluegen.patch"
-	"${FILESDIR}/${P}-fix-random-runtime-failure.patch"
-	"${FILESDIR}/${P}-accessviolation.patch"
-	"${FILESDIR}/${P}-missinglib.patch"
-	"${FILESDIR}/${P}-batik-1.8.patch"
-	"${FILESDIR}/${P}-fop-2.0.patch"
-	"${FILESDIR}/${P}-xmlgraphics-common-2.0.patch"
-	"${FILESDIR}/${P}-freehep.patch"
-)
-
-pkg_pretend() {
-	use doc && CHECKREQS_MEMORY="512M" check-reqs_pkg_pretend
-}
-
-pkg_setup() {
-	if use openmp; then
-		if [[ $(tc-getCC) == *gcc* ]] && ! tc-has-openmp; then
-			ewarn "You are using a gcc without OpenMP capabilities"
-			die "Need an OpenMP capable compiler"
-		fi
-		FORTRAN_NEED_OPENMP=1
-	fi
-	FORTRAN_STANDARD="77 90"
-	fortran-2_pkg_setup
-	#bug 8053
-	unset F77
-	java-pkg-opt-2_pkg_setup
-
-	ALL_L10N="en_US"
-	ALL_L10N_DOC="en_US"
-	for l in ${IUSE_L10N}; do
-		use l10n_${l} && ALL_L10N="${ALL_L10N} ${l}"
-	done
-	for l in ${L10N_DOC}; do
-		use l10n_${l} && ALL_L10N_DOC="${ALL_L10N_DOC} ${l}"
-	done
-	export ALL_L10N ALL_L10N_DOC
-}
-
-src_prepare() {
-	default
-
-	# works for me on x86, but users are having
-	# trouble without see #282 on github
-	append-ldflags $(no-as-needed)
-
-	# increases java heap to 512M when building docs (sync with cheqreqs above)
-	use doc && eapply "${FILESDIR}/${P}-java-heap.patch"
-
-	# use the L10N variable that we set
-	sed -i -e "/^ALL_LINGUAS=/d" -e "/^ALL_LINGUAS_DOC=/d" -i configure.ac ||die
-
-	# make sure the DOCBOOK_ROOT variable is set
-	sed -i -e "s/xsl-stylesheets-\*/xsl-stylesheets/g" bin/scilab* || die
-
-	# remove self closing <br /> (error our with javadoc8)
-	# already upstream commit 2103082c
-	find . -name '*.java' -exec sed -i "s|<br />|<BR>|" {} \; ||die
-
-	#add specific gentoo java directories
-	if use gui; then
-		sed -i -e "s|/usr/lib/jogl2|/usr/lib/jogl-2.2|" \
-			-e "s|/usr/lib64/jogl2|/usr/lib64/jogl-2.2|" configure.ac || die
-		sed -i -e "s|/usr/lib/gluegen2|/usr/lib/gluegen-2.2|" \
-			-e "s|/usr/lib64/gluegen2|/usr/lib64/gluegen-2.2|" \
-			-e "s|AC_CHECK_LIB(\[gluegen2-rt|AC_CHECK_LIB([gluegen-rt|" \
-			configure.ac || die
-
-		sed -i -e "s/jogl2/jogl-2.2/" -e "s/gluegen2/gluegen-2.2/" \
-			etc/librarypath.xml || die
-	fi
-
-	mkdir jar || die
-	pushd jar >/dev/null
-	if use gui; then
-		java-pkg_jar-from jlatexmath-1,flexdock,skinlf
-		java-pkg_jar-from jgoodies-looks-2.6,jrosetta
-		java-pkg_jar-from avalon-framework-4.2,jeuclid-core
-		java-pkg_jar-from xmlgraphics-commons-2,commons-io-1
-		java-pkg_jar-from jogl-2.2 jogl-all.jar jogl2.jar
-		java-pkg_jar-from gluegen-2.2 gluegen-rt.jar gluegen2-rt.jar
-		java-pkg_jar-from fop fop.jar
-		java-pkg_jar-from javahelp jhall.jar
-		java-pkg_jar-from jlatexmath-fop-1
-		use xcos &&	java-pkg_jar-from jgraphx-2.5
-		if use doc; then
-			java-pkg_jar-from --build-only batik-1.8 batik-all.jar
-			java-pkg_jar-from --build-only saxon-9 saxon.jar saxon9he.jar
-			java-pkg_jar-from --build-only xml-commons-external-1.4 xml-apis-ext.jar
-		fi
-	fi
-	if use emf; then
-		java-pkg_jar-from freehep-graphicsio-emf,freehep-graphics2d
-		java-pkg_jar-from freehep-graphicsio,freehep-io,freehep-graphicsbase
-	fi
-	if use test; then
-		java-pkg_jar-from junit-4 junit.jar junit4.jar
-		java-pkg_jar-from ant-junit
-	fi
-	popd
-
-	java-pkg-opt-2_src_prepare
-	eautoconf
-}
-
-src_configure() {
-	if use gui; then
-		export JAVA_HOME="$(java-config -O)"
-	else
-		unset JAVAC
-	fi
-
-	export BLAS_LIBS="$($(tc-getPKG_CONFIG) --libs blas)"
-	export LAPACK_LIBS="$($(tc-getPKG_CONFIG) --libs lapack)"
-	export F77_LDFLAGS="${LDFLAGS}"
-
-	econf \
-		--enable-relocatable \
-		--disable-rpath \
-		--with-docbook="${EPREFIX}/usr/share/sgml/docbook/xsl-stylesheets" \
-		--disable-static-system-lib \
-		$(use_enable debug) \
-		$(use_enable debug code-coverage) \
-		$(use_enable debug debug-C) \
-		$(use_enable debug debug-CXX) \
-		$(use_enable debug debug-fortran) \
-		$(use_enable debug debug-java) \
-		$(use_enable debug debug-linker) \
-		$(use_enable doc build-help) \
-		$(use_enable nls) \
-		$(use_enable nls build-localization) \
-		$(use_enable static-libs static) \
-		$(use_enable test compilation-tests) \
-		$(use_with emf) \
-		$(use_with fftw) \
-		$(use_with gui) \
-		$(use_with gui javasci) \
-		$(use_with matio) \
-		$(use_with openmp) \
-		$(use_with tk) \
-		$(use_with umfpack) \
-		$(use_with xcos) \
-		$(use_with xcos modelica) \
-		$(use_with mpi)
-}
-
-src_compile() {
-	addpredict /proc/mtrr
-	default
-	pax-mark m .libs/scilab-bin
-	use doc && emake doc
-}
-
-src_test() {
-	if use gui; then
-		Xemake check
-	else
-		emake check
-	fi
-}
-
-src_install() {
-	default
-	prune_libtool_files --all
-	rm -rf "${D}"/usr/share/scilab/modules/*/tests ||die
-	use bash-completion && newbashcomp "${FILESDIR}"/"${PN}".bash_completion "${PN}"
-	echo "SEARCH_DIRS_MASK=${EPREFIX}/usr/$(get_libdir)/scilab" \
-		> 50-"${PN}"
-	insinto /etc/revdep-rebuild && doins "50-${PN}"
-}
-
-pkg_postinst() {
-	xdg_mimeinfo_database_update
-	einfo "If you are using the NVIDIA binary drivers, and run into graphics"
-	einfo "crashes, you may try to run scilab as follows:"
-	einfo "EGL_DRIVER=egl_glx scilab"
-	einfo "See upstream http://bugzilla.scilab.org/show_bug.cgi?id=12940"
-}
-
-pkg_postrm() {
-	xdg_mimeinfo_database_update
-}
diff --git a/sci-mathematics/slepc/Manifest b/sci-mathematics/slepc/Manifest
deleted file mode 100644
index 8f4488e93..000000000
--- a/sci-mathematics/slepc/Manifest
+++ /dev/null
@@ -1,4 +0,0 @@
-DIST slepc-3.10.0.tar.gz 4565134 BLAKE2B 88546893525d1744b37d2190ba57c49c0c59022cc43b235f6fa91a4ff57b077ac114ce6e2cd72fee74cb35cb271821ccc7fc511dc5a2432fe436f2bf57fb69f4 SHA512 f182c5e612f1aa5ca436bcb0ad812f216f6e5eaebf16683cab5c8fba63d29ffd55c9fb69377dd9bce3b32f3e6dec4a681face5d960ed1c78bb78cdc0ffe913d9
-DIST slepc-3.10.2.tar.gz 4566198 BLAKE2B 3699f350871f1b48fe024ae55a4b27f3cd41558fc86968e9a54502fe5807a807e1aad5b8f6ed38d3eeac06aa41ccd298f03525441fed35927ed174410eec24d0 SHA512 07eacc8532dfdd8976fbffa0fc5664c377816f42ccba9bdcdc3f11fdc26557b0c86ed16c4d56f089837ef46206b82d99b97f782367137d16af2dae2b2250954f
-DIST slepc-3.8.2.tar.gz 4305725 BLAKE2B 7a8a0281cea19fb3c4b45ad98c277acff9d743c45e44af0600fe69c03b25d168994782daee01da7edb584adc1fce75badc6786752f70c1a751b59181b43476b3 SHA512 4d2cbcdd9ecc5e7fca10df85c0248874f379df4c7c5f6158e6896e9d5beced69c8755baf706418cd46dc2a82872a916d244b92b9fef4a7d6e8213d4899729a3e
-DIST slepc-3.9.0.tar.gz 4473419 BLAKE2B 1d64dc0ed0fd8617c6d17dcc53064ad3ceca8fd5392ea37ff82923c7d5c6740eaabdfc2b033f5e773e62c28d5e21cb3403d3f3b01c578f154aa9be80dbf6e97f SHA512 490403e42a2f02f56db7a9edda1c6f4d7454f6c14645ee12511a8a0551de5ea238d39dde4a5b854f82cc161582c73a5bf392b07c9161bb9a89e600ad53e28909
diff --git a/sci-mathematics/slepc/metadata.xml b/sci-mathematics/slepc/metadata.xml
deleted file mode 100644
index 046ec6c8f..000000000
--- a/sci-mathematics/slepc/metadata.xml
+++ /dev/null
@@ -1,15 +0,0 @@
-<?xml version="1.0" encoding="UTF-8"?>
-<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
-<pkgmetadata>
-	<maintainer type="person">
-		<email>tamiko@gentoo.org</email>
-		<name>Matthias Maier</name>
-	</maintainer>
-	<maintainer type="project">
-		<email>sci-mathematics@gentoo.org</email>
-		<name>Gentoo Mathematics Project</name>
-	</maintainer>
-	<use>
-		<flag name="complex-scalars">Make scalars complex</flag>
-	</use>
-</pkgmetadata>
diff --git a/sci-mathematics/slepc/slepc-3.10.0.ebuild b/sci-mathematics/slepc/slepc-3.10.0.ebuild
deleted file mode 100644
index 5bd6c4b95..000000000
--- a/sci-mathematics/slepc/slepc-3.10.0.ebuild
+++ /dev/null
@@ -1,74 +0,0 @@
-# Copyright 1999-2018 Gentoo Foundation
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=6
-
-PYTHON_COMPAT=( python2_7 )
-
-inherit eutils flag-o-matic python-any-r1 toolchain-funcs versionator
-
-DESCRIPTION="Scalable Library for Eigenvalue Problem Computations"
-HOMEPAGE="http://slepc.upv.es/"
-SRC_URI="http://slepc.upv.es/download/distrib/${P}.tar.gz"
-
-LICENSE="LGPL-3"
-SLOT="0"
-KEYWORDS="~amd64 ~x86"
-IUSE="complex-scalars doc mpi"
-
-PETSC_PV="$(get_version_component_range 1-2 ${PV})"
-RDEPEND="
-	=sci-mathematics/petsc-${PETSC_PV}*:=[mpi=,complex-scalars=]
-	sci-libs/arpack[mpi=]
-	mpi? ( virtual/mpi )
-"
-
-DEPEND="${RDEPEND}
-	${PYTHON_DEPS}
-	virtual/pkgconfig
-	dev-util/cmake
-"
-
-MAKEOPTS="${MAKEOPTS} -j1 V=1"
-
-src_prepare() {
-	default
-
-	sed -i -e 's%/usr/bin/env python%/usr/bin/env python2%' configure || die
-}
-
-src_configure() {
-	# *sigh*
-	addpredict "${PETSC_DIR}"/.nagged
-
-	# Make sure that the environment is set up correctly:
-	unset PETSC_DIR
-	unset PETSC_ARCH
-	unset SLEPC_DIR
-	source "${EPREFIX}"/etc/env.d/99petsc
-	export PETSC_DIR
-
-	# configure is a custom python script and doesn't want to have default
-	# configure arguments that we set with econf
-	./configure \
-		--prefix="${EPREFIX}/usr/$(get_libdir)/slepc" \
-		--with-arpack=1 \
-		--with-arpack-dir="${EPREFIX}/usr/$(get_libdir)" \
-		--with-arpack-flags="$(usex mpi "-lparpack,-larpack" "-larpack")"
-
-}
-
-src_install() {
-	emake SLEPC_DESTDIR="${D}/usr/$(get_libdir)/slepc" install
-
-	# add PETSC_DIR to environmental variables
-	cat >> 99slepc <<- EOF
-		SLEPC_DIR=${EPREFIX}/usr/$(get_libdir)/slepc
-	EOF
-	doenvd 99slepc
-
-	if use doc ; then
-		dodoc docs/slepc.pdf
-		dohtml -r docs/*.html docs/manualpages
-	fi
-}
diff --git a/sci-mathematics/slepc/slepc-3.10.2.ebuild b/sci-mathematics/slepc/slepc-3.10.2.ebuild
deleted file mode 100644
index 2009090c1..000000000
--- a/sci-mathematics/slepc/slepc-3.10.2.ebuild
+++ /dev/null
@@ -1,74 +0,0 @@
-# Copyright 1999-2019 Gentoo Authors
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=6
-
-PYTHON_COMPAT=( python2_7 )
-
-inherit eutils flag-o-matic python-any-r1 toolchain-funcs versionator
-
-DESCRIPTION="Scalable Library for Eigenvalue Problem Computations"
-HOMEPAGE="http://slepc.upv.es/"
-SRC_URI="http://slepc.upv.es/download/distrib/${P}.tar.gz"
-
-LICENSE="LGPL-3"
-SLOT="0"
-KEYWORDS="~amd64 ~x86"
-IUSE="complex-scalars doc mpi"
-
-PETSC_PV="$(get_version_component_range 1-2 ${PV})"
-RDEPEND="
-	=sci-mathematics/petsc-${PETSC_PV}*:=[mpi=,complex-scalars=]
-	sci-libs/arpack[mpi=]
-	mpi? ( virtual/mpi )
-"
-
-DEPEND="${RDEPEND}
-	${PYTHON_DEPS}
-	virtual/pkgconfig
-	dev-util/cmake
-"
-
-MAKEOPTS="${MAKEOPTS} -j1 V=1"
-
-src_prepare() {
-	default
-
-	sed -i -e 's%/usr/bin/env python%/usr/bin/env python2%' configure || die
-}
-
-src_configure() {
-	# *sigh*
-	addpredict "${PETSC_DIR}"/.nagged
-
-	# Make sure that the environment is set up correctly:
-	unset PETSC_DIR
-	unset PETSC_ARCH
-	unset SLEPC_DIR
-	source "${EPREFIX}"/etc/env.d/99petsc
-	export PETSC_DIR
-
-	# configure is a custom python script and doesn't want to have default
-	# configure arguments that we set with econf
-	./configure \
-		--prefix="${EPREFIX}/usr/$(get_libdir)/slepc" \
-		--with-arpack=1 \
-		--with-arpack-dir="${EPREFIX}/usr/$(get_libdir)" \
-		--with-arpack-flags="$(usex mpi "-lparpack,-larpack" "-larpack")"
-
-}
-
-src_install() {
-	emake SLEPC_DESTDIR="${D}/usr/$(get_libdir)/slepc" install
-
-	# add PETSC_DIR to environmental variables
-	cat >> 99slepc <<- EOF
-		SLEPC_DIR=${EPREFIX}/usr/$(get_libdir)/slepc
-	EOF
-	doenvd 99slepc
-
-	if use doc ; then
-		dodoc docs/slepc.pdf
-		dohtml -r docs/*.html docs/manualpages
-	fi
-}
diff --git a/sci-mathematics/slepc/slepc-3.8.2.ebuild b/sci-mathematics/slepc/slepc-3.8.2.ebuild
deleted file mode 100644
index 5bd6c4b95..000000000
--- a/sci-mathematics/slepc/slepc-3.8.2.ebuild
+++ /dev/null
@@ -1,74 +0,0 @@
-# Copyright 1999-2018 Gentoo Foundation
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=6
-
-PYTHON_COMPAT=( python2_7 )
-
-inherit eutils flag-o-matic python-any-r1 toolchain-funcs versionator
-
-DESCRIPTION="Scalable Library for Eigenvalue Problem Computations"
-HOMEPAGE="http://slepc.upv.es/"
-SRC_URI="http://slepc.upv.es/download/distrib/${P}.tar.gz"
-
-LICENSE="LGPL-3"
-SLOT="0"
-KEYWORDS="~amd64 ~x86"
-IUSE="complex-scalars doc mpi"
-
-PETSC_PV="$(get_version_component_range 1-2 ${PV})"
-RDEPEND="
-	=sci-mathematics/petsc-${PETSC_PV}*:=[mpi=,complex-scalars=]
-	sci-libs/arpack[mpi=]
-	mpi? ( virtual/mpi )
-"
-
-DEPEND="${RDEPEND}
-	${PYTHON_DEPS}
-	virtual/pkgconfig
-	dev-util/cmake
-"
-
-MAKEOPTS="${MAKEOPTS} -j1 V=1"
-
-src_prepare() {
-	default
-
-	sed -i -e 's%/usr/bin/env python%/usr/bin/env python2%' configure || die
-}
-
-src_configure() {
-	# *sigh*
-	addpredict "${PETSC_DIR}"/.nagged
-
-	# Make sure that the environment is set up correctly:
-	unset PETSC_DIR
-	unset PETSC_ARCH
-	unset SLEPC_DIR
-	source "${EPREFIX}"/etc/env.d/99petsc
-	export PETSC_DIR
-
-	# configure is a custom python script and doesn't want to have default
-	# configure arguments that we set with econf
-	./configure \
-		--prefix="${EPREFIX}/usr/$(get_libdir)/slepc" \
-		--with-arpack=1 \
-		--with-arpack-dir="${EPREFIX}/usr/$(get_libdir)" \
-		--with-arpack-flags="$(usex mpi "-lparpack,-larpack" "-larpack")"
-
-}
-
-src_install() {
-	emake SLEPC_DESTDIR="${D}/usr/$(get_libdir)/slepc" install
-
-	# add PETSC_DIR to environmental variables
-	cat >> 99slepc <<- EOF
-		SLEPC_DIR=${EPREFIX}/usr/$(get_libdir)/slepc
-	EOF
-	doenvd 99slepc
-
-	if use doc ; then
-		dodoc docs/slepc.pdf
-		dohtml -r docs/*.html docs/manualpages
-	fi
-}
diff --git a/sci-mathematics/slepc/slepc-3.9.0.ebuild b/sci-mathematics/slepc/slepc-3.9.0.ebuild
deleted file mode 100644
index 5bd6c4b95..000000000
--- a/sci-mathematics/slepc/slepc-3.9.0.ebuild
+++ /dev/null
@@ -1,74 +0,0 @@
-# Copyright 1999-2018 Gentoo Foundation
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=6
-
-PYTHON_COMPAT=( python2_7 )
-
-inherit eutils flag-o-matic python-any-r1 toolchain-funcs versionator
-
-DESCRIPTION="Scalable Library for Eigenvalue Problem Computations"
-HOMEPAGE="http://slepc.upv.es/"
-SRC_URI="http://slepc.upv.es/download/distrib/${P}.tar.gz"
-
-LICENSE="LGPL-3"
-SLOT="0"
-KEYWORDS="~amd64 ~x86"
-IUSE="complex-scalars doc mpi"
-
-PETSC_PV="$(get_version_component_range 1-2 ${PV})"
-RDEPEND="
-	=sci-mathematics/petsc-${PETSC_PV}*:=[mpi=,complex-scalars=]
-	sci-libs/arpack[mpi=]
-	mpi? ( virtual/mpi )
-"
-
-DEPEND="${RDEPEND}
-	${PYTHON_DEPS}
-	virtual/pkgconfig
-	dev-util/cmake
-"
-
-MAKEOPTS="${MAKEOPTS} -j1 V=1"
-
-src_prepare() {
-	default
-
-	sed -i -e 's%/usr/bin/env python%/usr/bin/env python2%' configure || die
-}
-
-src_configure() {
-	# *sigh*
-	addpredict "${PETSC_DIR}"/.nagged
-
-	# Make sure that the environment is set up correctly:
-	unset PETSC_DIR
-	unset PETSC_ARCH
-	unset SLEPC_DIR
-	source "${EPREFIX}"/etc/env.d/99petsc
-	export PETSC_DIR
-
-	# configure is a custom python script and doesn't want to have default
-	# configure arguments that we set with econf
-	./configure \
-		--prefix="${EPREFIX}/usr/$(get_libdir)/slepc" \
-		--with-arpack=1 \
-		--with-arpack-dir="${EPREFIX}/usr/$(get_libdir)" \
-		--with-arpack-flags="$(usex mpi "-lparpack,-larpack" "-larpack")"
-
-}
-
-src_install() {
-	emake SLEPC_DESTDIR="${D}/usr/$(get_libdir)/slepc" install
-
-	# add PETSC_DIR to environmental variables
-	cat >> 99slepc <<- EOF
-		SLEPC_DIR=${EPREFIX}/usr/$(get_libdir)/slepc
-	EOF
-	doenvd 99slepc
-
-	if use doc ; then
-		dodoc docs/slepc.pdf
-		dohtml -r docs/*.html docs/manualpages
-	fi
-}
diff --git a/sci-mathematics/tisean/Manifest b/sci-mathematics/tisean/Manifest
deleted file mode 100644
index 3139928c2..000000000
--- a/sci-mathematics/tisean/Manifest
+++ /dev/null
@@ -1 +0,0 @@
-DIST TISEAN_3.0.1.tar.gz 876454 BLAKE2B 5d1fb099fb28650d0a93b53ef52f332257ab87046f3ad4823c8c2b64e282ff681d839a193cec52a6a7b3934cdd1abaf5359e2954a501790f8fa06d61d49f41d9 SHA512 7c69f4189d0aeaadcd5d558f672bd2db0f4aa8d43bb390e54d283ae4a7a562446f909d46426da3de058c99ec54c84e8d7a69cec82a9b1772a946f5a7a5861f33
diff --git a/sci-mathematics/tisean/files/tisean-3.0.1-backport.patch b/sci-mathematics/tisean/files/tisean-3.0.1-backport.patch
deleted file mode 100644
index dc86d1f16..000000000
--- a/sci-mathematics/tisean/files/tisean-3.0.1-backport.patch
+++ /dev/null
@@ -1,752 +0,0 @@
-From 377911cf0ba30428e8e6095162ac9d63689838b8 Mon Sep 17 00:00:00 2001
-From: Rainer Hegger <hegger@theochem.uni-frankfurt.de>
-Date: Thu, 16 Apr 2015 15:49:31 +0200
-Subject: [PATCH] Collected changes over the last years
-
----
- configure                  |  22 +++++-----
- docs/docs_c/corr.html      |   5 +++
- docs/docs_c/lfo-ar.html    |   2 +-
- docs/docs_c/lyap_spec.html |   4 +-
- docs/tutorial/ex1.html     |   2 +-
- docs/tutorial/ex2.html     |  10 ++---
- docs/tutorial/ex3.html     |   2 +-
- source_c/corr.c            |  28 +++++++++---
- source_c/false_nearest.c   |  10 ++++-
- source_c/histogram.c       |  55 +++++++++++++++---------
- source_c/lzo-run.c         |   2 +-
- source_c/mem_spec.c        |   5 ++-
- source_c/mutual.c          | 105 +++++++++++++++++++++++++++++----------------
- source_c/polynom.c         |   7 ++-
- source_c/polynomp.c        |   2 +-
- source_c/xcor.c            |   2 +-
- source_f/cluster.f         |   3 +-
- 17 files changed, 172 insertions(+), 94 deletions(-)
-
-diff --git a/configure b/configure
-index c27cf28..095e16d 100755
---- a/configure
-+++ b/configure
-@@ -35,17 +35,17 @@ verbose=
- x_includes=NONE
- x_libraries=NONE
- bindir='bin'
--sbindir='${exec_prefix}/sbin'
--libexecdir='${exec_prefix}/libexec'
--datadir='${prefix}/share'
--sysconfdir='${prefix}/etc'
--sharedstatedir='${prefix}/com'
--localstatedir='${prefix}/var'
--libdir='${exec_prefix}/lib'
--includedir='${prefix}/include'
-+sbindir='sbin'
-+libexecdir='libexec'
-+datadir='share'
-+sysconfdir='etc'
-+sharedstatedir='com'
-+localstatedir='var'
-+libdir='lib'
-+includedir='include'
- oldincludedir='/usr/include'
--infodir='${prefix}/info'
--mandir='${prefix}/man'
-+infodir='info'
-+mandir='man'
- 
- # Initialize some other variables.
- subdirs=
-@@ -1020,7 +1020,7 @@ fi
- 
- 
- 
--for fff in "$FC" f77 g77 "f77 +U77" "f77 -q -f -B108 -lU77"; do
-+for fff in "$FC" f77 g77 gfortran "f77 +U77" "f77 -q -f -B108 -lU77"; do
-    if test -z "$fff"; then 
-       continue
-    fi
-diff --git a/docs/docs_c/corr.html b/docs/docs_c/corr.html
-index 8b2eb8c..f2aa4f2 100644
---- a/docs/docs_c/corr.html
-+++ b/docs/docs_c/corr.html
-@@ -57,6 +57,11 @@ <h2 align=center>Usage:</h2>
- <td>100
- </tr>
- <tr>
-+<th>-s#
-+<td>calculate the correlation only every #-th step
-+<td>1
-+</tr>
-+<tr>
- <th>-n
- <td>don't use normalization to standard deviation
- <td>not set
-diff --git a/docs/docs_c/lfo-ar.html b/docs/docs_c/lfo-ar.html
-index 59263b6..11a9b4e 100644
---- a/docs/docs_c/lfo-ar.html
-+++ b/docs/docs_c/lfo-ar.html
-@@ -117,7 +117,7 @@ <h2 align=center>Description of the Output:</h2>
- The output consists of 5 columns for each neighborhood size:</b>
- <ul>
- <li> neighborhood size (units of the data)
--<li> relative forecast error ((forecast error)/(variance of the data))
-+<li> relative forecast error ((forecast error)/(standard deviation of data))
- <li> fraction of points for which neighbors were found for this neighborhood 
- size
- <li> average number of neighbors found per point
-diff --git a/docs/docs_c/lyap_spec.html b/docs/docs_c/lyap_spec.html
-index ab67d84..189482a 100644
---- a/docs/docs_c/lyap_spec.html
-+++ b/docs/docs_c/lyap_spec.html
-@@ -58,7 +58,9 @@ <h2 align=center>Usage:</h2>
- -->
- <tr>
- <th>-r#
--<td>minimal neighborhood size
-+<td>minimal neighborhood size. This option dominates -k. This means
-+  that if -r is set and more than -k neighbors are found, the number
-+  of neighbors will not be reduced to the value given with -k.
- <td>not set
- </tr>
- <tr>
-diff --git a/docs/tutorial/ex1.html b/docs/tutorial/ex1.html
-index e77be7b..660811b 100644
---- a/docs/tutorial/ex1.html
-+++ b/docs/tutorial/ex1.html
-@@ -146,7 +146,7 @@
- variable <font color=blue>x </font> of the logistic equation for
- various parameter values (e.g.: <font color=green>
- gnuplot&#62; plot '&#60; henon -B0 -A2 -l10000 | histogram -b100' with
--hist</font>). When a sufficiently long transient has been
-+histeps</font>). When a sufficiently long transient has been
- discarded, such a histogram is the approximation to the invaraint
- measure on the bins of the histogram. Verify numerically:<br>
- <ul>
-diff --git a/docs/tutorial/ex2.html b/docs/tutorial/ex2.html
-index 5324a15..a0fbb11 100644
---- a/docs/tutorial/ex2.html
-+++ b/docs/tutorial/ex2.html
-@@ -82,7 +82,7 @@
- the two histograms, you thus should shift the one with respect to the
- other by the mean value of the data:<br>
- <font color=green>  
--set data style histep<br>
-+set style data histep<br>
- plot '&#60; histogram amplitude.dat' u ($1-.146):2,'&#60; histogram
- ar.dat' </font> 
- <br>Result: The data sets are differnt: the distribution of <font
-@@ -95,7 +95,7 @@
- <a href="../docs_f/spectrum.html">spectrum</a>) of both of them:<br>
- <font color=red> corr amplitude.dat -D500 -o<br>
- corr ar.dat -D500 -o</font><br>
--<font color=green>set data style lines</font><br>
-+<font color=green>set style data lines</font><br>
- <font color=green> plot 'ar.dat.cor','amplitude.dat.cor'</font><br>
- <font color=red>spectrum amplitude.dat -o<br>
- spectrum ar.dat -o</font><br>
-@@ -150,7 +150,7 @@
- <ul>
- <li> compute the false nearest neighbour statistics 
- (<a href="../docs_c/false_nearest.html">false_nearest</a>):<br>
--<font color=red> false_nearest  amplitude.dat -M8 -d8 -o
-+<font color=red> false_nearest  amplitude.dat -M1,8 -d8 -o
- -t200 -f5 </font><br>
- Study the output, <font color=blue>amplitude.dat.fnn</font>, and
- observe the invariance of the result (namely that the embedding dimension
-@@ -158,9 +158,9 @@
- <br><br>
- 
- <li> Use the zeorth-order predictor 
--(<a href="../docs_c/zeroth.html">zeroth</a>)
-+(<a href="../docs_c/lzo-test.html">zeroth</a>)
- on amplitude.dat and on ar.dat.<br>
--<font color=red> zeroth amplitude.dat -m1,4 -d8 -o
-+<font color=red> lzo-test amplitude.dat -m1,4 -d8 -o
- -s250<br>
- zeroth ar.dat -m1,4 -d8 -o
- -s250</font><br>
-diff --git a/docs/tutorial/ex3.html b/docs/tutorial/ex3.html
-index 91735dd..2894689 100644
---- a/docs/tutorial/ex3.html
-+++ b/docs/tutorial/ex3.html
-@@ -196,7 +196,7 @@
- <font color=red> ll-ar optimal.dat -d10 -m3 -i2000 -s1 -o</font>,<br>
- and compare the results:<br>
- <font color=green>
--set data style linespoints<br>
-+set style data linespoints<br>
- plot 'whatisit.dat.ll', 'whatisit.dat.ll' u 1:3,'optimal.dat.ll',
- 'optimal.dat.ll' u 1:3</font><br> 
- <br>
-diff --git a/source_c/corr.c b/source_c/corr.c
-index 06da07a..4c79b9a 100644
---- a/source_c/corr.c
-+++ b/source_c/corr.c
-@@ -30,7 +30,7 @@
- char *format,*outfile=NULL,stout=1,normalize=1;
- unsigned int column=1;
- unsigned int verbosity=0xff;
--unsigned long tau=100,length=ULONG_MAX,exclude=0;
-+unsigned long tau=100,step=1,length=ULONG_MAX,exclude=0;
- double *array;
- double av,var;
- char *infile=NULL;
-@@ -48,6 +48,8 @@ void show_options(char *progname)
-   fprintf(stderr,"\t-x # of lines to be ignored [default 0]\n");
-   fprintf(stderr,"\t-c column to read [default is 1]\n");
-   fprintf(stderr,"\t-D corrlength  [default is 100]\n");
-+  fprintf(stderr,"\t-s # calculate the correlation only every #-th step "
-+	  "[default is 1]\n");
-   fprintf(stderr,"\t-n don\'t normalize to the variance"
- 	  " of the data [not set]\n");
-   fprintf(stderr,"\t-o output_file  [default is 'datafile'.cor; no -o"
-@@ -72,6 +74,8 @@ void scan_options(int argc,char **argv)
-     sscanf(out,"%u",&column);
-   if ((out=check_option(argv,argc,'D','u')) != NULL)
-     sscanf(out,"%lu",&tau);
-+  if ((out=check_option(argv,argc,'s','u')) != NULL)
-+    sscanf(out,"%lu",&step);
-   if ((out=check_option(argv,argc,'n','n')) != NULL)
-     normalize=0;
-   if ((out=check_option(argv,argc,'V','u')) != NULL)
-@@ -88,16 +92,17 @@ double corr(long i)
-   long j;
-   double c=0.0;
-   
--  for (j=0;j<(length-i);j++)
-+  for (j=0;j<(length-i);j++) {
-     c += array[j]*array[j+i];
-+  }
- 
--  return c/(length-i);
-+  return c/(double)(length-i);
- }
- 
- int main(int argc,char** argv)
- {
--  char stdi=0;
--  long i;
-+  char stdi=0,done=0;
-+  unsigned long i;
-   FILE *fout=NULL;
-   
-   if (scan_help(argc,argv))
-@@ -157,14 +162,25 @@ int main(int argc,char** argv)
-   else
-     var=1.0;
- 
--  for (i=0;i<=tau;i++)
-+  for (i=0;i<=tau;i += step)
-     if (!stout) {
-       fprintf(fout,"%ld %e\n",i,corr(i)/var);
-       fflush(fout);
-+      if (i == tau) done=1;
-     }
-     else {
-       fprintf(stdout,"%ld %e\n",i,corr(i)/var);
-       fflush(stdout);
-+      if (i == tau) done=1;
-+    }
-+  if (!done)
-+    if (!stout) {
-+      fprintf(fout,"%ld %e\n",tau,corr(tau)/var);
-+      fflush(fout);
-+    }
-+    else {
-+      fprintf(stdout,"%ld %e\n",tau,corr(tau)/var);
-+      fflush(stdout);
-     }
-   if (!stout)
-     fclose(fout);
-diff --git a/source_c/false_nearest.c b/source_c/false_nearest.c
-index f8a16e9..f5eed04 100644
---- a/source_c/false_nearest.c
-+++ b/source_c/false_nearest.c
-@@ -21,6 +21,7 @@
- /*Changes:
-   12/10/05: It's multivariate now
-   12/16/05: Scaled <eps> and sigma(eps)
-+  03/08/09: delay was missing in delay embedding of univariate case
- */
- 
- #include <stdio.h>
-@@ -37,7 +38,7 @@ char *infile=NULL;
- char stdo=1,dimset=0;
- char *column=NULL;
- unsigned long length=ULONG_MAX,exclude=0,theiler=0;
--unsigned int delay=1,maxdim=5,minemb=1;
-+unsigned int delay=1,maxdim=6,minemb=1;
- unsigned int comp=1,maxemb=5;
- unsigned int verbosity=0xff;
- double rt=2.0;
-@@ -226,6 +227,11 @@ int main(int argc,char **argv)
-     series=(double**)get_multi_series(infile,&length,exclude,&comp,column,
- 				      dimset,verbosity);
- 
-+  if ((maxemb*delay+1) >= length) {
-+      fprintf(stderr,"Not enough points!\n");
-+      exit(FALSE_NEAREST_NOT_ENOUGH_POINTS);
-+  }
-+
-   for (i=0;i<comp;i++) {
-     rescale_data(series[i],length,&min,&ind_inter);
-     variance(series[i],length,&av,&ind_var);
-@@ -259,7 +265,7 @@ int main(int argc,char **argv)
-   for (i=0;i<maxdim;i++) {
-     if (comp == 1) {
-       vcomp[i]=0;
--      vemb[i]=i;
-+      vemb[i]=i*delay;
-     }
-     else {
-       vcomp[i]=i%comp;
-diff --git a/source_c/histogram.c b/source_c/histogram.c
-index 6ab9f02..a45576d 100644
---- a/source_c/histogram.c
-+++ b/source_c/histogram.c
-@@ -17,10 +17,8 @@
-  *   along with TISEAN; if not, write to the Free Software
-  *   Foundation, Inc., 51 Franklin St, Fifth Floor, Boston, MA  02110-1301  USA
-  */
--/*Author: Rainer Hegger. Last modified Dec 6, 2005*/
--/*Changes:
--  12/06/05: shift output x value to center of interval
--*/
-+/*Author: Rainer Hegger. Last modified May 16, 2014*/
-+
- #include <math.h>
- #include <limits.h>
- #include <stdio.h>
-@@ -28,7 +26,7 @@
- #include <string.h>
- #include "routines/tsa.h"
- 
--#define WID_STR "Makes a histogram of the data"
-+#define WID_STR "Creates a histogram of a onedimensional dataset"
- 
- unsigned long length=ULONG_MAX;
- unsigned long base=50;
-@@ -36,15 +34,10 @@ unsigned long exclude=0;
- unsigned int column=1;
- unsigned int verbosity=0xff;
- double size;
--char my_stdout=1,gotsize=0;
-+char my_stdout=1,gotsize=0,density=0;
- char *outfile=NULL;
- char *infile=NULL;
- 
--double *series;
--double average,var;
--double min,max;
--long *box;
--
- void show_options(char *progname)
- {
-   what_i_do(progname,WID_STR);
-@@ -57,6 +50,8 @@ void show_options(char *progname)
-   fprintf(stderr,"\t-x # of lines to ignore [default %ld]\n",exclude);
-   fprintf(stderr,"\t-c column to read [default %d]\n",column);
-   fprintf(stderr,"\t-b # of intervals [default %ld]\n",base);
-+  fprintf(stderr,"\t-D output densities not relative frequencies"
-+	  " [default not set]\n");
-   fprintf(stderr,"\t-o output file [default 'datafile'.dat ;"
- 	  " If no -o is given: stdout]\n");
-   fprintf(stderr,"\t-V verbosity level [default 1]\n\t\t"
-@@ -80,6 +75,8 @@ void scan_options(int n,char **str)
-     sscanf(out,"%lu",&base);
-   if ((out=check_option(str,n,'V','u')) != NULL)
-     sscanf(out,"%u",&verbosity);
-+  if ((out=check_option(str,n,'D','n')) != NULL)
-+    density=1;
-   if ((out=check_option(str,n,'o','o')) != NULL) {
-     my_stdout=0;
-     if (strlen(out) > 0)
-@@ -92,6 +89,10 @@ int main(int argc,char **argv)
-   char stdi=0;
-   unsigned long i,j;
-   double x,norm,size=1.0,size2=1.0;
-+  double min,max;
-+  double *series;
-+  double average,var;
-+  long *box;
-   FILE *fout;
- 
-   if (scan_help(argc,argv))
-@@ -123,24 +124,36 @@ int main(int argc,char **argv)
- 
-   series=(double*)get_series(infile,&length,exclude,column,verbosity);
-   variance(series,length,&average,&var);
--  rescale_data(series,length,&min,&max);
--  
--  
-+
-+  min=max=series[0];
-+  for (i=1;i<length;i++) {
-+    if (series[i] < min) min=series[i];
-+    else if (series[i] > max) max=series[i];
-+  }
-+  max -= min;
-+
-+  for (i=0;i<length;i++)
-+    series[i]=(series[i]-min);
-+
-   if (base > 0) {
-     check_alloc(box=(long*)malloc(sizeof(long)*base));
-     for (i=0;i<base;i++)
-       box[i]=0;
-     size=1./base;
--    size2=size/2.0;
-+    size2=(1.0-size/2.0)*max;
-     for (i=0;i<length;i++) {
--      if (series[i] > (1.0-size2))
--	series[i]=1.0-size2;
--      j=(long)(series[i]*base);
-+      if (series[i] > size2)
-+	series[i]=size2;
-+      j=(long)(series[i]*base/max);
-       box[j]++;
-     }
-   }
- 
--  norm=1.0/(double)length;
-+  if (!density)
-+    norm=1.0/(double)length;
-+  else
-+    norm=1.0/(double)length*(double)base/max;
-+
-   if (!my_stdout) {
-     fout=fopen(outfile,"w");
-     if (verbosity&VER_INPUT)
-@@ -150,7 +163,7 @@ int main(int argc,char **argv)
-     fprintf(fout,"#standard deviation= %e\n",var);
-     for (i=0;i<base;i++) {
-       x=(double)(i*size);
--      fprintf(fout,"%e %e\n",(x+size2)*max+min,(double)box[i]*norm);
-+      fprintf(fout,"%e %e\n",(x+size/2.0)*max+min,(double)box[i]*norm);
-     }
-     fclose(fout);
-   }
-@@ -162,7 +175,7 @@ int main(int argc,char **argv)
-     fprintf(stdout,"#standard deviation= %e\n",var);
-     for (i=0;i<base;i++) {
-       x=(double)(i*size);
--      fprintf(stdout,"%e %e\n",(x+size2)*max+min,(double)box[i]*norm);
-+      fprintf(stdout,"%e %e\n",(x+size/2.0)*max+min,(double)box[i]*norm);
-       fflush(stdout);
-     }
-   }
-diff --git a/source_c/lzo-run.c b/source_c/lzo-run.c
-index 5393e9f..bc54fb5 100644
---- a/source_c/lzo-run.c
-+++ b/source_c/lzo-run.c
-@@ -49,7 +49,7 @@ unsigned int MINN=50;
- unsigned int **indexes;
- unsigned long LENGTH=ULONG_MAX,FLENGTH=1000,exclude=0;
- unsigned long seed=0x9074325L;
--double EPS0=1.e-3,EPSF=1.2,Q=10.0;
-+double EPS0=1.e-3,EPSF=1.2,Q=0.0;
- 
- double **mat,*vec,*hsum,*newav;
- 
-diff --git a/source_c/mem_spec.c b/source_c/mem_spec.c
-index a38fcfd..9821488 100644
---- a/source_c/mem_spec.c
-+++ b/source_c/mem_spec.c
-@@ -22,6 +22,7 @@
-   Feb 19, 2007: changed meaning of -f flag and added -P flag to be 
-                 consistent with spectrum
-   Dec 5, 2006: Seg fault when poles > length;
-+  Mar 15, 2007: normalization now the same as in spectrum
-  */
- #include <stdio.h>
- #include <string.h>
-@@ -216,7 +217,7 @@ int main(int argc,char **argv)
-       fdt=i/(2.0*out);
-       pow_spec=powcoef(fdt,cof);
-       fprintf(fout,"%e %e\n",fdt*samplingrate,
--	      pm/pow_spec/sqrt((double)length));
-+	      pm/pow_spec/(double)length);
-       fflush(fout);
-     }
-     fclose(fout);
-@@ -233,7 +234,7 @@ int main(int argc,char **argv)
-       fdt=i/(2.0*out);
-       pow_spec=powcoef(fdt,cof);
-       fprintf(stdout,"%e %e\n",fdt*samplingrate,
--	      pm/pow_spec/*/sqrt((double)length)*/);
-+	      pm/pow_spec/(double)length);
-     }
-   }
-   
-diff --git a/source_c/mutual.c b/source_c/mutual.c
-index fbea470..0496e92 100644
---- a/source_c/mutual.c
-+++ b/source_c/mutual.c
-@@ -17,7 +17,7 @@
-  *   along with TISEAN; if not, write to the Free Software
-  *   Foundation, Inc., 51 Franklin St, Fifth Floor, Boston, MA  02110-1301  USA
-  */
--/*Author: Rainer Hegger. Last modified, Sep 20, 2000 */
-+/*Author: Rainer Hegger. Last modified, Jul 13, 2010 */
- #include <stdio.h>
- #include <stdlib.h>
- #include <math.h>
-@@ -26,16 +26,17 @@
- #include "routines/tsa.h"
- 
- #define WID_STR "Estimates the time delayed mutual information\n\t\
--of the data set"
-+of one or two data columns"
- 
- 
--char *file_out=NULL,stout=1;
-+char *file_out=NULL,stout=1,dimset=0;
- char *infile=NULL;
- unsigned long length=ULONG_MAX,exclude=0;
--unsigned int column=1;
-+unsigned int dim=1;
- unsigned int verbosity=0xff;
- long partitions=16,corrlength=20;
--long *array,*h1,*h11,**h2;
-+long **array,*h1,*h11,**h2;
-+char *column=NULL;
- 
- void show_options(char *progname)
- {
-@@ -48,7 +49,7 @@ void show_options(char *progname)
-           " means stdin\n");
-   fprintf(stderr,"\t-l # of points to be used [Default is all]\n");
-   fprintf(stderr,"\t-x # of lines to be ignored [Default is 0]\n");
--  fprintf(stderr,"\t-c column to read  [Default is 1]\n");
-+  fprintf(stderr,"\t-c columns to read  [Default is 1]\n");
-   fprintf(stderr,"\t-b # of boxes [Default is 16]\n");
-   fprintf(stderr,"\t-D max. time delay [Default is 20]\n");
-   fprintf(stderr,"\t-o output file [-o without name means 'datafile'.mut;"
-@@ -69,8 +70,8 @@ void scan_options(int n,char** in)
-     sscanf(out,"%lu",&length);
-   if ((out=check_option(in,n,'x','u')) != NULL)
-     sscanf(out,"%lu",&exclude);
--  if ((out=check_option(in,n,'c','u')) != NULL)
--    sscanf(out,"%u",&column);
-+  if ((out=check_option(in,n,'c','s')) != NULL)
-+    column=out;
-   if ((out=check_option(in,n,'b','u')) != NULL)
-     sscanf(out,"%lu",&partitions);
-   if ((out=check_option(in,n,'D','u')) != NULL)
-@@ -86,7 +87,7 @@ void scan_options(int n,char** in)
- 
- double make_cond_entropy(long t)
- {
--  long i,j,hi,hii,count=0;
-+  long i,j,hi,hii,count=0,start,stop;
-   double hpi,hpj,pij,cond_ent=0.0,norm;
- 
-   for (i=0;i<partitions;i++) {
-@@ -94,15 +95,23 @@ double make_cond_entropy(long t)
-     for (j=0;j<partitions;j++)
-       h2[i][j]=0;
-   }
--  for (i=0;i<length;i++)
--    if (i >= t) {
--      hii=array[i];
--      hi=array[i-t];
--      h1[hi]++;
--      h11[hii]++;
--      h2[hi][hii]++;
--      count++;
--    }
-+  if (t < 0) {
-+    start=0;
-+    stop=length+t;
-+  }
-+  else {
-+    start=t;
-+    stop=length;
-+  }
-+
-+  for (i=start;i<stop;i++) {
-+    hii=array[0][i];
-+    hi=array[1][i+t];
-+    h1[hi]++;
-+    h11[hii]++;
-+    h2[hi][hii]++;
-+    count++;
-+  }
- 
-   norm=1.0/(double)count;
-   cond_ent=0.0;
-@@ -127,8 +136,8 @@ double make_cond_entropy(long t)
- int main(int argc,char** argv)
- {
-   char stdi=0;
--  long tau,i;
--  double *series,min,interval,shannon;
-+  long tau,i,j;
-+  double **series,min1,min2,interval1,interval2,shannon,condent;
-   FILE *file;
-   
-   if (scan_help(argc,argv))
-@@ -140,7 +149,7 @@ int main(int argc,char** argv)
-     what_i_do(argv[0],WID_STR);
- #endif
- 
--  infile=search_datafile(argc,argv,&column,verbosity);
-+  infile=search_datafile(argc,argv,NULL,verbosity);
-   if (infile == NULL)
-     stdi=1;
- 
-@@ -158,20 +167,44 @@ int main(int argc,char** argv)
-   if (!stout)
-     test_outfile(file_out);
- 
--  series=(double*)get_series(infile,&length,exclude,column,verbosity);
--  rescale_data(series,length,&min,&interval);
-+  if (column == NULL) {
-+    series=(double**)get_multi_series(infile,&length,exclude,&dim,"",
-+				      dimset,verbosity);
-+  }
-+  else {
-+    series=(double**)get_multi_series(infile,&length,exclude,&dim,column,
-+                                      dimset,verbosity);
-+  }
- 
-   check_alloc(h1=(long *)malloc(sizeof(long)*partitions));
-   check_alloc(h11=(long *)malloc(sizeof(long)*partitions));
-   check_alloc(h2=(long **)malloc(sizeof(long *)*partitions));
-   for (i=0;i<partitions;i++) 
-     check_alloc(h2[i]=(long *)malloc(sizeof(long)*partitions));
--  check_alloc(array=(long *)malloc(sizeof(long)*length));
--  for (i=0;i<length;i++)
--    if (series[i] < 1.0)
--      array[i]=(long)(series[i]*(double)partitions);
--    else
--      array[i]=partitions-1;
-+  check_alloc(array=(long **)malloc(sizeof(long*)*2));
-+  check_alloc(array[0]=(long *)malloc(sizeof(long)*length));
-+  check_alloc(array[1]=(long *)malloc(sizeof(long)*length));
-+  if (dim == 1) {
-+    rescale_data(series[0],length,&min1,&interval1);
-+    for (i=0;i<length;i++)
-+      if (series[0][i] < 1.0)
-+	array[0][i]=array[1][i]=(long)(series[0][i]*(double)partitions);
-+      else
-+	array[0][i]=array[1][i]=partitions-1;
-+    free(series[0]);
-+  }
-+  else {
-+    rescale_data(series[0],length,&min1,&interval1);
-+    rescale_data(series[1],length,&min2,&interval2);
-+    for (j=0;j<2;j++) {
-+      for (i=0;i<length;i++)
-+	if (series[j][i] < 1.0)
-+	  array[j][i]=(long)(series[j][i]*(double)partitions);
-+	else
-+	  array[j][i]=partitions-1;
-+      free(series[j]);
-+    }
-+  }
-   free(series);
- 
-   shannon=make_cond_entropy(0);
-@@ -182,10 +215,9 @@ int main(int argc,char** argv)
-     file=fopen(file_out,"w");
-     if (verbosity&VER_INPUT)
-       fprintf(stderr,"Opened %s for writing\n",file_out);
--    fprintf(file,"#shannon= %e\n",shannon);
--    fprintf(file,"%d %e\n",0,shannon);
--    for (tau=1;tau<=corrlength;tau++) {
--      fprintf(file,"%ld %e\n",tau,make_cond_entropy(tau));
-+    for (tau=-corrlength;tau<=corrlength;tau++) {
-+      condent=make_cond_entropy(tau);
-+      fprintf(file,"%ld %e %e\n",tau,condent,condent/log((double)partitions));
-       fflush(file);
-     }
-     fclose(file);
-@@ -193,10 +225,9 @@ int main(int argc,char** argv)
-   else {
-     if (verbosity&VER_INPUT)
-       fprintf(stderr,"Writing to stdout\n");
--    fprintf(stdout,"#shannon= %e\n",shannon);
--    fprintf(stdout,"%d %e\n",0,shannon);
--    for (tau=1;tau<=corrlength;tau++) {
--      fprintf(stdout,"%ld %e\n",tau,make_cond_entropy(tau));
-+    for (tau=-corrlength;tau<=corrlength;tau++) {
-+      condent=make_cond_entropy(tau);
-+      fprintf(stdout,"%ld %e %e\n",tau,condent,condent/log((double)partitions));
-       fflush(stdout);
-     }
-   }
-diff --git a/source_c/polynom.c b/source_c/polynom.c
-index bc57ba8..6448f49 100644
---- a/source_c/polynom.c
-+++ b/source_c/polynom.c
-@@ -20,6 +20,8 @@
- /*Author: Rainer Hegger*/
- /* Changes:
-    6/30/2006: Norm of the errors was wrong
-+   6/5/2008: Norm was still wrong. Now its given as an absolute value in 
-+             units of the data
- */
- #include <stdio.h>
- #include <stdlib.h>
-@@ -265,6 +267,7 @@ int main(int argc,char **argv)
- 
-   series=(double*)get_series(infile,&LENGTH,exclude,COLUMN,verbosity);
-   variance(series,LENGTH,&av,&std_dev);
-+
-   for (i=0;i<LENGTH;i++)
-     series[i] /= std_dev;
- 
-@@ -307,11 +310,11 @@ int main(int argc,char **argv)
- 
-   in_error=make_error((unsigned long)0,INSAMPLE);
- 
--  fprintf(file,"#average insample error= %e\n",sqrt(in_error));
-+  fprintf(file,"#average insample error= %e\n",sqrt(in_error)*std_dev);
- 
-   if (INSAMPLE < LENGTH) {
-     out_error=make_error(INSAMPLE,LENGTH);
--    fprintf(file,"#average out of sample error= %e\n",sqrt(out_error));
-+    fprintf(file,"#average out of sample error= %e\n",sqrt(out_error)*std_dev);
-   }
- 
-   if (CAST)
-diff --git a/source_c/polynomp.c b/source_c/polynomp.c
-index 6021e19..5b32e58 100644
---- a/source_c/polynomp.c
-+++ b/source_c/polynomp.c
-@@ -239,7 +239,7 @@ int main(int argc,char **argv)
-   fclose(file);
- 
-   dummy=(double**)get_multi_series(parin,&plength,0LU,
--				   &dim,"",(char)"1",verbosity);
-+				   &dim,"",1,verbosity);
-   
-   check_alloc(order=(unsigned int**)malloc(sizeof(int*)*plength));
-   for (i=0;i<plength;i++) {
-diff --git a/source_c/xcor.c b/source_c/xcor.c
-index ec1ed7f..8f50609 100644
---- a/source_c/xcor.c
-+++ b/source_c/xcor.c
-@@ -30,7 +30,7 @@ given as two columns of one file."
- 
- char *columns=NULL,*outfile=NULL,stout=1;
- unsigned long length=ULONG_MAX,exclude=0;
--long tau=100;
-+unsigned long tau=100;
- unsigned int verbosity=0xff;
- double *array1,*array2;
- char *infile=NULL;
-diff --git a/source_f/cluster.f b/source_f/cluster.f
-index 61357ff..d564fc7 100644
---- a/source_f/cluster.f
-+++ b/source_f/cluster.f
-@@ -47,7 +47,8 @@
-       d(i,j)=dij
-       np=max(i,j,np)
-       goto 1
-- 999  if(iv_io(iverb).eq.1) write(0,'(a,i)') "matrix size ", np
-+c 999  if(iv_io(iverb).eq.1) write(0,'(a,i)') "matrix size ", np
-+ 999  if(iv_io(iverb).eq.1) write(0,*) "matrix size ", np
-       dmean=0
-       nd=0
-       do 20 i=1,np
diff --git a/sci-mathematics/tisean/files/tisean-3.0.1-gentoo.patch b/sci-mathematics/tisean/files/tisean-3.0.1-gentoo.patch
deleted file mode 100644
index 7f80f6276..000000000
--- a/sci-mathematics/tisean/files/tisean-3.0.1-gentoo.patch
+++ /dev/null
@@ -1,57 +0,0 @@
-diff --git a/Makefile.in b/Makefile.in
-index c1f3e0c..60f9720 100644
---- a/Makefile.in
-+++ b/Makefile.in
-@@ -9,8 +9,8 @@ HAVE_NR = @HAVE_NR@
- 
- all:
- 	@head -20 README
--	-if test -n "${FC}"; then (cd source_f && $(MAKE) $@); fi
--	-if test -n "${CC}"; then (cd source_c && $(MAKE) $@); fi
-+	$(MAKE) -C source_f $@
-+	$(MAKE) -C source_c $@
- 
- install: do_install missing
- 	@echo "******************************************************************"
-diff --git a/source_c/Makefile.in b/source_c/Makefile.in
-index 1ab10e4..2efb803 100644
---- a/source_c/Makefile.in
-+++ b/source_c/Makefile.in
-@@ -23,10 +23,10 @@ LOADLIBS = routines/libddtsa.a -lm
- all: $(ALL) 
- 
- routines/libddtsa.a:
--	(cd routines && $(MAKE))
-+	$(MAKE) -C routines
- 
- $(ALL): routines/libddtsa.a *.c
--	-$(CC) $(CFLAGS) $(COPTS) -o $@ $@.c $(LOADLIBS)
-+	-$(CC) $(LDFLAGS) $(CFLAGS) $(COPTS) -o $@ $@.c $(LOADLIBS)
- 
- install: all
- 	-for bin in $(ALL); do $(INSTALL) $$bin $(BINDIR); done
-diff --git a/source_f/Makefile.in b/source_f/Makefile.in
-index 6525b72..e45eea7 100644
---- a/source_f/Makefile.in
-+++ b/source_f/Makefile.in
-@@ -37,17 +37,17 @@ istdio.o: istdio_temp.f
- 	$(FC) $(FFLAGS) -c istdio.f -o istdio.o
- 
- $(BINS): libtsa.a libsla.a *.f
--	-$(FC) $(FFLAGS) -o $@ $@.f $(LOADLIBES) $(LDFLAGS)
-+	-$(FC) $(LDFLAGS) $(FFLAGS) -o $@ $@.f $(LOADLIBES)
- 
- libtsa.a: $(INC)
- 	$(AR) $(ARFLAGS) libtsa.a $?
- 	$(RANLIB) libtsa.a
- 
- libsla.a: slatec/*.f
--	(cd slatec && $(MAKE))
-+	$(MAKE) -C slatec
- 
- Randomize: libtsa.a libsla.a
--	-(cd randomize && $(MAKE))
-+	$(MAKE) -C randomize
- 
- clean:
- 	@rm -f istdio.f
diff --git a/sci-mathematics/tisean/metadata.xml b/sci-mathematics/tisean/metadata.xml
deleted file mode 100644
index 02d26ebf3..000000000
--- a/sci-mathematics/tisean/metadata.xml
+++ /dev/null
@@ -1,11 +0,0 @@
-<?xml version="1.0" encoding="UTF-8"?>
-<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
-<pkgmetadata>
-	<maintainer type="person">
-		<email>jlec@gentoo.org</email>
-		<name>Justin Lecher (jlec)</name>
-	</maintainer>
-	<upstream>
-		<remote-id type="github">heggus/Tisean</remote-id>
-	</upstream>
-</pkgmetadata>
diff --git a/sci-mathematics/tisean/tisean-3.0.1.ebuild b/sci-mathematics/tisean/tisean-3.0.1.ebuild
deleted file mode 100644
index f43138ee6..000000000
--- a/sci-mathematics/tisean/tisean-3.0.1.ebuild
+++ /dev/null
@@ -1,45 +0,0 @@
-# Copyright 1999-2017 Gentoo Foundation
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=5
-
-inherit eutils toolchain-funcs
-
-MY_P="Tisean_${PV}"
-
-DESCRIPTION="Time series analytics with theory of non-liner deterministic dynamical systems"
-HOMEPAGE="
-	https://github.com/heggus/Tisean
-	http://www.mpipks-dresden.mpg.de/%7Etisean/Tisean_3.0.1/index.html"
-SRC_URI="http://www.mpipks-dresden.mpg.de/~tisean/TISEAN_3.0.1.tar.gz"
-
-LICENSE="GPL-2"
-SLOT="0"
-KEYWORDS="~amd64 ~x86"
-IUSE=""
-
-S="${WORKDIR}/${MY_P}"
-
-src_prepare() {
-	tc-export FC CC
-	epatch \
-		"${FILESDIR}"/${P}-gentoo.patch \
-		"${FILESDIR}"/${P}-backport.patch
-}
-
-src_configure() {
-	econf \
-		--prefix="${ED}/usr"
-}
-
-src_install() {
-	# TODO: fix file collisions with:
-	# media-gfx/graphviz: /usr/bin/cluster
-	# media-gfx/imagemagick: /usr/bin/compare
-	dodir /usr/bin
-	default
-}
-
-pkg_postinst() {
-	optfeature "plotting support" sci-visualization/gnuplot
-}
diff --git a/sci-mathematics/ufc/Manifest b/sci-mathematics/ufc/Manifest
deleted file mode 100644
index 2a3e180a7..000000000
--- a/sci-mathematics/ufc/Manifest
+++ /dev/null
@@ -1,2 +0,0 @@
-DIST ufc-1.4.2.tar.gz 560547 SHA256 7f67e67c1e51753cbc0755db4122e2ece585af53a7869ddb670ee6aae7f2ff91 SHA512 6737e2125d7551d893c2034ad0fb5e623c51524510b072f3ad11c1851313d6c67c71bef14426f0a29ca3e92f821b9b320f1dbe7d98ba936a393b29a98ee89ece WHIRLPOOL d5fa9db8f07108b7345c8435915779ec6a5d8535c30f5b28b4173254fe1fbe9824a422d56eb21f33a513fa84b784c72854186b3149c8a70d55ab62971505c211
-DIST ufc-2.3.0.tar.gz 93771 BLAKE2B 6cbe24bf66da9300e9d4eed09aae15c15e8b92549c1dd18f4499d2debb873a7d1adf04c14498c8618e377418cdb81bbee6b9a3c7ec3efc85ab314b287ee7d692 SHA512 b60a7641fcd694466e0388989e8405ebb1cb2e15320dede45c1edc1fb80ea320e5177bdbed826b3a54c8e7fcd68180bc13fb18f458b2e3fca8af9f4994b51ad6
diff --git a/sci-mathematics/ufc/metadata.xml b/sci-mathematics/ufc/metadata.xml
deleted file mode 100644
index 062f16a24..000000000
--- a/sci-mathematics/ufc/metadata.xml
+++ /dev/null
@@ -1,15 +0,0 @@
-<?xml version="1.0" encoding="UTF-8"?>
-<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
-<pkgmetadata>
-	<maintainer type="project">
-		<email>sci-mathematics@gentoo.org</email>
-		<name>Gentoo Mathematics Project</name>
-	</maintainer>
-	<longdescription lang="en">
-UFC (Unified Form-assembly Code) is a unified framework for finite element assembly. More precisely, it defines a fixed interface for communicating low level routines (functions) for evaluating and assembling finite element variational forms. The UFC interface consists of a single header file ufc.h that specifies a C++ interface that must be implemented by code that complies with the UFC specification.
-</longdescription>
-	<upstream>
-		<remote-id type="bitbucket">fenics-project/ufc-deprecated</remote-id>
-		<remote-id type="launchpad">ufc</remote-id>
-	</upstream>
-</pkgmetadata>
diff --git a/sci-mathematics/ufc/ufc-1.4.2.ebuild b/sci-mathematics/ufc/ufc-1.4.2.ebuild
deleted file mode 100644
index 90700be9b..000000000
--- a/sci-mathematics/ufc/ufc-1.4.2.ebuild
+++ /dev/null
@@ -1,19 +0,0 @@
-# Copyright 1999-2014 Gentoo Foundation
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=5
-
-inherit cmake-utils
-
-DESCRIPTION="Unified framework for finite element assembly"
-HOMEPAGE="http://launchpad.net/ufc"
-SRC_URI="http://launchpad.net/${PN}/trunk/${PV}/+download/${P}.tar.gz"
-
-LICENSE="public-domain"
-SLOT="0"
-KEYWORDS="~amd64"
-
-IUSE=""
-
-DEPEND=""
-RDEPEND="${DEPEND}"
diff --git a/sci-mathematics/ufc/ufc-2.3.0.ebuild b/sci-mathematics/ufc/ufc-2.3.0.ebuild
deleted file mode 100644
index bf9b9330b..000000000
--- a/sci-mathematics/ufc/ufc-2.3.0.ebuild
+++ /dev/null
@@ -1,18 +0,0 @@
-# Copyright 1999-2014 Gentoo Foundation
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=5
-
-inherit cmake-utils
-
-DESCRIPTION="Unified framework for finite element assembly"
-HOMEPAGE="https://bitbucket.org/fenics-project/${PN}-deprecated/"
-SRC_URI="https://bitbucket.org/fenics-project/${PN}-deprecated/downloads/${P}.tar.gz"
-
-LICENSE="public-domain"
-SLOT="0"
-KEYWORDS="~amd64 ~x86"
-IUSE=""
-
-DEPEND=""
-RDEPEND="${DEPEND}"
diff --git a/sci-mathematics/why/Manifest b/sci-mathematics/why/Manifest
deleted file mode 100644
index 9b986a8e8..000000000
--- a/sci-mathematics/why/Manifest
+++ /dev/null
@@ -1 +0,0 @@
-DIST why-2.34.tar.gz 4019877 BLAKE2B f7f26b993ffb6b47b5822ad555d55e766738a7f158797408af79a1b90b5becc87f14581b569981e37d3fbf6cd120fd1c9bf1b10b48cc057acc4c92458bb65cb7 SHA512 e4abf6573cff52fcfe5c6b867ec15f6f65a88c9892143681b74e3a35caa870acdf04fdda6fc67790af608975bb688c6ec14fc12f2e44b319abdd262ac59384a7
diff --git a/sci-mathematics/why/files/why-flocq23.patch b/sci-mathematics/why/files/why-flocq23.patch
deleted file mode 100644
index b54d85a38..000000000
--- a/sci-mathematics/why/files/why-flocq23.patch
+++ /dev/null
@@ -1,11 +0,0 @@
---- lib/coq/WhyFloats.v.orig	2014-03-17 16:01:46.000000000 -0600
-+++ lib/coq/WhyFloats.v	2014-04-21 15:39:55.680771647 -0600
-@@ -108,7 +108,7 @@
- generalize (Zeq_bool_eq _ _ H1). clear.
- rewrite Fcalc_digits.Z_of_nat_S_digits2_Pnat.
- intros H.
--apply (Fcalc_digits.Zpower_gt_Zdigits Fcalc_digits.radix2 (Zpos prec) (Zpos m)).
-+apply (Fcore_digits.Zpower_gt_Zdigits Fcalc_digits.radix2 (Zpos prec) (Zpos m)).
- revert H.
- unfold FLT_exp.
- generalize (Fcore_digits.Zdigits radix2 (Zpos m)).
diff --git a/sci-mathematics/why/metadata.xml b/sci-mathematics/why/metadata.xml
deleted file mode 100644
index 70e1eb45f..000000000
--- a/sci-mathematics/why/metadata.xml
+++ /dev/null
@@ -1,25 +0,0 @@
-<?xml version="1.0" encoding="UTF-8"?>
-<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
-<pkgmetadata>
-	<maintainer type="project">
-		<email>sci@gentoo.org</email>
-		<name>Gentoo Science Project</name>
-	</maintainer>
-	<longdescription>
-Why is a software verification platform. It contains a general-purpose
-verification condition generator (VCG) which is used as a back-end
-by other verification tools but it can also be used directly to verify
-programs. It also provides Krakatoa, a tool or the verification of Java
-programs and Caduceus, a tool for the verification of C programs.
-</longdescription>
-	<use>
-		<flag name="apron">Use <pkg>sci-mathematics/apron</pkg> library for
-abstract interpretation</flag>
-		<flag name="coq">Add <pkg>sci-mathematics/coq</pkg> support</flag>
-		<flag name="float">Add <pkg>sci-mathematics/flocq</pkg> support</flag>
-		<flag name="gappa">Add <pkg>sci-mathematics/gappalib-coq</pkg> support</flag>
-		<flag name="frama-c">Add <pkg>sci-mathematics/frama-c</pkg> support</flag>
-		<flag name="pff">Add <pkg>sci-mathematics/pff</pkg> support</flag>
-		<flag name="why3">Add <pkg>sci-mathematics/why3</pkg> support</flag>
-	</use>
-</pkgmetadata>
diff --git a/sci-mathematics/why/why-2.34.ebuild b/sci-mathematics/why/why-2.34.ebuild
deleted file mode 100644
index 4851cd7c9..000000000
--- a/sci-mathematics/why/why-2.34.ebuild
+++ /dev/null
@@ -1,69 +0,0 @@
-# Copyright 1999-2016 Gentoo Foundation
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=5
-
-inherit autotools eutils
-
-DESCRIPTION="Why is a software verification platform"
-HOMEPAGE="http://why.lri.fr/"
-SRC_URI="http://why.lri.fr/download/${P}.tar.gz"
-
-LICENSE="GPL-2"
-SLOT="0"
-KEYWORDS="~amd64"
-IUSE="apron coq doc examples float gappa frama-c gtk pff why3"
-
-DEPEND=">=dev-lang/ocaml-3.12.1
-		>=dev-ml/ocamlgraph-1.5
-		gtk? ( >=dev-ml/lablgtk-2.14 )
-		apron? ( sci-mathematics/apron )
-		coq? ( sci-mathematics/coq )
-		gappa? ( sci-mathematics/gappalib-coq )
-		pff? ( sci-mathematics/pff )
-		frama-c? ( >=sci-mathematics/frama-c-20140301 )
-		float? ( sci-mathematics/flocq )
-		why3? ( sci-mathematics/why3 )"
-RDEPEND="${DEPEND}"
-
-DOCS=( CHANGES README Version )
-
-src_prepare() {
-	sed -i Makefile.in \
-		-e "s/DESTDIR =.*//g" \
-		-e "s/@COQLIB@/\$(DESTDIR)\/@COQLIB@/g" || die
-
-	#to build with apron-0.9.10
-	sed -i configure.in \
-		-e "s/pvs/sri-pvs/g" \
-		-e "s/oct_caml/octMPQ_caml/g" \
-		-e "s/box_caml/boxMPQ_caml/g" \
-		-e "s/polka_caml/polkaMPQ_caml/g" || die
-
-	epatch "${FILESDIR}"/why-flocq23.patch
-	eautoreconf
-}
-
-src_configure() {
-	econf $(use_enable apron) PATH="/usr/bin:$PATH"
-}
-
-src_compile(){
-	MAKEOPTS+=" -j1"
-	emake DESTDIR="/"
-}
-
-src_install(){
-	default
-
-	doman doc/why.1
-
-	if use doc; then
-		dodoc doc/manual.ps
-	fi
-
-	if use examples; then
-		insinto /usr/share/doc/${PF}
-		doins -r examples examples-c
-	fi
-}
diff --git a/sci-mathematics/why3/Manifest b/sci-mathematics/why3/Manifest
deleted file mode 100644
index 6ba945696..000000000
--- a/sci-mathematics/why3/Manifest
+++ /dev/null
@@ -1 +0,0 @@
-DIST why3-0.83.tar.gz 5347628 BLAKE2B d405eec88a66312f6f39ab64e121650256395c01396d47b1b18d68cb5a501cc60698d5498df3a25ccd780f6ff592ffb5a5f9f1fd2ac6fe252213b1df42480b0f SHA512 e1c4d462986835aa0e9a1ca117e4c3bbaf307b45b6de03da6ea8dd706770b8d9894031ea22ec732dfa7340d613b023ab499837203a132db5f138e51596e64177
diff --git a/sci-mathematics/why3/metadata.xml b/sci-mathematics/why3/metadata.xml
deleted file mode 100644
index 5f92771c1..000000000
--- a/sci-mathematics/why3/metadata.xml
+++ /dev/null
@@ -1,24 +0,0 @@
-<?xml version="1.0" encoding="UTF-8"?>
-<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
-<pkgmetadata>
-	<maintainer type="project">
-		<email>sci-mathematics@gentoo.org</email>
-		<name>Gentoo Mathematics Project</name>
-	</maintainer>
-	<longdescription>
-Why3 is a platform for deductive program verification. It provides
-a rich language for specification and programming, called WhyML,
-and relies on external theorem provers, both automated and interactive,
-to discharge verification conditions. Why3 comes with a standard
-library of logical theories (integer and real arithmetic, Boolean
-operations, sets and maps, etc.) and basic programming data structures
-(arrays, queues, hash tables, etc.). A user can write WhyML programs
-directly and get correct-by-construction OCaml programs through an
-automated extraction mechanism. WhyML is also used as an intermediate
-language for the verification of C, Java, or Ada programs.
-</longdescription>
-	<use>
-		<flag name="float">Add <pkg>sci-mathematics/flocq</pkg> support</flag>
-		<flag name="frama-c">Enable Frama-C plugin</flag>
-	</use>
-</pkgmetadata>
diff --git a/sci-mathematics/why3/why3-0.83.ebuild b/sci-mathematics/why3/why3-0.83.ebuild
deleted file mode 100644
index ac914306c..000000000
--- a/sci-mathematics/why3/why3-0.83.ebuild
+++ /dev/null
@@ -1,59 +0,0 @@
-# Copyright 1999-2016 Gentoo Foundation
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=5
-
-inherit eutils
-
-DESCRIPTION=" Why3 is a platform for deductive program verification"
-HOMEPAGE="http://why3.lri.fr/"
-SRC_URI="https://gforge.inria.fr/frs/download.php/33490/${P}.tar.gz"
-
-LICENSE="LGPL-2"
-SLOT="0"
-KEYWORDS="~amd64"
-IUSE="float frama-c doc examples"
-
-DEPEND=">=dev-lang/ocaml-3.12.1
-		dev-ml/zarith
-		sci-mathematics/coq
-		frama-c? ( >=sci-mathematics/frama-c-20140301 )
-		float? ( sci-mathematics/flocq )
-		doc? ( dev-tex/rubber )"
-RDEPEND="${DEPEND}"
-
-DOCS=( CHANGES README Version )
-
-src_prepare() {
-	mv doc/why.1 doc/why3.1 || die
-	sed -i configure.in -e "s/\"pvs\"/\"sri-pvs\"/g" || die
-	sed -i configure -e "s/\"pvs\"/\"sri-pvs\"/g" || die
-	sed -i Makefile.in -e "s:DESTDIR =::g" \
-		-e "s:\$(RUBBER) --warn all --pdf manual.tex:makeindex manual.tex; \$(RUBBER) --warn all --pdf manual.tex; cd ..:g" || die
-}
-
-src_configure() {
-	econf $(use_enable frama-c)
-}
-
-src_compile() {
-	MAKEOPTS+=" -j1"
-
-	default
-	if use doc; then
-		emake doc/manual.pdf
-	fi
-}
-
-src_install(){
-	default
-
-	doman doc/why3.1
-	if use doc; then
-		dodoc doc/manual.pdf
-	fi
-	if use examples; then
-		insinto /usr/share/doc/${PF}
-		doins -r examples
-	fi
-}
diff --git a/sci-mathematics/z3/Manifest b/sci-mathematics/z3/Manifest
deleted file mode 100644
index 5232371ed..000000000
--- a/sci-mathematics/z3/Manifest
+++ /dev/null
@@ -1 +0,0 @@
-DIST z3-4.3.1.tar.xz 1841796 BLAKE2B 50049ad94c1a35559b6f064daef73366d1b1756842f4eda67fd0f835b769e2e991369a54ad4976958dd1288eb2bfbdfe8ee44abbe932afdd15d58acc5346da55 SHA512 ccffb07c6468911685db28030e012a6504c2ce5d50b33163cfac0f12bdbd25b5365b39e61ad514ede01bc138cbc7004de6a9efa6264bc5d2f9fc8db63c989c91
diff --git a/sci-mathematics/z3/metadata.xml b/sci-mathematics/z3/metadata.xml
deleted file mode 100644
index ae9640ffb..000000000
--- a/sci-mathematics/z3/metadata.xml
+++ /dev/null
@@ -1,8 +0,0 @@
-<?xml version="1.0" encoding="UTF-8"?>
-<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
-<pkgmetadata>
-	<maintainer type="project">
-		<email>sci@gentoo.org</email>
-		<name>Gentoo Science Project</name>
-	</maintainer>
-</pkgmetadata>
diff --git a/sci-mathematics/z3/z3-4.3.1.ebuild b/sci-mathematics/z3/z3-4.3.1.ebuild
deleted file mode 100644
index 751fc10ad..000000000
--- a/sci-mathematics/z3/z3-4.3.1.ebuild
+++ /dev/null
@@ -1,74 +0,0 @@
-# Copyright 1999-2015 Gentoo Foundation
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=5
-
-PYTHON_COMPAT=( python2_7 )
-
-inherit autotools flag-o-matic python-r1 toolchain-funcs vcs-snapshot
-
-DESCRIPTION="An efficient theorem prover"
-HOMEPAGE="http://z3.codeplex.com/"
-SRC_URI="http://dev.gentoo.org/~jlec/distfiles/${P}.tar.xz"
-
-SLOT="0"
-LICENSE="MIT"
-KEYWORDS="~amd64 ~x86"
-IUSE="gmp"
-
-REQUIRED_USE="${PYTHON_REQUIRED_USE}"
-
-RDEPEND="${PYTHON_DEPS}
-	gmp? ( dev-libs/gmp:0 )"
-DEPEND="${RDEPEND}"
-
-pkg_setup() {
-	if [[ ${MERGE_TYPE} != binary ]]; then
-		if [[ $(tc-getCXX)$ == *g++* ]] && ! tc-has-openmp; then
-			ewarn "Please use an openmp compatible compiler"
-			ewarn "like >gcc-4.2 with USE=openmp"
-			die "Openmp support missing in compiler"
-		fi
-	fi
-}
-
-src_prepare() {
-	sed \
-		-e 's:-O3::g' \
-		-e 's:-fomit-frame-pointer::' \
-		-e 's:-msse2::g' \
-		-e 's:-msse::g' \
-		-e "/LINK_EXTRA_FLAGS/s:@LDFLAGS@:-lrt $(usex gmp -lgmp):g" \
-		-e 's:t@\$:t\$:g' \
-		-i scripts/*mk* || die
-
-	append-ldflags -fopenmp
-
-	eautoreconf
-}
-
-src_configure() {
-	python_export_best
-	econf \
-		--host="" \
-		--with-python="${PYTHON}" \
-		$(use_with gmp) \
-		SLIBFLAGS=" -Wl,-soname,lib${PN}.so.0.1 "
-	${EPYTHON} scripts/mk_make.py || die
-}
-
-src_compile() {
-	emake \
-		--directory="build" \
-		CXX=$(tc-getCXX) \
-		LINK="$(tc-getCXX) ${LDFLAGS}" \
-		LINK_FLAGS="${LDFLAGS}"
-}
-
-src_install() {
-	doheader src/api/z3*.h src/api/c++/z3*.h
-	dolib.so build/*.so
-	dobin build/z3
-
-	python_foreach_impl python_domodule src/api/python/*.py
-}
diff --git a/sci-mathematics/z3/z3-9999.ebuild b/sci-mathematics/z3/z3-9999.ebuild
deleted file mode 100644
index 589751a60..000000000
--- a/sci-mathematics/z3/z3-9999.ebuild
+++ /dev/null
@@ -1,79 +0,0 @@
-# Copyright 1999-2015 Gentoo Foundation
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=5
-
-PYTHON_COMPAT=( python2_7 )
-
-inherit autotools flag-o-matic git-r3 python-r1 toolchain-funcs
-
-DESCRIPTION="An efficient theorem prover"
-HOMEPAGE="http://z3.codeplex.com/"
-SRC_URI=""
-EGIT_REPO_URI="https://git01.codeplex.com/z3"
-EGIT_MIN_CLONE_TYPE=single
-
-SLOT="0"
-LICENSE="MIT"
-KEYWORDS=""
-IUSE="gmp"
-
-REQUIRED_USE="${PYTHON_REQUIRED_USE}"
-
-RDEPEND="${PYTHON_DEPS}
-	gmp? ( dev-libs/gmp:0 )"
-# A new curl is needed because codeplex has a bug and early version of libcurl
-# will cause a failed git clone.
-DEPEND="${RDEPEND}
-	>=net-misc/curl-7.33"
-
-pkg_setup() {
-	if [[ ${MERGE_TYPE} != binary ]]; then
-		if [[ $(tc-getCXX)$ == *g++* ]] && ! tc-has-openmp; then
-			ewarn "Please use an openmp compatible compiler"
-			ewarn "like >gcc-4.2 with USE=openmp"
-			die "Openmp support missing in compiler"
-		fi
-	fi
-}
-
-src_prepare() {
-	sed \
-		-e 's:-O3::g' \
-		-e 's:-fomit-frame-pointer::' \
-		-e 's:-msse2::g' \
-		-e 's:-msse::g' \
-		-e "/LINK_EXTRA_FLAGS/s:@LDFLAGS@:-lrt $(usex gmp -lgmp):g" \
-		-e 's:t@\$:t\$:g' \
-		-i scripts/*mk* || die
-
-	append-ldflags -fopenmp
-
-	eautoreconf
-}
-
-src_configure() {
-	python_export_best
-	econf \
-		--host="" \
-		--with-python="${PYTHON}" \
-		$(use_with gmp) \
-		SLIBFLAGS=" -Wl,-soname,lib${PN}.so.0.1 "
-	${EPYTHON} scripts/mk_make.py || die
-}
-
-src_compile() {
-	emake \
-		--directory="build" \
-		CXX=$(tc-getCXX) \
-		LINK="$(tc-getCXX) ${LDFLAGS}" \
-		LINK_FLAGS="${LDFLAGS}"
-}
-
-src_install() {
-	doheader src/api/z3*.h src/api/c++/z3*.h
-	dolib.so build/*.so
-	dobin build/z3
-
-	python_foreach_impl python_domodule src/api/python/*.py
-}
diff --git a/sci-misc/elmer-elmergrid/Manifest b/sci-misc/elmer-elmergrid/Manifest
deleted file mode 100644
index 1a895c9f0..000000000
--- a/sci-misc/elmer-elmergrid/Manifest
+++ /dev/null
@@ -1 +0,0 @@
-DIST elmer-elmergrid-6.0_p4651.tar.gz 717102 SHA256 3ffd59716892aaeb2605a70c4ca00c872e2aff07ba9be0a50b09868bea75950c SHA512 64d1d907016f65fa324279cc0a73af818df1e86bd05f74e949b6e6166ad77787e465bb27b599767d7a31a3dd5f3744226a0cfbcf58e65693280eb1c59a11b87d WHIRLPOOL 9807abc30d566ce8c536465776d58e168377a04e05d77ed3e3a6d05ce39e7835e7e01a985ffdc8f01bd07ef7e64db21ab514dbd95461b1a32449bec306a6e461
diff --git a/sci-misc/elmer-elmergrid/elmer-elmergrid-6.0_p4651.ebuild b/sci-misc/elmer-elmergrid/elmer-elmergrid-6.0_p4651.ebuild
deleted file mode 100644
index 025d8aed1..000000000
--- a/sci-misc/elmer-elmergrid/elmer-elmergrid-6.0_p4651.ebuild
+++ /dev/null
@@ -1,36 +0,0 @@
-# Copyright 1999-2014 Gentoo Foundation
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=5
-
-AUTOTOOLS_AUTORECONF=true
-
-inherit autotools-utils multilib
-
-ELMER_ROOT="elmerfem"
-MY_PN=${PN/elmer-/}
-
-DESCRIPTION="Finite element programs, libraries, and visualization tools - elmergrid"
-HOMEPAGE="http://www.csc.fi/english/pages/elmer"
-SRC_URI="http://elmerfem.svn.sourceforge.net/viewvc/${ELMER_ROOT}/release/${PV%_p*}/${MY_PN}/?view=tar&pathrev=4651 -> ${P}.tar.gz"
-
-LICENSE="GPL-2"
-SLOT="0"
-KEYWORDS="~amd64 ~x86"
-IUSE="debug"
-
-RDEPEND="
-	sci-libs/matc
-	sci-libs/metis"
-DEPEND="${RDEPEND}"
-
-S="${WORKDIR}/elmergrid"
-
-src_configure() {
-	local myeconfargs=(
-		$(use_with debug)
-		--with-metis-libs="${EPREFIX}"/usr/$(get_libdir)
-		--with-metis-include="${EPREFIX}"/usr/include/metis
-	)
-	autotools-utils_src_configure
-}
diff --git a/sci-misc/elmer-elmergrid/elmer-elmergrid-9999.ebuild b/sci-misc/elmer-elmergrid/elmer-elmergrid-9999.ebuild
deleted file mode 100644
index 46d58ec57..000000000
--- a/sci-misc/elmer-elmergrid/elmer-elmergrid-9999.ebuild
+++ /dev/null
@@ -1,43 +0,0 @@
-# Copyright 1999-2014 Gentoo Foundation
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=5
-
-AUTOTOOLS_AUTORECONF=true
-
-inherit autotools-utils subversion
-
-ELMER_ROOT="elmerfem"
-MY_PN=${PN/elmer-/}
-
-DESCRIPTION="Finite element programs, libraries, and visualization tools - elmergrid"
-HOMEPAGE="http://www.csc.fi/english/pages/elmer"
-SRC_URI=""
-ESVN_REPO_URI="https://elmerfem.svn.sourceforge.net/svnroot/elmerfem/trunk/${MY_PN}"
-ESVN_PROJECT="${MY_PN}"
-
-LICENSE="GPL-2"
-SLOT="0"
-KEYWORDS=""
-IUSE="debug"
-
-RDEPEND="
-	sci-libs/matc
-	sci-libs/metis"
-DEPEND="${RDEPEND}"
-
-S="${WORKDIR}/elmergrid"
-
-src_prepare() {
-	subversion_src_prepare
-	autotools-utils_src_prepare
-}
-
-src_configure() {
-	local myeconfargs=(
-		$(use_with debug)
-		--with-metis-libs="${EPREFIX}"/usr/$(get_libdir)
-		--with-metis-include="${EPREFIX}"/usr/include/metis
-	)
-	autotools-utils_src_configure
-}
diff --git a/sci-misc/elmer-elmergrid/metadata.xml b/sci-misc/elmer-elmergrid/metadata.xml
deleted file mode 100644
index 070aa2029..000000000
--- a/sci-misc/elmer-elmergrid/metadata.xml
+++ /dev/null
@@ -1,11 +0,0 @@
-<?xml version="1.0" encoding="UTF-8"?>
-<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
-<pkgmetadata>
-	<maintainer type="project">
-		<email>sci@gentoo.org</email>
-		<name>Gentoo Science Project</name>
-	</maintainer>
-	<upstream>
-		<remote-id type="sourceforge">svn</remote-id>
-	</upstream>
-</pkgmetadata>
diff --git a/sci-misc/elmer-fem/Manifest b/sci-misc/elmer-fem/Manifest
index 6b759e17e..9412ee2dc 100644
--- a/sci-misc/elmer-fem/Manifest
+++ b/sci-misc/elmer-fem/Manifest
@@ -1 +1 @@
-DIST elmer-fem-6.0_p4651.tar.gz 10915056 SHA256 1672a7a4f1e1030fd66217563c73dc99f7ebdbec6880539c778c43d0e94e1eb8 SHA512 824e26193ca2b55651c1bdddd73b28d06dff47914855ed67353c941851ba57961c68c2dd28d19bd4e8406b67efeb997bf441a3225ecd1fb66cdc575cb4f575dd WHIRLPOOL 4e2e2f3e6cafccc47cfea618f40d0fd949448d38279fe8dc699cfbda7ff4dcf61495ddbb1b01a0d282a4091fbbf5d0f51cc31c15e37a7b3b2bbcd8a41f7b1255
+DIST elmer-fem-9.0.tar.gz 64060003 BLAKE2B 54c1ee1c7c8f8337aadd7afed60a7c0f20184a4114c8b998d940c27836b654149a27d2bf44421d9ac25255781971ca377fa1d43bcb729fb285629453e2e8fbfb SHA512 0affb0420b674ebf4d089c4039ba78dd29650f0daf956eab59bd7bea1c466ba6dfdf17c1ca6c953f36bbf95ed127dc9e6e025ee3edb1d2a56e55e61e24e97254
diff --git a/sci-misc/elmer-fem/elmer-fem-6.0_p4651.ebuild b/sci-misc/elmer-fem/elmer-fem-6.0_p4651.ebuild
deleted file mode 100644
index ebc4ea74a..000000000
--- a/sci-misc/elmer-fem/elmer-fem-6.0_p4651.ebuild
+++ /dev/null
@@ -1,53 +0,0 @@
-# Copyright 1999-2014 Gentoo Foundation
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=5
-
-AUTOTOOLS_AUTORECONF=true
-FORTRAN_STANDARD=90
-
-inherit autotools-utils fortran-2 multilib
-
-ELMER_ROOT="elmerfem"
-MY_PN=${PN/elmer-/}
-
-DESCRIPTION="Finite element programs, libraries, and visualization tools - main fem"
-HOMEPAGE="http://www.csc.fi/english/pages/elmer"
-SRC_URI="http://elmerfem.svn.sourceforge.net/viewvc/${ELMER_ROOT}/release/${PV%_p*}/${MY_PN}/?view=tar&pathrev=4651 -> ${P}.tar.gz"
-
-LICENSE="GPL-2"
-SLOT="0"
-KEYWORDS="~amd64 ~x86"
-IUSE="mpi debug"
-
-RDEPEND="
-	virtual/blas
-	virtual/lapack
-	sci-libs/arpack
-	sci-libs/matc
-	sci-libs/elmer-hutiter
-	sci-libs/elmer-eio
-	mpi?     ( sys-cluster/mpich2 )"
-DEPEND="${RDEPEND}"
-# Note this seems to only configure correctly with the elmer version of umfpack
-# But this doesn't stop it from compiling / working without it
-
-S="${WORKDIR}/fem"
-
-PATCHES=(
-	"${FILESDIR}"/${P}-oos.patch
-	"${FILESDIR}"/${P}-underlinking.patch
-)
-
-src_configure() {
-	local myeconfargs=(
-		$(use_with debug)
-		$(usex mpi --with-mpi "")
-		$(usex mpi --with-mpi-dir="${EPREFIX}"/usr "")
-		--with-arpack="$($(tc-getPKG_CONFIG) --libs arpack)"
-		--with-blas="$($(tc-getPKG_CONFIG) --libs blas)"
-		--with-lapack="$($(tc-getPKG_CONFIG) --libs lapack)"
-		--with-huti	--with-eiof --with-matc
-	)
-	autotools-utils_src_configure
-}
diff --git a/sci-misc/elmer-fem/elmer-fem-9.0-r2.ebuild b/sci-misc/elmer-fem/elmer-fem-9.0-r2.ebuild
new file mode 100644
index 000000000..82e1c796f
--- /dev/null
+++ b/sci-misc/elmer-fem/elmer-fem-9.0-r2.ebuild
@@ -0,0 +1,78 @@
+# Copyright 1999-2021 Gentoo Authors
+# Distributed under the terms of the GNU General Public License v2
+
+EAPI=8
+
+FORTRAN_STANDARD=90
+
+inherit fortran-2 flag-o-matic cmake
+
+ELMER_ROOT="elmerfem"
+MY_PN=${PN/elmer-/}
+
+DESCRIPTION="Finite element programs, libraries, and visualization tools"
+HOMEPAGE="https://www.csc.fi/web/elmer https://www.elmerfem.org/blog/"
+SRC_URI="https://github.com/ElmerCSC/elmerfem/archive/release-${PV}.tar.gz -> ${P}.tar.gz"
+
+LICENSE="GPL-2"
+SLOT="0"
+KEYWORDS="~amd64 ~x86"
+
+IUSE="ice gui matc mumps mpi post test"
+RESTRICT="!test? ( test )"
+
+RDEPEND="
+	virtual/blas
+	virtual/lapack
+	sci-libs/arpack
+	mumps? ( sci-libs/mumps )
+	mpi? ( sys-cluster/openmpi )
+	post? (
+		dev-lang/tcl:0=
+		dev-lang/tk:0=
+	)
+	gui? ( x11-libs/qwt:6 )
+"
+DEPEND="${RDEPEND}"
+# Note this seems to only configure correctly with the elmer version of umfpack
+# But this doesn't stop it from compiling / working without it
+
+PATCHES=(
+	"${FILESDIR}/${PN}-DCRComplexSolve-compile-error.patch"
+	"${FILESDIR}/${PN}-ElmerIce-compile.patch"
+	"${FILESDIR}/${PN}-rpath.patch"
+	"${FILESDIR}/${P}-qwt-6.2.patch"
+)
+
+S="${WORKDIR}/elmerfem-release-${PV}"
+
+src_prepare() {
+	cmake_src_prepare
+	sed -i '/#include <QPainter>/a #include <QPainterPath>' ElmerGUI/Application/twod/renderarea.cpp || die
+	test-flag-FC -fallow-argument-mismatch && append-fflags -fallow-argument-mismatch
+	test-flag-FC -fallow-invalid-boz && append-fflags -fallow-invalid-boz
+	# TODO: fix the tests, fails in compile phase: multiple rules to make target
+	rm -r fem/tests/* || die
+	touch fem/tests/CMakeLists.txt || die
+}
+
+src_configure() {
+	local mycmakeargs=(
+		-DMPI_Fortran_COMPILE_FLAGS="$FCFLAGS"
+		-DCMAKE_Fortran_FLAGS="$FCFLAGS"
+		-DELMER_INSTALL_LIB_DIR="/usr/$(get_libdir)/elmersolver"
+		-DWITH_MPI="$(usex mpi)"
+		-DWITH_OpenMP="$(usex mpi)"
+		-DWITH_MATC="$(usex matc)"
+		-DWITH_Mumps="$(usex mumps)"
+		-DWITH_ElmerIce="$(usex ice)"
+		-DWITH_ELMERPOST="$(usex post)"
+		-DWITH_ELMERGUI="$(usex gui)"
+		-DWITH_QT5="$(usex gui)"
+		-DWITH_QWT="$(usex gui)"
+		-DQWT_INCLUDE_DIR="/usr/include/qwt6"
+		-DQWT_LIBRARY="/usr/$(get_libdir)/libqwt6-qt5.so"
+		-DBUILD_TESTING="$(usex test)"
+	)
+	cmake_src_configure
+}
diff --git a/sci-misc/elmer-fem/elmer-fem-9999.ebuild b/sci-misc/elmer-fem/elmer-fem-9999.ebuild
deleted file mode 100644
index 8683aed51..000000000
--- a/sci-misc/elmer-fem/elmer-fem-9999.ebuild
+++ /dev/null
@@ -1,55 +0,0 @@
-# Copyright 1999-2014 Gentoo Foundation
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=5
-
-AUTOTOOLS_AUTORECONF=true
-FORTRAN_STANDARD=90
-
-inherit autotools-utils fortran-2 multilib subversion
-
-ELMER_ROOT="elmerfem"
-MY_PN=${PN/elmer-/}
-
-DESCRIPTION="Finite element programs, libraries, and visualization tools - main fem"
-HOMEPAGE="http://www.csc.fi/english/pages/elmer"
-SRC_URI=""
-ESVN_REPO_URI="https://elmerfem.svn.sourceforge.net/svnroot/elmerfem/trunk/${MY_PN}"
-ESVN_PROJECT="${MY_PN}"
-
-LICENSE="GPL-2"
-SLOT="0"
-KEYWORDS=""
-IUSE="mpi debug"
-
-RDEPEND="
-	virtual/blas
-	virtual/lapack
-	sci-libs/arpack
-	sci-libs/matc
-	sci-libs/elmer-hutiter
-	sci-libs/elmer-eio
-	mpi?     ( sys-cluster/mpich2 )"
-DEPEND="${RDEPEND}"
-# Note this seems to only configure correctly with the elmer version of umfpack
-# But this doesn't stop it from compiling / working without it
-
-S="${WORKDIR}/fem"
-
-PATCHES=(
-	"${FILESDIR}"/${PN}-6.0_p4651-oos.patch
-	"${FILESDIR}"/${PN}-6.0_p4651-underlinking.patch
-)
-
-src_configure() {
-	local myeconfargs=(
-		$(use_with debug)
-		$(usex mpi --with-mpi "")
-		$(usex mpi --with-mpi-dir="${EPREFIX}"/usr "")
-		--with-arpack="$($(tc-getPKG_CONFIG) --libs arpack)"
-		--with-blas="$($(tc-getPKG_CONFIG) --libs blas)"
-		--with-lapack="$($(tc-getPKG_CONFIG) --libs lapack)"
-		--with-huti	--with-eiof --with-matc
-	)
-	autotools-utils_src_configure
-}
diff --git a/sci-misc/elmer-fem/files/elmer-fem-6.0_p4651-oos.patch b/sci-misc/elmer-fem/files/elmer-fem-6.0_p4651-oos.patch
deleted file mode 100644
index 00291bc56..000000000
--- a/sci-misc/elmer-fem/files/elmer-fem-6.0_p4651-oos.patch
+++ /dev/null
@@ -1,75 +0,0 @@
- src/Makefile.am | 6 +++---
- 1 file changed, 3 insertions(+), 3 deletions(-)
-
-diff --git a/src/Makefile.am b/src/Makefile.am
-index 9e48c31..b94705c 100644
---- a/src/Makefile.am
-+++ b/src/Makefile.am
-@@ -182,11 +182,11 @@ SC2Elmer_SOURCES = SC2Elmer.c
- 
- if USE_LOCAL_MPIF_H
- mpif: mpif_stub.h
--	$(CP) mpif_stub.h mpif.h
--	$(CP) mpif_stub.h mpif
-+	$(CP) $(srcdir)/mpif_stub.h mpif.h
-+	$(CP) $(srcdir)/mpif_stub.h mpif
- else 
- mpif: mpif_stub.h
--	$(CP) mpif_stub.h mpif
-+	$(CP) $(srcdir)/mpif_stub.h mpif
- endif
- 
- EXTRA_DIST = \
- src/Makefile.am | 25 +++++++++++++------------
- 1 file changed, 13 insertions(+), 12 deletions(-)
-
-diff --git a/src/Makefile.am b/src/Makefile.am
-index 92de7a4..89a2236 100644
---- a/src/Makefile.am
-+++ b/src/Makefile.am
-@@ -144,32 +144,33 @@ ELMER_SOLVER_DATADIR=$(prefix)/share/elmersolver
- install-data-local:
- 	@echo "Installing solvers to ${ELMER_SOLVER_DATADIR}/lib"
- 
--	mkdir -p $(DESTDIR)$(ELMER_SOLVER_DATADIR)/lib
--	$(CP) `ls -f *$(SHL_EXT) | grep -v libelmersolver` $(DESTDIR)$(ELMER_SOLVER_DATADIR)/lib
--	$(CP) elements.def $(DESTDIR)$(ELMER_SOLVER_DATADIR)/lib
--	$(CP) SOLVER.KEYWORDS $(DESTDIR)$(ELMER_SOLVER_DATADIR)/lib
-+	mkdir -p $(DESTDIR)$(ELMER_SOLVER_DATADIR)/$(libdir)
-+	$(CP) `ls -f $(builddir)/*$(SHL_EXT) | grep -v libelmersolver` $(DESTDIR)$(ELMER_SOLVER_DATADIR)/$(libdir)
-+	$(CP) $(srcdir)/elements.def $(DESTDIR)$(ELMER_SOLVER_DATADIR)/$(libdir)
-+	$(CP) $(srcdir)/SOLVER.KEYWORDS $(DESTDIR)$(ELMER_SOLVER_DATADIR)/$(libdir)
- 
- 	@echo "Installing *.mod to ${ELMER_SOLVER_DATADIR}/include"
- 	mkdir -p $(DESTDIR)$(ELMER_SOLVER_DATADIR)/include
--	$(CP) *.mod $(DESTDIR)$(ELMER_SOLVER_DATADIR)/include
-+	$(CP) $(builddir)/*.mod $(DESTDIR)$(ELMER_SOLVER_DATADIR)/include
- 
- 
- install-exec-local:
- 	@echo "Installing stuff to ${prefix}/bin"
- 	$(MKDIR) $(DESTDIR)$(prefix)/bin
--	$(CP) ElmerSolver$(EXEEXT) $(DESTDIR)$(prefix)/bin
--	$(CP) ViewFactors$(EXEEXT) $(DESTDIR)$(prefix)/bin
--	$(CP) GebhardtFactors$(EXEEXT) $(DESTDIR)$(prefix)/bin
-+	$(CP) $(builddir)/ElmerSolver$(EXEEXT) $(DESTDIR)$(prefix)/bin
-+	$(CP) $(builddir)/ViewFactors$(EXEEXT) $(DESTDIR)$(prefix)/bin
-+	$(CP) $(builddir)/GebhardtFactors$(EXEEXT) $(DESTDIR)$(prefix)/bin
- if USE_WINDOWS_COMPILER
- 	$(CP) libelmersolver*$(SHL_EXT) $(DESTDIR)$(prefix)/lib
- else
--	$(CP) libelmersolver-$(VERSION)$(SHL_EXT) $(DESTDIR)$(prefix)/lib
-+	mkdir -p $(DESTDIR)$(prefix)/$(libdir)
-+	$(CP) $(builddir)/libelmersolver-$(VERSION)$(SHL_EXT) $(DESTDIR)$(prefix)/$(libdir)
- 	$(LN) -sf libelmersolver-$(VERSION)$(SHL_EXT)\
--              $(DESTDIR)$(prefix)/lib/libelmersolver$(SHL_EXT)
-+              $(DESTDIR)$(prefix)/$(libdir)/libelmersolver$(SHL_EXT)
- endif
--	$(CP) elmerf90 elmerf90-nosh elmerld $(DESTDIR)$(prefix)/bin
-+	$(CP) $(builddir)/elmerf90 $(builddir)/elmerf90-nosh elmerld $(DESTDIR)$(prefix)/bin
- if USE_MPI
--	$(CP) ElmerSolver_mpi$(EXEEXT) $(DESTDIR)$(prefix)/bin
-+	$(CP) $(builddir)/ElmerSolver_mpi$(EXEEXT) $(DESTDIR)$(prefix)/bin
- endif
- 
- clean-local:
diff --git a/sci-misc/elmer-fem/files/elmer-fem-6.0_p4651-underlinking.patch b/sci-misc/elmer-fem/files/elmer-fem-6.0_p4651-underlinking.patch
deleted file mode 100644
index 7c6be1d8c..000000000
--- a/sci-misc/elmer-fem/files/elmer-fem-6.0_p4651-underlinking.patch
+++ /dev/null
@@ -1,23 +0,0 @@
- src/Makefile.am | 4 ++--
- 1 file changed, 2 insertions(+), 2 deletions(-)
-
-diff --git a/src/Makefile.am b/src/Makefile.am
-index b94705c..92de7a4 100644
---- a/src/Makefile.am
-+++ b/src/Makefile.am
-@@ -122,13 +122,13 @@ if USE_WINDOWS_COMPILER
- else
- 	$(FC) $(SH_LINKING_TO_FLAGS) $(RPATH_ELMER) $(B64FLAGS) $(LDFLAGS) \
- 	      -o ViewFactors$(EXE_EXT) ViewFactors$(OBJ_EXT) mpi_stubs$(OBJ_EXT) \
--	      -L. -lelmersolver viewaxis/libviewaxis.a view3d/libview3d.a $(EXTRA_LIBS) $(BLAS_LIBS) $(STDCXX_LIBS)
-+	      -L. -lelmersolver viewaxis/libviewaxis.a view3d/libview3d.a $(EXTRA_LIBS) $(BLAS_LIBS) $(STDCXX_LIBS) -lhuti
- endif
- 
- GebhardtFactors$(EXE_EXT): libelmersolver$(SHL_EXT) GebhardtFactors$(OBJ_EXT) mpi_stubs$(OBJ_EXT)
- 	$(FC) $(SH_LINKING_TO_FLAGS) $(RPATH_ELMER) $(B64FLAGS) $(LDFLAGS) \
- 	      -o GebhardtFactors$(EXE_EXT) GebhardtFactors$(OBJ_EXT) mpi_stubs$(OBJ_EXT) \
--	      -L. -lelmersolver viewaxis/libviewaxis.a view3d/libview3d.a $(EXTRA_LIBS)
-+	      -L. -lelmersolver viewaxis/libviewaxis.a view3d/libview3d.a $(EXTRA_LIBS) -lhuti
- 
- 
- 
diff --git a/sci-misc/elmer-fem/files/elmer-fem-9.0-qwt-6.2.patch b/sci-misc/elmer-fem/files/elmer-fem-9.0-qwt-6.2.patch
new file mode 100644
index 000000000..13eaf1c5f
--- /dev/null
+++ b/sci-misc/elmer-fem/files/elmer-fem-9.0-qwt-6.2.patch
@@ -0,0 +1,35 @@
+From 48e9430ccb858ca5bda28b967a0c84b51e2404b2 Mon Sep 17 00:00:00 2001
+From: "E. Albiter" <ealbiter@gmail.com>
+Date: Fri, 15 Oct 2021 13:12:48 -0500
+Subject: [PATCH] Compatibility with Qwt 6.2. Fix for #293
+
+---
+ ElmerGUI/Application/src/convergenceview.h | 8 ++++----
+ 1 file changed, 4 insertions(+), 4 deletions(-)
+
+diff --git a/ElmerGUI/Application/src/convergenceview.h b/ElmerGUI/Application/src/convergenceview.h
+index 377b644b99..4259eb730e 100755
+--- a/ElmerGUI/Application/src/convergenceview.h
++++ b/ElmerGUI/Application/src/convergenceview.h
+@@ -51,8 +51,8 @@
+ #include <qwt_plot_curve.h>

+ #include <qwt_plot_grid.h>

+ #include <qwt_legend.h>

+-/*#include <qwt_data.h> <-- deprecated in Qwt6, using qwt_compat.h instead*/

+-#include <qwt_compat.h>

++/*#include <qwt_data.h> <-- deprecated in Qwt6, using qwt_compat.h instead

++#include <qwt_compat.h> <-- Removed in Qwt 6.2 */

+ #include <qwt_text.h>

+ #include <qwt_scale_engine.h>

+ 

+@@ -76,8 +76,8 @@ class CurveData
+   

+ private:

+   int d_count;

+-  QwtArray<double> d_x;

+-  QwtArray<double> d_y;

++  QVector<double> d_x;

++  QVector<double> d_y;

+ };

+ 

+ class Curve

diff --git a/sci-misc/elmer-fem/files/elmer-fem-DCRComplexSolve-compile-error.patch b/sci-misc/elmer-fem/files/elmer-fem-DCRComplexSolve-compile-error.patch
new file mode 100644
index 000000000..6f9cdf289
--- /dev/null
+++ b/sci-misc/elmer-fem/files/elmer-fem-DCRComplexSolve-compile-error.patch
@@ -0,0 +1,70 @@
+From 8ea87194fb50ff052a75212f9d2a2ae217edad95 Mon Sep 17 00:00:00 2001
+From: Mathias <mathias@localhost.localdomain>
+Date: Sun, 2 May 2021 12:06:15 +0200
+Subject: [PATCH] fixed DCRComplexSolve compile error
+
+---
+ fem/src/modules/DCRComplexSolve.F90 | 12 ++++++------
+ 1 file changed, 6 insertions(+), 6 deletions(-)
+
+diff --git a/fem/src/modules/DCRComplexSolve.F90 b/fem/src/modules/DCRComplexSolve.F90
+index cfa71dee..b6bb59bc 100644
+--- a/fem/src/modules/DCRComplexSolve.F90
++++ b/fem/src/modules/DCRComplexSolve.F90
+@@ -426,7 +426,7 @@ CONTAINS
+    SUBROUTINE InputTensor( Tensor, IsScalar, Name, Material, n, NodeIndexes )
+ !------------------------------------------------------------------------------
+       REAL(KIND=dp) :: Tensor(:,:,:)
+-      INTEGER :: n, NodeIndexes(:)
++      INTEGER :: n, i, j, NodeIndexes(:)
+       LOGICAL :: IsScalar
+       CHARACTER(LEN=*) :: Name
+       TYPE(ValueList_t), POINTER :: Material
+@@ -485,7 +485,7 @@ CONTAINS
+    SUBROUTINE InputVector( Tensor, IsScalar, Name, Material, n, NodeIndexes )
+ !------------------------------------------------------------------------------
+       REAL(KIND=dp) :: Tensor(:,:)
+-      INTEGER :: n, NodeIndexes(:)
++      INTEGER :: n, i, NodeIndexes(:)
+       LOGICAL :: IsScalar
+       CHARACTER(LEN=*) :: Name
+       TYPE(ValueList_t), POINTER :: Material
+@@ -543,7 +543,7 @@ CONTAINS
+     REAL(KIND=dp) :: DiffCoef(3,3), Velo(3)
+     COMPLEX(KIND=dp) :: LSTIFF(2*n,2*n), LFORCE(2*n), A
+     LOGICAL :: Stat
+-    INTEGER :: i,p,q,t,dim, NBasis, CoordSys
++    INTEGER :: i,j,p,q,t,dim, NBasis, CoordSys
+     TYPE(GaussIntegrationPoints_t) :: IntegStuff
+ 
+     REAL(KIND=dp) :: X,Y,Z,Metric(3,3),SqrtMetric,Symb(3,3,3),dSymb(3,3,3,3)
+@@ -678,7 +678,7 @@ CONTAINS
+          C1(3), C0
+     COMPLEX(KIND=dp) :: LSTIFF(n,n), LFORCE(n), A
+     LOGICAL :: Stat
+-    INTEGER :: i,p,q,t,dim,CoordSys
++    INTEGER :: i,j,p,q,t,dim,CoordSys
+     TYPE(GaussIntegrationPoints_t) :: IntegStuff
+ !------------------------------------------------------------------------------
+     dim = CoordinateSystemDimension()
+@@ -1374,7 +1374,7 @@ contains
+    SUBROUTINE InputTensor( Tensor, IsScalar, Name, Material, n, NodeIndexes )
+ !------------------------------------------------------------------------------
+       REAL(KIND=dp) :: Tensor(:,:,:)
+-      INTEGER :: n, NodeIndexes(:)
++      INTEGER :: n, i, NodeIndexes(:)
+       LOGICAL :: IsScalar
+       CHARACTER(LEN=*) :: Name
+       TYPE(ValueList_t), POINTER :: Material
+@@ -1426,7 +1426,7 @@ contains
+    SUBROUTINE InputVector( Tensor, IsScalar, Name, Material, n, NodeIndexes )
+ !------------------------------------------------------------------------------
+       REAL(KIND=dp) :: Tensor(:,:)
+-      INTEGER :: n, NodeIndexes(:)
++      INTEGER :: n, i, NodeIndexes(:)
+       LOGICAL :: IsScalar
+       CHARACTER(LEN=*) :: Name
+       TYPE(ValueList_t), POINTER :: Material
+-- 
+2.31.1
+
diff --git a/sci-misc/elmer-fem/files/elmer-fem-ElmerIce-compile.patch b/sci-misc/elmer-fem/files/elmer-fem-ElmerIce-compile.patch
new file mode 100644
index 000000000..c8a065e30
--- /dev/null
+++ b/sci-misc/elmer-fem/files/elmer-fem-ElmerIce-compile.patch
@@ -0,0 +1,58 @@
+diff --color -Naur a/elmerice/Solvers/CalvingRemeshMMG.F90 b/elmerice/Solvers/CalvingRemeshMMG.F90
+--- a/elmerice/Solvers/CalvingRemeshMMG.F90	2018-12-19 12:34:45.000000000 +0300
++++ b/elmerice/Solvers/CalvingRemeshMMG.F90	2020-12-12 22:39:24.040363020 +0300
+@@ -71,6 +71,7 @@
+   TYPE(ValueList_t), POINTER :: SolverParams
+   TYPE(Mesh_t),POINTER :: Mesh,GatheredMesh,NewMeshR,FinalMesh
+   TYPE(Element_t),POINTER :: Element, ParentElem
++  TYPE(MMG5_DATA_PTR_T),POINTER :: mmgMet
+   INTEGER :: i,j,k,NNodes,GNBulk, GNBdry, GNNode, NBulk, Nbdry, ierr, &
+        my_cboss,MyPE, PEs,CCount, counter, GlNode_min, GlNode_max,adjList(4),front_BC_ID, &
+        my_calv_front,calv_front, ncalv_parts, group_calve, comm_calve, group_world,ecode, NElNodes
+@@ -426,7 +427,7 @@
+ 
+       !> ------------------------------ STEP  II --------------------------
+       !! remesh function
+-      CALL MMG3D_mmg3dls(mmgMesh,mmgSol,ierr)
++      CALL MMG3D_mmg3dls(mmgMesh,mmgSol,mmgMet,ierr)
+ 
+       CALL MMG3D_SaveMesh(mmgMesh,"test_out.mesh",LEN(TRIM("test_out.mesh")),ierr)
+ 
+diff --color -Naur a/elmerice/Solvers/MeshAdaptation_2D/MMG2DSolver.F90 b/elmerice/Solvers/MeshAdaptation_2D/MMG2DSolver.F90
+--- a/elmerice/Solvers/MeshAdaptation_2D/MMG2DSolver.F90	2018-12-19 12:34:45.000000000 +0300
++++ b/elmerice/Solvers/MeshAdaptation_2D/MMG2DSolver.F90	2020-12-12 22:42:32.639562150 +0300
+@@ -310,14 +310,14 @@
+ !------------------------------------------------------------------------------
+       TYPE(Element_t),POINTER ::  Element
+       INTEGER, POINTER :: NodeIndexes(:)
+-      INTEGER :: np,nt,na,ier
++      INTEGER :: np,nt,na,ier,nquad
+       INTEGER :: ref,corner,required,ridge
+       INTEGER :: parent,ied
+       INTEGER :: tt, jj, kk, ll
+ 
+ 
+      !> a) get the size of the mesh: vertices,  triangles, edges
+-      CALL MMG2D_Get_meshSize(mmgMesh,np,nt,na,ier)
++      CALL MMG2D_Get_meshSize(mmgMesh,np,nt,nquad,na,ier)
+       IF ( ier == 0 ) CALL FATAL('MMGSolver',&
+                            'CALL TO MMGS_Get_meshSize FAILED')
+       IF (DEBUG) PRINT *,'--**-- MMG2D_Get_meshSize DONE'    
+@@ -467,7 +467,7 @@
+       TYPE(Element_t),POINTER :: Element
+       INTEGER, POINTER :: NodeIndexes(:)
+ 
+-      INTEGER :: NVert,NEle,NEdge
++      INTEGER :: NVert,NEle,NEdge,NQuad
+       INTEGER :: n
+       INTEGER :: ier
+       INTEGER :: ii,tt
+@@ -476,7 +476,7 @@
+       NEle=Mesh%NumberOfBulkElements
+       NEdge=Mesh%NumberOfBoundaryElements
+ 
+-      CALL MMG2D_Set_meshSize(mmgMesh,NVert,NEle,NEdge,ier)
++      CALL MMG2D_Set_meshSize(mmgMesh,NVert,NEle,NQuad,NEdge,ier)
+       IF ( ier == 0 ) CALL FATAL('MMGSolver',&
+                         'CALL TO MMG2D_Set_meshSize FAILED')
+       IF (DEBUG) PRINT *,'--**-- MMG2D_Set_meshSize DONE'
diff --git a/sci-misc/elmer-fem/files/elmer-fem-Makefile-install.patch b/sci-misc/elmer-fem/files/elmer-fem-Makefile-install.patch
deleted file mode 100644
index d0de4fe8b..000000000
--- a/sci-misc/elmer-fem/files/elmer-fem-Makefile-install.patch
+++ /dev/null
@@ -1,13 +0,0 @@
---- fem/src/Makefile.am.old	2012-11-12 14:50:05.435767716 +0100
-+++ fem/src/Makefile.am	2012-11-12 14:51:29.271802187 +0100
-@@ -154,8 +154,9 @@
- 
- 
- install-exec-local:
--	@echo "Installing stuff to ${prefix}/bin"
-+	@echo "Installing stuff to ${DESTDIR}${prefix}/bin"
- 	$(MKDIR) $(DESTDIR)$(prefix)/bin
-+	$(MKDIR) $(DESTDIR)$(prefix)/lib
- 	$(CP) ElmerSolver$(EXEEXT) $(DESTDIR)$(prefix)/bin
- 	$(CP) ViewFactors$(EXEEXT) $(DESTDIR)$(prefix)/bin
- 	$(CP) GebhardtFactors$(EXEEXT) $(DESTDIR)$(prefix)/bin
diff --git a/sci-misc/elmer-fem/files/elmer-fem-rpath.patch b/sci-misc/elmer-fem/files/elmer-fem-rpath.patch
new file mode 100644
index 000000000..27249fef9
--- /dev/null
+++ b/sci-misc/elmer-fem/files/elmer-fem-rpath.patch
@@ -0,0 +1,11 @@
+--- a/CMakeLists.txt.orig	2022-08-24 21:50:59.940905698 -0500
++++ b/CMakeLists.txt	2022-08-24 21:51:08.610804464 -0500
+@@ -479,7 +479,7 @@
+ 
+ # Set up rpaths to point ELMER_INSTALL_LIB_DIR
+ IF(${CMAKE_SYSTEM_NAME} MATCHES "Linux")   
+-  SET(ELMERSOLVER_RPATH_STRING "\$ORIGIN/../${ELMER_INSTALL_LIB_DIR}")
++  SET(ELMERSOLVER_RPATH_STRING "${ELMER_INSTALL_LIB_DIR}")
+   SET(ELMERLIB_RPATH_STRING "\$ORIGIN/")
+ ELSEIF(APPLE)                               
+   SET(ELMERSOLVER_RPATH_STRING "@loader_path/../${ELMER_INSTALL_LIB_DIR}")
diff --git a/sci-misc/elmer-fem/metadata.xml b/sci-misc/elmer-fem/metadata.xml
index 070aa2029..37464c70a 100644
--- a/sci-misc/elmer-fem/metadata.xml
+++ b/sci-misc/elmer-fem/metadata.xml
@@ -7,5 +7,13 @@
 	</maintainer>
 	<upstream>
 		<remote-id type="sourceforge">svn</remote-id>
+		<remote-id type="github">ElmerCSC/elmerfem</remote-id>
 	</upstream>
+	<use>
+		<flag name="gui">Build the ElmerGUI</flag>
+		<flag name="matc">Build the Elmer matc library</flag>
+		<flag name="ice">Build ElmerICE</flag>
+		<flag name="mumps">Build with Mumps</flag>
+		<flag name="post">Build ElmerPOST</flag>
+	</use>
 </pkgmetadata>
diff --git a/sci-misc/elmer-front/Manifest b/sci-misc/elmer-front/Manifest
deleted file mode 100644
index 1afe23899..000000000
--- a/sci-misc/elmer-front/Manifest
+++ /dev/null
@@ -1 +0,0 @@
-DIST elmer-front-6.0_p4651.tar.gz 1458292 SHA256 5613131bd35778975cd4fd2cb2c05d7165a83cc8a0afbe4aa0e0be9d8f1f89f7 SHA512 6970290749884e52deac47d5ccf94447ee8518cf71471bca77793fb8edfd417959e01248a886f3459db506c8e12396e76a048db40b0c13980ee99734f4e58e78 WHIRLPOOL 13c068399b8601d6e1bbba21549026a3181d0a18a909f2cbfc58816ddd402e8e587e3a7fc4017ecc40426c54735df56b8adb6877d7f86a05fd8a1edcb8fe86cc
diff --git a/sci-misc/elmer-front/elmer-front-6.0_p4651.ebuild b/sci-misc/elmer-front/elmer-front-6.0_p4651.ebuild
deleted file mode 100644
index 250a300e8..000000000
--- a/sci-misc/elmer-front/elmer-front-6.0_p4651.ebuild
+++ /dev/null
@@ -1,43 +0,0 @@
-# Copyright 1999-2015 Gentoo Foundation
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=5
-
-AUTOTOOLS_AUTORECONF=true
-
-inherit autotools-utils multilib
-
-ELMER_ROOT="elmerfem"
-MY_PN=${PN/elmer-/}
-
-DESCRIPTION="Finite element programs, libraries, and visualization tools - elmer frontend"
-HOMEPAGE="http://www.csc.fi/english/pages/elmer"
-SRC_URI="http://elmerfem.svn.sourceforge.net/viewvc/${ELMER_ROOT}/release/${PV%_p*}/${MY_PN}/?view=tar&pathrev=4651 -> ${P}.tar.gz"
-
-LICENSE="GPL-2"
-SLOT="0"
-KEYWORDS="~amd64 ~x86"
-IUSE=""
-
-RDEPEND="
-	dev-lang/tcl:0=
-	dev-lang/tk:0=
-	sci-libs/matc
-	sci-libs/elmer-eio
-	virtual/opengl"
-DEPEND="${RDEPEND}"
-
-S="${WORKDIR}"/front/front
-
-PATCHES=(
-	"${FILESDIR}"/${P}-tcltk8.6.patch
-	"${FILESDIR}"/${P}-underlinking.patch
-	"${FILESDIR}"/${P}-out-of-source.patch
-)
-
-src_configure() {
-	local myeconfargs=(
-		--with-eioc --with-matc --with-tcltk --with-x
-	)
-	autotools-utils_src_configure
-}
diff --git a/sci-misc/elmer-front/elmer-front-9999.ebuild b/sci-misc/elmer-front/elmer-front-9999.ebuild
deleted file mode 100644
index 71c9ef327..000000000
--- a/sci-misc/elmer-front/elmer-front-9999.ebuild
+++ /dev/null
@@ -1,50 +0,0 @@
-# Copyright 1999-2015 Gentoo Foundation
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=5
-
-AUTOTOOLS_AUTORECONF=true
-
-inherit autotools-utils multilib subversion
-
-ELMER_ROOT="elmerfem"
-MY_PN=${PN/elmer-/}
-
-DESCRIPTION="Finite element programs, libraries, and visualization tools - elmer frontend"
-HOMEPAGE="http://www.csc.fi/english/pages/elmer"
-SRC_URI=""
-ESVN_REPO_URI="https://elmerfem.svn.sourceforge.net/svnroot/elmerfem/trunk/${MY_PN}"
-ESVN_PROJECT="${MY_PN}"
-
-LICENSE="GPL-2"
-SLOT="0"
-KEYWORDS=""
-IUSE=""
-
-RDEPEND="
-	dev-lang/tcl:0=
-	dev-lang/tk:0=
-	sci-libs/matc
-	sci-libs/elmer-eio
-	virtual/opengl"
-DEPEND="${RDEPEND}"
-
-S="${WORKDIR}/front"
-
-PATCHES=(
-	"${FILESDIR}"/${PN}-6.0_p4651-tcltk8.6.patch
-	"${FILESDIR}"/${PN}-6.0_p4651-underlinking.patch
-	"${FILESDIR}"/${PN}-6.0_p4651-out-of-source.patch
-)
-
-src_prepare() {
-	subversion_src_prepare
-	autotools-utils_src_prepare
-}
-
-src_configure() {
-	local myeconfargs=(
-		--with-eioc --with-matc --with-tcltk --with-x
-	)
-	autotools-utils_src_configure
-}
diff --git a/sci-misc/elmer-front/files/elmer-front-6.0_p4651-out-of-source.patch b/sci-misc/elmer-front/files/elmer-front-6.0_p4651-out-of-source.patch
deleted file mode 100644
index 872c03f21..000000000
--- a/sci-misc/elmer-front/files/elmer-front-6.0_p4651-out-of-source.patch
+++ /dev/null
@@ -1,30 +0,0 @@
- src/Makefile.am | 9 +++++----
- 1 file changed, 5 insertions(+), 4 deletions(-)
-
-diff --git a/src/Makefile.am b/src/Makefile.am
-old mode 100755
-new mode 100644
-index 894a547..dc7c77b
---- a/src/Makefile.am
-+++ b/src/Makefile.am
-@@ -87,15 +87,16 @@ endif
- ElmerFront_LDADD = -lX11
- 
- install-data-local:
--	@echo "Installing tcl scripts to ${prefix}/share/elmerfront/tcl"
-+	@echo "Installing tcl scripts to ${DESTDIR}${prefix}/share/elmerfront/tcl"
- 
- 	mkdir -p "$(DESTDIR)${prefix}/share/elmerfront/tcl"
--	cp -r ./tcl/* "$(DESTDIR)${prefix}/share/elmerfront/tcl"
-+	cp -r "${srcdir}"/tcl/* "$(DESTDIR)${prefix}/share/elmerfront/tcl"
-+	cp -r "${builddir}"/tcl/* "$(DESTDIR)${prefix}/share/elmerfront/tcl"
- 	rm -rf `find $(DESTDIR)$(prefix)/share/elmerfront/tcl -name .svn`
- 
--	@echo "Installing *.edf *.rgb to ${prefix}/share/elmerfront/lib"
-+	@echo "Installing *.edf *.rgb to ${DESTDIR}${prefix}/share/elmerfront/lib"
- 	mkdir -p "$(DESTDIR)${prefix}/share/elmerfront/lib"
--	cp -r ./lib/* "$(DESTDIR)${prefix}/share/elmerfront/lib"
-+	cp -r "${srcdir}"/lib/* "$(DESTDIR)${prefix}/share/elmerfront/lib"
- 	rm -rf `find $(DESTDIR)$(prefix)/share/elmerfront/lib -name .svn`
- 
- 
diff --git a/sci-misc/elmer-front/files/elmer-front-6.0_p4651-tcltk8.6.patch b/sci-misc/elmer-front/files/elmer-front-6.0_p4651-tcltk8.6.patch
deleted file mode 100644
index 7fa7605b7..000000000
--- a/sci-misc/elmer-front/files/elmer-front-6.0_p4651-tcltk8.6.patch
+++ /dev/null
@@ -1,55 +0,0 @@
- src/ecif_userinterface_TCL.cpp | 18 +++++++++++++++++-
- 1 file changed, 17 insertions(+), 1 deletion(-)
-
-diff --git a/src/ecif_userinterface_TCL.cpp b/src/ecif_userinterface_TCL.cpp
-index 7f581a8..53e0432 100644
---- a/src/ecif_userinterface_TCL.cpp
-+++ b/src/ecif_userinterface_TCL.cpp
-@@ -622,7 +622,11 @@ UserInterface_TCL::createTclEnvironment(Hinst application)
- 
-   // *** Invoke application-specific initialization.
-   if (My_Tcl_AppInit(interp) != TCL_OK) {
-+#if TCL_MAJOR_VERSION <=8 && TCL_MINOR_VERSION < 6
-     WishPanic("My_Tcl_AppInit failed: %s\n", interp->result);
-+#else
-+    WishPanic("My_Tcl_AppInit failed: %s\n", Tcl_GetStringResult(interp));
-+#endif
-   }
- 
-   // Result value is the Tcl interpreter
-@@ -4685,11 +4689,19 @@ UserInterface_TCL::sendCommandToGui(Tcl_Interp* interp, const char* cmd, const c
-     Tcl_DStringFree( &dstring );
-   }
- 
-+#if TCL_MAJOR_VERSION <=8 && TCL_MINOR_VERSION < 6
-   if (interp->result[0] != '\0') {
-+#else
-+  if (Tcl_GetStringResult(interp)[0] != '\0') {
-+#endif
- 
-     char err_buf[256];
-     err_buf[255] = '\0';
-+#if TCL_MAJOR_VERSION <=8 && TCL_MINOR_VERSION < 6
-     strncpy(err_buf, interp->result, 255);
-+#else
-+    strncpy(err_buf, Tcl_GetStringResult(interp), 255);
-+#endif
- 
-     char cmd_buf[256];
-     cmd_buf[255] = '\0';
-@@ -5350,10 +5362,14 @@ UserInterface_TCL::start(int argc, char** argv)
-   //--If we can't load the script (= start CONTROL-SIDE interpreter)
-   if (code != TCL_OK) {
- 
--    char* p = (char *)Tcl_GetVar(theInterp, "errorInfo", glob_flag);
-+    const char* p = (const char *)Tcl_GetVar(theInterp, "errorInfo", glob_flag);
- 
-     if ((p == NULL) || (*p == '\0')) {
-+#if TCL_MAJOR_VERSION <=8 && TCL_MINOR_VERSION < 6
-       p = theInterp->result;
-+#else
-+      p = Tcl_GetStringResult(theInterp);
-+#endif
-     }
- 
-     ((ofstream*)debugFile)->open("ElmerFront.log", ios::out);
diff --git a/sci-misc/elmer-front/files/elmer-front-6.0_p4651-underlinking.patch b/sci-misc/elmer-front/files/elmer-front-6.0_p4651-underlinking.patch
deleted file mode 100644
index b370ed494..000000000
--- a/sci-misc/elmer-front/files/elmer-front-6.0_p4651-underlinking.patch
+++ /dev/null
@@ -1,16 +0,0 @@
- src/Makefile.am | 2 ++
- 1 file changed, 2 insertions(+)
-
-diff --git a/src/Makefile.am b/src/Makefile.am
-index 01e3e48..894a547 100755
---- a/src/Makefile.am
-+++ b/src/Makefile.am
-@@ -84,6 +84,8 @@ ElmerFront_SOURCES =  $(COMMON_SRCS)
- 
- endif
- 
-+ElmerFront_LDADD = -lX11
-+
- install-data-local:
- 	@echo "Installing tcl scripts to ${prefix}/share/elmerfront/tcl"
- 
diff --git a/sci-misc/elmer-front/files/elmer-front-Makefile-install.patch b/sci-misc/elmer-front/files/elmer-front-Makefile-install.patch
deleted file mode 100644
index 6ecbe6f8e..000000000
--- a/sci-misc/elmer-front/files/elmer-front-Makefile-install.patch
+++ /dev/null
@@ -1,18 +0,0 @@
---- front/src/Makefile.am.old	2012-11-12 13:25:34.331046988 +0100
-+++ front/src/Makefile.am	2012-11-12 13:27:36.055100527 +0100
-@@ -85,13 +85,13 @@
- endif
- 
- install-data-local:
--	@echo "Installing tcl scripts to ${prefix}/share/elmerfront/tcl"
-+	@echo "Installing tcl scripts to ${DESTDIR}${prefix}/share/elmerfront/tcl"
- 
- 	mkdir -p "$(DESTDIR)${prefix}/share/elmerfront/tcl"
- 	cp -r ./tcl/* "$(DESTDIR)${prefix}/share/elmerfront/tcl"
- 	rm -rf `find $(DESTDIR)$(prefix)/share/elmerfront/tcl -name .svn`
- 
--	@echo "Installing *.edf *.rgb to ${prefix}/share/elmerfront/lib"
-+	@echo "Installing *.edf *.rgb to ${DESTDIR}${prefix}/share/elmerfront/lib"
- 	mkdir -p "$(DESTDIR)${prefix}/share/elmerfront/lib"
- 	cp -r ./lib/* "$(DESTDIR)${prefix}/share/elmerfront/lib"
- 	rm -rf `find $(DESTDIR)$(prefix)/share/elmerfront/lib -name .svn`
diff --git a/sci-misc/elmer-front/metadata.xml b/sci-misc/elmer-front/metadata.xml
deleted file mode 100644
index 070aa2029..000000000
--- a/sci-misc/elmer-front/metadata.xml
+++ /dev/null
@@ -1,11 +0,0 @@
-<?xml version="1.0" encoding="UTF-8"?>
-<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
-<pkgmetadata>
-	<maintainer type="project">
-		<email>sci@gentoo.org</email>
-		<name>Gentoo Science Project</name>
-	</maintainer>
-	<upstream>
-		<remote-id type="sourceforge">svn</remote-id>
-	</upstream>
-</pkgmetadata>
diff --git a/sci-misc/elmer-meshgen2d/Manifest b/sci-misc/elmer-meshgen2d/Manifest
deleted file mode 100644
index 8b83c109b..000000000
--- a/sci-misc/elmer-meshgen2d/Manifest
+++ /dev/null
@@ -1 +0,0 @@
-DIST elmer-meshgen2d-6.0_p4651.tar.gz 1758048 SHA256 8c8f5c86445ad78ddd3284e45b759b03331e65e6d949ee7d177de626b8c0316c SHA512 1522473ef314bb2e093e820f91194ee30d9e76aa693c2e258b0585246048c9c5368db56195838f27b6c31c286dfd32dae787be1079227e36ff1af07928075e30 WHIRLPOOL cd69f8a02a69f9cef0160c406a9f238bb08dd9d097d76a4657b3d4821e93e904790e8cc51fb487fce827846d8097f4a42e0c16f3d00d4c352d8dca475df00b58
diff --git a/sci-misc/elmer-meshgen2d/elmer-meshgen2d-6.0_p4651.ebuild b/sci-misc/elmer-meshgen2d/elmer-meshgen2d-6.0_p4651.ebuild
deleted file mode 100644
index b61443e6a..000000000
--- a/sci-misc/elmer-meshgen2d/elmer-meshgen2d-6.0_p4651.ebuild
+++ /dev/null
@@ -1,33 +0,0 @@
-# Copyright 1999-2014 Gentoo Foundation
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=5
-
-AUTOTOOLS_AUTORECONF=true
-
-inherit autotools-utils
-
-ELMER_ROOT="elmerfem"
-MY_PN=${PN/elmer-/}
-
-DESCRIPTION="Finite element programs, libraries, and visualization tools - meshgen2d"
-HOMEPAGE="http://www.csc.fi/english/pages/elmer"
-SRC_URI="http://elmerfem.svn.sourceforge.net/viewvc/${ELMER_ROOT}/release/${PV%_p*}/${MY_PN}/?view=tar&pathrev=4651 -> ${P}.tar.gz"
-
-LICENSE="GPL-2"
-SLOT="0"
-KEYWORDS="~amd64 ~x86"
-IUSE="debug"
-
-S="${WORKDIR}/meshgen2d"
-
-PATCHES=(
-	"${FILESDIR}"/${P}-oof.patch
-)
-
-src_configure() {
-	local myeconfargs=(
-		$(use_with debug)
-	)
-	autotools-utils_src_configure
-}
diff --git a/sci-misc/elmer-meshgen2d/elmer-meshgen2d-9999.ebuild b/sci-misc/elmer-meshgen2d/elmer-meshgen2d-9999.ebuild
deleted file mode 100644
index fed4beca0..000000000
--- a/sci-misc/elmer-meshgen2d/elmer-meshgen2d-9999.ebuild
+++ /dev/null
@@ -1,40 +0,0 @@
-# Copyright 1999-2014 Gentoo Foundation
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=5
-
-AUTOTOOLS_AUTORECONF=true
-
-inherit autotools-utils subversion
-
-ELMER_ROOT="elmerfem"
-MY_PN=${PN/elmer-/}
-
-DESCRIPTION="Finite element programs, libraries, and visualization tools - meshgen2d"
-HOMEPAGE="http://www.csc.fi/english/pages/elmer"
-SRC_URI=""
-ESVN_REPO_URI="https://elmerfem.svn.sourceforge.net/svnroot/elmerfem/trunk/${MY_PN}"
-ESVN_PROJECT="${MY_PN}"
-
-LICENSE="GPL-2"
-SLOT="0"
-KEYWORDS=""
-IUSE="debug"
-
-S="${WORKDIR}/meshgen2d"
-
-PATCHES=(
-	"${FILESDIR}"/${PN}-6.0_p4651-oof.patch
-)
-
-src_prepare() {
-	subversion_src_prepare
-	autotools-utils_src_prepare
-}
-
-src_configure() {
-	local myeconfargs=(
-		$(use_with debug)
-	)
-	autotools-utils_src_configure
-}
diff --git a/sci-misc/elmer-meshgen2d/files/elmer-meshgen2d-6.0_p4651-oof.patch b/sci-misc/elmer-meshgen2d/files/elmer-meshgen2d-6.0_p4651-oof.patch
deleted file mode 100644
index 49ab50640..000000000
--- a/sci-misc/elmer-meshgen2d/files/elmer-meshgen2d-6.0_p4651-oof.patch
+++ /dev/null
@@ -1,17 +0,0 @@
- src/Makefile.am | 3 ++-
- 1 file changed, 2 insertions(+), 1 deletion(-)
-
-diff --git a/src/Makefile.am b/src/Makefile.am
-index d33d999..8111609 100755
---- a/src/Makefile.am
-+++ b/src/Makefile.am
-@@ -2,7 +2,8 @@
- SUBDIRS=include
- 
- INCLUDES = \
--        -I./include       
-+        -I$(srcdir)/include       \
-+        -I$(builddir)/include       
- 
- bin_PROGRAMS = ElmerMesh2D Mesh2D
- 
diff --git a/sci-misc/elmer-meshgen2d/metadata.xml b/sci-misc/elmer-meshgen2d/metadata.xml
deleted file mode 100644
index 070aa2029..000000000
--- a/sci-misc/elmer-meshgen2d/metadata.xml
+++ /dev/null
@@ -1,11 +0,0 @@
-<?xml version="1.0" encoding="UTF-8"?>
-<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
-<pkgmetadata>
-	<maintainer type="project">
-		<email>sci@gentoo.org</email>
-		<name>Gentoo Science Project</name>
-	</maintainer>
-	<upstream>
-		<remote-id type="sourceforge">svn</remote-id>
-	</upstream>
-</pkgmetadata>
diff --git a/sci-misc/elmer-meta/elmer-meta-6.0_p4651.ebuild b/sci-misc/elmer-meta/elmer-meta-6.0_p4651.ebuild
deleted file mode 100644
index c4c866374..000000000
--- a/sci-misc/elmer-meta/elmer-meta-6.0_p4651.ebuild
+++ /dev/null
@@ -1,27 +0,0 @@
-# Copyright 1999-2017 Gentoo Foundation
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=6
-
-DESCRIPTION="Collection of finite element programs, libraries, and visualization tools"
-HOMEPAGE="http://www.csc.fi/english/pages/elmer"
-
-LICENSE="GPL-2"
-SLOT="0"
-KEYWORDS="~amd64 ~x86"
-IUSE=""
-
-DEPEND="
-	~sci-libs/matc-${PV}
-	~sci-misc/elmer-elmergrid-${PV}
-	~sci-misc/elmer-meshgen2d-${PV}
-	~sci-libs/elmer-eio-${PV}
-	~sci-libs/elmer-hutiter-${PV}
-	~sci-misc/elmer-fem-${PV}
-	~sci-misc/elmer-post-${PV}
-	~sci-misc/elmer-front-${PV}"
-
-pkg_postinst() {
-	einfo "Elmer ebuilds may need further development."
-	einfo "Please inform any problems or improvements in http://bugs.gentoo.org/show_bug.cgi?id=221013"
-}
diff --git a/sci-misc/elmer-meta/elmer-meta-9999.ebuild b/sci-misc/elmer-meta/elmer-meta-9999.ebuild
deleted file mode 100644
index 9bd892a40..000000000
--- a/sci-misc/elmer-meta/elmer-meta-9999.ebuild
+++ /dev/null
@@ -1,27 +0,0 @@
-# Copyright 1999-2017 Gentoo Foundation
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=6
-
-DESCRIPTION="Collection of finite element programs, libraries, and visualization tools"
-HOMEPAGE="http://www.csc.fi/english/pages/elmer"
-
-LICENSE="GPL-2"
-SLOT="0"
-KEYWORDS=""
-IUSE=""
-
-DEPEND="
-	~sci-libs/matc-${PV}
-	~sci-misc/elmer-elmergrid-${PV}
-	~sci-misc/elmer-meshgen2d-${PV}
-	~sci-libs/elmer-eio-${PV}
-	~sci-libs/elmer-hutiter-${PV}
-	~sci-misc/elmer-fem-${PV}
-	~sci-misc/elmer-post-${PV}
-	~sci-misc/elmer-front-${PV}"
-
-pkg_postinst() {
-	einfo "Elmer ebuilds may need further development."
-	einfo "Please inform any problems or improvements in http://bugs.gentoo.org/show_bug.cgi?id=221013"
-}
diff --git a/sci-misc/elmer-meta/metadata.xml b/sci-misc/elmer-meta/metadata.xml
deleted file mode 100644
index ae9640ffb..000000000
--- a/sci-misc/elmer-meta/metadata.xml
+++ /dev/null
@@ -1,8 +0,0 @@
-<?xml version="1.0" encoding="UTF-8"?>
-<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
-<pkgmetadata>
-	<maintainer type="project">
-		<email>sci@gentoo.org</email>
-		<name>Gentoo Science Project</name>
-	</maintainer>
-</pkgmetadata>
diff --git a/sci-misc/elmer-post/Manifest b/sci-misc/elmer-post/Manifest
deleted file mode 100644
index 8ce95fea2..000000000
--- a/sci-misc/elmer-post/Manifest
+++ /dev/null
@@ -1 +0,0 @@
-DIST elmer-post-6.0_p4651.tar.gz 5213917 SHA256 6c54ea46701e95a7ef574198668013169231dd453faa6562aa01ce388bc49aba SHA512 4ff54ea1831923a9522f19cb1adb8a2b56959c31be26b2da61f6af56571bc9174a743fbb7457062c3bbf528056b53c0cb67fedede4e28871fe2a42d1dd6f9bc2 WHIRLPOOL d0f7363c7b5f8faeb6f8279e86e3050c98e3d1d96debc3ecbfd4d9e94152867363e2bfae7ad5ef214b6b249998d85577ab91527d61b94cfacbd4553b89a22eac
diff --git a/sci-misc/elmer-post/elmer-post-6.0_p4651.ebuild b/sci-misc/elmer-post/elmer-post-6.0_p4651.ebuild
deleted file mode 100644
index 75f6c0887..000000000
--- a/sci-misc/elmer-post/elmer-post-6.0_p4651.ebuild
+++ /dev/null
@@ -1,59 +0,0 @@
-# Copyright 1999-2015 Gentoo Foundation
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=5
-
-AUTOTOOLS_AUTORECONF=true
-
-inherit autotools-utils flag-o-matic multilib toolchain-funcs
-
-ELMER_ROOT="elmerfem"
-MY_PN=${PN/elmer-/}
-
-DESCRIPTION="Finite element programs, libraries, and visualization tools - elmerpost"
-HOMEPAGE="http://www.csc.fi/english/pages/elmer"
-SRC_URI="http://elmerfem.svn.sourceforge.net/viewvc/${ELMER_ROOT}/release/${PV%_p*}/${MY_PN}/?view=tar&pathrev=4651 -> ${P}.tar.gz"
-
-LICENSE="GPL-2"
-SLOT="0"
-KEYWORDS="~amd64 ~x86"
-IUSE="debug opengl"
-
-RDEPEND="
-	dev-lang/tcl:0=
-	dev-lang/tk:0=
-	opengl? (
-		virtual/opengl
-		media-libs/ftgl
-		)
-	sci-libs/matc"
-DEPEND="${RDEPEND}
-	virtual/pkgconfig"
-
-S="${WORKDIR}/post"
-
-PATCHES=(
-	"${FILESDIR}"/${P}-oof.patch
-	"${FILESDIR}"/${P}-underlinking.patch
-	"${FILESDIR}"/${P}-tcltk8.6.patch
-	"${FILESDIR}"/${P}-bfr-overflow.patch
-	"${FILESDIR}"/${P}-impl-dec.patch
-)
-
-src_prepare() {
-	use opengl && append-cppflags $($(tc-getPKG_CONFIG) --cflags ftgl)
-	autotools-utils_src_prepare
-}
-
-src_configure() {
-	local myeconfargs=(
-		$(use_with debug)
-		--with-matc
-		--with-x
-	)
-	autotools-utils_src_configure
-}
-
-src_install() {
-	autotools-utils_src_install ELMER_POST_DATADIR="/usr/share/elmerpost"
-}
diff --git a/sci-misc/elmer-post/elmer-post-9999.ebuild b/sci-misc/elmer-post/elmer-post-9999.ebuild
deleted file mode 100644
index 3b7c2b47e..000000000
--- a/sci-misc/elmer-post/elmer-post-9999.ebuild
+++ /dev/null
@@ -1,61 +0,0 @@
-# Copyright 1999-2015 Gentoo Foundation
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=5
-
-AUTOTOOLS_AUTORECONF=true
-
-inherit autotools-utils flag-o-matic multilib subversion toolchain-funcs
-
-ELMER_ROOT="elmerfem"
-MY_PN=${PN/elmer-/}
-
-DESCRIPTION="Finite element programs, libraries, and visualization tools - elmerpost"
-HOMEPAGE="http://www.csc.fi/english/pages/elmer"
-SRC_URI=""
-ESVN_REPO_URI="https://elmerfem.svn.sourceforge.net/svnroot/elmerfem/trunk/${MY_PN}"
-ESVN_PROJECT="${MY_PN}"
-
-LICENSE="GPL-2"
-SLOT="0"
-KEYWORDS=""
-IUSE="debug opengl"
-
-RDEPEND="
-	dev-lang/tcl:0=
-	dev-lang/tk:0=
-	opengl? (
-		virtual/opengl
-		media-libs/ftgl
-		)
-	sci-libs/matc"
-DEPEND="${RDEPEND}
-	virtual/pkgconfig"
-
-S="${WORKDIR}/post"
-
-PATCHES=(
-	"${FILESDIR}"/${PN}-6.0_p4651-oof.patch
-	"${FILESDIR}"/${PN}-6.0_p4651-underlinking.patch
-	"${FILESDIR}"/${PN}-6.0_p4651-tcltk8.6.patch
-	"${FILESDIR}"/${PN}-6.0_p4651-bfr-overflow.patch
-	"${FILESDIR}"/${PN}-6.0_p4651-impl-dec.patch
-)
-
-src_prepare() {
-	use opengl && append-cppflags $($(tc-getPKG_CONFIG) --cflags ftgl)
-	autotools-utils_src_prepare
-}
-
-src_configure() {
-	local myeconfargs=(
-		$(use_with debug)
-		--with-matc
-		--with-x
-	)
-	autotools-utils_src_configure
-}
-
-src_install() {
-	autotools-utils_src_install ELMER_POST_DATADIR="/usr/share/elmerpost"
-}
diff --git a/sci-misc/elmer-post/files/elmer-post-6.0_p4651-bfr-overflow.patch b/sci-misc/elmer-post/files/elmer-post-6.0_p4651-bfr-overflow.patch
deleted file mode 100644
index b5d78116c..000000000
--- a/sci-misc/elmer-post/files/elmer-post-6.0_p4651-bfr-overflow.patch
+++ /dev/null
@@ -1,16 +0,0 @@
- src/sico2elmer/sico2elmerc.c | 2 +-
- 1 file changed, 1 insertion(+), 1 deletion(-)
-
-diff --git a/src/sico2elmer/sico2elmerc.c b/src/sico2elmer/sico2elmerc.c
-index 1522030..6ae875c 100755
---- a/src/sico2elmer/sico2elmerc.c
-+++ b/src/sico2elmer/sico2elmerc.c
-@@ -27,7 +27,7 @@ void STDCALLBULL FC_FUNC(postgrid,POSTGRID) (float  *xi, /* unscaled x coordinat
-   int   imax, jmax, kcmax, ktmax;
-   float *staggered_grid[2];
-   float actual_scaled_coord[3];
--  char  groupid[4], filename[80], yes_no, *suffix=".ep";
-+  char  groupid[8], filename[80], yes_no, *suffix=".ep";
-   FILE  *ptFile;
-   
-   /* constants */
diff --git a/sci-misc/elmer-post/files/elmer-post-6.0_p4651-impl-dec.patch b/sci-misc/elmer-post/files/elmer-post-6.0_p4651-impl-dec.patch
deleted file mode 100644
index 30c82595e..000000000
--- a/sci-misc/elmer-post/files/elmer-post-6.0_p4651-impl-dec.patch
+++ /dev/null
@@ -1,15 +0,0 @@
- src/screensave.c | 1 +
- 1 file changed, 1 insertion(+)
-
-diff --git a/src/screensave.c b/src/screensave.c
-index ae4f577..810f54c 100755
---- a/src/screensave.c
-+++ b/src/screensave.c
-@@ -26,6 +26,7 @@
- #include <math.h>
- #include <stdlib.h>
- #include <strings.h>
-+#include <string.h>
- 
-   
- #include <GL/gl.h>
diff --git a/sci-misc/elmer-post/files/elmer-post-6.0_p4651-oof.patch b/sci-misc/elmer-post/files/elmer-post-6.0_p4651-oof.patch
deleted file mode 100644
index cd9368748..000000000
--- a/sci-misc/elmer-post/files/elmer-post-6.0_p4651-oof.patch
+++ /dev/null
@@ -1,181 +0,0 @@
- src/ElmerPost.c              |  2 +-
- src/Makefile.am              | 16 ++++++++--------
- src/camera/context.cc        |  2 +-
- src/camera/file.cc           |  2 +-
- src/camera/glp.h             |  4 ++--
- src/elmerpost.h              |  2 +-
- src/fttext.cpp               |  2 +-
- src/graphics/graphics.h      |  2 +-
- src/second.c                 |  2 +-
- src/sico2elmer/sico2elmerc.c |  2 +-
- 10 files changed, 18 insertions(+), 18 deletions(-)
-
-diff --git a/src/ElmerPost.c b/src/ElmerPost.c
-index 2a238b0..9c63113 100644
---- a/src/ElmerPost.c
-+++ b/src/ElmerPost.c
-@@ -45,7 +45,7 @@
- 
- #define MODULE_MAIN
- #include "elmerpost.h"
--#include "../config.h"
-+#include "config.h"
- 
- #include <tcl.h>
- #include <tk.h>
-diff --git a/src/Makefile.am b/src/Makefile.am
-index f4234a1..cd35e72 100755
---- a/src/Makefile.am
-+++ b/src/Makefile.am
-@@ -98,31 +98,31 @@ install-data-local:
- 
- 	@echo "Instaling help to ${ELMER_POST_DATADIR}/help"
- 	mkdir -p $(DESTDIR)$(ELMER_POST_DATADIR)/help
--	cp -r help/* $(DESTDIR)$(ELMER_POST_DATADIR)/help
-+	cp -r $(srcdir)/help/* $(DESTDIR)$(ELMER_POST_DATADIR)/help
- 	rm -rf `find $(DESTDIR)$(ELMER_POST_DATADIR)/help -name .svn`
- 
- 	@echo "Instaling tcl scripts to ${ELMER_POST_DATADIR}/tcl"
- 	mkdir -p $(DESTDIR)$(ELMER_POST_DATADIR)/tcl
--	cp -r tcl/* $(DESTDIR)$(ELMER_POST_DATADIR)/tcl
-+	cp -r $(srcdir)/tcl/* $(DESTDIR)$(ELMER_POST_DATADIR)/tcl
- 	rm -rf `find $(DESTDIR)$(ELMER_POST_DATADIR)/tcl -name .svn`
- 
- 	@echo "Instaling initialization scripts to ${ELMER_POST_DATADIR}/lib"
- 	mkdir -p $(DESTDIR)$(ELMER_POST_DATADIR)/lib
--	cp -r lib/* $(DESTDIR)$(ELMER_POST_DATADIR)/lib
-+	cp -r $(srcdir)/lib/* $(DESTDIR)$(ELMER_POST_DATADIR)/lib
- 	rm -rf `find $(DESTDIR)$(ELMER_POST_DATADIR)/lib -name .svn`
- 
- 	@echo "Installing fonts to $(ELMER_POST_DATADIR)/fonts"
- 	mkdir -p $(DESTDIR)$(ELMER_POST_DATADIR)/fonts
--	cp -r fonts/* $(DESTDIR)$(ELMER_POST_DATADIR)/fonts
-+	cp -r $(srcdir)/fonts/* $(DESTDIR)$(ELMER_POST_DATADIR)/fonts
- 	rm -rf `find $(DESTDIR)$(ELMER_POST_DATADIR)/fonts -name .svn`
- #
- # Copy the help and tcl
- #
- dist-hook:
--	cp -r tcl $(distdir)
--	cp -r help $(distdir)
--	cp -r lib $(distdir)
--	cp -r fonts $(distdir)
-+	cp -r $(srcdir)/tcl $(distdir)
-+	cp -r $(srcdir)/help $(distdir)
-+	cp -r $(srcdir)/lib $(distdir)
-+	cp -r $(srcdir)/fonts $(distdir)
- 	rm -rf `find $(distdir)/ -name .svn`
- 	rm -rf `find $(distdir)/ -name CVS`
- 	rm -rf `find $(distdir)/ -name \#*`
-diff --git a/src/camera/context.cc b/src/camera/context.cc
-index c2bcbd4..e7926b3 100755
---- a/src/camera/context.cc
-+++ b/src/camera/context.cc
-@@ -38,7 +38,7 @@
- // Include necessary headers.
- //
- 
--#include <../../config.h>
-+#include <config.h>
- 
- #include "glp.h"
- #include <math.h>
-diff --git a/src/camera/file.cc b/src/camera/file.cc
-index 1f4cd30..6544830 100755
---- a/src/camera/file.cc
-+++ b/src/camera/file.cc
-@@ -47,7 +47,7 @@
- //
- 
- 
--#include <../../config.h>
-+#include <config.h>
- 
- #include <stdio.h>
- #include <stdlib.h>
-diff --git a/src/camera/glp.h b/src/camera/glp.h
-index 8c65318..31a2e49 100755
---- a/src/camera/glp.h
-+++ b/src/camera/glp.h
-@@ -35,7 +35,7 @@
- 
- #ifndef _GL_GLP_H_
- #  define _GL_GLP_H_
--#include "../../config.h"
-+#include "config.h"
- 
- #if defined(WIN32) ||defined(MINGW32)
- #include <windows.h>
-@@ -49,7 +49,7 @@
- // Include necessary headers.
- //
- #include <GL/gl.h>
--#include "../../config.h"
-+#include "config.h"
- 
- 
- 
-diff --git a/src/elmerpost.h b/src/elmerpost.h
-index 53560c0..7d312df 100755
---- a/src/elmerpost.h
-+++ b/src/elmerpost.h
-@@ -44,7 +44,7 @@
-  *
-  ******************************************************************************/
- 
--#include "../config.h"
-+#include "config.h"
- 
- #if defined(WIN32) || defined(MINGW32)
- #include <windows.h>
-diff --git a/src/fttext.cpp b/src/fttext.cpp
-index 9ee88f8..48a3e0a 100644
---- a/src/fttext.cpp
-+++ b/src/fttext.cpp
-@@ -10,7 +10,7 @@
- // Date:        15. Jan 2008
- //-----------------------------------------------------------------------------------
- #if defined(HAVE_CONFIG_H)
--#include "../config.h"
-+#include "config.h"
- #endif
- 
- #if defined(HAVE_FTGL_NEW) || defined(HAVE_FTGL_OLD)
-diff --git a/src/graphics/graphics.h b/src/graphics/graphics.h
-index 6e702c1..5d6d81b 100755
---- a/src/graphics/graphics.h
-+++ b/src/graphics/graphics.h
-@@ -67,7 +67,7 @@
-  *
-  ******************************************************************************/
- 
--#include "../../config.h"
-+#include "config.h"
- 
- #ifndef MINGW32
- 
-diff --git a/src/second.c b/src/second.c
-index b719556..128e404 100755
---- a/src/second.c
-+++ b/src/second.c
-@@ -45,7 +45,7 @@
-  ******************************************************************************/
- 
- 
--#include "../config.h"
-+#include "config.h"
- #ifndef WIN32
- 
- #include <sys/types.h>
-diff --git a/src/sico2elmer/sico2elmerc.c b/src/sico2elmer/sico2elmerc.c
-index 1522030..23f3abb 100755
---- a/src/sico2elmer/sico2elmerc.c
-+++ b/src/sico2elmer/sico2elmerc.c
-@@ -1,6 +1,6 @@
- #include "sico2elmer.h"
- 
--#include "../../config.h"
-+#include "config.h"
- 
- /*
-   jv: added fortran function name and char ptr macros to (hopefully) enhance portability
diff --git a/sci-misc/elmer-post/files/elmer-post-6.0_p4651-tcltk8.6.patch b/sci-misc/elmer-post/files/elmer-post-6.0_p4651-tcltk8.6.patch
deleted file mode 100644
index 31596e6f4..000000000
--- a/sci-misc/elmer-post/files/elmer-post-6.0_p4651-tcltk8.6.patch
+++ /dev/null
@@ -1,355 +0,0 @@
- src/ElmerPost.c          | 48 ++++++++++++++++++++++++++++++++++++++++++++++++
- src/modules/matctcl.c    |  8 ++++++++
- src/modules/readfile.c   |  4 ++++
- src/modules/transforms.c | 40 ++++++++++++++++++++++++++++++++++++++++
- src/screensave.c         | 12 ++++++++++++
- 5 files changed, 112 insertions(+)
-
-diff --git a/src/ElmerPost.c b/src/ElmerPost.c
-index 2a238b0..b9e8df5 100644
---- a/src/ElmerPost.c
-+++ b/src/ElmerPost.c
-@@ -183,7 +183,11 @@ static int SetParentObject( ClientData cl,Tcl_Interp *interp,int argc,char **arg
-    obj = (object_t *)obj_find( &VisualObject,argv[1] );
-    if ( !obj )
-    {
-+#if TCL_MAJOR_VERSION <=8 && TCL_MINOR_VERSION < 6
-       sprintf( interp->result, "parent: no such object [%s]", argv[1] );
-+#else
-+      sprintf( Tcl_GetStringResult(interp), "parent: no such object [%s]", argv[1] );
-+#endif
-       return TCL_ERROR;
-    }
- 
-@@ -346,13 +350,21 @@ static int ClipPlane( ClientData cl,Tcl_Interp *interp,int argc,char **argv)
-     int i,id;
- 
-     if ( argc != 6 ) {
-+#if TCL_MAJOR_VERSION <=8 && TCL_MINOR_VERSION < 6
-         sprintf( interp->result, "clip: Wrong number of arguments.\n" );
-+#else
-+        sprintf( Tcl_GetStringResult(interp), "clip: Wrong number of arguments.\n" );
-+#endif
-         return TCL_ERROR;
-     }
- 
-     sscanf( argv[1], "%d",  &id );
-     if ( id < 0 || id > 5 ) {
-+#if TCL_MAJOR_VERSION <=8 && TCL_MINOR_VERSION < 6
-         sprintf( interp->result, "clip: Plane argument should be from a int from 0..5.\n" );
-+#else
-+        sprintf( Tcl_GetStringResult(interp), "clip: Plane argument should be from a int from 0..5.\n" );
-+#endif
-         return TCL_ERROR;
-     }
-     CurrentObject->ClipPlane[id] = id;
-@@ -779,7 +791,11 @@ static int TimeStep(ClientData cl,Tcl_Interp *interp,int argc,char **argv)
- 
-     if ( argc != 2 )
-     {
-+#if TCL_MAJOR_VERSION <=8 && TCL_MINOR_VERSION < 6
-         sprintf( interp->result, "c_TimeStep: wrong number of parameters.\n" );
-+#else
-+        sprintf( Tcl_GetStringResult(interp), "c_TimeStep: wrong number of parameters.\n" );
-+#endif
-         return TCL_ERROR;
-     }
- 
-@@ -790,7 +806,11 @@ static int TimeStep(ClientData cl,Tcl_Interp *interp,int argc,char **argv)
- 
-     if ( n < 0  || n >= ElementModel->NofTimesteps )
-     {
-+#if TCL_MAJOR_VERSION <=8 && TCL_MINOR_VERSION < 6
-         sprintf( interp->result, "c_TimeStep: Invalid timestep.\n" );
-+#else
-+        sprintf( Tcl_GetStringResult(interp), "c_TimeStep: Invalid timestep.\n" );
-+#endif
-         return TCL_ERROR;
-     }
- 
-@@ -1028,7 +1048,11 @@ static int CurrentCamera(ClientData cl,Tcl_Interp *interp,int argc,char **argv)
- 
-     if ( argc != 2 )
-     {
-+#if TCL_MAJOR_VERSION <=8 && TCL_MINOR_VERSION < 6
-         sprintf( interp->result, "camera: wrong number of arguments\n" );
-+#else
-+        sprintf( Tcl_GetStringResult(interp), "camera: wrong number of arguments\n" );
-+#endif
-         return TCL_ERROR;
-     }
- 
-@@ -1038,7 +1062,11 @@ static int CurrentCamera(ClientData cl,Tcl_Interp *interp,int argc,char **argv)
-         if ( strcmp( cam->Name, argv[1] ) == 0 )
-         {
-             cam_set_current( cam );
-+#if TCL_MAJOR_VERSION <=8 && TCL_MINOR_VERSION < 6
-             sprintf( interp->result, "%d", i );
-+#else
-+            sprintf( Tcl_GetStringResult(interp), "%d", i );
-+#endif
-             return TCL_OK;
-         }
-     }
-@@ -1548,7 +1576,11 @@ static int ShowString( ClientData cl,Tcl_Interp *interp,int argc,char **argv )
- 
-     if ( argc < 5 )
-     {
-+#if TCL_MAJOR_VERSION <=8 && TCL_MINOR_VERSION < 6
-         sprintf( interp->result, "string: Wrong number of arguments.\n" );
-+#else
-+        sprintf( Tcl_GetStringResult(interp), "string: Wrong number of arguments.\n" );
-+#endif
-         return TCL_ERROR;
-     }
- 
-@@ -1587,7 +1619,11 @@ static int SetFont( ClientData cl,Tcl_Interp *interp,int argc,char **argv )
-   int i;
-     if ( argc < 1 )
-     {
-+#if TCL_MAJOR_VERSION <=8 && TCL_MINOR_VERSION < 6
-         sprintf( interp->result, "Set font: Wrong number of arguments.\n" );
-+#else
-+        sprintf( Tcl_GetStringResult(interp), "Set font: Wrong number of arguments.\n" );
-+#endif
-         return TCL_ERROR;
-     }
- 
-@@ -2146,7 +2182,11 @@ static int WindowSize( ClientData cl,Tcl_Interp *interp,int argc,char **argv )
- 
- 
-    if ( argc < 3 ) {
-+#if TCL_MAJOR_VERSION <=8 && TCL_MINOR_VERSION < 6
-       sprintf( interp->result, "Usage: winsize width height" );
-+#else
-+      sprintf( Tcl_GetStringResult(interp), "Usage: winsize width height" );
-+#endif
-       return TCL_ERROR;
-    }
- 
-@@ -2184,7 +2224,11 @@ static int WindowSize( ClientData cl,Tcl_Interp *interp,int argc,char **argv )
- static int WindowPosition( ClientData cl,Tcl_Interp *interp,int argc,char **argv )
- {
-    if ( argc < 3 ) {
-+#if TCL_MAJOR_VERSION <=8 && TCL_MINOR_VERSION < 6
-       sprintf( interp->result, "Usage: winpos xpos ypos" );
-+#else
-+      sprintf( Tcl_GetStringResult(interp), "Usage: winpos xpos ypos" );
-+#endif
-       return TCL_ERROR;
-    }
- 
-@@ -2210,7 +2254,11 @@ static int MPlayer( ClientData cl, Tcl_Interp *interp, int argc, char **argv )
- #else
- 
-   if( argc < 2 ) {
-+#if TCL_MAJOR_VERSION <=8 && TCL_MINOR_VERSION < 6
-     sprintf( interp->result, "Usage: mplayer filename");
-+#else
-+    sprintf( Tcl_GetStringResult(interp), "Usage: mplayer filename");
-+#endif
-     return TCL_ERROR;
-   }
- 
-diff --git a/src/modules/matctcl.c b/src/modules/matctcl.c
-index 4d6b64f..b69f9ba 100755
---- a/src/modules/matctcl.c
-+++ b/src/modules/matctcl.c
-@@ -79,11 +79,19 @@ static VARIABLE *matc_tcl( VARIABLE *ptr )
- 
-    FREEMEM( command );
- 
-+#if TCL_MAJOR_VERSION <=8 && TCL_MINOR_VERSION < 6
-    if ( TCLInterp->result && (n=strlen(TCLInterp->result))>0 )
-    {
-        res = var_temp_new( TYPE_STRING,1,n );
-        for( i=0; i<n; i++ ) M( res,0,i ) = TCLInterp->result[i];
-    }
-+#else
-+   if ( Tcl_GetStringResult(TCLInterp) && (n=strlen(Tcl_GetStringResult(TCLInterp)))>0 )
-+   {
-+       res = var_temp_new( TYPE_STRING,1,n );
-+       for( i=0; i<n; i++ ) M( res,0,i ) = Tcl_GetStringResult(TCLInterp)[i];
-+   }
-+#endif
- 
-    return res;
- }
-diff --git a/src/modules/readfile.c b/src/modules/readfile.c
-index 254601c..0bcc8f7 100755
---- a/src/modules/readfile.c
-+++ b/src/modules/readfile.c
-@@ -90,7 +90,11 @@ static int epReadFile( ClientData cl,Tcl_Interp *interp,int argc,char **argv )
-     fp = fopen( argv[1], "r" ); 
-     if ( !fp )
-     {
-+#if TCL_MAJOR_VERSION <=8 && TCL_MINOR_VERSION < 6
-        sprintf( interp->result, "ReadModel: can't open file [%s]\n",argv[1] );
-+#else
-+       sprintf( Tcl_GetStringResult(interp), "ReadModel: can't open file [%s]\n",argv[1] );
-+#endif
-        return TCL_ERROR;
-     }
- 
-diff --git a/src/modules/transforms.c b/src/modules/transforms.c
-index 19808ff..4038210 100755
---- a/src/modules/transforms.c
-+++ b/src/modules/transforms.c
-@@ -72,7 +72,11 @@ static int TrnPriority(ClientData cl,Tcl_Interp *interp,int argc,char **argv)
- 
-     if ( argc != 2 )
-     {
-+#if TCL_MAJOR_VERSION <=8 && TCL_MINOR_VERSION < 6
-         sprintf( interp->result, "cTrnPriority: wrong number of parameters\n" );
-+#else
-+        sprintf( Tcl_GetStringResult(interp), "cTrnPriority: wrong number of parameters\n" );
-+#endif
-         return TCL_ERROR;
-     }
- 
-@@ -80,7 +84,11 @@ static int TrnPriority(ClientData cl,Tcl_Interp *interp,int argc,char **argv)
- 
-     if ( n <= 0 )
-     {
-+#if TCL_MAJOR_VERSION <=8 && TCL_MINOR_VERSION < 6
-         sprintf( interp->result, "cTrnPriority: wrong number of parameters\n" );
-+#else
-+        sprintf( Tcl_GetStringResult(interp), "cTrnPriority: wrong number of parameters\n" );
-+#endif
-         return TCL_ERROR;
-     }
- 
-@@ -96,7 +104,11 @@ static int RotPriority(ClientData cl,Tcl_Interp *interp,int argc,char **argv)
- 
-     if ( argc != 2 )
-     {
-+#if TCL_MAJOR_VERSION <=8 && TCL_MINOR_VERSION < 6
-         sprintf( interp->result, "cRotPrioryty: wrong number of parameters\n" );
-+#else
-+        sprintf( Tcl_GetStringResult(interp), "cRotPrioryty: wrong number of parameters\n" );
-+#endif
-         return TCL_ERROR;
-     }
- 
-@@ -104,7 +116,11 @@ static int RotPriority(ClientData cl,Tcl_Interp *interp,int argc,char **argv)
- 
-     if ( n <= 0 )
-     {
-+#if TCL_MAJOR_VERSION <=8 && TCL_MINOR_VERSION < 6
-         sprintf( interp->result, "cRotPriority: wrong number of parameters\n" );
-+#else
-+        sprintf( Tcl_GetStringResult(interp), "cRotPriority: wrong number of parameters\n" );
-+#endif
-         return TCL_ERROR;
-     }
- 
-@@ -130,7 +146,11 @@ static int Rotate(ClientData cl,Tcl_Interp *interp,int argc,char **argv)
- 
-     if ( argc != 4 )
-     {
-+#if TCL_MAJOR_VERSION <=8 && TCL_MINOR_VERSION < 6
-         sprintf( interp->result, "cRotate: wrong number of parameters\n" );
-+#else
-+        sprintf( Tcl_GetStringResult(interp), "cRotate: wrong number of parameters\n" );
-+#endif
-         return TCL_ERROR;
-     }
- 
-@@ -138,7 +158,11 @@ static int Rotate(ClientData cl,Tcl_Interp *interp,int argc,char **argv)
- 
-     if ( n <= 0 )
-     {
-+#if TCL_MAJOR_VERSION <=8 && TCL_MINOR_VERSION < 6
-         sprintf( interp->result, "cRotate: wrong number of parameters\n" );
-+#else
-+        sprintf( Tcl_GetStringResult(interp), "cRotate: wrong number of parameters\n" );
-+#endif
-         return TCL_ERROR;
-     }
- 
-@@ -156,7 +180,11 @@ static int Scale(ClientData cl,Tcl_Interp *interp,int argc,char **argv)
- 
-     if ( argc != 4 )
-     {
-+#if TCL_MAJOR_VERSION <=8 && TCL_MINOR_VERSION < 6
-         sprintf( interp->result, "cScale: wrong number of parameters\n" );
-+#else
-+        sprintf( Tcl_GetStringResult(interp), "cScale: wrong number of parameters\n" );
-+#endif
-         return TCL_ERROR;
-     }
- 
-@@ -164,7 +192,11 @@ static int Scale(ClientData cl,Tcl_Interp *interp,int argc,char **argv)
- 
-     if ( n <= 0 )
-     {
-+#if TCL_MAJOR_VERSION <=8 && TCL_MINOR_VERSION < 6
-         sprintf( interp->result, "cScale: wrong number of parameters\n" );
-+#else
-+        sprintf( Tcl_GetStringResult(interp), "cScale: wrong number of parameters\n" );
-+#endif
-         return TCL_ERROR;
-     }
- 
-@@ -182,13 +214,21 @@ static int Translate(ClientData cl,Tcl_Interp *interp,int argc,char **argv)
- 
-     if ( argc != 4 )
-     {
-+#if TCL_MAJOR_VERSION <=8 && TCL_MINOR_VERSION < 6
-         sprintf( interp->result, "cScale: wrong number of parameters\n" );
-+#else
-+        sprintf( Tcl_GetStringResult(interp), "cScale: wrong number of parameters\n" );
-+#endif
-         return TCL_ERROR;
-     }
- 
-     if ( (n = sscanf( argv[3], "%lf %lf %lf", &x,&y,&z ) ) <= 0 )
-     {
-+#if TCL_MAJOR_VERSION <=8 && TCL_MINOR_VERSION < 6
-         sprintf( interp->result, "cScale: wrong number of parameters\n" );
-+#else
-+        sprintf( Tcl_GetStringResult(interp), "cScale: wrong number of parameters\n" );
-+#endif
-         return TCL_ERROR;
-     }
- 
-diff --git a/src/screensave.c b/src/screensave.c
-index ae4f577..703fe24 100755
---- a/src/screensave.c
-+++ b/src/screensave.c
-@@ -56,7 +56,11 @@ static int ScreenSave( ClientData cl,Tcl_Interp *interp,int argc,char **argv )
-       sprintf( interp->result, 
-        "screensave: can't open [%s] for writing!\n", argv[1] );
- #else
-+#if TCL_MAJOR_VERSION <=8 && TCL_MINOR_VERSION < 6
-       sprintf( interp->result, 
-+#else
-+      sprintf( Tcl_GetStringResult(interp), 
-+#endif
-         "screensave: can't open [%s] for writing:\n%s\n", 
-               argv[1], strerror(errno) );
- #endif
-@@ -76,7 +80,11 @@ static int ScreenSave( ClientData cl,Tcl_Interp *interp,int argc,char **argv )
-       sprintf( interp->result,
-             "screensave: can't allocate enough memory!\n" );
- #else
-+#if TCL_MAJOR_VERSION <=8 && TCL_MINOR_VERSION < 6
-       sprintf( interp->result,
-+#else
-+      sprintf( Tcl_GetStringResult(interp),
-+#endif
-         "screensave: can't allocate enough memory:\n%s\n",
-             strerror(errno) );
- #endif
-@@ -100,7 +108,11 @@ static int ScreenSave( ClientData cl,Tcl_Interp *interp,int argc,char **argv )
-          sprintf( interp->result,
-            "screensave: error writing to [%s]!\n", argv[1] );
- #else
-+#if TCL_MAJOR_VERSION <=8 && TCL_MINOR_VERSION < 6
-          sprintf( interp->result,
-+#else
-+         sprintf( Tcl_GetStringResult(interp),
-+#endif
-            "screensave: error writing to [%s]:\n%s\n",
-                argv[1], strerror(errno) );
- #endif
diff --git a/sci-misc/elmer-post/files/elmer-post-6.0_p4651-underlinking.patch b/sci-misc/elmer-post/files/elmer-post-6.0_p4651-underlinking.patch
deleted file mode 100644
index 45e0d3e71..000000000
--- a/sci-misc/elmer-post/files/elmer-post-6.0_p4651-underlinking.patch
+++ /dev/null
@@ -1,20 +0,0 @@
- src/Makefile.am | 4 +++-
- 1 file changed, 3 insertions(+), 1 deletion(-)
-
-diff --git a/src/Makefile.am b/src/Makefile.am
-index f4234a1..6d99d31 100755
---- a/src/Makefile.am
-+++ b/src/Makefile.am
-@@ -23,9 +23,11 @@ ElmerPost_LDADD=\
- 	./visuals/libvisuals.a \
- 	./graphics/libgraphics.a \
- 	./glaux/libglaux.a \
--	./tk/libtk.a
-+	./tk/libtk.a \
-+	-lX11
- 
- QueryGLXExt_SOURCES=QueryGLXExt.c 
-+QueryGLXExt_LDADD=-lX11
- 
- all-local: screensave.so
- clean-local:
diff --git a/sci-misc/elmer-post/metadata.xml b/sci-misc/elmer-post/metadata.xml
deleted file mode 100644
index 070aa2029..000000000
--- a/sci-misc/elmer-post/metadata.xml
+++ /dev/null
@@ -1,11 +0,0 @@
-<?xml version="1.0" encoding="UTF-8"?>
-<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
-<pkgmetadata>
-	<maintainer type="project">
-		<email>sci@gentoo.org</email>
-		<name>Gentoo Science Project</name>
-	</maintainer>
-	<upstream>
-		<remote-id type="sourceforge">svn</remote-id>
-	</upstream>
-</pkgmetadata>
diff --git a/sci-misc/finomaton/Manifest b/sci-misc/finomaton/Manifest
index b4edb51ab..1bb6119bb 100644
--- a/sci-misc/finomaton/Manifest
+++ b/sci-misc/finomaton/Manifest
@@ -1 +1 @@
-DIST finomaton.zip 72250 BLAKE2B 086e4db9185b9ead1b9375c090d927fad32095a4adfd066bd5f1821fe19ce580436ad68164aa2b2e626fe5966bc7876643e3ba9a28e1fd4f3e08f5e9656dde38 SHA512 0e69da93ffa049eb4b8efbb51f6eeaacce3496a60fdfa0b3fc7379ee969dcbe937c311fcb0e0ca26ed0047e704b29f5b7cbb15bbf88455c3cdd41e37d6c1f1ce
+DIST finomaton-1.0.zip 72250 BLAKE2B 086e4db9185b9ead1b9375c090d927fad32095a4adfd066bd5f1821fe19ce580436ad68164aa2b2e626fe5966bc7876643e3ba9a28e1fd4f3e08f5e9656dde38 SHA512 0e69da93ffa049eb4b8efbb51f6eeaacce3496a60fdfa0b3fc7379ee969dcbe937c311fcb0e0ca26ed0047e704b29f5b7cbb15bbf88455c3cdd41e37d6c1f1ce
diff --git a/sci-misc/finomaton/finomaton-1.0.ebuild b/sci-misc/finomaton/finomaton-1.0.ebuild
index 83edf89bf..8e1bf3c0d 100644
--- a/sci-misc/finomaton/finomaton-1.0.ebuild
+++ b/sci-misc/finomaton/finomaton-1.0.ebuild
@@ -1,13 +1,13 @@
-# Copyright 1999-2015 Gentoo Foundation
+# Copyright 1999-2021 Gentoo Authors
 # Distributed under the terms of the GNU General Public License v2
 
-EAPI=5
+EAPI=7
 
 # N.B. this is from CTAN
 
 DESCRIPTION="Simple tcl/tk script to draw finite state automata"
 HOMEPAGE="https://www.ctan.org/pkg/finomaton"
-SRC_URI="http://mirrors.ctan.org/graphics/finomaton.zip"
+SRC_URI="http://mirrors.ctan.org/graphics/finomaton.zip -> ${P}.zip"
 
 LICENSE="GPL-2"
 SLOT="0"
@@ -15,13 +15,14 @@ KEYWORDS="~amd64 ~x86"
 IUSE="examples"
 
 # script only
-DEPEND=""
+BDEPEND="app-arch/unzip"
 # tex for metapost
 RDEPEND="
 	dev-lang/tk:0
-	dev-texlive/texlive-metapost"
+	dev-texlive/texlive-metapost
+"
 
-S="${WORKDIR}"/${PN}
+S="${WORKDIR}/${PN}"
 
 src_install() {
 	dobin finomaton.tcl
diff --git a/sci-misc/foma/Manifest b/sci-misc/foma/Manifest
deleted file mode 100644
index d55de986c..000000000
--- a/sci-misc/foma/Manifest
+++ /dev/null
@@ -1,2 +0,0 @@
-DIST foma-0.9.14alpha.tar.gz 306549 BLAKE2B 5b52c3449cbf8edc1944b526740709776e280bc61b485b01e6affe7c5e994c6ac0bb0d71887413510a8b8183d6833dd947403ec41137a75db6190b7a0f38241f SHA512 deb1a2086d21020d84941025f4e131b6a20262b816def2a43261dedfa928823e59704336cdecf28a56b5fb270786b8a7cc2f3ad8b861920e3e0d5a6fd51a7add
-DIST foma-0.9.16alpha.tar.gz 328482 SHA256 dc019dcdf6dc8f7e881394f3d76821006e7f0cf6e3fe1c12ac2887fa48d81208 SHA512 8c33de29be11dbbf808243222369ee1e8c17f4659fb2d88ce7b1e53f1161538415e50792981110cf46e50890933573f70d034b258a7d7c596e3c61317d56f369 WHIRLPOOL 2cf481210eef4f46eb42f8c98f157074985d2030fbf0aea8cf1f89b1827f7fabf43c0607cefe40d831a5fb15f92f81a04b546a878b299939c1895d8a4c829787
diff --git a/sci-misc/foma/foma-0.9.14_alpha.ebuild b/sci-misc/foma/foma-0.9.14_alpha.ebuild
deleted file mode 100644
index 5d300b6bc..000000000
--- a/sci-misc/foma/foma-0.9.14_alpha.ebuild
+++ /dev/null
@@ -1,43 +0,0 @@
-# Copyright 1999-2015 Gentoo Foundation
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=5
-
-MY_P=${P/_alpha/alpha}
-
-DESCRIPTION="Finite state toolkit compatible with Xerox tools"
-HOMEPAGE="http://foma.sf.net/"
-SRC_URI="http://dingo.sbs.arizona.edu/~mhulden/${MY_P}.tar.gz"
-
-LICENSE="GPL-2"
-SLOT="0"
-KEYWORDS="~amd64 ~x86"
-IUSE=""
-
-RDEPEND="
-	sys-libs/libtermcap-compat
-	sys-libs/readline:0="
-DEPEND="${RDEPEND}
-	>=sys-devel/bison-2.3
-	>=sys-devel/flex-2.5.35"
-
-S="${WORKDIR}/${PN}"
-
-src_prepare() {
-	sed \
-		-e "s/^CFLAGS =/CFLAGS = ${CFLAGS} -fPIC/" \
-		-e 's/ltermcap/lcurses/' \
-		-e 's/ldconfig/true/g' \
-		-i Makefile || die
-}
-
-src_compile() {
-	default
-	emake libfoma
-}
-
-src_install() {
-	dobin foma
-	dolib.so libfoma.so.0.9.14
-	dodoc README README.symbols
-}
diff --git a/sci-misc/foma/foma-0.9.16_alpha.ebuild b/sci-misc/foma/foma-0.9.16_alpha.ebuild
deleted file mode 100644
index 01cec152b..000000000
--- a/sci-misc/foma/foma-0.9.16_alpha.ebuild
+++ /dev/null
@@ -1,45 +0,0 @@
-# Copyright 1999-2015 Gentoo Foundation
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=5
-
-MY_P=${P/_alpha/alpha}
-
-DESCRIPTION="Finite state toolkit compatible with Xerox tools"
-HOMEPAGE="http://code.google.com/p/foma/"
-SRC_URI="http://${PN}.googlecode.com/files/${MY_P}.tar.gz"
-
-LICENSE="GPL-2"
-SLOT="0"
-KEYWORDS="~amd64 ~x86"
-IUSE=""
-
-RDEPEND="
-	sys-libs/libtermcap-compat
-	sys-libs/readline:0="
-DEPEND="${RDEPEND}
-	>=sys-devel/bison-2.3
-	>=sys-devel/flex-2.5.35"
-
-S="${WORKDIR}/${PN}"
-
-src_prepare() {
-	sed \
-		-e "s/^CFLAGS =/CFLAGS = ${CFLAGS} -fPIC/" \
-		-e 's/ltermcap/lcurses/' \
-		-e 's/ldconfig/true/g' \
-		-i Makefile || die
-}
-
-src_compile() {
-	default
-	emake libfoma
-}
-
-src_install() {
-	# since install target doesn't have DESTDIR
-	dobin foma flookup cgflookup
-	dolib.so libfoma.so.${PV/_alpha/}
-	doheader foma.h fomalib.h fomalibconf.h
-	dodoc README README.symbols
-}
diff --git a/sci-misc/foma/metadata.xml b/sci-misc/foma/metadata.xml
deleted file mode 100644
index 2d4fb61e6..000000000
--- a/sci-misc/foma/metadata.xml
+++ /dev/null
@@ -1,7 +0,0 @@
-<?xml version="1.0" encoding="UTF-8"?>
-<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
-<pkgmetadata>
-	<maintainer type="person">
-		<email>flammie@gentoo.org</email>
-	</maintainer>
-</pkgmetadata>
diff --git a/sci-misc/hfst/Manifest b/sci-misc/hfst/Manifest
deleted file mode 100644
index cb92aac04..000000000
--- a/sci-misc/hfst/Manifest
+++ /dev/null
@@ -1 +0,0 @@
-DIST hfst-3.3.12.tar.gz 1419137 BLAKE2B c2b7a42080e6e9444406d4f3b672f757ebf66473ba324c9be9478bd8a7736a0396cb4ebf22162afd7cd64a317ed975923cddbc48887d6763963fa9753761a53a SHA512 b4b754767cb750cb420b9c8eafbc33dd89a6deec58012f5a4aa90c0219d7e0737a08215b7f4c3277f40180a7fe970c9ee9aafc8077520d0e49eba398b7d8f269
diff --git a/sci-misc/hfst/hfst-3.3.12.ebuild b/sci-misc/hfst/hfst-3.3.12.ebuild
deleted file mode 100644
index 92d0eb714..000000000
--- a/sci-misc/hfst/hfst-3.3.12.ebuild
+++ /dev/null
@@ -1,34 +0,0 @@
-# Copyright 1999-2017 Gentoo Foundation
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=6
-
-DESCRIPTION="Helsinki Finite State Transducer API and tools"
-HOMEPAGE="http://hfst.sourceforge.net/"
-SRC_URI="mirror://sourceforge/${PN}/${P}.tar.gz"
-
-LICENSE="GPL-3"
-SLOT="0"
-KEYWORDS="~amd64 ~x86"
-IUSE="+openfst sfst foma xml +glib"
-
-RDEPEND="
-	foma? ( >sci-misc/foma-0.9.13 )
-	glib? ( dev-libs/glib:2 )
-	openfst? ( >sci-misc/openfst-1.2 )
-	sfst? ( >sci-misc/sfst-1.3 )
-	xml? ( dev-libs/libxml2:2= dev-cpp/libxmlpp:3.0= )
-"
-DEPEND="${RDEPEND}
-	>=sys-devel/flex-2.5.35
-	sys-devel/bison"
-
-src_configure() {
-	econf \
-		$(use_with openfst) \
-		$(use_with sfst) \
-		$(use_with foma) \
-		$(use_enable xml apertium2fst) \
-		$(use_with glib unicodehandler glib) \
-		--enable-lexc
-}
diff --git a/sci-misc/hfst/metadata.xml b/sci-misc/hfst/metadata.xml
deleted file mode 100644
index 1bda309e1..000000000
--- a/sci-misc/hfst/metadata.xml
+++ /dev/null
@@ -1,31 +0,0 @@
-<?xml version="1.0" encoding="UTF-8"?>
-<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
-<pkgmetadata>
-	<longdescription lang="en">
-Open Source API for FSTs, a set of command line tools, and clones of
-traditional FST-based linguistic morphology tools.
-</longdescription>
-	<use>
-		<flag name="openfst">
-Add optional support for openfst backend library
-(<pkg>sci-misc/openfst</pkg>)
-</flag>
-		<flag name="foma">
-Add optional support for foma backend library
-(<pkg>sci-misc/foma</pkg>)</flag>
-		<flag name="sfst">
-Add optional support for sfst backend library
-(<pkg>sci-misc/sfst</pkg>)
-</flag>
-		<flag name="glib">
-Parse UTF-8 and collate unicode using glib instead of
-homebrewn methods
-</flag>
-		<flag name="xml">
-Include parsers for grammars and formats that require XML support
-</flag>
-	</use>
-	<upstream>
-		<remote-id type="sourceforge">hfst</remote-id>
-	</upstream>
-</pkgmetadata>
diff --git a/sci-misc/irstlm/files/irstlm-6.00.05-doc-obey-docdir.patch b/sci-misc/irstlm/files/irstlm-6.00.05-doc-obey-docdir.patch
new file mode 100644
index 000000000..0b25ead22
--- /dev/null
+++ b/sci-misc/irstlm/files/irstlm-6.00.05-doc-obey-docdir.patch
@@ -0,0 +1,22 @@
+Remove doc/irstlm-manual.pdf from install in --prefix to instead obey --docdir
+
+--- a/doc/Makefile.am
++++ b/doc/Makefile.am
+@@ -1,5 +1,3 @@
+-documentationdir = @prefix@/doc
+-
+ if DOC_COMPILATION
+ 
+ irstlm-manual.pdf: irstlm-manual.tex
+@@ -14,10 +12,6 @@ clean-local:
+ 
+ all: irstlm-manual.pdf
+  
+-dist_documentation_SCRIPTS = irstlm-manual.pdf
++dist_doc_DATA = irstlm-manual.pdf
+ 
+ endif
+-
+-EXTRA_DIST = irstlm-manual.tex 
+-
+-
diff --git a/sci-misc/irstlm/files/irstlm-6.00.05-remove-lib-linking.patch b/sci-misc/irstlm/files/irstlm-6.00.05-remove-lib-linking.patch
new file mode 100644
index 000000000..c0cfcfe32
--- /dev/null
+++ b/sci-misc/irstlm/files/irstlm-6.00.05-remove-lib-linking.patch
@@ -0,0 +1,18 @@
+Remove Makefile.am lib linking operation
+Taken from upstream PR: https://github.com/irstlm-team/irstlm/pull/12
+
+--- a/Makefile.am
++++ b/Makefile.am
+@@ -7,12 +7,3 @@ SUBDIRS = src scripts doc
+ EXTRA_DIST = README RELEASE Copyright
+ 
+ ACLOCAL_AMFLAGS = -I m4
+-
+-LN_S=@LN_S@
+-
+-install-exec-hook:
+-	cd ${exec_prefix}/ && \
+-	  ${LN_S} -n -f lib lib64
+-
+-dist-hook:
+-	rm -rf `find $(distdir)/doc -type d -name .svn`
diff --git a/sci-misc/irstlm/irstlm-6.00.05-r1.ebuild b/sci-misc/irstlm/irstlm-6.00.05-r1.ebuild
new file mode 100644
index 000000000..73786fd4a
--- /dev/null
+++ b/sci-misc/irstlm/irstlm-6.00.05-r1.ebuild
@@ -0,0 +1,38 @@
+# Copyright 1999-2021 Gentoo Authors
+# Distributed under the terms of the GNU General Public License v2
+
+EAPI=8
+
+inherit autotools
+
+DESCRIPTION="A tool to estimate, store, and access very large n-gram language models"
+HOMEPAGE="https://hlt-mt.fbk.eu/technologies/irstlm"
+SRC_URI="https://github.com/irstlm-team/${PN}/archive/v${PV}.tar.gz -> ${P}.tar.gz"
+
+LICENSE="LGPL-3"
+SLOT="0"
+KEYWORDS="~amd64"
+IUSE="doc static-libs"
+
+BDEPEND="doc? ( app-text/texlive[extra] )"
+
+PATCHES=(
+	"${FILESDIR}"/${P}-remove-lib-linking.patch
+	"${FILESDIR}"/${P}-doc-obey-docdir.patch
+)
+
+src_prepare() {
+	default
+	# Remove AM_CXXFLAGS that are breaking the package or should not be there
+	# Bug: https://bugs.gentoo.org/755473
+	sed -e 's/-static -isystem\/usr\/include -W //' -i src/Makefile.am || die
+	# Needed for doc
+	cp "${S}/doc/RELEASE" "${S}/RELEASE.tex" || die
+	eautoreconf
+}
+
+src_configure() {
+	econf \
+		$(use_enable static-libs static) \
+		$(use_enable doc)
+}
diff --git a/sci-misc/irstlm/irstlm-6.00.05.ebuild b/sci-misc/irstlm/irstlm-6.00.05.ebuild
index 49fb5a8c4..de884e3c3 100644
--- a/sci-misc/irstlm/irstlm-6.00.05.ebuild
+++ b/sci-misc/irstlm/irstlm-6.00.05.ebuild
@@ -1,7 +1,7 @@
-# Copyright 1999-2016 Gentoo Foundation
+# Copyright 1999-2021 Gentoo Authors
 # Distributed under the terms of the GNU General Public License v2
 
-EAPI=6
+EAPI=7
 
 inherit autotools
 
@@ -15,5 +15,5 @@ KEYWORDS="~amd64"
 
 src_prepare() {
 	eautoreconf
-	eapply_user
+	default
 }
diff --git a/sci-misc/jwnl/Manifest b/sci-misc/jwnl/Manifest
index b63c83247..6ec349e7a 100644
--- a/sci-misc/jwnl/Manifest
+++ b/sci-misc/jwnl/Manifest
@@ -1,2 +1 @@
-DIST jwnl13rc3.zip 640112 BLAKE2B ab69cc0cf848de3fed20231a8e2d12539c13c487e3538997072415270a5d03c1e998530f1b10b97161254e3e6867bbde8ed31fce6d864f03cf544f196b5038a3 SHA512 655497849698518bffb651f67fd2e40546ff5700b4ffa3fa7ee63125b4523a4720f5644e8f06266072342ee583ad5383f5e0cf01fda23bfe90419b06438ef697
-DIST jwnl13rc3_src.zip 109993 BLAKE2B f5bdb5bb87cf70aa3640273dd8ee410173d1c4be0daa06a531810f80668af655ca2a866fab9860205ba2ca9dd944ceba8bcba32f522465d0ceb5af5ddd890201 SHA512 89524c349a50fae09a8dcbc6fa9ba03227200eb389ba8903b7d3a2ca678e5bcd4c25ae20da67728dac8f563b9f535aadb6ecdd838c79961c5788148951a386e5
+DIST jwnl14-rc2.zip 1554168 BLAKE2B d73747b161f0a1183d00f8953e7317783b88d6da99d0829f9d3912862b6e6e6953265c49ed4764df2dae7703750881765fafe50455ea8ae5ce6fe56de1b3a51b SHA512 2d279803489e1259563f671efa707902e85b338851df69a73b5f863fc0b520fb85aab4ce41e2781cab8dccfb5cf8c320150f54f798022e186945584d7c5c70d9
diff --git a/sci-misc/jwnl/jwnl-1.3_rc3.ebuild b/sci-misc/jwnl/jwnl-1.3_rc3.ebuild
deleted file mode 100644
index abf81be22..000000000
--- a/sci-misc/jwnl/jwnl-1.3_rc3.ebuild
+++ /dev/null
@@ -1,47 +0,0 @@
-# Copyright 1999-2014 Gentoo Foundation
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=5
-
-inherit eutils java-pkg-2 java-utils-2 versionator
-
-MY_P=${PN}$(delete_all_version_separators)
-
-DESCRIPTION="Java interface to WordNet dictionary data"
-HOMEPAGE="http://jwordnet.sf.net"
-SRC_URI="
-	mirror://sourceforge/jwordnet/${MY_P}_src.zip
-	mirror://sourceforge/jwordnet/${MY_P}.zip"
-
-LICENSE="BSD"
-SLOT="0"
-KEYWORDS="~x86"
-IUSE=""
-
-COMMON_DEP="dev-java/commons-logging"
-DEPEND=">=virtual/jdk-1.4
-	${COMMON_DEP}"
-RDEPEND=">=virtual/jre-1.4
-	${COMMON_DEP}"
-
-S="${WORKDIR}"
-
-src_prepare() {
-	rm -v commons-logging.jar jwnl.jar || die
-}
-
-src_compile() {
-	# picked up from dev-java/ant-eclipse-ecj
-	ejavac -classpath "$(java-pkg_getjars commons-logging)" \
-		`find net -name '*.java'` || die "ejavac failed"
-	find net -name '*.class' -o -name '*.properties' | \
-		xargs jar cf "${S}/${PN}.jar" || die "jar failed"
-}
-
-src_install() {
-	java-pkg_dojar ${PN}.jar utilities.jar
-	insinto /usr/share/${PN}
-	doins create.sql database_properties.xml file_properties.xml \
-		jwnl_properties.dtd jwnl_properties.xsd map_properties.xml
-	dodoc changes.txt
-}
diff --git a/sci-misc/jwnl/jwnl-1.4_rc2.ebuild b/sci-misc/jwnl/jwnl-1.4_rc2.ebuild
new file mode 100644
index 000000000..7c5137bca
--- /dev/null
+++ b/sci-misc/jwnl/jwnl-1.4_rc2.ebuild
@@ -0,0 +1,48 @@
+# Copyright 1999-2021 Gentoo Authors
+# Distributed under the terms of the GNU General Public License v2
+
+EAPI=7
+
+inherit java-pkg-2
+
+MY_P=${PN}${PV//.}
+
+DESCRIPTION="Java interface to WordNet dictionary data"
+HOMEPAGE="https://sourceforge.net/projects/jwordnet/"
+SRC_URI="https://downloads.sourceforge.net/jwordnet/${MY_P//_rc/-rc}.zip"
+
+LICENSE="BSD"
+SLOT="0"
+KEYWORDS="~amd64 ~x86"
+
+COMMON_DEP="
+	dev-java/commons-logging:0
+	dev-java/junit:4
+"
+DEPEND=">=virtual/jdk-1.7
+	${COMMON_DEP}"
+RDEPEND=">=virtual/jre-1.7
+	${COMMON_DEP}"
+BDEPEND="app-arch/unzip"
+
+S="${WORKDIR}/${MY_P//_rc/-rc}"
+
+src_prepare() {
+	rm jwnl.jar lib/commons-logging.jar lib/junit-4.1.jar || die
+	default
+}
+
+src_compile() {
+	# picked up from dev-java/ant-eclipse-ecj
+	ejavac -classpath "$(java-pkg_getjars commons-logging):$(java-pkg_getjars junit:4)" \
+		`find -name '*.java'` || die "ejavac failed"
+	find -name '*.class' -o -name '*.properties' | \
+		xargs jar cf "${S}/${PN}.jar" || die "jar failed"
+}
+
+src_install() {
+	java-pkg_dojar ${PN}.jar
+	insinto /usr/share/${PN}
+	doins -r sql config
+	dodoc changes.txt
+}
diff --git a/sci-misc/jwnl/metadata.xml b/sci-misc/jwnl/metadata.xml
index 09c9fed59..8f0d2663f 100644
--- a/sci-misc/jwnl/metadata.xml
+++ b/sci-misc/jwnl/metadata.xml
@@ -4,10 +4,6 @@
 	<maintainer type="person">
 		<email>flammie@gentoo.org</email>
 	</maintainer>
-	<longdescription>
-Java based programming interface for accessing wordnet style dictionary
-data.
-</longdescription>
 	<upstream>
 		<remote-id type="sourceforge">jwordnet</remote-id>
 	</upstream>
diff --git a/sci-misc/kaldi/Manifest b/sci-misc/kaldi/Manifest
deleted file mode 100644
index 0aa4d1beb..000000000
--- a/sci-misc/kaldi/Manifest
+++ /dev/null
@@ -1,2 +0,0 @@
-DIST kaldi-0_p20160628.tar.gz 8280371 SHA256 c14b88921fc1d80a0285df77670013c4ea568e1d9506e7a7f3532115061ef145 SHA512 31132feb3a3d971a55d4e5f3c37e5ac4bf56c527bb3aa1381e4bb6e149e542ec9f3117943515b57e75c1f7c51db415f0436f7f4d801babd0dc27fd521b939e76 WHIRLPOOL 56145409bf66814526c2027bac955ef3abfdad35ee0e3b6cf1bafa24bcb762003ae40be04b1c1b3ca41873125c31214cc5a17e8e10e3c1a483c0518f6c709f33
-DIST kaldi-5.1.65.tar.gz 9177937 SHA256 8b3f60cdf62c8f80b56ed0f5e3da90477728941a5193bae9d9f198b9c081c4c1 SHA512 731e76eb387977a303cf4b466381705682253adfe7c32bb82b75e1eea86ce236a224e2bb217cc0654728f6648a7be5c902bca3826c3e6e760317e46f6ca82448 WHIRLPOOL 1088a64b1b9e265591c9707567f8e6e1c1feb358ffad5348f4a4be2ee3885a232f91b3572cfefdff9b02af5dc5e6f32b96ec4704b381b7eacd4f749a8d73849e
diff --git a/sci-misc/kaldi/files/Makefile.0d5e4b1.patch b/sci-misc/kaldi/files/Makefile.0d5e4b1.patch
deleted file mode 100644
index 80b9862c6..000000000
--- a/sci-misc/kaldi/files/Makefile.0d5e4b1.patch
+++ /dev/null
@@ -1,45 +0,0 @@
---- src/Makefile.orig	2017-03-03 01:33:22.000000000 +0100
-+++ src/Makefile	2017-03-03 18:06:59.912864196 +0100
-@@ -32,7 +32,6 @@
- # Reset the default goal, so that the all target will become default
- .DEFAULT_GOAL :=
- all: 
--	$(MAKE) checkversion 
- 	$(MAKE) kaldi.mk 
- 	$(MAKE) mklibdir
- 	$(MAKE) subdirs
-@@ -52,18 +51,6 @@
- 	@true
- endif
- 
--.PHONY: checkversion
--checkversion:
--ifeq ($(shell ./configure --version),$(CONFIGURE_VERSION))
--	@echo "The version of configure script matches kaldi.mk version. Good."
--else
--	@echo ""
--	@echo "The kaldi.mk file was generated using a different version of configure script. Please rerun the configure again"
--	@test -f ./kaldi.mk && echo  "Hint: Previous configure command line: " && head -n 2 ./kaldi.mk | grep configure | sed 's/^# *//g'
--	@echo ""
--	@false
--endif
--
- biglib: $(SUBDIRS_LIB)
- ifeq ($(KALDI_FLAVOR), dynamic)
- ifeq ($(shell uname), Darwin)
-@@ -136,6 +123,15 @@
- ext_depend: check_portaudio
- 	-for x in $(EXT_SUBDIRS); do $(MAKE) -C $$x depend; done
- 
-+print-binfiles: $(addsuffix /print-binfiles, $(SUBDIRS))
-+
-+%/print-binfiles:
-+	@$(MAKE) --no-print-directory -C $(dir $@) print-binfiles
-+
-+print-libfiles: $(addsuffix /print-libfiles, $(SUBDIRS))
-+
-+%/print-libfiles:
-+	@$(MAKE) --no-print-directory -C $(dir $@) print-libfiles
- 
- .PHONY: $(SUBDIRS)
- $(SUBDIRS) : mklibdir
diff --git a/sci-misc/kaldi/files/Makefile.patch b/sci-misc/kaldi/files/Makefile.patch
deleted file mode 100644
index 0556e2531..000000000
--- a/sci-misc/kaldi/files/Makefile.patch
+++ /dev/null
@@ -1,60 +0,0 @@
---- src/Makefile.orig	2015-11-06 18:43:31.000000000 -0400
-+++ src/Makefile	2015-11-17 20:15:14.452502675 -0400
-@@ -30,7 +30,7 @@
- 
- # Reset the default goal, so that the all target will become default
- .DEFAULT_GOAL :=
--all: checkversion test_dependencies kaldi.mk mklibdir $(SUBDIRS)
-+all: kaldi.mk mklibdir $(SUBDIRS)
- 	-echo Done
- 
- mklibdir:
-@@ -45,14 +45,6 @@
- 	@true
- endif
- 
--.PHONY: checkversion
--checkversion:
--ifeq ($(shell ./configure --version),$(CONFIGURE_VERSION))
--	@echo "The version of configure script matches kaldi.mk version. Good."
--else
--	$(error The kaldi.mk file was generated using a different version of configure script. Run the configure script again.)
--endif
--
- biglib: $(SUBDIRS_LIB)
- ifeq ($(KALDI_FLAVOR), dynamic)
- ifeq ($(shell uname), Darwin)
-@@ -88,16 +80,6 @@
- ext: test_dependencies ext_depend $(SUBDIRS) $(EXT_SUBDIRS)
- 	-echo Done
- 
--ifndef OPENFST_VER
--$(error Please rerun configure: OPENFST_VER is not defined, likely kaldi.mk was produced by older configure script.)
--endif
--# Note: OPENFST_VER is determined by configure and added to kaldi.mk
--OPENFST_VER_NUM := $(shell echo $(OPENFST_VER) | sed 's/\./ /g' | xargs printf "%d%02d%02d")
--test_dependencies:
--ifeq ("$(shell expr $(OPENFST_VER_NUM) \< 10302)","1")
--	$(error OpenFst $(OPENFST_VER) is not supported. You now need OpenFst >= 1.3.2.)
--endif
--
- check_portaudio:
- 	@[ -d ../tools/portaudio ] || ( cd ../tools;  ./install_portaudio.sh )
- 
-@@ -131,6 +113,16 @@
- ext_depend: check_portaudio
- 	-for x in $(EXT_SUBDIRS); do $(MAKE) -C $$x depend; done
- 
-+print-binfiles: $(addsuffix /print-binfiles, $(SUBDIRS))
-+
-+%/print-binfiles:
-+	@$(MAKE) --no-print-directory -C $(dir $@) print-binfiles
-+
-+print-libfiles: $(addsuffix /print-libfiles, $(SUBDIRS))
-+
-+%/print-libfiles:
-+	@$(MAKE) --no-print-directory -C $(dir $@) print-libfiles
-+
- 
- .PHONY: $(SUBDIRS)
- $(SUBDIRS) : mklibdir
diff --git a/sci-misc/kaldi/files/default_rules.mk.96eec2b.patch b/sci-misc/kaldi/files/default_rules.mk.96eec2b.patch
deleted file mode 100644
index 89a3103ba..000000000
--- a/sci-misc/kaldi/files/default_rules.mk.96eec2b.patch
+++ /dev/null
@@ -1,30 +0,0 @@
---- src/makefiles/default_rules.mk.orig	2017-03-03 01:33:22.000000000 +0100
-+++ src/makefiles/default_rules.mk	2017-03-03 18:24:54.159740235 +0100
-@@ -12,7 +12,7 @@
-     ifdef LIBNAME
-       LIBFILE = lib$(LIBNAME).so
-     endif
--    LDFLAGS += -Wl,-rpath=$(shell readlink -f $(KALDILIBDIR))
-+    LDFLAGS += -L. $(foreach dep,$(ADDLIBS), -L$(dir $(dep)))
-     EXTRA_LDLIBS += $(foreach dep,$(ADDLIBS), $(dir $(dep))lib$(notdir $(basename $(dep))).so)
-   else  # Platform not supported
-     $(error Dynamic libraries not supported on this platform. Run configure with --static flag.)
-@@ -82,7 +82,7 @@
- 	for x in $(TESTFILES); do	\
- 	  printf "Running $$x ...";	\
-       timestamp1=$$(date +"%s"); \
--	  ./$$x >$$x.testlog 2>&1;	\
-+	  LD_LIBRARY_PATH=$(KALDILIBDIR):${LD_LIBRARY_PATH} ./$$x >$$x.testlog 2>&1;	\
-       ret=$$? \
-       timestamp2=$$(date +"%s"); \
-       time_taken=$$[timestamp2-timestamp1]; \
-@@ -121,3 +121,9 @@
- # removing automatic making of "depend" as it's quite slow.
- #.depend.mk: depend
- -include .depend.mk
-+
-+print-binfiles:
-+	@echo $(addprefix $(shell pwd)/, $(BINFILES))
-+
-+print-libfiles:
-+	@echo $(addsuffix .so, $(addprefix $(shell pwd)/lib, $(LIBNAME)))
diff --git a/sci-misc/kaldi/files/default_rules.mk.a7d9824.patch b/sci-misc/kaldi/files/default_rules.mk.a7d9824.patch
deleted file mode 100644
index a51fd2035..000000000
--- a/sci-misc/kaldi/files/default_rules.mk.a7d9824.patch
+++ /dev/null
@@ -1,30 +0,0 @@
---- src/makefiles/default_rules.mk.orig	2015-11-06 18:43:31.000000000 -0400
-+++ src/makefiles/default_rules.mk	2015-11-09 18:42:33.609774157 -0400
-@@ -14,7 +14,7 @@
-         LIBFILE = lib$(LIBNAME).so
-         #LDLIBS  += -l$(LIBNAME)
-       endif
--      LDFLAGS += -Wl,-rpath=$(shell readlink -f $(KALDILIBDIR)) -L.
-+      LDFLAGS += -L.
-       LDFLAGS += $(foreach dep,$(ADDLIBS), -L$(dir $(dep)) )
-       XDEPENDS = $(foreach dep,$(ADDLIBS), $(dir $(dep))/lib$(notdir $(basename $(dep))).so )
-     else  # Platform not supported
-@@ -75,7 +75,7 @@
- 	@{ result=0;			\
- 	for x in $(TESTFILES); do	\
- 	  printf "Running $$x ...";	\
--	  ./$$x >$$x.testlog 2>&1;	\
-+	  LD_LIBRARY_PATH=$(KALDILIBDIR):${LD_LIBRARY_PATH} ./$$x >$$x.testlog 2>&1;	\
- 	  if [ $$? -ne 0 ]; then	\
- 	    echo "... FAIL $$x";	\
- 	    result=1;			\
-@@ -99,3 +99,9 @@
- # removing automatic making of "depend" as it's quite slow.
- #.depend.mk: depend
- -include .depend.mk
-+
-+print-binfiles:
-+	@echo $(addprefix $(shell pwd)/, $(BINFILES))
-+
-+print-libfiles:
-+	@echo $(addsuffix .so, $(addprefix $(shell pwd)/lib, $(LIBNAME)))
diff --git a/sci-misc/kaldi/kaldi-0_p20160628.ebuild b/sci-misc/kaldi/kaldi-0_p20160628.ebuild
deleted file mode 100644
index 520d7cfa4..000000000
--- a/sci-misc/kaldi/kaldi-0_p20160628.ebuild
+++ /dev/null
@@ -1,135 +0,0 @@
-# Copyright 1999-2016 Gentoo Foundation
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=6
-
-inherit toolchain-funcs cuda flag-o-matic
-
-COMMIT_ID="16e69f1aacce8ad0665d2b6666c053b1421a9e91"
-DESCRIPTION="A toolkit for speech recognition"
-HOMEPAGE="http://kaldi-asr.org/"
-SRC_URI="https://github.com/kaldi-asr/kaldi/archive/${COMMIT_ID}.tar.gz -> ${P}.tar.gz"
-
-S=${WORKDIR}/${PN}-${COMMIT_ID}/src
-
-LICENSE="Apache-2.0"
-SLOT="0"
-IUSE="cuda doc speex test"
-KEYWORDS="~amd64"
-
-RDEPEND="
-	speex? ( media-libs/speex )
-	virtual/cblas
-	virtual/lapack
-	virtual/lapacke
-	<sci-misc/openfst-1.5.0
-	cuda? ( dev-util/nvidia-cuda-toolkit )"
-DEPEND="${RDEPEND}
-	virtual/pkgconfig
-	doc? ( app-doc/doxygen )"
-
-# We need write acccess /dev/nvidiactl, /dev/nvidia0 and /dev/nvidia-uvm and the portage
-# user is (usually) not in the video group
-RESTRICT="cuda? ( userpriv )"
-
-pkg_pretend() {
-	local cblas_provider=$(eselect cblas show)
-
-	if [[ ! ${cblas_provider} =~ (atlas|mkl|openblas) ]]; then
-		die "Build with '${cblas_provider}' CBLAS is not supported"
-	fi
-}
-
-src_prepare() {
-	eapply \
-		"${FILESDIR}"/Makefile.patch \
-		"${FILESDIR}"/default_rules.mk.a7d9824.patch
-	eapply_user
-
-	use cuda && cuda_src_prepare
-}
-
-src_configure() {
-	append-cxxflags \
-		-DHAVE_EXECINFO_H=1 \
-		-DHAVE_CXXABI_H \
-		-DHAVE_OPENFST_GE_10400 \
-		-std=c++11 \
-		-Wall \
-		-I.. \
-		-pthread \
-		-Wno-sign-compare \
-		-Wno-unused-local-typedefs \
-		-Winit-self \
-		-rdynamic \
-		-fPIC \
-		$($(tc-getPKG_CONFIG) --cflags cblas) \
-		$($(tc-getPKG_CONFIG) --cflags lapack)
-
-	append-libs \
-		-lfst \
-		-lm \
-		-lpthread \
-		-ldl \
-		$($(tc-getPKG_CONFIG) --libs cblas) \
-		$($(tc-getPKG_CONFIG) --libs lapack)
-
-	local cblas_provider=$(eselect cblas show)
-
-	if [[ ${cblas_provider} =~ atlas ]]; then
-		append-cxxflags -DHAVE_ATLAS
-	elif [[ ${cblas_provider} =~ mkl ]]; then
-		append-cxxflags -DHAVE_MKL
-	elif [[ ${cblas_provider} =~ openblas ]]; then
-		append-cxxflags -DHAVE_OPENBLAS $($(tc-getPKG_CONFIG) --cflags lapacke)
-	fi
-
-	use test || append-cxxflags -DNDEBUG
-
-	if use speex; then
-		append-cxxflags -DHAVE_SPEEX
-		append-libs -lspeex
-	fi
-
-	cat <<-EOF > kaldi.mk
-		KALDI_FLAVOR := dynamic
-		KALDILIBDIR := "${S}"/lib
-		CC = $(tc-getCXX)
-		RANLIB = $(tc-getRANLIB)
-		LDLIBS = ${LIBS}
-		DOUBLE_PRECISION = 0
-	EOF
-
-	if use cuda; then
-		cat <<-EOF >> kaldi.mk
-			CUDA = true
-			CUDATKDIR = "${EPREFIX}"/opt/cuda
-			CUDA_ARCH :=
-			CUDA_ARCH +=
-		EOF
-		cat makefiles/cuda_64bit.mk >> kaldi.mk
-		sed -i \
-			-e "s:CUDA_FLAGS = -g:CUDA_FLAGS = ${NVCCFLAGS}:" \
-			kaldi.mk || die "sed unix/kaldi.mk failed"
-	fi
-}
-
-src_compile() {
-	default
-	use doc && doxygen
-}
-
-src_test() {
-	if use cuda; then
-		addwrite /dev/nvidiactl
-		addwrite /dev/nvidia0
-		addwrite /dev/nvidia-uvm
-	fi
-	default
-}
-
-src_install() {
-	dolib.so $(make print-libfiles)
-	dobin $(make print-binfiles)
-	use doc && dodoc -r html
-}
diff --git a/sci-misc/kaldi/kaldi-5.1.65.ebuild b/sci-misc/kaldi/kaldi-5.1.65.ebuild
deleted file mode 100644
index 4304f695c..000000000
--- a/sci-misc/kaldi/kaldi-5.1.65.ebuild
+++ /dev/null
@@ -1,146 +0,0 @@
-# Copyright 1999-2017 Gentoo Foundation
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=6
-
-inherit toolchain-funcs cuda flag-o-matic
-
-COMMIT_ID="9e06caa1fb0306898632c6fa3ad67571c4d06cf5"
-DESCRIPTION="A toolkit for speech recognition"
-HOMEPAGE="http://kaldi-asr.org/"
-SRC_URI="https://github.com/kaldi-asr/kaldi/archive/${COMMIT_ID}.tar.gz -> ${P}.tar.gz"
-
-LICENSE="Apache-2.0"
-SLOT="0"
-KEYWORDS="~amd64"
-IUSE="cuda doc double-precision speex test"
-REQUIRED_USE="double-precision? ( !speex )"
-
-RDEPEND="
-	>=sci-misc/openfst-1.6.0
-	virtual/cblas
-	virtual/lapack
-	virtual/lapacke
-	cuda? ( dev-util/nvidia-cuda-toolkit )
-	speex? ( media-libs/speex )"
-DEPEND="${RDEPEND}
-	virtual/pkgconfig
-	doc? ( app-doc/doxygen )"
-
-S=${WORKDIR}/${PN}-${COMMIT_ID}/src
-
-PATCHES=(
-	"${FILESDIR}"/Makefile.0d5e4b1.patch
-	"${FILESDIR}"/default_rules.mk.96eec2b.patch
-)
-
-# We need write acccess /dev/nvidiactl, /dev/nvidia0 and /dev/nvidia-uvm and the portage
-# user is (usually) not in the video group
-RESTRICT="cuda? ( userpriv )"
-
-pkg_pretend() {
-	local cblas_provider=$(eselect cblas show)
-
-	if [[ ! ${cblas_provider} =~ (atlas|openblas) ]]; then
-		die "Build with '${cblas_provider}' CBLAS is not supported"
-	fi
-}
-
-src_prepare() {
-	default
-	use cuda && cuda_src_prepare
-}
-
-src_configure() {
-	cat <<-EOF > base/version.h
-		#define KALDI_VERSION "${PV}-${COMMIT_ID:0:5}"
-		#define KALDI_GIT_HEAD "${COMMIT_ID}"
-	EOF
-
-	echo "true" > base/get_version.sh
-
-	append-cxxflags \
-		$($(tc-getPKG_CONFIG) --cflags cblas) \
-		$($(tc-getPKG_CONFIG) --cflags lapack)
-
-	append-libs \
-		$($(tc-getPKG_CONFIG) --libs cblas) \
-		$($(tc-getPKG_CONFIG) --libs lapack)
-
-	use test || append-cppflags -DNDEBUG
-
-	if use speex; then
-		append-cppflags -DHAVE_SPEEX
-		append-libs -lspeex
-	fi
-
-	cat <<-EOF > kaldi.mk
-		KALDI_FLAVOR := dynamic
-		KALDILIBDIR := "${S}"/lib
-		CXX = $(tc-getCXX)
-		AR = $(tc-getAR)
-		AS = $(tc-getAS)
-		RANLIB = $(tc-getRANLIB)
-		DOUBLE_PRECISION = $(usex double-precision 1 0)
-		OPENFSTINC = "."
-		OPENFSTLIBS = -lfst
-	EOF
-
-	local cblas_provider=$(eselect cblas show)
-
-	if [[ ${cblas_provider} =~ atlas ]]; then
-		cat <<-EOF >> kaldi.mk
-			ATLASINC = "."
-			ATLASLIBS = -L.
-		EOF
-
-		cat makefiles/linux_atlas.mk >> kaldi.mk
-	elif [[ ${cblas_provider} =~ openblas ]]; then
-		append-cxxflags $($(tc-getPKG_CONFIG) --cflags lapacke)
-
-		cat <<-EOF >> kaldi.mk
-			OPENBLASINC = "."
-			OPENBLASLIBS = -L.
-		EOF
-
-		cat makefiles/linux_openblas.mk >> kaldi.mk
-	fi
-
-	cat <<-EOF >> kaldi.mk
-		CXXFLAGS += ${CXXFLAGS}
-		LDLIBS += ${LIBS}
-	EOF
-
-	if use cuda; then
-		cat <<-EOF >> kaldi.mk
-			CUDA = true
-			CUDATKDIR = "${EPREFIX}"/opt/cuda
-			CUDA_ARCH :=
-			CUDA_ARCH +=
-		EOF
-		cat makefiles/cuda_64bit.mk >> kaldi.mk
-		sed -i \
-			-e "s:CUDA_FLAGS = -g:CUDA_FLAGS = ${NVCCFLAGS}:" \
-			kaldi.mk || die "sed unix/kaldi.mk failed"
-	fi
-}
-
-src_compile() {
-	default
-	use doc && doxygen
-}
-
-src_test() {
-	if use cuda; then
-		addwrite /dev/nvidiactl
-		addwrite /dev/nvidia0
-		addwrite /dev/nvidia-uvm
-	fi
-	default
-}
-
-src_install() {
-	dolib.so $(make print-libfiles)
-	dobin $(make print-binfiles)
-	use doc && dodoc -r html
-}
diff --git a/sci-misc/kaldi/metadata.xml b/sci-misc/kaldi/metadata.xml
deleted file mode 100644
index df4524e1f..000000000
--- a/sci-misc/kaldi/metadata.xml
+++ /dev/null
@@ -1,24 +0,0 @@
-<?xml version="1.0" encoding="UTF-8"?>
-<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
-<pkgmetadata>
-	<maintainer type="person">
-		<email>pavel.a.denisov@gmail.com</email>
-		<name>Pavel Denisov</name>
-	</maintainer>
-	<longdescription lang="en">
-Kaldi is a toolkit for speech recognition written
-in C++ and licensed under the Apache License v2.0.
-Kaldi is intended for use by speech recognition researchers.
-</longdescription>
-	<upstream>
-		<remote-id type="github">kaldi-asr/kaldi</remote-id>
-	</upstream>
-	<use>
-		<flag name="cuda">
-Build with CUDA support.
-</flag>
-		<flag name="double-precision">
-Build in double precision mode.
-</flag>
-	</use>
-</pkgmetadata>
diff --git a/sci-misc/kotus-sanalista/Manifest b/sci-misc/kotus-sanalista/Manifest
deleted file mode 100644
index 5c547bd4c..000000000
--- a/sci-misc/kotus-sanalista/Manifest
+++ /dev/null
@@ -1 +0,0 @@
-DIST kotus-sanalista-v1-r1.tar.bz2 461303 BLAKE2B ae86eaee7b08a40a7f204c39c8fa7465f452e5bc683eae1e894642eb6463c5ce87458e26c41db0b0724a679497f5997fc921176b91b330ffe7e06ffb873f2940 SHA512 73b870c619511424c52b9984b3d4d3f5aa3e638d837c4f9dccf49d646fc1630aa1b8fa2e7685b5ff754b92450b2568b73948bc6b0cc60eb3f07dc76a692dda4d
diff --git a/sci-misc/kotus-sanalista/kotus-sanalista-1-r1.ebuild b/sci-misc/kotus-sanalista/kotus-sanalista-1-r1.ebuild
deleted file mode 100644
index e83251299..000000000
--- a/sci-misc/kotus-sanalista/kotus-sanalista-1-r1.ebuild
+++ /dev/null
@@ -1,20 +0,0 @@
-# Copyright 1999-2014 Gentoo Foundation
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=5
-
-MY_P=${PN}-v${PVR}
-
-DESCRIPTION="Finnish dictionary word list"
-HOMEPAGE="http://home.gna.org/omorfi/"
-SRC_URI="http://download.gna.org/omorfi/${MY_P}.tar.bz2"
-
-LICENSE="GPL-3"
-SLOT="0"
-KEYWORDS="~x86"
-IUSE=""
-
-DEPEND="dev-java/saxon"
-RDEPEND=""
-
-S="${WORKDIR}/${MY_P}"
diff --git a/sci-misc/kotus-sanalista/metadata.xml b/sci-misc/kotus-sanalista/metadata.xml
deleted file mode 100644
index cfcdc4ea3..000000000
--- a/sci-misc/kotus-sanalista/metadata.xml
+++ /dev/null
@@ -1,12 +0,0 @@
-<?xml version="1.0" encoding="UTF-8"?>
-<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
-<pkgmetadata>
-	<maintainer type="person">
-		<email>flammie@gentoo.org</email>
-	</maintainer>
-	<longdescription lang="en">
-Kotus-sanalista is an XML list of Finnish words dictionary forms and
-morphological data. It was released by Research Institute of Languages in
-Finland.
-</longdescription>
-</pkgmetadata>
diff --git a/sci-misc/mitlm/Manifest b/sci-misc/mitlm/Manifest
index f0acc3be4..1ef6f8edd 100644
--- a/sci-misc/mitlm/Manifest
+++ b/sci-misc/mitlm/Manifest
@@ -1 +1 @@
-DIST mitlm-0.4.1.tar.gz 460787 BLAKE2B b7a175b0185d8370e1ff5f8e5130ca2678aa6c31b29b360f5d4b15f95ef2a30b645d1c46c9dddc11f4a5fcf3048cebf78d685283ef17d57a47c192b62189c452 SHA512 11b217473ea41197838ed86acdc9ea1f264e077e00d4b2131ddae9121096145292b0b01d8a8300be4e2aa2ff09563fe66307a31278cfbfbd0d8f36ffc4b8624c
+DIST mitlm-0.4.2.tar.xz 321508 BLAKE2B c57eb92d0df3a816c9feb967d715c69b0ee56fb480a098869ad7f621367eae780b754761081455eb5520c71a956bc50b93ecc764b20035553e45e592a38f1ee5 SHA512 8e5100f8c564eb47a8d008f129c17affbea6b2cdd65a48e44abdc2c0e5ee1413cd31da8afca5b5971ba446092311eea35eb6ef71f9cd51b86d214427fc427d80
diff --git a/sci-misc/mitlm/mitlm-0.4.1.ebuild b/sci-misc/mitlm/mitlm-0.4.1.ebuild
deleted file mode 100644
index 9b70b4bb8..000000000
--- a/sci-misc/mitlm/mitlm-0.4.1.ebuild
+++ /dev/null
@@ -1,19 +0,0 @@
-# Copyright 1999-2016 Gentoo Foundation
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=5
-
-inherit autotools
-
-DESCRIPTION="Tools designed for efficient estimation of statistical n-gram language models"
-HOMEPAGE="https://github.com/mitlm/mitlm"
-SRC_URI="https://github.com/${PN}/${PN}/releases/download/v${PV}/${PN}_${PV}.tar.gz -> ${P}.tar.gz"
-
-LICENSE="MIT"
-SLOT="0"
-KEYWORDS="~amd64 ~x86"
-
-src_prepare() {
-	echo "m4_ifdef([AM_PROG_AR], [AM_PROG_AR])" >> configure.ac
-	eautoreconf
-}
diff --git a/sci-misc/mitlm/mitlm-0.4.2.ebuild b/sci-misc/mitlm/mitlm-0.4.2.ebuild
new file mode 100644
index 000000000..00e8ea63b
--- /dev/null
+++ b/sci-misc/mitlm/mitlm-0.4.2.ebuild
@@ -0,0 +1,20 @@
+# Copyright 1999-2021 Gentoo Authors
+# Distributed under the terms of the GNU General Public License v2
+
+EAPI=7
+
+inherit autotools
+
+DESCRIPTION="Tools designed for efficient estimation of statistical n-gram language models"
+HOMEPAGE="https://github.com/mitlm/mitlm"
+SRC_URI="https://github.com/${PN}/${PN}/releases/download/v${PV}/${P}.tar.xz"
+
+LICENSE="MIT"
+SLOT="0"
+KEYWORDS="~amd64 ~x86"
+
+src_prepare() {
+	default
+	echo "m4_ifdef([AM_PROG_AR], [AM_PROG_AR])" >> configure.ac
+	eautoreconf
+}
diff --git a/sci-misc/nltk/Manifest b/sci-misc/nltk/Manifest
deleted file mode 100644
index 5dd7cc42d..000000000
--- a/sci-misc/nltk/Manifest
+++ /dev/null
@@ -1 +0,0 @@
-DIST nltk-2.0.4.tar.gz 2066069 SHA256 a5821642e15e8d20dd715d4ff37c0466fe2b28735baf11d0f445caea9e07a239 SHA512 93dea108759e53c52dc6128c556f4926b9983061473771aba941afcf9dc3a19d8a6f82322eea5a923eefe40be14a441207940f27d472cff4149740d641c3c8a8 WHIRLPOOL 8ea2afaf3246e579c8679dca3ea3d03a164815cb0d944e0ef2cbb8c8b482719f08bc7effe578715bcf0a563a79d3268a765d6da7f468396cbf8d15d21d5a2a60
diff --git a/sci-misc/nltk/metadata.xml b/sci-misc/nltk/metadata.xml
deleted file mode 100644
index 844f6974f..000000000
--- a/sci-misc/nltk/metadata.xml
+++ /dev/null
@@ -1,14 +0,0 @@
-<?xml version="1.0" encoding="UTF-8"?>
-<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
-<pkgmetadata>
-	<maintainer type="person">
-		<email>flammie@gentoo.org</email>
-	</maintainer>
-	<longdescription>
-NLTK is collection of natural language tools written in python language. It
-also contains huge corpora.
-</longdescription>
-	<upstream>
-		<remote-id type="github">nltk/nltk</remote-id>
-	</upstream>
-</pkgmetadata>
diff --git a/sci-misc/nltk/nltk-2.0.4.ebuild b/sci-misc/nltk/nltk-2.0.4.ebuild
deleted file mode 100644
index de413e07e..000000000
--- a/sci-misc/nltk/nltk-2.0.4.ebuild
+++ /dev/null
@@ -1,28 +0,0 @@
-# Copyright 1999-2014 Gentoo Foundation
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=5
-
-PYTHON_COMPAT=( python2_7 )
-PYTHON_REQ_USE="tk"
-
-inherit distutils-r1
-
-DESCRIPTION="Natural language processing tool collection"
-HOMEPAGE="http://www.nltk.org/"
-SRC_URI="https://github.com/nltk/nltk/archive/2.0.4.tar.gz -> ${P}.tar.gz"
-
-LICENSE="GPL-2"
-SLOT="0"
-KEYWORDS=""
-IUSE=""
-
-DEPEND="
-	dev-python/numpy[${PYTHON_USEDEP}]
-	dev-python/matplotlib[${PYTHON_USEDEP}]
-	dev-python/pyyaml[${PYTHON_USEDEP}]
-	>=app-dicts/wordnet-2.0
-	sci-misc/pywordnet[${PYTHON_USEDEP}]"
-RDEPEND="${DEPEND}"
-
-S="${WORKDIR}"/${P/_rc/rc}
diff --git a/sci-misc/omorfi/Manifest b/sci-misc/omorfi/Manifest
deleted file mode 100644
index b0e963918..000000000
--- a/sci-misc/omorfi/Manifest
+++ /dev/null
@@ -1 +0,0 @@
-DIST omorfi-0.1-alpha.tar.bz2 110111 BLAKE2B 59aa0c1388a69b56dbb1aa8ba6d93bfaf7f7fbe45b31c1dcc119a25d1c4313309a3f3f6fac5f315f4b8e16b5b93b211164a0fc2cf92b9f960248d1d11ecb5444 SHA512 3bab188661b994d1c2589ff52a202db2f78a9b511c7ccb0475fc1e8599c579e9a5d00be02efdefa1e2b22341d8c7e9c164208596329ba01843839d39e55d25de
diff --git a/sci-misc/omorfi/metadata.xml b/sci-misc/omorfi/metadata.xml
deleted file mode 100644
index 738386c91..000000000
--- a/sci-misc/omorfi/metadata.xml
+++ /dev/null
@@ -1,11 +0,0 @@
-<?xml version="1.0" encoding="UTF-8"?>
-<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
-<pkgmetadata>
-	<maintainer type="person">
-		<email>flammie@gentoo.org</email>
-	</maintainer>
-	<longdescription lang="en">
-Omorfi is a free open source implementation of Finnish word form
-morphology.
-</longdescription>
-</pkgmetadata>
diff --git a/sci-misc/omorfi/omorfi-0.1_alpha.ebuild b/sci-misc/omorfi/omorfi-0.1_alpha.ebuild
deleted file mode 100644
index 2486d97ab..000000000
--- a/sci-misc/omorfi/omorfi-0.1_alpha.ebuild
+++ /dev/null
@@ -1,25 +0,0 @@
-# Copyright 1999-2014 Gentoo Foundation
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=5
-
-MY_P="${PN}-${PV/_alpha/-alpha}"
-
-DESCRIPTION="Open morphology for Finnish language"
-HOMEPAGE="http://gna.org/projects/omorfi"
-SRC_URI="http://download.gna.org/omorfi/${MY_P}.tar.bz2"
-
-LICENSE="LGPL-3"
-SLOT="0"
-KEYWORDS="~x86"
-IUSE=""
-
-DEPEND="
-	>=sci-misc/kotus-sanalista-1
-	dev-java/saxon
-	sci-misc/sfst"
-RDEPEND=""
-
-S="${WORKDIR}/${MY_P}"
-
-MAKEOPTS+=" -j1"
diff --git a/sci-misc/openfst/Manifest b/sci-misc/openfst/Manifest
index 999086ae3..f89088f0a 100644
--- a/sci-misc/openfst/Manifest
+++ b/sci-misc/openfst/Manifest
@@ -1,3 +1 @@
-DIST openfst-1.3.4.tar.gz 769158 BLAKE2B b150e158b3a28b073b33612ef747b7632ef0f357571ce428f87c3b636dac464675c79247074aa5a52626bbde918f053a130d58926dbfee2a87ce90531bd7da44 SHA512 6ed87cbb949776b8702545a51d129e03f33428369b20255d637191e054ce04e529969aef49549b098b144cfde45cd9b741e6cba6680f815c04ad5717fdb0cbd9
-DIST openfst-1.4.1.tar.gz 824020 BLAKE2B 87fd131ed3a6efa878ef07100de590601dfb9e3e6dbc3244824ce392c789217014cea285b0c6d16962b18c0ecd07dd76c4975ca3bc7443271faafa0f6cfeb13c SHA512 8cb3b3e83155d1b2bd0075bab4fcf5d7160b427af87a2c03217a614a9dd1f9d7d1a67d404d897ad8659532686a7ad2fd20270de7cf838c6f38d4ae807369c51f
-DIST openfst-1.6.1.tar.gz 1208654 BLAKE2B d0e783013e199b27a204a2fa60195c1c05a2744a71de890cbfb87443fea18132905ed05c2af1cfaaf415013e7b9b4bfda53164c01674268b1b7133ed52f5adb6 SHA512 e75b706a825c3569271677226a47852744da20e1afc765d6a0f16b34a2e7af80b79b562a1c6bb3c17e1b819f8bd89958074cb671f3747deb31d8dccbb21abec2
+DIST openfst-1.8.2.tar.gz 1342793 BLAKE2B bae3ff40e1234a5c2a9bbd642ba5a7e29b0ecef2e304b2a952d1ebb354c3fb4d772dfdf85710fcd4940e01798ac4064226377e59f1a3f46b2331219e1bd3f8cf SHA512 ca7f9f19e24141e1f1d0bbabf43795e6e278bce3887c14261d9ce204a0e01b1588eaf982755a9105247510a19f67da2f566e9b14b1d869497148f95b55606d5c
diff --git a/sci-misc/openfst/files/kaldi-openfst-1.4.1.patch b/sci-misc/openfst/files/kaldi-openfst-1.4.1.patch
deleted file mode 100644
index 140ea4e24..000000000
--- a/sci-misc/openfst/files/kaldi-openfst-1.4.1.patch
+++ /dev/null
@@ -1,269 +0,0 @@
-diff -crB openfst-1.4.1.orig/src/include/fst/lock.h openfst-1.4.1/src/include/fst/lock.h
-*** openfst-1.4.1.orig/src/include/fst/lock.h	2012-04-25 19:43:47.000000000 -0400
---- openfst-1.4.1/src/include/fst/lock.h	2015-02-28 14:12:29.009385600 -0400
-***************
-*** 78,85 ****
-    RefCounter() : count_(1) {}
-  
-    int count() const { return count_; }
-!   int Incr() const { return ++count_; }
-!   int Decr() const {  return --count_; }
-  
-   private:
-    mutable int count_;
---- 78,93 ----
-    RefCounter() : count_(1) {}
-  
-    int count() const { return count_; }
-! 
-! // below lines are modifications of openfst for multi-thrads support,
-! // from tools/extras/openfst_gcc41up.patch, applied by tools/Makefile,
-! // applicable to gcc 4.1 or above
-!   // int Incr() const { return ++count_; }
-!   // int Decr() const {  return --count_; }
-! 
-!   int Incr() const { return __sync_add_and_fetch(&count_, 1); }
-!   int Decr() const { return __sync_sub_and_fetch(&count_, 1); }
-! // end modifications
-  
-   private:
-    mutable int count_;
-diff -crB openfst-1.4.1.orig/src/include/fst/minimize.h openfst-1.4.1/src/include/fst/minimize.h
-*** openfst-1.4.1.orig/src/include/fst/minimize.h	2014-04-29 18:15:17.000000000 -0400
---- openfst-1.4.1/src/include/fst/minimize.h	2015-02-28 14:11:39.270566070 -0400
-***************
-*** 134,140 ****
-    typedef typename A::Weight Weight;
-    typedef ReverseArc<A> RevA;
-  
-!   CyclicMinimizer(const ExpandedFst<A>& fst) {
-      Initialize(fst);
-      Compute(fst);
-    }
---- 134,147 ----
-    typedef typename A::Weight Weight;
-    typedef ReverseArc<A> RevA;
-  
-!   CyclicMinimizer(const ExpandedFst<A>& fst):
-!       // tell the Partition data-member to expect multiple repeated
-!       // calls to SplitOn with the same element if we are non-deterministic.
-!       P_(fst.Properties(kIDeterministic, true) == 0) {
-!     if(fst.Properties(kIDeterministic, true) == 0)
-!       CHECK(Weight::Properties() & kIdempotent); // this minimization
-!     // algorithm for non-deterministic FSTs can only work with idempotent
-!     // semirings.
-      Initialize(fst);
-      Compute(fst);
-    }
-***************
-*** 315,321 ****
-    typedef typename A::StateId ClassId;
-    typedef typename A::Weight Weight;
-  
-!   AcyclicMinimizer(const ExpandedFst<A>& fst) {
-      Initialize(fst);
-      Refine(fst);
-    }
---- 322,334 ----
-    typedef typename A::StateId ClassId;
-    typedef typename A::Weight Weight;
-  
-!   AcyclicMinimizer(const ExpandedFst<A>& fst):
-!       // tell the Partition data-member to expect multiple repeated
-!       // calls to SplitOn with the same element if we are non-deterministic.
-!       partition_(fst.Properties(kIDeterministic, true) == 0) {
-!     if(fst.Properties(kIDeterministic, true) == 0)
-!       CHECK(Weight::Properties() & kIdempotent); // minimization for
-!     // non-deterministic FSTs can only work with idempotent semirings.
-      Initialize(fst);
-      Refine(fst);
-    }
-***************
-*** 531,543 ****
-  void Minimize(MutableFst<A>* fst,
-                MutableFst<A>* sfst = 0,
-                float delta = kDelta) {
-!   uint64 props = fst->Properties(kAcceptor | kIDeterministic|
-!                                  kWeighted | kUnweighted, true);
-!   if (!(props & kIDeterministic)) {
-!     FSTERROR() << "FST is not deterministic";
-!     fst->SetProperties(kError, kError);
-!     return;
-!   }
-  
-    if (!(props & kAcceptor)) {  // weighted transducer
-      VectorFst< GallicArc<A, GALLIC_LEFT> > gfst;
---- 544,550 ----
-  void Minimize(MutableFst<A>* fst,
-                MutableFst<A>* sfst = 0,
-                float delta = kDelta) {
-!   uint64 props = fst->Properties(kAcceptor | kWeighted | kUnweighted, true);
-  
-    if (!(props & kAcceptor)) {  // weighted transducer
-      VectorFst< GallicArc<A, GALLIC_LEFT> > gfst;
-diff -crB openfst-1.4.1.orig/src/include/fst/partition.h openfst-1.4.1/src/include/fst/partition.h
-*** openfst-1.4.1.orig/src/include/fst/partition.h	2014-04-29 18:15:17.000000000 -0400
---- openfst-1.4.1/src/include/fst/partition.h	2015-02-28 14:11:39.271566087 -0400
-***************
-*** 43,50 ****
-    friend class PartitionIterator<T>;
-  
-    struct Element {
-!    Element() : value(0), next(0), prev(0) {}
-!    Element(T v) : value(v), next(0), prev(0) {}
-  
-     T        value;
-     Element* next;
---- 43,50 ----
-    friend class PartitionIterator<T>;
-  
-    struct Element {
-!     Element() : value(0), next(0), prev(0) {}
-!     Element(T v) : value(v), next(0), prev(0) {}
-  
-     T        value;
-     Element* next;
-***************
-*** 52,60 ****
-    };
-  
-   public:
-!   Partition() {}
-  
-!   Partition(T num_states) {
-      Initialize(num_states);
-    }
-  
---- 52,62 ----
-    };
-  
-   public:
-!   Partition(bool allow_repeated_split):
-!       allow_repeated_split_(allow_repeated_split) {}
-  
-!   Partition(bool allow_repeated_split, T num_states):
-!       allow_repeated_split_(allow_repeated_split) {
-      Initialize(num_states);
-    }
-  
-***************
-*** 137,152 ****
-      if (class_size_[class_id] == 1) return;
-  
-      // first time class is split
-!     if (split_size_[class_id] == 0)
-        visited_classes_.push_back(class_id);
-! 
-      // increment size of split (set of element at head of chain)
-      split_size_[class_id]++;
-! 
-      // update split point
-!     if (class_split_[class_id] == 0)
-!       class_split_[class_id] = classes_[class_id];
-!     if (class_split_[class_id] == elements_[element_id])
-        class_split_[class_id] = elements_[element_id]->next;
-  
-      // move to head of chain in same class
---- 139,154 ----
-      if (class_size_[class_id] == 1) return;
-  
-      // first time class is split
-!     if (split_size_[class_id] == 0) { 
-        visited_classes_.push_back(class_id);
-!       class_split_[class_id] = classes_[class_id];
-!     }
-      // increment size of split (set of element at head of chain)
-      split_size_[class_id]++;
-!     
-      // update split point
-!     if (class_split_[class_id] != 0
-!         && class_split_[class_id] == elements_[element_id])
-        class_split_[class_id] = elements_[element_id]->next;
-  
-      // move to head of chain in same class
-***************
-*** 157,165 ****
-    // class indices of the newly created class. Returns the new_class id
-    // or -1 if no new class was created.
-    T SplitRefine(T class_id) {
-      // only split if necessary
-!     if (class_size_[class_id] == split_size_[class_id]) {
-!       class_split_[class_id] = 0;
-        split_size_[class_id] = 0;
-        return -1;
-      } else {
---- 159,169 ----
-    // class indices of the newly created class. Returns the new_class id
-    // or -1 if no new class was created.
-    T SplitRefine(T class_id) {
-+ 
-+     Element* split_el = class_split_[class_id];
-      // only split if necessary
-!     //if (class_size_[class_id] == split_size_[class_id]) {
-!     if(split_el == NULL) { // we split on everything...
-        split_size_[class_id] = 0;
-        return -1;
-      } else {
-***************
-*** 163,180 ****
-        split_size_[class_id] = 0;
-        return -1;
-      } else {
-- 
-        T new_class = AddClass();
-        size_t remainder = class_size_[class_id] - split_size_[class_id];
-        if (remainder < split_size_[class_id]) {  // add smaller
--         Element* split_el   = class_split_[class_id];
-          classes_[new_class] = split_el;
--         class_size_[class_id] = split_size_[class_id];
--         class_size_[new_class] = remainder;
-          split_el->prev->next = 0;
-          split_el->prev = 0;
-        } else {
--         Element* split_el   = class_split_[class_id];
-          classes_[new_class] = classes_[class_id];
-          class_size_[class_id] = remainder;
-          class_size_[new_class] = split_size_[class_id];
---- 167,189 ----
-        split_size_[class_id] = 0;
-        return -1;
-      } else {
-        T new_class = AddClass();
-+ 
-+       if(allow_repeated_split_) { // split_size_ is possibly
-+         // inaccurate, so work it out exactly.
-+         size_t split_count;  Element *e;
-+         for(split_count=0,e=classes_[class_id];
-+             e != split_el; split_count++, e=e->next);
-+         split_size_[class_id] = split_count;
-+       }
-        size_t remainder = class_size_[class_id] - split_size_[class_id];
-        if (remainder < split_size_[class_id]) {  // add smaller
-          classes_[new_class] = split_el;
-          split_el->prev->next = 0;
-          split_el->prev = 0;
-+         class_size_[class_id] = split_size_[class_id];
-+         class_size_[new_class] = remainder;
-        } else {
-          classes_[new_class] = classes_[class_id];
-          class_size_[class_id] = remainder;
-          class_size_[new_class] = split_size_[class_id];
-***************
-*** 245,254 ****
---- 254,269 ----
-    vector<T> class_size_;
-  
-    // size of split for each class
-+   // in the nondeterministic case, split_size_ is actually an upper
-+   // bound on the size of split for each class.
-    vector<T> split_size_;
-  
-    // set of visited classes to be used in split refine
-    vector<T> visited_classes_;
-+ 
-+   // true if input fst was deterministic: we can make
-+   // certain assumptions in this case that speed up the algorithm.
-+   bool allow_repeated_split_;
-  };
-  
-  
diff --git a/sci-misc/openfst/files/kaldi.patch b/sci-misc/openfst/files/kaldi.patch
deleted file mode 100644
index 3a3854eff..000000000
--- a/sci-misc/openfst/files/kaldi.patch
+++ /dev/null
@@ -1,599 +0,0 @@
-diff -crB openfst-1.3.4.orig/src/include/fst/interval-set.h openfst-1.3.4/src/include/fst/interval-set.h
-*** openfst-1.3.4.orig/src/include/fst/interval-set.h	2013-01-24 06:36:23.000000000 +0400
---- openfst-1.3.4/src/include/fst/interval-set.h	2013-11-21 15:59:08.541136087 +0400
-***************
-*** 37,74 ****
-  class IntervalSet {
-   public:
-    struct Interval {
-!     T begin;
-!     T end;
-  
-!     Interval() : begin(-1), end(-1) {}
-  
-!     Interval(T b, T e) : begin(b), end(e) {}
-  
-      bool operator<(const Interval &i) const {
-!       return begin < i.begin || (begin == i.begin && end > i.end);
-      }
-  
-      bool operator==(const Interval &i) const {
-!       return begin == i.begin && end == i.end;
-      }
-  
-      bool operator!=(const Interval &i) const {
-!       return begin != i.begin || end != i.end;
-      }
-  
-      istream &Read(istream &strm) {
-        T n;
-        ReadType(strm, &n);
-!       begin = n;
-        ReadType(strm, &n);
-!       end = n;
-        return strm;
-      }
-  
-      ostream &Write(ostream &strm) const {
-!       T n = begin;
-        WriteType(strm, n);
-!       n = end;
-        WriteType(strm, n);
-        return strm;
-      }
---- 37,74 ----
-  class IntervalSet {
-   public:
-    struct Interval {
-!     T begin_;
-!     T end_;
-  
-!     Interval() : begin_(-1), end_(-1) {}
-  
-!     Interval(T b, T e) : begin_(b), end_(e) {}
-  
-      bool operator<(const Interval &i) const {
-!       return begin_ < i.begin_ || (begin_ == i.begin_ && end_ > i.end_);
-      }
-  
-      bool operator==(const Interval &i) const {
-!       return begin_ == i.begin_ && end_ == i.end_;
-      }
-  
-      bool operator!=(const Interval &i) const {
-!       return begin_ != i.begin_ || end_ != i.end_;
-      }
-  
-      istream &Read(istream &strm) {
-        T n;
-        ReadType(strm, &n);
-!       begin_ = n;
-        ReadType(strm, &n);
-!       end_ = n;
-        return strm;
-      }
-  
-      ostream &Write(ostream &strm) const {
-!       T n = begin_;
-        WriteType(strm, n);
-!       n = end_;
-        WriteType(strm, n);
-        return strm;
-      }
-***************
-*** 108,114 ****
-          lower_bound(intervals_.begin(), intervals_.end(), interval);
-      if (lb == intervals_.begin())
-        return false;
-!     return (--lb)->end > value;
-    }
-  
-    // Requires intervals be normalized.
---- 108,114 ----
-          lower_bound(intervals_.begin(), intervals_.end(), interval);
-      if (lb == intervals_.begin())
-        return false;
-!     return (--lb)->end_ > value;
-    }
-  
-    // Requires intervals be normalized.
-***************
-*** 123,129 ****
-  
-    bool Singleton() const {
-      return intervals_.size() == 1 &&
-!         intervals_[0].begin + 1 == intervals_[0].end;
-    }
-  
-  
---- 123,129 ----
-  
-    bool Singleton() const {
-      return intervals_.size() == 1 &&
-!         intervals_[0].begin_ + 1 == intervals_[0].end_;
-    }
-  
-  
-***************
-*** 178,194 ****
-    T size = 0;
-    for (T i = 0; i < intervals_.size(); ++i) {
-      Interval &inti = intervals_[i];
-!     if (inti.begin == inti.end)
-        continue;
-      for (T j = i + 1; j < intervals_.size(); ++j) {
-        Interval &intj = intervals_[j];
-!       if (intj.begin > inti.end)
-          break;
-!       if (intj.end > inti.end)
-!         inti.end = intj.end;
-        ++i;
-      }
-!     count_ += inti.end - inti.begin;
-      intervals_[size++] = inti;
-    }
-    intervals_.resize(size);
---- 178,194 ----
-    T size = 0;
-    for (T i = 0; i < intervals_.size(); ++i) {
-      Interval &inti = intervals_[i];
-!     if (inti.begin_ == inti.end_)
-        continue;
-      for (T j = i + 1; j < intervals_.size(); ++j) {
-        Interval &intj = intervals_[j];
-!       if (intj.begin_ > inti.end_)
-          break;
-!       if (intj.end_ > inti.end_)
-!         inti.end_ = intj.end_;
-        ++i;
-      }
-!     count_ += inti.end_ - inti.begin_;
-      intervals_[size++] = inti;
-    }
-    intervals_.resize(size);
-***************
-*** 208,224 ****
-    oset->count_ = 0;
-  
-    while (it1 != intervals_.end() && it2 != iintervals->end()) {
-!     if (it1->end <= it2->begin) {
-        ++it1;
-!     } else if (it2->end <= it1->begin) {
-        ++it2;
-      } else {
-        Interval interval;
-!       interval.begin = max(it1->begin, it2->begin);
-!       interval.end = min(it1->end, it2->end);
-        ointervals->push_back(interval);
-!       oset->count_ += interval.end - interval.begin;
-!       if (it1->end < it2->end)
-          ++it1;
-        else
-          ++it2;
---- 208,224 ----
-    oset->count_ = 0;
-  
-    while (it1 != intervals_.end() && it2 != iintervals->end()) {
-!     if (it1->end_ <= it2->begin_) {
-        ++it1;
-!     } else if (it2->end_ <= it1->begin_) {
-        ++it2;
-      } else {
-        Interval interval;
-!       interval.begin_ = max(it1->begin_, it2->begin_);
-!       interval.end_ = min(it1->end_, it2->end_);
-        ointervals->push_back(interval);
-!       oset->count_ += interval.end_ - interval.begin_;
-!       if (it1->end_ < it2->end_)
-          ++it1;
-        else
-          ++it2;
-***************
-*** 235,255 ****
-    oset->count_ = 0;
-  
-    Interval interval;
-!   interval.begin = 0;
-    for (typename vector<Interval>::const_iterator it = intervals_.begin();
-         it != intervals_.end();
-         ++it) {
-!     interval.end = min(it->begin, maxval);
-!     if (interval.begin < interval.end) {
-        ointervals->push_back(interval);
-!       oset->count_ += interval.end - interval.begin;
-      }
-!     interval.begin = it->end;
-    }
-!   interval.end = maxval;
-!   if (interval.begin < interval.end) {
-      ointervals->push_back(interval);
-!     oset->count_ += interval.end - interval.begin;
-    }
-  }
-  
---- 235,255 ----
-    oset->count_ = 0;
-  
-    Interval interval;
-!   interval.begin_ = 0;
-    for (typename vector<Interval>::const_iterator it = intervals_.begin();
-         it != intervals_.end();
-         ++it) {
-!     interval.end_ = min(it->begin_, maxval);
-!     if (interval.begin_ < interval.end_) {
-        ointervals->push_back(interval);
-!       oset->count_ += interval.end_ - interval.begin_;
-      }
-!     interval.begin_ = it->end_;
-    }
-!   interval.end_ = maxval;
-!   if (interval.begin_ < interval.end_) {
-      ointervals->push_back(interval);
-!     oset->count_ += interval.end_ - interval.begin_;
-    }
-  }
-  
-***************
-*** 263,269 ****
-      oset->count_ = 0;
-    } else {
-      IntervalSet<T> cset;
-!     iset.Complement(intervals_.back().end, &cset);
-      Intersect(cset, oset);
-    }
-  }
---- 263,269 ----
-      oset->count_ = 0;
-    } else {
-      IntervalSet<T> cset;
-!     iset.Complement(intervals_.back().end_, &cset);
-      Intersect(cset, oset);
-    }
-  }
-***************
-*** 277,285 ****
-    typename vector<Interval>::const_iterator it2 = intervals->begin();
-  
-    while (it1 != intervals_.end() && it2 != intervals->end()) {
-!     if (it1->end <= it2->begin) {
-        ++it1;
-!     } else if (it2->end <= it1->begin) {
-        ++it2;
-      } else {
-        return true;
---- 277,285 ----
-    typename vector<Interval>::const_iterator it2 = intervals->begin();
-  
-    while (it1 != intervals_.end() && it2 != intervals->end()) {
-!     if (it1->end_ <= it2->begin_) {
-        ++it1;
-!     } else if (it2->end_ <= it1->begin_) {
-        ++it2;
-      } else {
-        return true;
-***************
-*** 300,320 ****
-    bool overlap = false; // point in both intervals_ and intervals
-  
-    while (it1 != intervals_.end() && it2 != intervals->end()) {
-!     if (it1->end <= it2->begin) {  // no overlap - it1 first
-        only1 = true;
-        ++it1;
-!     } else if (it2->end <= it1->begin) {  // no overlap - it2 first
-        only2 = true;
-        ++it2;
-!     } else if (it2->begin == it1->begin && it2->end == it1->end) {  // equals
-        overlap = true;
-        ++it1;
-        ++it2;
-!     } else if (it2->begin <= it1->begin && it2->end >= it1->end) {  // 1 c 2
-        only2 = true;
-        overlap = true;
-        ++it1;
-!     } else if (it1->begin <= it2->begin && it1->end >= it2->end) {  // 2 c 1
-        only1 = true;
-        overlap = true;
-        ++it2;
---- 300,320 ----
-    bool overlap = false; // point in both intervals_ and intervals
-  
-    while (it1 != intervals_.end() && it2 != intervals->end()) {
-!     if (it1->end_ <= it2->begin_) {  // no overlap - it1 first
-        only1 = true;
-        ++it1;
-!     } else if (it2->end_ <= it1->begin_) {  // no overlap - it2 first
-        only2 = true;
-        ++it2;
-!     } else if (it2->begin_ == it1->begin_ && it2->end_ == it1->end_) {  // equals
-        overlap = true;
-        ++it1;
-        ++it2;
-!     } else if (it2->begin_ <= it1->begin_ && it2->end_ >= it1->end_) {  // 1 c 2
-        only2 = true;
-        overlap = true;
-        ++it1;
-!     } else if (it1->begin_ <= it2->begin_ && it1->end_ >= it2->end_) {  // 2 c 1
-        only1 = true;
-        overlap = true;
-        ++it2;
-***************
-*** 346,356 ****
-    typename vector<Interval>::const_iterator it2 = intervals->begin();
-  
-    while (it1 != intervals_.end() && it2 != intervals->end()) {
-!     if (it1->end <= it2->begin) {  // no overlap - it1 first
-        ++it1;
-!     } else if (it2->begin < it1->begin || it2->end > it1->end) {  // no C
-        return false;
-!     } else if (it2->end == it1->end) {
-        ++it1;
-        ++it2;
-      } else {
---- 346,356 ----
-    typename vector<Interval>::const_iterator it2 = intervals->begin();
-  
-    while (it1 != intervals_.end() && it2 != intervals->end()) {
-!     if (it1->end_ <= it2->begin_) {  // no overlap - it1 first
-        ++it1;
-!     } else if (it2->begin_ < it1->begin_ || it2->end_ > it1->end_) {  // no C
-        return false;
-!     } else if (it2->end_ == it1->end_) {
-        ++it1;
-        ++it2;
-      } else {
-***************
-*** 370,376 ****
-         ++it) {
-      if (it != intervals->begin())
-        strm << ",";
-!     strm << "[" << it->begin << "," << it->end << ")";
-    }
-    strm << "}";
-    return strm;
---- 370,376 ----
-         ++it) {
-      if (it != intervals->begin())
-        strm << ",";
-!     strm << "[" << it->begin_ << "," << it->end_ << ")";
-    }
-    strm << "}";
-    return strm;
-diff -crB openfst-1.3.4.orig/src/include/fst/minimize.h openfst-1.3.4/src/include/fst/minimize.h
-*** openfst-1.3.4.orig/src/include/fst/minimize.h	2013-01-24 06:36:23.000000000 +0400
---- openfst-1.3.4/src/include/fst/minimize.h	2013-11-21 15:59:08.539136087 +0400
-***************
-*** 134,140 ****
-    typedef typename A::Weight Weight;
-    typedef ReverseArc<A> RevA;
-  
-!   CyclicMinimizer(const ExpandedFst<A>& fst) {
-      Initialize(fst);
-      Compute(fst);
-    }
---- 134,147 ----
-    typedef typename A::Weight Weight;
-    typedef ReverseArc<A> RevA;
-  
-!   CyclicMinimizer(const ExpandedFst<A>& fst):
-!       // tell the Partition data-member to expect multiple repeated
-!       // calls to SplitOn with the same element if we are non-deterministic.
-!       P_(fst.Properties(kIDeterministic, true) == 0) {
-!     if(fst.Properties(kIDeterministic, true) == 0)
-!       CHECK(Weight::Properties() & kIdempotent); // this minimization
-!     // algorithm for non-deterministic FSTs can only work with idempotent
-!     // semirings.
-      Initialize(fst);
-      Compute(fst);
-    }
-***************
-*** 315,321 ****
-    typedef typename A::StateId ClassId;
-    typedef typename A::Weight Weight;
-  
-!   AcyclicMinimizer(const ExpandedFst<A>& fst) {
-      Initialize(fst);
-      Refine(fst);
-    }
---- 322,334 ----
-    typedef typename A::StateId ClassId;
-    typedef typename A::Weight Weight;
-  
-!   AcyclicMinimizer(const ExpandedFst<A>& fst):
-!       // tell the Partition data-member to expect multiple repeated
-!       // calls to SplitOn with the same element if we are non-deterministic.
-!       partition_(fst.Properties(kIDeterministic, true) == 0) {
-!     if(fst.Properties(kIDeterministic, true) == 0)
-!       CHECK(Weight::Properties() & kIdempotent); // minimization for
-!     // non-deterministic FSTs can only work with idempotent semirings.
-      Initialize(fst);
-      Refine(fst);
-    }
-***************
-*** 531,543 ****
-  void Minimize(MutableFst<A>* fst,
-                MutableFst<A>* sfst = 0,
-                float delta = kDelta) {
-!   uint64 props = fst->Properties(kAcceptor | kIDeterministic|
-!                                  kWeighted | kUnweighted, true);
-!   if (!(props & kIDeterministic)) {
-!     FSTERROR() << "FST is not deterministic";
-!     fst->SetProperties(kError, kError);
-!     return;
-!   }
-  
-    if (!(props & kAcceptor)) {  // weighted transducer
-      VectorFst< GallicArc<A, STRING_LEFT> > gfst;
---- 544,550 ----
-  void Minimize(MutableFst<A>* fst,
-                MutableFst<A>* sfst = 0,
-                float delta = kDelta) {
-!   uint64 props = fst->Properties(kAcceptor | kWeighted | kUnweighted, true);
-  
-    if (!(props & kAcceptor)) {  // weighted transducer
-      VectorFst< GallicArc<A, STRING_LEFT> > gfst;
-diff -crB openfst-1.3.4.orig/src/include/fst/partition.h openfst-1.3.4/src/include/fst/partition.h
-*** openfst-1.3.4.orig/src/include/fst/partition.h	2013-01-24 06:36:23.000000000 +0400
---- openfst-1.3.4/src/include/fst/partition.h	2013-11-21 15:59:08.539136087 +0400
-***************
-*** 43,50 ****
-    friend class PartitionIterator<T>;
-  
-    struct Element {
-!    Element() : value(0), next(0), prev(0) {}
-!    Element(T v) : value(v), next(0), prev(0) {}
-  
-     T        value;
-     Element* next;
---- 43,50 ----
-    friend class PartitionIterator<T>;
-  
-    struct Element {
-!     Element() : value(0), next(0), prev(0) {}
-!     Element(T v) : value(v), next(0), prev(0) {}
-  
-     T        value;
-     Element* next;
-***************
-*** 52,60 ****
-    };
-  
-   public:
-!   Partition() {}
-  
-!   Partition(T num_states) {
-      Initialize(num_states);
-    }
-  
---- 52,62 ----
-    };
-  
-   public:
-!   Partition(bool allow_repeated_split):
-!       allow_repeated_split_(allow_repeated_split) {}
-  
-!   Partition(bool allow_repeated_split, T num_states):
-!       allow_repeated_split_(allow_repeated_split) {
-      Initialize(num_states);
-    }
-  
-***************
-*** 137,152 ****
-      if (class_size_[class_id] == 1) return;
-  
-      // first time class is split
-!     if (split_size_[class_id] == 0)
-        visited_classes_.push_back(class_id);
-! 
-      // increment size of split (set of element at head of chain)
-      split_size_[class_id]++;
-! 
-      // update split point
-!     if (class_split_[class_id] == 0)
-!       class_split_[class_id] = classes_[class_id];
-!     if (class_split_[class_id] == elements_[element_id])
-        class_split_[class_id] = elements_[element_id]->next;
-  
-      // move to head of chain in same class
---- 139,154 ----
-      if (class_size_[class_id] == 1) return;
-  
-      // first time class is split
-!     if (split_size_[class_id] == 0) { 
-        visited_classes_.push_back(class_id);
-!       class_split_[class_id] = classes_[class_id];
-!     }
-      // increment size of split (set of element at head of chain)
-      split_size_[class_id]++;
-!     
-      // update split point
-!     if (class_split_[class_id] != 0
-!         && class_split_[class_id] == elements_[element_id])
-        class_split_[class_id] = elements_[element_id]->next;
-  
-      // move to head of chain in same class
-***************
-*** 157,165 ****
-    // class indices of the newly created class. Returns the new_class id
-    // or -1 if no new class was created.
-    T SplitRefine(T class_id) {
-      // only split if necessary
-!     if (class_size_[class_id] == split_size_[class_id]) {
-!       class_split_[class_id] = 0;
-        split_size_[class_id] = 0;
-        return -1;
-      } else {
---- 159,169 ----
-    // class indices of the newly created class. Returns the new_class id
-    // or -1 if no new class was created.
-    T SplitRefine(T class_id) {
-+ 
-+     Element* split_el = class_split_[class_id];
-      // only split if necessary
-!     //if (class_size_[class_id] == split_size_[class_id]) {
-!     if(split_el == NULL) { // we split on everything...
-        split_size_[class_id] = 0;
-        return -1;
-      } else {
-***************
-*** 163,180 ****
-        split_size_[class_id] = 0;
-        return -1;
-      } else {
-- 
-        T new_class = AddClass();
-        size_t remainder = class_size_[class_id] - split_size_[class_id];
-        if (remainder < split_size_[class_id]) {  // add smaller
--         Element* split_el   = class_split_[class_id];
-          classes_[new_class] = split_el;
--         class_size_[class_id] = split_size_[class_id];
--         class_size_[new_class] = remainder;
-          split_el->prev->next = 0;
-          split_el->prev = 0;
-        } else {
--         Element* split_el   = class_split_[class_id];
-          classes_[new_class] = classes_[class_id];
-          class_size_[class_id] = remainder;
-          class_size_[new_class] = split_size_[class_id];
---- 167,189 ----
-        split_size_[class_id] = 0;
-        return -1;
-      } else {
-        T new_class = AddClass();
-+ 
-+       if(allow_repeated_split_) { // split_size_ is possibly
-+         // inaccurate, so work it out exactly.
-+         size_t split_count;  Element *e;
-+         for(split_count=0,e=classes_[class_id];
-+             e != split_el; split_count++, e=e->next);
-+         split_size_[class_id] = split_count;
-+       }
-        size_t remainder = class_size_[class_id] - split_size_[class_id];
-        if (remainder < split_size_[class_id]) {  // add smaller
-          classes_[new_class] = split_el;
-          split_el->prev->next = 0;
-          split_el->prev = 0;
-+         class_size_[class_id] = split_size_[class_id];
-+         class_size_[new_class] = remainder;
-        } else {
-          classes_[new_class] = classes_[class_id];
-          class_size_[class_id] = remainder;
-          class_size_[new_class] = split_size_[class_id];
-***************
-*** 245,254 ****
---- 254,269 ----
-    vector<T> class_size_;
-  
-    // size of split for each class
-+   // in the nondeterministic case, split_size_ is actually an upper
-+   // bound on the size of split for each class.
-    vector<T> split_size_;
-  
-    // set of visited classes to be used in split refine
-    vector<T> visited_classes_;
-+ 
-+   // true if input fst was deterministic: we can make
-+   // certain assumptions in this case that speed up the algorithm.
-+   bool allow_repeated_split_;
-  };
-  
-  
diff --git a/sci-misc/openfst/files/openfst-20080422_beta-gcc-4.3.patch b/sci-misc/openfst/files/openfst-20080422_beta-gcc-4.3.patch
deleted file mode 100644
index 8eb3116d0..000000000
--- a/sci-misc/openfst/files/openfst-20080422_beta-gcc-4.3.patch
+++ /dev/null
@@ -1,83 +0,0 @@
-diff -Naur -Naur OpenFst/fst/bin/main.cc OpenFst-nu/fst/bin/main.cc
---- OpenFst/fst/bin/main.cc	2008-03-17 17:42:00.000000000 +0200
-+++ OpenFst-nu/fst/bin/main.cc	2008-10-20 16:30:36.000000000 +0300
-@@ -18,6 +18,8 @@
- // Classes and functions for registering and invoking Fst main
- // functions that support multiple and extensible arc types.
- 
-+#include <cstring>
-+#include <climits>
- #include <iostream>
- 
- #include "fst/bin/main.h"
-diff -Naur -Naur OpenFst/fst/bin/Makefile OpenFst-nu/fst/bin/Makefile
---- OpenFst/fst/bin/Makefile	2008-03-17 17:42:00.000000000 +0200
-+++ OpenFst-nu/fst/bin/Makefile	2008-10-20 16:31:12.000000000 +0300
-@@ -15,7 +15,7 @@
- FSTLIBMAIN=libfstmain.$(LIBTYPE)
- LIBS=-lfstmain -lfst -lm -lpthread -ldl
- CC=g++
--OPT=-O2
-+OPT=-O2 -fPIC
- CFLAGS=-I../.. $(OPT) -DFST_DL
- LDLFLAGS=-Wl,-L$(LIBDIR),-L$(BINDIR)
- LDRFLAGS=-Wl,-rpath,$(LIBDIR),-rpath,$(BINDIR) # empty on macosx
-diff -Naur -Naur OpenFst/fst/lib/compat.h OpenFst-nu/fst/lib/compat.h
---- OpenFst/fst/lib/compat.h	2008-03-17 17:41:56.000000000 +0200
-+++ OpenFst-nu/fst/lib/compat.h	2008-10-20 16:25:49.000000000 +0300
-@@ -27,7 +27,7 @@
- #include <map>
- #include <string>
- #include <vector>
--
-+#include <cstring>
- #include <ext/hash_map>
- #include <fcntl.h>
- #include <pthread.h>
-diff -Naur -Naur OpenFst/fst/lib/Makefile OpenFst-nu/fst/lib/Makefile
---- OpenFst/fst/lib/Makefile	2008-03-17 17:41:56.000000000 +0200
-+++ OpenFst-nu/fst/lib/Makefile	2008-10-20 16:23:05.000000000 +0300
-@@ -2,7 +2,7 @@
- SRCS=fst.cc properties.cc symbol-table.cc compat.cc
- OBJS=fst.o properties.o symbol-table.o compat.o
- CC=g++
--OPT=-O2
-+OPT=-fPIC -O2
- CFLAGS=$(OPT) -I../.. -DFST_DL
- LIBTYPE=so # "dylib" on macosx
- SOFLAGS=-shared  # "-dynamiclib -flat_namespace -undefined suppress" on macosx
-diff -Naur -Naur OpenFst/fst/lib/randgen.h OpenFst-nu/fst/lib/randgen.h
---- OpenFst/fst/lib/randgen.h	2008-03-17 17:41:56.000000000 +0200
-+++ OpenFst-nu/fst/lib/randgen.h	2008-10-20 16:44:33.000000000 +0300
-@@ -23,6 +23,7 @@
- #include <cmath>
- #include <cstdlib>
- #include <ctime>
-+#include <climits>
- 
- #include "fst/lib/mutable-fst.h"
- 
-diff -Naur -Naur OpenFst/fst/lib/symbol-table.cc OpenFst-nu/fst/lib/symbol-table.cc
---- OpenFst/fst/lib/symbol-table.cc	2008-03-17 17:41:56.000000000 +0200
-+++ OpenFst-nu/fst/lib/symbol-table.cc	2008-10-20 16:21:16.000000000 +0300
-@@ -17,6 +17,8 @@
- // \file
- // Classes to provide symbol-to-integer and integer-to-symbol mappings.
- 
-+#include <cstring>
-+
- #include "fst/lib/symbol-table.h"
- #include "fst/lib/util.h"
- 
-diff -Naur -Naur OpenFst/fst/lib/vector-fst.h OpenFst-nu/fst/lib/vector-fst.h
---- OpenFst/fst/lib/vector-fst.h	2008-03-17 17:41:56.000000000 +0200
-+++ OpenFst-nu/fst/lib/vector-fst.h	2008-10-20 16:21:25.000000000 +0300
-@@ -21,6 +21,8 @@
- #ifndef FST_LIB_VECTOR_FST_H__
- #define FST_LIB_VECTOR_FST_H__
- 
-+#include <cstring>
-+
- #include "fst/lib/mutable-fst.h"
- #include "fst/lib/test-properties.h"
- 
diff --git a/sci-misc/openfst/metadata.xml b/sci-misc/openfst/metadata.xml
index 2d4fb61e6..8b44b5491 100644
--- a/sci-misc/openfst/metadata.xml
+++ b/sci-misc/openfst/metadata.xml
@@ -4,4 +4,8 @@
 	<maintainer type="person">
 		<email>flammie@gentoo.org</email>
 	</maintainer>
+	<maintainer type="project">
+		<email>sci@gentoo.org</email>
+		<name>Gentoo Science Project</name>
+	</maintainer>
 </pkgmetadata>
diff --git a/sci-misc/openfst/openfst-1.3.4.ebuild b/sci-misc/openfst/openfst-1.3.4.ebuild
deleted file mode 100644
index f38da4642..000000000
--- a/sci-misc/openfst/openfst-1.3.4.ebuild
+++ /dev/null
@@ -1,23 +0,0 @@
-# Copyright 1999-2014 Gentoo Foundation
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=5
-
-inherit eutils flag-o-matic multilib
-
-DESCRIPTION="Finite State Transducer tools by Google et al"
-HOMEPAGE="http://www.openfst.org"
-SRC_URI="http://www.openfst.org/twiki/pub/FST/FstDownload/${P}.tar.gz"
-
-LICENSE="Apache-2.0"
-SLOT="0"
-KEYWORDS="~amd64 ~x86"
-
-src_prepare() {
-	epatch "${FILESDIR}/kaldi.patch"
-}
-
-src_test() {
-	einfo "make test can take a few hours on moderately modern systems"
-	make test || die "check failed"
-}
diff --git a/sci-misc/openfst/openfst-1.4.1.ebuild b/sci-misc/openfst/openfst-1.4.1.ebuild
deleted file mode 100644
index 002ce42c0..000000000
--- a/sci-misc/openfst/openfst-1.4.1.ebuild
+++ /dev/null
@@ -1,18 +0,0 @@
-# Copyright 1999-2015 Gentoo Foundation
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=5
-
-inherit eutils
-
-DESCRIPTION="Finite State Transducer tools by Google et al"
-HOMEPAGE="http://www.openfst.org"
-SRC_URI="http://www.openfst.org/twiki/pub/FST/FstDownload/${P}.tar.gz"
-
-LICENSE="Apache-2.0"
-SLOT="0"
-KEYWORDS="~amd64 ~x86"
-
-src_prepare() {
-	epatch "${FILESDIR}/kaldi-${P}.patch"
-}
diff --git a/sci-misc/openfst/openfst-1.6.1.ebuild b/sci-misc/openfst/openfst-1.6.1.ebuild
deleted file mode 100644
index 4507b7e87..000000000
--- a/sci-misc/openfst/openfst-1.6.1.ebuild
+++ /dev/null
@@ -1,30 +0,0 @@
-# Copyright 1999-2017 Gentoo Foundation
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=6
-
-DESCRIPTION="Finite State Transducer tools by Google et al"
-HOMEPAGE="http://www.openfst.org"
-SRC_URI="http://www.openfst.org/twiki/pub/FST/FstDownload/${P}.tar.gz"
-
-LICENSE="Apache-2.0"
-SLOT="0"
-KEYWORDS="~amd64 ~x86"
-
-src_configure() {
-	local myeconfargs=(
-		--enable-compact-fsts
-		--enable-compress
-		--enable-const-fsts
-		--enable-far
-		--enable-linear-fsts
-		--enable-lookahead-fsts
-		--enable-mpdt
-		--enable-ngram-fsts
-		--enable-pdt
-		--enable-special
-		--enable-bin
-		--enable-grm
-	)
-	econf ${myeconfargs[@]}
-}
diff --git a/sci-misc/openfst/openfst-1.8.2.ebuild b/sci-misc/openfst/openfst-1.8.2.ebuild
new file mode 100644
index 000000000..923a36f64
--- /dev/null
+++ b/sci-misc/openfst/openfst-1.8.2.ebuild
@@ -0,0 +1,30 @@
+# Copyright 1999-2023 Gentoo Authors
+# Distributed under the terms of the GNU General Public License v2
+
+EAPI=8
+
+DESCRIPTION="Finite State Transducer tools by Google et al"
+HOMEPAGE="http://www.openfst.org"
+SRC_URI="http://www.openfst.org/twiki/pub/FST/FstDownload/${P}.tar.gz"
+
+LICENSE="Apache-2.0"
+SLOT="0"
+KEYWORDS="~amd64 ~x86"
+
+src_configure() {
+	local myeconfargs=(
+		--enable-compact-fsts
+		--enable-compress
+		--enable-const-fsts
+		--enable-far
+		--enable-linear-fsts
+		--enable-lookahead-fsts
+		--enable-mpdt
+		--enable-ngram-fsts
+		--enable-pdt
+		--enable-special
+		--enable-bin
+		--enable-grm
+	)
+	econf ${myeconfargs[@]}
+}
diff --git a/sci-misc/opennlp-maxent/Manifest b/sci-misc/opennlp-maxent/Manifest
deleted file mode 100644
index 03e5dea9a..000000000
--- a/sci-misc/opennlp-maxent/Manifest
+++ /dev/null
@@ -1 +0,0 @@
-DIST maxent-2.4.0.tgz 1242290 BLAKE2B 49dac8ec8af1ed46d8dc1ee349b2d7550de75719737a55c77d29ee833a73d267d9f325b7a0b80f93035428b3afbfbc36d49d1fb8d6ea3ed3a51a2f7bbb47a88b SHA512 bba7e1e546f30d15e3d2cf1fffb5e2785174533acee25ed8b3fab97999431e1e4335f228f59da95770229c0c8d115152c140b9ca0d59cdc3b1e50090d6d8a2ac
diff --git a/sci-misc/opennlp-maxent/metadata.xml b/sci-misc/opennlp-maxent/metadata.xml
deleted file mode 100644
index 7ba312978..000000000
--- a/sci-misc/opennlp-maxent/metadata.xml
+++ /dev/null
@@ -1,14 +0,0 @@
-<?xml version="1.0" encoding="UTF-8"?>
-<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
-<pkgmetadata>
-	<maintainer type="person">
-		<email>flammie@gentoo.org</email>
-	</maintainer>
-	<longdescription>
-Implementation of statistical classification using
-maximum entropy models in opennlp framework.
-</longdescription>
-	<upstream>
-		<remote-id type="sourceforge">maxent</remote-id>
-	</upstream>
-</pkgmetadata>
diff --git a/sci-misc/opennlp-maxent/opennlp-maxent-2.4.0.ebuild b/sci-misc/opennlp-maxent/opennlp-maxent-2.4.0.ebuild
deleted file mode 100644
index fdd89655a..000000000
--- a/sci-misc/opennlp-maxent/opennlp-maxent-2.4.0.ebuild
+++ /dev/null
@@ -1,54 +0,0 @@
-# Copyright 1999-2015 Gentoo Foundation
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=5
-
-JAVA_PKG_IUSE="source examples doc"
-
-inherit eutils java-pkg-2 java-ant-2
-
-MY_PN="maxent"
-MY_P="${MY_PN}-${PV}"
-
-DESCRIPTION="Maximum entropy model implementation for opennlp"
-HOMEPAGE="http://maxent.sf.net/"
-SRC_URI="mirror://sourceforge/maxent/${MY_P}.tgz"
-
-LICENSE="LGPL-2.1"
-SLOT="0"
-KEYWORDS="~x86"
-IUSE="${IUSE}"
-
-COMMON_DEP="
-	dev-java/java-getopt
-	dev-java/trove:0"
-DEPEND=">=virtual/jdk-1.4:*
-	${COMMON_DEP}"
-RDEPEND=">=virtual/jre-1.4:*
-	${COMMON_DEP}"
-
-EANT_BUILD_TARGET="compile package"
-S="${WORKDIR}/${MY_P}"
-
-src_prepare() {
-	cd "${S}"/lib || die
-	rm -v *.jar || die "failed to rm jars"
-	java-pkg_jarfrom java-getopt-1 gnu.getopt.jar java-getopt.jar
-	java-pkg_jarfrom trove
-}
-
-src_install() {
-	java-pkg_newjar output/${MY_P}.jar
-	java-pkg_dohtml docs/*html docs/*css docs/*jpg
-	if use doc ; then
-		java-pkg_dojavadoc docs/api
-	fi
-	if use source ; then
-		java-pkg_dosrc src/java/opennlp
-	fi
-	if use examples ; then
-		java-pkg_doexamples samples
-	fi
-	dodoc AUTHORS CHANGES COMMANDLINE README
-	# java-pkg_dolauncher
-}
diff --git a/sci-misc/pqdump/Manifest b/sci-misc/pqdump/Manifest
new file mode 100644
index 000000000..f738c3ede
--- /dev/null
+++ b/sci-misc/pqdump/Manifest
@@ -0,0 +1,119 @@
+DIST adler-1.0.2.crate 12778 BLAKE2B a1dc17786adae945ac09d3525e609ed944e6465690787bbb831a1b9d53793cba1989793d0a5606d5d23ee20d36457923d451b1b3530c9ec7072a487aa3e55bbd SHA512 7ab190d31890fc05b0b55d8e2c6527a505e06793d5496be0b3831e0513412f9ba97f8148f6f68ed0770fa9cd980a5092d885e058becf1d5506b7c74b82674aa1
+DIST ahash-0.8.3.crate 42416 BLAKE2B 84836a4e33451012ff32c1a1a90500d87eb7ce649b60dff4eecfb0d25b9782a186376c154673c3121b154ff4616016d1718dfd687b88f4772c2c89eeb2f119b6 SHA512 cf2d2f1201ac0969cf4e2a0c47090bee971b2287ac44b5e091c90a9eced03cf6ff56d7900cc0f529d4acedc30bd400261c15e50efabdd1731f79951b449af53e
+DIST alloc-no-stdlib-2.0.4.crate 10105 BLAKE2B afa0bfeb7df1d742edb412dca4c22957fc21c2a1be21c64c58503d4b943c06e3163d0f3c90525b25323b8dc38e6c64136ec4f9608758c5c6f3bd07c2c033ee74 SHA512 6518856fa524ee0fe8e04cf133c11028efcf2f6a28f3a70e401566a4eb343c954dba34aec2a02c0d0359757dfb5dcf48279610646215eea190d699708d838904
+DIST alloc-stdlib-0.2.2.crate 6693 BLAKE2B a22faf3482e416664f2e104f5f45c4e6d116a42b890216b80102e266f7a3a3accd2933aeca71650a4c4626e3d9da76b6488ffc9ea2ae4229cdfbf1ce9ca6c7cf SHA512 9c4169052ad460af2be6f2a128056661b2f26da0122877f13fcd4f4f3e2e9537783cb2b2bec47af43569629639aa8ad507ab010833982e5d942f5b26cfd46c14
+DIST android-tzdata-0.1.1.crate 7674 BLAKE2B 4385a4875aadaacd5284a9ca7d1bf8a7bf14bf8925d1563d52fbabacc3af2c1ea08bfcf77106f3648f4fa052ac295158a21e7a0131d31eb9aecd99ea4ba20055 SHA512 4294024c21ddd0090c42c8eedf708d40d917f55ad5a4cb7aa3e64cfb6551b6df60f2e36bc08620c1d2fc8c7ba7207411518ee5c8635f60ed8ad9efdd458a2077
+DIST android_system_properties-0.1.5.crate 5243 BLAKE2B 86f68ec3bdabf8c6ec47881d794970f08a9eefc7417fc8a2bf4fe9faf9bdd2a2024a94adb0cbf96673409f5fbbd4d0111a1ac371339e7a90a277b6cd5003524e SHA512 b09f51339f9772c0e2e4241b36cf51573c6b96b19ffc1fbbc94b1c1d1d2fdfe8eac3134af54174a675ab05d18ef4f6bcb2c7fcc20114bbeef6e17e3692202191
+DIST anstream-0.5.0.crate 19646 BLAKE2B 770dc99092e1c48ad5c1658e83abff3b8c9e0915e360048bfe0fe04faf61991e01e88ca4adca23533bf11fe078066e351778661128d69381756688341022f29d SHA512 8e285cc8f92708cf9482e7b4dc84dd891e5ec0bd8c57894c6bb368eede1127b7b903adb4c40b37287e3644535cc60c92662951c2c8fb5b92e10f49ff5374d359
+DIST anstyle-1.0.2.crate 13983 BLAKE2B 4274b101d1cab2b62f9bb7637dab35f4b16e8c08a080355a2ea53e2b7b353ff230aa77fb3a244e0d6ff0dcd27abe5895eb306c630aa0822d0c608f041d4abfea SHA512 09220abfc844192ca698589897845752e02666b4ecd6529af4cde9f260ef36694e6e631c7503fc0e438ac72c88c419043b78399385cb248e789e86404503935a
+DIST anstyle-parse-0.2.1.crate 24802 BLAKE2B 6304a56c6a9fbaf1bb4d1d177b2315684345dc9d71c35836f9544145364f8d6eb56e25c03076690c594ab7db5914501acb569f6c136952e59c93179ced527fb2 SHA512 5c8fc7d88ffc3a6e78340ffe0f3c2d72e865512030ade4509de9c673eba955c536bb1873dac11f6ba11cc8367fb30c67451ed65d19f81507c9e917c702bfd176
+DIST anstyle-query-1.0.0.crate 8620 BLAKE2B 2d296b5066fd6284a2410923215571e6df650c5ef892d6de7a7088a0996ca30608797feabc84f3c325ff4d07001dac80ac5067d2a9c9d15d9ba59a276b399f53 SHA512 2781be5c82293b7ae338ec5046fbeb130de9eb2dbf2e4dfaa73ca5233032e1e52c133e141b02f33d4bc36d996a0a3f680ac82d42d614a5305005f60547133c7a
+DIST anstyle-wincon-2.1.0.crate 11757 BLAKE2B b7c1071da1ab24accc33d7af70f09ace8edb2dcbb53936ed5ac13552c6082c0f16ce501f041d2c1792cee7dd9cc3877d29505e12a65022bec44285f13e1f422f SHA512 6c379c46f791b6b1367f3d6f3531dcd16589cc2e12f6f5ce52a3fa32d42e62b719d2277699d1bc8526099a6f791f2e7d5b1068e1295cbcd2997841f0eafc4eeb
+DIST arrow-array-46.0.0.crate 156326 BLAKE2B e65de2cd1e0fc718ca841abb1e97e38d78dce63fb41024884ef08f6101858af544578d80bc63d9344705b339e97ce110221bb14565588a6c21bd97aaa67cd335 SHA512 62b62688a7c2b0c2dce3ae2e6b43d5547787cc4d28851b59d21cd62bc997326d55d36ffd28f09fc2e0916a263fe5fcb9790c5fd909abc202792a813246c64d31
+DIST arrow-buffer-46.0.0.crate 54546 BLAKE2B 861ca8d55c8e0091101ef201afcda7e299fd562d9cc354f9535326f6887a808985b5fa04ff6efbe1a47baa60993e9cb2d9417c3106b82cb8c70791534de94948 SHA512 80f6b3b6b146126cee536a1ab34e2081d57224e8419a75a6c4de508337d22ad0009b1de344c79a9d83e1c9146bc6ee5c82ed7051a0e92fdce726e1be2b5a0cb8
+DIST arrow-cast-46.0.0.crate 64841 BLAKE2B 981245caa13230e26399148a99c67d53b232d358459677e8bdd7fa07b472ed1c2a20411a83e16164b0b411dbd63baefc231e52cb6fd7a1dd9341f25fdbe2265d SHA512 6ccddcdeeea9c827f499f031e2cb0fcbdfa0ade2a066325da13b65580f49547d08879940319bce42a545f638d6ce53e627bb762c8c9db319d1d6cca899cecae1
+DIST arrow-data-46.0.0.crate 41443 BLAKE2B a9b2b0a08dd96610685afa3d181f14bfa531b8e717eca3c56524c087ff8c3f1c33a0bd2b6abb58f5879fe994e1639f8b833a531b254c1b828f9fc291f04c167c SHA512 b9b7e3f6ada368fa6f0bc25de98dc7364e76091f3f2ca5f5ca82fbe273204520e5b524fdeb0b6a462ba33281245b56dbe97f4280515c3ff77fa67c4aa1184d51
+DIST arrow-ipc-46.0.0.crate 75756 BLAKE2B 5d0c8be5c3ce0bb03a5bbf64fda03720e4d9dceb40ce717753d2626b07aed9c94d2e702290f941bd7903653a7ed9f9412bfd28329aa174ca121bb94d38afd4a3 SHA512 976084028ee304795a4f9a8f2d7112f18ea04662448dfe92cb7993e5c1b672feec808b63662be31ea82f0ae1015466d6ac58c519d3f3e7da223241bfa3ddf4e1
+DIST arrow-schema-46.0.0.crate 28737 BLAKE2B a2bedb59ebfc1c087e89a0e391e55a8fe1ddb727ae5cfb0911fd8090c2f6b025501deea5878e6cab5cf6c4256e5d54316944c227896c05ac5fa682a11e9a095f SHA512 1070afa6106b5a424864bdb16a5a91fe2308d86d6c3622df1c74c8296f93bc9b8764421945d36527d817cb3cb5ea8e3f8692e0b3d5a01e2dffb76767db891124
+DIST arrow-select-46.0.0.crate 33837 BLAKE2B c2067b23b8a977276a55a135cb7990370cddbd9840b067f49b944d819a7699bc18c844508363180d0ad22fa115780a23023ac17254dbb1ac81eace9aa45bbd60 SHA512 3aeec63751532bdd60dc3f7ed284ef3374f81e8f0444ac6042f25b8017994072af1b2349b08c7ce63dc11b12367025f500882ec8de095b9debbf3b53fdb827fd
+DIST autocfg-1.1.0.crate 13272 BLAKE2B 7724055c337d562103f191f4e36cab469e578f0c51cc24d33624dea155d108a07578703766341fd6a4cc1ef52acda406e7dba1650d59115f18261281e5b40203 SHA512 df972c09abbdc0b6cb6bb55b1e29c7fed706ece38a62613d9e275bac46a19574a7f96f0152cccb0239efea04ee90083a146b58b15307696c4c81878cd12de28f
+DIST base64-0.21.3.crate 76898 BLAKE2B 09dc56f20321ea9e4af6a9bbbb83aec13b78e52d9f0007630b0ea21bd4ba24d7dd604a50001488656f2e18fedf6ba76328c673ae986fc8e8516d546cd167cf8e SHA512 75745fe54f321d21fb94d6481aa35f8fac29c8fa514a36043d10eb1a08f5566ee0ad0cdc7358a20b8086babd2afe043efad6720df1289495b5df4a788dbe920c
+DIST bitflags-1.3.2.crate 23021 BLAKE2B eb990bb27b2bdeb66fd7212ce582cb36e1c616debbac85df642d0c82b25439e6bf9b1e811fac76b59e58ea3c1bbea6170d03a61e8f9a395e4334a0e2e2987eda SHA512 3c698f757b5cc62f815f9a1cce365c3d2dd88e4db71f331dff8bba86c2865f755b81cb4c9bfc59bd86b7643b0943f9e09a7c4f8ad75eb2ab0e714803d0129f62
+DIST brotli-3.3.4.crate 1369026 BLAKE2B b46085e324a6fb90ef4f6198154e2f45d58b91302f07b0e7ec3394183e1981d8e25c2d617425bb656756988cac57fdee15d6de3510e6e0b3ea1fe450ff06b8df SHA512 e312842abd713b5dd750ae92dbac297136291bef22b95572b52141c7d991f9d8bc84dc605f30c062a9cdd42d610ba5eb2f8e1ce3a8489f4ba816fca5eca7e5d8
+DIST brotli-decompressor-2.3.4.crate 192085 BLAKE2B 8ae8a47410215cbae102bbf19aa87f05e8739d6fe31e8eaff25948b1b4138ffed36e699947be30faf0b48891a010c10aafa835065cbd9a31f0c2628564a02359 SHA512 2698f1d9fc33ae37efc4587a448255320c864d1bba498ead93c5e28167ef696bcb5ddec9d4292b5fde93c3acddb7e99b453d6507780d0034e325bd20e5222c62
+DIST bumpalo-3.13.0.crate 82114 BLAKE2B 62a930b165e853aeeb40558079f570c75ed13ff5e8436d99309dc6252aa28ae69d327c4b438913d6c7543bc156f2714f0c1e80d759ea0d44babe24ef0f268ac0 SHA512 419368d6ca37474c2867751fe5706d0c747326bebce323d571cfc07ee0f022d8e8a7ef5692091b0fa804995b081998dafc55da19a53e51135a767bc0afdb9605
+DIST byteorder-1.4.3.crate 22512 BLAKE2B d39c546ba7346df315297fc53da4bfc77ecb1f38567ddb788549ee31cae2719a8bc0b7d1f1705abb3cff033aa57af004987d90748f5a31765273b3223a011c0d SHA512 8c8000eb8ecf40351c9ce36a3a8acd7a02f81786d1b11aab85adfeffa0f2267ed74df29b2ca5d1d38128484d1d3cad2b673aa0d0441dcd0620dfd3934bb888fa
+DIST bytes-1.4.0.crate 58080 BLAKE2B 99a9d343424e04649bd209bf2a6c3a089a6cc9fdb799968f8c3a711189328e4499df2e09cc6a2a8ce05d2cc668149b364cf30cb3b09e96e21d50a39519c2f49f SHA512 502c63b9fdcd36ed28ede55a63cd359dc7b28658ecd43020511d17d48d7c34e45aa8ff7e4b17770f12197451040c2b724fe68d2aa3ab4f81c9171d052f2aa000
+DIST cc-1.0.83.crate 68343 BLAKE2B 33245b33fa845ea2f36da36e3830ec835f937e4319865b357ee9d5ea29a0f9f8392eadb38bf1d95e3c15ed201e561acaa87aedcef744f8db3dabff87a96c7f02 SHA512 742a248c3a7547bb220a0b9c97b67a831fab9b4ac21daa08c85a3966b9fe576088def33e16132fcabec9a2828a6fc437088bb045bfc98b2cea829df6742565a7
+DIST cfg-if-1.0.0.crate 7934 BLAKE2B e99a5589c11d79d77a4537b34ce0a45d37b981c123b79b807cea836c89fc3926d693458893baca2882448d3d44e3f64e06141f6d916b748daa10b8cc1ae16d1b SHA512 0fb16a8882fd30e86b62c5143b1cb18ab564e84e75bd1f28fd12f24ffdc4a42e0d2e012a99abb606c12efe3c11061ff5bf8e24ab053e550ae083f7d90f6576ff
+DIST chrono-0.4.26.crate 191501 BLAKE2B eae49ee247607995c28463b8c3e2119497141e69d19a756c408f2b72d94bea39397ea2d0d3cd2ccbf1348ef973dd8bae6d29a0d0590e8dd34633f365a9170adb SHA512 2b66faf4d8374cfb0485710ceb2c9c1ce63aa6f9670e405a0810af4aca01c57d8dcd198a1f4cad498d5efd89e00003ba1b4f0bab599422af4f9bd6fb74494c47
+DIST clap-4.4.0.crate 54523 BLAKE2B 0292f888fc6426d4e79fbc82fe382be091c222371d2920cfca93cce9a16b3781d7d9bdddb1be62c4593a18d1bc0be0424139ef26745cb26e2ffbe33e684e30df SHA512 359d61374fe40f00a3b3af0e2962e80829cdd34f91b05c7c2347cf58568913037acda79409e44b25f7529901def008c0da0acf5837f784acc45d14936172f2eb
+DIST clap_builder-4.4.0.crate 162489 BLAKE2B 0856a43db80c074ee98477a5a83260b56c8fbf73b00855e0120969fb643211955403045c7354878d4774d81df2e3035b9aa361172cd5286adf164565391f6d8b SHA512 2a79dda8d5dc4a0fc7d43f714d003096bacbb6a2c58f5085732f1a9b73d5f8f6346f4d9195a2e5a8d683cc206d59e54e400c9c748c0bc7abb176f6ed62bb3c33
+DIST clap_derive-4.4.0.crate 29055 BLAKE2B 1cc5364e48025c21dbf72808270ae6c9c1d130307a5e8047335ffc2bb6153a98e55967d11a04fbe2fcb8afb4cca230ec0f637dfb5023309270e62b145bf73ab4 SHA512 4c8fc71e2480a93b98c723a1282e68047acace1474fdbd1f6cf76fd6fe95d1564d0929a336da4eed090da0f119f029d087d38e95c05f0f078158c755eabb01a0
+DIST clap_lex-0.5.1.crate 11793 BLAKE2B 8e3d2dc120401fdd0cf0bf069119c8b7eafa13e5f682c56499062fc09acc05f443caafa6fca791ea53e693a83de69e98fd0488726a4170db037c37118ce0edf1 SHA512 ea5e49e9a8536093f7de89be30add7c3d880b232b0ce393b0429fd4402db2518036998689817bdfd472b6400224fd3c42fec1b5f8538dc433c31dadeb6281e80
+DIST colorchoice-1.0.0.crate 6857 BLAKE2B a0818be1299717461ffc1bcfb6fc53a0b3b645aa8c45fb72e045cf2d876fa207948610e58d6a837aad24838ea9616e80b0558ca3eae03fdf9bc4c03a8e5ba52f SHA512 53363f2889cd8e8a3b3ed10c48356896c0daa72f3c12c9c7804707ab0dbc07c0e34ef52fa4f0fb1647311ce5913168c1bf62c2407ff86a33f765a9e6fccad551
+DIST comfy-table-7.0.1.crate 72831 BLAKE2B af07dc0551c133dc8d8e29375055eb7092c93f02c9ba62e4cf67e66eb3678e34161da2394efdbcd4554037feb51dc2209e1bcb4e2fc8de1840a1cb68121fd48d SHA512 4ce73693e659ad12fed827b7b6e6e2260577f25eb41849dc66375e032fcd0dcf9928aca6101fb3f4327100e6c0875ca91ac7d9d17572ae0d5cd09c0e27c42d55
+DIST const-random-0.1.15.crate 6699 BLAKE2B 2580963485d51a910a23d4d5723a0a1da66788328d4988f39f9ef50d89625f8d07707eac7caee2dae803772b1b6e93961dfe9471ca8b821eca377e27a79ad600 SHA512 efda06434f62ad74eca1a8768de065367a6e2466b98fade93a6714834b71092c9009219f92969da233b329bc4bcf630944fbf666bc5fb852aacd4dfddc881c40
+DIST const-random-macro-0.1.15.crate 6680 BLAKE2B 597bfb60bcf1e9007abf0f81e4d9f2a328622a8379b91898826f8409ec72345cccaab8bab9aad850d47d19f3cfb4f669aad24f142dd4679849e1248428fb2874 SHA512 2dfc7248fab80463df8e848855dc91e82810cb302e047ac6a5c4afd6140784b86203f3a9f30559079d26b6f29fa3974b367ec4aa78b9d00f1d79339703163d9d
+DIST core-foundation-sys-0.8.4.crate 17725 BLAKE2B 8afe47838dc91c8848c0d6a96a604149e5f0762228dbc10c17b85e4e9cd2c3928712bd0b28e1071f5fd6fd76d4ef972cb86c6c929246fb6e84577776933a8ac7 SHA512 15da472316d6decc213e4e5f08ecd22a108ebefe427b890741de4f9199614f19123e64329da76de5e8b4c9ff74ffc31738fd929acc1460fc757b4aa1fd3fdbb6
+DIST crc32fast-1.3.2.crate 38661 BLAKE2B ce3762b03d24d5367d89738991c060f4b3af7840e0a7ac7fc17d01ed438caf964bbaefad0fc4d0c438dafa5a578429ddd353c71197f8b54b1ec441395f2f7ee0 SHA512 a683943e252afdb1b9d626a07533ed11cf7a63af603c19640056c5d2b9c884ad9aff33ac54c0853ffca2f6cf94b0730eae6c05abf3e53e55e709d180c8152357
+DIST crunchy-0.2.2.crate 2995 BLAKE2B 74ddf8c5e0deb2ceab65c20a2743e1230739ac6aa3af60c9e867a7852270697a1278b7dee00df8949fc4268f9756a4a098df1211ab3b3e31a122652c3ba0a6fb SHA512 36dc0aebc41a3aac5f1b178a7e61b65bcd9bb5c8539b2024f79428200f7c62daa7098af55c6ab0765febd2f8969bd6c0ac8096f73cdc0958e5c4e4eb6a4f7025
+DIST flatbuffers-23.5.26.crate 23943 BLAKE2B 30b05e7463f2e1146834c74f69bec341d0894a9e3e07a7311f0029c093f08798bb25ae3ff96abbe66b05ba37ad3f8cafce1ff2eb656ff99ed34b22e87a309885 SHA512 b4d6caeec11c9c731ac1ee8b88b72dc1b2c2b0a6a6351732686b26fbd89c966db8ab389a37cb0556e097ca43224372ef0fbac5d4628bed9af9032499c65e20f1
+DIST flate2-1.0.27.crate 73460 BLAKE2B 5603848098ac02c9c83893df79ea9d9ad3df5b7e02ffa155ac74602bda7e28e14e6b7de2ff321b38d24fa3741ccea8a4c811abb47690cc295f90d4cf2bdd0bbf SHA512 e76e76444686433acabd16513e6e5860d4d6fa53a810f37266f36900f154acacac6dcd77b0373599a6d33a09175f5f02146d84726b982c59a78926950e19ff09
+DIST getrandom-0.2.10.crate 34955 BLAKE2B 8e7b8554ae360484ceca2a05f834c2664b08f41cbc6c955663e1f8f22fb5750481518bf1c7b49f49223a99a66914ef013347b9186acc97a20249f3222a13f9d4 SHA512 82af9e0417bff9272ed0478be4ac90426405ce210014b21899c6b95fde1b16893bf46295388ff5f13fa712a04c99c46b770fab83f41a1343af1590a86ca8da3b
+DIST half-2.3.1.crate 50257 BLAKE2B 073192254d98ea786b450eb4e29d36c3a661ee2ac6e57b8f303a7da483ac60451de59a91fb4d4be3fab23ceb109674416162f8224d3e9bc05883e4f998182225 SHA512 b29acbca7b8f8fed6392346d03c710dad0f51cb2e358e7ea74a3aad4e10ffd22edb4154a56f877adc375da831a7597b51f7049335c0781a1b1110103e5eafc35
+DIST hashbrown-0.14.0.crate 116103 BLAKE2B 24bab03e8a8cb7623b92282c83bf8acaf0752c696ee1c010249e3ebb3646e7549d8d6d798b02c9d5b621afbebba7320f8a859d9a1af1523dbd46377b857dbb5f SHA512 f0fbdf81517f59a0b67f792a4097f1131d346b2b4cbda93590749cef7f9f1c9029e0e182f58c23b74d3028f7502c30b9593c1eb4da37f95388d74b14582b8959
+DIST heck-0.4.1.crate 11567 BLAKE2B 520aeea740cfa30b0cca12f73594ffa655f32959673b1c9caaca1ea0162e455546ae3033881394c0ba0516bcd5c9a997da02162e1585522d665813b9096eabd9 SHA512 8c80e959d2f10a2893f9a71994720f90747742bb5b61fc0a539eed3ea5679b140c48fd7f7690d7122cd6af5f7f20a19d412e3569fe741c6d31f6b2ce1e0b80e8
+DIST iana-time-zone-0.1.57.crate 19785 BLAKE2B 2304a63e4d3a477125ed07fccd5a84832f775c4a0fbd60a995e6f1850aaf3f5047c6f70975c9f6334f96def12770d470677e1f536e9817f8ab1df8a312622cfe SHA512 79bc0fe559dce022cd3c15ffc3b6f870c14a40de6d5a61b4a5a6ad28fe7efce82a16ac5102073a3510f3ba683843475f7fb8a4029bbafbc1cc25e48b98ce2fe8
+DIST iana-time-zone-haiku-0.1.2.crate 7185 BLAKE2B 37fa14b589ff092377b9271c414d4e584c5a531f13f70ac48df26df3cc03353db635b4630ba192fc65b800cce11823e91b91f03dfad85e4bed55aa18398156cb SHA512 448224ecafa935472ff6f0aab7cb71f9dabdbe71569c4b94fcc65baea925ef48841577687c9a31106a1826c2105e8dd73c748e9d27fd002648e5b0ce838af6b2
+DIST integer-encoding-3.0.4.crate 12446 BLAKE2B bcdb01101c3af348c299ccdf54ad006c7cee26570639cd390d42a98a40b84f3a5906a5de95a301e22633a62f57a9aaec038cbdc8f73a78d17c1ef5dbb127fcd5 SHA512 453686fa64aae578c5f8954ee1b34dcd895f6757a3c71dfa7eb944da85cab7c39498bb6b42aac93e1df473cb52de07316beedf59ade63a4dcba921c1dbce2ee3
+DIST jobserver-0.1.26.crate 22645 BLAKE2B 44bcc15330268ea29650e58605c7f21c35108eb64b790c005968955238e948d27b3d12e6bb06bfc0eb4a3fe5f9e5322bc0657200212bf87e08d9e043e008a5a8 SHA512 ad3ebb693018928daf399e918ce35ed0d4e643cfb5c78bde04697e41dc8adf2861023ea1cf2c5033a3026048ca0ebeb7f2f57a966ba8e420558e42dde8d494f7
+DIST js-sys-0.3.64.crate 80313 BLAKE2B 7cf5dcb2b9e0b63cb82771c9e98518a4cda70372c5aed07866a07d2aa51274622357e4b5a665499328f5a3c38f7c515303da50421bad4a496fbb658e2132325f SHA512 a4f389a4eb45c2122e7bcf365dccdce8fcf14b1b521b8b839746bba8783296e2f1b959d73bdd874743f49c61a24c4077dec52f63cc7d594cd42e9cd6ea9c2e64
+DIST lexical-core-0.8.5.crate 26680 BLAKE2B 71f3cc95f47fa636f68d6d25612a47d4a178e2ffe484aa66760e78fb71e55633c055892647decaac08120d1b8b3b79d80d1a23d46a74d13b5e52d6b912839ea0 SHA512 f98d2b5afd331c6f4f599d24599ed8791ee3628a2fa2b8172b698cfe9a180e1ccd2da4dca4dd33fc76ef3417114c580399106d01a8d6153b45b38bceacee1018
+DIST lexical-parse-float-0.8.5.crate 180161 BLAKE2B 881e4db32a21c26a1919fd1373aef1ea16a6fca3d799edb18ff0c9e4a79d481f8ade7a93f9ded2a660ad10cf815eb757f6eec7887945f8203c467e700af7a9a3 SHA512 ef012cbf18f2e306724dd700ac259aaa73b44f6c4531377deb9979c80d31ae66fc1a8b2671bd677e0ebfad8f77e9a5cf25707c67a1c5b1f554953c036cb39d46
+DIST lexical-parse-integer-0.8.6.crate 33647 BLAKE2B a0ebd7a51c271a163796b0f55bb85e16830bf06e26e3f10d9b13dc5b65af590c77f47fb64360a8738c5ad4be6e6932d58e83e1594a80c067859645c35b907c53 SHA512 e9a814d2928bf5bb2d9dce53e26c65356191c9e21c3aa0e674d58ed879aa52293272f3897f64372d996a3f8c471b0f59348ad48f15a21c2f35ed15f522ac2daa
+DIST lexical-util-0.8.5.crate 85152 BLAKE2B 42a968c6f9d20cb4cb10906399d37d6581b425eadb31439fec4a71395819133249c4fb75b1d962100e77ba35b6f6b4cd428d5b5c161b405b22333ee390e671a6 SHA512 449c7f2a22c109cd179937c36e14d91c742e1a837a85fcf4fb58c21f05317511d1281b564d216a34760ae54a0df2d0ff5caf49da4aa9d43a8d87fcec0033cc39
+DIST lexical-write-float-0.8.5.crate 100281 BLAKE2B d5885d793ddcb8414fc9cd3085f0a0360b683df093b458f09fa4cf1dd670fbca7d9f86a19eca3082b32c4eb224cc9ab24a526350af0f894907391833888ca56f SHA512 35afe75db2fb4664e335349978fb8376a2b6cad48000e06652a3d3ce0b5fdbc422679821389856729724babc6cfe08ac8a1511c06bb743709787a4a47f956fd4
+DIST lexical-write-integer-0.8.5.crate 55427 BLAKE2B 54bb11be6c9377518384ad843d90d3bd344edadb889e1049ca8b58e34862e6d2a6730cd772c38859372d1068e110fd67db147c2d4c90bdd9bdb232ced7be4710 SHA512 a749846f8beb9b01ce61473f6ce123afb1b9f6efd91428cfff1fbbdd77422867e6eed4cd04c3ef25cd2d5be59864fa0e213ce296735e4021ac4632634b345838
+DIST libc-0.2.147.crate 686772 BLAKE2B ab2f0c65d071d46b8b88149add1c8429237ef6d9e0563d56ee1adbf23e6147dbb57fb68fbd02498f8ec75327693237a47e5e5259615ce8b0d5ed7a03bbf4fffb SHA512 bfb3c230b59d623b98726f92b7c3f897b47ba3d22fe9834c15f5b4c1b662289aba35a0ae3acfc704ad74696db8c691ee007b9cc6fa03ae65a18eb6bedc81931e
+DIST libm-0.2.7.crate 115688 BLAKE2B e180347d10847c40a88e43d321e08561df053e6fea0cea2cac480c4162c2f31d8697b4572a384edae323d43781d3c6462b2d77220dd71b2fd0da3a2757487db1 SHA512 b7adbf657be812451fc50cd5e5f92b7a71d43b4e48761bd2738d65498c9abad851f8e86d3be06ae75cf39c7798c23cafe767bc5fd40f596774e858f69fcb46d9
+DIST log-0.4.20.crate 38307 BLAKE2B cb9c9a401b49bd68c18d5e42f2ed94446f1aeb184caa23cefacad4ce54a2a357143af54a5595c45d6f3c3d20b054c451d9e6ccdc09c19cca99ffffdaf8bbfc72 SHA512 8661b0c71d3b7fc0d679aa3d7f06910e6d3da1c53862aa06526000e1bcaa0b0b068415a1a9ab317c318f00d15346dba8a4f5d2a60d8850790bed9cfaaf757b3e
+DIST lz4-1.24.0.crate 13361 BLAKE2B e0ebfab2aceb6817fea87d703b9c63d7248156d6ff4a051b4d41beceb0462551e9b4b7250a1bba8724fafbb90ab3618aed115d3f2f90cf184013d4eac76e93d4 SHA512 971e6265f12306ad228841ab5b72cfb80f001e57c2e3a815a8fe4a343ee2d93cfef6155ad4ff019873555b7e843ddffb1b70e22a057bb79b4688903c9407bcbc
+DIST lz4-sys-1.9.4.crate 354842 BLAKE2B ced6f5f681003284d6720f3bf4af4089b991320fc1ba52a445d67ae118a573edbba9dac656a4f04dab50e3d4ea8c1b32339f3413a5e590a597c2407a963da646 SHA512 a0cd903494db1089965f5316694eb23e219002c147aad68794d57e7206aff641824e54f25f7c4cbe08bb06a63e6f5ee4c44447aa7f7057c8467872d69c6f0b06
+DIST miniz_oxide-0.7.1.crate 55194 BLAKE2B 56afbe0c0b3eca98105ae2d507493f365353cce29a6b04910ff26bc75899400fdbd067756cbda7b3d86f047fb8f3d737de00043a4a7348a813cc43e45824e33f SHA512 5eb6ffe34a866403273ff0267ff7838aeb50722ca57a03d5a1d842a5f19a3b4af570b133a3b9d64d78eafe49e4b9732b92dd63fd9c6b0ce59b3295daf10f6a3c
+DIST num-0.4.1.crate 9522 BLAKE2B a7235566f657ea9dd3c15d4cf5ce85ac94f9f0e15ef5f4dd4f6bc7f8f09b9f654635a61785dfafef56dea980ee1f7441ea6fa366e51b9db707992a6b9d036bf9 SHA512 ea3b49c1b7a361266ee44213cd65765e58bfc51b9e805bdc71bed120a3b43f87ca60ba81b231a2c9a0ced617e10024d4e0961d8a3a52f26dbce1a22d550b7a84
+DIST num-bigint-0.4.4.crate 99369 BLAKE2B 09a44754e3a3d4f949b3714d96ddd7f3915164d611036675e3df421d6c0863e368eb0180978a4ec27fbfff529b4999d2593e411903516670c24c08fbed6a79de SHA512 0dcef3344a933509fdfe87d6adb0bb1bf67af3c692ccaeec5663a8f18ad0a251199ef9c7a24c25b95d1b255b413947e70f0a205669d549b13e54b6f4864ab3b5
+DIST num-complex-0.4.4.crate 29564 BLAKE2B 8ae65e8f2d87de96ec0a3d0e6d580584aff8cfbd0ebe56272dcf7cc5eea1b545fb9d597cbe4b1e25562b99a217a03ceef60e6cbda47c1e8cbd29b38d16cbe428 SHA512 632f9486df426d9254d2b6484c560b31e4ac0270de85878b9c4d14339a05ab318a90019f0724d2fac4d8496b03680650f899cedb1741c58eb7536cf3732db600
+DIST num-integer-0.1.45.crate 22529 BLAKE2B 4da3e801f71ba8f92c692497e200bfc8d32183c94eaad91260683b09f4697c03175fec7cff5a9ff3782d5db5d514d74f22f7a61a102c0f0d2e67a7a4b4f29222 SHA512 731bdc09c3af7f9d8b171041f2957aa60facef93b06886000d8ba60d410aabbbee358d700bf31b2588b2e077464f290f24a0b712df7bb7f12972675b6c9bd735
+DIST num-iter-0.1.43.crate 10655 BLAKE2B 41ee6d80f38f0767e134835ac84dacee8b50395b29c3e620b74cf4a843cfedfa71dc690e787b291a2b08750cd8386f1dad768e1b506ce088df33cf9e51b90a8e SHA512 97ac20f16d4518c8cbe944e5c80089fa6bb75d4632fb9f3c9d9891aaddb0e0f2209f6e854317f3d3b41bfb330c9d3ed830f3797f0120d4b1863b1d6fa3b9c07b
+DIST num-rational-0.4.1.crate 27889 BLAKE2B c6db5b2165eb341268cc8b81df44caf25a18242d0ff1cc0959444ed9a51ba9985c1238d6d79433c3927267ceb181da6d491bf282560db6bafd7768b79ec65842 SHA512 a7547ca663543e9da9e18dd079762cde371b85d55874a54d6b343ba775a9373392c85cebad511c53b5af5db298bd5d57ccef6161c1c28587a6c9fa2c5962a0bd
+DIST num-traits-0.2.16.crate 50130 BLAKE2B 1101d28cb4dce477657684a068792b94c7008a965e655edbabfeff51cbe6f008450dc6d7e4fc5dc4fe9c3ee8623ed77a7bde83ce2f68e75d618295fe6cebe0a8 SHA512 2ef65e2f6275b1000f611cc4d019b2f4846a8964b54d9b96462da10e3ac9edbf3d1de82e40094c76f7f5205740361b0eb0ced414bcddbaba5955144f728c6f94
+DIST once_cell-1.18.0.crate 32969 BLAKE2B a08d5beee50a7add28bd9e50b18709e7b34574f0f55f80909d5efb7ac5917e5f30bdcf3fb43ddd0a4f420a427390c7ffe1cc1c7191a3a1d939bc6e3139e6eef7 SHA512 9328968afdf3535b2d9e0113d75afa725259d76994ef2e1948ad7efa4ec8a65bac7cfdc31b749d5cd55ad4e28d2e28ac57b871e3067b89182453c7e2413a13b8
+DIST ordered-float-2.10.0.crate 15589 BLAKE2B 76561b2ab32b61ae69bef039f5f4636a05533cb8002b894ea18ce776ada1b5911c3067af2318126f359a305d7a9d3844053be62af1cbd2c3c9c1f45443a1cc9c SHA512 cb883ddd723d1bedfe13d16c9546dcb84d17d4fb1c6dc6d632a0c385d80b0b881694b3364a406e5d7f073c5a7e9e80810f343dd1d6f22df6188322b3e89cf77f
+DIST parquet-46.0.0.crate 413516 BLAKE2B ccc95d99d5ac4f948404916920bd1a05fdc1bc340160dff894f28efe772b25d47aa2737f92fe82b48eec894990f972442a4260f04dbf2493e9de4f3767084956 SHA512 2bd2d7b69c7ea09528eb5dd6f216db4db9197ee99234151ab635221860d5d30e6383ccad71c9437bf2bc8a165021ece953bd221f1f8355954cda06038b0834e9
+DIST paste-1.0.14.crate 18157 BLAKE2B 35e8548611c51ee75f4d04926149e5e54870d7073d9b635d550a6fa0f85891f57f326bdbcff3dd8618cf40f8e08cf903ef87d9c034d5921d8b91e1db842cdd7c SHA512 3a793f0e5e773a7f7defc798a4c17ae9a40d715144632ea6cb0a8c785e14c4212046491df016bb9838281f8eaf327a79f01c1e2ac5f26785c028bc880faff9ee
+DIST pkg-config-0.3.27.crate 18838 BLAKE2B 1295eb4f08751b3663cb2c7c2753f29bf2ccd80f4e5856909fe10b6f006c37fb9672c9518b9b416546469faa18821512673a66543c0bd1e848bddabc456d0a90 SHA512 41e9b8d4fce6b8244c2ac8566318a001b481bd42a182f1a832c81ce93c6a023e18af03aa3500b134c30195219d35080433bdba69b2594e9665081debfbb4533a
+DIST pqdump-0.1.0.tar.gz 10707 BLAKE2B 331578f96328015147c9ba7d679559e85fac6b831ac5a6a72d578f7499f90516e09741e59d08f3bca646187a3891ec903d34fee94799a23da705ccab69da826c SHA512 d8f0171e868c03e994490c7fc43f9da3b73dc5c14b02eac08ea31f41a19bf4bfa818eda37c0d5c64e7df3cd6ae7f2f446e6146e7070e6ee8187d5e8822e00acb
+DIST proc-macro-hack-0.5.20+deprecated.crate 15045 BLAKE2B fb7b9fa57ad64f2920e801482bfccc762bb7b2c8c1db7da32f393c7b47414fab37234c8a408a4ca9d7072a541df22b07775fc509f76f352fb6be9fe822f84dfd SHA512 278e786f8e0c93e346de900666b3d55d366324167a2e5e553565870c4444bfe661cf8c151a29cbd3176a4905ec49d69cffb81ae1e4a129f30404f930972c4b43
+DIST proc-macro2-1.0.66.crate 43575 BLAKE2B 9eb3e816b00fcf625c280ba14ad269f5893d0523473a24de07c21945f6f932fbd08efb3c339b35d903245510e3f065e1478439b024a325f2bb9f97bc7bcbb18d SHA512 85f5a762f9411142e5ac28144bd380f07f0633ed2e44d8a2545be9fb8f42abaca6b5d45631b4be83b8e8b9beca7438bc52f25615c3a410a3a1249474b1aca407
+DIST quote-1.0.33.crate 28090 BLAKE2B 77c4b166f1200e1ee2ab94a5014acd334c1fe4b7d72851d73768d491c56c6779a0882a304c1f30c88732a6168351f0f786b10516ae537cff993892a749175848 SHA512 c1e76c3c017e8554eebe309f8167fd56fce931981c06798aa85a0cc6d64a9cba6ab103f5a1324e69c6f9ca5dc47a8e31ff2e847850542748697afcd265b5939c
+DIST rustc_version-0.4.0.crate 12175 BLAKE2B 6fda2ce03eab45d7193fa0d70175cc7ffb56b7be85fb1314092bdcfd3948ea145420569ace3a47218a4a2a6e44a818862cea6dd8cfb945475496f63b591c29da SHA512 f66da7c6efe431db06cd01180d84ba67fcd38f8cd6ef693762957c00ccc2211f23c08079d7f184776e08f28d2d6ca3bdb5f5016f7de245c6193d4722891ba1db
+DIST rustversion-1.0.14.crate 17261 BLAKE2B db30d01914059a893bdb4c448ed0bf04852085c2d948bfbed8819a1d2317c34133cf609abdd806ad628b86974a9c1ab9d09f79743cb8e13257ef32cd444f49c6 SHA512 466d753c28c4899ab3da3e9f3366f7ecc435d484f51e0c07acfa5f3367af0de27ea3bc75efda22159b4990c976b1466a27e7c31c834c72a87d8234318357454b
+DIST semver-1.0.18.crate 29703 BLAKE2B b1867f552ac87968d895c5e49123bcce0f8aa0ad384e421e5ac88bd04ae203ed6b731d5c77fb8488ec6601f1f02a8f2a207a9d21f1cc66d433032628f5d7beda SHA512 698dcd37b354cfd6ee452dce02d16051f23088ce53f0b4d099e1e4ad0f9350996f0b9b2e1c3ac7d5ed258accd92773266892e945fcae28055d4671c7ae5aac02
+DIST seq-macro-0.3.5.crate 13332 BLAKE2B 2e93de606214852f2d5818398565770d01425fa2cd8361397e877dfba2c890e472d46eebe2c8ea2483f99dd783c8e80383f700b81dab3cc019cbea977f4ec96d SHA512 5eea67d40e6c6217512140791dba33e0909bdef6ddbc09ab14ebf5ec862126be68413e0c4ea34dda416ef1a9b2e64e32d7c69ae14dff44a7965b04606b6ed596
+DIST snap-1.1.0.crate 33163 BLAKE2B f9441def95039050ff4cee05771524cc966959300d1206e472c26728213eabc64716da00273ce254e2504e83d7542a45f92d13d1cafd1028f9b7cd833e8b18c4 SHA512 3d374ece917ab052b260e2a6b5bd509c94b8545601b910c964368612055ba5cf7b748f23873f2ba5adcc47f0f4eb6063e52f6d4ba186653d43e5f5d03c0363b9
+DIST static_assertions-1.1.0.crate 18480 BLAKE2B 358dd5ac413d06f62da0388e2016c5fcb8ec68fd7dceb0dbbcb97665c032b7509b7e083c20701648b6a9174485f117c02682ae4bde7ef037e80a85cdf6a0c86e SHA512 46d0e35f77941dee6f60f574c130472248063dc38494c1c4f84f7c048244cc2a58a86fe17c0990e3f0f01406b75ed385a13d00058612b27cf0e867c8d31c92ee
+DIST strsim-0.10.0.crate 11355 BLAKE2B bcb25ad0a7284e24e4f17ebe0ccb621bdc4118e499b50b094d98aa7e8fcc0b96716c9953c3516ce7ea78309d41d424892ded595259696a5bbffdcb07802b5c2f SHA512 78b318532addfcf5c1ccc1e14539e258aab9d3cd893cc45d82342549bde838c177d90f13c560671f8f32929af47d0b467db35e6876bd7697d8b3f9e055aeeac1
+DIST strum-0.24.1.crate 5636 BLAKE2B 81959b4ed8b78313bcd370eca0de10dd86b63c27eeacab66afb6e0c620bf1a13b66ee4a06ff90ce09b46dfd29d8ce32218414900a077ddcdbd8debfb05de243c SHA512 d842464b762790f4b785e494f72f7bae47b5a068cd06ddaad7a491d1abff53fa9cde280b06bbbb6b39a3a8f350a2384080ec4b3e4f16226cb076b1df153e6197
+DIST strum_macros-0.24.3.crate 20696 BLAKE2B fa86022cd1f701d8755fbf3e6356a38d46f4f168a1abd19d1d8fa63cbecf41746165791955c8cf1fba86cadf85ddb427ffd17bb360567187b55dfb9a899503c1 SHA512 8276343808afe71d68d7984d5a223a4fc630df0adb5a547cbcc6912fbffcf7e4ad38f115888a2dd3a8443d6fa7b9c7726318d4f5d1ab43f463dd97ec20df9134
+DIST syn-1.0.109.crate 237611 BLAKE2B e827445d00c79a8eeb91eacde472f1987addd6ce9e1df95d7abf6446a77ff4173a8006845f3ae71c1da47193cfb72e0ead9a6d6bad2573be12c17e90735d9ad9 SHA512 12816b9e8cf984024b2fbce9f0ae14cf94d4d2c06f08cc54fb793ce78770bb4cc1288eb7df0ba5e8e937756e1e8e295c53fe07a0c5dde1ea8ddba03b6203b37d
+DIST syn-2.0.29.crate 241664 BLAKE2B 5b339433249d7ee17b032cc9ecb118169957d91f438619940aeba0003ab0015b01cc6afb00656b5492539a5396325ec16c37e33764b00d6f9b8dc6b5b5e6a9f0 SHA512 a6319ee743a7690c7858da8492ffb6a963d102beba07009e82b08082d33ac8e8ea2675bdfc3ac3684392b3bc3d7f2624983dc508dd8b8f1fb9a57ec8a5b82828
+DIST thrift-0.17.0.crate 45286 BLAKE2B 93fb20bd82fe6320c4348779fcb84d83feb050b7686fde4a7082a4658152f514621ddffe294d0c53718d85506b12659ac03e7cc808bfbc983f36ade5d44fd0c5 SHA512 760fc20570ec63f5b60350518a4acbfe5f85f93416c846b84ffdc757510792e9cf5623c290b98715dd35def7076a38a3239ae7d7099f8b52a9643749c222c934
+DIST tiny-keccak-2.0.2.crate 20129 BLAKE2B 105a2d2af36cc053cd95721ea563108f33b8a3feb2ae84c75a04a65ed5d548dfe35d8b2e48977a82f725c0ebcf914f21157c547f4a74bb4d98c2e894385139be SHA512 c0219f23361eb07e0a68575c461a36b7286d9bdebae89080d9e259178d402b0c7762ccf33e65a16951ea168392322c44a24eb55189cf143e22d09d6dfc4acec1
+DIST twox-hash-1.6.3.crate 21842 BLAKE2B 67c261b2b0a93293717a4e2e07dc11df2abde09da6fe713b9d04917ace73de1b59b8d4fd9449ab46cb7cf496fad1e440effdfa1fae6f5cae4ca78af8cd019c42 SHA512 f7ce63e6e5ca79ce9330caf40b32578a5d2088c5d8ed371604268760d6e212d447d9e3a95378378a283024155bccdaea47597902c488a94c5d5f79770baec8fc
+DIST unicode-ident-1.0.11.crate 42067 BLAKE2B 3c7cac3d2bf1cbf1cf04716a482f130123e8e6940f7a90a17bc62fca44ac0069688165538f5329b95a72f735b594cfb85e3250738393ffd1b53cb0cd95077d89 SHA512 9682bbee339fb987c9d0bb6a54406d37b28b5c3587372d406402e4341900fec97e3234cd03b5c98b90b6378fd533dc452cac3de90d3ade19c4b09657e4abf6df
+DIST unicode-width-0.1.10.crate 18968 BLAKE2B 6174e307fd3ee290d0a5d1d31233baaa5315cdb73f19b8580718e9f9eb04cfd3aeaeb474af1e50c4b9fecc6fc777937dedc527c9dc9ed14ccf42af099e591f31 SHA512 9836a8d489d18ea1ecfe1957ed6d5da7dce825e138cd1848aef093fa8d2eb83fcf01eabb1a2446df4f5ede4e67316e9e81b5d58b59d4e8c5d67870e8fa5dca3b
+DIST utf8parse-0.2.1.crate 13435 BLAKE2B a1c111d7ffc60690f2aaa86f034c66ba1abe4e126f1774a4377d41eba3269369862f57515af387ea785d69a8adf46338b5e53761b5ee6f4f4380473f4d9cab0a SHA512 51fba8f1e7eb74b7020fd831e30a67fc8353ac2ee07335c8c3374a5570ac8117f165f6905d4b7f0360095b7b5ed3e739001d02a8cc3c89195baf2cd679136050
+DIST version_check-0.9.4.crate 14895 BLAKE2B fa1fa4008af165bfc1fdbe560488afd9d232cfafee94104fbcc4cbc52f234849bff9ddfa88109a1ac682f6d9c1d86b0459893d223f64e65adc08966aaf93dc89 SHA512 b172dc9a3759a4a683ffc39b9a40b03b9974b626a088217de87090466cef695226557c226cf3e469b2b25ee7297b7eb0d7719878cab42457f80146a81943c0c8
+DIST wasi-0.11.0+wasi-snapshot-preview1.crate 28131 BLAKE2B fe501889f25d65e2d032f885cc50c4f8bf7dd70fd5cbc438de349838370d8699e9627b0a4fc76030ea9fe6d508f41d0c9928a875fdbc47e73bfb17241cf7b155 SHA512 043500ab28cd9cb779475255da5d109ebab7fccca72b64873dc28d77bc5a157ba8d96b9e8f05223b5b36c7089bb7b4ba87657fc69bac16b78972f897294a865f
+DIST wasm-bindgen-0.2.87.crate 175052 BLAKE2B bf8cf4aa1786ac5c2ba76e80500b5c54313adf9690ef370e60b894401bd1b81416da7bb46b90c014412c96f30f995bd1e52cf7f3a6be1111aea40866e8178396 SHA512 0c3099155ef079d2b91d2d5b135243d687bf865cdd9ae9d97d8cc2eb4c9bf7439b66b28d5b1d7e95048e53be63ed4909b6b3f2427951348de25ca7abb7a03705
+DIST wasm-bindgen-backend-0.2.87.crate 26821 BLAKE2B e230aa256a1f681ab3ffd2c83c3f6a810c305bb79a5e1d806b8b2b9f54ef0babc83809f6153b9ca511faa4b122f80bd1cc9eb97e7ae3cb4cba9e2dc1c6bd0b51 SHA512 317ee2bdf85067cb7f4b4ed6ff475ff9e5063143e9b7c8a28572211c09025935815227c4afa8c92823ac92102562d4d34531aa4891d8c922048d37e27377ee94
+DIST wasm-bindgen-macro-0.2.87.crate 13897 BLAKE2B 0926975b0328cdd5525820358795b7b68b4ab9dc460715ed84e5d276e76e936057140efb1ba875acf25f3d2862e680f9827bd05cc47560d54f7ec673f30244cb SHA512 af366d8d853b280014cdf5286f3b1f6d7fb0837ce6e359a81cb6f85161537c8e2cd06d7f893c957f5bf1548d34084d33a213670b471937782b56033a23cb15a6
+DIST wasm-bindgen-macro-support-0.2.87.crate 20006 BLAKE2B d32dfc7231e4fbc226586e66063538208f9e299fbf803c4e2d1e1e61b4a22f51cc7509bdd269a44f072f9843a083ee84d2326408fb3211009ce93542c3fdc6ce SHA512 9390aa2767fed1027be168612c424d4c7cd4423addd83b79afd8c67886f66303ca4846e6454302ecc78b47bc62e8ee46849a4c0d3edb98849ce8476901424e33
+DIST wasm-bindgen-shared-0.2.87.crate 7248 BLAKE2B 0393ce9452119fd5f92836a76b28d3a697f91fb09de39d1af0a2a83e81d48bd4a17f39b48f15ae97edca3e361d4f8fedae8de04173c4ba1711decc73f64000d5 SHA512 cb9ff537554f56fd07052ddc4adc904a57ee64e13298df1dfca58b361ce163c34640e7dd9ed301ec1375f335dfa424230e22638ea7569ceb34aeca4505f6c008
+DIST winapi-0.3.9.crate 1200382 BLAKE2B cb5799749ccd935ea2d7068d953cecf19f543d9db7dc16ad4584bb7005373ada34937a3ced7225544d8bc765da599911c7a3190efefb3a25b7c1bb7123b4f673 SHA512 ff8b7b78065f3d8999ec03c725a0460ebc059771bf071c7a3df3f0ecd733edf3b0a2450024d4e24e1aedddaecd9038ce1376c0d8bbf45132068cf45cf4a53a97
+DIST winapi-i686-pc-windows-gnu-0.4.0.crate 2918815 BLAKE2B 4d357e4d30f9552972170d65b9a5358b69c46a3e772fe05efc22f3d4ffc1caeeaad7aacdc7abd503a7ad0545f8bd7d22bf351dcb6df76f812fa4d45c34d65df0 SHA512 a672ccefd0730a8166fef1d4e39f9034d9ae426a3f5e28d1f4169fa5c5790767693f281d890e7804773b34acdb0ae1febac33cde8c50c0044a5a6152c7209ec2
+DIST winapi-x86_64-pc-windows-gnu-0.4.0.crate 2947998 BLAKE2B 2ad1ea8b5fa07d544e910ccba043ae925269b76b26c9da356305b34b86741dd8b9aff0b9ffe3d562db4fcd7d7c46a11ce9e3168b782b1d89ae6881742b7ede82 SHA512 4a654af6a5d649dc87e00497245096b35a2894ae66f155cb62389902c3b93ddcc5cf7d0d8b9dd97b291d2d80bc686af2298e80abef6ac69883f4a54e79712513
+DIST windows-0.48.0.crate 11864177 BLAKE2B 39c0e4f058f68a829ee08721818a0b04287af20dfe6e03a125b75566b4c8a58b56557d685600f1f9c215811154f9782f12368d42848445d54dcf9bfd6471349d SHA512 7c906f885fa0a730f1cb1ef4e62f5b602a49d44343febe1d38fcd4cbc28e0342766983796042585fe457aa229333558715b6270e378946faa8f398a7ecc2af8c
+DIST windows-sys-0.48.0.crate 2628884 BLAKE2B 551e900de4f67187ef034b60df9fd0e0d8f82a3100ef28e1eabd543ac129d882dc86ffcc1714071aba09e4cb2ae2d2f07ace1a32b99fd989ce525cf05991edab SHA512 bdf534bcf3face31e9ebe11427a911a53f89f4ff5eaea8cccd094e139bfe14b2aec602b1cab1df774794d999477439d9adc6b627a8e33c20334fc348ba2c47ed
+DIST windows-targets-0.48.5.crate 6904 BLAKE2B 7396bb210f37bd51da86f39fca3425c8f6610721d5c4e94f9fafa0a8a8046303b3fcc6979146bcfaa32f4406d242a0455f6cbb220f84c6ff84650e755acf5223 SHA512 e079eeef255a046be7f8e6a31c14f7b230254ebcf05eed2944827bb3d2a0dc30940d87593cf544d5e7ef35f6312b99430efcfb01421d91b02bb9c4bef7d98709
+DIST windows_aarch64_gnullvm-0.48.5.crate 418492 BLAKE2B 5c6f7d73ad05740f0bac304ed1ef9b2ea63b0d6ca8f875552ae299a0b73b1557e8fe996f1c2b69be9f2df350c9288690f49ee62239a2896991364331d6c55462 SHA512 20158d31454488f6053d3ad7b97d7fc6eae6cf37e4ba0e50c28bd29b368505eed64199ae31104d5f97b66846be54e5ed25c0ad31ea850819205c573a31ac0996
+DIST windows_aarch64_msvc-0.48.5.crate 798483 BLAKE2B 60c466d6536426425a34b5ca20da97c8127ebeb4fb9b1363911165bada484f8913fcd50e90410b5661e0c27dbfe8f4eeaa62fb17d1f3566bfc82b6255e11619b SHA512 223f016c6f1a44dbc5c8a8428b39438f75380ea06951b7c26ed0877b19d79410c6fde5e4c7f2c839b6e76159131f39a1230e0e3a208dfc425ba9117e3665c4ff
+DIST windows_i686_gnu-0.48.5.crate 844891 BLAKE2B fdc37cd74a4982056bf22fdb7b84e1c55dc838f3cb19ff3648730a77e673ef4ecc0380b3e4277bb8df2fcfa25f57b69014713d9e3ed27c28e19b25b3ea2ab774 SHA512 931ba5c1e4eb8ae73248e00d9611298d1c4b4b0dae719fdeb9243930cd420a103a7bc2738e0a4887c42c8f25728d6c5d64ad141dc092bc3f1d0f35dbe37d303a
+DIST windows_i686_msvc-0.48.5.crate 864300 BLAKE2B 3d3ea8be55e2d6ced0eeda18abe1dffb925a1a78f456d683e4450d9f2fd287ad2e8494d65b2b770c677a12b3a60d10f0435e16c61880e3867c3657fd44892442 SHA512 70e2fb4fdb006a4cbd43ab2c7e940b277a15fb1790dfa2d1fc1f1fd18bead4886f6dc046e44326603e4894d988578917b8932aba5d9a6a4cc8424911cad9dc7e
+DIST windows_x86_64_gnu-0.48.5.crate 801619 BLAKE2B aa7e7e6a6ff9f9553ada3a0a39a9aa798e9d995a8eef36e0b6fdb2a0db93ddecee5548970575271fe43aec74797a420d0ee231d503b5bad1bd999059261e0e33 SHA512 1d6056fae430b3d042bdff3c6217c76be4b8b9f5dada9bad06beaac2db7d7ab9b0a82e44f498ec88e61afa73e99f56d84d445dc3847732b9ce5d947e08485f74
+DIST windows_x86_64_gnullvm-0.48.5.crate 418486 BLAKE2B 12a2199d434617c1df1a839e9f435620ad64b40c579f6d0c3677553ad7a48e5765d12c266b04946402e15c92cff2e4ac4979ce2130750ef426e2672119680284 SHA512 c016d5b5e73832b61ff67929d92fa8c16e154656294357266ad29ce1f44db4ca2d2935dba31a6b571187dc838b1d22f1e3b41fefffd1d719a338439adf1646aa
+DIST windows_x86_64_msvc-0.48.5.crate 798412 BLAKE2B 8abc0721e2fb337fe17c91d278947d36122d9045b839ba0cf3e690202d242265b676f23cc301da5f9d98c56ca4ecb76f7d6f072ee71bf986a1deca87020b90e5 SHA512 fa1c5cd14ca2ff0082e2504cf59d317dc4dc6f7138d35c12f95d4476a9c13d8b7f5537d0ee251eee7c99411ad31b22263171b7fbd391daa5d3ea3488ceaa61a0
+DIST zstd-0.12.4.crate 30434 BLAKE2B 39dc5c1aaee0c6973ec27ca3447f7d3f0460ca7382c46660c1c72ad9af9c9dc85778b6e0addb6ed90ffd90848f5da7006fae7c0d41c8915965707b923ed7b1cd SHA512 69b94d18982d7adbf0d3a79dc013c98af97ec2b10e10ef4cd6c15a89049f343fd83db3a79c393a43e9d12d8c071a728b8666680cc5a23817a126340ba9500715
+DIST zstd-safe-6.0.6.crate 20828 BLAKE2B 426bf142868de682082d3b5fb4ac711a96b963856af763f3cc4544aa5bac32f14fc4c40f3b95cf2e91e0145cb0a1c67823c258ceaab48d368c8d56ddc6f8f440 SHA512 33f8aee9c584a2abdd3d965fa9ff15fad310fc3f9d73e04d5a3a871c3b7e96b7a833cf563ef81656c9226ec793f42bb9c08b1c5cc53c9ead3e29802d8fcfbc6a
+DIST zstd-sys-2.0.8+zstd.1.5.5.crate 736270 BLAKE2B 9ee3bae57279efca7305f6ac9456c71eb5714b595cf75b0faac7232c91f9df127c75c02f68021291ea01d6ab42a51a550d84cec246cd47bb8f502bbd32ceee09 SHA512 acfbf6c464678438bcab289c8be2e67a2bdfb910143d77363bf1ad5227dffc4b60e224388b7e59186fd4d1e017b63fef49734e99e383cbda19b82b4ed382fcd8
diff --git a/sci-misc/pqdump/pqdump-0.1.0.ebuild b/sci-misc/pqdump/pqdump-0.1.0.ebuild
new file mode 100644
index 000000000..377b17549
--- /dev/null
+++ b/sci-misc/pqdump/pqdump-0.1.0.ebuild
@@ -0,0 +1,146 @@
+# Copyright 2023 Gentoo Authors
+# Distributed under the terms of the GNU General Public License v2
+
+# Auto-Generated by cargo-ebuild 0.5.4
+
+EAPI=8
+
+CRATES="
+	adler-1.0.2
+	ahash-0.8.3
+	alloc-no-stdlib-2.0.4
+	alloc-stdlib-0.2.2
+	android-tzdata-0.1.1
+	android_system_properties-0.1.5
+	anstream-0.5.0
+	anstyle-1.0.2
+	anstyle-parse-0.2.1
+	anstyle-query-1.0.0
+	anstyle-wincon-2.1.0
+	arrow-array-46.0.0
+	arrow-buffer-46.0.0
+	arrow-cast-46.0.0
+	arrow-data-46.0.0
+	arrow-ipc-46.0.0
+	arrow-schema-46.0.0
+	arrow-select-46.0.0
+	autocfg-1.1.0
+	base64-0.21.3
+	bitflags-1.3.2
+	brotli-3.3.4
+	brotli-decompressor-2.3.4
+	bumpalo-3.13.0
+	byteorder-1.4.3
+	bytes-1.4.0
+	cc-1.0.83
+	cfg-if-1.0.0
+	chrono-0.4.26
+	clap-4.4.0
+	clap_builder-4.4.0
+	clap_derive-4.4.0
+	clap_lex-0.5.1
+	colorchoice-1.0.0
+	comfy-table-7.0.1
+	const-random-0.1.15
+	const-random-macro-0.1.15
+	core-foundation-sys-0.8.4
+	crc32fast-1.3.2
+	crunchy-0.2.2
+	flatbuffers-23.5.26
+	flate2-1.0.27
+	getrandom-0.2.10
+	half-2.3.1
+	hashbrown-0.14.0
+	heck-0.4.1
+	iana-time-zone-0.1.57
+	iana-time-zone-haiku-0.1.2
+	integer-encoding-3.0.4
+	jobserver-0.1.26
+	js-sys-0.3.64
+	lexical-core-0.8.5
+	lexical-parse-float-0.8.5
+	lexical-parse-integer-0.8.6
+	lexical-util-0.8.5
+	lexical-write-float-0.8.5
+	lexical-write-integer-0.8.5
+	libc-0.2.147
+	libm-0.2.7
+	log-0.4.20
+	lz4-1.24.0
+	lz4-sys-1.9.4
+	miniz_oxide-0.7.1
+	num-0.4.1
+	num-bigint-0.4.4
+	num-complex-0.4.4
+	num-integer-0.1.45
+	num-iter-0.1.43
+	num-rational-0.4.1
+	num-traits-0.2.16
+	once_cell-1.18.0
+	ordered-float-2.10.0
+	parquet-46.0.0
+	paste-1.0.14
+	pkg-config-0.3.27
+	proc-macro-hack-0.5.20+deprecated
+	proc-macro2-1.0.66
+	quote-1.0.33
+	rustc_version-0.4.0
+	rustversion-1.0.14
+	semver-1.0.18
+	seq-macro-0.3.5
+	snap-1.1.0
+	static_assertions-1.1.0
+	strsim-0.10.0
+	strum-0.24.1
+	strum_macros-0.24.3
+	syn-1.0.109
+	syn-2.0.29
+	thrift-0.17.0
+	tiny-keccak-2.0.2
+	twox-hash-1.6.3
+	unicode-ident-1.0.11
+	unicode-width-0.1.10
+	utf8parse-0.2.1
+	version_check-0.9.4
+	wasi-0.11.0+wasi-snapshot-preview1
+	wasm-bindgen-0.2.87
+	wasm-bindgen-backend-0.2.87
+	wasm-bindgen-macro-0.2.87
+	wasm-bindgen-macro-support-0.2.87
+	wasm-bindgen-shared-0.2.87
+	winapi-0.3.9
+	winapi-i686-pc-windows-gnu-0.4.0
+	winapi-x86_64-pc-windows-gnu-0.4.0
+	windows-0.48.0
+	windows-sys-0.48.0
+	windows-targets-0.48.5
+	windows_aarch64_gnullvm-0.48.5
+	windows_aarch64_msvc-0.48.5
+	windows_i686_gnu-0.48.5
+	windows_i686_msvc-0.48.5
+	windows_x86_64_gnu-0.48.5
+	windows_x86_64_gnullvm-0.48.5
+	windows_x86_64_msvc-0.48.5
+	zstd-0.12.4
+	zstd-safe-6.0.6
+	zstd-sys-2.0.8+zstd.1.5.5
+"
+
+inherit cargo
+
+DESCRIPTION="simple program to dump Parquet files"
+HOMEPAGE="https://github.com/Berrysoft/pqdump"
+SRC_URI="
+    https://github.com/Berrysoft/${PN}/archive/v${PV}.tar.gz -> ${P}.tar.gz
+    $(cargo_crate_uris)
+"
+
+LICENSE="BSD Apache-2.0 Apache-2.0-with-LLVM-exceptions BSD CC0-1.0 MIT Unicode-DFS-2016 Unlicense ZLIB"
+SLOT="0"
+KEYWORDS="~amd64"
+
+DEPEND=""
+RDEPEND="${DEPEND}"
+BDEPEND=""
+
+QA_FLAGS_IGNORED="usr/bin/${PN}"
diff --git a/sci-misc/praat/Manifest b/sci-misc/praat/Manifest
index eb6c460d5..552567989 100644
--- a/sci-misc/praat/Manifest
+++ b/sci-misc/praat/Manifest
@@ -1 +1 @@
-DIST praat-6.0.26.tar.gz 11631820 BLAKE2B c6cbd695e00954ea61084b43a43882f7e410127f500ff6a350e72b95ad7a27d8a64ff123d5d4d1a361b5da46f33ea4ef4d427a70f34a676fca609b1dc94446b0 SHA512 56a480ea6caf0226b048b1472eaa77761ad5e3f5cd4c65c5f11bd84e8655988e8c1f729f42af130d19fb6d6ee36814bde4c121d824292b35714beeb7ea666ed0
+DIST praat-6.1.42.tar.gz 33628783 BLAKE2B b406ae2d0242c3a093a99db45a083cf54180be6632946596e5b3cebf20b133e29fcac5081f5fc997cf6b6c313128b4f2813b00c2b096fc5c085c8be1642cc6c7 SHA512 eb3f6b5f0a74a1eba4dd4fb6f9231322e2accf127e8d9e104066c4341120e72c00f3773b38636891094d9912dd4081e2b6719f1c07883e592341dbb81f2db9ce
diff --git a/sci-misc/praat/metadata.xml b/sci-misc/praat/metadata.xml
index 8b2f625ef..5ca31b49e 100644
--- a/sci-misc/praat/metadata.xml
+++ b/sci-misc/praat/metadata.xml
@@ -4,10 +4,6 @@
 	<maintainer type="person">
 		<email>flammie@gentoo.org</email>
 	</maintainer>
-	<longdescription lang="en">
-Praat is a phonetic program for computer. It includes speech synthesis,
-analysis and other tools.
-</longdescription>
 	<upstream>
 		<remote-id type="github">praat/praat</remote-id>
 	</upstream>
diff --git a/sci-misc/praat/praat-6.0.26.ebuild b/sci-misc/praat/praat-6.0.26.ebuild
deleted file mode 100644
index 01f910d56..000000000
--- a/sci-misc/praat/praat-6.0.26.ebuild
+++ /dev/null
@@ -1,37 +0,0 @@
-# Copyright 1999-2017 Gentoo Foundation
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=6
-
-DESCRIPTION="Speech analysis and synthesis"
-HOMEPAGE="http://www.fon.hum.uva.nl/praat/ https://github.com/praat/praat"
-SRC_URI="https://github.com/${PN}/${PN}/archive/v${PV}.tar.gz -> ${P}.tar.gz"
-
-KEYWORDS="~amd64 ~x86"
-IUSE=""
-LICENSE="GPL-2"
-SLOT="0"
-
-DEPEND="
-	x11-libs/gtk+:2
-	media-libs/alsa-lib
-	media-sound/pulseaudio"
-RDEPEND="${DEPEND}"
-
-src_prepare() {
-	eapply_user
-	# TODO: following line should be updated for non-linux etc. builds
-	# (Flammie does not have testing equipment)
-	cp makefiles/makefile.defs.linux.pulse makefile.defs || die
-
-	cat <<-EOF >> makefile.defs
-		CFLAGS += ${CFLAGS}
-		CXXFLAGS += ${CXXFLAGS}
-	EOF
-}
-
-src_install() {
-	dobin ${PN}
-	insinto /usr/share/${PN}
-	doins -r test
-}
diff --git a/sci-misc/praat/praat-6.1.42.ebuild b/sci-misc/praat/praat-6.1.42.ebuild
new file mode 100644
index 000000000..5a60b5149
--- /dev/null
+++ b/sci-misc/praat/praat-6.1.42.ebuild
@@ -0,0 +1,60 @@
+# Copyright 1999-2021 Gentoo Authors
+# Distributed under the terms of the GNU General Public License v2
+
+EAPI=7
+
+DESCRIPTION="Speech analysis and synthesis"
+SRC_URI="https://github.com/praat/praat/archive/v${PV}.tar.gz -> ${P}.tar.gz"
+HOMEPAGE="http://www.fon.hum.uva.nl/praat/"
+
+KEYWORDS="~amd64 ~x86"
+IUSE="+pulseaudio static-libs +X"
+LICENSE="GPL-2"
+SLOT="0"
+
+DEPEND="
+	pulseaudio? ( media-sound/pulseaudio )
+	static-libs? ( media-libs/alsa-lib )
+	X? ( x11-libs/gtk+:3 )
+	!X? ( x11-libs/pango )"
+
+RDEPEND="${DEPEND}"
+
+S="${WORKDIR}/praat-${PV}"
+
+src_prepare() {
+	if use X; then
+		if use static-libs; then
+			if use pulseaudio; then
+				cp "${S}/makefiles/makefile.defs.linux.pulse_static" "${S}/makefile.defs"
+			else
+				cp "${S}/makefiles/makefile.defs.linux.alsa" "${S}/makefile.defs"
+			fi
+		else
+			if use pulseaudio; then
+				cp "${S}/makefiles/makefile.defs.linux.pulse" "${S}/makefile.defs"
+			else
+				cp "${S}/makefiles/makefile.defs.linux.silent" "${S}/makefile.defs"
+			fi
+		fi
+	else
+		cp "${S}/makefiles/makefile.defs.linux.nogui" "${S}/makefile.defs"
+	fi
+	cat <<-EOF >> makefile.defs
+		CFLAGS += ${CFLAGS}
+		LDFLAGS += ${LDFLAGS}
+		CXXFLAGS += ${CXXFLAGS}
+	EOF
+	default
+}
+
+src_install() {
+	if [ -e praat_nogui ]; then
+		mv praat_nogui praat
+	elif [ -e praat_static ]; then
+		mv praat_static praat
+	fi
+	dobin praat
+	insinto /usr/share/${PN}/test
+	doins -r test/*
+}
diff --git a/sci-misc/pywordnet/Manifest b/sci-misc/pywordnet/Manifest
deleted file mode 100644
index 80a757de5..000000000
--- a/sci-misc/pywordnet/Manifest
+++ /dev/null
@@ -1 +0,0 @@
-DIST pywordnet-2.0.1.tar.gz 38052 BLAKE2B 598f24f486583c0447f2510efc3b73782fea9a01978ca3f66445e7ccca77aea33f757d268cc29a22f6cb2da235f4639168537e430bfe9628255cc15b8da95378 SHA512 2073765c2fa2a2b91c200ded22c60412af1ff89d5104d24d8624602872f34cb6c657aaa9f4ff2c2b203403437f198f908f8e9f9714b2a3f24b6a1ce4375e8d2b
diff --git a/sci-misc/pywordnet/metadata.xml b/sci-misc/pywordnet/metadata.xml
deleted file mode 100644
index bedc00164..000000000
--- a/sci-misc/pywordnet/metadata.xml
+++ /dev/null
@@ -1,13 +0,0 @@
-<?xml version="1.0" encoding="UTF-8"?>
-<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
-<pkgmetadata>
-	<maintainer type="person">
-		<email>flammie@gentoo.org</email>
-	</maintainer>
-	<longdescription>
-Pywordnet contains python bindings to handle wordnet databases.
-</longdescription>
-	<upstream>
-		<remote-id type="sourceforge">pywordnet</remote-id>
-	</upstream>
-</pkgmetadata>
diff --git a/sci-misc/pywordnet/pywordnet-2.0.1.ebuild b/sci-misc/pywordnet/pywordnet-2.0.1.ebuild
deleted file mode 100644
index 51066d9d7..000000000
--- a/sci-misc/pywordnet/pywordnet-2.0.1.ebuild
+++ /dev/null
@@ -1,22 +0,0 @@
-# Copyright 1999-2014 Gentoo Foundation
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=5
-
-PYTHON_COMPAT=( python2_7 )
-
-inherit distutils-r1
-
-DESCRIPTION="Python bindings for wordnet"
-HOMEPAGE="http://pywordnet.sourceforge.net/"
-SRC_URI="mirror://sourceforge/${PN}/${P}.tar.gz"
-
-LICENSE="Artistic"
-SLOT="0"
-KEYWORDS="~amd64 ~x86"
-IUSE=""
-
-DEPEND=">=app-dicts/wordnet-2.0"
-RDEPEND="${DEPEND}"
-
-DOCS=( docs/. )
diff --git a/sci-misc/sfst/Manifest b/sci-misc/sfst/Manifest
deleted file mode 100644
index 303a0b2d7..000000000
--- a/sci-misc/sfst/Manifest
+++ /dev/null
@@ -1,5 +0,0 @@
-DIST SFST-1.4.2.tar.gz 490458 BLAKE2B 63bbf850a38698cdb492760c2b30274980408b6c8a492a301e87f8c09972aa5afcc67baee0b95c40ab13e6d83295d7715958592d35465ca7df987bea0c532ae1 SHA512 9466d929e33141db7e2e19eb9dbcdf095a561677ba0e0ae9158a813a92ac3b389462a47a253fca5c61d14413c2559e0f1cfe3d3222f456836b5b5f93b33b42ea
-DIST SFST-1.4.6g.tar.gz 486334 BLAKE2B 87800c1f88a7d001d5deb746d501d8a88842c07d4229d6637f9ac9e61966969a4b1d8840d1116b2502c4aa3447ed66d3f00b4bfa4d4c9774488fa29e365ad580 SHA512 8535ffd7b0a62dd27bc24d95d048afc7f56c81bfc3c989255a3d65b18a7be99c6b474a6ca0c196f7dc68eea4e4a5e1d744413252d909a9db2f0be843bb8fc518
-DIST SFST-1.4.7d.tar.gz 666828 BLAKE2B 3ec54d4203854e0becbe9443ea4c9a2296281f5c87975e87d783ebb801c39b031e28b165f90f7f8ac95771b2dea4156349bb01ef4d17b0b1ee91b10dddab4544 SHA512 905a606aa11c7d480d0714d195f864a73ed55637a81867bc1659e789367730be68e7d3f90a186330cb24ef7b0404b66ab58e9b8a1e78f4b6a185b07eddd6501b
-DIST sfst.el 4752 SHA256 b47ff59f5ff24482dbbb2f1e71a8b9ca234c4154487f83eb2118f1a62bb9eb5f SHA512 88c808044919d49b7c647c16caffb0e67d6fae9ae948434247dbcef7d78168a7b67e7a5b64c5dbeb634f273d6b8ccb93d449af097a1418a6d48a7852f6ad9bbe WHIRLPOOL c8075858fde4c0986acdebab6e5935b1a8022065db09f722d0844d5a020414e8b19d3f321a6f1eeb96e4609643ed4dc62375d8c11be471b5d2e6b7212f6af273
-DIST vim-mode.tar.gz 1104 SHA256 a62ba91c40da75be389a334db62cc2b4904bedfac657b185012b10f3f55dfe09 SHA512 8b808553dbf7a6d6aebb0d6382339bfbe56584effe0b1b0b9096969f81324305e4b66760188dc8fdfbb69118aa5688c66e2bd880dabb57b494068fd620ff540d WHIRLPOOL 252b7bd1110f3522caf0e2921550a52a552611227fd0da0029485f6eaf467ad476758deaee2774cf3c0e882d5dca63b82362e3e5a8fd378171286f7c1682fa77
diff --git a/sci-misc/sfst/files/50sfst-gentoo.el b/sci-misc/sfst/files/50sfst-gentoo.el
deleted file mode 100644
index e3e9da983..000000000
--- a/sci-misc/sfst/files/50sfst-gentoo.el
+++ /dev/null
@@ -1,9 +0,0 @@
-
-;;; site-lisp configuration for sfst-syntax
-
-(add-to-list 'load-path "@SITELISP@")
-
-(autoload 'sfst-mode "ebuild-mode"
-  "Major mode for SFST-PL files" t)
-
-(add-to-list 'auto-mode-alist '("\\.fst\\'" . sfst-mode))
diff --git a/sci-misc/sfst/files/SFST-1.3-gcc43.patch b/sci-misc/sfst/files/SFST-1.3-gcc43.patch
deleted file mode 100644
index 3198d6b0f..000000000
--- a/sci-misc/sfst/files/SFST-1.3-gcc43.patch
+++ /dev/null
@@ -1,37 +0,0 @@
-diff -Naur SFST-1.3/src/alphabet.C SFST/src/alphabet.C
---- SFST-1.3/src/alphabet.C	2008-09-11 10:59:11.000000000 +0000
-+++ SFST/src/alphabet.C	2008-09-11 11:01:44.000000000 +0000
-@@ -10,6 +10,9 @@
- /*                                                                 */
- /*******************************************************************/
- 
-+#include <climits>
-+#include <cstring>
-+
- #include "utf8.h"
- #include "alphabet.h"
- 
-diff -Naur SFST-1.3/src/alphabet.h SFST/src/alphabet.h
---- SFST-1.3/src/alphabet.h	2008-09-11 10:59:11.000000000 +0000
-+++ SFST/src/alphabet.h	2008-09-11 10:59:54.000000000 +0000
-@@ -21,6 +21,8 @@
- 
- #include <iostream>
- 
-+#include <cstring>
-+
- #ifndef CODE_DATA_TYPE
- typedef unsigned short Character;  // data type of the symbol codes
- #else
-diff -Naur SFST-1.3/src/interface.h SFST/src/interface.h
---- SFST-1.3/src/interface.h	2008-09-11 10:59:11.000000000 +0000
-+++ SFST/src/interface.h	2008-09-11 11:03:32.000000000 +0000
-@@ -82,7 +82,7 @@
- Transducer *optional( Transducer *a );
- Transducer *make_rule( Transducer *lc, Range *r1, Twol_Type type,
- 		      Range *r2, Transducer *rc );
--Transducer *freely_insert( Transducer *a, Character c, Character c );
-+Transducer *freely_insert( Transducer *a, Character lc, Character uc );
- Transducer *make_mapping( Ranges*, Ranges* );
- Ranges *add_range( Range*, Ranges* );
- Contexts *make_context( Transducer *l, Transducer *r );
diff --git a/sci-misc/sfst/files/ftdetect-sfst.vim b/sci-misc/sfst/files/ftdetect-sfst.vim
deleted file mode 100644
index df702ad49..000000000
--- a/sci-misc/sfst/files/ftdetect-sfst.vim
+++ /dev/null
@@ -1,2 +0,0 @@
-" SFST ftdetect for vim sfst-syntax
-au BufRead,BufNewFile *.sfst	set filetype=sfst
diff --git a/sci-misc/sfst/metadata.xml b/sci-misc/sfst/metadata.xml
deleted file mode 100644
index e1523edf0..000000000
--- a/sci-misc/sfst/metadata.xml
+++ /dev/null
@@ -1,13 +0,0 @@
-<?xml version="1.0" encoding="UTF-8"?>
-<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
-<pkgmetadata>
-	<maintainer type="person">
-		<email>flammie@gentoo.org</email>
-		<description>N.B. This is used in my master’s thesis project</description>
-	</maintainer>
-	<longdescription>
-SFST is open source package for compiling and using Finite State
-Transducers, mainly for linguistic uses, made in university of
-Stuttgart, Germany.
-</longdescription>
-</pkgmetadata>
diff --git a/sci-misc/sfst/sfst-1.4.2.ebuild b/sci-misc/sfst/sfst-1.4.2.ebuild
deleted file mode 100644
index 3fe2847a0..000000000
--- a/sci-misc/sfst/sfst-1.4.2.ebuild
+++ /dev/null
@@ -1,80 +0,0 @@
-# Copyright 1999-2015 Gentoo Foundation
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=5
-
-inherit elisp eutils
-
-MY_PN="SFST"
-MY_P="${MY_PN}-${PV}"
-
-DESCRIPTION="Uni Stuttgart Finite State Transducer tools"
-HOMEPAGE="http://www.ims.uni-stuttgart.de/projekte/gramotron/SOFTWARE/SFST.html"
-SRC_URI="
-	ftp://ftp.ims.uni-stuttgart.de/pub/corpora/${MY_PN}/${MY_P}.tar.gz
-	vim-syntax? ( ftp://ftp.ims.uni-stuttgart.de/pub/corpora/${MY_PN}/vim-mode.tar.gz )
-	emacs? ( http://www.cis.uni-muenchen.de/~wastl/emacs/sfst.el )"
-
-LICENSE="GPL-2"
-SLOT="0"
-KEYWORDS="~amd64 ~x86"
-IUSE="emacs vim-syntax"
-
-RDEPEND="sys-libs/readline:0="
-DEPEND="${RDEPEND}
-	sys-devel/bison
-	sys-devel/flex"
-
-S="${WORKDIR}/${MY_PN}"
-
-src_prepare() {
-	# settings in makefile are a bit hacky
-	#epatch "${FILESDIR}"/SFST-1.3-gcc43.patch || die "patch failed"
-	sed \
-		-e "s/^CFLAGS = -O3/CFLAGS = ${CFLAGS}/g" \
-		-e "s/local//g" \
-		-e 's/strip/echo strip removed: /g' \
-		-e 's/# FPIC/FPIC/' \
-		-e 's/ $(PREFIX/ $(DESTDIR)$(PREFIX/g' \
-		-e 's/ldconfig/true/' \
-		-e 's/$(INSTALL_LIBS)/$(INSTALL_DIR) $(DESTDIR)$(PREFIX)\/lib\n\t\0/' \
-		-i "${S}"/src/Makefile || die "sed failed"
-	cd "${S}" || die
-	if use emacs ; then
-		cp "${DISTDIR}/sfst.el" "${S}" || die
-	fi
-	if use vim-syntax ; then
-		mv "${WORKDIR}"/INSTALL "${S}"/INSTALL-vim-syntax || die
-		mv "${WORKDIR}"/sfst.vim "${S}"/ || die
-	fi
-}
-
-src_compile() {
-	emake -C "${S}/src"
-	if use emacs ; then
-		cd "${S}" || die
-		elisp_src_compile
-	fi
-}
-
-src_install() {
-	cd "${S}/src" || die
-	# destdir works but prefix fails
-	emake DESTDIR="${D}" install maninstall libinstall
-	cd "${S}" || die
-	dodoc README
-	insinto /usr/share/doc/${PF}/
-	doins doc/SFST-Manual.pdf doc/SFST-Tutorial.pdf
-	insinto /usr/share/${PN}
-	doins -r data/*
-	if use vim-syntax ; then
-		insinto /usr/share/vim/vimfiles/syntax/
-		doins sfst.vim
-		insinto /usr/share/vim/vimfiles/ftdetect/
-		newins "${FILESDIR}"/ftdetect-sfst.vim sfst.vim
-		dodoc INSTALL-vim-syntax
-	fi
-	if use emacs ; then
-		elisp_src_install
-	fi
-}
diff --git a/sci-misc/sfst/sfst-1.4.6g.ebuild b/sci-misc/sfst/sfst-1.4.6g.ebuild
deleted file mode 100644
index 1049b4f28..000000000
--- a/sci-misc/sfst/sfst-1.4.6g.ebuild
+++ /dev/null
@@ -1,82 +0,0 @@
-# Copyright 1999-2015 Gentoo Foundation
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=5
-
-inherit elisp-common eutils
-
-MY_PN="SFST"
-MY_P="${MY_PN}-${PV}"
-
-DESCRIPTION="Uni Stuttgart Finite State Transducer tools"
-HOMEPAGE="http://www.ims.uni-stuttgart.de/projekte/gramotron/SOFTWARE/SFST.html"
-SRC_URI="
-	ftp://ftp.ims.uni-stuttgart.de/pub/corpora/${MY_PN}/${MY_P}.tar.gz
-	vim-syntax? ( ftp://ftp.ims.uni-stuttgart.de/pub/corpora/${MY_PN}/vim-mode.tar.gz )
-	emacs? ( http://www.cis.uni-muenchen.de/~wastl/emacs/sfst.el )"
-
-LICENSE="GPL-2"
-SLOT="0"
-KEYWORDS="~amd64 ~x86"
-IUSE="emacs vim-syntax"
-
-RDEPEND="
-	sys-libs/readline:0=
-	emacs? ( virtual/emacs )"
-DEPEND="${RDEPEND}
-	sys-devel/bison
-	sys-devel/flex"
-
-S="${WORKDIR}/${MY_PN}"
-
-src_prepare() {
-	# settings in makefile are a bit hacky
-	#epatch "${FILESDIR}"/SFST-1.3-gcc43.patch || die "patch failed"
-	sed \
-		-e "s/^CFLAGS = -O3/CFLAGS = ${CFLAGS}/g" \
-		-e "s/local//g" \
-		-e 's/strip/echo strip removed: /g' \
-		-e 's/# FPIC/FPIC/' \
-		-e 's/ $(PREFIX/ $(DESTDIR)$(PREFIX/g' \
-		-e 's/ldconfig/true/' \
-		-e 's/$(INSTALL_LIBS)/$(INSTALL_DIR) $(DESTDIR)$(PREFIX)\/lib\n\t\0/' \
-		-i "${S}"/src/Makefile || die "sed failed"
-	cd "${S}" || die
-	if use emacs ; then
-		cp "${DISTDIR}/sfst.el" "${S}" || die
-	fi
-	if use vim-syntax ; then
-		mv "${WORKDIR}"/INSTALL "${S}"/INSTALL-vim-syntax || die
-		mv "${WORKDIR}"/sfst.vim "${S}"/ || die
-	fi
-}
-
-src_compile() {
-	emake -C "${S}/src"
-	if use emacs ; then
-		cd "${S}" || die
-		elisp-compile *.el || die "could not compile elisp"
-	fi
-}
-
-src_install() {
-	cd "${S}/src" || die
-	# destdir works but prefix fails
-	emake DESTDIR="${D}" install maninstall libinstall
-	cd "${S}" || die
-	dodoc README
-	insinto /usr/share/doc/${PF}/
-	doins doc/SFST-Manual.pdf doc/SFST-Tutorial.pdf
-	insinto /usr/share/${PN}
-	doins -r data/*
-	if use vim-syntax ; then
-		insinto /usr/share/vim/vimfiles/syntax/
-		doins sfst.vim
-		insinto /usr/share/vim/vimfiles/ftdetect/
-		newins "${FILESDIR}"/ftdetect-sfst.vim sfst.vim
-		dodoc INSTALL-vim-syntax
-	fi
-	if use emacs ; then
-		elisp-install ${PN} *.el *.elc
-	fi
-}
diff --git a/sci-misc/sfst/sfst-1.4.7d.ebuild b/sci-misc/sfst/sfst-1.4.7d.ebuild
deleted file mode 100644
index c0210963f..000000000
--- a/sci-misc/sfst/sfst-1.4.7d.ebuild
+++ /dev/null
@@ -1,83 +0,0 @@
-# Copyright 1999-2017 Gentoo Foundation
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=6
-
-inherit elisp-common eutils
-
-MY_PN="SFST"
-MY_P="${MY_PN}-${PV}"
-
-DESCRIPTION="Uni Stuttgart Finite State Transducer tools"
-HOMEPAGE="http://www.cis.uni-muenchen.de/~schmid/tools/SFST/"
-SRC_URI="
-	http://www.cis.uni-muenchen.de/~schmid/tools/${MY_PN}/data/${MY_P}.tar.gz
-	vim-syntax? ( http://www.cis.uni-muenchen.de/~schmid/tools/${MY_PN}/data/vim-mode.tar.gz )
-	emacs? ( http://www.cis.uni-muenchen.de/~wastl/emacs/sfst.el )"
-
-LICENSE="GPL-2"
-SLOT="0"
-KEYWORDS="~amd64 ~x86"
-IUSE="emacs vim-syntax"
-
-RDEPEND="
-	sys-libs/readline:0=
-	emacs? ( virtual/emacs )"
-DEPEND="${RDEPEND}
-	sys-devel/bison
-	sys-devel/flex"
-
-S="${WORKDIR}/${MY_PN}"
-
-src_prepare() {
-	# settings in makefile are a bit hacky
-	sed \
-		-e "s/^CFLAGS = -O3/CFLAGS = ${CFLAGS}/g" \
-		-e "s/local//g" \
-		-e 's/strip/echo strip removed: /g' \
-		-e 's/# FPIC/FPIC/' \
-		-e 's/ $(PREFIX/ $(DESTDIR)$(PREFIX/g' \
-		-e 's/ldconfig/true/' \
-		-e 's/$(INSTALL_LIBS)/$(INSTALL_DIR) $(DESTDIR)$(PREFIX)\/lib\n\t\0/' \
-		-i "${S}"/src/Makefile || die "sed failed"
-	cd "${S}" || die
-	if use emacs ; then
-		cp "${DISTDIR}/sfst.el" "${S}" || die
-	fi
-	if use vim-syntax ; then
-		mv "${WORKDIR}"/INSTALL "${S}"/INSTALL-vim-syntax || die
-		mv "${WORKDIR}"/sfst.vim "${S}"/ || die
-	fi
-
-	eapply_user
-}
-
-src_compile() {
-	emake -C "${S}/src"
-	if use emacs ; then
-		cd "${S}" || die
-		elisp-compile *.el || die "could not compile elisp"
-	fi
-}
-
-src_install() {
-	cd "${S}/src" || die
-	# destdir works but prefix fails
-	emake DESTDIR="${D}" install maninstall libinstall
-	cd "${S}" || die
-	dodoc README
-	insinto /usr/share/doc/${PF}/
-	doins doc/SFST-Manual.pdf doc/SFST-Tutorial.pdf
-	insinto /usr/share/${PN}
-	doins -r data/*
-	if use vim-syntax ; then
-		insinto /usr/share/vim/vimfiles/syntax/
-		doins sfst.vim
-		insinto /usr/share/vim/vimfiles/ftdetect/
-		newins "${FILESDIR}"/ftdetect-sfst.vim sfst.vim
-		dodoc INSTALL-vim-syntax
-	fi
-	if use emacs ; then
-		elisp-install ${PN} *.el *.elc
-	fi
-}
diff --git a/sci-misc/simx/Manifest b/sci-misc/simx/Manifest
deleted file mode 100644
index 34a0d55d9..000000000
--- a/sci-misc/simx/Manifest
+++ /dev/null
@@ -1 +0,0 @@
-DIST simx-0.2.tar.gz 595766 BLAKE2B d2aaea3f30e5e03ce400d0bb9965cb36e5e10d75364fa03a063467e8dc886d652ad7459fcb77dabaca0427699cef0a7330127a5720eb5007b8d6804bad9a2c0f SHA512 f03ed149b369d60ea9eafa7bff0b2a08007808f6ea280d12c413583a30a55cb80e660a062d701ff745bb30a2f63d4c958c63e76d6b00264221c3c830cb526116
diff --git a/sci-misc/simx/metadata.xml b/sci-misc/simx/metadata.xml
deleted file mode 100644
index b1adaa806..000000000
--- a/sci-misc/simx/metadata.xml
+++ /dev/null
@@ -1,11 +0,0 @@
-<?xml version="1.0" encoding="UTF-8"?>
-<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
-<pkgmetadata>
-	<maintainer type="project">
-		<email>sci@gentoo.org</email>
-		<name>Gentoo Science Project</name>
-	</maintainer>
-	<upstream>
-		<remote-id type="github">sim-x</remote-id>
-	</upstream>
-</pkgmetadata>
diff --git a/sci-misc/simx/simx-0.2.ebuild b/sci-misc/simx/simx-0.2.ebuild
deleted file mode 100644
index fb74b984f..000000000
--- a/sci-misc/simx/simx-0.2.ebuild
+++ /dev/null
@@ -1,32 +0,0 @@
-# Copyright 1999-2016 Gentoo Foundation
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=6
-
-PYTHON_COMPAT=( python2_7 )
-
-inherit cmake-utils distutils-r1
-
-DESCRIPTION="Library for developing parallel, discrete-event simulations in Python"
-HOMEPAGE="https://github.com/sim-x"
-SRC_URI="https://github.com/sim-x/${PN}/archive/v${PV}.tar.gz -> ${P}.tar.gz"
-
-SLOT="0"
-LICENSE="LGPL-2.1"
-KEYWORDS="~amd64"
-IUSE=""
-
-RDEPEND="
-	virtual/mpi
-	dev-libs/boost[python,${PYTHON_USEDEP}]
-	dev-python/greenlet[${PYTHON_USEDEP}]"
-DEPEND="${RDEPEND}
-	dev-util/cmake"
-
-python_prepare_all() {
-	# don't do egg install
-	sed \
-		-e 's/self.do_egg_install()/_install.install.run(self)/' \
-		-i setup.py || die
-	distutils-r1_python_prepare_all
-}
diff --git a/sci-misc/simx/simx-9999.ebuild b/sci-misc/simx/simx-9999.ebuild
deleted file mode 100644
index 940aa7643..000000000
--- a/sci-misc/simx/simx-9999.ebuild
+++ /dev/null
@@ -1,33 +0,0 @@
-# Copyright 1999-2016 Gentoo Foundation
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=6
-
-PYTHON_COMPAT=( python2_7 )
-
-inherit cmake-utils distutils-r1 git-r3
-
-DESCRIPTION="Library for developing parallel, discrete-event simulations in Python"
-HOMEPAGE="https://github.com/sim-x"
-SRC_URI=""
-EGIT_REPO_URI="git://github.com/sim-x/${PN}.git http://github.com/sim-x/${PN}.git"
-
-SLOT="0"
-LICENSE="LGPL-2.1"
-KEYWORDS=""
-IUSE=""
-
-RDEPEND="
-	virtual/mpi
-	dev-libs/boost[python,${PYTHON_USEDEP}]
-	dev-python/greenlet[${PYTHON_USEDEP}]"
-DEPEND="${RDEPEND}
-	dev-util/cmake"
-
-python_prepare_all() {
-	# don't do egg install
-	sed \
-		-e 's/self.do_egg_install()/_install.install.run(self)/' \
-		-i setup.py || die
-	distutils-r1_python_prepare_all
-}
diff --git a/sci-misc/stanford-parser/Manifest b/sci-misc/stanford-parser/Manifest
index 259d4e9b1..27d5a0eae 100644
--- a/sci-misc/stanford-parser/Manifest
+++ b/sci-misc/stanford-parser/Manifest
@@ -1 +1 @@
-DIST stanford-parser-2007-08-19.tar.gz 60783166 BLAKE2B c35d9f501bd5e204bb58d55eeaaef08d4a6f53513e6103ce8a31f7ff66b870493916058dac72cbe495d73828b74d05d0178796ea9b0e59e14555e8e6e0c2c8d4 SHA512 d22812d9786cc68315969b2a19efbb0ac2a48b24f0a25635a02c87e441f2e605146ec86625e0282a28bab4336918cf249ee1d9a793dc0bfe0268eda0c88b5470
+DIST stanford-parser-4.2.0.zip 182285548 BLAKE2B d9838011b43b849d5ed247d8e0a58fad047a173d5c2ccadf7e18ab45a8f1365302130541802de9790274057d3180644db5e29cb386cb8aae6c58a67cfd6cd9b7 SHA512 9ab4a510ad7b69c23886cc5f865c6020a23888460b0dcced8c0c22870eb246f04bd866777e47ff07d37556a51ff6b14e61aacfd3fe0555aca5e87b67c0140a94
diff --git a/sci-misc/stanford-parser/stanford-parser-1.6.ebuild b/sci-misc/stanford-parser/stanford-parser-1.6.ebuild
deleted file mode 100644
index 81b297db0..000000000
--- a/sci-misc/stanford-parser/stanford-parser-1.6.ebuild
+++ /dev/null
@@ -1,44 +0,0 @@
-# Copyright 1999-2014 Gentoo Foundation
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=5
-
-JAVA_PKG_IUSE="doc source"
-inherit eutils java-pkg-2 java-ant-2
-
-MY_PV=2007-08-19
-MY_P=${PN}-${MY_PV}
-
-DESCRIPTION="Stanfords statistical natural language parsers"
-HOMEPAGE="http://www-nlp.stanford.edu/software/"
-SRC_URI="http://www-nlp.stanford.edu/software/${MY_P}.tar.gz"
-
-LICENSE="GPL-2"
-SLOT="0"
-KEYWORDS="~x86"
-IUSE="${IUSE}"
-
-COMMON_DEP=""
-DEPEND=">=virtual/jdk-1.5
-	${COMMON_DEP}"
-RDEPEND=">=virtual/jre-1.5
-	${COMMON_DEP}"
-
-S="${WORKDIR}/${MY_P}"
-
-EANT_BUILD_TARGET="compile"
-
-src_install() {
-	java-pkg_dojar stanford-parser.jar
-	if use doc ; then
-		java-pkg_dojavadoc javadoc
-	fi
-	if use source ; then
-		java-pkg_dosrc src
-	fi
-	dodoc README.txt README_dependencies.txt cedict_readme.txt
-	insinto /usr/share/${PN}
-	doins *ser.gz
-	java-pkg_dolauncher stanford-lexparser --java_args -Xmx200m --main edu.stanford.nlp.parser.lexparser.LexicalizedParser
-	java-pkg_dolauncher stanford-lexparser-gui --java_args "-server -Xmx600m" --main edu.stanford.nlp.parser.ui.Parser
-}
diff --git a/sci-misc/stanford-parser/stanford-parser-4.2.0.ebuild b/sci-misc/stanford-parser/stanford-parser-4.2.0.ebuild
new file mode 100644
index 000000000..bb70e918f
--- /dev/null
+++ b/sci-misc/stanford-parser/stanford-parser-4.2.0.ebuild
@@ -0,0 +1,49 @@
+# Copyright 1999-2021 Gentoo Authors
+# Distributed under the terms of the GNU General Public License v2
+
+EAPI=7
+
+JAVA_PKG_IUSE="doc source"
+
+inherit java-pkg-2
+
+DATE="2020-11-17"
+
+DESCRIPTION="Stanfords statistical natural language parsers"
+HOMEPAGE="https://www-nlp.stanford.edu/software/lex-parser.html"
+SRC_URI="http://www-nlp.stanford.edu/software/${P}.zip"
+
+LICENSE="GPL-2"
+SLOT="0"
+KEYWORDS="~amd64 ~x86"
+
+COMMON_DEP=""
+DEPEND=">=virtual/jdk-1.7
+	${COMMON_DEP}"
+RDEPEND=">=virtual/jre-1.7
+	${COMMON_DEP}"
+BDEPEND="app-arch/unzip"
+
+S="${WORKDIR}/${PN}-full-${DATE}"
+
+EANT_BUILD_TARGET="compile"
+
+src_prepare() {
+	mkdir -p src || die
+	pushd src || die
+	jar xf ../${P}-sources.jar || die
+	popd || die
+	default
+}
+
+src_install() {
+	java-pkg_dojar ${PN}.jar
+	if use doc ; then
+		java-pkg_dojavadoc javadoc
+	fi
+	if use source ; then
+		java-pkg_dosrc src
+	fi
+	java-pkg_dolauncher stanford-lexparser --java_args -Xmx200m --main edu.stanford.nlp.parser.lexparser.LexicalizedParser
+	java-pkg_dolauncher stanford-lexparser-gui --java_args "-server -Xmx600m" --main edu.stanford.nlp.parser.ui.Parser
+}
diff --git a/sci-misc/stanford-tagger/Manifest b/sci-misc/stanford-tagger/Manifest
index d35aa5bb6..4099c1d16 100644
--- a/sci-misc/stanford-tagger/Manifest
+++ b/sci-misc/stanford-tagger/Manifest
@@ -1 +1 @@
-DIST postagger-2006-05-21.tar.gz 10722420 BLAKE2B eada87ca6282d0d4d7a3601d0a694c723e888a0385baff2e55848749b238e58fe180c12a2ad5768604d5b6ed65a348d12629d934b7d52e32ab052c1d9c543c45 SHA512 ff54d13367b1402144ea36e0e42a98817fe8ac8ce47a1114c51fecf03e203b1fdcf048a15692688796978992c71eb0c35d76b66f5a07c749e1c3a7f99174caca
+DIST stanford-tagger-4.2.0.zip 78034596 BLAKE2B 63fd2f62644b430e47dd8a9f455a00a95c81304954cc8dc7ba4fffa22584fa340509fe5d504251e205cf94ed0bfce20b57470d873dfd05a4c28bcfd15a630d24 SHA512 56c2c12f71d39338052a80c1b7e63e232847df4d9aac1211d6ea5afddebe1689ab6314f3097278af1058f9f07332b243da75ad8b61301db12b7eb087c13452bc
diff --git a/sci-misc/stanford-tagger/stanford-tagger-20060521.ebuild b/sci-misc/stanford-tagger/stanford-tagger-20060521.ebuild
deleted file mode 100644
index a844dd05c..000000000
--- a/sci-misc/stanford-tagger/stanford-tagger-20060521.ebuild
+++ /dev/null
@@ -1,61 +0,0 @@
-# Copyright 1999-2014 Gentoo Foundation
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=5
-
-JAVA_PKG_IUSE="doc source"
-inherit java-pkg-2
-
-MY_PV=2006-05-21
-MY_P=postagger-${MY_PV}
-DESCRIPTION="Stanfords log linear POS taggers"
-HOMEPAGE="http://nlp.stanford.edu/software/tagger.shtml"
-SRC_URI="http://nlp.stanford.edu/software/${MY_P}.tar.gz"
-
-LICENSE="GPL-2"
-SLOT="0"
-KEYWORDS="~x86"
-IUSE="${IUSE}"
-
-COMMON_DEP=""
-DEPEND=">=virtual/jdk-1.5
-	${COMMON_DEP}"
-RDEPEND=">=virtual/jre-1.5
-	${COMMON_DEP}"
-
-S="${WORKDIR}/${MY_P}"
-
-src_prepare() {
-	jar xf ${MY_P}-source.jar
-	rm -v ${MY_P}.jar || die
-	sed \
-		-e 's/import edu.stanford.nlp.ling.IndexedFeatureLabe/\/\/\0/g' \
-		-i edu/stanford/nlp/stats/Counters.java || die "sed failed"
-	sed \
-		-e 's/import edu.stanford.nlp.sequences.BeamBestSequenceFinder/\/\/\0/g' \
-		-i edu/stanford/nlp/tagger/maxent/TestSentence.java || die "sed failed"
-}
-
-src_compile() {
-	ejavac `find edu -name *.java` || die "ejavac failed"
-	find edu -name '*.class' -o -name '*.properties' | \
-		xargs jar cf "${S}/${PN}.jar" || die "jar failed"
-}
-
-src_install() {
-	java-pkg_dojar ${PN}.jar
-	insinto /usr/share/${PN}/wsj3t0-18-bidirectional
-	doins wsj3t0-18-bidirectional/*
-
-	insinto /usr/share/${PN}/wsj3t0-18-left3words
-	doins wsj3t0-18-left3words/*
-	if use doc ; then
-		java-pkg_dojavadoc javadoc
-	fi
-	if use source ; then
-		java-pkg_dosrc edu
-	fi
-	java-pkg_dolauncher stanford-postagger --java_args -Xmx300m --main edu.stanford.nlp.tagger.maxent.MaxentTagger
-	java-pkg_dolauncher stanford-postrainer --main edu.stanford.nlp.tagger.maxent.Train
-	java-pkg_dolauncher stanford-postester --main edu.stanford.nlp.tagger.maxent.Test
-}
diff --git a/sci-misc/stanford-tagger/stanford-tagger-4.2.0.ebuild b/sci-misc/stanford-tagger/stanford-tagger-4.2.0.ebuild
new file mode 100644
index 000000000..f3e5339dd
--- /dev/null
+++ b/sci-misc/stanford-tagger/stanford-tagger-4.2.0.ebuild
@@ -0,0 +1,59 @@
+# Copyright 1999-2021 Gentoo Authors
+# Distributed under the terms of the GNU General Public License v2
+
+EAPI=7
+
+JAVA_PKG_IUSE="doc source"
+
+inherit java-pkg-2
+
+MY_PN=stanford-postagger
+MY_P="${MY_PN}-${PV}"
+DATE="2020-11-17"
+
+DESCRIPTION="Stanfords log linear POS taggers"
+HOMEPAGE="http://nlp.stanford.edu/software/tagger.shtml"
+SRC_URI="http://nlp.stanford.edu/software/${P}.zip"
+
+LICENSE="GPL-2"
+SLOT="0"
+KEYWORDS="~amd64 ~x86"
+
+COMMON_DEP=""
+DEPEND=">=virtual/jdk-1.7
+	${COMMON_DEP}"
+RDEPEND=">=virtual/jre-1.7
+	${COMMON_DEP}"
+BDEPEND="app-arch/unzip"
+
+S="${WORKDIR}/${MY_PN}-full-${DATE}"
+
+src_prepare() {
+	mkdir -p src || die
+	pushd src || die
+	jar xf ../${MY_P}-sources.jar || die
+	sed \
+		-e 's/import edu.stanford.nlp.ling.IndexedFeatureLabe/\/\/\0/g' \
+		-i edu/stanford/nlp/stats/Counters.java || die "sed failed"
+	sed \
+		-e 's/import edu.stanford.nlp.sequences.BeamBestSequenceFinder/\/\/\0/g' \
+		-i edu/stanford/nlp/tagger/maxent/TestSentence.java || die "sed failed"
+	popd || die
+	rm -v ${MY_P}.jar || die
+	default
+}
+
+src_install() {
+	java-pkg_newjar ${MY_PN}.jar ${PN}.jar
+	insinto /usr/share/${PN}/wsj3t0-18-bidirectional
+
+	if use doc ; then
+		java-pkg_dojavadoc javadoc
+	fi
+	if use source ; then
+		java-pkg_dosrc src
+	fi
+	java-pkg_dolauncher stanford-postagger --java_args -Xmx300m --main edu.stanford.nlp.tagger.maxent.MaxentTagger
+	java-pkg_dolauncher stanford-postrainer --main edu.stanford.nlp.tagger.maxent.Train
+	java-pkg_dolauncher stanford-postester --main edu.stanford.nlp.tagger.maxent.Test
+}
diff --git a/sci-physics/apfelxx/Manifest b/sci-physics/apfelxx/Manifest
new file mode 100644
index 000000000..b461f2a76
--- /dev/null
+++ b/sci-physics/apfelxx/Manifest
@@ -0,0 +1 @@
+DIST apfelxx-4.8.0.tar.gz 21695802 BLAKE2B f28d28bafed79ec679fd44bbd3cba668b108668dceaffbc80091a022d1884121a9d2fb08e89ae439663765877aadb7c214b6196d2ea35ad8c25ba545ec3492ee SHA512 23fcde7262637cbe0ff0173a530d0e2d3f39a9daa8b8757e4769c41c4af72569b0e0b8ab59ad5a8dc08ec7718d40bd34abed66671d2116f4242d06b6c2e7c1cc
diff --git a/sci-physics/apfelxx/apfelxx-4.8.0.ebuild b/sci-physics/apfelxx/apfelxx-4.8.0.ebuild
new file mode 100644
index 000000000..d31224fa3
--- /dev/null
+++ b/sci-physics/apfelxx/apfelxx-4.8.0.ebuild
@@ -0,0 +1,39 @@
+# Copyright 2022 Gentoo Authors
+# Distributed under the terms of the GNU General Public License v2
+
+EAPI=8
+
+CMAKE_MAKEFILE_GENERATOR="emake"
+PYTHON_COMPAT=( python3_{10..12} )
+
+inherit cmake python-single-r1
+
+DESCRIPTION="Object oriented rewriting of the APFEL evolution code"
+HOMEPAGE="https://github.com/vbertone/apfelxx"
+SRC_URI="https://github.com/vbertone/apfelxx/archive/${PV}.tar.gz -> ${P}.tar.gz"
+
+LICENSE="GPL-3+"
+SLOT="0"
+KEYWORDS="~amd64"
+
+REQUIRED_USE="${PYTHON_REQUIRED_USE}"
+RDEPEND="${PYTHON_DEPS}"
+
+src_prepare() {
+	default
+	cmake_src_prepare
+	sed -i "/prefix./s/\/lib/\/$(get_libdir)/g" CMakeLists.txt || die
+	sed -i "s#DESTINATION lib#DESTINATION $(get_libdir)#g" CMakeLists.txt || die
+}
+
+src_configure() {
+	local mycmakeargs=(
+		-DCMAKE_INSTALL_PREFIX="${EPREFIX}"/usr
+	)
+	cmake_src_configure
+}
+
+src_install() {
+	cmake_src_install
+	python_optimize
+}
diff --git a/sci-physics/apfelxx/metadata.xml b/sci-physics/apfelxx/metadata.xml
new file mode 100644
index 000000000..27c6de8e1
--- /dev/null
+++ b/sci-physics/apfelxx/metadata.xml
@@ -0,0 +1,18 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
+<pkgmetadata>
+	<maintainer type="person">
+		<email>alexander@neuwirth-informatik.de</email>
+		<name>Alexander Puck Neuwirth</name>
+	</maintainer>
+	<maintainer type="project">
+		<email>sci-physics@gentoo.org</email>
+		<name>Gentoo Physics Project</name>
+	</maintainer>
+	<longdescription lang="en">
+	APFEL++ is a C++ rewriting of the Fortran 77 evolution code APFEL. However, APFEL++ is based on a completely new code design and guarantees a better performance along with a more optimal memory management. The new modular structure allows for better maintainability and easier extensibility. This makes APFEL++ suitable for a wide range of tasks: from the solution of the DGLAP evolution equations to the computation of deep-inelastic-scattering (DIS) and single-inclusive-annihilation cross sections. Also more complex computations, such as differential semi-inclusive DIS and Drell-Yan cross sections, are easily implementable in APFEL++.
+	</longdescription>
+	<upstream>
+		<remote-id type="github">vbertone/apfelxx</remote-id> 
+	</upstream>
+</pkgmetadata>
diff --git a/sci-physics/atompaw/Manifest b/sci-physics/atompaw/Manifest
index 0b5678f74..5460cf85d 100644
--- a/sci-physics/atompaw/Manifest
+++ b/sci-physics/atompaw/Manifest
@@ -1,3 +1,3 @@
-DIST atompaw-4.0.0.14.tar.gz 5616545 BLAKE2B ac929050cfe203be7f9dcc28ef355fac642ae18e64cf0146886abeee629381d389699a69528a1dbe2356a616e750b1707220b9273f7b52fb41b816561807a937 SHA512 2df089ffa5c76cfc9dddfc4a40ec4e347ef05e2f65c757cebde549be28e98ffcbcffbf528d36e6a11fad20cb26edda65694857d8a51e8433fe78596038c45c71
-DIST atompaw.pdf 334715 SHA256 10a70f0c31e4a0a06e31b2b922b938742daf8635c87b95f5a48609555d9397ed SHA512 287f521a10b144bf8c6f59f21a025a8b1e0f6a23d576abe347be8fd41f8577dec0febd289618384d6e7796f0f68bfb41672c9d6d7bf1658f245cff20463ffff7 WHIRLPOOL ae9280374777fd61751d60b4944f3d21aceb86d3b6f4879ced1c26200e33d8ebb08b99e81cffd562e43643274f83bd6d4263360d399acee7eefad3f36791606a
-DIST atompawEqns.pdf 198480 SHA256 181af33190b77b630c1fb94882d0cbc5f79281346f93c25ef4d645806f2c1dc6 SHA512 e0b7fcbce906ceda953e000378786d3b679b68a5dd3d1a53b8d41a61e80bfa5a83fa04a6b8945b274ffe351491bffe3bdd801937f1b838f90b21e462fb09b9e9 WHIRLPOOL 9ba9c90df0c368b935fce573a6be30c492819fda4245f10d217bff3576f82b21036aeee837c28e5b694220f2749a6cf7e26b797b2690624dbfbc3bb598cc2bdd
+DIST atompaw-4.1.1.0.tar.gz 5675066 BLAKE2B 8c2f46538c89b4a01c17f928c599042d6db986841e3d443db2f94652dc02ddff82540ae486846c9714ea05c55f30c53db275bea5bbe622bb06f6225e49817153 SHA512 cb0569af1aa89973efd5c59c4ec3c5ce23850e42c8fa78d2037dc121ca77be928fb24f8513b75854bc45714d45155d236fe86b9075f81f9927ec15c127b6e969
+DIST atompaw.pdf 334715 BLAKE2B 80005a0a6808a645ea975cdb7289d5438c6347eaec227f56c1e4f39833b8de931eaef8cac9d55d3f819bcd473bd24178a9a8597b4ba8173ef1925e710cbc43df SHA512 287f521a10b144bf8c6f59f21a025a8b1e0f6a23d576abe347be8fd41f8577dec0febd289618384d6e7796f0f68bfb41672c9d6d7bf1658f245cff20463ffff7
+DIST atompawEqns.pdf 198480 BLAKE2B fe4ad827ae1cc34724c9fdab5785521f231f6ba0b0ea3066c4a1fc403bcdf87463ebf3315c653088c701de5f0e5542187d4284a874627f2e99456757e04f12ed SHA512 e0b7fcbce906ceda953e000378786d3b679b68a5dd3d1a53b8d41a61e80bfa5a83fa04a6b8945b274ffe351491bffe3bdd801937f1b838f90b21e462fb09b9e9
diff --git a/sci-physics/atompaw/atompaw-4.0.0.14.ebuild b/sci-physics/atompaw/atompaw-4.0.0.14.ebuild
deleted file mode 100644
index 1c272ace6..000000000
--- a/sci-physics/atompaw/atompaw-4.0.0.14.ebuild
+++ /dev/null
@@ -1,68 +0,0 @@
-# Copyright 1999-2017 Gentoo Foundation
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=5
-
-inherit autotools-utils eutils fortran-2 multilib toolchain-funcs
-
-DESCRIPTION="PAW atomic data generator"
-HOMEPAGE="http://www.wfu.edu/~natalie/papers/pwpaw/man.html"
-SRC_URI="
-	http://www.wfu.edu/~natalie/papers/pwpaw/${P}.tar.gz
-	doc? (
-		http://www.wfu.edu/~natalie/papers/pwpaw/atompaw.pdf
-		http://www.wfu.edu/~natalie/papers/pwpaw/notes/atompaw/atompawEqns.pdf )"
-
-LICENSE="GPL-2"
-SLOT="0"
-KEYWORDS="~amd64 ~x86"
-IUSE="doc libxc longplot test"
-
-RDEPEND="
-	virtual/blas
-	virtual/lapack
-	libxc? ( >=sci-libs/libxc-2.0.1[fortran] )"
-DEPEND="${RDEPEND}
-	virtual/pkgconfig"
-
-DOCS=( README )
-
-FORTRAN_STANDARD=90
-
-src_unpack() {
-	unpack ${P}.tar.gz
-	if use doc; then
-		cp "${DISTDIR}"/atompaw.pdf "${DISTDIR}"/atompawEqns.pdf "${S}"/doc/ || die
-	fi
-}
-
-src_prepare() {
-	use longplot && epatch "${FILESDIR}"/4.0-longplot.patch
-}
-
-src_configure() {
-	local myeconfargs=(
-		$(use_enable libxc)
-		--with-linalg-flavor=atlas
-		--with-linalg-libs="$($(tc-getPKG_CONFIG) --libs lapack)"
-		--with-libxc-incs="-I/usr/include $($(tc-getPKG_CONFIG) --cflags libxc)"
-		--with-libxc-libs="$($(tc-getPKG_CONFIG) --libs libxc)"
-		FC="$(tc-getFC)" FCFLAGS="${FCFLAGS:- ${FFLAGS:- -O2}}"
-		CC="$(tc-getCC)" LDFLAGS="${LDFLAGS:- ${CFLAGS:- -O2}}"
-	)
-	autotools-utils_src_configure
-}
-
-src_compile() {
-	autotools-utils_src_compile -j1
-}
-
-src_test() {
-	use test && autotools-utils_src_test
-}
-
-src_install() {
-	autotools-utils_src_install
-
-	use doc && dodoc doc/atompaw.pdf doc/atompawEqns.pdf
-}
diff --git a/sci-physics/atompaw/atompaw-4.1.1.0.ebuild b/sci-physics/atompaw/atompaw-4.1.1.0.ebuild
new file mode 100644
index 000000000..b9d8912b8
--- /dev/null
+++ b/sci-physics/atompaw/atompaw-4.1.1.0.ebuild
@@ -0,0 +1,55 @@
+# Copyright 1999-2021 Gentoo Authors
+# Distributed under the terms of the GNU General Public License v2
+
+EAPI=7
+
+inherit fortran-2 toolchain-funcs
+
+DESCRIPTION="PAW atomic data generator"
+HOMEPAGE="http://users.wfu.edu/natalie/papers/pwpaw/man.html"
+SRC_URI="
+	http://users.wfu.edu/natalie/papers/pwpaw/${P}.tar.gz
+	http://users.wfu.edu/natalie/papers/pwpaw/atompaw.pdf
+	http://users.wfu.edu/natalie/papers/pwpaw/notes/atompaw/atompawEqns.pdf
+"
+
+LICENSE="GPL-2"
+SLOT="0"
+KEYWORDS="~amd64 ~x86"
+
+IUSE="libxc longplot"
+
+RDEPEND="
+	virtual/blas
+	virtual/lapack
+	libxc? ( >=sci-libs/libxc-2.0.1[fortran] )
+"
+DEPEND="${RDEPEND}"
+BDEPEND="virtual/pkgconfig"
+
+FORTRAN_STANDARD=90
+
+src_unpack() {
+	unpack ${P}.tar.gz
+	cp "${DISTDIR}"/atompaw.pdf "${DISTDIR}"/atompawEqns.pdf "${S}"/doc/ || die
+}
+
+src_prepare() {
+	default
+	use longplot && eapply "${FILESDIR}"/4.0-longplot.patch
+}
+
+src_configure() {
+	econf \
+		$(use_enable libxc) \
+		--with-linalg-libs="$($(tc-getPKG_CONFIG) --libs blas lapack)" \
+		--with-libxc-incs="-I/usr/include $($(tc-getPKG_CONFIG) --cflags libxc)" \
+		--with-libxc-libs="$($(tc-getPKG_CONFIG) --libs libxc)" \
+		FC="$(tc-getFC)" FCFLAGS="${FCFLAGS:- ${FFLAGS:- -O2}}" \
+		CC="$(tc-getCC)" LDFLAGS="${LDFLAGS:- ${CFLAGS:- -O2}}"
+}
+
+src_install() {
+	default
+	dodoc doc/atompaw.pdf doc/atompawEqns.pdf
+}
diff --git a/sci-physics/bigdft/Manifest b/sci-physics/bigdft/Manifest
deleted file mode 100644
index 91f834fe8..000000000
--- a/sci-physics/bigdft/Manifest
+++ /dev/null
@@ -1,2 +0,0 @@
-DIST bigdft-1.7.1.tar.bz2 12028799 BLAKE2B fcc991c2b4bd65893a0f00276ef55d2f386ea7a891576d902582f68d55f04f2c3a520ad172db15e278eba49f7e37085c3d73bbc7820589dd48f2e12e9d4817e0 SHA512 e26abe7743106764ea6779e29d85da8a7d9272fa3ebd10f668d74c6ef196ff52283e38669fc815ce9409f1ff245ba74d56b2d300a309f5a69baf445317aafd2e
-DIST bigdft-1.7.6.tar.xz 10399604 BLAKE2B ffe58ea7d2a76a6ce16bdddd8828a1f7dd98250ba129b5a213902bbda36c7aca017912a0a921a32ce01f5ff841ec010880fd9f3ddadf9cef0339e05291b00747 SHA512 cdadda8e9105355e48a9f301ac5d8178955fff90593935143db5219de867f1461bfb7c934a9fe0dcbb7af7c77bb0aedfc5f1d078d1eeeeca76c3e868ee8d3919
diff --git a/sci-physics/bigdft/bigdft-1.7.1.ebuild b/sci-physics/bigdft/bigdft-1.7.1.ebuild
deleted file mode 100644
index b82c3c03b..000000000
--- a/sci-physics/bigdft/bigdft-1.7.1.ebuild
+++ /dev/null
@@ -1,171 +0,0 @@
-# Copyright 1999-2015 Gentoo Foundation
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=5
-
-PYTHON_COMPAT=(  python2_7 )
-
-inherit autotools-utils eutils flag-o-matic fortran-2 python-any-r1 toolchain-funcs
-
-DESCRIPTION="A DFT electronic structure code using a wavelet basis set"
-HOMEPAGE="http://bigdft.org/"
-SRC_URI="http://launchpad.net/${PN}/${PV%.*}/${PV}/+download/${P}.tar.bz2"
-
-LICENSE="GPL-3"
-SLOT="0"
-KEYWORDS="~amd64 ~x86 ~amd64-linux"
-IUSE="cuda doc etsf_io glib mpi netcdf openmp opencl scalapack test"
-
-RDEPEND="
-	( >=sci-libs/libxc-1.2.0-r1[fortran]
-		<sci-libs/libxc-2.2 )
-	virtual/blas
-	virtual/fortran
-	virtual/lapack
-	dev-libs/libyaml
-	mpi? ( virtual/mpi )
-	cuda? ( dev-util/nvidia-cuda-sdk )
-	opencl? ( virtual/opencl )
-	glib? ( >=dev-libs/glib-2.22 )
-	etsf_io? ( >=sci-libs/etsf_io-1.0.4[pic] )
-	netcdf? ( || (
-				sci-libs/netcdf[fortran]
-				sci-libs/netcdf-fortran
-				)
-			)
-	scalapack? ( virtual/scalapack )"
-DEPEND="${RDEPEND}
-	virtual/pkgconfig
-	>=sys-devel/autoconf-2.59
-	doc? ( virtual/latex-base )
-	${PYTHON_DEPS}
-	dev-python/pyyaml[libyaml]
-	dev-util/gdbus-codegen
-	app-arch/tar
-	app-arch/gzip"
-
-DOCS=( README INSTALL ChangeLog AUTHORS NEWS )
-
-FORTRAN_STANDARD=90
-
-pkg_setup() {
-	# fortran-2.eclass does not handle mpi wrappers
-	if use mpi; then
-		export FC="mpif90"
-		export F77="mpif77"
-		export CC="mpicc"
-		export CXX="mpic++"
-	else
-		tc-export FC F77 CC CXX
-	fi
-
-	use openmp && FORTRAN_NEED_OPENMP=1
-
-	fortran-2_pkg_setup
-
-	if use openmp; then
-		# based on _fortran-has-openmp() of fortran-2.eclass
-		local openmp=""
-		local fcode=ebuild-openmp-flags.f
-		local _fc=$(tc-getFC)
-
-		pushd "${T}"
-		cat <<- EOF > "${fcode}"
-		1     call omp_get_num_threads
-		2     end
-		EOF
-
-		for openmp in -fopenmp -xopenmp -openmp -mp -omp -qsmp=omp; do
-			"${_fc}" "${openmp}" "${fcode}" -o "${fcode}.x" && break
-		done
-
-		rm -f "${fcode}.*"
-		popd
-
-		append-flags "${openmp}"
-	fi
-
-	python-any-r1_pkg_setup
-}
-
-src_prepare() {
-	epatch \
-		"${FILESDIR}"/"${P}"-pkgconfig.patch \
-		"${FILESDIR}"/"${P}"-longline.patch
-
-	eautoreconf
-}
-
-src_configure() {
-	local modules="${EPREFIX}/usr/include"
-	local netcdff_libs="-lnetcdff"
-	filter-flags '-m*' '-O*' "-pipe"
-	local nvcflags="${CFLAGS}"
-	_filter-var nvcflags '-m*' '-O*' "-pipe" "-W*"
-	use cuda && filter-ldflags '-m*' '-O*' "-pipe" "-W*"
-	local mylapack="lapack"
-	use scalapack && mylapack="scalapack"
-	local myeconfargs=(
-		$(use_enable mpi)
-		--enable-optimised-convolution
-		--enable-pseudo
-		--enable-libbigdft
-		--enable-binaries
-		--disable-bindings
-		--disable-minima-hopping
-		--disable-internal-libyaml
-		--enable-internal-libabinit
-		--with-moduledir="${modules}"
-		--with-ext-linalg="$($(tc-getPKG_CONFIG) --libs-only-l "${mylapack}")"
-		--with-ext-linalg-path="$($(tc-getPKG_CONFIG) --libs-only-L "${mylapack}")"
-		--with-libxc="yes"
-		--disable-internal-libxc
-		$(use_enable cuda cuda-gpu)
-		$(use_with cuda cuda-path /opt/cuda)
-		$(use_with cuda nvcc-flags "${nvcflags}")
-		$(use_enable opencl)
-		$(use_with etsf_io etsf-io)
-		"$(use etsf_io && echo "--with-netcdf-libs=$($(tc-getPKG_CONFIG) --libs netcdf) ${netcdff_libs}")"
-		$(use_with glib gobject)
-		$(use_with scalapack)
-		$(use_with scalapack scalapack-path "${EPREFIX}/usr/$(get_libdir)")
-		$(use_with scalapack blacs)
-		$(use_with scalapack blacs-path "${EPREFIX}/usr/$(get_libdir)")
-		PKG_CONFIG="$(tc-getPKG_CONFIG)"
-		FCFLAGS="${FCFLAGS} -I${modules}"
-		LD="$(tc-getLD)"
-		CPP="$(tc-getCPP)"
-		)
-	autotools-utils_src_configure
-}
-
-src_compile() {
-	#autotools-utils_src_compile() expanded
-	_check_build_dir
-	pushd "${AUTOTOOLS_BUILD_DIR}" > /dev/null
-	emake -j1
-	sed -i -e's%\$(top_builddir)/[^ ]*/lib\([^ /$-]*\)\.a%-l\1%g' bigdft.pc
-	popd > /dev/null
-
-	#autotools-utils_src_compile
-	if use doc; then
-		VARTEXFONTS="${T}/fonts"
-		autotools-utils_src_compile doc
-	fi
-}
-
-src_test() {
-	if use test; then
-		#autotools-utils_src_test() expanded
-		_check_build_dir
-		pushd "${BUILD_DIR}" > /dev/null || die
-		# Run default src_test as defined in ebuild.sh
-		cd tests
-		emake -j1 check
-		popd > /dev/null
-	fi
-}
-
-src_install() {
-	autotools-utils_src_install
-}
diff --git a/sci-physics/bigdft/bigdft-1.7.6.ebuild b/sci-physics/bigdft/bigdft-1.7.6.ebuild
deleted file mode 100644
index fcb9c7fa2..000000000
--- a/sci-physics/bigdft/bigdft-1.7.6.ebuild
+++ /dev/null
@@ -1,171 +0,0 @@
-# Copyright 1999-2015 Gentoo Foundation
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=5
-
-PYTHON_COMPAT=(  python2_7 )
-
-inherit autotools-utils eutils flag-o-matic fortran-2 python-any-r1 toolchain-funcs
-
-DESCRIPTION="A DFT electronic structure code using a wavelet basis set"
-HOMEPAGE="http://bigdft.org/"
-SRC_URI="http://launchpad.net/${PN}/${PV%.*}/${PV}/+download/${P}.tar.xz"
-
-LICENSE="GPL-3"
-SLOT="0"
-KEYWORDS="~amd64 ~x86 ~amd64-linux"
-IUSE="cuda doc etsf_io glib mpi netcdf openmp opencl scalapack test"
-
-RDEPEND="
-	( >=sci-libs/libxc-2.0[fortran]
-		<sci-libs/libxc-2.2 )
-	virtual/blas
-	virtual/fortran
-	virtual/lapack
-	dev-libs/libyaml
-	mpi? ( virtual/mpi )
-	cuda? ( dev-util/nvidia-cuda-sdk )
-	opencl? ( virtual/opencl )
-	glib? ( >=dev-libs/glib-2.22 )
-	etsf_io? ( >=sci-libs/etsf_io-1.0.4[pic] )
-	netcdf? ( || (
-				sci-libs/netcdf[fortran]
-				sci-libs/netcdf-fortran
-				)
-			)
-	scalapack? ( virtual/scalapack )"
-DEPEND="${RDEPEND}
-	virtual/pkgconfig
-	>=sys-devel/autoconf-2.59
-	doc? ( virtual/latex-base )
-	${PYTHON_DEPS}
-	dev-python/pyyaml[libyaml]
-	dev-util/gdbus-codegen
-	app-arch/tar
-	app-arch/gzip"
-
-DOCS=( README INSTALL ChangeLog AUTHORS NEWS )
-
-FORTRAN_STANDARD=90
-
-pkg_setup() {
-	# fortran-2.eclass does not handle mpi wrappers
-	if use mpi; then
-		export FC="mpif90"
-		export F77="mpif77"
-		export CC="mpicc"
-		export CXX="mpic++"
-	else
-		tc-export FC F77 CC CXX
-	fi
-
-	use openmp && FORTRAN_NEED_OPENMP=1
-
-	fortran-2_pkg_setup
-
-	if use openmp; then
-		# based on _fortran-has-openmp() of fortran-2.eclass
-		local openmp=""
-		local fcode=ebuild-openmp-flags.f
-		local _fc=$(tc-getFC)
-
-		pushd "${T}"
-		cat <<- EOF > "${fcode}"
-		1     call omp_get_num_threads
-		2     end
-		EOF
-
-		for openmp in -fopenmp -xopenmp -openmp -mp -omp -qsmp=omp; do
-			"${_fc}" "${openmp}" "${fcode}" -o "${fcode}.x" && break
-		done
-
-		rm -f "${fcode}.*"
-		popd
-
-		append-flags "${openmp}"
-	fi
-
-	python-any-r1_pkg_setup
-}
-
-src_prepare() {
-	epatch \
-		"${FILESDIR}"/"${PN}"-1.7.1-pkgconfig.patch \
-		"${FILESDIR}"/"${PN}"-1.7.5-dynamic_memory.patch
-
-	eautoreconf
-}
-
-src_configure() {
-	local modules="${EPREFIX}/usr/include"
-	local netcdff_libs="-lnetcdff"
-	filter-flags '-m*' '-O*' "-pipe"
-	local nvcflags="${CFLAGS}"
-	_filter-var nvcflags '-m*' '-O*' "-pipe" "-W*"
-	use cuda && filter-ldflags '-m*' '-O*' "-pipe" "-W*"
-	local mylapack="lapack"
-	use scalapack && mylapack="scalapack"
-	local myeconfargs=(
-		$(use_enable mpi)
-		--enable-optimised-convolution
-		--enable-pseudo
-		--enable-libbigdft
-		--enable-binaries
-		--disable-bindings
-		--disable-minima-hopping
-		--disable-internal-libyaml
-		--enable-internal-libabinit
-		--with-moduledir="${modules}"
-		--with-ext-linalg="$($(tc-getPKG_CONFIG) --libs-only-l "${mylapack}")"
-		--with-ext-linalg-path="$($(tc-getPKG_CONFIG) --libs-only-L "${mylapack}")"
-		--with-libxc="yes"
-		--disable-internal-libxc
-		$(use_enable cuda cuda-gpu)
-		$(use_with cuda cuda-path /opt/cuda)
-		$(use_with cuda nvcc-flags "${nvcflags}")
-		$(use_enable opencl)
-		$(use_with etsf_io etsf-io)
-		"$(use etsf_io && echo "--with-netcdf-libs=$($(tc-getPKG_CONFIG) --libs netcdf) ${netcdff_libs}")"
-		$(use_with glib gobject)
-		$(use_with scalapack)
-		$(use_with scalapack scalapack-path "${EPREFIX}/usr/$(get_libdir)")
-		$(use_with scalapack blacs)
-		$(use_with scalapack blacs-path "${EPREFIX}/usr/$(get_libdir)")
-		PKG_CONFIG="$(tc-getPKG_CONFIG)"
-		FCFLAGS="${FCFLAGS} -I${modules}"
-		LD="$(tc-getLD)"
-		CPP="$(tc-getCPP)"
-		)
-	autotools-utils_src_configure
-}
-
-src_compile() {
-	#autotools-utils_src_compile() expanded
-	_check_build_dir
-	pushd "${AUTOTOOLS_BUILD_DIR}" > /dev/null
-	emake -j1
-	sed -i -e's%\$(top_builddir)/[^ ]*/lib\([^ /$-]*\)\.a%-l\1%g' bigdft.pc
-	popd > /dev/null
-
-	#autotools-utils_src_compile
-	if use doc; then
-		VARTEXFONTS="${T}/fonts"
-		autotools-utils_src_compile doc
-	fi
-}
-
-src_test() {
-	if use test; then
-		#autotools-utils_src_test() expanded
-		_check_build_dir
-		pushd "${BUILD_DIR}" > /dev/null || die
-		# Run default src_test as defined in ebuild.sh
-		cd tests
-		emake -j1 check
-		popd > /dev/null
-	fi
-}
-
-src_install() {
-	autotools-utils_src_install
-}
diff --git a/sci-physics/bigdft/files/bigdft-1.7.1-longline.patch b/sci-physics/bigdft/files/bigdft-1.7.1-longline.patch
deleted file mode 100644
index 29dadb545..000000000
--- a/sci-physics/bigdft/files/bigdft-1.7.1-longline.patch
+++ /dev/null
@@ -1,14 +0,0 @@
-diff -Naurp bigdft-1.7.1.orig/libABINIT/src/16_hideleave/m_errors.F90 bigdft-1.7.1/libABINIT/src/16_hideleave/m_errors.F90
---- bigdft-1.7.1.orig/libABINIT/src/16_hideleave/m_errors.F90	2013-12-11 09:31:00.000000000 +0000
-+++ bigdft-1.7.1/libABINIT/src/16_hideleave/m_errors.F90	2015-04-21 08:35:18.781370070 +0000
-@@ -777,7 +777,9 @@ subroutine sentinel(level,mode_paral,fun
-  else if (level==2) then
-   msg = ' '//TRIM(my_funcname)//' : exit '//ch10
-  else 
--  call die('Wrong level',__FILE__,__LINE__)
-+  call die('Wrong level',&
-+&  __FILE__,&
-+&  __LINE__)
-  end if
- 
-  call wrtout(std_out,msg,my_mode) 
diff --git a/sci-physics/bigdft/files/bigdft-1.7.1-pkgconfig.patch b/sci-physics/bigdft/files/bigdft-1.7.1-pkgconfig.patch
deleted file mode 100644
index d1832d280..000000000
--- a/sci-physics/bigdft/files/bigdft-1.7.1-pkgconfig.patch
+++ /dev/null
@@ -1,10 +0,0 @@
-diff -Naurp bigdft-1.7.1.orig/bigdft.pc.in bigdft-1.7.1/bigdft.pc.in
---- bigdft-1.7.1.orig/bigdft.pc.in	2013-12-11 09:31:00.000000000 +0000
-+++ bigdft-1.7.1/bigdft.pc.in	2014-01-27 10:17:14.314387505 +0000
-@@ -7,5 +7,5 @@ Name: libbigdft
- Description: Library for DFT calculation over wavelets.
- Requires: 
- Version: @VERSION@
--Libs: -L${libdir} @LIBS_DEPENDENCIES@ @FCLIBS@
-+Libs: -L${libdir} -lbigdft-1 @LIBS_SHORT_DEPS@ @FCLIBS@
- Cflags: -I${includedir}
diff --git a/sci-physics/bigdft/files/bigdft-1.7.5-dynamic_memory.patch b/sci-physics/bigdft/files/bigdft-1.7.5-dynamic_memory.patch
deleted file mode 100644
index 7271223ea..000000000
--- a/sci-physics/bigdft/files/bigdft-1.7.5-dynamic_memory.patch
+++ /dev/null
@@ -1,106 +0,0 @@
-diff -Naurp bigdft-1.7.5_orig/src/wavelib/i-o-etsf.f90 bigdft-1.7.5/src/wavelib/i-o-etsf.f90
---- bigdft-1.7.5_orig/src/wavelib/i-o-etsf.f90	2014-07-09 12:56:18.000000000 +0000
-+++ bigdft-1.7.5/src/wavelib/i-o-etsf.f90	2014-09-04 07:05:36.256646737 +0000
-@@ -178,6 +178,7 @@ module internal_etsf
-    subroutine etsf_gcoordToLocreg(n1, n2, n3, nvctr_c, nvctr, gcoord, lr)
-       use module_defs
-       use module_types
-+      use dynamic_memory
- 
-       implicit none
- 
-@@ -401,6 +402,7 @@ subroutine read_waves_from_list_etsf(ipr
-       &   wfd,psi,norb,nspinor,iorbparr,isorb,eval)
-    use module_base
-    use module_types
-+   use dynamic_memory
-    use etsf_io_low_level
-    use etsf_io
-    use internal_etsf
-@@ -744,11 +746,18 @@ subroutine read_waves_etsf(iproc,filenam
-    character(len = *), intent(in) :: filename
-    ! Local variables
-    integer :: i
-+   real(wp), dimension(:), allocatable :: eval
-+
-+   eval = f_malloc(size(orbs%eval),id='eval')
-+   eval = orbs%eval
- 
-    i = 0
-    call read_waves_from_list_etsf(iproc,filename,n1,n2,n3,hx,hy,hz,at,rxyz_old,rxyz, & 
-       &   wfd,psi,orbs%norbp,orbs%nspinor,(/ (i, i=1, orbs%norbp*orbs%nspinor) /), &
--      & orbs%isorb,orbs%eval(orbs%isorb + 1))
-+      & orbs%isorb,eval(orbs%isorb + 1))
-+
-+   orbs%eval = eval
-+   call f_free(eval)
- END SUBROUTINE read_waves_etsf
- 
- subroutine read_one_wave_etsf(iproc,filename,iorbp,isorb,nspinor,n1,n2,n3,&
-@@ -765,14 +774,16 @@ subroutine read_one_wave_etsf(iproc,file
-    real(gp), dimension(3,at%astruct%nat), intent(out) :: rxyz_old
-    real(wp), dimension(wfd%nvctr_c+7*wfd%nvctr_f,nspinor), intent(out) :: psi
-    character(len = *), intent(in) :: filename
-+   real(wp), dimension(1) :: eval1
- 
-    if (nspinor == 1) then
-       call read_waves_from_list_etsf(iproc,filename,n1,n2,n3,hx,hy,hz,at,rxyz_old,rxyz, & 
--         &   wfd,psi,1,nspinor,(/ iorbp /),isorb,eval)
-+         &   wfd,psi,1,nspinor,(/ iorbp /),isorb,eval1)
-    else
-       call read_waves_from_list_etsf(iproc,filename,n1,n2,n3,hx,hy,hz,at,rxyz_old,rxyz, & 
--         &   wfd,psi,1,nspinor,(/ 2 * iorbp - 1, 2 * iorbp /),isorb,eval)
-+         &   wfd,psi,1,nspinor,(/ 2 * iorbp - 1, 2 * iorbp /),isorb,eval1)
-    end if
-+   eval = eval1(1)
- END SUBROUTINE read_one_wave_etsf
- 
- subroutine write_psi_compress_etsf(ncid, iorbp, orbs, nvctr, wfd, psi)
-@@ -1062,7 +1073,7 @@ subroutine write_waves_etsf(iproc,filena
-       end do
-       znucl = f_malloc(at%astruct%ntypes,id='znucl')
-       znucl = real(at%nzatom)
--      spnames = f_malloc(at%astruct%ntypes,id='spnames')
-+      spnames = f_malloc_str(etsf_chemlen,at%astruct%ntypes,id='spnames')
-       do iat = 1, at%astruct%ntypes, 1
-          !call nzsymbol(at%nzatom(iat), spnames(iat))
-          call atomic_info(at%nzatom(iat),at%nelpsp(iat),symbol=spnames(iat))
-@@ -1080,7 +1091,7 @@ subroutine write_waves_etsf(iproc,filena
-       if (.not. lstat) call etsf_error(error)
-       call f_free(xred)
-       call f_free(znucl)
--      call f_free(spnames)
-+      call f_free_str(etsf_chemlen,spnames)
-       ! The eigenvalues & occupation.
-       if (dims%number_of_spins == 1) then
-          elec%eigenvalues%data1D => orbs%eval
-@@ -1138,6 +1149,8 @@ subroutine write_waves_etsf(iproc,filena
-    END SUBROUTINE etsf_write_global
- 
-    subroutine build_grid(n1,n2,n3,nvctr, gcoord, wfd)
-+      use dynamic_memory
-+
-       integer, intent(in) :: n1, n2, n3
-       type(wavefunctions_descriptors), intent(in) :: wfd
-       integer, intent(out) :: nvctr(wfd%nvctr_c)
-diff -Naurp bigdft-1.7.5_orig/src/wavelib/plotting-etsf.f90 bigdft-1.7.5/src/wavelib/plotting-etsf.f90
---- bigdft-1.7.5_orig/src/wavelib/plotting-etsf.f90	2014-06-05 14:07:35.000000000 +0000
-+++ bigdft-1.7.5/src/wavelib/plotting-etsf.f90	2014-09-04 07:04:42.335813661 +0000
-@@ -141,7 +141,7 @@ subroutine write_etsf_density(filename,m
-   end do
-   znucl = f_malloc(at%astruct%ntypes,id='znucl')
-   znucl = real(at%nzatom)
--  spnames = f_malloc(at%astruct%ntypes,id='spnames')
-+  spnames = f_malloc_str(etsf_chemlen,at%astruct%ntypes,id='spnames')
-   do iat = 1, at%astruct%ntypes, 1
-      !call nzsymbol(at%nzatom(iat), spnames(iat))
-      call atomic_info(at%nzatom(iat),at%nelpsp(iat),symbol=spnames(iat))
-@@ -159,7 +159,7 @@ subroutine write_etsf_density(filename,m
-   end if
-   call f_free(xred)
-   call f_free(znucl)
--  call f_free(spnames)
-+  call f_free_str(etsf_chemlen,spnames)
- 
-   ! We switch to write mode.
-   call etsf_io_low_set_write_mode(ncid, lstat, error_data = error)
diff --git a/sci-physics/bigdft/metadata.xml b/sci-physics/bigdft/metadata.xml
deleted file mode 100644
index 56b5a0e32..000000000
--- a/sci-physics/bigdft/metadata.xml
+++ /dev/null
@@ -1,28 +0,0 @@
-<?xml version="1.0" encoding="UTF-8"?>
-<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
-<pkgmetadata>
-	<maintainer type="project">
-		<email>sci-physics@gentoo.org</email>
-		<name>Gentoo Physics Project</name>
-	</maintainer>
-	<longdescription lang="en">
-BigDFT is a DFT massively parallel electronic structure code (GPL license) using a wavelet basis set. Wavelets form a real space basis set distributed on an adaptive mesh (two levels of resolution in our implementation). GTH or HGH pseudopotentials are used to remove the core electrons. Thanks to our Poisson solver based on a Green function formalism, periodic systems, surfaces and isolated systems can be simulated with the proper boundary conditions.
-</longdescription>
-	<use>
-		<flag name="cuda">Enable support for nVidia CUDA GPU acceleration</flag>
-		<flag name="etsf_io">
-Enable support for reading and writing the European Theoretical
-Spectroscopy facility (ETSF) file format.
-</flag>
-		<flag name="glib">
-Compile with GLib Object System support
-</flag>
-		<flag name="opencl">Enable support for OpenCL GPU acceleration</flag>
-		<flag name="scalapack">
-Use ScaLAPACK, a subset of LAPACK routines redesigned for heterogenous computing
-</flag>
-	</use>
-	<upstream>
-		<remote-id type="launchpad">bigdft</remote-id>
-	</upstream>
-</pkgmetadata>
diff --git a/sci-physics/cernlib/Manifest b/sci-physics/cernlib/Manifest
new file mode 100644
index 000000000..d8be46729
--- /dev/null
+++ b/sci-physics/cernlib/Manifest
@@ -0,0 +1,2 @@
+DIST cernlib-2023.10.31.0-free.tar.gz 39191038 BLAKE2B 941592a65f0c8d7d0c6c3907c96d8209568579dac455ed28657a5635677d73e6580f48667a641a6ca9dd296bf82a40f6a75c5fc801fcefb7f8e9101b4dcd3202 SHA512 d015f89942bab695444d37847a8138c3a8736ceeb6f4826c659553bf1ae5eab2a77b2871645a125ea189e62520856955070fbb3ed2d208d35f82ee8b8559d089
+DIST cernlib-2023.10.31.0.tar.gz 39547453 BLAKE2B f37686e4a43b969a8cb604874b6181adf8529b9fc383ccd2e42fc369f92d4693ca8db682bc58638cb58e9941cf22551cfec26b33075e15fc6a0b3fab3dcf7d82 SHA512 9bc866d08e3bce2f571f9f4e21e34ca6c99467088d4dce4cbc9b6c62d8ee2b9018668fd66795996a5f6abb1082ac9559cf08bc7f5201421dbffcdd0db9459008
diff --git a/sci-physics/cernlib/cernlib-2023.10.31.0-r2.ebuild b/sci-physics/cernlib/cernlib-2023.10.31.0-r2.ebuild
new file mode 100644
index 000000000..93220dffb
--- /dev/null
+++ b/sci-physics/cernlib/cernlib-2023.10.31.0-r2.ebuild
@@ -0,0 +1,79 @@
+EAPI=8
+
+CMAKE_MAKEFILE_GENERATOR="emake"
+inherit cmake fortran-2 flag-o-matic
+
+DESCRIPTION="CERN program library for High Energy Physics"
+HOMEPAGE="https://cernlib.web.cern.ch/cernlib/"
+SRC_URI="
+	free? ( https://cernlib.web.cern.ch/download/2023_source/tar/${P}-free.tar.gz )
+	!free? ( https://cernlib.web.cern.ch/download/2023_source/tar/${P}.tar.gz )
+"
+
+LICENSE="
+	free? ( BSD LGPL-2+ GPL-1+ )
+	!free? ( all-rights-reserved )
+"
+SLOT="0"
+KEYWORDS="~amd64"
+# static-libs as default since otherwise test fail...
+IUSE="+free +static-libs"
+RESTRICT="mirror"
+
+RDEPEND="
+	x11-libs/motif:0
+	x11-libs/libXaw
+	x11-libs/libXau
+	virtual/lapack
+	dev-lang/cfortran
+	x11-libs/xbae
+	net-libs/libnsl
+	virtual/libcrypt:=
+"
+DEPEND="${RDEPEND}"
+BDEPEND="
+	virtual/pkgconfig
+"
+
+PATCHES=(
+	"${FILESDIR}"/${P}-cfortran.patch
+	"${FILESDIR}"/${P}-ctest.patch
+	"${FILESDIR}"/${P}-man.patch
+)
+
+src_unpack() {
+	default
+	if use free; then
+		mv ${P}-free ${P} || die
+	fi
+}
+
+src_prepare() {
+	cmake_src_prepare
+	# cfortran.patch
+	# Remove cfortran.h since it is already installed from dev-lang/cfortran
+	# thereby we avoid collisions if e.g. sci-physics/root[fortran] is installed.
+	rm cfortran/cfortran.h || die
+}
+
+src_configure() {
+	# docs follow rpm like spliting into packages cernlib, cernlib-devel, etc.
+	# we move them into a folder that agrees with gentoo doc structure.
+	sed -i "s#/doc/#/doc/${PF}/#g" CMakeLists.txt || die
+	# with -O2 some tests fail
+	# let upstream decide on optimization (-O0) since code is fragile
+	filter-flags -O1 -O2 -O3 -Os -Oz -Og -Ofast
+	local mycmakeargs=(
+		-DBUILD_SHARED_LIBS=$(usex static-libs OFF ON)
+	)
+	cmake_src_configure
+}
+
+src_install() {
+	cmake_src_install
+	# man.patch
+	# The CMakeLists.txt already compresses the manual before install
+	# therefore we install it manually and avoid QA problems.
+	doman contrib/man/man1/*.1
+	doman contrib/man/man8/*.8
+}
diff --git a/sci-physics/cernlib/files/cernlib-2023.10.31.0-cfortran.patch b/sci-physics/cernlib/files/cernlib-2023.10.31.0-cfortran.patch
new file mode 100644
index 000000000..b4426b3eb
--- /dev/null
+++ b/sci-physics/cernlib/files/cernlib-2023.10.31.0-cfortran.patch
@@ -0,0 +1,21 @@
+diff --git a/CMakeLists.txt b/CMakeLists.txt
+index 0b56fc85..ead47c54 100644
+--- a/CMakeLists.txt
++++ b/CMakeLists.txt
+@@ -735,7 +735,6 @@ add_subdirectory(code_motif)
+ ########################################################################
+ set(CERNLIB_MMAP 1)
+ install(FILES
+-${CMAKE_CURRENT_SOURCE_DIR}/cfortran/cfortran.h
+ ${CMAKE_CURRENT_SOURCE_DIR}/cfortran/comis.h
+ ${CMAKE_CURRENT_SOURCE_DIR}/cfortran/cspack.h
+ ${CMAKE_CURRENT_SOURCE_DIR}/cfortran/geant315.h
+@@ -757,7 +756,7 @@ ${CMAKE_CURRENT_SOURCE_DIR}/cfortran/paw.h
+ ${CMAKE_CURRENT_SOURCE_DIR}/cfortran/zebra.h
+ DESTINATION ${CMAKE_INSTALL_INCLUDEDIR}/  COMPONENT libs  )
+ 
+-set(head cfortran.h comis.h cspack.h geant315.h geant321.h gen.h graflib.h hbook.h hbook_94b.h higz.h hplot.h jetset74.h kernlib.h kuip.h lapack.h lepto62.h minuit.h packlib.h paw.h zebra.h )
++set(head comis.h cspack.h geant315.h geant321.h gen.h graflib.h hbook.h hbook_94b.h higz.h hplot.h jetset74.h kernlib.h kuip.h lapack.h lepto62.h minuit.h packlib.h paw.h zebra.h )
+ 
+ install(CODE "execute_process(COMMAND ${CMAKE_COMMAND} -E make_directory ${CMAKE_INSTALL_INCLUDEDIR}/cfortran/)")
+ foreach ( m ${head} )
diff --git a/sci-physics/cernlib/files/cernlib-2023.10.31.0-ctest.patch b/sci-physics/cernlib/files/cernlib-2023.10.31.0-ctest.patch
new file mode 100644
index 000000000..b329bb900
--- /dev/null
+++ b/sci-physics/cernlib/files/cernlib-2023.10.31.0-ctest.patch
@@ -0,0 +1,31 @@
+diff --git a/CMakeLists.txt b/CMakeLists.txt
+index 0b56fc85..78a28e11 100644
+--- a/CMakeLists.txt
++++ b/CMakeLists.txt
+@@ -162,9 +162,10 @@ macro(CLATestTarget ast)
+   list(FIND a "<" NEEDSHELL)
+   list(JOIN a " " MYCMD)
+   if (NEEDSHELL STREQUAL "-1")
+-    add_test(NAME test${exec} COMMAND  ${CMAKE_CURRENT_BINARY_DIR}/${exec} {MYCMD}           WORKING_DIRECTORY ${CMAKE_CURRENT_BINARY_DIR})
++    add_test(NAME test${exec} COMMAND  ${CMAKE_CURRENT_BINARY_DIR}/${exec} ${MYCMD}           WORKING_DIRECTORY ${CMAKE_CURRENT_BINARY_DIR})
+     if (CERNLIB_ENABLE_MEMORYTEST)
+-       add_test(NAME memory_test${exec} COMMAND ${VG} ${VGOPTIONS} ${CMAKE_CURRENT_BINARY_DIR}/${exec} {MYCMD}           WORKING_DIRECTORY ${CMAKE_CURRENT_BINARY_DIR})
++       add_test(NAME memory_test${exec} COMMAND ${VG} ${VGOPTIONS}
++	       ${CMAKE_CURRENT_BINARY_DIR}/${exec} ${MYCMD}           WORKING_DIRECTORY ${CMAKE_CURRENT_BINARY_DIR})
+     endif()
+   else()
+     add_test(NAME test${exec} COMMAND sh -c "${CMAKE_CURRENT_BINARY_DIR}/${exec} ${MYCMD}"  WORKING_DIRECTORY ${CMAKE_CURRENT_BINARY_DIR})
+@@ -182,9 +183,11 @@ macro(CLBTestTarget ast)
+   list(JOIN a " " MYCMD)
+   if (NEEDSHELL STREQUAL "-1")
+     if (CERNLIB_ENABLE_MEMORYTEST)
+-      add_test(NAME memory_test${exec} COMMAND ${VG} ${VGOPTIONS} ${CMAKE_CURRENT_BINARY_DIR}/${exec}/${exec} {MYCMD}           WORKING_DIRECTORY ${CMAKE_CURRENT_BINARY_DIR}/${exec})
++      add_test(NAME memory_test${exec} COMMAND ${VG} ${VGOPTIONS}
++	      ${CMAKE_CURRENT_BINARY_DIR}/${exec}/${exec} ${MYCMD}           WORKING_DIRECTORY ${CMAKE_CURRENT_BINARY_DIR}/${exec})
+     endif()
+-    add_test(NAME test${exec} COMMAND ${CMAKE_CURRENT_BINARY_DIR}/${exec}/${exec} {MYCMD}           WORKING_DIRECTORY ${CMAKE_CURRENT_BINARY_DIR}/${exec})
++    add_test(NAME test${exec} COMMAND
++	    ${CMAKE_CURRENT_BINARY_DIR}/${exec}/${exec} ${MYCMD}           WORKING_DIRECTORY ${CMAKE_CURRENT_BINARY_DIR}/${exec})
+   else()
+     if (CERNLIB_ENABLE_MEMORYTEST)
+       add_test(NAME memory_test${exec} COMMAND sh -c "${VG} ${VGOPTIONS} ${CMAKE_CURRENT_BINARY_DIR}/${exec}/${exec} ${MYCMD}"  WORKING_DIRECTORY ${CMAKE_CURRENT_BINARY_DIR}/${exec})
diff --git a/sci-physics/cernlib/files/cernlib-2023.10.31.0-man.patch b/sci-physics/cernlib/files/cernlib-2023.10.31.0-man.patch
new file mode 100644
index 000000000..636943899
--- /dev/null
+++ b/sci-physics/cernlib/files/cernlib-2023.10.31.0-man.patch
@@ -0,0 +1,22 @@
+diff --git a/CMakeLists.txt b/CMakeLists.txt
+index 0b56fc85..0db67942 100644
+--- a/CMakeLists.txt
++++ b/CMakeLists.txt
+@@ -410,7 +413,7 @@ else()
+         COMMENT "GZipping to ${CMAKE_CURRENT_BINARY_DIR}/${m}.gz."
+     )
+ endif()
+-  install(FILES  ${CMAKE_CURRENT_BINARY_DIR}/${m}.gz DESTINATION ${CMAKE_INSTALL_DATADIR}/man/man1)
++#install(FILES  ${CMAKE_CURRENT_BINARY_DIR}/${m}.gz DESTINATION ${CMAKE_INSTALL_DATADIR}/man/man1)
+ endforeach ( m ${man1} )
+ 
+ foreach ( m ${man8} )
+@@ -425,7 +428,7 @@ else()
+         COMMENT "GZipping to ${CMAKE_CURRENT_BINARY_DIR}/${m}.gz."
+     )
+ endif()
+-  install(FILES  ${CMAKE_CURRENT_BINARY_DIR}/${m}.gz DESTINATION ${CMAKE_INSTALL_DATADIR}/man/man8)
++#install(FILES  ${CMAKE_CURRENT_BINARY_DIR}/${m}.gz DESTINATION ${CMAKE_INSTALL_DATADIR}/man/man8)
+ endforeach ( m ${man8} )
+ 
+ #install(PROGRAMS ${CMAKE_CURRENT_SOURCE_DIR}/patchy5/yexpand.script  DESTINATION ${CMAKE_INSTALL_BINDIR}/ RENAME yexpand.script${COMPSUFFIXBIN} )
diff --git a/sci-physics/cernlib/metadata.xml b/sci-physics/cernlib/metadata.xml
new file mode 100644
index 000000000..dcbfb9b47
--- /dev/null
+++ b/sci-physics/cernlib/metadata.xml
@@ -0,0 +1,24 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
+<pkgmetadata>
+  <maintainer type="person">
+    <email>alexander@neuwirth-informatik.de</email>
+    <name>Alexander Puck Neuwirth</name>
+  </maintainer>
+  <maintainer type="project">
+    <email>sci-physics@gentoo.org</email>
+    <name>Gentoo Physics Project</name>
+  </maintainer>
+  <longdescription lang="en">
+  The CERN Program Library is a large collection of general purpose
+  libraries and modules maintained and offered in both source and
+  object code form on the CERN central computers. Most of these
+  programs were developed at CERN and are therefore oriented towards
+  the needs of a physics research laboratory that is general
+  mathematics, data analysis, detectors simulation, data-handling
+  etc... applicable to a wide range of problems.
+  </longdescription>
+  <use>
+    <flag name="free"> Use free sources </flag>
+  </use>
+</pkgmetadata>
diff --git a/sci-physics/collier/Manifest b/sci-physics/collier/Manifest
new file mode 100644
index 000000000..709444249
--- /dev/null
+++ b/sci-physics/collier/Manifest
@@ -0,0 +1 @@
+DIST collier-1.2.8.tar.gz 933258 BLAKE2B 9849ae140ed055a24010f020920f377a78665cb6f2c16ba060082c3573594a2f5772779b4a5596d306220b49ec2ffb7249705c0f05ea4eb22784518acb1038a0 SHA512 119b597da04dcd529efc35b5f96d2b2ad1f2f4403c3d0521a24b49fba973c5557378b68994ea6d30ca92057d32a30a6de299b2c707d56c231d197f33632297d9
diff --git a/sci-physics/collier/collier-1.2.8.ebuild b/sci-physics/collier/collier-1.2.8.ebuild
new file mode 100644
index 000000000..c9410cf34
--- /dev/null
+++ b/sci-physics/collier/collier-1.2.8.ebuild
@@ -0,0 +1,34 @@
+# Copyright 2022 Gentoo Authors
+# Distributed under the terms of the GNU General Public License v2
+
+EAPI=8
+
+CMAKE_MAKEFILE_GENERATOR="emake"
+
+inherit fortran-2 cmake
+
+MY_P=COLLIER-${PV}
+
+DESCRIPTION="A Complex One-Loop LIbrary with Extended Regularizations"
+HOMEPAGE="https://collier.hepforge.org/index.html"
+SRC_URI="https://collier.hepforge.org/downloads/?f=${P}.tar.gz -> ${P}.tar.gz"
+S="${WORKDIR}/${MY_P}"
+
+LICENSE="GPL-3"
+SLOT="0"
+KEYWORDS="~amd64"
+
+IUSE="static-libs"
+
+PATCHES=(
+	"${FILESDIR}/${PN}-1.2.7-mod.patch"
+)
+
+src_configure() {
+	local mycmakeargs=(
+		-Dstatic=$(usex static-libs ON OFF)
+		-DLIB_INSTALL_DIR="${EPREFIX}"/usr/$(get_libdir)
+		-DSYSCONFIG_INSTALL_DIR="${EPREFIX}"/usr/$(get_libdir)/cmake/collier
+	)
+	cmake_src_configure
+}
diff --git a/sci-physics/collier/files/collier-1.2.7-mod.patch b/sci-physics/collier/files/collier-1.2.7-mod.patch
new file mode 100644
index 000000000..030900b5c
--- /dev/null
+++ b/sci-physics/collier/files/collier-1.2.7-mod.patch
@@ -0,0 +1,40 @@
+--- a/CMakeLists.txt	2023-05-08 17:21:39.559979698 +0200
++++ b/CMakeLists.txt	2023-05-08 17:43:20.599147534 +0200
+@@ -282,7 +282,36 @@
+ message("Collier install include prefix: ${INCLUDE_INSTALL_DIR}")
+ message("Collier install library prefix: ${LIB_INSTALL_DIR}")
+ 
+-set(COLLIER_HEADERS "${CMAKE_Fortran_MODULE_DIRECTORY}/collier.mod")
++set(COLLIER_HEADERS "${CMAKE_Fortran_MODULE_DIRECTORY}/collier.mod"
++	"${CMAKE_Fortran_MODULE_DIRECTORY}/cache.mod"
++	"${CMAKE_Fortran_MODULE_DIRECTORY}/buildtensors.mod"
++	"${CMAKE_Fortran_MODULE_DIRECTORY}/coli_aux2.mod"
++	"${CMAKE_Fortran_MODULE_DIRECTORY}/coli_stat.mod"
++	"${CMAKE_Fortran_MODULE_DIRECTORY}/collier_aux.mod"
++	"${CMAKE_Fortran_MODULE_DIRECTORY}/collier_coefs.mod"
++	"${CMAKE_Fortran_MODULE_DIRECTORY}/collier_global.mod"
++	"${CMAKE_Fortran_MODULE_DIRECTORY}/collier_init.mod"
++	"${CMAKE_Fortran_MODULE_DIRECTORY}/collier.mod"
++	"${CMAKE_Fortran_MODULE_DIRECTORY}/collier_tensors.mod"
++	"${CMAKE_Fortran_MODULE_DIRECTORY}/combinatorics.mod"
++	"${CMAKE_Fortran_MODULE_DIRECTORY}/dd_2pt.mod"
++	"${CMAKE_Fortran_MODULE_DIRECTORY}/dd_3pt.mod"
++	"${CMAKE_Fortran_MODULE_DIRECTORY}/dd_4pt.mod"
++	"${CMAKE_Fortran_MODULE_DIRECTORY}/dd_5pt.mod"
++	"${CMAKE_Fortran_MODULE_DIRECTORY}/dd_6pt.mod"
++	"${CMAKE_Fortran_MODULE_DIRECTORY}/dd_global.mod"
++	"${CMAKE_Fortran_MODULE_DIRECTORY}/dd_statistics.mod"
++	"${CMAKE_Fortran_MODULE_DIRECTORY}/globalc.mod"
++	"${CMAKE_Fortran_MODULE_DIRECTORY}/globald.mod"
++	"${CMAKE_Fortran_MODULE_DIRECTORY}/inittensors.mod"
++	"${CMAKE_Fortran_MODULE_DIRECTORY}/master.mod"
++	"${CMAKE_Fortran_MODULE_DIRECTORY}/reductionab.mod"
++	"${CMAKE_Fortran_MODULE_DIRECTORY}/reductionc.mod"
++	"${CMAKE_Fortran_MODULE_DIRECTORY}/reductiond.mod"
++	"${CMAKE_Fortran_MODULE_DIRECTORY}/reductionefg.mod"
++	"${CMAKE_Fortran_MODULE_DIRECTORY}/reductiontn.mod"
++	"${CMAKE_Fortran_MODULE_DIRECTORY}/tensorreduction.mod"
++)
+ set_target_properties(collier PROPERTIES PUBLIC_HEADER "${COLLIER_HEADERS}")
+ 
+ include(PackageConfigInstall)
diff --git a/sci-physics/collier/metadata.xml b/sci-physics/collier/metadata.xml
new file mode 100644
index 000000000..72f8361a4
--- /dev/null
+++ b/sci-physics/collier/metadata.xml
@@ -0,0 +1,19 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<!DOCTYPE pkgmetadata SYSTEM "https://www.gentoo.org/dtd/metadata.dtd">
+<pkgmetadata>
+  <maintainer type="person">
+    <email>alexander@neuwirth-informatik.de</email>
+    <name>Alexander Puck Neuwirth</name>
+  </maintainer>
+  <maintainer type="project">
+    <email>sci-physics@gentoo.org</email>
+    <name>Gentoo Physics Project</name>
+  </maintainer>
+  <longdescription>
+  A package for evaluation of scalar and tensor one-loop integrals 
+  based on the FF package by G.J. van Oldenborgh.
+  It features an easy Fortran, C++, and Mathematica interface 
+  to the scalar one-loop functions of FF and in addition provides 
+  the 2-, 3-, and 4-point tensor coefficient functions.
+  </longdescription>
+</pkgmetadata>
diff --git a/sci-physics/elk/Manifest b/sci-physics/elk/Manifest
deleted file mode 100644
index adb5a0410..000000000
--- a/sci-physics/elk/Manifest
+++ /dev/null
@@ -1,2 +0,0 @@
-DIST elk-1.4.22.tgz 1866287 BLAKE2B 34e11f23823a274154732f11cb8b2891f68b1ac15cc2179e4e6d471983382ac1a3fbf5e3b891be8eba26031302957ef276dc90fb213ad04e320613373e4e2b86 SHA512 7c512ac6738d883fe1c76964c8bd44ef34269f58f4c8d97ee63949949391ef1040dc41cf0c2626492f6c94649b696d7b67eef8292011dc75c312a3c4b3c21da6
-DIST elk-2.1.25.tgz 1932025 BLAKE2B 8fb20518eba4b64be7bd4a71e1e9d45eb9cf8d990016ccf7b9c18d72da89bd646f0e16f8e4b904d096883c7e509d528bf7b59998073b84080fd1afd8d15928d0 SHA512 ef121946f992a6de2d05681a08a94a50eeab72d0dc6cc81de82ccd3460020eccd266f5f584e7e52c8c79eb8ad1d29ed8a0decc9fa0ecf9ae07fb54c3235b389c
diff --git a/sci-physics/elk/elk-1.4.22.ebuild b/sci-physics/elk/elk-1.4.22.ebuild
deleted file mode 100644
index cf22468c1..000000000
--- a/sci-physics/elk/elk-1.4.22.ebuild
+++ /dev/null
@@ -1,108 +0,0 @@
-# Copyright 1999-2014 Gentoo Foundation
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=5
-
-inherit eutils flag-o-matic fortran-2 multilib toolchain-funcs
-
-DESCRIPTION="All-electron full-potential linearised augmented-plane wave (FP-LAPW)"
-HOMEPAGE="http://elk.sourceforge.net/"
-SRC_URI="mirror://sourceforge/${PN}/${P}.tgz"
-
-LICENSE="GPL-3"
-SLOT="0"
-KEYWORDS="~amd64 ~x86"
-IUSE="-debug lapack libxc mpi openmp perl test"
-
-RDEPEND="
-	lapack? (
-		virtual/blas
-		virtual/lapack )
-	libxc? ( >=sci-libs/libxc-1.2.0-r1[fortran] )
-	mpi? ( virtual/mpi )"
-DEPEND="${RDEPEND}
-	perl? ( dev-lang/perl )
-	virtual/pkgconfig"
-
-DOCS=( README  )
-
-FORTRAN_STANDARD=90
-
-pkg_setup() {
-	# fortran-2.eclass does not handle mpi wrappers
-	if use mpi; then
-		export FC="mpif90"
-		export F77="mpif77"
-		export CC="mpicc"
-		export CXX="mpic++"
-	else
-		tc-export FC F77 CC CXX
-	fi
-
-	use openmp && FORTRAN_NEED_OPENMP=1
-
-	fortran-2_pkg_setup
-
-	use openmp && append-flags -fopenmp
-}
-
-src_prepare() {
-	rm -rf src/{BLAS,LAPACK} || die
-	if use libxc; then
-		sed -i -e's/^\(SRC_libxc =\)/#\1/' "${S}/src/Makefile" || die
-	fi
-	if use mpi; then
-		sed -i -e's/^\(SRC_mpi =\)/#\1/' "${S}/src/Makefile" || die
-	fi
-
-	sed \
-		-e "s: -o : ${LDFLAGS} -o :g" \
-		-i src/{,eos,spacegroup}/Makefile || die
-}
-
-src_configure() {
-	append-fflags -I/usr/include -I/usr/$(get_libdir)/finclude
-
-	cat > make.inc <<- EOF
-	MAKE = make
-	F90 = $(tc-getFC)
-	F90_OPTS = ${FCFLAGS}
-	F77 = $(tc-getF77)
-	F77_OPTS = ${FFLAGS}
-	CC = $(tc-getCC)
-	CXX = $(tc-getCXX)
-	CFLAGS = ${CFLAGS}
-	CXXFLAGS = ${CXXFLAGS}
-	LD = $(tc-getLD)
-	AR = $(tc-getAR)
-	LIB_SYS =
-	LIB_LPK = $($(tc-getPKG_CONFIG) --libs lapack)
-	LIB_FFT = fftlib.a
-	EOF
-
-	if use libxc; then
-		echo "LIB_XC = -L/usr/$(get_libdir) -lxc" >> make.inc
-		echo "SRC_libxc = libxc_funcs.f90 libxc.f90 libxcifc.f90" >>make.inc
-	fi
-}
-
-MAKEOPTS+=" -j1"
-
-src_compile() {
-	emake -C src fft
-	emake -C src elk
-	emake -C src/eos
-	emake -C src/spacegroup
-}
-
-src_install() {
-	dobin src/elk src/protex src/eos/eos src/spacegroup/spacegroup
-	dobin utilities/elk-bands
-	use perl && dobin utilities/xps_exc.pl utilities/se.pl
-	dodoc README
-	for doc in docs/*; do
-		dodoc $doc
-	done
-	insinto /usr/share/${P}
-	doins -r species utilities examples tests
-}
diff --git a/sci-physics/elk/elk-2.1.25.ebuild b/sci-physics/elk/elk-2.1.25.ebuild
deleted file mode 100644
index 39054114b..000000000
--- a/sci-physics/elk/elk-2.1.25.ebuild
+++ /dev/null
@@ -1,134 +0,0 @@
-# Copyright 1999-2015 Gentoo Foundation
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=5
-
-PYTHON_COMPAT=( python2_7 )
-
-inherit eutils flag-o-matic fortran-2 multilib toolchain-funcs python-single-r1
-
-DESCRIPTION="All-electron full-potential linearised augmented-plane wave (FP-LAPW)"
-HOMEPAGE="http://elk.sourceforge.net/"
-SRC_URI="mirror://sourceforge/${PN}/${P}.tgz"
-
-LICENSE="GPL-3"
-SLOT="0"
-KEYWORDS="~amd64 ~x86"
-IUSE="-debug lapack libxc mpi openmp perl python test"
-
-REQUIRED_USE="${PYTHON_REQUIRED_USE}"
-
-RDEPEND="
-	lapack? (
-		virtual/blas
-		virtual/lapack )
-	libxc? ( >=sci-libs/libxc-1.2.0-r1[fortran] )
-	perl? ( dev-lang/perl )
-	python? ( ${PYTHON_DEPS} )
-	mpi? ( virtual/mpi )"
-DEPEND="${RDEPEND}
-	virtual/pkgconfig"
-
-DOCS=( README  )
-
-FORTRAN_STANDARD=90
-
-pkg_setup() {
-	# fortran-2.eclass does not handle mpi wrappers
-	if use mpi; then
-		export FC="mpif90"
-		export F77="mpif77"
-		export CC="mpicc"
-		export CXX="mpic++"
-	else
-		tc-export FC F77 CC CXX
-	fi
-
-	use openmp && FORTRAN_NEED_OPENMP=1
-
-	fortran-2_pkg_setup
-
-	if use openmp; then
-		# based on _fortran-has-openmp() of fortran-2.eclass
-		local openmp=""
-		local fcode=ebuild-openmp-flags.f
-		local _fc=$(tc-getFC)
-
-		pushd "${T}"
-		cat <<- EOF > "${fcode}"
-		1     call omp_get_num_threads
-		2     end
-		EOF
-
-		for openmp in -fopenmp -xopenmp -openmp -mp -omp -qsmp=omp; do
-			"${_fc}" "${openmp}" "${fcode}" -o "${fcode}.x" && break
-		done
-
-		rm -f "${fcode}.*"
-		popd
-
-		append-flags "${openmp}"
-	fi
-}
-
-src_prepare() {
-	rm -rf src/{BLAS,LAPACK} || die
-	if use libxc; then
-		sed -i -e's/^\(SRC_libxc =\)/#\1/' "${S}/src/Makefile" || die
-	fi
-	if use mpi; then
-		sed -i -e's/^\(SRC_mpi =\)/#\1/' "${S}/src/Makefile" || die
-	fi
-
-	sed \
-		-e "s: -o : ${LDFLAGS} -o :g" \
-		-i src/{,eos,spacegroup}/Makefile || die
-}
-
-src_configure() {
-	append-fflags -I/usr/include
-
-	cat > make.inc <<- EOF
-	MAKE = make
-	F90 = $(tc-getFC)
-	F90_OPTS = ${FCFLAGS}
-	F77 = $(tc-getF77)
-	F77_OPTS = ${FFLAGS}
-	CC = $(tc-getCC)
-	CXX = $(tc-getCXX)
-	CFLAGS = ${CFLAGS}
-	CXXFLAGS = ${CXXFLAGS}
-	LD = $(tc-getLD)
-	AR = $(tc-getAR)
-	LIB_SYS =
-	LIB_LPK = $($(tc-getPKG_CONFIG) --libs lapack)
-	LIB_FFT = fftlib.a
-	EOF
-
-	if use libxc; then
-		echo "LIB_XC = -L/usr/$(get_libdir) -lxc" >> make.inc
-		echo "SRC_libxc = libxc_funcs.f90 libxc.f90 libxcifc.f90" >>make.inc
-	fi
-}
-
-MAKEOPTS+=" -j1"
-
-src_compile() {
-	emake -C src fft
-	emake -C src elk
-	emake -C src/eos
-	emake -C src/spacegroup
-}
-
-src_install() {
-	dobin src/elk src/protex src/eos/eos src/spacegroup/spacegroup
-	dobin utilities/elk-bands/elk-bands
-	use perl && dobin utilities/xps/xps_exc.pl utilities/wien2k-elk/se.pl
-	use python && dobin utilities/blocks2columns/blocks2columns.py
-	dodoc README
-	for doc in docs/*; do
-		dodoc $doc
-	done
-	insinto /usr/share/${P}
-	doins -r species utilities examples tests
-}
diff --git a/sci-physics/elk/metadata.xml b/sci-physics/elk/metadata.xml
deleted file mode 100644
index d00045595..000000000
--- a/sci-physics/elk/metadata.xml
+++ /dev/null
@@ -1,25 +0,0 @@
-<?xml version="1.0" encoding="UTF-8"?>
-<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
-<pkgmetadata>
-	<maintainer type="project">
-		<email>sci-physics@gentoo.org</email>
-		<name>Gentoo Physics Project</name>
-	</maintainer>
-	<longdescription lang="en">
-Elk is an all-electron full-potential linearised augmented-plane wave (FP-LAPW) code with many advanced features. Written originally at Karl-Franzens-Universität Graz as a milestone of the EXCITING EU Research and Training Network, the code is designed to be as simple as possible so that new developments in the field of density functional theory (DFT) can be added quickly and reliably. The code is freely available under the GNU General Public License.
-</longdescription>
-	<use>
-		<flag name="libxc">
-Use sci-libs/libxc library of exchange-correlation functionals by ETSF.
-</flag>
-		<flag name="perl">
-Install perl scripts.
-</flag>
-		<flag name="python">
-Install python scripts.
-</flag>
-	</use>
-	<upstream>
-		<remote-id type="sourceforge">elk</remote-id>
-	</upstream>
-</pkgmetadata>
diff --git a/sci-physics/feynarts/Manifest b/sci-physics/feynarts/Manifest
new file mode 100644
index 000000000..d66304b21
--- /dev/null
+++ b/sci-physics/feynarts/Manifest
@@ -0,0 +1 @@
+DIST FeynArts-3.11.tar.gz 3146405 BLAKE2B d22a19faecaa3a87ebf48b035736a04a6ae9b28e47300240edac541cb86438781092bf0a16d84808fb0256cf7547ba9d04024934007fa017cab08811d6b2b41b SHA512 2032172c86316b1703c0ff0c9cc511db0b97d6268bde30b6948ea98c5f2b39996071675d25aba4ed65af99f0c6535bce4e5eca8ca942be3591f922937c4aa79b
diff --git a/sci-physics/feynarts/feynarts-3.11.ebuild b/sci-physics/feynarts/feynarts-3.11.ebuild
new file mode 100644
index 000000000..ecf46b127
--- /dev/null
+++ b/sci-physics/feynarts/feynarts-3.11.ebuild
@@ -0,0 +1,29 @@
+# Copyright 2022 Gentoo Authors
+# Distributed under the terms of the GNU General Public License v2
+
+EAPI=8
+
+MY_PN=FeynArts
+MY_P=${MY_PN}-${PV}
+
+DESCRIPTION="FeynArts renders Feynman diagrams and generates their topologies."
+HOMEPAGE="https://feynarts.de"
+SRC_URI="https://feynarts.de/${MY_P}.tar.gz"
+S="${WORKDIR}/${MY_P}"
+
+LICENSE="LGPL-3+"
+SLOT="0"
+KEYWORDS="~amd64"
+
+RDEPEND="
+	sci-mathematics/mathematica
+	"
+DEPEND="${RDEPEND}"
+
+src_install() {
+	MMADIR=/usr/share/Mathematica/Applications
+	dosym "${MY_P}" "${MMADIR}/${MY_PN}"
+	dodir "${MMADIR}/${MY_P}"
+	insinto ${MMADIR}
+	doins -r "${S}"
+}
diff --git a/sci-physics/feynarts/metadata.xml b/sci-physics/feynarts/metadata.xml
new file mode 100644
index 000000000..14606c162
--- /dev/null
+++ b/sci-physics/feynarts/metadata.xml
@@ -0,0 +1,19 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
+<pkgmetadata>
+	<maintainer type="project">
+		<email>sci@gentoo.org</email>
+		<name>Gentoo Science Project</name>
+	</maintainer>
+	<maintainer type="project">
+		<email>sci-physics@gentoo.org</email>
+		<name>Gentoo Physics Project</name>
+	</maintainer>
+	<maintainer type="person">
+		<email>alexander@neuwirth-informatik.de</email>
+		<name>Alexander Puck Neuwirth</name>
+	</maintainer>
+	<longdescription lang="en">
+	FeynArts is a Mathematica package for the generation and visualization of Feynman diagrams and amplitudes.
+	</longdescription>
+</pkgmetadata>
diff --git a/sci-physics/feyncalc/Manifest b/sci-physics/feyncalc/Manifest
new file mode 100644
index 000000000..9514cfd33
--- /dev/null
+++ b/sci-physics/feyncalc/Manifest
@@ -0,0 +1,2 @@
+DIST FeynCalc-9.3.1.tar.gz 4296784 BLAKE2B bb9e2e17ee8c51ec9417f900982af494e44a19cad651065d769820756056d6accfa8955da1c03dcc054e32c8ca5a5b1974594e77f95cc0a8e7100919783d20ad SHA512 3e7f4e87920e26712008754498f2d7e3a5873f6adf3e7dbea1e98f7f0f9ff20e1e08941b959e18143d3f602aa3f0c1ac4c574f450bcd6d2e8ad68e775e95aeee
+DIST FeynCalc-9999.tar.gz 4298804 BLAKE2B a4b404aed41d510f32ddf5a242d0c6129174ace1eeb92a19c2cf6f9620f82b37f3b01709d063619567590d38d4506431b5d9af6fbf3fe1184c07c683c1f2d3b4 SHA512 30ef3f0249b9dd639e0d83767d1aaea272c6ce3083d0a36a96ced11c68bd4d9c499efcd95abb209d56cd8ae3142b925c6b723c541821c7856e4ac787c2c52e34
diff --git a/sci-physics/feyncalc/feyncalc-9.3.1.ebuild b/sci-physics/feyncalc/feyncalc-9.3.1.ebuild
new file mode 100644
index 000000000..2f54f878b
--- /dev/null
+++ b/sci-physics/feyncalc/feyncalc-9.3.1.ebuild
@@ -0,0 +1,43 @@
+# Copyright 2022 Gentoo Authors
+# Distributed under the terms of the GNU General Public License v2
+
+EAPI=8
+
+MY_PV=$(ver_rs 1-3 '_')
+MY_PN=FeynCalc
+
+DESCRIPTION="FeynCalc is a Mathematica package for computing Feynman diagrams."
+HOMEPAGE="https://feyncalc.github.io/"
+SLOT="0"
+SRC_URI="https://github.com/FeynCalc/feyncalc/archive/refs/tags/Release-${MY_PV}.tar.gz -> ${MY_PN}-${PV}.tar.gz"
+S="${WORKDIR}/feyncalc-Release-${MY_PV}"
+
+LICENSE="GPL-3+"
+KEYWORDS="~amd64"
+IUSE="+FCtraditionalFormOutput"
+
+RDEPEND="
+	sci-mathematics/mathematica
+	"
+DEPEND="${RDEPEND}"
+
+src_configure() {
+	mv "${MY_PN}/DocOutput" "${MY_PN}/Documentation" || die
+	if use FCtraditionalFormOutput; then
+		echo '$FCTraditionalFormOutput=True;' > "${MY_PN}/FCConfig.m" || die
+	fi
+}
+
+src_install() {
+	MMADIR=/usr/share/Mathematica/Applications
+	dodir "${MMADIR}/${MY_PN}"
+	insinto "${MMADIR}/"
+	doins -r "${S}/${MY_PN}"
+	# copy permissions
+	for f in $(find "${MY_PN}/*" ! -type l); do
+		fperms --reference="${S}/$f" "${MMADIR}/$f"
+	done
+	# documentation are notebook(.nb) files
+	dodoc -r ${MY_PN}/Documentation/English/*
+	docompress -x /usr/share/doc/${PF}/
+}
diff --git a/sci-physics/feyncalc/feyncalc-9999.ebuild b/sci-physics/feyncalc/feyncalc-9999.ebuild
new file mode 100644
index 000000000..1c26d976e
--- /dev/null
+++ b/sci-physics/feyncalc/feyncalc-9999.ebuild
@@ -0,0 +1,47 @@
+# Copyright 2020 Gentoo Authors
+# Distributed under the terms of the GNU General Public License v2
+
+# Copyright 1999-2020 Gentoo Authors
+# Distributed under the terms of the GNU General Public License v2
+
+EAPI=8
+
+MY_PV=$(ver_rs 1-3 '_')
+MY_PN=FeynCalc
+
+DESCRIPTION="FeynCalc is a Mathematica package for computing Feynman diagrams."
+HOMEPAGE="https://feyncalc.github.io/"
+SLOT="0"
+SRC_URI="https://github.com/FeynCalc/feyncalc/archive/hotfix-stable.tar.gz -> ${MY_PN}-${PV}.tar.gz"
+S="${WORKDIR}/feyncalc-hotfix-stable"
+
+LICENSE="GPL-3+"
+IUSE="+FCtraditionalFormOutput"
+REQUIRED_USE=""
+PROPERTIES+=" live"
+
+RDEPEND="
+	sci-mathematics/mathematica
+	"
+DEPEND="${RDEPEND}"
+
+src_configure() {
+	mv "${MY_PN}/DocOutput" "${MY_PN}/Documentation" || die
+	if use FCtraditionalFormOutput; then
+		echo '$FCTraditionalFormOutput=True;' > "${MY_PN}/FCConfig.m" || die
+	fi
+}
+
+src_install() {
+	MMADIR=/usr/share/Mathematica/Applications
+	dodir "${MMADIR}/${MY_PN}"
+	insinto "${MMADIR}/"
+	doins -r "${S}/${MY_PN}"
+	# copy permissions
+	for f in $(find "${MY_PN}/*" ! -type l); do
+		fperms --reference="${S}/$f" "${MMADIR}/$f"
+	done
+	# documentation are notebook(.nb) files
+	dodoc -r ${MY_PN}/Documentation/English/*
+	docompress -x /usr/share/doc/${PF}/
+}
diff --git a/sci-physics/feyncalc/metadata.xml b/sci-physics/feyncalc/metadata.xml
new file mode 100644
index 000000000..826061ef4
--- /dev/null
+++ b/sci-physics/feyncalc/metadata.xml
@@ -0,0 +1,25 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
+<pkgmetadata>
+	<maintainer type="project">
+		<email>sci@gentoo.org</email>
+		<name>Gentoo Science Project</name>
+	</maintainer>
+	<maintainer type="project">
+		<email>sci-physics@gentoo.org</email>
+		<name>Gentoo Physics Project</name>
+	</maintainer>
+	<maintainer type="person">
+		<email>alexander@neuwirth-informatik.de</email>
+		<name>Alexander Puck Neuwirth</name>
+	</maintainer>
+	<longdescription lang="en">
+	FeynCalc is a Mathematica package for symbolic evaluation of Feynman diagrams and algebraic calculations in quantum field theory and elementary particle physics.
+	</longdescription>
+	<use>
+		<flag name="FCtraditionalFormOutput">Use TraditionalForm typesetting.</flag>
+	</use>
+	<upstream>
+		<remote-id type="github">FeynCalc/feyncalc</remote-id>
+	</upstream>
+</pkgmetadata>
diff --git a/sci-physics/formcalc/Manifest b/sci-physics/formcalc/Manifest
new file mode 100644
index 000000000..6ac4c74b1
--- /dev/null
+++ b/sci-physics/formcalc/Manifest
@@ -0,0 +1,2 @@
+DIST FormCalc-9.10.tar.gz 32070519 BLAKE2B e789d7eea0cc92f27033373fd6516e94ec66d1780ae7bb1254537fa508640436a4595dbf09594a2cad8b4178d1e950806089ae4584bff0f2848674325a734212 SHA512 30519fcd6a9e616f6bfa23825056afdc27111605ca66e35f6baebac5bcb7ff43e07c7d40ed90157c584be82392fc85a32b769e637a793817377a8ffc5601af6d
+DIST FormCalc-9.9.tar.gz 32059045 BLAKE2B 69e3d063bf746d86d02f63d3a1fdce314582b190bafc66d063a6f25575476fcb6b60121b9133f850ffd5d173e437b160a2661072051083b3f4affc48fcb4bda7 SHA512 9661a07fac13348de13ec09dc8f043df02ef9a5391be64217d432e04d4d82ad3dea94f43951f839fbe8947338bc0ab721a9a9ebdc0900979e16ea89d857c87c7
diff --git a/sci-physics/formcalc/files/formcalc-9.9-compile.patch b/sci-physics/formcalc/files/formcalc-9.9-compile.patch
new file mode 100644
index 000000000..48be7f06e
--- /dev/null
+++ b/sci-physics/formcalc/files/formcalc-9.9-compile.patch
@@ -0,0 +1,50 @@
+--- a/compile	2022-07-20 14:51:59.605328833 +0200
++++ b/compile	2022-07-20 15:37:09.122446647 +0200
+@@ -96,7 +96,7 @@
+ 
+ mcc="REALCC=\"$CC\" CC=\"$t/fcc\" \
+ REALCXX=\"$CXX\" CXX=\"$t/f++\" \
+-PATH=\""'$$PATH'":$t\" $MCC -st $MCFLAGS $CFLAGS"
++PATH=\""'$$PATH'":$t\" $MCC -st -g $MCFLAGS $CFLAGS"
+ 
+ # Mma 5.1's mcc needs -lpthread for static linking
+ mclibs="-lpthread"
+@@ -104,37 +104,28 @@
+ cc="$CC $CFLAGS"
+ 
+ make -f - << _EOF_ || exit 1
+-all: $DEST/tform$exe \
++all: \
+   $DEST/ReadForm$exe $DEST/ToForm$exe \
+   $DEST/ToFortran$exe $DEST/ToC$exe \
+   $DEST/ReadData$exe $DEST/reorder$exe
+ 
+-$DEST/tform$exe: $SRC/bin/$BIN/tform$exe
+-	cp -p $SRC/bin/$BIN/* $DEST/
+-
+ $DEST/ReadForm$exe: $SRC/FormCalc/ReadForm.tm
+ 	$mcc -o $DEST/ReadForm$exe $SRC/FormCalc/ReadForm.tm $mclibs
+-	-strip $DEST/ReadForm$exe
+ 
+ $DEST/ToForm$exe: $SRC/FormCalc/ToForm.c
+ 	$cc -o $DEST/ToForm$exe $SRC/FormCalc/ToForm.c
+-	-strip $DEST/ToForm$exe
+ 
+ $DEST/ToFortran$exe: $SRC/FormCalc/ToFortran.c
+ 	$cc -o $DEST/ToFortran$exe $SRC/FormCalc/ToFortran.c
+-	-strip $DEST/ToFortran$exe
+ 
+ $DEST/ToC$exe: $SRC/FormCalc/ToC.c
+ 	$cc -o $DEST/ToC$exe $SRC/FormCalc/ToC.c
+-	-strip $DEST/ToC$exe
+ 
+ $DEST/ReadData$exe: $SRC/tools/ReadData.tm
+ 	$mcc -o $DEST/ReadData$exe $SRC/tools/ReadData.tm $mclibs
+-	-strip $DEST/ReadData$exe
+ 
+ $DEST/reorder$exe: $SRC/tools/reorder.c
+ 	$cc -o $DEST/reorder$exe $SRC/tools/reorder.c
+-	-strip $DEST/reorder$exe
+ _EOF_
+ 
+ 
diff --git a/sci-physics/formcalc/formcalc-9.10-r1.ebuild b/sci-physics/formcalc/formcalc-9.10-r1.ebuild
new file mode 100644
index 000000000..fb57ea648
--- /dev/null
+++ b/sci-physics/formcalc/formcalc-9.10-r1.ebuild
@@ -0,0 +1,49 @@
+# Copyright 2022 Gentoo Authors
+# Distributed under the terms of the GNU General Public License v2
+
+EAPI=8
+
+inherit fortran-2
+
+MY_PN=FormCalc
+MY_P=${MY_PN}-${PV}
+
+DESCRIPTION="FormCalc can be used for automatic Feynman diagram computation."
+HOMEPAGE="https://feynarts.de/formcalc"
+SRC_URI="https://feynarts.de/formcalc/${MY_P}.tar.gz"
+S="${WORKDIR}/${MY_P}"
+
+LICENSE="LGPL-3+"
+SLOT="0"
+KEYWORDS="~amd64"
+
+RDEPEND="
+	sci-mathematics/mathematica
+	sci-mathematics/form[threads]
+	"
+DEPEND="${RDEPEND}"
+BDEPEND="
+	sci-mathematics/mathematica
+	sci-mathematics/form
+	"
+PATCHES=( "${FILESDIR}"/${PN}-9.9-compile.patch )
+
+src_compile() {
+	# remove shipped binaries
+	rm bin/Linux-x86-64/* || die
+	rm bin/Linux-x86-64-kernel2.6/* || die
+	export DEST=Linux-x86-64
+	./compile ${LDFLAGS} || die
+}
+
+src_install() {
+	MMADIR=/usr/share/Mathematica/Applications
+	# unversioned directory
+	dosym ${MY_P} ${MMADIR}/${MY_PN}
+	mv "${WORKDIR}/${MY_P}" "${ED}${MMADIR}" || die
+	# switch to system form
+	dosym `command -v form` ${MMADIR}/${MY_P}/Linux-x86-64/form
+	dosym `command -v tform` ${MMADIR}/${MY_P}/Linux-x86-64/tform
+
+	dodoc manual/*.pdf
+}
diff --git a/sci-physics/formcalc/formcalc-9.9-r1.ebuild b/sci-physics/formcalc/formcalc-9.9-r1.ebuild
new file mode 100644
index 000000000..91d88dd99
--- /dev/null
+++ b/sci-physics/formcalc/formcalc-9.9-r1.ebuild
@@ -0,0 +1,51 @@
+# Copyright 2022 Gentoo Authors
+# Distributed under the terms of the GNU General Public License v2
+
+EAPI=8
+
+inherit fortran-2
+
+MY_PN=FormCalc
+MY_P=${MY_PN}-${PV}
+
+DESCRIPTION="FormCalc can be used for automatic Feynman diagram computation."
+HOMEPAGE="https://feynarts.de/formcalc"
+SRC_URI="https://feynarts.de/formcalc/${MY_P}.tar.gz"
+S="${WORKDIR}/${MY_P}"
+
+LICENSE="LGPL-3+"
+SLOT="0"
+KEYWORDS="~amd64"
+
+RDEPEND="
+	sci-mathematics/mathematica
+	sci-mathematics/form[threads]
+	"
+DEPEND="${RDEPEND}"
+BDEPEND="
+	sci-mathematics/mathematica
+	sci-mathematics/form
+	"
+
+PATCHES=( "${FILESDIR}"/${P}-compile.patch )
+
+src_compile() {
+	# remove shipped binaries
+	rm bin/Linux-x86-64/* || die
+	rm bin/Linux-x86-64-old/* || die
+
+	export DEST=Linux-x86-64
+	./compile ${LDFLAGS} || die
+}
+
+src_install() {
+	MMADIR=/usr/share/Mathematica/Applications
+	# unversioned directory
+	dosym ${MY_P} ${MMADIR}/${MY_PN}
+	mv "${WORKDIR}/${MY_P}" "${ED}${MMADIR}" || die
+	# switch to system form
+	dosym `command -v form` ${MMADIR}/${MY_P}/Linux-x86-64/form
+	dosym `command -v tform` ${MMADIR}/${MY_P}/Linux-x86-64/tform
+
+	dodoc manual/*.pdf
+}
diff --git a/sci-physics/formcalc/metadata.xml b/sci-physics/formcalc/metadata.xml
new file mode 100644
index 000000000..b103d8f63
--- /dev/null
+++ b/sci-physics/formcalc/metadata.xml
@@ -0,0 +1,19 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
+<pkgmetadata>
+	<maintainer type="project">
+		<email>sci@gentoo.org</email>
+		<name>Gentoo Science Project</name>
+	</maintainer>
+	<maintainer type="project">
+		<email>sci-physics@gentoo.org</email>
+		<name>Gentoo Physics Project</name>
+	</maintainer>
+	<maintainer type="person">
+		<email>alexander@neuwirth-informatik.de</email>
+		<name>Alexander Puck Neuwirth</name>
+	</maintainer>
+	<longdescription lang="en">
+	FormCalc is a Mathematica package for the calculation of tree-level and one-loop Feynman diagrams. It makes extensive use of the form tool.
+	</longdescription>
+</pkgmetadata>
diff --git a/sci-physics/fullprof-bin/Manifest b/sci-physics/fullprof-bin/Manifest
index be51fa085..eb20213f3 100644
--- a/sci-physics/fullprof-bin/Manifest
+++ b/sci-physics/fullprof-bin/Manifest
@@ -1 +1 @@
-DIST FullProf_Suite_April2013_Lin.tgz 67231541 SHA256 8e3248471e7fa8e2be6a4b87212d280ae71f19f03bd5b7d304bac8a91b39a8a1 SHA512 e56bcec33a4b587cc299084c08b352b992e75434e3550eb7c83d3f908895bdf92248872f9781fcb76b6672b438955b7cb0be01fe4bf67296d0e93b4de74cf68f WHIRLPOOL 4fd25c610d46920be287ae8ce4ae7d9c9231f4598a804b005c42f661da41adaf02667c8a1857d24e0f60566462bbaafd266f482e1e11c1ea893c8de75e39dc9d
+DIST FullProf_Suite_September2020_Linux64.tgz 115771268 BLAKE2B 436f3a8ba2fba85f91595ccd70ae10c9a04abb2b80a06d16fc07a640e5a11539cc364a54bb0bb3dfe8e99a1c986af8630e328b94d58cb819eaf9b9d6f9ef3e85 SHA512 cdbab81ab8a2b6c16c73ed64224638e2a11a6f3a42467bf6452260fabfdc396a71cf636e92dbc5fabb41aa636145777379f493367290a1112960224d9cb3226c
diff --git a/sci-physics/fullprof-bin/fullprof-bin-2020.09.ebuild b/sci-physics/fullprof-bin/fullprof-bin-2020.09.ebuild
new file mode 100644
index 000000000..929f61bb1
--- /dev/null
+++ b/sci-physics/fullprof-bin/fullprof-bin-2020.09.ebuild
@@ -0,0 +1,44 @@
+# Copyright 1999-2021 Gentoo Authors
+# Distributed under the terms of the GNU General Public License v2
+
+EAPI=7
+
+DESCRIPTION="Crystallographic tools mainly for Rietveld analysis"
+HOMEPAGE="https://www.ill.eu/sites/fullprof/index.html"
+# Does not fetch correctly with wget, we get the index.html file instead
+# their website seems to explicitly not want us to do this so we
+# add RESTRICT="fetch"
+#SRC_URI="https://www.ill.eu/sites/fullprof/downloads/FullProf_Suite_September2020_Linux64.tgz"
+SRC_URI="FullProf_Suite_September2020_Linux64.tgz"
+RESTRICT="fetch"
+
+LICENSE="freedist HPND"
+# There is no clear license specified. But according to Docs/Readme_Fp_Suite.txt
+# those two seem to be appropriate.
+SLOT="0"
+KEYWORDS="-* ~amd64 ~x86"
+
+RDEPEND="x11-libs/motif"
+DEPEND="${RDEPEND}"
+
+S="${WORKDIR}"
+
+QA_PREBUILT="opt/.*"
+
+pkg_nofetch() {
+	einfo "Please access https://www.ill.eu/sites/fullprof/downloads/${SRC_URI} using a browser"
+	einfo "and place the tgz file in your DISTDIR directory."
+}
+
+src_install() {
+	BASEDIR="/opt/fullprof"
+	echo "FULLPROF=\"${BASEDIR}\"" > "${T}"/99fullprof
+	doenvd "${T}"/99fullprof
+
+	dodir "${BASEDIR}"
+	# make symlinks
+	for i in * ; do
+		[[ -x $i && ! -d $i ]] && dosym "../fullprof/${i}" /opt/bin/"${i##*/}"
+	done
+	mv "${S}"/* "${ED}/${BASEDIR}" || die
+}
diff --git a/sci-physics/fullprof-bin/fullprof-bin-20313.04.ebuild b/sci-physics/fullprof-bin/fullprof-bin-20313.04.ebuild
deleted file mode 100644
index 8a4df4509..000000000
--- a/sci-physics/fullprof-bin/fullprof-bin-20313.04.ebuild
+++ /dev/null
@@ -1,65 +0,0 @@
-# Copyright 1999-2014 Gentoo Foundation
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=5
-
-DESCRIPTION="Crystallographic tools mainly for Rietveld analysis"
-HOMEPAGE="http://www.ill.eu/sites/fullprof/index.html"
-SRC_URI="http://www.ill.eu/sites/fullprof/downloads/FullProf_Suite_April2013_Lin.tgz"
-
-LICENSE="freedist HPND"
-# There is no clear license specified. But according to Docs/Readme_Fp_Suite.txt
-# those two seem to be appropriate.
-SLOT="0"
-KEYWORDS="-* ~amd64 ~x86"
-IUSE="+doc +examples +X"
-
-RDEPEND="X? ( x11-libs/motif:0 )"
-DEPEND=""
-S="${WORKDIR}"
-
-QA_PREBUILT="opt/.*"
-
-src_install() {
-	BASEDIR="/opt/fullprof"
-	echo "FULLPROF=\"${BASEDIR}\"" > "${T}"/99fullprof
-	doenvd "${T}"/99fullprof
-
-	if ! use examples; then
-		rm -r Examples || die
-	fi
-
-	if ! use doc; then
-		rm -r Docs Html || die
-	else
-		# fix (html) documentation to actually work
-		# as upstream is using inconsistent upper and lower case
-		mv Docs docs || die
-		cd docs || die
-		for i in *.HTM; do
-			mv "$i" "${i,,}" || die
-		done
-		mv "FullProf_Manual.pdf" "Fullprof_Manual.pdf" || die
-		mv "Manual_FullProf_Studio.pdf" "Manual_Fullprof_Studio.pdf" || die
-		mv "FullProf_News.htm" "Fullprof_News.htm" || die
-		for i in FullProf_News_200?.htm; do
-			mv "$i" "${i/FullProf/Fullprof}" || die
-		done
-		cd .. || die
-	fi
-
-	if ! use X; then
-		rm -rf \
-			tfp tfp.set winplotr-2006 check_group cryscal edpcr fp_studio \
-			gbasireps gbond_str gdatared gfourier gfourier.hlp gxlens \
-			powderpat resvis symmcal wfp2k winplotr.* \
-			Fps_Icons || die
-	fi
-
-	dodir "${BASEDIR}"
-	# make symlinks
-	for i in * ; do
-		[[ -x $i && ! -d $i ]] && dosym "../fullprof/${i}" /opt/bin/"${i##*/}"
-	done
-	mv "${S}"/* "${ED}/${BASEDIR}" || die
-}
diff --git a/sci-physics/geant-vmc/Manifest b/sci-physics/geant-vmc/Manifest
deleted file mode 100644
index 5d79abf8e..000000000
--- a/sci-physics/geant-vmc/Manifest
+++ /dev/null
@@ -1,3 +0,0 @@
-DIST geant321+_vmc.1.15a.tar.gz 11301200 BLAKE2B d0b486bb004b7c6c4cf15c20d7ccf40d2830718c009456e0f4018b4595ccf42e35333fc802078f41096849414452f04f19128cc3176e832bb500788ba9e358e3 SHA512 a5d92cbd0b4199feeedace3e0b09f7cdef6e8270bed44ae7adb024a3a8e6f0fdce51ed6ade3dd58a841594ebf1b4430c2702b71e262075b790e8a82c24c2ac0a
-DIST geant4_vmc.2.15a.tar.gz 18180065 BLAKE2B dab8c2329aff4b954f33098e054e7d936890d8dc9e876f128d944c415799f28a6756be60563f405da8f0d0fb9917412a8a0c552b1d12ab3e60fb738b5210c05c SHA512 b2ea376c44fbf27010572112e1cfbb20c09850a458487f80d6fbe5f4150d8de0bf45d5b134875aff458ed143ad0c6a9db43fda9c7323d2fd625c1bc7adfe9b7a
-DIST geant4_vmc.3.3.tar.gz 1072223 BLAKE2B cb532dd56bbaa87b6fae28ae0355db02ebc24aaca2508a34eb7bee81bee80465b2120261a4c5ae950d2cd3613feb06686de47f3be6228ad1ced28c442e46fb52 SHA512 77ec63c6502f193694a595a822edca5363b057304bc5603c0919000399cd76727b0f2782f347c1bf9ce5fabd05550b1698cca211690680aab8eb832796337acf
diff --git a/sci-physics/geant-vmc/geant-vmc-3.1.15a.ebuild b/sci-physics/geant-vmc/geant-vmc-3.1.15a.ebuild
deleted file mode 100644
index 840fe03ce..000000000
--- a/sci-physics/geant-vmc/geant-vmc-3.1.15a.ebuild
+++ /dev/null
@@ -1,38 +0,0 @@
-# Copyright 1999-2016 Gentoo Foundation
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=5
-
-inherit fortran-2 versionator
-
-MPV=$(get_version_component_range 2-)
-
-DESCRIPTION="Virtual Monte Carlo Geant3 implementation"
-HOMEPAGE="http://root.cern.ch/root/vmc/VirtualMC.html"
-SRC_URI="http://root.cern.ch/download/vmc/geant321+_vmc.${MPV}.tar.gz"
-
-LICENSE="GPL-2"
-SLOT="3"
-
-KEYWORDS="~amd64 ~x86 ~amd64-linux ~x86-linux"
-IUSE="examples"
-
-RDEPEND="
-	sci-physics/root:=[pythia6]
-	!sci-physics/geant:3"
-DEPEND="${RDEPEND}"
-
-S="${WORKDIR}/geant3"
-
-src_install() {
-	dolib.so lib/*/*.so
-	insinto /usr/include/TGeant3
-	doins TGeant3/TGeant3.h
-	insinto /usr/include/geant321
-	doins geant321/*.inc
-
-	if use examples; then
-		insinto /usr/shared/doc/${PF}
-		doins -r examples
-	fi
-}
diff --git a/sci-physics/geant-vmc/geant-vmc-4.2.15a.ebuild b/sci-physics/geant-vmc/geant-vmc-4.2.15a.ebuild
deleted file mode 100644
index 2109a907c..000000000
--- a/sci-physics/geant-vmc/geant-vmc-4.2.15a.ebuild
+++ /dev/null
@@ -1,60 +0,0 @@
-# Copyright 1999-2016 Gentoo Foundation
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=5
-
-inherit versionator
-
-MPV=$(get_version_component_range 2-)
-
-DESCRIPTION="Virtual Monte Carlo Geant4 implementation"
-HOMEPAGE="http://root.cern.ch/root/vmc/VirtualMC.html"
-SRC_URI="http://root.cern.ch/download/vmc/geant4_vmc.${MPV}.tar.gz"
-
-LICENSE="GPL-2"
-SLOT="4"
-KEYWORDS="~amd64 ~x86 ~amd64-linux ~x86-linux"
-IUSE="doc examples vgm"
-
-RDEPEND="
-	sci-physics/root:=
-	>=sci-physics/geant-4.9.6[opengl,geant3,examples?]
-	vgm? ( sci-physics/vgm )"
-DEPEND="${RDEPEND}
-	doc? ( app-doc/doxygen )"
-
-S="${WORKDIR}/geant4_vmc"
-
-src_compile() {
-	use vgm && export USE_VGM=1
-	local dirs="g4root source"
-	use examples && dirs+=" examples"
-	local d
-	source $(ls -1 "${EROOT}"usr/share/Geant4-*/geant4make/geant4make.sh) || die
-	for d in ${dirs}; do
-		pushd ${d} > /dev/null || die
-		default
-		if use doc; then
-			doxygen || die
-		fi
-		popd > /dev/null
-	done
-}
-
-src_test() {
-	cd examples || die
-	default
-	./run_suite.sh || die
-}
-
-src_install() {
-	dolib.so lib/tgt_*/{libg4root,libgeant4vmc}.so
-	doheader -r include/*
-	dodoc README history version_number
-	use doc && dohtml -r Geant4VMC.html doc/*
-	if use examples; then
-		insinto /usr/share/doc/${PF}
-		emake -C examples clean
-		doins -r examples
-	fi
-}
diff --git a/sci-physics/geant-vmc/geant-vmc-4.3.3.ebuild b/sci-physics/geant-vmc/geant-vmc-4.3.3.ebuild
deleted file mode 100644
index 2852a47e0..000000000
--- a/sci-physics/geant-vmc/geant-vmc-4.3.3.ebuild
+++ /dev/null
@@ -1,71 +0,0 @@
-# Copyright 1999-2016 Gentoo Foundation
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=6
-
-inherit cmake-utils versionator
-
-if [[ ${PV} == *9999* ]]; then
-	inherit git-r3
-	EGIT_REPO_URI=" http://root.cern.ch/git/geant4_vmc.git"
-	KEYWORDS=""
-else
-	MPV=$(get_version_component_range 2-)
-	SRC_URI="http://root.cern.ch/download/vmc/geant4_vmc.${MPV}.tar.gz"
-	S="${WORKDIR}/geant4_vmc.${MPV}"
-	KEYWORDS="~amd64 ~x86 ~amd64-linux ~x86-linux"
-fi
-
-DESCRIPTION="Virtual Monte Carlo Geant4 implementation"
-HOMEPAGE="http://root.cern.ch/root/vmc/VirtualMC.html"
-
-LICENSE="GPL-2"
-SLOT="4"
-IUSE="doc examples geant3 +g4root +mtroot vgm test"
-
-RDEPEND="
-	sci-physics/root:=
-	>=sci-physics/geant-4.9.6[opengl,geant3?]
-	vgm? ( >=sci-physics/vgm-4.00 )"
-DEPEND="${RDEPEND}
-	doc? ( app-doc/doxygen )"
-
-src_configure() {
-	local mycmakeargs=(
-			-DGeant4VMC_USE_VGM="$(usex vgm)"
-			-DGeant4VMC_USE_GEANT4_G3TOG4="$(usex geant3)"
-			-DGeant4VMC_USE_G4Root="$(usex g4root)"
-			-DGeant4VMC_USE_MTRoot="$(usex mtroot)"
-			-DGeant4VMC_BUILD_EXAMPLES="$(usex test)"
-			-DGeant4VMC_INSTALL_EXAMPLES="$(usex examples)"
-			)
-	cmake-utils_src_configure
-}
-
-src_compile() {
-	cmake-utils_src_compile
-	local dirs="source"
-	use g4root && dirs+=" g4root "
-	use mtroot && dirs+=" mtroot "
-	use examples && dirs+=" examples "
-	local d
-	for d in ${dirs}; do
-		pushd ${d} > /dev/null || die
-		if use doc; then
-			doxygen || die
-		fi
-		popd > /dev/null
-	done
-}
-
-src_test() {
-	cd examples || die
-	./test_suite.sh --g3=off --builddir="${BUILD_DIR}" || die
-	./test_suite_exe.sh --g3=off --builddir="${BUILD_DIR}" || die
-}
-
-src_install() {
-	cmake-utils_src_install
-	dodoc README history
-	use doc && dohtml -r Geant4VMC.html doc/*
-}
diff --git a/sci-physics/geant-vmc/geant-vmc-9999.ebuild b/sci-physics/geant-vmc/geant-vmc-9999.ebuild
deleted file mode 100644
index 2852a47e0..000000000
--- a/sci-physics/geant-vmc/geant-vmc-9999.ebuild
+++ /dev/null
@@ -1,71 +0,0 @@
-# Copyright 1999-2016 Gentoo Foundation
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=6
-
-inherit cmake-utils versionator
-
-if [[ ${PV} == *9999* ]]; then
-	inherit git-r3
-	EGIT_REPO_URI=" http://root.cern.ch/git/geant4_vmc.git"
-	KEYWORDS=""
-else
-	MPV=$(get_version_component_range 2-)
-	SRC_URI="http://root.cern.ch/download/vmc/geant4_vmc.${MPV}.tar.gz"
-	S="${WORKDIR}/geant4_vmc.${MPV}"
-	KEYWORDS="~amd64 ~x86 ~amd64-linux ~x86-linux"
-fi
-
-DESCRIPTION="Virtual Monte Carlo Geant4 implementation"
-HOMEPAGE="http://root.cern.ch/root/vmc/VirtualMC.html"
-
-LICENSE="GPL-2"
-SLOT="4"
-IUSE="doc examples geant3 +g4root +mtroot vgm test"
-
-RDEPEND="
-	sci-physics/root:=
-	>=sci-physics/geant-4.9.6[opengl,geant3?]
-	vgm? ( >=sci-physics/vgm-4.00 )"
-DEPEND="${RDEPEND}
-	doc? ( app-doc/doxygen )"
-
-src_configure() {
-	local mycmakeargs=(
-			-DGeant4VMC_USE_VGM="$(usex vgm)"
-			-DGeant4VMC_USE_GEANT4_G3TOG4="$(usex geant3)"
-			-DGeant4VMC_USE_G4Root="$(usex g4root)"
-			-DGeant4VMC_USE_MTRoot="$(usex mtroot)"
-			-DGeant4VMC_BUILD_EXAMPLES="$(usex test)"
-			-DGeant4VMC_INSTALL_EXAMPLES="$(usex examples)"
-			)
-	cmake-utils_src_configure
-}
-
-src_compile() {
-	cmake-utils_src_compile
-	local dirs="source"
-	use g4root && dirs+=" g4root "
-	use mtroot && dirs+=" mtroot "
-	use examples && dirs+=" examples "
-	local d
-	for d in ${dirs}; do
-		pushd ${d} > /dev/null || die
-		if use doc; then
-			doxygen || die
-		fi
-		popd > /dev/null
-	done
-}
-
-src_test() {
-	cd examples || die
-	./test_suite.sh --g3=off --builddir="${BUILD_DIR}" || die
-	./test_suite_exe.sh --g3=off --builddir="${BUILD_DIR}" || die
-}
-
-src_install() {
-	cmake-utils_src_install
-	dodoc README history
-	use doc && dohtml -r Geant4VMC.html doc/*
-}
diff --git a/sci-physics/geant-vmc/metadata.xml b/sci-physics/geant-vmc/metadata.xml
deleted file mode 100644
index ef6deebdf..000000000
--- a/sci-physics/geant-vmc/metadata.xml
+++ /dev/null
@@ -1,25 +0,0 @@
-<?xml version="1.0" encoding="UTF-8"?>
-<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
-<pkgmetadata>
-	<maintainer type="project">
-		<email>sci-physics@gentoo.org</email>
-		<name>Gentoo Physics Project</name>
-	</maintainer>
-	<longdescription lang="en">
-The Virtual Monte Carlo (VMC) allows to run different simulation
-Monte Carlo without changing the user code and therefore the input
-and output format as well as the geometry and detector response
-definition.
-The core of the VMC is the category of classes vmc in ROOT. It
-provides a set of interfaces which completely decouple the
-dependencies between the user code and the concrete Monte Carlo. 
-Geant3 VMC (C++) is provided within a single package together with
-GEANT3 (Fortran) - geant3.
-</longdescription>
-	<use>
-		<flag name="vgm">Enable the Virtual Geometry Model (<pkg>sci-physics/vgm</pkg>)</flag>
-		<flag name="g4root">Build G4Root (interface for GEANT4 simulation with a ROOT geometry)</flag>
-		<flag name="geant3">Build with Geant4 G3toG4 library</flag>
-		<flag name="mtroot">Build MTRoot (provides ROOT IO manager classes with multi-threading support)</flag>
-	</use>
-</pkgmetadata>
diff --git a/sci-physics/genfit/Manifest b/sci-physics/genfit/Manifest
index f2403a31a..0fc9e67d3 100644
--- a/sci-physics/genfit/Manifest
+++ b/sci-physics/genfit/Manifest
@@ -1 +1 @@
-DIST genfit-code-1688-tags-v02-00-00.zip 2251113 BLAKE2B f8cc8bec5730d8bd239bb23b50fb6d3efe8c0b18224433257404af713bb111ff376b42b39ab34fb320c67c51a16b0138a0518ddf21dde78b1e481ad5938114eb SHA512 1dc13174b39cfa450bcb6eb3395f84d8a5b189bdc67aadc744aebb2ffbe039db1a34742897ba6fd9b11e5704987cb1e8efbd6a494942eb3b676b72d15fd79c09
+DIST genfit-02.00.00_p20201231.tar.gz 336441 BLAKE2B 3b3280e5cbf3a2c75c57d2d99f3a1d9c885d2b7ed77d291f4766f8c8cdf94b886dcc589b2f738fc1ed47b8ee090e9b801adad3084ba8697917be648fc4ceee26 SHA512 7077cb2b7480f7eee15ce9198bbf3e4616edf1fcb7185ea977949139e9d186b95226479c51ae9af9ff3d3177a3916bf59630346c722465e775d46eff7f39c09d
diff --git a/sci-physics/genfit/genfit-02.00.00.ebuild b/sci-physics/genfit/genfit-02.00.00.ebuild
deleted file mode 100644
index 40a4cce10..000000000
--- a/sci-physics/genfit/genfit-02.00.00.ebuild
+++ /dev/null
@@ -1,58 +0,0 @@
-# Copyright 1999-2014 Gentoo Foundation
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=5
-
-inherit cmake-utils versionator
-
-if [[ ${PV} == *9999* ]]; then
-	inherit subversion
-	ESVN_REPO_URI="https://svn.code.sf.net/p/${PN}/code/trunk"
-	ESVN_PROJECT="${PN}.${PV}"
-	KEYWORDS=""
-else
-	# .zip-snapshot can be recreated by visiting
-	# http://sourceforge.net/p/${PN}/code/${COMMIT}/tarball?path=/tags/v$(replace_all_version_separators '-')
-	TAG_VER=${PN}-code-1688-tags-v$(replace_all_version_separators '-')
-	#SRC_URI="http://sourceforge.net/code-snapshots/svn/g/ge/genfit/code/${TAG_VER}.zip"
-	SRC_URI="http://dev.gentoo.org/~jlec/distfiles/${TAG_VER}.zip"
-	KEYWORDS="~amd64 ~x86 ~amd64-linux ~x86-linux"
-	S=${WORKDIR}/${TAG_VER}
-fi
-
-DESCRIPTION="Generic toolkit for track reconstruction in physics experiments"
-HOMEPAGE="http://genfit.sourceforge.net/Main.html"
-
-LICENSE="LGPL-3"
-SLOT="0"
-IUSE="doc examples"
-
-RDEPEND="
-	sci-physics/root:=
-	dev-libs/boost:="
-DEPEND="${RDEPEND}
-	doc? ( app-doc/doxygen[dot] )"
-
-src_compile() {
-	cmake-utils_src_compile
-	use doc      && cmake-utils_src_compile doc
-	use examples && cmake-utils_src_compile tests
-}
-
-src_install() {
-	cmake-utils_src_install
-	if use examples; then
-		insinto /usr/share/doc/${PF}
-		doins -r "${BUILD_DIR}/bin"
-		doins test/makeGeom.C
-		doins test/README
-	fi
-	use doc && dohtml -r doc/html/*
-	echo
-	elog "Note that there is no support in this ebuild for RAVE yet,"
-	elog "which is also not in portage."
-	elog "It should be possible to use a local installation of RAVE"
-	elog "and set:"
-	elog "  export RAVEPATH=<yourRaveDirectory>"
-	echo
-}
diff --git a/sci-physics/genfit/genfit-02.00.00_p20201231.ebuild b/sci-physics/genfit/genfit-02.00.00_p20201231.ebuild
new file mode 100644
index 000000000..88cf6d216
--- /dev/null
+++ b/sci-physics/genfit/genfit-02.00.00_p20201231.ebuild
@@ -0,0 +1,58 @@
+# Copyright 1999-2021 Gentoo Authors
+# Distributed under the terms of the GNU General Public License v2
+
+EAPI=7
+
+inherit cmake
+
+if [[ ${PV} == *9999* ]]; then
+	inherit git-r3
+	EGIT_REPO_URI="https://github.com/GenFit/GenFit.git"
+else
+	EGIT_COMMIT="c3546c073e732abc942a08430b6ca3cb36f5339e"
+	MY_PN="GenFit"
+	SRC_URI="https://github.com/GenFit/GenFit/archive/${EGIT_COMMIT}.tar.gz -> ${P}.tar.gz"
+	KEYWORDS="~amd64 ~x86"
+	S="${WORKDIR}/${MY_PN}-${EGIT_COMMIT}"
+fi
+
+DESCRIPTION="Generic toolkit for track reconstruction in physics experiments"
+HOMEPAGE="https://github.com/GenFit/GenFit"
+
+LICENSE="LGPL-3"
+SLOT="0"
+
+IUSE="doc examples"
+
+RDEPEND="
+	sci-physics/root:=
+	dev-libs/boost:=
+"
+DEPEND="${RDEPEND}"
+
+src_compile() {
+	cmake_src_compile
+	use doc && cmake_src_compile doc
+	use examples && cmake_src_compile tests
+}
+
+src_install() {
+	cmake_src_install
+	if use doc; then
+		docinto html
+		dodoc -r doc/html/.
+	fi
+	if use examples; then
+		docinto examples
+		dodoc -r "${BUILD_DIR}/bin"
+		dodoc test/makeGeom.C
+		dodoc test/README
+	fi
+	echo
+	elog "Note that there is no support in this ebuild for RAVE yet,"
+	elog "which is also not in portage."
+	elog "It should be possible to use a local installation of RAVE"
+	elog "and set:"
+	elog "  export RAVEPATH=<yourRaveDirectory>"
+	echo
+}
diff --git a/sci-physics/genfit/genfit-9999.ebuild b/sci-physics/genfit/genfit-9999.ebuild
index d4960e9fd..5afb43063 100644
--- a/sci-physics/genfit/genfit-9999.ebuild
+++ b/sci-physics/genfit/genfit-9999.ebuild
@@ -1,52 +1,53 @@
-# Copyright 1999-2014 Gentoo Foundation
+# Copyright 1999-2021 Gentoo Authors
 # Distributed under the terms of the GNU General Public License v2
 
-EAPI=5
+EAPI=7
 
-inherit cmake-utils versionator
+inherit cmake
 
 if [[ ${PV} == *9999* ]]; then
 	inherit git-r3
 	EGIT_REPO_URI="https://github.com/GenFit/GenFit.git"
-	KEYWORDS=""
 else
-	# .zip-snapshot can be recreated by visiting
-	# http://sourceforge.net/p/${PN}/code/${COMMIT}/tarball?path=/tags/v$(replace_all_version_separators '-')
-	TAG_VER=${PN}-code-1688-tags-v$(replace_all_version_separators '-')
-	#SRC_URI="http://sourceforge.net/code-snapshots/svn/g/ge/genfit/code/${TAG_VER}.zip"
-	SRC_URI="http://dev.gentoo.org/~jlec/distfiles/${TAG_VER}.zip"
-	KEYWORDS="~amd64 ~x86 ~amd64-linux ~x86-linux"
-	S=${WORKDIR}/${TAG_VER}
+	EGIT_COMMIT=""
+	MY_PN="GenFit"
+	SRC_URI="https://github.com/GenFit/GenFit/archive/${EGIT_COMMIT}.tar.gz -> ${P}.tar.gz"
+	KEYWORDS="~amd64 ~x86"
+	S="${WORKDIR}/${MY_PN}-${EGIT_COMMIT}"
 fi
 
 DESCRIPTION="Generic toolkit for track reconstruction in physics experiments"
-HOMEPAGE="http://genfit.sourceforge.net/Main.html"
+HOMEPAGE="https://github.com/GenFit/GenFit"
 
 LICENSE="LGPL-3"
 SLOT="0"
+
 IUSE="doc examples"
 
 RDEPEND="
 	sci-physics/root:=
-	dev-libs/boost:="
-DEPEND="${RDEPEND}
-	doc? ( app-doc/doxygen[dot] )"
+	dev-libs/boost:=
+"
+DEPEND="${RDEPEND}"
 
 src_compile() {
-	cmake-utils_src_compile
-	use doc      && cmake-utils_src_compile doc
-	use examples && cmake-utils_src_compile tests
+	cmake_src_compile
+	use doc && cmake_src_compile doc
+	use examples && cmake_src_compile tests
 }
 
 src_install() {
-	cmake-utils_src_install
+	cmake_src_install
+	if use doc; then
+		docinto html
+		dodoc -r doc/html/.
+	fi
 	if use examples; then
-		insinto /usr/share/doc/${PF}
-		doins -r "${BUILD_DIR}/bin"
-		doins test/makeGeom.C
-		doins test/README
+		docinto examples
+		dodoc -r "${BUILD_DIR}/bin"
+		dodoc test/makeGeom.C
+		dodoc test/README
 	fi
-	use doc && dohtml -r doc/html/*
 	echo
 	elog "Note that there is no support in this ebuild for RAVE yet,"
 	elog "which is also not in portage."
diff --git a/sci-physics/genfit/metadata.xml b/sci-physics/genfit/metadata.xml
index 90b22390e..2796af0dc 100644
--- a/sci-physics/genfit/metadata.xml
+++ b/sci-physics/genfit/metadata.xml
@@ -1,6 +1,10 @@
 <?xml version="1.0" encoding="UTF-8"?>
 <!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
 <pkgmetadata>
+	<maintainer type="person">
+		<email>o.freyermuth@googlemail.com</email>
+		<name>Oliver Freyermuth</name>
+	</maintainer>
 	<maintainer type="project">
 		<email>sci-physics@gentoo.org</email>
 		<name>Gentoo Physics Project</name>
@@ -32,6 +36,6 @@ FAIR, Darmstadt, Germany.
 It is also used in the Belle-2, Fopi, and GEM-TPC experiments.
 </longdescription>
 	<upstream>
-		<remote-id type="sourceforge">genfit</remote-id>
+		<remote-id type="github">GenFit/GenFit</remote-id>
 	</upstream>
 </pkgmetadata>
diff --git a/sci-physics/hepunits/Manifest b/sci-physics/hepunits/Manifest
new file mode 100644
index 000000000..9b6a3c900
--- /dev/null
+++ b/sci-physics/hepunits/Manifest
@@ -0,0 +1,2 @@
+DIST hepunits-2.3.2.tar.gz 13327 BLAKE2B 16986f4cf96eb927e5ae7268dc2975957846678bff0569fc5d5b9d36bb5dae251905283a07e5fcdd895b20982e1e2d32bce5048752d654ca085286e89b65837f SHA512 48d0a4939e19fc6f26b3bb5f8515d8e0d9d4cbed172c14ae30609c2039bdb77625dad8e1e628178481ee0f203d7d36cd2e0d3306f3b344fe14cd68827c4d9477
+DIST hepunits-2.3.3.tar.gz 13491 BLAKE2B ec212be4e53e7ea5aa195852ea6ad4f3aac8e3eb49676e6bef76d525be861ecd4480821b248d746950b45affccd31bf23d5232aee13058bb48ec8d76c4f70a14 SHA512 7a29dd6220c1fbe610f15ef66f02e499d7e2ade8c39827e3229ae74035d127ca7805b9e32c3859c5af4b001725d21514fd81f0408d7f0dc76e9ee34aa66191e8
diff --git a/sci-physics/hepunits/hepunits-2.3.2.ebuild b/sci-physics/hepunits/hepunits-2.3.2.ebuild
new file mode 100644
index 000000000..34b3977a8
--- /dev/null
+++ b/sci-physics/hepunits/hepunits-2.3.2.ebuild
@@ -0,0 +1,23 @@
+EAPI=8
+
+PYTHON_COMPAT=( python3_{9..11} )
+DISTUTILS_USE_PEP517=hatchling
+inherit distutils-r1
+
+DESCRIPTION="units and constants in the HEP system of units"
+HOMEPAGE="https://github.com/scikit-hep/hepunits"
+
+LICENSE="BSD"
+SLOT="0"
+if [[ ${PV} == 9999 ]]; then
+	inherit git-r3
+	EGIT_REPO_URI="https://github.com/scikit-hep/hepunits"
+else
+	inherit pypi
+	KEYWORDS="~amd64"
+fi
+
+RDEPEND="
+	>=dev-python/attrs-19.2[${PYTHON_USEDEP}]
+"
+DEPEND="${RDEPEND}"
diff --git a/sci-physics/hepunits/hepunits-2.3.3.ebuild b/sci-physics/hepunits/hepunits-2.3.3.ebuild
new file mode 100644
index 000000000..2fb8bb148
--- /dev/null
+++ b/sci-physics/hepunits/hepunits-2.3.3.ebuild
@@ -0,0 +1,25 @@
+EAPI=8
+
+PYTHON_COMPAT=( python3_{10..12} )
+DISTUTILS_USE_PEP517=hatchling
+inherit distutils-r1
+
+DESCRIPTION="units and constants in the HEP system of units"
+HOMEPAGE="https://github.com/scikit-hep/hepunits"
+
+LICENSE="BSD"
+SLOT="0"
+if [[ ${PV} == 9999 ]]; then
+	inherit git-r3
+	EGIT_REPO_URI="https://github.com/scikit-hep/hepunits"
+else
+	inherit pypi
+	KEYWORDS="~amd64"
+fi
+
+RDEPEND="
+	>=dev-python/attrs-19.2[${PYTHON_USEDEP}]
+"
+DEPEND="${RDEPEND}"
+
+distutils_enable_tests pytest
diff --git a/sci-physics/hepunits/hepunits-9999.ebuild b/sci-physics/hepunits/hepunits-9999.ebuild
new file mode 100644
index 000000000..2fb8bb148
--- /dev/null
+++ b/sci-physics/hepunits/hepunits-9999.ebuild
@@ -0,0 +1,25 @@
+EAPI=8
+
+PYTHON_COMPAT=( python3_{10..12} )
+DISTUTILS_USE_PEP517=hatchling
+inherit distutils-r1
+
+DESCRIPTION="units and constants in the HEP system of units"
+HOMEPAGE="https://github.com/scikit-hep/hepunits"
+
+LICENSE="BSD"
+SLOT="0"
+if [[ ${PV} == 9999 ]]; then
+	inherit git-r3
+	EGIT_REPO_URI="https://github.com/scikit-hep/hepunits"
+else
+	inherit pypi
+	KEYWORDS="~amd64"
+fi
+
+RDEPEND="
+	>=dev-python/attrs-19.2[${PYTHON_USEDEP}]
+"
+DEPEND="${RDEPEND}"
+
+distutils_enable_tests pytest
diff --git a/sci-physics/hepunits/metadata.xml b/sci-physics/hepunits/metadata.xml
new file mode 100644
index 000000000..41d598fa2
--- /dev/null
+++ b/sci-physics/hepunits/metadata.xml
@@ -0,0 +1,19 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
+<pkgmetadata>
+	<maintainer type="project">
+		<email>sci@gentoo.org</email>
+		<name>Gentoo Science Project</name>
+	</maintainer>
+	<maintainer type="person">
+		<email>alexander@neuwirth-informatik.de</email>
+		<name>Alexander Puck Neuwirth</name>
+	</maintainer>
+	<longdescription lang="en">
+	hepunits collects the most commonly used units and constants in the HEP System of Units, as derived from the basic units originally defined by the CLHEP project
+	</longdescription>
+	<upstream>
+		<remote-id type="pypi">hepunits</remote-id>
+		<remote-id type="github">scikit-hep/hepunits</remote-id>
+	</upstream>
+</pkgmetadata>
diff --git a/sci-physics/hoppet/Manifest b/sci-physics/hoppet/Manifest
new file mode 100644
index 000000000..cc73bfc3b
--- /dev/null
+++ b/sci-physics/hoppet/Manifest
@@ -0,0 +1 @@
+DIST hoppet-1.2.0.tgz 575911 BLAKE2B 4d4dc1874b45b7237384ad3955808b5f4995c86b4d44165ef0c4d8b1da21880cdd1a3f1f1537f02ad7928baef5207e950be411465989ab876bcb806f355725cf SHA512 65ceb170cd417f229f8a974aa995138b8ee7ea5ef04538a5382b353181951e9d4489045234cd45c1ea8f88a5faf4755e3a0e246065711f137676bbf726a29f1f
diff --git a/sci-physics/hoppet/hoppet-1.2.0.ebuild b/sci-physics/hoppet/hoppet-1.2.0.ebuild
new file mode 100644
index 000000000..337881026
--- /dev/null
+++ b/sci-physics/hoppet/hoppet-1.2.0.ebuild
@@ -0,0 +1,35 @@
+# Copyright 2022-2024 Gentoo Authors
+# Distributed under the terms of the GNU General Public License v2
+
+EAPI=8
+
+inherit fortran-2
+
+DESCRIPTION="Higher Order Perturbative Parton Evolution Toolkit"
+HOMEPAGE="
+	https://hoppet.hepforge.org/
+	https://github.com/gavinsalam/hoppet
+"
+SRC_URI="https://hoppet.hepforge.org/downloads/${P}.tgz"
+
+SLOT="0"
+LICENSE="GPL-3+"
+KEYWORDS="~amd64"
+
+
+src_configure() {
+	default
+	# own custom configure
+	./configure --prefix="${EPREFIX}"/usr FFLAGS="${FFLAGS} -fPIC" || die
+}
+
+src_install() {
+	# Fix install to ED
+	sed -i "s#scripts/install-sh hoppet-config#\##g" Makefile || die
+	sed -i "s#/usr/lib/libhoppet#${ED}/usr/$(get_libdir)/libhoppet#g" src/Makefile || die
+	sed -i "s#/usr/include/hoppet#${ED}/usr/include/hoppet#g" src/Makefile || die
+	emake install
+	emake install-mod
+	dobin hoppet-config
+	find "${ED}" -name '*.la' -delete || die
+}
diff --git a/sci-physics/hoppet/metadata.xml b/sci-physics/hoppet/metadata.xml
new file mode 100644
index 000000000..37900a238
--- /dev/null
+++ b/sci-physics/hoppet/metadata.xml
@@ -0,0 +1,19 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
+<pkgmetadata>
+	<maintainer type="person">
+		<email>alexander@neuwirth-informatik.de</email>
+		<name>Alexander Puck Neuwirth</name>
+	</maintainer>
+	<maintainer type="project">
+		<email>sci-physics@gentoo.org</email>
+		<name>Gentoo Physics Project</name>
+	</maintainer>
+
+	<longdescription lang="en">
+	HOPPET is a Fortran 95 package for carrying out DGLAP evolution and other common manipulations of parton distribution functions (PDFs).
+	</longdescription>
+	<upstream>
+		<remote-id type="github">gavinsalam/hoppet</remote-id> 
+	</upstream>
+</pkgmetadata>
diff --git a/sci-physics/jaxodraw-bin/Manifest b/sci-physics/jaxodraw-bin/Manifest
new file mode 100644
index 000000000..a449139fe
--- /dev/null
+++ b/sci-physics/jaxodraw-bin/Manifest
@@ -0,0 +1,3 @@
+DIST axodraw4j_2008_11_19.tar.gz 20930 BLAKE2B f2478df46f47c931bba71b1f43717d2d01a1a8282acc54582ed1ba5596dec8f03600e01f93a61ef4949f95a274a00b8ec62d2dffb283353de244950c4763531e SHA512 81bfcbd1b121104e0058654ac5520d0f570f9a915e9f6dfb8c52c11e9cf92f1e01c800182c2dc34e503a6eceafdff462b4f57dfa5bb5db979101a106c10d88c8
+DIST jaxodraw-2.1-0-bin.tar.gz 1241010 BLAKE2B 6dd5bbc09ed5b497c9c39a235a2f15c3b9cf2135f121af7d866a11a3458856c87a613e702f6dc71523506870fd94063992af42d1fc8ddd26c1be9ab83bf363b0 SHA512 4dbccabe22e8849af71e386b464201c2616d0f6475b905feb9fffc2687420b2b72af5c751d05aa1374a2806693ab2d6e256c3029bb0167f9ba6ea699b253669a
+DIST jaxodraw-2.1-0-src.tar.gz 3777234 BLAKE2B df659a27762e7a05b461b520b9076a7eef1b5006a9ef3338fb0d5ec173a8cc6b0abf2f2de3d90a6c998439b19dad5dc9965a82622afc4e85227f175a9355183b SHA512 a829249823ec6b23248000a70ed5ccdc70d10f7212614e64162ba8bef53e6b59db042ff1f5205f07b1d521899f6505562311955fc95d8f374e81eec1135391aa
diff --git a/sci-physics/jaxodraw-bin/jaxodraw-bin-2.1.0.ebuild b/sci-physics/jaxodraw-bin/jaxodraw-bin-2.1.0.ebuild
new file mode 100644
index 000000000..e23381514
--- /dev/null
+++ b/sci-physics/jaxodraw-bin/jaxodraw-bin-2.1.0.ebuild
@@ -0,0 +1,54 @@
+# Copyright 2022 Gentoo Authors
+# Distributed under the terms of the GNU General Public License v2
+
+EAPI=8
+JAVA_PKG_IUSE="doc source"
+
+inherit desktop java-pkg-2 latex-package
+
+MY_PN="jaxodraw"
+MY_PV=$(ver_rs 2 '-')
+MY_P=${MY_PN}-${MY_PV}
+
+DESCRIPTION="Java program for drawing Feynman diagrams"
+HOMEPAGE="
+	https://jaxodraw.sourceforge.io/index.html
+	http://jaxodraw.sourceforge.net/
+"
+SRC_URI="
+	https://${MY_PN}.sourceforge.net/download/pkgs/${MY_P}-bin.tar.gz
+	https://${MY_PN}.sourceforge.net/download/pkgs/${MY_P}-src.tar.gz
+	latex? ( https://downloads.sourceforge.net/${MY_PN}/axodraw4j_2008_11_19.tar.gz )
+"
+S="${WORKDIR}/${MY_P}"
+
+LICENSE="GPL-2"
+SLOT="0"
+KEYWORDS="~amd64 ~x86"
+IUSE="+latex"
+
+DEPEND="
+	>=virtual/jdk-1.8
+	latex? ( dev-texlive/texlive-pstricks:0 )
+"
+
+RDEPEND=">=virtual/jre-1.8"
+
+src_install() {
+	java-pkg_newjar ${MY_P}.jar
+
+	newicon src/site/resources/images/favicon.ico jaxodraw.ico
+	make_desktop_entry jaxodraw JaxoDraw jaxodraw.ico
+
+	use source && java-pkg_dosrc src/main/java/net
+
+	dodoc src/doc/BUGS src/doc/CHANGELOG src/doc/README src/doc/TODO
+	use doc && java-pkg_dojavadoc build/javadoc
+
+	java-pkg_dolauncher "${MY_P}"
+
+	if use latex; then
+		cd "${WORKDIR}" || die "Failed to cd ${WORKDIR}"
+		latex-package_src_doinstall
+	fi
+}
diff --git a/sci-physics/jaxodraw-bin/metadata.xml b/sci-physics/jaxodraw-bin/metadata.xml
new file mode 100644
index 000000000..7a665fa37
--- /dev/null
+++ b/sci-physics/jaxodraw-bin/metadata.xml
@@ -0,0 +1,15 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
+<pkgmetadata>
+	<maintainer type="person">
+		<email>alexander@neuwirth-informatik.de</email>
+		<name>Alexander Puck Neuwirth</name>
+	</maintainer>
+	<maintainer type="project">
+		<email>sci-physics@gentoo.org</email>
+		<name>Gentoo Physics Project</name>
+	</maintainer>
+	<upstream>
+		<remote-id type="sourceforge">jaxodraw</remote-id>
+	</upstream>
+</pkgmetadata>
diff --git a/sci-physics/lhapdf-sets/Manifest b/sci-physics/lhapdf-sets/Manifest
new file mode 100644
index 000000000..6e1d34375
--- /dev/null
+++ b/sci-physics/lhapdf-sets/Manifest
@@ -0,0 +1,14 @@
+DIST CT10.tar.gz 10246366 BLAKE2B f0daf0a3ca6cd2f178f993944cdc29de5deb1f441d197e47c8b1c285a56abc0fdb1cd53ec5a8e7736e200397bea9ec9cf4d04420ce206e5c396b85b63f695d00 SHA512 90406bd102ab54b683fa3e6f3fc759febea2454a0b96c6a8d373cdec297f5d652097057a015c7d87241792ed9b5d9ac658a33155cdd7362f59110f8f06ecce73
+DIST CT14lo.tar.gz 474954 BLAKE2B 60e8d3695fa64a997f0431516086f037d8843a9310cb52910c28a8a8960838409bafb280cf776b25fde1b31225743b72a48a3d467b1f7a4ff5478d515607645b SHA512 bc6acfcf522262da227411555f10dd73456fb5d0ab9db334b99cf7953463e1fa3de8c78bbb95269e9a47629860d906d43948e6cf1719b00402645ec18249f959
+DIST CT14nlo.tar.gz 27067462 BLAKE2B b8d46593a62e80c320c76fb89f646ba0f31ab98811076120de1d21ef3b4849ff3d2e7b8d01d01dff5f1ee05a2266d94664e7f4a27347fa32c8ac4c68b0e72acb SHA512 1fcdfd24569966c1bc9c98f8ae2bf7d3a306700387b1351c92bc2b4f061db5d59d048c6cdd25095e1dc58344afa7f65a6526c611d747a5894398754483db77a2
+DIST CT14qed_proton.tar.gz 11064380 BLAKE2B b0b5834473a90d2adfedfa4dd467847349fc1b60907d387d1007387dcf557fac37871ea7430161edc0ecf6f8e8839077283dc8fcad610f03dd192efd70890c3f SHA512 a41f6f82e5505f66014e5523210c272254fb8018bbfac542eb1941e60c1c897ee687bfef1afbd981132cb772240fdd4d19b5dcd2b36b01f8e34ea959d9acd4f7
+DIST MRST2004qed.tar.gz 185079 BLAKE2B 62e0371de965698100755b14b0c282095b84b40800a58cd6776c458b03982f032f3b2464eb76174084dd22de9fd962e202a4896327b0a00579c3a632dac24ccc SHA512 404aacf0e241f572cc42ad4cf963deef1acd3d365fa68cfa3518878f921858046377ea39caf663fdced2cdde07af2f6ce695737f7fea229489df3d3f38283c95
+DIST MRST2007lomod.tar.gz 56685 BLAKE2B 8515b6f77302621f4b37f550840f07f0351e7ea98de16a37ceb4cb0f2ea64aa4b027462ffc442f34d1f4c349d67fac7b35353606d8920f17621c7187e508c689 SHA512 8e55627a01c85d90a62e4fb11b115c2faac2220479b6d558d3d6f1b801fc5c3e88abc377cd5437ccaeedd34b2ca42d6e833014566b796e5e1eebcf4d620e5dc0
+DIST NNPDF23_nlo_as_0118.tar.gz 21655966 BLAKE2B f92d0b90f27d1a096f327e5aa45cc4d36ad3789db6fcc477b21d6170495c8508edcc86000baf20e50366895a8a1fd1b7d30c136b77ea35c466b65016b66c3829 SHA512 5570273743d4efb9676e3b5f461d8944b841cbcb3f80949f63520f05c184bd551a2a3be3961d20d5de80e7e35e88f26e5eb5c20903d20ed44e2f33038d6c66af
+DIST NNPDF23_nlo_as_0119_qed_mc.tar.gz 25223180 BLAKE2B 05dd8772d559e8f08e28dc16da6b256d875563b140e1954cedac9b5f541e9cd325c4dfd5adbb13af434e036cbafa9bfe19325f69ae00ed599cfac6791629d989 SHA512 fc6998d50a61bbe65eef827021c0f453164795c079daef6a4932f825f8db4ae318bbf0e8781b61f1d3ffa9a495b5c4813af3aa31c77694657a44356d93fa970f
+DIST NNPDF23_nnlo_as_0119_qed_mc.tar.gz 28940412 BLAKE2B 57c7c98bb863258f87e236fea2d0233ac61350012aec6ba5cced75de0b4b945a5633d7fd487b0913b822df1c3ef804de2aacf34b1319d6973d959dc02ebbc9b2 SHA512 5088c30acbd1da4e412ba9f6a997ceaa34f426f41c7ebacaf4d2e8aa49b8b45052913e8d873b293d9f140c01e82c05735b66dd527a9aa124b86f73bf5e4d8c53
+DIST NNPDF31_nnlo_as_0118.tar.gz 43193739 BLAKE2B b826eaebb6483b844bc18cfca36be8ead1dc409641e445f8d31db58f31bde623b7e7753a94c0e2ee0dfe24b28909b9d06b17641a783c223d8ab7ce8e55902a5c SHA512 a62330979f4001933b52e2b1bd3142b4dacd27aeed1e49969108a842e00e7db59a7fe8d80b755c283f3bc706b36e3ec4597e124d95ad3a7f334fb956bebe7ae0
+DIST NNPDF31_nnlo_as_0118_luxqed.tar.gz 47462442 BLAKE2B 2b473d943ec49e28de63d002e4eadfd3002c63aa6ef9b4e792adf7acf8bb3a771f91298ac6575034407653d15aa4191da6090aaaa34d8a8091cb1a5d4562479a SHA512 5faafc9a2b23dc0a82c7f3ca26a6691cfa476f83741beab2b41a77e63fa5f10428bf43579670636689c0080421f4b08ec058aa63c047f04f6d892b1b848fd702
+DIST PDF4LHC15_nlo_asvar.tar.gz 578871 BLAKE2B a42a24d4af82f892e0dccfeeacedfcbb074be1ddc9649d55ff6c15e3923901173337ba4197248410d2a40e72ab627af9a0cea09e5ee98c37130aceb34402d9d4 SHA512 ef96970050b78f5a5bc54b43ee2d7ed0eb76796ea23ce864f1c8ff6de2d68f99023d5c4530f4e73197948c39886fcb832ed26dfa126ca0396e4fd08e353df8a0
+DIST cteq66.tar.gz 8647237 BLAKE2B 3ac47b6eee434f89ff329cfcb8268782af4ffa552ca4b412a59254e9b10410518f9fe9543b47f193d9cd31b06fc1101556df2be01c25ca17febcb9fb1855e5ca SHA512 25d0fa01dcdb59d71c7092367af8258471a2bc6dfd146766cc79f90ffb0feafa0f2011d0a37a7d75315c10ba7c7a6e3fa583d9c0a28119b072228ac800294e48
+DIST cteq6l1.tar.gz 317834 BLAKE2B eccad131853f9a760d0dfd43a3f8705f8edbac3ec7373de9ef9a8936f13ba06500ba5758cd04649dd1b85ac04fc778e9d96222877e74e9ff02263455b233fa41 SHA512 7177608e97077eaf45a292db4ea74eb9a28b4b500ab8be02098b4837a5583cd397828abc3bf43ead448926eaa75ae3968bd059ecde333d90ed6e4295cbe1873c
diff --git a/sci-physics/lhapdf-sets/lhapdf-sets-0.ebuild b/sci-physics/lhapdf-sets/lhapdf-sets-0.ebuild
new file mode 100644
index 000000000..784d94f97
--- /dev/null
+++ b/sci-physics/lhapdf-sets/lhapdf-sets-0.ebuild
@@ -0,0 +1,70 @@
+# Copyright 1999-2022 Gentoo Authors
+# Distributed under the terms of the GNU General Public License v2
+
+EAPI=8
+LHA_VER="6.2.1"
+
+IUSE_LHAPDF_SETS="
+	lhapdf_sets_nnpdf31_nnlo_as_0118_luxqed
+	lhapdf_sets_pdf4lhc15_nlo_asvar
+	lhapdf_sets_ct14qed_proton
+	lhapdf_sets_ct14lo
+	lhapdf_sets_ct14nlo
+	lhapdf_sets_ct10
+	lhapdf_sets_mrst2007lomod
+	lhapdf_sets_nnpdf23_nlo_as_0119_qed_mc
+	lhapdf_sets_nnpdf23_nnlo_as_0119_qed_mc
+	lhapdf_sets_cteq66
+	lhapdf_sets_cteq6l1
+	lhapdf_sets_mrst2004qed
+	lhapdf_sets_nnpdf23_nlo_as_0118
+	lhapdf_sets_nnpdf31_nnlo_as_0118
+"
+
+COMMON_URI="https://lhapdfsets.web.cern.ch/lhapdfsets/current"
+HEPFORGE_URI="https://www.hepforge.org/downloads/lhapdf/pdfsets/v6.backup/${LHA_VER}"
+# Alternatively to fetching them here already the user can install them by lhapdf install,
+# BUT some codes need them during test and even compile (Herwig) stage.
+# Also since it belongs to LHAPDF it is better to fetch them here.
+SRC_URI="
+	lhapdf_sets_nnpdf31_nnlo_as_0118_luxqed? ( ${COMMON_URI}/NNPDF31_nnlo_as_0118_luxqed.tar.gz )
+	lhapdf_sets_pdf4lhc15_nlo_asvar?         ( ${COMMON_URI}/PDF4LHC15_nlo_asvar.tar.gz         )
+	lhapdf_sets_ct14qed_proton?              ( ${COMMON_URI}/CT14qed_proton.tar.gz              )
+	lhapdf_sets_ct14lo?                      ( ${COMMON_URI}/CT14lo.tar.gz                      )
+	lhapdf_sets_ct14nlo?                     ( ${COMMON_URI}/CT14nlo.tar.gz                     )
+	lhapdf_sets_ct10?                        ( ${COMMON_URI}/CT10.tar.gz                        )
+	lhapdf_sets_mrst2007lomod?               ( ${COMMON_URI}/MRST2007lomod.tar.gz               )
+	lhapdf_sets_nnpdf23_nlo_as_0119_qed_mc?  ( ${COMMON_URI}/NNPDF23_nlo_as_0119_qed_mc.tar.gz  )
+	lhapdf_sets_nnpdf23_nnlo_as_0119_qed_mc? ( ${COMMON_URI}/NNPDF23_nnlo_as_0119_qed_mc.tar.gz )
+	lhapdf_sets_cteq66?                      ( ${COMMON_URI}/cteq66.tar.gz                      )
+	lhapdf_sets_cteq6l1?                     ( ${COMMON_URI}/cteq6l1.tar.gz                     )
+	lhapdf_sets_mrst2004qed?                 ( ${HEPFORGE_URI}/MRST2004qed.tar.gz               )
+	lhapdf_sets_nnpdf23_nlo_as_0118?         ( ${COMMON_URI}/NNPDF23_nlo_as_0118.tar.gz         )
+	lhapdf_sets_nnpdf31_nnlo_as_0118?        ( ${COMMON_URI}/NNPDF31_nnlo_as_0118.tar.gz        )
+"
+
+MY_PV=$(ver_cut 1-3)
+MY_PF=LHAPDF-${MY_PV}
+
+DESCRIPTION="LHAPDF data grids"
+HOMEPAGE="https://lhapdf.hepforge.org/"
+KEYWORDS="~amd64 ~x86"
+S="${WORKDIR}"
+
+LICENSE="public-domain"
+SLOT="0"
+IUSE="${IUSE_LHAPDF_SETS}"
+SLOT="0"
+RDEPEND="sci-physics/lhapdf"
+DEPEND="${RDEPEND}"
+
+src_unpack() {
+	# unpack in destination only to avoid copy
+	return
+}
+
+src_install() {
+	dodir /usr/share/LHAPDF/
+	cd "${ED}/usr/share/LHAPDF/" || die
+	unpack ${A}
+}
diff --git a/sci-physics/lhapdf-sets/metadata.xml b/sci-physics/lhapdf-sets/metadata.xml
new file mode 100644
index 000000000..73a7063eb
--- /dev/null
+++ b/sci-physics/lhapdf-sets/metadata.xml
@@ -0,0 +1,12 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
+<pkgmetadata>
+	<maintainer type="project">
+		<email>sci@gentoo.org</email>
+		<name>Gentoo Science Project</name>
+	</maintainer>
+	<maintainer type="person">
+		<email>alexander@neuwirth-informatik.de</email>
+		<name>Alexander Puck Neuwirth</name>
+	</maintainer>
+</pkgmetadata>
diff --git a/sci-physics/mc-tester/files/mc-tester-1.25.0-compare.sh.patch b/sci-physics/mc-tester/files/mc-tester-1.25.0-compare.sh.patch
index 180dcb029..bb8695fca 100644
--- a/sci-physics/mc-tester/files/mc-tester-1.25.0-compare.sh.patch
+++ b/sci-physics/mc-tester/files/mc-tester-1.25.0-compare.sh.patch
@@ -1,5 +1,5 @@
---- analyze/compare.sh
-+++ analyze/compare.sh
+--- a/analyze/compare.sh
++++ b/analyze/compare.sh
 @@ -6,13 +6,14 @@
  #----------------------------------
  # Change these variables
diff --git a/sci-physics/mc-tester/mc-tester-1.25.0.ebuild b/sci-physics/mc-tester/mc-tester-1.25.0.ebuild
index 6126cde65..5a08d1b3e 100644
--- a/sci-physics/mc-tester/mc-tester-1.25.0.ebuild
+++ b/sci-physics/mc-tester/mc-tester-1.25.0.ebuild
@@ -1,48 +1,53 @@
-# Copyright 1999-2015 Gentoo Foundation
+# Copyright 1999-2021 Gentoo Authors
 # Distributed under the terms of the GNU General Public License v2
 
-EAPI=5
+EAPI=7
 
-inherit eutils
+MYPN="MC-TESTER"
 
-MYPN=MC-TESTER
+DOCS_BUILDER="doxygen"
+DOCS_DIR="doc"
+DOCS_DEPEND="media-gfx/graphviz"
+
+inherit docs
 
 DESCRIPTION="Comparisons of Monte Carlo predictions in High Energy Physics"
 HOMEPAGE="http://mc-tester.web.cern.ch/MC-TESTER/"
 SRC_URI="http://mc-tester.web.cern.ch/MC-TESTER/${MYPN}-${PV}.tar.gz"
-LICENSE="CPC GPL-2+"
-#HepMC interface is licensed under GPL, other code under CPC
 
+#HepMC interface is licensed under GPL, other code under CPC
+LICENSE="CPC GPL-2+"
 SLOT="0"
 KEYWORDS="~amd64 ~x86"
-IUSE="doc examples hepmc"
 
-RDEPEND="sci-physics/root
+IUSE="examples hepmc pythia"
+
+RDEPEND="sci-physics/root:=
 	hepmc? ( sci-physics/hepmc )
+	pythia? ( sci-physics/pythia:8 )
 "
-DEPEND="${RDEPEND}
-	doc? ( app-doc/doxygen )"
+DEPEND="${RDEPEND}"
 
 S="${WORKDIR}/${MYPN}"
 
-src_prepare() {
-	epatch "${FILESDIR}/${P}-compare.sh.patch"
-}
+PATCHES=(
+	"${FILESDIR}/${P}-compare.sh.patch"
+)
 
 src_configure() {
 	econf \
 		--with-root="${EPREFIX}/usr" \
-		--without-Pythia8 \
+		$(use_with pythia Pythia8 "${EPREFIX}/usr") \
 		$(use_with hepmc HepMC "${EPREFIX}/usr")
 }
 
 src_compile() {
+	docs_compile
 	default
-	use doc && cd doc && default
 }
 
 src_install() {
-	emake PREFIX="${D}/usr" install
+	default
 	newbin analyze/compare.sh mc-tester-compare
 
 	insinto /usr/libexec/${PN}/analyze
@@ -50,11 +55,6 @@ src_install() {
 	insinto /usr/share/${PN}
 	doins analyze/*.tex
 
-	if use doc; then
-		dohtml doc/doxygenDocs/html/*
-		dodoc doc/{README*,USER-TESTS,tester.ps.gz}
-	fi
-
 	use examples && dodoc -r examples-*
 }
 
diff --git a/sci-physics/mc-tester/metadata.xml b/sci-physics/mc-tester/metadata.xml
index 53b89a9c9..7d0535abc 100644
--- a/sci-physics/mc-tester/metadata.xml
+++ b/sci-physics/mc-tester/metadata.xml
@@ -8,10 +8,8 @@
 		<email>sci-physics@gentoo.org</email>
 		<name>Gentoo Physics Project</name>
 	</maintainer>
-	<longdescription>
-A universal tool for comparisons of Monte Carlo predictions in High Energy Physics
-</longdescription>
 	<use>
 		<flag name="hepmc">Compile <pkg>sci-physics/hepmc</pkg> interface</flag>
+		<flag name="pythia">Compile <pkg>sci-physics/pythia</pkg> interface</flag>
 	</use>
 </pkgmetadata>
diff --git a/sci-physics/mcfm/Manifest b/sci-physics/mcfm/Manifest
new file mode 100644
index 000000000..9163b57a5
--- /dev/null
+++ b/sci-physics/mcfm/Manifest
@@ -0,0 +1 @@
+DIST MCFM-10.2.1.tar.gz 39365160 BLAKE2B 59b6fc55e4a21d4dea979d973cac0378763585088b7b5f032d671a30358e6bd8b6332fd3fa0eeca573177e46f642b3ba8b0c78c503bf37ac4ee0d6c0b962e4df SHA512 994f243b5460784eb5d62f81adf6c08d7ffd03df0d2fa8ac8e4522ab5127f54c3218cd4fe9984adff505c02804613c570d228f88c9343804e20d08f7187575c1
diff --git a/sci-physics/mcfm/files/mcfm-10.2.1-rest.patch b/sci-physics/mcfm/files/mcfm-10.2.1-rest.patch
new file mode 100644
index 000000000..f43a1cb48
--- /dev/null
+++ b/sci-physics/mcfm/files/mcfm-10.2.1-rest.patch
@@ -0,0 +1,251 @@
+--- a/CMakeLists.txt	2022-09-19 02:30:49.215050000 +0200
++++ b/CMakeLists.txt	2022-09-19 21:03:05.409746266 +0200
+@@ -41,48 +41,48 @@
+ 
+ include(ExternalProject)
+ 
+-ExternalProject_Add(qd
+-    DOWNLOAD_COMMAND mkdir -p ${CMAKE_BINARY_DIR}/lib && cp -r ${CMAKE_SOURCE_DIR}/lib/qd-2.3.22 ${CMAKE_BINARY_DIR}/lib/
+-    PREFIX ${CMAKE_BINARY_DIR}/lib/qd-2.3.22
+-    SOURCE_DIR ${CMAKE_BINARY_DIR}/lib/qd-2.3.22
+-    BUILD_IN_SOURCE ON
+-    PATCH_COMMAND mkdir -p ${CMAKE_BINARY_DIR}/local
+-    CONFIGURE_COMMAND CC=${CMAKE_C_COMPILER} CXX=${CMAKE_CXX_COMPILER} FC=${CMAKE_Fortran_COMPILER} ./configure --with-pic --enable-fortran --enable-fma --prefix=${CMAKE_BINARY_DIR}/local --enable-shared --libdir=${CMAKE_BINARY_DIR}/local/lib
+-    BUILD_COMMAND ${MAKE}
+-    INSTALL_COMMAND ${CMAKE_MAKE_PROGRAM} install
+-)
+-
+-ExternalProject_Add(qcdloop
+-    DOWNLOAD_COMMAND mkdir -p ${CMAKE_BINARY_DIR}/lib && cp -r ${CMAKE_SOURCE_DIR}/lib/qcdloop-2.0.5 ${CMAKE_BINARY_DIR}/lib
+-    PREFIX ${CMAKE_BINARY_DIR}/lib/qcdloop-2.0.5
+-    SOURCE_DIR ${CMAKE_BINARY_DIR}/lib/qcdloop-2.0.5
+-    BUILD_IN_SOURCE ON
+-    PATCH_COMMAND mkdir -p ${CMAKE_BINARY_DIR}/local
+-    CMAKE_ARGS -DCMAKE_BUILD_TYPE=${CMAKE_BUILD_TYPE} -DENABLE_FORTRAN_WRAPPER=ON -DCMAKE_INSTALL_PREFIX=${CMAKE_BINARY_DIR}/local -DCMAKE_CXX_COMPILER=${CMAKE_CXX_COMPILER} -DCMAKE_C_COMPILER=${CMAKE_C_COMPILER} -DCMAKE_INSTALL_LIBDIR=lib
+-    BUILD_COMMAND ${MAKE}
+-    INSTALL_COMMAND ${CMAKE_MAKE_PROGRAM} install
+-)
+-
+-ExternalProject_Add(liboneloop
+-    DOWNLOAD_COMMAND mkdir -p ${CMAKE_BINARY_DIR}/lib && cp -r ${CMAKE_SOURCE_DIR}/lib/oneloop ${CMAKE_BINARY_DIR}/lib/
+-    PREFIX ${CMAKE_BINARY_DIR}/lib/oneloop
+-    SOURCE_DIR ${CMAKE_BINARY_DIR}/lib/oneloop
+-    BUILD_IN_SOURCE ON
+-    CMAKE_ARGS -DCMAKE_BUILD_TYPE=${CMAKE_BUILD_TYPE} -DCMAKE_Fortran_COMPILER=${CMAKE_Fortran_COMPILER} -DCMAKE_Fortran_FLAGS=-fPIC
+-    BUILD_COMMAND ${MAKE}
+-    INSTALL_COMMAND mkdir -p ${CMAKE_BINARY_DIR}/local/include && cp ${CMAKE_BINARY_DIR}/lib/oneloop/avh_olo.mod ${CMAKE_BINARY_DIR}/local/include 
+-)
+-
+-ExternalProject_Add(handyg
+-    DOWNLOAD_COMMAND mkdir -p ${CMAKE_BINARY_DIR}/lib && cp -r ${CMAKE_SOURCE_DIR}/lib/handyG ${CMAKE_BINARY_DIR}/lib/
+-    PREFIX ${CMAKE_BINARY_DIR}/lib/handyG
+-    SOURCE_DIR ${CMAKE_BINARY_DIR}/lib/handyG
+-    BUILD_IN_SOURCE ON
+-    PATCH_COMMAND mkdir -p ${CMAKE_BINARY_DIR}/local
+-    CONFIGURE_COMMAND CC=${CMAKE_C_COMPILER} CXX=${CMAKE_CXX_COMPILER} FC=${CMAKE_Fortran_COMPILER} CFLAGS=-fPIC CXXFLAGS=-fPIC FFLAGS=-fPIC  ./configure --prefix=${CMAKE_BINARY_DIR}/local --moduledir=${CMAKE_BINARY_DIR}/local/include
+-    BUILD_COMMAND ${MAKE}
+-    INSTALL_COMMAND ${CMAKE_MAKE_PROGRAM} install
+-)
++#ExternalProject_Add(qd
++#    DOWNLOAD_COMMAND mkdir -p ${CMAKE_BINARY_DIR}/lib && cp -r ${CMAKE_SOURCE_DIR}/lib/qd-2.3.22 ${CMAKE_BINARY_DIR}/lib/
++#    PREFIX ${CMAKE_BINARY_DIR}/lib/qd-2.3.22
++#    SOURCE_DIR ${CMAKE_BINARY_DIR}/lib/qd-2.3.22
++#    BUILD_IN_SOURCE ON
++#    PATCH_COMMAND mkdir -p ${CMAKE_BINARY_DIR}/local
++#    CONFIGURE_COMMAND CC=${CMAKE_C_COMPILER} CXX=${CMAKE_CXX_COMPILER} FC=${CMAKE_Fortran_COMPILER} ./configure --with-pic --enable-fortran --enable-fma --prefix=${CMAKE_BINARY_DIR}/local --enable-shared --libdir=${CMAKE_BINARY_DIR}/local/lib
++#    BUILD_COMMAND ${MAKE}
++#    INSTALL_COMMAND ${CMAKE_MAKE_PROGRAM} install
++#)
++#
++#ExternalProject_Add(qcdloop
++#    DOWNLOAD_COMMAND mkdir -p ${CMAKE_BINARY_DIR}/lib && cp -r ${CMAKE_SOURCE_DIR}/lib/qcdloop-2.0.5 ${CMAKE_BINARY_DIR}/lib
++#    PREFIX ${CMAKE_BINARY_DIR}/lib/qcdloop-2.0.5
++#    SOURCE_DIR ${CMAKE_BINARY_DIR}/lib/qcdloop-2.0.5
++#    BUILD_IN_SOURCE ON
++#    PATCH_COMMAND mkdir -p ${CMAKE_BINARY_DIR}/local
++#    CMAKE_ARGS -DCMAKE_BUILD_TYPE=${CMAKE_BUILD_TYPE} -DENABLE_FORTRAN_WRAPPER=ON -DCMAKE_INSTALL_PREFIX=${CMAKE_BINARY_DIR}/local -DCMAKE_CXX_COMPILER=${CMAKE_CXX_COMPILER} -DCMAKE_C_COMPILER=${CMAKE_C_COMPILER} -DCMAKE_INSTALL_LIBDIR=lib
++#    BUILD_COMMAND ${MAKE}
++#    INSTALL_COMMAND ${CMAKE_MAKE_PROGRAM} install
++#)
++#
++#ExternalProject_Add(liboneloop
++#    DOWNLOAD_COMMAND mkdir -p ${CMAKE_BINARY_DIR}/lib && cp -r ${CMAKE_SOURCE_DIR}/lib/oneloop ${CMAKE_BINARY_DIR}/lib/
++#    PREFIX ${CMAKE_BINARY_DIR}/lib/oneloop
++#    SOURCE_DIR ${CMAKE_BINARY_DIR}/lib/oneloop
++#    BUILD_IN_SOURCE ON
++#    CMAKE_ARGS -DCMAKE_BUILD_TYPE=${CMAKE_BUILD_TYPE} -DCMAKE_Fortran_COMPILER=${CMAKE_Fortran_COMPILER} -DCMAKE_Fortran_FLAGS=-fPIC
++#    BUILD_COMMAND ${MAKE}
++#    INSTALL_COMMAND mkdir -p ${CMAKE_BINARY_DIR}/local/include && cp ${CMAKE_BINARY_DIR}/lib/oneloop/avh_olo.mod ${CMAKE_BINARY_DIR}/local/include 
++#)
++#
++#ExternalProject_Add(handyg
++#    DOWNLOAD_COMMAND mkdir -p ${CMAKE_BINARY_DIR}/lib && cp -r ${CMAKE_SOURCE_DIR}/lib/handyG ${CMAKE_BINARY_DIR}/lib/
++#    PREFIX ${CMAKE_BINARY_DIR}/lib/handyG
++#    SOURCE_DIR ${CMAKE_BINARY_DIR}/lib/handyG
++#    BUILD_IN_SOURCE ON
++#    PATCH_COMMAND mkdir -p ${CMAKE_BINARY_DIR}/local
++#    CONFIGURE_COMMAND CC=${CMAKE_C_COMPILER} CXX=${CMAKE_CXX_COMPILER} FC=${CMAKE_Fortran_COMPILER} CFLAGS=-fPIC CXXFLAGS=-fPIC FFLAGS=-fPIC  ./configure --prefix=${CMAKE_BINARY_DIR}/local --moduledir=${CMAKE_BINARY_DIR}/local/include
++#    BUILD_COMMAND ${MAKE}
++#    INSTALL_COMMAND ${CMAKE_MAKE_PROGRAM} install
++#)
+ 
+ ## Configuration options
+ 
+@@ -169,7 +169,7 @@
+ add_subdirectory(lib/SpecialFunctions)
+ add_subdirectory(lib/AMOS)
+ 
+-add_dependencies(objlib qd qcdloop liboneloop handyg)
++#add_dependencies(objlib qd qcdloop liboneloop handyg)
+ 
+ if(${with_vvamp})
+     add_compile_definitions(WITH_VVAMP=1)
+@@ -182,7 +182,7 @@
+         PATCH_COMMAND mkdir -p ${CMAKE_BINARY_DIR}/local
+         CMAKE_ARGS -DCMAKE_BUILD_TYPE=${CMAKE_BUILD_TYPE} -DCMAKE_Fortran_COMPILER=${CMAKE_Fortran_COMPILER} -DCMAKE_Fortran_FLAGS=-fPIC
+         BUILD_COMMAND ${MAKE}
+-        INSTALL_COMMAND mkdir -p ${CMAKE_BINARY_DIR}/local/include && cp ${CMAKE_BINARY_DIR}/VVamp/mod_vvamp.mod ${CMAKE_BINARY_DIR}/local/include 
++        INSTALL_COMMAND mv ${CMAKE_BINARY_DIR}/VVamp/mod_vvamp.mod ${CMAKE_BINARY_DIR}/local/include 
+     )
+     add_library(vvamp STATIC IMPORTED)
+     set_property(TARGET vvamp PROPERTY IMPORTED_LOCATION "${CMAKE_BINARY_DIR}/VVamp/libvvamp.a")
+@@ -192,7 +192,6 @@
+ else()
+     set(linkvvamp "")
+ endif()
+-
+ set_target_properties(objlib PROPERTIES
+     CXX_STANDARD 11
+     Fortran_MODULE_DIRECTORY "${CMAKE_BINARY_DIR}/include"
+@@ -222,48 +221,51 @@
+     target_link_libraries(mcfm ${OpenMP_Fortran_LIBRARIES})
+ endif()
+ 
+-add_library(oneloop STATIC IMPORTED)
+-set_property(TARGET oneloop PROPERTY IMPORTED_LOCATION "${CMAKE_BINARY_DIR}/lib/oneloop/liboneloop.a")
++find_library(qcdloop qcdloop)
+ 
+-add_library(qcdloop_lib_static STATIC IMPORTED)
+-set_property(TARGET qcdloop_lib_static PROPERTY IMPORTED_LOCATION "${CMAKE_BINARY_DIR}/local/lib/libqcdloop.a")
+-set_property(TARGET qcdloop_lib_static PROPERTY IMPORTED_NO_SONAME TRUE)
+-add_dependencies(qcdloop_lib_static qcdloop)
+-
+-add_library(qcdloop_lib_shared SHARED IMPORTED)
+-set_property(TARGET qcdloop_lib_shared PROPERTY IMPORTED_LOCATION "${CMAKE_BINARY_DIR}/local/lib/libqcdloop.${CMAKE_SHARED_LIBRARY_SUFFIX}")
+-set_property(TARGET qcdloop_lib_shared PROPERTY IMPORTED_NO_SONAME TRUE)
+-add_dependencies(qcdloop_lib_shared qcdloop)
+-
+-add_library(qd_lib_static STATIC IMPORTED)
+-set_property(TARGET qd_lib_static PROPERTY IMPORTED_LOCATION "${CMAKE_BINARY_DIR}/local/lib/libqd.a")
+-set_property(TARGET qd_lib_static PROPERTY IMPORTED_NO_SONAME TRUE)
+-add_dependencies(qd_lib_static qd)
+-
+-add_library(qd_lib_shared SHARED IMPORTED)
+-set_property(TARGET qd_lib_shared PROPERTY IMPORTED_LOCATION "${CMAKE_BINARY_DIR}/local/lib/libqd.${CMAKE_SHARED_LIBRARY_SUFFIX}")
+-set_property(TARGET qd_lib_shared PROPERTY IMPORTED_NO_SONAME TRUE)
+-add_dependencies(qd_lib_shared qd)
+-
+-add_library(qdmod_lib_static STATIC IMPORTED)
+-set_property(TARGET qdmod_lib_static PROPERTY IMPORTED_LOCATION "${CMAKE_BINARY_DIR}/local/lib/libqdmod.a")
+-set_property(TARGET qdmod_lib_static PROPERTY IMPORTED_NO_SONAME TRUE)
+-add_dependencies(qdmod_lib_static qd)
+-
+-add_library(qdmod_lib_shared SHARED IMPORTED)
+-set_property(TARGET qdmod_lib_shared PROPERTY IMPORTED_LOCATION "${CMAKE_BINARY_DIR}/local/lib/libqdmod.${CMAKE_SHARED_LIBRARY_SUFFIX}")
+-set_property(TARGET qdmod_lib_shared PROPERTY IMPORTED_NO_SONAME TRUE)
+-add_dependencies(qdmod_lib_shared qd)
+-
+-add_library(handyg_lib_static STATIC IMPORTED)
+-set_property(TARGET handyg_lib_static PROPERTY IMPORTED_LOCATION "${CMAKE_BINARY_DIR}/local/lib/libhandyg.a")
+-set_property(TARGET handyg_lib_static PROPERTY IMPORTED_NO_SONAME TRUE)
+-add_dependencies(handyg_lib_static handyg)
+-
+-add_dependencies(objlib qdmod_lib_static)
+-add_dependencies(objlib qd_lib_static)
+-add_dependencies(objlib qcdloop_lib_static)
+-add_dependencies(objlib handyg_lib_static)
++#add_library(oneloop STATIC IMPORTED)
++#set_property(TARGET oneloop PROPERTY IMPORTED_LOCATION "${CMAKE_BINARY_DIR}/lib/oneloop/liboneloop.a")
++#
++#add_library(qcdloop_lib_static STATIC IMPORTED)
++#set_property(TARGET qcdloop_lib_static PROPERTY IMPORTED_LOCATION "${CMAKE_BINARY_DIR}/local/lib/libqcdloop.a")
++#set_property(TARGET qcdloop_lib_static PROPERTY IMPORTED_NO_SONAME TRUE)
++#add_dependencies(qcdloop_lib_static qcdloop)
++
++#add_library(qcdloop_lib_shared SHARED IMPORTED)
++#set_property(TARGET qcdloop_lib_shared PROPERTY IMPORTED_LOCATION "${CMAKE_BINARY_DIR}/local/lib/libqcdloop.${CMAKE_SHARED_LIBRARY_SUFFIX}")
++#set_property(TARGET qcdloop_lib_shared PROPERTY IMPORTED_NO_SONAME TRUE)
++#add_dependencies(qcdloop_lib_shared qcdloop)
++#
++#add_library(qd_lib_static STATIC IMPORTED)
++#set_property(TARGET qd_lib_static PROPERTY IMPORTED_LOCATION "${CMAKE_BINARY_DIR}/local/lib/libqd.a")
++#set_property(TARGET qd_lib_static PROPERTY IMPORTED_NO_SONAME TRUE)
++#add_dependencies(qd_lib_static qd)
++#
++#add_library(qd_lib_shared SHARED IMPORTED)
++#set_property(TARGET qd_lib_shared PROPERTY IMPORTED_LOCATION "${CMAKE_BINARY_DIR}/local/lib/libqd.${CMAKE_SHARED_LIBRARY_SUFFIX}")
++#set_property(TARGET qd_lib_shared PROPERTY IMPORTED_NO_SONAME TRUE)
++#add_dependencies(qd_lib_shared qd)
++#
++#add_library(qdmod_lib_static STATIC IMPORTED)
++#set_property(TARGET qdmod_lib_static PROPERTY IMPORTED_LOCATION "${CMAKE_BINARY_DIR}/local/lib/libqdmod.a")
++#set_property(TARGET qdmod_lib_static PROPERTY IMPORTED_NO_SONAME TRUE)
++#add_dependencies(qdmod_lib_static qd)
++#
++#add_library(qdmod_lib_shared SHARED IMPORTED)
++#set_property(TARGET qdmod_lib_shared PROPERTY IMPORTED_LOCATION "${CMAKE_BINARY_DIR}/local/lib/libqdmod.${CMAKE_SHARED_LIBRARY_SUFFIX}")
++#set_property(TARGET qdmod_lib_shared PROPERTY IMPORTED_NO_SONAME TRUE)
++#add_dependencies(qdmod_lib_shared qd)
++#
++#add_library(handyg_lib_static STATIC IMPORTED)
++#set_property(TARGET handyg_lib_static PROPERTY IMPORTED_LOCATION "${CMAKE_BINARY_DIR}/local/lib/libhandyg.a")
++#set_property(TARGET handyg_lib_static PROPERTY IMPORTED_NO_SONAME TRUE)
++#add_dependencies(handyg_lib_static handyg)
++
++#add_dependencies(objlib qdmod_lib_static)
++#add_dependencies(objlib qd_lib_static)
++#add_dependencies(objlib qcdloop_lib_static)
++#add_dependencies(objlib handyg_lib_static)
++target_link_libraries(objlib qdmod qd qcdloop handyg)
+ 
+ if(use_internal_lhapdf)
+     ExternalProject_Add(lhapdf
+@@ -285,13 +287,15 @@
+ 
+     add_dependencies(lhapdf_lib_static lhapdf)
+     target_link_libraries(mcfm lhapdf_lib_static)
+-    target_include_directories(objlib PRIVATE "${CMAKE_BINARY_DIR}/local/include" "${CMAKE_BINARY_DIR}/local/include/qd")
++    target_include_directories(objlib PRIVATE
++	   "${CMAKE_BINARY_DIR}/include" "/usr/include" "/usr/include/qd")
+     add_dependencies(objlib lhapdf)
+ elseif(use_external_lhapdf)
+     find_library(lhapdf_lib NAMES LHAPDF REQUIRED)
+     target_link_libraries(mcfm ${lhapdf_lib})
+     if (${lhapdf_include_path})
+-        target_include_directories(objlib PRIVATE "${LHAPDF_INCLUDE_PATH}" "${CMAKE_BINARY_DIR}/local/include" "${CMAKE_BINARY_DIR}/local/include/qd")
++        target_include_directories(objlib PRIVATE "${LHAPDF_INCLUDE_PATH}"
++          "${CMAKE_BINARY_DIR}/include" "/usr/include" "/usr/include/qd")
+     endif()
+ endif()
+ 
+@@ -299,9 +303,9 @@
+ 
+ if(${with_library})
+     if(use_internal_lhapdf)
+-        target_link_libraries(libmcfm qdmod_lib_static qd_lib_static qcdloop_lib_static oneloop handyg_lib_static ${linkvvamp} quadmath stdc++ lhapdf_lib_static)
++        target_link_libraries(libmcfm qdmod qd qcdloop avh_olo handyg ${linkvvamp} quadmath stdc++ lhapdf_lib_static)
+     else()
+-        target_link_libraries(libmcfm qdmod_lib_static qd_lib_static qcdloop_lib_static oneloop handyg_lib_static ${linkvvamp} quadmath stdc++ ${lhapdf_lib})
++        target_link_libraries(libmcfm qdmod qd qcdloop avh_olo handyg ${linkvvamp} quadmath stdc++ ${lhapdf_lib})
+     endif()
+     if (DEFINED OLDIR)
+       target_link_libraries(oltest libmcfm ${openloops_lib})
+@@ -320,7 +324,7 @@
+     endif()
+ endif()
+ 
+-target_link_libraries(mcfm qdmod_lib_static qd_lib_static qcdloop_lib_static oneloop handyg_lib_static ${linkvvamp} quadmath stdc++)
++target_link_libraries(mcfm qdmod qd qcdloop avh_olo handyg ${linkvvamp} quadmath stdc++)
+ 
+ set(CMAKE_INSTALL_RPATH_USE_LINK_PATH TRUE)
+ set(CMAKE_INSTALL_RPATH "${CMAKE_BINARY_DIR}/local/lib")
diff --git a/sci-physics/mcfm/mcfm-10.2.1.ebuild b/sci-physics/mcfm/mcfm-10.2.1.ebuild
new file mode 100644
index 000000000..bfc795247
--- /dev/null
+++ b/sci-physics/mcfm/mcfm-10.2.1.ebuild
@@ -0,0 +1,68 @@
+# Copyright 2022 Gentoo Authors
+# Distributed under the terms of the GNU General Public License v2
+
+EAPI=8
+
+CMAKE_MAKEFILE_GENERATOR="emake"
+
+inherit cmake fortran-2
+
+MY_PN=MCFM
+MY_P=${MY_PN}-${PV}
+
+DESCRIPTION="Monte Carlo for FeMtobarn processes"
+HOMEPAGE="https://mcfm.fnal.gov"
+SRC_URI="https://mcfm.fnal.gov/downloads/${MY_P}.tar.gz"
+S="${WORKDIR}/${MY_P}"
+
+LICENSE="GPL-3+"
+SLOT="0"
+KEYWORDS="~amd64"
+
+# Manual states multithreading bug in lhapdf-6.3.0 ?!
+# MCFM has been tested against lhapdf-6.2.0 which ::gentoo already dropped
+DEPEND="
+	sci-physics/lhapdf
+	>=sci-libs/qd-2.3.22
+	>=sci-physics/qcdloop-2.0.5
+	>=sci-physics/oneloop-2020.07.31
+	>=sci-libs/handyg-0.1.5
+"
+RDEPEND="${DEPEND}"
+
+PATCHES=(
+	"${FILESDIR}"/${P}-rest.patch
+)
+src_prepare() {
+	sed -i -e 's/\(name=".*\)"/\1_"/g' src/Mods/mod_qcdloop_c.f || die
+	cmake_src_prepare
+}
+
+src_configure() {
+	local mycmakeargs=(
+		-Duse_external_lhapdf=ON
+		-Duse_internal_lhapdf=OFF
+		-Dlhapdf_include_path=ON
+		-Dwith_library=ON
+		-Dwith_vvamp=OFF
+	)
+	cmake_src_configure
+	# Fix relative path in working dir to something absolute
+	sed -i "s/process\.DAT/${EPREFIX}\/usr\/share\/${MY_PN}\/process\.DAT/g" src/Procdep/chooser.f || die
+}
+
+src_compile() {
+	# Single thread force needed since fortan mods depend on each other
+	# This problem only happend very rarely
+	export MAKEOPTS=-j1
+	cmake_src_compile
+}
+
+src_install() {
+	# this did not work
+	#cmake_src_install
+	dobin "${BUILD_DIR}"/mcfm
+	dolib.so "${BUILD_DIR}"/libmcfm.so
+	insinto "/usr/share/${MY_PN}/"
+	doins "Bin/process.DAT"
+}
diff --git a/sci-physics/mcfm/metadata.xml b/sci-physics/mcfm/metadata.xml
new file mode 100644
index 000000000..a8720d7dd
--- /dev/null
+++ b/sci-physics/mcfm/metadata.xml
@@ -0,0 +1,15 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
+<pkgmetadata>
+	<maintainer type="person">
+		<email>APN-Pucky@users.noreply.github.com</email>
+		<name>APN-Pucky</name>
+	</maintainer>
+	<maintainer type="project">
+		<email>sci-physics@gentoo.org</email>
+		<name>Gentoo Physics Project</name>
+	</maintainer>
+	<longdescription lang="en">
+	The program calculates cross-sections for various femtobarn-level processes at hadron-hadron colliders. A number of processes can be calculated at NLO order in QCD, while most other processes are included at NNLO order in QCD. The calculation of some processes can also account for next-to-leading order weak effects.
+	</longdescription>
+</pkgmetadata>
diff --git a/sci-physics/oneloop/Manifest b/sci-physics/oneloop/Manifest
new file mode 100644
index 000000000..f698d0a23
--- /dev/null
+++ b/sci-physics/oneloop/Manifest
@@ -0,0 +1 @@
+DIST oneloop-2020.07.31.zip 166257 BLAKE2B 7869806c6e70388311b62ae1ad15b35292c81d5d87ff7f24ad53bb8e562631664545f36e3e32d6f31a39ca9489d7da64284ad10ed988cb7c4375626121d0a84f SHA512 eee46cfe60b1d887cb40033e63d7a04ca24b329692e443d28ecb9f070182d5c56ea5bbaefd2ae21b2776d907ea280ebf81cae0c332391e7e7e7d5e3be3084220
diff --git a/sci-physics/oneloop/files/oneloop-2020.07.31-config.patch b/sci-physics/oneloop/files/oneloop-2020.07.31-config.patch
new file mode 100644
index 000000000..4af47e066
--- /dev/null
+++ b/sci-physics/oneloop/files/oneloop-2020.07.31-config.patch
@@ -0,0 +1,11 @@
+--- a/Config	2022-05-19 17:34:51.000000000 +0200
++++ b/Config	2022-05-19 17:34:51.000000000 +0200
+@@ -3,7 +3,7 @@
+ #FFLAGS = -Wall
+ 
+ DPKIND = kind(1d0)
+-QPKIND = kind(1q0)
++#QPKIND = kind(1q0)
+ #DPKIND = selected_real_kind(15)
+ #QPKIND = 16
+ #DDTYPE = ddfun90
diff --git a/sci-physics/oneloop/metadata.xml b/sci-physics/oneloop/metadata.xml
new file mode 100644
index 000000000..35b6c2bd9
--- /dev/null
+++ b/sci-physics/oneloop/metadata.xml
@@ -0,0 +1,15 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
+<pkgmetadata>
+	<maintainer type="person">
+		<email>alexander@neuwirth-informatik.de</email>
+		<name>Alexander Puck Neuwirth</name>
+	</maintainer>
+	<maintainer type="project">
+		<email>sci-physics@gentoo.org</email>
+		<name>Gentoo Physics Project</name>
+	</maintainer>
+	<upstream>
+		<remote-id type="bitbucket">hameren/oneloop</remote-id>
+	</upstream>
+</pkgmetadata>
diff --git a/sci-physics/oneloop/oneloop-2020.07.31.ebuild b/sci-physics/oneloop/oneloop-2020.07.31.ebuild
new file mode 100644
index 000000000..9344d1513
--- /dev/null
+++ b/sci-physics/oneloop/oneloop-2020.07.31.ebuild
@@ -0,0 +1,46 @@
+# Copyright 2022 Gentoo Authors
+# Distributed under the terms of the GNU General Public License v2
+
+EAPI=8
+
+# python only needed for create.py to get binaries
+PYTHON_COMPAT=( python3_{10..11} )
+inherit toolchain-funcs python-any-r1 fortran-2
+
+DESCRIPTION="Library of one-loop scalar functions"
+HOMEPAGE="https://bitbucket.org/hameren/oneloop"
+SRC_URI="https://bitbucket.org/hameren/oneloop/get/3762b8bad6ad.zip -> ${P}.zip"
+S="${WORKDIR}/hameren-oneloop-3762b8bad6ad"
+
+LICENSE="GPL-3+"
+SLOT="0"
+KEYWORDS="~amd64"
+
+BDEPEND="
+	${PYTHON_DEPS}
+	app-arch/unzip
+"
+
+PATCHES=(
+	"${FILESDIR}"/${P}-config.patch
+)
+
+src_configure() {
+	tc-export FC
+	sed -i "/FC = /s/gfortran/${FC}/g" Config || die
+	sed -i "/FFLAGS = /s/ -O/${FFLAGS} -fPIC/g" Config || die
+}
+
+src_compile() {
+	tc-export FC
+	emake -f make_cuttools
+	${EPYTHON} ./create.py || die "Failed to compile"
+	#./create.py dynamic || die
+	${FC} ${LDFLAGS} -Wl,-soname,libavh_olo.so -shared -o libavh_olo.so avh_olo.o || die "Failed to link"
+}
+
+src_install() {
+	dolib.a libavh_olo.a
+	dolib.so libavh_olo.so
+	doheader avh_olo.mod
+}
diff --git a/sci-physics/openmx/Manifest b/sci-physics/openmx/Manifest
index 429fb1ea5..030db9f8c 100644
--- a/sci-physics/openmx/Manifest
+++ b/sci-physics/openmx/Manifest
@@ -1,4 +1,2 @@
-DIST openmx3.6.tar.gz 83023744 SHA256 e344914a615d4179e724877207335e44f9d629cd3931b70e135011877355ab71 SHA512 f4d59e839bbd216893149c83d1059aa4dc4fb011d113cb40efbd99db96d558501b371628f0ea064d3091d8ef0d2c8664412b0c3541fa2a7135811e3536cb0018 WHIRLPOOL 54c72309133dbb010218ce138992362e98eb4c345eb3b2897e1d86f3f2469cc95a2024c8547cc3dc0db78befaf620e624640b6a64522c0937bf7158658a28109
-DIST openmx3.7.tar.gz 117784869 BLAKE2B 7b9229058e7f6999a66ca2342819603dd730e88f2ef1de531979940447b9e885b5e34f6cb59088ed87a3b9527a91ebde6ee5a1eef132b51dce2e10ba1d350f84 SHA512 e05e2839776be17d0df71818444ff7234b75f00177111ff4003eacbe3663a025965990c293cd1dfa078c3960fe89385cbe16393c9cfaf5953e1c683e7964423a
-DIST patch3.6.1.tar.gz 202531 SHA256 56cba052a84c73bf332ff3a65787001376f8d50ec50e7e363a67dfb5b417febd SHA512 1f1c2c156c80a21649826cfaeb79a9b2b7d81b46920e713fb0e4489eeceb8cc6a9193c49efb0d4c1a1a69313e21186e10ed4fd97d27e63b555ce1092425c641d WHIRLPOOL 006cb7ec822ef485c03a371b9c3a99c426fc5e6e1249fd17d9f5527f0220f09df1acc049e31a59d6834a3ce44431ae385268954898613a9fe31ff892262a5503
-DIST patch3.7.8.tar.gz 147931 BLAKE2B 2263893bbcd899375b4fa29c82ec4c5ae0f4c50352616f773ae5297afa5d6881d9a4c6cc3b4e4d0f2c2d25a71b977ef7a07db67d069c9693dddd7aa8c7d2d627 SHA512 4fa088e121b63db68be47c5a105fcdce660ef4a6d705d5390e8ce3405fbedf98abefeb10099034bd4046541cba7c050a06afccd67eaab2f413bb1d160a1ba460
+DIST openmx3.9.tar.gz 166014953 BLAKE2B 1aba4107a2b8d014da40e7851ac33c3678fa1d25e30b7cbfc02017d349d89ed577f2bbd0341cb44e519fc2879879adca83140a9c216fd102842deff6c5d35ec2 SHA512 dc8f0712ccf02be749b640f9e1678fcc83cb9821589f1f5091d18b2ba68b909389c80dc1e469ba4d81105281f45790f1b699198c0e12590aeb6a73cf2d2c4ac2
+DIST patch3.9.9.tar.gz 1074993 BLAKE2B ed539788a5f6dedf41814c69339dc0ec3ac8d9da1beec363edfbd691571d22c0bb984f50e386687c75ae0eb9d5fdee2085067cd81451869703fa749f22dc2f3d SHA512 5b7d12f17150b0403a0afae5d206379270b2fa734755a48f52902893e5610a7edb710caee634abd98c230261ec6faea4cc607eb82bd8603e16815aebf0d5c85a
diff --git a/sci-physics/openmx/files/3.7-fortran_objects.patch b/sci-physics/openmx/files/3.7-fortran_objects.patch
deleted file mode 100644
index 62521a4da..000000000
--- a/sci-physics/openmx/files/3.7-fortran_objects.patch
+++ /dev/null
@@ -1,15 +0,0 @@
-diff -Naurp openmx3.7.orig/source/makefile openmx3.7/source/makefile
---- openmx3.7.orig/source/makefile	2013-06-18 11:22:23.000000000 +0000
-+++ openmx3.7/source/makefile	2013-06-18 11:36:31.118716378 +0000
-@@ -818,8 +818,8 @@ TRAN_Set_SurfOverlap_NC.o: TRAN_Set_Surf
- 
- 
- elpa1.o: elpa1.f90 
--	$(FC) -c elpa1.f90
-+	$(FC) -c elpa1.f90 -o elpa1.o
- solve_evp_real.o: solve_evp_real.f90 
--	$(FC) -c solve_evp_real.f90 
-+	$(FC) -c solve_evp_real.f90 -o solve_evp_real.o
- solve_evp_complex.o: solve_evp_complex.f90 
--	$(FC) -c solve_evp_complex.f90
-+	$(FC) -c solve_evp_complex.f90 -o solve_evp_complex.o
diff --git a/sci-physics/openmx/openmx-3.6.ebuild b/sci-physics/openmx/openmx-3.6.ebuild
deleted file mode 100644
index 4da849ef5..000000000
--- a/sci-physics/openmx/openmx-3.6.ebuild
+++ /dev/null
@@ -1,96 +0,0 @@
-# Copyright 1999-2014 Gentoo Foundation
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=5
-
-inherit eutils multilib toolchain-funcs
-
-DESCRIPTION="Material eXplorer"
-HOMEPAGE="http://www.openmx-square.org/"
-SRC_URI="
-	http://www.openmx-square.org/${PN}${PV}.tar.gz
-	http://www.openmx-square.org/bugfixed/11Nov14/patch${PV}.1.tar.gz"
-
-LICENSE="GPL-3"
-SLOT="0"
-KEYWORDS="~amd64 ~x86"
-IUSE="-debug mpi openmp test"
-
-RDEPEND="
-	virtual/blas
-	virtual/lapack
-	sci-libs/fftw:3.0[mpi?,openmp?]
-	mpi? ( virtual/mpi )"
-DEPEND="${RDEPEND}
-	virtual/pkgconfig"
-
-S="${WORKDIR}/${PN}${PV}"
-
-pkg_setup() {
-	if use mpi; then
-		export CC="mpicc"
-	else
-		tc-export CC
-	fi
-
-	if use openmp; then
-		if tc-has-openmp; then
-			export CC="${CC} -fopenmp"
-		else
-			die "Please switch to an openmp compatible compiler"
-		fi
-	fi
-}
-
-src_prepare() {
-	cd "${WORKDIR}"
-	mv *.out "${PN}${PV}"/work/input_example
-	mv *.[hc] "${PN}${PV}"/source
-}
-
-src_configure() {
-	local FFTW_FLAVOUR=fftw3
-	if use openmp; then
-	   FFTW_FLAVOUR=fftw3_omp
-	else
-	   export CFLAGS="${CFLAGS} -Dnoomp"
-	fi
-	if use mpi; then
-	   FFTW_FLAVOUR=fftw3_mpi
-	else
-	   export CFLAGS="${CFLAGS} -Dnompi"
-	fi
-	CFLAGS="${CFLAGS} $($(tc-getPKG_CONFIG) --cflags lapack)"
-	CFLAGS="${CFLAGS} $($(tc-getPKG_CONFIG) --cflags ${FFTW_FLAVOUR})"
-	export CFLAGS
-
-	local MX_LIB="$($(tc-getPKG_CONFIG) --static --libs lapack)"
-	local MX_LIB="${MX_LIB} $($(tc-getPKG_CONFIG) --static --libs ${FFTW_FLAVOUR})"
-
-	sed \
-		-e "s%^CC *=.*$%CC  = ${CC} ${CFLAGS}%" \
-		-e "s%^LIB *=.*$%LIB = ${MX_LIB}%" \
-		-i source/makefile || die
-}
-
-src_compile() {
-	emake -C source
-}
-
-src_test() {
-	cd work
-	../source/openmx -runtest || die
-}
-
-src_install() {
-	insinto /usr/share/${P}
-	doins -r DFT_DATA11
-	cd work
-	insinto /usr/share/${P}/examples
-	doins -r *
-	cd ../source
-	dodir /usr/bin
-	emake DESTDIR="${D}/usr/bin" install
-	dodoc "${S}/${PN}${PV}.pdf"
-	use test && dodoc "${S}"/work/runtest.result
-}
diff --git a/sci-physics/openmx/openmx-3.7.8.ebuild b/sci-physics/openmx/openmx-3.7.8.ebuild
deleted file mode 100644
index 3a9758c85..000000000
--- a/sci-physics/openmx/openmx-3.7.8.ebuild
+++ /dev/null
@@ -1,170 +0,0 @@
-# Copyright 1999-2014 Gentoo Foundation
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=5
-
-inherit eutils multilib toolchain-funcs fortran-2
-
-PATCHDATE="14Feb17"
-
-DESCRIPTION="Material eXplorer"
-HOMEPAGE="http://www.openmx-square.org/"
-SRC_URI="
-	http://www.openmx-square.org/${PN}${PV%.[0-9]}.tar.gz
-	http://www.openmx-square.org/bugfixed/${PATCHDATE}/patch${PV}.tar.gz"
-
-LICENSE="GPL-3"
-SLOT="0"
-KEYWORDS="~amd64 ~x86"
-IUSE="-debug mpi openmp test"
-
-RDEPEND="
-	virtual/blas
-	virtual/lapack
-	sci-libs/fftw:3.0[mpi?,openmp?]
-	mpi? ( virtual/mpi )"
-DEPEND="${RDEPEND}
-	virtual/pkgconfig"
-
-S="${WORKDIR}/${PN}${PV%.[0-9]}"
-
-MAKEOPTS+=" -j1"
-
-FORTRAN_STANDARD=90
-
-pkg_setup() {
-	# Link in the GNU Fortran library for Fortran code.
-	# Other compilers may need other hacks.
-	FC_LIB=""
-	if [[ $(tc-getCC)$ == *gcc* ]]; then
-		FC_LIB="-lgfortran"
-	fi
-	export FC_LIB
-
-	if use mpi; then
-		export CC="mpicc"
-		export FC="mpif90"
-	else
-		tc-export CC
-		tc-export FC
-	fi
-
-	if use openmp; then FORTRAN_NEED_OPENMP=1; fi
-
-	fortran-2_pkg_setup
-
-	if use openmp; then
-		# based on _fortran-has-openmp() of fortran-2.eclass
-		local code=ebuild-openmp-flags
-		local ret
-		local openmp
-
-		pushd "${T}"
-		cat <<- EOF > "${code}.c"
-		# include <omp.h>
-		main () {
-			int nthreads;
-			nthreads=omp_get_num_threads();
-		}
-		EOF
-
-		for openmp in -fopenmp -xopenmp -openmp -mp -omp -qsmp=omp; do
-			${CC} ${openmp} "${code}.c" -o "${code}.o" &>> "${T}"/_c_compile_test.log
-			ret=$?
-			(( ${ret} )) || break
-		done
-
-		rm -f "${code}.*"
-		popd
-
-		if (( ${ret} )); then
-			die "Please switch to an openmp compatible C compiler"
-		else
-			export CC="${CC} ${openmp}"
-		fi
-
-		pushd "${T}"
-		cat <<- EOF > "${code}.f"
-		1     call omp_get_num_threads
-		2     end
-		EOF
-
-		for openmp in -fopenmp -xopenmp -openmp -mp -omp -qsmp=omp; do
-			${FC} ${openmp} "${code}.f" -o "${code}.o" &>> "${T}"/_f_compile_test.log
-			ret=$?
-			(( ${ret} )) || break
-		done
-
-		rm -f "${code}.*"
-		popd
-
-		if (( ${ret} )); then
-			die "Please switch to an openmp compatible fortran compiler"
-		else
-			export FC="${FC} ${openmp}"
-		fi
-	fi
-
-}
-
-src_prepare() {
-	cd "${WORKDIR}"
-	mv *.[hc] "${S}"/source
-	epatch "${FILESDIR}/3.7-fortran_objects.patch"
-}
-
-src_configure() {
-	local FFTW_FLAVOUR=fftw3
-	if use openmp; then
-	   FFTW_FLAVOUR=fftw3_omp
-	else
-	   export CFLAGS="${CFLAGS} -Dnoomp"
-	fi
-	if use mpi; then
-	   FFTW_FLAVOUR=fftw3_mpi
-	else
-	   export CFLAGS="${CFLAGS} -Dnompi"
-	fi
-	CFLAGS="${CFLAGS} $($(tc-getPKG_CONFIG) --cflags lapack)"
-	CFLAGS="${CFLAGS} $($(tc-getPKG_CONFIG) --cflags ${FFTW_FLAVOUR})"
-	export CFLAGS
-
-	FCFLAGS="${FCFLAGS} -I/usr/include"
-	FCFLAGS="${FCFLAGS} $($(tc-getPKG_CONFIG) --cflags lapack)"
-	FCFLAGS="${FCFLAGS} $($(tc-getPKG_CONFIG) --cflags ${FFTW_FLAVOUR})"
-	export FCFLAGS
-
-	local MX_LIB="$($(tc-getPKG_CONFIG) --static --libs lapack)"
-	MX_LIB="${MX_LIB} $($(tc-getPKG_CONFIG) --static --libs ${FFTW_FLAVOUR})"
-	if use mpi; then
-		MX_LIB="${MX_LIB} $(mpif90 -showme:link)"
-	fi
-
-	sed \
-		-e "s%^CC *=.*$%CC  = ${CC} ${CFLAGS}%" \
-		-e "s%^FC *=.*$%FC  = ${FC} ${FCFLAGS}%" \
-		-e "s%^LIB *=.*$%LIB = ${MX_LIB} ${FC_LIB}%" \
-		-i source/makefile || die
-}
-
-src_compile() {
-	emake -C source
-}
-
-src_test() {
-	cd work
-	../source/openmx -runtest || die
-}
-
-src_install() {
-	insinto /usr/share/${P}
-	doins -r DFT_DATA13
-	cd work
-	insinto /usr/share/${P}/examples
-	doins -r *
-	cd ../source
-	dodir /usr/bin
-	emake DESTDIR="${D}/usr/bin" install
-	dodoc "${S}/${PN}${PV%.?}.pdf"
-	use test && dodoc "${S}"/work/runtest.result
-}
diff --git a/sci-physics/openmx/openmx-3.9_p20211017.ebuild b/sci-physics/openmx/openmx-3.9_p20211017.ebuild
new file mode 100644
index 000000000..2d1e50397
--- /dev/null
+++ b/sci-physics/openmx/openmx-3.9_p20211017.ebuild
@@ -0,0 +1,174 @@
+# Copyright 1999-2022 Gentoo Authors
+# Distributed under the terms of the GNU General Public License v2
+
+EAPI=8
+
+inherit toolchain-funcs flag-o-matic fortran-2
+
+DESCRIPTION="Material eXplorer"
+HOMEPAGE="http://www.openmx-square.org/" # no https, SSL invalid
+SRC_URI="
+	http://t-ozaki.issp.u-tokyo.ac.jp/${PN}${PV//_*}.tar.gz
+	http://www.openmx-square.org/bugfixed/21Oct17/patch${PV//_*}.9.tar.gz
+"
+S="${WORKDIR}/${PN}${PV//_*}/source"
+
+LICENSE="GPL-3"
+SLOT="0"
+KEYWORDS="~amd64"
+
+IUSE="debug openmp test"
+RESTRICT="!test? ( test )"
+
+RDEPEND="
+	virtual/blas
+	virtual/lapack
+	virtual/mpi
+	sci-libs/scalapack
+	sys-cluster/openmpi
+	sci-libs/fftw:3.0[mpi,openmp?]"
+DEPEND="${RDEPEND}"
+BDEPEND="virtual/pkgconfig"
+
+FORTRAN_STANDARD=90
+
+pkg_setup() {
+	# Link in the GNU Fortran library for Fortran code.
+	# Other compilers may need other hacks.
+	FC_LIB=""
+	if [[ $(tc-getCC)$ == *gcc* ]]; then
+		FC_LIB="-lgfortran"
+	fi
+	export FC_LIB
+
+	export CC="mpicc"
+	export FC="mpif90"
+
+	if use openmp; then FORTRAN_NEED_OPENMP=1; fi
+
+	fortran-2_pkg_setup
+
+	if use openmp; then
+		# based on _fortran-has-openmp() of fortran-2.eclass
+		local code=ebuild-openmp-flags
+		local ret
+		local openmp
+
+		pushd "${T}"
+		cat <<- EOF > "${code}.c"
+		# include <omp.h>
+		main () {
+			int nthreads;
+			nthreads=omp_get_num_threads();
+		}
+		EOF
+
+		for openmp in -fopenmp -xopenmp -openmp -mp -omp -qsmp=omp; do
+			${CC} ${openmp} "${code}.c" -o "${code}.o" &>> "${T}"/_c_compile_test.log
+			ret=$?
+			(( ${ret} )) || break
+		done
+
+		rm "${code}."* || die
+		popd
+
+		if (( ${ret} )); then
+			die "Please switch to an openmp compatible C compiler"
+		else
+			export CC="${CC} ${openmp}"
+		fi
+
+		pushd "${T}"
+		cat <<- EOF > "${code}.f"
+		1     call omp_get_num_threads
+		2     end
+		EOF
+
+		for openmp in -fopenmp -xopenmp -openmp -mp -omp -qsmp=omp; do
+			${FC} ${openmp} "${code}.f" -o "${code}.o" &>> "${T}"/_f_compile_test.log
+			ret=$?
+			(( ${ret} )) || break
+		done
+
+		rm "${code}."* || die
+		popd
+
+		if (( ${ret} )); then
+			die "Please switch to an openmp compatible fortran compiler"
+		else
+			export FC="${FC} ${openmp}"
+		fi
+	fi
+
+}
+
+src_unpack() {
+	unpack "${PN}${PV//_*}.tar.gz"
+	# copy patched files to source
+	cd "${S}" || die
+	unpack "patch${PV//_*}.9.tar.gz"
+}
+
+src_configure() {
+	local FFTW_FLAVOUR=fftw3
+	if use openmp; then
+	   FFTW_FLAVOUR=fftw3_omp
+	   append-cflag -fopenmp
+	else
+	   append-cflag -Dnoomp
+	fi
+	append-cflag -Dkcomp
+	append-cflag -ffast-math
+	append-cflags $($(tc-getPKG_CONFIG) --cflags lapack)
+	append-cflags $($(tc-getPKG_CONFIG) --cflags scalapack)
+	append-cflags $($(tc-getPKG_CONFIG) --cflags openmpi)
+	append-cflags $($(tc-getPKG_CONFIG) --cflags ${FFTW_FLAVOUR})
+
+	append-fflags -I/usr/include
+	append-fflags -Dkcomp
+	append-fflags -ffast-math
+	append-fflags $($(tc-getPKG_CONFIG) --cflags lapack)
+	append-fflags $($(tc-getPKG_CONFIG) --cflags scalapack)
+	append-fflags $($(tc-getPKG_CONFIG) --cflags openmpi)
+	append-fflags $($(tc-getPKG_CONFIG) --cflags ${FFTW_FLAVOUR})
+
+	# otherwise we get Error: Rank mismatch between actual argument
+	# at (1) and actual argument at (2) (rank-1 and scalar)
+	append-fflags -fallow-argument-mismatch
+
+	local MX_LIB="$($(tc-getPKG_CONFIG) --static --libs lapack)"
+	MX_LIB="${MX_LIB} $($(tc-getPKG_CONFIG) --static --libs scalapack)"
+	MX_LIB="${MX_LIB} $($(tc-getPKG_CONFIG) --static --libs openmpi)"
+	MX_LIB="${MX_LIB} $($(tc-getPKG_CONFIG) --static --libs ${FFTW_FLAVOUR})"
+	MX_LIB="${MX_LIB} $(mpif90 -showme:link)"
+
+	sed \
+		-e "s%^CC *=.*$%CC  = ${CC} ${CFLAGS}%" \
+		-e "s%^FC *=.*$%FC  = ${FC} ${FCFLAGS}%" \
+		-e "s%^LIB *=.*$%LIB = ${MX_LIB} ${FC_LIB}%" \
+		-i makefile || die
+}
+
+src_compile() {
+	# does not properly parallelize
+	# file 1 says can't find file 2
+	# and at the same time file 2 can't find file 3
+	emake -j1
+}
+
+src_test() {
+	cd ../work || die
+	../source/openmx -runtest || die
+}
+
+src_install() {
+	insinto /usr/share/${P}
+	doins -r DFT_DATA19
+	cd ../work || die
+	insinto /usr/share/${P}/examples
+	doins -r *
+	cd ../source || die
+	emake DESTDIR="${D}/usr/bin" install
+	dodoc "${S}/${PN}${PV%.?}.pdf"
+	use test && dodoc "${S}"/work/runtest.result
+}
diff --git a/sci-physics/particle/Manifest b/sci-physics/particle/Manifest
new file mode 100644
index 000000000..2f92c548b
--- /dev/null
+++ b/sci-physics/particle/Manifest
@@ -0,0 +1,3 @@
+DIST particle-0.23.0.tar.gz 313512 BLAKE2B 33a0dc1cf612af8242b5080d0862f3b1e587254b46fa90f235cd6edba3919594c5077733600dfe88ad0959be889271c301324789abf0511a7fbe588942086877 SHA512 582c42beade0b28f28f3ee9f83f6d8cc75558f8a9aa5fbe3679c7aa68af40bd04f374741211d6f214bb828c24a017a89b541f780739a36d61d85a2fd5e00b530
+DIST particle-0.23.1.tar.gz 313729 BLAKE2B fc35163955e065b350dfa0825612a64214baeb1f5be41404af259136e6689e23419891513c059ccdfbe2cbf5891596fccd0b0b7f283031bb3352600b5be43441 SHA512 1b4f4516357fd9725d9d5b0a481467896e93e23a8956b2ce321b9cac1d200a8ee8dd9cc1b22d940b4708f29abe3417988677ac685b78287abe10afafa79fb381
+DIST particle-0.24.0.tar.gz 314302 BLAKE2B bbb2d52a80b4d9aafaf86a3cc1b28106253bf0edfe5a6127c03242a32973feaefeb32562063e5ff0438f5df946a905d03baa36c445093ce185d3be71c10e5135 SHA512 5a73079d9120ab509162189ba5992c615fc00e00d37a6556338130739bbf53fd5db01e973cb1b509ef7ce569021c0462ac77e5fcafe40df31e5cef0a89923a2a
diff --git a/sci-physics/particle/metadata.xml b/sci-physics/particle/metadata.xml
new file mode 100644
index 000000000..1ec9e9afb
--- /dev/null
+++ b/sci-physics/particle/metadata.xml
@@ -0,0 +1,19 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
+<pkgmetadata>
+	<maintainer type="project">
+		<email>sci@gentoo.org</email>
+		<name>Gentoo Science Project</name>
+	</maintainer>
+	<maintainer type="person">
+		<email>alexander@neuwirth-informatik.de</email>
+		<name>Alexander Puck Neuwirth</name>
+	</maintainer>
+	<longdescription lang="en">
+	Particle provides a pythonic interface to the Particle Data Group (PDG) particle data tables and particle identification codes, with extended particle information and extra goodies.
+	</longdescription>
+	<upstream>
+		<remote-id type="pypi">particle</remote-id>
+		<remote-id type="github">scikit-hep/particle</remote-id>
+	</upstream>
+</pkgmetadata>
diff --git a/sci-physics/particle/particle-0.23.0.ebuild b/sci-physics/particle/particle-0.23.0.ebuild
new file mode 100644
index 000000000..88da33c3e
--- /dev/null
+++ b/sci-physics/particle/particle-0.23.0.ebuild
@@ -0,0 +1,44 @@
+EAPI=8
+
+PYTHON_COMPAT=( python3_11 )
+DISTUTILS_USE_PEP517=hatchling
+inherit distutils-r1
+
+DESCRIPTION="PDG particle data and identification codes"
+HOMEPAGE="https://github.com/scikit-hep/particle"
+
+LICENSE="BSD"
+SLOT="0"
+
+if [[ ${PV} == 9999 ]]; then
+	inherit git-r3
+	EGIT_REPO_URI="https://github.com/scikit-hep/particle"
+else
+	inherit pypi
+	KEYWORDS="~amd64"
+fi
+
+RDEPEND="
+	>=dev-python/attrs-19.2[${PYTHON_USEDEP}]
+	>=sci-physics/hepunits-2.0.0[${PYTHON_USEDEP}]
+	dev-python/deprecated[${PYTHON_USEDEP}]
+"
+DEPEND="${RDEPEND}"
+BDEPEND="
+	test? (
+		>=dev-python/pytest-6.0.0[${PYTHON_USEDEP}]
+		dev-python/pandas[${PYTHON_USEDEP}]
+		dev-python/tabulate[${PYTHON_USEDEP}]
+	)
+"
+distutils_enable_tests pytest
+
+src_prepare() {
+	default
+
+	sed -i -e 's:--benchmark-disable::' pyproject.toml || die
+}
+
+python_test() {
+	epytest --ignore tests/particle/test_performance.py
+}
diff --git a/sci-physics/particle/particle-0.23.1.ebuild b/sci-physics/particle/particle-0.23.1.ebuild
new file mode 100644
index 000000000..43f1e67ca
--- /dev/null
+++ b/sci-physics/particle/particle-0.23.1.ebuild
@@ -0,0 +1,44 @@
+EAPI=8
+
+PYTHON_COMPAT=( python3_{11..12} )
+DISTUTILS_USE_PEP517=hatchling
+inherit distutils-r1
+
+DESCRIPTION="PDG particle data and identification codes"
+HOMEPAGE="https://github.com/scikit-hep/particle"
+
+LICENSE="BSD"
+SLOT="0"
+
+if [[ ${PV} == 9999 ]]; then
+	inherit git-r3
+	EGIT_REPO_URI="https://github.com/scikit-hep/particle"
+else
+	inherit pypi
+	KEYWORDS="~amd64"
+fi
+
+RDEPEND="
+	>=dev-python/attrs-19.2[${PYTHON_USEDEP}]
+	>=sci-physics/hepunits-2.0.0[${PYTHON_USEDEP}]
+	dev-python/deprecated[${PYTHON_USEDEP}]
+"
+DEPEND="${RDEPEND}"
+BDEPEND="
+	test? (
+		>=dev-python/pytest-6.0.0[${PYTHON_USEDEP}]
+		dev-python/pandas[${PYTHON_USEDEP}]
+		dev-python/tabulate[${PYTHON_USEDEP}]
+	)
+"
+distutils_enable_tests pytest
+
+src_prepare() {
+	default
+
+	sed -i -e 's:--benchmark-disable::' pyproject.toml || die
+}
+
+python_test() {
+	epytest --ignore tests/particle/test_performance.py
+}
diff --git a/sci-physics/particle/particle-0.24.0.ebuild b/sci-physics/particle/particle-0.24.0.ebuild
new file mode 100644
index 000000000..43f1e67ca
--- /dev/null
+++ b/sci-physics/particle/particle-0.24.0.ebuild
@@ -0,0 +1,44 @@
+EAPI=8
+
+PYTHON_COMPAT=( python3_{11..12} )
+DISTUTILS_USE_PEP517=hatchling
+inherit distutils-r1
+
+DESCRIPTION="PDG particle data and identification codes"
+HOMEPAGE="https://github.com/scikit-hep/particle"
+
+LICENSE="BSD"
+SLOT="0"
+
+if [[ ${PV} == 9999 ]]; then
+	inherit git-r3
+	EGIT_REPO_URI="https://github.com/scikit-hep/particle"
+else
+	inherit pypi
+	KEYWORDS="~amd64"
+fi
+
+RDEPEND="
+	>=dev-python/attrs-19.2[${PYTHON_USEDEP}]
+	>=sci-physics/hepunits-2.0.0[${PYTHON_USEDEP}]
+	dev-python/deprecated[${PYTHON_USEDEP}]
+"
+DEPEND="${RDEPEND}"
+BDEPEND="
+	test? (
+		>=dev-python/pytest-6.0.0[${PYTHON_USEDEP}]
+		dev-python/pandas[${PYTHON_USEDEP}]
+		dev-python/tabulate[${PYTHON_USEDEP}]
+	)
+"
+distutils_enable_tests pytest
+
+src_prepare() {
+	default
+
+	sed -i -e 's:--benchmark-disable::' pyproject.toml || die
+}
+
+python_test() {
+	epytest --ignore tests/particle/test_performance.py
+}
diff --git a/sci-physics/particle/particle-9999.ebuild b/sci-physics/particle/particle-9999.ebuild
new file mode 100644
index 000000000..43f1e67ca
--- /dev/null
+++ b/sci-physics/particle/particle-9999.ebuild
@@ -0,0 +1,44 @@
+EAPI=8
+
+PYTHON_COMPAT=( python3_{11..12} )
+DISTUTILS_USE_PEP517=hatchling
+inherit distutils-r1
+
+DESCRIPTION="PDG particle data and identification codes"
+HOMEPAGE="https://github.com/scikit-hep/particle"
+
+LICENSE="BSD"
+SLOT="0"
+
+if [[ ${PV} == 9999 ]]; then
+	inherit git-r3
+	EGIT_REPO_URI="https://github.com/scikit-hep/particle"
+else
+	inherit pypi
+	KEYWORDS="~amd64"
+fi
+
+RDEPEND="
+	>=dev-python/attrs-19.2[${PYTHON_USEDEP}]
+	>=sci-physics/hepunits-2.0.0[${PYTHON_USEDEP}]
+	dev-python/deprecated[${PYTHON_USEDEP}]
+"
+DEPEND="${RDEPEND}"
+BDEPEND="
+	test? (
+		>=dev-python/pytest-6.0.0[${PYTHON_USEDEP}]
+		dev-python/pandas[${PYTHON_USEDEP}]
+		dev-python/tabulate[${PYTHON_USEDEP}]
+	)
+"
+distutils_enable_tests pytest
+
+src_prepare() {
+	default
+
+	sed -i -e 's:--benchmark-disable::' pyproject.toml || die
+}
+
+python_test() {
+	epytest --ignore tests/particle/test_performance.py
+}
diff --git a/sci-physics/pyhepmc/Manifest b/sci-physics/pyhepmc/Manifest
new file mode 100644
index 000000000..1351fa866
--- /dev/null
+++ b/sci-physics/pyhepmc/Manifest
@@ -0,0 +1 @@
+DIST pyhepmc-2.11.0.tar.gz 361596 BLAKE2B 18264f61bdef3c27f8aa4d48d25257c03f98cc89745533641119cf7ba6d5fe36c084d25ccaeed6769dc9226fd5f2c27060006030447a8ac8409ff6d752437d2c SHA512 31975d0bee5037c1cc36753ce6324342ed6a48b2d3f91f53d61f445f38f0fa3ecbeb0e29fcbc7f6778bafcc23c1f6a689b9516eae8da4cc620cd7c72b89e0b00
diff --git a/sci-physics/pyhepmc/metadata.xml b/sci-physics/pyhepmc/metadata.xml
new file mode 100644
index 000000000..6f6a9a0bb
--- /dev/null
+++ b/sci-physics/pyhepmc/metadata.xml
@@ -0,0 +1,19 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
+<pkgmetadata>
+	<maintainer type="project">
+		<email>sci@gentoo.org</email>
+		<name>Gentoo Science Project</name>
+	</maintainer>
+	<maintainer type="person">
+		<email>alexander@neuwirth-informatik.de</email>
+		<name>Alexander Puck Neuwirth</name>
+	</maintainer>
+	<longdescription lang="en">
+	pyhepmc largely mirrors the C++ interface of the HepMC3 library, which is documented here. Parts of the documentation have been copied from HepMC3. Documentation is available as Python docstrings, so you can use Python's help() browser to learn about the API. Alternatively, you can consult the online reference generated from these docstrings which includes some examples.
+	</longdescription>
+	<upstream>
+		<remote-id type="pypi">pyhepmc</remote-id>
+		<remote-id type="github">scikit-hep/pyhepmc</remote-id>
+	</upstream>
+</pkgmetadata>
diff --git a/sci-physics/pyhepmc/pyhepmc-2.11.0.ebuild b/sci-physics/pyhepmc/pyhepmc-2.11.0.ebuild
new file mode 100644
index 000000000..c28b094bb
--- /dev/null
+++ b/sci-physics/pyhepmc/pyhepmc-2.11.0.ebuild
@@ -0,0 +1,20 @@
+EAPI=8
+
+PYTHON_COMPAT=( python3_{10..12} )
+DISTUTILS_USE_PEP517=setuptools
+inherit distutils-r1 pypi
+
+DESCRIPTION="A Pythonic wrapper for the HepMC3 C++ library."
+HOMEPAGE="https://github.com/scikit-hep/pyhepmc"
+
+LICENSE="MIT"
+SLOT="0"
+KEYWORDS="~amd64"
+
+RDEPEND="
+	>=dev-python/numpy-1.0[${PYTHON_USEDEP}]
+"
+BDEPEND="
+        ${RDEPEND}
+        dev-build/cmake
+"
diff --git a/sci-physics/pyhf/Manifest b/sci-physics/pyhf/Manifest
new file mode 100644
index 000000000..3155872d4
--- /dev/null
+++ b/sci-physics/pyhf/Manifest
@@ -0,0 +1,2 @@
+DIST pyhf-0.7.3.tar.gz 113423 BLAKE2B 216ef186c539481e2819e3f3a198203f085aa99652ab335b1153309a780857c5ad53bc848bb1b12615cfa9b8ee97a67553cef5a0f899bbcf178bfea1b2ca11c5 SHA512 904491f9c161f0231d1e109cfa3a12b31a31b1aa7477752e1eafd1e6c4cec75551e53ce1f6d447bed8f295371dc20b032888a5175af0f2eb808e03c0a8993930
+DIST pyhf-0.7.5.tar.gz 113812 BLAKE2B 747dc59de4e80d883145dd6b5643507c6faca2c1cb53b2aaea93cfcf31ed474ed3807f9f5a79d45f49a330f9c6260d5373e8134be814b07e1a1ae161844ad960 SHA512 83a5e02d7278e3e835ecf49d5b01fd6614923bf5e80d58ec2a96da89a67ad80bcdad4be90b598d314caf83a293c3bb69c3e995c292c0b62ef109662c061d91e8
diff --git a/sci-physics/pyhf/metadata.xml b/sci-physics/pyhf/metadata.xml
new file mode 100644
index 000000000..47738d1db
--- /dev/null
+++ b/sci-physics/pyhf/metadata.xml
@@ -0,0 +1,18 @@
+<?xml version="1.0" encoding="UTF-8"?> <!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
+<pkgmetadata>
+	<maintainer type="project">
+		<email>sci@gentoo.org</email>
+		<name>Gentoo Science Project</name>
+	</maintainer>
+	<maintainer type="person">
+		<email>alexander@neuwirth-informatik.de</email>
+		<name>Alexander Puck Neuwirth</name>
+	</maintainer>
+	<longdescription lang="en">
+	The HistFactory p.d.f. template [CERN-OPEN-2012-016] is per-se independent of its implementation in ROOT and sometimes, it’s useful to be able to run statistical analysis outside of ROOT, RooFit, RooStats framework.
+	</longdescription>
+	<upstream>
+		<remote-id type="pypi">particle</remote-id>
+		<remote-id type="github">scikit-hep/particle</remote-id>
+	</upstream>
+</pkgmetadata>
diff --git a/sci-physics/pyhf/pyhf-0.7.3.ebuild b/sci-physics/pyhf/pyhf-0.7.3.ebuild
new file mode 100644
index 000000000..d97cd71f9
--- /dev/null
+++ b/sci-physics/pyhf/pyhf-0.7.3.ebuild
@@ -0,0 +1,35 @@
+# Copyright 2023 Gentoo Authors
+# Distributed under the terms of the GNU General Public License v2
+
+EAPI=8
+
+PYTHON_COMPAT=( python3_11 )
+DISTUTILS_USE_PEP517=hatchling
+
+inherit distutils-r1 pypi
+
+DESCRIPTION="pure-python fitting/limit-setting/interval estimation HistFactory-style"
+HOMEPAGE="
+	https://github.com/scikit-hep/pyhf
+	https://doi.org/10.5281/zenodo.1169739
+	https://zenodo.org/record/8256635
+	https://doi.org/10.21105/joss.02823
+	https://inspirehep.net/literature/2598491
+	https://arxiv.org/abs/2211.15838
+	https://doi.org/10.22323/1.414.0245
+"
+
+LICENSE="BSD"
+SLOT="0"
+KEYWORDS="~amd64"
+
+RDEPEND="
+	dev-python/numpy[${PYTHON_USEDEP}]
+	>=dev-python/scipy-1.5.1[${PYTHON_USEDEP}]
+	>=dev-python/pyyaml-5.1[${PYTHON_USEDEP}]
+	>=dev-python/tqdm-4.56.0[${PYTHON_USEDEP}]
+	>=dev-python/jsonschema-4.15.0[${PYTHON_USEDEP}]
+	>=dev-python/jsonpatch-1.15[${PYTHON_USEDEP}]
+	>=dev-python/click-8.0.0[${PYTHON_USEDEP}]
+"
+DEPEND="${RDEPEND}"
diff --git a/sci-physics/pyhf/pyhf-0.7.5.ebuild b/sci-physics/pyhf/pyhf-0.7.5.ebuild
new file mode 100644
index 000000000..22a36af7f
--- /dev/null
+++ b/sci-physics/pyhf/pyhf-0.7.5.ebuild
@@ -0,0 +1,37 @@
+# Copyright 2023 Gentoo Authors
+# Distributed under the terms of the GNU General Public License v2
+
+EAPI=8
+
+PYTHON_COMPAT=( python3_{11..12} )
+DISTUTILS_USE_PEP517=hatchling
+
+inherit distutils-r1 pypi
+
+DESCRIPTION="pure-python fitting/limit-setting/interval estimation HistFactory-style"
+HOMEPAGE="
+	https://github.com/scikit-hep/pyhf
+	https://doi.org/10.5281/zenodo.1169739
+	https://zenodo.org/record/8256635
+	https://doi.org/10.21105/joss.02823
+	https://inspirehep.net/literature/2598491
+	https://arxiv.org/abs/2211.15838
+	https://doi.org/10.22323/1.414.0245
+"
+
+LICENSE="BSD"
+SLOT="0"
+KEYWORDS="~amd64"
+# test needs missing scrapbook papermill pydocstyle ...
+RESTRICT="test"
+
+RDEPEND="
+	>=dev-python/click-8.0.0[${PYTHON_USEDEP}]
+	>=dev-python/jsonpatch-1.15[${PYTHON_USEDEP}]
+	>=dev-python/jsonschema-4.15.0[${PYTHON_USEDEP}]
+	>=dev-python/pyyaml-5.1[${PYTHON_USEDEP}]
+	>=dev-python/scipy-1.5.2[${PYTHON_USEDEP}]
+	>=dev-python/tqdm-4.56.0[${PYTHON_USEDEP}]
+	dev-python/numpy[${PYTHON_USEDEP}]
+"
+DEPEND="${RDEPEND}"
diff --git a/sci-physics/pylhe/Manifest b/sci-physics/pylhe/Manifest
new file mode 100644
index 000000000..11dbc6d26
--- /dev/null
+++ b/sci-physics/pylhe/Manifest
@@ -0,0 +1,2 @@
+DIST pylhe-0.7.0.gh.tar.gz 140203 BLAKE2B 6c167b37bb6c978752de79586e4f655169b5134c6cd7637807e649323ebaca50d8a360b1ca32eeff2cc162efe5e13d7de92f72d5a9263a7b2c48a5b87b7b919c SHA512 1a338ab4e1c5dd1d8d80e4a03ad84eb59f19ebb151a4b1393b68ee6ecade920c88db6cb940d56bd1f238e833f59b266507ab678124ea49b4086fe05b7f9baa88
+DIST pylhe-0.8.0.gh.tar.gz 144541 BLAKE2B 5c6a6511acd1adefad6bf3769fdb5ac2a528a8cc939bb1209d7fd4dc31eef9060d129c330b34e3cfc7b640c9b82f68f043e4604f3a535865240ceda0a33dd691 SHA512 6fc3c525cbb5f2ebe8678d1e03940fde8bdc837f1da6a667c70069584de476ea73c72e817cc84637e018ca7cf21e8bb0f7b2721fe54ef78a9b0eee7900ec400e
diff --git a/sci-physics/pylhe/files/pylhe-0.7.0-coverage.patch b/sci-physics/pylhe/files/pylhe-0.7.0-coverage.patch
new file mode 100644
index 000000000..ea678ce8c
--- /dev/null
+++ b/sci-physics/pylhe/files/pylhe-0.7.0-coverage.patch
@@ -0,0 +1,8 @@
+--- a/pytest.ini	2024-03-20 07:36:32.600030197 +0100
++++ b/pytest.ini	2024-03-20 07:36:45.896874886 +0100
+@@ -1,4 +1,4 @@
+ [pytest]
+ docstyle_convention = numpy
+ junit_family = xunit2
+-addopts = --ignore=setup.py --ignore=binder/ --ignore=docs/ --cov=pylhe --cov-report=term-missing --cov-config=.coveragerc --cov-report xml --doctest-modules --doctest-glob='*.rst'
++addopts = --ignore=setup.py --ignore=binder/ --ignore=docs/ --doctest-modules --doctest-glob='*.rst'
diff --git a/sci-physics/pylhe/metadata.xml b/sci-physics/pylhe/metadata.xml
new file mode 100644
index 000000000..86ede8deb
--- /dev/null
+++ b/sci-physics/pylhe/metadata.xml
@@ -0,0 +1,19 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
+<pkgmetadata>
+	<maintainer type="project">
+		<email>sci@gentoo.org</email>
+		<name>Gentoo Science Project</name>
+	</maintainer>
+	<maintainer type="person">
+		<email>alexander@neuwirth-informatik.de</email>
+		<name>Alexander Puck Neuwirth</name>
+	</maintainer>
+	<longdescription lang="en">
+	Small and thin Python interface to read Les Houches Event (LHE) files.
+	</longdescription>
+	<upstream>
+		<remote-id type="pypi">pylhe</remote-id>
+		<remote-id type="github">scikit-hep/pylhe</remote-id>
+	</upstream>
+</pkgmetadata>
diff --git a/sci-physics/pylhe/pylhe-0.7.0.ebuild b/sci-physics/pylhe/pylhe-0.7.0.ebuild
new file mode 100644
index 000000000..45ef91695
--- /dev/null
+++ b/sci-physics/pylhe/pylhe-0.7.0.ebuild
@@ -0,0 +1,35 @@
+EAPI=8
+
+PYTHON_COMPAT=( python3_{11..12} )
+DISTUTILS_USE_PEP517=setuptools
+inherit distutils-r1 pypi
+
+DESCRIPTION="Lightweight Python interface to read Les Houches Event (LHE) files"
+HOMEPAGE="https://github.com/scikit-hep/pylhe"
+# pypi does not include tests
+SRC_URI="https://github.com/scikit-hep/${PN}/archive/refs/tags/v${PV}.tar.gz -> ${P}.gh.tar.gz"
+# export is needed here!
+export SETUPTOOLS_SCM_PRETEND_VERSION=${PV}
+
+LICENSE="Apache-2.0"
+SLOT="0"
+KEYWORDS="~amd64"
+
+RDEPEND="
+	>=dev-python/graphviz-0.12.0[${PYTHON_USEDEP}]
+	>=sci-physics/particle-0.16[${PYTHON_USEDEP}]
+	>=dev-python/awkward-1.2.0[${PYTHON_USEDEP}]
+	>=dev-python/vector-0.8.1[${PYTHON_USEDEP}]
+"
+DEPEND="${RDEPEND}"
+BDEPEND="
+	dev-python/setuptools-scm[${PYTHON_USEDEP}]
+	test? (
+		>=sci-physics/scikit-hep-testdata-0.4.36[${PYTHON_USEDEP}]
+	)
+"
+PATCHES=(
+	"${FILESDIR}/${PN}"-0.7.0-coverage.patch
+)
+
+distutils_enable_tests pytest
diff --git a/sci-physics/pylhe/pylhe-0.8.0.ebuild b/sci-physics/pylhe/pylhe-0.8.0.ebuild
new file mode 100644
index 000000000..45ef91695
--- /dev/null
+++ b/sci-physics/pylhe/pylhe-0.8.0.ebuild
@@ -0,0 +1,35 @@
+EAPI=8
+
+PYTHON_COMPAT=( python3_{11..12} )
+DISTUTILS_USE_PEP517=setuptools
+inherit distutils-r1 pypi
+
+DESCRIPTION="Lightweight Python interface to read Les Houches Event (LHE) files"
+HOMEPAGE="https://github.com/scikit-hep/pylhe"
+# pypi does not include tests
+SRC_URI="https://github.com/scikit-hep/${PN}/archive/refs/tags/v${PV}.tar.gz -> ${P}.gh.tar.gz"
+# export is needed here!
+export SETUPTOOLS_SCM_PRETEND_VERSION=${PV}
+
+LICENSE="Apache-2.0"
+SLOT="0"
+KEYWORDS="~amd64"
+
+RDEPEND="
+	>=dev-python/graphviz-0.12.0[${PYTHON_USEDEP}]
+	>=sci-physics/particle-0.16[${PYTHON_USEDEP}]
+	>=dev-python/awkward-1.2.0[${PYTHON_USEDEP}]
+	>=dev-python/vector-0.8.1[${PYTHON_USEDEP}]
+"
+DEPEND="${RDEPEND}"
+BDEPEND="
+	dev-python/setuptools-scm[${PYTHON_USEDEP}]
+	test? (
+		>=sci-physics/scikit-hep-testdata-0.4.36[${PYTHON_USEDEP}]
+	)
+"
+PATCHES=(
+	"${FILESDIR}/${PN}"-0.7.0-coverage.patch
+)
+
+distutils_enable_tests pytest
diff --git a/sci-physics/qcdloop/Manifest b/sci-physics/qcdloop/Manifest
new file mode 100644
index 000000000..84ca31226
--- /dev/null
+++ b/sci-physics/qcdloop/Manifest
@@ -0,0 +1,2 @@
+DIST qcdloop-2.0.5.tar.gz 199141 BLAKE2B b16c193bd267b838535a572dd3b1cf50ac9af03b65347877b550bcbdcc9cfdd42f08e198732c513cff8298632ea65be82f2986701de75cee80cec2f9c30e3368 SHA512 9bfa3bad7a8c808b2db5eda32a755da4dadf67eba10845eb798d447fd47062bd40aa877929b60d95ec6b4e3b4a2cbba6384a3d1b13f92cfdec06e76177532c0f
+DIST qcdloop-2.0.9.tar.gz 214697 BLAKE2B 19d426cc61b8a8f08fc56522b5a2d48c7fea7027225e1317c2e2908b8a87367ff69077bfe5508ee50ee585d8d0f68ae4c1fdad312b4cbc73ca4f3fd735fa94c9 SHA512 c8031dbee1c83d2bd0fcca0b1d94f18e7d07b77c247ca7a15cfec9bc402391e89036a64507c48e743eeecb3a19fe25d4e766ff13ede9f042d4d723adc8adb238
diff --git a/sci-physics/qcdloop/files/qcdloop-2.0.5-cxx.patch b/sci-physics/qcdloop/files/qcdloop-2.0.5-cxx.patch
new file mode 100644
index 000000000..56a665de2
--- /dev/null
+++ b/sci-physics/qcdloop/files/qcdloop-2.0.5-cxx.patch
@@ -0,0 +1,11 @@
+--- a/CMakeLists.txt	2022-09-19 11:13:08.777453946 +0200
++++ b/CMakeLists.txt	2022-09-19 11:13:27.315507011 +0200
+@@ -20,7 +20,7 @@
+ set(CMAKE_CXX_STANDARD_REQUIRED ON)
+ set(CMAKE_CXX_EXTENSIONS OFF)
+ set(VERSION "\"2.0.5\"")
+-set(CMAKE_CXX_FLAGS "-Wall -Wextra -march=nocona -mtune=haswell -fvisibility-inlines-hidden -fmessage-length=0 -ftree-vectorize -fPIC -fstack-protector-strong -O2 -pipe -fext-numeric-literals")
++set(CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} -fext-numeric-literals")
+ set(CMAKE_CXX_FLAGS_DEBUG "${CMAKE_CXX_FLAGS_DEBUG} -fsanitize=address -fPIC ${CMAKE_CXX_FLAGS}" CACHE STRING "debug compile flags" FORCE)
+ set(CMAKE_EXE_LINKER_FLAGS_DEBUG "-fsanitize=address" CACHE STRING "debug linker flags" FORCE)
+ set(prefix ${CMAKE_INSTALL_PREFIX})
diff --git a/sci-physics/qcdloop/files/qcdloop-2.0.9-cxx.patch b/sci-physics/qcdloop/files/qcdloop-2.0.9-cxx.patch
new file mode 100644
index 000000000..b3babf764
--- /dev/null
+++ b/sci-physics/qcdloop/files/qcdloop-2.0.9-cxx.patch
@@ -0,0 +1,11 @@
+--- a/CMakeLists.txt	2022-09-19 11:13:08.777453946 +0200
++++ b/CMakeLists.txt	2022-09-19 11:13:27.315507011 +0200
+@@ -20,7 +20,7 @@
+ set(CMAKE_CXX_STANDARD_REQUIRED ON)
+ set(CMAKE_CXX_EXTENSIONS OFF)
+ set(VERSION "\"2.0.9\"")
+-set(CMAKE_CXX_FLAGS "-Wall -Wextra -march=nocona -mtune=haswell -fvisibility-inlines-hidden -fmessage-length=0 -ftree-vectorize -fPIC -fstack-protector-strong -O2 -pipe -fext-numeric-literals")
++set(CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} -fext-numeric-literals")
+ set(CMAKE_CXX_FLAGS_DEBUG "${CMAKE_CXX_FLAGS_DEBUG} -fsanitize=address -fPIC ${CMAKE_CXX_FLAGS}" CACHE STRING "debug compile flags" FORCE)
+ set(CMAKE_EXE_LINKER_FLAGS_DEBUG "-fsanitize=address" CACHE STRING "debug linker flags" FORCE)
+ set(prefix ${CMAKE_INSTALL_PREFIX})
diff --git a/sci-physics/qcdloop/metadata.xml b/sci-physics/qcdloop/metadata.xml
new file mode 100644
index 000000000..84c79dc3b
--- /dev/null
+++ b/sci-physics/qcdloop/metadata.xml
@@ -0,0 +1,18 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
+<pkgmetadata>
+	<maintainer type="person">
+		<email>alexander@neuwirth-informatik.de</email>
+		<name>Alexander Puck Neuwirth</name>
+	</maintainer>
+	<maintainer type="project">
+		<email>sci-physics@gentoo.org</email>
+		<name>Gentoo Physics Project</name>
+	</maintainer>
+	<longdescription lang="en">
+	QCDLoop is a library of one-loop scalar Feynman integrals, evaluated close to four dimensions. First documented in arXiv:0712.1851 and recently in arXiv:1605.03181.
+	</longdescription>
+	<upstream>
+		<remote-id type="github">scarrazza/qcdloop</remote-id>
+	</upstream>
+</pkgmetadata>
diff --git a/sci-physics/qcdloop/qcdloop-2.0.5.ebuild b/sci-physics/qcdloop/qcdloop-2.0.5.ebuild
new file mode 100644
index 000000000..672957c56
--- /dev/null
+++ b/sci-physics/qcdloop/qcdloop-2.0.5.ebuild
@@ -0,0 +1,27 @@
+# Copyright 2022 Gentoo Authors
+# Distributed under the terms of the GNU General Public License v2
+
+EAPI=8
+
+CMAKE_MAKEFILE_GENERATOR="emake"
+
+inherit cmake fortran-2
+
+DESCRIPTION="An object-oriented one-loop scalar Feynman integrals framework"
+HOMEPAGE="https://qcdloop.web.cern.ch/qcdloop/"
+SRC_URI="https://github.com/scarrazza/${PN}/archive/refs/tags/${PV}.tar.gz -> ${P}.tar.gz"
+
+LICENSE="GPL-3+"
+SLOT="0"
+KEYWORDS="~amd64"
+
+PATCHES=(
+	"${FILESDIR}"/${P}-cxx.patch
+)
+
+src_configure() {
+	local mycmakeargs=(
+		-DCMAKE_INSTALL_PREFIX="${ESYSROOT}/usr/$(get_libdir)"
+	)
+	cmake_src_configure
+}
diff --git a/sci-physics/qcdloop/qcdloop-2.0.9.ebuild b/sci-physics/qcdloop/qcdloop-2.0.9.ebuild
new file mode 100644
index 000000000..6486e70b9
--- /dev/null
+++ b/sci-physics/qcdloop/qcdloop-2.0.9.ebuild
@@ -0,0 +1,44 @@
+# Copyright 2022 Gentoo Authors
+# Distributed under the terms of the GNU General Public License v2
+
+EAPI=8
+
+CMAKE_MAKEFILE_GENERATOR="emake"
+
+inherit cmake fortran-2
+
+DESCRIPTION="An object-oriented one-loop scalar Feynman integrals framework"
+HOMEPAGE="https://qcdloop.web.cern.ch/qcdloop/"
+SRC_URI="https://github.com/scarrazza/${PN}/archive/refs/tags/${PV}.tar.gz -> ${P}.tar.gz"
+
+LICENSE="GPL-3+"
+SLOT="0"
+KEYWORDS="~amd64"
+
+PATCHES=(
+	"${FILESDIR}"/${P}-cxx.patch
+)
+
+src_prepare() {
+	cmake_src_prepare
+
+	# gentoo libdir love
+	sed -i \
+		-e '/DESTINATION/s/lib/lib${LIB_SUFFIX}/g' \
+		CMakeLists.txt || die
+	sed -i \
+		-e '/libdir.*/s/lib/lib${LIB_SUFFIX}/g' \
+		CMakeLists.txt || die
+
+	#sed -i \
+	#	-e '/qcdloop/s/SHARED/STATIC/g' \
+	#	CMakeLists.txt || die
+}
+
+src_configure() {
+	local mycmakeargs=(
+		-DCMAKE_INSTALL_PREFIX="${ESYSROOT}"/usr
+		-DENABLE_FORTRAN_WRAPPER=ON
+	)
+	cmake_src_configure
+}
diff --git a/sci-physics/qgraf/Manifest b/sci-physics/qgraf/Manifest
new file mode 100644
index 000000000..32519be3c
--- /dev/null
+++ b/sci-physics/qgraf/Manifest
@@ -0,0 +1,3 @@
+DIST qgraf-3.4.2.tgz 358979 BLAKE2B 06c5cf82faab531d6d17387d62e80b2e395ad0ffd80a69dc49608588f4acdf23d226877db047d3906963b5f64d85329665fed0e10359ddbb649122fb328b78f8 SHA512 e86f94480eaf7cd0b4d79b60ec1420c21f0285133f2184d1c0a1d05ec0d9abc3e483d100d43c38fafc06bf8cecea413c0304adcb64d900522e877b1a24e7b61b
+DIST qgraf-3.5.2.tgz 426930 BLAKE2B 0bd50cbefee9a91cdfe9a15a53fb018c1b15088b211a03dde63f08410bbac4acd7586ef4cece17debd5197d3d5b7a8c889aeec27d7f3f137df7ef95f1687a709 SHA512 1e1fbafc80c60a663537a5ca555f405ec1517beccf09e2f68fcd9c84963b4b20d3a66e77980c4c4ff68f82950dc41f4492dc0272fdf5e3c105861fcf4c0e8c80
+DIST qgraf-3.6.7.tgz 460592 BLAKE2B d4275d7e5b9138eab3a2848b1e75883a4d52b61bdddd2ecbefe674559a56d9315bb03bd86c5a607f01d708c634f35b180f4cfde99242e65a40bf3f81ce6fa9e3 SHA512 c721eb82975a6077da77a82f7875d0e0346e21932d0312109d1bab68391a0210fc3f7ff79327d515668dedee0c5fce4e01d7433177232c43a4e39d8204f01405
diff --git a/sci-physics/qgraf/metadata.xml b/sci-physics/qgraf/metadata.xml
new file mode 100644
index 000000000..3fa7c9624
--- /dev/null
+++ b/sci-physics/qgraf/metadata.xml
@@ -0,0 +1,15 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<!DOCTYPE pkgmetadata SYSTEM "https://www.gentoo.org/dtd/metadata.dtd">
+<pkgmetadata>
+  <maintainer type="person">
+    <email>alexander@neuwirth-informatik.de</email>
+    <name>Alexander Puck Neuwirth</name>
+  </maintainer>
+  <maintainer type="project" proxied="proxy">
+    <email>sci-physics@gentoo.org</email>
+    <name>Gentoo Physics Project</name>
+  </maintainer>
+  <longdescription lang="en">
+    Qgraf is a computer program that generates Feynman diagrams for various types of QFT models — it is a research tool created with the obvious aim of contributing to extend the range of feasible, perturbative QFT calculations. It generates neither 0-point nor non-connected diagrams, though. Diagrams are represented by symbolic expressions only; nevertheless, if some kind of graphical representation is required, have a look at the external links.
+  </longdescription>
+</pkgmetadata>
diff --git a/sci-physics/qgraf/qgraf-3.4.2.ebuild b/sci-physics/qgraf/qgraf-3.4.2.ebuild
new file mode 100644
index 000000000..cdab94002
--- /dev/null
+++ b/sci-physics/qgraf/qgraf-3.4.2.ebuild
@@ -0,0 +1,32 @@
+# Copyright 2022 Gentoo Authors
+# Distributed under the terms of the GNU General Public License v2
+
+EAPI=8
+
+inherit toolchain-funcs fortran-2
+
+DESCRIPTION="qgraf generates Feynman diagrams for various types of QFT models"
+HOMEPAGE="http://cfif.ist.utl.pt/~paulo/qgraf.html"
+SRC_URI="http://anonymous:anonymous@qgraf.tecnico.ulisboa.pt/v$(ver_cut 1-2)/qgraf-${PV}.tgz"
+S="${WORKDIR}"
+
+LICENSE="all-rights-reserved"
+RESTRICT="bindist mirror"
+SLOT="0"
+KEYWORDS="~amd64"
+IUSE="doc examples"
+
+src_compile() {
+	$(tc-getFC) ${P}.f -o ${PN} ${FFLAGS} ${LDFLAGS} || die "Failed to compile"
+}
+
+src_install() {
+	dobin ${PN}
+
+	use doc && dodoc *.pdf
+	if use examples; then
+		docinto examples
+		dodoc phi3 qed qcd *.sty *.dat
+		docompress -x /usr/share/doc/${PF}/examples
+	fi
+}
diff --git a/sci-physics/qgraf/qgraf-3.5.2.ebuild b/sci-physics/qgraf/qgraf-3.5.2.ebuild
new file mode 100644
index 000000000..4194295a4
--- /dev/null
+++ b/sci-physics/qgraf/qgraf-3.5.2.ebuild
@@ -0,0 +1,32 @@
+# Copyright 2022 Gentoo Authors
+# Distributed under the terms of the GNU General Public License v2
+
+EAPI=8
+
+inherit toolchain-funcs fortran-2
+
+DESCRIPTION="qgraf generates Feynman diagrams for various types of QFT models"
+HOMEPAGE="http://cfif.ist.utl.pt/~paulo/qgraf.html"
+SRC_URI="http://anonymous:anonymous@qgraf.tecnico.ulisboa.pt/v$(ver_cut 1-2)/qgraf-${PV}.tgz"
+S="${WORKDIR}"
+
+LICENSE="all-rights-reserved"
+RESTRICT="bindist mirror"
+SLOT="0"
+KEYWORDS="~amd64"
+IUSE="doc examples"
+
+src_compile() {
+	$(tc-getFC) ${P}.f08 -o ${PN} ${FFLAGS} ${LDFLAGS} || die "Failed to compile"
+}
+
+src_install() {
+	dobin ${PN}
+
+	use doc && dodoc *.pdf
+	if use examples; then
+		docinto examples
+		dodoc phi3 qed qcd *.sty *.dat
+		docompress -x /usr/share/doc/${PF}/examples
+	fi
+}
diff --git a/sci-physics/qgraf/qgraf-3.6.7.ebuild b/sci-physics/qgraf/qgraf-3.6.7.ebuild
new file mode 100644
index 000000000..4194295a4
--- /dev/null
+++ b/sci-physics/qgraf/qgraf-3.6.7.ebuild
@@ -0,0 +1,32 @@
+# Copyright 2022 Gentoo Authors
+# Distributed under the terms of the GNU General Public License v2
+
+EAPI=8
+
+inherit toolchain-funcs fortran-2
+
+DESCRIPTION="qgraf generates Feynman diagrams for various types of QFT models"
+HOMEPAGE="http://cfif.ist.utl.pt/~paulo/qgraf.html"
+SRC_URI="http://anonymous:anonymous@qgraf.tecnico.ulisboa.pt/v$(ver_cut 1-2)/qgraf-${PV}.tgz"
+S="${WORKDIR}"
+
+LICENSE="all-rights-reserved"
+RESTRICT="bindist mirror"
+SLOT="0"
+KEYWORDS="~amd64"
+IUSE="doc examples"
+
+src_compile() {
+	$(tc-getFC) ${P}.f08 -o ${PN} ${FFLAGS} ${LDFLAGS} || die "Failed to compile"
+}
+
+src_install() {
+	dobin ${PN}
+
+	use doc && dodoc *.pdf
+	if use examples; then
+		docinto examples
+		dodoc phi3 qed qcd *.sty *.dat
+		docompress -x /usr/share/doc/${PF}/examples
+	fi
+}
diff --git a/sci-physics/quinoa/metadata.xml b/sci-physics/quinoa/metadata.xml
deleted file mode 100644
index 2e043b786..000000000
--- a/sci-physics/quinoa/metadata.xml
+++ /dev/null
@@ -1,12 +0,0 @@
-<?xml version="1.0" encoding="UTF-8"?>
-<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
-<pkgmetadata>
-	<maintainer type="person">
-		<email>junghans@gentoo.org</email>
-		<name>Christoph Junghans</name>
-	</maintainer>
-	<maintainer type="project">
-		<email>sci-physics@gentoo.org</email>
-		<name>Gentoo Physics Project</name>
-	</maintainer>
-</pkgmetadata>
diff --git a/sci-physics/quinoa/quinoa-9999.ebuild b/sci-physics/quinoa/quinoa-9999.ebuild
deleted file mode 100644
index 68b4e20b2..000000000
--- a/sci-physics/quinoa/quinoa-9999.ebuild
+++ /dev/null
@@ -1,32 +0,0 @@
-# Copyright 1999-2017 Gentoo Foundation
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=6
-
-inherit cmake-utils git-r3
-
-DESCRIPTION="Adaptive computational fluid dynamics"
-HOMEPAGE="http://quinoacomputing.org/"
-EGIT_REPO_URI="git://github.com/quinoacomputing/${PN}.git https://github.com/quinoacomputing/${PN}.git"
-
-LICENSE="BSD"
-SLOT="0"
-KEYWORDS=""
-IUSE="test"
-
-DEPEND=">=sci-libs/trilinos-12.10.1[netcdf]
-	sci-libs/h5part
-	>=sys-cluster/charm-6.7.1[mpi]
-	dev-libs/boost
-	dev-libs/boost-mpl-cartesian_product
-	dev-libs/tut
-	dev-libs/pugixml
-	dev-cpp/pstreams
-	sci-libs/hypre[mpi]
-	>=dev-libs/pegtl-2
-	dev-cpp/random123
-	virtual/lapacke
-	dev-util/mad-numdiff"
-RDEPEND="${DEPEND}"
-
-CMAKE_USE_DIR="${S}/src"
diff --git a/sci-physics/scikit-hep-testdata/Manifest b/sci-physics/scikit-hep-testdata/Manifest
new file mode 100644
index 000000000..1051bc85d
--- /dev/null
+++ b/sci-physics/scikit-hep-testdata/Manifest
@@ -0,0 +1 @@
+DIST scikit-hep-testdata-0.4.39.gh.tar.gz 340561478 BLAKE2B 9d0fc60c8bd9c11b5cd786389489b095a5498c7e08c744106d3bacd3f203f4b186f50a5e1ef6cbdcb23fc5d975807277cc25397ea8049e2acccbbc06c53f65d2 SHA512 fe31302178b8148b0486fe314a9d40c7a4318e53113878769484cc79dd55e5adb977357a175ffad887a205e1ea3e99a4f5be192581cca61554ba2187daad3bd2
diff --git a/sci-physics/scikit-hep-testdata/metadata.xml b/sci-physics/scikit-hep-testdata/metadata.xml
new file mode 100644
index 000000000..ea2e37599
--- /dev/null
+++ b/sci-physics/scikit-hep-testdata/metadata.xml
@@ -0,0 +1,19 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
+<pkgmetadata>
+	<maintainer type="project">
+		<email>sci@gentoo.org</email>
+		<name>Gentoo Science Project</name>
+	</maintainer>
+	<maintainer type="person">
+		<email>alexander@neuwirth-informatik.de</email>
+		<name>Alexander Puck Neuwirth</name>
+	</maintainer>
+	<longdescription lang="en">
+	A common package to provide example files (e.g. ROOT) for testing and developing packages against. The sample of files is representative of typical files found "in the wild".
+	</longdescription>
+	<upstream>
+		<remote-id type="pypi">scikit-hep-testdata</remote-id>
+		<remote-id type="github">scikit-hep/scikit-hep-testdata</remote-id>
+	</upstream>
+</pkgmetadata>
diff --git a/sci-physics/scikit-hep-testdata/scikit-hep-testdata-0.4.39.ebuild b/sci-physics/scikit-hep-testdata/scikit-hep-testdata-0.4.39.ebuild
new file mode 100644
index 000000000..47d0f0bbd
--- /dev/null
+++ b/sci-physics/scikit-hep-testdata/scikit-hep-testdata-0.4.39.ebuild
@@ -0,0 +1,30 @@
+EAPI=8
+
+PYTHON_COMPAT=( python3_{10..12} )
+DISTUTILS_USE_PEP517=setuptools
+inherit distutils-r1 pypi
+
+DESCRIPTION="A package to provide example files for testing and developing packages against."
+HOMEPAGE="https://github.com/scikit-hep/scikit-hep-testdata"
+# pypi does not include the data nor tests
+SRC_URI="https://github.com/scikit-hep/${PN}/archive/refs/tags/v${PV}.tar.gz -> ${P}.gh.tar.gz"
+S="${WORKDIR}/${P}"
+# export is needed here!
+export SETUPTOOLS_SCM_PRETEND_VERSION=${PV}
+# otherwise we don't install the data
+export SKHEP_DATA=1
+
+LICENSE="MIT"
+SLOT="0"
+KEYWORDS="~amd64"
+
+RDEPEND="
+	dev-python/pyyaml[${PYTHON_USEDEP}]
+	dev-python/requests[${PYTHON_USEDEP}]
+"
+DEPEND="${RDEPEND}"
+BDEPEND="
+	dev-python/setuptools-scm[${PYTHON_USEDEP}]
+"
+
+distutils_enable_tests pytest
diff --git a/sci-physics/spheno/Manifest b/sci-physics/spheno/Manifest
new file mode 100644
index 000000000..5db72217b
--- /dev/null
+++ b/sci-physics/spheno/Manifest
@@ -0,0 +1,2 @@
+DIST spheno-3.3.8.tar.gz 1415645 BLAKE2B 830cdbcd8f213f0de0cd0b72455d5919e390069f097bca5a0cabdbfb77ec21549c9455139ff960a0cdbd425368805c1f2d11384c240a8e82f66e33864f4fce7b SHA512 e6c923586eae198f62121e0410f9f1f87e7badfd58d90e3b5f600e8364ea054dfb8b58c1c39d74ec6067112fa6cad727797230bce6cfc6040e2bf4c6d01b0eae
+DIST spheno-4.0.5.tar.gz 1587855 BLAKE2B d3cb92740be416934a928147d980e180be623dbbfeac7a1b0b16e7e4a36d2b3088e455b5348f6e65cfa2ac8d90286c0b65a81498527419ed4eaa42622651408b SHA512 387099c3d9c9c7baf4a5da6d46b819d53dc703f72cc3a73fac7c2e63b66623e328294ac131e128253002ab03a81e96c686702ac90a58479ae573f228d3a51379
diff --git a/sci-physics/spheno/files/spheno-3.3.8-gfortran.patch b/sci-physics/spheno/files/spheno-3.3.8-gfortran.patch
new file mode 100644
index 000000000..8f6fa7e19
--- /dev/null
+++ b/sci-physics/spheno/files/spheno-3.3.8-gfortran.patch
@@ -0,0 +1,32 @@
+--- a/src/Makefile	2022-07-20 11:47:44.078639381 +0200
++++ b/src/Makefile	2022-07-24 02:16:38.972041809 +0200
+@@ -9,10 +9,11 @@
+ # options for various compilers
+ #
+ 
+-# Intels ifort, default in optimized mode
+-F90 = ifort
+-comp = -c -O -module ${Mdir} -I${InDir} 
+-LFlagsB = -O  
++
++# gentoo toolchain
++F90 = ${F90}
++comp = -c -O -J${Mdir} -I${InDir}  ${FFLAGS} ${FCFLAGS} ${CFLAGS}
++LFlagsB = -O ${LDFLAGS}
+ 
+ # Intels ifort, debug modus
+ ifeq (${F90},ifortg)
+@@ -70,11 +71,11 @@
+ #
+ .f90.a:
+ 	${F90} ${comp} $<
+-	ar -ruc $@ $*.o
++	$(AR) -ruc $@ $*.o
+ 	rm -f $*.o
+ .F90.a:
+ 	${F90} ${comp}  ${PreDef} $<
+-	ar -ruc $@ $*.o
++	$(AR) -ruc $@ $*.o
+ 	rm -f $*.o
+ .f90.o: 
+ 	${F90} ${comp}  $< 
diff --git a/sci-physics/spheno/files/spheno-4.0.5-gfortran.patch b/sci-physics/spheno/files/spheno-4.0.5-gfortran.patch
new file mode 100644
index 000000000..1abf36367
--- /dev/null
+++ b/sci-physics/spheno/files/spheno-4.0.5-gfortran.patch
@@ -0,0 +1,29 @@
+--- a/src/Makefile	2023-05-04 12:33:44.804394098 +0200
++++ b/src/Makefile	2023-05-04 12:34:37.023776033 +0200
+@@ -21,9 +21,9 @@
+ #

+ 

+ # Intels ifort, default in optimized mode

+-F90 = ifort

+-comp = -c -O -module ${Mdir} -I${InDir} 

+-LFlagsB = -O  

++F90 = ${F90}

++comp = -c -O -J${Mdir} -I${InDir}  ${FFLAGS} ${FCFLAGS} ${CFLAGS}

++LFlagsB = -O ${LDFLAGS}

+ 

+ # Intels ifort, debug modus

+ ifeq (${F90},ifortg)

+@@ -81,11 +81,11 @@
+ #

+ .f90.a:

+ 	${F90} ${comp} $<

+-	ar ${linker} $@ $*.o

++	$(AR) ${linker} $@ $*.o

+ 	rm -f $*.o

+ .F90.a:

+ 	${F90} ${comp}  ${PreDef} $<

+-	ar ${linker} $@ $*.o

++	$(AR) ${linker} $@ $*.o

+ 	rm -f $*.o

+ .f90.o: 

+ 	${F90} ${comp}  $< 

diff --git a/sci-physics/spheno/metadata.xml b/sci-physics/spheno/metadata.xml
new file mode 100644
index 000000000..277841e1a
--- /dev/null
+++ b/sci-physics/spheno/metadata.xml
@@ -0,0 +1,19 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
+<pkgmetadata>
+	<maintainer type="project">
+		<email>sci@gentoo.org</email>
+		<name>Gentoo Science Project</name>
+	</maintainer>
+	<maintainer type="project">
+		<email>sci-physics@gentoo.org</email>
+		<name>Gentoo Physics Project</name>
+	</maintainer>
+	<maintainer type="person">
+		<email>alexander@neuwirth-informatik.de</email>
+		<name>Alexander Puck Neuwirth</name>
+	</maintainer>
+	<longdescription lang="en">
+The code calculates the SUSY spectrum using low energy data and a user supplied high scale model as input. The spectrum is used to calculate two- and three body decay modes of supersymmetric particle as well as of Higgs bosons. In addition the production cross sections for supersymmetric particle and Higgs bosons in e^+ e^- annihilation is calculated. Moreover, the branching of the decay $b \to s \gamma$, the SUSY contribution to anomalous magnetic moment of the muon as well as the SUSY contributions to the rho parameter due to sfermions are calculated. The code is written in F90 with an emphasis on easy generalisability. The structure is set such that complex phases as well as the extension to include the flavour structure can be done in a straight forward way. The 2-loop renormalization group equations as well as the one-loop finite corrections a la Bagger, Matchev, Pierce and Zhang are included. In addition the two-loop corrections to the neutral Higgs boson masses (a la Brignole, Degrassi, Slavich and Zwirner) and to the mu-parameter (a la Dedes and Slavich) are included. Starting with version 2.2.2 the SUSY Les Houches Accord is supported as well as the SPA conventions (for details see hep-ph/0511344).
+	</longdescription>
+</pkgmetadata>
diff --git a/sci-physics/spheno/spheno-3.3.8-r1.ebuild b/sci-physics/spheno/spheno-3.3.8-r1.ebuild
new file mode 100644
index 000000000..7ed53c4c7
--- /dev/null
+++ b/sci-physics/spheno/spheno-3.3.8-r1.ebuild
@@ -0,0 +1,39 @@
+# Copyright 2022 Gentoo Authors
+# Distributed under the terms of the GNU General Public License v2
+
+EAPI=8
+
+inherit fortran-2
+
+MY_PN=SPheno
+MY_P=${MY_PN}-${PV}
+
+DESCRIPTION="SPheno stands for S(upersymmetric) Pheno(menology)"
+HOMEPAGE="https://spheno.hepforge.org/"
+SRC_URI="https://spheno.hepforge.org/downloads/?f=${MY_P}.tar.gz -> ${P}.tar.gz"
+S="${WORKDIR}/${MY_P}"
+
+LICENSE="all-rights-reserved"
+RESTRICT="bindist mirror"
+SLOT="0"
+KEYWORDS="~amd64"
+
+PATCHES=( "${FILESDIR}"/${P}-gfortran.patch )
+
+src_compile() {
+	# single thread force needed since fortan mods depend on each other
+	emake -j1 F90="${FC}"
+}
+
+src_install() {
+	dobin bin/${MY_PN}
+	# convenience symlink since the package is lowercase but the default produced binary is uppercase
+	dosym ${MY_PN} /usr/bin/${PN}
+	dolib.a lib/lib${MY_PN}.a
+	mv include ${PN}
+	doheader -r ${PN}
+	dodoc doc/*
+	docinto examples
+	dodoc input/*
+	docompress -x /usr/share/doc/${PF}/examples
+}
diff --git a/sci-physics/spheno/spheno-4.0.5.ebuild b/sci-physics/spheno/spheno-4.0.5.ebuild
new file mode 100644
index 000000000..7ed53c4c7
--- /dev/null
+++ b/sci-physics/spheno/spheno-4.0.5.ebuild
@@ -0,0 +1,39 @@
+# Copyright 2022 Gentoo Authors
+# Distributed under the terms of the GNU General Public License v2
+
+EAPI=8
+
+inherit fortran-2
+
+MY_PN=SPheno
+MY_P=${MY_PN}-${PV}
+
+DESCRIPTION="SPheno stands for S(upersymmetric) Pheno(menology)"
+HOMEPAGE="https://spheno.hepforge.org/"
+SRC_URI="https://spheno.hepforge.org/downloads/?f=${MY_P}.tar.gz -> ${P}.tar.gz"
+S="${WORKDIR}/${MY_P}"
+
+LICENSE="all-rights-reserved"
+RESTRICT="bindist mirror"
+SLOT="0"
+KEYWORDS="~amd64"
+
+PATCHES=( "${FILESDIR}"/${P}-gfortran.patch )
+
+src_compile() {
+	# single thread force needed since fortan mods depend on each other
+	emake -j1 F90="${FC}"
+}
+
+src_install() {
+	dobin bin/${MY_PN}
+	# convenience symlink since the package is lowercase but the default produced binary is uppercase
+	dosym ${MY_PN} /usr/bin/${PN}
+	dolib.a lib/lib${MY_PN}.a
+	mv include ${PN}
+	doheader -r ${PN}
+	dodoc doc/*
+	docinto examples
+	dodoc input/*
+	docompress -x /usr/share/doc/${PF}/examples
+}
diff --git a/sci-physics/tauola/Manifest b/sci-physics/tauola/Manifest
index 5f335bd72..37adec18a 100644
--- a/sci-physics/tauola/Manifest
+++ b/sci-physics/tauola/Manifest
@@ -1 +1 @@
-DIST TAUOLA.1.1.5.tar.gz 11986900 BLAKE2B 11198bfddddfbd7b7d93acea2a96fe06209dbadb3af95b24ad47a6bf7e5eb028c4c05b6597f15bb33bef16a6b5a9a6505b38e2abff7229cfc5f99a73b0326066 SHA512 1eb6e4b9b649cdd62b77d65899ae3e74cfdd0e8015d115690c020a06f0ff27c22a745db7c7acb12eeffacb9140b069c57c4135037eaf8feb26f8be32aced182a
+DIST TAUOLA.1.1.8.tar.gz 14434046 BLAKE2B b8d37001b445b6433f7eae61a0a90d5ddc51eb7955f93c0dade3dfcfa50a75721346fff1506d9d5b699a254250557a53cc4b3b7b878e4a0760f7d02891ee7fbd SHA512 633b61fc6f0068f1de0329db77197cdcd1869cc224f81e8e102067c02d8db555305fc30d38af8c1d54fdc594644ca202651e3a5055ef54c17ea8678ccefb5612
diff --git a/sci-physics/tauola/files/tauola-1.1.4-makefile.patch b/sci-physics/tauola/files/tauola-1.1.4-makefile.patch
deleted file mode 100644
index 00be27f59..000000000
--- a/sci-physics/tauola/files/tauola-1.1.4-makefile.patch
+++ /dev/null
@@ -1,12 +0,0 @@
---- a/Makefile
-+++ b/Makefile
-@@ -38,8 +38,7 @@
- 
- install:
- 	mkdir -p $(PREFIX)/include
--	mkdir -p $(PREFIX)/include/Tauola
--	cp include/Tauola/* $(PREFIX)/include/Tauola/.
-+	cp -r include/* $(PREFIX)/include
- 	mkdir -p $(PREFIX)/lib
- 	cp lib/* $(PREFIX)/lib/.
- 
diff --git a/sci-physics/tauola/files/tauola-1.1.5-doc.patch b/sci-physics/tauola/files/tauola-1.1.5-doc.patch
deleted file mode 100644
index b33fe1b06..000000000
--- a/sci-physics/tauola/files/tauola-1.1.5-doc.patch
+++ /dev/null
@@ -1,11 +0,0 @@
---- a/documentation/latex_documentation/Tauola_interface_design.tex
-+++ b/documentation/latex_documentation/Tauola_interface_design.tex
-@@ -2652,6 +2652,7 @@
-         there is a mismatch in the {\tt TAUOLA} version number given,
-         but otherwise all information on the generated sample, 
-         as explained eg. in \cite{Jadach:1990mz,Jezabek:1991qp,Jadach:1993hs}, is printed correctly. 
-+  }
- \end{itemize}
- 
- 
-
diff --git a/sci-physics/tauola/metadata.xml b/sci-physics/tauola/metadata.xml
index 1afd606d4..b0f8228f8 100644
--- a/sci-physics/tauola/metadata.xml
+++ b/sci-physics/tauola/metadata.xml
@@ -8,9 +8,6 @@
 		<email>sci-physics@gentoo.org</email>
 		<name>Gentoo Physics Project</name>
 	</maintainer>
-	<longdescription>
-tau decay Monte Carlo generator
-</longdescription>
 	<use>
 		<flag name="hepmc">Compile <pkg>sci-physics/hepmc</pkg> interface</flag>
 		<flag name="tau-spinner">Compile with TauSpinner library</flag>
diff --git a/sci-physics/tauola/tauola-1.1.5.ebuild b/sci-physics/tauola/tauola-1.1.5.ebuild
deleted file mode 100644
index 1ee8b98ea..000000000
--- a/sci-physics/tauola/tauola-1.1.5.ebuild
+++ /dev/null
@@ -1,71 +0,0 @@
-# Copyright 1999-2017 Gentoo Foundation
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=6
-
-inherit eutils
-
-MYPN=TAUOLA
-
-DESCRIPTION="Tau decay Monte Carlo generator"
-HOMEPAGE="http://tauolapp.web.cern.ch/tauolapp/"
-SRC_URI="http://tauolapp.web.cern.ch/tauolapp/resources/${MYPN}.${PV}/${MYPN}.${PV}.tar.gz"
-
-#HepMC interface is licensed under GPL, other code under CPC
-LICENSE="CPC GPL-2+"
-SLOT="0"
-KEYWORDS="~amd64 ~x86"
-IUSE="doc examples hepmc tau-spinner"
-
-RDEPEND="
-	hepmc? ( sci-physics/hepmc )
-	tau-spinner? ( sci-physics/lhapdf )
-"
-DEPEND="${RDEPEND}
-	doc? (
-		app-doc/doxygen
-		app-text/ghostscript-gpl
-		app-text/texlive
-	)
-"
-
-S="${WORKDIR}/${MYPN}"
-
-PATCHES=(
-	"${FILESDIR}"/${P}-doc.patch
-	"${FILESDIR}"/${PN}-1.1.4-makefile.patch
-	"${FILESDIR}"/${PN}-1.1.3-tau-spinner-makefile.patch
-)
-
-src_configure() {
-	econf \
-		--without-mc-tester \
-		--without-pythia8 \
-		$(use_with hepmc hepmc "${EPREFIX}/usr") \
-		$(use_with tau-spinner) \
-		$(use_with tau-spinner lhapdf "${EPREFIX}/usr")
-}
-
-src_compile() {
-	emake -j1
-	if use doc; then
-		cd "${S}/documentation/doxy_documentation" || die
-		default
-		cd "${S}/documentation/latex_documentation" || die
-		default
-	fi
-}
-
-src_install() {
-	emake PREFIX="${D}/usr" install
-
-	if use doc; then
-		dohtml documentation/doxy_documentation/html/*
-		dodoc documentation/latex_documentation/Tauola_interface_design.pdf
-	fi
-
-	if use examples; then
-		dodoc -r examples
-		use tau-spinner && docinto tau-spinner && dodoc -r TauSpinner/examples
-	fi
-}
diff --git a/sci-physics/tauola/tauola-1.1.8.ebuild b/sci-physics/tauola/tauola-1.1.8.ebuild
new file mode 100644
index 000000000..4d4742dd1
--- /dev/null
+++ b/sci-physics/tauola/tauola-1.1.8.ebuild
@@ -0,0 +1,68 @@
+# Copyright 1999-2021 Gentoo Authors
+# Distributed under the terms of the GNU General Public License v2
+
+EAPI=7
+
+MYPN=TAUOLA
+
+DESCRIPTION="Tau decay Monte Carlo generator"
+HOMEPAGE="https://tauolapp.web.cern.ch/tauolapp/"
+SRC_URI="https://tauolapp.web.cern.ch/tauolapp/resources/${MYPN}.${PV}/${MYPN}.${PV}.tar.gz"
+
+#HepMC interface is licensed under GPL, other code under CPC
+LICENSE="CPC GPL-2+"
+SLOT="0"
+KEYWORDS="~amd64 ~x86"
+IUSE="doc examples hepmc tau-spinner"
+
+RDEPEND="
+	hepmc? ( sci-physics/hepmc )
+	tau-spinner? ( sci-physics/lhapdf )
+"
+DEPEND="${RDEPEND}
+	doc? (
+		app-text/doxygen[dot]
+		app-text/ghostscript-gpl
+		app-text/texlive
+	)
+"
+
+S="${WORKDIR}/${MYPN}"
+
+PATCHES=(
+	"${FILESDIR}"/${PN}-1.1.3-tau-spinner-makefile.patch
+)
+
+src_configure() {
+	econf \
+		--without-mc-tester \
+		--without-pythia8 \
+		$(use_with hepmc hepmc "${EPREFIX}/usr") \
+		--without-hepmc3 \
+		$(use_with tau-spinner) \
+		$(use_with tau-spinner lhapdf "${EPREFIX}/usr")
+}
+
+src_compile() {
+	emake -j1
+	if use doc; then
+		cd "${S}/documentation/doxy_documentation" || die
+		default
+		cd "${S}/documentation/latex_documentation" || die
+		default
+	fi
+}
+
+src_install() {
+	emake DESTDIR="${ED}" install
+
+	if use doc; then
+		dodoc documentation/doxy_documentation/html/*
+		dodoc documentation/latex_documentation/Tauola_interface_design.pdf
+	fi
+
+	if use examples; then
+		dodoc -r examples
+		use tau-spinner && docinto tau-spinner && dodoc -r TauSpinner/examples
+	fi
+}
diff --git a/sci-physics/tauola/tauola-9999.ebuild b/sci-physics/tauola/tauola-9999.ebuild
deleted file mode 100644
index 8e968923c..000000000
--- a/sci-physics/tauola/tauola-9999.ebuild
+++ /dev/null
@@ -1,75 +0,0 @@
-# Copyright 1999-2017 Gentoo Foundation
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=6
-
-MYPN=TAUOLA
-
-DESCRIPTION="Tau decay Monte Carlo generator"
-HOMEPAGE="http://tauolapp.web.cern.ch/tauolapp/"
-SRC_URI=""
-
-#HepMC interface is licensed under GPL, other code under CPC
-LICENSE="CPC GPL-2+"
-SLOT="0"
-KEYWORDS=""
-IUSE="doc examples hepmc tau-spinner"
-
-RDEPEND="
-	hepmc? ( sci-physics/hepmc )
-	tau-spinner? ( sci-physics/lhapdf )
-"
-DEPEND="${RDEPEND}
-	net-misc/wget
-	doc? (
-		app-doc/doxygen
-		app-text/ghostscript-gpl
-		app-text/texlive
-)
-"
-
-S="${WORKDIR}/${MYPN}"
-
-src_unpack() {
-	#there is no public svn, just generated tarball, so fetch it
-	wget "http://tauolapp.web.cern.ch/tauolapp/resources/${MYPN}.development.version/${MYPN}.development.version.tar.gz" || die
-	unpack "./${MYPN}.development.version.tar.gz"
-}
-
-PATCHES=(
-	"${FILESDIR}"/${PN}-1.1.4-makefile.patch
-	"${FILESDIR}"/${PN}-1.1.3-tau-spinner-makefile.patch
-)
-
-src_configure() {
-	econf \
-		--without-mc-tester \
-		--without-pythia8 \
-		$(use_with hepmc hepmc "${EPREFIX}/usr") \
-		$(use_with tau-spinner) \
-		$(use_with tau-spinner lhapdf "${EPREFIX}/usr")
-}
-
-src_compile() {
-	emake -j1
-	if use doc; then
-		cd "${S}/documentation/doxy_documentation" || die
-		default
-		cd "${S}/documentation/latex_documentation" || die
-		default
-	fi
-}
-
-src_install() {
-	emake PREFIX="${D}/usr" install
-
-	if use doc; then
-		dohtml documentation/doxy_documentation/html/*
-		dodoc documentation/latex_documentation/Tauola_interface_design.pdf
-	fi
-
-	if use examples; then
-		dodoc -r examples
-		use tau-spinner && docinto tau-spinner && dodoc -r TauSpinner/examples
-	fi
-}
diff --git a/sci-physics/uproot/Manifest b/sci-physics/uproot/Manifest
new file mode 100644
index 000000000..bb52077be
--- /dev/null
+++ b/sci-physics/uproot/Manifest
@@ -0,0 +1 @@
+DIST uproot-5.3.1.tar.gz 919910 BLAKE2B 6c138a56ecabb08905e1edde8c776c3dfae6cca3213bbc3546e7241979052178e1c9718c1fcf298573669bcc4c004806cd54ab16050405038f76f3ef356fb184 SHA512 2525f372caa3b25e3a11b170ce981ce253a7b9ca1fdb2c04b6bb1093b166d206a28e9bc22ffa19dead76870f521cee44a812cbf41a087b34fb9a3bc52c210733
diff --git a/sci-physics/uproot/metadata.xml b/sci-physics/uproot/metadata.xml
new file mode 100644
index 000000000..1b293facb
--- /dev/null
+++ b/sci-physics/uproot/metadata.xml
@@ -0,0 +1,21 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
+<pkgmetadata>
+	<maintainer type="project">
+		<email>sci@gentoo.org</email>
+		<name>Gentoo Science Project</name>
+	</maintainer>
+	<maintainer type="person">
+		<email>alexander@neuwirth-informatik.de</email>
+		<name>Alexander Puck Neuwirth</name>
+	</maintainer>
+	<longdescription lang="en">
+		Uproot is a library for reading and writing ROOT files in pure Python and NumPy.
+
+		Unlike the standard C++ ROOT implementation, Uproot is only an I/O library, primarily intended to stream data into machine learning libraries in Python. Unlike PyROOT and root_numpy, Uproot does not depend on C++ ROOT. Instead, it uses Numpy to cast blocks of data from the ROOT file as Numpy arrays.
+	</longdescription>
+	<upstream>
+		<remote-id type="pypi">uproot</remote-id>
+		<remote-id type="github">scikit-hep/uproot5</remote-id>
+	</upstream>
+</pkgmetadata>
diff --git a/sci-physics/uproot/uproot-5.3.1.ebuild b/sci-physics/uproot/uproot-5.3.1.ebuild
new file mode 100644
index 000000000..cfc3880e9
--- /dev/null
+++ b/sci-physics/uproot/uproot-5.3.1.ebuild
@@ -0,0 +1,28 @@
+EAPI=8
+
+PYTHON_COMPAT=( python3_{10..12} )
+DISTUTILS_USE_PEP517=hatchling
+SETUPTOOLS_SCM_PRETEND_VERSION=${PV}
+inherit distutils-r1 pypi
+
+DESCRIPTION="ROOT I/O in pure Python and Numpy."
+HOMEPAGE="https://github.com/scikit-hep/uproot"
+
+LICENSE="BSD"
+SLOT="0"
+KEYWORDS="~amd64"
+
+RDEPEND="
+	>=dev-python/awkward-2.4.6[${PYTHON_USEDEP}]
+	>=dev-python/cramjam-2.5.0[${PYTHON_USEDEP}]
+	dev-python/numpy[${PYTHON_USEDEP}]
+	dev-python/fsspec[${PYTHON_USEDEP}]
+	dev-python/packaging[${PYTHON_USEDEP}]
+"
+DEPEND="${RDEPEND}"
+BDEPEND="
+	dev-python/hatch-vcs[${PYTHON_USEDEP}]
+"
+
+# way too many missing packages, isal, deflate, xxhash, http servers etc
+# distutils_enable_tests pytest
diff --git a/sci-physics/vgm/Manifest b/sci-physics/vgm/Manifest
deleted file mode 100644
index c70815e95..000000000
--- a/sci-physics/vgm/Manifest
+++ /dev/null
@@ -1,2 +0,0 @@
-DIST vgm-code-731-tags-v3-06.zip 3668484 BLAKE2B 0d20e16f731ca565b1807ffd0b154f349e295f1e4de9380436b25eb03a810371ec385a9ef23c4365b1644de9717a1b571bc8d20f9c7080bde20a2a17b95a224c SHA512 27b275f4710bfd4f445147854260a768ca1808bad7fc0c4b38e28a4ade22acd80ff80d519341b279c81b9e9e303135f681003381acee2e28e549c93d74858f01
-DIST vgm.4.3.tar.gz 2989397 BLAKE2B 4939c66da33f081fd9cc6952737f6ed8bfe12aa1e4d51301991f6dbce68607e0fb9aca5401c7b54dac77e3fc7beea827f33eb52786cb0498575a6e7df673c93c SHA512 2e832639becc098ade28d965bc05da56dc54899ea80e475990098ceef39b00e64458c8a18df8995a82afaa7fa8e983c3f104ff1440254cd0b29213039081c12d
diff --git a/sci-physics/vgm/metadata.xml b/sci-physics/vgm/metadata.xml
deleted file mode 100644
index dba956aa1..000000000
--- a/sci-physics/vgm/metadata.xml
+++ /dev/null
@@ -1,16 +0,0 @@
-<?xml version="1.0" encoding="UTF-8"?>
-<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
-<pkgmetadata>
-	<maintainer type="project">
-		<email>sci-physics@gentoo.org</email>
-		<name>Gentoo Physics Project</name>
-	</maintainer>
-	<longdescription lang="en">
-The Virtual Geometry Model (VGM) is an
-abstraction layer between the Geant4 and ROOT software.
-</longdescription>
-	<use>
-		<flag name="geant4">Enable interaction with Geant4(<pkg>sci-physics/geant</pkg>:4) </flag>
-		<flag name="root">Enable interactions with ROOT (<pkg>sci-physics/root</pkg>) </flag>
-	</use>
-</pkgmetadata>
diff --git a/sci-physics/vgm/vgm-3.06.ebuild b/sci-physics/vgm/vgm-3.06.ebuild
deleted file mode 100644
index b0a867f54..000000000
--- a/sci-physics/vgm/vgm-3.06.ebuild
+++ /dev/null
@@ -1,70 +0,0 @@
-# Copyright 1999-2014 Gentoo Foundation
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=5
-
-inherit cmake-utils versionator
-
-#ESVN_REPO_URI="https://vgm.svn.sourceforge.net/svnroot/${PN}/tags/v$(replace_all_version_separators '-')/${PN}"
-#ESVN_PROJECT="${PN}.${PV}"
-
-# .zip-snapshot can be recreated by visiting
-# http://sourceforge.net/p/${PN}/code/${COMMIT}/tarball?path=/tags/v$(replace_all_version_separators '-')
-TAG_VER="${PN}-code-731-tags-v$(replace_all_version_separators '-')"
-
-DESCRIPTION="Virtual Geometry Model for High Energy Physics Experiments"
-HOMEPAGE="http://ivana.home.cern.ch/ivana/VGM.html"
-#SRC_URI="http://sourceforge.net/code-snapshots/svn/v/vg/vgm/code/${TAG_VER}.zip"
-SRC_URI="http://dev.gentoo.org/~jlec/distfiles/${TAG_VER}.zip"
-
-LICENSE="GPL-2"
-SLOT="0"
-KEYWORDS="~amd64 ~x86 ~amd64-linux ~x86-linux"
-IUSE="doc examples +geant4 +root test xml"
-
-RDEPEND="
-	sci-physics/clhep:=
-	root? ( sci-physics/root:= )
-	geant4? ( >=sci-physics/geant-4.9.6[examples?] )
-	xml? ( dev-libs/xerces-c )"
-DEPEND="${RDEPEND}
-	doc? ( app-doc/doxygen[dot] )
-	test? ( geant4? ( xml? ( >=sci-physics/geant-4.9.6[gdml] ) ) )"
-
-S=${WORKDIR}/${TAG_VER}/${PN}
-
-src_configure() {
-	local mycmakeargs=(
-		-DCLHEP_DIR="${EROOT}usr"
-		$(cmake-utils_use_with examples)
-		$(cmake-utils_use_with geant4)
-		$(cmake-utils_use_with root)
-		$(cmake-utils_use_with test)
-		$(cmake-utils_use_with xml xercesc)
-	)
-	cmake-utils_src_configure
-}
-
-src_compile() {
-	cmake-utils_src_compile
-	if use doc; then
-		cd packages
-		doxygen || die
-	fi
-}
-
-src_test() {
-	cd "${BUILD_DIR}"/test
-	./test_suite.sh || die
-}
-
-src_install() {
-	cmake-utils_src_install
-	if use examples; then
-		insinto /usr/share/doc/${PF}
-		doins -r examples
-	fi
-	cd doc || die
-	dodoc README todo.txt VGMhistory.txt VGM.html VGMversions.html
-	use doc && dohtml -r html/*
-}
diff --git a/sci-physics/vgm/vgm-4.3.ebuild b/sci-physics/vgm/vgm-4.3.ebuild
deleted file mode 100644
index f9b13101a..000000000
--- a/sci-physics/vgm/vgm-4.3.ebuild
+++ /dev/null
@@ -1,69 +0,0 @@
-# Copyright 1999-2016 Gentoo Foundation
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=6
-
-inherit cmake-utils versionator
-
-if [[ ${PV} == *9999* ]]; then
-	inherit subversion
-	ESVN_REPO_URI="svn://svn.code.sf.net/p/vgm/code/trunk/vgm"
-	KEYWORDS=""
-else
-	SRC_URI="http://ivana.home.cern.ch/ivana/${PN}.${PV}.tar.gz"
-	S="${WORKDIR}/${PN}.${PV}"
-	KEYWORDS="~amd64 ~x86 ~amd64-linux ~x86-linux"
-fi
-
-DESCRIPTION="Virtual Geometry Model for High Energy Physics Experiments"
-HOMEPAGE="http://ivana.home.cern.ch/ivana/VGM.html"
-
-LICENSE="GPL-2"
-SLOT="0"
-IUSE="doc examples +geant4 +root test xml"
-
-RDEPEND="
-	sci-physics/clhep:=
-	root? ( sci-physics/root:= )
-	geant4? ( >=sci-physics/geant-4.9.6 )
-	xml? ( dev-libs/xerces-c )"
-DEPEND="${RDEPEND}
-	doc? ( app-doc/doxygen[dot] )
-	test? ( geant4? ( xml? ( >=sci-physics/geant-4.9.6[gdml] ) ) )"
-
-src_prepare() {
-	default
-}
-
-src_configure() {
-	local mycmakeargs=(
-		-DCLHEP_DIR="${EROOT}usr"
-		-Dexamples="$(usex examples)"
-		-DVGM_INSTALL_EXAMPLES="$(usex examples)"
-		-Dgeant4="$(usex geant4)"
-		-Droot="$(usex root)"
-		-Dtest="$(usex test)"
-		-Dxercesc="$(usex xml)"
-	)
-	cmake-utils_src_configure
-}
-
-src_compile() {
-	cmake-utils_src_compile
-	if use doc; then
-		cd packages
-		doxygen || die
-	fi
-}
-
-src_test() {
-	cd "${BUILD_DIR}"/test
-	./test_suite.sh || die
-}
-
-src_install() {
-	cmake-utils_src_install
-	cd doc || die
-	dodoc README todo.txt VGMhistory.txt VGM.html VGMversions.html
-	use doc && dohtml -r html/*
-}
diff --git a/sci-physics/vgm/vgm-9999.ebuild b/sci-physics/vgm/vgm-9999.ebuild
deleted file mode 100644
index f9b13101a..000000000
--- a/sci-physics/vgm/vgm-9999.ebuild
+++ /dev/null
@@ -1,69 +0,0 @@
-# Copyright 1999-2016 Gentoo Foundation
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=6
-
-inherit cmake-utils versionator
-
-if [[ ${PV} == *9999* ]]; then
-	inherit subversion
-	ESVN_REPO_URI="svn://svn.code.sf.net/p/vgm/code/trunk/vgm"
-	KEYWORDS=""
-else
-	SRC_URI="http://ivana.home.cern.ch/ivana/${PN}.${PV}.tar.gz"
-	S="${WORKDIR}/${PN}.${PV}"
-	KEYWORDS="~amd64 ~x86 ~amd64-linux ~x86-linux"
-fi
-
-DESCRIPTION="Virtual Geometry Model for High Energy Physics Experiments"
-HOMEPAGE="http://ivana.home.cern.ch/ivana/VGM.html"
-
-LICENSE="GPL-2"
-SLOT="0"
-IUSE="doc examples +geant4 +root test xml"
-
-RDEPEND="
-	sci-physics/clhep:=
-	root? ( sci-physics/root:= )
-	geant4? ( >=sci-physics/geant-4.9.6 )
-	xml? ( dev-libs/xerces-c )"
-DEPEND="${RDEPEND}
-	doc? ( app-doc/doxygen[dot] )
-	test? ( geant4? ( xml? ( >=sci-physics/geant-4.9.6[gdml] ) ) )"
-
-src_prepare() {
-	default
-}
-
-src_configure() {
-	local mycmakeargs=(
-		-DCLHEP_DIR="${EROOT}usr"
-		-Dexamples="$(usex examples)"
-		-DVGM_INSTALL_EXAMPLES="$(usex examples)"
-		-Dgeant4="$(usex geant4)"
-		-Droot="$(usex root)"
-		-Dtest="$(usex test)"
-		-Dxercesc="$(usex xml)"
-	)
-	cmake-utils_src_configure
-}
-
-src_compile() {
-	cmake-utils_src_compile
-	if use doc; then
-		cd packages
-		doxygen || die
-	fi
-}
-
-src_test() {
-	cd "${BUILD_DIR}"/test
-	./test_suite.sh || die
-}
-
-src_install() {
-	cmake-utils_src_install
-	cd doc || die
-	dodoc README todo.txt VGMhistory.txt VGM.html VGMversions.html
-	use doc && dohtml -r html/*
-}
diff --git a/sci-visualization/clip/Manifest b/sci-visualization/clip/Manifest
new file mode 100644
index 000000000..cdbc6b05a
--- /dev/null
+++ b/sci-visualization/clip/Manifest
@@ -0,0 +1 @@
+DIST clip-0.7.tar.gz 2842638 BLAKE2B 676ec642b0480eeda1da918bd99b374b11fb6e6d2c7b67c1856395100c794724c071266d81214cc3ec7b5eaa235a185466bcddd470922e27b7c5f46c4fdcee01 SHA512 b08cb2c4112364e5dc80e975021af33709fb5322f19a78a998a2e1b2720807a1b6f92623005ad5d6f609e58338c0c37bc743ac31bc737c669545fd27df31be19
diff --git a/sci-visualization/clip/clip-0.7-r1.ebuild b/sci-visualization/clip/clip-0.7-r1.ebuild
new file mode 100644
index 000000000..5de823101
--- /dev/null
+++ b/sci-visualization/clip/clip-0.7-r1.ebuild
@@ -0,0 +1,30 @@
+# Copyright 1999-2022 Gentoo Authors
+# Distributed under the terms of the GNU General Public License v2
+
+EAPI=8
+
+CMAKE_BUILD_TYPE=Release
+CMAKE_IN_SOURCE_BUILD=1
+CMAKE_MAKEFILE_GENERATOR=emake
+inherit cmake
+
+DESCRIPTION="command line chart creator"
+HOMEPAGE="https://clip-lang.org"
+SRC_URI="https://github.com/asmuth/clip/archive/v${PV}.tar.gz -> ${P}.tar.gz"
+
+KEYWORDS="~amd64"
+LICENSE="Apache-2.0"
+SLOT="0"
+
+RDEPEND="
+	dev-libs/fribidi
+	dev-libs/libfmt
+	media-libs/freetype
+	media-libs/fontconfig
+	media-libs/harfbuzz
+	media-libs/libpng
+	x11-libs/cairo
+"
+DEPEND="${RDEPEND}"
+
+PATCHES=( "${FILESDIR}"/${PN}-0.7-libdir.patch )
diff --git a/sci-visualization/clip/files/clip-0.7-libdir.patch b/sci-visualization/clip/files/clip-0.7-libdir.patch
new file mode 100644
index 000000000..ceafecb80
--- /dev/null
+++ b/sci-visualization/clip/files/clip-0.7-libdir.patch
@@ -0,0 +1,15 @@
+diff --git a/CMakeLists.txt b/CMakeLists.txt
+index c86ddca..8653311 100644
+--- a/CMakeLists.txt
++++ b/CMakeLists.txt
+@@ -102,8 +102,8 @@ set_target_properties(clip-cli PROPERTIES OUTPUT_NAME clip)
+ 
+ # Installation
+ # -----------------------------------------------------------------------------
+-install(TARGETS clip-lib-a ARCHIVE DESTINATION lib PUBLIC_HEADER DESTINATION include/clip)
+-install(TARGETS clip-lib-so LIBRARY DESTINATION lib PUBLIC_HEADER DESTINATION include/clip)
++install(TARGETS clip-lib-a ARCHIVE DESTINATION ${CMAKE_INSTALL_LIBDIR} PUBLIC_HEADER DESTINATION include/clip)
++install(TARGETS clip-lib-so LIBRARY DESTINATION ${CMAKE_INSTALL_LIBDIR} PUBLIC_HEADER DESTINATION include/clip)
+ install(TARGETS clip-cli DESTINATION bin)
+ 
+ 
diff --git a/sci-visualization/clip/metadata.xml b/sci-visualization/clip/metadata.xml
new file mode 100644
index 000000000..8f000a818
--- /dev/null
+++ b/sci-visualization/clip/metadata.xml
@@ -0,0 +1,15 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
+<pkgmetadata>
+	<maintainer type="person">
+		<email>gentoo@aisha.cc</email>
+		<name>Aisha Tammy</name>
+	</maintainer>
+	<maintainer type="project">
+		<email>sci@gentoo.org</email>
+		<name>Gentoo Science Project</name>
+	</maintainer>
+	<upstream>
+		<remote-id type="github">asmuth/clip</remote-id>
+	</upstream>
+</pkgmetadata>
diff --git a/sci-visualization/forge/Manifest b/sci-visualization/forge/Manifest
index 41a57ac1c..4af43c3f5 100644
--- a/sci-visualization/forge/Manifest
+++ b/sci-visualization/forge/Manifest
@@ -1,4 +1,2 @@
-DIST forge-0.9.0.tar.gz 798695 BLAKE2B a1ab587141ed25624f4d478733863c8df0e025278d9282ccaff3b9116bfc40a5e85dee6ea9431afb7e13455a07aa887636f5ee8149c490ac229743ec85eb8fd6 SHA512 88e0590d1e4da308a91919f0a9169ebbd8f605e8bb0fea4e5e728924535c329f3fab1740b760969c4790500d52202e3730b8d2228eaeff526a1f235ee645c00f
-DIST forge-0.9.2.tar.gz 735452 BLAKE2B d9c16f2981b0ee516e4aa88d6567905c89eb61f6530301169b8d5ec31efc8aa9c0797f7524160aebf01f57ccd42e2c9509d1ea2af504404e8830734ec5e6e5e1 SHA512 6bf92462f4e599faeb4665efedb1461780f2b886670f5e7ea4e6bb8c9ce4909652d778ed274c260970342e61e11057861b67dcc4ed0d01248ca1a36d1556e626
-DIST forge-3.1.2.tar.gz 222873 BLAKE2B e8d70c90927628ec774d4192f7d89d958e5c8652f06b5f63739a4bc4bcbad29d7536aa60f6739706c4f11bc500eba063c56d3177f9ecd5a7011903ff3a8ba01a SHA512 cbc9a754ef3110120cffe0882321bc236e0f655f95b2115203c98743bd39bac870bd866eeddf923497370c497dc349fd394dc84f77eb3f8b30b64d9b3173e377
-DIST forge-3.2.2.tar.gz 232250 BLAKE2B 6ba82c0e83d27a5845cac6b55cb1de60986d98a3f9007877a96b689eca0710e009e709159d48ef6fc88b01147687035eb767e9dae09f98b6c223d65d892faf70 SHA512 069fed370043cd782879788cf62658374c9326a3b18cc69a86b97a0d42de76874c65cc96efe0ec75b6bc5074933c74decfaf5c8457e024515cac7da8ee1f6142
+DIST forge-1.0.5.tar.gz 1076708 BLAKE2B 9615e9b6d684ce9dab3600350f66654fa65d987ebd921d304c1106e2fe6111ff9efabac89b06a046cf060f13ee4bd1776ac91459afc25172d93483399a04b068 SHA512 01dc17f202bc79734bb997065c8cbc8d950204a47f979afddd8df14e40774dc712ecb7c34b11f0e312b1598fcbc9d25dd0bb089956d86508aac5b10fe1789fc3
+DIST forge-1.0.7.tar.gz 6146823 BLAKE2B 50ab2425f44216dd9e67e513b6e5a27d0a12729c2622b8139ba783668cb09ac23bdce2b1ce5313c21c669349cece47cc1e28972a1582bf043d37a7aa8a702baa SHA512 d341d5c6bdccf7d2f085162d1d8209b0b28d73b8a9f3173546b26f06bf8e422b3fdf1cfbaa7d122ea75cee5cf5f6bb6dbd2bffc10d8e0c336b5b8695c39f7b54
diff --git a/sci-visualization/forge/forge-0.9.0-r1.ebuild b/sci-visualization/forge/forge-0.9.0-r1.ebuild
deleted file mode 100644
index 3df07a527..000000000
--- a/sci-visualization/forge/forge-0.9.0-r1.ebuild
+++ /dev/null
@@ -1,47 +0,0 @@
-# Copyright 1999-2017 Gentoo Foundation
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=6
-
-inherit cmake-utils multilib
-
-DESCRIPTION="High Performance Visualizations for ArrayFire"
-HOMEPAGE="http://www.arrayfire.com/"
-SRC_URI="https://github.com/arrayfire/${PN}/archive/v${PV}.tar.gz -> ${P}.tar.gz"
-
-LICENSE="BSD"
-SLOT="0"
-KEYWORDS="~amd64"
-IUSE="examples"
-
-RDEPEND="
-	media-libs/glew:=
-	>=media-libs/glfw-3.1.1
-	media-libs/freetype:2
-	media-libs/fontconfig:1.0
-	media-libs/glbinding
-	>=media-libs/glm-0.9.7.1
-	virtual/opengl
-	"
-DEPEND="${RDEPEND}"
-
-#S="${WORKDIR}/${PN}-af${PV}"
-
-pkg_pretend() {
-	if [[ ${MERGE_TYPE} != binary ]]; then
-		if [[ $(gcc-major-version) -lt 4 ]] || ( [[ $(gcc-major-version) -eq 4 && $(gcc-minor-version) -lt 7 ]] ) ; then
-			die "Compilation with gcc older than 4.7 is not supported."
-		fi
-	fi
-}
-
-src_configure() {
-	local mycmakeargs=(
-	   -DBUILD_EXAMPLES="$(examples EXAMPLES)"
-	   -DUSE_SYSTEM_GLBINDING=ON
-	   -DUSE_SYSTEM_GLM=ON
-	   -DUSE_SYSTEM_FREETYPE=ON
-	   -DFG_INSTALL_CMAKE_DIR=/usr/$(get_libdir)/cmake/Forge
-	)
-	cmake-utils_src_configure
-}
diff --git a/sci-visualization/forge/forge-0.9.2-r1.ebuild b/sci-visualization/forge/forge-0.9.2-r1.ebuild
deleted file mode 100644
index 3df07a527..000000000
--- a/sci-visualization/forge/forge-0.9.2-r1.ebuild
+++ /dev/null
@@ -1,47 +0,0 @@
-# Copyright 1999-2017 Gentoo Foundation
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=6
-
-inherit cmake-utils multilib
-
-DESCRIPTION="High Performance Visualizations for ArrayFire"
-HOMEPAGE="http://www.arrayfire.com/"
-SRC_URI="https://github.com/arrayfire/${PN}/archive/v${PV}.tar.gz -> ${P}.tar.gz"
-
-LICENSE="BSD"
-SLOT="0"
-KEYWORDS="~amd64"
-IUSE="examples"
-
-RDEPEND="
-	media-libs/glew:=
-	>=media-libs/glfw-3.1.1
-	media-libs/freetype:2
-	media-libs/fontconfig:1.0
-	media-libs/glbinding
-	>=media-libs/glm-0.9.7.1
-	virtual/opengl
-	"
-DEPEND="${RDEPEND}"
-
-#S="${WORKDIR}/${PN}-af${PV}"
-
-pkg_pretend() {
-	if [[ ${MERGE_TYPE} != binary ]]; then
-		if [[ $(gcc-major-version) -lt 4 ]] || ( [[ $(gcc-major-version) -eq 4 && $(gcc-minor-version) -lt 7 ]] ) ; then
-			die "Compilation with gcc older than 4.7 is not supported."
-		fi
-	fi
-}
-
-src_configure() {
-	local mycmakeargs=(
-	   -DBUILD_EXAMPLES="$(examples EXAMPLES)"
-	   -DUSE_SYSTEM_GLBINDING=ON
-	   -DUSE_SYSTEM_GLM=ON
-	   -DUSE_SYSTEM_FREETYPE=ON
-	   -DFG_INSTALL_CMAKE_DIR=/usr/$(get_libdir)/cmake/Forge
-	)
-	cmake-utils_src_configure
-}
diff --git a/sci-visualization/forge/forge-1.0.5.ebuild b/sci-visualization/forge/forge-1.0.5.ebuild
new file mode 100644
index 000000000..dd708d35f
--- /dev/null
+++ b/sci-visualization/forge/forge-1.0.5.ebuild
@@ -0,0 +1,54 @@
+# Copyright 2019-2021 Gentoo Authors
+# Distributed under the terms of the GNU General Public License v2
+
+EAPI=7
+
+inherit cmake
+
+DESCRIPTION="High Performance Visualizations for ArrayFire"
+HOMEPAGE="http://www.arrayfire.com/"
+
+if [[ ${PV} == 9999 ]]; then
+	inherit git-r3
+	EGIT_REPO_URI="https://github.com/arrayfire/forge"
+else
+	SRC_URI="https://github.com/arrayfire/forge/archive/v${PV}.tar.gz -> ${P}.tar.gz"
+	KEYWORDS="~amd64"
+fi
+
+LICENSE="BSD"
+SLOT="0"
+IUSE="doc examples"
+
+RDEPEND="
+	dev-libs/boost
+	media-libs/glfw
+	media-libs/fontconfig:1.0
+	media-libs/freeimage
+	media-libs/freetype:2
+	media-libs/glbinding
+	media-libs/glm
+	virtual/opengl
+	"
+DEPEND="${RDEPEND}"
+BDEPEND="
+	doc? (
+		app-text/doxygen
+		dev-python/breathe
+		dev-python/recommonmark
+		dev-python/sphinx
+	)
+"
+
+src_configure() {
+	local mycmakeargs=(
+		-DBUILD_SHARED_LIBS=ON
+		-DFG_USE_STATIC_CPPFLAGS=OFF
+		-DFG_BUILD_DOCS=$(usex doc ON OFF)
+		-DFG_BUILD_EXAMPLES=$(usex examples ON OFF)
+		-DFG_WITH_FREEIMAGE=ON
+		-DFG_USE_STATIC_FREEIMAGE=OFF
+		-DFG_INSTALL_CMAKE_DIR=/usr/$(get_libdir)/cmake/Forge
+	)
+	cmake_src_configure
+}
diff --git a/sci-visualization/forge/forge-1.0.7.ebuild b/sci-visualization/forge/forge-1.0.7.ebuild
new file mode 100644
index 000000000..dd708d35f
--- /dev/null
+++ b/sci-visualization/forge/forge-1.0.7.ebuild
@@ -0,0 +1,54 @@
+# Copyright 2019-2021 Gentoo Authors
+# Distributed under the terms of the GNU General Public License v2
+
+EAPI=7
+
+inherit cmake
+
+DESCRIPTION="High Performance Visualizations for ArrayFire"
+HOMEPAGE="http://www.arrayfire.com/"
+
+if [[ ${PV} == 9999 ]]; then
+	inherit git-r3
+	EGIT_REPO_URI="https://github.com/arrayfire/forge"
+else
+	SRC_URI="https://github.com/arrayfire/forge/archive/v${PV}.tar.gz -> ${P}.tar.gz"
+	KEYWORDS="~amd64"
+fi
+
+LICENSE="BSD"
+SLOT="0"
+IUSE="doc examples"
+
+RDEPEND="
+	dev-libs/boost
+	media-libs/glfw
+	media-libs/fontconfig:1.0
+	media-libs/freeimage
+	media-libs/freetype:2
+	media-libs/glbinding
+	media-libs/glm
+	virtual/opengl
+	"
+DEPEND="${RDEPEND}"
+BDEPEND="
+	doc? (
+		app-text/doxygen
+		dev-python/breathe
+		dev-python/recommonmark
+		dev-python/sphinx
+	)
+"
+
+src_configure() {
+	local mycmakeargs=(
+		-DBUILD_SHARED_LIBS=ON
+		-DFG_USE_STATIC_CPPFLAGS=OFF
+		-DFG_BUILD_DOCS=$(usex doc ON OFF)
+		-DFG_BUILD_EXAMPLES=$(usex examples ON OFF)
+		-DFG_WITH_FREEIMAGE=ON
+		-DFG_USE_STATIC_FREEIMAGE=OFF
+		-DFG_INSTALL_CMAKE_DIR=/usr/$(get_libdir)/cmake/Forge
+	)
+	cmake_src_configure
+}
diff --git a/sci-visualization/forge/forge-3.1.2.ebuild b/sci-visualization/forge/forge-3.1.2.ebuild
deleted file mode 100644
index 9ff3957d8..000000000
--- a/sci-visualization/forge/forge-3.1.2.ebuild
+++ /dev/null
@@ -1,44 +0,0 @@
-# Copyright 1999-2017 Gentoo Foundation
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=5
-
-inherit cmake-utils
-
-DESCRIPTION="High Performance Visualizations for ArrayFire"
-HOMEPAGE="http://www.arrayfire.com/"
-SRC_URI="https://github.com/arrayfire/${PN}/archive/af${PV}.tar.gz -> ${P}.tar.gz"
-KEYWORDS="~amd64"
-
-LICENSE="BSD"
-SLOT="0"
-IUSE="examples"
-
-RDEPEND="
-	media-libs/glew:=
-	>=media-libs/glfw-3.1.1
-	media-libs/freetype:2
-	media-libs/fontconfig:1.0
-	>=media-libs/glm-0.9.7.1
-	virtual/opengl
-	"
-DEPEND="${RDEPEND}"
-
-S="${WORKDIR}/${PN}-af${PV}"
-
-pkg_pretend() {
-	if [[ ${MERGE_TYPE} != binary ]]; then
-		if [[ $(gcc-major-version) -lt 4 ]] || ( [[ $(gcc-major-version) -eq 4 && $(gcc-minor-version) -lt 7 ]] ) ; then
-			die "Compilation with gcc older than 4.7 is not supported."
-		fi
-	fi
-}
-
-src_configure() {
-	local mycmakeargs=(
-	   $(cmake-utils_use_build examples EXAMPLES)
-	   -DUSE_SYSTEM_GLM=ON
-	   -DUSE_SYSTEM_FREETYPE=ON
-	)
-	cmake-utils_src_configure
-}
diff --git a/sci-visualization/forge/forge-3.2.2.ebuild b/sci-visualization/forge/forge-3.2.2.ebuild
deleted file mode 100644
index 1fa0c53bc..000000000
--- a/sci-visualization/forge/forge-3.2.2.ebuild
+++ /dev/null
@@ -1,45 +0,0 @@
-# Copyright 1999-2017 Gentoo Foundation
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=5
-
-inherit cmake-utils multilib
-
-DESCRIPTION="High Performance Visualizations for ArrayFire"
-HOMEPAGE="http://www.arrayfire.com/"
-SRC_URI="https://github.com/arrayfire/${PN}/archive/af${PV}.tar.gz -> ${P}.tar.gz"
-
-LICENSE="BSD"
-SLOT="0"
-KEYWORDS="~amd64"
-IUSE="examples"
-
-RDEPEND="
-	media-libs/glew:=
-	>=media-libs/glfw-3.1.1
-	media-libs/freetype:2
-	media-libs/fontconfig:1.0
-	>=media-libs/glm-0.9.7.1
-	virtual/opengl
-	"
-DEPEND="${RDEPEND}"
-
-S="${WORKDIR}/${PN}-af${PV}"
-
-pkg_pretend() {
-	if [[ ${MERGE_TYPE} != binary ]]; then
-		if [[ $(gcc-major-version) -lt 4 ]] || ( [[ $(gcc-major-version) -eq 4 && $(gcc-minor-version) -lt 7 ]] ) ; then
-			die "Compilation with gcc older than 4.7 is not supported."
-		fi
-	fi
-}
-
-src_configure() {
-	local mycmakeargs=(
-	   $(cmake-utils_use_build examples EXAMPLES)
-	   -DUSE_SYSTEM_GLM=ON
-	   -DUSE_SYSTEM_FREETYPE=ON
-	   -DFG_INSTALL_CMAKE_DIR=/usr/$(get_libdir)/cmake/Forge
-	)
-	cmake-utils_src_configure
-}
diff --git a/sci-visualization/forge/forge-9999.ebuild b/sci-visualization/forge/forge-9999.ebuild
index d34b350ee..dd708d35f 100644
--- a/sci-visualization/forge/forge-9999.ebuild
+++ b/sci-visualization/forge/forge-9999.ebuild
@@ -1,45 +1,54 @@
-# Copyright 1999-2017 Gentoo Foundation
+# Copyright 2019-2021 Gentoo Authors
 # Distributed under the terms of the GNU General Public License v2
 
-EAPI=6
+EAPI=7
 
-inherit cmake-utils multilib git-r3
+inherit cmake
 
 DESCRIPTION="High Performance Visualizations for ArrayFire"
 HOMEPAGE="http://www.arrayfire.com/"
-EGIT_REPO_URI="https://github.com/arrayfire/${PN}.git git://github.com/arrayfire/${PN}.git"
+
+if [[ ${PV} == 9999 ]]; then
+	inherit git-r3
+	EGIT_REPO_URI="https://github.com/arrayfire/forge"
+else
+	SRC_URI="https://github.com/arrayfire/forge/archive/v${PV}.tar.gz -> ${P}.tar.gz"
+	KEYWORDS="~amd64"
+fi
 
 LICENSE="BSD"
 SLOT="0"
-KEYWORDS=""
-IUSE="examples"
+IUSE="doc examples"
 
 RDEPEND="
-	media-libs/glew:=
-	>=media-libs/glfw-3.1.1
-	media-libs/freetype:2
+	dev-libs/boost
+	media-libs/glfw
 	media-libs/fontconfig:1.0
+	media-libs/freeimage
+	media-libs/freetype:2
 	media-libs/glbinding
-	>=media-libs/glm-0.9.7.1
+	media-libs/glm
 	virtual/opengl
 	"
 DEPEND="${RDEPEND}"
-
-pkg_pretend() {
-	if [[ ${MERGE_TYPE} != binary ]]; then
-		if [[ $(gcc-major-version) -lt 4 ]] || ( [[ $(gcc-major-version) -eq 4 && $(gcc-minor-version) -lt 7 ]] ) ; then
-			die "Compilation with gcc older than 4.7 is not supported."
-		fi
-	fi
-}
+BDEPEND="
+	doc? (
+		app-text/doxygen
+		dev-python/breathe
+		dev-python/recommonmark
+		dev-python/sphinx
+	)
+"
 
 src_configure() {
 	local mycmakeargs=(
-	   -DBUILD_EXAMPLES="$(examples EXAMPLES)"
-	   -DUSE_SYSTEM_GLBINDING=ON
-	   -DUSE_SYSTEM_GLM=ON
-	   -DUSE_SYSTEM_FREETYPE=ON
-	   -DFG_INSTALL_CMAKE_DIR=/usr/$(get_libdir)/cmake/Forge
+		-DBUILD_SHARED_LIBS=ON
+		-DFG_USE_STATIC_CPPFLAGS=OFF
+		-DFG_BUILD_DOCS=$(usex doc ON OFF)
+		-DFG_BUILD_EXAMPLES=$(usex examples ON OFF)
+		-DFG_WITH_FREEIMAGE=ON
+		-DFG_USE_STATIC_FREEIMAGE=OFF
+		-DFG_INSTALL_CMAKE_DIR=/usr/$(get_libdir)/cmake/Forge
 	)
-	cmake-utils_src_configure
+	cmake_src_configure
 }
diff --git a/sci-visualization/forge/metadata.xml b/sci-visualization/forge/metadata.xml
index 3e7207c7f..610245a28 100644
--- a/sci-visualization/forge/metadata.xml
+++ b/sci-visualization/forge/metadata.xml
@@ -5,17 +5,21 @@
 		<email>marbre@linux.sungazer.de</email>
 		<name>Marius Brehler</name>
 	</maintainer>
+	<maintainer type="person">
+		<email>gentoo@aisha.cc</email>
+		<name>Aisha Tammy</name>
+	</maintainer>
 	<maintainer type="project">
 		<email>sci@gentoo.org</email>
 		<name>Gentoo Science Project</name>
 	</maintainer>
 	<longdescription>
-A prototype of the OpenGL interop library that can be used with
-ArrayFire. The goal of Forge is to provide high performance OpenGL
-visualizations for C/C++ applications that use CUDA/OpenCL. Forge
-uses OpenGL &gt;=3.3 forward compatible contexts, so please make sure
-you have capable hardware before trying it out.
-</longdescription>
+		A prototype of the OpenGL interop library that can be used with
+		ArrayFire. The goal of Forge is to provide high performance OpenGL
+		visualizations for C/C++ applications that use CUDA/OpenCL. Forge
+		uses OpenGL &gt;=3.3 forward compatible contexts, so please make sure
+		you have capable hardware before trying it out.
+	</longdescription>
 	<upstream>
 		<remote-id type="github">arrayfire/forge</remote-id>
 	</upstream>
diff --git a/sci-visualization/fsleyes-props/Manifest b/sci-visualization/fsleyes-props/Manifest
new file mode 100644
index 000000000..6cafd64da
--- /dev/null
+++ b/sci-visualization/fsleyes-props/Manifest
@@ -0,0 +1 @@
+DIST props-1.8.2.tar.gz 124579 BLAKE2B 5a4a399c18b3a8299fa62d378713988c42f25fba7baa90f52b81aad6786dafeda1dc3fb273f159e88d17b5319977ca007854253eba781b579fd771a84d812bba SHA512 66c6e6d47ecd17e7bde245a6b8c94b3710dbec01e16d1829a257c3315d2f013dcce878f972eb65d0642a0231445f1cc1b0b16987676f5c2ea19e62fe19a9432f
diff --git a/sci-visualization/fsleyes-props/fsleyes-props-1.8.2.ebuild b/sci-visualization/fsleyes-props/fsleyes-props-1.8.2.ebuild
new file mode 100644
index 000000000..12364b0cc
--- /dev/null
+++ b/sci-visualization/fsleyes-props/fsleyes-props-1.8.2.ebuild
@@ -0,0 +1,45 @@
+# Copyright 1999-2022 Gentoo Authors
+# Distributed under the terms of the GNU General Public License v2
+
+EAPI=8
+
+PYTHON_COMPAT=( python3_10 )
+DISTUTILS_USE_PEP517=setuptools
+inherit distutils-r1 virtualx
+
+MY_PN="props"
+
+DESCRIPTION="Object attribute management for the FSLeyes viewer"
+HOMEPAGE="https://git.fmrib.ox.ac.uk/fsl/fsleyes/fsleyes/tree/master"
+SRC_URI="https://git.fmrib.ox.ac.uk/fsl/fsleyes/${MY_PN}/-/archive/${PV}/${MY_PN}-${PV}.tar.gz"
+S="${WORKDIR}/${MY_PN}-${PV}"
+
+LICENSE="BSD"
+SLOT="0"
+KEYWORDS="~amd64 ~x86"
+
+RDEPEND="
+	dev-python/numpy[${PYTHON_USEDEP}]
+	dev-python/matplotlib[${PYTHON_USEDEP}]
+	>=dev-python/wxpython-3.0.2.0[${PYTHON_USEDEP}]
+	>=sci-visualization/fsleyes-widgets-0.6[${PYTHON_USEDEP}]
+	>=dev-python/fslpy-1.4[${PYTHON_USEDEP}]
+"
+
+distutils_enable_tests pytest
+distutils_enable_sphinx doc dev-python/sphinx-rtd-theme
+
+python_prepare_all() {
+	# do not depend on pytest-cov
+	sed -i -e '/addopts/d' setup.cfg || die
+
+	distutils-r1_python_prepare_all
+}
+
+src_test() {
+	virtx distutils-r1_src_test
+}
+
+python_test() {
+	epytest || die "Tests failed with ${EPYTHON}"
+}
diff --git a/sci-visualization/fsleyes-props/metadata.xml b/sci-visualization/fsleyes-props/metadata.xml
new file mode 100644
index 000000000..332860a00
--- /dev/null
+++ b/sci-visualization/fsleyes-props/metadata.xml
@@ -0,0 +1,19 @@
+<?xml version='1.0' encoding='UTF-8'?>
+<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
+<pkgmetadata>
+	<maintainer type="person">
+		<email>gentoo@chymera.eu</email>
+		<name>Horea Christian</name>
+	</maintainer>
+	<maintainer type="project">
+		<email>sci@gentoo.org</email>
+		<name>Gentoo Science Project</name>
+	</maintainer>
+	<longdescription lang="en">
+		FSLeyes-props is a library which is used by FSLeyes, and which allows you to
+		listen for change to attributes on a python object, automatically generate
+		wxpython widgets which are bound to attributes of a python object, and
+		automatically generate a command line interface to set values of the attributes
+		of a Python object.
+	</longdescription>
+</pkgmetadata>
diff --git a/sci-visualization/fsleyes-widgets/Manifest b/sci-visualization/fsleyes-widgets/Manifest
new file mode 100644
index 000000000..b88ec6d0e
--- /dev/null
+++ b/sci-visualization/fsleyes-widgets/Manifest
@@ -0,0 +1 @@
+DIST fsleyes-widgets-0.12.3.tar.gz 1138692 BLAKE2B beb4125760b4aff463bc3f9ccb03ae3aa0c88a35af4d992a1f2cb728cb607e846e616a0c91bc3c725db613ef82d3d5acefd47195342aa7bfce2d9bfbcb90428c SHA512 93ebf267eee345ce57bc0096b294f399be9815848d5d2b3c8644a4d177ce37b77a37036bc7825541a7e3a8b364701ab5f6a24532a156b258787e0a0961657aed
diff --git a/sci-visualization/fsleyes-widgets/fsleyes-widgets-0.12.3.ebuild b/sci-visualization/fsleyes-widgets/fsleyes-widgets-0.12.3.ebuild
new file mode 100644
index 000000000..fdbb611c2
--- /dev/null
+++ b/sci-visualization/fsleyes-widgets/fsleyes-widgets-0.12.3.ebuild
@@ -0,0 +1,61 @@
+# Copyright 1999-2022 Gentoo Authors
+# Distributed under the terms of the GNU General Public License v2
+
+EAPI=8
+
+PYTHON_COMPAT=( python3_10 )
+DISTUTILS_USE_PEP517=setuptools
+inherit distutils-r1 virtualx
+
+MY_P="widgets-${PV}"
+
+DESCRIPTION="GUI widgets and utilities for the FSLeyes viewer"
+HOMEPAGE="https://git.fmrib.ox.ac.uk/fsl/fsleyes/fsleyes/tree/master"
+SRC_URI="https://git.fmrib.ox.ac.uk/fsl/fsleyes/widgets/-/archive/${PV}/${MY_P}.tar.gz -> ${P}.tar.gz"
+S="${WORKDIR}/${MY_P}"
+
+LICENSE="BSD"
+SLOT="0"
+KEYWORDS="~amd64 ~x86"
+
+RDEPEND="
+	=dev-python/numpy-1*[${PYTHON_USEDEP}]
+	>=dev-python/matplotlib-1.5[${PYTHON_USEDEP}]
+	>=dev-python/wxpython-3.0.2.0[${PYTHON_USEDEP}]
+"
+
+distutils_enable_tests pytest
+distutils_enable_sphinx doc dev-python/sphinx-rtd-theme
+
+python_prepare_all() {
+	# do not depend on pytest-cov
+	sed -i -e '/addopts/d' setup.cfg || die
+
+	# assert 0 == 1
+	sed -i -e 's:test_FloatSlider_mouse_non_gtk:_&:' \
+		-e 's:test_FloatSlider_mouse_gtk:_&:' \
+		-e 's:test_SliderSpinPanel_events:_&:' \
+		tests/test_floatslider.py || die
+
+	# assert None == 0
+	sed -i -e 's:test_notebook_events:_&:' \
+		tests/test_notebook.py || die
+
+	# assert 25.0 < 5
+	sed -i -e 's:test_RangePanel_events_slider:_&:' \
+		-e 's:test_RangeSliderSpinPanel_onchange:_&:' \
+		tests/test_rangeslider.py || die
+
+	distutils-r1_python_prepare_all
+}
+
+src_test() {
+	virtx distutils-r1_src_test
+}
+
+python_test() {
+	# If this could be set for the eclass, it might fix some of the tests:
+	# https://github.com/pauldmccarthy/fsleyes-widgets/issues/1#issuecomment-575387724
+	#xvfbargs="-screen 0 1920x1200x24 +extension RANDR"
+	epytest
+}
diff --git a/sci-visualization/fsleyes-widgets/metadata.xml b/sci-visualization/fsleyes-widgets/metadata.xml
new file mode 100644
index 000000000..275610888
--- /dev/null
+++ b/sci-visualization/fsleyes-widgets/metadata.xml
@@ -0,0 +1,17 @@
+<?xml version='1.0' encoding='UTF-8'?>
+<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
+<pkgmetadata>
+	<maintainer type="person">
+		<email>gentoo@chymera.eu</email>
+		<name>Horea Christian</name>
+	</maintainer>
+	<maintainer type="project">
+		<email>sci@gentoo.org</email>
+		<name>Gentoo Science Project</name>
+	</maintainer>
+	<longdescription lang="en">
+		The fsleyes-widgets package contains a collection of GUI widgets and
+		utilities, based on wxPython, which are These widgets are used by
+		fsleyes-props and FSLeyes.
+	</longdescription>
+</pkgmetadata>
diff --git a/sci-visualization/fsleyes/Manifest b/sci-visualization/fsleyes/Manifest
new file mode 100644
index 000000000..a22884a06
--- /dev/null
+++ b/sci-visualization/fsleyes/Manifest
@@ -0,0 +1 @@
+DIST fsleyes-1.5.0.tar.gz 98895209 BLAKE2B 1f8b7545a894c281fb596b94d38330662fd5e6fa92e6bf88e480b214b925355e6f660e9312c7b82da41a1217edf1b7026d95832f31a08cbb0a3106e5bd3123e6 SHA512 cc74244ff56b66fca6ffeb10ae21dc69a0a771a1fb0fbaa6b95837cf8a25e674e7b0f81e96ce7583c22844e217f5b258ec0bd3639559de4e74e85847afdd70b7
diff --git a/sci-visualization/fsleyes/files/fsleyes-0.26.2-fsldir.patch b/sci-visualization/fsleyes/files/fsleyes-0.26.2-fsldir.patch
new file mode 100644
index 000000000..51392f52e
--- /dev/null
+++ b/sci-visualization/fsleyes/files/fsleyes-0.26.2-fsldir.patch
@@ -0,0 +1,14 @@
+--- a/fsleyes/main.py	2018-09-24 17:46:07.756686411 +0200
++++ b/fsleyes/main.py	2018-10-06 14:36:53.328135230 +0200
+@@ -325,11 +325,6 @@
+         app.SetTopWindow(frame)
+         frame.Show()
+ 
+-        # Check that $FSLDIR is set, complain
+-        # to the user if it isn't
+-        if not namespace[0].skipfslcheck:
+-            wx.CallAfter(fslDirWarning, frame)
+-
+         # Check for updates. Ignore point
+         # releases, otherwise users might
+         # get swamped with update notifications.
diff --git a/sci-visualization/fsleyes/fsleyes-1.5.0.ebuild b/sci-visualization/fsleyes/fsleyes-1.5.0.ebuild
new file mode 100644
index 000000000..2b608c0d0
--- /dev/null
+++ b/sci-visualization/fsleyes/fsleyes-1.5.0.ebuild
@@ -0,0 +1,65 @@
+# Copyright 1999-2022 Gentoo Authors
+# Distributed under the terms of the GNU General Public License v2
+
+EAPI=8
+
+PYTHON_COMPAT=( python3_10 )
+DISTUTILS_USE_PEP517=setuptools
+inherit xdg distutils-r1 desktop virtualx
+
+DESCRIPTION="The new FSL image viewer, released with FSL 5.0.10"
+HOMEPAGE="https://git.fmrib.ox.ac.uk/fsl/fsleyes/fsleyes/tree/master"
+SRC_URI="
+	https://git.fmrib.ox.ac.uk/fsl/fsleyes/fsleyes/-/archive/${PV}/${P}.tar.gz
+	https://github.com/pauldmccarthy/fsleyes/archive/${PV}.tar.gz -> ${P}.tar.gz
+"
+
+LICENSE="Apache-2.0"
+SLOT="0"
+KEYWORDS="~amd64"
+
+RDEPEND="
+	>=dev-python/fslpy-3.9[${PYTHON_USEDEP}]
+	>=dev-python/jinja-2[${PYTHON_USEDEP}]
+	>=dev-python/matplotlib-1.5.1[${PYTHON_USEDEP}]
+	>=dev-python/numpy-1.14[${PYTHON_USEDEP}]
+	>=dev-python/pillow-3.2.0[${PYTHON_USEDEP}]
+	>=dev-python/pyopengl-3.1.0[${PYTHON_USEDEP}]
+	>=dev-python/pyopengl_accelerate-3.1.0[${PYTHON_USEDEP}]
+	>=dev-python/pyparsing-2[${PYTHON_USEDEP}]
+	>=dev-python/wxpython-4[${PYTHON_USEDEP}]
+	>=dev-python/scipy-0.18[${PYTHON_USEDEP}]
+	>=sci-libs/nibabel-2.3[${PYTHON_USEDEP}]
+	>=sci-visualization/fsleyes-widgets-0.12.3[${PYTHON_USEDEP}]
+	>=sci-visualization/fsleyes-props-1.8[${PYTHON_USEDEP}]
+	"
+
+PATCHES=(
+	"${FILESDIR}/${PN}-0.26.2-fsldir.patch"
+)
+
+distutils_enable_tests pytest
+distutils_enable_sphinx userdoc dev-python/sphinx-rtd-theme
+
+python_prepare_all() {
+	# do not depend on pytest-cov
+	sed -i -e '/addopts/d' setup.cfg || die
+
+	distutils-r1_python_prepare_all
+}
+
+python_install_all() {
+	distutils-r1_python_install_all
+	doicon -s 48 fsleyes/assets/linux/hicolor/48x48/apps/*.png
+	domenu fsleyes/assets/linux/*.desktop
+	insinto /usr/share/metainfo
+	doins fsleyes/assets/linux/*.appdata.xml
+	local size
+	for size in 16 32 128 256 512 ; do
+		newicon -s ${size} fsleyes/assets/icons/app_icon/${PN}.iconset/icon_${size}x${size}.png "${PN}.png"
+	done
+}
+
+python_test() {
+	virtx epytest
+}
diff --git a/sci-visualization/fsleyes/metadata.xml b/sci-visualization/fsleyes/metadata.xml
new file mode 100644
index 000000000..d38edeff2
--- /dev/null
+++ b/sci-visualization/fsleyes/metadata.xml
@@ -0,0 +1,21 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
+<pkgmetadata>
+	<maintainer type="person">
+		<email>gentoo@chymera.eu</email>
+		<name>Horea Christian</name>
+	</maintainer>
+	<maintainer type="project">
+		<email>sci@gentoo.org</email>
+		<name>Gentoo Science Project</name>
+	</maintainer>
+	<longdescription lang="en">
+		FSLeyes is a viewer for 3D and 4D neuroimaging data. It is intended as a
+		replacement for the much loved FSLView. FSLeyes offers similar functionality
+		to FSLView, and aims to improve and expand upon this functionality in many
+		ways.
+	</longdescription>
+	<upstream>
+		<remote-id type="github">pauldmccarthy/fsleyes</remote-id>
+	</upstream>
+</pkgmetadata>
diff --git a/sci-visualization/mricrogl/Manifest b/sci-visualization/mricrogl/Manifest
index a73b5e67e..8abe973fd 100644
--- a/sci-visualization/mricrogl/Manifest
+++ b/sci-visualization/mricrogl/Manifest
@@ -1,4 +1,2 @@
-DIST mricrogl-1.0.20170401.tar.gz 75578721 BLAKE2B 2d84d20954a1d877ed45ce4effbcef2912cae0117159235b34acb03d5fc86793dd22b89f67ef3bb3f628817e2d7df0f1cad6adda2fcef908059207ab306461fa SHA512 50bbf1451a7b7848d3bc9c8ae6a30ec43ddf45520eacb168b4217b2dc5ab44de680cea55a5223bdb3cc5ebd78ccfdb10559dd212287aecede3165853a30ec082
-DIST mricrogl-1.0.20170714.tar.gz 75803499 BLAKE2B b3b160fb6c1986693ea4bb76dcf27ef691476cbb6acb2eabfe0a5bc78f7d45718d79a7b042a53530d34252757d13bb5b5440fc9a19faa109bf7feb4dc25fd302 SHA512 ce544669343c77aa60698805e5c3b55d22be3b41278b321232695baf4f7f5811cdc898a36b4fd4a08abdcaa5268eda5ec761ced8f7764322cf1a03ec3df3086d
-DIST mricrogl-1.0.20180402.tar.gz 76341660 BLAKE2B 2a94bf9821dc60803efb9bf311846fbcb83881fbb21b69351d109e89a4261c3bd927b8639f85736adade5b8352fa4e20a63d60928210fed4ccc74c6cfd1364f5 SHA512 80c6451707472f5181e8a8c4dbae72ded140f1bd5481f0e5aa1eee2d3367ffab8248d093ecc1bdbca491c0e3d9e8ebd5f97c147b2408077b15c3d9f08d9a947f
-DIST mricrogl-1.0.20180623.tar.gz 81494878 BLAKE2B f90b9a153048676a77a93c067119604a58a55c03992b645cf3fdef936e402728148a772469ad83c2283951fe6a4a931deb39a58cd83a9b27123ddc97556b48d7 SHA512 b3bd3b74b6dfac904b404f6cef7379b06071ae79f44ac71ce3fc40bc8b138f960abbf516e6544db8ae1d8d9cc2cf2df610befa2bdd6b2dfae3d589568e13da04
+DIST mricrogl-1.2.20211007.tar.gz 59766871 BLAKE2B c9ea15b55cc58c2a350e369094098d107ba5464adb8f098c0d8941d7a471ea132d96eec9d7c684fdb87b726594421fd9bcead326dec685066c26b0786597a7af SHA512 faa3409f5ea711927c5f31c869136170cb3a6fc67b7f821e77a867aa2acda76e99f3a1aeeac60ae63df7eff34c163283df024add0dc6c02fa421b5f66f7f5dea
+DIST mricrogl-1.2.20220720.tar.gz 59769179 BLAKE2B 2e7310c8e15db700988100acb5a4173a5411d9cbdbf56832c9acf9031dfe08dbc344b39657cc99e3b27275c0656c2e7ac1aaee39d2acc6731045f2332cf61622 SHA512 58eaf0f4ceacb0e39cb054a1761f3c0734a34c30dd9723bd9790bcc0f5665cd59bac4689ec28a07b2ac5f569b1cac10e005eb1017ad18384a318cee1e15fec2f
diff --git a/sci-visualization/mricrogl/metadata.xml b/sci-visualization/mricrogl/metadata.xml
index a9107b897..076b1ca19 100644
--- a/sci-visualization/mricrogl/metadata.xml
+++ b/sci-visualization/mricrogl/metadata.xml
@@ -6,11 +6,14 @@
 		<name>Gentoo Science Project</name>
 	</maintainer>
 	<longdescription lang="en">
-MRIcroGL is a program designed to display 3D medical imaging.
-By using your computer's graphics card, it can allow real-time
-interactive rendering. It includes scripts to show you some of
-the many effects.
-</longdescription>
+		MRIcroGL is a program designed to display 3D medical imaging.
+		By using your computer's graphics card, it can allow real-time
+		interactive rendering. It includes scripts to show you some of
+		the many effects.
+	</longdescription>
+	<use>
+		<flag name="dicom">Adds limited read support for the DICOM imaging format.</flag>
+	</use>
 	<upstream>
 		<remote-id type="github">neurolabusc/MRIcroGL</remote-id>
 	</upstream>
diff --git a/sci-visualization/mricrogl/mricrogl-1.0.20170401.ebuild b/sci-visualization/mricrogl/mricrogl-1.0.20170401.ebuild
deleted file mode 100644
index b3df3546f..000000000
--- a/sci-visualization/mricrogl/mricrogl-1.0.20170401.ebuild
+++ /dev/null
@@ -1,41 +0,0 @@
-# Copyright 1999-2017 Gentoo Foundation
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=6
-
-inherit gnome2-utils
-
-DESCRIPTION="A simple medical imaging visualization tool"
-HOMEPAGE="https://github.com/neurolabusc/MRIcroGL"
-SRC_URI="https://github.com/neurolabusc/MRIcroGL/archive/v${PV}.tar.gz -> ${P}.tar.gz"
-
-LICENSE="BSD"
-SLOT="0"
-KEYWORDS="~amd64 ~x86"
-
-RDEPEND=""
-DEPEND="dev-lang/fpc
-	>=dev-lang/lazarus-1.6.2"
-
-S="${WORKDIR}/MRIcroGL-${PV}"
-
-src_compile() {
-	lazbuild -B --lazarusdir="${EPREFIX}/usr/share/lazarus/" simplelaz.lpi || die
-}
-
-src_install() {
-	dobin MRIcroGL
-
-	insinto /usr/share/mricrogl
-	doins -r lut script shaders
-
-	doicon -s scalable mricrogl.svg
-	make_desktop_entry MRIcroGL MRIcroGL /usr/share/icons/hicolor/scalable/apps/mricrogl.svg
-}
-
-pkg_postinst() {
-	gnome2_icon_cache_update
-}
-pkg_postrm() {
-	gnome2_icon_cache_update
-}
diff --git a/sci-visualization/mricrogl/mricrogl-1.0.20170714.ebuild b/sci-visualization/mricrogl/mricrogl-1.0.20170714.ebuild
deleted file mode 100644
index 388c8a3e1..000000000
--- a/sci-visualization/mricrogl/mricrogl-1.0.20170714.ebuild
+++ /dev/null
@@ -1,41 +0,0 @@
-# Copyright 1999-2017 Gentoo Foundation
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=6
-
-inherit eutils gnome2-utils
-
-DESCRIPTION="A simple medical imaging visualization tool"
-HOMEPAGE="https://github.com/neurolabusc/MRIcroGL"
-SRC_URI="https://github.com/neurolabusc/MRIcroGL/archive/v${PV}.tar.gz -> ${P}.tar.gz"
-
-LICENSE="BSD"
-SLOT="0"
-KEYWORDS="~amd64 ~x86"
-
-RDEPEND=""
-DEPEND="dev-lang/fpc
-	>=dev-lang/lazarus-1.6.2"
-
-S="${WORKDIR}/MRIcroGL-${PV}"
-
-src_compile() {
-	lazbuild -B --lazarusdir="${EPREFIX}/usr/share/lazarus/" simplelaz.lpi || die
-}
-
-src_install() {
-	dobin MRIcroGL
-
-	insinto /usr/share/mricrogl
-	doins -r lut script shaders
-
-	doicon -s scalable mricrogl.svg
-	make_desktop_entry MRIcroGL MRIcroGL /usr/share/icons/hicolor/scalable/apps/mricrogl.svg
-}
-
-pkg_postinst() {
-	gnome2_icon_cache_update
-}
-pkg_postrm() {
-	gnome2_icon_cache_update
-}
diff --git a/sci-visualization/mricrogl/mricrogl-1.0.20180402.ebuild b/sci-visualization/mricrogl/mricrogl-1.0.20180402.ebuild
deleted file mode 100644
index ab87019a2..000000000
--- a/sci-visualization/mricrogl/mricrogl-1.0.20180402.ebuild
+++ /dev/null
@@ -1,41 +0,0 @@
-# Copyright 1999-2018 Gentoo Foundation
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=6
-
-inherit eutils gnome2-utils
-
-DESCRIPTION="A simple medical imaging visualization tool"
-HOMEPAGE="https://github.com/neurolabusc/MRIcroGL"
-SRC_URI="https://github.com/neurolabusc/MRIcroGL/archive/v${PV}.tar.gz -> ${P}.tar.gz"
-
-LICENSE="BSD"
-SLOT="0"
-KEYWORDS="~amd64 ~x86"
-
-RDEPEND=""
-DEPEND="dev-lang/fpc
-	>=dev-lang/lazarus-1.6.2"
-
-S="${WORKDIR}/MRIcroGL-${PV}"
-
-src_compile() {
-	lazbuild -B --lazarusdir="${EPREFIX}/usr/share/lazarus/" simplelaz.lpi || die
-}
-
-src_install() {
-	dobin MRIcroGL
-
-	insinto /usr/share/mricrogl
-	doins -r lut script shaders
-
-	doicon -s scalable mricrogl.svg
-	make_desktop_entry MRIcroGL MRIcroGL /usr/share/icons/hicolor/scalable/apps/mricrogl.svg
-}
-
-pkg_postinst() {
-	gnome2_icon_cache_update
-}
-pkg_postrm() {
-	gnome2_icon_cache_update
-}
diff --git a/sci-visualization/mricrogl/mricrogl-1.0.20180623.ebuild b/sci-visualization/mricrogl/mricrogl-1.0.20180623.ebuild
deleted file mode 100644
index 3c54c1576..000000000
--- a/sci-visualization/mricrogl/mricrogl-1.0.20180623.ebuild
+++ /dev/null
@@ -1,44 +0,0 @@
-# Copyright 1999-2018 Gentoo Foundation
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=6
-
-inherit eutils gnome2-utils
-
-DESCRIPTION="A simple medical imaging visualization tool"
-HOMEPAGE="https://github.com/neurolabusc/MRIcroGL"
-SRC_URI="https://github.com/neurolabusc/MRIcroGL/archive/v${PV}.tar.gz -> ${P}.tar.gz"
-
-LICENSE="BSD"
-SLOT="0"
-KEYWORDS="~amd64 ~x86"
-
-RDEPEND=""
-DEPEND="dev-lang/fpc
-	>=dev-lang/lazarus-1.6.2[python]"
-
-S="${WORKDIR}/MRIcroGL-${PV}"
-
-src_compile() {
-	# Python support will only be vaialable for the default implementation:
-	# https://github.com/neurolabusc/MRIcroGL/issues/30#issuecomment-423216197
-	cp -rf /etc/lazarus system-lazarus-config
-	lazbuild -B --lazarusdir="/usr/share/lazarus/" --pcp="system-lazarus-config" simplelaz.lpi || die
-}
-
-src_install() {
-	dobin MRIcroGL
-
-	insinto /usr/share/mricrogl
-	doins -r lut script shaders
-
-	doicon -s scalable mricrogl.svg
-	make_desktop_entry MRIcroGL MRIcroGL /usr/share/icons/hicolor/scalable/apps/mricrogl.svg
-}
-
-pkg_postinst() {
-	gnome2_icon_cache_update
-}
-pkg_postrm() {
-	gnome2_icon_cache_update
-}
diff --git a/sci-visualization/mricrogl/mricrogl-1.2.20211007-r1.ebuild b/sci-visualization/mricrogl/mricrogl-1.2.20211007-r1.ebuild
new file mode 100644
index 000000000..da8e446cf
--- /dev/null
+++ b/sci-visualization/mricrogl/mricrogl-1.2.20211007-r1.ebuild
@@ -0,0 +1,66 @@
+# Copyright 1999-2023 Gentoo Authors
+# Distributed under the terms of the GNU General Public License v2
+
+EAPI=8
+
+MY_PN="MRIcroGL"
+inherit desktop xdg-utils
+
+DESCRIPTION="A simple medical imaging visualization tool"
+HOMEPAGE="https://github.com/neurolabusc/MRIcroGL"
+SRC_URI="https://github.com/rordenlab/${MY_PN}/archive/v${PV}.tar.gz -> ${P}.tar.gz"
+
+LICENSE="BSD"
+SLOT="0"
+KEYWORDS="~amd64 ~x86"
+IUSE="dicom python"
+
+BDEPEND="dev-lang/lazarus"
+DEPEND="
+	dev-lang/fpc
+	x11-misc/appmenu-gtk-module[gtk2]
+	"
+RDEPEND="dicom? ( sci-biology/dcm2niix )"
+
+S="${WORKDIR}/${MY_PN}-${PV}"
+
+src_compile() {
+	# Allegedly the Debian recipe contains some sort of Python support, wasn't able to test.
+	if use python; then
+		lazbuild -B \
+			--lazarusdir="/usr/share/lazarus/" \
+			--pcp="system-lazarus-config" \
+			MRIcroGL_Debian.lpi || die
+	else
+		lazbuild -B \
+			--lazarusdir="/usr/share/lazarus/" \
+			--pcp="system-lazarus-config" \
+			MRIcroGL_NoPython.lpi || die
+	fi
+}
+
+src_install() {
+	dobin MRIcroGL
+
+	pushd Resources > /dev/null
+		insinto /usr/share/MRIcroGL
+		doins -r lut matcap Roboto.* script shader
+		doicon -s scalable mricrogl.svg
+		make_desktop_entry MRIcroGL MRIcroGL /usr/share/icons/hicolor/scalable/apps/mricrogl.svg
+	popd
+}
+
+pkg_postinst(){
+	xdg_icon_cache_update
+
+	ewarn "This package might exhibit nondeterministic lag at startup manifesting as a blank"
+	ewarn "window, which can either be closed (e.g. Alt+F4) manually leading to the actual"
+	ewarn "interface being launched, or will close itself after 10-20s and start the proper GUI"
+	ewarn "For more details on this look up: https://github.com/rordenlab/MRIcroGL/issues/49"
+}
+
+pkg_postrm() {
+	xdg_icon_cache_update
+	xdg_mimeinfo_database_update
+	xdg_desktop_database_update
+}
diff --git a/sci-visualization/mricrogl/mricrogl-1.2.20220720-r1.ebuild b/sci-visualization/mricrogl/mricrogl-1.2.20220720-r1.ebuild
new file mode 100644
index 000000000..da8e446cf
--- /dev/null
+++ b/sci-visualization/mricrogl/mricrogl-1.2.20220720-r1.ebuild
@@ -0,0 +1,66 @@
+# Copyright 1999-2023 Gentoo Authors
+# Distributed under the terms of the GNU General Public License v2
+
+EAPI=8
+
+MY_PN="MRIcroGL"
+inherit desktop xdg-utils
+
+DESCRIPTION="A simple medical imaging visualization tool"
+HOMEPAGE="https://github.com/neurolabusc/MRIcroGL"
+SRC_URI="https://github.com/rordenlab/${MY_PN}/archive/v${PV}.tar.gz -> ${P}.tar.gz"
+
+LICENSE="BSD"
+SLOT="0"
+KEYWORDS="~amd64 ~x86"
+IUSE="dicom python"
+
+BDEPEND="dev-lang/lazarus"
+DEPEND="
+	dev-lang/fpc
+	x11-misc/appmenu-gtk-module[gtk2]
+	"
+RDEPEND="dicom? ( sci-biology/dcm2niix )"
+
+S="${WORKDIR}/${MY_PN}-${PV}"
+
+src_compile() {
+	# Allegedly the Debian recipe contains some sort of Python support, wasn't able to test.
+	if use python; then
+		lazbuild -B \
+			--lazarusdir="/usr/share/lazarus/" \
+			--pcp="system-lazarus-config" \
+			MRIcroGL_Debian.lpi || die
+	else
+		lazbuild -B \
+			--lazarusdir="/usr/share/lazarus/" \
+			--pcp="system-lazarus-config" \
+			MRIcroGL_NoPython.lpi || die
+	fi
+}
+
+src_install() {
+	dobin MRIcroGL
+
+	pushd Resources > /dev/null
+		insinto /usr/share/MRIcroGL
+		doins -r lut matcap Roboto.* script shader
+		doicon -s scalable mricrogl.svg
+		make_desktop_entry MRIcroGL MRIcroGL /usr/share/icons/hicolor/scalable/apps/mricrogl.svg
+	popd
+}
+
+pkg_postinst(){
+	xdg_icon_cache_update
+
+	ewarn "This package might exhibit nondeterministic lag at startup manifesting as a blank"
+	ewarn "window, which can either be closed (e.g. Alt+F4) manually leading to the actual"
+	ewarn "interface being launched, or will close itself after 10-20s and start the proper GUI"
+	ewarn "For more details on this look up: https://github.com/rordenlab/MRIcroGL/issues/49"
+}
+
+pkg_postrm() {
+	xdg_icon_cache_update
+	xdg_mimeinfo_database_update
+	xdg_desktop_database_update
+}
diff --git a/sci-visualization/mricrogl/mricrogl-9999.ebuild b/sci-visualization/mricrogl/mricrogl-9999.ebuild
deleted file mode 100644
index 45eb77642..000000000
--- a/sci-visualization/mricrogl/mricrogl-9999.ebuild
+++ /dev/null
@@ -1,44 +0,0 @@
-# Copyright 1999-2018 Gentoo Foundation
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=6
-
-inherit git-r3 gnome2-utils
-
-DESCRIPTION="A simple medical imaging visualization tool"
-HOMEPAGE="https://github.com/neurolabusc/MRIcroGL"
-SRC_URI=""
-EGIT_REPO_URI="https://github.com/neurolabusc/MRIcroGL.git"
-
-LICENSE="BSD"
-SLOT="0"
-
-RDEPEND=""
-DEPEND="dev-lang/fpc
-	>=dev-lang/lazarus-1.6.2
-	media-libs/mesa
-	"
-
-src_compile() {
-	# Python support will only be vaialable for the default implementation:
-	# https://github.com/neurolabusc/MRIcroGL/issues/30#issuecomment-423216197
-	cp -rf /etc/lazarus system-lazarus-config
-	lazbuild -B --lazarusdir="/usr/share/lazarus/" --pcp="system-lazarus-config" simplelaz.lpi || die
-}
-
-src_install() {
-	dobin MRIcroGL
-
-	insinto /usr/share/mricrogl
-	doins -r lut script shaders
-
-	doicon -s scalable mricrogl.svg
-	make_desktop_entry MRIcroGL MRIcroGL /usr/share/icons/hicolor/scalable/apps/mricrogl.svg
-}
-
-pkg_postinst() {
-	gnome2_icon_cache_update
-}
-pkg_postrm() {
-	gnome2_icon_cache_update
-}
diff --git a/sci-visualization/mricron/metadata.xml b/sci-visualization/mricron/metadata.xml
deleted file mode 100644
index 4e582b27d..000000000
--- a/sci-visualization/mricron/metadata.xml
+++ /dev/null
@@ -1,14 +0,0 @@
-<?xml version="1.0" encoding="UTF-8"?>
-<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
-<pkgmetadata>
-	<maintainer type="project">
-		<email>sci@gentoo.org</email>
-		<name>Gentoo Science Project</name>
-	</maintainer>
-	<longdescription lang="en">
-MRIcron is a simple medical imaging visualization tool written in Lazarus.
-</longdescription>
-	<upstream>
-		<remote-id type="github">neurolabusc/MRIcron</remote-id>
-	</upstream>
-</pkgmetadata>
diff --git a/sci-visualization/mricron/mricron-9999.ebuild b/sci-visualization/mricron/mricron-9999.ebuild
deleted file mode 100644
index 7605d5bcd..000000000
--- a/sci-visualization/mricron/mricron-9999.ebuild
+++ /dev/null
@@ -1,37 +0,0 @@
-# Copyright 1999-2016 Gentoo Foundation
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=6
-
-inherit git-r3 gnome2-utils
-
-DESCRIPTION="A simple medical imaging visualization tool"
-HOMEPAGE="https://github.com/neurolabusc/MRIcron"
-SRC_URI=""
-EGIT_REPO_URI="https://github.com/neurolabusc/MRIcron.git"
-
-LICENSE="BSD"
-SLOT="0"
-
-RDEPEND=""
-DEPEND="dev-lang/fpc
-	dev-lang/lazarus"
-
-src_compile() {
-	lazbuild -B --lazarusdir="/usr/share/lazarus/" mricron.lpr || die
-}
-
-src_install() {
-	dobin mricron
-	dobin dcm2nii/dcm2nii
-	dobin dcm2nii/dcm2niigui
-	doicon icons/mricron.png
-	make_desktop_entry mricron MRIcron mricron
-}
-
-pkg_postinst() {
-	gnome2_icon_cache_update
-}
-pkg_postrm() {
-	gnome2_icon_cache_update
-}
diff --git a/sci-visualization/nodemon/Manifest b/sci-visualization/nodemon/Manifest
deleted file mode 100644
index 1c1cf3280..000000000
--- a/sci-visualization/nodemon/Manifest
+++ /dev/null
@@ -1 +0,0 @@
-DIST nodemon-0.3.5.tar.gz 697412 BLAKE2B 9d986fb230e6aee3d4cb6f8383343319a62f29a7a27514846fb40b1c14765efe82566de350349e67c737ff22e22159d687ed45f07815b4198ceea7733eb64b7e SHA512 145f8a8a8d8594b9c035d7c538571006a7052d6a9714e449f1efe15302faecfb5274d639531652d2bccd658308ee93633dd15246589ceb52afde701fd27ba615
diff --git a/sci-visualization/nodemon/metadata.xml b/sci-visualization/nodemon/metadata.xml
deleted file mode 100644
index 3bbffb9b5..000000000
--- a/sci-visualization/nodemon/metadata.xml
+++ /dev/null
@@ -1,23 +0,0 @@
-<?xml version="1.0" encoding="UTF-8"?>
-<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
-<pkgmetadata>
-	<maintainer type="person">
-		<email>bryan.d.green@nasa.gov</email>
-		<name>Bryan Green</name>
-	</maintainer>
-	<maintainer type="project">
-		<email>sci@gentoo.org</email>
-		<name>Gentoo Science Project</name>
-	</maintainer>
-	<longdescription>
-NodeMon is a distributed visualization tool for monitoring system resource
-utilization.  It is primarily intended for clusters and large-scale NUMA
-systems.
-</longdescription>
-	<use>
-		<flag name="pbs">Enable support for the Portable Batch System.</flag>
-	</use>
-	<upstream>
-		<remote-id type="sourceforge">downloads</remote-id>
-	</upstream>
-</pkgmetadata>
diff --git a/sci-visualization/nodemon/nodemon-0.3.5.ebuild b/sci-visualization/nodemon/nodemon-0.3.5.ebuild
deleted file mode 100644
index 60496ec7c..000000000
--- a/sci-visualization/nodemon/nodemon-0.3.5.ebuild
+++ /dev/null
@@ -1,29 +0,0 @@
-# Copyright 1999-2015 Gentoo Foundation
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=5
-
-DESCRIPTION="Distributed visualization tool for monitoring system resource utilization"
-HOMEPAGE="http://nodemon.sourceforge.net/"
-SRC_URI="http://downloads.sourceforge.net/nodemon/nodemon-${PV}.tar.gz"
-
-LICENSE="NOSA"
-SLOT="0"
-KEYWORDS="~amd64 ~x86"
-IUSE="gtk pbs"
-
-RDEPEND="
-	>=dev-cpp/growler-arch-0.3.7.1
-	gtk? (
-		>=x11-libs/gtkglext-1.0
-		x11-libs/gtk+:2
-	)"
-DEPEND="${RDEPEND}"
-
-DOCS="README NEWS AUTHORS NOSA ChangeLog"
-
-src_configure() {
-	econf \
-		$(use_enable gtk) \
-		$(use_with pbs)
-}
diff --git a/sci-visualization/surf-ice/Manifest b/sci-visualization/surf-ice/Manifest
index b7b7b498f..b65215cb2 100644
--- a/sci-visualization/surf-ice/Manifest
+++ b/sci-visualization/surf-ice/Manifest
@@ -1,2 +1 @@
-DIST surf-ice-1.0.20170202.tar.gz 40179987 BLAKE2B 94c396f2813d37664988ddf1402421799bb6e4d2bdfb016db4420c810b38466bb274c8d43ea4d8ddba870155fdea5873a6ef6aea286961741726b61bd8eb7f61 SHA512 526828d12a75f103fa04ef6e2bd1a5f75eabd47243797392ac8275e9bfaacd66285272241171745c3d7aa5669dc24eee736d597ad89d066d8cbeb4ad4a0954df
-DIST surf-ice-1.0.20180622.tar.gz 29653902 BLAKE2B f68d2746d7bb2c97e4e998d394c1028173164d855ada695d65846f78ec7c6d1b43b6bab66444da27000d7d0539b2b1adfe0499321085980ba3d528423315d84e SHA512 dcad99c7add43d9e5b3196f64236a64c7315cd5bbbd744911c322b4ac821d8a81f268e43a367e9e09cd22972abb64f9419346a8119332551ae02a9261751c5f8
+DIST surf-ice-1.0.20201102.tar.gz 31088319 BLAKE2B 08b0f234776dbcc568dd6f5cd024e06759bece6deaac759e44b30887c171ea4619ca0c422d6fba2948bdf5efa57a2e8d82950a1ef0eafea9646b939eccce6c1a SHA512 3158733e9910440900f9bc3a00d5ba7635613e72a3d40b64e3ae80927ad69d8103c78097e6b4230d802008a0d1d81164904862edf715dc66782fa74cf227c23b
diff --git a/sci-visualization/surf-ice/metadata.xml b/sci-visualization/surf-ice/metadata.xml
index 8c0be2bba..190e6c026 100644
--- a/sci-visualization/surf-ice/metadata.xml
+++ b/sci-visualization/surf-ice/metadata.xml
@@ -6,7 +6,7 @@
 		<name>Gentoo Science Project</name>
 	</maintainer>
 	<maintainer type="person">
-		<email>horea.christ@gmail.com</email>
+		<email>gentoo@chymera.eu</email>
 		<name>Horea Christian</name>
 	</maintainer>
 	<longdescription lang="en">
diff --git a/sci-visualization/surf-ice/surf-ice-1.0.20170202.ebuild b/sci-visualization/surf-ice/surf-ice-1.0.20170202.ebuild
deleted file mode 100644
index bd983444a..000000000
--- a/sci-visualization/surf-ice/surf-ice-1.0.20170202.ebuild
+++ /dev/null
@@ -1,44 +0,0 @@
-# Copyright 1999-2017 Gentoo Foundation
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=6
-
-inherit gnome2-utils
-
-DESCRIPTION="A simple medical imaging visualization tool"
-HOMEPAGE="https://github.com/neurolabusc/surf-ice"
-SRC_URI="https://github.com/neurolabusc/surf-ice/archive/v${PV}.tar.gz -> ${P}.tar.gz"
-
-LICENSE="BSD"
-SLOT="0"
-KEYWORDS="~amd64 ~x86"
-
-RDEPEND=""
-DEPEND="dev-lang/fpc
-	>=dev-lang/lazarus-1.6.2"
-
-#S="${WORKDIR}/surf-ice-${PV}"
-
-src_compile() {
-	lazbuild -B --lazarusdir="/usr/share/lazarus/" surfice.lpi || die
-}
-
-src_install() {
-	dobin surfice
-
-	insinto /usr/bin/shaders
-	doins shaders/*.txt
-
-	insinto /usr/bin/shadersOld
-	doins shadersOld/*.txt
-
-	doicon -s scalable Surfice.jpg
-	make_desktop_entry surfice surfice /usr/share/icons/hicolor/scalable/apps/Surfice.jpg
-}
-
-pkg_postinst() {
-	gnome2_icon_cache_update
-}
-pkg_postrm() {
-	gnome2_icon_cache_update
-}
diff --git a/sci-visualization/surf-ice/surf-ice-1.0.20180622.ebuild b/sci-visualization/surf-ice/surf-ice-1.0.20180622.ebuild
deleted file mode 100644
index 477d3a0c8..000000000
--- a/sci-visualization/surf-ice/surf-ice-1.0.20180622.ebuild
+++ /dev/null
@@ -1,45 +0,0 @@
-# Copyright 1999-2018 Gentoo Foundation
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=6
-
-inherit gnome2-utils
-
-DESCRIPTION="A simple medical imaging visualization tool"
-HOMEPAGE="https://github.com/neurolabusc/surf-ice"
-SRC_URI="https://github.com/neurolabusc/surf-ice/archive/v${PV}.tar.gz -> ${P}.tar.gz"
-
-LICENSE="BSD"
-SLOT="0"
-KEYWORDS="~amd64 ~x86"
-
-RDEPEND=""
-DEPEND="dev-lang/fpc
-	>=dev-lang/lazarus-1.6.2[python]"
-
-src_compile() {
-	# Python support will only be vaialable for the default implementation:
-	# https://github.com/neurolabusc/MRIcroGL/issues/30#issuecomment-423216197
-	cp -rf /etc/lazarus system-lazarus-config
-	lazbuild -B --lazarusdir="/usr/share/lazarus/" --pcp="system-lazarus-config" surfice.lpi || die
-}
-
-src_install() {
-	dobin surfice
-
-	insinto /usr/bin/shaders
-	doins shaders/*.txt
-
-	insinto /usr/bin/shadersOld
-	doins shadersOld/*.txt
-
-	doicon -s scalable Surfice.jpg
-	make_desktop_entry surfice surfice /usr/share/icons/hicolor/scalable/apps/Surfice.jpg
-}
-
-pkg_postinst() {
-	gnome2_icon_cache_update
-}
-pkg_postrm() {
-	gnome2_icon_cache_update
-}
diff --git a/sci-visualization/surf-ice/surf-ice-1.0.20201102.ebuild b/sci-visualization/surf-ice/surf-ice-1.0.20201102.ebuild
new file mode 100644
index 000000000..e2e0ae462
--- /dev/null
+++ b/sci-visualization/surf-ice/surf-ice-1.0.20201102.ebuild
@@ -0,0 +1,34 @@
+# Copyright 1999-2022 Gentoo Authors
+# Distributed under the terms of the GNU General Public License v2
+
+EAPI=7
+
+inherit desktop xdg
+
+DESCRIPTION="A simple medical imaging visualization tool"
+HOMEPAGE="https://github.com/neurolabusc/surf-ice"
+SRC_URI="https://github.com/neurolabusc/surf-ice/archive/v${PV}.tar.gz -> ${P}.tar.gz"
+
+LICENSE="BSD"
+SLOT="0"
+KEYWORDS="~amd64 ~x86"
+
+RDEPEND=""
+DEPEND="${RDEPEND}
+	dev-lang/fpc
+	>=dev-lang/lazarus-1.6.2
+"
+
+src_compile() {
+	# Python support will only be vaialable for the default implementation:
+	# https://github.com/neurolabusc/MRIcroGL/issues/30#issuecomment-423216197
+	cp -rf /etc/lazarus system-lazarus-config
+	lazbuild -B --lazarusdir="/usr/share/lazarus/" --pcp="system-lazarus-config" surfice.lpi || die
+}
+
+src_install() {
+	dobin surfice
+
+	doicon -s scalable Surfice.jpg
+	make_desktop_entry surfice surfice /usr/share/icons/hicolor/scalable/apps/Surfice.jpg
+}
diff --git a/sci-visualization/surf-ice/surf-ice-9999.ebuild b/sci-visualization/surf-ice/surf-ice-9999.ebuild
index 6858805e5..1419f17be 100644
--- a/sci-visualization/surf-ice/surf-ice-9999.ebuild
+++ b/sci-visualization/surf-ice/surf-ice-9999.ebuild
@@ -1,21 +1,22 @@
-# Copyright 1999-2018 Gentoo Foundation
+# Copyright 1999-2022 Gentoo Authors
 # Distributed under the terms of the GNU General Public License v2
 
-EAPI=6
+EAPI=7
 
-inherit git-r3 gnome2-utils
+inherit git-r3 desktop xdg
 
 DESCRIPTION="A surface rendering tool supporting neuroimaging data"
 HOMEPAGE="https://github.com/neurolabusc/surf-ice"
-SRC_URI=""
 EGIT_REPO_URI="https://github.com/neurolabusc/surf-ice.git"
 
 LICENSE="BSD"
 SLOT="0"
 
 RDEPEND=""
-DEPEND="dev-lang/fpc
-	>=dev-lang/lazarus-1.6.2"
+DEPEND="${RDEPEND}
+	dev-lang/fpc
+	>=dev-lang/lazarus-1.6.2
+"
 
 src_compile() {
 	# Python support will only be vaialable for the default implementation:
@@ -27,16 +28,6 @@ src_compile() {
 src_install() {
 	dobin surfice
 
-	insinto /usr/share/surfice
-	doins -r lut script shaders shadersOld
-
 	doicon -s scalable Surfice.jpg
 	make_desktop_entry surfice surfice /usr/share/icons/hicolor/scalable/apps/Surfice.jpg
 }
-
-pkg_postinst() {
-	gnome2_icon_cache_update
-}
-pkg_postrm() {
-	gnome2_icon_cache_update
-}
diff --git a/sci-visualization/yt/Manifest b/sci-visualization/yt/Manifest
deleted file mode 100644
index 48134f975..000000000
--- a/sci-visualization/yt/Manifest
+++ /dev/null
@@ -1 +0,0 @@
-DIST yt-2.6.tar.gz 2327271 BLAKE2B 7d441a9866b6a1dc0f3b35194b6ccc135741e29951bb3c3923658f3595976bb970e983c836a24dfb958efcf0ac7e2a3f802d7d12916f92b95962381d9da7052d SHA512 cbd20db03b1cd5fe8fff3b24d51de13ef620add8f0808a50e45efe9568efba008c23625f1cd8edb3adc5315bc2ebc2898032bdf9f9611df1148569975c9fdf1c
diff --git a/sci-visualization/yt/metadata.xml b/sci-visualization/yt/metadata.xml
deleted file mode 100644
index 5957457f4..000000000
--- a/sci-visualization/yt/metadata.xml
+++ /dev/null
@@ -1,21 +0,0 @@
-<?xml version="1.0" encoding="UTF-8"?>
-<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
-<pkgmetadata>
-	<maintainer type="person">
-		<email>xarthisius@gentoo.org</email>
-		<name>Kacper Kowalik</name>
-	</maintainer>
-	<maintainer type="project">
-		<email>sci@gentoo.org</email>
-		<name>Gentoo Science Project</name>
-	</maintainer>
-	<longdescription>yt is an analysis and visualization system written in Python,
-designed for use with Astrophysical Simulation codes. yt can process data in a
-myriad of ways and make a variety of visualizations. It is designed to be portable
-across simulation codes, and it is developed by developers from a variety of
-institutions and backgrounds.
-</longdescription>
-	<upstream>
-		<remote-id type="pypi">yt</remote-id>
-	</upstream>
-</pkgmetadata>
diff --git a/sci-visualization/yt/yt-2.6.ebuild b/sci-visualization/yt/yt-2.6.ebuild
deleted file mode 100644
index 37efad0fd..000000000
--- a/sci-visualization/yt/yt-2.6.ebuild
+++ /dev/null
@@ -1,50 +0,0 @@
-# Copyright 1999-2014 Gentoo Foundation
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=5
-PYTHON_COMPAT=( python2_7 )
-DISTUTILS_IN_SOURCE_BUILD=1
-
-inherit distutils-r1 flag-o-matic
-
-DESCRIPTION="Astrophysical Simulation Analysis and Vizualization package"
-HOMEPAGE="http://yt-project.org/"
-SRC_URI="mirror://pypi/${PN:0:1}/${PN}/${P}.tar.gz"
-
-LICENSE="BSD"
-SLOT="0"
-KEYWORDS="~amd64 ~x86 ~amd64-linux ~x86-linux"
-IUSE="test"
-
-CDEPEND="media-libs/freetype:2
-	media-libs/libpng:0=
-	sci-libs/hdf5:="
-RDEPEND="${CDEPEND}
-	dev-python/ipython[notebook,${PYTHON_USEDEP}]
-	dev-python/pyx[${PYTHON_USEDEP}]
-	dev-python/numpy[${PYTHON_USEDEP}]
-	dev-python/h5py[${PYTHON_USEDEP}]
-	dev-python/matplotlib[${PYTHON_USEDEP}]
-	dev-python/sympy[${PYTHON_USEDEP}]"
-DEPEND="${CDEPEND}
-	dev-python/Forthon[${PYTHON_USEDEP}]
-	>=dev-python/cython-0.19[${PYTHON_USEDEP}]
-	>=dev-python/setuptools-0.7[${PYTHON_USEDEP}]
-	test? ( ${RDEPEND}
-		dev-python/nose[${PYTHON_USEDEP}]
-	)"
-
-python_prepare_all() {
-	append-flags -fno-strict-aliasing
-	sed -i setup.py \
-		-e 's:build/lib:../../../&:' || die
-	sed -i yt/utilities/setup.py \
-		-e "s:/usr:${EPREFIX}/usr:g"  || die
-	mv yt/utilities/kdtree/fKD.{f,F}90 || die # Forthon-0.8.13
-	distutils-r1_python_prepare_all
-}
-
-# TODO
-#python_test() {
-#	nosetests || die
-#}
diff --git a/sci-visualization/yt/yt-9999.ebuild b/sci-visualization/yt/yt-9999.ebuild
deleted file mode 100644
index f6c4869a7..000000000
--- a/sci-visualization/yt/yt-9999.ebuild
+++ /dev/null
@@ -1,53 +0,0 @@
-# Copyright 1999-2014 Gentoo Foundation
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=5
-
-PYTHON_COMPAT=( python2_7 )
-DISTUTILS_IN_SOURCE_BUILD=1
-EHG_REPO_URI="https://bitbucket.org/yt_analysis/yt"
-EHG_REVISION="yt"
-
-inherit distutils-r1 mercurial
-
-DESCRIPTION="Astrophysical Simulation Analysis and Vizualization package"
-HOMEPAGE="http://yt-project.org/"
-SRC_URI=""
-
-LICENSE="BSD"
-SLOT="0"
-KEYWORDS=""
-IUSE="test"
-
-CDEPEND="media-libs/freetype:2
-	media-libs/libpng:0=
-	sci-libs/hdf5:="
-RDEPEND="${CDEPEND}
-	dev-python/ipython[notebook,${PYTHON_USEDEP}]
-	dev-python/pyx[${PYTHON_USEDEP}]
-	dev-python/numpy[${PYTHON_USEDEP}]
-	dev-python/h5py[${PYTHON_USEDEP}]
-	dev-python/matplotlib[${PYTHON_USEDEP}]
-	dev-python/sympy[${PYTHON_USEDEP}]"
-DEPEND="${CDEPEND}
-	dev-python/Forthon[${PYTHON_USEDEP}]
-	>=dev-python/cython-0.19[${PYTHON_USEDEP}]
-	>=dev-python/setuptools-0.7[${PYTHON_USEDEP}]
-	test? ( ${RDEPEND}
-		dev-python/nose[${PYTHON_USEDEP}]
-	)"
-
-python_prepare_all() {
-	append-flags -fno-strict-aliasing
-	sed -i setup.py \
-		-e 's:build/lib:../../../&:' || die
-	sed -i yt/utilities/setup.py \
-		-e "s:/usr:${EPREFIX}/usr:g" || die
-	mv yt/utilities/kdtree/fKD.{f,F}90 || die # Forthon-0.8.13
-	distutils-r1_python_prepare_all
-}
-
-# TODO
-#python_test() {
-#	nosetests || die
-#}
diff --git a/scripts/check-duplicates.sh b/scripts/check-duplicates.sh
new file mode 100755
index 000000000..56c5bf1dd
--- /dev/null
+++ b/scripts/check-duplicates.sh
@@ -0,0 +1,76 @@
+#! /usr/bin/env bash
+# Maintainer: Andrew Ammerlaan <andrewammerlaan@gentoo.org>
+# Maintainer: Theo Anderson <telans@posteo.de>
+#
+# This checks for potential and exact package matches within an overlay & ::gentoo
+# Note that this is not going to be 100% accurate
+
+GENTOO_DIR="/var/db/repos/gentoo"
+GENTOO_PACKAGES=(
+	$(find ${GENTOO_DIR} -mindepth 2 -maxdepth 2 -printf "%P\n" \
+		| sort | grep -Ev "^(.git|.github|metadata|profiles|scripts)/|metadata.xml"
+	)
+)
+REPO_PACKAGES=(
+	$(find . -mindepth 2 -maxdepth 2 -printf "%P\n" \
+		| sort | grep -Ev "^(.git|.github|metadata|profiles|scripts)/|metadata.xml"
+	)
+)
+
+REPO_NAME="$(cat profiles/repo_name)"
+
+printf "\nChecking for duplicates...\n"
+
+for GENTOO_PKG in ${GENTOO_PACKAGES[@]}; do
+	GENTOO_CATEGORIES+=( ${GENTOO_PKG%%/*} )	# Separate category
+	GENTOO_PKG_NAME=${GENTOO_PKG##*/}			# Separate name
+	GENTOO_PKG_NAME=${GENTOO_PKG_NAME,,}		# Force lower case, e.g. to match foobar and FooBar
+	GENTOO_PKG_NAME=${GENTOO_PKG_NAME/[-_]}		# Remove underscores and dashes, e.g. to match foo-bar and foo_bar
+	GENTOO_PKG_NAMES+=( ${GENTOO_PKG_NAME} )
+done
+
+printf "Testing ${#REPO_PACKAGES[@]} ${REPO_NAME^} packages against ${#GENTOO_PKG_NAMES[@]} Gentoo packages\n"
+
+for REPO_PKG in ${REPO_PACKAGES[@]}; do
+	REPO_PKG_CATEGORY=${REPO_PKG%%/*}
+	REPO_PKG_NAME=${REPO_PKG##*/}
+	REPO_PKG_NAME=${REPO_PKG_NAME,,}
+	REPO_PKG_NAME=${REPO_PKG_NAME/[-_]}
+
+	if [[ ${GENTOO_PKG_NAMES[@]} =~ " ${REPO_PKG_NAME} " ]]; then	# Check for a matcing name in the Gentoo tree,
+		for (( i=0; i<${#GENTOO_PKG_NAMES[@]}; i++ )); do			# otherwise there is no need to continue
+			[[ ${GENTOO_PKG_NAMES[$i]} == ${REPO_PKG_NAME} ]] && index+=( $i ) # Find the category/index for multiple matching names
+		done
+
+		for i in ${index[@]}; do	# For each possible match
+			if [[ ${GENTOO_PACKAGES[$i]} == ${REPO_PKG} ]]; then
+				PKG_EXACT_MATCH+="\t${REPO_PKG}::${REPO_NAME} exact match of ${GENTOO_PACKAGES[$i]}::gentoo\n"
+				break	# An exact match is fatal, no need to continue
+			elif [[ ${GENTOO_CATEGORIES[$i]} == ${REPO_PKG_CATEGORY} ]]; then # Possible match within the same category
+				PKG_CATEGORY_MATCH+="\t${REPO_PKG}::${REPO_NAME} possible duplicate of ${GENTOO_PACKAGES[$i]}::gentoo\n"
+			else # Possible match in a different category
+				PKG_SPECULATIVE_MATCH+="\t${REPO_PKG}::${REPO_NAME} possible duplicate of ${GENTOO_PACKAGES[$i]}::gentoo\n"
+			fi
+		done
+		unset index
+	fi
+done
+
+if [[ -n ${PKG_SPECULATIVE_MATCH} ]]; then
+	printf "\nWARNING: The following packages closely match packages in the main Gentoo repository:\n"
+	printf "${PKG_SPECULATIVE_MATCH}"
+	printf "Please check these manually.\n"
+fi
+
+if [[ -n ${PKG_CATEGORY_MATCH} ]]; then
+	printf "\nWARNING: The following packages closely match packages in the main Gentoo repository, in the same category:\n"
+	printf "${PKG_CATEGORY_MATCH}"
+	printf "Please check these manually.\n"
+fi
+
+if [[ -n ${PKG_EXACT_MATCH} ]]; then
+	printf "\nERROR: The following packages override packages in the main Gentoo repository:\n"
+	printf "${PKG_EXACT_MATCH}"
+	printf "Please remove these packages.\n"
+	# exit 1
+fi
diff --git a/scripts/lapack-migration.sh b/scripts/lapack-migration.sh
deleted file mode 100755
index cd932c130..000000000
--- a/scripts/lapack-migration.sh
+++ /dev/null
@@ -1,25 +0,0 @@
-#!/usr/bin/env bash
-set -e
-
-EPREFIX=${1}
-
-#Link to the workaround automated by this script: https://wiki.gentoo.org/wiki/User_talk:Houseofsuns#Migration_to_science_overlay_from_main_tree
-#Efforts to more permanently address the issue: https://github.com/gentoo/sci/issues/805
-echo ""
-echo "Setting Up Eselect for Gentoo Science:"
-echo "~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~"
-if [ ! -d ${EPREFIX}/etc/portage/package.mask/ ]; then
-	mkdir -p ${EPREFIX}/etc/portage/package.mask/;
-fi
-cp "sci-lapack" "${EPREFIX}/etc/portage/package.mask/"
-emerge --oneshot --verbose dev-util/cmake >> /dev/null
-emerge --oneshot --verbose app-admin/eselect::science >> /dev/null
-FEATURES="-preserve-libs":$FEATURES emerge --oneshot --verbose sci-libs/blas-reference::science
-eselect blas set reference
-FEATURES="-preserve-libs":$FEATURES emerge --oneshot --verbose sci-libs/cblas-reference::science
-eselect cblas set reference
-FEATURES="-preserve-libs":$FEATURES emerge --oneshot --verbose sci-libs/lapack-reference::science
-eselect lapack set reference
-FEATURES="-preserve-libs":$FEATURES emerge --oneshot --verbose --exclude sci-libs/blas-reference --exclude sci-libs/cblas-reference --exclude sci-libs/lapack-reference `eix --only-names --installed --in-overlay science`
-
-emerge -1qv @preserved-rebuild
diff --git a/scripts/make_path64_snapshot.sh b/scripts/make_path64_snapshot.sh
deleted file mode 100644
index 35924953a..000000000
--- a/scripts/make_path64_snapshot.sh
+++ /dev/null
@@ -1,37 +0,0 @@
-#!/bin/bash
-
-clean_git() {
-   for f in $(find ./"$1" -name ".git"); do rm -rf $f; done
-}
-
-TEMP=/dev/shm/path64
-TODAY=$(date -u +%Y%m%d)
-
-[[ -d ${TEMP} ]] && rm -rf ${TEMP}
-mkdir "${TEMP}" && cd "${TEMP}"
-
-git clone git://github.com/pathscale/path64-suite.git path64
-clean_git path64
-ver=$(grep 'SET(PSC_FULL_VERSION' path64/CMakeLists.txt | cut -d'"' -f2)
-tar cjf path64-suite-${ver}_pre${TODAY}.tbz2 path64
-
-[[ -d ${TEMP}/path64/compiler ]] || mkdir -p ${TEMP}/path64/compiler
-cd ${TEMP}/path64/compiler
-
-for f in compiler assembler ; do 
-   git clone git://github.com/path64/$f.git
-done
-git clone git://github.com/path64/debugger.git pathdb
-for f in compiler-rt libcxxrt libdwarf-bsd libunwind stdcxx ; do 
-	git clone git://github.com/pathscale/$f.git
-done
-
-clean_git
-cd "${TEMP}"
-tar cjf path64-compiler-${ver}_pre${TODAY}.tbz2 \
-	path64/compiler/{compiler,compiler-rt,libcxxrt,libdwarf-bsd,libunwind,stdcxx}
-tar cjf path64-debugger-${ver}_pre${TODAY}.tbz2 \
-	path64/compiler/pathdb
-tar cjf path64-assembler-${ver}_pre${TODAY}.tbz2 \
-	path64/compiler/assembler
-
diff --git a/scripts/sci-lapack b/scripts/sci-lapack
deleted file mode 100644
index 691059927..000000000
--- a/scripts/sci-lapack
+++ /dev/null
@@ -1,18 +0,0 @@
-## mask packages superseded by science overlay
-app-admin/eselect::gentoo
-app-eselect/eselect-blas
-app-eselect/eselect-cblas
-app-eselect/eselect-lapack
-virtual/blas::gentoo
-virtual/cblas::gentoo
-virtual/lapack::gentoo
-sci-libs/gsl::gentoo
-app-doc/blas-docs::gentoo
-app-doc/lapack-docs::gentoo
-sci-libs/blas-reference::gentoo
-sci-libs/cblas-reference::gentoo
-sci-libs/lapack-reference::gentoo
-sci-libs/mkl::gentoo
-
-## more recently requires (see: https://github.com/gentoo/sci/issues/878 )
->=dev-util/cmake-3.12.0
diff --git a/scripts/setup-master-gentoo.sh b/scripts/setup-master-gentoo.sh
new file mode 100755
index 000000000..1a19d18df
--- /dev/null
+++ b/scripts/setup-master-gentoo.sh
@@ -0,0 +1,10 @@
+#! /usr/bin/env bash
+# Maintainer: Andrew Ammerlaan <andrewammerlaan@gentoo.org>
+#
+# Fetch and setup the latest ::gentoo
+
+sudo mkdir -p /var/db/repos/gentoo /etc/portage /var/cache/distfiles
+wget -qO - "https://github.com/gentoo-mirror/gentoo/archive/master.tar.gz" | sudo tar xz -C /var/db/repos/gentoo --strip-components=1
+sudo wget "https://www.gentoo.org/dtd/metadata.dtd" -O /var/cache/distfiles/metadata.dtd
+sudo wget "https://gitweb.gentoo.org/proj/portage.git/plain/cnf/repos.conf" -O /etc/portage/repos.conf
+sudo ln -s /var/db/repos/gentoo/profiles/default/linux/amd64/17.1 /etc/portage/make.profile
diff --git a/skel.ebuild b/skel.ebuild
deleted file mode 100644
index 0114d8c26..000000000
--- a/skel.ebuild
+++ /dev/null
@@ -1,162 +0,0 @@
-# Copyright 1999-2018 Gentoo Authors
-# Distributed under the terms of the GNU General Public License v2
-
-# NOTE: The comments in this file are for instruction and documentation.
-# They're not meant to appear with your final, production ebuild.  Please
-# remember to remove them before submitting or committing your ebuild.  That
-# doesn't mean you can't add your own comments though.
-
-# The EAPI variable tells the ebuild format in use.
-# It is suggested that you use the latest EAPI approved by the Council.
-# The PMS contains specifications for all EAPIs. Eclasses will test for this
-# variable if they need to use features that are not universal in all EAPIs.
-EAPI=6
-
-# inherit lists eclasses to inherit functions from. For example, an ebuild
-# that needs the eautoreconf function from autotools.eclass won't work
-# without the following line:
-#inherit autotools
-#
-# eclasses tend to list descriptions of how to use their functions properly.
-# take a look at /usr/portage/eclass/ for more examples.
-
-# Short one-line description of this package.
-DESCRIPTION="This is a sample skeleton ebuild file"
-
-# Homepage, not used by Portage directly but handy for developer reference
-HOMEPAGE="https://foo.example.org/"
-
-# Point to any required sources; these will be automatically downloaded by
-# Portage.
-SRC_URI="ftp://foo.example.org/${P}.tar.gz"
-
-
-# License of the package.  This must match the name of file(s) in
-# /usr/portage/licenses/.  For complex license combination see the developer
-# docs on gentoo.org for details.
-LICENSE=""
-
-# The SLOT variable is used to tell Portage if it's OK to keep multiple
-# versions of the same package installed at the same time.  For example,
-# if we have a libfoo-1.2.2 and libfoo-1.3.2 (which is not compatible
-# with 1.2.2), it would be optimal to instruct Portage to not remove
-# libfoo-1.2.2 if we decide to upgrade to libfoo-1.3.2.  To do this,
-# we specify SLOT="1.2" in libfoo-1.2.2 and SLOT="1.3" in libfoo-1.3.2.
-# emerge clean understands SLOTs, and will keep the most recent version
-# of each SLOT and remove everything else.
-# Note that normal applications should use SLOT="0" if possible, since
-# there should only be exactly one version installed at a time.
-# Do not use SLOT="", because the SLOT variable must not be empty.
-SLOT="0"
-
-# Using KEYWORDS, we can record masking information *inside* an ebuild
-# instead of relying on an external package.mask file.  Right now, you should
-# set the KEYWORDS variable for every ebuild so that it contains the names of
-# all the architectures with which the ebuild works.  All of the official
-# architectures can be found in the arch.list file which is in
-# /usr/portage/profiles/.  Usually you should just set this to "~amd64".
-# The ~ in front of the architecture indicates that the package is new and
-# should be considered unstable until testing proves its stability.  So, if
-# you've confirmed that your ebuild works on amd64 and ppc, you'd specify:
-# KEYWORDS="~amd64 ~ppc"
-# Once packages go stable, the ~ prefix is removed.
-# For binary packages, use -* and then list the archs the bin package
-# exists for.  If the package was for an x86 binary package, then
-# KEYWORDS would be set like this: KEYWORDS="-* x86"
-# Do not use KEYWORDS="*"; this is not valid in an ebuild context.
-KEYWORDS="~amd64"
-
-# Comprehensive list of any and all USE flags leveraged in the ebuild,
-# with some exceptions, e.g., ARCH specific flags like "amd64" or "ppc".
-# Not needed if the ebuild doesn't use any USE flags.
-IUSE="gnome X"
-
-# A space delimited list of portage features to restrict. man 5 ebuild
-# for details.  Usually not needed.
-#RESTRICT="strip"
-
-
-# Build-time dependencies, such as
-#    ssl? ( >=dev-libs/openssl-0.9.6b )
-#    >=dev-lang/perl-5.6.1-r1
-# It is advisable to use the >= syntax show above, to reflect what you
-# had installed on your system when you tested the package.  Then
-# other users hopefully won't be caught without the right version of
-# a dependency.
-#DEPEND=""
-
-# Run-time dependencies. Must be defined to whatever this depends on to run.
-# The below is valid if the same run-time depends are required to compile.
-RDEPEND="${DEPEND}"
-
-# Source directory; the dir where the sources can be found (automatically
-# unpacked) inside ${WORKDIR}.  The default value for S is ${WORKDIR}/${P}
-# If you don't need to change it, leave the S= line out of the ebuild
-# to keep it tidy.
-#S=${WORKDIR}/${P}
-
-
-# The following src_configure function is implemented as default by portage, so
-# you only need to call it if you need a different behaviour.
-#src_configure() {
-	# Most open-source packages use GNU autoconf for configuration.
-	# The default, quickest (and preferred) way of running configure is:
-	#econf
-	#
-	# You could use something similar to the following lines to
-	# configure your package before compilation.  The "|| die" portion
-	# at the end will stop the build process if the command fails.
-	# You should use this at the end of critical commands in the build
-	# process.  (Hint: Most commands are critical, that is, the build
-	# process should abort if they aren't successful.)
-	#./configure \
-	#	--host=${CHOST} \
-	#	--prefix=/usr \
-	#	--infodir=/usr/share/info \
-	#	--mandir=/usr/share/man || die
-	# Note the use of --infodir and --mandir, above. This is to make
-	# this package FHS 2.2-compliant.  For more information, see
-	#   https://www.pathname.com/fhs/
-#}
-
-# The following src_compile function is implemented as default by portage, so
-# you only need to call it, if you need different behaviour.
-#src_compile() {
-	# emake is a script that calls the standard GNU make with parallel
-	# building options for speedier builds (especially on SMP systems).
-	# Try emake first.  It might not work for some packages, because
-	# some makefiles have bugs related to parallelism, in these cases,
-	# use emake -j1 to limit make to a single process.  The -j1 is a
-	# visual clue to others that the makefiles have bugs that have been
-	# worked around.
-
-	#emake
-#}
-
-# The following src_install function is implemented as default by portage, so
-# you only need to call it, if you need different behaviour.
-#src_install() {
-	# You must *personally verify* that this trick doesn't install
-	# anything outside of DESTDIR; do this by reading and
-	# understanding the install part of the Makefiles.
-	# This is the preferred way to install.
-	#emake DESTDIR="${D}" install
-
-	# When you hit a failure with emake, do not just use make. It is
-	# better to fix the Makefiles to allow proper parallelization.
-	# If you fail with that, use "emake -j1", it's still better than make.
-
-	# For Makefiles that don't make proper use of DESTDIR, setting
-	# prefix is often an alternative.  However if you do this, then
-	# you also need to specify mandir and infodir, since they were
-	# passed to ./configure as absolute paths (overriding the prefix
-	# setting).
-	#emake \
-	#	prefix="${D}"/usr \
-	#	mandir="${D}"/usr/share/man \
-	#	infodir="${D}"/usr/share/info \
-	#	libdir="${D}"/usr/$(get_libdir) \
-	#	install
-	# Again, verify the Makefiles!  We don't want anything falling
-	# outside of ${D}.
-#}
diff --git a/skel.metadata.xml b/skel.metadata.xml
deleted file mode 100644
index 42444c655..000000000
--- a/skel.metadata.xml
+++ /dev/null
@@ -1,31 +0,0 @@
-<?xml version="1.0" encoding="UTF-8"?>
-<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
-<!--
-This is the example metadata file.
-The root element of this file is <pkgmetadata>. Within this element a
-number of subelements are allowed, the most common being maintainer.
-
-For a full description look at:
-https://devmanual.gentoo.org/ebuild-writing/misc-files/metadata/
-
-Before committing, please remove the comments from this file. They are
-not relevant for general metadata.xml files.
--->
-<pkgmetadata>
-<maintainer type="person">
-	<email>exampledev@gentoo.org</email>
-	<description>Primary maintainer</description>
-</maintainer>
-<maintainer type="project">
-	<email>exampleproject@gentoo.org</email>
-	<name>Gentoo Example Project</name>
-</maintainer>
-<longdescription>Long description of the package</longdescription>
-<use>
-	<flag name="aspell">Uses <pkg>app-text/aspell</pkg> for spell checking.
-		Requires an installed dictionary from <cat>app-dicts</cat></flag>
-	<flag name="flag">Description of how USE='flag' affects this package</flag>
-	<flag name="userland_GNU">Description of how USERLAND='GNU' affects this
-		package</flag>
-</use>
-</pkgmetadata>
diff --git a/sys-cluster/blcr/Manifest b/sys-cluster/blcr/Manifest
deleted file mode 100644
index 31fa4f64d..000000000
--- a/sys-cluster/blcr/Manifest
+++ /dev/null
@@ -1 +0,0 @@
-DIST blcr-0.8.5.tar.gz 921596 BLAKE2B 6c507c20e0e4389c4c0ae12e2bc28fa1ee259dbeb46bc8b0e917c63f8612a052c69d43adbf60eba05573d37a78d9e85a1485558c9db482da858e815aab5bbe0d SHA512 9089b9f04d948f6a470dd54026167ca8a4330b51f0ee74a2dd98b5cf17d9090950b82f66727a7d09da746a450b061c0ac9991e21de23dd596180be469c28d795
diff --git a/sys-cluster/blcr/blcr-0.8.5.ebuild b/sys-cluster/blcr/blcr-0.8.5.ebuild
deleted file mode 100644
index 87880e460..000000000
--- a/sys-cluster/blcr/blcr-0.8.5.ebuild
+++ /dev/null
@@ -1,58 +0,0 @@
-# Copyright 1999-2017 Gentoo Foundation
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=6
-
-inherit linux-mod
-
-DESCRIPTION="Berkeley Lab Checkpoint/Restart for Linux"
-HOMEPAGE="https://ftg.lbl.gov/projects/CheckpointRestart"
-SRC_URI="https://crd.lbl.gov/assets/Uploads/FTG/Projects/CheckpointRestart/downloads/${P}.tar.gz"
-
-LICENSE="BSD"
-SLOT="0"
-KEYWORDS="~amd64 ~x86"
-IUSE=""
-
-# up to kernel 2.6.38
-
-pkg_setup() {
-	local msg
-	linux-info_pkg_setup
-
-	# kernel version check
-	if kernel_is gt 3 8; then
-		eerror "${PN} is being developed and tested up to linux-3.7.x."
-		eerror "It is known not to work with 3.8.x kernels"
-		eerror "Make sure you have a proper kernel version and point"
-		eerror "  /usr/src/linux symlink or env variable KERNEL_DIR to it!"
-		die "Wrong kernel version ${KV_FULL}"
-	fi
-
-	linux-mod_pkg_setup
-	MODULE_NAMES="blcr(blcr::${S}/cr_module/kbuild)
-		blcr_imports(blcr::${S}/blcr_imports/kbuild)"
-	BUILD_TARGETS="clean all"
-	ECONF_PARAMS="--with-kernel=${KV_DIR}"
-
-	MAKEOPTS+=" -j1"
-}
-
-src_install() {
-	dodoc README NEWS
-	cd "${S}"/util || die
-	default
-	cd "${S}"/libcr || die
-	default
-	cd "${S}"/man || die
-	default
-	cd "${S}"/include || die
-	default
-	linux-mod_src_install
-}
-
-pkg_postinst() {
-	linux-mod_pkg_postinst
-	einfo "Be sure to add blcr to your modules.autoload.d to"
-	einfo "ensure that the modules get loaded on your next boot"
-}
diff --git a/sys-cluster/blcr/metadata.xml b/sys-cluster/blcr/metadata.xml
deleted file mode 100644
index 76dfb6d1d..000000000
--- a/sys-cluster/blcr/metadata.xml
+++ /dev/null
@@ -1,11 +0,0 @@
-<?xml version="1.0" encoding="UTF-8"?>
-<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
-<pkgmetadata>
-	<maintainer type="project">
-		<email>cluster@gentoo.org</email>
-		<name>Gentoo Cluster Project</name>
-	</maintainer>
-	<longdescription>
-Berkeley Lab Checkpoint/Restart for Linux
-</longdescription>
-</pkgmetadata>
diff --git a/sys-cluster/easybuild-easyblocks/Manifest b/sys-cluster/easybuild-easyblocks/Manifest
new file mode 100644
index 000000000..955f41791
--- /dev/null
+++ b/sys-cluster/easybuild-easyblocks/Manifest
@@ -0,0 +1,2 @@
+DIST easybuild-easyblocks-4.6.2.tar.gz 539757 BLAKE2B e33db4b390cdbe11237c5f5750426f15d264cf081e2846c7b9de9254f7a0fbdc1459795920fcc131ceb5681f0acc905a74f96cd841b73b523e030246b78393e8 SHA512 72cb4c057efdfeb4c45fbf1e036a6f231e7f01ad6e593d1c2352b27f002ed4f45cd625c4125b90b708b15f226fb9519a345217f7882c2155b399894986a4505c
+DIST easybuild-easyblocks-4.9.0.tar.gz 574066 BLAKE2B 404ea11287d03edf497c85e9d58eba05d3257aed609eb3f65e3d1543e08e0be27a64fd7459ba30578a3bd2be2051020f711f6598af082d2cdec3fad65116a0ed SHA512 c75695c66f4683128be268471e996abde83fc9cc5f937699b81da5ea94bf02df84bc6b0a88c657a904730afbc4048e3a44cfbc5288a546c1962a51960393d5c7
diff --git a/sys-cluster/easybuild-easyblocks/easybuild-easyblocks-4.6.2.ebuild b/sys-cluster/easybuild-easyblocks/easybuild-easyblocks-4.6.2.ebuild
new file mode 100644
index 000000000..6c5f7a6e6
--- /dev/null
+++ b/sys-cluster/easybuild-easyblocks/easybuild-easyblocks-4.6.2.ebuild
@@ -0,0 +1,29 @@
+EAPI=8
+
+PYTHON_COMPAT=( python3_{10..11} )
+DISTUTILS_USE_PEP517=setuptools
+PYPI_NO_NORMALIZE=1
+inherit distutils-r1 pypi
+
+SUB_P=$(ver_cut 1)
+
+DESCRIPTION="Provides a collection of easyblocks for EasyBuild."
+HOMEPAGE="
+	https://easybuild.io/
+	https://github.com/easybuilders/easybuild-easyblocks
+"
+
+LICENSE="GPL-2"
+SLOT="0"
+KEYWORDS="~amd64"
+
+RDEPEND="
+	>=sys-cluster/easybuild-framework-${SUB_P}[${PYTHON_USEDEP}]
+"
+DEPEND="${RDEPEND}"
+
+src_prepare() {
+	# already there from easybuild_framework
+	rm easybuild/__init__.py || die
+	default
+}
diff --git a/sys-cluster/easybuild-easyblocks/easybuild-easyblocks-4.9.0.ebuild b/sys-cluster/easybuild-easyblocks/easybuild-easyblocks-4.9.0.ebuild
new file mode 100644
index 000000000..d4cc85067
--- /dev/null
+++ b/sys-cluster/easybuild-easyblocks/easybuild-easyblocks-4.9.0.ebuild
@@ -0,0 +1,36 @@
+EAPI=8
+
+PYTHON_COMPAT=( python3_{10..11} )
+DISTUTILS_USE_PEP517=setuptools
+PYPI_NO_NORMALIZE=1
+
+inherit distutils-r1
+
+SUB_P=$(ver_cut 1)
+
+DESCRIPTION="Provides a collection of easyblocks for EasyBuild."
+HOMEPAGE="
+	https://easybuild.io/
+	https://github.com/easybuilders/easybuild-easyblocks
+"
+
+LICENSE="GPL-2"
+SLOT="0"
+if [[ ${PV} == 9999 ]]; then
+	inherit git-r3
+	EGIT_REPO_URI="https://github.com/easybuilders/easybuild-easyblocks"
+else
+	inherit pypi
+	KEYWORDS="~amd64"
+fi
+
+RDEPEND="
+	>=sys-cluster/easybuild-framework-${SUB_P}[${PYTHON_USEDEP}]
+"
+DEPEND="${RDEPEND}"
+
+src_prepare() {
+	# already there from easybuild_framework
+	rm easybuild/__init__.py || die
+	default
+}
diff --git a/sys-cluster/easybuild-easyblocks/easybuild-easyblocks-9999.ebuild b/sys-cluster/easybuild-easyblocks/easybuild-easyblocks-9999.ebuild
new file mode 100644
index 000000000..b32a81c59
--- /dev/null
+++ b/sys-cluster/easybuild-easyblocks/easybuild-easyblocks-9999.ebuild
@@ -0,0 +1,37 @@
+EAPI=8
+
+PYTHON_COMPAT=( python3_{10..11} )
+DISTUTILS_USE_PEP517=setuptools
+PYPI_NO_NORMALIZE=1
+
+inherit distutils-r1
+
+SUB_P=$(ver_cut 1)
+
+DESCRIPTION="Provides a collection of easyblocks for EasyBuild."
+HOMEPAGE="
+	https://easybuild.io/
+	https://github.com/easybuilders/easybuild-easyblocks
+"
+
+LICENSE="GPL-2"
+SLOT="0"
+if [[ ${PV} == 9999 ]]; then
+	inherit git-r3
+	EGIT_REPO_URI="https://github.com/easybuilders/easybuild-easyblocks"
+	SUB_P=9999
+else
+	inherit pypi
+	KEYWORDS="~amd64"
+fi
+
+RDEPEND="
+	>=sys-cluster/easybuild-framework-${SUB_P}[${PYTHON_USEDEP}]
+"
+DEPEND="${RDEPEND}"
+
+src_prepare() {
+	# already there from easybuild_framework
+	rm easybuild/__init__.py || die
+	default
+}
diff --git a/sys-cluster/easybuild-easyblocks/metadata.xml b/sys-cluster/easybuild-easyblocks/metadata.xml
new file mode 100644
index 000000000..d7dba6355
--- /dev/null
+++ b/sys-cluster/easybuild-easyblocks/metadata.xml
@@ -0,0 +1,20 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
+<pkgmetadata>
+	<maintainer type="project">
+		<email>sci@gentoo.org</email>
+		<name>Gentoo Science Project</name>
+	</maintainer>
+	<maintainer type="person">
+		<email>alexander@neuwirth-informatik.de</email>
+		<name>Alexander Puck Neuwirth</name>
+	</maintainer>
+	<longdescription lang="en">
+	The easybuild-easyblocks package provides a collection of easyblocks for EasyBuild. Easyblocks are Python modules that implement the install procedure for a (group of) software package(s). Together with the EasyBuild framework, they allow to easily build and install supported software packages.
+	</longdescription>
+	<upstream>
+		<remote-id type="pypi">easybuild-easyblocks</remote-id>
+		<remote-id type="github">easybuilders/easybuild-easyblocks</remote-id>
+		<bugs-to>https://github.com/easybuilders/easybuild-easyblocks/issues</bugs-to>
+	</upstream>
+</pkgmetadata>
diff --git a/sys-cluster/easybuild-easyconfigs/Manifest b/sys-cluster/easybuild-easyconfigs/Manifest
new file mode 100644
index 000000000..b8328d6aa
--- /dev/null
+++ b/sys-cluster/easybuild-easyconfigs/Manifest
@@ -0,0 +1,2 @@
+DIST easybuild-easyconfigs-4.6.2.tar.gz 7991765 BLAKE2B 02e7b629858177db19b7a63fcacd4898805ccfabd7bac343e05015d545d057bb04416b0b89245d3e3c206bc0f129920dda7d7ae1e421e9f7ce690ee6d01acd90 SHA512 4632dc0714b3e070b58a8192cb8054f0e21357701f59df054593ea754f5598c8e6446acd77c0e41f2fb920d31297ea5a5164fd81b26b926835868f24623cdce8
+DIST easybuild-easyconfigs-4.9.0.tar.gz 9636057 BLAKE2B 5b7710c99eb0d728d4df6582db40b7dc72d86cfca32548c79344a2b918e53e56360c97225ab2cf577bf2ba170bf67de211758afb83e696ec157165316b01cf02 SHA512 a39dc1eddc569163b21abdca9633a4c35519f609a03012ef7ec3f58c40a58961450b626c3701c325a2e485e5a00d161d737239c19ea657546b52b2c16de307f5
diff --git a/sys-cluster/easybuild-easyconfigs/easybuild-easyconfigs-4.6.2.ebuild b/sys-cluster/easybuild-easyconfigs/easybuild-easyconfigs-4.6.2.ebuild
new file mode 100644
index 000000000..08434dc1c
--- /dev/null
+++ b/sys-cluster/easybuild-easyconfigs/easybuild-easyconfigs-4.6.2.ebuild
@@ -0,0 +1,25 @@
+EAPI=8
+
+PYTHON_COMPAT=( python3_{10..11} )
+DISTUTILS_USE_PEP517=setuptools
+PYPI_NO_NORMALIZE=1
+inherit distutils-r1 pypi
+
+SUB_P=$(ver_cut 1)
+SUB_PP=$(ver_cut 2)
+
+DESCRIPTION="Provides a collection of well-tested easyconfig files for EasyBuild."
+HOMEPAGE="
+	https://easybuild.io/
+	https://github.com/easybuilders/easybuild-easyconfigs
+"
+
+LICENSE="GPL-2"
+SLOT="0"
+KEYWORDS="~amd64"
+
+RDEPEND="
+	>=sys-cluster/easybuild-framework-${SUB_P}[${PYTHON_USEDEP}]
+	>=sys-cluster/easybuild-easyblocks-${SUB_P}.${SUB_PP}[${PYTHON_USEDEP}]
+"
+DEPEND="${RDEPEND}"
diff --git a/sys-cluster/easybuild-easyconfigs/easybuild-easyconfigs-4.9.0.ebuild b/sys-cluster/easybuild-easyconfigs/easybuild-easyconfigs-4.9.0.ebuild
new file mode 100644
index 000000000..5d5750a61
--- /dev/null
+++ b/sys-cluster/easybuild-easyconfigs/easybuild-easyconfigs-4.9.0.ebuild
@@ -0,0 +1,34 @@
+EAPI=8
+
+PYTHON_COMPAT=( python3_{10..11} )
+DISTUTILS_USE_PEP517=setuptools
+PYPI_NO_NORMALIZE=1
+
+inherit distutils-r1
+
+SUB_P=$(ver_cut 1)
+SUB_PP=${SUB_P}.$(ver_cut 2)
+
+DESCRIPTION="Provides a collection of well-tested easyconfig files for EasyBuild."
+HOMEPAGE="
+	https://easybuild.io/
+	https://github.com/easybuilders/easybuild-easyconfigs
+"
+
+LICENSE="GPL-2"
+SLOT="0"
+if [[ ${PV} == 9999 ]]; then
+	inherit git-r3
+	EGIT_REPO_URI="https://github.com/easybuilders/easybuild-easyconfigs"
+	SUB_P=9999
+	SUB_PP=9999
+else
+	inherit pypi
+	KEYWORDS="~amd64"
+fi
+
+RDEPEND="
+	>=sys-cluster/easybuild-framework-${SUB_P}[${PYTHON_USEDEP}]
+	>=sys-cluster/easybuild-easyblocks-${SUB_PP}[${PYTHON_USEDEP}]
+"
+DEPEND="${RDEPEND}"
diff --git a/sys-cluster/easybuild-easyconfigs/easybuild-easyconfigs-9999.ebuild b/sys-cluster/easybuild-easyconfigs/easybuild-easyconfigs-9999.ebuild
new file mode 100644
index 000000000..5d5750a61
--- /dev/null
+++ b/sys-cluster/easybuild-easyconfigs/easybuild-easyconfigs-9999.ebuild
@@ -0,0 +1,34 @@
+EAPI=8
+
+PYTHON_COMPAT=( python3_{10..11} )
+DISTUTILS_USE_PEP517=setuptools
+PYPI_NO_NORMALIZE=1
+
+inherit distutils-r1
+
+SUB_P=$(ver_cut 1)
+SUB_PP=${SUB_P}.$(ver_cut 2)
+
+DESCRIPTION="Provides a collection of well-tested easyconfig files for EasyBuild."
+HOMEPAGE="
+	https://easybuild.io/
+	https://github.com/easybuilders/easybuild-easyconfigs
+"
+
+LICENSE="GPL-2"
+SLOT="0"
+if [[ ${PV} == 9999 ]]; then
+	inherit git-r3
+	EGIT_REPO_URI="https://github.com/easybuilders/easybuild-easyconfigs"
+	SUB_P=9999
+	SUB_PP=9999
+else
+	inherit pypi
+	KEYWORDS="~amd64"
+fi
+
+RDEPEND="
+	>=sys-cluster/easybuild-framework-${SUB_P}[${PYTHON_USEDEP}]
+	>=sys-cluster/easybuild-easyblocks-${SUB_PP}[${PYTHON_USEDEP}]
+"
+DEPEND="${RDEPEND}"
diff --git a/sys-cluster/easybuild-easyconfigs/metadata.xml b/sys-cluster/easybuild-easyconfigs/metadata.xml
new file mode 100644
index 000000000..4f1fac641
--- /dev/null
+++ b/sys-cluster/easybuild-easyconfigs/metadata.xml
@@ -0,0 +1,20 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
+<pkgmetadata>
+	<maintainer type="project">
+		<email>sci@gentoo.org</email>
+		<name>Gentoo Science Project</name>
+	</maintainer>
+	<maintainer type="person">
+		<email>alexander@neuwirth-informatik.de</email>
+		<name>Alexander Puck Neuwirth</name>
+	</maintainer>
+	<longdescription lang="en">
+	The easybuild-easyconfigs package provides a collection of well-tested example easyconfig files for EasyBuild. Easyconfig files are used to specify which software to build, which version of the software (and its dependencies), which build parameters to use (e.g., which compiler toolchain to use), etc.
+	</longdescription>
+	<upstream>
+		<remote-id type="pypi">easybuild-easyconfigs</remote-id>
+		<remote-id type="github">easybuilders/easybuild-easyconfigs</remote-id>
+		<bugs-to>https://github.com/easybuilders/easybuild-easyconfigs/issues</bugs-to>
+	</upstream>
+</pkgmetadata>
diff --git a/sys-cluster/easybuild-framework/Manifest b/sys-cluster/easybuild-framework/Manifest
new file mode 100644
index 000000000..6845b4e9c
--- /dev/null
+++ b/sys-cluster/easybuild-framework/Manifest
@@ -0,0 +1,2 @@
+DIST easybuild-framework-4.6.2.tar.gz 2019284 BLAKE2B a32ae1fc43d490b32fc6c44790493204de935d16257846ec46830fc4d18a7343b860317c0ba33a16d89f12f657c33f7bb7359a70bf26a17c4e0dd16b8c78e2cd SHA512 ac8a06301c6c95edded262cb55b02ea8ada9ea14dfb7b7354a3bb29fcd9ad9a8d0011edbf2175085b8cec721f08a2b5f5e74aaa191d381a787eb5438c6c7f8cc
+DIST easybuild-framework-4.9.0.tar.gz 2064113 BLAKE2B 637498e7d52f0e9a6e9bd25c843052d9fc3c730f93b40c37381263b8861b0dd1b8ebf1d13af514d841d43284eb81b7555fcdaacbc1ac2c1bd655748c01540677 SHA512 b7b52d8987f13d9f859df0874adb7b855f8b4961215d9e9cb4a63a15911affe1591d718076277419be0c31e76845cf5cbe4fe553676ac71b8ff33a82d3c17a0e
diff --git a/sys-cluster/easybuild-framework/easybuild-framework-4.6.2.ebuild b/sys-cluster/easybuild-framework/easybuild-framework-4.6.2.ebuild
new file mode 100644
index 000000000..0f7421835
--- /dev/null
+++ b/sys-cluster/easybuild-framework/easybuild-framework-4.6.2.ebuild
@@ -0,0 +1,33 @@
+EAPI=8
+
+PYTHON_COMPAT=( python3_{10..11} )
+DISTUTILS_USE_PEP517=setuptools
+PYPI_NO_NORMALIZE=1
+inherit distutils-r1 pypi
+
+DESCRIPTION="The easybuild-framework package is the core of EasyBuild."
+HOMEPAGE="
+	https://easybuild.io/
+	https://github.com/easybuilders/easybuild-framework
+"
+
+LICENSE="GPL-2"
+SLOT="0"
+KEYWORDS="~amd64"
+
+RDEPEND="
+dev-python/flake8[${PYTHON_USEDEP}]
+dev-python/keyring[${PYTHON_USEDEP}]
+dev-python/GitPython[${PYTHON_USEDEP}]
+dev-python/pyyaml[${PYTHON_USEDEP}]
+dev-python/autopep8[${PYTHON_USEDEP}]
+dev-python/requests[${PYTHON_USEDEP}]
+dev-python/cryptography[${PYTHON_USEDEP}]
+dev-python/rich[${PYTHON_USEDEP}]
+dev-python/archspec[${PYTHON_USEDEP}]
+"
+DEPEND="${RDEPEND}"
+
+PATCHES=(
+	"${FILESDIR}"/${P}-test.patch
+)
diff --git a/sys-cluster/easybuild-framework/easybuild-framework-4.9.0.ebuild b/sys-cluster/easybuild-framework/easybuild-framework-4.9.0.ebuild
new file mode 100644
index 000000000..c88f89f6f
--- /dev/null
+++ b/sys-cluster/easybuild-framework/easybuild-framework-4.9.0.ebuild
@@ -0,0 +1,40 @@
+EAPI=8
+
+PYTHON_COMPAT=( python3_{10..11} )
+DISTUTILS_USE_PEP517=setuptools
+PYPI_NO_NORMALIZE=1
+
+inherit distutils-r1
+
+DESCRIPTION="The easybuild-framework package is the core of EasyBuild."
+HOMEPAGE="
+	https://easybuild.io/
+	https://github.com/easybuilders/easybuild-framework
+"
+
+LICENSE="GPL-2"
+SLOT="0"
+if [[ ${PV} == 9999 ]]; then
+	inherit git-r3
+	EGIT_REPO_URI="https://github.com/easybuilders/easybuild-framework"
+else
+	inherit pypi
+	KEYWORDS="~amd64"
+fi
+
+RDEPEND="
+	dev-python/flake8[${PYTHON_USEDEP}]
+	dev-python/keyring[${PYTHON_USEDEP}]
+	dev-python/GitPython[${PYTHON_USEDEP}]
+	dev-python/pyyaml[${PYTHON_USEDEP}]
+	dev-python/autopep8[${PYTHON_USEDEP}]
+	dev-python/requests[${PYTHON_USEDEP}]
+	dev-python/archspec[${PYTHON_USEDEP}]
+	dev-python/cryptography[${PYTHON_USEDEP}]
+	dev-python/rich[${PYTHON_USEDEP}]
+"
+DEPEND="${RDEPEND}"
+
+PATCHES=(
+	"${FILESDIR}"/${PN}-4.6.2-test.patch
+)
diff --git a/sys-cluster/easybuild-framework/easybuild-framework-9999.ebuild b/sys-cluster/easybuild-framework/easybuild-framework-9999.ebuild
new file mode 100644
index 000000000..c88f89f6f
--- /dev/null
+++ b/sys-cluster/easybuild-framework/easybuild-framework-9999.ebuild
@@ -0,0 +1,40 @@
+EAPI=8
+
+PYTHON_COMPAT=( python3_{10..11} )
+DISTUTILS_USE_PEP517=setuptools
+PYPI_NO_NORMALIZE=1
+
+inherit distutils-r1
+
+DESCRIPTION="The easybuild-framework package is the core of EasyBuild."
+HOMEPAGE="
+	https://easybuild.io/
+	https://github.com/easybuilders/easybuild-framework
+"
+
+LICENSE="GPL-2"
+SLOT="0"
+if [[ ${PV} == 9999 ]]; then
+	inherit git-r3
+	EGIT_REPO_URI="https://github.com/easybuilders/easybuild-framework"
+else
+	inherit pypi
+	KEYWORDS="~amd64"
+fi
+
+RDEPEND="
+	dev-python/flake8[${PYTHON_USEDEP}]
+	dev-python/keyring[${PYTHON_USEDEP}]
+	dev-python/GitPython[${PYTHON_USEDEP}]
+	dev-python/pyyaml[${PYTHON_USEDEP}]
+	dev-python/autopep8[${PYTHON_USEDEP}]
+	dev-python/requests[${PYTHON_USEDEP}]
+	dev-python/archspec[${PYTHON_USEDEP}]
+	dev-python/cryptography[${PYTHON_USEDEP}]
+	dev-python/rich[${PYTHON_USEDEP}]
+"
+DEPEND="${RDEPEND}"
+
+PATCHES=(
+	"${FILESDIR}"/${PN}-4.6.2-test.patch
+)
diff --git a/sys-cluster/easybuild-framework/files/easybuild-framework-4.6.2-test.patch b/sys-cluster/easybuild-framework/files/easybuild-framework-4.6.2-test.patch
new file mode 100644
index 000000000..db1a65b5a
--- /dev/null
+++ b/sys-cluster/easybuild-framework/files/easybuild-framework-4.6.2-test.patch
@@ -0,0 +1,11 @@
+--- a/setup.py	2022-10-22 17:31:01.312465269 +0200
++++ b/setup.py	2022-10-22 17:30:50.826310864 +0200
+@@ -72,7 +72,7 @@
+     "easybuild.toolchains.fft", "easybuild.toolchains.linalg", "easybuild.tools", "easybuild.tools.containers",
+     "easybuild.tools.deprecated", "easybuild.tools.job", "easybuild.tools.toolchain",
+     "easybuild.tools.module_naming_scheme", "easybuild.tools.package", "easybuild.tools.package.package_naming_scheme",
+-    "easybuild.tools.py2vs3", "easybuild.tools.repository", "test.framework", "test",
++    "easybuild.tools.py2vs3", "easybuild.tools.repository",
+ ]
+ 
+ setup(
diff --git a/sys-cluster/easybuild-framework/metadata.xml b/sys-cluster/easybuild-framework/metadata.xml
new file mode 100644
index 000000000..5d61e5c64
--- /dev/null
+++ b/sys-cluster/easybuild-framework/metadata.xml
@@ -0,0 +1,20 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
+<pkgmetadata>
+	<maintainer type="project">
+		<email>sci@gentoo.org</email>
+		<name>Gentoo Science Project</name>
+	</maintainer>
+	<maintainer type="person">
+		<email>alexander@neuwirth-informatik.de</email>
+		<name>Alexander Puck Neuwirth</name>
+	</maintainer>
+	<longdescription lang="en">
+	The easybuild-framework package is the core of EasyBuild. It supports the implementation and use of so-called easyblocks which implement the software install procedure for a particular (group of) software package(s).
+	</longdescription>
+	<upstream>
+		<remote-id type="pypi">easybuild-framework</remote-id>
+		<remote-id type="github">easybuilders/easybuild-framework</remote-id>
+		<bugs-to>https://github.com/easybuilders/easybuild-framework/issues</bugs-to>
+	</upstream>
+</pkgmetadata>
diff --git a/sys-cluster/easybuild/Manifest b/sys-cluster/easybuild/Manifest
new file mode 100644
index 000000000..b17222baf
--- /dev/null
+++ b/sys-cluster/easybuild/Manifest
@@ -0,0 +1,2 @@
+DIST easybuild-4.6.2.tar.gz 10680 BLAKE2B ed9dcaf1e138dd0d56fbff51151b5e0a6c0842495a950fe6a37a16435ab679bd0f60d34a703f6791b1486001fa3508e23d8a82ae6cc39f90137f03b5a93f5a0e SHA512 34097122968d31cf7fa8503f1566ff43c4fd34849c02050eb2f7304028479afd224128a0b83c195150b9ff6680b903a6b20fee715c9511bde292e2c4ac88397b
+DIST easybuild-4.9.0.tar.gz 10622 BLAKE2B bf7c69db95d49e2d992541baa145346e173fc35eab6002afd59a62d7c2007fea41672d81a3f1cf0e170f630dcf4bbea957b254fbffd5237738180d2df0976964 SHA512 3a1a4433e58d90f90dd8ba2700f7dcc07a07333d7f103ea23f82145af76a41af436d9e606fbe95fc5cfcf4be07399a3b3d5cc10c57c0bd77ea8018ba4e852c8d
diff --git a/sys-cluster/easybuild/easybuild-4.6.2.ebuild b/sys-cluster/easybuild/easybuild-4.6.2.ebuild
new file mode 100644
index 000000000..fe08d45ad
--- /dev/null
+++ b/sys-cluster/easybuild/easybuild-4.6.2.ebuild
@@ -0,0 +1,31 @@
+EAPI=8
+
+PYTHON_COMPAT=( python3_{10..11} )
+DISTUTILS_USE_PEP517=setuptools
+inherit distutils-r1 pypi
+
+DESCRIPTION="EasyBuild is a software build and installation framework."
+HOMEPAGE="
+	https://easybuild.io/
+	https://github.com/easybuilders/easybuild
+"
+
+LICENSE="GPL-2"
+SLOT="0"
+KEYWORDS="~amd64"
+
+RDEPEND="
+	dev-libs/openssl
+	dev-tcltk/tclx
+	|| ( >=sys-cluster/lmod-6.5.1 >=sys-cluster/modules-4.6.0-r1 )
+	~sys-cluster/easybuild-framework-${PV}[${PYTHON_USEDEP}]
+	~sys-cluster/easybuild-easyblocks-${PV}[${PYTHON_USEDEP}]
+	~sys-cluster/easybuild-easyconfigs-${PV}[${PYTHON_USEDEP}]
+"
+DEPEND="${RDEPEND}"
+
+pkg_postinst() {
+	elog "Remember to set the module install path"
+	elog "ml use \$installpath/modules/all"
+	elog "where --installpath is passed to eb"
+}
diff --git a/sys-cluster/easybuild/easybuild-4.9.0.ebuild b/sys-cluster/easybuild/easybuild-4.9.0.ebuild
new file mode 100644
index 000000000..9a38672aa
--- /dev/null
+++ b/sys-cluster/easybuild/easybuild-4.9.0.ebuild
@@ -0,0 +1,40 @@
+EAPI=8
+
+PYTHON_COMPAT=( python3_{10..11} )
+DISTUTILS_USE_PEP517=setuptools
+
+inherit distutils-r1 optfeature
+
+DESCRIPTION="EasyBuild is a software build and installation framework."
+HOMEPAGE="
+	https://easybuild.io/
+	https://github.com/easybuilders/easybuild
+"
+
+LICENSE="GPL-2"
+SLOT="0"
+if [[ ${PV} == 9999 ]]; then
+	inherit git-r3
+	EGIT_REPO_URI="https://github.com/easybuilders/easybuild"
+else
+	inherit pypi
+	KEYWORDS="~amd64"
+fi
+
+RDEPEND="
+	dev-libs/openssl
+	dev-tcltk/tclx
+	|| ( >=sys-cluster/lmod-6.5.1 >=sys-cluster/modules-4.6.0-r1 )
+	~sys-cluster/easybuild-framework-${PV}[${PYTHON_USEDEP}]
+	~sys-cluster/easybuild-easyblocks-${PV}[${PYTHON_USEDEP}]
+	~sys-cluster/easybuild-easyconfigs-${PV}[${PYTHON_USEDEP}]
+"
+DEPEND="${RDEPEND}"
+
+pkg_postinst() {
+	elog "Remember to set the module install path"
+	elog "ml use \$installpath/modules/all"
+	elog "where --installpath is passed to eb"
+
+	optfeature "GitHub PR integration" dev-python/keyring dev-python/GitPython
+}
diff --git a/sys-cluster/easybuild/easybuild-9999.ebuild b/sys-cluster/easybuild/easybuild-9999.ebuild
new file mode 100644
index 000000000..9a38672aa
--- /dev/null
+++ b/sys-cluster/easybuild/easybuild-9999.ebuild
@@ -0,0 +1,40 @@
+EAPI=8
+
+PYTHON_COMPAT=( python3_{10..11} )
+DISTUTILS_USE_PEP517=setuptools
+
+inherit distutils-r1 optfeature
+
+DESCRIPTION="EasyBuild is a software build and installation framework."
+HOMEPAGE="
+	https://easybuild.io/
+	https://github.com/easybuilders/easybuild
+"
+
+LICENSE="GPL-2"
+SLOT="0"
+if [[ ${PV} == 9999 ]]; then
+	inherit git-r3
+	EGIT_REPO_URI="https://github.com/easybuilders/easybuild"
+else
+	inherit pypi
+	KEYWORDS="~amd64"
+fi
+
+RDEPEND="
+	dev-libs/openssl
+	dev-tcltk/tclx
+	|| ( >=sys-cluster/lmod-6.5.1 >=sys-cluster/modules-4.6.0-r1 )
+	~sys-cluster/easybuild-framework-${PV}[${PYTHON_USEDEP}]
+	~sys-cluster/easybuild-easyblocks-${PV}[${PYTHON_USEDEP}]
+	~sys-cluster/easybuild-easyconfigs-${PV}[${PYTHON_USEDEP}]
+"
+DEPEND="${RDEPEND}"
+
+pkg_postinst() {
+	elog "Remember to set the module install path"
+	elog "ml use \$installpath/modules/all"
+	elog "where --installpath is passed to eb"
+
+	optfeature "GitHub PR integration" dev-python/keyring dev-python/GitPython
+}
diff --git a/sys-cluster/easybuild/metadata.xml b/sys-cluster/easybuild/metadata.xml
new file mode 100644
index 000000000..d7af184b5
--- /dev/null
+++ b/sys-cluster/easybuild/metadata.xml
@@ -0,0 +1,20 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
+<pkgmetadata>
+	<maintainer type="project">
+		<email>sci@gentoo.org</email>
+		<name>Gentoo Science Project</name>
+	</maintainer>
+	<maintainer type="person">
+		<email>alexander@neuwirth-informatik.de</email>
+		<name>Alexander Puck Neuwirth</name>
+	</maintainer>
+	<longdescription lang="en">
+	EasyBuild is a software build and installation framework that allows you to manage (scientific) software on High Performance Computing (HPC) systems in an efficient way.
+	</longdescription>
+	<upstream>
+		<remote-id type="pypi">easybuild</remote-id>
+		<remote-id type="github">easybuilders/easybuild</remote-id>
+		<bugs-to>https://github.com/easybuilders/easybuild/issues</bugs-to>
+	</upstream>
+</pkgmetadata>
diff --git a/sys-cluster/empi/empi-0.10.ebuild b/sys-cluster/empi/empi-0.10.ebuild
deleted file mode 100644
index 5f24f1107..000000000
--- a/sys-cluster/empi/empi-0.10.ebuild
+++ /dev/null
@@ -1,31 +0,0 @@
-# Copyright 1999-2014 Gentoo Foundation
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=5
-
-inherit eutils
-
-DESCRIPTION="Handling Multiple MPI Implementations"
-HOMEPAGE="http://dev.gentoo.org/~jsbronder/empi.xml"
-SRC_URI=""
-
-LICENSE="GPL-2"
-SLOT="0"
-KEYWORDS="~amd64 ~x86"
-IUSE=""
-DEPEND="app-admin/eselect"
-RDEPEND="${DEPEND}"
-
-S="${WORKDIR}"
-
-src_install() {
-	newbin "${FILESDIR}"/${P} ${PN}
-	dodoc "${FILESDIR}"/README.txt
-	dodoc "${FILESDIR}"/ChangeLog-${PV}
-
-	insinto /usr/share/eselect/modules
-	newins "${FILESDIR}"/eselect.mpi-${PV} mpi.eselect
-	exeinto /etc/profile.d
-	doexe "${FILESDIR}"/mpi.sh
-	doexe "${FILESDIR}"/mpi.csh
-}
diff --git a/sys-cluster/empi/files/ChangeLog-0.10 b/sys-cluster/empi/files/ChangeLog-0.10
deleted file mode 100644
index ac5eff065..000000000
--- a/sys-cluster/empi/files/ChangeLog-0.10
+++ /dev/null
@@ -1,121 +0,0 @@
-commit ab2dc2e2210f81d24b42180359d0842eb33f994a (HEAD, tag: v0.10, origin/master, origin/HEAD, master)
-Author: Justin Bronder <jsbronder@gmail.com>
-Date:   Wed Jul 10 20:22:13 2013 -0400
-
-    empi-0.10
-
-commit d84c6ce3949f9eeeb1bab816e3e25eef0dd75661
-Author: Justin Bronder <jsbronder@gmail.com>
-Date:   Tue Jul 9 18:48:01 2013 -0400
-
-    empi:  support make.conf move
-    
-    Later versions of portage moved /etc/make.conf to /etc/portage/make.conf
-    by default while still supporting the old location.
-
-commit 914c277799fd0f44266864fa16fef338046be5f6
-Author: Justin Bronder <jsbronder@gmail.com>
-Date:   Tue Jul 9 18:12:50 2013 -0400
-
-    eclass: add sys-cluster/mpich
-    
-    upstream renamed mpich2 to mpich.
-
-commit 5c80290f4f0d90fe84fa0f18f2264052c544c008
-Author: Justin Bronder <jsbronder@gmail.com>
-Date:   Mon Jul 1 22:16:04 2013 -0400
-
-    Revert "eclass:  workaround OpenMPI build issue #462602"
-    
-    This reverts commit 5e9b1be531ca02607e730a5b43765850eae9a0c5.
-
-commit a5d63455bf53a1ca6ab0220e3f308707a852b0cc (tag: v0.9)
-Author: Justin Bronder <jsbronder@gmail.com>
-Date:   Mon Jul 1 20:06:50 2013 -0400
-
-    empi-0.9
-
-commit 4540a319542ddc7c0fbcea47174fe85e1810561c
-Author: Justin Bronder <jsbronder@gmail.com>
-Date:   Mon Jul 1 20:05:35 2013 -0400
-
-    empi:  better filtering of emerge output
-    
-    Ignore extra information spit out by emerge, like news.
-
-commit 5e9b1be531ca02607e730a5b43765850eae9a0c5
-Author: Justin Bronder <jsbronder@gmail.com>
-Date:   Mon Jul 1 20:04:58 2013 -0400
-
-    eclass:  workaround OpenMPI build issue #462602
-    
-    export FAKEROOTKEY=1 to stop OpenMPI from replacing malloc.
-
-commit a17e4452cb93014e2a4d5f7615e5d09f2df9c6a2 (tag: v0.8)
-Author: Justin Bronder <jsbronder@gmail.com>
-Date:   Thu Feb 21 22:56:27 2013 -0500
-
-    empi-0.8
-
-commit b38f48aa70933858d410abce58964e55708471c9
-Author: Justin Bronder <jsbronder@gmail.com>
-Date:   Thu Feb 21 22:54:28 2013 -0500
-
-    empi:  manage overlay metadata
-    
-    Add overlay metadata management.  Snagged from crossdev.
-    http://git.overlays.gentoo.org/gitweb/?p=proj/crossdev.git
-
-commit 4305d879c232acd663a8bb13505e5cfa403c5df5
-Author: Justin Bronder <jsbronder@gmail.com>
-Date:   Thu Feb 21 21:05:19 2013 -0500
-
-    empi:  provide and set overlay default
-    
-    Set default overlay path to /var/cache/overlays/mpi
-
-commit fd7eed35034cb54dbe0d8f553c57abceee3c0eea
-Author: Justin Bronder <jsbronder@gmail.com>
-Date:   Thu Feb 21 20:40:36 2013 -0500
-
-    empi:  allow all users to see usage screen
-
-commit 84aa3a41dbbf2924dc223614c267ff6e79bfce2e
-Author: Justin Bronder <jsbronder@gmail.com>
-Date:   Fri Jan 11 16:43:08 2013 -0500
-
-    rename MPI_PORTDIR and pull it from the portage env
-
-commit 77318d28462f05b4a8a6f1ac7b270aa07b5ebc8a
-Author: Justin Bronder <jsbronder@gmail.com>
-Date:   Fri Jan 11 16:07:14 2013 -0500
-
-    rename global variables to be obvious
-
-commit 07beb4baf6af2a45bd382d6b7ba87d8bcbeda7a7
-Author: Justin Bronder <jsbronder@gmail.com>
-Date:   Fri Jan 11 15:44:50 2013 -0500
-
-    sanitize whitespace
-
-commit 7c7fb4f0669d554a5301e70a46ae82e584685aff
-Author: Justin Bronder <jsbronder@gmail.com>
-Date:   Tue Mar 22 10:27:53 2011 -0400
-
-    mpi.eclass:  Improve handling of unclassed dep strings
-    
-    Instead of requiring a list of packages to block when calculating the
-    dep list for an unclassed ebuild, simply inject a dep string.  This
-    will allow the use of USE-conditional blockers.
-
-commit 0319e9cac8325bda7440f0f48eeac30056658b7e
-Author: Nicolas Bigaouette <nbigaouette@gmail.com>
-Date:   Wed Nov 24 22:42:49 2010 -0500
-
-    Typo: 'classs' to 'classes'
-
-commit 7f0ce9ea97ee8f72dc275ebdf3ce7ab44ad6538a
-Author: Justin Bronder <jsbronder@gmail.com>
-Date:   Mon Nov 29 11:51:31 2010 -0500
-
-    Initial import to git.
diff --git a/sys-cluster/empi/files/README.txt b/sys-cluster/empi/files/README.txt
deleted file mode 100644
index 0148775fd..000000000
--- a/sys-cluster/empi/files/README.txt
+++ /dev/null
@@ -1,76 +0,0 @@
-= Introduction =
-Empi is basically a reworking of vapier's crossdev script to
-handle installing multiple mpi implementations and applications
-that depend on them.  This is done through trickery involving
-adding categories that portage will recognize, moving mpi-enabled
-packages (defined as those using mpi.eclass) to a local overlay
-directory and then emerging these packages using the new
-category.
-
-Empi handles getting mpi application ebuilds into the overlay,
-copying anything in package.{use,keywords}, and wrapping the
-emerge process.  The eclass handles putting the package files
-into separate "root" directories based on the category name as
-well as making sure the applications build against the
-appropriate environment.
-
-I also provide eselect-mpi, which unlike every other eselect
-module I've ever used, is designed to manage a users personal
-environment by writing to ${HOME}/.env.d/mpi.  This provides a
-quick and easy way for users to experiment with various
-implementations while imposing on any other user's ability to
-use their preferred implementation.
-
-The newly written mpi.eclass should handle empi-based and standard
-emerging of packages in a manner that enables package maintainers
-to quickly port their applications without much knowledge of the
-underlying mechanics.  At least, that was my intent, maybe I
-succeeded.
-
-
-= Definitions =
-Class:  Fake category name used by empi.  Must be
-    prefixed with mpi-
-Base Implementation:  Actual mpi-implementation package that will
-    provide all mpi functionality to the above.
-
-
-= Instructions =
-
-The following creates a class called "mpi-openmpi"
-using sys-cluster/openmpi as the base implementation.  We also
-set some USE flags and make sure to unmask the appropriate
-version of sys-cluster/openmpi.  Long options and full package
-atoms are used, but not required.
-
-1.) Sync the science overlay.
-
-2.) Emerge empi
-
-3.) Setup /etc/portage/package stuff.
-    # echo ">=sys-cluster/openmpi-1.2.5-r1 pbs fortran romio smp" >> /etc/portage/package.use
-    # echo ">=sys-cluster/openmpi-1.2.5-r1" >> /etc/portage/package.keywords
-
-4.) Create the implementation.
-    # empi --create --class mpi-openmpi =sys-cluster/openmpi-1.2.5-r1
-
-5.) Add packages.
-    # empi --add --class mpi-openmpi hpl mpi-examples
-
-6.) Setup your user.
-    $ eselect mpi set mpi-openmpi
-    $ echo <<-EOF >> .bash_profile
-for i in $(ls ${HOME}/.env.d/*); do
-    source ${i}
-done
-EOF
-    $ source .bash_profile
-
-7.) Do stuff, or decide this is all worthless and cleanup the mess.
-    # empi --delete mpi-openmpi
-
-
-= Links =
-http://dev.gentoo.org/~vapier/CROSS-COMPILE-HOWTO
-http://archives.gentoo.org/gentoo-cluster/msg_f29032b0d85f7f47d9e52940e9322d91.xml
-http://dev.gentoo.org/~jsbronder/empi.xml
diff --git a/sys-cluster/empi/files/empi-0.10 b/sys-cluster/empi/files/empi-0.10
deleted file mode 100644
index cf41dbbce..000000000
--- a/sys-cluster/empi/files/empi-0.10
+++ /dev/null
@@ -1,497 +0,0 @@
-#!/bin/bash
-VERSION=0.10
-
-source /etc/init.d/functions.sh
-
-die(){
-    if [ -n "${1}" ]; then
-        echo; eerror $1; echo
-    fi
-    exit 1
-}
-
-has() {
-    [[ " ${@:2} " == *" $1 "* ]]
-}
-
-usage(){
-    local rc=${1:-0}
-    shift
-cat <<-EOF
-empi-${VERSION}
-Usage: ${HILITE}empi${NORMAL} ${GOOD}[actions]${NORMAL} ${BRACKET}[options]${NORMAL}
-
-Actions:
-    ${GOOD}-c, --create${NORMAL} pkgspec        (Re)Initialize setup for mpi class.
-    ${GOOD}-a, --add${NORMAL} pkgspec(s)        Add packages using specified mpi class.
-    ${GOOD}-d, --delete${NORMAL} class          Remove everything related to specified class.
-
-Options:
-    ${GOOD}-C, --class${NORMAL} class           MPI class to use.
-    ${GOOD}-t, --tree${NORMAL} path             Path to portage tree to use ebuilds from.
-    ${GOOD}-o, --overlaydir${NORMAL} path       Directory to use for the empi portage overlay.
-                                Defaults to MPI_OVERLAY_DIR [${DEFAULT_MPI_OVERLAY_DIR}]
-    ${GOOD}    --noemerge${NORMAL}              Do not call emerge, only preform overlay setup.
-
-Notes:
-    ${HILITE}-${NORMAL} pkgspec is specified by a package string.  Without a version, the
-      portageq best_visible is used.  For example, all of the following
-      are valid: openmpi, sys-cluster/openmpi, =sys-cluster/openmpi-1.2.5.
-    ${HILITE}-${NORMAL} class (-c) is user defined but must be prefixed with "mpi-"
-
-Examples:
-${BRACKET}Create a new class based on openmpi.${NORMAL}
-    empi --create sys-cluster/openmpi --class mpi-ompi
-${BRACKET}Rebuild the above.${NORMAL}
-    emerge mpi-ompi/openmpi
-${BRACKET}Add hpl to mpi-ompi${NORMAL}
-    empi --class mpi-ompi --add sys-cluster/hpl
-EOF
-    [[ -n $* ]] && echo && eerror "Error: $*"
-    exit ${rc}
-}
-
-class_is_valid() {
-    [[ -z ${CLASS} ]] && usage 1 "No class defined."
-    [[ ${CLASS} != mpi-* ]] && usage 1 "Classes must be prefixed with mpi-"
-    [[ ${CLASS//./} != ${CLASS} ]] && usage 1 "Classes cannot contain . (period)"
-}
-
-is_class_category() {
-    local i
-    for i in $(eselect mpi list -p); do
-        [[ ${1} == ${i} ]] && return 0
-    done
-    return 1
-}
-
-split_atom() {
-    local cpv c pf pn pv
-    cpv=$(portageq best_visible / ${1})
-    if [[ -z ${cpv} || ${rc} -ne 0 ]]; then
-        cpv=$(portageq best_visible / =${1})
-        [[ -z ${cpv} || ${rc} -ne 0 ]] && return 1
-    fi
-    c=${cpv%/*}; pf=${cpv#${c}/}; pn=${pf%%-[0-9]*}; pv=${pf#${pn}-}
-    echo "${c} ${pn} ${pv}"
-}
-
-parse_pkgspecs() {
-    local atom i
-    for ((i=0; i<${#TARGETS[@]}; i++)); do
-        atom=($(split_atom ${TARGETS[i]}))
-        if [[ $? -ne 0 ]]; then
-            eerror "Unable to find a unique package or valid version for ${TARGETS[i]}"
-            eerror "Is the package unmasked and unblocked normally?"
-            die ""
-        fi
-        TARGETS[i]=${atom[0]}/${atom[1]}-${atom[2]}
-    done
-}
-
-# handle_etc_portage package_spec
-# parses /etc/portage/package.{keywords,use}.  If ${CLASS}/${pn} is seen, we don't
-# do a thing.  Otherwise copy any lines that have ${cat}/${pn} inserting them again
-# with the new category.  Also keywords virtual/${CLASS} if necessary.
-handle_etc_portage() {
-    local atom=( $(split_atom ${1}) )
-    local ext line gfiles f
-
-    for ext in "keywords" "use"; do
-        if [ -d /etc/portage/package.${ext} ]; then
-            gfiles="/etc/portage/package.${ext}/*"
-            f=/etc/portage/package.${ext}/${CLASS}
-        else
-            gfiles="/etc/portage/package.${ext}"
-            f=/etc/portage/package.${ext}
-        fi
-
-        if ! grep "^[>=<]*${CLASS}/${atom[1]}" ${gfiles} &>/dev/null; then
-            grep -h "^[>=<]*${atom[0]}/${atom[1]}" ${gfiles} 2>/dev/null \
-                | sed "s,${atom[0]},${CLASS}," \
-            | while read line; do
-               echo "${line}" >> ${f}
-                [[ ${VERBOSE} -ne 0 ]] \
-                    && einfo "Addition to ${f}: ${line}"
-            done
-        elif [[ ${VERBOSE} -ne 0 ]]; then
-            ewarn "Keys for ${CLASS}/${atom[1]} already exist in ${f}.  Will not replicate them."
-        fi
-
-        if ! grep "^${CLASS}/mpi" ${gfiles} &>/dev/null; then
-            grep -h "^virtual/mpi" ${gfiles} 2>/dev/null \
-                | sed "s,/mpi,/${CLASS}," \
-            | while read line; do
-                echo "${line}" >> ${f}
-            [[ ${VERBOSE} -ne 0 ]] \
-                && einfo "Addition to ${f}: ${line}"
-            done
-        elif [[ ${VERBOSE} -ne 0 ]]; then
-            ewarn "Keys for virtual/${CLASS} already exist.  Will not replicate."
-        fi
-    done
-}
-
-
-
-get_ebuild_dir() {
-    local d a
-    local want_uses_mpi=${2:-0}
-    local found=0
-
-    a=($(split_atom ${1}))
-    [[ $? -ne 0 ]] && die "Unable to find a unique package or valid version for ${1}."
-    is_class_category ${a[0]} && die "It makes no sense to build a new mpi-class from a current one."
-
-    if [[ -z ${PORTAGE_TREE} ]]; then
-        for d in $(portageq portdir_overlay) $(portageq portdir); do
-            if [[ ${want_uses_mpi} -ne 0 ]]; then
-                [[ -f "${d}/${a[0]}/${a[1]}/${a[1]}-${a[2]}.ebuild" ]] \
-                    && ebuild_uses_mpi ${d}/${a[0]}/${a[1]} ${a[1]}-${a[2]} \
-                    && found=1
-            else
-                [[ -f "${d}/${a[0]}/${a[1]}/${a[1]}-${a[2]}.ebuild" ]] && found=1
-            fi
-            [[ ${found} -ne 0 ]] && break
-        done
-        if [[ ${found} -ne 0 ]]; then
-            PORTAGE_TREE=${d}
-        else
-            die "Could not find an ebuild for ${a[0]}/${a[1]}-${a[2]}."
-        fi
-    fi
-
-    EBUILD_DIR="${PORTAGE_TREE}/${a[0]}/${a[1]}"
-}
-
-ebuild_uses_mpi() {
-    grep 'inherit .*mpi' "${1}/${2##*/}.ebuild" &>/dev/null
-}
-
-link_ebuild_dir() {
-    ln -snf "${EBUILD_DIR}" "${MPI_OVERLAY_DIR}"/${CLASS}/${EBUILD_DIR##*/} \
-        || die "Failed to link ${EBUILD_DIR} to ${MPI_OVERLAY_DIR}/${CLASS}/${EBUILD_DIR##*/}"
-}
-
-# TODO:  Needs to be called after get_ebuild_dir which sets $PORTAGE_TREE
-create_virtual_mpi() {
-    local d_dir="${MPI_OVERLAY_DIR}"/virtual/${CLASS}
-    local version d_file mpi_ebuild s_dir
-
-    # Try to get virtual/mpi from the same tree as the other ebuilds.
-    # Otherwise we fall back and get it from anywhere.
-    version=$(portageq best_visible / ${__VIRTUAL_MPI_VERSION})
-    version=${version#virtual/mpi-}
-
-    for s_dir in ${PORTAGE_TREE} $(portageq portdir_overlay) $(portageq portdir); do
-        mpi_ebuild="${s_dir}"/virtual/mpi/mpi-${version}.ebuild
-        [ -f "${mpi_ebuild}" ] && break;
-    done
-
-    [[ ! -f "${mpi_ebuild}" ]] \
-        && die "Cannot satisfy ${__VIRTUAL_MPI_VERSION}"
-
-    d_file=${CLASS}-${version}.ebuild
-
-    mkdir -p "${d_dir}" || die "Could not create ${d_dir}"
-
-    cp "${mpi_ebuild}" "${d_dir}"/${d_file} \
-        || die "Could not copy ${mpi_ebuild} to ${d_dir}/${d_file}"
-
-    sed -i "s,sys-cluster/,${CLASS}/," ${d_dir}/${d_file}
-    ebuild ${d_dir}/${d_file} digest > /dev/null \
-        || die "Failed to digest ${d_dir}/${d_file}"
-}
-
-set_metadata() {
-    # Snagged from crossdev:  http://git.overlays.gentoo.org/gitweb/?p=proj/crossdev.git
-    # 3cab8c394fec72f2353e209d98429dd1aaf1d337
-
-    # for people who have eclasses spread over their overlays, generate
-    # a layout.conf file so portage can find them.  this is a crapshoot
-    # when diff overlay sources have conflicting eclasses, but nothing
-    # we really can do about that.
-    local autogen_tag="# Autogenerated and managed by empi"
-    local meta=${MPI_OVERLAY_DIR}/metadata
-    local layout=${meta}/layout.conf
-    local d name masters thin_manifests="false"
-
-    mkdir -p "${meta}"
-    if [[ -e ${layout} ]] ; then
-        if ! grep -qs "^${autogen_tag}" "${layout}" ; then
-            einfo "leaving metadata/layout.conf alone in ${MPI_OVERLAY_DIR}"
-            return
-        fi
-
-        # We are managing it, so blow it away
-        rm -f "${layout}"
-    fi
-
-    # build up a list of possible repos where we can pull from
-    for d in ${PORTDIR_OVERLAY} "${PORTDIR}" ; do
-        [[ -z ${d} ]] && continue
-
-        name=
-        if [[ -e ${d}/profiles/repo_name ]] ; then
-            name=$(<"${d}"/profiles/repo_name)
-        fi
-        [[ -z ${name} ]] && continue
-
-        # If this repo has an eclass dir, mark it as a master.
-        # Note: portage reads the masters list in reverse order,
-        #       so we have to prepare it the same way.
-        if [[ -d ${d}/eclass ]] ; then
-            has ${name} ${masters} || masters="${name} ${masters}"
-        fi
-
-        # If one of the overlays uses thin manifests, then turn it on
-        if [[ -z ${this_manifests} ]] && has ${name} ${masters} && \
-            sed \
-                -e 's:#.*::' \
-                -e 's:^[[:space:]]*::' \
-                -e 's:[[:space:]]*$::' \
-                -e 's:[[:space:]]*=[[:space:]]*:=:' \
-                "${d}/metadata/layout.conf" 2>/dev/null | \
-            gawk -F= '{
-                    if ($1 == "use-manifests") um = $2
-                    if ($1 == "thin-manifests") tm = $2
-                }
-                END {
-                    exit !(um != "false" && tm == "true")
-                }'
-        then
-            einfo "enabling thin-manifests due to ${d}"
-            this_manifests="use-manifests = true\nthin-manifests = true"
-        fi
-    done
-
-    # write out that layout.conf!
-    cat <<-EOF > "${layout}"
-	${autogen_tag}
-	# Delete the above line if you want to manage this file yourself
-	masters = ${masters% }
-	$(printf '%b' "${this_manifests}")
-	EOF
-}
-
-do_emerge() {
-    [[ ${DO_EMERGE} -eq 0 ]] && return 0
-    einfo "Emerging $*"
-    emerge ${EMERGE_OPTS} $* || die "emerge failed!"
-}
-
-# We should have only one target here.
-create_class() {
-    local mpi_class_pkg d mpi_class_pn
-
-    [[ ${#TARGETS[@]} -ne 1 ]] && die "Can only create one class at a time."
-
-    for d in $(eselect mpi list -p); do
-        [ "${d}" == "${CLASS}" ] && die "${CLASS} has already been created."
-    done
-
-    # Prevent laziness
-    [[ ${TARGETS[0]} == ${TARGETS[0]##*/} ]] \
-        && TARGETS[0]="sys-cluster/${TARGETS[0]}"
-
-    parse_pkgspecs
-    get_ebuild_dir ${TARGETS[0]} 1
-    create_virtual_mpi
-    mpi_class_pn=${EBUILD_DIR##*/}
-    mpi_class_pkg=${TARGETS[0]}
-    handle_etc_portage ${TARGETS[0]}
-    TARGETS[0]="=${CLASS}/${TARGETS[0]##*/}"
-
-    # Refuse to break systems.  If there is already a class
-    # installed in that directory, we're not going to add another one as
-    # the eclass doesn't fix one problem just to introduce a bigger one.
-    for d in $(find ${MPI_OVERLAY_DIR}/${CLASS} -maxdepth 1 -mindepth 1 -type l 2>/dev/null);do
-        d=${d##*/}
-        [[ ${d} == ${mpi_class_pn} ]] && continue
-        for i in ${MPI_ALL_IMPS}; do
-            [[ ${i} == ${d} ]] \
-                && die "${CLASS} already has MPI implementation ${d}, refusing to add ${mpi_class_pn}"
-        done
-    done
-
-    if [[ -d "${MPI_OVERLAY_DIR}"/${CLASS} ]]; then
-        [[ ${VERBOSE} -ne 0 ]] && ewarn "Overlay for ${CLASS} has already been created."
-    else
-        mkdir -p ${MPI_OVERLAY_DIR}/${CLASS}
-        link_ebuild_dir
-		set_metadata
-    fi
-    if ! grep "^${CLASS}$" /etc/portage/categories &>/dev/null; then
-        echo "${CLASS}" >> /etc/portage/categories
-    fi
-
-
-cat << EOF
-Creating ${HILITE}${CLASS}${NORMAL}
-    Class:                  ${GOOD}${CLASS}${NORMAL}
-    MPI Implementation:     ${GOOD}${mpi_class_pkg}${NORMAL}
-    Source:                 ${GOOD}${EBUILD_DIR}${NORMAL}
-    Destination:            ${GOOD}${MPI_OVERLAY_DIR}/${CLASS}${NORMAL}
-EOF
-    do_emerge ${TARGETS[0]}
-}
-
-
-add_packages(){
-    local i j deps
-
-    [[ -d "${MPI_OVERLAY_DIR}"/${CLASS} ]] || die "Class ${CLASS} has not been created yet."
-    [[ ${#TARGETS[@]} -lt 1 ]] && die "You need to specify at least one package"
-
-    parse_pkgspecs
-    for ((i=0;i<${#TARGETS[@]};i++)); do
-        get_ebuild_dir ${TARGETS[i]}
-        create_virtual_mpi
-        if ebuild_uses_mpi ${EBUILD_DIR} ${TARGETS[i]}; then
-            link_ebuild_dir
-            handle_etc_portage ${TARGETS[i]}
-            TARGETS[i]="=${CLASS}/${TARGETS[i]##*/}"
-        else
-            TARGETS[i]="=${TARGETS[i]}"
-        fi
-
-        # I don't know about this, but do you have a better idea?
-        deps="$(emerge --color=n --onlydeps -p --quiet ${TARGETS[i]} | grep '^\[')"
-        if [[ $? -ne 0 ]]; then
-            emerge --onlydeps -p ${TARGETS[i]}
-            die "Unable to calculate deps for ${TARGETS[i]}"
-        fi
-        deps=( $(echo ${deps} | sed -e 's:\[[a-z]* [A-Z] \] :=:g') )
-        for ((j=0;j<${#deps[@]};j++)); do
-            get_ebuild_dir ${deps[j]}
-            if ebuild_uses_mpi ${deps[i]}; then
-                link_ebuild_dir
-            fi
-        done
-    done
-cat << EOF
-Adding packages to ${HILIGHT}${CLASS}${NORMAL}
-    Packages:       ${GOOD}${TARGETS[@]}${NORMAL}
-EOF
-    do_emerge ${TARGETS[@]}
-}
-
-
-delete_class() {
-    local pkgs=( $(ls /var/db/pkg/${CLASS}/ 2>/dev/null) )
-    local ext d i rc
-    [[ -d "${MPI_OVERLAY_DIR}"/${CLASS} ]] || die "Class ${CLASS} has not been created yet."
-    rc=0
-
-    for (( i=0; i<${#pkgs[@]}; i++)); do
-        pkgs[i]="=${CLASS}/${pkgs[i]}"
-    done
-
-    if [[ ${#pkgs[@]} -gt 0 ]] && ! emerge -C ${EMERGE_OPTS/-u/} ${pkgs[@]}; then
-        die "Failed to unmerge ${pkgs[@]}"
-    fi
-
-    for ext in "keywords" "use"; do
-        if [ -d /etc/portage/package.${ext} ]; then
-            rm /etc/portage/package.${ext}/${CLASS} &>/dev/null
-            rc=$((rc+$?))
-        elif [ -f /etc/portage/package.${ext} ]; then
-            sed -i -e "/^${CLASS}\//d" /etc/portage/package.${ext}
-            rc=$((rc+$?))
-        fi
-    done
-
-    [ ! -f /etc/portage/categories ] || sed -i -e "/^${CLASS}$/d" /etc/portage/categories
-    rc=$((rc+$?))
-
-   for d in $(ls "${MPI_OVERLAY_DIR}"/${CLASS}/ 2>/dev/null); do
-        rm "${MPI_OVERLAY_DIR}"/${CLASS}/${d}
-        rc=$((rc+$?))
-    done
-
-    for d in "${MPI_OVERLAY_DIR}/${CLASS}" /var/db/pkg/${CLASS}; do
-        [ ! -d "${d}" ] || rmdir "${d}"
-        rc=$((rc+$?))
-    done
-
-    [[ ${rc} -ne 0 ]] \
-        && ewarn "Errors were encountered during delete_class()"
-    return ${rc}
-}
-
-# Internal variables.
-__VIRTUAL_MPI_VERSION=">=virtual/mpi-2.0"
-
-ACTION=""
-CLASS=""
-PORTAGE_TREE=""
-MPI_OVERLAY_DIR=""
-VERBOSE=0
-DO_EMERGE=1
-EMERGE_OPTS="-u"  # Packages can be recompiled by hand if necessary.
-TARGETS=""
-DEFAULT_MPI_OVERLAY_DIR=/var/cache/overlays/mpi
-MAKE_CONF=/etc/make.conf
-
-PORTDIR_OVERLAY=""
-PKGDIR=""
-
-EBUILD_DIR=""
-
-while [[ $# -gt 0 ]]; do
-    case $1 in
-        -h|--help)
-            usage;;
-        -c|--create)
-            ACTION="${ACTION}create";;
-        -a|--add)
-            ACTION="${ACTION}add";;
-        -d|--delete)
-            ACTION="${ACTION}delete"
-            shift; CLASS=${1};;
-        -C|--class)
-            shift; CLASS=${1};;
-        -t|--tree)
-            shift; PORTAGE_TREE=${1};;
-        -o|--overlaydir)
-            shift; MPI_OVERLAY_DIR=${1};;
-        -v|--verbose)
-            VERBOSE=1;;
-        --noemerge)
-            DO_EMERGE=0;;
-        -*)
-            EMERGE_OPTS="${EMERGE_OPTS} ${1}";;
-        *)
-            TARGETS=( $(echo ${TARGETS[@]}) ${1} );;
-    esac
-    shift
-done
-
-[[ ${UID} -ne 0 ]] && die "You must be root to preform any actions."
-
-if [ -s /etc/portage/make.conf ]; then
-    MAKE_CONF=/etc/portage/make.conf
-fi
-
-: ${MPI_OVERLAY_DIR:=$(portageq envvar MPI_OVERLAY_DIR)}
-if [ -z "${MPI_OVERLAY_DIR}" ]; then
-    MPI_OVERLAY_DIR=${DEFAULT_MPI_OVERLAY_DIR}
-    einfo "MPI_OVERLAY_DIR not set, defaulting to ${MPI_OVERLAY_DIR} and updating make.conf"
-    echo "MPI_OVERLAY_DIR=\"${MPI_OVERLAY_DIR}\"" >> ${MAKE_CONF}
-fi
-
-if [ ! -d "${MPI_OVERLAY_DIR}" ]; then
-    mkdir -p "${MPI_OVERLAY_DIR}" || die "Failed to mkdir ${MPI_OVERLAY_DIR}"
-fi
-
-export PORTDIR_OVERLAY="${MPI_OVERLAY_DIR} $(portageq portdir_overlay)"
-export PKGDIR="$(portageq envvar PKGDIR)/mpi/${CLASS}"
-export PORTDIR="$(portageq envvar PORTDIR)"
-
-[[ -z ${ACTION} ]] && usage 1 "No action defined."
-class_is_valid
-
-set_metadata
-[[ ${ACTION} == *create* ]] && create_class
-[[ ${ACTION} == *add* ]]    && add_packages
-[[ ${ACTION} == *delete* ]] && delete_class
diff --git a/sys-cluster/empi/files/eselect.mpi-0.10 b/sys-cluster/empi/files/eselect.mpi-0.10
deleted file mode 100644
index 2c7a56776..000000000
--- a/sys-cluster/empi/files/eselect.mpi-0.10
+++ /dev/null
@@ -1,273 +0,0 @@
-# Copyright 1999-2013 Gentoo Foundation
-# Distributed under the terms of the GNU General Public License v2
-
-DESCRIPTION="Manage MPI classes"
-MAINTAINER="jsbronder@gentoo.org"
-SVN_DATE='$Date: $'
-VERSION="0.0.2"
-
-inherit path-manipulation config
-
-# The basic idea is we want to allow every use to select their own mpi
-# implementation they want, and a ${HOME}/.env.d/mpi file is created for them.
-#   A user then is -required- to source the env file.  This sets PATH, MANPATH,
-# and LD_LIBRARY_PATH.  I'm sure I'm forgetting something here.
-# Calling unset only wipes out the env file, replacing it with what we
-# previously added stripped out.
-
-# If you can think of a better way to do this, while still allowing user's
-# freedom, please let me know.
-
-# List the valid mpi classes currently installed.
-find_classes() {
-	local classes
-	for f in ${ROOT}/etc/env.d/mpi/*; do
-		[[ -f ${f} ]] || continue
-		f=$(basename ${f})
-		[[ "${f#mpi-}" == "${f}" ]] && continue
-		classes=(${classes[@]} ${f})
-	done
-	echo ${classes[@]}
-}
-
-# User's current environment has the class configured in it.
-is_in_use() { [ "${ESELECT_MPI_IMP}" == "${1}" ]; }
-
-# User's env file is ready for sourcing for this class
-is_enabled() {
-	[ "$(var_from_user_envd ESELECT_MPI_IMP)" == "${1}" ]
-}
-
-var_from_user_envd(){
-	[ ! -f ${user_ev_sh} ] && return 0
-	echo "$(source ${user_ev_sh}; echo ${!1})"
-}
-
-# Is this a valid class?
-is_class() {
-	local classes=$(find_classes)
-	for i in ${classes[@]}; do
-		[[ "${i}" == "${1}" ]] && return 0
-	done
-	return 1
-}
-
-init() {
-	local d
-	[[ ${UID} -eq 0 ]] && HOME="${ROOT}/root"
-	d="$(canonicalise "${ROOT}/${HOME}")"
-	d="${d}/.env.d/"
-	user_ev_sh="${d}mpi.sh"; 
-	user_ev_csh="${d}mpi.csh"; 
-	
-	if [[ ! -d "${d}" ]]; then
-		mkdir "${d}" || die -q "Failed to create ${d}."
-	elif [[ ! -w "${d}" ]]; then
-		die -q "You do not have permission to mkdir ${d}."
-	fi
-	[[ -f "${user_ev_sh}" && ! -w "${user_ev_sh}" \
-		&& -f "${user_ev_csh}" && ! -w "${user_ev_csh}" ]] \
-		&& die -q "You do not have permission to write to ${user_ev_sh} or ${user_ev_csh}."
-}
-
-global_env() {
-	local d=$(canonicalise "${ROOT}/etc/env.d/mpi/${1}")
-	[ -z "${d}" ] && die "Cannot find global env file for ${1}"
-	ev=${d}
-}
-
-### list action ###
-
-describe_list() {  echo "List available classs"; }
-describe_list_parameters() { echo "[-p]"; }
-
-do_list() {
-	classes=( $(find_classes) )
-	init
-	if [[ ${@} == *-p* ]]; then
-		echo "${classes[@]}"
-	else
-		write_list_start "Available MPI classs:"
-		if [[ -n "${classes[@]}" ]]; then
-			for (( i=0; i<${#classes[@]}; i++ )); do
-				if is_in_use ${classes[$i]} && is_enabled ${classes[$i]}; then
-					write_kv_list_entry "${classes[$i]}" "Enabled, In Use"
-				elif is_in_use ${classes[$i]}; then
-					write_kv_list_entry "${classes[$i]}" "In Use"
-				elif is_enabled ${classes[$i]}; then
-					write_kv_list_entry "${classes[$i]}" "Enabled"
-				else
-					write_kv_list_entry "${classes[$i]}" "--"
-				fi
-			done
-		else
-			write_kv_list_entry "(none found)" ""
-		fi
-	fi
-	return 0
-}
-
-
-### set action ###
-
-describe_set() {
-	echo "Select a MPI class."
-}
-
-describe_set_parameters() {
-	echo "<target>"
-}
-
-do_set() {
-	local binpath lld manpath current_imp
-
-	init
-	current_imp="$(var_from_user_envd ESELECT_MPI_IMP)"
-	global_env ${1}
-
-	[[ -z ${1} ]] && die -q "You didnt specifiy any class for use."
-	[[ ${#@} -ne 1 ]] && die -q "You may only select exactly one class."
-	! is_class ${1} && die -q "${1} is not an class."
-	if is_enabled ${1}; then
-		echo "${1} implemention is currently in use.  This is a no-op."
-		return
-	elif [ -n "${current_imp}" ]; then
-		echo "Cannot select ${1} when ${current_imp} is in use."
-		return 1
-	fi
-	
-   binpath="$(load_config ${ev} PATH)"
-   lld="$(load_config ${ev} LD_LIBRARY_PATH)"
-   manpath="$(load_config ${ev} MANPATH)"
-
-cat <<-EOF >${user_ev_sh}
-bpl=\`expr "\${PATH}" : ".*${binpath}:"\`
-mpl=\`expr "\${MANPATH}" : ".*${manpath}:"\`
-llpl=\`expr "\${LD_LIBRARY_PATH}" : ".*${lld}:"\`
-
-if [ \${bpl} -eq 0 ]; then
-	export PATH="${binpath}:\${PATH}"
-fi
-
-if [ \${mpl} -eq 0 ]; then
-	export MANPATH="${manpath}:\${MANPATH}"
-fi
-
-if [ \${llpl} -eq 0 ]; then
-	export LD_LIBRARY_PATH="${lld}:\${LD_LIBRARY_PATH}"
-fi
-export ESELECT_MPI_IMP="${1}"
-EOF
-
-cat <<-EOF >${user_ev_csh}
-set bpl=\`expr "\${PATH}" : ".*${binpath}:"\`
-set mpl=\`expr "\${MANPATH}" : ".*${manpath}:"\`
-set llpl=\`expr "\${LD_LIBRARY_PATH}" : ".*${lld}:"\`
-
-if ( \$bpl == 0 ) \
-	setenv PATH "${binpath}:\${PATH}"
-
-if ( \$mpl == 0 ) \
-	setenv MANPATH "${manpath}:\${MANPATH}"
-
-if ( \$llpl  == 0 ) \
-	setenv LD_LIBRARY_PATH "${lld}:\${LD_LIBRARY_PATH}"
-
-setenv ESELECT_MPI_IMP "${1}"
-EOF
-
-	echo "Remember to source /etc/profile or /etc/csh.login"
-}
-
-
-### unset action ###
-describe_unset() {
-	echo "Restore MPI-less environment."
-}
-
-do_unset() {
-   	local lld current_imp
-   	init
-
-	current_imp="$(var_from_user_envd ESELECT_MPI_IMP)"
-
-	if [ -z "${current_imp}" ]; then
-		echo "No implemention currently in use.  This is a no-op."
-		return
-	fi
-	
-	global_env "${ESELECT_MPI_IMP}"
-	lld="$(load_config ${ev} LD_LIBRARY_PATH)"
-
-   # PATH and MANPATH are reset in /etc/profile.
-cat <<-EOF > ${user_ev_sh}
-unset ESELECT_MPI_IMP
-l=\`expr "\${LD_LIBRARY_PATH}:" : ".*${lld}:"\`
-l=\$(( \${l} + 1 ))
-
-if [ \${l} -gt 1 ]; then
-	export LD_LIBRARY_PATH="\`expr substr \${LD_LIBRARY_PATH} \${l} 1024\`"
-fi
-EOF
-
-cat <<-EOF > ${user_ev_csh}
-unsetenv ESELECT_MPI_IMP
-set l=\`expr "\${LD_LIBRARY_PATH}:" : ".*${lld}:"\`
-@ l = ( \${l} + 1 )
-
-if ( \${l} > 1 ) \
-	setenv LD_LIBRARY_PATH "\`expr substr \${LD_LIBRARY_PATH} \${l} 1024\`"
-EOF
-
-   echo "Remember to source /etc/profile or /etc/csh.login"
-}
-
-### add action (from skel pretty much)
-describe_add() {
-	echo "Add a new mpi class"
-}
-
-describe_add_parameters() {
-	echo "<file>"
-}
-
-do_add() {
-	local class
-	[[ ${#@} -ne 1 ]] \
-		&& die -q "Bad arguments, use:  mpi add /some/full/path/<class>.eselect"
-
-	# If $D is set, we're adding from portage so we want to respect sandbox.
-	# Otherwise, respect the ROOT variable.
-	local PREFIX=${D:-${ROOT}/}
-
-	# Create directory if necessary
-	if [[ ! -e ${PREFIX}/etc/env.d/mpi/ ]]; then
-		mkdir -p ${PREFIX}/etc/env.d/mpi/
-	else
-		if [[ ! -d ${PREFIX}/etc/env.d/mpi/ ]]; then
-			die -q "${PREFIX}/etc/env.d/mpi/ exists but isn't a directory!"
-		fi
-	fi
-
-	class=$(basename ${1}); class=${class%.eselect}
-	if ! cp ${1} ${PREFIX}/etc/env.d/mpi/${class}; then
-		die -q "Installing ${1} as ${PREFIX}/etc/env.d/mpi/${class} failed!"
-	fi
-}
-
-
-### printvar action ###
-describe_printvar() { echo "Print variables stored in global env.d file."; }
-describe_printvar_parameters() { echo "<class> <variable>"; }
-
-do_printvar() {
-	if [[ ${#@} -ne 2 ]] \
-		|| ! is_class ${1}; then
-		die -q "Specify exactly 1 class and 1 variable."
-	fi
-	global_env ${1}
-	echo "$(load_config ${ev} ${2})"
-}
-
-# vim: ft=eselect:noet
-
diff --git a/sys-cluster/empi/files/mpi.csh b/sys-cluster/empi/files/mpi.csh
deleted file mode 100644
index 32506b4cc..000000000
--- a/sys-cluster/empi/files/mpi.csh
+++ /dev/null
@@ -1,3 +0,0 @@
-if ( -d "${HOME}"/.env.d && -f "${HOME}"/.env.d/mpi.csh ) then
-    source "${HOME}"/.env.d/mpi.csh
-endif
diff --git a/sys-cluster/empi/files/mpi.sh b/sys-cluster/empi/files/mpi.sh
deleted file mode 100644
index 5483247e5..000000000
--- a/sys-cluster/empi/files/mpi.sh
+++ /dev/null
@@ -1,3 +0,0 @@
-if [ -d "${HOME}"/.env.d -a -f "${HOME}"/.env.d/mpi.sh ]; then
-    source "${HOME}"/.env.d/mpi.sh
-fi
diff --git a/sys-cluster/empi/metadata.xml b/sys-cluster/empi/metadata.xml
deleted file mode 100644
index c74b39b01..000000000
--- a/sys-cluster/empi/metadata.xml
+++ /dev/null
@@ -1,11 +0,0 @@
-<?xml version="1.0" encoding="UTF-8"?>
-<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
-<pkgmetadata>
-	<maintainer type="person">
-		<email>jsbronder@gentoo.org</email>
-	</maintainer>
-	<maintainer type="project">
-		<email>cluster@gentoo.org</email>
-		<name>Gentoo Cluster Project</name>
-	</maintainer>
-</pkgmetadata>
diff --git a/sys-cluster/hpl/Manifest b/sys-cluster/hpl/Manifest
deleted file mode 100644
index 492955e56..000000000
--- a/sys-cluster/hpl/Manifest
+++ /dev/null
@@ -1,2 +0,0 @@
-DIST hpl-2.0.tar.gz 591087 BLAKE2B d3fd738c40f89916c7a5a7cbb561d30c8b9defd08d552b6aeea707f2b6b87a4774d6dce4b9fd7983ee12b112f319e574b89fd8158a381e997dfb86a3572d5f95 SHA512 3aa76144526b01ec40d940cae50d47e480e2760a36d1e95bc6e431b216407db190946fc3d99a6a7caf7b61bcc76d805d28da3ef0b141ff467854e1cdf10bb274
-DIST hpl-2.1.tar.gz 527433 BLAKE2B ccc3f881c3e584ef36801ac5584b5d5e4a354723100c4ffae943689c95763609ea5058b1eb376fe802c8a8c84ce24995aa12301f01cf122462f90308f7ba3588 SHA512 ed39e407341d1cfe2d4d7e50f029e3ca62c7e87e82c3b09a89fd231c5cb4f1c95857f050a940bfd60b724eaa9fdab8631a0693a14b6e9dac82c05897bff557a4
diff --git a/sys-cluster/hpl/hpl-2.0-r1.ebuild b/sys-cluster/hpl/hpl-2.0-r1.ebuild
deleted file mode 100644
index 8b80e4c1c..000000000
--- a/sys-cluster/hpl/hpl-2.0-r1.ebuild
+++ /dev/null
@@ -1,67 +0,0 @@
-# Copyright 1999-2016 Gentoo Foundation
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=6
-
-inherit eutils mpi toolchain-funcs
-
-DESCRIPTION="High-Performance Linpack Benchmark for Distributed-Memory Computers"
-HOMEPAGE="http://www.netlib.org/benchmark/hpl/"
-SRC_URI="http://www.netlib.org/benchmark/hpl/hpl-${PV}.tar.gz"
-
-SLOT="0"
-LICENSE="HPL"
-KEYWORDS="~amd64 ~x86"
-IUSE="doc"
-
-RDEPEND="
-	$(mpi_pkg_deplist)
-	virtual/blas
-	virtual/lapack"
-DEPEND="${RDEPEND}
-	virtual/pkgconfig"
-
-src_prepare() {
-	local mpicc_path="$(mpi_pkg_cc)"
-
-	cp setup/Make.Linux_PII_FBLAS Make.gentoo_hpl_fblas_x86 || die
-	sed -i \
-		-e "/^TOPdir/s,= .*,= ${S}," \
-		-e '/^HPL_OPTS\>/s,=,= -DHPL_DETAILED_TIMING -DHPL_COPY_L,' \
-		-e '/^ARCH\>/s,= .*,= gentoo_hpl_fblas_x86,' \
-		-e '/^MPdir\>/s,= .*,=,' \
-		-e '/^MPlib\>/s,= .*,=,' \
-		-e "/^LAlib\>/s,= .*,= $($(tc-getPKG_CONFIG) --libs-only-l blas lapack)," \
-		-e "/^LINKER\>/s,= .*,= ${mpicc_path}," \
-		-e "/^CC\>/s,= .*,= ${mpicc_path}," \
-		-e "/^LINKFLAGS\>/s|= .*|= ${LDFLAGS} $($(tc-getPKG_CONFIG) --libs-only-L blas lapack)|" \
-		Make.gentoo_hpl_fblas_x86 || die
-	default
-}
-
-src_compile() {
-	# do NOT use emake here
-	mpi_pkg_set_env
-	# parallel make failure bug #321539
-	HOME=${WORKDIR} emake -j1 arch=gentoo_hpl_fblas_x86
-	mpi_pkg_restore_env
-}
-
-src_install() {
-	mpi_dobin bin/gentoo_hpl_fblas_x86/xhpl
-	mpi_dolib.a lib/gentoo_hpl_fblas_x86/libhpl.a
-	mpi_dodoc INSTALL BUGS COPYRIGHT HISTORY README TUNING \
-		bin/gentoo_hpl_fblas_x86/HPL.dat
-	mpi_doman man/man3/*.3
-	if use doc; then
-		mpi_dohtml -r www/*
-	fi
-}
-
-pkg_postinst() {
-	local d=$(mpi_root)
-	einfo "Remember to copy $(mpi_root)usr/share/doc/${PF}/HPL.dat to your working directory first!"
-	einfo "Typically one may run hpl by executing the following:"
-	einfo "\"mpiexec -np 4 /usr/bin/xhpl\""
-	einfo "where -np specifies the number of processes."
-}
diff --git a/sys-cluster/hpl/hpl-2.1.ebuild b/sys-cluster/hpl/hpl-2.1.ebuild
deleted file mode 100644
index ba91a5d66..000000000
--- a/sys-cluster/hpl/hpl-2.1.ebuild
+++ /dev/null
@@ -1,71 +0,0 @@
-# Copyright 1999-2016 Gentoo Foundation
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=6
-
-inherit eutils mpi multilib
-
-DESCRIPTION="High-Performance Linpack Benchmark for Distributed-Memory Computers"
-HOMEPAGE="http://www.netlib.org/benchmark/hpl/"
-SRC_URI="http://www.netlib.org/benchmark/hpl/hpl-${PV}.tar.gz"
-
-SLOT="0"
-LICENSE="HPL"
-KEYWORDS="~amd64 ~x86"
-IUSE="doc"
-
-RDEPEND="
-	$(mpi_pkg_deplist)
-	virtual/blas
-	virtual/lapack"
-DEPEND="${RDEPEND}
-	virtual/pkgconfig"
-
-src_prepare() {
-	local mpicc_path="$(mpi_pkg_cc)"
-	local a=""
-	local locallib="${EPREFIX}/usr/$(get_libdir)/lib"
-
-	cp setup/Make.Linux_PII_FBLAS Make.gentoo_hpl_fblas_x86 || die
-	sed -i \
-		-e "/^TOPdir/s,= .*,= ${S}," \
-		-e '/^HPL_OPTS\>/s,=,= -DHPL_DETAILED_TIMING -DHPL_COPY_L,' \
-		-e '/^ARCH\>/s,= .*,= gentoo_hpl_fblas_x86,' \
-		-e '/^MPdir\>/s,= .*,=,' \
-		-e '/^MPlib\>/s,= .*,=,' \
-		-e "/^LAlib\>/s%= .*%= $($(tc-getPKG_CONFIG) --libs blas lapack)%" \
-		-e "/^LINKER\>/s,= .*,= ${mpicc_path}," \
-		-e "/^CC\>/s,= .*,= ${mpicc_path}," \
-		-e "/^CCFLAGS\>/s|= .*|= \$(HPL_DEFS) ${CFLAGS}|" \
-		-e "/^LINKFLAGS\>/s|= .*|= ${LDFLAGS}|" \
-		Make.gentoo_hpl_fblas_x86 || die
-	default
-}
-
-src_compile() {
-	# do NOT use emake here
-	mpi_pkg_set_env
-	# parallel make failure bug #321539
-	HOME=${WORKDIR} emake -j1 arch=gentoo_hpl_fblas_x86
-	mpi_pkg_restore_env
-}
-
-src_install() {
-	mpi_dobin bin/gentoo_hpl_fblas_x86/xhpl
-	mpi_dolib.a lib/gentoo_hpl_fblas_x86/libhpl.a
-	mpi_dodoc INSTALL BUGS COPYRIGHT HISTORY README TUNING
-	mpi_doman man/man3/*.3
-	if use doc; then
-		mpi_dohtml -r www/*
-	fi
-	insinto $(mpi_root)usr/share/hpl
-	mpi_doins bin/gentoo_hpl_fblas_x86/HPL.dat
-}
-
-pkg_postinst() {
-	local d=$(mpi_root)
-	einfo "Remember to copy $(mpi_root)usr/share/hpl/HPL.dat to your working directory"
-	einfo "before running xhpl. Typically one may run hpl by executing:"
-	einfo "\"mpiexec -np 4 /usr/bin/xhpl\""
-	einfo "where -np specifies the number of processes."
-}
diff --git a/sys-cluster/hpl/metadata.xml b/sys-cluster/hpl/metadata.xml
deleted file mode 100644
index 8bf4b5f36..000000000
--- a/sys-cluster/hpl/metadata.xml
+++ /dev/null
@@ -1,8 +0,0 @@
-<?xml version="1.0" encoding="UTF-8"?>
-<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
-<pkgmetadata>
-	<maintainer type="project">
-		<email>cluster@gentoo.org</email>
-		<name>Gentoo Cluster Project</name>
-	</maintainer>
-</pkgmetadata>
diff --git a/sys-cluster/htcondor/Manifest b/sys-cluster/htcondor/Manifest
deleted file mode 100644
index 44889bcaa..000000000
--- a/sys-cluster/htcondor/Manifest
+++ /dev/null
@@ -1,2 +0,0 @@
-DIST condor_src-8.0.0-all-all.tar.gz 18636227 SHA256 b1fe7cedcab17d713a64b57dbb2a5f0426979316b8f309f9492ff60f7b43d3a8 SHA512 a335d0cb200f1899711f6f87968a01a2f5dcd37fede2ef973f2863a3f628d6f04421abbaaa22a310711ea1367af3a4f68e31c5e91e8cee1149cc5957d6ac0119 WHIRLPOOL 4c755644cd2ba5f7414ac3c8374df141b98d3e830f07a0ea0e0cc46b575ac8b42c1e47135cb9a87342bd41309b03df1693de1836cd250ea7e6ace1c3445ebd25
-DIST htcondor-8.3.2.tar.gz 18451391 BLAKE2B ab30e6bb2bfbcd67e1f4e03e10ec7b52fb7b5c707bb7451c97327032c1be663db145b378113bcd1f46cb6dc4edd32298afba0bb554504368db3b4c92a669a98b SHA512 588d2dd4586be6d135a658cc54b01ed2c02a1127495af68c73f69d33df98bdafe7e1fc248950e4af3ca14fc1bd6329f003a61daf875580646eddabe6201b353c
diff --git a/sys-cluster/htcondor/files/0001-Apply-the-user-s-condor_config-last-rather-than-firs.patch b/sys-cluster/htcondor/files/0001-Apply-the-user-s-condor_config-last-rather-than-firs.patch
deleted file mode 100644
index 0664fe764..000000000
--- a/sys-cluster/htcondor/files/0001-Apply-the-user-s-condor_config-last-rather-than-firs.patch
+++ /dev/null
@@ -1,90 +0,0 @@
---- a/src/condor_utils/condor_config.cpp
-+++ b/src/condor_utils/condor_config.cpp
-@@ -110,6 +110,7 @@ void check_params();
- // External variables
- extern int	ConfigLineNo;
- }  /* End extern "C" */
-+bool find_user_file(std::string &);
- 
- // Global variables
- BUCKET	*ConfigTab[TABLESIZE];
-@@ -654,6 +655,14 @@ real_config(char* host, int wantsQuiet, bool wantExtraInfo)
- 	if(dirlist) { free(dirlist); dirlist = NULL; }
- 	if(newdirlist) { free(newdirlist); newdirlist = NULL; }
- 
-+		// Now, insert overrides from the user config file
-+	std::string file_location;
-+	if (find_user_file(file_location))
-+	{
-+		process_config_source( file_location.c_str(), "user local source", host, false );
-+		local_config_sources.append(file_location.c_str());
-+	}
-+	
- 		// Now, insert any macros defined in the environment.
- 	char **my_environ = GetEnviron();
- 	for( int i = 0; my_environ[i]; i++ ) {
-@@ -996,6 +1005,38 @@ find_global()
- }
- 
- 
-+// Find user-specific location of a file
-+// Returns true if found, and puts the location in the file_location argument.
-+// If not found, returns false.  The contents of file_location are undefined.
-+bool
-+find_user_file(std::string &file_location)
-+{
-+#ifdef UNIX
-+	// $HOME/.condor/condor_config
-+	struct passwd *pw = getpwuid( geteuid() );
-+	std::stringstream ss;
-+	if ( can_switch_ids() || !pw || !pw->pw_dir ) {
-+		return false;
-+	}
-+	ss << pw->pw_dir << "/." << myDistro->Get() << "/" << myDistro->Get() << "_config";
-+	file_location = ss.str();
-+
-+	int fd;
-+	if ((fd = safe_open_wrapper_follow(file_location.c_str(), O_RDONLY)) < 0) {
-+		return false;
-+	} else {
-+		close(fd);
-+		dprintf(D_FULLDEBUG, "Reading condor configuration from '%s'\n", file_location.c_str());
-+	}
-+
-+	return true;
-+#else
-+	// To get rid of warnings...
-+	file_location = "";
-+	return false;
-+#endif
-+}
-+
- // Find location of specified file
- char*
- find_file(const char *env_name, const char *file_name)
-@@ -1052,21 +1093,15 @@ find_file(const char *env_name, const char *file_name)
- 	if (!config_source) {
- 			// List of condor_config file locations we'll try to open.
- 			// As soon as we find one, we'll stop looking.
--		const int locations_length = 4;
-+		const int locations_length = 3;
- 		MyString locations[locations_length];
--			// 1) $HOME/.condor/condor_config
--		struct passwd *pw = getpwuid( geteuid() );
--		if ( !can_switch_ids() && pw && pw->pw_dir ) {
--			formatstr( locations[0], "%s/.%s/%s", pw->pw_dir, myDistro->Get(),
--					 file_name );
--		}
- 			// 2) /etc/condor/condor_config
--		locations[1].formatstr( "/etc/%s/%s", myDistro->Get(), file_name );
-+		locations[0].formatstr( "/etc/%s/%s", myDistro->Get(), file_name );
- 			// 3) /usr/local/etc/condor_config (FreeBSD)
--		locations[2].formatstr( "/usr/local/etc/%s", file_name );
-+		locations[1].formatstr( "/usr/local/etc/%s", file_name );
- 		if (tilde) {
- 				// 4) ~condor/condor_config
--			locations[3].formatstr( "%s/%s", tilde, file_name );
-+			locations[2].formatstr( "%s/%s", tilde, file_name );
- 		}
- 
- 		int ctr;	
diff --git a/sys-cluster/htcondor/files/condor.confd b/sys-cluster/htcondor/files/condor.confd
deleted file mode 100644
index bbb955811..000000000
--- a/sys-cluster/htcondor/files/condor.confd
+++ /dev/null
@@ -1,2 +0,0 @@
-CONDOR_CENTRAL_MANAGER="$(cat /etc/condor/central_manager)"
-CONDOR_OPTS=""
diff --git a/sys-cluster/htcondor/files/condor.initd b/sys-cluster/htcondor/files/condor.initd
deleted file mode 100644
index a9904536f..000000000
--- a/sys-cluster/htcondor/files/condor.initd
+++ /dev/null
@@ -1,63 +0,0 @@
-#!/sbin/openrc-run
-# Copyright 1999-2017 Gentoo Foundation
-# Distributed under the terms of the GNU General Public License v2
-
-CONDOR_USER=condor
-
-CONDOR_CONFIG_LOCAL=$(condor_config_val LOCAL_CONFIG_FILE)
-CONDOR_MASTER=$(condor_config_val MASTER)
-CONDOR_RUN=$(condor_config_val RUN)
-CONDOR_LOCK=$(condor_config_val LOCK)
-
-depend() {
-    need net
-    use logger
-}
-
-setup_central_manager() {
-    # delete current condor host, replace it with central manager
-    sed -e '/CONDOR_HOST/d' \
-	/etc/condor/condor_config.local > ${CONDOR_CONFIG_LOCAL}
-    echo "CONDOR_HOST=${CONDOR_CENTRAL_MANAGER}" >> ${CONDOR_CONFIG_LOCAL}	
-    chown ${CONDOR_USER}:${CONDOR_USER} ${CONDOR_CONFIG_LOCAL}
-}
-
-# set up condor ccb if only private networking is available (assumes ifconfig)
-setup_ccb() {
-    /sbin/ifconfig | grep "inet addr" | egrep -v "addr:127.|addr:192.|addr:172.|addr:10." > /dev/null
-    retval=$?
-    if [ ${retval} -ne 0 ]; then # all addresses are local
-	echo \
-	    "$(/sbin/ifconfig | grep "inet addr" | grep -v 127. | awk '{print $2}' | sed s/addr://)" \
-	    "$(hostname)" \
-	    "# Added for Condor CCB" \
-	    >> /etc/hosts
-    fi
-}
-
-cleanup_ccb() {
-    sed -i '/# Added for Condor CCB/d' /etc/hosts
-}
-
-start() {
-    ebegin "Starting condor"
-    setup_central_manager
-    setup_ccb
-    start-stop-daemon --start --quiet --user ${CONDOR_USER} \
-	--pidfile ${CONDOR_RUN}/condor.pid \
-	--exec ${CONDOR_MASTER} -- ${CONDOR_OPTS}
-    retval=$?
-    [ $retval -eq 0 ] && touch /var/lock/subsys/condor
-    eend ${retval}
-}
-
-stop() {
-    ebegin "Stopping condor"
-    cleanup_ccb
-    start-stop-daemon --stop --quiet \
-	--pidfile ${CONDOR_RUN}/condor.pid \
-	--exec ${CONDOR_MASTER}
-    retval=$?
-    [ ${retval} -eq 0 ] && rm -f /var/lock/subsys/condor
-    eend ${retval}
-}
diff --git a/sys-cluster/htcondor/files/condor_config.generic.patch b/sys-cluster/htcondor/files/condor_config.generic.patch
deleted file mode 100644
index 5a986227c..000000000
--- a/sys-cluster/htcondor/files/condor_config.generic.patch
+++ /dev/null
@@ -1,257 +0,0 @@
---- a/src/condor_examples/condor_config.generic
-+++ b/src/condor_examples/condor_config.generic
-@@ -1,12 +1,31 @@
- ######################################################################
-+######################################################################
-+###                                                                ###
-+###  N O T I C E:   D O   N O T   E D I T   T H I S   F I L E      ###
-+###                                                                ###
-+###      Customization should be done via the LOCAL_CONFIG_DIR.    ###
-+###                                                                ###
-+######################################################################
-+######################################################################
-+
-+
-+######################################################################
- ##
- ##  condor_config
- ##
- ##  This is the global configuration file for condor.  Any settings
--##  made here may potentially be overridden in the local configuration
--##  file.  KEEP THAT IN MIND!  To double-check that a variable is
--##  getting set from the configuration file that you expect, use
--##  condor_config_val -v <variable name>
-+##  found here * * s h o u l d   b e   c u s t o m i z e d   i n
-+##  a   l o c a l   c o n f i g u r a t i o n   f i l e. * *
-+##
-+##  The local configuration files are located in LOCAL_CONFIG_DIR, set
-+##  below.
-+##
-+##  For a basic configuration, you may only want to start by
-+##  customizing CONDOR_HOST and DAEMON_LIST.
-+##
-+##  Note: To double-check where a configuration variable is set from
-+##  you can use condor_config_val -v -config <variable name>,
-+##  e.g. condor_config_val -v -config CONDOR_HOST.
- ##
- ##  The file is divided into four main parts:
- ##  Part 1:  Settings you likely want to customize 
-@@ -53,7 +72,7 @@
- ##  Pathnames:
- ##--------------------------------------------------------------------
- ##  Where have you installed the bin, sbin and lib condor directories?   
--RELEASE_DIR		= /usr/local/condor
-+RELEASE_DIR		= /usr
- 
- ##  Where is the local condor directory for each host?  
- ##  This is where the local config file(s), logs and
-@@ -61,17 +80,20 @@
- LOCAL_DIR		= $(TILDE)
- #LOCAL_DIR		= $(RELEASE_DIR)/hosts/$(HOSTNAME)
- 
--##  Where is the machine-specific local config file for each host?
--LOCAL_CONFIG_FILE	= $(LOCAL_DIR)/condor_config.local
--#LOCAL_CONFIG_FILE	= $(RELEASE_DIR)/etc/$(HOSTNAME).local
-+## Looking for LOCAL_CONFIG_FILE? You will not find it here. Instead
-+## put a file in the LOCAL_CONFIG_DIR below. It is a more extensible
-+## means to manage configuration. The order in which configuration
-+## files are read from the LOCAL_CONFIG_DIR is lexicographic. For
-+## instance, config in 00MyConfig will be overridden by config in
-+## 97MyConfig.
- 
- ##  Where are optional machine-specific local config files located?
- ##  Config files are included in lexicographic order.
--LOCAL_CONFIG_DIR	= $(LOCAL_DIR)/config
--#LOCAL_CONFIG_DIR	= $(LOCAL_DIR)/config
-+##  No default.
-+LOCAL_CONFIG_DIR        = $(ETC)/config.d
- 
- ## Blacklist for file processing in the LOCAL_CONFIG_DIR
--## LOCAL_CONFIG_DIR_EXCLUDE_REGEXP = ^((\..*)|(.*~)|(#.*)|(.*\.rpmsave)|(.*\.rpmnew))$
-+LOCAL_CONFIG_DIR_EXCLUDE_REGEXP = ^((\..*)|(.*~)|(#.*)|(.*\.rpmsave)|(.*\.rpmnew))$
- 
- ## If the local config file is not present, is it an error?
- ## WARNING: This is a potential security issue. 
-@@ -409,7 +431,22 @@
- ##  condor account, it's probably condor.  Otherwise, it's whatever
- ##  you've set in the CONDOR_IDS environment variable.  See the Admin
- ##  manual for details on this.
--LOCK		= $(LOG)
-+LOCK = /var/lock/condor
-+
-+# Condor allows for creating surrogate lock files that always live on
-+# local disk. This is useful for the times when Condor would otherwise
-+# lock a file on a network filesystem, such as a UserLog.
-+# CREATE_LOCKS_ON_LOCAL_DISK controls this feature, and
-+# LOCAL_DISK_LOCK_DIR controls where the lock files are created. The
-+# local dir must have tmp-like permissions (1777), because multiple
-+# users, e.g. via condor_submit or condor_dagman, will need to
-+# add/remove lock files.
-+# NOTE: This will not provide proper locking if a shared file is
-+# simultaneously accessed from multiple machines. However, that is not
-+# a common event. One example where it is possible is remote
-+# submission with condor_submit -remote.
-+#CREATE_LOCKS_ON_LOCAL_DISK = TRUE
-+LOCAL_DISK_LOCK_DIR = $(LOCK)/local
- 
- ##  If you don't use a fully qualified name in your /etc/hosts file
- ##  (or NIS, etc.) for either your official hostname or as an alias,
-@@ -475,7 +512,8 @@
- ##  the execute machine and just make sure the two strings match.  The
- ##  default for this setting is False, since it is more secure this
- ##  way.
--#TRUST_UID_DOMAIN = False
-+##   Default is False
-+TRUST_UID_DOMAIN = True
- 
- ## If you would like to be informed in near real-time via condor_q when
- ## a vanilla/standard/java job is in a suspension state, set this attribute to
-@@ -514,8 +552,9 @@
- ## just disable it).
- #NEGOTIATOR_IGNORE_USER_PRIORITIES = False
- 
--## This is a list of libraries containing ClassAd plug-in functions.
--#CLASSAD_USER_LIBS =
-+## These are the directories used to locate classad plug-in functions
-+#CLASSAD_SCRIPT_DIRECTORY =
-+#CLASSAD_LIB_PATH =
- 
- ## This setting tells Condor whether to delegate or copy GSI X509
- ## credentials when sending them over the wire between daemons.
-@@ -605,6 +644,9 @@
- MAX_HDFS_LOG            = 1000000
- HDFS_DEBUG              =
- 
-+MAX_TRIGGERD_LOG	= 1000000
-+TRIGGERD_DEBUG        	=
-+
- # High Availability Logs
- MAX_HAD_LOG		= 1000000
- HAD_DEBUG		=
-@@ -932,14 +974,18 @@ TESTINGMODE_CLAIM_WORKLIFE = 1200
- ######################################################################
- 
- ##  Pathnames
--LOG		= $(LOCAL_DIR)/log
-+LOG         = /var/log/condor
- SPOOL		= $(LOCAL_DIR)/spool
- EXECUTE		= $(LOCAL_DIR)/execute
- BIN		= $(RELEASE_DIR)/bin
- LIB		= $(RELEASE_DIR)/lib
--INCLUDE		= $(RELEASE_DIR)/include
-+INCLUDE     = $(RELEASE_DIR)/include/condor
- SBIN		= $(RELEASE_DIR)/sbin
--LIBEXEC		= $(RELEASE_DIR)/libexec
-+SHARE   = $(RELEASE_DIR)/share/condor
-+RUN     = /var/run/condor
-+DATA		= $(SPOOL)
-+ETC     = /etc/condor
-+LIBEXEC		= $(RELEASE_DIR)/libexec/condor
- 
- ## If you leave HISTORY undefined (comment it out), no history file
- ## will be created. 
-@@ -963,6 +1009,7 @@ HAD_LOG		= $(LOG)/HADLog
- REPLICATION_LOG	= $(LOG)/ReplicationLog
- TRANSFERER_LOG	= $(LOG)/TransfererLog
- HDFS_LOG	= $(LOG)/HDFSLog
-+TRIGGERD_LOG	= $(LOG)/TriggerLog
- 
- ##  Lock files
- SHADOW_LOCK	= $(LOCK)/ShadowLock
-@@ -1084,7 +1131,7 @@ DAEMON_LIST			= MASTER, STARTD, SCHEDD
- #MASTER, STARTD, SCHEDD, KBDD, COLLECTOR, NEGOTIATOR, EVENTD, \
- #VIEW_SERVER, CONDOR_VIEW, VIEW_COLLECTOR, HAWKEYE, CREDD, HAD, \
- #DBMSD, QUILL, JOB_ROUTER, ROOSTER, LEASEMANAGER, HDFS, SHARED_PORT, \
--#DEFRAG
-+#DEFRAG TRIGGERD
- 
- 
- ##  Where are the binaries for these daemons?
-@@ -1094,7 +1141,6 @@ SCHEDD				= $(SBIN)/condor_schedd
- KBDD				= $(SBIN)/condor_kbdd
- NEGOTIATOR			= $(SBIN)/condor_negotiator
- COLLECTOR			= $(SBIN)/condor_collector
--CKPT_SERVER			= $(SBIN)/condor_ckpt_server
- STARTER_LOCAL			= $(SBIN)/condor_starter
- JOB_ROUTER                      = $(LIBEXEC)/condor_job_router
- ROOSTER                         = $(LIBEXEC)/condor_rooster
-@@ -1102,6 +1148,7 @@ HDFS				= $(SBIN)/condor_hdfs
- SHARED_PORT			= $(LIBEXEC)/condor_shared_port
- TRANSFERER			= $(LIBEXEC)/condor_transferer
- DEFRAG                          = $(LIBEXEC)/condor_defrag
-+TRIGGERD			= $(sbin)/condor_triggerd
- 
- ##  When the master starts up, it can place it's address (IP and port)
- ##  into a file.  This way, tools running on the local machine don't
-@@ -1178,11 +1225,13 @@ PREEN_ARGS			= -m -r
- ##--------------------------------------------------------------------
- ## Address to which Condor will send a weekly e-mail with output of
- ## condor_status.
--#CONDOR_DEVELOPERS = condor-admin@cs.wisc.edu
-+##  Default is condor-admin@cs.wisc.edu
-+CONDOR_DEVELOPERS = NONE
- 
- ## Global Collector to periodically advertise basic information about
- ## your pool.
--#CONDOR_DEVELOPERS_COLLECTOR = condor.cs.wisc.edu
-+##  Default is condor.cs.wisc.edu
-+CONDOR_DEVELOPERS_COLLECTOR = NONE
- 
- ##  When the collector starts up, it can place it's address (IP and port)
- ##  into a file.  This way, tools running on the local machine don't
-@@ -1199,6 +1248,7 @@ COLLECTOR_ADDRESS_FILE = $(LOG)/.collector_address
- ## Determine if the Negotiator will honor SlotWeight attributes, which
- ## may be used to give a slot greater weight when calculating usage.
- #NEGOTIATOR_USE_SLOT_WEIGHTS = True
-+NEGOTIATOR_USE_SLOT_WEIGHTS = True
- 
- 
- ## How often the Negotaitor starts a negotiation cycle, defined in
-@@ -1668,7 +1718,7 @@ QUEUE_SUPER_USERS	= root, condor
- ##  Such as when when Condor is running as a service.
- ##   /s is delete subdirectories
- ##   /c is continue on error
--WINDOWS_RMDIR = $(SBIN)\condor_rmdir.exe
-+#WINDOWS_RMDIR = $(SBIN)\condor_rmdir.exe
- #WINDOWS_RMDIR_OPTIONS = /s /c
- 
- ##--------------------------------------------------------------------
-@@ -1689,13 +1739,15 @@ PROCD = $(SBIN)/condor_procd
- #     UNIX); the name will be something like:
- #         \\.\pipe\condor_procd
- #
--PROCD_ADDRESS = $(LOCK)/procd_pipe
-+PROCD_ADDRESS = $(RUN)/procd_pipe
- 
--# Note that in other Condor daemons, turning on D_PROCFAMILY will
--# result in that daemon logging all of its interactions with the
--# ProcD.
-+# The procd currently uses a very simplistic logging system. Since this
-+# log will not be rotated like other Condor logs, it is only recommended
-+# to set PROCD_LOG when attempting to debug a problem. In other Condor
-+# daemons, turning on D_PROCFAMILY will result in that daemon logging
-+# all of its interactions with the ProcD.
- #
--PROCD_LOG = $(LOG)/ProcLog
-+#PROCD_LOG = $(LOG)/ProcLog
- 
- # This is the maximum period that the procd will use for taking
- # snapshots (the actual period may be lower if a condor daemon registers
-@@ -1788,7 +1840,7 @@ JAVA = /usr/bin/java
- ## them here.  However, do not remove the existing entries, as Condor
- ## needs them.
- 
--JAVA_CLASSPATH_DEFAULT = $(LIB) $(LIB)/scimark2lib.jar .
-+JAVA_CLASSPATH_DEFAULT = $(SHARE) $(SHARE)/scimark2lib.jar .
- 
- ##  JAVA_CLASSPATH_ARGUMENT describes the command-line parameter
- ##  used to introduce a new classpath:
-@@ -2458,7 +2510,7 @@ KBDD_ADDRESS_FILE = $(LOG)/.kbdd_address
- #SSH_TO_JOB_SSHD_ARGS = "-i -e -f %f"
- 
- # sshd configuration template used by condor_ssh_to_job_sshd_setup.
--#SSH_TO_JOB_SSHD_CONFIG_TEMPLATE = $(LIB)/condor_ssh_to_job_sshd_config_template
-+SSH_TO_JOB_SSHD_CONFIG_TEMPLATE = $(ETC)/condor_ssh_to_job_sshd_config_template
- 
- # Path to ssh-keygen
- #SSH_TO_JOB_SSH_KEYGEN = /usr/bin/ssh-keygen
diff --git a/sys-cluster/htcondor/files/condor_config.local b/sys-cluster/htcondor/files/condor_config.local
deleted file mode 100644
index cada046bd..000000000
--- a/sys-cluster/htcondor/files/condor_config.local
+++ /dev/null
@@ -1,11 +0,0 @@
-CONDOR_DEVELOPERS = NONE
-CONDOR_HOST = $(FULL_HOSTNAME)
-COLLECTOR_NAME = Personal Condor
-START = TRUE
-SUSPEND = FALSE
-CONTINUE =  TRUE
-PREEMPT = FALSE
-KILL = FALSE
-DAEMON_LIST = COLLECTOR, MASTER, NEGOTIATOR, SCHEDD, STARTD
-NEGOTIATOR_INTERVAL = 20
-TRUST_UID_DOMAIN = TRUE
diff --git a/sys-cluster/htcondor/files/condor_shadow_dlopen-8.0.0.patch b/sys-cluster/htcondor/files/condor_shadow_dlopen-8.0.0.patch
deleted file mode 100644
index 50a4556da..000000000
--- a/sys-cluster/htcondor/files/condor_shadow_dlopen-8.0.0.patch
+++ /dev/null
@@ -1,11 +0,0 @@
---- build/cmake/CondorConfigure.cmake.orig      2013-06-17 19:49:16.067968000 +0100
-+++ build/cmake/CondorConfigure.cmake   2013-06-17 19:51:27.105306000 +0100
-@@ -704,7 +704,7 @@
- set (CONDOR_TOOL_LIBS "condor_utils;${CLASSADS_FOUND};${VOMS_FOUND};${GLOBUS_FOUND};${EXPAT_FOUND};${PCRE_FOUND};${COREDUMPER_FOUND}")
- set (CONDOR_SCRIPT_PERMS OWNER_READ OWNER_WRITE OWNER_EXECUTE GROUP_READ GROUP_EXECUTE WORLD_READ WORLD_EXECUTE)
- if (LINUX OR DARWIN)
--  set (CONDOR_LIBS_FOR_SHADOW "condor_utils_s;classads;${VOMS_FOUND};${GLOBUS_FOUND};${EXPAT_FOUND};${PCRE_FOUND};${OPENSSL_FOUND};${KRB5_FOUND};${POSTGRESQL_FOUND};${COREDUMPER_FOUND};${IOKIT_FOUND};${COREFOUNDATION_FOUND}")
-+  set (CONDOR_LIBS_FOR_SHADOW "condor_utils_s;classads;${VOMS_FOUND};${GLOBUS_FOUND};${EXPAT_FOUND};${PCRE_FOUND};${OPENSSL_FOUND};${KRB5_FOUND};${POSTGRESQL_FOUND};${COREDUMPER_FOUND};${IOKIT_FOUND};${COREFOUNDATION_FOUND};dl")
-   if (DARWIN)
-     set (CONDOR_LIBS_FOR_SHADOW "${CONDOR_LIBS_FOR_SHADOW};resolv" )
-   endif (DARWIN)
\ No newline at end of file
diff --git a/sys-cluster/htcondor/files/fix_sandbox_violations-8.0.0.patch b/sys-cluster/htcondor/files/fix_sandbox_violations-8.0.0.patch
deleted file mode 100644
index cb4629993..000000000
--- a/sys-cluster/htcondor/files/fix_sandbox_violations-8.0.0.patch
+++ /dev/null
@@ -1,31 +0,0 @@
---- src/condor_scripts/CMakeLists.txt.orig	2013-06-17 23:02:02.815939000 +0100
-+++ src/condor_scripts/CMakeLists.txt	2013-06-17 23:02:34.476727000 +0100
-@@ -27,9 +27,6 @@
-         install ( FILES condor_configure DESTINATION ${C_SBIN} PERMISSIONS ${CONDOR_SCRIPT_PERMS} )
-         install ( FILES condor_configure DESTINATION ${C_SBIN} RENAME condor_install PERMISSIONS ${CONDOR_SCRIPT_PERMS} )
-         install ( FILES condor_configure DESTINATION ${C_SBIN} RENAME bosco_install PERMISSIONS ${CONDOR_SCRIPT_PERMS} )
--        install ( CODE "EXECUTE_PROCESS(COMMAND ${CMAKE_COMMAND} -E create_symlink ./sbin/bosco_install \${CMAKE_INSTALL_PREFIX}/bosco_install)" )
--        install ( CODE "EXECUTE_PROCESS(COMMAND ${CMAKE_COMMAND} -E create_symlink ./sbin/condor_install \${CMAKE_INSTALL_PREFIX}/condor_install)" )
--        install ( CODE "EXECUTE_PROCESS(COMMAND ${CMAKE_COMMAND} -E create_symlink ./sbin/condor_configure \${CMAKE_INSTALL_PREFIX}/condor_configure)" )
-     endif(WANT_FULL_DEPLOYMENT)
- 
- 	install ( FILES condor_ssh sshd.sh DESTINATION ${C_LIBEXEC} PERMISSIONS ${CONDOR_SCRIPT_PERMS} )
---- src/condor_tools/CMakeLists.txt.orig	2013-06-17 22:50:20.459572000 +0100
-+++ src/condor_tools/CMakeLists.txt	2013-06-17 22:52:59.841733000 +0100
-@@ -102,13 +102,13 @@
- if ( LINUX AND NOT CONDOR_PACKAGE_BUILD )
- 	set( SRC_DIR ${CMAKE_SOURCE_DIR} )
- 	set( BIN_DIR ${CMAKE_BINARY_DIR} )
--	install( CODE "execute_process(COMMAND mkdir -p ${CMAKE_INSTALL_PREFIX}/lib/condor)" )
-+	install( CODE "execute_process(COMMAND mkdir -p \$ENV{DESTDIR}\${CMAKE_INSTALL_PREFIX}/lib/condor)" )
- 	install( CODE "execute_process(COMMAND ${SRC_DIR}/src/condor_scripts/print-libs ${BIN_DIR}/src/condor_tools/condor_version ${SRC_DIR}/src/condor_scripts/syslib-patterns
--		 COMMAND xargs -isrc cp src ${CMAKE_INSTALL_PREFIX}/lib/condor
-+		 COMMAND xargs -isrc cp src \$ENV{DESTDIR}\${CMAKE_INSTALL_PREFIX}/lib/condor
- 		 )" )
- 	# This is required for opensuse, where the system's libssl and
- 	# libcrypto files don't have owner write permission.
--	install( CODE "execute_process(COMMAND chmod -R u+w ${CMAKE_INSTALL_PREFIX}/lib/condor/)" )
-+	install( CODE "execute_process(COMMAND chmod -R u+w \$ENV{DESTDIR}\${CMAKE_INSTALL_PREFIX}/lib/condor/)" )
- endif()
- 
- ############################################################
diff --git a/sys-cluster/htcondor/files/htcondor-8.3.2-Apply-the-users-condor_config-last-rather-than-first.patch b/sys-cluster/htcondor/files/htcondor-8.3.2-Apply-the-users-condor_config-last-rather-than-first.patch
deleted file mode 100644
index f906ec89e..000000000
--- a/sys-cluster/htcondor/files/htcondor-8.3.2-Apply-the-users-condor_config-last-rather-than-first.patch
+++ /dev/null
@@ -1,29 +0,0 @@
-Apply the users condor_config last, rather than first.
-Ported patch from htcondor-8.0.0 to 8.3.2
-
-Patch by Marius Brehler.
---- src/condor_utils/condor_config.cpp
-+++ src/condor_utils/condor_config.cpp
-@@ -1454,18 +1454,14 @@ find_file(const char *env_name, const ch
- 	if (!config_source) {
- 			// List of condor_config file locations we'll try to open.
- 			// As soon as we find one, we'll stop looking.
--		const int locations_length = 4;
-+		const int locations_length = 3;
- 		MyString locations[locations_length];
--			// 1) $HOME/.condor/condor_config
--		// $HOME/.condor/condor_config was added for BOSCO and never used, We are removing it in 8.3.1, but may put it back if users complain.
--		//find_user_file(locations[0], file_name, false);
--			// 2) /etc/condor/condor_config
--		locations[1].formatstr( "/etc/%s/%s", myDistro->Get(), file_name );
-+		locations[0].formatstr( "/etc/%s/%s", myDistro->Get(), file_name );
- 			// 3) /usr/local/etc/condor_config (FreeBSD)
--		locations[2].formatstr( "/usr/local/etc/%s", file_name );
-+		locations[1].formatstr( "/usr/local/etc/%s", file_name );
- 		if (tilde) {
- 				// 4) ~condor/condor_config
--			locations[3].formatstr( "%s/%s", tilde, file_name );
-+			locations[2].formatstr( "%s/%s", tilde, file_name );
- 		}
- 
- 		int ctr;	
diff --git a/sys-cluster/htcondor/files/htcondor-8.3.2-condor_config.generic.patch b/sys-cluster/htcondor/files/htcondor-8.3.2-condor_config.generic.patch
deleted file mode 100644
index 7b6d337aa..000000000
--- a/sys-cluster/htcondor/files/htcondor-8.3.2-condor_config.generic.patch
+++ /dev/null
@@ -1,47 +0,0 @@
-Adjust the generic condor_config to Gentoo's needs.
-Ported patch from htcondor-8.0.0 to 8.3.2
-
-Patch by Marius Brehler.
---- b/src/condor_examples/condor_config.generic
-+++ a/src/condor_examples/condor_config.generic
-@@ -19,7 +19,7 @@
- ######################################################################
- 
- ##  Where have you installed the bin, sbin and lib condor directories?   
--RELEASE_DIR = /usr/local/condor
-+RELEASE_DIR = /usr
- 
- ##  Where is the local condor directory for each host?  This is where the local config file(s), logs and
- ##  spool/execute directories are located. this is the default for Linux and Unix systems.
-@@ -27,18 +27,22 @@ RELEASE_DIR = /usr/local/condor
- ##  this is the default on Windows sytems
- #LOCAL_DIR = $(RELEASE_DIR)
- 
--##  Where is the machine-specific local config file for each host?
--LOCAL_CONFIG_FILE = $(LOCAL_DIR)/condor_config.local
--##  If your configuration is on a shared file system, then this might be a better default
--#LOCAL_CONFIG_FILE = $(RELEASE_DIR)/etc/$(HOSTNAME).local
-+## Looking for LOCAL_CONFIG_FILE? You will not find it here. Instead
-+## put a file in the LOCAL_CONFIG_DIR below. It is a more extensible
-+## means to manage configuration. The order in which configuration
-+## files are read from the LOCAL_CONFIG_DIR is lexicographic. For
-+## instance, config in 00MyConfig will be overridden by config in
-+## 97MyConfig.
- ##  If the local config file is not present, is it an error? (WARNING: This is a potential security issue.)
--#REQUIRE_LOCAL_CONFIG_FILE = true
-+REQUIRE_LOCAL_CONFIG_FILE = false
- 
--##  The normal way to do configuration with RPMs is to read all of the
--##  files in a given directory that don't match a regex as configuration files.
-+##  Where are optional machine-specific local config files located?
- ##  Config files are read in lexicographic order.
--LOCAL_CONFIG_DIR = $(LOCAL_DIR)/config
--#LOCAL_CONFIG_DIR_EXCLUDE_REGEXP = ^((\..*)|(.*~)|(#.*)|(.*\.rpmsave)|(.*\.rpmnew))$
-+##  No default.
-+LOCAL_CONFIG_DIR        = $(ETC)/config.d
-+
-+## Blacklist for file processing in the LOCAL_CONFIG_DIR
-+LOCAL_CONFIG_DIR_EXCLUDE_REGEXP = ^((\..*)|(.*~)|(#.*)|(.*\.rpmsave)|(.*\.rpmnew))$
- 
- ##  Use a host-based security policy. By default CONDOR_HOST and the local machine will be allowed
- use SECURITY : HOST_BASED
diff --git a/sys-cluster/htcondor/files/htcondor-8.3.2-packaging_directories.patch b/sys-cluster/htcondor/files/htcondor-8.3.2-packaging_directories.patch
deleted file mode 100644
index 8acd7c7e0..000000000
--- a/sys-cluster/htcondor/files/htcondor-8.3.2-packaging_directories.patch
+++ /dev/null
@@ -1,36 +0,0 @@
-Adjust the package directories.
-Ported patch from htcondor-8.0.0 to 8.3.2
-
-Patch by Marius Brehler.
---- b/build/cmake/CondorPackageConfig.cmake
-+++ a/build/cmake/CondorPackageConfig.cmake
-@@ -406,6 +406,29 @@ elseif( ${OS_NAME} STREQUAL "LINUX" AND
- 		set(CMAKE_INSTALL_PREFIX "")
- 		set(CPACK_SET_DESTDIR "ON")
- 
-+	else()
-+
-+		#Directory overrides
-+		set( C_BIN			usr/bin )
-+		set( C_LIB			usr/lib\${LIB_SUFFIX}/condor )
-+		set( C_LIB_PUBLIC		usr/lib\${LIB_SUFFIX} )
-+		set( C_LIB32		usr/lib\${LIB_SUFFIX}/condor )
-+		set( C_SBIN			usr/sbin )
-+		set( C_INCLUDE		usr/include/condor )
-+		set( C_INCLUDE_PUBLIC		usr/include )
-+		set( C_MAN			usr/share/man )
-+		set( C_SRC			usr/src)
-+		set( C_SQL			usr/share/condor/sql)
-+		set( C_INIT			etc/init.d )
-+		set( C_ETC			etc/condor )
-+		set( C_CONFIGD		etc/condor/config.d )
-+
-+		set( C_ETC_EXAMPLES	usr/share/doc/htcondor-${VERSION}/etc/examples )
-+		set( C_SHARE_EXAMPLES usr/share/doc/htcondor-${VERSION} )
-+		set( C_DOC			usr/share/doc/htcondor-${VERSION} )
-+		set( C_LIBEXEC		usr/lib\${LIB_SUFFIX}/condor/libexec )
-+		set( C_SYSCONFIG	etc/default )
-+
- 	endif()
- 
- 	set( EXTERNALS_LIB "${C_LIB}" )
diff --git a/sys-cluster/htcondor/files/htcondor-8.3.2-shadow_dlopen.patch b/sys-cluster/htcondor/files/htcondor-8.3.2-shadow_dlopen.patch
deleted file mode 100644
index 010adbd55..000000000
--- a/sys-cluster/htcondor/files/htcondor-8.3.2-shadow_dlopen.patch
+++ /dev/null
@@ -1,14 +0,0 @@
-Ported patch from htcondor-8.0.0 to 8.3.2
-
-Patch by Marius Brehler.
--- b/build/cmake/CondorConfigure.cmake
-+++ a/build/cmake/CondorConfigure.cmake
-@@ -841,7 +841,7 @@ set (CONDOR_LIBS "condor_utils;${RT_FOUN
- set (CONDOR_TOOL_LIBS "condor_utils;${RT_FOUND};${CLASSADS_FOUND};${SECURITY_LIBS};${PCRE_FOUND};${COREDUMPER_FOUND}")
- set (CONDOR_SCRIPT_PERMS OWNER_READ OWNER_WRITE OWNER_EXECUTE GROUP_READ GROUP_EXECUTE WORLD_READ WORLD_EXECUTE)
- if (LINUX OR DARWIN)
--  set (CONDOR_LIBS_FOR_SHADOW "condor_utils_s;classads;${SECURITY_LIBS};${RT_FOUND};${PCRE_FOUND};${OPENSSL_FOUND};${KRB5_FOUND};${POSTGRESQL_FOUND};${COREDUMPER_FOUND};${IOKIT_FOUND};${COREFOUNDATION_FOUND}")
-+  set (CONDOR_LIBS_FOR_SHADOW "condor_utils_s;classads;${SECURITY_LIBS};${RT_FOUND};${PCRE_FOUND};${OPENSSL_FOUND};${KRB5_FOUND};${POSTGRESQL_FOUND};${COREDUMPER_FOUND};${IOKIT_FOUND};${COREFOUNDATION_FOUND};dl")
-   if (DARWIN)
-     set (CONDOR_LIBS_FOR_SHADOW "${CONDOR_LIBS_FOR_SHADOW};resolv" )
-   endif (DARWIN)
diff --git a/sys-cluster/htcondor/files/packaging_directories-8.0.0.patch b/sys-cluster/htcondor/files/packaging_directories-8.0.0.patch
deleted file mode 100644
index d0882644c..000000000
--- a/sys-cluster/htcondor/files/packaging_directories-8.0.0.patch
+++ /dev/null
@@ -1,32 +0,0 @@
---- build/cmake/CondorPackageConfig.cmake.orig	2013-06-29 22:54:28.964316000 +0100
-+++ build/cmake/CondorPackageConfig.cmake	2013-06-29 22:56:26.258961000 +0100
-@@ -401,6 +401,29 @@
- 		set(CMAKE_INSTALL_PREFIX "")
- 		set(CPACK_SET_DESTDIR "ON")
- 
-+	else()
-+
-+		#Directory overrides
-+		set( C_BIN			usr/bin )
-+		set( C_LIB			usr/lib\${LIB_SUFFIX}/condor )
-+		set( C_LIB_PUBLIC		usr/lib\${LIB_SUFFIX} )
-+		set( C_LIB32		usr/lib\${LIB_SUFFIX}/condor )
-+		set( C_SBIN			usr/sbin )
-+		set( C_INCLUDE		usr/include/condor )
-+		set( C_INCLUDE_PUBLIC		usr/include )
-+		set( C_MAN			usr/share/man )
-+		set( C_SRC			usr/src)
-+		set( C_SQL			usr/share/condor/sql)
-+		set( C_INIT			etc/init.d )
-+		set( C_ETC			etc/condor )
-+		set( C_CONFIGD		etc/condor/config.d )
-+
-+		set( C_ETC_EXAMPLES	usr/share/doc/htcondor-${VERSION}/etc/examples )
-+		set( C_SHARE_EXAMPLES usr/share/doc/htcondor-${VERSION} )
-+		set( C_DOC			usr/share/doc/htcondor-${VERSION} )
-+		set( C_LIBEXEC		usr/lib\${LIB_SUFFIX}/condor/libexec )
-+		set( C_SYSCONFIG	etc/default )
-+
- 	endif()
- 
- 	set( EXTERNALS_LIB "${C_LIB}" )
diff --git a/sys-cluster/htcondor/htcondor-8.0.0.ebuild b/sys-cluster/htcondor/htcondor-8.0.0.ebuild
deleted file mode 100644
index 5e25f0325..000000000
--- a/sys-cluster/htcondor/htcondor-8.0.0.ebuild
+++ /dev/null
@@ -1,113 +0,0 @@
-# Copyright 1999-2017 Gentoo Foundation
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=5
-
-CMAKE_MIN_VERSION=2.8
-
-PYTHON_COMPAT=( python2_7 )
-
-inherit cmake-utils python-single-r1 user
-
-DESCRIPTION="Workload management system for compute-intensive jobs"
-HOMEPAGE="http://www.cs.wisc.edu/htcondor/"
-SRC_URI="condor_src-${PV}-all-all.tar.gz"
-
-LICENSE="Apache-2.0"
-SLOT="0"
-KEYWORDS="~amd64 ~x86"
-IUSE="boinc cgroup contrib curl doc kerberos libvirt minimal postgres python soap ssl test X xml"
-
-REQUIRED_USE="python? ( ${PYTHON_REQUIRED_USE} )"
-
-CDEPEND="
-	sys-libs/zlib
-	>=dev-libs/libpcre-7.6
-	>=dev-libs/boost-1.49.0[${PYTHON_USEDEP}]
-	net-nds/openldap
-	boinc? ( sci-misc/boinc )
-	cgroup? ( >=dev-libs/libcgroup-0.37 )
-	curl? ( >=net-misc/curl-7.19.7[ssl?] )
-	libvirt? ( >=app-emulation/libvirt-0.6.2 )
-	kerberos? ( virtual/krb5 )
-	X? ( x11-libs/libX11 )
-	postgres? ( >=dev-db/postgresql-8.2.4:= )
-	python? ( ${PYTHON_DEPS} )
-	soap? ( >=net-libs/gsoap-2.7.11[ssl?] )
-	ssl? ( >=dev-libs/openssl-0.9.8i:0 )
-	xml? ( >=dev-libs/libxml2-2.7.3 )"
-
-DEPEND="${CDEPEND}
-	test? ( dev-util/valgrind )"
-
-RDEPEND="${CDEPEND}
-	mail-client/mailx"
-
-RESTRICT=fetch
-
-S="${WORKDIR}/condor-${PV}"
-PATCHES=(
-	"${FILESDIR}"/condor_shadow_dlopen-${PV}.patch
-	"${FILESDIR}"/condor_config.generic.patch
-	"${FILESDIR}"/0001-Apply-the-user-s-condor_config-last-rather-than-firs.patch
-	"${FILESDIR}"/packaging_directories-${PV}.patch
-	"${FILESDIR}"/fix_sandbox_violations-${PV}.patch
-)
-
-pkg_setup() {
-	enewgroup condor
-	enewuser condor -1 "${ROOT}"bin/bash "${ROOT}var/lib/condor" condor
-}
-
-src_configure() {
-	# All the hard coded -DWITH_X=OFF flags are for packages that aren't in portage
-	# I also haven't included support for HAVE_VMWARE because I don't know what it requires
-	local mycmakeargs="
-		-DCONDOR_PACKAGE_BUILD=ON
-		-DCMAKE_INSTALL_PREFIX=/
-		-DWITH_BLAHP=OFF
-		-DWITH_CAMPUSFACTORY=OFF
-		-DWITH_CLUSTER_RA=OFF
-		-DWITH_COREDUMPER=OFF
-		-DWITH_CREAM=OFF
-		-DWITH_GLOBUS=OFF
-		-DWITH_LIBDELTACLOUD=OFF
-		-DWITH_BLAHP=OFF
-		-DWITH_QPID=OFF
-		-DWITH_UNICOREGAHP=OFF
-		-DWITH_VOMS=OFF
-		-DWITH_WSO2=OFF
-		-DWITH_MANAGEMENT=OFF
-		$(cmake-utils_use_has boinc BACKFILL)
-		$(cmake-utils_use_has boinc)
-		$(cmake-utils_use_with cgroup LIBCGROUP)
-		$(cmake-utils_use_want contrib)
-		$(cmake-utils_use_with curl)
-		$(cmake-utils_use_want doc MAN_PAGES)
-		$(cmake-utils_use_with libvirt)
-		$(cmake-utils_use_has X KBDD)
-		$(cmake-utils_use_with kerberos KRB5)
-		$(cmake-utils_use_with postgres POSTGRESQL)
-		$(cmake-utils_use_with python PYTHON_BINDINGS)
-		$(cmake-utils_use minimal CLIPPED)
-		$(cmake-utils_use_with soap AVIARY)
-		$(cmake-utils_use_with soap GSOAP)
-		$(cmake-utils_use_with ssl OPENSSL)
-		$(cmake-utils_use_build test TESTING)
-		$(cmake-utils_use_with xml LIBXML2)"
-	cmake-utils_src_configure
-}
-
-src_install() {
-	cmake-utils_src_install
-
-	dodir /var/lib/condor
-	dodir /var/log/condor
-	dodir /var/run/condor
-	dodir /var/lock/condor
-
-	fperms 750 /var/lib/condor /var/log/condor
-	fperms 755 /var/run/condor
-	fperms 0775 /var/lock/condor
-	fowners condor:condor /var/lib/condor /var/log/condor /var/run/condor
-}
diff --git a/sys-cluster/htcondor/htcondor-8.3.2.ebuild b/sys-cluster/htcondor/htcondor-8.3.2.ebuild
deleted file mode 100644
index c4464b88f..000000000
--- a/sys-cluster/htcondor/htcondor-8.3.2.ebuild
+++ /dev/null
@@ -1,110 +0,0 @@
-# Copyright 1999-2017 Gentoo Foundation
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=5
-
-CMAKE_MIN_VERSION=2.8
-
-PYTHON_COMPAT=( python2_7 )
-
-inherit cmake-utils python-single-r1 user vcs-snapshot
-
-DESCRIPTION="Workload management system for compute-intensive jobs"
-HOMEPAGE="http://htcondorproject.org/"
-SRC_URI="https://github.com/${PN}/${PN}/archive/V${PV//./_}.tar.gz -> ${P}.tar.gz"
-
-LICENSE="Apache-2.0"
-SLOT="0"
-#KEYWORDS="~amd64 ~x86"
-IUSE="boinc cgroup contrib curl dmtcp doc kerberos libvirt minimal postgres python soap ssl test X xml"
-
-REQUIRED_USE="python? ( ${PYTHON_REQUIRED_USE} )"
-
-CDEPEND="sys-libs/zlib
-	>=dev-libs/libpcre-7.6
-	>=dev-libs/boost-1.49.0[${PYTHON_USEDEP}]
-	net-nds/openldap
-	boinc? ( sci-misc/boinc )
-	cgroup? ( >=dev-libs/libcgroup-0.37 )
-	curl? ( >=net-misc/curl-7.19.7[ssl?] )
-	dmtcp? ( sys-apps/dmtcp )
-	libvirt? ( >=app-emulation/libvirt-0.6.2 )
-	kerberos? ( virtual/krb5 )
-	X? ( x11-libs/libX11 )
-	postgres? ( >=dev-db/postgresql-8.2.4:= )
-	python? ( ${PYTHON_DEPS} )
-	soap? ( >=net-libs/gsoap-2.7.11[ssl?] )
-	ssl? ( >=dev-libs/openssl-0.9.8i:0 )
-	xml? ( >=dev-libs/libxml2-2.7.3 )"
-
-DEPEND="${CDEPEND}
-	test? ( dev-util/valgrind )"
-
-RDEPEND="${CDEPEND}
-	virtual/mailx"
-
-PATCHES=(
-	"${FILESDIR}"/${P}-shadow_dlopen.patch
-	"${FILESDIR}"/${P}-condor_config.generic.patch
-	"${FILESDIR}"/${P}-Apply-the-users-condor_config-last-rather-than-first.patch
-	"${FILESDIR}"/${P}-packaging_directories.patch
-	"${FILESDIR}"/fix_sandbox_violations-8.0.0.patch
-)
-
-pkg_setup() {
-	enewgroup condor
-	enewuser condor -1 "${ROOT}"bin/bash "${ROOT}var/lib/condor" condor
-}
-
-src_configure() {
-	# All the hard coded -DWITH_X=OFF flags are for packages that aren't in portage
-	# I also haven't included support for HAVE_VMWARE because I don't know what it requires
-	local mycmakeargs="
-		-DCONDOR_PACKAGE_BUILD=ON
-		-DCMAKE_INSTALL_PREFIX=/
-		-DWITH_BLAHP=OFF
-		-DWITH_CAMPUSFACTORY=OFF
-		-DWITH_CLUSTER_RA=OFF
-		-DWITH_COREDUMPER=OFF
-		-DWITH_CREAM=OFF
-		-DWITH_GLOBUS=OFF
-		-DWITH_LIBDELTACLOUD=OFF
-		-DWITH_BLAHP=OFF
-		-DWITH_QPID=OFF
-		-DWITH_UNICOREGAHP=OFF
-		-DWITH_VOMS=OFF
-		-DWITH_WSO2=OFF
-		-DWITH_MANAGEMENT=OFF
-		$(cmake-utils_use_has boinc BACKFILL)
-		$(cmake-utils_use_has boinc)
-		$(cmake-utils_use_with cgroup LIBCGROUP)
-		$(cmake-utils_use_want contrib)
-		$(cmake-utils_use_with curl)
-		$(cmake-utils_use_want doc MAN_PAGES)
-		$(cmake-utils_use_with libvirt)
-		$(cmake-utils_use_has X KBDD)
-		$(cmake-utils_use_with kerberos KRB5)
-		$(cmake-utils_use_with postgres POSTGRESQL)
-		$(cmake-utils_use_with python PYTHON_BINDINGS)
-		$(cmake-utils_use minimal CLIPPED)
-		$(cmake-utils_use_with soap AVIARY)
-		$(cmake-utils_use_with soap GSOAP)
-		$(cmake-utils_use_with ssl OPENSSL)
-		$(cmake-utils_use_build test TESTING)
-		$(cmake-utils_use_with xml LIBXML2)"
-	cmake-utils_src_configure
-}
-
-src_install() {
-	cmake-utils_src_install
-
-	dodir /var/lib/condor
-	dodir /var/log/condor
-	dodir /var/run/condor
-	dodir /var/lock/condor
-
-	fperms 750 /var/lib/condor /var/log/condor
-	fperms 755 /var/run/condor
-	fperms 0775 /var/lock/condor
-	fowners condor:condor /var/lib/condor /var/log/condor /var/run/condor
-}
diff --git a/sys-cluster/htcondor/metadata.xml b/sys-cluster/htcondor/metadata.xml
deleted file mode 100644
index 3846c294e..000000000
--- a/sys-cluster/htcondor/metadata.xml
+++ /dev/null
@@ -1,34 +0,0 @@
-<?xml version="1.0" encoding="UTF-8"?>
-<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
-<pkgmetadata>
-	<maintainer type="person">
-		<email>cjk34@cam.ac.uk</email>
-	</maintainer>
-	<maintainer type="project">
-		<email>cluster@gentoo.org</email>
-		<name>Gentoo Cluster Project</name>
-	</maintainer>
-	<longdescription lang="en">
-HTCondor is a open-source, specialized workload management system for
-compute-intensive jobs. Like other full-featured batch systems, HTCondor
-provides a job queueing mechanism, scheduling policy, priority scheme,
-resource monitoring, and resource management. Users submit their serial
-or parallel jobs to HTCondor, HTCondor places them into a queue, chooses
-when and where to run the jobs based upon a policy, carefully monitors
-their progress, and ultimately informs the user upon completion. HTCondor
-also contains mechanisms to submit jobs to grid-sites and supports many
-different grid toolkits.
-</longdescription>
-	<use>
-		<flag name="boinc">Enable backfill with BOINC jobs when the cluster is not being used</flag>
-		<flag name="cgroup">Use <pkg>dev-libs/libcgroup</pkg> for kernel control groups</flag>
-		<flag name="contrib">Build contrib modules</flag>
-		<flag name="dmtcp">Use <pkg>sys-apps/dmtcp</pkg> for checkpointing</flag>
-		<flag name="libvirt">Use <pkg>app-emulation/libvirt</pkg> for virtualisation</flag>
-		<flag name="minimal">Don't support standard universe jobs</flag>
-		<flag name="X">Enable the HTCondor Keyboard Daemon to monitor logged in X users for activity</flag>
-	</use>
-	<upstream>
-		<remote-id type="github">htcondor/htcondor</remote-id>
-	</upstream>
-</pkgmetadata>
diff --git a/sys-cluster/lustre/Manifest b/sys-cluster/lustre/Manifest
deleted file mode 100644
index a2b8f9bf1..000000000
--- a/sys-cluster/lustre/Manifest
+++ /dev/null
@@ -1 +0,0 @@
-DIST lustre-2.10.1.tar.gz 15281445 BLAKE2B 53961a97c435d3eb03dae1fd0a8e080659d2997222ec847c612f9aff27d0e0c0a2ab07255dd958f61737480c18bd08db0965e072501b4ffa331367b984ab71a9 SHA512 a76bf9f489dc4aedce6716e26421c85a99628153c7644fa537a91cc6db8e1a8540d444acac6b2da4a77da52b0962e146c10427347a5f3916a4338de19e11b1a7
diff --git a/sys-cluster/lustre/files/lnet.initd b/sys-cluster/lustre/files/lnet.initd
deleted file mode 100644
index 227780c52..000000000
--- a/sys-cluster/lustre/files/lnet.initd
+++ /dev/null
@@ -1,45 +0,0 @@
-#!/sbin/openrc-run
-# Copyright 1999-2017 Gentoo Foundation
-# Distributed under the terms of the GNU General Public License v2
-
-description="Loads lnet module and configures network."
-
-depend() {
-        need net
-        after bootmisc
-}
-
-start() {
-        if [ "${RC_CMD}" = "restart" ];
-        then
-                einfo "Restarting..."
-        fi
-
-        ebegin "Loading LNet modules:"
-        modprobe lnet
-        eend $*
-
-        ebegin "Bringing up LNet"
-        lnetctl lnet configure --all
-        eend $*
-}
-
-stop() {
-        local LNETMODULES=( "ko2iblnd" "lnet" "libcfs" )
-        ebegin "Bringing down LNet"
-        lnetctl lnet unconfigure --all
-        eend $*
-
-        einfo "Unloading LNet modules:"
-        for mod in ${LNETMODULES[@]}; do
-                ebegin "... ${mod}"
-                modprobe -r ${mod}
-                eend $*
-        done
-}
-
-status()
-{
-        einfo "LNet status:"
-        lnetctl net show
-}
diff --git a/sys-cluster/lustre/files/lustre-client.initd b/sys-cluster/lustre/files/lustre-client.initd
deleted file mode 100644
index 2978b42b9..000000000
--- a/sys-cluster/lustre/files/lustre-client.initd
+++ /dev/null
@@ -1,47 +0,0 @@
-#!/sbin/openrc-run
-# Copyright 1999-2017 Gentoo Foundation
-# Distributed under the terms of the GNU General Public License v2
-
-description="Load lustre modules"
-
-extra_commands="checkmodule"
-
-depend() {
-        need lnet
-        before netmount
-}
-
-checkmodule() {
-        local LOADED="$(lctl modules | awk -F"/" /lustre/'{print $2F}')"
-        for mod in ${LOADED[@]}; do
-                ewarn "Module is still loaded: ${mod}"
-                eend $*
-        done
-}
-
-start() {
-        if [ "${RC_CMD}" = "restart" ];
-        then
-                einfo "Restarting Lustre..."
-                checkmodule
-        fi
-
-        ebegin "Loading Lustre modules..."
-        modprobe lustre
-        eend $*
-}
-
-stop() {
-        local LMODULES=( "lustre" "osc" "mgc" "lmv" "fld" "mdc" "fid" "lov" "ptlrpc" )
-        ebegin "Trying to unmount all Lustre fs"
-        umount -a -t lustre
-        eend $*
-        einfo "Unloading lustre modules:"
-        for mod in ${LMODULES[@]}; do
-                ebegin "... ${mod}"
-                modprobe -r ${mod}
-                eend $*
-        done
-
-        checkmodule
-}
diff --git a/sys-cluster/lustre/lustre-2.10.1.ebuild b/sys-cluster/lustre/lustre-2.10.1.ebuild
deleted file mode 100644
index b2b1d1b35..000000000
--- a/sys-cluster/lustre/lustre-2.10.1.ebuild
+++ /dev/null
@@ -1,120 +0,0 @@
-# Copyright 1999-2017 Gentoo Foundation
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=6
-
-WANT_AUTOCONF="2.5"
-WANT_AUTOMAKE="1.15"
-WANT_LIBTOOL="latest"
-
-if [[ $PV = *9999* ]]; then
-	scm="git-r3"
-	SRC_URI=""
-	EGIT_REPO_URI="git://git.whamcloud.com/fs/lustre-release.git"
-	KEYWORDS=""
-	EGIT_BRANCH="master"
-else
-	scm=""
-	SRC_URI="https://dev.gentoo.org/~alexxy/distfiles/${P}.tar.gz"
-	KEYWORDS="~amd64"
-fi
-
-SUPPORTED_KV_MAJOR=4
-SUPPORTED_KV_MINOR=9
-
-inherit ${scm} autotools linux-info linux-mod toolchain-funcs udev flag-o-matic
-
-DESCRIPTION="Lustre is a parallel distributed file system"
-HOMEPAGE="http://wiki.whamcloud.com/"
-
-LICENSE="GPL-2"
-SLOT="0"
-IUSE="+client +utils +modules +dlc server readline tests"
-
-RDEPEND="
-	virtual/awk
-	dlc? ( dev-libs/libyaml )
-	readline? ( sys-libs/readline:0 )
-	server? (
-		>=sys-kernel/spl-0.6.1
-		>=sys-fs/zfs-kmod-0.6.1
-		sys-fs/zfs
-	)
-	"
-DEPEND="${RDEPEND}
-	dev-python/docutils
-	virtual/linux-sources"
-
-REQUIRED_USE="
-	client? ( modules )
-	server? ( modules )"
-
-pkg_pretend() {
-	KVSUPP=${SUPPORTED_KV_MAJOR}.${SUPPORTED_KV_MINOR}.x
-	if kernel_is gt ${SUPPORTED_KV_MAJOR} ${SUPPORTED_KV_MINOR}; then
-		eerror "Unsupported kernel version! Latest supported one is ${KVSUPP}"
-		die
-	fi
-}
-
-pkg_setup() {
-	filter-mfpmath sse
-	filter-mfpmath i386
-	filter-flags -msse* -mavx* -mmmx -m3dnow
-	linux-mod_pkg_setup
-	ARCH="$(tc-arch-kernel)"
-	ABI="${KERNEL_ABI}"
-}
-
-src_prepare() {
-	if [ ${#PATCHES[0]} -ne 0 ]; then
-		epatch ${PATCHES[@]}
-	fi
-	eapply_user
-	if [[ ${PV} == "9999" ]]; then
-	# replace upstream autogen.sh by our src_prepare()
-		local DIRS="libcfs lnet lustre snmp"
-		local ACLOCAL_FLAGS
-		for dir in $DIRS ; do
-			ACLOCAL_FLAGS="$ACLOCAL_FLAGS -I $dir/autoconf"
-		done
-		_elibtoolize -q
-		eaclocal -I config $ACLOCAL_FLAGS
-		eautoheader
-		eautomake
-		eautoconf
-	fi
-}
-
-src_configure() {
-	local myconf
-	if use server; then
-		SPL_PATH=$(basename $(echo "${EROOT}usr/src/spl-"*)) \
-			myconf="${myconf} --with-spl=${EROOT}usr/src/${SPL_PATH} \
-							--with-spl-obj=${EROOT}usr/src/${SPL_PATH}/${KV_FULL}"
-		ZFS_PATH=$(basename $(echo "${EROOT}usr/src/zfs-"*)) \
-			myconf="${myconf} --with-zfs=${EROOT}usr/src/${ZFS_PATH} \
-							--with-zfs-obj=${EROOT}usr/src/${ZFS_PATH}/${KV_FULL}"
-	fi
-	econf \
-		${myconf} \
-		--without-ldiskfs \
-		--with-linux="${KERNEL_DIR}" \
-		$(use_enable dlc) \
-		$(use_enable client) \
-		$(use_enable utils) \
-		$(use_enable modules) \
-		$(use_enable server) \
-		$(use_enable readline) \
-		$(use_enable tests)
-}
-
-src_compile() {
-	default
-}
-
-src_install() {
-	default
-	newinitd "${FILESDIR}/lnet.initd" lnet
-	newinitd "${FILESDIR}/lustre-client.initd" lustre-client
-}
diff --git a/sys-cluster/lustre/lustre-2.8.0.ebuild b/sys-cluster/lustre/lustre-2.8.0.ebuild
deleted file mode 100644
index 3cf01dd73..000000000
--- a/sys-cluster/lustre/lustre-2.8.0.ebuild
+++ /dev/null
@@ -1,116 +0,0 @@
-# Copyright 1999-2016 Gentoo Foundation
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=6
-
-WANT_AUTOCONF="2.5"
-WANT_AUTOMAKE="1.15"
-WANT_LIBTOOL="latest"
-
-if [[ $PV = *9999* ]]; then
-	KEYWORDS=""
-	EGIT_BRANCH="master"
-else
-	KEYWORDS="~amd64"
-	EGIT_COMMIT="${PV}"
-fi
-
-SUPPORTED_KV_MAJOR=4
-SUPPORTED_KV_MINOR=1
-
-inherit git-r3 autotools linux-info linux-mod toolchain-funcs udev flag-o-matic
-
-DESCRIPTION="Lustre is a parallel distributed file system"
-HOMEPAGE="http://wiki.whamcloud.com/"
-SRC_URI=""
-EGIT_REPO_URI="git://git.whamcloud.com/fs/lustre-release.git"
-
-LICENSE="GPL-2"
-SLOT="0"
-IUSE="+client +utils +modules +dlc server readline tests"
-
-RDEPEND="
-	virtual/awk
-	dlc? ( dev-libs/libyaml )
-	readline? ( sys-libs/readline:0 )
-	server? (
-		>=sys-kernel/spl-0.6.1
-		>=sys-fs/zfs-kmod-0.6.1
-		sys-fs/zfs
-	)
-	"
-DEPEND="${RDEPEND}
-	dev-python/docutils
-	virtual/linux-sources"
-
-REQUIRED_USE="
-	client? ( modules )
-	server? ( modules )"
-
-pkg_pretend() {
-	KVSUPP=${SUPPORTED_KV_MAJOR}.${SUPPORTED_KV_MINOR}.x
-	if kernel_is gt ${SUPPORTED_KV_MAJOR} ${SUPPORTED_KV_MINOR}; then
-		eerror "Unsupported kernel version! Latest supported one is ${KVSUPP}"
-		die
-	fi
-}
-
-pkg_setup() {
-	filter-mfpmath sse
-	filter-mfpmath i386
-	filter-flags -msse* -mavx* -mmmx -m3dnow
-	linux-mod_pkg_setup
-	ARCH="$(tc-arch-kernel)"
-	ABI="${KERNEL_ABI}"
-}
-
-src_prepare() {
-	if [ ${#PATCHES[0]} -ne 0 ]; then
-		epatch ${PATCHES[@]}
-	fi
-	eapply_user
-	# replace upstream autogen.sh by our src_prepare()
-	local DIRS="libcfs lnet lustre snmp"
-	local ACLOCAL_FLAGS
-	for dir in $DIRS ; do
-		ACLOCAL_FLAGS="$ACLOCAL_FLAGS -I $dir/autoconf"
-	done
-	_elibtoolize -q
-	eaclocal -I config $ACLOCAL_FLAGS
-	eautoheader
-	eautomake
-	eautoconf
-}
-
-src_configure() {
-	local myconf
-	if use server; then
-		SPL_PATH=$(basename $(echo "${EROOT}usr/src/spl-"*)) \
-			myconf="${myconf} --with-spl=${EROOT}usr/src/${SPL_PATH} \
-							--with-spl-obj=${EROOT}usr/src/${SPL_PATH}/${KV_FULL}"
-		ZFS_PATH=$(basename $(echo "${EROOT}usr/src/zfs-"*)) \
-			myconf="${myconf} --with-zfs=${EROOT}usr/src/${ZFS_PATH} \
-							--with-zfs-obj=${EROOT}usr/src/${ZFS_PATH}/${KV_FULL}"
-	fi
-	econf \
-		${myconf} \
-		--without-ldiskfs \
-		--with-linux="${KERNEL_DIR}" \
-		$(use_enable dlc) \
-		$(use_enable client) \
-		$(use_enable utils) \
-		$(use_enable modules) \
-		$(use_enable server) \
-		$(use_enable readline) \
-		$(use_enable tests)
-}
-
-src_compile() {
-	default
-}
-
-src_install() {
-	default
-	newinitd "${FILESDIR}/lnet.initd" lnet
-	newinitd "${FILESDIR}/lustre-client.initd" lustre-client
-}
diff --git a/sys-cluster/lustre/lustre-9999.ebuild b/sys-cluster/lustre/lustre-9999.ebuild
deleted file mode 100644
index 1f17955bb..000000000
--- a/sys-cluster/lustre/lustre-9999.ebuild
+++ /dev/null
@@ -1,118 +0,0 @@
-# Copyright 1999-2017 Gentoo Foundation
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=6
-
-WANT_AUTOCONF="2.5"
-WANT_AUTOMAKE="1.15"
-WANT_LIBTOOL="latest"
-
-if [[ $PV = *9999* ]]; then
-	scm="git-r3"
-	SRC_URI=""
-	EGIT_REPO_URI="git://git.whamcloud.com/fs/lustre-release.git"
-	KEYWORDS=""
-	EGIT_BRANCH="master"
-else
-	scm=""
-	SRC_URI="https://dev.gentoo.org/~alexxy/distfiles/${P}.tar.gz"
-	KEYWORDS="~amd64"
-fi
-
-SUPPORTED_KV_MAJOR=4
-SUPPORTED_KV_MINOR=9
-
-inherit ${scm} autotools linux-info linux-mod toolchain-funcs udev flag-o-matic
-
-DESCRIPTION="Lustre is a parallel distributed file system"
-HOMEPAGE="http://wiki.whamcloud.com/"
-
-LICENSE="GPL-2"
-SLOT="0"
-IUSE="+client +utils +modules +dlc server readline tests"
-
-RDEPEND="
-	virtual/awk
-	dlc? ( dev-libs/libyaml )
-	readline? ( sys-libs/readline:0 )
-	server? (
-		>=sys-kernel/spl-0.6.1
-		>=sys-fs/zfs-kmod-0.6.1
-		sys-fs/zfs
-	)
-	"
-DEPEND="${RDEPEND}
-	dev-python/docutils
-	virtual/linux-sources"
-
-REQUIRED_USE="
-	client? ( modules )
-	server? ( modules )"
-
-pkg_pretend() {
-	KVSUPP=${SUPPORTED_KV_MAJOR}.${SUPPORTED_KV_MINOR}.x
-	if kernel_is gt ${SUPPORTED_KV_MAJOR} ${SUPPORTED_KV_MINOR}; then
-		eerror "Unsupported kernel version! Latest supported one is ${KVSUPP}"
-		die
-	fi
-}
-
-pkg_setup() {
-	filter-mfpmath sse
-	filter-mfpmath i386
-	filter-flags -msse* -mavx* -mmmx -m3dnow
-	linux-mod_pkg_setup
-	ARCH="$(tc-arch-kernel)"
-	ABI="${KERNEL_ABI}"
-}
-
-src_prepare() {
-	if [ ${#PATCHES[0]} -ne 0 ]; then
-		epatch ${PATCHES[@]}
-	fi
-	eapply_user
-	# replace upstream autogen.sh by our src_prepare()
-	local DIRS="libcfs lnet lustre snmp"
-	local ACLOCAL_FLAGS
-	for dir in $DIRS ; do
-		ACLOCAL_FLAGS="$ACLOCAL_FLAGS -I $dir/autoconf"
-	done
-	_elibtoolize -q
-	eaclocal -I config $ACLOCAL_FLAGS
-	eautoheader
-	eautomake
-	eautoconf
-}
-
-src_configure() {
-	local myconf
-	if use server; then
-		SPL_PATH=$(basename $(echo "${EROOT}usr/src/spl-"*)) \
-			myconf="${myconf} --with-spl=${EROOT}usr/src/${SPL_PATH} \
-							--with-spl-obj=${EROOT}usr/src/${SPL_PATH}/${KV_FULL}"
-		ZFS_PATH=$(basename $(echo "${EROOT}usr/src/zfs-"*)) \
-			myconf="${myconf} --with-zfs=${EROOT}usr/src/${ZFS_PATH} \
-							--with-zfs-obj=${EROOT}usr/src/${ZFS_PATH}/${KV_FULL}"
-	fi
-	econf \
-		${myconf} \
-		--without-ldiskfs \
-		--with-linux="${KERNEL_DIR}" \
-		$(use_enable dlc) \
-		$(use_enable client) \
-		$(use_enable utils) \
-		$(use_enable modules) \
-		$(use_enable server) \
-		$(use_enable readline) \
-		$(use_enable tests)
-}
-
-src_compile() {
-	default
-}
-
-src_install() {
-	default
-	newinitd "${FILESDIR}/lnet.initd" lnet
-	newinitd "${FILESDIR}/lustre-client.initd" lustre-client
-}
diff --git a/sys-cluster/lustre/metadata.xml b/sys-cluster/lustre/metadata.xml
deleted file mode 100644
index bb4904291..000000000
--- a/sys-cluster/lustre/metadata.xml
+++ /dev/null
@@ -1,18 +0,0 @@
-<?xml version="1.0" encoding="UTF-8"?>
-<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
-<pkgmetadata>
-	<maintainer type="project">
-		<email>cluster@gentoo.org</email>
-		<name>Gentoo Cluster Project</name>
-	</maintainer>
-	<longdescription>
-Lustre is a parallel distributed file system, generally used for large scale cluster computing
-</longdescription>
-	<use>
-		<flag name="client">Enable kernel client modules</flag>
-		<flag name="dlc">Enable Dynamic LNET Configuration</flag>
-		<flag name="server">Enable kernels server modules</flag>
-		<flag name="utils">Enable lustre utils</flag>
-		<flag name="tests">Enable installation of tests</flag>
-	</use>
-</pkgmetadata>
diff --git a/sys-cluster/modules/Manifest b/sys-cluster/modules/Manifest
index b2428f699..d58d72d46 100644
--- a/sys-cluster/modules/Manifest
+++ b/sys-cluster/modules/Manifest
@@ -1,2 +1 @@
-DIST modules-3.2.10.tar.bz2 327611 BLAKE2B 48579b23c72dd973c393a066b788258ba02cc6483536c2177b6fe9d5535c479c54c1384339ecbf46f96128a29b6d808579e5576f443b94835a2c49473f7d15ef SHA512 97715a691e19e7196f7b79464f758aefb703d8712edd2d571faa1501ed9134b7a0b0e82126de089ddbf406f3ca67837a495a3afdf5fbb49c6231f27dc2654032
-DIST modules-3.2.9c.tar.bz2 340529 BLAKE2B 7b7bdedf3d631849df8f10d38f62ec44dcbe076b4978739671bcbde0fe18d40796165af224b8a63c7afc28f83ffb4131f0c08fd2c0c27984d9f3a057355738a8 SHA512 f65c9b7a56b2836256b9eef337c68272cff6137f2df46dcb75d1f8e0d6b023d908117023ee2e32acceb2b9482d0e2aeae7ab13505902b8a12858cb7307ba0ca0
+DIST modules-4.6.0.tar.bz2 1589367 BLAKE2B 0fed7eadd95562a58a6d7ab903bbc442138f41f1fe533d3ea07ff988b57d564de0e5304954fdf379e4c35286e37cf8397fc525dc73d2aa9d76f87e15a487594d SHA512 7412e5e1107d4ea664734d0bc8c473e3f9c756d3b2bd9960c8d5db7733c6e798d98157dd7bf8b0311eb357ec46b9f900617054c47199a94c26744b0efc26eed2
diff --git a/sys-cluster/modules/files/createmodule.py b/sys-cluster/modules/files/createmodule.py
deleted file mode 100644
index 60c6ba7fa..000000000
--- a/sys-cluster/modules/files/createmodule.py
+++ /dev/null
@@ -1,186 +0,0 @@
-#!/usr/bin/python
-#
-# createmodule.py - Takes the name of a environment init script and 
-# produces a modulefile that duplicates the changes made by the init script
-#
-# Copyright (C) 2012 by Orion E. Poplawski <orion@cora.nwra.com>
-#
-# This program is free software: you can redistribute it and/or modify
-# it under the terms of the GNU General Public License as published by
-# the Free Software Foundation, either version 2 of the License, or
-# (at your option) any later version.
-
-# This program is distributed in the hope that it will be useful,
-# but WITHOUT ANY WARRANTY; without even the implied warranty of
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
-# GNU General Public License for more details.
-
-# You should have received a copy of the GNU General Public License
-# along with this program.  If not, see <http://www.gnu.org/licenses/>.
-
-from optparse import OptionParser
-import os,sys
-from subprocess import *
-
-# Handle options
-usage = "Usage: %prog [-p prefix] <initscript> [args]"
-parser = OptionParser()
-parser.set_usage(usage)
-parser.add_option('-p', '--prefix', dest='prefix', help='Specify path prefix')
-(options, args) = parser.parse_args()
-
-# Need a script name
-if not args:
-    parser.print_usage()
-    exit(1)
-
-# Return environment after a command
-def getenv(cmd = ':'):
-    env = {}
-    p = Popen(cmd + ";env", shell=True, stdout=PIPE, stderr=PIPE)
-    (stdout, stderr) = p.communicate()
-    if p.returncode != 0:
-        print "EROR: Could not execute initscript:"
-        print "%s returned exit code %d" % (cmd, p.returncode)
-        print stderr
-        exit(1)
-    if stderr != '':
-        print "WARNING: initscript sent the following to stderr:"
-        print stderr
-    # Parse the output key=value pairs
-    for line in stdout.splitlines():
-        try:
-            (var,value) = line.split('=',1)
-        except ValueError:
-            print "ERROR: Could not parse output:"
-            print stdout
-            exit(1)
-        env[var] = value
-    return env
-
-#Record initial environment
-env1=getenv()
-
-#Record environment after sourcing the initscript
-env2=getenv(". " + " ".join(args))
-
-# Initialize our variables for storing modifications
-chdir = None
-appendpath = {}
-prependpath = {}
-setenv = {}
-unsetenv = []
-pathnames = []
-
-# Function to nomalize all paths in a list of paths and remove duplicate items
-def normpaths(paths):
-    newpaths = []
-    for path in paths:
-        normpath = os.path.normpath(path)
-        if normpath not in newpaths:
-             newpaths.append(os.path.normpath(path))
-    return newpaths
-
-# Start with existing keys and look for changes
-for key in env1.keys():
-    # Test for delete
-    if key not in env2:
-        unsetenv.append(key)
-        continue
-    # No change
-    if env1[key] == env2[key]:
-        del env2[key]
-        continue
-    #Working directory change
-    if key == 'PWD':
-	chdir=os.path.normpath(env2[key])
-        pathnames.append(chdir)
-        del env2[key]
-        continue
-    # Determine modifcations to beginning and end of the string
-    (prepend,append) = env2[key].split(env1[key])
-    if prepend:
-        prependpaths = prepend.strip(':').split(':')
-        # LICENSE variables often include paths outside install directory
-        if 'LICENSE' not in key:
-            pathnames += prependpaths
-        prependpath[key] = ':'.join(normpaths(prependpaths))
-    if append:
-        appendpaths = append.strip(':').split(':')
-        # LICENSE variables often include paths outside install directory
-        if 'LICENSE' not in key:
-            pathnames += appendpaths
-        appendpath[key] = ':'.join(normpaths(appendpaths))
-    del env2[key]
-      
-# We're left with new keys in env2
-for key in env2.keys():
-    # Use prepend-path for new paths
-    if ('PATH' in key) or (':' in env2[key]):
-        prependpaths = env2[key].strip(':').split(':')
-        # MANPATH can have system defaults added it it wasn't previously set
-        # LICENSE variables often include paths outside install directory
-        if key != 'MANPATH' and 'LICENSE' not in key:
-            pathnames += prependpaths
-        prependpath[key] = ':'.join(normpaths(prependpaths))
-        continue
-    # Set new variables
-    setenv[key] = os.path.normpath(env2[key])
-    if 'LICENSE' not in key:
-        pathnames.append(setenv[key])
-
-# Determine a prefix
-prefix = None
-if options.prefix:
-    prefix = options.prefix
-else:
-    prefix = os.path.commonprefix(pathnames).rstrip('/')
-    if prefix == '':
-          prefix = None
-
-# Print out the modulefile
-print "#%Module 1.0"
-
-# Prefix
-if prefix is not None:
-    print "\nset prefix " + prefix + "\n"
-
-# Chdir
-if chdir is not None:
-    print "chdir\t" + chdir
-
-# Function to format output line with tabs and substituting prefix
-def formatline(item, key, value=None):
-    print item,
-    print "\t"*(2-(len(item)+1)/8),
-    print key,
-    if value is not None:
-        print "\t"*(3-(len(key)+1)/8),
-        if prefix is not None:
-            print value.replace(prefix,'$prefix')
-        else:
-            print value
-
-# Paths first, grouped by variable name
-pathkeys = appendpath.keys() + prependpath.keys()
-pathkeys.sort()
-for key in pathkeys:
-    if key in prependpath:
-        formatline("prepend-path",key,prependpath[key])
-    if key in appendpath:
-        formatline("append-path",key,appendpath[key])
-
-# Setenv
-setenvkeys = setenv.keys()
-setenvkeys.sort()
-if setenvkeys:
-    print
-for key in setenvkeys:
-    formatline("setenv",key,setenv[key])
-
-# Unsetenv
-unsetenv.sort()
-if unsetenv:
-    print
-for key in unsetenv:
-    formatline("unsetenv",key)
diff --git a/sys-cluster/modules/files/createmodule.sh b/sys-cluster/modules/files/createmodule.sh
deleted file mode 100644
index b44cf0512..000000000
--- a/sys-cluster/modules/files/createmodule.sh
+++ /dev/null
@@ -1,166 +0,0 @@
-#!/bin/bash
-#
-# createmodule.sh - Takes the name of a environment init script and 
-# produces a modulefile that duplicates the changes made by the init script
-#
-# Copyright (C) 2010-2012 by Orion E. Poplawski <orion@cora.nwra.com>
-#
-# This program is free software: you can redistribute it and/or modify
-# it under the terms of the GNU General Public License as published by
-# the Free Software Foundation, either version 2 of the License, or
-# (at your option) any later version.
-
-# This program is distributed in the hope that it will be useful,
-# but WITHOUT ANY WARRANTY; without even the implied warranty of
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
-# GNU General Public License for more details.
-
-# You should have received a copy of the GNU General Public License
-# along with this program.  If not, see <http://www.gnu.org/licenses/>.
-
-usage="Usage: $0 [-p prefix] <initscript> [args]"
-
-usage() {
-  echo $usage 1>&2
-  exit 1
-}
-
-while getopts "p:" opt
-do
-  case $opt in
-    p) prefix=$OPTARG; shift 2;;
-    *) usage;;
-  esac
-done
-
-# Need a script name
-[ -z "$1" ] && usage
-
-# Need to be a readable script
-if [ ! -r "$1" ]
-then
-  echo "ERROR: Cannot read $1" 1>&2
-  exit 1 
-fi
-
-#Will print out array assignment list
-printenvarray () {
-  env | while read x
-  do
-    key=${x%%=*}
-    value=${x#*=}
-    echo [$key]="'$value'"
-  done
-}
-
-#Apparently we need to declare the associative arrays
-declare -A env1 env2
-
-#Record starting environment
-eval env1=(`printenvarray`)
-
-#Source the environment script
-. "$@"
-
-#Record ending environment
-eval env2=(`printenvarray`)
-
-#Print out the modulefile
-echo "#%Module 1.0"
-
-#Prefix
-[ -n "$prefix" ] && echo -e "\nset prefix $prefix\n"
-
-#Subshell so we can sort the output
-(
-dedup() {
-  list=`mktemp`
-  echo $1 | sed -r -e 's,[^/]+/\.\./,,g' -e 's,[^/]+/\.\./,,g' -e 's/:/\n/g' |
-    while read x
-    do
-      grep -Fx ${x} $list && continue
-      if [ -n "$prefix" ]
-      then
-        echo $x | sed -e s,$prefix,\$prefix,
-      else
-        echo $x
-      fi
-      echo $x >> $list
-    done | tr '\n' : | sed -e 's/:$//'
-  rm $list
-} 
-    
-#Keys that changed
-for key in "${!env1[@]}"
-do
-  if [ "${env1[$key]}" != "${env2[$key]}" ]
-  then
-    #Working directory change
-    if [ "$key" = PWD ]
-    then
-      if [ -n "$prefix" ]
-      then
-        echo -e "chdir\t\t${env2[PWD]}" | sed -e s,$prefix,\$prefix,g
-      else
-        echo -e "chdir\t\t${env2[PWD]}"
-      fi
-    #Test for delete
-    elif [ -z "${env2[$key]}" ]
-    then
-      echo -e "unsetenv\t${key}\t${env2[$key]}"
-    #Test for prepend
-    elif [ "${env2[$key]%${env1[$key]}}" != "${env2[$key]}" ]
-    then
-      added=$(dedup ${env2[$key]%:${env1[$key]}})
-      echo -e "prepend-path\t$key\t${added}"
-    #Test for prepend plus : added at end (MANPATH)
-    elif [ "${env2[$key]%${env1[$key]}:}" != "${env2[$key]}" ]
-    then
-      added=$(dedup ${env2[$key]%${env1[$key]}:})
-      echo -e "prepend-path\t$key\t${added}"
-    #Test for append
-    elif [ "${env2[$key]#${env1[$key]}}" != "${env2[$key]}" ]
-    then
-      added=$(dedup ${env2[$key]#:${env1[$key]}})
-      echo -e "append-path\t$key\t${added}"
-    #Test for prepend plus append
-    elif [ "${env2[$key]%${env1[$key]}:*}" != "${env2[$key]}" ]
-    then
-      added=$(dedup ${env2[$key]%:${env1[$key]}*})
-      echo -e "prepend-path\t$key\t${added}"
-      added=$(dedup ${env2[$key]#*${env1[$key]}:})
-      echo -e "append-path\t$key\t${added}"
-    else
-      #Unhandled
-      echo "Unhandled change of $key" 1>&2
-      echo "Before <${env1[$key]}>" 1>&2
-      echo "After  <${env2[$key]}>" 1>&2
-    fi
-  fi
-  #Delete keys we've handled
-  unset env1[$key]
-  unset env2[$key]
-done
-
-#New keys
-for key in "${!env2[@]}"
-do
-  if [ "$key" = OLDPWD ]
-  then
-    continue
-  fi
-  #Use prepend-path for new paths
-  if [ "${key/PATH/}" != "$key" ]
-  then
-    # TODO - Need to handle stripping of default MANPATH
-    echo -e "prepend-path\t${key}\t"$(dedup ${env2[$key]})
-  else
-    if [ -n "$prefix" ]
-    then
-      echo -e "setenv\t\t${key}\t${env2[$key]}" | sed -e s,$prefix,\$prefix,g
-    else
-      echo -e "setenv\t\t${key}\t${env2[$key]}"
-    fi
-  fi
-done
-) | sort
diff --git a/sys-cluster/modules/files/modules-3.2.10-avail.patch b/sys-cluster/modules/files/modules-3.2.10-avail.patch
deleted file mode 100644
index 8d6f52b92..000000000
--- a/sys-cluster/modules/files/modules-3.2.10-avail.patch
+++ /dev/null
@@ -1,12 +0,0 @@
-diff -up modules-3.2.10/init/bash_completion.in.avail modules-3.2.10/init/bash_completion.in
---- modules-3.2.10/init/bash_completion.in.avail	2012-10-25 13:33:34.000000000 -0600
-+++ modules-3.2.10/init/bash_completion.in	2013-01-15 12:05:37.247309733 -0700
-@@ -56,7 +56,7 @@ _module() {
- 	unuse)		COMPREPLY=( $(IFS=: compgen -W "${MODULEPATH}" -- "$cur") );;
- 	use|*-a*)	;;			# let readline handle the completion
- 	-u|--userlvl)	COMPREPLY=( $(compgen -W "novice expert advanced" -- "$cur") );;
--	display|help|show|whatis)
-+	av*|disp*|help|show|whatis)
- 			COMPREPLY=( $(compgen -W "$(_module_avail)" -- "$cur") );;
- 	*) if test $COMP_CWORD -gt 2
- 	   then
diff --git a/sys-cluster/modules/files/modules-3.2.10-bindir.patch b/sys-cluster/modules/files/modules-3.2.10-bindir.patch
deleted file mode 100644
index 2066d7f13..000000000
--- a/sys-cluster/modules/files/modules-3.2.10-bindir.patch
+++ /dev/null
@@ -1,11 +0,0 @@
---- modules-3.2.10.orig/init/Makefile.in	2009-09-22 12:13:52.000000000 -0600
-+++ modules-3.2.10/init/Makefile.in	2009-09-23 12:19:50.797470155 -0600
-@@ -404,7 +404,7 @@
- 	sed -e "/@$(if $(subst 0,,$(WANTS_VERSIONING)),NOT,)VERSIONING\@/d; \
- 	s,@$(if $(subst 0,,$(WANTS_VERSIONING)),,NOT)VERSIONING\@,,g; \
- 	s,@prefix\@,${prefix},g; \
--	s,@bindir\@,${exec_prefix}/bin,g; \
-+	s,@bindir\@,${bindir},g; \
- 	s,@VERSION\@,@VERSION@,g; \
- 	s,@BASEPREFIX\@,@BASEPREFIX@,g;" < $< > $@
- 
diff --git a/sys-cluster/modules/files/modules-3.2.10-clear.patch b/sys-cluster/modules/files/modules-3.2.10-clear.patch
deleted file mode 100644
index 0817db5c2..000000000
--- a/sys-cluster/modules/files/modules-3.2.10-clear.patch
+++ /dev/null
@@ -1,11 +0,0 @@
---- modules-3.2.9/utility.c	2011-11-28 22:27:13.000000000 +0100
-+++ modules-3.2.9-new/utility.c	2012-06-13 15:17:41.570629148 +0200
-@@ -727,7 +727,7 @@ int Output_Modulefile_Changes(	Tcl_Inter
- 			output_unset_variable( (char*) key);
- 		} else {
- 			val = EMGetEnv(interp, key);
--			if(val && *val)
-+			if(val)
- 				output_set_variable(interp, (char*) key, val);
- 			null_free((void *)&val);
- 		}
diff --git a/sys-cluster/modules/files/modules-3.2.10-defs.patch b/sys-cluster/modules/files/modules-3.2.10-defs.patch
deleted file mode 100644
index 412abebd7..000000000
--- a/sys-cluster/modules/files/modules-3.2.10-defs.patch
+++ /dev/null
@@ -1,20 +0,0 @@
---- modules-3.2.10/modules_def.h.orig	2017-04-21 19:33:52.698720482 +0300
-+++ modules-3.2.10/modules_def.h	2017-04-21 19:35:19.506727343 +0300
-@@ -616,6 +616,9 @@
- /**  ModuleCmd_Purge.c  **/
- extern	int	  ModuleCmd_Purge( Tcl_Interp*, int, char*[]);
- 
-+/**  ModuleCmd_Refresh.c **/
-+extern	int	  ModuleCmd_Refresh( Tcl_Interp*,	int	argc, char*[]);
-+
- /**  ModuleCmd_Switch.c  **/
- extern	int	  ModuleCmd_Switch( Tcl_Interp*, int, char*[]);
- 
-@@ -753,6 +756,7 @@
- extern	char 	 *EMGetEnv(Tcl_Interp *, char const *);
- extern	char 	 *EMSetEnv(Tcl_Interp *, char const *, char const *);
- extern	int	  is_interactive(void);
-+extern	void	 regex_quote(const char	*, char	*, int len);
- 
- #ifndef HAVE_STRDUP
- #  undef strdup
diff --git a/sys-cluster/modules/files/modules-3.2.10-errorline.patch b/sys-cluster/modules/files/modules-3.2.10-errorline.patch
deleted file mode 100644
index b2962f104..000000000
--- a/sys-cluster/modules/files/modules-3.2.10-errorline.patch
+++ /dev/null
@@ -1,14 +0,0 @@
-diff -ru modules-3.2.9-old/cmdModule.c modules-3.2.9/cmdModule.c
---- modules-3.2.9-old/cmdModule.c	2013-06-02 22:46:09.196302980 +0200
-+++ modules-3.2.9/cmdModule.c	2013-06-02 22:53:36.706298800 +0200
-@@ -640,8 +640,8 @@
-             case TCL_OK:	gotPartial = 0;
- 			        continue;	/** while **/
- 	    
--            case TCL_ERROR:	interp->errorLine = ((linenum-1)-gotPartial) +
--				    interp->errorLine;
-+		case TCL_ERROR:	Tcl_SetErrorLine(interp, ((linenum-1)-gotPartial) +
-+										 Tcl_GetErrorLine(interp));
- 	    			/* FALLTHROUGH */
- 
-             case TCL_LEVEL0_RETURN:
diff --git a/sys-cluster/modules/files/modules-3.2.10-versioning.patch b/sys-cluster/modules/files/modules-3.2.10-versioning.patch
deleted file mode 100644
index 7bda92023..000000000
--- a/sys-cluster/modules/files/modules-3.2.10-versioning.patch
+++ /dev/null
@@ -1,10 +0,0 @@
-diff -up modules-3.2.10/modulefiles/modules.in.versioning modules-3.2.10/modulefiles/modules.in
---- modules-3.2.10/modulefiles/modules.in.versioning	2012-10-25 13:33:34.000000000 -0600
-+++ modules-3.2.10/modulefiles/modules.in	2013-01-15 11:30:22.046031158 -0700
-@@ -26,5 +26,5 @@ setenv		MODULESHOME	$prefix
- prepend-path    PATH   		@bindir@
- prepend-path    MANPATH		@mandir@
- 
--module		use		@VERSIONPATH@
-+@VERSIONING@module		use		@VERSIONPATH@
- 
diff --git a/sys-cluster/modules/files/modules-3.2.9c-errorline.patch b/sys-cluster/modules/files/modules-3.2.9c-errorline.patch
deleted file mode 100644
index b2962f104..000000000
--- a/sys-cluster/modules/files/modules-3.2.9c-errorline.patch
+++ /dev/null
@@ -1,14 +0,0 @@
-diff -ru modules-3.2.9-old/cmdModule.c modules-3.2.9/cmdModule.c
---- modules-3.2.9-old/cmdModule.c	2013-06-02 22:46:09.196302980 +0200
-+++ modules-3.2.9/cmdModule.c	2013-06-02 22:53:36.706298800 +0200
-@@ -640,8 +640,8 @@
-             case TCL_OK:	gotPartial = 0;
- 			        continue;	/** while **/
- 	    
--            case TCL_ERROR:	interp->errorLine = ((linenum-1)-gotPartial) +
--				    interp->errorLine;
-+		case TCL_ERROR:	Tcl_SetErrorLine(interp, ((linenum-1)-gotPartial) +
-+										 Tcl_GetErrorLine(interp));
- 	    			/* FALLTHROUGH */
- 
-             case TCL_LEVEL0_RETURN:
diff --git a/sys-cluster/modules/files/modules.sh.in b/sys-cluster/modules/files/modules.sh.in
deleted file mode 100644
index e3d6d43b2..000000000
--- a/sys-cluster/modules/files/modules.sh.in
+++ /dev/null
@@ -1,7 +0,0 @@
-shell=$(basename $(ps -p $$ -ocomm=))
-if [ -f @EPREFIX@/usr/share/Modules/init/${shell} ]
-then
-  . @EPREFIX@/usr/share/Modules/init/${shell}
-else
-  . @EPREFIX@/usr/share/Modules/init/sh
-fi
diff --git a/sys-cluster/modules/metadata.xml b/sys-cluster/modules/metadata.xml
index 60ab20673..4842f7c2c 100644
--- a/sys-cluster/modules/metadata.xml
+++ b/sys-cluster/modules/metadata.xml
@@ -2,21 +2,26 @@
 <!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
 <pkgmetadata>
 	<maintainer type="person">
-		<email>nicolasbock@gentoo.org</email>
-		<name>Nicolas Bock</name>
+		<email>btbn@btbn.de</email>
+		<name>Timo Rothenpieler</name>
 	</maintainer>
 	<maintainer type="project">
-		<email>cluster@gentoo.org</email>
-		<name>Gentoo Cluster Project</name>
+		<email>sci@gentoo.org</email>
+		<name>Gentoo Science Project</name>
 	</maintainer>
 	<longdescription lang="en">
-The environment modules package provides for an easy dynamic
-modification of a user's environment via modulefiles. which
-typically instruct the module command to alter or set shell
-environment variables such as PATH, MANPATH, etc. as well as define
-aliases over a variety of shells.
-</longdescription>
+		The environment modules package provides for an easy dynamic
+		modification of a user's environment via modulefiles. which
+		typically instruct the module command to alter or set shell
+		environment variables such as PATH, MANPATH, etc. as well as define
+		aliases over a variety of shells.
+	</longdescription>
 	<upstream>
 		<remote-id type="sourceforge">modules</remote-id>
+		<remote-id type="github">cea-hpc/modules</remote-id>
+		<bugs-to>https://github.com/cea-hpc/modules/issues</bugs-to>
 	</upstream>
+	<use>
+		<flag name="compat">Build Modules version 3 compat support</flag>
+	</use>
 </pkgmetadata>
diff --git a/sys-cluster/modules/modules-3.2.10-r2.ebuild b/sys-cluster/modules/modules-3.2.10-r2.ebuild
deleted file mode 100644
index 33ff8a591..000000000
--- a/sys-cluster/modules/modules-3.2.10-r2.ebuild
+++ /dev/null
@@ -1,66 +0,0 @@
-# Copyright 1999-2017 Gentoo Foundation
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=6
-
-inherit autotools
-
-DESCRIPTION="Dynamic modification of a user's environment via modulefiles"
-HOMEPAGE="http://modules.sourceforge.net/"
-SRC_URI="mirror://sourceforge/${PN}/${P}.tar.bz2"
-
-LICENSE="GPL-2"
-SLOT="0"
-KEYWORDS="~amd64 ~x86 ~amd64-linux ~x86-linux"
-IUSE="test X"
-
-RDEPEND="
-	dev-lang/tcl:0=
-	dev-tcltk/tclx
-	X? ( x11-libs/libX11 )"
-DEPEND="${RDEPEND}
-	test? ( dev-util/dejagnu )"
-
-S="${WORKDIR}/${P%[a-z]}"
-
-PATCHES=(
-	"${FILESDIR}"/${P}-bindir.patch
-	"${FILESDIR}"/${P}-versioning.patch
-	"${FILESDIR}"/${P}-clear.patch
-	"${FILESDIR}"/${P}-avail.patch
-	"${FILESDIR}"/${P}-defs.patch
-)
-
-DOCS=(ChangeLog README NEWS TODO)
-
-src_prepare() {
-	has_version ">=dev-lang/tcl-8.6.0" &&
-		eapply "${FILESDIR}"/${P}-errorline.patch
-	default
-	sed -e "s:@EPREFIX@:${EPREFIX}:g" \
-		"${FILESDIR}"/modules.sh.in > modules.sh || die
-
-	eautoreconf
-}
-
-src_configure() {
-	local myconf=(
-		--disable-versioning
-		--prefix="${EPREFIX}/usr/share"
-		--exec-prefix="${EPREFIX}/usr/share/Modules"
-		--with-module-path="${EPREFIX}/etc/modulefiles"
-		--with-tcl="${EPREFIX}/usr/$(get_libdir)"
-		$(use_with X x)
-	)
-	econf ${myconf[@]}
-}
-
-src_install() {
-	default
-	insinto /etc/profile.d
-	doins modules.sh
-	exeinto /usr/share/Modules/bin
-	doexe "${FILESDIR}"/createmodule.{sh,py}
-	dosym ../../../usr/share/Modules/init/csh /etc/profile.d/modules.csh
-	dodir /etc/modulefiles
-}
diff --git a/sys-cluster/modules/modules-3.2.9c-r1.ebuild b/sys-cluster/modules/modules-3.2.9c-r1.ebuild
deleted file mode 100644
index 43f0ab91d..000000000
--- a/sys-cluster/modules/modules-3.2.9c-r1.ebuild
+++ /dev/null
@@ -1,48 +0,0 @@
-# Copyright 1999-2015 Gentoo Foundation
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=5
-
-inherit autotools-utils
-
-DESCRIPTION="Dynamic modification of a user's environment via modulefiles"
-HOMEPAGE="http://modules.sourceforge.net/"
-SRC_URI="http://sourceforge.net/projects/modules/files/Modules/${P%[a-z]}/${P}.tar.bz2/download -> ${P}.tar.bz2"
-
-LICENSE="GPL-2"
-SLOT="0"
-KEYWORDS="~amd64 ~x86"
-IUSE="X"
-
-DEPEND="
-	dev-lang/tcl:0=
-	dev-tcltk/tclx
-	X? ( x11-libs/libX11 )
-	"
-RDEPEND="${DEPEND}"
-
-S="${WORKDIR}/${P%[a-z]}"
-
-DOCS=(ChangeLog README NEWS TODO)
-
-src_prepare() {
-	has_version ">=dev-lang/tcl-8.6.0" && epatch "${FILESDIR}/${P}-errorline.patch"
-}
-
-src_configure() {
-	local myeconfargs=(
-		$(use_with X x)
-		--prefix=/opt
-	)
-	autotools-utils_src_configure
-}
-
-src_install() {
-	autotools-utils_src_install
-	dosym ${PV%[a-z]} /opt/Modules/default
-}
-
-pkg_postinst() {
-	elog "Add this line at the end of your bashrc:"
-	elog "[ -f /opt/Modules/default/init/bash ] && source /opt/Modules/default/init/bash"
-}
diff --git a/sys-cluster/modules/modules-4.6.0-r1.ebuild b/sys-cluster/modules/modules-4.6.0-r1.ebuild
new file mode 100644
index 000000000..3aade0b38
--- /dev/null
+++ b/sys-cluster/modules/modules-4.6.0-r1.ebuild
@@ -0,0 +1,82 @@
+# Copyright 2020 Gentoo Authors
+# Distributed under the terms of the GNU General Public License v2
+
+EAPI=8
+
+PYTHON_COMPAT=( python3_{10..11} )
+
+inherit autotools python-single-r1
+
+DESCRIPTION="Dynamic modification of a user's environment via modulefiles"
+HOMEPAGE="http://modules.sourceforge.net/"
+SRC_URI="https://github.com/cea-hpc/modules/releases/download/v${PV}/${P}.tar.bz2"
+
+LICENSE="GPL-2"
+SLOT="0"
+KEYWORDS="~amd64 ~x86"
+IUSE="compat test"
+REQUIRED_USE="${PYTHON_REQUIRED_USE}"
+RESTRICT="!test? ( test )"
+
+DEPEND="
+	${PYTHON_DEPS}
+	dev-lang/tcl:0=
+	dev-tcltk/tclx
+	compat? ( x11-libs/libX11 )
+"
+# lmod is strong blocked since both want to install a module binary
+RDEPEND="
+	${DEPEND}
+	!sys-cluster/lmod
+"
+BDEPEND="
+	test? ( dev-util/dejagnu )
+"
+
+src_prepare() {
+	default
+
+	cd "${S}/lib" || die
+	eautoreconf
+
+	if use compat; then
+		cd "${S}/compat" || die
+		eautoreconf
+	fi
+}
+
+src_configure() {
+	local myconf=(
+		--disable-versioning
+		--with-initconf-in=etcdir
+		--enable-multilib-support
+		--disable-set-shell-startup
+		--prefix="${EPREFIX}/usr/share/Modules"
+		--mandir="${EPREFIX}/usr/share/man"
+		--docdir="${EPREFIX}/usr/share/doc/${P}"
+		--libdir="${EPREFIX}/usr/share/Modules/$(get_libdir)"
+		--datarootdir="${EPREFIX}/usr/share"
+		--modulefilesdir="${EPREFIX}/etc/modulefiles"
+		--with-tcl="${EPREFIX}/usr/$(get_libdir)"
+		--with-python="${PYTHON}"
+		--with-quarantine-vars="LD_LIBRARY_PATH LD_PRELOAD"
+		$(use_enable compat compat-version)
+	)
+	econf "${myconf[@]}" "${EXTRA_ECONF[@]}" || die "configure failed"
+}
+
+src_test() {
+	# Remove known-broken tests
+	# These test fine, but fail for random differences in the gentoo environment
+	rm "${S}"/testsuite/modules.70-maint/210-clear.exp || die "rm failed"
+	rm "${S}"/testsuite/modules.00-init/110-quar.exp || die "rm failed"
+
+	RUNTESTARGS=-v emake test
+}
+
+src_install() {
+	default
+	dosym ../../usr/share/Modules/init/profile.sh /etc/profile.d/modules.sh
+	dosym ../../usr/share/Modules/init/profile.csh /etc/profile.d/modules.csh
+	dodir /etc/modulefiles
+}
diff --git a/sys-cluster/mpe2/Manifest b/sys-cluster/mpe2/Manifest
deleted file mode 100644
index 7b0ec3089..000000000
--- a/sys-cluster/mpe2/Manifest
+++ /dev/null
@@ -1 +0,0 @@
-DIST mpe2-1.3.0.tar.gz 9703024 BLAKE2B 1fe8db10968602270e296368ea90ede3998d480fe27c68b6fb9375d83a193e8d909fc27055541561acd97b03b8cf6c56b13d1e3032e6ff3018d17ed31f6942fe SHA512 84f0be89f4c17e5b86bc4d067be650b65938af4f7e71224e8f65b723f217649da3d5b8991f3eb9c83823d9c0831d9847c90e6940d9f30958803984efb2e028ca
diff --git a/sys-cluster/mpe2/metadata.xml b/sys-cluster/mpe2/metadata.xml
deleted file mode 100644
index 8bf4b5f36..000000000
--- a/sys-cluster/mpe2/metadata.xml
+++ /dev/null
@@ -1,8 +0,0 @@
-<?xml version="1.0" encoding="UTF-8"?>
-<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
-<pkgmetadata>
-	<maintainer type="project">
-		<email>cluster@gentoo.org</email>
-		<name>Gentoo Cluster Project</name>
-	</maintainer>
-</pkgmetadata>
diff --git a/sys-cluster/mpe2/mpe2-1.3.0.ebuild b/sys-cluster/mpe2/mpe2-1.3.0.ebuild
deleted file mode 100644
index d1bf59c08..000000000
--- a/sys-cluster/mpe2/mpe2-1.3.0.ebuild
+++ /dev/null
@@ -1,147 +0,0 @@
-# Copyright 1999-2016 Gentoo Foundation
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=6
-
-FORTRAN_NEEDED=fortran
-
-inherit eutils fortran-2 java-utils-2 toolchain-funcs
-
-MY_P=${P/_/}
-DESCRIPTION="MPI development tools"
-HOMEPAGE="http://www-unix.mcs.anl.gov/perfvis/download/index.htm"
-SRC_URI="ftp://ftp.mcs.anl.gov/pub/mpi/${PN%2}/${MY_P}.tar.gz"
-
-LICENSE="mpich2"
-SLOT="0"
-KEYWORDS="~amd64 ~x86"
-IUSE="minimal fortran threads debug"
-
-COMMON_DEPEND="
-	!minimal? (
-		x11-libs/libXtst
-		x11-libs/libXi
-	)
-	|| (
-		sys-cluster/openmpi[fortran?,threads?]
-		sys-cluster/mpich2[fortran?,threads?]
-	)"
-
-DEPEND="!minimal? ( >=virtual/jdk-1.4 )
-	${COMMON_DEPEND}"
-
-RDEPEND="
-!minimal? ( >=virtual/jre-1.4 )
-	${COMMON_DEPEND}"
-
-S="${WORKDIR}"/${MY_P}
-MPE_IMP=""
-
-# README:
-# This ebuild is created to handle building with both mpich2 and openmpi.
-# However, without empi (in the science overlay), and some further
-# conversion to use mpi.eclass, we can only handle one implementation
-# at a time.  I still believe it's better to have the ebuild setup
-# correctly in preperation.
-
-pkg_setup() {
-	fortran-2_pkg_setup
-	local i
-
-	if has_version sys-cluster/openmpi; then
-		MPE_IMP=openmpi
-	elif has_version sys-cluster/mpich2; then
-		MPE_IMP=mpich2
-	else
-		die "Unknown MPI implementation"
-	fi
-
-	export JFLAGS="${JFLAGS} $(java-pkg_javac-args)"
-
-	if [[ "${MPE_IMP}" == openmpi ]] && [ -z "${MPE2_FORCE_OPENMPI_TEST}" ]; then
-		echo
-		elog "Currently src_test fails on collchk with openmpi, hence"
-		elog "testing is disabled by default.  If you would like to"
-		elog "force testing, please add MPE_FORCE_OPENMPI_TEST=1"
-		elog "to your environment."
-		echo
-	fi
-
-	einfo "Building with support for: sys-cluster/${MPE_IMP}"
-}
-
-src_prepare() {
-	default
-	# Don't assume path contains ./
-	sed -i 's,\($MPERUN\) $pgm,\1 ./$pgm,' sbin/mpetestexeclog.in || die
-
-	# No parallel make:
-	# http://trac.mcs.anl.gov/projects/mpich2/ticket/1095#comment:1
-	MAKEOPTS+=" -j1"
-}
-
-src_configure() {
-	local c="--with-mpicc=/usr/bin/mpicc"
-
-	if use fortran; then
-		c="${c} --with-mpif77=/usr/bin/mpif77"
-	else
-		c="${c} --disable-f77"
-	fi
-
-	if use minimal; then
-		c="${c} --enable-slog2=no --disable-rlog --disable-sample"
-	else
-		c="${c} --with-java2=$(java-config --jdk-home) --enable-slog2=build"
-	fi
-
-	if [[ "${MPE_IMP}" == openmpi ]]; then
-		c="${c} --disable-rlog --disable-sample"
-	fi
-
-	econf ${c} \
-		--sysconfdir=/etc/${PN} \
-		--datadir=/usr/share/${PN} \
-		--with-htmldir=/usr/share/${PN} \
-		--with-docdir=/usr/share/${PN} \
-		--enable-collchk \
-		--enable-wrappers \
-		$(use_enable !minimal graphics) \
-		$(use_enable threads threadlogging) \
-		$(use_enable debug g)
-}
-
-src_test() {
-	local rc
-
-	cd "${S}" || die
-	if [[ "${MPE_IMP}" == mpich2 ]]; then
-		echo "MPD_SECRETWORD=junk" > "${T}"/mpd.conf
-		chmod 600 "${T}"/mpd.conf
-		export MPD_CONF_FILE="${T}/mpd.conf"
-		"${ROOT}"usr/bin/mpd -d --pidfile="${T}"/mpd.pid
-	elif [[ "${MPE_IMP}" == openmpi* ]] && [ -z "${MPE2_FORCE_OPENMPI_TEST}" ]; then
-		elog
-		elog "Skipping tests for openmpi"
-		elog
-		return 0
-	fi
-
-	emake \
-		CC="${S}"/bin/mpecc \
-		FC="${S}"/bin/mpefc \
-		MPERUN="${ROOT}/usr/bin/mpiexec -n 4" \
-		CLOG2TOSLOG2="${S}/src/slog2sdk/bin/clog2TOslog2" \
-		check;
-		rc=${?}
-	if [[ "${MPE_IMP}" == mpich2 ]]; then
-		"${ROOT}"usr/bin/mpdallexit || kill $(<"${T}"/mpd.pid)
-	fi
-
-	return ${rc}
-}
-
-src_install() {
-	default
-	rm -f "${D}"/usr/sbin/mpeuninstall || die
-}
diff --git a/sys-cluster/mpich/Manifest b/sys-cluster/mpich/Manifest
deleted file mode 100644
index d96bcb053..000000000
--- a/sys-cluster/mpich/Manifest
+++ /dev/null
@@ -1,5 +0,0 @@
-DIST mpich-3.0.4.tar.gz 10921075 BLAKE2B 341aaac23277aed05a4448ea03d9caf1ee14cfe327a770c95d620fc1ee1ea7bfa6df36860aa44aad162eb6d630d35fdfb30ae9a866d67680ab71c7b4326c109c SHA512 f9d8b2cf561fe5f85c12512ef4dd7b0cf5ec8b53ddb07bfa0d1db2e3c8ae0382c77e0661f46b82ec96b05d18ea2d25328bb84e9528ac06e5925f30ec8ef030d0
-DIST mpich-3.1.3.tar.gz 11487313 BLAKE2B 15d39d8617e7b503bd1cb7d05ef098898736c2d634da2e50f33d7d3a92f2c0aeeb72ec152ee1907ab0658e5c485bd7ed8c2639b8d2abf1839981c542cfe2fc29 SHA512 3071d75e925808c13ea528aaff81a2ee44a4eb9732c74005a0cedd5a710aeafc691d30c7a035ae0aba14bd2b837c1c788202a7612599d3ffac8e5a9299467c09
-DIST mpich-3.1.4.tar.gz 11325036 BLAKE2B 606003f4a9120930841a261698ff9c572f289a88d1db40bf02c8ed89f67a7ba1081652ce39acbf995b7c42e7becb9336fbb262c04873f25a939e5f963eec7de3 SHA512 55bd4d12a42b9ebc116016bd777eb2b8ed8c51e69f5ea5faf823eba0aeb7eadfe2848c4cca3032aa38841a25a4902c07cec2409811149a057c4aa99a25c6b6da
-DIST mpich-3.2.1.tar.gz 11908154 BLAKE2B 86437d9fefae06e32b5d1ba983e6d70f61e6e7a99b92527b966f5dcd1c7fb44fbfe155226c369fb5dede15a554d89ff674eaeeedfb47753b7e73e93ecdca91ce SHA512 659a11cf02302f27eb1db77667dd4c7a4f8008b1d73f5f0f0f28ee6b5d9cca2130bac3d010a132136ba15a25a738ec9cbda67255133aeb42f0d82a2ded23d23d
-DIST mpich-3.2.tar.gz 11862150 BLAKE2B 2e0414b2e11b08a59497fa255d464a2130c754ba8798b99a8b84f7232179906bb27906abbe58b9546833541c238f42ae06df90bfe1133d3ff2d85921d9736452 SHA512 083c51655b4355827bd7fa4fe528046e2bc77b7747d869ff87b79fa324c3cc2a9b5640ccb7271490ccc0dd627e354a33a449bbab448501bbfddcfe5f999ee717
diff --git a/sys-cluster/mpich/files/eselect.mpi.mpich b/sys-cluster/mpich/files/eselect.mpi.mpich
deleted file mode 100644
index 703d71176..000000000
--- a/sys-cluster/mpich/files/eselect.mpi.mpich
+++ /dev/null
@@ -1,8 +0,0 @@
-MPI_CC=@ROOT@usr/bin/mpicc
-MPI_CXX=@ROOT@usr/bin/mpicxx
-MPI_F77=@ROOT@usr/bin/mpif77
-MPI_FC=@ROOT@usr/bin/mpif90
-CLASS_BASE_MPI_IMP=@BASE_IMP@
-PATH=@ROOT@usr/bin
-MANPATH=@ROOT@usr/share/man
-LD_LIBRARY_PATH=@ROOT@usr/@LIBDIR@
diff --git a/sys-cluster/mpich/files/mpich-3.2.1-hwloc2.patch b/sys-cluster/mpich/files/mpich-3.2.1-hwloc2.patch
deleted file mode 100644
index 415a40932..000000000
--- a/sys-cluster/mpich/files/mpich-3.2.1-hwloc2.patch
+++ /dev/null
@@ -1,42 +0,0 @@
-From ab59467c51206ac72546e4b734a1b41bf3d0345d Mon Sep 17 00:00:00 2001
-From: Kavitha Tiptur Madhu <kmadhu@anl.gov>
-Date: Fri, 19 Jan 2018 10:44:56 -0600
-Subject: [PATCH] hydra: remove replicate membind option
-
-The "replicate" option of membind is not well supported on a number of
-operating systems, and has been removed from hwloc (in v2.0) as well.
-This patch gets rid of that option in Hydra, in preparation for an
-upgrade to hwloc-2.0.
-
-Signed-off-by: Pavan Balaji <balaji@anl.gov>
----
- src/pm/hydra/tools/topo/hwloc/topo_hwloc.c | 3 ---
- src/pm/hydra/ui/mpich/utils.c              | 1 -
- 2 files changed, 4 deletions(-)
-
-diff --git a/src/pm/hydra/tools/topo/hwloc/topo_hwloc.c b/src/pm/hydra/tools/topo/hwloc/topo_hwloc.c
-index ce15fe7702..74029fad61 100644
---- a/src/pm/hydra/tools/topo/hwloc/topo_hwloc.c
-+++ b/src/pm/hydra/tools/topo/hwloc/topo_hwloc.c
-@@ -424,9 +424,6 @@ HYD_status HYDT_topo_hwloc_init(const char *binding, const char *mapping, const
-     else if (!strncmp(membind, "interleave:", strlen("interleave:"))) {
-         HYDT_topo_hwloc_info.membind = HWLOC_MEMBIND_INTERLEAVE;
-     }
--    else if (!strncmp(membind, "replicate:", strlen("replicate:"))) {
--        HYDT_topo_hwloc_info.membind = HWLOC_MEMBIND_REPLICATE;
--    }
-     else {
-         HYDU_ERR_SETANDJUMP(status, HYD_INTERNAL_ERROR,
-                             "unrecognized membind policy \"%s\"\n", membind);
-diff --git a/src/pm/hydra/ui/mpich/utils.c b/src/pm/hydra/ui/mpich/utils.c
-index 9e18a754b5..a9c9dde015 100644
---- a/src/pm/hydra/ui/mpich/utils.c
-+++ b/src/pm/hydra/ui/mpich/utils.c
-@@ -940,7 +940,6 @@ static void bind_to_help_fn(void)
-     printf("            nexttouch         -- closest to process that next touches memory\n");
-     printf("            bind:<list>       -- bind to memory node list\n");
-     printf("            interleave:<list> -- interleave among memory node list\n");
--    printf("            replicate:<list>  -- replicate among memory node list\n");
- }
- 
- static HYD_status bind_to_fn(char *arg, char ***argv)
diff --git a/sys-cluster/mpich/metadata.xml b/sys-cluster/mpich/metadata.xml
deleted file mode 100644
index 6cbe440fa..000000000
--- a/sys-cluster/mpich/metadata.xml
+++ /dev/null
@@ -1,21 +0,0 @@
-<?xml version="1.0" encoding="UTF-8"?>
-<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
-<pkgmetadata>
-	<maintainer type="person">
-		<email>jsbronder@gentoo.org</email>
-		<name>Justin Bronder</name>
-	</maintainer>
-	<maintainer type="person">
-		<email>balaji@mcs.anl.gov</email>
-		<name>Pavan Balaji</name>
-		<description>Upstream Contact</description>
-	</maintainer>
-	<maintainer type="project">
-		<email>cluster@gentoo.org</email>
-		<name>Gentoo Cluster Project</name>
-	</maintainer>
-	<use>
-		<flag name="mpi-threads">Enable MPI_THREAD_MULTIPLE</flag>
-		<flag name="romio">Build the ROMIO MPI-IO component</flag>
-	</use>
-</pkgmetadata>
diff --git a/sys-cluster/mpich/mpich-3.0.4.ebuild b/sys-cluster/mpich/mpich-3.0.4.ebuild
deleted file mode 100644
index 6a32941cd..000000000
--- a/sys-cluster/mpich/mpich-3.0.4.ebuild
+++ /dev/null
@@ -1,121 +0,0 @@
-# Copyright 1999-2014 Gentoo Foundation
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=5
-
-FORTRAN_NEEDED=fortran
-
-inherit fortran-2 mpi
-
-MY_PV=${PV/_/}
-DESCRIPTION="A high performance and portable MPI implementation"
-HOMEPAGE="http://www.mpich.org/"
-SRC_URI="http://www.mpich.org/static/downloads/${PV}/${P}.tar.gz"
-
-SLOT="0"
-LICENSE="mpich"
-KEYWORDS="~amd64 ~x86"
-IUSE="+cxx doc fortran mpi-threads romio threads"
-
-COMMON_DEPEND="
-	dev-libs/libaio
-	sys-apps/hwloc
-	romio? ( net-fs/nfs-utils )
-	$(mpi_imp_deplist)"
-
-DEPEND="${COMMON_DEPEND}
-	dev-lang/perl
-	sys-devel/libtool"
-
-RDEPEND="${COMMON_DEPEND}"
-
-S="${WORKDIR}"/${PN}-${MY_PV}
-
-pkg_setup() {
-	FORTRAN_STANDARD="77 90"
-	fortran-2_pkg_setup
-	MPI_ESELECT_FILE="eselect.mpi.mpich"
-
-	if use mpi-threads && ! use threads; then
-		ewarn "mpi-threads requires threads, assuming that's what you want"
-	fi
-}
-
-src_prepare() {
-	# Using MPICHLIB_LDFLAGS doesn't seem to fully work.
-	sed -i 's| *@WRAPPER_LDFLAGS@ *||' \
-		src/packaging/pkgconfig/mpich.pc.in \
-		src/env/*.in \
-		|| die
-}
-
-src_configure() {
-	local c="--enable-shared"
-
-	# The configure statements can be somewhat confusing, as they
-	# don't all show up in the top level configure, however, they
-	# are picked up in the children directories.
-
-	if use mpi-threads; then
-		# MPI-THREAD requries threading.
-		c="${c} --with-thread-package=pthreads"
-		c="${c} --enable-threads=runtime"
-	else
-		if use threads ; then
-			c="${c} --with-thread-package=pthreads"
-		else
-			c="${c} --with-thread-package=none"
-		fi
-		c="${c} --enable-threads=single"
-	fi
-
-	if ! mpi_classed; then
-		c="${c} --sysconfdir=${EPREFIX}/etc/${PN}"
-		c="${c} --docdir=${EPREFIX}/usr/share/doc/${PF}"
-	else
-		c="${c} --docdir=$(mpi_root)/usr/share/doc/${PF}"
-	fi
-
-	export MPICHLIB_CFLAGS=${CFLAGS}
-	export MPICHLIB_CPPFLAGS=${CPPFLAGS}
-	export MPICHLIB_CXXFLAGS=${CXXFLAGS}
-	export MPICHLIB_FFLAGS=${FFLAGS}
-	export MPICHLIB_FCFLAGS=${FCFLAGS}
-	export MPICHLIB_LDFLAGS=${LDFLAGS}
-	unset CFLAGS CPPFLAGS CXXFLAGS FFLAGS FCFLAGS LDFLAGS
-
-	econf $(mpi_econf_args) ${c} \
-		--with-pm=hydra \
-		--disable-mpe \
-		--disable-fast \
-		--enable-smpcoll \
-		--enable-versioning \
-		--with-hwloc-prefix=/usr \
-		$(use_enable romio) \
-		$(use_enable cxx) \
-		$(use_enable fortran f77) \
-		$(use_enable fortran fc)
-}
-
-src_test() {
-	emake -j1 check
-}
-
-src_install() {
-	local d=$(echo ${ED}/$(mpi_root)/ | sed 's,///*,/,g')
-
-	default
-
-	mpi_dodir /usr/share/doc/${PF}
-	mpi_dodoc COPYRIGHT README{,.envvar} CHANGES RELEASE_NOTES
-	mpi_newdoc src/pm/hydra/README README.hydra
-	if use romio; then
-		mpi_newdoc src/mpi/romio/README README.romio
-	fi
-
-	if ! use doc; then
-		rm -rf "${d}"usr/share/doc/${PF}/www*
-	fi
-
-	mpi_imp_add_eselect
-}
diff --git a/sys-cluster/mpich/mpich-3.1.3-r2.ebuild b/sys-cluster/mpich/mpich-3.1.3-r2.ebuild
deleted file mode 100644
index 4657ded7f..000000000
--- a/sys-cluster/mpich/mpich-3.1.3-r2.ebuild
+++ /dev/null
@@ -1,121 +0,0 @@
-# Copyright 1999-2014 Gentoo Foundation
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=5
-
-FORTRAN_NEEDED=fortran
-
-inherit fortran-2 mpi
-
-MY_PV=${PV/_/}
-DESCRIPTION="A high performance and portable MPI implementation"
-HOMEPAGE="http://www.mpich.org/"
-SRC_URI="http://www.mpich.org/static/downloads/${PV}/${P}.tar.gz"
-
-SLOT="0"
-LICENSE="mpich"
-KEYWORDS="~amd64 ~x86 ~amd64-linux ~x86-linux"
-IUSE="+cxx doc fortran mpi-threads romio threads"
-
-COMMON_DEPEND="
-	dev-libs/libaio
-	>=sys-apps/hwloc-1.9
-	romio? ( net-fs/nfs-utils )
-	$(mpi_imp_deplist)"
-
-DEPEND="${COMMON_DEPEND}
-	dev-lang/perl
-	sys-devel/libtool"
-
-RDEPEND="${COMMON_DEPEND}"
-
-S="${WORKDIR}"/${PN}-${MY_PV}
-
-pkg_setup() {
-	FORTRAN_STANDARD="77 90"
-	fortran-2_pkg_setup
-	MPI_ESELECT_FILE="eselect.mpi.mpich"
-
-	if use mpi-threads && ! use threads; then
-		ewarn "mpi-threads requires threads, assuming that's what you want"
-	fi
-}
-
-src_prepare() {
-	# Using MPICHLIB_LDFLAGS doesn't seem to fully work.
-	sed -i 's| *@WRAPPER_LDFLAGS@ *||' \
-		src/packaging/pkgconfig/mpich.pc.in \
-		src/env/*.in \
-		|| die
-}
-
-src_configure() {
-	local c="--enable-shared"
-
-	# The configure statements can be somewhat confusing, as they
-	# don't all show up in the top level configure, however, they
-	# are picked up in the children directories.
-
-	if use mpi-threads; then
-		# MPI-THREAD requries threading.
-		c="${c} --with-thread-package=pthreads"
-		c="${c} --enable-threads=runtime"
-	else
-		if use threads ; then
-			c="${c} --with-thread-package=pthreads"
-		else
-			c="${c} --with-thread-package=none"
-		fi
-		c="${c} --enable-threads=single"
-	fi
-
-	if ! mpi_classed; then
-		c="${c} --sysconfdir=${EPREFIX}/etc/${PN}"
-		c="${c} --docdir=${EPREFIX}/usr/share/doc/${PF}"
-	else
-		c="${c} --docdir=$(mpi_root)/usr/share/doc/${PF}"
-	fi
-
-	export MPICHLIB_CFLAGS=${CFLAGS}
-	export MPICHLIB_CPPFLAGS=${CPPFLAGS}
-	export MPICHLIB_CXXFLAGS=${CXXFLAGS}
-	export MPICHLIB_FFLAGS=${FFLAGS}
-	export MPICHLIB_FCFLAGS=${FCFLAGS}
-	export MPICHLIB_LDFLAGS=${LDFLAGS}
-	unset CFLAGS CPPFLAGS CXXFLAGS FFLAGS FCFLAGS LDFLAGS
-
-	econf $(mpi_econf_args) ${c} \
-		--with-pm=hydra \
-		--disable-mpe \
-		--disable-fast \
-		--enable-smpcoll \
-		--enable-versioning \
-		--with-hwloc-prefix=/usr \
-		$(use_enable romio) \
-		$(use_enable cxx) \
-		$(use_enable fortran f77) \
-		$(use_enable fortran fc)
-}
-
-src_test() {
-	emake -j1 check
-}
-
-src_install() {
-	local d=$(echo ${ED}/$(mpi_root)/ | sed 's,///*,/,g')
-
-	default
-
-	mpi_dodir /usr/share/doc/${PF}
-	mpi_dodoc COPYRIGHT README{,.envvar} CHANGES RELEASE_NOTES
-	mpi_newdoc src/pm/hydra/README README.hydra
-	if use romio; then
-		mpi_newdoc src/mpi/romio/README README.romio
-	fi
-
-	if ! use doc; then
-		rm -rf "${d}"usr/share/doc/${PF}/www*
-	fi
-
-	mpi_imp_add_eselect
-}
diff --git a/sys-cluster/mpich/mpich-3.1.4-r1.ebuild b/sys-cluster/mpich/mpich-3.1.4-r1.ebuild
deleted file mode 100644
index 2db9c9e60..000000000
--- a/sys-cluster/mpich/mpich-3.1.4-r1.ebuild
+++ /dev/null
@@ -1,121 +0,0 @@
-# Copyright 1999-2015 Gentoo Foundation
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=5
-
-FORTRAN_NEEDED=fortran
-
-inherit fortran-2 mpi
-
-MY_PV=${PV/_/}
-DESCRIPTION="A high performance and portable MPI implementation"
-HOMEPAGE="http://www.mpich.org/"
-SRC_URI="http://www.mpich.org/static/downloads/${PV}/${P}.tar.gz"
-
-SLOT="0"
-LICENSE="mpich"
-KEYWORDS="~amd64 ~x86 ~amd64-linux ~x86-linux"
-IUSE="+cxx doc fortran mpi-threads romio threads"
-
-COMMON_DEPEND="
-	dev-libs/libaio
-	>=sys-apps/hwloc-1.9
-	romio? ( net-fs/nfs-utils )
-	$(mpi_imp_deplist)"
-
-DEPEND="${COMMON_DEPEND}
-	dev-lang/perl
-	sys-devel/libtool"
-
-RDEPEND="${COMMON_DEPEND}"
-
-S="${WORKDIR}"/${PN}-${MY_PV}
-
-pkg_setup() {
-	FORTRAN_STANDARD="77 90"
-	fortran-2_pkg_setup
-	MPI_ESELECT_FILE="eselect.mpi.mpich"
-
-	if use mpi-threads && ! use threads; then
-		ewarn "mpi-threads requires threads, assuming that's what you want"
-	fi
-}
-
-src_prepare() {
-	# Using MPICHLIB_LDFLAGS doesn't seem to fully work.
-	sed -i 's| *@WRAPPER_LDFLAGS@ *||' \
-		src/packaging/pkgconfig/mpich.pc.in \
-		src/env/*.in \
-		|| die
-}
-
-src_configure() {
-	local c="--enable-shared"
-	local hydra_c="--with-hwloc-prefix=/usr"
-
-	# The configure statements can be somewhat confusing, as they
-	# don't all show up in the top level configure, however, they
-	# are picked up in the children directories.  Hence the separate
-	# local vars.
-
-	if use mpi-threads; then
-		# MPI-THREAD requries threading.
-		c="${c} --with-thread-package=pthreads"
-		c="${c} --enable-threads=runtime"
-	else
-		if use threads ; then
-			c="${c} --with-thread-package=pthreads"
-		else
-			c="${c} --with-thread-package=none"
-		fi
-		c="${c} --enable-threads=single"
-	fi
-
-	if ! mpi_classed; then
-		c="${c} --sysconfdir=${EPREFIX}/etc/${PN}"
-		c="${c} --docdir=${EPREFIX}/usr/share/doc/${PF}"
-	else
-		c="${c} --docdir=$(mpi_root)/usr/share/doc/${PF}"
-	fi
-
-	export MPICHLIB_CFLAGS=${CFLAGS}
-	export MPICHLIB_CPPFLAGS=${CPPFLAGS}
-	export MPICHLIB_CXXFLAGS=${CXXFLAGS}
-	export MPICHLIB_FFLAGS=${FFLAGS}
-	export MPICHLIB_FCFLAGS=${FCFLAGS}
-	export MPICHLIB_LDFLAGS=${LDFLAGS}
-	unset CFLAGS CPPFLAGS CXXFLAGS FFLAGS FCFLAGS LDFLAGS
-
-	econf $(mpi_econf_args) ${c} \
-		--with-pm=hydra \
-		--disable-fast \
-		--enable-versioning \
-		${hydra_c} \
-		$(use_enable romio) \
-		$(use_enable cxx) \
-		$(use_enable fortran f77) \
-		$(use_enable fortran fc)
-}
-
-src_test() {
-	emake -j1 check
-}
-
-src_install() {
-	local d=$(echo ${ED}/$(mpi_root)/ | sed 's,///*,/,g')
-
-	default
-
-	mpi_dodir /usr/share/doc/${PF}
-	mpi_dodoc COPYRIGHT README{,.envvar} CHANGES RELEASE_NOTES
-	mpi_newdoc src/pm/hydra/README README.hydra
-	if use romio; then
-		mpi_newdoc src/mpi/romio/README README.romio
-	fi
-
-	if ! use doc; then
-		rm -rf "${d}"usr/share/doc/${PF}/www*
-	fi
-
-	mpi_imp_add_eselect
-}
diff --git a/sys-cluster/mpich/mpich-3.2-r1.ebuild b/sys-cluster/mpich/mpich-3.2-r1.ebuild
deleted file mode 100644
index 2db9c9e60..000000000
--- a/sys-cluster/mpich/mpich-3.2-r1.ebuild
+++ /dev/null
@@ -1,121 +0,0 @@
-# Copyright 1999-2015 Gentoo Foundation
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=5
-
-FORTRAN_NEEDED=fortran
-
-inherit fortran-2 mpi
-
-MY_PV=${PV/_/}
-DESCRIPTION="A high performance and portable MPI implementation"
-HOMEPAGE="http://www.mpich.org/"
-SRC_URI="http://www.mpich.org/static/downloads/${PV}/${P}.tar.gz"
-
-SLOT="0"
-LICENSE="mpich"
-KEYWORDS="~amd64 ~x86 ~amd64-linux ~x86-linux"
-IUSE="+cxx doc fortran mpi-threads romio threads"
-
-COMMON_DEPEND="
-	dev-libs/libaio
-	>=sys-apps/hwloc-1.9
-	romio? ( net-fs/nfs-utils )
-	$(mpi_imp_deplist)"
-
-DEPEND="${COMMON_DEPEND}
-	dev-lang/perl
-	sys-devel/libtool"
-
-RDEPEND="${COMMON_DEPEND}"
-
-S="${WORKDIR}"/${PN}-${MY_PV}
-
-pkg_setup() {
-	FORTRAN_STANDARD="77 90"
-	fortran-2_pkg_setup
-	MPI_ESELECT_FILE="eselect.mpi.mpich"
-
-	if use mpi-threads && ! use threads; then
-		ewarn "mpi-threads requires threads, assuming that's what you want"
-	fi
-}
-
-src_prepare() {
-	# Using MPICHLIB_LDFLAGS doesn't seem to fully work.
-	sed -i 's| *@WRAPPER_LDFLAGS@ *||' \
-		src/packaging/pkgconfig/mpich.pc.in \
-		src/env/*.in \
-		|| die
-}
-
-src_configure() {
-	local c="--enable-shared"
-	local hydra_c="--with-hwloc-prefix=/usr"
-
-	# The configure statements can be somewhat confusing, as they
-	# don't all show up in the top level configure, however, they
-	# are picked up in the children directories.  Hence the separate
-	# local vars.
-
-	if use mpi-threads; then
-		# MPI-THREAD requries threading.
-		c="${c} --with-thread-package=pthreads"
-		c="${c} --enable-threads=runtime"
-	else
-		if use threads ; then
-			c="${c} --with-thread-package=pthreads"
-		else
-			c="${c} --with-thread-package=none"
-		fi
-		c="${c} --enable-threads=single"
-	fi
-
-	if ! mpi_classed; then
-		c="${c} --sysconfdir=${EPREFIX}/etc/${PN}"
-		c="${c} --docdir=${EPREFIX}/usr/share/doc/${PF}"
-	else
-		c="${c} --docdir=$(mpi_root)/usr/share/doc/${PF}"
-	fi
-
-	export MPICHLIB_CFLAGS=${CFLAGS}
-	export MPICHLIB_CPPFLAGS=${CPPFLAGS}
-	export MPICHLIB_CXXFLAGS=${CXXFLAGS}
-	export MPICHLIB_FFLAGS=${FFLAGS}
-	export MPICHLIB_FCFLAGS=${FCFLAGS}
-	export MPICHLIB_LDFLAGS=${LDFLAGS}
-	unset CFLAGS CPPFLAGS CXXFLAGS FFLAGS FCFLAGS LDFLAGS
-
-	econf $(mpi_econf_args) ${c} \
-		--with-pm=hydra \
-		--disable-fast \
-		--enable-versioning \
-		${hydra_c} \
-		$(use_enable romio) \
-		$(use_enable cxx) \
-		$(use_enable fortran f77) \
-		$(use_enable fortran fc)
-}
-
-src_test() {
-	emake -j1 check
-}
-
-src_install() {
-	local d=$(echo ${ED}/$(mpi_root)/ | sed 's,///*,/,g')
-
-	default
-
-	mpi_dodir /usr/share/doc/${PF}
-	mpi_dodoc COPYRIGHT README{,.envvar} CHANGES RELEASE_NOTES
-	mpi_newdoc src/pm/hydra/README README.hydra
-	if use romio; then
-		mpi_newdoc src/mpi/romio/README README.romio
-	fi
-
-	if ! use doc; then
-		rm -rf "${d}"usr/share/doc/${PF}/www*
-	fi
-
-	mpi_imp_add_eselect
-}
diff --git a/sys-cluster/mpich/mpich-3.2-r2.ebuild b/sys-cluster/mpich/mpich-3.2-r2.ebuild
deleted file mode 100644
index dc2e80944..000000000
--- a/sys-cluster/mpich/mpich-3.2-r2.ebuild
+++ /dev/null
@@ -1,136 +0,0 @@
-# Copyright 1999-2016 Gentoo Foundation
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=6
-
-FORTRAN_NEEDED=fortran
-FORTRAN_STANDARD="77 90"
-
-inherit fortran-2 multilib-minimal mpi
-
-MY_PV=${PV/_/}
-DESCRIPTION="A high performance and portable MPI implementation"
-HOMEPAGE="http://www.mpich.org/"
-SRC_URI="http://www.mpich.org/static/downloads/${PV}/${P}.tar.gz"
-
-SLOT="0"
-LICENSE="mpich"
-KEYWORDS="~amd64 ~x86 ~amd64-linux ~x86-linux"
-IUSE="+cxx doc fortran mpi-threads romio threads"
-
-COMMON_DEPEND="
-	>=dev-libs/libaio-0.3.109-r5[${MULTILIB_USEDEP}]
-	>=sys-apps/hwloc-1.10.0-r2[${MULTILIB_USEDEP}]
-	romio? ( net-fs/nfs-utils )
-	$(mpi_imp_deplist)"
-
-DEPEND="${COMMON_DEPEND}
-	dev-lang/perl
-	sys-devel/libtool"
-
-RDEPEND="${COMMON_DEPEND}"
-
-S="${WORKDIR}"/${PN}-${MY_PV}
-
-MULTILIB_WRAPPED_HEADERS=(
-	/usr/include/mpicxx.h
-	/usr/include/mpi.h
-	/usr/include/opa_config.h
-)
-
-src_prepare() {
-	default
-
-	# Using MPICHLIB_LDFLAGS doesn't seem to fully work.
-	sed -i 's| *@WRAPPER_LDFLAGS@ *||' \
-		src/packaging/pkgconfig/mpich.pc.in \
-		src/env/*.in \
-		|| die
-}
-
-multilib_src_configure() {
-	# The configure statements can be somewhat confusing, as they
-	# don't all show up in the top level configure, however, they
-	# are picked up in the children directories.  Hence the separate
-	# local vars.
-
-	local c=
-	if use mpi-threads; then
-		# MPI-THREAD requries threading.
-		c="${c} --with-thread-package=pthreads"
-		c="${c} --enable-threads=runtime"
-	else
-		if use threads ; then
-			c="${c} --with-thread-package=pthreads"
-		else
-			c="${c} --with-thread-package=none"
-		fi
-		c="${c} --enable-threads=single"
-	fi
-
-	if ! mpi_classed; then
-		c="${c} --sysconfdir=${EPREFIX}/etc/${PN}"
-		c="${c} --docdir=${EPREFIX}/usr/share/doc/${PF}"
-	else
-		c="${c} --docdir=$(mpi_root)/usr/share/doc/${PF}"
-	fi
-
-	export MPICHLIB_CFLAGS="${CFLAGS}"
-	export MPICHLIB_CPPFLAGS="${CPPFLAGS}"
-	export MPICHLIB_CXXFLAGS="${CXXFLAGS}"
-	export MPICHLIB_FFLAGS="${FFLAGS}"
-	export MPICHLIB_FCFLAGS="${FCFLAGS}"
-	export MPICHLIB_LDFLAGS="${LDFLAGS}"
-	unset CFLAGS CPPFLAGS CXXFLAGS FFLAGS FCFLAGS LDFLAGS
-
-	ECONF_SOURCE=${S} econf $(mpi_econf_args) \
-		--enable-shared \
-		--with-hwloc-prefix="${EPREFIX}/usr" \
-		${c} \
-		--with-pm=hydra \
-		--disable-fast \
-		--enable-versioning \
-		$(use_enable romio) \
-		$(use_enable cxx) \
-		$(multilib_native_use_enable fortran fortran all)
-}
-
-multilib_src_test() {
-	emake -j1 check
-}
-
-multilib_src_install() {
-	default
-
-	# fortran header cannot be wrapped (bug #540508), workaround part 1
-	if multilib_is_native_abi && use fortran; then
-		mkdir "${T}"/fortran || die
-		mv "${ED}"/$(mpi_root)/usr/include/mpif* "${T}"/fortran || die
-		mv "${ED}"/$(mpi_root)/usr/include/*.mod "${T}"/fortran || die
-	else
-		# some fortran files get installed unconditionally
-		rm "${ED}"/$(mpi_root)/usr/include/mpif* "${ED}"usr/include/*.mod || die
-	fi
-}
-
-multilib_src_install_all() {
-	# fortran header cannot be wrapped (bug #540508), workaround part 2
-	if use fortran; then
-		mv "${T}"/fortran/* "${ED}"/$(mpi_root)/usr/include || die
-	fi
-
-	mpi_dodir /usr/share/doc/${PF}
-	mpi_dodoc COPYRIGHT README{,.envvar} CHANGES RELEASE_NOTES
-	mpi_newdoc src/pm/hydra/README README.hydra
-	if use romio; then
-		mpi_newdoc src/mpi/romio/README README.romio
-	fi
-
-	local d=$(echo ${ED}/$(mpi_root)/ | sed 's,///*,/,g')
-	if ! use doc; then
-		rm -rf "${d}"usr/share/doc/${PF}/www* || die
-	fi
-
-	MPI_ESELECT_FILE="eselect.mpi.mpich"
-	mpi_imp_add_eselect
-}
diff --git a/sys-cluster/mpich/mpich-3.2.1.ebuild b/sys-cluster/mpich/mpich-3.2.1.ebuild
deleted file mode 100644
index ae3166474..000000000
--- a/sys-cluster/mpich/mpich-3.2.1.ebuild
+++ /dev/null
@@ -1,140 +0,0 @@
-# Copyright 1999-2018 Gentoo Authors
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=6
-
-FORTRAN_NEEDED=fortran
-FORTRAN_STANDARD="77 90"
-
-inherit fortran-2 multilib-minimal mpi
-
-MY_PV=${PV/_/}
-DESCRIPTION="A high performance and portable MPI implementation"
-HOMEPAGE="http://www.mpich.org/"
-SRC_URI="http://www.mpich.org/static/downloads/${PV}/${P}.tar.gz"
-
-SLOT="0"
-LICENSE="mpich"
-KEYWORDS="~amd64 ~x86 ~amd64-linux ~x86-linux"
-IUSE="+cxx doc fortran mpi-threads romio threads"
-
-COMMON_DEPEND="
-	>=dev-libs/libaio-0.3.109-r5[${MULTILIB_USEDEP}]
-	>=sys-apps/hwloc-1.10.0-r2[${MULTILIB_USEDEP}]
-	romio? ( net-fs/nfs-utils )
-	$(mpi_imp_deplist)"
-
-DEPEND="${COMMON_DEPEND}
-	dev-lang/perl
-	sys-devel/libtool"
-
-RDEPEND="${COMMON_DEPEND}"
-
-PATCHES=(
-	"${FILESDIR}/${P}-hwloc2.patch"
-)
-
-S="${WORKDIR}"/${PN}-${MY_PV}
-
-MULTILIB_WRAPPED_HEADERS=(
-	/usr/include/mpicxx.h
-	/usr/include/mpi.h
-	/usr/include/opa_config.h
-)
-
-src_prepare() {
-	default
-
-	# Using MPICHLIB_LDFLAGS doesn't seem to fully work.
-	sed -i 's| *@WRAPPER_LDFLAGS@ *||' \
-		src/packaging/pkgconfig/mpich.pc.in \
-		src/env/*.in \
-		|| die
-}
-
-multilib_src_configure() {
-	# The configure statements can be somewhat confusing, as they
-	# don't all show up in the top level configure, however, they
-	# are picked up in the children directories.  Hence the separate
-	# local vars.
-
-	local c=
-	if use mpi-threads; then
-		# MPI-THREAD requries threading.
-		c="${c} --with-thread-package=pthreads"
-		c="${c} --enable-threads=runtime"
-	else
-		if use threads ; then
-			c="${c} --with-thread-package=pthreads"
-		else
-			c="${c} --with-thread-package=none"
-		fi
-		c="${c} --enable-threads=single"
-	fi
-
-	if ! mpi_classed; then
-		c="${c} --sysconfdir=${EPREFIX}/etc/${PN}"
-		c="${c} --docdir=${EPREFIX}/usr/share/doc/${PF}"
-	else
-		c="${c} --docdir=$(mpi_root)/usr/share/doc/${PF}"
-	fi
-
-	export MPICHLIB_CFLAGS="${CFLAGS}"
-	export MPICHLIB_CPPFLAGS="${CPPFLAGS}"
-	export MPICHLIB_CXXFLAGS="${CXXFLAGS}"
-	export MPICHLIB_FFLAGS="${FFLAGS}"
-	export MPICHLIB_FCFLAGS="${FCFLAGS}"
-	export MPICHLIB_LDFLAGS="${LDFLAGS}"
-	unset CFLAGS CPPFLAGS CXXFLAGS FFLAGS FCFLAGS LDFLAGS
-
-	ECONF_SOURCE=${S} econf $(mpi_econf_args) \
-		--enable-shared \
-		--with-hwloc-prefix="${EPREFIX}/usr" \
-		${c} \
-		--with-pm=hydra \
-		--disable-fast \
-		--enable-versioning \
-		$(use_enable romio) \
-		$(use_enable cxx) \
-		$(multilib_native_use_enable fortran fortran all)
-}
-
-multilib_src_test() {
-	emake -j1 check
-}
-
-multilib_src_install() {
-	default
-
-	# fortran header cannot be wrapped (bug #540508), workaround part 1
-	if multilib_is_native_abi && use fortran; then
-		mkdir "${T}"/fortran || die
-		mv "${ED}"/$(mpi_root)/usr/include/mpif* "${T}"/fortran || die
-		mv "${ED}"/$(mpi_root)/usr/include/*.mod "${T}"/fortran || die
-	else
-		# some fortran files get installed unconditionally
-		rm "${ED}"/$(mpi_root)/usr/include/mpif* "${ED}"usr/include/*.mod || die
-	fi
-}
-
-multilib_src_install_all() {
-	# fortran header cannot be wrapped (bug #540508), workaround part 2
-	if use fortran; then
-		mv "${T}"/fortran/* "${ED}"/$(mpi_root)/usr/include || die
-	fi
-
-	mpi_dodir /usr/share/doc/${PF}
-	mpi_dodoc COPYRIGHT README{,.envvar} CHANGES RELEASE_NOTES
-	mpi_newdoc src/pm/hydra/README README.hydra
-	if use romio; then
-		mpi_newdoc src/mpi/romio/README README.romio
-	fi
-
-	local d=$(echo ${ED}/$(mpi_root)/ | sed 's,///*,/,g')
-	if ! use doc; then
-		rm -rf "${d}"usr/share/doc/${PF}/www* || die
-	fi
-
-	MPI_ESELECT_FILE="eselect.mpi.mpich"
-	mpi_imp_add_eselect
-}
diff --git a/sys-cluster/mpich2/Manifest b/sys-cluster/mpich2/Manifest
deleted file mode 100644
index 8ae78c914..000000000
--- a/sys-cluster/mpich2/Manifest
+++ /dev/null
@@ -1 +0,0 @@
-DIST mpich2-1.5.tar.gz 22826035 BLAKE2B 75075fbdd0111725e5bce1e828561125cdba2c91ecfb5af7c6ebd0603f8de05aa5813e57bf05b276607d0a6c0a378862b5631ab988f87e67299e7f651efdc76b SHA512 01ef68accdd60af805705c1c7a144a570eee6f01984939fe151a093f963c956fba366247b1058885ba1a2ff626278d30e928e03d394bd6cf2a4b6dab99586c15
diff --git a/sys-cluster/mpich2/files/0001-MPD_CONF_FILE-should-be-readable.patch b/sys-cluster/mpich2/files/0001-MPD_CONF_FILE-should-be-readable.patch
deleted file mode 100644
index fa685e364..000000000
--- a/sys-cluster/mpich2/files/0001-MPD_CONF_FILE-should-be-readable.patch
+++ /dev/null
@@ -1,32 +0,0 @@
-From 4daa0519150f38bd322964157157fb3369ee0f38 Mon Sep 17 00:00:00 2001
-From: Justin Bronder <jsbronder@gmail.com>
-Date: Wed, 16 Sep 2009 11:43:59 -0400
-Subject: [PATCH 1/3] MPD_CONF_FILE should be readable
-
-When looking for the MPD_CONF_FILE, the existance is not enough, the
-file also needs to be readable by the current user.
----
- src/pm/mpd/mpdlib.py |    4 ++--
- 1 files changed, 2 insertions(+), 2 deletions(-)
-
-diff --git a/src/pm/mpd/mpdlib.py b/src/pm/mpd/mpdlib.py
-index 8ea8a05..31ddcb4 100644
---- a/src/pm/mpd/mpdlib.py
-+++ b/src/pm/mpd/mpdlib.py
-@@ -1359,11 +1359,11 @@ class MPDParmDB(dict):
-             if os.environ.has_key(k):
-                 self[('env',k)] = os.environ[k]
-     def get_parms_from_rcfile(self,parmsToOverride,errIfMissingFile=0):
--        if os.environ.has_key('MPD_CONF_FILE'):
-+        if os.environ.has_key('MPD_CONF_FILE') and os.access(os.environ['MPD_CONF_FILE'], os.R_OK):
-             parmsRCFilename = os.environ['MPD_CONF_FILE']
-         elif hasattr(os,'getuid')  and  os.getuid() == 0:    # if ROOT
-             parmsRCFilename = os.path.abspath('/etc/mpd.conf')
--        elif os.environ.has_key('HOME'):
-+        elif os.environ.has_key('HOME') and os.access(os.path.join(os.environ['HOME'], '.mpd.conf'), os.R_OK):
-             parmsRCFilename = os.path.join(os.environ['HOME'],'.mpd.conf')
-         elif os.environ.has_key('HOMEPATH'):    # e.g. win32
-             parmsRCFilename = os.path.join(os.environ['HOMEPATH'],'.mpd.conf')
--- 
-1.6.3.3
-
diff --git a/sys-cluster/mpich2/files/0002-mpd_conf_file-search-order.patch b/sys-cluster/mpich2/files/0002-mpd_conf_file-search-order.patch
deleted file mode 100644
index 2bb59e7c2..000000000
--- a/sys-cluster/mpich2/files/0002-mpd_conf_file-search-order.patch
+++ /dev/null
@@ -1,98 +0,0 @@
-From c5c6b5677854d2e835ed7d8d0497ab4f475c63fc Mon Sep 17 00:00:00 2001
-From: Justin Bronder <jsbronder@gmail.com>
-Date: Wed, 16 Sep 2009 11:50:20 -0400
-Subject: [PATCH 2/3] mpd_conf_file search order.
-
-Make sure the search order for mpd.conf is the following:
-    - MPD_CONF_FILE set in environment
-    - .mpd.conf in the user's home directory
-    - The system wide default in SYSCONFDIR/mpd.conf
----
- src/pm/mpd/Makefile.in |    9 ++++++---
- src/pm/mpd/mpdroot.c   |   27 +++++++++++++++++++++++++--
- 2 files changed, 31 insertions(+), 5 deletions(-)
-
-diff --git a/src/pm/mpd/Makefile.in b/src/pm/mpd/Makefile.in
-index e1752f8..4ef65fc 100644
---- a/src/pm/mpd/Makefile.in
-+++ b/src/pm/mpd/Makefile.in
-@@ -74,7 +74,7 @@ mpdroot: ${mpdroot_OBJECTS}
- 	$(C_LINK) -o mpdroot ${mpdroot_OBJECTS} $(LIBS)
- 
- mpdroot.o: ${srcdir}/mpdroot.c ${srcdir}/mpdroot.h mpdconf.h
--	${C_COMPILE} -c  $< 
-+	${C_COMPILE} -DSYSCONFDIR=\"@sysconfdir@\" -c  $< 
- 
- # The following lines provide the right libraries for all example programs
- .c:
-@@ -128,7 +128,10 @@ install: all
- 	@echo "copying python files/links into " $(DESTDIR)${bindir}
- 	-@for cmd in ${PYTHON_SOURCE} ; do \
- 	    if [ ! -s $(srcdir)/$$cmd.py ] ; then continue ; fi ; \
--	    sed -e 's#/usr/bin/env python.*#/usr/bin/env ${PYTHON}#' ${srcdir}/$$cmd.py > $(DESTDIR)${bindir}/temp$$cmd.py ; \
-+		sed \
-+			-e 's#/usr/bin/env python.*#/usr/bin/env ${PYTHON}#' \
-+			-e 's,/etc/mpd.conf,@sysconfdir@/mpd.conf,g' \
-+			${srcdir}/$$cmd.py > $(DESTDIR)${bindir}/temp$$cmd.py ; \
- 	    ${INSTALL} -m 755 $(DESTDIR)${bindir}/temp$$cmd.py $(DESTDIR)${bindir}/$$cmd.py; \
- 	    ( rm -f $(DESTDIR)${bindir}/temp$$cmd.py >/dev/null 2>&1 || exit 0 ) ; \
- 	done
-@@ -210,7 +213,7 @@ mpich2-mpdroot: mpich2-mpdroot.o
- 
- mpich2-mpdroot.o: ${srcdir}/mpdroot.c ${srcdir}/mpdroot.h mpdconf.h
- 	${INSTALL} -m 644 ${srcdir}/mpdroot.c mpich2-mpdroot.c
--	${C_COMPILE} -c mpich2-mpdroot.c
-+	${C_COMPILE} -DSYSCONFDIR=\"@sysconfdir@\" -c mpich2-mpdroot.c
- 	rm -f mpich2-mpdroot.c
- 
- # A special alternate installation target when using multiple process managers
-diff --git a/src/pm/mpd/mpdroot.c b/src/pm/mpd/mpdroot.c
-index 348c7b6..1a4f2a5 100644
---- a/src/pm/mpd/mpdroot.c
-+++ b/src/pm/mpd/mpdroot.c
-@@ -19,6 +19,7 @@ int main(int argc, char *argv[])
-     struct passwd *pwent;
-     char input_line[NAME_LEN+1], secretword[NAME_LEN+1];
-     FILE *conf_file;
-+    char *mpdconf_path = NULL;
- 
-     if ((pwent = getpwuid(getuid())) == NULL)    /* for real id */
-     {
-@@ -26,10 +27,32 @@ int main(int argc, char *argv[])
-         exit(-1);
-     }
- 
--    conf_file = fopen("/etc/mpd.conf","r");
-+    /*
-+     * We look for a readable mpd.conf in the following order.
-+     * - MPD_CONF_FILE set in environment
-+     * - .mpd.conf in the user's home directory
-+     * - The system wide default in SYSCONFDIR/mpd.conf
-+     */
-+    mpdconf_path = getenv("MPD_CONF_FILE");
-+    if ( ! (mpdconf_path && access( mpdconf_path, R_OK ) == 0) ){
-+        /* By far, the largest we'll need */
-+        size_t mpdconf_path_len = strlen(pwent->pw_dir) \
-+            + strlen(SYSCONFDIR) + strlen("/.mpd.conf");
-+
-+        mpdconf_path = (char*) malloc( sizeof(char) * mpdconf_path_len ); 
-+        if ( ! mpdconf_path ){
-+            fprintf( stderr, "%s:  Failed to allocate a buffer for path to mpd.conf\n", argv[0]);
-+            exit(-1);
-+        }
-+        snprintf( mpdconf_path, mpdconf_path_len-1, "%s/.mpd.conf", pwent->pw_dir );
-+        if ( access( mpdconf_path, R_OK ) != 0 )
-+            snprintf( mpdconf_path, mpdconf_path_len-1, "%s/mpd.conf", SYSCONFDIR );
-+    }
-+    conf_file = fopen( mpdconf_path, "r");
-+
-     if (conf_file == NULL)
-     {
--        printf("%s: open failed for root's mpd conf file",argv[0]);
-+        printf("%s: open failed for root's mpd conf file\n",argv[0]);
-         exit(-1);
-     }
-     secretword[0] = '\0';
--- 
-1.6.3.3
-
diff --git a/sys-cluster/mpich2/files/0003-Fix-pkgconfig-for-mpich2-ch3-v1.2.1.patch b/sys-cluster/mpich2/files/0003-Fix-pkgconfig-for-mpich2-ch3-v1.2.1.patch
deleted file mode 100644
index 266990c0b..000000000
--- a/sys-cluster/mpich2/files/0003-Fix-pkgconfig-for-mpich2-ch3-v1.2.1.patch
+++ /dev/null
@@ -1,36 +0,0 @@
-From 6572e098d5463bdcdcb9563ee9a736efed4a01c9 Mon Sep 17 00:00:00 2001
-From: Justin Bronder <jsbronder@gmail.com>
-Date: Tue, 24 Nov 2009 10:27:51 -0500
-Subject: [PATCH] Fix pkgconfig for mpich2-ch3 v1.2.1
-
-Variables were undefined, see http://bugs.gentoo.org/257821
-
-$ pkg-config --list-all
-[lots of output, then]
-Variable 'exec_prefix' not defined in '/usr/lib/pkgconfig/mpich2-ch3.pc'
----
- src/packaging/pkgconfig/mpich2-ch3.pc.in |    8 ++++++--
- 1 files changed, 6 insertions(+), 2 deletions(-)
-
-diff --git a/src/packaging/pkgconfig/mpich2-ch3.pc.in b/src/packaging/pkgconfig/mpich2-ch3.pc.in
-index b061464..275b535 100644
---- a/src/packaging/pkgconfig/mpich2-ch3.pc.in
-+++ b/src/packaging/pkgconfig/mpich2-ch3.pc.in
-@@ -1,8 +1,12 @@
- # this gives access to the mpich2 header files
-+prefix=@prefix@
-+exec_prefix=@exec_prefix@ 
-+libdir=@libdir@
-+includedir=@includedir@
- 
- Name: mpich2
- Description: MPICH2 is an implementation of the Message-Passing Interface (MPI). The goals of MPICH2 are to provide an MPI implementation for important platforms, including clusters, SMPs, and massively parallel processors. It also provides a vehicle for MPI implementation research and for developing new and better parallel programming environments.
- Version: @MPICH2_VERSION@
- Requires: 
--Libs: -L@libdir@ -lmpich -lmpichcxx -lopa @LIBS@
--Cflags: @CFLAGS@ -I@includedir@ -DMPICH_IGNORE_CXX_SEEK
-+Libs: -L${libdir} -lmpich -lmpichcxx -lopa @LIBS@
-+Cflags: @CFLAGS@ -I${includedir} -DMPICH_IGNORE_CXX_SEEK
--- 
-1.6.3.3
-
diff --git a/sys-cluster/mpich2/files/0003-Fix-pkgconfig-for-mpich2-ch3.patch b/sys-cluster/mpich2/files/0003-Fix-pkgconfig-for-mpich2-ch3.patch
deleted file mode 100644
index 04be31337..000000000
--- a/sys-cluster/mpich2/files/0003-Fix-pkgconfig-for-mpich2-ch3.patch
+++ /dev/null
@@ -1,36 +0,0 @@
-From 06eaaf72d12ca70275fd4f403af14bcb2d609718 Mon Sep 17 00:00:00 2001
-From: Justin Bronder <jsbronder@gmail.com>
-Date: Wed, 16 Sep 2009 11:59:57 -0400
-Subject: [PATCH 3/3] Fix pkgconfig for mpich2-ch3
-
-Variables were undefined, see http://bugs.gentoo.org/257821
-
-$ pkg-config --list-all
-[lots of output, then]
-Variable 'exec_prefix' not defined in '/usr/lib/pkgconfig/mpich2-ch3.pc'
----
- src/packaging/pkgconfig/mpich2-ch3.pc.in |    8 ++++++--
- 1 files changed, 6 insertions(+), 2 deletions(-)
-
-diff --git a/src/packaging/pkgconfig/mpich2-ch3.pc.in b/src/packaging/pkgconfig/mpich2-ch3.pc.in
-index df10b7f..8621ef5 100644
---- a/src/packaging/pkgconfig/mpich2-ch3.pc.in
-+++ b/src/packaging/pkgconfig/mpich2-ch3.pc.in
-@@ -1,8 +1,12 @@
- # this gives access to the mpich2 header files
-+prefix=@prefix@
-+exec_prefix=@exec_prefix@ 
-+libdir=@libdir@
-+includedir=@includedir@
- 
- Name: mpich2
- Description: MPICH2 is an implementation of the Message-Passing Interface (MPI). The goals of MPICH2 are to provide an MPI implementation for important platforms, including clusters, SMPs, and massively parallel processors. It also provides a vehicle for MPI implementation research and for developing new and better parallel programming environments.
- Version: @VERSION@
- Requires: 
--Libs: -L@libdir@ -lmpich -lmpichcxx @LIBS@
--Cflags: @CFLAGS@ -I@includedir@ -DMPICH_IGNORE_CXX_SEEK
-+Libs: -L${libdir} -lmpich -lmpichcxx @LIBS@
-+Cflags: @CFLAGS@ -I${includedir} -DMPICH_IGNORE_CXX_SEEK
--- 
-1.6.3.3
-
diff --git a/sys-cluster/mpich2/files/eselect.mpi.mpich2 b/sys-cluster/mpich2/files/eselect.mpi.mpich2
deleted file mode 100644
index 703d71176..000000000
--- a/sys-cluster/mpich2/files/eselect.mpi.mpich2
+++ /dev/null
@@ -1,8 +0,0 @@
-MPI_CC=@ROOT@usr/bin/mpicc
-MPI_CXX=@ROOT@usr/bin/mpicxx
-MPI_F77=@ROOT@usr/bin/mpif77
-MPI_FC=@ROOT@usr/bin/mpif90
-CLASS_BASE_MPI_IMP=@BASE_IMP@
-PATH=@ROOT@usr/bin
-MANPATH=@ROOT@usr/share/man
-LD_LIBRARY_PATH=@ROOT@usr/@LIBDIR@
diff --git a/sys-cluster/mpich2/files/fix-pkg-config-files.patch b/sys-cluster/mpich2/files/fix-pkg-config-files.patch
deleted file mode 100644
index d9c311e31..000000000
--- a/sys-cluster/mpich2/files/fix-pkg-config-files.patch
+++ /dev/null
@@ -1,119 +0,0 @@
-From cba731049a24735beb660dc236f61070aa6e387a Mon Sep 17 00:00:00 2001
-From: Justin Bronder <jsbronder@gmail.com>
-Date: Thu, 5 Jan 2012 22:20:31 -0500
-Subject: [PATCH] fix pkg config files
-
-Conditionals are not supported.
-https://trac.mcs.anl.gov/projects/mpich2/ticket/1044
----
- configure.in                             |    6 ++++++
- src/packaging/pkgconfig/mpich2-c.pc.in   |    8 +-------
- src/packaging/pkgconfig/mpich2-cxx.pc.in |    8 +-------
- src/packaging/pkgconfig/mpich2-f77.pc.in |    8 +-------
- src/packaging/pkgconfig/mpich2-f90.pc.in |    8 +-------
- 5 files changed, 10 insertions(+), 28 deletions(-)
-
-diff --git a/configure.in b/configure.in
-index 294dc85..44b1010 100644
---- a/configure.in
-+++ b/configure.in
-@@ -5332,6 +5332,12 @@ AC_SUBST(MPICH_TIMER_KIND)
- # Setup other replaceable values
- AC_SUBST(MPILIBNAME)
- AC_SUBST(PMPILIBNAME)
-+PKGCONFIG_PMPILIB=""
-+if test "$NEEDSPLIB" = yes -a test -n "${PMPILIBNAME}" ; then
-+    PKGCONFIG_PMPILIB="-l${PMPILIBNAME}"
-+fi
-+AC_SUBST(PKGCONFIG_PMPILIB)
-+
- # Note that aint_size must be used instead of void_p where the desired check
- # is on the size of MPI_Aint
- aint_size=$ac_cv_sizeof_void_p
-diff --git a/src/packaging/pkgconfig/mpich2-c.pc.in b/src/packaging/pkgconfig/mpich2-c.pc.in
-index 394630b..e0ab3fa 100644
---- a/src/packaging/pkgconfig/mpich2-c.pc.in
-+++ b/src/packaging/pkgconfig/mpich2-c.pc.in
-@@ -4,15 +4,9 @@ exec_prefix=@exec_prefix@
- libdir=@libdir@
- includedir=@includedir@
- 
--if test "@NEEDSPLIB@" = "yes" ; then
--   plib=@PMPILIBNAME@
--else
--   plib=
--fi
--
- Name: mpich2
- Description: MPICH2 is an implementation of the Message-Passing Interface (MPI). The goals of MPICH2 are to provide an MPI implementation for important platforms, including clusters, SMPs, and massively parallel processors. It also provides a vehicle for MPI implementation research and for developing new and better parallel programming environments.
- Version: @MPICH2_VERSION@
- Requires:
--Libs: @WRAPPER_LDFLAGS@ -L${libdir} -l${plib} -l@MPILIBNAME@ @WRAPPER_LIBS@
-+Libs: @WRAPPER_LDFLAGS@ -L${libdir} @PKGCONFIG_PMPILIB@ -l@MPILIBNAME@ @WRAPPER_LIBS@
- Cflags: @WRAPPER_CPPFLAGS@ @WRAPPER_CFLAGS@ -I${includedir}
-diff --git a/src/packaging/pkgconfig/mpich2-cxx.pc.in b/src/packaging/pkgconfig/mpich2-cxx.pc.in
-index 936ade6..d82e184 100644
---- a/src/packaging/pkgconfig/mpich2-cxx.pc.in
-+++ b/src/packaging/pkgconfig/mpich2-cxx.pc.in
-@@ -4,15 +4,9 @@ exec_prefix=@exec_prefix@
- libdir=@libdir@
- includedir=@includedir@
- 
--if test "@NEEDSPLIB@" = "yes" ; then
--   plib=@PMPILIBNAME@
--else
--   plib=
--fi
--
- Name: mpich2
- Description: MPICH2 is an implementation of the Message-Passing Interface (MPI). The goals of MPICH2 are to provide an MPI implementation for important platforms, including clusters, SMPs, and massively parallel processors. It also provides a vehicle for MPI implementation research and for developing new and better parallel programming environments.
- Version: @MPICH2_VERSION@
- Requires:
--Libs: @WRAPPER_LDFLAGS@ -L${libdir} -l${plib} -l@MPILIBNAME@ @WRAPPER_LIBS@
-+Libs: @WRAPPER_LDFLAGS@ -L${libdir} @PKGCONFIG_PMPILIB@ -l@MPILIBNAME@ @WRAPPER_LIBS@
- Cxxflags: @WRAPPER_CPPFLAGS@ @WRAPPER_CXXFLAGS@ -I${includedir}
-diff --git a/src/packaging/pkgconfig/mpich2-f77.pc.in b/src/packaging/pkgconfig/mpich2-f77.pc.in
-index 291462e..193c2ab 100644
---- a/src/packaging/pkgconfig/mpich2-f77.pc.in
-+++ b/src/packaging/pkgconfig/mpich2-f77.pc.in
-@@ -4,15 +4,9 @@ exec_prefix=@exec_prefix@
- libdir=@libdir@
- includedir=@includedir@
- 
--if test "@NEEDSPLIB@" = "yes" ; then
--   plib=@PMPILIBNAME@
--else
--   plib=
--fi
--
- Name: mpich2
- Description: MPICH2 is an implementation of the Message-Passing Interface (MPI). The goals of MPICH2 are to provide an MPI implementation for important platforms, including clusters, SMPs, and massively parallel processors. It also provides a vehicle for MPI implementation research and for developing new and better parallel programming environments.
- Version: @MPICH2_VERSION@
- Requires:
--Libs: @WRAPPER_LDFLAGS@ -L${libdir} -l${plib} -l@MPILIBNAME@ @WRAPPER_LIBS@
-+Libs: @WRAPPER_LDFLAGS@ -L${libdir} @PKGCONFIG_PMPILIB@ -l@MPILIBNAME@ @WRAPPER_LIBS@
- Fflags: @WRAPPER_FFLAGS@ -I${includedir}
-diff --git a/src/packaging/pkgconfig/mpich2-f90.pc.in b/src/packaging/pkgconfig/mpich2-f90.pc.in
-index ca15e18..700976f 100644
---- a/src/packaging/pkgconfig/mpich2-f90.pc.in
-+++ b/src/packaging/pkgconfig/mpich2-f90.pc.in
-@@ -4,15 +4,9 @@ exec_prefix=@exec_prefix@
- libdir=@libdir@
- includedir=@includedir@
- 
--if test "@NEEDSPLIB@" = "yes" ; then
--   plib=@PMPILIBNAME@
--else
--   plib=
--fi
--
- Name: mpich2
- Description: MPICH2 is an implementation of the Message-Passing Interface (MPI). The goals of MPICH2 are to provide an MPI implementation for important platforms, including clusters, SMPs, and massively parallel processors. It also provides a vehicle for MPI implementation research and for developing new and better parallel programming environments.
- Version: @MPICH2_VERSION@
- Requires:
--Libs: @WRAPPER_LDFLAGS@ -L${libdir} -l${plib} -l@MPILIBNAME@ @WRAPPER_LIBS@
-+Libs: @WRAPPER_LDFLAGS@ -L${libdir} @PKGCONFIG_PMPILIB@ -l@MPILIBNAME@ @WRAPPER_LIBS@
- Fcflags: @WRAPPER_FCFLAGS@ -I${includedir}
--- 
-1.7.3.4
-
diff --git a/sys-cluster/mpich2/files/mpd.conf b/sys-cluster/mpich2/files/mpd.conf
deleted file mode 100644
index 07dd98250..000000000
--- a/sys-cluster/mpich2/files/mpd.conf
+++ /dev/null
@@ -1,2 +0,0 @@
-secretword=test69hike
-MPD_SECRETWORD=test69hike
diff --git a/sys-cluster/mpich2/files/mpich2-1.0.8-gforker-install-alt-fix.patch b/sys-cluster/mpich2/files/mpich2-1.0.8-gforker-install-alt-fix.patch
deleted file mode 100644
index 00774049f..000000000
--- a/sys-cluster/mpich2/files/mpich2-1.0.8-gforker-install-alt-fix.patch
+++ /dev/null
@@ -1,12 +0,0 @@
---- mpich2-1.0.8/src/pm/gforker/Makefile.in-orig	2008-11-01 13:18:37.685990975 -0400
-+++ mpich2-1.0.8/src/pm/gforker/Makefile.in	2008-11-01 13:19:03.584804978 -0400
-@@ -176,6 +176,9 @@
- 
- # A special alternate installation target when using multiple process managers
- install-alt: mpiexec
-+	if [ ! -d ${DESTDIR}${exec_prefix} ] ; then $(MKDIR_P) ${DESTDIR}${exec_prefix} ; fi
-+	if [ ! -d ${DESTDIR}${prefix} ] ; then $(MKDIR_P) ${DESTDIR}${prefix} ; fi
-+	if [ ! -d ${DESTDIR}${bindir} ] ; then $(MKDIR_P) ${DESTDIR}${bindir} ; fi
- 	$(INSTALL_PROGRAM) $(INSTALL_STRIP_FLAG) mpiexec $(DESTDIR)${bindir}/mpiexec.gforker
- 
- 
diff --git a/sys-cluster/mpich2/files/mpich2-1.0.8-mpdconf-env.patch b/sys-cluster/mpich2/files/mpich2-1.0.8-mpdconf-env.patch
deleted file mode 100644
index af3bbb239..000000000
--- a/sys-cluster/mpich2/files/mpich2-1.0.8-mpdconf-env.patch
+++ /dev/null
@@ -1,112 +0,0 @@
-diff -urN a/mpich2-1.0.8/src/pm/mpd/Makefile.in b/mpich2-1.0.8/src/pm/mpd/Makefile.in
---- a/mpich2-1.0.8/src/pm/mpd/Makefile.in	2008-09-17 16:40:53.000000000 -0400
-+++ b/mpich2-1.0.8/src/pm/mpd/Makefile.in	2009-04-01 16:38:02.236018295 -0400
-@@ -74,7 +74,7 @@
- 	$(C_LINK) -o mpdroot ${mpdroot_OBJECTS} $(LIBS)
- 
- mpdroot.o: ${srcdir}/mpdroot.c ${srcdir}/mpdroot.h mpdconf.h
--	${C_COMPILE} -c  $< 
-+	${C_COMPILE} -DSYSCONFDIR=\"@sysconfdir@\" -c  $< 
- 
- # The following lines provide the right libraries for all example programs
- .c:
-@@ -128,8 +128,11 @@
- 	@echo "copying python files/links into " $(DESTDIR)${bindir}
- 	-@for cmd in ${PYTHON_SOURCE} ; do \
- 	    if [ ! -s $(srcdir)/$$cmd.py ] ; then continue ; fi ; \
--	    sed -e 's#/usr/bin/env python.*#/usr/bin/env ${PYTHON}#' ${srcdir}/$$cmd.py > $(DESTDIR)${bindir}/temp$$cmd.py ; \
--	    ${INSTALL} -m 755 $(DESTDIR)${bindir}/temp$$cmd.py $(DESTDIR)${bindir}/$$cmd.py; \
-+	    sed \
-+			-e 's#/usr/bin/env python.*#/usr/bin/env ${PYTHON}#' \
-+			-e 's,/etc/mpd.conf,@sysconfdir@/mpd.conf,g' \
-+			${srcdir}/$$cmd.py > $(DESTDIR)${bindir}/temp$$cmd.py ; \
-+		${INSTALL} -m 755 $(DESTDIR)${bindir}/temp$$cmd.py $(DESTDIR)${bindir}/$$cmd.py; \
- 	    ( rm -f $(DESTDIR)${bindir}/temp$$cmd.py >/dev/null 2>&1 || exit 0 ) ; \
- 	done
- 	-@cd $(DESTDIR)${bindir} && rm -f mpd
-@@ -210,7 +213,7 @@
- 
- mpich2-mpdroot.o: ${srcdir}/mpdroot.c ${srcdir}/mpdroot.h mpdconf.h
- 	${INSTALL} -m 644 ${srcdir}/mpdroot.c mpich2-mpdroot.c
--	${C_COMPILE} -c mpich2-mpdroot.c
-+	${C_COMPILE} -DSYSCONFDIR=\"@sysconfdir@\" -c mpich2-mpdroot.c
- 	rm -f mpich2-mpdroot.c
- 
- # A special alternate installation target when using multiple process managers
-@@ -226,8 +229,11 @@
- 	fi   
- 	for cmd in ${PYTHON_SOURCE} ; do \
- 	    if [ ! -s $(srcdir)/$$cmd.py ] ; then continue ; fi ; \
--	    sed -e 's#/usr/bin/env python.*#/usr/bin/env ${PYTHON}#' ${srcdir}/$$cmd.py > $(DESTDIR)${bindir}/temp$$cmd.py ; \
--	    ${INSTALL} -m 755 $(DESTDIR)${bindir}/temp$$cmd.py $(DESTDIR)${bindir}/$$cmd.py; \
-+		sed \
-+			-e 's#/usr/bin/env python.*#/usr/bin/env ${PYTHON}#' \
-+			-e 's,/etc/mpd.conf,@sysconfdir@/mpd.conf,g' \
-+			${srcdir}/$$cmd.py > $(DESTDIR)${bindir}/temp$$cmd.py ; \
-+		${INSTALL} -m 755 $(DESTDIR)${bindir}/temp$$cmd.py $(DESTDIR)${bindir}/$$cmd.py; \
- 	    ( rm -f $(DESTDIR)${bindir}/temp$$cmd.py >/dev/null 2>&1 || exit 0 ) ; \
- 	done
- 	cd $(DESTDIR)${bindir} && rm -f mpd
-diff -urN a/mpich2-1.0.8/src/pm/mpd/mpdlib.py b/mpich2-1.0.8/src/pm/mpd/mpdlib.py
---- a/mpich2-1.0.8/src/pm/mpd/mpdlib.py	2007-11-08 18:47:44.000000000 -0500
-+++ b/mpich2-1.0.8/src/pm/mpd/mpdlib.py	2009-04-01 16:35:08.899627072 -0400
-@@ -1341,11 +1341,11 @@
-             if os.environ.has_key(k):
-                 self[('env',k)] = os.environ[k]
-     def get_parms_from_rcfile(self,parmsToOverride,errIfMissingFile=0):
--        if os.environ.has_key('MPD_CONF_FILE'):
-+        if os.environ.has_key('MPD_CONF_FILE') and os.access(os.environ['MPD_CONF_FILE'], os.R_OK):
-             parmsRCFilename = os.environ['MPD_CONF_FILE']
-         elif hasattr(os,'getuid')  and  os.getuid() == 0:    # if ROOT
-             parmsRCFilename = os.path.abspath('/etc/mpd.conf')
--        elif os.environ.has_key('HOME'):
-+        elif os.environ.has_key('HOME') and os.access(os.path.join(os.environ['HOME'],'.mpd.conf'), os.R_OK):
-             parmsRCFilename = os.path.join(os.environ['HOME'],'.mpd.conf')
-         elif os.environ.has_key('HOMEPATH'):    # e.g. win32
-             parmsRCFilename = os.path.join(os.environ['HOMEPATH'],'.mpd.conf')
-diff -urN a/mpich2-1.0.8/src/pm/mpd/mpdroot.c b/mpich2-1.0.8/src/pm/mpd/mpdroot.c
---- a/mpich2-1.0.8/src/pm/mpd/mpdroot.c	2007-11-02 18:50:19.000000000 -0400
-+++ b/mpich2-1.0.8/src/pm/mpd/mpdroot.c	2009-04-01 16:35:08.899627072 -0400
-@@ -19,6 +19,7 @@
-     struct passwd *pwent;
-     char input_line[NAME_LEN+1], secretword[NAME_LEN+1];
-     FILE *conf_file;
-+    char *mpdconf_path = NULL;
- 
-     if ((pwent = getpwuid(getuid())) == NULL)    /* for real id */
-     {
-@@ -26,10 +27,32 @@
-         exit(-1);
-     }
- 
--    conf_file = fopen("/etc/mpd.conf","r");
-+    /*
-+     * We look for a readable mpd.conf in the following order.
-+     * - MPD_CONF_FILE set in environment
-+     * - .mpd.conf in the user's home directory
-+     * - The system wide default in SYSCONFDIR/mpd.conf
-+     */
-+    mpdconf_path = getenv("MPD_CONF_FILE");
-+    if ( ! (mpdconf_path && access( mpdconf_path, R_OK ) == 0) ){
-+        /* By far, the largest we'll need */
-+        size_t mpdconf_path_len = strlen(pwent->pw_dir) \
-+            + strlen(SYSCONFDIR) + strlen("/.mpd.conf");
-+
-+        mpdconf_path = (char*) malloc( sizeof(char) * mpdconf_path_len ); 
-+        if ( ! mpdconf_path ){
-+            fprintf( stderr, "%s:  Failed to allocate a buffer for path to mpd.conf\n", argv[0]);
-+            exit(-1);
-+        }
-+        snprintf( mpdconf_path, mpdconf_path_len-1, "%s/.mpd.conf", pwent->pw_dir );
-+        if ( access( mpdconf_path, R_OK ) != 0 )
-+            snprintf( mpdconf_path, mpdconf_path_len-1, "%s/mpd.conf", SYSCONFDIR );
-+    }
-+    conf_file = fopen( mpdconf_path, "r");
-+
-     if (conf_file == NULL)
-     {
--        printf("%s: open failed for root's mpd conf file",argv[0]);
-+        printf("%s: open failed for root's mpd conf file\n",argv[0]);
-         exit(-1);
-     }
-     secretword[0] = '\0';
diff --git a/sys-cluster/mpich2/files/mpich2-1.0.8-pkgconfig.patch b/sys-cluster/mpich2/files/mpich2-1.0.8-pkgconfig.patch
deleted file mode 100644
index 1d3a456bd..000000000
--- a/sys-cluster/mpich2/files/mpich2-1.0.8-pkgconfig.patch
+++ /dev/null
@@ -1,17 +0,0 @@
---- a/mpich2-1.0.8/src/pkgconfig/mpich2-ch3.pc.in	2008-11-04 20:36:38.931970012 -0500
-+++ b/mpich2-1.0.8/src/pkgconfig/mpich2-ch3.pc.in	2009-02-11 21:39:00.279871039 -0500
-@@ -1,8 +1,12 @@
- # this gives access to the mpich2 header files
-+prefix=@prefix@
-+exec_prefix=@exec_prefix@
-+libdir=@libdir@
-+includedir=@includedir@
- 
- Name: mpich2
- Description: MPICH2 is an implementation of the Message-Passing Interface (MPI). The goals of MPICH2 are to provide an MPI implementation for important platforms, including clusters, SMPs, and massively parallel processors. It also provides a vehicle for MPI implementation research and for developing new and better parallel programming environments.
- Version: @VERSION@
- Requires: 
--Libs: -L@libdir@ -lmpich -lmpichcxx @LIBS@
--Cflags: @CFLAGS@ -I@includedir@ -DMPICH_IGNORE_CXX_SEEK
-+Libs: -L${libdir} -lmpich -lmpichcxx @LIBS@
-+Cflags: @CFLAGS@ -I${includedir} -DMPICH_IGNORE_CXX_SEEK
diff --git a/sys-cluster/mpich2/files/mpich2-1.2.1-fix-missing-libs.patch b/sys-cluster/mpich2/files/mpich2-1.2.1-fix-missing-libs.patch
deleted file mode 100644
index 1f2ba04cf..000000000
--- a/sys-cluster/mpich2/files/mpich2-1.2.1-fix-missing-libs.patch
+++ /dev/null
@@ -1,33 +0,0 @@
-From 94707148dc8c33a1d3245e1f0dd7e28542f91e75 Mon Sep 17 00:00:00 2001
-From: Steve Arnold <nerdboy@gentoo.org>
-Date: Wed, 4 Aug 2010 23:34:06 -0400
-Subject: [PATCH] Added missing library references for the f90 and C++ shared libraries
-
-Backport of upstream r6848.  Directly modifies the Makefile.in to avoid
-having to call simplemake to regenerate the entire build system.
-
-http://trac.mcs.anl.gov/projects/mpich2/changeset/6848
----
- Makefile.in |    4 ++--
- 1 files changed, 2 insertions(+), 2 deletions(-)
-
-diff --git a/Makefile.in b/Makefile.in
-index cbe4a93..d12babb 100644
---- a/Makefile.in
-+++ b/Makefile.in
-@@ -143,10 +143,10 @@ lib/libf${MPILIBNAME}.@SHLIB_EXT@: lib/libf${MPILIBNAME}.la
- 	(cd lib && $(CREATESHLIB) --mode=link -version-info "@ABIVERSION@" -o libf${MPILIBNAME}.la  -rpath $(libdir) -L. -l$(MPILIBNAME) -ldflags "$(LDFLAGS)" $(LIBS))
- # Build the shared library from the shared object files
- lib/lib${MPILIBNAME}f90.@SHLIB_EXT@: lib/lib${MPILIBNAME}f90.la
--	(cd lib && $(CREATESHLIB) --mode=link -version-info "@ABIVERSION@" -o lib${MPILIBNAME}f90.la  -rpath $(libdir)  -ldflags "$(LDFLAGS)" $(LIBS))
-+	(cd lib && $(CREATESHLIB) --mode=link -version-info "@ABIVERSION@" -o lib${MPILIBNAME}f90.la  -rpath $(libdir) -L. -l$(MPILIBNAME) -ldflags "$(LDFLAGS)" $(LIBS))
- # Build the shared library from the shared object files
- lib/lib${MPICXXLIBNAME}.@SHLIB_EXT@: lib/lib${MPICXXLIBNAME}.la
--	(cd lib && $(CREATESHLIB) --mode=link -version-info "@ABIVERSION@" -o lib${MPICXXLIBNAME}.la  -rpath $(libdir)  -ldflags "$(LDFLAGS)" $(LIBS))
-+	(cd lib && $(CREATESHLIB) --mode=link -version-info "@ABIVERSION@" -o lib${MPICXXLIBNAME}.la  -rpath $(libdir) -L. -l$(MPILIBNAME) -ldflags "$(LDFLAGS)" $(LIBS))
- 
- # --------------------------------------------------------------------------
- .libstamp0: 
--- 
-1.7.1
-
diff --git a/sys-cluster/mpich2/files/mpich2-1.3-libtvmpich2.so-respect-user-LDFLAGS.patch b/sys-cluster/mpich2/files/mpich2-1.3-libtvmpich2.so-respect-user-LDFLAGS.patch
deleted file mode 100644
index 2a7ba2fb1..000000000
--- a/sys-cluster/mpich2/files/mpich2-1.3-libtvmpich2.so-respect-user-LDFLAGS.patch
+++ /dev/null
@@ -1,25 +0,0 @@
-From e51d6ec114dafc10a7eeeeb04c1dfdc7a7b7514c Mon Sep 17 00:00:00 2001
-From: Justin Bronder <jsbronder@gmail.com>
-Date: Sat, 25 Sep 2010 12:04:35 -0400
-Subject: [PATCH] debugger:  make libtvmpich2.so respect user LDFLAGS
-
----
- src/mpi/debugger/Makefile.in |    2 +-
- 1 files changed, 1 insertions(+), 1 deletions(-)
-
-diff --git a/src/mpi/debugger/Makefile.in b/src/mpi/debugger/Makefile.in
-index 834079f..8723e6f 100644
---- a/src/mpi/debugger/Makefile.in
-+++ b/src/mpi/debugger/Makefile.in
-@@ -172,7 +172,7 @@ SOURCEFILES     = $(SOURCES)
- # There is no static debugger interface library
- # Force a custom target
- ./libtvmpich2.@SHLIB_EXT@: ./libtvmpich2.la
--	(cd . && $(CREATESHLIB) -libtype=@DBG_SHLIB_TYPE@ --mode=link -cc="@CC_SHL_DBG@" -clink="@C_LINK_SHL_DBG@" -o libtvmpich2.la  -rpath $(libdir) )
-+	(cd . && $(CREATESHLIB) -libtype=@DBG_SHLIB_TYPE@ --mode=link -cc="@CC_SHL_DBG@" -clink="@C_LINK_SHL_DBG@" -o libtvmpich2.la  -rpath $(libdir) -ldflags "$(LDFLAGS)" )
- 
- #
- # We need to make sure that dbginit is compiled with -g, so
--- 
-1.7.2.2
-
diff --git a/sys-cluster/mpich2/files/mpich2-hvector.patch b/sys-cluster/mpich2/files/mpich2-hvector.patch
deleted file mode 100644
index 9d67561e3..000000000
--- a/sys-cluster/mpich2/files/mpich2-hvector.patch
+++ /dev/null
@@ -1,63 +0,0 @@
---- src/binding/f90/buildiface	2011-12-06 09:57:04.000000000 +0100
-+++ src/binding/f90/buildiface	2011-12-06 09:57:54.000000000 +0100
-@@ -117,9 +117,13 @@
- 		  'Type_hindexed-3' => 'int[]',
- 		  'Type_indexed-2' => 'int[]',
- 		  'Type_indexed-3' => 'int[]',
-+		  'Type_hvector-3' => 'int', 
- 		  'Type_struct-2' => 'int[]',
- 		  'Type_struct-3' => 'int[]',
- 		  'Type_struct-4' => 'MPI_Datatype[]',
-+		  'Type_extent-2' => 'int',
-+		  'Type_lb-2' => 'int',
-+		  'Type_ub-2' => 'int',
- 		  'Waitall-2' => 'MPI_Request[]',
- 		  'Waitall-3' => 'MPI_Status[]',
- 		  'Waitany-2' => 'MPI_Request[]',
---- src/binding/f90/mpi_base.f90.in	2011-12-06 09:58:42.000000000 +0100
-+++ src/binding/f90/mpi_base.f90.in	2011-12-06 10:00:30.000000000 +0100
-@@ -15,9 +15,7 @@
-        END SUBROUTINE MPI_COMM_FREE_KEYVAL
- 
-        SUBROUTINE MPI_TYPE_EXTENT(v0,v1,ierror)
--       USE MPI_CONSTANTS,ONLY:MPI_ADDRESS_KIND
--       INTEGER v0
--       INTEGER(KIND=MPI_ADDRESS_KIND) v1
-+       INTEGER v0, v1
-        INTEGER ierror
-        END SUBROUTINE MPI_TYPE_EXTENT
- 
-@@ -114,9 +112,7 @@
-        END SUBROUTINE MPI_OP_COMMUTATIVE
- 
-        SUBROUTINE MPI_TYPE_LB(v0,v1,ierror)
--       USE MPI_CONSTANTS,ONLY:MPI_ADDRESS_KIND
--       INTEGER v0
--       INTEGER(KIND=MPI_ADDRESS_KIND) v1
-+       INTEGER v0, v1
-        INTEGER ierror
-        END SUBROUTINE MPI_TYPE_LB
- 
-@@ -562,9 +558,7 @@
-        END SUBROUTINE MPI_TYPE_CREATE_RESIZED
- 
-        SUBROUTINE MPI_TYPE_UB(v0,v1,ierror)
--       USE MPI_CONSTANTS,ONLY:MPI_ADDRESS_KIND
--       INTEGER v0
--       INTEGER(KIND=MPI_ADDRESS_KIND) v1
-+       INTEGER v0, v1
-        INTEGER ierror
-        END SUBROUTINE MPI_TYPE_UB
- 
-@@ -822,10 +816,7 @@
-        END SUBROUTINE MPI_GET_VERSION
- 
-        SUBROUTINE MPI_TYPE_HVECTOR(v0,v1,v2,v3,v4,ierror)
--       USE MPI_CONSTANTS,ONLY:MPI_ADDRESS_KIND
--       INTEGER v0, v1
--       INTEGER(KIND=MPI_ADDRESS_KIND) v2
--       INTEGER v3, v4
-+       INTEGER v0, v1, v2, v3, v4
-        INTEGER ierror
-        END SUBROUTINE MPI_TYPE_HVECTOR
- 
diff --git a/sys-cluster/mpich2/metadata.xml b/sys-cluster/mpich2/metadata.xml
deleted file mode 100644
index 6cbe440fa..000000000
--- a/sys-cluster/mpich2/metadata.xml
+++ /dev/null
@@ -1,21 +0,0 @@
-<?xml version="1.0" encoding="UTF-8"?>
-<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
-<pkgmetadata>
-	<maintainer type="person">
-		<email>jsbronder@gentoo.org</email>
-		<name>Justin Bronder</name>
-	</maintainer>
-	<maintainer type="person">
-		<email>balaji@mcs.anl.gov</email>
-		<name>Pavan Balaji</name>
-		<description>Upstream Contact</description>
-	</maintainer>
-	<maintainer type="project">
-		<email>cluster@gentoo.org</email>
-		<name>Gentoo Cluster Project</name>
-	</maintainer>
-	<use>
-		<flag name="mpi-threads">Enable MPI_THREAD_MULTIPLE</flag>
-		<flag name="romio">Build the ROMIO MPI-IO component</flag>
-	</use>
-</pkgmetadata>
diff --git a/sys-cluster/mpich2/mpich2-1.5.ebuild b/sys-cluster/mpich2/mpich2-1.5.ebuild
deleted file mode 100644
index 29288ffcc..000000000
--- a/sys-cluster/mpich2/mpich2-1.5.ebuild
+++ /dev/null
@@ -1,127 +0,0 @@
-# Copyright 1999-2014 Gentoo Foundation
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=5
-
-FORTRAN_NEEDED=fortran
-
-inherit fortran-2 mpi
-
-MY_PV=${PV/_/}
-DESCRIPTION="A high performance and portable MPI implementation"
-HOMEPAGE="http://www.mcs.anl.gov/research/projects/mpich2/index.php"
-SRC_URI="http://www.mcs.anl.gov/research/projects/mpich2/downloads/tarballs/${MY_PV}/${PN}-${MY_PV}.tar.gz"
-
-SLOT="0"
-LICENSE="mpich2"
-KEYWORDS="~amd64 ~x86"
-IUSE="+cxx doc fortran mpi-threads romio threads"
-
-COMMON_DEPEND="
-	dev-libs/libaio
-	sys-apps/hwloc
-	romio? ( net-fs/nfs-utils )
-	$(mpi_imp_deplist)"
-
-DEPEND="${COMMON_DEPEND}
-	dev-lang/perl
-	sys-devel/libtool"
-
-RDEPEND="${COMMON_DEPEND}"
-
-S="${WORKDIR}"/${PN}-${MY_PV}
-
-pkg_setup() {
-	FORTRAN_STANDARD="77 90"
-	fortran-2_pkg_setup
-	MPI_ESELECT_FILE="eselect.mpi.mpich2"
-
-	if use mpi-threads && ! use threads; then
-		ewarn "mpi-threads requires threads, assuming that's what you want"
-	fi
-
-	if mpi_classed; then
-		MPD_CONF_FILE_DIR=/etc/$(mpi_class)
-	else
-		MPD_CONF_FILE_DIR=/etc/${PN}
-	fi
-
-}
-
-src_prepare() {
-	# Using MPICH2LIB_LDFLAGS doesn't seem to full work.
-	sed -i 's| *@WRAPPER_LDFLAGS@ *||' \
-		src/packaging/pkgconfig/mpich2.pc.in \
-		src/env/*.in \
-		|| die
-}
-
-src_configure() {
-	local c="--enable-shared"
-
-	# The configure statements can be somewhat confusing, as they
-	# don't all show up in the top level configure, however, they
-	# are picked up in the children directories.
-
-	if use mpi-threads; then
-		# MPI-THREAD requries threading.
-		c="${c} --with-thread-package=pthreads"
-		c="${c} --enable-threads=runtime"
-	else
-		if use threads ; then
-			c="${c} --with-thread-package=pthreads"
-		else
-			c="${c} --with-thread-package=none"
-		fi
-		c="${c} --enable-threads=single"
-	fi
-
-	if ! mpi_classed; then
-		c="${c} --sysconfdir=${EPREFIX}/etc/${PN}"
-		c="${c} --docdir=${EPREFIX}/usr/share/doc/${PF}"
-	else
-		c="${c} --docdir=$(mpi_root)/usr/share/doc/${PF}"
-	fi
-
-	export MPICH2LIB_CFLAGS=${CFLAGS}
-	export MPICH2LIB_CPPFLAGS=${CPPFLAGS}
-	export MPICH2LIB_CXXFLAGS=${CXXFLAGS}
-	export MPICH2LIB_FFLAGS=${FFLAGS}
-	export MPICH2LIB_FCFLAGS=${FCFLAGS}
-	export MPICH2LIB_LDFLAGS=${LDFLAGS}
-	unset CFLAGS CPPFLAGS CXXFLAGS FFLAGS FCFLAGS LDFLAGS
-
-	econf $(mpi_econf_args) ${c} \
-		--with-pm=hydra \
-		--disable-mpe \
-		--disable-fast \
-		--enable-smpcoll \
-		--enable-versioning \
-		$(use_enable romio) \
-		$(use_enable cxx) \
-		$(use_enable fortran f77) \
-		$(use_enable fortran fc)
-}
-
-src_test() {
-	emake -j1 check
-}
-
-src_install() {
-	local d=$(echo ${ED}/$(mpi_root)/ | sed 's,///*,/,g')
-
-	default
-
-	mpi_dodir /usr/share/doc/${PF}
-	mpi_dodoc COPYRIGHT README{,.envvar} CHANGES RELEASE_NOTES
-	mpi_newdoc src/pm/hydra/README README.hydra
-	if use romio; then
-		mpi_newdoc src/mpi/romio/README README.romio
-	fi
-
-	if ! use doc; then
-		rm -rf "${d}"usr/share/doc/${PF}/www*
-	fi
-
-	mpi_imp_add_eselect
-}
diff --git a/sys-cluster/mvapich2/Manifest b/sys-cluster/mvapich2/Manifest
deleted file mode 100644
index 9c59e1fd9..000000000
--- a/sys-cluster/mvapich2/Manifest
+++ /dev/null
@@ -1 +0,0 @@
-DIST mvapich2-1.6.tgz 23239787 BLAKE2B 4cdd286d7a13f70b50ced6ac6cb3df51065225a33141410b699246f2b99d0f4b57611cd95f39806387c71d0f07257560c6f210ed4bbb8ce5fa5d2b8b7071db2c SHA512 4a4aac17742f347c4daed40a8360576ff4c644c549d4a3b364c7d2b1eada6aecc514b447b4613111e113d8f9be79b5101a999298cf89ff19ce63523a54702289
diff --git a/sys-cluster/mvapich2/files/eselect.mpi.mvapich2 b/sys-cluster/mvapich2/files/eselect.mpi.mvapich2
deleted file mode 100644
index d1d2131a1..000000000
--- a/sys-cluster/mvapich2/files/eselect.mpi.mvapich2
+++ /dev/null
@@ -1,8 +0,0 @@
-MPI_CC=@ROOT@/usr/bin/mpicc
-MPI_CXX=@ROOT@/usr/bin/mpic++
-MPI_F77=@ROOT@/usr/bin/mpif77
-MPI_F90=@ROOT@/usr/bin/mpif90
-MPI_BUILT_WITH=@BUILT_WITH@
-PATH=@ROOT@/usr/bin
-MANPATH=@ROOT@/usr/share/man
-LD_LIBRARY_PATH=@ROOT@/usr/@LIBDIR@
diff --git a/sys-cluster/mvapich2/metadata.xml b/sys-cluster/mvapich2/metadata.xml
deleted file mode 100644
index 50e4975c9..000000000
--- a/sys-cluster/mvapich2/metadata.xml
+++ /dev/null
@@ -1,16 +0,0 @@
-<?xml version="1.0" encoding="UTF-8"?>
-<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
-<pkgmetadata>
-	<maintainer type="project">
-		<email>cluster@gentoo.org</email>
-		<name>Gentoo Cluster Project</name>
-	</maintainer>
-	<longdescription>
-MVAPICH2 MPI-over-infiniband package auto-configured for OpenIB.
-</longdescription>
-	<use>
-		<flag name="large-cluster">Automatically generated description for large-cluster</flag>
-		<flag name="medium-cluster">Automatically generated description for medium-cluster</flag>
-		<flag name="romio">Automatically generated description for romio</flag>
-	</use>
-</pkgmetadata>
diff --git a/sys-cluster/mvapich2/mvapich2-1.6-r1.ebuild b/sys-cluster/mvapich2/mvapich2-1.6-r1.ebuild
deleted file mode 100644
index 8ed791509..000000000
--- a/sys-cluster/mvapich2/mvapich2-1.6-r1.ebuild
+++ /dev/null
@@ -1,145 +0,0 @@
-# Copyright 1999-2015 Gentoo Foundation
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=5
-
-inherit flag-o-matic fortran-2 mpi
-
-DESCRIPTION="MVAPICH2 MPI-over-infiniband package auto-configured for OpenIB"
-HOMEPAGE="http://mvapich.cse.ohio-state.edu/"
-SRC_URI="${HOMEPAGE}/download/mvapich2/mvapich2-${PV/_/-}.tgz"
-
-SLOT="0"
-LICENSE="BSD"
-KEYWORDS="~amd64 ~x86"
-IUSE="debug fortran large-cluster medium-cluster romio threads"
-
-RDEPEND="
-	sys-fabric/libibverbs:=
-	sys-fabric/libibumad:=
-	sys-fabric/libibmad:=
-	sys-fabric/librdmacm:=
-	"
-DEPEND="${RDEPEND}"
-
-S="${WORKDIR}/mvapich2-${PV/_/-}"
-
-pkg_setup() {
-	fortran-2_pkg_setup
-	MPI_ESELECT_FILE="eselect.mpi.mvapich2"
-
-	if [ -z "${MVAPICH_HCA_TYPE}" ]; then
-		elog "${PN} needs to know which HCA it should optimize for.  This is"
-		elog "passed to the ebuild with the variable, \${MVAPICH_HCA_TYPE}."
-		elog "Please choose one of:  _MLX_PCI_EX_SDR_, _MLX_PCI_EX_DDR_,"
-		elog "_MLX_PCI_X, _PATH_HT_, or _IBM_EHCA_."
-		elog "See make.mvapich2.detect in ${S} for more information."
-		die "MVAPICH_HCA_TYPE undefined"
-	fi
-
-	case ${ARCH} in
-		amd64)
-			if grep Intel /proc/cpuinfo &>/dev/null; then
-				BUILD_ARCH=-D_EM64T_
-			else
-				BUILD_ARCH=-D_X86_64_
-			fi
-			;;
-		x86)
-			BUILD_ARCH=-D_IA32_
-			;;
-		ia64)
-			BUILD_ARCH=-D_IA64_
-			;;
-		ppc64)
-			BUILD_ARCH=-D_PPC64_
-			;;
-		*)
-			die "unsupported architecture: ${ARCH}"
-			;;
-	esac
-}
-
-src_prepare() {
-	einfo "Disabling examples"
-	# Examples are always compiled with the default 'all' target.  This
-	# causes problems when we don't build support for everything, including
-	# threads, mpe2, etc.  So we're not going to build them.
-	sed -i 's:.*cd examples && ${MAKE} all.*::' Makefile.in || die
-}
-
-src_configure() {
-	local c="--with-device=osu_ch3:mrail
-		--with-rdma=gen2
-		--with-pm=mpd
-		$(use_enable romio)
-		--with-mpe=no"
-
-	# TODO Shared libs should build with this, but they don't
-	# --enable-shared=gcc"
-
-	local enable_srq
-	local vcluster=-D_SMALL_CLUSTER
-
-	use large-cluster 	&& vcluster=-D_LARGE_CLUSTER
-	use medium-cluster 	&& vcluster=-D_MEDIUM_CLUSTER
-	[ "${MVAPICH_HCA_TYPE}" == "_MLX_PCI_X_" ] && enable_srq="-DSRQ"
-
-	append-ldflags "-lrdmacm"
-	append-flags "-DADAPTIVE_RDMA_FAST_PATH -DRDMA_CM"
-	append-ldflags "-libverbs -libumad -libmad"
-
-	append-flags "${BUILD_ARCH} -DUSE_INLINE -D_SMP_ -D_GNU_SOURCE"
-	append-flags "${enable_srq} -DUSE_HEADER_CACHING -DLAZY_MEM_UNREGISTER"
-	append-flags "-DONE_SIDED -D${MVAPICH_HCA_TYPE} ${vcluster}"
-	append-flags "-DMPID_USE_SEQUENCE_NUMBERS -DUSE_MPD_RING"
-
-	use debug && c="${c} --enable-g=all --enable-debuginfo"
-
-	if use threads; then
-		c="${c} --enable-threads=multiple --with-thread-package=pthreads"
-		append-flags "-pthread"
-	else
-		c="${c} --with-thread-package=none"
-	fi
-
-	# enable f90 support for appropriate compilers
-	if use fortran; then
-		case "$(tc-getFC)" in
-			gfortran|ifort|f95)
-				c="${c} --enable-f77 --enable-f90";;
-			g77|f77|f2c)
-				c="${c} --enable-f77 --disable-f90";;
-		esac
-	else
-		c="${c} --disable-f77 --disable-f90"
-	fi
-
-	sed -i \
-		-e 's/ ${exec_prefix}/ ${DESTDIR}${exec_prefix}/' \
-		-e 's/ ${libdir}/ ${DESTDIR}${libdir}/' \
-		${S/-beta2/}/Makefile.in || die
-	sed -i '/bindir/s/ ${bindir}/ ${DESTDIR}${bindir}/' ${S/-beta2/}/src/pm/mpd/Makefile.in || die
-	cd ${S/-beta2/} || die
-
-	! mpi_classed && c="${c} --sysconfdir=/etc/${PN}"
-	econf $(mpi_econf_args)	${c}
-}
-
-src_install() {
-	emake  DESTDIR="${D}"
-	mpi_dodoc CHANGES_MPICH2 COPYRIGHT COPYRIGHT_MVAPICH2 LICENSE.TXT \
-		README* RELEASE_NOTES*
-	mpi_imp_add_eselect
-}
-
-pkg_postinst() {
-	einfo "To allow normal users to use infiniband, it is necessary to"
-	einfo "increase the system limits on locked memory."
-	einfo "You must increase the kernel.shmmax sysctl value, and increase"
-	einfo "the memlock limits in /etc/security/limits.conf.  i.e.:"
-	echo
-	einfo "echo 'kernel.shmmax = 512000000' >> /etc/sysctl.conf"
-	einfo "echo 512000000 > /proc/sys/kernel/shmmax"
-	einfo "echo -e '* soft memlock 500000\n* hard memlock 500000' > /etc/security/limits.conf"
-}
diff --git a/sys-cluster/openmpi/Manifest b/sys-cluster/openmpi/Manifest
deleted file mode 100644
index e4dc0cd12..000000000
--- a/sys-cluster/openmpi/Manifest
+++ /dev/null
@@ -1,7 +0,0 @@
-DIST openmpi-1.10.7.tar.bz2 13435131 BLAKE2B c1914e6842f59a4a21a27d015275eff00092e57784c4219f58424fbc69c6d9e58109aa1b2ff4e1e340ddc3b93f07d7271e728928772c66c271442e375c08315e SHA512 9c5470f9959ca37650a59e56fb8343c028422c709876ab9d25a411dd09a07cdde927c45d8f3db1ad524b1f2847fe799471d469fa1efee48f8018b2ff24427ecb
-DIST openmpi-1.8.8.tar.bz2 13231433 BLAKE2B d196fd0bb08cfb0c86a29ae39015eb15e1465554e322c1ae039b61cee3a027ea0ba8d7fecd02e310309caec416147611a233861e464db4449da3b449387b1dca SHA512 8ca2e3ebb9d9ba0f33faba9bef76fe95293721b73619cbc18176611074a56c277e9ab6cae7fa6c87ace11f16151c1bc495b2a8dbc8ad064d5a8f89f5d431a660
-DIST openmpi-2.0.4.tar.bz2 8272983 BLAKE2B 7d0a392fbc8c896cdccefb9bf0ff83fbd8db8a42d17f06cb23ac88ba896e2c75e1b1b7a79559d0ce3c2b881f197f54ce1bd8967c889bafe2b97f95fb6b957501 SHA512 2cccb83847d44f6282ec24f7bc12ab51b84dc5ac1a2a919ef0761847ff7cdcb31cfb1f38dca33df7063a98c27a64575a108002716d207cbba3a54773b999e6c5
-DIST openmpi-2.1.6.tar.bz2 8324626 BLAKE2B 4aed4b397c0e0ead24ed5e9bbf45ee8f6719a7566d74405cccf119ddf535891ece91c04cbcad96be5a5d9805c620aa13a1b51c0edd67c049827357e7668008b9 SHA512 f552f47961e040476e7d2949cdd3e5a0b5ad74bea2b6532608117ec893473a160cd368251d1f439fd773f4846950857baf939e7b3586bac2a099495f7bc0e349
-DIST openmpi-3.0.3.tar.bz2 9316109 BLAKE2B e67e649917911eff3286c0f3d15e181b30e4ac6061891f6e13c75570368edb943fff55e4d41ffaa4a095b2060c84d24f8c32975758ad4632bae1813accd9f516 SHA512 12bbc5add4160e732ac10f302106c4bc2fa61ef2cde955e1fdd4a7aaad44b022d6babdd4bd529f687bb03fc5e5c3804ba6b1869e9609c9725bc291524c8304d7
-DIST openmpi-3.1.3.tar.bz2 9442937 BLAKE2B 40067e1694a106d96e5ba41884a6facec9e605b5afba03ab908e4cf124f35b0691f0ab626e5190cffebc9c28d05b11b5c6401a5aa39ac17ec04650ed29e0976e SHA512 700821df676de5f85ce2793298242dcaea73f585f89540e30999792a568f193545a9f9b2bcb3ea22effa3bf14744531c4eb5fc4c84a8d7bbe5e5fdd76ab3a04a
-DIST openmpi-4.0.0.tar.bz2 9812193 BLAKE2B e5307c22ce4c9aac8d0efe5a659dfa79b4471020ece095e84026914eab8edf030b59bbac2a37405851a904aeb4d4b3a33ce8de4cd25218dcb9f37626a3540ff5 SHA512 978097dcbb16df2a616dcbbef9536fed0f7be40914daa8f927882d91bdda9265e54334fc12aeef49b41073d8782321b5611a7e9c71182258a45bca5f640e927b
diff --git a/sys-cluster/openmpi/files/eselect.mpi.openmpi b/sys-cluster/openmpi/files/eselect.mpi.openmpi
deleted file mode 100644
index c1a9373f3..000000000
--- a/sys-cluster/openmpi/files/eselect.mpi.openmpi
+++ /dev/null
@@ -1,8 +0,0 @@
-MPI_CC=@ROOT@usr/bin/mpicc
-MPI_CXX=@ROOT@usr/bin/mpic++
-MPI_F77=@ROOT@usr/bin/mpif77
-MPI_FC=@ROOT@usr/bin/mpif90
-CLASS_BASE_MPI_IMP=@BASE_IMP@
-PATH=@ROOT@usr/bin
-MANPATH=@ROOT@usr/share/man
-LD_LIBRARY_PATH=@ROOT@usr/@LIBDIR@
diff --git a/sys-cluster/openmpi/files/hooks-disable-malloc-override-inside-of-Gentoo-sandb.patch b/sys-cluster/openmpi/files/hooks-disable-malloc-override-inside-of-Gentoo-sandb.patch
deleted file mode 100644
index 197430aee..000000000
--- a/sys-cluster/openmpi/files/hooks-disable-malloc-override-inside-of-Gentoo-sandb.patch
+++ /dev/null
@@ -1,42 +0,0 @@
-From 3bd5897c7ca8ab61fb024957aeae891e204b3e3f Mon Sep 17 00:00:00 2001
-From: Justin Bronder <jsbronder@gmail.com>
-Date: Mon, 1 Jul 2013 20:37:17 -0400
-Subject: [PATCH] hooks:  disable malloc override inside of Gentoo sandbox
-
-As described in the comments in the source, Gentoo's own version of
-fakeroot, sandbox, also runs into hangs when malloc is overridden.
-Sandbox environments can easily be detected by looking for SANDBOX_PID
-in the environment.  When detected, employ the same fix used for
-fakeroot.
-
-See https://bugs.gentoo.org/show_bug.cgi?id=462602
----
- opal/mca/memory/linux/hooks.c | 11 +++++++++--
- 1 file changed, 9 insertions(+), 2 deletions(-)
-
-diff --git a/opal/mca/memory/linux/hooks.c b/opal/mca/memory/linux/hooks.c
-index 6a1646f..5ded08c 100644
---- a/opal/mca/memory/linux/hooks.c
-+++ b/opal/mca/memory/linux/hooks.c
-@@ -747,9 +747,16 @@ static void opal_memory_linux_malloc_init_hook(void)
-        "fakeroot" build environment that allocates memory during
-        stat() (see http://bugs.debian.org/531522).  It may not be
-        necessary any more since we're using access(), not stat().  But
--       we'll leave the check, anyway. */
-+       we'll leave the check, anyway.
-+
-+       This is also an issue when using Gentoo's version of 'fakeroot',
-+       sandbox v2.5.  Sandbox environments can also be detected fairly
-+       easily by looking for SANDBOX_ON.
-+    */
-+
-     if (getenv("FAKEROOTKEY") != NULL ||
--        getenv("FAKED_MODE") != NULL) {
-+        getenv("FAKED_MODE") != NULL ||
-+        getenv("SANDBOX_ON") != NULL ) {
-         return;
-     }
- 
--- 
-1.8.1.5
-
diff --git a/sys-cluster/openmpi/files/openmpi-ltdl.patch b/sys-cluster/openmpi/files/openmpi-ltdl.patch
deleted file mode 100644
index a288ea272..000000000
--- a/sys-cluster/openmpi/files/openmpi-ltdl.patch
+++ /dev/null
@@ -1,78 +0,0 @@
-diff -up openmpi-1.6.3/ompi/debuggers/dlopen_test.c.ltdl openmpi-1.6.3/ompi/debuggers/dlopen_test.c
---- openmpi-1.6.3/ompi/debuggers/dlopen_test.c.ltdl	2012-04-03 08:30:25.000000000 -0600
-+++ openmpi-1.6.3/ompi/debuggers/dlopen_test.c	2012-11-02 14:50:12.613702426 -0600
-@@ -13,7 +13,17 @@
- #include <string.h>
- #include <stdlib.h>
- 
--#include "opal/libltdl/ltdl.h"
-+#if OPAL_WANT_LIBLTDL
-+  #ifndef __WINDOWS__
-+    #if OPAL_LIBLTDL_INTERNAL
-+      #include "opal/libltdl/ltdl.h"
-+    #else
-+      #include "ltdl.h"
-+    #endif
-+  #else
-+    #include "ltdl.h"
-+  #endif
-+#endif
- 
- static int do_test(void);
- 
-diff -up openmpi-1.6.3/ompi/debuggers/Makefile.am.ltdl openmpi-1.6.3/ompi/debuggers/Makefile.am
---- openmpi-1.6.3/ompi/debuggers/Makefile.am.ltdl	2012-04-03 08:30:25.000000000 -0600
-+++ openmpi-1.6.3/ompi/debuggers/Makefile.am	2012-11-02 15:04:53.636926260 -0600
-@@ -47,7 +47,7 @@ headers = \
- 
- dlopen_test_SOURCES = dlopen_test.c
- dlopen_test_CPPFLAGS = -I$(top_srcdir)/opal/libltdl
--dlopen_test_LDADD = $(top_builddir)/opal/libltdl/libltdlc.la
-+dlopen_test_LDADD = $(LIBLTDL)
- 
- predefined_gap_test_SOURCES = predefined_gap_test.c
- predefined_gap_test_LDFLAGS = $(WRAPPER_EXTRA_LDFLAGS)
-diff -up openmpi-1.6.3/test/support/components.c.ltdl openmpi-1.6.3/test/support/components.c
---- openmpi-1.6.3/test/support/components.c.ltdl	2012-04-03 08:29:44.000000000 -0600
-+++ openmpi-1.6.3/test/support/components.c	2012-11-02 14:50:29.204705380 -0600
-@@ -24,7 +24,17 @@
- 
- #include "opal/constants.h"
- #include "opal/mca/mca.h"
--#include "opal/libltdl/ltdl.h"
-+#if OPAL_WANT_LIBLTDL
-+  #ifndef __WINDOWS__
-+    #if OPAL_LIBLTDL_INTERNAL
-+      #include "opal/libltdl/ltdl.h"
-+    #else
-+      #include "ltdl.h"
-+    #endif
-+  #else
-+    #include "ltdl.h"
-+  #endif
-+#endif
- 
- #include "components.h"
- 
-diff -up openmpi-1.6.3/test/support/components.h.ltdl openmpi-1.6.3/test/support/components.h
---- openmpi-1.6.3/test/support/components.h.ltdl	2012-04-03 08:29:44.000000000 -0600
-+++ openmpi-1.6.3/test/support/components.h	2012-11-02 14:50:22.409703519 -0600
-@@ -20,7 +20,17 @@
- #ifndef OMPI_SUPPORT_COMPONENTS_H
- #define OMPI_SUPPORT_COMPONENTS_H
- 
--#include "opal/libltdl/ltdl.h"
-+#if OPAL_WANT_LIBLTDL
-+  #ifndef __WINDOWS__
-+    #if OPAL_LIBLTDL_INTERNAL
-+      #include "opal/libltdl/ltdl.h"
-+    #else
-+      #include "ltdl.h"
-+    #endif
-+  #else
-+    #include "ltdl.h"
-+  #endif
-+#endif
- #include "opal/mca/mca.h"
- 
- BEGIN_C_DECLS
diff --git a/sys-cluster/openmpi/files/openmpi-r24328.patch b/sys-cluster/openmpi/files/openmpi-r24328.patch
deleted file mode 100644
index bbd689d3a..000000000
--- a/sys-cluster/openmpi/files/openmpi-r24328.patch
+++ /dev/null
@@ -1,54 +0,0 @@
-From cf054cd92dfac55f3920e805d01c11dcfc2cd4fa Mon Sep 17 00:00:00 2001
-From: jsquyres <jsquyres@cisco.com>
-Date: Mon, 28 Mar 2011 12:44:06 -0400
-Subject: [PATCH] Fix some fairly-important typos (!)
-
-Upstream commit r24328.
----
- test/datatype/ddt_lib.c      |    2 +-
- test/datatype/ddt_raw.c      |    2 +-
- test/datatype/opal_ddt_lib.c |    2 +-
- 3 files changed, 3 insertions(+), 3 deletions(-)
-
-diff --git a/test/datatype/ddt_lib.c b/test/datatype/ddt_lib.c
-index 015419d..c349384 100644
---- a/test/datatype/ddt_lib.c
-+++ b/test/datatype/ddt_lib.c
-@@ -209,7 +209,7 @@ int mpich_typeub2( void )
- 
- int mpich_typeub3( void )
- {
--   int blocklen[2], err = 0, idisp[3];
-+   int blocklen[3], err = 0, idisp[3];
-    size_t sz;
-    MPI_Aint disp[3], lb, ub, ex;
-    ompi_datatype_t *types[3], *dt1, *dt2, *dt3, *dt4, *dt5;
-diff --git a/test/datatype/ddt_raw.c b/test/datatype/ddt_raw.c
-index eea9004..7effe65 100644
---- a/test/datatype/ddt_raw.c
-+++ b/test/datatype/ddt_raw.c
-@@ -45,7 +45,7 @@ static int test_upper( unsigned int length )
- {
-     ompi_datatype_t *pdt;
-     opal_convertor_t * pConv;
--    int rc;
-+    int rc = OMPI_SUCCESS;
-     unsigned int i, iov_count, split_chunk, total_length;
-     size_t max_data;
-     struct iovec iov[5];
-diff --git a/test/datatype/opal_ddt_lib.c b/test/datatype/opal_ddt_lib.c
-index e05bb06..dffd86c 100644
---- a/test/datatype/opal_ddt_lib.c
-+++ b/test/datatype/opal_ddt_lib.c
-@@ -759,7 +759,7 @@ int mpich_typeub2( void )
- 
- int mpich_typeub3( void )
- {
--   int blocklen[2], err = 0, idisp[3];
-+   int blocklen[3], err = 0, idisp[3];
-    size_t sz;
-    OPAL_PTRDIFF_TYPE disp[3], lb, ub, ex;
-    opal_datatype_t *types[3], *dt1, *dt2, *dt3, *dt4, *dt5;
--- 
-1.7.3.4
-
diff --git a/sys-cluster/openmpi/metadata.xml b/sys-cluster/openmpi/metadata.xml
deleted file mode 100644
index 08b693bf5..000000000
--- a/sys-cluster/openmpi/metadata.xml
+++ /dev/null
@@ -1,21 +0,0 @@
-<?xml version="1.0" encoding="UTF-8"?>
-<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
-<pkgmetadata>
-	<maintainer type="person">
-		<email>jsbronder@gentoo.org</email>
-	</maintainer>
-	<maintainer type="project">
-		<email>cluster@gentoo.org</email>
-		<name>Gentoo Cluster Project</name>
-	</maintainer>
-	<use>
-		<flag name="cma">Enable the CMA (Cross Memory Attach) MCA</flag>
-		<flag name="cuda">Add GPU direct support</flag>
-		<flag name="heterogeneous">Enable features required for heterogeneous
-platform support</flag>
-		<flag name="romio">Build the ROMIO MPI-IO component</flag>
-		<flag name="mpi-threads">Enable MPI_THREAD_MULTIPLE</flag>
-		<flag name="numa">Enable numactl to allow binding processes to CPUs</flag>
-		<flag name="vt">Enable bundled VampirTrace support</flag>
-	</use>
-</pkgmetadata>
diff --git a/sys-cluster/openmpi/openmpi-1.10.7.ebuild b/sys-cluster/openmpi/openmpi-1.10.7.ebuild
deleted file mode 100644
index de982dc42..000000000
--- a/sys-cluster/openmpi/openmpi-1.10.7.ebuild
+++ /dev/null
@@ -1,194 +0,0 @@
-# Copyright 1999-2018 Gentoo Foundation
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=6
-
-FORTRAN_NEEDED=fortran
-
-inherit cuda flag-o-matic fortran-2 java-pkg-opt-2 toolchain-funcs versionator multilib-minimal mpi
-
-MY_P=${P/-mpi}
-S=${WORKDIR}/${MY_P}
-
-IUSE_OPENMPI_FABRICS="
-	openmpi_fabrics_ofed
-	openmpi_fabrics_knem
-	openmpi_fabrics_psm"
-
-IUSE_OPENMPI_RM="
-	openmpi_rm_pbs
-	openmpi_rm_slurm"
-
-IUSE_OPENMPI_OFED_FEATURES="
-	openmpi_ofed_features_control-hdr-padding
-	openmpi_ofed_features_connectx-xrc
-	openmpi_ofed_features_udcm
-	openmpi_ofed_features_rdmacm
-	openmpi_ofed_features_dynamic-sl
-	openmpi_ofed_features_failover"
-
-DESCRIPTION="A high-performance message passing library (MPI)"
-HOMEPAGE="http://www.open-mpi.org"
-SRC_URI="http://www.open-mpi.org/software/ompi/v$(get_version_component_range 1-2)/downloads/${MY_P}.tar.bz2"
-LICENSE="BSD"
-SLOT="0"
-KEYWORDS="~amd64 ~x86 ~amd64-linux"
-IUSE="cma cuda +cxx elibc_FreeBSD fortran heterogeneous ipv6 java mpi-threads numa romio threads vt
-	${IUSE_OPENMPI_FABRICS} ${IUSE_OPENMPI_RM} ${IUSE_OPENMPI_OFED_FEATURES}"
-
-REQUIRED_USE="openmpi_rm_slurm? ( !openmpi_rm_pbs )
-	openmpi_rm_pbs? ( !openmpi_rm_slurm )
-	openmpi_fabrics_psm? ( openmpi_fabrics_ofed )
-	openmpi_ofed_features_control-hdr-padding? ( openmpi_fabrics_ofed )
-	openmpi_ofed_features_connectx-xrc? ( openmpi_fabrics_ofed )
-	openmpi_ofed_features_udcm? ( openmpi_fabrics_ofed )
-	openmpi_ofed_features_rdmacm? ( openmpi_fabrics_ofed )
-	openmpi_ofed_features_dynamic-sl? ( openmpi_fabrics_ofed )
-	openmpi_ofed_features_failover? ( openmpi_fabrics_ofed )"
-
-MPI_UNCLASSED_DEP_STR="
-	!sys-cluster/pmix
-	vt? (
-		!dev-libs/libotf
-		!app-text/lcdf-typetools
-	)"
-
-CDEPEND="
-	>=dev-libs/libevent-2.0.21[${MULTILIB_USEDEP}]
-	dev-libs/libltdl:0[${MULTILIB_USEDEP}]
-	<sys-apps/hwloc-2[${MULTILIB_USEDEP},numa?]
-	>=sys-libs/zlib-1.2.8-r1[${MULTILIB_USEDEP}]
-	cuda? ( >=dev-util/nvidia-cuda-toolkit-6.5.19-r1 )
-	elibc_FreeBSD? ( dev-libs/libexecinfo )
-	openmpi_fabrics_ofed? ( sys-fabric/ofed:* )
-	openmpi_fabrics_knem? ( sys-cluster/knem )
-	openmpi_fabrics_psm? ( sys-fabric/infinipath-psm:* )
-	openmpi_rm_pbs? ( sys-cluster/torque )
-	openmpi_rm_slurm? ( sys-cluster/slurm )
-	openmpi_ofed_features_rdmacm? ( sys-fabric/librdmacm:* )
-	$(mpi_imp_deplist)"
-
-RDEPEND="${CDEPEND}
-	java? ( >=virtual/jre-1.6 )"
-
-DEPEND="${CDEPEND}
-	java? ( >=virtual/jdk-1.6 )"
-
-MULTILIB_WRAPPED_HEADERS=(
-	/usr/include/mpi.h
-	/usr/include/openmpi/ompi/mpi/java/mpiJava.h
-)
-
-pkg_setup() {
-	fortran-2_pkg_setup
-	java-pkg-opt-2_pkg_setup
-	MPI_ESELECT_FILE="eselect.mpi.openmpi"
-
-	if use mpi-threads; then
-		ewarn
-		ewarn "WARNING: use of MPI_THREAD_MULTIPLE is still disabled by"
-		ewarn "default and officially unsupported by upstream."
-		ewarn "You may stop now and set USE=-mpi-threads"
-		ewarn
-	fi
-
-	elog
-	elog "OpenMPI has an overwhelming count of configuration options."
-	elog "Don't forget the EXTRA_ECONF environment variable can let you"
-	elog "specify configure options if you find them necessary."
-	elog
-}
-
-src_prepare() {
-	default
-
-	# Necessary for scalibility, see
-	# http://www.open-mpi.org/community/lists/users/2008/09/6514.php
-	if use threads; then
-		echo 'oob_tcp_listen_mode = listen_thread' \
-			>> opal/etc/openmpi-mca-params.conf || die
-	fi
-}
-
-multilib_src_configure() {
-	if use java; then
-		# We must always build with the right -source and -target
-		# flags. Passing flags to javac isn't explicitly supported here
-		# but we can cheat by overriding the configure test for javac.
-		export ac_cv_path_JAVAC="$(java-pkg_get-javac) $(java-pkg_javac-args)"
-	fi
-
-	ECONF_SOURCE=${S} econf $(mpi_econf_args) \
-		--sysconfdir="${EPREFIX}/etc/${PN}" \
-		--enable-pretty-print-stacktrace \
-		--enable-orterun-prefix-by-default \
-		--with-hwloc="${EPREFIX}/usr" \
-		--with-libltdl="${EPREFIX}/usr" \
-		--enable-mpi-fortran=$(usex fortran all no) \
-		$(usex !vt --enable-contrib-no-build=vt "") \
-		$(use_enable cxx mpi-cxx) \
-		$(use_with cma) \
-		$(use_with cuda cuda "${EPREFIX}"/opt/cuda) \
-		$(use_enable romio io-romio) \
-		$(use_enable heterogeneous) \
-		$(use_enable ipv6) \
-		$(multilib_native_use_enable java) \
-		$(multilib_native_use_enable java mpi-java) \
-		$(multilib_native_use_enable mpi-threads mpi-thread-multiple) \
-		$(multilib_native_use_with openmpi_fabrics_ofed verbs "${EPREFIX}"/usr) \
-		$(multilib_native_use_with openmpi_fabrics_knem knem "${EPREFIX}"/usr) \
-		$(multilib_native_use_with openmpi_fabrics_psm psm "${EPREFIX}"/usr) \
-		$(multilib_native_use_enable openmpi_ofed_features_control-hdr-padding openib-control-hdr-padding) \
-		$(multilib_native_use_enable openmpi_ofed_features_connectx-xrc openib-connectx-xrc) \
-		$(multilib_native_use_enable openmpi_ofed_features_rdmacm openib-rdmacm) \
-		$(multilib_native_use_enable openmpi_ofed_features_udcm openib-udcm) \
-		$(multilib_native_use_enable openmpi_ofed_features_dynamic-sl openib-dynamic-sl) \
-		$(multilib_native_use_enable openmpi_ofed_features_failover btl-openib-failover) \
-		$(multilib_native_use_with openmpi_rm_pbs tm) \
-		$(multilib_native_use_with openmpi_rm_slurm slurm)
-}
-
-multilib_src_test() {
-	# Doesn't work with the default src_test as the dry run (-n) fails.
-	emake -j1 check
-}
-
-multilib_src_install() {
-	default
-
-	# fortran header cannot be wrapped (bug #540508), workaround part 1
-	if multilib_is_native_abi && use fortran; then
-		mkdir "${T}"/fortran || die
-		mv "${ED}"/$(mpi_root)/usr/include/mpif* "${T}"/fortran || die
-	else
-		# some fortran files get installed unconditionally
-		rm "${ED}"/$(mpi_root)/usr/include/mpif* "${ED}"usr/bin/mpif* || die
-	fi
-}
-
-multilib_src_install_all() {
-	# From USE=vt see #359917
-	rm -rf "${ED}"/$(mpi_root)/usr/share/libtool &> /dev/null
-
-	# fortran header cannot be wrapped (bug #540508), workaround part 2
-	if use fortran; then
-		mv "${T}"/fortran/mpif* "${ED}"/$(mpi_root)/usr/include || die
-	fi
-
-	# Avoid collisions with libevent
-	rm -rf "${ED}"/$(mpi_root)/usr/include/event2 &> /dev/null || die
-
-	# Remove la files, no static libs are installed and we have pkg-config
-	find "${ED}" -name '*.la' -delete || die
-
-	if use java; then
-		local mpi_jar="${ED}"/$(mpi_root)/usr/$(get_libdir)/mpi.jar
-		java-pkg_dojar "${mpi_jar}"
-		# We don't want to install the jar file twice
-		# so let's clean after ourselves.
-		rm "${mpi_jar}" || die
-	fi
-
-	mpi_dodoc README AUTHORS NEWS VERSION
-	mpi_imp_add_eselect
-}
diff --git a/sys-cluster/openmpi/openmpi-1.8.8.ebuild b/sys-cluster/openmpi/openmpi-1.8.8.ebuild
deleted file mode 100644
index b7fa7fabd..000000000
--- a/sys-cluster/openmpi/openmpi-1.8.8.ebuild
+++ /dev/null
@@ -1,180 +0,0 @@
-# Copyright 1999-2018 Gentoo Foundation
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=5
-
-FORTRAN_NEEDED=fortran
-
-inherit cuda eutils flag-o-matic fortran-2 java-pkg-opt-2 multilib mpi toolchain-funcs versionator
-
-MY_P=${P/-mpi}
-S=${WORKDIR}/${MY_P}
-
-IUSE_OPENMPI_FABRICS="
-	openmpi_fabrics_ofed
-	openmpi_fabrics_knem
-	openmpi_fabrics_open-mx
-	openmpi_fabrics_psm"
-
-IUSE_OPENMPI_RM="
-	openmpi_rm_pbs
-	openmpi_rm_slurm"
-
-IUSE_OPENMPI_OFED_FEATURES="
-	openmpi_ofed_features_control-hdr-padding
-	openmpi_ofed_features_connectx-xrc
-	openmpi_ofed_features_udcm
-	openmpi_ofed_features_rdmacm
-	openmpi_ofed_features_dynamic-sl
-	openmpi_ofed_features_failover"
-
-DESCRIPTION="A high-performance message passing library (MPI)"
-HOMEPAGE="http://www.open-mpi.org"
-SRC_URI="http://www.open-mpi.org/software/ompi/v$(get_version_component_range 1-2)/downloads/${MY_P}.tar.bz2"
-LICENSE="BSD"
-SLOT="0"
-KEYWORDS="~amd64 ~x86 ~amd64-linux"
-IUSE="cma cuda +cxx elibc_FreeBSD fortran heterogeneous ipv6 java mpi-threads numa romio threads vt
-	${IUSE_OPENMPI_FABRICS} ${IUSE_OPENMPI_RM} ${IUSE_OPENMPI_OFED_FEATURES}"
-
-REQUIRED_USE="openmpi_rm_slurm? ( !openmpi_rm_pbs )
-	openmpi_rm_pbs? ( !openmpi_rm_slurm )
-	openmpi_fabrics_psm? ( openmpi_fabrics_ofed )
-	openmpi_ofed_features_control-hdr-padding? ( openmpi_fabrics_ofed )
-	openmpi_ofed_features_connectx-xrc? ( openmpi_fabrics_ofed )
-	openmpi_ofed_features_udcm? ( openmpi_fabrics_ofed )
-	openmpi_ofed_features_rdmacm? ( openmpi_fabrics_ofed )
-	openmpi_ofed_features_dynamic-sl? ( openmpi_fabrics_ofed )
-	openmpi_ofed_features_failover? ( openmpi_fabrics_ofed )"
-
-MPI_UNCLASSED_DEP_STR="
-	!sys-cluster/pmix
-	vt? (
-		!dev-libs/libotf
-		!app-text/lcdf-typetools
-	)"
-
-RDEPEND="
-	dev-libs/libevent
-	dev-libs/libltdl:0
-	<sys-apps/hwloc-2[numa?]
-	sys-libs/zlib
-	cuda? ( dev-util/nvidia-cuda-toolkit )
-	elibc_FreeBSD? ( dev-libs/libexecinfo )
-	java? ( >=virtual/jre-1.6:* )
-	openmpi_fabrics_ofed? ( sys-fabric/ofed:* )
-	openmpi_fabrics_knem? ( sys-cluster/knem )
-	openmpi_fabrics_open-mx? ( sys-cluster/open-mx )
-	openmpi_fabrics_psm? ( sys-fabric/infinipath-psm:* )
-	openmpi_rm_pbs? ( sys-cluster/torque )
-	openmpi_rm_slurm? ( sys-cluster/slurm )
-	openmpi_ofed_features_rdmacm? ( sys-fabric/librdmacm:* )
-	$(mpi_imp_deplist)"
-DEPEND="${RDEPEND}
-	java? ( >=virtual/jdk-1.6 )"
-
-pkg_setup() {
-	fortran-2_pkg_setup
-	java-pkg-opt-2_pkg_setup
-	MPI_ESELECT_FILE="eselect.mpi.openmpi"
-
-	if use mpi-threads; then
-		echo
-		ewarn "WARNING: use of MPI_THREAD_MULTIPLE is still disabled by"
-		ewarn "default and officially unsupported by upstream."
-		ewarn "You may stop now and set USE=-mpi-threads"
-		echo
-	fi
-
-	echo
-	elog "OpenMPI has an overwhelming count of configuration options."
-	elog "Don't forget the EXTRA_ECONF environment variable can let you"
-	elog "specify configure options if you find them necessary."
-	echo
-}
-
-src_prepare() {
-	# Necessary for scalibility, see
-	# http://www.open-mpi.org/community/lists/users/2008/09/6514.php
-	if use threads; then
-		echo 'oob_tcp_listen_mode = listen_thread' \
-			>> opal/etc/openmpi-mca-params.conf
-	fi
-}
-
-src_configure() {
-	local myconf=(
-		--sysconfdir="${EPREFIX}/etc/${PN}"
-		--enable-pretty-print-stacktrace
-		--enable-orterun-prefix-by-default
-		--with-hwloc="${EPREFIX}/usr"
-		--with-libltdl="${EPREFIX}/usr"
-		)
-
-	if use fortran; then
-		myconf+=(--enable-mpi-fortran=all)
-	else
-		myconf+=(--enable-mpi-fortran=no)
-	fi
-
-	if use java; then
-		# We must always build with the right -source and -target
-		# flags. Passing flags to javac isn't explicitly supported here
-		# but we can cheat by overriding the configure test for javac.
-		export ac_cv_path_JAVAC="$(java-pkg_get-javac) $(java-pkg_javac-args)"
-	fi
-
-	! use vt && myconf+=(--enable-contrib-no-build=vt)
-
-	econf $(mpi_econf_args) "${myconf[@]}" \
-		$(use_enable cxx mpi-cxx) \
-		$(use_with cma) \
-		$(use_with cuda cuda "${EPREFIX}"/opt/cuda) \
-		$(use_enable romio io-romio) \
-		$(use_enable heterogeneous) \
-		$(use_enable ipv6) \
-		$(use_enable java) \
-		$(use_enable java mpi-java) \
-		$(use_enable mpi-threads mpi-thread-multiple) \
-		$(use_with openmpi_fabrics_ofed verbs "${EPREFIX}"/usr) \
-		$(use_with openmpi_fabrics_knem knem "${EPREFIX}"/usr) \
-		$(use_with openmpi_fabrics_open-mx mx "${EPREFIX}"/usr) \
-		$(use_with openmpi_fabrics_psm psm "${EPREFIX}"/usr) \
-		$(use_enable openmpi_ofed_features_control-hdr-padding openib-control-hdr-padding) \
-		$(use_enable openmpi_ofed_features_connectx-xrc openib-connectx-xrc) \
-		$(use_enable openmpi_ofed_features_rdmacm openib-rdmacm) \
-		$(use_enable openmpi_ofed_features_udcm openib-udcm) \
-		$(use_enable openmpi_ofed_features_dynamic-sl openib-dynamic-sl) \
-		$(use_enable openmpi_ofed_features_failover btl-openib-failover) \
-		$(use_with openmpi_rm_pbs tm) \
-		$(use_with openmpi_rm_slurm slurm)
-}
-
-src_install () {
-	default
-
-	# From USE=vt see #359917
-	rm "${ED}"/$(mpi_root)/usr/share/libtool &> /dev/null
-
-	# Avoid collisions with libevent
-	rm -rf "${ED}"/$(mpi_root)/usr/include/event2 &> /dev/null
-
-	# Remove la files, no static libs are installed and we have pkg-config
-	find "${ED}"/$(mpi_root)/usr/$(get_libdir)/ -type f -name '*.la' -delete
-
-	if use java; then
-		local mpi_jar="${ED}"/$(mpi_root)/usr/$(get_libdir)/mpi.jar
-		java-pkg_dojar "${mpi_jar}"
-		# We don't want to install the jar file twice
-		# so let's clean after ourselves.
-		rm "${mpi_jar}" || die
-	fi
-
-	mpi_dodoc README AUTHORS NEWS VERSION
-	mpi_imp_add_eselect
-}
-
-src_test() {
-	# Doesn't work with the default src_test as the dry run (-n) fails.
-	emake -j1 check
-}
diff --git a/sys-cluster/openmpi/openmpi-2.0.4.ebuild b/sys-cluster/openmpi/openmpi-2.0.4.ebuild
deleted file mode 100644
index bfd34c9b0..000000000
--- a/sys-cluster/openmpi/openmpi-2.0.4.ebuild
+++ /dev/null
@@ -1,177 +0,0 @@
-# Copyright 1999-2018 Gentoo Foundation
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=6
-
-FORTRAN_NEEDED=fortran
-
-inherit cuda flag-o-matic fortran-2 java-pkg-opt-2 toolchain-funcs versionator multilib-minimal mpi
-
-MY_P=${P/-mpi}
-S=${WORKDIR}/${MY_P}
-
-IUSE_OPENMPI_FABRICS="
-	openmpi_fabrics_ofed
-	openmpi_fabrics_knem
-	openmpi_fabrics_psm"
-
-IUSE_OPENMPI_RM="
-	openmpi_rm_pbs
-	openmpi_rm_slurm"
-
-IUSE_OPENMPI_OFED_FEATURES="
-	openmpi_ofed_features_control-hdr-padding
-	openmpi_ofed_features_connectx-xrc
-	openmpi_ofed_features_udcm
-	openmpi_ofed_features_rdmacm
-	openmpi_ofed_features_dynamic-sl
-	openmpi_ofed_features_failover"
-
-DESCRIPTION="A high-performance message passing library (MPI)"
-HOMEPAGE="http://www.open-mpi.org"
-SRC_URI="http://www.open-mpi.org/software/ompi/v$(get_version_component_range 1-2)/downloads/${MY_P}.tar.bz2"
-LICENSE="BSD"
-SLOT="0"
-KEYWORDS="~amd64 ~x86 ~amd64-linux"
-IUSE="cma cuda cxx elibc_FreeBSD fortran heterogeneous ipv6 java mpi-threads numa romio threads
-	${IUSE_OPENMPI_FABRICS} ${IUSE_OPENMPI_RM} ${IUSE_OPENMPI_OFED_FEATURES}"
-
-REQUIRED_USE="openmpi_rm_slurm? ( !openmpi_rm_pbs )
-	openmpi_rm_pbs? ( !openmpi_rm_slurm )
-	openmpi_fabrics_psm? ( openmpi_fabrics_ofed )
-	openmpi_ofed_features_control-hdr-padding? ( openmpi_fabrics_ofed )
-	openmpi_ofed_features_connectx-xrc? ( openmpi_fabrics_ofed )
-	openmpi_ofed_features_udcm? ( openmpi_fabrics_ofed )
-	openmpi_ofed_features_rdmacm? ( openmpi_fabrics_ofed )
-	openmpi_ofed_features_dynamic-sl? ( openmpi_fabrics_ofed )
-	openmpi_ofed_features_failover? ( openmpi_fabrics_ofed )"
-
-MPI_UNCLASSED_DEP_STR="
-	!sys-cluster/pmix
-"
-
-CDEPEND="
-	>=dev-libs/libevent-2.0.22[${MULTILIB_USEDEP},threads]
-	dev-libs/libltdl:0[${MULTILIB_USEDEP}]
-	<sys-apps/hwloc-2[${MULTILIB_USEDEP},numa?]
-	>=sys-libs/zlib-1.2.8-r1[${MULTILIB_USEDEP}]
-	cuda? ( >=dev-util/nvidia-cuda-toolkit-6.5.19-r1 )
-	elibc_FreeBSD? ( dev-libs/libexecinfo )
-	openmpi_fabrics_ofed? ( sys-fabric/ofed:* )
-	openmpi_fabrics_knem? ( sys-cluster/knem )
-	openmpi_fabrics_psm? ( sys-fabric/infinipath-psm:* )
-	openmpi_rm_pbs? ( sys-cluster/torque )
-	openmpi_rm_slurm? ( sys-cluster/slurm )
-	openmpi_ofed_features_rdmacm? ( sys-fabric/librdmacm:* )
-	$(mpi_imp_deplist)"
-
-RDEPEND="${CDEPEND}
-	java? ( >=virtual/jre-1.6 )"
-
-DEPEND="${CDEPEND}
-	java? ( >=virtual/jdk-1.6 )"
-
-MULTILIB_WRAPPED_HEADERS=(
-	/usr/include/mpi.h
-	/usr/include/openmpi/ompi/mpi/java/mpiJava.h
-)
-
-pkg_setup() {
-	fortran-2_pkg_setup
-	java-pkg-opt-2_pkg_setup
-	MPI_ESELECT_FILE="eselect.mpi.openmpi"
-
-	elog
-	elog "OpenMPI has an overwhelming count of configuration options."
-	elog "Don't forget the EXTRA_ECONF environment variable can let you"
-	elog "specify configure options if you find them necessary."
-	elog
-}
-
-src_prepare() {
-	default
-
-	# Necessary for scalibility, see
-	# http://www.open-mpi.org/community/lists/users/2008/09/6514.php
-	if use threads; then
-		echo 'oob_tcp_listen_mode = listen_thread' \
-			>> opal/etc/openmpi-mca-params.conf || die
-	fi
-}
-
-multilib_src_configure() {
-	if use java; then
-		# We must always build with the right -source and -target
-		# flags. Passing flags to javac isn't explicitly supported here
-		# but we can cheat by overriding the configure test for javac.
-		export ac_cv_path_JAVAC="$(java-pkg_get-javac) $(java-pkg_javac-args)"
-	fi
-
-	ECONF_SOURCE=${S} econf $(mpi_econf_args) \
-		--sysconfdir="${EPREFIX}/etc/${PN}" \
-		--enable-pretty-print-stacktrace \
-		--enable-orterun-prefix-by-default \
-		--with-hwloc="${EPREFIX}/usr" \
-		--with-libltdl="${EPREFIX}/usr" \
-		--with-libevent="${EPREFIX}/usr" \
-		--enable-mpi-fortran=$(usex fortran all no) \
-		$(use_enable cxx mpi-cxx) \
-		$(use_with cma) \
-		$(use_with cuda cuda "${EPREFIX}"/opt/cuda) \
-		$(use_enable romio io-romio) \
-		$(use_enable heterogeneous) \
-		$(use_enable ipv6) \
-		$(multilib_native_use_enable java) \
-		$(multilib_native_use_enable java mpi-java) \
-		$(multilib_native_use_enable mpi-threads mpi-thread-multiple) \
-		$(multilib_native_use_with openmpi_fabrics_ofed verbs "${EPREFIX}"/usr) \
-		$(multilib_native_use_with openmpi_fabrics_knem knem "${EPREFIX}"/usr) \
-		$(multilib_native_use_with openmpi_fabrics_psm psm "${EPREFIX}"/usr) \
-		$(multilib_native_use_enable openmpi_ofed_features_control-hdr-padding openib-control-hdr-padding) \
-		$(multilib_native_use_enable openmpi_ofed_features_connectx-xrc openib-connectx-xrc) \
-		$(multilib_native_use_enable openmpi_ofed_features_rdmacm openib-rdmacm) \
-		$(multilib_native_use_enable openmpi_ofed_features_udcm openib-udcm) \
-		$(multilib_native_use_enable openmpi_ofed_features_dynamic-sl openib-dynamic-sl) \
-		$(multilib_native_use_enable openmpi_ofed_features_failover btl-openib-failover) \
-		$(multilib_native_use_with openmpi_rm_pbs tm) \
-		$(multilib_native_use_with openmpi_rm_slurm slurm)
-}
-
-multilib_src_test() {
-	# Doesn't work with the default src_test as the dry run (-n) fails.
-	emake -j1 check
-}
-
-multilib_src_install() {
-	default
-
-	# fortran header cannot be wrapped (bug #540508), workaround part 1
-	if multilib_is_native_abi && use fortran; then
-		mkdir "${T}"/fortran || die
-		mv "${ED}"/$(mpi_root)/usr/include/mpif* "${T}"/fortran || die
-	else
-		# some fortran files get installed unconditionally
-		rm "${ED}"/$(mpi_root)/usr/include/mpif* "${ED}"usr/bin/mpif* || die
-	fi
-}
-
-multilib_src_install_all() {
-	# fortran header cannot be wrapped (bug #540508), workaround part 2
-	if use fortran; then
-		mv "${T}"/fortran/mpif* "${ED}"/$(mpi_root)/usr/include || die
-	fi
-
-	# Remove la files, no static libs are installed and we have pkg-config
-	find "${ED}" -name '*.la' -delete || die
-
-	if use java; then
-		local mpi_jar="${ED}"/$(mpi_root)/usr/$(get_libdir)/mpi.jar
-		java-pkg_dojar "${mpi_jar}"
-		# We don't want to install the jar file twice
-		# so let's clean after ourselves.
-		rm "${mpi_jar}" || die
-	fi
-
-	mpi_dodoc README AUTHORS NEWS VERSION
-	mpi_imp_add_eselect
-}
diff --git a/sys-cluster/openmpi/openmpi-2.1.6.ebuild b/sys-cluster/openmpi/openmpi-2.1.6.ebuild
deleted file mode 100644
index f616b2844..000000000
--- a/sys-cluster/openmpi/openmpi-2.1.6.ebuild
+++ /dev/null
@@ -1,176 +0,0 @@
-# Copyright 1999-2019 Gentoo Authors
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=6
-
-FORTRAN_NEEDED=fortran
-
-inherit cuda flag-o-matic fortran-2 java-pkg-opt-2 toolchain-funcs versionator multilib-minimal mpi
-
-MY_P=${P/-mpi}
-S=${WORKDIR}/${MY_P}
-
-IUSE_OPENMPI_FABRICS="
-	openmpi_fabrics_ofed
-	openmpi_fabrics_knem
-	openmpi_fabrics_psm"
-
-IUSE_OPENMPI_RM="
-	openmpi_rm_pbs
-	openmpi_rm_slurm"
-
-IUSE_OPENMPI_OFED_FEATURES="
-	openmpi_ofed_features_control-hdr-padding
-	openmpi_ofed_features_udcm
-	openmpi_ofed_features_rdmacm
-	openmpi_ofed_features_dynamic-sl"
-
-DESCRIPTION="A high-performance message passing library (MPI)"
-HOMEPAGE="http://www.open-mpi.org"
-SRC_URI="http://www.open-mpi.org/software/ompi/v$(get_version_component_range 1-2)/downloads/${MY_P}.tar.bz2"
-LICENSE="BSD"
-SLOT="0"
-KEYWORDS="~amd64 ~x86 ~amd64-linux"
-IUSE="cma cuda cxx elibc_FreeBSD fortran heterogeneous ipv6 java mpi-threads numa romio threads
-	${IUSE_OPENMPI_FABRICS} ${IUSE_OPENMPI_RM} ${IUSE_OPENMPI_OFED_FEATURES}"
-
-REQUIRED_USE="openmpi_rm_slurm? ( !openmpi_rm_pbs )
-	openmpi_rm_pbs? ( !openmpi_rm_slurm )
-	openmpi_fabrics_psm? ( openmpi_fabrics_ofed )
-	openmpi_ofed_features_control-hdr-padding? ( openmpi_fabrics_ofed )
-	openmpi_ofed_features_udcm? ( openmpi_fabrics_ofed )
-	openmpi_ofed_features_rdmacm? ( openmpi_fabrics_ofed )
-	openmpi_ofed_features_dynamic-sl? ( openmpi_fabrics_ofed )"
-
-MPI_UNCLASSED_DEP_STR="
-	!sys-cluster/pmix
-"
-
-CDEPEND="
-	>=dev-libs/libevent-2.0.22[${MULTILIB_USEDEP},threads]
-	dev-libs/libltdl:0[${MULTILIB_USEDEP}]
-	<sys-apps/hwloc-2[${MULTILIB_USEDEP},numa?]
-	>=sys-libs/zlib-1.2.8-r1[${MULTILIB_USEDEP}]
-	cuda? ( >=dev-util/nvidia-cuda-toolkit-6.5.19-r1 )
-	elibc_FreeBSD? ( dev-libs/libexecinfo )
-	openmpi_fabrics_ofed? ( sys-fabric/ofed:* )
-	openmpi_fabrics_knem? ( sys-cluster/knem )
-	openmpi_fabrics_psm? ( sys-fabric/infinipath-psm:* )
-	openmpi_rm_pbs? ( sys-cluster/torque )
-	openmpi_rm_slurm? ( sys-cluster/slurm )
-	openmpi_ofed_features_rdmacm? ( sys-fabric/librdmacm:* )
-	$(mpi_imp_deplist)"
-
-RDEPEND="${CDEPEND}
-	java? ( >=virtual/jre-1.6 )"
-
-DEPEND="${CDEPEND}
-	java? ( >=virtual/jdk-1.6 )"
-
-MULTILIB_WRAPPED_HEADERS=(
-	/usr/include/mpi.h
-	/usr/include/openmpi/ompi/mpi/java/mpiJava.h
-)
-
-pkg_setup() {
-	fortran-2_pkg_setup
-	java-pkg-opt-2_pkg_setup
-	MPI_ESELECT_FILE="eselect.mpi.openmpi"
-
-	elog
-	elog "OpenMPI has an overwhelming count of configuration options."
-	elog "Don't forget the EXTRA_ECONF environment variable can let you"
-	elog "specify configure options if you find them necessary."
-	elog
-}
-
-src_prepare() {
-	default
-
-	# Necessary for scalibility, see
-	# http://www.open-mpi.org/community/lists/users/2008/09/6514.php
-	if use threads; then
-		echo 'oob_tcp_listen_mode = listen_thread' \
-			>> opal/etc/openmpi-mca-params.conf || die
-	fi
-}
-
-multilib_src_configure() {
-	if use java; then
-		# We must always build with the right -source and -target
-		# flags. Passing flags to javac isn't explicitly supported here
-		# but we can cheat by overriding the configure test for javac.
-		export ac_cv_path_JAVAC="$(java-pkg_get-javac) $(java-pkg_javac-args)"
-	fi
-
-	ECONF_SOURCE=${S} econf $(mpi_econf_args) \
-		--sysconfdir="${EPREFIX}/etc/${PN}" \
-		--enable-pretty-print-stacktrace \
-		--enable-orterun-prefix-by-default \
-		--with-hwloc="${EPREFIX}/usr" \
-		--with-libltdl="${EPREFIX}/usr" \
-		--with-libevent="${EPREFIX}/usr" \
-		--enable-mpi-fortran=$(usex fortran all no) \
-		$(use_enable cxx mpi-cxx) \
-		$(use_with cma) \
-		$(use_with cuda cuda "${EPREFIX}"/opt/cuda) \
-		$(use_enable romio io-romio) \
-		$(use_enable heterogeneous) \
-		$(use_enable ipv6) \
-		$(multilib_native_use_enable java) \
-		$(multilib_native_use_enable java mpi-java) \
-		$(multilib_native_use_enable mpi-threads mpi-thread-multiple) \
-		$(multilib_native_use_with openmpi_fabrics_ofed verbs "${EPREFIX}"/usr) \
-		$(multilib_native_use_with openmpi_fabrics_knem knem "${EPREFIX}"/usr) \
-		$(multilib_native_use_with openmpi_fabrics_psm psm "${EPREFIX}"/usr) \
-		$(multilib_native_use_enable openmpi_ofed_features_control-hdr-padding openib-control-hdr-padding) \
-		$(multilib_native_use_enable openmpi_ofed_features_rdmacm openib-rdmacm) \
-		$(multilib_native_use_enable openmpi_ofed_features_udcm openib-udcm) \
-		$(multilib_native_use_enable openmpi_ofed_features_dynamic-sl openib-dynamic-sl) \
-		$(multilib_native_use_with openmpi_rm_pbs tm) \
-		$(multilib_native_use_with openmpi_rm_slurm slurm)
-}
-
-multilib_src_test() {
-	# Doesn't work with the default src_test as the dry run (-n) fails.
-	emake -j1 check
-}
-
-multilib_src_install() {
-	default
-
-	# fortran header cannot be wrapped (bug #540508), workaround part 1
-	if multilib_is_native_abi && use fortran; then
-		mkdir "${T}"/fortran || die
-		mv "${ED}"/$(mpi_root)/usr/include/mpif* "${T}"/fortran || die
-	else
-		# some fortran files get installed unconditionally
-		rm \
-			"${ED}"/$(mpi_root)/usr/include/mpif* \
-			"${ED}"/$(mpi_root)/usr/bin/mpif* \
-			"${ED}"/$(mpi_root)/usr/bin/oshfort \
-			"${ED}"/$(mpi_root)/usr/bin/shmemfort \
-			|| die
-	fi
-}
-
-multilib_src_install_all() {
-	# fortran header cannot be wrapped (bug #540508), workaround part 2
-	if use fortran; then
-		mv "${T}"/fortran/mpif* "${ED}"/$(mpi_root)/usr/include || die
-	fi
-
-	# Remove la files, no static libs are installed and we have pkg-config
-	find "${ED}" -name '*.la' -delete || die
-
-	if use java; then
-		local mpi_jar="${ED}"/$(mpi_root)/usr/$(get_libdir)/mpi.jar
-		java-pkg_dojar "${mpi_jar}"
-		# We don't want to install the jar file twice
-		# so let's clean after ourselves.
-		rm "${mpi_jar}" || die
-	fi
-
-	mpi_dodoc README AUTHORS NEWS VERSION
-	mpi_imp_add_eselect
-}
diff --git a/sys-cluster/openmpi/openmpi-3.0.3.ebuild b/sys-cluster/openmpi/openmpi-3.0.3.ebuild
deleted file mode 100644
index fd6168349..000000000
--- a/sys-cluster/openmpi/openmpi-3.0.3.ebuild
+++ /dev/null
@@ -1,173 +0,0 @@
-# Copyright 1999-2018 Gentoo Foundation
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=6
-
-FORTRAN_NEEDED=fortran
-
-inherit cuda flag-o-matic fortran-2 java-pkg-opt-2 toolchain-funcs versionator multilib-minimal mpi
-
-MY_P=${P/-mpi}
-S=${WORKDIR}/${MY_P}
-
-IUSE_OPENMPI_FABRICS="
-	openmpi_fabrics_ofed
-	openmpi_fabrics_knem
-	openmpi_fabrics_psm"
-
-IUSE_OPENMPI_RM="
-	openmpi_rm_pbs
-	openmpi_rm_slurm"
-
-IUSE_OPENMPI_OFED_FEATURES="
-	openmpi_ofed_features_control-hdr-padding
-	openmpi_ofed_features_udcm
-	openmpi_ofed_features_rdmacm
-	openmpi_ofed_features_dynamic-sl"
-
-DESCRIPTION="A high-performance message passing library (MPI)"
-HOMEPAGE="http://www.open-mpi.org"
-SRC_URI="http://www.open-mpi.org/software/ompi/v$(get_version_component_range 1-2)/downloads/${MY_P}.tar.bz2"
-LICENSE="BSD"
-SLOT="0"
-KEYWORDS="~amd64 ~x86 ~amd64-linux"
-IUSE="cma cuda cxx elibc_FreeBSD fortran heterogeneous ipv6 java numa romio
-	${IUSE_OPENMPI_FABRICS} ${IUSE_OPENMPI_RM} ${IUSE_OPENMPI_OFED_FEATURES}"
-
-REQUIRED_USE="openmpi_rm_slurm? ( !openmpi_rm_pbs )
-	openmpi_rm_pbs? ( !openmpi_rm_slurm )
-	openmpi_fabrics_psm? ( openmpi_fabrics_ofed )
-	openmpi_ofed_features_control-hdr-padding? ( openmpi_fabrics_ofed )
-	openmpi_ofed_features_udcm? ( openmpi_fabrics_ofed )
-	openmpi_ofed_features_rdmacm? ( openmpi_fabrics_ofed )
-	openmpi_ofed_features_dynamic-sl? ( openmpi_fabrics_ofed )"
-
-MPI_UNCLASSED_DEP_STR="
-	!sys-cluster/pmix
-"
-
-CDEPEND="
-	>=dev-libs/libevent-2.0.22[${MULTILIB_USEDEP},threads]
-	dev-libs/libltdl:0[${MULTILIB_USEDEP}]
-	<sys-apps/hwloc-2[${MULTILIB_USEDEP},numa?]
-	>=sys-libs/zlib-1.2.8-r1[${MULTILIB_USEDEP}]
-	cuda? ( >=dev-util/nvidia-cuda-toolkit-6.5.19-r1 )
-	elibc_FreeBSD? ( dev-libs/libexecinfo )
-	openmpi_fabrics_ofed? ( sys-fabric/ofed:* )
-	openmpi_fabrics_knem? ( sys-cluster/knem )
-	openmpi_fabrics_psm? ( sys-fabric/infinipath-psm:* )
-	openmpi_rm_pbs? ( sys-cluster/torque )
-	openmpi_rm_slurm? ( sys-cluster/slurm )
-	openmpi_ofed_features_rdmacm? ( sys-fabric/librdmacm:* )
-	$(mpi_imp_deplist)"
-
-RDEPEND="${CDEPEND}
-	java? ( >=virtual/jre-1.6 )"
-
-DEPEND="${CDEPEND}
-	java? ( >=virtual/jdk-1.6 )"
-
-MULTILIB_WRAPPED_HEADERS=(
-	/usr/include/mpi.h
-	/usr/include/openmpi/ompi/mpi/java/mpiJava.h
-)
-
-pkg_setup() {
-	fortran-2_pkg_setup
-	java-pkg-opt-2_pkg_setup
-	MPI_ESELECT_FILE="eselect.mpi.openmpi"
-
-	elog
-	elog "OpenMPI has an overwhelming count of configuration options."
-	elog "Don't forget the EXTRA_ECONF environment variable can let you"
-	elog "specify configure options if you find them necessary."
-	elog
-}
-
-src_prepare() {
-	default
-
-	# Necessary for scalibility, see
-	# http://www.open-mpi.org/community/lists/users/2008/09/6514.php
-	echo 'oob_tcp_listen_mode = listen_thread' \
-		>> opal/etc/openmpi-mca-params.conf || die
-}
-
-multilib_src_configure() {
-	if use java; then
-		# We must always build with the right -source and -target
-		# flags. Passing flags to javac isn't explicitly supported here
-		# but we can cheat by overriding the configure test for javac.
-		export ac_cv_path_JAVAC="$(java-pkg_get-javac) $(java-pkg_javac-args)"
-	fi
-
-	ECONF_SOURCE=${S} econf $(mpi_econf_args) \
-		--sysconfdir="${EPREFIX}/etc/${PN}" \
-		--enable-pretty-print-stacktrace \
-		--enable-orterun-prefix-by-default \
-		--with-hwloc="${EPREFIX}/usr" \
-		--with-libltdl="${EPREFIX}/usr" \
-		--with-libevent="${EPREFIX}/usr" \
-		--enable-mpi-fortran=$(usex fortran all no) \
-		$(use_enable cxx mpi-cxx) \
-		$(use_with cma) \
-		$(use_with cuda cuda "${EPREFIX}"/opt/cuda) \
-		$(use_enable romio io-romio) \
-		$(use_enable heterogeneous) \
-		$(use_enable ipv6) \
-		$(multilib_native_use_enable java) \
-		$(multilib_native_use_enable java mpi-java) \
-		$(multilib_native_use_with openmpi_fabrics_ofed verbs "${EPREFIX}"/usr) \
-		$(multilib_native_use_with openmpi_fabrics_knem knem "${EPREFIX}"/usr) \
-		$(multilib_native_use_with openmpi_fabrics_psm psm "${EPREFIX}"/usr) \
-		$(multilib_native_use_enable openmpi_ofed_features_control-hdr-padding openib-control-hdr-padding) \
-		$(multilib_native_use_enable openmpi_ofed_features_rdmacm openib-rdmacm) \
-		$(multilib_native_use_enable openmpi_ofed_features_udcm openib-udcm) \
-		$(multilib_native_use_enable openmpi_ofed_features_dynamic-sl openib-dynamic-sl) \
-		$(multilib_native_use_with openmpi_rm_pbs tm) \
-		$(multilib_native_use_with openmpi_rm_slurm slurm)
-}
-
-multilib_src_test() {
-	# Doesn't work with the default src_test as the dry run (-n) fails.
-	emake -j1 check
-}
-
-multilib_src_install() {
-	default
-
-	# fortran header cannot be wrapped (bug #540508), workaround part 1
-	if multilib_is_native_abi && use fortran; then
-		mkdir "${T}"/fortran || die
-		mv "${ED}"/$(mpi_root)/usr/include/mpif* "${T}"/fortran || die
-	else
-		# some fortran files get installed unconditionally
-		rm \
-			"${ED}"/$(mpi_root)/usr/include/mpif* \
-			"${ED}"/$(mpi_root)/usr/bin/mpif* \
-			"${ED}"/$(mpi_root)/usr/bin/oshfort \
-			"${ED}"/$(mpi_root)/usr/bin/shmemfort \
-			|| die
-	fi
-}
-
-multilib_src_install_all() {
-	# fortran header cannot be wrapped (bug #540508), workaround part 2
-	if use fortran; then
-		mv "${T}"/fortran/mpif* "${ED}"/$(mpi_root)/usr/include || die
-	fi
-
-	# Remove la files, no static libs are installed and we have pkg-config
-	find "${ED}" -name '*.la' -delete || die
-
-	if use java; then
-		local mpi_jar="${ED}"/$(mpi_root)/usr/$(get_libdir)/mpi.jar
-		java-pkg_dojar "${mpi_jar}"
-		# We don't want to install the jar file twice
-		# so let's clean after ourselves.
-		rm "${mpi_jar}" || die
-	fi
-
-	mpi_dodoc README AUTHORS NEWS VERSION
-	mpi_imp_add_eselect
-}
diff --git a/sys-cluster/openmpi/openmpi-3.1.3.ebuild b/sys-cluster/openmpi/openmpi-3.1.3.ebuild
deleted file mode 100644
index fd6168349..000000000
--- a/sys-cluster/openmpi/openmpi-3.1.3.ebuild
+++ /dev/null
@@ -1,173 +0,0 @@
-# Copyright 1999-2018 Gentoo Foundation
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=6
-
-FORTRAN_NEEDED=fortran
-
-inherit cuda flag-o-matic fortran-2 java-pkg-opt-2 toolchain-funcs versionator multilib-minimal mpi
-
-MY_P=${P/-mpi}
-S=${WORKDIR}/${MY_P}
-
-IUSE_OPENMPI_FABRICS="
-	openmpi_fabrics_ofed
-	openmpi_fabrics_knem
-	openmpi_fabrics_psm"
-
-IUSE_OPENMPI_RM="
-	openmpi_rm_pbs
-	openmpi_rm_slurm"
-
-IUSE_OPENMPI_OFED_FEATURES="
-	openmpi_ofed_features_control-hdr-padding
-	openmpi_ofed_features_udcm
-	openmpi_ofed_features_rdmacm
-	openmpi_ofed_features_dynamic-sl"
-
-DESCRIPTION="A high-performance message passing library (MPI)"
-HOMEPAGE="http://www.open-mpi.org"
-SRC_URI="http://www.open-mpi.org/software/ompi/v$(get_version_component_range 1-2)/downloads/${MY_P}.tar.bz2"
-LICENSE="BSD"
-SLOT="0"
-KEYWORDS="~amd64 ~x86 ~amd64-linux"
-IUSE="cma cuda cxx elibc_FreeBSD fortran heterogeneous ipv6 java numa romio
-	${IUSE_OPENMPI_FABRICS} ${IUSE_OPENMPI_RM} ${IUSE_OPENMPI_OFED_FEATURES}"
-
-REQUIRED_USE="openmpi_rm_slurm? ( !openmpi_rm_pbs )
-	openmpi_rm_pbs? ( !openmpi_rm_slurm )
-	openmpi_fabrics_psm? ( openmpi_fabrics_ofed )
-	openmpi_ofed_features_control-hdr-padding? ( openmpi_fabrics_ofed )
-	openmpi_ofed_features_udcm? ( openmpi_fabrics_ofed )
-	openmpi_ofed_features_rdmacm? ( openmpi_fabrics_ofed )
-	openmpi_ofed_features_dynamic-sl? ( openmpi_fabrics_ofed )"
-
-MPI_UNCLASSED_DEP_STR="
-	!sys-cluster/pmix
-"
-
-CDEPEND="
-	>=dev-libs/libevent-2.0.22[${MULTILIB_USEDEP},threads]
-	dev-libs/libltdl:0[${MULTILIB_USEDEP}]
-	<sys-apps/hwloc-2[${MULTILIB_USEDEP},numa?]
-	>=sys-libs/zlib-1.2.8-r1[${MULTILIB_USEDEP}]
-	cuda? ( >=dev-util/nvidia-cuda-toolkit-6.5.19-r1 )
-	elibc_FreeBSD? ( dev-libs/libexecinfo )
-	openmpi_fabrics_ofed? ( sys-fabric/ofed:* )
-	openmpi_fabrics_knem? ( sys-cluster/knem )
-	openmpi_fabrics_psm? ( sys-fabric/infinipath-psm:* )
-	openmpi_rm_pbs? ( sys-cluster/torque )
-	openmpi_rm_slurm? ( sys-cluster/slurm )
-	openmpi_ofed_features_rdmacm? ( sys-fabric/librdmacm:* )
-	$(mpi_imp_deplist)"
-
-RDEPEND="${CDEPEND}
-	java? ( >=virtual/jre-1.6 )"
-
-DEPEND="${CDEPEND}
-	java? ( >=virtual/jdk-1.6 )"
-
-MULTILIB_WRAPPED_HEADERS=(
-	/usr/include/mpi.h
-	/usr/include/openmpi/ompi/mpi/java/mpiJava.h
-)
-
-pkg_setup() {
-	fortran-2_pkg_setup
-	java-pkg-opt-2_pkg_setup
-	MPI_ESELECT_FILE="eselect.mpi.openmpi"
-
-	elog
-	elog "OpenMPI has an overwhelming count of configuration options."
-	elog "Don't forget the EXTRA_ECONF environment variable can let you"
-	elog "specify configure options if you find them necessary."
-	elog
-}
-
-src_prepare() {
-	default
-
-	# Necessary for scalibility, see
-	# http://www.open-mpi.org/community/lists/users/2008/09/6514.php
-	echo 'oob_tcp_listen_mode = listen_thread' \
-		>> opal/etc/openmpi-mca-params.conf || die
-}
-
-multilib_src_configure() {
-	if use java; then
-		# We must always build with the right -source and -target
-		# flags. Passing flags to javac isn't explicitly supported here
-		# but we can cheat by overriding the configure test for javac.
-		export ac_cv_path_JAVAC="$(java-pkg_get-javac) $(java-pkg_javac-args)"
-	fi
-
-	ECONF_SOURCE=${S} econf $(mpi_econf_args) \
-		--sysconfdir="${EPREFIX}/etc/${PN}" \
-		--enable-pretty-print-stacktrace \
-		--enable-orterun-prefix-by-default \
-		--with-hwloc="${EPREFIX}/usr" \
-		--with-libltdl="${EPREFIX}/usr" \
-		--with-libevent="${EPREFIX}/usr" \
-		--enable-mpi-fortran=$(usex fortran all no) \
-		$(use_enable cxx mpi-cxx) \
-		$(use_with cma) \
-		$(use_with cuda cuda "${EPREFIX}"/opt/cuda) \
-		$(use_enable romio io-romio) \
-		$(use_enable heterogeneous) \
-		$(use_enable ipv6) \
-		$(multilib_native_use_enable java) \
-		$(multilib_native_use_enable java mpi-java) \
-		$(multilib_native_use_with openmpi_fabrics_ofed verbs "${EPREFIX}"/usr) \
-		$(multilib_native_use_with openmpi_fabrics_knem knem "${EPREFIX}"/usr) \
-		$(multilib_native_use_with openmpi_fabrics_psm psm "${EPREFIX}"/usr) \
-		$(multilib_native_use_enable openmpi_ofed_features_control-hdr-padding openib-control-hdr-padding) \
-		$(multilib_native_use_enable openmpi_ofed_features_rdmacm openib-rdmacm) \
-		$(multilib_native_use_enable openmpi_ofed_features_udcm openib-udcm) \
-		$(multilib_native_use_enable openmpi_ofed_features_dynamic-sl openib-dynamic-sl) \
-		$(multilib_native_use_with openmpi_rm_pbs tm) \
-		$(multilib_native_use_with openmpi_rm_slurm slurm)
-}
-
-multilib_src_test() {
-	# Doesn't work with the default src_test as the dry run (-n) fails.
-	emake -j1 check
-}
-
-multilib_src_install() {
-	default
-
-	# fortran header cannot be wrapped (bug #540508), workaround part 1
-	if multilib_is_native_abi && use fortran; then
-		mkdir "${T}"/fortran || die
-		mv "${ED}"/$(mpi_root)/usr/include/mpif* "${T}"/fortran || die
-	else
-		# some fortran files get installed unconditionally
-		rm \
-			"${ED}"/$(mpi_root)/usr/include/mpif* \
-			"${ED}"/$(mpi_root)/usr/bin/mpif* \
-			"${ED}"/$(mpi_root)/usr/bin/oshfort \
-			"${ED}"/$(mpi_root)/usr/bin/shmemfort \
-			|| die
-	fi
-}
-
-multilib_src_install_all() {
-	# fortran header cannot be wrapped (bug #540508), workaround part 2
-	if use fortran; then
-		mv "${T}"/fortran/mpif* "${ED}"/$(mpi_root)/usr/include || die
-	fi
-
-	# Remove la files, no static libs are installed and we have pkg-config
-	find "${ED}" -name '*.la' -delete || die
-
-	if use java; then
-		local mpi_jar="${ED}"/$(mpi_root)/usr/$(get_libdir)/mpi.jar
-		java-pkg_dojar "${mpi_jar}"
-		# We don't want to install the jar file twice
-		# so let's clean after ourselves.
-		rm "${mpi_jar}" || die
-	fi
-
-	mpi_dodoc README AUTHORS NEWS VERSION
-	mpi_imp_add_eselect
-}
diff --git a/sys-cluster/openmpi/openmpi-4.0.0.ebuild b/sys-cluster/openmpi/openmpi-4.0.0.ebuild
deleted file mode 100644
index 5fd6e1b85..000000000
--- a/sys-cluster/openmpi/openmpi-4.0.0.ebuild
+++ /dev/null
@@ -1,172 +0,0 @@
-# Copyright 1999-2019 Gentoo Authors
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=6
-
-FORTRAN_NEEDED=fortran
-
-inherit cuda eapi7-ver flag-o-matic fortran-2 java-pkg-opt-2 toolchain-funcs multilib-minimal mpi
-
-MY_P=${P/-mpi}
-S=${WORKDIR}/${MY_P}
-
-IUSE_OPENMPI_FABRICS="
-	openmpi_fabrics_ofed
-	openmpi_fabrics_knem
-	openmpi_fabrics_psm"
-
-IUSE_OPENMPI_RM="
-	openmpi_rm_pbs
-	openmpi_rm_slurm"
-
-IUSE_OPENMPI_OFED_FEATURES="
-	openmpi_ofed_features_control-hdr-padding
-	openmpi_ofed_features_udcm
-	openmpi_ofed_features_rdmacm
-	openmpi_ofed_features_dynamic-sl"
-
-DESCRIPTION="A high-performance message passing library (MPI)"
-HOMEPAGE="http://www.open-mpi.org"
-SRC_URI="http://www.open-mpi.org/software/ompi/v$(ver_cut 1-2)/downloads/${MY_P}.tar.bz2"
-LICENSE="BSD"
-SLOT="0"
-KEYWORDS="~amd64 ~x86 ~amd64-linux"
-IUSE="cma cuda cxx elibc_FreeBSD fortran heterogeneous ipv6 java numa romio
-	${IUSE_OPENMPI_FABRICS} ${IUSE_OPENMPI_RM} ${IUSE_OPENMPI_OFED_FEATURES}"
-
-REQUIRED_USE="openmpi_rm_slurm? ( !openmpi_rm_pbs )
-	openmpi_rm_pbs? ( !openmpi_rm_slurm )
-	openmpi_fabrics_psm? ( openmpi_fabrics_ofed )
-	openmpi_ofed_features_control-hdr-padding? ( openmpi_fabrics_ofed )
-	openmpi_ofed_features_udcm? ( openmpi_fabrics_ofed )
-	openmpi_ofed_features_rdmacm? ( openmpi_fabrics_ofed )
-	openmpi_ofed_features_dynamic-sl? ( openmpi_fabrics_ofed )"
-
-MPI_UNCLASSED_DEP_STR="
-	!sys-cluster/pmix
-"
-
-CDEPEND="
-	>=dev-libs/libevent-2.0.22[${MULTILIB_USEDEP},threads]
-	dev-libs/libltdl:0[${MULTILIB_USEDEP}]
-	>=sys-apps/hwloc-2.0.2[${MULTILIB_USEDEP},numa?]
-	>=sys-libs/zlib-1.2.8-r1[${MULTILIB_USEDEP}]
-	cuda? ( >=dev-util/nvidia-cuda-toolkit-6.5.19-r1:= )
-	elibc_FreeBSD? ( dev-libs/libexecinfo )
-	openmpi_fabrics_ofed? ( sys-fabric/ofed:* )
-	openmpi_fabrics_knem? ( sys-cluster/knem )
-	openmpi_fabrics_psm? ( sys-fabric/infinipath-psm:* )
-	openmpi_rm_pbs? ( sys-cluster/torque )
-	openmpi_rm_slurm? ( sys-cluster/slurm )
-	openmpi_ofed_features_rdmacm? ( sys-fabric/librdmacm:* )
-	$(mpi_imp_deplist)"
-
-RDEPEND="${CDEPEND}
-	java? ( >=virtual/jre-1.6 )"
-
-DEPEND="${CDEPEND}
-	java? ( >=virtual/jdk-1.6 )"
-
-MULTILIB_WRAPPED_HEADERS=(
-	/usr/include/mpi.h
-	/usr/include/openmpi/ompi/mpi/java/mpiJava.h
-)
-
-pkg_setup() {
-	fortran-2_pkg_setup
-	java-pkg-opt-2_pkg_setup
-	MPI_ESELECT_FILE="eselect.mpi.openmpi"
-
-	elog
-	elog "OpenMPI has an overwhelming count of configuration options."
-	elog "Don't forget the EXTRA_ECONF environment variable can let you"
-	elog "specify configure options if you find them necessary."
-	elog
-}
-
-src_prepare() {
-	default
-
-	# Necessary for scalibility, see
-	# http://www.open-mpi.org/community/lists/users/2008/09/6514.php
-	echo 'oob_tcp_listen_mode = listen_thread' \
-		>> opal/etc/openmpi-mca-params.conf || die
-}
-
-multilib_src_configure() {
-	if use java; then
-		# We must always build with the right -source and -target
-		# flags. Passing flags to javac isn't explicitly supported here
-		# but we can cheat by overriding the configure test for javac.
-		export ac_cv_path_JAVAC="$(java-pkg_get-javac) $(java-pkg_javac-args)"
-	fi
-
-	ECONF_SOURCE=${S} econf $(mpi_econf_args) \
-		--sysconfdir="${EPREFIX}/etc/${PN}" \
-		--enable-pretty-print-stacktrace \
-		--enable-orterun-prefix-by-default \
-		--with-hwloc="${EPREFIX}/usr" \
-		--with-libltdl="${EPREFIX}/usr" \
-		--with-libevent="${EPREFIX}/usr" \
-		--enable-mpi-fortran=$(usex fortran all no) \
-		$(use_enable cxx mpi-cxx) \
-		$(use_with cma) \
-		$(multilib_native_use_with cuda cuda "${EPREFIX}"/opt/cuda) \
-		$(use_enable romio io-romio) \
-		$(use_enable heterogeneous) \
-		$(use_enable ipv6) \
-		$(multilib_native_use_enable java mpi-java) \
-		$(multilib_native_use_with openmpi_fabrics_ofed verbs "${EPREFIX}"/usr) \
-		$(multilib_native_use_with openmpi_fabrics_knem knem "${EPREFIX}"/usr) \
-		$(multilib_native_use_with openmpi_fabrics_psm psm "${EPREFIX}"/usr) \
-		$(multilib_native_use_enable openmpi_ofed_features_control-hdr-padding openib-control-hdr-padding) \
-		$(multilib_native_use_enable openmpi_ofed_features_rdmacm openib-rdmacm) \
-		$(multilib_native_use_enable openmpi_ofed_features_udcm openib-udcm) \
-		$(multilib_native_use_enable openmpi_ofed_features_dynamic-sl openib-dynamic-sl) \
-		$(multilib_native_use_with openmpi_rm_pbs tm) \
-		$(multilib_native_use_with openmpi_rm_slurm slurm)
-}
-
-multilib_src_test() {
-	# Doesn't work with the default src_test as the dry run (-n) fails.
-	emake -j1 check
-}
-
-multilib_src_install() {
-	default
-
-	# fortran header cannot be wrapped (bug #540508), workaround part 1
-	if multilib_is_native_abi && use fortran; then
-		mkdir "${T}"/fortran || die
-		mv "${ED}"/$(mpi_root)/usr/include/mpif* "${T}"/fortran || die
-	else
-		# some fortran files get installed unconditionally
-		rm \
-			"${ED}"/$(mpi_root)/usr/include/mpif* \
-			"${ED}"/$(mpi_root)/usr/bin/mpif* \
-			"${ED}"/$(mpi_root)/usr/bin/oshfort \
-			"${ED}"/$(mpi_root)/usr/bin/shmemfort \
-			|| die
-	fi
-}
-
-multilib_src_install_all() {
-	# fortran header cannot be wrapped (bug #540508), workaround part 2
-	if use fortran; then
-		mv "${T}"/fortran/mpif* "${ED}"/$(mpi_root)/usr/include || die
-	fi
-
-	# Remove la files, no static libs are installed and we have pkg-config
-	find "${ED}" -name '*.la' -delete || die
-
-	if use java; then
-		local mpi_jar="${ED}"/$(mpi_root)/usr/$(get_libdir)/mpi.jar
-		java-pkg_dojar "${mpi_jar}"
-		# We don't want to install the jar file twice
-		# so let's clean after ourselves.
-		rm "${mpi_jar}" || die
-	fi
-
-	mpi_dodoc README AUTHORS NEWS VERSION
-	mpi_imp_add_eselect
-}
diff --git a/sys-cluster/pyslice/Manifest b/sys-cluster/pyslice/Manifest
deleted file mode 100644
index 3bb447557..000000000
--- a/sys-cluster/pyslice/Manifest
+++ /dev/null
@@ -1 +0,0 @@
-DIST pyslice-1.7.tar.gz 24422 SHA256 83a832779eb3f38ee16e5eee179e38e715e905865148330ea6899c4475221798 SHA512 a2213deaf7d7873e1f2ecdb42d11df4dd823b7556b840b43978164f3a24911a9ffbeb17747032a2df0331ce1b6fb31c0c904e2be48330ab5ad30f5ce12ce4fee WHIRLPOOL 40bc25533d6c04eafe701d88eb35bd555d60e3e6e850c616cdc1621cf984e7284212bdd25215931c72a01be0c1c8dd18835b62cee9f8c933e1db425d9d8a89a2
diff --git a/sys-cluster/pyslice/metadata.xml b/sys-cluster/pyslice/metadata.xml
deleted file mode 100644
index 7624e48f8..000000000
--- a/sys-cluster/pyslice/metadata.xml
+++ /dev/null
@@ -1,15 +0,0 @@
-<?xml version="1.0" encoding="UTF-8"?>
-<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
-<pkgmetadata>
-	<maintainer type="project">
-		<email>cluster@gentoo.org</email>
-		<name>Gentoo Cluster Project</name>
-	</maintainer>
-	<longdescription>
-Templating system for parametric modeling.
-</longdescription>
-	<upstream>
-		<remote-id type="pypi">pyslice</remote-id>
-		<remote-id type="sourceforge">pyslice</remote-id>
-	</upstream>
-</pkgmetadata>
diff --git a/sys-cluster/pyslice/pyslice-1.7.ebuild b/sys-cluster/pyslice/pyslice-1.7.ebuild
deleted file mode 100644
index 7177ab13f..000000000
--- a/sys-cluster/pyslice/pyslice-1.7.ebuild
+++ /dev/null
@@ -1,20 +0,0 @@
-# Copyright 1999-2017 Gentoo Foundation
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=6
-
-PYTHON_COMPAT=( python2_7 )
-
-inherit distutils-r1
-
-DESCRIPTION="Templating system for parametric modeling"
-HOMEPAGE="http://pyslice.sourceforge.net/"
-SRC_URI="mirror://pypi/${PN:0:1}/${PN}/${P}.tar.gz"
-
-LICENSE="GPL-2"
-SLOT="0"
-KEYWORDS="~amd64 ~x86"
-IUSE=""
-
-RDEPEND=""
-DEPEND="dev-python/setuptools[${PYTHON_USEDEP}]"
diff --git a/sys-devel/DPC++/DPC++-2021.12.ebuild b/sys-devel/DPC++/DPC++-2021.12.ebuild
new file mode 100644
index 000000000..348b6f8d6
--- /dev/null
+++ b/sys-devel/DPC++/DPC++-2021.12.ebuild
@@ -0,0 +1,177 @@
+# Copyright 2022 Gentoo Authors
+# Distributed under the terms of the GNU General Public License v2
+
+EAPI=8
+
+PYTHON_COMPAT=( python3_{10..12} )
+inherit cmake python-any-r1
+DOCS_BUILDER="doxygen"
+DOCS_DIR="build/docs"
+DOCS_CONFIG_NAME="doxygen.cfg"
+DOCS_DEPEND="
+	media-gfx/graphviz
+	virtual/latex-base
+	$(python_gen_any_dep '
+		dev-python/sphinx[${PYTHON_USEDEP}]
+		dev-python/recommonmark[${PYTHON_USEDEP}]
+		dev-python/myst-parser[${PYTHON_USEDEP}]
+	')
+"
+inherit docs
+
+# We cannot unbundle this because it has to be compiled with the clang/llvm
+# that we are building here. Otherwise we run into problems running the compiler.
+CPU_EMUL_PV="2022-08-22"
+VC_INTR_PV="0.8.1" # Newer versions cause compile failure
+
+DESCRIPTION="oneAPI Data Parallel C++ compiler"
+HOMEPAGE="https://github.com/intel/llvm"
+SRC_URI="
+	https://github.com/intel/llvm/archive/refs/tags/${PV//./-}.tar.gz -> ${P}.tar.gz
+	https://github.com/intel/vc-intrinsics/archive/refs/tags/v${VC_INTR_PV}.tar.gz -> ${P}-vc-intrinsics-${VC_INTR_PV}.tar.gz
+	esimd_emulator? ( https://github.com/intel/cm-cpu-emulation/archive/refs/tags/v${CPU_EMUL_PV}.tar.gz -> ${P}-cm-cpu-emulation-${CPU_EMUL_PV}.tar.gz )
+"
+S="${WORKDIR}/llvm-${PV//./-}"
+CMAKE_USE_DIR="${S}/llvm"
+BUILD_DIR="${S}/build"
+
+LICENSE="Apache-2.0 MIT"
+SLOT="0/5" # Based on libsycl.so
+KEYWORDS="~amd64"
+
+ALL_LLVM_TARGETS=( AArch64 AMDGPU ARM AVR BPF Hexagon Lanai Mips MSP430
+	NVPTX PowerPC RISCV Sparc SystemZ WebAssembly X86 XCore )
+ALL_LLVM_TARGETS=( "${ALL_LLVM_TARGETS[@]/#/llvm_targets_}" )
+LLVM_TARGET_USEDEPS=${ALL_LLVM_TARGETS[@]/%/(-)?}
+
+IUSE="cuda hip test esimd_emulator ${ALL_LLVM_TARGETS[*]}"
+REQUIRED_USE="
+	?? ( cuda hip )
+	cuda? ( llvm_targets_NVPTX )
+	hip? ( llvm_targets_AMDGPU )
+"
+RESTRICT="!test? ( test )"
+
+BDEPEND="virtual/pkgconfig"
+
+DEPEND="
+	dev-libs/boost:=
+	dev-libs/level-zero:=
+	dev-libs/opencl-icd-loader
+	dev-util/opencl-headers
+	dev-util/spirv-headers
+	dev-util/spirv-tools
+	media-libs/libva
+	dev-build/libtool
+	esimd_emulator? ( dev-libs/libffi:= )
+	cuda? ( dev-util/nvidia-cuda-toolkit:= )
+	hip? ( dev-util/hip:= )
+"
+RDEPEND="${DEPEND}"
+
+PATCHES=(
+	"${FILESDIR}/${P}-system-libs.patch"
+)
+
+src_configure() {
+	# Extracted from buildbot/configure.py
+	local mycmakeargs=(
+		-DLLVM_ENABLE_ASSERTIONS=ON
+		-DLLVM_TARGETS_TO_BUILD="${LLVM_TARGETS// /;}"
+		-DLLVM_EXTERNAL_PROJECTS="sycl;llvm-spirv;opencl;libdevice;xpti;xptifw"
+		-DLLVM_EXTERNAL_SYCL_SOURCE_DIR="${S}/sycl"
+		-DLLVM_EXTERNAL_LLVM_SPIRV_SOURCE_DIR="${S}/llvm-spirv"
+		-DLLVM_EXTERNAL_XPTI_SOURCE_DIR="${S}/xpti"
+		-DXPTI_SOURCE_DIR="${S}/xpti"
+		-DLLVM_EXTERNAL_XPTIFW_SOURCE_DIR="${S}/xptifw"
+		-DLLVM_EXTERNAL_LIBDEVICE_SOURCE_DIR="${S}/libdevice"
+		-DLLVM_ENABLE_PROJECTS="clang;sycl;llvm-spirv;opencl;libdevice;xpti;xptifw"
+		-DLLVM_BUILD_TOOLS=ON
+		-DSYCL_ENABLE_WERROR=OFF
+		-DSYCL_INCLUDE_TESTS="$(usex test)"
+		-DCLANG_INCLUDE_TESTS="$(usex test)"
+		-DLLVM_INCLUDE_TESTS="$(usex test)"
+		-DLLVM_SPIRV_INCLUDE_TESTS="$(usex test)"
+		-DLLVM_ENABLE_DOXYGEN="$(usex doc)"
+		-DLLVM_ENABLE_SPHINX="$(usex doc)"
+		-DLLVM_BUILD_DOCS="$(usex doc)"
+		-DSYCL_ENABLE_XPTI_TRACING=ON
+		-DLLVM_ENABLE_LLD=OFF
+		-DXPTI_ENABLE_WERROR=OFF
+		-DSYCL_BUILD_PI_ESIMD_EMULATOR="$(usex esimd_emulator)"
+		-DSYCL_BUILD_PI_CUDA="$(usex cuda)"
+		-DSYCL_BUILD_PI_HIP="$(usex hip)"
+		-DLLVM_EXTERNAL_SPIRV_HEADERS_SOURCE_DIR="${ESYSROOT}/usr"
+		-DLEVEL_ZERO_LIBRARY="${ESYSROOT}/usr/lib64/libze_loader.so"
+		-DLEVEL_ZERO_INCLUDE_DIR="${ESYSROOT}/usr/include"
+		-DLLVMGenXIntrinsics_SOURCE_DIR="${WORKDIR}/vc-intrinsics-${VC_INTR_PV}"
+		-DSYCL_CLANG_EXTRA_FLAGS="${CXXFLAGS}"
+		# The sycl part of the build system insists on installing during compiling
+		# Install it to some temporary directory
+		-DCMAKE_INSTALL_PREFIX="${BUILD_DIR}/install"
+		-DCMAKE_INSTALL_MANDIR="${BUILD_DIR}/install/share/man"
+		-DCMAKE_INSTALL_INFODIR="${BUILD_DIR}/install/share/info"
+		-DCMAKE_INSTALL_DOCDIR="${BUILD_DIR}/install/share/doc/${PF}"
+	)
+
+	if use hip; then
+		mycmakeargs+=(
+			-DSYCL_BUILD_PI_HIP_PLATFORM=AMD
+			-DLIBCLC_GENERATE_REMANGLED_VARIANTS=ON
+			-DLIBCLC_TARGETS_TO_BUILD=";amdgcn--;amdgcn--amdhsa"
+		)
+	fi
+
+	if use cuda; then
+		mycmakeargs+=(
+			-DLIBCLC_GENERATE_REMANGLED_VARIANTS=ON
+			-DLIBCLC_TARGETS_TO_BUILD=";nvptx64--;nvptx64--nvidiacl"
+		)
+	fi
+
+	if use esimd_emulator; then
+		mycmakeargs+=(
+			-DLibFFI_INCLUDE_DIR="${ESYSROOT}/usr/lib64/libffi/include"
+			-DUSE_LOCAL_CM_EMU_SOURCE="${WORKDIR}/cm-cpu-emulation-${CPU_EMUL_PV}"
+		)
+	fi
+
+	if use doc; then
+		mycmakeargs+=( -DSPHINX_WARNINGS_AS_ERRORS=OFF )
+	fi
+
+	cmake_src_configure
+}
+
+src_compile() {
+	# Build sycl (this also installs some stuff already)
+	cmake_build deploy-sycl-toolchain
+
+	use doc && cmake_build doxygen-sycl
+
+	# Install all other files into the same temporary directory
+	cmake_build install
+}
+
+src_test() {
+	cmake_build check
+}
+
+src_install() {
+	einstalldocs
+
+	local LLVM_INTEL_DIR="/usr/lib/llvm/intel"
+	dodir "${LLVM_INTEL_DIR}"
+
+	# Copy our temporary directory to the image directory
+	mv "${BUILD_DIR}/install"/* "${ED}/${LLVM_INTEL_DIR}" || die
+
+	# Copied from llvm ebuild, put env file last so we don't overwrite main llvm/clang
+	newenvd - "60llvm-intel" <<-_EOF_
+		PATH="${EPREFIX}${LLVM_INTEL_DIR}/bin"
+		# we need to duplicate it in ROOTPATH for Portage to respect...
+		ROOTPATH="${EPREFIX}${LLVM_INTEL_DIR}/bin"
+		MANPATH="${EPREFIX}${LLVM_INTEL_DIR}/share/man"
+		LDPATH="${EPREFIX}${LLVM_INTEL_DIR}/lib:${EPREFIX}${LLVM_INTEL_DIR}/lib64"
+	_EOF_
+}
diff --git a/sys-devel/DPC++/DPC++-2022.09.ebuild b/sys-devel/DPC++/DPC++-2022.09.ebuild
new file mode 100644
index 000000000..ee2077566
--- /dev/null
+++ b/sys-devel/DPC++/DPC++-2022.09.ebuild
@@ -0,0 +1,176 @@
+# Copyright 2022 Gentoo Authors
+# Distributed under the terms of the GNU General Public License v2
+
+EAPI=8
+
+PYTHON_COMPAT=( python3_{10..12} )
+inherit cmake python-any-r1
+DOCS_BUILDER="doxygen"
+DOCS_DIR="build/docs"
+DOCS_CONFIG_NAME="doxygen.cfg"
+DOCS_DEPEND="
+	media-gfx/graphviz
+	virtual/latex-base
+	$(python_gen_any_dep '
+		dev-python/sphinx[${PYTHON_USEDEP}]
+		dev-python/recommonmark[${PYTHON_USEDEP}]
+		dev-python/myst-parser[${PYTHON_USEDEP}]
+	')
+"
+inherit docs
+
+# We cannot unbundle this because it has to be compiled with the clang/llvm
+# that we are building here. Otherwise we run into problems running the compiler.
+CPU_EMUL_PV="2022-08-22"
+VC_INTR_PV="0.8.1" # Newer versions cause compile failure
+
+DESCRIPTION="oneAPI Data Parallel C++ compiler"
+HOMEPAGE="https://github.com/intel/llvm"
+SRC_URI="
+	https://github.com/intel/llvm/archive/refs/tags/${PV//./-}.tar.gz -> ${P}.tar.gz
+	https://github.com/intel/vc-intrinsics/archive/refs/tags/v${VC_INTR_PV}.tar.gz -> ${P}-vc-intrinsics-${VC_INTR_PV}.tar.gz
+	esimd_emulator? ( https://github.com/intel/cm-cpu-emulation/archive/refs/tags/v${CPU_EMUL_PV}.tar.gz -> ${P}-cm-cpu-emulation-${CPU_EMUL_PV}.tar.gz )
+"
+S="${WORKDIR}/llvm-${PV//./-}"
+CMAKE_USE_DIR="${S}/llvm"
+BUILD_DIR="${S}/build"
+
+LICENSE="Apache-2.0 MIT"
+SLOT="0/6" # Based on libsycl.so
+KEYWORDS="~amd64"
+
+ALL_LLVM_TARGETS=( AArch64 AMDGPU ARM AVR BPF Hexagon Lanai Mips MSP430
+	NVPTX PowerPC RISCV Sparc SystemZ WebAssembly X86 XCore )
+ALL_LLVM_TARGETS=( "${ALL_LLVM_TARGETS[@]/#/llvm_targets_}" )
+LLVM_TARGET_USEDEPS=${ALL_LLVM_TARGETS[@]/%/(-)?}
+
+IUSE="cuda hip test esimd_emulator ${ALL_LLVM_TARGETS[*]}"
+REQUIRED_USE="
+	?? ( cuda hip )
+	cuda? ( llvm_targets_NVPTX )
+	hip? ( llvm_targets_AMDGPU )
+"
+RESTRICT="!test? ( test )"
+
+BDEPEND="virtual/pkgconfig"
+
+DEPEND="
+	dev-libs/boost:=
+	dev-libs/level-zero:=
+	dev-libs/opencl-icd-loader
+	dev-util/opencl-headers
+	dev-util/spirv-headers
+	dev-util/spirv-tools
+	media-libs/libva
+	dev-build/libtool
+	esimd_emulator? ( dev-libs/libffi:= )
+	cuda? ( dev-util/nvidia-cuda-toolkit:= )
+	hip? ( dev-util/hip:= )
+"
+RDEPEND="${DEPEND}"
+
+PATCHES=(
+	"${FILESDIR}/${P}-system-libs.patch"
+)
+
+src_configure() {
+	# Extracted from buildbot/configure.py
+	local mycmakeargs=(
+		-DLLVM_ENABLE_ASSERTIONS=ON
+		-DLLVM_TARGETS_TO_BUILD="${LLVM_TARGETS// /;}"
+		-DLLVM_EXTERNAL_PROJECTS="sycl;llvm-spirv;opencl;libdevice;xpti;xptifw"
+		-DLLVM_EXTERNAL_SYCL_SOURCE_DIR="${S}/sycl"
+		-DLLVM_EXTERNAL_LLVM_SPIRV_SOURCE_DIR="${S}/llvm-spirv"
+		-DLLVM_EXTERNAL_XPTI_SOURCE_DIR="${S}/xpti"
+		-DXPTI_SOURCE_DIR="${S}/xpti"
+		-DLLVM_EXTERNAL_XPTIFW_SOURCE_DIR="${S}/xptifw"
+		-DLLVM_EXTERNAL_LIBDEVICE_SOURCE_DIR="${S}/libdevice"
+		-DLLVM_ENABLE_PROJECTS="clang;sycl;llvm-spirv;opencl;libdevice;xpti;xptifw"
+		-DLLVM_BUILD_TOOLS=ON
+		-DSYCL_ENABLE_WERROR=OFF
+		-DSYCL_INCLUDE_TESTS="$(usex test)"
+		-DCLANG_INCLUDE_TESTS="$(usex test)"
+		-DLLVM_INCLUDE_TESTS="$(usex test)"
+		-DLLVM_SPIRV_INCLUDE_TESTS="$(usex test)"
+		-DLLVM_ENABLE_DOXYGEN="$(usex doc)"
+		-DLLVM_ENABLE_SPHINX="$(usex doc)"
+		-DLLVM_BUILD_DOCS="$(usex doc)"
+		-DSYCL_ENABLE_XPTI_TRACING=ON
+		-DLLVM_ENABLE_LLD=OFF
+		-DXPTI_ENABLE_WERROR=OFF
+		-DSYCL_ENABLE_PLUGINS="level_zero;opencl;$(usev esimd_emulator);$(usev hip);$(usev cuda)"
+		-DLLVM_EXTERNAL_SPIRV_HEADERS_SOURCE_DIR="${ESYSROOT}/usr"
+		-DBOOST_MP11_SOURCE_DIR="${ESYSROOT}/usr "
+		-DLEVEL_ZERO_LIBRARY="${ESYSROOT}/usr/lib64/libze_loader.so"
+		-DLEVEL_ZERO_INCLUDE_DIR="${ESYSROOT}/usr/include"
+		-DLLVMGenXIntrinsics_SOURCE_DIR="${WORKDIR}/vc-intrinsics-${VC_INTR_PV}"
+		-DSYCL_CLANG_EXTRA_FLAGS="${CXXFLAGS}"
+		# The sycl part of the build system insists on installing during compiling
+		# Install it to some temporary directory
+		-DCMAKE_INSTALL_PREFIX="${BUILD_DIR}/install"
+		-DCMAKE_INSTALL_MANDIR="${BUILD_DIR}/install/share/man"
+		-DCMAKE_INSTALL_INFODIR="${BUILD_DIR}/install/share/info"
+		-DCMAKE_INSTALL_DOCDIR="${BUILD_DIR}/install/share/doc/${PF}"
+	)
+
+	if use hip; then
+		mycmakeargs+=(
+			-DSYCL_BUILD_PI_HIP_PLATFORM=AMD
+			-DLIBCLC_GENERATE_REMANGLED_VARIANTS=ON
+			-DLIBCLC_TARGETS_TO_BUILD=";amdgcn--;amdgcn--amdhsa"
+		)
+	fi
+
+	if use cuda; then
+		mycmakeargs+=(
+			-DLIBCLC_GENERATE_REMANGLED_VARIANTS=ON
+			-DLIBCLC_TARGETS_TO_BUILD=";nvptx64--;nvptx64--nvidiacl"
+		)
+	fi
+
+	if use esimd_emulator; then
+		mycmakeargs+=(
+			-DLibFFI_INCLUDE_DIR="${ESYSROOT}/usr/lib64/libffi/include"
+			-DUSE_LOCAL_CM_EMU_SOURCE="${WORKDIR}/cm-cpu-emulation-${CPU_EMUL_PV}"
+		)
+	fi
+
+	if use doc; then
+		mycmakeargs+=( -DSPHINX_WARNINGS_AS_ERRORS=OFF )
+	fi
+
+	cmake_src_configure
+}
+
+src_compile() {
+	# Build sycl (this also installs some stuff already)
+	cmake_build deploy-sycl-toolchain
+
+	use doc && cmake_build doxygen-sycl
+
+	# Install all other files into the same temporary directory
+	cmake_build install
+}
+
+src_test() {
+	cmake_build check
+}
+
+src_install() {
+	einstalldocs
+
+	local LLVM_INTEL_DIR="/usr/lib/llvm/intel"
+	dodir "${LLVM_INTEL_DIR}"
+
+	# Copy our temporary directory to the image directory
+	mv "${BUILD_DIR}/install"/* "${ED}/${LLVM_INTEL_DIR}" || die
+
+	# Copied from llvm ebuild, put env file last so we don't overwrite main llvm/clang
+	newenvd - "60llvm-intel" <<-_EOF_
+		PATH="${EPREFIX}${LLVM_INTEL_DIR}/bin"
+		# we need to duplicate it in ROOTPATH for Portage to respect...
+		ROOTPATH="${EPREFIX}${LLVM_INTEL_DIR}/bin"
+		MANPATH="${EPREFIX}${LLVM_INTEL_DIR}/share/man"
+		LDPATH="${EPREFIX}${LLVM_INTEL_DIR}/lib:${EPREFIX}${LLVM_INTEL_DIR}/lib64"
+	_EOF_
+}
diff --git a/sys-devel/DPC++/DPC++-2022.12.ebuild b/sys-devel/DPC++/DPC++-2022.12.ebuild
new file mode 100644
index 000000000..be9a59fec
--- /dev/null
+++ b/sys-devel/DPC++/DPC++-2022.12.ebuild
@@ -0,0 +1,184 @@
+# Copyright 2022 Gentoo Authors
+# Distributed under the terms of the GNU General Public License v2
+
+EAPI=8
+
+PYTHON_COMPAT=( python3_{10..12} )
+inherit cmake python-any-r1
+DOCS_BUILDER="doxygen"
+DOCS_DIR="build/docs"
+DOCS_CONFIG_NAME="doxygen.cfg"
+DOCS_DEPEND="
+	media-gfx/graphviz
+	virtual/latex-base
+	$(python_gen_any_dep '
+		dev-python/sphinx[${PYTHON_USEDEP}]
+		dev-python/recommonmark[${PYTHON_USEDEP}]
+		dev-python/myst-parser[${PYTHON_USEDEP}]
+	')
+"
+inherit docs
+
+# We cannot unbundle this because it has to be compiled with the clang/llvm
+# that we are building here. Otherwise we run into problems running the compiler.
+CPU_EMUL_PV="2022-08-22"
+VC_INTR_PV="0.10.0" # Newer versions cause compile failure
+UR_COMMIT="fd711c920acc4434cb52ff18b078c082d9d7f44d"
+
+DESCRIPTION="oneAPI Data Parallel C++ compiler"
+HOMEPAGE="https://github.com/intel/llvm"
+SRC_URI="
+	https://github.com/intel/llvm/archive/refs/tags/${PV//./-}.tar.gz -> ${P}.tar.gz
+	https://github.com/intel/vc-intrinsics/archive/refs/tags/v${VC_INTR_PV}.tar.gz -> ${P}-vc-intrinsics-${VC_INTR_PV}.tar.gz
+	https://github.com/oneapi-src/unified-runtime/archive/${UR_COMMIT}.tar.gz -> ${P}-unified-runtime-${UR_COMMIT}.tar.gz
+	esimd_emulator? ( https://github.com/intel/cm-cpu-emulation/archive/refs/tags/v${CPU_EMUL_PV}.tar.gz -> ${P}-cm-cpu-emulation-${CPU_EMUL_PV}.tar.gz )
+"
+S="${WORKDIR}/llvm-${PV//./-}"
+CMAKE_USE_DIR="${S}/llvm"
+BUILD_DIR="${S}/build"
+
+LICENSE="Apache-2.0 MIT"
+SLOT="0/6" # Based on libsycl.so
+KEYWORDS="~amd64"
+
+ALL_LLVM_TARGETS=( AArch64 AMDGPU ARM AVR BPF Hexagon Lanai Mips MSP430
+	NVPTX PowerPC RISCV Sparc SystemZ WebAssembly X86 XCore )
+ALL_LLVM_TARGETS=( "${ALL_LLVM_TARGETS[@]/#/llvm_targets_}" )
+LLVM_TARGET_USEDEPS=${ALL_LLVM_TARGETS[@]/%/(-)?}
+
+IUSE="cuda hip test esimd_emulator ${ALL_LLVM_TARGETS[*]}"
+REQUIRED_USE="
+	?? ( cuda hip )
+	cuda? ( llvm_targets_NVPTX )
+	hip? ( llvm_targets_AMDGPU )
+"
+RESTRICT="!test? ( test )"
+
+BDEPEND="virtual/pkgconfig"
+
+DEPEND="
+	dev-libs/boost:=
+	dev-libs/level-zero:=
+	dev-libs/opencl-icd-loader
+	dev-util/opencl-headers
+	dev-util/spirv-headers
+	dev-util/spirv-tools
+	media-libs/libva
+	dev-build/libtool
+	esimd_emulator? ( dev-libs/libffi:= )
+	cuda? ( dev-util/nvidia-cuda-toolkit:= )
+	hip? ( dev-util/hip:= )
+"
+RDEPEND="${DEPEND}"
+
+PATCHES=(
+	"${FILESDIR}/${P}-system-libs.patch"
+	"${FILESDIR}/${P}-gcc13.patch"
+)
+
+src_configure() {
+	# Extracted from buildbot/configure.py
+	local mycmakeargs=(
+		-DLLVM_ENABLE_ASSERTIONS=ON
+		-DLLVM_TARGETS_TO_BUILD="${LLVM_TARGETS// /;}"
+		-DLLVM_EXTERNAL_PROJECTS="sycl;llvm-spirv;opencl;libdevice;xpti;xptifw"
+		-DLLVM_EXTERNAL_SYCL_SOURCE_DIR="${S}/sycl"
+		-DLLVM_EXTERNAL_LLVM_SPIRV_SOURCE_DIR="${S}/llvm-spirv"
+		-DLLVM_EXTERNAL_XPTI_SOURCE_DIR="${S}/xpti"
+		-DXPTI_SOURCE_DIR="${S}/xpti"
+		-DLLVM_EXTERNAL_XPTIFW_SOURCE_DIR="${S}/xptifw"
+		-DLLVM_EXTERNAL_LIBDEVICE_SOURCE_DIR="${S}/libdevice"
+		-DLLVM_ENABLE_PROJECTS="clang;sycl;llvm-spirv;opencl;libdevice;xpti;xptifw"
+		-DLLVM_BUILD_TOOLS=ON
+		-DSYCL_ENABLE_WERROR=OFF
+		-DSYCL_INCLUDE_TESTS="$(usex test)"
+		-DCLANG_INCLUDE_TESTS="$(usex test)"
+		-DLLVM_INCLUDE_TESTS="$(usex test)"
+		-DLLVM_SPIRV_INCLUDE_TESTS="$(usex test)"
+		-DLLVM_ENABLE_DOXYGEN="$(usex doc)"
+		-DLLVM_ENABLE_SPHINX="$(usex doc)"
+		-DLLVM_BUILD_DOCS="$(usex doc)"
+		-DSYCL_ENABLE_XPTI_TRACING=ON
+		-DLLVM_ENABLE_LLD=OFF
+		-DXPTI_ENABLE_WERROR=OFF
+		-DSYCL_ENABLE_PLUGINS="level_zero;opencl;$(usev esimd_emulator);$(usev hip);$(usev cuda)"
+		-DLLVM_EXTERNAL_SPIRV_HEADERS_SOURCE_DIR="${ESYSROOT}/usr"
+		-DBOOST_MP11_SOURCE_DIR="${ESYSROOT}/usr "
+		-DLEVEL_ZERO_LIBRARY="${ESYSROOT}/usr/lib64/libze_loader.so"
+		-DLEVEL_ZERO_INCLUDE_DIR="${ESYSROOT}/usr/include"
+		-DLLVMGenXIntrinsics_SOURCE_DIR="${WORKDIR}/vc-intrinsics-${VC_INTR_PV}"
+		-DSYCL_CLANG_EXTRA_FLAGS="${CXXFLAGS}"
+		-DUNIFIED_RUNTIME_SOURCE_DIR="${WORKDIR}/unified-runtime-${UR_COMMIT}"
+		# The sycl part of the build system insists on installing during compiling
+		# Install it to some temporary directory
+		-DCMAKE_INSTALL_PREFIX="${BUILD_DIR}/install"
+		-DCMAKE_INSTALL_MANDIR="${BUILD_DIR}/install/share/man"
+		-DCMAKE_INSTALL_INFODIR="${BUILD_DIR}/install/share/info"
+		-DCMAKE_INSTALL_DOCDIR="${BUILD_DIR}/install/share/doc/${PF}"
+	)
+
+	if use hip; then
+		mycmakeargs+=(
+			-DSYCL_BUILD_PI_HIP_PLATFORM=AMD
+			-DLIBCLC_GENERATE_REMANGLED_VARIANTS=ON
+			-DLIBCLC_TARGETS_TO_BUILD=";amdgcn--;amdgcn--amdhsa"
+		)
+	fi
+
+	if use cuda; then
+		mycmakeargs+=(
+			-DLIBCLC_GENERATE_REMANGLED_VARIANTS=ON
+			-DLIBCLC_TARGETS_TO_BUILD=";nvptx64--;nvptx64--nvidiacl"
+		)
+	fi
+
+	if use esimd_emulator; then
+		mycmakeargs+=(
+			-DLibFFI_INCLUDE_DIR="${ESYSROOT}/usr/lib64/libffi/include"
+			-DUSE_LOCAL_CM_EMU_SOURCE="${WORKDIR}/cm-cpu-emulation-${CPU_EMUL_PV}"
+		)
+	fi
+
+	if use doc; then
+		mycmakeargs+=( -DSPHINX_WARNINGS_AS_ERRORS=OFF )
+	fi
+
+	cmake_src_configure
+}
+
+src_compile() {
+	# Build sycl (this also installs some stuff already)
+	cmake_build deploy-sycl-toolchain
+
+	use doc && cmake_build doxygen-sycl
+
+	# Install all other files into the same temporary directory
+	cmake_build install
+}
+
+src_test() {
+	cmake_build check
+}
+
+src_install() {
+	einstalldocs
+
+	local LLVM_INTEL_DIR="/usr/lib/llvm/intel"
+	dodir "${LLVM_INTEL_DIR}"
+
+	# Copy our temporary directory to the image directory
+	mv "${BUILD_DIR}/install"/* "${ED}/${LLVM_INTEL_DIR}" || die
+
+	# Convienence symlinks
+	dosym "${LLVM_INTEL_DIR}/bin/clang" "/usr/bin/icx"
+	dosym "${LLVM_INTEL_DIR}/bin/clang++" "/usr/bin/icpx"
+
+	# Copied from llvm ebuild, put env file last so we don't overwrite main llvm/clang
+	newenvd - "60llvm-intel" <<-_EOF_
+		PATH="${EPREFIX}${LLVM_INTEL_DIR}/bin"
+		# we need to duplicate it in ROOTPATH for Portage to respect...
+		ROOTPATH="${EPREFIX}${LLVM_INTEL_DIR}/bin"
+		MANPATH="${EPREFIX}${LLVM_INTEL_DIR}/share/man"
+		LDPATH="${EPREFIX}${LLVM_INTEL_DIR}/lib:${EPREFIX}${LLVM_INTEL_DIR}/lib64"
+	_EOF_
+}
diff --git a/sys-devel/DPC++/Manifest b/sys-devel/DPC++/Manifest
new file mode 100644
index 000000000..324ee6cfc
--- /dev/null
+++ b/sys-devel/DPC++/Manifest
@@ -0,0 +1,10 @@
+DIST DPC++-2021.12-cm-cpu-emulation-2022-08-22.tar.gz 328563 BLAKE2B 86dfbf9163e77675227eb1db2242edf0de6e3f6be45ddfc1077d4cfb83e997f4839f2abb4e15688f4e657c263a0102d7fda627d6c57f1bcc2582560f3fdb5664 SHA512 fabd973739c17c3c702d8ea1345df165a272053fe7c6564fb81f00a3a316e1ed69d4fdbd73f408841600cf9705e31fc688c6d88e7b095e8f97b1090b3ecd8ccc
+DIST DPC++-2021.12-vc-intrinsics-0.8.1.tar.gz 138462 BLAKE2B 0f86f5fbeb7931a564eb598d527fd67e96489d0f2e7dba7166ffa468470022eff05e150877c3dd380ad003beb8651a0ac9ffe9c3dceeae6552c46b5f3e00aa64 SHA512 9763f1b624121694d6880ca3ffdf2e344ce3ed1a39c1c1e7dc06195b79acccce5e3d86032bba5c0de440376821c383f8ff59fdd57b0ae93fede17595b0fe0b42
+DIST DPC++-2021.12.tar.gz 160365844 BLAKE2B c741afc109ceb9d1b5e62e1299d400b4009979621363e173cded514ed9417e4728ad2079f7f74f3ff8038a898950aca7157a60bb9d9017e8e3c453990d301481 SHA512 7128f325d5f68fb408c14a595612fdde45e69f3d60807fd68888f4715a96976fd8881fb5421177fab5add84a1d717ec136ba47f78e2211a4c7db33d9e40b7060
+DIST DPC++-2022.09-cm-cpu-emulation-2022-08-22.tar.gz 328563 BLAKE2B 86dfbf9163e77675227eb1db2242edf0de6e3f6be45ddfc1077d4cfb83e997f4839f2abb4e15688f4e657c263a0102d7fda627d6c57f1bcc2582560f3fdb5664 SHA512 fabd973739c17c3c702d8ea1345df165a272053fe7c6564fb81f00a3a316e1ed69d4fdbd73f408841600cf9705e31fc688c6d88e7b095e8f97b1090b3ecd8ccc
+DIST DPC++-2022.09-vc-intrinsics-0.8.1.tar.gz 138462 BLAKE2B 0f86f5fbeb7931a564eb598d527fd67e96489d0f2e7dba7166ffa468470022eff05e150877c3dd380ad003beb8651a0ac9ffe9c3dceeae6552c46b5f3e00aa64 SHA512 9763f1b624121694d6880ca3ffdf2e344ce3ed1a39c1c1e7dc06195b79acccce5e3d86032bba5c0de440376821c383f8ff59fdd57b0ae93fede17595b0fe0b42
+DIST DPC++-2022.09.tar.gz 171848301 BLAKE2B 48f57fee53370135b25a4e5f27926375fe9e4b707909f5841afa4c0d27a53932404f066db6384b8e8c327f1328cd00339e1c055935eb38fca2a8ce34f3556727 SHA512 f17ac91d4ec03c067595abd8355a54484c2cd8b79bb8b1ed8c90fabd8d83b73cce0271a8b3aa26e2c92e8083a2b3cf145c7e78b68e568c3cb036c80b8a4f9e12
+DIST DPC++-2022.12-cm-cpu-emulation-2022-08-22.tar.gz 328563 BLAKE2B 86dfbf9163e77675227eb1db2242edf0de6e3f6be45ddfc1077d4cfb83e997f4839f2abb4e15688f4e657c263a0102d7fda627d6c57f1bcc2582560f3fdb5664 SHA512 fabd973739c17c3c702d8ea1345df165a272053fe7c6564fb81f00a3a316e1ed69d4fdbd73f408841600cf9705e31fc688c6d88e7b095e8f97b1090b3ecd8ccc
+DIST DPC++-2022.12-unified-runtime-fd711c920acc4434cb52ff18b078c082d9d7f44d.tar.gz 249206 BLAKE2B 52da2e773e3d617ca1fd491a71c0c9ce0d943f550278339aa9fa14c8997aff26a5cd642a414f4fb2aece198a7d912b7c9092a9d89c7f62f417f43406f73bf4a6 SHA512 356351abe965b5129d0c0ec2c459e950461192762c501b5089d12a1135fd970ff2572ac99255bb743798f890f485621fc21173124d67a9b142d36ac07c09d936
+DIST DPC++-2022.12-vc-intrinsics-0.10.0.tar.gz 138920 BLAKE2B a73ccbbc56bff3cf0656eb505b5201db1889dec0c2b608c1a999bb0302a9bc9c275480a2d3aa31e04faed5c827a55aa6d36e4603f4716b5998ed4f2df4ec8850 SHA512 5c9e5eae2da9f4975f9d11249a27751c387dd2a425b40d9ff67890857557cfc503e93f0315329658443d060c48b72fd4eee776d5592f0b9e5cb485d659d55658
+DIST DPC++-2022.12.tar.gz 176940515 BLAKE2B ef4ca7096ae18c2ae19c8e781dd120621f59741533d76f3f3739d8d043a11edfff036a45aed187735c5e7fe34d707f2dd85c336b4995ac64acd0f91f1558c4ca SHA512 132c016af101f5fb1f86a77ad7714883adf30803700bcf5349bc5f16618606e6697f920992bb6bd61ddaa8f6c9259eabbc1a163a05249f7731400c7b584fb222
diff --git a/sys-devel/DPC++/files/DPC++-2021.12-system-libs.patch b/sys-devel/DPC++/files/DPC++-2021.12-system-libs.patch
new file mode 100644
index 000000000..a9d7f468f
--- /dev/null
+++ b/sys-devel/DPC++/files/DPC++-2021.12-system-libs.patch
@@ -0,0 +1,274 @@
+diff --git a/opencl/CMakeLists.txt b/opencl/CMakeLists.txt
+index ad6fc3327..f68e18b51 100644
+--- a/opencl/CMakeLists.txt
++++ b/opencl/CMakeLists.txt
+@@ -23,29 +23,8 @@ set(OCL_LOADER_REPO
+ set(OCL_HEADERS_TAG 23710f1b99186065c1768fc3098ba681adc0f253)
+ set(OCL_LOADER_TAG 5f8249691ec8c25775789498951f8e9eb62c201d)
+ 
+-# OpenCL Headers
+-if(NOT OpenCL_HEADERS)
+-  message(STATUS "Will fetch OpenCL headers from ${OCL_HEADERS_REPO}")
+-
+-  FetchContent_Declare(ocl-headers
+-    GIT_REPOSITORY    ${OCL_HEADERS_REPO}
+-    GIT_TAG           ${OCL_HEADERS_TAG}
+-  )
+-else()
+-  message(STATUS "OpenCL headers are added manually ${OpenCL_HEADERS}")
+-
+-  FetchContent_Declare(ocl-headers
+-    URL               ${OpenCL_HEADERS}
+-  )
+-endif()
+-
+-FetchContent_MakeAvailable(ocl-headers)
+-FetchContent_GetProperties(ocl-headers)
+ set(OpenCL_INCLUDE_DIR
+-  ${ocl-headers_SOURCE_DIR} CACHE PATH "Path to OpenCL Headers")
+-
+-target_compile_definitions(Headers INTERFACE -DCL_TARGET_OPENCL_VERSION=220)
+-add_library(OpenCL-Headers ALIAS Headers)
++  /usr/include CACHE PATH "Path to OpenCL Headers")
+ 
+ # OpenCL Library (ICD Loader)
+ 
+@@ -57,25 +36,4 @@ set(OPENCL_ICD_LOADER_HEADERS_DIR
+ # library.
+ set(BUILD_SHARED_LIBS ON)
+ 
+-if(NOT OpenCL_LIBRARY_SRC)
+-  message(STATUS "Will fetch OpenCL ICD Loader from ${OCL_LOADER_REPO}")
+-
+-  FetchContent_Declare(ocl-icd
+-    GIT_REPOSITORY    ${OCL_LOADER_REPO}
+-    GIT_TAG           ${OCL_LOADER_TAG}
+-  )
+-else()
+-  # TODO: add possibility to use prebuilt OpenCL library rather than building
+-  #       together with llvm.
+-  message(STATUS
+-    "OpenCL ICD Loader sources added manually ${OpenCL_LIBRARY_SRC}")
+-
+-  FetchContent_Declare(ocl-icd
+-    URL               ${OpenCL_LIBRARY_SRC}
+-  )
+-endif()
+-
+-FetchContent_MakeAvailable(ocl-icd)
+-add_library(OpenCL-ICD ALIAS OpenCL)
+-
+ add_subdirectory(opencl-aot)
+diff --git a/opencl/opencl-aot/CMakeLists.txt b/opencl/opencl-aot/CMakeLists.txt
+index ff905fd88..5232fe7a6 100644
+--- a/opencl/opencl-aot/CMakeLists.txt
++++ b/opencl/opencl-aot/CMakeLists.txt
+@@ -19,5 +19,4 @@ endif()
+ 
+ target_link_libraries(${OPENCL_AOT_PROJECT_NAME}
+   PRIVATE
+-    OpenCL-Headers
+-    OpenCL-ICD)
++    OpenCL)
+diff --git a/sycl/CMakeLists.txt b/sycl/CMakeLists.txt
+index 0894e7413..5645799a8 100644
+--- a/sycl/CMakeLists.txt
++++ b/sycl/CMakeLists.txt
+@@ -103,7 +103,7 @@ file(COPY ${OpenCL_INCLUDE_DIR}/CL
+ # Include OpenCL Headers into final bundle.
+ install(DIRECTORY ${OpenCL_INCLUDE_DIR}/CL
+         DESTINATION ${SYCL_INCLUDE_DIR}/sycl
+-        COMPONENT OpenCL-Headers)
++        COMPONENT OpenCL)
+ 
+ option(SYCL_BUILD_PI_CUDA
+   "Enables the CUDA backend for the Plugin Interface" OFF)
+@@ -295,7 +295,7 @@ set( SYCL_TOOLCHAIN_DEPLOY_COMPONENTS
+      sycl-post-link
+      sycl-ls
+      clang-resource-headers
+-     OpenCL-Headers
++     OpenCL
+      opencl-aot
+      sycl-headers
+      sycl-headers-extras
+@@ -306,8 +306,8 @@ set( SYCL_TOOLCHAIN_DEPLOY_COMPONENTS
+      ${XPTIFW_LIBS}
+ )
+ 
+-if(OpenCL_INSTALL_KHRONOS_ICD_LOADER AND TARGET OpenCL-ICD)
+-  list(APPEND SYCL_TOOLCHAIN_DEPLOY_COMPONENTS OpenCL-ICD)
++if(OpenCL_INSTALL_KHRONOS_ICD_LOADER AND TARGET OpenCL)
++  list(APPEND SYCL_TOOLCHAIN_DEPLOY_COMPONENTS OpenCL)
+ endif()
+ 
+ if(SYCL_BUILD_PI_CUDA)
+diff --git a/sycl/cmake/modules/AddSYCLUnitTest.cmake b/sycl/cmake/modules/AddSYCLUnitTest.cmake
+index 030ff6139..235522b58 100644
+--- a/sycl/cmake/modules/AddSYCLUnitTest.cmake
++++ b/sycl/cmake/modules/AddSYCLUnitTest.cmake
+@@ -31,7 +31,7 @@ macro(add_sycl_unittest test_dirname link_variant)
+   target_link_libraries(${test_dirname}
+     PRIVATE
+       LLVMTestingSupport
+-      OpenCL-Headers
++      OpenCL
+       ${SYCL_LINK_LIBS}
+     )
+   target_include_directories(${test_dirname}
+diff --git a/sycl/plugins/cuda/CMakeLists.txt b/sycl/plugins/cuda/CMakeLists.txt
+index ff6dd8bc6..260b10268 100644
+--- a/sycl/plugins/cuda/CMakeLists.txt
++++ b/sycl/plugins/cuda/CMakeLists.txt
+@@ -41,7 +41,7 @@ target_include_directories(pi_cuda
+ 
+ target_link_libraries(pi_cuda
+   PRIVATE
+-    OpenCL-Headers
++    OpenCL
+     cudadrv
+ )
+ 
+diff --git a/sycl/plugins/esimd_emulator/CMakeLists.txt b/sycl/plugins/esimd_emulator/CMakeLists.txt
+index 4ce9e1ff5..5b6cbf1bf 100755
+--- a/sycl/plugins/esimd_emulator/CMakeLists.txt
++++ b/sycl/plugins/esimd_emulator/CMakeLists.txt
+@@ -40,6 +40,7 @@ if (DEFINED CM_LOCAL_SOURCE_DIR)
+       INSTALL_DIR       ${CMAKE_CURRENT_BINARY_DIR}/cm-emu_install
+       CMAKE_ARGS        -DLIBVA_INSTALL_PATH=/usr
+                         -D__SYCL_EXPLICIT_SIMD_PLUGIN__=true
++                        -DLibFFI_INCLUDE_DIR=${LibFFI_INCLUDE_DIR}
+                         -DCMAKE_INSTALL_PREFIX=<INSTALL_DIR>
+       BUILD_BYPRODUCTS  ${LIBCM} ${LIBIGFXCMRT_EMU}
+     )
+@@ -123,7 +124,7 @@ else()
+   )
+ endif()
+ 
+-add_dependencies(pi_esimd_emulator OpenCL-Headers)
++add_dependencies(pi_esimd_emulator OpenCL)
+ add_dependencies(pi_esimd_emulator cm-emu)
+ add_dependencies(sycl-toolchain pi_esimd_emulator)
+ 
+diff --git a/sycl/plugins/hip/CMakeLists.txt b/sycl/plugins/hip/CMakeLists.txt
+index 7b3d9c395..e696ceeb0 100644
+--- a/sycl/plugins/hip/CMakeLists.txt
++++ b/sycl/plugins/hip/CMakeLists.txt
+@@ -17,7 +17,7 @@ add_library(pi_hip SHARED
+ )
+ add_dependencies(sycl-toolchain pi_hip)
+ set_target_properties(pi_hip PROPERTIES LINKER_LANGUAGE CXX)
+-target_link_libraries(pi_hip PUBLIC OpenCL-Headers)
++target_link_libraries(pi_hip PUBLIC OpenCL)
+ 
+ # Setup include directories
+ target_include_directories(pi_hip
+diff --git a/sycl/plugins/level_zero/CMakeLists.txt b/sycl/plugins/level_zero/CMakeLists.txt
+index f4e6a48bc..f674c6a57 100755
+--- a/sycl/plugins/level_zero/CMakeLists.txt
++++ b/sycl/plugins/level_zero/CMakeLists.txt
+@@ -48,7 +48,7 @@ if (NOT DEFINED LEVEL_ZERO_LIBRARY OR NOT DEFINED LEVEL_ZERO_INCLUDE_DIR)
+                LOG_BUILD 1
+                LOG_INSTALL 1
+     STEP_TARGETS      configure,build,install
+-    DEPENDS           OpenCL-Headers
++    DEPENDS           OpenCL
+     BUILD_BYPRODUCTS ${LEVEL_ZERO_LOADER}
+   )
+   ExternalProject_Add_Step(level-zero-loader llvminstall
+@@ -82,7 +82,7 @@ else()
+       COMMAND
+ 	  ${CMAKE_COMMAND} -E copy ${LEVEL_ZERO_LIBRARY_SRC} ${LLVM_LIBRARY_OUTPUT_INTDIR}
+       COMMAND
+-	  ${CMAKE_COMMAND} -E copy_directory ${LEVEL_ZERO_INCLUDE_DIR} ${LLVM_BINARY_DIR}/include/sycl
++	  ${CMAKE_COMMAND} -E copy_directory ${LEVEL_ZERO_INCLUDE_DIR}/level_zero ${LLVM_BINARY_DIR}/include/sycl/level_zero
+       DEPENDS
+ 	  ${LEVEL_ZERO_LIBRARY}
+           ${LEVEL_ZERO_INCLUDE_DIR}
+@@ -140,7 +140,7 @@ add_dependencies(sycl-toolchain pi_level_zero)
+ target_link_libraries(pi_level_zero
+   PRIVATE
+     "${LEVEL_ZERO_LOADER}"
+-    OpenCL-Headers
++    OpenCL
+ )
+ 
+ if (UNIX)
+diff --git a/sycl/plugins/opencl/CMakeLists.txt b/sycl/plugins/opencl/CMakeLists.txt
+index d3d5c3a4c..d08809c99 100644
+--- a/sycl/plugins/opencl/CMakeLists.txt
++++ b/sycl/plugins/opencl/CMakeLists.txt
+@@ -25,8 +25,7 @@ target_include_directories(pi_opencl PRIVATE "${sycl_inc_dir}")
+ #link pi_opencl with OpenCL headers and ICD Loader.
+ target_link_libraries(pi_opencl
+   PRIVATE
+-    OpenCL-Headers
+-    OpenCL-ICD
++    OpenCL
+ )
+ if (MSVC)
+   # by defining __SYCL_BUILD_SYCL_DLL, we can use __declspec(dllexport)
+diff --git a/sycl/source/CMakeLists.txt b/sycl/source/CMakeLists.txt
+index 46f33bdb4..6e65cd6a8 100644
+--- a/sycl/source/CMakeLists.txt
++++ b/sycl/source/CMakeLists.txt
+@@ -76,14 +76,14 @@ function(add_sycl_rt_library LIB_NAME)
+   )
+   #TODO: Remove dependency on icd loader and opencl headers.
+   target_link_libraries(${LIB_OBJ_NAME}
+-    PRIVATE OpenCL-Headers
++    PRIVATE OpenCL
+   )
+ 
+   find_package(Threads REQUIRED)
+ 
+   target_link_libraries(${LIB_NAME}
+     PRIVATE
+-      OpenCL-ICD
++      OpenCL
+       ${CMAKE_DL_LIBS}
+       ${CMAKE_THREAD_LIBS_INIT}
+     PUBLIC
+diff --git a/sycl/tools/CMakeLists.txt b/sycl/tools/CMakeLists.txt
+index a4f567482..7af557fd2 100644
+--- a/sycl/tools/CMakeLists.txt
++++ b/sycl/tools/CMakeLists.txt
+@@ -20,9 +20,8 @@ endif()
+ 
+ target_link_libraries(get_device_count_by_type
+   PRIVATE
+-    OpenCL-Headers
++    OpenCL
+     LevelZeroLoader::Headers
+-    OpenCL-ICD
+     ${LEVEL_ZERO_LIBRARY}
+     # The CUDA and HIP for NVIDA plugins need cudadrv
+     $<$<OR:$<BOOL:${SYCL_BUILD_PI_CUDA}>,$<AND:$<BOOL:${SYCL_BUILD_PI_HIP}>,$<STREQUAL:${SYCL_BUILD_PI_HIP_PLATFORM},NVIDIA>>>:cudadrv>
+diff --git a/sycl/tools/pi-trace/CMakeLists.txt b/sycl/tools/pi-trace/CMakeLists.txt
+index e305fd22d..5aea609ff 100644
+--- a/sycl/tools/pi-trace/CMakeLists.txt
++++ b/sycl/tools/pi-trace/CMakeLists.txt
+@@ -1,8 +1,8 @@
+ add_library(pi_trace SHARED pi_trace.cpp)
+ target_compile_definitions(pi_trace PRIVATE XPTI_CALLBACK_API_EXPORTS)
+ target_link_libraries(pi_trace PRIVATE xptifw)
+-if (TARGET OpenCL-Headers)
+-  target_link_libraries(pi_trace PRIVATE OpenCL-Headers)
++if (TARGET OpenCL)
++  target_link_libraries(pi_trace PRIVATE OpenCL)
+ endif()
+ 
+ target_include_directories(pi_trace PRIVATE
+diff --git a/sycl/tools/sycl-ls/CMakeLists.txt b/sycl/tools/sycl-ls/CMakeLists.txt
+index f5909cf49..f9c52e3a3 100644
+--- a/sycl/tools/sycl-ls/CMakeLists.txt
++++ b/sycl/tools/sycl-ls/CMakeLists.txt
+@@ -11,7 +11,7 @@ endif()
+ target_link_libraries(sycl-ls
+   PRIVATE
+     ${sycl_lib}
+-    OpenCL-Headers
++    OpenCL
+ )
+ install(TARGETS sycl-ls
+   RUNTIME DESTINATION "bin" COMPONENT sycl-ls)
diff --git a/sys-devel/DPC++/files/DPC++-2022.09-system-libs.patch b/sys-devel/DPC++/files/DPC++-2022.09-system-libs.patch
new file mode 100644
index 000000000..7d2cdc823
--- /dev/null
+++ b/sys-devel/DPC++/files/DPC++-2022.09-system-libs.patch
@@ -0,0 +1,217 @@
+diff --git a/opencl/CMakeLists.txt b/opencl/CMakeLists.txt
+index 954317fe2..ba3bf19d3 100644
+--- a/opencl/CMakeLists.txt
++++ b/opencl/CMakeLists.txt
+@@ -23,29 +23,8 @@ set(OCL_LOADER_REPO
+ set(OCL_HEADERS_TAG dcd5bede6859d26833cd85f0d6bbcee7382dc9b3)
+ set(OCL_LOADER_TAG 792682ad3d877ab38573b997808bab3b43902b70)
+ 
+-# OpenCL Headers
+-if(NOT OpenCL_HEADERS)
+-  message(STATUS "Will fetch OpenCL headers from ${OCL_HEADERS_REPO}")
+-
+-  FetchContent_Declare(ocl-headers
+-    GIT_REPOSITORY    ${OCL_HEADERS_REPO}
+-    GIT_TAG           ${OCL_HEADERS_TAG}
+-  )
+-else()
+-  message(STATUS "OpenCL headers are added manually ${OpenCL_HEADERS}")
+-
+-  FetchContent_Declare(ocl-headers
+-    URL               ${OpenCL_HEADERS}
+-  )
+-endif()
+-
+-FetchContent_MakeAvailable(ocl-headers)
+-FetchContent_GetProperties(ocl-headers)
+ set(OpenCL_INCLUDE_DIR
+-  ${ocl-headers_SOURCE_DIR} CACHE PATH "Path to OpenCL Headers")
+-
+-target_compile_definitions(Headers INTERFACE -DCL_TARGET_OPENCL_VERSION=220)
+-add_library(OpenCL-Headers ALIAS Headers)
++  /usr/include CACHE PATH "Path to OpenCL Headers")
+ 
+ # OpenCL Library (ICD Loader)
+ 
+@@ -57,25 +36,4 @@ set(OPENCL_ICD_LOADER_HEADERS_DIR
+ # library.
+ set(BUILD_SHARED_LIBS ON)
+ 
+-if(NOT OpenCL_LIBRARY_SRC)
+-  message(STATUS "Will fetch OpenCL ICD Loader from ${OCL_LOADER_REPO}")
+-
+-  FetchContent_Declare(ocl-icd
+-    GIT_REPOSITORY    ${OCL_LOADER_REPO}
+-    GIT_TAG           ${OCL_LOADER_TAG}
+-  )
+-else()
+-  # TODO: add possibility to use prebuilt OpenCL library rather than building
+-  #       together with llvm.
+-  message(STATUS
+-    "OpenCL ICD Loader sources added manually ${OpenCL_LIBRARY_SRC}")
+-
+-  FetchContent_Declare(ocl-icd
+-    URL               ${OpenCL_LIBRARY_SRC}
+-  )
+-endif()
+-
+-FetchContent_MakeAvailable(ocl-icd)
+-add_library(OpenCL-ICD ALIAS OpenCL)
+-
+ add_subdirectory(opencl-aot)
+diff --git a/opencl/opencl-aot/CMakeLists.txt b/opencl/opencl-aot/CMakeLists.txt
+index ff905fd88..b673f79a4 100644
+--- a/opencl/opencl-aot/CMakeLists.txt
++++ b/opencl/opencl-aot/CMakeLists.txt
+@@ -19,5 +19,5 @@ endif()
+ 
+ target_link_libraries(${OPENCL_AOT_PROJECT_NAME}
+   PRIVATE
+-    OpenCL-Headers
+-    OpenCL-ICD)
++    OpenCL
++)
+diff --git a/sycl/cmake/modules/AddSYCL.cmake b/sycl/cmake/modules/AddSYCL.cmake
+index aa0cfcadd..9cfa5aadd 100644
+--- a/sycl/cmake/modules/AddSYCL.cmake
++++ b/sycl/cmake/modules/AddSYCL.cmake
+@@ -47,7 +47,7 @@ function(add_sycl_plugin PLUGIN_NAME)
+       ${sycl_inc_dir}
+     LIBRARIES
+       ${ARG_LIBRARIES}
+-      OpenCL-Headers
++      OpenCL
+   )
+ 
+   install(TARGETS pi_${PLUGIN_NAME}
+diff --git a/sycl/cmake/modules/AddSYCLUnitTest.cmake b/sycl/cmake/modules/AddSYCLUnitTest.cmake
+index 9f5e6dc30..fe0e18b2f 100644
+--- a/sycl/cmake/modules/AddSYCLUnitTest.cmake
++++ b/sycl/cmake/modules/AddSYCLUnitTest.cmake
+@@ -53,7 +53,7 @@ macro(add_sycl_unittest test_dirname link_variant)
+   target_link_libraries(${test_dirname}
+     PRIVATE
+       LLVMTestingSupport
+-      OpenCL-Headers
++      OpenCL
+       ${SYCL_LINK_LIBS}
+     )
+   target_include_directories(${test_dirname}
+diff --git a/sycl/plugins/esimd_emulator/CMakeLists.txt b/sycl/plugins/esimd_emulator/CMakeLists.txt
+index 0b32c3925..e8b8616bc 100755
+--- a/sycl/plugins/esimd_emulator/CMakeLists.txt
++++ b/sycl/plugins/esimd_emulator/CMakeLists.txt
+@@ -58,6 +58,7 @@ if ((DEFINED USE_DEFAULT_CM_EMU_SOURCE) OR (DEFINED USE_LOCAL_CM_EMU_SOURCE))
+       INSTALL_DIR       ${CMAKE_CURRENT_BINARY_DIR}/cm-emu_install
+       CMAKE_ARGS        -DLIBVA_INSTALL_PATH=/usr
+                         -D__SYCL_EXPLICIT_SIMD_PLUGIN__=true
++                        -DLibFFI_INCLUDE_DIR=${LibFFI_INCLUDE_DIR}
+                         -DCMAKE_INSTALL_PREFIX=<INSTALL_DIR>
+       BUILD_BYPRODUCTS  ${LIBCM} ${LIBIGFXCMRT_EMU}
+     )
+diff --git a/sycl/plugins/level_zero/CMakeLists.txt b/sycl/plugins/level_zero/CMakeLists.txt
+index 9391ff1e5..aa823e8fa 100755
+--- a/sycl/plugins/level_zero/CMakeLists.txt
++++ b/sycl/plugins/level_zero/CMakeLists.txt
+@@ -82,7 +82,7 @@ else()
+       COMMAND
+ 	  ${CMAKE_COMMAND} -E copy ${LEVEL_ZERO_LIBRARY_SRC} ${LLVM_LIBRARY_OUTPUT_INTDIR}
+       COMMAND
+-	  ${CMAKE_COMMAND} -E copy_directory ${LEVEL_ZERO_INCLUDE_DIR} ${LLVM_BINARY_DIR}/include/sycl
++	  ${CMAKE_COMMAND} -E copy_directory ${LEVEL_ZERO_INCLUDE_DIR}/level_zero ${LLVM_BINARY_DIR}/include/sycl/level_zero
+       DEPENDS
+ 	  ${LEVEL_ZERO_LIBRARY}
+           ${LEVEL_ZERO_INCLUDE_DIR}
+diff --git a/sycl/plugins/opencl/CMakeLists.txt b/sycl/plugins/opencl/CMakeLists.txt
+index 9943827e4..29fae166e 100644
+--- a/sycl/plugins/opencl/CMakeLists.txt
++++ b/sycl/plugins/opencl/CMakeLists.txt
+@@ -15,7 +15,7 @@ add_sycl_plugin(opencl
+     "${sycl_inc_dir}/sycl/detail/pi.h"
+     "pi_opencl.cpp"
+   LIBRARIES
+-    OpenCL-ICD
++    OpenCL
+ )
+ 
+ set_target_properties(pi_opencl PROPERTIES LINKER_LANGUAGE CXX)
+diff --git a/sycl/source/CMakeLists.txt b/sycl/source/CMakeLists.txt
+index 23b161480..4a5c48625 100644
+--- a/sycl/source/CMakeLists.txt
++++ b/sycl/source/CMakeLists.txt
+@@ -82,7 +82,7 @@ function(add_sycl_rt_library LIB_NAME LIB_OBJ_NAME)
+   )
+   #TODO: Remove dependency on opencl headers.
+   target_link_libraries(${LIB_OBJ_NAME}
+-    PRIVATE OpenCL-Headers
++    PRIVATE OpenCL
+   )
+ 
+   find_package(Threads REQUIRED)
+diff --git a/sycl/tools/CMakeLists.txt b/sycl/tools/CMakeLists.txt
+index eb62c48e1..6a7ff9aef 100644
+--- a/sycl/tools/CMakeLists.txt
++++ b/sycl/tools/CMakeLists.txt
+@@ -38,9 +38,8 @@ endif()
+ 
+ target_link_libraries(get_device_count_by_type
+   PRIVATE
+-    OpenCL-Headers
++    OpenCL
+     LevelZeroLoader::Headers
+-    OpenCL-ICD
+     ${LEVEL_ZERO_LIBRARY}
+     # The CUDA and HIP for NVIDA plugins need cudadrv
+     $<$<OR:$<BOOL:${SYCL_BUILD_PI_CUDA}>,$<AND:$<BOOL:${SYCL_BUILD_PI_HIP}>,$<STREQUAL:${SYCL_BUILD_PI_HIP_PLATFORM},NVIDIA>>>:cudadrv>
+diff --git a/sycl/tools/sycl-ls/CMakeLists.txt b/sycl/tools/sycl-ls/CMakeLists.txt
+index f5909cf49..f9c52e3a3 100644
+--- a/sycl/tools/sycl-ls/CMakeLists.txt
++++ b/sycl/tools/sycl-ls/CMakeLists.txt
+@@ -11,7 +11,7 @@ endif()
+ target_link_libraries(sycl-ls
+   PRIVATE
+     ${sycl_lib}
+-    OpenCL-Headers
++    OpenCL
+ )
+ install(TARGETS sycl-ls
+   RUNTIME DESTINATION "bin" COMPONENT sycl-ls)
+diff --git a/sycl/tools/sycl-prof/CMakeLists.txt b/sycl/tools/sycl-prof/CMakeLists.txt
+index 09586c1b8..ff708db67 100644
+--- a/sycl/tools/sycl-prof/CMakeLists.txt
++++ b/sycl/tools/sycl-prof/CMakeLists.txt
+@@ -16,7 +16,7 @@ add_library(sycl_profiler_collector SHARED collector.cpp)
+ target_compile_definitions(sycl_profiler_collector PRIVATE XPTI_CALLBACK_API_EXPORTS)
+ target_link_libraries(sycl_profiler_collector PRIVATE xptifw)
+ if (TARGET OpenCL-Headers)
+-  target_link_libraries(sycl_profiler_collector PRIVATE OpenCL-Headers)
++  target_link_libraries(sycl_profiler_collector PRIVATE OpenCL)
+ endif()
+ target_include_directories(sycl_profiler_collector PRIVATE
+     "${sycl_inc_dir}"
+diff --git a/sycl/tools/sycl-sanitize/CMakeLists.txt b/sycl/tools/sycl-sanitize/CMakeLists.txt
+index 16e7a1a49..e27b2cb21 100644
+--- a/sycl/tools/sycl-sanitize/CMakeLists.txt
++++ b/sycl/tools/sycl-sanitize/CMakeLists.txt
+@@ -14,7 +14,7 @@ add_library(sycl_sanitizer_collector SHARED collector.cpp)
+ target_compile_definitions(sycl_sanitizer_collector PRIVATE XPTI_CALLBACK_API_EXPORTS)
+ target_link_libraries(sycl_sanitizer_collector PRIVATE xptifw)
+ if (TARGET OpenCL-Headers)
+-  target_link_libraries(sycl_sanitizer_collector PRIVATE OpenCL-Headers)
++  target_link_libraries(sycl_sanitizer_collector PRIVATE OpenCL)
+ endif()
+ 
+ target_include_directories(sycl_sanitizer_collector PRIVATE
+diff --git a/sycl/tools/sycl-trace/CMakeLists.txt b/sycl/tools/sycl-trace/CMakeLists.txt
+index 385a348f6..721e29125 100644
+--- a/sycl/tools/sycl-trace/CMakeLists.txt
++++ b/sycl/tools/sycl-trace/CMakeLists.txt
+@@ -46,7 +46,7 @@ add_custom_target(ze-pretty-printers
+ target_compile_definitions(sycl_pi_trace_collector PRIVATE XPTI_CALLBACK_API_EXPORTS)
+ target_link_libraries(sycl_pi_trace_collector PRIVATE xptifw)
+ if (TARGET OpenCL-Headers)
+-  target_link_libraries(sycl_pi_trace_collector PRIVATE OpenCL-Headers)
++  target_link_libraries(sycl_pi_trace_collector PRIVATE OpenCL)
+ endif()
+ 
+ target_include_directories(sycl_pi_trace_collector PRIVATE
diff --git a/sys-devel/DPC++/files/DPC++-2022.12-gcc13.patch b/sys-devel/DPC++/files/DPC++-2022.12-gcc13.patch
new file mode 100644
index 000000000..047170cd3
--- /dev/null
+++ b/sys-devel/DPC++/files/DPC++-2022.12-gcc13.patch
@@ -0,0 +1,12 @@
+diff --git a/sycl/include/sycl/sycl_span.hpp b/sycl/include/sycl/sycl_span.hpp
+index 33b942fbc..395694573 100644
+--- a/sycl/include/sycl/sycl_span.hpp
++++ b/sycl/include/sycl/sycl_span.hpp
+@@ -128,6 +128,7 @@ template<class Container>
+ #include <cassert>     // for assert
+ #include <cstddef>     // for byte
+ #include <iterator>    // for iterators
++#include <cstdint>
+ #include <type_traits> // for remove_cv, etc
+ 
+ #define _SYCL_SPAN_TEMPLATE_VIS
diff --git a/sys-devel/DPC++/files/DPC++-2022.12-system-libs.patch b/sys-devel/DPC++/files/DPC++-2022.12-system-libs.patch
new file mode 100644
index 000000000..c5d9d138b
--- /dev/null
+++ b/sys-devel/DPC++/files/DPC++-2022.12-system-libs.patch
@@ -0,0 +1,273 @@
+diff --git a/opencl/CMakeLists.txt b/opencl/CMakeLists.txt
+index 954317fe2..ba3bf19d3 100644
+--- a/opencl/CMakeLists.txt
++++ b/opencl/CMakeLists.txt
+@@ -23,29 +23,8 @@ set(OCL_LOADER_REPO
+ set(OCL_HEADERS_TAG dcd5bede6859d26833cd85f0d6bbcee7382dc9b3)
+ set(OCL_LOADER_TAG 792682ad3d877ab38573b997808bab3b43902b70)
+ 
+-# OpenCL Headers
+-if(NOT OpenCL_HEADERS)
+-  message(STATUS "Will fetch OpenCL headers from ${OCL_HEADERS_REPO}")
+-
+-  FetchContent_Declare(ocl-headers
+-    GIT_REPOSITORY    ${OCL_HEADERS_REPO}
+-    GIT_TAG           ${OCL_HEADERS_TAG}
+-  )
+-else()
+-  message(STATUS "OpenCL headers are added manually ${OpenCL_HEADERS}")
+-
+-  FetchContent_Declare(ocl-headers
+-    URL               ${OpenCL_HEADERS}
+-  )
+-endif()
+-
+-FetchContent_MakeAvailable(ocl-headers)
+-FetchContent_GetProperties(ocl-headers)
+ set(OpenCL_INCLUDE_DIR
+-  ${ocl-headers_SOURCE_DIR} CACHE PATH "Path to OpenCL Headers")
+-
+-target_compile_definitions(Headers INTERFACE -DCL_TARGET_OPENCL_VERSION=220)
+-add_library(OpenCL-Headers ALIAS Headers)
++  /usr/include CACHE PATH "Path to OpenCL Headers")
+ 
+ # OpenCL Library (ICD Loader)
+ 
+@@ -57,25 +36,4 @@ set(OPENCL_ICD_LOADER_HEADERS_DIR
+ # library.
+ set(BUILD_SHARED_LIBS ON)
+ 
+-if(NOT OpenCL_LIBRARY_SRC)
+-  message(STATUS "Will fetch OpenCL ICD Loader from ${OCL_LOADER_REPO}")
+-
+-  FetchContent_Declare(ocl-icd
+-    GIT_REPOSITORY    ${OCL_LOADER_REPO}
+-    GIT_TAG           ${OCL_LOADER_TAG}
+-  )
+-else()
+-  # TODO: add possibility to use prebuilt OpenCL library rather than building
+-  #       together with llvm.
+-  message(STATUS
+-    "OpenCL ICD Loader sources added manually ${OpenCL_LIBRARY_SRC}")
+-
+-  FetchContent_Declare(ocl-icd
+-    URL               ${OpenCL_LIBRARY_SRC}
+-  )
+-endif()
+-
+-FetchContent_MakeAvailable(ocl-icd)
+-add_library(OpenCL-ICD ALIAS OpenCL)
+-
+ add_subdirectory(opencl-aot)
+diff --git a/opencl/opencl-aot/CMakeLists.txt b/opencl/opencl-aot/CMakeLists.txt
+index ff905fd88..b673f79a4 100644
+--- a/opencl/opencl-aot/CMakeLists.txt
++++ b/opencl/opencl-aot/CMakeLists.txt
+@@ -19,5 +19,5 @@ endif()
+ 
+ target_link_libraries(${OPENCL_AOT_PROJECT_NAME}
+   PRIVATE
+-    OpenCL-Headers
+-    OpenCL-ICD)
++    OpenCL
++)
+diff --git a/sycl/CMakeLists.txt b/sycl/CMakeLists.txt
+index 86c5b420d..1d834de4f 100644
+--- a/sycl/CMakeLists.txt
++++ b/sycl/CMakeLists.txt
+@@ -142,7 +142,7 @@ file(COPY ${OpenCL_INCLUDE_DIR}/CL
+ # Include OpenCL Headers into final bundle.
+ install(DIRECTORY ${OpenCL_INCLUDE_DIR}/CL
+         DESTINATION ${SYCL_INCLUDE_DIR}/sycl
+-        COMPONENT OpenCL-Headers)
++        COMPONENT OpenCL)
+ 
+ # Option to enable online kernel fusion via a JIT compiler
+ option(SYCL_ENABLE_KERNEL_FUSION "Enable kernel fusion via JIT compiler" OFF)
+@@ -371,7 +371,7 @@ set( SYCL_TOOLCHAIN_DEPLOY_COMPONENTS
+      sycl-post-link
+      sycl-ls
+      clang-resource-headers
+-     OpenCL-Headers
++     OpenCL
+      opencl-aot
+      sycl-headers
+      sycl-headers-extras
+@@ -391,9 +391,7 @@ if (TARGET sycl-trace)
+   list(APPEND SYCL_TOOLCHAIN_DEPLOY_COMPONENTS sycl-trace)
+ endif()
+ 
+-if(OpenCL_INSTALL_KHRONOS_ICD_LOADER AND TARGET OpenCL-ICD)
+-  list(APPEND SYCL_TOOLCHAIN_DEPLOY_COMPONENTS OpenCL-ICD)
+-endif()
++list(APPEND SYCL_TOOLCHAIN_DEPLOY_COMPONENTS OpenCL)
+ 
+ # Build and install lld as part of the sycl-toolchain if available
+ if("lld" IN_LIST LLVM_ENABLE_PROJECTS)
+diff --git a/sycl/cmake/modules/AddSYCL.cmake b/sycl/cmake/modules/AddSYCL.cmake
+index dbf539e9a..5933b9770 100644
+--- a/sycl/cmake/modules/AddSYCL.cmake
++++ b/sycl/cmake/modules/AddSYCL.cmake
+@@ -47,7 +47,7 @@ function(add_sycl_plugin PLUGIN_NAME)
+       ${sycl_inc_dir}
+     LIBRARIES
+       ${ARG_LIBRARIES}
+-      OpenCL-Headers
++      OpenCL
+   )
+ 
+   install(TARGETS pi_${PLUGIN_NAME}
+diff --git a/sycl/cmake/modules/AddSYCLUnitTest.cmake b/sycl/cmake/modules/AddSYCLUnitTest.cmake
+index 9f5e6dc30..fe0e18b2f 100644
+--- a/sycl/cmake/modules/AddSYCLUnitTest.cmake
++++ b/sycl/cmake/modules/AddSYCLUnitTest.cmake
+@@ -53,7 +53,7 @@ macro(add_sycl_unittest test_dirname link_variant)
+   target_link_libraries(${test_dirname}
+     PRIVATE
+       LLVMTestingSupport
+-      OpenCL-Headers
++      OpenCL
+       ${SYCL_LINK_LIBS}
+     )
+   target_include_directories(${test_dirname}
+diff --git a/sycl/plugins/esimd_emulator/CMakeLists.txt b/sycl/plugins/esimd_emulator/CMakeLists.txt
+index 0b32c3925..e8b8616bc 100755
+--- a/sycl/plugins/esimd_emulator/CMakeLists.txt
++++ b/sycl/plugins/esimd_emulator/CMakeLists.txt
+@@ -58,6 +58,7 @@ if ((DEFINED USE_DEFAULT_CM_EMU_SOURCE) OR (DEFINED USE_LOCAL_CM_EMU_SOURCE))
+       INSTALL_DIR       ${CMAKE_CURRENT_BINARY_DIR}/cm-emu_install
+       CMAKE_ARGS        -DLIBVA_INSTALL_PATH=/usr
+                         -D__SYCL_EXPLICIT_SIMD_PLUGIN__=true
++                        -DLibFFI_INCLUDE_DIR=${LibFFI_INCLUDE_DIR}
+                         -DCMAKE_INSTALL_PREFIX=<INSTALL_DIR>
+       BUILD_BYPRODUCTS  ${LIBCM} ${LIBIGFXCMRT_EMU}
+     )
+diff --git a/sycl/plugins/level_zero/CMakeLists.txt b/sycl/plugins/level_zero/CMakeLists.txt
+index 7b0ce7eae..b9ee52376 100755
+--- a/sycl/plugins/level_zero/CMakeLists.txt
++++ b/sycl/plugins/level_zero/CMakeLists.txt
+@@ -44,7 +44,7 @@ if (NOT DEFINED LEVEL_ZERO_LIBRARY OR NOT DEFINED LEVEL_ZERO_INCLUDE_DIR)
+                LOG_BUILD 1
+                LOG_INSTALL 1
+     STEP_TARGETS      configure,build,install
+-    DEPENDS           OpenCL-Headers
++    DEPENDS           OpenCL
+     BUILD_BYPRODUCTS ${LEVEL_ZERO_LOADER}
+   )
+   ExternalProject_Add_Step(level-zero-loader llvminstall
+@@ -78,7 +78,7 @@ else()
+       COMMAND
+ 	  ${CMAKE_COMMAND} -E copy ${LEVEL_ZERO_LIBRARY_SRC} ${LLVM_LIBRARY_OUTPUT_INTDIR}
+       COMMAND
+-	  ${CMAKE_COMMAND} -E copy_directory ${LEVEL_ZERO_INCLUDE_DIR} ${LLVM_BINARY_DIR}/include/sycl
++	  ${CMAKE_COMMAND} -E copy_directory ${LEVEL_ZERO_INCLUDE_DIR}/level_zero ${LLVM_BINARY_DIR}/include/sycl/level_zero
+       DEPENDS
+ 	  ${LEVEL_ZERO_LIBRARY}
+           ${LEVEL_ZERO_INCLUDE_DIR}
+diff --git a/sycl/plugins/opencl/CMakeLists.txt b/sycl/plugins/opencl/CMakeLists.txt
+index 9943827e4..29fae166e 100644
+--- a/sycl/plugins/opencl/CMakeLists.txt
++++ b/sycl/plugins/opencl/CMakeLists.txt
+@@ -15,7 +15,7 @@ add_sycl_plugin(opencl
+     "${sycl_inc_dir}/sycl/detail/pi.h"
+     "pi_opencl.cpp"
+   LIBRARIES
+-    OpenCL-ICD
++    OpenCL
+ )
+ 
+ set_target_properties(pi_opencl PROPERTIES LINKER_LANGUAGE CXX)
+diff --git a/sycl/plugins/unified_runtime/CMakeLists.txt b/sycl/plugins/unified_runtime/CMakeLists.txt
+index f442db4a4..9ca733695 100755
+--- a/sycl/plugins/unified_runtime/CMakeLists.txt
++++ b/sycl/plugins/unified_runtime/CMakeLists.txt
+@@ -3,18 +3,6 @@
+ 
+ include(FetchContent)
+ 
+-set(UNIFIED_RUNTIME_REPO "https://github.com/oneapi-src/unified-runtime.git")
+-set(UNIFIED_RUNTIME_TAG fd711c920acc4434cb52ff18b078c082d9d7f44d)
+-
+-message(STATUS "Will fetch Unified Runtime from ${UNIFIED_RUNTIME_REPO}")
+-FetchContent_Declare(unified-runtime
+-  GIT_REPOSITORY    ${UNIFIED_RUNTIME_REPO}
+-  GIT_TAG           ${UNIFIED_RUNTIME_TAG}
+-)
+-
+-FetchContent_MakeAvailable(unified-runtime)
+-FetchContent_GetProperties(unified-runtime)
+-
+ set(UNIFIED_RUNTIME_SOURCE_DIR
+   ${unified-runtime_SOURCE_DIR} CACHE PATH "Path to Unified Runtime Headers")
+ set(UNIFIED_RUNTIME_INCLUDE_DIR "${UNIFIED_RUNTIME_SOURCE_DIR}/include")
+diff --git a/sycl/source/CMakeLists.txt b/sycl/source/CMakeLists.txt
+index c61b10da7..02a7fab32 100644
+--- a/sycl/source/CMakeLists.txt
++++ b/sycl/source/CMakeLists.txt
+@@ -84,7 +84,7 @@ function(add_sycl_rt_library LIB_NAME LIB_OBJ_NAME)
+   )
+   #TODO: Remove dependency on opencl headers.
+   target_link_libraries(${LIB_OBJ_NAME}
+-    PRIVATE OpenCL-Headers
++    PRIVATE OpenCL
+   )
+ 
+   find_package(Threads REQUIRED)
+diff --git a/sycl/tools/sycl-ls/CMakeLists.txt b/sycl/tools/sycl-ls/CMakeLists.txt
+index f5909cf49..f9c52e3a3 100644
+--- a/sycl/tools/sycl-ls/CMakeLists.txt
++++ b/sycl/tools/sycl-ls/CMakeLists.txt
+@@ -11,7 +11,7 @@ endif()
+ target_link_libraries(sycl-ls
+   PRIVATE
+     ${sycl_lib}
+-    OpenCL-Headers
++    OpenCL
+ )
+ install(TARGETS sycl-ls
+   RUNTIME DESTINATION "bin" COMPONENT sycl-ls)
+diff --git a/sycl/tools/sycl-prof/CMakeLists.txt b/sycl/tools/sycl-prof/CMakeLists.txt
+index 09586c1b8..bc8f37379 100644
+--- a/sycl/tools/sycl-prof/CMakeLists.txt
++++ b/sycl/tools/sycl-prof/CMakeLists.txt
+@@ -15,9 +15,7 @@ target_compile_options(sycl-prof PRIVATE -fno-exceptions -fno-rtti)
+ add_library(sycl_profiler_collector SHARED collector.cpp)
+ target_compile_definitions(sycl_profiler_collector PRIVATE XPTI_CALLBACK_API_EXPORTS)
+ target_link_libraries(sycl_profiler_collector PRIVATE xptifw)
+-if (TARGET OpenCL-Headers)
+-  target_link_libraries(sycl_profiler_collector PRIVATE OpenCL-Headers)
+-endif()
++target_link_libraries(sycl_profiler_collector PRIVATE OpenCL)
+ target_include_directories(sycl_profiler_collector PRIVATE
+     "${sycl_inc_dir}"
+     "${sycl_src_dir}"
+diff --git a/sycl/tools/sycl-sanitize/CMakeLists.txt b/sycl/tools/sycl-sanitize/CMakeLists.txt
+index 16e7a1a49..4ef93e8e2 100644
+--- a/sycl/tools/sycl-sanitize/CMakeLists.txt
++++ b/sycl/tools/sycl-sanitize/CMakeLists.txt
+@@ -13,9 +13,7 @@ target_compile_options(sycl-sanitize PRIVATE -fno-exceptions -fno-rtti)
+ add_library(sycl_sanitizer_collector SHARED collector.cpp)
+ target_compile_definitions(sycl_sanitizer_collector PRIVATE XPTI_CALLBACK_API_EXPORTS)
+ target_link_libraries(sycl_sanitizer_collector PRIVATE xptifw)
+-if (TARGET OpenCL-Headers)
+-  target_link_libraries(sycl_sanitizer_collector PRIVATE OpenCL-Headers)
+-endif()
++target_link_libraries(sycl_sanitizer_collector PRIVATE OpenCL)
+ 
+ target_include_directories(sycl_sanitizer_collector PRIVATE
+     "${CMAKE_CURRENT_SOURCE_DIR}/../xpti_helpers/"
+diff --git a/sycl/tools/sycl-trace/CMakeLists.txt b/sycl/tools/sycl-trace/CMakeLists.txt
+index 6f36b83a2..24f0d115b 100644
+--- a/sycl/tools/sycl-trace/CMakeLists.txt
++++ b/sycl/tools/sycl-trace/CMakeLists.txt
+@@ -62,9 +62,7 @@ endif()
+ 
+ target_compile_definitions(sycl_pi_trace_collector PRIVATE XPTI_CALLBACK_API_EXPORTS)
+ target_link_libraries(sycl_pi_trace_collector PRIVATE xptifw)
+-if (TARGET OpenCL-Headers)
+-  target_link_libraries(sycl_pi_trace_collector PRIVATE OpenCL-Headers)
+-endif()
++target_link_libraries(sycl_pi_trace_collector PRIVATE OpenCL)
+ 
+ target_include_directories(sycl_pi_trace_collector PRIVATE
+     "${CMAKE_CURRENT_SOURCE_DIR}/../xpti_helpers/"
diff --git a/sys-devel/DPC++/metadata.xml b/sys-devel/DPC++/metadata.xml
new file mode 100644
index 000000000..771c45a25
--- /dev/null
+++ b/sys-devel/DPC++/metadata.xml
@@ -0,0 +1,16 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
+<pkgmetadata>
+	<maintainer type="project">
+		<email>sci@gentoo.org</email>
+		<name>Gentoo Science Project</name>
+	</maintainer>
+	<upstream>
+		<remote-id type="github">intel/llvm</remote-id>
+	</upstream>
+	<use>
+		<flag name="cuda">use the cuda backend</flag>
+		<flag name="esimd_emulator">enable ESIMD CPU emulation</flag>
+		<flag name="hip">use the HIP backend</flag>
+	</use>
+</pkgmetadata>
diff --git a/sys-devel/gdebugger/Manifest b/sys-devel/gdebugger/Manifest
deleted file mode 100644
index d3427aab6..000000000
--- a/sys-devel/gdebugger/Manifest
+++ /dev/null
@@ -1,2 +0,0 @@
-DIST AMDgDEBugger6.2.438x86.tar.gz 26645419 SHA256 659c544eaf80a9bd1e33aa685a30b5fff8cd75117fef45dd14008fb966e4edbb SHA512 b2d1e048c1319b4060398c354b970977896babb9aeebe628f0f8528e7c201e8c3114c5a024d7c1eeacb42f326b5fc69df7513488b4070e3c055a8f234cb9a56e WHIRLPOOL 7156292a1210af572fc73c0bc6e0b9aa99f409be072719ff417c429745ace4e5af78bf5fd06173026a8176b63314b74780c59a13d958fa8f8171b1e29d411e64
-DIST AMDgDEBugger6.2.438x86_64.tar.gz 26814026 SHA256 78d67e68b441fea446d22bd49e192bd561973ce734589e05e0c610ba5870120c SHA512 b6b601894354636b95fa3280393b23f78315b5369117a2749d7ec75bd7d46adff5422201e8e8159325c0ae5e01f3f89b5500dfef733b5505358486aaba07593b WHIRLPOOL 79bfe124dde3d77b9679edc2b8135cea81f12cd84071323d40ea4cfce7b7fbafcac257ce00ddc75c4209bc416e092932975edc4cdb01728ffd12666342fde684
diff --git a/sys-devel/gdebugger/gdebugger-6.2.438.ebuild b/sys-devel/gdebugger/gdebugger-6.2.438.ebuild
deleted file mode 100644
index efc26cda3..000000000
--- a/sys-devel/gdebugger/gdebugger-6.2.438.ebuild
+++ /dev/null
@@ -1,98 +0,0 @@
-# Copyright 1999-2016 Gentoo Foundation
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=6
-
-inherit eutils toolchain-funcs versionator
-
-MY_PN=gDEBugger
-MY_PV=$(delete_all_version_separators)
-MY_P=${MY_PN}${PV}
-
-DESCRIPTION="OpenCL and OpenGL debugger and memory analyzer"
-HOMEPAGE="http://developer.amd.com/tools/gDEBugger/Pages/default.aspx"
-SRC_URI="
-	x86? ( http://developer.amd.com/Downloads/AMD${MY_P}x86.tar.gz )
-	amd64? ( http://developer.amd.com/Downloads/AMD${MY_P}x86_64.tar.gz )"
-
-LICENSE="gDEBugger"
-SLOT="0"
-KEYWORDS="~amd64 ~x86"
-IUSE="examples"
-
-DEPEND=""
-RDEPEND="
-	virtual/libstdc++
-	dev-libs/atk
-	dev-libs/glib:2
-	media-libs/fontconfig
-	media-libs/freetype
-	media-libs/libpng:1.2
-	media-libs/mesa
-	sys-libs/zlib
-	x11-libs/cairo
-	x11-libs/gdk-pixbuf
-	x11-libs/gtk+:2
-	x11-libs/libICE
-	x11-libs/libSM
-	x11-libs/libX11
-	x11-libs/libXext
-	x11-libs/libXrender
-	x11-libs/libXxf86vm
-	x11-libs/pango"
-
-RESTRICT="mirror strip"
-
-S=${WORKDIR}
-
-QA_PREBUILT="
-	/opt/${MY_PN}/libGROSWrappers.so
-	/opt/${MY_PN}/libGRProcessDebugger.so
-	/opt/${MY_PN}/libGRAPIClasses.so
-	/opt/${MY_PN}/libgDEBuggerAppCode.so
-	/opt/${MY_PN}/libGRApiFunctions.so
-	/opt/${MY_PN}/libAMDTApplicationFramework.so
-	/opt/${MY_PN}/libGRApplicationComponents.so
-	/opt/${MY_PN}/libAMDTgDEBuggerAppWrapper.so
-	/opt/${MY_PN}/libGRSpiesUtilities.so
-	/opt/${MY_PN}/libGRBaseTools.so
-	/opt/${MY_PN}/gDEBugger
-"
-
-src_prepare() {
-	cat >> "${T}"/99${PN} <<- EOF
-		PATH="/opt/${MY_PN}"
-		LDPATH="/opt/${MY_PN}"
-	EOF
-}
-
-src_install() {
-	pushd ${MY_P}-$(tc-arch-kernel) &> /dev/null
-	local _dest=/opt/${MY_PN}
-
-	exeinto ${_dest}
-	doexe $(find . -maxdepth 1 -type f -name '*.so*')
-	for f in lib*.so.?.?.?; do
-		dosym $f ${_dest}/${f%.?.?.?}
-		dosym $f ${_dest}/${f%.?.?}
-	done
-	newexe ${MY_PN}-bin ${MY_PN}
-
-	insinto ${_dest}
-	doins -r Images webhelp	tutorial
-
-	insinto ${_dest}/Legal
-	doins Legal/EndUserLicenseAgreement.htm
-
-	if use examples ; then
-		insinto ${_dest}/examples
-		doins -r examples/*
-	fi
-
-	newicon tutorial/images/applicationicon_64.png ${MY_PN}.png
-	popd &> /dev/null
-
-	doenvd "${T}"/99${PN}
-	make_desktop_entry ${MY_PN} ${MY_PN} ${MY_PN} \
-		"Application;Development"
-}
diff --git a/sys-devel/gdebugger/metadata.xml b/sys-devel/gdebugger/metadata.xml
deleted file mode 100644
index 670dc201d..000000000
--- a/sys-devel/gdebugger/metadata.xml
+++ /dev/null
@@ -1,12 +0,0 @@
-<?xml version="1.0" encoding="UTF-8"?>
-<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
-<pkgmetadata>
-	<maintainer type="person">
-		<email>nbigaouette@gmail.com</email>
-		<name>Nicolas Bigaouette</name>
-	</maintainer>
-	<maintainer type="project">
-		<email>sci@gentoo.org</email>
-		<name>Gentoo Science Project</name>
-	</maintainer>
-</pkgmetadata>
diff --git a/sys-devel/ittapi/Manifest b/sys-devel/ittapi/Manifest
new file mode 100644
index 000000000..f8d38ff32
--- /dev/null
+++ b/sys-devel/ittapi/Manifest
@@ -0,0 +1,2 @@
+DIST ittapi-3.23.0.tar.gz 132481 BLAKE2B c1caf9755e3f0dfa0de2d3e1bca29f3596b68669d8b119822ab23617fdfc33df8d049ed9e8fd66b0865abd311a72b8362e9f26ff45875880cedd1d545f475500 SHA512 2e4aae2e3867588d38734f4425e416fb1ee6fd7df64c72823b481256cf9b7c18a50b6dba22727e16ada9ba0ac10ad0a96fc0d7c6d68edd2b64a899ea047651b5
+DIST ittapi-3.24.0.tar.gz 209498 BLAKE2B f7d13bf8a9633f01719c54cd6e29c2106572dc2bb883d9166af420b6c856cc126a398933cdda73f556b020128292dddb68f67eb97dc1bc597253cea7ade3ca6a SHA512 8d0b8213c0d18514eca581ebb868d7458094bb53760815c68e0648c785d4be0634b09c44bc6565483014425ae422ff390d19e365c19110cc8b5e1a4cced7a51b
diff --git a/sys-devel/ittapi/ittapi-3.23.0.ebuild b/sys-devel/ittapi/ittapi-3.23.0.ebuild
new file mode 100644
index 000000000..38ae1b432
--- /dev/null
+++ b/sys-devel/ittapi/ittapi-3.23.0.ebuild
@@ -0,0 +1,26 @@
+# Copyright 2022 Gentoo Authors
+# Distributed under the terms of the GNU General Public License v2
+
+EAPI=8
+
+inherit cmake
+
+DESCRIPTION="Intel Instrumentation and Tracing Technology and Just-In-Time API "
+HOMEPAGE="https://github.com/intel/ittapi"
+SRC_URI="https://github.com/intel/ittapi/archive/refs/tags/v${PV}.tar.gz -> ${P}.tar.gz"
+
+LICENSE="|| ( GPL-2 BSD )"
+SLOT="0"
+KEYWORDS="~amd64"
+
+src_prepare() {
+	# Make it a shared library
+	sed -i -e 's/STATIC/SHARED/g' CMakeLists.txt || die
+	cmake_src_prepare
+}
+
+src_install() {
+	dolib.so "${BUILD_DIR}/bin/"*.so
+	doheader -r "${S}/include/"*
+	einstalldocs
+}
diff --git a/sys-devel/ittapi/ittapi-3.24.0.ebuild b/sys-devel/ittapi/ittapi-3.24.0.ebuild
new file mode 100644
index 000000000..38ae1b432
--- /dev/null
+++ b/sys-devel/ittapi/ittapi-3.24.0.ebuild
@@ -0,0 +1,26 @@
+# Copyright 2022 Gentoo Authors
+# Distributed under the terms of the GNU General Public License v2
+
+EAPI=8
+
+inherit cmake
+
+DESCRIPTION="Intel Instrumentation and Tracing Technology and Just-In-Time API "
+HOMEPAGE="https://github.com/intel/ittapi"
+SRC_URI="https://github.com/intel/ittapi/archive/refs/tags/v${PV}.tar.gz -> ${P}.tar.gz"
+
+LICENSE="|| ( GPL-2 BSD )"
+SLOT="0"
+KEYWORDS="~amd64"
+
+src_prepare() {
+	# Make it a shared library
+	sed -i -e 's/STATIC/SHARED/g' CMakeLists.txt || die
+	cmake_src_prepare
+}
+
+src_install() {
+	dolib.so "${BUILD_DIR}/bin/"*.so
+	doheader -r "${S}/include/"*
+	einstalldocs
+}
diff --git a/sys-devel/ittapi/metadata.xml b/sys-devel/ittapi/metadata.xml
new file mode 100644
index 000000000..f71d530b0
--- /dev/null
+++ b/sys-devel/ittapi/metadata.xml
@@ -0,0 +1,11 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
+<pkgmetadata>
+	<maintainer type="project">
+		<email>sci@gentoo.org</email>
+		<name>Gentoo Science Project</name>
+	</maintainer>
+	<upstream>
+		<remote-id type="github">intel/ittapi</remote-id>
+	</upstream>
+</pkgmetadata>
diff --git a/sys-devel/oneDPL/Manifest b/sys-devel/oneDPL/Manifest
new file mode 100644
index 000000000..c3002057c
--- /dev/null
+++ b/sys-devel/oneDPL/Manifest
@@ -0,0 +1,3 @@
+DIST oneDPL-2021.7.1-release.tar.gz 3704195 BLAKE2B 32b47a8ed27a59487b030af8a1cb5f521fb9c03c25bebeb682d601a92594fd2e7c0437b209fead1e3a2b7ad0ad9b6afe736fcef97266619f19cac32d965fb5fa SHA512 264b5e866985e23c28e411d89a5e2e4bb306ac70976c4b3d40991d53dc70a211ab67821f7ea94ff57f093205b1e9f0bb41308e394b4dc0d439b771a6316c1709
+DIST oneDPL-2022.0.0-release.tar.gz 3729700 BLAKE2B f1da5c7a69583b08646ba5dd55fc9a178c2174804518b1ef6af094f2bde9b9df61ff45856a79a98cff91baee43e58e54d701e924e2f7f0d059f0ded2bd09fbc6 SHA512 c254cabd98328303e47b6054ffd0893aaa5862abda48febcbaca82190d901c6e49c9c64cdd91b08417e1618eae05cbaf392dfdbec5f6f03535a89d74d368689b
+DIST oneDPL-2022.2.0-rc1.tar.gz 3764454 BLAKE2B 32f2bdc43df7209dc0b14c5bbe8ef8352af04aed8848be10378a4c0cf2877e4e76b05dc5e68dcf392256ca7e0f16a086f1f1cec8e4c7cf2a021705406ad0ec94 SHA512 006ade274211b767874e7375cad5a3763266104484092d9b4177f47699f36d920cdecb3fbb45b6e5fd45cce721ae8aec5b4ae90139ef9f5497d2661fa5d1fec0
diff --git a/sys-devel/oneDPL/metadata.xml b/sys-devel/oneDPL/metadata.xml
new file mode 100644
index 000000000..474176a00
--- /dev/null
+++ b/sys-devel/oneDPL/metadata.xml
@@ -0,0 +1,14 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
+<pkgmetadata>
+	<maintainer type="project">
+		<email>sci@gentoo.org</email>
+		<name>Gentoo Science Project</name>
+	</maintainer>
+	<upstream>
+		<remote-id type="github">oneapi-src/oneDPL</remote-id>
+	</upstream>
+	<use>
+		<flag name="esimd_emulator">enable ESIMD CPU emulation</flag>
+	</use>
+</pkgmetadata>
diff --git a/sys-devel/oneDPL/oneDPL-2021.7.1.ebuild b/sys-devel/oneDPL/oneDPL-2021.7.1.ebuild
new file mode 100644
index 000000000..7db9cb0b6
--- /dev/null
+++ b/sys-devel/oneDPL/oneDPL-2021.7.1.ebuild
@@ -0,0 +1,58 @@
+# Copyright 2022 Gentoo Authors
+# Distributed under the terms of the GNU General Public License v2
+
+EAPI=8
+
+# Missing deps for documentation
+# PYTHON_COMPAT=( python3_{10..11} )
+# DOCS_BUILDER="sphinx"
+# DOCS_DIR="documentation/library_guide"
+# DOCS_AUTODOC=0
+inherit cmake #python-any-r1 docs
+
+DESCRIPTION="oneAPI Data Parallel C++ Library"
+HOMEPAGE="https://github.com/oneapi-src/oneDPL"
+SRC_URI="https://github.com/oneapi-src/oneDPL/archive/refs/tags/${P}-release.tar.gz"
+S="${WORKDIR}/${PN}-${P}-release"
+
+LICENSE="Apache-2.0-with-LLVM-exceptions"
+SLOT="0"
+KEYWORDS="~amd64"
+
+#TODO: Figure out how to use the test
+RESTRICT="test"
+
+BDEPEND="virtual/pkgconfig"
+
+DEPEND="
+	sys-devel/DPC++:0/5
+	dev-libs/level-zero
+	dev-cpp/tbb
+"
+RDEPEND="${DEPEND}"
+
+src_prepare() {
+	# Not using the DPC++ compiler doesn't really make sense here
+	export CXX="${ESYSROOT}/usr/lib/llvm/intel/bin/clang++"
+	export CC="${ESYSROOT}/usr/lib/llvm/intel/bin/clang"
+	cmake_src_prepare
+}
+
+src_configure() {
+	local mycmakeargs=(
+		-DONEDPL_DEVICE_BACKEND="level_zero"
+		-DONEDPL_BACKEND="dpcpp"
+	)
+
+	cmake_src_configure
+}
+
+src_compile() {
+	cmake_src_compile
+	# docs_compile
+}
+
+src_install() {
+	einstalldocs
+	doheader -r "${S}/include/oneapi"
+}
diff --git a/sys-devel/oneDPL/oneDPL-2022.0.0-r1.ebuild b/sys-devel/oneDPL/oneDPL-2022.0.0-r1.ebuild
new file mode 100644
index 000000000..895c53c37
--- /dev/null
+++ b/sys-devel/oneDPL/oneDPL-2022.0.0-r1.ebuild
@@ -0,0 +1,65 @@
+# Copyright 2022 Gentoo Authors
+# Distributed under the terms of the GNU General Public License v2
+
+EAPI=8
+
+# Missing deps for documentation
+# PYTHON_COMPAT=( python3_{10..11} )
+# DOCS_BUILDER="sphinx"
+# DOCS_DIR="documentation/library_guide"
+# DOCS_AUTODOC=0
+inherit cmake #python-any-r1 docs
+
+DESCRIPTION="oneAPI Data Parallel C++ Library"
+HOMEPAGE="https://github.com/oneapi-src/oneDPL"
+SRC_URI="https://github.com/oneapi-src/oneDPL/archive/refs/tags/${P}-release.tar.gz"
+S="${WORKDIR}/${PN}-${P}-release"
+
+LICENSE="Apache-2.0-with-LLVM-exceptions"
+SLOT="0"
+KEYWORDS="~amd64"
+
+IUSE="esimd_emulator"
+#TODO: Figure out how to use the test
+RESTRICT="test"
+
+BDEPEND="virtual/pkgconfig"
+
+DEPEND="
+	sys-devel/DPC++:0/6[esimd_emulator?]
+	dev-libs/level-zero
+	dev-cpp/tbb
+"
+RDEPEND="${DEPEND}"
+
+src_prepare() {
+	# Not using the DPC++ compiler doesn't really make sense here
+	export CXX="${ESYSROOT}/usr/lib/llvm/intel/bin/clang++"
+	export CC="${ESYSROOT}/usr/lib/llvm/intel/bin/clang"
+	cmake_src_prepare
+}
+
+src_configure() {
+	local mycmakeargs=(
+		-DONEDPL_DEVICE_BACKEND="level_zero"
+		-DONEDPL_BACKEND="dpcpp"
+		-DONEDPL_ENABLE_SIMD="$(usex esimd_emulator)"
+	)
+
+	cmake_src_configure
+}
+
+src_compile() {
+	cmake_src_compile
+	cmake -P cmake/scripts/generate_config.cmake || die
+	# docs_compile
+}
+
+src_install() {
+	einstalldocs
+	doheader -r "${S}/include/oneapi"
+	insinto "/usr/$(get_libdir)/cmake/oneDPL/"
+	doins output/*.cmake
+	insinto "/usr/$(get_libdir)/pkgconfig/"
+	doins output/pkgconfig-lin/*.pc
+}
diff --git a/sys-devel/oneDPL/oneDPL-2022.2.0.ebuild b/sys-devel/oneDPL/oneDPL-2022.2.0.ebuild
new file mode 100644
index 000000000..7b1010ab1
--- /dev/null
+++ b/sys-devel/oneDPL/oneDPL-2022.2.0.ebuild
@@ -0,0 +1,66 @@
+# Copyright 2022 Gentoo Authors
+# Distributed under the terms of the GNU General Public License v2
+
+EAPI=8
+
+# Missing deps for documentation
+# PYTHON_COMPAT=( python3_{10..11} )
+# DOCS_BUILDER="sphinx"
+# DOCS_DIR="documentation/library_guide"
+# DOCS_AUTODOC=0
+inherit cmake #python-any-r1 docs
+
+DESCRIPTION="oneAPI Data Parallel C++ Library"
+HOMEPAGE="https://github.com/oneapi-src/oneDPL"
+SRC_URI="https://github.com/oneapi-src/oneDPL/archive/refs/tags/${P}-rc1.tar.gz"
+S="${WORKDIR}/${PN}-${P}-rc1"
+
+LICENSE="Apache-2.0-with-LLVM-exceptions"
+SLOT="0"
+KEYWORDS="~amd64"
+
+IUSE="esimd_emulator"
+#TODO: Figure out how to use the test
+RESTRICT="test"
+
+BDEPEND="virtual/pkgconfig"
+
+DEPEND="
+	sys-devel/DPC++:0/6[esimd_emulator?]
+	dev-libs/level-zero
+	dev-cpp/tbb
+"
+RDEPEND="${DEPEND}"
+
+src_prepare() {
+	# Not using the DPC++ compiler doesn't really make sense here
+	export CXX="${ESYSROOT}/usr/lib/llvm/intel/bin/clang++"
+	export CC="${ESYSROOT}/usr/lib/llvm/intel/bin/clang"
+	cmake_src_prepare
+}
+
+src_configure() {
+	local mycmakeargs=(
+		-DONEDPL_DEVICE_TYPE="GPU"
+		-DONEDPL_DEVICE_BACKEND="level_zero"
+		-DONEDPL_BACKEND="dpcpp"
+		-DONEDPL_ENABLE_SIMD="$(usex esimd_emulator)"
+	)
+
+	cmake_src_configure
+}
+
+src_compile() {
+	cmake_src_compile
+	cmake -P cmake/scripts/generate_config.cmake || die
+	# docs_compile
+}
+
+src_install() {
+	einstalldocs
+	doheader -r "${S}/include/oneapi"
+	insinto "/usr/$(get_libdir)/cmake/oneDPL/"
+	doins output/*.cmake
+	insinto "/usr/$(get_libdir)/pkgconfig/"
+	doins output/pkgconfig-lin/*.pc
+}
diff --git a/virtual/blacs/blacs-1.1-r1.ebuild b/virtual/blacs/blacs-1.1-r1.ebuild
deleted file mode 100644
index ba94ffaa2..000000000
--- a/virtual/blacs/blacs-1.1-r1.ebuild
+++ /dev/null
@@ -1,24 +0,0 @@
-# Copyright 1999-2017 Gentoo Foundation
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=6
-
-inherit multilib-build
-
-DESCRIPTION="Virtual for BLACS implementation"
-HOMEPAGE=""
-SRC_URI=""
-
-LICENSE=""
-SLOT="0"
-KEYWORDS="~amd64 ~x86 ~amd64-linux"
-IUSE="doc int64"
-
-RDEPEND="
-	|| (
-		sci-libs/mkl[int64?,${MULTILIB_USEDEP}]
-		abi_x86_64? ( !abi_x86_32? ( >=sci-libs/mpiblacs-1.1 ) )
-	)
-	int64? ( sci-libs/mkl[int64,${MULTILIB_USEDEP}] )
-	doc? ( >=app-doc/blacs-docs-1 )"
-DEPEND=""
diff --git a/virtual/blacs/metadata.xml b/virtual/blacs/metadata.xml
deleted file mode 100644
index 5f25087f3..000000000
--- a/virtual/blacs/metadata.xml
+++ /dev/null
@@ -1,15 +0,0 @@
-<?xml version="1.0" encoding="UTF-8"?>
-<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
-<pkgmetadata>
-	<maintainer type="project">
-		<email>sci@gentoo.org</email>
-		<name>Gentoo Science Project</name>
-	</maintainer>
-	<longdescription lang="en">
-Gentoo virtual package for the Basic Linear Algebra Communication Subprograms implementation.
-</longdescription>
-	<use>
-		<flag name="int64">Add eselect module for blas libraries built with 64 bits
-integer ABI</flag>
-	</use>
-</pkgmetadata>
diff --git a/virtual/blas/blas-2.1-r5.ebuild b/virtual/blas/blas-2.1-r5.ebuild
deleted file mode 100644
index d30ea7186..000000000
--- a/virtual/blas/blas-2.1-r5.ebuild
+++ /dev/null
@@ -1,53 +0,0 @@
-# Copyright 1999-2017 Gentoo Foundation
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=6
-
-inherit multilib-build multilib
-
-DESCRIPTION="Virtual for FORTRAN 77 BLAS implementation"
-HOMEPAGE=""
-SRC_URI=""
-
-LICENSE=""
-SLOT="0"
-KEYWORDS="~amd64 ~x86 ~amd64-linux ~x86-linux"
-IUSE="doc int64"
-
-RDEPEND="
-	!app-eselect/eselect-blas
-	|| (
-		sci-libs/blas-reference[int64?,${MULTILIB_USEDEP}]
-		>=sci-libs/openblas-0.2.11[int64?,${MULTILIB_USEDEP}]
-		sci-libs/gotoblas2[int64?,${MULTILIB_USEDEP}]
-		sci-libs/mkl[int64?,${MULTILIB_USEDEP}]
-		abi_x86_64? (
-			!abi_x86_32? (
-				|| (
-					>=dev-cpp/eigen-3.1.4[fortran]
-					sci-libs/atlas[fortran]
-				)
-			)
-		)
-	)
-	doc? ( >=app-doc/blas-docs-3.2 )
-	int64? (
-		|| (
-			sci-libs/blas-reference[int64,${MULTILIB_USEDEP}]
-			>=sci-libs/openblas-0.2.11[int64,${MULTILIB_USEDEP}]
-			sci-libs/gotoblas2[int64,${MULTILIB_USEDEP}]
-			sci-libs/mkl[int64,${MULTILIB_USEDEP}]
-		)
-	)
-"
-DEPEND=""
-
-pkg_pretend() {
-	if [[ -e "${EROOT%/}"/usr/$(get_libdir)/lib${PN}.so ]]; then
-		ewarn "You have still the old ${PN} library symlink present"
-		ewarn "Please delete"
-		ewarn "${EROOT%/}/usr/$(get_libdir)/lib${PN}.so"
-		ewarn "to avoid problems with new ${PN} structure"
-		die "Old lib${PN} detected"
-	fi
-}
diff --git a/virtual/blas/blas-3.6-r100.ebuild b/virtual/blas/blas-3.6-r100.ebuild
deleted file mode 100644
index 37afd2e29..000000000
--- a/virtual/blas/blas-3.6-r100.ebuild
+++ /dev/null
@@ -1,53 +0,0 @@
-# Copyright 1999-2017 Gentoo Foundation
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=6
-
-inherit multilib-build multilib
-
-DESCRIPTION="Virtual for FORTRAN 77 BLAS implementation"
-HOMEPAGE=""
-SRC_URI=""
-
-LICENSE=""
-SLOT="0"
-KEYWORDS="~amd64 ~x86 ~amd64-linux ~x86-linux"
-IUSE="doc int64"
-
-RDEPEND="
-	!app-eselect/eselect-blas
-	|| (
-		>=sci-libs/blas-reference-20151113-r100[int64?,${MULTILIB_USEDEP}]
-		>=sci-libs/openblas-0.2.11[int64?,${MULTILIB_USEDEP}]
-		sci-libs/gotoblas2[int64?,${MULTILIB_USEDEP}]
-		sci-libs/mkl[int64?,${MULTILIB_USEDEP}]
-		abi_x86_64? (
-			!abi_x86_32? (
-				|| (
-					>=dev-cpp/eigen-3.1.4[fortran]
-					sci-libs/atlas[fortran]
-				)
-			)
-		)
-	)
-	doc? ( >=app-doc/blas-docs-3.2 )
-	int64? (
-		|| (
-			sci-libs/blas-reference[int64,${MULTILIB_USEDEP}]
-			>=sci-libs/openblas-0.2.11[int64,${MULTILIB_USEDEP}]
-			sci-libs/gotoblas2[int64,${MULTILIB_USEDEP}]
-			sci-libs/mkl[int64,${MULTILIB_USEDEP}]
-		)
-	)
-"
-DEPEND=""
-
-pkg_pretend() {
-	if [[ -e "${EROOT%/}"/usr/$(get_libdir)/lib${PN}.so ]]; then
-		ewarn "You have still the old ${PN} library symlink present"
-		ewarn "Please delete"
-		ewarn "${EROOT%/}/usr/$(get_libdir)/lib${PN}.so"
-		ewarn "to avoid problems with new ${PN} structure"
-		die "Old lib${PN} detected"
-	fi
-}
diff --git a/virtual/blas/blas-3.7-r100.ebuild b/virtual/blas/blas-3.7-r100.ebuild
deleted file mode 100644
index 2c17daa33..000000000
--- a/virtual/blas/blas-3.7-r100.ebuild
+++ /dev/null
@@ -1,53 +0,0 @@
-# Copyright 1999-2017 Gentoo Foundation
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=6
-
-inherit multilib-build multilib
-
-DESCRIPTION="Virtual for FORTRAN 77 BLAS implementation"
-HOMEPAGE=""
-SRC_URI=""
-
-LICENSE=""
-SLOT="0"
-KEYWORDS="~amd64 ~x86 ~amd64-linux ~x86-linux"
-IUSE="doc int64"
-
-RDEPEND="
-	!app-eselect/eselect-blas
-	|| (
-		>=sci-libs/blas-reference-20161223-r100[int64?,${MULTILIB_USEDEP}]
-		>=sci-libs/openblas-0.2.11[int64?,${MULTILIB_USEDEP}]
-		sci-libs/gotoblas2[int64?,${MULTILIB_USEDEP}]
-		sci-libs/mkl[int64?,${MULTILIB_USEDEP}]
-		abi_x86_64? (
-			!abi_x86_32? (
-				|| (
-					>=dev-cpp/eigen-3.1.4[fortran]
-					sci-libs/atlas[fortran]
-				)
-			)
-		)
-	)
-	doc? ( >=app-doc/blas-docs-3.2 )
-	int64? (
-		|| (
-			sci-libs/blas-reference[int64,${MULTILIB_USEDEP}]
-			>=sci-libs/openblas-0.2.11[int64,${MULTILIB_USEDEP}]
-			sci-libs/gotoblas2[int64,${MULTILIB_USEDEP}]
-			sci-libs/mkl[int64,${MULTILIB_USEDEP}]
-		)
-	)
-"
-DEPEND=""
-
-pkg_pretend() {
-	if [[ -e "${EROOT%/}"/usr/$(get_libdir)/lib${PN}.so ]]; then
-		ewarn "You have still the old ${PN} library symlink present"
-		ewarn "Please delete"
-		ewarn "${EROOT%/}/usr/$(get_libdir)/lib${PN}.so"
-		ewarn "to avoid problems with new ${PN} structure"
-		die "Old lib${PN} detected"
-	fi
-}
diff --git a/virtual/blas/metadata.xml b/virtual/blas/metadata.xml
deleted file mode 100644
index f683eb986..000000000
--- a/virtual/blas/metadata.xml
+++ /dev/null
@@ -1,16 +0,0 @@
-<?xml version="1.0" encoding="UTF-8"?>
-<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
-<pkgmetadata>
-	<maintainer type="project">
-		<email>sci@gentoo.org</email>
-		<name>Gentoo Science Project</name>
-	</maintainer>
-	<longdescription lang="en">
-Gentoo virtual package for the Basic Linear Algebra Subprograms
-FORTRAN 77 implementation.
-</longdescription>
-	<use>
-		<flag name="int64">Add eselect module for blas libraries built with 64 bits
-integer ABI</flag>
-	</use>
-</pkgmetadata>
diff --git a/virtual/cblas/cblas-2.0-r4.ebuild b/virtual/cblas/cblas-2.0-r4.ebuild
deleted file mode 100644
index 14a030651..000000000
--- a/virtual/cblas/cblas-2.0-r4.ebuild
+++ /dev/null
@@ -1,34 +0,0 @@
-# Copyright 1999-2017 Gentoo Foundation
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=6
-
-inherit multilib-build
-
-DESCRIPTION="Virtual for BLAS C implementation"
-HOMEPAGE=""
-SRC_URI=""
-
-LICENSE=""
-SLOT="0"
-KEYWORDS="~amd64 ~x86 ~amd64-linux ~x86-linux"
-IUSE="int64"
-
-RDEPEND="
-	|| (
-		>=sci-libs/cblas-reference-20110218-r1[int64?,${MULTILIB_USEDEP}]
-		>=sci-libs/openblas-0.2.11[int64?,${MULTILIB_USEDEP}]
-		>=sci-libs/gsl-1.16-r2[-cblas-external,${MULTILIB_USEDEP}]
-		>=sci-libs/gotoblas2-1.13[int64?,${MULTILIB_USEDEP}]
-		sci-libs/mkl[int64?,${MULTILIB_USEDEP}]
-		abi_x86_64? ( !abi_x86_32? ( >=sci-libs/atlas-3.9.34 ) )
-	)
-	int64? (
-		|| (
-			>=sci-libs/openblas-0.2.11[int64,${MULTILIB_USEDEP}]
-			>=sci-libs/cblas-reference-20110218-r1[int64,${MULTILIB_USEDEP}]
-			>=sci-libs/gotoblas2-1.13[int64,${MULTILIB_USEDEP}]
-			sci-libs/mkl[int64,${MULTILIB_USEDEP}]
-		)
-	)"
-DEPEND=""
diff --git a/virtual/cblas/cblas-3.6-r100.ebuild b/virtual/cblas/cblas-3.6-r100.ebuild
deleted file mode 100644
index 4adf7906c..000000000
--- a/virtual/cblas/cblas-3.6-r100.ebuild
+++ /dev/null
@@ -1,34 +0,0 @@
-# Copyright 1999-2017 Gentoo Foundation
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=6
-
-inherit multilib-build
-
-DESCRIPTION="Virtual for BLAS C implementation"
-HOMEPAGE=""
-SRC_URI=""
-
-LICENSE=""
-SLOT="0"
-KEYWORDS="~amd64 ~x86 ~amd64-linux ~x86-linux"
-IUSE="int64"
-
-RDEPEND="
-	|| (
-		>=sci-libs/cblas-reference-20151113-r100[int64?,${MULTILIB_USEDEP}]
-		>=sci-libs/openblas-0.2.11[int64?,${MULTILIB_USEDEP}]
-		>=sci-libs/gsl-1.16-r2[-cblas-external,${MULTILIB_USEDEP}]
-		>=sci-libs/gotoblas2-1.13[int64?,${MULTILIB_USEDEP}]
-		sci-libs/mkl[int64?,${MULTILIB_USEDEP}]
-		abi_x86_64? ( !abi_x86_32? ( >=sci-libs/atlas-3.9.34 ) )
-	)
-	int64? (
-		|| (
-			>=sci-libs/openblas-0.2.11[int64,${MULTILIB_USEDEP}]
-			>=sci-libs/cblas-reference-20110218-r1[int64,${MULTILIB_USEDEP}]
-			>=sci-libs/gotoblas2-1.13[int64,${MULTILIB_USEDEP}]
-			sci-libs/mkl[int64,${MULTILIB_USEDEP}]
-		)
-	)"
-DEPEND=""
diff --git a/virtual/cblas/cblas-3.7-r100.ebuild b/virtual/cblas/cblas-3.7-r100.ebuild
deleted file mode 100644
index 51ed1b464..000000000
--- a/virtual/cblas/cblas-3.7-r100.ebuild
+++ /dev/null
@@ -1,34 +0,0 @@
-# Copyright 1999-2017 Gentoo Foundation
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=6
-
-inherit multilib-build
-
-DESCRIPTION="Virtual for BLAS C implementation"
-HOMEPAGE=""
-SRC_URI=""
-
-LICENSE=""
-SLOT="0"
-KEYWORDS="~amd64 ~x86 ~amd64-linux ~x86-linux"
-IUSE="int64"
-
-RDEPEND="
-	|| (
-		>=sci-libs/cblas-reference-20161223-r100[int64?,${MULTILIB_USEDEP}]
-		>=sci-libs/openblas-0.2.11[int64?,${MULTILIB_USEDEP}]
-		>=sci-libs/gsl-1.16-r2[-cblas-external,${MULTILIB_USEDEP}]
-		>=sci-libs/gotoblas2-1.13[int64?,${MULTILIB_USEDEP}]
-		sci-libs/mkl[int64?,${MULTILIB_USEDEP}]
-		abi_x86_64? ( !abi_x86_32? ( >=sci-libs/atlas-3.9.34 ) )
-	)
-	int64? (
-		|| (
-			>=sci-libs/openblas-0.2.11[int64,${MULTILIB_USEDEP}]
-			>=sci-libs/cblas-reference-20110218-r1[int64,${MULTILIB_USEDEP}]
-			>=sci-libs/gotoblas2-1.13[int64,${MULTILIB_USEDEP}]
-			sci-libs/mkl[int64,${MULTILIB_USEDEP}]
-		)
-	)"
-DEPEND=""
diff --git a/virtual/cblas/metadata.xml b/virtual/cblas/metadata.xml
deleted file mode 100644
index 1f78cc421..000000000
--- a/virtual/cblas/metadata.xml
+++ /dev/null
@@ -1,16 +0,0 @@
-<?xml version="1.0" encoding="UTF-8"?>
-<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
-<pkgmetadata>
-	<maintainer type="project">
-		<email>sci@gentoo.org</email>
-		<name>Gentoo Science Project</name>
-	</maintainer>
-	<longdescription lang="en">
-Gentoo virtual package for the Basic Linear Algebra Subprograms
-C implementation.
-</longdescription>
-	<use>
-		<flag name="int64">Add eselect module for cblas libraries built with 64 bits
-integer ABI</flag>
-	</use>
-</pkgmetadata>
diff --git a/virtual/geant/geant-3.ebuild b/virtual/geant/geant-3.ebuild
deleted file mode 100644
index 69f961c5e..000000000
--- a/virtual/geant/geant-3.ebuild
+++ /dev/null
@@ -1,16 +0,0 @@
-# Copyright 1999-2016 Gentoo Foundation
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=6
-
-DESCRIPTION="Virtual for Geant-3"
-HOMEPAGE=""
-SRC_URI=""
-
-LICENSE=""
-SLOT="3"
-KEYWORDS="~amd64 ~x86 ~amd64-linux ~x86-linux"
-IUSE=""
-
-DEPEND=""
-RDEPEND="|| ( sci-physics/geant:3 sci-physics/geant-vmc:3 )"
diff --git a/virtual/geant/metadata.xml b/virtual/geant/metadata.xml
deleted file mode 100644
index 723432dfb..000000000
--- a/virtual/geant/metadata.xml
+++ /dev/null
@@ -1,11 +0,0 @@
-<?xml version="1.0" encoding="UTF-8"?>
-<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
-<pkgmetadata>
-	<maintainer type="project">
-		<email>sci-physics@gentoo.org</email>
-		<name>Gentoo Physics Project</name>
-	</maintainer>
-	<longdescription lang="en">
-Gentoo virtual package for GEANT-3 implementation
-</longdescription>
-</pkgmetadata>
diff --git a/virtual/lapack/lapack-3.6-r100.ebuild b/virtual/lapack/lapack-3.6-r100.ebuild
deleted file mode 100644
index 64256ca6d..000000000
--- a/virtual/lapack/lapack-3.6-r100.ebuild
+++ /dev/null
@@ -1,40 +0,0 @@
-# Copyright 1999-2017 Gentoo Foundation
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=6
-
-inherit multilib-build
-
-DESCRIPTION="Virtual for Linear Algebra Package FORTRAN 77 implementation"
-HOMEPAGE=""
-SRC_URI=""
-
-LICENSE=""
-SLOT="0"
-KEYWORDS="~amd64 ~x86 ~amd64-linux ~x86-linux"
-IUSE="doc int64"
-
-RDEPEND="
-	!app-eselect/eselect-lapack
-	|| (
-		>=sci-libs/lapack-reference-${PV}-r100[int64?,${MULTILIB_USEDEP}]
-		sci-libs/mkl[int64?,${MULTILIB_USEDEP}]
-		abi_x86_64? ( !abi_x86_32? ( >=sci-libs/atlas-3.9.34[lapack] ) )
-	)
-	int64? (
-		|| (
-			>=sci-libs/lapack-reference-${PV}[int64,${MULTILIB_USEDEP}]
-			sci-libs/mkl[int64,${MULTILIB_USEDEP}]
-		)
-	)
-	doc? ( >=app-doc/lapack-docs-3.3 )"
-DEPEND=""
-
-pkg_pretend() {
-	if [[ -e "${EROOT%/}"/usr/$(get_libdir)/lib${PN}.so ]]; then
-		ewarn "You have still the old ${PN} library symlink present"
-		ewarn "Please delete"
-		ewarn "${EROOT%/}/usr/$(get_libdir)/lib${PN}.so"
-		ewarn "to avoid problems with new ${PN} structure"
-	fi
-}
diff --git a/virtual/lapack/lapack-3.7-r100.ebuild b/virtual/lapack/lapack-3.7-r100.ebuild
deleted file mode 100644
index 64256ca6d..000000000
--- a/virtual/lapack/lapack-3.7-r100.ebuild
+++ /dev/null
@@ -1,40 +0,0 @@
-# Copyright 1999-2017 Gentoo Foundation
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=6
-
-inherit multilib-build
-
-DESCRIPTION="Virtual for Linear Algebra Package FORTRAN 77 implementation"
-HOMEPAGE=""
-SRC_URI=""
-
-LICENSE=""
-SLOT="0"
-KEYWORDS="~amd64 ~x86 ~amd64-linux ~x86-linux"
-IUSE="doc int64"
-
-RDEPEND="
-	!app-eselect/eselect-lapack
-	|| (
-		>=sci-libs/lapack-reference-${PV}-r100[int64?,${MULTILIB_USEDEP}]
-		sci-libs/mkl[int64?,${MULTILIB_USEDEP}]
-		abi_x86_64? ( !abi_x86_32? ( >=sci-libs/atlas-3.9.34[lapack] ) )
-	)
-	int64? (
-		|| (
-			>=sci-libs/lapack-reference-${PV}[int64,${MULTILIB_USEDEP}]
-			sci-libs/mkl[int64,${MULTILIB_USEDEP}]
-		)
-	)
-	doc? ( >=app-doc/lapack-docs-3.3 )"
-DEPEND=""
-
-pkg_pretend() {
-	if [[ -e "${EROOT%/}"/usr/$(get_libdir)/lib${PN}.so ]]; then
-		ewarn "You have still the old ${PN} library symlink present"
-		ewarn "Please delete"
-		ewarn "${EROOT%/}/usr/$(get_libdir)/lib${PN}.so"
-		ewarn "to avoid problems with new ${PN} structure"
-	fi
-}
diff --git a/virtual/lapack/metadata.xml b/virtual/lapack/metadata.xml
deleted file mode 100644
index 6148c6b10..000000000
--- a/virtual/lapack/metadata.xml
+++ /dev/null
@@ -1,17 +0,0 @@
-<?xml version="1.0" encoding="UTF-8"?>
-<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
-<pkgmetadata>
-	<maintainer type="project">
-		<email>sci@gentoo.org</email>
-		<name>Gentoo Science Project</name>
-	</maintainer>
-	<longdescription lang="en">
-Gentoo virtual package for the Linear Algebra PACKAge
-FORTRAN 77 implementation. The version number corresponds to the
-version of the LAPACK reference implementation.
-</longdescription>
-	<use>
-		<flag name="int64">Add eselect module for lapack libraries built with 64 bits
-integer ABI</flag>
-	</use>
-</pkgmetadata>
diff --git a/virtual/lapacke/lapacke-3.6.ebuild b/virtual/lapacke/lapacke-3.6.ebuild
deleted file mode 100644
index 594d6e640..000000000
--- a/virtual/lapacke/lapacke-3.6.ebuild
+++ /dev/null
@@ -1,24 +0,0 @@
-# Copyright 1999-2017 Gentoo Foundation
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=6
-
-inherit multilib-build
-
-DESCRIPTION="Virtual for LAPACK C implementation"
-HOMEPAGE=""
-SRC_URI=""
-
-LICENSE=""
-SLOT="0"
-KEYWORDS="~amd64 ~x86 ~amd64-linux ~x86-linux"
-IUSE="int64"
-
-RDEPEND="
-	|| (
-		abi_x86_64? ( !abi_x86_32? ( >=sci-libs/lapacke-reference-${PV} ) )
-		sci-libs/mkl[int64?,${MULTILIB_USEDEP}]
-	)
-	int64? ( sci-libs/mkl[int64,${MULTILIB_USEDEP}] )
-	"
-DEPEND=""
diff --git a/virtual/lapacke/metadata.xml b/virtual/lapacke/metadata.xml
deleted file mode 100644
index 52b90821b..000000000
--- a/virtual/lapacke/metadata.xml
+++ /dev/null
@@ -1,16 +0,0 @@
-<?xml version="1.0" encoding="UTF-8"?>
-<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
-<pkgmetadata>
-	<maintainer type="project">
-		<email>sci@gentoo.org</email>
-		<name>Gentoo Science Project</name>
-	</maintainer>
-	<longdescription lang="en">
-Gentoo virtual package for the Linear Algebra PACKAge
-C implementation.
-</longdescription>
-	<use>
-		<flag name="int64">Add eselect module for blas libraries built with 64 bits
-integer ABI</flag>
-	</use>
-</pkgmetadata>
diff --git a/virtual/perl-encoding-warnings/metadata.xml b/virtual/perl-encoding-warnings/metadata.xml
deleted file mode 100644
index ae9640ffb..000000000
--- a/virtual/perl-encoding-warnings/metadata.xml
+++ /dev/null
@@ -1,8 +0,0 @@
-<?xml version="1.0" encoding="UTF-8"?>
-<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
-<pkgmetadata>
-	<maintainer type="project">
-		<email>sci@gentoo.org</email>
-		<name>Gentoo Science Project</name>
-	</maintainer>
-</pkgmetadata>
diff --git a/virtual/perl-encoding-warnings/perl-encoding-warnings-0.11.ebuild b/virtual/perl-encoding-warnings/perl-encoding-warnings-0.11.ebuild
deleted file mode 100644
index d3dfa34a1..000000000
--- a/virtual/perl-encoding-warnings/perl-encoding-warnings-0.11.ebuild
+++ /dev/null
@@ -1,15 +0,0 @@
-# Copyright 1999-2016 Gentoo Foundation
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=6
-
-DESCRIPTION="Virtual for ${PN#perl-}"
-HOMEPAGE=""
-SRC_URI=""
-
-LICENSE=""
-SLOT="0"
-KEYWORDS="~amd64 ~x86"
-IUSE=""
-
-RDEPEND="~perl-core/${PN#perl-}-${PV}"
diff --git a/virtual/scalapack/metadata.xml b/virtual/scalapack/metadata.xml
deleted file mode 100644
index a39ef098a..000000000
--- a/virtual/scalapack/metadata.xml
+++ /dev/null
@@ -1,17 +0,0 @@
-<?xml version="1.0" encoding="UTF-8"?>
-<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
-<pkgmetadata>
-	<maintainer type="project">
-		<email>sci@gentoo.org</email>
-		<name>Gentoo Science Project</name>
-	</maintainer>
-	<longdescription lang="en">
-Gentoo virtual package for the Scalable LAPACK implementation. The
-version number corresponds to the version of the ScaLAPACK reference
-implementation.
-</longdescription>
-	<use>
-		<flag name="int64">Add eselect module for blas libraries built with 64 bits
-integer ABI</flag>
-	</use>
-</pkgmetadata>
diff --git a/virtual/scalapack/scalapack-2.0.2.ebuild b/virtual/scalapack/scalapack-2.0.2.ebuild
deleted file mode 100644
index a68e13002..000000000
--- a/virtual/scalapack/scalapack-2.0.2.ebuild
+++ /dev/null
@@ -1,24 +0,0 @@
-# Copyright 1999-2017 Gentoo Foundation
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=6
-
-inherit multilib-build
-
-DESCRIPTION="Virtual for ScaLAPACK implementation"
-HOMEPAGE=""
-SRC_URI=""
-
-LICENSE=""
-SLOT="0"
-KEYWORDS="~amd64 ~x86 ~amd64-linux"
-IUSE="doc int64"
-
-RDEPEND="
-	|| (
-		>=sci-libs/scalapack-${PV}
-		sci-libs/mkl[int64?,${MULTILIB_USEDEP}]
-	)
-	int64? ( sci-libs/mkl[int64,${MULTILIB_USEDEP}] )
-	doc? ( >=app-doc/scalapack-docs-2.0 )"
-DEPEND=""
diff --git a/x11-libs/tr/Manifest b/x11-libs/tr/Manifest
deleted file mode 100644
index ea572644d..000000000
--- a/x11-libs/tr/Manifest
+++ /dev/null
@@ -1 +0,0 @@
-DIST tr-1.3.tar.gz 23598 BLAKE2B 4cb3a33d6fbc0cdc2292b78c8e20aee75361a9135970efbde26a2c08fafa95f260b8c0bb2906c82df4b8acb373a140587cf59e9eb19c1341e1e46bb491432fdb SHA512 530a6a4885340cb2efee181bfa52598c93a4cdbfbd197e2c854265175758beb5a27c68dd5a23c2e14fdeded2a2f8b5079b0478a18cbdbfdd854280ab4d6e26c1
diff --git a/x11-libs/tr/files/1.3-Makefile.patch b/x11-libs/tr/files/1.3-Makefile.patch
deleted file mode 100644
index 6f3a2afe8..000000000
--- a/x11-libs/tr/files/1.3-Makefile.patch
+++ /dev/null
@@ -1,29 +0,0 @@
---- a/Makefile	2005-08-25 22:18:31.000000000 +0200
-+++ b/Makefile	2009-03-21 15:11:55.000000000 +0100
-@@ -4,8 +4,8 @@
- # You'll probably have to tweak this for your platform.
- 
- 
--CC = cc
--CFLAGS = -c -g -ansi -I/usr/local/include
-+CC ?= gcc
-+CFLAGS += -c -ansi -I/usr/include
- LIBS = -L/usr/X11R6/lib -lglut -lGLU -lGL -lX11 -lXmu -lXext -lm
- 
- 
-@@ -19,13 +19,13 @@
- 	$(CC) $(CFLAGS) tr.c
- 
- trdemo1: trdemo1.o tr.o
--	$(CC) trdemo1.o tr.o $(LIBS) -o $@
-+	$(CC) $(LDFLAGS) trdemo1.o tr.o $(LIBS) -o $@
- 
- trdemo1.o: trdemo1.c tr.h
- 	$(CC) $(CFLAGS) trdemo1.c
- 
- trdemo2: trdemo2.o tr.o
--	$(CC) trdemo2.o tr.o $(LIBS) -o $@
-+	$(CC) $(LDFLAGS) trdemo2.o tr.o $(LIBS) -o $@
- 
- trdemo2.o: trdemo2.c tr.h
- 	$(CC) $(CFLAGS) trdemo2.c
diff --git a/x11-libs/tr/metadata.xml b/x11-libs/tr/metadata.xml
deleted file mode 100644
index ae9640ffb..000000000
--- a/x11-libs/tr/metadata.xml
+++ /dev/null
@@ -1,8 +0,0 @@
-<?xml version="1.0" encoding="UTF-8"?>
-<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
-<pkgmetadata>
-	<maintainer type="project">
-		<email>sci@gentoo.org</email>
-		<name>Gentoo Science Project</name>
-	</maintainer>
-</pkgmetadata>
diff --git a/x11-libs/tr/tr-1.3.ebuild b/x11-libs/tr/tr-1.3.ebuild
deleted file mode 100644
index 105e296bc..000000000
--- a/x11-libs/tr/tr-1.3.ebuild
+++ /dev/null
@@ -1,33 +0,0 @@
-# Copyright 1999-2016 Gentoo Foundation
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=6
-
-inherit eutils toolchain-funcs
-
-DESCRIPTION="An OpenGL utility library for doing tiled rendering"
-HOMEPAGE="http://www.mesa3d.org/brianp/TR.html"
-SRC_URI="http://www.mesa3d.org/brianp/tr-1.3.tar.gz"
-
-LICENSE="GPL-2"
-SLOT="0"
-KEYWORDS="~amd64 ~x86"
-IUSE=""
-
-RDEPEND="media-libs/freeglut"
-DEPEND="${RDEPEND}"
-
-PATCHES=( "${FILESDIR}"/${PV}-Makefile.patch )
-
-src_prepare() {
-	default
-	tc-export CC
-}
-
-src_install() {
-	doheader tr.h
-	dobin trdemo{1,2}
-	dodoc README
-	docinto html
-	dodoc tr.htm
-}
diff --git a/x11-libs/xview-bin/Manifest b/x11-libs/xview-bin/Manifest
index 96a7e7dce..5a495242c 100644
--- a/x11-libs/xview-bin/Manifest
+++ b/x11-libs/xview-bin/Manifest
@@ -1 +1 @@
-DIST xviewg_3.2p1.4-28.1_i386.deb 781214 BLAKE2B 33fe4552341ae8f96ab788b6a2c7060ac55d1f55631f510d062776607eadcccaa96b6296c2d860a439f57d97f4dd3415c893dc4d763dc891a80ba33a6441ba28 SHA512 f6a5b969c74596f6b7376ce76174b0381425fd01ffd3fc13c28331e19572b978707cc392ca0c26c9c526c3e3fdb2a91e4de89c90264adafa5446960be5ee7df1
+DIST xview-3.2p1.4-21.1.fc8.i386.rpm 2156462 BLAKE2B e1900f644907c28258aecfbab59f84ac7c2f60ab5c0ccd3361c84ba5dc4c9fe837d0153abaf40f18bc924b6cecc6564920318447abe5cba6d140b0493af25910 SHA512 d29c1f6c892e9d5aae4dab5609b586e7f00ff431eaf2ec8f6317ff34bb20004ed6a87cd65ce893b7e708351c17684c426ac8d446374c106c82677bfd750136f9
diff --git a/x11-libs/xview-bin/xview-bin-3.2_p14211.ebuild b/x11-libs/xview-bin/xview-bin-3.2_p14211.ebuild
new file mode 100644
index 000000000..6bb1ac03d
--- /dev/null
+++ b/x11-libs/xview-bin/xview-bin-3.2_p14211.ebuild
@@ -0,0 +1,24 @@
+# Copyright 1999-2021 Gentoo Authors
+# Distributed under the terms of the GNU General Public License v2
+
+EAPI=7
+
+inherit rpm
+
+RPMVER="3.2p1.4-21.1"
+
+DESCRIPTION="The X Window-System-based Visual/Integrated Environment - binary package"
+HOMEPAGE="https://archive.physionet.org/physiotools/xview/"
+SRC_URI="https://archive.physionet.org/physiotools/xview/i386-Fedora/xview-${RPMVER}.fc8.i386.rpm"
+
+LICENSE="XVIEW"
+SLOT="0"
+KEYWORDS="~amd64 ~x86"
+
+S="${WORKDIR}"
+
+QA_PREBUILT="*"
+
+src_install() {
+	dolib.so usr/*/lib/*.so.*
+}
diff --git a/x11-libs/xview-bin/xview-bin-3.2_p1428.ebuild b/x11-libs/xview-bin/xview-bin-3.2_p1428.ebuild
deleted file mode 100644
index 50ccb3804..000000000
--- a/x11-libs/xview-bin/xview-bin-3.2_p1428.ebuild
+++ /dev/null
@@ -1,35 +0,0 @@
-# Copyright 1999-2016 Gentoo Foundation
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=6
-
-DEBVER="3.2p1.4-28.1"
-
-DESCRIPTION="The X Window-System-based Visual/Integrated Environment - binary package"
-HOMEPAGE="http://physionet.caregroup.harvard.edu/physiotools/xview/"
-SRC_URI="mirror://debian/pool/main/x/xview/xviewg_${DEBVER}_i386.deb"
-
-LICENSE="XVIEW"
-SLOT="0"
-KEYWORDS=""
-IUSE="static-libs"
-
-S=${WORKDIR}
-
-QA_PREBUILT="*"
-
-src_unpack() {
-	unpack ${A}
-	unpack ./data.tar.gz
-}
-
-src_install() {
-	local lib_dir
-	if use prefix; then
-		lib_dir=lib
-	else
-		lib_dir=lib32
-	fi
-	dodir /usr/${lib_dir}/
-	mv usr/lib/* "${ED}"/usr/${lib_dir}/ || die
-}
diff --git a/x11-misc/envytools/Manifest b/x11-misc/envytools/Manifest
new file mode 100644
index 000000000..a34198fc4
--- /dev/null
+++ b/x11-misc/envytools/Manifest
@@ -0,0 +1 @@
+DIST envytools-0_pre20200928.tar.gz 1412065 BLAKE2B ce60047f44115f287d23065df63f5a0f5e8967e6daba1b2f4206b247c0e6ad0e525d9dfb057ba411adb0b4329a819746474459889ce0917edf567f6c4e53e586 SHA512 4f9e018834390768e92f398c1617973b0fe46a270e1f7dfa402e900c9c8c0e859dba8c865364339a6060d16d94de3a74abacea182c0c7c17f749ce8c8c1a27d2
diff --git a/x11-misc/envytools/envytools-0_pre20200928.ebuild b/x11-misc/envytools/envytools-0_pre20200928.ebuild
new file mode 100644
index 000000000..057c97f9e
--- /dev/null
+++ b/x11-misc/envytools/envytools-0_pre20200928.ebuild
@@ -0,0 +1,36 @@
+# Copyright 1999-2021 Gentoo Authors
+# Distributed under the terms of the GNU General Public License v2
+
+EAPI=7
+
+inherit cmake
+
+DESCRIPTION="Tools for people envious of nvidia's blob driver"
+HOMEPAGE="https://envytools.readthedocs.io/en/latest/"
+if [[ ${PV} == 9999 ]]; then
+	inherit git-r3
+	EGIT_REPO_URI="https://github.com/envytools/envytools"
+else
+	COMMIT="2d9931313aa14dfdf26f85be2576b181a14ad387"
+	SRC_URI="https://github.com/envytools/envytools/archive/${COMMIT}.tar.gz -> ${P}.tar.gz"
+	S="${WORKDIR}"/${PN}-${COMMIT}
+	KEYWORDS="~amd64"
+fi
+
+LICENSE="MIT"
+SLOT="0"
+
+RDEPEND="
+	dev-libs/libxml2
+	x11-libs/libpciaccess
+"
+DEPEND="${RDEPEND}"
+BDEPEND="
+	virtual/pkgconfig
+	sys-devel/bison
+	sys-devel/flex
+"
+
+DOCS=( README.rst )
+
+PATCHES=( "${FILESDIR}"/${PN}-bison.patch )
diff --git a/x11-misc/envytools/envytools-9999.ebuild b/x11-misc/envytools/envytools-9999.ebuild
index d01476085..057c97f9e 100644
--- a/x11-misc/envytools/envytools-9999.ebuild
+++ b/x11-misc/envytools/envytools-9999.ebuild
@@ -1,27 +1,35 @@
-# Copyright 1999-2016 Gentoo Foundation
+# Copyright 1999-2021 Gentoo Authors
 # Distributed under the terms of the GNU General Public License v2
 
-EAPI=6
+EAPI=7
 
-inherit cmake-utils git-r3
+inherit cmake
 
 DESCRIPTION="Tools for people envious of nvidia's blob driver"
-HOMEPAGE="https://github.com/pathscale/envytools"
-EGIT_REPO_URI="
-	https://github.com/envytools/envytools.git"
+HOMEPAGE="https://envytools.readthedocs.io/en/latest/"
+if [[ ${PV} == 9999 ]]; then
+	inherit git-r3
+	EGIT_REPO_URI="https://github.com/envytools/envytools"
+else
+	COMMIT="2d9931313aa14dfdf26f85be2576b181a14ad387"
+	SRC_URI="https://github.com/envytools/envytools/archive/${COMMIT}.tar.gz -> ${P}.tar.gz"
+	S="${WORKDIR}"/${PN}-${COMMIT}
+	KEYWORDS="~amd64"
+fi
 
 LICENSE="MIT"
 SLOT="0"
-KEYWORDS=""
-IUSE=""
 
 RDEPEND="
 	dev-libs/libxml2
-	x11-libs/libpciaccess"
-DEPEND="${RDEPEND}
+	x11-libs/libpciaccess
+"
+DEPEND="${RDEPEND}"
+BDEPEND="
 	virtual/pkgconfig
 	sys-devel/bison
-	sys-devel/flex"
+	sys-devel/flex
+"
 
 DOCS=( README.rst )
 
diff --git a/x11-misc/xdg-java/Manifest b/x11-misc/xdg-java/Manifest
new file mode 100644
index 000000000..1cad78fa2
--- /dev/null
+++ b/x11-misc/xdg-java/Manifest
@@ -0,0 +1 @@
+DIST xdg-java-0.1.1-sources.tar.gz 19734 BLAKE2B 402eedd9d0c6e8fd2ddb138fcbd16b06d653af6e219f5ca91df73dce9cbbed3764e39e886a67b4290fd079c71a2b86b2be2a31cee368d12f2e022deeb8887612 SHA512 01f63339bc21a502693c803f38762e66fc0ad570acf0ba6fde17519d820e9f6b94183f30b265ab68467a7c37a9df65612aed3774b6b6f955113c2bac9f1f7077
diff --git a/x11-misc/xdg-java/metadata.xml b/x11-misc/xdg-java/metadata.xml
new file mode 100644
index 000000000..45a5f9d39
--- /dev/null
+++ b/x11-misc/xdg-java/metadata.xml
@@ -0,0 +1,14 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
+<pkgmetadata>
+  <longdescription>
+    This is a Java API that provides an easy to use implementations of various Free Desktop specifications. Use the correct application specific configuration, data and cache directories. Safely read and write desktop entries without worrying about parsing and escaping.
+  </longdescription>
+  <maintainer type="project">
+    <email>sci@gentoo.org</email>
+    <name>Gentoo Science Project</name>
+  </maintainer>
+  <upstream>
+    <remote-id type="github">kothar/xdg-java</remote-id>
+  </upstream>
+</pkgmetadata>
diff --git a/x11-misc/xdg-java/xdg-java-0.1.1.ebuild b/x11-misc/xdg-java/xdg-java-0.1.1.ebuild
new file mode 100644
index 000000000..8723b0774
--- /dev/null
+++ b/x11-misc/xdg-java/xdg-java-0.1.1.ebuild
@@ -0,0 +1,45 @@
+# Copyright 1999-2023 Gentoo Authors
+# Distributed under the terms of the GNU General Public License v2
+
+EAPI=8
+
+JAVA_PKG_IUSE="doc source test"
+JAVA_TESTING_FRAMEWORKS="junit-4"
+
+inherit java-pkg-2 java-pkg-simple
+
+DESCRIPTION="Java bindings for various FreeDesktop.org standards"
+HOMEPAGE="https://github.com/kothar/xdg-java"
+
+if [[ ${PV} == 9999 ]]; then
+	inherit git-r3
+	EGIT_REPO_URI="https://github.com/kothar/xdg-java.git"
+	S="${WORKDIR}/${P}"
+	MAVEN_ID="net.kothar:xdg-java:9999"
+else
+	SRC_URI="
+		https://github.com/kothar/${PN}/archive/refs/tags/${PV}.tar.gz -> ${P}-sources.tar.gz
+		"
+	S="${WORKDIR}/${P}"
+	MAVEN_ID="net.kothar:xdg-java:0.1.1"
+	KEYWORDS="~amd64"
+fi
+
+LICENSE="LGPL-2.1"
+SLOT="0"
+
+DEPEND=">=virtual/jdk-1.8:*"
+
+BDEPEND="
+	>=virtual/jdk-1.8:*
+	test? (
+	      >=dev-java/junit-4.13.2:4
+	      )
+"
+
+RDEPEND=">=virtual/jre-1.8:*"
+
+JAVA_SRC_DIR="src/main/java"
+
+JAVA_TEST_GENTOO_CLASSPATH="junit-4"
+JAVA_TEST_SRC_DIR="src/test/java"
diff --git a/x11-misc/xdg-java/xdg-java-9999.ebuild b/x11-misc/xdg-java/xdg-java-9999.ebuild
new file mode 100644
index 000000000..8723b0774
--- /dev/null
+++ b/x11-misc/xdg-java/xdg-java-9999.ebuild
@@ -0,0 +1,45 @@
+# Copyright 1999-2023 Gentoo Authors
+# Distributed under the terms of the GNU General Public License v2
+
+EAPI=8
+
+JAVA_PKG_IUSE="doc source test"
+JAVA_TESTING_FRAMEWORKS="junit-4"
+
+inherit java-pkg-2 java-pkg-simple
+
+DESCRIPTION="Java bindings for various FreeDesktop.org standards"
+HOMEPAGE="https://github.com/kothar/xdg-java"
+
+if [[ ${PV} == 9999 ]]; then
+	inherit git-r3
+	EGIT_REPO_URI="https://github.com/kothar/xdg-java.git"
+	S="${WORKDIR}/${P}"
+	MAVEN_ID="net.kothar:xdg-java:9999"
+else
+	SRC_URI="
+		https://github.com/kothar/${PN}/archive/refs/tags/${PV}.tar.gz -> ${P}-sources.tar.gz
+		"
+	S="${WORKDIR}/${P}"
+	MAVEN_ID="net.kothar:xdg-java:0.1.1"
+	KEYWORDS="~amd64"
+fi
+
+LICENSE="LGPL-2.1"
+SLOT="0"
+
+DEPEND=">=virtual/jdk-1.8:*"
+
+BDEPEND="
+	>=virtual/jdk-1.8:*
+	test? (
+	      >=dev-java/junit-4.13.2:4
+	      )
+"
+
+RDEPEND=">=virtual/jre-1.8:*"
+
+JAVA_SRC_DIR="src/main/java"
+
+JAVA_TEST_GENTOO_CLASSPATH="junit-4"
+JAVA_TEST_SRC_DIR="src/test/java"